Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007761.1 Hibiscus syriacus cultivar Beakdansim tig00110030_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: 1497221
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:310581 original size:36 final size:36
Alignment explanation
Indices: 310541--310609 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
310531 CTGGAATTAA
*
310541 GTGATAAAAGAATCAGCCATCGATATGTAGATTTAC
1 GTGATAAAAGAATCAACCATCGATATGTAGATTTAC
*
310577 GTGATAAAAGAATCAACCATGGATATGTAGATT
1 GTGATAAAAGAATCAACCATCGATATGTAGATT
310610 ATAATTTATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.28
Consensus pattern (36 bp):
GTGATAAAAGAATCAACCATCGATATGTAGATTTAC
Found at i:310766 original size:17 final size:18
Alignment explanation
Indices: 310731--310767 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
310721 TGGATTAATA
310731 ATCTGAAAAGAATTATTG
1 ATCTGAAAAGAATTATTG
310749 ATCTGATAAA-AA-TATTG
1 ATCTGA-AAAGAATTATTG
310766 AT
1 AT
310768 GTGCATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 8 0.44
19 3 0.17
ACGTcount: A:0.46, C:0.05, G:0.14, T:0.35
Consensus pattern (18 bp):
ATCTGAAAAGAATTATTG
Found at i:312800 original size:10 final size:9
Alignment explanation
Indices: 312783--312829 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
312773 ATGTAAAATA
312783 AAAT-AAAG
1 AAATAAAAG
312791 ATAATAAAAG
1 A-AATAAAAG
312801 -AATAAAAG
1 AAATAAAAG
*
312809 AATTAAAAG
1 AAATAAAAG
312818 AAATCAAAAG
1 AAAT-AAAAG
312828 AA
1 AA
312830 TCATGAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
8 9 0.27
9 13 0.39
10 11 0.33
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (9 bp):
AAATAAAAG
Found at i:312806 original size:17 final size:17
Alignment explanation
Indices: 312783--312830 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 17
312773 ATGTAAAATA
*
312783 AAATAAAGATAATAAAAG
1 AAATAAA-AGAATAAAAG
312801 -AATAAAAGAATTAAAAG
1 AAATAAAAGAA-TAAAAG
312818 AAATCAAAAGAAT
1 AAAT-AAAAGAAT
312831 CATGAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 3 0.12
17 12 0.46
18 4 0.15
19 7 0.27
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.17
Consensus pattern (17 bp):
AAATAAAAGAATAAAAG
Found at i:313768 original size:2 final size:2
Alignment explanation
Indices: 313715--313749 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
313705 AATATGGAAC
313715 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
313750 CTTAAATAAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:317023 original size:103 final size:103
Alignment explanation
Indices: 316845--317051 Score: 310
Period size: 103 Copynumber: 2.0 Consensus size: 103
316835 GTAACTTCAA
* *
316845 TTTTTTTTAAGCATACTTTAAGGGGAGTCAGCTCATAACACTACCATCCCACACTCTAAGTGAAA
1 TTTTTTTTAAGCATACTTTAAGGGGAGTCAACCCATAACACTACCATCCCACACTCTAAGTGAAA
*
316910 GGCAGCATACCTT-TACCCCCGAGCTAGTCAGGTAGAG
66 GGCAGCATACCTTCCACCCCCGAGCTAGTCAGGTAGAG
* * * *
316947 TTTTTTTTAA-CACTGCTTTGAGGGGAGTCAACCCATCACACCTACCATCCCACACTCTAGGTGA
1 TTTTTTTTAAGCA-TACTTTAAGGGGAGTCAACCCATAACA-CTACCATCCCACACTCTAAGTGA
*
317011 AAGGGAGCATACCTTCCACCCCCGAGCTAGTCAGGTAGAG
64 AAGGCAGCATACCTTCCACCCCCGAGCTAGTCAGGTAGAG
317051 T
1 T
317052 CATCTCGTGA
Statistics
Matches: 94, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
101 2 0.02
102 32 0.34
103 36 0.38
104 24 0.26
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (103 bp):
TTTTTTTTAAGCATACTTTAAGGGGAGTCAACCCATAACACTACCATCCCACACTCTAAGTGAAA
GGCAGCATACCTTCCACCCCCGAGCTAGTCAGGTAGAG
Found at i:318692 original size:21 final size:21
Alignment explanation
Indices: 318666--318707 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
318656 TAAGGCCTTA
* *
318666 GTTGAGGTCGTGAAATCTTGT
1 GTTGAGGTCATAAAATCTTGT
318687 GTTGAGGTCATAAAATCTTGT
1 GTTGAGGTCATAAAATCTTGT
318708 AGTGAAGCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.10, G:0.29, T:0.38
Consensus pattern (21 bp):
GTTGAGGTCATAAAATCTTGT
Found at i:324289 original size:39 final size:39
Alignment explanation
Indices: 324235--324318 Score: 114
Period size: 39 Copynumber: 2.2 Consensus size: 39
324225 GACCTTACTA
* ** *
324235 CTTACCGCAAGCTCCTTGGCTTTCTACTCAGGGTAAGTC
1 CTTACTGCAAGCTCCTCAGCTTTCTACTAAGGGTAAGTC
* *
324274 CTTACTGCAAGCTCCTCAGCTTTGTGCTAAGGGTAAGTC
1 CTTACTGCAAGCTCCTCAGCTTTCTACTAAGGGTAAGTC
324313 CTTACT
1 CTTACT
324319 ACAGGATCTC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.19, C:0.29, G:0.20, T:0.32
Consensus pattern (39 bp):
CTTACTGCAAGCTCCTCAGCTTTCTACTAAGGGTAAGTC
Found at i:324354 original size:38 final size:38
Alignment explanation
Indices: 324307--324395 Score: 108
Period size: 38 Copynumber: 2.3 Consensus size: 38
324297 GTGCTAAGGG
* *
324307 TAAGTCCTTACTACAGGAT-CTCTGCTTTGTGCACATGA
1 TAAGACCTTACTACAGG-TCCTCTGCTTTGTGCACAAGA
* * *
324345 TAAGACCTTACCACATGTCCTCTGCTTTGTGCACAAGG
1 TAAGACCTTACTACAGGTCCTCTGCTTTGTGCACAAGA
*
324383 TAAGCCCTTACTA
1 TAAGACCTTACTA
324396 GGTGTACAAG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
37 1 0.02
38 42 0.98
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (38 bp):
TAAGACCTTACTACAGGTCCTCTGCTTTGTGCACAAGA
Found at i:325305 original size:21 final size:20
Alignment explanation
Indices: 325281--325320 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
325271 TAGCATCAAG
*
325281 TTAAAATTAAGTATGAAATTT
1 TTAAAATTAA-TATCAAATTT
325302 TTAAAATTAATATCAAATT
1 TTAAAATTAATATCAAATT
325321 ATATAAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (20 bp):
TTAAAATTAATATCAAATTT
Found at i:325327 original size:21 final size:20
Alignment explanation
Indices: 325282--325333 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
325272 AGCATCAAGT
* *
325282 TAAAATTAAGTATGAAATTTT
1 TAAAATTAA-TATCAAATTTA
325303 TAAAATTAATATCAAATTATA
1 TAAAATTAATATCAAATT-TA
*
325324 TAAAACTAAT
1 TAAAATTAAT
325334 TCTAATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (20 bp):
TAAAATTAATATCAAATTTA
Found at i:326362 original size:6 final size:6
Alignment explanation
Indices: 326351--326377 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
326341 ATTTCATTTT
326351 ATTAAA ATTAAA ATTAAA ATTAAA ATT
1 ATTAAA ATTAAA ATTAAA ATTAAA ATT
326378 TAATAAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
ATTAAA
Found at i:329319 original size:21 final size:20
Alignment explanation
Indices: 329281--329323 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
329271 TATTTTTTCT
* *
329281 TTAGTTCATTTAGTTGCATA
1 TTAGTTCATGTAGCTGCATA
329301 TTAGTTTCATGTAGCTGCATA
1 TTAG-TTCATGTAGCTGCATA
329322 TT
1 TT
329324 TCATGAATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.23, C:0.12, G:0.16, T:0.49
Consensus pattern (20 bp):
TTAGTTCATGTAGCTGCATA
Found at i:342873 original size:8 final size:8
Alignment explanation
Indices: 342860--342898 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
342850 TTAGTATTTT
342860 TTTAATTA
1 TTTAATTA
342868 TTTAATTA
1 TTTAATTA
342876 TTTAATT-
1 TTTAATTA
*
342883 TTATATTTA
1 TT-TAATTA
342892 TTTAATT
1 TTTAATT
342899 TTTTGCAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 2 0.07
8 23 0.85
9 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTAATTA
Found at i:343171 original size:13 final size:13
Alignment explanation
Indices: 343153--343213 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
343143 AACTGCAAAA
343153 AAATAAAATAATT
1 AAATAAAATAATT
343166 AAATAAAATAA-T
1 AAATAAAATAATT
* *
343178 AAAAAAAATTAAAT
1 AAATAAAA-TAATT
*
343192 -AATATAATAATT
1 AAATAAAATAATT
343204 AAATAAAATA
1 AAATAAAATA
343214 CTAACAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
12 12 0.30
13 27 0.68
14 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATAAAATAATT
Found at i:343187 original size:22 final size:22
Alignment explanation
Indices: 343149--343201 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
343139 TTTTAACTGC
* *
343149 AAAAAAAT-AAAATAATTAAAT
1 AAAATAATAAAAAAAATTAAAT
343170 AAAATAATAAAAAAAATTAAAT
1 AAAATAATAAAAAAAATTAAAT
*
343192 AATATAATAA
1 AAAATAATAA
343202 TTAAATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 7 0.25
22 21 0.75
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (22 bp):
AAAATAATAAAAAAAATTAAAT
Found at i:350252 original size:18 final size:19
Alignment explanation
Indices: 350231--350267 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
350221 TTTTTGATCC
350231 CTTGTTTGT-TTTGAATTT
1 CTTGTTTGTATTTGAATTT
*
350249 CTTGTTTGTATTTTAATTT
1 CTTGTTTGTATTTGAATTT
350268 GTAATTTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.14, C:0.05, G:0.14, T:0.68
Consensus pattern (19 bp):
CTTGTTTGTATTTGAATTT
Found at i:351313 original size:21 final size:21
Alignment explanation
Indices: 351292--351362 Score: 108
Period size: 21 Copynumber: 3.4 Consensus size: 21
351282 CCAAGGACGA
*
351292 GAAGACCATTCGTAAAGACGA-
1 GAAGACCATTCATAAAGAC-AT
351313 GAAGACCATTCATAAAGACAT
1 GAAGACCATTCATAAAGACAT
*
351334 GAAGACCCTTCATAAAGACAT
1 GAAGACCATTCATAAAGACAT
351355 GAAGACCA
1 GAAGACCA
351363 CTTCGCATTG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 1 0.02
21 45 0.98
ACGTcount: A:0.45, C:0.21, G:0.18, T:0.15
Consensus pattern (21 bp):
GAAGACCATTCATAAAGACAT
Found at i:355873 original size:13 final size:13
Alignment explanation
Indices: 355855--355880 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
355845 CTGTCATAGT
355855 CAATTTCACACGA
1 CAATTTCACACGA
355868 CAATTTCACACGA
1 CAATTTCACACGA
355881 GCACTTAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (13 bp):
CAATTTCACACGA
Found at i:358742 original size:208 final size:211
Alignment explanation
Indices: 358264--358820 Score: 876
Period size: 208 Copynumber: 2.6 Consensus size: 211
358254 GAAGCAAACT
* * *
358264 CATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATTTGTAAGCTTTTAGAGCAAG
1 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAG
* *
358329 ATGATAAGTCCTTCGAGCCATCCATAAGACCTTAGGGTATGATGTTTTCACATGAATTTGG--A-
66 ATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTATGATGTTTTCACATGAATTTGGAAAT
*
358391 AAAAAAAATTATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCA
131 AAAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTC--AA--T-A
*
358456 CAATTTATAAGTTCTTCGGGC
191 CAATTTATAAGTCCTTCGGGC
358477 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAG
1 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAG
* * *
358542 ATGACAACTCCTTCGGGCCATCCATAAAACCTTCGGGTATGATGTTTTCACATGAATTTGGAAAT
66 ATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTATGATGTTTTCACATGAATTTGGAAAT
358607 AAAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTC-A-A-AATT
131 AAAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAATACAATT
358669 TATAAGTCCTTCGGGC
196 TATAAGTCCTTCGGGC
* *
358685 CATCAGTAAGTCTTTCGAGCATGATGCTTAAAACCTTCAGGTCATCTGTAAGCCTTTAGAGCAAG
1 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAG
* *
358750 ATGATAAGTCCTTCGGG-CATTCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
66 ATGATAAGTCCTTCGGGCCA-TCCATAAGACCTTCGGGTATGATGTTTTCACATGAATTTGGAAA
*
358814 TGAAAAA
130 TAAAAAA
358821 TGATGAAATC
Statistics
Matches: 322, Mismatches: 18, Indels: 13
0.91 0.05 0.04
Matches are distributed among these distances:
207 2 0.01
208 144 0.45
209 1 0.00
213 119 0.37
215 1 0.00
216 55 0.17
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (211 bp):
CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAG
ATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTATGATGTTTTCACATGAATTTGGAAAT
AAAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAATACAATT
TATAAGTCCTTCGGGC
Found at i:359040 original size:37 final size:38
Alignment explanation
Indices: 358987--359069 Score: 123
Period size: 37 Copynumber: 2.2 Consensus size: 38
358977 CGAGCAATCT
** * *
358987 TAAGCCTTCATTGAAGAGTAGTGAAGCAAATTCATCA-
1 TAAGCCTTCACGGAAGAATAATGAAGCAAATTCATCAG
359024 TAAGCCTTCACGGAAGAATAATGAAGCAAATTCATCAG
1 TAAGCCTTCACGGAAGAATAATGAAGCAAATTCATCAG
359062 TAAGCCTT
1 TAAGCCTT
359070 ACGAGCATGA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
37 33 0.80
38 8 0.20
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (38 bp):
TAAGCCTTCACGGAAGAATAATGAAGCAAATTCATCAG
Found at i:359133 original size:79 final size:80
Alignment explanation
Indices: 359019--359213 Score: 266
Period size: 81 Copynumber: 2.4 Consensus size: 80
359009 GAAGCAAATT
* ** * *
359019 CATCATAAGCCTTCACGGAAGAATAATGAAGCAAATTCATCAGTAAGCCTTACGAGC-ATGATGA
1 CATCTTAAGCCTTCACCAAAGAGTAATGAAGCAAATTCATCAGTAAGCCTTACGAGCAATGATAA
359083 TTAAGTCATCCGGGC
66 TTAAGTCATCCGGGC
* * *
359098 CATCTTAAACCTTCACCAAAGAGTAATGAAGCAAATTCATCAGTAAGCTTTCCGAGCATATGATA
1 CATCTTAAGCCTTCACCAAAGAGTAATGAAGCAAATTCATCAGTAAGCCTTACGAGCA-ATGATA
* *
359163 ATTAAGTCCTCTGGGC
65 ATTAAGTCATCCGGGC
* *
359179 CATCTTAAGCCTTCACCAAAGAGTAGTAAAGCAAA
1 CATCTTAAGCCTTCACCAAAGAGTAATGAAGCAAA
359214 ATCAATTTTA
Statistics
Matches: 101, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
79 50 0.50
81 51 0.50
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.24
Consensus pattern (80 bp):
CATCTTAAGCCTTCACCAAAGAGTAATGAAGCAAATTCATCAGTAAGCCTTACGAGCAATGATAA
TTAAGTCATCCGGGC
Found at i:359237 original size:38 final size:37
Alignment explanation
Indices: 359183--359256 Score: 121
Period size: 38 Copynumber: 2.0 Consensus size: 37
359173 CTGGGCCATC
359183 TTAAGCCTTCACCAAAGAGTAGTAAAGCAAAATCAATT
1 TTAAGCCTTCACCAAAGAGTAGTAAAGC-AAATCAATT
* *
359221 TTAAGCCTTCATCAAAGAGTAGTGAAGCAAATCAAT
1 TTAAGCCTTCACCAAAGAGTAGTAAAGCAAATCAAT
359257 CTCGAGTTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 8 0.24
38 26 0.76
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.24
Consensus pattern (37 bp):
TTAAGCCTTCACCAAAGAGTAGTAAAGCAAATCAATT
Found at i:363216 original size:23 final size:23
Alignment explanation
Indices: 363189--363252 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
363179 AAAGATATAT
*
363189 CCTTTTGTTTTAAAGAGACATGC
1 CCTTTTGTTTTAAAGAGACACGC
*
363212 CCTTTTGTTTTAAAGAGATACGC
1 CCTTTTGTTTTAAAGAGACACGC
* * *
363235 CTTTTTCTTGTAAAGAGA
1 CCTTTTGTTTTAAAGAGA
363253 AATGTCCTAC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.41
Consensus pattern (23 bp):
CCTTTTGTTTTAAAGAGACACGC
Found at i:364384 original size:24 final size:24
Alignment explanation
Indices: 364357--364408 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
364347 AACGGATATA
*
364357 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
364381 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
364405 TCAA
1 TCAA
364409 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:364409 original size:24 final size:24
Alignment explanation
Indices: 364377--364495 Score: 152
Period size: 24 Copynumber: 5.0 Consensus size: 24
364367 AAACATAAAT
364377 CAGGTCAAGTATCATATCAGAAAT-
1 CAGGTCAAGTATCATATCAG-AATC
* *
364401 CAGGTCAAGTAACAGATCAGAATC
1 CAGGTCAAGTATCATATCAGAATC
*
364425 CAAGTCAAGTATCATATCAGAATC
1 CAGGTCAAGTATCATATCAGAATC
*
364449 CATGTCATA-TATCATATCAGAATC
1 CAGGTCA-AGTATCATATCAGAATC
* *
364473 CATGTCAAGTATCAGATCAGAAT
1 CAGGTCAAGTATCATATCAGAAT
364496 TCAAATCGAA
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
23 4 0.05
24 80 0.94
25 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.25
Consensus pattern (24 bp):
CAGGTCAAGTATCATATCAGAATC
Found at i:364525 original size:72 final size:72
Alignment explanation
Indices: 364386--364525 Score: 167
Period size: 72 Copynumber: 1.9 Consensus size: 72
364376 TCAGGTCAAG
* * * * *
364386 TATCATATCAGAAATCAGGTCAAGTAACAGATCAGAATCCAAGTCAAGTATCATATCAGAATCCA
1 TATCATATCAGAAATCAGGTCAAGTAACAGATCAGAATCCAAATCAAGAATCAGATAAAAATCCA
364451 TGTCATA
66 TGTCATA
* * * *
364458 TATCATATCAG-AATCCATGTCAAGTATCAGATCAGAATTCAAATCGAA-AATCAGATAAAAATT
1 TATCATATCAGAAAT-CAGGTCAAGTAACAGATCAGAATCCAAATC-AAGAATCAGATAAAAATC
364521 CATGT
64 CATGT
364526 GAGTAGGGAA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
71 3 0.05
72 52 0.91
73 2 0.04
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (72 bp):
TATCATATCAGAAATCAGGTCAAGTAACAGATCAGAATCCAAATCAAGAATCAGATAAAAATCCA
TGTCATA
Found at i:367033 original size:13 final size:13
Alignment explanation
Indices: 367015--367050 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
367005 CGGTCAACGA
367015 TCAACGGGTCGGG
1 TCAACGGGTCGGG
367028 TCAACGGGTCGGG
1 TCAACGGGTCGGG
*
367041 TCAACAGGTC
1 TCAACGGGTC
367051 AGGTAAATGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.19, C:0.25, G:0.39, T:0.17
Consensus pattern (13 bp):
TCAACGGGTCGGG
Found at i:369276 original size:24 final size:24
Alignment explanation
Indices: 369161--369276 Score: 137
Period size: 24 Copynumber: 4.8 Consensus size: 24
369151 TATAAATCAG
* * *
369161 GTCAAGTCTCATATCAGAAAT-CAG
1 GTCAAGTATCAGATCAG-AATCCAT
* * * *
369185 GTCAAGCAACAGATCAAAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
369209 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
369233 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
369257 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
369277 TCAAATCGAA
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
23 5 0.06
24 72 0.91
25 2 0.03
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:371809 original size:13 final size:13
Alignment explanation
Indices: 371791--371844 Score: 72
Period size: 13 Copynumber: 4.2 Consensus size: 13
371781 CAACGATTAA
371791 CGGGTCAACGGGT
1 CGGGTCAACGGGT
371804 CGGGTCAACGGGT
1 CGGGTCAACGGGT
**
371817 CGGGTCAACAAGT
1 CGGGTCAACGGGT
* *
371830 CAGGTAAACGGGT
1 CGGGTCAACGGGT
371843 CG
1 CG
371845 AGTCGGGTCG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.22, C:0.22, G:0.41, T:0.15
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:374060 original size:24 final size:24
Alignment explanation
Indices: 373945--374060 Score: 137
Period size: 24 Copynumber: 4.8 Consensus size: 24
373935 CATAAATCAG
* * *
373945 GTCAAGTCTCATATCAGAAAT-CAG
1 GTCAAGTATCAGATCAG-AATCCAT
* * * *
373969 GTCAAGCAACAGATCAAAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
373993 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
374017 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
374041 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
374061 TCAAATCGAA
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
23 5 0.06
24 72 0.91
25 2 0.03
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:374076 original size:48 final size:48
Alignment explanation
Indices: 373978--374083 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 48
373968 GGTCAAGCAA
** *
373978 CAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCATGTCAGATAT
1 CAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAAAT
* * *
374026 CAGATCAGAATCCATGTCAAGTATCAGATCAGAATTCAAATC-GAAAAT
1 CAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAG-AAAT
374074 CAGAT-AAAAT
1 CAGATCAAAAT
374084 ATTCATGTGA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
47 5 0.10
48 45 0.90
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.23
Consensus pattern (48 bp):
CAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAAAT
Found at i:376584 original size:8 final size:8
Alignment explanation
Indices: 376533--376594 Score: 56
Period size: 8 Copynumber: 7.5 Consensus size: 8
376523 TCAAAGTTTT
376533 GGTCAACAG
1 GGTCAAC-G
376542 TGGTCAACG
1 -GGTCAACG
376551 CCGGTCAAC-
1 --GGTCAACG
376560 GGTCAAC-
1 GGTCAACG
*
376567 AGTCAACG
1 GGTCAACG
*
376575 GGTTAACG
1 GGTCAACG
376583 GGTCAACG
1 GGTCAACG
376591 GGTC
1 GGTC
376595 GAGTCGGGTC
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
7 13 0.29
8 17 0.38
9 1 0.02
10 14 0.31
ACGTcount: A:0.26, C:0.26, G:0.32, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:385413 original size:45 final size:45
Alignment explanation
Indices: 385280--385603 Score: 452
Period size: 45 Copynumber: 7.2 Consensus size: 45
385270 ATTATTCATT
* *
385280 ATTTCCATTTATGGCATCCATTCATGCCTTCAATGCACCGTTATGC
1 ATTT-CATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* ***
385326 ATTTCATTTATGGCATCC-TTCATGCCTTTAATACATTATTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
385370 ATTTCATTTATGGCATCCTTTCAGGCCTTTAATGCACCGTTATGG
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * * *
385415 ATTTCATTTATGGCATCCTTTTATGCCTTTAATGAACCATTATGT
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * *
385460 ATTTCATTTATGACATCCATTCATGCCTTTAATGCACCGTTATGT
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
385505 ATTTCATTTATGGTATCCTTTCATGCCTTTAATGCACCGTTATGG
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * *
385550 ATTTCATTTATGGAACCCTTTCATTCCTTTAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
385595 ATTTCATTT
1 ATTTCATTT
385604 GTGTAATAAA
Statistics
Matches: 248, Mismatches: 29, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
44 39 0.16
45 205 0.83
46 4 0.02
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (45 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
Found at i:389149 original size:24 final size:24
Alignment explanation
Indices: 389103--389154 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
389093 CCTTGGCACT
* * *
389103 TCAAGTGGCACATCTTTTTGAACA
1 TCAAGTGGCACAACTGTTGGAACA
* *
389127 TCAAGTGGCATAACTGTTGGAACG
1 TCAAGTGGCACAACTGTTGGAACA
389151 TCAA
1 TCAA
389155 ATGACATGTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (24 bp):
TCAAGTGGCACAACTGTTGGAACA
Found at i:390473 original size:23 final size:24
Alignment explanation
Indices: 390430--390482 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
390420 TTTCTTTTTT
390430 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* * *
390454 TTTCTTCTTTT-GAGTTCTTTTAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
390477 TTTCTT
1 TTTCTT
390483 TGCTGATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.09, C:0.17, G:0.09, T:0.64
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:398093 original size:45 final size:45
Alignment explanation
Indices: 397985--398266 Score: 442
Period size: 45 Copynumber: 6.3 Consensus size: 45
397975 TATTCATTAT
* **
397985 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACAAATTATGCA
1 TTTCATTTATGTCATCCTTTCATGCCTTTAATGCAC-CGTTATGCA
398031 TTTCATTTATGAT-ATCCTTTCATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATG-TCATCCTTTCATGCCTTTAATGCACCGTTATGCA
398076 TTTCATTTATGTCATCCTTTCATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGTCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* **
398121 TTTCATTGATGGAATCCTTTCATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGTCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* *
398166 TTTCATTTATG-GATCCTTTCATGCCTTTAATGCATCGTTATGCA
1 TTTCATTTATGTCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* *
398210 TTTTATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGTCATCCTTTCATGCCTTTAATGCACCGTTATGCA
398255 TTTCATTTATGT
1 TTTCATTTATGT
398267 AATGAAACAT
Statistics
Matches: 219, Mismatches: 14, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
44 42 0.19
45 143 0.65
46 34 0.16
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (45 bp):
TTTCATTTATGTCATCCTTTCATGCCTTTAATGCACCGTTATGCA
Found at i:398205 original size:134 final size:136
Alignment explanation
Indices: 397985--398261 Score: 468
Period size: 134 Copynumber: 2.1 Consensus size: 136
397975 TATTCATTAT
* * *
397985 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACAAATTATGCATTTCATTTATGATATCCTT
1 TTTCATTGATGGAATCCTTTCATGCCTTTAATGCACAAATTATGCATTTCATTTATGAGATCCTT
*
398050 TCATGCCTTTAATGCACCGTTATGCATTTCATTTATGTCATCCTTTCATGCCTTTAATGCACCGT
66 TCATGCCTTTAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCGT
398115 TATGCA
131 TATGCA
**
398121 TTTCATTGATGGAATCCTTTCATGCCTTTAATGCAC-CGTTATGCATTTCATTTATG-GATCCTT
1 TTTCATTGATGGAATCCTTTCATGCCTTTAATGCACAAATTATGCATTTCATTTATGAGATCCTT
* *
398184 TCATGCCTTTAATGCATCGTTATGCATTTTATTTATGACATCCTTTCATGCCTTTAATGCACCGT
66 TCATGCCTTTAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCGT
398249 TATGCA
131 TATGCA
398255 TTTCATT
1 TTTCATT
398262 TATGTAATGA
Statistics
Matches: 133, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
134 81 0.61
135 18 0.14
136 34 0.26
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (136 bp):
TTTCATTGATGGAATCCTTTCATGCCTTTAATGCACAAATTATGCATTTCATTTATGAGATCCTT
TCATGCCTTTAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCGT
TATGCA
Found at i:398231 original size:89 final size:87
Alignment explanation
Indices: 397985--398265 Score: 445
Period size: 89 Copynumber: 3.1 Consensus size: 87
397975 TATTCATTAT
*
397985 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACAAATTATGCATTTCATTTATGATATCCTT
1 TTTCATTTATGG-ATCCTTTCATGCCTTTAATGCAC--GTTATGCATTTCATTTATGA-ATCCTT
398050 TCATGCCTTTAATGCACCGTTATGCA
62 TCATGCCTTTAATGCACCGTTATGCA
* *
398076 TTTCATTTATGTCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTGATGGAATCCTTT
1 TTTCATTTATG-GATCCTTTCATGCCTTTAATGCA-CGTTATGCATTTCATTTAT-GAATCCTTT
398141 CATGCCTTTAATGCACCGTTATGCA
63 CATGCCTTTAATGCACCGTTATGCA
*
398166 TTTCATTTATGGATCCTTTCATGCCTTTAATGCATCGTTATGCATTTTATTTATGACATCCTTTC
1 TTTCATTTATGGATCCTTTCATGCCTTTAATGCA-CGTTATGCATTTCATTTATGA-ATCCTTTC
398231 ATGCCTTTAATGCACCGTTATGCA
64 ATGCCTTTAATGCACCGTTATGCA
398255 TTTCATTTATG
1 TTTCATTTATG
398266 TAATGAAACA
Statistics
Matches: 179, Mismatches: 7, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
88 2 0.01
89 82 0.46
90 59 0.33
91 35 0.20
92 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (87 bp):
TTTCATTTATGGATCCTTTCATGCCTTTAATGCACGTTATGCATTTCATTTATGAATCCTTTCAT
GCCTTTAATGCACCGTTATGCA
Found at i:400780 original size:44 final size:44
Alignment explanation
Indices: 400665--400970 Score: 393
Period size: 44 Copynumber: 7.0 Consensus size: 44
400655 ATACCATGAG
* * * * *
400665 TGGCACCTTTCTGTCAATAATGTACCGCTATGCATTTTAATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
400709 TGTCACATTT-T-CCAATAATGCACCATTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
** *
400751 TGGCATGTTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * * *
400795 TGTCACATTTCTGCCAAAAATGCACCATTATGCATTTTGATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
400839 TGGCACCTTTCTGCCAATAATGCACCGTTATACATTTTCATGTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
400883 TGGTACCTTTCTGCCAATAATGCACCGTTATACATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
**
400927 TGGCACATTTCTGGTAATAATGCACCGTTA-GCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
400970 T
1 T
400971 TTTAGAGCAT
Statistics
Matches: 231, Mismatches: 29, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
42 33 0.14
43 15 0.06
44 183 0.79
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (44 bp):
TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:405825 original size:2 final size:2
Alignment explanation
Indices: 405820--405848 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
405810 ATTCTTTAAT
405820 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 T
405849 TAAACACTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:406503 original size:44 final size:44
Alignment explanation
Indices: 406426--406872 Score: 482
Period size: 44 Copynumber: 10.2 Consensus size: 44
406416 ATACCATGAG
** ** ** *
406426 TGGCACCTTTCTGCCAATAATATAATGCAATGCATTTTTATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
406470 TGGCACCTTTCT-CCTAATAATGCATCATTATGCATTTTCATTAA
1 TGGCACCTTTCTGCC-AATAATGCACCGTTATGCATTTTCATTTA
* * *
406514 TGACACCTTTCAGCCAATAATACACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * * *
406558 TGTCACCTTTCTACTAAAAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * * * *
406602 TGGAACCTTTCTACCAATAAAGCACCTTTATACATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
*
406646 TGGCACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
** * ** * *
406690 TGGCATTTTTCTGCCAAAAATGCACTTTTTTGTATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * **
406734 TGACACATTTCTGCCAATAATGCATTGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * * * * * *
406778 TGACACCTTTTTGCCAAAAATGCATCATCATGCATTTTCAATTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
406822 TGGCACCTTTTTGCTAATAATGCACCGTTATGTATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
406866 TGGCACC
1 TGGCACC
406873 GTTATGTAAT
Statistics
Matches: 336, Mismatches: 65, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
43 2 0.01
44 332 0.99
45 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.41
Consensus pattern (44 bp):
TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:406603 original size:132 final size:131
Alignment explanation
Indices: 406455--407331 Score: 656
Period size: 132 Copynumber: 6.5 Consensus size: 131
406445 ATATAATGCA
* * * *
406455 ATGCATTTTTATTTATGGCACCTTTCTCCTAATAATGCATCATTATGCATTTTCATTAATGACAC
1 ATGCATTTTCATTTATGGCACCTTTCTCC-AATAATGCATCGTTATGCATTTTCATTTATGGCAC
* * * * *
406520 CTTTCAGCCAATAATACACCGTTATGCATTTTCATTTATGTCACCTTTCTACTAAAAATGCACCG
65 CTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACCTTTCTGCTAATAATGCACCG
406585 TT
130 TT
* * * * *
406587 ATGCATTTTCATTTATGGAACCTTTCTACCAATAAAGCACCTTTATACATTTTCATTTATGGCAC
1 ATGCATTTTCATTTATGGCACCTTTCT-CCAATAATGCATCGTTATGCATTTTCATTTATGGCAC
* ** * * **
406652 CTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTATGGCATTTTTCTGCCAAAAATGCACTT
65 CTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACCTTTCTGCTAATAATGCACCG
406717 TT
130 TT
* * * * * *
406719 TTGTATTTTCATTTATGACACATTTCTGCCAATAATGCATTGTTATGCATTTTCATTTATGACAC
1 ATGCATTTTCATTTATGGCACCTTTCT-CCAATAATGCATCGTTATGCATTTTCATTTATGGCAC
* * * * * * *
406784 CTTTTTGCCAAAAATGCATCATCATGCATTTTCAATTATGGCACCTTTTTGCTAATAATGCACCG
65 CTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACCTTTCTGCTAATAATGCACCG
406849 TT
130 TT
* * * ** * * *
406851 ATGTATTTTCATTTATGGCACCGTTATGTAAT--TTCAT--TTATGGCACCTTTCTGTCAATAAT
1 ATGCATTTTCATTTATGGCACCTTTCTCCAATAATGCATCGTTAT-GCA---TT-T-TCATTTAT
** * * * * * * * *
406912 -GCACCATTATGCATTTTCATTTATGGCACCTTTCTGTCAATAATGCACCATTAT-GCA-TTTTC
60 GGCACC-TT-T-C--TGCCAATAAT-GCACCGTTATG-C-AT-TTTCA--TTTATGGCACCTTTC
* * * * ***
406974 AT-TTATGTCACCTTTCTACCAAAA
114 -TGCTA-AT-A--ATGC-ACC-GTT
* * *
406998 ATACAATGTT-ACGCTTTTTCATTTATGGCACCTTTCTTCCAATAATGCATCGTTATGGATTTTC
1 ATGC-ATTTTCA----------TTTATGGCACCTTTC-TCCAATAATGCATCGTTATGCATTTTC
* * * *
407062 ATTTATGGCACCTTTCTTCCAAAAATGTACCGTTATGCATTTTCATTTATGGCACATTTCTGCTA
54 ATTTATGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACCTTTCTGCTA
407127 ATAATGCACCGTT
119 ATAATGCACCGTT
* * *
407140 ATGCATTTTCATTTATGGCACCTTTCTTCCAATAATGCACCGTTATGTATTTTCACTTATGGCAC
1 ATGCATTTTCATTTATGGCACCTTTC-TCCAATAATGCATCGTTATGCATTTTCATTTATGGCAC
* * *
407205 CTTTCTTCCAATAATGCACCGTTATGCATTTTCATTTATGGCACCTTTCTGCCAATAATGCACCA
65 CTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACCTTTCTGCTAATAATGCACCG
407270 TT
130 TT
* *
407272 ATGCATTTTCATTTATGACACCTTTCTTCCAATAATGCACCGTTATGCATTTTCATTTAT
1 ATGCATTTTCATTTATGGCACCTTTC-TCCAATAATGCATCGTTATGCATTTTCATTTAT
407332 TTTAGAGCAG
Statistics
Matches: 583, Mismatches: 116, Indels: 92
0.74 0.15 0.12
Matches are distributed among these distances:
127 4 0.01
128 3 0.01
129 4 0.01
131 5 0.01
132 416 0.71
133 10 0.02
134 1 0.00
137 5 0.01
138 7 0.01
139 1 0.00
140 2 0.00
141 12 0.02
142 9 0.02
143 9 0.02
144 2 0.00
145 2 0.00
146 8 0.01
147 8 0.01
148 13 0.02
149 2 0.00
150 1 0.00
151 8 0.01
152 6 0.01
154 1 0.00
155 1 0.00
156 8 0.01
157 19 0.03
158 6 0.01
160 4 0.01
161 2 0.00
162 4 0.01
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.42
Consensus pattern (131 bp):
ATGCATTTTCATTTATGGCACCTTTCTCCAATAATGCATCGTTATGCATTTTCATTTATGGCACC
TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACCTTTCTGCTAATAATGCACCGT
T
Found at i:406871 original size:25 final size:25
Alignment explanation
Indices: 406843--406897 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
406833 TGCTAATAAT
*
406843 GCACCGTTATGTATTTTCATTTATG
1 GCACCGTTATGTAATTTCATTTATG
406868 GCACCGTTATGTAATTTCATTTATG
1 GCACCGTTATGTAATTTCATTTATG
406893 GCACC
1 GCACC
406898 TTTCTGTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (25 bp):
GCACCGTTATGTAATTTCATTTATG
Found at i:406896 original size:69 final size:69
Alignment explanation
Indices: 406813--406941 Score: 206
Period size: 69 Copynumber: 1.9 Consensus size: 69
406803 CATCATGCAT
* * *
406813 TTTCAATTATGGCACCTTTTTG-CTAATAATGCACCGTTATGTATTTTCATTTATGGCACCGTTA
1 TTTCAATTATGGCACCTTTCTGTC-AATAATGCACCATTATGCATTTTCATTTATGGCACCGTTA
406877 TGTAA
65 TGTAA
*
406882 TTTCATTTATGGCACCTTTCTGTCAATAATGCACCATTATGCATTTTCATTTATGGCACC
1 TTTCAATTATGGCACCTTTCTGTCAATAATGCACCATTATGCATTTTCATTTATGGCACC
406942 TTTCTGTCAA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
69 54 0.98
70 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (69 bp):
TTTCAATTATGGCACCTTTCTGTCAATAATGCACCATTATGCATTTTCATTTATGGCACCGTTAT
GTAA
Found at i:406914 original size:113 final size:113
Alignment explanation
Indices: 406760--406985 Score: 319
Period size: 113 Copynumber: 2.0 Consensus size: 113
406750 ATAATGCATT
* * *
406760 GTTATGCATTTTCATTTATGACACCTTTTTGCCAAAAATGCATCATCATGCATTTTCAATTATGG
1 GTTATGCAATTTCATTTATGACACCTTTCTGCCAAAAATGCACCATCATGCATTTTCAATTATGG
* * *
406825 CACCTTTTTG-CTAATAATGCACCGTTATGTATTTTCATTTATGGCACC
66 CACCTTTCTGTC-AATAATGCACCATTATGCATTTTCATTTATGGCACC
* * * * * *
406873 GTTATGTAATTTCATTTATGGCACCTTTCTGTCAATAATGCACCATTATGCATTTTCATTTATGG
1 GTTATGCAATTTCATTTATGACACCTTTCTGCCAAAAATGCACCATCATGCATTTTCAATTATGG
*
406938 CACCTTTCTGTCAATAATGCACCATTATGCATTTTCATTTATGTCACC
66 CACCTTTCTGTCAATAATGCACCATTATGCATTTTCATTTATGGCACC
406986 TTTCTACCAA
Statistics
Matches: 99, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
113 98 0.99
114 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (113 bp):
GTTATGCAATTTCATTTATGACACCTTTCTGCCAAAAATGCACCATCATGCATTTTCAATTATGG
CACCTTTCTGTCAATAATGCACCATTATGCATTTTCATTTATGGCACC
Found at i:406931 original size:44 final size:44
Alignment explanation
Indices: 406868--407331 Score: 680
Period size: 44 Copynumber: 10.5 Consensus size: 44
406858 TTCATTTATG
* *
406868 GCACCGTTATGTAATTTCATTTATGGCACCTTTCTGT-CAATAAT
1 GCACCGTTATGCATTTTCATTTATGGCACCTTTCT-TCCAATAAT
*
406912 GCACCATTATGCATTTTCATTTATGGCACCTTTCTGT-CAATAAT
1 GCACCGTTATGCATTTTCATTTATGGCACCTTTCT-TCCAATAAT
* * * *
406956 GCACCATTATGCATTTTCATTTATGTCACCTTTCTACCAAAAAT
1 GCACCGTTATGCATTTTCATTTATGGCACCTTTCTTCCAATAAT
* ** * *
407000 ACAATGTTACGCTTTTTCATTTATGGCACCTTTCTTCCAATAAT
1 GCACCGTTATGCATTTTCATTTATGGCACCTTTCTTCCAATAAT
* * *
407044 GCATCGTTATGGATTTTCATTTATGGCACCTTTCTTCCAAAAAT
1 GCACCGTTATGCATTTTCATTTATGGCACCTTTCTTCCAATAAT
* * * *
407088 GTACCGTTATGCATTTTCATTTATGGCACATTTCTGCTAATAAT
1 GCACCGTTATGCATTTTCATTTATGGCACCTTTCTTCCAATAAT
407132 GCACCGTTATGCATTTTCATTTATGGCACCTTTCTTCCAATAAT
1 GCACCGTTATGCATTTTCATTTATGGCACCTTTCTTCCAATAAT
* *
407176 GCACCGTTATGTATTTTCACTTATGGCACCTTTCTTCCAATAAT
1 GCACCGTTATGCATTTTCATTTATGGCACCTTTCTTCCAATAAT
*
407220 GCACCGTTATGCATTTTCATTTATGGCACCTTTCTGCCAATAAT
1 GCACCGTTATGCATTTTCATTTATGGCACCTTTCTTCCAATAAT
* *
407264 GCACCATTATGCATTTTCATTTATGACACCTTTCTTCCAATAAT
1 GCACCGTTATGCATTTTCATTTATGGCACCTTTCTTCCAATAAT
407308 GCACCGTTATGCATTTTCATTTAT
1 GCACCGTTATGCATTTTCATTTAT
407332 TTTAGAGCAG
Statistics
Matches: 377, Mismatches: 42, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
44 377 1.00
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (44 bp):
GCACCGTTATGCATTTTCATTTATGGCACCTTTCTTCCAATAAT
Found at i:406940 original size:25 final size:24
Alignment explanation
Indices: 406843--406987 Score: 94
Period size: 25 Copynumber: 6.3 Consensus size: 24
406833 TGCTAATAAT
*
406843 GCACCGTTATGTATTTTCATTTATG
1 GCACC-TTATGCATTTTCATTTATG
* *
406868 GCACCGTTATGTAATTTCATTTATG
1 GCACC-TTATGCATTTTCATTTATG
* * *
406893 GCACCTT-T-C--TGTCAATAAT-
1 GCACCTTATGCATTTTCATTTATG
406912 GCACCATTATGCATTTTCATTTATG
1 GCACC-TTATGCATTTTCATTTATG
* * *
406937 GCACCTT-T-C--TGTCAATAAT-
1 GCACCTTATGCATTTTCATTTATG
406956 GCACCATTATGCATTTTCATTTATG
1 GCACC-TTATGCATTTTCATTTATG
*
406981 TCACCTT
1 GCACCTT
406988 TCTACCAAAA
Statistics
Matches: 93, Mismatches: 15, Indels: 25
0.70 0.11 0.19
Matches are distributed among these distances:
19 10 0.11
20 18 0.19
21 2 0.02
22 3 0.03
23 2 0.02
24 20 0.22
25 38 0.41
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.43
Consensus pattern (24 bp):
GCACCTTATGCATTTTCATTTATG
Found at i:407017 original size:157 final size:157
Alignment explanation
Indices: 406720--407205 Score: 398
Period size: 176 Copynumber: 3.0 Consensus size: 157
406710 TGCACTTTTT
* ***
406720 TGTATTTTCATTTATGACACATTTCTGCCAATAATGCATTGTTATGCATTTTCATTTATGACACC
1 TGTAATTTCATTTATGACACATTTCTGCCAATAATGCACCATTATGCATTTTCATTTATGACACC
* * * * * * * *
406785 TTTTTGCCAAAAATGCATCATCATGCATTTTCAATTATGGCACCTTTTTGCTAATAATGCACCGT
66 TTTCTGCCAAAAATGCACCATCATGCATTTTCAATTATGGCACCTTTCTACCAAAAATACAACGT
*
406850 TATGTATTTTCATTTATGGCACCGTTA
131 TACGTATTTTCATTTATGGCACCGTTA
* * * *
406877 TGTAATTTCATTTATGGCACCTTTCTGTCAATAATGCACCATTATGCATTTTCATTTATGGCACC
1 TGTAATTTCATTTATGACACATTTCTGCCAATAATGCACCATTATGCATTTTCATTTATGACACC
* * * * * *
406942 TTTCTGTCAATAATGCACCATTATGCATTTTCATTTATGTCACCTTTCTACCAAAAATACAATGT
66 TTTCTGCCAAAAATGCACCATCATGCATTTTCAATTATGGCACCTTTCTACCAAAAATACAACGT
*
407007 TACGCT-TTTTCATTTATGGCACCTTTCTTCCAATAATGCA
131 TACG-TATTTTCATTTATGGCA--------CC-GT--T--A
* * * * * *
407047 TCGTTATGGATTTTCATTTATGGCACCTTTCTTCCAAAAATGTACCGTTATGCATTTTCATTTAT
1 T-G-TA---A-TTTCATTTATGACACATTTCTGCCAATAATGCACCATTATGCATTTTCATTTAT
* * * * * * * * * *
407112 GGCACATTTCTGCTAATAATGCACCGTTATGCATTTTCATTTATGGCACCTTTCTTCCAATAATG
60 GACACCTTTCTGCCAAAAATGCACCATCATGCATTTTCAATTATGGCACCTTTCTACCAAAAATA
* * *
407177 CACCGTTATGTATTTTCACTTATGGCACC
125 CAACGTTACGTATTTTCATTTATGGCACC
407206 TTTCTTCCAA
Statistics
Matches: 267, Mismatches: 41, Indels: 31
0.79 0.12 0.09
Matches are distributed among these distances:
157 126 0.47
158 1 0.00
165 2 0.01
166 1 0.00
168 3 0.01
170 2 0.01
171 1 0.00
172 2 0.01
175 2 0.01
176 127 0.48
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (157 bp):
TGTAATTTCATTTATGACACATTTCTGCCAATAATGCACCATTATGCATTTTCATTTATGACACC
TTTCTGCCAAAAATGCACCATCATGCATTTTCAATTATGGCACCTTTCTACCAAAAATACAACGT
TACGTATTTTCATTTATGGCACCGTTA
Found at i:407161 original size:25 final size:25
Alignment explanation
Indices: 407132--407249 Score: 80
Period size: 20 Copynumber: 5.2 Consensus size: 25
407122 TGCTAATAAT
*
407132 GCACCGTTATGCATTTTCATTTATG
1 GCACCGTTATGCATTTTCAATTATG
* *
407157 GCACC-TT-T-C--TTCCAATAAT-
1 GCACCGTTATGCATTTTCAATTATG
* *
407176 GCACCGTTATGTATTTTCACTTATG
1 GCACCGTTATGCATTTTCAATTATG
* *
407201 GCACC-TT-T-C--TTCCAATAAT-
1 GCACCGTTATGCATTTTCAATTATG
*
407220 GCACCGTTATGCATTTTCATTTATG
1 GCACCGTTATGCATTTTCAATTATG
407245 GCACC
1 GCACC
407250 TTTCTGCCAA
Statistics
Matches: 67, Mismatches: 14, Indels: 24
0.64 0.13 0.23
Matches are distributed among these distances:
19 10 0.15
20 18 0.27
21 2 0.03
22 2 0.03
23 2 0.03
24 18 0.27
25 15 0.22
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.40
Consensus pattern (25 bp):
GCACCGTTATGCATTTTCAATTATG
Found at i:410980 original size:3 final size:3
Alignment explanation
Indices: 410972--410997 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
410962 TCGTGGAATA
410972 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
410998 AAAGATGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:411004 original size:9 final size:9
Alignment explanation
Indices: 410969--411007 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
410959 TTTTCGTGGA
410969 ATAATGATG
1 ATAATGATG
*
410978 ATGATGATG
1 ATAATGATG
*
410987 ATGATGATG
1 ATAATGATG
*
410996 ATAAAGATG
1 ATAATGATG
411005 ATA
1 ATA
411008 GATAAATGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.31
Consensus pattern (9 bp):
ATAATGATG
Found at i:412783 original size:57 final size:57
Alignment explanation
Indices: 412695--412828 Score: 259
Period size: 57 Copynumber: 2.4 Consensus size: 57
412685 AATAAGAAAA
412695 ACATCGATAAGAAACCCTTCCAGTCATCTTCTTCCTCTTCCTCCGTTGTCGTCGAAG
1 ACATCGATAAGAAACCCTTCCAGTCATCTTCTTCCTCTTCCTCCGTTGTCGTCGAAG
*
412752 ACATCAATAAGAAACCCTTCCAGTCATCTTCTTCCTCTTCCTCCGTTGTCGTCGAAG
1 ACATCGATAAGAAACCCTTCCAGTCATCTTCTTCCTCTTCCTCCGTTGTCGTCGAAG
412809 ACATCGATAAGAAACCCTTC
1 ACATCGATAAGAAACCCTTC
412829 TGGTCCTACA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 75 1.00
ACGTcount: A:0.25, C:0.33, G:0.13, T:0.30
Consensus pattern (57 bp):
ACATCGATAAGAAACCCTTCCAGTCATCTTCTTCCTCTTCCTCCGTTGTCGTCGAAG
Found at i:412978 original size:10 final size:10
Alignment explanation
Indices: 412963--412993 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
412953 AATATATTTT
412963 TATAACAATA
1 TATAACAATA
412973 TATAACAATA
1 TATAACAATA
412983 TATAACAATA
1 TATAACAATA
412993 T
1 T
412994 TAGAATGGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (10 bp):
TATAACAATA
Found at i:414263 original size:15 final size:13
Alignment explanation
Indices: 414243--414277 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 13
414233 TTACCCATAA
414243 AAAATAATAAATGAT
1 AAAATAATAAA--AT
414258 AAAATAATAAAAT
1 AAAATAATAAAAT
414271 AAAATAA
1 AAAATAA
414278 ATAGGGGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 9 0.45
15 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (13 bp):
AAAATAATAAAAT
Found at i:415699 original size:29 final size:29
Alignment explanation
Indices: 415640--415704 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
415630 TTTATGTTCA
* * *
415640 TTTC-ATTTTTATTCTATGTTTTTACTAT
1 TTTCTATTTTTATTATATGTTTTAAATAT
*
415668 TTTCTATTTTTATTATTTGTTTTAAAT-T
1 TTTCTATTTTTATTATATGTTTTAAATAT
*
415696 TTTTTATTT
1 TTTCTATTT
415705 AAGTTTATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 13 0.42
29 18 0.58
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.72
Consensus pattern (29 bp):
TTTCTATTTTTATTATATGTTTTAAATAT
Found at i:421568 original size:288 final size:288
Alignment explanation
Indices: 421046--421906 Score: 1221
Period size: 288 Copynumber: 3.0 Consensus size: 288
421036 TAGTTGTAAA
* * * * ** * *
421046 TGGACATTTAAAACGAAGATGGTTGCAAAAGGTGACATTGACATGTATAAGGTATATTTTGTATC
1 TGGATATTTAAAACCAAGATGGATGCAAAATGTGATGTTGACATGTATAAGGAATATCTTGTATC
* * ** ****
421111 TGAAGGATATATTCAAAAATAATGTATTAATTTAATAGTCTTTCTTTTTGGTTTCATTGAAAGAC
66 TGAAGGATATACTCAGAAATAATGTATTAATTTTGTAGAGACTCTTTTTGGTTTCATTGAAAGAC
* * * * *
421176 TATTTTAGGATAATCATAATACTTGTTG-CTCATATTTGATATTGAGTTACATAAGTTGGATTTC
131 TCTTTCAGGATAATCATGATACTTGTTGCCT-ATATTTGGTCTTGAGTTACATAAGTTGGATTTC
* *
421240 AATATTGTGTTTCTTAATGGTAACATTGATGAGATGGTTTATACGGTACAATTAGAAAATTGTAT
195 AATATTGTGTTTCTCAATGGTAACATTGATGAGATGGTTTATACGGTGCAATTAGAAAATTGTAT
421305 CAAATGATACAAAATTAATGATATGCAAG
260 CAAATGATACAAAATTAATGATATGCAAG
* * *
421334 TGGATTTTTAAAACCAAGATGGATGCAAAATGTGATGTTAACATGCATAAGGAATATCTTGTATC
1 TGGATATTTAAAACCAAGATGGATGCAAAATGTGATGTTGACATGTATAAGGAATATCTTGTATC
* *
421399 TAAAGGATATACTCAGAAATATTGTATTAATTTTGTAGAGACTCTTTTTGGTTTCATTGAAAGAC
66 TGAAGGATATACTCAGAAATAATGTATTAATTTTGTAGAGACTCTTTTTGGTTTCATTGAAAGAC
421464 TCTTTCAGGATAATCATGATACTTGTTGCCTATATTTGGTCTTGAGTTACATAAGTTGGATTTCA
131 TCTTTCAGGATAATCATGATACTTGTTGCCTATATTTGGTCTTGAGTTACATAAGTTGGATTTCA
* *
421529 ATATTGTGTTTCTCAAAGGTAACATTGATGAGATGGTTTATACTGTGCAATTAGAAAATTGTATC
196 ATATTGTGTTTCTCAATGGTAACATTGATGAGATGGTTTATACGGTGCAATTAGAAAATTGTATC
* *
421594 AAACGATAC--AA--AATGATATACAAG
261 AAATGATACAAAATTAATGATATGCAAG
* * * *
421618 TGGATATTTAAAGCCAAGATGGATTCAAAATGTGATGTTGACATGTATAAGGCATATCTTGTATG
1 TGGATATTTAAAACCAAGATGGATGCAAAATGTGATGTTGACATGTATAAGGAATATCTTGTATC
* *
421683 TGAAGGATATACTCAGAAATAATGTATTAATTTTGTAGAGACTCTCTTTTTAGTTTCATTGAAAT
66 TGAAGGATATACTCAGAAATAATGTATTAATTTTGTAGAGA--CTCTTTTTGGTTTCATTGAAAG
421748 ACTCTTTCAGGATAATCATGATACTTGTTGCAC-ATATTTGGTCTTGAGTTACATAAGTTGGATT
129 ACTCTTTCAGGATAATCATGATACTTGTTGC-CTATATTTGGTCTTGAGTTACATAAGTTGGATT
* * * * ** * *
421812 TCAAAATTCTGTTTCTGAATGGTAACATTCATGAGATTATTTATACGATGCAATTAAAAAATTGT
193 TCAATATTGTGTTTCTCAATGGTAACATTGATGAGATGGTTTATACGGTGCAATTAGAAAATTGT
*
421877 ACCAAATGATACAAAATTAATGATATGCAA
258 ATCAAATGATACAAAATTAATGATATGCAA
421907 ATTAAAGAAA
Statistics
Matches: 509, Mismatches: 56, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
284 109 0.21
286 149 0.29
287 1 0.00
288 237 0.47
289 2 0.00
290 11 0.02
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (288 bp):
TGGATATTTAAAACCAAGATGGATGCAAAATGTGATGTTGACATGTATAAGGAATATCTTGTATC
TGAAGGATATACTCAGAAATAATGTATTAATTTTGTAGAGACTCTTTTTGGTTTCATTGAAAGAC
TCTTTCAGGATAATCATGATACTTGTTGCCTATATTTGGTCTTGAGTTACATAAGTTGGATTTCA
ATATTGTGTTTCTCAATGGTAACATTGATGAGATGGTTTATACGGTGCAATTAGAAAATTGTATC
AAATGATACAAAATTAATGATATGCAAG
Found at i:422149 original size:46 final size:46
Alignment explanation
Indices: 422096--422185 Score: 171
Period size: 46 Copynumber: 2.0 Consensus size: 46
422086 GATCGGTGTC
422096 CTAAGAATGATTTTGAAACTAAGGAAATTCAAAAAGGTTCCTTATA
1 CTAAGAATGATTTTGAAACTAAGGAAATTCAAAAAGGTTCCTTATA
*
422142 CTAAGAATGATTTTGAAACTAAGGAAATTGAAAAAGGTTCCTTA
1 CTAAGAATGATTTTGAAACTAAGGAAATTCAAAAAGGTTCCTTA
422186 CTTCAAAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (46 bp):
CTAAGAATGATTTTGAAACTAAGGAAATTCAAAAAGGTTCCTTATA
Found at i:422795 original size:25 final size:25
Alignment explanation
Indices: 422761--422822 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
422751 AAACACAATC
*
422761 TCAGTTACTTTAGTCTAAGGATATT
1 TCAGTTACTTCAGTCTAAGGATATT
*
422786 TCAGTTACTTCAGTTTAAGGATATT
1 TCAGTTACTTCAGTCTAAGGATATT
*
422811 TCATTTACTTCA
1 TCAGTTACTTCA
422823 ATTTCCACAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (25 bp):
TCAGTTACTTCAGTCTAAGGATATT
Found at i:424217 original size:23 final size:23
Alignment explanation
Indices: 424189--424248 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
424179 AGCTCATATA
*
424189 AAATGCACCGAAGTGTCATGTAG
1 AAATGCACCGAAGTGTCACGTAG
* * *
424212 AAATGCATCAAAGTGTCGCGTAG
1 AAATGCACCGAAGTGTCACGTAG
424235 AAATGCACCGAAGT
1 AAATGCACCGAAGT
424249 ACCATATAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (23 bp):
AAATGCACCGAAGTGTCACGTAG
Found at i:429398 original size:48 final size:48
Alignment explanation
Indices: 429342--429450 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 48
429332 GGTAGAGCAT
* * * * * *
429342 TTAGCACGTTTGATGTTTGTGTGATGTTGGTGCTACTATTAATGATAA
1 TTAGCACGTTTGATGTCTATGTGACGGTGCTGCTACTATCAATGATAA
* * *
429390 TTAGCACGTCTGATGTCTATGTGACGGTGCTGCTACTATCAATGGTAC
1 TTAGCACGTTTGATGTCTATGTGACGGTGCTGCTACTATCAATGATAA
*
429438 CTAGCACGTTTGA
1 TTAGCACGTTTGA
429451 CGTTACTTAT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.38
Consensus pattern (48 bp):
TTAGCACGTTTGATGTCTATGTGACGGTGCTGCTACTATCAATGATAA
Found at i:431172 original size:11 final size:11
Alignment explanation
Indices: 431149--431233 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
431139 ACAATATGTC
431149 CATCACCATTAT
1 CATCACCA-TAT
431161 CA-CACCTATAT
1 CATCACC-ATAT
431172 CATCACCATAGT
1 CATCACCATA-T
*
431184 CTATCACCATTGT
1 C-ATCACCA-TAT
*
431197 CA-CGCCTATAT
1 CATCACC-ATAT
431208 CATCACCATATT
1 CATCACCATA-T
431220 CCATCACCATAT
1 -CATCACCATAT
431232 CA
1 CA
431234 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 16 0.27
13 19 0.32
14 1 0.02
ACGTcount: A:0.32, C:0.35, G:0.04, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:431205 original size:36 final size:36
Alignment explanation
Indices: 431146--431250 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 36
431136 GATACAATAT
*
431146 GTCCATCACCATTATCACACCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
431182 GTCTATCACCATTGTCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
431218 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
431251 ACTTATAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
35 20 0.32
36 42 0.68
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:431718 original size:14 final size:15
Alignment explanation
Indices: 431684--431730 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
431674 AATTTGGAGT
431684 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
431699 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
431713 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
431730 G
1 G
431731 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:433919 original size:21 final size:21
Alignment explanation
Indices: 433878--433919 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
433868 TACTTTATCT
* *
433878 TATATTTACTTATTTATGCAC
1 TATATATACTTATTTAAGCAC
433899 TATATATA-TTATTATAAGCAC
1 TATATATACTTATT-TAAGCAC
433920 ACAATTTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.48
Consensus pattern (21 bp):
TATATATACTTATTTAAGCAC
Found at i:435273 original size:13 final size:12
Alignment explanation
Indices: 435255--435315 Score: 56
Period size: 13 Copynumber: 5.0 Consensus size: 12
435245 CACGCCTATA
435255 TCATCACCATAGT
1 TCATCACCATA-T
435268 TCATCACCAT-T
1 TCATCACCATAT
*
435279 GTCA-CGCC-TAT
1 -TCATCACCATAT
435290 ATCATCACCATAT
1 -TCATCACCATAT
435303 TCAATCACCATAT
1 TC-ATCACCATAT
435316 CACGCCTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
10 1 0.03
11 8 0.20
12 8 0.20
13 23 0.57
ACGTcount: A:0.31, C:0.33, G:0.05, T:0.31
Consensus pattern (12 bp):
TCATCACCATAT
Found at i:435284 original size:36 final size:35
Alignment explanation
Indices: 435233--435334 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 35
435223 ACAATATGTC
435233 CATCACCATTATCACGCCTATATCATCACCATAGTT
1 CATCACCATTATCACGCCTATATCATCACCATA-TT
*
435269 CATCACCATTGTCACGCCTATATCATCACCATATT
1 CATCACCATTATCACGCCTATATCATCACCATATT
*
435304 CAATCACCA-TATCACGCCTATATTATCACCA
1 C-ATCACCATTATCACGCCTATATCATCACCA
435335 ACTTATAAAT
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
35 23 0.37
36 39 0.63
ACGTcount: A:0.31, C:0.34, G:0.05, T:0.29
Consensus pattern (35 bp):
CATCACCATTATCACGCCTATATCATCACCATATT
Found at i:435801 original size:14 final size:15
Alignment explanation
Indices: 435767--435813 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
435757 AATTTGGAGT
435767 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
435782 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
435796 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
435813 G
1 G
435814 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:439357 original size:36 final size:36
Alignment explanation
Indices: 439310--439414 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
439300 GATACAATCT
439310 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
439346 GTCCATCACCATTGTCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
439382 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
439415 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.30, C:0.36, G:0.06, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:439395 original size:13 final size:13
Alignment explanation
Indices: 439313--439395 Score: 56
Period size: 13 Copynumber: 6.8 Consensus size: 13
439303 ACAATCTGTC
439313 CATCACCAT-TAT
1 CATCACCATATAT
*
439325 CA-CGCC-TATAT
1 CATCACCATATAT
*
439336 CATCACCATAGT-C
1 CATCACCATA-TAT
*
439349 CATCACCAT-TGT
1 CATCACCATATAT
*
439361 CA-CGCC-TATAT
1 CATCACCATATAT
439372 CATCACCATAT-T
1 CATCACCATATAT
439384 CCATCACCATAT
1 -CATCACCATAT
439396 CACGCCTATA
Statistics
Matches: 55, Mismatches: 7, Indels: 17
0.70 0.09 0.22
Matches are distributed among these distances:
10 2 0.04
11 16 0.29
12 11 0.20
13 25 0.45
14 1 0.02
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (13 bp):
CATCACCATATAT
Found at i:444656 original size:48 final size:48
Alignment explanation
Indices: 444600--444724 Score: 160
Period size: 48 Copynumber: 2.6 Consensus size: 48
444590 ACGCTTGTTT
* * *
444600 TTTGTGTGACGGTGGTACTATTATTAATTATAATTAGCACATCTGACG
1 TTTGTGTGACGATGGTACTACTATTAATGATAATTAGCACATCTGACG
* * *
444648 TTTGTGTGATGATGGTGCTACTATTAATGATAATTAGCACGTCTGACG
1 TTTGTGTGACGATGGTACTACTATTAATGATAATTAGCACATCTGACG
** * *
444696 AATGTGTGACGATGGTGCTACTATGAATG
1 TTTGTGTGACGATGGTACTACTATTAATG
444725 GTACATAGCA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 67 1.00
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.37
Consensus pattern (48 bp):
TTTGTGTGACGATGGTACTACTATTAATGATAATTAGCACATCTGACG
Found at i:446972 original size:228 final size:217
Alignment explanation
Indices: 446667--447078 Score: 565
Period size: 228 Copynumber: 1.8 Consensus size: 217
446657 ATTCAGGTCA
* * * *
446667 GGTCGAGTTCGGGTTTAGGTTGAAAAATACCCGACCCGAAAATATATATAATTTTACCTTATATA
1 GGTCGAGTTCGGGTTTAGGGTGAAAAAAACCCGACCAGAAAAAATATATAATTTTACCTTATATA
* *
446732 TTTAGGAATAATTACAATAATACCCCTCTATATAT-ATTTTTTCAATTAAGTCACTGTTTTTATT
66 TTTAGAAATAATTACAATAATACCCCTCTATATATAATTTTTTCAATTAAGTCAATGTTTTT-TT
*
446796 AAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGGTTGGATTTCTAATTCATATATTCGGG
130 ---T--AAAT-ATTTTTTATTATTTCGGGTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGG
446861 TTGGGTTGGGTGAAACTTTATTTTGTTCG
189 TTGGGTTGGGTGAAACTTTATTTTGTTCG
*
446890 GGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCAGAAAAAAATATATAATTTTACCTT
1 GGTCGAGTTCGGGTTTAGGGTGAAAAAAA-C---CCGACCAG-AAAAAATATATAATTTTACCTT
* *
446955 ATATATTTAGAAATAATTACAATAATACCCCTCTATATATAATTTTTTTAATTAATTCAATGTTT
61 ATATATTTAGAAATAATTACAATAATACCCCTCTATATATAATTTTTTCAATTAAGTCAATGTTT
* * * * * *
447020 TTTTTGAATTTTTTTTATTATTTTGTGTCGTGTCGGGTCGGGTTTCTAATTCATATATT
126 TTTTTAAATATTTTTTATTATTTCGGGTCGGGTCGGGTCGGATTTCTAATTCATATATT
447079 GAATAAAAAT
Statistics
Matches: 167, Mismatches: 16, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
222 44 0.26
223 29 0.17
224 1 0.01
225 1 0.01
227 7 0.04
228 62 0.37
229 23 0.14
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.42
Consensus pattern (217 bp):
GGTCGAGTTCGGGTTTAGGGTGAAAAAAACCCGACCAGAAAAAATATATAATTTTACCTTATATA
TTTAGAAATAATTACAATAATACCCCTCTATATATAATTTTTTCAATTAAGTCAATGTTTTTTTT
AAATATTTTTTATTATTTCGGGTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTTGGGTT
GGGTGAAACTTTATTTTGTTCG
Found at i:448291 original size:60 final size:58
Alignment explanation
Indices: 448115--448295 Score: 191
Period size: 60 Copynumber: 3.0 Consensus size: 58
448105 TATTATATAT
* * * * *
448115 TCTCAAACTATGACCCTCATTCTAATCTAGTCACTAAAGTTTTAAATATTCTAATTCCA
1 TCTCAAACTATGACCCTCATTCAAAT-TAGTCCCTAAACTTTTAAATATTCAAATTTCA
** * * * * *
448174 TTCTCAAACTATGAAACTCATTTTAAATTAGTCCTTAAACTTTTGAACATTCCAATTTCA
1 -TCTCAAACTATGACCCTCA-TTCAAATTAGTCCCTAAACTTTTAAATATTCAAATTTCA
* *
448234 TCATCAAACTAAGACCCTCATTCAAAATTGGTCCCTAAACTTTTAAATATTCAAATTTCA
1 TC-TCAAACTATGACCCTCATTC-AAATTAGTCCCTAAACTTTTAAATATTCAAATTTCA
448294 TC
1 TC
448296 CCCAAATTCA
Statistics
Matches: 98, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
59 4 0.04
60 89 0.91
61 5 0.05
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.37
Consensus pattern (58 bp):
TCTCAAACTATGACCCTCATTCAAATTAGTCCCTAAACTTTTAAATATTCAAATTTCA
Found at i:452089 original size:21 final size:21
Alignment explanation
Indices: 452063--452103 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
452053 CCGTACAGGG
452063 GGTATCGGTACCCATTCATAT
1 GGTATCGGTACCCATTCATAT
*
452084 GGTATCGGTACCCCTTCATA
1 GGTATCGGTACCCATTCATA
452104 AAATTCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (21 bp):
GGTATCGGTACCCATTCATAT
Found at i:452186 original size:16 final size:15
Alignment explanation
Indices: 452151--452180 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
452141 GGATACCCCT
452151 GGGGGTATCAATACC
1 GGGGGTATCAATACC
*
452166 GGGGGTATCGATACC
1 GGGGGTATCAATACC
452181 ATGGGGGGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.20, G:0.37, T:0.20
Consensus pattern (15 bp):
GGGGGTATCAATACC
Found at i:452360 original size:29 final size:29
Alignment explanation
Indices: 452339--452396 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
452329 AAACTTTGAA
452339 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
452368 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
452397 TGCCTTAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:452386 original size:30 final size:30
Alignment explanation
Indices: 452339--452398 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
452329 AAACTTTGAA
452339 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
452368 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
452399 CCTTAAAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:453654 original size:19 final size:19
Alignment explanation
Indices: 453618--453663 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
453608 CTAAATCCTT
*
453618 TTTCAAAATTTCATTTTGGC
1 TTTCAAAATCTCATTTT-GC
*
453638 TTTCAAAATCT-ATTTTGT
1 TTTCAAAATCTCATTTTGC
453656 TTTCAAAA
1 TTTCAAAA
453664 GAAAATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.38
19 5 0.21
20 10 0.42
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (19 bp):
TTTCAAAATCTCATTTTGC
Found at i:454938 original size:15 final size:15
Alignment explanation
Indices: 454918--454947 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
454908 GTTGCAGCCA
454918 GGGGGTATCGATACC
1 GGGGGTATCGATACC
454933 GGGGGTATCGATACC
1 GGGGGTATCGATACC
454948 ATAGATACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.40, T:0.20
Consensus pattern (15 bp):
GGGGGTATCGATACC
Found at i:460292 original size:21 final size:19
Alignment explanation
Indices: 460263--460301 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
460253 GAGATATATC
460263 ATTTGGTTAAAGGGGTCAATA
1 ATTTGGTT--AGGGGTCAATA
*
460284 ATTTTGTTAGGGGTCAAT
1 ATTTGGTTAGGGGTCAAT
460302 CCTTTGAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
21 7 0.41
ACGTcount: A:0.28, C:0.05, G:0.28, T:0.38
Consensus pattern (19 bp):
ATTTGGTTAGGGGTCAATA
Found at i:461149 original size:12 final size:12
Alignment explanation
Indices: 461132--461159 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
461122 GATATTTCTA
461132 ACAATCAATGAC
1 ACAATCAATGAC
461144 ACAATCAATGAC
1 ACAATCAATGAC
461156 ACAA
1 ACAA
461160 GAAATAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.25, G:0.07, T:0.14
Consensus pattern (12 bp):
ACAATCAATGAC
Found at i:461906 original size:2 final size:2
Alignment explanation
Indices: 461901--461933 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
461891 TTTATACATG
461901 TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
461934 CATAGAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:462072 original size:19 final size:20
Alignment explanation
Indices: 462032--462072 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
462022 TTATTTTAAA
* *
462032 AATGAAAGATTTAGAATTAT
1 AATGAAAGATTTACAATCAT
462052 AATG-AAGATTTACAATCAT
1 AATGAAAGATTTACAATCAT
462071 AA
1 AA
462073 CCGTAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.51, C:0.05, G:0.12, T:0.32
Consensus pattern (20 bp):
AATGAAAGATTTACAATCAT
Found at i:474271 original size:46 final size:46
Alignment explanation
Indices: 474242--474550 Score: 411
Period size: 46 Copynumber: 6.7 Consensus size: 46
474232 AATACACTCG
* *
474242 TTCATACATTTTAATCATGGCATCCTTTCATGCCTTAATGCATCAT
1 TTCATGCATTTTAATCATGGCATCCTTTCATGCCTTAATGCATCCT
* * * * *
474288 TTCATGCATTTTAGTTATGGCAACCTTTCATGCCTTAATCCATCCG
1 TTCATGCATTTTAATCATGGCATCCTTTCATGCCTTAATGCATCCT
* *
474334 TTGATGCATTTCAATCATGGCATCCTTTCATGCCTTAATGCATCCT
1 TTCATGCATTTTAATCATGGCATCCTTTCATGCCTTAATGCATCCT
* * * * *
474380 TTCATGCATTTTTATCACGACATCCTATAATGCCTTAATGCATCCT
1 TTCATGCATTTTAATCATGGCATCCTTTCATGCCTTAATGCATCCT
* * * * *
474426 TTCATGCATTTTAGTTATGACATCCGTTCATGCCTTAATGCATCAT
1 TTCATGCATTTTAATCATGGCATCCTTTCATGCCTTAATGCATCCT
* * * *
474472 TTCATGCATTTTAGTTATGGCATTCTTTCATGCCTTAATGCATCCG
1 TTCATGCATTTTAATCATGGCATCCTTTCATGCCTTAATGCATCCT
474518 TTCATGCATTTTAATCATGGCATCCTTTCATGC
1 TTCATGCATTTTAATCATGGCATCCTTTCATGC
474551 ATTTTAGTTA
Statistics
Matches: 226, Mismatches: 37, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 226 1.00
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.41
Consensus pattern (46 bp):
TTCATGCATTTTAATCATGGCATCCTTTCATGCCTTAATGCATCCT
Found at i:474353 original size:92 final size:92
Alignment explanation
Indices: 474221--474550 Score: 457
Period size: 92 Copynumber: 3.6 Consensus size: 92
474211 TATGGTCTCT
* * *
474221 TTTCATGCATTAATACA-CTCGTTCATACATTTTAATCATGGCATCCTTTCATGCCTTAATGCAT
1 TTTCATGCCTTAATGCATC-CGTTCATGCATTTTAATCATGGCATCCTTTCATGCCTTAATGCAT
*
474285 CATTTCATGCATTTTAGTTATGGCAACC
65 CATTTCATGCATTTTAGTTATGGCATCC
* * *
474313 TTTCATGCCTTAATCCATCCGTTGATGCATTTCAATCATGGCATCCTTTCATGCCTTAATGCATC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATCATGGCATCCTTTCATGCCTTAATGCATC
* * * *
474378 CTTTCATGCATTTTTA-TCACGACATCC
66 ATTTCATGCA-TTTTAGTTATGGCATCC
* * * * * * *
474405 TATAATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGACATCCGTTCATGCCTTAATGCATC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATCATGGCATCCTTTCATGCCTTAATGCATC
*
474470 ATTTCATGCATTTTAGTTATGGCATTC
66 ATTTCATGCATTTTAGTTATGGCATCC
474497 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATCATGGCATCCTTTCATGC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATCATGGCATCCTTTCATGC
474551 ATTTTAGTTA
Statistics
Matches: 203, Mismatches: 32, Indels: 6
0.84 0.13 0.02
Matches are distributed among these distances:
91 5 0.02
92 192 0.95
93 6 0.03
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.41
Consensus pattern (92 bp):
TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATCATGGCATCCTTTCATGCCTTAATGCATC
ATTTCATGCATTTTAGTTATGGCATCC
Found at i:474563 original size:26 final size:26
Alignment explanation
Indices: 474419--474563 Score: 125
Period size: 26 Copynumber: 6.0 Consensus size: 26
474409 ATGCCTTAAT
474419 GCATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
* * *
474445 ACATCCGTTCATGC--CTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
*
474465 GCATCATTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
* *
474491 GCATTCTTTCATGC--CTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
* * *
474511 GCATCCGTTCATGCATTTTAATCATG
1 GCATCCTTTCATGCATTTTAGTTATG
474537 GCATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
474563 G
1 G
474564 ATTCGGTTTA
Statistics
Matches: 91, Mismatches: 16, Indels: 24
0.69 0.12 0.18
Matches are distributed among these distances:
20 23 0.25
21 4 0.04
22 6 0.07
24 6 0.07
25 4 0.04
26 48 0.53
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.43
Consensus pattern (26 bp):
GCATCCTTTCATGCATTTTAGTTATG
Found at i:481414 original size:46 final size:46
Alignment explanation
Indices: 481358--481718 Score: 263
Period size: 46 Copynumber: 7.7 Consensus size: 46
481348 AATACATCCG
*
481358 TTCATGCATTTTAATCATGGCATCCTTTCATGACTTAATGCATCAT
1 TTCATGCATTTTAATTATGGCATCCTTTCATGACTTAATGCATCAT
* * * * * *
481404 TTTATGCATTTTAGTTATGGTATCCTTTCATGCCTTAAAGCATCCT
1 TTCATGCATTTTAATTATGGCATCCTTTCATGACTTAATGCATCAT
* * * * * * *
481450 TTAATGCATTTTAGTTATTGTATCCTTTCAAGCATTTTAGTTATGGCATCCT
1 TTCATGCATTTTAATTATGGCATCCTTTCATG-A-CTTA---AT-GCATCAT
* * *
481502 TTCATGC--CTT-A--AT-GCATCCATTCATGCCTTAATGCATCTAT
1 TTCATGCATTTTAATTATGGCATCCTTTCATGACTTAATGCATC-AT
** *
481543 TT-ATGCATTTTAACCATGGCATCCTTTCATGCATTTTAAT-CATGGCAT
1 TTCATGCATTTTAATTATGGCATCCTTTCATG-A-CTTAATGCAT--CAT
* * * *
481591 CCTTCCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATACATCCT
1 --TT-CATGCATTTTAATTATGGCATCCTTTCATGACTTAATGCATCAT
* * *
481640 TTCATGCATTTTAGTTATGGCATTCTTTCATGATTTAATGCATCCA-
1 TTCATGCATTTTAATTATGGCATCCTTTCATGACTTAATGCAT-CAT
* *
481686 TTCATGCATTTTAATCATGTCATCCTTTCATGA
1 TTCATGCATTTTAATTATGGCATCCTTTCATGA
481719 ATTTTAGTTA
Statistics
Matches: 251, Mismatches: 41, Indels: 46
0.74 0.12 0.14
Matches are distributed among these distances:
40 9 0.04
41 5 0.02
42 2 0.01
43 1 0.00
44 3 0.01
45 2 0.01
46 156 0.62
47 8 0.03
48 10 0.04
49 3 0.01
50 9 0.04
51 4 0.02
52 39 0.16
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.43
Consensus pattern (46 bp):
TTCATGCATTTTAATTATGGCATCCTTTCATGACTTAATGCATCAT
Found at i:481548 original size:20 final size:20
Alignment explanation
Indices: 481495--481539 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
481485 TTTAGTTATG
*
481495 GCATCCTTTCATGCCTTAAT
1 GCATCCATTCATGCCTTAAT
481515 GCATCCATTCATGCCTTAAT
1 GCATCCATTCATGCCTTAAT
481535 GCATC
1 GCATC
481540 TATTTATGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.31, G:0.11, T:0.36
Consensus pattern (20 bp):
GCATCCATTCATGCCTTAAT
Found at i:481710 original size:26 final size:26
Alignment explanation
Indices: 481352--481744 Score: 214
Period size: 26 Copynumber: 16.5 Consensus size: 26
481342 TGCATTAATA
*
481352 CATCCGTTCATGCATTTTAATCATGG
1 CATCCTTTCATGCATTTTAATCATGG
*
481378 CATCCTTTCATG-A-CTTAATGCAT--
1 CATCCTTTCATGCATTTTAAT-CATGG
* *
481401 CAT--TTT-ATGCATTTTAGTTATGG
1 CATCCTTTCATGCATTTTAATCATGG
* *
481424 TATCCTTTCATGC--CTTAA--A--G
1 CATCCTTTCATGCATTTTAATCATGG
* * * *
481444 CATCCTTTAATGCATTTTAGTTATTG
1 CATCCTTTCATGCATTTTAATCATGG
* * * *
481470 TATCCTTTCAAGCATTTTAGTTATGG
1 CATCCTTTCATGCATTTTAATCATGG
*
481496 CATCCTTTCATGC--CTT-A--AT-G
1 CATCCTTTCATGCATTTTAATCATGG
* *
481516 CATCCATTCATGC--CTT-A--AT-G
1 CATCCTTTCATGCATTTTAATCATGG
* *
481536 CAT-CTATTTATGCATTTTAACCATGG
1 CATCCT-TTCATGCATTTTAATCATGG
481562 CATCCTTTCATGCATTTTAATCATGG
1 CATCCTTTCATGCATTTTAATCATGG
* * *
481588 CATCCTTCCATGCATTTTAGTTATGG
1 CATCCTTTCATGCATTTTAATCATGG
*
481614 CATCCTTTCATGC--CTTAAT-A---
1 CATCCTTTCATGCATTTTAATCATGG
* *
481634 CATCCTTTCATGCATTTTAGTTATGG
1 CATCCTTTCATGCATTTTAATCATGG
*
481660 CATTCTTTCATG-A-TTT-A--AT-G
1 CATCCTTTCATGCATTTTAATCATGG
* *
481680 CATCCATTCATGCATTTTAATCATGT
1 CATCCTTTCATGCATTTTAATCATGG
* * *
481706 CATCCTTTCATGAATTTTAGTTATGG
1 CATCCTTTCATGCATTTTAATCATGG
*
481732 TATCCTTTCATGC
1 CATCCTTTCATGC
481745 CTTAATGAAT
Statistics
Matches: 287, Mismatches: 46, Indels: 68
0.72 0.11 0.17
Matches are distributed among these distances:
19 1 0.00
20 68 0.24
21 11 0.04
22 17 0.06
23 9 0.03
24 18 0.06
25 12 0.04
26 149 0.52
27 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.44
Consensus pattern (26 bp):
CATCCTTTCATGCATTTTAATCATGG
Found at i:481710 original size:72 final size:71
Alignment explanation
Indices: 481352--481770 Score: 235
Period size: 72 Copynumber: 5.9 Consensus size: 71
481342 TGCATTAATA
* * * * *
481352 CATCCGTTCATGCATTTTAATCATGGCATCCTTTCATGACTTAATGCAT-CATTTTATGCATTTT
1 CATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGATTTAATGCATCCA-TTCATGCATTTT
* *
481416 AGTTATGG
65 AATCAT-G
* * * * * * *
481424 TATCCTTTCATGC--CTTA---A-AGCATCCTTTAATGCATTTTAGTTATTGTATCCTTTCAAGC
1 CATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATG-A-TTTA---A-TGCATCCATTCATGC
* *
481483 ATTTTAGTTATGG
60 ATTTTAATCAT-G
* * ** * *
481496 CATCCTTTCATGC--CTTA---AT-GCATCCATTCATGCCTTAATGCATCTATTTATGCATTTTA
1 CATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGATTTAATGCATCCATTCATGCATTTTA
*
481555 ACCATGG
66 ATCAT-G
* * * *
481562 CATCCTTTCATGCATTTTAATCATGGCATCCTTCCATGCATTTTAGTTATGGCATCCTTTCATGC
1 CATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATG-A-TTTA---AT-GCATCCATTCATGC
*
481627 --CTTAAT-A--
60 ATTTTAATCATG
*
481634 CATCCTTTCATGCATTTTAGTTATGGCATTCTTTCATGATTTAATGCATCCATTCATGCATTTTA
1 CATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGATTTAATGCATCCATTCATGCATTTTA
481699 ATCATG
66 ATCATG
* * ** * * *
481705 TCATCCTTTCATGAATTTTAGTTATGGTATCCTTTCATGCCTTAATGAATCCGTTCATGCCTTTT
1 -CATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGATTTAATGCATCCATTCATGCATTTT
481770 A
65 A
481771 GTGATGGATT
Statistics
Matches: 274, Mismatches: 47, Indels: 52
0.73 0.13 0.14
Matches are distributed among these distances:
66 58 0.21
67 5 0.02
68 11 0.04
69 1 0.00
70 10 0.04
71 4 0.01
72 163 0.59
73 1 0.00
74 3 0.01
75 1 0.00
76 4 0.01
77 2 0.01
78 11 0.04
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.43
Consensus pattern (71 bp):
CATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGATTTAATGCATCCATTCATGCATTTTA
ATCATG
Found at i:481770 original size:118 final size:118
Alignment explanation
Indices: 481352--481781 Score: 457
Period size: 118 Copynumber: 3.7 Consensus size: 118
481342 TGCATTAATA
* * * * * * *
481352 CATCCGTTCATGCATTTTAATCATGGCATCCTTTCATGACTTAATGCATCATTTTATGCATTTTA
1 CATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGAATCCTTTCATGCATTTTA
* * ** * * * *
481417 GTTATGGTATCCTTTCATGCCTTAAAGCATCCTTTAATGCATTTTAGTTATTGT
66 GTTATGGCATTCTTTCATGATTTAATGCATCCTTTCATGCATTTTAATCA-TGT
* * * *
481471 -ATCCTTTCAAGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCATTCATGC--CTTA
1 CATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGAATCCTTTCATGCATTTTA
* *
481533 ---AT-GCA-TCTATTTATGCATTTTAACCATGGCATCCTTTCATGCATTTTAATCATGG
66 GTTATGGCATTCT-TTCATG-A-TTT-A--AT-GCATCCTTTCATGCATTTTAATCATGT
*
481588 CATCCTTCCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT-ACATCCTTTCATGCATTTT
1 CATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGA-ATCCTTTCATGCATTTT
*
481652 AGTTATGGCATTCTTTCATGATTTAATGCATCCATTCATGCATTTTAATCATGT
65 AGTTATGGCATTCTTTCATGATTTAATGCATCCTTTCATGCATTTTAATCATGT
* * * *
481706 CATCCTTTCATGAATTTTAGTTATGGTATCCTTTCATGCCTTAATGAATCCGTTCATGCCTTTTA
1 CATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGAATCCTTTCATGCATTTTA
*
481771 GTGATGG-ATTC
66 GTTATGGCATTC
481782 GGTTTTGAGC
Statistics
Matches: 261, Mismatches: 33, Indels: 36
0.79 0.10 0.11
Matches are distributed among these distances:
111 2 0.01
112 7 0.03
113 2 0.01
114 2 0.01
115 1 0.00
116 3 0.01
117 7 0.03
118 213 0.82
119 3 0.01
120 3 0.01
121 1 0.00
122 3 0.01
123 3 0.01
124 8 0.03
125 3 0.01
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.43
Consensus pattern (118 bp):
CATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGAATCCTTTCATGCATTTTA
GTTATGGCATTCTTTCATGATTTAATGCATCCTTTCATGCATTTTAATCATGT
Found at i:485680 original size:19 final size:19
Alignment explanation
Indices: 485659--485747 Score: 67
Period size: 19 Copynumber: 4.7 Consensus size: 19
485649 AAGGAGTACA
485659 AAAACAAAAGAAAATCACA-
1 AAAA-AAAAGAAAATCACAG
* *
485678 AAAAATAAGAAACTCA-AG
1 AAAAAAAAGAAAATCACAG
* *
485696 TAAAGAAAAGAAAATCACAT
1 -AAAAAAAAGAAAATCACAG
* *
485716 AAAAACAAGAAACTCA-AG
1 AAAAAAAAGAAAATCACAG
*
485734 CAAAGAAAAGAAAA
1 -AAAAAAAAGAAAA
485748 GCAAAACAAA
Statistics
Matches: 53, Mismatches: 13, Indels: 8
0.72 0.18 0.11
Matches are distributed among these distances:
17 1 0.02
18 11 0.21
19 40 0.75
20 1 0.02
ACGTcount: A:0.70, C:0.12, G:0.10, T:0.08
Consensus pattern (19 bp):
AAAAAAAAGAAAATCACAG
Found at i:485714 original size:37 final size:38
Alignment explanation
Indices: 485664--485747 Score: 143
Period size: 38 Copynumber: 2.2 Consensus size: 38
485654 GTACAAAAAC
* *
485664 AAAAGAAAATCACA-AAAAATAAGAAACTCAAGTAAAG
1 AAAAGAAAATCACATAAAAACAAGAAACTCAAGCAAAG
485701 AAAAGAAAATCACATAAAAACAAGAAACTCAAGCAAAG
1 AAAAGAAAATCACATAAAAACAAGAAACTCAAGCAAAG
485739 AAAAGAAAA
1 AAAAGAAAA
485748 GCAAAACAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
37 14 0.32
38 30 0.68
ACGTcount: A:0.69, C:0.12, G:0.11, T:0.08
Consensus pattern (38 bp):
AAAAGAAAATCACATAAAAACAAGAAACTCAAGCAAAG
Found at i:492557 original size:37 final size:37
Alignment explanation
Indices: 492507--492593 Score: 138
Period size: 37 Copynumber: 2.4 Consensus size: 37
492497 TAGAAGAATC
* *
492507 GAGGTTGGTTTTTAGCAGTTAACAACCATATAGAGAG
1 GAGGTTAGTTTTTAGCAGTTAACAACCAGATAGAGAG
492544 GAGGTTAGTTTTTAGCAGTTAACAACCAGATAGAGAG
1 GAGGTTAGTTTTTAGCAGTTAACAACCAGATAGAGAG
**
492581 GAGGCCAGTTTTT
1 GAGGTTAGTTTTT
492594 CATTAGGGGA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.30
Consensus pattern (37 bp):
GAGGTTAGTTTTTAGCAGTTAACAACCAGATAGAGAG
Found at i:496823 original size:19 final size:20
Alignment explanation
Indices: 496799--496836 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
496789 TTTTTTACTT
496799 TTTTTGCAATGCA-TCTTAA
1 TTTTTGCAATGCATTCTTAA
*
496818 TTTTTGCATTGCATTCTTA
1 TTTTTGCAATGCATTCTTA
496837 TTCATTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.21, C:0.16, G:0.11, T:0.53
Consensus pattern (20 bp):
TTTTTGCAATGCATTCTTAA
Found at i:500731 original size:37 final size:36
Alignment explanation
Indices: 500566--500748 Score: 233
Period size: 36 Copynumber: 5.1 Consensus size: 36
500556 TTCTCCATGC
500566 CATCTTAAGCCTTCACGGAAGTA-TAGTGAAGCAAAT
1 CATCTTAAGCCTTCACGGAAG-AGTAGTGAAGCAAAT
* * *
500602 CATCTTAAGCCTTCACGGAATAGTAATAAAGCAAAT
1 CATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAAT
* * *
500638 CATTTTAAGCCTTCACGAAAGAGTAATGAAGCAAAT
1 CATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAAT
* * *
500674 CGTCTTAAGCCTTCATGGAAGAGTAGTGGAGCAAAT
1 CATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAAT
* * *
500710 CATGTATAAGCCTTCAAGGAAGAGTAGTGAAGAAAAT
1 CATCT-TAAGCCTTCACGGAAGAGTAGTGAAGCAAAT
500747 CA
1 CA
500749 AGATCGAGTC
Statistics
Matches: 127, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
35 1 0.01
36 96 0.76
37 30 0.24
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (36 bp):
CATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAAT
Found at i:500828 original size:55 final size:56
Alignment explanation
Indices: 500752--501300 Score: 595
Period size: 55 Copynumber: 10.0 Consensus size: 56
500742 AAAATCAAGA
* * * * * *
500752 TCGAGTCCTATACTCCTTGAAATAATAGTGAGCAG-ACACGTTTGCTGAAGATTGT
1 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCAGAACCCGTTTTCTGAAGATTGT
* ** *
500807 TCGAGTTCTATACTCCCTGAAAGAATAGGGAG-AGAACCCATTTTCAAAATATTGT
1 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCAGAACCCGTTTTCTGAAGATTGT
* *
500862 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGC-GAACCCATTTT-TAGAAGATTAT
1 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCAGAACCCGTTTTCT-GAAGATTGT
* * * * *
500917 TCGAGTTCTATAATCCCTGAAAGAATAGGGAGC-GAACTCGTTTTCAGAATATTTT
1 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCAGAACCCGTTTTCTGAAGATTGT
* * * ** * *
500972 TCGAGTTCTATACTCCCTGAAGGAATATGGAGC-GAACTCGTTTTCAAAATATTAT
1 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCAGAACCCGTTTTCTGAAGATTGT
* *
501027 TCGAGTTTTATACT-CCTCGAAAGATTAGGGAGCA-AACCCGTTTT-TAGAAGATTGT
1 TCGAGTTCTATACTCCCT-GAAAGAATAGGGAGCAGAACCCGTTTTCT-GAAGATTGT
* * * * *
501082 TTGAGTTCTATAATCCCTGAAAGAATAGGGAG-TGAACCCATTTTCAGAAGATTGT
1 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCAGAACCCGTTTTCTGAAGATTGT
* * * ** *
501137 TAGAGTTCTATACTCCCTGAAAGAATAGGGAGC-GGACCC-ATTTCCAAATCATTGT
1 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCAGAACCCGTTTTCTGAA-GATTGT
* * *
501192 TCGAGTTCTATACACCCTGAAAAAATAGGGAGCA-AACCCGTTTTTTAGAAGATTGT
1 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCAGAACCCGTTTTCT-GAAGATTGT
501248 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCA-AACCCGTTTTCTGAAGATT
1 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCAGAACCCGTTTTCTGAAGATT
501301 TTTCAAGATT
Statistics
Matches: 419, Mismatches: 60, Indels: 30
0.82 0.12 0.06
Matches are distributed among these distances:
54 11 0.03
55 352 0.84
56 54 0.13
57 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (56 bp):
TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCAGAACCCGTTTTCTGAAGATTGT
Found at i:501078 original size:165 final size:164
Alignment explanation
Indices: 500752--501300 Score: 726
Period size: 165 Copynumber: 3.3 Consensus size: 164
500742 AAAATCAAGA
* * * * * * * *
500752 TCGAGTCCTATACTCCTTGAAATAATAGTGAGC-AGACACGTTTGCTGAAGATTGTTCGAGTTCT
1 TCGAGTTCTATAATCCCTGAAAGAATAGGGAGCGA-ACCCGTTTTCAGAAGATTGTTCGAGTTCT
*
500816 ATACTCCCTGAAAGAATAGGGAGAGAACCCATTTTCAAAATATTGTTCGAGTTCTATACTCCCTG
65 ATACTCCCTGAAAGAATAGGGAGCGAA-CCATTTTCAAAATATTGTTCGAGTTCTATACTCCCTG
* * *
500881 AAAGAATAGGGAGCGAACCCATTTTTAGAAGATTAT
129 AAAGAATAGGGAGCAAACCCGTTTTTAGAAGATTGT
* * *
500917 TCGAGTTCTATAATCCCTGAAAGAATAGGGAGCGAACTCGTTTTCAGAATATTTTTCGAGTTCTA
1 TCGAGTTCTATAATCCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGATTGTTCGAGTTCTA
* * * * *
500982 TACTCCCTGAAGGAATATGGAGCGAACTCGTTTTCAAAATATTATTCGAGTTTTATACT-CCTCG
66 TACTCCCTGAAAGAATAGGGAGCGAAC-CATTTTCAAAATATTGTTCGAGTTCTATACTCCCT-G
*
501046 AAAGATTAGGGAGCAAACCCGTTTTTAGAAGATTGT
129 AAAGAATAGGGAGCAAACCCGTTTTTAGAAGATTGT
* * * *
501082 TTGAGTTCTATAATCCCTGAAAGAATAGGGAGTGAACCCATTTTCAGAAGATTGTTAGAGTTCTA
1 TCGAGTTCTATAATCCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGATTGTTCGAGTTCTA
* * *
501147 TACTCCCTGAAAGAATAGGGAGCGGACCCA-TTTCCAAATCATTGTTCGAGTTCTATACACCCTG
66 TACTCCCTGAAAGAATAGGGAGC-GAACCATTTTCAAAAT-ATTGTTCGAGTTCTATACTCCCTG
*
501211 AAAAAATAGGGAGCAAACCCGTTTTTTAGAAGATTGT
129 AAAGAATAGGGAGCAAACCCG-TTTTTAGAAGATTGT
* * *
501248 TCGAGTTCTATACTCCCTGAAAGAATAGGGAGCAAACCCGTTTTCTGAAGATT
1 TCGAGTTCTATAATCCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGATT
501301 TTTCAAGATT
Statistics
Matches: 334, Mismatches: 43, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
164 12 0.04
165 253 0.76
166 69 0.21
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (164 bp):
TCGAGTTCTATAATCCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGATTGTTCGAGTTCTA
TACTCCCTGAAAGAATAGGGAGCGAACCATTTTCAAAATATTGTTCGAGTTCTATACTCCCTGAA
AGAATAGGGAGCAAACCCGTTTTTAGAAGATTGT
Found at i:503297 original size:18 final size:19
Alignment explanation
Indices: 503255--503290 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
503245 GCTGAAGAAG
*
503255 ATTAATTTATGTTAGGTTT
1 ATTATTTTATGTTAGGTTT
503274 ATTATTTTA-GTTAGGTT
1 ATTATTTTATGTTAGGTT
503291 ATATATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.25, C:0.00, G:0.17, T:0.58
Consensus pattern (19 bp):
ATTATTTTATGTTAGGTTT
Found at i:505874 original size:46 final size:45
Alignment explanation
Indices: 505804--505925 Score: 127
Period size: 49 Copynumber: 2.6 Consensus size: 45
505794 GTAACCATGC
* *
505804 AAATAAGCTTATTAGCTTACGGAATAATGGCAAGTATATTGAAAAA
1 AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTG-AAAA
* * * **
505850 AAATAAGCTTACGAGCTTATGGAATTTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTATGGAA---T-AATGGCAAGTATATTGAAAA
*
505899 AAATAAGCTTATGAGCTTATGGGATAA
1 AAATAAGCTTATGAGCTTATGGAATAA
505926 AAGGTAAGAA
Statistics
Matches: 63, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
45 2 0.03
46 22 0.35
49 25 0.40
50 14 0.22
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAA
Found at i:507665 original size:37 final size:36
Alignment explanation
Indices: 507591--507661 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
507581 GAAATATTTA
507591 ATTATTTAATTTTTTTCGAGAAAAGATTGTTAGAAT
1 ATTATTTAATTTTTTTCGAGAAAAGATTGTTAGAAT
507627 ATTATTTAATTTTTTTCGAGAAAAGATTGTTAGAA
1 ATTATTTAATTTTTTTCGAGAAAAGATTGTTAGAA
507662 ATATCTAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.37, C:0.03, G:0.14, T:0.46
Consensus pattern (36 bp):
ATTATTTAATTTTTTTCGAGAAAAGATTGTTAGAAT
Found at i:509088 original size:17 final size:17
Alignment explanation
Indices: 509066--509115 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
509056 AATTAAGAGT
509066 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
*
509083 TAGTTTAATGAATGAAC
1 TAGTTTAATAAATGAAC
* *
509100 TAACTTTATTAAATGA
1 T-AGTTTAATAAATGA
509116 CTATATGCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 17 0.61
18 11 0.39
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:514761 original size:17 final size:17
Alignment explanation
Indices: 514739--514809 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
514729 AATTAAGAGT
514739 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
514756 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
* *
514773 TAGTTTAATTAATAAAC
1 TAGTTTAATAAATGAAC
**
514790 TAACTTAATTAAAT-AAC
1 TAGTTTAA-TAAATGAAC
514807 TAG
1 TAG
514810 ATGCATGAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
17 40 0.91
18 4 0.09
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:515362 original size:17 final size:17
Alignment explanation
Indices: 515340--515389 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
515330 AATTAAGAGT
515340 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
*
515357 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
* *
515374 TAACTTTATTAAATGA
1 T-AGTTTAATAAATGA
515390 CTAAATGAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 17 0.61
18 11 0.39
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:516482 original size:33 final size:33
Alignment explanation
Indices: 516414--516482 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
516404 ACACTTTTGT
*
516414 TTTTCAATGTGCTCATTTTCACTCTCAATTCTC
1 TTTTCAATGTGCTCATTTTCACTCTCAAATCTC
*
516447 TTTTCAATGCT-CTCATTTTCAACTCT-AAATGTC
1 TTTTCAATG-TGCTCATTTTC-ACTCTCAAATCTC
516480 TTT
1 TTT
516483 GTTTCCTCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 26 0.81
34 6 0.19
ACGTcount: A:0.20, C:0.25, G:0.06, T:0.49
Consensus pattern (33 bp):
TTTTCAATGTGCTCATTTTCACTCTCAAATCTC
Found at i:517327 original size:22 final size:22
Alignment explanation
Indices: 517302--517349 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
517292 AAGTTGTGGC
*
517302 TAAAATAAAAATAATAATTAAA
1 TAAAAGAAAAATAATAATTAAA
517324 TAAAAGAAAAATAATAATTAAA
1 TAAAAGAAAAATAATAATTAAA
517346 TAAA
1 TAAA
517350 CAAATTAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (22 bp):
TAAAAGAAAAATAATAATTAAA
Found at i:518090 original size:75 final size:77
Alignment explanation
Indices: 517990--518131 Score: 198
Period size: 76 Copynumber: 1.9 Consensus size: 77
517980 AATACCTAAA
* * * * * * *
517990 AAAATATAATATTCTAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACAAAGATA
1 AAAATATAATATCCTAAAACCTAATTAAAAAACGAAAAACCTAATGAAAATAAAATACAAAGATA
518054 AAGATAAAATAC
66 AAGATAAAATAC
*
518066 AAAA-ATAATATCCTAAAACTTAATTAAAAAACGAAAAACCTAATGAAAATAAAATACAAAGATA
1 AAAATATAATATCCTAAAACCTAATTAAAAAACGAAAAACCTAATGAAAATAAAATACAAAGATA
518130 AA
66 AA
518132 ATATAATGTT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
75 24 0.42
76 33 0.58
ACGTcount: A:0.61, C:0.11, G:0.04, T:0.24
Consensus pattern (77 bp):
AAAATATAATATCCTAAAACCTAATTAAAAAACGAAAAACCTAATGAAAATAAAATACAAAGATA
AAGATAAAATAC
Found at i:519988 original size:15 final size:14
Alignment explanation
Indices: 519970--520009 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
519960 TAAAGTTCGC
519970 GAAAATAAATAAAAT
1 GAAAATAAA-AAAAT
519985 GAAAATAAAAAAAT
1 GAAAATAAAAAAAT
* *
519999 AAAAACAAAAA
1 GAAAATAAAAA
520010 TATAACGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 14 0.61
15 9 0.39
ACGTcount: A:0.80, C:0.03, G:0.05, T:0.12
Consensus pattern (14 bp):
GAAAATAAAAAAAT
Found at i:520003 original size:14 final size:14
Alignment explanation
Indices: 519971--520014 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
519961 AAAGTTCGCG
*
519971 AAAATAAATAAAATG
1 AAAATAAA-AAAATA
519986 AAAATAAAAAAATA
1 AAAATAAAAAAATA
* *
520000 AAAACAAAAATATA
1 AAAATAAAAAAATA
520014 A
1 A
520015 CGAAATGGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 18 0.69
15 8 0.31
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (14 bp):
AAAATAAAAAAATA
Found at i:520008 original size:19 final size:20
Alignment explanation
Indices: 519971--520008 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
519961 AAAGTTCGCG
**
519971 AAAATAAATAAAATGAAAAT
1 AAAATAAATAAAAACAAAAT
519991 AAAA-AAATAAAAACAAAA
1 AAAATAAATAAAAACAAAA
520009 ATATAACGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.13
Consensus pattern (20 bp):
AAAATAAATAAAAACAAAAT
Found at i:524146 original size:15 final size:15
Alignment explanation
Indices: 524126--524159 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
524116 TTCCTCTTGT
524126 TCTTCCTGATGTGCG
1 TCTTCCTGATGTGCG
524141 TCTTCCTGATGTGCG
1 TCTTCCTGATGTGCG
524156 TCTT
1 TCTT
524160 TTTCTGCTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.06, C:0.26, G:0.24, T:0.44
Consensus pattern (15 bp):
TCTTCCTGATGTGCG
Found at i:525828 original size:16 final size:19
Alignment explanation
Indices: 525802--525839 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
525792 GATGAAGTTG
525802 AAAAGATATAT-TAA-AAT
1 AAAAGATATATATAATAAT
525819 AAAA-ATATATATAATAAT
1 AAAAGATATATATAATAAT
525837 AAA
1 AAA
525840 TATTAATAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.32
17 7 0.37
18 6 0.32
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (19 bp):
AAAAGATATATATAATAAT
Found at i:525828 original size:18 final size:18
Alignment explanation
Indices: 525802--525839 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
525792 GATGAAGTTG
525802 AAAAGATATATTAA-AATA
1 AAAAGATATA-TAATAATA
*
525820 AAAATATATATAATAATA
1 AAAAGATATATAATAATA
525838 AA
1 AA
525840 TATTAATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAAGATATATAATAATA
Found at i:525840 original size:16 final size:17
Alignment explanation
Indices: 525807--525859 Score: 60
Period size: 16 Copynumber: 3.3 Consensus size: 17
525797 AGTTGAAAAG
525807 ATATATTAA-AATAA-AA
1 ATATA-TAATAATAATAA
525823 ATATAT-ATAATAATAA
1 ATATATAATAATAATAA
*
525839 ATAT-TAATAGTAATAA
1 ATATATAATAATAATAA
525855 ATATA
1 ATATA
525860 AAATTGTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
14 1 0.03
15 7 0.22
16 24 0.75
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
ATATATAATAATAATAA
Found at i:526668 original size:75 final size:76
Alignment explanation
Indices: 526576--526745 Score: 200
Period size: 76 Copynumber: 2.2 Consensus size: 76
526566 AATACCTAAA
* * * * * *
526576 AAAATATAATATTCTAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACAAAGATA
1 AAAA-ATAATATCCTAAATCCTAATTAAAAAACGAAAAACCTAATGAAAATAAAATACAAAGATA
526640 AAGATAAAAT-AT
65 AA-ATAAAATGAT
* *
526652 AAAAATAATATCCTAAAACTTAATTAAAAAACGAAAAACCTAATGAAAATAAAATACAAAGATAA
1 AAAAATAATATCCTAAATCCTAATTAAAAAACGAAAAACCTAATGAAAATAAAATACAAAGATAA
* *
526717 AATATAATGTT
66 AATAAAATGAT
* *
526728 TAAAATATTATCCTAAAT
1 AAAAATAATATCCTAAAT
526746 TTGAGTTTAA
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
75 30 0.38
76 49 0.62
ACGTcount: A:0.59, C:0.10, G:0.04, T:0.28
Consensus pattern (76 bp):
AAAAATAATATCCTAAATCCTAATTAAAAAACGAAAAACCTAATGAAAATAAAATACAAAGATAA
AATAAAATGAT
Found at i:530417 original size:17 final size:17
Alignment explanation
Indices: 530374--530475 Score: 66
Period size: 17 Copynumber: 5.9 Consensus size: 17
530364 TAAGAGTTAG
* *
530374 TTAATAAATGAACTAGA
1 TTAATTAATGAACTAGT
* *
530391 TTGATGAATGAACTAGT
1 TTAATTAATGAACTAGT
* *
530408 TTAATTAATGAAATGACT
1 TTAATTAATGAACT-AGT
530426 TT-ATTCAATGAACT--T
1 TTAATT-AATGAACTAGT
*
530441 GTAATCTTGAATGAACTAGT
1 TTAA--TT-AATGAACTAGT
*
530461 TTAATTAATCAACTA
1 TTAATTAATGAACTA
530476 CTTAGTTAAA
Statistics
Matches: 66, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
15 2 0.03
16 1 0.02
17 36 0.55
18 23 0.35
20 4 0.06
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (17 bp):
TTAATTAATGAACTAGT
Found at i:534302 original size:54 final size:54
Alignment explanation
Indices: 534220--534667 Score: 556
Period size: 54 Copynumber: 8.3 Consensus size: 54
534210 TTACCAAATA
* * *
534220 GGCACTAAGTGTGCAATTCA-AGGAATTCATCATATGTTGTTAAACAACCATTTC
1 GGCACTAAGTGTGCAATTCACA-GAATTCATCATATGTTGATGAACAACCGTTTC
* * * * *
534274 GGCACTAAGTATGCAGTTCACAGAATTCATCATATGTTGATGAACAATCATTTT
1 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAACAACCGTTTC
** * * * *
534328 AACACTAAGTTTGCAATTAACGGAATTCATCATATGTTGATGAACAACCGTTTT
1 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAACAACCGTTTC
* * *
534382 GGCACTAAGTGTACAATTCACAGAATTCATCATATGTTGATGAACAATCGTTTT
1 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAACAACCGTTTC
* * **
534436 GGCACTAAGTGTGCAATTCATAAAATTCATCATATGTTGATGAACAACTATTTC
1 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAACAACCGTTTC
** * *
534490 GGCTTTAAGTGTCCAATTCACTGAATTCATCATATGTTGATGAACAACCGTTTC
1 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAACAACCGTTTC
* * * * * *
534544 GGCACTAACTGTGCATTTCACGGAATTCATCTTATGTTGATGAACAACCTTTTT
1 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAACAACCGTTTC
** *
534598 GGCACTAAGTGTGCAATTCAGGGAATTCATCATTTGTTGATGAACAACCGTTTC
1 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAACAACCGTTTC
* *
534652 GACACTATGTGTGCAA
1 GGCACTAAGTGTGCAA
534668 CCCACGAAAT
Statistics
Matches: 339, Mismatches: 54, Indels: 2
0.86 0.14 0.01
Matches are distributed among these distances:
54 338 1.00
55 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Consensus pattern (54 bp):
GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAACAACCGTTTC
Found at i:534708 original size:108 final size:108
Alignment explanation
Indices: 534222--534720 Score: 550
Period size: 108 Copynumber: 4.6 Consensus size: 108
534212 ACCAAATAGG
* * * * ** * *
534222 CACTAAGTGTGCAATTCAAGGAATTCATCATATGTTGTTAAACAACCATTTCGGCACTAAGTATG
1 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAACAACTGTTTTGGCACTAAGTGTG
* * * **
534287 CAGTTCACAGAATTCATCATATGTTGATGAACAATCATTTTAA
66 CAATTCACAGAATTCATCATATGTTGATGAACAACCGTTTCGA
* * * * *
534330 CACTAAGTTTGCAATTAACGGAATTCATCATATGTTGATGAACAACCGTTTTGGCACTAAGTGTA
1 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAACAACTGTTTTGGCACTAAGTGTG
* * *
534395 CAATTCACAGAATTCATCATATGTTGATGAACAATCGTTTTGG
66 CAATTCACAGAATTCATCATATGTTGATGAACAACCGTTTCGA
** * * ** *
534438 CACTAAGTGTGCAATTCATAAAATTCATCATATGTTGATGAACAACTATTTCGGCTTTAAGTGTC
1 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAACAACTGTTTTGGCACTAAGTGTG
* *
534503 CAATTCACTGAATTCATCATATGTTGATGAACAACCGTTTCGG
66 CAATTCACAGAATTCATCATATGTTGATGAACAACCGTTTCGA
* * * *
534546 CACTAACTGTGCATTTCACGGAATTCATCTTATGTTGATGAACAACCT-TTTTGGCACTAAGTGT
1 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAACAA-CTGTTTTGGCACTAAGTGT
** *
534610 GCAATTCAGGGAATTCATCATTTGTTGATGAACAACCGTTTCGA
65 GCAATTCACAGAATTCATCATATGTTGATGAACAACCGTTTCGA
* ** * * * * ** * *
534654 CACTATGTGTGCAACCCACGAAATTCATAATATATTTATAAATGACTGTATTGGCACTATGTGTG
1 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAACAACTGTTTTGGCACTAAGTGTG
534719 CA
66 CA
534721 TCTTAATAAA
Statistics
Matches: 333, Mismatches: 56, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
107 2 0.01
108 329 0.99
109 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (108 bp):
CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAACAACTGTTTTGGCACTAAGTGTG
CAATTCACAGAATTCATCATATGTTGATGAACAACCGTTTCGA
Found at i:538290 original size:15 final size:15
Alignment explanation
Indices: 538270--538309 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
538260 TCACGAAGAG
538270 GTGCCTTTTCGGGTT
1 GTGCCTTTTCGGGTT
*
538285 GTGCCTTTTCTGGTT
1 GTGCCTTTTCGGGTT
* *
538300 ATACCTTTTC
1 GTGCCTTTTC
538310 ATGAGGTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.05, C:0.23, G:0.23, T:0.50
Consensus pattern (15 bp):
GTGCCTTTTCGGGTT
Found at i:541154 original size:20 final size:21
Alignment explanation
Indices: 541108--541156 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
541098 CTAAAGAAAG
*
541108 TGAGCTAATATAAACATAACA
1 TGAGCTAAAATAAACATAACA
* * *
541129 TAAGCTAAAAT-AACATGACT
1 TGAGCTAAAATAAACATAACA
541149 TGAGCTAA
1 TGAGCTAA
541157 TAAATGAATG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.24
Consensus pattern (21 bp):
TGAGCTAAAATAAACATAACA
Done.