Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_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: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 89
Found at i:237439 original size:36 final size:36
Alignment explanation
Indices: 237392--237669 Score: 430
Period size: 36 Copynumber: 7.7 Consensus size: 36
237382 GTGCTACATT
* *
237392 CTTCCGTTCGACTTGAATCGGAAGTACCGATGCTTC
1 CTTCCGTTCGACTTGAATCGGAAGTGCCGATGCCTC
* *
237428 CTTCAGTTCGACTTGAATCGGAAGTGCCGATGCTTC
1 CTTCCGTTCGACTTGAATCGGAAGTGCCGATGCCTC
*
237464 TTTCCGTTCGACTTGAATCGGAAGTGCCGATGCCTC
1 CTTCCGTTCGACTTGAATCGGAAGTGCCGATGCCTC
**
237500 CTTCCGTTCCTCTTGAATCGGAAGTGCCGATGCCTC
1 CTTCCGTTCGACTTGAATCGGAAGTGCCGATGCCTC
*
237536 CTTCCGTTCGAATTGAATCGGAAGTGCCGATGCCTC
1 CTTCCGTTCGACTTGAATCGGAAGTGCCGATGCCTC
* *
237572 ATTCCGTTCGACTTGAATCAGAAGTGCCGATGCCTC
1 CTTCCGTTCGACTTGAATCGGAAGTGCCGATGCCTC
* * * *
237608 CTTCCGTTCAACTTGAATCGGAAGTACCGATTCTTC
1 CTTCCGTTCGACTTGAATCGGAAGTGCCGATGCCTC
237644 CTTCCGTTCGACTTGAATCGGAAGTG
1 CTTCCGTTCGACTTGAATCGGAAGTG
237670 TAGATGAAAT
Statistics
Matches: 220, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 220 1.00
ACGTcount: A:0.19, C:0.28, G:0.23, T:0.30
Consensus pattern (36 bp):
CTTCCGTTCGACTTGAATCGGAAGTGCCGATGCCTC
Found at i:241597 original size:2 final size:2
Alignment explanation
Indices: 241592--241620 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
241582 TTTACATTAT
241592 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
241621 TAATGACCTA
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:248894 original size:6 final size:6
Alignment explanation
Indices: 248883--248919 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
248873 GACACGTTTT
248883 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
248920 GCCGAGCCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:248927 original size:5 final size:5
Alignment explanation
Indices: 248917--248950 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
248907 ACCACGACCA
* *
248917 CGAGC CGAGC CGAGC CGAGA CGAGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
248951 ACGGCGGCGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.26, C:0.32, G:0.41, T:0.00
Consensus pattern (5 bp):
CGAGC
Found at i:248932 original size:10 final size:10
Alignment explanation
Indices: 248916--248950 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
248906 GACCACGACC
248916 ACGAGCCGAG
1 ACGAGCCGAG
*
248926 CCGAGCCGAG
1 ACGAGCCGAG
248936 ACGAGCCGAG
1 ACGAGCCGAG
248946 ACGAG
1 ACGAG
248951 ACGGCGGCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.29, C:0.31, G:0.40, T:0.00
Consensus pattern (10 bp):
ACGAGCCGAG
Found at i:248940 original size:15 final size:15
Alignment explanation
Indices: 248916--248953 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
248906 GACCACGACC
*
248916 ACGAGCCGAGCCGAG
1 ACGAGACGAGCCGAG
*
248931 CCGAGACGAGCCGAG
1 ACGAGACGAGCCGAG
248946 ACGAGACG
1 ACGAGACG
248954 GCGGCGGCGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.32, G:0.39, T:0.00
Consensus pattern (15 bp):
ACGAGACGAGCCGAG
Found at i:249749 original size:28 final size:28
Alignment explanation
Indices: 249714--249767 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
249704 TTATATTATA
249714 TTACATTACATTACATTACATTACATAC
1 TTACATTACATTACATTACATTACATAC
249742 TTACATTACATTACATTACATTACAT
1 TTACATTACATTACATTACATTACAT
249768 TATTTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (28 bp):
TTACATTACATTACATTACATTACATAC
Found at i:249818 original size:5 final size:5
Alignment explanation
Indices: 249543--249802 Score: 304
Period size: 5 Copynumber: 52.4 Consensus size: 5
249533 TGTCTGGGAA
249543 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
249593 A-TAT ATTAT ATTAT ATTAT ATTAT -TTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
249641 ATTAT A-TAT ATT-T ATTAT A-TAT ATTAT ATATAT ATTATT ATT-T ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT-TAT ATTA-T ATTAT ATTAT
* * * * *
249689 ATTAT ATTAT ATGA- ATTAT ATTAT ATTAC ATTAC ATTAC ATTAC ATTACAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATT--AT
* * * * *
249740 ACTTAC ATTAC ATTAC ATTAC ATTAC ATTATTT ATTAT ATTAT A-TAT
1 A-TTAT ATTAT ATTAT ATTAT ATTAT ATTA--T ATTAT ATTAT ATTAT
249787 A-TAT ATTAT ATTAT AT
1 ATTAT ATTAT ATTAT AT
249803 ATTACATTTA
Statistics
Matches: 234, Mismatches: 6, Indels: 30
0.87 0.02 0.11
Matches are distributed among these distances:
4 35 0.15
5 180 0.77
6 11 0.05
7 6 0.03
8 2 0.01
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (5 bp):
ATTAT
Found at i:249834 original size:18 final size:17
Alignment explanation
Indices: 249544--249830 Score: 135
Period size: 19 Copynumber: 16.2 Consensus size: 17
249534 GTCTGGGAAA
249544 TTATATTATATTATATTAT
1 TTATATTATA-TAT-TTAT
249563 ATTATATTATATTATATTAT
1 -TTATATTATA-TAT-TTAT
249583 ATTATATTATATATATTAT
1 -TTATATTATATAT-TTAT
249602 ATTATATTATATTATTTAT
1 -TTATATTATA-TATTTAT
*
249621 ATTATATTATAT-TATA-
1 -TTATATTATATATTTAT
249637 TTATATTATATA--TAT
1 TTATATTATATATTTAT
249652 TTAT-TATATATATTATAT
1 TTATAT-TATATATT-TAT
*
249670 ATATATTAT-TATTTA-
1 TTATATTATATATTTAT
* *
249685 TTATATTATATTATATGAA
1 TTATATTATA-TAT-TTAT
* *
249704 TTATATTATATTACATTACA
1 TTATATTATA-TA-TTTA-T
* * ** *
249724 TTACATTACATTACATAC
1 TTATATTATA-TATTTAT
* * **
249742 TTACATTACAT-TACA-
1 TTATATTATATATTTAT
* *
249757 TTACATTACATTATTTA-
1 TTATATTATA-TATTTAT
*
249774 TTATATTATATATATAT
1 TTATATTATATATTTAT
*
249791 ATTATATTATATATTACAT
1 -TTATATTATATATT-TAT
*
249810 TTATATTATTTATTTAT
1 TTATATTATATATTTAT
249827 TTAT
1 TTAT
249831 TATTTTAGGT
Statistics
Matches: 226, Mismatches: 22, Indels: 41
0.78 0.08 0.14
Matches are distributed among these distances:
14 3 0.01
15 39 0.17
16 10 0.04
17 27 0.12
18 48 0.21
19 54 0.24
20 45 0.20
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATATTATATATTTAT
Found at i:258860 original size:28 final size:28
Alignment explanation
Indices: 258828--258882 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
258818 CTCTGTTTAC
258828 ATTATGTCATCGAGACAATGCTTGAAAT
1 ATTATGTCATCGAGACAATGCTTGAAAT
* *
258856 ATTATGTTATCGAGCCAATGCTTGAAA
1 ATTATGTCATCGAGACAATGCTTGAAA
258883 CCAATGTCGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Consensus pattern (28 bp):
ATTATGTCATCGAGACAATGCTTGAAAT
Found at i:259981 original size:22 final size:23
Alignment explanation
Indices: 259951--259994 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
259941 ATCCGAAGAA
259951 AAAACATATTACAAAAA-TAAAT
1 AAAACATATTACAAAAAGTAAAT
* *
259973 AAAATATATTATAAAAAGTAAA
1 AAAACATATTACAAAAAGTAAA
259995 GTCATTCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (23 bp):
AAAACATATTACAAAAAGTAAAT
Found at i:263062 original size:22 final size:23
Alignment explanation
Indices: 263032--263075 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
263022 ATCCGAAGAA
263032 AAAACATATTACAAAAA-TAAAT
1 AAAACATATTACAAAAAGTAAAT
* *
263054 AAAATATATTATAAAAAGTAAA
1 AAAACATATTACAAAAAGTAAA
263076 GTCATTCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (23 bp):
AAAACATATTACAAAAAGTAAAT
Found at i:269799 original size:6 final size:6
Alignment explanation
Indices: 269788--269818 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
269778 GACACATTTT
269788 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
269819 GCCGAGCCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:269826 original size:5 final size:5
Alignment explanation
Indices: 269815--269848 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
269805 GACCACGACC
* *
269815 ACGAG CCGAG CCGAG ACGAG ACGAG ACGAG ACGA
1 ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGA
269849 AATAGACGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.35, C:0.26, G:0.38, T:0.00
Consensus pattern (5 bp):
ACGAG
Found at i:271256 original size:4 final size:5
Alignment explanation
Indices: 270448--271274 Score: 724
Period size: 5 Copynumber: 167.8 Consensus size: 5
270438 TCTAGGATAT
270448 TTATA TT-TA TATATA TTATA TTATA TTATA TTATA TTTATA TTATA TTATA
1 TTATA TTATA T-TATA TTATA TTATA TTATA TTATA -TTATA TTATA TTATA
270499 TTATA TTATA TTATA TTATA TTATA -TATA TTATA TTATA -TATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
270547 TT-TA TTATA TT-TA TTATA TTATA TTATA TTATA TTATA -T-TA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
270593 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA -TATA -TATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
*
270641 TTATA TTATA TTATA TTATA TTATA TTTATA TTATA TTAT- CTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA -TTATA TTATA TTATA TTATA TTATA
270691 TTATA TTATA TTATA -TATA TT-TA TTATA TTATA -TATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
270738 TTATA TTATA TTATA -TATA TTATA -TATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* * * * * * * * *
270786 TTATA TTCTA TTCTA TTCTA TTCTA TTCTA TTCTA TTCTA TTCTA TTCTA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* * * * * *
270836 TTCTA TTCTA TTCTA TTCTA TTCTA TTCTA TTATA TTATATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA -T-TATA TTATA TTATA
270888 TTATA TTTATA TTATA TTATA TTATA TTATA TTA-A -TATA TTATATA
1 TTATA -TTATA TTATA TTATA TTATA TTATA TTATA TTATA -T-TATA
* * * * * * * * *
270934 TTATA TTCTA TTCTA TTCTA TTCTA TTCTA TTCTA TTCTA TTCTA TTCTA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* * * * * * * * * * * * *
270984 TTCTA -T-TA TTCTA TTCTA CTCTA CTCTA TTCTA CTCTCTA CTCTA CTCTA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA -T-TATA TTATA TTATA
* * * * * * * * * * * *
271034 CTCTA CTCTA CTCTA CTCTACTA CTCTA CTCTA CTCTACTA TTCTA TTCTA
1 TTATA TTATA TTATA -T-TA-TA TTATA TTATA -T-TA-TA TTATA TTATA
* * * * * * * * *
271085 TTCTA TTCTA TTCTA TTTATTA TTCTA TTCTA TTCTA TTCTA TTCTA TTCTA
1 TTATA TTATA TTATA -TTA-TA TTATA TTATA TTATA TTATA TTATA TTATA
* * *
271137 TTCTA TTCTA TTCTA TTATA TTATA -T-TA TTATA TTATA TTATA -TATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
271184 TTATA -TATA TT-TA TTATA TTATA -TATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
271231 TTATA TTATA TTATA -TATA TTA-A TTATA TTAT- TTAT- TTAT- TTAT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTAT
271275 TATTTAAGGT
Statistics
Matches: 760, Mismatches: 18, Indels: 89
0.88 0.02 0.10
Matches are distributed among these distances:
3 8 0.01
4 94 0.12
5 609 0.80
6 28 0.04
7 17 0.02
8 4 0.01
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:271276 original size:20 final size:22
Alignment explanation
Indices: 270448--271275 Score: 367
Period size: 23 Copynumber: 36.9 Consensus size: 22
270438 TCTAGGATAT
* *
270448 TTATATT-TA-TATATATTATA
1 TTATATTATATTATTTATTCTA
* *
270468 TTATATTATATTATAT-TTATA
1 TTATATTATATTATTTATTCTA
*
270489 TTATATTATATTA--TATTATA
1 TTATATTATATTATTTATTCTA
*
270509 TTATATTATATTATATATATTATA
1 TTATATTATATTAT-T-TATTCTA
*
270533 TTATA-TATATTATATTTATTATA
1 TTATATTATA-T-TATTTATTCTA
*
270556 TT-TATTATATTA--TATTATA
1 TTATATTATATTATTTATTCTA
*
270575 TTATATTATATTATTATATTATA
1 TTATATTATATTATT-TATTCTA
*
270598 TTATATTATATTA--TATTATA
1 TTATATTATATTATTTATTCTA
* *
270618 TTATATTATATTATATATATATA
1 TTATATTATATTATTTAT-TCTA
*
270641 TTATATTATATTATATTATATTATA
1 TTATATTATA-T-TATT-TATTCTA
*
270666 TTTATATTATATTATCTATATTATA
1 -TTATATTATATTAT-T-TATTCTA
270691 TTATATTATATTATATATATT-TA
1 TTATATTATATTAT-T-TATTCTA
*
270714 TTATATTATATATATTATATTATA
1 TTATATTATAT-TATT-TATTCTA
*
270738 TTATATTATATTATATATAT-TA
1 TTATATTATATTATTTAT-TCTA
*
270760 TATATATTATATTA--TATTATA
1 T-TATATTATATTATTTATTCTA
270781 TTATATTATATTCTATTCTATTCTA
1 TTATATTATA-T-TATT-TATTCTA
* *
270806 TTCTATTCTATTCTATTCTATTCTA
1 TTATATTATA-T-TATT-TATTCTA
* *
270831 TTCTATTCTATTCTATTCTATTCTA
1 TTATATTATA-T-TATT-TATTCTA
* * *
270856 TTCTATTCTATTATATTA-TATA
1 TTATATTATATTAT-TTATTCTA
* *
270878 TTATATTATATTATAT-TTATA
1 TTATATTATATTATTTATTCTA
270899 TTATATTATATTATATTATAT-TA
1 TTATATTATATTAT-TTAT-TCTA
*
270922 ATATATTATA-TATTATATTCTA
1 TTATATTATATTATT-TATTCTA
* * *
270944 TTCTATTCTA-T-TCTATTCTA
1 TTATATTATATTATTTATTCTA
* * *
270964 TTCTATTCTA-T-TCTATTCTA
1 TTATATTATATTATTTATTCTA
* *
270984 TTCTATTAT-TCTATTCTACTCTA
1 TTATATTATAT-TATT-TATTCTA
* * * * * * *
271007 CTCTATTCTACTCTCTACTCTA
1 TTATATTATATTATTTATTCTA
* * * * *
271029 CTCTACTCTACTCTACTCTACTCTACTA
1 TTATATTATA-T-TA-TTTA-T-T-CTA
* * * * *
271057 CTCTACTCTACTCTA-CTATTCTA
1 TTATATTATA-T-TATTTATTCTA
* * *
271080 TTCTATTCTA-T-TCTATTCTA
1 TTATATTATATTATTTATTCTA
271100 TT-TATTAT-TCTATTCTATTCTA
1 TTATATTATAT-TATT-TATTCTA
* *
271122 TTCTATTCTATTCTATTCTATTCTA
1 TTATATTATA-T-TATT-TATTCTA
* *
271147 TTCTATTATATTATATTATTATA
1 TTATATTATATTAT-TTATTCTA
*
271170 TTATATTATA-TATATTATATATA
1 TTATATTATATTAT-TTAT-TCTA
*
271193 TT-TATTATATTATATATATTATA
1 TTATATTATATTAT-T-TATTCTA
*
271216 TTATATTATATTA--TATTATA
1 TTATATTATATTATTTATTCTA
* *
271236 TTATATTATATATATTAATTATA
1 TTATATTATAT-TATTTATTCTA
271259 TTAT-TTAT-TTATTTATT
1 TTATATTATATTATTTATT
271276 ATTTAAGGTC
Statistics
Matches: 704, Mismatches: 38, Indels: 132
0.81 0.04 0.15
Matches are distributed among these distances:
19 15 0.02
20 137 0.19
21 56 0.08
22 96 0.14
23 179 0.25
24 74 0.11
25 112 0.16
26 16 0.02
27 1 0.00
28 18 0.03
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (22 bp):
TTATATTATATTATTTATTCTA
Found at i:271277 original size:15 final size:17
Alignment explanation
Indices: 270454--271280 Score: 286
Period size: 18 Copynumber: 47.7 Consensus size: 17
270444 ATATTTATAT
*
270454 TTATATATATTATATTATA
1 TTATAT-TATT-TATTCTA
* *
270473 TTATATTATAT-TTATA
1 TTATATTATTTATTCTA
*
270489 TTATATTA--TATTATA
1 TTATATTATTTATTCTA
270504 TTATATTATATTATAT-TA
1 TTATATTAT-TTAT-TCTA
*
270522 TATATATTATATTATATATA
1 T-TATATTAT-TTAT-TCTA
270542 TTATATTTATTATATT-TA
1 TTATA-TTATT-TATTCTA
*
270560 TTATATTA--TATTATA
1 TTATATTATTTATTCTA
*
270575 TTATATTATATTATTATA
1 TTATATTAT-TTATTCTA
*
270593 TTATATTA--TATTATA
1 TTATATTATTTATTCTA
*
270608 TTATATTA--TATTATA
1 TTATATTATTTATTCTA
* *
270623 TTATATTATATATATATA
1 TTATATTATTTAT-TCTA
*
270641 TTATATTA--TATTATA
1 TTATATTATTTATTCTA
* *
270656 TTATATTATAT-TTATA
1 TTATATTATTTATTCTA
*
270672 TTATATTATCTA---TA
1 TTATATTATTTATTCTA
*
270686 TTATATTA--TATTATA
1 TTATATTATTTATTCTA
*
270701 TTATATATATTTATTATA
1 TTATAT-TATTTATTCTA
*
270719 TTATATATATTATATTATA
1 TTATAT-TATT-TATTCTA
*
270738 TTATATTA--TATTATA
1 TTATATTATTTATTCTA
*
270753 -TATATTATATATATTATA
1 TTATATTAT-T-TATTCTA
*
270771 TTATATTA--TATTATA
1 TTATATTATTTATTCTA
270786 TTATATTCTATTCTATTCTA
1 TTATA-T-TATT-TATTCTA
*
270806 TTCTATTCTATTCTATTCTA
1 TTATA-T-TATT-TATTCTA
*
270826 TTCTATTCTATTCTATTCTA
1 TTATA-T-TATT-TATTCTA
*
270846 TTCTATTCTATTCTATTCTA
1 TTATA-T-TATT-TATTCTA
* *
270866 TTATATTATATATTATA
1 TTATATTATTTATTCTA
* *
270883 TTATATTATAT-TTATA
1 TTATATTATTTATTCTA
*
270899 TTATATTA--TATTATA
1 TTATATTATTTATTCTA
*
270914 TTATATTA---A-TATA
1 TTATATTATTTATTCTA
270927 TTATA-TATTATATTCTA
1 TTATATTATT-TATTCTA
*
270944 TTCTATTCTATTCTATTCTA
1 TTATA-T-TATT-TATTCTA
*
270964 TTCTATTCTATTCTATTCTA
1 TTATA-T-TATT-TATTCTA
*
270984 TTCTATTATTCTATTCTA
1 TTATATTATT-TATTCTA
* *
271002 CTCTACTCTATTCTACTCTCTA
1 TTATA-T-TATT-TA-T-TCTA
* *
271024 CTCTACTCTACTCTACTCTACTCTA
1 -T-TA---TA-T-TA-TTTATTCTA
* * * * *
271049 CTCTACTACTCTACTCTA
1 TTATATTA-TTTATTCTA
* * *
271067 CTCTACTATTCTATTCTA
1 TTATATTATT-TATTCTA
* *
271085 TTCTA-T-TCTATTCTA
1 TTATATTATTTATTCTA
271100 TT-TATTATTCTATTCTA
1 TTATATTATT-TATTCTA
*
271117 TTCTATTCTATTCTATTCTA
1 TTATA-T-TATT-TATTCTA
* *
271137 TTCTA-T-TCTATTCTA
1 TTATATTATTTATTCTA
*
271152 TTATATTATATTATTATA
1 TTATATTAT-TTATTCTA
*
271170 TTATATTA--TA-TATA
1 TTATATTATTTATTCTA
*
271184 TTATATATATTTATTATA
1 TTATAT-TATTTATTCTA
*
271202 TTATATATATTATATTATA
1 TTATAT-TATT-TATTCTA
*
271221 TTATATTA--TATTATA
1 TTATATTATTTATTCTA
*
271236 TTATATTATATATATT-AA
1 TTATATTAT-T-TATTCTA
271254 TTATATTATTTATT-TA
1 TTATATTATTTATTCTA
271270 TT-TATTATTTA
1 TTATATTATTTA
271281 AGGTCTAAAA
Statistics
Matches: 705, Mismatches: 29, Indels: 152
0.80 0.03 0.17
Matches are distributed among these distances:
12 4 0.01
13 9 0.01
14 36 0.05
15 154 0.22
16 59 0.08
17 50 0.07
18 162 0.23
19 69 0.10
20 141 0.20
21 1 0.00
22 4 0.01
23 1 0.00
24 1 0.00
25 4 0.01
27 9 0.01
28 1 0.00
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATATTATTTATTCTA
Found at i:280326 original size:28 final size:28
Alignment explanation
Indices: 280280--280334 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
280270 CTCTGTTTAC
280280 ATTATGTCATCGAGACAATGCTTGAAAT
1 ATTATGTCATCGAGACAATGCTTGAAAT
* * *
280308 ATTATGTTATCGTGCCAATGCTTGAAA
1 ATTATGTCATCGAGACAATGCTTGAAA
280335 CCAATGTCGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (28 bp):
ATTATGTCATCGAGACAATGCTTGAAAT
Found at i:280550 original size:30 final size:31
Alignment explanation
Indices: 280487--280550 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
280477 AACTTTTAAA
* * * *
280487 AGTCAGAGGACTCAACAAAACATCATTCTAT
1 AGTCAGAGAACTCAAAAAAACAGCATCCTAT
*
280518 AGTCAGAGAACTCAAAAAAATAGCA-CCTAT
1 AGTCAGAGAACTCAAAAAAACAGCATCCTAT
280548 AGT
1 AGT
280551 TGATGAACCA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 7 0.25
31 21 0.75
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.20
Consensus pattern (31 bp):
AGTCAGAGAACTCAAAAAAACAGCATCCTAT
Found at i:297174 original size:8 final size:8
Alignment explanation
Indices: 297161--297203 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
297151 TGTTATGAGT
297161 AAATTTTA
1 AAATTTTA
297169 AAATTTTA
1 AAATTTTA
* **
297177 AAAATAAA
1 AAATTTTA
297185 AAATTTT-
1 AAATTTTA
297192 AAATTTTA
1 AAATTTTA
297200 AAAT
1 AAAT
297204 AAACAAAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
7 7 0.25
8 21 0.75
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
AAATTTTA
Found at i:302398 original size:6 final size:6
Alignment explanation
Indices: 302383--302419 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
302373 CGATAAAAAC
*
302383 AAAATAT AAAACT AAAATT AAAATT AAAATT AAAATT
1 AAAAT-T AAAATT AAAATT AAAATT AAAATT AAAATT
302420 TGGGAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
6 24 0.86
7 4 0.14
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (6 bp):
AAAATT
Found at i:302404 original size:12 final size:12
Alignment explanation
Indices: 302378--302417 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
302368 AATCCCGATA
302378 AAAAC-AAAATAT
1 AAAACTAAAAT-T
302390 AAAACTAAAATT
1 AAAACTAAAATT
*
302402 AAAATTAAAATT
1 AAAACTAAAATT
302414 AAAA
1 AAAA
302418 TTTGGGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 21 0.81
13 5 0.19
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAACTAAAATT
Found at i:302968 original size:17 final size:17
Alignment explanation
Indices: 302946--302996 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
302936 CTATTACATA
302946 AATTTTATAATGATATT
1 AATTTTATAATGATATT
*** *
302963 AATTTTGCCATTATA-T
1 AATTTTATAATGATATT
302979 AAGTTTTATAATGATATT
1 AA-TTTTATAATGATATT
302997 TCAATGTTCT
Statistics
Matches: 24, Mismatches: 8, Indels: 3
0.69 0.23 0.09
Matches are distributed among these distances:
16 3 0.12
17 20 0.83
18 1 0.04
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.51
Consensus pattern (17 bp):
AATTTTATAATGATATT
Found at i:302986 original size:34 final size:34
Alignment explanation
Indices: 302927--302996 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
302917 TTTTAAAATT
*
302927 TTAACTTTGCTATTACATAAATTTTATAATGATA
1 TTAACTTTGCCATTACATAAATTTTATAATGATA
* * *
302961 TTAATTTTGCCATTATATAAGTTTTATAATGATA
1 TTAACTTTGCCATTACATAAATTTTATAATGATA
302995 TT
1 TT
302997 TCAATGTTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (34 bp):
TTAACTTTGCCATTACATAAATTTTATAATGATA
Found at i:305035 original size:13 final size:12
Alignment explanation
Indices: 305017--305046 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
305007 CCACACCGAT
305017 CGTCGTCCTTTA
1 CGTCGTCCTTTA
305029 CCGTCGTCCTTTA
1 -CGTCGTCCTTTA
305042 CGTCG
1 CGTCG
305047 ACAAAGCTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.07, C:0.37, G:0.20, T:0.37
Consensus pattern (12 bp):
CGTCGTCCTTTA
Found at i:310544 original size:21 final size:20
Alignment explanation
Indices: 310501--310548 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
310491 ATAAAGACTT
*
310501 AAAC-ATAAAATAAATGCCC
1 AAACTATAAAATAAATGCAC
* *
310520 AAACATATAAAATAAGTGCAT
1 AAAC-TATAAAATAAATGCAC
310541 AAACTATA
1 AAACTATA
310549 GTGCCTAACG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 4 0.17
20 4 0.17
21 16 0.67
ACGTcount: A:0.58, C:0.15, G:0.06, T:0.21
Consensus pattern (20 bp):
AAACTATAAAATAAATGCAC
Found at i:311532 original size:30 final size:30
Alignment explanation
Indices: 311469--311525 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
311459 AGAACCGGAA
** *
311469 GAACCGGCTAAAAACCGGGAAAACCGGGGT
1 GAACCGGCTAAAAACCGACAAAACCGAGGT
*
311499 GAACCGGCTGAAAACCGACAAAACCGA
1 GAACCGGCTAAAAACCGACAAAACCGA
311526 TTTGAACTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.40, C:0.26, G:0.28, T:0.05
Consensus pattern (30 bp):
GAACCGGCTAAAAACCGACAAAACCGAGGT
Found at i:311772 original size:25 final size:24
Alignment explanation
Indices: 311744--311814 Score: 79
Period size: 24 Copynumber: 2.9 Consensus size: 24
311734 AACTCAAAAA
* * *
311744 AAAATTAGAAGTTCGATTGAAGCCT
1 AAAATTAG-AGCTCAATCGAAGCCT
*
311769 AAAATTTGAGCTCAATCGAAGCCT
1 AAAATTAGAGCTCAATCGAAGCCT
* *
311793 AAAATTTGAGCTCAATTGAAGC
1 AAAATTAGAGCTCAATCGAAGC
311815 GAAAGAATAG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
24 34 0.83
25 7 0.17
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (24 bp):
AAAATTAGAGCTCAATCGAAGCCT
Found at i:311791 original size:24 final size:24
Alignment explanation
Indices: 311762--311814 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
311752 AAGTTCGATT
311762 GAAGCCTAAAATTTGAGCTCAATC
1 GAAGCCTAAAATTTGAGCTCAATC
*
311786 GAAGCCTAAAATTTGAGCTCAATT
1 GAAGCCTAAAATTTGAGCTCAATC
311810 GAAGC
1 GAAGC
311815 GAAAGAATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
GAAGCCTAAAATTTGAGCTCAATC
Found at i:312361 original size:35 final size:34
Alignment explanation
Indices: 312313--312425 Score: 154
Period size: 35 Copynumber: 3.2 Consensus size: 34
312303 AAAACAATTC
*
312313 TCAATTTCATTCTAAACCACAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAATAAT
*
312348 TCAATTTCGTTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
* * *
312383 TCAATTACATTCTAAAACCCAAATTCTAAAATACT
1 TCAATTTCATTCT-AAACCCAAATTCCAAAATAAT
312418 TCAATTTC
1 TCAATTTC
312426 TGTCTTTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
34 1 0.01
35 62 0.90
36 6 0.09
ACGTcount: A:0.42, C:0.23, G:0.02, T:0.34
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:313476 original size:35 final size:35
Alignment explanation
Indices: 313421--313532 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
313411 ATTTCTCCTT
* *
313421 AAATTGAAGTATTTTAGAATTTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
* * *
313456 TAATTTAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
* * * *
313491 AAATTGAATTACTTTGAAATTTGGGATTTATAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
313526 AAATTGA
1 AAATTGA
313533 GGAATGTTTT
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.36, C:0.01, G:0.21, T:0.43
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
Found at i:324067 original size:71 final size:70
Alignment explanation
Indices: 323950--324106 Score: 251
Period size: 71 Copynumber: 2.2 Consensus size: 70
323940 TATCATAATC
* * *
323950 ATGTAATTAAGATATTTTTTCTCAACAAGATATTTTTATTACATATAAAGTACAAATCTTACCCG
1 ATGTAATTAAGATATTTTTTCTCAACAAGATAATTTTATTACATATAAAGCACAAACCTTACCCG
324015 ATTGT
66 ATTGT
* * *
324020 ATGTAATTAAGATTTTTTTTCCTCAACAAGATAATTTTATTAGATATAAAGCACAAGCCTTACCC
1 ATGTAATTAAGATATTTTTT-CTCAACAAGATAATTTTATTACATATAAAGCACAAACCTTACCC
324085 GATTGT
65 GATTGT
324091 ATGTAATTAAGATATT
1 ATGTAATTAAGATATT
324107 ATTATATGTA
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
70 19 0.24
71 60 0.76
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (70 bp):
ATGTAATTAAGATATTTTTTCTCAACAAGATAATTTTATTACATATAAAGCACAAACCTTACCCG
ATTGT
Found at i:326717 original size:2 final size:2
Alignment explanation
Indices: 326712--326744 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
326702 ACATACATAC
326712 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
326745 AACAGATCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:329757 original size:59 final size:58
Alignment explanation
Indices: 329694--329833 Score: 138
Period size: 59 Copynumber: 2.4 Consensus size: 58
329684 GGGTAAAGTA
*
329694 TATAAATGGTCCTTTGACTATAGAATA-ATGCTTTATTAAATCCCTTGACTATTAAAAAT
1 TATAAATGGTCCTTTGACTATAG-ATAGATGCTTT-TTAAATCCCTTAACTATTAAAAAT
** ** * * *
329753 TATAAAATAATCCTTCAACTATTGATAGTTGCTTTTTAAGTCCCTTAACTATTAAAAAT
1 TAT-AAATGGTCCTTTGACTATAGATAGATGCTTTTTAAATCCCTTAACTATTAAAAAT
* * *
329812 TACAAAATGGTCATCTGACTAT
1 TA-TAAATGGTCCTTTGACTAT
329834 TTATTATGTT
Statistics
Matches: 63, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
59 42 0.67
60 21 0.33
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (58 bp):
TATAAATGGTCCTTTGACTATAGATAGATGCTTTTTAAATCCCTTAACTATTAAAAAT
Found at i:330152 original size:60 final size:60
Alignment explanation
Indices: 330042--330163 Score: 149
Period size: 60 Copynumber: 2.0 Consensus size: 60
330032 TAATCGAGTA
* ** *
330042 ACCATTTTGTAACTTTTAATAGTTGAGAGACTCAATAAAGAAACTCCCTATAGTCGAGGG
1 ACCATTTTATAACTTTTAATAGTCAAGAGACTCAATAAAGAAACTCCCTATAGTCAAGGG
* * *
330102 ACCATTTTATAATTTTTAATAGTCAAGAGACTCAATATAGCAGTA-T-CCTATAGTCAAGGG
1 ACCATTTTATAACTTTTAATAGTCAAGAGACTCAATAAAG-A-AACTCCCTATAGTCAAGGG
330162 AC
1 AC
330164 TGTTTATCTA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
60 50 0.94
61 2 0.04
62 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (60 bp):
ACCATTTTATAACTTTTAATAGTCAAGAGACTCAATAAAGAAACTCCCTATAGTCAAGGG
Found at i:333368 original size:19 final size:19
Alignment explanation
Indices: 333344--333380 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
333334 ATGACCAACA
*
333344 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
333363 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
333381 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:333475 original size:20 final size:21
Alignment explanation
Indices: 333425--333476 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
333415 CATTTTGACT
* *
333425 ATCGCATTGCGATTTTCCAAA
1 ATCGCAATGCGATTTTCAAAA
* *
333446 TTCGC-GTGCGATTTT-AAAA
1 ATCGCAATGCGATTTTCAAAA
333465 ATCGCAATGCGA
1 ATCGCAATGCGA
333477 ATATGTAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 7 0.28
20 14 0.56
21 4 0.16
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (21 bp):
ATCGCAATGCGATTTTCAAAA
Found at i:333486 original size:20 final size:20
Alignment explanation
Indices: 333463--333516 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
333453 GCGATTTTAA
333463 AAATCGCAATGCGAATATGT
1 AAATCGCAATGCGAATATGT
*
333483 AAATCGCAATGAGAATATGT
1 AAATCGCAATGCGAATATGT
*
333503 AAATCGCAACGCGA
1 AAATCGCAATGCGA
333517 TTCTGACTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAATGCGAATATGT
Found at i:333528 original size:20 final size:20
Alignment explanation
Indices: 333505--333552 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
333495 GAATATGTAA
*
333505 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
333525 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
333545 GTCGCAAC
1 ATCGCAAC
333553 ACTGAATTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:334626 original size:15 final size:15
Alignment explanation
Indices: 334608--334644 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
334598 AGAAAAAGAA
334608 GAAGAAAAAATCCCC
1 GAAGAAAAAATCCCC
*
334623 GAAG-AAAAGTCCCC
1 GAAGAAAAAATCCCC
334637 GAAGAAAA
1 GAAGAAAA
334645 TGCCACGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.54, C:0.22, G:0.19, T:0.05
Consensus pattern (15 bp):
GAAGAAAAAATCCCC
Found at i:336976 original size:20 final size:20
Alignment explanation
Indices: 336880--336976 Score: 122
Period size: 20 Copynumber: 4.8 Consensus size: 20
336870 TTACACATTC
* *
336880 ATTTGAATATCGTAACGCGA
1 ATTTGACTATCGCAACGCGA
*
336900 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
**
336920 ATTTGACTATCGCAACATGA
1 ATTTGACTATCGCAACGCGA
* *
336940 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
*
336960 ATTTGACTATCACAACG
1 ATTTGACTATCGCAACG
336977 AAAAAATCAC
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.29
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:337044 original size:20 final size:20
Alignment explanation
Indices: 337015--337076 Score: 106
Period size: 20 Copynumber: 3.1 Consensus size: 20
337005 GCAACATGAA
*
337015 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCATTGCGATT
*
337035 TTGGCTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
337055 TTGACTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
337075 TT
1 TT
337077 AAGTTTAGCG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:337090 original size:20 final size:19
Alignment explanation
Indices: 337020--337092 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
337010 ATGAATTGAC
* *
337020 TTTCGCGTTGCGATTTTGG
1 TTTCGCATTGCGATTTTAG
*
337039 CTTTCGCATTGCGATTTTGAC
1 -TTTCGCATTGCGATTTT-AG
337060 TTTCGCATTGCGATTTTAAG
1 TTTCGCATTGCGATTTT-AG
* *
337080 TTTAGCGTTGCGA
1 TTTCGCATTGCGA
337093 AAGTGTACCT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.14, C:0.18, G:0.25, T:0.44
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTAG
Found at i:337091 original size:40 final size:40
Alignment explanation
Indices: 337015--337092 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
337005 GCAACATGAA
* * *
337015 TTGACTTTCGCGTTGCGATTTTGGCTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATTTTAGCTTTAGCATTGCGATT
*
337055 TTGACTTTCGCATTGCGATTTTAAG-TTTAGCGTTGCGA
1 TTGACTTTCGCATTGCGATTTT-AGCTTTAGCATTGCGA
337093 AAGTGTACCT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 32 0.97
41 1 0.03
ACGTcount: A:0.14, C:0.18, G:0.24, T:0.44
Consensus pattern (40 bp):
TTGACTTTCGCATTGCGATTTTAGCTTTAGCATTGCGATT
Found at i:337233 original size:14 final size:14
Alignment explanation
Indices: 337214--337248 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
337204 TCAATTAAAA
337214 AAATCAACTTTTAC
1 AAATCAACTTTTAC
337228 AAATCAACTTTTAC
1 AAATCAACTTTTAC
337242 AAATCAA
1 AAATCAA
337249 TTAAACAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATCAACTTTTAC
Found at i:337270 original size:81 final size:81
Alignment explanation
Indices: 337145--337320 Score: 191
Period size: 81 Copynumber: 2.1 Consensus size: 81
337135 ATTGAAATCA
*
337145 ACAAATCAACTTTTACATTTCAATCAATTAAACAAGCACAAATAATAA-TTA-TTTACACATCAA
1 ACAAATCAACTTTTACA--T-AATCAATTAAACAAGCAAAAATAATAATTTATTTTACACATCAA
337208 TTAAAAAAATCA-ACTTTT
63 TTAAAAAAATCAGACTTTT
* *
337226 ACAAATCAACTTTTACA-AATCAATTAAACAAGCAAAAAATAATAATAATTCTTATTTTCCTCAT
1 ACAAATCAACTTTTACATAATCAATTAAACAAGC---AAA-AATAATAA-T-TTATTTTACACAT
*
337290 CAATTAAACAAATCAGACTTTT
60 CAATTAAAAAAATCAGACTTTT
337312 A-AGAATCAA
1 ACA-AATCAA
337321 TTAAACAATA
Statistics
Matches: 81, Mismatches: 4, Indels: 15
0.81 0.04 0.15
Matches are distributed among these distances:
77 16 0.20
80 2 0.02
81 25 0.31
84 3 0.04
85 22 0.27
86 13 0.16
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.31
Consensus pattern (81 bp):
ACAAATCAACTTTTACATAATCAATTAAACAAGCAAAAATAATAATTTATTTTACACATCAATTA
AAAAAATCAGACTTTT
Found at i:338714 original size:18 final size:20
Alignment explanation
Indices: 338691--338730 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
338681 CTCTTGAGGG
338691 ATGATA-AG-GGCCTCTTGA
1 ATGATAGAGAGGCCTCTTGA
338709 ATGATAGGAGAGGCCTCTTGA
1 ATGATA-GAGAGGCCTCTTGA
338730 A
1 A
338731 CGATGACAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
20 2 0.11
21 11 0.58
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.25
Consensus pattern (20 bp):
ATGATAGAGAGGCCTCTTGA
Found at i:338727 original size:42 final size:42
Alignment explanation
Indices: 338618--338738 Score: 138
Period size: 42 Copynumber: 2.9 Consensus size: 42
338608 GTGAATCAGG
* * *
338618 CTCTTGAATGGTAGGAGAGACCTCTTCAACGATGACATGGGC
1 CTCTTGAATGGTAGGAGAGGCCTCTTGAACGATGACAAGGGC
* ** *
338660 CTCTTGAACGGT-GG-GAGGCGACTCTTGAGGGATGATAAGGGC
1 CTCTTGAATGGTAGGAGAGGC--CTCTTGAACGATGACAAGGGC
*
338702 CTCTTGAATGATAGGAGAGGCCTCTTGAACGATGACA
1 CTCTTGAATGGTAGGAGAGGCCTCTTGAACGATGACA
338739 GGTGAGTCAG
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
40 4 0.06
41 2 0.03
42 50 0.79
43 2 0.03
44 5 0.08
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (42 bp):
CTCTTGAATGGTAGGAGAGGCCTCTTGAACGATGACAAGGGC
Found at i:339241 original size:20 final size:20
Alignment explanation
Indices: 339216--339259 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
339206 AATTGTTTCT
339216 GAAACTTAAAATCACAACAC
1 GAAACTTAAAATCACAACAC
* *
339236 GAAACTTAAAATCTCAACGC
1 GAAACTTAAAATCACAACAC
339256 GAAA
1 GAAA
339260 ATGACTATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.23, G:0.09, T:0.16
Consensus pattern (20 bp):
GAAACTTAAAATCACAACAC
Found at i:339301 original size:20 final size:19
Alignment explanation
Indices: 339250--339301 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 19
339240 CTTAAAATCT
339250 CAACGCGAAAATGACTATCG
1 CAACGC-AAAATGACTATCG
339270 CAACGCAGAAATGACTATCG
1 CAACGCA-AAATGACTATCG
339290 CAACGACAAAAT
1 CAACG-CAAAAT
339302 CACAACGCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 1 0.03
20 27 0.90
21 2 0.07
ACGTcount: A:0.44, C:0.25, G:0.17, T:0.13
Consensus pattern (19 bp):
CAACGCAAAATGACTATCG
Found at i:339320 original size:19 final size:19
Alignment explanation
Indices: 339296--339333 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
339286 ATCGCAACGA
339296 CAAAATCACAACGCGAAAC
1 CAAAATCACAACGCGAAAC
*
339315 CAAAATCGCAACGCGAAAC
1 CAAAATCACAACGCGAAAC
339334 TAAATCCGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.32, G:0.13, T:0.05
Consensus pattern (19 bp):
CAAAATCACAACGCGAAAC
Found at i:339413 original size:33 final size:34
Alignment explanation
Indices: 339343--339417 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 34
339333 CTAAATCCGT
* * * *
339343 GTTGCGATTTTTATTTTTACATTGCGTTTTTGAC
1 GTTGCGATTTTTATTTTCACATTGCGATTATCAC
* *
339377 GTTGCGATTTTTA-TTTCGCATTGCGATTATCCC
1 GTTGCGATTTTTATTTTCACATTGCGATTATCAC
339410 GTTGCGAT
1 GTTGCGAT
339418 AGTCAAATTC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
33 22 0.63
34 13 0.37
ACGTcount: A:0.15, C:0.16, G:0.20, T:0.49
Consensus pattern (34 bp):
GTTGCGATTTTTATTTTCACATTGCGATTATCAC
Found at i:339434 original size:20 final size:20
Alignment explanation
Indices: 339409--339477 Score: 120
Period size: 20 Copynumber: 3.5 Consensus size: 20
339399 GCGATTATCC
339409 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
339429 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
339449 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
339469 CGTTGCGAT
1 CGTTGCGAT
339478 TTTAAGTTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:339487 original size:20 final size:20
Alignment explanation
Indices: 339409--339496 Score: 81
Period size: 20 Copynumber: 4.4 Consensus size: 20
339399 GCGATTATCC
*
339409 CGTTGCGATAGTCAA-ATTCG
1 CGTTGCGATAGT-AAGTTTCG
*
339429 CGTTGCGATAGTCAA-ATTCG
1 CGTTGCGATAGT-AAGTTTCG
* *
339449 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAGTTTCG
**
339469 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATAGTAAGTTTCG
*
339489 TGTTGCGA
1 CGTTGCGA
339497 CTATTCTTCT
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
19 1 0.02
20 59 0.98
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTAAGTTTCG
Found at i:341416 original size:20 final size:20
Alignment explanation
Indices: 341393--341460 Score: 84
Period size: 21 Copynumber: 3.4 Consensus size: 20
341383 TTTGAAACTT
*
341393 AAAATTGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
341413 AAAATCGCAACACGAAAAATG
1 AAAATCGCAACACG-AAAATG
** *
341434 ACTATCGCAACACGAAACT-
1 AAAATCGCAACACGAAAATG
341453 AAAATCGC
1 AAAATCGC
341461 GTTGCAATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 6 0.15
20 17 0.41
21 18 0.44
ACGTcount: A:0.51, C:0.22, G:0.13, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:341879 original size:22 final size:22
Alignment explanation
Indices: 341849--341899 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
341839 GATGGAGATA
*
341849 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGAAGATGGG
* *
341871 GATGGATTTCGTCGAAGATGGG
1 GACGGATTTCGCCGAAGATGGG
341893 GACGGAT
1 GACGGAT
341900 GTCACCGTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.14, G:0.43, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGCCGAAGATGGG
Found at i:342143 original size:20 final size:20
Alignment explanation
Indices: 342099--342203 Score: 113
Period size: 20 Copynumber: 5.2 Consensus size: 20
342089 GCGTTGCGAC
* *
342099 TCGCGTTGCGATAATACAAAA
1 TCGCATTGCGAT-ATTCAAAA
*
342120 TCGCATTGCGATATTCAGAA
1 TCGCATTGCGATATTCAAAA
* * *
342140 TCGCGTTGCGAT-TTACATAT
1 TCGCATTGCGATATT-CAAAA
*
342160 TCGCATTGCGATAGTCAAAA
1 TCGCATTGCGATATTCAAAA
*
342180 TCGCATTGCGATAGTCAAAA
1 TCGCATTGCGATATTCAAAA
342200 TCGC
1 TCGC
342204 CCTGCGAATC
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.03
20 58 0.81
21 12 0.17
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (20 bp):
TCGCATTGCGATATTCAAAA
Found at i:342210 original size:40 final size:41
Alignment explanation
Indices: 342099--342203 Score: 133
Period size: 40 Copynumber: 2.6 Consensus size: 41
342089 GCGTTGCGAC
* *
342099 TCGCGTTGCGATAATACAAAATCGCATTGCGATATTCAGAA
1 TCGCGTTGCGATAATACAAAATCGCATTGCGATAGTCAAAA
* * *
342140 TCGCGTTGCGAT-TTACATATTCGCATTGCGATAGTCAAAA
1 TCGCGTTGCGATAATACAAAATCGCATTGCGATAGTCAAAA
* *
342180 TCGCATTGCGATAGT-CAAAATCGC
1 TCGCGTTGCGATAATACAAAATCGC
342204 CCTGCGAATC
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
40 41 0.76
41 13 0.24
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (41 bp):
TCGCGTTGCGATAATACAAAATCGCATTGCGATAGTCAAAA
Found at i:342248 original size:20 final size:19
Alignment explanation
Indices: 342225--342270 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
342215 GGAAACTGAT
* *
342225 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
342245 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
342264 TTGCGAT
1 TTGCGAT
342271 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:342260 original size:19 final size:19
Alignment explanation
Indices: 342236--342272 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
342226 TGCGATACTG
*
342236 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
342255 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
342273 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:350645 original size:8 final size:8
Alignment explanation
Indices: 350634--350684 Score: 54
Period size: 8 Copynumber: 6.8 Consensus size: 8
350624 AAAATAAAAA
350634 AAGTTAGT
1 AAGTTAGT
350642 AAGTTAG-
1 AAGTTAGT
*
350649 AAGTCAGT
1 AAGTTAGT
350657 AAGTTA-T
1 AAGTTAGT
*
350664 AAATTAGT
1 AAGTTAGT
*
350672 AAATTAG-
1 AAGTTAGT
350679 AAGTTA
1 AAGTTA
350685 ATATATTAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
7 17 0.46
8 20 0.54
ACGTcount: A:0.45, C:0.02, G:0.20, T:0.33
Consensus pattern (8 bp):
AAGTTAGT
Found at i:350657 original size:15 final size:15
Alignment explanation
Indices: 350634--350684 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
350624 AAAATAAAAA
350634 AAGTTAGTAAGTTAG
1 AAGTTAGTAAGTTAG
* *
350649 AAGTCAGTAAGTTAT
1 AAGTTAGTAAGTTAG
* *
350664 AAATTAGTAAATTAG
1 AAGTTAGTAAGTTAG
350679 AAGTTA
1 AAGTTA
350685 ATATATTAGA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.45, C:0.02, G:0.20, T:0.33
Consensus pattern (15 bp):
AAGTTAGTAAGTTAG
Found at i:350682 original size:22 final size:22
Alignment explanation
Indices: 350634--350700 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
350624 AAAATAAAAA
* * * *
350634 AAGTTAGTAAGTTAGAAGTCAG
1 AAGTTAATAAATTAGAAATTAG
350656 TAAGTT-ATAAATTAGTAAATTAG
1 -AAGTTAATAAATTAG-AAATTAG
*
350679 AAGTTAATATATTAGAAATTAG
1 AAGTTAATAAATTAGAAATTAG
350701 GGAATTAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
22 19 0.51
23 18 0.49
ACGTcount: A:0.46, C:0.01, G:0.18, T:0.34
Consensus pattern (22 bp):
AAGTTAATAAATTAGAAATTAG
Found at i:350698 original size:30 final size:30
Alignment explanation
Indices: 350637--350700 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
350627 ATAAAAAAAG
* * *
350637 TTAGTAAGTTAGAAGTCAGTAAGTTATAAA
1 TTAGTAAATTAGAAGTCAATAAGTTAGAAA
*
350667 TTAGTAAATTAGAAGTTAATATA-TTAGAAA
1 TTAGTAAATTAGAAGTCAATA-AGTTAGAAA
350697 TTAG
1 TTAG
350701 GGAATTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.17, T:0.36
Consensus pattern (30 bp):
TTAGTAAATTAGAAGTCAATAAGTTAGAAA
Found at i:352782 original size:19 final size:19
Alignment explanation
Indices: 352758--352795 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
352748 AAAAATATGT
352758 TCATCACAATTATTTTTTA
1 TCATCACAATTATTTTTTA
352777 TCATCACAATTATTTTTTA
1 TCATCACAATTATTTTTTA
352796 ACATAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.53
Consensus pattern (19 bp):
TCATCACAATTATTTTTTA
Found at i:355907 original size:15 final size:15
Alignment explanation
Indices: 355841--355911 Score: 63
Period size: 15 Copynumber: 4.7 Consensus size: 15
355831 ATTTTATTGG
* *
355841 TAAGTGAATATGTTT
1 TAAGTGAAAATGTTC
355856 TATA-TGAAAATGTTC
1 TA-AGTGAAAATGTTC
* * *
355871 TATGGGAAAATGTGC
1 TAAGTGAAAATGTTC
*
355886 CAAGTGAAAATGTTC
1 TAAGTGAAAATGTTC
*
355901 TACGTGAAAAT
1 TAAGTGAAAAT
355912 ACCCTATGTG
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
15 42 0.98
16 1 0.02
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (15 bp):
TAAGTGAAAATGTTC
Found at i:356141 original size:24 final size:24
Alignment explanation
Indices: 356047--356141 Score: 109
Period size: 24 Copynumber: 3.9 Consensus size: 24
356037 TCGAAGGTTG
* *
356047 TACGTGGTCCTTCGGGACAAATTTT
1 TACGCGGTCCTTCGGGACAAA-TTC
* * **
356072 TATGTGGTTTTTCGGGACAAATTC
1 TACGCGGTCCTTCGGGACAAATTC
*
356096 TACGCGGTCCTTCGAGACAAATTC
1 TACGCGGTCCTTCGGGACAAATTC
*
356120 TACGCGGTCCTTCGGGAAAAAT
1 TACGCGGTCCTTCGGGACAAAT
356142 CTATGTGGCA
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
24 41 0.69
25 18 0.31
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (24 bp):
TACGCGGTCCTTCGGGACAAATTC
Found at i:362964 original size:25 final size:25
Alignment explanation
Indices: 362924--362997 Score: 87
Period size: 24 Copynumber: 3.0 Consensus size: 25
362914 GAGTCGAGGG
* *
362924 TTCTACACGGTCCTTCAGGATAAAT
1 TTCTACGCGGTCCTTCGGGATAAAT
* * *
362949 TTCTACGTGGTTCTTCGGGACAAA-
1 TTCTACGCGGTCCTTCGGGATAAAT
*
362973 TTCTACGCGGTCCTTTGGGATAAAT
1 TTCTACGCGGTCCTTCGGGATAAAT
362998 CTATGTGGCA
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
24 20 0.51
25 19 0.49
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (25 bp):
TTCTACGCGGTCCTTCGGGATAAAT
Found at i:368200 original size:116 final size:116
Alignment explanation
Indices: 367982--368339 Score: 409
Period size: 116 Copynumber: 3.1 Consensus size: 116
367972 GAAAAGGTTG
* * * * * * * * *
367982 ATGCTGATCCAGCTCCTTATGTGATAGATGAG-CTAGGTTAAATAAGTT-TTTTAATTAAGAAAT
1 ATGCTGATCCAACTCCTTATGTGATGGATAAGCCAAGGTTGAACAAGTTCTTCTAATTAGGAACT
* * * * *
368045 TCTTCTCCCTTATGAGATGAGTTCTTCTCATTATAAACCCTTCCATTGGAA
66 TTTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACCCTTCCATTGAAA
* *
368096 ATACTGATCCAACTCCTTATGTGATGGATAAGCCAAGGTTGAACAAGTTCTTCTCATTAGGAACT
1 ATGCTGATCCAACTCCTTATGTGATGGATAAGCCAAGGTTGAACAAGTTCTTCTAATTAGGAACT
* * * *
368161 TTTTCTCTCTCATCAGACGAGTTCTTCTCATTAGGAACCCTTCAACTT-AAA
66 TTTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACCCTTCCA-TTGAAA
* * *
368212 ATGCTGATCCAACTCCTTATGTGATGGAGAAGCCACA-GTTGAGCAAGTTCTTCTTATTAGGAAC
1 ATGCTGATCCAACTCCTTATGTGATGGATAAGCCA-AGGTTGAACAAGTTCTTCTAATTAGGAAC
* * * * *
368276 TTTTTCCCCCGCTTCGGATGAGTTTTTCTCATTATGAACCCTTCCATTGAAA
65 TTTTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACCCTTCCATTGAAA
*
368328 ATGTTGATCCAA
1 ATGCTGATCCAA
368340 GAACTTCTTC
Statistics
Matches: 205, Mismatches: 34, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
114 28 0.14
115 15 0.07
116 159 0.78
117 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.35
Consensus pattern (116 bp):
ATGCTGATCCAACTCCTTATGTGATGGATAAGCCAAGGTTGAACAAGTTCTTCTAATTAGGAACT
TTTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACCCTTCCATTGAAA
Found at i:369442 original size:22 final size:21
Alignment explanation
Indices: 369413--369462 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
369403 TTTATTTCTT
*
369413 TTCTTTTCTCTTTTCTTTTCA
1 TTCTTTTCTCTTCTCTTTTCA
*
369434 TTCTATTTCTCTTCTCTTTTTA
1 TTCT-TTTCTCTTCTCTTTTCA
*
369456 CTCTTTT
1 TTCTTTT
369463 TTGTTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.70
Consensus pattern (21 bp):
TTCTTTTCTCTTCTCTTTTCA
Found at i:372828 original size:48 final size:48
Alignment explanation
Indices: 372736--372830 Score: 111
Period size: 48 Copynumber: 2.0 Consensus size: 48
372726 TGTTTGACAA
* * * *
372736 ATAAATCCTAACCGCATGCTTTTCTAGATCACGTGATTTGTACAAAAT
1 ATAAAACCTAACCACATACTTTTCTAGATCACATGATTTGTACAAAAT
* * *
372784 ATAAAACCTAACCACATATTTTTCTAGTTCTCATGCATTT-TACAAAA
1 ATAAAACCTAACCACATACTTTTCTAGATCACATG-ATTTGTACAAAA
372831 GGTAAATCTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
48 35 0.90
49 4 0.10
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.35
Consensus pattern (48 bp):
ATAAAACCTAACCACATACTTTTCTAGATCACATGATTTGTACAAAAT
Found at i:374177 original size:33 final size:31
Alignment explanation
Indices: 374135--374235 Score: 96
Period size: 31 Copynumber: 3.2 Consensus size: 31
374125 TAAATAGCAG
*
374135 AAAAATAAAGTCCTTAAATGTAAATAGCA-AAA
1 AAAAATAAAGTCCATAAATGTAAATA--ATAAA
** * *
374167 ATAAAATAAAGGGCAAAAATGTAAATAATAAG
1 A-AAAATAAAGTCCATAAATGTAAATAATAAA
*
374199 AAAAATAAAGTTCATAAATGTAAATAAATAAA
1 AAAAATAAAGTCCATAAATGTAAAT-AATAAA
*
374231 TAAAA
1 AAAAA
374236 GTTAGCGGTT
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
31 22 0.39
32 13 0.23
33 21 0.38
ACGTcount: A:0.63, C:0.05, G:0.10, T:0.22
Consensus pattern (31 bp):
AAAAATAAAGTCCATAAATGTAAATAATAAA
Found at i:374453 original size:17 final size:17
Alignment explanation
Indices: 374441--374474 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
374431 AAAAATAGCA
374441 AAAAAATAGAAATTA-AT
1 AAAAAATAGAAA-TAGAT
374458 AAAAAATAGAAATAGAT
1 AAAAAATAGAAATAGAT
374475 GACTAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (17 bp):
AAAAAATAGAAATAGAT
Found at i:376405 original size:17 final size:17
Alignment explanation
Indices: 376335--376406 Score: 60
Period size: 17 Copynumber: 4.2 Consensus size: 17
376325 AATTTTATTT
*
376335 TATAATATTTATCTACA
1 TATAATATATATCTACA
* *
376352 TATATTATATATTTA-A
1 TATAATATATATCTACA
*
376368 -ATAATTATATTTCTAACA
1 TATAA-TATATATCT-ACA
376386 TATAATATATAT-TGACA
1 TATAATATATATCT-ACA
376403 TATA
1 TATA
376407 TTGTAATGTT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
15 3 0.07
16 8 0.19
17 21 0.49
18 7 0.16
19 4 0.09
ACGTcount: A:0.44, C:0.07, G:0.01, T:0.47
Consensus pattern (17 bp):
TATAATATATATCTACA
Found at i:378146 original size:29 final size:29
Alignment explanation
Indices: 378104--378185 Score: 164
Period size: 29 Copynumber: 2.8 Consensus size: 29
378094 TGATCGCCAT
378104 AGGACGCCATGCAATCCAGGCGACCTTGG
1 AGGACGCCATGCAATCCAGGCGACCTTGG
378133 AGGACGCCATGCAATCCAGGCGACCTTGG
1 AGGACGCCATGCAATCCAGGCGACCTTGG
378162 AGGACGCCATGCAATCCAGGCGAC
1 AGGACGCCATGCAATCCAGGCGAC
378186 ATACGGGGTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.26, C:0.32, G:0.30, T:0.12
Consensus pattern (29 bp):
AGGACGCCATGCAATCCAGGCGACCTTGG
Found at i:378209 original size:13 final size:13
Alignment explanation
Indices: 378183--378217 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
378173 CAATCCAGGC
378183 GACATACG-GGGT
1 GACATACGAGGGT
378195 GACATACGAGGGT
1 GACATACGAGGGT
378208 GACATACGAG
1 GACATACGAG
378218 CCATATACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.31, C:0.17, G:0.37, T:0.14
Consensus pattern (13 bp):
GACATACGAGGGT
Found at i:378305 original size:28 final size:29
Alignment explanation
Indices: 378232--378405 Score: 147
Period size: 28 Copynumber: 5.8 Consensus size: 29
378222 ATACGATCAT
* ** *
378232 ACGAGCCAATGGGGAGCATGCAACGAGCCAT
1 ACGAGCCAATGGGGAGCATGC-AGGA-ATAG
378263 ACGAGCCAATGGGGAGCATGCAGGAATAG
1 ACGAGCCAATGGGGAGCATGCAGGAATAG
* * *
378292 A-GAGCCAATAGGGAGCATGCAATGAGCCATAT
1 ACGAGCCAATGGGGAGCATGC-A-G-G-AATAG
** *
378324 ACGAGCC-ATGGGGAGCATGCAACAAGCCATAT
1 ACGAGCCAATGGGGAGCATG---C-AGGAATAG
378356 ACGAGCCAATGGGGAGCATGCAGGAATAG
1 ACGAGCCAATGGGGAGCATGCAGGAATAG
378385 A-GAGCCAATGGGGAGCATGCA
1 ACGAGCCAATGGGGAGCATGCA
378406 ACGAGCCATA
Statistics
Matches: 122, Mismatches: 12, Indels: 21
0.79 0.08 0.14
Matches are distributed among these distances:
28 38 0.31
29 9 0.07
30 5 0.04
31 22 0.18
32 27 0.22
33 17 0.14
34 1 0.01
35 3 0.02
ACGTcount: A:0.34, C:0.21, G:0.33, T:0.11
Consensus pattern (29 bp):
ACGAGCCAATGGGGAGCATGCAGGAATAG
Found at i:378381 original size:93 final size:91
Alignment explanation
Indices: 378230--378425 Score: 338
Period size: 93 Copynumber: 2.1 Consensus size: 91
378220 ATATACGATC
*
378230 ATACGAGCCAATGGGGAGCATGCAACGAGCCATACGAGCCAATGGGGAGCATGCAGGAATAGAGA
1 ATACGAGCC-ATGGGGAGCATGCAACAAGCCATACGAGCCAATGGGGAGCATGCAGGAATAGAGA
*
378295 GCCAATAGGGAGCATGCAATGAGCCAT
65 GCCAATAGGGAGCATGCAACGAGCCAT
378322 ATACGAGCCATGGGGAGCATGCAACAAGCCATATACGAGCCAATGGGGAGCATGCAGGAATAGAG
1 ATACGAGCCATGGGGAGCATGCAACAAGCC--ATACGAGCCAATGGGGAGCATGCAGGAATAGAG
*
378387 AGCCAATGGGGAGCATGCAACGAGCCAT
64 AGCCAATAGGGAGCATGCAACGAGCCAT
378415 ATACGAGCCAT
1 ATACGAGCCAT
378426 ACGAGCCAAT
Statistics
Matches: 99, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
91 20 0.20
92 9 0.09
93 70 0.71
ACGTcount: A:0.35, C:0.21, G:0.32, T:0.12
Consensus pattern (91 bp):
ATACGAGCCATGGGGAGCATGCAACAAGCCATACGAGCCAATGGGGAGCATGCAGGAATAGAGAG
CCAATAGGGAGCATGCAACGAGCCAT
Found at i:378413 original size:61 final size:64
Alignment explanation
Indices: 378230--378424 Score: 230
Period size: 61 Copynumber: 3.2 Consensus size: 64
378220 ATATACGATC
* *
378230 ATACGAGCCAATGGGGAGCATGCAACGAGCCATACGAGCCAATGGGGAGCATGC-A-G-G-AAT
1 ATACGAGCCAATGGGGAGCATGCAACGAGCCATAAGAGCCAATGGGGAGCATGCAACGAGCCAT
* * * *
378290 AGA-GAGCCAATAGGGAGCATGCAATGAGCCATATACGAGCC-ATGGGGAGCATGCAACAAGCCA
1 ATACGAGCCAATGGGGAGCATGCAACGAGCCATA-A-GAGCCAATGGGGAGCATGCAACGAGCCA
378353 T
64 T
*
378354 ATACGAGCCAATGGGGAGCATGC-A-G-G-AATAGAGAGCCAATGGGGAGCATGCAACGAGCCAT
1 ATACGAGCCAATGGGGAGCATGCAACGAGCCATA-AGAGCCAATGGGGAGCATGCAACGAGCCAT
378415 ATACGAGCCA
1 ATACGAGCCA
378425 TACGAGCCAA
Statistics
Matches: 116, Mismatches: 11, Indels: 15
0.82 0.08 0.11
Matches are distributed among these distances:
59 28 0.24
60 20 0.17
61 42 0.36
62 1 0.01
63 2 0.02
64 5 0.04
65 18 0.16
ACGTcount: A:0.35, C:0.22, G:0.32, T:0.12
Consensus pattern (64 bp):
ATACGAGCCAATGGGGAGCATGCAACGAGCCATAAGAGCCAATGGGGAGCATGCAACGAGCCAT
Found at i:378512 original size:28 final size:28
Alignment explanation
Indices: 378456--378560 Score: 144
Period size: 28 Copynumber: 3.8 Consensus size: 28
378446 AGGAATAGAG
*
378456 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC--GGCGACCTTGT
378485 AGGTCGCCATGTAGTCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCGGCGACCTTGT
378513 AGGT--CCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGT-CCGGCGACCTTGT
*
378540 AGGTCGCCATGTAGCCCGGCG
1 AGGTCGCCATGTAGTCCGGCG
378561 CCATTCCCAC
Statistics
Matches: 70, Mismatches: 2, Indels: 9
0.86 0.02 0.11
Matches are distributed among these distances:
26 9 0.13
27 17 0.24
28 21 0.30
29 21 0.30
30 2 0.03
ACGTcount: A:0.15, C:0.30, G:0.32, T:0.22
Consensus pattern (28 bp):
AGGTCGCCATGTAGTCCGGCGACCTTGT
Found at i:378663 original size:18 final size:18
Alignment explanation
Indices: 378640--378674 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
378630 CCCAATGCAT
378640 GCATGTGAACCATTTGAG
1 GCATGTGAACCATTTGAG
378658 GCATGTGAACCATTTGA
1 GCATGTGAACCATTTGA
378675 TTATTGGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (18 bp):
GCATGTGAACCATTTGAG
Found at i:378833 original size:25 final size:23
Alignment explanation
Indices: 378779--378824 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
378769 GAAAGAAAGA
378779 AAGAAAGAGGAGAGAGATTGCAG
1 AAGAAAGAGGAGAGAGATTGCAG
378802 AAGAAAG-GGAGAAGAGATTGCAG
1 AAGAAAGAGGAG-AGAGATTGCAG
378825 CCGAGAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.48, C:0.04, G:0.39, T:0.09
Consensus pattern (23 bp):
AAGAAAGAGGAGAGAGATTGCAG
Found at i:378861 original size:11 final size:11
Alignment explanation
Indices: 378834--378865 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
378824 GCCGAGAAAG
378834 AAAG-AAAGAA
1 AAAGAAAAGAA
378844 AAA-AAAAGAA
1 AAAGAAAAGAA
378854 AAAGAAAAGAA
1 AAAGAAAAGAA
378865 A
1 A
378866 GGGAGAAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 12 0.60
11 8 0.40
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:378872 original size:13 final size:13
Alignment explanation
Indices: 378856--378898 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
378846 AAAAAGAAAA
378856 AGAAAAGAAAGGG
1 AGAAAAGAAAGGG
* **
378869 AGAAAGGAAAGTA
1 AGAAAAGAAAGGG
378882 AGAAGAAGAAAGGG
1 AGAA-AAGAAAGGG
378896 AGA
1 AGA
378899 TAAGTAAATT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.02
Consensus pattern (13 bp):
AGAAAAGAAAGGG
Found at i:379108 original size:40 final size:40
Alignment explanation
Indices: 379039--379155 Score: 110
Period size: 41 Copynumber: 2.8 Consensus size: 40
379029 TACATAAATT
* * * * *
379039 AAAAATTATTAATTAGTATATGTTGATAGTTA-TATAGTTAA
1 AAAAATAATTAGTTTGTAT-TGTTAATAGTTAGTATA-TAAA
379080 AAAAATAATTAGTTTGTATTGTTAATAGTTAGTTATATAAA
1 AAAAATAATTAGTTTGTATTGTTAATAGTTAG-TATATAAA
*
379121 AAAAATTTAATTAGTTTGTGTTAGTTAAATAGTTA
1 AAAAA--TAATTAGTTTGTATT-GTT-AATAGTTA
379156 AGTTATATTT
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
40 11 0.17
41 24 0.38
42 4 0.06
43 14 0.22
44 3 0.05
45 8 0.12
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.44
Consensus pattern (40 bp):
AAAAATAATTAGTTTGTATTGTTAATAGTTAGTATATAAA
Found at i:379137 original size:43 final size:44
Alignment explanation
Indices: 379078--379163 Score: 124
Period size: 43 Copynumber: 2.0 Consensus size: 44
379068 TTATATAGTT
379078 AAAAAAATAATTAGTTTGTATT-GTT-AATAGTT-AGTTATATA
1 AAAAAAATAATTAGTTTGTATTAGTTAAATAGTTAAGTTATATA
*
379119 AAAAAAATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAAA--TAATTAGTTTGTATTAGTTAAATAGTTAAGTTATAT
379164 TTGTTTGTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
41 7 0.18
43 14 0.36
44 3 0.08
45 7 0.18
46 8 0.21
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.44
Consensus pattern (44 bp):
AAAAAAATAATTAGTTTGTATTAGTTAAATAGTTAAGTTATATA
Found at i:379349 original size:15 final size:15
Alignment explanation
Indices: 379326--379363 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
379316 GTTTGTTAGT
*
379326 TTATTAGTTATTATA
1 TTATAAGTTATTATA
379341 TTATAAGTTATTATA
1 TTATAAGTTATTATA
379356 TTA-AAGTT
1 TTATAAGTT
379364 TAGTGTTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (15 bp):
TTATAAGTTATTATA
Found at i:381506 original size:17 final size:17
Alignment explanation
Indices: 381484--381516 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
381474 CAATGATTTT
*
381484 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
381501 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
381517 AATATTAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:381747 original size:26 final size:25
Alignment explanation
Indices: 381612--381797 Score: 157
Period size: 25 Copynumber: 7.3 Consensus size: 25
381602 TTGTTAGTAT
*
381612 TAAATCATTATTATAAATCATTATTA
1 TAAATCATTATTAT-AATGATTATTA
* * *
381638 TAAATAATTACTA-AAT-AATATTA
1 TAAATCATTATTATAATGATTATTA
*
381661 TAAAATAATTATTATAATGA-TATTA
1 T-AAATCATTATTATAATGATTATTA
* * * *
381686 TCAAATCATTACTA-AATCATCAAATCA
1 T-AAATCATTATTATAATGAT--TATTA
*
381713 TTAAATCATTTTTATAATGATTATTA
1 -TAAATCATTATTATAATGATTATTA
381739 CTAAATCATTATTA-AATGATTATTA
1 -TAAATCATTATTATAATGATTATTA
*
381764 TCAAATCATTACTATAATGATTATTA
1 T-AAATCATTATTATAATGATTATTA
*
381790 TCAATCAT
1 TAAATCAT
381798 ACTAATCATC
Statistics
Matches: 131, Mismatches: 19, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
23 7 0.05
24 19 0.15
25 47 0.36
26 39 0.30
27 13 0.10
28 6 0.05
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.42
Consensus pattern (25 bp):
TAAATCATTATTATAATGATTATTA
Found at i:384668 original size:26 final size:24
Alignment explanation
Indices: 384610--384668 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
384600 CTAATAAACC
*
384610 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
384634 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
384662 TAATAAT
1 TAATAAT
384669 AATATGATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:385454 original size:41 final size:43
Alignment explanation
Indices: 385379--385483 Score: 110
Period size: 41 Copynumber: 2.5 Consensus size: 43
385369 GTTTAAAGAC
* *
385379 ACTAACAAATTAATTAATATTTTTTATAT-TTA-ATA-ACTTAA
1 ACTAACAAACTAATTAATATTTTTTATATATAATATATACTT-A
* *
385420 ACTAAGAAACTAATTAA-CTTTTTTATAATATAATATATACTTA
1 ACTAACAAACTAATTAATATTTTTTAT-ATATAATATATACTTA
*
385463 ACTAATAAACTAATATAATAT
1 ACTAACAAACTAAT-TAATAT
385484 ACTTAAACTA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
40 8 0.15
41 17 0.33
42 2 0.04
43 17 0.33
44 7 0.13
45 1 0.02
ACGTcount: A:0.49, C:0.09, G:0.01, T:0.42
Consensus pattern (43 bp):
ACTAACAAACTAATTAATATTTTTTATATATAATATATACTTA
Found at i:385500 original size:27 final size:28
Alignment explanation
Indices: 385445--385504 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
385435 AACTTTTTTA
*
385445 TAATATAATATATACTTAACTAATAAAC
1 TAATATAATATATACTTAACTAACAAAC
385473 TAATAT-A-ATATACTTAAACTAACAAAC
1 TAATATAATATATACTT-AACTAACAAAC
385500 TAATA
1 TAATA
385505 ATTTATACTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 8 0.27
27 16 0.53
28 6 0.20
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (28 bp):
TAATATAATATATACTTAACTAACAAAC
Found at i:385511 original size:27 final size:26
Alignment explanation
Indices: 385449--385513 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 26
385439 TTTTTATAAT
*
385449 ATAATATATACTTAACTAATAAACTA
1 ATAATATATACTTAACTAACAAACTA
385475 AT-ATAATATACTTAAACTAACAAACTA
1 ATAAT-ATATACTT-AACTAACAAACTA
*
385502 ATAATTTATACT
1 ATAATATATACT
385514 AACAAACTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 2 0.06
26 10 0.29
27 20 0.59
28 2 0.06
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (26 bp):
ATAATATATACTTAACTAACAAACTA
Found at i:386077 original size:25 final size:25
Alignment explanation
Indices: 386023--386080 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
386013 GTTCCCACGT
* *
386023 CCCATGCACAGCATGCATCTGCATG
1 CCCATGCACAGCATGCATCTCCATC
* *
386048 GCCATGCACAGCATGCATC-CCCTCC
1 CCCATGCACAGCATGCATCTCCAT-C
386073 CCCATGCA
1 CCCATGCA
386081 TTCCCACAGC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 2 0.07
25 25 0.93
ACGTcount: A:0.22, C:0.43, G:0.17, T:0.17
Consensus pattern (25 bp):
CCCATGCACAGCATGCATCTCCATC
Found at i:386171 original size:29 final size:29
Alignment explanation
Indices: 386139--386218 Score: 142
Period size: 29 Copynumber: 2.8 Consensus size: 29
386129 TCCACCTTGG
*
386139 AGGTCGCCCGGATTGCATGGCGACCTCCA
1 AGGTCGCCTGGATTGCATGGCGACCTCCA
*
386168 AGGTCGCCTGGATTGCATGGCGACCTCTA
1 AGGTCGCCTGGATTGCATGGCGACCTCCA
386197 AGGTCGCCTGGATTGCATGGCG
1 AGGTCGCCTGGATTGCATGGCG
386219 TCCTATGGCG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.16, C:0.29, G:0.34, T:0.21
Consensus pattern (29 bp):
AGGTCGCCTGGATTGCATGGCGACCTCCA
Found at i:391605 original size:6 final size:6
Alignment explanation
Indices: 391568--391602 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
391558 TTTTCCATTT
* *
391568 TATTAC TATTAA TATTAA TATTAA TATTAT TATTA
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATTA
391603 TTAAAAATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (6 bp):
TATTAA
Found at i:392697 original size:2 final size:2
Alignment explanation
Indices: 392690--392717 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
392680 TTAGTCCCTA
392690 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
392718 TAGGGTAAAA
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:393048 original size:22 final size:20
Alignment explanation
Indices: 393035--393083 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
393025 TATTCATATG
393035 AATATATATATTTAATTAAAT
1 AATATATATATTT-ATTAAAT
* *
393056 AATAATATATATTTATTTATT
1 AAT-ATATATATTTATTAAAT
393077 AATATAT
1 AATATAT
393084 TATGAAAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 4 0.16
21 11 0.44
22 10 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATATATATATTTATTAAAT
Found at i:403476 original size:22 final size:22
Alignment explanation
Indices: 403451--403504 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
403441 CAGAGGAAAT
*
403451 CGATACCCCCTTGAAGGGGAAC
1 CGATTCCCCCTTGAAGGGGAAC
* *
403473 CGATTCCCTCTTTGAAGGGGAAT
1 CGATTCCC-CCTTGAAGGGGAAC
403496 CGATTCCCC
1 CGATTCCCC
403505 TAGGGGAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 8 0.29
23 20 0.71
ACGTcount: A:0.22, C:0.31, G:0.24, T:0.22
Consensus pattern (22 bp):
CGATTCCCCCTTGAAGGGGAAC
Found at i:403511 original size:18 final size:18
Alignment explanation
Indices: 403488--403529 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
403478 CCCTCTTTGA
*
403488 AGGGGAATCGATTCCCCT
1 AGGGGAATCGATACCCCT
403506 AGGGGAATCGATACCCCT
1 AGGGGAATCGATACCCCT
403524 ATGGGG
1 A-GGGG
403530 TTCTGGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.24, C:0.24, G:0.33, T:0.19
Consensus pattern (18 bp):
AGGGGAATCGATACCCCT
Found at i:407452 original size:90 final size:90
Alignment explanation
Indices: 407213--407445 Score: 367
Period size: 90 Copynumber: 2.6 Consensus size: 90
407203 AGTCTGTTAT
* * *
407213 GCTTGAGTTGTCCCCCTAAAGCAATTTGTTAATCACCCCGGCTTTATGGATAATATTCAGCTAGC
1 GCTTGAGTTGTCCCTCTAAAGCAATTAGTTAATCACCCCGGCTTTATGGATAATATTCAACTAGC
407278 CTATTATACTATTATATGCAATAAA
66 CTATTATACTATTATATGCAATAAA
* * *
407303 GCTTGAGTTGTCCCTCTAGAGCAATTGGTTAATCGCCCCGGCTTTATGGATAATATTCAACTAGC
1 GCTTGAGTTGTCCCTCTAAAGCAATTAGTTAATCACCCCGGCTTTATGGATAATATTCAACTAGC
*
407368 CTATTATATTATTATATGCAATAAA
66 CTATTATACTATTATATGCAATAAA
* * **
407393 GCTTGAGTTATCCCTCTAAAGCAATTAGTTAATAACCCTAGCTTTATGGATAA
1 GCTTGAGTTGTCCCTCTAAAGCAATTAGTTAATCACCCCGGCTTTATGGATAA
407446 GTTTCAAATA
Statistics
Matches: 130, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 130 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (90 bp):
GCTTGAGTTGTCCCTCTAAAGCAATTAGTTAATCACCCCGGCTTTATGGATAATATTCAACTAGC
CTATTATACTATTATATGCAATAAA
Found at i:410746 original size:16 final size:18
Alignment explanation
Indices: 410721--410766 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
410711 AATATTTTTC
410721 TATT-TTATTA-CTA-AT
1 TATTATTATTATCTATAT
*
410736 TATTATTATTATTTTATAT
1 TATTATTATTA-TCTATAT
410755 TATTATTATTAT
1 TATTATTATTAT
410767 TAAAACTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 4 0.15
16 6 0.23
18 3 0.12
19 13 0.50
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTATTATTATCTATAT
Found at i:410778 original size:13 final size:13
Alignment explanation
Indices: 410762--410796 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
410752 TATTATTATT
410762 ATTATTA-AAACTA
1 ATTATTACAAA-TA
410775 ATTATTACAAATA
1 ATTATTACAAATA
410788 ATTATTACA
1 ATTATTACA
410797 GGCTCATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 18 0.86
14 3 0.14
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTATTACAAATA
Found at i:410778 original size:22 final size:21
Alignment explanation
Indices: 410730--410781 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 21
410720 CTATTTTATT
**
410730 ACTAATTATTATTATTATTTT
1 ACTAATTATTATTATTATTAA
410751 A-T-ATTATTATTATTATTAAA
1 ACTAATTATTATTATTATT-AA
410771 ACTAATTATTA
1 ACTAATTATTA
410782 CAAATAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 15 0.58
20 2 0.08
21 2 0.08
22 7 0.27
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (21 bp):
ACTAATTATTATTATTATTAA
Found at i:410781 original size:3 final size:3
Alignment explanation
Indices: 410721--410768 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
410711 AATATTTTTC
*
410721 TAT T-T TAT TACT AAT TAT TAT TAT TAT T-T TA- TAT TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
410764 TAT TA
1 TAT TA
410769 AAACTAATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 6 0.15
3 31 0.79
4 2 0.05
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:414488 original size:12 final size:12
Alignment explanation
Indices: 414461--414500 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
414451 ACATTTGAAA
* *
414461 TTATTTTTAGGA
1 TTATTTTTATGT
*
414473 TTATTTTTATTT
1 TTATTTTTATGT
414485 TTATTTTTATGT
1 TTATTTTTATGT
414497 TTAT
1 TTAT
414501 CTCTAGGGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.72
Consensus pattern (12 bp):
TTATTTTTATGT
Found at i:415449 original size:43 final size:43
Alignment explanation
Indices: 415382--415474 Score: 159
Period size: 43 Copynumber: 2.2 Consensus size: 43
415372 TATTATGTAT
* *
415382 TTCCTTTATTTATAAGCGACGATCGAGTTAAAAATGACGAAAC
1 TTCCTTTATTTATAAGCGAAGATCGAGTTAAAAATGACAAAAC
*
415425 TTCCTTTATTTATAAGTGAAGATCGAGTTAAAAATGACAAAAC
1 TTCCTTTATTTATAAGCGAAGATCGAGTTAAAAATGACAAAAC
415468 TTCCTTT
1 TTCCTTT
415475 TGAGTTTTAC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (43 bp):
TTCCTTTATTTATAAGCGAAGATCGAGTTAAAAATGACAAAAC
Found at i:417108 original size:30 final size:30
Alignment explanation
Indices: 417041--417113 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
417031 TTGGGGCCTG
**
417041 AGAGCCTACCCAAAAAGTTCTCAGGGCCAC
1 AGAGCCTACCCAAAAAAATCTCAGGGCCAC
* ** * *
417071 AGGGCCTACCCAAAAAAATCTTGGGGTCAT
1 AGAGCCTACCCAAAAAAATCTCAGGGCCAC
417101 AGAGCCTACCCAA
1 AGAGCCTACCCAA
417114 GGGTCCCTTA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.34, C:0.30, G:0.21, T:0.15
Consensus pattern (30 bp):
AGAGCCTACCCAAAAAAATCTCAGGGCCAC
Found at i:421269 original size:25 final size:24
Alignment explanation
Indices: 421232--421294 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 24
421222 TAGTTTTATA
421232 AAGTTATTTTTTTT-CTTTTATTTT
1 AAGTT-TTTTTTTTGCTTTTATTTT
*
421256 CAAGTTTTTGTTTTTGTTTTTATTTT
1 -AAGTTTTT-TTTTTGCTTTTATTTT
*
421282 AAGTTTTATTTTT
1 AAGTTTTTTTTTT
421295 AAACATGCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
24 8 0.24
25 17 0.50
26 9 0.26
ACGTcount: A:0.16, C:0.03, G:0.08, T:0.73
Consensus pattern (24 bp):
AAGTTTTTTTTTTGCTTTTATTTT
Found at i:421296 original size:13 final size:13
Alignment explanation
Indices: 421247--421293 Score: 53
Period size: 12 Copynumber: 3.7 Consensus size: 13
421237 ATTTTTTTTC
421247 TTTTATTTTCAAGT
1 TTTTATTTT-AAGT
* *
421261 TTTTGTTTT-TGT
1 TTTTATTTTAAGT
421273 TTTTATTTTAAG-
1 TTTTATTTTAAGT
421285 TTTTATTTT
1 TTTTATTTT
421294 TAAACATGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 19 0.68
13 1 0.04
14 8 0.29
ACGTcount: A:0.15, C:0.02, G:0.09, T:0.74
Consensus pattern (13 bp):
TTTTATTTTAAGT
Found at i:434092 original size:20 final size:23
Alignment explanation
Indices: 434053--434098 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
434043 TTCTATTGTT
434053 TTTTTAGGCCTTTAAAGTTC-TG
1 TTTTTAGGCCTTTAAAGTTCTTG
434075 TTTTTA-GCCTTT-AAGTTCTTG
1 TTTTTAGGCCTTTAAAGTTCTTG
434096 TTT
1 TTT
434099 GTTATTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.26
21 11 0.48
22 6 0.26
ACGTcount: A:0.15, C:0.13, G:0.15, T:0.57
Consensus pattern (23 bp):
TTTTTAGGCCTTTAAAGTTCTTG
Found at i:434241 original size:20 final size:20
Alignment explanation
Indices: 434180--434241 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
434170 CTTTTTTTAA
* *
434180 TTTTTAATTTTTTCTTCATAT
1 TTTTTATTTTTTTCATCAT-T
*
434201 TGTTTTATTTTATTT-AACATT
1 T-TTTTATTTT-TTTCATCATT
434222 TTTTTATTTTTTTCATCATT
1 TTTTTATTTTTTTCATCATT
434242 ATTATTTAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
19 3 0.09
20 14 0.41
21 3 0.09
22 11 0.32
23 3 0.09
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTTATTTTTTTCATCATT
Found at i:434280 original size:17 final size:18
Alignment explanation
Indices: 434260--434293 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
434250 GTATTTATTA
434260 TTATTTACCTTT-TTATC
1 TTATTTACCTTTATTATC
*
434277 TTATTTCCCTTTATTAT
1 TTATTTACCTTTATTAT
434294 TATTTATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTTACCTTTATTATC
Found at i:434354 original size:13 final size:13
Alignment explanation
Indices: 434321--434369 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
434311 TTTGTTTTCG
*
434321 TTTTA-TTAATAT
1 TTTTATTTATTAT
434333 TTTTATTTATTCAT
1 TTTTATTTATT-AT
*
434347 TTTT-TTTATTTT
1 TTTTATTTATTAT
434359 TTTTATTTATT
1 TTTTATTTATT
434370 TTCCTCTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 10 0.31
13 16 0.50
14 6 0.19
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTATTTATTAT
Found at i:439706 original size:84 final size:84
Alignment explanation
Indices: 439499--440032 Score: 611
Period size: 84 Copynumber: 6.4 Consensus size: 84
439489 TAAACAAACT
* * * * *
439499 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCGACCAAAGACCCCCGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTCTGAGTTCGACTACG
*
439564 CTCAGCTTCGAGGGCACATC
66 CTCAGC-TCCAGGGCACATC
* *
439584 ATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTCTGAGTTCGACTACG
*
439649 CTCAGCTCCAAGGCACATC
66 CTCAGCTCCAGGGCACATC
* * * * *
439668 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAGGACC-CTGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTCTGAGTTCGACTACG
*
439728 CTCAGCTTCGAGGGCACATC
66 CTCAGC-TCCAGGGCACATC
* * * * * ** *
439748 ATTTACAACATAACTCAAGGCTAGAAGGGTTATCTG-TGACCAAAAGACCTTTGAGTTCGACTAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTCTGAGTTCGACTAC
439812 GCTCAGCTCCAGGGCACATC
65 GCTCAGCTCCAGGGCACATC
* * * *
439832 ATTTGCAGCATAGCTTAATTCGAGAAGGGTTATCTGCCAA--AGA-ACC-CCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTCTGAGTTCGACTACG
*
439893 CTCAGCTCCAGGGCATATC
66 CTCAGCTCCAGGGCACATC
* * * * * * *
439912 ATTTGCAGTACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCTACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTCTGAGTTCGACTACG
* * *
439977 CTCAGCTCAACGACACATC
66 CTCAGCTCCAGGGCACATC
* *
439996 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGC
440033 TAAAGACCTT
Statistics
Matches: 375, Mismatches: 63, Indels: 23
0.81 0.14 0.05
Matches are distributed among these distances:
79 18 0.05
80 113 0.30
81 3 0.01
82 4 0.01
83 5 0.01
84 149 0.40
85 83 0.22
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (84 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTCTGAGTTCGACTACG
CTCAGCTCCAGGGCACATC
Found at i:439776 original size:164 final size:164
Alignment explanation
Indices: 439499--440054 Score: 776
Period size: 164 Copynumber: 3.4 Consensus size: 164
439489 TAAACAAACT
* *
439499 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCGACCAAAGACCCCCGAGTTCGATTACA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT---G-CCAAAGA-CCCCGAGTTCGATTACA
*
439564 CTCAGCTTCGAGGGCACATCATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAA
61 CTCAGCTTCGAGGGCACATCATTTGCAGTATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAA
439629 GACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
126 GACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* *
439668 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAGGACCCTGAGTTCGATTACACTCAG
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCGAGTTCGATTACACTCAG
* ** * * **
439733 CTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTG-TGACCAAAAGACC
66 CTTCGAGGGCACATCATTTGCAGTATAACTTAAGTCTAGAAGGGTTATCTGCCAACC-AAAGACC
*
439797 TTTGAGTTCGACTACGCTCAGCTCCAGGGCACATC
130 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* * * *
439832 ATTTGCAGCATAGCTTAATTCGAGAAGGGTTATCTGCCAAAGAACCCCGAGTTCGACTACGCTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG-ACCCCGAGTTCGATTACACTCA
* * * * *
439897 GC-TCCAGGGCATATCATTTGCAGTACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACC
65 GCTTCGAGGGCACATCATTTGCAGTATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACC
* *
439961 TTTGAGTTCTACTACGCTCAGCT-CAACGACACATC
130 TTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATC
* *
439996 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCTAAAGACCTTCGAGTTCGATTA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC-CCGAGTTCGATTA
440055 TATTCAACTT
Statistics
Matches: 343, Mismatches: 39, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
163 8 0.02
164 272 0.79
165 29 0.08
166 1 0.00
169 33 0.10
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.25
Consensus pattern (164 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCGAGTTCGATTACACTCAG
CTTCGAGGGCACATCATTTGCAGTATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCT
TTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
Found at i:440148 original size:164 final size:159
Alignment explanation
Indices: 439499--440135 Score: 598
Period size: 164 Copynumber: 3.8 Consensus size: 159
439489 TAAACAAACT
* * *
439499 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCGACCAAAGACCCCCGAGTTCGATTACA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT---G-CCAAAGA-CCTCGAGTTCGATTACA
* * * * * * * *
439564 CTCAGCTTCGAGGGCACATCATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAA
61 CTCAGCTTAGA-GGCAAATCATTTACAGAATAACTCAAGGCTAGAAGGGTTATCTGTCAA--AAA
*
439629 GACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATC
123 -A-CTTTGAGTTCGACTACGCTCAGCT-CAACGACACATC
*
439668 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAGGACC-CTGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTC-GAGTTCGATTACACTCA
* * *
439732 GCTTCGAGGGCACATCATTTACA-ACATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGAC
65 GCTTAGA-GGCAAATCATTTACAGA-ATAACTCAAGGCTAGAAGGGTTATCTGT---CAAAA-AA
* * *
439796 CTTTGAGTTCGACTACGCTCAGCTCCAGGGCACATC
124 CTTTGAGTTCGACTACGCTCAGCTCAACGACACATC
* * * * *
439832 ATTTGCAGCATAGCTTAATTCGAGAAGGGTTATCTGCCAAAGAACCCCGAGTTCGACTACGCTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG-ACCTCGAGTTCGATTACACTCA
* * * * * * * * *
439897 GCTCCAG-GGCATATCATTTGCAGTACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACC
65 GCT-TAGAGGCAAATCATTTACAGAATAACTCAAGGCTAGAAGGGTTATCTGTC-A-AAAA-A-C
*
439961 TTTGAGTTCTACTACGCTCAGCTCAACGACACATC
125 TTTGAGTTCGACTACGCTCAGCTCAACGACACATC
* * *
439996 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCTAAAGACCTTCGAGTTCGATTATATTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC-TCGAGTTCGATTACACTCA
* * * * *
440061 ACTTAGAGGCAAATCAAGCTTACAGAATAGCTCAAGGCAAGAAGGGCTATCTGTCAATAAAACTG
65 GCTTAGAGGCAAATC-A-TTTACAGAATAACTCAAGGCTAGAAGGGTTATCTGTCAA-AAAACT-
*
440126 TCGAGTTCGA
126 TTGAGTTCGA
440136 TTCCAATCAG
Statistics
Matches: 392, Mismatches: 55, Indels: 47
0.79 0.11 0.10
Matches are distributed among these distances:
161 1 0.00
162 2 0.01
163 13 0.03
164 276 0.70
165 34 0.09
166 30 0.08
167 3 0.01
169 33 0.08
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (159 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTCGAGTTCGATTACACTCAG
CTTAGAGGCAAATCATTTACAGAATAACTCAAGGCTAGAAGGGTTATCTGTCAAAAAACTTTGAG
TTCGACTACGCTCAGCTCAACGACACATC
Found at i:440148 original size:328 final size:329
Alignment explanation
Indices: 439499--440148 Score: 866
Period size: 328 Copynumber: 2.0 Consensus size: 329
439489 TAAACAAACT
* *
439499 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCGACCAAAGACCCCCGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT--CGACCAAAGAACCCCGAGTTCGACTACA
* * *
439564 CTCAGCTTCGAGGGCACATCATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAA
64 CTCAGCTTCCAGGGCACATCATTTGCAGTACAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAA
*
439629 GACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAA
129 GACCTTTGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCATAGCTTAAGTCGAGAA
* * * * *
439694 GGGCTATCTGCCAAGGACCCTGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACAT
194 GGGCTATCTGCCAAAGACCCTGAGTTCGATTACACTCAACTTAGAGGGCAAATCACTTACAACAT
* * * * **
439759 AACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAG
259 AACTCAAGGCAAGAAGGGCTATCTGT-A-CAAAAGAACTTCGAGTTCGACTACAATCAGCTCCAG
439824 GGCACATC
322 GGCACATC
* * *
439832 ATTTGCAGCATAGCTTAATTCGAGAAGGGTTATCT-G-CCAAAGAACCCCGAGTTCGACTACGCT
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTCGACCAAAGAACCCCGAGTTCGACTACACT
* * *
439895 CAGC-TCCAGGGCATATCATTTGCAGTACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGA
66 CAGCTTCCAGGGCACATCATTTGCAGTACAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGA
*
439959 CCTTTGAGTTCTACTACGCTCAGCT-CAACGACACATCATTTGCAGCATAGCTTAAGTCGAGAAG
131 CCTTTGAGTTCGACTACGCTCAGCTCCAA-GACACATCATTTGCAGCATAGCTTAAGTCGAGAAG
* * * *
440023 GGCTATCTGCTAAAGACCTTCGAGTTCGATTATATTCAACTTAGA-GGCAAATCAAGCTTACAGA
195 GGCTATCTGCCAAAGACCCT-GAGTTCGATTACACTCAACTTAGAGGGCAAATC-A-CTTACA-A
* * *
440087 -ATAGCTCAAGGCAAGAAGGGCTATCTGT-CAATAA-AACTGTCGAGTTCGATTCCAATCAGCTC
256 CATAACTCAAGGCAAGAAGGGCTATCTGTACAA-AAGAACT-TCGAGTTCGACTACAATCAGCTC
440149 GATGACACCT
Statistics
Matches: 279, Mismatches: 31, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
327 9 0.03
328 156 0.56
329 49 0.18
330 31 0.11
331 1 0.00
333 33 0.12
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (329 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTCGACCAAAGAACCCCGAGTTCGACTACACT
CAGCTTCCAGGGCACATCATTTGCAGTACAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGA
CCTTTGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGG
GCTATCTGCCAAAGACCCTGAGTTCGATTACACTCAACTTAGAGGGCAAATCACTTACAACATAA
CTCAAGGCAAGAAGGGCTATCTGTACAAAAGAACTTCGAGTTCGACTACAATCAGCTCCAGGGCA
CATC
Found at i:440335 original size:81 final size:80
Alignment explanation
Indices: 440241--440444 Score: 228
Period size: 84 Copynumber: 2.5 Consensus size: 80
440231 TGATAAAAAA
* ** * *
440241 ATCATTTCCAGCATAGTTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACAC
1 ATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCCCGAGTTCGACTACAC
* *
440306 TCAGCTTCGAGGGCAC
66 TCAGC-TCAACGGCAC
* * * **
440322 ATCATTTGCAGCATAACTTAAGTCGAGAAAGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACT
1 ATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATC-T---GCCAAAGACCCCCGAGTTCGACT
*
440387 ACACTCAGCTCAACGGCGC
62 ACACTCAGCTCAACGGCAC
* *
440406 ATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTG
1 ATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTG
440445 TTACAAAGAC
Statistics
Matches: 102, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
81 32 0.31
82 1 0.01
83 1 0.01
84 40 0.39
85 28 0.27
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (80 bp):
ATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCCCGAGTTCGACTACAC
TCAGCTCAACGGCAC
Found at i:440440 original size:84 final size:85
Alignment explanation
Indices: 440280--440443 Score: 231
Period size: 84 Copynumber: 1.9 Consensus size: 85
440270 GGGCTATCTG
* * * * * *
440280 CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGT
1 CCAAAGACCCCCGAGTTCGACTACACTCAGCTTCAACGGCACATCATTTACAGCATAACTCAAGG
440345 CGAGAAAGGTTATCTTCCAA
66 CGAGAAAGGTTATCTTCCAA
** *
440365 CCAAAGACCTTCGAGTTCGACTACACTCAGC-TCAACGGCGCATCATTTACAGCATAACTCAAGG
1 CCAAAGACCCCCGAGTTCGACTACACTCAGCTTCAACGGCACATCATTTACAGCATAACTCAAGG
*
440429 CGAGAAGGGTTATCT
66 CGAGAAAGGTTATCT
440444 GTTACAAAGA
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
84 41 0.59
85 28 0.41
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (85 bp):
CCAAAGACCCCCGAGTTCGACTACACTCAGCTTCAACGGCACATCATTTACAGCATAACTCAAGG
CGAGAAAGGTTATCTTCCAA
Done.