Multiple sequence alignment - TraesCS7D01G511900

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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 TraesCS7D01G511900 chr7D 100.000 3642 0 0 1 3642 613798361 613802002 0.000000e+00 6726.0
1 TraesCS7D01G511900 chr7D 90.354 1721 132 15 941 2644 613828185 613826482 0.000000e+00 2228.0
2 TraesCS7D01G511900 chr7D 90.164 61 6 0 720 780 402509301 402509361 3.010000e-11 80.5
3 TraesCS7D01G511900 chr7D 85.366 82 4 6 719 794 81228162 81228241 1.080000e-10 78.7
4 TraesCS7D01G511900 chr7D 85.366 82 4 6 719 794 81644247 81644326 1.080000e-10 78.7
5 TraesCS7D01G511900 chr7D 84.146 82 5 6 719 794 81375688 81375609 5.040000e-09 73.1
6 TraesCS7D01G511900 chr7A 92.517 2646 142 28 720 3326 705677971 705680599 0.000000e+00 3738.0
7 TraesCS7D01G511900 chr7A 91.304 437 28 7 856 1284 705595066 705595500 4.050000e-164 588.0
8 TraesCS7D01G511900 chr7A 83.284 341 31 10 1 340 705676961 705677276 1.280000e-74 291.0
9 TraesCS7D01G511900 chr7A 79.615 260 38 7 455 711 705677684 705677931 4.830000e-39 172.0
10 TraesCS7D01G511900 chr7B 91.701 2458 128 30 860 3267 705109901 705112332 0.000000e+00 3339.0
11 TraesCS7D01G511900 chr7B 91.080 1704 122 14 954 2644 705128018 705126332 0.000000e+00 2278.0
12 TraesCS7D01G511900 chr7B 91.221 262 22 1 3322 3583 598296145 598296405 4.470000e-94 355.0
13 TraesCS7D01G511900 chr7B 81.855 248 40 4 2668 2914 329794769 329795012 1.710000e-48 204.0
14 TraesCS7D01G511900 chr7B 86.243 189 20 5 408 595 705109641 705109824 2.220000e-47 200.0
15 TraesCS7D01G511900 chr7B 84.524 84 13 0 2785 2868 207908412 207908495 2.330000e-12 84.2
16 TraesCS7D01G511900 chr7B 100.000 28 0 0 833 860 705109813 705109840 7.000000e-03 52.8
17 TraesCS7D01G511900 chr5B 86.752 936 109 9 972 1904 586534218 586535141 0.000000e+00 1027.0
18 TraesCS7D01G511900 chr5B 85.886 666 78 10 1985 2650 586535344 586535993 0.000000e+00 695.0
19 TraesCS7D01G511900 chr5B 84.314 102 12 4 609 707 490126193 490126093 2.990000e-16 97.1
20 TraesCS7D01G511900 chr5D 84.926 816 95 16 948 1743 478689807 478689000 0.000000e+00 800.0
21 TraesCS7D01G511900 chr5D 84.441 662 82 13 1984 2635 478598797 478599447 1.850000e-177 632.0
22 TraesCS7D01G511900 chr5D 86.989 538 70 0 1985 2522 478688986 478688449 1.120000e-169 606.0
23 TraesCS7D01G511900 chr5D 90.602 266 23 2 3318 3583 193041030 193041293 5.790000e-93 351.0
24 TraesCS7D01G511900 chr1A 84.029 814 111 15 1100 1902 560881509 560880704 0.000000e+00 765.0
25 TraesCS7D01G511900 chr1A 84.083 289 41 4 3036 3320 581212828 581213115 1.290000e-69 274.0
26 TraesCS7D01G511900 chr3A 83.666 802 104 14 1109 1904 52963186 52963966 0.000000e+00 730.0
27 TraesCS7D01G511900 chr3A 80.360 667 113 3 1976 2642 52981935 52982583 1.180000e-134 490.0
28 TraesCS7D01G511900 chr1D 83.149 813 120 12 1100 1902 467863292 467862487 0.000000e+00 726.0
29 TraesCS7D01G511900 chr1D 90.909 264 23 1 3324 3587 365804560 365804822 1.610000e-93 353.0
30 TraesCS7D01G511900 chr3D 79.254 670 119 4 1975 2642 41055112 41055763 1.990000e-122 449.0
31 TraesCS7D01G511900 chr4D 91.571 261 21 1 3323 3583 3381090 3381349 3.460000e-95 359.0
32 TraesCS7D01G511900 chr5A 91.288 264 20 2 3322 3583 34841903 34842165 1.240000e-94 357.0
33 TraesCS7D01G511900 chr5A 95.349 43 2 0 722 764 582982638 582982680 6.530000e-08 69.4
34 TraesCS7D01G511900 chr2D 91.255 263 21 2 3322 3583 70277788 70277527 1.240000e-94 357.0
35 TraesCS7D01G511900 chr2D 91.221 262 22 1 3324 3585 112870950 112871210 4.470000e-94 355.0
36 TraesCS7D01G511900 chr2B 91.221 262 22 1 3322 3583 166592115 166592375 4.470000e-94 355.0
37 TraesCS7D01G511900 chr2B 81.818 231 38 1 2675 2901 134377757 134377527 1.330000e-44 191.0
38 TraesCS7D01G511900 chr2B 82.673 202 34 1 2668 2869 518584762 518584962 1.040000e-40 178.0
39 TraesCS7D01G511900 chr2B 84.211 95 9 6 616 706 778472268 778472176 1.800000e-13 87.9
40 TraesCS7D01G511900 chr6A 90.909 264 23 1 3323 3586 138271294 138271032 1.610000e-93 353.0
41 TraesCS7D01G511900 chr2A 84.559 272 33 5 3057 3320 3506955 3506685 1.000000e-65 261.0
42 TraesCS7D01G511900 chr2A 79.787 94 17 2 616 707 764891351 764891258 2.350000e-07 67.6
43 TraesCS7D01G511900 chr4A 79.894 189 33 5 2682 2867 271812345 271812531 2.280000e-27 134.0
44 TraesCS7D01G511900 chr4A 80.702 114 14 3 719 824 546476829 546476942 8.380000e-12 82.4
45 TraesCS7D01G511900 chr3B 81.897 116 13 3 719 826 512937796 512937681 1.390000e-14 91.6
46 TraesCS7D01G511900 chr6D 79.825 114 14 6 719 824 350062314 350062426 1.400000e-09 75.0
47 TraesCS7D01G511900 chr6D 85.714 56 7 1 719 773 71008835 71008780 1.410000e-04 58.4
48 TraesCS7D01G511900 chr4B 79.091 110 21 2 599 706 453261968 453261859 1.400000e-09 75.0


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 TraesCS7D01G511900 chr7D 613798361 613802002 3641 False 6726.000000 6726 100.000000 1 3642 1 chr7D.!!$F4 3641
1 TraesCS7D01G511900 chr7D 613826482 613828185 1703 True 2228.000000 2228 90.354000 941 2644 1 chr7D.!!$R2 1703
2 TraesCS7D01G511900 chr7A 705676961 705680599 3638 False 1400.333333 3738 85.138667 1 3326 3 chr7A.!!$F2 3325
3 TraesCS7D01G511900 chr7B 705126332 705128018 1686 True 2278.000000 2278 91.080000 954 2644 1 chr7B.!!$R1 1690
4 TraesCS7D01G511900 chr7B 705109641 705112332 2691 False 1197.266667 3339 92.648000 408 3267 3 chr7B.!!$F4 2859
5 TraesCS7D01G511900 chr5B 586534218 586535993 1775 False 861.000000 1027 86.319000 972 2650 2 chr5B.!!$F1 1678
6 TraesCS7D01G511900 chr5D 478688449 478689807 1358 True 703.000000 800 85.957500 948 2522 2 chr5D.!!$R1 1574
7 TraesCS7D01G511900 chr5D 478598797 478599447 650 False 632.000000 632 84.441000 1984 2635 1 chr5D.!!$F2 651
8 TraesCS7D01G511900 chr1A 560880704 560881509 805 True 765.000000 765 84.029000 1100 1902 1 chr1A.!!$R1 802
9 TraesCS7D01G511900 chr3A 52963186 52963966 780 False 730.000000 730 83.666000 1109 1904 1 chr3A.!!$F1 795
10 TraesCS7D01G511900 chr3A 52981935 52982583 648 False 490.000000 490 80.360000 1976 2642 1 chr3A.!!$F2 666
11 TraesCS7D01G511900 chr1D 467862487 467863292 805 True 726.000000 726 83.149000 1100 1902 1 chr1D.!!$R1 802
12 TraesCS7D01G511900 chr3D 41055112 41055763 651 False 449.000000 449 79.254000 1975 2642 1 chr3D.!!$F1 667

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
524 863 0.034863 TTATTTGGACGGTGGCCTCC 60.035 55.0 14.20 14.20 0.0 4.30 F
814 1192 0.319555 CATAGGACCGGGTGTATGCG 60.320 60.0 3.30 0.00 0.0 4.73 F
819 1197 0.320421 GACCGGGTGTATGCGCATAT 60.320 55.0 31.14 14.82 0.0 1.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1904 2373 1.137513 GATATGTACGCGTTGGAGGC 58.862 55.0 20.78 0.0 0.00 4.70 R
2546 3155 0.389948 GCCTCGGTCATGTCGAACTT 60.390 55.0 13.00 0.0 36.15 2.66 R
2661 3282 6.459923 AGTAGACTCTTTTTAAGGAGCACTG 58.540 40.0 1.93 0.0 33.29 3.66 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
20 22 1.927487 TAAGCACAACTCGACCCCTA 58.073 50.000 0.00 0.00 0.00 3.53
32 34 2.516930 CCCCTAAGGCATGCGGTG 60.517 66.667 12.44 1.63 0.00 4.94
74 76 3.432252 CCTTGAGTTTTGCTACACCTACG 59.568 47.826 0.00 0.00 0.00 3.51
90 92 1.612463 CTACGAAGGATTACGAGGGGG 59.388 57.143 0.00 0.00 0.00 5.40
139 141 0.673644 GAGCTTTAGTGGAGGCGCAA 60.674 55.000 10.83 0.00 0.00 4.85
152 154 2.597217 CGCAAAGCCCACCCTGAA 60.597 61.111 0.00 0.00 0.00 3.02
153 155 2.199652 CGCAAAGCCCACCCTGAAA 61.200 57.895 0.00 0.00 0.00 2.69
154 156 1.367471 GCAAAGCCCACCCTGAAAC 59.633 57.895 0.00 0.00 0.00 2.78
155 157 1.115326 GCAAAGCCCACCCTGAAACT 61.115 55.000 0.00 0.00 0.00 2.66
156 158 0.961753 CAAAGCCCACCCTGAAACTC 59.038 55.000 0.00 0.00 0.00 3.01
157 159 0.555769 AAAGCCCACCCTGAAACTCA 59.444 50.000 0.00 0.00 0.00 3.41
158 160 0.555769 AAGCCCACCCTGAAACTCAA 59.444 50.000 0.00 0.00 0.00 3.02
159 161 0.111253 AGCCCACCCTGAAACTCAAG 59.889 55.000 0.00 0.00 0.00 3.02
160 162 0.895559 GCCCACCCTGAAACTCAAGG 60.896 60.000 0.00 0.00 34.17 3.61
161 163 0.895559 CCCACCCTGAAACTCAAGGC 60.896 60.000 0.00 0.00 31.08 4.35
162 164 1.237285 CCACCCTGAAACTCAAGGCG 61.237 60.000 0.00 0.00 31.08 5.52
163 165 0.250295 CACCCTGAAACTCAAGGCGA 60.250 55.000 0.00 0.00 31.08 5.54
164 166 0.693049 ACCCTGAAACTCAAGGCGAT 59.307 50.000 0.00 0.00 31.08 4.58
165 167 1.089920 CCCTGAAACTCAAGGCGATG 58.910 55.000 0.00 0.00 0.00 3.84
166 168 1.611673 CCCTGAAACTCAAGGCGATGT 60.612 52.381 0.00 0.00 0.00 3.06
167 169 2.154462 CCTGAAACTCAAGGCGATGTT 58.846 47.619 0.00 0.00 0.00 2.71
168 170 2.554032 CCTGAAACTCAAGGCGATGTTT 59.446 45.455 0.00 0.00 35.64 2.83
187 189 3.405823 TTGGTTAAGGTGTAAGGGACG 57.594 47.619 0.00 0.00 0.00 4.79
244 246 2.080286 TTTTCGCCCTCTTCTCTTCG 57.920 50.000 0.00 0.00 0.00 3.79
245 247 0.389948 TTTCGCCCTCTTCTCTTCGC 60.390 55.000 0.00 0.00 0.00 4.70
247 249 1.226831 CGCCCTCTTCTCTTCGCTC 60.227 63.158 0.00 0.00 0.00 5.03
255 257 1.136110 CTTCTCTTCGCTCCCTCCTTC 59.864 57.143 0.00 0.00 0.00 3.46
263 265 1.728068 GCTCCCTCCTTCGAGAAAAC 58.272 55.000 0.00 0.00 38.52 2.43
264 266 1.997669 CTCCCTCCTTCGAGAAAACG 58.002 55.000 0.00 0.00 38.52 3.60
269 271 1.000506 CTCCTTCGAGAAAACGGACCA 59.999 52.381 0.00 0.00 38.52 4.02
274 276 0.317479 CGAGAAAACGGACCACCTCT 59.683 55.000 0.00 0.00 0.00 3.69
276 278 0.396811 AGAAAACGGACCACCTCTGG 59.603 55.000 0.00 0.00 44.26 3.86
286 288 0.890996 CCACCTCTGGTTGACAAGGC 60.891 60.000 0.00 0.00 31.02 4.35
290 292 0.535780 CTCTGGTTGACAAGGCAGCA 60.536 55.000 0.00 0.00 0.00 4.41
294 296 0.038892 GGTTGACAAGGCAGCACATG 60.039 55.000 0.00 0.00 0.00 3.21
313 315 1.751351 TGACTAGAATCTCGCAGGTGG 59.249 52.381 0.00 0.00 0.00 4.61
342 680 1.202964 GGGCCTCCTACTCCTAGTCTC 60.203 61.905 0.84 0.00 0.00 3.36
349 687 2.553466 CCTACTCCTAGTCTCCGGATGG 60.553 59.091 3.57 2.82 0.00 3.51
364 702 1.565305 GATGGTAGCACAAGAGAGCG 58.435 55.000 0.00 0.00 36.39 5.03
369 707 1.135083 GTAGCACAAGAGAGCGGCTAA 60.135 52.381 0.60 0.00 38.64 3.09
371 709 0.108615 GCACAAGAGAGCGGCTAAGA 60.109 55.000 0.60 0.00 0.00 2.10
372 710 1.919918 CACAAGAGAGCGGCTAAGAG 58.080 55.000 0.60 0.00 0.00 2.85
373 711 0.174617 ACAAGAGAGCGGCTAAGAGC 59.825 55.000 0.60 0.00 41.46 4.09
374 712 0.174389 CAAGAGAGCGGCTAAGAGCA 59.826 55.000 0.60 0.00 44.75 4.26
375 713 1.118838 AAGAGAGCGGCTAAGAGCAT 58.881 50.000 0.60 0.00 44.75 3.79
376 714 0.673437 AGAGAGCGGCTAAGAGCATC 59.327 55.000 0.60 0.00 44.75 3.91
403 741 0.736325 GCGCGCCTCATATCCGTAAT 60.736 55.000 23.24 0.00 0.00 1.89
406 744 2.096980 CGCGCCTCATATCCGTAATAGA 59.903 50.000 0.00 0.00 0.00 1.98
425 763 1.141053 GATGCCCTTTGGACTACCGAT 59.859 52.381 0.00 0.00 39.42 4.18
427 765 0.252197 GCCCTTTGGACTACCGATGT 59.748 55.000 0.00 0.00 39.42 3.06
428 766 2.012051 GCCCTTTGGACTACCGATGTG 61.012 57.143 0.00 0.00 39.42 3.21
429 767 1.278127 CCCTTTGGACTACCGATGTGT 59.722 52.381 0.00 0.00 39.42 3.72
430 768 2.346803 CCTTTGGACTACCGATGTGTG 58.653 52.381 0.00 0.00 39.42 3.82
431 769 2.028476 CCTTTGGACTACCGATGTGTGA 60.028 50.000 0.00 0.00 39.42 3.58
432 770 3.556213 CCTTTGGACTACCGATGTGTGAA 60.556 47.826 0.00 0.00 39.42 3.18
434 772 3.973206 TGGACTACCGATGTGTGAATT 57.027 42.857 0.00 0.00 39.42 2.17
437 775 3.374058 GGACTACCGATGTGTGAATTTGG 59.626 47.826 0.00 0.00 0.00 3.28
438 776 4.250464 GACTACCGATGTGTGAATTTGGA 58.750 43.478 0.00 0.00 0.00 3.53
439 777 4.843728 ACTACCGATGTGTGAATTTGGAT 58.156 39.130 0.00 0.00 0.00 3.41
440 778 4.635765 ACTACCGATGTGTGAATTTGGATG 59.364 41.667 0.00 0.00 0.00 3.51
441 779 3.684908 ACCGATGTGTGAATTTGGATGA 58.315 40.909 0.00 0.00 0.00 2.92
442 780 4.272489 ACCGATGTGTGAATTTGGATGAT 58.728 39.130 0.00 0.00 0.00 2.45
443 781 4.096833 ACCGATGTGTGAATTTGGATGATG 59.903 41.667 0.00 0.00 0.00 3.07
444 782 4.336153 CCGATGTGTGAATTTGGATGATGA 59.664 41.667 0.00 0.00 0.00 2.92
445 783 5.268544 CGATGTGTGAATTTGGATGATGAC 58.731 41.667 0.00 0.00 0.00 3.06
446 784 5.065602 CGATGTGTGAATTTGGATGATGACT 59.934 40.000 0.00 0.00 0.00 3.41
450 788 4.701651 TGTGAATTTGGATGATGACTGACC 59.298 41.667 0.00 0.00 0.00 4.02
516 855 7.419204 TGTGTTCTTACTTTTTATTTGGACGG 58.581 34.615 0.00 0.00 0.00 4.79
521 860 2.297880 ACTTTTTATTTGGACGGTGGCC 59.702 45.455 0.00 0.00 0.00 5.36
524 863 0.034863 TTATTTGGACGGTGGCCTCC 60.035 55.000 14.20 14.20 0.00 4.30
537 876 3.776969 GGTGGCCTCCATCATCATATCTA 59.223 47.826 19.19 0.00 34.21 1.98
563 902 5.163468 TGGAGATGCTCTGAGATTTGAGTAC 60.163 44.000 9.28 0.00 33.22 2.73
569 908 4.991056 GCTCTGAGATTTGAGTACACAACA 59.009 41.667 9.28 0.21 33.22 3.33
578 917 9.736023 AGATTTGAGTACACAACATTCTTTTTC 57.264 29.630 5.14 0.00 0.00 2.29
582 921 7.184106 TGAGTACACAACATTCTTTTTCGAAC 58.816 34.615 0.00 0.00 0.00 3.95
585 924 6.189677 ACACAACATTCTTTTTCGAACAGA 57.810 33.333 0.00 0.00 0.00 3.41
595 934 9.801873 ATTCTTTTTCGAACAGAAGAAATTCAA 57.198 25.926 23.28 9.41 40.34 2.69
597 936 8.240682 TCTTTTTCGAACAGAAGAAATTCAACA 58.759 29.630 12.75 0.00 40.40 3.33
604 943 7.462724 CGAACAGAAGAAATTCAACAAACCAAC 60.463 37.037 0.00 0.00 0.00 3.77
606 945 5.231991 CAGAAGAAATTCAACAAACCAACCG 59.768 40.000 0.00 0.00 0.00 4.44
607 946 4.993029 AGAAATTCAACAAACCAACCGA 57.007 36.364 0.00 0.00 0.00 4.69
614 953 6.939132 TTCAACAAACCAACCGATAGTTAA 57.061 33.333 0.00 0.00 36.18 2.01
618 957 6.262193 ACAAACCAACCGATAGTTAAATGG 57.738 37.500 0.00 0.00 36.18 3.16
624 963 6.070078 ACCAACCGATAGTTAAATGGTTAGGA 60.070 38.462 13.70 0.00 40.80 2.94
625 964 6.996282 CCAACCGATAGTTAAATGGTTAGGAT 59.004 38.462 0.00 0.00 40.80 3.24
626 965 7.041372 CCAACCGATAGTTAAATGGTTAGGATG 60.041 40.741 0.00 0.00 40.80 3.51
636 975 4.755266 ATGGTTAGGATGACAGTGGTAC 57.245 45.455 0.00 0.00 0.00 3.34
637 976 2.835764 TGGTTAGGATGACAGTGGTACC 59.164 50.000 4.43 4.43 0.00 3.34
639 978 2.169978 GTTAGGATGACAGTGGTACCCC 59.830 54.545 10.07 0.00 0.00 4.95
640 979 0.620700 AGGATGACAGTGGTACCCCC 60.621 60.000 10.07 0.00 0.00 5.40
641 980 0.912487 GGATGACAGTGGTACCCCCA 60.912 60.000 10.07 0.36 42.51 4.96
651 990 0.546598 GGTACCCCCAACTCATCAGG 59.453 60.000 0.00 0.00 0.00 3.86
652 991 0.546598 GTACCCCCAACTCATCAGGG 59.453 60.000 0.00 0.00 43.88 4.45
660 999 3.490348 CCAACTCATCAGGGTTCAAGTT 58.510 45.455 0.00 0.00 0.00 2.66
661 1000 3.503748 CCAACTCATCAGGGTTCAAGTTC 59.496 47.826 0.00 0.00 0.00 3.01
670 1009 1.476833 GGGTTCAAGTTCTGGTGCTCA 60.477 52.381 0.00 0.00 0.00 4.26
678 1017 4.833478 AGTTCTGGTGCTCACATTATCT 57.167 40.909 2.21 0.00 0.00 1.98
684 1024 5.819379 TCTGGTGCTCACATTATCTTGATTC 59.181 40.000 2.21 0.00 0.00 2.52
708 1048 2.621338 TCAGGATTTCTGACGATGCAC 58.379 47.619 0.00 0.00 46.71 4.57
709 1049 1.325640 CAGGATTTCTGACGATGCACG 59.674 52.381 7.07 7.07 46.18 5.34
738 1110 5.147330 TGTACGGTGACTTCATCAATCTT 57.853 39.130 0.00 0.00 39.72 2.40
741 1113 6.811665 TGTACGGTGACTTCATCAATCTTAAG 59.188 38.462 0.00 0.00 39.72 1.85
752 1124 7.838771 TCATCAATCTTAAGATGATATGGCG 57.161 36.000 18.61 10.61 44.04 5.69
760 1132 1.274728 AGATGATATGGCGGCTCAGTC 59.725 52.381 11.43 3.98 0.00 3.51
764 1136 2.139118 GATATGGCGGCTCAGTCTTTC 58.861 52.381 11.43 0.00 0.00 2.62
768 1140 1.355066 GGCGGCTCAGTCTTTCGAAG 61.355 60.000 0.00 0.00 0.00 3.79
769 1141 1.355066 GCGGCTCAGTCTTTCGAAGG 61.355 60.000 0.00 0.00 0.00 3.46
773 1145 1.063806 CTCAGTCTTTCGAAGGTGCG 58.936 55.000 7.20 0.00 0.00 5.34
799 1177 4.371786 AGGATGTGCGTGTGTATTCATAG 58.628 43.478 0.00 0.00 0.00 2.23
801 1179 3.878160 TGTGCGTGTGTATTCATAGGA 57.122 42.857 0.00 0.00 0.00 2.94
802 1180 3.517602 TGTGCGTGTGTATTCATAGGAC 58.482 45.455 0.00 0.00 0.00 3.85
803 1181 2.864343 GTGCGTGTGTATTCATAGGACC 59.136 50.000 0.00 0.00 0.00 4.46
804 1182 2.124903 GCGTGTGTATTCATAGGACCG 58.875 52.381 0.00 0.00 0.00 4.79
811 1189 4.282703 GTGTATTCATAGGACCGGGTGTAT 59.717 45.833 3.30 0.00 0.00 2.29
812 1190 4.282449 TGTATTCATAGGACCGGGTGTATG 59.718 45.833 3.30 11.74 0.00 2.39
814 1192 0.319555 CATAGGACCGGGTGTATGCG 60.320 60.000 3.30 0.00 0.00 4.73
815 1193 2.095978 ATAGGACCGGGTGTATGCGC 62.096 60.000 3.30 0.00 0.00 6.09
816 1194 4.460683 GGACCGGGTGTATGCGCA 62.461 66.667 14.96 14.96 0.00 6.09
817 1195 2.203015 GACCGGGTGTATGCGCAT 60.203 61.111 28.23 28.23 0.00 4.73
818 1196 1.068417 GACCGGGTGTATGCGCATA 59.932 57.895 25.78 25.78 0.00 3.14
819 1197 0.320421 GACCGGGTGTATGCGCATAT 60.320 55.000 31.14 14.82 0.00 1.78
820 1198 0.970640 ACCGGGTGTATGCGCATATA 59.029 50.000 31.14 26.17 0.00 0.86
821 1199 1.553248 ACCGGGTGTATGCGCATATAT 59.447 47.619 31.14 11.92 0.00 0.86
822 1200 2.761767 ACCGGGTGTATGCGCATATATA 59.238 45.455 31.14 18.33 0.00 0.86
823 1201 3.386726 ACCGGGTGTATGCGCATATATAT 59.613 43.478 31.14 8.90 0.00 0.86
880 1319 2.820197 GTCTTTTGTCCATTCCTCCACC 59.180 50.000 0.00 0.00 0.00 4.61
1843 2312 2.061220 CTCCTGAGGGTGCAGAACA 58.939 57.895 0.00 0.00 38.14 3.18
1904 2373 0.924090 GCCGTCATCTTCGTAAGCAG 59.076 55.000 0.00 0.00 37.18 4.24
2661 3282 2.932614 AGCTAGTTGATTCACGTGCATC 59.067 45.455 19.53 19.53 0.00 3.91
2662 3283 2.672874 GCTAGTTGATTCACGTGCATCA 59.327 45.455 24.08 24.08 0.00 3.07
2681 3311 6.175712 CATCAGTGCTCCTTAAAAAGAGTC 57.824 41.667 0.00 0.00 0.00 3.36
2919 3560 2.420058 AAAAGGAGGAAGTATGCGGG 57.580 50.000 0.00 0.00 0.00 6.13
2935 3576 1.794222 GGGAAACAAGCCGTCATCG 59.206 57.895 0.00 0.00 0.00 3.84
3014 3659 2.951229 AACGGGAGATGGACTTGTTT 57.049 45.000 0.00 0.00 0.00 2.83
3075 3720 0.398098 CTACCGGGTAGTGGGATGGT 60.398 60.000 23.36 0.00 32.09 3.55
3095 3740 3.886505 GGTGCATATTTCGTTTGGGGATA 59.113 43.478 0.00 0.00 0.00 2.59
3120 3765 5.171476 GTGCATGTATCGCTCTATTATGGT 58.829 41.667 0.00 0.00 0.00 3.55
3183 3828 6.757947 CCTTCTCTCTTCTTCAATCAAGCTAG 59.242 42.308 0.00 0.00 31.26 3.42
3246 3891 1.689273 GAAGCCCCACGATAGAGTGAT 59.311 52.381 0.00 0.00 44.43 3.06
3293 3939 5.034200 AGTAGTATTACATCCCACCAACCA 58.966 41.667 0.00 0.00 31.96 3.67
3302 3948 4.904853 ACATCCCACCAACCAATACTTTTT 59.095 37.500 0.00 0.00 0.00 1.94
3305 3951 5.707495 TCCCACCAACCAATACTTTTTAGT 58.293 37.500 0.00 0.00 0.00 2.24
3307 3953 5.047590 CCCACCAACCAATACTTTTTAGTCC 60.048 44.000 0.00 0.00 0.00 3.85
3320 3968 6.665465 ACTTTTTAGTCCGAACATAGTTTGC 58.335 36.000 0.00 0.00 0.00 3.68
3326 3974 5.488341 AGTCCGAACATAGTTTGCAGTATT 58.512 37.500 0.00 0.00 0.00 1.89
3327 3975 5.581085 AGTCCGAACATAGTTTGCAGTATTC 59.419 40.000 0.00 0.00 0.00 1.75
3328 3976 4.873827 TCCGAACATAGTTTGCAGTATTCC 59.126 41.667 0.00 0.00 0.00 3.01
3329 3977 4.035208 CCGAACATAGTTTGCAGTATTCCC 59.965 45.833 0.00 0.00 0.00 3.97
3330 3978 4.876107 CGAACATAGTTTGCAGTATTCCCT 59.124 41.667 0.00 0.00 0.00 4.20
3331 3979 5.006746 CGAACATAGTTTGCAGTATTCCCTC 59.993 44.000 0.00 0.00 0.00 4.30
3332 3980 4.781934 ACATAGTTTGCAGTATTCCCTCC 58.218 43.478 0.00 0.00 0.00 4.30
3333 3981 4.227300 ACATAGTTTGCAGTATTCCCTCCA 59.773 41.667 0.00 0.00 0.00 3.86
3334 3982 5.103940 ACATAGTTTGCAGTATTCCCTCCAT 60.104 40.000 0.00 0.00 0.00 3.41
3335 3983 4.322057 AGTTTGCAGTATTCCCTCCATT 57.678 40.909 0.00 0.00 0.00 3.16
3336 3984 4.677182 AGTTTGCAGTATTCCCTCCATTT 58.323 39.130 0.00 0.00 0.00 2.32
3337 3985 4.706962 AGTTTGCAGTATTCCCTCCATTTC 59.293 41.667 0.00 0.00 0.00 2.17
3338 3986 4.591321 TTGCAGTATTCCCTCCATTTCT 57.409 40.909 0.00 0.00 0.00 2.52
3339 3987 4.591321 TGCAGTATTCCCTCCATTTCTT 57.409 40.909 0.00 0.00 0.00 2.52
3340 3988 4.934356 TGCAGTATTCCCTCCATTTCTTT 58.066 39.130 0.00 0.00 0.00 2.52
3341 3989 5.332743 TGCAGTATTCCCTCCATTTCTTTT 58.667 37.500 0.00 0.00 0.00 2.27
3342 3990 5.779771 TGCAGTATTCCCTCCATTTCTTTTT 59.220 36.000 0.00 0.00 0.00 1.94
3343 3991 6.951198 TGCAGTATTCCCTCCATTTCTTTTTA 59.049 34.615 0.00 0.00 0.00 1.52
3344 3992 7.122650 TGCAGTATTCCCTCCATTTCTTTTTAG 59.877 37.037 0.00 0.00 0.00 1.85
3345 3993 7.122799 GCAGTATTCCCTCCATTTCTTTTTAGT 59.877 37.037 0.00 0.00 0.00 2.24
3346 3994 8.678199 CAGTATTCCCTCCATTTCTTTTTAGTC 58.322 37.037 0.00 0.00 0.00 2.59
3347 3995 8.615705 AGTATTCCCTCCATTTCTTTTTAGTCT 58.384 33.333 0.00 0.00 0.00 3.24
3348 3996 7.709149 ATTCCCTCCATTTCTTTTTAGTCTG 57.291 36.000 0.00 0.00 0.00 3.51
3349 3997 5.010282 TCCCTCCATTTCTTTTTAGTCTGC 58.990 41.667 0.00 0.00 0.00 4.26
3350 3998 4.766891 CCCTCCATTTCTTTTTAGTCTGCA 59.233 41.667 0.00 0.00 0.00 4.41
3351 3999 5.420104 CCCTCCATTTCTTTTTAGTCTGCAT 59.580 40.000 0.00 0.00 0.00 3.96
3352 4000 6.603201 CCCTCCATTTCTTTTTAGTCTGCATA 59.397 38.462 0.00 0.00 0.00 3.14
3353 4001 7.286316 CCCTCCATTTCTTTTTAGTCTGCATAT 59.714 37.037 0.00 0.00 0.00 1.78
3354 4002 9.342308 CCTCCATTTCTTTTTAGTCTGCATATA 57.658 33.333 0.00 0.00 0.00 0.86
3369 4017 8.806146 AGTCTGCATATAAAAATTGGTCAAAGT 58.194 29.630 0.00 0.00 0.00 2.66
3370 4018 9.076596 GTCTGCATATAAAAATTGGTCAAAGTC 57.923 33.333 0.00 0.00 0.00 3.01
3371 4019 8.801299 TCTGCATATAAAAATTGGTCAAAGTCA 58.199 29.630 0.00 0.00 0.00 3.41
3372 4020 9.421806 CTGCATATAAAAATTGGTCAAAGTCAA 57.578 29.630 0.00 0.00 0.00 3.18
3373 4021 9.770097 TGCATATAAAAATTGGTCAAAGTCAAA 57.230 25.926 0.00 0.00 0.00 2.69
3427 4075 9.932207 AAAAAGACATCAAGATTTGCAATATGA 57.068 25.926 0.00 3.22 0.00 2.15
3428 4076 9.932207 AAAAGACATCAAGATTTGCAATATGAA 57.068 25.926 0.00 0.00 0.00 2.57
3429 4077 9.932207 AAAGACATCAAGATTTGCAATATGAAA 57.068 25.926 0.00 0.00 0.00 2.69
3431 4079 9.745880 AGACATCAAGATTTGCAATATGAAATC 57.254 29.630 0.00 0.00 38.38 2.17
3432 4080 9.524106 GACATCAAGATTTGCAATATGAAATCA 57.476 29.630 0.00 0.00 39.88 2.57
3433 4081 9.878667 ACATCAAGATTTGCAATATGAAATCAA 57.121 25.926 0.00 0.00 39.88 2.57
3523 4171 7.876896 TTTGTTTCTACAAAGTTGGTCAAAC 57.123 32.000 9.53 9.53 46.46 2.93
3580 4228 7.625828 ATGTAGATTAAAAAGAAACGGAGGG 57.374 36.000 0.00 0.00 0.00 4.30
3581 4229 6.771573 TGTAGATTAAAAAGAAACGGAGGGA 58.228 36.000 0.00 0.00 0.00 4.20
3582 4230 6.877322 TGTAGATTAAAAAGAAACGGAGGGAG 59.123 38.462 0.00 0.00 0.00 4.30
3583 4231 4.700692 AGATTAAAAAGAAACGGAGGGAGC 59.299 41.667 0.00 0.00 0.00 4.70
3584 4232 2.358322 AAAAAGAAACGGAGGGAGCA 57.642 45.000 0.00 0.00 0.00 4.26
3585 4233 2.586648 AAAAGAAACGGAGGGAGCAT 57.413 45.000 0.00 0.00 0.00 3.79
3586 4234 1.826385 AAAGAAACGGAGGGAGCATG 58.174 50.000 0.00 0.00 0.00 4.06
3587 4235 0.984230 AAGAAACGGAGGGAGCATGA 59.016 50.000 0.00 0.00 0.00 3.07
3588 4236 0.984230 AGAAACGGAGGGAGCATGAA 59.016 50.000 0.00 0.00 0.00 2.57
3589 4237 1.561542 AGAAACGGAGGGAGCATGAAT 59.438 47.619 0.00 0.00 0.00 2.57
3590 4238 2.025887 AGAAACGGAGGGAGCATGAATT 60.026 45.455 0.00 0.00 0.00 2.17
3591 4239 3.199946 AGAAACGGAGGGAGCATGAATTA 59.800 43.478 0.00 0.00 0.00 1.40
3592 4240 3.864789 AACGGAGGGAGCATGAATTAT 57.135 42.857 0.00 0.00 0.00 1.28
3593 4241 4.974645 AACGGAGGGAGCATGAATTATA 57.025 40.909 0.00 0.00 0.00 0.98
3594 4242 5.505181 AACGGAGGGAGCATGAATTATAT 57.495 39.130 0.00 0.00 0.00 0.86
3595 4243 4.836825 ACGGAGGGAGCATGAATTATATG 58.163 43.478 0.00 0.00 0.00 1.78
3596 4244 4.287067 ACGGAGGGAGCATGAATTATATGT 59.713 41.667 0.00 0.00 0.00 2.29
3597 4245 5.221925 ACGGAGGGAGCATGAATTATATGTT 60.222 40.000 0.00 0.00 0.00 2.71
3598 4246 5.707298 CGGAGGGAGCATGAATTATATGTTT 59.293 40.000 0.00 0.00 0.00 2.83
3599 4247 6.207417 CGGAGGGAGCATGAATTATATGTTTT 59.793 38.462 0.00 0.00 0.00 2.43
3600 4248 7.373493 GGAGGGAGCATGAATTATATGTTTTG 58.627 38.462 0.00 0.00 0.00 2.44
3601 4249 7.231317 GGAGGGAGCATGAATTATATGTTTTGA 59.769 37.037 0.00 0.00 0.00 2.69
3602 4250 8.537728 AGGGAGCATGAATTATATGTTTTGAA 57.462 30.769 0.00 0.00 0.00 2.69
3603 4251 8.416329 AGGGAGCATGAATTATATGTTTTGAAC 58.584 33.333 0.00 0.00 0.00 3.18
3604 4252 8.196771 GGGAGCATGAATTATATGTTTTGAACA 58.803 33.333 0.00 0.00 46.94 3.18
3605 4253 9.585099 GGAGCATGAATTATATGTTTTGAACAA 57.415 29.630 0.00 0.00 45.86 2.83
3625 4273 8.664798 TGAACAAAATATCAGATTGACTAACCG 58.335 33.333 0.00 0.00 0.00 4.44
3626 4274 8.561738 AACAAAATATCAGATTGACTAACCGT 57.438 30.769 0.00 0.00 0.00 4.83
3627 4275 8.561738 ACAAAATATCAGATTGACTAACCGTT 57.438 30.769 0.00 0.00 0.00 4.44
3628 4276 9.010029 ACAAAATATCAGATTGACTAACCGTTT 57.990 29.630 0.00 0.00 0.00 3.60
3629 4277 9.277565 CAAAATATCAGATTGACTAACCGTTTG 57.722 33.333 0.00 0.00 0.00 2.93
3630 4278 7.553881 AATATCAGATTGACTAACCGTTTGG 57.446 36.000 0.00 0.00 42.84 3.28
3631 4279 4.610605 TCAGATTGACTAACCGTTTGGA 57.389 40.909 0.00 0.00 39.21 3.53
3632 4280 5.160607 TCAGATTGACTAACCGTTTGGAT 57.839 39.130 0.00 0.00 39.21 3.41
3633 4281 6.288941 TCAGATTGACTAACCGTTTGGATA 57.711 37.500 0.00 0.00 39.21 2.59
3634 4282 6.884832 TCAGATTGACTAACCGTTTGGATAT 58.115 36.000 0.00 0.00 39.21 1.63
3635 4283 7.335627 TCAGATTGACTAACCGTTTGGATATT 58.664 34.615 0.00 0.00 39.21 1.28
3636 4284 8.479689 TCAGATTGACTAACCGTTTGGATATTA 58.520 33.333 0.00 0.00 39.21 0.98
3637 4285 8.765219 CAGATTGACTAACCGTTTGGATATTAG 58.235 37.037 0.00 0.00 39.21 1.73
3638 4286 8.483758 AGATTGACTAACCGTTTGGATATTAGT 58.516 33.333 0.00 0.00 37.31 2.24
3639 4287 9.754382 GATTGACTAACCGTTTGGATATTAGTA 57.246 33.333 0.00 0.00 35.70 1.82
3641 4289 9.537192 TTGACTAACCGTTTGGATATTAGTATG 57.463 33.333 0.00 0.00 35.70 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 40 2.058595 CAAGGAGGGGGTCGATCGT 61.059 63.158 15.94 0.00 0.00 3.73
39 41 1.739338 CTCAAGGAGGGGGTCGATCG 61.739 65.000 9.36 9.36 0.00 3.69
44 46 1.911057 CAAAACTCAAGGAGGGGGTC 58.089 55.000 0.00 0.00 33.35 4.46
49 51 2.814336 GGTGTAGCAAAACTCAAGGAGG 59.186 50.000 0.00 0.00 33.35 4.30
90 92 4.394920 ACACCGACAAATCATCACATAACC 59.605 41.667 0.00 0.00 0.00 2.85
139 141 0.555769 TTGAGTTTCAGGGTGGGCTT 59.444 50.000 0.00 0.00 0.00 4.35
144 146 2.247790 CGCCTTGAGTTTCAGGGTG 58.752 57.895 8.72 7.58 45.47 4.61
145 147 0.693049 ATCGCCTTGAGTTTCAGGGT 59.307 50.000 8.72 0.00 44.60 4.34
146 148 1.089920 CATCGCCTTGAGTTTCAGGG 58.910 55.000 3.09 3.09 45.46 4.45
147 149 1.813513 ACATCGCCTTGAGTTTCAGG 58.186 50.000 0.00 0.00 0.00 3.86
148 150 3.558505 CAAACATCGCCTTGAGTTTCAG 58.441 45.455 0.00 0.00 32.34 3.02
149 151 2.293122 CCAAACATCGCCTTGAGTTTCA 59.707 45.455 0.00 0.00 32.34 2.69
150 152 2.293399 ACCAAACATCGCCTTGAGTTTC 59.707 45.455 0.00 0.00 32.34 2.78
151 153 2.306847 ACCAAACATCGCCTTGAGTTT 58.693 42.857 0.00 0.00 34.78 2.66
152 154 1.981256 ACCAAACATCGCCTTGAGTT 58.019 45.000 0.00 0.00 0.00 3.01
153 155 1.981256 AACCAAACATCGCCTTGAGT 58.019 45.000 0.00 0.00 0.00 3.41
154 156 3.119849 CCTTAACCAAACATCGCCTTGAG 60.120 47.826 0.00 0.00 0.00 3.02
155 157 2.817258 CCTTAACCAAACATCGCCTTGA 59.183 45.455 0.00 0.00 0.00 3.02
156 158 2.556622 ACCTTAACCAAACATCGCCTTG 59.443 45.455 0.00 0.00 0.00 3.61
157 159 2.556622 CACCTTAACCAAACATCGCCTT 59.443 45.455 0.00 0.00 0.00 4.35
158 160 2.159382 CACCTTAACCAAACATCGCCT 58.841 47.619 0.00 0.00 0.00 5.52
159 161 1.883926 ACACCTTAACCAAACATCGCC 59.116 47.619 0.00 0.00 0.00 5.54
160 162 4.379082 CCTTACACCTTAACCAAACATCGC 60.379 45.833 0.00 0.00 0.00 4.58
161 163 4.155280 CCCTTACACCTTAACCAAACATCG 59.845 45.833 0.00 0.00 0.00 3.84
162 164 5.182570 GTCCCTTACACCTTAACCAAACATC 59.817 44.000 0.00 0.00 0.00 3.06
163 165 5.074804 GTCCCTTACACCTTAACCAAACAT 58.925 41.667 0.00 0.00 0.00 2.71
164 166 4.463070 GTCCCTTACACCTTAACCAAACA 58.537 43.478 0.00 0.00 0.00 2.83
165 167 3.499537 CGTCCCTTACACCTTAACCAAAC 59.500 47.826 0.00 0.00 0.00 2.93
166 168 3.136260 ACGTCCCTTACACCTTAACCAAA 59.864 43.478 0.00 0.00 0.00 3.28
167 169 2.705127 ACGTCCCTTACACCTTAACCAA 59.295 45.455 0.00 0.00 0.00 3.67
168 170 2.328319 ACGTCCCTTACACCTTAACCA 58.672 47.619 0.00 0.00 0.00 3.67
200 202 6.846350 TGCTAGACCTACGTAAACTTCTTAC 58.154 40.000 0.00 0.00 0.00 2.34
216 218 1.134371 AGAGGGCGAAAATGCTAGACC 60.134 52.381 0.00 0.00 34.52 3.85
244 246 1.728068 GTTTTCTCGAAGGAGGGAGC 58.272 55.000 0.00 0.00 40.85 4.70
245 247 1.404315 CCGTTTTCTCGAAGGAGGGAG 60.404 57.143 0.00 0.00 40.85 4.30
247 249 0.606604 TCCGTTTTCTCGAAGGAGGG 59.393 55.000 0.00 0.00 40.85 4.30
255 257 0.317479 AGAGGTGGTCCGTTTTCTCG 59.683 55.000 0.00 0.00 39.05 4.04
269 271 0.109342 CTGCCTTGTCAACCAGAGGT 59.891 55.000 3.45 0.00 37.65 3.85
274 276 0.467844 ATGTGCTGCCTTGTCAACCA 60.468 50.000 0.00 0.00 0.00 3.67
276 278 0.953727 TCATGTGCTGCCTTGTCAAC 59.046 50.000 0.00 0.00 0.00 3.18
278 280 0.109153 AGTCATGTGCTGCCTTGTCA 59.891 50.000 0.00 0.00 0.00 3.58
282 284 3.199508 AGATTCTAGTCATGTGCTGCCTT 59.800 43.478 0.00 0.00 0.00 4.35
286 288 2.793790 GCGAGATTCTAGTCATGTGCTG 59.206 50.000 0.00 0.00 0.00 4.41
290 292 3.027412 ACCTGCGAGATTCTAGTCATGT 58.973 45.455 0.00 0.00 0.00 3.21
294 296 1.751924 ACCACCTGCGAGATTCTAGTC 59.248 52.381 0.00 0.00 0.00 2.59
298 300 1.599047 CCACCACCTGCGAGATTCT 59.401 57.895 0.00 0.00 0.00 2.40
342 680 0.824109 TCTCTTGTGCTACCATCCGG 59.176 55.000 0.00 0.00 38.77 5.14
349 687 0.456221 TAGCCGCTCTCTTGTGCTAC 59.544 55.000 0.00 0.00 33.63 3.58
364 702 1.269831 CGGTGGTAGATGCTCTTAGCC 60.270 57.143 0.00 0.00 41.51 3.93
369 707 2.808315 CGCGGTGGTAGATGCTCT 59.192 61.111 0.00 0.00 0.00 4.09
371 709 4.873129 CGCGCGGTGGTAGATGCT 62.873 66.667 24.84 0.00 0.00 3.79
379 717 4.969196 ATATGAGGCGCGCGGTGG 62.969 66.667 33.06 3.25 0.00 4.61
380 718 3.406361 GATATGAGGCGCGCGGTG 61.406 66.667 33.06 3.70 0.00 4.94
381 719 4.664677 GGATATGAGGCGCGCGGT 62.665 66.667 33.06 15.55 0.00 5.68
383 721 3.604494 TACGGATATGAGGCGCGCG 62.604 63.158 28.44 28.44 0.00 6.86
391 729 6.406370 CAAAGGGCATCTATTACGGATATGA 58.594 40.000 0.00 0.00 0.00 2.15
393 731 5.487488 TCCAAAGGGCATCTATTACGGATAT 59.513 40.000 0.00 0.00 0.00 1.63
400 738 4.039973 CGGTAGTCCAAAGGGCATCTATTA 59.960 45.833 0.00 0.00 0.00 0.98
403 741 1.760613 CGGTAGTCCAAAGGGCATCTA 59.239 52.381 0.00 0.00 0.00 1.98
406 744 1.134098 CATCGGTAGTCCAAAGGGCAT 60.134 52.381 0.00 0.00 0.00 4.40
425 763 5.181811 GTCAGTCATCATCCAAATTCACACA 59.818 40.000 0.00 0.00 0.00 3.72
427 765 4.701651 GGTCAGTCATCATCCAAATTCACA 59.298 41.667 0.00 0.00 0.00 3.58
428 766 4.701651 TGGTCAGTCATCATCCAAATTCAC 59.298 41.667 0.00 0.00 0.00 3.18
429 767 4.920999 TGGTCAGTCATCATCCAAATTCA 58.079 39.130 0.00 0.00 0.00 2.57
430 768 6.461110 AATGGTCAGTCATCATCCAAATTC 57.539 37.500 0.00 0.00 0.00 2.17
431 769 5.066893 CGAATGGTCAGTCATCATCCAAATT 59.933 40.000 0.00 0.00 0.00 1.82
432 770 4.577693 CGAATGGTCAGTCATCATCCAAAT 59.422 41.667 0.00 0.00 0.00 2.32
434 772 3.197549 TCGAATGGTCAGTCATCATCCAA 59.802 43.478 0.00 0.00 0.00 3.53
437 775 3.247173 GCTTCGAATGGTCAGTCATCATC 59.753 47.826 0.00 0.00 0.00 2.92
438 776 3.201290 GCTTCGAATGGTCAGTCATCAT 58.799 45.455 0.00 0.00 0.00 2.45
439 777 2.028203 TGCTTCGAATGGTCAGTCATCA 60.028 45.455 0.00 0.00 0.00 3.07
440 778 2.621338 TGCTTCGAATGGTCAGTCATC 58.379 47.619 0.00 0.00 0.00 2.92
441 779 2.768253 TGCTTCGAATGGTCAGTCAT 57.232 45.000 0.00 0.00 0.00 3.06
442 780 2.542020 TTGCTTCGAATGGTCAGTCA 57.458 45.000 0.00 0.00 0.00 3.41
443 781 2.096496 CCATTGCTTCGAATGGTCAGTC 59.904 50.000 7.26 0.00 45.16 3.51
444 782 2.086869 CCATTGCTTCGAATGGTCAGT 58.913 47.619 7.26 0.00 45.16 3.41
445 783 2.838386 CCATTGCTTCGAATGGTCAG 57.162 50.000 7.26 0.00 45.16 3.51
450 788 5.046910 AGTTTGTACCATTGCTTCGAATG 57.953 39.130 0.00 0.00 33.74 2.67
516 855 3.996921 AGATATGATGATGGAGGCCAC 57.003 47.619 5.01 0.00 35.80 5.01
524 863 8.596271 GAGCATCTCCAATAGATATGATGATG 57.404 38.462 0.00 0.00 43.42 3.07
563 902 6.966632 TCTTCTGTTCGAAAAAGAATGTTGTG 59.033 34.615 19.41 10.58 32.25 3.33
569 908 9.801873 TTGAATTTCTTCTGTTCGAAAAAGAAT 57.198 25.926 22.17 13.99 37.52 2.40
578 917 6.033341 TGGTTTGTTGAATTTCTTCTGTTCG 58.967 36.000 0.00 0.00 32.29 3.95
582 921 5.231991 CGGTTGGTTTGTTGAATTTCTTCTG 59.768 40.000 0.00 0.00 32.29 3.02
585 924 5.331876 TCGGTTGGTTTGTTGAATTTCTT 57.668 34.783 0.00 0.00 0.00 2.52
595 934 5.771165 ACCATTTAACTATCGGTTGGTTTGT 59.229 36.000 0.00 0.00 38.75 2.83
597 936 6.904463 AACCATTTAACTATCGGTTGGTTT 57.096 33.333 0.00 0.00 40.41 3.27
604 943 7.214381 TGTCATCCTAACCATTTAACTATCGG 58.786 38.462 0.00 0.00 0.00 4.18
606 945 9.046296 CACTGTCATCCTAACCATTTAACTATC 57.954 37.037 0.00 0.00 0.00 2.08
607 946 7.993183 CCACTGTCATCCTAACCATTTAACTAT 59.007 37.037 0.00 0.00 0.00 2.12
614 953 4.080526 GGTACCACTGTCATCCTAACCATT 60.081 45.833 7.15 0.00 0.00 3.16
636 975 0.034089 GAACCCTGATGAGTTGGGGG 60.034 60.000 0.00 0.00 44.97 5.40
637 976 0.698238 TGAACCCTGATGAGTTGGGG 59.302 55.000 0.00 0.00 44.97 4.96
639 978 3.146104 ACTTGAACCCTGATGAGTTGG 57.854 47.619 0.00 0.00 0.00 3.77
640 979 4.214971 CAGAACTTGAACCCTGATGAGTTG 59.785 45.833 0.00 0.00 0.00 3.16
641 980 4.392940 CAGAACTTGAACCCTGATGAGTT 58.607 43.478 0.00 0.00 0.00 3.01
642 981 3.244700 CCAGAACTTGAACCCTGATGAGT 60.245 47.826 0.00 0.00 0.00 3.41
644 983 2.711009 ACCAGAACTTGAACCCTGATGA 59.289 45.455 0.00 0.00 0.00 2.92
651 990 1.604278 GTGAGCACCAGAACTTGAACC 59.396 52.381 0.00 0.00 0.00 3.62
652 991 2.288666 TGTGAGCACCAGAACTTGAAC 58.711 47.619 0.00 0.00 0.00 3.18
660 999 4.824479 TCAAGATAATGTGAGCACCAGA 57.176 40.909 0.00 0.00 0.00 3.86
661 1000 5.587443 TGAATCAAGATAATGTGAGCACCAG 59.413 40.000 0.00 0.00 0.00 4.00
701 1041 3.181528 ACCGTACAAAAATACGTGCATCG 60.182 43.478 0.00 7.07 45.17 3.84
702 1042 4.085884 CACCGTACAAAAATACGTGCATC 58.914 43.478 0.00 0.00 45.17 3.91
704 1044 3.059733 GTCACCGTACAAAAATACGTGCA 60.060 43.478 0.00 0.00 45.17 4.57
705 1045 3.184986 AGTCACCGTACAAAAATACGTGC 59.815 43.478 0.00 0.00 45.17 5.34
706 1046 4.977741 AGTCACCGTACAAAAATACGTG 57.022 40.909 0.00 3.90 45.17 4.49
707 1047 5.049167 TGAAGTCACCGTACAAAAATACGT 58.951 37.500 0.00 0.00 45.17 3.57
708 1048 5.579384 TGAAGTCACCGTACAAAAATACG 57.421 39.130 0.00 0.00 45.99 3.06
709 1049 7.124347 TGATGAAGTCACCGTACAAAAATAC 57.876 36.000 0.00 0.00 0.00 1.89
710 1050 7.731882 TTGATGAAGTCACCGTACAAAAATA 57.268 32.000 0.00 0.00 36.32 1.40
711 1051 6.627395 TTGATGAAGTCACCGTACAAAAAT 57.373 33.333 0.00 0.00 36.32 1.82
713 1053 5.995282 AGATTGATGAAGTCACCGTACAAAA 59.005 36.000 0.00 0.00 36.32 2.44
714 1054 5.547465 AGATTGATGAAGTCACCGTACAAA 58.453 37.500 0.00 0.00 36.32 2.83
715 1055 5.147330 AGATTGATGAAGTCACCGTACAA 57.853 39.130 0.00 0.00 36.32 2.41
718 1058 7.165460 TCTTAAGATTGATGAAGTCACCGTA 57.835 36.000 0.00 0.00 36.32 4.02
719 1059 6.037786 TCTTAAGATTGATGAAGTCACCGT 57.962 37.500 0.00 0.00 36.32 4.83
720 1060 6.758416 TCATCTTAAGATTGATGAAGTCACCG 59.242 38.462 15.49 0.00 43.90 4.94
738 1110 2.899900 ACTGAGCCGCCATATCATCTTA 59.100 45.455 0.00 0.00 0.00 2.10
741 1113 1.274728 AGACTGAGCCGCCATATCATC 59.725 52.381 0.00 0.00 0.00 2.92
749 1121 1.355066 CTTCGAAAGACTGAGCCGCC 61.355 60.000 0.00 0.00 41.84 6.13
750 1122 1.355066 CCTTCGAAAGACTGAGCCGC 61.355 60.000 0.00 0.00 41.84 6.53
752 1124 1.433534 CACCTTCGAAAGACTGAGCC 58.566 55.000 0.00 0.00 41.84 4.70
760 1132 1.683790 CCTACGCGCACCTTCGAAAG 61.684 60.000 5.73 0.00 0.00 2.62
764 1136 2.104331 ATCCTACGCGCACCTTCG 59.896 61.111 5.73 0.00 0.00 3.79
768 1140 3.564027 GCACATCCTACGCGCACC 61.564 66.667 5.73 0.00 0.00 5.01
769 1141 3.913573 CGCACATCCTACGCGCAC 61.914 66.667 5.73 0.00 42.79 5.34
773 1145 0.457166 TACACACGCACATCCTACGC 60.457 55.000 0.00 0.00 0.00 4.42
799 1177 2.372040 TATGCGCATACACCCGGTCC 62.372 60.000 25.78 0.00 0.00 4.46
801 1179 0.970640 TATATGCGCATACACCCGGT 59.029 50.000 31.17 16.40 0.00 5.28
802 1180 2.309528 ATATATGCGCATACACCCGG 57.690 50.000 31.17 0.00 0.00 5.73
803 1181 8.926715 ATATAATATATATGCGCATACACCCG 57.073 34.615 31.17 0.00 0.00 5.28
821 1199 9.817809 GCCGTGAATTTCTCCTCATATATAATA 57.182 33.333 0.00 0.00 0.00 0.98
822 1200 7.770897 GGCCGTGAATTTCTCCTCATATATAAT 59.229 37.037 0.00 0.00 0.00 1.28
823 1201 7.038302 AGGCCGTGAATTTCTCCTCATATATAA 60.038 37.037 0.00 0.00 0.00 0.98
880 1319 5.180117 CCTAGGTATGAAATCAAAGATGCGG 59.820 44.000 0.00 0.00 0.00 5.69
1035 1490 3.362797 AGCACGACGAGGAGCGAA 61.363 61.111 0.00 0.00 44.57 4.70
1087 1545 4.749310 CCGCAGCTTGTCCTCGCT 62.749 66.667 0.00 0.00 36.83 4.93
1119 1577 4.457496 ATCACCGGCAGCGTCCAG 62.457 66.667 0.00 0.00 0.00 3.86
1350 1814 1.526887 GAAGATGATGTCCCGGCCA 59.473 57.895 2.24 0.00 0.00 5.36
1904 2373 1.137513 GATATGTACGCGTTGGAGGC 58.862 55.000 20.78 0.00 0.00 4.70
1944 2431 2.396601 CGAAACGGTTAGTGTAGTGCA 58.603 47.619 0.00 0.00 0.00 4.57
2546 3155 0.389948 GCCTCGGTCATGTCGAACTT 60.390 55.000 13.00 0.00 36.15 2.66
2661 3282 6.459923 AGTAGACTCTTTTTAAGGAGCACTG 58.540 40.000 1.93 0.00 33.29 3.66
2662 3283 6.673839 AGTAGACTCTTTTTAAGGAGCACT 57.326 37.500 1.93 4.91 33.29 4.40
2666 3287 9.549078 AGTTGAAAGTAGACTCTTTTTAAGGAG 57.451 33.333 0.58 0.58 37.70 3.69
2667 3288 9.901172 AAGTTGAAAGTAGACTCTTTTTAAGGA 57.099 29.630 0.00 0.00 37.70 3.36
2799 3431 6.861065 TGCCACTAAATTAGTAGCATTAGC 57.139 37.500 19.37 8.66 45.91 3.09
2809 3441 7.132213 CACCGACATTTATGCCACTAAATTAG 58.868 38.462 0.00 0.00 30.68 1.73
2901 3541 1.580059 TCCCGCATACTTCCTCCTTT 58.420 50.000 0.00 0.00 0.00 3.11
2902 3542 1.580059 TTCCCGCATACTTCCTCCTT 58.420 50.000 0.00 0.00 0.00 3.36
2919 3560 1.732259 ACATCGATGACGGCTTGTTTC 59.268 47.619 31.33 0.00 40.21 2.78
2935 3576 7.329226 CCACAAACTGAACCAATCAAATACATC 59.671 37.037 0.00 0.00 37.67 3.06
3061 3706 1.136828 TATGCACCATCCCACTACCC 58.863 55.000 0.00 0.00 0.00 3.69
3075 3720 5.009510 CACATATCCCCAAACGAAATATGCA 59.990 40.000 0.00 0.00 34.93 3.96
3095 3740 5.814188 CCATAATAGAGCGATACATGCACAT 59.186 40.000 0.00 0.00 33.85 3.21
3136 3781 7.043961 AGGTAGTGTGATGTATATGTGTCAG 57.956 40.000 0.00 0.00 0.00 3.51
3202 3847 1.134280 GCTAGCTGTCCCACATGTCAT 60.134 52.381 7.70 0.00 0.00 3.06
3246 3891 7.229106 ACTTTTTACTTCAAACATACCCGCTAA 59.771 33.333 0.00 0.00 0.00 3.09
3287 3933 6.016943 TGTTCGGACTAAAAAGTATTGGTTGG 60.017 38.462 0.00 0.00 0.00 3.77
3302 3948 4.530710 ACTGCAAACTATGTTCGGACTA 57.469 40.909 0.00 0.00 0.00 2.59
3305 3951 4.873827 GGAATACTGCAAACTATGTTCGGA 59.126 41.667 0.00 0.00 0.00 4.55
3307 3953 4.876107 AGGGAATACTGCAAACTATGTTCG 59.124 41.667 0.00 0.00 0.00 3.95
3320 3968 8.581253 ACTAAAAAGAAATGGAGGGAATACTG 57.419 34.615 0.00 0.00 0.00 2.74
3326 3974 5.010282 GCAGACTAAAAAGAAATGGAGGGA 58.990 41.667 0.00 0.00 0.00 4.20
3327 3975 4.766891 TGCAGACTAAAAAGAAATGGAGGG 59.233 41.667 0.00 0.00 0.00 4.30
3328 3976 5.964958 TGCAGACTAAAAAGAAATGGAGG 57.035 39.130 0.00 0.00 0.00 4.30
3343 3991 8.806146 ACTTTGACCAATTTTTATATGCAGACT 58.194 29.630 0.00 0.00 0.00 3.24
3344 3992 8.986477 ACTTTGACCAATTTTTATATGCAGAC 57.014 30.769 0.00 0.00 0.00 3.51
3345 3993 8.801299 TGACTTTGACCAATTTTTATATGCAGA 58.199 29.630 0.00 0.00 0.00 4.26
3346 3994 8.984891 TGACTTTGACCAATTTTTATATGCAG 57.015 30.769 0.00 0.00 0.00 4.41
3347 3995 9.770097 TTTGACTTTGACCAATTTTTATATGCA 57.230 25.926 0.00 0.00 0.00 3.96
3401 4049 9.932207 TCATATTGCAAATCTTGATGTCTTTTT 57.068 25.926 1.71 0.00 0.00 1.94
3402 4050 9.932207 TTCATATTGCAAATCTTGATGTCTTTT 57.068 25.926 1.71 0.00 0.00 2.27
3403 4051 9.932207 TTTCATATTGCAAATCTTGATGTCTTT 57.068 25.926 1.71 0.00 0.00 2.52
3405 4053 9.745880 GATTTCATATTGCAAATCTTGATGTCT 57.254 29.630 1.71 0.00 36.47 3.41
3406 4054 9.524106 TGATTTCATATTGCAAATCTTGATGTC 57.476 29.630 1.71 6.41 39.04 3.06
3407 4055 9.878667 TTGATTTCATATTGCAAATCTTGATGT 57.121 25.926 1.71 0.00 39.04 3.06
3500 4148 7.222000 AGTTTGACCAACTTTGTAGAAACAA 57.778 32.000 0.00 0.00 43.89 2.83
3501 4149 6.827586 AGTTTGACCAACTTTGTAGAAACA 57.172 33.333 0.00 0.00 43.89 2.83
3554 4202 9.338622 CCCTCCGTTTCTTTTTAATCTACATAT 57.661 33.333 0.00 0.00 0.00 1.78
3555 4203 8.542080 TCCCTCCGTTTCTTTTTAATCTACATA 58.458 33.333 0.00 0.00 0.00 2.29
3556 4204 7.399634 TCCCTCCGTTTCTTTTTAATCTACAT 58.600 34.615 0.00 0.00 0.00 2.29
3557 4205 6.771573 TCCCTCCGTTTCTTTTTAATCTACA 58.228 36.000 0.00 0.00 0.00 2.74
3558 4206 6.183360 GCTCCCTCCGTTTCTTTTTAATCTAC 60.183 42.308 0.00 0.00 0.00 2.59
3559 4207 5.878669 GCTCCCTCCGTTTCTTTTTAATCTA 59.121 40.000 0.00 0.00 0.00 1.98
3560 4208 4.700692 GCTCCCTCCGTTTCTTTTTAATCT 59.299 41.667 0.00 0.00 0.00 2.40
3561 4209 4.457949 TGCTCCCTCCGTTTCTTTTTAATC 59.542 41.667 0.00 0.00 0.00 1.75
3562 4210 4.403734 TGCTCCCTCCGTTTCTTTTTAAT 58.596 39.130 0.00 0.00 0.00 1.40
3563 4211 3.822940 TGCTCCCTCCGTTTCTTTTTAA 58.177 40.909 0.00 0.00 0.00 1.52
3564 4212 3.495434 TGCTCCCTCCGTTTCTTTTTA 57.505 42.857 0.00 0.00 0.00 1.52
3565 4213 2.358322 TGCTCCCTCCGTTTCTTTTT 57.642 45.000 0.00 0.00 0.00 1.94
3566 4214 2.162681 CATGCTCCCTCCGTTTCTTTT 58.837 47.619 0.00 0.00 0.00 2.27
3567 4215 1.351017 TCATGCTCCCTCCGTTTCTTT 59.649 47.619 0.00 0.00 0.00 2.52
3568 4216 0.984230 TCATGCTCCCTCCGTTTCTT 59.016 50.000 0.00 0.00 0.00 2.52
3569 4217 0.984230 TTCATGCTCCCTCCGTTTCT 59.016 50.000 0.00 0.00 0.00 2.52
3570 4218 2.044123 ATTCATGCTCCCTCCGTTTC 57.956 50.000 0.00 0.00 0.00 2.78
3571 4219 2.514458 AATTCATGCTCCCTCCGTTT 57.486 45.000 0.00 0.00 0.00 3.60
3572 4220 3.864789 ATAATTCATGCTCCCTCCGTT 57.135 42.857 0.00 0.00 0.00 4.44
3573 4221 4.287067 ACATATAATTCATGCTCCCTCCGT 59.713 41.667 0.00 0.00 0.00 4.69
3574 4222 4.836825 ACATATAATTCATGCTCCCTCCG 58.163 43.478 0.00 0.00 0.00 4.63
3575 4223 7.231317 TCAAAACATATAATTCATGCTCCCTCC 59.769 37.037 0.00 0.00 0.00 4.30
3576 4224 8.169977 TCAAAACATATAATTCATGCTCCCTC 57.830 34.615 0.00 0.00 0.00 4.30
3577 4225 8.416329 GTTCAAAACATATAATTCATGCTCCCT 58.584 33.333 0.00 0.00 0.00 4.20
3578 4226 8.196771 TGTTCAAAACATATAATTCATGCTCCC 58.803 33.333 0.00 0.00 36.25 4.30
3579 4227 9.585099 TTGTTCAAAACATATAATTCATGCTCC 57.415 29.630 0.00 0.00 41.79 4.70
3599 4247 8.664798 CGGTTAGTCAATCTGATATTTTGTTCA 58.335 33.333 0.00 0.00 0.00 3.18
3600 4248 8.665685 ACGGTTAGTCAATCTGATATTTTGTTC 58.334 33.333 0.00 0.00 0.00 3.18
3601 4249 8.561738 ACGGTTAGTCAATCTGATATTTTGTT 57.438 30.769 0.00 0.00 0.00 2.83
3602 4250 8.561738 AACGGTTAGTCAATCTGATATTTTGT 57.438 30.769 0.00 0.00 0.00 2.83
3603 4251 9.277565 CAAACGGTTAGTCAATCTGATATTTTG 57.722 33.333 0.00 0.00 0.00 2.44
3604 4252 8.458843 CCAAACGGTTAGTCAATCTGATATTTT 58.541 33.333 0.00 0.00 0.00 1.82
3605 4253 7.827236 TCCAAACGGTTAGTCAATCTGATATTT 59.173 33.333 0.00 0.00 0.00 1.40
3606 4254 7.335627 TCCAAACGGTTAGTCAATCTGATATT 58.664 34.615 0.00 0.00 0.00 1.28
3607 4255 6.884832 TCCAAACGGTTAGTCAATCTGATAT 58.115 36.000 0.00 0.00 0.00 1.63
3608 4256 6.288941 TCCAAACGGTTAGTCAATCTGATA 57.711 37.500 0.00 0.00 0.00 2.15
3609 4257 5.160607 TCCAAACGGTTAGTCAATCTGAT 57.839 39.130 0.00 0.00 0.00 2.90
3610 4258 4.610605 TCCAAACGGTTAGTCAATCTGA 57.389 40.909 0.00 0.00 0.00 3.27
3611 4259 7.553881 AATATCCAAACGGTTAGTCAATCTG 57.446 36.000 0.00 0.00 0.00 2.90
3612 4260 8.483758 ACTAATATCCAAACGGTTAGTCAATCT 58.516 33.333 0.00 0.00 31.87 2.40
3613 4261 8.658499 ACTAATATCCAAACGGTTAGTCAATC 57.342 34.615 0.00 0.00 31.87 2.67
3615 4263 9.537192 CATACTAATATCCAAACGGTTAGTCAA 57.463 33.333 0.00 0.00 37.01 3.18


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

AutoCloner maintained by Alex Coulton.