Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008772.1 Hibiscus syriacus cultivar Beakdansim tig00111877_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: 3098974
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 16
Found at i:449911 original size:113 final size:113
Alignment explanation
Indices: 449701--450388 Score: 850
Period size: 113 Copynumber: 6.0 Consensus size: 113
449691 CAAAGATTTA
* *
449701 AATCCATCATTCAATGGATCAACATTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * *
449765 A-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTTG
* * * * *
449812 AATTCATCATTCGATGGATCATCATTTCAAGTGAAAGTTCATAATGAGAAGAACTTATCTGAAGA
1 AATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
449877 AGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTTG
* *
449925 AATTCATCATTCGATGGATCAGCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-
1 AATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
449989 AGGAAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTCGCTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTTG
* *
450037 AATCCATCACTAGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* **
450102 AGGAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTGCTCA
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTTG
* * * *
450150 AATCCATCACTGGATGGATAAGCATTTCCAGAGAAAGTTCATAATGAGAAGAATTCATCTGAAGA
1 AATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * *
450215 AGGAAGAAGAAGTTCATAATGAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTT-AT--T---CA-ACCTT-TT---GC--TTG
* * *
450276 -CTCAAATCCA-TC-ACTGGATGGATCAGCATTTCCAGAGAAAGTTCATAATAAGAAGAACTCAT
1 AATC-CAT-CATTCGA-TGG----ATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCAT
* *
450338 CTGAAG-AGGAAGAACAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
59 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGC
450389 ATGACTCTAT
Statistics
Matches: 507, Mismatches: 47, Indels: 39
0.85 0.08 0.07
Matches are distributed among these distances:
111 28 0.06
112 136 0.27
113 237 0.47
114 2 0.00
116 1 0.00
118 1 0.00
119 1 0.00
120 4 0.01
121 4 0.01
122 4 0.01
123 1 0.00
124 1 0.00
125 3 0.01
126 8 0.02
127 2 0.00
128 1 0.00
129 29 0.06
130 44 0.09
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (113 bp):
AATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTTG
Found at i:450099 original size:225 final size:225
Alignment explanation
Indices: 449700--450388 Score: 941
Period size: 225 Copynumber: 3.0 Consensus size: 225
449690 GCAAAGATTT
* *
449700 AAATCCATCATTCAATGGATCAACATTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * * * * * *
449764 AAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTCGATGG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTTGAATCCATCACTAGATGG
* * * *
449829 ATCATCATTTCAAGTGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCAT
131 ATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
449894 AATGAGAAGAGCTTGTTCAACCTTTTGCTT
196 AATGAGAAGAGCTTGTTCAACCTTTTGCTC
* * *
449924 GAATTCATCATTCGATGGATCAGCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
449989 AGGAAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTCGCTTGAATCCATCACTAGATGG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTTGAATCCATCACTAGATGG
450054 ATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
131 ATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
450119 AATGAGAAGAGCTTATTCAACCTTTTGCTC
196 AATGAGAAGAGCTTGTTCAACCTTTTGCTC
* * * *
450149 AAATCCATCACTGGATGGATAAGCATTTCCAGAGAAAGTTCATAATGAGAAGAATTCATCTGAAG
1 AAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT----
*
450214 AAGGAAGAAGAAGTTCATAATGAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTC
62 ---GAAG-AG--G------A--AGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTT
* * *
450279 AAATCCATCACTGGATGGATCAGCATTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAG
113 GAATCCATCACTAGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
450344 -AGGAAGAACAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
178 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
450389 ATGACTCTAT
Statistics
Matches: 412, Mismatches: 34, Indels: 20
0.88 0.07 0.04
Matches are distributed among these distances:
224 29 0.07
225 230 0.56
232 4 0.01
233 2 0.00
235 1 0.00
241 1 0.00
242 42 0.10
243 103 0.25
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (225 bp):
AAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AGGAAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTTGAATCCATCACTAGATGG
ATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAGCTTGTTCAACCTTTTGCTC
Found at i:450239 original size:24 final size:23
Alignment explanation
Indices: 450196--450240 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
450186 GTTCATAATG
*
450196 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
450219 AGAAGAAGTTCATAATG-AGAAG
1 AGAAGAA-TTCAT-ATGAAGAAG
450241 AAGTTCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:450240 original size:130 final size:129
Alignment explanation
Indices: 450106--450371 Score: 478
Period size: 130 Copynumber: 2.1 Consensus size: 129
450096 TGAAGAAGGA
*
450106 AGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTGCTCAAATCCATCACTGGATGGATAA
1 AGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTCAAATCCATCACTGGATGGATAA
* * *
450171 GCATTTCCAGAGAAAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
66 GCATTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAG-AGGAAGAACAAGTTCATAATG
*
450236 AGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTCAAATCCATCACTGGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTCAAATCCATCACTGGATGGATAA
450301 GCATTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAACAAGTTCATAATG
66 GCATTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAACAAGTTCATAATG
450365 AGAAGAA
1 AGAAGAA
450372 CTTGTTCAAC
Statistics
Matches: 131, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
129 27 0.21
130 104 0.79
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (129 bp):
AGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTCAAATCCATCACTGGATGGATAA
GCATTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAACAAGTTCATAATG
Found at i:450241 original size:17 final size:17
Alignment explanation
Indices: 450219--450259 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
450209 TGAAGAAGGA
450219 AGAAGAAGTTCATAATG
1 AGAAGAAGTTCATAATG
450236 AGAAGAAGTTCATAATG
1 AGAAGAAGTTCATAATG
450253 AGAAGAA
1 AGAAGAA
450260 CTTATTCAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.51, C:0.05, G:0.24, T:0.20
Consensus pattern (17 bp):
AGAAGAAGTTCATAATG
Found at i:450518 original size:84 final size:84
Alignment explanation
Indices: 450356--450518 Score: 238
Period size: 84 Copynumber: 1.9 Consensus size: 84
450346 GAAGAACAAG
* * * * *
450356 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATTAGCA
1 TTCATAATAAGAAGAAATTGTTCAACCTTTTGCAAGACTCTATCACAGAAGAAGATAGATCAGCA
* *
450421 TACACTTTTCCAGAGAAAA
66 TACACATTGCCAGAGAAAA
*
450440 TTCATAATAAGAAGAAATTGTTCAACCTTTTGCAAGATTCTATCACAGAAGAAGATAGATCAGCA
1 TTCATAATAAGAAGAAATTGTTCAACCTTTTGCAAGACTCTATCACAGAAGAAGATAGATCAGCA
450505 T-CAACATTGCCAGA
66 TAC-ACATTGCCAGA
450519 AGTGTTCATA
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
83 1 0.01
84 69 0.99
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.28
Consensus pattern (84 bp):
TTCATAATAAGAAGAAATTGTTCAACCTTTTGCAAGACTCTATCACAGAAGAAGATAGATCAGCA
TACACATTGCCAGAGAAAA
Found at i:450814 original size:3 final size:3
Alignment explanation
Indices: 450799--450866 Score: 77
Period size: 3 Copynumber: 23.0 Consensus size: 3
450789 ATTTGGTTTT
* * *
450799 TTA TTA -TA TTTA TTA TTT TTA TTA CTA TTA TTA TTA TTA ATA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
450844 TTT TTA TTA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
450867 CATATACAAC
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
2 4 0.07
3 48 0.89
4 2 0.04
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:450817 original size:18 final size:18
Alignment explanation
Indices: 450778--450866 Score: 78
Period size: 18 Copynumber: 5.0 Consensus size: 18
450768 AGACACTACT
**
450778 TTTTTATATATATTTGGT-
1 TTTTTAT-TATATTTATTA
450796 TTTTTATTATATTTATTA
1 TTTTTATTATATTTATTA
450814 TTTTTATTACTA-TTATTA
1 TTTTTATTA-TATTTATTA
* *
450832 TTATTAATATTATTT-TTA
1 TTTTTATTA-TATTTATTA
*
450850 TTATTATTAT-TTTATTA
1 TTTTTATTATATTTATTA
450867 CATATACAAC
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
16 3 0.05
17 12 0.20
18 42 0.69
19 4 0.07
ACGTcount: A:0.28, C:0.01, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTTTATTATATTTATTA
Found at i:452295 original size:15 final size:13
Alignment explanation
Indices: 452264--452291 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
452254 CATTGTTTAG
452264 TTATATGTTAATT
1 TTATATGTTAATT
452277 TTATATGTTAATT
1 TTATATGTTAATT
452290 TT
1 TT
452292 TTATTATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (13 bp):
TTATATGTTAATT
Found at i:452300 original size:3 final size:3
Alignment explanation
Indices: 452292--452323 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
452282 TGTTAATTTT
*
452292 TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
452324 TAACGATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:452645 original size:33 final size:33
Alignment explanation
Indices: 452597--452660 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
452587 CTGATATTTC
452597 TAAATAAATAAATATTTTATTT-ATAAATATATA
1 TAAATAAATAAATATTTT-TTTCATAAATATATA
* * *
452630 TAAATTAATATATATTTTTTTCATAATTATA
1 TAAATAAATAAATATTTTTTTCATAAATATA
452661 ATCTTAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 3 0.11
33 24 0.89
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (33 bp):
TAAATAAATAAATATTTTTTTCATAAATATATA
Found at i:457554 original size:36 final size:35
Alignment explanation
Indices: 457506--457643 Score: 181
Period size: 36 Copynumber: 3.9 Consensus size: 35
457496 TGAATAAGAA
*
457506 GAAC-GAAAGAAGCATCAGCACTTTCGATTCAAAGT
1 GAACGGAAGGAAGCATCAGCACTTTCGATTC-AAGT
* *
457541 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGAA
1 GAACGGAAGGAAGCATCAGCACTTTCGATTCAAG-T
* * *
457577 GAACGAAAGGAAGCACCGGCACTTTCGA-TCAAGT
1 GAACGGAAGGAAGCATCAGCACTTTCGATTCAAGT
*
457611 GAACGGAAGGAAGCGTCAGCACTTTCGATTCAA
1 GAACGGAAGGAAGCATCAGCACTTTCGATTCAA
457644 TTGTTCATCT
Statistics
Matches: 90, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
34 24 0.27
35 16 0.18
36 50 0.56
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.17
Consensus pattern (35 bp):
GAACGGAAGGAAGCATCAGCACTTTCGATTCAAGT
Found at i:457623 original size:70 final size:71
Alignment explanation
Indices: 457501--457643 Score: 227
Period size: 70 Copynumber: 2.0 Consensus size: 71
457491 GAAGGTGAAT
* *
457501 AAGAAGAACGAAAGAAGCATCAGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCGGCACTTT
1 AAGAAGAACGAAAGAAGCACCAGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCAGCACTTT
457566 CGATTC
66 CGATTC
* *
457572 AAGAAGAACGAAAGGAAGCACCGGCACTTTCGA-TC-AAGTGAACGGAAGGAAGCGTCAGCACTT
1 AAGAAGAACGAAA-GAAGCACCAGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCAGCACTT
457635 TCGATTC
65 TCGATTC
457642 AA
1 AA
457644 TTGTTCATCT
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
70 35 0.52
71 15 0.22
72 17 0.25
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.17
Consensus pattern (71 bp):
AAGAAGAACGAAAGAAGCACCAGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCAGCACTTT
CGATTC
Found at i:462623 original size:20 final size:21
Alignment explanation
Indices: 462598--462640 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
462588 GAACAAAATC
462598 CAAGTTATGGA-TTTTTTGGT
1 CAAGTTATGGATTTTTTTGGT
462618 CAAGTTATGGATTTTTTTGGT
1 CAAGTTATGGATTTTTTTGGT
462639 CA
1 CA
462641 TCATTTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.21, C:0.07, G:0.23, T:0.49
Consensus pattern (21 bp):
CAAGTTATGGATTTTTTTGGT
Found at i:464269 original size:101 final size:99
Alignment explanation
Indices: 464017--464284 Score: 364
Period size: 99 Copynumber: 2.7 Consensus size: 99
464007 TTTTTATTTA
* * * *
464017 TTTTATTAATTT-TC-AAATCATTATACGACCTTTTGGTGACCCGATCCGGGGTGTGATCTGCAT
1 TTTTATTAATTTGTCTGAATCATTATACGACCTTGTGGTGACCCGATCTGGGGTATGATCTGCAT
464080 TATTATGGTCAGGACTCTATTAACTCCTAACCTT
66 TATTATGGTCAGGACTCTATTAACTCCTAACCTT
464114 TTTTATTAATTTGTCTGAATCATTATACGACCTTGTGGTGACCCGATCTGGGGTATGATCAT-CA
1 TTTTATTAATTTGTCTGAATCATTATACGACCTTGTGGTGACCCGATCTGGGGTATGATC-TGCA
464178 TTATTATGGT-ACGGACTCTATTAACTCCTAACCTTTT
65 TTATTATGGTCA-GGACTCTATTAACTCCTAACC--TT
* * ** * * * *
464215 TTTTATTAATTTGTTTGAATTATTATACGACCTTGCAGTGACCCGATCTAGGGTACGACCCGCAT
1 TTTTATTAATTTGTCTGAATCATTATACGACCTTGTGGTGACCCGATCTGGGGTATGATCTGCAT
464280 TATTA
66 TATTA
464285 CGATTTAGAC
Statistics
Matches: 152, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
97 12 0.08
98 3 0.02
99 73 0.48
100 1 0.01
101 63 0.41
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (99 bp):
TTTTATTAATTTGTCTGAATCATTATACGACCTTGTGGTGACCCGATCTGGGGTATGATCTGCAT
TATTATGGTCAGGACTCTATTAACTCCTAACCTT
Found at i:464315 original size:101 final size:101
Alignment explanation
Indices: 464017--464302 Score: 294
Period size: 101 Copynumber: 2.9 Consensus size: 101
464007 TTTTTATTTA
* *** ** ** * *
464017 TTTTATTAATTT-TC-AAATCATTATACGACCTTTTGGTGACCCGATCCGGGGTGTGATCTGCAT
1 TTTTATTAATTTGTCTGAATCATTATACGACCTTGCAGTGACCCGATCTAGGGTACGACCAGCAT
* *
464080 TATTATGGT-CAGGACTCTATTAACTCCTAACC--TT
66 TATTACGATACA-GACTCTATTAACTCCTAACCTTTT
** * * * *
464114 TTTTATTAATTTGTCTGAATCATTATACGACCTTGTGGTGACCCGATCTGGGGTATGATCATCAT
1 TTTTATTAATTTGTCTGAATCATTATACGACCTTGCAGTGACCCGATCTAGGGTACGACCAGCAT
* * *
464179 TATTATGGTACGGACTCTATTAACTCCTAACCTTTT
66 TATTACGATACAGACTCTATTAACTCCTAACCTTTT
* * *
464215 TTTTATTAATTTGTTTGAATTATTATACGACCTTGCAGTGACCCGATCTAGGGTACGACCCGCAT
1 TTTTATTAATTTGTCTGAATCATTATACGACCTTGCAGTGACCCGATCTAGGGTACGACCAGCAT
**
464280 TATTACGATTTAGACTCTATTAA
66 TATTACGATACAGACTCTATTAA
464303 TTTTAGTACT
Statistics
Matches: 163, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
97 12 0.07
98 2 0.01
99 72 0.44
100 1 0.01
101 76 0.47
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (101 bp):
TTTTATTAATTTGTCTGAATCATTATACGACCTTGCAGTGACCCGATCTAGGGTACGACCAGCAT
TATTACGATACAGACTCTATTAACTCCTAACCTTTT
Found at i:465347 original size:7 final size:8
Alignment explanation
Indices: 465324--465349 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
465314 ATGTTATTTC
465324 AAGGAAAA
1 AAGGAAAA
465332 AAGGAAAA
1 AAGGAAAA
465340 AAGGAAAA
1 AAGGAAAA
465348 AA
1 AA
465350 TATTTTCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (8 bp):
AAGGAAAA
Found at i:470996 original size:55 final size:55
Alignment explanation
Indices: 470931--471749 Score: 1217
Period size: 55 Copynumber: 14.9 Consensus size: 55
470921 ACCAATATGA
*
470931 AAATTCATAAACTTATTATGAATTTCTTATTTTTGCACACAAAGTGCCCATACGG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGG
*
470986 AAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACGA
1 AAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACAAAGTGCCCATACGG
* * * *
471042 AAATTCATAAAATCATTATGAATTTATTAGTTTTGCACACAAAGTTCCCATACGG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGG
* *
471097 AAATTCATAAACTCATTATGAATTTCTTAGCTTTGCACACAAAGTGCCCATACGG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGG
* *
471152 AAATTCATAAA-TTCATTATGAATTTCTTAGGTTTGCACACAAAGTGCCCATACAG
1 AAATTCATAAACTT-ATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGG
* * *
471207 AAATTCATAAACTCATTATGAATTTATTAGCTTTGCACACAAAGTGCCCATACGG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGG
* *
471262 AAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGG
* * * *
471317 AAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAATGTGCTCATACTG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGG
* * * *
471372 AAATTCAAAAACTTATTATGAATCTCTTAGTTTTGCACACAAAGTGCCCATAAGA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGG
* * *
471427 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACATAAAGTGCCCATATGA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGG
* * * *
471482 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACATACTGCCCAAATGG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGG
* * *
471537 AAATTCACAAACTTATTATGAATTGCTTAGTTTTGCACACAAAGTGCCCATATGG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGG
* *
471592 AAATTCATAAACTTATTATGAATTTCTTAGTTTTTCACACAAAGTGCCCATACGA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGG
* * **
471647 AAATTCATAAACTTATTATGAATTTCATAGTTTTTCACACAAAGTGCCCATACAT
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGG
* * ** *
471702 AAATTGATAAACTTATTATGAAATTCTTAGTTTTATACACATAGTGCC
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCC
471750 ATTTGATAAT
Statistics
Matches: 701, Mismatches: 60, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
54 1 0.00
55 648 0.92
56 52 0.07
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (55 bp):
AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGG
Found at i:475575 original size:139 final size:139
Alignment explanation
Indices: 475320--475995 Score: 967
Period size: 139 Copynumber: 4.9 Consensus size: 139
475310 TATAAACCAG
* * * * * *
475320 TCAATATTTCCAGTGGAGGGTTCATAATGAGAAGAACTCATTCAATGAGGGAGAATAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCCGATGAGGGAGAAGAAGTTCATA
* * * * *
475385 ATGAGAAAAACTTGTTCAACTTTAGTTCGATTCATCGCATATAGAGTTGAATCAGTGACACCTCA
66 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCGACACCTCA
475450 CTCGAGGGA
131 CTCGAGGGA
* * * *
475459 TCAACATTTCCAGTGGAGAGTTTATAATGAGAATAACTCATCCAATGAGAGAGAAGAATTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCCGATGAGGGAGAAGAAGTTCATA
* * *
475524 ATGAGAATAACTTGTAT-AACCTTAACTCGATTCATCGCATATGGAGTTGAATCAGCGACATCTC
66 ATGAGAAGAACTTGT-TCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCGACACCTC
475588 ACTCGAGGGA
130 ACTCGAGGGA
* * * * ** *
475598 TCAACATTTCTAGTGGAGATTTCATAATGAGAAGAATTCATCCGATGAAAGAGAAAAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCCGATGAGGGAGAAGAAGTTCATA
* * *
475663 ATGAGAAGAACTTGTTCAATCTTAGCTCGATTCATCGTATATGGAGTTAAATCAGCGACACCTCA
66 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCGACACCTCA
*
475728 CTCGGGGGA
131 CTCGAGGGA
475737 TCAACATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCCGATGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCCGATGAGGGAGAAGAAGTTCATA
* * *
475802 ATGAGAAGAACTTATTCAACCTTAGATCGATTCATTGCATATGGAGTTGAATCAGCGACACCTCA
66 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCGACACCTCA
*
475867 CTCAAGGGA
131 CTCGAGGGA
* * * *
475876 TCAACATTTCCAGTGAAGAGTTCATAATGAGAATAACTCATCTGATAAGGGAGAAGGAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCCGATGAGGGAGAAGAAGTTCATA
* * * *
475941 ATGAGAAGAACGTGTTCAACCTTAGCTCAATTCATCTCATATGGAGTTCAATCAG
66 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAG
475996 TGATTTTGTG
Statistics
Matches: 478, Mismatches: 57, Indels: 4
0.89 0.11 0.01
Matches are distributed among these distances:
138 1 0.00
139 476 1.00
140 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (139 bp):
TCAACATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCCGATGAGGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCGACACCTCA
CTCGAGGGA
Found at i:479635 original size:200 final size:200
Alignment explanation
Indices: 479292--479691 Score: 800
Period size: 200 Copynumber: 2.0 Consensus size: 200
479282 TTCTAGTTGT
479292 TATTATGGCATTGAGCTAGTTAGCTCAACATTTGGAATTTGTTTCCTTAAGCAGATTAGGTGGAG
1 TATTATGGCATTGAGCTAGTTAGCTCAACATTTGGAATTTGTTTCCTTAAGCAGATTAGGTGGAG
479357 CATTCGAGGAAGCCTTAGAGCGACCGAGGTCCAACAGATCAGAGTCCGTCTCAAGTTTTTGAAAG
66 CATTCGAGGAAGCCTTAGAGCGACCGAGGTCCAACAGATCAGAGTCCGTCTCAAGTTTTTGAAAG
479422 GCATGCATATTTATAAACCTTGTTGTAAAGTTGAGTCGTAAAGTTAATTTAAGTTGGTTTGTATA
131 GCATGCATATTTATAAACCTTGTTGTAAAGTTGAGTCGTAAAGTTAATTTAAGTTGGTTTGTATA
479487 TTTTG
196 TTTTG
479492 TATTATGGCATTGAGCTAGTTAGCTCAACATTTGGAATTTGTTTCCTTAAGCAGATTAGGTGGAG
1 TATTATGGCATTGAGCTAGTTAGCTCAACATTTGGAATTTGTTTCCTTAAGCAGATTAGGTGGAG
479557 CATTCGAGGAAGCCTTAGAGCGACCGAGGTCCAACAGATCAGAGTCCGTCTCAAGTTTTTGAAAG
66 CATTCGAGGAAGCCTTAGAGCGACCGAGGTCCAACAGATCAGAGTCCGTCTCAAGTTTTTGAAAG
479622 GCATGCATATTTATAAACCTTGTTGTAAAGTTGAGTCGTAAAGTTAATTTAAGTTGGTTTGTATA
131 GCATGCATATTTATAAACCTTGTTGTAAAGTTGAGTCGTAAAGTTAATTTAAGTTGGTTTGTATA
479687 TTTTG
196 TTTTG
479692 AATGTAGATA
Statistics
Matches: 200, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 200 1.00
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.34
Consensus pattern (200 bp):
TATTATGGCATTGAGCTAGTTAGCTCAACATTTGGAATTTGTTTCCTTAAGCAGATTAGGTGGAG
CATTCGAGGAAGCCTTAGAGCGACCGAGGTCCAACAGATCAGAGTCCGTCTCAAGTTTTTGAAAG
GCATGCATATTTATAAACCTTGTTGTAAAGTTGAGTCGTAAAGTTAATTTAAGTTGGTTTGTATA
TTTTG
Found at i:482300 original size:31 final size:30
Alignment explanation
Indices: 482265--482351 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
482255 TCAATAAAGT
482265 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAATA-TTATTAAATTTA
* *
482296 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAA-TATTATTAAATTTA
* *
482327 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAAT-ATTATTA
482352 TATTATCGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 44 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (30 bp):
TTAAAAAATTATAAAATATTATTAAATTTA
Found at i:482327 original size:20 final size:20
Alignment explanation
Indices: 482260--482327 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 20
482250 TTTCGTCAAT
*
482260 AAAG-TTTAAAAAATTA-TA
1 AAAGATTTATAAAATTATTA
* * *
482278 AAATACTTATTAAATTTATTA
1 AAAGATTTA-TAAAATTATTA
482299 AAAGA-TTATAAAATTATTA
1 AAAGATTTATAAAATTATTA
482318 ATAA-ATTTAT
1 A-AAGATTTAT
482328 CTAAATACTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 3 0.08
19 15 0.38
20 15 0.38
21 6 0.15
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (20 bp):
AAAGATTTATAAAATTATTA
Found at i:484723 original size:44 final size:44
Alignment explanation
Indices: 484655--484755 Score: 150
Period size: 44 Copynumber: 2.3 Consensus size: 44
484645 GACCGAAACA
484655 AAGAAGAAGACAAAGAGGACTAACGGCCAAGGAATAAGAAGAAG
1 AAGAAGAAGACAAAGAGGACTAACGGCCAAGGAATAAGAAGAAG
* **
484699 AAGAAGAAGACAAAG-GGAATTAACGGCTGAGGAATAAGAAGAAG
1 AAGAAGAAGACAAAGAGG-ACTAACGGCCAAGGAATAAGAAGAAG
*
484743 AAGAAGAATACAA
1 AAGAAGAAGACAA
484756 CAAAGCGGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
43 2 0.04
44 50 0.96
ACGTcount: A:0.55, C:0.09, G:0.29, T:0.07
Consensus pattern (44 bp):
AAGAAGAAGACAAAGAGGACTAACGGCCAAGGAATAAGAAGAAG
Found at i:484759 original size:47 final size:44
Alignment explanation
Indices: 484655--484777 Score: 140
Period size: 44 Copynumber: 2.7 Consensus size: 44
484645 GACCGAAACA
* * * *
484655 AAGAAGAAGACAAAGAGGACTAACGGCCAAGGAATAAGAAGAAG
1 AAGAAGAAAACAAAGCGGATTAACGGCCGAGGAATAAGAAGAAG
* *
484699 AAGAAGAAGACAAAG-GGAATTAACGGCTGAGGAATAAGAAGAAG
1 AAGAAGAAAACAAAGCGG-ATTAACGGCCGAGGAATAAGAAGAAG
*
484743 AAGAAGAATACAACAAAGCGGATCAACGGCCGAGG
1 AAGAAG-A-A-AACAAAGCGGATTAACGGCCGAGG
484778 GACTTAAACT
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
43 2 0.03
44 44 0.65
45 1 0.01
46 1 0.01
47 18 0.26
48 2 0.03
ACGTcount: A:0.51, C:0.12, G:0.30, T:0.07
Consensus pattern (44 bp):
AAGAAGAAAACAAAGCGGATTAACGGCCGAGGAATAAGAAGAAG
Found at i:485160 original size:148 final size:148
Alignment explanation
Indices: 484892--485187 Score: 574
Period size: 148 Copynumber: 2.0 Consensus size: 148
484882 AGAGTACTGA
484892 AGTTGCAAAATTGTGTTTGTGTAAATCATGCTTATTTATTGTGTGACACTCTTAATGCTGCAGGA
1 AGTTGCAAAATTGTGTTTGTGTAAATCATGCTTATTTATTGTGTGACACTCTTAATGCTGCAGGA
* *
484957 AATTTAGTGACTGAGGAAGAACAAGTCAGTTTCGCTTTAGCTGGCTAATCGATGAAGTATAAGTT
66 AATTTAGTGACTGAGGAAGAACAAGTCAGTTTCGCTTTAGCCGGCTAACCGATGAAGTATAAGTT
485022 TGTTATTGCAATAGCTTC
131 TGTTATTGCAATAGCTTC
485040 AGTTGCAAAATTGTGTTTGTGTAAATCATGCTTATTTATTGTGTGACACTCTTAATGCTGCAGGA
1 AGTTGCAAAATTGTGTTTGTGTAAATCATGCTTATTTATTGTGTGACACTCTTAATGCTGCAGGA
485105 AATTTAGTGACTGAGGAAGAACAAGTCAGTTTCGCTTTAGCCGGCTAACCGATGAAGTATAAGTT
66 AATTTAGTGACTGAGGAAGAACAAGTCAGTTTCGCTTTAGCCGGCTAACCGATGAAGTATAAGTT
485170 TGTTATTGCAATAGCTTC
131 TGTTATTGCAATAGCTTC
485188 TCGAGAATCA
Statistics
Matches: 146, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
148 146 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (148 bp):
AGTTGCAAAATTGTGTTTGTGTAAATCATGCTTATTTATTGTGTGACACTCTTAATGCTGCAGGA
AATTTAGTGACTGAGGAAGAACAAGTCAGTTTCGCTTTAGCCGGCTAACCGATGAAGTATAAGTT
TGTTATTGCAATAGCTTC
Found at i:487221 original size:6 final size:6
Alignment explanation
Indices: 487210--487280 Score: 70
Period size: 6 Copynumber: 10.8 Consensus size: 6
487200 TTTCCTTACT
* *
487210 TTTTTC TTTTTC TTTTTTTC TTTTTC TTTTTTTC TTTTTC TTTTGC TTTTAC
1 TTTTTC TTTTTC --TTTTTC TTTTTC --TTTTTC TTTTTC TTTTTC TTTTTC
487262 TTTTTTC TTTTTAC TTTTT
1 -TTTTTC TTTTT-C TTTTT
487281 TGAAACAAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
6 33 0.59
7 11 0.20
8 12 0.21
ACGTcount: A:0.03, C:0.14, G:0.01, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:487226 original size:14 final size:14
Alignment explanation
Indices: 487209--487281 Score: 98
Period size: 14 Copynumber: 5.4 Consensus size: 14
487199 TTTTCCTTAC
487209 TTTTTTCTTTTTCT
1 TTTTTTCTTTTTCT
487223 TTTTTTCTTTTTCT
1 TTTTTTCTTTTTCT
487237 TTTTTTCTTTTTC-
1 TTTTTTCTTTTTCT
* *
487250 -TTTTGCTTTTAC-
1 TTTTTTCTTTTTCT
487262 TTTTTTCTTTTTACT
1 TTTTTTCTTTTT-CT
487277 TTTTT
1 TTTTT
487282 GAAACAAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
12 10 0.19
13 9 0.17
14 28 0.54
15 5 0.10
ACGTcount: A:0.03, C:0.14, G:0.01, T:0.82
Consensus pattern (14 bp):
TTTTTTCTTTTTCT
Found at i:487227 original size:8 final size:8
Alignment explanation
Indices: 487216--487248 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
487206 TACTTTTTTC
487216 TTTTTCTT
1 TTTTTCTT
487224 TTTTTC--
1 TTTTTCTT
487230 TTTTTCTT
1 TTTTTCTT
487238 TTTTTCTT
1 TTTTTCTT
487246 TTT
1 TTT
487249 CTTTTGCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 6 0.26
8 17 0.74
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTCTT
Found at i:487233 original size:20 final size:20
Alignment explanation
Indices: 487210--487280 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
487200 TTTCCTTACT
487210 TTTTTCTTTTTCTTTTTTTC
1 TTTTTCTTTTTCTTTTTTTC
487230 TTTTTCTTTTT-TTCTTTTTC
1 TTTTTCTTTTTCTT-TTTTTC
* *
487250 TTTTGCTTTTAC-TTTTTTC
1 TTTTTCTTTTTCTTTTTTTC
487269 TTTTTACTTTTT
1 TTTTT-CTTTTT
487281 TGAAACAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
19 12 0.27
20 32 0.73
ACGTcount: A:0.03, C:0.14, G:0.01, T:0.82
Consensus pattern (20 bp):
TTTTTCTTTTTCTTTTTTTC
Found at i:487770 original size:91 final size:91
Alignment explanation
Indices: 487615--487867 Score: 313
Period size: 91 Copynumber: 2.8 Consensus size: 91
487605 AAAAGTTGAG
* * * *
487615 CAAGTTCTTCTCATTATGAAC--TTTCTCC-TCTAGGACAAGTTCTTCTCATTATGAACTCTACA
1 CAAGTTCTTCTCATTATGAACTTTTTCTCCTTGTTGGACGAGTTCTTCTCATTATGAACTCTCCA
*
487677 CTGGAAATGTTGATCCAAGGTCGA-A
66 CTGGAAATGTTGATCAAAGGTCGAGA
487702 CAAGTTCTTCTCATTATGAACTTTTTCTCCCTTGTTGGACGAGTTCTTCTCATTATGAACTCTCC
1 CAAGTTCTTCTCATTATGAACTTTTTCT-CCTTGTTGGACGAGTTCTTCTCATTATGAACTCTCC
* * *
487767 ACTGGGAACGTTGATCAAAGGTTGAGA
65 ACTGGAAATGTTGATCAAAGGTCGAGA
* * *
487794 -AAGTTCTTCAT-ATTATGAACTTCTTCTTCGTTGTTGGATGAGTTCTTCTCATTTATGAACTCT
1 CAAGTTCTTC-TCATTATGAACTTTTTC-TCCTTGTTGGACGAGTTCTTCTCA-TTATGAACTCT
487857 CCA-TCGGAAAT
63 CCACT-GGAAAT
487868 TCCAATCCCT
Statistics
Matches: 144, Mismatches: 13, Indels: 13
0.85 0.08 0.08
Matches are distributed among these distances:
87 21 0.15
89 5 0.03
90 2 0.01
91 95 0.66
92 21 0.15
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (91 bp):
CAAGTTCTTCTCATTATGAACTTTTTCTCCTTGTTGGACGAGTTCTTCTCATTATGAACTCTCCA
CTGGAAATGTTGATCAAAGGTCGAGA
Found at i:488360 original size:73 final size:73
Alignment explanation
Indices: 488279--488622 Score: 409
Period size: 73 Copynumber: 4.8 Consensus size: 73
488269 AATCTATTTG
* * * * * * * * *
488279 AAGAGAAACTATCTCAAGTGAGATAATATTTGTTTCAAGGGGAATTGTATCTAGAGAGACAAAAC
1 AAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAC
488344 TTTGTTTC
66 TTTGTTTC
* * *
488352 AAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGAT-TC-A-A-AG----AT
1 AAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC-TATCTCAAGAGAGACAAAA
*
488409 TTTGTGTTTC
65 CTT-TGTTTC
* * *
488419 AAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAAC
1 AAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAC
488484 -TTGTTTC
66 TTTGTTTC
* * * *
488491 AAGAGAAACTGTCTTAAGGGAGACAAAACTTGATTCAAAGGAAACTATCTCAAGAGAGACAAAAC
1 AAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAC
488556 TTTGTTTC
66 TTTGTTTC
* *
488564 AAGAGAAACTGTCTCAAGGGAGACAAAACTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 AAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGA
488623 GAGAAATTGT
Statistics
Matches: 233, Mismatches: 27, Indels: 22
0.83 0.10 0.08
Matches are distributed among these distances:
66 5 0.02
67 50 0.21
68 1 0.00
70 4 0.02
71 1 0.00
72 65 0.28
73 105 0.45
74 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (73 bp):
AAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAC
TTTGTTTC
Found at i:488396 original size:36 final size:36
Alignment explanation
Indices: 488279--488640 Score: 346
Period size: 36 Copynumber: 10.1 Consensus size: 36
488269 AATCTATTTG
* * *
488279 AAGAGAAACTATCTCAAGTGAGATAATATTTGTTTC
1 AAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTC
* * * * * *
488315 AAGGGGAATTGTATCTAGAGAGACAAAACTTTGTTTC
1 AAGAGAAACTATCTCAAGAGAGACAAAA-TTTGTTTC
*
488352 AAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTC
1 AAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTC
* * **
488388 AAGGGAAACAGAT-TC-A-A-AG---ATTTTGTGTTTC
1 AAGAGAAAC-TATCTCAAGAGAGACAAAATT-TGTTTC
*
488419 AAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTC
1 AAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTC
* *
488455 AAGAGAAACTATCTCAAGGGAGACAAAACTTGTTTC
1 AAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTC
* * * * *
488491 AAGAGAAACTGTCTTAAGGGAGACAAAACTTGATTC
1 AAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTC
488527 AA-AGGAAACTATCTCAAGAGAGACAAAACTTTGTTTC
1 AAGA-GAAACTATCTCAAGAGAGACAAAA-TTTGTTTC
* * *
488564 AAGAGAAACTGTCTCAAGGGAGACAAAACTTGTTTC
1 AAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTC
* * * *
488600 AAGGGAAACTGTCTCAAGAGAGAGAGAAA-TTGTCTC
1 AAGAGAAACTATCTCAAGAGAGACA-AAATTTGTTTC
488636 AAGAG
1 AAGAG
488641 GGACAACATT
Statistics
Matches: 267, Mismatches: 45, Indels: 28
0.79 0.13 0.08
Matches are distributed among these distances:
30 4 0.01
31 16 0.06
32 1 0.00
33 3 0.01
34 2 0.01
35 2 0.01
36 171 0.64
37 67 0.25
38 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (36 bp):
AAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTC
Found at i:488585 original size:109 final size:108
Alignment explanation
Indices: 488423--488622 Score: 346
Period size: 109 Copynumber: 1.8 Consensus size: 108
488413 TGTTTCAAGA
*
488423 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAACTTGT
1 GAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAACTTGT
* *
488488 TTCAAGAGAAACTGTCTTAAGGGAGACAAAACTTGATTCAAAG
66 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGATTCAAAG
*
488531 GAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTG
1 GAAACTATCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAACTTG
*
488596 TTTCAAGGGAAACTGTCTCAAGAGAGA
65 TTTCAAGAGAAACTGTCTCAAGAGAGA
488623 GAGAAATTGT
Statistics
Matches: 86, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
108 23 0.27
109 63 0.73
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23
Consensus pattern (108 bp):
GAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAACTTGT
TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGATTCAAAG
Found at i:488626 original size:57 final size:57
Alignment explanation
Indices: 488565--488679 Score: 169
Period size: 57 Copynumber: 2.0 Consensus size: 57
488555 CTTTGTTTCA
488565 AGAGAAACTGTCTCAAG-GGAGACAAAACTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 AGAGAAACTGTCTCAAGAGG-GACAAAACTTGTTTCAAGGGAAACTGTCTCAAGAGAG
* * * * *
488622 AGAGAAATTGTCTCAAGAGGGACAACATTTGTTTCAATGGAAACTGTCTCAAGGGAG
1 AGAGAAACTGTCTCAAGAGGGACAAAACTTGTTTCAAGGGAAACTGTCTCAAGAGAG
488679 A
1 A
488680 CGAAATTAGT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
57 50 0.96
58 2 0.04
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (57 bp):
AGAGAAACTGTCTCAAGAGGGACAAAACTTGTTTCAAGGGAAACTGTCTCAAGAGAG
Found at i:488670 original size:36 final size:35
Alignment explanation
Indices: 488625--488699 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 35
488615 AAGAGAGAGA
* *
488625 GAAATTGTCTCAAGAGG-GAC-AACATTTGTTTCAATG
1 GAAACTGTCTCAAG-GGAGACGAA-ATTAGTTTC-ATG
488661 GAAACTGTCTCAAGGGAGACGAAATTAGTTTCATG
1 GAAACTGTCTCAAGGGAGACGAAATTAGTTTCATG
488696 GAAA
1 GAAA
488700 ACGTTTTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
35 9 0.26
36 24 0.69
37 2 0.06
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (35 bp):
GAAACTGTCTCAAGGGAGACGAAATTAGTTTCATG
Found at i:488775 original size:36 final size:36
Alignment explanation
Indices: 488716--488803 Score: 106
Period size: 36 Copynumber: 2.4 Consensus size: 36
488706 TCAAAGTTTA
* *
488716 TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAATT
1 TGTTTCAAGGGAAACTGTATCAAGAGAGAAAAAATT
** *
488752 TGTTTCAAGGGAAA-TGGTATCAAGAGAGGCATAATT
1 TGTTTCAAGGGAAACT-GTATCAAGAGAGAAAAAATT
488788 TGTTTCAAGAGGAAAC
1 TGTTTCAAG-GGAAAC
488804 AATCTCAAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
35 1 0.02
36 38 0.86
37 5 0.11
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTATCAAGAGAGAAAAAATT
Found at i:491304 original size:8 final size:8
Alignment explanation
Indices: 491291--491334 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
491281 TATATATAAT
491291 GATGCAAA
1 GATGCAAA
491299 GATGC-AA
1 GATGCAAA
491306 -ATGC-AA
1 GATGCAAA
*
491312 -ATGTAAA
1 GATGCAAA
491319 GATGCAAA
1 GATGCAAA
491327 GATGCAAA
1 GATGCAAA
491335 AATGGGAGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 9 0.28
7 4 0.12
8 19 0.59
ACGTcount: A:0.50, C:0.11, G:0.23, T:0.16
Consensus pattern (8 bp):
GATGCAAA
Found at i:491348 original size:14 final size:15
Alignment explanation
Indices: 491326--491362 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
491316 AAAGATGCAA
491326 AGATGCAAAAATGGG
1 AGATGCAAAAATGGG
*
491341 AG-TGC-AAAATGTG
1 AGATGCAAAAATGGG
491354 AGATGCAAA
1 AGATGCAAA
491363 TGCGACAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
13 9 0.47
14 6 0.32
15 4 0.21
ACGTcount: A:0.46, C:0.08, G:0.30, T:0.16
Consensus pattern (15 bp):
AGATGCAAAAATGGG
Found at i:491877 original size:29 final size:31
Alignment explanation
Indices: 491820--491877 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 31
491810 CAACAAAAGC
* *
491820 AGACAAAAGGAAATCATTGTTAGTAGAAACA
1 AGACAAAAAGAAATCATAGTTAGTAGAAACA
*
491851 AGACAAAAAG-AATCA-AGTTAGTTGAAA
1 AGACAAAAAGAAATCATAGTTAGTAGAAA
491878 TGATTAGTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 10 0.42
30 5 0.21
31 9 0.38
ACGTcount: A:0.53, C:0.09, G:0.19, T:0.19
Consensus pattern (31 bp):
AGACAAAAAGAAATCATAGTTAGTAGAAACA
Found at i:497785 original size:29 final size:28
Alignment explanation
Indices: 497743--497798 Score: 103
Period size: 29 Copynumber: 2.0 Consensus size: 28
497733 ATTTCACTGT
497743 ATAATCTTCGTTAAGCGCCCATACAACG
1 ATAATCTTCGTTAAGCGCCCATACAACG
497771 ATAATCTTTCGTTAAGCGCCCATACAAC
1 ATAATC-TTCGTTAAGCGCCCATACAAC
497799 TAGAATCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.27
Consensus pattern (28 bp):
ATAATCTTCGTTAAGCGCCCATACAACG
Found at i:497805 original size:29 final size:28
Alignment explanation
Indices: 497745--497805 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 28
497735 TTCACTGTAT
*
497745 AATCTTCGTTAAGCGCCCATACAACGAT
1 AATCTTCGTTAAGCGCCCATACAACGAG
*
497773 AATCTTTCGTTAAGCGCCCATACAACTAG
1 AATC-TTCGTTAAGCGCCCATACAACGAG
497802 AATC
1 AATC
497806 AAGTAACGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 4 0.13
29 26 0.87
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (28 bp):
AATCTTCGTTAAGCGCCCATACAACGAG
Found at i:498935 original size:12 final size:11
Alignment explanation
Indices: 498912--498952 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
498902 GGGAGTGTTT
*
498912 AATATAAAATA
1 AATAAAAAATA
498923 AATAAACAAATA
1 AATAAA-AAATA
498935 AATAATAAAATA
1 AATAA-AAAATA
498947 AATAAA
1 AATAAA
498953 TTGAGATAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 6 0.22
12 20 0.74
13 1 0.04
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (11 bp):
AATAAAAAATA
Found at i:499770 original size:72 final size:73
Alignment explanation
Indices: 499694--499830 Score: 242
Period size: 72 Copynumber: 1.9 Consensus size: 73
499684 AATAAAGAAA
499694 TAAATCCTAATTAAAATACTTAAAACTATTTAAAAT-AAATATC-TAAAACAAAGATAAGATAAA
1 TAAATCCTAATTAAAATACTTAAAACTATTTAAAATAAAATA-CATAAAACAAAGATAAGATAAA
499757 ATAATATCT
65 ATAATATCT
*
499766 TAAATCCTAATTAAAATACTTAAAATTATTTAAAATAAAATACATAAAACAAAGATAAGATAAAA
1 TAAATCCTAATTAAAATACTTAAAACTATTTAAAATAAAATACATAAAACAAAGATAAGATAAAA
499831 ATATAATATT
Statistics
Matches: 62, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
72 36 0.58
73 26 0.42
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (73 bp):
TAAATCCTAATTAAAATACTTAAAACTATTTAAAATAAAATACATAAAACAAAGATAAGATAAAA
TAATATCT
Found at i:500171 original size:39 final size:39
Alignment explanation
Indices: 500127--500207 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
500117 GATTAAGGAA
*
500127 CAATTTAAAAGCAAAATATTAACCAAATAAAGTACTTAT
1 CAATTTAAAAGCAAAATATTAACCAAATAAAGCACTTAT
500166 CAATTTAAAAGCAAAATATTAACCAAATAAAGCACTTAT
1 CAATTTAAAAGCAAAATATTAACCAAATAAAGCACTTAT
500205 CAA
1 CAA
500208 ATTCCCCCTC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.54, C:0.15, G:0.05, T:0.26
Consensus pattern (39 bp):
CAATTTAAAAGCAAAATATTAACCAAATAAAGCACTTAT
Found at i:501312 original size:92 final size:92
Alignment explanation
Indices: 501155--501340 Score: 372
Period size: 92 Copynumber: 2.0 Consensus size: 92
501145 TTGGCACCAT
501155 AACAATGTATAGAAAGATTTCAACTTTGAAATTGTGGGTCCATCGATTCACCTAGAGGCCTATTT
1 AACAATGTATAGAAAGATTTCAACTTTGAAATTGTGGGTCCATCGATTCACCTAGAGGCCTATTT
501220 TGGATTGGAGGAAAAAAAATTAAAAGA
66 TGGATTGGAGGAAAAAAAATTAAAAGA
501247 AACAATGTATAGAAAGATTTCAACTTTGAAATTGTGGGTCCATCGATTCACCTAGAGGCCTATTT
1 AACAATGTATAGAAAGATTTCAACTTTGAAATTGTGGGTCCATCGATTCACCTAGAGGCCTATTT
501312 TGGATTGGAGGAAAAAAAATTAAAAGA
66 TGGATTGGAGGAAAAAAAATTAAAAGA
501339 AA
1 AA
501341 TATACCAATG
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 94 1.00
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (92 bp):
AACAATGTATAGAAAGATTTCAACTTTGAAATTGTGGGTCCATCGATTCACCTAGAGGCCTATTT
TGGATTGGAGGAAAAAAAATTAAAAGA
Found at i:503562 original size:31 final size:34
Alignment explanation
Indices: 503524--503588 Score: 109
Period size: 31 Copynumber: 2.0 Consensus size: 34
503514 TTGAGCACGT
503524 GTATAAACGACGCAGT-GGGG-AACGT-GTTCGC
1 GTATAAACGACGCAGTGGGGGAAACGTAGTTCGC
503555 GTATAAACGACGCAGTGGGGGAAACGTAGTTCGC
1 GTATAAACGACGCAGTGGGGGAAACGTAGTTCGC
503589 CTTTATGGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 16 0.52
32 4 0.13
33 5 0.16
34 6 0.19
ACGTcount: A:0.28, C:0.18, G:0.35, T:0.18
Consensus pattern (34 bp):
GTATAAACGACGCAGTGGGGGAAACGTAGTTCGC
Found at i:509103 original size:15 final size:15
Alignment explanation
Indices: 509085--509114 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
509075 CCACGGTGCT
509085 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
509100 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
509115 GATTGTGATA
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:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:511146 original size:85 final size:85
Alignment explanation
Indices: 511037--511207 Score: 342
Period size: 85 Copynumber: 2.0 Consensus size: 85
511027 ATGTGAAATG
511037 CGAAATGTACCTCCACACTGGTAACCAACAGGGCGATCAACAATGTTGCAGCGTTTCGGAATGGT
1 CGAAATGTACCTCCACACTGGTAACCAACAGGGCGATCAACAATGTTGCAGCGTTTCGGAATGGT
511102 CACTGCAATTTCCGGCCTCA
66 CACTGCAATTTCCGGCCTCA
511122 CGAAATGTACCTCCACACTGGTAACCAACAGGGCGATCAACAATGTTGCAGCGTTTCGGAATGGT
1 CGAAATGTACCTCCACACTGGTAACCAACAGGGCGATCAACAATGTTGCAGCGTTTCGGAATGGT
511187 CACTGCAATTTCCGGCCTCA
66 CACTGCAATTTCCGGCCTCA
511207 C
1 C
511208 TCCCGCATTG
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 86 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (85 bp):
CGAAATGTACCTCCACACTGGTAACCAACAGGGCGATCAACAATGTTGCAGCGTTTCGGAATGGT
CACTGCAATTTCCGGCCTCA
Found at i:512732 original size:49 final size:49
Alignment explanation
Indices: 512676--512773 Score: 144
Period size: 49 Copynumber: 2.0 Consensus size: 49
512666 AAAGTTCGCG
*
512676 GCGTTTGT-TCAACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT
1 GCGTTTGTCT-AACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTT
* * *
512725 GCGTTTGTCTTACAACCGCCGCAATAGGTTTTGAGATTTAGCGGCGTTT
1 GCGTTTGTCTAACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTT
512774 TTTGGATACA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 43 0.98
50 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (49 bp):
GCGTTTGTCTAACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTT
Found at i:512812 original size:44 final size:44
Alignment explanation
Indices: 512763--513079 Score: 370
Period size: 44 Copynumber: 7.2 Consensus size: 44
512753 TTTTGAGATT
* * *
512763 TAGCGGCGTTTTTTGGATACAAGCGCCTCTAAAGGTCTGGTATA
1 TAGCGGCGTTTTTAGGATACAAACGCCGCTAAAGGTCTGGTATA
* ** * *
512807 TAGCGGCGTTTTTAGGATGCAAACATCGTTAAAGGTGTGGTATA
1 TAGCGGCGTTTTTAGGATACAAACGCCGCTAAAGGTCTGGTATA
*
512851 TAGC-ACGTTTTTAGGATACAAACGCCGCTAAAGGTCTGGTATA
1 TAGCGGCGTTTTTAGGATACAAACGCCGCTAAAGGTCTGGTATA
* * * *
512894 TATCGACATTTTTAGGATACAAACGCCGCTAAAAGTCTGGTATA
1 TAGCGGCGTTTTTAGGATACAAACGCCGCTAAAGGTCTGGTATA
** * * *
512938 TAGTTGCGTTTTTAGTACACAAACGCCGCTATAGGTCTGGTATA
1 TAGCGGCGTTTTTAGGATACAAACGCCGCTAAAGGTCTGGTATA
* * *
512982 TATCGACATTTTTAGGATACAAACGCCGCTAAAGGTCTGGTATA
1 TAGCGGCGTTTTTAGGATACAAACGCCGCTAAAGGTCTGGTATA
* * * * *
513026 TAACGGCGTTTTTAGTACACAAACGCCGCTATAGGT-TGATA-A
1 TAGCGGCGTTTTTAGGATACAAACGCCGCTAAAGGTCTGGTATA
513068 CTAGCGGCGTTT
1 -TAGCGGCGTTT
513080 GTTACAAAAA
Statistics
Matches: 229, Mismatches: 42, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
42 1 0.00
43 50 0.22
44 178 0.78
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.31
Consensus pattern (44 bp):
TAGCGGCGTTTTTAGGATACAAACGCCGCTAAAGGTCTGGTATA
Found at i:515521 original size:39 final size:36
Alignment explanation
Indices: 515437--515522 Score: 154
Period size: 36 Copynumber: 2.4 Consensus size: 36
515427 AACCTTTCGT
515437 TTTCCATAATAATCTAACTCAATAATGTCCGTAAGA
1 TTTCCATAATAATCTAACTCAATAATGTCCGTAAGA
* *
515473 TTTCCATAATAATCTAACTCAATAATTTTCGTAAGA
1 TTTCCATAATAATCTAACTCAATAATGTCCGTAAGA
515509 TTTCCATAATAATC
1 TTTCCATAATAATC
515523 GACCTCTCCT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (36 bp):
TTTCCATAATAATCTAACTCAATAATGTCCGTAAGA
Found at i:517240 original size:161 final size:164
Alignment explanation
Indices: 516975--517300 Score: 631
Period size: 161 Copynumber: 2.0 Consensus size: 164
516965 TAAACGAAAT
516975 TAAGAATCGGCATAACACAGGTGGCAAGTGTAAAACCTGATCCGGGTATTTCATAATTTCGTGGT
1 TAAGAATCGGCATAACACAGGTGGCAAGTGTAAAACCTGATCCGGGTATTTCATAATTTCGTGGT
517040 AAGCTGATATCCTGCAAGGCTGCAACTTTTGAATCAAACTTCAAGCTGGCAACTTTATCCTCAGC
66 AAGCTGATATCCTGCAAGGCTGCAACTTTTGAATCAAACTTCAAGCTGGCAACTTTATCCTCAGC
517105 GTGGATGCA-CTGAAATATGAATGT-A-ATTCAG
131 GTGGATGCATCTGAAATATGAATGTCACATTCAG
517136 TAAGAATCGGCATAACACAGGTGGCAAGTGTAAAACCTGATCCGGGTATTTCATAATTTCGTGGT
1 TAAGAATCGGCATAACACAGGTGGCAAGTGTAAAACCTGATCCGGGTATTTCATAATTTCGTGGT
517201 AAGCTGATATCCTGCAAGGCTGCAACTTTTGAATCAAACTTCAAGCTGGCAACTTTATCCTCAGC
66 AAGCTGATATCCTGCAAGGCTGCAACTTTTGAATCAAACTTCAAGCTGGCAACTTTATCCTCAGC
517266 GTGGATGCATCTGAAATATGAATGTCACATTCAG
131 GTGGATGCATCTGAAATATGAATGTCACATTCAG
517300 T
1 T
517301 CAATCATGAG
Statistics
Matches: 162, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
161 139 0.86
162 15 0.09
163 1 0.01
164 7 0.04
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (164 bp):
TAAGAATCGGCATAACACAGGTGGCAAGTGTAAAACCTGATCCGGGTATTTCATAATTTCGTGGT
AAGCTGATATCCTGCAAGGCTGCAACTTTTGAATCAAACTTCAAGCTGGCAACTTTATCCTCAGC
GTGGATGCATCTGAAATATGAATGTCACATTCAG
Found at i:518948 original size:41 final size:41
Alignment explanation
Indices: 518870--519057 Score: 202
Period size: 41 Copynumber: 4.5 Consensus size: 41
518860 CATATATATC
* * *
518870 GCGGCGTTTGGGTA-AAAAACGCCACTATTGTTCAACTCGATT
1 GCGGCGTTT--GTAGAAAAACGCCTCTATTATTCAACTCTATT
*
518912 GCGGCGTTTGTAGAAAAACGCCTCTATTATTTAACTCTATT
1 GCGGCGTTTGTAGAAAAACGCCTCTATTATTCAACTCTATT
*
518953 GCGGCATTTGTAGAAAAACGCCTCTATTATTCAACTCTATT
1 GCGGCGTTTGTAGAAAAACGCCTCTATTATTCAACTCTATT
* ** * * *
518994 GCGGCATTTACATAACAAACACCTCTATAGATT-ACAC-CTATT
1 GCGGCGTTTGTAGAA-AAACGCCTCTAT-TATTCA-ACTCTATT
*
519036 GCGGCGTTTGTACAAAAACGCC
1 GCGGCGTTTGTAGAAAAACGCC
519058 GCTAATGTAT
Statistics
Matches: 126, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
40 3 0.02
41 81 0.64
42 37 0.29
43 5 0.04
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (41 bp):
GCGGCGTTTGTAGAAAAACGCCTCTATTATTCAACTCTATT
Found at i:519055 original size:83 final size:81
Alignment explanation
Indices: 518870--519057 Score: 209
Period size: 83 Copynumber: 2.3 Consensus size: 81
518860 CATATATATC
* * ** *
518870 GCGGCGTTTGGGTAAAAAACGCCACTATTGTTCAACTCGATTGCGGCGTTTGTAGAAAAACGCCT
1 GCGGCGTTT--GTAAAAAACGCCACTATTATTCAACTCGATTGCGGCATTTACAGAAAAACACCT
*
518935 CTATTATTTAACTCTATT
64 CTATTAATTAACTCTATT
* * * *
518953 GCGGCATTTGTAGAAAAACGCCTCTATTATTCAACTCTATTGCGGCATTTACATAACAAACACCT
1 GCGGCGTTTGTA-AAAAACGCCACTATTATTCAACTCGATTGCGGCATTTACAGAA-AAACACCT
519018 CTA-TAGATTACAC-CTATT
64 CTATTA-ATTA-ACTCTATT
519036 GCGGCGTTTGTACAAAAACGCC
1 GCGGCGTTTGTA-AAAAACGCC
519058 GCTAATGTAT
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
81 3 0.03
82 38 0.43
83 46 0.52
84 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (81 bp):
GCGGCGTTTGTAAAAAACGCCACTATTATTCAACTCGATTGCGGCATTTACAGAAAAACACCTCT
ATTAATTAACTCTATT
Found at i:520304 original size:22 final size:22
Alignment explanation
Indices: 520269--520310 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
520259 TTCAGAAGCT
*
520269 ATTATTTTCCTATTCGAAATCA
1 ATTATTTTCATATTCGAAATCA
* *
520291 ATTATTTTTATATTTGAAAT
1 ATTATTTTCATATTCGAAAT
520311 GTTAAGTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.52
Consensus pattern (22 bp):
ATTATTTTCATATTCGAAATCA
Found at i:521101 original size:64 final size:63
Alignment explanation
Indices: 521032--521190 Score: 214
Period size: 65 Copynumber: 2.5 Consensus size: 63
521022 TGCACTAAGA
* *
521032 GTGCATCGATGCATGAAGTGCATTCGATGTTTCA-AACAAGCC-AGAGTGCATCGATGCATGGTC
1 GTGCATCGATGCAT-AAATGCATTCGATGTTTCATAA-AA-CCTAGAGTGCATCGATGCATGGTA
521095 T
63 T
* *
521096 GTGCATCGATGCATAAAATGCATTCGATTTTTTCATAAAACCTTGAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCAT-AAATGCATTCGA-TGTTTCATAAAACCTAGAGTGCATCGATGCATGGTAT
*
521161 GTGCATAGATGCATAAATGCATTCGATGTT
1 GTGCATCGATGCATAAATGCATTCGATGTT
521191 CAATTTATTC
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
63 3 0.04
64 39 0.46
65 41 0.48
66 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATAAATGCATTCGATGTTTCATAAAACCTAGAGTGCATCGATGCATGGTAT
Found at i:527897 original size:22 final size:22
Alignment explanation
Indices: 527879--527921 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
527869 CAGAAGCTAT
527879 TATTTTCCTATTCGAAAGCAAG
1 TATTTTCCTATTCGAAAGCAAG
* *
527901 TATTTTTCTATTTGAAAGCAA
1 TATTTTCCTATTCGAAAGCAA
527922 AAAAACACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.42
Consensus pattern (22 bp):
TATTTTCCTATTCGAAAGCAAG
Found at i:528455 original size:83 final size:82
Alignment explanation
Indices: 528350--528665 Score: 285
Period size: 83 Copynumber: 3.8 Consensus size: 82
528340 AAACACCATG
* * ** *
528350 ATAAACAACA-TATTACGGCGTTTGTAGGACAAAAGTTGCTAAATTATTACTCTATTGCGGCATT
1 ATAAACAACACTATTACGGCGTTTATA-GAAAAAAGCCGCTAAATTATTACTCTATTGCGGCGTT
* *
528414 TTTTGCACAAACGCCACT
65 TGTTGAACAAACGCCACT
* * * * * *
528432 ATAAACAATACTATTACGGCGTTTATTTGATAAACGCCGCTAAATTACTT-CTCTATAGCGTCGT
1 ATAAACAACACTATTACGGCGTTTA-TAGAAAAAAGCCGCTAAATTA-TTACTCTATTGCGGCGT
528496 TTGTTGAACAAACGCCACT
64 TTGTTGAACAAACGCCACT
** * ** **
528515 ATAAACAACACTATCGCGGCGTTTATATAAAAAAGCCGCTAAATTACCACTCTATTATGGCGTTT
1 ATAAACAACACTATTACGGCGTTTATAGAAAAAAGCCGCTAAATTATTACTCTATTGCGGCGTTT
* *
528580 GTTGAAAAAATGCCACT
66 GTTGAACAAACGCCACT
* * *** * * ** * *
528597 ATAGACAACTCTATTACGGCGTTTGACCTATAAACGCCGCTAAATTACCACTCTATTACGGTGTT
1 ATAAACAACACTATTACGGCGTTT-ATAGAAAAAAGCCGCTAAATTATTACTCTATTGCGGCGTT
528662 TGTT
65 TGTT
528666 TACAAAACGT
Statistics
Matches: 192, Mismatches: 37, Indels: 9
0.81 0.16 0.04
Matches are distributed among these distances:
82 73 0.38
83 116 0.60
84 3 0.02
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.31
Consensus pattern (82 bp):
ATAAACAACACTATTACGGCGTTTATAGAAAAAAGCCGCTAAATTATTACTCTATTGCGGCGTTT
GTTGAACAAACGCCACT
Found at i:528674 original size:42 final size:41
Alignment explanation
Indices: 528442--528674 Score: 150
Period size: 41 Copynumber: 5.6 Consensus size: 41
528432 ATAAACAATA
* * **
528442 CTATTACGGCGTTTATTTGATAAACGCCGCTAAATTACTTCT
1 CTATTACGGCGTTTGTTT-AAAAACGCCGCTAAATTACCACT
* * * * *
528484 CTA-TAGCGTCGTTTGTTGAACAAACGCCACTATAA--ACAACA
1 CTATTA-CGGCGTTTGTTTAA-AAACGCCGCTA-AATTACCACT
** * * *
528525 CTATCGCGGCGTTTATATAAAAAAGCCGCTAAATTACCACT
1 CTATTACGGCGTTTGTTTAAAAACGCCGCTAAATTACCACT
* * * * * * *
528566 CTATTATGGCGTTTGTTGAAAAAATGCCACTATA-GACAACT
1 CTATTACGGCGTTTGTT-TAAAAACGCCGCTAAATTACCACT
** *
528607 CTATTACGGCGTTTGACCTATAAACGCCGCTAAATTACCACT
1 CTATTACGGCGTTTG-TTTAAAAACGCCGCTAAATTACCACT
*
528649 CTATTACGGTGTTTGTTTACAAAACG
1 CTATTACGGCGTTTGTTTA-AAAACG
528675 TCGTTAAAGT
Statistics
Matches: 138, Mismatches: 43, Indels: 20
0.69 0.21 0.10
Matches are distributed among these distances:
39 2 0.01
40 9 0.07
41 67 0.49
42 58 0.42
43 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31
Consensus pattern (41 bp):
CTATTACGGCGTTTGTTTAAAAACGCCGCTAAATTACCACT
Found at i:531295 original size:26 final size:26
Alignment explanation
Indices: 531259--531315 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
531249 TTAACTTAAA
531259 ATGCTGGATATCACAATGAATCCAGC
1 ATGCTGGATATCACAATGAATCCAGC
531285 ATGCTGGATATCACAATGAATCCAGC
1 ATGCTGGATATCACAATGAATCCAGC
531311 ATGCT
1 ATGCT
531316 TATACTGCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (26 bp):
ATGCTGGATATCACAATGAATCCAGC
Found at i:533350 original size:4 final size:4
Alignment explanation
Indices: 533341--533379 Score: 60
Period size: 4 Copynumber: 9.5 Consensus size: 4
533331 GTGTTTAAAT
*
533341 ATAA ATAA ATAA ACAA ATAA ATAA ATAAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATAA ATAA AT
533380 TGAGATAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 28 0.88
5 4 0.12
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:533362 original size:16 final size:17
Alignment explanation
Indices: 533341--533379 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
533331 GTGTTTAAAT
533341 ATAAATAAAT-AAACAA
1 ATAAATAAATAAAACAA
*
533357 ATAAATAAATAAAATAA
1 ATAAATAAATAAAACAA
533374 ATAAAT
1 ATAAAT
533380 TGAGATAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (17 bp):
ATAAATAAATAAAACAA
Found at i:533373 original size:13 final size:13
Alignment explanation
Indices: 533336--533379 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
533326 GGGGAGTGTT
533336 TAAATATAAATAAA
1 TAAATA-AAATAAA
*
533350 TAAA-CAAATAAA
1 TAAATAAAATAAA
533362 TAAATAAAATAAA
1 TAAATAAAATAAA
533375 TAAAT
1 TAAAT
533380 TGAGATAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 11 0.41
13 12 0.44
14 4 0.15
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (13 bp):
TAAATAAAATAAA
Found at i:534220 original size:72 final size:73
Alignment explanation
Indices: 534144--534280 Score: 233
Period size: 72 Copynumber: 1.9 Consensus size: 73
534134 AATAAAGAAA
534144 TAAATCCTAATTAAAATACTTAAAACTATTTAAAAT-AAATATC-TAAAACAAAGATAAGATAAA
1 TAAATCCTAATTAAAATACTTAAAACTATTTAAAATAAAATA-CATAAAACAAAGATAAGATAAA
534207 ATAATATCT
65 ATAATATCT
* *
534216 TAAATCCTAATTAAAATACTTAAAATTATTTAAACTAAAATACATAAAACAAAGATAAGATAAAA
1 TAAATCCTAATTAAAATACTTAAAACTATTTAAAATAAAATACATAAAACAAAGATAAGATAAAA
534281 ATATAATATT
Statistics
Matches: 61, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
72 35 0.57
73 26 0.43
ACGTcount: A:0.58, C:0.09, G:0.03, T:0.29
Consensus pattern (73 bp):
TAAATCCTAATTAAAATACTTAAAACTATTTAAAATAAAATACATAAAACAAAGATAAGATAAAA
TAATATCT
Found at i:534611 original size:22 final size:22
Alignment explanation
Indices: 534586--534650 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 22
534576 AGGAACAATT
534586 TAAAAGCAAAATATTAACCAAA
1 TAAAAGCAAAATATTAACCAAA
* * *
534608 T-AAAGC---A-CTT-ATCAAT
1 TAAAAGCAAAATATTAACCAAA
534624 TTAAAAGCAAAATATTAACCAAA
1 T-AAAAGCAAAATATTAACCAAA
534647 TAAA
1 TAAA
534651 GCACTTATCA
Statistics
Matches: 30, Mismatches: 6, Indels: 14
0.60 0.12 0.28
Matches are distributed among these distances:
16 5 0.17
17 2 0.07
18 6 0.20
21 6 0.20
22 6 0.20
23 5 0.17
ACGTcount: A:0.58, C:0.14, G:0.05, T:0.23
Consensus pattern (22 bp):
TAAAAGCAAAATATTAACCAAA
Found at i:534613 original size:21 final size:21
Alignment explanation
Indices: 534588--534653 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
534578 GAACAATTTA
534588 AAAGCAAAATATTAACCAAAT
1 AAAGCAAAATATTAACCAAAT
** * ***
534609 AAAGC-ACTTATCAA-TTTA-
1 AAAGCAAAATATTAACCAAAT
534627 AAAGCAAAATATTAACCAAAT
1 AAAGCAAAATATTAACCAAAT
534648 AAAGCA
1 AAAGCA
534654 CTTATCAAAT
Statistics
Matches: 30, Mismatches: 12, Indels: 6
0.62 0.25 0.12
Matches are distributed among these distances:
18 5 0.17
19 7 0.23
20 7 0.23
21 11 0.37
ACGTcount: A:0.58, C:0.15, G:0.06, T:0.21
Consensus pattern (21 bp):
AAAGCAAAATATTAACCAAAT
Found at i:534625 original size:39 final size:39
Alignment explanation
Indices: 534581--534661 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
534571 GATTAAGGAA
534581 CAATTTAAAAGCAAAATATTAACCAAATAAAGCACTTAT
1 CAATTTAAAAGCAAAATATTAACCAAATAAAGCACTTAT
534620 CAATTTAAAAGCAAAATATTAACCAAATAAAGCACTTAT
1 CAATTTAAAAGCAAAATATTAACCAAATAAAGCACTTAT
534659 CAA
1 CAA
534662 ATTCCCCCTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.54, C:0.16, G:0.05, T:0.25
Consensus pattern (39 bp):
CAATTTAAAAGCAAAATATTAACCAAATAAAGCACTTAT
Found at i:535701 original size:91 final size:92
Alignment explanation
Indices: 535546--535726 Score: 355
Period size: 91 Copynumber: 2.0 Consensus size: 92
535536 TTGGCACCAT
535546 AACAATGTATAGAAAGATTTCAACTTTGAAATTGTGGGTCCATCGATTCACCTAGAGGCCTATTT
1 AACAATGTATAGAAAGATTTCAACTTTGAAATTGTGGGTCCATCGATTCACCTAGAGGCCTATTT
535611 TGGATTGGAGG-AAAAAAATTAAAAGA
66 TGGATTGGAGGAAAAAAAATTAAAAGA
535637 AACAATGTATAGAAAGATTTCAACTTTGAAATTGTGGGTCCATCGATTCACCTAGAGGCCTATTT
1 AACAATGTATAGAAAGATTTCAACTTTGAAATTGTGGGTCCATCGATTCACCTAGAGGCCTATTT
535702 TGGATTGGAGGAAAAAAAATTAAAA
66 TGGATTGGAGGAAAAAAAATTAAAA
535727 CAAATATACC
Statistics
Matches: 89, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
91 76 0.85
92 13 0.15
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (92 bp):
AACAATGTATAGAAAGATTTCAACTTTGAAATTGTGGGTCCATCGATTCACCTAGAGGCCTATTT
TGGATTGGAGGAAAAAAAATTAAAAGA
Found at i:537677 original size:5 final size:5
Alignment explanation
Indices: 537667--537693 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
537657 TAAATAAATT
537667 TAATA TAATA TAATA TAATA TAATA TA
1 TAATA TAATA TAATA TAATA TAATA TA
537694 TTACTATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:540646 original size:2 final size:2
Alignment explanation
Indices: 540639--540665 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
540629 ATGATAATAC
540639 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 A
540666 CATGTATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:541423 original size:6 final size:6
Alignment explanation
Indices: 541412--541503 Score: 130
Period size: 6 Copynumber: 15.3 Consensus size: 6
541402 GGTTCAGTAG
* * * * * *
541412 TGGTGC TGGTGC TGGTGC TGGTGC TGGTGC TGGTGC TGGTGT TGGTGT
1 TGGTGT TGGTGT TGGTGT TGGTGT TGGTGT TGGTGT TGGTGT TGGTGT
541460 TGGTGT TGGTGT TGGTGT TGGTGT TGGTGT TGGTGT TGGTGT TG
1 TGGTGT TGGTGT TGGTGT TGGTGT TGGTGT TGGTGT TGGTGT TG
541504 TATCTACGAG
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 85 1.00
ACGTcount: A:0.00, C:0.07, G:0.50, T:0.43
Consensus pattern (6 bp):
TGGTGT
Found at i:543446 original size:18 final size:19
Alignment explanation
Indices: 543418--543455 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
543408 ATAAGGAAAG
543418 TTAGTTTTTTTATAAATGT
1 TTAGTTTTTTTATAAATGT
543437 TTAGTTTTTTTATAAATGT
1 TTAGTTTTTTTATAAATGT
543456 CATATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (19 bp):
TTAGTTTTTTTATAAATGT
Found at i:543463 original size:19 final size:19
Alignment explanation
Indices: 543419--543465 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
543409 TAAGGAAAGT
*
543419 TAGTTTTTTTATAAATGTT
1 TAGTTTTTTTATAAATGTA
543438 TAGTTTTTTTATAAATGTCA
1 TAGTTTTTTTATAAATGT-A
543458 TA-TTTTTT
1 TAGTTTTTT
543466 AATATTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 24 0.92
20 2 0.08
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.64
Consensus pattern (19 bp):
TAGTTTTTTTATAAATGTA
Found at i:544078 original size:21 final size:22
Alignment explanation
Indices: 544039--544081 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
544029 ATTAGTAAAA
544039 ATTAATTTTTTTAAAAATAATTAT
1 ATTAATTTTTTT--AAATAATTAT
544063 ATTAATTTTTTT-AATAATT
1 ATTAATTTTTTTAAATAATT
544082 TTCAACCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
24 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTAATTTTTTTAAATAATTAT
Found at i:545338 original size:20 final size:20
Alignment explanation
Indices: 545313--545352 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
545303 ATTAGTAACA
545313 AATAATTAAA-TATAAATTTT
1 AATAA-TAAATTATAAATTTT
*
545333 AATAATAAATTTTAAATTTT
1 AATAATAAATTATAAATTTT
545353 TTTACTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATAATAAATTATAAATTTT
Found at i:546552 original size:44 final size:42
Alignment explanation
Indices: 546345--546739 Score: 295
Period size: 43 Copynumber: 9.3 Consensus size: 42
546335 AATTGATGTT
* * * * * *
546345 CTAATTTTATCCAATCTCAATTTTTATCTTTACAATTGAAGTCT
1 CTAATTTT-TTCAATCTCAATTTCTA-CTTTATAATTGAGGCCC
** * *
546389 CTAATTTTTT-AATCTCTTTTTTTACCTTTATAATTGA-GACC
1 CTAATTTTTTCAATCTCAATTTCTA-CTTTATAATTGAGGCCC
* * * * * *
546430 ATAATTTTTT-AGTCCCACTTTTTAACTTTATAATTGATGCCC
1 CTAATTTTTTCAATCTCAATTTCT-ACTTTATAATTGAGGCCC
* * * * *
546472 TTAAGTTTTTCAATATCACTTTCTACCTTTACAATTGAGGCCC
1 CTAATTTTTTCAATCTCAATTTCTA-CTTTATAATTGAGGCCC
* *
546515 CTAAGTTTTTTCAATCTCAATTTCCACTCTTATAATTGAGGTCC
1 CTAA-TTTTTTCAATCTCAATTTCTACT-TTATAATTGAGGCCC
** *
546559 CTAATTTTTT-AATCTCGCTTTTTTAACTTTATAATTGAGG-CC
1 CTAATTTTTTCAATCTC-AATTTCT-ACTTTATAATTGAGGCCC
* * * *
546601 C---TTTTTTCAATCTCACTTTCTATTTTATAATTGATGTCC
1 CTAATTTTTTCAATCTCAATTTCTACTTTATAATTGAGGCCC
*
546640 CTAATTTTTTCCAATCTCAA-TTATACGTTTATAATTGAGGCCC
1 CTAATTTTTT-CAATCTCAATTTCTAC-TTTATAATTGAGGCCC
* * * *
546683 CTAATTTTTTCAATCTCAATTTCTGCCTTTATAATTAATGCCT
1 CTAATTTTTTCAATCTCAATTTCT-ACTTTATAATTGAGGCCC
*
546726 CTATTTTTTTCAAT
1 CTAATTTTTTCAAT
546740 TTCATAAATT
Statistics
Matches: 286, Mismatches: 48, Indels: 35
0.78 0.13 0.09
Matches are distributed among these distances:
38 13 0.05
39 13 0.05
40 6 0.02
41 32 0.11
42 64 0.22
43 112 0.39
44 46 0.16
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.48
Consensus pattern (42 bp):
CTAATTTTTTCAATCTCAATTTCTACTTTATAATTGAGGCCC
Found at i:546671 original size:81 final size:83
Alignment explanation
Indices: 546498--546706 Score: 230
Period size: 81 Copynumber: 2.5 Consensus size: 83
546488 CACTTTCTAC
* *
546498 CTTTACAATTGAGGCCCCTAAGTTTTTTCAATCTCAATTTCCACTCTTATAATTGAGGTCCCTAA
1 CTTTATAATTGAGGCCCC--A-TTTTTTCAATCTCAATTTCTACTCTTATAATTGAGGTCCCTAA
** *
546563 TTTTTTAATCTCGCTTTTTTAA
63 TTTTTTAATCTC-CAATTATAA
* * *
546585 CTTTATAATTGAGG-CCC-TTTTTTCAATCTCACTTTCTA-TTTTATAATTGATGTCCCTAATTT
1 CTTTATAATTGAGGCCCCATTTTTTCAATCTCAATTTCTACTCTTATAATTGAGGTCCCTAATTT
546647 TTTCCAATCT-CAATTAT-A
66 TTT--AATCTCCAATTATAA
546665 CGTTTATAATTGAGGCCCCTAATTTTTTCAATCTCAATTTCT
1 C-TTTATAATTGAGGCCCC--ATTTTTTCAATCTCAATTTCT
546707 GCCTTTATAA
Statistics
Matches: 106, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
80 2 0.02
81 42 0.40
82 22 0.21
83 5 0.05
85 19 0.18
86 3 0.03
87 13 0.12
ACGTcount: A:0.24, C:0.21, G:0.08, T:0.46
Consensus pattern (83 bp):
CTTTATAATTGAGGCCCCATTTTTTCAATCTCAATTTCTACTCTTATAATTGAGGTCCCTAATTT
TTTAATCTCCAATTATAA
Found at i:546686 original size:168 final size:168
Alignment explanation
Indices: 546345--546705 Score: 435
Period size: 168 Copynumber: 2.1 Consensus size: 168
546335 AATTGATGTT
* ** * *
546345 CTAATTTTATCCAATCTCAATTTTTATCTTTACAATTGAAGTCTCTAATTTTTTAATCTCTTTTT
1 CTAATTTT-TTCAATCTCAATTTCCATCTTTACAATTGAAGTCCCTAATTTTTTAATCTCCTTTT
* * * *
546410 TTACCTTTATAATTGAGACCATAATTTTTTAGTCCCACTTTTTAACTTTATAATTGATGCCCTTA
65 TTAACTTTATAATTGAGACCAT-ATTTTTCAATCCCACTTTCTAACTTTATAATTGATGCCCTTA
* *
546475 AGTTTTTCAATATCACTTTCTACCTTTACAATTGAGGCCC
129 AGTTTTTCAATATCACATTATACCTTTACAATTGAGGCCC
* *
546515 CTAAGTTTTTTCAATCTCAATTTCCA-CTCTTATAATTGAGGTCCCTAATTTTTTAATCTCGCTT
1 CTAA-TTTTTTCAATCTCAATTTCCATCT-TTACAATTGAAGTCCCTAATTTTTTAATCTC-CTT
* * * *
546579 TTTTAACTTTATAATTGAGGCCCT-TTTTTCAATCTCACTTTCT-ATTTTATAATTGATGTCCC-
63 TTTTAACTTTATAATTGAGACCATATTTTTCAATCCCACTTTCTAACTTTATAATTGATG-CCCT
* * * *
546641 TAATTTTTTCCAATCTCA-ATTATACGTTTATAATTGAGGCCC
127 TAAGTTTTT-CAATATCACATTATACCTTTACAATTGAGGCCC
546683 CTAATTTTTTCAATCTCAATTTC
1 CTAATTTTTTCAATCTCAATTTC
546706 TGCCTTTATA
Statistics
Matches: 165, Mismatches: 21, Indels: 13
0.83 0.11 0.07
Matches are distributed among these distances:
167 19 0.12
168 46 0.28
169 27 0.16
170 46 0.28
171 27 0.16
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.48
Consensus pattern (168 bp):
CTAATTTTTTCAATCTCAATTTCCATCTTTACAATTGAAGTCCCTAATTTTTTAATCTCCTTTTT
TAACTTTATAATTGAGACCATATTTTTCAATCCCACTTTCTAACTTTATAATTGATGCCCTTAAG
TTTTTCAATATCACATTATACCTTTACAATTGAGGCCC
Found at i:547400 original size:12 final size:11
Alignment explanation
Indices: 547383--547416 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
547373 TAAAGATTTT
547383 ATTTTTTATTA
1 ATTTTTTATTA
*
547394 ATATTTTAGTTA
1 ATTTTTTA-TTA
547406 ATTTTTTATTA
1 ATTTTTTATTA
547417 GATTGTGTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (11 bp):
ATTTTTTATTA
Found at i:547427 original size:24 final size:23
Alignment explanation
Indices: 547383--547430 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
547373 TAAAGATTTT
*
547383 ATTTTTTATTAATATTTTAGTTA
1 ATTTTTTATTAATATTGTAGTTA
547406 ATTTTTTATTAGAT-TGTGTAGTTA
1 ATTTTTTATTA-ATAT-TGTAGTTA
547430 A
1 A
547431 AAATGTGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.60
Consensus pattern (23 bp):
ATTTTTTATTAATATTGTAGTTA
Found at i:547704 original size:2 final size:2
Alignment explanation
Indices: 547697--547728 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
547687 CCAATGTTTA
547697 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
547729 TTACCTAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:549151 original size:60 final size:60
Alignment explanation
Indices: 549042--549155 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
549032 TTAGGTGACC
* * **
549042 ATTTTATAACTTTTAATAGCTGAAGGACTAAACAAAGAAATGTCATATAGTCAATGAACT
1 ATTTTATAAATTTTAATAGCTGAACGACTAAACAAAGAAACATCATATAGTCAATGAACT
* * * *
549102 ATTTTATAAATTTTAATAG-TCGAACGACTCAATAAAGCAACATCCTATAGTCAA
1 ATTTTATAAATTTTAATAGCT-GAACGACTAAACAAAGAAACATCATATAGTCAA
549156 CGGATCATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
59 1 0.02
60 44 0.98
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (60 bp):
ATTTTATAAATTTTAATAGCTGAACGACTAAACAAAGAAACATCATATAGTCAATGAACT
Found at i:549632 original size:2 final size:2
Alignment explanation
Indices: 549621--549654 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
549611 AGCAATTGAA
549621 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
549655 TTGTGTATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:551276 original size:21 final size:21
Alignment explanation
Indices: 551252--551291 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
551242 TACCCTAAAA
*
551252 ATTAGGATT-AATTATATTATT
1 ATTAGG-TTAAATCATATTATT
551273 ATTAGGTTAAATCATATTA
1 ATTAGGTTAAATCATATTA
551292 AATATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (21 bp):
ATTAGGTTAAATCATATTATT
Found at i:552840 original size:21 final size:21
Alignment explanation
Indices: 552810--553007 Score: 160
Period size: 21 Copynumber: 9.6 Consensus size: 21
552800 GATTTACATA
* *
552810 TTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
*
552831 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
552852 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
552873 TT--CGTTGCGATAGTCAAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
552892 TTCACGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
552915 TT--TGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
552934 TTCGCGTTGCGATTTATTACAAA
1 TTCGCGTTGCGA--TAGTCCAAG
552957 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
552976 TT--CGTTGCGATAATCGAAG
1 TTCGCGTTGCGATAGTCCAAG
552995 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
553008 TTATTCCAAA
Statistics
Matches: 143, Mismatches: 24, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
19 49 0.34
21 78 0.55
23 16 0.11
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:552862 original size:42 final size:40
Alignment explanation
Indices: 552835--552987 Score: 202
Period size: 42 Copynumber: 3.8 Consensus size: 40
552825 TCGAAGTTCG
* *
552835 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATATTCCAAATT
* *
552875 CGTTGCGATAGTCAAAGTTCACGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGA--TATTCCAAATT
* *
552917 TGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGA--TATTCCAAATT
552959 CGTTGCGATAGTCCAAGTT--CGTTGCGATA
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATA
552988 ATCGAAGTTC
Statistics
Matches: 103, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
38 2 0.02
40 35 0.34
42 66 0.64
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (40 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATATTCCAAATT
Found at i:552937 original size:103 final size:102
Alignment explanation
Indices: 552816--553035 Score: 291
Period size: 103 Copynumber: 2.1 Consensus size: 102
552806 CATATTCGCA
* * **
552816 TTGCGATAGTCGAAGTTCGCGTTGCGA-TAGT-CGAAGTTCGCGTTGCGATTTTCCAAATTCGTT
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTAGTAC-AAATT--CGTTGCGATAGTCCAAATTCGTT
* *
552879 GCGATAGTCAAAGTTCACGTTGCGATTTATTCCAAATTTG
63 GCGATAATCAAAGTTCACGTTGCGATTTATTCCAAATTCG
* *
552919 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCGTTGC
1 TTGCGATAGTCCAAGTTCGCGTTGCGA-TTAGTACAAATTCGTTGCGATAGTCCAAATTCGTTGC
* *
552984 GATAATCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
65 GATAATCAAAGTTCACGTTGCGATTTATTCCAAATTCG
*
553022 TTGTGATAGTCCAA
1 TTGCGATAGTCCAA
553036 AATCGCAACG
Statistics
Matches: 103, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
103 95 0.92
105 7 0.07
106 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (102 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTAGTACAAATTCGTTGCGATAGTCCAAATTCGTTGCG
ATAATCAAAGTTCACGTTGCGATTTATTCCAAATTCG
Found at i:552974 original size:61 final size:61
Alignment explanation
Indices: 552909--553036 Score: 202
Period size: 61 Copynumber: 2.1 Consensus size: 61
552899 TGCGATTTAT
* *
552909 TCCAAATTTGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAATCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAG
* * * *
552970 TCCAAGTTCGTTGCGATAATCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGTGATAG
1 TCCAAATTCGTTGCGATAATCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAG
553031 TCCAAA
1 TCCAAA
553037 ATCGCAACGA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (61 bp):
TCCAAATTCGTTGCGATAATCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAG
Found at i:552982 original size:82 final size:81
Alignment explanation
Indices: 552836--552986 Score: 241
Period size: 82 Copynumber: 1.8 Consensus size: 81
552826 CGAAGTTCGC
* *
552836 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCAAAGTTCACGTTG
1 GTTGCGATAGTCCAAGTTCGCGTTGCGATTTTACAAATTCGTTGCGATAGTCAAAGTT-ACGTTG
552901 CGATTTATTCCAAATTT
65 CGATTTATTCCAAATTT
*
552918 GTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTT-CGTT
1 GTTGCGATAGTCCAAGTTCGCGTTGCGA-TT-TTACAAATTCGTTGCGATAGTCAAAGTTACGTT
552982 GCGAT
64 GCGAT
552987 AATCGAAGTT
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
82 36 0.56
83 2 0.03
84 26 0.41
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.36
Consensus pattern (81 bp):
GTTGCGATAGTCCAAGTTCGCGTTGCGATTTTACAAATTCGTTGCGATAGTCAAAGTTACGTTGC
GATTTATTCCAAATTT
Found at i:553136 original size:6 final size:6
Alignment explanation
Indices: 553125--553161 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
553115 GACACGTATT
*
553125 ACCACG ACCACG ACCACG ACCACG ACCATG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
553162 GACAGACGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.35, C:0.46, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:553912 original size:19 final size:19
Alignment explanation
Indices: 553889--554015 Score: 119
Period size: 19 Copynumber: 6.3 Consensus size: 19
553879 CGTTGCGATT
*
553889 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
*
553908 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
*
553931 TTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
* *
553950 TTAGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
*
553973 TTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
*
553992 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
554011 TTGGA
1 TTGGA
554016 AAATCGCATT
Statistics
Matches: 90, Mismatches: 10, Indels: 16
0.78 0.09 0.14
Matches are distributed among these distances:
19 43 0.48
21 28 0.31
23 19 0.21
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.22
Consensus pattern (19 bp):
TTGGACTATCGCAACGAAC
Found at i:553957 original size:42 final size:42
Alignment explanation
Indices: 553892--553993 Score: 186
Period size: 42 Copynumber: 2.4 Consensus size: 42
553882 TGCGATTTTG
* *
553892 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTAGAATAAATCGCAACGCGAACTTC
553934 GACTATCGCAACGAACTTAGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTAGAATAAATCGCAACGCGAACTTC
553976 GACTATCGCAACGAACTT
1 GACTATCGCAACGAACTT
553994 GGACTATCGC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTAGAATAAATCGCAACGCGAACTTC
Found at i:554048 original size:21 final size:21
Alignment explanation
Indices: 554019--554071 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
554009 ATTTGGAAAA
*
554019 TCGCATTGCGATAATCGAAGT
1 TCGCGTTGCGATAATCGAAGT
* * *
554040 TCGCGTTGCAATAGTCGATGT
1 TCGCGTTGCGATAATCGAAGT
554061 TCGCGTTGCGA
1 TCGCGTTGCGA
554072 ATCTGGAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAATCGAAGT
Found at i:554467 original size:12 final size:13
Alignment explanation
Indices: 554435--554468 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
554425 GAGTCAAAAA
554435 AATTAAATTTTCT
1 AATTAAATTTTCT
554448 AATTAAATTTT-T
1 AATTAAATTTTCT
*
554460 ATTTAAATT
1 AATTAAATT
554469 ATTGTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (13 bp):
AATTAAATTTTCT
Found at i:554479 original size:19 final size:18
Alignment explanation
Indices: 554457--554521 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 18
554447 TAATTAAATT
554457 TTTATTTAAATTATTGTAA
1 TTTATTTAAATTATT-TAA
554476 TTTA-TTAAATTTATATTTAA
1 TTTATTTAAA--T-TATTTAA
* *
554496 -TTATTGTAATTTATTAAA
1 TTTATT-TAAATTATTTAA
554514 TTTATTTA
1 TTTATTTA
554522 TTTTTGTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
18 13 0.34
19 13 0.34
20 5 0.13
21 7 0.18
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTATTTAAATTATTTAA
Found at i:554507 original size:29 final size:30
Alignment explanation
Indices: 554449--554518 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 30
554439 AAATTTTCTA
*
554449 ATTAAATTTTTATTTAAATTATTGTAATTT
1 ATTAAATTTATATTTAAATTATTGTAATTT
554479 ATTAAATTTATATTT-AATTATTGTAATTT
1 ATTAAATTTATATTTAAATTATTGTAATTT
554508 ATTAAATTTAT
1 ATTAAATTTAT
554519 TTATTTTTGT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 25 0.64
30 14 0.36
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.59
Consensus pattern (30 bp):
ATTAAATTTATATTTAAATTATTGTAATTT
Found at i:554534 original size:29 final size:28
Alignment explanation
Indices: 554449--554535 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 28
554439 AAATTTTCTA
* *
554449 ATTAAATTTTTATTTAAATTATTGTAATTT
1 ATTAAATTTATATTT--ATTATTATAATTT
*
554479 ATTAAATTTATATTTAATTATTGTAATTT
1 ATTAAATTTATATTT-ATTATTATAATTT
*
554508 ATTAAATTTATTTATTT-TTGTTATAATT
1 ATTAAATTTA--TATTTATTATTATAATT
554536 CGATTGATTT
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
29 33 0.63
30 14 0.27
31 5 0.10
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (28 bp):
ATTAAATTTATATTTATTATTATAATTT
Found at i:558514 original size:18 final size:18
Alignment explanation
Indices: 558491--558525 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
558481 ATCGGATTAT
558491 AAATATTATAT-GTAAATA
1 AAATATTA-ATGGTAAATA
558509 AAATATTAATGGTAAAT
1 AAATATTAATGGTAAAT
558526 GCTTAATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (18 bp):
AAATATTAATGGTAAATA
Found at i:559612 original size:21 final size:21
Alignment explanation
Indices: 559572--559612 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
559562 TTTTAAAATT
*
559572 TATTTTTTAAAAATAGTATTA
1 TATTTTTTAAAAATACTATTA
559593 TATTTATTTAAAAA-ACTATT
1 TATTT-TTTAAAAATACTATT
559613 TTCTCTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TATTTTTTAAAAATACTATTA
Found at i:560011 original size:20 final size:20
Alignment explanation
Indices: 559967--560004 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
559957 GTGTTATTTC
559967 AAAATTTTTATTTTTAATAT
1 AAAATTTTTATTTTTAATAT
559987 AAAATTTATT-TTTTTAAT
1 AAAATTT-TTATTTTTAAT
560005 TTTAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
AAAATTTTTATTTTTAATAT
Found at i:561608 original size:18 final size:18
Alignment explanation
Indices: 561587--561630 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
561577 GTGAAGTAAT
561587 TTTTTTTTGGATA-AATGA
1 TTTTTTTT-GATAGAATGA
**
561605 TTTTAATTGATAGAATGA
1 TTTTTTTTGATAGAATGA
561623 TTTTTTTT
1 TTTTTTTT
561631 TTTTTGTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.27, C:0.00, G:0.14, T:0.59
Consensus pattern (18 bp):
TTTTTTTTGATAGAATGA
Found at i:561853 original size:30 final size:30
Alignment explanation
Indices: 561814--561885 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
561804 GAAAAGTCAC
*
561814 AAATCGATCATTAACGTTATCGTTTGTTACA
1 AAAT-GATCACTAACGTTATCGTTTGTTACA
*
561845 AAATGATCACTAACGTTGTCGTTTGTTACA
1 AAATGATCACTAACGTTATCGTTTGTTACA
*
561875 AAATGGTCACT
1 AAATGATCACT
561886 CGATGTTAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 34 0.89
31 4 0.11
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (30 bp):
AAATGATCACTAACGTTATCGTTTGTTACA
Found at i:562371 original size:21 final size:22
Alignment explanation
Indices: 562347--562390 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
562337 CCTGTTGATA
*
562347 TTTGTTCTCCAA-TGAAAGAAT
1 TTTGATCTCCAAGTGAAAGAAT
*
562368 TTTGATCTGCAAGTGAAAGAAT
1 TTTGATCTCCAAGTGAAAGAAT
562390 T
1 T
562391 CAGTAAGTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.36
Consensus pattern (22 bp):
TTTGATCTCCAAGTGAAAGAAT
Found at i:563569 original size:85 final size:85
Alignment explanation
Indices: 563426--563595 Score: 324
Period size: 85 Copynumber: 2.0 Consensus size: 85
563416 ATGTATTCAG
563426 CTTCAGTTGTAGATAGTGCCACGACAGATTGAACAGTAGACTTCCAAAAATAGGCCCTCCACCAA
1 CTTCAGTTGTAGATAGTGCCACGACAGATTGAACAGTAGACTTCCAAAAATAGGCCCTCCACCAA
563491 GAGTAAACACATACCCTGTC
66 GAGTAAACACATACCCTGTC
563511 CTTCAGTTGTAGATAGTGCCACGACAGATTGAACAGTAGACTTCCAACAAA-AGGCCCTCCACCA
1 CTTCAGTTGTAGATAGTGCCACGACAGATTGAACAGTAGACTTCCAA-AAATAGGCCCTCCACCA
563575 AGAGTAAACACATACCCTGTC
65 AGAGTAAACACATACCCTGTC
563596 GTAGATTCTT
Statistics
Matches: 84, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
85 81 0.96
86 3 0.04
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.21
Consensus pattern (85 bp):
CTTCAGTTGTAGATAGTGCCACGACAGATTGAACAGTAGACTTCCAAAAATAGGCCCTCCACCAA
GAGTAAACACATACCCTGTC
Found at i:565226 original size:187 final size:186
Alignment explanation
Indices: 564912--565284 Score: 721
Period size: 187 Copynumber: 2.0 Consensus size: 186
564902 TGGAAACTGC
564912 TCGAAATCTACCACTGTCGTGTCTTGCTTCTGCTGCAACATAGACTGTTCATCAAAACGACATCT
1 TCGAAATCTACCACTGTCGTGTCTTGCTTCTGCTGCAACATAGACTGTTCATCAAAACGACATCT
564977 CTACTAATCACAACTTTCTTCGCAACTGGTCCCAGAACTTGAAATCCTTTGACACCTTTCTTGTA
66 CTACTAATCACAACTTTCTTCGCAACTGGTCCCAGAACTTGAAATCCTTTGACACCTTTCTTGTA
565042 ACCCAGAAAAATGCACTCCTTCGATTTTGCATCAAGTTTGGATCTCTCATCAGCAG
131 ACCCAGAAAAATGCACTCCTTCGATTTTGCATCAAGTTTGGATCTCTCATCAGCAG
565098 TCGAAATCTACCACTGTCGTGTCTTGCTTCTGCTGCAACATAGACTGTTCATCAAAAACGACATC
1 TCGAAATCTACCACTGTCGTGTCTTGCTTCTGCTGCAACATAGACTGTTCATC-AAAACGACATC
565163 TCTACTAATCACAACTTTCTTCGCAACTGGATCCCAGAACTTG-AATCCTTTGACACCTTTCTTG
65 TCTACTAATCACAACTTTCTTCGCAACTGG-TCCCAGAACTTGAAATCCTTTGACACCTTTCTTG
565227 TAACCCAGAAAAATGCACTCCTTCGATTTTGCATCAAGTTTGGATCTCTCATCAGCAG
129 TAACCCAGAAAAATGCACTCCTTCGATTTTGCATCAAGTTTGGATCTCTCATCAGCAG
565285 GTACATGCAC
Statistics
Matches: 185, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
186 53 0.29
187 120 0.65
188 12 0.06
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (186 bp):
TCGAAATCTACCACTGTCGTGTCTTGCTTCTGCTGCAACATAGACTGTTCATCAAAACGACATCT
CTACTAATCACAACTTTCTTCGCAACTGGTCCCAGAACTTGAAATCCTTTGACACCTTTCTTGTA
ACCCAGAAAAATGCACTCCTTCGATTTTGCATCAAGTTTGGATCTCTCATCAGCAG
Found at i:568170 original size:30 final size:30
Alignment explanation
Indices: 568105--568170 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
568095 GTTAATGTTG
*
568105 AGTGACTATTTTGTAACAAAGGATAACGTT
1 AGTGATTATTTTGTAACAAAGGATAACGTT
* * *
568135 AGTGATTATTTTGTAATAAATGATAGCGTT
1 AGTGATTATTTTGTAACAAAGGATAACGTT
568165 AGTGAT
1 AGTGAT
568171 AGATTTGTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (30 bp):
AGTGATTATTTTGTAACAAAGGATAACGTT
Found at i:568178 original size:30 final size:30
Alignment explanation
Indices: 568105--568178 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
568095 GTTAATGTTG
* *
568105 AGTGACTATTTTGTAACAAAGGATAACGTT
1 AGTGATTAATTTGTAACAAAGGATAACGTT
* * * *
568135 AGTGATTATTTTGTAATAAATGATAGCGTT
1 AGTGATTAATTTGTAACAAAGGATAACGTT
568165 AGTGA-TAGATTTGT
1 AGTGATTA-ATTTGT
568179 GACTTCCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 2 0.05
30 36 0.95
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.39
Consensus pattern (30 bp):
AGTGATTAATTTGTAACAAAGGATAACGTT
Found at i:569698 original size:21 final size:21
Alignment explanation
Indices: 569674--569721 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
569664 CGTTAACCTG
*
569674 TTGATTGTGATATGATAACAT
1 TTGATTGTAATATGATAACAT
*
569695 TTGACTGTAATATGATAACAT
1 TTGATTGTAATATGATAACAT
569716 TTGATT
1 TTGATT
569722 ACAAAATATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (21 bp):
TTGATTGTAATATGATAACAT
Found at i:573552 original size:2 final size:2
Alignment explanation
Indices: 573541--573600 Score: 99
Period size: 2 Copynumber: 31.5 Consensus size: 2
573531 TCGTTTGGTT
573541 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
573582 TA TA TA TA TA T- TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA T
573601 TTTTACAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 3 0.05
2 52 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:580494 original size:22 final size:22
Alignment explanation
Indices: 580463--580505 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
580453 ACATCCTACA
580463 TATTACTATTTCTAGTTGTTAC
1 TATTACTATTTCTAGTTGTTAC
* *
580485 TATTATTATTTCTGGTTGTTA
1 TATTACTATTTCTAGTTGTTA
580506 TTGAGTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.09, G:0.12, T:0.58
Consensus pattern (22 bp):
TATTACTATTTCTAGTTGTTAC
Found at i:584940 original size:40 final size:42
Alignment explanation
Indices: 584889--585025 Score: 120
Period size: 42 Copynumber: 3.3 Consensus size: 42
584879 TTTTTCCAAA
* *
584889 AAACGCTGCAATAGAGAAG-AATTTTGCAGCGTTT-TACGC-C
1 AAACGCCGCAATAGAGAAGTAATTTAGCAGCGTTTATAC-CAC
* ** *
584929 AAACGCCGCAATATAGTGGTAATTTAGCGGCGTTTATACCAC
1 AAACGCCGCAATAGAGAAGTAATTTAGCAGCGTTTATACCAC
* * * * * *
584971 AAACGCCGCAATAGA-ATGATAAATTAGCGGCATTTATATCTC
1 AAACGCCGCAATAGAGAAG-TAATTTAGCAGCGTTTATACCAC
585013 AAACGCCGCAATA
1 AAACGCCGCAATA
585026 AATAATGCTT
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
40 15 0.19
41 15 0.19
42 50 0.62
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (42 bp):
AAACGCCGCAATAGAGAAGTAATTTAGCAGCGTTTATACCAC
Found at i:584980 original size:42 final size:42
Alignment explanation
Indices: 584928--585025 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
584918 CGTTTTACGC
* * * * *
584928 CAAACGCCGCAATATAGTGGTAATTTAGCGGCGTTTATACCA
1 CAAACGCCGCAATAGAATGATAAATTAGCGGCATTTATACCA
* *
584970 CAAACGCCGCAATAGAATGATAAATTAGCGGCATTTATATCT
1 CAAACGCCGCAATAGAATGATAAATTAGCGGCATTTATACCA
585012 CAAACGCCGCAATA
1 CAAACGCCGCAATA
585026 AATAATGCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.23
Consensus pattern (42 bp):
CAAACGCCGCAATAGAATGATAAATTAGCGGCATTTATACCA
Found at i:586588 original size:41 final size:41
Alignment explanation
Indices: 586503--586606 Score: 120
Period size: 41 Copynumber: 2.5 Consensus size: 41
586493 TAATTAGCGA
* **
586503 CGTTTTCATAGAAACGCCGCAAAATAGTTGGACTATAGTGG
1 CGTTTTCATAGAAACGCCGCAAAATAGTTGGAATATAGCAG
* *
586544 CGTTTTCATAGAAACGCCGCAAAATA-TTAGTAATTTAGCAG
1 CGTTTTCATAGAAACGCCGCAAAATAGTT-GGAATATAGCAG
* * *
586585 CGTTTTTACAAAAACGCCGCAA
1 CGTTTTCATAGAAACGCCGCAA
586607 TAGGTTCCAC
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
40 2 0.04
41 52 0.96
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (41 bp):
CGTTTTCATAGAAACGCCGCAAAATAGTTGGAATATAGCAG
Found at i:590611 original size:749 final size:747
Alignment explanation
Indices: 589069--590822 Score: 3337
Period size: 749 Copynumber: 2.3 Consensus size: 747
589059 GTATTTTCTT
* *
589069 TAATTGAGTATCAGTGATTAAAATCAATAATTCATCTGTTTCTCTCTTCATAGGTGCTAATTAAG
1 TAATTGAGTATCAGTGATTAAAATCAATAATTCATCTGTTTCTCTCTTCGTAGGTGCTAATTGAG
* *
589134 TTGAGCATCTCAAATTTTATTCGTTTCTGAGGAACTCATTTGTCAAGAAACAAAGGTAATCTTCT
66 TTGAGCATATCGAATTTTATTCGTTTCTGAGGAACTCATTTGTCAAGAAACAAAGGTAATCTTCT
589199 ATCTGTTATACTTTTGGGTTACTATTTTTCTATTTTTCTTGAACCTGTCTGACATGGAACAAAGG
131 ATCTGTTATACTTTTGGGTTACTATTTTTCTATTTTTCTTGAACCTGTCTGACATGGAACAAAGG
589264 TAATGAACTCCGTTGTAAGTTCTTCATGCCTCTATCTTTACCATTGAAACATGAGTTTGTTTATA
196 TAATGAACTCCGTTGTAAGTTCTTCATGCCTCTATCTTTACCATTGAAACATGAGTTTGTTTATA
589329 AAAAAAATAGTGCTTGTAATCAATTTAAAACCCATTATCTAAAAAAATATGAGAACCGAAACGAG
261 AAAAAAATAGTGCTTGTAATCAATTTAAAACCCATTATCTAAAAAAATATGAGAACCGAAACGAG
*
589394 TACAATTAAATACACTTACTCTATATGTATTAGAAAAAGAATATTATACCTTGAGATCTTAAGTT
326 TACAATTAAATACACTTACACTATATGTATTAGAAAAAGAATATTATACCTTGAGATCTTAAGTT
589459 TAAAAAACTATATTTATAAAAAAATATTATTAATAATTAAAAAATTATAAATATATATTATATTA
391 TAAAAAACTATATTTATAAAAAAATATTATTAATAATTAAAAAATTATAAATATATATTATATTA
589524 TAATCACTTGGATTATTAGATTTGTAAGGGAGAATTACATGCGGGGAAAAAGAAGCTGATAGAGT
456 TAATCACTTGGATTATTAGATTTGTAAGGGAGAATTACATGCGGGGAAAAAGAAGCTGATAGAGT
* *
589589 CAGTGGGGTGTTAAGTCAACCAAATGGACGTTATCGACATGGCCACGTCAAAGATAATCTCAGAT
521 CAGTGGGGTGTTAAATCAACCAAATGGACGTTACCGACATGGCCACGTCAAAGATAATCTCAGAT
589654 TTCCTACATTACGATAGTGTTAACATTCAAGACTAATTCAAATTTTATTATGGGAGGGTACAAGG
586 TTCCTACATTACGATAGTGTTAACATTCAAGACTAATTCAAATTTTATTATGGGAGGGTACAAGG
589719 TGGATTGATTTCCTACATTACTGCTATTTTGTATGATCTTGTTGGCAGAGCATGCATAATAAAAA
651 TGGATTGATTTCCTACATTACTGCTATTTTGTATGATCTTGTTGGCAGAGCATGCATAATAAAAA
589784 TAAATAGTTTGACACTACCCTATTGATGGATG
716 TAAATAGTTTGACACTACCCTATTGATGGATG
589816 TAATTGAGTATCAGTGATTAAAATCAATAATTCATCTGTTTCTCTCTTCGTAGGTGCTAATTGAG
1 TAATTGAGTATCAGTGATTAAAATCAATAATTCATCTGTTTCTCTCTTCGTAGGTGCTAATTGAG
589881 TTGAGCATATCGAATTTTATTCGTTTCTGAGGAACTCATTTGTCAAGAAACAAAGGTAATCTTCT
66 TTGAGCATATCGAATTTTATTCGTTTCTGAGGAACTCATTTGTCAAGAAACAAAGGTAATCTTCT
589946 ATCTGTTATACTTTTGGGTTACTATTTTTCTATTTTTCTTGAACCTGTCTGACATGGAACAAAGG
131 ATCTGTTATACTTTTGGGTTACTATTTTTCTATTTTTCTTGAACCTGTCTGACATGGAACAAAGG
590011 TAATGAACTCCGTTGTAAGTTCTTCATGCCTCTATCTTTACCATTGAAACATGAGTTTGTTTATA
196 TAATGAACTCCGTTGTAAGTTCTTCATGCCTCTATCTTTACCATTGAAACATGAGTTTGTTTATA
590076 AAAAAAATAGTGCTTGTAATCAATTTAAAACCCATTATCTAAAAAAATATGAGAACCGAAACGAG
261 AAAAAAATAGTGCTTGTAATCAATTTAAAACCCATTATCTAAAAAAATATGAGAACCGAAACGAG
590141 TACAATTAAATACACTTACACTATATGTATTAGAAAAAGAATATTATACCTTGAGATCTTAAGTT
326 TACAATTAAATACACTTACACTATATGTATTAGAAAAAGAATATTATACCTTGAGATCTTAAGTT
590206 TAAAAAACTATATTTATAAAAAAAATATTATTAATAATTAAAAAAATTATAAATATATATTATAT
391 TAAAAAACTATATTTAT-AAAAAAATATTATTAATAATT-AAAAAATTATAAATATATATTATAT
*
590271 TATAATCACTTGGATTATTAGATTTGTAAGGGAGAATTACATGCGGGGAAAAAGTAGCTGATAGA
454 TATAATCACTTGGATTATTAGATTTGTAAGGGAGAATTACATGCGGGGAAAAAGAAGCTGATAGA
590336 GTCAGTGGGGTGTTAAATCAACCAAATGGACGTTACCGACATGGCCACGTCAAAGATAATCTCAG
519 GTCAGTGGGGTGTTAAATCAACCAAATGGACGTTACCGACATGGCCACGTCAAAGATAATCTCAG
590401 ATTTCCTACATTACGATAGTGTTAACATTCAAGACTAATTCAAATTTTATTATGGGAGGGTACAA
584 ATTTCCTACATTACGATAGTGTTAACATTCAAGACTAATTCAAATTTTATTATGGGAGGGTACAA
*
590466 GGTGGATTGATTTCCTACATTACTGTTATTTTGTATGATCTTGTTGGCAGAGCATGCATAATAAA
649 GGTGGATTGATTTCCTACATTACTGCTATTTTGTATGATCTTGTTGGCAGAGCATGCATAATAAA
590531 AATAAATAGTTTGACACTACCCTATTGATGGATG
714 AATAAATAGTTTGACACTACCCTATTGATGGATG
* *
590565 TAATTGAGTATCAATGATTAAAATCAATAATTCATTTGTTTCTCTCTTCGTAGGTGCTAATTGAG
1 TAATTGAGTATCAGTGATTAAAATCAATAATTCATCTGTTTCTCTCTTCGTAGGTGCTAATTGAG
*
590630 TTGAGCATATCGAATTTTATTCGTTTCTGAGGAACTCATTTGTCAAAAAACAAAGGTAATCTTCT
66 TTGAGCATATCGAATTTTATTCGTTTCTGAGGAACTCATTTGTCAAGAAACAAAGGTAATCTTCT
* *
590695 ATCCGTTATACTTTTGGGTTACTATTTTTCTATTTTTCTTGAACCTTTCTGACATGGAACAAAGG
131 ATCTGTTATACTTTTGGGTTACTATTTTTCTATTTTTCTTGAACCTGTCTGACATGGAACAAAGG
** *
590760 TAATGAACTCATTTGTAAGTTCTTCATGCCTCTATTTTTACCATTGAAACATGAGTTTGTTTA
196 TAATGAACTCCGTTGTAAGTTCTTCATGCCTCTATCTTTACCATTGAAACATGAGTTTGTTTA
590823 GATATAAATG
Statistics
Matches: 988, Mismatches: 17, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
747 402 0.41
748 21 0.02
749 565 0.57
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.36
Consensus pattern (747 bp):
TAATTGAGTATCAGTGATTAAAATCAATAATTCATCTGTTTCTCTCTTCGTAGGTGCTAATTGAG
TTGAGCATATCGAATTTTATTCGTTTCTGAGGAACTCATTTGTCAAGAAACAAAGGTAATCTTCT
ATCTGTTATACTTTTGGGTTACTATTTTTCTATTTTTCTTGAACCTGTCTGACATGGAACAAAGG
TAATGAACTCCGTTGTAAGTTCTTCATGCCTCTATCTTTACCATTGAAACATGAGTTTGTTTATA
AAAAAAATAGTGCTTGTAATCAATTTAAAACCCATTATCTAAAAAAATATGAGAACCGAAACGAG
TACAATTAAATACACTTACACTATATGTATTAGAAAAAGAATATTATACCTTGAGATCTTAAGTT
TAAAAAACTATATTTATAAAAAAATATTATTAATAATTAAAAAATTATAAATATATATTATATTA
TAATCACTTGGATTATTAGATTTGTAAGGGAGAATTACATGCGGGGAAAAAGAAGCTGATAGAGT
CAGTGGGGTGTTAAATCAACCAAATGGACGTTACCGACATGGCCACGTCAAAGATAATCTCAGAT
TTCCTACATTACGATAGTGTTAACATTCAAGACTAATTCAAATTTTATTATGGGAGGGTACAAGG
TGGATTGATTTCCTACATTACTGCTATTTTGTATGATCTTGTTGGCAGAGCATGCATAATAAAAA
TAAATAGTTTGACACTACCCTATTGATGGATG
Found at i:593219 original size:21 final size:22
Alignment explanation
Indices: 593193--593258 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 22
593183 AGCGAAAAAT
*
593193 GAAGCAAG-GGAAGCCGAGAGA
1 GAAGCAAGCGGAAGCAGAGAGA
*
593214 GCAGC-AGCGGAAGCAGAGAGA
1 GAAGCAAGCGGAAGCAGAGAGA
* * *
593235 GAAGC-AGTGGCAGCACAGAGA
1 GAAGCAAGCGGAAGCAGAGAGA
593256 GAA
1 GAA
593259 TCAACATATC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 2 0.05
21 36 0.95
ACGTcount: A:0.41, C:0.17, G:0.41, T:0.02
Consensus pattern (22 bp):
GAAGCAAGCGGAAGCAGAGAGA
Found at i:593715 original size:43 final size:43
Alignment explanation
Indices: 593668--593848 Score: 247
Period size: 43 Copynumber: 4.2 Consensus size: 43
593658 CCAATTTTTA
* * * * * *
593668 GCGGCGTTTGTA-TTAAAAAAGCCGCTAAACCTCAGCGCCTATT
1 GCGGCGTTT-TAGCTAAAAACGCCGCTAAATCTCAACACATATT
* *
593711 GCGGCATTTTAGCTAAAAACGTCGCTAAATCTCAACACATATT
1 GCGGCGTTTTAGCTAAAAACGCCGCTAAATCTCAACACATATT
*
593754 GCGGCGTTTTAGCTAAAAACGTCGCTAAATCTCAACACATATT
1 GCGGCGTTTTAGCTAAAAACGCCGCTAAATCTCAACACATATT
*
593797 GCGGCGTTTTCGCTAAAAACGCCGCTAAATCTCAACACATATT
1 GCGGCGTTTTAGCTAAAAACGCCGCTAAATCTCAACACATATT
*
593840 GCAGCGTTT
1 GCGGCGTTT
593849 GTGAAGAAAA
Statistics
Matches: 125, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
42 2 0.02
43 123 0.98
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (43 bp):
GCGGCGTTTTAGCTAAAAACGCCGCTAAATCTCAACACATATT
Found at i:593886 original size:86 final size:86
Alignment explanation
Indices: 593705--593888 Score: 230
Period size: 86 Copynumber: 2.1 Consensus size: 86
593695 AACCTCAGCG
* * * *
593705 CCTATTGCGGCATTTTAGCTAAAAACGTCGCTAAATCTCAACACATATTGCGGCGTTTTAGCTAA
1 CCTATTGCGGCGTTTTAGCTAAAAACGCCGCTAAATCTCAACACATATTGCAGCGTTTTAGCAAA
** *
593770 AAACGTCGCTAAATCTCAACA
66 AAACACCGCTAAATCTCAAAA
* *
593791 CATATTGCGGCGTTTTCGCTAAAAACGCCGCTAAATCTCAACACATATTGCAGCGTTTGT-G-AA
1 CCTATTGCGGCGTTTTAGCTAAAAACGCCGCTAAATCTCAACACATATTGCAGCGTTT-TAGCAA
593854 GAAAACACCGCTAAA-CATCAAAA
65 -AAAACACCGCTAAATC-TCAAAA
*
593877 CCTACTGCGGCG
1 CCTATTGCGGCG
593889 CTTGTGAAGA
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
85 2 0.02
86 81 0.96
87 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.25
Consensus pattern (86 bp):
CCTATTGCGGCGTTTTAGCTAAAAACGCCGCTAAATCTCAACACATATTGCAGCGTTTTAGCAAA
AAACACCGCTAAATCTCAAAA
Found at i:593902 original size:86 final size:86
Alignment explanation
Indices: 593725--593919 Score: 202
Period size: 86 Copynumber: 2.3 Consensus size: 86
593715 CATTTTAGCT
* * * ** *
593725 AAAAACGTCGCTAAATCTCAACACATATTGCGGCGTTTTAGCTAAAAACGTCGCTAAATCTCAAC
1 AAAAACGCCGCTAAATCTCAACACATATTGCAGCGTTTTAGCAAAAAACACCGCTAAATCTCAAA
* * *
593790 ACATATTGCGGCGTTTTCGCT
66 ACATACTGCGGCGTTGTCGCA
593811 AAAAACGCCGCTAAATCTCAACACATATTGCAGCGTTTGT-G-AAGAAAACACCGCTAAA-CATC
1 AAAAACGCCGCTAAATCTCAACACATATTGCAGCGTTT-TAGCAA-AAAACACCGCTAAATC-TC
*
593873 AAAACCTACTGCGGCGCTTGT-G-A
63 AAAACATACTGCGGCG-TTGTCGCA
* *
593896 AGAAAACGCCACTAAATATCAACA
1 A-AAAACGCCGCTAAATCTCAACA
593920 ACTTTGGCGG
Statistics
Matches: 92, Mismatches: 12, Indels: 10
0.81 0.11 0.09
Matches are distributed among these distances:
85 3 0.03
86 85 0.92
87 4 0.04
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (86 bp):
AAAAACGCCGCTAAATCTCAACACATATTGCAGCGTTTTAGCAAAAAACACCGCTAAATCTCAAA
ACATACTGCGGCGTTGTCGCA
Found at i:593930 original size:43 final size:43
Alignment explanation
Indices: 593726--593931 Score: 133
Period size: 43 Copynumber: 4.8 Consensus size: 43
593716 ATTTTAGCTA
* * * *
593726 AAAACGTCGCTAAATCTCAAC-ACATATTGCGGCG-TTTTAGCTA-
1 AAAACGCCGCTAAATATCAACAAC-TATTGCGGCGCTTGT-G-AAG
* * * *
593769 AAAACGTCGCTAAATCTCAAC-ACATATTGCGGCG-TTTTCGCTA-
1 AAAACGCCGCTAAATATCAACAAC-TATTGCGGCGCTTGT-G-AAG
* * *
593812 AAAACGCCGCTAAATCTCAAC-ACATATTGCAGCGTTTGTGAAG
1 AAAACGCCGCTAAATATCAACAAC-TATTGCGGCGCTTGTGAAG
* * *
593855 AAAACACCGCTAAACATCAA-AACCTACTGCGGCGCTTGTGAAG
1 AAAACGCCGCTAAATATCAACAA-CTATTGCGGCGCTTGTGAAG
*
593898 AAAACGCCACTAAATATCAACAACT-TTGGCGGCG
1 AAAACGCCGCTAAATATCAACAACTATT-GCGGCG
593932 TTTTTCAACA
Statistics
Matches: 142, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
42 2 0.01
43 134 0.94
44 6 0.04
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (43 bp):
AAAACGCCGCTAAATATCAACAACTATTGCGGCGCTTGTGAAG
Found at i:595247 original size:10 final size:10
Alignment explanation
Indices: 595223--595257 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
595213 CCGCGGGCTA
*
595223 CCCGCGAAA-
1 CCCGCTAAAG
595232 CCCGCTAAAG
1 CCCGCTAAAG
595242 CCCGCTAAAG
1 CCCGCTAAAG
595252 CCCGCT
1 CCCGCT
595258 TAATTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.26, C:0.46, G:0.20, T:0.09
Consensus pattern (10 bp):
CCCGCTAAAG
Done.