Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008577.1 Hibiscus syriacus cultivar Beakdansim tig00111506_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: 1329373
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:4562 original size:19 final size:19
Alignment explanation
Indices: 4538--4574 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4528 ACCCTTCATT
4538 TTTTATCGTGGAACCATCC
1 TTTTATCGTGGAACCATCC
*
4557 TTTTATCTTGGAACCATC
1 TTTTATCGTGGAACCATC
4575 GAAACTAAAG
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:0.24, G:0.14, T:0.41
Consensus pattern (19 bp):
TTTTATCGTGGAACCATCC
Found at i:7536 original size:60 final size:61
Alignment explanation
Indices: 7442--7564 Score: 146
Period size: 60 Copynumber: 2.0 Consensus size: 61
7432 CTTTTAAATG
* * * *
7442 TTTCAGTTTCATCCCTAAATTATGATTGTCATTCTAAATT-AGTCCTCAAAC-TTTTGAACA
1 TTTCAGTTTCATCCCCAAAATATGATTGTCATTCTAAATTGA-CCCCCAAACTTTTTGAACA
*
7502 TTTCAGTTTCATCCCCAAAATGTGACATT-T-ATTCTAAATTGACCCCCAAACTTTTTGAACA
1 TTTCAGTTTCATCCCCAAAATATG--ATTGTCATTCTAAATTGACCCCCAAACTTTTTGAACA
7563 TT
1 TT
7565 CTAATTTTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
60 38 0.70
61 13 0.24
62 3 0.06
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (61 bp):
TTTCAGTTTCATCCCCAAAATATGATTGTCATTCTAAATTGACCCCCAAACTTTTTGAACA
Found at i:7880 original size:59 final size:59
Alignment explanation
Indices: 7696--7873 Score: 189
Period size: 59 Copynumber: 3.0 Consensus size: 59
7686 TTCGGATGAA
* * * *
7696 TTTAGGGATATAATTGGAATATTTAAAAGTTTAGGGACCCATTTAGAAA-GAGGGTCATAG
1 TTTAGGGATA-AATTAGAATATTAAAAAGTTTAAGGACCAATTTA-AAATGAGGGTCATAG
* * *** ** *
7756 TTTAGTGATAAATTAGAATATTCAAAAGTTTAAGGA-TGTTTTAAAATGAAAGCCATAG
1 TTTAGGGATAAATTAGAATATTAAAAAGTTTAAGGACCAATTTAAAATGAGGGTCATAG
* *
7814 TTTAGGGATCAAATTAGAATATTAAAAAGTTTAAGTACCAATTTAAAATGAGGGTTATAG
1 TTTAGGGAT-AAATTAGAATATTAAAAAGTTTAAGGACCAATTTAAAATGAGGGTCATAG
7874 GTAGGGAAAT
Statistics
Matches: 95, Mismatches: 20, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
57 3 0.03
58 20 0.21
59 48 0.51
60 24 0.25
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.33
Consensus pattern (59 bp):
TTTAGGGATAAATTAGAATATTAAAAAGTTTAAGGACCAATTTAAAATGAGGGTCATAG
Found at i:8399 original size:2 final size:2
Alignment explanation
Indices: 8392--8427 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
8382 TATAAAAGAG
8392 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8428 GTTTCTTAGT
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):
TA
Found at i:8801 original size:30 final size:30
Alignment explanation
Indices: 8531--8833 Score: 164
Period size: 30 Copynumber: 10.1 Consensus size: 30
8521 ATTGAGTTTA
*
8531 TTTATTCTTATCTTAA-T-TGAAAAATGTAT
1 TTTATTCTTATCTTAACTAT-AAAAATATAT
* *
8560 TTTAATCTTATCTTAACT-TATAAAATGTAT
1 TTTATTCTTATCTTAACTATA-AAAATATAT
* *
8590 TTTATTCCTAACTTAACT-TAAAAATATAT
1 TTTATTCTTATCTTAACTATAAAAATATAT
* ** *
8619 TTTATTTTTATCTTAACT-TGTTACATATAT
1 TTTATTCTTATCTTAACTAT-AAAAATATAT
* ** * * *
8649 TATATTCTTAAGTTAAAT-TATTAAATATAA
1 TTTATTCTTATCTTAACTATA-AAAATATAT
* * * *
8679 TATATTCTTACCTTAAAT-TATTAAATAT-T
1 TTTATTCTTATCTTAACTATA-AAAATATAT
*
8708 ATTTATTCTTATCTTAACT-TGAAAATATACAT
1 -TTTATTCTTATCTTAACTAT-AAAA-ATATAT
* **
8740 TTTATT-TTAAT-TTAAAAAATATATTAATATAT
1 TTTATTCTT-ATCTT---AACTATAAAAATATAT
* *
8772 TTTATTCTTATTTTTAA-TTTAAAAATATAT
1 TTTATTCTTA-TCTTAACTATAAAAATATAT
*
8802 TTTATTTTTATCTTAACTATAAAAA-ATAT
1 TTTATTCTTATCTTAACTATAAAAATATAT
8831 TTT
1 TTT
8834 TTTATCTCAA
Statistics
Matches: 220, Mismatches: 37, Indels: 34
0.76 0.13 0.12
Matches are distributed among these distances:
29 52 0.24
30 130 0.59
31 14 0.06
32 13 0.06
33 8 0.04
34 3 0.01
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (30 bp):
TTTATTCTTATCTTAACTATAAAAATATAT
Found at i:8806 original size:93 final size:89
Alignment explanation
Indices: 8531--8819 Score: 228
Period size: 89 Copynumber: 3.2 Consensus size: 89
8521 ATTGAGTTTA
* * * * * ** * * * * *
8531 TTTATTCTTATCTTAA-TTGAAAAATGTATTTTAATCTTATCTTAACTTATAAAATGTATTTTAT
1 TTTATTTTTATCTTAACTTGTAAAATATATTATATTCTTAAGTTAAATTATTAAATATAATATAT
* * *
8595 TCCTAACTTAACTTAAAAATATAT
66 TCTTACCTTAAATTAAAAATATAT
* *
8619 TTTATTTTTATCTTAACTTGTTACATATATTATATTCTTAAGTTAAATTATTAAATATAATATAT
1 TTTATTTTTATCTTAACTTGTAAAATATATTATATTCTTAAGTTAAATTATTAAATATAATATAT
*
8684 TCTTACCTTAAATTATTAAATAT-T
66 TCTTACCTTAAATTA-AAAATATAT
* * *
8708 ATTTATTCTTATCTTAACTTG-AAAATATACATTTTATT-TTAATTTAAAAAATATATT-AATAT
1 -TTTATTTTTATCTTAACTTGTAAAATAT--ATTATATTCTTAAGTT---AAAT-TATTAAATAT
* * ** *
8770 ATTTTATTCTTATTTTTAATTTAAAAATATAT
59 AATATATTCTTA-CCTTAAATTAAAAATATAT
8802 TTTATTTTTATCTTAACT
1 TTTATTTTTATCTTAACT
8820 ATAAAAAATA
Statistics
Matches: 160, Mismatches: 30, Indels: 17
0.77 0.14 0.08
Matches are distributed among these distances:
88 15 0.09
89 53 0.33
90 31 0.19
91 7 0.04
93 42 0.26
94 12 0.08
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (89 bp):
TTTATTTTTATCTTAACTTGTAAAATATATTATATTCTTAAGTTAAATTATTAAATATAATATAT
TCTTACCTTAAATTAAAAATATAT
Found at i:11674 original size:2 final size:2
Alignment explanation
Indices: 11669--11696 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11659 GACAAGGGGG
11669 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
11697 ACTTTAACGC
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17901 original size:2 final size:2
Alignment explanation
Indices: 17889--17932 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
17879 TATTTGACTA
*
17889 AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17931 AT
1 AT
17933 TGTCTAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:20267 original size:19 final size:20
Alignment explanation
Indices: 20229--20268 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
20219 TCTCTCTCAA
*
20229 TTTAACCTTCACTCTTTATT
1 TTTAACCTTCACTATTTATT
*
20249 TTTAGCCTTCA-TATTTATT
1 TTTAACCTTCACTATTTATT
20268 T
1 T
20269 GACACATTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.20, C:0.20, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTAACCTTCACTATTTATT
Found at i:22508 original size:21 final size:21
Alignment explanation
Indices: 22442--22508 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
22432 AGAAACCATG
22442 GTTTTAGTCCATCATGTTCGA
1 GTTTTAGTCCATCATGTTCGA
** ** * *
22463 G-TTTAAACCATGGTTTTAGA
1 GTTTTAGTCCATCATGTTCGA
*
22483 CTTTTAGTCCATCATGTTCGA
1 GTTTTAGTCCATCATGTTCGA
22504 GTTTT
1 GTTTT
22509 TAATCTCATT
Statistics
Matches: 31, Mismatches: 14, Indels: 2
0.66 0.30 0.04
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.21, C:0.16, G:0.18, T:0.45
Consensus pattern (21 bp):
GTTTTAGTCCATCATGTTCGA
Found at i:38073 original size:26 final size:26
Alignment explanation
Indices: 38044--38094 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
38034 TTAACTCGAG
*
38044 TCGAGTTTTAATTTTA-AATTTTAAAT
1 TCGAG-TTTAATTTAATAATTTTAAAT
38070 TCGAGTTTAATTTAATAATTTTAAA
1 TCGAGTTTAATTTAATAATTTTAAA
38095 CTCGTAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.51
Consensus pattern (26 bp):
TCGAGTTTAATTTAATAATTTTAAAT
Found at i:45668 original size:22 final size:22
Alignment explanation
Indices: 45636--45680 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
45626 GCCTTACATC
45636 AATATAACTTGTTTAATTAATT
1 AATATAACTTGTTTAATTAATT
*
45658 AATATATCTTGTTTAATTAATT
1 AATATAACTTGTTTAATTAATT
45680 A
1 A
45681 GAATTGAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (22 bp):
AATATAACTTGTTTAATTAATT
Found at i:46562 original size:15 final size:15
Alignment explanation
Indices: 46542--46573 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
46532 TTTCAGACAC
46542 TGGTCTGAGAATAGT
1 TGGTCTGAGAATAGT
*
46557 TGGTCTGATAATAGT
1 TGGTCTGAGAATAGT
46572 TG
1 TG
46574 AGGACAGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.31, T:0.38
Consensus pattern (15 bp):
TGGTCTGAGAATAGT
Found at i:47525 original size:2 final size:2
Alignment explanation
Indices: 47518--47558 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
47508 TGTACTAATT
47518 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
47559 TTTAGTTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:69142 original size:19 final size:21
Alignment explanation
Indices: 69106--69144 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
69096 ACTAAAATTA
69106 TAAATATATAATATAATAAAG
1 TAAATATATAATATAATAAAG
69127 TAAATA-ATAA-ATAATAAA
1 TAAATATATAATATAATAAA
69145 TACATACAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 4 0.22
21 6 0.33
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (21 bp):
TAAATATATAATATAATAAAG
Found at i:71032 original size:332 final size:332
Alignment explanation
Indices: 70634--71304 Score: 1042
Period size: 338 Copynumber: 2.0 Consensus size: 332
70624 TAATAAATTC
* * *
70634 TAATTTTACTAAAAATGAATAAATATTATTAATTGTTGTTAAAAATAATAATTAATGAATAATAA
1 TAATTTTACTAAAAATAAATAAACATTATTAACTGTTGTTAAAAATAATAATTAATGAATAATAA
*
70699 TTCATTTGATCCCTCAATTGTAATTAAAAGTTTA-TTT-TA-ATATTTTTAAACAATTAATTTTA
66 TTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTATATATATTTTTAAACAAATAATTTTA
* *
70761 AAATTCAATAATATTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTTATTA
131 AAAGTCAATAAAATTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTTATTA
* * * * *
70826 TCATCATCGTCGTCGTCATTTTATAAAAGAAATACTGGTTATAAAACTTTTATAAAATTATTCAT
196 TCATCA---TCATCATCATTTTATAAAAGAAATAATAGTCATAAAACTTTTATAAAATTATTCAT
* * * * * *
70891 ATTTTAAAATACTTACCCTCAAAGTTTTCCTATAATAGATTATATATATTGTTTAATTTCATGCA
258 ATTTTAAAACACTTACCCTCAAAGTTTTCCTATAAGAAATTATACATATTGTGTAATTTCATACA
*
70956 AAAATCAAAA
323 AAAATAAAAA
*
70966 TAATTTTATTAAAAATAAATAAACATTATTAACTGTTGTTAAAAATAATAATTAATGAATAATAA
1 TAATTTTACTAAAAATAAATAAACATTATTAACTGTTGTTAAAAATAATAATTAATGAATAATAA
71031 TTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAAATA
66 TTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTT-ATA-----TATATTTTTAAACAAATA
71096 ATTTTAAAAGTCAATAAAATTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATAT
125 ATTTTAAAAGTCAATAAAATTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATAT
*
71161 TTATTATCATCATCATCATCATTTTGTAAAAGAAATAATAGTCATAAAACTTTTATAAAATTATT
190 TTATTATCATCATCATCATCATTTTATAAAAGAAATAATAGTCATAAAACTTTTATAAAATTATT
* *
71226 CATATTTTAAAACACTTACCCTCAAAGTTTTCCTATACGAAATTATACGTATTGTGTAATTTCAT
255 CATATTTTAAAACACTTACCCTCAAAGTTTTCCTATAAGAAATTATACATATTGTGTAATTTCAT
71291 ACAAAAATAAAAA
320 ACAAAAATAAAAA
71304 T
1 T
71305 TTATCGAGTT
Statistics
Matches: 308, Mismatches: 22, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
332 95 0.31
333 3 0.01
335 2 0.01
338 117 0.38
341 91 0.30
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (332 bp):
TAATTTTACTAAAAATAAATAAACATTATTAACTGTTGTTAAAAATAATAATTAATGAATAATAA
TTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTATATATATTTTTAAACAAATAATTTTA
AAAGTCAATAAAATTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTTATTA
TCATCATCATCATCATTTTATAAAAGAAATAATAGTCATAAAACTTTTATAAAATTATTCATATT
TTAAAACACTTACCCTCAAAGTTTTCCTATAAGAAATTATACATATTGTGTAATTTCATACAAAA
ATAAAAA
Found at i:73105 original size:2 final size:2
Alignment explanation
Indices: 73100--73131 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
73090 TTTTTTTCAC
*
73100 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
73132 ATTGGCATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:76553 original size:35 final size:35
Alignment explanation
Indices: 76513--76633 Score: 100
Period size: 35 Copynumber: 3.2 Consensus size: 35
76503 TTAAATACAA
76513 TATTAATGGCTTTCTTCTGAATTTATTTGAATACT
1 TATTAATGGCTTTCTTCTGAATTTATTTGAATACT
* * * * *
76548 TATTAATGACCTTAAT-TTTTAGAATATATTCGATTAAATACAA
1 TATTAATG-GCTT--TCTTCT-GAATTTA-T---TTGAATAC-T
*
76591 TATTAATGGCTTCCTTCTGAATTTATTTGAATACT
1 TATTAATGGCTTTCTTCTGAATTTATTTGAATACT
76626 TATTAATG
1 TATTAATG
76634 ACCTTAATTT
Statistics
Matches: 65, Mismatches: 11, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
35 16 0.25
36 10 0.15
37 3 0.05
38 7 0.11
39 2 0.03
40 6 0.09
41 3 0.05
42 10 0.15
43 8 0.12
ACGTcount: A:0.32, C:0.11, G:0.10, T:0.47
Consensus pattern (35 bp):
TATTAATGGCTTTCTTCTGAATTTATTTGAATACT
Found at i:76579 original size:78 final size:78
Alignment explanation
Indices: 76493--76655 Score: 317
Period size: 78 Copynumber: 2.1 Consensus size: 78
76483 GTTCACAAAT
*
76493 ATATATTCGATTAAATACAATATTAATGGCTTTCTTCTGAATTTATTTGAATACTTATTAATGAC
1 ATATATTCGATTAAATACAATATTAATGGCTTCCTTCTGAATTTATTTGAATACTTATTAATGAC
76558 CTTAATTTTTAGA
66 CTTAATTTTTAGA
76571 ATATATTCGATTAAATACAATATTAATGGCTTCCTTCTGAATTTATTTGAATACTTATTAATGAC
1 ATATATTCGATTAAATACAATATTAATGGCTTCCTTCTGAATTTATTTGAATACTTATTAATGAC
76636 CTTAATTTTTAGA
66 CTTAATTTTTAGA
76649 ATATATT
1 ATATATT
76656 ATTTTCAATT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 84 1.00
ACGTcount: A:0.35, C:0.10, G:0.09, T:0.46
Consensus pattern (78 bp):
ATATATTCGATTAAATACAATATTAATGGCTTCCTTCTGAATTTATTTGAATACTTATTAATGAC
CTTAATTTTTAGA
Found at i:78973 original size:3 final size:3
Alignment explanation
Indices: 78965--79017 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
78955 CATCAGTTTA
78965 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
79013 ATT AT
1 ATT AT
79018 GGTGTAAGTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:82655 original size:24 final size:23
Alignment explanation
Indices: 82600--82655 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
82590 TCAAAACAAA
82600 TTTATTAAATTTATCATCATTTTT
1 TTTA-TAAATTTATCATCATTTTT
* * *
82624 TTAAATAATTTTATCATTATTCTTT
1 TT-TATAAATTTATCATCATT-TTT
82649 TTTATAA
1 TTTATAA
82656 CTTAACATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
24 20 0.77
25 6 0.23
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTATAAATTTATCATCATTTTT
Found at i:93849 original size:2 final size:2
Alignment explanation
Indices: 93842--93871 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
93832 GGATTCACCA
93842 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
93872 TACATTGACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:96015 original size:21 final size:21
Alignment explanation
Indices: 95991--96044 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
95981 TATCGCAAAT
95991 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
*
96012 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAA
96033 TCGCGTTGCGAT
1 TCGCGTTGCGAT
96045 TTTCCATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Found at i:96061 original size:20 final size:20
Alignment explanation
Indices: 96033--96203 Score: 134
Period size: 20 Copynumber: 8.4 Consensus size: 20
96023 TAGTTGAAAA
96033 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* *
96053 TCGCATTGCGACTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
96073 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCATT
* * * *
96093 TCGTGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCATT
*
96115 T-GTCGTTGCGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-ATT
* * *
96136 T--CGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCATT
96156 T-GCCGTTGCGATTTTCCATT
1 TCG-CGTTGCGATTTTCCATT
* *
96176 TCGCGTTGCGATTTTTCAGT
1 TCGCGTTGCGATTTTCCATT
96196 TCGCGTTG
1 TCGCGTTG
96204 TGATAGTTAA
Statistics
Matches: 122, Mismatches: 20, Indels: 18
0.76 0.12 0.11
Matches are distributed among these distances:
19 9 0.07
20 81 0.66
21 8 0.07
22 24 0.20
ACGTcount: A:0.13, C:0.23, G:0.23, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:96122 original size:22 final size:22
Alignment explanation
Indices: 96089--96167 Score: 76
Period size: 22 Copynumber: 3.7 Consensus size: 22
96079 TGCGATTTTC
96089 CAGTTCGT-GTTGCGATAGTCTA
1 CAGTT-GTCGTTGCGATAGTCTA
* *
96111 CAGTTGTCGTTGCGAT--TTTC
1 CAGTTGTCGTTGCGATAGTCTA
**
96131 CAAAT-TCGTTGCGATAGTCTA
1 CAGTTGTCGTTGCGATAGTCTA
*
96152 CAGTTGCCGTTGCGAT
1 CAGTTGTCGTTGCGAT
96168 TTTCCATTTC
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
19 10 0.23
20 5 0.11
21 7 0.16
22 22 0.50
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (22 bp):
CAGTTGTCGTTGCGATAGTCTA
Found at i:96130 original size:42 final size:41
Alignment explanation
Indices: 96076--96187 Score: 163
Period size: 41 Copynumber: 2.7 Consensus size: 41
96066 TTCCATTTCG
* *
96076 CGTTGCGATTTTCCAGTTCGTGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAATTCG-GTTGCGATAGTCTACAGTTGC
96118 CGTTGCGATTTTCCAAATTC-GTTGCGATAGTCTACAGTTGC
1 CGTTGCGATTTTCC-AATTCGGTTGCGATAGTCTACAGTTGC
*
96159 CGTTGCGATTTTCCATTTCGCGTTGCGAT
1 CGTTGCGATTTTCCAATTCG-GTTGCGAT
96188 TTTTCAGTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
40 4 0.06
41 34 0.53
42 22 0.34
43 4 0.06
ACGTcount: A:0.15, C:0.21, G:0.24, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTTCCAATTCGGTTGCGATAGTCTACAGTTGC
Found at i:96286 original size:6 final size:6
Alignment explanation
Indices: 96275--96305 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
96265 GACACGTATT
96275 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
96306 GACGGCGGCG
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:96802 original size:6 final size:6
Alignment explanation
Indices: 96786--96827 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
96776 GTCCGTCTCG
*
96786 GGTCGT TGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
96828 CGACACGTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.17, G:0.48, T:0.36
Consensus pattern (6 bp):
GGTCGT
Found at i:97031 original size:22 final size:21
Alignment explanation
Indices: 96962--97038 Score: 93
Period size: 22 Copynumber: 3.7 Consensus size: 21
96952 CATTTTAGAC
96962 TATCGCAACGCGAAATGGAAA
1 TATCGCAACGCGAAATGGAAA
** ** *
96983 -ATCGCAACGCGATTTTCAAC
1 TATCGCAACGCGAAATGGAAA
97003 TATCGCAACGCGAAATGGAAAA
1 TATCGCAACGCGAAATGG-AAA
97025 TATCGCAACGCGAA
1 TATCGCAACGCGAA
97039 TTTGCGATAG
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
20 15 0.34
21 13 0.30
22 16 0.36
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (21 bp):
TATCGCAACGCGAAATGGAAA
Found at i:101065 original size:41 final size:42
Alignment explanation
Indices: 101005--101084 Score: 126
Period size: 41 Copynumber: 1.9 Consensus size: 42
100995 TTTGTGATAA
*
101005 ACTTTTTAGATTTAAGATTTTTAGTTTGATTATTTTATTATT
1 ACTTTTTAGATTTAAGATTTTTAGTTTAATTATTTTATTATT
* *
101047 ACTTTTT-TATTTAGGATTTTTAGTTTAATTATTTTATT
1 ACTTTTTAGATTTAAGATTTTTAGTTTAATTATTTTATT
101085 TAGGAATTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
41 28 0.80
42 7 0.20
ACGTcount: A:0.25, C:0.03, G:0.09, T:0.64
Consensus pattern (42 bp):
ACTTTTTAGATTTAAGATTTTTAGTTTAATTATTTTATTATT
Found at i:101106 original size:28 final size:27
Alignment explanation
Indices: 101051--101106 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
101041 ATTATTACTT
*
101051 TTTTATTTAGGATTTTTAGTTTAATTA
1 TTTTATTTAGGATTGTTAGTTTAATTA
*
101078 TTTTATTTAGGAATTAGTTA-TTTTATTA
1 TTTTATTTAGG-ATT-GTTAGTTTAATTA
101106 T
1 T
101107 AACTCTTGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 11 0.44
28 11 0.44
29 3 0.12
ACGTcount: A:0.27, C:0.00, G:0.11, T:0.62
Consensus pattern (27 bp):
TTTTATTTAGGATTGTTAGTTTAATTA
Found at i:105402 original size:29 final size:29
Alignment explanation
Indices: 105369--105444 Score: 152
Period size: 29 Copynumber: 2.6 Consensus size: 29
105359 CTCTGGGGGT
105369 AGGTCGCCATGCACGCCCAGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
105398 AGGTCGCCATGCACGCCCAGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
105427 AGGTCGCCATGCACGCCC
1 AGGTCGCCATGCACGCCC
105445 CAACACGCTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.20, C:0.45, G:0.25, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCAGCGACCTACC
Found at i:105483 original size:14 final size:14
Alignment explanation
Indices: 105460--105506 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
105450 CGCTGGGCAT
*
105460 CCGAGACCATCCGA
1 CCGAGGCCATCCGA
105474 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
105488 CCGATGCCATCCGA
1 CCGAGGCCATCCGA
*
105502 ACGAG
1 CCGAG
105507 CTATGCGAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.26, C:0.40, G:0.26, T:0.09
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:105527 original size:10 final size:10
Alignment explanation
Indices: 105512--105568 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
105502 ACGAGCTATG
105512 CGAGGGCATC
1 CGAGGGCATC
*
105522 CGAGGGCAAC
1 CGAGGGCATC
*
105532 CGAGCGAGCTATG
1 CGAG-G-GC-ATC
*
105545 CGAGGGAATC
1 CGAGGGCATC
*
105555 CGAGGGCAAC
1 CGAGGGCATC
105565 CGAG
1 CGAG
105569 CGAGGGTAGG
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
10 27 0.73
11 2 0.05
12 3 0.08
13 5 0.14
ACGTcount: A:0.26, C:0.26, G:0.40, T:0.07
Consensus pattern (10 bp):
CGAGGGCATC
Found at i:105545 original size:33 final size:33
Alignment explanation
Indices: 105498--105572 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
105488 CCGATGCCAT
* *
105498 CCGAACGAGCTATGCGAGGGCATCCGAGGGCAA
1 CCGAGCGAGCTATGCGAGGGAATCCGAGGGCAA
105531 CCGAGCGAGCTATGCGAGGGAATCCGAGGGCAA
1 CCGAGCGAGCTATGCGAGGGAATCCGAGGGCAA
105564 CCGAGCGAG
1 CCGAGCGAG
105573 GGTAGGTCGC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.27, C:0.27, G:0.39, T:0.08
Consensus pattern (33 bp):
CCGAGCGAGCTATGCGAGGGAATCCGAGGGCAA
Found at i:105658 original size:10 final size:10
Alignment explanation
Indices: 105639--105726 Score: 59
Period size: 10 Copynumber: 8.5 Consensus size: 10
105629 CCTACCCTCG
*
105639 CTCGGTTGCC
1 CTCGGATGCC
105649 CTCGGATGCC
1 CTCGGATGCC
*
105659 CTCGCATTGCTC
1 CTCGGA-TGC-C
* * *
105671 GTTCAGATGGC
1 -CTCGGATGCC
*
105682 CTCGGATGCT
1 CTCGGATGCC
*
105692 CTCGGATGGC
1 CTCGGATGCC
*
105702 CTCGGATGCT
1 CTCGGATGCC
* *
105712 TTCGGATGGC
1 CTCGGATGCC
105722 CTCGG
1 CTCGG
105727 TCGAATGGCC
Statistics
Matches: 57, Mismatches: 18, Indels: 6
0.70 0.22 0.07
Matches are distributed among these distances:
10 47 0.82
11 4 0.07
12 3 0.05
13 3 0.05
ACGTcount: A:0.09, C:0.32, G:0.32, T:0.27
Consensus pattern (10 bp):
CTCGGATGCC
Found at i:105701 original size:20 final size:20
Alignment explanation
Indices: 105639--105726 Score: 95
Period size: 20 Copynumber: 4.2 Consensus size: 20
105629 CCTACCCTCG
* * *
105639 CTCGGTTGCCCTCGGATGCC
1 CTCGGATGCTCTCGGATGGC
* *
105659 CTCGCATTGCTCGTTCAGATGGC
1 CTCGGA-TGCTC--TCGGATGGC
105682 CTCGGATGCTCTCGGATGGC
1 CTCGGATGCTCTCGGATGGC
*
105702 CTCGGATGCTTTCGGATGGC
1 CTCGGATGCTCTCGGATGGC
105722 CTCGG
1 CTCGG
105727 TCGAATGGCC
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
20 36 0.63
21 4 0.07
22 5 0.09
23 12 0.21
ACGTcount: A:0.09, C:0.32, G:0.32, T:0.27
Consensus pattern (20 bp):
CTCGGATGCTCTCGGATGGC
Found at i:105849 original size:29 final size:30
Alignment explanation
Indices: 105791--105863 Score: 112
Period size: 29 Copynumber: 2.5 Consensus size: 30
105781 CTGCATGGAT
105791 TGCATGGCGACCTACCTAGGTCACTGGGCG
1 TGCATGGCGACCTACCTAGGTCACTGGGCG
** *
105821 TGCATGGCGACCT-GGTAGGTCGCTGGGCG
1 TGCATGGCGACCTACCTAGGTCACTGGGCG
105850 TGCATGGCGACCTA
1 TGCATGGCGACCTA
105864 TATGGGGACT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
29 26 0.67
30 13 0.33
ACGTcount: A:0.15, C:0.27, G:0.37, T:0.21
Consensus pattern (30 bp):
TGCATGGCGACCTACCTAGGTCACTGGGCG
Found at i:111241 original size:21 final size:21
Alignment explanation
Indices: 111212--111252 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
111202 CATCATTCTC
* *
111212 TTAAATATATAATTATATTTT
1 TTAAATATAAAATTAAATTTT
*
111233 TTAATTATAAAATTAAATTT
1 TTAAATATAAAATTAAATTT
111253 GATGATAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTAAATATAAAATTAAATTTT
Found at i:112609 original size:19 final size:19
Alignment explanation
Indices: 112587--112631 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
112577 AACTTTTAAA
*
112587 TATTTAAATATTTGTTAG-T
1 TATTTAAATAATT-TTAGTT
112606 TA-TTAAATAATTTTAGTT
1 TATTTAAATAATTTTAGTT
112624 TATTTAAA
1 TATTTAAA
112632 AATATTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 4 0.17
18 12 0.52
19 7 0.30
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (19 bp):
TATTTAAATAATTTTAGTT
Found at i:113116 original size:13 final size:15
Alignment explanation
Indices: 113098--113138 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
113088 TTAAAAAAAT
113098 TAAA-TTTATTT-TA
1 TAAATTTTATTTATA
113111 TAAATTTTATTTATA
1 TAAATTTTATTTATA
113126 TACTAATTTTATT
1 TA--AATTTTATT
113139 ATGGTAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.17
14 7 0.29
15 4 0.17
17 9 0.38
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (15 bp):
TAAATTTTATTTATA
Found at i:118329 original size:2 final size:2
Alignment explanation
Indices: 118322--118361 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
118312 TTTTATAACC
118322 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
118362 TTCTTCATTT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:123276 original size:12 final size:13
Alignment explanation
Indices: 123239--123273 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
123229 ATAATGCTAG
123239 ATTTTTATTTAA-
1 ATTTTTATTTAAT
123251 ATTTTTATTTTAAT
1 ATTTTTA-TTTAAT
123265 ATTTTTATT
1 ATTTTTATT
123274 AATTTAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.33
13 7 0.33
14 7 0.33
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
ATTTTTATTTAAT
Found at i:128938 original size:29 final size:29
Alignment explanation
Indices: 128905--128986 Score: 110
Period size: 29 Copynumber: 2.8 Consensus size: 29
128895 AATTAAATTA
128905 ATGTCATTGTTTACATCATTTAAGTAAAG
1 ATGTCATTGTTTACATCATTTAAGTAAAG
* * *
128934 ATGTCATTGTTTACACCATTAAAGTAATG
1 ATGTCATTGTTTACATCATTTAAGTAAAG
* *
128963 ATGACATTGCTTACATCAATTTAA
1 ATGTCATTGTTTACATC-ATTTAA
128987 TTAAGTGAGA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 40 0.89
30 5 0.11
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.39
Consensus pattern (29 bp):
ATGTCATTGTTTACATCATTTAAGTAAAG
Found at i:130167 original size:15 final size:15
Alignment explanation
Indices: 130144--130173 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
130134 ACCAGGCTGG
130144 AATTACAACAACAAC
1 AATTACAACAACAAC
*
130159 AATTCCAACAACAAC
1 AATTACAACAACAAC
130174 TATAAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.13
Consensus pattern (15 bp):
AATTACAACAACAAC
Found at i:131781 original size:18 final size:18
Alignment explanation
Indices: 131760--131800 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
131750 GCAACTCCAC
131760 CCACTTCACCAACATCAA
1 CCACTTCACCAACATCAA
*
131778 CCACTTCACCAATATCAA
1 CCACTTCACCAACATCAA
131796 CCACT
1 CCACT
131801 CAAGGAGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.37, C:0.44, G:0.00, T:0.20
Consensus pattern (18 bp):
CCACTTCACCAACATCAA
Found at i:133538 original size:29 final size:29
Alignment explanation
Indices: 133496--133576 Score: 144
Period size: 29 Copynumber: 2.8 Consensus size: 29
133486 AACTAAATTA
133496 ATGTCATTGCTTACATCATTTAAGTAAAG
1 ATGTCATTGCTTACATCATTTAAGTAAAG
*
133525 ATGTCATTGCTTACATCATTTAAGTAATG
1 ATGTCATTGCTTACATCATTTAAGTAAAG
133554 ATGTCATTGCTTACATCAATTTA
1 ATGTCATTGCTTACATC-ATTTA
133577 TTAGGTGAGA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (29 bp):
ATGTCATTGCTTACATCATTTAAGTAAAG
Found at i:134006 original size:27 final size:27
Alignment explanation
Indices: 133958--134037 Score: 87
Period size: 28 Copynumber: 3.0 Consensus size: 27
133948 TAATTATTTT
*
133958 ATATT-TAT-TTTTTTATCT-TTTAAA
1 ATATTATATATTTTTTATTTATTTAAA
*
133982 GTATTATATATTTTTTATTTATTTAAA
1 ATATTATATATTTTTTATTTATTTAAA
*
134009 AT-TTAGTATATATTTTTTTTTATTTAAA
1 ATATTA-TATAT-TTTTTATTTATTTAAA
134037 A
1 A
134038 GATGTTTGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
24 4 0.09
25 3 0.06
26 12 0.26
27 12 0.26
28 16 0.34
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.64
Consensus pattern (27 bp):
ATATTATATATTTTTTATTTATTTAAA
Found at i:134808 original size:81 final size:84
Alignment explanation
Indices: 134672--134888 Score: 352
Period size: 81 Copynumber: 2.6 Consensus size: 84
134662 TGGTAGTAAA
*
134672 TTTAGCGATATTAAGAG-GGGTTGTATATATATAGCTACTACTGAACCAGCTGGTATGGAAGATA
1 TTTAGCGATATTAAGAGTGGGTTG-ATATATATAGCTACTACTGAACCAGATGGTATGGAAGATA
134736 GGG-T-CATGCAATGGTGGT
65 GGGTTCCATGCAATGGTGGT
134754 TTTAGCGATATTAAGAGTGGGTTG-TATATATAGCTACTACTGAACCAGATGGTATGGAAGATAG
1 TTTAGCGATATTAAGAGTGGGTTGATATATATAGCTACTACTGAACCAGATGGTATGGAAGATAG
134818 GGTTTCCCATGCAATGGTGGT
66 GG-TT-CCATGCAATGGTGGT
*
134839 TTTAGCGATATTAAGAGTGGGTTGTATATATATAGCTACCACTGAACCAG
1 TTTAGCGATATTAAGAGTGGGTTG-ATATATATAGCTACTACTGAACCAG
134889 CTTCATATTT
Statistics
Matches: 126, Mismatches: 2, Indels: 9
0.92 0.01 0.07
Matches are distributed among these distances:
81 41 0.33
82 17 0.13
83 7 0.06
85 38 0.30
87 23 0.18
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.31
Consensus pattern (84 bp):
TTTAGCGATATTAAGAGTGGGTTGATATATATAGCTACTACTGAACCAGATGGTATGGAAGATAG
GGTTCCATGCAATGGTGGT
Found at i:136327 original size:13 final size:13
Alignment explanation
Indices: 136309--136337 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
136299 CCACAGTACT
136309 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
136322 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
136335 CCG
1 CCG
136338 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:136597 original size:1 final size:1
Alignment explanation
Indices: 136591--136629 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
136581 GTATAGCTTA
* * *
136591 TTTTTTTTCTTTCTGTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
136630 GTTTCTGTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.05, G:0.03, T:0.92
Consensus pattern (1 bp):
T
Found at i:137022 original size:3 final size:3
Alignment explanation
Indices: 137014--137184 Score: 190
Period size: 3 Copynumber: 56.7 Consensus size: 3
137004 ATATTTATTA
*
137014 AAT AAT AAT AAT ATAT AAT AAT -AT ATAT ATT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
**
137060 ATAT AAT -AT AAT AAT -AT AAT AAT AAT AAT AAAT GCT AAT AAT AAT
1 A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
* * *
137105 AAT AAT ACT AAT AAT AAT AAT ATT AAT AAAT AAT -AT AAT AAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
*
137150 AAT AAT AAT ATT AAT AAT AAT AAT AA- ATAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AA
137185 AATGGATAAA
Statistics
Matches: 143, Mismatches: 14, Indels: 22
0.80 0.08 0.12
Matches are distributed among these distances:
2 9 0.06
3 118 0.83
4 16 0.11
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:138133 original size:221 final size:224
Alignment explanation
Indices: 137473--138460 Score: 1273
Period size: 221 Copynumber: 4.5 Consensus size: 224
137463 GATATCAAAC
** *
137473 AAGGTTGAACAAGCTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTC
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT-
* * * * * * *
137538 ATGAA-CTTTTTTGGCCATGTTGA-CCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTC
65 ATGAACCTTCTCTGGCAATGATGATCCATCAAATGATGGATTCAAACAAAAAGTTGAACAAGATC
*
137601 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
130 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAA
* * * **
137666 AAGAATGATCCACCAAATGATGGATTCAGGA
195 AAG-ATAATCCACCAGATGATGGATTGAAAA
137697 AAGGTTGAAC-AA--CTTCTCATTATGAA---CTTCTTCCTTCTTC-GATGAGTTC-TCTC-TTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * *** *
137753 TGAACTTTCTCTGG-AAAGATGATCCACCAAATGATGGATTC-AGGTAAAGGTTGAACAA-ATTC
66 TGAACCTTCTCTGGCAATGATGATCCATCAAATGATGGATTCAAACAAAAAGTTGAACAAGA-TC
* *
137815 TTCTCATTATGAACTTCTTCTTCCTTCTTCA-ATGAGTTC-T-TCATCATGAACTTTCTCTGGAA
130 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAA
* * **
137877 AAGATGATTCACCA-ATGATGGATTCAGGTAA
195 AAGATAATCCACCAGATGATGGATT--GAAAA
137908 AAGGTTTGAACAAATTCTTCTCATTA-GAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAGG-TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *** *
137972 ATGAACCTTCTCTGGTAATGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAA-AT-
65 ATGAACCTTCTCTGGCAATGATGATCCATCAAATGATGGATTCAAACAAAAAGTTGAACAAGATC
*
138035 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT-TCATTATGAACCTTCTCTGGCA
130 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAA
* **
138099 ATGATAATCCATTAGATGATGGATTGAAAA
195 AAGATAATCCACCAGATGATGGATTGAAAA
*
138129 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * *
138194 TGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAACAAAAAGTTGAACAAGTTCT
66 TGAACCTTCTCTGGCAATGATGATCCATCAAATGATGGATTCAAACAAAAAGTTGAACAAGATCT
* *
138259 TCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGCAA
131 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAA
* *
138324 TGATAATCCATCAGATGATGGATTTGAACAA
196 AGATAATCCACCAGATGATGGA-TTGAA-AA
*
138355 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * *
138420 TGAACTTTCTCTGGAAATGCTGATCCATCGAATGATGGATT
66 TGAACCTTCTCTGGCAATGATGATCCATCAAATGATGGATT
138461 TGAACTTTGC
Statistics
Matches: 681, Mismatches: 57, Indels: 50
0.86 0.07 0.06
Matches are distributed among these distances:
209 10 0.01
210 10 0.01
211 29 0.04
212 7 0.01
213 10 0.01
214 59 0.09
215 33 0.05
216 4 0.01
217 23 0.03
218 22 0.03
219 4 0.01
220 68 0.10
221 145 0.21
222 45 0.07
223 52 0.08
224 54 0.08
225 5 0.01
226 101 0.15
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (224 bp):
AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACCTTCTCTGGCAATGATGATCCATCAAATGATGGATTCAAACAAAAAGTTGAACAAGATCT
TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAA
AGATAATCCACCAGATGATGGATTGAAAA
Found at i:138465 original size:113 final size:112
Alignment explanation
Indices: 137473--138460 Score: 1273
Period size: 113 Copynumber: 8.9 Consensus size: 112
137463 GATATCAAAC
** *
137473 AAGGTTGAACAAGCTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTC
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT-
* ** * * *
137538 ATGAACTTT-TTTGGCCATGTTGA-CCATCAAATGATGAATTTAAACAA
65 ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGA-TTCAACAA
* *
137585 AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * **
137650 TGAACTTTCTCTGGAAAAGAATGATCCACCAAATGATGGATTC-AGGA
66 TGAACTTTCTCTGGAAATG-ATGATCCATCAAATGATGGATTCAACAA
137697 AAGGTTGAAC-AA--CTTCTCATTATGAA---CTTCTTCCTTCTTC-GATGAGTTC-TCTC-TTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* ***
137753 TGAACTTTCTCTGGAAA-GATGATCCACCAAATGATGGATTCAGGTA
66 TGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAACAA
*
137799 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA-ATGAGTTC-T-TCATCA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * **
137861 TGAACTTTCTCTGGAAAAGATGATTCA-CCAATGATGGATTCAGGTAA
66 TGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCA-ACAA
137908 AAGGTTTGAACAAATTCTTCTCATTA-GAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAGG-TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * **
137972 ATGAACCTTCTCTGGTAATGATGATCCACCAAATGATGGATTCAGGTAA
65 ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCA-ACAA
138021 AAGGTTGAACAAA-T-TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT-TCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * * * *
138083 TGAACCTTCTCTGGCAATGATAATCCATTAGATGATGGATTGAA-AA
66 TGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAACAA
*
138129 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * * *
138194 TGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAACAA
66 TGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTC-AACAA
* * *
138242 AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * * *
138307 TGAACCTTCTCTGGCAATGATAATCCATCAGATGATGGATTTGAACAA
66 TGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGA-TTCAACAA
*
138355 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* *
138420 TGAACTTTCTCTGGAAATGCTGATCCATCGAATGATGGATT
66 TGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATT
138461 TGAACTTTGC
Statistics
Matches: 791, Mismatches: 59, Indels: 52
0.88 0.07 0.06
Matches are distributed among these distances:
101 23 0.03
102 13 0.02
103 22 0.03
104 4 0.01
105 23 0.03
106 14 0.02
107 2 0.00
108 71 0.09
109 50 0.06
110 122 0.15
111 87 0.11
112 119 0.15
113 226 0.29
114 15 0.02
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (112 bp):
AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAACAA
Found at i:138888 original size:22 final size:22
Alignment explanation
Indices: 138863--138917 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
138853 GATAAAGCTT
*
138863 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
138885 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
138907 TCATCTTTGAA
1 TCATCTTTGAA
138918 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:141618 original size:82 final size:82
Alignment explanation
Indices: 141480--141659 Score: 283
Period size: 82 Copynumber: 2.2 Consensus size: 82
141470 CTTATTTCTA
* *
141480 CTATGAGCAAATTCATCTTCCAATTCAATGATTGGTTCTGTCCAACCAGATTAGATAACTCAAAG
1 CTATGAGCAAATTCATCTTCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAG
141545 AACACTTCCAGAAGATG
66 AACACTTCCAGAAGATG
* *
141562 CTATGAACAAATTCATCTTCTAAATTCAATGATT-GTTTTG-CCAAACCAGATCAGATAACTCAA
1 CTATGAGCAAATTCATCTTC-AAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAA
141625 AGAACACTTCCAGAAGATG
64 AGAACACTTCCAGAAGATG
*
141644 CTATGAGCACATTCAT
1 CTATGAGCAAATTCAT
141660 TTGTTCCATT
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
81 2 0.02
82 76 0.84
83 12 0.13
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (82 bp):
CTATGAGCAAATTCATCTTCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATG
Found at i:143321 original size:32 final size:32
Alignment explanation
Indices: 143280--143341 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
143270 GAAGAAATGA
*
143280 TTGTTATGCTCATCTTGTAGAGATACTTCTCG
1 TTGTTATGCTCATCTGGTAGAGATACTTCTCG
143312 TTGTTATGCTCATCTGGTAGAGATACTTCT
1 TTGTTATGCTCATCTGGTAGAGATACTTCT
143342 TGTGTCTGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.44
Consensus pattern (32 bp):
TTGTTATGCTCATCTGGTAGAGATACTTCTCG
Found at i:147197 original size:14 final size:14
Alignment explanation
Indices: 147163--147215 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
147153 TTGTGCAATA
* *
147163 CAAATGCAAAGATG
1 CAAATGTAAAAATG
* *
147177 CCAAATGTAGATATG
1 -CAAATGTAAAAATG
147192 CAAATGTAAAAATG
1 CAAATGTAAAAATG
*
147206 TAAATGTAAA
1 CAAATGTAAA
147216 TTATTTAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 21 0.66
15 11 0.34
ACGTcount: A:0.51, C:0.09, G:0.17, T:0.23
Consensus pattern (14 bp):
CAAATGTAAAAATG
Found at i:150226 original size:13 final size:13
Alignment explanation
Indices: 150208--150236 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
150198 CCACCGTACT
150208 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
150221 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
150234 CCG
1 CCG
150237 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:150939 original size:3 final size:3
Alignment explanation
Indices: 150931--151104 Score: 237
Period size: 3 Copynumber: 58.7 Consensus size: 3
150921 TTATTTATTA
*
150931 AAT AAT AAT AAT -AT AAT AAT AAT -AT ATAT ATT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
* **
150975 AAT ACT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT GCT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
151022 AAT AAT AAT ACT AAT AAT AAT AAT ATT AAT AAT AAT AAT AAT ATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
151070 AAT GAT AAT AAT AAT ATT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
151105 AATGGATAAA
Statistics
Matches: 149, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
2 6 0.04
3 140 0.94
4 3 0.02
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:151674 original size:2 final size:2
Alignment explanation
Indices: 151667--151705 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
151657 CCTAACCCAT
151667 TA TA TA TA TA 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 TA TA TA TA TA T
151706 CACCCATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:155386 original size:23 final size:23
Alignment explanation
Indices: 155342--155386 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
155332 GTATTCATGC
*
155342 ATTAAATATAAATTTATATAATG
1 ATTAAATATAAATTAATATAATG
*
155365 ATTAAA-ATAATATTAATCTAAT
1 ATTAAATATAA-ATTAATATAAT
155387 TCAGAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
ATTAAATATAAATTAATATAATG
Found at i:169446 original size:31 final size:31
Alignment explanation
Indices: 169411--169470 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
169401 TAATGAATTG
169411 ATCACTAATATTA-TCATTTTATAATAAATCA
1 ATCACTAATATTATTCA-TTTATAATAAATCA
* *
169442 ATCACTAATTTTATTGATTTATAATAAAT
1 ATCACTAATATTATTCATTTATAATAAAT
169471 TGATCATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (31 bp):
ATCACTAATATTATTCATTTATAATAAATCA
Found at i:169630 original size:6 final size:6
Alignment explanation
Indices: 169619--169647 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
169609 TTTCTCTCAA
169619 TTTCTC TTTCTC TTTCTC TTTCTC TTTCT
1 TTTCTC TTTCTC TTTCTC TTTCTC TTTCT
169648 AATAAAGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTCTC
Found at i:171058 original size:10 final size:10
Alignment explanation
Indices: 171043--171085 Score: 68
Period size: 10 Copynumber: 4.1 Consensus size: 10
171033 TCCCTACATT
171043 AGGAGAAAGA
1 AGGAGAAAGA
171053 AGGAGAAAGA
1 AGGAGAAAGA
171063 AGGAGAAAGA
1 AGGAGAAAGA
171073 GAGAGAGAAAGA
1 -AG-GAGAAAGA
171085 A
1 A
171086 TATGTAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 20 0.65
11 3 0.10
12 8 0.26
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (10 bp):
AGGAGAAAGA
Found at i:176764 original size:24 final size:24
Alignment explanation
Indices: 176737--176786 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
176727 AGGTTACTCA
*
176737 AATTTGTATTAGTTTTTGAATTGT
1 AATTTGTATTACTTTTTGAATTGT
*
176761 AATTTGTATTACTTTTTGAGTTGT
1 AATTTGTATTACTTTTTGAATTGT
176785 AA
1 AA
176787 CAAAACATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.26, C:0.02, G:0.16, T:0.56
Consensus pattern (24 bp):
AATTTGTATTACTTTTTGAATTGT
Found at i:178931 original size:23 final size:23
Alignment explanation
Indices: 178882--178937 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
178872 TGTTCGTTCG
* * * *
178882 TTTAACGTTCGTGAACGTATTCG
1 TTTAACGTTCATGAACATACTCA
*
178905 TTTAACGTTCATGAATATACTCA
1 TTTAACGTTCATGAACATACTCA
*
178928 TTTAATGTTC
1 TTTAACGTTC
178938 GTTTAATGTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (23 bp):
TTTAACGTTCATGAACATACTCA
Found at i:182290 original size:29 final size:29
Alignment explanation
Indices: 182258--182318 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
182248 TTATTACAAC
* * * *
182258 GATATATTATATACTTAAAATGGTTGAGT
1 GATAAATTATATACTAAAAATGATTGAAT
* *
182287 GATAAATTCTATGCTAAAAATGATTGAAT
1 GATAAATTATATACTAAAAATGATTGAAT
182316 GAT
1 GAT
182319 GGATGAGAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (29 bp):
GATAAATTATATACTAAAAATGATTGAAT
Found at i:183230 original size:26 final size:26
Alignment explanation
Indices: 183171--183222 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
183161 ATTTAGATCT
183171 AAACCCTAAACCCCAAATTATACCCC
1 AAACCCTAAACCCCAAATTATACCCC
*
183197 AAACCCTAAATCCCAAATTATACCCC
1 AAACCCTAAACCCCAAATTATACCCC
183223 CTACCCTACC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.40, G:0.00, T:0.17
Consensus pattern (26 bp):
AAACCCTAAACCCCAAATTATACCCC
Found at i:190077 original size:2 final size:2
Alignment explanation
Indices: 190070--190095 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
190060 AACTTATTAA
190070 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
190096 ACATATTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:190220 original size:2 final size:2
Alignment explanation
Indices: 190213--190239 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
190203 ATAATTGACT
190213 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 T
190240 TTCTAAGCAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:190441 original size:21 final size:21
Alignment explanation
Indices: 190399--190441 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
190389 GTATCCGCAC
* *
190399 TCTTGTATAGGGTATTCATTA
1 TCTTGTAGAGGGTATGCATTA
* *
190420 TCTTGTAGATGGTATGCCTTA
1 TCTTGTAGAGGGTATGCATTA
190441 T
1 T
190442 TTAGATAATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.47
Consensus pattern (21 bp):
TCTTGTAGAGGGTATGCATTA
Found at i:197655 original size:15 final size:15
Alignment explanation
Indices: 197635--197668 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
197625 ATTTTGATCG
197635 AAAATTAAAATGCTT
1 AAAATTAAAATGCTT
* *
197650 AAAATTAAAGTGTTT
1 AAAATTAAAATGCTT
197665 AAAA
1 AAAA
197669 AAATAGAGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.09, T:0.32
Consensus pattern (15 bp):
AAAATTAAAATGCTT
Found at i:206808 original size:3 final size:3
Alignment explanation
Indices: 206787--206854 Score: 61
Period size: 3 Copynumber: 22.3 Consensus size: 3
206777 ATGTAAAAAT
* *
206787 ATA ATA TTA ATA A-A ATA ATA AT- ATA A-A TATA AAA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
206830 ATAA ATA TATAA ATA ATA ATA ATA A
1 AT-A ATA -AT-A ATA ATA ATA ATA A
206855 AAAAGACCCG
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
2 5 0.09
3 40 0.74
4 8 0.15
5 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:206835 original size:21 final size:21
Alignment explanation
Indices: 206798--206855 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
206788 TAATATTAAT
206798 AAAATAATAAT-ATAAATATA
1 AAAATAATAATAATAAATATA
206818 AAAATAATAATAATAAATATA
1 AAAATAATAATAATAAATATA
*
206839 TAAATAATAATAATAAA
1 AAAATAATAATAATAAA
206856 AAAGACCCGG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 11 0.31
21 25 0.69
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAATAATAATAATAAATATA
Found at i:207189 original size:43 final size:44
Alignment explanation
Indices: 207124--207369 Score: 174
Period size: 43 Copynumber: 5.7 Consensus size: 44
207114 GTTCTTGGCC
*
207124 ATCTCAAGGTGATAACACGGTTCCTACGTGATGAGGACTACTGGTT
1 ATCT-AAGG-GATGACACGGTTCCTACGTGATGAGGACTACTGGTT
* *
207170 ATCTAAGGG-TGACCCGGTTCCTACGTGATGAGGA-AATCTGG--
1 ATCTAAGGGATGACACGGTTCCTACGTGATGAGGACTA-CTGGTT
* * * * * * **
207211 -TC-AGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCC
1 ATCTAAGGGATGACACGGTTCCTACGTGATGAGGACTACTGGTT
* **
207253 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTT
1 ATCT-AAGG-GATGACACGGTTCCTACGTGATGAGGACTACTGGTT
* * * *
207299 ATCT-ATGGTTGACACGGCTCCTACGTGATGAGGA-GATCTGG--
1 ATCTAAGGGATGACACGGTTCCTACGTGATGAGGACTA-CTGGTT
* *
207340 -TCT-GGGGATGACACGGTTCCTACATGATGA
1 ATCTAAGGGATGACACGGTTCCTACGTGATGA
207370 AGACGGCTGG
Statistics
Matches: 160, Mismatches: 30, Indels: 26
0.74 0.14 0.12
Matches are distributed among these distances:
39 4 0.03
40 52 0.32
42 2 0.01
43 57 0.36
44 3 0.02
45 7 0.04
46 35 0.22
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (44 bp):
ATCTAAGGGATGACACGGTTCCTACGTGATGAGGACTACTGGTT
Found at i:207303 original size:46 final size:45
Alignment explanation
Indices: 207124--207379 Score: 186
Period size: 40 Copynumber: 6.0 Consensus size: 45
207114 GTTCTTGGCC
*
207124 ATCTCAAGGTGATAACACGGTTCCTACGTGATGAGGAC-TACTGGTT
1 ATCT-AAGGTGATGACACGGTTCCTACGTGATGAGGACGT-CTGGTT
* **
207170 ATCTAAGG-G-TGACCCGGTTCCTACGTGATGAGGAAATCTGG--
1 ATCTAAGGTGATGACACGGTTCCTACGTGATGAGGACGTCTGGTT
* * * * **
207211 -TC--AGGGGATGACACGGCTCATACGTGATGAAGA-GTTCTGGCC
1 ATCTAAGGTGATGACACGGTTCCTACGTGATGAGGACG-TCTGGTT
* *
207253 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTT
1 ATCT-AAGGTGATGACACGGTTCCTACGTGATGAGGACGTCTGGTT
* *
207299 ATCTATGGT--TGACACGGCTCCTACGTGATGAGGA-GATCTGG--
1 ATCTAAGGTGATGACACGGTTCCTACGTGATGAGGACG-TCTGGTT
* * * *
207340 -TCT--GGGGATGACACGGTTCCTACATGATGAAGACGGCTGG
1 ATCTAAGGTGATGACACGGTTCCTACGTGATGAGGACGTCTGG
207380 CCATCTTTAG
Statistics
Matches: 170, Mismatches: 25, Indels: 36
0.74 0.11 0.16
Matches are distributed among these distances:
38 5 0.03
39 1 0.01
40 57 0.34
41 1 0.01
42 1 0.01
43 56 0.33
44 2 0.01
45 8 0.05
46 38 0.22
47 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (45 bp):
ATCTAAGGTGATGACACGGTTCCTACGTGATGAGGACGTCTGGTT
Found at i:207321 original size:129 final size:128
Alignment explanation
Indices: 207042--207385 Score: 474
Period size: 129 Copynumber: 2.7 Consensus size: 128
207032 TTCGGGTCGA
* * * * **
207042 CTAAGGGTGACTCGGTTCCTACGTGATGAAGACATCTGGTCGAAGGATGACACTACTCATACATG
1 CTAAGGGTGACACGGTTCCTACGTGATGAGGAAATCTGGTCG-GGGATGACACGGCTCATACATG
* *
207107 ATGAAGAGTTCTTGGCCATCTCAAGGTGATAACACGGTTCCTACGTGATGAGGACTACTGGTTAT
65 ATGAAGAGTTC-TGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTAT
* *
207172 CTAAGGGTGACCCGGTTCCTACGTGATGAGGAAATCTGGTCAGGGGATGACACGGCTCATACGTG
1 CTAAGGGTGACACGGTTCCTACGTGATGAGGAAATCTGGTC-GGGGATGACACGGCTCATACATG
*
207237 ATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTAT
65 ATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTAT
* * * * * *
207301 CTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGTTCCTACATG
1 CTAAGGGTGACACGGTTCCTACGTGATGAGGAAATCTGGTC-GGGGATGACACGGCTCATACATG
*
207366 ATGAAGACG-GCTGGCCATCT
65 ATGAAGA-GTTCTGGCCATCT
207386 TTAGGAGTTA
Statistics
Matches: 192, Mismatches: 20, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
129 123 0.64
130 68 0.35
131 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (128 bp):
CTAAGGGTGACACGGTTCCTACGTGATGAGGAAATCTGGTCGGGGATGACACGGCTCATACATGA
TGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTAT
Found at i:207438 original size:28 final size:28
Alignment explanation
Indices: 207398--207494 Score: 83
Period size: 28 Copynumber: 3.4 Consensus size: 28
207388 AGGAGTTATG
* *
207398 GTTTCAAGAGAAACCA-AATTAAAGATTT
1 GTTTCAAAAGAAA-CAGAATCAAAGATTT
*
207426 GTTTCAAAAGAAACAGACTCAAAGATTT
1 GTTTCAAAAGAAACAGAATCAAAGATTT
*
207454 GTTTCAAGAA-AAACA-AGCTCAAAGATAATGT
1 GTTTCAA-AAGAAACAGA-ATCAAAGAT--T-T
207485 GTTTCAAAAG
1 GTTTCAAAAG
207495 CAACTGTCTC
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
27 3 0.05
28 43 0.73
29 2 0.03
30 3 0.05
31 8 0.14
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.26
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGAATCAAAGATTT
Found at i:207491 original size:31 final size:28
Alignment explanation
Indices: 207418--207494 Score: 95
Period size: 28 Copynumber: 2.6 Consensus size: 28
207408 AAACCAAATT
207418 AAAGATTTGTTTCAAAAGAAACAGACTC
1 AAAGATTTGTTTCAAAAGAAACAGACTC
207446 AAAGATTTGTTTCAAGAA-AAACA-AGCTC
1 AAAGATTTGTTTCAA-AAGAAACAGA-CTC
207474 AAAGATAATGTGTTTCAAAAG
1 AAAGAT--T-TGTTTCAAAAG
207495 CAACTGTCTC
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
27 1 0.02
28 29 0.67
29 2 0.05
30 3 0.07
31 8 0.19
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.26
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAGACTC
Found at i:207685 original size:66 final size:64
Alignment explanation
Indices: 207496--207685 Score: 159
Period size: 66 Copynumber: 2.9 Consensus size: 64
207486 TTTCAAAAGC
** * *
207496 AACTGTCTCGAAAGAGACAAAATTCATTTCAAATGAAAC-AACTCAAAAGATG-ACGTTTAAAGG
1 AACTGTCTC-AAAGAGACAAAATTCATTTCAAGGGAAACGATCTC-AAAGATGTATGTTTAAAGG
207559 G
64 G
* * * ** * * * * * * *
207560 AATTGTCTCAAGCGAGATAAAATTTGTTTTTAAGGGAAACGTTCTCAAATATCTGTGTTTCATGG
1 AACTGTCTCAA-AGAGACAAAA-TTCATTTCAAGGGAAACGATCTCAAAGATGTATGTTTAAAGG
207625 G
64 G
*
207626 AAACTGTCTCAAATGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGTTTGTTT
1 -AACTGTCTCAAA-GAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGTATGTTT
207686 TGTTTCAAGG
Statistics
Matches: 94, Mismatches: 26, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
63 2 0.02
64 16 0.17
65 17 0.18
66 41 0.44
67 18 0.19
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (64 bp):
AACTGTCTCAAAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGTATGTTTAAAGGG
Found at i:208507 original size:66 final size:66
Alignment explanation
Indices: 208430--208555 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 66
208420 AAACTGTCTC
* *
208430 AAGAGAGACAAAAATCAT-TTT-AAGAGAAACAGATTCAAAGATTTTTGTTTCAAAAGAAATTAT
1 AAGAGAGAC-AAAATCATGTTTCAA-AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTAT
208493 CTT
64 CTT
**
208496 AAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAA
1 AAGAGAGACAAAATCATGTTT-CAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAA
208556 CAATCTCAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
65 6 0.11
66 12 0.23
67 33 0.62
68 2 0.04
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.29
Consensus pattern (66 bp):
AAGAGAGACAAAATCATGTTTCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCT
T
Found at i:208543 original size:30 final size:30
Alignment explanation
Indices: 208509--208572 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
208499 AGAGACAAAA
*
208509 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
*
208539 TTTTGTTTCAAAAGAAACAATCTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
208569 TTTT
1 TTTT
208573 TTCACAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAAACTCAAAGAT
Found at i:208581 original size:30 final size:29
Alignment explanation
Indices: 208504--208581 Score: 97
Period size: 30 Copynumber: 2.7 Consensus size: 29
208494 TTAAGAGAGA
208504 CAAA-ATTTTGTTTCC-AAAGAAACAAACT
1 CAAAGATTTT-TTTCCAAAAGAAACAAACT
* *
208532 CAAAGATTTTTGTTTCAAAAGAAACAATCT
1 CAAAGATTTTT-TTCCAAAAGAAACAAACT
208562 CAAAGATTTTTTTCACAAAA
1 CAAAGATTTTTTTC-CAAAA
208582 TTGTCTCAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
28 5 0.12
29 10 0.23
30 28 0.65
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (29 bp):
CAAAGATTTTTTTCCAAAAGAAACAAACT
Found at i:208635 original size:52 final size:53
Alignment explanation
Indices: 208560--208663 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 53
208550 AAGAAACAAT
208560 CTCAAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
1 CTCAAAGA-TTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
*
208614 CTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
208664 AAATAAATAG
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 41 0.84
54 8 0.16
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (53 bp):
CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
Found at i:208742 original size:29 final size:28
Alignment explanation
Indices: 208659--208782 Score: 153
Period size: 29 Copynumber: 4.4 Consensus size: 28
208649 CAAAACTTTG
* * *
208659 TTTCAAAATAAATAGACTCAAAGATTTT
1 TTTCAAAAGAAACAAACTCAAAGATTTT
208687 TTTCAAAAGAAAC-AACTCAAAGATTTT
1 TTTCAAAAGAAACAAACTCAAAGATTTT
* *
208714 TATTCAAAAGTAACAAACTCCAAGATTTT
1 T-TTCAAAAGAAACAAACTCAAAGATTTT
*
208743 TGTTCAAAAGGAACAAACTCAAAGA-TTT
1 T-TTCAAAAGAAACAAACTCAAAGATTTT
*
208771 TTTCAAGAGAAA
1 TTTCAAAAGAAA
208783 TTGTCTCAAG
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
27 23 0.27
28 26 0.31
29 35 0.42
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.30
Consensus pattern (28 bp):
TTTCAAAAGAAACAAACTCAAAGATTTT
Found at i:209798 original size:4 final size:4
Alignment explanation
Indices: 209778--209858 Score: 78
Period size: 4 Copynumber: 20.2 Consensus size: 4
209768 ATATAACATA
* *
209778 TATG TATG TGT- TGATG TATG TATG TATG CATG TATG TATG TATG TATG
1 TATG TATG TATG T-ATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
209826 TAT- TGATA TATG TTTG TAT- TGATG TATG TATG T
1 TATG T-ATG TATG TATG TATG T-ATG TATG TATG T
209859 TGATTTGTGA
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
3 3 0.05
4 58 0.91
5 3 0.05
ACGTcount: A:0.23, C:0.01, G:0.25, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:213460 original size:30 final size:31
Alignment explanation
Indices: 213402--213461 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
213392 ATGAAAAATG
*
213402 ACACAAACAAATGAGAAAAAATGAGTTAGTA
1 ACACAAACAAATGAGAAAAAACGAGTTAGTA
*
213433 ACACAAACAAAAT-AG-AGAAACGAGTTAGT
1 ACACAAAC-AAATGAGAAAAAACGAGTTAGT
213462 GCAAGCAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 12 0.46
31 10 0.38
32 4 0.15
ACGTcount: A:0.57, C:0.12, G:0.17, T:0.15
Consensus pattern (31 bp):
ACACAAACAAATGAGAAAAAACGAGTTAGTA
Found at i:217133 original size:17 final size:17
Alignment explanation
Indices: 217108--217161 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
217098 AAAATATGTA
217108 AAAAT-ATAATATTAAT
1 AAAATAATAATATTAAT
*
217124 AAAATAATAATATAAAT
1 AAAATAATAATATTAAT
*
217141 ATAAA-AATAATAATAAT
1 A-AAATAATAATATTAAT
217158 AAAA
1 AAAA
217162 AAGACCCGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 8 0.24
17 22 0.67
18 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAATAATAATATTAAT
Found at i:226177 original size:14 final size:16
Alignment explanation
Indices: 226146--226178 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
226136 TTATCATTGT
226146 TCTCACAATCTCCATA
1 TCTCACAATCTCCATA
226162 TCTC-CAATCT-CATA
1 TCTCACAATCTCCATA
226176 TCT
1 TCT
226179 ACCTTAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 6 0.35
16 4 0.24
ACGTcount: A:0.27, C:0.36, G:0.00, T:0.36
Consensus pattern (16 bp):
TCTCACAATCTCCATA
Found at i:233318 original size:31 final size:30
Alignment explanation
Indices: 233283--233342 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
233273 CAAACAAGTT
*
233283 TTGGCAATCGATCACTTCAAAAAAAAAAAAG
1 TTGGCAATCGAT-ACTTAAAAAAAAAAAAAG
*
233314 TTGGCAATCGATATTTAAAAAAAAAAAAA
1 TTGGCAATCGATACTTAAAAAAAAAAAAA
233343 AAGTTTTGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 15 0.56
31 12 0.44
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.22
Consensus pattern (30 bp):
TTGGCAATCGATACTTAAAAAAAAAAAAAG
Found at i:233343 original size:31 final size:33
Alignment explanation
Indices: 233282--233358 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 33
233272 ACAAACAAGT
*
233282 TTTGGCAATCGATCACTT-CAAAAAAAAAAAAG
1 TTTGGCAATCGATCACTTAAAAAAAAAAAAAAG
*
233314 -TTGGCAATCGAT-ATTTAAAAAAAAAAAAAAAG
1 TTTGGCAATCGATCACTT-AAAAAAAAAAAAAAG
233346 TTTTGGCAATCGA
1 -TTTGGCAATCGA
233359 AATAGAGAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
30 3 0.08
31 12 0.31
32 13 0.33
34 11 0.28
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (33 bp):
TTTGGCAATCGATCACTTAAAAAAAAAAAAAAG
Found at i:236032 original size:16 final size:16
Alignment explanation
Indices: 236011--236041 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
236001 TAATAAATAA
236011 ACGAACATAAACGAAT
1 ACGAACATAAACGAAT
236027 ACGAACATAAACGAA
1 ACGAACATAAACGAA
236042 CAATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.19, G:0.13, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAT
Found at i:236133 original size:16 final size:16
Alignment explanation
Indices: 236108--236146 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
236098 CATTTAATAA
*
236108 ATAAAGGAACACGAAC
1 ATAAACGAACACGAAC
236124 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
236140 ATAAACG
1 ATAAACG
236147 TTGGAGTCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.56, C:0.21, G:0.15, T:0.08
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:237074 original size:14 final size:14
Alignment explanation
Indices: 237052--237100 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 14
237042 GATTGGGTTA
237052 AACATAAATGAATG
1 AACATAAATGAATG
*
237066 AATATAAATGAATG
1 AACATAAATGAATG
* *
237080 AACATAAACGAACG
1 AACATAAATGAATG
237094 AACATAA
1 AACATAA
237101 CAGAACGTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.59, C:0.10, G:0.12, T:0.18
Consensus pattern (14 bp):
AACATAAATGAATG
Found at i:238538 original size:210 final size:210
Alignment explanation
Indices: 238322--238804 Score: 598
Period size: 210 Copynumber: 2.3 Consensus size: 210
238312 GTGGGGAGAC
** * *
238322 AGAGTTCATAGTAATGTCACATACCAAGGATCTGACAATGGCTCAAGTGAATCTTCTGGTTCTCA
1 AGAGTTCATAGTAATGTCACATATGAAGGATATGACAATGGATCAAGTGAATCTTCTGGTTCTCA
* * * * *
238387 AATAAATGATTCGTATGG-TAGTTCTAATAAGAGTAG-AAGTA-AGGGATTTTGTGATTTGGGTT
66 AATAAAGGATTCG-ACGGATAGTTCCAATAAGAGT-GCAAGTATAGGG-TTTGGGGATTTGGGTT
* * * * ** * *
238449 CTGAAAATTTGGAGAAATCTAATGATATTAATGTTTTAGGTTCCTCAATTTCTCAGCGTTCGAGA
128 CGGAAAATTTGGAGAAATCTAATGAGAGTAATGTTGTAGGTTCCTCAATCCCTCAACATTCGAGA
*
238514 TCTGGAAGAACG-AGAGTG
193 TCTGGAAGAACGAAGA-AG
* * *
238532 AGAGTTCATAGTAATGTCACATATGAAGGATAT-AGCAATGGATCAAGAGAATCTTCAGGTTCAC
1 AGAGTTCATAGTAATGTCACATATGAAGGATATGA-CAATGGATCAAGTGAATCTTCTGGTTCTC
* * *
238596 AAATGAAGGATTCGCCGGATAGTTCCAATAAGAGTGCATGTATAGGGTTTGGGGATTTGGGTTCG
65 AAATAAAGGATTCGACGGATAGTTCCAATAAGAGTGCAAGTATAGGGTTTGGGGATTTGGGTTCG
* * * *
238661 GAAAATTTGGAGAAGTTTAATGAGAGTGATGTTGTAGGTTCCTCAATCCCTGAACATTCGAGATC
130 GAAAATTTGGAGAAATCTAATGAGAGTAATGTTGTAGGTTCCTCAATCCCTCAACATTCGAGATC
*
238726 TGGAAGAATGAAGAAG
195 TGGAAGAACGAAGAAG
* * *
238742 AGAGTTCATCGTAATGTCACATATGAAGGATTTGGCAATGGATCAAGTGAATCTTCTGGTTCT
1 AGAGTTCATAGTAATGTCACATATGAAGGATATGACAATGGATCAAGTGAATCTTCTGGTTCT
238805 AATAAGAGTA
Statistics
Matches: 232, Mismatches: 35, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
209 4 0.02
210 221 0.95
211 7 0.03
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (210 bp):
AGAGTTCATAGTAATGTCACATATGAAGGATATGACAATGGATCAAGTGAATCTTCTGGTTCTCA
AATAAAGGATTCGACGGATAGTTCCAATAAGAGTGCAAGTATAGGGTTTGGGGATTTGGGTTCGG
AAAATTTGGAGAAATCTAATGAGAGTAATGTTGTAGGTTCCTCAATCCCTCAACATTCGAGATCT
GGAAGAACGAAGAAG
Found at i:247504 original size:23 final size:24
Alignment explanation
Indices: 247474--247527 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
247464 TTAGTGAGAC
247474 AATA-ATATTAAAG-A-CGAGAATA
1 AATATATATTAAAGTATCGA-AATA
247496 AATATATA-TAAAGTATCGAAATA
1 AATATATATTAAAGTATCGAAATA
*
247519 TATATATAT
1 AATATATAT
247528 AAACATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 9 0.33
23 15 0.56
24 3 0.11
ACGTcount: A:0.56, C:0.04, G:0.09, T:0.31
Consensus pattern (24 bp):
AATATATATTAAAGTATCGAAATA
Found at i:254229 original size:60 final size:59
Alignment explanation
Indices: 254119--254301 Score: 174
Period size: 60 Copynumber: 3.1 Consensus size: 59
254109 GTATATATGA
** *
254119 ATAGTTTGGGG-TGAAATTGAAATATTCAAAAAGTTCAGAGACTAATTTAGAATGAAGGTC
1 ATAGTTTGGGGATGAAATTGAAATATTCAAAATTTTAAG-GAC-AATTTAGAATGAAGGTC
* * *
254179 ATAGTTTGGGGATGAAATTGAAATGTTCAAAATTTTGAGGATCAATTTAGAGTGATA-GTC
1 ATAGTTTGGGGATGAAATTGAAATATTCAAAATTTTAAGGA-CAATTTAGAATGA-AGGTC
* * * * * * *
254239 ATAGTTTAGGGATAAAATTTAAACACTT-AAAATTTTAAAGACCAATTTAAAATGAGGGTC
1 ATAGTTTGGGGATGAAATTGAAATA-TTCAAAATTTTAAGGA-CAATTTAGAATGAAGGTC
254299 ATA
1 ATA
254302 TATTGAGGAC
Statistics
Matches: 102, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
60 75 0.74
61 27 0.26
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (59 bp):
ATAGTTTGGGGATGAAATTGAAATATTCAAAATTTTAAGGACAATTTAGAATGAAGGTC
Found at i:257966 original size:2 final size:2
Alignment explanation
Indices: 257959--257985 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
257949 TTTTTGTTAT
257959 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 T
257986 TTAAAAAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:260987 original size:29 final size:29
Alignment explanation
Indices: 260952--261033 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
260942 AAACTAAATT
*
260952 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
260981 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
261010 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
261034 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:265619 original size:29 final size:29
Alignment explanation
Indices: 265584--265665 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
265574 AAACTAAATT
*
265584 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
265613 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
265642 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
265666 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:270967 original size:25 final size:26
Alignment explanation
Indices: 270939--270996 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
270929 AATAATAATT
270939 TAATGATTTTATA-CAAATAATTTAG
1 TAATGATTTTATATCAAATAATTTAG
** *
270964 TAATGA-TTTATATTTAATGATTTAG
1 TAATGATTTTATATCAAATAATTTAG
270989 TAATGATT
1 TAATGATT
270997 ACTAATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 6 0.21
25 21 0.75
26 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (26 bp):
TAATGATTTTATATCAAATAATTTAG
Found at i:271005 original size:25 final size:25
Alignment explanation
Indices: 270958--271005 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
270948 TATACAAATA
*
270958 ATTTAGTAATGATTTATATTTAATG
1 ATTTAGTAATGATTTATAATTAATG
270983 ATTTAGTAATGA-TTACTAATTAA
1 ATTTAGTAATGATTTA-TAATTAA
271006 AATCATGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (25 bp):
ATTTAGTAATGATTTATAATTAATG
Found at i:271062 original size:15 final size:14
Alignment explanation
Indices: 271038--271079 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
271028 ATTAATAATG
*
271038 ATTTACTAATTATT
1 ATTTAATAATTATT
271052 AATTTAATAATTATT
1 -ATTTAATAATTATT
*
271067 A-CTAATAATTATT
1 ATTTAATAATTATT
271080 TAGTAGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 11 0.44
14 1 0.04
15 13 0.52
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTTAATAATTATT
Found at i:273103 original size:23 final size:20
Alignment explanation
Indices: 273048--273099 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
273038 TCGAATATTA
* *
273048 TTACTATTATATTGAGTTTT
1 TTACTACTAAATTGAGTTTT
273068 TTACTACTAAATTGAGTTTT
1 TTACTACTAAATTGAGTTTT
273088 TTACTACTAAAT
1 TTACTACTAAAT
273100 AATTATTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.52
Consensus pattern (20 bp):
TTACTACTAAATTGAGTTTT
Found at i:273169 original size:26 final size:25
Alignment explanation
Indices: 273092--273177 Score: 79
Period size: 26 Copynumber: 3.4 Consensus size: 25
273082 AGTTTTTTAC
*
273092 TACTAAATAATTATTAGTA-ATAAT
1 TACTAAATCATTATTAGTATATAAT
* *
273116 TATTAAATCATTATTA-AATTAATAAT
1 TACTAAATCATTATTAGTA-T-ATAAT
* *
273142 TAGTAAATCATTATTAGTATCATTAT
1 TACTAAATCATTATTAGTAT-ATAAT
273168 TACT-AATCAT
1 TACTAAATCAT
273178 GATTTTAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
23 1 0.02
24 14 0.28
25 6 0.12
26 28 0.56
27 1 0.02
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.44
Consensus pattern (25 bp):
TACTAAATCATTATTAGTATATAAT
Found at i:273339 original size:13 final size:12
Alignment explanation
Indices: 273300--273352 Score: 58
Period size: 13 Copynumber: 4.6 Consensus size: 12
273290 TGATGAAATC
*
273300 ATTATTATTAA-
1 ATTATTACTAAT
273311 ATT-TTACTAA-
1 ATTATTACTAAT
273321 ATTATTACTAAT
1 ATTATTACTAAT
273333 CATTATTACTAAT
1 -ATTATTACTAAT
*
273346 ATAATTA
1 ATTATTA
273353 ACGTCATTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
10 9 0.24
11 10 0.27
12 6 0.16
13 12 0.32
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (12 bp):
ATTATTACTAAT
Found at i:277695 original size:61 final size:61
Alignment explanation
Indices: 277563--277695 Score: 162
Period size: 61 Copynumber: 2.2 Consensus size: 61
277553 GTTTTGAAAG
* * * *
277563 ATATGTTTTTACAATCTTAAAAATTAATAAATTCTATATATTCAGATATTTTTTATTAAAA
1 ATATGATTTTACAATCTTAAAAATTAATAAATTCTATATATTCAGAAATTTTTAAATAAAA
* * * *
277624 ATATGTTTTTACAATCTTAAAAATTAATAAATTTTATTATATTTA-AAATTTTATAAATATAA
1 ATATGATTTTACAATCTTAAAAATTAATAAATTCTA-TATATTCAGAAATTTT-TAAATAAAA
277686 ATAT-ATTTTA
1 ATATGATTTTA
277696 ATATAAAATT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
61 46 0.73
62 17 0.27
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (61 bp):
ATATGATTTTACAATCTTAAAAATTAATAAATTCTATATATTCAGAAATTTTTAAATAAAA
Found at i:278415 original size:21 final size:21
Alignment explanation
Indices: 278389--278432 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
278379 GGTAAAAAAA
* *
278389 TTATTTAAAATATTATTATTT
1 TTATTTAAAATATCAATATTT
278410 TTATTTAAAATATCAATATTT
1 TTATTTAAAATATCAATATTT
278431 TT
1 TT
278433 TAACATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTTAAAATATCAATATTT
Found at i:278488 original size:21 final size:21
Alignment explanation
Indices: 278458--278503 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
278448 AGTGTCCAAC
* *
278458 AATAATAAAATCGGTAGAAAA
1 AATAACAAAATCGATAGAAAA
*
278479 AATAACAAAATCGATAGAAAT
1 AATAACAAAATCGATAGAAAA
278500 AATA
1 AATA
278504 TTATTTCCGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.63, C:0.07, G:0.11, T:0.20
Consensus pattern (21 bp):
AATAACAAAATCGATAGAAAA
Found at i:279333 original size:16 final size:16
Alignment explanation
Indices: 279309--279347 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
279299 ATATATAATA
*
279309 TAATATAATATAATTT
1 TAATTTAATATAATTT
*
279325 TAATTTAATTTAATTT
1 TAATTTAATATAATTT
*
279341 TATTTTA
1 TAATTTA
279348 TTTATATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTAATATAATTT
Found at i:287260 original size:5 final size:5
Alignment explanation
Indices: 287250--287350 Score: 69
Period size: 5 Copynumber: 18.8 Consensus size: 5
287240 AACGGTTAAC
* *
287250 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
* * * *
287299 GGTCA GATC- GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG
287347 GGTC
1 GGTC
287351 AGACCGGTCA
Statistics
Matches: 77, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
4 3 0.04
5 58 0.75
7 16 0.21
ACGTcount: A:0.10, C:0.23, G:0.49, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:287275 original size:22 final size:22
Alignment explanation
Indices: 287247--287350 Score: 183
Period size: 22 Copynumber: 4.8 Consensus size: 22
287237 GTTAACGGTT
287247 AACGGTCGGGTCGGGTCGGGTC
1 AACGGTCGGGTCGGGTCGGGTC
287269 AACGGTCGGGTCGGGTCGGGTC
1 AACGGTCGGGTCGGGTCGGGTC
* *
287291 AACGGTCGGGTCAGATC-GGTC
1 AACGGTCGGGTCGGGTCGGGTC
287312 AACGGTCGGGTCGGGTCGGGTC
1 AACGGTCGGGTCGGGTCGGGTC
287334 AACGGTCGGGTCGGGTC
1 AACGGTCGGGTCGGGTC
287351 AGACCGGTCA
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
21 19 0.25
22 58 0.75
ACGTcount: A:0.12, C:0.23, G:0.47, T:0.18
Consensus pattern (22 bp):
AACGGTCGGGTCGGGTCGGGTC
Found at i:287277 original size:17 final size:17
Alignment explanation
Indices: 287277--287351 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 17
287267 TCAACGGTCG
287277 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
287294 GGTCGGGTCAGATCGGTCAACGGTC
1 GGTCGGGTC-G---GGTCAA----C
287319 GGGTCGGGTCGGGTCAAC
1 -GGTCGGGTCGGGTCAAC
287337 GGTCGGGTCGGGTCA
1 GGTCGGGTCGGGTCA
287352 GACCGGTCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 18
0.73 0.00 0.27
Matches are distributed among these distances:
17 24 0.49
18 2 0.04
21 6 0.12
22 6 0.12
25 2 0.04
26 9 0.18
ACGTcount: A:0.12, C:0.23, G:0.47, T:0.19
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAC
Found at i:287312 original size:43 final size:44
Alignment explanation
Indices: 287247--287345 Score: 173
Period size: 43 Copynumber: 2.3 Consensus size: 44
287237 GTTAACGGTT
* *
287247 AACGGTCGGGTCGGGTCGGGTCAACGGTCGGGTCGGGTCGGGTC
1 AACGGTCGGGTCAGATCGGGTCAACGGTCGGGTCGGGTCGGGTC
287291 AACGGTCGGGTCAGATC-GGTCAACGGTCGGGTCGGGTCGGGTC
1 AACGGTCGGGTCAGATCGGGTCAACGGTCGGGTCGGGTCGGGTC
287334 AACGGTCGGGTC
1 AACGGTCGGGTC
287346 GGGTCAGACC
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
43 38 0.72
44 15 0.28
ACGTcount: A:0.12, C:0.23, G:0.46, T:0.18
Consensus pattern (44 bp):
AACGGTCGGGTCAGATCGGGTCAACGGTCGGGTCGGGTCGGGTC
Found at i:287375 original size:19 final size:19
Alignment explanation
Indices: 287353--287407 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
287343 GTCGGGTCAG
*
287353 ACCGGTCAAACCGGTTCGA
1 ACCGGTCAAACCGGTTCAA
*
287372 ACCGGTTGAAACCGG-TCAA
1 ACCGG-TCAAACCGGTTCAA
287391 ACCGGTCAGAACCGGTT
1 ACCGGTCA-AACCGGTT
287408 TCCAGCAGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 2 0.07
19 19 0.63
20 9 0.30
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCAA
Found at i:294009 original size:33 final size:33
Alignment explanation
Indices: 293947--294037 Score: 136
Period size: 33 Copynumber: 2.9 Consensus size: 33
293937 GTAGCCAGAA
*
293947 AATCAAATAAAACAT--C--AGTGTCATTGTAT
1 AATCAAATAAAACATCACTTAGTTTCATTGTAT
293976 AATCAAATAAAACATCACTTAGTTTCATTGTAT
1 AATCAAATAAAACATCACTTAGTTTCATTGTAT
*
294009 AATCAAATAAAATATCACTTAGTTTCATT
1 AATCAAATAAAACATCACTTAGTTTCATT
294038 CTTCATTCCT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
29 15 0.27
31 1 0.02
33 40 0.71
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (33 bp):
AATCAAATAAAACATCACTTAGTTTCATTGTAT
Found at i:297624 original size:22 final size:22
Alignment explanation
Indices: 297599--297640 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
297589 TTTTTTGGGG
297599 GTTTAA-TTCCTTTGTGTTTTCA
1 GTTTAACTT-CTTTGTGTTTTCA
*
297621 GTTTAACTTCTTTGTTTTTT
1 GTTTAACTTCTTTGTGTTTT
297641 ACTAGTTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.64
Consensus pattern (22 bp):
GTTTAACTTCTTTGTGTTTTCA
Found at i:299771 original size:16 final size:16
Alignment explanation
Indices: 299744--299787 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
299734 TAATAATTTA
299744 TTTTAT-TATTTTTGT
1 TTTTATATATTTTTGT
299759 TTTTATATATTTTTGT
1 TTTTATATATTTTTGT
*
299775 TTTTATAAATTTT
1 TTTTATATATTTT
299788 AACTTCACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
15 6 0.22
16 21 0.78
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (16 bp):
TTTTATATATTTTTGT
Found at i:310633 original size:27 final size:27
Alignment explanation
Indices: 310603--310661 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
310593 CCTAAACCCA
*
310603 ACCCGAATATCACACTTAAAAAACTCG
1 ACCCGAATATCAAACTTAAAAAACTCG
310630 ACCCGAATATCAAACTTAAAAAACTCG
1 ACCCGAATATCAAACTTAAAAAACTCG
310657 ACCCG
1 ACCCG
310662 GCCCGACCCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.44, C:0.31, G:0.08, T:0.17
Consensus pattern (27 bp):
ACCCGAATATCAAACTTAAAAAACTCG
Done.