Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008959.1 Hibiscus syriacus cultivar Beakdansim tig00112293_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: 4521124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 21
Found at i:1190967 original size:32 final size:32
Alignment explanation
Indices: 1190927--1190987 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
1190917 TAGAAACAAG
*
1190927 AAGTATCTCTACGAGATGAGCATAACAACGAA
1 AAGTATCTCTACAAGATGAGCATAACAACGAA
1190959 AAGTATCTCTACAAGATGAGCATAACAAC
1 AAGTATCTCTACAAGATGAGCATAACAAC
1190988 CATTTCTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (32 bp):
AAGTATCTCTACAAGATGAGCATAACAACGAA
Found at i:1191280 original size:166 final size:167
Alignment explanation
Indices: 1191085--1191419 Score: 654
Period size: 166 Copynumber: 2.0 Consensus size: 167
1191075 TAAATCAATC
1191085 AATAATTTTGACACTTGCCATAGGACTATGATTTTTGAATAATTTAAAAGAGTGGTTGATTTATT
1 AATAATTTTGACACTTGCCATAGGACTATGATTTTTGAATAATTTAAAAGAGTGGTTGATTTATT
1191150 TGATATTCATTAATTTCATGTATTATAATGTGATTCTATTGTGAACCTAT-ATAGGCAATATTTT
66 TGATATTCATTAATTTCATGTATTATAATGTGATTCTATTGTGAACCTATAATAGGCAATATTTT
1191214 ACAAAATTCTTTCATTCTTCGATAAAGAAAGGAGAAA
131 ACAAAATTCTTTCATTCTTCGATAAAGAAAGGAGAAA
*
1191251 AATAATTTTGACACTTGCCATAGGACTATGATTTTTGAATAATTTAAAAGAGTTGTTGATTTATT
1 AATAATTTTGACACTTGCCATAGGACTATGATTTTTGAATAATTTAAAAGAGTGGTTGATTTATT
1191316 TGATATTCATTAATTTCATGTATTATAATGTGATTCTATTGTGAACCTATAATAGGCAATATTTT
66 TGATATTCATTAATTTCATGTATTATAATGTGATTCTATTGTGAACCTATAATAGGCAATATTTT
1191381 ACAAAATTCTTTCATTCTTCGATAAAGAAAGGAGAAA
131 ACAAAATTCTTTCATTCTTCGATAAAGAAAGGAGAAA
1191418 AA
1 AA
1191420 AACATTTTCA
Statistics
Matches: 167, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
166 114 0.68
167 53 0.32
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (167 bp):
AATAATTTTGACACTTGCCATAGGACTATGATTTTTGAATAATTTAAAAGAGTGGTTGATTTATT
TGATATTCATTAATTTCATGTATTATAATGTGATTCTATTGTGAACCTATAATAGGCAATATTTT
ACAAAATTCTTTCATTCTTCGATAAAGAAAGGAGAAA
Found at i:1193932 original size:58 final size:58
Alignment explanation
Indices: 1193842--1193957 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
1193832 GCTACATTAT
1193842 GGTTGCATGAATAAGGATGGTCCCCAGGCAAACCATTTGATCCAGGGTTCAGTTCCTC
1 GGTTGCATGAATAAGGATGGTCCCCAGGCAAACCATTTGATCCAGGGTTCAGTTCCTC
1193900 GGTTGCATGAATAAGGATGGTCCCCAGGCAAACCATTTGATCCAGGGTTCAGTTCCTC
1 GGTTGCATGAATAAGGATGGTCCCCAGGCAAACCATTTGATCCAGGGTTCAGTTCCTC
1193958 AAAATCTCGG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (58 bp):
GGTTGCATGAATAAGGATGGTCCCCAGGCAAACCATTTGATCCAGGGTTCAGTTCCTC
Found at i:1194632 original size:54 final size:54
Alignment explanation
Indices: 1194524--1194641 Score: 166
Period size: 54 Copynumber: 2.2 Consensus size: 54
1194514 CTTCCCTGAC
* *
1194524 CAAACTTCTGGACAGAAGCCACAAGAAAAGATGAATGTGTTGTCAAATATTTTA
1 CAAACATCTGGACAGAAGCCACAAGAAAAGATGAATGTGTTGTCAAATACTTTA
* * * *
1194578 CGAACCTCTGGCCAGAAGCCAC-AGTAAAAGATGAATGTGTTGTCAAATGCTTTA
1 CAAACATCTGGACAGAAGCCACAAG-AAAAGATGAATGTGTTGTCAAATACTTTA
1194632 CAAACATCTG
1 CAAACATCTG
1194642 AGTAGAAACC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
53 2 0.04
54 54 0.96
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (54 bp):
CAAACATCTGGACAGAAGCCACAAGAAAAGATGAATGTGTTGTCAAATACTTTA
Found at i:1194654 original size:54 final size:54
Alignment explanation
Indices: 1194524--1194685 Score: 157
Period size: 54 Copynumber: 3.0 Consensus size: 54
1194514 CTTCCCTGAC
* * * * **
1194524 CAAACTTCTGGACAGAAGCCACAAGAAAAGATGAATGTGTTGTCAAATATTTTA
1 CAAACATCTGGCCAGAAACCACATGAAAAGATGAATGTGTTGTCAAATGCTTTA
* * *
1194578 CGAACCTCTGGCCAGAAGCCACA-GTAAAAGATGAATGTGTTGTCAAATGCTTTA
1 CAAACATCTGGCCAGAAACCACATG-AAAAGATGAATGTGTTGTCAAATGCTTTA
* * * * * *
1194632 CAAACATCTGAG-TAGAAACCACATGAGATGATGAATGTATTATCAAATGGTTTA
1 CAAACATCTG-GCCAGAAACCACATGAAAAGATGAATGTGTTGTCAAATGCTTTA
1194686 TGAACCAGTT
Statistics
Matches: 91, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
53 1 0.01
54 88 0.97
55 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (54 bp):
CAAACATCTGGCCAGAAACCACATGAAAAGATGAATGTGTTGTCAAATGCTTTA
Found at i:1195080 original size:22 final size:22
Alignment explanation
Indices: 1195054--1195155 Score: 150
Period size: 22 Copynumber: 4.6 Consensus size: 22
1195044 TACATCTACA
*
1195054 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTTT
*
1195076 CTCTTCAAAGATGATATATTTT
1 CTCTTCAAAGATGATAGATTTT
* *
1195098 CTCTTCAAATATGATAGCTTTT
1 CTCTTCAAAGATGATAGATTTT
*
1195120 CTCTTCAAAGATGATAGATTAT
1 CTCTTCAAAGATGATAGATTTT
*
1195142 CTTTTCAAAGATGA
1 CTCTTCAAAGATGA
1195156 AAGCTTTATT
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 71 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTTT
Found at i:1195908 original size:45 final size:45
Alignment explanation
Indices: 1195859--1195972 Score: 138
Period size: 45 Copynumber: 2.5 Consensus size: 45
1195849 GGGAACTTTT
** * *
1195859 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCA
* * *
1195904 TGATGCTTTCAAAACCTTTGTGTCATCCATAAGACCTGCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCA
*
1195949 GGATGTTTTCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
1195973 ATGTTTTTGA
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
45 46 0.82
46 4 0.07
47 6 0.11
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.32
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCA
Found at i:1196025 original size:121 final size:121
Alignment explanation
Indices: 1195806--1196091 Score: 402
Period size: 121 Copynumber: 2.4 Consensus size: 121
1195796 CTATTTCCCA
* * *
1195806 CATCTATAAGCCCTACAATGCAGGATGTTTTCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAA
1 CATCTATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAACTTTTTGATATTTTCAA
* *
1195871 AACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTT-TCAAAACCTT-TGTGT
66 AACATTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG-TTATCAAAACCTTCAG-GT
* * ** *
1195927 CATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGATGTTTTTGATATTTTTAA
1 CATCTATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAACTTTTTGATATTTTCAA
1195992 AACATTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCAGGT
66 AACATTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCAGGT
* *
1196048 CATCTATAA-ACCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGG
1 CATCTATAAGA-CCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGG
1196092 TCATCCGTAA
Statistics
Matches: 149, Mismatches: 13, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
119 8 0.05
120 7 0.05
121 133 0.89
122 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (121 bp):
CATCTATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAACTTTTTGATATTTTCAA
AACATTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCAGGT
Found at i:1196039 original size:45 final size:45
Alignment explanation
Indices: 1195980--1196128 Score: 199
Period size: 45 Copynumber: 3.3 Consensus size: 45
1195970 GGGATGTTTT
* * *
1195980 TGATATTTTTAAAACATTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * * *
1196025 TGATGTTATCAAAACCTTCAGGTCATCTATAAACCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
1196070 TGATGTTTTCAAAACCTTCGGGTCATCCGTAAGCCCTACAGTGTA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
1196115 GGATGTTTTCAAAA
1 TGATGTTTTCAAAA
1196129 AAGCCTTCGG
Statistics
Matches: 89, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 89 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.33
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:1196173 original size:122 final size:122
Alignment explanation
Indices: 1196025--1196365 Score: 529
Period size: 122 Copynumber: 2.8 Consensus size: 122
1196015 CTTCAGTGCA
* * * *
1196025 TGATGTTATCAAAACCTTCAGGTCATCTATAAACCCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
*
1196090 GGTCATCCGTAAGCCCTACAGTGTAGGATGTTTTCAAAAAAGCCTTCGGAAGCTTTT
66 GGTCATCCGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAAGCCTTCGGAAGCTTTT
* *
1196147 TGATGTTTTCAAAAACTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTTG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
* *
1196212 GGTCATCCGTAAGCTCTACAATGCAGGATGTTTTCAAAAAAGCCTTCGGAAGCTTTT
66 GGTCATCCGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAAGCCTTCGGAAGCTTTT
* * * *
1196269 TGATGTTTTCAAAACCTTCGGGTTATTTGTAAGCCCTTCAGTGCATGATGTTCTCAAAACCTTCT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
* * * *
1196334 GGTCATCTGTAAGACCTTCAGTGCATGATGTT
66 GGTCATCCGTAAGCCCTACAGTGCAGGATGTT
1196366 CTTAAATCCT
Statistics
Matches: 198, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
122 198 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (122 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
GGTCATCCGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAAGCCTTCGGAAGCTTTT
Found at i:1196196 original size:45 final size:45
Alignment explanation
Indices: 1196147--1196251 Score: 147
Period size: 45 Copynumber: 2.3 Consensus size: 45
1196137 GGAAGCTTTT
* * *
1196147 TGATGTTTTCAAAAACTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAAACTTCGGGTCATCCGTAAGCCCTACAATGCA
* * *
1196192 TGATGTTTTCAAAACCTTTGGGTCATCCGTAAGCTCTACAATGCA
1 TGATGTTTTCAAAAACTTCGGGTCATCCGTAAGCCCTACAATGCA
*
1196237 GGATGTTTTCAAAAA
1 TGATGTTTTCAAAAA
1196252 AGCCTTCGGA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (45 bp):
TGATGTTTTCAAAAACTTCGGGTCATCCGTAAGCCCTACAATGCA
Found at i:1196209 original size:167 final size:166
Alignment explanation
Indices: 1195859--1196250 Score: 563
Period size: 167 Copynumber: 2.4 Consensus size: 166
1195849 GGGAACTTTT
* *
1195859 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTTG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
* * *
1195924 TGTCATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGATGTTTTTGATATTTT
66 GGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAAGTTTTTGATATTTT
*
1195989 TAAAACATTCGGGTCATCTGTAAGCCCTTCAGTGCA
131 AAAAACATTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * * *
1196025 TGATGTTATCAAAACCTTCAGGTCATCTATAAACCCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
* * * *
1196090 GGTCATCCGTAAGCCCTACAGTGTAGGATGTTTTCAAAAAAGCCTTC-GGAAGCTTTTTGATGTT
66 GGTCATCCATAAGACCTACAGTGCAGGATGTTTTC-AAAAAGCCTTCGGGAAG-TTTTTGATATT
1196154 TTCAAAAAC-TTCGGGTCATCTGTAAGCCCTTCAGTGCA
129 TT-AAAAACATTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * * * * *
1196192 TGATGTTTTCAAAACCTTTGGGTCATCCGTAAGCTCTACAATGCAGGATGTTTTCAAAA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAA
1196251 AAGCCTTCGG
Statistics
Matches: 199, Mismatches: 24, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
166 93 0.47
167 101 0.51
168 5 0.03
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.33
Consensus pattern (166 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
GGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAAGTTTTTGATATTTT
AAAAACATTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:1196318 original size:45 final size:45
Alignment explanation
Indices: 1196269--1196395 Score: 184
Period size: 45 Copynumber: 2.8 Consensus size: 45
1196259 GGAAGCTTTT
* * *
1196269 TGATGTTTTCAAAACCTTCGGGTTATTTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
* *
1196314 TGATGTTCTCAAAACCTTCTGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
*
1196359 TGATGTTCTT-AAATCCTTCGGGTCATCTGTAAGACCT
1 TGATGTT-TTCAAAACCTTCGGGTCATCTGTAAGACCT
1196396 ACAATGCAAG
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
45 72 0.99
46 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
Found at i:1196590 original size:3 final size:3
Alignment explanation
Indices: 1196577--1196643 Score: 80
Period size: 3 Copynumber: 21.7 Consensus size: 3
1196567 TTTTTCATTC
* * * *
1196577 TAT TTT TAT TAT TAT TAT TAT TAA AAT TAT TAT TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1196625 TAT TAT ATAT ATAT TAT TA
1 TAT TAT -TAT -TAT TAT TA
1196644 AATAAATAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
3 48 0.87
4 7 0.13
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1197483 original size:20 final size:20
Alignment explanation
Indices: 1197460--1197515 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
1197450 GAACGGGAGG
*
1197460 AGACATAGAGCAATCCAAAA
1 AGACAGAGAGCAATCCAAAA
* *
1197480 AGACAGAGAGAAAACCAAAA
1 AGACAGAGAGCAATCCAAAA
*
1197500 A-ATAGAGAGCAATCCA
1 AGACAGAGAGCAATCCA
1197516 GAAACAGAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.57, C:0.18, G:0.18, T:0.07
Consensus pattern (20 bp):
AGACAGAGAGCAATCCAAAA
Found at i:1198565 original size:22 final size:21
Alignment explanation
Indices: 1198528--1198574 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
1198518 TTCTGATATT
*
1198528 TTTTATAAATAAATATTTTAC
1 TTTTATAAATAAATATATTAC
* *
1198549 TTTTATAAATTATATATATTAT
1 TTTTATAAA-TAAATATATTAC
1198571 TTTT
1 TTTT
1198575 TAATGTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTATAAATAAATATATTAC
Found at i:1198738 original size:2 final size:2
Alignment explanation
Indices: 1198699--1198728 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1198689 AAATAAATAA
1198699 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
1198729 TCACATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1208198 original size:33 final size:34
Alignment explanation
Indices: 1208135--1208214 Score: 119
Period size: 33 Copynumber: 2.4 Consensus size: 34
1208125 ATTTGATTTT
*
1208135 AAATTTTATAGAATGGTCTTATATGGTGGTTTAC
1 AAATTTTATAGAATAGTCTTATATGGTGGTTTAC
1208169 AAATATTT-TAGAATAGTCTT-TATGGTGGTTTAC
1 AAAT-TTTATAGAATAGTCTTATATGGTGGTTTAC
*
1208202 AAATTTTAAAGAA
1 AAATTTTATAGAA
1208215 ATTTTTGGGT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
32 3 0.07
33 21 0.50
34 15 0.36
35 3 0.07
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.42
Consensus pattern (34 bp):
AAATTTTATAGAATAGTCTTATATGGTGGTTTAC
Found at i:1209241 original size:23 final size:23
Alignment explanation
Indices: 1209184--1209241 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
1209174 AAATGGATTG
*
1209184 ATCCC-TTTGAAAAAAATGATCC
1 ATCCCTTTTGAAAAAAAAGATCC
**
1209206 ATCCCTTGGGAAAAAAAAGATCC
1 ATCCCTTTTGAAAAAAAAGATCC
1209229 ATCCCTTTTGAAA
1 ATCCCTTTTGAAA
1209242 CTTTGCATAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 5 0.17
23 25 0.83
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.26
Consensus pattern (23 bp):
ATCCCTTTTGAAAAAAAAGATCC
Found at i:1210019 original size:16 final size:16
Alignment explanation
Indices: 1209998--1210028 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1209988 GCAACTAAGG
*
1209998 TAGCTTCGCTACACAC
1 TAGCTTAGCTACACAC
1210014 TAGCTTAGCTACACA
1 TAGCTTAGCTACACA
1210029 TACTAAAGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.32, G:0.13, T:0.26
Consensus pattern (16 bp):
TAGCTTAGCTACACAC
Found at i:1210764 original size:20 final size:20
Alignment explanation
Indices: 1210731--1210768 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1210721 ATTCATCTCA
* *
1210731 GTTCATCCAGTATCGATATT
1 GTTCAACCAATATCGATATT
1210751 GTTCAACCAATATCGATA
1 GTTCAACCAATATCGATA
1210769 CTCGAACCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (20 bp):
GTTCAACCAATATCGATATT
Found at i:1212251 original size:26 final size:27
Alignment explanation
Indices: 1212222--1212273 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 27
1212212 AAAAAAAAAA
1212222 AAAGAAGAATCCAGAAATTA-CATAAC
1 AAAGAAGAATCCAGAAATTATCATAAC
1212248 AAAGAAGAATCCAGAAATTATCATAA
1 AAAGAAGAATCCAGAAATTATCATAA
1212274 AGCATTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.58, C:0.13, G:0.12, T:0.17
Consensus pattern (27 bp):
AAAGAAGAATCCAGAAATTATCATAAC
Found at i:1214773 original size:18 final size:18
Alignment explanation
Indices: 1214739--1214772 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1214729 TTTATTTTTA
1214739 AAGAAAAAAAATGAAAAC
1 AAGAAAAAAAATGAAAAC
*
1214757 AAGAAAAGAAA-GAAAA
1 AAGAAAAAAAATGAAAA
1214773 AAAAAAGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (18 bp):
AAGAAAAAAAATGAAAAC
Found at i:1220960 original size:153 final size:153
Alignment explanation
Indices: 1220682--1220988 Score: 598
Period size: 153 Copynumber: 2.0 Consensus size: 153
1220672 CCGGTCATTT
1220682 CGGCATGTGGCAAAGTGAGGTTCTAGATGCCCTATTTCAACAGGGTCTAGACATTGCTATTGAAG
1 CGGCATGTGGCAAAGTGAGGTTCTAGATGCCCTATTTCAACAGGGTCTAGACATTGCTATTGAAG
1220747 GAGAGAAACCGATGATGTTGAGGAGAAAGAATGGAAGAGGATCAATAGATTGGCATGTGGTACTA
66 GAGAGAAACCGATGATGTTGAGGAGAAAGAATGGAAGAGGATCAATAGATTGGCATGTGGTACTA
1220812 TTCGATCGTGTCTTTATAGAGAG
131 TTCGATCGTGTCTTTATAGAGAG
1220835 CGGCATGTGGCAAAGTGAGGTTCTAGATGCCCTATTTCAACA-GGTCTAGACATTGCTATTGAAG
1 CGGCATGTGGCAAAGTGAGGTTCTAGATGCCCTATTTCAACAGGGTCTAGACATTGCTATTGAAG
1220899 GAGAGAAACCAGATGATGTTGAGGAGAAAGAATGGAAGAGGATCAATAGATTGGCATGTGGTACT
66 GAGAGAAACC-GATGATGTTGAGGAGAAAGAATGGAAGAGGATCAATAGATTGGCATGTGGTACT
1220964 ATTCGATCGTGTCTTTATAGAGAG
130 ATTCGATCGTGTCTTTATAGAGAG
1220988 C
1 C
1220989 ATAAGTATGC
Statistics
Matches: 153, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
152 32 0.21
153 121 0.79
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.26
Consensus pattern (153 bp):
CGGCATGTGGCAAAGTGAGGTTCTAGATGCCCTATTTCAACAGGGTCTAGACATTGCTATTGAAG
GAGAGAAACCGATGATGTTGAGGAGAAAGAATGGAAGAGGATCAATAGATTGGCATGTGGTACTA
TTCGATCGTGTCTTTATAGAGAG
Found at i:1222501 original size:93 final size:92
Alignment explanation
Indices: 1222342--1222524 Score: 348
Period size: 93 Copynumber: 2.0 Consensus size: 92
1222332 TAGATTGCTT
*
1222342 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1222407 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
1222435 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1222500 TTTGTCTTTGTTTGTCTTTTGGTTG
66 TTTGTCTTTGTTTGTCTTTTGGTTG
1222525 TTTGTCTTTT
Statistics
Matches: 89, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
92 15 0.17
93 74 0.83
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.46
Consensus pattern (92 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTGTCTTTTGGTTGAA
Found at i:1222527 original size:15 final size:15
Alignment explanation
Indices: 1222507--1222539 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1222497 GTATTTGTCT
1222507 TTGTTTGTCTTTTGG
1 TTGTTTGTCTTTTGG
1222522 TTGTTTGTCTTTTGG
1 TTGTTTGTCTTTTGG
1222537 TTG
1 TTG
1222540 AAAGTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.06, G:0.27, T:0.67
Consensus pattern (15 bp):
TTGTTTGTCTTTTGG
Found at i:1222608 original size:104 final size:105
Alignment explanation
Indices: 1222418--1222720 Score: 438
Period size: 104 Copynumber: 3.0 Consensus size: 105
1222408 TTGTCTTTGT
1222418 TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT
1 TTTGTCTTTTGGTTGAAAGTAAA-TTGTTCGGTTGCTGCCAATTCTGCTAAAC-GTGTATTCTTT
1222483 AACACTGTGAAATAGTATTTGTCTTTGTTTGTCTTTTGGTTG
64 AACACTGTGAAATAGTATTTGTCTTTGTTTGTCTTTTGGTTG
1222525 TTTGTCTTTTGGTTGAAAGTAAATTGTTCGGTTGCTGCCAATTCTGCTAAAC-TGTATTCTTTAA
1 TTTGTCTTTTGGTTGAAAGTAAATTGTTCGGTTGCTGCCAATTCTGCTAAACGTGTATTCTTTAA
1222589 CACTGTGAAATAGTATTTGTCTTTGTTTGTCTTTT-G--G
66 CACTGTGAAATAGTATTTGTCTTTGTTTGTCTTTTGGTTG
*** *
1222626 -TTG----AAAG-T-AAA-T---TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTTTTTA
1 TTTGTCTTTTGGTTGAAAGTAAATTGTTCGGTTGCTGCCAATTCTGCTAAAC-GTGTATTCTTTA
1222680 ACACTGTGAAATAGTATTTGTCTTTGTTTGTCTTTTGGTTG
65 ACACTGTGAAATAGTATTTGTCTTTGTTTGTCTTTTGGTTG
1222721 AAGTAATCAT
Statistics
Matches: 187, Mismatches: 4, Indels: 22
0.88 0.02 0.10
Matches are distributed among these distances:
90 29 0.16
92 46 0.25
93 2 0.01
94 3 0.02
95 2 0.01
96 1 0.01
100 3 0.02
101 1 0.01
103 1 0.01
104 47 0.25
106 29 0.16
107 23 0.12
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.48
Consensus pattern (105 bp):
TTTGTCTTTTGGTTGAAAGTAAATTGTTCGGTTGCTGCCAATTCTGCTAAACGTGTATTCTTTAA
CACTGTGAAATAGTATTTGTCTTTGTTTGTCTTTTGGTTG
Found at i:1222615 original size:89 final size:91
Alignment explanation
Indices: 1222522--1222726 Score: 371
Period size: 92 Copynumber: 2.3 Consensus size: 91
1222512 TGTCTTTTGG
1222522 TTGTTTGTCTTTTGGTTGAAAGTAAA-TTGTTCGGTTGCTGCCAATTCTGCTAAAC-TGTATTCT
1 TTGTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACGTGTATTCT
1222585 TTAACACTGTGAAATAGTATTTGTCT
66 TTAACACTGTGAAATAGTATTTGTCT
*
1222611 TTGTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTT
1 TTGTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAC-GTGTATTC
1222676 TTTAACACTGTGAAATAGTATTTGTCT
65 TTTAACACTGTGAAATAGTATTTGTCT
1222703 TTGTTTGTCTTTTGGTTG-AAGTAA
1 TTGTTTGTCTTTTGGTTGAAAGTAA
1222727 TCATCCATTC
Statistics
Matches: 112, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
89 26 0.23
90 29 0.26
91 6 0.05
92 51 0.46
ACGTcount: A:0.21, C:0.12, G:0.20, T:0.47
Consensus pattern (91 bp):
TTGTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACGTGTATTCT
TTAACACTGTGAAATAGTATTTGTCT
Found at i:1222689 original size:196 final size:199
Alignment explanation
Indices: 1222342--1222720 Score: 710
Period size: 196 Copynumber: 1.9 Consensus size: 199
1222332 TAGATTGCTT
1222342 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAAC-GTGTATTCTTTAACACTGTGAAATAGTA
1222407 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1222472 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTGTCTTTTGGTTGTTTGTCTTTTGG
130 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTGTCTTTTGGTTGTTTGTCTTTTGG
1222537 TTGAA
195 TTGAA
*
1222542 AGTAAA-TTGTTCGGTTGCTGCCAATTCTGCTAAAC-TGTATTCTTTAACACTGTGAAATAGTAT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACGTGTATTCTTTAACACTGTGAAATAGTAT
1222605 TTGTCTTTG-TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
*
1222669 TGTATTTTTTAACACTGTGAAATAGTATTTGTCTTTGTTTGTCTTTTGGTTG
131 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTGTCTTTTGGTTG
1222721 AAGTAATCAT
Statistics
Matches: 177, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
196 106 0.60
197 37 0.21
199 28 0.16
200 6 0.03
ACGTcount: A:0.21, C:0.13, G:0.20, T:0.47
Consensus pattern (199 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACGTGTATTCTTTAACACTGTGAAATAGTAT
TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTGTCTTTTGGTTGTTTGTCTTTTGGT
TGAA
Found at i:1222794 original size:21 final size:20
Alignment explanation
Indices: 1222770--1222836 Score: 75
Period size: 19 Copynumber: 3.4 Consensus size: 20
1222760 TAGTTTACTT
1222770 TCGCAACACGAAACTTAAAAA
1 TCGCAACACGAAAC-TAAAAA
* *
1222791 TCGCAACGCGAAAC-CAAAA
1 TCGCAACACGAAACTAAAAA
* *
1222810 TCGCAACGCGAAA-TGAAAA
1 TCGCAACACGAAACTAAAAA
1222829 TCGCAACA
1 TCGCAACA
1222837 AAAGAATCGC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 28 0.68
21 13 0.32
ACGTcount: A:0.48, C:0.27, G:0.15, T:0.10
Consensus pattern (20 bp):
TCGCAACACGAAACTAAAAA
Found at i:1222811 original size:19 final size:19
Alignment explanation
Indices: 1222787--1222899 Score: 129
Period size: 19 Copynumber: 6.5 Consensus size: 19
1222777 ACGAAACTTA
1222787 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
**
1222806 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAACC
1222825 AAAATCGCAA--C-AAA--
1 AAAATCGCAACGCGAAACC
*
1222839 AGAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
1222858 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAACC
1222872 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
1222891 AAAATCGCA
1 AAAATCGCA
1222900 TTGCGATTTT
Statistics
Matches: 80, Mismatches: 4, Indels: 20
0.77 0.04 0.19
Matches are distributed among these distances:
14 20 0.25
15 1 0.01
16 6 0.08
17 6 0.08
18 1 0.01
19 46 0.57
ACGTcount: A:0.50, C:0.27, G:0.16, T:0.07
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACC
Found at i:1222845 original size:33 final size:33
Alignment explanation
Indices: 1222806--1222899 Score: 145
Period size: 33 Copynumber: 2.8 Consensus size: 33
1222796 ACGCGAAACC
**
1222806 AAAATCGCAACGCGAAATGAAAATCGCAAC-AA
1 AAAATCGCAACGCGAAACCAAAATCGCAACGAA
*
1222838 AAGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 AA-AATCGCAACGCGAAACCAAAATCGCAACGAA
1222872 AAAATCGCAACGCGAAACCAAAATCGCA
1 AAAATCGCAACGCGAAACCAAAATCGCA
1222900 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 2 0.04
33 52 0.91
34 3 0.05
ACGTcount: A:0.50, C:0.27, G:0.16, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGCGAAACCAAAATCGCAACGAA
Found at i:1222876 original size:14 final size:14
Alignment explanation
Indices: 1222857--1222883 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1222847 AACGCGAAAC
1222857 CAAAATCGCAACGA
1 CAAAATCGCAACGA
1222871 CAAAATCGCAACG
1 CAAAATCGCAACG
1222884 CGAAACCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.30, G:0.15, T:0.07
Consensus pattern (14 bp):
CAAAATCGCAACGA
Found at i:1222897 original size:52 final size:51
Alignment explanation
Indices: 1222786--1222899 Score: 140
Period size: 52 Copynumber: 2.2 Consensus size: 51
1222776 CACGAAACTT
* * *
1222786 AAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACA
1 AAAAATCGCAACGCGAAACCAAAATCGCAACGCAAAATGAAAAGCGAAACA
* *
1222837 AAAGAATCGCAACGCGAAACCAAAATCGCAACGACAAAATCGCAACGCGAAAC-
1 AAA-AATCGCAACGCGAAACCAAAATCGCAACG-CAAAAT-GAAAAGCGAAACA
*
1222890 CAAAATCGCA
1 AAAAATCGCA
1222900 TTGCGATTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
51 3 0.06
52 36 0.67
53 7 0.13
54 8 0.15
ACGTcount: A:0.50, C:0.27, G:0.16, T:0.07
Consensus pattern (51 bp):
AAAAATCGCAACGCGAAACCAAAATCGCAACGCAAAATGAAAAGCGAAACA
Found at i:1222917 original size:19 final size:19
Alignment explanation
Indices: 1222895--1223067 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
1222885 GAAACCAAAA
*
1222895 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1222914 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1222930 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* * *
1222947 TCGCATTACGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1222963 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1222980 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
1222999 TCGCGTTGCGATTTTTGTT
1 TCGCGTTGCGATTTTCATT
* * *
1223018 TCTCTTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATT
*
1223037 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1223057 TCGTGTTGCGA
1 TCGCGTTGCGA
1223068 AAGTAAAACT
Statistics
Matches: 123, Mismatches: 20, Indels: 21
0.75 0.12 0.13
Matches are distributed among these distances:
14 14 0.11
16 11 0.09
17 11 0.09
19 75 0.61
20 12 0.10
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1222936 original size:14 final size:14
Alignment explanation
Indices: 1222917--1222973 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1222907 TTTCATTTCG
1222917 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1222931 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
* *
1222948 CGCATTACGATTCTGT
1 CG--TTGCGATTCTTT
1222964 CGTTGCGATT
1 CGTTGCGATT
1222974 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 15 0.43
16 7 0.20
17 8 0.23
19 5 0.14
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1222942 original size:33 final size:33
Alignment explanation
Indices: 1222900--1222992 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
1222890 CAAAATCGCA
*
1222900 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
* *
1222933 TTGCGATTTTCATTTCGCATTACGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1222966 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1222993 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1223027 original size:38 final size:38
Alignment explanation
Indices: 1222895--1223067 Score: 150
Period size: 33 Copynumber: 4.8 Consensus size: 38
1222885 GAAACCAAAA
*
1222895 TCGCATTGCGATTTTCATTTCGCGTTGCGA-T-TC-TT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* * *
1222930 T--CGTTGCGATTTTCATTTCGCATTACGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* **
1222963 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
** * *
1222999 TCGCGTTGCGATTTTTGTTTCTCTTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* *
1223037 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
1223068 AAGTAAAACT
Statistics
Matches: 112, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
33 54 0.48
34 1 0.01
35 2 0.02
36 2 0.02
38 43 0.38
39 10 0.09
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
Found at i:1225117 original size:19 final size:19
Alignment explanation
Indices: 1225093--1225213 Score: 118
Period size: 19 Copynumber: 6.8 Consensus size: 19
1225083 GCATTATGTT
1225093 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
1225112 GAAATGAAAATCGCAA---
1 GAAATGAAAATCGCAATGC
* * *
1225128 -AGA-GAGAATCGCAAAGC
1 GAAATGAAAATCGCAATGC
*
1225145 AAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
1225162 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
1225178 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
1225197 GGAAATGAAAATCGCAA
1 -GAAATGAAAATCGCAA
1225214 CGAGAGAATC
Statistics
Matches: 84, Mismatches: 7, Indels: 21
0.75 0.06 0.19
Matches are distributed among these distances:
14 20 0.24
15 3 0.04
16 2 0.02
17 1 0.01
18 3 0.04
19 39 0.46
20 16 0.19
ACGTcount: A:0.50, C:0.16, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:1225150 original size:33 final size:33
Alignment explanation
Indices: 1225101--1225193 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
1225091 TTGAAATGAA
1225101 AATCGCAATGCGAAATGAAAATCGCAAAGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAAAGAGAG
* * *
1225134 AATCGCAAAGCAAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAAAGAGAG
1225167 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
1225194 TGCGGAAATG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.49, C:0.17, G:0.22, T:0.12
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAAAGAGAG
Found at i:1225250 original size:19 final size:19
Alignment explanation
Indices: 1225222--1225464 Score: 265
Period size: 19 Copynumber: 13.7 Consensus size: 19
1225212 AACGAGAGAA
*
1225222 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1225241 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1225260 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
1225277 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1225294 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1225313 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1225329 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1225346 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1225365 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
1225382 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1225399 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1225418 TCCGCAGTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
1225436 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
1225452 TCGCATTGCGATT
1 TCGCATTGCGATT
1225465 CTCTCGTTGC
Statistics
Matches: 190, Mismatches: 11, Indels: 46
0.77 0.04 0.19
Matches are distributed among these distances:
14 28 0.15
16 19 0.10
17 20 0.11
18 7 0.04
19 81 0.43
20 35 0.18
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1225304 original size:33 final size:33
Alignment explanation
Indices: 1225246--1225411 Score: 167
Period size: 33 Copynumber: 4.8 Consensus size: 33
1225236 TCATTTCGCA
1225246 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
*
1225280 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
1225316 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
1225351 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
1225385 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
1225412 TTCATTTCCG
Statistics
Matches: 108, Mismatches: 12, Indels: 25
0.74 0.08 0.17
Matches are distributed among these distances:
31 4 0.04
32 6 0.06
33 34 0.31
34 33 0.31
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.07
39 3 0.03
40 9 0.08
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:1225317 original size:105 final size:105
Alignment explanation
Indices: 1225208--1225419 Score: 343
Period size: 105 Copynumber: 2.0 Consensus size: 105
1225198 GAAATGAAAA
1225208 TCGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGAT
1 TCGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGAT
1225273 TCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
66 TCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
** * *** * **
1225313 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGAT
1 TCGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGAT
1225378 TCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
66 TCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1225418 TC
1 TC
1225420 CGCAGTGCGA
Statistics
Matches: 98, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
105 98 1.00
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.43
Consensus pattern (105 bp):
TCGCAACGAGAGAATCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGAT
TCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:1225486 original size:33 final size:33
Alignment explanation
Indices: 1225299--1225478 Score: 152
Period size: 33 Copynumber: 5.2 Consensus size: 33
1225289 TCATTTCGCA
1225299 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1225332 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG
* * * * *
1225369 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
* *
1225404 TTGCGATTTTCATTTCCGCAGTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
1225438 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1225471 TTGCGATT
1 TTGCGATT
1225479 GTAATTTCCG
Statistics
Matches: 115, Mismatches: 17, Indels: 30
0.71 0.10 0.19
Matches are distributed among these distances:
31 4 0.03
32 6 0.05
33 58 0.50
34 16 0.14
35 4 0.03
36 3 0.03
37 2 0.02
38 2 0.02
39 8 0.07
40 3 0.03
41 9 0.08
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:1225493 original size:53 final size:53
Alignment explanation
Indices: 1225228--1225464 Score: 424
Period size: 53 Copynumber: 4.5 Consensus size: 53
1225218 AGAATCGCAA
1225228 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1225281 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1225333 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
* *
1225386 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAGTGCGATTTTCAT-GT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTC-TCGT
*
1225439 TGGGATTTTCATTTCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
1225465 CTCTCGTTGC
Statistics
Matches: 179, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
52 52 0.29
53 126 0.70
54 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (53 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
Found at i:1227986 original size:24 final size:24
Alignment explanation
Indices: 1227952--1227998 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1227942 CTGAAACATC
1227952 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1227976 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1227999 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1228719 original size:20 final size:20
Alignment explanation
Indices: 1228691--1228919 Score: 253
Period size: 20 Copynumber: 11.4 Consensus size: 20
1228681 AAATTTCAGT
* * *
1228691 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1228711 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1228731 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1228751 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1228771 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1228791 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1228811 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1228831 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
1228851 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1228871 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1228891 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1228911 GTTGCGATT
1 GTTGCGATT
1228920 CTGGAAAATC
Statistics
Matches: 185, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
20 184 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1236813 original size:5 final size:5
Alignment explanation
Indices: 1236779--1236828 Score: 82
Period size: 5 Copynumber: 9.6 Consensus size: 5
1236769 ACGGCACGGC
1236779 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG
1236829 TGGTAATACG
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 33 0.75
6 11 0.25
ACGTcount: A:0.00, C:0.20, G:0.56, T:0.24
Consensus pattern (5 bp):
TCGGG
Found at i:1237093 original size:16 final size:16
Alignment explanation
Indices: 1237072--1237102 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1237062 GACGTCTTTT
1237072 AAAACAATTTTAAGAA
1 AAAACAATTTTAAGAA
*
1237088 AAAACATTTTTAAGA
1 AAAACAATTTTAAGA
1237103 CGAAAACTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (16 bp):
AAAACAATTTTAAGAA
Found at i:1239424 original size:40 final size:42
Alignment explanation
Indices: 1239322--1239439 Score: 134
Period size: 40 Copynumber: 2.8 Consensus size: 42
1239312 TTGTTGGTGG
** * * *
1239322 GGATGACACGACTCATACGCAATGAAAAGGTCTGGTCGTTTAAA
1 GGATGACACGACTCATACGTGATGAAGAGATCTGGTCGTGT--A
*
1239366 GG-TGACACGACTCCTACGTGATGAAGAGATCTGGTCG-GT-
1 GGATGACACGACTCATACGTGATGAAGAGATCTGGTCGTGTA
*
1239405 GGATGACACGACTCATACGTGATGAAGAGTTCTGG
1 GGATGACACGACTCATACGTGATGAAGAGATCTGG
1239440 CCATCTTTAG
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 2 0.03
40 30 0.46
42 1 0.02
43 30 0.46
44 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.23
Consensus pattern (42 bp):
GGATGACACGACTCATACGTGATGAAGAGATCTGGTCGTGTA
Found at i:1239716 original size:134 final size:133
Alignment explanation
Indices: 1239366--1239697 Score: 414
Period size: 134 Copynumber: 2.5 Consensus size: 133
1239356 GTCGTTTAAA
* * * *
1239366 GGTGACACGACTCCTACGTGATGAAGAGATCTGGTCGGTGGATGACACGACTCATACGTGATGAA
1 GGTGACACGGCTCCTACATGATGAGGAGATCTGGTCGG-GGATGACACGGCTCATACGTGATGAA
* * * **
1239431 GAGTTCTGGCCATCTTTAGGAATGATGATAACTCGGTTCCTACGTGATGAGGACAGTTGGTTATC
65 GAGTTCTGGCCATCTTTAGAAAGGATGATAACTCGGTTCCTACGTGATGAGGACAGCTAATTATC
*
1239496 TATG
130 TAAG
* * * * *
1239500 GGTGACACGGCTCCTACATGATGAGGAGGTCTGGTCGAGGGATGATACTGCTCATACGCGATAAA
1 GGTGACACGGCTCCTACATGATGAGGAGATCTGGTCG-GGGATGACACGGCTCATACGTGATGAA
* *
1239565 GAGTTCTGGCCATCTTTATAAAGGGTGATAACTCGGTTCCTACGTGATGAGGAC-GACTAATTAT
65 GAGTTCTGGCCATCTTTAGAAAGGATGATAACTCGGTTCCTACGTGATGAGGACAG-CTAATTAT
1239629 CTAAG
129 CTAAG
* ** * * *
1239634 GTTGATGCGGCTTCTACATGATGAGGAGATCTGGTCAGGGGATGACACGGTTCCTACGTGATGA
1 GGTGACACGGCTCCTACATGATGAGGAGATCTGGTC-GGGGATGACACGGCTCATACGTGATGA
1239698 TGATGGCTGA
Statistics
Matches: 167, Mismatches: 28, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
133 1 0.01
134 164 0.98
135 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (133 bp):
GGTGACACGGCTCCTACATGATGAGGAGATCTGGTCGGGGATGACACGGCTCATACGTGATGAAG
AGTTCTGGCCATCTTTAGAAAGGATGATAACTCGGTTCCTACGTGATGAGGACAGCTAATTATCT
AAG
Found at i:1239860 original size:30 final size:30
Alignment explanation
Indices: 1239826--1239932 Score: 117
Period size: 30 Copynumber: 3.6 Consensus size: 30
1239816 GAGACAAAAT
* * * *
1239826 GTGTTTCAAGGGAAACGATCTCAAAGGTGG
1 GTGTTTCAAGAGAAACGAACTCAAAGATAG
*
1239856 GTGTTTCAAGAGAAACTAACTCAAAGATAG
1 GTGTTTCAAGAGAAACGAACTCAAAGATAG
* **
1239886 GTGTTTCAAAAGAAAC-AACTCAAAGATTT
1 GTGTTTCAAGAGAAACGAACTCAAAGATAG
* *
1239915 TTGTTTCAAAAGAAACGA
1 GTGTTTCAAGAGAAACGA
1239933 CTTGAATATT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
29 26 0.39
30 41 0.61
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.25
Consensus pattern (30 bp):
GTGTTTCAAGAGAAACGAACTCAAAGATAG
Found at i:1239919 original size:29 final size:29
Alignment explanation
Indices: 1239857--1240141 Score: 173
Period size: 29 Copynumber: 9.5 Consensus size: 29
1239847 CAAAGGTGGG
* ***
1239857 TGTTTCAAGAGAAACTAACTCAAAGATAGG
1 TGTTTCAAAAGAAAC-AACTCAAAGATTTT
1239887 TGTTTCAAAAGAAACAACTCAAAGATTTT
1 TGTTTCAAAAGAAACAACTCAAAGATTTT
* ** *
1239916 TGTTTCAAAAGAAACGACTTGAATATTTT
1 TGTTTCAAAAGAAACAACTCAAAGATTTT
** *** * * *
1239945 T-TCACGAAAAATTGTCTCAAGC-GAGAGAAAATTT
1 TGTTTC--AAAA--GAAACAA-CTCA-A-AGATTTT
* *
1239979 TGTTTCAAAATAAACAGACTCAAAG-GTTT
1 TGTTTCAAAAGAAACA-ACTCAAAGATTTT
1240008 T-TTTCAAAAGAAACAACTCAAAGATTTT
1 TGTTTCAAAAGAAACAACTCAAAGATTTT
* * *
1240036 TATTTCAAAAGAAACAACTCACAGACTTT
1 TGTTTCAAAAGAAACAACTCAAAGATTTT
*
1240065 TGTTTCAAGAGAAACAGACTCAAAGATAGGTTT
1 TGTTTCAAAAGAAACA-ACTCAAAGAT---TTT
** *
1240098 TGTTTCAAGTGAAACAATCTCAAAGATGTT
1 TGTTTCAAAAGAAACAA-CTCAAAGATTTT
* *
1240128 TGTTTTAAGAGAAA
1 TGTTTCAAAAGAAA
1240142 TTGTCTCAAA
Statistics
Matches: 199, Mismatches: 39, Indels: 34
0.73 0.14 0.12
Matches are distributed among these distances:
27 8 0.04
28 19 0.10
29 80 0.40
30 41 0.21
31 4 0.02
32 6 0.03
33 33 0.17
34 6 0.03
35 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (29 bp):
TGTTTCAAAAGAAACAACTCAAAGATTTT
Found at i:1240299 original size:68 final size:65
Alignment explanation
Indices: 1240095--1240329 Score: 244
Period size: 68 Copynumber: 3.5 Consensus size: 65
1240085 CAAAGATAGG
* * *
1240095 TTTTGTTTCAAGTGAAACA-ATCTCAAAGATGTTTGTTTTAAGAGAAAT-TGTCTCAAAAGAGAC
1 TTTTGTTTCAA-AGAAACAGA-CTCAAAGATTTTTG-TTTAAAAG-AATCTGTCTCAAAAGAGAC
1240158 AAAA
62 AAAA
* * * * *
1240162 CTTTGTTTTCATAA-AAATAGACTCAAAGATTTTTCTTTAAACGGAA-CTGTCTCATAAGAGACA
1 TTTTG-TTTCA-AAGAAACAGACTCAAAGATTTTTGTTTAAA-AGAATCTGTCTCAAAAGAGACA
1240225 AAA
63 AAA
*
1240228 TTTTGTTTCCAAAGAAACAGACTCAAAGATTCTTTGTTTCAAAAGAATCTTTCTCAAAAGAGACA
1 TTTTGTTT-CAAAGAAACAGACTCAAAGATT-TTTGTTT-AAAAGAATCTGTCTCAAAAGAGACA
1240293 AAA
63 AAA
* *
1240296 TTTTGCTATCAAAGAAACATACTCAAAGATTTTT
1 TTTTG-TTTCAAAGAAACAGACTCAAAGATTTTT
1240330 CATTTTGTTT
Statistics
Matches: 141, Mismatches: 16, Indels: 22
0.79 0.09 0.12
Matches are distributed among these distances:
65 5 0.04
66 47 0.33
67 33 0.23
68 53 0.38
69 3 0.02
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (65 bp):
TTTTGTTTCAAAGAAACAGACTCAAAGATTTTTGTTTAAAAGAATCTGTCTCAAAAGAGACAAAA
Found at i:1240335 original size:36 final size:36
Alignment explanation
Indices: 1240295--1240367 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
1240285 AAGAGACAAA
1240295 ATTTTGCTATCAA-AGAAACATACTCAAAGATTTTTC
1 ATTTTG-TATCAAGAGAAACATACTCAAAGATTTTTC
* * *
1240331 ATTTTGTTTTAAGTGAAACATACTCAAAGATTTTTC
1 ATTTTGTATCAAGAGAAACATACTCAAAGATTTTTC
1240367 A
1 A
1240368 AGAAAATCTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 4 0.12
36 29 0.88
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.40
Consensus pattern (36 bp):
ATTTTGTATCAAGAGAAACATACTCAAAGATTTTTC
Found at i:1240640 original size:211 final size:208
Alignment explanation
Indices: 1240376--1240802 Score: 576
Period size: 211 Copynumber: 2.0 Consensus size: 208
1240366 CAAGAAAATC
**
1240376 TGTCTCAAGAAAGACAAAGTTTTGTTTTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTA
1 TGTCTCAAGAAAGACAAAGTTTTGTTTTAAGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTA
* *
1240441 ATGTGAAACAAATTCAAAATTTGTATTCTCAAAGG-AAAAATGTCTCAAACGAGACGAAATTTAT
66 ATGTGAAACAAATTCAAAATTTGTA-TATCAAAGGAAAAAATGTCTCAAACAAGACGAAATTTAT
* * * *
1240505 TTTGAA-AGAAATAACAATCTCAAGTGAGATTAATTTTTGTTTCAA-GTGAATCAAATTCGAAAT
130 TTT-AAGAG-AA-AACAATCTCAAATGAGATCAA-CTTTGTTT-AATGTGAAACAAATTCGAAAT
1240568 TTGTATATCAAAGGAAAAAA
190 TTGTATATCAAAGG-AAAAA
* * *
1240588 TGTCTCAAGCAAGATAAAG-TTTGTTTTAAGAGAAAGCGATCTCTAA-TGAGATCAACTTTGTTT
1 TGTCTCAAGAAAGACAAAGTTTTGTTTTAAGAGAAAACGATCTC-AAGTGAGATCAACTTTGTTT
** * * *
1240651 AATGTGAAACAAATTTGAAATTTGTATATCAAAGGAAAAAATGTCTCAAGCAAGACGAAGTTTGT
65 AATGTGAAACAAATTCAAAATTTGTATATCAAAGGAAAAAATGTCTCAAACAAGACGAAATTTAT
* *
1240716 TTTAAGAGAAAGCGATCTCAAATGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTA
130 TTTAAGAGAAAACAATCTCAAATGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTA
*
1240781 TCTCAAAGGAAAAA
195 TATCAAAGGAAAAA
1240795 TGTCTCAA
1 TGTCTCAA
1240803 ATGAGACGAA
Statistics
Matches: 192, Mismatches: 19, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
207 15 0.08
208 37 0.19
209 17 0.09
210 12 0.06
211 92 0.48
212 19 0.10
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (208 bp):
TGTCTCAAGAAAGACAAAGTTTTGTTTTAAGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTA
ATGTGAAACAAATTCAAAATTTGTATATCAAAGGAAAAAATGTCTCAAACAAGACGAAATTTATT
TTAAGAGAAAACAATCTCAAATGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTAT
ATCAAAGGAAAAA
Found at i:1240676 original size:104 final size:103
Alignment explanation
Indices: 1240376--1240802 Score: 556
Period size: 104 Copynumber: 4.1 Consensus size: 103
1240366 CAAGAAAATC
* **
1240376 TGTCTCAAGAAAGACAAAGTTTTGTTTTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTA
1 TGTCTCAAGCAAGACAAAG-TTTGTTTTAAGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTA
* *
1240441 ATGTGAAACAAATTCAAAATTTGTATTCTCAAAGGAAAAA
65 ATGTGAAACAAATTCGAAATTTGTA-TATCAAAGGAAAAA
* * * * * *
1240481 TGTCTCAAACGAGACGAAA-TTTATTTTGAA-AGAAATAACAATCTCAAGTGAGATTAATTTTTG
1 TGTCTCAAGCAAGAC-AAAGTTTGTTTT-AAGAG-AA-AACGATCTCAAGTGAGATCAA-CTTTG
*
1240544 TTTCAA-GTGAATCAAATTCGAAATTTGTATATCAAAGGAAAAAA
61 TTT-AATGTGAAACAAATTCGAAATTTGTATATCAAAGG-AAAAA
* *
1240588 TGTCTCAAGCAAGATAAAGTTTGTTTTAAGAGAAAGCGATCTCTAA-TGAGATCAACTTTGTTTA
1 TGTCTCAAGCAAGACAAAGTTTGTTTTAAGAGAAAACGATCTC-AAGTGAGATCAACTTTGTTTA
*
1240652 ATGTGAAACAAATTTGAAATTTGTATATCAAAGGAAAAAA
65 ATGTGAAACAAATTCGAAATTTGTATATCAAAGG-AAAAA
* * *
1240692 TGTCTCAAGCAAGACGAAGTTTGTTTTAAGAGAAAGCGATCTCAAATGAGATCAACTTTGTTTAA
1 TGTCTCAAGCAAGACAAAGTTTGTTTTAAGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAA
*
1240757 TGTGAAACAAATTCGAAATTTGTATCTCAAAGGAAAAA
66 TGTGAAACAAATTCGAAATTTGTATATCAAAGGAAAAA
1240795 TGTCTCAA
1 TGTCTCAA
1240803 ATGAGACGAA
Statistics
Matches: 284, Mismatches: 26, Indels: 26
0.85 0.08 0.08
Matches are distributed among these distances:
103 17 0.06
104 143 0.50
105 29 0.10
106 39 0.14
107 54 0.19
108 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (103 bp):
TGTCTCAAGCAAGACAAAGTTTGTTTTAAGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAA
TGTGAAACAAATTCGAAATTTGTATATCAAAGGAAAAA
Found at i:1240901 original size:72 final size:72
Alignment explanation
Indices: 1240789--1240930 Score: 205
Period size: 72 Copynumber: 2.0 Consensus size: 72
1240779 TATCTCAAAG
* *
1240789 GAAAAATGTCTCAAATGAGACGAAATTTGTTTTGAAAGAAATTGTCTCAAGCGAAAC-AAAATTT
1 GAAAAATGTCTCAAACGAGACAAAATTTGTTTTGAAAGAAATTGTCTCAAGCGAAACAAAAATTT
1240853 ATTTTTA
66 ATTTTTA
* * * *
1240860 GAAAACTGTCTCAAGCGAGACAAAAATTTGTTTTGAGAGAAATTGTCTCAAGCGAGACAAAAATT
1 GAAAAATGTCTCAAACGAGAC-AAAATTTGTTTTGAAAGAAATTGTCTCAAGCGAAACAAAAATT
*
1240925 TGTTTT
65 TATTTT
1240931 AAAATTCTCA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
71 18 0.29
72 33 0.53
73 11 0.18
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (72 bp):
GAAAAATGTCTCAAACGAGACAAAATTTGTTTTGAAAGAAATTGTCTCAAGCGAAACAAAAATTT
ATTTTTA
Found at i:1240912 original size:37 final size:37
Alignment explanation
Indices: 1240811--1240930 Score: 181
Period size: 37 Copynumber: 3.3 Consensus size: 37
1240801 AAATGAGACG
* *
1240811 AAATTTGTTTTGAAAGAAATTGTCTCAAGCGAAAC-A
1 AAATTTGTTTTGAGAGAAATTGTCTCAAGCGAGACAA
* * *
1240847 AAATTTATTTTTAGA-AAACTGTCTCAAGCGAGACAA
1 AAATTTGTTTTGAGAGAAATTGTCTCAAGCGAGACAA
1240883 AAATTTGTTTTGAGAGAAATTGTCTCAAGCGAGACAA
1 AAATTTGTTTTGAGAGAAATTGTCTCAAGCGAGACAA
1240920 AAATTTGTTTT
1 AAATTTGTTTT
1240931 AAAATTCTCA
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
35 17 0.23
36 26 0.35
37 31 0.42
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (37 bp):
AAATTTGTTTTGAGAGAAATTGTCTCAAGCGAGACAA
Found at i:1241546 original size:33 final size:32
Alignment explanation
Indices: 1241494--1241561 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
1241484 AGAAATCTTC
* * *
1241494 GTTGAATTCCAAGATATGCCTCCAATATTCGAT
1 GTTGAATTCCAAGAGATGCC-CCAACATTCAAT
1241527 GTTGAATCTCCAA-AGATGCCCCAACATTCAAT
1 GTTGAAT-TCCAAGAGATGCCCCAACATTCAAT
1241559 GTT
1 GTT
1241562 TCTTACTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 13 0.42
33 13 0.42
34 5 0.16
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (32 bp):
GTTGAATTCCAAGAGATGCCCCAACATTCAAT
Found at i:1242616 original size:15 final size:13
Alignment explanation
Indices: 1242592--1242677 Score: 61
Period size: 14 Copynumber: 6.2 Consensus size: 13
1242582 TTGTTCTTTG
1242592 TTTT-TCTTTGCTT
1 TTTTCTCTTTG-TT
1242605 CTTTTCTCTTTGTT
1 -TTTTCTCTTTGTT
* *
1242619 TTTGCTCTTTTTTTTT
1 TTT--TC-TCTTTGTT
1242635 TTTTGCTCTTTG-T
1 TTTT-CTCTTTGTT
1242648 TTTT-TCTTTGCTT
1 TTTTCTCTTTG-TT
1242661 CTTTTCTCTTTGTT
1 -TTTTCTCTTTGTT
1242675 TTT
1 TTT
1242678 CTGTTCTCTT
Statistics
Matches: 59, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 6 0.10
13 12 0.20
14 17 0.29
15 15 0.25
16 9 0.15
ACGTcount: A:0.00, C:0.16, G:0.08, T:0.76
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:1242684 original size:22 final size:25
Alignment explanation
Indices: 1242586--1242677 Score: 87
Period size: 26 Copynumber: 3.4 Consensus size: 25
1242576 CTCTTTTTGT
1242586 TCTTTG-TTTTTCTTTGCTTCTTTTC
1 TCTTTGTTTTTTC-TTGCTTCTTTTC
** *
1242611 TCTTTGTTTTTGCTCTTTTTTTTTTTTTGC
1 TCTTTGTTTTT--TC--TTGCTTCTTTT-C
1242641 TCTTTGTTTTTTCTTTGCTTCTTTTC
1 TCTTTGTTTTTTC-TTGCTTCTTTTC
1242667 TCTTTGTTTTT
1 TCTTTGTTTTT
1242678 CTGTTCTCTT
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
25 6 0.11
26 16 0.29
27 9 0.16
28 4 0.07
29 9 0.16
30 12 0.21
ACGTcount: A:0.00, C:0.16, G:0.09, T:0.75
Consensus pattern (25 bp):
TCTTTGTTTTTTCTTGCTTCTTTTC
Found at i:1244005 original size:12 final size:12
Alignment explanation
Indices: 1243967--1244020 Score: 72
Period size: 12 Copynumber: 4.2 Consensus size: 12
1243957 CTTAAAAATA
1243967 AAATACAGATGC
1 AAATACAGATGC
*
1243979 AAAATGCAAAGATGC
1 -AAAT--ACAGATGC
1243994 AAATACAGATGC
1 AAATACAGATGC
1244006 AAATACAGATGC
1 AAATACAGATGC
1244018 AAA
1 AAA
1244021 AATGTTGATC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
12 22 0.59
13 4 0.11
14 4 0.11
15 7 0.19
ACGTcount: A:0.54, C:0.15, G:0.17, T:0.15
Consensus pattern (12 bp):
AAATACAGATGC
Found at i:1246534 original size:23 final size:23
Alignment explanation
Indices: 1246508--1246567 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
1246498 AATCTTATAT
1246508 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* *
1246531 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
*
1246554 GGCACTTTGGTGCA
1 GGCACTTCGGTGCA
1246568 TTTATATGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:1250354 original size:123 final size:123
Alignment explanation
Indices: 1250136--1250363 Score: 343
Period size: 123 Copynumber: 1.9 Consensus size: 123
1250126 TAATTGTTAG
* * *
1250136 AAAAATTAAAGGTTAACAGAGTTCGAACCATAATAATGTAGATCATACTCCGGATCAGGTCACCA
1 AAAAATTAAAGGTTAACAGAGTCCGAACCATAATAATGCAGATCATACCCCGGATCAGGTCACCA
* *
1250201 CAAAGCCGAATCAAATATTATAAATAATAAATAAATAAATGTTATAATGCAATAAAAT
66 CAAAGCCGAATCAAATAATAGAAATAATAAATAAATAAATGTTATAATGCAATAAAAT
* * *
1250259 AAAAATTAATA-GTTAACAGAGTCCGAACCATAATAATGCGGATTATACCCCGGATCGGGTCACC
1 AAAAATTAA-AGGTTAACAGAGTCCGAACCATAATAATGCAGATCATACCCCGGATCAGGTCACC
*
1250323 AC-AAGACCGAATCGAATAATAGAAATAATAAATAAATAAAT
65 ACAAAG-CCGAATCAAATAATAGAAATAATAAATAAATAAAT
1250364 AAAGGTTAGA
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
122 3 0.03
123 90 0.96
124 1 0.01
ACGTcount: A:0.48, C:0.15, G:0.14, T:0.23
Consensus pattern (123 bp):
AAAAATTAAAGGTTAACAGAGTCCGAACCATAATAATGCAGATCATACCCCGGATCAGGTCACCA
CAAAGCCGAATCAAATAATAGAAATAATAAATAAATAAATGTTATAATGCAATAAAAT
Found at i:1250439 original size:29 final size:29
Alignment explanation
Indices: 1250377--1250440 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
1250367 GGTTAGAGTG
*
1250377 CAATAAAATAAAAGTTAGTGATTAATATA
1 CAATAAAATAAAAGTTAGTGATTAAAATA
*
1250406 CAATAAAATAAAATTTAGT-AGTTAGAAATA
1 CAATAAAATAAAAGTTAGTGA-TTA-AAATA
1250436 -AATAA
1 CAATAA
1250441 CATAGCAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 1 0.03
29 26 0.84
30 4 0.13
ACGTcount: A:0.58, C:0.03, G:0.09, T:0.30
Consensus pattern (29 bp):
CAATAAAATAAAAGTTAGTGATTAAAATA
Found at i:1258859 original size:55 final size:55
Alignment explanation
Indices: 1258775--1258888 Score: 228
Period size: 55 Copynumber: 2.1 Consensus size: 55
1258765 CACCCTTCTT
1258775 CAATGGAGAAATATACACATTGGAAGAATAATATGATGTACTTTATTCAATCCTA
1 CAATGGAGAAATATACACATTGGAAGAATAATATGATGTACTTTATTCAATCCTA
1258830 CAATGGAGAAATATACACATTGGAAGAATAATATGATGTACTTTATTCAATCCTA
1 CAATGGAGAAATATACACATTGGAAGAATAATATGATGTACTTTATTCAATCCTA
1258885 CAAT
1 CAAT
1258889 ACAATCTAGG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 59 1.00
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (55 bp):
CAATGGAGAAATATACACATTGGAAGAATAATATGATGTACTTTATTCAATCCTA
Found at i:1263303 original size:27 final size:28
Alignment explanation
Indices: 1263255--1263313 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
1263245 GGCTTAGAGG
* * *
1263255 TATTTTAGATCATTTTATACTTTAGGGA
1 TATTTTAGATCATTGTACACTTCAGGGA
*
1263283 TATTTT-GGTCATTGTACACTTCAGGGA
1 TATTTTAGATCATTGTACACTTCAGGGA
1263310 TATT
1 TATT
1263314 CTATACTTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.47
Consensus pattern (28 bp):
TATTTTAGATCATTGTACACTTCAGGGA
Found at i:1264328 original size:14 final size:14
Alignment explanation
Indices: 1264309--1264402 Score: 107
Period size: 14 Copynumber: 6.6 Consensus size: 14
1264299 AAGTCAACGG
1264309 GTTGACTCAGACGA
1 GTTGACTCAGACGA
*
1264323 GTTGACTCAGATGA
1 GTTGACTCAGACGA
*
1264337 GTTGACTCAGACGG
1 GTTGACTCAGACGA
*
1264351 GTTGACTCATACCGA
1 GTTGACTCAGA-CGA
** *
1264366 GTTGACTTGGACGG
1 GTTGACTCAGACGA
*
1264380 GTTGACTCGGACCGA
1 GTTGACTCAGA-CGA
1264395 GTTGACTC
1 GTTGACTC
1264403 GATGACTGGA
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
14 47 0.70
15 20 0.30
ACGTcount: A:0.22, C:0.21, G:0.31, T:0.26
Consensus pattern (14 bp):
GTTGACTCAGACGA
Found at i:1264378 original size:29 final size:29
Alignment explanation
Indices: 1264309--1264402 Score: 127
Period size: 29 Copynumber: 3.3 Consensus size: 29
1264299 AAGTCAACGG
* *
1264309 GTTGACTCAGACGAGTTGACTCAGA-TGA
1 GTTGACTCAGACGGGTTGACTCAGACCGA
*
1264337 GTTGACTCAGACGGGTTGACTCATACCGA
1 GTTGACTCAGACGGGTTGACTCAGACCGA
** *
1264366 GTTGACTTGGACGGGTTGACTCGGACCGA
1 GTTGACTCAGACGGGTTGACTCAGACCGA
1264395 GTTGACTC
1 GTTGACTC
1264403 GATGACTGGA
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 23 0.40
29 34 0.60
ACGTcount: A:0.22, C:0.21, G:0.31, T:0.26
Consensus pattern (29 bp):
GTTGACTCAGACGGGTTGACTCAGACCGA
Found at i:1264384 original size:43 final size:42
Alignment explanation
Indices: 1264305--1264402 Score: 115
Period size: 43 Copynumber: 2.3 Consensus size: 42
1264295 GTCAAAGTCA
*
1264305 ACGGGTTGACTCAGACGAGTTGACTCAGATGAGTTGACTCAG
1 ACGGGTTGACTCAGACGAGTTGACTCAGACGAGTTGACTCAG
* ** * *
1264347 ACGGGTTGACTCATACCGAGTTGACTTGGACGGGTTGACTCGG
1 ACGGGTTGACTCAGA-CGAGTTGACTCAGACGAGTTGACTCAG
*
1264390 ACCGAGTTGACTC
1 A-CGGGTTGACTC
1264403 GATGACTGGA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 14 0.30
43 23 0.49
44 10 0.21
ACGTcount: A:0.22, C:0.21, G:0.32, T:0.24
Consensus pattern (42 bp):
ACGGGTTGACTCAGACGAGTTGACTCAGACGAGTTGACTCAG
Found at i:1264917 original size:29 final size:29
Alignment explanation
Indices: 1264877--1264946 Score: 131
Period size: 29 Copynumber: 2.4 Consensus size: 29
1264867 TCTTAATGTA
1264877 ATCATTCAGCGCTGAATGCTGAACGGTTC
1 ATCATTCAGCGCTGAATGCTGAACGGTTC
1264906 ATCATTCAGCGCTGAATGCTGAACGGTTC
1 ATCATTCAGCGCTGAATGCTGAACGGTTC
*
1264935 AGCATTCAGCGC
1 ATCATTCAGCGC
1264947 ATTTGTTTCG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (29 bp):
ATCATTCAGCGCTGAATGCTGAACGGTTC
Found at i:1265002 original size:23 final size:23
Alignment explanation
Indices: 1264972--1265037 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
1264962 CTGAATGATT
*
1264972 CAGTGCTGATTGATTCAGCAAAA
1 CAGTGCTGAATGATTCAGCAAAA
*
1264995 CAGTGCTGACTGATTCAGCAAAA
1 CAGTGCTGAATGATTCAGCAAAA
* * *
1265018 CAATACTAAATGATTCAGCA
1 CAGTGCTGAATGATTCAGCA
1265038 CAGAAGTACA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (23 bp):
CAGTGCTGAATGATTCAGCAAAA
Found at i:1266785 original size:18 final size:18
Alignment explanation
Indices: 1266750--1266788 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1266740 TTTAGAATTT
*
1266750 TATATAATTTTTAAAAAA
1 TATATAATTTTAAAAAAA
*
1266768 TATATAATTTAAAGAAAAA
1 TATATAATTTTAA-AAAAA
1266787 TA
1 TA
1266789 AAAAATTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
TATATAATTTTAAAAAAA
Found at i:1272866 original size:27 final size:27
Alignment explanation
Indices: 1272828--1272882 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
1272818 TCATACTTAG
1272828 CTCGAAGAGAATAGATGCATCAATTGT
1 CTCGAAGAGAATAGATGCATCAATTGT
*
1272855 CTCGAAGAGAATAGATGCATCGATTGT
1 CTCGAAGAGAATAGATGCATCAATTGT
1272882 C
1 C
1272883 AGGCTAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (27 bp):
CTCGAAGAGAATAGATGCATCAATTGT
Found at i:1282291 original size:43 final size:41
Alignment explanation
Indices: 1282242--1282462 Score: 187
Period size: 43 Copynumber: 5.2 Consensus size: 41
1282232 AGAACAAAAC
*
1282242 ACGCCGCAATAGGTGAAGAGATATAGCGGCGTTTTTTGAACAA
1 ACGCCGCAAAAGGT-AA-AGATATAGCGGCGTTTTTTGAACAA
* ** *
1282285 ACGCCGCAAAAGGTCGATATCTATAGCGGTG-TTTTT-AACAA
1 ACGCCGCAAAAGGT--AAAGATATAGCGGCGTTTTTTGAACAA
* * *
1282326 ACACCGCAAAAGGTCAAGATATAGCGGCGTTTTCTAGATACAA
1 ACGCCGCAAAAGGTAAAGATATAGCGGCGTTTT-TTGA-ACAA
* **
1282369 ACGCCGCAAAAGTCTAAATCTATAGCGGCGTTTTTT-AACAA
1 ACGCCGCAAAAG-GTAAAGATATAGCGGCGTTTTTTGAACAA
* * * * *
1282410 ACGACGTAAAAGGTCAGGTATATAGCGGTGTTTTTTGATACAA
1 ACGCCGCAAAAGGTAAAG-ATATAGCGGCGTTTTTTGA-ACAA
*
1282453 ACGTCGCAAA
1 ACGCCGCAAA
1282463 TATCTAATTT
Statistics
Matches: 141, Mismatches: 28, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
39 10 0.07
40 5 0.04
41 48 0.34
42 8 0.06
43 51 0.36
44 19 0.13
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.25
Consensus pattern (41 bp):
ACGCCGCAAAAGGTAAAGATATAGCGGCGTTTTTTGAACAA
Found at i:1282336 original size:41 final size:42
Alignment explanation
Indices: 1282263--1282454 Score: 164
Period size: 41 Copynumber: 4.5 Consensus size: 42
1282253 GGTGAAGAGA
*
1282263 TATAGCGGCGTTTTTTGAACAAACGCCGCAAAAGGTCGATATC
1 TATAGCGGCG-TTTTTGAACAAACACCGCAAAAGGTCGATATC
* **
1282306 TATAGCGGTGTTTTT-AACAAACACCGCAAAAGGTC-A-AGA
1 TATAGCGGCGTTTTTGAACAAACACCGCAAAAGGTCGATATC
* * *
1282345 TATAGCGGCGTTTTCTAGATACAAACGCCGCAAAA-GTCTAAATC
1 TATAGCGGCGTTTT-T-GA-ACAAACACCGCAAAAGGTCGATATC
* * *
1282389 TATAGCGGCGTTTTTTAACAAACGA-CGTAAAAGGTCAGGTA--
1 TATAGCGGCGTTTTTGAACAAAC-ACCGCAAAAGGTC-GATATC
*
1282430 TATAGCGGTGTTTTTTGATACAAAC
1 TATAGCGGCG-TTTTTGA-ACAAAC
1282455 GTCGCAAATA
Statistics
Matches: 122, Mismatches: 16, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
39 14 0.11
40 2 0.02
41 40 0.33
42 19 0.16
43 32 0.26
44 15 0.12
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (42 bp):
TATAGCGGCGTTTTTGAACAAACACCGCAAAAGGTCGATATC
Found at i:1282404 original size:84 final size:83
Alignment explanation
Indices: 1282260--1282462 Score: 277
Period size: 84 Copynumber: 2.4 Consensus size: 83
1282250 ATAGGTGAAG
* *
1282260 AGATATAGCGGCGTTTTTTGA-ACAAACGCCGCAAAAGGTCGATATCTATAGCGGTGTTTTTAAC
1 AGATATAGCGGCGTTTTTTGATACAAACGCCGCAAAAGGTCGAAATCTATAGCGGCGTTTTTAAC
1282324 AAAC-ACCGCAAAAGGTCA
66 AAACGA-CGCAAAAGGTCA
* *
1282342 AGATATAGCGGCGTTTTCTAGATACAAACGCCGCAAAA-GTCTAAATCTATAGCGGCGTTTTTTA
1 AGATATAGCGGCGTTTT-TTGATACAAACGCCGCAAAAGGTCGAAATCTATAGCGGCG-TTTTTA
*
1282406 ACAAACGACGTAAAAGGTCA
64 ACAAACGACGCAAAAGGTCA
* * *
1282426 GGTATATAGCGGTGTTTTTTGATACAAACGTCGCAAA
1 AG-ATATAGCGGCGTTTTTTGATACAAACGCCGCAAA
1282463 TATCTAATTT
Statistics
Matches: 107, Mismatches: 9, Indels: 8
0.86 0.07 0.06
Matches are distributed among these distances:
82 17 0.16
83 19 0.18
84 56 0.52
85 15 0.14
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (83 bp):
AGATATAGCGGCGTTTTTTGATACAAACGCCGCAAAAGGTCGAAATCTATAGCGGCGTTTTTAAC
AAACGACGCAAAAGGTCA
Found at i:1290875 original size:41 final size:43
Alignment explanation
Indices: 1290776--1290879 Score: 124
Period size: 44 Copynumber: 2.4 Consensus size: 43
1290766 CGTTTATAAT
* * * *
1290776 AAAAACGCCGCTAATGTACATGACTATTGGGGCCTTTATTGCAA
1 AAAAACGCCACTAAAGTACATGACTATTGCGGCCATTATT-CAA
*
1290820 AAAAATGCCACTAAAGTACATGACTATTGCGG-CATT-TT-AA
1 AAAAACGCCACTAAAGTACATGACTATTGCGGCCATTATTCAA
1290860 CAAAAACGCCACTAAAGTAC
1 -AAAAACGCCACTAAAGTAC
1290880 GAGTCTATAG
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
40 2 0.04
41 18 0.34
42 2 0.04
43 3 0.06
44 28 0.53
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.24
Consensus pattern (43 bp):
AAAAACGCCACTAAAGTACATGACTATTGCGGCCATTATTCAA
Found at i:1290906 original size:41 final size:41
Alignment explanation
Indices: 1290861--1290957 Score: 131
Period size: 41 Copynumber: 2.4 Consensus size: 41
1290851 GCATTTTAAC
* *
1290861 AAAAACGCCACTAAAGTACGAGTCTATAGCGATGTTTGCAT
1 AAAAACGCCACTAAAGTAAGAGTCTATAGCGACGTTTGCAT
* * * *
1290902 AAAAACGCCACTAAAGTAAGAGTCTTTCGCGGCGTTTTCAT
1 AAAAACGCCACTAAAGTAAGAGTCTATAGCGACGTTTGCAT
*
1290943 ACAAACGCCACTAAA
1 AAAAACGCCACTAAA
1290958 CATTTTGATT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.23
Consensus pattern (41 bp):
AAAAACGCCACTAAAGTAAGAGTCTATAGCGACGTTTGCAT
Found at i:1291130 original size:41 final size:40
Alignment explanation
Indices: 1291068--1291196 Score: 120
Period size: 41 Copynumber: 3.2 Consensus size: 40
1291058 CGTTTGTGTT
* * *
1291068 TAAAAACACCGCTAAAGTACGAGTCTATAGCGACACTTTTTA
1 TAAAAACACCACTAAAGTACGAGTATATAGCG--ACTTTGTA
*
1291110 TAAAAA-ACCACTAAAGTACGAGTATATATCGACTTTGTA
1 TAAAAACACCACTAAAGTACGAGTATATAGCGACTTTGTA
* * * *
1291149 TAAAAATGA-CACTAACA-TATGAGTATATAGCGGCGTTTTTA
1 TAAAAA-CACCACTAA-AGTACGAGTATATAGCGAC-TTTGTA
1291190 TAAAAAC
1 TAAAAAC
1291197 TCCGCTAAGG
Statistics
Matches: 74, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
39 13 0.18
40 20 0.27
41 35 0.47
42 6 0.08
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (40 bp):
TAAAAACACCACTAAAGTACGAGTATATAGCGACTTTGTA
Found at i:1291262 original size:41 final size:40
Alignment explanation
Indices: 1291217--1291337 Score: 95
Period size: 41 Copynumber: 3.0 Consensus size: 40
1291207 TACAACTATG
1291217 TTGCGGCGTTTGTTGAAAAATGCCACTATAGATAAACCTT
1 TTGCGGCGTTTGTTGAAAAATGCCACTATAGATAAACCTT
* * *
1291257 ATTGCGGCATTT-TT-ATATAAATGCCGCTAAAG-TAATACTCTT
1 -TTGCGGCGTTTGTTGA-A-AAATGCCACTATAGATAA-AC-CTT
** * * * *
1291299 TAACGGTGTTTGTTGAGAAACGCCACTATAGATGAACCT
1 TTGCGGCGTTTGTTGAAAAATGCCACTATAGATAAACCT
1291338 ATTACTTCGT
Statistics
Matches: 61, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
39 1 0.02
40 8 0.13
41 44 0.72
42 7 0.11
43 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (40 bp):
TTGCGGCGTTTGTTGAAAAATGCCACTATAGATAAACCTT
Found at i:1291264 original size:82 final size:82
Alignment explanation
Indices: 1291178--1291337 Score: 191
Period size: 82 Copynumber: 2.0 Consensus size: 82
1291168 TGAGTATATA
* * * *
1291178 GCGGCGTTTTTATAAAAACT-CCGCTAAGGTACA-ACTATGTT-GCGGCGTTTGTTGAAAAATGC
1 GCGGCATTTTTATAAAAA-TGCCGCTAAAGTA-ATACTAT-TTAACGGCGTTTGTTGAAAAACGC
1291240 CACTATAGATAAACCTTATT
63 CACTATAGATAAACCTTATT
* * * *
1291260 GCGGCATTTTTATATAAATGCCGCTAAAGTAATACTCTTTAACGGTGTTTGTTGAGAAACGCCAC
1 GCGGCATTTTTATAAAAATGCCGCTAAAGTAATACTATTTAACGGCGTTTGTTGAAAAACGCCAC
*
1291325 TATAGATGAACCT
66 TATAGATAAACCT
1291338 ATTACTTCGT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
81 4 0.06
82 62 0.94
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (82 bp):
GCGGCATTTTTATAAAAATGCCGCTAAAGTAATACTATTTAACGGCGTTTGTTGAAAAACGCCAC
TATAGATAAACCTTATT
Found at i:1297263 original size:2 final size:2
Alignment explanation
Indices: 1297256--1297282 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1297246 GATTTCCTTT
1297256 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1297283 GTATTCGAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1297759 original size:3 final size:3
Alignment explanation
Indices: 1297751--1297841 Score: 159
Period size: 3 Copynumber: 30.7 Consensus size: 3
1297741 TTTGGGTTTG
1297751 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
1297796 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1297842 CTGTAATGTA
Statistics
Matches: 85, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.05
3 78 0.92
4 3 0.04
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1298479 original size:3 final size:3
Alignment explanation
Indices: 1298473--1298513 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
1298463 TTTTAAAATA
1298473 AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1298514 GTAAGGTGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1298498 original size:20 final size:19
Alignment explanation
Indices: 1298469--1298512 Score: 79
Period size: 20 Copynumber: 2.3 Consensus size: 19
1298459 ATATTTTTAA
1298469 AATAAATAATAATAATAAT
1 AATAAATAATAATAATAAT
1298488 AATATAATAATAATAATAAT
1 AATA-AATAATAATAATAAT
1298508 AATAA
1 AATAA
1298513 TGTAAGGTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AATAAATAATAATAATAAT
Found at i:1299026 original size:114 final size:114
Alignment explanation
Indices: 1298779--1299031 Score: 334
Period size: 114 Copynumber: 2.2 Consensus size: 114
1298769 GCTAATGCTA
* * *
1298779 ATCCAACTCTTTATATGATGG-AT-GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTT
1 ATCCACCTCTTTATATGATGGAATCGAACCAAGGTTGAACAAG-T-TTCTCATTATAAACTTCTT
* * *
1298842 CTCCATCATCGGATGAGTTCTTCTTATATGAACTCTCCATTGGAAATATTG
64 CTCCATCATCGGATGAGTTCTTCTCATATGAACTATCAATTGGAAATATTG
* *
1298893 ATCCACCTCATTCTATGATGGAATCGAACCAAGGTTGAACAAG-TTCTCATTATAAACTTCTTCT
1 ATCCACCTCTTTATATGATGGAATCGAACCAAGGTTGAACAAGTTTCTCATTATAAACTTCTTCT
* * *
1298957 CCCTCGTCGGATGAGTTCTTCTCATTATGAACTATCAATTGGAAATGTAT-
66 CCATCATCGGATGAGTTCTTCTCA-TATGAACTATCAATTGGAAATAT-TG
*
1299007 ATCCACCTCTTTATGTGATGGAATC
1 ATCCACCTCTTTATATGATGGAATC
1299032 AGACAAAGTG
Statistics
Matches: 121, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
113 41 0.34
114 60 0.50
115 3 0.02
116 17 0.14
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (114 bp):
ATCCACCTCTTTATATGATGGAATCGAACCAAGGTTGAACAAGTTTCTCATTATAAACTTCTTCT
CCATCATCGGATGAGTTCTTCTCATATGAACTATCAATTGGAAATATTG
Found at i:1305584 original size:23 final size:23
Alignment explanation
Indices: 1305558--1305639 Score: 114
Period size: 23 Copynumber: 3.7 Consensus size: 23
1305548 CTCGTATAAA
1305558 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
1305581 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* * * *
1305604 TGCACCGTAGTACCGCGTATAAT
1 TGCACCGAAGTGCCACGTAGAAT
1305627 TGCACC--AGTGCCA
1 TGCACCGAAGTGCCA
1305640 TATAATAATG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
21 5 0.09
23 48 0.91
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1306635 original size:21 final size:21
Alignment explanation
Indices: 1306603--1306643 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1306593 TGTTTGTTTA
1306603 ATTGAGAGTGCATCGATGCAC
1 ATTGAGAGTGCATCGATGCAC
1306624 ATTGA-AGATGCATCGATGCA
1 ATTGAGAG-TGCATCGATGCA
1306644 TATAACCCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (21 bp):
ATTGAGAGTGCATCGATGCAC
Found at i:1315732 original size:2 final size:2
Alignment explanation
Indices: 1315727--1315756 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1315717 TTTTTTCGTG
1315727 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1315757 TCTAAAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1316213 original size:3 final size:3
Alignment explanation
Indices: 1316207--1316250 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
1316197 ATATTTTTAA
1316207 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1316251 GTAAGGTGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1318805 original size:60 final size:60
Alignment explanation
Indices: 1318683--1318913 Score: 179
Period size: 60 Copynumber: 3.9 Consensus size: 60
1318673 AACATAATAA
* *
1318683 ATAGTTGAGTGATCATTTTGTAACTTTTAATAGTAGGAGAATTCAACAAAGCAACACTCT
1 ATAGTTGAGTGATCATTTTGTAACTTTTAATAGCAGGAGAACTCAACAAAGCAACACTCT
* * *
1318743 ATAGTTGAGGGATTATTTTGTAACTTTTAATAGCCAGG-GAACTCAACAAAGTGAA-A-TCCT
1 ATAGTTGAGTGATCATTTTGTAACTTTTAATAG-CAGGAGAACTCAACAAAG-CAACACT-CT
* * ** * *
1318803 ATAGTT-AGATAATCATTTTGTAAATTTTAATAGTC--GATGAACTCAACGTAGCAACGCACT
1 ATAGTTGAG-TGATCATTTTGTAACTTTTAATAG-CAGGA-GAACTCAACAAAGCAACACTCT
* * ** * * * *
1318863 ATAATCGAGCAACCATTTTATAACTTTTAATAGTTA-AAGAACTCAACAAAG
1 ATAGTTGAGTGATCATTTTGTAACTTTTAATAG-CAGGAGAACTCAACAAAG
1318914 TAAGATCCTA
Statistics
Matches: 136, Mismatches: 25, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
58 1 0.01
59 5 0.04
60 122 0.90
61 8 0.06
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (60 bp):
ATAGTTGAGTGATCATTTTGTAACTTTTAATAGCAGGAGAACTCAACAAAGCAACACTCT
Found at i:1319901 original size:75 final size:75
Alignment explanation
Indices: 1319778--1319960 Score: 287
Period size: 75 Copynumber: 2.4 Consensus size: 75
1319768 CTTAACCGGT
* ** * *
1319778 TAAAATAAAATAGGTGCTATGTATTATGTTAAACTACCTACTGGTTTGTTTGAAGGTTACTAATA
1 TAAAATAAAATAGGCGCTACCTATTATGTTAAAATACCTACTGGTTTGTTTAAAGGTTACTAATA
1319843 ATGTAAACGG
66 ATGTAAACGG
* *
1319853 TAAAATAAAATAGGCGCTACCTATTACGTTAAAATACTTACAT-GTTTGTTTAAAGGTTACTAAT
1 TAAAATAAAATAGGCGCTACCTATTATGTTAAAATACCTAC-TGGTTTGTTTAAAGGTTACTAAT
1319917 AATGTAAACGG
65 AATGTAAACGG
1319928 TAAAATAAAATAGGCGCTACCTATTATGTTAAA
1 TAAAATAAAATAGGCGCTACCTATTATGTTAAA
1319961 TAAGCTCTAC
Statistics
Matches: 99, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
75 98 0.99
76 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (75 bp):
TAAAATAAAATAGGCGCTACCTATTATGTTAAAATACCTACTGGTTTGTTTAAAGGTTACTAATA
ATGTAAACGG
Found at i:1319970 original size:23 final size:23
Alignment explanation
Indices: 1319935--1320006 Score: 108
Period size: 23 Copynumber: 3.1 Consensus size: 23
1319925 CGGTAAAATA
*
1319935 AAATAGGCGCTACCTATTATGTT
1 AAATAAGCGCTACCTATTATGTT
*
1319958 AAATAAGCTCTACCTATTATGTT
1 AAATAAGCGCTACCTATTATGTT
**
1319981 AAATAAGCGCTATTTATTATGTT
1 AAATAAGCGCTACCTATTATGTT
1320004 AAA
1 AAA
1320007 CTAGCCACCG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (23 bp):
AAATAAGCGCTACCTATTATGTT
Found at i:1320080 original size:75 final size:75
Alignment explanation
Indices: 1319981--1320156 Score: 264
Period size: 75 Copynumber: 2.3 Consensus size: 75
1319971 CTATTATGTT
* * * * *
1319981 AAATAAGCGCTATTTATTATGTTAAACTAGCC-ACCGGTTTGTTTAAATGTTAATAATAATGTAA
1 AAATAGGCGCTATCTATTACGTTAAAATA-CCTACCGGTTTGTTTAAAGGTTAATAATAATGTAA
1320045 ACGGTAAAATA
65 ACGGTAAAATA
* *
1320056 AAATAGGCGCTACCTATTACGTTAAAATACCTACCGGTTTGTTTAAAGGTTACTAATAATGTAAA
1 AAATAGGCGCTATCTATTACGTTAAAATACCTACCGGTTTGTTTAAAGGTTAATAATAATGTAAA
1320121 CGGTAAAATA
66 CGGTAAAATA
*
1320131 AAATAGACGCTATCTATTACGTTAAA
1 AAATAGGCGCTATCTATTACGTTAAA
1320157 TAGACGCTAC
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
74 2 0.02
75 89 0.98
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (75 bp):
AAATAGGCGCTATCTATTACGTTAAAATACCTACCGGTTTGTTTAAAGGTTAATAATAATGTAAA
CGGTAAAATA
Found at i:1320133 original size:196 final size:196
Alignment explanation
Indices: 1319793--1320251 Score: 679
Period size: 196 Copynumber: 2.3 Consensus size: 196
1319783 TAAAATAGGT
* * * *
1319793 GCTATGTATTATGTTAAACTA-CCTACTGGTTTGTTTGAAGGTTACTAATAATGTAAACGGTAAA
1 GCTATATATTATGTTAAACTAGCC-ACCGGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAA
* *
1319857 ATAAAATAGGCGCTACCTATTACGTTAAAATACTTACATGTTTGTTTAAAGGTTACTAATAATGT
65 ATAAAATAGGCGCTACCTATTACGTTAAAATACCTACAGGTTTGTTTAAAGGTTACTAATAATGT
* * * *
1319922 AAACGGTAAAATAAAATAGGCGCTACCTATTATGTTAAATA-AGCTCTACCTATTATGTTAAATA
130 AAACGGTAAAATAAAATAGACGCTACCTATTACGTTAAATAGA-CGCTACCTATTACGTTAAATA
1319986 AGC
194 AGC
* *
1319989 GCTATTTATTATGTTAAACTAGCCACCGGTTTGTTTAAATGTTAATAATAATGTAAACGGTAAAA
1 GCTATATATTATGTTAAACTAGCCACCGGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAA
*
1320054 TAAAATAGGCGCTACCTATTACGTTAAAATACCTACCGGTTTGTTTAAAGGTTACTAATAATGTA
66 TAAAATAGGCGCTACCTATTACGTTAAAATACCTACAGGTTTGTTTAAAGGTTACTAATAATGTA
*
1320119 AACGGTAAAATAAAATAGACGCTATCTATTACGTTAAATAGACGCTACCTATTACGTTAAATAAG
131 AACGGTAAAATAAAATAGACGCTACCTATTACGTTAAATAGACGCTACCTATTACGTTAAATAAG
1320184 C
196 C
** * * * * ** *
1320185 GCTGCATATTACGCTAAACTAGCTACCAGTTTGTTTAAAGGTTAACGATTATGTAAACGGTAAAA
1 GCTATATATTATGTTAAACTAGCCACCGGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAA
1320250 TA
66 TA
1320252 TATACAACTT
Statistics
Matches: 237, Mismatches: 24, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
196 234 0.99
197 3 0.01
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.33
Consensus pattern (196 bp):
GCTATATATTATGTTAAACTAGCCACCGGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAA
TAAAATAGGCGCTACCTATTACGTTAAAATACCTACAGGTTTGTTTAAAGGTTACTAATAATGTA
AACGGTAAAATAAAATAGACGCTACCTATTACGTTAAATAGACGCTACCTATTACGTTAAATAAG
C
Found at i:1320187 original size:23 final size:23
Alignment explanation
Indices: 1320131--1320181 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
1320121 CGGTAAAATA
*
1320131 AAATAGACGCTATCTATTACGTT
1 AAATAGACGCTACCTATTACGTT
1320154 AAATAGACGCTACCTATTACGTT
1 AAATAGACGCTACCTATTACGTT
1320177 AAATA
1 AAATA
1320182 AGCGCTGCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (23 bp):
AAATAGACGCTACCTATTACGTT
Found at i:1320194 original size:23 final size:23
Alignment explanation
Indices: 1320131--1320202 Score: 85
Period size: 23 Copynumber: 3.1 Consensus size: 23
1320121 CGGTAAAATA
1320131 AAATAGACGCTATC-TATTACGTT
1 AAATAGACGCTA-CATATTACGTT
*
1320154 AAATAGACGCTACCTATTACGTT
1 AAATAGACGCTACATATTACGTT
* *
1320177 AAATA-AGCGCTGCATATTACGCT
1 AAATAGA-CGCTACATATTACGTT
1320200 AAA
1 AAA
1320203 CTAGCTACCA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
22 2 0.05
23 42 0.95
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (23 bp):
AAATAGACGCTACATATTACGTT
Found at i:1321932 original size:35 final size:36
Alignment explanation
Indices: 1321843--1321946 Score: 126
Period size: 35 Copynumber: 2.9 Consensus size: 36
1321833 AATAATATTC
1321843 TTTTGAATATTTCAAATTAAAAGATATCTATTATCT
1 TTTTGAATATTTCAAATTAAAAGATATCTATTATCT
* * *
1321879 ATTT-AAT-TTTGAATATTAAAATATAAT-TA-TATCT
1 TTTTGAATATTTCAA-ATTAAAAGAT-ATCTATTATCT
*
1321913 TTTTGAATATTTCAAATTAAAAAATATCTATTAT
1 TTTTGAATATTTCAAATTAAAAGATATCTATTAT
1321947 GTCTTTTAAG
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
34 15 0.27
35 28 0.50
36 13 0.23
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (36 bp):
TTTTGAATATTTCAAATTAAAAGATATCTATTATCT
Found at i:1322955 original size:16 final size:15
Alignment explanation
Indices: 1322936--1322978 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
1322926 TTATGAGGTG
1322936 AAAATATTATTATTGT
1 AAAATATTATTATT-T
*
1322952 AAAAAATTAATTATTT
1 AAAATATT-ATTATTT
*
1322968 AAAATAATATT
1 AAAATATTATT
1322979 TAATTTTGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 3 0.13
16 14 0.61
17 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
AAAATATTATTATTT
Found at i:1324214 original size:19 final size:19
Alignment explanation
Indices: 1324173--1324211 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1324163 TCCTCCATCA
* *
1324173 TCTTTTTCTTCTTCTTCTT
1 TCTTTTTCTTATCCTTCTT
1324192 TCTTTTTCTATATCCTTCTT
1 TCTTTTTCT-TATCCTTCTT
1324212 CTTCCCTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.69
Consensus pattern (19 bp):
TCTTTTTCTTATCCTTCTT
Found at i:1325223 original size:20 final size:20
Alignment explanation
Indices: 1325182--1325251 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
1325172 ACAATTTTTG
* * *
1325182 GTATCGATAC-CAAGTGTGA
1 GTATCTATACTCAAGGGTTA
1325201 GTATCTATACTCAAGGGTTA
1 GTATCTATACTCAAGGGTTA
*
1325221 GTAT-TGATACTAAAGGGCTTA
1 GTATCT-ATACTCAAGGG-TTA
* *
1325242 ATATCAATAC
1 GTATCTATAC
1325252 CCTTATTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
19 10 0.24
20 21 0.51
21 10 0.24
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCTATACTCAAGGGTTA
Found at i:1327352 original size:21 final size:20
Alignment explanation
Indices: 1327313--1327366 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 20
1327303 CTCGGAGGGA
1327313 ACCGATTCCCCCCAAGGGGT
1 ACCGATTCCCCCCAAGGGGT
*
1327333 ACCGATTCCCTCCCAGGGGGT
1 ACCGATTCCC-CCCAAGGGGT
1327354 ACCGATTCCCCCC
1 ACCGATTCCCCCC
1327367 TTGTATAACG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.17, C:0.44, G:0.22, T:0.17
Consensus pattern (20 bp):
ACCGATTCCCCCCAAGGGGT
Found at i:1333147 original size:20 final size:22
Alignment explanation
Indices: 1333122--1333182 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
1333112 TTTGGTGCAG
*
1333122 AGGGAATCG-TTCCCCCCTT-A
1 AGGGAACCGATTCCCCCCTTGA
*
1333142 AGGGAACCGATTCCCCCTTTGA
1 AGGGAACCGATTCCCCCCTTGA
1333164 AGGGGAACCGATTCCCCCC
1 A-GGGAACCGATTCCCCCC
1333183 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 8 0.23
21 9 0.26
22 2 0.06
23 16 0.46
ACGTcount: A:0.21, C:0.36, G:0.23, T:0.20
Consensus pattern (22 bp):
AGGGAACCGATTCCCCCCTTGA
Found at i:1338407 original size:34 final size:34
Alignment explanation
Indices: 1338358--1338436 Score: 99
Period size: 34 Copynumber: 2.3 Consensus size: 34
1338348 ATTCTAAAGC
*
1338358 TTAAATTGAAGTATTT-TGAATTTAGGGTTTAAAA
1 TTAAATTGAAGTATTTAT-AATTTAGGATTTAAAA
* *
1338392 TGT-AATTGAATTATTTATAATTTAGGATTTAGAA
1 T-TAAATTGAAGTATTTATAATTTAGGATTTAAAA
1338426 TTAAATTGAAG
1 TTAAATTGAAG
1338437 ACTGTGTTAC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
33 1 0.03
34 35 0.92
35 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.44
Consensus pattern (34 bp):
TTAAATTGAAGTATTTATAATTTAGGATTTAAAA
Found at i:1339933 original size:23 final size:23
Alignment explanation
Indices: 1339907--1339973 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
1339897 CACCACATCT
*
1339907 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
1339930 CGTAGAATTGCAACGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
1339953 CGTAGAAATGCACCGAAGTGC
1 CGTAGAAATGCACCGAAGTGC
1339974 TATATAAGGT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1340939 original size:2 final size:2
Alignment explanation
Indices: 1340932--1340961 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1340922 ATCTTATGTT
1340932 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1340962 ATATATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1345165 original size:23 final size:23
Alignment explanation
Indices: 1345110--1345169 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
1345100 ACGCTCGTAT
1345110 AAATGCACCGAAGTGCCACATAG
1 AAATGCACCGAAGTGCCACATAG
* * * **
1345133 AATTGTACCGTAGTGCCATGTAG
1 AAATGCACCGAAGTGCCACATAG
1345156 AAATGCACCGAAGT
1 AAATGCACCGAAGT
1345170 TCTATATAAG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACATAG
Found at i:1345817 original size:39 final size:39
Alignment explanation
Indices: 1345740--1345818 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 39
1345730 TATCATTAAC
*
1345740 CTATAAACTTACTCATATATCATATATACTCTTTATATAA
1 CTATAAACTTACTCATATATCA-ATATACTCTTAATATAA
1345780 CTATAAACTTACTCATATACTC-ATATACTCTTAATATAA
1 CTATAAACTTACTCATATA-TCAATATACTCTTAATATAA
1345819 TTTGTATAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
39 16 0.43
40 19 0.51
41 2 0.05
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (39 bp):
CTATAAACTTACTCATATATCAATATACTCTTAATATAA
Found at i:1346219 original size:2 final size:2
Alignment explanation
Indices: 1346212--1346245 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1346202 TCTTATGTTC
1346212 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1346246 CAATGGTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1348441 original size:39 final size:39
Alignment explanation
Indices: 1348349--1348463 Score: 144
Period size: 39 Copynumber: 2.9 Consensus size: 39
1348339 TGCTTTCTGT
1348349 AGGCTCCTTGGCTTTGTGCTCAGGGTAAGTCCTTACTAA
1 AGGCTCCTTGGCTTTGTGCTCAGGGTAAGTCCTTACTAA
* * * *
1348388 AGGCTCATTGGCTTTATACTCAGGGTAAGTCCTTAC-AGC
1 AGGCTCCTTGGCTTTGTGCTCAGGGTAAGTCCTTACTA-A
* *
1348427 AGGCTCCTCT-GCTTTGTGCACAGGGTAAGCCCTTACT
1 AGGCTCCT-TGGCTTTGTGCTCAGGGTAAGTCCTTACT
1348464 GAGTGTATAT
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
38 1 0.02
39 62 0.97
40 1 0.02
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.31
Consensus pattern (39 bp):
AGGCTCCTTGGCTTTGTGCTCAGGGTAAGTCCTTACTAA
Found at i:1358348 original size:169 final size:167
Alignment explanation
Indices: 1358069--1358405 Score: 631
Period size: 169 Copynumber: 2.0 Consensus size: 167
1358059 TTGAGACGAT
1358069 AGAATTGCCCGAGCGTAAATGCGGGAGATAAACTATTGTGCCTAATAACCGAAACATTGCCTCGG
1 AGAATTGCCCGAGCGTAAATGCGGGAGATAAACTATTGTGCCTAATAACCG-AACATTGCCTCGG
1358134 TTTTAGAAAATAGATTTGGTTTGAAAAGGATGTCGACCTATTTAGGGAATTATCAGTAGTCACCC
65 TTTTAGAAAATAGATTTGGTTTGAAAAGGATGTCGACCTATTTAGGGAATTATCAGTAGTCA-CC
1358199 CCTGAGCACGATCGCGGAGATATACTATTAATTCCTTAA
129 CCTGAGCACGATCGCGGAGATATACTATTAATTCCTTAA
1358238 AGAATTGCCCGAGCGTAAATGCGGGAGATAAACTATTGTGCCTAATAACCG-ACATTGCCTCGGT
1 AGAATTGCCCGAGCGTAAATGCGGGAGATAAACTATTGTGCCTAATAACCGAACATTGCCTCGGT
1358302 TTTAGAAAATATGATTTGGTTTTGAAAAGGATGTCGACCTATTTAGGGAATTATCAGTAGTCACC
66 TTTAGAAAATA-GATTTGG-TTTGAAAAGGATGTCGACCTATTTAGGGAATTATCAGTAGTCACC
1358367 CCTGAGCACGATCGCGGAGATATACTATTAATTCCTTAA
129 CCTGAGCACGATCGCGGAGATATACTATTAATTCCTTAA
1358406 TAAGTGAAAC
Statistics
Matches: 166, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
167 24 0.14
168 48 0.29
169 94 0.57
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.28
Consensus pattern (167 bp):
AGAATTGCCCGAGCGTAAATGCGGGAGATAAACTATTGTGCCTAATAACCGAACATTGCCTCGGT
TTTAGAAAATAGATTTGGTTTGAAAAGGATGTCGACCTATTTAGGGAATTATCAGTAGTCACCCC
TGAGCACGATCGCGGAGATATACTATTAATTCCTTAA
Found at i:1359736 original size:286 final size:285
Alignment explanation
Indices: 1359210--1359799 Score: 1041
Period size: 287 Copynumber: 2.1 Consensus size: 285
1359200 TAAGTCTAAA
1359210 ATCGAAATAAAATAAAATACATGCAAAATAAAATAAATAGAATAAAATGAAGTGACCAAAGTGTA
1 ATCGAAATAAAATAAAATACATGCAAAATAAAATAAATAGAATAAAATGAAGTGACCAAAGTGTA
1359275 AAACACGCTAAATTAAAGGTACTGAAACAGTAAATTTACCAGAAAAATAAAGCATGCATAGAGAA
66 AAACACGCTAAATTAAAGGTACTGAAACAGTAAATTTACCAGAAAAATAAAGCATGCATAGAGAA
1359340 ATGGCTAAACATCAATTTCGGTCCTTACAGTGACTAAAATGTAAAAAACGGGAAAGTTAGAGGCA
131 ATGGCTAAACATCAATTTCGGTCCTTACAGTGACTAAAATGTAAAAAACGGGAAAGTTAGAGGCA
1359405 TTTAAGATGTAATTTTACCATTAATCTAGTCTATATATACCAACCTTTACT-TTTTTTGTTTCA-
196 TTTAAGATGTAATTTTACCATTAATCTAGTCTATATATACCAACCTTTACTCTTTTTTGTTTCAT
1359468 TTTTTACCCAAAACACAAAAAAAAGG
261 TTTTTACCCAAAACAC-AAAAAAAGG
1359494 ATCGAAATAAAATAAAATACATGCCAAAATAAAA-AAATAGAAATAAAAGATGAAGTGACCAAAG
1 ATCGAAATAAAATAAAATACATG-CAAAATAAAATAAATAG-AAT-AAA-ATGAAGTGACCAAAG
1359558 TGTAAAAACACGCTAAAATTAAAGGTACTGAAACAGTAAATTTACCAGAAAAATAAAGCATGCAT
62 TGT-AAAACACGCT-AAATTAAAGGTACTGAAACAGTAAATTTACCAGAAAAATAAAGCATGCAT
1359623 AGAG-AAT-GCTAAACATCAATTTCGGTCCTTACAGTGACTAAAATGT-AAAAACGGGAAAGTTA
125 AGAGAAATGGCTAAACATCAATTTCGGTCCTTACAGTGACTAAAATGTAAAAAACGGGAAAGTTA
1359685 -AGGGCATTTAAGATGTAATTTTACCATTAATCTAGTCTATATATACCAACCTTTACTCTTTTTT
190 GA-GGCATTTAAGATGTAATTTTACCATTAATCTAGTCTATATATACCAACCTTTACTCTTTTTT
1359749 GTTTCATTTTTTACCCAAAACACAAAAAAAGG
254 GTTTCATTTTTTACCCAAAACACAAAAAAAGG
1359781 ATTTCGAAATAAAATAAAA
1 A--TCGAAATAAAATAAAA
1359800 AATTGAACGT
Statistics
Matches: 295, Mismatches: 0, Indels: 17
0.95 0.00 0.05
Matches are distributed among these distances:
284 29 0.10
285 14 0.05
286 74 0.25
287 79 0.27
288 29 0.10
289 70 0.24
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.27
Consensus pattern (285 bp):
ATCGAAATAAAATAAAATACATGCAAAATAAAATAAATAGAATAAAATGAAGTGACCAAAGTGTA
AAACACGCTAAATTAAAGGTACTGAAACAGTAAATTTACCAGAAAAATAAAGCATGCATAGAGAA
ATGGCTAAACATCAATTTCGGTCCTTACAGTGACTAAAATGTAAAAAACGGGAAAGTTAGAGGCA
TTTAAGATGTAATTTTACCATTAATCTAGTCTATATATACCAACCTTTACTCTTTTTTGTTTCAT
TTTTTACCCAAAACACAAAAAAAGG
Found at i:1360271 original size:33 final size:33
Alignment explanation
Indices: 1360199--1360278 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 33
1360189 TCTTCGTTGG
* *
1360199 AGATGTCAATCCACTTCCTTATGTGATGAATTA
1 AGATGTCGATCCACTTCCTCATGTGATGAATTA
*
1360232 AAATGTCGATCCAGC-TCCTCATGTGAT-ATATTA
1 AGATGTCGATCCA-CTTCCTCATGTGATGA-ATTA
*
1360265 TGATGTCGATCCAC
1 AGATGTCGATCCAC
1360279 CCCTTTCTGT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
32 2 0.05
33 37 0.93
34 1 0.03
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (33 bp):
AGATGTCGATCCACTTCCTCATGTGATGAATTA
Found at i:1360375 original size:44 final size:44
Alignment explanation
Indices: 1360327--1360773 Score: 209
Period size: 44 Copynumber: 10.1 Consensus size: 44
1360317 ATCTACCTCA
* * *
1360327 TTCTGTGATAGAATCGAGCAAAAAGTTAAAGTTGATCCAACTCC
1 TTCTGTGATGGAATCGAGCGAAAAGTTGAAGTTGATCCAACTCC
* * * ** * *
1360371 TTCTGCGATGGATTTGAGCGAAAA-TAAAAATGTCGATCCACCTCC
1 TTCTGTGATGGAATCGAGCGAAAAGT-TGAA-GTTGATCCAACTCC
* * * * * * * * *
1360416 TTCAGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCTCC
1 TTCTGTGATGGAATCGAGCGAAAAGTTGAAGTTGATCCAACTCC
* * *
1360460 TTCTTTGATAGAATCGAGCAAAAAGTTGAAGTTGATCCAACTCC
1 TTCTGTGATGGAATCGAGCGAAAAGTTGAAGTTGATCCAACTCC
* * * ** * *
1360504 TTCTGCGATGGATTTGAGCGAAAA-TAAAAATGTCGATCCACCTCC
1 TTCTGTGATGGAATCGAGCGAAAAGT-TGAA-GTTGATCCAACTCC
* * * * * * * * *
1360549 TTCAGTGATGGAATCGAACGAGATGTCGATGCTGATCTATCTCC
1 TTCTGTGATGGAATCGAGCGAAAAGTTGAAGTTGATCCAACTCC
* * * * *
1360593 TTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTTC
1 TTCTGTGATGGAATCGAGCGAAAAGTTGAAGTTGATCCAACTCC
* * ** ** * *
1360637 TTCTGAGATGGATTTAAGCGAAAA-TAAAAATGTCGATCCACCTCC
1 TTCTGTGATGGAATCGAGCGAAAAGT-TGAA-GTTGATCCAACTCC
* * * * * * * * * *
1360682 TTCTGTGATGAAATCGAACGAGATGTCGATGCTGATCTACCTTC
1 TTCTGTGATGGAATCGAGCGAAAAGTTGAAGTTGATCCAACTCC
* * * * *
1360726 TTCTGTGATAGAATCGAGCAAAAAGTAGACA-CTGATCTAACTCC
1 TTCTGTGATGGAATCGAGCGAAAAGTTGA-AGTTGATCCAACTCC
1360770 TTCT
1 TTCT
1360774 CCTTCTGTGA
Statistics
Matches: 287, Mismatches: 106, Indels: 20
0.69 0.26 0.05
Matches are distributed among these distances:
43 3 0.01
44 194 0.68
45 87 0.30
46 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (44 bp):
TTCTGTGATGGAATCGAGCGAAAAGTTGAAGTTGATCCAACTCC
Found at i:1360452 original size:89 final size:89
Alignment explanation
Indices: 1360359--1360749 Score: 261
Period size: 89 Copynumber: 4.4 Consensus size: 89
1360349 AAGTTAAAGT
* * * *
1360359 TGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCAGTGA
1 TGATCCAACTCCTTCTGTGATGGAATCGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGA
*
1360424 TGGAATCGAACGAGATGTCGATGC
66 TGGAATCGAACGAAATGTCGATGC
* * * * * ** * * *
1360448 TGATCTACCTCCTTCTTTGATAGAATCGAGCAAAAAGT-TGAA-GTTGATCCAACTCCTTCTGCG
1 TGATCCAACTCCTTCTGTGATGGAATCGAGCGAAAA-TAAAAATGTCGATCCACCTCCTTCTGTG
* * * ****
1360511 ATGGATTTGAGCGAAAATAAAAATG-
65 ATGGAATCGAACG-AAATGTCGATGC
* * * * **** * *
1360536 TCGATCCACCTCCTTCAGTGATGGAATCGAACG-AGATGTCGATG-CTGATCTATCTCCTTCTGT
1 T-GATCCAACTCCTTCTGTGATGGAATCGAGCGAAAATAAAAATGTC-GATCCACCTCCTTCTGT
* * * * * *
1360599 GATAGAATCGAGCAAAAAGTTGACGC
64 GATGGAATCGAACGAAATGTCGATGC
* * * **
1360625 TGATCCAACTTCTTCTGAGATGGATTTAAGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGA
1 TGATCCAACTCCTTCTGTGATGGAATCGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGA
* *
1360690 TGAAATCGAACGAGATGTCGATGC
66 TGGAATCGAACGAAATGTCGATGC
* * * * *
1360714 TGATCTACCTTCTTCTGTGATAGAATCGAGCAAAAA
1 TGATCCAACTCCTTCTGTGATGGAATCGAGCGAAAA
1360750 GTAGACACTG
Statistics
Matches: 217, Mismatches: 76, Indels: 18
0.70 0.24 0.06
Matches are distributed among these distances:
87 1 0.00
88 60 0.28
89 154 0.71
90 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (89 bp):
TGATCCAACTCCTTCTGTGATGGAATCGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGA
TGGAATCGAACGAAATGTCGATGC
Found at i:1360505 original size:133 final size:133
Alignment explanation
Indices: 1360267--1360773 Score: 820
Period size: 133 Copynumber: 3.8 Consensus size: 133
1360257 ATATATTATG
* * * *
1360267 ATGTCGATCCACC-CCTTTCTGTAATGGATTCGAACGAGATGTCGATGCTGATCTACCTCATTCT
1 ATGTCGATCCACCTCC-TTCAGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCT
* *
1360331 GTGATAGAATCGAGCAAAAAGTTAAAGTTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAAT
65 GTGATAGAATCGAGCAAAAAGTTGAAGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAAT
1360396 AAAA
130 AAAA
*
1360400 ATGTCGATCCACCTCCTTCAGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTT
1 ATGTCGATCCACCTCCTTCAGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTG
*
1360465 TGATAGAATCGAGCAAAAAGTTGAAGTTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATA
66 TGATAGAATCGAGCAAAAAGTTGAAGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATA
1360530 AAA
131 AAA
*
1360533 ATGTCGATCCACCTCCTTCAGTGATGGAATCGAACGAGATGTCGATGCTGATCTATCTCCTTCTG
1 ATGTCGATCCACCTCCTTCAGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTG
* * * *
1360598 TGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTTCTTCTGAGATGGATTTAAGCGAAAATA
66 TGATAGAATCGAGCAAAAAGTTGAAGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATA
1360663 AAA
131 AAA
* * *
1360666 ATGTCGATCCACCTCCTTCTGTGATGAAATCGAACGAGATGTCGATGCTGATCTACCTTCTTCTG
1 ATGTCGATCCACCTCCTTCAGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTG
* *
1360731 TGATAGAATCGAGCAAAAAGTAGACA-CTGATCTAACTCCTTCT
66 TGATAGAATCGAGCAAAAAGTTGA-AGCTGATCCAACTCCTTCT
1360774 CCTTCTGTGA
Statistics
Matches: 351, Mismatches: 21, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
133 349 0.99
134 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.28
Consensus pattern (133 bp):
ATGTCGATCCACCTCCTTCAGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTG
TGATAGAATCGAGCAAAAAGTTGAAGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATA
AAA
Found at i:1361609 original size:18 final size:18
Alignment explanation
Indices: 1361586--1361623 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1361576 GGTTTTCACC
1361586 TCGAACCTCTCCTTTTTT
1 TCGAACCTCTCCTTTTTT
1361604 TCGAACCTCTCCTTTTTT
1 TCGAACCTCTCCTTTTTT
1361622 TC
1 TC
1361624 TTTTTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.11, C:0.34, G:0.05, T:0.50
Consensus pattern (18 bp):
TCGAACCTCTCCTTTTTT
Found at i:1361629 original size:6 final size:6
Alignment explanation
Indices: 1361618--1361652 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
1361608 ACCTCTCCTT
1361618 TTTTTC TTTTTC TTTTTTC TTTTTC TTTTTC TTTT
1 TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC TTTT
1361653 CAGGCGTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Done.