Multiple sequence alignment - TraesCS4D01G244900

Loading Multiple Alignment...

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 TraesCS4D01G244900 chr4D 100.000 4610 0 0 1562 6171 409636361 409640970 0.000000e+00 8514
1 TraesCS4D01G244900 chr4D 100.000 1166 0 0 1 1166 409634800 409635965 0.000000e+00 2154
2 TraesCS4D01G244900 chr4A 97.439 2811 62 4 1562 4368 64151244 64148440 0.000000e+00 4783
3 TraesCS4D01G244900 chr4A 96.721 854 24 2 4457 5306 64148242 64147389 0.000000e+00 1419
4 TraesCS4D01G244900 chr4A 94.952 416 12 2 5762 6171 64147080 64146668 1.450000e-180 643
5 TraesCS4D01G244900 chr4A 93.857 293 12 3 874 1166 64152016 64151730 2.640000e-118 436
6 TraesCS4D01G244900 chr4A 93.925 214 10 1 5449 5659 64147308 64147095 2.780000e-83 320
7 TraesCS4D01G244900 chr4A 92.593 216 13 3 1 215 64173252 64173039 2.160000e-79 307
8 TraesCS4D01G244900 chr4A 91.241 137 8 2 4319 4455 64148455 64148323 3.800000e-42 183
9 TraesCS4D01G244900 chr4A 95.349 86 3 1 716 800 64164113 64164028 1.080000e-27 135
10 TraesCS4D01G244900 chr4A 89.655 87 5 4 5337 5423 64147390 64147308 2.350000e-19 108
11 TraesCS4D01G244900 chr4B 96.235 2842 72 13 1562 4368 506148274 506145433 0.000000e+00 4623
12 TraesCS4D01G244900 chr4B 96.552 986 26 4 4511 5491 506145052 506144070 0.000000e+00 1626
13 TraesCS4D01G244900 chr4B 85.433 762 72 24 5 749 506149545 506148806 0.000000e+00 756
14 TraesCS4D01G244900 chr4B 93.720 414 20 3 5762 6171 506143634 506143223 3.160000e-172 616
15 TraesCS4D01G244900 chr4B 88.831 385 14 12 783 1164 506148820 506148462 4.390000e-121 446
16 TraesCS4D01G244900 chr4B 98.421 190 3 0 5452 5641 506144071 506143882 9.910000e-88 335
17 TraesCS4D01G244900 chr4B 95.050 101 5 0 5666 5766 56355740 56355640 6.400000e-35 159
18 TraesCS4D01G244900 chr4B 95.050 101 5 0 5666 5766 64948561 64948661 6.400000e-35 159
19 TraesCS4D01G244900 chr4B 98.246 57 1 0 4457 4513 506145231 506145175 3.940000e-17 100
20 TraesCS4D01G244900 chr5B 97.030 101 3 0 5666 5766 277079076 277078976 2.960000e-38 171
21 TraesCS4D01G244900 chr3B 96.040 101 4 0 5666 5766 523209912 523210012 1.380000e-36 165
22 TraesCS4D01G244900 chr3B 93.396 106 7 0 5666 5771 822718662 822718767 2.300000e-34 158
23 TraesCS4D01G244900 chr2A 94.340 106 5 1 5666 5770 73898446 73898551 1.780000e-35 161
24 TraesCS4D01G244900 chr2A 93.396 106 7 0 5666 5771 333768725 333768830 2.300000e-34 158
25 TraesCS4D01G244900 chr2A 91.892 111 9 0 5666 5776 180979165 180979275 8.280000e-34 156
26 TraesCS4D01G244900 chr3A 91.964 112 8 1 5666 5776 1921252 1921363 8.280000e-34 156


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 TraesCS4D01G244900 chr4D 409634800 409640970 6170 False 5334.000000 8514 100.000000 1 6171 2 chr4D.!!$F1 6170
1 TraesCS4D01G244900 chr4A 64146668 64152016 5348 True 1127.428571 4783 93.970000 874 6171 7 chr4A.!!$R3 5297
2 TraesCS4D01G244900 chr4B 506143223 506149545 6322 True 1214.571429 4623 93.919714 5 6171 7 chr4B.!!$R2 6166

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
868 900 0.100682 CCATATCCGCGATACCTCCG 59.899 60.000 8.23 0.0 0.00 4.63 F
887 919 0.107459 GGAGTAGGCCTGCCAAGAAG 60.107 60.000 17.99 0.0 38.92 2.85 F
888 920 0.905357 GAGTAGGCCTGCCAAGAAGA 59.095 55.000 17.99 0.0 38.92 2.87 F
889 921 1.488393 GAGTAGGCCTGCCAAGAAGAT 59.512 52.381 17.99 0.0 38.92 2.40 F
2527 2649 1.223487 CCGTTCCACATTCCCGGAT 59.777 57.895 0.73 0.0 41.08 4.18 F
3127 3253 0.331616 GGTATGGGGCAGTTTGGACT 59.668 55.000 0.00 0.0 36.25 3.85 F
4990 5387 0.318784 GTCTCCGTTGTTCGCTGTCT 60.319 55.000 0.00 0.0 38.35 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1867 1989 0.116342 TGAACTGCTCCTCCCAGGTA 59.884 55.000 0.00 0.0 36.53 3.08 R
2525 2647 0.319727 CGCTGCATCTCCTCTGGATC 60.320 60.000 0.00 0.0 0.00 3.36 R
2527 2649 2.429767 CCGCTGCATCTCCTCTGGA 61.430 63.158 0.00 0.0 0.00 3.86 R
3127 3253 1.948834 CAATCTGCAGTGTTGTCACCA 59.051 47.619 14.67 0.0 44.83 4.17 R
3958 4115 0.040058 TGATTTCTGGCCCTGCATGT 59.960 50.000 0.00 0.0 0.00 3.21 R
5002 5399 0.539518 TACGCTTCTAGCATTGCCCA 59.460 50.000 4.70 0.0 42.58 5.36 R
5864 6434 0.589708 TGTATCGGATGTACGCGAGG 59.410 55.000 15.93 0.0 0.00 4.63 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
28 29 5.238650 AGTTAGCATGCATTTTACCGTATCC 59.761 40.000 21.98 0.00 0.00 2.59
33 34 4.481368 TGCATTTTACCGTATCCTCAGT 57.519 40.909 0.00 0.00 0.00 3.41
42 43 2.766828 CCGTATCCTCAGTTTCCTCCTT 59.233 50.000 0.00 0.00 0.00 3.36
117 118 1.207329 ACGAAAGGACCTAGATGCCAC 59.793 52.381 0.00 0.00 0.00 5.01
135 136 2.584608 CGAGTGGGCTAGGTTGGG 59.415 66.667 0.00 0.00 0.00 4.12
169 170 2.031157 GCACGATACATGCATAAACCCC 60.031 50.000 0.00 0.00 42.88 4.95
170 171 3.210227 CACGATACATGCATAAACCCCA 58.790 45.455 0.00 0.00 0.00 4.96
171 172 3.820467 CACGATACATGCATAAACCCCAT 59.180 43.478 0.00 0.00 0.00 4.00
172 173 5.000591 CACGATACATGCATAAACCCCATA 58.999 41.667 0.00 0.00 0.00 2.74
173 174 5.001232 ACGATACATGCATAAACCCCATAC 58.999 41.667 0.00 0.00 0.00 2.39
174 175 4.092821 CGATACATGCATAAACCCCATACG 59.907 45.833 0.00 0.00 0.00 3.06
175 176 1.953686 ACATGCATAAACCCCATACGC 59.046 47.619 0.00 0.00 0.00 4.42
176 177 1.069296 CATGCATAAACCCCATACGCG 60.069 52.381 3.53 3.53 0.00 6.01
177 178 0.178301 TGCATAAACCCCATACGCGA 59.822 50.000 15.93 0.00 0.00 5.87
190 191 4.440663 CCCATACGCGATATCATCACTCAT 60.441 45.833 15.93 0.00 0.00 2.90
218 219 1.132365 AGGTGGAATCCCCTATCCCTC 60.132 57.143 7.43 0.00 34.68 4.30
289 292 2.151202 CGTAAGAACTGCACACCCAAT 58.849 47.619 0.00 0.00 43.02 3.16
303 306 3.961408 ACACCCAATCGCTCTATTAGACT 59.039 43.478 0.00 0.00 0.00 3.24
328 331 2.742053 CCATCTACTTCACACCCAAACG 59.258 50.000 0.00 0.00 0.00 3.60
338 341 2.224784 CACACCCAAACGTTAACCTAGC 59.775 50.000 0.00 0.00 0.00 3.42
346 349 1.209128 CGTTAACCTAGCATGAGCCG 58.791 55.000 0.00 0.00 43.56 5.52
363 366 4.082787 TGAGCCGATTTTCTTCCATTTGTC 60.083 41.667 0.00 0.00 0.00 3.18
365 368 4.463891 AGCCGATTTTCTTCCATTTGTCAT 59.536 37.500 0.00 0.00 0.00 3.06
366 369 5.047092 AGCCGATTTTCTTCCATTTGTCATT 60.047 36.000 0.00 0.00 0.00 2.57
405 432 1.002011 GCGGCCTCCTTCCTTTCTT 60.002 57.895 0.00 0.00 0.00 2.52
406 433 0.609406 GCGGCCTCCTTCCTTTCTTT 60.609 55.000 0.00 0.00 0.00 2.52
407 434 1.454201 CGGCCTCCTTCCTTTCTTTC 58.546 55.000 0.00 0.00 0.00 2.62
408 435 1.003696 CGGCCTCCTTCCTTTCTTTCT 59.996 52.381 0.00 0.00 0.00 2.52
409 436 2.717390 GGCCTCCTTCCTTTCTTTCTC 58.283 52.381 0.00 0.00 0.00 2.87
410 437 2.040412 GGCCTCCTTCCTTTCTTTCTCA 59.960 50.000 0.00 0.00 0.00 3.27
411 438 3.308760 GGCCTCCTTCCTTTCTTTCTCAT 60.309 47.826 0.00 0.00 0.00 2.90
412 439 4.339748 GCCTCCTTCCTTTCTTTCTCATT 58.660 43.478 0.00 0.00 0.00 2.57
413 440 4.769488 GCCTCCTTCCTTTCTTTCTCATTT 59.231 41.667 0.00 0.00 0.00 2.32
414 441 5.244851 GCCTCCTTCCTTTCTTTCTCATTTT 59.755 40.000 0.00 0.00 0.00 1.82
415 442 6.571344 GCCTCCTTCCTTTCTTTCTCATTTTC 60.571 42.308 0.00 0.00 0.00 2.29
416 443 6.718912 CCTCCTTCCTTTCTTTCTCATTTTCT 59.281 38.462 0.00 0.00 0.00 2.52
417 444 7.094420 CCTCCTTCCTTTCTTTCTCATTTTCTC 60.094 40.741 0.00 0.00 0.00 2.87
418 445 6.717084 TCCTTCCTTTCTTTCTCATTTTCTCC 59.283 38.462 0.00 0.00 0.00 3.71
419 446 6.718912 CCTTCCTTTCTTTCTCATTTTCTCCT 59.281 38.462 0.00 0.00 0.00 3.69
420 447 7.232330 CCTTCCTTTCTTTCTCATTTTCTCCTT 59.768 37.037 0.00 0.00 0.00 3.36
421 448 8.539117 TTCCTTTCTTTCTCATTTTCTCCTTT 57.461 30.769 0.00 0.00 0.00 3.11
422 449 8.539117 TCCTTTCTTTCTCATTTTCTCCTTTT 57.461 30.769 0.00 0.00 0.00 2.27
423 450 8.633561 TCCTTTCTTTCTCATTTTCTCCTTTTC 58.366 33.333 0.00 0.00 0.00 2.29
424 451 7.869937 CCTTTCTTTCTCATTTTCTCCTTTTCC 59.130 37.037 0.00 0.00 0.00 3.13
425 452 8.539117 TTTCTTTCTCATTTTCTCCTTTTCCT 57.461 30.769 0.00 0.00 0.00 3.36
426 453 8.539117 TTCTTTCTCATTTTCTCCTTTTCCTT 57.461 30.769 0.00 0.00 0.00 3.36
427 454 8.539117 TCTTTCTCATTTTCTCCTTTTCCTTT 57.461 30.769 0.00 0.00 0.00 3.11
428 455 8.981659 TCTTTCTCATTTTCTCCTTTTCCTTTT 58.018 29.630 0.00 0.00 0.00 2.27
429 456 9.254133 CTTTCTCATTTTCTCCTTTTCCTTTTC 57.746 33.333 0.00 0.00 0.00 2.29
430 457 7.290110 TCTCATTTTCTCCTTTTCCTTTTCC 57.710 36.000 0.00 0.00 0.00 3.13
431 458 7.069344 TCTCATTTTCTCCTTTTCCTTTTCCT 58.931 34.615 0.00 0.00 0.00 3.36
462 489 6.496338 TTTTCCTCTTCTCCTAAAATTCGC 57.504 37.500 0.00 0.00 0.00 4.70
483 510 5.917447 TCGCGAACATTTTCAAATTTCATGA 59.083 32.000 6.20 0.00 0.00 3.07
740 770 8.650143 ATTAAAGATAAAAGAAACCTGAGGCA 57.350 30.769 0.00 0.00 0.00 4.75
741 771 6.581171 AAAGATAAAAGAAACCTGAGGCAG 57.419 37.500 0.00 0.00 0.00 4.85
742 772 4.013050 AGATAAAAGAAACCTGAGGCAGC 58.987 43.478 0.00 0.00 0.00 5.25
743 773 2.071778 AAAAGAAACCTGAGGCAGCA 57.928 45.000 0.00 0.00 0.00 4.41
744 774 2.299326 AAAGAAACCTGAGGCAGCAT 57.701 45.000 0.00 0.00 0.00 3.79
745 775 1.831580 AAGAAACCTGAGGCAGCATC 58.168 50.000 0.00 0.00 0.00 3.91
746 776 0.990374 AGAAACCTGAGGCAGCATCT 59.010 50.000 8.81 0.00 0.00 2.90
747 777 1.353694 AGAAACCTGAGGCAGCATCTT 59.646 47.619 8.81 0.00 0.00 2.40
748 778 2.165998 GAAACCTGAGGCAGCATCTTT 58.834 47.619 8.81 0.40 0.00 2.52
749 779 3.009473 AGAAACCTGAGGCAGCATCTTTA 59.991 43.478 8.81 0.00 0.00 1.85
750 780 2.706339 ACCTGAGGCAGCATCTTTAG 57.294 50.000 8.81 0.00 0.00 1.85
751 781 1.307097 CCTGAGGCAGCATCTTTAGC 58.693 55.000 8.81 0.00 0.00 3.09
752 782 1.134159 CCTGAGGCAGCATCTTTAGCT 60.134 52.381 8.81 0.00 44.62 3.32
753 783 2.641305 CTGAGGCAGCATCTTTAGCTT 58.359 47.619 8.81 0.00 41.14 3.74
754 784 3.015327 CTGAGGCAGCATCTTTAGCTTT 58.985 45.455 8.81 0.00 41.14 3.51
755 785 3.012518 TGAGGCAGCATCTTTAGCTTTC 58.987 45.455 8.81 0.00 41.14 2.62
756 786 3.277715 GAGGCAGCATCTTTAGCTTTCT 58.722 45.455 0.00 0.00 41.14 2.52
757 787 3.693578 GAGGCAGCATCTTTAGCTTTCTT 59.306 43.478 0.00 0.00 41.14 2.52
758 788 4.085009 AGGCAGCATCTTTAGCTTTCTTT 58.915 39.130 0.00 0.00 41.14 2.52
759 789 4.082354 AGGCAGCATCTTTAGCTTTCTTTG 60.082 41.667 0.00 0.00 41.14 2.77
760 790 4.082571 GGCAGCATCTTTAGCTTTCTTTGA 60.083 41.667 0.00 0.00 41.14 2.69
761 791 5.464168 GCAGCATCTTTAGCTTTCTTTGAA 58.536 37.500 0.00 0.00 41.14 2.69
762 792 5.572126 GCAGCATCTTTAGCTTTCTTTGAAG 59.428 40.000 0.00 0.00 41.14 3.02
763 793 6.091437 CAGCATCTTTAGCTTTCTTTGAAGG 58.909 40.000 0.00 0.00 41.14 3.46
764 794 4.861462 GCATCTTTAGCTTTCTTTGAAGGC 59.139 41.667 6.34 6.34 0.00 4.35
765 795 4.749245 TCTTTAGCTTTCTTTGAAGGCG 57.251 40.909 8.37 0.00 0.00 5.52
766 796 4.385825 TCTTTAGCTTTCTTTGAAGGCGA 58.614 39.130 8.37 1.73 0.00 5.54
767 797 4.819630 TCTTTAGCTTTCTTTGAAGGCGAA 59.180 37.500 8.37 7.17 0.00 4.70
768 798 4.749245 TTAGCTTTCTTTGAAGGCGAAG 57.251 40.909 8.37 0.00 36.94 3.79
769 799 2.851195 AGCTTTCTTTGAAGGCGAAGA 58.149 42.857 8.37 0.00 41.66 2.87
770 800 2.550180 AGCTTTCTTTGAAGGCGAAGAC 59.450 45.455 8.37 0.00 42.77 3.01
779 809 2.358003 GGCGAAGACTGCAGCTGT 60.358 61.111 15.27 4.29 0.00 4.40
780 810 1.963338 GGCGAAGACTGCAGCTGTT 60.963 57.895 15.27 4.37 0.00 3.16
781 811 1.495069 GCGAAGACTGCAGCTGTTC 59.505 57.895 15.27 12.91 0.00 3.18
809 839 4.328983 CAGCCTACTTTTAATTTCGCGAGA 59.671 41.667 9.59 4.97 39.20 4.04
818 848 3.247046 TTCGCGAGAACGACGAGA 58.753 55.556 9.59 0.00 46.92 4.04
821 853 0.452287 TCGCGAGAACGACGAGAAAG 60.452 55.000 3.71 0.00 40.59 2.62
839 871 0.392193 AGGGAATGAGAGCGCTGTTG 60.392 55.000 18.48 0.00 0.00 3.33
844 876 2.049063 GAGAGCGCTGTTGTCGGT 60.049 61.111 18.48 0.00 40.58 4.69
858 890 2.357517 CGGTCAGCCCATATCCGC 60.358 66.667 0.00 0.00 35.01 5.54
859 891 2.357517 GGTCAGCCCATATCCGCG 60.358 66.667 0.00 0.00 0.00 6.46
860 892 2.734591 GTCAGCCCATATCCGCGA 59.265 61.111 8.23 0.00 0.00 5.87
861 893 1.293498 GTCAGCCCATATCCGCGAT 59.707 57.895 8.23 1.39 0.00 4.58
862 894 0.530744 GTCAGCCCATATCCGCGATA 59.469 55.000 8.23 4.01 0.00 2.92
863 895 0.530744 TCAGCCCATATCCGCGATAC 59.469 55.000 8.23 0.00 0.00 2.24
864 896 0.460284 CAGCCCATATCCGCGATACC 60.460 60.000 8.23 0.00 0.00 2.73
865 897 0.614979 AGCCCATATCCGCGATACCT 60.615 55.000 8.23 0.00 0.00 3.08
866 898 0.179108 GCCCATATCCGCGATACCTC 60.179 60.000 8.23 0.00 0.00 3.85
867 899 0.460311 CCCATATCCGCGATACCTCC 59.540 60.000 8.23 0.00 0.00 4.30
868 900 0.100682 CCATATCCGCGATACCTCCG 59.899 60.000 8.23 0.00 0.00 4.63
886 918 1.899437 CGGAGTAGGCCTGCCAAGAA 61.899 60.000 17.99 0.00 38.92 2.52
887 919 0.107459 GGAGTAGGCCTGCCAAGAAG 60.107 60.000 17.99 0.00 38.92 2.85
888 920 0.905357 GAGTAGGCCTGCCAAGAAGA 59.095 55.000 17.99 0.00 38.92 2.87
889 921 1.488393 GAGTAGGCCTGCCAAGAAGAT 59.512 52.381 17.99 0.00 38.92 2.40
905 937 7.201767 GCCAAGAAGATGCACAAAATCTACTAT 60.202 37.037 0.00 0.00 33.17 2.12
913 945 3.739300 CACAAAATCTACTATACGGCCCG 59.261 47.826 0.00 0.00 0.00 6.13
1065 1097 2.052690 CCCAGACCAGATCCGACGT 61.053 63.158 0.00 0.00 0.00 4.34
1589 1711 2.444706 CCCTCCGCCTCCAGATCA 60.445 66.667 0.00 0.00 0.00 2.92
2035 2157 3.771160 CCGGGGGTTGAGGAGTCG 61.771 72.222 0.00 0.00 0.00 4.18
2038 2160 1.916777 GGGGGTTGAGGAGTCGGAA 60.917 63.158 0.00 0.00 0.00 4.30
2083 2205 2.161012 TGTGTTCGAGTATCTCCACGAC 59.839 50.000 0.00 0.00 34.59 4.34
2207 2329 1.998530 CTTGCACCAGGGTGGGATA 59.001 57.895 19.41 0.00 43.37 2.59
2217 2339 4.547367 GTGGGATAGCGCGGCCTT 62.547 66.667 8.83 0.00 0.00 4.35
2220 2342 2.031163 GGATAGCGCGGCCTTGAT 59.969 61.111 8.83 0.00 0.00 2.57
2323 2445 5.108187 AGGATGTGATCAAGCAGTACATT 57.892 39.130 0.00 0.00 32.58 2.71
2428 2550 1.491274 TTGCTGGAGTGGATGCTGGA 61.491 55.000 0.00 0.00 0.00 3.86
2525 2647 1.743995 GACCGTTCCACATTCCCGG 60.744 63.158 0.00 0.00 44.06 5.73
2527 2649 1.223487 CCGTTCCACATTCCCGGAT 59.777 57.895 0.73 0.00 41.08 4.18
3127 3253 0.331616 GGTATGGGGCAGTTTGGACT 59.668 55.000 0.00 0.00 36.25 3.85
3163 3289 4.279420 GCAGATTGGGATCACCTTAAATCC 59.721 45.833 0.00 0.00 40.69 3.01
3554 3682 8.746052 ATCGAGGAAAATTTATTACCATGACA 57.254 30.769 0.00 0.00 0.00 3.58
3565 3693 8.806429 TTTATTACCATGACATGACTTCACAT 57.194 30.769 17.24 2.13 0.00 3.21
3730 3879 7.937394 GGTATTCATTGTTGCCCTACTATTACT 59.063 37.037 0.00 0.00 0.00 2.24
4100 4257 2.579410 TACCAAGCTTCCAAAGGTCC 57.421 50.000 8.58 0.00 38.49 4.46
4194 4351 5.073428 TGGTATGTCAAACATGTTTGCCTA 58.927 37.500 35.90 26.24 46.92 3.93
4210 4367 5.818136 TTGCCTATGTAAACATCTTGCTC 57.182 39.130 0.00 0.00 37.76 4.26
4235 4392 9.403583 TCTTTGGTAACTCATAATCCCATTTAC 57.596 33.333 0.00 0.00 37.61 2.01
4245 4402 9.921637 CTCATAATCCCATTTACTAGTTCTCTC 57.078 37.037 0.00 0.00 0.00 3.20
4246 4403 9.661954 TCATAATCCCATTTACTAGTTCTCTCT 57.338 33.333 0.00 0.00 0.00 3.10
4269 4426 8.510243 TCTGTGATGTGCAAATAGTCATTAAT 57.490 30.769 0.00 0.00 0.00 1.40
4339 4496 4.685924 AGTTGCATGTGAACCTTTTTCTG 58.314 39.130 0.00 0.00 0.00 3.02
4347 4538 7.378728 GCATGTGAACCTTTTTCTGTACTAAAC 59.621 37.037 0.00 0.00 0.00 2.01
4353 4544 6.735130 ACCTTTTTCTGTACTAAACACATGC 58.265 36.000 0.00 0.00 33.45 4.06
4379 4570 2.431057 TGTGAGCCTTACTTAGCTAGCC 59.569 50.000 12.13 0.00 40.11 3.93
4400 4591 3.493350 CCCCTTCCAGATTAGTCGATGTG 60.493 52.174 0.00 0.00 0.00 3.21
4455 4646 7.922811 GCAATGCTTGTTAAATTATTAGGCTCT 59.077 33.333 0.00 0.00 0.00 4.09
4508 4778 6.395629 TCTGTTTGGTTGATGTAGCTACTAC 58.604 40.000 23.84 17.09 37.46 2.73
4522 4917 6.933521 TGTAGCTACTACCTACATACTAGTGC 59.066 42.308 23.84 0.00 39.98 4.40
4536 4931 4.803098 ACTAGTGCGGTTTATTCTCTGT 57.197 40.909 0.00 0.00 0.00 3.41
4592 4989 2.903135 GGTGATAGCCCTCAATAGCTCT 59.097 50.000 0.00 0.00 40.56 4.09
4633 5030 6.530019 ACTTTATGTGGATGATGGGAAAAC 57.470 37.500 0.00 0.00 0.00 2.43
4761 5158 5.484173 TTCAACTGAGTGTGTGATTGAAC 57.516 39.130 0.00 0.00 32.61 3.18
4934 5331 7.303182 TGTAGATGATTGGACGATAAGGATT 57.697 36.000 0.00 0.00 0.00 3.01
4959 5356 4.370094 TGATATGCAGCCCATTCACATA 57.630 40.909 0.00 0.00 35.34 2.29
4990 5387 0.318784 GTCTCCGTTGTTCGCTGTCT 60.319 55.000 0.00 0.00 38.35 3.41
5002 5399 3.887621 TCGCTGTCTGGCTATAAACTT 57.112 42.857 0.00 0.00 0.00 2.66
5298 5697 8.613482 GGATAGTTCTTTGCCTAAGATTGTAAC 58.387 37.037 0.00 0.00 42.32 2.50
5368 5768 4.326826 CACACACTATCCTCCAACACAAT 58.673 43.478 0.00 0.00 0.00 2.71
5420 5820 6.674694 ATGCACATACTTTAAGAGCTTGAG 57.325 37.500 0.00 0.00 0.00 3.02
5421 5821 5.551233 TGCACATACTTTAAGAGCTTGAGT 58.449 37.500 0.00 0.00 0.00 3.41
5422 5822 5.997746 TGCACATACTTTAAGAGCTTGAGTT 59.002 36.000 0.00 0.00 0.00 3.01
5623 6064 3.903090 TCTGTTCCGACCTAAAAGGGTAA 59.097 43.478 0.00 0.00 40.58 2.85
5659 6120 6.870769 AGTGGCGTATAACAACATAAGTAGT 58.129 36.000 0.00 0.00 0.00 2.73
5661 6122 7.917505 AGTGGCGTATAACAACATAAGTAGTAC 59.082 37.037 0.00 0.00 0.00 2.73
5662 6123 7.701924 GTGGCGTATAACAACATAAGTAGTACA 59.298 37.037 2.52 0.00 0.00 2.90
5664 6125 9.086336 GGCGTATAACAACATAAGTAGTACAAA 57.914 33.333 2.52 0.00 0.00 2.83
5671 6132 9.609346 AACAACATAAGTAGTACAAAGTTCACT 57.391 29.630 2.52 0.00 0.00 3.41
5682 6143 7.681903 AGTACAAAGTTCACTTTTGTAAGTCG 58.318 34.615 10.95 0.00 43.07 4.18
5683 6144 6.490566 ACAAAGTTCACTTTTGTAAGTCGT 57.509 33.333 2.01 0.00 43.07 4.34
5685 6146 7.364970 ACAAAGTTCACTTTTGTAAGTCGTTT 58.635 30.769 2.01 0.00 43.07 3.60
5686 6147 7.863877 ACAAAGTTCACTTTTGTAAGTCGTTTT 59.136 29.630 2.01 0.00 43.07 2.43
5687 6148 9.332301 CAAAGTTCACTTTTGTAAGTCGTTTTA 57.668 29.630 2.01 0.00 43.07 1.52
5689 6150 8.483307 AGTTCACTTTTGTAAGTCGTTTTAGA 57.517 30.769 0.00 0.00 42.67 2.10
5690 6151 8.385858 AGTTCACTTTTGTAAGTCGTTTTAGAC 58.614 33.333 0.00 0.00 42.67 2.59
5691 6152 7.830940 TCACTTTTGTAAGTCGTTTTAGACA 57.169 32.000 0.00 0.00 42.67 3.41
5692 6153 8.254178 TCACTTTTGTAAGTCGTTTTAGACAA 57.746 30.769 0.00 0.00 42.67 3.18
5693 6154 8.170553 TCACTTTTGTAAGTCGTTTTAGACAAC 58.829 33.333 0.00 0.00 42.67 3.32
5695 6156 8.385858 ACTTTTGTAAGTCGTTTTAGACAACTC 58.614 33.333 0.00 0.00 40.60 3.01
5697 6158 7.830940 TTGTAAGTCGTTTTAGACAACTCAA 57.169 32.000 0.00 0.00 43.24 3.02
5698 6159 7.830940 TGTAAGTCGTTTTAGACAACTCAAA 57.169 32.000 0.00 0.00 43.24 2.69
5699 6160 8.254178 TGTAAGTCGTTTTAGACAACTCAAAA 57.746 30.769 0.00 0.00 43.24 2.44
5700 6161 8.885722 TGTAAGTCGTTTTAGACAACTCAAAAT 58.114 29.630 0.00 0.00 43.24 1.82
5701 6162 9.155053 GTAAGTCGTTTTAGACAACTCAAAATG 57.845 33.333 0.00 0.00 43.24 2.32
5702 6163 6.725246 AGTCGTTTTAGACAACTCAAAATGG 58.275 36.000 0.00 0.00 43.24 3.16
5703 6164 6.540914 AGTCGTTTTAGACAACTCAAAATGGA 59.459 34.615 0.00 0.00 43.24 3.41
5704 6165 6.631636 GTCGTTTTAGACAACTCAAAATGGAC 59.368 38.462 0.00 0.00 40.65 4.02
5705 6166 6.540914 TCGTTTTAGACAACTCAAAATGGACT 59.459 34.615 0.00 0.00 31.88 3.85
5708 6169 7.639113 TTTAGACAACTCAAAATGGACTGTT 57.361 32.000 0.00 0.00 0.00 3.16
5711 6172 6.332630 AGACAACTCAAAATGGACTGTTTTG 58.667 36.000 5.27 5.27 44.10 2.44
5712 6173 4.869861 ACAACTCAAAATGGACTGTTTTGC 59.130 37.500 6.49 0.00 43.04 3.68
5713 6174 4.734398 ACTCAAAATGGACTGTTTTGCA 57.266 36.364 6.49 0.00 43.04 4.08
5714 6175 4.432712 ACTCAAAATGGACTGTTTTGCAC 58.567 39.130 6.49 0.00 43.04 4.57
5715 6176 4.081752 ACTCAAAATGGACTGTTTTGCACA 60.082 37.500 6.49 0.00 43.04 4.57
5716 6177 5.021033 TCAAAATGGACTGTTTTGCACAT 57.979 34.783 6.49 0.00 43.04 3.21
5718 6179 5.293814 TCAAAATGGACTGTTTTGCACATTG 59.706 36.000 6.49 0.00 43.04 2.82
5719 6180 4.405116 AATGGACTGTTTTGCACATTGT 57.595 36.364 0.00 0.00 33.76 2.71
5720 6181 3.435105 TGGACTGTTTTGCACATTGTC 57.565 42.857 0.00 0.00 33.76 3.18
5722 6183 3.181488 TGGACTGTTTTGCACATTGTCTG 60.181 43.478 0.00 0.00 33.15 3.51
5723 6184 3.066621 GGACTGTTTTGCACATTGTCTGA 59.933 43.478 0.00 0.00 33.15 3.27
5724 6185 4.439974 GGACTGTTTTGCACATTGTCTGAA 60.440 41.667 0.00 0.00 33.15 3.02
5725 6186 5.070770 ACTGTTTTGCACATTGTCTGAAA 57.929 34.783 0.00 0.00 33.76 2.69
5726 6187 5.663456 ACTGTTTTGCACATTGTCTGAAAT 58.337 33.333 0.00 0.00 33.76 2.17
5727 6188 5.521010 ACTGTTTTGCACATTGTCTGAAATG 59.479 36.000 0.00 9.50 42.21 2.32
5729 6190 5.519566 TGTTTTGCACATTGTCTGAAATGTC 59.480 36.000 12.25 9.51 45.47 3.06
5731 6192 5.518848 TTGCACATTGTCTGAAATGTCTT 57.481 34.783 12.25 0.00 45.47 3.01
5734 6195 7.036996 TGCACATTGTCTGAAATGTCTTAAA 57.963 32.000 12.25 0.00 45.47 1.52
5735 6196 7.140705 TGCACATTGTCTGAAATGTCTTAAAG 58.859 34.615 12.25 5.42 45.47 1.85
5736 6197 6.583806 GCACATTGTCTGAAATGTCTTAAAGG 59.416 38.462 12.25 4.96 45.47 3.11
5737 6198 6.583806 CACATTGTCTGAAATGTCTTAAAGGC 59.416 38.462 12.25 0.00 45.47 4.35
5738 6199 5.705609 TTGTCTGAAATGTCTTAAAGGCC 57.294 39.130 0.00 0.00 0.00 5.19
5739 6200 4.985538 TGTCTGAAATGTCTTAAAGGCCT 58.014 39.130 0.00 0.00 0.00 5.19
5742 6203 7.175104 TGTCTGAAATGTCTTAAAGGCCTTAT 58.825 34.615 20.84 11.72 0.00 1.73
5743 6204 8.325787 TGTCTGAAATGTCTTAAAGGCCTTATA 58.674 33.333 20.84 10.67 0.00 0.98
5750 6211 9.528489 AATGTCTTAAAGGCCTTATAAAAGTGA 57.472 29.630 20.84 9.87 0.00 3.41
5751 6212 8.927675 TGTCTTAAAGGCCTTATAAAAGTGAA 57.072 30.769 20.84 7.75 0.00 3.18
5752 6213 8.789762 TGTCTTAAAGGCCTTATAAAAGTGAAC 58.210 33.333 20.84 13.59 0.00 3.18
5754 6215 9.010029 TCTTAAAGGCCTTATAAAAGTGAACAG 57.990 33.333 20.84 5.01 0.00 3.16
5755 6216 8.927675 TTAAAGGCCTTATAAAAGTGAACAGA 57.072 30.769 20.84 0.00 0.00 3.41
5756 6217 7.454260 AAAGGCCTTATAAAAGTGAACAGAG 57.546 36.000 20.84 0.00 0.00 3.35
5757 6218 5.501156 AGGCCTTATAAAAGTGAACAGAGG 58.499 41.667 0.00 0.00 0.00 3.69
5758 6219 5.250774 AGGCCTTATAAAAGTGAACAGAGGA 59.749 40.000 0.00 0.00 0.00 3.71
5760 6221 6.094186 GGCCTTATAAAAGTGAACAGAGGAAG 59.906 42.308 0.00 0.00 0.00 3.46
5852 6422 4.261031 CGAAAACAAAACCTCATCTTCGGT 60.261 41.667 0.00 0.00 32.83 4.69
5869 6439 2.159282 TCGGTAAGAAGAATGACCTCGC 60.159 50.000 0.00 0.00 0.00 5.03
5876 6446 2.493713 AGAATGACCTCGCGTACATC 57.506 50.000 5.77 0.44 0.00 3.06
5903 6475 8.604890 CGATACAAGGATTAAGAGAGGAAAAAC 58.395 37.037 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.142708 CGGTAAAATGCATGCTAACTGACA 60.143 41.667 20.33 0.00 0.00 3.58
1 2 4.142687 ACGGTAAAATGCATGCTAACTGAC 60.143 41.667 20.33 9.62 0.00 3.51
2 3 4.006989 ACGGTAAAATGCATGCTAACTGA 58.993 39.130 20.33 0.00 0.00 3.41
3 4 4.355543 ACGGTAAAATGCATGCTAACTG 57.644 40.909 20.33 15.44 0.00 3.16
13 14 5.220796 GGAAACTGAGGATACGGTAAAATGC 60.221 44.000 0.00 0.00 46.39 3.56
14 15 6.113411 AGGAAACTGAGGATACGGTAAAATG 58.887 40.000 0.00 0.00 41.03 2.32
42 43 1.549243 TATGTGCTTGAGGTGCCCGA 61.549 55.000 0.00 0.00 0.00 5.14
75 76 5.220719 CGTGTTCAGCATATGTCATCATTGT 60.221 40.000 4.29 0.00 35.70 2.71
117 118 2.584608 CCAACCTAGCCCACTCGG 59.415 66.667 0.00 0.00 34.87 4.63
130 131 2.137528 CACCCCCACCAAACCCAAC 61.138 63.158 0.00 0.00 0.00 3.77
131 132 2.283809 CACCCCCACCAAACCCAA 59.716 61.111 0.00 0.00 0.00 4.12
135 136 3.601685 CGTGCACCCCCACCAAAC 61.602 66.667 12.15 0.00 32.10 2.93
162 163 4.221041 TGATGATATCGCGTATGGGGTTTA 59.779 41.667 5.77 0.00 0.00 2.01
164 165 2.565391 TGATGATATCGCGTATGGGGTT 59.435 45.455 5.77 0.00 0.00 4.11
167 168 3.119495 TGAGTGATGATATCGCGTATGGG 60.119 47.826 5.77 0.00 44.25 4.00
169 170 4.435877 CGATGAGTGATGATATCGCGTATG 59.564 45.833 5.77 0.00 44.25 2.39
170 171 4.496507 CCGATGAGTGATGATATCGCGTAT 60.497 45.833 5.77 3.23 44.25 3.06
171 172 3.181510 CCGATGAGTGATGATATCGCGTA 60.182 47.826 5.77 0.00 44.25 4.42
172 173 2.414691 CCGATGAGTGATGATATCGCGT 60.415 50.000 5.77 0.00 44.25 6.01
173 174 2.180397 CCGATGAGTGATGATATCGCG 58.820 52.381 0.00 0.00 44.25 5.87
174 175 2.164422 TCCCGATGAGTGATGATATCGC 59.836 50.000 0.00 0.00 40.61 4.58
175 176 4.026293 CTCCCGATGAGTGATGATATCG 57.974 50.000 0.00 0.00 41.35 2.92
190 191 0.398098 GGGATTCCACCTACTCCCGA 60.398 60.000 4.80 0.00 38.15 5.14
225 226 4.346418 ACAAGCGAGAATAGAGGATTCCAT 59.654 41.667 5.29 0.00 44.54 3.41
257 260 7.915923 TGTGCAGTTCTTACGAATATCTCTTAG 59.084 37.037 0.00 0.00 0.00 2.18
278 281 0.541392 ATAGAGCGATTGGGTGTGCA 59.459 50.000 0.00 0.00 0.00 4.57
289 292 5.632118 AGATGGGTTAGTCTAATAGAGCGA 58.368 41.667 0.00 0.00 0.00 4.93
303 306 3.522759 TGGGTGTGAAGTAGATGGGTTA 58.477 45.455 0.00 0.00 0.00 2.85
328 331 2.596904 TCGGCTCATGCTAGGTTAAC 57.403 50.000 0.00 0.00 39.59 2.01
338 341 4.644103 AATGGAAGAAAATCGGCTCATG 57.356 40.909 0.00 0.00 0.00 3.07
387 414 0.609406 AAAGAAAGGAAGGAGGCCGC 60.609 55.000 0.00 0.00 0.00 6.53
405 432 7.565029 AGGAAAAGGAAAAGGAGAAAATGAGAA 59.435 33.333 0.00 0.00 0.00 2.87
406 433 7.069344 AGGAAAAGGAAAAGGAGAAAATGAGA 58.931 34.615 0.00 0.00 0.00 3.27
407 434 7.295322 AGGAAAAGGAAAAGGAGAAAATGAG 57.705 36.000 0.00 0.00 0.00 2.90
408 435 7.675161 AAGGAAAAGGAAAAGGAGAAAATGA 57.325 32.000 0.00 0.00 0.00 2.57
409 436 8.737168 AAAAGGAAAAGGAAAAGGAGAAAATG 57.263 30.769 0.00 0.00 0.00 2.32
436 463 7.094762 GCGAATTTTAGGAGAAGAGGAAAAAGA 60.095 37.037 0.00 0.00 0.00 2.52
450 477 6.003234 TGAAAATGTTCGCGAATTTTAGGA 57.997 33.333 26.23 12.19 36.40 2.94
636 663 7.986085 ACATGCTATGGGTTTATTGATAGAC 57.014 36.000 0.00 0.00 33.60 2.59
723 753 3.222173 TGCTGCCTCAGGTTTCTTTTA 57.778 42.857 0.00 0.00 31.21 1.52
733 763 2.328819 AGCTAAAGATGCTGCCTCAG 57.671 50.000 7.66 0.00 39.56 3.35
734 764 2.795231 AAGCTAAAGATGCTGCCTCA 57.205 45.000 7.66 0.00 41.03 3.86
735 765 3.277715 AGAAAGCTAAAGATGCTGCCTC 58.722 45.455 0.00 0.00 41.03 4.70
736 766 3.362870 AGAAAGCTAAAGATGCTGCCT 57.637 42.857 0.00 0.00 41.03 4.75
737 767 4.082571 TCAAAGAAAGCTAAAGATGCTGCC 60.083 41.667 0.00 0.00 41.03 4.85
738 768 5.051891 TCAAAGAAAGCTAAAGATGCTGC 57.948 39.130 0.00 0.00 41.03 5.25
739 769 6.091437 CCTTCAAAGAAAGCTAAAGATGCTG 58.909 40.000 0.00 0.00 41.03 4.41
740 770 5.336293 GCCTTCAAAGAAAGCTAAAGATGCT 60.336 40.000 0.00 0.00 43.32 3.79
741 771 4.861462 GCCTTCAAAGAAAGCTAAAGATGC 59.139 41.667 0.00 0.00 0.00 3.91
742 772 5.091431 CGCCTTCAAAGAAAGCTAAAGATG 58.909 41.667 0.00 0.00 0.00 2.90
743 773 5.003804 TCGCCTTCAAAGAAAGCTAAAGAT 58.996 37.500 0.00 0.00 0.00 2.40
744 774 4.385825 TCGCCTTCAAAGAAAGCTAAAGA 58.614 39.130 0.00 0.00 0.00 2.52
745 775 4.749245 TCGCCTTCAAAGAAAGCTAAAG 57.251 40.909 0.00 0.00 0.00 1.85
746 776 4.819630 TCTTCGCCTTCAAAGAAAGCTAAA 59.180 37.500 0.00 0.00 0.00 1.85
747 777 4.213482 GTCTTCGCCTTCAAAGAAAGCTAA 59.787 41.667 0.00 0.00 33.53 3.09
748 778 3.746492 GTCTTCGCCTTCAAAGAAAGCTA 59.254 43.478 0.00 0.00 33.53 3.32
749 779 2.550180 GTCTTCGCCTTCAAAGAAAGCT 59.450 45.455 0.00 0.00 33.53 3.74
750 780 2.550180 AGTCTTCGCCTTCAAAGAAAGC 59.450 45.455 0.00 0.00 33.53 3.51
751 781 3.608008 GCAGTCTTCGCCTTCAAAGAAAG 60.608 47.826 0.00 0.00 33.53 2.62
752 782 2.290641 GCAGTCTTCGCCTTCAAAGAAA 59.709 45.455 0.00 0.00 33.53 2.52
753 783 1.873591 GCAGTCTTCGCCTTCAAAGAA 59.126 47.619 0.00 0.00 33.53 2.52
754 784 1.202639 TGCAGTCTTCGCCTTCAAAGA 60.203 47.619 0.00 0.00 0.00 2.52
755 785 1.196354 CTGCAGTCTTCGCCTTCAAAG 59.804 52.381 5.25 0.00 0.00 2.77
756 786 1.229428 CTGCAGTCTTCGCCTTCAAA 58.771 50.000 5.25 0.00 0.00 2.69
757 787 1.230635 GCTGCAGTCTTCGCCTTCAA 61.231 55.000 16.64 0.00 0.00 2.69
758 788 1.669115 GCTGCAGTCTTCGCCTTCA 60.669 57.895 16.64 0.00 0.00 3.02
759 789 1.375268 AGCTGCAGTCTTCGCCTTC 60.375 57.895 16.64 0.00 0.00 3.46
760 790 1.670406 CAGCTGCAGTCTTCGCCTT 60.670 57.895 16.64 0.00 0.00 4.35
761 791 2.047465 CAGCTGCAGTCTTCGCCT 60.047 61.111 16.64 0.00 0.00 5.52
762 792 1.905922 GAACAGCTGCAGTCTTCGCC 61.906 60.000 15.27 0.00 0.00 5.54
763 793 1.495069 GAACAGCTGCAGTCTTCGC 59.505 57.895 15.27 0.00 0.00 4.70
764 794 1.621301 CCGAACAGCTGCAGTCTTCG 61.621 60.000 22.54 22.54 34.78 3.79
765 795 0.601311 ACCGAACAGCTGCAGTCTTC 60.601 55.000 15.27 8.78 0.00 2.87
766 796 0.882042 CACCGAACAGCTGCAGTCTT 60.882 55.000 15.27 0.00 0.00 3.01
767 797 1.301244 CACCGAACAGCTGCAGTCT 60.301 57.895 15.27 10.20 0.00 3.24
768 798 2.959357 GCACCGAACAGCTGCAGTC 61.959 63.158 15.27 8.11 0.00 3.51
769 799 2.974698 GCACCGAACAGCTGCAGT 60.975 61.111 15.27 2.92 0.00 4.40
770 800 2.974148 TGCACCGAACAGCTGCAG 60.974 61.111 15.27 10.11 36.00 4.41
771 801 2.974148 CTGCACCGAACAGCTGCA 60.974 61.111 15.27 3.71 38.60 4.41
776 806 0.320771 AAGTAGGCTGCACCGAACAG 60.321 55.000 5.14 0.00 46.52 3.16
777 807 0.107831 AAAGTAGGCTGCACCGAACA 59.892 50.000 5.14 0.00 46.52 3.18
778 808 1.235724 AAAAGTAGGCTGCACCGAAC 58.764 50.000 5.14 0.00 46.52 3.95
779 809 2.843401 TAAAAGTAGGCTGCACCGAA 57.157 45.000 5.14 0.00 46.52 4.30
780 810 2.843401 TTAAAAGTAGGCTGCACCGA 57.157 45.000 5.14 0.00 46.52 4.69
781 811 4.412207 GAAATTAAAAGTAGGCTGCACCG 58.588 43.478 5.14 0.00 46.52 4.94
809 839 2.561419 TCTCATTCCCTTTCTCGTCGTT 59.439 45.455 0.00 0.00 0.00 3.85
811 841 2.803451 CTCTCATTCCCTTTCTCGTCG 58.197 52.381 0.00 0.00 0.00 5.12
812 842 2.545731 GCTCTCATTCCCTTTCTCGTC 58.454 52.381 0.00 0.00 0.00 4.20
818 848 0.326264 ACAGCGCTCTCATTCCCTTT 59.674 50.000 7.13 0.00 0.00 3.11
821 853 0.674895 ACAACAGCGCTCTCATTCCC 60.675 55.000 7.13 0.00 0.00 3.97
839 871 1.006102 CGGATATGGGCTGACCGAC 60.006 63.158 0.00 0.00 45.31 4.79
844 876 0.530744 GTATCGCGGATATGGGCTGA 59.469 55.000 6.13 0.00 0.00 4.26
864 896 3.541713 GGCAGGCCTACTCCGGAG 61.542 72.222 30.11 30.11 0.00 4.63
865 897 3.916438 TTGGCAGGCCTACTCCGGA 62.916 63.158 3.98 2.93 36.94 5.14
866 898 3.391665 CTTGGCAGGCCTACTCCGG 62.392 68.421 3.98 0.00 36.94 5.14
867 899 1.899437 TTCTTGGCAGGCCTACTCCG 61.899 60.000 3.98 0.00 36.94 4.63
868 900 0.107459 CTTCTTGGCAGGCCTACTCC 60.107 60.000 3.98 8.04 36.94 3.85
886 918 5.696724 GCCGTATAGTAGATTTTGTGCATCT 59.303 40.000 0.00 0.00 35.13 2.90
887 919 5.107065 GGCCGTATAGTAGATTTTGTGCATC 60.107 44.000 0.00 0.00 0.00 3.91
888 920 4.755123 GGCCGTATAGTAGATTTTGTGCAT 59.245 41.667 0.00 0.00 0.00 3.96
889 921 4.124238 GGCCGTATAGTAGATTTTGTGCA 58.876 43.478 0.00 0.00 0.00 4.57
1640 1762 2.679287 GTCGGGGAGGAGGACGTT 60.679 66.667 0.00 0.00 0.00 3.99
1867 1989 0.116342 TGAACTGCTCCTCCCAGGTA 59.884 55.000 0.00 0.00 36.53 3.08
2035 2157 0.611714 TGAAGAGGCGGTAAGGTTCC 59.388 55.000 0.00 0.00 0.00 3.62
2038 2160 0.323957 GGTTGAAGAGGCGGTAAGGT 59.676 55.000 0.00 0.00 0.00 3.50
2207 2329 4.845580 CTCCATCAAGGCCGCGCT 62.846 66.667 5.56 0.00 37.29 5.92
2215 2337 5.298777 GTCAATTCTCCCATTCTCCATCAAG 59.701 44.000 0.00 0.00 0.00 3.02
2217 2339 4.227982 TGTCAATTCTCCCATTCTCCATCA 59.772 41.667 0.00 0.00 0.00 3.07
2220 2342 3.619733 CGTGTCAATTCTCCCATTCTCCA 60.620 47.826 0.00 0.00 0.00 3.86
2428 2550 9.695155 TCATATGGAATATCATGCTCATCAAAT 57.305 29.630 2.13 0.00 37.44 2.32
2525 2647 0.319727 CGCTGCATCTCCTCTGGATC 60.320 60.000 0.00 0.00 0.00 3.36
2527 2649 2.429767 CCGCTGCATCTCCTCTGGA 61.430 63.158 0.00 0.00 0.00 3.86
3127 3253 1.948834 CAATCTGCAGTGTTGTCACCA 59.051 47.619 14.67 0.00 44.83 4.17
3163 3289 7.011482 CCAAGAGTTAAAACCATCGGAATAGAG 59.989 40.741 0.00 0.00 0.00 2.43
3730 3879 2.828520 CACTAGCCTCTTGGAACAGAGA 59.171 50.000 0.00 0.00 42.39 3.10
3958 4115 0.040058 TGATTTCTGGCCCTGCATGT 59.960 50.000 0.00 0.00 0.00 3.21
4194 4351 7.448469 AGTTACCAAAGAGCAAGATGTTTACAT 59.552 33.333 0.00 0.00 39.70 2.29
4210 4367 9.408648 AGTAAATGGGATTATGAGTTACCAAAG 57.591 33.333 0.00 0.00 0.00 2.77
4235 4392 4.446994 TGCACATCACAGAGAGAACTAG 57.553 45.455 0.00 0.00 0.00 2.57
4245 4402 9.874215 CTATTAATGACTATTTGCACATCACAG 57.126 33.333 0.00 0.00 0.00 3.66
4246 4403 9.394767 ACTATTAATGACTATTTGCACATCACA 57.605 29.630 0.00 0.00 0.00 3.58
4310 4467 4.874970 AGGTTCACATGCAACTTTTCATC 58.125 39.130 7.80 0.00 0.00 2.92
4353 4544 2.611292 GCTAAGTAAGGCTCACATGCAG 59.389 50.000 0.00 0.00 34.04 4.41
4363 4554 1.425694 AGGGGCTAGCTAAGTAAGGC 58.574 55.000 15.72 0.00 35.21 4.35
4379 4570 3.493350 CCACATCGACTAATCTGGAAGGG 60.493 52.174 0.00 0.00 0.00 3.95
4400 4591 7.055667 TGATGTATAGTTGATCCTCAGAACC 57.944 40.000 0.00 0.00 0.00 3.62
4508 4778 6.746120 AGAATAAACCGCACTAGTATGTAGG 58.254 40.000 0.00 0.00 0.00 3.18
4557 4954 4.098349 GGCTATCACCTGATCATTGCAAAA 59.902 41.667 1.71 0.00 36.05 2.44
4592 4989 1.490490 AGTTCACCTTCTGCAGAACCA 59.510 47.619 25.16 5.68 40.82 3.67
4633 5030 4.401022 TGCCCCTTGCTGATAATCATAAG 58.599 43.478 0.00 0.00 42.00 1.73
4761 5158 7.411912 CGATGATAACCCAAGCACTATAATTCG 60.412 40.741 0.00 0.00 0.00 3.34
4990 5387 2.430332 GCATTGCCCAAGTTTATAGCCA 59.570 45.455 0.00 0.00 0.00 4.75
5002 5399 0.539518 TACGCTTCTAGCATTGCCCA 59.460 50.000 4.70 0.00 42.58 5.36
5344 5743 2.038557 GTGTTGGAGGATAGTGTGTGGT 59.961 50.000 0.00 0.00 0.00 4.16
5368 5768 8.598916 TGTCTGAGAAGGTATTATTTGTTACCA 58.401 33.333 2.29 0.00 35.15 3.25
5420 5820 3.694072 TGATGGCTGCCATAACTAACAAC 59.306 43.478 32.63 17.51 45.26 3.32
5421 5821 3.961849 TGATGGCTGCCATAACTAACAA 58.038 40.909 32.63 9.41 45.26 2.83
5422 5822 3.643199 TGATGGCTGCCATAACTAACA 57.357 42.857 32.63 21.84 45.26 2.41
5659 6120 7.599630 ACGACTTACAAAAGTGAACTTTGTA 57.400 32.000 9.11 10.34 46.09 2.41
5661 6122 7.790861 AAACGACTTACAAAAGTGAACTTTG 57.209 32.000 9.11 6.53 46.09 2.77
5662 6123 9.550811 CTAAAACGACTTACAAAAGTGAACTTT 57.449 29.630 2.56 2.56 46.09 2.66
5664 6125 8.385858 GTCTAAAACGACTTACAAAAGTGAACT 58.614 33.333 0.00 0.00 46.09 3.01
5665 6126 8.170553 TGTCTAAAACGACTTACAAAAGTGAAC 58.829 33.333 0.00 0.00 46.09 3.18
5666 6127 8.254178 TGTCTAAAACGACTTACAAAAGTGAA 57.746 30.769 0.00 0.00 46.09 3.18
5667 6128 7.830940 TGTCTAAAACGACTTACAAAAGTGA 57.169 32.000 0.00 0.00 46.09 3.41
5668 6129 8.307031 GTTGTCTAAAACGACTTACAAAAGTG 57.693 34.615 0.00 0.00 46.09 3.16
5679 6140 6.631636 GTCCATTTTGAGTTGTCTAAAACGAC 59.368 38.462 0.00 0.00 41.93 4.34
5682 6143 7.480810 ACAGTCCATTTTGAGTTGTCTAAAAC 58.519 34.615 0.00 0.00 32.28 2.43
5683 6144 7.639113 ACAGTCCATTTTGAGTTGTCTAAAA 57.361 32.000 0.00 0.00 32.28 1.52
5685 6146 7.639113 AAACAGTCCATTTTGAGTTGTCTAA 57.361 32.000 0.00 0.00 0.00 2.10
5686 6147 7.479980 CAAAACAGTCCATTTTGAGTTGTCTA 58.520 34.615 4.56 0.00 45.75 2.59
5687 6148 6.332630 CAAAACAGTCCATTTTGAGTTGTCT 58.667 36.000 4.56 0.00 45.75 3.41
5689 6150 4.869861 GCAAAACAGTCCATTTTGAGTTGT 59.130 37.500 13.00 0.00 45.75 3.32
5690 6151 4.869297 TGCAAAACAGTCCATTTTGAGTTG 59.131 37.500 13.00 0.00 45.75 3.16
5691 6152 4.869861 GTGCAAAACAGTCCATTTTGAGTT 59.130 37.500 13.00 0.00 45.75 3.01
5692 6153 4.081752 TGTGCAAAACAGTCCATTTTGAGT 60.082 37.500 13.00 0.00 45.75 3.41
5693 6154 4.431809 TGTGCAAAACAGTCCATTTTGAG 58.568 39.130 13.00 0.00 45.75 3.02
5695 6156 5.064962 ACAATGTGCAAAACAGTCCATTTTG 59.935 36.000 5.96 5.96 45.68 2.44
5697 6158 4.768583 ACAATGTGCAAAACAGTCCATTT 58.231 34.783 0.00 0.00 43.64 2.32
5698 6159 4.099881 AGACAATGTGCAAAACAGTCCATT 59.900 37.500 0.00 0.00 43.64 3.16
5699 6160 3.638160 AGACAATGTGCAAAACAGTCCAT 59.362 39.130 0.00 0.00 43.64 3.41
5700 6161 3.023119 AGACAATGTGCAAAACAGTCCA 58.977 40.909 0.00 0.00 43.64 4.02
5701 6162 3.066621 TCAGACAATGTGCAAAACAGTCC 59.933 43.478 0.00 0.00 43.64 3.85
5702 6163 4.291540 TCAGACAATGTGCAAAACAGTC 57.708 40.909 0.00 0.00 43.64 3.51
5703 6164 4.717233 TTCAGACAATGTGCAAAACAGT 57.283 36.364 0.00 0.00 43.64 3.55
5704 6165 5.521010 ACATTTCAGACAATGTGCAAAACAG 59.479 36.000 0.00 0.00 44.19 3.16
5705 6166 5.417811 ACATTTCAGACAATGTGCAAAACA 58.582 33.333 0.00 0.00 44.19 2.83
5708 6169 5.518848 AGACATTTCAGACAATGTGCAAA 57.481 34.783 12.82 0.00 45.55 3.68
5711 6172 6.583806 CCTTTAAGACATTTCAGACAATGTGC 59.416 38.462 12.82 7.29 45.55 4.57
5712 6173 6.583806 GCCTTTAAGACATTTCAGACAATGTG 59.416 38.462 12.82 2.69 45.55 3.21
5714 6175 6.071728 AGGCCTTTAAGACATTTCAGACAATG 60.072 38.462 0.00 0.00 39.67 2.82
5715 6176 6.012745 AGGCCTTTAAGACATTTCAGACAAT 58.987 36.000 0.00 0.00 0.00 2.71
5716 6177 5.385198 AGGCCTTTAAGACATTTCAGACAA 58.615 37.500 0.00 0.00 0.00 3.18
5718 6179 5.966742 AAGGCCTTTAAGACATTTCAGAC 57.033 39.130 13.78 0.00 0.00 3.51
5719 6180 9.747898 TTTATAAGGCCTTTAAGACATTTCAGA 57.252 29.630 26.08 0.00 0.00 3.27
5724 6185 9.528489 TCACTTTTATAAGGCCTTTAAGACATT 57.472 29.630 26.08 0.00 35.61 2.71
5725 6186 9.528489 TTCACTTTTATAAGGCCTTTAAGACAT 57.472 29.630 26.08 12.46 35.61 3.06
5726 6187 8.789762 GTTCACTTTTATAAGGCCTTTAAGACA 58.210 33.333 26.08 4.20 35.61 3.41
5727 6188 8.789762 TGTTCACTTTTATAAGGCCTTTAAGAC 58.210 33.333 26.08 15.04 35.61 3.01
5729 6190 9.010029 TCTGTTCACTTTTATAAGGCCTTTAAG 57.990 33.333 26.08 21.73 35.61 1.85
5731 6192 7.610305 CCTCTGTTCACTTTTATAAGGCCTTTA 59.390 37.037 26.08 12.91 35.61 1.85
5734 6195 5.250774 TCCTCTGTTCACTTTTATAAGGCCT 59.749 40.000 0.00 0.00 35.61 5.19
5735 6196 5.497474 TCCTCTGTTCACTTTTATAAGGCC 58.503 41.667 0.00 0.00 35.61 5.19
5736 6197 6.655425 ACTTCCTCTGTTCACTTTTATAAGGC 59.345 38.462 0.00 0.00 35.61 4.35
5737 6198 9.152595 GTACTTCCTCTGTTCACTTTTATAAGG 57.847 37.037 0.00 0.00 35.61 2.69
5738 6199 9.930693 AGTACTTCCTCTGTTCACTTTTATAAG 57.069 33.333 0.00 0.00 37.40 1.73
5743 6204 9.628500 AAATTAGTACTTCCTCTGTTCACTTTT 57.372 29.630 0.00 0.00 0.00 2.27
5747 6208 8.603242 TGAAAATTAGTACTTCCTCTGTTCAC 57.397 34.615 0.00 0.00 0.00 3.18
5749 6210 7.604545 AGCTGAAAATTAGTACTTCCTCTGTTC 59.395 37.037 0.00 0.00 0.00 3.18
5750 6211 7.454225 AGCTGAAAATTAGTACTTCCTCTGTT 58.546 34.615 0.00 0.00 0.00 3.16
5751 6212 7.010339 AGCTGAAAATTAGTACTTCCTCTGT 57.990 36.000 0.00 0.00 0.00 3.41
5752 6213 7.148340 CCAAGCTGAAAATTAGTACTTCCTCTG 60.148 40.741 0.00 0.00 0.00 3.35
5754 6215 6.879458 TCCAAGCTGAAAATTAGTACTTCCTC 59.121 38.462 0.00 0.00 0.00 3.71
5755 6216 6.779860 TCCAAGCTGAAAATTAGTACTTCCT 58.220 36.000 0.00 0.00 0.00 3.36
5756 6217 6.094186 CCTCCAAGCTGAAAATTAGTACTTCC 59.906 42.308 0.00 0.00 0.00 3.46
5757 6218 6.655425 ACCTCCAAGCTGAAAATTAGTACTTC 59.345 38.462 0.00 0.00 0.00 3.01
5758 6219 6.543735 ACCTCCAAGCTGAAAATTAGTACTT 58.456 36.000 0.00 0.00 0.00 2.24
5760 6221 6.819397 AACCTCCAAGCTGAAAATTAGTAC 57.181 37.500 0.00 0.00 0.00 2.73
5765 6333 5.357742 AACAAACCTCCAAGCTGAAAATT 57.642 34.783 0.00 0.00 0.00 1.82
5806 6376 7.521529 TCGAGCTGAGAAATAAAATTGTCTTG 58.478 34.615 0.00 0.00 0.00 3.02
5852 6422 3.441222 TGTACGCGAGGTCATTCTTCTTA 59.559 43.478 15.93 0.00 0.00 2.10
5863 6433 0.590195 GTATCGGATGTACGCGAGGT 59.410 55.000 15.93 0.00 0.00 3.85
5864 6434 0.589708 TGTATCGGATGTACGCGAGG 59.410 55.000 15.93 0.00 0.00 4.63
5869 6439 6.675026 TCTTAATCCTTGTATCGGATGTACG 58.325 40.000 0.00 0.00 40.31 3.67
5876 6446 6.406692 TTCCTCTCTTAATCCTTGTATCGG 57.593 41.667 0.00 0.00 0.00 4.18
5903 6475 6.015350 ACATTGGTCTATCCCTAGTTATGTCG 60.015 42.308 0.00 0.00 34.77 4.35
6073 6652 5.567037 TGGGGTATTGGAGTTAGATGATG 57.433 43.478 0.00 0.00 0.00 3.07
6074 6653 5.456763 GCTTGGGGTATTGGAGTTAGATGAT 60.457 44.000 0.00 0.00 0.00 2.45
6075 6654 4.141482 GCTTGGGGTATTGGAGTTAGATGA 60.141 45.833 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.