Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008258.1 Hibiscus syriacus cultivar Beakdansim tig00110911_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: 1617810
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:1073430 original size:28 final size:28
Alignment explanation
Indices: 1073390--1073477 Score: 108
Period size: 28 Copynumber: 3.1 Consensus size: 28
1073380 CCAAAGAAAC
1073390 CAACTTGAAACACATTACATTCCCAAAT
1 CAACTTGAAACACATTACATTCCCAAAT
*
1073418 CAACTTGAAACACATT--ATCTCCTTAAAT
1 CAACTTGAAACACATTACAT-TCC-CAAAT
* * *
1073446 TAACTTGAAACACATTACCTTCCCAAGT
1 CAACTTGAAACACATTACATTCCCAAAT
1073474 CAAC
1 CAAC
1073478 CTAAGCCTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
26 2 0.04
27 3 0.06
28 41 0.82
29 3 0.06
30 1 0.02
ACGTcount: A:0.40, C:0.28, G:0.05, T:0.27
Consensus pattern (28 bp):
CAACTTGAAACACATTACATTCCCAAAT
Found at i:1074920 original size:56 final size:54
Alignment explanation
Indices: 1074783--1074935 Score: 179
Period size: 55 Copynumber: 2.8 Consensus size: 54
1074773 TGATATCTTT
* * * * *
1074783 AAATGAATTTTGAAATAAACTAAGCC-AGATTTTCAGGGG-TTCTTGATGTCTCC
1 AAATGAATTTTTAAAGAAGCTAAGCCTA-ATTTTTAGGGGTTTCTTAATGTCTCC
* *
1074836 AAAT-AAGTTTTT-AAGAAGCTAAGCCTAATTTTTTAGGGGATTTCTTAATGTTTTC
1 AAATGAA-TTTTTAAAGAAGCTAAGCCTAA-TTTTTAGGGG-TTTCTTAATGTCTCC
1074891 AAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTT
1 AAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTT
1074936 GATGATTACT
Statistics
Matches: 86, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
52 14 0.16
53 18 0.21
54 6 0.07
55 30 0.35
56 18 0.21
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (54 bp):
AAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTAATGTCTCC
Found at i:1074981 original size:58 final size:54
Alignment explanation
Indices: 1074802--1074996 Score: 166
Period size: 55 Copynumber: 3.5 Consensus size: 54
1074792 TTGAAATAAA
* * * *
1074802 CTAAGCC-AGATTTTCAGGGG-TTCTTGATGTCTCCAAA-TAAGTTTTTAAGAAG
1 CTAAGCCTA-ATTTTTAGGGGTTTCTTGATGTTTTCAAACGAAGTTTTTAAGAAG
* *
1074854 CTAAGCCTAATTTTTTAGGGGATTTCTTAATGTTTTCAAATGAA-TTTTTAAAGAAG
1 CTAAGCCTAA-TTTTTAGGGG-TTTCTTGATGTTTTCAAACGAAGTTTTT-AAGAAG
*
1074910 CTAAGCCTAATTTTTAGGGGTTTCTTGATGATTACTAT-AAACGAGAGTTTTTAAGAAA
1 CTAAGCCTAATTTTTAGGGGTTTCTTGATG-TT--T-TCAAACGA-AGTTTTTAAGAAG
* * * * *
1074968 CTAAGCTTGATTTTCAAGAGTTTCTTGAT
1 CTAAGCCTAATTTTTAGGGGTTTCTTGAT
1074997 AAATAAGTCC
Statistics
Matches: 118, Mismatches: 13, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
52 8 0.07
53 10 0.08
54 9 0.08
55 31 0.26
56 18 0.15
57 6 0.05
58 31 0.26
59 5 0.04
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (54 bp):
CTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAACGAAGTTTTTAAGAAG
Found at i:1075516 original size:249 final size:240
Alignment explanation
Indices: 1075000--1075836 Score: 1140
Period size: 249 Copynumber: 3.5 Consensus size: 240
1074990 TCTTGATAAA
* * * * *
1075000 TAAGTCCTTCGGGCTATCAGTAAGTCTTTCGAGTATGATGTTTAAATTCTTAGGGTCATCTATAA
1 TAAGTCCTTCGGGCCATCAGTAAGGCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTATAA
* * * *
1075065 GTCTTTCGAGCAAGATGATATGTCCTTCGAGTCATCCATAAGACCTTCGGACAGGACGTTTTCAC
66 GTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGACAGGATGTTTTCAC
*
1075130 ATGATTTTCAAAAAAATGAGAAAGCAATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATTG
131 ATGATTTTCAAAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATTG
* *
1075195 ATTTTTTTAAAAGGAACAAAACGATTTCCAAAGTTTCTTACTTAG
196 ATTTTTTTAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTAG
* ** * * * *
1075240 TAAGTCCTCCGGTTCTTCAGTAAGGCTTTTGAGCATGATGCTTAAATCCTAT-GGGTCATCTTTA
1 TAAGTCCTTCGGGCCATCAGTAAGGCTTTCGAGCATGATGTTTAAATCCT-TCGGGTCATCTATA
* * * * * * *
1075304 AATATTTCAAGCGAGATGATAAGTCCTTCGGGCTATCCATAAGACCTTAGGACATGATGTTTTCA
65 AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGACAGGATGTTTTCA
* *
1075369 TATGATTTTCAAAAAAAAAAAGAAAAGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTC
130 CATGATTTTC-------AAAA-AAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTC
*
1075434 TGAAAAATTGATTTTTTTAAAAGTAAGAAAACAATTTCCAAAGTTTCTTACTTAG
187 TG-AAAATTGATTTTTTTAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTAG
* * *
1075489 TAAGTCCTTAGGGCCATCAGTAAGGCTTTCGAGCATGATGTTTAAATCTTTCGAGTCATCTATAA
1 TAAGTCCTTCGGGCCATCAGTAAGGCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTATAA
* * * * *
1075554 GTCTTTCGAGTAAGATGATAAATCATTCGGGCCATCTATAAGACCTTCGGGCAGGATGTTTTCAC
66 GTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGACAGGATGTTTTCAC
* * *
1075619 ATGATTTTC-AAAAAATGAGAAACCGATTTCCAAAGTTTCTTATTTAAATCTTTTCTGAAATTTG
131 ATGATTTTCAAAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATTG
*
1075683 A-TTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTAG
196 ATTTTTTTAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTAG
* * **
1075727 TAAGTCATTCGGGTCATCAGTAACTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTATAA
1 TAAGTCCTTCGGGCCATCAGTAAGGCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTATAA
*
1075792 GTCTTTCGAGCATGATGATTAAGTCCTTCGGGCCATCCATAAGAC
66 GTCTTTCGAGCAAGATGA-TAAGTCCTTCGGGCCATCCATAAGAC
1075837 TTTCAAACAT
Statistics
Matches: 516, Mismatches: 69, Indels: 25
0.85 0.11 0.04
Matches are distributed among these distances:
238 115 0.22
239 30 0.06
240 156 0.30
241 4 0.01
247 4 0.01
248 44 0.09
249 163 0.32
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (240 bp):
TAAGTCCTTCGGGCCATCAGTAAGGCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTATAA
GTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGACAGGATGTTTTCAC
ATGATTTTCAAAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATTG
ATTTTTTTAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTAG
Found at i:1075590 original size:41 final size:42
Alignment explanation
Indices: 1075499--1075595 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 42
1075489 TAAGTCCTTA
* * *
1075499 GGGCCATC-AGTAAGGCTTTCGAGCATGATGTTTAAATCTTTC
1 GGGCCATCTA-TAAGGCTTTCGAGCAAGATGTATAAATCATTC
* * * *
1075541 GAGTCATCTATAAGTCTTTCGAGTAAGATG-ATAAATCATTC
1 GGGCCATCTATAAGGCTTTCGAGCAAGATGTATAAATCATTC
1075582 GGGCCATCTATAAG
1 GGGCCATCTATAAG
1075596 ACCTTCGGGC
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
41 21 0.47
42 23 0.51
43 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.32
Consensus pattern (42 bp):
GGGCCATCTATAAGGCTTTCGAGCAAGATGTATAAATCATTC
Found at i:1075797 original size:42 final size:41
Alignment explanation
Indices: 1075734--1075850 Score: 144
Period size: 42 Copynumber: 2.8 Consensus size: 41
1075724 TAGTAAGTCA
* *
1075734 TTCGGGTCATCAGTAACTCTTTCGAGCATGATGTTTAAATCC
1 TTCGGGTCATCA-TAAGTCTTTCGAGCATGATGATTAAATCC
*
1075776 TTCGGGTCATCTATAAGTCTTTCGAGCATGATGATTAAGTCC
1 TTCGGGTCATC-ATAAGTCTTTCGAGCATGATGATTAAATCC
* * * *
1075818 TTCGGGCCATCCATAAGACTTTCAAACATGATG
1 TTCGGGTCAT-CATAAGTCTTTCGAGCATGATG
1075851 CATTTAAAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
42 64 0.97
43 2 0.03
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (41 bp):
TTCGGGTCATCATAAGTCTTTCGAGCATGATGATTAAATCC
Found at i:1075814 original size:22 final size:22
Alignment explanation
Indices: 1075754--1075821 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
1075744 CAGTAACTCT
* *
1075754 TTCGAGCATGATGTTTAAATCC
1 TTCGAGCATGATGATTAAGTCC
* * *
1075776 TTCGGGTCAT-CT-A-TAAGTCT
1 TTCGAG-CATGATGATTAAGTCC
1075796 TTCGAGCATGATGATTAAGTCC
1 TTCGAGCATGATGATTAAGTCC
1075818 TTCG
1 TTCG
1075822 GGCCATCCAT
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
19 3 0.09
20 11 0.32
21 1 0.03
22 16 0.47
23 3 0.09
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.37
Consensus pattern (22 bp):
TTCGAGCATGATGATTAAGTCC
Found at i:1076452 original size:135 final size:134
Alignment explanation
Indices: 1076165--1076509 Score: 439
Period size: 135 Copynumber: 2.6 Consensus size: 134
1076155 TGAATCGATC
* * *
1076165 AACATTTCCAATGGAGAGTTCGTAATGAGAAAGACTCA-TCTGACAGAGGGAGAAGAAGTTCATA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAA-ACTCATTC-GATAGAGGGAGAAAAAGTTCATA
* *
1076229 ATGAGAAGAACTTGTTCGACCTATGATCGATTCACGACACTTTAAATAAGCAACGCCTTGCTTAA
64 ATGAGAAGAACTTGTTCGACCTATGATCGATTCACAACACTTTAAATAAGCAACGCCTCGCTTAA
*
1076294 GGGATT
129 GGGAGT
* * *
1076300 AACATTTCTAATGGAGAGTTCATAATTAGAACAACTCATTCAATAGAGGGAGAAAAAGTTCATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAA-AACTCATTCGATAGAGGGAGAAAAAGTTCATAA
* * * *
1076365 TGAGAAGAACTTGTTCGACCTATTGCTCGGTTCACAACA-TTTCGAATCAA-CAATGCCTCGCTT
65 TGAGAAGAACTTGTTCGACCTA-TGATCGATTCACAACACTTT-AAAT-AAGCAACGCCTCGCTT
*
1076428 GAGGGAGT
127 AAGGGAGT
* *
1076436 AACATTTCCAAT-GAGAGTTCATAATGAGAAAAATTCATCCGATAGAGGGA-AAATAAGTTCATA
1 AACATTTCCAATGGAGAGTTCATAATGAG-AAAACTCATTCGATAGAGGGAGAAA-AAGTTCATA
1076499 ATGAGAAGAAC
64 ATGAGAAGAAC
1076510 ATTTGAATTA
Statistics
Matches: 184, Mismatches: 19, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
134 3 0.02
135 130 0.71
136 49 0.27
137 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.26
Consensus pattern (134 bp):
AACATTTCCAATGGAGAGTTCATAATGAGAAAACTCATTCGATAGAGGGAGAAAAAGTTCATAAT
GAGAAGAACTTGTTCGACCTATGATCGATTCACAACACTTTAAATAAGCAACGCCTCGCTTAAGG
GAGT
Found at i:1078432 original size:29 final size:28
Alignment explanation
Indices: 1078382--1078447 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
1078372 TTGTCGTATT
*
1078382 TTTTCATTTTAGTCATTAAATTTTATTTA
1 TTTTCATTTTAGTCATTAAA-TTTAATTA
* *
1078411 TTTTGATTTTAG-CATATTAATTTAATTA
1 TTTTCATTTTAGTCAT-TAAATTTAATTA
1078439 TTTTACATT
1 TTTT-CATT
1078448 CTGGTCACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 14 0.45
29 17 0.55
ACGTcount: A:0.29, C:0.06, G:0.05, T:0.61
Consensus pattern (28 bp):
TTTTCATTTTAGTCATTAAATTTAATTA
Found at i:1078638 original size:29 final size:29
Alignment explanation
Indices: 1078606--1078661 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1078596 TATATTTCTA
* *
1078606 ATTAACTACTATCTTTCATTTTATTGCAT
1 ATTAACCACTAACTTTCATTTTATTGCAT
*
1078635 ATTAACCACTAACTTTTATTTTATTGC
1 ATTAACCACTAACTTTCATTTTATTGC
1078662 GCTCTAACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.50
Consensus pattern (29 bp):
ATTAACCACTAACTTTCATTTTATTGCAT
Found at i:1080409 original size:24 final size:25
Alignment explanation
Indices: 1080375--1080422 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1080365 ACTTGTTTTG
1080375 TCTTTCAAAAGGA-ATTTCTTAAATT
1 TCTTTCAAAA-GATATTTCTTAAATT
*
1080400 TCTTT-AAAAGATATTTTTTAAAT
1 TCTTTCAAAAGATATTTCTTAAAT
1080423 ATTCGACCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 14 0.67
25 5 0.24
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (25 bp):
TCTTTCAAAAGATATTTCTTAAATT
Found at i:1080867 original size:2 final size:2
Alignment explanation
Indices: 1080860--1080931 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
1080850 TTTTATCCCC
1080860 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1080902 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
1080932 TATTAGGTAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1084362 original size:12 final size:12
Alignment explanation
Indices: 1084345--1084369 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1084335 CTCGCTGTCA
1084345 TCATCATCGTCG
1 TCATCATCGTCG
1084357 TCATCATCGTCG
1 TCATCATCGTCG
1084369 T
1 T
1084370 AGTCCTGAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (12 bp):
TCATCATCGTCG
Found at i:1086444 original size:16 final size:16
Alignment explanation
Indices: 1086419--1086468 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
1086409 CTACAAAAAA
*
1086419 ATTAATTAAATTAAAT
1 ATTAAATAAATTAAAT
1086435 ATTAAATAAATTAAAT
1 ATTAAATAAATTAAAT
1086451 ACTTAAATAAATTAAAT
1 A-TTAAATAAATTAAAT
1086468 A
1 A
1086469 CAATATATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 16 0.50
17 16 0.50
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTAAATAAATTAAAT
Found at i:1086458 original size:17 final size:17
Alignment explanation
Indices: 1086420--1086469 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
1086410 TACAAAAAAA
*
1086420 TTAATTAAATTAAATA-
1 TTAAATAAATTAAATAC
1086436 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
1086453 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
1086470 AATATATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 15 0.47
17 17 0.53
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAATAAATTAAATAC
Found at i:1086468 original size:9 final size:9
Alignment explanation
Indices: 1086417--1086468 Score: 65
Period size: 9 Copynumber: 6.1 Consensus size: 9
1086407 ATCTACAAAA
*
1086417 AAATTAATT
1 AAATTAAAT
1086426 AAATTAAAT
1 AAATTAAAT
1086435 --ATTAAAT
1 AAATTAAAT
1086442 AAATTAAAT
1 AAATTAAAT
*
1086451 -ACTTAAAT
1 AAATTAAAT
1086459 AAATTAAAT
1 AAATTAAAT
1086468 A
1 A
1086469 CAATATATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
7 7 0.19
8 7 0.19
9 23 0.62
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (9 bp):
AAATTAAAT
Found at i:1088716 original size:37 final size:38
Alignment explanation
Indices: 1088632--1088719 Score: 135
Period size: 38 Copynumber: 2.3 Consensus size: 38
1088622 CCTAAACCTG
*
1088632 AACCCGACCCGAC-CTGACCCGAATATCACACTTAAAAA
1 AACCCGACCTGACTC-GACCCGAATATCACACTTAAAAA
1088670 AACCCGACCTGACTCGACCCGAATATCACACTT-AAAA
1 AACCCGACCTGACTCGACCCGAATATCACACTTAAAAA
*
1088707 AACCTGACCTGAC
1 AACCCGACCTGAC
1088720 CCGAAAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
37 16 0.34
38 30 0.64
39 1 0.02
ACGTcount: A:0.38, C:0.36, G:0.11, T:0.15
Consensus pattern (38 bp):
AACCCGACCTGACTCGACCCGAATATCACACTTAAAAA
Found at i:1089087 original size:257 final size:260
Alignment explanation
Indices: 1088583--1089160 Score: 864
Period size: 257 Copynumber: 2.2 Consensus size: 260
1088573 TATAAGGTAA
* * ** * *
1088583 AATTATATATTTTTTTCGAGTCGGTCTGGGTTTTTTCACCCTAAACCTGAACCCGACCCGACCTG
1 AATTATATA-TATTTTCGGGTCGGTC-CAGTTTTTTTACCCTAAACCCGAACCCGACCCGACCTG
* * *
1088648 ACCCGAATATCACACTTAAAAAAACCCGACCTGACTCGACCCGAATATCACACTTAAAAAACCTG
64 ACCCGAATATCACACTTAAAAAAACACGACCCGACTCGACCCAAATATCACACTTAAAAAACC--
* * *
1088713 ACCTGACCCGAAAAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATTCGACC
127 ACCTAACCCGAAAAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCAACC
* * *
1088778 TGACCCAACCCGAAATAATAAAAAATATTTTTATTTAATAAAAATAGTGACTTAATCTGACCCGA
192 CGACCCAACCCGAAATAATAAAAAATATTTTTATTTAATAAAAAAAGTGACTTAATCCGACCCGA
1088843 CAC-G
257 C-CTG
*
1088847 AATTATATATATTTTCGGGTCGGTCCAGTTTTTTTACCCTAAACCCGAA-CCGAACCCGACTTGA
1 AATTATATATATTTTCGGGTCGGTCCAGTTTTTTTACCCTAAACCCGAACCCG-ACCCGACCTGA
*
1088911 CCCGAATATCACACTTAAAAAAACATGACCCGACTCGACCCAAATATCACACTTAAAAAA-C-CC
65 CCCGAATATCACACTTAAAAAAACACGACCCGACTCGACCCAAATATCACACTTAAAAAACCACC
* *
1088974 -AACTCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCAACCCGA
130 TAACCCGAAAAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCAACCCGA
* *
1089038 CCCGACCCGAATTAATAAAAAATATTTTTATTTAATAAAAAAAGTGACTTAATCCGACCCGACCT
195 CCCAACCCGAAATAATAAAAAATATTTTTATTTAATAAAAAAAGTGACTTAATCCGACCCGACCT
1089103 G
260 G
1089104 AATTATATATATTTTCGGGTCGGTCCA--TTTTTTACCCTAAACCCGAACCCGACCCGA
1 AATTATATATATTTTCGGGTCGGTCCAGTTTTTTTACCCTAAACCCGAACCCGACCCGA
1089161 ATATCACACT
Statistics
Matches: 290, Mismatches: 21, Indels: 15
0.89 0.06 0.05
Matches are distributed among these distances:
255 26 0.09
256 4 0.01
257 145 0.50
258 2 0.01
261 4 0.01
262 86 0.30
263 14 0.05
264 9 0.03
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.25
Consensus pattern (260 bp):
AATTATATATATTTTCGGGTCGGTCCAGTTTTTTTACCCTAAACCCGAACCCGACCCGACCTGAC
CCGAATATCACACTTAAAAAAACACGACCCGACTCGACCCAAATATCACACTTAAAAAACCACCT
AACCCGAAAAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCAACCCGAC
CCAACCCGAAATAATAAAAAATATTTTTATTTAATAAAAAAAGTGACTTAATCCGACCCGACCTG
Found at i:1091022 original size:19 final size:19
Alignment explanation
Indices: 1090998--1091036 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1090988 AATTCATGTT
1090998 TGGGTAGGATATACTTTAA
1 TGGGTAGGATATACTTTAA
*
1091017 TGGGTAGGATCTACTTTAA
1 TGGGTAGGATATACTTTAA
1091036 T
1 T
1091037 AAATCATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (19 bp):
TGGGTAGGATATACTTTAA
Found at i:1091173 original size:3 final size:3
Alignment explanation
Indices: 1091167--1091193 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1091157 ATTGCATTTG
1091167 CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT
1091194 GACATAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:1092942 original size:15 final size:15
Alignment explanation
Indices: 1092916--1093019 Score: 75
Period size: 15 Copynumber: 6.9 Consensus size: 15
1092906 GTTTTCATTT
1092916 TATTAGTATGTGAAAA
1 TATTA-TATGTGAAAA
*
1092932 TATTATATGTGAATA
1 TATTATATGTGAAAA
*
1092947 TATT-TAATATGAAAA
1 TATTAT-ATGTGAAAA
* *
1092962 TGTTCTATGTGAAAA
1 TATTATATGTGAAAA
* ** *
1092977 TGTGGTAAGTGAAAA
1 TATTATATGTGAAAA
* * *
1092992 TGTTCTACGTGAAAA
1 TATTATATGTGAAAA
*
1093007 TATCATATGTGAA
1 TATTATATGTGAA
1093020 TGTGCTCTAT
Statistics
Matches: 71, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
14 1 0.01
15 64 0.90
16 6 0.08
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (15 bp):
TATTATATGTGAAAA
Found at i:1093019 original size:30 final size:30
Alignment explanation
Indices: 1092956--1093019 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1092946 ATATTTAATA
* * **
1092956 TGAAAATGTTCTATGTGAAAATGTGGTAAG
1 TGAAAATGTTCTACGTGAAAATATCATAAG
*
1092986 TGAAAATGTTCTACGTGAAAATATCATATG
1 TGAAAATGTTCTACGTGAAAATATCATAAG
1093016 TGAA
1 TGAA
1093020 TGTGCTCTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (30 bp):
TGAAAATGTTCTACGTGAAAATATCATAAG
Found at i:1093233 original size:23 final size:24
Alignment explanation
Indices: 1093199--1093253 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
1093189 CTAAGCGTTC
*
1093199 CTTCGG-GACATA-TCTATATGGCA
1 CTTCGGTG-CATATTCTACATGGCA
* *
1093222 CTTTGGTGCATATTCTACGTGGCA
1 CTTCGGTGCATATTCTACATGGCA
1093246 CTTCGGTG
1 CTTCGGTG
1093254 TAAATTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 9 0.35
24 17 0.65
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (24 bp):
CTTCGGTGCATATTCTACATGGCA
Found at i:1099932 original size:15 final size:15
Alignment explanation
Indices: 1099912--1099997 Score: 93
Period size: 15 Copynumber: 5.7 Consensus size: 15
1099902 ATTTTATTGG
* *
1099912 TATGTGAAAATTTTA
1 TATGTGAAAATGTTC
*
1099927 TATGTGAATATGTT-
1 TATGTGAAAATGTTC
*
1099941 TAATATGAAAATGTTC
1 T-ATGTGAAAATGTTC
* *
1099957 TATGTGAGAATGTGC
1 TATGTGAAAATGTTC
*
1099972 TAAGTGAAAATGTTC
1 TATGTGAAAATGTTC
1099987 TATGTGAAAAT
1 TATGTGAAAAT
1099998 ACCCTATGTG
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
14 1 0.02
15 56 0.97
16 1 0.02
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.40
Consensus pattern (15 bp):
TATGTGAAAATGTTC
Found at i:1100009 original size:30 final size:30
Alignment explanation
Indices: 1099946--1100009 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1099936 ATGTTTAATA
* ***
1099946 TGAAAATGTTCTATGTGAGAATGTGCTAAG
1 TGAAAATGTTCTATGTGAAAATACCCTAAG
*
1099976 TGAAAATGTTCTATGTGAAAATACCCTATG
1 TGAAAATGTTCTATGTGAAAATACCCTAAG
1100006 TGAA
1 TGAA
1100010 TGTGCTCTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (30 bp):
TGAAAATGTTCTATGTGAAAATACCCTAAG
Found at i:1100168 original size:24 final size:24
Alignment explanation
Indices: 1100136--1100197 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
1100126 GGTTCTAAGT
*
1100136 GGTCATTCGGGACAAATT-TCACGC
1 GGTCCTTCGGGACAAATTCT-ACGC
*
1100160 GGTCCTTCGGGATAAATTCTACGC
1 GGTCCTTCGGGACAAATTCTACGC
1100184 GGTCCTTCGGGACA
1 GGTCCTTCGGGACA
1100198 TATCTATGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 33 0.97
25 1 0.03
ACGTcount: A:0.21, C:0.26, G:0.27, T:0.26
Consensus pattern (24 bp):
GGTCCTTCGGGACAAATTCTACGC
Found at i:1100214 original size:23 final size:24
Alignment explanation
Indices: 1100175--1100239 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 24
1100165 TTCGGGATAA
*
1100175 ATTCTACGCGGTC-CTTCGG-GACAT
1 ATTCTACGTGG-CACTTCGGTG-CAT
*
1100199 A-TCTATGTGGCACTTCGGTGCAT
1 ATTCTACGTGGCACTTCGGTGCAT
1100222 ATTCTACGTGGCACTTCG
1 ATTCTACGTGGCACTTCG
1100240 ATGCCAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
22 1 0.03
23 17 0.49
24 17 0.49
ACGTcount: A:0.17, C:0.26, G:0.25, T:0.32
Consensus pattern (24 bp):
ATTCTACGTGGCACTTCGGTGCAT
Found at i:1100232 original size:24 final size:24
Alignment explanation
Indices: 1100164--1100239 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
1100154 TCACGCGGTC
* * *
1100164 CTTCGGGATAAATTCTACGCGGTC-
1 CTTCGGGACATATTCTACGTGG-CA
*
1100188 CTTCGGGACATA-TCTATGTGGCA
1 CTTCGGGACATATTCTACGTGGCA
1100211 CTTCGGTG-CATATTCTACGTGGCA
1 CTTCGG-GACATATTCTACGTGGCA
1100235 CTTCG
1 CTTCG
1100240 ATGCCAATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
22 1 0.02
23 17 0.39
24 26 0.59
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (24 bp):
CTTCGGGACATATTCTACGTGGCA
Found at i:1104196 original size:16 final size:15
Alignment explanation
Indices: 1104162--1104190 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1104152 TACATAAATT
1104162 TACATCTTTGCATCA
1 TACATCTTTGCATCA
1104177 TACATCTTT-CATCA
1 TACATCTTTGCATCA
1104191 CATACAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.28, C:0.28, G:0.03, T:0.41
Consensus pattern (15 bp):
TACATCTTTGCATCA
Found at i:1104765 original size:100 final size:99
Alignment explanation
Indices: 1104600--1104787 Score: 227
Period size: 100 Copynumber: 1.9 Consensus size: 99
1104590 TGTTTCCTTC
* ** *
1104600 AAACAAATTTCATCTCGCTCGAGAAGTTTCTCTTGAAACACAAGCAAAAGATCGTTTCAATTTAA
1 AAACAAATTTCATCTCGCTCGAAAAGTTTCTCTCAAAACACAACCAAAAGATCGTTTCAATTTAA
1104665 A-AAAA-TTACCTCACTCGAGATTTTTTCTTTGG
66 ACAAAATTTACCTCACTCGAGATTTTTTCTTTGG
* * ** **
1104697 AAACAAAGTTTTATCTCGCTGGAAATAGTTTCTCTCAAAACACAAACCTCAAGATCGTTTCTCTT
1 AAACAAA-TTTCATCTCGCTCGAAA-AGTTTCTCTCAAAACAC-AACCAAAAGATCGTTTCAATT
* *
1104762 TAAACAAAATTTATCTCGCTCGAGAT
63 TAAACAAAATTTACCTCACTCGAGAT
1104788 AATTTCCCTT
Statistics
Matches: 74, Mismatches: 12, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
97 7 0.09
98 14 0.19
99 15 0.20
100 20 0.27
101 4 0.05
102 14 0.19
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (99 bp):
AAACAAATTTCATCTCGCTCGAAAAGTTTCTCTCAAAACACAACCAAAAGATCGTTTCAATTTAA
ACAAAATTTACCTCACTCGAGATTTTTTCTTTGG
Found at i:1104878 original size:35 final size:36
Alignment explanation
Indices: 1104754--1104893 Score: 123
Period size: 35 Copynumber: 3.9 Consensus size: 36
1104744 CTCAAGATCG
* *
1104754 TTTCTCTTTAAACAAAATTT-ATCTCGCTCGAGATAA
1 TTTCTCTTGAAACAAAATTTCATCTCACTCGAGAT-A
* * * *
1104790 TTTCCCTTGAAATAAAATTTCA-CT---T-GAAATTG
1 TTTCTCTTGAAACAAAATTTCATCTCACTCGAGA-TA
1104822 TTTCTCTTGAAACAAACAAATTTCATCTCACTCGAGAT-
1 TTTCTCTTGAAAC--A-AAATTTCATCTCACTCGAGATA
*
1104860 TTTCTCTTGAAACAAAATTTCATCTCACTTGAGA
1 TTTCTCTTGAAACAAAATTTCATCTCACTCGAGA
1104894 CAGTTTCCCA
Statistics
Matches: 85, Mismatches: 9, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
32 14 0.16
33 2 0.02
34 1 0.01
35 27 0.32
36 22 0.26
37 1 0.01
38 13 0.15
39 2 0.02
40 3 0.04
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.38
Consensus pattern (36 bp):
TTTCTCTTGAAACAAAATTTCATCTCACTCGAGATA
Found at i:1110893 original size:65 final size:64
Alignment explanation
Indices: 1110759--1110919 Score: 216
Period size: 65 Copynumber: 2.5 Consensus size: 64
1110749 GTGCACTAAG
* * *
1110759 TGTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAGCCTGAGTGCATCGATGCATGGCT
1 TGTGCATCGATGCATAAAATGCATTCAATGTTTTCAAAAACCCTGAGTGCATCGATGCATGGCT
* * * * *
1110823 GGTGCATCGATGCATCAAGTGTATTCAATGTTTTCATAAAACCCTGAGTGTATCGATGCATGG-T
1 TGTGCATCGATGCATAAAATGCATTCAATGTTTTCA-AAAACCCTGAGTGCATCGATGCATGGCT
*
1110887 ATGTGCATCGATGCATGAAATGCATTCAATGTT
1 -TGTGCATCGATGCATAAAATGCATTCAATGTT
1110920 CAATTTATTC
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 31 0.37
65 52 0.63
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.32
Consensus pattern (64 bp):
TGTGCATCGATGCATAAAATGCATTCAATGTTTTCAAAAACCCTGAGTGCATCGATGCATGGCT
Found at i:1110958 original size:65 final size:64
Alignment explanation
Indices: 1110760--1110969 Score: 205
Period size: 65 Copynumber: 3.2 Consensus size: 64
1110750 TGCACTAAGT
* * * *
1110760 GTGCATCGATGCATAAAATGCATTCGATGTTTTGA-AAAAGCC-TGAGTGCATCGATGCATGGCT
1 GTGCATCGATGCATCAAATGCATTCAATG-TTTCATAAAA-CCATGAGTGCATCGATGCATGGTT
1110823 G
64 G
* * * *
1110824 GTGCATCGATGCATCAAGTGTATTCAATGTTTTCATAAAACCCTGAGTGTATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCAATG-TTTCATAAAACCATGAGTGCATCGATGCATGGT-T
1110889 -
64 G
* * **
1110889 GTGCATCGATGCATGAAATGCATTCAATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCAATGTTTC-A-TAAAACCATGAGTGCATCGATGCATGG-T
1110952 TG
63 TG
*
1110954 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
1110970 CTTTGAAAAA
Statistics
Matches: 122, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
63 3 0.02
64 49 0.40
65 69 0.57
66 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCAATGTTTCATAAAACCATGAGTGCATCGATGCATGGTTG
Found at i:1119062 original size:34 final size:34
Alignment explanation
Indices: 1119019--1119096 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 34
1119009 AGCTCGATAC
* * *
1119019 TCAAACTCGATTGAAACTCGATTTTGAGCTCAAT
1 TCAAGCTCGATTCAAACTCGACTTTGAGCTCAAT
* *
1119053 TCAAGCTCGATTCAATCTTGACTTTGAGCTCAAT
1 TCAAGCTCGATTCAAACTCGACTTTGAGCTCAAT
1119087 TCAAGCTCGA
1 TCAAGCTCGA
1119097 CTTTGAGCTC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.32
Consensus pattern (34 bp):
TCAAGCTCGATTCAAACTCGACTTTGAGCTCAAT
Found at i:1119082 original size:23 final size:23
Alignment explanation
Indices: 1119056--1119141 Score: 127
Period size: 23 Copynumber: 3.7 Consensus size: 23
1119046 GCTCAATTCA
* *
1119056 AGCTCGATTCAATCTTGACTTTG
1 AGCTCGATTCAAGCTCGACTTTG
*
1119079 AGCTCAATTCAAGCTCGACTTTG
1 AGCTCGATTCAAGCTCGACTTTG
*
1119102 AGCTCGATTCAAGCTCGACTTTA
1 AGCTCGATTCAAGCTCGACTTTG
*
1119125 AGCTCGATTGAAGCTCG
1 AGCTCGATTCAAGCTCG
1119142 TTTGAAGCTT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (23 bp):
AGCTCGATTCAAGCTCGACTTTG
Found at i:1119141 original size:11 final size:11
Alignment explanation
Indices: 1119024--1119150 Score: 71
Period size: 11 Copynumber: 11.2 Consensus size: 11
1119014 GATACTCAAA
*
1119024 CTCGATTGAAA
1 CTCGATTGAAG
1119035 CTCGATTTTG-AG
1 CTCGA--TTGAAG
* *
1119047 CTCAATTCAAG
1 CTCGATTGAAG
* *
1119058 CTCGATTCAAT
1 CTCGATTGAAG
*
1119069 CTTGACTTTG-AG
1 CTCGA--TTGAAG
* *
1119081 CTCAATTCAAG
1 CTCGATTGAAG
1119092 CTCGACTTTG-AG
1 CTCGA--TTGAAG
*
1119104 CTCGATTCAAG
1 CTCGATTGAAG
*
1119115 CTCGACTTTAAG
1 CTCGA-TTGAAG
1119127 CTCGATTGAAG
1 CTCGATTGAAG
*
1119138 CTCGTTTGAAG
1 CTCGATTGAAG
1119149 CT
1 CT
1119151 TGAAGACGGG
Statistics
Matches: 89, Mismatches: 17, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
10 6 0.07
11 50 0.56
12 26 0.29
13 7 0.08
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (11 bp):
CTCGATTGAAG
Found at i:1121368 original size:14 final size:14
Alignment explanation
Indices: 1121325--1121361 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1121315 ATGATGTAAG
*
1121325 TATAATTTAAGGTT
1 TATAGTTTAAGGTT
*
1121339 TATGGTTTAAGGTT
1 TATAGTTTAAGGTT
1121353 TATAGTTTA
1 TATAGTTTA
1121362 GGATTTAAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (14 bp):
TATAGTTTAAGGTT
Found at i:1124969 original size:24 final size:24
Alignment explanation
Indices: 1124942--1124995 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1124932 AATTTTTGAC
1124942 TTTTTTAG-CTTTTGGCTTTTTCTA
1 TTTTTTAGCCTTTT-GCTTTTTCTA
* * *
1124966 TTTTTTGGCCTTTTTCTTTTTCTT
1 TTTTTTAGCCTTTTGCTTTTTCTA
1124990 TTTTTT
1 TTTTTT
1124996 TGAAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.04, C:0.13, G:0.09, T:0.74
Consensus pattern (24 bp):
TTTTTTAGCCTTTTGCTTTTTCTA
Found at i:1124971 original size:17 final size:17
Alignment explanation
Indices: 1124951--1124986 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1124941 CTTTTTTAGC
1124951 TTTTGG-CTTTTTCTATT
1 TTTTGGCCTTTTTCT-TT
1124968 TTTTGGCCTTTTTCTTT
1 TTTTGGCCTTTTTCTTT
1124985 TT
1 TT
1124987 CTTTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.03, C:0.14, G:0.11, T:0.72
Consensus pattern (17 bp):
TTTTGGCCTTTTTCTTT
Found at i:1129245 original size:13 final size:13
Alignment explanation
Indices: 1129218--1129262 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
1129208 AAATAAAATG
1129218 AAGATAAATGAAAA
1 AAGA-AAATGAAAA
*
1129232 AAGAAAATGGAAA
1 AAGAAAATGAAAA
1129245 AAG-AAATGAAAA
1 AAGAAAATGAAAA
1129257 AAGAAA
1 AAGAAA
1129263 GAGGAAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 11 0.39
13 13 0.46
14 4 0.14
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (13 bp):
AAGAAAATGAAAA
Found at i:1129251 original size:12 final size:12
Alignment explanation
Indices: 1129223--1129262 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
1129213 AAATGAAGAT
1129223 AAATGAAAAAAG
1 AAATGAAAAAAG
*
1129235 AAAATGGAAAAAG
1 -AAATGAAAAAAG
1129248 AAATGAAAAAAG
1 AAATGAAAAAAG
1129260 AAA
1 AAA
1129263 GAGGAAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.07
Consensus pattern (12 bp):
AAATGAAAAAAG
Found at i:1129251 original size:25 final size:24
Alignment explanation
Indices: 1129223--1129274 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 24
1129213 AAATGAAGAT
1129223 AAATGAAAAAAGAAA-ATGGAAAAAG
1 AAATGAAAAAAGAAAGA-GG-AAAAG
1129248 AAATGAAAAAAGAAAGAGGAAAAG
1 AAATGAAAAAAGAAAGAGGAAAAG
1129272 AAA
1 AAA
1129275 AGGGGGTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 8 0.31
25 17 0.65
26 1 0.04
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (24 bp):
AAATGAAAAAAGAAAGAGGAAAAG
Found at i:1130394 original size:105 final size:105
Alignment explanation
Indices: 1130192--1130383 Score: 233
Period size: 105 Copynumber: 1.8 Consensus size: 105
1130182 TAATGACTTT
* ** * * * * *
1130192 AATCAATCACAGAAGGATGTGGATTGACATTTCCAAAAGAGTTGATAATGAGAAGAACTCGTTCC
1 AATCAATCACAGAAGGATGTGAATCAACATTTCCAAAAGAATTCATAATGAGAAAAACTCATCCC
*
1130257 AAAGGAGAAAGTACATAATGAGAAAATCTTATTCCTTTCA
66 AAAGGAAAAAGTACATAATGAGAAAATCTTATTCCTTTCA
* *
1130297 AATCCATCACAGAAGGA-GATGAATCAACATTTCCAGAAGAATTCATAATGAGAAAAACTCATCC
1 AATCAATCACAGAAGGATG-TGAATCAACATTTCCAAAAGAATTCATAATGAGAAAAACTCATCC
* * *
1130361 CGATGAGAAAAAGTTCATAATGA
65 CAAAG-GAAAAAGTACATAATGA
1130384 AATAACTTAT
Statistics
Matches: 71, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
104 1 0.01
105 55 0.77
106 15 0.21
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.23
Consensus pattern (105 bp):
AATCAATCACAGAAGGATGTGAATCAACATTTCCAAAAGAATTCATAATGAGAAAAACTCATCCC
AAAGGAAAAAGTACATAATGAGAAAATCTTATTCCTTTCA
Found at i:1130990 original size:14 final size:14
Alignment explanation
Indices: 1130906--1131010 Score: 62
Period size: 14 Copynumber: 7.9 Consensus size: 14
1130896 ATAATGTTAG
*
1130906 TATTATTATTATAA
1 TATTATTATTATTA
* *
1130920 TATCATTA-CATTA
1 TATTATTATTATTA
1130933 TTATTATTACTTATTA
1 -TATTATTA-TTATTA
1130949 -A--ATTATT-TT-
1 TATTATTATTATTA
* *
1130958 TAGTACTATTATT-
1 TATTATTATTATTA
* *
1130971 TTTTATTGTTATTA
1 TATTATTATTATTA
1130985 TATTATTATTATTA
1 TATTATTATTATTA
**
1130999 TACCATTATTAT
1 TATTATTATTAT
1131011 ACTTTAAAAA
Statistics
Matches: 69, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
10 3 0.04
11 2 0.03
12 9 0.13
13 14 0.20
14 37 0.54
16 4 0.06
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:1131010 original size:3 final size:3
Alignment explanation
Indices: 1130906--1130999 Score: 65
Period size: 3 Copynumber: 33.0 Consensus size: 3
1130896 ATAATGTTAG
* * *
1130906 TAT TAT TAT TA- TAA TAT CAT TA- CAT TAT TAT TAT TACT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
* * * * *
1130949 AAT TAT TTT TAG TAC TAT TAT T-T T-T TAT TGT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1130994 TAT TAT
1 TAT TAT
1131000 ACCATTATTA
Statistics
Matches: 71, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
2 10 0.14
3 58 0.82
4 3 0.04
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1134743 original size:18 final size:18
Alignment explanation
Indices: 1134710--1134744 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1134700 ATGTACTAAC
*
1134710 TCATTTCTTTTATTTTTT
1 TCATTTCTTGTATTTTTT
*
1134728 TCATTTCTTGTCTTTTT
1 TCATTTCTTGTATTTTT
1134745 GCATTGCATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.14, G:0.03, T:0.74
Consensus pattern (18 bp):
TCATTTCTTGTATTTTTT
Found at i:1138307 original size:38 final size:38
Alignment explanation
Indices: 1138222--1138340 Score: 112
Period size: 38 Copynumber: 3.1 Consensus size: 38
1138212 AACTTTTTTG
* * * * *
1138222 TCCTTAAGATTGTTTCCCTAGAAACCTGAATTTTGTCT
1 TCCTTAAGACTGTTTCTCTAGAAACCTCAACTTTATCT
* *
1138260 TCCTCAAGACTGTTTCTCTAAAAACCTCAACTTTATCT
1 TCCTTAAGACTGTTTCTCTAGAAACCTCAACTTTATCT
* ** * * *
1138298 TTCTTAAGACCATTTTTCTAGAAACTTCAACTTTGTCT
1 TCCTTAAGACTGTTTCTCTAGAAACCTCAACTTTATCT
*
1138336 CCCTT
1 TCCTT
1138341 GAGATAGTTT
Statistics
Matches: 64, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.25, C:0.25, G:0.08, T:0.41
Consensus pattern (38 bp):
TCCTTAAGACTGTTTCTCTAGAAACCTCAACTTTATCT
Found at i:1138389 original size:38 final size:39
Alignment explanation
Indices: 1138333--1138432 Score: 123
Period size: 38 Copynumber: 2.6 Consensus size: 39
1138323 TTCAACTTTG
*
1138333 TCTCCCTTGAGATAGTTTCCCTTAAAACACC-AAATTCA
1 TCTCACTTGAGATAGTTTCCCTTAAAACACCGAAATTCA
* * *
1138371 TCT-ATCTTGAGATAGTTTCCCTTGAAACACCGAATTTTA
1 TCTCA-CTTGAGATAGTTTCCCTTAAAACACCGAAATTCA
* *
1138410 TCTCACTCGAGACAGTTTCCCTT
1 TCTCACTTGAGATAGTTTCCCTT
1138433 GAAATTAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
38 28 0.53
39 24 0.45
40 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.35
Consensus pattern (39 bp):
TCTCACTTGAGATAGTTTCCCTTAAAACACCGAAATTCA
Found at i:1138431 original size:39 final size:38
Alignment explanation
Indices: 1138341--1138436 Score: 122
Period size: 39 Copynumber: 2.5 Consensus size: 38
1138331 TGTCTCCCTT
* *
1138341 GAGATAGTTTCCCTTAAAACACCAAATTCATCTATCTT
1 GAGATAGTTTCCCTTGAAACACCAAATTCATCTATCTC
* *
1138379 GAGATAGTTTCCCTTGAAACACCGAATTTTATCTCA-CTC
1 GAGATAGTTTCCCTTGAAACACC-AAATTCATCT-ATCTC
*
1138418 GAGACAGTTTCCCTTGAAA
1 GAGATAGTTTCCCTTGAAA
1138437 TTAAAAGTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
38 22 0.43
39 28 0.55
40 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.32
Consensus pattern (38 bp):
GAGATAGTTTCCCTTGAAACACCAAATTCATCTATCTC
Found at i:1138669 original size:142 final size:141
Alignment explanation
Indices: 1138376--1138682 Score: 431
Period size: 142 Copynumber: 2.2 Consensus size: 141
1138366 ATTCATCTAT
* *
1138376 CTTGAGATAGTTTCCCTTGAAACACCGAATTTTATCTCACTCGAGACAGTTTCCCTTGAAATTAA
1 CTTGAGATAGTTTCTCTTGAAACA-C-AATTTTATCTCACTCAAGACAGTTTCCCTTGAAATTAA
* *
1138441 AAGTTTACTTTACTTGAGGAATTTTCCCTTGAAATGAAAAATCAAGATTATTTCGCTCGAAACAA
64 AAGTTTACTTCACTTGAGGAATTTTCCCTTGAAATCAAAAATCAAGATTATTTCGCTCGAAACAA
1138506 AAACTTTATCTCA
129 AAACTTTATCTCA
*
1138519 CTTGAGATAGTGTCTCTTGAAACA-AA-TTTATTCTCACTCAAGACAGTTTCCCTTGAAATTAAA
1 CTTGAGATAGTTTCTCTTGAAACACAATTTTA-TCTCACTCAAGACAGTTTCCCTTGAAATTAAA
* ** * * * *
1138582 ATTTTTGTCTCACTTGAGGAATTTTCCCTTGAAATACAAAAATCGATATTGTTTCGTTC-AAACC
65 AGTTTACT-TCACTTGAGGAATTTTCCCTTGAAAT-CAAAAATCAAGATTATTTCGCTCGAAA-C
1138646 AAAAACTTTATCTCA
127 AAAAACTTTATCTCA
1138661 CTTGAGATAGTTTCTCTTGAAA
1 CTTGAGATAGTTTCTCTTGAAA
1138683 GAGATTTCAT
Statistics
Matches: 147, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
139 4 0.03
140 38 0.26
141 28 0.19
142 55 0.37
143 22 0.15
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (141 bp):
CTTGAGATAGTTTCTCTTGAAACACAATTTTATCTCACTCAAGACAGTTTCCCTTGAAATTAAAA
GTTTACTTCACTTGAGGAATTTTCCCTTGAAATCAAAAATCAAGATTATTTCGCTCGAAACAAAA
ACTTTATCTCA
Found at i:1140092 original size:15 final size:15
Alignment explanation
Indices: 1140069--1140111 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
1140059 CGTGTTATAT
*
1140069 ATATGAAAATGTTCT
1 ATATGAAAATGTTCC
* **
1140084 ATGTGAAAACATTCC
1 ATATGAAAATGTTCC
1140099 ATATGAAAATGTT
1 ATATGAAAATGTT
1140112 ATACACGAAT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (15 bp):
ATATGAAAATGTTCC
Found at i:1140346 original size:24 final size:24
Alignment explanation
Indices: 1140319--1140365 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1140309 AAATATATGC
* *
1140319 GGCAATTCGATGCATATTCTACGT
1 GGCAATTCGATGCAAATTATACGT
* *
1140343 GGCACTTCGGTGCAAATTATACG
1 GGCAATTCGATGCAAATTATACG
1140366 AGTAGTGGTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (24 bp):
GGCAATTCGATGCAAATTATACGT
Found at i:1149299 original size:23 final size:23
Alignment explanation
Indices: 1149269--1149318 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
1149259 GCCTTAAAGA
*
1149269 CCATTTACAGATCCAACATTCGC
1 CCATTTACAGATCCAACATTCAC
1149292 CCATTTACAGATCCAACATTCAC
1 CCATTTACAGATCCAACATTCAC
1149315 CCAT
1 CCAT
1149319 AATCCAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.32, C:0.36, G:0.06, T:0.26
Consensus pattern (23 bp):
CCATTTACAGATCCAACATTCAC
Found at i:1151235 original size:22 final size:22
Alignment explanation
Indices: 1151189--1151232 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1151179 TGTAGCAGTA
**
1151189 CTGTAGCAAGGGTATCGGTACC
1 CTGTAGCAAGGGTATCAATACC
1151211 CTGTAGC-AGGGTATCAATACC
1 CTGTAGCAAGGGTATCAATACC
1151232 C
1 C
1151233 CTGATGTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (22 bp):
CTGTAGCAAGGGTATCAATACC
Found at i:1154054 original size:29 final size:29
Alignment explanation
Indices: 1154022--1154133 Score: 70
Period size: 30 Copynumber: 3.8 Consensus size: 29
1154012 TAAAGTTTAT
1154022 GTTTTGTCATTTTAGTCTTTTAAATTTCA
1 GTTTTGTCATTTTAGTCTTTTAAATTTCA
* * **
1154051 G-TTTGTGATATTTGGTCTTCAAAATTTCTA
1 GTTTTGTCAT-TTTAGTCTTTTAAATTTC-A
**
1154081 -TTTT-TACTATTTTAGT-TTTTGAAATTTTT
1 GTTTTGT-C-ATTTTAGTCTTTT-AAATTTCA
*
1154110 GTTTGTGTCATTTTATTTCTTTTA
1 GTTT-TGTCATTTTA-GTCTTTTA
1154134 CTTTCTATTT
Statistics
Matches: 61, Mismatches: 11, Indels: 20
0.66 0.12 0.22
Matches are distributed among these distances:
28 7 0.11
29 19 0.31
30 24 0.39
31 6 0.10
32 5 0.08
ACGTcount: A:0.20, C:0.08, G:0.12, T:0.61
Consensus pattern (29 bp):
GTTTTGTCATTTTAGTCTTTTAAATTTCA
Found at i:1155612 original size:27 final size:28
Alignment explanation
Indices: 1155565--1155618 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
1155555 TCTTACATGT
* *
1155565 ACACTAATTTCTTCTCTTTTGTTTGTGG
1 ACACTAACTTATTCTCTTTTGTTTGTGG
1155593 ACACTAACTTATT-TCTTTTGTTTGTG
1 ACACTAACTTATTCTCTTTTGTTTGTG
1155619 TCATTTTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.17, C:0.17, G:0.13, T:0.54
Consensus pattern (28 bp):
ACACTAACTTATTCTCTTTTGTTTGTGG
Found at i:1159099 original size:10 final size:10
Alignment explanation
Indices: 1159084--1159167 Score: 94
Period size: 9 Copynumber: 9.1 Consensus size: 10
1159074 CTCATCCATC
1159084 AGAGAAAAAA
1 AGAGAAAAAA
*
1159094 AGAGAAAAGA
1 AGAGAAAAAA
1159104 A-A-AAAAAA
1 AGAGAAAAAA
1159112 AGA-AAAAAGA
1 AGAGAAAAA-A
1159122 AGA-AAAAAA
1 AGAGAAAAAA
1159131 A-AG-AAAAA
1 AGAGAAAAAA
1159139 AGAG-AAAAA
1 AGAGAAAAAA
1159148 AGAGAAAAAA
1 AGAGAAAAAA
1159158 AG-GAAAAAA
1 AGAGAAAAAA
1159167 A
1 A
1159168 TTGAATCAAG
Statistics
Matches: 67, Mismatches: 2, Indels: 11
0.84 0.03 0.14
Matches are distributed among these distances:
8 13 0.19
9 28 0.42
10 26 0.39
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AGAGAAAAAA
Found at i:1159103 original size:7 final size:6
Alignment explanation
Indices: 1159090--1159156 Score: 57
Period size: 7 Copynumber: 10.8 Consensus size: 6
1159080 CATCAGAGAA
*
1159090 AAAAAG AGAAAAG AAAAA- AAAAAG AAAAAAG AAGAAAA AAAAAG AAAAAAG
1 AAAAAG A-AAAAG AAAAAG AAAAAG -AAAAAG AA-AAAG AAAAAG -AAAAAG
* *
1159141 AGAAA- AAAGAG AAAAA
1 AAAAAG AAAAAG AAAAA
1159157 AAGGAAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
5 8 0.16
6 18 0.37
7 23 0.47
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1159124 original size:21 final size:21
Alignment explanation
Indices: 1159100--1159148 Score: 84
Period size: 20 Copynumber: 2.4 Consensus size: 21
1159090 AAAAAGAGAA
1159100 AAGAAAAAAAAAAGAAAAAAG
1 AAGAAAAAAAAAAGAAAAAAG
1159121 AAG-AAAAAAAAAGAAAAAAG
1 AAGAAAAAAAAAAGAAAAAAG
1159141 -AGAAAAAA
1 AAGAAAAAA
1159149 GAGAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (21 bp):
AAGAAAAAAAAAAGAAAAAAG
Found at i:1159140 original size:38 final size:37
Alignment explanation
Indices: 1159088--1159167 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 37
1159078 TCCATCAGAG
*
1159088 AAAAAAAGAGAAAAGAAAAAAAAAAGAAAAAAGAAGAA
1 AAAAAAAGAAAAAAGAAAAAAAAAAGAAAAAA-AAGAA
* * *
1159126 AAAAAAAGAAAAAAGAGAAAAAAGAGAAAAAAAGGAA
1 AAAAAAAGAAAAAAGAAAAAAAAAAGAAAAAAAAGAA
1159163 AAAAA
1 AAAAA
1159168 TTGAATCAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
37 9 0.24
38 29 0.76
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (37 bp):
AAAAAAAGAAAAAAGAAAAAAAAAAGAAAAAAAAGAA
Found at i:1162326 original size:69 final size:70
Alignment explanation
Indices: 1162247--1162407 Score: 254
Period size: 70 Copynumber: 2.3 Consensus size: 70
1162237 CCTAAAAGAG
*
1162247 AAAGTTCATAATGAGAAGAACTT-TTCCTTTCAAATTCACCACAGAA-GATGGTGAACCAGCATT
1 AAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATTCACCACAGAAGGA-GGTGAACCAACATT
*
1162310 TCCATA
65 TCCAGA
* *
1162316 AAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATTCACTATAGAAGGAGGTGAACCAACATTT
1 AAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATTCACCACAGAAGGAGGTGAACCAACATTT
1162381 CCAGA
66 CCAGA
*
1162386 AGAGTTCATAATGAGAAGAACT
1 AAAGTTCATAATGAGAAGAACT
1162408 CACTCAAAGA
Statistics
Matches: 85, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
69 23 0.27
70 60 0.71
71 2 0.02
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (70 bp):
AAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATTCACCACAGAAGGAGGTGAACCAACATTT
CCAGA
Found at i:1162451 original size:20 final size:20
Alignment explanation
Indices: 1162388--1162452 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
1162378 TTTCCAGAAG
1162388 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* **
1162408 CA-CTCA-AA-GAAGAAGAAGA
1 -AGTTCATAATG-AGAAGAACT
1162427 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
1162447 TGTTCA
1 AGTTCA
1162453 ACCTTGGTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 9
0.67 0.14 0.18
Matches are distributed among these distances:
18 2 0.06
19 12 0.36
20 17 0.52
21 2 0.06
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.22
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:1162556 original size:78 final size:78
Alignment explanation
Indices: 1162427--1162602 Score: 327
Period size: 78 Copynumber: 2.3 Consensus size: 78
1162417 AAGAAGAAGA
1162427 AGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTTGATTCCATCACAGAAGGAGGTGGATCAAC
1 AGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTTGATTCCATCACAGAAGGAGGTGGATCAAC
1162492 ATTTTCAA-TGGAG
66 A-TTTCAAGTGGAG
*
1162505 AGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTTGATTCCATCACAGAAGGAGGTGGATCAAT
1 AGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTTGATTCCATCACAGAAGGAGGTGGATCAAC
1162570 ATTTCAAGTGGAG
66 ATTTCAAGTGGAG
1162583 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
1162603 CATCCAACGA
Statistics
Matches: 96, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
77 6 0.06
78 90 0.94
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (78 bp):
AGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTTGATTCCATCACAGAAGGAGGTGGATCAAC
ATTTCAAGTGGAG
Found at i:1162719 original size:38 final size:39
Alignment explanation
Indices: 1162669--1162762 Score: 156
Period size: 38 Copynumber: 2.5 Consensus size: 39
1162659 TGTTTCCAGT
* *
1162669 GAAG-AGTTCATAATGAGAATAACTTATCCAACAAG-GA
1 GAAGAAGTTCATAATGAGAAGAACTCATCCAACAAGAGA
1162706 GAAGAAGTTCATAATGAGAAGAACTCATCCAACAAGAGA
1 GAAGAAGTTCATAATGAGAAGAACTCATCCAACAAGAGA
1162745 GAAGAAGTTCATAATGAG
1 GAAGAAGTTCATAATGAG
1162763 TCACCCACGA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
37 4 0.08
38 29 0.55
39 20 0.38
ACGTcount: A:0.47, C:0.13, G:0.21, T:0.19
Consensus pattern (39 bp):
GAAGAAGTTCATAATGAGAAGAACTCATCCAACAAGAGA
Found at i:1165114 original size:30 final size:30
Alignment explanation
Indices: 1165036--1165114 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 30
1165026 TCTTCAAAAT
**
1165036 TTTCTATTTTTACTATTTTAGTTTTTGAAA
1 TTTCTATTTTTGTTATTTTAGTTTTTGAAA
* * * * *
1165066 TTTTTGTTTGTGTCATTTTAGTTCTTT-AAC
1 TTTCTATTTTTGTTATTTTAGTT-TTTGAAA
1165096 TTTCTATTTTTGTTATTTT
1 TTTCTATTTTTGTTATTTT
1165115 GATCCTTAAA
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
30 34 0.92
31 3 0.08
ACGTcount: A:0.16, C:0.08, G:0.09, T:0.67
Consensus pattern (30 bp):
TTTCTATTTTTGTTATTTTAGTTTTTGAAA
Found at i:1167024 original size:12 final size:13
Alignment explanation
Indices: 1167000--1167032 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
1166990 TCTGACCCGA
1167000 CCGACCCGTTGAC
1 CCGACCCGTTGAC
1167013 CCGACCCG-TGAC
1 CCGACCCGTTGAC
1167025 CCGACCCG
1 CCGACCCG
1167033 ACCCGGTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.15, C:0.52, G:0.24, T:0.09
Consensus pattern (13 bp):
CCGACCCGTTGAC
Found at i:1167093 original size:29 final size:29
Alignment explanation
Indices: 1167041--1167138 Score: 144
Period size: 29 Copynumber: 3.4 Consensus size: 29
1167031 CGACCCGGTG
* *
1167041 ACATTTTGGAAAATATTTTGAAAAA-GTA
1 ACATTCTGGGAAATATTTTGAAAAAGGTA
*
1167069 ACATTCTGGGAAATATTTTGAAAAAGGTT
1 ACATTCTGGGAAATATTTTGAAAAAGGTA
* *
1167098 ACATCCTGGGAAATATTTTGAAAAAGGTG
1 ACATTCTGGGAAATATTTTGAAAAAGGTA
1167127 ACATTCTGGGAA
1 ACATTCTGGGAA
1167139 TTTTCGAATG
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
28 23 0.37
29 40 0.63
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (29 bp):
ACATTCTGGGAAATATTTTGAAAAAGGTA
Found at i:1174351 original size:9 final size:8
Alignment explanation
Indices: 1174335--1174406 Score: 72
Period size: 10 Copynumber: 8.0 Consensus size: 8
1174325 GGTGTTAATT
1174335 GGTTGACC
1 GGTTGACC
1174343 GGCTTGACC
1 GG-TTGACC
1174352 GGTCTGAACC
1 GGT-TG-ACC
1174362 GGTTGAACC
1 GGTTG-ACC
1174371 GGTCTGAACC
1 GGT-TG-ACC
1174381 GGTTGACC
1 GGTTGACC
1174389 GGGGTTGACC
1 --GGTTGACC
1174399 GGTTGACC
1 GGTTGACC
1174407 CGTTAACTCG
Statistics
Matches: 58, Mismatches: 0, Indels: 12
0.83 0.00 0.17
Matches are distributed among these distances:
8 14 0.24
9 21 0.36
10 23 0.40
ACGTcount: A:0.15, C:0.26, G:0.36, T:0.22
Consensus pattern (8 bp):
GGTTGACC
Found at i:1174371 original size:19 final size:18
Alignment explanation
Indices: 1174340--1174390 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 18
1174330 TAATTGGTTG
1174340 ACCGGCTTGACCGGTCTGA
1 ACCGG-TTGACCGGTCTGA
1174359 ACCGGTTGAACCGGTCTGA
1 ACCGGTTG-ACCGGTCTGA
1174378 ACCGGTTGACCGG
1 ACCGGTTGACCGG
1174391 GGTTGACCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.26
19 23 0.74
ACGTcount: A:0.18, C:0.29, G:0.33, T:0.20
Consensus pattern (18 bp):
ACCGGTTGACCGGTCTGA
Found at i:1174508 original size:27 final size:28
Alignment explanation
Indices: 1174439--1174539 Score: 141
Period size: 29 Copynumber: 3.5 Consensus size: 28
1174429 ACCCGACCCG
*
1174439 GTGACATTCTGGGAAATATTTTTGAAAAA
1 GTGACATCCTGGGAAATA-TTTTGAAAAA
*
1174468 GGTGACCTCCTGGGAAATATTTTGAAAAA
1 -GTGACATCCTGGGAAATATTTTGAAAAA
1174497 -TGACATCCTGGGAAATATTTTGAAAAAA
1 GTGACATCCTGGGAAATATTTTG-AAAAA
*
1174525 GTGACATTCTGGGAA
1 GTGACATCCTGGGAA
1174540 TTTTAGAATG
Statistics
Matches: 65, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
27 21 0.32
28 5 0.08
29 23 0.35
30 16 0.25
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.30
Consensus pattern (28 bp):
GTGACATCCTGGGAAATATTTTGAAAAA
Found at i:1174524 original size:29 final size:29
Alignment explanation
Indices: 1174439--1174539 Score: 143
Period size: 27 Copynumber: 3.5 Consensus size: 29
1174429 ACCCGACCCG
* *
1174439 GTGACATTCTGGGAAATATTTTTGAAAAAG
1 GTGACATCCTGGGAAATA-TTTTGAAAAAA
*
1174469 GTGACCTCCTGGGAAATATTTTG-AAAAA
1 GTGACATCCTGGGAAATATTTTGAAAAAA
1174497 -TGACATCCTGGGAAATATTTTGAAAAAA
1 GTGACATCCTGGGAAATATTTTGAAAAAA
*
1174525 GTGACATTCTGGGAA
1 GTGACATCCTGGGAA
1174540 TTTTAGAATG
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 21 0.33
28 9 0.14
29 18 0.28
30 16 0.25
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.30
Consensus pattern (29 bp):
GTGACATCCTGGGAAATATTTTGAAAAAA
Found at i:1178798 original size:21 final size:20
Alignment explanation
Indices: 1178773--1178811 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1178763 CATCAAGGTC
*
1178773 TTTGTTAAGGCCATGAAATCT
1 TTTGTCAAGGCCAT-AAATCT
*
1178794 TTTGTCGAGGCCATAAAT
1 TTTGTCAAGGCCATAAAT
1178812 TCCTGCAACG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (20 bp):
TTTGTCAAGGCCATAAATCT
Found at i:1184904 original size:21 final size:20
Alignment explanation
Indices: 1184880--1184930 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
1184870 CGAATGAACA
1184880 TATCGATACCGAT-TGAAGAAG
1 TATCGATACCGATGTGAAG--G
* *
1184901 TATCGATACTGATGTGTAGG
1 TATCGATACCGATGTGAAGG
1184921 TATCGATACC
1 TATCGATACC
1184931 AAGGGAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 10 0.38
21 12 0.46
22 4 0.15
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (20 bp):
TATCGATACCGATGTGAAGG
Found at i:1185481 original size:15 final size:15
Alignment explanation
Indices: 1185436--1185482 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1185426 ACGTGTTATA
*
1185436 TATATAAAAATGTTC
1 TATATGAAAATGTTC
* **
1185451 TATGTGAAAACATTC
1 TATATGAAAATGTTC
1185466 TATATGAAAATGTTC
1 TATATGAAAATGTTC
1185481 TA
1 TA
1185483 CGCGAATGTG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.38
Consensus pattern (15 bp):
TATATGAAAATGTTC
Found at i:1185538 original size:15 final size:16
Alignment explanation
Indices: 1185518--1185550 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1185508 AGACATTTTG
1185518 AATAATGATAT-GTTA
1 AATAATGATATGGTTA
*
1185533 AATAATTATATGGTTA
1 AATAATGATATGGTTA
1185549 AA
1 AA
1185551 GCCCAAAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39
Consensus pattern (16 bp):
AATAATGATATGGTTA
Found at i:1186895 original size:36 final size:39
Alignment explanation
Indices: 1186812--1186910 Score: 125
Period size: 36 Copynumber: 2.6 Consensus size: 39
1186802 TAATTGAGAA
* * *
1186812 TTCATAATGAGAATAACTCATC-AAGAGGAAGAAGATAG
1 TTCATAATGAGAATAACTCGTCTAAGAGGAAGAAAAAAG
*
1186850 TTCATAATGAGAAGAACTCGTCTAA-A-GAA-AAAAAAG
1 TTCATAATGAGAATAACTCGTCTAAGAGGAAGAAAAAAG
*
1186886 TTCATAATGAGAATAACTTGTCTAA
1 TTCATAATGAGAATAACTCGTCTAA
1186911 TCTTTTTACT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
36 28 0.52
37 3 0.06
38 21 0.39
39 2 0.04
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.24
Consensus pattern (39 bp):
TTCATAATGAGAATAACTCGTCTAAGAGGAAGAAAAAAG
Found at i:1186970 original size:152 final size:154
Alignment explanation
Indices: 1186693--1186971 Score: 323
Period size: 152 Copynumber: 1.8 Consensus size: 154
1186683 TTCAATGAAG
* * * *
1186693 AGTTCATAATGAGAAGAACTCATCCAAAGAAGAAGCAGAAGTTTATAATGAAAAGAACTTGTTTG
1 AGTTCATAATGAGAAGAACTCATCCAAAGAAGAA-CAAAAGTTCATAATGAAAAGAACTTGTCTA
* * * * ** *
1186758 ACATTTTGCTTAAATCCATCGCAGAAAGAGGTGGATCAACATTTTAATTGAGAATTCATAATGAG
65 ACATTTTACTCAAATCCATCACAGAAAGAGGTGGATCAACATTTCAAAAGAGAATCCATAATGAG
1186823 AATAACTCATCAAGAGGAAGAAGAT
130 AATAACTCATCAAGAGGAAGAAGAT
* * * *
1186848 AGTTCATAATGAGAAGAACTCGTCTAAAGAA-AA-AAAAGTTCATAATGAGAATAACTTGTCTAA
1 AGTTCATAATGAGAAGAACTCATCCAAAGAAGAACAAAAGTTCATAATGAAAAGAACTTGTCTAA
* * * * *
1186911 TCTTTTTACTCAAGTCCATCACA-AAA-AGGTGGATTAACATTTCCAAAAGGGAGTCCATAAT
66 -CATTTTACTCAAATCCATCACAGAAAGAGGTGGATCAACATTT-CAAAAGAGAATCCATAAT
1186972 AATAAATACT
Statistics
Matches: 102, Mismatches: 20, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
151 15 0.15
152 39 0.38
153 17 0.17
154 2 0.02
155 29 0.28
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.27
Consensus pattern (154 bp):
AGTTCATAATGAGAAGAACTCATCCAAAGAAGAACAAAAGTTCATAATGAAAAGAACTTGTCTAA
CATTTTACTCAAATCCATCACAGAAAGAGGTGGATCAACATTTCAAAAGAGAATCCATAATGAGA
ATAACTCATCAAGAGGAAGAAGAT
Found at i:1188514 original size:23 final size:21
Alignment explanation
Indices: 1188468--1188514 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
1188458 TTCTTTCGAA
*
1188468 TTTCATTTATTTAATTTATGT
1 TTTCATTTATTTAATTTATAT
*
1188489 TTTCATTTTAGTTTCATTTATAT
1 TTTCA-TTTA-TTTAATTTATAT
1188512 TTT
1 TTT
1188515 TCTGTAATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 4 0.18
23 13 0.59
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.68
Consensus pattern (21 bp):
TTTCATTTATTTAATTTATAT
Found at i:1188974 original size:2 final size:2
Alignment explanation
Indices: 1188969--1189014 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1188959 TTATATACAA
1188969 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1189010 AT AT A
1 AT AT A
1189015 CTAAATTAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1189022 original size:12 final size:12
Alignment explanation
Indices: 1188960--1189020 Score: 68
Period size: 12 Copynumber: 4.9 Consensus size: 12
1188950 AATAAGTAGT
*
1188960 TATATACAAATA
1 TATATATAAATA
*
1188972 TATATATATATA
1 TATATATAAATA
*
1188984 TATATATATATA
1 TATATATAAATA
*
1188996 TATATATATATA
1 TATATATAAATA
1189008 TTATATACTAAAT
1 -TATATA-TAAAT
1189021 TAAGCATGCA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
12 34 0.77
13 6 0.14
14 4 0.09
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (12 bp):
TATATATAAATA
Found at i:1189112 original size:45 final size:46
Alignment explanation
Indices: 1189053--1189146 Score: 172
Period size: 45 Copynumber: 2.1 Consensus size: 46
1189043 CTCATATTAC
*
1189053 ATAGATTTTTTTAACATGGTGGATACTATTATTATTATATTTATGA
1 ATAGATTTTTTTAACATGGTGGATACTATTATTATAATATTTATGA
1189099 ATAG-TTTTTTTAACATGGTGGATACTATTATTATAATATTTATGA
1 ATAGATTTTTTTAACATGGTGGATACTATTATTATAATATTTATGA
1189144 ATA
1 ATA
1189147 TTGATTTCTA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 43 0.91
46 4 0.09
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.49
Consensus pattern (46 bp):
ATAGATTTTTTTAACATGGTGGATACTATTATTATAATATTTATGA
Found at i:1194385 original size:38 final size:39
Alignment explanation
Indices: 1194317--1194404 Score: 108
Period size: 38 Copynumber: 2.3 Consensus size: 39
1194307 ATCCCAACCC
* * *
1194317 TCTAAATTCTTAATTTTTTAAAGTACTTTAC-CATAGCAT
1 TCTAAATTATTAATTTTTTAAAGTACTTTACTC-TAACAA
* *
1194356 TCTAAATTATTAATTTTTT-AATTATTTTACTCTAACAA
1 TCTAAATTATTAATTTTTTAAAGTACTTTACTCTAACAA
1194394 TCTAAATTATT
1 TCTAAATTATT
1194405 TCTCATATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
38 24 0.56
39 19 0.44
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.50
Consensus pattern (39 bp):
TCTAAATTATTAATTTTTTAAAGTACTTTACTCTAACAA
Found at i:1195329 original size:35 final size:36
Alignment explanation
Indices: 1195283--1195353 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
1195273 TATATGAAGG
1195283 GGGAACAGATTCCCCCT-GGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
1195318 GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
1195354 CTAAATGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 17 0.49
36 18 0.51
ACGTcount: A:0.17, C:0.31, G:0.32, T:0.20
Consensus pattern (36 bp):
GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
Found at i:1195732 original size:15 final size:14
Alignment explanation
Indices: 1195712--1195746 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
1195702 ATGATATACA
1195712 TGATATATGCATATG
1 TGATATATGC-TATG
1195727 TGATATATGCTATG
1 TGATATATGCTATG
*
1195741 AGATAT
1 TGATAT
1195747 GACCAATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (14 bp):
TGATATATGCTATG
Found at i:1202375 original size:14 final size:15
Alignment explanation
Indices: 1202356--1202384 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1202346 TACATGATAT
1202356 GCAT-AAACATAAGA
1 GCATAAAACATAAGA
1202370 GCATAAAACATAAGA
1 GCATAAAACATAAGA
1202385 TATATGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (15 bp):
GCATAAAACATAAGA
Found at i:1202669 original size:15 final size:15
Alignment explanation
Indices: 1202651--1202685 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1202641 CGAGGGTATT
*
1202651 GTAGTCCTTCGGGAC
1 GTAGTCCTTAGGGAC
1202666 GTAGTCCTTAGGGAC
1 GTAGTCCTTAGGGAC
1202681 GTAGT
1 GTAGT
1202686 GGTCCTACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.34, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTAGGGAC
Found at i:1204379 original size:21 final size:21
Alignment explanation
Indices: 1204330--1204379 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1204320 TAGCATTATC
*
1204330 CAATAAACTTGAAATCCATAA
1 CAATAAATTTGAAATCCATAA
*
1204351 CAACAAATTTGAAATCCATAA
1 CAATAAATTTGAAATCCATAA
*
1204372 TAATAAAT
1 CAATAAAT
1204380 CAAAGTTTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.54, C:0.16, G:0.04, T:0.26
Consensus pattern (21 bp):
CAATAAATTTGAAATCCATAA
Found at i:1207804 original size:14 final size:14
Alignment explanation
Indices: 1207778--1207812 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1207768 ATTCATTGCC
1207778 ACTTTGC-TTTTTG
1 ACTTTGCTTTTTTG
1207791 ACTTTGCTTTTTTG
1 ACTTTGCTTTTTTG
*
1207805 TCTTTGCT
1 ACTTTGCT
1207813 GGTGTTGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.06, C:0.17, G:0.14, T:0.63
Consensus pattern (14 bp):
ACTTTGCTTTTTTG
Found at i:1207991 original size:26 final size:27
Alignment explanation
Indices: 1207944--1207995 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
1207934 TAAAAATCGG
*
1207944 TTTTTGAAACATATATATAATATATAA
1 TTTTTGAAACATATATAGAATATATAA
1207971 TTTTTGAAAACAT-T-TAGAATATATA
1 TTTTTG-AAACATATATAGAATATATA
1207996 TATAATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 10 0.43
27 7 0.30
28 6 0.26
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (27 bp):
TTTTTGAAACATATATAGAATATATAA
Found at i:1208084 original size:109 final size:106
Alignment explanation
Indices: 1207945--1208311 Score: 370
Period size: 109 Copynumber: 3.3 Consensus size: 106
1207935 AAAAATCGGT
* *
1207945 TTTTGAAACATATATATAATATATAATTTTTGAAAACATTTAGAATATATATATAATATATAGTT
1 TTTTG-AA-ATATATATAATATA-AATTTTTGAAAATATTTAGAAAATATATATAATATATAGTT
* *
1208010 TCGAAAACAT-TTTTGAAAATATATATATTATATAGTTTTGAAAACA
63 TTGAAAA-ATGTTTT-AAAATATATATATTATATAGTTTT-AAAAAA
*
1208056 TTTTGAATATATATATAA-ATAAAGTTTTTGAAAATATTTTGAAAATATATATAATATATAGTTT
1 TTTTGAA-ATATATATAATATAAA-TTTTTGAAAATATTTAGAAAATATATATAATATATAGTTT
* * *
1208120 TTAAAAATGTTTTAAAAATATATATAATATATAGTTTTTAAAAATG
64 TGAAAAATGTTTT-AAAATATATATATTATATAG-TTTTAAAAA-A
* * * * *
1208166 TTTTAAAAATATATATAATAT--ATTTTTG-AATTTTTTAAAAAAAATGTATATAATATATAGTT
1 TTTT-GAAATATATATAATATAAATTTTTGAAAATATTT--AGAAAATATATATAATATATAGTT
1208228 TTG-AAAATGTTTTAAAATATATATATAATATATAGTTTTAAAAATA
63 TTGAAAAATGTTTTAAAATATATATAT--TATATAGTTTTAAAAA-A
* *
1208274 TTTTTGAAA-ACGTATATAATATATAGTTTTGAAAATAT
1 -TTTTGAAATA--TATATAATATAAATTTTTGAAAATAT
1208312 ATTATATAGT
Statistics
Matches: 217, Mismatches: 23, Indels: 31
0.80 0.08 0.11
Matches are distributed among these distances:
107 19 0.09
108 33 0.15
109 116 0.53
110 30 0.14
111 15 0.07
112 4 0.02
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.45
Consensus pattern (106 bp):
TTTTGAAATATATATAATATAAATTTTTGAAAATATTTAGAAAATATATATAATATATAGTTTTG
AAAAATGTTTTAAAATATATATATTATATAGTTTTAAAAAA
Found at i:1208132 original size:11 final size:11
Alignment explanation
Indices: 1208118--1208175 Score: 53
Period size: 11 Copynumber: 4.9 Consensus size: 11
1208108 AATATATAGT
1208118 TTTTAAAAATG
1 TTTTAAAAATG
*
1208129 TTTTAAAAATA
1 TTTTAAAAATG
* *
1208140 TATATAATATATAG
1 T-TTTAA-AAAT-G
1208154 TTTTTAAAAATG
1 -TTTTAAAAATG
1208166 TTTTAAAAAT
1 TTTTAAAAAT
1208176 ATATATAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
11 21 0.57
12 5 0.14
13 6 0.16
14 4 0.11
15 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (11 bp):
TTTTAAAAATG
Found at i:1208141 original size:146 final size:144
Alignment explanation
Indices: 1207945--1208308 Score: 398
Period size: 146 Copynumber: 2.5 Consensus size: 144
1207935 AAAAATCGGT
* * * *
1207945 TTTTGAAACATATATATAATATATAATTTTTGAAAA-CATTTAGAATATATATATAATATATAGT
1 TTTTGAAACATATATATAATATATAGTTTTTAAAAATCTTTTA-AAAATATATATAATATATAGT
* * * *
1208009 TTCGAAAACAT-TTTTGAAAATATATATATTATATAGTTTTGAAAACATTTT-GAATATATATAT
65 TTTGAAAA-ATGTTTT-AAAA-ATATATATAATATAGTTTTG--AACATTTTAAAAAATATATAT
1208072 AA-ATAAAGTTTTTGAAAATA
125 AATATAAAG-TTTTGAAAATA
*
1208092 TTTTGAAA-ATATATATAATATATAGTTTTTAAAAATGTTTTAAAAATATATATAATATATAGTT
1 TTTTGAAACATATATATAATATATAGTTTTTAAAAATCTTTTAAAAATATATATAATATATAGTT
* * ** *
1208156 TTTAAAAATGTTTTAAAAATATATATAATATATTTTTGAATTTTTTAAAAAAAATGTATATAATA
66 TTGAAAAATGTTTTAAAAATATATATAATATAGTTTTGAACATTTT--AAAAAATATATATAATA
* *
1208221 TATAGTTTTGAAAATG
129 TAAAGTTTTGAAAATA
* * * * **
1208237 TTTTAAAATATATATATAATATATAG-TTTTAAAAATATTTTTGAAAACGTATATAATATATAGT
1 TTTTGAAACATATATATAATATATAGTTTTTAAAAAT-CTTTTAAAAATATATATAATATATAGT
1208301 TTTGAAAA
65 TTTGAAAA
1208309 TATATTATAT
Statistics
Matches: 187, Mismatches: 22, Indels: 17
0.83 0.10 0.08
Matches are distributed among these distances:
142 6 0.03
144 18 0.10
145 44 0.24
146 107 0.57
147 12 0.06
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.45
Consensus pattern (144 bp):
TTTTGAAACATATATATAATATATAGTTTTTAAAAATCTTTTAAAAATATATATAATATATAGTT
TTGAAAAATGTTTTAAAAATATATATAATATAGTTTTGAACATTTTAAAAAATATATATAATATA
AAGTTTTGAAAATA
Found at i:1208303 original size:25 final size:22
Alignment explanation
Indices: 1208275--1208330 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
1208265 TTAAAAATAT
1208275 TTTTGAAAACGTATATAATATATAG
1 TTTTGAAAAC-TATAT--TATATAG
1208300 TTTTGAAAA-TATATTATATAG
1 TTTTGAAAACTATATTATATAG
*
1208321 TTTTAAAAAC
1 TTTTGAAAAC
1208331 AATTTTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 15 0.52
23 5 0.17
25 9 0.31
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.43
Consensus pattern (22 bp):
TTTTGAAAACTATATTATATAG
Found at i:1208309 original size:37 final size:37
Alignment explanation
Indices: 1207944--1208311 Score: 382
Period size: 37 Copynumber: 10.0 Consensus size: 37
1207934 TAAAAATCGG
* *
1207944 TTTTTGAAACATATATATAATATATAATTTTTGAAAACA
1 TTTTTGAAA-ATATATATAATATAT-AGTTTTGAAAATA
* * * *
1207983 -TTTAGAATATATATATAATATATAGTTTCGAAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAATA
* *
1208019 TTTTTGAAAATATATATATTATATAGTTTTGAAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAATA
* *
1208056 -TTTTGAATATATATATAA-ATAAAGTTTTTGAAAATA
1 TTTTTGAAAATATATATAATATATAG-TTTTGAAAATA
*
1208092 -TTTTGAAAATATATATAATATATAGTTTTTAAAA-A
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAATA
* *
1208127 TGTTTTAAAAATATATATAATATATAGTTTTTAAAA-A
1 T-TTTTGAAAATATATATAATATATAGTTTTGAAAATA
*
1208164 TGTTTTAAAAATATATATAATATAT--TTTTG--AAT-
1 T-TTTTGAAAATATATATAATATATAGTTTTGAAAATA
* *
1208197 TTTTTAAAAAAAATGTATATAATATATAGTTTTGAAAAT-
1 TTTTT---GAAAATATATATAATATATAGTTTTGAAAATA
* * *
1208236 GTTTTAAAATATATATATAATATATAGTTTTAAAAATA
1 TTTTTGAAA-ATATATATAATATATAGTTTTGAAAATA
**
1208274 TTTTTGAAAACGTATATAATATATAGTTTTGAAAATA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAATA
1208311 T
1 T
1208312 ATTATATAGT
Statistics
Matches: 288, Mismatches: 26, Indels: 32
0.83 0.08 0.09
Matches are distributed among these distances:
32 4 0.01
33 3 0.01
35 28 0.10
36 66 0.23
37 167 0.58
38 13 0.05
39 7 0.02
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (37 bp):
TTTTTGAAAATATATATAATATATAGTTTTGAAAATA
Found at i:1208320 original size:58 final size:55
Alignment explanation
Indices: 1208250--1208364 Score: 160
Period size: 58 Copynumber: 2.0 Consensus size: 55
1208240 TAAAATATAT
*
1208250 ATATAATATATAGTTTTAAAAA-TATTTTTGAAAACGTATATAATATATAGTTTTGAAA
1 ATATAATATATAGTTTTAAAAACAATTTTT-AAAA---ATATAATATATAGTTTTGAAA
* *
1208308 ATATATTATATAGTTTTAAAAACAATTTTTAAAAATATATTATATAGTTTTGAAA
1 ATATAATATATAGTTTTAAAAACAATTTTTAAAAATATAATATATAGTTTTGAAA
1208363 AT
1 AT
1208365 TAACTTTTTG
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
55 22 0.42
58 25 0.47
59 6 0.11
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (55 bp):
ATATAATATATAGTTTTAAAAACAATTTTTAAAAATATAATATATAGTTTTGAAA
Found at i:1208345 original size:34 final size:35
Alignment explanation
Indices: 1208300--1208403 Score: 120
Period size: 34 Copynumber: 2.9 Consensus size: 35
1208290 TAATATATAG
*
1208300 TTTTGAAAATATATTATATAGTTTTAAAAACAA-T
1 TTTTAAAAATATATTATATAGTTTTAAAAACAACT
**
1208334 TTTTAAAAATATATTATATAGTTTTGAAAATTAACT
1 TTTTAAAAATATATTATATAGTTTT-AAAAACAACT
*
1208370 TTTTGAAAACATATATGTTATATAGTTTAAAAAA
1 TTTT-AAAA-ATATA--TTATATAGTTTTAAAAA
1208404 ATCGACATAT
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
34 24 0.41
35 6 0.10
36 5 0.08
37 4 0.07
38 5 0.08
39 4 0.07
40 11 0.19
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (35 bp):
TTTTAAAAATATATTATATAGTTTTAAAAACAACT
Found at i:1208431 original size:12 final size:12
Alignment explanation
Indices: 1208414--1208479 Score: 54
Period size: 11 Copynumber: 5.9 Consensus size: 12
1208404 ATCGACATAT
1208414 TATTATATATTA
1 TATTATATATTA
*
1208426 TATTATA-ATAA
1 TATTATATATTA
1208437 TATTAT-TATATA
1 TATTATATAT-TA
*
1208449 TATTATTTATT-
1 TATTATATATTA
1208460 TATT-TAT-TTA
1 TATTATATATTA
*
1208470 T-TTATTTATT
1 TATTATATATT
1208480 TTTCTTCTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
9 4 0.09
10 5 0.11
11 17 0.39
12 15 0.34
13 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TATTATATATTA
Found at i:1208458 original size:4 final size:4
Alignment explanation
Indices: 1208451--1208480 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1208441 ATTATATATA
1208451 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1208481 TTCTTCTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:1210525 original size:13 final size:13
Alignment explanation
Indices: 1210507--1210536 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1210497 TGAATCGAGT
1210507 TTTTAAATTTTAA
1 TTTTAAATTTTAA
*
1210520 TTTTAATTTTTAA
1 TTTTAAATTTTAA
1210533 TTTT
1 TTTT
1210537 CGTAATTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:1211728 original size:18 final size:18
Alignment explanation
Indices: 1211707--1211741 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1211697 TCCAGAGTTC
1211707 TCTTCTTCTCCTTTTTCT
1 TCTTCTTCTCCTTTTTCT
*
1211725 TCTTCTTCTTCTTTTTC
1 TCTTCTTCTCCTTTTTC
1211742 ACGTGAAGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (18 bp):
TCTTCTTCTCCTTTTTCT
Found at i:1214077 original size:23 final size:23
Alignment explanation
Indices: 1214047--1214100 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
1214037 ACATTTTATA
1214047 TGGCACTTTGGTGCAATTCTACG
1 TGGCACTTTGGTGCAATTCTACG
1214070 TGGCACTTTGGTGCAATTCTACG
1 TGGCACTTTGGTGCAATTCTACG
1214093 TGGCACTT
1 TGGCACTT
1214101 CAGTTCATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (23 bp):
TGGCACTTTGGTGCAATTCTACG
Found at i:1214115 original size:23 final size:23
Alignment explanation
Indices: 1214047--1214115 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
1214037 ACATTTTATA
** *
1214047 TGGCACTTTGGTGCAATTCTACG
1 TGGCACTTCAGTGCAATTATACG
** *
1214070 TGGCACTTTGGTGCAATTCTACG
1 TGGCACTTCAGTGCAATTATACG
* *
1214093 TGGCACTTCAGTTCATTTATACG
1 TGGCACTTCAGTGCAATTATACG
1214116 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (23 bp):
TGGCACTTCAGTGCAATTATACG
Found at i:1215418 original size:45 final size:45
Alignment explanation
Indices: 1215307--1215523 Score: 264
Period size: 45 Copynumber: 4.9 Consensus size: 45
1215297 AACATAACAT
* **
1215307 CTTTTCTTTTGATAATGCACCCATATGCATTTCAAC-CATAGTATA
1 CTTTTCTATTGATAATGCACCCATATATATTTCAACTC-TAGTATA
* * *
1215352 C-TTT-TATTGATAATGTACCCATATATATATCAAC-CATTGTATA
1 CTTTTCTATTGATAATGCACCCATATATATTTCAACTC-TAGTATA
*
1215395 CTTTTCTATTGATAATGTACCCATATATATTTCAACTCTAGTATA
1 CTTTTCTATTGATAATGCACCCATATATATTTCAACTCTAGTATA
* *
1215440 ATTTTCTGTTGATAATGCACCCATAT-TCATTTCAACTCTAGTATA
1 CTTTTCTATTGATAATGCACCCATATAT-ATTTCAACTCTAGTATA
* **
1215485 CTTTTCTATTGATAATGCACCCTTATGCATTTCAACTCT
1 CTTTTCTATTGATAATGCACCCATATATATTTCAACTCT
1215524 GGCATCATTT
Statistics
Matches: 152, Mismatches: 15, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
43 34 0.22
44 7 0.05
45 110 0.72
46 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.42
Consensus pattern (45 bp):
CTTTTCTATTGATAATGCACCCATATATATTTCAACTCTAGTATA
Found at i:1215489 original size:90 final size:88
Alignment explanation
Indices: 1215307--1215560 Score: 280
Period size: 90 Copynumber: 2.8 Consensus size: 88
1215297 AACATAACAT
* * * *
1215307 CTTTTCTTTTGATAATGCACCCATATGCATTTCAAC-CATAGTATACTTTTATTGATAATGTACC
1 CTTTTCTATTGATAATGCACCCATATGCATTTCAACTC-TAGTATATTTTTGTTGATAATGCACC
* *
1215371 CATATAT-ATATCAACCATTGTATA
65 CATAT-TCATTTCAACCATAGTATA
* **
1215395 CTTTTCTATTGATAATGTACCCATATATATTTCAACTCTAGTATAATTTTCTGTTGATAATGCAC
1 CTTTTCTATTGATAATGCACCCATATGCATTTCAACTCTAGTAT-ATTTT-TGTTGATAATGCAC
1215460 CCATATTCATTTCAACTC-TAGTATA
64 CCATATTCATTTCAAC-CATAGTATA
* * * ***
1215485 CTTTTCTATTGATAATGCACCCTTATGCATTTCAACTCTGGCATCATTTTATGCCAATAATGCAC
1 CTTTTCTATTGATAATGCACCCATATGCATTTCAACTCTAGTAT-ATTTT-TGTTGATAATGCAC
*
1215550 CCATATGCATT
64 CCATATTCATT
1215561 ATTCTTTTAT
Statistics
Matches: 140, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
88 38 0.27
89 6 0.04
90 95 0.68
91 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.41
Consensus pattern (88 bp):
CTTTTCTATTGATAATGCACCCATATGCATTTCAACTCTAGTATATTTTTGTTGATAATGCACCC
ATATTCATTTCAACCATAGTATA
Found at i:1216019 original size:21 final size:20
Alignment explanation
Indices: 1215991--1216052 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 20
1215981 ATTTCTGGCC
1215991 CTTAGGTATTGATACCCCTA
1 CTTAGGTATTGATACCCCTA
* *
1216011 CTTATGGTATCGATAGTACCCTA
1 CTTA-GGTATTGATA--CCCCTA
1216034 -TTAGGGTATTGATACCCCT
1 CTTA-GGTATTGATACCCCT
1216053 CAATGTATCA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
20 8 0.24
21 9 0.26
22 12 0.35
23 5 0.15
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (20 bp):
CTTAGGTATTGATACCCCTA
Found at i:1216159 original size:18 final size:17
Alignment explanation
Indices: 1216128--1216162 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1216118 TATCCCTATG
*
1216128 CTATGGTATTGATACCC
1 CTATGGTATCGATACCC
1216145 CTATAGGTATCGATACCC
1 CTAT-GGTATCGATACCC
1216163 ATTTTAGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (17 bp):
CTATGGTATCGATACCC
Found at i:1226932 original size:84 final size:85
Alignment explanation
Indices: 1226707--1227213 Score: 711
Period size: 84 Copynumber: 6.0 Consensus size: 85
1226697 AAATTGTTCC
* * * *
1226707 CAGCATAACTCAAAGCGAGAAGGGCTATCTGTCAACAAAAACCTTTGAGTTCGATCACATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
*
1226772 TCAAGGTCATATCAAATTTA
66 TCAAGGGCATATCAAATTTA
* * * * *
1226792 CAACATAGCTCAAGCCGAGAAGGGCTATCTGTCAACAAAAACCATCAAGTTCGATTCCATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
*
1226857 TCAAGAGCATATCAAATTTA
66 TCAAGGGCATATCAAATTTA
* * *
1226877 CAGCATAGC-CAAGGCGAGAATGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
1226941 TCAAGGGCATATCAAATTTA
66 TCAAGGGCATATCAAATTTA
* * * *
1226961 CAAG-ATAGCTTAAGGC--GAAGGGCTCTCTGTCAACAAAAACCTTCGAAATTCGACTACATTCA
1 C-AGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCG-AGTTCGATTACATTCA
1227023 GCTCAAGGGCATATCAAATTTA
64 GCTCAAGGGCATATCAAATTTA
* * * * *
1227045 CAACATAACTCAAGGCGAGAAGGGTTATTTCTCAACAAAAACCTTCGAGTTCGATTACATTCA-C
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
1227109 TCAAGGGCATATCAAATTTA
66 TCAAGGGCATATCAAATTTA
* *
1227129 CAGCATAGCTTAAGGCGAGAAGGGTTATCTGTCAA-AAAAACCTTCGAGTTCGATTACATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
* *
1227193 TCAGGGGAATATCAAATTTA
66 TCAAGGGCATATCAAATTTA
1227213 C
1 C
1227214 TGAAGGGTTA
Statistics
Matches: 374, Mismatches: 41, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
83 54 0.14
84 192 0.51
85 103 0.28
86 25 0.07
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.25
Consensus pattern (85 bp):
CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGC
TCAAGGGCATATCAAATTTA
Found at i:1227127 original size:168 final size:169
Alignment explanation
Indices: 1226710--1227213 Score: 714
Period size: 169 Copynumber: 3.0 Consensus size: 169
1226700 TTGTTCCCAG
* * * *
1226710 CATAACTCAAAGCGAGAAGGGCTATCTGTCAACAAAAACCTTTGAGTTCGATCACATTCAGCTCA
1 CATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCA
* * * * *
1226775 AGGTCATATCAAATTTACAACATAGCTCAAGCCGAGAAGGGCTATCTGTCAACAAAAACCATC-A
66 AGGGCATATCAAATTTACAAGATAGCTTAAG--GCGAAGGGCTATCTGTCAACAAAAACCTTCGA
* * *
1226839 AGTTCGATTCCATTCAGCTCAAGAGCATATCAAATTTACAG
129 AGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTACAA
* * *
1226880 CATAGC-CAAGGCGAGAATGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAGCTCA
1 CATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCA
* *
1226944 AGGGCATATCAAATTTACAAGATAGCTTAAGGCGAAGGGCTCTCTGTCAACAAAAACCTTCGAAA
66 AGGGCATATCAAATTTACAAGATAGCTTAAGGCGAAGGGCTATCTGTCAACAAAAACCTTCGAAG
*
1227009 TTCGACTACATTCAGCTCAAGGGCATATCAAATTTACAA
131 TTCGATTACATTCAGCTCAAGGGCATATCAAATTTACAA
* *
1227048 CATAACTCAAGGCGAGAAGGGTTATTTCTCAACAAAAACCTTCGAGTTCGATTACATTCA-CTCA
1 CATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCA
*
1227112 AGGGCATATCAAATTTAC-AGCATAGCTTAAGGCGAGAAGGGTTATCTGTCAA-AAAAACCTTCG
66 AGGGCATATCAAATTTACAAG-ATAGCTTAAGGC--GAAGGGCTATCTGTCAACAAAAACCTTCG
* *
1227175 -AGTTCGATTACATTCAGCTCAGGGGAATATCAAATTTAC
128 AAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTAC
1227214 TGAAGGGTTA
Statistics
Matches: 300, Mismatches: 29, Indels: 12
0.88 0.09 0.04
Matches are distributed among these distances:
167 29 0.10
168 111 0.37
169 140 0.47
170 20 0.07
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (169 bp):
CATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCA
AGGGCATATCAAATTTACAAGATAGCTTAAGGCGAAGGGCTATCTGTCAACAAAAACCTTCGAAG
TTCGATTACATTCAGCTCAAGGGCATATCAAATTTACAA
Found at i:1227257 original size:68 final size:68
Alignment explanation
Indices: 1227147--1227281 Score: 227
Period size: 68 Copynumber: 2.0 Consensus size: 68
1227137 CTTAAGGCGA
*
1227147 GAAGGGTTATCTGTCAAAAAAACCTTCGAGTTCGATTACATTCAGCTCAGGGGAATATCAAATTT
1 GAAGGGTTATCTGTCAAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGAATATCAAATTT
1227212 ACT
66 ACT
* *
1227215 GAAGGGTTATC-GTCAATAAAAACCTTCGAGTTCGATTCCATTCAGCTCAAGGGCATATCAAATT
1 GAAGGGTTATCTGTCAA-AAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGAATATCAAATT
1227279 TAC
65 TAC
1227282 AGCATAGCTC
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
67 5 0.08
68 58 0.92
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (68 bp):
GAAGGGTTATCTGTCAAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGAATATCAAATTT
ACT
Found at i:1228029 original size:37 final size:37
Alignment explanation
Indices: 1227975--1228357 Score: 350
Period size: 37 Copynumber: 10.9 Consensus size: 37
1227965 AAAAAAATCG
*
1227975 TTTTTGAAACATATATATAATGTATAGTTTTTGAAAACA
1 TTTTTGAAA-ATATATATAATATATAG-TTTTGAAAACA
*
1228014 -TTTTGAAAATATATATATTATATAGTTTTGAAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
* *
1228050 TTTTTGAAAATGTATATATTATATAGTTTTGAAAAC-
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
* * *
1228086 GTTTTGAAAACATATATATAACATATTGTTTTTGAAAACA
1 TTTTTG-AAA-ATATATATAATATATAG-TTTTGAAAACA
*
1228126 -TTTTGAAAATATATATAATATATAGTTTTTAAAA-A
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
* * *
1228161 GTTTTAAAAATATATATAATATATAGTTTTGAAAATA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
*
1228198 TTTTTGAAAATGTATATAATATATAGTTTTG-AAA-A
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
*
1228233 TGTTT--AAATATATAT-ATATATA-TTTTG-AAA-A
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
*
1228264 ----TG------TATATAATATATAGTTTTGAAAATA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
*
1228291 TTTTTG-AAA-ATATAT--TATATAGTTTTGAAAATTAA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAA--CA
* * **
1228326 CTTTTGAAAACATATATGTTATATAGTTTTGA
1 TTTTTGAAAATATATATAATATATAGTTTTGA
1228358 TTTTTTCGAC
Statistics
Matches: 298, Mismatches: 20, Indels: 52
0.81 0.05 0.14
Matches are distributed among these distances:
23 5 0.02
24 7 0.02
25 5 0.02
26 3 0.01
27 2 0.01
31 11 0.04
32 7 0.02
33 25 0.08
35 17 0.06
36 62 0.21
37 102 0.34
38 24 0.08
39 28 0.09
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (37 bp):
TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
Found at i:1228091 original size:73 final size:73
Alignment explanation
Indices: 1227975--1228263 Score: 374
Period size: 73 Copynumber: 4.0 Consensus size: 73
1227965 AAAAAAATCG
* * *
1227975 TTTTTGAAACATATATATAATGTATAGTTTTTGAAAACATTTTGAAAATATATATATTATATAGT
1 TTTTTGAAA-ATATATATAATATATAG-TTTTGAAAACGTTTTGAAAATATATATAATATATAGT
1228040 TTTGAAAACA
64 TTTGAAAACA
* * * *
1228050 TTTTTGAAAATGTATATATTATATAGTTTTGAAAACGTTTTGAAAACATATATATAACATATTGT
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACGTTTTG-AAA-ATATATATAATATATAG-
1228115 TTTTGAAAACA
63 TTTTGAAAACA
* * *
1228126 -TTTTGAAAATATATATAATATATAGTTTTTAAAAAGTTTTAAAAATATATATAATATATAGTTT
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACGTTTTGAAAATATATATAATATATAGTTT
*
1228190 TGAAAATA
66 TGAAAACA
* *
1228198 TTTTTGAAAATGTATATAATATATAGTTTTGAAAATG-TTT--AAATATATAT-ATATATA-TTT
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACGTTTTGAAAATATATATAATATATAGTTT
1228258 TGAAAA
66 TGAAAA
1228264 TGTATATAAT
Statistics
Matches: 192, Mismatches: 18, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
68 9 0.05
69 7 0.04
70 10 0.05
72 13 0.07
73 63 0.33
74 20 0.10
75 59 0.31
76 11 0.06
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (73 bp):
TTTTTGAAAATATATATAATATATAGTTTTGAAAACGTTTTGAAAATATATATAATATATAGTTT
TGAAAACA
Found at i:1228103 original size:112 final size:110
Alignment explanation
Indices: 1227976--1228263 Score: 376
Period size: 112 Copynumber: 2.6 Consensus size: 110
1227966 AAAAAATCGT
*
1227976 TTTTGAAACATATATATAATGTATAGTTTTTGAAAACATTTTGAAAATATATATATTATATAGTT
1 TTTTGAAACATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATA-TATATAGTT
* * * * *
1228041 TTGAAAACATTTTTGAAAATGTATATATTATATAGTTTTGAAAA-CG
65 TTGAAAA-AGTTTTAAAAATATATATAATATATAGTTTTGAAAATAG
* *
1228087 TTTTGAAAACATATATATAACATATTGTTTTTGAAAACATTTTGAAAATATATATAATATATAGT
1 TTTTG-AAACATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATAT-ATATATAGT
* *
1228152 TTTTAAAAAGTTTTAAAAATATATATAATATATAGTTTTGAAAATAT
64 TTTGAAAAAGTTTTAAAAATATATATAATATATAGTTTTGAAAATAG
*
1228199 TTTTGAAA-ATGTATATAATATATAG-TTTTG-AAA-ATGTTT--AAATATATATATATATA-TT
1 TTTTGAAACATATATATAATATATAGTTTTTGAAAACAT-TTTGAAAATATATATATATATAGTT
1228257 TTGAAAA
65 TTGAAAA
1228264 TGTATATAAT
Statistics
Matches: 159, Mismatches: 14, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
104 8 0.05
105 7 0.04
106 10 0.06
107 2 0.01
108 6 0.04
109 5 0.03
110 14 0.09
111 40 0.25
112 66 0.42
113 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (110 bp):
TTTTGAAACATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATATATATAGTTT
TGAAAAAGTTTTAAAAATATATATAATATATAGTTTTGAAAATAG
Found at i:1228227 original size:25 final size:25
Alignment explanation
Indices: 1228199--1228289 Score: 119
Period size: 25 Copynumber: 3.4 Consensus size: 25
1228189 TTGAAAATAT
1228199 TTTTGAAAATGTATATAATATATAG
1 TTTTGAAAATGTATATAATATATAG
*
1228224 TTTTGAAAATGTTTAAATATATATATATATA
1 TTTTGAAAATG--T--ATATA-ATATATA-G
1228255 TTTTGAAAATGTATATAATATATAG
1 TTTTGAAAATGTATATAATATATAG
1228280 TTTTGAAAAT
1 TTTTGAAAAT
1228290 ATTTTTGAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
25 21 0.36
26 7 0.12
27 6 0.10
29 6 0.10
30 7 0.12
31 11 0.19
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (25 bp):
TTTTGAAAATGTATATAATATATAG
Found at i:1228269 original size:56 final size:57
Alignment explanation
Indices: 1228195--1228322 Score: 192
Period size: 56 Copynumber: 2.3 Consensus size: 57
1228185 AGTTTTGAAA
1228195 ATAT-TTTTGAAAATGTATATAATATATAGTTTTG-AAA-ATGTTT-AAATATATATAT
1 ATATATTTTGAAAATGTATATAATATATAGTTTTGAAAATATGTTTGAAA-ATATAT-T
*
1228250 ATATATTTTGAAAATGTATATAATATATAGTTTTGAAAATATTTTTGAAAATATATT
1 ATATATTTTGAAAATGTATATAATATATAGTTTTGAAAATATGTTTGAAAATATATT
1228307 ATATAGTTTTGAAAAT
1 ATATA-TTTTGAAAAT
1228323 TAACTTTTGA
Statistics
Matches: 67, Mismatches: 1, Indels: 7
0.89 0.01 0.09
Matches are distributed among these distances:
55 4 0.06
56 30 0.45
57 9 0.13
58 21 0.31
59 3 0.04
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (57 bp):
ATATATTTTGAAAATGTATATAATATATAGTTTTGAAAATATGTTTGAAAATATATT
Found at i:1228275 original size:32 final size:31
Alignment explanation
Indices: 1228136--1228278 Score: 108
Period size: 36 Copynumber: 4.2 Consensus size: 31
1228126 TTTTGAAAAT
* * *
1228136 ATATATAATATATAGTTTTTAAAAAGTTTTAAAAA
1 ATATATAATATATAG-TTTTGAAAA--TGT-ATAA
* *
1228171 TATATATAATATATAGTTTTGAAAATATTTTTGAAA
1 -ATATATAATATATAGTTTTG-AAA-ATGTAT--AA
*
1228207 ATGTATATAATATATAGTTTTGAAAATGTTTAA
1 A--TATATAATATATAGTTTTGAAAATGTATAA
1228240 ATATATATATATATA-TTTTGAAAATGTATATA
1 ATATATA-ATATATAGTTTTGAAAATGTATA-A
1228272 ATATATA
1 ATATATA
1228279 GTTTTGAAAA
Statistics
Matches: 94, Mismatches: 5, Indels: 20
0.79 0.04 0.17
Matches are distributed among these distances:
31 20 0.21
32 15 0.16
33 3 0.03
35 13 0.14
36 23 0.24
37 20 0.21
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (31 bp):
ATATATAATATATAGTTTTGAAAATGTATAA
Found at i:1228310 original size:33 final size:37
Alignment explanation
Indices: 1228267--1228357 Score: 118
Period size: 33 Copynumber: 2.5 Consensus size: 37
1228257 TTGAAAATGT
* *
1228267 ATATAATATATAGTTTTGAAAA-T-ATTTTTG-AAA-
1 ATATATTATATAGTTTTGAAAATTAACTTTTGAAAAC
1228300 ATATATTATATAGTTTTGAAAATTAACTTTTGAAAAC
1 ATATATTATATAGTTTTGAAAATTAACTTTTGAAAAC
1228337 ATATATGTTATATAGTTTTGA
1 ATATA--TTATATAGTTTTGA
1228358 TTTTTTCGAC
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
33 21 0.42
34 1 0.02
35 6 0.12
36 3 0.06
37 5 0.10
39 14 0.28
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (37 bp):
ATATATTATATAGTTTTGAAAATTAACTTTTGAAAAC
Found at i:1228381 original size:128 final size:127
Alignment explanation
Indices: 1228125--1228357 Score: 319
Period size: 129 Copynumber: 1.8 Consensus size: 127
1228115 TTTTGAAAAC
*
1228125 ATTTTGAAAATATATATAATATATAGTTTTTAAAAAGTTTTAAAAATATATATAATATATAGTTT
1 ATTTTGAAAATATATATAATATATAGTTTTGAAAAAGTTTTAAAAATATATAT-ATATATAGTTT
* **
1228190 TGAAAATATTTTTGAAAATGTATATAATATATAGTTTTGAAAATGTTTAAATATATATATATAT
65 TGAAAATACTTTTGAAAACATATATAATATATAGTTTTG-AAATGTTTAAATATATATATATAT
* **
1228254 ATTTTGAAAATGTATATAATATATAGTTTTGAAAATA-TTTTTGAAA-ATATAT-TATATAGTTT
1 ATTTTGAAAATATATATAATATATAGTTTTGAAAA-AGTTTTAAAAATATATATATATATAGTTT
**
1228316 TGAAAATTAACTTTTGAAAACATATATGTTATATAGTTTTGA
65 TGAAAA-T-ACTTTTGAAAACATATATAATATATAGTTTTGA
1228358 TTTTTTCGAC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
126 16 0.17
127 2 0.02
128 33 0.36
129 40 0.43
130 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.09, T:0.46
Consensus pattern (127 bp):
ATTTTGAAAATATATATAATATATAGTTTTGAAAAAGTTTTAAAAATATATATATATATAGTTTT
GAAAATACTTTTGAAAACATATATAATATATAGTTTTGAAATGTTTAAATATATATATATAT
Found at i:1228385 original size:3 final size:3
Alignment explanation
Indices: 1228370--1228449 Score: 67
Period size: 3 Copynumber: 26.0 Consensus size: 3
1228360 TTTTCGACGC
1228370 ATT ATT ATAT ATT ATT A-T ATT ATT ATT ATT ATAT ATAT ATT ATTT ATTT
1 ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT AT-T AT-T ATT A-TT A-TT
* * *
1228419 ATT -TT CTT CTT ATT TTT ATT -TT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1228450 TTTGTTAGGG
Statistics
Matches: 68, Mismatches: 3, Indels: 12
0.82 0.04 0.14
Matches are distributed among these distances:
2 6 0.09
3 45 0.66
4 17 0.25
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:1228401 original size:24 final size:24
Alignment explanation
Indices: 1228370--1228417 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
1228360 TTTTCGACGC
1228370 ATTATTATATAT-TATTATATTATT
1 ATTATTATATATATATTAT-TTATT
1228394 ATTATTATATATATATTATTTATT
1 ATTATTATATATATATTATTTATT
1228418 TATTTTCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTATTATATATATATTATTTATT
Found at i:1228451 original size:11 final size:11
Alignment explanation
Indices: 1228371--1228451 Score: 53
Period size: 11 Copynumber: 7.2 Consensus size: 11
1228361 TTTCGACGCA
1228371 TTATTATATATT
1 TTATTAT-TATT
1228383 ATTA-TATTATT
1 -TTATTATTATT
1228394 ATTATTA-TATAT
1 -TTATTATTAT-T
*
1228406 ATATTATT-TAT
1 TTATTATTAT-T
*
1228417 TTATT-TTCTT
1 TTATTATTATT
*
1228427 CTTATTTTTATT
1 -TTATTATTATT
1228439 TTATTATTATT
1 TTATTATTATT
1228450 TT
1 TT
1228452 TGTTAGGGTC
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
10 3 0.05
11 41 0.71
12 11 0.19
13 3 0.05
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATTATTATT
Done.