Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009067.1 Hibiscus syriacus cultivar Beakdansim tig00112491_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: 2329927
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 10
Found at i:1103908 original size:29 final size:29
Alignment explanation
Indices: 1103866--1103921 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
1103856 AAATATCCAA
* *
1103866 AGAAAGTT-CAAAAACAAGTTCCAAACATG
1 AGAAAGTTAAAAAAACAAATT-CAAACATG
1103895 AGAAAGTTAAAAAAACAAATTCAAACA
1 AGAAAGTTAAAAAAACAAATTCAAACA
1103922 AGACGCCTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.59, C:0.14, G:0.11, T:0.16
Consensus pattern (29 bp):
AGAAAGTTAAAAAAACAAATTCAAACATG
Found at i:1106502 original size:6 final size:6
Alignment explanation
Indices: 1106491--1106515 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1106481 ATCGAATAAA
1106491 TAAATT TAAATT TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT T
1106516 GTAATTTTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAAATT
Found at i:1107015 original size:3 final size:3
Alignment explanation
Indices: 1107007--1107038 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1106997 TAAACAAAAG
*
1107007 AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1107039 AAAAACAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:1108319 original size:5 final size:5
Alignment explanation
Indices: 1108309--1108388 Score: 58
Period size: 5 Copynumber: 15.2 Consensus size: 5
1108299 CCTGGAAAGA
* *
1108309 AAAAT AAAAT AAAA- AGGAAAT -TAAT AAAAT AAAAA AGGAAAT -AAAT
1 AAAAT AAAAT AAAAT A--AAAT AAAAT AAAAT AAAAT A--AAAT AAAAT
1108355 AATAAT AATAAT AAAGAT AAAAT AAAAT AAAAT A
1 AA-AAT AA-AAT AAA-AT AAAAT AAAAT AAAAT A
1108389 TTTTTCGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
4 8 0.13
5 32 0.52
6 19 0.31
7 3 0.05
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1108345 original size:21 final size:21
Alignment explanation
Indices: 1108310--1108386 Score: 86
Period size: 21 Copynumber: 3.6 Consensus size: 21
1108300 CTGGAAAGAA
1108310 AAATAAAAT-AAAAAGGAAAT
1 AAATAAAATAAAAAAGGAAAT
*
1108330 TAATAAAATAAAAAAGGAAAT
1 AAATAAAATAAAAAAGGAAAT
* *
1108351 AAATAATAATAATAATAAAGATA-
1 AAATAA-AATAA-AA-AAGGAAAT
1108374 AAATAAAATAAAA
1 AAATAAAATAAAA
1108387 TATTTTTCGA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
20 8 0.16
21 18 0.37
22 10 0.20
23 8 0.16
24 5 0.10
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (21 bp):
AAATAAAATAAAAAAGGAAAT
Found at i:1108491 original size:29 final size:29
Alignment explanation
Indices: 1108453--1108509 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
1108443 ATTATATATT
* *
1108453 TTTTGAAAAATGCTTTCAAAGCTATATAG
1 TTTTCAAAAATGCTTTCAAAACTATATAG
* *
1108482 TTTTCAAAAATGTTTTTAAAACTATATA
1 TTTTCAAAAATGCTTTCAAAACTATATA
1108510 CTATATAAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (29 bp):
TTTTCAAAAATGCTTTCAAAACTATATAG
Found at i:1108572 original size:29 final size:29
Alignment explanation
Indices: 1108539--1108612 Score: 87
Period size: 31 Copynumber: 2.5 Consensus size: 29
1108529 GATTTCAAAA
*
1108539 TTAAATAA-TATATATGTTTTCAAAATATT
1 TTAAA-AACTATATATATTTTCAAAATATT
* *
1108568 TTAAAAAAGCTATATTTATTTTCAAAATGTT
1 TT-AAAAA-CTATATATATTTTCAAAATATT
1108599 TTAAAAACTATATA
1 TTAAAAACTATATA
1108613 ATATATAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
29 10 0.26
30 8 0.21
31 20 0.53
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (29 bp):
TTAAAAACTATATATATTTTCAAAATATT
Found at i:1108611 original size:103 final size:106
Alignment explanation
Indices: 1108470--1108664 Score: 274
Period size: 103 Copynumber: 1.9 Consensus size: 106
1108460 AAATGCTTTC
* *
1108470 AAAGCTATATAGTTTTCAAAAATGTTTTTAAAACTATATACTATAT-AA-GTTTTCAAA-ATGAT
1 AAAGCTATATAGTTTTCAAAAATGTTTTAAAAACTATATAATATATAAACGTTTTCAAACATGAT
* *
1108532 TTCAAAATTAAATAATATATATGTTTTCAAAATATTTTAAA
66 TTCAAAACTAAATAATATATATATTTTCAAAATATTTTAAA
1108573 AAAGCTATATTTA-TTTTC-AAAATGTTTTAAAAACTATATAATATATAAACGTTTTCAAACATG
1 AAAGCTATA--TAGTTTTCAAAAATGTTTTAAAAACTATATAATATATAAACGTTTTCAAACATG
* * *
1108636 TTTTCAAAACTATATATTATATATATTTT
64 ATTTCAAAACTAAATAATATATATATTTT
1108665 TTAAAAATGT
Statistics
Matches: 80, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
103 35 0.44
104 7 0.09
105 11 0.14
106 27 0.34
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.43
Consensus pattern (106 bp):
AAAGCTATATAGTTTTCAAAAATGTTTTAAAAACTATATAATATATAAACGTTTTCAAACATGAT
TTCAAAACTAAATAATATATATATTTTCAAAATATTTTAAA
Found at i:1108630 original size:38 final size:36
Alignment explanation
Indices: 1108475--1108697 Score: 181
Period size: 36 Copynumber: 6.2 Consensus size: 36
1108465 CTTTCAAAGC
* *
1108475 TATAT-AGTTTTCAAAAATGTTTTTAAAACTATATAC
1 TATATAAGTTTTC-AAAATGTTTTAAAAACTATATAA
* * * *
1108511 TATATAAGTTTTCAAAATGATTTCAAAATTAAATAA
1 TATATAAGTTTTCAAAATGTTTTAAAAACTATATAA
* * **
1108547 TATATATGTTTTCAAAATATTTTAAAAA--AGCT-A
1 TATATAAGTTTTCAAAATGTTTTAAAAACTATATAA
*
1108580 TAT-TTA-TTTTCAAAATGTTTTAAAAACTATATAA
1 TATATAAGTTTTCAAAATGTTTTAAAAACTATATAA
*
1108614 TATATAAACGTTTTCAAACATGTTTTCAAAACTATATATTA
1 TATAT-AA-GTTTTCAAA-ATGTTTTAAAAACTATATA--A
** * *
1108655 TATATATTTTTTAAAAATGTTTT-CAAACTATAATATA
1 TATATAAGTTTTCAAAATGTTTTAAAAACTAT-ATA-A
1108692 TATATA
1 TATATA
1108698 TAAATGGGAC
Statistics
Matches: 153, Mismatches: 22, Indels: 23
0.77 0.11 0.12
Matches are distributed among these distances:
31 19 0.12
32 1 0.01
33 6 0.04
34 6 0.04
35 1 0.01
36 48 0.31
37 22 0.14
38 18 0.12
39 25 0.16
40 1 0.01
41 6 0.04
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (36 bp):
TATATAAGTTTTCAAAATGTTTTAAAAACTATATAA
Found at i:1108696 original size:37 final size:36
Alignment explanation
Indices: 1108475--1108698 Score: 124
Period size: 38 Copynumber: 6.2 Consensus size: 36
1108465 CTTTCAAAGC
* * *
1108475 TATATAGTTTTCAAAAATGTTTTTAAAACTATATACTA
1 TATATATTTTTTAAAAATG-TTTTCAAACTATATA-TA
* * * * *
1108513 TATA-A-GTTTTCAAAATGATTTCAAAAT-TAAATAA
1 TATATATTTTTTAAAAATGTTTTCAAACTATATAT-A
* * * **
1108547 TATATATGTTTTCAAAATATTTT-AAA--A-A-AGC
1 TATATATTTTTTAAAAATGTTTTCAAACTATATATA
* *
1108578 TATAT-TTATTTTCAAAATGTTTTAAAAACTATATAATA
1 TATATATT-TTTTAAAAATGTTTT-CAAACTATAT-ATA
* * * *
1108616 TATAAACGTTTTCAAACATGTTTTCAAAACTATATATTA
1 TATATA-TTTTTTAAAAATGTTTTC-AAACTATATA-TA
1108655 TATATATTTTTTAAAAATGTTTTCAAACTATAATATA
1 TATATATTTTTTAAAAATGTTTTCAAACTAT-ATATA
1108692 TATATAT
1 TATATAT
1108699 AAATGGGACG
Statistics
Matches: 144, Mismatches: 25, Indels: 35
0.71 0.12 0.17
Matches are distributed among these distances:
30 1 0.01
31 19 0.13
32 1 0.01
33 5 0.03
34 8 0.06
35 12 0.08
36 24 0.17
37 17 0.12
38 28 0.19
39 28 0.19
40 1 0.01
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (36 bp):
TATATATTTTTTAAAAATGTTTTCAAACTATATATA
Found at i:1111824 original size:30 final size:30
Alignment explanation
Indices: 1111790--1111849 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1111780 AGTGATTGAG
1111790 ATTTTATCCTCTAGGTGATCATTTAGAGGT
1 ATTTTATCCTCTAGGTGATCATTTAGAGGT
1111820 ATTTTATCCTCTAGGTGATCATTTAGAGGT
1 ATTTTATCCTCTAGGTGATCATTTAGAGGT
1111850 GTTATTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.43
Consensus pattern (30 bp):
ATTTTATCCTCTAGGTGATCATTTAGAGGT
Found at i:1113579 original size:44 final size:44
Alignment explanation
Indices: 1113523--1113664 Score: 239
Period size: 44 Copynumber: 3.2 Consensus size: 44
1113513 TATTTATTAT
* *
1113523 TTTTATTTATGACATCCTTTCATGCCTTAATGGACCATTATGCA
1 TTTTAGTTATGACATCCTTTCATGCCTTAATGCACCATTATGCA
* *
1113567 TTTCAGTTATGACATCCTTTAATGCCTTAATGCACCATTATGCA
1 TTTTAGTTATGACATCCTTTCATGCCTTAATGCACCATTATGCA
*
1113611 TTTTAGTTATGGCATCCTTTCATGCCTTAATGCACCATTATGCA
1 TTTTAGTTATGACATCCTTTCATGCCTTAATGCACCATTATGCA
1113655 TTTTAGTTAT
1 TTTTAGTTAT
1113665 TAATTCGGTT
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 91 1.00
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.43
Consensus pattern (44 bp):
TTTTAGTTATGACATCCTTTCATGCCTTAATGCACCATTATGCA
Found at i:1114237 original size:20 final size:19
Alignment explanation
Indices: 1114187--1114242 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
1114177 AACCAATAAT
1114187 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
*
1114206 GATGAAAA-AAAATGAAATTG
1 AAT-AAAATAAAAT-AAATTG
1114226 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
1114243 GAAGATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 15 0.48
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:1114349 original size:28 final size:28
Alignment explanation
Indices: 1114318--1114374 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
1114308 AATAAGAGCA
*
1114318 AAAAACTAAAAATATAATAA-AAATAAAT
1 AAAAACTAAAAATAAAATAATAAA-AAAT
* *
1114346 AAAAAGTATAAATAAAATAATAAAAAAT
1 AAAAACTAAAAATAAAATAATAAAAAAT
1114374 A
1 A
1114375 TACATATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 22 0.88
29 3 0.12
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (28 bp):
AAAAACTAAAAATAAAATAATAAAAAAT
Found at i:1114350 original size:22 final size:22
Alignment explanation
Indices: 1114325--1114395 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
1114315 GCAAAAAACT
1114325 AAAAATATAATAAAAATAAATA
1 AAAAATATAATAAAAATAAATA
*
1114347 AAAAGTATAA-ATAAAAT-AATA
1 AAAAATATAATA-AAAATAAATA
* *
1114368 AAAAATATACATATATA-AAATA
1 AAAAATATA-ATAAAAATAAATA
1114390 AAAAAT
1 AAAAAT
1114396 GTATGTATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
21 13 0.32
22 27 0.66
23 1 0.02
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.24
Consensus pattern (22 bp):
AAAAATATAATAAAAATAAATA
Found at i:1114410 original size:25 final size:26
Alignment explanation
Indices: 1114329--1114419 Score: 77
Period size: 25 Copynumber: 3.7 Consensus size: 26
1114319 AAAACTAAAA
*
1114329 ATATAAT-AAA-AATAAATAAA-AAGT
1 ATATAATAAAATAATAAA-AAATATGT
**
1114353 ATA-AATAAAATAATAAAAAATATAC
1 ATATAATAAAATAATAAAAAATATGT
**
1114378 ATAT-ATAAAATAA-AAAATGTATGT
1 ATATAATAAAATAATAAAAAATATGT
*
1114402 ATATAATAAAATACTAAA
1 ATATAATAAAATAATAAA
1114420 TAGTAATAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
23 3 0.06
24 20 0.38
25 27 0.51
26 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.27
Consensus pattern (26 bp):
ATATAATAAAATAATAAAAAATATGT
Found at i:1114438 original size:19 final size:18
Alignment explanation
Indices: 1114405--1114440 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1114395 TGTATGTATA
*
1114405 TAATAAAATACTAAATAG
1 TAATAAAATAATAAATAG
1114423 TAATAATAATAATAAATA
1 TAATAA-AATAATAAATA
1114441 AAAAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (18 bp):
TAATAAAATAATAAATAG
Found at i:1114589 original size:2 final size:2
Alignment explanation
Indices: 1114584--1114612 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1114574 TAAAAAAATA
1114584 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1114613 CATAAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1115165 original size:37 final size:37
Alignment explanation
Indices: 1115072--1115173 Score: 132
Period size: 37 Copynumber: 2.8 Consensus size: 37
1115062 ATGCTTGTGG
* * ** ** *
1115072 ATCCTATCTTTAGGAGTTTAAATAATAATAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
*
1115109 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTAT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
1115146 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
1115174 TAGGACGAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
Found at i:1116065 original size:106 final size:106
Alignment explanation
Indices: 1115873--1117127 Score: 1945
Period size: 106 Copynumber: 11.9 Consensus size: 106
1115863 GCATTGTTCT
* * * * * * *
1115873 GAGTCTAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATCGGAAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
1115938 CCAGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1115979 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTAC-GAAATTGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT-CTGAAATTGGGAAGTTGTTTGTTGACA
** * * *
1116043 GTCAGCGGTCCCTTCATCGTGAAGTTGAACTTACGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1116085 GAGTCCAATATCCTTCGTTGTGCAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1116150 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGAT-TG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG-TCTG
* *
1116191 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1116256 CCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1116297 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1116362 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1116403 GAGTCCAATATCTTTCGTTGTGAAGTTAAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1116468 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC--
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1116507 ---T-C--TATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
1116566 CCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGAGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1116607 GAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1116672 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1116713 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
1116778 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
1116819 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATCGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1116884 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1116925 GAGTACAATATCCTTCGTTATGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1116990 CCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1117031 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTGGGAAGTTGTTTGTTAACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
1117096 CCAGCTGTCCCTTCGTTGTGAAGTTGAACTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
1117128 TGTTATCTCG
Statistics
Matches: 1061, Mismatches: 76, Indels: 24
0.91 0.07 0.02
Matches are distributed among these distances:
98 89 0.08
100 1 0.00
101 1 0.00
103 1 0.00
105 2 0.00
106 965 0.91
107 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1117910 original size:24 final size:22
Alignment explanation
Indices: 1117853--1117911 Score: 57
Period size: 24 Copynumber: 2.6 Consensus size: 22
1117843 TTTTATTTTC
*
1117853 AAAGTTCTG-AAAATGTCAATA
1 AAAGTTTTGAAAAATGTCAATA
* *
1117874 AAGAGTTTCGAAAAATGTTTAATCA
1 AA-AGTTTTGAAAAATG-TCAAT-A
1117899 AAAGTTTTGAAAA
1 AAAGTTTTGAAAA
1117912 TATTGTCTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
21 2 0.07
22 5 0.17
23 6 0.20
24 14 0.47
25 3 0.10
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.31
Consensus pattern (22 bp):
AAAGTTTTGAAAAATGTCAATA
Found at i:1117911 original size:23 final size:21
Alignment explanation
Indices: 1117853--1117912 Score: 57
Period size: 23 Copynumber: 2.7 Consensus size: 21
1117843 TTTTATTTTC
*
1117853 AAAGTTCTGAAAATGTCAATA
1 AAAGTTTTGAAAATGTCAATA
* *
1117874 AAGAGTTTCGAAAAATGTTTAATCA
1 AA-AGTTTTG-AAAATG-TCAAT-A
1117899 AAAGTTTTGAAAAT
1 AAAGTTTTGAAAAT
1117913 ATTGTCTCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
21 2 0.06
22 5 0.16
23 11 0.35
24 10 0.32
25 3 0.10
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.32
Consensus pattern (21 bp):
AAAGTTTTGAAAATGTCAATA
Found at i:1118761 original size:26 final size:27
Alignment explanation
Indices: 1118732--1118796 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 27
1118722 TTTTTTGTCC
*
1118732 CTTTTTCTTTTTGATTTTTG-TTC-TTT
1 CTTTTT-TTTTTCATTTTTGCTTCTTTT
*
1118758 CTTTTTTTTTTCTTTTTTGCTTCTTTT
1 CTTTTTTTTTTCATTTTTGCTTCTTTT
1118785 CTTTTTTGTTTT
1 CTTTTTT-TTTT
1118797 TGCCCTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 11 0.32
26 9 0.26
27 10 0.29
28 4 0.12
ACGTcount: A:0.02, C:0.12, G:0.06, T:0.80
Consensus pattern (27 bp):
CTTTTTTTTTTCATTTTTGCTTCTTTT
Found at i:1118787 original size:31 final size:30
Alignment explanation
Indices: 1118733--1118797 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
1118723 TTTTTGTCCC
* *
1118733 TTTTTCTTTTTGATTTTTGTTCTTTCTTTTT
1 TTTTTCTTTTTGATTCTTGTTCTTT-TTTGT
*
1118764 TTTTTCTTTTTTGCTTCTT-TTCTTTTTTGT
1 TTTTTC-TTTTTGATTCTTGTTCTTTTTTGT
1118794 TTTT
1 TTTT
1118798 GCCCTTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 8 0.27
31 12 0.40
32 10 0.33
ACGTcount: A:0.02, C:0.11, G:0.06, T:0.82
Consensus pattern (30 bp):
TTTTTCTTTTTGATTCTTGTTCTTTTTTGT
Found at i:1118798 original size:22 final size:22
Alignment explanation
Indices: 1118756--1118799 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1118746 TTTTTGTTCT
*
1118756 TTCTTTTTTTTTTCTTTTTTGC
1 TTCTTTTTTTTTTCGTTTTTGC
1118778 TTCTTTTCTTTTTT-GTTTTTGC
1 TTCTTTT-TTTTTTCGTTTTTGC
1118800 CCTTTTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.80
Consensus pattern (22 bp):
TTCTTTTTTTTTTCGTTTTTGC
Found at i:1118806 original size:22 final size:23
Alignment explanation
Indices: 1118723--1118806 Score: 66
Period size: 23 Copynumber: 3.7 Consensus size: 23
1118713 TGCATGTGTT
1118723 TTTTTGTCCCTTTTTC-TTTTTG
1 TTTTTGTCCCTTTTTCTTTTTTG
* * * *
1118745 ATTTTTGTTCTTTCTTTTTTTTTTC
1 -TTTTTGTCCCTT-TTTCTTTTTTG
* *
1118770 TTTTT-TGCTTCTTTTCTTTTTTG
1 TTTTTGTCCCT-TTTTCTTTTTTG
1118793 TTTTTG-CCCTTTTT
1 TTTTTGTCCCTTTTT
1118807 GTTCTGATTG
Statistics
Matches: 48, Mismatches: 9, Indels: 9
0.73 0.14 0.14
Matches are distributed among these distances:
22 4 0.08
23 30 0.62
24 9 0.19
25 5 0.10
ACGTcount: A:0.01, C:0.15, G:0.07, T:0.76
Consensus pattern (23 bp):
TTTTTGTCCCTTTTTCTTTTTTG
Found at i:1123124 original size:20 final size:19
Alignment explanation
Indices: 1123073--1123129 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
1123063 AACCAATAAT
1123073 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
* *
1123092 GATGAAAAAAAAATGAAATTG
1 AAT-AAAATAAAAT-AAATTG
1123113 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
1123130 GAAGATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 12 0.39
20 12 0.39
21 7 0.23
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:1123236 original size:28 final size:27
Alignment explanation
Indices: 1123204--1123260 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
1123194 TAATAAGAGC
* *
1123204 AAAAAACTAAAAATATAATGAAAATAAAT
1 AAAAAA-TAAAAATAAAAT-AAAAAAAAT
*
1123233 AAAAAATATAAATAAAATAAAAAAAAT
1 AAAAAATAAAAATAAAATAAAAAAAAT
1123260 A
1 A
1123261 TACATTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 9 0.36
28 10 0.40
29 6 0.24
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (27 bp):
AAAAAATAAAAATAAAATAAAAAAAAT
Found at i:1123237 original size:22 final size:19
Alignment explanation
Indices: 1123212--1123262 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 19
1123202 GCAAAAAACT
1123212 AAAAATATAATGAAAATAAATA
1 AAAAATATAAT-AAAAT-AA-A
1123234 AAAAATATAAATAAAATAAA
1 AAAAATAT-AATAAAATAAA
1123254 AAAAATATA
1 AAAAATATA
1123263 CATTTATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.04
20 9 0.32
21 2 0.07
22 13 0.46
23 3 0.11
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (19 bp):
AAAAATATAATAAAATAAA
Found at i:1124143 original size:37 final size:37
Alignment explanation
Indices: 1124050--1124151 Score: 150
Period size: 37 Copynumber: 2.8 Consensus size: 37
1124040 ATGCTTGTAG
* * ** *
1124050 ATCCTATCTTTAGGAGTTTAAATAATAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
*
1124087 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
1124124 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
1124152 TAGAACGAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:1144222 original size:21 final size:21
Alignment explanation
Indices: 1144198--1144240 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1144188 TTAGAGTGAA
*
1144198 AGTTTACAATATTGATATGAC
1 AGTTTACAATATTGACATGAC
* *
1144219 AGTTTACGATGTTGACATGAC
1 AGTTTACAATATTGACATGAC
1144240 A
1 A
1144241 ATATACAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (21 bp):
AGTTTACAATATTGACATGAC
Found at i:1144326 original size:23 final size:23
Alignment explanation
Indices: 1144300--1144351 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
1144290 AATACTTATT
* *
1144300 TAAAATTATATAAATTTAAAATA-
1 TAAAATTAT-TAAAATGAAAATAC
1144323 TAAAAATTATTAAAATGAAAATAC
1 T-AAAATTATTAAAATGAAAATAC
1144347 TAAAA
1 TAAAA
1144352 ATTAAATCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
TAAAATTATTAAAATGAAAATAC
Found at i:1144329 original size:15 final size:16
Alignment explanation
Indices: 1144297--1144330 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1144287 CAAAATACTT
*
1144297 ATTTAAAATTATATAA
1 ATTTAAAATTATAAAA
1144313 ATTTAAAA-TATAAAA
1 ATTTAAAATTATAAAA
1144328 ATT
1 ATT
1144331 ATTAAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTTAAAATTATAAAA
Found at i:1144329 original size:24 final size:24
Alignment explanation
Indices: 1144301--1144355 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
1144291 ATACTTATTT
* *
1144301 AAAATTATATAAATTTAAAATA-TA
1 AAAATTAT-TAAAATGAAAATACTA
1144325 AAAATTATTAAAATGAAAATACTA
1 AAAATTATTAAAATGAAAATACTA
1144349 AAAATTA
1 AAAATTA
1144356 AATCGTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 11 0.39
24 17 0.61
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (24 bp):
AAAATTATTAAAATGAAAATACTA
Found at i:1146753 original size:84 final size:84
Alignment explanation
Indices: 1146612--1146784 Score: 310
Period size: 84 Copynumber: 2.1 Consensus size: 84
1146602 TCCCAGTAGT
* *
1146612 TTATAATTAATCACAATGAATGGTTGAAAAACTAAAGCAAAAGAGGGTTAAATGTTAGTACGGTC
1 TTATAAGTAATCACAATGAATGGTTGAAAAACTAAAGCAAAAGAGGGTTAAATGTTAGTACCGTC
1146677 CTTATATAATACATTGAAC
66 CTTATATAATACATTGAAC
* *
1146696 TTATAAGTAATCACAATGCATGGTTGAAAAACTAAAGCAAAAGAGGGTTGAATGTTAGTACCGTC
1 TTATAAGTAATCACAATGAATGGTTGAAAAACTAAAGCAAAAGAGGGTTAAATGTTAGTACCGTC
1146761 CTTATATAATACATTGAAC
66 CTTATATAATACATTGAAC
1146780 TTATA
1 TTATA
1146785 TCAGTGGAAA
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.30
Consensus pattern (84 bp):
TTATAAGTAATCACAATGAATGGTTGAAAAACTAAAGCAAAAGAGGGTTAAATGTTAGTACCGTC
CTTATATAATACATTGAAC
Found at i:1148301 original size:62 final size:62
Alignment explanation
Indices: 1148197--1148401 Score: 347
Period size: 62 Copynumber: 3.3 Consensus size: 62
1148187 ATTGCAAAAT
* * ** *
1148197 TAGTAAGGCTTGTGGTTTTAAGATCTCGTTATTAGCAGTTGGATAGGTATGGTAGTAATAAA
1 TAGTAAGGCTTGTAGTTTTAAGATCTCATTAGAAGCACTTGGATAGGTATGGTAGTAATAAA
1148259 TAGTAAGGCTTGTAGTTTTAAGATCTCATTAGAAGCACTTGGATAGGTATGGTAGTAATAAA
1 TAGTAAGGCTTGTAGTTTTAAGATCTCATTAGAAGCACTTGGATAGGTATGGTAGTAATAAA
1148321 TAGTAAGGCTTGTAGTTTTAAGATCTCATTAGAAGCACTTGGATAGGTATGGTAGTAATAAA
1 TAGTAAGGCTTGTAGTTTTAAGATCTCATTAGAAGCACTTGGATAGGTATGGTAGTAATAAA
**
1148383 TAGTAAGATTTGTAGTTTT
1 TAGTAAGGCTTGTAGTTTT
1148402 TTAAATAGTC
Statistics
Matches: 136, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 136 1.00
ACGTcount: A:0.32, C:0.07, G:0.25, T:0.37
Consensus pattern (62 bp):
TAGTAAGGCTTGTAGTTTTAAGATCTCATTAGAAGCACTTGGATAGGTATGGTAGTAATAAA
Found at i:1152094 original size:82 final size:82
Alignment explanation
Indices: 1152004--1152168 Score: 321
Period size: 82 Copynumber: 2.0 Consensus size: 82
1151994 AAATCTTAGG
1152004 CATACTCTCTATTTATAAAGTTAAATATTTGGTCACATAGAATCCTTATTCAATAAAAATTCTGA
1 CATACTCTCTATTTATAAAGTTAAATATTTGGTCACATAGAATCCTTATTCAATAAAAATTCTGA
1152069 CTAAATAAACTTAATCA
66 CTAAATAAACTTAATCA
*
1152086 CATACTCTCTATTTATAAAGTTAAATATTTGGTCACATAGAATCCTTATTCAATAAGAATTCTGA
1 CATACTCTCTATTTATAAAGTTAAATATTTGGTCACATAGAATCCTTATTCAATAAAAATTCTGA
1152151 CTAAATAAACTTAATCA
66 CTAAATAAACTTAATCA
1152168 C
1 C
1152169 TGAGTAAATA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (82 bp):
CATACTCTCTATTTATAAAGTTAAATATTTGGTCACATAGAATCCTTATTCAATAAAAATTCTGA
CTAAATAAACTTAATCA
Found at i:1153724 original size:23 final size:25
Alignment explanation
Indices: 1153679--1153724 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1153669 TAAATAAAGA
1153679 CATGAAATAAATAAGTTTATTGTGT
1 CATGAAATAAATAAGTTTATTGTGT
1153704 CATGATAA-AAATAA-TTT-TTGT
1 CATGA-AATAAATAAGTTTATTGT
1153725 TTTAGAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.20
24 3 0.15
25 11 0.55
26 2 0.10
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.41
Consensus pattern (25 bp):
CATGAAATAAATAAGTTTATTGTGT
Found at i:1160303 original size:81 final size:81
Alignment explanation
Indices: 1160168--1160329 Score: 288
Period size: 81 Copynumber: 2.0 Consensus size: 81
1160158 AAAGTAAGAA
* * *
1160168 AACCATAGAATCATGTTTTTAGTTTAATGCTCGAAAAGAAGATGAACTAGTATCTTCTACGTGAC
1 AACCATAGAATCATGTTTCTAGTTTAATGCTCGAAAAGAAGATGAACAAGTATCTTCTACATGAC
1160233 TCGCATTCACATAACC
66 TCGCATTCACATAACC
*
1160249 AACCATAGAATCATGTTTCTAGTTTACTGCTCGAAAAGAAGATGAACAAGTATCTTCTACATGAC
1 AACCATAGAATCATGTTTCTAGTTTAATGCTCGAAAAGAAGATGAACAAGTATCTTCTACATGAC
1160314 TCGCATTCACATAACC
66 TCGCATTCACATAACC
1160330 CGCACACATT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (81 bp):
AACCATAGAATCATGTTTCTAGTTTAATGCTCGAAAAGAAGATGAACAAGTATCTTCTACATGAC
TCGCATTCACATAACC
Found at i:1163361 original size:31 final size:31
Alignment explanation
Indices: 1163326--1163434 Score: 182
Period size: 31 Copynumber: 3.5 Consensus size: 31
1163316 CTGCTACTTG
1163326 ATAGTACTCTGCTAGTAACTATACTAGTTAC
1 ATAGTACTCTGCTAGTAACTATACTAGTTAC
1163357 ATAGTACTCTGCTAGTAACTATACTAGTTAC
1 ATAGTACTCTGCTAGTAACTATACTAGTTAC
* *
1163388 ATAGTACTCTGCTAGTATCTATACTAGTTAG
1 ATAGTACTCTGCTAGTAACTATACTAGTTAC
* *
1163419 ATTGTACTCTGTTAGT
1 ATAGTACTCTGCTAGT
1163435 TATTGATAGT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 74 1.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (31 bp):
ATAGTACTCTGCTAGTAACTATACTAGTTAC
Found at i:1163659 original size:77 final size:77
Alignment explanation
Indices: 1163567--1163721 Score: 292
Period size: 77 Copynumber: 2.0 Consensus size: 77
1163557 ACATTTCCTA
1163567 CTGGTCATGTAGAAAATGGCAAATACCACTTGAACTCCAAGTGAAGAAATGCCTTTTTGTATCAT
1 CTGGTCATGTAGAAAATGGCAAATACCACTTGAACTCCAAGTGAAGAAATGCCTTTTTGTATCAT
*
1163632 AATATGCCACTT
66 AATATGACACTT
*
1163644 CTGGTCATGTAGAAAATGGCAAATACCACTTGAACTCCATGTGAAGAAATGCCTTTTTGTATCAT
1 CTGGTCATGTAGAAAATGGCAAATACCACTTGAACTCCAAGTGAAGAAATGCCTTTTTGTATCAT
1163709 AATATGACACTT
66 AATATGACACTT
1163721 C
1 C
1163722 AATCTAAATA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (77 bp):
CTGGTCATGTAGAAAATGGCAAATACCACTTGAACTCCAAGTGAAGAAATGCCTTTTTGTATCAT
AATATGACACTT
Found at i:1166312 original size:22 final size:23
Alignment explanation
Indices: 1166260--1166312 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
1166250 ATTCGATTTA
*
1166260 ATTTTATATTATTTAAATATTAAT
1 ATTTTA-AGTATTTAAATATTAAT
*
1166284 TTTTTAAGTATTTAAATA-TAAT
1 ATTTTAAGTATTTAAATATTAAT
1166306 ATTTTAA
1 ATTTTAA
1166313 ATTTACATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 10 0.38
23 11 0.42
24 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
ATTTTAAGTATTTAAATATTAAT
Found at i:1174795 original size:243 final size:240
Alignment explanation
Indices: 1174337--1174823 Score: 856
Period size: 247 Copynumber: 2.0 Consensus size: 240
1174327 AAAGGTCTGC
1174337 CCTCATGCATCCTCGGGAAGCAGAAACGGTTTCCGTTATTTGAACCACTCGTAATAACCGTCAGT
1 CCTCATGCATCCTCGGGAAGCAGAAACGGTTTCCGTTATTTGAACCACTCGTAATAACCGTCAGT
*
1174402 AACCATCAAGAGGTCAAGAAAAATGGCTCTCTACGGGGAAGGCGCCGATGTCGATCCTCCCACAA
66 AACCATCAAGAGGTCAAGAAAAATGGC-CTCTACGGGGAAGGCGACGATGTCGATCCTCCCACAA
1174467 CACACGACCACCCATGATGCCTCACCAGTCAATCTGTATCTGTCTTTGCCGCGTCTATCTGTGCT
130 CACAC-ACCACCCATGATGCCTCACCAGTCAATCTGTATCTGTCTTTGCCGCGTCTATCTGTGCT
1174532 ATGCAACTGTCCATATTGCGAGGGTGCTTCCGGAATTGGTTGAAAACAA
194 ATGCAACTGTCCATATTGCGA-GG-GCTTCCGGAATTGGTTGAAAACAA
1174581 CCTCATGCATCCTCGGGAAGCAGAAACGGTTTCCCGTTATTATTGAACCACTCGTAATAACCGTC
1 CCTCATGCATCCTCGGGAAGCAGAAACGGTTT-CCGTTA-T-TTGAACCACTCGTAATAACCGTC
1174646 AGTAACCATCAAGAGGTCAAGAAAAATGG-CTCTACGGGGAAGGCGACGATGTCGATCCTCCCAC
63 AGTAACCATCAAGAGGTCAAGAAAAATGGCCTCTACGGGGAAGGCGACGATGTCGATCCTCCCAC
1174710 AACACGAC-CCA-CCATGATGCCTCACCAGTCAATCTGTATCTGTC-TTGCCGCGTCTATCTGTG
128 AACAC-ACACCACCCATGATGCCTCACCAGTCAATCTGTATCTGTCTTTGCCGCGTCTATCTGTG
1174772 CTATGCAACTCGTCCATATTGCGAGGGCTTCCGGAATTGGTTGAAAACAA
192 CTATGCAACT-GTCCATATTGCGAGGGCTTCCGGAATTGGTTGAAAACAA
1174822 CC
1 CC
1174824 AAATTGCCGG
Statistics
Matches: 237, Mismatches: 1, Indels: 13
0.94 0.00 0.05
Matches are distributed among these distances:
241 26 0.11
242 30 0.13
243 46 0.19
244 35 0.15
245 45 0.19
246 3 0.01
247 52 0.22
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (240 bp):
CCTCATGCATCCTCGGGAAGCAGAAACGGTTTCCGTTATTTGAACCACTCGTAATAACCGTCAGT
AACCATCAAGAGGTCAAGAAAAATGGCCTCTACGGGGAAGGCGACGATGTCGATCCTCCCACAAC
ACACACCACCCATGATGCCTCACCAGTCAATCTGTATCTGTCTTTGCCGCGTCTATCTGTGCTAT
GCAACTGTCCATATTGCGAGGGCTTCCGGAATTGGTTGAAAACAA
Found at i:1176376 original size:59 final size:59
Alignment explanation
Indices: 1176313--1176425 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
1176303 CATATTTTAG
* ** * * * *
1176313 GGATGAAATTAGAACGTTCAAAAGTTTAAGGACTAATTTATAATGATAGTTATAGTTGA
1 GGATGAAATTAGAACATTCAAAAAATTAAGAACCAATTTAAAATGAGAGTTATAGTTGA
*
1176372 GGATGAAATTAGAATATTCAAAAAATTAAGAACCAATTTAAAATGAGAGTTATA
1 GGATGAAATTAGAACATTCAAAAAATTAAGAACCAATTTAAAATGAGAGTTATA
1176426 ATTTAGGGAC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 46 1.00
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.31
Consensus pattern (59 bp):
GGATGAAATTAGAACATTCAAAAAATTAAGAACCAATTTAAAATGAGAGTTATAGTTGA
Found at i:1179503 original size:11 final size:11
Alignment explanation
Indices: 1179483--1179565 Score: 53
Period size: 11 Copynumber: 7.3 Consensus size: 11
1179473 ATTAATTATT
*
1179483 TTATTCTAATA
1 TTATTTTAATA
*
1179494 TTATTTTAATG
1 TTATTTTAATA
*
1179505 TTTTTTTAA-A
1 TTATTTTAATA
*
1179515 GTTATTAT-ATA
1 -TTATTTTAATA
1179526 TATATATTTAACTA
1 T-TAT-TTTAA-TA
*
1179540 TTATATTTATTA
1 TTAT-TTTAATA
*
1179552 TTATTTTACTA
1 TTATTTTAATA
1179563 TTA
1 TTA
1179566 AGTATAAATA
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
10 2 0.04
11 35 0.61
12 8 0.14
13 9 0.16
14 3 0.05
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:1179556 original size:23 final size:21
Alignment explanation
Indices: 1179517--1179580 Score: 65
Period size: 23 Copynumber: 2.9 Consensus size: 21
1179507 TTTTTAAAGT
1179517 TATTATATATATATATTTAAC
1 TATTATATATATATATTTAAC
* *
1179538 TATTATATTTATTATTATTTTAC
1 TATTATATATA-TA-TATTTAAC
*
1179561 TATTAAGTATAAATATATTT
1 TATT-A-TATATATATATTT
1179581 TTCTCTTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 10 0.29
22 2 0.06
23 16 0.46
24 3 0.09
25 4 0.11
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (21 bp):
TATTATATATATATATTTAAC
Found at i:1179761 original size:21 final size:22
Alignment explanation
Indices: 1179735--1179784 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1179725 ATATTACATT
*
1179735 ATTATTATTTTACTTTATTA-A
1 ATTATTATTTTACGTTATTATA
*
1179756 ATTATT-TTTTTCGTTATTATA
1 ATTATTATTTTACGTTATTATA
*
1179777 TTTATTAT
1 ATTATTAT
1179785 ATATATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 11 0.46
21 12 0.50
22 1 0.04
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (22 bp):
ATTATTATTTTACGTTATTATA
Found at i:1179783 original size:9 final size:9
Alignment explanation
Indices: 1179770--1179803 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1179760 TTTTTTTCGT
*
1179770 TATTATATT
1 TATTATATA
1179779 TATTATATA
1 TATTATATA
1179788 TA-TATATA
1 TATTATATA
1179796 TATTATAT
1 TATTATAT
1179804 CATAATGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATTATATA
Found at i:1184209 original size:21 final size:20
Alignment explanation
Indices: 1184185--1184237 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
1184175 AACAAAAAGG
1184185 GCAAAAAGAAAAAAGAAAGAA
1 GCAAAAAGAAAAAA-AAAGAA
*
1184206 GCAAAAAGGAAAAAACAAGAA
1 GCAAAAA-GAAAAAAAAAGAA
1184227 -CAAAAAAGAAA
1 GC-AAAAAGAAA
1184238 GAACAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 5 0.17
21 17 0.59
22 7 0.24
ACGTcount: A:0.75, C:0.08, G:0.17, T:0.00
Consensus pattern (20 bp):
GCAAAAAGAAAAAAAAAGAA
Found at i:1184882 original size:22 final size:22
Alignment explanation
Indices: 1184854--1184904 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1184844 CCCCATCAAT
1184854 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
1184876 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
1184898 CCTTTGA
1 CCTTTGA
1184905 CCAAACACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:1185727 original size:35 final size:36
Alignment explanation
Indices: 1185642--1185739 Score: 153
Period size: 36 Copynumber: 2.8 Consensus size: 36
1185632 CTCACCATTG
*
1185642 TCTCTTGAGACAGTTTCCCTTGAAACAAACTTTGTC
1 TCTCTTGAGACAGTTTCCCTTGAAACAAAATTTGTC
* *
1185678 TCTCTTGAGACAGTTTCCCTTTAAACAAAATTTTTC
1 TCTCTTGAGACAGTTTCCCTTGAAACAAAATTTGTC
*
1185714 TC-CTTGAGACAGTTTCTCTTGAAACA
1 TCTCTTGAGACAGTTTCCCTTGAAACA
1185740 TAAACATTGA
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 22 0.39
36 35 0.61
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (36 bp):
TCTCTTGAGACAGTTTCCCTTGAAACAAAATTTGTC
Found at i:1185918 original size:37 final size:36
Alignment explanation
Indices: 1185852--1185937 Score: 111
Period size: 37 Copynumber: 2.4 Consensus size: 36
1185842 ATTGGAAACA
** * *
1185852 TTTCCCTTGAAA-TGAATTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACAG
1185887 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAA-TTTGTCTCCCTTGAGACAG
*
1185924 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
1185938 TAAACATTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
35 12 0.27
36 2 0.05
37 30 0.68
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACAG
Found at i:1185925 original size:100 final size:101
Alignment explanation
Indices: 1185655--1186100 Score: 712
Period size: 100 Copynumber: 4.5 Consensus size: 101
1185645 CTTGAGACAG
** * *
1185655 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTTAAACAAAATTTT-TCT-CCT
1 TTTCCCTTGAAATGAA-TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1185718 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
65 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * * *
1185755 TTTCCCTTGAAATGAGTTT-TGTCTCTTGAGAT--TTTCCCTTGAAACAAAATTTCGTCTCCATT
1 TTTCCCTTGAAATGAATTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTT
*
1185817 GAGACAGTTTCTCTTGAAACAT-AACATTGGAAACA
66 GAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
1185852 TTTCCCTTGAAATGAATTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTT
1 TTTCCCTTGAAATGAATTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTT
1185917 GAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 GAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
1185953 TTTCCC-TGAAATGAATTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAAAATTTTGTCTCCCTT
1 TTTCCCTTGAAATGAATTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTT
1186017 GAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 GAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
1186053 TTTCCCTTGAAATGAA-TT-TCGTCTCTTGAGATAGTTTCTCTTGAAACA
1 TTTCCCTTGAAATGAATTTGTC-TCTCTTGAGATAGTTTCCCTTGAAACA
1186101 TAAACATTGA
Statistics
Matches: 321, Mismatches: 17, Indels: 16
0.91 0.05 0.05
Matches are distributed among these distances:
96 19 0.06
97 33 0.10
98 48 0.15
99 5 0.02
100 189 0.59
101 27 0.08
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (101 bp):
TTTCCCTTGAAATGAATTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTT
GAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:1186089 original size:63 final size:64
Alignment explanation
Indices: 1186014--1186165 Score: 279
Period size: 63 Copynumber: 2.4 Consensus size: 64
1186004 TTTTGTCTCC
1186014 CTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCG-TCT
1 CTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCGCTCT
*
1186077 CTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCGTCTCT
1 CTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCG-CTCT
1186142 CTTGAGACAGTTTCTCTTGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
1186166 AAATTTTGTC
Statistics
Matches: 85, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
63 59 0.69
65 26 0.31
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (64 bp):
CTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCGCTCT
Found at i:1186191 original size:165 final size:166
Alignment explanation
Indices: 1185887--1186200 Score: 517
Period size: 165 Copynumber: 1.9 Consensus size: 166
1185877 CTTGAGATAG
*
1185887 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTCGTCT-CCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
*
1185952 ATTTCCCTGAAATGAATTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAAAATTTTGTCTCCCTT
65 ATTTCCCTGAAATGAATTTGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAATTTTGTCTCCCTT
1186017 GAGACAG-TTTCTCTTGAAACATAAACATTGAAAACA
130 GAGACAGTTTTCTCTTGAAACATAAACATTGAAAACA
** *
1186053 TTTCCCTTGAAA-TGAATTTCGTCT-CTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACA
1 TTTCCCTTGAAACAAAATTTCGTCTCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
1186116 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCCCT
66 TTTCCC-TGAAATGAATTT-GTCTCTCTTGAGACAGTTTCCCTCGAAACAAAATTTTGTCTCCCT
1186181 TGAGACAGTTTTCTCTTGAA
129 TGAGACAGTTTTCTCTTGAA
1186201 GCATCATCTT
Statistics
Matches: 138, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
163 44 0.32
164 12 0.09
165 59 0.43
166 23 0.17
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (166 bp):
TTTCCCTTGAAACAAAATTTCGTCTCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
TTTCCCTGAAATGAATTTGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAATTTTGTCTCCCTTG
AGACAGTTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:1186275 original size:265 final size:265
Alignment explanation
Indices: 1185787--1186302 Score: 684
Period size: 265 Copynumber: 1.9 Consensus size: 265
1185777 CTCTTGAGAT
*
1185787 TTTCCCTTGAAACAAAATTTCGTCTCCATTGAGACAGTTTCTCTTGAAACATAACATTGGAAACA
1 TTTCCCTTGAAACAAAATTTCGTCTCCATTGAGACAGTTTCTCTTGAAACATAACATTGAAAACA
*
1185852 TTTCCCTTGAAATGAATTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTT
66 TTTCCCTTGAAATGAATTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTT
* * *
1185917 GAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTGAAATGAATTTGTCTCTCTTGA
131 GAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTGAAATGAATTTATCTCCCGTGA
* * *
1185982 GATAGTTTCCCTCGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTG
196 GACAATTT-CCTCGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTAAAACATAAACATTG
1186047 AAAACA
260 AAAACA
** *
1186053 TTTCCCTTGAAA-TGAATTTCGTCT-C-TTGAGATAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTCGTCTCCATTGAGACAGTTTCTCTTGAAACAT-AACATTGAAAAC
*
1186115 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCCC
65 ATTTCCCTTGAAATGAATTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCC
* * * * *** * *
1186180 TTGAGACAGTTTTCTCTTGAAGCATCATCTTTGAATATGTTTTCCTTGGAACT-AATTTCATC-C
129 TTGAGACAG-TTTCTCTTGAAACATAAACATTGAA-AACATTTCCCT-GAAATGAATTT-ATCTC
* * * * * *
1186243 CCGTGAGACAATTT-CTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACA
190 CCGTGAGACAATTTCCTCGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTAAAACA
1186303 AAATTTTGTC
Statistics
Matches: 217, Mismatches: 27, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
263 23 0.11
264 32 0.15
265 100 0.46
266 33 0.15
267 23 0.11
268 6 0.03
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.37
Consensus pattern (265 bp):
TTTCCCTTGAAACAAAATTTCGTCTCCATTGAGACAGTTTCTCTTGAAACATAACATTGAAAACA
TTTCCCTTGAAATGAATTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTT
GAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTGAAATGAATTTATCTCCCGTGA
GACAATTTCCTCGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTAAAACATAAACATTGA
AAACA
Found at i:1186339 original size:37 final size:37
Alignment explanation
Indices: 1186269--1186340 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
1186259 TGGAACTAAG
* * **
1186269 TTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
* *
1186306 TTTTGTCTCCCTTAAGACCGTTTCCCTTGAAACAA
1 TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAA
1186341 CAAATATCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.40
Consensus pattern (37 bp):
TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
Found at i:1186979 original size:96 final size:97
Alignment explanation
Indices: 1186689--1187045 Score: 396
Period size: 96 Copynumber: 3.6 Consensus size: 97
1186679 GTCAATTTCG
* * * * *
1186689 ACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGAG-GGC
1 ACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAAG-TCAACTTCACAGCGAA-GGAGCAGC
** * * *
1186753 TGGTTGTCAACAATAATTTCCCAGTTTCAGG-GCCAATTTCA
64 TGACTGTCGAC-A-AA-----CAATTTC-GGAGCCAATCTCA
* * *
1186794 ACTTCACGGCGAAGGATATTGGACCCAAGATAGCACAAGCTCAACTTCACAGCGAAGGGGCAGCT
1 ACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAAG-TCAACTTCACAGCGAAGGAGCAGCT
1186859 GACTGTCGACAAACAATTTCGGAGCCAATCTCA
65 GACTGTCGACAAACAATTTCGGAGCCAATCTCA
*
1186892 ACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAA-TCAACTTCACAGCGAAGGAGCGGCTG
1 ACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAAGTCAACTTCACAGCGAAGGAGCAGCTG
*
1186956 ACTGTCGACAAGCAATTTCGGAGCCAATCTCA
66 ACTGTCGACAAACAATTTCGGAGCCAATCTCA
* ** * * *
1186988 ACTTCACAGCGAATGATATTGGATTCGAGACAACACAAGTTTAACTTCACAGCGAAGG
1 ACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAAG-TCAACTTCACAGCGAAGG
1187046 GACGGTTGGT
Statistics
Matches: 223, Mismatches: 25, Indels: 15
0.85 0.10 0.06
Matches are distributed among these distances:
96 88 0.39
97 2 0.01
98 68 0.30
103 2 0.01
104 4 0.02
105 59 0.26
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (97 bp):
ACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAAGTCAACTTCACAGCGAAGGAGCAGCTG
ACTGTCGACAAACAATTTCGGAGCCAATCTCA
Found at i:1187383 original size:106 final size:105
Alignment explanation
Indices: 1186676--1187544 Score: 730
Period size: 109 Copynumber: 8.4 Consensus size: 105
1186666 GGTTTTAGCT
* *
1186676 AGAGTCAATTTCGACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* * * *
1186741 CGAAGGGAGGGCTGGTTGTCAAC-AATAATTTCCCAGTTTC
66 CGAAGGGACGGCTGGTTGTCAACAAACAATTT-TCAATTTC
* * * * * * * *
1186781 AGGGCCAATTTCAACTTCACGGCGAAGGATATTGGACCCAAGATAGCACAAGCTCAACTTCACAG
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* * ** *
1186846 CGAAGGGGCAGCTGACTGTCGAC--A-AA----CAATTTC
66 CGAAGGGACGGCTGGTTGTCAACAAACAATTTTCAATTTC
* * * * * *
1186879 GGAGCCAATCTCAACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAA--TCAACTTCACAG
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
** * *
1186942 CGAA-GGAGCGGCTGACTGT---C-GACAA---GCAATTTC
66 CGAAGGGA-CGGCTGGTTGTCAACAAACAATTTTCAATTTC
* * * * * *
1186975 GGAGCCAATCTCAACTTCACAGCGAATGATATTGGATTCGAGACAACACAAGTTTAACTTCACAG
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* * * *
1187040 CGAAGGGACGGTTGGTTGTCAGCAAACAATTTCCCAATTCC
66 CGAAGGGACGGCTGGTTGTCAACAAACAATTT-TCAATTTC
* * * * * *
1187081 AGAGCCGATTTCAACTCCAC-GACGGAGGATATCGTG-CTATCTGAGATAACACAAGTTCAACAT
1 AGAGCCAATTTCAACTTCACAG-CGAAGGATATTG-GAC--TC-GAGACAACACAAGTTCAACTT
* *
1187144 CACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTTTCAGTTTC
61 CACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTTCAATTTC
** * * *
1187190 A-TCCGCGATTTCAACTCCAC-GACGGAGGATATTGTGCCACTCGAGACAACACAAGTTCAACTT
1 AGAGC-CAATTTCAACTTCACAG-CGAAGGATATTG-G--ACTCGAGACAACACAAGTTCAACTT
* *
1187253 CACAACGAAGGGACGACTGGTTGTCAACAAACATTTTTCAAATTTC
61 CACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTC-AATTTC
* *
1187299 AGAGCCAATTTCAATTTCGCAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* * *
1187364 CGAAGGGACGGCTGATTGTCAAC-AA-GA-TTTC--GTTC
66 CGAAGGGACGGCTGGTTGTCAACAAACAATTTTCAATTTC
** * * * *
1187399 AGATTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGCTCAACTTCACAG
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* ** * * ** *
1187464 CGAAGGGGCGGCTGACTGTCAACAAATAATTTCCCGGTTCC
66 CGAAGGGACGGCTGGTTGTCAACAAACAATTT-TCAATTTC
* *
1187505 AGAACCAATTTCAACTTCACAGCGGAGGATATTGGACTCG
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
1187545 GAACAATATT
Statistics
Matches: 637, Mismatches: 93, Indels: 67
0.80 0.12 0.08
Matches are distributed among these distances:
93 1 0.00
94 1 0.00
95 4 0.01
96 79 0.12
98 75 0.12
99 3 0.00
100 81 0.13
101 3 0.00
102 5 0.01
103 8 0.01
104 2 0.00
105 75 0.12
106 120 0.19
107 1 0.00
108 9 0.01
109 162 0.25
110 7 0.01
112 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (105 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
CGAAGGGACGGCTGGTTGTCAACAAACAATTTTCAATTTC
Found at i:1188068 original size:35 final size:37
Alignment explanation
Indices: 1188005--1188079 Score: 109
Period size: 35 Copynumber: 2.1 Consensus size: 37
1187995 TTTCGTCCTA
1188005 CTAGGATTCAAACTCTCAAAAATAGGATAAAATTCTG
1 CTAGGATTCAAACTCTCAAAAATAGGATAAAATTCTG
* * *
1188042 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTTTG
1 CTAGGATTCAAACTCTCAAAAATAGGATAAAATTCTG
1188077 CTA
1 CTA
1188080 TATTTTAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
35 21 0.60
36 5 0.14
37 9 0.26
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (37 bp):
CTAGGATTCAAACTCTCAAAAATAGGATAAAATTCTG
Found at i:1188586 original size:15 final size:15
Alignment explanation
Indices: 1188548--1188586 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1188538 TTTTTTAAAG
1188548 TTATTATATATATTTA
1 TTATTAT-TATATTTA
* *
1188564 TAACTATTATATTTA
1 TTATTATTATATTTA
1188579 TTATTATT
1 TTATTATT
1188587 TTACTATTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATTATTATATTTA
Found at i:1188656 original size:17 final size:16
Alignment explanation
Indices: 1188636--1188671 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1188626 TATTATTATC
1188636 ATTATATGTATATTTTT
1 ATTATAT-TATATTTTT
*
1188653 ATTATATTTTATTTTT
1 ATTATATTATATTTTT
1188669 ATT
1 ATT
1188672 TTTACTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (16 bp):
ATTATATTATATTTTT
Found at i:1188784 original size:59 final size:59
Alignment explanation
Indices: 1188657--1188784 Score: 170
Period size: 59 Copynumber: 2.2 Consensus size: 59
1188647 ATTTTTATTA
* *
1188657 TATTTTATTTTTATTTTTACTTTTTTTAAACATATGCATATATATATATATACATTTAAT
1 TATTTT-TTTATATTTTTACTTTTTTTAAACATATGCATATATATATATATACATTAAAT
* * *
1188717 TATATTTTTATATTTTTACTTTTTTTAAACATATGCATATATA-ATTTA-ATTATATAAAT
1 TATTTTTTTATATTTTTACTTTTTTTAAACATATGCATATATATATATATA-CAT-TAAAT
1188776 TATTTTTTT
1 TATTTTTTT
1188785 TTTCGTTATT
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
57 1 0.02
58 6 0.10
59 48 0.80
60 5 0.08
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (59 bp):
TATTTTTTTATATTTTTACTTTTTTTAAACATATGCATATATATATATATACATTAAAT
Found at i:1196298 original size:18 final size:18
Alignment explanation
Indices: 1196275--1196310 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1196265 CTAATTGTTA
1196275 CTGTTACTTAGTATTTAG
1 CTGTTACTTAGTATTTAG
1196293 CTGTTACTTAGTATTTAG
1 CTGTTACTTAGTATTTAG
1196311 TATTGATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.50
Consensus pattern (18 bp):
CTGTTACTTAGTATTTAG
Found at i:1197264 original size:21 final size:22
Alignment explanation
Indices: 1197226--1197268 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
1197216 ATTTAAAAAT
1197226 ATTAAAGGAAGTACCGATACTC
1 ATTAAAGGAAGTACCGATACTC
*
1197248 ATTAAAGG-AGTATCGATACTC
1 ATTAAAGGAAGTACCGATACTC
1197269 CTTGTATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.26
Consensus pattern (22 bp):
ATTAAAGGAAGTACCGATACTC
Found at i:1197655 original size:3 final size:3
Alignment explanation
Indices: 1197647--1197681 Score: 52
Period size: 3 Copynumber: 11.0 Consensus size: 3
1197637 AAATCCTAAC
1197647 TAT TAT TAT TAT TGAT TAT TGAT TAT TAT TAT TAT
1 TAT TAT TAT TAT T-AT TAT T-AT TAT TAT TAT TAT
1197682 ATGAAACTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 24 0.80
4 6 0.20
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1206111 original size:21 final size:21
Alignment explanation
Indices: 1206085--1206129 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1206075 GATTTCTGGG
*
1206085 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGATACCCATT
*
1206106 CAAGGGGAATCGATACCCCTT
1 CAAGGGGAATCGATACCCATT
1206127 CAA
1 CAA
1206130 ACGAACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGATACCCATT
Found at i:1207574 original size:23 final size:22
Alignment explanation
Indices: 1207548--1207613 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
1207538 TATTATATGG
1207548 CACTTCGGTGCATTTCTACGCGA
1 CACTTCGGTGCATTT-TACGCGA
* ** *
1207571 CACTACGGTGCAATTTTACATGG
1 CACTTCGGTGC-ATTTTACGCGA
1207594 CACTTCGGTGCATTTATACG
1 CACTTCGGTGCATTT-TACG
1207614 AGTTGTGGTG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
22 4 0.11
23 27 0.77
24 4 0.11
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (22 bp):
CACTTCGGTGCATTTTACGCGA
Found at i:1209432 original size:21 final size:23
Alignment explanation
Indices: 1209396--1209456 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
1209386 TATAGGGCAG
*
1209396 AGGGAATCGATACCCCC-TTGAA
1 AGGGAACCGATACCCCCTTTGAA
*
1209418 AGGG-ACCGATTCCCCCTTTGAA
1 AGGGAACCGATACCCCCTTTGAA
*
1209440 GGGGAACCGATACCCCC
1 AGGGAACCGATACCCCC
1209457 ATGGAGTTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 10 0.30
22 12 0.36
23 11 0.33
ACGTcount: A:0.26, C:0.33, G:0.25, T:0.16
Consensus pattern (23 bp):
AGGGAACCGATACCCCCTTTGAA
Found at i:1214888 original size:32 final size:32
Alignment explanation
Indices: 1214845--1214932 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 32
1214835 CATGCATTAT
*
1214845 TATGAAGAAGACGCCGAGACATCC-CCCTCCCA
1 TATGAAGAAGACGCCGAGACATCCACCC-CCAA
* *
1214877 TGTGAAGAAGACGCCGAGTA-TTCCACCCCCAA
1 TATGAAGAAGACGCCGAG-ACATCCACCCCCAA
*
1214909 TATGAAGAAGACGTCGAGACATCC
1 TATGAAGAAGACGCCGAGACATCC
1214933 TCTACTTAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
31 1 0.02
32 42 0.89
33 4 0.09
ACGTcount: A:0.33, C:0.31, G:0.22, T:0.15
Consensus pattern (32 bp):
TATGAAGAAGACGCCGAGACATCCACCCCCAA
Found at i:1215016 original size:20 final size:20
Alignment explanation
Indices: 1214991--1215035 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1214981 CATCTTTCTT
*
1214991 TGCTCACCCCGTGAATTCCA
1 TGCTCACCACGTGAATTCCA
* *
1215011 TGCTCACCATGTGAATTCCC
1 TGCTCACCACGTGAATTCCA
1215031 TGCTC
1 TGCTC
1215036 CAGCTCTACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.18, C:0.38, G:0.16, T:0.29
Consensus pattern (20 bp):
TGCTCACCACGTGAATTCCA
Found at i:1218123 original size:25 final size:25
Alignment explanation
Indices: 1218095--1218169 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
1218085 TTAATTATGC
1218095 ATTTTATTCATATGTTTAACATTTA
1 ATTTTATTCATATGTTTAACATTTA
* *
1218120 ATTTT-TT--TA--ATT-A-ATTATGC
1 ATTTTATTCATATGTTTAACATT-T-A
1218140 ATTTTATTCATATGTTTAACATTTA
1 ATTTTATTCATATGTTTAACATTTA
1218165 ATTTT
1 ATTTT
1218170 TTTAATTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 18
0.63 0.07 0.31
Matches are distributed among these distances:
18 3 0.08
19 2 0.05
20 7 0.19
21 2 0.05
22 2 0.05
23 2 0.05
24 2 0.05
25 12 0.32
26 2 0.05
27 3 0.08
ACGTcount: A:0.31, C:0.07, G:0.04, T:0.59
Consensus pattern (25 bp):
ATTTTATTCATATGTTTAACATTTA
Found at i:1218145 original size:45 final size:45
Alignment explanation
Indices: 1218084--1218179 Score: 192
Period size: 45 Copynumber: 2.1 Consensus size: 45
1218074 GAATGTATTT
1218084 ATTAATTATGCATTTTATTCATATGTTTAACATTTAATTTTTTTA
1 ATTAATTATGCATTTTATTCATATGTTTAACATTTAATTTTTTTA
1218129 ATTAATTATGCATTTTATTCATATGTTTAACATTTAATTTTTTTA
1 ATTAATTATGCATTTTATTCATATGTTTAACATTTAATTTTTTTA
1218174 ATTAAT
1 ATTAAT
1218180 CATTGTTATC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.57
Consensus pattern (45 bp):
ATTAATTATGCATTTTATTCATATGTTTAACATTTAATTTTTTTA
Found at i:1230769 original size:25 final size:25
Alignment explanation
Indices: 1230728--1230781 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
1230718 AATTATTACT
1230728 TTTATTTTATTTTAATATCTAAA-A
1 TTTATTTTATTTTAATATCTAAATA
*
1230752 TTTATTTT-TTTTAAAATATTTAAATA
1 TTTATTTTATTTT--AATATCTAAATA
1230778 TTTA
1 TTTA
1230782 ATAGTTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 4 0.15
24 8 0.31
25 9 0.35
26 5 0.19
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (25 bp):
TTTATTTTATTTTAATATCTAAATA
Found at i:1230969 original size:21 final size:22
Alignment explanation
Indices: 1230937--1231008 Score: 87
Period size: 21 Copynumber: 3.3 Consensus size: 22
1230927 GTTATATATG
*
1230937 AAATTTAAAAAAATA--TATTA
1 AAATATAAAAAAATAATTATTA
1230957 AAATATAACAAAATAATAATTATTA
1 AAATAT-A-AAAA-AATAATTATTA
1230982 AAATA-AAAAAAATAATTATTA
1 AAATATAAAAAAATAATTATTA
1231003 AAATAT
1 AAATAT
1231009 TAAATGTGTA
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
20 5 0.11
21 17 0.38
22 8 0.18
23 5 0.11
25 10 0.22
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (22 bp):
AAATATAAAAAAATAATTATTA
Found at i:1231442 original size:38 final size:36
Alignment explanation
Indices: 1231400--1231573 Score: 176
Period size: 37 Copynumber: 4.7 Consensus size: 36
1231390 TTTAAGTAGT
*
1231400 GTTTTAAAAATATTTTTTGAAAATATATATAATATATT
1 GTTTT-AAAATA-TTTTTGAAAATATATATAATATATA
1231438 GTTTTAAAATATTTTTGAAAACTATATA-ATATATATA
1 GTTTTAAAATATTTTTGAAAA-TATATATA-ATATATA
* *
1231475 GTTTTGAAAACA-TTTT-CAAA-ATATATAATATATA
1 GTTTT-AAAATATTTTTGAAAATATATATAATATATA
* * *
1231509 GTTTTAAAGTATTTTTGGAATATATATATTATTATATA
1 GTTTTAAAATATTTTT-GAAAATATATA-TAATATATA
* *
1231547 GTTTTGGAAATATTTTTGAGAATATAT
1 GTTTT-AAAATATTTTTGAAAATATAT
1231574 TATTATTATT
Statistics
Matches: 114, Mismatches: 12, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
33 4 0.04
34 21 0.18
35 1 0.01
36 16 0.14
37 32 0.28
38 31 0.27
39 9 0.08
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.48
Consensus pattern (36 bp):
GTTTTAAAATATTTTTGAAAATATATATAATATATA
Found at i:1231522 original size:71 final size:72
Alignment explanation
Indices: 1231424--1231562 Score: 201
Period size: 71 Copynumber: 1.9 Consensus size: 72
1231414 TTTTGAAAAT
*
1231424 ATATATAATATATTGTTTTAAAATATTTTT-GAAAACTATATAATA-TATATAGTTTTGAAAACA
1 ATATATAATATATAGTTTTAAAATATTTTTGGAAAA-TATATAATATTATATAGTTTTGAAAACA
1231487 TTTTCAAA
65 TTTTCAAA
* * * * *
1231495 ATATATAATATATAGTTTTAAAGTATTTTTGGAATATATATATTATTATATAGTTTTGGAAATAT
1 ATATATAATATATAGTTTTAAAATATTTTTGGAAAATATATAATATTATATAGTTTTGAAAACAT
1231560 TTT
66 TTT
1231563 TGAGAATATA
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
71 36 0.60
72 24 0.40
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (72 bp):
ATATATAATATATAGTTTTAAAATATTTTTGGAAAATATATAATATTATATAGTTTTGAAAACAT
TTTCAAA
Found at i:1232953 original size:15 final size:15
Alignment explanation
Indices: 1232935--1233087 Score: 58
Period size: 15 Copynumber: 10.0 Consensus size: 15
1232925 ATTTAACATT
1232935 TTTTTATTTATTTTA
1 TTTTTATTTATTTTA
*
1232950 -TTTTATTTTATTTCA
1 TTTTTA-TTTATTTTA
*
1232965 -TTTCATTTCA-TTTA
1 TTTTTATTT-ATTTTA
1232979 --TTTATTTATTATT-
1 TTTTTATTTATT-TTA
* *
1232992 TTTCTT-TTTA-CTAA
1 TTT-TTATTTATTTTA
1233006 TTTTTTATTTATCTTTA
1 -TTTTTATTTAT-TTTA
1233023 TTTATTA-TTATTATTA
1 TTT-TTATTTATT-TTA
*
1233039 TTATTATTATATTAATATA
1 TTTTTATT-TATT--T-TA
1233058 TTTTTATTT-TTTATA
1 TTTTTATTTATTT-TA
1233073 TTTATT-TTTATTTTA
1 TTT-TTATTTATTTTA
1233088 CAATCTGACA
Statistics
Matches: 108, Mismatches: 10, Indels: 40
0.68 0.06 0.25
Matches are distributed among these distances:
12 1 0.01
13 8 0.07
14 15 0.14
15 41 0.38
16 20 0.19
17 11 0.10
18 3 0.03
19 9 0.08
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTATTTATTTTA
Found at i:1232954 original size:10 final size:10
Alignment explanation
Indices: 1232936--1233087 Score: 56
Period size: 10 Copynumber: 15.0 Consensus size: 10
1232926 TTTAACATTT
1232936 TTTTA-TTTA
1 TTTTATTTTA
1232945 TTTTATTTTA
1 TTTTATTTTA
*
1232955 TTTTATTTCA
1 TTTTATTTTA
* *
1232965 TTTCATTTCA
1 TTTTATTTTA
1232975 -TTTA-TTTA
1 TTTTATTTTA
1232983 -TTTATTATT-
1 TTTTATT-TTA
1232992 TTTCT-TTTTA
1 TTT-TATTTTA
*
1233002 CTAATT-TTTTA
1 -T-TTTATTTTA
1233013 -TTTATCTTTA
1 TTTTAT-TTTA
1233023 -TTTATTATTA
1 TTTTATT-TTA
1233033 TTATTATTATTA
1 TT-TTATT-TTA
*
1233045 TTATATTAATATA
1 TTTTATT--T-TA
*
1233058 TTTT-TATT-
1 TTTTATTTTA
1233066 TTTTATATTTA
1 TTTTAT-TTTA
1233077 TTTTTATTTTA
1 -TTTTATTTTA
1233088 CAATCTGACA
Statistics
Matches: 114, Mismatches: 10, Indels: 36
0.71 0.06 0.22
Matches are distributed among these distances:
8 13 0.11
9 15 0.13
10 43 0.38
11 17 0.15
12 21 0.18
13 5 0.04
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:1233001 original size:23 final size:23
Alignment explanation
Indices: 1232975--1233078 Score: 81
Period size: 23 Copynumber: 4.6 Consensus size: 23
1232965 TTTCATTTCA
*
1232975 TTTATTTATTTATTATTTTTCTT
1 TTTATTTATTTATTATTTTTATT
* * * *
1232998 TTTACTAATTT-TT-TATTTATC
1 TTTATTTATTTATTATTTTTATT
*
1233019 TTTATTTA-TTATTATTATTATT
1 TTTATTTATTTATTATTTTTATT
* *
1233041 ATTATTATATTAATATATTTTTATT
1 TTTATT-TATTTAT-TATTTTTATT
*
1233066 TTT-TATATTTATT
1 TTTATTTATTTATT
1233079 TTTATTTTAC
Statistics
Matches: 60, Mismatches: 16, Indels: 11
0.69 0.18 0.13
Matches are distributed among these distances:
20 2 0.03
21 13 0.22
22 13 0.22
23 17 0.28
24 4 0.07
25 11 0.18
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTATTTATTTATTATTTTTATT
Found at i:1233032 original size:3 final size:3
Alignment explanation
Indices: 1233024--1233065 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
1233014 TTATCTTTAT
* *
1233024 TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA ATA -TA TTT TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1233066 TTTTATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1233066 original size:6 final size:6
Alignment explanation
Indices: 1232979--1233086 Score: 56
Period size: 6 Copynumber: 16.3 Consensus size: 6
1232969 ATTTCATTTA
* *
1232979 TTTATT TATTATT TTTCTT TTTACTAAT TTT-TT ATTTATC TTTATT TATTATT
1 TTTATT T-TTATT TTTATT TTTA-T--T TTTATT -TTTATT TTTATT T-TTATT
* * * *
1233032 ATTATT ATTATT ATTATATT AATATATT TTTATTT TTTATA TTTATT TTTATT
1 TTTATT TTTATT -TT-TATT --TTTATT TTTA-TT TTTATT TTTATT TTTATT
1233085 TT
1 TT
1233087 ACAATCTGAC
Statistics
Matches: 81, Mismatches: 10, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
5 1 0.01
6 45 0.56
7 21 0.26
8 8 0.10
9 6 0.07
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (6 bp):
TTTATT
Found at i:1241572 original size:5 final size:5
Alignment explanation
Indices: 1241562--1241598 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
1241552 GCTTTGTAAT
1241562 TTGTA TTGTA TTGTA TTGTA TTGTA TTGTA TTGTA TT
1 TTGTA TTGTA TTGTA TTGTA TTGTA TTGTA TTGTA TT
1241599 TCTTTCTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62
Consensus pattern (5 bp):
TTGTA
Found at i:1252226 original size:34 final size:34
Alignment explanation
Indices: 1252188--1252288 Score: 141
Period size: 34 Copynumber: 3.0 Consensus size: 34
1252178 TTAATCAAGG
*
1252188 AGGGTTATAGTGTAATGTGTATCTTATGTATTTC
1 AGGGTTATAGTGTAATGTGTATCTTATGTAATTC
*
1252222 AGGGTTAGAGTGTAATGTGTATCTTATGTAATTC
1 AGGGTTATAGTGTAATGTGTATCTTATGTAATTC
* * *
1252256 AGGGTT-TGAGTGCATTTTGTATCTTATGTAATT
1 AGGGTTAT-AGTGTAATGTGTATCTTATGTAATT
1252289 TAGGTTAATT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
34 60 1.00
ACGTcount: A:0.24, C:0.06, G:0.25, T:0.46
Consensus pattern (34 bp):
AGGGTTATAGTGTAATGTGTATCTTATGTAATTC
Found at i:1262234 original size:34 final size:34
Alignment explanation
Indices: 1262191--1262268 Score: 129
Period size: 34 Copynumber: 2.3 Consensus size: 34
1262181 TCGAAATATG
1262191 CATCTCCCACACGTTCCTCACACCAGTAGCTTTC
1 CATCTCCCACACGTTCCTCACACCAGTAGCTTTC
*
1262225 CATCTCCCACACGTTCCTCACACTAGTAGCTTTC
1 CATCTCCCACACGTTCCTCACACCAGTAGCTTTC
* *
1262259 CGTTTCCCAC
1 CATCTCCCAC
1262269 CCTCCACATT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.19, C:0.44, G:0.09, T:0.28
Consensus pattern (34 bp):
CATCTCCCACACGTTCCTCACACCAGTAGCTTTC
Found at i:1271800 original size:28 final size:27
Alignment explanation
Indices: 1271769--1271836 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
1271759 AATACAAGTA
**
1271769 AATTTGTAATTTTTGAAATTTATATAAT
1 AATTTGTAATAATT-AAATTTATATAAT
* *
1271797 AATTAGATAAAAATTAAATTTATATAAT
1 AATTTG-TAATAATTAAATTTATATAAT
1271825 AATTT-TAATAAT
1 AATTTGTAATAAT
1271837 AAAAGAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
26 6 0.18
28 22 0.67
29 5 0.15
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (27 bp):
AATTTGTAATAATTAAATTTATATAAT
Found at i:1272079 original size:6 final size:6
Alignment explanation
Indices: 1272068--1272094 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1272058 CTTTTGTTGG
1272068 GAAGGT GAAGGT GAAGGT GAAGGT GAA
1 GAAGGT GAAGGT GAAGGT GAAGGT GAA
1272095 CATCACTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.48, T:0.15
Consensus pattern (6 bp):
GAAGGT
Found at i:1277780 original size:53 final size:53
Alignment explanation
Indices: 1277701--1277921 Score: 345
Period size: 53 Copynumber: 4.2 Consensus size: 53
1277691 CTCTTCTTTG
* * * *
1277701 AACAATCTTC-GACTAGCGGGTTCGCTCCATCTTGCTTTAGGGAGTAGAACTCG
1 AACAATCTTCTGCCTA-CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCA
*
1277754 AACAGTCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCA
1 AACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCA
**
1277807 AGTAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCA
1 AACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCA
* *
1277860 AACAATCTTCTGCCTACGGGTTCGCTGCCTCTTGCTTCAGGGAGTAAAACTCA
1 AACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCA
1277913 AACAATCTT
1 AACAATCTT
1277922 ATGGTGTGAT
Statistics
Matches: 155, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
53 151 0.97
54 4 0.03
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.29
Consensus pattern (53 bp):
AACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCA
Found at i:1278484 original size:122 final size:122
Alignment explanation
Indices: 1278317--1278631 Score: 497
Period size: 122 Copynumber: 2.6 Consensus size: 122
1278307 CGAATGACTT
* ** * * *
1278317 ATCATCTTGCTCGAAAGACTTACAAATGACCCGAATGATTTCATCATCATGCTCGAAAGACTTAC
1 ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTAC
*** *
1278382 TGATGGATTTGCTTCACTACTCTTTGGTAAAGGCTTACAAATTA-CCTGAAGGATTTA
66 TGATGGATTTGCTTCACTACTCTTCCATAAAGGCTTACAAATTACCCT-AAGAATTTA
1278439 ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTAC
1 ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTAC
* *
1278504 TGATGGGTTTGCTTCACTACTCTTCCATGAAGGCTTACAAATTACCCTAAGAATTTA
66 TGATGGATTTGCTTCACTACTCTTCCATAAAGGCTTACAAATTACCCTAAGAATTTA
*
1278561 ATCATCATGCTCGAAAGACTTATTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTAC
1 ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTAC
1278626 TGATGG
66 TGATGG
1278632 CCCGAAGGAC
Statistics
Matches: 179, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
122 176 0.98
123 3 0.02
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (122 bp):
ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTAC
TGATGGATTTGCTTCACTACTCTTCCATAAAGGCTTACAAATTACCCTAAGAATTTA
Found at i:1278500 original size:22 final size:21
Alignment explanation
Indices: 1278439--1278502 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 21
1278429 GAAGGATTTA
1278439 ATCATCATGCTCGAAAGACTT
1 ATCATCATGCTCGAAAGACTT
* * *
1278460 A-C-TGATGGCCCGAAGGACTT
1 ATCATCAT-GCTCGAAAGACTT
1278480 CATCATCATGCTCGAAAGACTT
1 -ATCATCATGCTCGAAAGACTT
1278502 A
1 A
1278503 CTGATGGGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
19 3 0.09
20 12 0.36
21 3 0.09
22 12 0.36
23 3 0.09
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (21 bp):
ATCATCATGCTCGAAAGACTT
Found at i:1278613 original size:164 final size:164
Alignment explanation
Indices: 1278429--1278798 Score: 704
Period size: 164 Copynumber: 2.3 Consensus size: 164
1278419 CAAATTACCT
* *
1278429 GAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCG
1 GAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCG
1278494 AAAGACTTACTGATGGGTTTGCTTCACTACTCTTCCATGAAGGCTTACAAATTACCCTAAGAATT
66 AAAGACTTACTGATGGGTTTGCTTCACTACTCTTCCATGAAGGCTTACAAATTACCCTAAGAATT
1278559 TAATCATCATGCTCGAAAGACTTATTGATGGCCC
131 TAATCATCATGCTCGAAAGACTTATTGATGGCCC
1278593 GAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCG
1 GAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCG
*
1278658 AAAGACTTACTGATGGGTTTGCTTCACTACTCTTCCGTGAAGGCTTACAAATTACCCTAAGAATT
66 AAAGACTTACTGATGGGTTTGCTTCACTACTCTTCCATGAAGGCTTACAAATTACCCTAAGAATT
*
1278723 TAATCATCATGCTTGAAAGACTTATTGATGGCCC
131 TAATCATCATGCTCGAAAGACTTATTGATGGCCC
1278757 GAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGCCC
1 GAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGCCC
1278799 TCGAAAGACT
Statistics
Matches: 202, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
164 202 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (164 bp):
GAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCG
AAAGACTTACTGATGGGTTTGCTTCACTACTCTTCCATGAAGGCTTACAAATTACCCTAAGAATT
TAATCATCATGCTCGAAAGACTTATTGATGGCCC
Found at i:1278622 original size:22 final size:21
Alignment explanation
Indices: 1278561--1278666 Score: 94
Period size: 20 Copynumber: 5.0 Consensus size: 21
1278551 TAAGAATTTA
1278561 ATCATCATGCTCGAAAGACTT
1 ATCATCATGCTCGAAAGACTT
* * *
1278582 AT--TGATGGCCCGAAGGACTT
1 ATCATCAT-GCTCGAAAGACTT
1278602 CATCATCATGCTCGAAAGACTT
1 -ATCATCATGCTCGAAAGACTT
* * *
1278624 A-C-TGATGGCCCGAAGGACTT
1 ATCATCAT-GCTCGAAAGACTT
1278644 CATCATCATGCTCGAAAGACTT
1 -ATCATCATGCTCGAAAGACTT
1278666 A
1 A
1278667 CTGATGGGTT
Statistics
Matches: 65, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
19 6 0.09
20 23 0.35
21 7 0.11
22 23 0.35
23 6 0.09
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (21 bp):
ATCATCATGCTCGAAAGACTT
Found at i:1278668 original size:42 final size:42
Alignment explanation
Indices: 1278301--1278798 Score: 295
Period size: 42 Copynumber: 12.2 Consensus size: 42
1278291 AAGGCTTAAA
* * **
1278301 ATGGCCCGAATGACTT-ATCATCTTGCTCGAAAGACTTACAA
1 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
* * *
1278342 ATGACCCGAATGATTTCATCATCATGCTCGAAAGACTTACTG
1 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
** * * * **
1278384 AT-G---GATTTG-CTTCA-CTACTC-T-TTGGTAAAGGCTTACAA
1 ATGGCCCGA-AGGACTTCATC-A-TCATGCTCG-AAAGACTTACTG
** * * *
1278422 ATTACCTGAAGGATTTAATCATCATGCTCGAAAGACTTACTG
1 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
1278464 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
1 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
*** * * * **
1278506 ATGG---GTTTG-CTTCA-CTACTCTTCCAT-G-AAGGCTTACAA
1 ATGGCCCGAAGGACTTCATC-A-TCATGC-TCGAAAGACTTACTG
** * * * * *
1278544 ATTACCCTAAGAATTTAATCATCATGCTCGAAAGACTTATTG
1 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
1278586 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
1 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
1278628 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
1 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
*** * * * **
1278670 ATGG---GTTTG-CTTCA-CTACTC-TTC-CGTGAAGGCTTACAA
1 ATGGCCCGAAGGACTTCATC-A-TCATGCTCG-AAAGACTTACTG
** * * * * * *
1278708 ATTACCCTAAGAATTTAATCATCATGCTTGAAAGACTTATTG
1 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
1278750 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
1 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
1278792 ATGGCCC
1 ATGGCCC
1278799 TCGAAAGACT
Statistics
Matches: 334, Mismatches: 90, Indels: 65
0.68 0.18 0.13
Matches are distributed among these distances:
37 7 0.02
38 53 0.16
39 15 0.04
40 2 0.01
41 24 0.07
42 227 0.68
43 6 0.02
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (42 bp):
ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
Found at i:1278786 original size:22 final size:21
Alignment explanation
Indices: 1278725--1278788 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
1278715 TAAGAATTTA
*
1278725 ATCATCATGCTTGAAAGACTT
1 ATCATCATGCTCGAAAGACTT
* * *
1278746 AT--TGATGGCCCGAAGGACTT
1 ATCATCAT-GCTCGAAAGACTT
1278766 CATCATCATGCTCGAAAGACTT
1 -ATCATCATGCTCGAAAGACTT
1278788 A
1 A
1278789 CTGATGGCCC
Statistics
Matches: 32, Mismatches: 7, Indels: 8
0.68 0.15 0.17
Matches are distributed among these distances:
19 3 0.09
20 10 0.31
21 5 0.16
22 11 0.34
23 3 0.09
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (21 bp):
ATCATCATGCTCGAAAGACTT
Found at i:1278801 original size:22 final size:21
Alignment explanation
Indices: 1278737--1278832 Score: 92
Period size: 22 Copynumber: 4.6 Consensus size: 21
1278727 CATCATGCTT
*
1278737 GAAAGACTTATTGATGGCC-C
1 GAAAGACTTACTGATGGCCTC
* *
1278757 GAAGGACTTCATCATCAT-G-CTC
1 GAAAGACTT-A-C-TGATGGCCTC
1278779 GAAAGACTTACTGATGGCCCTC
1 GAAAGACTTACTGATGG-CCTC
*
1278801 GAAAGACTTATTGATGGCC-C
1 GAAAGACTTACTGATGGCCTC
1278821 GAAAGACTTACT
1 GAAAGACTTACT
1278833 AAGTGGGGAA
Statistics
Matches: 62, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.05
20 22 0.35
21 5 0.08
22 29 0.47
23 3 0.05
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (21 bp):
GAAAGACTTACTGATGGCCTC
Found at i:1285844 original size:47 final size:46
Alignment explanation
Indices: 1285787--1285897 Score: 125
Period size: 45 Copynumber: 2.4 Consensus size: 46
1285777 TATCTACCCC
* * *
1285787 CATGCTTTGTTTGAACATTAAAACCCTAACCGCATAATATCTAATTCG
1 CATGCTTTGTTCGAAAAAT-AAA-CCTAACCGCATAATATCTAATTCG
* * *
1285835 CATGC-TTGTTCGAAAAATAAACTTAACCGCATGATATCTAGTTCG
1 CATGCTTTGTTCGAAAAATAAACCTAACCGCATAATATCTAATTCG
*
1285880 CATGCATTTATTCGAAAA
1 CATGC-TTTGTTCGAAAA
1285898 GTGAAAATAA
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
45 26 0.48
46 3 0.06
47 20 0.37
48 5 0.09
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (46 bp):
CATGCTTTGTTCGAAAAATAAACCTAACCGCATAATATCTAATTCG
Found at i:1289401 original size:53 final size:53
Alignment explanation
Indices: 1289188--1289408 Score: 336
Period size: 53 Copynumber: 4.2 Consensus size: 53
1289178 CTCTTCTTTG
* * * *
1289188 AACAATCTTC-GACTAGCGGGTTCGCTCCATCTTGCTTTAGGGAGTAGAACTCG
1 AACAATCTTCTGCCTA-CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCA
* *
1289241 AATAGTCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCA
1 AACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCA
**
1289294 AGTAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCA
1 AACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCA
* *
1289347 AACAATCTTCTGCCTACGGGTTCGCTACCTCTTGCTTCAGGGAGTAAAACTCA
1 AACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCA
1289400 AACAATCTT
1 AACAATCTT
1289409 ATGGTGTGAT
Statistics
Matches: 155, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
53 151 0.97
54 4 0.03
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.29
Consensus pattern (53 bp):
AACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCA
Found at i:1289971 original size:122 final size:122
Alignment explanation
Indices: 1289804--1290118 Score: 506
Period size: 122 Copynumber: 2.6 Consensus size: 122
1289794 CGAATGACTT
* ** * * *
1289804 ATCATCTTGCTCGAAAGACTTACAAATGACCCGAATGATTTCATCATCATGCTCGAAAGACTTAC
1 ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTAC
** *
1289869 TGATGGATTTGCTTCACTACTCTTTGGTAAAGGCTTACAAATTA-CCTGAAGGATTTA
66 TGATGGATTTGCTTCACTACTCTTCCGTAAAGGCTTACAAATTACCCT-AAGAATTTA
1289926 ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTAC
1 ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTAC
* *
1289991 TGATGGGTTTGCTTCACTACTCTTCCGTGAAGGCTTACAAATTACCCTAAGAATTTA
66 TGATGGATTTGCTTCACTACTCTTCCGTAAAGGCTTACAAATTACCCTAAGAATTTA
*
1290048 ATCATCATGCTCGAAAGACTTATTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTAC
1 ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTAC
1290113 TGATGG
66 TGATGG
1290119 CCCGAAGGAC
Statistics
Matches: 180, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
122 177 0.98
123 3 0.02
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (122 bp):
ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTAC
TGATGGATTTGCTTCACTACTCTTCCGTAAAGGCTTACAAATTACCCTAAGAATTTA
Found at i:1289987 original size:22 final size:21
Alignment explanation
Indices: 1289926--1289989 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 21
1289916 GAAGGATTTA
1289926 ATCATCATGCTCGAAAGACTT
1 ATCATCATGCTCGAAAGACTT
* * *
1289947 A-C-TGATGGCCCGAAGGACTT
1 ATCATCAT-GCTCGAAAGACTT
1289967 CATCATCATGCTCGAAAGACTT
1 -ATCATCATGCTCGAAAGACTT
1289989 A
1 A
1289990 CTGATGGGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
19 3 0.09
20 12 0.36
21 3 0.09
22 12 0.36
23 3 0.09
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (21 bp):
ATCATCATGCTCGAAAGACTT
Found at i:1290100 original size:164 final size:164
Alignment explanation
Indices: 1289916--1290285 Score: 695
Period size: 164 Copynumber: 2.3 Consensus size: 164
1289906 CAAATTACCT
* *
1289916 GAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCG
1 GAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCG
*
1289981 AAAGACTTACTGATGGGTTTGCTTCACTACTCTTCCGTGAAGGCTTACAAATTACCCTAAGAATT
66 AAAGACTTACTGATGGGTTTGCTTCACTACTCTTCCGTGAAGGCTTACAAATTACCCTAAAAATT
1290046 TAATCATCATGCTCGAAAGACTTATTGATGGCCC
131 TAATCATCATGCTCGAAAGACTTATTGATGGCCC
1290080 GAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCG
1 GAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCG
1290145 AAAGACTTACTGATGGGTTTGCTTCACTACTCTTCCGTGAAGGCTTACAAATTACCCTAAAAATT
66 AAAGACTTACTGATGGGTTTGCTTCACTACTCTTCCGTGAAGGCTTACAAATTACCCTAAAAATT
*
1290210 TAATCATCATGCTTGAAAGACTTATTGATGGCCC
131 TAATCATCATGCTCGAAAGACTTATTGATGGCCC
*
1290244 GAAGGACTTCATTATCATGCTCGAAAGACTTACTGATGGCCC
1 GAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGCCC
1290286 TCGAAAGACT
Statistics
Matches: 201, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
164 201 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (164 bp):
GAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCG
AAAGACTTACTGATGGGTTTGCTTCACTACTCTTCCGTGAAGGCTTACAAATTACCCTAAAAATT
TAATCATCATGCTCGAAAGACTTATTGATGGCCC
Found at i:1290109 original size:22 final size:21
Alignment explanation
Indices: 1290048--1290153 Score: 94
Period size: 20 Copynumber: 5.0 Consensus size: 21
1290038 TAAGAATTTA
1290048 ATCATCATGCTCGAAAGACTT
1 ATCATCATGCTCGAAAGACTT
* * *
1290069 AT--TGATGGCCCGAAGGACTT
1 ATCATCAT-GCTCGAAAGACTT
1290089 CATCATCATGCTCGAAAGACTT
1 -ATCATCATGCTCGAAAGACTT
* * *
1290111 A-C-TGATGGCCCGAAGGACTT
1 ATCATCAT-GCTCGAAAGACTT
1290131 CATCATCATGCTCGAAAGACTT
1 -ATCATCATGCTCGAAAGACTT
1290153 A
1 A
1290154 CTGATGGGTT
Statistics
Matches: 65, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
19 6 0.09
20 23 0.35
21 7 0.11
22 23 0.35
23 6 0.09
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (21 bp):
ATCATCATGCTCGAAAGACTT
Found at i:1290155 original size:42 final size:42
Alignment explanation
Indices: 1289788--1290285 Score: 277
Period size: 42 Copynumber: 12.2 Consensus size: 42
1289778 AAGGCTTAAA
* * **
1289788 ATGGCCCGAATGACTT-ATCATCTTGCTCGAAAGACTTACAA
1 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
* * *
1289829 ATGACCCGAATGATTTCATCATCATGCTCGAAAGACTTACTG
1 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
** * * * **
1289871 AT-G---GATTTG-CTTCA-CTACTC-T-TTGGTAAAGGCTTACAA
1 ATGGCCCGA-AGGACTTCATC-A-TCATGCTCG-AAAGACTTACTG
** * * *
1289909 ATTACCTGAAGGATTTAATCATCATGCTCGAAAGACTTACTG
1 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
1289951 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
1 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
*** * * * **
1289993 ATGG---GTTTG-CTTCA-CTACTC-TTC-CGTGAAGGCTTACAA
1 ATGGCCCGAAGGACTTCATC-A-TCATGCTCG-AAAGACTTACTG
** * * * * *
1290031 ATTACCCTAAGAATTTAATCATCATGCTCGAAAGACTTATTG
1 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
1290073 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
1 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
1290115 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
1 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
*** * * * **
1290157 ATGG---GTTTG-CTTCA-CTACTC-TTC-CGTGAAGGCTTACAA
1 ATGGCCCGAAGGACTTCATC-A-TCATGCTCG-AAAGACTTACTG
** * ** * * * *
1290195 ATTACCCTAAAAATTTAATCATCATGCTTGAAAGACTTATTG
1 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
*
1290237 ATGGCCCGAAGGACTTCATTATCATGCTCGAAAGACTTACTG
1 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
1290279 ATGGCCC
1 ATGGCCC
1290286 TCGAAAGACT
Statistics
Matches: 332, Mismatches: 92, Indels: 65
0.68 0.19 0.13
Matches are distributed among these distances:
37 9 0.03
38 55 0.17
39 12 0.04
41 21 0.06
42 227 0.68
43 8 0.02
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (42 bp):
ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
Found at i:1290230 original size:80 final size:80
Alignment explanation
Indices: 1289968--1290240 Score: 300
Period size: 80 Copynumber: 3.4 Consensus size: 80
1289958 GAAGGACTTC
1289968 ATCATCATGCTCGAAAGACTTACTGATGGGTTTGCTTCACTACTCTTCCGTGAAGGCTTACAAAT
1 ATCATCATGCTCGAAAGACTTACTGATGGGTTTGCTTCACTACTCTTCCGTGAAGGCTTACAAAT
1290033 TACCCTAAGAATTTA
66 TACCCTAAGAATTTA
* *** * * *
1290048 ATCATCATGCTCGAAAGACTTATTGATGGCCCGAAGGACTTCA-T-CATCATGCTCG-AAAGACT
1 ATCATCATGCTCGAAAGACTTACTGATGG---GTTTG-CTTCACTAC-TC-TTC-CGTGAAGGCT
** ** * * * *
1290110 TACTGATGGCCCGAAGGACTTC
59 TACAAATTACCCTAAGAATTTA
1290132 ATCATCATGCTCGAAAGACTTACTGATGGGTTTGCTTCACTACTCTTCCGTGAAGGCTTACAAAT
1 ATCATCATGCTCGAAAGACTTACTGATGGGTTTGCTTCACTACTCTTCCGTGAAGGCTTACAAAT
*
1290197 TACCCTAAAAATTTA
66 TACCCTAAGAATTTA
* *
1290212 ATCATCATGCTTGAAAGACTTATTGATGG
1 ATCATCATGCTCGAAAGACTTACTGATGG
1290241 CCCGAAGGAC
Statistics
Matches: 150, Mismatches: 33, Indels: 20
0.74 0.16 0.10
Matches are distributed among these distances:
79 2 0.01
80 80 0.53
81 5 0.03
82 2 0.01
83 5 0.03
84 54 0.36
85 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (80 bp):
ATCATCATGCTCGAAAGACTTACTGATGGGTTTGCTTCACTACTCTTCCGTGAAGGCTTACAAAT
TACCCTAAGAATTTA
Found at i:1290288 original size:22 final size:21
Alignment explanation
Indices: 1290263--1290319 Score: 89
Period size: 22 Copynumber: 2.7 Consensus size: 21
1290253 CATTATCATG
1290263 CTCGAAAGACTTACTGATGGCC
1 CTCGAAAGACTTACTGATGG-C
*
1290285 CTCGAAAGACTTATTGATGGC
1 CTCGAAAGACTTACTGATGGC
1290306 C-CGAAAGACTTACT
1 CTCGAAAGACTTACT
1290320 AAGTGGGGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.36
21 2 0.06
22 19 0.58
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (21 bp):
CTCGAAAGACTTACTGATGGC
Found at i:1290499 original size:42 final size:41
Alignment explanation
Indices: 1290436--1290536 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 41
1290426 AGGTCTTATG
* * ** *
1290436 GATGTCCCGAAGGACTTATCATCTTGCTTTAAAGGCTTACA
1 GATGACCCGAAGGACTTATCATCATGCTCGAAAGACTTACA
* * *
1290477 GATGACCCGAGGGATTTCATCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGACTT-ATCATCATGCTCGAAAGACTTACA
*
1290519 GATGGCCCGAAGGACTTA
1 GATGACCCGAAGGACTTA
1290537 AATTGTTTAT
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
41 15 0.31
42 33 0.69
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.27
Consensus pattern (41 bp):
GATGACCCGAAGGACTTATCATCATGCTCGAAAGACTTACA
Found at i:1296723 original size:16 final size:16
Alignment explanation
Indices: 1296699--1296729 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1296689 TCAATAGTTG
1296699 GATGCAAAACTAAAAA
1 GATGCAAAACTAAAAA
*
1296715 GATGTAAAACTAAAA
1 GATGCAAAACTAAAA
1296730 GTTTTACACT
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:0.61, C:0.10, G:0.13, T:0.16
Consensus pattern (16 bp):
GATGCAAAACTAAAAA
Found at i:1296776 original size:4 final size:4
Alignment explanation
Indices: 1296767--1296810 Score: 74
Period size: 4 Copynumber: 11.5 Consensus size: 4
1296757 AACTCGAATA
1296767 GTAT GTAT GTAT GTAT GTAT G-AT GTAT GTAT GTAT GTAT G-AT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
1296811 GGAAGCCAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 6 0.16
4 32 0.84
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.48
Consensus pattern (4 bp):
GTAT
Found at i:1296793 original size:19 final size:19
Alignment explanation
Indices: 1296769--1296810 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
1296759 CTCGAATAGT
1296769 ATGTATGTATGTATGTATG
1 ATGTATGTATGTATGTATG
1296788 ATGTATGTATGTATGTATG
1 ATGTATGTATGTATGTATG
1296807 ATGT
1 ATGT
1296811 GGAAGCCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (19 bp):
ATGTATGTATGTATGTATG
Found at i:1300733 original size:30 final size:32
Alignment explanation
Indices: 1300669--1300733 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 32
1300659 CTAAATAAAT
* *
1300669 AAAAAATCCTAAAATAATTATAATTTTTAATA
1 AAAAAATCATAAAATAATTATAATTCTTAATA
* *
1300701 AAAAAAT-ATAAATTAATTAT-ATTCTTATTA
1 AAAAAATCATAAAATAATTATAATTCTTAATA
1300731 AAA
1 AAA
1300734 TTAAAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 11 0.38
31 11 0.38
32 7 0.24
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (32 bp):
AAAAAATCATAAAATAATTATAATTCTTAATA
Found at i:1301061 original size:18 final size:19
Alignment explanation
Indices: 1301038--1301118 Score: 89
Period size: 18 Copynumber: 4.3 Consensus size: 19
1301028 AATTTTTCAT
1301038 TTATTATTATTA-AAATTA
1 TTATTATTATTATAAATTA
1301056 TTATTATTATTATAAA-TA
1 TTATTATTATTATAAATTA
*
1301074 TTATTATTA-TATTATATATA
1 TTATTATTATTA-TAAAT-TA
*
1301094 TTA-TATTATTATTAAATAA
1 TTATTATTATTA-TAAATTA
1301113 TTATTA
1 TTATTA
1301119 CAAGCCCAGA
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.04
18 26 0.48
19 12 0.22
20 14 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATTATTATTATAAATTA
Found at i:1301118 original size:3 final size:3
Alignment explanation
Indices: 1301038--1301107 Score: 74
Period size: 3 Copynumber: 24.0 Consensus size: 3
1301028 AATTTTTCAT
** * *
1301038 TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1301085 TTA -TA TATA TTA -TA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA
1301108 AATAATTATT
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
2 6 0.11
3 46 0.84
4 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1302398 original size:15 final size:15
Alignment explanation
Indices: 1302378--1302407 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1302368 GGAGCTCTTA
1302378 ATTTTAATAATTGAT
1 ATTTTAATAATTGAT
*
1302393 ATTTTAATCATTGAT
1 ATTTTAATAATTGAT
1302408 TAATAATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (15 bp):
ATTTTAATAATTGAT
Found at i:1308743 original size:7 final size:7
Alignment explanation
Indices: 1308733--1308808 Score: 59
Period size: 7 Copynumber: 10.7 Consensus size: 7
1308723 AAGAAAGAAG
1308733 AAGAAAA
1 AAGAAAA
1308740 AAGAAAA
1 AAGAAAA
1308747 AAGAAAGA
1 AAGAAA-A
1308755 AATGAAAA
1 AA-GAAAA
1308763 AA-AAGAA
1 AAGAA-AA
*
1308770 AA-AGAA
1 AAGAAAA
*
1308776 ATGAAAA
1 AAGAAAA
*
1308783 ATGAAAAA
1 AAG-AAAA
1308791 AAGAAAA
1 AAGAAAA
*
1308798 AA-AAAG
1 AAGAAAA
1308804 AAGAA
1 AAGAA
1308809 GGAGAAATTG
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
6 10 0.17
7 32 0.55
8 12 0.21
9 4 0.07
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (7 bp):
AAGAAAA
Found at i:1308751 original size:20 final size:20
Alignment explanation
Indices: 1308726--1308805 Score: 67
Period size: 18 Copynumber: 4.0 Consensus size: 20
1308716 TCCAGCAAAG
1308726 AAAGAAGAAGAAAAAAGAAA
1 AAAGAAGAAGAAAAAAGAAA
*
1308746 AAAGAAAGAAATGAAAAAAAAGAA
1 AAAG-AAG-AA-GAAAAAAGA-AA
* *
1308770 AAAGAA-ATGAAAAATG-AA
1 AAAGAAGAAGAAAAAAGAAA
*
1308788 AAA-AAGAAAAAAAAAGAA
1 AAAGAAGAAGAAAAAAGAA
1308806 GAAGGAGAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 13
0.70 0.10 0.19
Matches are distributed among these distances:
17 2 0.04
18 12 0.26
19 1 0.02
20 10 0.21
21 4 0.09
22 2 0.04
23 10 0.21
24 6 0.13
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (20 bp):
AAAGAAGAAGAAAAAAGAAA
Found at i:1308761 original size:5 final size:4
Alignment explanation
Indices: 1308722--1308805 Score: 51
Period size: 4 Copynumber: 22.5 Consensus size: 4
1308712 CTCATCCAGC
1308722 AAAG AAAG -AAG -AAG AAA- AAAG AAA- AAAG AAAG AAATG AAA- AAA-
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA-G AAAG AAAG
* * *
1308765 AAGAA AAAG AAATG AAA- AATG AAAA AAAG AAA- AAA- AAAG AA
1 AA-AG AAAG AAA-G AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA
1308806 GAAGGAGAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
3 25 0.38
4 31 0.47
5 10 0.15
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.04
Consensus pattern (4 bp):
AAAG
Found at i:1311203 original size:114 final size:114
Alignment explanation
Indices: 1311003--1311226 Score: 394
Period size: 114 Copynumber: 2.0 Consensus size: 114
1310993 CACATTCTCG
* *
1311003 TAGTAGAAATAATGAGACCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 TAGTAGAAATAAGGAGACACAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
*
1311068 GGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATTTGCTCA
66 GGTATGAACCCCAAAACCAATCATTAGATTTAAAAGATGAATTTGCTCA
* *
1311117 TAGTATAAATAAGGAGACACAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 TAGTAGAAATAAGGAGACACAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
*
1311182 GGTATGAACCCCAAAATCAATCATTAGATTTAAAAGATGAATTTG
66 GGTATGAACCCCAAAACCAATCATTAGATTTAAAAGATGAATTTG
1311227 ATGATAGTCT
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 104 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACACAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
GGTATGAACCCCAAAACCAATCATTAGATTTAAAAGATGAATTTGCTCA
Found at i:1313736 original size:22 final size:22
Alignment explanation
Indices: 1313710--1313786 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
1313700 ATCTACACTC
1313710 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
1313732 TTCAAAGACGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
1313754 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
1313776 TTCAAAGATGA
1 TTCAAAGATGA
1313787 AAGCTTTATT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:1315326 original size:76 final size:76
Alignment explanation
Indices: 1314460--1315325 Score: 1507
Period size: 76 Copynumber: 11.4 Consensus size: 76
1314450 CTATTTCCCA
*
1314460 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1314525 AACCTTAGGGT
66 AGCCTTAGGGT
* *
1314536 CATATGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1314601 AGCCTTAGGGT
66 AGCCTTAGGGT
1314612 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1314677 AGTCTTAGGGT
66 AGCCTTAGGGT
* * * *
1314688 CATCTGTAAGTCCTGCGGTGCATGATGTTTCCAAAAATCATTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1314753 AACCTTAGGGT
66 AGCCTTAGGGT
*
1314764 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1314829 AACCTTAGGGT
66 AGCCTTAGGGT
* *
1314840 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTAAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1314905 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1314916 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1314981 AGCCTTAGGGT
66 AGCCTTAGGGT
*** *
1314992 CAAGAGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1315057 AGCCTTAGGGT
66 AGCCTTAGGGT
1315068 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1315133 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1315144 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1315209 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1315220 CATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
1315285 AACCTTTGGGT
66 AGCCTTAGGGT
* *
1315296 CATCTGTAAGCCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
1315326 TTAAGACCTC
Statistics
Matches: 753, Mismatches: 37, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 753 1.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:1315525 original size:18 final size:18
Alignment explanation
Indices: 1315472--1315549 Score: 85
Period size: 18 Copynumber: 4.4 Consensus size: 18
1315462 ATTTTTCATT
1315472 TATTATTATTA-A--AAA
1 TATTATTATTATATTAAA
1315487 TATTATTATTAT-TATAAA
1 TATTATTATTATAT-TAAA
*
1315505 TATTATTATTATATTATA
1 TATTATTATTATATTAAA
1315523 TATTA-TATTATTATTAAA
1 TATTATTATTA-TATTAAA
1315541 TAATTATTA
1 T-ATTATTA
1315550 CAAGCCCAGA
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
15 11 0.21
17 5 0.09
18 30 0.57
19 5 0.09
20 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTATTATTATATTAAA
Found at i:1315549 original size:3 final size:3
Alignment explanation
Indices: 1315471--1315538 Score: 68
Period size: 3 Copynumber: 23.0 Consensus size: 3
1315461 AATTTTTCAT
** * * *
1315471 TTA TTA TTA TTA AAA ATA TTA TTA TTA TTA TAA ATA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1315518 TTA TATA TTA -TA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA
1315539 AATAATTATT
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
2 4 0.07
3 47 0.87
4 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Done.