Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001582.1 Hibiscus syriacus cultivar Beakdansim tig00003151_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: 1162828
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:448439 original size:4 final size:4
Alignment explanation
Indices: 448401--448493 Score: 70
Period size: 4 Copynumber: 23.0 Consensus size: 4
448391 GGGAAAATGT
* * *
448401 TAAA TAAA GT-AA TAAAA TAAA AAAA GAAG TAAA TAAA T-AA -AAA TAAA
1 TAAA TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
448448 TAAA TAAA TAAA TAAA -AATA TAAA TAAA -AATA TAAAA TAAAA TAAA
1 TAAA TAAA TAAA TAAA TAA-A TAAA TAAA TAA-A T-AAA T-AAA TAAA
448494 AACATACTAA
Statistics
Matches: 74, Mismatches: 5, Indels: 20
0.75 0.05 0.20
Matches are distributed among these distances:
3 9 0.12
4 50 0.68
5 13 0.18
6 2 0.03
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (4 bp):
TAAA
Found at i:448490 original size:24 final size:23
Alignment explanation
Indices: 448401--448491 Score: 89
Period size: 24 Copynumber: 3.8 Consensus size: 23
448391 GGGAAAATGT
*
448401 TAAATAAAGT-AATAAAATAAAAA
1 TAAATAAA-TAAATAAAATATAAA
*
448424 AAGAAGTAAATAAATAAAA-ATAAA
1 TA-AA-TAAATAAATAAAATATAAA
448448 TAAATAAATAAATAAAAATATAAA
1 TAAATAAATAAAT-AAAATATAAA
448472 TAAA-AATATAAAATAAAATA
1 TAAATAA-AT-AAATAAAATA
448492 AAAACATACT
Statistics
Matches: 58, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
22 9 0.16
23 9 0.16
24 25 0.43
25 15 0.26
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (23 bp):
TAAATAAATAAATAAAATATAAA
Found at i:448517 original size:23 final size:23
Alignment explanation
Indices: 448473--448535 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
448463 AAATATAAAT
*
448473 AAAAATA-TAAAA-T-AAAATAA
1 AAAAATACTAAAATTAAAAAGAA
*
448493 AAACATACTAAAATTAAAAAGAA
1 AAAAATACTAAAATTAAAAAGAA
*
448516 AAAAATGCTAAAATTAAAAA
1 AAAAATACTAAAATTAAAAA
448536 ATGAATAACT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 6 0.17
21 5 0.14
22 1 0.03
23 24 0.67
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (23 bp):
AAAAATACTAAAATTAAAAAGAA
Found at i:449657 original size:37 final size:38
Alignment explanation
Indices: 449607--449785 Score: 237
Period size: 37 Copynumber: 4.8 Consensus size: 38
449597 ACCTGGACCG
449607 AAAATGATTTC-AAAACTATATATTATATAAGTTTTTC
1 AAAATGATTTCAAAAACTATATATTATATAAGTTTTTC
*
449644 AAAATGATTTC-AAAACTATATATTATATAAG-TTTTG
1 AAAATGATTTCAAAAACTATATATTATATAAGTTTTTC
* *
449680 AAAATGTTTTCAAAAACTATATATTATATATATTTTTTC
1 AAAATGATTTCAAAAACTATATATTATATA-AGTTTTTC
449719 AAAAT-ATTTTCAAAAACTATATATTATAT-A-TATTTTC
1 AAAATGA-TTTCAAAAACTATATATTATATAAGT-TTTTC
*
449756 AAAATG-TCTTCAAAAACTATATAATATATA
1 AAAATGAT-TTCAAAAACTATATATTATATA
449786 CATTTTAAAA
Statistics
Matches: 128, Mismatches: 6, Indels: 15
0.86 0.04 0.10
Matches are distributed among these distances:
36 16 0.12
37 80 0.62
38 1 0.01
39 31 0.24
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (38 bp):
AAAATGATTTCAAAAACTATATATTATATAAGTTTTTC
Found at i:449747 original size:76 final size:74
Alignment explanation
Indices: 449606--449791 Score: 261
Period size: 76 Copynumber: 2.5 Consensus size: 74
449596 GACCTGGACC
* *
449606 GAAAATGATTTC-AAAACTATATATTATATAAGTTTTTCAAAATGATTTCAAAACTATATATTAT
1 GAAAATGTTTTCAAAAACTATATATTATATAATTTTTTCAAAATGATTTCAAAACTATATATTAT
449670 ATA-AGTTTT
66 ATATA-TTTT
449679 GAAAATGTTTTCAAAAACTATATATTATATATATTTTTTCAAAAT-ATTTTCAAAAACTATATAT
1 GAAAATGTTTTCAAAAACTATATATTATATA-ATTTTTTCAAAATGA-TTTC-AAAACTATATAT
449743 TATATATATTTT
63 TATATATATTTT
* * *
449755 CAAAATGTCTTCAAAAACTATATAATATATACATTTT
1 GAAAATGTTTTCAAAAACTATATATTATATA-ATTTT
449792 AAAAAATCGT
Statistics
Matches: 102, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
73 11 0.11
74 19 0.19
75 16 0.16
76 55 0.54
77 1 0.01
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (74 bp):
GAAAATGTTTTCAAAAACTATATATTATATAATTTTTTCAAAATGATTTCAAAACTATATATTAT
ATATATTTT
Found at i:449791 original size:37 final size:36
Alignment explanation
Indices: 449607--449811 Score: 234
Period size: 37 Copynumber: 5.5 Consensus size: 36
449597 ACCTGGACCG
*
449607 AAAATGATTTC-AAAACTATATATTATATAAGTTTTTC
1 AAAATGTTTTCAAAAACTATATATTATATAA--TTTTC
* *
449644 AAAATGATTTC-AAAACTATATATTATATAAGTTTTG
1 AAAATGTTTTCAAAAACTATATATTATATAA-TTTTC
449680 AAAATGTTTTCAAAAACTATATATTATATATATTTTTTC
1 AAAATGTTTTCAAAAACTATATATTATATA-A--TTTTC
*
449719 AAAATATTTTCAAAAACTATATATTATATATATTTTC
1 AAAATGTTTTCAAAAACTATATATTATATA-ATTTTC
* * *
449756 AAAATGTCTTCAAAAACTATATAATATATACATTTTAA
1 AAAATGTTTTCAAAAACTATATATTATATA-ATTTT-C
*
449794 AAAATCGTTTTGAAAAAC
1 AAAAT-GTTTTCAAAAAC
449812 ATTTTCAAAA
Statistics
Matches: 150, Mismatches: 13, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
36 14 0.09
37 85 0.57
38 6 0.04
39 45 0.30
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.42
Consensus pattern (36 bp):
AAAATGTTTTCAAAAACTATATATTATATAATTTTC
Found at i:449836 original size:2 final size:2
Alignment explanation
Indices: 449824--449878 Score: 101
Period size: 2 Copynumber: 27.0 Consensus size: 2
449814 TTTCAAAAAT
449824 TA TA CTA 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 TA TA TA
449867 TA TA TA TA TA TA
1 TA TA TA TA TA TA
449879 AAATAAAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 50 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:451718 original size:20 final size:20
Alignment explanation
Indices: 451693--451734 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
451683 ATACAAAACA
451693 AAAGTACAAGTTCCCAACCC
1 AAAGTACAAGTTCCCAACCC
*
451713 AAAGTACCAGTTCCCAACCC
1 AAAGTACAAGTTCCCAACCC
451733 AA
1 AA
451735 GGCTGAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.36, G:0.10, T:0.14
Consensus pattern (20 bp):
AAAGTACAAGTTCCCAACCC
Found at i:452746 original size:20 final size:20
Alignment explanation
Indices: 452721--452764 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
452711 ATATTGTTAT
452721 ATTATATTTTAAAAATATTA
1 ATTATATTTTAAAAATATTA
* *
452741 ATTATATTTTAAATATATTT
1 ATTATATTTTAAAAATATTA
452761 ATTA
1 ATTA
452765 AAATTATTAT
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTATATTTTAAAAATATTA
Found at i:452777 original size:14 final size:15
Alignment explanation
Indices: 452718--452794 Score: 50
Period size: 14 Copynumber: 4.7 Consensus size: 15
452708 GTAATATTGT
452718 TATATTATATTTTAAAAA
1 TATATTATA--TT-AAAA
*
452736 TATTAATTATATTTTAAA
1 TA-T-ATTATA-TTAAAA
452754 TATATT-TATTAAAA
1 TATATTATATTAAAA
452768 T-TATTATATTAATTAA
1 TATATTATATTAA--AA
452784 TATATATATAT
1 TATAT-TATAT
452795 AATATTATTC
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
13 4 0.08
14 12 0.24
15 2 0.04
16 6 0.12
17 4 0.08
18 12 0.24
19 4 0.08
20 6 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATTATATTAAAA
Found at i:452788 original size:30 final size:29
Alignment explanation
Indices: 452752--452831 Score: 92
Period size: 30 Copynumber: 2.8 Consensus size: 29
452742 TTATATTTTA
*
452752 AATATATTTATTAAAATTATTATATTAATT
1 AATATATTTATTAATATTATT-TATTAATT
* *
452782 AATATATATATATAATATTATTCATT-ATT
1 AATATATTTAT-TAATATTATTTATTAATT
*
452811 AATA-ATTTAATAATATTATTT
1 AATATATTTATTAATATTATTT
452832 TATGAAATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
27 10 0.23
28 4 0.09
29 7 0.16
30 13 0.30
31 9 0.21
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (29 bp):
AATATATTTATTAATATTATTTATTAATT
Found at i:453895 original size:19 final size:19
Alignment explanation
Indices: 453871--453916 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
453861 AATTTGATTT
*
453871 TTTATATTAATTCCAATTC
1 TTTATATTAATTACAATTC
* *
453890 TTTATATTATTTATAATTC
1 TTTATATTAATTACAATTC
453909 -TTATATTA
1 TTTATATTA
453917 TTATTTTATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTATATTAATTACAATTC
Found at i:454538 original size:23 final size:23
Alignment explanation
Indices: 454508--454558 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
454498 ACAGCAACCG
*
454508 ACAAGCATCAATGTACCAATTCA
1 ACAAGCATCAATGCACCAATTCA
* *
454531 ACAAGCATCATTGCATCAATTCA
1 ACAAGCATCAATGCACCAATTCA
*
454554 GCAAG
1 ACAAG
454559 TTTCCTGCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.41, C:0.25, G:0.12, T:0.22
Consensus pattern (23 bp):
ACAAGCATCAATGCACCAATTCA
Found at i:455739 original size:21 final size:21
Alignment explanation
Indices: 455710--455758 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
455700 ACCGTGATTG
*
455710 CGGCCGTCGCGGGCGCTATTA
1 CGGCCGTCGCGGACGCTATTA
*
455731 CGGCTGTCGCGGACGCTATTA
1 CGGCCGTCGCGGACGCTATTA
455752 CGGCCGT
1 CGGCCGT
455759 GGGTAACTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.10, C:0.33, G:0.37, T:0.20
Consensus pattern (21 bp):
CGGCCGTCGCGGACGCTATTA
Found at i:457526 original size:28 final size:28
Alignment explanation
Indices: 457471--457529 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
457461 AATAAATAAT
* *
457471 TTATAATTAATATTAAAATAATTATATA
1 TTATAATTAATACTAAAATAACTATATA
*
457499 TTATAATTAATACTAATATTAACT-TATA
1 TTATAATTAATACTAA-AATAACTATATA
457527 TTA
1 TTA
457530 ATATAATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (28 bp):
TTATAATTAATACTAAAATAACTATATA
Found at i:457532 original size:50 final size:51
Alignment explanation
Indices: 457471--457567 Score: 119
Period size: 50 Copynumber: 1.9 Consensus size: 51
457461 AATAAATAAT
457471 TTATAATTAATATTAAAATAA-TTAT-ATATTATAATTAATACTAATATTAAC
1 TTATAATTAATA-TAAAATAATTTATAAT-TTATAATTAATACTAATATTAAC
* * * *
457522 TTAT-ATTAATATAATATAGTTTATAATTTGTAATTAATATTAATAT
1 TTATAATTAATATAAAATAATTTATAATTTATAATTAATACTAATAT
457568 AAAATATAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
49 6 0.15
50 28 0.70
51 6 0.15
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (51 bp):
TTATAATTAATATAAAATAATTTATAATTTATAATTAATACTAATATTAAC
Found at i:457605 original size:24 final size:25
Alignment explanation
Indices: 457560--457606 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
457550 TGTAATTAAT
**
457560 ATTAATATAAAATATAGTCTATAAA
1 ATTAATATAAAATATAAACTATAAA
*
457585 ATTAATAT-TAATATAAACTATA
1 ATTAATATAAAATATAAACTATA
457607 TGTTATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTAATATAAAATATAAACTATAAA
Found at i:457633 original size:14 final size:14
Alignment explanation
Indices: 457616--457677 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
457606 ATGTTATAAA
457616 TTATATAGTATAGT
1 TTATATAGTATAGT
* *
457630 TTATAAACTATAGT
1 TTATATAGTATAGT
* *
457644 TAATATAATTAATA-T
1 TTATAT-AGT-ATAGT
*
457659 TAATATAGTATAGT
1 TTATATAGTATAGT
457673 TTATA
1 TTATA
457678 AACTATATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
13 3 0.08
14 23 0.61
15 9 0.24
16 3 0.08
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (14 bp):
TTATATAGTATAGT
Found at i:457663 original size:15 final size:15
Alignment explanation
Indices: 457643--457728 Score: 50
Period size: 15 Copynumber: 5.4 Consensus size: 15
457633 TAAACTATAG
457643 TTAATATAATTAATA
1 TTAATATAATTAATA
* *
457658 TTAATATAGTATAGTTTA
1 TTAATATAAT-TA--ATA
*
457676 TAAACTATATATT-ATA
1 TTAA-TATA-ATTAATA
457692 TTAATATAAATT-ATA
1 TTAATAT-AATTAATA
* *
457707 GTTAAGATAATTAACA
1 -TTAATATAATTAATA
457723 TTAATA
1 TTAATA
457729 CAAACTATAT
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
15 27 0.50
16 16 0.30
18 5 0.09
19 5 0.09
20 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (15 bp):
TTAATATAATTAATA
Found at i:457667 original size:43 final size:40
Alignment explanation
Indices: 457618--457708 Score: 128
Period size: 43 Copynumber: 2.2 Consensus size: 40
457608 GTTATAAATT
*
457618 ATATAGTATAGTTTATAAACTATAGTTAATATAATTAATATTA
1 ATATAGTATAGTTTATAAACTATA--TAATAT-ATTAATATAA
*
457661 ATATAGTATAGTTTATAAACTATATATTATATTAATATAA
1 ATATAGTATAGTTTATAAACTATATAATATATTAATATAA
457701 ATTATAGT
1 A-TATAGT
457709 TAAGATAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 10 0.22
41 11 0.24
43 24 0.53
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (40 bp):
ATATAGTATAGTTTATAAACTATATAATATATTAATATAA
Found at i:457671 original size:29 final size:30
Alignment explanation
Indices: 457552--457728 Score: 94
Period size: 31 Copynumber: 5.5 Consensus size: 30
457542 TTATAATTTG
*
457552 TAATTAATATTAATATAAAATATAGTCT-ATA
1 TAATTAATATTAATAT-AAGTATAGT-TAATA
* *
457583 AAATTAATATTAATATAAACTATATGTT-ATA
1 TAATTAATATTAATAT-AAGTATA-GTTAATA
* *
457614 -AATTATATAGTATAGTTTATAAACTATAGTTAATA
1 TAATTA-ATA-T-TA--ATAT-AAGTATAGTTAATA
457649 TAATTAATATTAATAT-AGTATAGTTTATAAACTA
1 TAATTAATATTAATATAAGTATAG--T-T-AA-TA
* *
457683 TATATT-ATATTAATATAAATTATAGTTAAGA
1 TA-ATTAATATTAATAT-AAGTATAGTTAATA
*
457714 TAATTAACATTAATA
1 TAATTAATATTAATA
457729 CAAACTATAT
Statistics
Matches: 121, Mismatches: 8, Indels: 34
0.74 0.05 0.21
Matches are distributed among these distances:
29 6 0.05
30 8 0.07
31 44 0.36
32 6 0.05
33 7 0.06
34 19 0.16
35 20 0.17
36 11 0.09
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (30 bp):
TAATTAATATTAATATAAGTATAGTTAATA
Found at i:457693 original size:131 final size:132
Alignment explanation
Indices: 457524--457773 Score: 321
Period size: 131 Copynumber: 1.9 Consensus size: 132
457514 ATATTAACTT
** *
457524 ATATTAATATAATATAGTTTATAATTTGTAATTAATATTAATATAAAATATAGTCTATA-A-AAT
1 ATATTAATATAATATAGTTTATAAACTATAATTAATATTAATATAAAATATAGT-TA-AGATAAT
* * * * *
457587 TAATATTAATATAAACTATAT-GT-TATAAATTATATAGTATAGTTTATAAACTATAGTTAATAT
64 TAACATTAATACAAACTATATAGTACATAAA-TATAAACTATAGTTTATAAACTATAGTTAATAT
457650 AATTA
128 AATTA
* *
457655 ATATTAATATAGTATAGTTTATAAACTATATATT-ATATTAATATAAATTATAGTTAAGATAATT
1 ATATTAATATAATATAGTTTATAAACTATA-ATTAATATTAATATAAAATATAGTTAAGATAATT
* *
457719 AACATTAATACAAACTATATAGTACATTAATATAAACTATAGTTTATAAATTATA
65 AACATTAATACAAACTATATAGTACATAAATATAAACTATAGTTTATAAACTATA
457774 TACTATAGGT
Statistics
Matches: 102, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
129 1 0.01
130 3 0.03
131 67 0.66
132 27 0.26
133 4 0.04
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (132 bp):
ATATTAATATAATATAGTTTATAAACTATAATTAATATTAATATAAAATATAGTTAAGATAATTA
ACATTAATACAAACTATATAGTACATAAATATAAACTATAGTTTATAAACTATAGTTAATATAAT
TA
Found at i:457718 original size:65 final size:64
Alignment explanation
Indices: 457524--457728 Score: 222
Period size: 65 Copynumber: 3.1 Consensus size: 64
457514 ATATTAACTT
* *
457524 ATATTAATATAATATAGTTTATAATTTGTA-ATTAATATTAATATAAAATATAGTCTATAA-AAT
1 ATATTAATATAATATAGTTTATAAATTATATATT-ATATTAATATAAAATATAGT-TA-AATAAT
457587 TA
63 TA
* *
457589 ATATTAATATAAACTATA-TGTTATAAATTATATAGTATAGTT--TATAAACTATAGTTAATATA
1 ATATTAATAT-AA-TATAGT-TTATAAATTATATATTATA-TTAATATAAAATATAGTTAA-ATA
457651 ATTA
61 ATTA
* * *
457655 ATATTAATATAGTATAGTTTATAAACTATATATTATATTAATATAAATTATAGTTAAGATAATTA
1 ATATTAATATAATATAGTTTATAAATTATATATTATATTAATATAAAATATAGTTAA-ATAATTA
*
457720 ACATTAATA
1 ATATTAATA
457729 CAAACTATAT
Statistics
Matches: 120, Mismatches: 10, Indels: 20
0.80 0.07 0.13
Matches are distributed among these distances:
63 2 0.02
64 22 0.18
65 45 0.38
66 30 0.25
67 17 0.14
68 4 0.03
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.44
Consensus pattern (64 bp):
ATATTAATATAATATAGTTTATAAATTATATATTATATTAATATAAAATATAGTTAAATAATTA
Found at i:457778 original size:21 final size:21
Alignment explanation
Indices: 457749--457801 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
457739 AGTACATTAA
* *
457749 TATAAACTATAGTTTATAAAT
1 TATAAACTATAGGTTATAAAG
*
457770 TATATACTATAGGTTATAAAG
1 TATAAACTATAGGTTATAAAG
457791 TATAAACTATA
1 TATAAACTATA
457802 TAGTACACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.40
Consensus pattern (21 bp):
TATAAACTATAGGTTATAAAG
Found at i:457895 original size:24 final size:20
Alignment explanation
Indices: 457844--457902 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 20
457834 TATAGGTTAC
457844 ATATATAGTTTATATAACAT
1 ATATATAGTTTATATAACAT
*
457864 ATAAATAGATTGTATATATACAT
1 ATATATAG-TT-TATATA-ACAT
*
457887 ATACTATAGGTTATAT
1 ATA-TATAGTTTATAT
457903 TTATAGTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
20 7 0.22
21 2 0.06
22 11 0.34
23 8 0.25
24 4 0.12
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.42
Consensus pattern (20 bp):
ATATATAGTTTATATAACAT
Found at i:457895 original size:57 final size:55
Alignment explanation
Indices: 457834--457967 Score: 144
Period size: 57 Copynumber: 2.4 Consensus size: 55
457824 GTTTATAAAT
* *
457834 TATAGGTTACATATATAGTTTATATA-ACATATAAATAGATTGTATATATACATATAC
1 TATAGGTTACATATATAGTTTATATATA-ATATAAATAG-TT-CATACATACATATAC
* * * * *
457891 TATAGGTTATATTTATAGTTTATATATATTATACATAGTTCATACATACATGTAC
1 TATAGGTTACATATATAGTTTATATATAATATAAATAGTTCATACATACATATAC
* * *
457946 TATAAGCTACATATATATTTTA
1 TATAGGTTACATATATAGTTTA
457968 CATGTATACA
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
55 29 0.45
56 2 0.03
57 32 0.50
58 1 0.02
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.43
Consensus pattern (55 bp):
TATAGGTTACATATATAGTTTATATATAATATAAATAGTTCATACATACATATAC
Found at i:459515 original size:23 final size:23
Alignment explanation
Indices: 459469--459521 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 23
459459 TACCCAGCTC
*
459469 TATATAAACTATAGTTTATATAAA
1 TATATAAAATATAG-TTATATAAA
459493 TAGTATAAAATATAG-TATATAAA
1 TA-TATAAAATATAGTTATATAAA
459516 TATATA
1 TATATA
459522 TAGTATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 4 0.15
23 10 0.37
24 2 0.07
25 11 0.41
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.40
Consensus pattern (23 bp):
TATATAAAATATAGTTATATAAA
Found at i:459524 original size:17 final size:17
Alignment explanation
Indices: 459502--459536 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
459492 ATAGTATAAA
459502 ATATAGTATATAAATAT
1 ATATAGTATATAAATAT
459519 ATATAGTATATAAATAT
1 ATATAGTATATAAATAT
459536 A
1 A
459537 AACTATAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (17 bp):
ATATAGTATATAAATAT
Found at i:459595 original size:18 final size:18
Alignment explanation
Indices: 459574--459608 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
459564 AACTATAATT
*
459574 TATATATATAGTGTATAC
1 TATATAAATAGTGTATAC
*
459592 TATATAAATAGTTTATA
1 TATATAAATAGTGTATA
459609 TAGTTCACTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.46
Consensus pattern (18 bp):
TATATAAATAGTGTATAC
Found at i:459724 original size:20 final size:20
Alignment explanation
Indices: 459649--459730 Score: 64
Period size: 20 Copynumber: 4.1 Consensus size: 20
459639 ATACGTAAAC
* *
459649 TATATAGTGTAC--ATAGTT
1 TATATAGTTTACATATAGTA
459667 TATATAGTTTATACATATAGT-
1 TATATAG-TT-TACATATAGTA
**
459688 TCATAT-GTAAACTATATAGTA
1 T-ATATAGTTTAC-ATATAGTA
459709 TATATAGTTTACATATAGTA
1 TATATAGTTTACATATAGTA
459729 TA
1 TA
459731 AGTTAGTTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
18 7 0.14
19 3 0.06
20 25 0.49
21 7 0.14
22 9 0.18
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (20 bp):
TATATAGTTTACATATAGTA
Found at i:459860 original size:22 final size:22
Alignment explanation
Indices: 459827--459993 Score: 81
Period size: 22 Copynumber: 8.0 Consensus size: 22
459817 ACCTTAAACC
*
459827 ATAATATATATATATATAAACTAT
1 ATAATTTATAT-TA-ATAAACTAT
*
459851 ATAGTTTATATTAATAAACTAT
1 ATAATTTATATTAATAAACTAT
*
459873 ATAATTTATA-CAAT--A-TAT
1 ATAATTTATATTAATAAACTAT
* *
459891 ATTATTTATAATT-ATACA-TA-
1 ATAATTTAT-ATTAATAAACTAT
** * * *
459911 AT-ATACA-AAT-ATAAATTGT
1 ATAATTTATATTAATAAACTAT
* **
459930 ATAGTTTATATATAATTCA-TAT
1 ATAATTTATAT-TAATAAACTAT
*
459952 ATAATTTTTA-T-ATAAACTAT
1 ATAATTTATATTAATAAACTAT
459972 ATAATTTATATTAATAAACTAT
1 ATAATTTATATTAATAAACTAT
459994 TTAGTTTCTA
Statistics
Matches: 107, Mismatches: 23, Indels: 28
0.68 0.15 0.18
Matches are distributed among these distances:
17 6 0.06
18 12 0.11
19 12 0.11
20 17 0.16
21 8 0.07
22 38 0.36
23 5 0.05
24 9 0.08
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.46
Consensus pattern (22 bp):
ATAATTTATATTAATAAACTAT
Found at i:459964 original size:13 final size:11
Alignment explanation
Indices: 459929--459986 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
459919 ATATAAATTG
*
459929 TATAGTTTATA
1 TATAATTTATA
*
459940 TATAATTCATA
1 TATAATTTATA
*
459951 TATAATTTTTA
1 TATAATTTATA
459962 TATAA---ACTA
1 TATAATTTA-TA
459971 TATAATTTATA
1 TATAATTTATA
459982 T-TAAT
1 TATAAT
459987 AAACTATTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
9 7 0.18
10 4 0.11
11 26 0.68
12 1 0.03
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (11 bp):
TATAATTTATA
Found at i:459973 original size:81 final size:81
Alignment explanation
Indices: 459826--459981 Score: 185
Period size: 81 Copynumber: 1.9 Consensus size: 81
459816 AACCTTAAAC
*
459826 CATAATATATATATATATAAACTATATAGTTTATATTAATAAACTATATAATTTATACAATATAT
1 CATAATATACATATATATAAACTATATAGTTTATATTAATAAACTATATAATTTATACAATATAT
*
459891 ATTATTTATAATTATA
66 ATAATTTATAATTATA
* * ** *
459907 CATAATATACA-A-ATATAAATTGTATAGTTTATATATAATTCA-TATATAATTTTTATATAA-A
1 CATAATATACATATATATAAACTATATAGTTTATAT-TAATAAACTATATAA--TTTATACAATA
459968 CTATATAATTTATA
63 -TATATAATTTATA
459982 TTAATAAACT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
79 27 0.42
80 7 0.11
81 30 0.47
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (81 bp):
CATAATATACATATATATAAACTATATAGTTTATATTAATAAACTATATAATTTATACAATATAT
ATAATTTATAATTATA
Found at i:460063 original size:2 final size:2
Alignment explanation
Indices: 460056--460202 Score: 76
Period size: 2 Copynumber: 74.0 Consensus size: 2
460046 TTATACATGG
* * *
460056 TA TA TA TA GTT TA TA CA TA -A TA TA TA TA TA TA -A TA TA TA GTT
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * *
460098 TT TA TA TA GTA TA TA -A TA -A TA TA AA TA TA AA CTA TA TA GTT
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* * * *
460139 TA TA TA TA TA -A TA CA TA TA CTT TA TA TA TA AA T- TA TA TA GTT
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA
460181 TA TA T- TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
460203 GTTGTTTCAA
Statistics
Matches: 110, Mismatches: 20, Indels: 30
0.69 0.12 0.19
Matches are distributed among these distances:
1 8 0.07
2 94 0.85
3 8 0.07
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:460067 original size:20 final size:20
Alignment explanation
Indices: 460042--460083 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
460032 TATAGTATTG
**
460042 TAGTTTATACATGGTATATA
1 TAGTTTATACATAATATATA
460062 TAGTTTATACATAATATATA
1 TAGTTTATACATAATATATA
460082 TA
1 TA
460084 TATAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (20 bp):
TAGTTTATACATAATATATA
Found at i:460091 original size:9 final size:9
Alignment explanation
Indices: 460067--460195 Score: 52
Period size: 9 Copynumber: 13.9 Consensus size: 9
460057 ATATATAGTT
*
460067 TATACATAA
1 TATATATAA
460076 TATATATATA
1 TATATATA-A
*
460086 TAATATATAG
1 T-ATATATAA
* *
460096 TTTTTAT-A
1 TATATATAA
460104 TAGTATATAA
1 TA-TATATAA
460114 TA-ATATAA
1 TATATATAA
460122 -ATATA-AA
1 TATATATAA
*
460129 CTATATAGTTTA
1 -TATATA--TAA
460141 TATATATAA
1 TATATATAA
* *
460150 TACATATACTT
1 TATATATA--A
460161 TATATATAA
1 TATATATAA
*
460170 -ATTATATAG
1 TA-TATATAA
* *
460179 TTTATATTA
1 TATATATAA
460188 TATATATA
1 TATATATA
460196 TATTATAGTT
Statistics
Matches: 87, Mismatches: 19, Indels: 28
0.65 0.14 0.21
Matches are distributed among these distances:
7 3 0.03
8 11 0.13
9 46 0.53
10 6 0.07
11 20 0.23
12 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (9 bp):
TATATATAA
Found at i:460095 original size:31 final size:33
Alignment explanation
Indices: 460057--460126 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 33
460047 TATACATGGT
460057 ATATATAGTTTATACATAATATAT-AT-ATATA
1 ATATATAGTTTATACATAATATATAATAATATA
* * *
460088 ATATATAGTTTTTATATAGTATATAATAATATA
1 ATATATAGTTTATACATAATATATAATAATATA
460121 A-ATATA
1 ATATATA
460127 AACTATATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 21 0.62
32 7 0.21
33 6 0.18
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (33 bp):
ATATATAGTTTATACATAATATATAATAATATA
Found at i:460105 original size:20 final size:20
Alignment explanation
Indices: 460078--460197 Score: 104
Period size: 22 Copynumber: 5.8 Consensus size: 20
460068 ATACATAATA
460078 TATATATATAATATATAGTT
1 TATATATATAATATATAGTT
* * *
460098 T-T-TATATAGTATATAATAA
1 TATATATATAATATATAGT-T
*
460117 TATAAATATAAACTATATAGTT
1 TATATATAT-AA-TATATAGTT
*
460139 TATATATATAATACATATACTT
1 TATATATATAAT--ATATAGTT
460161 TATATATA-AATTATATAGTT
1 TATATATATAA-TATATAGTT
460181 TATAT-TATATATATATA
1 TATATATATA-ATATATA
460198 TTATAGTTGT
Statistics
Matches: 80, Mismatches: 10, Indels: 20
0.73 0.09 0.18
Matches are distributed among these distances:
18 13 0.16
19 4 0.05
20 22 0.28
21 9 0.11
22 25 0.31
23 7 0.09
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (20 bp):
TATATATATAATATATAGTT
Found at i:460126 original size:41 final size:42
Alignment explanation
Indices: 460056--460195 Score: 155
Period size: 42 Copynumber: 3.4 Consensus size: 42
460046 TTATACATGG
* *
460056 TATATATAGTTTATACATAATATATATATATAA-TATATAGTT
1 TATATATAGTATATACATAATATAAATATA-AACTATATAGTT
*
460098 TTTATATAGTATATA-ATAATATAAATATAAACTATATAGTT
1 TATATATAGTATATACATAATATAAATATAAACTATATAGTT
* * *
460139 TATATATA-TA-ATACATATACTTTATATATAAATTATATAGTT
1 TATATATAGTATATACATA-A-TATAAATATAAACTATATAGTT
460181 TATATTATA-TATATA
1 TATA-TATAGTATATA
460196 TATTATAGTT
Statistics
Matches: 85, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
39 3 0.04
40 7 0.08
41 30 0.35
42 36 0.42
43 6 0.07
44 3 0.04
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (42 bp):
TATATATAGTATATACATAATATAAATATAAACTATATAGTT
Found at i:460202 original size:11 final size:11
Alignment explanation
Indices: 460056--460196 Score: 64
Period size: 11 Copynumber: 12.8 Consensus size: 11
460046 TTATACATGG
460056 TATATATAGTT-
1 TATATATA-TTA
* *
460067 TATACATAATA
1 TATATATATTA
460078 TATATATA-TA
1 TATATATATTA
460088 -ATATATAGTT-
1 TATATATA-TTA
* *
460098 TTTATATAGTA
1 TATATATATTA
*
460109 TATA-ATAATA
1 TATATATATTA
* *
460119 TAAATATA-AA
1 TATATATATTA
460129 CTATATAGT-TTA
1 -TATATA-TATTA
*
460141 TATATATAATA
1 TATATATATTA
*
460152 CATATACT-TTA
1 TATATA-TATTA
*
460163 TATATAAATTA
1 TATATATATTA
460174 TATAGTTTATATTA
1 TATA---TATATTA
460188 TATATATAT
1 TATATATAT
460197 ATTATAGTTG
Statistics
Matches: 98, Mismatches: 17, Indels: 30
0.68 0.12 0.21
Matches are distributed among these distances:
9 7 0.07
10 14 0.14
11 64 0.65
12 3 0.03
14 10 0.10
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.48
Consensus pattern (11 bp):
TATATATATTA
Found at i:460672 original size:215 final size:215
Alignment explanation
Indices: 460301--461001 Score: 1085
Period size: 215 Copynumber: 3.3 Consensus size: 215
460291 GATCCCTGTT
*
460301 TGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTTCTTAAAATT
1 TGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAAATT
* *
460366 ATATTTGCATCTGAAATTGACCTATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTT
66 ATATTTGCATCTGAAATTGACCCATACTTATTACTTATTTATATTTTTTAATTGGCCCATAACTT
**
460431 TTTAAATAAATATAATTTAGTACTTTTTGTATTAATTTAAACCTCACAATTTAAAATTATTTCAA
131 TTTAAATGGATATAATTTAGTACTTTTTGTATTAATTTAAACCTCACAATTTAAAATTATTTCAA
460496 TTTGATCCCTCATCAATGTG
196 TTTGATCCCTCATCAATGTG
*
460516 TGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTATTCAATTTAGTCCTTAAAATT
1 TGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAAATT
* *
460581 ATATATGCATCTGAAATTGACCCATACTTATTACTTATTTATATTTTTTAATTGGCCAATAACTT
66 ATATTTGCATCTGAAATTGACCCATACTTATTACTTATTTATATTTTTTAATTGGCCCATAACTT
* * * *
460646 TTTATATGGGTATAGTTTAGTACTTTTTTGTATTAATTTAAATCTCACAATTTAAAATTATTTCA
131 TTTAAATGGATATAATTTAGTAC-TTTTTGTATTAATTTAAACCTCACAATTTAAAATTATTTCA
*
460711 ATTTGAT---TC--C--TTTG
195 ATTTGATCCCTCATCAATGTG
* **
460725 TGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATT
1 TGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAAATT
*
460790 ATATTTGCATCTGAAATTGACCCATACTTATTACTTATTTATA-TTTTTAATTGGCCCATAATTT
66 ATATTTGCATCTGAAATTGACCCATACTTATTACTTATTTATATTTTTTAATTGGCCCATAACTT
* * * *
460854 TTTAAATGGATATAATTTAGTACTTTGTTTTATTAATTTCAACCTCACAATTTATAATTATTTCT
131 TTTAAATGGATATAATTTAGTACTTT-TTGTATTAATTTAAACCTCACAATTTAAAATTATTTCA
*
460919 ATTTGATCCCTCATCAATGAG
195 ATTTGATCCCTCATCAATGTG
* * * * *
460940 TGTTATTTAATTTATTTAAATTTTAATTTTTAATTTCATATTCGTTCAATTTAATTCTTAAA
1 TGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAA
461002 TTTGTATTAT
Statistics
Matches: 439, Mismatches: 38, Indels: 18
0.89 0.08 0.04
Matches are distributed among these distances:
207 3 0.01
208 79 0.18
209 106 0.24
211 3 0.01
213 3 0.01
215 198 0.45
216 47 0.11
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (215 bp):
TGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAAATT
ATATTTGCATCTGAAATTGACCCATACTTATTACTTATTTATATTTTTTAATTGGCCCATAACTT
TTTAAATGGATATAATTTAGTACTTTTTGTATTAATTTAAACCTCACAATTTAAAATTATTTCAA
TTTGATCCCTCATCAATGTG
Found at i:462178 original size:60 final size:62
Alignment explanation
Indices: 462059--462195 Score: 176
Period size: 60 Copynumber: 2.3 Consensus size: 62
462049 GGCACAAAGA
* * *
462059 CGCATCCCTAGGGAC-TCGTTTTACCTGGGTTTTTGCTGAGTAGGATGCCACGCGTGTAAGG
1 CGCATCCCTGGGGACGTCGTTTTACCTGGGGTTTTGCTGAGTAGGATGCCACGCGGGTAAGG
*
462120 CGCATCCCTGGGGACGTAC-TTTTA-C-GGGGTTTTGCTGAGTCA-GATGCCACGGGGGTAAGG
1 CGCATCCCTGGGGACGT-CGTTTTACCTGGGGTTTTGCTGAGT-AGGATGCCACGCGGGTAAGG
*
462180 CGCATCCCCGGGGACG
1 CGCATCCCTGGGGACG
462196 CACCTTTCAT
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
60 45 0.66
61 16 0.24
62 6 0.09
63 1 0.01
ACGTcount: A:0.16, C:0.25, G:0.34, T:0.25
Consensus pattern (62 bp):
CGCATCCCTGGGGACGTCGTTTTACCTGGGGTTTTGCTGAGTAGGATGCCACGCGGGTAAGG
Found at i:462632 original size:23 final size:24
Alignment explanation
Indices: 462601--462649 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
462591 ATTTTAGTGA
462601 TATGATAATATTT-TT-TTATATTT
1 TATGATAATATTTATTATTAT-TTT
*
462624 TATGTTAATATTTATTATTATTTT
1 TATGATAATATTTATTATTATTTT
462648 TA
1 TA
462650 ATTTAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 12 0.52
24 7 0.30
25 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (24 bp):
TATGATAATATTTATTATTATTTT
Found at i:464321 original size:21 final size:20
Alignment explanation
Indices: 464255--464318 Score: 83
Period size: 21 Copynumber: 3.1 Consensus size: 20
464245 ATCTCCTCAG
*
464255 GGTTACATTCCTAGCCTGCCA
1 GGTTACATTCCTAGCCCG-CA
*
464276 GCTTACATTCCTAGCCCGCTA
1 GGTTACATTCCTAGCCCGC-A
*
464297 GGTTACATGCCTAGCCCGCA
1 GGTTACATTCCTAGCCCGCA
464317 GG
1 GG
464319 GTTTTATGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 4 0.11
21 34 0.89
ACGTcount: A:0.19, C:0.34, G:0.22, T:0.25
Consensus pattern (20 bp):
GGTTACATTCCTAGCCCGCA
Found at i:464878 original size:34 final size:34
Alignment explanation
Indices: 464835--464907 Score: 146
Period size: 34 Copynumber: 2.1 Consensus size: 34
464825 TTAAATGTTT
464835 TTAAAATACAAATTATAGTATTCGAAATTTAACA
1 TTAAAATACAAATTATAGTATTCGAAATTTAACA
464869 TTAAAATACAAATTATAGTATTCGAAATTTAACA
1 TTAAAATACAAATTATAGTATTCGAAATTTAACA
464903 TTAAA
1 TTAAA
464908 TTCAACTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (34 bp):
TTAAAATACAAATTATAGTATTCGAAATTTAACA
Found at i:467269 original size:26 final size:26
Alignment explanation
Indices: 467239--467318 Score: 82
Period size: 24 Copynumber: 3.3 Consensus size: 26
467229 TTTTAAAACG
467239 ATTAATTA-TAATTATTGAATATAATA
1 ATTAATTATTAATTATT-AATATAATA
*
467265 ATTAA-TATTATTTATT-ATA-AATA
1 ATTAATTATTAATTATTAATATAATA
* *
467288 ATTTATTATTAATT-TTAATATTATA
1 ATTAATTATTAATTATTAATATAATA
467313 A-TAATT
1 ATTAATT
467319 TCACCTTCTA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
23 10 0.22
24 17 0.38
25 6 0.13
26 12 0.27
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (26 bp):
ATTAATTATTAATTATTAATATAATA
Found at i:469251 original size:15 final size:15
Alignment explanation
Indices: 469233--469288 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
469223 TAACCGGTTT
469233 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
469248 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
469265 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
469280 CGATTTTAA
1 CGGTTTTAA
469289 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:469261 original size:17 final size:17
Alignment explanation
Indices: 469236--469286 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
469226 CCGGTTTCGG
469236 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
469253 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
469268 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
469285 TT
1 TT
469287 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:469706 original size:13 final size:13
Alignment explanation
Indices: 469685--469739 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
469675 AAGTTCGATA
*
469685 AATTCAAATACTT
1 AATTGAAATACTT
469698 AATTGAAATACTT
1 AATTGAAATACTT
* *
469711 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
469725 AATTGAAATACTT
1 AATTGAAATACTT
469738 AA
1 AA
469740 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:469821 original size:32 final size:33
Alignment explanation
Indices: 469725--469823 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
469715 AACTCAACAT
* * *
469725 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
469758 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
469791 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
469823 A
1 A
469824 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:469842 original size:21 final size:21
Alignment explanation
Indices: 469818--469857 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
469808 ACTTCAAGTT
469818 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
469839 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
469858 AAAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:476655 original size:12 final size:12
Alignment explanation
Indices: 476638--476662 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
476628 GCAGAAAATT
476638 AGTCGAGGTAAC
1 AGTCGAGGTAAC
476650 AGTCGAGGTAAC
1 AGTCGAGGTAAC
476662 A
1 A
476663 ATGCCAGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (12 bp):
AGTCGAGGTAAC
Found at i:491421 original size:20 final size:20
Alignment explanation
Indices: 491396--491433 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
491386 GTCTACGTGG
*
491396 TCCTTCGGGACATATATGTA
1 TCCTTCGGAACATATATGTA
*
491416 TCCTTCGGAACATTTATG
1 TCCTTCGGAACATATATG
491434 AGGCCCTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (20 bp):
TCCTTCGGAACATATATGTA
Found at i:491566 original size:23 final size:23
Alignment explanation
Indices: 491522--491575 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
491512 CATTTTATTT
* *
491522 GGCACTTCGATGCATTTCTACGC
1 GGCACTTCGATGCAATTATACGC
* *
491545 GGCACTTCGGTGCAATTATACGT
1 GGCACTTCGATGCAATTATACGC
*
491568 GGTACTTC
1 GGCACTTC
491576 AGTGTATTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (23 bp):
GGCACTTCGATGCAATTATACGC
Found at i:492420 original size:24 final size:24
Alignment explanation
Indices: 492393--492478 Score: 91
Period size: 24 Copynumber: 3.6 Consensus size: 24
492383 GATATCAAAA
*
492393 ATCAAAACAGAATTTAGATCAGAT
1 ATCAGAACAGAATTTAGATCAGAT
** *
492417 ATCAGAACAGAATCCAGATCAGAA
1 ATCAGAACAGAATTTAGATCAGAT
* * *
492441 ATCAGAACATAATTTAGGTCATAT
1 ATCAGAACAGAATTTAGATCAGAT
* *
492465 ATCATAACATAATT
1 ATCAGAACAGAATT
492479 CAAGTTAGAA
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.48, C:0.15, G:0.12, T:0.26
Consensus pattern (24 bp):
ATCAGAACAGAATTTAGATCAGAT
Found at i:492489 original size:48 final size:48
Alignment explanation
Indices: 492386--492494 Score: 121
Period size: 48 Copynumber: 2.3 Consensus size: 48
492376 AAACAGAGAT
* * *
492386 ATCAAAAATCAAAACAGAATTTAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTTAGATCAGATATCAGAACAGAATCAAG
* * * * *
492434 ATCAGAAATCAGAACATAATTTAGGTCATATATCATAACATAATTCAAG
1 ATCAGAAATCAGAACAGAATTTAGATCAGATATCAGAACAGAA-TCAAG
*
492483 -TTAGAAATCAGA
1 ATCAGAAATCAGA
492495 TAAAATATTT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
48 47 0.92
49 4 0.08
ACGTcount: A:0.50, C:0.15, G:0.12, T:0.24
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTTAGATCAGATATCAGAACAGAATCAAG
Found at i:492492 original size:24 final size:24
Alignment explanation
Indices: 492411--492494 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 24
492401 AGAATTTAGA
* * *
492411 TCAGATATCAGAACAGAA-TCCAG
1 TCAGAAATCAGAACATAATTCAAG
* *
492434 ATCAGAAATCAGAACATAATTTAGG
1 -TCAGAAATCAGAACATAATTCAAG
* * *
492459 TCATATATCATAACATAATTCAAG
1 TCAGAAATCAGAACATAATTCAAG
*
492483 TTAGAAATCAGA
1 TCAGAAATCAGA
492495 TAAAATATTT
Statistics
Matches: 45, Mismatches: 14, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
24 43 0.96
25 2 0.04
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.25
Consensus pattern (24 bp):
TCAGAAATCAGAACATAATTCAAG
Found at i:500653 original size:23 final size:23
Alignment explanation
Indices: 500627--500686 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
500617 TTAATATGGC
*
500627 ACTTCGGTGTATTTCTACACGGT
1 ACTTCGGTGCATTTCTACACGGT
* *
500650 ACTTCGGTGCAATTCTACATGGT
1 ACTTCGGTGCATTTCTACACGGT
*
500673 ACTTTGGTGCATTT
1 ACTTCGGTGCATTT
500687 ATATGTGTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (23 bp):
ACTTCGGTGCATTTCTACACGGT
Found at i:503067 original size:43 final size:42
Alignment explanation
Indices: 503020--503103 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 42
503010 GTTTCAAAAA
503020 CGCCGCAAAA-GT-GATATATCTATAGCAGCGTTTTTGGAACAAT
1 CGCCGCAAAAGGTCGATAT-T-TATAGCAGCG-TTTTGGAACAAT
*
503063 CGCCGCAAAAGGTCGATATTTATAGCGGCGTTTTGGAACAA
1 CGCCGCAAAAGGTCGATATTTATAGCAGCGTTTTGGAACAA
503104 ACACAGCAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
42 11 0.29
43 19 0.50
44 3 0.08
45 5 0.13
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (42 bp):
CGCCGCAAAAGGTCGATATTTATAGCAGCGTTTTGGAACAAT
Found at i:503310 original size:43 final size:43
Alignment explanation
Indices: 503037--503320 Score: 220
Period size: 43 Copynumber: 6.7 Consensus size: 43
503027 AAAGTGATAT
* * * *
503037 ATCTATAGCAGCGTTTTTGGA-ACAATCGCCGCAAAAGGTCGAT
1 ATCTATAGCGGCGTTTTTGGATACAAACTCCGCAAAAGGTC-AG
* * * *
503080 ATTTATAGCGGCG-TTTTGGA-ACAAACACAGC-AAAGGTTGAG
1 ATCTATAGCGGCGTTTTTGGATACAAACTCCGCAAAAGG-TCAG
* * * ** *
503121 ATATATAGTGGCATTTTTTAATACAAACGCCGCAAAAGGTCAG
1 ATCTATAGCGGCGTTTTTGGATACAAACTCCGCAAAAGGTCAG
* * ** * *
503164 ATCTATAGCGACATTTTTTTATACAAACGT-TGCAAAAGGTTAG
1 ATCTATAGCGGCGTTTTTGGATACAAAC-TCCGCAAAAGGTCAG
* *
503207 ATCTATAGTGGCGTTTTTGGATACAAA-TGCCGCAAAAGGCCAG
1 ATCTATAGCGGCGTTTTTGGATACAAACT-CCGCAAAAGGTCAG
* * ** * * *
503250 TTCTACAATGGTGTTTTTGGAGACAAACTCCGCAAAAGGTCAA
1 ATCTATAGCGGCGTTTTTGGATACAAACTCCGCAAAAGGTCAG
*
503293 ATCTATAGCGGCCTTTTTGGATACAAAC
1 ATCTATAGCGGCGTTTTTGGATACAAAC
503321 GTCGATAATT
Statistics
Matches: 189, Mismatches: 44, Indels: 16
0.76 0.18 0.06
Matches are distributed among these distances:
41 17 0.09
42 21 0.11
43 145 0.77
44 6 0.03
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (43 bp):
ATCTATAGCGGCGTTTTTGGATACAAACTCCGCAAAAGGTCAG
Found at i:505175 original size:90 final size:88
Alignment explanation
Indices: 505023--505192 Score: 286
Period size: 90 Copynumber: 1.9 Consensus size: 88
505013 ACACACCCTT
505023 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAACTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAACTAATTAAATCTATATTTA
*
505088 ATTAATTAGAATTTAATAATCCTC
66 ATTAATT-GAAATTAATAATCCTC
* * *
505112 TTATATCCAAGTTACCCTAATCATATTGGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAACTAATTAAATCTATATTT
505177 AATTAATTGAAATTAA
65 AATTAATTGAAATTAA
505193 ATATTTGGGA
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
89 36 0.47
90 40 0.53
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.44
Consensus pattern (88 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAACTAATTAAATCTATATTTA
ATTAATTGAAATTAATAATCCTC
Found at i:513424 original size:41 final size:40
Alignment explanation
Indices: 513379--513513 Score: 105
Period size: 41 Copynumber: 3.3 Consensus size: 40
513369 CATTTTCTGA
*
513379 AAAAACGCCACTATAGATTAATCTTATTGCGGCGTTTGTAT
1 AAAAATGCCACTATAGATTAATC-TATTGCGGCGTTTGTAT
* * * * * *
513420 AAAAATGCCGCTAAAGTACTATTCTGTTGTGGCGTTTGT-T
1 AAAAATGCCACTATAG-ATTAATCTATTGCGGCGTTTGTAT
* * * *
513460 GAACAAATGCCACTATAGATGAACCCTATTGCGGTGTTTATAT
1 -AA-AAATGCCACTATAGATTAA-TCTATTGCGGCGTTTGTAT
513503 -AAAA-GCCACTA
1 AAAAATGCCACTA
513514 AAGTACTATT
Statistics
Matches: 72, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
39 7 0.10
40 4 0.06
41 31 0.43
42 29 0.40
43 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Consensus pattern (40 bp):
AAAAATGCCACTATAGATTAATCTATTGCGGCGTTTGTAT
Found at i:513492 original size:83 final size:83
Alignment explanation
Indices: 513376--513693 Score: 340
Period size: 83 Copynumber: 3.9 Consensus size: 83
513366 CGACATTTTC
* * * * * * *
513376 TGAAAAAACGCCACTATAGATTAATCTTATTGCGGCGTTTGTATAAAAATGCCGCTAAAGTACTA
1 TGAAGAAACACCACTATAGATGAACCCTATTGCGGCGTTTGTATAAAAACGCCACTAAAGTACTA
* *
513441 TTCTGTTGTGGCGTTTGT
66 CTCTGTTATGGCGTTTGT
* ** * *
513459 TGAACAAATGCCACTATAGATGAACCCTATTGCGGTGTTTATAT-AAAA-GCCACTAAAGTACTA
1 TGAAGAAACACCACTATAGATGAACCCTATTGCGGCGTTTGTATAAAAACGCCACTAAAGTACTA
* * *
513522 TTTTTTTCATGGCGTTTGT
66 CTCTGTT-ATGGCGTTTGT
* ** * *
513541 T-AAGAAACACCACTATGGATGAA-CCTATTATGGCGTTTGTATAAAAACACCGCTAAAGTACTA
1 TGAAGAAACACCACTATAGATGAACCCTATTGCGGCGTTTGTATAAAAACGCCACTAAAGTACTA
* * *
513604 CTCTATTATAGCATTTGT
66 CTCTGTTATGGCGTTTGT
* *
513622 TGAAGAAACACCACTATAGATGAACCCAATTGCGGCGTTAT-TATATAAACGCCACTAAAGTACT
1 TGAAGAAACACCACTATAGATGAACCCTATTGCGGCGTT-TGTATAAAAACGCCACTAAAGTACT
513686 ACTCTGTT
65 ACTCTGTT
513694 GCGATGTTTT
Statistics
Matches: 195, Mismatches: 34, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
80 15 0.08
81 51 0.26
82 53 0.27
83 75 0.38
84 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (83 bp):
TGAAGAAACACCACTATAGATGAACCCTATTGCGGCGTTTGTATAAAAACGCCACTAAAGTACTA
CTCTGTTATGGCGTTTGT
Found at i:513575 original size:40 final size:40
Alignment explanation
Indices: 513530--513647 Score: 125
Period size: 40 Copynumber: 2.9 Consensus size: 40
513520 TATTTTTTTC
*
513530 ATGGCGTTTGTTAAGAAACACCACTATGGATGAACCTATT
1 ATGGCGTTTGTTAAGAAACACCACTATAGATGAACCTATT
* *
513570 ATGGCGTTTGTATAA-AAACACCGCTAAAG-T-ACTACTCTATT
1 ATGGCGTTTGT-TAAGAAACACCACTATAGATGA--AC-CTATT
* *
513611 ATAGCATTTGTTGAAGAAACACCACTATAGATGAACC
1 ATGGCGTTTGTT-AAGAAACACCACTATAGATGAACC
513648 CAATTGCGGC
Statistics
Matches: 63, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
38 1 0.02
39 1 0.02
40 25 0.40
41 20 0.32
42 14 0.22
43 1 0.02
44 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29
Consensus pattern (40 bp):
ATGGCGTTTGTTAAGAAACACCACTATAGATGAACCTATT
Found at i:522870 original size:120 final size:120
Alignment explanation
Indices: 522651--522876 Score: 319
Period size: 120 Copynumber: 1.9 Consensus size: 120
522641 CAAATAACTC
* * *
522651 ACCAGCTTCACACAACTCCATAACAAAATGGACCGCATTGTCATCCTCATAAGTAGACTTCAAGG
1 ACCACCTTCACACAACTCCATAACAAAATAGACCGCACTGTCATCCTCATAAGTAGACTTCAAGG
* * *
522716 GATCAATATTTGCGTGCTGAGGCAAATGCGAAGAAAGAAAGAAAGAAAGTGACTT
66 GAACAATATTAGCGTGCTGAGGCAAATGCAAAGAAAGAAAGAAAGAAAGTGACTT
* * * * * *
522771 ACCACCTTCACACAATTCTATAACCAAATAGATCGCACTGTCATCCTCATAATTAGCCTTCAAGG
1 ACCACCTTCACACAACTCCATAACAAAATAGACCGCACTGTCATCCTCATAAGTAGACTTCAAGG
*
522836 TAACAATATTCAG-GTGCTGAGGCAAATGCAAAGAAAGAAAG
66 GAACAATATT-AGCGTGCTGAGGCAAATGCAAAGAAAGAAAG
522877 TGACTCTCCA
Statistics
Matches: 92, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
120 91 0.99
121 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (120 bp):
ACCACCTTCACACAACTCCATAACAAAATAGACCGCACTGTCATCCTCATAAGTAGACTTCAAGG
GAACAATATTAGCGTGCTGAGGCAAATGCAAAGAAAGAAAGAAAGAAAGTGACTT
Found at i:535787 original size:21 final size:21
Alignment explanation
Indices: 535761--535808 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
535751 GATTCTTCCA
*
535761 TTTCAACCATTAGCAATGACT
1 TTTCAACCATTAGCAATAACT
*
535782 TTTCAACCATTAGTAATAACT
1 TTTCAACCATTAGCAATAACT
535803 TTTCAA
1 TTTCAA
535809 AATGTTAGCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (21 bp):
TTTCAACCATTAGCAATAACT
Found at i:537157 original size:161 final size:162
Alignment explanation
Indices: 536833--537183 Score: 449
Period size: 161 Copynumber: 2.1 Consensus size: 162
536823 GGGAATTTTT
* *
536833 AATATTTGGGTGCTGAGGTAAATGCAAAGGAAGAAAGAAAGAATAACAATAGTTAGGTGCTGAGG
1 AATATTTGGGTGCTGAGGCAAAT-CAAA-GAAGAAAGAAAGAATAACAATAGTTAGGTGCTGAGA
* * *
536898 CAAATGCAAAAAAAGAAAGAAAGAATGGGACTCACAACCCTCACACAATTGCATAACCAAATGGA
64 CAAATGCAAAAAAAGAAAGAAAGAA---GACTCACAACCCTCACACAACTCCATAACCAAATAGA
*
536963 CAGTATTGTCATCCTCATAAGTAGCCTTCAAGGTAAAC
126 CAGCATTGTCATCCTCATAAGTAGCCTTCAAGGT-AAC
* * * * *
537001 TATATTTGGGTGCTGAGGCAAAT-ACA-AAGAAAGAAAGAATAACAATATTTGGGTGGTGAGACA
1 AATATTTGGGTGCTGAGGCAAATCAAAGAAGAAAGAAAGAATAACAATAGTTAGGTGCTGAGACA
* * *
537064 AATGCAAATAAAGAAAGAAAGCAA-ACTCACCACCTTCACACAACTCCATAACCAAATAGACCA-
66 AATGCAAAAAAAGAAAGAAAG-AAGACTCACAACCCTCACACAACTCCATAACCAAATAGA-CAG
* *
537127 CATTTTTATCCTCATAAGTAGCCTTCAAGGTAAC
129 CATTGTCATCCTCATAAGTAGCCTTCAAGGTAAC
*
537161 AATATTCGGGTGCTGAGGCAAAT
1 AATATTTGGGTGCTGAGGCAAAT
537184 GCTTCATGAT
Statistics
Matches: 163, Mismatches: 18, Indels: 12
0.84 0.09 0.06
Matches are distributed among these distances:
160 24 0.15
161 59 0.36
162 2 0.01
164 53 0.33
165 2 0.01
166 2 0.01
168 21 0.13
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.21
Consensus pattern (162 bp):
AATATTTGGGTGCTGAGGCAAATCAAAGAAGAAAGAAAGAATAACAATAGTTAGGTGCTGAGACA
AATGCAAAAAAAGAAAGAAAGAAGACTCACAACCCTCACACAACTCCATAACCAAATAGACAGCA
TTGTCATCCTCATAAGTAGCCTTCAAGGTAAC
Found at i:537391 original size:16 final size:15
Alignment explanation
Indices: 537366--537396 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
537356 ATAAAAAGAA
537366 TAAAATCCAAGCTTT
1 TAAAATCCAAGCTTT
537381 TAAAGATCCAAGCTTT
1 TAAA-ATCCAAGCTTT
537397 GAGATATAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (15 bp):
TAAAATCCAAGCTTT
Found at i:539118 original size:4 final size:4
Alignment explanation
Indices: 539109--539133 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
539099 TTAACCATTG
539109 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
539134 GTTTCTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:539308 original size:127 final size:127
Alignment explanation
Indices: 539117--539460 Score: 382
Period size: 127 Copynumber: 2.7 Consensus size: 127
539107 TGTTATTTAT
* *
539117 TTATTTATTTATTTATTGTTTCTAATATTCAATTCGACCTTGTGGTGACCAGATCCGGGTTATGA
1 TTATTTATTTATTTATTGTTTCTAATATTCAATTCGACCTTATGGTGACCAGATCCGGGGTATGA
* *
539182 TCCACATTATTATGGTTCGAACTCTACTAACTACTGACTTTTATTTTATTGCACTCTAACCA
66 TCCACATTATTATGGTTCGAACTCTACTAACCACTAACTTTTATTTTATTGCACTCTAACCA
* * *
539244 TTATTTATTTATTTATTGTTTCTAATATTTGAA-TCGACCTTATGGTGACCCGATCTGGGGTATG
1 TTATTTATTTATTTATTGTTTCTAATA-TTCAATTCGACCTTATGGTGACCAGATCCGGGGTATG
* * * * * **
539308 ATCCACATTATTATGGTTCGGACTCTACTAACCACTAACTTTT-TTATATT-TA-TTTTA-TT
65 ATCCACATTATTATGGTTCGAACTCTACTAACCACTAACTTTTATTTTATTGCACTCTAACCA
* * * * **
539367 TTATTT-TGTTA-AT-TTGTTT-TGAATTATTCAATTCGACCTTGTGGTGACTACATCTAGGGTA
1 TTATTTAT-TTATTTATTGTTTCT-AA-TATTCAATTCGACCTTATGGTGACCAGATCCGGGGTA
* * *
539428 TAATCCACATTATTATGGTTCAAACTCTGCTAA
63 TGATCCACATTATTATGGTTCGAACTCTACTAA
539461 TTGCTAACTT
Statistics
Matches: 187, Mismatches: 25, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
120 1 0.01
121 12 0.06
122 57 0.30
123 9 0.05
124 3 0.02
125 1 0.01
126 6 0.03
127 94 0.50
128 4 0.02
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.45
Consensus pattern (127 bp):
TTATTTATTTATTTATTGTTTCTAATATTCAATTCGACCTTATGGTGACCAGATCCGGGGTATGA
TCCACATTATTATGGTTCGAACTCTACTAACCACTAACTTTTATTTTATTGCACTCTAACCA
Found at i:539476 original size:16 final size:16
Alignment explanation
Indices: 539465--539509 Score: 90
Period size: 16 Copynumber: 2.8 Consensus size: 16
539455 TGCTAATTGC
539465 TAACTTTTCTAACTGT
1 TAACTTTTCTAACTGT
539481 TAACTTTTCTAACTGT
1 TAACTTTTCTAACTGT
539497 TAACTTTTCTAAC
1 TAACTTTTCTAAC
539510 AACTAACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.27, C:0.20, G:0.04, T:0.49
Consensus pattern (16 bp):
TAACTTTTCTAACTGT
Found at i:539516 original size:16 final size:16
Alignment explanation
Indices: 539457--539531 Score: 87
Period size: 16 Copynumber: 4.7 Consensus size: 16
539447 TCAAACTCTG
*
539457 CTAATTGCTAACTTTT
1 CTAACTGCTAACTTTT
*
539473 CTAACTGTTAACTTTT
1 CTAACTGCTAACTTTT
*
539489 CTAACTGTTAACTTTT
1 CTAACTGCTAACTTTT
** *
539505 CTAACAACTAACATTT
1 CTAACTGCTAACTTTT
*
539521 CTAACCGCTAA
1 CTAACTGCTAA
539532 TTACTAACTA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (16 bp):
CTAACTGCTAACTTTT
Found at i:539522 original size:32 final size:32
Alignment explanation
Indices: 539463--539550 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 32
539453 TCTGCTAATT
** * *
539463 GCTAACTTTTCTAACTGTTAACTTTTCTAACT
1 GCTAACTTTTCTAACTACTAACATTTCTAACC
* *
539495 GTTAACTTTTCTAACAACTAACATTTCTAACC
1 GCTAACTTTTCTAACTACTAACATTTCTAACC
*
539527 GCTAA--TTACTAACTACTAACATTT
1 GCTAACTTTTCTAACTACTAACATTT
539551 TATTTTTATT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
30 17 0.36
32 30 0.64
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.41
Consensus pattern (32 bp):
GCTAACTTTTCTAACTACTAACATTTCTAACC
Found at i:539847 original size:15 final size:14
Alignment explanation
Indices: 539809--539851 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
539799 GTATAGATAT
539809 TATATATTTATTTG
1 TATATATTTATTTG
539823 TAT-TATTTATGTATG
1 TATATATTTAT-T-TG
539838 TATATA-TTATTTG
1 TATATATTTATTTG
539851 T
1 T
539852 TCTTGGGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 10 0.38
14 5 0.19
15 9 0.35
16 2 0.08
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (14 bp):
TATATATTTATTTG
Found at i:542731 original size:110 final size:110
Alignment explanation
Indices: 542537--542734 Score: 335
Period size: 110 Copynumber: 1.8 Consensus size: 110
542527 GACATTCGAA
*
542537 GAATGATGGGGCATTATGAAGCTAGTCAAGAGGAGATCTTTGCATCTATCATGAAGCTTTCCTGC
1 GAATGATGGGGCATTATGAAGCTAGTCAAGAAGAGATCTTTGCATCTATCATGAAGCTTTCCTGC
* **
542602 ACTTGCATTAAGAGTATTGTTTTGAACTCGTTTTTTGTTCTATTT
66 ACTTCCATTAAGAACATTGTTTTGAACTCGTTTTTTGTTCTATTT
*
542647 GAATGATGGGGCATTCTGATA-CTAGTCAAGAAGAGATCTTTGCATCTATCATGAAGCTTTCCTG
1 GAATGATGGGGCATTATGA-AGCTAGTCAAGAAGAGATCTTTGCATCTATCATGAAGCTTTCCTG
542711 CACTTCCATTAAGAACATTGTTTT
65 CACTTCCATTAAGAACATTGTTTT
542735 TGTTTGAACT
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
110 81 0.99
111 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (110 bp):
GAATGATGGGGCATTATGAAGCTAGTCAAGAAGAGATCTTTGCATCTATCATGAAGCTTTCCTGC
ACTTCCATTAAGAACATTGTTTTGAACTCGTTTTTTGTTCTATTT
Found at i:543794 original size:24 final size:26
Alignment explanation
Indices: 543757--543825 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 26
543747 CCAAGCTGTC
*
543757 ATAACTATTTTTTTGAAAAAACAATT
1 ATAACTATTATTTTGAAAAAACAATT
*
543783 A-AA-TATTATTTT-AAAAAACAGTT
1 ATAACTATTATTTTGAAAAAACAATT
* *
543806 ATAACTTTTATTTGGAAAAA
1 ATAACTATTATTTTGAAAAA
543826 TTGGTGATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 11 0.31
24 10 0.28
25 9 0.25
26 6 0.17
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.41
Consensus pattern (26 bp):
ATAACTATTATTTTGAAAAAACAATT
Found at i:543929 original size:16 final size:17
Alignment explanation
Indices: 543910--543945 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
543900 TTTAAAACAA
543910 TTTTAAGA-AAAAATCG
1 TTTTAAGACAAAAATCG
*
543926 TTTTAAGACAAAAATGG
1 TTTTAAGACAAAAATCG
543943 TTT
1 TTT
543946 GTGTTTACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (17 bp):
TTTTAAGACAAAAATCG
Found at i:544236 original size:14 final size:14
Alignment explanation
Indices: 544217--544246 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
544207 ATTATTTTTA
544217 TCCGTAAAGAATAT
1 TCCGTAAAGAATAT
544231 TCCGTAAAGAATAT
1 TCCGTAAAGAATAT
544245 TC
1 TC
544247 TCTCTTCGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (14 bp):
TCCGTAAAGAATAT
Found at i:544641 original size:20 final size:20
Alignment explanation
Indices: 544600--544641 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
544590 TTAATAAATT
*
544600 TAACATATATATATTATTCA
1 TAACATATATATATTATACA
544620 TAACATA-ATATATTCATACA
1 TAACATATATATATT-ATACA
544640 TA
1 TA
544642 TAATGACAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (20 bp):
TAACATATATATATTATACA
Found at i:546268 original size:3 final size:3
Alignment explanation
Indices: 546260--546291 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
546250 AATATGTATT
546260 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
546292 TTTTTTTGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:547829 original size:20 final size:20
Alignment explanation
Indices: 547804--547843 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
547794 ACTTGTTCTA
547804 AATCTGGGTGAGACCAAACT
1 AATCTGGGTGAGACCAAACT
547824 AATCTGGGTGAGACCAAACT
1 AATCTGGGTGAGACCAAACT
547844 GCTGTTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (20 bp):
AATCTGGGTGAGACCAAACT
Found at i:550122 original size:59 final size:59
Alignment explanation
Indices: 550056--550192 Score: 213
Period size: 59 Copynumber: 2.3 Consensus size: 59
550046 GAGTCTATTT
*
550056 ACTATTAAAAGTTACAAAACAGTCCCCCAATTATAGGGTGTTACTTTATTGTGTCCTTA
1 ACTATTAAAAGTTACAAAACAGTCCCCCAATTATAGGGTGTTACTTTATTGAGTCCTTA
* * * *
550115 ACTATTAAAAATTACAAAACAGTTCTCCAATTATAGGGTGTTACTTTGTTGAGTCCTTA
1 ACTATTAAAAGTTACAAAACAGTCCCCCAATTATAGGGTGTTACTTTATTGAGTCCTTA
550174 ACT-TCTAAAAGTTACAAAA
1 ACTAT-TAAAAGTTACAAAA
550193 TGATTACTCA
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
58 1 0.01
59 70 0.99
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (59 bp):
ACTATTAAAAGTTACAAAACAGTCCCCCAATTATAGGGTGTTACTTTATTGAGTCCTTA
Found at i:552029 original size:16 final size:15
Alignment explanation
Indices: 552010--552044 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
552000 AGACCCTGTT
552010 TCAAAAGATGGAACAC
1 TCAAAAGATGGAAC-C
552026 TCAAAAGATGGAACC
1 TCAAAAGATGGAACC
552041 TCAA
1 TCAA
552045 CATAAGTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.49, C:0.20, G:0.17, T:0.14
Consensus pattern (15 bp):
TCAAAAGATGGAACC
Found at i:552578 original size:17 final size:18
Alignment explanation
Indices: 552558--552598 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
552548 AAGATATATA
*
552558 AAAATAA-AATAAATAAT
1 AAAATAAGAAAAAATAAT
552575 AAAA-AAGAAAAAATAAT
1 AAAATAAGAAAAAATAAT
*
552592 ATAATAA
1 AAAATAA
552599 CAAATATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 2 0.10
17 16 0.80
18 2 0.10
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (18 bp):
AAAATAAGAAAAAATAAT
Found at i:552667 original size:19 final size:18
Alignment explanation
Indices: 552648--552696 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 18
552638 AGTTGTTTTA
552648 AAATAAAAAATAATAATT
1 AAATAAAAAATAATAATT
*
552666 AAATAAAAGAAAAATAATT
1 AAATAAAA-AATAATAATT
552685 AAATAAACAAAT
1 AAATAAA-AAAT
552697 TAAAGAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 8 0.30
19 18 0.67
20 1 0.04
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (18 bp):
AAATAAAAAATAATAATT
Found at i:553296 original size:20 final size:18
Alignment explanation
Indices: 553273--553316 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
553263 AAAAACAAGC
*
553273 TAAACATCTTAAATCCTATT
1 TAAACA-CTTAAA-ACTATT
553293 TAAAACACTTAAAACTATT
1 T-AAACACTTAAAACTATT
553312 TAAAC
1 TAAAC
553317 TAAGATACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 4 0.18
19 6 0.27
20 7 0.32
21 5 0.23
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAACACTTAAAACTATT
Found at i:553312 original size:19 final size:21
Alignment explanation
Indices: 553274--553315 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
553264 AAAACAAGCT
*
553274 AAACATCTTAAATCCTATTTA
1 AAACATCTTAAATACTATTTA
553295 AAACA-CTTAAA-ACTATTTA
1 AAACATCTTAAATACTATTTA
553314 AA
1 AA
553316 CTAAGATACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 6 0.30
21 5 0.25
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (21 bp):
AAACATCTTAAATACTATTTA
Found at i:555100 original size:10 final size:10
Alignment explanation
Indices: 555085--555120 Score: 56
Period size: 9 Copynumber: 3.6 Consensus size: 10
555075 TAAGCATCTG
555085 ATAAAATAAA
1 ATAAAATAAA
555095 ATAAAAT-AA
1 ATAAAATAAA
555104 ATAAAATGAAA
1 ATAAAAT-AAA
555115 ATAAAA
1 ATAAAA
555121 CGAAATGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.38
10 7 0.29
11 8 0.33
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (10 bp):
ATAAAATAAA
Found at i:555107 original size:4 final size:5
Alignment explanation
Indices: 555085--555120 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
555075 TAAGCATCTG
555085 ATAAA ATAAA ATAAA AT-AA ATAAA ATGAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA AT-AAA ATAAA A
555121 CGAAATGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
5 20 0.69
6 5 0.17
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:555107 original size:14 final size:15
Alignment explanation
Indices: 555088--555119 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
555078 GCATCTGATA
555088 AAATAAAAT-AAAAT
1 AAATAAAATGAAAAT
555102 AAATAAAATGAAAAT
1 AAATAAAATGAAAAT
555117 AAA
1 AAA
555120 ACGAAATGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (15 bp):
AAATAAAATGAAAAT
Found at i:560632 original size:19 final size:18
Alignment explanation
Indices: 560594--560637 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
560584 GTTGTTTTAA
*
560594 AAATAAAAAATAAGAATT
1 AAATAAAAAAAAAGAATT
*
560612 AAATAAAAGAAAAATAATT
1 AAATAAAA-AAAAAGAATT
560631 AAATAAA
1 AAATAAA
560638 CAAATTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (18 bp):
AAATAAAAAAAAAGAATT
Found at i:561118 original size:12 final size:12
Alignment explanation
Indices: 561103--561132 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
561093 AAAAGTATGC
561103 GAAAAATAGAGA
1 GAAAAATAGAGA
*
561115 GAAAACTAGAGA
1 GAAAAATAGAGA
561127 GAAAAA
1 GAAAAA
561133 GAATATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.07
Consensus pattern (12 bp):
GAAAAATAGAGA
Found at i:561426 original size:76 final size:73
Alignment explanation
Indices: 561270--561413 Score: 173
Period size: 76 Copynumber: 1.9 Consensus size: 73
561260 ACTTAAAAAA
* * *
561270 ATAATATAATATTCTAAATCCTAATTAAAAAACTAAAACCTATTTAAACTAAAATACCTAAAACA
1 ATAAAATAATATCCTAAAACCTAATTAAAAAACTAAAACCTATTTAAACTAAAATA-C-AAAACA
*
561335 AAGATGAAAT
64 AAAATGAAAT
* * * *
561345 ATAAAAATAATATCCTAAAACTTAATTAAAATATTAAAAACCTATTTAAACTAAAATA-AAAATA
1 AT-AAAATAATATCCTAAAACCTAATTAAAAAACT-AAAACCTATTTAAACTAAAATACAAAACA
561409 AAAAT
64 AAAAT
561414 ATAATGTTTA
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
74 9 0.15
75 2 0.03
76 26 0.44
77 22 0.37
ACGTcount: A:0.59, C:0.11, G:0.01, T:0.28
Consensus pattern (73 bp):
ATAAAATAATATCCTAAAACCTAATTAAAAAACTAAAACCTATTTAAACTAAAATACAAAACAAA
AATGAAAT
Found at i:567133 original size:20 final size:17
Alignment explanation
Indices: 567097--567137 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
567087 ACTTGAGTTA
567097 CTGCCCAAGTTTTGCTG
1 CTGCCCAAGTTTTGCTG
*
567114 CTGCCCAAGTTTTGTTG
1 CTGCCCAAGTTTTGCTG
567131 CTGCCCA
1 CTGCCCA
567138 CTCATATCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.12, C:0.32, G:0.22, T:0.34
Consensus pattern (17 bp):
CTGCCCAAGTTTTGCTG
Found at i:580675 original size:233 final size:232
Alignment explanation
Indices: 580245--581598 Score: 1713
Period size: 233 Copynumber: 5.8 Consensus size: 232
580235 GGAAAAGAGG
* * ** * * *
580245 GACATGT-AAAAAATCCTGCCCAAAGGTCTTATTAATGGCCTGAAAGACTTATCACCTTGTTCGA
1 GACATGTGAAAACATCATGCCCAAAGGTCTTATGGATGGCCTGAAGGACTTATCATCTTGCTCGA
*
580309 AAGACTTATAGATGACCCGAAGGATTTAAGCATCATGCTC-AAATGACTTACTGATGGCCTGAAG
66 AAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAA-GACTTACTGATGGCC-GAAG
* *
580373 GACTTATAAATTTTGGAAATAGTTTACTAAGTAAGAAACCTTTCTTACTTTTCAAAACTTTCAAT
129 GACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAAT
*
580438 TTTCAAATTTGAACGAGAAACCTTTCTCATTTTTCGAGA
194 TTTCAAATTTGAATGAGAAACCTTTCTCATTTTTCGAGA
* * *
580477 GACATGTGAAAACATCATGCCCAAAGGTATTATGGATGGCCCGAAGGACTTACCATCTTGCTCGA
1 GACATGTGAAAACATCATGCCCAAAGGTCTTATGGATGGCCTGAAGGACTTATCATCTTGCTCGA
* * *
580542 AAGACTTACAGATAACCCTAAAGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCTCGAAGG
66 AAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGC-CGAAGG
* ** * *
580607 ACTTATAAATTTTCGAAATAGTTTTTTATGTAAGAAACCTTTCTTACTTTTCAAAAATTTCTATT
130 ACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATT
* * *
580672 TTCAAATCTGAATGAGAAATCTTTATCATTTTTCGAGA
195 TTCAAATTTGAATGAGAAACCTTTCTCATTTTTCGAGA
* * * * * * *
580710 GACATGTGAAAACATCTTACCCGAAGGACTTATAGATGGCCAGAATGACTTATCATCTTGCTCGA
1 GACATGTGAAAACATCATGCCCAAAGGTCTTATGGATGGCCTGAAGGACTTATCATCTTGCTCGA
* * *
580775 AAGACTTA-AAAGTGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTGCTGATGGACCGAAT
66 AAGACTTACAGA-TGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGG-CCGAAG
*
580839 GACTTATAAATTTTGGAAATAGTTTACTAGATAAGAAACCTTTCTTACTTTTCAAAAATTTCAAA
129 GACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTC-AA
* * * * * *
580904 ATTTCAGATTTAAATGAGGAACCTTTCTCATATTTCGATA
193 TTTTCAAATTTGAATGAGAAACCTTTCTCATTTTTCGAGA
* * ** * * * * *
580944 GACATGTGAAAACAT-ACTGCCGAAAGTTCTTATAAAAGGCCCGAAGGATTTATGATCTTGCTCA
1 GACATGTGAAAACATCA-TGCCCAAAGGTCTTATGGATGGCCTGAAGGACTTATCATCTTGCTCG
* * * * ** *
581008 AAATACTTACAGATAACCCGAATGATTTAAGAATCAAACTCGAAAGACTTACTGATGACCCGAAG
65 AAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATG-GCCGAAG
* *
581073 GACTTAT-AATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTATAAAAAATTTCAAT
129 GACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAAT
581137 TTTCAAATTTGAATGAGAAACCTTTCTCATTTTTCGAGA
194 TTTCAAATTTGAATGAGAAACCTTTCTCATTTTTCGAGA
* * * ** * * * *
581176 GACGTATGAAAACATCCTGCCTGAATGTCTTATGGATGGCCTAAAAGACTTATCATCTTACTCGA
1 GACATGTGAAAACATCATGCCCAAAGGTCTTATGGATGGCCTGAAGGACTTATCATCTTGCTCGA
* * * *
581241 AAGACTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATAGCCCAAAGA
66 AAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCGAAGGA
*
581306 CTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTAC-TTTCAAAAAATATCAATT
131 CTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTC-AAAAATTTCAATT
* * *
581370 TTCAAATTTAAATAAGAAACCTTTCTCATATTTT-GATA
195 TTCAAATTTGAATGAGAAACCTTTCTCAT-TTTTCGAGA
* * * * * *
581408 GACATG-AAAAATATCATGCCGAAAGGTCTTAAGGATGGCTTGAAGTACTTATCATCTTGCTCTG
1 GACATGTGAAAACATCATGCCCAAAGGTCTTATGGATGGCCTGAAGGACTTATCATCTTGCTC-G
* * * *
581472 -AAGGCTTACAGATGACCCGTAGGATTTAGGCATCATGCTCAAAAGACTTACTGATGGCCCGAAG
65 AAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGG-CCGAAG
* *
581536 GACTTATAAA-TTT-GAAATTAGTTTACTATGTAAGAAACCATTCTTACTTTTCAAAAATTTCAA
129 GACTTATAAATTTTGGAAA-TAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAA
581599 ATTTGATTGA
Statistics
Matches: 960, Mismatches: 145, Indels: 35
0.84 0.13 0.03
Matches are distributed among these distances:
230 4 0.00
231 148 0.15
232 245 0.26
233 416 0.43
234 145 0.15
235 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (232 bp):
GACATGTGAAAACATCATGCCCAAAGGTCTTATGGATGGCCTGAAGGACTTATCATCTTGCTCGA
AAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCGAAGGA
CTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTT
TCAAATTTGAATGAGAAACCTTTCTCATTTTTCGAGA
Found at i:588326 original size:6 final size:6
Alignment explanation
Indices: 588317--588364 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
588307 GAAAAATAAA
* *
588317 AATATT AATATT AATTAAT AAT-TAT AATAAT AATATT AATATT AATAT
1 AATATT AATATT AA-TATT AATAT-T AATATT AATATT AATATT AATAT
588365 CAAATGGGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 30 0.86
7 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
AATATT
Found at i:588517 original size:38 final size:40
Alignment explanation
Indices: 588470--588549 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 40
588460 TTTGAAATAT
*
588470 GATAAGGGAT-A-TGTTCCGCTGTTACTCAGGGAATATCA
1 GATAAGGGATAACTGTTCCGCTGTCACTCAGGGAATATCA
* *
588508 GATATGGGATAGACTTGTTCCGTTGTCACTCAGGGAATATCA
1 GATAAGGGATA-AC-TGTTCCGCTGTCACTCAGGGAATATCA
588550 AATCTTGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
38 9 0.26
40 1 0.03
42 25 0.71
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (40 bp):
GATAAGGGATAACTGTTCCGCTGTCACTCAGGGAATATCA
Found at i:589187 original size:234 final size:234
Alignment explanation
Indices: 588570--589961 Score: 1694
Period size: 234 Copynumber: 6.0 Consensus size: 234
588560 AAGAGGGACC
*
588570 TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGTCCA-AAAGAATTATCATCTTGCTC-AACA
1 TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGG-CCAGAAAGACTTATCATCTTGCTCGAA-A
* * * *
588633 GACTTACAAATGACCCAAAGGATTTAAGCATCATGCTCAAAAGAGTTACTGATTG-CCTGAAGGA
64 GACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGACC-GAAGGA
* * * ***
588697 CTTATAAATTATGGAAATAGTTTACTAAGTAAGAAACCTTTCTTACTTTTTGAAAAA-AAAATTA
128 CTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTAC-TTTTCAAAAATTTCA-TA
* * *
588761 TTTTCAAATTTGAATAAGAAACCTTTCTCATTTTTCGAGAGACA
191 TTTTTAAATTTGAATGAGAAACCTTTCTCATTTTTTGAGAGACA
* * *
588805 TGTGAAAACATCATGCCCAAAGGTCTTATGGATGGGCC-GAAGGACTTACCATCTTGCTCGAAAG
1 TGTGAAAACATCCTGCCCAAAGGTCTTATGGAT-GGCCAGAAAGACTTATCATCTTGCTCGAAAG
* * * * * *
588869 ACTTAGAGATGACCGACCCAAAGGATTTAGGCATCATGCTAAAAAAGACTTATTGAAGG-CTCGA
65 ACTTACAGAT----GACCCGAAGGATTTAAGCATCATGCT-CAAAAGACTTACTGATGGAC-CGA
* * * *
588933 AGGAATTATAAATTTTGGAAATAGTTTTCTATGTTAGAAACCATTT-TTACTTTTCAAAAATTT-
124 AGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACC-TTTCTTACTTTTCAAAAATTTC
** * *
588996 ATATTTGCAAATATGAATGAGAAACCTTTCTCATTTTTTGAGAGATA
188 ATATTTTTAAATTTGAATGAGAAACCTTTCTCATTTTTTGAGAGACA
* * * * *
589043 TGTGAAAACATCTTACCCTGAAGGACTTATGGATGGCCAGAAAGACTTATCATCTTTCTCGAAAG
1 TGTGAAAACATCCTGCCC-AAAGGTCTTATGGATGGCCAGAAAGACTTATCATCTTGCTCGAAAG
* * * *
589108 AATTATAGATGACCCGAAGGATTTAAGAATCATGCTCAAAAGACTTGCTGATGGACCGAAGGACT
65 ACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGACCGAAGGACT
* * *
589173 TATAAATTTTGGAAATAGATTACTAGGTAAGAAACCTTTCTTAGTTTTCAAAAATTTCAAATTTT
130 TATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCATATTTT
* * * * *
589238 TAGAA-TTAAATAAGAAACCTTTCTCATATTTCGATAGACA
195 TA-AATTTGAATGAGAAACCTTTCTCATTTTTTGAGAGACA
* * * * * * * * *
589278 TATGAAAATATACTGCCGAAAGGTCTTATGGATTGCCCGAATGATTTATCATCTTGCTCAAAAGA
1 TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCAGAAAGACTTATCATCTTGCTCGAAAGA
*
589343 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGAT-GACCCGAAGGACT
66 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGA-CCGAAGGACT
*
589407 TAT-AATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCA-ATTTT
130 TATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCATATTTT
*
589470 TAAATTTGAATGAGAAACCTTTCTCATTTTTTGAGAGACG
195 TAAATTTGAATGAGAAACCTTTCTCATTTTTTGAGAGACA
* *
589510 TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCC-TAAAGAACTTATCATCTTGCTTGAAAG
1 TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCAGAAAG-ACTTATCATCTTGCTCGAAAG
* * * * * * * *
589574 GCTTACAGATGACCCGAAGGATTTAAGGATCATCCTCGAAATACTTACTAATGGTCCGAAGAACT
65 ACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGACCGAAGGACT
*
589639 TATAAAATTTT-GAAATAGTTTACTAGGTTAGAAACCTTTCTTACTTTT-AAAAATTTTCA-ATT
130 TAT-AAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAA-TTTCATATT
* * *
589701 TTTAAATTTAAATGAGAAACCTTTCTCATATTTTGATAGACA
193 TTTAAATTTGAATGAGAAACCTTTCTCATTTTTTGAGAGACA
** * * *
589743 --CAAAAACATCCTTCCCAAAGGTCTTAAGGATGGCCAGAATGACTTATCATCTTGCTCTG-AAG
1 TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCAGAAAGACTTATCATCTTGCTC-GAAAG
*
589805 TCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGAT-GACCCGAAGGAC
65 ACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGA-CCGAAGGAC
* * *
589869 TTATAAA-TTTGAAAATAGTTTACTAGGTAAGAAACCGTTCTTACATTTCAAAAATTTCA-ATTT
129 TTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCATATTT
589932 TTAAATTTGAATGAGAAACCTTTCTCATTT
194 TTAAATTTGAATGAGAAACCTTTCTCATTT
589962 CATTTTCTTT
Statistics
Matches: 999, Mismatches: 129, Indels: 63
0.84 0.11 0.05
Matches are distributed among these distances:
229 3 0.00
230 74 0.07
231 117 0.12
232 154 0.15
233 139 0.14
234 174 0.17
235 131 0.13
236 6 0.01
238 61 0.06
239 79 0.08
240 57 0.06
241 4 0.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (234 bp):
TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCAGAAAGACTTATCATCTTGCTCGAAAGA
CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGACCGAAGGACTT
ATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCATATTTTT
AAATTTGAATGAGAAACCTTTCTCATTTTTTGAGAGACA
Found at i:589386 original size:42 final size:41
Alignment explanation
Indices: 589313--589404 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 41
589303 TTATGGATTG
* * *
589313 CCCGAATGATTTATCATCTTGCTCAAAAGACTTACAGATGA
1 CCCGAAGGATTTAGCATCATGCTCAAAAGACTTACAGATGA
* *
589354 CCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGA
1 CCCGAAGGATTT-AGCATCATGCTCAAAAGACTTACAGATGA
589396 CCCGAAGGA
1 CCCGAAGGA
589405 CTTATAATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 11 0.24
42 34 0.76
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.24
Consensus pattern (41 bp):
CCCGAAGGATTTAGCATCATGCTCAAAAGACTTACAGATGA
Found at i:589406 original size:20 final size:20
Alignment explanation
Indices: 589341--589408 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
589331 TTGCTCAAAA
*
589341 GACTTACAGATGACCCGAAG
1 GACTTACTGATGACCCGAAG
* * * *
589361 GATTTAAGCATCATG-CTCGAAA
1 GACTT-A-C-TGATGACCCGAAG
589383 GACTTACTGATGACCCGAAG
1 GACTTACTGATGACCCGAAG
589403 GACTTA
1 GACTTA
589409 TAATTTTGGA
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
19 4 0.11
20 16 0.46
21 2 0.06
22 10 0.29
23 3 0.09
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (20 bp):
GACTTACTGATGACCCGAAG
Found at i:589871 original size:463 final size:459
Alignment explanation
Indices: 588570--589961 Score: 1742
Period size: 463 Copynumber: 3.0 Consensus size: 459
588560 AAGAGGGACC
*
588570 TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGTCCAAAAGAA-TTATCATCTTGC-TCAACA
1 TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGG-CCAAAAGAACTTATCATCTTGCTTGAA-A
* * * * *
588633 GACTTACAAATGACCCAAAGGATTTAAGCATCATGCTCAAAAGAGTTACTGATTGCCTGAAGGAC
64 GACTTACAGATGACCCGAAGGATTTAAGAATCATGCTCAAAAGACTTACTGATGGCC-GAAGGAC
* * *
588698 TTATAAATTATGGAAATAGTTTACTAAGTAAGAAACCTTTCTTACTTTTTGAAAAAAAAATT--A
128 TTATAAATT-TTGAAATAGTTTACTAGGTAAGAAACCTTTCTTAC-TTTT---AAAAAATTTCAA
* * * * *
588761 TTTTCAAATTTGAATAAGAAACCTTTCTCAT-TTTTCGAGAGACATGTGAAAACATCATGCCCAA
188 TTTTTAAATTTAAATAAGAAACCTTTCTCATATTTT-GATAGACA--TAAAAACATCCTGCCCAA
* * * *
588825 AGGTCTTATGGATGGGCCGAAGGACTTACCATCTTGCTCGAAAGACTTAGAGATGACCGACCCAA
250 AGGTCTTATGGAT-GGCCGAATGACTTATCATCTTGCTCG-AAGACTTACAGAT----GACCCGA
* * * * * * *
588890 AGGATTTAGGCATCATGCTAAAAAAGACTTATTGAAGGCTCGAAGGAATTATAAATTTTGGAAAT
309 AGGATTTAAGCATCATGCT-CAAAAGACTTACTGATGACCCGAAGGACTTAT-AATTTTGGAAAT
* * ** *
588955 AGTTTT-CTATGTTAGAAACCATTT-TTACTTTTCAAAAATTT-ATATTTGCAAATATGAATGAG
372 A-TTTTACTAGGTAAGAAACC-TTTCTTACTTTTCAAAAATTTCA-ATTTTTAAATTTGAATGAG
*
589017 AAACCTTTCTCATTTTTTGAGAGATA
434 AAACCTTTCTCATTTTTTGAGAGACA
* * * * * *
589043 TGTGAAAACATCTTACCCTGAAGGACTTATGGATGGCCAGAAAG-ACTTATCATCTTTCTCGAAA
1 TGTGAAAACATCCTGCCC-AAAGGTCTTATGGATGGCCA-AAAGAACTTATCATCTTGCTTGAAA
* * *
589107 GAATTATAGATGACCCGAAGGATTTAAGAATCATGCTCAAAAGACTTGCTGATGGACCGAAGGAC
64 GACTTACAGATGACCCGAAGGATTTAAGAATCATGCTCAAAAGACTTACTGATGG-CCGAAGGAC
* * *
589172 TTATAAATTTTGGAAATAGATTACTAGGTAAGAAACCTTTCTTAGTTTTCAAAAATTTCAAATTT
128 TTATAAATTTT-GAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTAAAAAATTTC-AATTT
* * * *
589237 TTAGAA-TTAAATAAGAAACCTTTCTCATATTTCGATAGACATATGAAAATATACTGCCGAAAGG
191 TTA-AATTTAAATAAGAAACCTTTCTCATATTTTGATAGACATA--AAAACATCCTGCCCAAAGG
* * *
589301 TCTTATGGATTGCCCGAATGATTTATCATCTTGCTCAAAAGACTTACAGATGACCCGAAGGATTT
253 TCTTATGGA-TGGCCGAATGACTTATCATCTTGCTC-GAAGACTTACAGATGACCCGAAGGATTT
*
589366 AAGCATCATGCTCGAAAGACTTACTGATGACCCGAAGGACTTATAATTTTGGAAATATTTTACTA
316 AAGCATCATGCTCAAAAGACTTACTGATGACCCGAAGGACTTATAATTTTGGAAATATTTTACTA
589431 GGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTTAAATTTGAATGAGAAACCTTTCTCA
381 GGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTTAAATTTGAATGAGAAACCTTTCTCA
*
589496 TTTTTTGAGAGACG
446 TTTTTTGAGAGACA
* *
589510 TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCTAAAGAACTTATCATCTTGCTTGAAAGG
1 TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCAAAAGAACTTATCATCTTGCTTGAAAGA
* * * * * *
589575 CTTACAGATGACCCGAAGGATTTAAGGATCATCCTCGAAATACTTACTAATGGTCCGAAGAACTT
66 CTTACAGATGACCCGAAGGATTTAAGAATCATGCTCAAAAGACTTACTGATGG-CCGAAGGACTT
* *
589640 ATAAAATTTTGAAATAGTTTACTAGGTTAGAAACCTTTCTTACTTTTAAAAATTTTCAATTTTTA
130 AT-AAATTTTGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTAAAAAATTTCAATTTTTA
* * * *
589705 AATTTAAATGAGAAACCTTTCTCATATTTTGATAGACACAAAAACATCCTTCCCAAAGGTCTTAA
194 AATTTAAATAAGAAACCTTTCTCATATTTTGATAGACATAAAAACATCCTGCCCAAAGGTCTTAT
*
589770 GGATGGCCAGAATGACTTATCATCTTGCTCTGAAGTCTTACAGATGACCCGAAGGATTTAAGCAT
259 GGATGGCC-GAATGACTTATCATCTTGCTC-GAAGACTTACAGATGACCCGAAGGATTTAAGCAT
* * *
589835 CATGCTCAAAAGACTTACTGATGACCCGAAGGACTTATAAATTTGAAAATAGTTTACTAGGTAAG
322 CATGCTCAAAAGACTTACTGATGACCCGAAGGACTTATAATTTTGGAAATATTTTACTAGGTAAG
* *
589900 AAACCGTTCTTACATTTCAAAAATTTCAATTTTTAAATTTGAATGAGAAACCTTTCTCATTT
387 AAACCTTTCTTACTTTTCAAAAATTTCAATTTTTAAATTTGAATGAGAAACCTTTCTCATTT
589962 CATTTTCTTT
Statistics
Matches: 803, Mismatches: 94, Indels: 54
0.84 0.10 0.06
Matches are distributed among these distances:
462 4 0.00
463 196 0.24
464 2 0.00
465 46 0.06
466 142 0.18
467 105 0.13
468 26 0.03
469 24 0.03
470 7 0.01
471 1 0.00
473 116 0.14
474 130 0.16
475 4 0.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (459 bp):
TGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCAAAAGAACTTATCATCTTGCTTGAAAGA
CTTACAGATGACCCGAAGGATTTAAGAATCATGCTCAAAAGACTTACTGATGGCCGAAGGACTTA
TAAATTTTGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTAAAAAATTTCAATTTTTAAA
TTTAAATAAGAAACCTTTCTCATATTTTGATAGACATAAAAACATCCTGCCCAAAGGTCTTATGG
ATGGCCGAATGACTTATCATCTTGCTCGAAGACTTACAGATGACCCGAAGGATTTAAGCATCATG
CTCAAAAGACTTACTGATGACCCGAAGGACTTATAATTTTGGAAATATTTTACTAGGTAAGAAAC
CTTTCTTACTTTTCAAAAATTTCAATTTTTAAATTTGAATGAGAAACCTTTCTCATTTTTTGAGA
GACA
Found at i:597079 original size:233 final size:231
Alignment explanation
Indices: 596665--599182 Score: 3085
Period size: 233 Copynumber: 10.9 Consensus size: 231
596655 AAGAGGGACT
* * *
596665 TGTGAAAACATCCTGCCCAAAAGTCTTATGGATGGCCCGAATGACTTATCATCTTGCTCGAAAGA
1 TGTGAAAACATCATGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
*
596730 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCTGAAGGACTT
66 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCC-GAAGGACTT
** * *
596795 ATAAATTTTGGAAATAGTTTACTAAATCAA-AAACCTATCTTACTATTCAAAAATTTCAATTTTC
130 ATAAATTTTGGAAATAGTTTACTAGGT-AAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTC
*
596859 AAATTTGAAAGAGAAACCTTTCTCATTTTGCAAGAGACA
194 AAATTTGAAAGAGAAACCTTTCTCATTTT-CGAGAGACA
* *
596898 TGTGAAAACATCATGCCCAAAGGTCTTATGAATGGCCCGAAGGACTTATCAACTTGCTCGAAAGA
1 TGTGAAAACATCATGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
* * *
596963 GTTACAGATGACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCTCAAAGGACTT
66 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGC-CGAAGGACTT
* * * * *
597028 ATAAATTTTGGAAATAGTTTTCTACGTAAGAAACCTTTCTTATTTTTCAAAAAAATTCTATTTTC
130 ATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTC-AAAAATTTCAATTTTC
* * *
597093 AAATTTGAATGAGAAACCTTTCTCATTTTTTGAGATACA
194 AAATTTGAAAGAGAAACCTTTCTCA-TTTTCGAGAGACA
* * * *
597132 TGTGAAAACATCCTACCCGAAGGACTTATGGAT--------GG---------C---C-CGAAAGA
1 TGTGAAAACATCATGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
* * *
597176 CTTACAGATGACTCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTAATGGCCGAAGGACTTA
66 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCGAAGGACTTA
* *
597241 TAAATTTTGGAAATAGTTTACTAGATAAGAAACATTTCTTACTTTTCAAAAATTTCAAATTTTCA
131 TAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTC-AATTTTCA
* * * *
597306 GATTT-AAATGAGAAACATTTCTTATATTTCGATAGACA
195 AATTTGAAA-GAGAAACCTTTCTCAT-TTTCGAGAGACA
* * * * *
597344 TGTGAAAACAT-ACTGTCGAAAGGTATTATTGATGGCCCGAAGGACTTATCATCTTGCTAGAAAG
1 TGTGAAAACATCA-TGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAG
* * *
597408 ACTTACAGATGACCCGAAGGATTTAAGCATCATGTTTGAAAGACTTACTGATGACCCGAAGGACT
65 ACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATG-GCCGAAGGACT
* *
597473 TCT-AATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTT
129 TATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTC
* **
597537 AAATTTGAATGAGAAACCTTTCTCATTTTCGAGAGATG
194 AAATTTGAAAGAGAAACCTTTCTCATTTTCGAGAGACA
* * * * *
597575 TGTTAAAACATCTTGCTCGAAGGTCTTATGGATGG-CCGAAGGACTTATCATCTTGGTCGAAAGA
1 TGTGAAAACATCATGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
* *
597639 CTTACAAATGACTCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCTCGAATGG-CT
66 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGC-CGAA-GGACT
* *
597703 TATAAATTTTGGAAATAGTTTACTAGGTTAGAAACCTTTCTTAC-TTTCAAAAATTTCAATTTAC
129 TATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTC
* * **
597767 AAATTT-AAATGAGAAACGTTTCTCATATTTTGATTGACA
194 AAATTTGAAA-GAGAAACCTTTCTCAT-TTTCGAGAGACA
* * *
597806 --TGAAAATATCCTGCCCAAAGGTCTTAAGGATGGCCCGAAGGACTTATCATCTT-CATCGAAAG
1 TGTGAAAACATCATGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGC-TCGAAAG
*
597868 ACTTACAGATGACCCGAAAGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACT
65 ACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGG-CCGAAGGACT
* *
597933 TATAAA-TTTGAAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT-AAACAATTTTCTATTT
129 TATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAA-AA-TTTCAATTT
* * *
597996 TCAAATTTGAATGAGAAACCTTTCTCATTTTTTGAGATACA
192 TCAAATTTGAAAGAGAAACCTTTCTCA-TTTTCGAGAGACA
* * *
598037 TGTGAAAAAATCATACCCGAAA-GACTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAG
1 TGTGAAAACATCATGCCC-AAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAG
* * * *
598101 ACTTACAGATGACCCGAAGGATTTAAGCATCATGCTTGAAAGACTTATTGATGGTCGAATGACTT
65 ACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCGAAGGACTT
* * *
598166 ATAAATTTTGGAAATACTTTACTAGGTAAGAAACCTTTCTTAATTTTCAAAATTTTCAAATTTTC
130 ATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTC-AATTTTC
* * *
598231 AGATTT-AAATGAGAAA-C-ATCTCATATTTCGATAGACA
194 AAATTTGAAA-GAGAAACCTTTCTCAT-TTTCGAGAGACA
* * * * * * * *
598268 TGTGAAAACATCCTGTCGAAAGGTATTATGGATGGCCCGAATGACTTATTATATTGCTAGAAAGA
1 TGTGAAAACATCATGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
* * *
598333 CTTACTTG-TGACCCGAAGGATTTAAGCATCATGCTTGAAAGACTTACTGATGACCCGAAGGACT
66 CTTAC-AGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATG-GCCGAAGGACT
** * * * *
598397 TAT-AATTTTAAAAATAGTTTATTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTAAAATTTA
129 TATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTC
*
598461 AAATTTGAATA-AGAAACCTTTCTCATTTTTCGAGAGACG
194 AAATTTGAA-AGAGAAACCTTTCTCA-TTTTCGAGAGACA
** * * *
598500 TGTTTAAACATCTTTCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
1 TGTGAAAACATCATGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
* **
598565 CTTATAGATGACTTGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCAGAAGGACTT
66 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCC-GAAGGACTT
* * * *
598630 ATAAATTTTGGAAATACTTTACTAGGTAAGAAAACTTTCTTAATTTTCAAAATTTTCAAATTTTC
130 ATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTC-AATTTTC
* *
598695 AGATTT-AAATGAGAAACCTTTCTCATATTTCGATAGACA
194 AAATTTGAAA-GAGAAACCTTTCTCAT-TTTCGAGAGACA
* * * * * * * *
598734 TGTGAAAGCATCCTGTCGAAAGGTATTATGGATGGCCCGAATGACTTATTATCTTGCTAGAAAGA
1 TGTGAAAACATCATGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
* * *
598799 CTTACTTG-TGACCCGAAGGATTTAAGCATCATGCTTGAAAGACTTACTGATGACCCGAAGGACT
66 CTTAC-AGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATG-GCCGAAGGACT
* * * * * * *
598863 TAT-AATTTTGGAAATAGTTTATTAGGTAAGAAAACTTTCTTACATTTCAAAAATTTAAAATCTA
129 TATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTC
*
598927 AAATTTGAATA-AGAAACCTTTCTCATTTTTCGAGAGACG
194 AAATTTGAA-AGAGAAACCTTTCTCA-TTTTCGAGAGACA
** * *
598966 TGTTTAAACATCTTGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
1 TGTGAAAACATCATGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
* *
599031 CTTATAGATGACTCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCAGAAGGACTT
66 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCC-GAAGGACTT
* * *
599096 ATAAATTTTGGAAACAATTTACTAGGTAAGAAACCTTTCTTAATTTTCAAAAATTTCAATTTTCA
130 ATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCA
599161 AATTT-AAATGAGAAACCTTTCT
195 AATTTGAAA-GAGAAACCTTTCT
599183 TAATTTTCAA
Statistics
Matches: 1951, Mismatches: 254, Indels: 160
0.82 0.11 0.07
Matches are distributed among these distances:
211 11 0.01
212 109 0.06
213 56 0.03
214 1 0.00
217 1 0.00
220 2 0.00
226 2 0.00
229 71 0.04
230 235 0.12
231 291 0.15
232 336 0.17
233 593 0.30
234 236 0.12
235 7 0.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (231 bp):
TGTGAAAACATCATGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCGAAGGACTTA
TAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAA
ATTTGAAAGAGAAACCTTTCTCATTTTCGAGAGACA
Found at i:597185 original size:20 final size:20
Alignment explanation
Indices: 597147--597185 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
597137 AAACATCCTA
* **
597147 CCCGAAGGACTTATGGATGG
1 CCCGAAAGACTTACAGATGG
597167 CCCGAAAGACTTACAGATG
1 CCCGAAAGACTTACAGATG
597186 ACTCGAAGGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.23, G:0.28, T:0.18
Consensus pattern (20 bp):
CCCGAAAGACTTACAGATGG
Found at i:597424 original size:41 final size:42
Alignment explanation
Indices: 597374--597473 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
597364 AGGTATTATT
* * *
597374 GATGGCCCGAAGGACTT-ATCATCTTGCTAGAAAGACTTACA
1 GATGACCCGAAGGACTTAAGCATCATGCTAGAAAGACTTACA
* * * *
597415 GATGACCCGAAGGATTTAAGCATCATGTTTGAAAGACTTACT
1 GATGACCCGAAGGACTTAAGCATCATGCTAGAAAGACTTACA
597457 GATGACCCGAAGGACTT
1 GATGACCCGAAGGACTT
597474 CTAATTTTGG
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
41 15 0.30
42 35 0.70
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (42 bp):
GATGACCCGAAGGACTTAAGCATCATGCTAGAAAGACTTACA
Found at i:597696 original size:42 final size:41
Alignment explanation
Indices: 597583--597697 Score: 117
Period size: 42 Copynumber: 2.8 Consensus size: 41
597573 TGTGTTAAAA
* * *
597583 CATCTTGCTCGAAGGTCTTA-TGGATGGC-CGAAGGACTTAT
1 CATCTTGCTCGAAAGACTTACT-GATGGCTCGAAGGACTTAG
* ** * *
597623 CATCTTGGTCGAAAGACTTACAAATGACTCGAAGGATTTAAG
1 CATCTTGCTCGAAAGACTTACTGATGGCTCGAAGGACTT-AG
*
597665 CATCATGCTCGAAAGACTTACTGATGGCTCGAA
1 CATCTTGCTCGAAAGACTTACTGATGGCTCGAA
597698 TGGCTTATAA
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
40 21 0.36
41 9 0.15
42 29 0.49
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (41 bp):
CATCTTGCTCGAAAGACTTACTGATGGCTCGAAGGACTTAG
Found at i:597887 original size:20 final size:20
Alignment explanation
Indices: 597862--597934 Score: 58
Period size: 20 Copynumber: 3.5 Consensus size: 20
597852 TCATCTTCAT
597862 CGAAAGACTTACAGATGACC
1 CGAAAGACTTACAGATGACC
* * *
597882 CGAAAGATTTA-AGCATCATGCT
1 CGAAAGACTTACAG-ATGA--CC
* *
597904 CGAAAGACTTACTGATGGCC
1 CGAAAGACTTACAGATGACC
*
597924 CGAAGGACTTA
1 CGAAAGACTTA
597935 TAAATTTGAA
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
19 2 0.05
20 24 0.60
22 13 0.32
23 1 0.03
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.21
Consensus pattern (20 bp):
CGAAAGACTTACAGATGACC
Found at i:598100 original size:41 final size:41
Alignment explanation
Indices: 598054--598167 Score: 122
Period size: 41 Copynumber: 2.8 Consensus size: 41
598044 AAATCATACC
* *
598054 CGAAAGACTTATGGATGGCCCGAAGGACTTATCATCTTGCT
1 CGAAAGACTTATAGATGGCCCGAAGGACTTATCATCATGCT
* * * *
598095 CGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCT
1 CGAAAGACTTATAGATGGCCCGAAGGACTT-ATCATCATGCT
* * * *
598137 TGAAAGACTTATTGATGG-TCGAATGACTTAT
1 CGAAAGACTTATAGATGGCCCGAAGGACTTAT
598168 AAATTTTGGA
Statistics
Matches: 58, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
40 1 0.02
41 34 0.59
42 23 0.40
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (41 bp):
CGAAAGACTTATAGATGGCCCGAAGGACTTATCATCATGCT
Found at i:598348 original size:41 final size:41
Alignment explanation
Indices: 598298--598399 Score: 109
Period size: 42 Copynumber: 2.5 Consensus size: 41
598288 AGGTATTATG
* * *
598298 GATGGCCCGAATGACTTATTAT-ATTGCTAGAAAGACTTACTT
1 GATGACCCGAAGGACTTATCATCA-TGCTAGAAAGACTTAC-T
* * *
598340 G-TGACCCGAAGGATTTAAGCATCATGCTTGAAAGACTTACT
1 GATGACCCGAAGGACTT-ATCATCATGCTAGAAAGACTTACT
598381 GATGACCCGAAGGACTTAT
1 GATGACCCGAAGGACTTAT
598400 AATTTTAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
41 15 0.31
42 33 0.67
43 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (41 bp):
GATGACCCGAAGGACTTATCATCATGCTAGAAAGACTTACT
Found at i:598625 original size:42 final size:41
Alignment explanation
Indices: 598524--598630 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 41
598514 TCCCGAAGGT
* * * *
598524 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
1 CTTATAGATGGCCAGAAGGACTTAGCATCATGCTCGAAAGA
* ** *
598565 CTTATAGATGACTTGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGGCCAGAAGGACTT-AGCATCATGCTCGAAAGA
598607 CTTACT-GATGGCCAGAAGGACTTA
1 CTTA-TAGATGGCCAGAAGGACTTA
598631 TAAATTTTGG
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
41 19 0.36
42 33 0.62
43 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (41 bp):
CTTATAGATGGCCAGAAGGACTTAGCATCATGCTCGAAAGA
Found at i:598814 original size:41 final size:41
Alignment explanation
Indices: 598764--598865 Score: 116
Period size: 42 Copynumber: 2.5 Consensus size: 41
598754 AGGTATTATG
* * * *
598764 GATGGCCCGAATGACTTATTATCTTGCTAGAAAGACTTACTT
1 GATGACCCGAAGGACTTATCATCATGCTAGAAAGACTTAC-T
* * *
598806 G-TGACCCGAAGGATTTAAGCATCATGCTTGAAAGACTTACT
1 GATGACCCGAAGGACTT-ATCATCATGCTAGAAAGACTTACT
598847 GATGACCCGAAGGACTTAT
1 GATGACCCGAAGGACTTAT
598866 AATTTTGGAA
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
41 15 0.31
42 34 0.69
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (41 bp):
GATGACCCGAAGGACTTATCATCATGCTAGAAAGACTTACT
Found at i:599091 original size:42 final size:40
Alignment explanation
Indices: 598990--599096 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 40
598980 GCCCGAAGGT
* * *
598990 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
1 CTTATAGATGG-CCGAAGGACTTAGCATCATGCTCGAAAGA
* *
599031 CTTATAGATGACTCGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGGC-CGAAGGACTT-AGCATCATGCTCGAAAGA
599073 CTTACT-GATGGCCAGAAGGACTTA
1 CTTA-TAGATGGCC-GAAGGACTTA
599097 TAAATTTTGG
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
40 1 0.02
41 20 0.36
42 33 0.60
43 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (40 bp):
CTTATAGATGGCCGAAGGACTTAGCATCATGCTCGAAAGA
Found at i:599158 original size:16 final size:16
Alignment explanation
Indices: 599137--599209 Score: 53
Period size: 16 Copynumber: 4.6 Consensus size: 16
599127 AACCTTTCTT
599137 AATTTTCAAAAATTTC
1 AATTTTCAAAAATTTC
599153 AATTTTC--AAATTT-
1 AATTTTCAAAAATTTC
* *** **
599166 AAATGAGAAACCTTTC
1 AATTTTCAAAAATTTC
599182 TTAATTTTCAAAAATTTC
1 --AATTTTCAAAAATTTC
599200 AATTTTCAAA
1 AATTTTCAAA
599210 TTTAAATGAG
Statistics
Matches: 40, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
13 3 0.08
14 6 0.15
15 4 0.10
16 17 0.43
18 10 0.25
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (16 bp):
AATTTTCAAAAATTTC
Found at i:599176 original size:47 final size:47
Alignment explanation
Indices: 599124--599229 Score: 212
Period size: 47 Copynumber: 2.3 Consensus size: 47
599114 TTACTAGGTA
599124 AGAAACCTTTCTTAATTTTCAAAAATTTCAATTTTCAAATTTAAATG
1 AGAAACCTTTCTTAATTTTCAAAAATTTCAATTTTCAAATTTAAATG
599171 AGAAACCTTTCTTAATTTTCAAAAATTTCAATTTTCAAATTTAAATG
1 AGAAACCTTTCTTAATTTTCAAAAATTTCAATTTTCAAATTTAAATG
599218 AGAAACCTTTCT
1 AGAAACCTTTCT
599230 CATATTTTGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 59 1.00
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.42
Consensus pattern (47 bp):
AGAAACCTTTCTTAATTTTCAAAAATTTCAATTTTCAAATTTAAATG
Found at i:599290 original size:278 final size:278
Alignment explanation
Indices: 598891--599452 Score: 826
Period size: 278 Copynumber: 2.0 Consensus size: 278
598881 TTATTAGGTA
*
598891 AGAAAACTTTCTTACATTTCAAAAATTTAAAATCTAAAATTTGAATAAGAAACCTTTCTCATTTT
1 AGAAAACTTTCTTACATTTCAAAAATTTAAAATCTAAAATTTAAATAAGAAACCTTTCTCATTTT
* * * * *
598956 TCGAGAGACGTGTTTAAACATCTTGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTT
66 TCGAGAGACATG-TAAAACATCCTACCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTT
*
599021 GCTCGAAAGACTTATAGATGA-CTCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGC
130 GCTCGAAAGACTTATAGATGACCT-GAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGC
*
599085 CAGAAGGACTTATAAATTTTGGAAACAATTTACTAGGTAAGAAACCTTTCTTAATTTTCAAAAAT
194 CAGAAGGACTTATAAA-TTTGAAAACAATTTACTAGGTAAGAAACCTTTCTTAATTTTCAAAAAT
599150 TTCAATTTTCAAATTTAAATG
258 TTCAATTTTCAAATTTAAATG
* * * * * *
599171 AGAAACCTTTCTTA-ATTTTCAAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCTCATAT
1 AGAAAACTTTCTTACA-TTTCAAAAATTTAAAATCTAAAATTTAAATAAGAAACCTTTCTCAT-T
**
599235 TTT-GATTGACATG-AAAACATCCTACCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCT
64 TTTCGAGAGACATGTAAAACATCCTACCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCT
* *
599298 TTCTCGAAAGGCTTATAGATGACCTGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGC
129 TGCTCGAAAGACTTATAGATGACCTGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGC
* * * * * *
599363 CCGAAGGACTTATAAATTTGAAAATAGTTTACTAGGTAAGAATCCTTTCTTACTTTTCAAAATTT
194 CAGAAGGACTTATAAATTTGAAAACAATTTACTAGGTAAGAAACCTTTCTTAATTTTCAAAAATT
*
599428 TCAATTTTCAAATTTGAATG
259 TCAATTTTCAAATTTAAATG
599448 AGAAA
1 AGAAA
599453 TCATTCTCAT
Statistics
Matches: 254, Mismatches: 25, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
277 67 0.26
278 120 0.47
279 3 0.01
280 60 0.24
281 4 0.02
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (278 bp):
AGAAAACTTTCTTACATTTCAAAAATTTAAAATCTAAAATTTAAATAAGAAACCTTTCTCATTTT
TCGAGAGACATGTAAAACATCCTACCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTG
CTCGAAAGACTTATAGATGACCTGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCA
GAAGGACTTATAAATTTGAAAACAATTTACTAGGTAAGAAACCTTTCTTAATTTTCAAAAATTTC
AATTTTCAAATTTAAATG
Found at i:599370 original size:42 final size:41
Alignment explanation
Indices: 599268--599374 Score: 108
Period size: 42 Copynumber: 2.6 Consensus size: 41
599258 ACCCAAAGGT
* * * * * *
599268 CTTATGGATGGCCCGAAGGACTTATCATCTTTCTCGAAAGG
1 CTTATAGATGGCCCGAAGGACTTAGCATCATGCTCAAAAGA
* * *
599309 CTTATAGATGACCTGAAGGATTTAAGCATCATGCTCAAAAGA
1 CTTATAGATGGCCCGAAGGACTT-AGCATCATGCTCAAAAGA
599351 CTTACT-GATGGCCCGAAGGACTTA
1 CTTA-TAGATGGCCCGAAGGACTTA
599375 TAAATTTGAA
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
41 20 0.38
42 31 0.60
43 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTAGCATCATGCTCAAAAGA
Found at i:602848 original size:13 final size:13
Alignment explanation
Indices: 602832--602865 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
602822 TCTCGAAATG
602832 TTTTTCATTCTCT
1 TTTTTCATTCTCT
* *
602845 TTTTTCTTTTTCT
1 TTTTTCATTCTCT
602858 TTTTTCAT
1 TTTTTCAT
602866 GGAGCATACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTCATTCTCT
Found at i:618065 original size:3 final size:3
Alignment explanation
Indices: 618036--618079 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
618026 GGGATTGAAA
* * *
618036 AAT AAA AAT ATT AAT ATT AATT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT A
618080 TTGAATGGGA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:618067 original size:22 final size:22
Alignment explanation
Indices: 618036--618078 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
618026 GGGATTGAAA
* *
618036 AATAAAAATATTAATATTAATT
1 AATAAAAATAATAATAATAATT
*
618058 AATAATAATAATAATAATAAT
1 AATAAAAATAATAATAATAAT
618079 ATTGAATGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AATAAAAATAATAATAATAATT
Found at i:625719 original size:120 final size:120
Alignment explanation
Indices: 625506--625730 Score: 353
Period size: 120 Copynumber: 1.9 Consensus size: 120
625496 ATATCAAATA
* *
625506 ACTCACCACCTTCACACGACTTCATAACAAAATGGACCGCATTGTCATCCTCATAATTAGCCTTC
1 ACTCACCACCTTCACACGAATTCATAACAAAATGGACCGCATTGTCATCCTCATAAGTAGCCTTC
* * *
625571 AAGGTATCAATATTTGAGTGCTTAGGCAAGCGCAAAGAAATAAAGAAAGAAAGTG
66 AAGGTAACAATATTTGAGTGCTGAGGCAAACGCAAAGAAATAAAGAAAGAAAGTG
* *
625626 ACTCACCACCTTCACAC-AATTCCATAACCAAATGGACTGCATTGTCATCCTCATAAGTAGCCTT
1 ACTCACCACCTTCACACGAATT-CATAACAAAATGGACCGCATTGTCATCCTCATAAGTAGCCTT
* *
625690 CAAGGTAACAATATTTGGGTGCTGAGGCAAATGCAAAGAAA
65 CAAGGTAACAATATTTGAGTGCTGAGGCAAACGCAAAGAAA
625731 GAATGTGACT
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
119 3 0.03
120 92 0.97
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (120 bp):
ACTCACCACCTTCACACGAATTCATAACAAAATGGACCGCATTGTCATCCTCATAAGTAGCCTTC
AAGGTAACAATATTTGAGTGCTGAGGCAAACGCAAAGAAATAAAGAAAGAAAGTG
Found at i:627912 original size:32 final size:31
Alignment explanation
Indices: 627876--627950 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
627866 GGGCCACAGT
* * * *
627876 GCCTACCTAAGAATACATCTTAGGGTTGTAGG
1 GCCTACCTAAGAAT-CATCTCAGGGTCGCAGA
** *
627908 GCCTACCCGAGAATGATCTCAGGGTCGCAGA
1 GCCTACCTAAGAATCATCTCAGGGTCGCAGA
627939 GCCTACCTAAGA
1 GCCTACCTAAGA
627951 GTCACATTAG
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
31 22 0.65
32 12 0.35
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.21
Consensus pattern (31 bp):
GCCTACCTAAGAATCATCTCAGGGTCGCAGA
Done.