Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397267.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_204.0, 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: 6982396
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 27749 characters in sequence are not A, C, G, or T
File 2 of 12
Found at i:933664 original size:2 final size:2
Alignment explanation
Indices: 933659--933689 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
933649 ATATATATAT
933659 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
933690 CTGCCAAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:964422 original size:18 final size:18
Alignment explanation
Indices: 964385--964457 Score: 67
Period size: 18 Copynumber: 4.0 Consensus size: 18
964375 ATATATTTAA
* *
964385 TTAATTATATTAATTATAT
1 TTAAATATA-TAAATATAT
964404 TTAAATATATAAATATAT
1 TTAAATATATAAATATAT
* * *
964422 TT-AATCATATTATTATGT
1 TTAAAT-ATATAAATATAT
*
964440 TTAAATATATATATATAT
1 TTAAATATATAAATATAT
964458 ATAATTTATT
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
17 3 0.07
18 29 0.67
19 11 0.26
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (18 bp):
TTAAATATATAAATATAT
Found at i:964444 original size:36 final size:37
Alignment explanation
Indices: 964385--964473 Score: 119
Period size: 36 Copynumber: 2.5 Consensus size: 37
964375 ATATATTTAA
*
964385 TTAATTATATTAATTATATTTAAATATATAAATATAT
1 TTAATCATATTAATTATATTTAAATATATAAATATAT
* *
964422 TTAATCATATT-ATTATGTTTAAATATATATATATAT
1 TTAATCATATTAATTATATTTAAATATATAAATATAT
* *
964458 ATAAT-TTATTAATTAT
1 TTAATCATATTAATTAT
964474 TAAAAATTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
35 4 0.09
36 32 0.70
37 10 0.22
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (37 bp):
TTAATCATATTAATTATATTTAAATATATAAATATAT
Found at i:964622 original size:23 final size:21
Alignment explanation
Indices: 964595--964645 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 21
964585 TCTAATTTTA
964595 AATTTTATTTTACTATTTATTATT
1 AATTTTATTTT--TATTT-TTATT
964619 -ATTTTATTTTTATTTTTATT
1 AATTTTATTTTTATTTTTATT
964639 AATTTTA
1 AATTTTA
964646 AATTTAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.19
21 11 0.42
23 10 0.38
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (21 bp):
AATTTTATTTTTATTTTTATT
Found at i:964679 original size:19 final size:18
Alignment explanation
Indices: 964647--964712 Score: 62
Period size: 19 Copynumber: 3.6 Consensus size: 18
964637 TTAATTTTAA
* *
964647 ATTTAAATAATAAAATTAT
1 ATTTAATTATTAAAA-TAT
*
964666 ATTTAATTATTAAAAAATT
1 ATTTAATTATTAAAATA-T
*
964685 ATTTAATTATATTAAATAT
1 ATTTAATTAT-TAAAATAT
964704 A-TTAATTAT
1 ATTTAATTAT
964713 ATTATCAATC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
18 9 0.22
19 26 0.65
20 5 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATTTAATTATTAAAATAT
Found at i:964704 original size:9 final size:9
Alignment explanation
Indices: 964681--964716 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
964671 ATTATTAAAA
964681 AATTAT-TT
1 AATTATATT
964689 AATTATATT
1 AATTATATT
*
964698 AAATATATT
1 AATTATATT
964707 AATTATATT
1 AATTATATT
964716 A
1 A
964717 TCAATCGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 6 0.24
9 19 0.76
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
AATTATATT
Found at i:972897 original size:174 final size:174
Alignment explanation
Indices: 972597--972927 Score: 432
Period size: 174 Copynumber: 1.9 Consensus size: 174
972587 CAAACATATT
* * * *
972597 AGCCGTCGAATATTACTTTGAATTTTTATTGTTGTTTGCTTTTGCTTCAAAAAACTCCTTCTTAA
1 AGCCGTCGAAAATTACTTTGAATTTTTATTATTGCTTGCTTCTGCTTCAAAAAACTCCTTCTTAA
* ** * *
972662 CTGCCAACCACGGAAATGACTCTGAATTTTGGTTGCAGCAAATGTCTGATTTTGAAGAGATCTAT
66 CCGCCAACCACGGAAATGACTCTGAATTTTAATTGCAGCAAATGTCTGATTGTGAAGAGATCTAC
972727 AGACAAAATCCTCCCAAGCAATCTGAAAGGCCCTCCAGCATTTC
131 AGACAAAATCCTCCCAAGCAATCTGAAAGGCCCTCCAGCATTTC
* *
972771 AGCCGTCGAAAATTACTTTGAATTTTTGTTATTGCTTGCTTCTGCTTCATAAAACTCCTTCTTAA
1 AGCCGTCGAAAATTACTTTGAATTTTTATTATTGCTTGCTTCTGCTTCAAAAAACTCCTTCTTAA
* * * * * *
972836 CCGCCAACCCCGGTAATTG-CTCTGAATTTTAATTGCAGCACTAT-TTTTATTGTGTAGAGATCT
66 CCGCCAACCACGG-AAATGACTCTGAATTTTAATTGCAGCA-AATGTCTGATTGTGAAGAGATCT
* * * * *
972899 GCAGACAAACTTCTTCCATGCAATCTGAA
129 ACAGACAAAATCCTCCCAAGCAATCTGAA
972928 TCCTGGTTGC
Statistics
Matches: 133, Mismatches: 22, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
174 127 0.95
175 6 0.05
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.35
Consensus pattern (174 bp):
AGCCGTCGAAAATTACTTTGAATTTTTATTATTGCTTGCTTCTGCTTCAAAAAACTCCTTCTTAA
CCGCCAACCACGGAAATGACTCTGAATTTTAATTGCAGCAAATGTCTGATTGTGAAGAGATCTAC
AGACAAAATCCTCCCAAGCAATCTGAAAGGCCCTCCAGCATTTC
Found at i:991468 original size:26 final size:26
Alignment explanation
Indices: 991400--991452 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 26
991390 AAACAAAAAT
991400 ATTA-AAATT-AAATACATAATATAAGA
1 ATTAGAAATTAAAATA-A-AATATAAGA
991426 ATTAGAAATTAAAATAAAATATAAGA
1 ATTAGAAATTAAAATAAAATATAAGA
991452 A
1 A
991453 ATTGCAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 14 0.56
27 6 0.24
28 5 0.20
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (26 bp):
ATTAGAAATTAAAATAAAATATAAGA
Found at i:991537 original size:33 final size:33
Alignment explanation
Indices: 991500--991572 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
991490 TAAAAGATAT
* *
991500 AATATA-AAAATTATATTAAAGAAATGAAAATAA
1 AATATATAAAACTATAAT-AAGAAATGAAAATAA
*
991533 AATATATAAAACTATAATAAGAATTGAAAATAA
1 AATATATAAAACTATAATAAGAAATGAAAATAA
991566 AATATAT
1 AATATAT
991573 TTAAGAGATG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 27 0.75
34 9 0.25
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.29
Consensus pattern (33 bp):
AATATATAAAACTATAATAAGAAATGAAAATAA
Found at i:992312 original size:32 final size:32
Alignment explanation
Indices: 992260--992320 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
992250 ATTCTTATAA
*
992260 TTTTATTTTGAGTCACATAAATCTTTATATTT
1 TTTTATTTTGAGTCAAATAAATCTTTATATTT
* *
992292 TTTTGTTTTGTGTCAAATAAATCTTTATA
1 TTTTATTTTGAGTCAAATAAATCTTTATA
992321 GCATTAATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (32 bp):
TTTTATTTTGAGTCAAATAAATCTTTATATTT
Found at i:1010622 original size:15 final size:14
Alignment explanation
Indices: 1010602--1010650 Score: 62
Period size: 15 Copynumber: 3.4 Consensus size: 14
1010592 TCATTTCACC
1010602 AAAAAACAAAGAAAA
1 AAAAAAC-AAGAAAA
1010617 AAAAAACAAGAAAA
1 AAAAAACAAGAAAA
* *
1010631 GCAAGAACAAGAAAA
1 -AAAAAACAAGAAAA
1010646 AAAAA
1 AAAAA
1010651 GAAAAAGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 10 0.34
15 19 0.66
ACGTcount: A:0.82, C:0.08, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAACAAGAAAA
Found at i:1027110 original size:2 final size:2
Alignment explanation
Indices: 1027105--1027148 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
1027095 AAAAAGGCAT
* * *
1027105 GA GA GA CA GA GA GA GA TA CA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1027147 GA
1 GA
1027149 ATGTTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.50, C:0.05, G:0.43, T:0.02
Consensus pattern (2 bp):
GA
Found at i:1044594 original size:5 final size:5
Alignment explanation
Indices: 1044584--1044618 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
1044574 GAACTTAACC
* *
1044584 AGAGG AGAGG AGAGG AAAGG AAAGG AGAGG AGAGG
1 AGAGG AGAGG AGAGG AGAGG AGAGG AGAGG AGAGG
1044619 TTTATCTTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (5 bp):
AGAGG
Found at i:1047524 original size:23 final size:22
Alignment explanation
Indices: 1047490--1047532 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
1047480 GGGATATTTG
1047490 AAAAAGATTTAA-TTATGGCTAC
1 AAAAAGATTTAAGTT-TGGCTAC
*
1047512 AAAAAGTTATTAAGTTTGGCT
1 AAAAAGAT-TTAAGTTTGGCT
1047533 TTCAATTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 7 0.39
23 9 0.50
24 2 0.11
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.35
Consensus pattern (22 bp):
AAAAAGATTTAAGTTTGGCTAC
Found at i:1050768 original size:14 final size:14
Alignment explanation
Indices: 1050727--1050771 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
1050717 TTTAATTTTA
*
1050727 ATAATATTAAATAAT
1 ATAA-ATTAAATATT
1050742 ATAAATATAAATATT
1 ATAAAT-TAAATATT
*
1050757 TTAAATTAAATATT
1 ATAAATTAAATATT
1050771 A
1 A
1050772 ATATTATTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATAAATTAAATATT
Found at i:1050936 original size:19 final size:20
Alignment explanation
Indices: 1050898--1050935 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1050888 GTATACGATG
1050898 TTTTATATTTAAAACAAAAT
1 TTTTATATTTAAAACAAAAT
* *
1050918 TTTTATTTTTTAAACAAA
1 TTTTATATTTAAAACAAA
1050936 TATAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTATATTTAAAACAAAAT
Found at i:1057888 original size:21 final size:22
Alignment explanation
Indices: 1057812--1057888 Score: 74
Period size: 21 Copynumber: 3.7 Consensus size: 22
1057802 ATAAGATATA
*
1057812 TAATTATAAATAATATTT-TTAT
1 TAATTATAAA-AAAATTTATTAT
** *
1057834 TAA-TATAAATTAATTAATTAT
1 TAATTATAAAAAAATTTATTAT
1057855 TAATTAT--AAAAATTTATTA-
1 TAATTATAAAAAAATTTATTAT
1057874 TAATTATAAAAAAAT
1 TAATTATAAAAAAAT
1057889 AATTAAATGT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
19 7 0.16
20 12 0.27
21 19 0.43
22 6 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATTATAAAAAAATTTATTAT
Found at i:1057893 original size:20 final size:20
Alignment explanation
Indices: 1057848--1057908 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 20
1057838 ATAAATTAAT
*
1057848 TAATTATTAATTAT-AAAAAT
1 TAATTA-TAATTATAAAAAAA
*
1057868 TTATTATAATTATAAAAAAA
1 TAATTATAATTATAAAAAAA
1057888 TAATTA-AATGTA-AAAAAAA
1 TAATTATAAT-TATAAAAAAA
1057907 TA
1 TA
1057909 TAAAAATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 19 0.53
20 17 0.47
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
TAATTATAATTATAAAAAAA
Found at i:1060617 original size:23 final size:23
Alignment explanation
Indices: 1060569--1060618 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1060559 GTTTTTTATT
* *
1060569 TTTTTTAAAAAATATAATAATAA
1 TTTTTTAAAAAATAGAAAAATAA
*
1060592 TTTTTTAAATTAATAGAAAAAT-A
1 TTTTTTAAA-AAATAGAAAAATAA
1060615 TTTT
1 TTTT
1060619 AATTTTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
TTTTTTAAAAAATAGAAAAATAA
Found at i:1062639 original size:25 final size:25
Alignment explanation
Indices: 1062611--1062658 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1062601 ATTTTGTTAT
*
1062611 AATTTTTTTTAAATT-TAAATAATAA
1 AATTTTATTT-AATTGTAAATAATAA
1062636 AATTTTATTTAATTGTAAATAAT
1 AATTTTATTTAATTGTAAATAAT
1062659 TTTATTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
AATTTTATTTAATTGTAAATAATAA
Found at i:1073784 original size:19 final size:19
Alignment explanation
Indices: 1073760--1073801 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
1073750 TCACGAGAGA
1073760 ATATTCTAATGTAACAGCG
1 ATATTCTAATGTAACAGCG
1073779 ATATTCTAATGTAACAGCG
1 ATATTCTAATGTAACAGCG
1073798 ATAT
1 ATAT
1073802 ACTGCTAGGA
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:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (19 bp):
ATATTCTAATGTAACAGCG
Found at i:1078159 original size:2 final size:2
Alignment explanation
Indices: 1078152--1078183 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1078142 CCAAGGGGAG
*
1078152 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1078184 GTATGCATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1078184 original size:8 final size:8
Alignment explanation
Indices: 1078153--1078203 Score: 57
Period size: 8 Copynumber: 6.4 Consensus size: 8
1078143 CAAGGGGAGA
*
1078153 TATATATA
1 TATATATG
*
1078161 TATATATA
1 TATATATG
1078169 TATATATG
1 TATATATG
1078177 TATATATG
1 TATATATG
**
1078185 TATGCATG
1 TATATATG
*
1078193 TATGTATG
1 TATATATG
1078201 TAT
1 TAT
1078204 GCAAATTGGC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 39 1.00
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (8 bp):
TATATATG
Found at i:1078188 original size:12 final size:12
Alignment explanation
Indices: 1078153--1078203 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
1078143 CAAGGGGAGA
*
1078153 TATATATATATA
1 TATATATATATG
1078165 TATATATATATG
1 TATATATATATG
*
1078177 TATATATGTATG
1 TATATATATATG
* * *
1078189 CATGTATGTATG
1 TATATATATATG
1078201 TAT
1 TAT
1078204 GCAAATTGGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (12 bp):
TATATATATATG
Found at i:1080183 original size:15 final size:15
Alignment explanation
Indices: 1080156--1080202 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1080146 CATGTTCATG
1080156 ACAATGCAATGTGATT
1 ACAA-GCAATGTGATT
* *
1080172 ACAGGTAATGTGATT
1 ACAAGCAATGTGATT
*
1080187 GCAAGCAATGTGATT
1 ACAAGCAATGTGATT
1080202 A
1 A
1080203 TTGGGAAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
15 22 0.88
16 3 0.12
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (15 bp):
ACAAGCAATGTGATT
Found at i:1080472 original size:23 final size:23
Alignment explanation
Indices: 1080420--1080820 Score: 143
Period size: 23 Copynumber: 18.1 Consensus size: 23
1080410 TTTTAATATC
*
1080420 ATATATTTTATTTATTTATTATT-
1 ATATATTTTATAT-TTTATTATTA
*
1080443 ATAATATTTTATATTTTATTTTTA
1 AT-ATATTTTATATTTTATTATTA
1080467 ATATA-TTTATATTTTTATTATTA
1 ATATATTTTATA-TTTTATTATTA
* * * *
1080490 AT-T-TTATATAATATCATTTCTTA
1 ATATATTTTAT-ATTTTA-TTATTA
* *
1080513 A-ATA---TAT-TTTTAATA-TC
1 ATATATTTTATATTTTATTATTA
*
1080530 ATATATTTTATTTTATTTATTATT-
1 ATATATTTTA-TAT-TTTATTATTA
*
1080554 ATAATATTTTATATTTTATTTTTA
1 AT-ATATTTTATATTTTATTATTA
*
1080578 ATATA-TTTATATTTTTTATATTA
1 ATATATTTTATATTTTAT-TATTA
* * *
1080601 AT-T-TTTATATAATATCATTTTTA
1 ATATATTT-TAT-ATTTTATTATTA
* *
1080624 ATATATTTT-TAATATCATATATT-
1 ATATATTTTAT-ATTTTAT-TATTA
1080647 -T-TATTTT-TA-TTTATTATT-
1 ATATATTTTATATTTTATTATTA
*
1080665 ATAATATTTTATATTTTATTTTTA
1 AT-ATATTTTATATTTTATTATTA
* *
1080689 ATAT-TTGTAT-TTATATTATTA
1 ATATATTTTATATTTTATTATTA
** *
1080710 AT-T-TTTATATAATCATATTTTTA
1 ATATATTT-TAT-ATTTTATTATTA
* *
1080733 ATATATTTT-TAATGTCATATATT-
1 ATATATTTTAT-ATTTTAT-TATTA
1080756 -T-TATTTT-TA-TTTATTATT-
1 ATATATTTTATATTTTATTATTA
*
1080774 ATA-ATATTT-TATTTTATTTTTA
1 ATATAT-TTTATATTTTATTATTA
*
1080796 ATATATTTGTAT-TTATATTATTA
1 ATATATTT-TATATTTTATTATTA
1080819 AT
1 AT
1080821 TTTATATAAT
Statistics
Matches: 293, Mismatches: 40, Indels: 90
0.69 0.09 0.21
Matches are distributed among these distances:
17 2 0.01
18 12 0.04
19 13 0.04
20 10 0.03
21 47 0.16
22 43 0.15
23 110 0.38
24 41 0.14
25 15 0.05
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (23 bp):
ATATATTTTATATTTTATTATTA
Found at i:1080567 original size:111 final size:111
Alignment explanation
Indices: 1080351--1080907 Score: 886
Period size: 110 Copynumber: 5.0 Consensus size: 111
1080341 AAAATATAAG
1080351 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
1 TTTAATATATTTATA-TTTTTATTATTAATTTTTATATAATATCATTT-TT-AATATATTTTTAA
1080416 TATCATATATTTTA--TTTATTTATTATTATAATATTTTATATTTTATT
63 TATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
1080463 TTTAATATATTTATATTTTTATTATTAA-TTTTATATAATATCATTTCTTAAATATATTTTTAAT
1 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTT-TT-AATATATTTTTAAT
1080527 ATCATATATTTTA-TTTTATTTATTATTATAATATTTTATATTTTATT
64 ATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
1080574 TTTAATATATTTATATTTTT-TATATTAATTTTTATATAATATCATTTTTAATATATTTTTAATA
1 TTTAATATATTTATATTTTTAT-TATTAATTTTTATATAATATCATTTTTAATATATTTTTAATA
1080638 TCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
65 TCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
* * *
1080685 TTT-A-ATATTTGTATTTATATTATTAATTTTTATATAATCAT-ATTTTTAATATATTTTTAATG
1 TTTAATATATTTATATTTTTATTATTAATTTTTATATAAT-ATCATTTTTAATATATTTTTAATA
1080747 TCATATATTTTATTTTTATTTATTATTATAATA-TTT-TATTTTATT
65 TCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
* *
1080792 TTTAATATATTTGTATTTATATTATTAA-TTTTATATAATATCATATTTTTAATATATTTTTAAT
1 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATC--ATTTTTAATATATTTTTAAT
*
1080856 GTCATATATTTTATTTTTATTTATTATTATAAT-TTTATATATTTTATT
64 ATCATATATTTTATTTTTATTTATTATTATAATATTT-TATATTTTATT
1080904 TTTA
1 TTTA
1080908 TTTTTTAATA
Statistics
Matches: 428, Mismatches: 3, Indels: 28
0.93 0.01 0.06
Matches are distributed among these distances:
107 14 0.03
108 15 0.04
109 105 0.25
110 136 0.32
111 112 0.26
112 46 0.11
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (111 bp):
TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTTTAATATATTTTTAATAT
CATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
Found at i:1080672 original size:21 final size:21
Alignment explanation
Indices: 1080648--1080816 Score: 95
Period size: 21 Copynumber: 7.9 Consensus size: 21
1080638 TCATATATTT
1080648 TATTTTTATTTATTATTATAA
1 TATTTTTATTTATTATTATAA
1080669 TATTTTATATTTTATT-TT-TAA
1 TATTTT-TA-TTTATTATTATAA
* *
1080690 TATTTGTATTTA-TATTATTA
1 TATTTTTATTTATTATTATAA
* *
1080710 -ATTTTTATATAATCATATTTTTAA
1 TATTTTTAT-TTAT--TA-TTATAA
* * **
1080734 TATATTT-TTAATGTCATATATTT
1 TATTTTTATTTAT-T-AT-TATAA
1080757 TATTTTTATTTATTATTATAA
1 TATTTTTATTTATTATTATAA
1080778 TA-TTTTATTTTATT-TT-TAA
1 TATTTTTA-TTTATTATTATAA
1080797 TATATTTGTATTTA-TATTAT
1 TAT-TTT-TATTTATTATTAT
1080817 TAATTTTATA
Statistics
Matches: 114, Mismatches: 15, Indels: 37
0.69 0.09 0.22
Matches are distributed among these distances:
18 1 0.01
19 18 0.16
20 14 0.12
21 34 0.30
22 11 0.10
23 22 0.19
24 9 0.08
25 5 0.04
ACGTcount: A:0.31, C:0.01, G:0.02, T:0.66
Consensus pattern (21 bp):
TATTTTTATTTATTATTATAA
Found at i:1080705 original size:33 final size:34
Alignment explanation
Indices: 1080659--1080942 Score: 87
Period size: 39 Copynumber: 8.0 Consensus size: 34
1080649 ATTTTTATTT
1080659 ATTATTATAATATT-TTATATTTTATTTTTAATATT
1 ATTATTATAATATTATTATATTTTATTTTT-AT-TT
*
1080694 -TGTATT-T-ATATTATTA-ATTTTTATATAATCATATTT
1 AT-TATTATAATATTATTATA-TTTTAT-T--T-TTATTT
* * *
1080730 -TTAATATATTTTTAATGTCATATATTTTATTTTTATTT
1 ATTATTATAATATT-AT-T-ATAT-TT-TATTTTTATTT
*
1080768 ATTATTATAATA-T-TT-TATTTTATTTTTAATAT
1 ATTATTATAATATTATTATATTTTATTTTT-ATTT
*
1080800 ATT-TGTATTTATATTATTA-ATTTTATATAATATCATATTT
1 ATTAT-TA-TAATATTATTATATTTTAT-T--T-T--TATTT
* * *
1080840 -TTAATATATTTTTAATGTCATATATTTTATTTTTATTT
1 ATTATTATAATATT-AT-T-ATA--TTTTATTTTTATTT
*
1080878 ATTATTATAATTTTA-TATATTTTATTTTTATTT
1 ATTATTATAATATTATTATATTTTATTTTTATTT
* * *
1080911 -TT-TAAT-ATATTTTTATATTATATATTTTATTT
1 ATTATTATAATATTATTATATTTTAT-TTTTATTT
1080943 TAATTTGTTT
Statistics
Matches: 190, Mismatches: 21, Indels: 79
0.66 0.07 0.27
Matches are distributed among these distances:
30 4 0.02
31 20 0.11
32 20 0.11
33 27 0.14
34 12 0.06
35 21 0.11
36 7 0.04
37 6 0.03
38 20 0.11
39 28 0.15
40 7 0.04
41 7 0.04
42 4 0.02
43 1 0.01
44 6 0.03
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (34 bp):
ATTATTATAATATTATTATATTTTATTTTTATTT
Found at i:1080800 original size:47 final size:46
Alignment explanation
Indices: 1080749--1080851 Score: 118
Period size: 47 Copynumber: 2.2 Consensus size: 46
1080739 TTTTAATGTC
* ** **
1080749 ATATATTTTATTTTTATTTATT-ATTATAATATTTTATTTTATTTTTA
1 ATATATTTTATTTATA-TTATTAATT-TAATATAATATCATATTTTTA
*
1080796 ATATATTTGTATTTATATTATTAATTTTATATAATATCATATTTTTA
1 ATATATTT-TATTTATATTATTAATTTAATATAATATCATATTTTTA
1080843 ATATATTTT
1 ATATATTTT
1080852 TAATGTCATA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
46 1 0.02
47 37 0.77
48 10 0.21
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (46 bp):
ATATATTTTATTTATATTATTAATTTAATATAATATCATATTTTTA
Found at i:1080817 original size:31 final size:31
Alignment explanation
Indices: 1080725--1080964 Score: 113
Period size: 31 Copynumber: 7.9 Consensus size: 31
1080715 TATATAATCA
1080725 TATTTTTAATATATTTT-TAATGTCATA-TATTT
1 TATTTTTAATATATTTTAT-AT-T-ATATTATTT
* * *
1080757 TATTTTT-ATTTATTATTATAATATTTTATTT
1 TATTTTTAATATATT-TTATATTATATTATTT
1080788 TATTTTTAATATATTTGTAT-TTATATTA--T
1 TATTTTTAATATATTT-TATATTATATTATTT
* * * * *
1080817 TAATTTT-ATATAATATCATATT-T-TTAATA
1 TATTTTTAATAT-ATTTTATATTATATTATTT
1080846 TATTTTTAATGTCATATATTT-TATT-T-TTA-TT
1 TATTTTTAA--T-ATAT-TTTATATTATATTATTT
* *
1080877 TATTATT-ATA-ATTTTATA-TATTTTATTTT
1 TATTTTTAATATATTTTATATTATATTA-TTT
1080906 TATTTTTTAATATATTTTTATATTATA-TATTT
1 TA-TTTTTAATATA-TTTTATATTATATTATTT
* * *
1080938 TA-TTTTAATTTGTTTTAT-CTATATTAT
1 TATTTTTAATATATTTTATATTATATTAT
1080965 ATAAATATTA
Statistics
Matches: 163, Mismatches: 20, Indels: 53
0.69 0.08 0.22
Matches are distributed among these distances:
25 4 0.02
26 5 0.03
27 7 0.04
28 12 0.07
29 31 0.19
30 16 0.10
31 36 0.22
32 36 0.22
33 13 0.08
34 3 0.02
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (31 bp):
TATTTTTAATATATTTTATATTATATTATTT
Found at i:1081020 original size:44 final size:41
Alignment explanation
Indices: 1080895--1081029 Score: 67
Period size: 44 Copynumber: 3.0 Consensus size: 41
1080885 TAATTTTATA
* * *
1080895 TATTTTATTTTTATTTTTTAATATATTTTTATATTATATATTT
1 TATTTTATTTTTA-TTTTTATTTTATTTTAAT-TTATATATTT
* *
1080938 TATTTTAATTTGTT-TTATCTATATTATATAAATATTAATTTTTATATTT
1 TATTTT-ATTT-TTATT-T-T-TATT-T-T--ATTTTAATTTATATATTT
*
1080987 TATTTTATTTTAATTTATATATATTTATTTTAA-TTATAATATT
1 TATTTTATTTTTATTT-T-TAT-TTTATTTTAATTTAT-ATATT
1081030 ATAAAATATT
Statistics
Matches: 71, Mismatches: 9, Indels: 23
0.69 0.09 0.22
Matches are distributed among these distances:
43 11 0.15
44 16 0.23
45 3 0.04
46 4 0.06
47 8 0.11
48 8 0.11
49 15 0.21
50 6 0.08
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.67
Consensus pattern (41 bp):
TATTTTATTTTTATTTTTATTTTATTTTAATTTATATATTT
Found at i:1081433 original size:15 final size:15
Alignment explanation
Indices: 1081413--1081453 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
1081403 TTTTTCCTGT
1081413 AATCACATTACTTGC
1 AATCACATTACTTGC
1081428 AATCACATTACTTGC
1 AATCACATTACTTGC
1081443 AATCACATTAC
1 AATCACATTAC
1081454 CTATAATTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.32
Consensus pattern (15 bp):
AATCACATTACTTGC
Found at i:1117894 original size:51 final size:51
Alignment explanation
Indices: 1117825--1117926 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
1117815 TGTGATGTGT
1117825 GGCCTTAATGAGGACATCAAATCAAGGATTTGAGTGAGTGAGATTGTGATA
1 GGCCTTAATGAGGACATCAAATCAAGGATTTGAGTGAGTGAGATTGTGATA
1117876 GGCCTTAATGAGGACATCAAATCAAGGATTTGAGTGAGTGAGATTGTGATA
1 GGCCTTAATGAGGACATCAAATCAAGGATTTGAGTGAGTGAGATTGTGATA
1117927 CCCAACATCT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.27
Consensus pattern (51 bp):
GGCCTTAATGAGGACATCAAATCAAGGATTTGAGTGAGTGAGATTGTGATA
Found at i:1118003 original size:22 final size:22
Alignment explanation
Indices: 1117977--1118020 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1117967 ATATAACAAT
1117977 CTAAGTCTACTACTACAATGTG
1 CTAAGTCTACTACTACAATGTG
1117999 CTAAGTCTACTACTACAATGTG
1 CTAAGTCTACTACTACAATGTG
1118021 ATGTGTGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (22 bp):
CTAAGTCTACTACTACAATGTG
Found at i:1118130 original size:64 final size:64
Alignment explanation
Indices: 1118029--1118156 Score: 238
Period size: 64 Copynumber: 2.0 Consensus size: 64
1118019 TGATGTGTGG
1118029 CCTTGATGTACAATGTGATATGTGGCCTTAATGAGGACATCAAATCAAGGATTTAAGTGAGTGA
1 CCTTGATGTACAATGTGATATGTGGCCTTAATGAGGACATCAAATCAAGGATTTAAGTGAGTGA
* *
1118093 CCTTGATGTACAATGTGATGTGTGGCCTTAATGAGGACATCAAATCAAGGATTTGAGTGAGTGA
1 CCTTGATGTACAATGTGATATGTGGCCTTAATGAGGACATCAAATCAAGGATTTAAGTGAGTGA
1118157 GATTGTGATA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (64 bp):
CCTTGATGTACAATGTGATATGTGGCCTTAATGAGGACATCAAATCAAGGATTTAAGTGAGTGA
Found at i:1118185 original size:51 final size:51
Alignment explanation
Indices: 1118116--1118217 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
1118106 TGTGATGTGT
*
1118116 GGCCTTAATGAGGACATCAAATCAAGGATTTGAGTGAGTGAGATTGTGATA
1 GGCCTTAATGAGGACATCAAATCAAGGATTTGAGTGAGTGAGATTATGATA
1118167 GGCCTTAATGAGGACATCAAATCAAGGATTTGAGTGAGTGAGATTATGATA
1 GGCCTTAATGAGGACATCAAATCAAGGATTTGAGTGAGTGAGATTATGATA
1118218 CACAACATCC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.27
Consensus pattern (51 bp):
GGCCTTAATGAGGACATCAAATCAAGGATTTGAGTGAGTGAGATTATGATA
Found at i:1118310 original size:124 final size:124
Alignment explanation
Indices: 1118152--1118400 Score: 462
Period size: 124 Copynumber: 2.0 Consensus size: 124
1118142 GATTTGAGTG
*
1118152 AGTGAGATTGTGATAGGCCTTAATGAGGACATCAAATCAAGGATTTGAGTGAGTGAGATTATGAT
1 AGTGAGATTGTGATAGGCCTTAATAAGGACATCAAATCAAGGATTTGAGTGAGTGAGATTATGAT
*
1118217 ACACAACATCCCACATCTGATGAATATGATTGTTAAGACTTATATAACAATCTAAGTCT
66 ACACAACATCCCACATCTCATGAATATGATTGTTAAGACTTATATAACAATCTAAGTCT
*
1118276 AGTGAGATTGTGATAGGCCTTAATAAGGACATCAAATCAAGGATTTGAGTGAGTGAGATTGTGAT
1 AGTGAGATTGTGATAGGCCTTAATAAGGACATCAAATCAAGGATTTGAGTGAGTGAGATTATGAT
*
1118341 ACATAACATCCCACATCTCATGAATATGATTGTTAAGACTTATATAACAATCTAAGTCT
66 ACACAACATCCCACATCTCATGAATATGATTGTTAAGACTTATATAACAATCTAAGTCT
1118400 A
1 A
1118401 CTACTACAAT
Statistics
Matches: 121, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
124 121 1.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.30
Consensus pattern (124 bp):
AGTGAGATTGTGATAGGCCTTAATAAGGACATCAAATCAAGGATTTGAGTGAGTGAGATTATGAT
ACACAACATCCCACATCTCATGAATATGATTGTTAAGACTTATATAACAATCTAAGTCT
Found at i:1118418 original size:22 final size:22
Alignment explanation
Indices: 1118392--1118435 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1118382 ATATAACAAT
1118392 CTAAGTCTACTACTACAATGTG
1 CTAAGTCTACTACTACAATGTG
1118414 CTAAGTCTACTACTACAATGTG
1 CTAAGTCTACTACTACAATGTG
1118436 ATGTGTGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (22 bp):
CTAAGTCTACTACTACAATGTG
Found at i:1120886 original size:228 final size:228
Alignment explanation
Indices: 1119790--1120868 Score: 1340
Period size: 228 Copynumber: 4.7 Consensus size: 228
1119780 AGCTTAGAAA
* * * * * * * *
1119790 CCACCACGAAGGCGCAAGACCAGGTGAAGGGTGGACTCCTTCTGAATATTGTAATCAGCCAAAGT
1 CCACCACGTAGACGGAAGACCAGGTGGAGGGTCGACTCCTTCTGGATGTTGTAATCCGCCAAAGT
* * * * * ** * * * * *
1119855 CCTTCCATCTTCCAATTGCTTCCCAGCAAAAATCAA-CCTTTGCTGATCTGGTGGAATCCCTTCC
66 TCTGCCGTCCTCGAGCTGCTTCCCAGCAAAGAT-AAGCCTTTGCTGGTCCGGTGGGATTCCTTCC
* * * * * * * * * * * * * *
1119919 TTGTCCTGAATCTTTGCCTTAACATTATCAATCGTATCCGAGCTCTCCACCTCCAAAGTAATGGT
130 TTGTCCTGGATCTTGGCCTTCACGTTGTCGATGGTGTCGGAGCTTTCAACTTCCAAGGTTATGGT
* *
1119984 TTT-CCCTGTCAGAGTCTTGACGAAA-ATCTGCATC
195 TTTACCC-GTCAGGGTCTTGAC-AAAGATTTGCATC
* * ** * ** * * * * *
1120018 CCACCACGAAGCCTCAAAACCAAATGAAGGGTCGACTCTTTCTGAATGTTATAATCAGCCAAAGT
1 CCACCACGTAGACGGAAGACCAGGTGGAGGGTCGACTCCTTCTGGATGTTGTAATCCGCCAAAGT
* * * * *
1120083 TC-GACCGTCCTCGAGCTGCTTCCCTGCAAAGATAAGCCTTTGCTGATCTGGCGGAATTCCTTCC
66 TCTG-CCGTCCTCGAGCTGCTTCCCAGCAAAGATAAGCCTTTGCTGGTCCGGTGGGATTCCTTCC
*
1120147 TTGTCCTGGATCTTGGCCTTCACGTTGTCGATGGTGTCGGAACTTTCAACTTCCAAGGTTATGGT
130 TTGTCCTGGATCTTGGCCTTCACGTTGTCGATGGTGTCGGAGCTTTCAACTTCCAAGGTTATGGT
1120212 TTTACCCGTCAGGGTCTTGACAAAGATTTGCATC
195 TTTACCCGTCAGGGTCTTGACAAAGATTTGCATC
* * * *
1120246 CCACCACGGAGACGTAAGACCAGGTGGAGGGTTGACTCCTTTTGGATGTTGTAATCCGCCAAAGT
1 CCACCACGTAGACGGAAGACCAGGTGGAGGGTCGACTCCTTCTGGATGTTGTAATCCGCCAAAGT
* * *
1120311 TCGGCCGTCCTCGAGTTGCTTCCCAGCAAAGATAAGCCTTTGCTGGTCCGG-GGGAATTCCTTCT
66 TCTGCCGTCCTCGAGCTGCTTCCCAGCAAAGATAAGCCTTTGCTGGTCCGGTGGG-ATTCCTTCC
1120375 TTGTCCTGGATCTTGGCCTTCACGTTGTCGATGGTGTCGGAGCTTTCAACTTCCAAGGTTATGGT
130 TTGTCCTGGATCTTGGCCTTCACGTTGTCGATGGTGTCGGAGCTTTCAACTTCCAAGGTTATGGT
*
1120440 TTTGCCCGTCAGGGTCTTGACAAAGATTTGCATC
195 TTTACCCGTCAGGGTCTTGACAAAGATTTGCATC
* * * * * * *
1120474 CCACCACGTAAACGGAGGACGAGGTGGAGGGTTGACTCCTTTTGGATGTTGTAATCCGCTAAGGT
1 CCACCACGTAGACGGAAGACCAGGTGGAGGGTCGACTCCTTCTGGATGTTGTAATCCGCCAAAGT
1120539 TCTGCCGTCCTCGAGCTGCTTCCCAGCAAAGATAAGCCTTTGCTGGTCCGGTGGGATTCCTTCCT
66 TCTGCCGTCCTCGAGCTGCTTCCCAGCAAAGATAAGCCTTTGCTGGTCCGGTGGGATTCCTTCCT
* * *
1120604 TGTCCTGGATCTTGGCCTTCACGTTGTCAATGGTGTCGGAGCTTTCGACTTCCAGGGTTATGGTT
131 TGTCCTGGATCTTGGCCTTCACGTTGTCGATGGTGTCGGAGCTTTCAACTTCCAAGGTTATGGTT
*
1120669 TTACCCGTCAGGGTCTTGACGAAGATTTGCATC
196 TTACCCGTCAGGGTCTTGACAAAGATTTGCATC
* * * * **
1120702 CCACCACGTAGACGGAGGACGAGGTGGAGAGTCGACTCCTTCTGGATGTTGTAATCGGCCAGGGT
1 CCACCACGTAGACGGAAGACCAGGTGGAGGGTCGACTCCTTCTGGATGTTGTAATCCGCCAAAGT
* *
1120767 TCTGCCATCCTCGAGCTGCTTCCCAGCAAAGATAAGCCTTTGCTGGTCCGGTGGGATCCCTTCCT
66 TCTGCCGTCCTCGAGCTGCTTCCCAGCAAAGATAAGCCTTTGCTGGTCCGGTGGGATTCCTTCCT
*
1120832 TGTCCTGGATCTTGGCCTTCACGTTGTCGATCGTGTC
131 TGTCCTGGATCTTGGCCTTCACGTTGTCGATGGTGTC
1120869 AGAACTCTCG
Statistics
Matches: 759, Mismatches: 85, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
227 7 0.01
228 745 0.98
229 7 0.01
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.29
Consensus pattern (228 bp):
CCACCACGTAGACGGAAGACCAGGTGGAGGGTCGACTCCTTCTGGATGTTGTAATCCGCCAAAGT
TCTGCCGTCCTCGAGCTGCTTCCCAGCAAAGATAAGCCTTTGCTGGTCCGGTGGGATTCCTTCCT
TGTCCTGGATCTTGGCCTTCACGTTGTCGATGGTGTCGGAGCTTTCAACTTCCAAGGTTATGGTT
TTACCCGTCAGGGTCTTGACAAAGATTTGCATC
Found at i:1133937 original size:21 final size:21
Alignment explanation
Indices: 1133900--1133939 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1133890 ACTTTAAGTA
*
1133900 ATTAAAATATTAAATAATAAT
1 ATTAAAATAATAAATAATAAT
1133921 ATTAAAA-AATAACATAATA
1 ATTAAAATAATAA-ATAATA
1133940 TTTTTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (21 bp):
ATTAAAATAATAAATAATAAT
Found at i:1134624 original size:25 final size:25
Alignment explanation
Indices: 1134596--1134676 Score: 94
Period size: 24 Copynumber: 3.2 Consensus size: 25
1134586 ACAGGCCACA
**
1134596 AGAAGAAGGAAAAGAAGGCAAGGTG
1 AGAAGAAGGAAAAGAAGGCAAGAAG
*
1134621 AGAAGAAGG-AAAGAAAAGCAAGAAG
1 AGAAGAAGGAAAAG-AAGGCAAGAAG
*
1134646 -GAAGAAGGAGAAGAAGGCAAGAAG
1 AGAAGAAGGAAAAGAAGGCAAGAAG
1134670 AAGAAGA
1 -AGAAGA
1134677 GAAGAGTCGG
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
24 22 0.47
25 20 0.43
26 5 0.11
ACGTcount: A:0.58, C:0.04, G:0.37, T:0.01
Consensus pattern (25 bp):
AGAAGAAGGAAAAGAAGGCAAGAAG
Found at i:1134644 original size:33 final size:32
Alignment explanation
Indices: 1134598--1134676 Score: 83
Period size: 33 Copynumber: 2.4 Consensus size: 32
1134588 AGGCCACAAG
1134598 AAGAAGGAA-AAGAAGGCAAG-GTGAGAAGAAGGA
1 AAGAA-GAAGAAGAAGG-AAGAG-GAGAAGAAGGA
*
1134631 AAGAA-AAGCAAGAAGGAAGAAGGAGAAGAAGGC
1 AAGAAGAAG-AAGAAGGAAG-AGGAGAAGAAGGA
1134664 AAGAAGAAGAAGA
1 AAGAAGAAGAAGA
1134677 GAAGAGTCGG
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
31 2 0.05
32 3 0.08
33 31 0.77
34 4 0.10
ACGTcount: A:0.58, C:0.04, G:0.37, T:0.01
Consensus pattern (32 bp):
AAGAAGAAGAAGAAGGAAGAGGAGAAGAAGGA
Found at i:1146422 original size:25 final size:25
Alignment explanation
Indices: 1146394--1146448 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
1146384 TCTCACCCTA
1146394 TCCCCGACATTGTTCCCCGACGATG
1 TCCCCGACATTGTTCCCCGACGATG
* *
1146419 TCCCCGACATTGTTCTCTGACGATG
1 TCCCCGACATTGTTCCCCGACGATG
1146444 TCCCC
1 TCCCC
1146449 TGGGCGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.15, C:0.40, G:0.18, T:0.27
Consensus pattern (25 bp):
TCCCCGACATTGTTCCCCGACGATG
Found at i:1146424 original size:12 final size:13
Alignment explanation
Indices: 1146394--1146433 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1146384 TCTCACCCTA
1146394 TCCCCGACATTGT
1 TCCCCGACATTGT
1146407 TCCCCGACGA-TG-
1 TCCCCGAC-ATTGT
1146419 TCCCCGACATTGT
1 TCCCCGACATTGT
1146432 TC
1 TC
1146434 TCTGACGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 1 0.04
12 10 0.42
13 12 0.50
14 1 0.04
ACGTcount: A:0.15, C:0.40, G:0.17, T:0.28
Consensus pattern (13 bp):
TCCCCGACATTGT
Found at i:1151859 original size:18 final size:18
Alignment explanation
Indices: 1151836--1151877 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1151826 AAAAAAATTT
*
1151836 ATATGAGTATAAATTAAA
1 ATATGAATATAAATTAAA
* *
1151854 ATATGAATATTAATTTAA
1 ATATGAATATAAATTAAA
1151872 ATATGA
1 ATATGA
1151878 TAAAAGAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (18 bp):
ATATGAATATAAATTAAA
Found at i:1152203 original size:7 final size:7
Alignment explanation
Indices: 1152191--1152233 Score: 77
Period size: 7 Copynumber: 6.1 Consensus size: 7
1152181 GCGGTGGAGA
1152191 TGCTGGC
1 TGCTGGC
1152198 TGCTGGC
1 TGCTGGC
1152205 TGCTGGC
1 TGCTGGC
1152212 TGCTGGC
1 TGCTGGC
*
1152219 TGCTGCC
1 TGCTGGC
1152226 TGCTGGC
1 TGCTGGC
1152233 T
1 T
1152234 CATGTATTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.00, C:0.30, G:0.40, T:0.30
Consensus pattern (7 bp):
TGCTGGC
Found at i:1179637 original size:17 final size:17
Alignment explanation
Indices: 1179584--1179640 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 17
1179574 TTTTTATATC
*
1179584 ATTATT-TTTATTAATT
1 ATTATTATTTATTATTT
* *
1179600 -TTA-AATTT-TTATAT
1 ATTATTATTTATTATTT
1179614 ATT-TTATTTATTATTT
1 ATTATTATTTATTATTT
1179630 ATTATTATTTA
1 ATTATTATTTA
1179641 AAAAATGTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 9
0.69 0.11 0.20
Matches are distributed among these distances:
14 4 0.13
15 12 0.39
16 8 0.26
17 7 0.23
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTATTATTTATTATTT
Found at i:1190573 original size:21 final size:21
Alignment explanation
Indices: 1190520--1190573 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
1190510 GCATGGAGTG
* *
1190520 AGGTGAATATTGCTCCAAATA
1 AGGTGAATGTTGCACCAAATA
* *
1190541 AAGTGAACGTTGCACCAAATA
1 AGGTGAATGTTGCACCAAATA
*
1190562 AGGTGCATGTTG
1 AGGTGAATGTTG
1190574 AACTAGATTA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (21 bp):
AGGTGAATGTTGCACCAAATA
Found at i:1190788 original size:91 final size:91
Alignment explanation
Indices: 1190633--1190817 Score: 361
Period size: 91 Copynumber: 2.0 Consensus size: 91
1190623 TGATCAGCTT
*
1190633 ATTTACTAAGTCATATATACGTTGAAGTATAACCAGGTAAGGTAGGTAGAATTTTAGTATGATTC
1 ATTTACTAAGTCATATATACGTTGAAGTATAACCAGGTAAGGTAGGTAAAATTTTAGTATGATTC
1190698 AATCAAGGCTGAAAACTTTTAAAAAA
66 AATCAAGGCTGAAAACTTTTAAAAAA
1190724 ATTTACTAAGTCATATATACGTTGAAGTATAACCAGGTAAGGTAGGTAAAATTTTAGTATGATTC
1 ATTTACTAAGTCATATATACGTTGAAGTATAACCAGGTAAGGTAGGTAAAATTTTAGTATGATTC
1190789 AATCAAGGCTGAAAACTTTTAAAAAA
66 AATCAAGGCTGAAAACTTTTAAAAAA
1190815 ATT
1 ATT
1190818 AATACCAAAG
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 93 1.00
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.32
Consensus pattern (91 bp):
ATTTACTAAGTCATATATACGTTGAAGTATAACCAGGTAAGGTAGGTAAAATTTTAGTATGATTC
AATCAAGGCTGAAAACTTTTAAAAAA
Found at i:1208941 original size:11 final size:11
Alignment explanation
Indices: 1208912--1208941 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
1208902 TTCATATTCT
1208912 TAAATTTTAAA
1 TAAATTTTAAA
1208923 TGAAATTTTAAA
1 T-AAATTTTAAA
1208935 TAAATTT
1 TAAATTT
1208942 ATTAATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (11 bp):
TAAATTTTAAA
Found at i:1230961 original size:33 final size:34
Alignment explanation
Indices: 1230907--1230971 Score: 105
Period size: 33 Copynumber: 1.9 Consensus size: 34
1230897 ACTCGTTTAA
**
1230907 TTTCAAAAGAAAGTATAAAACCAAAAATAATACC
1 TTTCAAAAGAAAAAATAAAACCAAAAATAATACC
1230941 TTTCAAAA-AAAAAATAAAACCAAAAATAATA
1 TTTCAAAAGAAAAAATAAAACCAAAAATAATA
1230972 AGGTTTAAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 21 0.72
34 8 0.28
ACGTcount: A:0.65, C:0.12, G:0.03, T:0.20
Consensus pattern (34 bp):
TTTCAAAAGAAAAAATAAAACCAAAAATAATACC
Found at i:1232890 original size:2 final size:2
Alignment explanation
Indices: 1232883--1232907 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1232873 AACATTCATT
1232883 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1232908 TATTTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1233833 original size:15 final size:16
Alignment explanation
Indices: 1233797--1233857 Score: 51
Period size: 15 Copynumber: 4.0 Consensus size: 16
1233787 TTACAAAAAT
*
1233797 TATAACTTATAAAAT-
1 TATAACTTATAATATA
1233812 TATTAA-TTATAATATA
1 TA-TAACTTATAATATA
*
1233828 TATAA-TT-TACT-TA
1 TATAACTTATAATATA
1233841 TATAAACTTATAATATA
1 TAT-AACTTATAATATA
1233858 AAAACTTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
13 5 0.14
14 5 0.14
15 17 0.46
16 8 0.22
17 2 0.05
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (16 bp):
TATAACTTATAATATA
Found at i:1233941 original size:357 final size:339
Alignment explanation
Indices: 1233156--1234171 Score: 941
Period size: 357 Copynumber: 3.0 Consensus size: 339
1233146 CAAAAATTAT
* * * * * * *
1233156 AACTTATAATATATATAC-TTAAAAAGAATTTTTGAGATTA-TATAGTTTTGGAATCTAACTATT
1 AACTTATAATATAAAAACATTAAAAA-AAGTTATGAGATTAGAATAGTTTT-GAAACT-AGTA-T
* * ** * ** * *
1233219 TTTTTTAATTTTATGCAATTAAAGACAAA-TCCATATGGTTAATTAAATTAATTCATTAAACTAT
62 TTTTTAAATTTCATATAATTAAGGACAAACT-CATATAATTAATTAAATTAATTAATAAAACTAT
* ** * * * **
1233283 GATTATTAATTAACTTGGAATGT-TTTTTA-ATATATACATTA-ATATATGGGGTTCATTTATAA
126 AATTATTAATTAACTTATAATGTCTTTTAATATATATACTTTATAGATATTTGGTTCATTTATAA
* * * * *
1233345 GAAATATAATTACTA-TATTATCTATAT-TCT--AATACCTTTAACATATATA-TATTAAATATA
191 AAAATATAATTACTATTA-TA-C-ATATCACTAAAATACTTTTAATATATATACT-TTTAATATA
* * * *
1233405 AAAATATTTA--TT-T-TTAT-T-TTAACATTATAAAAATTATAACTTGTAAAATTATTAATTAT
252 AAGATATTTACTTTCTATTTTGTGTTAATATTA-AAAAATTATAACTTATAAAATTATTAATTAT
* * *
1233464 AATATATACACCTTTATTTATATA
316 AATATATATACATTTACTTATATA
* * * *
1233488 AACTTATAATATACAAACATTAAGAAAAGTTGTGAGATTGGAATAGTTTTGAAACTTAGTTATTT
1 AACTTATAATATAAAAACATTAAAAAAAGTTATGAGATTAGAATAGTTTTGAAAC-TAG-TATTT
* * *
1233553 TTTAAAATTTCATGTAATTAAGGACAAACTCATATAATTAATTAAATTAATTTATAAAATTATAA
64 TTT-AAATTTCATATAATTAAGGACAAACTCATATAATTAATTAAATTAATTAATAAAACTATAA
* * * * * *
1233618 TTATTAATTACCTTGTAATGTCTTTTAGTATATTTACTTTATATATA-TTGGATTTATTTATAAA
128 TTATTAATTAACTTATAATGTCTTTTAATATATATACTTTATAGATATTTGG-TTCATTTATAAA
*
1233682 AAATATAATTACTATTATACATAT-AGTAAAATACTTTGAGTATGTGTGTATATATGTATATACA
192 AAATATAATTACTATTATACATATCACTAAAATAC--------T-T-T-TA-ATA--TATATAC-
1233746 TTTTAAATATAAAGATATTTACTTTCTATTTTGTGTTAATATTACAAAAATTATAACTTATAAAA
242 TTTT-AATATAAAGATATTTACTTTCTATTTTGTGTTAATATTA-AAAAATTATAACTTATAAAA
1233811 TTATTAATTATAATATATATA-ATTTACTTATATA
305 TTATTAATTATAATATATATACATTTACTTATATA
*
1233845 AACTTATAATATAAAAACTTAATTAGCTATAAAGAAGTTATGAGATTATAATAGTTTTG-AA-TA
1 AACTTATAATATAAAAAC---ATTA---A-AAA-AAGTTATGAGATTAGAATAGTTTTGAAACTA
* * *
1233908 -T-TTTTTT-AATTTCATATAATTAAGGATAAACTCATATAATTAATTTAATTAATTAATGAAAC
58 GTATTTTTTAAATTTCATATAATTAAGGACAAACTCATATAATTAATTAAATTAATTAATAAAAC
*
1233970 TATAATTATTAATTAACTTATAATGTCTTTTAATATCTATACTTTATAGATATTTGGTTCATTTA
123 TATAATTATTAATTAACTTATAATGTCTTTTAATATATATACTTTATAGATATTTGGTTCATTTA
*** *
1234035 TAGGGAATATAATTACTATTATATATATGCACTAAAATACTTTTAATATATATACTTTTAATATA
188 TAAAAAATATAATTACTATTATACATAT-CACTAAAATACTTTTAATATATATACTTTTAATATA
* *
1234100 AATATATTTACTTTTTATTTTGTGTTAATATT-AAAAATTATAACTTATAAAATTATTAATTATA
252 AAGATATTTACTTTCTATTTTGTGTTAATATTAAAAAATTATAACTTATAAAATTATTAATTATA
1234164 ATATATAT
317 ATATATAT
1234172 TACACACACT
Statistics
Matches: 570, Mismatches: 67, Indels: 85
0.79 0.09 0.12
Matches are distributed among these distances:
332 38 0.07
333 85 0.15
334 10 0.02
335 13 0.02
336 36 0.06
337 2 0.00
341 40 0.07
343 36 0.06
344 4 0.01
345 8 0.01
346 1 0.00
347 5 0.01
348 4 0.01
349 1 0.00
350 7 0.01
351 3 0.01
352 16 0.03
354 2 0.00
355 1 0.00
356 3 0.01
357 155 0.27
358 51 0.09
359 15 0.03
360 5 0.01
362 2 0.00
363 1 0.00
364 4 0.01
365 22 0.04
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (339 bp):
AACTTATAATATAAAAACATTAAAAAAAGTTATGAGATTAGAATAGTTTTGAAACTAGTATTTTT
TAAATTTCATATAATTAAGGACAAACTCATATAATTAATTAAATTAATTAATAAAACTATAATTA
TTAATTAACTTATAATGTCTTTTAATATATATACTTTATAGATATTTGGTTCATTTATAAAAAAT
ATAATTACTATTATACATATCACTAAAATACTTTTAATATATATACTTTTAATATAAAGATATTT
ACTTTCTATTTTGTGTTAATATTAAAAAATTATAACTTATAAAATTATTAATTATAATATATATA
CATTTACTTATATA
Found at i:1233991 original size:18 final size:19
Alignment explanation
Indices: 1233944--1233993 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
1233934 TAAACTCATA
1233944 TAATTAA-TT-TAATTAAT
1 TAATTAACTTATAATTAAT
*
1233961 TAATGAAAC-TATAATT-AT
1 TAAT-TAACTTATAATTAAT
1233979 TAATTAACTTATAAT
1 TAATTAACTTATAAT
1233994 GTCTTTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
17 7 0.26
18 15 0.56
19 5 0.19
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (19 bp):
TAATTAACTTATAATTAAT
Found at i:1234109 original size:15 final size:15
Alignment explanation
Indices: 1234069--1234103 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1234059 ATATGCACTA
1234069 AAATACTTTTAATAT
1 AAATACTTTTAATAT
*
1234084 ATATACTTTTAATAT
1 AAATACTTTTAATAT
1234099 AAATA
1 AAATA
1234104 TATTTACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (15 bp):
AAATACTTTTAATAT
Found at i:1234289 original size:19 final size:19
Alignment explanation
Indices: 1234245--1234297 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
1234235 TGTTTATTTA
* *
1234245 TAAATAATATAATTACTAT
1 TAAATAATATAATAACTAC
*
1234264 TATATAAGT-TAATAACTAC
1 TAAATAA-TATAATAACTAC
*
1234283 TAAATAATAAAATAA
1 TAAATAATATAATAA
1234298 TATTGATTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 1 0.04
19 25 0.93
20 1 0.04
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.36
Consensus pattern (19 bp):
TAAATAATATAATAACTAC
Found at i:1237179 original size:21 final size:20
Alignment explanation
Indices: 1237155--1237196 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
1237145 CTTTCTTTAT
1237155 ATAATAATTAATTTAAACTAA
1 ATAATAATTAATTTAAA-TAA
*
1237176 ATAATAATTTATTTAAATAA
1 ATAATAATTAATTTAAATAA
1237196 A
1 A
1237197 AAAATCCTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAATAATTAATTTAAATAA
Found at i:1248369 original size:19 final size:19
Alignment explanation
Indices: 1248345--1248391 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
1248335 AATATTATTT
* *
1248345 TATTATTTAGTAGTTATTA
1 TATTATTTAATAGTAATTA
*
1248364 -ACTTATATAATAGTAATTA
1 TA-TTATTTAATAGTAATTA
1248383 TATTATTTA
1 TATTATTTA
1248392 TAAATAAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
18 1 0.05
19 20 0.91
20 1 0.05
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.53
Consensus pattern (19 bp):
TATTATTTAATAGTAATTA
Found at i:1248557 original size:15 final size:15
Alignment explanation
Indices: 1248539--1248567 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1248529 TAAATATATT
1248539 TATATTAAAAGTATA
1 TATATTAAAAGTATA
1248554 TATATTAAAAGTAT
1 TATATTAAAAGTAT
1248568 TTTAGTGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (15 bp):
TATATTAAAAGTATA
Found at i:1248668 original size:18 final size:19
Alignment explanation
Indices: 1248645--1248694 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
1248635 ATTAAAAGAC
1248645 ATTATAAGTTAATTAA-TA
1 ATTATAAGTTAATTAATTA
*
1248663 ATTAT-AGTTTCATTAATTA
1 ATTATAAG-TTAATTAATTA
1248682 ATTA-AA-TTAATTA
1 ATTATAAGTTAATTA
1248695 TATGAGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
17 8 0.30
18 12 0.44
19 7 0.26
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (19 bp):
ATTATAAGTTAATTAATTA
Found at i:1255170 original size:67 final size:66
Alignment explanation
Indices: 1255058--1255193 Score: 195
Period size: 67 Copynumber: 2.0 Consensus size: 66
1255048 TCTTGCTGTT
* *
1255058 TAAATATACTCCATATCTTTCACTTTCATTCTTTTTTTTCCTTTCACTTTCATTTAACACAAAGA
1 TAAATATACTCCATATCTTTCACTCTCATTCTTTTTTTTCCTTTCACTCTCATTTAACACAAAGA
1255123 A
66 A
* *
1255124 TAAACTATACTCCATATCTTTCACTCTCACTT-TGTTTTTTT-CTTTCACTCTCATTTCATACAA
1 TAAA-TATACTCCATATCTTTCACTCTCA-TTCT-TTTTTTTCCTTTCACTCTCATTTAACACAA
1255187 AGAA
63 AGAA
1255191 TAA
1 TAA
1255194 TTCGACATAA
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
66 4 0.06
67 50 0.79
68 9 0.14
ACGTcount: A:0.29, C:0.24, G:0.02, T:0.46
Consensus pattern (66 bp):
TAAATATACTCCATATCTTTCACTCTCATTCTTTTTTTTCCTTTCACTCTCATTTAACACAAAGA
A
Found at i:1270301 original size:18 final size:18
Alignment explanation
Indices: 1270263--1270300 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1270253 GAGTTATTTT
*
1270263 TCTCAAAAAGATCCTCTC
1 TCTCAAAAAGATACTCTC
1270281 TCTCAAAAA-ATACTC-C
1 TCTCAAAAAGATACTCTC
1270297 TCTC
1 TCTC
1270301 TTTCTCCCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 5 0.26
18 9 0.47
ACGTcount: A:0.34, C:0.34, G:0.03, T:0.29
Consensus pattern (18 bp):
TCTCAAAAAGATACTCTC
Found at i:1271499 original size:28 final size:28
Alignment explanation
Indices: 1271459--1271519 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
1271449 CCCATCCACT
*
1271459 CAAATATTTGATGTACTCTTCAAAGTCA
1 CAAATATTTGATGTACTCCTCAAAGTCA
1271487 CAAATATTTGATGTACTCCTCAAAGTCA
1 CAAATATTTGATGTACTCCTCAAAGTCA
1271515 CAAAT
1 CAAAT
1271520 CATCCATAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.33
Consensus pattern (28 bp):
CAAATATTTGATGTACTCCTCAAAGTCA
Found at i:1280591 original size:23 final size:24
Alignment explanation
Indices: 1280564--1280613 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 24
1280554 TCTCTACTCA
1280564 AACAAACACAATTGTCTATTTTT-
1 AACAAACACAATTGTCTATTTTTC
* * *
1280587 AAC-AATATAATTGTTTATTTTTC
1 AACAAACACAATTGTCTATTTTTC
1280610 AACA
1 AACA
1280614 CAGGTAACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.40, C:0.14, G:0.04, T:0.42
Consensus pattern (24 bp):
AACAAACACAATTGTCTATTTTTC
Found at i:1280659 original size:24 final size:24
Alignment explanation
Indices: 1280580--1280659 Score: 67
Period size: 23 Copynumber: 3.5 Consensus size: 24
1280570 CACAATTGTC
* *
1280580 TATTTTT-AAC-AATATAATTGTT
1 TATTTTTCAACAAAAATAATTATT
* ** * *
1280602 TATTTTTCAACACAGGTAACTATC
1 TATTTTTCAACAAAAATAATTATT
*
1280626 T-GTTTTCAACAAAAATAATTATT
1 TATTTTTCAACAAAAATAATTATT
1280649 TATTTTTCAAC
1 TATTTTTCAAC
1280660 CTAATTATTT
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
22 7 0.17
23 20 0.48
24 15 0.36
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.46
Consensus pattern (24 bp):
TATTTTTCAACAAAAATAATTATT
Found at i:1286943 original size:15 final size:15
Alignment explanation
Indices: 1286923--1286959 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
1286913 ATGAACTCAC
1286923 ATGCATCGATATGCT
1 ATGCATCGATATGCT
1286938 ATGCATCGATATGCT
1 ATGCATCGATATGCT
1286953 ATGCATC
1 ATGCATC
1286960 ATGCAACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (15 bp):
ATGCATCGATATGCT
Found at i:1290073 original size:17 final size:17
Alignment explanation
Indices: 1290051--1290107 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 17
1290041 CCGGCGCCGC
1290051 GGCGCGGGCGCGCGCGG
1 GGCGCGGGCGCGCGCGG
1290068 GGCGC-GGCG-GC-CGG
1 GGCGCGGGCGCGCGCGG
*
1290082 CGG-GCGGCCGCGCCGCGGG
1 -GGCGCGGGCGCG-CGC-GG
1290101 GGCGCGG
1 GGCGCGG
1290108 CGGACGCTGC
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
14 5 0.16
15 7 0.22
16 5 0.16
17 6 0.19
18 3 0.09
19 6 0.19
ACGTcount: A:0.00, C:0.37, G:0.63, T:0.00
Consensus pattern (17 bp):
GGCGCGGGCGCGCGCGG
Found at i:1290108 original size:33 final size:31
Alignment explanation
Indices: 1290042--1290110 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 31
1290032 CGCCCCCCCC
*
1290042 CGGC-GCCGCGGCGCGGGCGCGCGCGGGGCG
1 CGGCGGCCGCGGCGCGGCCGCGCGCGGGGCG
1290072 CGGCGGCCGGCGG-GCGGCCGCGCCGCGGGGGCG
1 CGGCGGCC-GCGGCGCGGCCGCG-CGC-GGGGCG
1290105 CGGCGG
1 CGGCGG
1290111 ACGCTGCGGC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
30 4 0.12
31 11 0.32
32 7 0.21
33 12 0.35
ACGTcount: A:0.00, C:0.39, G:0.61, T:0.00
Consensus pattern (31 bp):
CGGCGGCCGCGGCGCGGCCGCGCGCGGGGCG
Found at i:1297539 original size:29 final size:29
Alignment explanation
Indices: 1297507--1297570 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
1297497 TCTCTAAATT
1297507 ATTTTAAAAAATTTAAATAAACTTTTATA
1 ATTTTAAAAAATTTAAATAAACTTTTATA
** * *
1297536 ATTTTATTATATTTAAATAAATTTTTATA
1 ATTTTAAAAAATTTAAATAAACTTTTATA
*
1297565 TTTTTA
1 ATTTTA
1297571 TTTTAAACTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (29 bp):
ATTTTAAAAAATTTAAATAAACTTTTATA
Found at i:1297571 original size:29 final size:30
Alignment explanation
Indices: 1297519--1297654 Score: 148
Period size: 30 Copynumber: 4.5 Consensus size: 30
1297509 TTTAAAAAAT
* * * *
1297519 TTAAATAAACTTTTATAATTTTATTAT-AT
1 TTAAATAAATTTTTATATTTTTATTTTAAA
1297548 TTAAATAAATTTTTATATTTTTATTTTAAA
1 TTAAATAAATTTTTATATTTTTATTTTAAA
* * *
1297578 CTAAATAAATATTTATATTCTTATTTTAAA
1 TTAAATAAATTTTTATATTTTTATTTTAAA
* * * *
1297608 CTAAATAATTTTTTTTATATTTTTATTTTGAG
1 TTAAATAA--ATTTTTATATTTTTATTTTAAA
1297640 TTAAATAAATTTTTA
1 TTAAATAAATTTTTA
1297655 CAAATAATGA
Statistics
Matches: 90, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
29 24 0.27
30 42 0.47
32 24 0.27
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (30 bp):
TTAAATAAATTTTTATATTTTTATTTTAAA
Found at i:1298543 original size:25 final size:24
Alignment explanation
Indices: 1298496--1298543 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
1298486 AAAATAAATA
* *
1298496 TTTTTAAATTTATAAATAGTTTAT
1 TTTTTAAATTTATAAAAAATTTAT
1298520 TTTTTAATATTTATAAAAAATTTA
1 TTTTTAA-ATTTATAAAAAATTTA
1298544 AATTATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
TTTTTAAATTTATAAAAAATTTAT
Found at i:1304824 original size:25 final size:25
Alignment explanation
Indices: 1304790--1304846 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
1304780 TTTGAAGATT
*
1304790 GAAGAGATAAAAACATATTGGTAGA
1 GAAGAGATAAAAACATATTGGTAAA
1304815 GAAGAGATAAAAACATATTGGTAAA
1 GAAGAGATAAAAACATATTGGTAAA
1304840 GAAGAGA
1 GAAGAGA
1304847 AAAGGGTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.54, C:0.04, G:0.25, T:0.18
Consensus pattern (25 bp):
GAAGAGATAAAAACATATTGGTAAA
Found at i:1314294 original size:19 final size:19
Alignment explanation
Indices: 1314254--1314295 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1314244 TGAGAGTTTG
*
1314254 TCAAAAGCAACTTTTGAAC
1 TCAAAAGCAACTTTTCAAC
*
1314273 TCAAAAGCTAC-TTTCAACC
1 TCAAAAGCAACTTTTCAA-C
1314292 TCAA
1 TCAA
1314296 TGCCAAACGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.40, C:0.26, G:0.07, T:0.26
Consensus pattern (19 bp):
TCAAAAGCAACTTTTCAAC
Found at i:1345228 original size:3 final size:3
Alignment explanation
Indices: 1345220--1345254 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1345210 ATAGGTAATA
1345220 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1345255 GAGTTAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:1346337 original size:36 final size:35
Alignment explanation
Indices: 1346290--1346403 Score: 106
Period size: 35 Copynumber: 3.2 Consensus size: 35
1346280 TTTTTTATTT
* * *
1346290 TTATTTTTATTTTTAAAA-GTGTTGAGATAAAATTGA
1 TTATTTTTA-TTTTAAAATATGATAAGAT-AAATTGA
*
1346326 TTATTTTTATTTTAAAATATGATAAGATTAATTGA
1 TTATTTTTATTTTAAAATATGATAAGATAAATTGA
** * *
1346361 TTATTTTT-TTAAAAAATTTGATAAGATACGATTGA
1 TTATTTTTATTTTAAAATATGATAAGATA-AATTGA
*
1346396 TTTTTTTT
1 TTATTTTT
1346404 TTAAAGTGAT
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
34 16 0.24
35 34 0.52
36 16 0.24
ACGTcount: A:0.36, C:0.01, G:0.11, T:0.53
Consensus pattern (35 bp):
TTATTTTTATTTTAAAATATGATAAGATAAATTGA
Found at i:1346359 original size:35 final size:34
Alignment explanation
Indices: 1346320--1346408 Score: 108
Period size: 35 Copynumber: 2.6 Consensus size: 34
1346310 GTTGAGATAA
**
1346320 AATTGATTATTTTTATTTTAAAATATGATAAGATT
1 AATTGATTATTTTT-TTAAAAAATATGATAAGATT
*
1346355 AATTGATTATTTTTTTAAAAAATTTGATAAGA-T
1 AATTGATTATTTTTTTAAAAAATATGATAAGATT
*
1346388 ACGATTGATTTTTTTTTTAAA
1 A--ATTGATTATTTTTTTAAA
1346409 GTGATAACCT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
33 2 0.04
34 15 0.31
35 31 0.65
ACGTcount: A:0.38, C:0.01, G:0.09, T:0.52
Consensus pattern (34 bp):
AATTGATTATTTTTTTAAAAAATATGATAAGATT
Found at i:1350605 original size:28 final size:27
Alignment explanation
Indices: 1350565--1350773 Score: 124
Period size: 28 Copynumber: 7.6 Consensus size: 27
1350555 TATAATGACG
* *
1350565 TGTAATAATTAAATTTTTCAATATGTCA
1 TGTAACAACTAAATTTTTCAATATG-CA
* *
1350593 TATAACAACTAAATTTTTTACATGATG--
1 TGTAACAACTAAATTTTTCA-AT-ATGCA
* * * * *
1350620 TGTAATAATTATATTTTTTAATATAACA
1 TGTAACAACTAAATTTTTCAATAT-GCA
* **
1350648 TATATTAACTAAA--TTTCAATATAG-A
1 TGTAACAACTAAATTTTTCAATAT-GCA
* * *
1350673 GTCTAACAACCACATTTTTCAATATAGCA
1 -TGTAACAACTAAATTTTTCAATAT-GCA
* * *
1350702 TGTAATAACTAAATTTTT-AATATAACG
1 TGTAACAACTAAATTTTTCAATAT-GCA
*
1350729 TGTAACAACTAAATTTTTCAACATGGCA
1 TGTAACAACTAAATTTTTCAATAT-GCA
1350757 TGTAACAACTAAATTTT
1 TGTAACAACTAAATTTT
1350774 AAACATGATG
Statistics
Matches: 140, Mismatches: 31, Indels: 20
0.73 0.16 0.10
Matches are distributed among these distances:
25 3 0.02
26 19 0.14
27 40 0.29
28 72 0.51
29 3 0.02
30 3 0.02
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (27 bp):
TGTAACAACTAAATTTTTCAATATGCA
Found at i:1350623 original size:55 final size:55
Alignment explanation
Indices: 1350551--1350828 Score: 233
Period size: 55 Copynumber: 5.1 Consensus size: 55
1350541 TGCAATAATT
* *
1350551 TTTTTATA-ATGACGTGTAATAATTAAATTTTTCAATATGTCATATAACAACTAAA
1 TTTTTA-ACATGACGTGTAACAATTAAATTTTTCAATATGACATATAACAACTAAA
* * * * * * **
1350606 TTTTTTACATGATGTGTAATAATTATATTTTTTAATATAACATATATTAACTAAA
1 TTTTTAACATGACGTGTAACAATTAAATTTTTCAATATGACATATAACAACTAAA
* * * ** * * *
1350661 -TTTCAATATAGA-GTCTAACAACCACATTTTTCAATAT-AGCATGTAATAACTAAA
1 TTTTTAACAT-GACGTGTAACAATTAAATTTTTCAATATGA-CATATAACAACTAAA
* * * * * *
1350715 TTTTTAATATAACGTGTAACAACTAAATTTTTCAACATGGCATGTAACAACTAAA
1 TTTTTAACATGACGTGTAACAATTAAATTTTTCAATATGACATATAACAACTAAA
* * * *
1350770 TTTTAAACATGATGTGTAACAATTAAATTTTTAAAATATGACATATAAC-ACTACA
1 TTTTTAACATGACGTGTAACAATTAAATTTTT-CAATATGACATATAACAACTAAA
1350825 TTTT
1 TTTT
1350829 CCAAAGCTGT
Statistics
Matches: 179, Mismatches: 37, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
53 1 0.01
54 40 0.22
55 126 0.70
56 12 0.07
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (55 bp):
TTTTTAACATGACGTGTAACAATTAAATTTTTCAATATGACATATAACAACTAAA
Found at i:1353328 original size:19 final size:18
Alignment explanation
Indices: 1353304--1353344 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
1353294 ATGACTCTTT
*
1353304 TTTTATTTTTTTAATTTAA
1 TTTTATTTGTTTAATTT-A
*
1353323 TTTTATTTGTTTACTTTA
1 TTTTATTTGTTTAATTTA
1353341 TTTT
1 TTTT
1353345 CAACAAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTTATTTGTTTAATTTA
Found at i:1353979 original size:2 final size:2
Alignment explanation
Indices: 1353972--1353999 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1353962 TGTGGAACGG
1353972 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1354000 CTCAGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1358650 original size:14 final size:14
Alignment explanation
Indices: 1358633--1358659 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1358623 ATTTAAAATC
1358633 AATAATTATAACAA
1 AATAATTATAACAA
1358647 AATAATTATAACA
1 AATAATTATAACA
1358660 TCAAATATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (14 bp):
AATAATTATAACAA
Found at i:1358712 original size:25 final size:26
Alignment explanation
Indices: 1358664--1358712 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
1358654 ATAACATCAA
*
1358664 ATATAATAAAATTTAACATAAATAAC
1 ATATAATAAAATTCAACATAAATAAC
* *
1358690 ATAT-ATAAAATTCATCATTAATA
1 ATATAATAAAATTCAACATAAATA
1358713 TTAAACGTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (26 bp):
ATATAATAAAATTCAACATAAATAAC
Found at i:1359907 original size:74 final size:74
Alignment explanation
Indices: 1359781--1359930 Score: 264
Period size: 74 Copynumber: 2.0 Consensus size: 74
1359771 TATAGTGCAA
* * * *
1359781 GAACAGACGTGGGTGGTACGCAATGTCGATTAACCTTCCTCTTTTGCGTCTGTGTTCATCTTATC
1 GAACAGACGTGAGTGGTACGCAATGTCAATTAACCTTCCCCTTTTGCATCTGTGTTCATCTTATC
1359846 TTATTTGAG
66 TTATTTGAG
1359855 GAACAGACGTGAGTGGTACGCAATGTCAATTAACCTTCCCCTTTTGCATCTGTGTTCATCTTATC
1 GAACAGACGTGAGTGGTACGCAATGTCAATTAACCTTCCCCTTTTGCATCTGTGTTCATCTTATC
1359920 TTATTTGAG
66 TTATTTGAG
1359929 GA
1 GA
1359931 TCACATTTTA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (74 bp):
GAACAGACGTGAGTGGTACGCAATGTCAATTAACCTTCCCCTTTTGCATCTGTGTTCATCTTATC
TTATTTGAG
Found at i:1364588 original size:43 final size:43
Alignment explanation
Indices: 1364522--1364615 Score: 179
Period size: 43 Copynumber: 2.2 Consensus size: 43
1364512 NNNNNNNNNN
*
1364522 AGAGCGGACAAAACCATAGTCAAAGTTGTGGTTTGATCAGTGC
1 AGAGTGGACAAAACCATAGTCAAAGTTGTGGTTTGATCAGTGC
1364565 AGAGTGGACAAAACCATAGTCAAAGTTGTGGTTTGATCAGTGC
1 AGAGTGGACAAAACCATAGTCAAAGTTGTGGTTTGATCAGTGC
1364608 AGAGTGGA
1 AGAGTGGA
1364616 AAACCTATAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.23
Consensus pattern (43 bp):
AGAGTGGACAAAACCATAGTCAAAGTTGTGGTTTGATCAGTGC
Found at i:1368121 original size:14 final size:14
Alignment explanation
Indices: 1368104--1368141 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
1368094 GCACGATGGT
*
1368104 TTGCTTCAGGGGAG
1 TTGCCTCAGGGGAG
1368118 TTGCCTCAGGGGAG
1 TTGCCTCAGGGGAG
1368132 TTGCCTCAGG
1 TTGCCTCAGG
1368142 CGAAGGAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.13, C:0.21, G:0.39, T:0.26
Consensus pattern (14 bp):
TTGCCTCAGGGGAG
Found at i:1370324 original size:15 final size:15
Alignment explanation
Indices: 1370291--1370324 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1370281 TATTTTGTAT
*
1370291 AAAATATGATTATTG
1 AAAATATGATTATTA
*
1370306 AAAATGTGATTATTA
1 AAAATATGATTATTA
1370321 AAAA
1 AAAA
1370325 ATAATTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (15 bp):
AAAATATGATTATTA
Found at i:1370961 original size:8 final size:8
Alignment explanation
Indices: 1370948--1370976 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1370938 CCACTTTCCC
1370948 TTTTTTCT
1 TTTTTTCT
1370956 TTTTTTCT
1 TTTTTTCT
1370964 TTTTTT-T
1 TTTTTTCT
1370971 TTTTTT
1 TTTTTT
1370977 ACACCTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (8 bp):
TTTTTTCT
Found at i:1370976 original size:15 final size:15
Alignment explanation
Indices: 1370947--1370975 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1370937 TCCACTTTCC
1370947 CTTTTTTCTTTTTTT
1 CTTTTTTCTTTTTTT
1370962 CTTTTTT-TTTTTTT
1 CTTTTTTCTTTTTTT
1370976 TACACCTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
CTTTTTTCTTTTTTT
Found at i:1387046 original size:141 final size:141
Alignment explanation
Indices: 1386792--1387074 Score: 548
Period size: 141 Copynumber: 2.0 Consensus size: 141
1386782 AACAACTTTG
1386792 AAATTCTGAAAGAAATGCATGTCAGAACTTTATATAAATTTGAGGTAAAAATTGTATCTAATAAC
1 AAATTCTGAAAGAAATGCATGTCAGAACTTTATATAAATTTGAGGTAAAAATTGTATCTAATAAC
*
1386857 TTCCATCAACATTTACTTCTATCACCCCACCTCCTCCTGTGTCTTTAGAGAATAAAGCTCAAGGC
66 TTCCATCAACATTTACTTCTATCACCCCACCTCCTCCTGTGTCTTTAGAGAATAAAACTCAAGGC
1386922 TCATATGCACA
131 TCATATGCACA
1386933 AAATTCTGAAAGAAATGCATGTCAGAACTTTATATAAATTTGAGGTAAAAATTGTATCTAATAAC
1 AAATTCTGAAAGAAATGCATGTCAGAACTTTATATAAATTTGAGGTAAAAATTGTATCTAATAAC
*
1386998 TTCCATCAACATTTACTTCTATCACCCCACCTCCTCCTGTGTCTTTAGAGAATAAAACTTAAGGC
66 TTCCATCAACATTTACTTCTATCACCCCACCTCCTCCTGTGTCTTTAGAGAATAAAACTCAAGGC
1387063 TCATATGCACA
131 TCATATGCACA
1387074 A
1 A
1387075 TGATTTCAAG
Statistics
Matches: 140, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
141 140 1.00
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (141 bp):
AAATTCTGAAAGAAATGCATGTCAGAACTTTATATAAATTTGAGGTAAAAATTGTATCTAATAAC
TTCCATCAACATTTACTTCTATCACCCCACCTCCTCCTGTGTCTTTAGAGAATAAAACTCAAGGC
TCATATGCACA
Found at i:1395667 original size:21 final size:23
Alignment explanation
Indices: 1395623--1395670 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
1395613 CAATATTGAT
* *
1395623 ATTTTACTAATTATAATTAATTA
1 ATTTTAATAATTATAATAAATTA
1395646 ATTTTAATAA-TAT-ATAAATTA
1 ATTTTAATAATTATAATAAATTA
1395667 ATTT
1 ATTT
1395671 GATTTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
22 3 0.13
23 9 0.39
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTTTAATAATTATAATAAATTA
Found at i:1415777 original size:2 final size:2
Alignment explanation
Indices: 1415770--1415810 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1415760 ATTAAAGAGT
*
1415770 TC TC TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1415811 AGAGAGCTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:1420353 original size:22 final size:21
Alignment explanation
Indices: 1420288--1420353 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 21
1420278 TTGCATGCAA
1420288 ATTATTGAAATTTTAGATACTT
1 ATTATTGAAA-TTTAGATACTT
* *
1420310 A-TATTGGAATATTATA-AC-T
1 ATTATTGAAAT-TTAGATACTT
1420329 ATTATTGAAATTTCAGATACTT
1 ATTATTGAAATTT-AGATACTT
1420351 ATT
1 ATT
1420354 TAATTTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
19 4 0.11
20 13 0.37
21 13 0.37
22 5 0.14
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (21 bp):
ATTATTGAAATTTAGATACTT
Found at i:1420388 original size:18 final size:17
Alignment explanation
Indices: 1420356--1420389 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1420346 TACTTATTTA
1420356 ATTTTTTAAATATATAT
1 ATTTTTTAAATATATAT
*
1420373 ATTTTTTCAATA-ATAT
1 ATTTTTTAAATATATAT
1420389 A
1 A
1420390 CCTATGCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTTTAAATATATAT
Found at i:1425288 original size:19 final size:19
Alignment explanation
Indices: 1425264--1425302 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1425254 ATCGAAACTC
1425264 ATTGTCATGCATATAGAAA
1 ATTGTCATGCATATAGAAA
1425283 ATTGTCATGCATATAGAAA
1 ATTGTCATGCATATAGAAA
1425302 A
1 A
1425303 ACAGTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (19 bp):
ATTGTCATGCATATAGAAA
Found at i:1426942 original size:7 final size:7
Alignment explanation
Indices: 1426925--1426959 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
1426915 ACCATGATTT
1426925 CCATCAGG
1 CCAT-AGG
1426933 CCATAGG
1 CCATAGG
1426940 CCATAGG
1 CCATAGG
1426947 CCATAGG
1 CCATAGG
1426954 CCATAG
1 CCATAG
1426960 TTTATCATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 23 0.85
8 4 0.15
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (7 bp):
CCATAGG
Found at i:1435502 original size:44 final size:44
Alignment explanation
Indices: 1435439--1435536 Score: 142
Period size: 44 Copynumber: 2.2 Consensus size: 44
1435429 TTACAAGTTG
* ** *
1435439 TTGCAACAGTAGTTCAAGATATTGAAGTTATCTCCTTTTCCTTT
1 TTGCAACAATAGTTCAAGATACCGAAGTTATCTACTTTTCCTTT
* *
1435483 TTGCAACAATAGTTTAAGATACCGAAGTTATTTACTTTTCCTTT
1 TTGCAACAATAGTTCAAGATACCGAAGTTATCTACTTTTCCTTT
1435527 TTGCAACAAT
1 TTGCAACAAT
1435537 GGTGCCCAGT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (44 bp):
TTGCAACAATAGTTCAAGATACCGAAGTTATCTACTTTTCCTTT
Found at i:1438619 original size:17 final size:17
Alignment explanation
Indices: 1438597--1438630 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1438587 TTCATCACCT
1438597 AACCACAAAAGTGTGTA
1 AACCACAAAAGTGTGTA
1438614 AACCACAAAAGTGTGTA
1 AACCACAAAAGTGTGTA
1438631 CAAAGCAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (17 bp):
AACCACAAAAGTGTGTA
Found at i:1440566 original size:13 final size:14
Alignment explanation
Indices: 1440548--1440579 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
1440538 ACAAGCTGGG
1440548 AATAAAAAG-TGGA
1 AATAAAAAGATGGA
1440561 AATAAAAAGATGGA
1 AATAAAAAGATGGA
1440575 AATAA
1 AATAA
1440580 GTCACAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.16
Consensus pattern (14 bp):
AATAAAAAGATGGA
Found at i:1441013 original size:16 final size:17
Alignment explanation
Indices: 1440986--1441025 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
1440976 ACCTAAACAA
1440986 GTGTTGTTGAC-TTTTTT
1 GTGTT-TTGACTTTTTTT
1441003 GTGTTTTGACTTTTTTT
1 GTGTTTTGACTTTTTTT
1441020 GTGTTT
1 GTGTTT
1441026 ATAAGTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.05, C:0.05, G:0.23, T:0.68
Consensus pattern (17 bp):
GTGTTTTGACTTTTTTT
Found at i:1481253 original size:40 final size:39
Alignment explanation
Indices: 1481198--1481276 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 39
1481188 ACGTGAGTCA
1481198 GACCTCTCGTTCTTGTCCGATGTGGAATAGAAGCACTTTT
1 GACCTCTCGTTCTTGTCCGATGTGGAATAGAA-CACTTTT
*
1481238 GACCTCTCGTTCTTGTCCGATGTGGGATAGAACACTTTT
1 GACCTCTCGTTCTTGTCCGATGTGGAATAGAACACTTTT
1481277 CCACCTAGGA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 7 0.18
40 31 0.82
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (39 bp):
GACCTCTCGTTCTTGTCCGATGTGGAATAGAACACTTTT
Found at i:1500772 original size:22 final size:22
Alignment explanation
Indices: 1500745--1500786 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1500735 TTTCGCAACT
*
1500745 TTTTAAGACAGTAATGAAAACC
1 TTTTAAGACAGAAATGAAAACC
1500767 TTTTAAGACAGAAATGAAAA
1 TTTTAAGACAGAAATGAAAA
1500787 TTCAACTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (22 bp):
TTTTAAGACAGAAATGAAAACC
Found at i:1505328 original size:14 final size:14
Alignment explanation
Indices: 1505309--1505336 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1505299 TATGGAGGGT
1505309 CAACAAATTTTACC
1 CAACAAATTTTACC
1505323 CAACAAATTTTACC
1 CAACAAATTTTACC
1505337 AACGATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.29, G:0.00, T:0.29
Consensus pattern (14 bp):
CAACAAATTTTACC
Found at i:1508848 original size:2 final size:2
Alignment explanation
Indices: 1508837--1508892 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
1508827 TTGTGTGTAC
* *
1508837 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1508879 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1508893 GCAGTAAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1520194 original size:29 final size:29
Alignment explanation
Indices: 1520161--1520256 Score: 70
Period size: 31 Copynumber: 3.2 Consensus size: 29
1520151 GGAACAAACA
1520161 CTGCTTGATATCTCCAAAATGAGCACAAG
1 CTGCTTGATATCTCCAAAATGAGCACAAG
* * * * * *
1520190 CTGCTGCAGACATAT-GAAGAAGTG-GAACAAACA
1 CTGCT--TGATATCTCCAA-AA-TGAGCAC-AA-G
1520223 CTGCTTGATATCTCCAAAATGAGCACAAG
1 CTGCTTGATATCTCCAAAATGAGCACAAG
1520252 CTGCT
1 CTGCT
1520257 GCAGATGTTA
Statistics
Matches: 47, Mismatches: 12, Indels: 16
0.63 0.16 0.21
Matches are distributed among these distances:
29 10 0.21
30 6 0.13
31 20 0.43
32 6 0.13
33 5 0.11
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (29 bp):
CTGCTTGATATCTCCAAAATGAGCACAAG
Found at i:1520226 original size:62 final size:62
Alignment explanation
Indices: 1520129--1520261 Score: 257
Period size: 62 Copynumber: 2.1 Consensus size: 62
1520119 AGGGCGTGGT
*
1520129 TGCTGGAGACATATGAAGAAGTGGAACAAACACTGCTTGATATCTCCAAAATGAGCACAAGC
1 TGCTGCAGACATATGAAGAAGTGGAACAAACACTGCTTGATATCTCCAAAATGAGCACAAGC
1520191 TGCTGCAGACATATGAAGAAGTGGAACAAACACTGCTTGATATCTCCAAAATGAGCACAAGC
1 TGCTGCAGACATATGAAGAAGTGGAACAAACACTGCTTGATATCTCCAAAATGAGCACAAGC
1520253 TGCTGCAGA
1 TGCTGCAGA
1520262 TGTTAATGGC
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 70 1.00
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.20
Consensus pattern (62 bp):
TGCTGCAGACATATGAAGAAGTGGAACAAACACTGCTTGATATCTCCAAAATGAGCACAAGC
Found at i:1522884 original size:6 final size:6
Alignment explanation
Indices: 1522873--1522925 Score: 65
Period size: 6 Copynumber: 8.8 Consensus size: 6
1522863 ACACCTAGCA
*
1522873 GAGAGG GAGAGG GAGA-G GA-AGA GAGAGG GAGAGG GAGAGGAG GAGAGG
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGA-G-G GAGAGG
1522921 GAGAG
1 GAGAG
1522926 AGAGGAGAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 1 0.02
5 5 0.12
6 28 0.68
7 2 0.05
8 5 0.12
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:1522896 original size:14 final size:15
Alignment explanation
Indices: 1522879--1522939 Score: 81
Period size: 14 Copynumber: 4.1 Consensus size: 15
1522869 AGCAGAGAGG
*
1522879 GAGAG-GGAGAGGAA
1 GAGAGAGGAGAGGGA
1522893 GAGAGAGGGAGAGGGA
1 GAGAGA-GGAGAGGGA
1522909 GAG-GAGGAGAGGGA
1 GAGAGAGGAGAGGGA
*
1522923 GAGAGAGGAGAGAGA
1 GAGAGAGGAGAGGGA
1522938 GA
1 GA
1522940 ATCATAGAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
14 17 0.40
15 14 0.33
16 11 0.26
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (15 bp):
GAGAGAGGAGAGGGA
Found at i:1522899 original size:2 final size:2
Alignment explanation
Indices: 1522872--1522939 Score: 56
Period size: 2 Copynumber: 36.5 Consensus size: 2
1522862 AACACCTAGC
* * * *
1522872 AG AG AG GG AG AG GG AG AG -G A- AG AG AG AG GG AG AG GG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
1522912 -G AG -G AG AG GG AG AG AG AG -G AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1522940 ATCATAGAAG
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
1 5 0.10
2 46 0.90
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1522899 original size:22 final size:22
Alignment explanation
Indices: 1522872--1522939 Score: 99
Period size: 22 Copynumber: 3.2 Consensus size: 22
1522862 AACACCTAGC
1522872 AGAGAGGGAGAGGGAGAGGAAG
1 AGAGAGGGAGAGGGAGAGGAAG
1522894 AGAGAGGGAGAGGGAGAGG-AG
1 AGAGAGGGAGAGGGAGAGGAAG
1522915 -GAGAGGGAGA--GAGAGGAGAG
1 AGAGAGGGAGAGGGAGAGGA-AG
1522935 AGAGA
1 AGAGA
1522940 ATCATAGAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.14
20 12 0.28
21 6 0.14
22 19 0.44
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (22 bp):
AGAGAGGGAGAGGGAGAGGAAG
Found at i:1533565 original size:25 final size:25
Alignment explanation
Indices: 1533524--1533571 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1533514 GAATCCTGCT
* *
1533524 GGACTGGTGATTCGTTTTCTTCAAA
1 GGACTGGTCATTCGTTTTATTCAAA
*
1533549 GGACTGGTCATTTGTTTTATTCA
1 GGACTGGTCATTCGTTTTATTCA
1533572 CAGAAGAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.44
Consensus pattern (25 bp):
GGACTGGTCATTCGTTTTATTCAAA
Found at i:1550049 original size:35 final size:35
Alignment explanation
Indices: 1550001--1550067 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
1549991 TGTCACGGGC
1550001 CACAGTCCAGACCCACCAGGAGACCCAAGAGGTGA
1 CACAGTCCAGACCCACCAGGAGACCCAAGAGGTGA
* * *
1550036 CACAGTCCGGACCCGCCAGGAGGCCCAAGAGG
1 CACAGTCCAGACCCACCAGGAGACCCAAGAGG
1550068 GTGCCAGCCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.30, C:0.36, G:0.30, T:0.04
Consensus pattern (35 bp):
CACAGTCCAGACCCACCAGGAGACCCAAGAGGTGA
Found at i:1550161 original size:113 final size:113
Alignment explanation
Indices: 1549990--1550210 Score: 424
Period size: 113 Copynumber: 2.0 Consensus size: 113
1549980 ATTAGTCCTA
1549990 GTGTCACGGGCCACAGTCCAGACCCACCAGGAGACCCAAGAGGTGACACAGTCCGGACCCGCCAG
1 GTGTCACGGGCCACAGTCCAGACCCACCAGGAGACCCAAGAGGTGACACAGTCCGGACCCGCCAG
1550055 GAGGCCCAAGAGGGTGCCAGCCCACTAGACCCATGTAGGGGGGGCTGG
66 GAGGCCCAAGAGGGTGCCAGCCCACTAGACCCATGTAGGGGGGGCTGG
* *
1550103 GTGTCACGGGCCACAGTCCAGACCCACCAGGAGGCCCAAGAGGTGACACAGTCCGGACCCGTCAG
1 GTGTCACGGGCCACAGTCCAGACCCACCAGGAGACCCAAGAGGTGACACAGTCCGGACCCGCCAG
1550168 GAGGCCCAAGAGGGTGCCAGCCCACTAGACCCATGTAGGGGGG
66 GAGGCCCAAGAGGGTGCCAGCCCACTAGACCCATGTAGGGGGG
1550211 CTGTTGGAAA
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 106 1.00
ACGTcount: A:0.24, C:0.33, G:0.34, T:0.09
Consensus pattern (113 bp):
GTGTCACGGGCCACAGTCCAGACCCACCAGGAGACCCAAGAGGTGACACAGTCCGGACCCGCCAG
GAGGCCCAAGAGGGTGCCAGCCCACTAGACCCATGTAGGGGGGGCTGG
Found at i:1550162 original size:35 final size:35
Alignment explanation
Indices: 1550114--1550180 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
1550104 TGTCACGGGC
1550114 CACAGTCCAGACCCACCAGGAGGCCCAAGAGGTGA
1 CACAGTCCAGACCCACCAGGAGGCCCAAGAGGTGA
* **
1550149 CACAGTCCGGACCCGTCAGGAGGCCCAAGAGG
1 CACAGTCCAGACCCACCAGGAGGCCCAAGAGG
1550181 GTGCCAGCCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.28, C:0.34, G:0.31, T:0.06
Consensus pattern (35 bp):
CACAGTCCAGACCCACCAGGAGGCCCAAGAGGTGA
Found at i:1550347 original size:43 final size:44
Alignment explanation
Indices: 1550267--1550365 Score: 164
Period size: 43 Copynumber: 2.3 Consensus size: 44
1550257 TCCCAAATGT
* *
1550267 TTTGGAGTGAAATCTTTTGGGGGGGAATACTTTGAATTGAAAAC
1 TTTGGAGAGAAATCTTTTGGGGGGGAATACTTTGAATTAAAAAC
1550311 TTTGGAGAGAAATCTTTT-GGGGGGAATACTTTGAATTAAAAAC
1 TTTGGAGAGAAATCTTTTGGGGGGGAATACTTTGAATTAAAAAC
*
1550354 TTTGGAGGGAAA
1 TTTGGAGAGAAA
1550366 AGTGGGTGGG
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 35 0.67
44 17 0.33
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.32
Consensus pattern (44 bp):
TTTGGAGAGAAATCTTTTGGGGGGGAATACTTTGAATTAAAAAC
Found at i:1558029 original size:2 final size:2
Alignment explanation
Indices: 1558022--1558055 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1558012 ATGTCAAAAC
*
1558022 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1558056 TTTTATAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1560856 original size:18 final size:18
Alignment explanation
Indices: 1560835--1560874 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1560825 GCAGGTTCTT
*
1560835 GTTCCGGTTCTGGTTCGG
1 GTTCCGGTTCTGGTTCAG
* *
1560853 GTTCGGGTTCTGTTTCAG
1 GTTCCGGTTCTGGTTCAG
1560871 GTTC
1 GTTC
1560875 TTGTTTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.03, C:0.20, G:0.35, T:0.42
Consensus pattern (18 bp):
GTTCCGGTTCTGGTTCAG
Found at i:1564341 original size:16 final size:17
Alignment explanation
Indices: 1564309--1564341 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1564299 CATGAAGCAG
1564309 CTTAATAAAATAAGAAA
1 CTTAATAAAATAAGAAA
*
1564326 CTTAATGAAA-AAGAAA
1 CTTAATAAAATAAGAAA
1564342 AAATTTCAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.64, C:0.06, G:0.09, T:0.21
Consensus pattern (17 bp):
CTTAATAAAATAAGAAA
Found at i:1571745 original size:3 final size:3
Alignment explanation
Indices: 1571732--1571767 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
1571722 CGGGCCGTTG
*
1571732 TTC TCTC TTC TTC TTC TTC TTC TTC TTC TTC CTC TT
1 TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1571768 GCGCGGCTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Done.