Multiple sequence alignment - TraesCS4A01G216500

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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 TraesCS4A01G216500 chr4A 100.000 7146 0 0 1 7146 515460630 515467775 0.000000e+00 13197.0
1 TraesCS4A01G216500 chr4A 86.842 76 8 1 6706 6781 424369509 424369436 4.590000e-12 84.2
2 TraesCS4A01G216500 chr4A 84.146 82 10 2 6707 6787 599784420 599784499 7.690000e-10 76.8
3 TraesCS4A01G216500 chr4D 95.746 4537 128 28 1730 6258 66511717 66516196 0.000000e+00 7249.0
4 TraesCS4A01G216500 chr4D 92.746 896 34 12 850 1736 66508281 66509154 0.000000e+00 1266.0
5 TraesCS4A01G216500 chr4D 88.315 368 31 4 6779 7146 66517074 66517429 1.420000e-116 431.0
6 TraesCS4A01G216500 chr4D 94.022 184 10 1 6255 6438 66516276 66516458 1.960000e-70 278.0
7 TraesCS4A01G216500 chr4D 84.211 76 10 1 6706 6781 134627609 134627682 9.940000e-09 73.1
8 TraesCS4A01G216500 chr4B 95.111 2516 75 19 2842 5348 97072388 97074864 0.000000e+00 3921.0
9 TraesCS4A01G216500 chr4B 96.000 1075 27 7 5231 6304 97074860 97075919 0.000000e+00 1733.0
10 TraesCS4A01G216500 chr4B 94.033 972 21 13 1879 2844 97071367 97072307 0.000000e+00 1439.0
11 TraesCS4A01G216500 chr4B 92.342 888 36 12 988 1867 97070394 97071257 0.000000e+00 1234.0
12 TraesCS4A01G216500 chr4B 93.072 664 31 6 5583 6246 129101331 129101979 0.000000e+00 957.0
13 TraesCS4A01G216500 chr4B 90.547 603 34 6 6521 7122 97077043 97076463 0.000000e+00 776.0
14 TraesCS4A01G216500 chr4B 81.557 835 98 32 1 785 97068818 97069646 7.820000e-179 638.0
15 TraesCS4A01G216500 chr4B 95.899 317 13 0 5029 5345 129052335 129052651 1.370000e-141 514.0
16 TraesCS4A01G216500 chr4B 87.626 396 31 8 6240 6619 129103786 129104179 1.830000e-120 444.0
17 TraesCS4A01G216500 chr4B 85.870 368 36 6 6779 7146 129104457 129104808 1.880000e-100 377.0
18 TraesCS4A01G216500 chr4B 91.852 270 16 1 6877 7146 97076454 97076191 8.750000e-99 372.0
19 TraesCS4A01G216500 chr4B 92.233 206 15 1 5377 5582 129056766 129056970 2.520000e-74 291.0
20 TraesCS4A01G216500 chr5D 81.006 179 30 3 4999 5175 199084484 199084660 9.670000e-29 139.0
21 TraesCS4A01G216500 chr1B 85.526 76 8 2 6707 6781 29409009 29408936 7.690000e-10 76.8
22 TraesCS4A01G216500 chr7B 83.333 78 10 2 6706 6783 380716531 380716457 1.290000e-07 69.4
23 TraesCS4A01G216500 chr7B 81.579 76 10 3 6707 6781 519366662 519366734 7.740000e-05 60.2
24 TraesCS4A01G216500 chr3D 84.286 70 9 1 6711 6780 550996777 550996844 4.630000e-07 67.6
25 TraesCS4A01G216500 chr2A 82.667 75 11 1 6706 6780 509051655 509051727 1.660000e-06 65.8
26 TraesCS4A01G216500 chr5A 94.872 39 2 0 412 450 453190538 453190500 2.150000e-05 62.1
27 TraesCS4A01G216500 chr5B 100.000 29 0 0 6650 6678 534669902 534669874 4.000000e-03 54.7
28 TraesCS4A01G216500 chr2D 92.105 38 3 0 6650 6687 138293843 138293806 4.000000e-03 54.7
29 TraesCS4A01G216500 chr3B 100.000 28 0 0 6651 6678 119422000 119421973 1.300000e-02 52.8


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 TraesCS4A01G216500 chr4A 515460630 515467775 7145 False 13197.000000 13197 100.00000 1 7146 1 chr4A.!!$F1 7145
1 TraesCS4A01G216500 chr4D 66508281 66517429 9148 False 2306.000000 7249 92.70725 850 7146 4 chr4D.!!$F2 6296
2 TraesCS4A01G216500 chr4B 97068818 97075919 7101 False 1793.000000 3921 91.80860 1 6304 5 chr4B.!!$F3 6303
3 TraesCS4A01G216500 chr4B 129101331 129104808 3477 False 592.666667 957 88.85600 5583 7146 3 chr4B.!!$F4 1563
4 TraesCS4A01G216500 chr4B 97076191 97077043 852 True 574.000000 776 91.19950 6521 7146 2 chr4B.!!$R1 625


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
112 113 0.036388 TCGATGTCCAAGAACAGGGC 60.036 55.0 0.00 0.0 31.50 5.19 F
758 806 0.041839 CTGCGGCGCTGATTATGAAC 60.042 55.0 33.26 0.0 0.00 3.18 F
832 881 0.529378 GGACGTCTCCTTTAGCCGAA 59.471 55.0 16.46 0.0 33.07 4.30 F
1450 2069 0.543410 TTGCTCGTTCCCAGGGACTA 60.543 55.0 8.12 0.0 36.02 2.59 F
1582 2202 1.179152 TTTGCCACTGGATGCTCATG 58.821 50.0 0.00 0.0 0.00 3.07 F
2719 6030 0.537188 TCGCAGACTCCCTTGGATTC 59.463 55.0 0.00 0.0 32.48 2.52 F
4350 7749 0.452987 TTGCAATGGAGAATGCTCGC 59.547 50.0 0.00 0.0 42.97 5.03 F
4518 7917 0.420272 TTCTAGGGCCAGTTAGGGGT 59.580 55.0 6.18 0.0 38.09 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1524 2144 1.016627 AATTCATCCGACGCACATGG 58.983 50.000 0.00 0.00 0.00 3.66 R
2668 5979 0.041982 GGGGCCATAAAGGGTTTGGA 59.958 55.000 4.39 0.00 38.09 3.53 R
2669 5980 0.042581 AGGGGCCATAAAGGGTTTGG 59.957 55.000 4.39 0.00 38.09 3.28 R
2702 6013 0.250513 ACGAATCCAAGGGAGTCTGC 59.749 55.000 10.54 0.00 43.62 4.26 R
3107 6502 1.003718 GAAAGTGACCCAGGGACGG 60.004 63.158 14.54 0.00 0.00 4.79 R
4410 7809 1.414158 GACATCTCCCATTCCTCCGA 58.586 55.000 0.00 0.00 0.00 4.55 R
5581 9107 0.037326 CCAGCTTCCTCGTGCACTTA 60.037 55.000 16.19 1.63 0.00 2.24 R
6485 12033 1.228552 AGCCATGTCCCGCTGTTTT 60.229 52.632 0.00 0.00 32.98 2.43 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
27 28 4.191485 GTGCGAACGACGATGGCG 62.191 66.667 0.00 0.32 45.77 5.69
38 39 3.499737 GATGGCGGCGTGGTCAAG 61.500 66.667 9.10 0.00 0.00 3.02
47 48 2.031516 CGTGGTCAAGGCAGAGCTG 61.032 63.158 0.00 0.00 36.97 4.24
49 50 2.149383 TGGTCAAGGCAGAGCTGGT 61.149 57.895 0.00 0.00 36.97 4.00
60 61 1.520342 GAGCTGGTGACATCCTCGC 60.520 63.158 0.00 0.00 41.51 5.03
65 66 1.064946 GGTGACATCCTCGCTCTCG 59.935 63.158 0.00 0.00 0.00 4.04
68 69 0.960861 TGACATCCTCGCTCTCGTGT 60.961 55.000 0.00 0.00 36.96 4.49
83 84 1.599576 GTGTGCCTCCTCTTCCTCC 59.400 63.158 0.00 0.00 0.00 4.30
85 86 1.985116 GTGCCTCCTCTTCCTCCGT 60.985 63.158 0.00 0.00 0.00 4.69
86 87 1.682684 TGCCTCCTCTTCCTCCGTC 60.683 63.158 0.00 0.00 0.00 4.79
90 91 4.194720 CCTCTTCCTCCGTCGCCG 62.195 72.222 0.00 0.00 0.00 6.46
106 107 1.445410 CCGCGTCGATGTCCAAGAA 60.445 57.895 4.92 0.00 0.00 2.52
112 113 0.036388 TCGATGTCCAAGAACAGGGC 60.036 55.000 0.00 0.00 31.50 5.19
118 119 1.376037 CCAAGAACAGGGCGTCTCC 60.376 63.158 0.00 0.00 0.00 3.71
130 131 2.985456 GTCTCCCTCTGCCCACAG 59.015 66.667 0.00 0.00 45.95 3.66
151 152 4.166011 GTGCAACCGCCATCGCTC 62.166 66.667 0.00 0.00 37.32 5.03
167 168 3.758088 CTCGTGGTGGATCTCGCGG 62.758 68.421 6.13 0.00 37.47 6.46
193 194 0.734253 CAGTACGACAGGAGCAGCAC 60.734 60.000 0.00 0.00 0.00 4.40
235 237 2.234913 GACCGTCCGCCACCATAGTT 62.235 60.000 0.00 0.00 0.00 2.24
241 243 2.112190 TCCGCCACCATAGTTATGACA 58.888 47.619 0.74 0.00 35.75 3.58
264 266 4.719369 GTCGTTCGCCTGGTCGCT 62.719 66.667 5.78 0.00 0.00 4.93
265 267 4.717629 TCGTTCGCCTGGTCGCTG 62.718 66.667 5.78 0.00 0.00 5.18
266 268 4.717629 CGTTCGCCTGGTCGCTGA 62.718 66.667 5.78 0.00 0.00 4.26
267 269 3.112709 GTTCGCCTGGTCGCTGAC 61.113 66.667 5.78 0.79 0.00 3.51
302 304 2.811317 GCTGGTGCTCGTCGAAGG 60.811 66.667 0.00 0.00 36.03 3.46
303 305 2.962569 CTGGTGCTCGTCGAAGGA 59.037 61.111 0.00 0.00 0.00 3.36
304 306 1.153939 CTGGTGCTCGTCGAAGGAG 60.154 63.158 9.74 9.74 33.54 3.69
305 307 1.867919 CTGGTGCTCGTCGAAGGAGT 61.868 60.000 14.21 0.00 33.01 3.85
306 308 1.153997 GGTGCTCGTCGAAGGAGTC 60.154 63.158 14.21 8.59 33.01 3.36
317 319 1.962321 GAAGGAGTCGGGGAGAAGGC 61.962 65.000 0.00 0.00 0.00 4.35
319 321 4.516195 GAGTCGGGGAGAAGGCGC 62.516 72.222 0.00 0.00 0.00 6.53
336 338 3.107661 CGTACACCGGGTTGCGAC 61.108 66.667 6.32 0.00 0.00 5.19
361 363 1.659335 GACACTTTCGACCGACGCA 60.659 57.895 0.00 0.00 42.26 5.24
364 366 2.355363 CTTTCGACCGACGCACCA 60.355 61.111 0.00 0.00 42.26 4.17
374 376 1.568612 CGACGCACCACTTCAATGCT 61.569 55.000 0.00 0.00 37.20 3.79
381 383 1.093159 CCACTTCAATGCTGGCTCTC 58.907 55.000 0.00 0.00 0.00 3.20
382 384 1.612462 CCACTTCAATGCTGGCTCTCA 60.612 52.381 0.00 0.00 0.00 3.27
384 386 2.753452 CACTTCAATGCTGGCTCTCATT 59.247 45.455 0.00 0.00 33.56 2.57
393 395 3.390311 TGCTGGCTCTCATTAGATGTCAT 59.610 43.478 0.00 0.00 0.00 3.06
408 434 1.003839 TCATGTCCGTTGGTGCTCC 60.004 57.895 0.00 0.00 0.00 4.70
409 435 2.040544 CATGTCCGTTGGTGCTCCC 61.041 63.158 1.59 0.00 0.00 4.30
422 448 4.803426 CTCCCGAGCGGCACTGAC 62.803 72.222 1.45 0.00 0.00 3.51
431 457 4.693532 GGCACTGACCGACATGAA 57.306 55.556 0.00 0.00 0.00 2.57
433 459 2.309528 GGCACTGACCGACATGAATA 57.690 50.000 0.00 0.00 0.00 1.75
434 460 2.838736 GGCACTGACCGACATGAATAT 58.161 47.619 0.00 0.00 0.00 1.28
442 468 1.536766 CCGACATGAATATGCGGCAAT 59.463 47.619 6.82 0.00 42.51 3.56
450 476 3.884693 TGAATATGCGGCAATCACTTCAT 59.115 39.130 6.82 0.00 0.00 2.57
451 477 3.909776 ATATGCGGCAATCACTTCATG 57.090 42.857 6.82 0.00 0.00 3.07
459 485 2.159198 GCAATCACTTCATGCGGGAAAT 60.159 45.455 0.00 0.00 0.00 2.17
460 486 3.066621 GCAATCACTTCATGCGGGAAATA 59.933 43.478 0.00 0.00 0.00 1.40
462 488 3.627395 TCACTTCATGCGGGAAATAGT 57.373 42.857 0.00 0.00 0.00 2.12
475 501 4.072131 GGGAAATAGTGTGAGCAAGTGAA 58.928 43.478 0.00 0.00 0.00 3.18
490 516 1.007842 AGTGAAAGGGTTTTGGGTGGT 59.992 47.619 0.00 0.00 0.00 4.16
548 574 1.463674 CCCGCAAAGCATCCTAGTTT 58.536 50.000 0.00 0.00 0.00 2.66
558 584 2.911484 CATCCTAGTTTGCCTCTGGTC 58.089 52.381 0.00 0.00 0.00 4.02
559 585 1.276622 TCCTAGTTTGCCTCTGGTCC 58.723 55.000 0.00 0.00 0.00 4.46
563 589 1.966451 GTTTGCCTCTGGTCCGTGG 60.966 63.158 0.00 0.00 0.00 4.94
567 593 2.982130 CCTCTGGTCCGTGGAAGG 59.018 66.667 0.00 0.00 0.00 3.46
599 625 2.184322 CAGTCCACGGACCGATGG 59.816 66.667 23.38 22.66 45.59 3.51
600 626 2.036731 AGTCCACGGACCGATGGA 59.963 61.111 25.11 25.11 45.59 3.41
603 629 2.184322 CCACGGACCGATGGAGTG 59.816 66.667 23.38 6.94 38.34 3.51
623 649 5.189928 AGTGCCACGTTGGATGATAAAATA 58.810 37.500 8.04 0.00 40.96 1.40
624 650 5.650266 AGTGCCACGTTGGATGATAAAATAA 59.350 36.000 8.04 0.00 40.96 1.40
625 651 6.151985 AGTGCCACGTTGGATGATAAAATAAA 59.848 34.615 8.04 0.00 40.96 1.40
627 653 8.132362 GTGCCACGTTGGATGATAAAATAAATA 58.868 33.333 8.04 0.00 40.96 1.40
639 665 8.725405 TGATAAAATAAATACAGACCGCTTGA 57.275 30.769 0.00 0.00 0.00 3.02
659 685 2.048784 CGGATGGATGCGAGCGAT 60.049 61.111 0.00 0.00 44.78 4.58
660 686 1.665916 CGGATGGATGCGAGCGATT 60.666 57.895 0.00 0.00 44.78 3.34
661 687 1.224069 CGGATGGATGCGAGCGATTT 61.224 55.000 0.00 0.00 44.78 2.17
662 688 0.236711 GGATGGATGCGAGCGATTTG 59.763 55.000 0.00 0.00 0.00 2.32
663 689 1.220529 GATGGATGCGAGCGATTTGA 58.779 50.000 0.00 0.00 0.00 2.69
664 690 1.194098 GATGGATGCGAGCGATTTGAG 59.806 52.381 0.00 0.00 0.00 3.02
665 691 0.811219 TGGATGCGAGCGATTTGAGG 60.811 55.000 0.00 0.00 0.00 3.86
667 693 1.009829 GATGCGAGCGATTTGAGGTT 58.990 50.000 0.00 0.00 0.00 3.50
668 694 2.201732 GATGCGAGCGATTTGAGGTTA 58.798 47.619 0.00 0.00 0.00 2.85
669 695 1.640428 TGCGAGCGATTTGAGGTTAG 58.360 50.000 0.00 0.00 0.00 2.34
670 696 1.067142 TGCGAGCGATTTGAGGTTAGT 60.067 47.619 0.00 0.00 0.00 2.24
672 698 2.607187 CGAGCGATTTGAGGTTAGTGT 58.393 47.619 0.00 0.00 0.00 3.55
673 699 2.993899 CGAGCGATTTGAGGTTAGTGTT 59.006 45.455 0.00 0.00 0.00 3.32
674 700 3.181530 CGAGCGATTTGAGGTTAGTGTTG 60.182 47.826 0.00 0.00 0.00 3.33
675 701 3.074412 AGCGATTTGAGGTTAGTGTTGG 58.926 45.455 0.00 0.00 0.00 3.77
676 702 3.071479 GCGATTTGAGGTTAGTGTTGGA 58.929 45.455 0.00 0.00 0.00 3.53
677 703 3.500680 GCGATTTGAGGTTAGTGTTGGAA 59.499 43.478 0.00 0.00 0.00 3.53
679 705 4.994852 CGATTTGAGGTTAGTGTTGGAAGA 59.005 41.667 0.00 0.00 0.00 2.87
691 739 6.136541 AGTGTTGGAAGATCAAAGTTTGAC 57.863 37.500 20.26 13.70 43.48 3.18
698 746 9.739276 TTGGAAGATCAAAGTTTGACTACATAT 57.261 29.630 20.26 2.89 43.48 1.78
744 792 6.603237 TTATTCACATATTCAACTCTGCGG 57.397 37.500 0.00 0.00 0.00 5.69
745 793 2.279741 TCACATATTCAACTCTGCGGC 58.720 47.619 0.00 0.00 0.00 6.53
749 797 1.083806 TATTCAACTCTGCGGCGCTG 61.084 55.000 33.26 31.27 0.00 5.18
758 806 0.041839 CTGCGGCGCTGATTATGAAC 60.042 55.000 33.26 0.00 0.00 3.18
785 834 3.872771 GGAAACTGAACTTGGTGAACGTA 59.127 43.478 0.00 0.00 0.00 3.57
787 836 5.163733 GGAAACTGAACTTGGTGAACGTAAA 60.164 40.000 0.00 0.00 0.00 2.01
789 838 4.255301 ACTGAACTTGGTGAACGTAAACA 58.745 39.130 0.00 0.00 0.00 2.83
790 839 4.879545 ACTGAACTTGGTGAACGTAAACAT 59.120 37.500 0.00 0.00 0.00 2.71
791 840 5.007332 ACTGAACTTGGTGAACGTAAACATC 59.993 40.000 0.00 0.00 0.00 3.06
792 841 4.876679 TGAACTTGGTGAACGTAAACATCA 59.123 37.500 0.00 0.00 0.00 3.07
793 842 4.806342 ACTTGGTGAACGTAAACATCAC 57.194 40.909 8.49 8.49 42.08 3.06
794 843 4.193090 ACTTGGTGAACGTAAACATCACA 58.807 39.130 16.73 3.45 44.05 3.58
795 844 4.272504 ACTTGGTGAACGTAAACATCACAG 59.727 41.667 16.73 10.15 44.05 3.66
796 845 3.135225 TGGTGAACGTAAACATCACAGG 58.865 45.455 16.73 0.00 44.05 4.00
797 846 2.095919 GGTGAACGTAAACATCACAGGC 60.096 50.000 16.73 0.00 44.05 4.85
798 847 2.546368 GTGAACGTAAACATCACAGGCA 59.454 45.455 11.49 0.00 42.31 4.75
799 848 3.188460 GTGAACGTAAACATCACAGGCAT 59.812 43.478 11.49 0.00 42.31 4.40
802 851 4.846779 ACGTAAACATCACAGGCATTTT 57.153 36.364 0.00 0.00 0.00 1.82
803 852 4.545610 ACGTAAACATCACAGGCATTTTG 58.454 39.130 0.00 0.00 0.00 2.44
804 853 4.037446 ACGTAAACATCACAGGCATTTTGT 59.963 37.500 0.00 0.00 0.00 2.83
806 855 5.794945 CGTAAACATCACAGGCATTTTGTAG 59.205 40.000 0.00 0.00 0.00 2.74
808 857 5.789643 AACATCACAGGCATTTTGTAGTT 57.210 34.783 0.00 0.00 0.00 2.24
810 859 6.500684 ACATCACAGGCATTTTGTAGTTAG 57.499 37.500 0.00 0.00 0.00 2.34
811 860 5.106157 ACATCACAGGCATTTTGTAGTTAGC 60.106 40.000 0.00 0.00 0.00 3.09
812 861 3.435327 TCACAGGCATTTTGTAGTTAGCG 59.565 43.478 0.00 0.00 0.00 4.26
813 862 2.747446 ACAGGCATTTTGTAGTTAGCGG 59.253 45.455 0.00 0.00 0.00 5.52
814 863 2.097466 CAGGCATTTTGTAGTTAGCGGG 59.903 50.000 0.00 0.00 0.00 6.13
816 865 2.096980 GGCATTTTGTAGTTAGCGGGAC 59.903 50.000 0.00 0.00 0.00 4.46
830 879 1.141234 GGGACGTCTCCTTTAGCCG 59.859 63.158 16.46 0.00 36.68 5.52
832 881 0.529378 GGACGTCTCCTTTAGCCGAA 59.471 55.000 16.46 0.00 33.07 4.30
833 882 1.067354 GGACGTCTCCTTTAGCCGAAA 60.067 52.381 16.46 0.00 33.07 3.46
834 883 2.611224 GGACGTCTCCTTTAGCCGAAAA 60.611 50.000 16.46 0.00 33.07 2.29
835 884 2.410939 ACGTCTCCTTTAGCCGAAAAC 58.589 47.619 0.00 0.00 0.00 2.43
836 885 2.036862 ACGTCTCCTTTAGCCGAAAACT 59.963 45.455 0.00 0.00 0.00 2.66
838 887 4.240096 CGTCTCCTTTAGCCGAAAACTTA 58.760 43.478 0.00 0.00 0.00 2.24
840 889 5.005490 CGTCTCCTTTAGCCGAAAACTTATC 59.995 44.000 0.00 0.00 0.00 1.75
842 891 4.824289 TCCTTTAGCCGAAAACTTATCGT 58.176 39.130 0.00 0.00 38.60 3.73
845 894 5.220416 CCTTTAGCCGAAAACTTATCGTCAG 60.220 44.000 0.00 0.00 38.60 3.51
871 934 3.506398 TGGGGGTCATTCTTTTCTTTCC 58.494 45.455 0.00 0.00 0.00 3.13
891 954 6.721571 TTCCGAACAAACATTATCAGTCTC 57.278 37.500 0.00 0.00 0.00 3.36
909 1522 1.092921 TCTGGTTGTGTCGTGTTGCC 61.093 55.000 0.00 0.00 0.00 4.52
970 1583 5.968676 ACACTCCTTGCCCTATGTATTTA 57.031 39.130 0.00 0.00 0.00 1.40
971 1584 6.515512 ACACTCCTTGCCCTATGTATTTAT 57.484 37.500 0.00 0.00 0.00 1.40
972 1585 7.626999 ACACTCCTTGCCCTATGTATTTATA 57.373 36.000 0.00 0.00 0.00 0.98
973 1586 8.219660 ACACTCCTTGCCCTATGTATTTATAT 57.780 34.615 0.00 0.00 0.00 0.86
974 1587 8.103305 ACACTCCTTGCCCTATGTATTTATATG 58.897 37.037 0.00 0.00 0.00 1.78
975 1588 8.103305 CACTCCTTGCCCTATGTATTTATATGT 58.897 37.037 0.00 0.00 0.00 2.29
976 1589 9.333961 ACTCCTTGCCCTATGTATTTATATGTA 57.666 33.333 0.00 0.00 0.00 2.29
1003 1616 1.333524 GCCATTCGTGATCAATCGCAG 60.334 52.381 0.00 0.00 37.15 5.18
1011 1624 2.735663 GTGATCAATCGCAGCCATCTAG 59.264 50.000 0.00 0.00 37.27 2.43
1012 1625 2.629617 TGATCAATCGCAGCCATCTAGA 59.370 45.455 0.00 0.00 0.00 2.43
1245 1864 1.520787 GTACACGGCGGCTATGCTT 60.521 57.895 13.24 0.00 34.52 3.91
1308 1927 3.688159 GGACGCGTGGTGGTAGGT 61.688 66.667 20.70 0.00 0.00 3.08
1450 2069 0.543410 TTGCTCGTTCCCAGGGACTA 60.543 55.000 8.12 0.00 36.02 2.59
1524 2144 1.893137 AGGTGGAAATTTTCTTCCGGC 59.107 47.619 8.93 0.00 46.85 6.13
1570 2190 2.673368 CGTCTACTCCTTGATTTGCCAC 59.327 50.000 0.00 0.00 0.00 5.01
1582 2202 1.179152 TTTGCCACTGGATGCTCATG 58.821 50.000 0.00 0.00 0.00 3.07
1618 2238 3.886505 TCGTCCCAAAATTGTTTGTAGCT 59.113 39.130 0.00 0.00 42.26 3.32
1661 2281 2.937469 TTGTGTTGGCTGTTTGTGAG 57.063 45.000 0.00 0.00 0.00 3.51
1681 2309 6.478673 TGTGAGTTGTGACACAAATACAGTAG 59.521 38.462 22.16 0.00 40.15 2.57
1766 4963 2.887151 ATTTGGCTGCTTGTAGGAGT 57.113 45.000 0.00 0.00 35.94 3.85
1772 4969 2.432510 GGCTGCTTGTAGGAGTAGACAT 59.567 50.000 0.00 0.00 37.35 3.06
1791 4988 9.956720 GTAGACATCCATTGAATCCTTTATTTG 57.043 33.333 0.00 0.00 0.00 2.32
1797 4994 9.768662 ATCCATTGAATCCTTTATTTGTATTGC 57.231 29.630 0.00 0.00 0.00 3.56
1798 4995 8.980596 TCCATTGAATCCTTTATTTGTATTGCT 58.019 29.630 0.00 0.00 0.00 3.91
2556 5867 6.857437 TTCCTCAGAGTCATCTTGATTACA 57.143 37.500 0.00 0.00 31.64 2.41
2557 5868 7.429374 TTCCTCAGAGTCATCTTGATTACAT 57.571 36.000 0.00 0.00 31.64 2.29
2591 5902 3.814005 ACGAAACTCACTGTTGGTACT 57.186 42.857 0.00 0.00 39.13 2.73
2662 5973 9.823647 ATGATCCATGGTTCGATATTAACTATC 57.176 33.333 12.58 2.58 34.06 2.08
2663 5974 8.258007 TGATCCATGGTTCGATATTAACTATCC 58.742 37.037 12.58 0.00 33.89 2.59
2664 5975 7.547697 TCCATGGTTCGATATTAACTATCCA 57.452 36.000 12.58 0.00 33.89 3.41
2665 5976 7.969004 TCCATGGTTCGATATTAACTATCCAA 58.031 34.615 12.58 0.00 33.89 3.53
2666 5977 8.433599 TCCATGGTTCGATATTAACTATCCAAA 58.566 33.333 12.58 0.00 33.89 3.28
2667 5978 8.721478 CCATGGTTCGATATTAACTATCCAAAG 58.279 37.037 2.57 0.00 33.89 2.77
2668 5979 9.273016 CATGGTTCGATATTAACTATCCAAAGT 57.727 33.333 0.00 0.00 33.89 2.66
2669 5980 8.882415 TGGTTCGATATTAACTATCCAAAGTC 57.118 34.615 0.00 0.00 33.89 3.01
2670 5981 7.929785 TGGTTCGATATTAACTATCCAAAGTCC 59.070 37.037 0.00 0.00 33.89 3.85
2671 5982 7.929785 GGTTCGATATTAACTATCCAAAGTCCA 59.070 37.037 0.00 0.00 33.89 4.02
2672 5983 9.321562 GTTCGATATTAACTATCCAAAGTCCAA 57.678 33.333 0.00 0.00 33.89 3.53
2673 5984 9.893634 TTCGATATTAACTATCCAAAGTCCAAA 57.106 29.630 0.00 0.00 33.89 3.28
2674 5985 9.321562 TCGATATTAACTATCCAAAGTCCAAAC 57.678 33.333 0.00 0.00 33.89 2.93
2675 5986 8.557029 CGATATTAACTATCCAAAGTCCAAACC 58.443 37.037 0.00 0.00 33.89 3.27
2676 5987 8.762481 ATATTAACTATCCAAAGTCCAAACCC 57.238 34.615 0.00 0.00 0.00 4.11
2677 5988 4.741928 AACTATCCAAAGTCCAAACCCT 57.258 40.909 0.00 0.00 0.00 4.34
2678 5989 4.741928 ACTATCCAAAGTCCAAACCCTT 57.258 40.909 0.00 0.00 0.00 3.95
2679 5990 5.074746 ACTATCCAAAGTCCAAACCCTTT 57.925 39.130 0.00 0.00 0.00 3.11
2680 5991 6.208840 ACTATCCAAAGTCCAAACCCTTTA 57.791 37.500 0.00 0.00 30.06 1.85
2681 5992 6.800890 ACTATCCAAAGTCCAAACCCTTTAT 58.199 36.000 0.00 0.00 30.06 1.40
2682 5993 6.663523 ACTATCCAAAGTCCAAACCCTTTATG 59.336 38.462 0.00 0.00 30.06 1.90
2683 5994 4.156477 TCCAAAGTCCAAACCCTTTATGG 58.844 43.478 0.00 0.00 35.49 2.74
2684 5995 3.306710 CCAAAGTCCAAACCCTTTATGGC 60.307 47.826 0.00 0.00 34.13 4.40
2702 6013 1.032114 GCCCCTGGATTCCTGTTTCG 61.032 60.000 3.95 0.00 0.00 3.46
2719 6030 0.537188 TCGCAGACTCCCTTGGATTC 59.463 55.000 0.00 0.00 32.48 2.52
2913 6308 4.297299 ACTTCACAACATGTTTGCTCTG 57.703 40.909 8.77 0.00 0.00 3.35
3072 6467 9.869844 CTATTTTGCTTCTTTGTAGAATATCCG 57.130 33.333 0.00 0.00 39.58 4.18
3152 6547 3.396260 ACTAGCTCTGTAAAAACGCCA 57.604 42.857 0.00 0.00 0.00 5.69
3913 7312 5.815581 TGTTGCACCTTCCTTTGATATAGT 58.184 37.500 0.00 0.00 0.00 2.12
3926 7325 8.677300 TCCTTTGATATAGTGTCAAATTCTTGC 58.323 33.333 2.63 0.00 42.68 4.01
3927 7326 8.680903 CCTTTGATATAGTGTCAAATTCTTGCT 58.319 33.333 2.63 0.00 42.68 3.91
4149 7548 6.101650 TGATCAAGAAGAGTGCTTTGACTA 57.898 37.500 0.00 0.00 33.61 2.59
4237 7636 7.601856 TGGTGCCTGTTATTAAATCTTTTCAG 58.398 34.615 0.00 0.00 0.00 3.02
4350 7749 0.452987 TTGCAATGGAGAATGCTCGC 59.547 50.000 0.00 0.00 42.97 5.03
4410 7809 2.443255 AGTGATAAATCCCGAGGCCAAT 59.557 45.455 5.01 0.00 0.00 3.16
4518 7917 0.420272 TTCTAGGGCCAGTTAGGGGT 59.580 55.000 6.18 0.00 38.09 4.95
4589 7988 9.679661 TTACATCCAAGAATGATAAGTGCTTTA 57.320 29.630 0.00 0.00 0.00 1.85
4620 8019 3.118592 ACTGCAGTACTTAATGGAGCCTC 60.119 47.826 20.16 0.00 42.28 4.70
4662 8063 3.947196 TGCACATCATGTTCATTACTCCC 59.053 43.478 0.00 0.00 0.00 4.30
4674 8075 5.291100 TCATTACTCCCCAGGCTATCTAT 57.709 43.478 0.00 0.00 0.00 1.98
4893 8294 3.204158 TGGTAAATGTATCCTGCCACCAT 59.796 43.478 0.00 0.00 30.11 3.55
4899 8300 6.409524 AATGTATCCTGCCACCATAATTTG 57.590 37.500 0.00 0.00 0.00 2.32
4922 8323 3.640029 CAGATGCATTCCAATAGGCCTTT 59.360 43.478 12.58 0.00 33.74 3.11
5018 8422 1.179152 CAGGTTGGAATGATGCTGCA 58.821 50.000 4.13 4.13 0.00 4.41
5061 8465 2.826488 ACCTCACTCTATGTTGCCTCT 58.174 47.619 0.00 0.00 0.00 3.69
5136 8540 5.065474 TCCACTTCTACAAACAAAGGAAACG 59.935 40.000 0.00 0.00 0.00 3.60
5378 8895 1.105759 GGCATTCATCCAGACTGGCC 61.106 60.000 17.33 8.68 43.79 5.36
5464 8981 3.432749 CCTCATTTCCTGATCGGACACAT 60.433 47.826 2.08 0.00 42.97 3.21
5576 9102 4.927425 GCTTTGAGTAACCGTTGTCTGATA 59.073 41.667 0.00 0.00 0.00 2.15
5577 9103 5.581085 GCTTTGAGTAACCGTTGTCTGATAT 59.419 40.000 0.00 0.00 0.00 1.63
5578 9104 6.455646 GCTTTGAGTAACCGTTGTCTGATATG 60.456 42.308 0.00 0.00 0.00 1.78
5579 9105 5.654603 TGAGTAACCGTTGTCTGATATGT 57.345 39.130 0.00 0.00 0.00 2.29
5580 9106 5.647589 TGAGTAACCGTTGTCTGATATGTC 58.352 41.667 0.00 0.00 0.00 3.06
5581 9107 5.417894 TGAGTAACCGTTGTCTGATATGTCT 59.582 40.000 0.00 0.00 0.00 3.41
5592 9118 4.973051 GTCTGATATGTCTAAGTGCACGAG 59.027 45.833 12.01 13.09 0.00 4.18
5986 9513 9.455847 GTACCGATTTATGTACTTGTAAGTAGG 57.544 37.037 4.79 3.55 41.81 3.18
6261 11687 8.461249 TCCTGCCTAAACTAATACAGTAGTAG 57.539 38.462 12.58 12.58 36.04 2.57
6285 11711 6.765036 AGAGAGTATGCAACTTGGTATGATTG 59.235 38.462 0.00 0.00 39.07 2.67
6304 11730 3.257469 TGCTGTGCCAAACAAATGAAA 57.743 38.095 0.00 0.00 38.67 2.69
6366 11792 2.485122 GCACCGCATAACCTGTGC 59.515 61.111 0.00 0.00 46.09 4.57
6372 11798 3.442996 GCATAACCTGTGCGACTCT 57.557 52.632 0.00 0.00 32.29 3.24
6461 11993 7.294017 AGTTAATTAGCCTAATACAGCGGTA 57.706 36.000 0.00 0.00 0.00 4.02
6588 12136 2.871096 TAGATGAAAAGGCAACGGGT 57.129 45.000 0.00 0.00 46.39 5.28
6633 12181 6.273825 ACTATCAACATACTTACGGAAGCAG 58.726 40.000 7.48 0.00 35.97 4.24
6643 12191 6.134040 ACTTACGGAAGCAGTCTTATACTC 57.866 41.667 7.48 0.00 34.37 2.59
6644 12192 5.067544 ACTTACGGAAGCAGTCTTATACTCC 59.932 44.000 7.48 0.00 34.37 3.85
6650 12198 4.528076 AGCAGTCTTATACTCCCTCTGA 57.472 45.455 0.00 0.00 35.76 3.27
6682 12230 8.269317 ACTCCCTCCGTTTTTAAATATATGACA 58.731 33.333 0.00 0.00 0.00 3.58
6711 12259 6.213195 TGGTAGTTAGGAACGGAGGAAAATAA 59.787 38.462 0.00 0.00 36.23 1.40
6859 12597 9.383519 TGTGTTTATTTATTTTGGCTCAAACAA 57.616 25.926 0.00 0.00 36.66 2.83
6987 12727 5.244755 TGCTAGATCAAATATGCGCCATTA 58.755 37.500 4.18 0.00 0.00 1.90
6992 12732 1.888512 CAAATATGCGCCATTAGCCCT 59.111 47.619 4.18 0.00 38.78 5.19
7031 12771 4.133078 CCGATACCTTACTCGACCTTACT 58.867 47.826 0.00 0.00 37.05 2.24
7035 12775 4.582973 ACCTTACTCGACCTTACTACCT 57.417 45.455 0.00 0.00 0.00 3.08
7036 12776 4.928263 ACCTTACTCGACCTTACTACCTT 58.072 43.478 0.00 0.00 0.00 3.50
7074 12816 3.486375 GCAACCACATGATCTGAATGACG 60.486 47.826 0.00 0.00 0.00 4.35
7116 12858 5.129320 ACACATGCTACATCATCCTAGACAA 59.871 40.000 0.00 0.00 0.00 3.18
7132 13122 8.660295 TCCTAGACAACTAAAGAACCTAATGA 57.340 34.615 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.789075 ATCGTCGTTCGCACCCCG 62.789 66.667 0.00 0.00 39.67 5.73
7 8 3.186047 CATCGTCGTTCGCACCCC 61.186 66.667 0.00 0.00 39.67 4.95
27 28 2.743928 CTCTGCCTTGACCACGCC 60.744 66.667 0.00 0.00 0.00 5.68
36 37 0.035630 GATGTCACCAGCTCTGCCTT 60.036 55.000 0.00 0.00 0.00 4.35
38 39 1.451028 GGATGTCACCAGCTCTGCC 60.451 63.158 0.00 0.00 0.00 4.85
47 48 1.064946 CGAGAGCGAGGATGTCACC 59.935 63.158 0.00 0.00 40.82 4.02
49 50 0.960861 ACACGAGAGCGAGGATGTCA 60.961 55.000 0.00 0.00 41.64 3.58
60 61 0.172352 GAAGAGGAGGCACACGAGAG 59.828 60.000 0.00 0.00 0.00 3.20
65 66 1.599576 GGAGGAAGAGGAGGCACAC 59.400 63.158 0.00 0.00 0.00 3.82
68 69 1.682684 GACGGAGGAAGAGGAGGCA 60.683 63.158 0.00 0.00 0.00 4.75
90 91 0.716108 CTGTTCTTGGACATCGACGC 59.284 55.000 0.00 0.00 0.00 5.19
92 93 1.726853 CCCTGTTCTTGGACATCGAC 58.273 55.000 0.00 0.00 0.00 4.20
112 113 2.997315 TGTGGGCAGAGGGAGACG 60.997 66.667 0.00 0.00 0.00 4.18
130 131 4.759096 GATGGCGGTTGCACGTGC 62.759 66.667 33.11 33.11 45.35 5.34
146 147 2.761195 CGAGATCCACCACGAGCGA 61.761 63.158 0.00 0.00 0.00 4.93
151 152 4.873129 CCCGCGAGATCCACCACG 62.873 72.222 8.23 0.00 0.00 4.94
167 168 3.181967 CTGTCGTACTGCAGCGCC 61.182 66.667 15.27 0.00 0.00 6.53
170 171 1.807573 GCTCCTGTCGTACTGCAGC 60.808 63.158 15.27 0.00 0.00 5.25
172 173 1.586541 CTGCTCCTGTCGTACTGCA 59.413 57.895 0.00 0.00 0.00 4.41
179 180 3.559024 CAAGTGCTGCTCCTGTCG 58.441 61.111 0.00 0.00 0.00 4.35
214 216 1.076850 TATGGTGGCGGACGGTCTA 60.077 57.895 8.23 0.00 0.00 2.59
264 266 1.011968 CGCGGAGGAACAAATCGTCA 61.012 55.000 0.00 0.00 43.26 4.35
265 267 0.734942 TCGCGGAGGAACAAATCGTC 60.735 55.000 6.13 0.00 41.25 4.20
266 268 0.736325 CTCGCGGAGGAACAAATCGT 60.736 55.000 6.13 0.00 0.00 3.73
267 269 1.999051 CTCGCGGAGGAACAAATCG 59.001 57.895 6.13 0.00 0.00 3.34
300 302 2.364448 GCCTTCTCCCCGACTCCT 60.364 66.667 0.00 0.00 0.00 3.69
302 304 4.516195 GCGCCTTCTCCCCGACTC 62.516 72.222 0.00 0.00 0.00 3.36
306 308 4.867599 GTACGCGCCTTCTCCCCG 62.868 72.222 5.73 0.00 0.00 5.73
307 309 3.766691 TGTACGCGCCTTCTCCCC 61.767 66.667 5.73 0.00 0.00 4.81
308 310 2.508663 GTGTACGCGCCTTCTCCC 60.509 66.667 5.73 0.00 0.00 4.30
309 311 2.508663 GGTGTACGCGCCTTCTCC 60.509 66.667 5.73 0.76 41.88 3.71
319 321 3.107661 GTCGCAACCCGGTGTACG 61.108 66.667 0.00 6.41 43.80 3.67
344 346 1.947642 GTGCGTCGGTCGAAAGTGT 60.948 57.895 0.00 0.00 42.86 3.55
353 355 1.070786 ATTGAAGTGGTGCGTCGGT 59.929 52.632 0.00 0.00 0.00 4.69
357 359 1.518056 CCAGCATTGAAGTGGTGCGT 61.518 55.000 0.00 0.00 44.12 5.24
358 360 1.210931 CCAGCATTGAAGTGGTGCG 59.789 57.895 0.00 0.00 44.12 5.34
361 363 0.403271 AGAGCCAGCATTGAAGTGGT 59.597 50.000 0.00 0.00 33.51 4.16
364 366 2.803030 ATGAGAGCCAGCATTGAAGT 57.197 45.000 0.00 0.00 0.00 3.01
374 376 4.202295 GGACATGACATCTAATGAGAGCCA 60.202 45.833 0.00 0.00 34.35 4.75
381 383 4.034394 CACCAACGGACATGACATCTAATG 59.966 45.833 0.00 0.00 0.00 1.90
382 384 4.191544 CACCAACGGACATGACATCTAAT 58.808 43.478 0.00 0.00 0.00 1.73
384 386 2.676750 GCACCAACGGACATGACATCTA 60.677 50.000 0.00 0.00 0.00 1.98
393 395 4.308458 CGGGAGCACCAACGGACA 62.308 66.667 1.58 0.00 40.22 4.02
422 448 0.943673 TTGCCGCATATTCATGTCGG 59.056 50.000 12.85 12.85 46.07 4.79
425 451 3.216800 AGTGATTGCCGCATATTCATGT 58.783 40.909 0.00 0.00 34.40 3.21
431 457 2.030540 GCATGAAGTGATTGCCGCATAT 60.031 45.455 0.00 0.00 0.00 1.78
433 459 0.101759 GCATGAAGTGATTGCCGCAT 59.898 50.000 0.00 0.00 0.00 4.73
434 460 1.507630 GCATGAAGTGATTGCCGCA 59.492 52.632 0.00 0.00 0.00 5.69
438 464 0.810648 TTCCCGCATGAAGTGATTGC 59.189 50.000 0.00 0.00 0.00 3.56
442 468 3.270027 CACTATTTCCCGCATGAAGTGA 58.730 45.455 0.00 0.00 0.00 3.41
450 476 0.323302 TGCTCACACTATTTCCCGCA 59.677 50.000 0.00 0.00 0.00 5.69
451 477 1.398390 CTTGCTCACACTATTTCCCGC 59.602 52.381 0.00 0.00 0.00 6.13
459 485 2.438021 ACCCTTTCACTTGCTCACACTA 59.562 45.455 0.00 0.00 0.00 2.74
460 486 1.212935 ACCCTTTCACTTGCTCACACT 59.787 47.619 0.00 0.00 0.00 3.55
462 488 2.435372 AACCCTTTCACTTGCTCACA 57.565 45.000 0.00 0.00 0.00 3.58
475 501 0.757561 CGGAACCACCCAAAACCCTT 60.758 55.000 0.00 0.00 34.64 3.95
490 516 4.351938 CGCGACAGACACCCGGAA 62.352 66.667 0.73 0.00 0.00 4.30
540 566 1.276622 GGACCAGAGGCAAACTAGGA 58.723 55.000 0.00 0.00 0.00 2.94
548 574 2.525629 TTCCACGGACCAGAGGCA 60.526 61.111 0.00 0.00 0.00 4.75
559 585 2.126580 GACGTCCGTCCTTCCACG 60.127 66.667 3.51 0.00 39.08 4.94
583 609 2.036731 TCCATCGGTCCGTGGACT 59.963 61.111 23.49 0.00 44.04 3.85
588 614 3.771160 GGCACTCCATCGGTCCGT 61.771 66.667 11.88 0.00 0.00 4.69
589 615 3.770040 TGGCACTCCATCGGTCCG 61.770 66.667 4.39 4.39 37.47 4.79
599 625 2.309528 TATCATCCAACGTGGCACTC 57.690 50.000 16.72 0.00 37.47 3.51
600 626 2.779755 TTATCATCCAACGTGGCACT 57.220 45.000 16.72 0.00 37.47 4.40
603 629 8.132362 TGTATTTATTTTATCATCCAACGTGGC 58.868 33.333 0.00 0.00 37.47 5.01
623 649 2.550978 CGGATCAAGCGGTCTGTATTT 58.449 47.619 0.00 0.00 0.00 1.40
624 650 1.202533 CCGGATCAAGCGGTCTGTATT 60.203 52.381 0.00 0.00 0.00 1.89
625 651 0.389391 CCGGATCAAGCGGTCTGTAT 59.611 55.000 0.00 0.00 0.00 2.29
627 653 1.330655 ATCCGGATCAAGCGGTCTGT 61.331 55.000 12.38 0.00 0.00 3.41
652 678 2.607187 ACACTAACCTCAAATCGCTCG 58.393 47.619 0.00 0.00 0.00 5.03
656 682 4.994852 TCTTCCAACACTAACCTCAAATCG 59.005 41.667 0.00 0.00 0.00 3.34
659 685 5.935945 TGATCTTCCAACACTAACCTCAAA 58.064 37.500 0.00 0.00 0.00 2.69
660 686 5.560722 TGATCTTCCAACACTAACCTCAA 57.439 39.130 0.00 0.00 0.00 3.02
661 687 5.560722 TTGATCTTCCAACACTAACCTCA 57.439 39.130 0.00 0.00 0.00 3.86
662 688 5.998363 ACTTTGATCTTCCAACACTAACCTC 59.002 40.000 0.00 0.00 0.00 3.85
663 689 5.941788 ACTTTGATCTTCCAACACTAACCT 58.058 37.500 0.00 0.00 0.00 3.50
664 690 6.635030 AACTTTGATCTTCCAACACTAACC 57.365 37.500 0.00 0.00 0.00 2.85
665 691 7.644157 GTCAAACTTTGATCTTCCAACACTAAC 59.356 37.037 7.47 0.00 42.47 2.34
667 693 7.054124 AGTCAAACTTTGATCTTCCAACACTA 58.946 34.615 7.47 0.00 42.47 2.74
668 694 5.888161 AGTCAAACTTTGATCTTCCAACACT 59.112 36.000 7.47 0.00 42.47 3.55
669 695 6.136541 AGTCAAACTTTGATCTTCCAACAC 57.863 37.500 7.47 0.00 42.47 3.32
670 696 6.826231 TGTAGTCAAACTTTGATCTTCCAACA 59.174 34.615 7.47 5.76 42.47 3.33
672 698 9.739276 ATATGTAGTCAAACTTTGATCTTCCAA 57.261 29.630 7.47 0.00 42.47 3.53
673 699 9.739276 AATATGTAGTCAAACTTTGATCTTCCA 57.261 29.630 7.47 7.59 42.47 3.53
719 767 7.095229 GCCGCAGAGTTGAATATGTGAATAATA 60.095 37.037 0.00 0.00 0.00 0.98
742 790 1.564622 CGGTTCATAATCAGCGCCG 59.435 57.895 2.29 0.00 0.00 6.46
744 792 0.861837 CTCCGGTTCATAATCAGCGC 59.138 55.000 0.00 0.00 32.54 5.92
745 793 1.068588 TCCTCCGGTTCATAATCAGCG 59.931 52.381 0.00 0.00 0.00 5.18
749 797 4.766375 TCAGTTTCCTCCGGTTCATAATC 58.234 43.478 0.00 0.00 0.00 1.75
758 806 1.202770 ACCAAGTTCAGTTTCCTCCGG 60.203 52.381 0.00 0.00 0.00 5.14
767 816 4.255301 TGTTTACGTTCACCAAGTTCAGT 58.745 39.130 0.00 0.00 0.00 3.41
768 817 4.868450 TGTTTACGTTCACCAAGTTCAG 57.132 40.909 0.00 0.00 0.00 3.02
785 834 5.789643 ACTACAAAATGCCTGTGATGTTT 57.210 34.783 0.00 0.00 0.00 2.83
787 836 5.106157 GCTAACTACAAAATGCCTGTGATGT 60.106 40.000 0.00 0.00 0.00 3.06
789 838 4.094887 CGCTAACTACAAAATGCCTGTGAT 59.905 41.667 0.00 0.00 0.00 3.06
790 839 3.435327 CGCTAACTACAAAATGCCTGTGA 59.565 43.478 0.00 0.00 0.00 3.58
791 840 3.426159 CCGCTAACTACAAAATGCCTGTG 60.426 47.826 0.00 0.00 0.00 3.66
792 841 2.747446 CCGCTAACTACAAAATGCCTGT 59.253 45.455 0.00 0.00 0.00 4.00
793 842 2.097466 CCCGCTAACTACAAAATGCCTG 59.903 50.000 0.00 0.00 0.00 4.85
794 843 2.026636 TCCCGCTAACTACAAAATGCCT 60.027 45.455 0.00 0.00 0.00 4.75
795 844 2.096980 GTCCCGCTAACTACAAAATGCC 59.903 50.000 0.00 0.00 0.00 4.40
796 845 2.222953 CGTCCCGCTAACTACAAAATGC 60.223 50.000 0.00 0.00 0.00 3.56
797 846 2.997986 ACGTCCCGCTAACTACAAAATG 59.002 45.455 0.00 0.00 0.00 2.32
798 847 3.056322 AGACGTCCCGCTAACTACAAAAT 60.056 43.478 13.01 0.00 0.00 1.82
799 848 2.297033 AGACGTCCCGCTAACTACAAAA 59.703 45.455 13.01 0.00 0.00 2.44
802 851 1.089920 GAGACGTCCCGCTAACTACA 58.910 55.000 13.01 0.00 0.00 2.74
803 852 0.380024 GGAGACGTCCCGCTAACTAC 59.620 60.000 13.01 0.00 36.76 2.73
804 853 0.254178 AGGAGACGTCCCGCTAACTA 59.746 55.000 13.01 0.00 45.26 2.24
806 855 0.245813 AAAGGAGACGTCCCGCTAAC 59.754 55.000 13.01 0.00 45.26 2.34
808 857 1.386533 CTAAAGGAGACGTCCCGCTA 58.613 55.000 13.01 8.91 45.26 4.26
810 859 1.518792 GCTAAAGGAGACGTCCCGC 60.519 63.158 13.01 8.21 45.26 6.13
811 860 1.141234 GGCTAAAGGAGACGTCCCG 59.859 63.158 13.01 2.06 45.26 5.14
817 866 5.005490 CGATAAGTTTTCGGCTAAAGGAGAC 59.995 44.000 7.73 0.00 33.05 3.36
818 867 5.107133 CGATAAGTTTTCGGCTAAAGGAGA 58.893 41.667 7.73 0.00 33.05 3.71
819 868 4.868734 ACGATAAGTTTTCGGCTAAAGGAG 59.131 41.667 18.01 0.00 40.83 3.69
821 870 4.628333 TGACGATAAGTTTTCGGCTAAAGG 59.372 41.667 20.09 0.00 44.95 3.11
822 871 5.220416 CCTGACGATAAGTTTTCGGCTAAAG 60.220 44.000 20.09 10.69 44.95 1.85
824 873 4.082081 TCCTGACGATAAGTTTTCGGCTAA 60.082 41.667 20.09 2.81 44.95 3.09
826 875 2.232941 TCCTGACGATAAGTTTTCGGCT 59.767 45.455 20.09 1.36 44.95 5.52
829 878 5.447279 CCCAATTCCTGACGATAAGTTTTCG 60.447 44.000 13.25 13.25 42.20 3.46
830 879 5.163652 CCCCAATTCCTGACGATAAGTTTTC 60.164 44.000 0.00 0.00 0.00 2.29
832 881 4.270008 CCCCAATTCCTGACGATAAGTTT 58.730 43.478 0.00 0.00 0.00 2.66
833 882 3.371595 CCCCCAATTCCTGACGATAAGTT 60.372 47.826 0.00 0.00 0.00 2.66
834 883 2.172717 CCCCCAATTCCTGACGATAAGT 59.827 50.000 0.00 0.00 0.00 2.24
835 884 2.172717 ACCCCCAATTCCTGACGATAAG 59.827 50.000 0.00 0.00 0.00 1.73
836 885 2.171870 GACCCCCAATTCCTGACGATAA 59.828 50.000 0.00 0.00 0.00 1.75
838 887 0.546598 GACCCCCAATTCCTGACGAT 59.453 55.000 0.00 0.00 0.00 3.73
840 889 0.255890 ATGACCCCCAATTCCTGACG 59.744 55.000 0.00 0.00 0.00 4.35
842 891 2.287584 AGAATGACCCCCAATTCCTGA 58.712 47.619 0.00 0.00 0.00 3.86
845 894 4.096681 AGAAAAGAATGACCCCCAATTCC 58.903 43.478 0.00 0.00 0.00 3.01
871 934 5.639506 ACCAGAGACTGATAATGTTTGTTCG 59.360 40.000 0.00 0.00 32.44 3.95
891 954 1.095228 AGGCAACACGACACAACCAG 61.095 55.000 0.00 0.00 41.41 4.00
909 1522 9.729023 GATCGAATAGAGTGTATATGATCCAAG 57.271 37.037 9.08 0.00 0.00 3.61
970 1583 7.877612 TGATCACGAATGGCAAATACTACATAT 59.122 33.333 0.00 0.00 0.00 1.78
971 1584 7.213678 TGATCACGAATGGCAAATACTACATA 58.786 34.615 0.00 0.00 0.00 2.29
972 1585 6.054941 TGATCACGAATGGCAAATACTACAT 58.945 36.000 0.00 0.00 0.00 2.29
973 1586 5.423886 TGATCACGAATGGCAAATACTACA 58.576 37.500 0.00 0.00 0.00 2.74
974 1587 5.984233 TGATCACGAATGGCAAATACTAC 57.016 39.130 0.00 0.00 0.00 2.73
975 1588 6.073819 CGATTGATCACGAATGGCAAATACTA 60.074 38.462 0.00 0.00 0.00 1.82
976 1589 5.277490 CGATTGATCACGAATGGCAAATACT 60.277 40.000 0.00 0.00 0.00 2.12
984 1597 1.333524 GCTGCGATTGATCACGAATGG 60.334 52.381 9.68 0.00 0.00 3.16
986 1599 0.940126 GGCTGCGATTGATCACGAAT 59.060 50.000 9.68 0.00 0.00 3.34
1003 1616 9.534565 GAGGGAATTTTTATTTTTCTAGATGGC 57.465 33.333 0.00 0.00 0.00 4.40
1011 1624 5.444087 GCACGCGAGGGAATTTTTATTTTTC 60.444 40.000 15.93 0.00 35.60 2.29
1012 1625 4.387559 GCACGCGAGGGAATTTTTATTTTT 59.612 37.500 15.93 0.00 35.60 1.94
1282 1901 4.602259 CACGCGTCCACCACCTGT 62.602 66.667 9.86 0.00 0.00 4.00
1450 2069 7.287061 TGGGAATGGATCGAATAAACATTACT 58.713 34.615 10.73 0.00 33.83 2.24
1503 2122 2.094700 GCCGGAAGAAAATTTCCACCTC 60.095 50.000 5.05 3.04 45.66 3.85
1524 2144 1.016627 AATTCATCCGACGCACATGG 58.983 50.000 0.00 0.00 0.00 3.66
1570 2190 7.514784 TTATAATCAAACCATGAGCATCCAG 57.485 36.000 0.00 0.00 42.53 3.86
1582 2202 9.594478 AATTTTGGGACGATTTATAATCAAACC 57.406 29.630 0.00 0.00 0.00 3.27
1618 2238 3.894427 ACTTGGATGCAATGTGTGGTAAA 59.106 39.130 0.00 0.00 0.00 2.01
1661 2281 6.797033 GCATTCTACTGTATTTGTGTCACAAC 59.203 38.462 17.99 8.50 37.90 3.32
1699 2327 9.175312 CACCAGTTTCACTAGAGATTAGTACTA 57.825 37.037 0.00 0.00 0.00 1.82
1700 2328 7.122948 CCACCAGTTTCACTAGAGATTAGTACT 59.877 40.741 0.00 0.00 0.00 2.73
1701 2329 7.093858 ACCACCAGTTTCACTAGAGATTAGTAC 60.094 40.741 0.00 0.00 0.00 2.73
1736 4933 4.708726 AGCAGCCAAATTCAGTGTTATC 57.291 40.909 0.00 0.00 0.00 1.75
1737 4934 4.281688 ACAAGCAGCCAAATTCAGTGTTAT 59.718 37.500 0.00 0.00 0.00 1.89
1766 4963 9.699410 ACAAATAAAGGATTCAATGGATGTCTA 57.301 29.630 0.00 0.00 0.00 2.59
1772 4969 8.980596 AGCAATACAAATAAAGGATTCAATGGA 58.019 29.630 0.00 0.00 0.00 3.41
1875 5181 2.232452 AGAACTCGCATGCTACAGTCTT 59.768 45.455 17.13 0.96 0.00 3.01
1876 5182 1.821753 AGAACTCGCATGCTACAGTCT 59.178 47.619 17.13 8.84 0.00 3.24
1877 5183 1.923204 CAGAACTCGCATGCTACAGTC 59.077 52.381 17.13 6.64 0.00 3.51
1878 5184 1.273606 ACAGAACTCGCATGCTACAGT 59.726 47.619 17.13 11.74 0.00 3.55
1879 5185 2.001812 ACAGAACTCGCATGCTACAG 57.998 50.000 17.13 11.08 0.00 2.74
1880 5186 2.455674 AACAGAACTCGCATGCTACA 57.544 45.000 17.13 0.00 0.00 2.74
1881 5187 2.736721 TGAAACAGAACTCGCATGCTAC 59.263 45.455 17.13 2.45 0.00 3.58
1882 5188 3.038788 TGAAACAGAACTCGCATGCTA 57.961 42.857 17.13 3.43 0.00 3.49
1883 5189 1.882912 TGAAACAGAACTCGCATGCT 58.117 45.000 17.13 0.00 0.00 3.79
1983 5289 4.652822 TCTTTGACCTTTAAAGAGCTCCC 58.347 43.478 16.98 0.24 38.76 4.30
2556 5867 8.521176 AGTGAGTTTCGTTTCAGTAGTGTATAT 58.479 33.333 0.00 0.00 0.00 0.86
2557 5868 7.806487 CAGTGAGTTTCGTTTCAGTAGTGTATA 59.194 37.037 0.00 0.00 0.00 1.47
2575 5886 5.995897 GGTATTTCAGTACCAACAGTGAGTT 59.004 40.000 0.00 0.00 42.98 3.01
2576 5887 5.307196 AGGTATTTCAGTACCAACAGTGAGT 59.693 40.000 0.00 0.00 45.35 3.41
2577 5888 5.794894 AGGTATTTCAGTACCAACAGTGAG 58.205 41.667 0.00 0.00 45.35 3.51
2658 5969 6.096846 CCATAAAGGGTTTGGACTTTGGATAG 59.903 42.308 0.00 0.00 37.48 2.08
2661 5972 4.156477 CCATAAAGGGTTTGGACTTTGGA 58.844 43.478 0.00 0.00 37.48 3.53
2662 5973 3.306710 GCCATAAAGGGTTTGGACTTTGG 60.307 47.826 0.00 0.00 37.48 3.28
2663 5974 3.306710 GGCCATAAAGGGTTTGGACTTTG 60.307 47.826 0.00 0.00 37.48 2.77
2664 5975 2.903784 GGCCATAAAGGGTTTGGACTTT 59.096 45.455 0.00 0.00 39.91 2.66
2665 5976 2.536066 GGCCATAAAGGGTTTGGACTT 58.464 47.619 0.00 0.00 35.54 3.01
2666 5977 1.273041 GGGCCATAAAGGGTTTGGACT 60.273 52.381 4.39 0.00 38.68 3.85
2667 5978 1.191535 GGGCCATAAAGGGTTTGGAC 58.808 55.000 4.39 0.00 37.86 4.02
2668 5979 0.041982 GGGGCCATAAAGGGTTTGGA 59.958 55.000 4.39 0.00 38.09 3.53
2669 5980 0.042581 AGGGGCCATAAAGGGTTTGG 59.957 55.000 4.39 0.00 38.09 3.28
2670 5981 1.194218 CAGGGGCCATAAAGGGTTTG 58.806 55.000 4.39 0.00 38.09 2.93
2671 5982 0.042581 CCAGGGGCCATAAAGGGTTT 59.957 55.000 4.39 0.00 38.09 3.27
2672 5983 0.853586 TCCAGGGGCCATAAAGGGTT 60.854 55.000 4.39 0.00 38.09 4.11
2673 5984 0.630478 ATCCAGGGGCCATAAAGGGT 60.630 55.000 4.39 0.00 38.09 4.34
2674 5985 0.562674 AATCCAGGGGCCATAAAGGG 59.437 55.000 4.39 0.00 38.09 3.95
2675 5986 1.481242 GGAATCCAGGGGCCATAAAGG 60.481 57.143 4.39 0.00 41.84 3.11
2676 5987 1.500736 AGGAATCCAGGGGCCATAAAG 59.499 52.381 4.39 0.00 0.00 1.85
2677 5988 1.217689 CAGGAATCCAGGGGCCATAAA 59.782 52.381 4.39 0.00 0.00 1.40
2678 5989 0.852842 CAGGAATCCAGGGGCCATAA 59.147 55.000 4.39 0.00 0.00 1.90
2679 5990 0.328450 ACAGGAATCCAGGGGCCATA 60.328 55.000 4.39 0.00 0.00 2.74
2680 5991 1.224003 AACAGGAATCCAGGGGCCAT 61.224 55.000 4.39 0.00 0.00 4.40
2681 5992 1.442886 AAACAGGAATCCAGGGGCCA 61.443 55.000 4.39 0.00 0.00 5.36
2682 5993 0.684479 GAAACAGGAATCCAGGGGCC 60.684 60.000 0.61 0.00 0.00 5.80
2683 5994 1.032114 CGAAACAGGAATCCAGGGGC 61.032 60.000 0.61 0.00 0.00 5.80
2684 5995 1.032114 GCGAAACAGGAATCCAGGGG 61.032 60.000 0.61 0.00 0.00 4.79
2702 6013 0.250513 ACGAATCCAAGGGAGTCTGC 59.749 55.000 10.54 0.00 43.62 4.26
2719 6030 9.305110 GTTCATGCAAGAAATAAATTCAAAACG 57.695 29.630 5.85 0.00 40.72 3.60
2913 6308 8.948145 TCTCTGTTAGACTCAGATAAACACTAC 58.052 37.037 0.00 0.00 40.46 2.73
3072 6467 3.304928 CCAGTTTCTCCAAACACATCTGC 60.305 47.826 0.74 0.00 43.98 4.26
3104 6499 1.553690 AAGTGACCCAGGGACGGATG 61.554 60.000 14.54 0.00 0.00 3.51
3107 6502 1.003718 GAAAGTGACCCAGGGACGG 60.004 63.158 14.54 0.00 0.00 4.79
3277 6674 9.354673 AGACATAATGAAGTTTCTCTTTTCCAA 57.645 29.630 0.00 0.00 36.40 3.53
3913 7312 5.106712 CGCCTTTAGTAGCAAGAATTTGACA 60.107 40.000 0.00 0.00 36.36 3.58
3926 7325 7.502120 TGGTAGTATAGAACGCCTTTAGTAG 57.498 40.000 0.00 0.00 0.00 2.57
3927 7326 9.745018 ATATGGTAGTATAGAACGCCTTTAGTA 57.255 33.333 0.00 0.00 0.00 1.82
4149 7548 3.646162 TGAACTGACATGTACTTCCCACT 59.354 43.478 0.00 0.00 0.00 4.00
4195 7594 3.016031 CACCAACTAGCATGGCATTGTA 58.984 45.455 13.67 0.00 41.89 2.41
4237 7636 7.912250 CACAATCATCATAAAGCTTGGTCTTAC 59.088 37.037 0.00 0.00 0.00 2.34
4350 7749 2.586792 CCTCTCCAGCCCCTTTCG 59.413 66.667 0.00 0.00 0.00 3.46
4410 7809 1.414158 GACATCTCCCATTCCTCCGA 58.586 55.000 0.00 0.00 0.00 4.55
4577 7976 6.183360 GCAGTGGCAATTTTAAAGCACTTATC 60.183 38.462 0.00 0.00 40.72 1.75
4609 8008 4.640771 AAAACAGAGTGAGGCTCCATTA 57.359 40.909 12.86 0.00 45.21 1.90
4641 8042 3.316308 GGGGAGTAATGAACATGATGTGC 59.684 47.826 0.00 0.00 0.00 4.57
4662 8063 8.807118 TGTATTCTCTAACAATAGATAGCCTGG 58.193 37.037 0.00 0.00 37.52 4.45
4674 8075 7.062749 AGTGTCCAACTGTATTCTCTAACAA 57.937 36.000 0.00 0.00 37.88 2.83
4893 8294 6.739286 GCCTATTGGAATGCATCTGCAAATTA 60.739 38.462 9.20 7.55 45.26 1.40
4899 8300 1.271656 GGCCTATTGGAATGCATCTGC 59.728 52.381 0.00 0.00 37.22 4.26
4922 8323 6.140780 TAAGATCTCTTGGCAGCTTGCAGA 62.141 45.833 0.00 4.94 40.18 4.26
4991 8395 4.381825 GCATCATTCCAACCTGCATAAACA 60.382 41.667 0.00 0.00 33.13 2.83
5018 8422 5.078683 AGTATTATCAAACCCCATGCCAT 57.921 39.130 0.00 0.00 0.00 4.40
5136 8540 0.390998 GCTCCTCAGGTGAAGTGAGC 60.391 60.000 0.00 8.99 40.22 4.26
5403 8920 1.519408 GTTACAAAGGCTTCGCTCCA 58.481 50.000 0.00 0.00 0.00 3.86
5576 9102 2.675317 GCTTCCTCGTGCACTTAGACAT 60.675 50.000 16.19 0.00 0.00 3.06
5577 9103 1.336887 GCTTCCTCGTGCACTTAGACA 60.337 52.381 16.19 0.03 0.00 3.41
5578 9104 1.067495 AGCTTCCTCGTGCACTTAGAC 60.067 52.381 16.19 0.00 0.00 2.59
5579 9105 1.067565 CAGCTTCCTCGTGCACTTAGA 60.068 52.381 16.19 5.36 0.00 2.10
5580 9106 1.354040 CAGCTTCCTCGTGCACTTAG 58.646 55.000 16.19 11.88 0.00 2.18
5581 9107 0.037326 CCAGCTTCCTCGTGCACTTA 60.037 55.000 16.19 1.63 0.00 2.24
5592 9118 2.273776 GGGCCTTCTCCAGCTTCC 59.726 66.667 0.84 0.00 0.00 3.46
6034 9561 6.289834 TGGCATCTCTAGTCTACTACAGTAC 58.710 44.000 0.00 0.00 0.00 2.73
6035 9562 6.496144 TGGCATCTCTAGTCTACTACAGTA 57.504 41.667 0.00 0.00 0.00 2.74
6036 9563 5.375283 TGGCATCTCTAGTCTACTACAGT 57.625 43.478 0.00 0.00 0.00 3.55
6037 9564 6.701145 TTTGGCATCTCTAGTCTACTACAG 57.299 41.667 0.00 0.00 0.00 2.74
6038 9565 6.017026 CGATTTGGCATCTCTAGTCTACTACA 60.017 42.308 0.00 0.00 0.00 2.74
6261 11687 6.512415 GCAATCATACCAAGTTGCATACTCTC 60.512 42.308 0.00 0.00 44.63 3.20
6285 11711 7.775397 ATATATTTCATTTGTTTGGCACAGC 57.225 32.000 0.00 0.00 42.39 4.40
6366 11792 5.168569 TCTATTGCTTGGTGTAAAGAGTCG 58.831 41.667 0.00 0.00 0.00 4.18
6372 11798 7.759489 ATGAACTTCTATTGCTTGGTGTAAA 57.241 32.000 0.00 0.00 0.00 2.01
6466 11998 7.653311 GCTGTTTTTCTTTTCTGGTGTGATAAT 59.347 33.333 0.00 0.00 0.00 1.28
6485 12033 1.228552 AGCCATGTCCCGCTGTTTT 60.229 52.632 0.00 0.00 32.98 2.43
6614 12162 4.495422 AGACTGCTTCCGTAAGTATGTTG 58.505 43.478 0.00 0.00 34.99 3.33
6625 12173 2.959707 AGGGAGTATAAGACTGCTTCCG 59.040 50.000 0.00 0.00 45.50 4.30
6633 12181 8.296211 AGTAGTTTTCAGAGGGAGTATAAGAC 57.704 38.462 0.00 0.00 0.00 3.01
6643 12191 2.502130 GGAGGGAGTAGTTTTCAGAGGG 59.498 54.545 0.00 0.00 0.00 4.30
6644 12192 2.166664 CGGAGGGAGTAGTTTTCAGAGG 59.833 54.545 0.00 0.00 0.00 3.69
6650 12198 7.828508 ATTTAAAAACGGAGGGAGTAGTTTT 57.171 32.000 0.00 0.06 45.24 2.43
6682 12230 4.533311 TCCTCCGTTCCTAACTACCAAAAT 59.467 41.667 0.00 0.00 0.00 1.82
6825 12563 9.943163 GCCAAAATAAATAAACACACAAATGTT 57.057 25.926 0.00 0.00 44.76 2.71
6827 12565 9.810231 GAGCCAAAATAAATAAACACACAAATG 57.190 29.630 0.00 0.00 0.00 2.32
6987 12727 1.064832 GGCAGATTCTGAAGAAGGGCT 60.065 52.381 17.87 1.98 37.48 5.19
6992 12732 2.179427 TCGGAGGCAGATTCTGAAGAA 58.821 47.619 17.87 0.00 38.56 2.52
7042 12782 0.677731 ATGTGGTTGCGATGGAGGTG 60.678 55.000 0.00 0.00 0.00 4.00
7074 12816 1.150536 TGACAGGACCTTTGTGGCC 59.849 57.895 0.00 0.00 40.22 5.36
7116 12858 8.560124 AGATGGATCTCATTAGGTTCTTTAGT 57.440 34.615 0.00 0.00 35.97 2.24



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

AutoCloner maintained by Alex Coulton.