Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009636.1 Hibiscus syriacus cultivar Beakdansim tig00117040_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: 700957
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
File 3 of 4
Found at i:417419 original size:20 final size:20
Alignment explanation
Indices: 417375--417482 Score: 97
Period size: 19 Copynumber: 5.8 Consensus size: 20
417365 TGCAGAAGAG
*
417375 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
417396 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
*
417416 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
417435 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
417449 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
417468 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
417483 CGCAACGCGA
Statistics
Matches: 70, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
14 9 0.13
16 4 0.06
17 4 0.06
19 24 0.34
20 18 0.26
21 11 0.16
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:417452 original size:14 final size:14
Alignment explanation
Indices: 417433--417489 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
417423 GCGAAATGAA
417433 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
417447 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
417466 AATCGCAACGAGAG
1 AATCGCAACGAGAG
417480 AATCGCAACG
1 AATCGCAACG
417490 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:417458 original size:33 final size:33
Alignment explanation
Indices: 417387--417505 Score: 166
Period size: 33 Copynumber: 3.4 Consensus size: 33
417377 GCAACGAGAT
417387 AAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGCG
1 AAATGAAAATCGCAACGAGAG-A--A---TCGCAACGCG
417426 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
417459 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
417492 AAACCAAAATCGCA
1 AAATGAAAATCGCA
417506 TTGCGATTTT
Statistics
Matches: 78, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
33 55 0.71
36 1 0.01
38 1 0.01
39 21 0.27
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.10
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:417542 original size:14 final size:14
Alignment explanation
Indices: 417523--417612 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
417513 TTTTATTTCG
417523 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
417537 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
417556 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
417570 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
417589 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
417603 CGTTGCGATT
1 CGTTGCGATT
417613 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:417548 original size:33 final size:33
Alignment explanation
Indices: 417506--417620 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
417496 CAAAATCGCA
*
417506 TTGCGATTTTTATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
417539 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
417572 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
417605 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
417621 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:417561 original size:19 final size:19
Alignment explanation
Indices: 417501--417598 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
417491 GAAACCAAAA
* *
417501 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
417520 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
417534 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
417553 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
417567 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
417586 TCGCGTTGCGATT
1 TCGCGTTGCGATT
417599 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 5 0.08
19 32 0.52
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:419478 original size:93 final size:93
Alignment explanation
Indices: 419319--419694 Score: 727
Period size: 93 Copynumber: 4.1 Consensus size: 93
419309 TAGATTGCTT
*
419319 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
419384 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
419412 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
419477 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
419505 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
419570 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
419598 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTTTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
419663 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
419690 AGTAA
1 AGTAA
419695 TGCAATCCAT
Statistics
Matches: 281, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 6 0.02
93 275 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:419782 original size:19 final size:19
Alignment explanation
Indices: 419742--419870 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
419732 TAGTTTACTT
* *
419742 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
419762 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
419781 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
419800 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
419814 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
419833 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
419847 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
419866 TCGCA
1 TCGCA
419871 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:419821 original size:33 final size:32
Alignment explanation
Indices: 419778--419870 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
419768 CGCGAAACCA
**
419778 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
419810 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
419843 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
419871 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:419868 original size:52 final size:52
Alignment explanation
Indices: 419742--419870 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
419732 TAGTTTACTT
**
419742 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
419794 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
419847 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
419871 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:419888 original size:19 final size:19
Alignment explanation
Indices: 419866--420000 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
419856 GAAACCAAAA
*
419866 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
419885 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
419901 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
419918 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
419934 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
419951 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
419970 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
419990 TCGTGTTGCGA
1 TCGCGTTGCGA
420001 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:419907 original size:14 final size:14
Alignment explanation
Indices: 419888--419944 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
419878 TTTCATTTCG
419888 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
419902 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
419919 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
419935 CGTTGCGATT
1 CGTTGCGATT
419945 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:419913 original size:33 final size:33
Alignment explanation
Indices: 419871--419963 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
419861 CAAAATCGCA
*
419871 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
419904 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
419937 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
419964 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:421944 original size:14 final size:14
Alignment explanation
Indices: 421925--421960 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
421915 ATTGTTTAAT
421925 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
421939 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
421953 TGATTTGT
1 TGATTTGT
421961 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:422083 original size:19 final size:20
Alignment explanation
Indices: 422067--422116 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
422057 AAAAATGACT
422067 ATCGCAATGCG-AAATGAAA
1 ATCGCAATGCGAAAATGAAA
422086 ATCGCAATGCGAAAATGAAA
1 ATCGCAATGCGAAAATGAAA
422106 ATCGCAATGCG
1 ATCGCAATGCG
422117 TTTATAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGAAA
Found at i:422165 original size:33 final size:33
Alignment explanation
Indices: 422123--422418 Score: 192
Period size: 33 Copynumber: 8.5 Consensus size: 33
422113 TGCGTTTATA
422123 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
422156 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTGTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
422196 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
*
422227 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
*
422265 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
422305 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
422336 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* *
422369 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTC
*
422403 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
422419 GTAATTTCCG
Statistics
Matches: 212, Mismatches: 27, Indels: 48
0.74 0.09 0.17
Matches are distributed among these distances:
31 18 0.08
32 8 0.04
33 59 0.28
34 31 0.15
35 8 0.04
36 6 0.03
37 4 0.02
38 54 0.25
39 6 0.03
40 18 0.08
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:422169 original size:19 final size:19
Alignment explanation
Indices: 422145--422418 Score: 354
Period size: 19 Copynumber: 15.4 Consensus size: 19
422135 GATTCTCTCG
422145 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
422164 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
422183 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
422197 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
422216 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
422235 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
422254 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
422273 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
422292 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
422306 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
422325 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
422344 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
422358 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
422378 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
422392 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
422411 TTGCGATT
1 TTGCGATT
422419 GTAATTTCCG
Statistics
Matches: 226, Mismatches: 8, Indels: 42
0.82 0.03 0.15
Matches are distributed among these distances:
14 29 0.13
16 23 0.10
17 20 0.09
18 3 0.01
19 139 0.62
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:422180 original size:52 final size:52
Alignment explanation
Indices: 422123--422390 Score: 464
Period size: 52 Copynumber: 5.0 Consensus size: 52
422113 TGCGTTTATA
422123 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
422175 ATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
422227 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
422284 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
422336 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
422389 AT
1 AT
422391 GTTGGGATTT
Statistics
Matches: 207, Mismatches: 3, Indels: 11
0.94 0.01 0.05
Matches are distributed among these distances:
52 132 0.64
53 17 0.08
54 7 0.03
55 7 0.03
57 44 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:422274 original size:109 final size:102
Alignment explanation
Indices: 422145--422418 Score: 163
Period size: 109 Copynumber: 2.6 Consensus size: 102
422135 GATTCTCTCG
* *
422145 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TGTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTCATTTCGATTGCGATTTT
*
422207 CATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
61 CATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
422254 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TCTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTCATTTCGATTGCGATTTT
* * * * *
422316 CATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
61 CATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
* * *
422358 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCGTTGCGA-TTTCATTTCG-ATTGCGATT
422419 GTAATTTCCG
Statistics
Matches: 145, Mismatches: 10, Indels: 24
0.81 0.06 0.13
Matches are distributed among these distances:
100 5 0.03
102 12 0.08
103 11 0.08
104 20 0.14
105 19 0.13
107 2 0.01
109 76 0.52
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (102 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTCATTTCGATTGCGATTTTCATTT
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:424717 original size:12 final size:12
Alignment explanation
Indices: 424700--424724 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
424690 TCTTCGGGGA
424700 CTTTTTCTTCTT
1 CTTTTTCTTCTT
424712 CTTTTTCTTCTT
1 CTTTTTCTTCTT
424724 C
1 C
424725 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:424933 original size:24 final size:24
Alignment explanation
Indices: 424899--424945 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
424889 CTGAAACATC
424899 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
424923 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
424946 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:425656 original size:20 final size:20
Alignment explanation
Indices: 425628--425837 Score: 215
Period size: 20 Copynumber: 10.5 Consensus size: 20
425618 AGATTTCAGT
* * *
425628 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
425648 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
425668 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
425688 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
425708 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
425728 GTTGCGATATACGGAAACGC
1 GTTGCGATTTACGGATTCGC
* *
425748 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
425768 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
425788 ATTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
425808 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
425828 GTTGCGATTT
1 GTTGCGATTT
425838 TGGAAAATCG
Statistics
Matches: 164, Mismatches: 24, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
20 163 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:425854 original size:21 final size:20
Alignment explanation
Indices: 425804--425901 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
425794 ATTTATGTGT
* * * *
425804 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
425824 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
425845 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
425865 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
425886 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
425902 GACACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:425896 original size:41 final size:41
Alignment explanation
Indices: 425804--425901 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 41
425794 ATTTATGTGT
* * *
425804 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
425845 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
425886 TCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTG
425902 GACACTGATT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
40 2 0.04
41 42 0.91
42 2 0.04
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:426429 original size:18 final size:16
Alignment explanation
Indices: 426391--426432 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
426381 ATTATATGGA
426391 TATT-TTATTCATTTT
1 TATTATTATTCATTTT
*
426406 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TT-T
426424 TATTATTAT
1 TATTATTAT
426433 ATGTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 3 0.14
16 8 0.36
17 2 0.09
18 9 0.41
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (16 bp):
TATTATTATTCATTTT
Found at i:427572 original size:2 final size:2
Alignment explanation
Indices: 427565--427591 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
427555 CAATTAACTC
427565 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
427592 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:427596 original size:2 final size:2
Alignment explanation
Indices: 427591--427630 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
427581 ATATATATAT
427591 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
427631 TTAGAATCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:428432 original size:3 final size:3
Alignment explanation
Indices: 428424--428465 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
428414 TTATTTTTGC
428424 ATT ATT ATT ATT ATT ATT ATT ATTT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT AT
428466 CAAACGCCAC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:428825 original size:22 final size:23
Alignment explanation
Indices: 428800--428845 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
428790 AACATATGTA
428800 TTTGTAA-TTTTTTTTAATAATC
1 TTTGTAATTTTTTTTTAATAATC
428822 TTTGTAATTTTTTTTTAATAATC
1 TTTGTAATTTTTTTTTAATAATC
428845 T
1 T
428846 AAAGTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.65
Consensus pattern (23 bp):
TTTGTAATTTTTTTTTAATAATC
Found at i:428852 original size:24 final size:23
Alignment explanation
Indices: 428803--428854 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
428793 ATATGTATTT
**
428803 GTAA-TTTTTTTTAATAATCTTT
1 GTAATTTTTTTTTAATAATCTAA
428825 GTAATTTTTTTTTAATAATCTAAA
1 GTAATTTTTTTTTAATAATCT-AA
428849 GTAATT
1 GTAATT
428855 ATACGATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 4 0.15
23 16 0.62
24 6 0.23
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.58
Consensus pattern (23 bp):
GTAATTTTTTTTTAATAATCTAA
Found at i:429405 original size:2 final size:2
Alignment explanation
Indices: 429398--429433 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
429388 ATTAGAATTA
429398 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
429434 CACACACGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:436110 original size:81 final size:81
Alignment explanation
Indices: 435969--436129 Score: 225
Period size: 81 Copynumber: 2.0 Consensus size: 81
435959 CCAGTCTCCT
* *
435969 GTACAACCGGCTCGATAGCTTCTTGCTCTACACCTCTATGAGAGCTTGTCGATCCTCCATTTCGT
1 GTACAACCGGCTCGATAGCTTCCTGCTCTACACCTCTATGAGAGCTTGTCGATCCACCATTTCGT
436034 GTGCGAACCATTCTCG
66 GTGCGAACCATTCTCG
* * * * * *
436050 GTACAATCGGCTC-AGTAGCTTCCTGCTCTATACCTCTGTGAGAGCTTGTTGCTCCACCATTTTG
1 GTACAACCGGCTCGA-TAGCTTCCTGCTCTACACCTCTATGAGAGCTTGTCGATCCACCATTTCG
*
436114 TGTGCGGACCATTCTC
65 TGTGCGAACCATTCTC
436130 TATAACTCAC
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
80 1 0.01
81 69 0.99
ACGTcount: A:0.17, C:0.30, G:0.20, T:0.32
Consensus pattern (81 bp):
GTACAACCGGCTCGATAGCTTCCTGCTCTACACCTCTATGAGAGCTTGTCGATCCACCATTTCGT
GTGCGAACCATTCTCG
Found at i:436330 original size:55 final size:55
Alignment explanation
Indices: 436223--436375 Score: 146
Period size: 55 Copynumber: 2.8 Consensus size: 55
436213 TTGAATTAAC
* ** ** **
436223 GATTGAGCACCTTTGTGCTTCAACCGAGAGTTGACACCTCTGTGTAACTAAAAGT
1 GATTGAGCACCTATGTGCTTCAACCGAGAACTGACACCTCTGTACAACTAAAAAA
* * **
436278 GATTGAGCACCTATGTGCTTCAATCGAGAACTGATACCTCTGTACAGTTAAAAAA
1 GATTGAGCACCTATGTGCTTCAACCGAGAACTGACACCTCTGTACAACTAAAAAA
* * * * *
436333 GACTGAGAACCTCTGTGCTTCAGCC-AGGAGCTGACACCTCTGT
1 GATTGAGCACCTATGTGCTTCAACCGA-GAACTGACACCTCTGT
436376 GCTTCAGCCA
Statistics
Matches: 79, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
54 1 0.01
55 78 0.99
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.27
Consensus pattern (55 bp):
GATTGAGCACCTATGTGCTTCAACCGAGAACTGACACCTCTGTACAACTAAAAAA
Found at i:436376 original size:27 final size:27
Alignment explanation
Indices: 436341--436403 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
436331 AAGACTGAGA
436341 ACCTCTGTGCTTCAGCCAGGAGCTGAC
1 ACCTCTGTGCTTCAGCCAGGAGCTGAC
436368 ACCTCTGTGCTTCAGCCAGGAGCTGAC
1 ACCTCTGTGCTTCAGCCAGGAGCTGAC
436395 ACCTCTGTG
1 ACCTCTGTG
436404 TAGCTAAGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.17, C:0.33, G:0.25, T:0.24
Consensus pattern (27 bp):
ACCTCTGTGCTTCAGCCAGGAGCTGAC
Found at i:436481 original size:142 final size:137
Alignment explanation
Indices: 436230--436494 Score: 379
Period size: 142 Copynumber: 1.9 Consensus size: 137
436220 AACGATTGAG
* * * *
436230 CACCTTTGTGCTTCAACCGAGAGTTGACACCTCTGTGTAACTAAAAGTGATTGAGCACCTATGTG
1 CACCTCTGTGCTTCAACCGAGAGCTGACACCTCTGTGTAACTAAAACTAATTGAGCACCTATGTG
*
436295 CTTCAATCGAGAACTGATACCTCTGTACAGTTAAAAAAGACTGAGAACCTCTGTGCTTCAGCCAG
66 CTTCAATCGAGAACTGACACCTCTGTACAGTTAAAAAAGACTGAGAACCTCTGTGCTTCAGCCAG
436360 GAGCTGA
131 GAGCTGA
* * *
436367 CACCTCTGTGCTTCAGCC-AGGAGCTGACACCTCTGTGTAGCTAAGACTAATTGAGCACCTATGT
1 CACCTCTGTGCTTCAACCGA-GAGCTGACACCTCTGTGTAACTAAAACTAATTGAGCACC----T
* *
436431 GATGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAGACTGAGCACCTCTGTGCTT
61 -ATGTGCTTCAATCGAGAACTGACACCTCTGTACAGTTAAAAAAGACTGAGAACCTCTGTGCTT
436495 AAGTCTAAAA
Statistics
Matches: 112, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
136 1 0.01
137 50 0.45
141 1 0.01
142 60 0.54
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.26
Consensus pattern (137 bp):
CACCTCTGTGCTTCAACCGAGAGCTGACACCTCTGTGTAACTAAAACTAATTGAGCACCTATGTG
CTTCAATCGAGAACTGACACCTCTGTACAGTTAAAAAAGACTGAGAACCTCTGTGCTTCAGCCAG
GAGCTGA
Found at i:437961 original size:24 final size:24
Alignment explanation
Indices: 437909--437964 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 24
437899 TCTAAAAAAA
*
437909 TTAATTTT-TTTATATATTAAGTT
1 TTAATTTTATTTATATATGAAGTT
*
437932 TT-ATTTTATTT-TATATGAATTAT
1 TTAATTTTATTTATATATGAAGT-T
437955 TTAATTTTAT
1 TTAATTTTAT
437965 ACATTTGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 13 0.46
23 8 0.29
24 7 0.25
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (24 bp):
TTAATTTTATTTATATATGAAGTT
Found at i:442085 original size:16 final size:16
Alignment explanation
Indices: 442044--442085 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
442034 GTAGCTGGAC
*
442044 GAAACATTATTATGAT
1 GAAACATGATTATGAT
*
442060 GGAACATGATTATGAT
1 GAAACATGATTATGAT
*
442076 GAAACGTGAT
1 GAAACATGAT
442086 ATCTGCAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.31
Consensus pattern (16 bp):
GAAACATGATTATGAT
Found at i:443568 original size:19 final size:19
Alignment explanation
Indices: 443526--443570 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
443516 GAATAAGACG
443526 AGAAAAGATAGAAAAGAAA
1 AGAAAAGATAGAAAAGAAA
* * *
443545 GGAAAAGATAGAATATAAA
1 AGAAAAGATAGAAAAGAAA
443564 AGAAAAG
1 AGAAAAG
443571 GGAAAAAGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.69, C:0.00, G:0.22, T:0.09
Consensus pattern (19 bp):
AGAAAAGATAGAAAAGAAA
Found at i:448818 original size:81 final size:81
Alignment explanation
Indices: 448677--448836 Score: 223
Period size: 81 Copynumber: 2.0 Consensus size: 81
448667 CCAGTCTCCT
* *
448677 GTACAACCGGCTCGATAGCTTCTTGCTCTACACCTCTATGAGAGCTTGTCGATCCTCCATTTCGT
1 GTACAACCGGCTCGATAGCTTCCTGCTCTACACCTCTATGAGAGCTTGTCGATCCACCATTTCGT
448742 GTGCGAACCATTCTTG
66 GTGCGAACCATTCTTG
* * * * * *
448758 GTACAATCGGCTC-AGTAGCTTCCTGTTCTATACCTCTGTGAGAGCTTGTTGCTCCACCATTTCG
1 GTACAACCGGCTCGA-TAGCTTCCTGCTCTACACCTCTATGAGAGCTTGTCGATCCACCATTTCG
*
448822 TGTGCGGACCATTCT
65 TGTGCGAACCATTCT
448837 CTATAACTCA
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
80 1 0.01
81 68 0.99
ACGTcount: A:0.17, C:0.29, G:0.21, T:0.33
Consensus pattern (81 bp):
GTACAACCGGCTCGATAGCTTCCTGCTCTACACCTCTATGAGAGCTTGTCGATCCACCATTTCGT
GTGCGAACCATTCTTG
Found at i:448992 original size:55 final size:55
Alignment explanation
Indices: 448931--449170 Score: 241
Period size: 55 Copynumber: 4.4 Consensus size: 55
448921 TTGAATTAAC
* * * *
448931 GATTGAGCACCTTTGTGCTTCAACCGAGAGCTGACACCTCTGTGTAACTAAAAGT
1 GATTGAGCACCTATGTGCTTCAACCGAGAACTGACACCTCTGTGTAGCTAAAAAT
* * * *
448986 GATTGAGCACCTATGTGCTTCAATCGAGAACTGATACCTCTGTGCAGTTAAAAAAT
1 GATTGAGCACCTATGTGCTTCAACCGAGAACTGACACCTCTGTGTAGCT-AAAAAT
* * * * * * * *
449042 -ACTGAGAACCTCTATGCTTCAGCC-AGGAGCTGACACCTCTGTGTAGCTAAGACT
1 GATTGAGCACCTATGTGCTTCAACCGA-GAACTGACACCTCTGTGTAGCTAAAAAT
* * * * *
449096 AATTGAGCACCTATGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAA
1 GATTGAGCACCTATGTGCTTCAACCGAGAACTGACACCTCTGTGTAGCTAAAAAT
* *
449151 GACTGAGCACCTCTGTGCTT
1 GATTGAGCACCTATGTGCTT
449171 AAGTCTAAAA
Statistics
Matches: 146, Mismatches: 35, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
54 5 0.03
55 135 0.92
56 6 0.04
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.27
Consensus pattern (55 bp):
GATTGAGCACCTATGTGCTTCAACCGAGAACTGACACCTCTGTGTAGCTAAAAAT
Found at i:449108 original size:110 final size:110
Alignment explanation
Indices: 448958--449170 Score: 354
Period size: 110 Copynumber: 1.9 Consensus size: 110
448948 CTTCAACCGA
* * *
448958 GAGCTGACACCTCTGTGTAACTAAAAGTGATTGAGCACCTATGTGCTTCAATCGAGAACTGATAC
1 GAGCTGACACCTCTGTGTAACTAAAACTAATTGAGCACCTATGTGCTTCAATCGAGAACTGACAC
*
449023 CTCTGTGCAGTTAAAAAATACTGAGAACCTCTATGCTTCAGCCAG
66 CTCTGTGCAGTTAAAAAAGACTGAGAACCTCTATGCTTCAGCCAG
* *
449068 GAGCTGACACCTCTGTGTAGCTAAGACTAATTGAGCACCTATGTGCTTCAATCGAGAACTGACAC
1 GAGCTGACACCTCTGTGTAACTAAAACTAATTGAGCACCTATGTGCTTCAATCGAGAACTGACAC
* *
449133 CTCTGTGCAGTTAAAAAAGACTGAGCACCTCTGTGCTT
66 CTCTGTGCAGTTAAAAAAGACTGAGAACCTCTATGCTT
449171 AAGTCTAAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
110 95 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (110 bp):
GAGCTGACACCTCTGTGTAACTAAAACTAATTGAGCACCTATGTGCTTCAATCGAGAACTGACAC
CTCTGTGCAGTTAAAAAAGACTGAGAACCTCTATGCTTCAGCCAG
Found at i:450627 original size:24 final size:23
Alignment explanation
Indices: 450571--450630 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
450561 TTCTCTAAAA
450571 AATTTAATTTT-TTTTATATATT
1 AATTTAATTTTATTTTATATATT
*
450593 AAGTTTTATTTTATTTTATATGAATT
1 AA-TTTAATTTTATTTTATAT--ATT
450619 -ATTTAATTTTAT
1 AATTTAATTTTAT
450631 ACATTTGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 2 0.06
23 8 0.25
24 18 0.56
25 1 0.03
26 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (23 bp):
AATTTAATTTTATTTTATATATT
Found at i:454744 original size:16 final size:16
Alignment explanation
Indices: 454703--454744 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
454693 GTAGCTGGAC
*
454703 GAAACATTATTATGAT
1 GAAACATGATTATGAT
*
454719 GGAACATGATTATGAT
1 GAAACATGATTATGAT
*
454735 GAAACGTGAT
1 GAAACATGAT
454745 ATCTGCAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.31
Consensus pattern (16 bp):
GAAACATGATTATGAT
Found at i:456227 original size:19 final size:19
Alignment explanation
Indices: 456185--456229 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
456175 GAATAAGACG
456185 AGAAAAGATAGAAAAGAAA
1 AGAAAAGATAGAAAAGAAA
* * *
456204 GGAAAAGATAGAATATAAA
1 AGAAAAGATAGAAAAGAAA
456223 AGAAAAG
1 AGAAAAG
456230 GGAAAAAGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.69, C:0.00, G:0.22, T:0.09
Consensus pattern (19 bp):
AGAAAAGATAGAAAAGAAA
Found at i:458738 original size:37 final size:36
Alignment explanation
Indices: 458581--458925 Score: 229
Period size: 38 Copynumber: 9.2 Consensus size: 36
458571 TTATATATAT
* * *
458581 ACATATTTTGAAACTACGTATATAATATATAGTTTTTAAT
1 ACAT-TTTTGAAA--ACTTATAT-ATATATAGTTTTGAAA
* *
458621 A-GTTTTT-AAAACTATATA-ATATATAGTTTTAAAAAAA
1 ACATTTTTGAAAACT-TATATATATATAGTTTT---GAAA
* * *
458658 ACATTTTAGAAAA-TATATATAATATATAATTTTTAAA
1 ACATTTTTGAAAACT-TATAT-ATATATAGTTTTGAAA
458695 ATCATTTTTGAAAACTTATATATATATAGTTCTTGAAA
1 A-CATTTTTGAAAACTTATATATATATAGTT-TTGAAA
*
458733 ACATTTTTGAAAACATATATAT-TATAGTTTTGAAA
1 ACATTTTTGAAAACTTATATATATATAGTTTTGAAA
* *
458768 ACA-TTTTGAAAACATTTATATATTATATAATTTTTAAA
1 ACATTTTTGAAAAC--TTATATA-TATATAGTTTTGAAA
* * **
458806 ACGTTTTTGAAAACTTATATAATATTTTTTTTTTGAAA
1 ACATTTTTGAAAACTTATAT-ATA-TATAGTTTTGAAA
* * **
458844 ACA-TGTTGAAAACATTCGTATATTATATAGTTTAAAAA
1 ACATTTTTGAAAAC-TT-ATATA-TATATAGTTTTGAAA
* *
458882 AAATATTTTGAAAATTTATATAT-TATATGTTTTTGAAA
1 ACAT-TTTTGAAAACTTATATATATATA-G-TTTTGAAA
*
458920 ATATTT
1 ACATTT
458926 ATGTATATAT
Statistics
Matches: 245, Mismatches: 35, Indels: 53
0.74 0.11 0.16
Matches are distributed among these distances:
34 22 0.09
35 11 0.04
36 21 0.09
37 61 0.25
38 87 0.36
39 23 0.09
40 20 0.08
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (36 bp):
ACATTTTTGAAAACTTATATATATATAGTTTTGAAA
Found at i:458751 original size:35 final size:33
Alignment explanation
Indices: 458600--458790 Score: 141
Period size: 34 Copynumber: 5.3 Consensus size: 33
458590 GAAACTACGT
* * * *
458600 ATATAATATATAGTTTTTAATA-GTTTTTAAAAC
1 ATAT-ATATATAGTTTTGAAAACATTTTGAAAAC
* *
458633 TATATAATATATAGTTTTAAAAAAAACATTTTAGAAAATAT
1 -ATAT-ATATATAGTTTT---GAAAACATTTT-G-AAA-AC
* *
458674 ATATAATATATAATTTTTAAAATCATTTTTGAAAAC
1 ATAT-ATATATAGTTTTGAAAA-CA-TTTTGAAAAC
458710 TTATATATATATAGTTCTTGAAAACATTTTTGAAAAC
1 --ATATATATATAGTT-TTGAAAACA-TTTTGAAAAC
458747 ATATATATTATAGTTTTGAAAACATTTTGAAAAC
1 ATATATA-TATAGTTTTGAAAACATTTTGAAAAC
*
458781 ATTTATATAT
1 ATATATATAT
458791 TATATAATTT
Statistics
Matches: 133, Mismatches: 11, Indels: 27
0.78 0.06 0.16
Matches are distributed among these distances:
33 3 0.02
34 33 0.25
35 16 0.12
36 8 0.06
37 32 0.24
38 17 0.13
39 4 0.03
40 19 0.14
41 1 0.01
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.44
Consensus pattern (33 bp):
ATATATATATAGTTTTGAAAACATTTTGAAAAC
Found at i:458776 original size:11 final size:11
Alignment explanation
Indices: 458760--458784 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
458750 TATATTATAG
458760 TTTTGAAAACA
1 TTTTGAAAACA
458771 TTTTGAAAACA
1 TTTTGAAAACA
458782 TTT
1 TTT
458785 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:460308 original size:17 final size:17
Alignment explanation
Indices: 460286--460324 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
460276 AATTCGATCC
*
460286 TTTTTTTATATATTTTG
1 TTTTTTTATATATTTTA
* *
460303 TTTTTTTTTATGTTTTA
1 TTTTTTTATATATTTTA
460320 TTTTT
1 TTTTT
460325 GTTTATTCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.05, T:0.82
Consensus pattern (17 bp):
TTTTTTTATATATTTTA
Found at i:461865 original size:27 final size:23
Alignment explanation
Indices: 461835--461897 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 23
461825 ATAATAGCTT
461835 TGAATCATTCAGAATGTACTTCTGTGC
1 TGAATCATTCAGAAT-T-CTT-T-TGC
* *
461862 TGAATCATTCAGCATTGTTTTGC
1 TGAATCATTCAGAATTCTTTTGC
461885 TGAATCATTCAGA
1 TGAATCATTCAGA
461898 GGTGAGAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 15 0.45
24 1 0.03
25 2 0.06
26 1 0.03
27 14 0.42
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.38
Consensus pattern (23 bp):
TGAATCATTCAGAATTCTTTTGC
Found at i:462626 original size:181 final size:181
Alignment explanation
Indices: 462254--462679 Score: 671
Period size: 181 Copynumber: 2.4 Consensus size: 181
462244 TTGGGCCAAG
*
462254 ATGTTGTTGAATAAAAATGTTCTCACTTTGGAAAGTTGATTTAAGATCAATGTATTTAATGTTTT
1 ATGTTGTTGAATAAAAATGTTCACACTTTGGAAAGTTGATTTAAGATCAATGTATTTAATGTTTT
* * *
462319 CGTACATGGAAAGTTGTTATTCGTCGTCATACAAAGGCAGTTTAATGCACTGAAACGTAGTCCAT
66 CGTACATGGAAAGTGGTTATTCGTCGTCATACAAAGGAAATTTAATGCACTGAAACGTAGTCCAT
462384 AAATATAATTACCTGGGGGGAAATTGGAACATTTTTCCACACGTTAATGTAA
131 AAATATAATTACC-GGGGGGAAATTGGAACATTTTTCCACACGTTAATGTAA
* * *
462436 AT-ATGTTGAATAAAAATGTTCACACTTTGGAAAATTGATTTAAGATCAATGCATTTAATGTTTT
1 ATGTTGTTGAATAAAAATGTTCACACTTTGGAAAGTTGATTTAAGATCAATGTATTTAATGTTTT
* *
462500 -GTACATGG-AAGTGGTTATTCGTCGTCATACAAAGGAAATTTAGTGCACTGAAATGTAGTCCAT
66 CGTACATGGAAAGTGGTTATTCGTCGTCATACAAAGGAAATTTAATGCACTGAAACGTAGTCCAT
462563 AAATATAATTATCC-GGGGGAAATTGGAACATTTTTCCACACGTTAATGTAAA
131 AAATATAATTA-CCGGGGGGAAATTGGAACATTTTTCCACACGTTAATGT-AA
* * * *
462615 CATGTTGTTGAATAAGATTGTTCACACTTTGGAAAGTTGATTTAAAATCAATTTATTTAATGTTT
1 -ATGTTGTTGAATAAAAATGTTCACACTTTGGAAAGTTGATTTAAGATCAATGTATTTAATGTTT
462680 AATTTCCCCC
Statistics
Matches: 224, Mismatches: 16, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
178 35 0.16
179 63 0.28
180 12 0.05
181 112 0.50
182 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (181 bp):
ATGTTGTTGAATAAAAATGTTCACACTTTGGAAAGTTGATTTAAGATCAATGTATTTAATGTTTT
CGTACATGGAAAGTGGTTATTCGTCGTCATACAAAGGAAATTTAATGCACTGAAACGTAGTCCAT
AAATATAATTACCGGGGGGAAATTGGAACATTTTTCCACACGTTAATGTAA
Found at i:463729 original size:14 final size:14
Alignment explanation
Indices: 463710--463736 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
463700 ACAAGAACAA
463710 TAATCATTCGATTG
1 TAATCATTCGATTG
463724 TAATCATTCGATT
1 TAATCATTCGATT
463737 TTGTGAAAAA
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:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (14 bp):
TAATCATTCGATTG
Found at i:468496 original size:74 final size:74
Alignment explanation
Indices: 468401--468547 Score: 258
Period size: 74 Copynumber: 2.0 Consensus size: 74
468391 TCATTTGAGG
* *
468401 AAATTAATTTTTGGTAAAAAAGATGTTTTGACGAGCATTCTTTTCAACAAGACTTTTAAATTGGG
1 AAATTAATTTTTGGTAAAAAAGATATTTTGAAGAGCATTCTTTTCAACAAGACTTTTAAATTGGG
468466 AAATATCCA
66 AAATATCCA
* *
468475 AAATTAATTTTTGGTAAAAAAGATATTTTGAAGTGCATTCTTTTCAACAAGATTTTTAAATTGGG
1 AAATTAATTTTTGGTAAAAAAGATATTTTGAAGAGCATTCTTTTCAACAAGACTTTTAAATTGGG
468540 AAATATCC
66 AAATATCC
468548 GAAGAAATTT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 69 1.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (74 bp):
AAATTAATTTTTGGTAAAAAAGATATTTTGAAGAGCATTCTTTTCAACAAGACTTTTAAATTGGG
AAATATCCA
Found at i:469926 original size:18 final size:20
Alignment explanation
Indices: 469884--469926 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
469874 TATTGTTGAA
* *
469884 TGTTTGTGGAATACTATGCT
1 TGTTTGTGGAACACTATGAT
469904 TGTTTG-GGAACAC-ATGAT
1 TGTTTGTGGAACACTATGAT
469922 TGTTT
1 TGTTT
469927 AGGTTTGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
19 6 0.29
20 6 0.29
ACGTcount: A:0.21, C:0.09, G:0.26, T:0.44
Consensus pattern (20 bp):
TGTTTGTGGAACACTATGAT
Found at i:472204 original size:27 final size:30
Alignment explanation
Indices: 472148--472209 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
472138 ACAATCTTTA
*
472148 TTTTT-CTCATTTTTTTACCTTAATTAATT
1 TTTTTACTCATTTTATTACCTTAATTAATT
*
472177 TTTTTACTC-TTTTATTA-CTTAA-TCATT
1 TTTTTACTCATTTTATTACCTTAATTAATT
472204 TTTTTA
1 TTTTTA
472210 TCAAAACCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 10 0.33
28 5 0.17
29 12 0.40
30 3 0.10
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.66
Consensus pattern (30 bp):
TTTTTACTCATTTTATTACCTTAATTAATT
Found at i:473319 original size:130 final size:131
Alignment explanation
Indices: 473112--473444 Score: 445
Period size: 130 Copynumber: 2.5 Consensus size: 131
473102 TTGGTCGGAA
* * * * *
473112 TAATATATGACTACTTTAATGTATGAGAGGTCATTTATTCTCGATTGGAAATAATCAGATATTAT
1 TAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTAT
* * * * * * * * *
473177 CGTTTTCTCTCGAGTTAATATTGATTTTTAAGATGGAATAGTGATATTTCTTCATTTCGATTG-G
66 CGTTTTCACTCGAATCAATAATGAATTTTAAGACGAAATAGTGATATCTCTTCATTTCAATTGAG
473241 AG
131 -G
* *
473243 TAATAAATGACTGCTTTAAGGCATGAGAGGT-TTTTATTCTCGATTGGAAATCATTAGATATTAT
1 TAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTAT
* *
473307 CGTTTTCACTCGAATCAATAATGAATTTTAAGACGAAATGGTGATATCTCTTTATTTCAATTGAG
66 CGTTTTCACTCGAATCAATAATGAATTTTAAGACGAAATAGTGATATCTCTTCATTTCAATTGAG
473372 G
131 G
* * * *
473373 TAATAAATGATTGTTTTAAGGCATGAAATGTCATTTATTCTCGATTGGAAATAATTAGATATTAT
1 TAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTAT
473438 CGTTTTC
66 CGTTTTC
473445 TCTCTTAAAA
Statistics
Matches: 176, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
130 110 0.62
131 66 0.38
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (131 bp):
TAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTAT
CGTTTTCACTCGAATCAATAATGAATTTTAAGACGAAATAGTGATATCTCTTCATTTCAATTGAG
G
Found at i:477922 original size:2 final size:2
Alignment explanation
Indices: 477915--477979 Score: 71
Period size: 2 Copynumber: 32.5 Consensus size: 2
477905 TTTTATTAGT
* *
477915 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TCA T- TA GTA T- TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA -TA TA TA TA
*
477957 TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
477980 TTCCTATTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
1 2 0.04
2 47 0.89
3 4 0.08
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.54
Consensus pattern (2 bp):
TA
Found at i:478044 original size:26 final size:25
Alignment explanation
Indices: 478012--478076 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 25
478002 GTATATATAC
478012 ATATATTTTACTTATGATTTCCTATT
1 ATATATTTTACTTAT-ATTTCCTATT
* **
478038 ATATATTTT--TTCTATTTTTTATT
1 ATATATTTTACTTATATTTCCTATT
478061 AT-TATTTTACTTATAT
1 ATATATTTTACTTATAT
478077 ATATACTTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
22 6 0.18
23 10 0.30
24 8 0.24
26 9 0.27
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.65
Consensus pattern (25 bp):
ATATATTTTACTTATATTTCCTATT
Found at i:478126 original size:20 final size:20
Alignment explanation
Indices: 478097--478152 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
478087 ACCTTTTTTA
*
478097 TTTATCTATCTTCTTTTTATT
1 TTTAT-TATCTTCTTTTTATC
*
478118 TTTATTATC-TATTTTTATC
1 TTTATTATCTTCTTTTTATC
478137 TTT-TTATCTTCCTTTT
1 TTTATTATCTT-CTTTT
478153 GTTTGTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 5 0.17
19 12 0.40
20 8 0.27
21 5 0.17
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTATTATCTTCTTTTTATC
Found at i:481826 original size:18 final size:18
Alignment explanation
Indices: 481782--481826 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
481772 CAAAATTACT
481782 TTTATATTATATATTTGA
1 TTTATATTATATATTTGA
* *
481800 ATTATATTATTATATTTTA
1 TTTATATTA-TATATTTGA
481819 TTTA-ATTA
1 TTTATATTA
481827 ATCTTTGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTATATTATATATTTGA
Found at i:487429 original size:26 final size:28
Alignment explanation
Indices: 487368--487429 Score: 65
Period size: 31 Copynumber: 2.2 Consensus size: 28
487358 GAGTAGTGCT
* *
487368 GAGCTCGATTCGACTCGAAAACTCTGAAAT
1 GAGCTCGACTCGACTCGAAAACTCTG--AC
487398 GAAGCTCGACTCGACTCGAAAACTC-G-C
1 G-AGCTCGACTCGACTCGAAAACTCTGAC
487425 GAGCT
1 GAGCT
487430 TAAAATTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
26 4 0.14
27 1 0.03
30 2 0.07
31 22 0.76
ACGTcount: A:0.31, C:0.27, G:0.23, T:0.19
Consensus pattern (28 bp):
GAGCTCGACTCGACTCGAAAACTCTGAC
Found at i:498251 original size:29 final size:30
Alignment explanation
Indices: 498196--498253 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
498186 CATTTTGAAT
* *
498196 AACGGAATGAAACGTTAGGCAACAAACTAG
1 AACGAAATGAAACGTTAAGCAACAAACTAG
498226 AACGAAATG-AACGTTAAGC-ACTAAACTA
1 AACGAAATGAAACGTTAAGCAAC-AAACTA
498254 AAATAAAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.08
29 15 0.60
30 8 0.32
ACGTcount: A:0.48, C:0.17, G:0.19, T:0.16
Consensus pattern (30 bp):
AACGAAATGAAACGTTAAGCAACAAACTAG
Found at i:502483 original size:17 final size:17
Alignment explanation
Indices: 502461--502507 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
502451 AGCATCCGTT
*
502461 ACCATTATGAATTCTGG
1 ACCATTATGAATTATGG
502478 ACCATTATGAATTATGG
1 ACCATTATGAATTATGG
*
502495 ACAATTATGAATT
1 ACCATTATGAATT
502508 TATAATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (17 bp):
ACCATTATGAATTATGG
Found at i:503590 original size:31 final size:31
Alignment explanation
Indices: 503552--503633 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
503542 TTTTTTTTAT
*
503552 TTCGGGTCGGGTCGGGTTTCTAATTCAT-ATA
1 TTCGGGTCGGGTCGGGTTTCTAAGT-ATGATA
* * *
503583 TTCGGGTCGGGTCGGTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGGGTTTCTAAGTATGATA
*
503614 TTCGGGTCGAGTTCGGGTTT
1 TTCGGGTCG-GGTCGGGTTT
503634 TGGGTGAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
30 1 0.02
31 34 0.79
32 8 0.19
ACGTcount: A:0.12, C:0.13, G:0.34, T:0.40
Consensus pattern (31 bp):
TTCGGGTCGGGTCGGGTTTCTAAGTATGATA
Found at i:503898 original size:33 final size:33
Alignment explanation
Indices: 503834--503914 Score: 117
Period size: 33 Copynumber: 2.4 Consensus size: 33
503824 ATTTTGGTCG
* *
503834 GGTCGGGTCGGTTTTTTTTTAAGTGTGATATTCA
1 GGTCGGGTCGG-GTTTTTTTAAGTGTAATATTCA
* *
503868 GGTCGGGTCGGGTTTTTTTAATTGTAATATTCG
1 GGTCGGGTCGGGTTTTTTTAAGTGTAATATTCA
503901 GGTCGGGTCGGGTT
1 GGTCGGGTCGGGTT
503915 CGGGTTTAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.74
34 11 0.26
ACGTcount: A:0.12, C:0.10, G:0.35, T:0.43
Consensus pattern (33 bp):
GGTCGGGTCGGGTTTTTTTAAGTGTAATATTCA
Found at i:504170 original size:290 final size:288
Alignment explanation
Indices: 503615--504145 Score: 764
Period size: 290 Copynumber: 1.8 Consensus size: 288
503605 AGTGTGATAT
* * * * *
503615 TCGGGTCGAGTTCGGGTTTTGGGTGAAAAATATCTGACCCGAAAATATATATAATTTTATATTAT
1 TCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTACATTAT
* * *
503680 ATATTTAGGAATAATTACAATAATACCCCTTTATATATAATTTTTTTCAATTAAGTCACTGTTTT
66 ATATTTAGGAATAATTACAATAATACCCCTATATATATAATTATTTCCAATTAAGTCACTGTTTT
* * *
503745 TATTGAATAAATTTTTTTTTAATTTCGGGTCGGGTTGGATTTCTAATTCATATATTCGGGTCGGG
131 TATTGAATAAATTTTTTTTTAATTTCGGGTCAGGTCGGATTTCTAATTCATATATTCAGGTCGGG
* * ***** *
503810 TCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTTTAAGTGTGATATTCAGGTCGGG
196 TCGGGTGAAACTTTATTTTGGTCGAGTCGGGTCGGATGGAGGTTAACTGTGATATTCAGGTCGGG
503875 TCGGGTTTTTTTAATTGTAATATTCGGG
261 TCGGGTTTTTTTAATTGTAATATTCGGG
* *
503903 TCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCC-AAAAAATATATAATTTTACCTTAT
1 TCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTACATTAT
503967 ATATTTAGGAATAATTACAATAATACCCCTATATATAT-A-TATTTCCAATTAAGTCACTGTTTT
66 ATATTTAGGAATAATTACAATAATACCCCTATATATATAATTATTTCCAATTAAGTCACTGTTTT
*
504030 TATTGAATAAAAATAATATTTTTATT-ATTTCGGGTCAGGTCGGGTTTCTAATTCATATATTCAG
131 TATTGAAT--AAAT--T-TTTTT-TTAATTTCGGGTCAGGTCGGATTTCTAATTCATATATTCAG
504094 GTCGGGTCGGGTGAAACTTTATTTTGGTCGAGTCGGGTCTCGGATGGAGGTT
190 GTCGGGTCGGGTGAAACTTTATTTTGGTCGAGTCGGG--TCGGATGGAGGTT
504146 CCCTTGTTAT
Statistics
Matches: 214, Mismatches: 21, Indels: 12
0.87 0.09 0.05
Matches are distributed among these distances:
285 30 0.14
286 1 0.00
287 62 0.29
288 36 0.17
289 1 0.00
290 75 0.35
291 2 0.01
292 7 0.03
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (288 bp):
TCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTACATTAT
ATATTTAGGAATAATTACAATAATACCCCTATATATATAATTATTTCCAATTAAGTCACTGTTTT
TATTGAATAAATTTTTTTTTAATTTCGGGTCAGGTCGGATTTCTAATTCATATATTCAGGTCGGG
TCGGGTGAAACTTTATTTTGGTCGAGTCGGGTCGGATGGAGGTTAACTGTGATATTCAGGTCGGG
TCGGGTTTTTTTAATTGTAATATTCGGG
Found at i:504466 original size:17 final size:18
Alignment explanation
Indices: 504441--504487 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
504431 TATGGAATTG
* *
504441 GATTCCAATTCC-TGACA
1 GATTTCAATTCCTTCACA
504458 GATTTCAATTCCTTCACA
1 GATTTCAATTCCTTCACA
504476 GATTTCAATTCC
1 GATTTCAATTCC
504488 CTCAGAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 11 0.41
18 16 0.59
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.36
Consensus pattern (18 bp):
GATTTCAATTCCTTCACA
Found at i:505972 original size:21 final size:20
Alignment explanation
Indices: 505924--506018 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
505914 GTGATTCTTG
505924 AAAATCGCAATGCGATAGTC
1 AAAATCGCAATGCGATAGTC
* * **
505944 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAATGCGATAGT-C
* *
505965 AAAATCGCAACGCGAATA-TG
1 AAAATCGCAATGCG-ATAGTC
* **
505985 AAAATCGCAACGCGA-ACAC
1 AAAATCGCAATGCGATAGTC
506004 ATAAATCGCAATGCG
1 A-AAATCGCAATGCG
506019 TATCCGTAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
18 1 0.02
19 2 0.03
20 41 0.69
21 13 0.22
22 2 0.03
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (20 bp):
AAAATCGCAATGCGATAGTC
Found at i:506009 original size:20 final size:20
Alignment explanation
Indices: 505986--506156 Score: 107
Period size: 20 Copynumber: 8.6 Consensus size: 20
505976 GCGAATATGA
505986 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * *
506006 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
506026 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
** *
506046 AAATCGCAACGCGTTTCCGT
1 AAATCGCAACGCGTAACCAT
* * *
506066 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* *
506086 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTAA-CCAT
* **
506106 AAATCGCAACGAG-AATCTGT
1 AAATCGCAACGCGTAA-CCAT
* *
506126 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTAA-CCAT
506146 AAATCGCAACG
1 AAATCGCAACG
506157 AGAATCTGTA
Statistics
Matches: 131, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
19 2 0.02
20 127 0.97
21 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:506013 original size:61 final size:61
Alignment explanation
Indices: 505843--506018 Score: 171
Period size: 61 Copynumber: 2.9 Consensus size: 61
505833 AAATGACCAA
* * * *
505843 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGATCCCCAGAATCGCAAAT-C-AGTGTC
1 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGATACACAAAATCGC-AATGCGAGTGTC
* * * * ** * * * *
505902 CAAAATCGCAACGTGATTCTTGAAAATCGCAATGCGATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAAT-ATGAAAATCGCAACGCGATACACAAAATCGCAATGCGAGTGTC
505964 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA-ACACATAAATCGCAATGCG
1 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGATACACA-AAATCGCAATGCG
506019 TATCCGTAAA
Statistics
Matches: 91, Mismatches: 21, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
59 15 0.16
60 5 0.05
61 51 0.56
62 20 0.22
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (61 bp):
CAAAATCGCAACGCGAATATGAAAATCGCAACGCGATACACAAAATCGCAATGCGAGTGTC
Found at i:506051 original size:60 final size:58
Alignment explanation
Indices: 505966--506175 Score: 208
Period size: 60 Copynumber: 3.5 Consensus size: 58
505956 CGATTTTCCA
* ** * *
505966 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGCGAAC-CGTAAATCGCAA-GCGTATCCGT
* ** *
506026 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTTTCCGTATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGCG-AACCGTAAATCGCAA-GCGTATCCGT
* *
506086 AAATCGCAACGAT-AATCCGTAAATCGCAACGAGAATCTGTAAATCGCAA-CGATAATCCGT
1 AAATCGCAACG-TGAATCCGTAAATCGCAACGCGAA-CCGTAAATCGCAAGCG-T-ATCCGT
* * *
506146 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGTGAATCCGTAAATCGCAAC
506176 ACTGAAATTT
Statistics
Matches: 125, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
58 2 0.02
59 1 0.01
60 120 0.96
61 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (58 bp):
AAATCGCAACGTGAATCCGTAAATCGCAACGCGAACCGTAAATCGCAAGCGTATCCGT
Found at i:506157 original size:20 final size:20
Alignment explanation
Indices: 506020--506175 Score: 174
Period size: 20 Copynumber: 7.8 Consensus size: 20
506010 CGCAATGCGT
*
506020 ATCCGTAAATCGCAACG-TGT
1 ATCCGTAAATCGCAACGAT-A
*
506040 ATCCGTAAATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
* * *
506060 TTCCGTATATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
506080 ATCCGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
506100 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
*
506120 ATCTGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
506140 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
* *
506160 ATCTGTAAATCACAAC
1 ATCCGTAAATCGCAAC
506176 ACTGAAATTT
Statistics
Matches: 121, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
19 1 0.01
20 119 0.98
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (20 bp):
ATCCGTAAATCGCAACGATA
Found at i:506157 original size:40 final size:40
Alignment explanation
Indices: 505986--506175 Score: 208
Period size: 40 Copynumber: 4.8 Consensus size: 40
505976 GCGAATATGA
* *
505986 AAATCGCAACGCGAA-CACATAAATCGCAATGCG-T-ATCCGT
1 AAATCGCAACGAGAATC-CGTAAATCGCAA--CGATAATCCGT
* * * *
506026 AAATCGCAACGTGTATCCGTAAATCGCAACGCGT-TTCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACG-ATAATCCGT
* * *
506066 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
*
506106 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
* *
506146 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGAGAATCCGTAAATCGCAAC
506176 ACTGAAATTT
Statistics
Matches: 133, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
38 2 0.02
39 1 0.01
40 129 0.97
41 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (40 bp):
AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
Found at i:506896 original size:24 final size:24
Alignment explanation
Indices: 506857--506903 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
506847 AAATTTGGTC
506857 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
506881 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
506904 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:507095 original size:12 final size:12
Alignment explanation
Indices: 507078--507102 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
507068 ATATAATCCT
507078 GAAGAAGAAAAA
1 GAAGAAGAAAAA
507090 GAAGAAGAAAAA
1 GAAGAAGAAAAA
507102 G
1 G
507103 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:510293 original size:14 final size:14
Alignment explanation
Indices: 510274--510330 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
510264 GCGAAATGAA
*
510274 AATCGCAACGACAG
1 AATCGCAACGAAAG
510288 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
510305 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
510321 AATCGCAACG
1 AATCGCAACG
510331 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:510301 original size:33 final size:33
Alignment explanation
Indices: 510255--510347 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
510245 GCGAAACCAA
*
510255 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
510288 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
510321 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
510348 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:510312 original size:19 final size:19
Alignment explanation
Indices: 510218--510352 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
510208 TAGTTTACTT
* *
510218 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
510238 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
510257 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
510276 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
510290 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
510309 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
510323 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
510342 TCGCAATGCGA
1 TCGCAACGCGA
510353 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:510370 original size:19 final size:18
Alignment explanation
Indices: 510348--510476 Score: 94
Period size: 19 Copynumber: 7.3 Consensus size: 18
510338 AAAATCGCAA
510348 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
510367 TGCGA--TTCTTT--CGT
1 TGCGATTTTGTTTCGCGT
* *
510381 TGCGATTTTCATTTCGCAT
1 TGCGATTTT-GTTTCGCGT
*
510400 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
510414 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
510433 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
510452 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT--GTTTCGCGT
510472 TGCGA
1 TGCGA
510477 AAGTAAACTA
Statistics
Matches: 87, Mismatches: 12, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
14 18 0.21
16 6 0.07
17 6 0.07
19 44 0.51
20 13 0.15
ACGTcount: A:0.10, C:0.18, G:0.26, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:510383 original size:14 final size:14
Alignment explanation
Indices: 510364--510420 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
510354 TTTGGTTTCG
510364 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
510378 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
510395 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
510411 CGTTGCGATT
1 CGTTGCGATT
510421 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:510396 original size:33 final size:33
Alignment explanation
Indices: 510348--510439 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
510338 AAAATCGCAA
** *
510348 TGCGATTTTGGTTTCGCGTTGCGATTCTTTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
*
510381 TGCGATTTTCATTTCGCATTGCGATTCTGTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
510414 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTCATTTCGCGTTGCGATT
510440 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
Found at i:510640 original size:93 final size:93
Alignment explanation
Indices: 510524--510806 Score: 541
Period size: 93 Copynumber: 3.1 Consensus size: 93
510514 ATGGATTGCA
*
510524 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAAAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
510588 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
510616 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
510681 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
510709 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
510774 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
510802 TTACT
1 TTACT
510807 AAGCAATCTA
Statistics
Matches: 188, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
92 4 0.02
93 184 0.98
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:512551 original size:19 final size:20
Alignment explanation
Indices: 512507--512568 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
512497 TTTTGGTTGA
*
512507 AATGAAAATCGCAACGAGAG
1 AATGACAATCGCAACGAGAG
** *
512527 AATGACTGTCGCAACGCGA-
1 AATGACAATCGCAACGAGAG
512546 AATGACAATCGCAACGAGAG
1 AATGACAATCGCAACGAGAG
512566 AAT
1 AAT
512569 CGCAACGCGA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (20 bp):
AATGACAATCGCAACGAGAG
Found at i:512571 original size:14 final size:14
Alignment explanation
Indices: 512552--512608 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
512542 GCGAAATGAC
512552 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
512566 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
512585 AATCGCAACGAGAG
1 AATCGCAACGAGAG
512599 AATCGCAACG
1 AATCGCAACG
512609 CGAAATAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:512577 original size:33 final size:33
Alignment explanation
Indices: 512505--512625 Score: 170
Period size: 33 Copynumber: 3.5 Consensus size: 33
512495 TCTTTTGGTT
512505 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGC
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAACGC
*
512544 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
512577 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
512610 GAAATAAAAATCGCAA
1 GAAATGAAAATCGCAA
512626 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
33 56 0.71
36 1 0.01
38 1 0.01
39 21 0.27
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:512590 original size:19 final size:19
Alignment explanation
Indices: 512505--512630 Score: 92
Period size: 19 Copynumber: 7.1 Consensus size: 19
512495 TCTTTTGGTT
*
512505 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
***
512524 GAGAATGACTGTCGCAACGC
1 GA-AATGAAAATCGCAACGC
*
512544 GAAATGACAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
512561 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
512577 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
512594 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
512610 GAAATAAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
512629 GA
1 GA
512631 TTTTGGTTTC
Statistics
Matches: 84, Mismatches: 12, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
14 20 0.24
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 37 0.44
20 15 0.18
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:512661 original size:14 final size:14
Alignment explanation
Indices: 512642--512698 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
512632 TTTGGTTTCG
512642 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
512656 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
512675 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
512689 CGTTGCGATT
1 CGTTGCGATT
512699 GTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:512680 original size:19 final size:19
Alignment explanation
Indices: 512656--512744 Score: 80
Period size: 19 Copynumber: 4.9 Consensus size: 19
512646 GCGATTCTCT
512656 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
512675 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
512689 CGTTGCGATTGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*** *
512708 CGTTGCGACAGTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
512728 CGTTGCGATTTTCATTT
1 CGTTGCGATTTTCATTT
512745 ATCTCGTTGC
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 3 0.05
19 25 0.45
20 15 0.27
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:512736 original size:39 final size:33
Alignment explanation
Indices: 512626--512744 Score: 157
Period size: 33 Copynumber: 3.4 Consensus size: 33
512616 AAAATCGCAA
**
512626 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
512659 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
512692 TGCGATTGTCATTTCGCGTTGCGACAGTCATTCTCTCGT
1 TGCGATTTTCATTTCGCGTT--G-C-G--ATTCTCTCGT
512731 TGCGATTTTCATTT
1 TGCGATTTTCATTT
512745 ATCTCGTTGC
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
33 50 0.66
35 1 0.01
36 1 0.01
37 1 0.01
39 23 0.30
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:512878 original size:33 final size:33
Alignment explanation
Indices: 512836--512906 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
512826 AATACTAACT
512836 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
512869 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
512902 TGAAA
1 TGAAA
512907 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:513140 original size:22 final size:22
Alignment explanation
Indices: 513088--513142 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
513078 TGGTTGTGAG
**
513088 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
513110 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
513132 GGATTTCTTCG
1 GGATTTCTTCG
513143 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:513314 original size:20 final size:20
Alignment explanation
Indices: 513289--513482 Score: 203
Period size: 20 Copynumber: 9.7 Consensus size: 20
513279 CTTTAAATAT
513289 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
513309 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
513331 -TCGTTGCGATTTACCGATA
1 CGCGTTGCGATTTACGGATA
*
513350 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
513370 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
513390 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
513410 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
513430 CGCATTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
513450 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
513470 CGCGTTGCGATTT
1 CGCGTTGCGATTT
513483 TGGAAAATCG
Statistics
Matches: 143, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:513454 original size:60 final size:60
Alignment explanation
Indices: 513291--513462 Score: 236
Period size: 60 Copynumber: 2.9 Consensus size: 60
513281 TTAAATATCG
* ** *
513291 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACCGATACG
1 CGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTACCGATACA
* *** * *
513352 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACCGATACA
*
513412 CGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTT
513463 TCATATTCGC
Statistics
Matches: 95, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 69 0.73
61 26 0.27
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACCGATACA
Found at i:513476 original size:60 final size:60
Alignment explanation
Indices: 513288--513603 Score: 232
Period size: 60 Copynumber: 5.2 Consensus size: 60
513278 GCTTTAAATA
* ** * *
513288 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACCGAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTTCAGAT
* * *** * * *
513349 ACGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
* * * *
513409 ACACGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
* * * * * *
513469 TCGCGTTGCGATTT-TGGAAAATCGCAATGCGAATT-TG-ACTATCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTACGG-ATA-CGCATTGCGATTTATGTA-T-TCGCGTTGCGATTTTC-AGAT
* * ** * * *
513531 TCGCGTTGCGATTT-TGGAAACTG-ATTTGCGATTCTGGGGA-TCGCGTTGCGATTTTTA-TT
1 TCGCGTTGCGATTTACGGATAC-GCA-TTGCGATT-TATGTATTCGCGTTGCGATTTTCAGAT
513590 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
513604 TGTTGGTCAT
Statistics
Matches: 208, Mismatches: 37, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
59 16 0.08
60 92 0.44
61 78 0.38
62 20 0.10
63 1 0.00
64 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (60 bp):
TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
Found at i:513499 original size:21 final size:20
Alignment explanation
Indices: 513449--513546 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
513439 ATTTATGTGT
* * * *
513449 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
513469 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
513490 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
513510 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
513531 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
513547 GAAACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:513522 original size:61 final size:60
Alignment explanation
Indices: 513449--513605 Score: 176
Period size: 61 Copynumber: 2.6 Consensus size: 60
513439 ATTTATGTGT
*
513449 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATCGCA-ATGCGAATT-TGACTA
1 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAAT-G-ATATGCG-ATTCTGACGA
* * * * * **
513510 TCGCATTGCGATTTTCAAGAATCGCGTTGCGATTTTGGAAACTGATTTGCGATTCTGGGGA
1 TCGCGTTGCGATTTTC-ATATTCGCGTTGCGATTTTGGAAAATGATATGCGATTCTGACGA
*
513571 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTG
513606 TTGGTCATTT
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
59 16 0.20
60 5 0.06
61 37 0.46
62 23 0.28
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (60 bp):
TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATGATATGCGATTCTGACGA
Found at i:513541 original size:41 final size:41
Alignment explanation
Indices: 513449--513605 Score: 110
Period size: 41 Copynumber: 3.9 Consensus size: 41
513439 ATTTATGTGT
* * *
513449 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
513490 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
* * * ***
513531 TCGCGTTGCGATTTTGGAAACT-G-ATTTGCGATTCTG-GGGA
1 TCGCGTTGCGATTTT-GATATTCGCA-TTGCGATTTTGCAAAA
* *
513571 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTG
513606 TTGGTCATTT
Statistics
Matches: 89, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 19 0.21
41 52 0.58
42 5 0.06
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:517540 original size:20 final size:20
Alignment explanation
Indices: 517515--517566 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
517505 AGGTAAGAGA
517515 AGTATCGATACTCTCAAGAT
1 AGTATCGATACTCTCAAGAT
517535 AGTATCGATACTCTCAAGAT
1 AGTATCGATACTCTCAAGAT
517555 AGTATCGATACT
1 AGTATCGATACT
517567 ACCAGCTTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (20 bp):
AGTATCGATACTCTCAAGAT
Found at i:519042 original size:3 final size:3
Alignment explanation
Indices: 519030--519085 Score: 53
Period size: 3 Copynumber: 19.3 Consensus size: 3
519020 AGATGATGAT
* * * * *
519030 GAA GAA -AA GAA GAA GAA GAA TAA GAT GAT GAT GAA G-A GAA TAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
519076 GAA GAA GAA G
1 GAA GAA GAA G
519086 GAAGTGGACA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 4 0.09
3 41 0.91
ACGTcount: A:0.61, C:0.00, G:0.30, T:0.09
Consensus pattern (3 bp):
GAA
Found at i:519051 original size:32 final size:32
Alignment explanation
Indices: 519013--519081 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
519003 TTGATGGTAA
519013 AAGAATAAGATGATGATGAAGAAAAGAAGAAG
1 AAGAATAAGATGATGATGAAGAAAAGAAGAAG
* *
519045 AAGAATAAGATGATGATGAAGAGAATAAGAAG
1 AAGAATAAGATGATGATGAAGAAAAGAAGAAG
519077 AAGAA
1 AAGAA
519082 GAAGGAAGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.13
Consensus pattern (32 bp):
AAGAATAAGATGATGATGAAGAAAAGAAGAAG
Found at i:521219 original size:21 final size:22
Alignment explanation
Indices: 521187--521229 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
521177 TTTAAAAGTG
521187 TTAAAGGAAGTATTGATACTCA
1 TTAAAGGAAGTATTGATACTCA
521209 TTAAA-GAAGTATTGATACTCA
1 TTAAAGGAAGTATTGATACTCA
521230 CTGTCCATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (22 bp):
TTAAAGGAAGTATTGATACTCA
Found at i:522226 original size:15 final size:15
Alignment explanation
Indices: 522202--522245 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
522192 TTGGTTTTCC
522202 AGAAAATGAATTACT
1 AGAAAATGAATTACT
**
522217 AGAATTTGAATTACT
1 AGAAAATGAATTACT
*
522232 GGAAAATGAATTAC
1 AGAAAATGAATTAC
522246 ATTTCTGGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.48, C:0.07, G:0.16, T:0.30
Consensus pattern (15 bp):
AGAAAATGAATTACT
Found at i:522500 original size:49 final size:50
Alignment explanation
Indices: 522397--522501 Score: 119
Period size: 49 Copynumber: 2.1 Consensus size: 50
522387 ATTTATTACA
522397 AATTTT-AAATATAATAAATAATATTATTTATGATAAAACTTAATATTAT
1 AATTTTAAAATATAATAAATAATATTATTTATGATAAAACTTAATATTAT
* * * * *
522446 TATTTTAAAATATTA-AAATAAT-TTATTTATTATTAAATA-TTAGTTTTAT
1 AATTTTAAAATATAATAAATAATATTATTTATGA-TAAA-ACTTAATATTAT
522495 AATTTTA
1 AATTTTA
522502 TTAATAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
48 9 0.19
49 30 0.64
50 8 0.17
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (50 bp):
AATTTTAAAATATAATAAATAATATTATTTATGATAAAACTTAATATTAT
Found at i:522567 original size:91 final size:87
Alignment explanation
Indices: 522452--522621 Score: 202
Period size: 89 Copynumber: 1.9 Consensus size: 87
522442 TTATTATTTT
* * * *
522452 AAAATATTAAAATAATTTATTTA-TTATTAAA-TATTAGTTTTATAATTTTATTAATAAAAATAT
1 AAAATATTAAAATAATTTAATTATTTATTAAAGTAATAGTGTTAT-ATTATATT-ATAAAAATAT
*
522515 TAATATTGGTATATTTTAGTGAAATA
64 T-A-ATTAGTATATTTTAGTGAAATA
*
522541 AAAATATTATAAA-ATATATTAATTATTTATTAAAGTAATAGTGTTATATTATATTTTAAAAATA
1 AAAATATTA-AAATA-AT-TTAATTATTTATTAAAGTAATAGTGTTATATTATATTATAAAAATA
522605 TTAATTAGTATATTTTA
63 TTAATTAGTATATTTTA
522622 AATATCTCTA
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
89 23 0.33
90 6 0.09
91 16 0.23
92 15 0.21
93 10 0.14
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.48
Consensus pattern (87 bp):
AAAATATTAAAATAATTTAATTATTTATTAAAGTAATAGTGTTATATTATATTATAAAAATATTA
ATTAGTATATTTTAGTGAAATA
Found at i:522681 original size:19 final size:20
Alignment explanation
Indices: 522630--522681 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
522620 TAAATATCTC
522630 TATTAAA-ATATTATTTAAA
1 TATTAAATATATTATTTAAA
* *
522649 TATATAAATAATATTA-TTCAT
1 TAT-TAAAT-ATATTATTTAAA
522670 TATTAAATATAT
1 TATTAAATATAT
522682 AAATTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 6 0.21
22 6 0.21
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TATTAAATATATTATTTAAA
Found at i:522693 original size:28 final size:27
Alignment explanation
Indices: 522638--522800 Score: 82
Period size: 29 Copynumber: 5.7 Consensus size: 27
522628 TCTATTAAAA
522638 TATTATTTAAATATATAAATAATATTAT
1 TATTA-TTAAATATATAAATAATATTAT
**
522666 TCATTATTAAATATATAAATTTTTTTATTAT
1 T-ATTATTAAATATATAAA---TAATATTAT
*
522697 ATATTATTAAA-ATAAAAATATAATATCT-T
1 -TATTATTAAATAT-ATAA-ATAATAT-TAT
** * *
522726 ATATTATTATAATATAATTGATTATTTTAT
1 -TATTATTA-AATAT-ATAAATAATATTAT
* * *
522756 ATAATATTAAAAATATAATATTATATTAT
1 -TATTATTAAATATATAA-ATAATATTAT
522785 TATTA-TAAATAT-TAAA
1 TATTATTAAATATATAAA
522801 ATATTTTAAT
Statistics
Matches: 106, Mismatches: 17, Indels: 27
0.71 0.11 0.18
Matches are distributed among these distances:
25 1 0.01
26 3 0.03
27 6 0.06
28 20 0.19
29 32 0.30
30 19 0.18
31 23 0.22
32 2 0.02
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (27 bp):
TATTATTAAATATATAAATAATATTAT
Found at i:522710 original size:60 final size:60
Alignment explanation
Indices: 522637--522805 Score: 167
Period size: 59 Copynumber: 2.9 Consensus size: 60
522627 CTCTATTAAA
* *
522637 ATATTATTTAAATATATAA-ATAATATTATTCATTATTAAATATATAAATT-TTTTTATTAT
1 ATATTATTAAAATATATAATATAATATTATT-ATTATTAAATATATAAATTATTATT-TTAT
* *
522697 ATATTATTAAAATA-AAAATATAATATCT-TATATTATTATA-ATAT-AATTGATTATTTTAT
1 ATATTATTAAAATATATAATATAATAT-TAT-TATTATTAAATATATAAATT-ATTATTTTAT
* * *
522756 ATAATATTAAAA-ATATAATATTATATTATTATTA-TAAATAT-TAAAATATT
1 ATATTATTAAAATATATAATATAATATTATTATTATTAAATATATAAATTATT
522806 TTAATAATTA
Statistics
Matches: 91, Mismatches: 9, Indels: 21
0.75 0.07 0.17
Matches are distributed among these distances:
57 7 0.08
58 16 0.18
59 33 0.36
60 33 0.36
61 2 0.02
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (60 bp):
ATATTATTAAAATATATAATATAATATTATTATTATTAAATATATAAATTATTATTTTAT
Found at i:522764 original size:15 final size:16
Alignment explanation
Indices: 522726--522779 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 16
522716 ATAATATCTT
522726 ATATTATTATAATATA
1 ATATTATTATAATATA
*
522742 ATTGATTATT-TTATATA
1 A-T-ATTATTATAATATA
*
522759 ATATTA--AAAATATA
1 ATATTATTATAATATA
522773 ATATTAT
1 ATATTAT
522780 ATTATTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
14 11 0.35
15 4 0.13
16 2 0.06
17 8 0.26
18 6 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
ATATTATTATAATATA
Found at i:522806 original size:54 final size:53
Alignment explanation
Indices: 522709--522813 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 53
522699 ATTATTAAAA
* *
522709 TAAAAATATAATATCTTATATTATTATAATATAATTGATTATTTTATATAATAT
1 TAAAAATATAATATCTTATATTATTATAATATAATTAAATATTTTA-ATAATAT
522763 TAAAAATATAATAT-TATATTATTATTATAA-AT-ATTAAAATATTTTAATAAT
1 TAAAAATATAATATCT-TA-TATTATTATAATATAATT-AAATATTTTAATAAT
522814 TAATATTTTG
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
53 9 0.20
54 26 0.57
55 11 0.24
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (53 bp):
TAAAAATATAATATCTTATATTATTATAATATAATTAAATATTTTAATAATAT
Found at i:522812 original size:20 final size:21
Alignment explanation
Indices: 522758--522812 Score: 51
Period size: 20 Copynumber: 2.7 Consensus size: 21
522748 TATTTTATAT
** *
522758 AATATTAAAAATATAATATTAT
1 AATATTATTAATA-AATATTAA
*
522780 ATTATTATT-ATAAATATTAA
1 AATATTATTAATAAATATTAA
522800 AATATT-TTAATAA
1 AATATTATTAATAA
522813 TTAATATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.07
20 16 0.59
21 3 0.11
22 6 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATATTATTAATAAATATTAA
Found at i:523046 original size:42 final size:42
Alignment explanation
Indices: 522994--523109 Score: 171
Period size: 42 Copynumber: 2.8 Consensus size: 42
522984 ATGAATTATG
* * *
522994 TTCCGGAAAACGAATTACGTAAAACAAACAC-ATGAAAACATT
1 TTCCGAAAAACGAATTACATGAAACAAACACGA-GAAAACATT
523036 TTCCGAAAAACGAATTACATGAAACAAACACGAGAAAACATT
1 TTCCGAAAAACGAATTACATGAAACAAACACGAGAAAACATT
* *
523078 TTCCGAAAAATGAATTATATGAAACAAACACG
1 TTCCGAAAAACGAATTACATGAAACAAACACG
523110 GAATTTCGGG
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
42 67 0.99
43 1 0.01
ACGTcount: A:0.51, C:0.18, G:0.12, T:0.19
Consensus pattern (42 bp):
TTCCGAAAAACGAATTACATGAAACAAACACGAGAAAACATT
Found at i:524470 original size:10 final size:10
Alignment explanation
Indices: 524455--524481 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
524445 CATTTAATAA
524455 ATAAACGAAC
1 ATAAACGAAC
524465 ATAAACGAAC
1 ATAAACGAAC
524475 ATAAACG
1 ATAAACG
524482 TTAGAGACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.59, C:0.19, G:0.11, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:525118 original size:14 final size:14
Alignment explanation
Indices: 525101--525142 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
525091 GATTGGGTTA
* *
525101 AACATAAATGAGCG
1 AACATAAACGAACG
525115 AACATAAACGAACG
1 AACATAAACGAACG
*
525129 AACATAACCGAACG
1 AACATAAACGAACG
525143 TTCACGAACG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.52, C:0.21, G:0.17, T:0.10
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:526113 original size:25 final size:25
Alignment explanation
Indices: 526085--526134 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
526075 TTTTCGAGCT
526085 GCTCACAAGCATTTCGAGTCGAGTA
1 GCTCACAAGCATTTCGAGTCGAGTA
*
526110 GCTCACGAGCATTTCGAGTCGAGTA
1 GCTCACAAGCATTTCGAGTCGAGTA
526135 TCAAGTAGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (25 bp):
GCTCACAAGCATTTCGAGTCGAGTA
Found at i:528493 original size:37 final size:36
Alignment explanation
Indices: 528418--528493 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
528408 TTTTTATATT
*
528418 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
528454 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
528491 TTT
1 TTT
528494 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:528656 original size:18 final size:19
Alignment explanation
Indices: 528633--528676 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
528623 CCAGTAATCC
*
528633 TATTCC-CTGGTAATCTTT
1 TATTCCACTGGTAATCTTA
528651 TATTCCCACTGGTAATCTTA
1 TATT-CCACTGGTAATCTTA
528671 TATTCC
1 TATTCC
528677 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 15 0.65
ACGTcount: A:0.20, C:0.25, G:0.09, T:0.45
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTA
Found at i:528664 original size:20 final size:20
Alignment explanation
Indices: 528639--528676 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
528629 ATCCTATTCC
*
528639 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTATATTCCCA
528659 CTGGTAATCTTATATTCC
1 CTGGTAATCTTATATTCC
528677 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTATATTCCCA
Found at i:530180 original size:16 final size:16
Alignment explanation
Indices: 530145--530185 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
530135 GTTTACTTCA
* *
530145 GAATGATT-AAGCGTT
1 GAATGATTCAAACGCT
530160 GAATGATTCAAACGCT
1 GAATGATTCAAACGCT
530176 GAATGATTCA
1 GAATGATTCA
530186 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:536429 original size:2 final size:2
Alignment explanation
Indices: 536422--536450 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
536412 GAATCAAAAT
536422 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
536451 TATTAACCAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:537363 original size:23 final size:24
Alignment explanation
Indices: 537334--537390 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
537324 ATTTGTTTAC
* *
537334 GTTCGTTTATGTTCATTTATT-GT
1 GTTCGTTTACGTTCATTCATTAGT
**
537357 GTTCGTTTACGTTTGTTCATTAGT
1 GTTCGTTTACGTTCATTCATTAGT
537381 GTTCGTTTAC
1 GTTCGTTTAC
537391 ATCCGTTCGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 17 0.59
24 12 0.41
ACGTcount: A:0.12, C:0.12, G:0.19, T:0.56
Consensus pattern (24 bp):
GTTCGTTTACGTTCATTCATTAGT
Found at i:537400 original size:14 final size:14
Alignment explanation
Indices: 537381--537430 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
537371 GTTCATTAGT
537381 GTTCGTTTACATCC
1 GTTCGTTTACATCC
*
537395 GTTCGTTTATTAT--
1 GTTCGTTTA-CATCC
*
537408 GTTTGTTTACATCC
1 GTTCGTTTACATCC
537422 GTTCGTTTA
1 GTTCGTTTA
537431 TGTTCATTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
12 2 0.07
13 8 0.28
14 17 0.59
15 2 0.07
ACGTcount: A:0.14, C:0.18, G:0.16, T:0.52
Consensus pattern (14 bp):
GTTCGTTTACATCC
Done.