Multiple sequence alignment - TraesCS4D01G181900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G181900 chr4D 100.000 3909 0 0 1 3909 317606841 317602933 0.000000e+00 7219.0
1 TraesCS4D01G181900 chr4D 100.000 2294 0 0 4410 6703 317602432 317600139 0.000000e+00 4237.0
2 TraesCS4D01G181900 chr4D 100.000 41 0 0 5394 5434 280308880 280308840 7.210000e-10 76.8
3 TraesCS4D01G181900 chr4A 91.975 3190 151 38 792 3905 157203405 157206565 0.000000e+00 4375.0
4 TraesCS4D01G181900 chr4A 91.860 2371 108 29 4410 6702 157206808 157209171 0.000000e+00 3230.0
5 TraesCS4D01G181900 chr4A 92.922 438 29 2 95 532 157202665 157203100 2.640000e-178 636.0
6 TraesCS4D01G181900 chr4A 83.735 166 22 4 614 776 157202968 157202805 1.160000e-32 152.0
7 TraesCS4D01G181900 chr4A 88.496 113 9 3 4447 4557 528606315 528606205 4.220000e-27 134.0
8 TraesCS4D01G181900 chr4A 88.496 113 9 3 4447 4557 528646297 528646187 4.220000e-27 134.0
9 TraesCS4D01G181900 chr4A 86.179 123 13 4 4419 4539 356552051 356552171 5.460000e-26 130.0
10 TraesCS4D01G181900 chr4B 91.359 1759 94 21 2176 3905 394643200 394641471 0.000000e+00 2353.0
11 TraesCS4D01G181900 chr4B 94.136 1296 50 13 831 2104 394644750 394643459 0.000000e+00 1949.0
12 TraesCS4D01G181900 chr4B 93.562 963 38 8 4996 5943 394640652 394639699 0.000000e+00 1413.0
13 TraesCS4D01G181900 chr4B 90.099 808 37 12 5939 6703 394625758 394624951 0.000000e+00 1009.0
14 TraesCS4D01G181900 chr4B 95.302 596 20 5 4410 5002 394641286 394640696 0.000000e+00 939.0
15 TraesCS4D01G181900 chr4B 86.497 785 97 7 2 782 394707953 394707174 0.000000e+00 854.0
16 TraesCS4D01G181900 chr4B 95.385 65 3 0 2106 2170 394643295 394643231 3.310000e-18 104.0
17 TraesCS4D01G181900 chr3B 85.000 160 17 6 621 776 312195885 312196041 9.000000e-34 156.0
18 TraesCS4D01G181900 chr3B 77.959 245 51 3 220 462 807738943 807738700 4.190000e-32 150.0
19 TraesCS4D01G181900 chr5B 83.237 173 21 7 631 800 490730243 490730410 1.160000e-32 152.0
20 TraesCS4D01G181900 chr5B 88.679 53 5 1 5381 5433 499167797 499167746 5.610000e-06 63.9
21 TraesCS4D01G181900 chr2D 78.903 237 38 5 220 456 522626596 522626820 4.190000e-32 150.0
22 TraesCS4D01G181900 chr2D 94.340 53 3 0 4924 4976 17208600 17208652 1.550000e-11 82.4
23 TraesCS4D01G181900 chr7D 82.486 177 24 6 610 782 85027759 85027586 1.510000e-31 148.0
24 TraesCS4D01G181900 chr7D 97.778 45 1 0 428 472 638174484 638174528 2.000000e-10 78.7
25 TraesCS4D01G181900 chr1B 89.744 117 10 2 4423 4539 576362084 576361970 1.510000e-31 148.0
26 TraesCS4D01G181900 chr1B 81.875 160 18 8 621 774 24136258 24136104 2.540000e-24 124.0
27 TraesCS4D01G181900 chr1B 92.857 56 4 0 260 315 325294520 325294575 1.550000e-11 82.4
28 TraesCS4D01G181900 chr1B 92.105 38 3 0 4856 4893 623732186 623732149 3.000000e-03 54.7
29 TraesCS4D01G181900 chr1B 100.000 28 0 0 4868 4895 680782108 680782081 1.200000e-02 52.8
30 TraesCS4D01G181900 chr7B 91.509 106 8 1 4429 4533 715747187 715747082 1.950000e-30 145.0
31 TraesCS4D01G181900 chr7B 92.157 102 7 1 4431 4531 570465365 570465264 7.010000e-30 143.0
32 TraesCS4D01G181900 chr7B 100.000 41 0 0 428 468 735281959 735281999 7.210000e-10 76.8
33 TraesCS4D01G181900 chr7B 92.157 51 2 2 5385 5433 506624287 506624237 3.350000e-08 71.3
34 TraesCS4D01G181900 chr7B 93.333 45 1 2 5385 5427 228814585 228814629 1.560000e-06 65.8
35 TraesCS4D01G181900 chr1D 83.439 157 21 4 629 782 49429823 49429977 2.520000e-29 141.0
36 TraesCS4D01G181900 chr1A 90.000 110 10 1 4432 4541 489400704 489400812 2.520000e-29 141.0
37 TraesCS4D01G181900 chr6D 82.803 157 22 4 629 782 458065393 458065547 1.170000e-27 135.0
38 TraesCS4D01G181900 chr6D 97.917 48 1 0 4924 4971 221214302 221214255 4.310000e-12 84.2
39 TraesCS4D01G181900 chr3D 82.781 151 21 4 629 776 53560033 53560181 5.460000e-26 130.0
40 TraesCS4D01G181900 chr3D 96.078 51 2 0 4924 4974 43024240 43024290 4.310000e-12 84.2
41 TraesCS4D01G181900 chr3D 92.727 55 4 0 4927 4981 5616163 5616109 5.570000e-11 80.5
42 TraesCS4D01G181900 chr6B 79.268 164 28 5 220 380 392485348 392485508 7.110000e-20 110.0
43 TraesCS4D01G181900 chr6B 90.164 61 2 2 4914 4971 13965304 13965363 7.210000e-10 76.8
44 TraesCS4D01G181900 chr6A 97.917 48 1 0 4924 4971 262044765 262044718 4.310000e-12 84.2
45 TraesCS4D01G181900 chrUn 94.231 52 3 0 4927 4978 272240675 272240624 5.570000e-11 80.5
46 TraesCS4D01G181900 chrUn 92.453 53 3 1 420 472 150682768 150682717 2.590000e-09 75.0
47 TraesCS4D01G181900 chr5A 91.837 49 4 0 5382 5430 345350135 345350183 1.210000e-07 69.4
48 TraesCS4D01G181900 chr5D 91.304 46 4 0 5382 5427 260674940 260674985 5.610000e-06 63.9


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G181900 chr4D 317600139 317606841 6702 True 5728.0 7219 100.000000 1 6703 2 chr4D.!!$R2 6702
1 TraesCS4D01G181900 chr4A 157202665 157209171 6506 False 2747.0 4375 92.252333 95 6702 3 chr4A.!!$F2 6607
2 TraesCS4D01G181900 chr4B 394639699 394644750 5051 True 1351.6 2353 93.948800 831 5943 5 chr4B.!!$R3 5112
3 TraesCS4D01G181900 chr4B 394624951 394625758 807 True 1009.0 1009 90.099000 5939 6703 1 chr4B.!!$R1 764
4 TraesCS4D01G181900 chr4B 394707174 394707953 779 True 854.0 854 86.497000 2 782 1 chr4B.!!$R2 780

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
100 101 0.240145 CGGTCAGTGCGAGTTAGACA 59.760 55.000 0.0 0.0 0.00 3.41 F
1464 1513 0.319125 CTCTTCGAATAGCTCCCGCC 60.319 60.000 0.0 0.0 36.60 6.13 F
1465 1514 0.755698 TCTTCGAATAGCTCCCGCCT 60.756 55.000 0.0 0.0 36.60 5.52 F
1644 1693 1.075374 AGGAAGTGCCACCATTTAGCA 59.925 47.619 0.0 0.0 40.02 3.49 F
3118 3402 1.227674 CCTATGGCACTCGCTTCCC 60.228 63.158 0.0 0.0 38.60 3.97 F
3905 4189 0.107703 TTGTAGCCATTCAGCCCTCG 60.108 55.000 0.0 0.0 0.00 4.63 F
3907 4191 0.750850 GTAGCCATTCAGCCCTCGTA 59.249 55.000 0.0 0.0 0.00 3.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1628 1677 1.075374 TCCTTGCTAAATGGTGGCACT 59.925 47.619 18.45 0.00 35.62 4.40 R
3421 3705 0.032540 CCAACTTCACCAGCCTTTGC 59.967 55.000 0.00 0.00 37.95 3.68 R
3504 3788 6.460781 AGTACATAAAAGACCATTCGACACA 58.539 36.000 0.00 0.00 0.00 3.72 R
3540 3824 4.018415 ACCTGCAACCTTGATATTGGTAGT 60.018 41.667 0.00 0.00 35.17 2.73 R
4510 4804 1.135315 TCCGTCCGGAATTACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35 R
5029 5375 3.117851 TCACCTGTACCACAACCAATTGA 60.118 43.478 7.12 0.00 39.30 2.57 R
5803 6162 3.354089 AGCGTGACAAACAATCTTTGG 57.646 42.857 0.00 0.00 33.92 3.28 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 0.680061 CTAGGCCCTCCCGTCATTAC 59.320 60.000 0.00 0.00 39.21 1.89
40 41 1.520787 GTCATTACGCGTCCTGGGG 60.521 63.158 18.63 0.37 34.15 4.96
50 51 2.610859 TCCTGGGGCCTCTTGTCC 60.611 66.667 3.07 0.00 0.00 4.02
53 54 3.612247 CTGGGGCCTCTTGTCCACG 62.612 68.421 3.07 0.00 0.00 4.94
57 58 2.426023 GCCTCTTGTCCACGTGGT 59.574 61.111 32.74 0.00 36.34 4.16
60 61 0.600255 CCTCTTGTCCACGTGGTCAC 60.600 60.000 30.14 23.63 33.15 3.67
88 89 2.438975 CCATGCATGCCGGTCAGT 60.439 61.111 21.69 0.00 0.00 3.41
100 101 0.240145 CGGTCAGTGCGAGTTAGACA 59.760 55.000 0.00 0.00 0.00 3.41
201 203 4.692625 CAGTTCACCGAAAGAATCATGACT 59.307 41.667 0.00 0.00 0.00 3.41
254 257 7.768582 ACGTTGATGGTCATTGAACTTATCATA 59.231 33.333 2.91 0.00 38.03 2.15
300 303 9.937175 GTACTTAAGAATACGATTAGTACGGTT 57.063 33.333 10.09 0.00 38.29 4.44
371 374 3.713288 TCCGTATTCCAGCTATTTGACG 58.287 45.455 0.00 0.00 0.00 4.35
386 389 2.350057 TGACGGGTCAAACAATCCAA 57.650 45.000 0.00 0.00 36.53 3.53
387 390 1.950909 TGACGGGTCAAACAATCCAAC 59.049 47.619 0.00 0.00 36.53 3.77
424 427 7.663493 TCAGCTCATTTTCTCTCTCGATCTATA 59.337 37.037 0.00 0.00 0.00 1.31
459 462 1.070134 CAGTGGGTGGACGAAAGAAGA 59.930 52.381 0.00 0.00 0.00 2.87
497 500 0.738975 CGAGACCTCGCACTTATGGA 59.261 55.000 6.49 0.00 46.50 3.41
511 514 0.322456 TATGGACCAACTGCACCTGC 60.322 55.000 0.00 0.00 42.50 4.85
515 518 3.052082 CCAACTGCACCTGCCTCG 61.052 66.667 0.00 0.00 41.18 4.63
548 552 4.870991 CGACCAGAGGAGAAATCCTTTTAC 59.129 45.833 0.00 0.00 40.86 2.01
551 555 5.112686 CCAGAGGAGAAATCCTTTTACTCG 58.887 45.833 0.00 0.00 40.86 4.18
560 564 6.715264 AGAAATCCTTTTACTCGTTCAACCAT 59.285 34.615 0.00 0.00 0.00 3.55
564 568 5.237779 TCCTTTTACTCGTTCAACCATTCAC 59.762 40.000 0.00 0.00 0.00 3.18
580 584 4.938832 CCATTCACGTAACAACCATTAGGA 59.061 41.667 0.00 0.00 38.69 2.94
597 601 6.128580 CCATTAGGATTTTTCTTTTTGCGTGG 60.129 38.462 0.00 0.00 36.89 4.94
601 605 2.217429 TTTTCTTTTTGCGTGGGAGC 57.783 45.000 0.00 0.00 37.71 4.70
607 611 0.825425 TTTTGCGTGGGAGCCATTGA 60.825 50.000 0.00 0.00 35.28 2.57
618 622 2.427453 GGAGCCATTGAACTCTACGAGA 59.573 50.000 0.00 0.00 33.32 4.04
619 623 3.440228 GAGCCATTGAACTCTACGAGAC 58.560 50.000 0.00 0.00 33.32 3.36
659 663 6.645306 TGACCGGTCAAATAGATGAAATACA 58.355 36.000 34.60 5.64 36.53 2.29
662 666 7.509546 ACCGGTCAAATAGATGAAATACAGAT 58.490 34.615 0.00 0.00 0.00 2.90
698 702 8.000780 TGGATGATCGTATAATATCACCTCAG 57.999 38.462 1.40 0.00 35.06 3.35
699 703 7.615757 TGGATGATCGTATAATATCACCTCAGT 59.384 37.037 1.40 0.00 35.06 3.41
714 718 7.809546 TCACCTCAGTATGTATAGAGAACTG 57.190 40.000 8.21 8.21 39.10 3.16
715 719 6.263392 TCACCTCAGTATGTATAGAGAACTGC 59.737 42.308 9.23 0.00 37.94 4.40
716 720 6.039829 CACCTCAGTATGTATAGAGAACTGCA 59.960 42.308 9.23 0.00 37.94 4.41
717 721 6.780031 ACCTCAGTATGTATAGAGAACTGCAT 59.220 38.462 9.23 0.00 37.94 3.96
718 722 7.288852 ACCTCAGTATGTATAGAGAACTGCATT 59.711 37.037 9.23 0.00 37.94 3.56
719 723 7.598118 CCTCAGTATGTATAGAGAACTGCATTG 59.402 40.741 9.23 0.00 37.94 2.82
720 724 8.237811 TCAGTATGTATAGAGAACTGCATTGA 57.762 34.615 9.23 0.00 37.94 2.57
721 725 8.864087 TCAGTATGTATAGAGAACTGCATTGAT 58.136 33.333 9.23 0.00 37.94 2.57
722 726 9.486497 CAGTATGTATAGAGAACTGCATTGATT 57.514 33.333 0.00 0.00 32.02 2.57
723 727 9.486497 AGTATGTATAGAGAACTGCATTGATTG 57.514 33.333 0.00 0.00 0.00 2.67
724 728 9.265901 GTATGTATAGAGAACTGCATTGATTGT 57.734 33.333 0.00 0.00 0.00 2.71
727 731 9.836864 TGTATAGAGAACTGCATTGATTGTATT 57.163 29.630 0.00 0.00 0.00 1.89
730 734 7.934855 AGAGAACTGCATTGATTGTATTCTT 57.065 32.000 0.00 0.00 0.00 2.52
732 736 9.453572 AGAGAACTGCATTGATTGTATTCTTAA 57.546 29.630 0.00 0.00 0.00 1.85
733 737 9.713740 GAGAACTGCATTGATTGTATTCTTAAG 57.286 33.333 0.00 0.00 0.00 1.85
734 738 9.236006 AGAACTGCATTGATTGTATTCTTAAGT 57.764 29.630 1.63 0.00 0.00 2.24
737 741 9.448438 ACTGCATTGATTGTATTCTTAAGTACA 57.552 29.630 1.63 2.21 0.00 2.90
738 742 9.926751 CTGCATTGATTGTATTCTTAAGTACAG 57.073 33.333 1.63 0.00 32.87 2.74
739 743 9.448438 TGCATTGATTGTATTCTTAAGTACAGT 57.552 29.630 1.63 1.96 32.87 3.55
752 756 8.822652 TCTTAAGTACAGTAACCAAAGTAAGC 57.177 34.615 1.63 0.00 0.00 3.09
753 757 8.423349 TCTTAAGTACAGTAACCAAAGTAAGCA 58.577 33.333 1.63 0.00 0.00 3.91
754 758 9.216117 CTTAAGTACAGTAACCAAAGTAAGCAT 57.784 33.333 0.00 0.00 0.00 3.79
756 760 8.543862 AAGTACAGTAACCAAAGTAAGCATAC 57.456 34.615 0.00 0.00 0.00 2.39
757 761 7.673180 AGTACAGTAACCAAAGTAAGCATACA 58.327 34.615 1.44 0.00 34.29 2.29
758 762 6.796705 ACAGTAACCAAAGTAAGCATACAC 57.203 37.500 1.44 0.00 34.29 2.90
759 763 5.407387 ACAGTAACCAAAGTAAGCATACACG 59.593 40.000 1.44 0.00 34.29 4.49
760 764 5.636121 CAGTAACCAAAGTAAGCATACACGA 59.364 40.000 1.44 0.00 34.29 4.35
761 765 6.312918 CAGTAACCAAAGTAAGCATACACGAT 59.687 38.462 1.44 0.00 34.29 3.73
762 766 7.490079 CAGTAACCAAAGTAAGCATACACGATA 59.510 37.037 1.44 0.00 34.29 2.92
763 767 8.036575 AGTAACCAAAGTAAGCATACACGATAA 58.963 33.333 1.44 0.00 34.29 1.75
764 768 6.903883 ACCAAAGTAAGCATACACGATAAG 57.096 37.500 1.44 0.00 34.29 1.73
765 769 6.403878 ACCAAAGTAAGCATACACGATAAGT 58.596 36.000 1.44 0.00 34.29 2.24
766 770 6.877322 ACCAAAGTAAGCATACACGATAAGTT 59.123 34.615 1.44 0.00 34.29 2.66
767 771 7.064253 ACCAAAGTAAGCATACACGATAAGTTC 59.936 37.037 1.44 0.00 34.29 3.01
768 772 7.064134 CCAAAGTAAGCATACACGATAAGTTCA 59.936 37.037 1.44 0.00 34.29 3.18
769 773 8.440059 CAAAGTAAGCATACACGATAAGTTCAA 58.560 33.333 1.44 0.00 34.29 2.69
770 774 8.718102 AAGTAAGCATACACGATAAGTTCAAT 57.282 30.769 1.44 0.00 34.29 2.57
771 775 8.131455 AGTAAGCATACACGATAAGTTCAATG 57.869 34.615 1.44 0.00 34.29 2.82
772 776 7.979537 AGTAAGCATACACGATAAGTTCAATGA 59.020 33.333 1.44 0.00 34.29 2.57
773 777 6.589830 AGCATACACGATAAGTTCAATGAC 57.410 37.500 0.00 0.00 0.00 3.06
774 778 5.523916 AGCATACACGATAAGTTCAATGACC 59.476 40.000 0.00 0.00 0.00 4.02
775 779 5.293324 GCATACACGATAAGTTCAATGACCA 59.707 40.000 0.00 0.00 0.00 4.02
776 780 6.510157 GCATACACGATAAGTTCAATGACCAG 60.510 42.308 0.00 0.00 0.00 4.00
777 781 4.894784 ACACGATAAGTTCAATGACCAGT 58.105 39.130 0.00 0.00 0.00 4.00
778 782 6.032956 ACACGATAAGTTCAATGACCAGTA 57.967 37.500 0.00 0.00 0.00 2.74
779 783 6.100004 ACACGATAAGTTCAATGACCAGTAG 58.900 40.000 0.00 0.00 0.00 2.57
780 784 6.100004 CACGATAAGTTCAATGACCAGTAGT 58.900 40.000 0.00 0.00 0.00 2.73
781 785 6.035005 CACGATAAGTTCAATGACCAGTAGTG 59.965 42.308 0.00 0.00 0.00 2.74
821 868 3.814625 TGATCGCCCATGCATTTTACTA 58.185 40.909 0.00 0.00 37.32 1.82
822 869 3.563808 TGATCGCCCATGCATTTTACTAC 59.436 43.478 0.00 0.00 37.32 2.73
823 870 3.275617 TCGCCCATGCATTTTACTACT 57.724 42.857 0.00 0.00 37.32 2.57
824 871 2.942376 TCGCCCATGCATTTTACTACTG 59.058 45.455 0.00 0.00 37.32 2.74
873 920 2.559026 CCCCTTCTTCCCTTTAAACCCC 60.559 54.545 0.00 0.00 0.00 4.95
874 921 2.382305 CCCTTCTTCCCTTTAAACCCCT 59.618 50.000 0.00 0.00 0.00 4.79
976 1023 0.611714 TCCACGCTCCTAGGGTTTTC 59.388 55.000 9.46 0.00 39.54 2.29
1271 1320 1.870064 TGATCAGATGAGTGCTCCCA 58.130 50.000 0.00 0.00 0.00 4.37
1360 1409 1.101635 CGCTATCACCTCTGGACGGA 61.102 60.000 0.00 0.00 0.00 4.69
1378 1427 3.119352 ACGGACGGTACTTCAGGTTTATC 60.119 47.826 0.00 0.00 0.00 1.75
1459 1508 2.493713 TTCGGCTCTTCGAATAGCTC 57.506 50.000 27.99 19.25 43.12 4.09
1464 1513 0.319125 CTCTTCGAATAGCTCCCGCC 60.319 60.000 0.00 0.00 36.60 6.13
1465 1514 0.755698 TCTTCGAATAGCTCCCGCCT 60.756 55.000 0.00 0.00 36.60 5.52
1628 1677 4.350816 TCTCAAATTCCTGAGGTCAAGGAA 59.649 41.667 7.33 7.33 42.68 3.36
1637 1686 1.150536 GGTCAAGGAAGTGCCACCA 59.849 57.895 0.00 0.00 40.02 4.17
1644 1693 1.075374 AGGAAGTGCCACCATTTAGCA 59.925 47.619 0.00 0.00 40.02 3.49
1649 1698 2.102578 GTGCCACCATTTAGCAAGGAT 58.897 47.619 0.00 0.00 38.45 3.24
1662 1711 2.695127 CAAGGATGCTCAGCTCTTCT 57.305 50.000 0.00 0.00 0.00 2.85
1673 1722 3.693807 TCAGCTCTTCTTGGATGCAATT 58.306 40.909 0.00 0.00 0.00 2.32
1674 1723 3.442625 TCAGCTCTTCTTGGATGCAATTG 59.557 43.478 0.00 0.00 0.00 2.32
1745 1794 8.385898 AGAAAATAACTAACCATGACGTGAAA 57.614 30.769 0.00 0.00 0.00 2.69
1803 1852 2.561478 TCCAGAGGTTGCAAAGGTAC 57.439 50.000 0.00 0.00 0.00 3.34
1806 1855 2.571212 CAGAGGTTGCAAAGGTACACA 58.429 47.619 0.00 0.00 0.00 3.72
1807 1856 2.948979 CAGAGGTTGCAAAGGTACACAA 59.051 45.455 0.00 0.00 0.00 3.33
1819 1868 3.214328 AGGTACACAAGCTGGTTTTCAG 58.786 45.455 0.00 0.00 46.03 3.02
1837 1905 7.148804 GGTTTTCAGTTTTGAAGTGTTCACTTC 60.149 37.037 28.17 28.17 43.76 3.01
1839 1907 4.094294 TCAGTTTTGAAGTGTTCACTTCCG 59.906 41.667 30.19 17.49 43.94 4.30
1842 1910 5.048294 AGTTTTGAAGTGTTCACTTCCGTTT 60.048 36.000 30.19 16.43 43.94 3.60
1872 1940 8.659925 AGTCAACTATCATTCTGATCATGTTC 57.340 34.615 0.00 0.00 38.26 3.18
1917 1985 6.655003 TCCATTTTGGATGTACTTCTGAAGAC 59.345 38.462 23.36 16.07 42.67 3.01
1927 1995 5.758296 TGTACTTCTGAAGACATCAACAACC 59.242 40.000 23.36 0.00 37.67 3.77
1941 2009 3.054166 CAACAACCTGTCACATGCATTG 58.946 45.455 0.00 0.00 0.00 2.82
1966 2034 5.237236 TCTAAAAGAGGGGGTAAACACAG 57.763 43.478 0.00 0.00 0.00 3.66
1998 2066 3.062042 TGTGATGATCGATGTATGCAGC 58.938 45.455 0.54 0.00 0.00 5.25
2041 2109 1.398692 AAATGCACACGTCCCTTTGT 58.601 45.000 0.00 0.00 0.00 2.83
2055 2123 5.238650 CGTCCCTTTGTTGTCTAAAACTCAT 59.761 40.000 0.00 0.00 0.00 2.90
2066 2134 6.406370 TGTCTAAAACTCATGGACAGGTATG 58.594 40.000 0.00 0.00 33.74 2.39
2083 2151 5.030820 AGGTATGTAGAGCCACCTTTTAGT 58.969 41.667 0.00 0.00 38.23 2.24
2092 2160 7.124573 AGAGCCACCTTTTAGTTTTTGAATT 57.875 32.000 0.00 0.00 0.00 2.17
2196 2451 7.928307 ACATTGTTATGCAGTAGATTTGACT 57.072 32.000 0.00 0.00 35.03 3.41
2236 2491 8.347729 TGTTCTATTATGTAACATGTGCTACG 57.652 34.615 0.00 0.00 0.00 3.51
2238 2493 9.193133 GTTCTATTATGTAACATGTGCTACGAT 57.807 33.333 0.00 0.00 0.00 3.73
2256 2511 6.253083 GCTACGATAAACTTACTCGAGCTTTT 59.747 38.462 13.61 9.11 35.10 2.27
2288 2543 2.725637 TGCCATTGCTGCAATAAGAGA 58.274 42.857 25.85 9.34 38.71 3.10
2299 2554 5.469421 GCTGCAATAAGAGAGCATGAATAGT 59.531 40.000 0.00 0.00 37.68 2.12
2300 2555 6.566187 GCTGCAATAAGAGAGCATGAATAGTG 60.566 42.308 0.00 0.00 37.68 2.74
2315 2570 5.664457 TGAATAGTGATAACTCCTGCACAG 58.336 41.667 0.00 0.00 33.85 3.66
2316 2571 5.187772 TGAATAGTGATAACTCCTGCACAGT 59.812 40.000 0.00 0.00 33.85 3.55
2333 2588 4.321156 GCACAGTGCATACAAAGAATGGAA 60.321 41.667 21.22 0.00 44.26 3.53
2334 2589 5.156355 CACAGTGCATACAAAGAATGGAAC 58.844 41.667 0.00 0.00 0.00 3.62
2335 2590 5.048504 CACAGTGCATACAAAGAATGGAACT 60.049 40.000 0.00 0.00 0.00 3.01
2336 2591 5.048504 ACAGTGCATACAAAGAATGGAACTG 60.049 40.000 0.00 0.00 0.00 3.16
2337 2592 5.048504 CAGTGCATACAAAGAATGGAACTGT 60.049 40.000 0.00 0.00 0.00 3.55
2338 2593 5.048504 AGTGCATACAAAGAATGGAACTGTG 60.049 40.000 0.00 0.00 0.00 3.66
2339 2594 4.168760 GCATACAAAGAATGGAACTGTGC 58.831 43.478 0.00 0.00 0.00 4.57
2340 2595 4.321156 GCATACAAAGAATGGAACTGTGCA 60.321 41.667 0.00 0.00 0.00 4.57
2341 2596 5.771469 CATACAAAGAATGGAACTGTGCAA 58.229 37.500 0.00 0.00 0.00 4.08
2342 2597 4.045636 ACAAAGAATGGAACTGTGCAAC 57.954 40.909 0.00 0.00 37.35 4.17
2343 2598 3.701040 ACAAAGAATGGAACTGTGCAACT 59.299 39.130 0.00 0.00 38.04 3.16
2344 2599 3.996150 AAGAATGGAACTGTGCAACTG 57.004 42.857 0.00 0.00 42.04 3.16
2345 2600 2.233271 AGAATGGAACTGTGCAACTGG 58.767 47.619 0.00 0.00 40.44 4.00
2346 2601 1.956477 GAATGGAACTGTGCAACTGGT 59.044 47.619 0.00 0.00 38.93 4.00
2355 2610 3.181487 ACTGTGCAACTGGTCAAATTCAC 60.181 43.478 0.00 0.00 40.44 3.18
2358 2613 3.551485 GTGCAACTGGTCAAATTCACAAC 59.449 43.478 0.00 0.00 0.00 3.32
2360 2615 4.642437 TGCAACTGGTCAAATTCACAACTA 59.358 37.500 0.00 0.00 0.00 2.24
2392 2647 1.572415 ACTCCCAAGTCGATAGGGGTA 59.428 52.381 16.73 5.51 43.03 3.69
2395 2650 2.245546 TCCCAAGTCGATAGGGGTAGAA 59.754 50.000 16.73 0.00 43.03 2.10
2410 2665 7.232118 AGGGGTAGAATTGACAAGAAATTTG 57.768 36.000 0.00 0.00 0.00 2.32
2411 2666 6.211384 AGGGGTAGAATTGACAAGAAATTTGG 59.789 38.462 0.00 0.00 0.00 3.28
2428 2683 9.225436 AGAAATTTGGCTTTCTTTTAAAACACA 57.775 25.926 0.00 0.00 41.55 3.72
2433 2688 9.617975 TTTGGCTTTCTTTTAAAACACAAAATG 57.382 25.926 0.00 0.00 0.00 2.32
2469 2724 8.773404 AGATACTACTGTTACATGTTGTTTCC 57.227 34.615 2.30 0.00 0.00 3.13
2477 2732 2.159382 ACATGTTGTTTCCGGCCTAAG 58.841 47.619 0.00 0.00 0.00 2.18
2503 2758 9.255304 GCCTTGTGTAATTGTTTCTTTCATTTA 57.745 29.630 0.00 0.00 0.00 1.40
2515 2770 9.311916 TGTTTCTTTCATTTACTTGGACAAATG 57.688 29.630 0.00 0.00 41.44 2.32
2576 2831 6.127619 ACCACTTCTGCTAAAAATATGAAGGC 60.128 38.462 0.00 0.00 36.28 4.35
2584 2839 7.148641 TGCTAAAAATATGAAGGCGAAAAACA 58.851 30.769 0.00 0.00 0.00 2.83
2603 2858 7.816945 AAAACATTATTCAGTATTGCTGCAC 57.183 32.000 0.00 0.00 44.66 4.57
2605 2860 6.127810 ACATTATTCAGTATTGCTGCACTG 57.872 37.500 0.00 7.14 44.66 3.66
2629 2884 5.505654 GCAGAGTTTAGCAGTTTAGCACAAA 60.506 40.000 0.00 0.00 36.85 2.83
2633 2888 5.359860 AGTTTAGCAGTTTAGCACAAAGGTT 59.640 36.000 0.00 0.00 36.85 3.50
2634 2889 3.990318 AGCAGTTTAGCACAAAGGTTC 57.010 42.857 0.00 0.00 36.85 3.62
2635 2890 2.290641 AGCAGTTTAGCACAAAGGTTCG 59.709 45.455 0.00 0.00 36.85 3.95
2670 2925 8.426489 AGTCCAACTTAATAGACAACACTGTTA 58.574 33.333 0.00 0.00 35.30 2.41
2687 2942 3.997021 CTGTTAATTGACACGAGGCTTCT 59.003 43.478 0.00 0.00 0.00 2.85
2690 2945 5.810587 TGTTAATTGACACGAGGCTTCTATC 59.189 40.000 0.00 0.00 0.00 2.08
2698 2953 3.320541 CACGAGGCTTCTATCTTCCTGAT 59.679 47.826 0.00 0.00 39.11 2.90
2706 2961 6.013812 GGCTTCTATCTTCCTGATATGGACTT 60.014 42.308 0.00 0.00 37.07 3.01
2716 2971 5.131642 TCCTGATATGGACTTCTCAAGCAAT 59.868 40.000 0.00 0.00 0.00 3.56
2722 2977 2.289002 GGACTTCTCAAGCAATATGCCG 59.711 50.000 0.00 0.00 46.52 5.69
2816 3071 2.930950 TCACCAACAACTCTGGGAAAG 58.069 47.619 0.00 0.00 38.36 2.62
2873 3128 4.086706 TGGGAAGAGTTTTTCTGAGGTC 57.913 45.455 0.00 0.00 35.91 3.85
2897 3152 5.717119 AGATACTAGGGAAATTTGCTGGT 57.283 39.130 9.70 8.38 0.00 4.00
2936 3191 4.420522 TGCTGATGTAGTTGCATATCCA 57.579 40.909 0.00 0.00 0.00 3.41
3018 3273 8.988060 TCAATCCTTATGTTACTCAGGTGATTA 58.012 33.333 0.00 0.00 0.00 1.75
3117 3401 4.445699 CCTATGGCACTCGCTTCC 57.554 61.111 0.00 0.00 38.60 3.46
3118 3402 1.227674 CCTATGGCACTCGCTTCCC 60.228 63.158 0.00 0.00 38.60 3.97
3141 3425 9.101325 TCCCCTACTATTTACATTTCTATCAGG 57.899 37.037 0.00 0.00 0.00 3.86
3175 3459 9.547753 GTTCTGATGCAGTATTTATCCTCTTTA 57.452 33.333 0.00 0.00 32.61 1.85
3229 3513 6.597280 AGCTCTTCAATCTATTTGTCCAGTTC 59.403 38.462 0.00 0.00 36.65 3.01
3247 3531 5.504665 CCAGTTCAACATTGTCTTGACTGAC 60.505 44.000 17.14 4.77 33.35 3.51
3255 3539 5.647658 ACATTGTCTTGACTGACTTTGACAA 59.352 36.000 8.46 8.46 44.70 3.18
3266 3550 4.522114 TGACTTTGACAAAGACATGTGGA 58.478 39.130 30.01 8.06 41.02 4.02
3311 3595 5.178797 TCAAGCAGGTAAAGCTATGAAGAC 58.821 41.667 0.00 0.00 42.53 3.01
3315 3599 5.069781 AGCAGGTAAAGCTATGAAGACTAGG 59.930 44.000 0.00 0.00 41.32 3.02
3321 3605 6.985653 AAAGCTATGAAGACTAGGCTATCA 57.014 37.500 0.00 5.71 0.00 2.15
3329 3613 7.048629 TGAAGACTAGGCTATCATCAAAGAG 57.951 40.000 0.00 0.00 0.00 2.85
3408 3692 2.582636 ACTTACTCTGCATTCCCCCATT 59.417 45.455 0.00 0.00 0.00 3.16
3421 3705 6.576185 CATTCCCCCATTTTGTTTCAGATAG 58.424 40.000 0.00 0.00 0.00 2.08
3504 3788 8.635765 TTGAAAATAGTGAAGGCAATCTTAGT 57.364 30.769 0.00 0.00 35.50 2.24
3580 3864 7.499232 GGTTGCAGGTAATGTTATCACTTCTAT 59.501 37.037 0.00 0.00 0.00 1.98
3595 3879 7.265599 TCACTTCTATACTTGAATTTCCCCA 57.734 36.000 0.00 0.00 0.00 4.96
3609 3893 3.712016 TTCCCCATCTTCATTCGTCAA 57.288 42.857 0.00 0.00 0.00 3.18
3750 4034 2.232208 TCAATGACAGCGTGATCTCACT 59.768 45.455 8.57 0.00 44.34 3.41
3905 4189 0.107703 TTGTAGCCATTCAGCCCTCG 60.108 55.000 0.00 0.00 0.00 4.63
3906 4190 1.264749 TGTAGCCATTCAGCCCTCGT 61.265 55.000 0.00 0.00 0.00 4.18
3907 4191 0.750850 GTAGCCATTCAGCCCTCGTA 59.249 55.000 0.00 0.00 0.00 3.43
3908 4192 0.750850 TAGCCATTCAGCCCTCGTAC 59.249 55.000 0.00 0.00 0.00 3.67
4436 4720 8.721133 TTGCTCCCTATATAACTCAATACTCA 57.279 34.615 0.00 0.00 0.00 3.41
4440 4724 8.880991 TCCCTATATAACTCAATACTCACTCC 57.119 38.462 0.00 0.00 0.00 3.85
4441 4725 8.453681 TCCCTATATAACTCAATACTCACTCCA 58.546 37.037 0.00 0.00 0.00 3.86
4480 4764 7.343057 TGTCACAGAAATGGATGTATCTAGACT 59.657 37.037 0.00 0.00 32.14 3.24
4483 4767 9.469807 CACAGAAATGGATGTATCTAGACTTAC 57.530 37.037 0.00 0.00 0.00 2.34
4510 4804 5.542779 AGTTCTAGATACATCCATTTCCGC 58.457 41.667 0.00 0.00 0.00 5.54
4561 4855 3.069872 AGCATGGAACTGCAATTTGTGAA 59.930 39.130 0.00 0.00 44.77 3.18
4562 4856 3.998341 GCATGGAACTGCAATTTGTGAAT 59.002 39.130 0.00 0.00 41.87 2.57
4594 4888 9.153721 GAATGATGTTTATTTGGCTGAATTCAA 57.846 29.630 9.88 0.00 0.00 2.69
4729 5025 8.996024 TTGAAATATCGTTCTGAACATAGACA 57.004 30.769 19.56 13.02 0.00 3.41
4764 5060 6.072175 TGACAGACCTTGTGTTAATATTTGGC 60.072 38.462 0.00 0.00 41.05 4.52
4880 5178 9.951866 AAAATGGAACCAAATATATACTCCCTT 57.048 29.630 0.00 0.00 0.00 3.95
4935 5233 8.053026 ACACTAAAACGTGTCTGTATCTAGAT 57.947 34.615 10.73 10.73 44.32 1.98
5029 5375 6.913170 ACGACTGATTCATTATTGTTTTGCT 58.087 32.000 0.00 0.00 0.00 3.91
5161 5507 4.163078 TCATCCTCCCTTCAGTCTGATTTC 59.837 45.833 2.68 0.00 0.00 2.17
5229 5575 8.681486 TTATGATGTTTGTATGGATCTTGAGG 57.319 34.615 0.00 0.00 0.00 3.86
5334 5685 6.155475 TGTTTATTGTTTAAGCCTGCAGTT 57.845 33.333 13.81 3.71 0.00 3.16
5365 5716 5.127845 TCAAGTGGTCAAAGCCAAAACAATA 59.872 36.000 0.00 0.00 40.68 1.90
5379 5730 9.247861 AGCCAAAACAATAATTATTCTCACTCT 57.752 29.630 7.76 0.00 0.00 3.24
5380 5731 9.860898 GCCAAAACAATAATTATTCTCACTCTT 57.139 29.630 7.76 0.00 0.00 2.85
5764 6123 2.284457 CGACGACAGCGACAATAACATG 60.284 50.000 0.00 0.00 41.64 3.21
5779 6138 2.978156 ACATGGAAAGCTTCAAGGGA 57.022 45.000 0.00 0.00 0.00 4.20
5803 6162 2.470196 TCACATCGTAGCTTAGCGTC 57.530 50.000 0.00 0.00 0.00 5.19
5831 6190 9.691362 AAAGATTGTTTGTCACGCTAATTTATT 57.309 25.926 0.00 0.00 0.00 1.40
5857 6216 3.981211 TCTCATTGAAAAAGCTTGTGGC 58.019 40.909 0.00 0.00 42.19 5.01
5903 6264 6.018180 GGAATTGTACCATCACTATTCGTTCC 60.018 42.308 0.00 0.00 39.81 3.62
6036 6397 0.964358 GGTCGAGAAGTCTCCGGGAA 60.964 60.000 0.00 0.00 39.79 3.97
6076 6438 1.748493 TCTTCCAGTGCGCTTTTGTTT 59.252 42.857 9.73 0.00 0.00 2.83
6240 6624 2.844146 CGTTGGTGACGCGAAGAC 59.156 61.111 15.93 5.67 45.86 3.01
6241 6625 2.844146 GTTGGTGACGCGAAGACG 59.156 61.111 15.93 0.00 42.93 4.18
6259 6655 8.705323 GCGAAGACGTTGGTAACATTTTACTTG 61.705 40.741 1.99 0.00 43.36 3.16
6266 6662 2.723124 AACATTTTACTTGCCGGCAG 57.277 45.000 30.75 24.51 0.00 4.85
6282 6678 1.435408 GCAGCATTCTTCTCGGCTCC 61.435 60.000 0.00 0.00 33.60 4.70
6305 6701 1.196127 GCGAGGAAAATCGGAAAACGT 59.804 47.619 0.00 0.00 42.94 3.99
6306 6702 2.412770 GCGAGGAAAATCGGAAAACGTA 59.587 45.455 0.00 0.00 42.94 3.57
6320 6716 0.244450 AACGTAAATCGGTCGCTCCA 59.756 50.000 0.00 0.00 44.69 3.86
6326 6722 2.558554 AATCGGTCGCTCCAGTTCCG 62.559 60.000 0.00 0.00 42.12 4.30
6353 6749 1.340211 ACGTGAGAAGGGAGATCGTCT 60.340 52.381 0.00 0.00 0.00 4.18
6437 6833 0.676782 GGCCGTGAACCAATGCTACT 60.677 55.000 0.00 0.00 0.00 2.57
6499 6896 1.350684 TCAACTGCTGGGCACTATCAA 59.649 47.619 0.00 0.00 33.79 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.121378 GAGGGCCTAGGAGGTGTAAC 58.879 60.000 14.75 0.00 37.80 2.50
35 36 2.352805 GTGGACAAGAGGCCCCAG 59.647 66.667 0.00 0.00 0.00 4.45
40 41 1.668151 GACCACGTGGACAAGAGGC 60.668 63.158 40.21 8.90 38.94 4.70
62 63 1.876714 GCATGCATGGCGCTTTGAG 60.877 57.895 27.34 0.00 43.06 3.02
86 87 5.177696 GTCTTCAATTTGTCTAACTCGCACT 59.822 40.000 0.00 0.00 0.00 4.40
88 89 4.451096 GGTCTTCAATTTGTCTAACTCGCA 59.549 41.667 0.00 0.00 0.00 5.10
92 93 6.601332 TCCAAGGTCTTCAATTTGTCTAACT 58.399 36.000 0.00 0.00 0.00 2.24
100 101 6.723052 AGTGATTCATCCAAGGTCTTCAATTT 59.277 34.615 0.00 0.00 0.00 1.82
171 173 7.211573 TGATTCTTTCGGTGAACTGTTTACTA 58.788 34.615 14.04 2.08 0.00 1.82
180 182 4.670221 GCAGTCATGATTCTTTCGGTGAAC 60.670 45.833 0.00 0.00 0.00 3.18
254 257 4.267349 ACAGTAACCAAAGTGAGCGTAT 57.733 40.909 0.00 0.00 0.00 3.06
293 296 8.122952 ACTTCAACACGTATATAGTAACCGTAC 58.877 37.037 0.00 0.00 0.00 3.67
348 351 4.499188 CGTCAAATAGCTGGAATACGGAGA 60.499 45.833 0.00 0.00 0.00 3.71
371 374 1.000843 GCCAGTTGGATTGTTTGACCC 59.999 52.381 1.45 0.00 37.39 4.46
424 427 1.573108 CACTGACAGGTAGGACCCAT 58.427 55.000 7.51 0.00 39.75 4.00
459 462 6.342111 GTCTCGGGACTGAATCTTATTTTCT 58.658 40.000 8.58 0.00 39.24 2.52
497 500 2.113986 GAGGCAGGTGCAGTTGGT 59.886 61.111 4.01 0.00 44.36 3.67
511 514 2.432628 GTCGGACACTTGGCGAGG 60.433 66.667 6.71 0.00 0.00 4.63
515 518 1.374758 CTCTGGTCGGACACTTGGC 60.375 63.158 10.76 0.00 0.00 4.52
548 552 3.491639 TGTTACGTGAATGGTTGAACGAG 59.508 43.478 0.00 0.00 39.27 4.18
551 555 4.201930 TGGTTGTTACGTGAATGGTTGAAC 60.202 41.667 0.00 0.00 0.00 3.18
560 564 7.513371 AAAATCCTAATGGTTGTTACGTGAA 57.487 32.000 0.00 0.00 34.23 3.18
564 568 9.471084 AAAAGAAAAATCCTAATGGTTGTTACG 57.529 29.630 0.00 0.00 34.23 3.18
580 584 3.130633 GCTCCCACGCAAAAAGAAAAAT 58.869 40.909 0.00 0.00 0.00 1.82
591 595 1.971167 GTTCAATGGCTCCCACGCA 60.971 57.895 0.00 0.00 35.80 5.24
592 596 1.648467 GAGTTCAATGGCTCCCACGC 61.648 60.000 0.00 0.00 35.80 5.34
597 601 2.961526 TCGTAGAGTTCAATGGCTCC 57.038 50.000 3.05 0.00 32.47 4.70
618 622 1.269448 GTCAAACAATCCACATGGCGT 59.731 47.619 0.00 0.00 34.44 5.68
619 623 1.402720 GGTCAAACAATCCACATGGCG 60.403 52.381 0.00 0.00 34.44 5.69
674 678 8.001881 ACTGAGGTGATATTATACGATCATCC 57.998 38.462 0.00 5.31 34.30 3.51
688 692 9.508642 CAGTTCTCTATACATACTGAGGTGATA 57.491 37.037 0.00 0.00 38.74 2.15
689 693 7.040062 GCAGTTCTCTATACATACTGAGGTGAT 60.040 40.741 0.00 0.00 38.74 3.06
690 694 6.263392 GCAGTTCTCTATACATACTGAGGTGA 59.737 42.308 0.00 0.00 38.74 4.02
698 702 9.265901 ACAATCAATGCAGTTCTCTATACATAC 57.734 33.333 0.00 0.00 0.00 2.39
701 705 9.836864 AATACAATCAATGCAGTTCTCTATACA 57.163 29.630 0.00 0.00 0.00 2.29
711 715 9.448438 TGTACTTAAGAATACAATCAATGCAGT 57.552 29.630 10.09 0.00 0.00 4.40
712 716 9.926751 CTGTACTTAAGAATACAATCAATGCAG 57.073 33.333 10.09 0.00 31.09 4.41
713 717 9.448438 ACTGTACTTAAGAATACAATCAATGCA 57.552 29.630 10.09 0.00 31.09 3.96
726 730 9.264719 GCTTACTTTGGTTACTGTACTTAAGAA 57.735 33.333 10.09 0.00 0.00 2.52
727 731 8.423349 TGCTTACTTTGGTTACTGTACTTAAGA 58.577 33.333 10.09 0.00 0.00 2.10
728 732 8.597662 TGCTTACTTTGGTTACTGTACTTAAG 57.402 34.615 0.00 0.00 0.00 1.85
730 734 9.643693 GTATGCTTACTTTGGTTACTGTACTTA 57.356 33.333 2.60 0.00 0.00 2.24
731 735 8.152246 TGTATGCTTACTTTGGTTACTGTACTT 58.848 33.333 10.74 0.00 0.00 2.24
732 736 7.601508 GTGTATGCTTACTTTGGTTACTGTACT 59.398 37.037 10.74 0.00 0.00 2.73
733 737 7.411157 CGTGTATGCTTACTTTGGTTACTGTAC 60.411 40.741 10.74 0.00 0.00 2.90
734 738 6.587226 CGTGTATGCTTACTTTGGTTACTGTA 59.413 38.462 10.74 0.00 0.00 2.74
735 739 5.407387 CGTGTATGCTTACTTTGGTTACTGT 59.593 40.000 10.74 0.00 0.00 3.55
736 740 5.636121 TCGTGTATGCTTACTTTGGTTACTG 59.364 40.000 10.74 0.00 0.00 2.74
737 741 5.786311 TCGTGTATGCTTACTTTGGTTACT 58.214 37.500 10.74 0.00 0.00 2.24
738 742 6.657836 ATCGTGTATGCTTACTTTGGTTAC 57.342 37.500 10.74 0.00 0.00 2.50
739 743 8.036575 ACTTATCGTGTATGCTTACTTTGGTTA 58.963 33.333 10.74 0.00 0.00 2.85
740 744 6.877322 ACTTATCGTGTATGCTTACTTTGGTT 59.123 34.615 10.74 0.00 0.00 3.67
741 745 6.403878 ACTTATCGTGTATGCTTACTTTGGT 58.596 36.000 10.74 0.78 0.00 3.67
742 746 6.903883 ACTTATCGTGTATGCTTACTTTGG 57.096 37.500 10.74 0.00 0.00 3.28
743 747 7.959733 TGAACTTATCGTGTATGCTTACTTTG 58.040 34.615 10.74 1.84 0.00 2.77
744 748 8.542497 TTGAACTTATCGTGTATGCTTACTTT 57.458 30.769 10.74 0.00 0.00 2.66
745 749 8.604035 CATTGAACTTATCGTGTATGCTTACTT 58.396 33.333 10.74 0.00 0.00 2.24
746 750 7.979537 TCATTGAACTTATCGTGTATGCTTACT 59.020 33.333 10.74 0.00 0.00 2.24
747 751 8.056571 GTCATTGAACTTATCGTGTATGCTTAC 58.943 37.037 2.86 2.86 0.00 2.34
748 752 7.223971 GGTCATTGAACTTATCGTGTATGCTTA 59.776 37.037 0.00 0.00 0.00 3.09
749 753 6.037172 GGTCATTGAACTTATCGTGTATGCTT 59.963 38.462 0.00 0.00 0.00 3.91
750 754 5.523916 GGTCATTGAACTTATCGTGTATGCT 59.476 40.000 0.00 0.00 0.00 3.79
751 755 5.293324 TGGTCATTGAACTTATCGTGTATGC 59.707 40.000 2.91 0.00 0.00 3.14
752 756 6.535150 ACTGGTCATTGAACTTATCGTGTATG 59.465 38.462 2.91 0.00 0.00 2.39
753 757 6.640518 ACTGGTCATTGAACTTATCGTGTAT 58.359 36.000 2.91 0.00 0.00 2.29
754 758 6.032956 ACTGGTCATTGAACTTATCGTGTA 57.967 37.500 2.91 0.00 0.00 2.90
755 759 4.894784 ACTGGTCATTGAACTTATCGTGT 58.105 39.130 2.91 0.00 0.00 4.49
756 760 6.035005 CACTACTGGTCATTGAACTTATCGTG 59.965 42.308 2.91 1.21 0.00 4.35
757 761 6.100004 CACTACTGGTCATTGAACTTATCGT 58.900 40.000 2.91 0.00 0.00 3.73
758 762 5.520288 CCACTACTGGTCATTGAACTTATCG 59.480 44.000 2.91 0.00 32.03 2.92
759 763 6.640518 TCCACTACTGGTCATTGAACTTATC 58.359 40.000 2.91 0.00 38.90 1.75
760 764 6.213600 ACTCCACTACTGGTCATTGAACTTAT 59.786 38.462 2.91 0.00 38.90 1.73
761 765 5.542635 ACTCCACTACTGGTCATTGAACTTA 59.457 40.000 2.91 0.00 38.90 2.24
762 766 4.348168 ACTCCACTACTGGTCATTGAACTT 59.652 41.667 2.91 0.00 38.90 2.66
763 767 3.904339 ACTCCACTACTGGTCATTGAACT 59.096 43.478 2.91 0.00 38.90 3.01
764 768 4.273148 ACTCCACTACTGGTCATTGAAC 57.727 45.455 0.00 0.00 38.90 3.18
765 769 6.620877 AATACTCCACTACTGGTCATTGAA 57.379 37.500 0.00 0.00 38.90 2.69
766 770 6.620877 AAATACTCCACTACTGGTCATTGA 57.379 37.500 0.00 0.00 38.90 2.57
767 771 7.687941 AAAAATACTCCACTACTGGTCATTG 57.312 36.000 0.00 0.00 38.90 2.82
801 848 3.815401 AGTAGTAAAATGCATGGGCGATC 59.185 43.478 0.00 0.00 45.35 3.69
804 851 2.682856 ACAGTAGTAAAATGCATGGGCG 59.317 45.455 0.00 0.00 45.35 6.13
821 868 0.831966 TCGGGTGTGTTTGGTACAGT 59.168 50.000 0.00 0.00 42.39 3.55
822 869 1.508632 CTCGGGTGTGTTTGGTACAG 58.491 55.000 0.00 0.00 42.39 2.74
823 870 0.533308 GCTCGGGTGTGTTTGGTACA 60.533 55.000 0.00 0.00 0.00 2.90
824 871 0.533308 TGCTCGGGTGTGTTTGGTAC 60.533 55.000 0.00 0.00 0.00 3.34
873 920 1.687297 GGCGGAAAGGGAGGGTAGAG 61.687 65.000 0.00 0.00 0.00 2.43
874 921 1.688187 GGCGGAAAGGGAGGGTAGA 60.688 63.158 0.00 0.00 0.00 2.59
1360 1409 4.529377 TCCTTGATAAACCTGAAGTACCGT 59.471 41.667 0.00 0.00 0.00 4.83
1628 1677 1.075374 TCCTTGCTAAATGGTGGCACT 59.925 47.619 18.45 0.00 35.62 4.40
1644 1693 2.355920 CCAAGAAGAGCTGAGCATCCTT 60.356 50.000 7.39 6.84 0.00 3.36
1649 1698 1.678123 GCATCCAAGAAGAGCTGAGCA 60.678 52.381 7.39 0.00 0.00 4.26
1652 1701 2.865119 TTGCATCCAAGAAGAGCTGA 57.135 45.000 0.00 0.00 0.00 4.26
1673 1722 7.485810 CATCATTGATGCTAAAATCTTGGACA 58.514 34.615 13.43 0.00 33.17 4.02
1674 1723 7.925703 CATCATTGATGCTAAAATCTTGGAC 57.074 36.000 13.43 0.00 33.17 4.02
1745 1794 4.464244 TGCTTCAGATAGTACTCAACAGCT 59.536 41.667 0.00 0.00 0.00 4.24
1803 1852 4.493547 TCAAAACTGAAAACCAGCTTGTG 58.506 39.130 0.00 0.00 46.81 3.33
1806 1855 5.170748 CACTTCAAAACTGAAAACCAGCTT 58.829 37.500 0.00 0.00 46.81 3.74
1807 1856 4.220602 ACACTTCAAAACTGAAAACCAGCT 59.779 37.500 0.00 0.00 46.81 4.24
1837 1905 5.862924 ATGATAGTTGACTTCACAAACGG 57.137 39.130 0.00 0.00 0.00 4.44
1839 1907 8.087982 TCAGAATGATAGTTGACTTCACAAAC 57.912 34.615 0.00 0.00 42.56 2.93
1872 1940 4.790765 GAAGAATTCCAAAACCTGGGAG 57.209 45.455 0.65 0.00 46.44 4.30
1905 1973 5.991606 CAGGTTGTTGATGTCTTCAGAAGTA 59.008 40.000 10.09 1.58 35.27 2.24
1917 1985 2.293955 TGCATGTGACAGGTTGTTGATG 59.706 45.455 0.00 0.00 0.00 3.07
1927 1995 1.460504 AGAGCCAATGCATGTGACAG 58.539 50.000 0.00 0.00 41.13 3.51
1941 2009 3.009805 TGTTTACCCCCTCTTTTAGAGCC 59.990 47.826 0.00 0.00 40.98 4.70
1966 2034 4.693283 TCGATCATCACAGGGAACATAAC 58.307 43.478 0.00 0.00 0.00 1.89
1998 2066 2.529151 GTTGCCAAGGAACATATTGCG 58.471 47.619 0.00 0.00 0.00 4.85
2041 2109 5.304686 ACCTGTCCATGAGTTTTAGACAA 57.695 39.130 0.00 0.00 37.04 3.18
2055 2123 2.108168 GTGGCTCTACATACCTGTCCA 58.892 52.381 0.00 0.00 36.79 4.02
2066 2134 6.628919 TCAAAAACTAAAAGGTGGCTCTAC 57.371 37.500 0.00 0.00 0.00 2.59
2104 2334 6.761242 TCACACTAATACATCCACAAGCATAC 59.239 38.462 0.00 0.00 0.00 2.39
2165 2395 7.552458 TCTACTGCATAACAATGTTGTATGG 57.448 36.000 9.15 0.00 41.31 2.74
2170 2400 8.239314 AGTCAAATCTACTGCATAACAATGTTG 58.761 33.333 9.15 0.00 0.00 3.33
2171 2401 8.340618 AGTCAAATCTACTGCATAACAATGTT 57.659 30.769 3.43 3.43 0.00 2.71
2172 2402 7.928307 AGTCAAATCTACTGCATAACAATGT 57.072 32.000 0.00 0.00 0.00 2.71
2180 2435 8.646004 AGTCACATATAGTCAAATCTACTGCAT 58.354 33.333 0.00 0.00 0.00 3.96
2256 2511 3.747010 CAGCAATGGCAAGCAAACATAAA 59.253 39.130 16.10 0.00 44.61 1.40
2261 2516 0.881159 TGCAGCAATGGCAAGCAAAC 60.881 50.000 16.10 6.65 45.91 2.93
2288 2543 5.163269 TGCAGGAGTTATCACTATTCATGCT 60.163 40.000 10.17 0.00 31.22 3.79
2299 2554 2.099141 GCACTGTGCAGGAGTTATCA 57.901 50.000 26.70 0.00 44.26 2.15
2315 2570 5.156355 CACAGTTCCATTCTTTGTATGCAC 58.844 41.667 0.00 0.00 0.00 4.57
2316 2571 4.321156 GCACAGTTCCATTCTTTGTATGCA 60.321 41.667 0.00 0.00 0.00 3.96
2333 2588 3.023119 TGAATTTGACCAGTTGCACAGT 58.977 40.909 0.00 0.00 0.00 3.55
2334 2589 3.181488 TGTGAATTTGACCAGTTGCACAG 60.181 43.478 0.00 0.00 32.05 3.66
2335 2590 2.757314 TGTGAATTTGACCAGTTGCACA 59.243 40.909 0.00 0.00 33.18 4.57
2336 2591 3.435105 TGTGAATTTGACCAGTTGCAC 57.565 42.857 0.00 0.00 0.00 4.57
2337 2592 3.446873 AGTTGTGAATTTGACCAGTTGCA 59.553 39.130 0.00 0.00 0.00 4.08
2338 2593 4.045636 AGTTGTGAATTTGACCAGTTGC 57.954 40.909 0.00 0.00 0.00 4.17
2339 2594 5.630680 GCATAGTTGTGAATTTGACCAGTTG 59.369 40.000 0.00 0.00 0.00 3.16
2340 2595 5.536161 AGCATAGTTGTGAATTTGACCAGTT 59.464 36.000 0.00 0.00 0.00 3.16
2341 2596 5.048504 CAGCATAGTTGTGAATTTGACCAGT 60.049 40.000 0.00 0.00 0.00 4.00
2342 2597 5.048504 ACAGCATAGTTGTGAATTTGACCAG 60.049 40.000 0.00 0.00 0.00 4.00
2343 2598 4.826733 ACAGCATAGTTGTGAATTTGACCA 59.173 37.500 0.00 0.00 0.00 4.02
2344 2599 5.376854 ACAGCATAGTTGTGAATTTGACC 57.623 39.130 0.00 0.00 0.00 4.02
2345 2600 5.858581 GGAACAGCATAGTTGTGAATTTGAC 59.141 40.000 0.00 0.00 0.00 3.18
2346 2601 5.769662 AGGAACAGCATAGTTGTGAATTTGA 59.230 36.000 0.00 0.00 0.00 2.69
2355 2610 4.192317 GGGAGTTAGGAACAGCATAGTTG 58.808 47.826 0.00 0.00 0.00 3.16
2358 2613 4.080863 ACTTGGGAGTTAGGAACAGCATAG 60.081 45.833 0.00 0.00 29.87 2.23
2360 2615 2.644798 ACTTGGGAGTTAGGAACAGCAT 59.355 45.455 0.00 0.00 29.87 3.79
2392 2647 7.503549 AGAAAGCCAAATTTCTTGTCAATTCT 58.496 30.769 0.00 0.00 45.10 2.40
2410 2665 7.066404 TCCCATTTTGTGTTTTAAAAGAAAGCC 59.934 33.333 0.00 0.00 31.31 4.35
2411 2666 7.980062 TCCCATTTTGTGTTTTAAAAGAAAGC 58.020 30.769 0.00 0.00 31.31 3.51
2444 2699 7.544566 CGGAAACAACATGTAACAGTAGTATCT 59.455 37.037 0.00 0.00 0.00 1.98
2448 2703 4.753107 CCGGAAACAACATGTAACAGTAGT 59.247 41.667 0.00 0.00 0.00 2.73
2477 2732 7.713764 AATGAAAGAAACAATTACACAAGGC 57.286 32.000 0.00 0.00 0.00 4.35
2551 2806 6.127619 GCCTTCATATTTTTAGCAGAAGTGGT 60.128 38.462 0.00 0.00 38.25 4.16
2558 2813 7.328249 TGTTTTTCGCCTTCATATTTTTAGCAG 59.672 33.333 0.00 0.00 0.00 4.24
2571 2826 8.798153 CAATACTGAATAATGTTTTTCGCCTTC 58.202 33.333 0.00 0.00 0.00 3.46
2572 2827 7.275560 GCAATACTGAATAATGTTTTTCGCCTT 59.724 33.333 0.00 0.00 0.00 4.35
2605 2860 3.498397 TGTGCTAAACTGCTAAACTCTGC 59.502 43.478 0.00 0.00 0.00 4.26
2629 2884 6.786967 AGTTGGACTATTACATACGAACCT 57.213 37.500 0.00 0.00 0.00 3.50
2670 2925 4.744795 AGATAGAAGCCTCGTGTCAATT 57.255 40.909 0.00 0.00 0.00 2.32
2678 2933 5.394005 CCATATCAGGAAGATAGAAGCCTCG 60.394 48.000 0.00 0.00 42.26 4.63
2687 2942 7.256119 GCTTGAGAAGTCCATATCAGGAAGATA 60.256 40.741 0.00 0.00 43.11 1.98
2690 2945 5.055812 GCTTGAGAAGTCCATATCAGGAAG 58.944 45.833 0.00 0.00 39.92 3.46
2698 2953 5.065914 GGCATATTGCTTGAGAAGTCCATA 58.934 41.667 0.00 0.00 44.28 2.74
2716 2971 3.388024 ACAAAAGGCTAGATCTCGGCATA 59.612 43.478 20.83 0.00 0.00 3.14
2722 2977 4.256920 TCAGCAACAAAAGGCTAGATCTC 58.743 43.478 0.00 0.00 38.56 2.75
2852 3107 3.458118 TGACCTCAGAAAAACTCTTCCCA 59.542 43.478 0.00 0.00 29.07 4.37
2873 3128 5.888161 ACCAGCAAATTTCCCTAGTATCTTG 59.112 40.000 0.00 0.00 0.00 3.02
2897 3152 4.280425 TCAGCATTGTAATTTCCAACAGCA 59.720 37.500 13.99 0.00 31.98 4.41
2936 3191 5.189180 GTCATCTTAGGCCAGTCAATTTCT 58.811 41.667 5.01 0.00 0.00 2.52
2975 3230 5.510430 GGATTGAACTCCAAACCTAAGGAT 58.490 41.667 0.00 0.00 42.49 3.24
3002 3257 7.936847 AGTGACAAAATAATCACCTGAGTAACA 59.063 33.333 0.89 0.00 45.28 2.41
3018 3273 7.138736 CGTAAGGAACAATGAAGTGACAAAAT 58.861 34.615 0.00 0.00 0.00 1.82
3049 3315 0.179004 AAATGGTGCCCAAGACGTGA 60.179 50.000 0.00 0.00 36.95 4.35
3050 3316 0.673437 AAAATGGTGCCCAAGACGTG 59.327 50.000 0.00 0.00 36.95 4.49
3074 3340 7.147863 GCTCATCATACTGAGTCATATCTCCAT 60.148 40.741 0.00 0.00 43.75 3.41
3116 3400 9.101325 TCCTGATAGAAATGTAAATAGTAGGGG 57.899 37.037 0.00 0.00 0.00 4.79
3168 3452 6.314896 GTCATGAGGTTCAATCTGTAAAGAGG 59.685 42.308 0.00 0.00 0.00 3.69
3175 3459 8.489676 AGATATAGTCATGAGGTTCAATCTGT 57.510 34.615 0.00 0.00 0.00 3.41
3229 3513 5.967674 GTCAAAGTCAGTCAAGACAATGTTG 59.032 40.000 2.72 1.23 40.98 3.33
3247 3531 5.505173 AAGTCCACATGTCTTTGTCAAAG 57.495 39.130 17.73 17.73 39.88 2.77
3255 3539 6.051717 GCTGATATGTAAGTCCACATGTCTT 58.948 40.000 12.27 0.00 43.56 3.01
3266 3550 5.363868 TGAAGTAGCCTGCTGATATGTAAGT 59.636 40.000 0.97 0.00 0.00 2.24
3329 3613 8.694394 GTTCTTTCTTGCAGTATTGAATCAAAC 58.306 33.333 0.00 0.30 0.00 2.93
3337 3621 6.650807 TGAGTAGGTTCTTTCTTGCAGTATTG 59.349 38.462 0.00 0.00 0.00 1.90
3338 3622 6.769512 TGAGTAGGTTCTTTCTTGCAGTATT 58.230 36.000 0.00 0.00 0.00 1.89
3377 3661 6.071952 GGAATGCAGAGTAAGTTGAAATGGAA 60.072 38.462 0.00 0.00 0.00 3.53
3395 3679 2.707791 TGAAACAAAATGGGGGAATGCA 59.292 40.909 0.00 0.00 0.00 3.96
3421 3705 0.032540 CCAACTTCACCAGCCTTTGC 59.967 55.000 0.00 0.00 37.95 3.68
3504 3788 6.460781 AGTACATAAAAGACCATTCGACACA 58.539 36.000 0.00 0.00 0.00 3.72
3540 3824 4.018415 ACCTGCAACCTTGATATTGGTAGT 60.018 41.667 0.00 0.00 35.17 2.73
3580 3864 6.318648 CGAATGAAGATGGGGAAATTCAAGTA 59.681 38.462 0.00 0.00 35.47 2.24
3595 3879 6.808008 ATTCAGTTGTTGACGAATGAAGAT 57.192 33.333 16.43 2.39 44.40 2.40
3750 4034 7.035004 CCAAGTTTCTCAAAACAGTTGAATCA 58.965 34.615 4.09 0.00 45.94 2.57
4436 4720 1.982958 ACAAGTAATTCGGGGTGGAGT 59.017 47.619 0.00 0.00 0.00 3.85
4440 4724 2.742053 CTGTGACAAGTAATTCGGGGTG 59.258 50.000 0.00 0.00 0.00 4.61
4441 4725 2.635915 TCTGTGACAAGTAATTCGGGGT 59.364 45.455 0.00 0.00 0.00 4.95
4483 4767 9.197694 CGGAAATGGATGTATCTAGAACTAAAG 57.802 37.037 0.00 0.00 0.00 1.85
4510 4804 1.135315 TCCGTCCGGAATTACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
4561 4855 9.590451 CAGCCAAATAAACATCATTCAAGTAAT 57.410 29.630 0.00 0.00 0.00 1.89
4562 4856 8.801299 TCAGCCAAATAAACATCATTCAAGTAA 58.199 29.630 0.00 0.00 0.00 2.24
4655 4949 7.360113 TGATGTCCTGTTGAGTATAATAGCA 57.640 36.000 0.00 0.00 0.00 3.49
4729 5025 8.635765 AACACAAGGTCTGTCATTATTTATGT 57.364 30.769 0.00 0.00 35.47 2.29
4764 5060 6.404074 GGACAAGGTTTAGATGCAGAAAGATG 60.404 42.308 0.00 0.00 0.00 2.90
5006 5352 7.022979 TGAGCAAAACAATAATGAATCAGTCG 58.977 34.615 0.00 0.00 0.00 4.18
5029 5375 3.117851 TCACCTGTACCACAACCAATTGA 60.118 43.478 7.12 0.00 39.30 2.57
5161 5507 3.372060 CATGCAAGCATAGCACAATCAG 58.628 45.455 7.29 0.00 45.95 2.90
5210 5556 6.620877 AGTACCTCAAGATCCATACAAACA 57.379 37.500 0.00 0.00 0.00 2.83
5245 5596 7.549134 CACACAATAAGCACCTAATCTAGTCAA 59.451 37.037 0.00 0.00 0.00 3.18
5290 5641 6.753107 ACATAGTGGTGTATTTGCCTAAAC 57.247 37.500 0.00 0.00 0.00 2.01
5334 5685 4.072131 GGCTTTGACCACTTGAGAATACA 58.928 43.478 0.00 0.00 0.00 2.29
5764 6123 3.573967 TGATGTTTCCCTTGAAGCTTTCC 59.426 43.478 0.00 0.00 33.31 3.13
5779 6138 3.551890 CGCTAAGCTACGATGTGATGTTT 59.448 43.478 0.00 0.00 0.00 2.83
5803 6162 3.354089 AGCGTGACAAACAATCTTTGG 57.646 42.857 0.00 0.00 33.92 3.28
5831 6190 5.811613 CACAAGCTTTTTCAATGAGAACCAA 59.188 36.000 0.00 0.00 35.56 3.67
6076 6438 4.279982 TCAAAAAGCATCATATGAGGGCA 58.720 39.130 25.36 8.48 32.70 5.36
6188 6550 3.403038 CCGGATAAGGATGAACATGGTC 58.597 50.000 2.98 2.98 0.00 4.02
6237 6621 5.278120 GGCAAGTAAAATGTTACCAACGTCT 60.278 40.000 1.94 0.00 40.55 4.18
6239 6623 4.555116 CGGCAAGTAAAATGTTACCAACGT 60.555 41.667 1.94 0.00 40.55 3.99
6240 6624 3.909574 CGGCAAGTAAAATGTTACCAACG 59.090 43.478 1.94 0.00 40.55 4.10
6241 6625 4.231439 CCGGCAAGTAAAATGTTACCAAC 58.769 43.478 1.94 0.00 40.55 3.77
6242 6626 3.305471 GCCGGCAAGTAAAATGTTACCAA 60.305 43.478 24.80 0.00 40.55 3.67
6259 6655 2.817423 CGAGAAGAATGCTGCCGGC 61.817 63.158 22.73 22.73 42.22 6.13
6266 6662 0.813210 CTGGGAGCCGAGAAGAATGC 60.813 60.000 0.00 0.00 0.00 3.56
6282 6678 1.448985 TTTCCGATTTTCCTCGCTGG 58.551 50.000 0.00 0.00 37.33 4.85
6305 6701 1.134907 GGAACTGGAGCGACCGATTTA 60.135 52.381 0.00 0.00 42.61 1.40
6306 6702 0.391263 GGAACTGGAGCGACCGATTT 60.391 55.000 0.00 0.00 42.61 2.17
6320 6716 4.657824 CACGTGTCGGCCGGAACT 62.658 66.667 27.83 10.69 0.00 3.01
6326 6722 2.432628 CCTTCTCACGTGTCGGCC 60.433 66.667 16.51 0.00 0.00 6.13
6353 6749 2.690497 GCAGTAGCTAGATGGAGACACA 59.310 50.000 0.00 0.00 40.13 3.72
6437 6833 1.956043 GGTCGCAACCAGAAATGCA 59.044 52.632 0.00 0.00 45.68 3.96


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.