Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007976.1 Hibiscus syriacus cultivar Beakdansim tig00110413_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: 428971
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:146206 original size:12 final size:12
Alignment explanation
Indices: 146187--146235 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
146177 TCATTTACAA
146187 AATT-ATTTATT
1 AATTCATTTATT
*
146198 AATTCATTTATA
1 AATTCATTTATT
* *
146210 AACTCTTTTATT
1 AATTCATTTATT
*
146222 AGTTCATTTATT
1 AATTCATTTATT
146234 AA
1 AA
146236 AATTTCATAT
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
11 4 0.14
12 25 0.86
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (12 bp):
AATTCATTTATT
Found at i:146274 original size:21 final size:21
Alignment explanation
Indices: 146228--146274 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
146218 TATTAGTTCA
* *
146228 TTTATTAAAATTTCATATTTT
1 TTTATAAAAAATTCATATTTT
*
146249 ATTATAAAAAATT-ATATTTAT
1 TTTATAAAAAATTCATATTT-T
146270 TTTAT
1 TTTAT
146275 GGCAAAAGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTATAAAAAATTCATATTTT
Found at i:162768 original size:220 final size:220
Alignment explanation
Indices: 162386--162827 Score: 832
Period size: 220 Copynumber: 2.0 Consensus size: 220
162376 TCTCTTATTA
*
162386 ATAGATTAAGAATAATTTTAAAATATATTATCTTATAATCACTTCAAACTCTTAAAATCAAAAGA
1 ATAGATTAAGAATAATTTTAAAATATATTATCTTATAATCACCTCAAACTCTTAAAATCAAAAGA
**
162451 TACATTGTCAACGTTGCCTTCATAGAAGTTCTTTTAACGGATTTACATATGAACATGTAATTGGA
66 TACATCATCAACGTTGCCTTCATAGAAGTTCTTTTAACGGATTTACATATGAACATGTAATTGGA
162516 TGGTCAACAACTAAGCTTAAATTTTCATTCAAAATTTGCATATTATATTTGATCTAAAGAGGAGA
131 TGGTCAACAACTAAGCTTAAATTTTCATTCAAAATTTGCATATTATATTTGATCTAAAGAGGAGA
162581 CCAAATGAGAACACATGTATACACC
196 CCAAATGAGAACACATGTATACACC
*
162606 ATAGATTAAGAATAATTTTAAAATATATTATCTTATAATCACCTCAAACTCTTAAAATCAAAAGG
1 ATAGATTAAGAATAATTTTAAAATATATTATCTTATAATCACCTCAAACTCTTAAAATCAAAAGA
162671 TATC-TCATCAACGTTGCCTTCATAGAAGTTCTTTTAACGGATTTACATATGAACATGTAATTGG
66 TA-CATCATCAACGTTGCCTTCATAGAAGTTCTTTTAACGGATTTACATATGAACATGTAATTGG
162735 ATGGTCAACAACTAAGCTTAAATTTTCATTCAAAATTTGCATATTATATTTGATCTAAAGAGGAG
130 ATGGTCAACAACTAAGCTTAAATTTTCATTCAAAATTTGCATATTATATTTGATCTAAAGAGGAG
162800 ACCAAATGAGAACACATGTATACACC
195 ACCAAATGAGAACACATGTATACACC
162826 AT
1 AT
162828 CTCTTTCATT
Statistics
Matches: 217, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
220 216 1.00
221 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (220 bp):
ATAGATTAAGAATAATTTTAAAATATATTATCTTATAATCACCTCAAACTCTTAAAATCAAAAGA
TACATCATCAACGTTGCCTTCATAGAAGTTCTTTTAACGGATTTACATATGAACATGTAATTGGA
TGGTCAACAACTAAGCTTAAATTTTCATTCAAAATTTGCATATTATATTTGATCTAAAGAGGAGA
CCAAATGAGAACACATGTATACACC
Found at i:167557 original size:23 final size:23
Alignment explanation
Indices: 167516--167559 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
167506 ATGAGGGATC
*
167516 AAATTGAAATAATTTTAAAATGT
1 AAATTGAAATAATTATAAAATGT
167539 AAATTGAAATTAA-TATAAAAT
1 AAATTGAAA-TAATTATAAAAT
167560 TGGACTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (23 bp):
AAATTGAAATAATTATAAAATGT
Found at i:167898 original size:2 final size:2
Alignment explanation
Indices: 167891--168138 Score: 273
Period size: 2 Copynumber: 127.0 Consensus size: 2
167881 AATAATTCTA
*
167891 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT GA- AT GT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT -AT AT AT AT AT AT
* * *
167933 AT AT A- AT AC AT GT AC AT AT AT AT A- AT -T A- AT -T 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
167970 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
168012 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
* * * * *
168054 AT AT AT AT AT AT AT AC AT GT -T AT AC AT GT AT AT AT AT CAT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
* * * *
168096 AT GT AT AT AT AT AT AT GT AT AC GT -T AT AT AT AT A- AGT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
168137 AT
1 AT
168139 GTAATTATGT
Statistics
Matches: 210, Mismatches: 23, Indels: 26
0.81 0.09 0.10
Matches are distributed among these distances:
1 10 0.05
2 193 0.92
3 7 0.03
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:168172 original size:11 final size:11
Alignment explanation
Indices: 168156--168190 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
168146 TGTATGATCA
168156 ATGATGCATGT
1 ATGATGCATGT
*
168167 ATGATGTATGT
1 ATGATGCATGT
168178 ATGATGCATGT
1 ATGATGCATGT
168189 AT
1 AT
168191 ATATATATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.29, C:0.06, G:0.26, T:0.40
Consensus pattern (11 bp):
ATGATGCATGT
Found at i:168179 original size:4 final size:4
Alignment explanation
Indices: 168163--168219 Score: 73
Period size: 4 Copynumber: 14.8 Consensus size: 4
168153 TCAATGATGC
* * *
168163 ATGT ATG- ATGT ATGT ATG- ATGC ATGT ATAT ATAT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
168209 ATGT ATGT ATG
1 ATGT ATGT ATG
168220 ATCCATACAT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
3 6 0.12
4 42 0.88
ACGTcount: A:0.30, C:0.02, G:0.23, T:0.46
Consensus pattern (4 bp):
ATGT
Found at i:168236 original size:39 final size:38
Alignment explanation
Indices: 168163--168237 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 38
168153 TCAATGATGC
* ** *
168163 ATGTATGATGTATGTATGATGCATGTATATATATATGT
1 ATGTATGATGTATGTATGATCCATACATACATATATGT
168201 ATGTATGTATGTATGTATGATCCATACATACATATAT
1 ATGTATG-ATGTATGTATGATCCATACATACATATAT
168238 ATTTATATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 7 0.22
39 25 0.78
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (38 bp):
ATGTATGATGTATGTATGATCCATACATACATATATGT
Found at i:168282 original size:2 final size:2
Alignment explanation
Indices: 168277--168384 Score: 52
Period size: 2 Copynumber: 56.0 Consensus size: 2
168267 TAAAAAAATA
* *
168277 AT AT AT GT AT AT AT AT -T A- AT AT -T AT AT AT AT AC ACT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* * * *
168316 AT GT AT AT AT AT A- AGT AT A- AA AT AT AT AA AT A- ACT AT GT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT
* *
168357 AT AT AT A- AGT AT AT GT AA AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
168385 GTGATGTATG
Statistics
Matches: 79, Mismatches: 15, Indels: 24
0.67 0.13 0.20
Matches are distributed among these distances:
1 8 0.10
2 68 0.86
3 3 0.04
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.44
Consensus pattern (2 bp):
AT
Found at i:168317 original size:35 final size:35
Alignment explanation
Indices: 168278--168369 Score: 109
Period size: 35 Copynumber: 2.7 Consensus size: 35
168268 AAAAAAATAA
* * *
168278 TATATGTATATATATTAA-TATTATATATATACACT
1 TATATGTATATATATTAAGTATAAAATATATA-AAT
168313 TATATGTATATATA-TAAGTATAAAATATATAAAT
1 TATATGTATATATATTAAGTATAAAATATATAAAT
*
168347 AACTATGTATATATA-TAAGTATA
1 TA-TATGTATATATATTAAGTATA
168370 TGTAAATATA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
34 6 0.12
35 45 0.88
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (35 bp):
TATATGTATATATATTAAGTATAAAATATATAAAT
Found at i:182947 original size:21 final size:21
Alignment explanation
Indices: 182921--182960 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
182911 ATTCGTTGAA
182921 AATTATTAAAAAAATTAATAT
1 AATTATTAAAAAAATTAATAT
*
182942 AATTATTTAAAAAATTAAT
1 AATTATTAAAAAAATTAAT
182961 TTTTGCTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AATTATTAAAAAAATTAATAT
Found at i:188870 original size:21 final size:21
Alignment explanation
Indices: 188844--188886 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
188834 GTTTTTATGG
* *
188844 AAGATTTTATGGCTTCGACAA
1 AAGATTTCATGGCTTCAACAA
188865 AAGATTTCATGGCTTCAACAA
1 AAGATTTCATGGCTTCAACAA
188886 A
1 A
188887 GGCATTGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (21 bp):
AAGATTTCATGGCTTCAACAA
Found at i:189514 original size:42 final size:42
Alignment explanation
Indices: 189455--189537 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
189445 ATTGATCAGA
189455 TGCCTACTTATGCCAAATTTCTAAAGGATATCATCACAAAGG
1 TGCCTACTTATGCCAAATTTCTAAAGGATATCATCACAAAGG
*
189497 TGCCTACTTATGTCAAATTTCTAAAGGATATCATCACAAAG
1 TGCCTACTTATGCCAAATTTCTAAAGGATATCATCACAAAG
189538 AAGGGAAATG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.30
Consensus pattern (42 bp):
TGCCTACTTATGCCAAATTTCTAAAGGATATCATCACAAAGG
Found at i:194790 original size:20 final size:21
Alignment explanation
Indices: 194755--194793 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
194745 ATTACTAGTC
*
194755 ATATAATATTATATTATAATT
1 ATATAATATTAAATTATAATT
194776 ATATAA-ATTAAATTATAA
1 ATATAATATTAAATTATAA
194794 GGTATGCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATATAATATTAAATTATAATT
Found at i:196095 original size:12 final size:12
Alignment explanation
Indices: 196074--196132 Score: 68
Period size: 12 Copynumber: 5.1 Consensus size: 12
196064 CCTTCGGGCT
*
196074 ATATAAATAATA
1 ATATATATAATA
*
196086 ATATTTATAAT-
1 ATATATATAATA
*
196097 ATA-ATATAATC
1 ATATATATAATA
196108 ATATATATAATA
1 ATATATATAATA
*
196120 AAATATATAATA
1 ATATATATAATA
196132 A
1 A
196133 ACATCACTCG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
10 6 0.15
11 6 0.15
12 28 0.70
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (12 bp):
ATATATATAATA
Found at i:196111 original size:22 final size:22
Alignment explanation
Indices: 196074--196131 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
196064 CCTTCGGGCT
*
196074 ATATAA-ATAATAATATTTATA
1 ATATAATATAATAATATATATA
*
196095 ATATAATATAATCATATATATA
1 ATATAATATAATAATATATATA
*
196117 ATAAAATAT-ATAATA
1 ATATAATATAATAATA
196132 AACATCACTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 11 0.34
22 21 0.66
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATAATATAATAATATATATA
Found at i:210116 original size:2 final size:2
Alignment explanation
Indices: 210109--210140 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
210099 TTTAATATTA
210109 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
210141 GAGTAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:223314 original size:2 final size:2
Alignment explanation
Indices: 223298--223364 Score: 109
Period size: 2 Copynumber: 34.0 Consensus size: 2
223288 ATTATTAGTG
*
223298 AT AT -T AT AT AA 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
*
223339 AT AT AT AT AA AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
223365 TATTTGTTTA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
1 1 0.02
2 59 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:237060 original size:23 final size:23
Alignment explanation
Indices: 237034--237078 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
237024 GCTAAAGTTC
237034 AGTGAGTAAGAGTATAATTTACT
1 AGTGAGTAAGAGTATAATTTACT
*
237057 AGTGAGTAAGAGTGTAATTTAC
1 AGTGAGTAAGAGTATAATTTAC
237079 CTTTTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.33
Consensus pattern (23 bp):
AGTGAGTAAGAGTATAATTTACT
Found at i:250244 original size:17 final size:19
Alignment explanation
Indices: 250216--250264 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
250206 TATTTTGAAA
250216 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
250234 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
250253 CACCGATGCACT
1 CATCGATGCACT
250265 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:250260 original size:64 final size:64
Alignment explanation
Indices: 250085--250264 Score: 197
Period size: 65 Copynumber: 2.8 Consensus size: 64
250075 AATTAAATTG
* *
250085 AACATCGAATGCATTTCATGCATCGATGAACATAC-CATGCACCGATGCACTGAGGATTTTATGA
1 AACATCGAATGCATTTGATGCATCGATGAAC-T-CTCATGCACCGATGCACTCAGGATTTTATGA
250149 A
64 A
* * * *
250150 AACATCGAATGCATTTGATGCATCGATGTAC-CAGTCATGCATCGATGCACTCTGGCTATTT-TG
1 AACATCGAATGCATTTGATGCATCGATGAACTC--TCATGCACCGATGCACTCAGGAT-TTTATG
250213 -A
63 AA
* * *
250214 AACATCGAATGCACTTGATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTGATGCATCGATGAACTCTCA-TGCACCGATGCACT
250265 AAGGGTCCAA
Statistics
Matches: 99, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 43 0.43
65 50 0.51
66 3 0.03
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGAACTCTCATGCACCGATGCACTCAGGATTTTATGAA
Found at i:257669 original size:18 final size:19
Alignment explanation
Indices: 257632--257670 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
257622 ACTCCGGGAG
*
257632 CTAGTTCCTCACGCTGCTC
1 CTAGCTCCTCACGCTGCTC
*
257651 CTAGCTCCTCTCG-TGCTC
1 CTAGCTCCTCACGCTGCTC
257669 CT
1 CT
257671 CCTCCTCCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.08, C:0.44, G:0.15, T:0.33
Consensus pattern (19 bp):
CTAGCTCCTCACGCTGCTC
Found at i:258836 original size:64 final size:63
Alignment explanation
Indices: 258758--258933 Score: 193
Period size: 64 Copynumber: 2.8 Consensus size: 63
258748 GAATTAAATT
*
258758 AAACATCGAATGCATTTGATGCATCGATGCACTACCATGCACCGATGCACTGAGGAT-TTTATG
1 AAACATCGAATGCATTTGATGCATCGATGCACTACCATGCACCGATGCACTCAGGATATTT-TG
* * * *
258821 AAAACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCA---TTG-ACTCTGGCTATTTTG
1 -AAACATCGAATGCATTTGATGCATCGATGCACTA-CCATGCACCGATGCACTCAGGATATTTTG
* * *
258882 AAACATCGAATGCACTTGATACATCGATGCACT-CTTAGTGCACCGATGCACT
1 AAACATCGAATGCATTTGATGCATCGATGCACTAC-CA-TGCACCGATGCACT
258934 AAGGTCCAAC
Statistics
Matches: 94, Mismatches: 10, Indels: 16
0.78 0.08 0.13
Matches are distributed among these distances:
58 1 0.01
59 1 0.01
60 34 0.36
61 8 0.09
62 5 0.05
63 2 0.02
64 36 0.38
65 7 0.07
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (63 bp):
AAACATCGAATGCATTTGATGCATCGATGCACTACCATGCACCGATGCACTCAGGATATTTTG
Found at i:258913 original size:17 final size:18
Alignment explanation
Indices: 258879--258914 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
258869 TCTGGCTATT
258879 TTGAAACATCGAATGCAC
1 TTGAAACATCGAATGCAC
*
258897 TTGATACATCG-ATGCAC
1 TTGAAACATCGAATGCAC
258914 T
1 T
258915 CTTAGTGCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (18 bp):
TTGAAACATCGAATGCAC
Found at i:263564 original size:21 final size:21
Alignment explanation
Indices: 263535--263587 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
263525 ATTCTGACTA
263535 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
263556 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
263577 TCGCAATGCGA
1 TCGCATTGCGA
263588 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:263602 original size:20 final size:20
Alignment explanation
Indices: 263577--263688 Score: 161
Period size: 20 Copynumber: 5.5 Consensus size: 20
263567 TTTTCCTAAT
263577 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
263597 TCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
263617 TCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
263637 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
263658 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
263678 TCGCAATGCGA
1 TCGCAATGCGA
263689 TAGTGACTAT
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
20 65 0.78
21 18 0.22
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:263608 original size:41 final size:41
Alignment explanation
Indices: 263562--263689 Score: 168
Period size: 41 Copynumber: 3.1 Consensus size: 41
263552 AAATTCGCGT
* * *
263562 TGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAATGCGAATACGTAAATCGCAA
* * *
263603 CGCGA-TTACGTAAATCGCAACGCGATTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAATGCGAATACGTAAATCGCAA
* * *
263643 TGCGAATTAGGAAAATCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAATGCGAATACGTAAATCGCAA
263684 TGCGAT
1 TGCGAT
263690 AGTGACTATC
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
40 34 0.46
41 40 0.54
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.23
Consensus pattern (41 bp):
TGCGATTTACGTAAATCGCAATGCGAATACGTAAATCGCAA
Found at i:264284 original size:20 final size:20
Alignment explanation
Indices: 264238--264313 Score: 77
Period size: 18 Copynumber: 3.9 Consensus size: 20
264228 TTCTAAACTT
*
264238 AAAATCGCAACATGAAAA--
1 AAAATCGCAACACGAAAATG
264256 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
**
264276 ACTATCGCAACGA-GAGAAATG
1 AAAATCGCAAC-ACGA-AAATG
*
264297 AAAATCGCAACGCGAAA
1 AAAATCGCAACACGAAA
264314 CCAAAATCGC
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
18 17 0.36
20 13 0.28
21 17 0.36
ACGTcount: A:0.53, C:0.20, G:0.17, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:264297 original size:21 final size:21
Alignment explanation
Indices: 264238--264313 Score: 74
Period size: 21 Copynumber: 3.9 Consensus size: 21
264228 TTCTAAACTT
*
264238 AAAATCGCAAC-ATGAAAA--
1 AAAATCGCAACGACGAAAATG
264256 AAAATCGCAAC-ACGAAAATG
1 AAAATCGCAACGACGAAAATG
**
264276 ACTATCGCAACGA-GAGAAATG
1 AAAATCGCAACGACGA-AAATG
264297 AAAATCGCAACG-CGAAA
1 AAAATCGCAACGACGAAA
264314 CCAAAATCGC
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
18 17 0.35
20 13 0.27
21 18 0.38
ACGTcount: A:0.53, C:0.20, G:0.17, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACGACGAAAATG
Found at i:264342 original size:19 final size:18
Alignment explanation
Indices: 264320--264406 Score: 64
Period size: 19 Copynumber: 5.1 Consensus size: 18
264310 GAAACCAAAA
264320 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGATTTTCATT
*
264339 TCGCGTTGCGA--TTC-TC
1 TCGC-TTGCGATTTTCATT
*
264355 TCG-TTGCGATTTTAATT
1 TCGCTTGCGATTTTCATT
*
264372 TCGCTTTGCGA--TTC-TC
1 TCGC-TTGCGATTTTCATT
264388 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTTCATT
264405 TC
1 TC
264407 AACCAAAAGA
Statistics
Matches: 53, Mismatches: 7, Indels: 18
0.68 0.09 0.23
Matches are distributed among these distances:
14 12 0.23
16 13 0.25
17 12 0.23
19 16 0.30
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.47
Consensus pattern (18 bp):
TCGCTTGCGATTTTCATT
Found at i:264361 original size:14 final size:14
Alignment explanation
Indices: 264342--264398 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
264332 TTTCATTTCG
264342 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
264356 CGTTGCGATTTTAATTT
1 CGTTGCGA--TT-CTCT
264373 CGCTTTGCGATTCTCT
1 CG--TTGCGATTCTCT
264389 CGTTGCGATT
1 CGTTGCGATT
264399 TTCATTTCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 16 0.47
16 6 0.18
17 6 0.18
19 6 0.18
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:264367 original size:33 final size:33
Alignment explanation
Indices: 264325--264406 Score: 146
Period size: 33 Copynumber: 2.5 Consensus size: 33
264315 CAAAATCGCA
264325 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
264358 TTGCGATTTTAATTTCGCTTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
264391 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
264407 AACCAAAAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.11, C:0.22, G:0.18, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:266283 original size:94 final size:93
Alignment explanation
Indices: 266092--266465 Score: 616
Period size: 94 Copynumber: 4.1 Consensus size: 93
266082 TAGATTGCTT
* *
266092 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
266153 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
266182 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
266247 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
*
266276 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
266341 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * *
266370 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAG-TAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
266434 A-TTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
266461 AGTAA
1 AGTAA
266466 TGCAATCCAT
Statistics
Matches: 273, Mismatches: 6, Indels: 9
0.95 0.02 0.03
Matches are distributed among these distances:
90 35 0.13
91 6 0.02
92 28 0.10
93 27 0.10
94 177 0.65
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:266583 original size:20 final size:20
Alignment explanation
Indices: 266558--266619 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
266548 TTTTGGTTAA
266558 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
* *
266578 AATGAAAATCGTAACGCGA-
1 AATGAAAATCGCAACGAGAG
*
266597 AACGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
266617 AAT
1 AAT
266620 CGCAACGACA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 16 0.46
20 19 0.54
ACGTcount: A:0.50, C:0.16, G:0.23, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:266605 original size:19 final size:20
Alignment explanation
Indices: 266561--266618 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 20
266551 TGGTTAAAAT
*
266561 GAAAATCGCAACGAGAGAAT
1 GAAAATCGCAACGAGAGAAC
* *
266581 GAAAATCGTAACGCGA-AAC
1 GAAAATCGCAACGAGAGAAC
266600 GAAAATCGCAACGAGAGAA
1 GAAAATCGCAACGAGAGAA
266619 TCGCAACGAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.50, C:0.17, G:0.24, T:0.09
Consensus pattern (20 bp):
GAAAATCGCAACGAGAGAAC
Found at i:266622 original size:14 final size:14
Alignment explanation
Indices: 266601--266639 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
266591 ACGCGAAACG
*
266601 AAAATCGCAACGAG
1 AAAATCGCAACGAC
*
266615 AGAATCGCAACGAC
1 AAAATCGCAACGAC
266629 AAAATCGCAAC
1 AAAATCGCAAC
266640 TCGAAACCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.49, C:0.26, G:0.18, T:0.08
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:266654 original size:20 final size:20
Alignment explanation
Indices: 266629--266666 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
266619 TCGCAACGAC
*
266629 AAAATCGCAACTCGAAACCA
1 AAAATCGCAACGCGAAACCA
266649 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
266667 TATAATCGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.29, G:0.13, T:0.08
Consensus pattern (20 bp):
AAAATCGCAACGCGAAACCA
Found at i:266720 original size:21 final size:19
Alignment explanation
Indices: 266672--266766 Score: 100
Period size: 19 Copynumber: 4.8 Consensus size: 19
266662 GAAACTATAA
*
266672 TCGCGTTGCGATTTTCGTT
1 TCGCGTTGCGATTTTCATT
266691 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGA-TTTTCATT
*
266711 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
* **
266731 TCGCATTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
266752 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
266767 AAGTTCCAGA
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 24 0.39
20 15 0.24
21 23 0.37
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:266759 original size:40 final size:40
Alignment explanation
Indices: 266675--266766 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
266665 ACTATAATCG
* * ** *
266675 CGTTGCGATTTTCGTTTCGCGTTGCGATTTTTCATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTAGTCATTCTCA
*
266715 CGTTGCGATTTTCATTTCGCATTGCGA-TAGTCATTTTTCA
1 CGTTGCGATTTTCATTTCGCATTGCGATTAGTCA-TTCTCA
266755 CGTTGCGATTTT
1 CGTTGCGATTTT
266767 AAGTTCCAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 4 0.09
40 41 0.91
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.48
Consensus pattern (40 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTAGTCATTCTCA
Found at i:267240 original size:21 final size:21
Alignment explanation
Indices: 267216--267282 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
267206 TCATTCATCG
267216 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
267237 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
267258 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
267279 AGAG
1 AGAG
267283 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:268653 original size:14 final size:14
Alignment explanation
Indices: 268634--268665 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
268624 TGTTAATTGA
268634 TTGTAAAAGATGAT
1 TTGTAAAAGATGAT
*
268648 TTGTAAAAGTTGAT
1 TTGTAAAAGATGAT
268662 TTGT
1 TTGT
268666 TTAATTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TTGTAAAAGATGAT
Found at i:268865 original size:19 final size:19
Alignment explanation
Indices: 268843--268941 Score: 65
Period size: 19 Copynumber: 5.7 Consensus size: 19
268833 CGAAACTAAA
268843 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
268862 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
268877 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
268895 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
268910 -TCTCGTTGCGATTTTTAT
1 TTCGCGTTGCGATTTTCAT
*
268928 TTCGCATTGCGATT
1 TTCGCGTTGCGATT
268942 CTCTCGTTGC
Statistics
Matches: 58, Mismatches: 12, Indels: 20
0.64 0.13 0.22
Matches are distributed among these distances:
14 17 0.29
16 5 0.09
17 6 0.10
19 30 0.52
ACGTcount: A:0.11, C:0.23, G:0.19, T:0.46
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:268889 original size:33 final size:33
Alignment explanation
Indices: 268847--268963 Score: 207
Period size: 33 Copynumber: 3.5 Consensus size: 33
268837 ACTAAATTCG
* *
268847 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
268880 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
268913 CGTTGCGATTTTTATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
268946 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
268964 TTGTAGTACC
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.11, C:0.24, G:0.18, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:268920 original size:14 final size:14
Alignment explanation
Indices: 268868--268955 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
268858 TCATTTCGCT
*
268868 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
268882 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
268899 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
* *
268915 TTGCGATTTTTATTTCG
1 TTGCGA---TTCTCTCG
268932 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
268948 TTGCGATT
1 TTGCGATT
268956 TTCATTTCTT
Statistics
Matches: 57, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 20 0.35
16 13 0.23
17 12 0.21
19 12 0.21
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:271159 original size:20 final size:21
Alignment explanation
Indices: 271135--271297 Score: 147
Period size: 20 Copynumber: 8.0 Consensus size: 21
271125 CAGAATCTCG
271135 TTGCGATTTAC-TAAATCGCA
1 TTGCGATTTACGTAAATCGCA
*
271155 ATGCGA-TTACGTAAATCGCA
1 TTGCGATTTACGTAAATCGCA
* * * *
271175 ATGCGA-ATACGCAATTCGCA
1 TTGCGATTTACGTAAATCGCA
* * *
271195 TTGCGATTTACCTAATTCACA
1 TTGCGATTTACGTAAATCGCA
*
271216 TTGCAATTTACGT-AATCGCA
1 TTGCGATTTACGTAAATCGCA
* *
271236 TTGCGATTTACCTAATTCGCA
1 TTGCGATTTACGTAAATCGCA
* *
271257 TTGCGATTTACGT-ATTCGTA
1 TTGCGATTTACGTAAATCGCA
* * *
271277 TTGCGAATTAGGAAAATCGCA
1 TTGCGATTTACGTAAATCGCA
271298 ACGCGAATTT
Statistics
Matches: 116, Mismatches: 23, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
19 4 0.03
20 68 0.59
21 44 0.38
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (21 bp):
TTGCGATTTACGTAAATCGCA
Found at i:271237 original size:41 final size:41
Alignment explanation
Indices: 271190--271282 Score: 150
Period size: 41 Copynumber: 2.3 Consensus size: 41
271180 AATACGCAAT
271190 TCGCATTGCGATTTACCTAATTCACATTGCAATTTACGTAA
1 TCGCATTGCGATTTACCTAATTCACATTGCAATTTACGTAA
* * *
271231 TCGCATTGCGATTTACCTAATTCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACCTAATTCACATTGCAATTTACGTAA
*
271272 TCGTATTGCGA
1 TCGCATTGCGA
271283 ATTAGGAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.38
Consensus pattern (41 bp):
TCGCATTGCGATTTACCTAATTCACATTGCAATTTACGTAA
Found at i:271297 original size:41 final size:41
Alignment explanation
Indices: 271135--271297 Score: 109
Period size: 41 Copynumber: 4.0 Consensus size: 41
271125 CAGAATCTCG
* * **
271135 TTGCGATTTAC-TAAATCGCAATGCG-ATTACGTAAATCGCA
1 TTGCAATTTACGT-AATCGCATTGCGAATTACCAAAATCGCA
* * * * * *
271175 ATGCGAA--TACGCAATTCGCATTGCGATTTACCTAATTCACA
1 TTGC-AATTTACGTAA-TCGCATTGCGAATTACCAAAATCGCA
* * *
271216 TTGCAATTTACGTAATCGCATTGCGATTTACCTAATTCGCA
1 TTGCAATTTACGTAATCGCATTGCGAATTACCAAAATCGCA
* * * **
271257 TTGCGATTTACGTATTCGTATTGCGAATTAGGAAAATCGCA
1 TTGCAATTTACGTAATCGCATTGCGAATTACCAAAATCGCA
271298 ACGCGAATTT
Statistics
Matches: 98, Mismatches: 19, Indels: 11
0.77 0.15 0.09
Matches are distributed among these distances:
39 5 0.05
40 14 0.14
41 73 0.74
42 6 0.06
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (41 bp):
TTGCAATTTACGTAATCGCATTGCGAATTACCAAAATCGCA
Found at i:271305 original size:21 final size:21
Alignment explanation
Indices: 271279--271324 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
271269 TATTCGTATT
271279 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
271300 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
271321 GCGA
1 GCGA
271325 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:282877 original size:60 final size:59
Alignment explanation
Indices: 282756--282882 Score: 137
Period size: 60 Copynumber: 2.1 Consensus size: 59
282746 CGGCTGGCCG
* * * * *
282756 TTTTATAACTTTTAATAGTCAAGGACTCAACAAAACAACACCCTATAATCGATGGATCA
1 TTTTGTAACTTTTAAAAGTCAAAGACTCAACAAAACAACACCCTATAATCGAGGGACCA
** * * * *
282815 TTTTGTAACTTTTAAAAGTCGAAAGACTCAACAAAGTAATACCTTATAGTCGGGGGACCA
1 TTTTGTAACTTTTAAAAGTC-AAAGACTCAACAAAACAACACCCTATAATCGAGGGACCA
282875 TTTGTGTA
1 TTT-TGTA
282883 TTTTACCCTT
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
59 18 0.33
60 33 0.60
61 4 0.07
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (59 bp):
TTTTGTAACTTTTAAAAGTCAAAGACTCAACAAAACAACACCCTATAATCGAGGGACCA
Found at i:286922 original size:18 final size:17
Alignment explanation
Indices: 286892--286927 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
286882 AATTTCACTT
*
286892 AGAGATGATGAAGAAAA
1 AGAGATGAAGAAGAAAA
286909 AGAGAATGAAGAAGAAAA
1 AGAG-ATGAAGAAGAAAA
286927 A
1 A
286928 AAAAGAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (17 bp):
AGAGATGAAGAAGAAAA
Found at i:288502 original size:19 final size:19
Alignment explanation
Indices: 288478--288517 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
288468 ACCACATATT
288478 TAATATAAATAAATAAATA
1 TAATATAAATAAATAAATA
* * *
288497 TAATATATATATATATATA
1 TAATATAAATAAATAAATA
288516 TA
1 TA
288518 TATGTCATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAATATAAATAAATAAATA
Found at i:289350 original size:14 final size:14
Alignment explanation
Indices: 289333--289363 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
289323 TAAAATTATT
289333 TAAATAAATTCAAA
1 TAAATAAATTCAAA
*
289347 TAAATAAATTCTAA
1 TAAATAAATTCAAA
289361 TAA
1 TAA
289364 TTTAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAATAAATTCAAA
Found at i:289553 original size:8 final size:7
Alignment explanation
Indices: 289539--289637 Score: 51
Period size: 7 Copynumber: 13.6 Consensus size: 7
289529 AGTTTACAAT
289539 TAAATAA
1 TAAATAA
289546 TCAAATAA
1 T-AAATAA
289554 TAAATAA
1 TAAATAA
289561 -AAATAAA
1 TAAAT-AA
*
289568 TAAATAC
1 TAAATAA
289575 T-AA-AA
1 TAAATAA
289580 TAAAATAA
1 T-AAATAA
* *
289588 TTAATTACT
1 -TAAATA-A
289597 TAAATAA
1 TAAATAA
*
289604 TAAAAAA
1 TAAATAA
*
289611 TTTAATGAA
1 -TAAAT-AA
*
289620 TAAAAAA
1 TAAATAA
*
289627 TAAATTA
1 TAAATAA
289634 TAAA
1 TAAA
289638 AACAATTATA
Statistics
Matches: 69, Mismatches: 13, Indels: 20
0.68 0.13 0.20
Matches are distributed among these distances:
5 2 0.03
6 6 0.09
7 30 0.43
8 28 0.41
9 3 0.04
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (7 bp):
TAAATAA
Found at i:289596 original size:21 final size:21
Alignment explanation
Indices: 289555--289603 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
289545 ATCAAATAAT
289555 AAATAAAAATAAATAAATACTA
1 AAAT-AAAATAAATAAATACTA
* * *
289577 AAATAAAATAATTAATTACTT
1 AAATAAAATAAATAAATACTA
289598 AAATAA
1 AAATAA
289604 TAAAAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATAAAATAAATAAATACTA
Found at i:289615 original size:16 final size:15
Alignment explanation
Indices: 289536--289639 Score: 58
Period size: 15 Copynumber: 7.1 Consensus size: 15
289526 ATAAGTTTAC
*
289536 AATTAAATAATCAAAT
1 AATTAAATAAT-AAAA
289552 AA-TAAATAA-AAATA
1 AATTAAATAATAAA-A
*
289566 AA-TAAATACT--AA
1 AATTAAATAATAAAA
* **
289578 AATAAAATAATTAATT
1 AATTAAATAA-TAAAA
*
289594 ACTTAAATAATAAAA
1 AATTAAATAATAAAA
*
289609 AATTTAATGAATAAAA
1 AATTAAAT-AATAAAA
*
289625 AA-TAAATTATAAAA
1 AATTAAATAATAAAA
289639 A
1 A
289640 CAATTATACC
Statistics
Matches: 67, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
12 3 0.04
13 9 0.13
14 16 0.24
15 20 0.30
16 19 0.28
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (15 bp):
AATTAAATAATAAAA
Found at i:291147 original size:20 final size:21
Alignment explanation
Indices: 291124--291174 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
291114 CATAATTATT
*
291124 TAAAAAATTAAATAAAATA-C
1 TAAAAAATTAAATAAAAAATC
* *
291144 TAAAATATTTAATAAAAAATC
1 TAAAAAATTAAATAAAAAATC
*
291165 AAAAAAATTA
1 TAAAAAATTA
291175 TATTGAACCG
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (21 bp):
TAAAAAATTAAATAAAAAATC
Found at i:291712 original size:11 final size:10
Alignment explanation
Indices: 291691--291737 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
291681 TCAGATTTTA
*
291691 TATTTTTATT
1 TATTATTATT
*
291701 TTTTAATTATT
1 TATT-ATTATT
291712 TATTATTA-T
1 TATTATTATT
291721 TATTATTATT
1 TATTATTATT
*
291731 TAATATT
1 TATTATT
291738 TTTTTTTACT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 9 0.29
10 14 0.45
11 8 0.26
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TATTATTATT
Found at i:292039 original size:36 final size:36
Alignment explanation
Indices: 291992--292063 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
291982 GAGGAATTGG
291992 AGAGGGAGAGATGGAACCCACTTCCAGCTTCGAAAA
1 AGAGGGAGAGATGGAACCCACTTCCAGCTTCGAAAA
292028 AGAGGGAGAGATGGAACCCACTTCCAGCTTCGAAAA
1 AGAGGGAGAGATGGAACCCACTTCCAGCTTCGAAAA
292064 TGTCGATCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.22, G:0.28, T:0.14
Consensus pattern (36 bp):
AGAGGGAGAGATGGAACCCACTTCCAGCTTCGAAAA
Found at i:298033 original size:43 final size:43
Alignment explanation
Indices: 297985--298067 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
297975 CGAATGAGCC
*
297985 ATCCACGATTTCAACTCCAAGACGGAGGATATCATGCCCACAA
1 ATCCACGATTTCAACTCCAAGACGAAGGATATCATGCCCACAA
* * *
298028 ATCCACGATTTCAACTTCATGACGAAGGATATCGTGCCCA
1 ATCCACGATTTCAACTCCAAGACGAAGGATATCATGCCCA
298068 TCTACACAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.22
Consensus pattern (43 bp):
ATCCACGATTTCAACTCCAAGACGAAGGATATCATGCCCACAA
Found at i:298372 original size:116 final size:116
Alignment explanation
Indices: 298209--298420 Score: 363
Period size: 116 Copynumber: 1.8 Consensus size: 116
298199 CAATACAAGC
* *
298209 TTGGATTTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTTAACTTCACAACGAATG-GGCCA
1 TTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAGGCTCAACTTCACAACGAA-GAGGCCA
298273 TCCACGATTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGTAACATTCA
65 TCCACGATTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGTAACATTCA
*
298325 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGAGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAGGCTCAACTTCACAACGAAGAGGCCAT
* *
298390 CCACGGTTTCAACTTCACGACGTAGGGAATC
66 CCACGATTTCAACTTCACGACGAAGGGAATC
298421 CTGCCCATAA
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
115 1 0.01
116 89 0.99
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (116 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAGGCTCAACTTCACAACGAAGAGGCCAT
CCACGATTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGTAACATTCA
Found at i:298624 original size:21 final size:21
Alignment explanation
Indices: 298586--298665 Score: 91
Period size: 21 Copynumber: 4.0 Consensus size: 21
298576 AATTTACTCA
*
298586 AAACAAAGTTTTGTCTCTCTTG
1 AAACAAA-TTTTGCCTCTCTTG
298608 AAACAAATTTTGCCTCTCTTG
1 AAACAAATTTTGCCTCTCTTG
*
298629 AGAC-AA-TTT--C-C-CTTG
1 AAACAAATTTTGCCTCTCTTG
298644 AAACAAATTTTGCCTCTCTTG
1 AAACAAATTTTGCCTCTCTTG
298665 A
1 A
298666 GACAGTTTCC
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
15 7 0.14
16 3 0.06
17 4 0.08
19 4 0.08
20 3 0.06
21 21 0.43
22 7 0.14
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.38
Consensus pattern (21 bp):
AAACAAATTTTGCCTCTCTTG
Found at i:298645 original size:36 final size:36
Alignment explanation
Indices: 298604--298976 Score: 253
Period size: 36 Copynumber: 11.3 Consensus size: 36
298594 TTTTGTCTCT
*
298604 CTTGAAACAAATTTTGCCTCTCTTGAGACAATTTCC
1 CTTGAAACAAATTTTGCCTCTCTTGAGACAGTTTCC
298640 CTTGAAACAAATTTTGCCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAATTTTGCCTCTCTTGAGACAGTTTCC
* *
298676 ATTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAATTTTGCCTCTCTTGAGACAGTTTCC
* * * *
298712 CTTGAAACAAA------ATCT-TT-AAATATGTTTTC
1 CTTGAAACAAATTTTGCCTCTCTTGAGACA-GTTTCC
* * * * * *
298741 CTTTAAATAAATTTCGTCTCCCTAGAGACAGTTT-C
1 CTTGAAACAAATTTTGCCTCTCTTGAGACAGTTTCC
* * * * * * *
298776 TTTTAGAACTAAGTTTTGTCACTTTTGAGACAGTTTCT
1 CTTGA-AAC-AAATTTTGCCTCTCTTGAGACAGTTTCC
**
298814 CTTGAAACAAATTTTTTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAATTTTGCCTCTCTTGAGACAGTTTCC
298850 CTTGAAACAAA---------T-TTGAGACAGTTTCC
1 CTTGAAACAAATTTTGCCTCTCTTGAGACAGTTTCC
298876 CTTGAAACAAA-------T-T-TTGAGACAGTTTCC
1 CTTGAAACAAATTTTGCCTCTCTTGAGACAGTTTCC
298903 CTTGAAACAAA-------T-T-TTGAGACAGTTTCC
1 CTTGAAACAAATTTTGCCTCTCTTGAGACAGTTTCC
*
298930 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAATTTTGCCTCTCTTGAGACAGTTTCC
298966 CTTGAAACAAA
1 CTTGAAACAAA
298977 ATCTTTGAAT
Statistics
Matches: 284, Mismatches: 31, Indels: 44
0.79 0.09 0.12
Matches are distributed among these distances:
26 25 0.09
27 54 0.19
28 3 0.01
29 16 0.06
30 3 0.01
34 1 0.00
35 8 0.03
36 145 0.51
37 26 0.09
38 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (36 bp):
CTTGAAACAAATTTTGCCTCTCTTGAGACAGTTTCC
Found at i:298899 original size:27 final size:27
Alignment explanation
Indices: 298836--298945 Score: 213
Period size: 27 Copynumber: 4.1 Consensus size: 27
298826 TTTTTCTCTC
298836 TTGAGACAGTTTCCCTTGAAACAAA-T
1 TTGAGACAGTTTCCCTTGAAACAAATT
298862 TTGAGACAGTTTCCCTTGAAACAAATT
1 TTGAGACAGTTTCCCTTGAAACAAATT
298889 TTGAGACAGTTTCCCTTGAAACAAATT
1 TTGAGACAGTTTCCCTTGAAACAAATT
298916 TTGAGACAGTTTCCCTTGAAACAAATT
1 TTGAGACAGTTTCCCTTGAAACAAATT
298943 TTG
1 TTG
298946 TCTCTCTTGA
Statistics
Matches: 83, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
26 25 0.30
27 58 0.70
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (27 bp):
TTGAGACAGTTTCCCTTGAAACAAATT
Found at i:299039 original size:66 final size:64
Alignment explanation
Indices: 298889--299048 Score: 209
Period size: 66 Copynumber: 2.5 Consensus size: 64
298879 GAAACAAATT
*
298889 TTGAGACAGTTTCCCTTGAAAC-AAATTTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAAATTTTGAGACAGTTTCCCTTGAAACAAATTTTGCCTCTC
* *
298952 TTGAGACAGTTTCCCTTGAAACAAAATCTTTGA-ATATGTTTCTCTTGAAACAAAATTTTGCCT-
1 TTGAGACAGTTTCCCTTGAAACAAAAT-TTTGAGACA-GTTTCCCTTGAAAC-AAATTTTGCCTC
299015 TCC
63 T-C
* * *
299018 TTGAGATAATTTCTCTTGAAACAAAATTTTG
1 TTGAGACAGTTTCCCTTGAAACAAAATTTTG
299049 CCTCCCTTGA
Statistics
Matches: 86, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
63 22 0.26
64 6 0.07
65 23 0.27
66 35 0.41
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (64 bp):
TTGAGACAGTTTCCCTTGAAACAAAATTTTGAGACAGTTTCCCTTGAAACAAATTTTGCCTCTC
Found at i:299040 original size:37 final size:37
Alignment explanation
Indices: 298990--299080 Score: 164
Period size: 37 Copynumber: 2.5 Consensus size: 37
298980 TTTGAATATG
*
298990 TTTCTCTTGAAACAAAATTTTGCCTTCCTTGAGATAA
1 TTTCTCTTGAAACAAAATTTTGCCTCCCTTGAGATAA
*
299027 TTTCTCTTGAAACAAAATTTTGCCTCCCTTGAGATAG
1 TTTCTCTTGAAACAAAATTTTGCCTCCCTTGAGATAA
299064 TTTCTCTTGAAACAAAA
1 TTTCTCTTGAAACAAAA
299081 AAAAATATCA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (37 bp):
TTTCTCTTGAAACAAAATTTTGCCTCCCTTGAGATAA
Found at i:299267 original size:84 final size:84
Alignment explanation
Indices: 299119--299290 Score: 247
Period size: 84 Copynumber: 2.0 Consensus size: 84
299109 GAAACACCAA
*
299119 ACCTTCGAGTTGGATTATACTCAACTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAG
1 ACCTTCGAGTTGGACTATACTCAACTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAG
*
299184 GGCTAT-TTTCCAACCAAAG
66 GGCTATCTGT-CAACCAAAG
* * * * * * *
299203 ACCTTCGAGTTTGACTATGCTCAATTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAG
1 ACCTTCGAGTTGGACTATACTCAACTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAG
299268 GGCTATCTGTCAACCAAAG
66 GGCTATCTGTCAACCAAAG
299287 ACCT
1 ACCT
299291 GACGAATTCG
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
84 76 0.97
85 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (84 bp):
ACCTTCGAGTTGGACTATACTCAACTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAG
GGCTATCTGTCAACCAAAG
Found at i:302983 original size:137 final size:138
Alignment explanation
Indices: 302732--302987 Score: 460
Period size: 137 Copynumber: 1.9 Consensus size: 138
302722 GTGTCCCTGG
* *
302732 TTCTAACCTGTTTAGAGTTTGTCATGGAGCAAAATCATGGAATTCCCAGTTATATCCAATCCAAG
1 TTCTAACCTGTTTAGAGTTTGACATGGAGCAAAATCATGGAATTCCCAGTTATATACAATCCAAG
* * *
302797 TGGGTAGAATCAAATTTCATCTTTGGTTAATTATTTTTTGTTTGGTGTTGAATTCAGCTTAGTGC
66 TGGGTAAAATCAAATTTCATCTTTGGTTAATTATTGTTTGTTTGATGTTGAATTCAGCTTAGTGC
302862 TTTTAGTT
131 TTTTAGTT
302870 TTCTAACCTGTTTAGAGTTT-ACATGGAGCAAAATCATGGAATTCCCAGTTATATACAATCCAAG
1 TTCTAACCTGTTTAGAGTTTGACATGGAGCAAAATCATGGAATTCCCAGTTATATACAATCCAAG
302934 TGGGTAAAATCAAATTTCATCTTTGGTTAATTATTGTTTGTTTGATGTTGAATT
66 TGGGTAAAATCAAATTTCATCTTTGGTTAATTATTGTTTGTTTGATGTTGAATT
302988 AATGGATTCT
Statistics
Matches: 113, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
137 93 0.82
138 20 0.18
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (138 bp):
TTCTAACCTGTTTAGAGTTTGACATGGAGCAAAATCATGGAATTCCCAGTTATATACAATCCAAG
TGGGTAAAATCAAATTTCATCTTTGGTTAATTATTGTTTGTTTGATGTTGAATTCAGCTTAGTGC
TTTTAGTT
Found at i:311042 original size:18 final size:19
Alignment explanation
Indices: 311007--311043 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
310997 CACGGAATGT
311007 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
311027 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
311044 GGATTACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:311983 original size:36 final size:36
Alignment explanation
Indices: 311935--312077 Score: 130
Period size: 36 Copynumber: 4.0 Consensus size: 36
311925 CCAGAGCTTA
* *
311935 AGTGAGATAAAATAATATTTCAAGGAAAAC-ATCTCG
1 AGTGAGACAAAAT-TTATTTCAAGGAAAACTATCTCG
* **
311971 AGTGAGACAAAATTTATTTCAA-GAGAAACTACCTTA
1 AGTGAGACAAAATTTATTTCAAGGA-AAACTATCTCG
* ** * * *
312007 AGTGAGA-AAAAATTATTTTGAGGAAAAAATGTCTTG
1 AGTGAGACAAAATTTATTTCAAGG-AAAACTATCTCG
*
312043 AGTGAGACAAAATTTATTTCAAGGGAAACTATCTC
1 AGTGAGACAAAATTTATTTCAAGGAAAACTATCTC
312078 AAGGAAGATA
Statistics
Matches: 83, Mismatches: 19, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
34 2 0.02
35 23 0.28
36 44 0.53
37 14 0.17
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.28
Consensus pattern (36 bp):
AGTGAGACAAAATTTATTTCAAGGAAAACTATCTCG
Found at i:312048 original size:72 final size:72
Alignment explanation
Indices: 311931--312090 Score: 200
Period size: 72 Copynumber: 2.2 Consensus size: 72
311921 GTTTCCAGAG
*
311931 CTTAAGTGAGATAAAATAATATTTCAAGGAAAACATCTCGAGTGAGACAAAATTTATTTCAAGAG
1 CTTAAGTGAGATAAAATAATATTTCAAGGAAAAAATCTCGAGTGAGACAAAATTTATTTCAAGAG
311996 AAACTAC
66 AAACTAC
* ** *
312003 CTTAAGTGAGA-AAAA-ATTATTTTGAGGAAAAAATGTCTTGAGTGAGACAAAATTTATTTCAAG
1 CTTAAGTGAGATAAAATAATATTTCAAGGAAAAAA--TCTCGAGTGAGACAAAATTTATTTCAAG
* *
312066 GGAAACTAT
64 AGAAACTAC
*
312075 CTCAAG-GAAGATAAAA
1 CTTAAGTG-AGATAAAA
312091 AGTTTGTTTA
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
70 14 0.18
71 5 0.07
72 53 0.70
73 4 0.05
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (72 bp):
CTTAAGTGAGATAAAATAATATTTCAAGGAAAAAATCTCGAGTGAGACAAAATTTATTTCAAGAG
AAACTAC
Found at i:316152 original size:17 final size:17
Alignment explanation
Indices: 316130--316164 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
316120 TTAACTCTCA
316130 TTCGGAAAAGGCCTTTT
1 TTCGGAAAAGGCCTTTT
316147 TTCGGAAAAGGCCTTTT
1 TTCGGAAAAGGCCTTTT
316164 T
1 T
316165 GATAACATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (17 bp):
TTCGGAAAAGGCCTTTT
Found at i:318325 original size:18 final size:18
Alignment explanation
Indices: 318302--318345 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
318292 TTTGGAATTT
318302 GTTATTCTAGAATTCAGG
1 GTTATTCTAGAATTCAGG
318320 GTTATTCTAGAATTCAGG
1 GTTATTCTAGAATTCAGG
318338 GTTATTCT
1 GTTATTCT
318346 TCTTAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.43
Consensus pattern (18 bp):
GTTATTCTAGAATTCAGG
Found at i:319597 original size:21 final size:19
Alignment explanation
Indices: 319571--319674 Score: 82
Period size: 21 Copynumber: 5.1 Consensus size: 19
319561 CGTTAGACAA
*
319571 GGGGAATCGACACCCCCTGG
1 GGGGAATCG-TACCCCCTGG
* *
319591 GAGGGAATCTGTTCCCTCTGG
1 G-GGGAATC-GTACCCCCTGG
319612 GGGGAATCGGTACCCCCTGGG
1 GGGGAATC-GTACCCCCT-GG
* *
319633 GGGGAATCTGTTCCCTCTGG
1 GGGGAATC-GTACCCCCTGG
*
319653 GGAGGAATCTGTACCCCTTGG
1 GG-GGAATC-GTACCCCCTGG
319674 G
1 G
319675 CAATCTGATT
Statistics
Matches: 68, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
20 19 0.28
21 48 0.71
22 1 0.01
ACGTcount: A:0.15, C:0.27, G:0.37, T:0.21
Consensus pattern (19 bp):
GGGGAATCGTACCCCCTGG
Found at i:319618 original size:20 final size:20
Alignment explanation
Indices: 319587--319664 Score: 102
Period size: 21 Copynumber: 3.8 Consensus size: 20
319577 TCGACACCCC
319587 CTGGGAGGGAATCTGTTCCCT
1 CTGGG-GGGAATCTGTTCCCT
* * *
319608 CTGGGGGGAATCGGTACCCC
1 CTGGGGGGAATCTGTTCCCT
319628 CTGGGGGGGAATCTGTTCCCT
1 CT-GGGGGGAATCTGTTCCCT
319649 CTGGGGAGGAATCTGT
1 CTGGGG-GGAATCTGT
319665 ACCCCTTGGG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 18 0.37
21 31 0.63
ACGTcount: A:0.14, C:0.23, G:0.38, T:0.24
Consensus pattern (20 bp):
CTGGGGGGAATCTGTTCCCT
Found at i:319628 original size:41 final size:41
Alignment explanation
Indices: 319571--319674 Score: 154
Period size: 41 Copynumber: 2.5 Consensus size: 41
319561 CGTTAGACAA
**
319571 GGGGAATCGACACCCCCTGGGAGGGAATCTGTTCCCTCTGG
1 GGGGAATCGGTACCCCCTGGGAGGGAATCTGTTCCCTCTGG
*
319612 GGGGAATCGGTACCCCCTGGGGGGGAATCTGTTCCCTCTGG
1 GGGGAATCGGTACCCCCTGGGAGGGAATCTGTTCCCTCTGG
* *
319653 GGAGGAATCTGTACCCCTTGGG
1 GG-GGAATCGGTACCCCCTGGG
319675 CAATCTGATT
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 40 0.70
42 17 0.30
ACGTcount: A:0.15, C:0.27, G:0.37, T:0.21
Consensus pattern (41 bp):
GGGGAATCGGTACCCCCTGGGAGGGAATCTGTTCCCTCTGG
Found at i:321110 original size:19 final size:20
Alignment explanation
Indices: 321067--321114 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
321057 TCTAAATCCT
*
321067 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
321087 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
321106 TTTTCAAAA
1 TTTTCAAAA
321115 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:322367 original size:21 final size:20
Alignment explanation
Indices: 322341--322464 Score: 133
Period size: 21 Copynumber: 6.1 Consensus size: 20
322331 CCGTTAGAAA
*
322341 GGGGGAATCGGTACCCCCTAT
1 GGGGGAATCGGTACCCCCT-G
** *
322362 GGGGGAATATGTTCCCCCTG
1 GGGGGAATCGGTACCCCCTG
* *
322382 GGGGGAATTGGTACCCCTTGG
1 GGGGGAATCGGTACCCCCT-G
* *
322403 GGGGGAATCTGT-TCCCCTG
1 GGGGGAATCGGTACCCCCTG
322422 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTACCCCCT-G
*
322443 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
322463 GG
1 GG
322465 CAATCTAATT
Statistics
Matches: 85, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
19 12 0.14
20 27 0.32
21 46 0.54
ACGTcount: A:0.15, C:0.26, G:0.39, T:0.21
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCCTG
Found at i:322397 original size:41 final size:41
Alignment explanation
Indices: 322341--322464 Score: 187
Period size: 40 Copynumber: 3.0 Consensus size: 41
322331 CCGTTAGAAA
** *
322341 GGGGGAATCGGTACCCCCTATGGGGGAATATGTTCCCCCTG
1 GGGGGAATCGGTACCCCCTGGGGGGGAATCTGTTCCCCCTG
* *
322382 GGGGGAATTGGTACCCCTTGGGGGGGAATCTGTT-CCCCTG
1 GGGGGAATCGGTACCCCCTGGGGGGGAATCTGTTCCCCCTG
*
322422 GGGGGAATCGGTACCCCCTGGGGGGGAATCTGTACCCCCTG
1 GGGGGAATCGGTACCCCCTGGGGGGGAATCTGTTCCCCCTG
322463 GG
1 GG
322465 CAATCTAATT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 37 0.50
41 37 0.50
ACGTcount: A:0.15, C:0.26, G:0.39, T:0.21
Consensus pattern (41 bp):
GGGGGAATCGGTACCCCCTGGGGGGGAATCTGTTCCCCCTG
Found at i:322399 original size:40 final size:40
Alignment explanation
Indices: 322341--322464 Score: 162
Period size: 41 Copynumber: 3.0 Consensus size: 40
322331 CCGTTAGAAA
*
322341 GGGGGAATCGGTACCCCCTATGGGGGAATATGTTCCCCCTG
1 GGGGGAATCGGTACCCCCT-TGGGGGAATCTGTTCCCCCTG
*
322382 GGGGGAATTGGTA-CCCCTTGGGGGGGAATCTGTT-CCCCTG
1 GGGGGAATCGGTACCCCCTT--GGGGGAATCTGTTCCCCCTG
* *
322422 GGGGGAATCGGTACCCCCTGGGGGGGAATCTGTACCCCCTG
1 GGGGGAATCGGTACCCCCT-TGGGGGAATCTGTTCCCCCTG
322463 GG
1 GG
322465 CAATCTAATT
Statistics
Matches: 73, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
39 1 0.01
40 35 0.48
41 37 0.51
ACGTcount: A:0.15, C:0.26, G:0.39, T:0.21
Consensus pattern (40 bp):
GGGGGAATCGGTACCCCCTTGGGGGAATCTGTTCCCCCTG
Found at i:331081 original size:13 final size:13
Alignment explanation
Indices: 331063--331091 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
331053 ATTTTATTTG
331063 AAGTTTAGGGACT
1 AAGTTTAGGGACT
331076 AAGTTTAGGGACT
1 AAGTTTAGGGACT
331089 AAG
1 AAG
331092 GTGGTGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.07, G:0.31, T:0.28
Consensus pattern (13 bp):
AAGTTTAGGGACT
Found at i:339166 original size:20 final size:20
Alignment explanation
Indices: 339141--339178 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
339131 TTGACACCCT
339141 TTTCGAACACGGAAAATACC
1 TTTCGAACACGGAAAATACC
339161 TTTCGAACACGGAAAATA
1 TTTCGAACACGGAAAATA
339179 ATGGAGGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.21
Consensus pattern (20 bp):
TTTCGAACACGGAAAATACC
Found at i:344346 original size:19 final size:19
Alignment explanation
Indices: 344305--344346 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
344295 ATGACCAACA
* * *
344305 AATTCTCAATGCGATCTCG
1 AATTCTCAATACGAACTCC
344324 AATTCTCAATACGAACTCC
1 AATTCTCAATACGAACTCC
344343 AATT
1 AATT
344347 TCGCAACACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.10, T:0.31
Consensus pattern (19 bp):
AATTCTCAATACGAACTCC
Found at i:344369 original size:20 final size:20
Alignment explanation
Indices: 344340--344381 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
344330 CAATACGAAC
*
344340 TCCAATTTCGCAACACAGTT
1 TCCAAATTCGCAACACAGTT
* *
344360 TCCAAATTCGTAACTCAGTT
1 TCCAAATTCGCAACACAGTT
344380 TC
1 TC
344382 TGCAATCGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.33
Consensus pattern (20 bp):
TCCAAATTCGCAACACAGTT
Found at i:344448 original size:20 final size:20
Alignment explanation
Indices: 344407--344538 Score: 174
Period size: 20 Copynumber: 6.5 Consensus size: 20
344397 AATTTCTTTC
344407 TCGCAACGCGATTTTCCAAAT
1 TCGCAACGCGA-TTTCCAAAT
* *
344428 TTGCAACGCGATTTTCAAAT
1 TCGCAACGCGATTTCCAAAT
*
344448 TCACAACGCGATTTCCAAAT
1 TCGCAACGCGATTTCCAAAT
*
344468 TCGCAATGCGATTTCCAAAT
1 TCGCAACGCGATTTCCAAAT
*
344488 TCGCAATGCGATTTCCAAAT
1 TCGCAACGCGATTTCCAAAT
* **
344508 TCGCAACTCGATTTCTGAAT
1 TCGCAACGCGATTTCCAAAT
*
344528 TCGCAATGCGA
1 TCGCAACGCGA
344539 ACGAAACACA
Statistics
Matches: 98, Mismatches: 13, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
20 88 0.90
21 10 0.10
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (20 bp):
TCGCAACGCGATTTCCAAAT
Found at i:344600 original size:40 final size:40
Alignment explanation
Indices: 344556--344644 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 40
344546 ACAAGTTTCC
*
344556 TTTTCGCAAC-AAGATTTTCT-AAATCGCAACACGAATTTTG
1 TTTTCGCAACTAA-ATTTT-TGAAATCGCAACACGAATTTTA
* *
344596 TTTTCGCAACTCAATTTTTGAATTCGCAACACGAATTTTA
1 TTTTCGCAACTAAATTTTTGAAATCGCAACACGAATTTTA
*
344636 ATTTCGCAA
1 TTTTCGCAA
344645 TAGCTTTTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
39 1 0.02
40 41 0.95
41 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.37
Consensus pattern (40 bp):
TTTTCGCAACTAAATTTTTGAAATCGCAACACGAATTTTA
Found at i:344602 original size:20 final size:20
Alignment explanation
Indices: 344557--344665 Score: 75
Period size: 20 Copynumber: 5.5 Consensus size: 20
344547 CAAGTTTCCT
* *
344557 TTTCGCAACAAGATTTTCTAA
1 TTTCGCAACACGAATTT-TAA
* **
344578 -ATCGCAACACGAATTTTGT
1 TTTCGCAACACGAATTTTAA
*
344597 TTTCGCAACTC-AATTTTTGAA
1 TTTCGCAACACGAA-TTTT-AA
344618 -TTCGCAACACGAATTTTAA
1 TTTCGCAACACGAATTTTAA
* * *
344637 TTTCGCAATA-G-CTTTTAT
1 TTTCGCAACACGAATTTTAA
344655 TTTCGCAACAC
1 TTTCGCAACAC
344666 AAATGTTTTG
Statistics
Matches: 68, Mismatches: 14, Indels: 14
0.71 0.15 0.15
Matches are distributed among these distances:
18 14 0.21
19 6 0.09
20 46 0.68
21 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (20 bp):
TTTCGCAACACGAATTTTAA
Found at i:345639 original size:24 final size:24
Alignment explanation
Indices: 345588--345641 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
345578 GTATTCTAAA
*
345588 TTTGATCTTGGTCAATACCCGTAC
1 TTTGATCTTGGTCAATACCCGGAC
* * *
345612 TTTGTTCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
345636 TTTGAT
1 TTTGAT
345642 GATGTTTCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:349581 original size:49 final size:49
Alignment explanation
Indices: 349502--349604 Score: 152
Period size: 49 Copynumber: 2.1 Consensus size: 49
349492 CGTTGCGATT
* * * *
349502 TTCGCGTTGCGATTGTTGCGAAAGTCAAATTCACAACGTGAAAGTCAAA
1 TTCGCGTTGCGATTGTTGCGAAAGTCAAATTCAAAACGCGAAAATAAAA
* *
349551 TTCGTGTTGCGATTGTTGCGAAAGTTAAATTCAAAACGCGAAAATAAAA
1 TTCGCGTTGCGATTGTTGCGAAAGTCAAATTCAAAACGCGAAAATAAAA
349600 TTCGC
1 TTCGC
349605 AACGCGAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (49 bp):
TTCGCGTTGCGATTGTTGCGAAAGTCAAATTCAAAACGCGAAAATAAAA
Found at i:349649 original size:20 final size:20
Alignment explanation
Indices: 349608--349652 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
349598 AATTCGCAAC
**
349608 GCGAATTTGACTTTTGTGTT
1 GCGAATTTGACTTTTGCATT
349628 GCGAATTTGA-TTTTCGCATT
1 GCGAATTTGACTTTT-GCATT
349648 GCGAA
1 GCGAA
349653 AGTGTACCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.20, C:0.13, G:0.24, T:0.42
Consensus pattern (20 bp):
GCGAATTTGACTTTTGCATT
Found at i:351188 original size:17 final size:17
Alignment explanation
Indices: 351166--351201 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
351156 CCTCTTGAAC
*
351166 GATGAGAGGGGCCTCTT
1 GATGAGAGGGACCTCTT
351183 GATGAGAGGGACCTCTT
1 GATGAGAGGGACCTCTT
351200 GA
1 GA
351202 ACGATAGGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.17, G:0.39, T:0.22
Consensus pattern (17 bp):
GATGAGAGGGACCTCTT
Found at i:351226 original size:21 final size:21
Alignment explanation
Indices: 351136--351227 Score: 97
Period size: 21 Copynumber: 4.6 Consensus size: 21
351126 GTGAATCGGG
*
351136 CTCTTGAACG-GAGGAAGGGGC
1 CTCTTGAACGATAGG-AGGGGC
351157 CTCTTGAACGAT-GAGAGGGGC
1 CTCTTGAACGATAG-GAGGGGC
* *
351178 CTCTTG-ATG--A-GAGGGAC
1 CTCTTGAACGATAGGAGGGGC
351195 CTCTTGAACGATAGGAGGGGC
1 CTCTTGAACGATAGGAGGGGC
351216 CTCTTGAACGAT
1 CTCTTGAACGAT
351228 GACATGTGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
17 12 0.20
18 2 0.03
20 3 0.05
21 41 0.69
22 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.36, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATAGGAGGGGC
Found at i:351661 original size:21 final size:21
Alignment explanation
Indices: 351526--351686 Score: 85
Period size: 21 Copynumber: 7.7 Consensus size: 21
351516 TAGAGCGGCT
* ***
351526 ACCTCATCACGTAAAGTAGAT
1 ACCTCATCACGTAAAGCACCG
* *
351547 ACCTCACCACGTAAAACACC-
1 ACCTCATCACGTAAAGCACCG
* * * * * *
351567 ACTGTCATCGCATAAAACAGCT
1 AC-CTCATCACGTAAAGCACCG
*
351589 ACCTCACCACGTAAAG-ACCG
1 ACCTCATCACGTAAAGCACCG
** *
351609 TACCTCATCACGCCATGCACC-
1 -ACCTCATCACGTAAAGCACCG
** * *
351630 ATTTTCGTCACGTAAAGTACCG
1 A-CCTCATCACGTAAAGCACCG
*
351652 ACCTCATCACGTAAAGCACTG
1 ACCTCATCACGTAAAGCACCG
351673 ACCTCATCACGTAA
1 ACCTCATCACGTAA
351687 CTACCCTGAC
Statistics
Matches: 101, Mismatches: 33, Indels: 12
0.69 0.23 0.08
Matches are distributed among these distances:
20 5 0.05
21 90 0.89
22 6 0.06
ACGTcount: A:0.34, C:0.34, G:0.12, T:0.20
Consensus pattern (21 bp):
ACCTCATCACGTAAAGCACCG
Found at i:351848 original size:42 final size:42
Alignment explanation
Indices: 351801--351899 Score: 146
Period size: 42 Copynumber: 2.4 Consensus size: 42
351791 GTGATGGAAT
* * *
351801 AGGTAATGGCTCTCGGTGTGGAGGC-GTATAATCGGCTCGATC
1 AGGTAATGGCTCTCGGTGTCGA-GCTGTAGAATCGACTCGATC
351843 AGGTAATGGCTCTCGGTGTCGAGCTGTAGAATCGACTCGATC
1 AGGTAATGGCTCTCGGTGTCGAGCTGTAGAATCGACTCGATC
*
351885 AGGTGATGGCTCTCG
1 AGGTAATGGCTCTCG
351900 AAGTGGGGGG
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
41 2 0.04
42 50 0.96
ACGTcount: A:0.19, C:0.20, G:0.34, T:0.26
Consensus pattern (42 bp):
AGGTAATGGCTCTCGGTGTCGAGCTGTAGAATCGACTCGATC
Found at i:353404 original size:20 final size:20
Alignment explanation
Indices: 353381--353475 Score: 172
Period size: 20 Copynumber: 4.8 Consensus size: 20
353371 GTTTTTGAAA
*
353381 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGAATTTCATTT
353401 TCGCGTTGCGAATTTCATTT
1 TCGCGTTGCGAATTTCATTT
353421 TCGCGTTGCGAATTTCATTT
1 TCGCGTTGCGAATTTCATTT
353441 TCGCGTTGCGAATTTCATTT
1 TCGCGTTGCGAATTTCATTT
*
353461 TGGCGTTGCGAATTT
1 TCGCGTTGCGAATTT
353476 AAGTTTCAAA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 73 1.00
ACGTcount: A:0.14, C:0.19, G:0.22, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGAATTTCATTT
Found at i:354022 original size:15 final size:15
Alignment explanation
Indices: 354002--354041 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
353992 TAAACACGCT
354002 TTGCGAATTTTCACG
1 TTGCGAATTTTCACG
354017 TTGCGAATTTTCACG
1 TTGCGAATTTTCACG
354032 TTGCGAATTT
1 TTGCGAATTT
354042 GGAAAATCGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.42
Consensus pattern (15 bp):
TTGCGAATTTTCACG
Found at i:361007 original size:107 final size:107
Alignment explanation
Indices: 360891--361105 Score: 358
Period size: 107 Copynumber: 2.0 Consensus size: 107
360881 AAAATGAATC
*
360891 AAAATTGATAATTGATGTACTAAACATAAAATTTACCCTAGTTAAAACATAAATAAATACCATAT
1 AAAATTGATAATTGATATACTAAACATAAAATTTACCCTAGTTAAAACATAAATAAATACCATAT
* *
360956 GAATAATTATCAACAGTGCAATGAAAATCCCCATTACCGTAG
66 GAATAATTACCAACAGTGCAAGGAAAATCCCCATTACCGTAG
* * **
360998 AAAATTGATAATTTATATATTAAACATATTATTTACCCTAGTTAAAACATAAATAAATACCATAT
1 AAAATTGATAATTGATATACTAAACATAAAATTTACCCTAGTTAAAACATAAATAAATACCATAT
*
361063 GAATAATTACCAACAGTGCAGGGAAAATCCCCATTACCGTAG
66 GAATAATTACCAACAGTGCAAGGAAAATCCCCATTACCGTAG
361105 A
1 A
361106 GAAAATTTTA
Statistics
Matches: 100, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
107 100 1.00
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.29
Consensus pattern (107 bp):
AAAATTGATAATTGATATACTAAACATAAAATTTACCCTAGTTAAAACATAAATAAATACCATAT
GAATAATTACCAACAGTGCAAGGAAAATCCCCATTACCGTAG
Found at i:362221 original size:24 final size:24
Alignment explanation
Indices: 362194--362247 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
362184 TTCTCATTTT
* *
362194 CTAATTCCTCCTCTTTCAAAATCC
1 CTAACTCCTCCTCGTTCAAAATCC
362218 CTAACTCCTCCTCGTTCAAAATCC
1 CTAACTCCTCCTCGTTCAAAATCC
362242 CTAACT
1 CTAACT
362248 GAGGTAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.26, C:0.39, G:0.02, T:0.33
Consensus pattern (24 bp):
CTAACTCCTCCTCGTTCAAAATCC
Found at i:365467 original size:14 final size:14
Alignment explanation
Indices: 365448--365474 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
365438 AGCTACTGTG
365448 ATTACTAATGGTTT
1 ATTACTAATGGTTT
365462 ATTACTAATGGTT
1 ATTACTAATGGTT
365475 GAGTAGTTAC
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:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (14 bp):
ATTACTAATGGTTT
Found at i:367331 original size:24 final size:24
Alignment explanation
Indices: 367299--367376 Score: 129
Period size: 24 Copynumber: 3.2 Consensus size: 24
367289 TTCTCATTTT
* **
367299 CTAATTCCTCCTATTTCAAAATCC
1 CTAACTCCTCCTCGTTCAAAATCC
367323 CTAACTCCTCCTCGTTCAAAATCC
1 CTAACTCCTCCTCGTTCAAAATCC
367347 CTAACTCCTCCTCGTTCAAAATCC
1 CTAACTCCTCCTCGTTCAAAATCC
367371 CTAACT
1 CTAACT
367377 GAGGTAATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.27, C:0.38, G:0.03, T:0.32
Consensus pattern (24 bp):
CTAACTCCTCCTCGTTCAAAATCC
Found at i:370171 original size:23 final size:25
Alignment explanation
Indices: 370131--370181 Score: 63
Period size: 23 Copynumber: 2.1 Consensus size: 25
370121 AAAATTATTA
370131 AAATATTATTTTTGTATAA-AT-AC
1 AAATATTATTTTTGTATAATATAAC
*
370154 AAATATT-TTTTTATTATAATATAAC
1 AAATATTATTTTT-GTATAATATAAC
370179 AAA
1 AAA
370182 ATATACTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 5 0.21
23 12 0.50
24 2 0.08
25 5 0.21
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (25 bp):
AAATATTATTTTTGTATAATATAAC
Found at i:376249 original size:30 final size:30
Alignment explanation
Indices: 376214--376350 Score: 150
Period size: 30 Copynumber: 4.6 Consensus size: 30
376204 TAGTTCATCG
* *
376214 CTTTAACTTTCTATTTTTGCTATTTTAGTC
1 CTTTAACTTTCTGTTTTTACTATTTTAGTC
* * * *
376244 TTTTAAGTTTATGTCTTTACTATTTTAGTC
1 CTTTAACTTTCTGTTTTTACTATTTTAGTC
*
376274 CTTTAACTTTTTGTTTTTACTATTTTAGTC
1 CTTTAACTTTCTGTTTTTACTATTTTAGTC
* * * *
376304 CTTTAAGTTTTTG-TTTTGCTATTTTGGTC
1 CTTTAACTTTCTGTTTTTACTATTTTAGTC
* *
376333 CTTTAAATTTCTTTTTTT
1 CTTTAACTTTCTGTTTTT
376351 TTTTTTGCTA
Statistics
Matches: 90, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
29 24 0.27
30 66 0.73
ACGTcount: A:0.16, C:0.12, G:0.09, T:0.63
Consensus pattern (30 bp):
CTTTAACTTTCTGTTTTTACTATTTTAGTC
Found at i:376351 original size:60 final size:61
Alignment explanation
Indices: 376214--376380 Score: 196
Period size: 60 Copynumber: 2.7 Consensus size: 61
376204 TAGTTCATCG
* *
376214 CTTTAACTTTC-TATTTTTGCTATTTTAGTCTTTTAAGTTTATGTCTTTACTATTTTAGTC
1 CTTTAACTTTCTTATTTTTGCTATTTTAGTCCTTTAAGTTTTTGTCTTTACTATTTTAGTC
* * * *
376274 CTTTAACTTT-TTGTTTTTACTATTTTAGTCCTTTAAGTTTTTGT-TTTGCTATTTTGGTC
1 CTTTAACTTTCTTATTTTTGCTATTTTAGTCCTTTAAGTTTTTGTCTTTACTATTTTAGTC
* *
376333 CTTTAAATTTCTTTTTTTTTTTTTGCTATTTTAGTCCTTTAAGTTTTT
1 CTTT-AA---C-TTTCTTATTTTTGCTATTTTAGTCCTTTAAGTTTTT
376381 TCCTATTTTG
Statistics
Matches: 92, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
59 17 0.18
60 41 0.45
63 1 0.01
64 3 0.03
65 30 0.33
ACGTcount: A:0.16, C:0.12, G:0.09, T:0.63
Consensus pattern (61 bp):
CTTTAACTTTCTTATTTTTGCTATTTTAGTCCTTTAAGTTTTTGTCTTTACTATTTTAGTC
Found at i:376393 original size:24 final size:25
Alignment explanation
Indices: 376351--376398 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
376341 TTCTTTTTTT
* *
376351 TTTTTTGCTATTTTAGTCCTTTAAG
1 TTTTTTCCTATTTTAGTCCCTTAAG
376376 TTTTTTCCTATTTT-GTCCCTTAA
1 TTTTTTCCTATTTTAGTCCCTTAA
376399 ATCACTGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.15, C:0.17, G:0.08, T:0.60
Consensus pattern (25 bp):
TTTTTTCCTATTTTAGTCCCTTAAG
Found at i:378797 original size:14 final size:15
Alignment explanation
Indices: 378778--378806 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
378768 AATATTTTAC
378778 ATTTGCA-TTTGCAT
1 ATTTGCATTTTGCAT
378792 ATTTGCATTTTGCAT
1 ATTTGCATTTTGCAT
378807 CTGTATTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.52
Consensus pattern (15 bp):
ATTTGCATTTTGCAT
Found at i:380118 original size:14 final size:14
Alignment explanation
Indices: 380082--380161 Score: 71
Period size: 13 Copynumber: 5.7 Consensus size: 14
380072 ACATCAAAGA
380082 AAAGAAAAAAGAAC
1 AAAGAAAAAAGAAC
380096 AAAGGGAAAAAAGCAA-
1 AAA--GAAAAAAG-AAC
*
380112 AAAGAAAAAA-AAT
1 AAAGAAAAAAGAAC
380125 AAAG-AAAAAGAAGC
1 AAAGAAAAAAGAA-C
380139 AAAGAAAAAA-ATA-
1 AAAGAAAAAAGA-AC
380152 AAAGAAAAAA
1 AAAGAAAAAA
380162 AAAAGATAAG
Statistics
Matches: 57, Mismatches: 1, Indels: 17
0.76 0.01 0.23
Matches are distributed among these distances:
12 7 0.12
13 16 0.28
14 15 0.26
15 6 0.11
16 11 0.19
17 2 0.04
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.03
Consensus pattern (14 bp):
AAAGAAAAAAGAAC
Found at i:380128 original size:29 final size:27
Alignment explanation
Indices: 380077--380162 Score: 88
Period size: 27 Copynumber: 3.1 Consensus size: 27
380067 AGATCACATC
* *
380077 AAAG-AAAAGAAAAAAGAACAAAGGGAAA
1 AAAGCAAAAGAAAAAA-AATAAA-GAAAA
380105 AAAGCAAAAAGAAAAAAAATAAAGAAAA
1 AAAGC-AAAAGAAAAAAAATAAAGAAAA
380133 AGAAGC-AAAG-AAAAAAATAAAAGAAAA
1 A-AAGCAAAAGAAAAAAAAT-AAAGAAAA
380160 AAA
1 AAA
380163 AAAGATAAGA
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
26 10 0.19
27 13 0.25
28 9 0.17
29 9 0.17
30 11 0.21
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.02
Consensus pattern (27 bp):
AAAGCAAAAGAAAAAAAATAAAGAAAA
Found at i:380172 original size:16 final size:16
Alignment explanation
Indices: 380110--380173 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 16
380100 GGAAAAAAGC
380110 AAAAAGAAAA-AAAATA
1 AAAAAGAAAAGAAAA-A
380126 AAGAAA-AAGAAGCAAAGAA
1 AA-AAAGAA-AAG-AAA-AA
*
380145 AAAAATAAAAGAAAAA
1 AAAAAGAAAAGAAAAA
*
380161 AAAAAGATAAGAA
1 AAAAAGAAAAGAA
380174 GCAAATGCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
16 17 0.43
17 8 0.20
18 6 0.15
19 8 0.20
20 1 0.03
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.05
Consensus pattern (16 bp):
AAAAAGAAAAGAAAAA
Found at i:381543 original size:66 final size:67
Alignment explanation
Indices: 381402--381681 Score: 228
Period size: 66 Copynumber: 4.3 Consensus size: 67
381392 CTTTCGCTAA
* * * * * *
381402 AAAC-AAACTTTGTCTCACTTGAGACA--ATCTTTATTAAGACAAAAT-TTGAAATTT-TTTCTC
1 AAACAAAATTTTGTCTCTCTTGAGACAGTTTCTTT-TGAAGACAAAATCTTTAAGTTTGTTTCTC
*
381462 TTG
65 TGG
*
381465 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTTTGAAGA-AAAATCTTTAAGTTTGTTTCTCT
1 AAACAAAATTTTGTCTCTCTTGAGACAGTTTCTTTTGAAGACAAAATCTTTAAGTTTGTTTCTCT
381529 GG
66 GG
* * *
381531 AAACAAAATTTTGTCTCTCTTG-G---GTTTCTTTTGAA-AAAAAATCTTTGAA-TTTGCTTATC
1 AAACAAAATTTTGTCTCTCTTGAGACAGTTTCTTTTGAAGACAAAATCTTT-AAGTTTGTTTCTC
381590 TGG
65 TGG
* * * * ** * * * * *
381593 AAACAAATTTTTGTATCTCTTGACATAGTTTCCCTTGAA-ACACCAATCTTTGAGTCTATTTCCC
1 AAACAAAATTTTGTCTCTCTTGAGACAGTTTCTTTTGAAGACA-AAATCTTTAAGTTTGTTTCTC
*
381657 TTG
65 TGG
381660 AAAC-AAATTTTGTCTCTCTTGA
1 AAACAAAATTTTGTCTCTCTTGA
381682 AACACCCATC
Statistics
Matches: 177, Mismatches: 27, Indels: 23
0.78 0.12 0.10
Matches are distributed among these distances:
61 1 0.01
62 52 0.29
63 6 0.03
64 24 0.14
65 13 0.07
66 63 0.36
67 18 0.10
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.41
Consensus pattern (67 bp):
AAACAAAATTTTGTCTCTCTTGAGACAGTTTCTTTTGAAGACAAAATCTTTAAGTTTGTTTCTCT
GG
Found at i:381592 original size:62 final size:64
Alignment explanation
Indices: 381464--381615 Score: 202
Period size: 62 Copynumber: 2.4 Consensus size: 64
381454 TTTTTCTCTT
* * * *
381464 GAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTTTGAAGAAAAATCTTTAAGTTTGTTTCTCT
1 GAAACAAAATTTTGTCTCTCTTGAG--AGTTTCTTTTGAAAAAAAATCTTTAAGTTTGCTTATCT
381529 G
64 G
381530 GAAACAAAATTTTGTCTCTCTTG-G-GTTTCTTTTGAAAAAAAATCTTTGAA-TTTGCTTATCTG
1 GAAACAAAATTTTGTCTCTCTTGAGAGTTTCTTTTGAAAAAAAATCTTT-AAGTTTGCTTATCTG
* *
381592 GAAACAAATTTTTGTATCTCTTGA
1 GAAACAAAATTTTGTCTCTCTTGA
381616 CATAGTTTCC
Statistics
Matches: 78, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
62 53 0.68
63 2 0.03
65 1 0.01
66 22 0.28
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (64 bp):
GAAACAAAATTTTGTCTCTCTTGAGAGTTTCTTTTGAAAAAAAATCTTTAAGTTTGCTTATCTG
Found at i:381706 original size:51 final size:51
Alignment explanation
Indices: 381626--381732 Score: 171
Period size: 51 Copynumber: 2.1 Consensus size: 51
381616 CATAGTTTCC
381626 CTTGAAACACCAATCTTTGAGTCTATTTCCCTTGAAACAAATTTTGTCTCT
1 CTTGAAACACCAATCTTTGAGTCTATTTCCCTTGAAACAAATTTTGTCTCT
* * *
381677 CTTGAAACACCCATCTTTGAGATC-GTTTCCCTTGAAACGAATTTTGTCTCT
1 CTTGAAACACCAATCTTTGAG-TCTATTTCCCTTGAAACAAATTTTGTCTCT
381728 CTTGA
1 CTTGA
381733 GACAGCTTCT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
51 50 0.96
52 2 0.04
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.38
Consensus pattern (51 bp):
CTTGAAACACCAATCTTTGAGTCTATTTCCCTTGAAACAAATTTTGTCTCT
Found at i:381959 original size:48 final size:48
Alignment explanation
Indices: 381887--381995 Score: 146
Period size: 48 Copynumber: 2.3 Consensus size: 48
381877 TAACCAGCAG
* * * *
381887 TCCTCATCTCGTAGGAACCGTGTTATCATCCCTAAAGATGGCCTACCA
1 TCCTCATCACGTAAGAACCGTGTTATCAACCCTAAAGATAGCCTACCA
** **
381935 TCCTCATCACGTAAGAATTGTGTTATCAACCCTAAAGATAGCCTGTCA
1 TCCTCATCACGTAAGAACCGTGTTATCAACCCTAAAGATAGCCTACCA
381983 TCCTCATCACGTA
1 TCCTCATCACGTA
381996 GGACTGTGTC
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (48 bp):
TCCTCATCACGTAAGAACCGTGTTATCAACCCTAAAGATAGCCTACCA
Found at i:382389 original size:3 final size:3
Alignment explanation
Indices: 382381--382410 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
382371 ACTAATTTTA
382381 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
382411 ATTTACTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:383843 original size:30 final size:30
Alignment explanation
Indices: 383807--383965 Score: 203
Period size: 30 Copynumber: 5.3 Consensus size: 30
383797 ATAGTTCAGC
383807 CCTTTAAGTTTTTATTTTTGCTATTTTAGT
1 CCTTTAAGTTTTTATTTTTGCTATTTTAGT
*
383837 CCTTTAAGTTTTTATCTTTGCTATTTTAGT
1 CCTTTAAGTTTTTATTTTTGCTATTTTAGT
* * * * *
383867 CCTTTAACTTTCTATTTTTACTATTTCAAT
1 CCTTTAAGTTTTTATTTTTGCTATTTTAGT
* * *
383897 CCTTTACGTTTTT-GTTTTGCTATTTTGGT
1 CCTTTAAGTTTTTATTTTTGCTATTTTAGT
* *
383926 CCTTTAAATTTCTATTTTTGCTATTTTAGT
1 CCTTTAAGTTTTTATTTTTGCTATTTTAGT
*
383956 TCTTTAAGTT
1 CCTTTAAGTT
383966 AATGTTTTAT
Statistics
Matches: 106, Mismatches: 22, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
29 21 0.20
30 85 0.80
ACGTcount: A:0.17, C:0.14, G:0.09, T:0.60
Consensus pattern (30 bp):
CCTTTAAGTTTTTATTTTTGCTATTTTAGT
Found at i:383851 original size:59 final size:59
Alignment explanation
Indices: 383807--383965 Score: 219
Period size: 59 Copynumber: 2.7 Consensus size: 59
383797 ATAGTTCAGC
* *
383807 CCTTTAAGTTTTTATTTTTGCTATTTTAGTCCTTTAAGTTTTTATCTTTGCTATTTTAGT
1 CCTTTAAATTTCTATTTTTGCTATTTTAGTCCTTTAAGTTTTTAT-TTTGCTATTTTAGT
* * * * * * *
383867 CCTTTAACTTTCTATTTTTACTATTTCAATCCTTTACGTTTTTGTTTTGCTATTTTGGT
1 CCTTTAAATTTCTATTTTTGCTATTTTAGTCCTTTAAGTTTTTATTTTGCTATTTTAGT
*
383926 CCTTTAAATTTCTATTTTTGCTATTTTAGTTCTTTAAGTT
1 CCTTTAAATTTCTATTTTTGCTATTTTAGTCCTTTAAGTT
383966 AATGTTTTAT
Statistics
Matches: 85, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
59 47 0.55
60 38 0.45
ACGTcount: A:0.17, C:0.14, G:0.09, T:0.60
Consensus pattern (59 bp):
CCTTTAAATTTCTATTTTTGCTATTTTAGTCCTTTAAGTTTTTATTTTGCTATTTTAGT
Found at i:383980 original size:89 final size:90
Alignment explanation
Indices: 383807--383981 Score: 230
Period size: 89 Copynumber: 2.0 Consensus size: 90
383797 ATAGTTCAGC
* * *
383807 CCTTTAAGTTTTTATTTTTGCTATTTTAGTCCTTTAAGTTTTTATCTTTGCTATTTTAGTCCTTT
1 CCTTTAAGTTTTTAGTTTTGCTATTTTAGTCCTTTAAATTTCTATCTTTGCTATTTTAGTCCTTT
* *
383872 AACTTTCTATTTTTACTATTTCAAT
66 AACGTTCAATTTTTACTATTTCAAT
* * * *
383897 CCTTTACGTTTTT-GTTTTGCTATTTTGGTCCTTTAAATTTCTATTTTTGCTATTTTAGTTCTTT
1 CCTTTAAGTTTTTAGTTTTGCTATTTTAGTCCTTTAAATTTCTATCTTTGCTATTTTAGTCCTTT
383961 AA-GTT-AATGTTTTATCTATTT
66 AACGTTCAAT-TTTTA-CTATTT
383982 TGGTCCCTTA
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
87 2 0.03
88 7 0.09
89 53 0.72
90 12 0.16
ACGTcount: A:0.18, C:0.13, G:0.09, T:0.61
Consensus pattern (90 bp):
CCTTTAAGTTTTTAGTTTTGCTATTTTAGTCCTTTAAATTTCTATCTTTGCTATTTTAGTCCTTT
AACGTTCAATTTTTACTATTTCAAT
Found at i:392555 original size:21 final size:21
Alignment explanation
Indices: 392504--392556 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
392494 CTTCATCGCC
*
392504 ATCTTCTTCGTATCAGATTAA
1 ATCTTCTTTGTATCAGATTAA
392525 ATC-TCTTTTGTATCAGATTAA
1 ATCTTC-TTTGTATCAGATTAA
392546 ATCTTCTTTGT
1 ATCTTCTTTGT
392557 GGTTCCACTG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 2 0.07
21 25 0.86
22 2 0.07
ACGTcount: A:0.25, C:0.17, G:0.09, T:0.49
Consensus pattern (21 bp):
ATCTTCTTTGTATCAGATTAA
Found at i:409674 original size:20 final size:19
Alignment explanation
Indices: 409639--409684 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
409629 ATTTATAATT
*
409639 TATAAATAAAATATTATTA
1 TATATATAAAATATTATTA
*
409658 TATATATAAACATATTATTT
1 TATATATAAA-ATATTATTA
409678 TATATAT
1 TATATAT
409685 TAATTGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TATATATAAAATATTATTA
Found at i:411560 original size:2 final size:2
Alignment explanation
Indices: 411553--411587 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
411543 CATCCTCATC
411553 TA 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 TA T
411588 TTCCTTTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:423802 original size:136 final size:139
Alignment explanation
Indices: 423653--423940 Score: 359
Period size: 149 Copynumber: 2.0 Consensus size: 139
423643 ATTTTAATGT
** * *
423653 TAATATGGTTTTATCTTGTGGTGAGACATTAATAGCATCGTTAATTTTTTTAACAGTGGTGA-C-
1 TAATATGACTTTATCTTGTGGTGAGACATTAATAGCATCGTTAA-ATTTTTAACAATGGTGACCA
* *
423716 C-GAAACATAACATGAAGTATAA-TTTTAAAAAAAATAAATTATTAAAATAAAATTATGAGAACA
65 CAGAAACATAACATGAAGTATAATTTTTAAAAAAAATAAATGATTAAAATAAAATTACGAGAACA
*
423779 ATTAACTGAC
130 ATTAACCGAC
*
423789 TAATATGACTTTATCTTGTGGTGAGACATTAATAGTATCGTTAAATTTTTAACAATGGTGACCAA
1 TAATATGACTTTATCTTGTGGTGAGACATTAATAGCATCGTTAAATTTTTAACAATGGTGACC--
*
423854 AACAAAAAAGAAACATAACATGAAGTATAATTTTTTTAAAAAAGATAAATGATTAAAATAAAATT
64 -AC-----AGAAACATAACATGAAGTATAA--TTTTTAAAAAAAATAAATGATTAAAATAAAATT
*
423919 ACGAGAATAATTAACCGAC
121 ACGAGAACAATTAACCGAC
423938 TAA
1 TAA
423941 ATACATAGTT
Statistics
Matches: 128, Mismatches: 10, Indels: 15
0.84 0.07 0.10
Matches are distributed among these distances:
135 15 0.12
136 42 0.33
140 1 0.01
146 21 0.16
149 49 0.38
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.33
Consensus pattern (139 bp):
TAATATGACTTTATCTTGTGGTGAGACATTAATAGCATCGTTAAATTTTTAACAATGGTGACCAC
AGAAACATAACATGAAGTATAATTTTTAAAAAAAATAAATGATTAAAATAAAATTACGAGAACAA
TTAACCGAC
Found at i:425580 original size:2 final size:2
Alignment explanation
Indices: 425573--425604 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
425563 TATACATCCC
425573 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
425605 GAGTAGTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.