Multiple sequence alignment - TraesCS2D01G484700

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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 TraesCS2D01G484700 chr2D 100.000 6589 0 0 1 6589 585691307 585684719 0.000000e+00 12168.0
1 TraesCS2D01G484700 chr2D 81.399 2344 327 69 3495 5771 619702471 619704772 0.000000e+00 1812.0
2 TraesCS2D01G484700 chr2D 87.395 119 14 1 3473 3591 619702287 619702404 1.150000e-27 135.0
3 TraesCS2D01G484700 chr2D 78.689 183 23 14 435 611 30253802 30253630 2.510000e-19 108.0
4 TraesCS2D01G484700 chr2D 89.231 65 5 2 6526 6589 619576390 619576453 5.480000e-11 80.5
5 TraesCS2D01G484700 chr2B 93.733 2617 121 16 3469 6060 706923737 706921139 0.000000e+00 3884.0
6 TraesCS2D01G484700 chr2B 93.945 2494 113 20 3468 5937 706731801 706729322 0.000000e+00 3735.0
7 TraesCS2D01G484700 chr2B 89.401 2453 150 37 161 2560 706734190 706731795 0.000000e+00 2988.0
8 TraesCS2D01G484700 chr2B 91.483 1996 129 21 300 2287 706926075 706924113 0.000000e+00 2706.0
9 TraesCS2D01G484700 chr2B 82.581 1906 247 58 3495 5345 759440643 759442518 0.000000e+00 1602.0
10 TraesCS2D01G484700 chr2B 83.039 1757 215 52 3468 5167 759346373 759348103 0.000000e+00 1517.0
11 TraesCS2D01G484700 chr2B 80.730 1562 223 37 985 2532 759344853 759346350 0.000000e+00 1146.0
12 TraesCS2D01G484700 chr2B 80.781 947 134 30 2561 3466 246627258 246626319 0.000000e+00 697.0
13 TraesCS2D01G484700 chr2B 80.795 880 114 31 2562 3433 429261592 429262424 7.210000e-179 638.0
14 TraesCS2D01G484700 chr2B 91.244 217 16 3 2344 2560 706923945 706923732 6.460000e-75 292.0
15 TraesCS2D01G484700 chr2B 89.759 166 12 4 47 207 706926239 706926074 2.410000e-49 207.0
16 TraesCS2D01G484700 chr2B 93.600 125 6 2 1 125 706734315 706734193 1.130000e-42 185.0
17 TraesCS2D01G484700 chr2B 85.526 152 10 3 6435 6586 706921143 706921004 1.480000e-31 148.0
18 TraesCS2D01G484700 chr2A 95.723 1894 64 6 3466 5345 719730507 719728617 0.000000e+00 3033.0
19 TraesCS2D01G484700 chr2A 92.387 1944 110 22 649 2560 719732436 719730499 0.000000e+00 2736.0
20 TraesCS2D01G484700 chr2A 81.565 2083 266 72 3471 5489 751233149 751235177 0.000000e+00 1611.0
21 TraesCS2D01G484700 chr2A 81.644 2032 273 64 3468 5441 751268717 751270706 0.000000e+00 1594.0
22 TraesCS2D01G484700 chr2A 81.604 2033 273 64 3468 5441 751238330 751240320 0.000000e+00 1589.0
23 TraesCS2D01G484700 chr2A 83.390 1764 209 52 3468 5174 751208956 751210692 0.000000e+00 1557.0
24 TraesCS2D01G484700 chr2A 92.062 907 60 9 5387 6285 719728612 719727710 0.000000e+00 1266.0
25 TraesCS2D01G484700 chr2A 85.368 1155 167 2 985 2138 751231658 751232811 0.000000e+00 1195.0
26 TraesCS2D01G484700 chr2A 84.115 1152 183 0 985 2136 751207439 751208590 0.000000e+00 1114.0
27 TraesCS2D01G484700 chr2A 81.344 1399 218 24 773 2136 751236569 751237959 0.000000e+00 1098.0
28 TraesCS2D01G484700 chr2A 83.702 1129 184 0 1008 2136 751288144 751289272 0.000000e+00 1066.0
29 TraesCS2D01G484700 chr2A 83.702 1129 183 1 1008 2136 751267219 751268346 0.000000e+00 1064.0
30 TraesCS2D01G484700 chr2A 85.526 912 115 9 2560 3459 99478647 99477741 0.000000e+00 937.0
31 TraesCS2D01G484700 chr2A 84.633 898 117 14 2559 3444 296955924 296956812 0.000000e+00 874.0
32 TraesCS2D01G484700 chr2A 90.450 555 40 8 69 611 719735083 719734530 0.000000e+00 719.0
33 TraesCS2D01G484700 chr2A 83.420 386 47 9 5948 6321 719725326 719724946 6.330000e-90 342.0
34 TraesCS2D01G484700 chr2A 91.534 189 11 3 6326 6509 719727735 719727547 8.480000e-64 255.0
35 TraesCS2D01G484700 chr2A 89.032 155 17 0 6355 6509 751174503 751174657 6.740000e-45 193.0
36 TraesCS2D01G484700 chr2A 87.395 119 14 1 3473 3591 751268562 751268679 1.150000e-27 135.0
37 TraesCS2D01G484700 chr2A 87.395 119 14 1 3473 3591 751289488 751289605 1.150000e-27 135.0
38 TraesCS2D01G484700 chr2A 92.941 85 5 1 6506 6589 719727521 719727437 8.970000e-24 122.0
39 TraesCS2D01G484700 chr2A 89.231 65 5 2 6526 6589 751057195 751057258 5.480000e-11 80.5
40 TraesCS2D01G484700 chr2A 95.745 47 2 0 6541 6587 751016390 751016436 7.080000e-10 76.8
41 TraesCS2D01G484700 chr2A 95.745 47 2 0 6541 6587 751049845 751049891 7.080000e-10 76.8
42 TraesCS2D01G484700 chr2A 92.453 53 4 0 6535 6587 751174715 751174767 7.080000e-10 76.8
43 TraesCS2D01G484700 chr5A 86.492 918 93 16 2561 3464 115836280 115837180 0.000000e+00 979.0
44 TraesCS2D01G484700 chr5A 96.970 33 1 0 580 612 609791162 609791194 1.000000e-03 56.5
45 TraesCS2D01G484700 chr1D 86.026 916 86 22 2561 3462 356340322 356341209 0.000000e+00 944.0
46 TraesCS2D01G484700 chr6A 84.940 923 120 13 2559 3471 453411271 453410358 0.000000e+00 917.0
47 TraesCS2D01G484700 chr6A 78.889 900 165 20 2561 3446 306475324 306476212 2.650000e-163 586.0
48 TraesCS2D01G484700 chr1A 85.210 906 115 11 2565 3455 257604158 257605059 0.000000e+00 913.0
49 TraesCS2D01G484700 chr4D 85.088 912 109 19 2561 3458 37837363 37836465 0.000000e+00 905.0
50 TraesCS2D01G484700 chr4A 84.966 878 107 17 2558 3419 4226295 4227163 0.000000e+00 867.0
51 TraesCS2D01G484700 chr7A 85.771 759 90 11 2711 3458 189205280 189204529 0.000000e+00 787.0
52 TraesCS2D01G484700 chrUn 87.395 119 14 1 3473 3591 337512861 337512978 1.150000e-27 135.0
53 TraesCS2D01G484700 chr5D 96.970 33 1 0 580 612 488784999 488785031 1.000000e-03 56.5


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 TraesCS2D01G484700 chr2D 585684719 585691307 6588 True 12168.000000 12168 100.000000 1 6589 1 chr2D.!!$R2 6588
1 TraesCS2D01G484700 chr2D 619702287 619704772 2485 False 973.500000 1812 84.397000 3473 5771 2 chr2D.!!$F2 2298
2 TraesCS2D01G484700 chr2B 706729322 706734315 4993 True 2302.666667 3735 92.315333 1 5937 3 chr2B.!!$R2 5936
3 TraesCS2D01G484700 chr2B 759440643 759442518 1875 False 1602.000000 1602 82.581000 3495 5345 1 chr2B.!!$F2 1850
4 TraesCS2D01G484700 chr2B 706921004 706926239 5235 True 1447.400000 3884 90.349000 47 6586 5 chr2B.!!$R3 6539
5 TraesCS2D01G484700 chr2B 759344853 759348103 3250 False 1331.500000 1517 81.884500 985 5167 2 chr2B.!!$F3 4182
6 TraesCS2D01G484700 chr2B 246626319 246627258 939 True 697.000000 697 80.781000 2561 3466 1 chr2B.!!$R1 905
7 TraesCS2D01G484700 chr2B 429261592 429262424 832 False 638.000000 638 80.795000 2562 3433 1 chr2B.!!$F1 871
8 TraesCS2D01G484700 chr2A 751231658 751240320 8662 False 1373.250000 1611 82.470250 773 5489 4 chr2A.!!$F7 4716
9 TraesCS2D01G484700 chr2A 751207439 751210692 3253 False 1335.500000 1557 83.752500 985 5174 2 chr2A.!!$F6 4189
10 TraesCS2D01G484700 chr2A 719724946 719735083 10137 True 1210.428571 3033 91.216714 69 6589 7 chr2A.!!$R2 6520
11 TraesCS2D01G484700 chr2A 99477741 99478647 906 True 937.000000 937 85.526000 2560 3459 1 chr2A.!!$R1 899
12 TraesCS2D01G484700 chr2A 751267219 751270706 3487 False 931.000000 1594 84.247000 1008 5441 3 chr2A.!!$F8 4433
13 TraesCS2D01G484700 chr2A 296955924 296956812 888 False 874.000000 874 84.633000 2559 3444 1 chr2A.!!$F1 885
14 TraesCS2D01G484700 chr2A 751288144 751289605 1461 False 600.500000 1066 85.548500 1008 3591 2 chr2A.!!$F9 2583
15 TraesCS2D01G484700 chr5A 115836280 115837180 900 False 979.000000 979 86.492000 2561 3464 1 chr5A.!!$F1 903
16 TraesCS2D01G484700 chr1D 356340322 356341209 887 False 944.000000 944 86.026000 2561 3462 1 chr1D.!!$F1 901
17 TraesCS2D01G484700 chr6A 453410358 453411271 913 True 917.000000 917 84.940000 2559 3471 1 chr6A.!!$R1 912
18 TraesCS2D01G484700 chr6A 306475324 306476212 888 False 586.000000 586 78.889000 2561 3446 1 chr6A.!!$F1 885
19 TraesCS2D01G484700 chr1A 257604158 257605059 901 False 913.000000 913 85.210000 2565 3455 1 chr1A.!!$F1 890
20 TraesCS2D01G484700 chr4D 37836465 37837363 898 True 905.000000 905 85.088000 2561 3458 1 chr4D.!!$R1 897
21 TraesCS2D01G484700 chr4A 4226295 4227163 868 False 867.000000 867 84.966000 2558 3419 1 chr4A.!!$F1 861
22 TraesCS2D01G484700 chr7A 189204529 189205280 751 True 787.000000 787 85.771000 2711 3458 1 chr7A.!!$R1 747

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 2856 0.453793 TTTTGCACCTTGTGTGGTCG 59.546 50.0 0.00 0.00 45.55 4.79 F
1314 3391 0.252103 ACTCCCAAGGCCGAACTCTA 60.252 55.0 0.00 0.00 0.00 2.43 F
2340 9597 0.307760 CCGTCTTGCCAGTTCAACAC 59.692 55.0 0.00 0.00 0.00 3.32 F
2781 10174 0.324943 AAGGTACTCAGGTGCGCAAT 59.675 50.0 14.00 0.00 38.49 3.56 F
2830 10223 0.333993 ATTCCAGGAGCTTGTGGCAT 59.666 50.0 9.90 3.01 44.79 4.40 F
4559 12060 0.474184 ATATGCACCCGCTAAGGCTT 59.526 50.0 4.58 4.58 39.64 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1614 3691 0.398522 ACCCATCCCACGCAGATCTA 60.399 55.000 0.00 0.00 0.00 1.98 R
2809 10202 0.322816 GCCACAAGCTCCTGGAATGA 60.323 55.000 12.82 0.00 38.99 2.57 R
4004 11473 1.341531 CACCTCCTAATAGTCCCTGCG 59.658 57.143 0.00 0.00 0.00 5.18 R
4006 11475 2.700897 CACCACCTCCTAATAGTCCCTG 59.299 54.545 0.00 0.00 0.00 4.45 R
4827 12330 2.849943 TCCATAAGCTCCAGGCCTAAAA 59.150 45.455 3.98 0.00 43.05 1.52 R
5949 13499 2.358322 AGGCCCGTCTTTTGAAAAGA 57.642 45.000 15.81 15.81 0.00 2.52 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
35 36 1.509787 CATTGGCTTTGTCGCGTCG 60.510 57.895 5.77 0.00 0.00 5.12
157 163 1.292546 CCCTCCCTTACCTTCCTCTCT 59.707 57.143 0.00 0.00 0.00 3.10
250 256 2.188829 GCCATCGCCAGCAGCAATA 61.189 57.895 0.00 0.00 44.04 1.90
294 300 1.967066 CTTCGCCAGAGATGTATCCCT 59.033 52.381 0.00 0.00 0.00 4.20
305 311 5.314306 AGAGATGTATCCCTAATGGCCAATT 59.686 40.000 10.96 7.63 0.00 2.32
395 401 1.585006 CGCCTGACTGACGGTAACT 59.415 57.895 0.00 0.00 0.00 2.24
423 429 6.739331 TCTTCTCATATCCCCTTTCTTCTC 57.261 41.667 0.00 0.00 0.00 2.87
639 688 6.402456 AATATGAAACGGAGGGAGTACTAC 57.598 41.667 0.00 0.00 0.00 2.73
659 2733 2.299013 ACTTGTGCATCTAAGACCACGA 59.701 45.455 13.18 0.00 0.00 4.35
699 2773 3.447229 AGTGTGCAAATAATTGTAGCCCC 59.553 43.478 0.00 0.00 38.85 5.80
704 2778 3.551846 CAAATAATTGTAGCCCCCGAGT 58.448 45.455 0.00 0.00 0.00 4.18
726 2800 7.472334 AGTTATTTCTTGATGTGCAATTCCT 57.528 32.000 0.00 0.00 35.59 3.36
736 2810 1.741770 GCAATTCCTGACGGCGACT 60.742 57.895 16.62 0.00 0.00 4.18
746 2820 2.054140 GACGGCGACTGGCAAACAAA 62.054 55.000 16.62 0.00 46.16 2.83
761 2835 5.336690 GGCAAACAAAGCTGAATAATCCTCA 60.337 40.000 0.00 0.00 0.00 3.86
764 2838 7.373493 CAAACAAAGCTGAATAATCCTCACTT 58.627 34.615 0.00 0.00 0.00 3.16
782 2856 0.453793 TTTTGCACCTTGTGTGGTCG 59.546 50.000 0.00 0.00 45.55 4.79
813 2887 2.597510 GTTCCGGGCAAAGCTGGT 60.598 61.111 0.00 0.00 0.00 4.00
838 2912 4.223700 ACTCAGACTCCTGCAAATGTGATA 59.776 41.667 0.00 0.00 40.20 2.15
840 2914 5.748402 TCAGACTCCTGCAAATGTGATAAT 58.252 37.500 0.00 0.00 40.20 1.28
902 2977 0.924090 CAGCGTTAGATCGTCCAAGC 59.076 55.000 0.00 0.00 0.00 4.01
919 2994 3.548770 CAAGCCTCCAAGCATCTTCATA 58.451 45.455 0.00 0.00 34.23 2.15
982 3059 4.079787 TCCTTCCTTTTGATCATAGGGTGG 60.080 45.833 19.11 19.09 0.00 4.61
1044 3121 4.825085 GTCCTCCTGTCATTGGTTTGTTTA 59.175 41.667 0.00 0.00 0.00 2.01
1073 3150 1.380785 ATGACCGCCTTACTCCCGA 60.381 57.895 0.00 0.00 0.00 5.14
1078 3155 1.003928 ACCGCCTTACTCCCGAAAAAT 59.996 47.619 0.00 0.00 0.00 1.82
1092 3169 2.032030 CGAAAAATCACTCAACGCTGGT 60.032 45.455 0.00 0.00 0.00 4.00
1262 3339 1.377856 GTTCTCCTGGGAAGCTGGC 60.378 63.158 0.00 0.00 0.00 4.85
1273 3350 1.497223 GAAGCTGGCTATGAGCAGCG 61.497 60.000 13.47 0.00 44.75 5.18
1308 3385 2.119611 TCTGACTCCCAAGGCCGA 59.880 61.111 0.00 0.00 0.00 5.54
1314 3391 0.252103 ACTCCCAAGGCCGAACTCTA 60.252 55.000 0.00 0.00 0.00 2.43
1374 3451 4.878397 GGAACTGCTGCTATACTGTTTGAT 59.122 41.667 0.00 0.00 0.00 2.57
1496 3573 6.124340 TGAGCACAAATGATGGTATCTTGAT 58.876 36.000 0.00 0.00 0.00 2.57
1517 3594 3.930504 CCTCATTGCTTGGAGGGC 58.069 61.111 9.43 0.00 45.62 5.19
1575 3652 2.225142 TGGTGACTCTAGCTCAGACCTT 60.225 50.000 0.00 0.00 0.00 3.50
1661 3738 2.305635 TCTCTGCCCTGTATCAAAGCAA 59.694 45.455 0.00 0.00 32.14 3.91
1757 3834 1.515519 CACCAAGCATGCGCATGAC 60.516 57.895 45.47 35.28 39.19 3.06
1758 3835 1.972752 ACCAAGCATGCGCATGACA 60.973 52.632 45.47 11.19 39.19 3.58
1770 3847 2.412870 CGCATGACACTGGACTACAAA 58.587 47.619 0.00 0.00 0.00 2.83
1959 4036 0.603569 GCGTCAACTTCTCCAGAGGA 59.396 55.000 0.00 0.00 0.00 3.71
1991 9218 5.983333 AAGGAGGATCTGAAATGTGGTAT 57.017 39.130 0.00 0.00 33.73 2.73
2061 9288 5.808366 TCTTGTATGTCAGGAACAGAAGT 57.192 39.130 0.00 0.00 42.37 3.01
2139 9366 4.640771 TGCTAACCTGAGAAATGGAAGT 57.359 40.909 0.00 0.00 0.00 3.01
2202 9429 5.242838 CCAGTCAAGGTGCTTAATTTGGTTA 59.757 40.000 0.00 0.00 0.00 2.85
2287 9517 7.450074 CCTTGCCAGTTCAACAGGTATATATA 58.550 38.462 0.27 0.00 0.00 0.86
2340 9597 0.307760 CCGTCTTGCCAGTTCAACAC 59.692 55.000 0.00 0.00 0.00 3.32
2473 9863 9.899661 TTGCTGGACTATATTTCTAGCTTTTTA 57.100 29.630 17.70 1.70 45.31 1.52
2474 9864 9.326413 TGCTGGACTATATTTCTAGCTTTTTAC 57.674 33.333 17.70 0.00 45.31 2.01
2475 9865 9.326413 GCTGGACTATATTTCTAGCTTTTTACA 57.674 33.333 12.51 0.00 42.63 2.41
2487 9877 5.582689 AGCTTTTTACAAAGAGTGCAAGT 57.417 34.783 5.54 0.00 41.97 3.16
2488 9878 5.965922 AGCTTTTTACAAAGAGTGCAAGTT 58.034 33.333 5.54 0.00 41.97 2.66
2489 9879 5.807011 AGCTTTTTACAAAGAGTGCAAGTTG 59.193 36.000 5.54 0.00 41.97 3.16
2490 9880 5.576774 GCTTTTTACAAAGAGTGCAAGTTGT 59.423 36.000 5.54 9.61 41.97 3.32
2492 9882 4.530094 TTACAAAGAGTGCAAGTTGTCG 57.470 40.909 4.48 0.00 35.82 4.35
2494 9884 3.006940 ACAAAGAGTGCAAGTTGTCGAA 58.993 40.909 4.48 0.00 28.08 3.71
2496 9886 2.890808 AGAGTGCAAGTTGTCGAAGA 57.109 45.000 4.48 0.00 0.00 2.87
2497 9887 3.393089 AGAGTGCAAGTTGTCGAAGAT 57.607 42.857 4.48 0.00 40.67 2.40
2499 9889 3.496130 AGAGTGCAAGTTGTCGAAGATTG 59.504 43.478 4.48 0.00 40.67 2.67
2500 9890 3.206150 AGTGCAAGTTGTCGAAGATTGT 58.794 40.909 4.48 0.00 40.67 2.71
2502 9892 4.211374 AGTGCAAGTTGTCGAAGATTGTAC 59.789 41.667 4.48 11.52 40.67 2.90
2503 9893 4.211374 GTGCAAGTTGTCGAAGATTGTACT 59.789 41.667 4.48 0.00 40.67 2.73
2504 9894 4.447724 TGCAAGTTGTCGAAGATTGTACTC 59.552 41.667 4.48 0.00 40.67 2.59
2505 9895 4.143094 GCAAGTTGTCGAAGATTGTACTCC 60.143 45.833 4.48 0.00 40.67 3.85
2506 9896 4.189639 AGTTGTCGAAGATTGTACTCCC 57.810 45.455 0.00 0.00 40.67 4.30
2507 9897 3.833070 AGTTGTCGAAGATTGTACTCCCT 59.167 43.478 0.00 0.00 40.67 4.20
2508 9898 3.868757 TGTCGAAGATTGTACTCCCTG 57.131 47.619 0.00 0.00 40.67 4.45
2509 9899 3.162666 TGTCGAAGATTGTACTCCCTGT 58.837 45.455 0.00 0.00 40.67 4.00
2510 9900 4.338012 TGTCGAAGATTGTACTCCCTGTA 58.662 43.478 0.00 0.00 40.67 2.74
2511 9901 4.768448 TGTCGAAGATTGTACTCCCTGTAA 59.232 41.667 0.00 0.00 40.67 2.41
2512 9902 5.421056 TGTCGAAGATTGTACTCCCTGTAAT 59.579 40.000 0.00 0.00 40.67 1.89
2513 9903 5.749109 GTCGAAGATTGTACTCCCTGTAATG 59.251 44.000 0.00 0.00 40.67 1.90
2514 9904 5.050490 CGAAGATTGTACTCCCTGTAATGG 58.950 45.833 0.00 0.00 32.25 3.16
2515 9905 4.423625 AGATTGTACTCCCTGTAATGGC 57.576 45.455 0.00 0.00 32.25 4.40
2518 9908 1.837439 TGTACTCCCTGTAATGGCTGG 59.163 52.381 0.00 0.00 32.25 4.85
2520 9910 1.898863 ACTCCCTGTAATGGCTGGAT 58.101 50.000 0.00 0.00 0.00 3.41
2521 9911 1.492176 ACTCCCTGTAATGGCTGGATG 59.508 52.381 0.00 0.00 0.00 3.51
2522 9912 1.492176 CTCCCTGTAATGGCTGGATGT 59.508 52.381 0.00 0.00 0.00 3.06
2524 9914 1.683943 CCTGTAATGGCTGGATGTGG 58.316 55.000 0.00 0.00 0.00 4.17
2529 9919 2.442236 AATGGCTGGATGTGGTTAGG 57.558 50.000 0.00 0.00 0.00 2.69
2530 9920 1.595311 ATGGCTGGATGTGGTTAGGA 58.405 50.000 0.00 0.00 0.00 2.94
2532 9922 1.707989 TGGCTGGATGTGGTTAGGAAA 59.292 47.619 0.00 0.00 0.00 3.13
2533 9923 2.092323 GGCTGGATGTGGTTAGGAAAC 58.908 52.381 0.00 0.00 34.66 2.78
2540 9930 5.491078 TGGATGTGGTTAGGAAACTTAGGAT 59.509 40.000 0.00 0.00 43.67 3.24
2542 9932 5.174037 TGTGGTTAGGAAACTTAGGATGG 57.826 43.478 0.00 0.00 43.67 3.51
2543 9933 3.945921 GTGGTTAGGAAACTTAGGATGGC 59.054 47.826 0.00 0.00 43.67 4.40
2544 9934 3.589735 TGGTTAGGAAACTTAGGATGGCA 59.410 43.478 0.00 0.00 43.67 4.92
2546 9936 5.430417 TGGTTAGGAAACTTAGGATGGCATA 59.570 40.000 0.00 0.00 43.67 3.14
2547 9937 6.069323 TGGTTAGGAAACTTAGGATGGCATAA 60.069 38.462 0.00 0.00 43.67 1.90
2550 9940 9.569122 GTTAGGAAACTTAGGATGGCATAATAA 57.431 33.333 0.00 1.80 43.67 1.40
2587 9977 5.047092 CCATTTGCATTTCTGTCCCTAACTT 60.047 40.000 0.00 0.00 0.00 2.66
2640 10030 0.543646 AGCCTGCTCAAATTTGCCCT 60.544 50.000 13.54 0.72 0.00 5.19
2716 10106 4.999751 AAAGAGCTTTGATTGTCTCGAC 57.000 40.909 0.00 0.00 0.00 4.20
2781 10174 0.324943 AAGGTACTCAGGTGCGCAAT 59.675 50.000 14.00 0.00 38.49 3.56
2809 10202 6.034898 GCGTGCAAATTTTCATGCTATTTAGT 59.965 34.615 22.63 0.00 42.97 2.24
2830 10223 0.333993 ATTCCAGGAGCTTGTGGCAT 59.666 50.000 9.90 3.01 44.79 4.40
2863 10257 7.011109 ACAATAAATCTGTACGCCTGTGAATAC 59.989 37.037 0.00 0.00 0.00 1.89
2960 10356 5.671742 AGGTGCATGCAAAATTTTGTTAC 57.328 34.783 24.58 18.70 40.24 2.50
3082 10490 5.452078 ACAATGTCCGAACACATCAAAAT 57.548 34.783 0.00 0.00 38.48 1.82
3095 10506 3.876320 ACATCAAAATTTTGCACACACCC 59.124 39.130 23.36 0.00 38.05 4.61
3277 10705 5.773176 AGTACCTTCGATCCCACAAAATTTT 59.227 36.000 0.00 0.00 0.00 1.82
3285 10713 8.582433 TCGATCCCACAAAATTTTAGTTTTTC 57.418 30.769 2.44 0.00 0.00 2.29
3399 10849 1.512694 GGAGGGGCAAATTTGAGCG 59.487 57.895 22.31 0.00 0.00 5.03
3426 10876 3.450457 TCGCAATTAGGGGCAAATTTGAT 59.550 39.130 22.31 6.62 0.00 2.57
3569 11026 3.995199 TGCAGTTGACAAGGAGAGTAAG 58.005 45.455 0.00 0.00 0.00 2.34
3780 11243 8.251750 TCAAGGAGATTAAGAACAAACATACG 57.748 34.615 0.00 0.00 0.00 3.06
3782 11245 5.585047 AGGAGATTAAGAACAAACATACGCC 59.415 40.000 0.00 0.00 0.00 5.68
3939 11402 7.102847 TGGAAAAGTTTACAAGGTAACAAGG 57.897 36.000 0.00 0.00 41.41 3.61
4004 11473 2.229543 TGCTCAAGGATGATGTGTTTGC 59.770 45.455 0.00 0.00 34.37 3.68
4006 11475 1.199789 TCAAGGATGATGTGTTTGCGC 59.800 47.619 0.00 0.00 0.00 6.09
4156 11625 4.423625 AGACTTCTTGGTTACTGCACTT 57.576 40.909 0.00 0.00 0.00 3.16
4249 11719 9.601217 GTATGTTCTAACTTATGGTCATGTCTT 57.399 33.333 0.00 0.00 0.00 3.01
4257 11744 2.346766 TGGTCATGTCTTGCACAACT 57.653 45.000 0.00 0.00 38.97 3.16
4515 12016 1.804151 GCAACAAGCGAACACTATCCA 59.196 47.619 0.00 0.00 0.00 3.41
4559 12060 0.474184 ATATGCACCCGCTAAGGCTT 59.526 50.000 4.58 4.58 39.64 4.35
4560 12061 1.124780 TATGCACCCGCTAAGGCTTA 58.875 50.000 6.80 6.80 39.64 3.09
4712 12213 6.157211 CGTTCTACTGTTGGAGATTGTAAGT 58.843 40.000 0.00 0.00 0.00 2.24
5012 12525 4.009675 TCATGCTAGAAAATGAAACGGCT 58.990 39.130 0.00 0.00 29.97 5.52
5129 12648 4.546674 TGACTATCACTATGCAAGAGGGA 58.453 43.478 6.41 6.41 0.00 4.20
5276 12799 8.885722 GTCGTGGTTTATTTTCATAGATGGTTA 58.114 33.333 0.00 0.00 0.00 2.85
5326 12849 4.458989 TCATATGTTTCTCACCTTGCCAAC 59.541 41.667 1.90 0.00 0.00 3.77
5376 12899 6.523201 CGGATCACTGCTTACATTTGTTTTAC 59.477 38.462 0.00 0.00 0.00 2.01
5404 12930 6.885918 TCATGAATTTTCTGTATCCAGCTTCA 59.114 34.615 0.00 0.00 38.66 3.02
5407 12933 6.885918 TGAATTTTCTGTATCCAGCTTCATCA 59.114 34.615 0.00 0.00 38.66 3.07
5467 12993 5.485662 GGTAACAAGGCTGCTAGTAATTG 57.514 43.478 0.00 0.00 0.00 2.32
5549 13086 4.096984 GTGGCAAGCAAGCTAGATTTACAT 59.903 41.667 0.00 0.00 34.17 2.29
5553 13090 4.162040 AGCAAGCTAGATTTACATGCCT 57.838 40.909 0.00 0.00 32.95 4.75
5567 13104 3.759581 ACATGCCTGAAGTCTGACAATT 58.240 40.909 10.88 0.00 0.00 2.32
5678 13221 3.806949 AAAGTGGGGCTTCTGTGAATA 57.193 42.857 0.00 0.00 36.17 1.75
5775 13320 5.869888 CAGCCTAACTTATCCCGAATCATAC 59.130 44.000 0.00 0.00 0.00 2.39
5998 13548 1.452651 ATGGTGCTGCCGGAGAATG 60.453 57.895 5.05 0.00 41.21 2.67
6079 13629 8.308931 ACATTGTCTTTCATGTTGCTTTATGAT 58.691 29.630 0.00 0.00 33.68 2.45
6118 13668 2.584835 TAGGGTGTTTGAGCTGCATT 57.415 45.000 1.02 0.00 0.00 3.56
6124 13674 2.293122 GTGTTTGAGCTGCATTGTGGTA 59.707 45.455 1.02 0.00 0.00 3.25
6138 13688 5.404946 CATTGTGGTAGCTTTCATTGAAGG 58.595 41.667 4.25 4.25 0.00 3.46
6173 13723 9.239551 GAGTTAAATTCCAAGGTTACCATTAGT 57.760 33.333 3.51 0.00 0.00 2.24
6179 13729 8.721133 ATTCCAAGGTTACCATTAGTTCTTTT 57.279 30.769 3.51 0.00 0.00 2.27
6218 13768 5.460419 GTCAAGTTCTCTGACAAGTACACAG 59.540 44.000 0.00 0.00 33.20 3.66
6273 13823 9.784531 CAGAGGTTCAACTTTATATATCCATGT 57.215 33.333 0.00 0.00 0.00 3.21
6277 13827 9.337396 GGTTCAACTTTATATATCCATGTCACA 57.663 33.333 0.00 0.00 0.00 3.58
6303 13853 6.729690 AAAAATTGGTGTGATGAGGAGAAA 57.270 33.333 0.00 0.00 0.00 2.52
6304 13854 6.923199 AAAATTGGTGTGATGAGGAGAAAT 57.077 33.333 0.00 0.00 0.00 2.17
6305 13855 6.923199 AAATTGGTGTGATGAGGAGAAATT 57.077 33.333 0.00 0.00 0.00 1.82
6306 13856 8.421249 AAAATTGGTGTGATGAGGAGAAATTA 57.579 30.769 0.00 0.00 0.00 1.40
6307 13857 8.421249 AAATTGGTGTGATGAGGAGAAATTAA 57.579 30.769 0.00 0.00 0.00 1.40
6308 13858 8.599624 AATTGGTGTGATGAGGAGAAATTAAT 57.400 30.769 0.00 0.00 0.00 1.40
6309 13859 8.599624 ATTGGTGTGATGAGGAGAAATTAATT 57.400 30.769 0.00 0.00 0.00 1.40
6310 13860 9.699410 ATTGGTGTGATGAGGAGAAATTAATTA 57.301 29.630 0.01 0.00 0.00 1.40
6311 13861 9.699410 TTGGTGTGATGAGGAGAAATTAATTAT 57.301 29.630 0.01 0.00 0.00 1.28
6396 13950 3.415212 TGGAAGGCATTTTCTCTGTCAG 58.585 45.455 0.00 0.00 0.00 3.51
6425 13979 5.738909 ACACATATAGCTATGGGATCTTGC 58.261 41.667 16.77 0.00 40.62 4.01
6446 14000 2.789409 ACTGGAGATTGTAAGTGGGC 57.211 50.000 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 1.373497 CAGTGACGGTGCCTGACTC 60.373 63.158 0.00 0.00 0.00 3.36
132 137 1.557426 GGAAGGTAAGGGAGGGAAGGT 60.557 57.143 0.00 0.00 0.00 3.50
157 163 2.138179 GCCGGCCTGATACACCCTA 61.138 63.158 18.11 0.00 0.00 3.53
279 285 3.054802 GGCCATTAGGGATACATCTCTGG 60.055 52.174 0.00 0.00 38.31 3.86
294 300 3.907474 TCCCGAGAGATAATTGGCCATTA 59.093 43.478 6.09 8.19 0.00 1.90
305 311 1.040646 GTGCACCATCCCGAGAGATA 58.959 55.000 5.22 0.00 0.00 1.98
395 401 7.457380 AGAAAGGGGATATGAGAAGAAATGA 57.543 36.000 0.00 0.00 0.00 2.57
423 429 1.065418 ACGGAGGGAGCATTACAAAGG 60.065 52.381 0.00 0.00 0.00 3.11
537 555 7.989741 TGGAATACATGTTTTCCACATTGTTTT 59.010 29.630 33.84 0.00 44.40 2.43
575 593 9.385902 GACATTCACAATACCAAATGAATATCG 57.614 33.333 0.00 0.00 39.25 2.92
639 688 2.959516 TCGTGGTCTTAGATGCACAAG 58.040 47.619 0.00 0.00 0.00 3.16
687 2761 5.131475 AGAAATAACTCGGGGGCTACAATTA 59.869 40.000 0.00 0.00 0.00 1.40
699 2773 4.944962 TGCACATCAAGAAATAACTCGG 57.055 40.909 0.00 0.00 0.00 4.63
704 2778 7.315142 GTCAGGAATTGCACATCAAGAAATAA 58.685 34.615 0.00 0.00 38.22 1.40
726 2800 2.970324 GTTTGCCAGTCGCCGTCA 60.970 61.111 0.00 0.00 36.24 4.35
736 2810 4.527816 AGGATTATTCAGCTTTGTTTGCCA 59.472 37.500 0.00 0.00 0.00 4.92
746 2820 5.012239 TGCAAAAGTGAGGATTATTCAGCT 58.988 37.500 0.00 0.00 0.00 4.24
761 2835 1.476488 GACCACACAAGGTGCAAAAGT 59.524 47.619 0.00 0.00 46.50 2.66
764 2838 0.678366 ACGACCACACAAGGTGCAAA 60.678 50.000 0.00 0.00 46.50 3.68
813 2887 2.369860 ACATTTGCAGGAGTCTGAGTGA 59.630 45.455 0.00 0.00 43.49 3.41
838 2912 6.579666 TTGTTCAAGATAAGCTCAGCAATT 57.420 33.333 0.00 0.00 0.00 2.32
840 2914 6.389830 TTTTGTTCAAGATAAGCTCAGCAA 57.610 33.333 0.00 0.00 0.00 3.91
843 2917 6.638468 GTGGTTTTTGTTCAAGATAAGCTCAG 59.362 38.462 0.00 0.00 0.00 3.35
902 2977 3.565764 TGGTATGAAGATGCTTGGAGG 57.434 47.619 0.00 0.00 0.00 4.30
919 2994 4.853007 CCAATGAAGAGAAGGAGAATGGT 58.147 43.478 0.00 0.00 0.00 3.55
982 3059 7.430441 GGAGTCATACCTATTCAGACTTCTTC 58.570 42.308 0.00 0.00 39.47 2.87
1044 3121 1.447317 GGCGGTCATCGGATTTGCAT 61.447 55.000 0.00 0.00 39.69 3.96
1073 3150 2.948979 TCACCAGCGTTGAGTGATTTTT 59.051 40.909 15.75 0.00 35.67 1.94
1078 3155 2.930887 GCTTATCACCAGCGTTGAGTGA 60.931 50.000 19.80 19.80 44.11 3.41
1262 3339 1.268999 GGTCAGAGTCGCTGCTCATAG 60.269 57.143 0.00 0.00 44.52 2.23
1273 3350 3.319405 TCAGACAAGACAAGGTCAGAGTC 59.681 47.826 0.00 4.00 36.50 3.36
1308 3385 4.787551 TGTTTGTGGTTGTCCATAGAGTT 58.212 39.130 0.00 0.00 46.20 3.01
1314 3391 3.766591 TGAAGTTGTTTGTGGTTGTCCAT 59.233 39.130 0.00 0.00 46.20 3.41
1374 3451 1.609580 CGGATGACCAAGTTTCCGGAA 60.610 52.381 14.35 14.35 45.65 4.30
1496 3573 2.033911 TCCAAGCAATGAGGCGCA 59.966 55.556 10.83 0.00 39.27 6.09
1575 3652 3.849574 TCCCATTCCAGATTACAACCTGA 59.150 43.478 0.00 0.00 32.37 3.86
1584 3661 1.486726 GGTCTCGTCCCATTCCAGATT 59.513 52.381 0.00 0.00 0.00 2.40
1614 3691 0.398522 ACCCATCCCACGCAGATCTA 60.399 55.000 0.00 0.00 0.00 1.98
1661 3738 2.299013 TCAGTTACGATGAAGCCAGTGT 59.701 45.455 0.00 0.00 0.00 3.55
1757 3834 2.550830 AGTGCCTTTGTAGTCCAGTG 57.449 50.000 0.00 0.00 0.00 3.66
1758 3835 3.577805 AAAGTGCCTTTGTAGTCCAGT 57.422 42.857 0.10 0.00 31.98 4.00
1770 3847 5.011023 CCAGACCAGAAATTTAAAAGTGCCT 59.989 40.000 0.00 0.00 0.00 4.75
1791 3868 1.728971 GATGACGAGTTGCTGTTCCAG 59.271 52.381 0.00 0.00 34.12 3.86
1944 4021 2.417924 CCGACATCCTCTGGAGAAGTTG 60.418 54.545 0.00 0.00 34.05 3.16
1959 4036 2.697751 CAGATCCTCCTTTCTCCGACAT 59.302 50.000 0.00 0.00 0.00 3.06
1991 9218 5.800296 TCAGGGTCGAGAAATTATTGTCAA 58.200 37.500 0.00 0.00 0.00 3.18
2061 9288 3.953612 ACTCTTCTGTGCATTGGTCAAAA 59.046 39.130 0.00 0.00 0.00 2.44
2129 9356 5.358160 AGGTTAGCATAAGCACTTCCATTTC 59.642 40.000 0.00 0.00 45.49 2.17
2139 9366 5.714333 TCCATTTTTCAGGTTAGCATAAGCA 59.286 36.000 0.00 0.00 45.49 3.91
2202 9429 1.524863 CCGTGTCGACAAGTCCTCCT 61.525 60.000 26.11 0.00 0.00 3.69
2287 9517 3.686016 ACCGTTGCACAAGGAAAGATAT 58.314 40.909 8.13 0.00 0.00 1.63
2289 9519 1.981256 ACCGTTGCACAAGGAAAGAT 58.019 45.000 8.13 0.00 0.00 2.40
2292 9522 3.075884 GGTATACCGTTGCACAAGGAAA 58.924 45.455 6.06 0.00 0.00 3.13
2300 9557 2.965572 GGTACAGGTATACCGTTGCA 57.034 50.000 19.67 2.97 42.08 4.08
2340 9597 9.976511 TCTAGAATTCAACATAAAGGGTATACG 57.023 33.333 8.44 0.00 0.00 3.06
2473 9863 2.627945 TCGACAACTTGCACTCTTTGT 58.372 42.857 0.00 0.00 34.88 2.83
2474 9864 3.309682 TCTTCGACAACTTGCACTCTTTG 59.690 43.478 0.00 0.00 0.00 2.77
2475 9865 3.531538 TCTTCGACAACTTGCACTCTTT 58.468 40.909 0.00 0.00 0.00 2.52
2477 9867 2.890808 TCTTCGACAACTTGCACTCT 57.109 45.000 0.00 0.00 0.00 3.24
2478 9868 3.248602 ACAATCTTCGACAACTTGCACTC 59.751 43.478 0.00 0.00 0.00 3.51
2479 9869 3.206150 ACAATCTTCGACAACTTGCACT 58.794 40.909 0.00 0.00 0.00 4.40
2481 9871 4.377021 AGTACAATCTTCGACAACTTGCA 58.623 39.130 0.00 0.00 0.00 4.08
2483 9873 4.389077 GGGAGTACAATCTTCGACAACTTG 59.611 45.833 0.00 0.00 0.00 3.16
2487 9877 3.576982 ACAGGGAGTACAATCTTCGACAA 59.423 43.478 0.00 0.00 0.00 3.18
2488 9878 3.162666 ACAGGGAGTACAATCTTCGACA 58.837 45.455 0.00 0.00 0.00 4.35
2489 9879 3.870633 ACAGGGAGTACAATCTTCGAC 57.129 47.619 0.00 0.00 0.00 4.20
2490 9880 5.163447 CCATTACAGGGAGTACAATCTTCGA 60.163 44.000 0.00 0.00 30.91 3.71
2492 9882 4.816925 GCCATTACAGGGAGTACAATCTTC 59.183 45.833 0.00 0.00 30.91 2.87
2494 9884 4.040755 AGCCATTACAGGGAGTACAATCT 58.959 43.478 0.00 0.00 30.91 2.40
2496 9886 3.117888 CCAGCCATTACAGGGAGTACAAT 60.118 47.826 0.00 0.00 30.91 2.71
2497 9887 2.238646 CCAGCCATTACAGGGAGTACAA 59.761 50.000 0.00 0.00 30.91 2.41
2499 9889 2.116238 TCCAGCCATTACAGGGAGTAC 58.884 52.381 0.00 0.00 30.91 2.73
2500 9890 2.561209 TCCAGCCATTACAGGGAGTA 57.439 50.000 0.00 0.00 0.00 2.59
2502 9892 1.492176 ACATCCAGCCATTACAGGGAG 59.508 52.381 0.00 0.00 0.00 4.30
2503 9893 1.212688 CACATCCAGCCATTACAGGGA 59.787 52.381 0.00 0.00 0.00 4.20
2504 9894 1.683943 CACATCCAGCCATTACAGGG 58.316 55.000 0.00 0.00 0.00 4.45
2505 9895 1.064463 ACCACATCCAGCCATTACAGG 60.064 52.381 0.00 0.00 0.00 4.00
2506 9896 2.425143 ACCACATCCAGCCATTACAG 57.575 50.000 0.00 0.00 0.00 2.74
2507 9897 2.897271 AACCACATCCAGCCATTACA 57.103 45.000 0.00 0.00 0.00 2.41
2508 9898 3.118038 TCCTAACCACATCCAGCCATTAC 60.118 47.826 0.00 0.00 0.00 1.89
2509 9899 3.119319 TCCTAACCACATCCAGCCATTA 58.881 45.455 0.00 0.00 0.00 1.90
2510 9900 1.922447 TCCTAACCACATCCAGCCATT 59.078 47.619 0.00 0.00 0.00 3.16
2511 9901 1.595311 TCCTAACCACATCCAGCCAT 58.405 50.000 0.00 0.00 0.00 4.40
2512 9902 1.367346 TTCCTAACCACATCCAGCCA 58.633 50.000 0.00 0.00 0.00 4.75
2513 9903 2.092323 GTTTCCTAACCACATCCAGCC 58.908 52.381 0.00 0.00 0.00 4.85
2514 9904 3.073274 AGTTTCCTAACCACATCCAGC 57.927 47.619 0.00 0.00 34.71 4.85
2515 9905 5.045869 TCCTAAGTTTCCTAACCACATCCAG 60.046 44.000 0.00 0.00 34.71 3.86
2518 9908 5.823045 CCATCCTAAGTTTCCTAACCACATC 59.177 44.000 0.00 0.00 34.71 3.06
2520 9910 4.566907 GCCATCCTAAGTTTCCTAACCACA 60.567 45.833 0.00 0.00 34.71 4.17
2521 9911 3.945921 GCCATCCTAAGTTTCCTAACCAC 59.054 47.826 0.00 0.00 34.71 4.16
2522 9912 3.589735 TGCCATCCTAAGTTTCCTAACCA 59.410 43.478 0.00 0.00 34.71 3.67
2524 9914 9.569122 TTATTATGCCATCCTAAGTTTCCTAAC 57.431 33.333 0.00 0.00 34.36 2.34
2532 9922 9.860650 TGTTGTAATTATTATGCCATCCTAAGT 57.139 29.630 0.00 0.00 0.00 2.24
2540 9930 5.069781 GGCCCTTGTTGTAATTATTATGCCA 59.930 40.000 0.00 0.00 33.01 4.92
2542 9932 6.155475 TGGCCCTTGTTGTAATTATTATGC 57.845 37.500 0.00 0.00 0.00 3.14
2543 9933 9.044150 CAAATGGCCCTTGTTGTAATTATTATG 57.956 33.333 0.00 0.00 0.00 1.90
2544 9934 7.714813 GCAAATGGCCCTTGTTGTAATTATTAT 59.285 33.333 14.35 0.00 36.11 1.28
2546 9936 5.879777 GCAAATGGCCCTTGTTGTAATTATT 59.120 36.000 14.35 0.00 36.11 1.40
2547 9937 5.046014 TGCAAATGGCCCTTGTTGTAATTAT 60.046 36.000 14.35 0.00 43.89 1.28
2550 9940 2.636893 TGCAAATGGCCCTTGTTGTAAT 59.363 40.909 14.35 0.00 43.89 1.89
2552 9942 1.709578 TGCAAATGGCCCTTGTTGTA 58.290 45.000 14.35 4.48 43.89 2.41
2554 9944 2.188062 AATGCAAATGGCCCTTGTTG 57.812 45.000 14.35 8.11 43.89 3.33
2555 9945 2.372837 AGAAATGCAAATGGCCCTTGTT 59.627 40.909 14.35 3.44 43.89 2.83
2587 9977 3.559171 GGCAAATCTGAGTAGGTGGTTCA 60.559 47.826 0.00 0.00 0.00 3.18
2742 10134 7.042797 ACCTTCGATCCCATAAAATTTCATG 57.957 36.000 0.00 0.00 0.00 3.07
2753 10145 2.320781 CCTGAGTACCTTCGATCCCAT 58.679 52.381 0.00 0.00 0.00 4.00
2781 10174 1.526041 GCATGAAAATTTGCACGCACA 59.474 42.857 12.30 0.00 38.72 4.57
2809 10202 0.322816 GCCACAAGCTCCTGGAATGA 60.323 55.000 12.82 0.00 38.99 2.57
2830 10223 7.065324 CAGGCGTACAGATTTATTGTTTTCCTA 59.935 37.037 0.00 0.00 0.00 2.94
2913 10309 1.153107 CCCGAGCATCTTGGATGCA 60.153 57.895 27.00 0.00 46.77 3.96
2960 10356 0.379669 GCTCCTCGCATGTCATTTGG 59.620 55.000 0.00 0.00 38.92 3.28
3095 10506 1.376424 AAGATGCTCGGGTGTGCAG 60.376 57.895 0.00 0.00 46.58 4.41
3407 10857 6.762661 CCACTAATCAAATTTGCCCCTAATTG 59.237 38.462 13.54 3.29 0.00 2.32
3426 10876 3.173953 TCCCTAACTCGAACCCACTAA 57.826 47.619 0.00 0.00 0.00 2.24
3780 11243 1.528161 GAATTTTGCAAGTGCTGTGGC 59.472 47.619 0.00 0.00 42.66 5.01
3782 11245 2.823984 TGGAATTTTGCAAGTGCTGTG 58.176 42.857 0.00 0.00 42.66 3.66
4004 11473 1.341531 CACCTCCTAATAGTCCCTGCG 59.658 57.143 0.00 0.00 0.00 5.18
4006 11475 2.700897 CACCACCTCCTAATAGTCCCTG 59.299 54.545 0.00 0.00 0.00 4.45
4080 11549 6.625873 AGAACAACTTCATTTCTGAACTCC 57.374 37.500 0.00 0.00 36.46 3.85
4249 11719 3.188254 CGACCATCACATAAAGTTGTGCA 59.812 43.478 0.00 0.00 45.29 4.57
4515 12016 4.612264 ACTTACTATGTCCCAACAACGT 57.388 40.909 0.00 0.00 39.30 3.99
4676 12177 5.080969 ACAGTAGAACGCCAAAGCTATAA 57.919 39.130 0.00 0.00 36.60 0.98
4712 12213 3.308402 GGGATGAACTGATCTTTGACCCA 60.308 47.826 0.00 0.00 34.43 4.51
4825 12328 3.620488 CATAAGCTCCAGGCCTAAAACA 58.380 45.455 3.98 0.00 43.05 2.83
4827 12330 2.849943 TCCATAAGCTCCAGGCCTAAAA 59.150 45.455 3.98 0.00 43.05 1.52
4923 12436 7.097192 TGAACACACAAGAGACCTATATGAAC 58.903 38.462 0.00 0.00 0.00 3.18
5012 12525 1.005569 TCCTTCGGAGTAGGAAGCAGA 59.994 52.381 0.00 0.00 38.83 4.26
5167 12687 3.964688 TCACCTGTACAAACTGGAGAAGA 59.035 43.478 5.91 0.00 45.20 2.87
5237 12760 4.829872 AACCACGACCAGGATTACAATA 57.170 40.909 0.00 0.00 0.00 1.90
5276 12799 6.950860 AAATAGGGAAATTCCAAACATGGT 57.049 33.333 14.68 0.00 38.64 3.55
5326 12849 2.392662 TGATCAGGTAGCCTCTTCCAG 58.607 52.381 0.00 0.00 0.00 3.86
5404 12930 5.762179 TTCAGACCCATTGACTAACTGAT 57.238 39.130 0.00 0.00 33.90 2.90
5407 12933 5.308237 AGAGTTTCAGACCCATTGACTAACT 59.692 40.000 0.00 0.00 31.64 2.24
5467 12993 3.338249 TGCCAGCTCAAAGAGAACATAC 58.662 45.455 0.00 0.00 0.00 2.39
5534 13071 5.587844 ACTTCAGGCATGTAAATCTAGCTTG 59.412 40.000 0.00 0.00 34.14 4.01
5549 13086 8.579850 AAAATATAATTGTCAGACTTCAGGCA 57.420 30.769 1.31 0.00 0.00 4.75
5872 13421 6.689178 TTCAAGATTATTGTTTTGAAGCGC 57.311 33.333 0.00 0.00 35.34 5.92
5948 13498 2.661718 AGGCCCGTCTTTTGAAAAGAA 58.338 42.857 20.71 4.13 0.00 2.52
5949 13499 2.358322 AGGCCCGTCTTTTGAAAAGA 57.642 45.000 15.81 15.81 0.00 2.52
5963 13513 2.644798 ACCATGGATATACTGAAGGCCC 59.355 50.000 21.47 0.00 0.00 5.80
5966 13516 4.321718 CAGCACCATGGATATACTGAAGG 58.678 47.826 21.47 0.00 0.00 3.46
5998 13548 7.025963 CAGTCAAATTCAGCACCTTTATCTTC 58.974 38.462 0.00 0.00 0.00 2.87
6079 13629 4.998672 CCTAAGTTGGTGTAATGGTCGAAA 59.001 41.667 0.00 0.00 0.00 3.46
6118 13668 3.820467 CACCTTCAATGAAAGCTACCACA 59.180 43.478 0.00 0.00 0.00 4.17
6124 13674 5.360714 TCTGTTTTCACCTTCAATGAAAGCT 59.639 36.000 13.17 0.00 44.57 3.74
6138 13688 7.489160 ACCTTGGAATTTAACTCTGTTTTCAC 58.511 34.615 0.00 0.00 0.00 3.18
6173 13723 5.146010 ACTGTTTCTTGCCACAAAAAGAA 57.854 34.783 0.00 0.00 39.91 2.52
6179 13729 3.088532 ACTTGACTGTTTCTTGCCACAA 58.911 40.909 0.00 0.00 0.00 3.33
6280 13830 6.729690 TTTCTCCTCATCACACCAATTTTT 57.270 33.333 0.00 0.00 0.00 1.94
6281 13831 6.923199 ATTTCTCCTCATCACACCAATTTT 57.077 33.333 0.00 0.00 0.00 1.82
6282 13832 6.923199 AATTTCTCCTCATCACACCAATTT 57.077 33.333 0.00 0.00 0.00 1.82
6283 13833 8.599624 ATTAATTTCTCCTCATCACACCAATT 57.400 30.769 0.00 0.00 0.00 2.32
6284 13834 8.599624 AATTAATTTCTCCTCATCACACCAAT 57.400 30.769 0.00 0.00 0.00 3.16
6285 13835 9.699410 ATAATTAATTTCTCCTCATCACACCAA 57.301 29.630 5.91 0.00 0.00 3.67
6382 13932 2.996621 GTCGGACCTGACAGAGAAAATG 59.003 50.000 3.32 0.00 38.75 2.32
6383 13933 2.632996 TGTCGGACCTGACAGAGAAAAT 59.367 45.455 13.06 0.00 43.62 1.82
6396 13950 3.119101 CCCATAGCTATATGTGTCGGACC 60.119 52.174 5.77 0.00 37.65 4.46
6425 13979 3.452627 AGCCCACTTACAATCTCCAGTAG 59.547 47.826 0.00 0.00 0.00 2.57
6446 14000 3.196469 TGGTAAGGTGAGCTGATCTTCAG 59.804 47.826 0.51 0.08 46.90 3.02
6539 14123 3.689161 CCTGAAACATGGTCGAGCATAAA 59.311 43.478 28.12 11.98 0.00 1.40


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

AutoCloner maintained by Alex Coulton.