Multiple sequence alignment - TraesCS4B01G249700

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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 TraesCS4B01G249700 chr4B 100.000 9129 0 0 1 9129 515157813 515166941 0.000000e+00 16859.0
1 TraesCS4B01G249700 chr4B 100.000 32 0 0 8289 8320 493784677 493784646 9.900000e-05 60.2
2 TraesCS4B01G249700 chr4D 96.885 4302 87 17 4015 8289 418621071 418616790 0.000000e+00 7158.0
3 TraesCS4B01G249700 chr4D 96.380 2376 51 17 784 3144 418624197 418621842 0.000000e+00 3879.0
4 TraesCS4B01G249700 chr4D 97.465 710 17 1 3304 4013 418621845 418621137 0.000000e+00 1210.0
5 TraesCS4B01G249700 chr4D 91.688 794 43 11 8289 9081 234703726 234704497 0.000000e+00 1079.0
6 TraesCS4B01G249700 chr4D 92.226 566 33 7 1 564 418722598 418722042 0.000000e+00 791.0
7 TraesCS4B01G249700 chr4D 82.514 183 16 6 560 740 418626078 418625910 7.390000e-31 147.0
8 TraesCS4B01G249700 chr4D 97.619 42 1 0 9073 9114 234724548 234724589 1.270000e-08 73.1
9 TraesCS4B01G249700 chr4A 95.134 2281 59 12 5894 8131 46125743 46123472 0.000000e+00 3550.0
10 TraesCS4B01G249700 chr4A 94.796 2133 83 17 842 2951 46131261 46129134 0.000000e+00 3299.0
11 TraesCS4B01G249700 chr4A 98.148 1674 23 5 4225 5896 46127503 46125836 0.000000e+00 2913.0
12 TraesCS4B01G249700 chr4A 97.887 710 14 1 3304 4013 46128978 46128270 0.000000e+00 1227.0
13 TraesCS4B01G249700 chr4A 93.445 839 31 3 8285 9123 743341984 743341170 0.000000e+00 1223.0
14 TraesCS4B01G249700 chr4A 84.203 747 75 18 2 740 46133134 46132423 0.000000e+00 686.0
15 TraesCS4B01G249700 chr4A 92.593 216 9 4 4016 4230 46128200 46127991 4.140000e-78 303.0
16 TraesCS4B01G249700 chr4A 94.643 168 4 1 2977 3144 46129137 46128975 1.180000e-63 255.0
17 TraesCS4B01G249700 chr5B 99.278 831 5 1 8291 9121 325942528 325941699 0.000000e+00 1500.0
18 TraesCS4B01G249700 chr5B 99.777 448 1 0 8676 9123 535692193 535691746 0.000000e+00 822.0
19 TraesCS4B01G249700 chr5B 98.324 358 4 2 8270 8626 535692541 535692185 2.160000e-175 627.0
20 TraesCS4B01G249700 chr5B 97.688 173 3 1 3137 3309 93472270 93472099 6.930000e-76 296.0
21 TraesCS4B01G249700 chr5B 98.193 166 3 0 3143 3308 575812805 575812970 3.220000e-74 291.0
22 TraesCS4B01G249700 chr5B 79.444 180 14 15 1829 2005 37063389 37063548 1.250000e-18 106.0
23 TraesCS4B01G249700 chr2A 99.359 780 4 1 8342 9121 721607943 721608721 0.000000e+00 1411.0
24 TraesCS4B01G249700 chr2A 94.595 74 4 0 64 137 19032097 19032170 2.080000e-21 115.0
25 TraesCS4B01G249700 chr2A 100.000 56 0 0 8289 8344 721607807 721607862 4.510000e-18 104.0
26 TraesCS4B01G249700 chr3A 96.181 838 28 2 8287 9124 712528814 712527981 0.000000e+00 1367.0
27 TraesCS4B01G249700 chr3A 85.047 107 13 2 620 726 571174260 571174363 1.250000e-18 106.0
28 TraesCS4B01G249700 chr7A 95.579 837 33 2 8287 9123 98540872 98540040 0.000000e+00 1338.0
29 TraesCS4B01G249700 chr3B 91.737 835 40 11 8293 9119 338577365 338576552 0.000000e+00 1133.0
30 TraesCS4B01G249700 chr3B 85.714 119 15 2 624 740 578986334 578986216 3.460000e-24 124.0
31 TraesCS4B01G249700 chr3B 86.420 81 10 1 646 726 565265007 565265086 4.540000e-13 87.9
32 TraesCS4B01G249700 chr3B 75.000 152 32 6 236 386 822224211 822224065 2.130000e-06 65.8
33 TraesCS4B01G249700 chr3B 75.000 152 32 6 236 386 822314779 822314633 2.130000e-06 65.8
34 TraesCS4B01G249700 chr6B 88.849 278 13 4 8844 9121 705558322 705558581 8.840000e-85 326.0
35 TraesCS4B01G249700 chr1D 97.647 170 4 0 3138 3307 238940211 238940380 8.970000e-75 292.0
36 TraesCS4B01G249700 chr1D 96.571 175 6 0 3133 3307 196817853 196817679 3.220000e-74 291.0
37 TraesCS4B01G249700 chr2D 97.093 172 5 0 3136 3307 161906845 161907016 3.220000e-74 291.0
38 TraesCS4B01G249700 chr2D 96.089 179 5 2 3129 3307 560959473 560959649 3.220000e-74 291.0
39 TraesCS4B01G249700 chr2D 94.595 74 4 0 64 137 17635607 17635680 2.080000e-21 115.0
40 TraesCS4B01G249700 chr2D 93.243 74 5 0 64 137 17609868 17609941 9.690000e-20 110.0
41 TraesCS4B01G249700 chr2D 78.049 123 23 3 620 740 369239685 369239565 3.540000e-09 75.0
42 TraesCS4B01G249700 chr6A 97.076 171 5 0 3139 3309 287304227 287304057 1.160000e-73 289.0
43 TraesCS4B01G249700 chr6D 97.059 170 5 0 3139 3308 406391527 406391358 4.170000e-73 287.0
44 TraesCS4B01G249700 chr6D 85.556 90 8 5 625 710 469972904 469972992 1.260000e-13 89.8
45 TraesCS4B01G249700 chr6D 100.000 30 0 0 8233 8262 342022305 342022276 1.000000e-03 56.5
46 TraesCS4B01G249700 chr6D 100.000 28 0 0 8235 8262 89235560 89235587 1.700000e-02 52.8
47 TraesCS4B01G249700 chr3D 93.194 191 9 4 3117 3307 254826823 254827009 2.510000e-70 278.0
48 TraesCS4B01G249700 chr5D 96.479 142 1 3 8986 9123 330884592 330884733 1.980000e-56 231.0
49 TraesCS4B01G249700 chr1A 90.667 75 6 1 612 685 264222305 264222379 2.100000e-16 99.0
50 TraesCS4B01G249700 chr2B 84.946 93 12 2 625 715 438878969 438878877 9.760000e-15 93.5
51 TraesCS4B01G249700 chr2B 94.737 38 2 0 1944 1981 529499605 529499642 9.900000e-05 60.2
52 TraesCS4B01G249700 chrUn 75.000 152 32 6 236 386 334317573 334317427 2.130000e-06 65.8
53 TraesCS4B01G249700 chrUn 75.000 152 32 6 236 386 383435389 383435535 2.130000e-06 65.8


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 TraesCS4B01G249700 chr4B 515157813 515166941 9128 False 16859.000000 16859 100.000000 1 9129 1 chr4B.!!$F1 9128
1 TraesCS4B01G249700 chr4D 418616790 418626078 9288 True 3098.500000 7158 93.311000 560 8289 4 chr4D.!!$R2 7729
2 TraesCS4B01G249700 chr4D 234703726 234704497 771 False 1079.000000 1079 91.688000 8289 9081 1 chr4D.!!$F1 792
3 TraesCS4B01G249700 chr4D 418722042 418722598 556 True 791.000000 791 92.226000 1 564 1 chr4D.!!$R1 563
4 TraesCS4B01G249700 chr4A 46123472 46133134 9662 True 1747.571429 3550 93.914857 2 8131 7 chr4A.!!$R2 8129
5 TraesCS4B01G249700 chr4A 743341170 743341984 814 True 1223.000000 1223 93.445000 8285 9123 1 chr4A.!!$R1 838
6 TraesCS4B01G249700 chr5B 325941699 325942528 829 True 1500.000000 1500 99.278000 8291 9121 1 chr5B.!!$R2 830
7 TraesCS4B01G249700 chr5B 535691746 535692541 795 True 724.500000 822 99.050500 8270 9123 2 chr5B.!!$R3 853
8 TraesCS4B01G249700 chr2A 721607807 721608721 914 False 757.500000 1411 99.679500 8289 9121 2 chr2A.!!$F2 832
9 TraesCS4B01G249700 chr3A 712527981 712528814 833 True 1367.000000 1367 96.181000 8287 9124 1 chr3A.!!$R1 837
10 TraesCS4B01G249700 chr7A 98540040 98540872 832 True 1338.000000 1338 95.579000 8287 9123 1 chr7A.!!$R1 836
11 TraesCS4B01G249700 chr3B 338576552 338577365 813 True 1133.000000 1133 91.737000 8293 9119 1 chr3B.!!$R1 826

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
782 2831 0.185901 AAGGCAAGGAGAAGCAACCA 59.814 50.000 0.00 0.00 0.00 3.67 F
831 2975 0.472471 TCATATTCCGTTGGCCTCCC 59.528 55.000 3.32 0.00 0.00 4.30 F
2019 4194 0.396060 GAGGAGGCAGGGAGCTATTG 59.604 60.000 0.00 0.00 44.79 1.90 F
2660 4840 0.240945 GCAAACCCTGGTCATGTTCG 59.759 55.000 0.00 0.00 0.00 3.95 F
3263 5444 1.749063 TGCTCCGTATGTAGTCACCTG 59.251 52.381 0.00 0.00 0.00 4.00 F
4173 6422 1.729149 GCAAAAATTAGCTCGCACGCT 60.729 47.619 0.00 2.12 43.83 5.07 F
4263 7005 2.092212 CACCTAGGAATTGAGGCACCAT 60.092 50.000 17.98 0.00 36.17 3.55 F
4421 7165 2.103373 TCCTTCAGAAGACTGGATCCG 58.897 52.381 12.14 4.62 43.60 4.18 F
4472 7216 3.260740 CCTCAGCAGCTAACTTCTCAAG 58.739 50.000 0.00 0.00 0.00 3.02 F
6245 9123 4.246143 AGATATCCAACCACCCATCTCAT 58.754 43.478 0.00 0.00 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1797 3964 0.103026 GATTTCCAGCGCCCAAATCC 59.897 55.000 18.77 7.2 32.53 3.01 R
2628 4806 0.322008 GGTTTGCTGAGACTGGGAGG 60.322 60.000 0.00 0.0 0.00 4.30 R
3298 5479 0.033011 TCTCTGGCCACTACTCCCTC 60.033 60.000 0.00 0.0 0.00 4.30 R
3982 6163 3.119173 CGGATGCTTTAAAATCCAAGCCA 60.119 43.478 15.89 0.0 44.15 4.75 R
4822 7572 0.895559 AGCTGCAAAACACCCCTAGC 60.896 55.000 1.02 0.0 0.00 3.42 R
5768 8519 1.511850 CAGTCTTGCACGACAATCCA 58.488 50.000 23.55 0.0 37.72 3.41 R
6402 9280 9.302345 ACAGTATCGACACAAGTAAAGAATATG 57.698 33.333 0.00 0.0 0.00 1.78 R
6836 9716 9.720769 TTAAGTTGACTGATTAAACTTAGGAGG 57.279 33.333 7.16 0.0 43.51 4.30 R
6892 9772 9.739276 AATTATAGATGTGTGGTTCTTCAAAGA 57.261 29.630 0.00 0.0 0.00 2.52 R
8172 11063 0.036306 AGTAGGTGTTTGCTTCCCCG 59.964 55.000 0.00 0.0 0.00 5.73 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
169 171 8.349245 CAACGGTCTAAAATATAATGCATTGGA 58.651 33.333 22.27 9.74 0.00 3.53
388 392 8.584157 AGATACAATTCATTAGAGGAGCTACTG 58.416 37.037 0.99 0.00 32.61 2.74
497 501 4.319177 AGAGTGATCCTAAGTGCAACAAC 58.681 43.478 0.00 0.00 41.43 3.32
514 518 7.011669 GTGCAACAACACTAGTCCTAAGTTTAA 59.988 37.037 0.00 0.00 37.58 1.52
554 558 5.244755 ACAACAACAAACTTGCCTTTGATT 58.755 33.333 5.80 0.00 35.46 2.57
564 568 2.161855 TGCCTTTGATTGTGCAGGTAG 58.838 47.619 0.00 0.00 0.00 3.18
565 569 2.162681 GCCTTTGATTGTGCAGGTAGT 58.837 47.619 0.00 0.00 0.00 2.73
566 570 2.162408 GCCTTTGATTGTGCAGGTAGTC 59.838 50.000 0.00 0.00 0.00 2.59
567 571 3.411446 CCTTTGATTGTGCAGGTAGTCA 58.589 45.455 0.00 0.00 0.00 3.41
568 572 4.012374 CCTTTGATTGTGCAGGTAGTCAT 58.988 43.478 0.00 0.00 0.00 3.06
569 573 5.185454 CCTTTGATTGTGCAGGTAGTCATA 58.815 41.667 0.00 0.00 0.00 2.15
576 580 2.108168 TGCAGGTAGTCATAGTGTCCC 58.892 52.381 0.00 0.00 0.00 4.46
609 613 6.940739 GTGGTCTCAATGCTCCACTATATAT 58.059 40.000 11.66 0.00 44.57 0.86
618 624 6.824958 TGCTCCACTATATATTTATCCCCC 57.175 41.667 0.00 0.00 0.00 5.40
652 658 0.750546 GCCCCCTCGTATTTTGGGTC 60.751 60.000 0.00 0.00 39.31 4.46
658 664 5.137551 CCCCTCGTATTTTGGGTCATATTT 58.862 41.667 0.00 0.00 39.31 1.40
660 666 6.773685 CCCCTCGTATTTTGGGTCATATTTTA 59.226 38.462 0.00 0.00 39.31 1.52
740 748 3.382546 GCAACATTGAGATACCAAGCCAT 59.617 43.478 0.00 0.00 0.00 4.40
742 750 4.785346 ACATTGAGATACCAAGCCATCT 57.215 40.909 0.00 0.00 34.19 2.90
743 751 4.712476 ACATTGAGATACCAAGCCATCTC 58.288 43.478 4.93 4.93 44.92 2.75
747 2796 2.887783 GAGATACCAAGCCATCTCTCGA 59.112 50.000 4.68 0.00 42.54 4.04
782 2831 0.185901 AAGGCAAGGAGAAGCAACCA 59.814 50.000 0.00 0.00 0.00 3.67
788 2837 1.846712 AGGAGAAGCAACCAGCCTCC 61.847 60.000 0.00 0.00 46.29 4.30
799 2943 4.548513 AGCCTCCCCTCGCCTAGG 62.549 72.222 3.67 3.67 46.09 3.02
830 2974 1.594331 GTCATATTCCGTTGGCCTCC 58.406 55.000 3.32 0.00 0.00 4.30
831 2975 0.472471 TCATATTCCGTTGGCCTCCC 59.528 55.000 3.32 0.00 0.00 4.30
832 2976 0.537371 CATATTCCGTTGGCCTCCCC 60.537 60.000 3.32 0.00 0.00 4.81
833 2977 1.716028 ATATTCCGTTGGCCTCCCCC 61.716 60.000 3.32 0.00 0.00 5.40
863 3007 3.620488 CCGGAAATTCTCAAATCCCTCA 58.380 45.455 0.00 0.00 0.00 3.86
864 3008 3.629398 CCGGAAATTCTCAAATCCCTCAG 59.371 47.826 0.00 0.00 0.00 3.35
865 3009 4.517285 CGGAAATTCTCAAATCCCTCAGA 58.483 43.478 0.00 0.00 0.00 3.27
866 3010 4.574013 CGGAAATTCTCAAATCCCTCAGAG 59.426 45.833 0.00 0.00 0.00 3.35
867 3011 4.337836 GGAAATTCTCAAATCCCTCAGAGC 59.662 45.833 0.00 0.00 0.00 4.09
868 3012 3.574354 ATTCTCAAATCCCTCAGAGCC 57.426 47.619 0.00 0.00 0.00 4.70
869 3013 1.956869 TCTCAAATCCCTCAGAGCCA 58.043 50.000 0.00 0.00 0.00 4.75
870 3014 1.836166 TCTCAAATCCCTCAGAGCCAG 59.164 52.381 0.00 0.00 0.00 4.85
871 3015 1.558756 CTCAAATCCCTCAGAGCCAGT 59.441 52.381 0.00 0.00 0.00 4.00
941 3088 3.443681 CGACCAGCATTATTCCCTGTTTT 59.556 43.478 0.00 0.00 0.00 2.43
1418 3581 6.037098 CCATCGGTAAGGATAAGATCGATTC 58.963 44.000 0.00 0.00 34.31 2.52
1421 3584 6.621613 TCGGTAAGGATAAGATCGATTCATG 58.378 40.000 0.00 0.00 0.00 3.07
1456 3622 1.215382 GATTCGGTGCTTTTGGGGC 59.785 57.895 0.00 0.00 0.00 5.80
1683 3850 3.430929 CCAAGAGAGTTAGTCATTCGGGG 60.431 52.174 0.00 0.00 0.00 5.73
1762 3929 7.284489 TCTGTTATTGGCCAAAATGTAGTATCC 59.716 37.037 24.71 3.15 0.00 2.59
1796 3963 0.762418 TGAACCATCGACTGGGTTGT 59.238 50.000 19.27 0.55 45.28 3.32
1797 3964 1.156736 GAACCATCGACTGGGTTGTG 58.843 55.000 19.27 0.00 45.28 3.33
1927 4095 3.644884 ATCAGCTTTCCCTACGTATCG 57.355 47.619 0.00 0.00 0.00 2.92
2019 4194 0.396060 GAGGAGGCAGGGAGCTATTG 59.604 60.000 0.00 0.00 44.79 1.90
2020 4195 1.228094 GGAGGCAGGGAGCTATTGC 60.228 63.158 7.78 7.78 44.79 3.56
2208 4385 3.710209 ACCTCTGGAGATTTGAAGTGG 57.290 47.619 0.00 0.00 0.00 4.00
2255 4432 9.432982 TGGGTTTATGAATTATGATTAGGCTTT 57.567 29.630 0.00 0.00 0.00 3.51
2266 4443 9.813826 ATTATGATTAGGCTTTGGCTTAGTTAT 57.186 29.630 0.00 0.00 39.70 1.89
2267 4444 9.640952 TTATGATTAGGCTTTGGCTTAGTTATT 57.359 29.630 0.00 0.00 39.70 1.40
2268 4445 7.954666 TGATTAGGCTTTGGCTTAGTTATTT 57.045 32.000 0.00 0.00 39.70 1.40
2269 4446 7.996385 TGATTAGGCTTTGGCTTAGTTATTTC 58.004 34.615 0.00 0.00 39.70 2.17
2601 4779 6.305272 TCTGCTCTGACCTGATTAGATTTT 57.695 37.500 0.00 0.00 0.00 1.82
2628 4806 6.803366 TTTGGGTTACTAGATAGTTCTCCC 57.197 41.667 0.00 14.48 38.50 4.30
2660 4840 0.240945 GCAAACCCTGGTCATGTTCG 59.759 55.000 0.00 0.00 0.00 3.95
2749 4929 2.050985 GTTCGCTGCCTTGTGTGC 60.051 61.111 0.00 0.00 0.00 4.57
2910 5090 4.492646 TGAGATAGATGGCATAGGTCCAA 58.507 43.478 0.00 0.00 37.13 3.53
2929 5109 5.527214 GTCCAAATGCCTGCTTTTAACTTTT 59.473 36.000 3.10 0.00 0.00 2.27
3010 5191 7.913789 TGATAAGTCAAGTTACCACTTACCAT 58.086 34.615 4.26 0.00 41.69 3.55
3085 5266 4.037923 ACTCTTGAGCTTCTCTATAGCAGC 59.962 45.833 9.32 9.32 41.72 5.25
3138 5319 4.623932 TTTTGGCTCTTGAGCTTCTCTA 57.376 40.909 20.12 0.61 34.73 2.43
3140 5321 5.939764 TTTGGCTCTTGAGCTTCTCTATA 57.060 39.130 20.12 0.00 34.73 1.31
3141 5322 5.528043 TTGGCTCTTGAGCTTCTCTATAG 57.472 43.478 20.12 0.00 34.73 1.31
3142 5323 4.541705 TGGCTCTTGAGCTTCTCTATAGT 58.458 43.478 20.12 0.00 34.73 2.12
3143 5324 5.696030 TGGCTCTTGAGCTTCTCTATAGTA 58.304 41.667 20.12 0.00 34.73 1.82
3144 5325 5.533154 TGGCTCTTGAGCTTCTCTATAGTAC 59.467 44.000 20.12 2.04 34.73 2.73
3145 5326 5.768164 GGCTCTTGAGCTTCTCTATAGTACT 59.232 44.000 20.12 0.00 34.73 2.73
3146 5327 6.072673 GGCTCTTGAGCTTCTCTATAGTACTC 60.073 46.154 20.12 2.26 34.73 2.59
3147 5328 6.072673 GCTCTTGAGCTTCTCTATAGTACTCC 60.073 46.154 14.65 0.00 0.00 3.85
3148 5329 6.300703 TCTTGAGCTTCTCTATAGTACTCCC 58.699 44.000 0.00 0.00 0.00 4.30
3149 5330 5.915744 TGAGCTTCTCTATAGTACTCCCT 57.084 43.478 0.00 0.00 0.00 4.20
3150 5331 5.871834 TGAGCTTCTCTATAGTACTCCCTC 58.128 45.833 0.00 1.82 0.00 4.30
3151 5332 5.221966 TGAGCTTCTCTATAGTACTCCCTCC 60.222 48.000 0.00 0.00 0.00 4.30
3152 5333 4.004982 GCTTCTCTATAGTACTCCCTCCG 58.995 52.174 0.00 0.00 0.00 4.63
3153 5334 4.505390 GCTTCTCTATAGTACTCCCTCCGT 60.505 50.000 0.00 0.00 0.00 4.69
3154 5335 5.623169 CTTCTCTATAGTACTCCCTCCGTT 58.377 45.833 0.00 0.00 0.00 4.44
3155 5336 5.226194 TCTCTATAGTACTCCCTCCGTTC 57.774 47.826 0.00 0.00 0.00 3.95
3156 5337 4.041444 TCTCTATAGTACTCCCTCCGTTCC 59.959 50.000 0.00 0.00 0.00 3.62
3157 5338 3.979347 TCTATAGTACTCCCTCCGTTCCT 59.021 47.826 0.00 0.00 0.00 3.36
3158 5339 5.158141 TCTATAGTACTCCCTCCGTTCCTA 58.842 45.833 0.00 0.00 0.00 2.94
3159 5340 4.803329 ATAGTACTCCCTCCGTTCCTAA 57.197 45.455 0.00 0.00 0.00 2.69
3160 5341 3.463048 AGTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
3161 5342 3.991683 AGTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
3162 5343 5.134725 AGTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
3163 5344 5.713807 AGTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
3164 5345 6.141790 AGTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
3165 5346 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3166 5347 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3167 5348 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3168 5349 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3169 5350 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
3170 5351 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
3171 5352 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
3172 5353 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
3173 5354 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
3174 5355 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
3175 5356 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
3176 5357 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
3189 5370 9.573166 TTTGTCTTTCTAGAGATTTCAAATGGA 57.427 29.630 0.00 0.00 0.00 3.41
3190 5371 8.553459 TGTCTTTCTAGAGATTTCAAATGGAC 57.447 34.615 0.00 0.00 0.00 4.02
3191 5372 8.378565 TGTCTTTCTAGAGATTTCAAATGGACT 58.621 33.333 0.00 0.00 0.00 3.85
3192 5373 9.877178 GTCTTTCTAGAGATTTCAAATGGACTA 57.123 33.333 0.00 0.00 0.00 2.59
3193 5374 9.877178 TCTTTCTAGAGATTTCAAATGGACTAC 57.123 33.333 0.00 0.00 0.00 2.73
3194 5375 9.103861 CTTTCTAGAGATTTCAAATGGACTACC 57.896 37.037 0.00 0.00 0.00 3.18
3247 5428 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
3248 5429 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
3249 5430 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
3250 5431 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
3251 5432 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
3252 5433 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
3253 5434 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
3254 5435 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
3255 5436 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
3256 5437 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
3257 5438 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
3258 5439 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
3259 5440 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
3260 5441 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
3261 5442 2.953466 TTGCTCCGTATGTAGTCACC 57.047 50.000 0.00 0.00 0.00 4.02
3262 5443 2.139323 TGCTCCGTATGTAGTCACCT 57.861 50.000 0.00 0.00 0.00 4.00
3263 5444 1.749063 TGCTCCGTATGTAGTCACCTG 59.251 52.381 0.00 0.00 0.00 4.00
3264 5445 1.749634 GCTCCGTATGTAGTCACCTGT 59.250 52.381 0.00 0.00 0.00 4.00
3265 5446 2.165845 GCTCCGTATGTAGTCACCTGTT 59.834 50.000 0.00 0.00 0.00 3.16
3266 5447 3.770666 CTCCGTATGTAGTCACCTGTTG 58.229 50.000 0.00 0.00 0.00 3.33
3267 5448 3.423749 TCCGTATGTAGTCACCTGTTGA 58.576 45.455 0.00 0.00 0.00 3.18
3268 5449 3.827876 TCCGTATGTAGTCACCTGTTGAA 59.172 43.478 0.00 0.00 35.39 2.69
3269 5450 4.281435 TCCGTATGTAGTCACCTGTTGAAA 59.719 41.667 0.00 0.00 35.39 2.69
3270 5451 5.046878 TCCGTATGTAGTCACCTGTTGAAAT 60.047 40.000 0.00 0.00 35.39 2.17
3271 5452 5.291128 CCGTATGTAGTCACCTGTTGAAATC 59.709 44.000 0.00 0.00 35.39 2.17
3272 5453 6.100004 CGTATGTAGTCACCTGTTGAAATCT 58.900 40.000 0.00 0.00 35.39 2.40
3273 5454 6.253727 CGTATGTAGTCACCTGTTGAAATCTC 59.746 42.308 0.00 0.00 35.39 2.75
3274 5455 5.808366 TGTAGTCACCTGTTGAAATCTCT 57.192 39.130 0.00 0.00 35.39 3.10
3275 5456 6.911250 TGTAGTCACCTGTTGAAATCTCTA 57.089 37.500 0.00 0.00 35.39 2.43
3276 5457 6.925211 TGTAGTCACCTGTTGAAATCTCTAG 58.075 40.000 0.00 0.00 35.39 2.43
3277 5458 6.719829 TGTAGTCACCTGTTGAAATCTCTAGA 59.280 38.462 0.00 0.00 35.39 2.43
3278 5459 6.672266 AGTCACCTGTTGAAATCTCTAGAA 57.328 37.500 0.00 0.00 35.39 2.10
3279 5460 7.067496 AGTCACCTGTTGAAATCTCTAGAAA 57.933 36.000 0.00 0.00 35.39 2.52
3280 5461 7.158021 AGTCACCTGTTGAAATCTCTAGAAAG 58.842 38.462 0.00 0.00 35.39 2.62
3281 5462 7.015682 AGTCACCTGTTGAAATCTCTAGAAAGA 59.984 37.037 0.00 0.00 35.39 2.52
3282 5463 7.117092 GTCACCTGTTGAAATCTCTAGAAAGAC 59.883 40.741 0.00 0.00 35.39 3.01
3283 5464 6.931281 CACCTGTTGAAATCTCTAGAAAGACA 59.069 38.462 0.00 0.00 0.00 3.41
3284 5465 7.442364 CACCTGTTGAAATCTCTAGAAAGACAA 59.558 37.037 0.00 0.00 0.00 3.18
3285 5466 7.993183 ACCTGTTGAAATCTCTAGAAAGACAAA 59.007 33.333 0.00 0.00 0.00 2.83
3286 5467 9.007901 CCTGTTGAAATCTCTAGAAAGACAAAT 57.992 33.333 0.00 0.00 0.00 2.32
3298 5479 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
3299 5480 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
3300 5481 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
3301 5482 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
3302 5483 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3489 5670 4.142687 CCATGAGTTGTCGGTATTTTGGTC 60.143 45.833 0.00 0.00 0.00 4.02
3505 5686 9.614792 GTATTTTGGTCCTCTAGATGTGTATTT 57.385 33.333 0.00 0.00 0.00 1.40
3607 5788 4.142600 GGTGTAACTGTTGCAATCCTGATC 60.143 45.833 12.86 0.00 36.74 2.92
3682 5863 4.081807 GGGTGATTCTACGGTAAGACACTT 60.082 45.833 0.00 0.00 0.00 3.16
3695 5876 6.566564 CGGTAAGACACTTAACTCGTTGACTA 60.567 42.308 0.00 0.00 0.00 2.59
3696 5877 7.141363 GGTAAGACACTTAACTCGTTGACTAA 58.859 38.462 0.00 0.00 0.00 2.24
3885 6066 5.927115 GGAGATGAAGGATAACCATTACGAC 59.073 44.000 0.00 0.00 38.94 4.34
3933 6114 5.007385 AGGCTACGGTATGAAACTAACAG 57.993 43.478 0.00 0.00 0.00 3.16
4013 6194 6.262273 GGATTTTAAAGCATCCGAAGACCATA 59.738 38.462 3.67 0.00 29.78 2.74
4173 6422 1.729149 GCAAAAATTAGCTCGCACGCT 60.729 47.619 0.00 2.12 43.83 5.07
4184 6433 2.285084 GCTCGCACGCTATTTTACAGAC 60.285 50.000 0.00 0.00 0.00 3.51
4185 6434 2.921121 CTCGCACGCTATTTTACAGACA 59.079 45.455 0.00 0.00 0.00 3.41
4186 6435 3.517602 TCGCACGCTATTTTACAGACAT 58.482 40.909 0.00 0.00 0.00 3.06
4189 6438 5.401376 TCGCACGCTATTTTACAGACATATC 59.599 40.000 0.00 0.00 0.00 1.63
4190 6439 5.388475 CGCACGCTATTTTACAGACATATCC 60.388 44.000 0.00 0.00 0.00 2.59
4191 6440 5.465390 GCACGCTATTTTACAGACATATCCA 59.535 40.000 0.00 0.00 0.00 3.41
4192 6441 6.147821 GCACGCTATTTTACAGACATATCCAT 59.852 38.462 0.00 0.00 0.00 3.41
4193 6442 7.513132 CACGCTATTTTACAGACATATCCATG 58.487 38.462 0.00 0.00 38.21 3.66
4195 6444 7.715249 ACGCTATTTTACAGACATATCCATGTT 59.285 33.333 0.00 0.00 45.58 2.71
4221 6470 7.643569 TCTACATTGCATAATTGTGTTGGAT 57.356 32.000 4.00 0.00 0.00 3.41
4263 7005 2.092212 CACCTAGGAATTGAGGCACCAT 60.092 50.000 17.98 0.00 36.17 3.55
4421 7165 2.103373 TCCTTCAGAAGACTGGATCCG 58.897 52.381 12.14 4.62 43.60 4.18
4472 7216 3.260740 CCTCAGCAGCTAACTTCTCAAG 58.739 50.000 0.00 0.00 0.00 3.02
4788 7538 7.273188 CATGATATGCTCTTTGTTGTTTGTG 57.727 36.000 0.00 0.00 0.00 3.33
4804 7554 8.494347 TGTTGTTTGTGATCTTTTGAAAAAGTG 58.506 29.630 13.68 0.00 44.37 3.16
4822 7572 9.530129 GAAAAAGTGTATCTAACTCACATTTCG 57.470 33.333 0.00 0.00 33.84 3.46
4872 7622 7.987750 TGTAATTTACCATGACTTGCAACTA 57.012 32.000 0.00 0.00 0.00 2.24
4940 7691 8.776470 CAGTTCTGGTCATTTTGCAATTTTATT 58.224 29.630 0.00 0.00 0.00 1.40
5768 8519 5.351189 GGCTGTTCTTTGTGTCAAATGTTTT 59.649 36.000 0.00 0.00 0.00 2.43
6245 9123 4.246143 AGATATCCAACCACCCATCTCAT 58.754 43.478 0.00 0.00 0.00 2.90
6402 9280 6.454795 TGTTATCTTTTTGTCCAATTCTGGC 58.545 36.000 0.00 0.00 43.17 4.85
6836 9716 7.906010 GGTAACACATTTTAACCTTGCAAAAAC 59.094 33.333 0.00 0.00 0.00 2.43
6921 9801 7.761409 TGAAGAACCACACATCTATAATTTGC 58.239 34.615 0.00 0.00 0.00 3.68
6937 9817 5.811399 AATTTGCGCTGCATAGTTTAGTA 57.189 34.783 9.73 0.00 38.76 1.82
7013 9893 3.202906 TGTGCTGTCTAGTGTTCCAAAC 58.797 45.455 0.00 0.00 0.00 2.93
7015 9895 3.248602 GTGCTGTCTAGTGTTCCAAACTG 59.751 47.826 0.00 0.00 0.00 3.16
7111 9991 3.316308 GCAATCCTGTGTTGTCTTCACTT 59.684 43.478 0.00 0.00 36.83 3.16
7181 10061 8.598916 TGGGTATGAAGAATAGTTACTCACAAA 58.401 33.333 0.00 0.00 0.00 2.83
7241 10121 3.119849 GCTATAGTTGTTGGCACTGTTGG 60.120 47.826 0.84 0.00 0.00 3.77
7305 10187 4.833390 CCGGTCTTACTCTCTGGAAATTT 58.167 43.478 0.00 0.00 0.00 1.82
7407 10289 1.523758 ACCAAGAAAGCACGGACATC 58.476 50.000 0.00 0.00 0.00 3.06
7580 10462 4.189639 ACGACAGATAAGGACTTTGGAC 57.810 45.455 0.00 0.00 0.00 4.02
7683 10568 4.643784 GGAGGAAAGCAATCATCAGTGAAT 59.356 41.667 0.00 0.00 38.01 2.57
7809 10694 4.664150 TTGGTTGGTCATTCTTTTGGAC 57.336 40.909 0.00 0.00 0.00 4.02
7813 10698 4.499696 GGTTGGTCATTCTTTTGGACAGTG 60.500 45.833 0.00 0.00 33.26 3.66
8074 10965 4.318332 TGTAGTAGATATGCCATTGCTGC 58.682 43.478 0.00 0.00 38.71 5.25
8076 10967 2.037641 AGTAGATATGCCATTGCTGCGA 59.962 45.455 0.00 0.00 38.71 5.10
8213 11104 3.694566 TCGAGCTGATGTTAGAGCAACTA 59.305 43.478 0.00 0.00 37.70 2.24
8214 11105 4.157840 TCGAGCTGATGTTAGAGCAACTAA 59.842 41.667 0.00 0.00 37.70 2.24
8250 11141 4.573900 CTGATGTTAGAGCAACTCCAACT 58.426 43.478 7.29 0.00 34.24 3.16
8254 11145 0.324943 TAGAGCAACTCCAACTGGCC 59.675 55.000 0.00 0.00 34.44 5.36
8262 11153 2.672996 CCAACTGGCCGACCCAAG 60.673 66.667 0.00 0.00 44.81 3.61
8268 11159 4.717313 GGCCGACCCAAGTGGACC 62.717 72.222 0.00 0.00 37.39 4.46
8269 11160 4.717313 GCCGACCCAAGTGGACCC 62.717 72.222 0.00 0.00 37.39 4.46
8280 11171 1.033202 AGTGGACCCGCGTTTTGTTT 61.033 50.000 4.92 0.00 0.00 2.83
8759 11741 1.525535 GAAGCTGATGCGGCAGGAT 60.526 57.895 9.25 0.00 45.42 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 148 7.362056 CCCTCCAATGCATTATATTTTAGACCG 60.362 40.741 12.53 0.00 0.00 4.79
169 171 8.701643 ATTAAGATATAATCTAAGGGCACCCT 57.298 34.615 1.11 1.11 45.97 4.34
240 242 9.730705 AACACATGATATTTCTCTCTTTTCTCA 57.269 29.630 0.00 0.00 0.00 3.27
282 286 5.941788 AGTTGTCTTGGTCTTGGTTCTAAT 58.058 37.500 0.00 0.00 0.00 1.73
371 375 5.953571 TGGATACAGTAGCTCCTCTAATGA 58.046 41.667 6.42 0.00 43.89 2.57
441 445 7.698130 CCTCCTGATCGATGTTAAATTTTTGTC 59.302 37.037 0.54 0.00 0.00 3.18
457 461 0.248825 CTTCGACTGCCTCCTGATCG 60.249 60.000 0.00 0.00 0.00 3.69
497 501 6.128634 CCGTTTGCTTAAACTTAGGACTAGTG 60.129 42.308 0.00 0.00 0.00 2.74
505 509 8.568732 TTCATTTTCCGTTTGCTTAAACTTAG 57.431 30.769 0.00 0.00 0.00 2.18
514 518 4.499183 TGTTGTTTCATTTTCCGTTTGCT 58.501 34.783 0.00 0.00 0.00 3.91
554 558 2.496070 GGACACTATGACTACCTGCACA 59.504 50.000 0.00 0.00 0.00 4.57
564 568 1.755380 AGTAAGGCGGGACACTATGAC 59.245 52.381 0.00 0.00 0.00 3.06
565 569 1.754803 CAGTAAGGCGGGACACTATGA 59.245 52.381 0.00 0.00 0.00 2.15
566 570 1.480954 ACAGTAAGGCGGGACACTATG 59.519 52.381 0.00 0.00 0.00 2.23
567 571 1.480954 CACAGTAAGGCGGGACACTAT 59.519 52.381 0.00 0.00 0.00 2.12
568 572 0.892755 CACAGTAAGGCGGGACACTA 59.107 55.000 0.00 0.00 0.00 2.74
569 573 1.671742 CACAGTAAGGCGGGACACT 59.328 57.895 0.00 0.00 0.00 3.55
576 580 2.002586 CATTGAGACCACAGTAAGGCG 58.997 52.381 0.00 0.00 0.00 5.52
609 613 3.588396 AGTAAACCAAGACGGGGGATAAA 59.412 43.478 0.00 0.00 40.22 1.40
618 624 1.406477 GGGGGCTAGTAAACCAAGACG 60.406 57.143 0.00 0.00 0.00 4.18
718 726 2.754552 TGGCTTGGTATCTCAATGTTGC 59.245 45.455 0.00 0.00 0.00 4.17
726 734 2.887783 TCGAGAGATGGCTTGGTATCTC 59.112 50.000 0.00 0.00 46.11 2.75
742 750 4.116328 CTTCCGGCTGCGTCGAGA 62.116 66.667 0.00 0.00 29.41 4.04
743 751 4.116328 TCTTCCGGCTGCGTCGAG 62.116 66.667 0.00 0.00 29.41 4.04
747 2796 3.302347 CTTCCTCTTCCGGCTGCGT 62.302 63.158 0.00 0.00 0.00 5.24
768 2817 0.037447 GAGGCTGGTTGCTTCTCCTT 59.963 55.000 0.00 0.00 43.43 3.36
782 2831 4.548513 CCTAGGCGAGGGGAGGCT 62.549 72.222 5.64 0.00 46.54 4.58
811 2955 1.594331 GGAGGCCAACGGAATATGAC 58.406 55.000 5.01 0.00 0.00 3.06
812 2956 0.472471 GGGAGGCCAACGGAATATGA 59.528 55.000 5.01 0.00 0.00 2.15
863 3007 4.775236 CCTATCAGCTAAAAACTGGCTCT 58.225 43.478 0.00 0.00 40.48 4.09
864 3008 3.313803 GCCTATCAGCTAAAAACTGGCTC 59.686 47.826 0.00 0.00 40.48 4.70
865 3009 3.282885 GCCTATCAGCTAAAAACTGGCT 58.717 45.455 0.00 0.00 43.91 4.75
866 3010 2.359214 GGCCTATCAGCTAAAAACTGGC 59.641 50.000 0.00 0.00 35.78 4.85
867 3011 2.952310 GGGCCTATCAGCTAAAAACTGG 59.048 50.000 0.84 0.00 35.78 4.00
868 3012 2.952310 GGGGCCTATCAGCTAAAAACTG 59.048 50.000 0.84 0.00 36.44 3.16
869 3013 2.091830 GGGGGCCTATCAGCTAAAAACT 60.092 50.000 0.84 0.00 0.00 2.66
870 3014 2.307768 GGGGGCCTATCAGCTAAAAAC 58.692 52.381 0.84 0.00 0.00 2.43
871 3015 1.133915 CGGGGGCCTATCAGCTAAAAA 60.134 52.381 0.84 0.00 0.00 1.94
941 3088 0.481128 AGGGAGGCGAAAGGGAAAAA 59.519 50.000 0.00 0.00 0.00 1.94
1456 3622 2.513897 GATCCAAGGTTCGCCGGG 60.514 66.667 2.18 0.00 43.66 5.73
1683 3850 2.565841 AGCCGAAAGCCTGATCATAAC 58.434 47.619 0.00 0.00 45.47 1.89
1762 3929 4.351874 TGGTTCAAAACTAGGGAGTGAG 57.648 45.455 0.00 0.00 35.52 3.51
1796 3963 0.614415 ATTTCCAGCGCCCAAATCCA 60.614 50.000 2.29 0.00 0.00 3.41
1797 3964 0.103026 GATTTCCAGCGCCCAAATCC 59.897 55.000 18.77 7.20 32.53 3.01
1865 4032 6.549364 TCCTTTCTAATCCAGTTTTGCAAGAA 59.451 34.615 0.00 0.00 0.00 2.52
1927 4095 3.502211 ACAGTTGCAGCTTGTGGTATAAC 59.498 43.478 0.00 0.00 0.00 1.89
2208 4385 5.412904 CCCAAATCACTAACTCTCTTGGTTC 59.587 44.000 0.00 0.00 31.80 3.62
2379 4557 2.254546 AATCCAACAGTGCGTCTGAA 57.745 45.000 14.20 0.05 46.27 3.02
2431 4609 3.706594 TCAGGGTATCCTTTCTACTGCAG 59.293 47.826 13.48 13.48 42.67 4.41
2628 4806 0.322008 GGTTTGCTGAGACTGGGAGG 60.322 60.000 0.00 0.00 0.00 4.30
2910 5090 7.806409 AATCAAAAAGTTAAAAGCAGGCATT 57.194 28.000 0.00 0.00 0.00 3.56
3010 5191 4.469586 TGTCTATCACCAAAGGCATCAGTA 59.530 41.667 0.00 0.00 0.00 2.74
3085 5266 4.637483 ATTTGGCCAACATCAATAGTCG 57.363 40.909 20.35 0.00 0.00 4.18
3138 5319 4.803329 TTAGGAACGGAGGGAGTACTAT 57.197 45.455 0.00 0.00 0.00 2.12
3140 5321 3.463048 TTTAGGAACGGAGGGAGTACT 57.537 47.619 0.00 0.00 0.00 2.73
3141 5322 6.416631 AATATTTAGGAACGGAGGGAGTAC 57.583 41.667 0.00 0.00 0.00 2.73
3142 5323 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
3143 5324 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
3144 5325 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3145 5326 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3146 5327 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3147 5328 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
3148 5329 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
3149 5330 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
3150 5331 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
3163 5344 9.573166 TCCATTTGAAATCTCTAGAAAGACAAA 57.427 29.630 0.00 4.41 0.00 2.83
3164 5345 9.003658 GTCCATTTGAAATCTCTAGAAAGACAA 57.996 33.333 0.00 0.00 0.00 3.18
3165 5346 8.378565 AGTCCATTTGAAATCTCTAGAAAGACA 58.621 33.333 0.00 0.00 0.00 3.41
3166 5347 8.785329 AGTCCATTTGAAATCTCTAGAAAGAC 57.215 34.615 0.00 0.00 0.00 3.01
3167 5348 9.877178 GTAGTCCATTTGAAATCTCTAGAAAGA 57.123 33.333 0.00 0.00 0.00 2.52
3168 5349 9.103861 GGTAGTCCATTTGAAATCTCTAGAAAG 57.896 37.037 0.00 0.00 0.00 2.62
3169 5350 8.602424 TGGTAGTCCATTTGAAATCTCTAGAAA 58.398 33.333 0.00 0.00 39.03 2.52
3170 5351 8.146053 TGGTAGTCCATTTGAAATCTCTAGAA 57.854 34.615 0.00 0.00 39.03 2.10
3171 5352 7.733773 TGGTAGTCCATTTGAAATCTCTAGA 57.266 36.000 0.00 0.00 39.03 2.43
3186 5367 9.788889 CTATATACATCCGTATATGGTAGTCCA 57.211 37.037 10.85 3.57 46.31 4.02
3225 5406 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
3226 5407 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
3227 5408 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
3228 5409 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
3229 5410 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
3230 5411 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
3231 5412 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
3232 5413 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
3233 5414 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
3234 5415 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
3235 5416 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
3236 5417 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
3237 5418 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
3238 5419 4.034048 GGTGACTACATACGGAGCAAAATG 59.966 45.833 0.00 0.00 0.00 2.32
3239 5420 4.081087 AGGTGACTACATACGGAGCAAAAT 60.081 41.667 0.00 0.00 40.61 1.82
3240 5421 3.259876 AGGTGACTACATACGGAGCAAAA 59.740 43.478 0.00 0.00 40.61 2.44
3241 5422 2.829720 AGGTGACTACATACGGAGCAAA 59.170 45.455 0.00 0.00 40.61 3.68
3242 5423 2.165641 CAGGTGACTACATACGGAGCAA 59.834 50.000 0.00 0.00 40.21 3.91
3243 5424 1.749063 CAGGTGACTACATACGGAGCA 59.251 52.381 0.00 0.00 40.21 4.26
3244 5425 1.749634 ACAGGTGACTACATACGGAGC 59.250 52.381 0.00 0.00 40.21 4.70
3245 5426 3.442625 TCAACAGGTGACTACATACGGAG 59.557 47.826 0.00 0.00 40.21 4.63
3246 5427 3.423749 TCAACAGGTGACTACATACGGA 58.576 45.455 0.00 0.00 40.21 4.69
3247 5428 3.861276 TCAACAGGTGACTACATACGG 57.139 47.619 0.00 0.00 40.21 4.02
3248 5429 6.100004 AGATTTCAACAGGTGACTACATACG 58.900 40.000 0.00 0.00 40.21 3.06
3249 5430 7.324178 AGAGATTTCAACAGGTGACTACATAC 58.676 38.462 0.00 0.00 40.21 2.39
3250 5431 7.482169 AGAGATTTCAACAGGTGACTACATA 57.518 36.000 0.00 0.00 40.21 2.29
3251 5432 6.365970 AGAGATTTCAACAGGTGACTACAT 57.634 37.500 0.00 0.00 40.21 2.29
3252 5433 5.808366 AGAGATTTCAACAGGTGACTACA 57.192 39.130 0.00 0.00 40.21 2.74
3253 5434 7.159322 TCTAGAGATTTCAACAGGTGACTAC 57.841 40.000 0.00 0.00 40.21 2.73
3254 5435 7.776618 TTCTAGAGATTTCAACAGGTGACTA 57.223 36.000 0.00 0.00 40.21 2.59
3255 5436 6.672266 TTCTAGAGATTTCAACAGGTGACT 57.328 37.500 0.00 0.00 46.44 3.41
3256 5437 7.117092 GTCTTTCTAGAGATTTCAACAGGTGAC 59.883 40.741 0.00 0.00 35.39 3.67
3257 5438 7.155328 GTCTTTCTAGAGATTTCAACAGGTGA 58.845 38.462 0.00 0.00 0.00 4.02
3258 5439 6.931281 TGTCTTTCTAGAGATTTCAACAGGTG 59.069 38.462 0.00 0.00 0.00 4.00
3259 5440 7.067496 TGTCTTTCTAGAGATTTCAACAGGT 57.933 36.000 0.00 0.00 0.00 4.00
3260 5441 7.969536 TTGTCTTTCTAGAGATTTCAACAGG 57.030 36.000 0.00 0.00 0.00 4.00
3272 5453 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
3273 5454 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
3274 5455 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
3275 5456 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
3276 5457 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
3277 5458 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
3278 5459 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
3279 5460 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
3280 5461 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3281 5462 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3282 5463 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3283 5464 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3284 5465 6.041751 CACTACTCCCTCCGTTCCTAAATATT 59.958 42.308 0.00 0.00 0.00 1.28
3285 5466 5.539193 CACTACTCCCTCCGTTCCTAAATAT 59.461 44.000 0.00 0.00 0.00 1.28
3286 5467 4.891756 CACTACTCCCTCCGTTCCTAAATA 59.108 45.833 0.00 0.00 0.00 1.40
3287 5468 3.705072 CACTACTCCCTCCGTTCCTAAAT 59.295 47.826 0.00 0.00 0.00 1.40
3288 5469 3.094572 CACTACTCCCTCCGTTCCTAAA 58.905 50.000 0.00 0.00 0.00 1.85
3289 5470 2.622452 CCACTACTCCCTCCGTTCCTAA 60.622 54.545 0.00 0.00 0.00 2.69
3290 5471 1.064166 CCACTACTCCCTCCGTTCCTA 60.064 57.143 0.00 0.00 0.00 2.94
3291 5472 0.324460 CCACTACTCCCTCCGTTCCT 60.324 60.000 0.00 0.00 0.00 3.36
3292 5473 1.957765 GCCACTACTCCCTCCGTTCC 61.958 65.000 0.00 0.00 0.00 3.62
3293 5474 1.516423 GCCACTACTCCCTCCGTTC 59.484 63.158 0.00 0.00 0.00 3.95
3294 5475 1.988406 GGCCACTACTCCCTCCGTT 60.988 63.158 0.00 0.00 0.00 4.44
3295 5476 2.363925 GGCCACTACTCCCTCCGT 60.364 66.667 0.00 0.00 0.00 4.69
3296 5477 2.363795 TGGCCACTACTCCCTCCG 60.364 66.667 0.00 0.00 0.00 4.63
3297 5478 1.001760 TCTGGCCACTACTCCCTCC 59.998 63.158 0.00 0.00 0.00 4.30
3298 5479 0.033011 TCTCTGGCCACTACTCCCTC 60.033 60.000 0.00 0.00 0.00 4.30
3299 5480 0.639392 ATCTCTGGCCACTACTCCCT 59.361 55.000 0.00 0.00 0.00 4.20
3300 5481 1.044611 GATCTCTGGCCACTACTCCC 58.955 60.000 0.00 0.00 0.00 4.30
3301 5482 2.080654 AGATCTCTGGCCACTACTCC 57.919 55.000 0.00 0.00 0.00 3.85
3302 5483 2.102252 CCAAGATCTCTGGCCACTACTC 59.898 54.545 0.00 0.00 0.00 2.59
3407 5588 7.201767 GCTTGAGAAAAACATATGCCTACATCT 60.202 37.037 1.58 0.00 37.74 2.90
3489 5670 7.554118 ACATCCAACAAAATACACATCTAGAGG 59.446 37.037 2.12 2.12 0.00 3.69
3505 5686 7.871973 CCATAAGAAAAACATGACATCCAACAA 59.128 33.333 0.00 0.00 0.00 2.83
3682 5863 6.518493 ACCAACAGAATTAGTCAACGAGTTA 58.482 36.000 0.00 0.00 0.00 2.24
3696 5877 9.912634 CTACAAATCATGTTTTACCAACAGAAT 57.087 29.630 1.50 0.00 43.63 2.40
3933 6114 6.147164 TGCAACAGTACAGATTAAAGTAGCAC 59.853 38.462 0.00 0.00 0.00 4.40
3982 6163 3.119173 CGGATGCTTTAAAATCCAAGCCA 60.119 43.478 15.89 0.00 44.15 4.75
4013 6194 4.935352 TGAGCTGGCTAAACAACAAAAT 57.065 36.364 0.00 0.00 0.00 1.82
4192 6441 8.976471 CAACACAATTATGCAATGTAGAAAACA 58.024 29.630 0.00 0.00 43.86 2.83
4193 6442 8.434661 CCAACACAATTATGCAATGTAGAAAAC 58.565 33.333 0.00 0.00 0.00 2.43
4194 6443 8.363390 TCCAACACAATTATGCAATGTAGAAAA 58.637 29.630 0.00 0.00 0.00 2.29
4195 6444 7.890515 TCCAACACAATTATGCAATGTAGAAA 58.109 30.769 0.00 0.00 0.00 2.52
4221 6470 6.964086 AGGTGATACTTTCCCTTCCTAAGTTA 59.036 38.462 0.00 0.00 34.26 2.24
4314 7057 6.126825 ACAGCAGACATTCCTATCTCAAATCT 60.127 38.462 0.00 0.00 0.00 2.40
4421 7165 5.973565 GCCAAGTAGCAATACATGATTGTTC 59.026 40.000 0.00 1.61 45.88 3.18
4472 7216 6.153756 ACCCGTATCACAAAACAAATTTAGC 58.846 36.000 0.00 0.00 0.00 3.09
4658 7404 7.998383 ACAAGGGCAGAATTATCATGTACATTA 59.002 33.333 5.37 0.00 0.00 1.90
4659 7405 6.835488 ACAAGGGCAGAATTATCATGTACATT 59.165 34.615 5.37 0.00 0.00 2.71
4660 7406 6.263842 CACAAGGGCAGAATTATCATGTACAT 59.736 38.462 1.41 1.41 0.00 2.29
4661 7407 5.589855 CACAAGGGCAGAATTATCATGTACA 59.410 40.000 0.00 0.00 0.00 2.90
4662 7408 5.590259 ACACAAGGGCAGAATTATCATGTAC 59.410 40.000 0.00 0.00 0.00 2.90
4663 7409 5.589855 CACACAAGGGCAGAATTATCATGTA 59.410 40.000 0.00 0.00 0.00 2.29
4804 7554 5.921408 CCCTAGCGAAATGTGAGTTAGATAC 59.079 44.000 0.00 0.00 0.00 2.24
4822 7572 0.895559 AGCTGCAAAACACCCCTAGC 60.896 55.000 1.02 0.00 0.00 3.42
4872 7622 8.845227 CAAAAATGGCAAGGTAAAAGGTAATTT 58.155 29.630 0.00 0.00 0.00 1.82
5091 7842 5.008619 TGTTTTTCATCTGCAAAGAAGCA 57.991 34.783 0.00 0.00 43.35 3.91
5768 8519 1.511850 CAGTCTTGCACGACAATCCA 58.488 50.000 23.55 0.00 37.72 3.41
6402 9280 9.302345 ACAGTATCGACACAAGTAAAGAATATG 57.698 33.333 0.00 0.00 0.00 1.78
6836 9716 9.720769 TTAAGTTGACTGATTAAACTTAGGAGG 57.279 33.333 7.16 0.00 43.51 4.30
6892 9772 9.739276 AATTATAGATGTGTGGTTCTTCAAAGA 57.261 29.630 0.00 0.00 0.00 2.52
6921 9801 5.966636 TGACATTACTAAACTATGCAGCG 57.033 39.130 0.00 0.00 0.00 5.18
6937 9817 8.735692 AACATTTTCAAGTTGGAAATGACATT 57.264 26.923 38.73 26.44 36.71 2.71
7071 9951 8.645110 CAGGATTGCAGATAGGGAAATAAAATT 58.355 33.333 0.00 0.00 0.00 1.82
7111 9991 7.323420 CAAGTGTTTCACTCTATGTATGGAGA 58.677 38.462 11.55 0.00 44.62 3.71
7181 10061 9.213799 TCACAAAGTTTAAGCTTGAAACAAAAT 57.786 25.926 22.31 9.08 38.91 1.82
7407 10289 2.548057 TGCAGCCTTCTTAACACTTTCG 59.452 45.455 0.00 0.00 0.00 3.46
7683 10568 6.095021 GGGCGTGTCAGAGATATATGTATGTA 59.905 42.308 4.60 0.00 0.00 2.29
7809 10694 5.978814 AGCTACCCTTGATAGTTAACACTG 58.021 41.667 8.61 0.00 34.06 3.66
8000 10888 8.770438 TCACAAAACTAGCAGAACAAAATTTT 57.230 26.923 0.00 0.00 0.00 1.82
8074 10965 7.268199 TGTAACAATATCCTGTAGGTACTCG 57.732 40.000 0.00 0.00 41.75 4.18
8076 10967 8.475639 CAGTTGTAACAATATCCTGTAGGTACT 58.524 37.037 0.00 0.00 46.37 2.73
8172 11063 0.036306 AGTAGGTGTTTGCTTCCCCG 59.964 55.000 0.00 0.00 0.00 5.73
8250 11141 3.948719 GTCCACTTGGGTCGGCCA 61.949 66.667 9.07 0.00 38.11 5.36
8262 11153 0.868177 CAAACAAAACGCGGGTCCAC 60.868 55.000 12.47 0.00 0.00 4.02
8268 11159 1.555477 AAAGAGCAAACAAAACGCGG 58.445 45.000 12.47 0.00 0.00 6.46
8269 11160 2.719046 CCTAAAGAGCAAACAAAACGCG 59.281 45.455 3.53 3.53 0.00 6.01
8280 11171 2.602676 AAGCGGGGCCTAAAGAGCA 61.603 57.895 0.84 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.