Multiple sequence alignment - TraesCS1D01G450300

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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 TraesCS1D01G450300 chr1D 100.000 5710 0 0 1 5710 492644598 492638889 0.000000e+00 10545.0
1 TraesCS1D01G450300 chr1D 98.182 55 1 0 5656 5710 492638997 492638943 4.710000e-16 97.1
2 TraesCS1D01G450300 chr1B 91.419 3193 187 44 1187 4326 685291656 685288498 0.000000e+00 4298.0
3 TraesCS1D01G450300 chr1B 86.768 922 63 28 4328 5209 685288469 685287567 0.000000e+00 972.0
4 TraesCS1D01G450300 chr1B 85.915 355 34 9 781 1126 685292006 685291659 1.170000e-96 364.0
5 TraesCS1D01G450300 chr1A 90.825 3117 160 46 2615 5662 591149322 591146263 0.000000e+00 4056.0
6 TraesCS1D01G450300 chr1A 91.096 2628 119 50 3 2562 591152214 591149634 0.000000e+00 3450.0
7 TraesCS1D01G450300 chr1A 84.076 157 18 3 569 722 459273383 459273231 1.660000e-30 145.0
8 TraesCS1D01G450300 chr3B 84.570 512 77 2 2782 3292 372243723 372243213 1.840000e-139 507.0
9 TraesCS1D01G450300 chr3B 77.551 392 74 11 1877 2261 372244495 372244111 2.070000e-54 224.0
10 TraesCS1D01G450300 chr3B 92.308 52 4 0 5656 5707 257513606 257513555 2.210000e-09 75.0
11 TraesCS1D01G450300 chr3A 84.016 513 78 4 2782 3292 360828411 360827901 1.850000e-134 490.0
12 TraesCS1D01G450300 chr3A 96.078 51 2 0 5660 5710 222359469 222359419 3.670000e-12 84.2
13 TraesCS1D01G450300 chr3D 83.594 512 82 2 2782 3292 278447101 278447611 4.000000e-131 479.0
14 TraesCS1D01G450300 chr3D 77.749 391 69 11 1877 2258 278442860 278443241 2.070000e-54 224.0
15 TraesCS1D01G450300 chr3D 84.906 159 17 5 569 722 110398129 110398285 2.760000e-33 154.0
16 TraesCS1D01G450300 chr3D 84.146 164 19 3 562 722 170546942 170547101 9.910000e-33 152.0
17 TraesCS1D01G450300 chr3D 84.076 157 17 4 569 722 482599255 482599406 1.660000e-30 145.0
18 TraesCS1D01G450300 chr5D 83.333 498 78 5 2797 3291 543223939 543224434 6.740000e-124 455.0
19 TraesCS1D01G450300 chr5D 82.400 500 79 9 2797 3291 543214040 543214535 1.470000e-115 427.0
20 TraesCS1D01G450300 chr5D 75.923 731 151 14 3415 4122 543093681 543094409 9.100000e-93 351.0
21 TraesCS1D01G450300 chr5D 75.815 736 152 18 3415 4128 543272219 543272950 3.270000e-92 350.0
22 TraesCS1D01G450300 chr5D 92.045 88 7 0 2173 2260 543213875 543213962 2.160000e-24 124.0
23 TraesCS1D01G450300 chr5D 94.231 52 1 2 5660 5710 411994011 411993961 1.710000e-10 78.7
24 TraesCS1D01G450300 chr5D 94.231 52 1 2 5660 5710 412035771 412035721 1.710000e-10 78.7
25 TraesCS1D01G450300 chr5D 90.741 54 1 4 5180 5231 56235599 56235548 1.030000e-07 69.4
26 TraesCS1D01G450300 chr5B 82.495 497 84 3 2797 3291 684611194 684611689 3.160000e-117 433.0
27 TraesCS1D01G450300 chr5B 78.503 521 101 11 3415 3928 684745780 684746296 1.190000e-86 331.0
28 TraesCS1D01G450300 chr5B 75.101 739 158 16 3415 4131 684772387 684771653 7.140000e-84 322.0
29 TraesCS1D01G450300 chr5B 76.686 519 102 13 3559 4067 684656715 684656206 2.620000e-68 270.0
30 TraesCS1D01G450300 chr5B 93.182 88 6 0 2173 2260 684611050 684611137 4.640000e-26 130.0
31 TraesCS1D01G450300 chr5B 90.323 93 9 0 2168 2260 684089270 684089362 7.770000e-24 122.0
32 TraesCS1D01G450300 chr5B 93.878 49 1 2 5180 5226 211004093 211004045 7.940000e-09 73.1
33 TraesCS1D01G450300 chr4A 82.200 500 80 9 2797 3291 626021894 626021399 6.840000e-114 422.0
34 TraesCS1D01G450300 chr4A 81.964 499 83 7 2797 3291 626048939 626048444 3.180000e-112 416.0
35 TraesCS1D01G450300 chr4A 80.367 545 96 8 3396 3933 626013145 626012605 2.480000e-108 403.0
36 TraesCS1D01G450300 chr4A 75.000 736 153 15 3404 4131 625995332 625994620 1.540000e-80 311.0
37 TraesCS1D01G450300 chr4A 77.467 537 104 12 3415 3941 625959469 625958940 7.190000e-79 305.0
38 TraesCS1D01G450300 chr4A 76.163 516 108 11 3415 3921 695806180 695806689 2.040000e-64 257.0
39 TraesCS1D01G450300 chr4A 92.045 88 7 0 2173 2260 626049104 626049017 2.160000e-24 124.0
40 TraesCS1D01G450300 chr4A 93.671 79 5 0 2174 2252 626013877 626013799 1.010000e-22 119.0
41 TraesCS1D01G450300 chr4A 80.220 91 14 4 5575 5662 45708237 45708326 1.330000e-06 65.8
42 TraesCS1D01G450300 chr6D 89.815 216 16 3 734 943 406206895 406206680 7.290000e-69 272.0
43 TraesCS1D01G450300 chr6D 100.000 45 0 0 526 570 406206943 406206899 3.670000e-12 84.2
44 TraesCS1D01G450300 chr6D 92.453 53 1 2 5177 5226 341840241 341840189 7.940000e-09 73.1
45 TraesCS1D01G450300 chr6A 89.815 216 16 3 734 943 552744189 552743974 7.290000e-69 272.0
46 TraesCS1D01G450300 chr6A 100.000 45 0 0 526 570 552744237 552744193 3.670000e-12 84.2
47 TraesCS1D01G450300 chr6A 92.593 54 1 2 5176 5226 232780334 232780281 2.210000e-09 75.0
48 TraesCS1D01G450300 chr6B 88.426 216 19 3 734 943 610238801 610238586 7.340000e-64 255.0
49 TraesCS1D01G450300 chr6B 100.000 45 0 0 526 570 610238849 610238805 3.670000e-12 84.2
50 TraesCS1D01G450300 chr5A 86.667 165 14 4 562 722 660831258 660831098 5.880000e-40 176.0
51 TraesCS1D01G450300 chr7D 86.061 165 13 6 569 729 33102854 33102696 9.840000e-38 169.0
52 TraesCS1D01G450300 chr7D 80.220 91 14 4 5575 5662 95826720 95826809 1.330000e-06 65.8
53 TraesCS1D01G450300 chr2A 87.671 146 11 3 580 722 141506459 141506318 4.580000e-36 163.0
54 TraesCS1D01G450300 chr7B 87.075 147 10 4 579 722 78552570 78552430 2.130000e-34 158.0
55 TraesCS1D01G450300 chr7B 94.340 53 2 1 5656 5707 380064491 380064439 4.740000e-11 80.5
56 TraesCS1D01G450300 chr7B 94.000 50 3 0 5656 5705 668488832 668488783 6.130000e-10 76.8
57 TraesCS1D01G450300 chr7B 94.000 50 3 0 5656 5705 668499888 668499839 6.130000e-10 76.8
58 TraesCS1D01G450300 chr2B 85.714 84 9 2 5580 5662 594025470 594025389 1.020000e-12 86.1
59 TraesCS1D01G450300 chr2B 93.878 49 1 2 5180 5226 610937903 610937951 7.940000e-09 73.1
60 TraesCS1D01G450300 chr2B 89.474 57 2 4 5179 5231 469350221 469350165 1.030000e-07 69.4
61 TraesCS1D01G450300 chr7A 90.909 55 4 1 5656 5709 433729303 433729249 7.940000e-09 73.1
62 TraesCS1D01G450300 chr4D 93.878 49 1 2 5180 5226 363960571 363960523 7.940000e-09 73.1


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 TraesCS1D01G450300 chr1D 492638889 492644598 5709 True 10545.0 10545 100.0000 1 5710 1 chr1D.!!$R1 5709
1 TraesCS1D01G450300 chr1B 685287567 685292006 4439 True 1878.0 4298 88.0340 781 5209 3 chr1B.!!$R1 4428
2 TraesCS1D01G450300 chr1A 591146263 591152214 5951 True 3753.0 4056 90.9605 3 5662 2 chr1A.!!$R2 5659
3 TraesCS1D01G450300 chr3B 372243213 372244495 1282 True 365.5 507 81.0605 1877 3292 2 chr3B.!!$R2 1415
4 TraesCS1D01G450300 chr3A 360827901 360828411 510 True 490.0 490 84.0160 2782 3292 1 chr3A.!!$R2 510
5 TraesCS1D01G450300 chr3D 278442860 278447611 4751 False 351.5 479 80.6715 1877 3292 2 chr3D.!!$F4 1415
6 TraesCS1D01G450300 chr5D 543093681 543094409 728 False 351.0 351 75.9230 3415 4122 1 chr5D.!!$F1 707
7 TraesCS1D01G450300 chr5D 543272219 543272950 731 False 350.0 350 75.8150 3415 4128 1 chr5D.!!$F3 713
8 TraesCS1D01G450300 chr5D 543213875 543214535 660 False 275.5 427 87.2225 2173 3291 2 chr5D.!!$F4 1118
9 TraesCS1D01G450300 chr5B 684745780 684746296 516 False 331.0 331 78.5030 3415 3928 1 chr5B.!!$F2 513
10 TraesCS1D01G450300 chr5B 684771653 684772387 734 True 322.0 322 75.1010 3415 4131 1 chr5B.!!$R3 716
11 TraesCS1D01G450300 chr5B 684611050 684611689 639 False 281.5 433 87.8385 2173 3291 2 chr5B.!!$F3 1118
12 TraesCS1D01G450300 chr5B 684656206 684656715 509 True 270.0 270 76.6860 3559 4067 1 chr5B.!!$R2 508
13 TraesCS1D01G450300 chr4A 625994620 625995332 712 True 311.0 311 75.0000 3404 4131 1 chr4A.!!$R2 727
14 TraesCS1D01G450300 chr4A 625958940 625959469 529 True 305.0 305 77.4670 3415 3941 1 chr4A.!!$R1 526
15 TraesCS1D01G450300 chr4A 626048444 626049104 660 True 270.0 416 87.0045 2173 3291 2 chr4A.!!$R5 1118
16 TraesCS1D01G450300 chr4A 626012605 626013877 1272 True 261.0 403 87.0190 2174 3933 2 chr4A.!!$R4 1759
17 TraesCS1D01G450300 chr4A 695806180 695806689 509 False 257.0 257 76.1630 3415 3921 1 chr4A.!!$F2 506

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
254 269 0.108424 GCAACGAGTCTCCTGCTCAT 60.108 55.0 12.35 0.00 33.45 2.90 F
257 272 0.108424 ACGAGTCTCCTGCTCATTGC 60.108 55.0 0.00 0.00 43.25 3.56 F
261 276 0.179100 GTCTCCTGCTCATTGCGCTA 60.179 55.0 9.73 0.00 46.63 4.26 F
334 356 0.181114 TGTAGCAGATGGATGGTGCC 59.819 55.0 0.00 0.00 37.98 5.01 F
970 1011 0.250467 GGCTCTGCTCAACTCAACCA 60.250 55.0 0.00 0.00 0.00 3.67 F
2474 2615 0.984961 CCATGCCTCCTCTTCCCTCA 60.985 60.0 0.00 0.00 0.00 3.86 F
2846 6637 0.601046 GTGGCAAGCTTCCAAAAGGC 60.601 55.0 16.19 8.61 35.01 4.35 F
4200 8026 0.258774 AGGTTCCACAGCAAACACCT 59.741 50.0 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1469 1510 0.249405 GCTGGCTCTCGAAGATCTGG 60.249 60.000 0.00 0.00 33.89 3.86 R
2327 2437 9.280174 CGTTGGGGTAGATATATTTGTTTACAT 57.720 33.333 0.00 0.00 0.00 2.29 R
2411 2544 6.184789 ACAGACCGGTTGATTTGGTATTAAT 58.815 36.000 9.42 0.00 35.75 1.40 R
2455 2588 0.984961 TGAGGGAAGAGGAGGCATGG 60.985 60.000 0.00 0.00 0.00 3.66 R
2679 3270 1.139654 TCATCCCTACATGAGCAGTGC 59.860 52.381 7.13 7.13 0.00 4.40 R
4179 8005 0.307760 GTGTTTGCTGTGGAACCTCG 59.692 55.000 0.00 0.00 34.36 4.63 R
4569 8429 0.572590 GACACACATACGAGATGCGC 59.427 55.000 0.00 0.00 46.04 6.09 R
5555 9461 0.103208 ACTTCATCCTCGACGCCATC 59.897 55.000 0.00 0.00 0.00 3.51 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
99 100 1.697982 CTAGGGTTTATTAGGGCGCCT 59.302 52.381 28.56 15.07 37.71 5.52
101 102 0.536687 GGGTTTATTAGGGCGCCTCC 60.537 60.000 28.56 11.04 34.61 4.30
106 107 1.119574 TATTAGGGCGCCTCCAGTCC 61.120 60.000 28.56 7.55 34.61 3.85
225 240 2.809174 TGCCTGTCGAATCACGCG 60.809 61.111 3.53 3.53 42.26 6.01
251 266 2.659610 GGCAACGAGTCTCCTGCT 59.340 61.111 17.00 0.00 35.13 4.24
252 267 1.446966 GGCAACGAGTCTCCTGCTC 60.447 63.158 17.00 7.50 35.13 4.26
253 268 1.290324 GCAACGAGTCTCCTGCTCA 59.710 57.895 12.35 0.00 33.45 4.26
254 269 0.108424 GCAACGAGTCTCCTGCTCAT 60.108 55.000 12.35 0.00 33.45 2.90
255 270 1.674221 GCAACGAGTCTCCTGCTCATT 60.674 52.381 12.35 0.00 33.45 2.57
256 271 1.998315 CAACGAGTCTCCTGCTCATTG 59.002 52.381 0.00 0.00 31.45 2.82
257 272 0.108424 ACGAGTCTCCTGCTCATTGC 60.108 55.000 0.00 0.00 43.25 3.56
258 273 1.144565 CGAGTCTCCTGCTCATTGCG 61.145 60.000 0.00 0.00 46.63 4.85
259 274 1.427592 GAGTCTCCTGCTCATTGCGC 61.428 60.000 0.00 0.00 46.63 6.09
260 275 1.449246 GTCTCCTGCTCATTGCGCT 60.449 57.895 9.73 0.00 46.63 5.92
261 276 0.179100 GTCTCCTGCTCATTGCGCTA 60.179 55.000 9.73 0.00 46.63 4.26
262 277 0.755079 TCTCCTGCTCATTGCGCTAT 59.245 50.000 9.73 2.86 46.63 2.97
263 278 1.963515 TCTCCTGCTCATTGCGCTATA 59.036 47.619 9.73 0.00 46.63 1.31
264 279 2.064762 CTCCTGCTCATTGCGCTATAC 58.935 52.381 9.73 0.14 46.63 1.47
265 280 1.412343 TCCTGCTCATTGCGCTATACA 59.588 47.619 9.73 5.13 46.63 2.29
266 281 1.797046 CCTGCTCATTGCGCTATACAG 59.203 52.381 9.73 14.17 46.63 2.74
267 282 2.546584 CCTGCTCATTGCGCTATACAGA 60.547 50.000 21.48 9.28 46.63 3.41
268 283 2.473816 TGCTCATTGCGCTATACAGAC 58.526 47.619 9.73 3.74 46.63 3.51
272 287 4.480541 CTCATTGCGCTATACAGACTAGG 58.519 47.826 9.73 0.00 0.00 3.02
278 293 4.202336 TGCGCTATACAGACTAGGAGTAGT 60.202 45.833 9.73 0.00 42.59 2.73
284 299 7.094677 GCTATACAGACTAGGAGTAGTTTAGGC 60.095 44.444 0.00 0.00 39.78 3.93
290 305 9.352191 CAGACTAGGAGTAGTTTAGGCTAATTA 57.648 37.037 7.96 1.63 39.78 1.40
297 312 8.139989 GGAGTAGTTTAGGCTAATTATTCGTCA 58.860 37.037 7.96 0.00 0.00 4.35
309 331 9.170584 GCTAATTATTCGTCAAAAATAAGGCTC 57.829 33.333 0.00 0.00 33.40 4.70
310 332 9.370126 CTAATTATTCGTCAAAAATAAGGCTCG 57.630 33.333 0.00 0.00 33.40 5.03
334 356 0.181114 TGTAGCAGATGGATGGTGCC 59.819 55.000 0.00 0.00 37.98 5.01
356 378 3.372660 AGAATTTCTATCTCGGACCGC 57.627 47.619 9.66 0.00 0.00 5.68
408 430 8.030692 CCTTTATTCAGAAATCAGATGTTGCAA 58.969 33.333 0.00 0.00 0.00 4.08
470 496 0.305313 TTTGTTTGTACCGCTGTCGC 59.695 50.000 0.00 0.00 0.00 5.19
544 570 6.636562 ATGAATGAAGATGCTGGAGATTTC 57.363 37.500 0.00 0.00 0.00 2.17
568 594 7.280356 TCACTGTTAGAGAAAGGCTAAAAACT 58.720 34.615 0.00 0.00 30.34 2.66
574 600 6.435292 AGAGAAAGGCTAAAAACTACTCCA 57.565 37.500 0.00 0.00 0.00 3.86
575 601 6.838382 AGAGAAAGGCTAAAAACTACTCCAA 58.162 36.000 0.00 0.00 0.00 3.53
583 609 6.427974 GCTAAAAACTACTCCAACTGTTCAC 58.572 40.000 0.00 0.00 0.00 3.18
584 610 6.037830 GCTAAAAACTACTCCAACTGTTCACA 59.962 38.462 0.00 0.00 0.00 3.58
644 673 3.874543 TGCATATAGGCCACGTTTTACAG 59.125 43.478 5.01 0.00 0.00 2.74
649 678 3.196939 AGGCCACGTTTTACAGTGTTA 57.803 42.857 5.01 0.00 36.69 2.41
676 708 4.459337 CACTCACAGTCTGTATGTAGTCCA 59.541 45.833 4.85 0.00 0.00 4.02
789 821 2.555199 CTATTGGCCTCTTTGGACTCG 58.445 52.381 3.32 0.00 46.68 4.18
812 845 4.095483 GTGCTGCTTTTAGTCATGCATAGT 59.905 41.667 0.00 0.00 34.79 2.12
820 853 2.362736 AGTCATGCATAGTGCTTGGTG 58.637 47.619 15.05 5.00 45.26 4.17
842 875 5.239525 GTGTGTTTTAATCTCCACTTGAGCT 59.760 40.000 0.00 0.00 41.18 4.09
843 876 5.827797 TGTGTTTTAATCTCCACTTGAGCTT 59.172 36.000 0.00 0.00 41.18 3.74
844 877 6.017109 TGTGTTTTAATCTCCACTTGAGCTTC 60.017 38.462 0.00 0.00 41.18 3.86
845 878 5.473504 TGTTTTAATCTCCACTTGAGCTTCC 59.526 40.000 0.00 0.00 41.18 3.46
846 879 4.908601 TTAATCTCCACTTGAGCTTCCA 57.091 40.909 0.00 0.00 41.18 3.53
847 880 5.441718 TTAATCTCCACTTGAGCTTCCAT 57.558 39.130 0.00 0.00 41.18 3.41
848 881 2.775911 TCTCCACTTGAGCTTCCATG 57.224 50.000 0.00 0.00 41.18 3.66
883 916 7.336931 GTCACCTGATATGTGATTAACCTTGTT 59.663 37.037 0.00 0.00 43.98 2.83
884 917 7.336679 TCACCTGATATGTGATTAACCTTGTTG 59.663 37.037 0.00 0.00 37.80 3.33
886 919 8.055181 ACCTGATATGTGATTAACCTTGTTGAT 58.945 33.333 0.00 0.00 0.00 2.57
894 927 9.883142 TGTGATTAACCTTGTTGATTTTCTTTT 57.117 25.926 0.00 0.00 0.00 2.27
951 992 1.877637 TGGGTGTCGTTGTTGAGATG 58.122 50.000 0.00 0.00 0.00 2.90
956 997 1.344438 TGTCGTTGTTGAGATGGCTCT 59.656 47.619 0.00 0.00 41.84 4.09
968 1009 1.736681 GATGGCTCTGCTCAACTCAAC 59.263 52.381 0.00 0.00 0.00 3.18
970 1011 0.250467 GGCTCTGCTCAACTCAACCA 60.250 55.000 0.00 0.00 0.00 3.67
972 1013 1.736681 GCTCTGCTCAACTCAACCATC 59.263 52.381 0.00 0.00 0.00 3.51
975 1016 1.998315 CTGCTCAACTCAACCATCGAG 59.002 52.381 0.00 0.00 36.53 4.04
988 1029 2.006888 CCATCGAGTGCCGTATGTTTT 58.993 47.619 0.00 0.00 39.75 2.43
996 1037 5.574055 CGAGTGCCGTATGTTTTAACTTCTA 59.426 40.000 0.00 0.00 0.00 2.10
999 1040 7.971455 AGTGCCGTATGTTTTAACTTCTATTC 58.029 34.615 0.00 0.00 0.00 1.75
1000 1041 7.604927 AGTGCCGTATGTTTTAACTTCTATTCA 59.395 33.333 0.00 0.00 0.00 2.57
1033 1074 4.034258 GGCGGTCGTCGAGTGTGA 62.034 66.667 0.00 0.00 42.43 3.58
1048 1089 5.357032 TCGAGTGTGATCTACAATGAGCTAA 59.643 40.000 3.56 0.00 41.89 3.09
1049 1090 5.457148 CGAGTGTGATCTACAATGAGCTAAC 59.543 44.000 3.56 0.00 41.89 2.34
1112 1153 1.541672 CCTCCCTCCCTCTCTCTCC 59.458 68.421 0.00 0.00 0.00 3.71
1113 1154 1.541672 CTCCCTCCCTCTCTCTCCC 59.458 68.421 0.00 0.00 0.00 4.30
1128 1169 1.364678 TCTCCCCCAAGGACATACTGA 59.635 52.381 0.00 0.00 40.93 3.41
1129 1170 2.022035 TCTCCCCCAAGGACATACTGAT 60.022 50.000 0.00 0.00 40.93 2.90
1130 1171 2.105477 CTCCCCCAAGGACATACTGATG 59.895 54.545 0.00 0.00 40.93 3.07
1131 1172 1.477558 CCCCCAAGGACATACTGATGC 60.478 57.143 0.00 0.00 38.24 3.91
1132 1173 1.492176 CCCCAAGGACATACTGATGCT 59.508 52.381 0.00 0.00 36.43 3.79
1189 1230 5.742446 CCGAGCATTTCTTTCTATTAGTGC 58.258 41.667 0.00 0.00 0.00 4.40
1195 1236 5.545658 TTTCTTTCTATTAGTGCGGCAAG 57.454 39.130 3.23 0.00 0.00 4.01
1219 1260 2.879026 GAGTCTGTTTGAGTGTTTCCCC 59.121 50.000 0.00 0.00 0.00 4.81
1258 1299 5.776173 ATCTTACTGTATTCCAGGTCTCG 57.224 43.478 0.00 0.00 46.06 4.04
1311 1352 2.825532 ACTGTTTGCAAACTGAGGTTGT 59.174 40.909 39.33 22.43 39.36 3.32
1331 1372 6.294508 GGTTGTGTGTTCTAATTAATGCAGGT 60.295 38.462 0.00 0.00 0.00 4.00
1463 1504 6.954684 AGATCTACAGAAGTAACCCAGAAAGA 59.045 38.462 0.00 0.00 0.00 2.52
1469 1510 3.938289 AGTAACCCAGAAAGAGTCGTC 57.062 47.619 0.00 0.00 0.00 4.20
1619 1660 5.069914 TGGTCTCTACTGCTTCACTTAAACA 59.930 40.000 0.00 0.00 0.00 2.83
1620 1661 6.166982 GGTCTCTACTGCTTCACTTAAACAT 58.833 40.000 0.00 0.00 0.00 2.71
2357 2475 5.605488 ACAAATATATCTACCCCAACGAGGT 59.395 40.000 0.00 0.00 41.64 3.85
2362 2480 1.553248 TCTACCCCAACGAGGTTGATG 59.447 52.381 9.91 3.48 45.28 3.07
2435 2568 3.713826 ATACCAAATCAACCGGTCTGT 57.286 42.857 8.04 0.00 34.12 3.41
2436 2569 1.892209 ACCAAATCAACCGGTCTGTC 58.108 50.000 8.04 0.00 0.00 3.51
2446 2579 4.081142 TCAACCGGTCTGTCACATGATAAT 60.081 41.667 8.04 0.00 0.00 1.28
2449 2582 5.984725 ACCGGTCTGTCACATGATAATTTA 58.015 37.500 0.00 0.00 0.00 1.40
2450 2583 6.591935 ACCGGTCTGTCACATGATAATTTAT 58.408 36.000 0.00 0.00 0.00 1.40
2451 2584 7.732025 ACCGGTCTGTCACATGATAATTTATA 58.268 34.615 0.00 0.00 0.00 0.98
2453 2586 8.712363 CCGGTCTGTCACATGATAATTTATAAG 58.288 37.037 0.00 0.00 0.00 1.73
2454 2587 8.712363 CGGTCTGTCACATGATAATTTATAAGG 58.288 37.037 0.00 0.00 0.00 2.69
2455 2588 8.507249 GGTCTGTCACATGATAATTTATAAGGC 58.493 37.037 0.00 0.00 0.00 4.35
2474 2615 0.984961 CCATGCCTCCTCTTCCCTCA 60.985 60.000 0.00 0.00 0.00 3.86
2492 2633 9.323985 CTTCCCTCAATTTGTTGTGATTTTTAA 57.676 29.630 0.00 0.00 0.00 1.52
2493 2634 8.885494 TCCCTCAATTTGTTGTGATTTTTAAG 57.115 30.769 0.00 0.00 0.00 1.85
2495 2636 7.442062 CCCTCAATTTGTTGTGATTTTTAAGCT 59.558 33.333 0.00 0.00 0.00 3.74
2496 2637 8.490355 CCTCAATTTGTTGTGATTTTTAAGCTC 58.510 33.333 0.00 0.00 0.00 4.09
2498 2639 7.440856 TCAATTTGTTGTGATTTTTAAGCTCCC 59.559 33.333 0.00 0.00 0.00 4.30
2499 2640 5.860941 TTGTTGTGATTTTTAAGCTCCCA 57.139 34.783 0.00 0.00 0.00 4.37
2500 2641 5.452078 TGTTGTGATTTTTAAGCTCCCAG 57.548 39.130 0.00 0.00 0.00 4.45
2502 2643 5.596361 TGTTGTGATTTTTAAGCTCCCAGAA 59.404 36.000 0.00 0.00 0.00 3.02
2503 2644 5.964958 TGTGATTTTTAAGCTCCCAGAAG 57.035 39.130 0.00 0.00 0.00 2.85
2504 2645 4.766891 TGTGATTTTTAAGCTCCCAGAAGG 59.233 41.667 0.00 0.00 0.00 3.46
2505 2646 5.010282 GTGATTTTTAAGCTCCCAGAAGGA 58.990 41.667 0.00 0.00 44.91 3.36
2506 2647 5.476945 GTGATTTTTAAGCTCCCAGAAGGAA 59.523 40.000 0.00 0.00 46.94 3.36
2507 2648 5.476945 TGATTTTTAAGCTCCCAGAAGGAAC 59.523 40.000 0.00 0.00 46.94 3.62
2509 2650 3.703001 TTAAGCTCCCAGAAGGAACTG 57.297 47.619 0.00 0.00 46.94 3.16
2510 2651 1.734655 AAGCTCCCAGAAGGAACTGA 58.265 50.000 0.00 0.00 46.94 3.41
2511 2652 1.734655 AGCTCCCAGAAGGAACTGAA 58.265 50.000 0.00 0.00 46.94 3.02
2513 2654 3.454858 AGCTCCCAGAAGGAACTGAATA 58.545 45.455 0.00 0.00 46.94 1.75
2515 2656 5.219739 AGCTCCCAGAAGGAACTGAATATA 58.780 41.667 0.00 0.00 46.94 0.86
2518 2659 7.001073 GCTCCCAGAAGGAACTGAATATAATT 58.999 38.462 0.00 0.00 46.94 1.40
2546 2693 5.775195 TCATCTGGTCTTCTACAGAAACTCA 59.225 40.000 0.00 0.00 45.81 3.41
2594 2777 3.214328 TCTCCTGCCTTTCTGTTGAAAC 58.786 45.455 0.00 0.00 37.27 2.78
2601 2784 3.457234 CCTTTCTGTTGAAACCTTTGCC 58.543 45.455 0.00 0.00 37.27 4.52
2609 2794 1.208259 GAAACCTTTGCCGCACTTTG 58.792 50.000 0.00 0.00 0.00 2.77
2630 3019 4.397064 GCTTTGTAGCTGTTGAAGTCTC 57.603 45.455 0.00 0.00 44.27 3.36
2632 3021 4.319118 GCTTTGTAGCTGTTGAAGTCTCAC 60.319 45.833 0.00 0.00 44.27 3.51
2633 3022 3.013276 TGTAGCTGTTGAAGTCTCACG 57.987 47.619 0.00 0.00 0.00 4.35
2672 3263 7.533426 ACTATTGCTTTTCTCATGACATTGTC 58.467 34.615 9.93 9.93 0.00 3.18
2674 3265 4.401022 TGCTTTTCTCATGACATTGTCCT 58.599 39.130 14.05 1.38 0.00 3.85
2679 3270 7.306983 GCTTTTCTCATGACATTGTCCTTTTTG 60.307 37.037 14.05 4.82 0.00 2.44
2680 3271 5.125100 TCTCATGACATTGTCCTTTTTGC 57.875 39.130 14.05 0.00 0.00 3.68
2687 3278 2.869233 TTGTCCTTTTTGCACTGCTC 57.131 45.000 1.98 0.00 0.00 4.26
2688 3279 1.761449 TGTCCTTTTTGCACTGCTCA 58.239 45.000 1.98 0.00 0.00 4.26
2738 4738 7.448161 TGTTTTGATCTTCAATATGTGTGGAGT 59.552 33.333 0.00 0.00 36.11 3.85
2740 4740 8.408043 TTTGATCTTCAATATGTGTGGAGTTT 57.592 30.769 0.00 0.00 36.11 2.66
2741 4741 9.513906 TTTGATCTTCAATATGTGTGGAGTTTA 57.486 29.630 0.00 0.00 36.11 2.01
2754 4904 9.912634 ATGTGTGGAGTTTATCTATTTTGTTTG 57.087 29.630 0.00 0.00 0.00 2.93
2756 4906 9.394477 GTGTGGAGTTTATCTATTTTGTTTGAC 57.606 33.333 0.00 0.00 0.00 3.18
2770 4920 4.074627 TGTTTGACGTGATGTTCCCTTA 57.925 40.909 0.00 0.00 0.00 2.69
2846 6637 0.601046 GTGGCAAGCTTCCAAAAGGC 60.601 55.000 16.19 8.61 35.01 4.35
3306 7097 8.221944 TGTCAAAGGTAAAGAATCCTTCCTTAA 58.778 33.333 0.00 0.00 42.38 1.85
3394 7187 4.444876 CCTTTTCTCCCTGAACTGAACTGA 60.445 45.833 0.00 0.00 33.88 3.41
3852 7648 4.125695 GAGGTAACGTCGGGCGCT 62.126 66.667 7.64 0.00 46.11 5.92
4200 8026 0.258774 AGGTTCCACAGCAAACACCT 59.741 50.000 0.00 0.00 0.00 4.00
4395 8250 1.886777 GCCGCTGAAGAGAGCATCC 60.887 63.158 0.00 0.00 39.07 3.51
4483 8343 3.118811 AGCCTGAAGAAGAAGAAGATCCG 60.119 47.826 0.00 0.00 0.00 4.18
4516 8376 3.144506 GGATCCGCTGATTCATGTCAAT 58.855 45.455 0.00 0.00 0.00 2.57
4517 8377 3.567164 GGATCCGCTGATTCATGTCAATT 59.433 43.478 0.00 0.00 0.00 2.32
4569 8429 4.319046 CCTCTTATCATTTGATCGTTGCGG 60.319 45.833 0.00 0.00 36.05 5.69
4576 8436 3.264897 GATCGTTGCGGCGCATCT 61.265 61.111 36.69 19.47 38.76 2.90
4577 8437 3.215606 GATCGTTGCGGCGCATCTC 62.216 63.158 36.69 25.29 38.76 2.75
4580 8440 2.883730 GTTGCGGCGCATCTCGTA 60.884 61.111 36.69 17.33 38.76 3.43
4581 8441 2.106131 TTGCGGCGCATCTCGTAT 59.894 55.556 36.69 0.00 38.76 3.06
4582 8442 2.237066 TTGCGGCGCATCTCGTATG 61.237 57.895 36.69 0.00 38.76 2.39
4583 8443 2.658593 GCGGCGCATCTCGTATGT 60.659 61.111 29.21 0.00 41.07 2.29
4584 8444 2.932083 GCGGCGCATCTCGTATGTG 61.932 63.158 29.21 8.93 41.07 3.21
4612 8472 5.163893 CGCAATCTTGGATAAGTTGTAACGT 60.164 40.000 0.00 0.00 35.38 3.99
4624 8484 5.119931 AGTTGTAACGTGTCGGTTATACA 57.880 39.130 0.00 0.00 35.08 2.29
4625 8485 5.527951 AGTTGTAACGTGTCGGTTATACAA 58.472 37.500 0.00 0.00 35.08 2.41
4640 8500 3.940209 ATACAACGGTTTAGACGTCCA 57.060 42.857 13.01 0.00 44.83 4.02
4648 8509 2.804527 GGTTTAGACGTCCACCTTGTTC 59.195 50.000 13.01 0.00 0.00 3.18
4653 8514 0.818040 ACGTCCACCTTGTTCTTGCC 60.818 55.000 0.00 0.00 0.00 4.52
4706 8568 2.035449 CAGGAATGGCATGGCATTGTAG 59.965 50.000 41.86 28.34 0.00 2.74
4707 8569 2.091720 AGGAATGGCATGGCATTGTAGA 60.092 45.455 41.86 13.64 0.00 2.59
4708 8570 2.035066 GGAATGGCATGGCATTGTAGAC 59.965 50.000 41.86 28.97 0.00 2.59
4752 8617 7.345691 TGTTTCCTTTCTATATCTGCATGGAA 58.654 34.615 0.00 0.00 0.00 3.53
4788 8654 3.863400 GCAATTGCATCAGGTTCTTGCTT 60.863 43.478 25.36 0.00 41.59 3.91
4824 8691 1.879380 CTTTGACAAGGTCGGCAATGA 59.121 47.619 0.00 0.00 34.95 2.57
4828 8695 2.290260 TGACAAGGTCGGCAATGAGATT 60.290 45.455 0.00 0.00 34.95 2.40
4857 8726 1.141657 ACCTTGTGATCACAGCAGTGT 59.858 47.619 26.48 18.05 46.01 3.55
4901 8770 4.320608 TGTCTCCAAAATTTGTGGAAGC 57.679 40.909 9.60 6.07 44.55 3.86
4915 8784 3.697542 TGTGGAAGCATGAATGAATGGAG 59.302 43.478 0.00 0.00 0.00 3.86
5000 8870 1.141881 CCCACTGCGCGAAGTATCT 59.858 57.895 21.84 0.00 0.00 1.98
5006 8876 2.115595 CTGCGCGAAGTATCTTGAGAG 58.884 52.381 12.10 0.00 0.00 3.20
5007 8877 1.743394 TGCGCGAAGTATCTTGAGAGA 59.257 47.619 12.10 0.00 36.09 3.10
5008 8878 2.113289 GCGCGAAGTATCTTGAGAGAC 58.887 52.381 12.10 0.00 36.58 3.36
5009 8879 2.722071 CGCGAAGTATCTTGAGAGACC 58.278 52.381 0.00 0.00 36.99 3.85
5012 8882 4.553156 CGCGAAGTATCTTGAGAGACCTAC 60.553 50.000 0.00 0.00 36.99 3.18
5018 8888 9.515226 GAAGTATCTTGAGAGACCTACATAGAT 57.485 37.037 2.38 0.00 36.99 1.98
5019 8889 9.515226 AAGTATCTTGAGAGACCTACATAGATC 57.485 37.037 2.38 0.00 36.99 2.75
5020 8890 8.107095 AGTATCTTGAGAGACCTACATAGATCC 58.893 40.741 2.38 0.00 36.99 3.36
5021 8891 5.636123 TCTTGAGAGACCTACATAGATCCC 58.364 45.833 0.00 0.00 0.00 3.85
5023 8893 4.730966 TGAGAGACCTACATAGATCCCAC 58.269 47.826 0.00 0.00 0.00 4.61
5024 8894 4.417183 TGAGAGACCTACATAGATCCCACT 59.583 45.833 0.00 0.00 0.00 4.00
5060 8950 9.730705 CCCACATAGATAATCACAATCATAGTT 57.269 33.333 0.00 0.00 0.00 2.24
5123 9013 4.412796 TGCTTCCATGGTAGAATCTGAG 57.587 45.455 21.61 4.11 0.00 3.35
5124 9014 3.137533 GCTTCCATGGTAGAATCTGAGC 58.862 50.000 21.61 9.50 0.00 4.26
5125 9015 3.432749 GCTTCCATGGTAGAATCTGAGCA 60.433 47.826 21.61 0.00 0.00 4.26
5126 9016 4.378774 CTTCCATGGTAGAATCTGAGCAG 58.621 47.826 12.88 0.00 0.00 4.24
5127 9017 2.103771 TCCATGGTAGAATCTGAGCAGC 59.896 50.000 12.58 0.00 0.00 5.25
5129 9019 1.571955 TGGTAGAATCTGAGCAGCCA 58.428 50.000 0.00 0.00 0.00 4.75
5130 9020 2.121948 TGGTAGAATCTGAGCAGCCAT 58.878 47.619 0.00 0.00 0.00 4.40
5131 9021 2.158856 TGGTAGAATCTGAGCAGCCATG 60.159 50.000 0.00 0.00 0.00 3.66
5154 9053 0.249741 ACAACAGTACCGCACAGACC 60.250 55.000 0.00 0.00 0.00 3.85
5156 9055 1.741327 AACAGTACCGCACAGACCGT 61.741 55.000 0.00 0.00 0.00 4.83
5178 9079 5.446206 CGTTCGAACCTTGTGAACAACTTTA 60.446 40.000 22.07 0.00 41.52 1.85
5213 9114 8.897752 AGTTTGATTGATTTTGAGATAGCTACC 58.102 33.333 0.00 0.00 0.00 3.18
5237 9138 3.754850 GCTTATTCCAAACGGTACCTTGT 59.245 43.478 10.90 0.00 0.00 3.16
5297 9198 9.110502 CATACAGCTCATATCAGCAATTCATAT 57.889 33.333 0.03 0.00 42.40 1.78
5412 9318 5.647658 TGTTTGGCCTTATGAAGTAGATGTG 59.352 40.000 3.32 0.00 0.00 3.21
5460 9366 8.450578 TTGATAGACTACATAAGCCAAAATGG 57.549 34.615 0.00 0.00 41.55 3.16
5465 9371 7.172342 AGACTACATAAGCCAAAATGGTTACA 58.828 34.615 0.00 0.00 40.46 2.41
5466 9372 7.336931 AGACTACATAAGCCAAAATGGTTACAG 59.663 37.037 0.00 0.00 40.46 2.74
5467 9373 7.172342 ACTACATAAGCCAAAATGGTTACAGA 58.828 34.615 0.00 0.00 40.46 3.41
5468 9374 7.834181 ACTACATAAGCCAAAATGGTTACAGAT 59.166 33.333 0.00 0.00 40.46 2.90
5533 9439 6.719365 CCGTATCATCTTTTGCTTCTAAAGG 58.281 40.000 0.00 0.00 34.22 3.11
5551 9457 3.963428 AGGTGGACTATCGGATTATGC 57.037 47.619 0.00 0.00 0.00 3.14
5586 9492 7.378966 GTCGAGGATGAAGTGATGGAAATATA 58.621 38.462 0.00 0.00 0.00 0.86
5589 9495 7.493971 CGAGGATGAAGTGATGGAAATATATCC 59.506 40.741 0.00 0.00 40.10 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.356818 GATCCAAGCTCCCCGAGACG 62.357 65.000 0.00 0.00 0.00 4.18
8 9 3.154473 CCGATCCAAGCTCCCCGA 61.154 66.667 0.00 0.00 0.00 5.14
9 10 4.918201 GCCGATCCAAGCTCCCCG 62.918 72.222 0.00 0.00 0.00 5.73
10 11 4.570874 GGCCGATCCAAGCTCCCC 62.571 72.222 0.00 0.00 34.01 4.81
11 12 4.918201 CGGCCGATCCAAGCTCCC 62.918 72.222 24.07 0.00 34.01 4.30
65 66 2.782222 CCTAGCTAGCACCGCGGAA 61.782 63.158 35.90 13.11 0.00 4.30
73 74 3.326880 GCCCTAATAAACCCTAGCTAGCA 59.673 47.826 18.83 1.89 0.00 3.49
101 102 4.655762 TGAATATTCCAGAGTCGGACTG 57.344 45.455 16.72 2.70 33.75 3.51
106 107 3.467803 GGGGTTGAATATTCCAGAGTCG 58.532 50.000 12.90 0.00 0.00 4.18
136 137 2.586900 GCGCGGTAAGATCTATCTGTC 58.413 52.381 8.83 0.00 37.19 3.51
138 139 1.729472 CGGCGCGGTAAGATCTATCTG 60.729 57.143 8.83 0.00 37.19 2.90
161 176 1.432657 GACGGCGGAGGAGAAGTAC 59.567 63.158 13.24 0.00 0.00 2.73
210 225 1.154016 ACTCGCGTGATTCGACAGG 60.154 57.895 16.04 0.00 42.86 4.00
240 255 1.427592 GCGCAATGAGCAGGAGACTC 61.428 60.000 0.30 0.00 46.13 3.36
242 257 0.179100 TAGCGCAATGAGCAGGAGAC 60.179 55.000 11.47 0.00 46.13 3.36
243 258 0.755079 ATAGCGCAATGAGCAGGAGA 59.245 50.000 11.47 0.00 46.13 3.71
245 260 1.412343 TGTATAGCGCAATGAGCAGGA 59.588 47.619 11.47 0.00 46.13 3.86
246 261 1.797046 CTGTATAGCGCAATGAGCAGG 59.203 52.381 11.47 0.00 46.13 4.85
247 262 2.474359 GTCTGTATAGCGCAATGAGCAG 59.526 50.000 11.47 10.10 46.13 4.24
248 263 2.101415 AGTCTGTATAGCGCAATGAGCA 59.899 45.455 11.47 0.00 46.13 4.26
249 264 2.748605 AGTCTGTATAGCGCAATGAGC 58.251 47.619 11.47 0.00 40.87 4.26
250 265 4.216472 TCCTAGTCTGTATAGCGCAATGAG 59.784 45.833 11.47 0.00 0.00 2.90
251 266 4.142038 TCCTAGTCTGTATAGCGCAATGA 58.858 43.478 11.47 0.00 0.00 2.57
252 267 4.022762 ACTCCTAGTCTGTATAGCGCAATG 60.023 45.833 11.47 0.00 0.00 2.82
253 268 4.145807 ACTCCTAGTCTGTATAGCGCAAT 58.854 43.478 11.47 0.00 0.00 3.56
254 269 3.552875 ACTCCTAGTCTGTATAGCGCAA 58.447 45.455 11.47 0.00 0.00 4.85
255 270 3.210232 ACTCCTAGTCTGTATAGCGCA 57.790 47.619 11.47 0.00 0.00 6.09
256 271 4.317488 ACTACTCCTAGTCTGTATAGCGC 58.683 47.826 0.00 0.00 0.00 5.92
257 272 6.864360 AAACTACTCCTAGTCTGTATAGCG 57.136 41.667 0.00 0.00 31.42 4.26
258 273 7.094677 GCCTAAACTACTCCTAGTCTGTATAGC 60.095 44.444 0.00 0.00 31.42 2.97
259 274 8.158789 AGCCTAAACTACTCCTAGTCTGTATAG 58.841 40.741 0.00 0.00 31.42 1.31
260 275 8.043429 AGCCTAAACTACTCCTAGTCTGTATA 57.957 38.462 0.00 0.00 31.42 1.47
261 276 6.913545 AGCCTAAACTACTCCTAGTCTGTAT 58.086 40.000 0.00 0.00 31.42 2.29
262 277 6.324601 AGCCTAAACTACTCCTAGTCTGTA 57.675 41.667 0.00 0.00 31.42 2.74
263 278 5.195848 AGCCTAAACTACTCCTAGTCTGT 57.804 43.478 0.00 0.00 31.42 3.41
264 279 7.826918 ATTAGCCTAAACTACTCCTAGTCTG 57.173 40.000 0.00 0.00 31.42 3.51
268 283 9.843334 CGAATAATTAGCCTAAACTACTCCTAG 57.157 37.037 0.00 0.00 0.00 3.02
272 287 9.525409 TTGACGAATAATTAGCCTAAACTACTC 57.475 33.333 0.00 0.00 0.00 2.59
284 299 9.370126 CGAGCCTTATTTTTGACGAATAATTAG 57.630 33.333 0.00 0.00 30.88 1.73
290 305 5.873179 TTCGAGCCTTATTTTTGACGAAT 57.127 34.783 0.00 0.00 34.51 3.34
297 312 5.880332 TGCTACAGATTCGAGCCTTATTTTT 59.120 36.000 6.00 0.00 35.24 1.94
334 356 4.477780 GCGGTCCGAGATAGAAATTCTAG 58.522 47.826 17.49 0.00 31.67 2.43
408 430 0.034089 GGTAGCCACTGCCTTGGATT 60.034 55.000 4.86 0.00 39.24 3.01
470 496 0.389426 GGCATGCCAAACAGAGCAAG 60.389 55.000 32.08 0.00 43.36 4.01
518 544 5.883685 TCTCCAGCATCTTCATTCATAGT 57.116 39.130 0.00 0.00 0.00 2.12
544 570 7.497925 AGTTTTTAGCCTTTCTCTAACAGTG 57.502 36.000 0.00 0.00 0.00 3.66
644 673 7.385205 ACATACAGACTGTGAGTGAAATAACAC 59.615 37.037 18.58 0.00 40.60 3.32
649 678 7.233389 ACTACATACAGACTGTGAGTGAAAT 57.767 36.000 18.58 0.00 0.00 2.17
789 821 2.995466 TGCATGACTAAAAGCAGCAC 57.005 45.000 0.00 0.00 32.48 4.40
812 845 4.037446 GTGGAGATTAAAACACACCAAGCA 59.963 41.667 0.00 0.00 34.16 3.91
842 875 2.644299 AGGTGACTCATGGAACATGGAA 59.356 45.455 9.15 0.00 39.75 3.53
843 876 2.026915 CAGGTGACTCATGGAACATGGA 60.027 50.000 9.15 0.00 41.99 3.41
844 877 2.026915 TCAGGTGACTCATGGAACATGG 60.027 50.000 9.15 3.47 41.99 3.66
845 878 3.339253 TCAGGTGACTCATGGAACATG 57.661 47.619 2.91 2.91 41.99 3.21
846 879 5.131642 ACATATCAGGTGACTCATGGAACAT 59.868 40.000 0.00 0.00 41.99 2.71
847 880 4.471025 ACATATCAGGTGACTCATGGAACA 59.529 41.667 0.00 0.00 42.00 3.18
848 881 4.813161 CACATATCAGGTGACTCATGGAAC 59.187 45.833 0.00 0.00 40.21 3.62
934 975 0.517316 GCCATCTCAACAACGACACC 59.483 55.000 0.00 0.00 0.00 4.16
935 976 1.461127 GAGCCATCTCAACAACGACAC 59.539 52.381 0.00 0.00 39.16 3.67
941 982 1.348696 TGAGCAGAGCCATCTCAACAA 59.651 47.619 0.00 0.00 41.81 2.83
943 984 2.105006 TTGAGCAGAGCCATCTCAAC 57.895 50.000 0.00 0.00 40.63 3.18
951 992 0.250467 TGGTTGAGTTGAGCAGAGCC 60.250 55.000 0.00 0.00 0.00 4.70
956 997 1.344438 ACTCGATGGTTGAGTTGAGCA 59.656 47.619 0.00 0.00 44.00 4.26
968 1009 1.651987 AAACATACGGCACTCGATGG 58.348 50.000 0.00 0.00 42.43 3.51
970 1011 4.501071 AGTTAAAACATACGGCACTCGAT 58.499 39.130 0.00 0.00 42.43 3.59
972 1013 4.387862 AGAAGTTAAAACATACGGCACTCG 59.612 41.667 0.00 0.00 45.88 4.18
975 1016 7.745015 TGAATAGAAGTTAAAACATACGGCAC 58.255 34.615 0.00 0.00 0.00 5.01
988 1029 5.355071 CAGCCTGCAACATGAATAGAAGTTA 59.645 40.000 0.00 0.00 0.00 2.24
996 1037 1.822990 CTTCCAGCCTGCAACATGAAT 59.177 47.619 0.00 0.00 0.00 2.57
999 1040 1.888018 CCTTCCAGCCTGCAACATG 59.112 57.895 0.00 0.00 0.00 3.21
1000 1041 1.980772 GCCTTCCAGCCTGCAACAT 60.981 57.895 0.00 0.00 0.00 2.71
1033 1074 6.694877 TGTACTCGTTAGCTCATTGTAGAT 57.305 37.500 0.00 0.00 0.00 1.98
1048 1089 2.364324 TCCTGAAAGCACTTGTACTCGT 59.636 45.455 0.00 0.00 0.00 4.18
1049 1090 2.731976 GTCCTGAAAGCACTTGTACTCG 59.268 50.000 0.00 0.00 0.00 4.18
1112 1153 1.492176 AGCATCAGTATGTCCTTGGGG 59.508 52.381 0.00 0.00 37.40 4.96
1113 1154 2.437281 AGAGCATCAGTATGTCCTTGGG 59.563 50.000 0.00 0.00 37.82 4.12
1128 1169 4.338879 AGCTTGTTTCCACATAAGAGCAT 58.661 39.130 0.00 0.00 36.05 3.79
1129 1170 3.753272 GAGCTTGTTTCCACATAAGAGCA 59.247 43.478 0.00 0.00 36.05 4.26
1130 1171 3.127721 GGAGCTTGTTTCCACATAAGAGC 59.872 47.826 0.00 0.00 34.47 4.09
1131 1172 4.394300 CAGGAGCTTGTTTCCACATAAGAG 59.606 45.833 0.00 0.00 37.18 2.85
1132 1173 4.326826 CAGGAGCTTGTTTCCACATAAGA 58.673 43.478 0.00 0.00 37.18 2.10
1189 1230 2.478134 CTCAAACAGACTCTTCTTGCCG 59.522 50.000 0.00 0.00 0.00 5.69
1195 1236 4.273724 GGGAAACACTCAAACAGACTCTTC 59.726 45.833 0.00 0.00 0.00 2.87
1258 1299 2.291465 TCATGAGCAACAACTGAAGCAC 59.709 45.455 0.00 0.00 0.00 4.40
1311 1352 5.565509 TCCACCTGCATTAATTAGAACACA 58.434 37.500 0.00 0.00 0.00 3.72
1331 1372 0.673644 GCAGCGCCTTAAGAACTCCA 60.674 55.000 2.29 0.00 0.00 3.86
1391 1432 1.547372 GTGTCAAAGTCCCGTAGCCTA 59.453 52.381 0.00 0.00 0.00 3.93
1400 1441 0.307760 CACTTGGCGTGTCAAAGTCC 59.692 55.000 0.00 0.00 38.84 3.85
1421 1462 3.386402 AGATCTCTTTAAGAAGGGAGGCG 59.614 47.826 0.00 0.00 45.24 5.52
1463 1504 2.285083 CTCTCGAAGATCTGGACGACT 58.715 52.381 13.31 0.00 33.89 4.18
1469 1510 0.249405 GCTGGCTCTCGAAGATCTGG 60.249 60.000 0.00 0.00 33.89 3.86
2327 2437 9.280174 CGTTGGGGTAGATATATTTGTTTACAT 57.720 33.333 0.00 0.00 0.00 2.29
2411 2544 6.184789 ACAGACCGGTTGATTTGGTATTAAT 58.815 36.000 9.42 0.00 35.75 1.40
2428 2561 8.712363 CCTTATAAATTATCATGTGACAGACCG 58.288 37.037 0.00 0.00 0.00 4.79
2435 2568 7.093814 GGCATGGCCTTATAAATTATCATGTGA 60.094 37.037 8.35 0.00 46.69 3.58
2436 2569 7.037438 GGCATGGCCTTATAAATTATCATGTG 58.963 38.462 8.35 0.00 46.69 3.21
2454 2587 2.194326 GGGAAGAGGAGGCATGGC 59.806 66.667 12.14 12.14 0.00 4.40
2455 2588 0.984961 TGAGGGAAGAGGAGGCATGG 60.985 60.000 0.00 0.00 0.00 3.66
2466 2607 7.790823 AAAAATCACAACAAATTGAGGGAAG 57.209 32.000 0.00 0.00 39.30 3.46
2474 2615 7.278875 TGGGAGCTTAAAAATCACAACAAATT 58.721 30.769 0.00 0.00 0.00 1.82
2493 2634 2.797177 ATTCAGTTCCTTCTGGGAGC 57.203 50.000 0.00 0.00 46.01 4.70
2518 2659 8.816894 AGTTTCTGTAGAAGACCAGATGAATAA 58.183 33.333 0.00 0.00 37.54 1.40
2521 2662 6.267699 TGAGTTTCTGTAGAAGACCAGATGAA 59.732 38.462 0.00 0.00 37.54 2.57
2523 2664 6.030548 TGAGTTTCTGTAGAAGACCAGATG 57.969 41.667 0.00 0.00 37.54 2.90
2524 2665 6.672266 TTGAGTTTCTGTAGAAGACCAGAT 57.328 37.500 0.00 0.00 37.54 2.90
2609 2794 4.319118 GTGAGACTTCAACAGCTACAAAGC 60.319 45.833 0.00 0.00 41.29 3.51
2659 3250 4.682860 GTGCAAAAAGGACAATGTCATGAG 59.317 41.667 15.86 0.85 38.62 2.90
2672 3263 2.806608 ACATGAGCAGTGCAAAAAGG 57.193 45.000 19.20 3.73 0.00 3.11
2674 3265 2.557924 CCCTACATGAGCAGTGCAAAAA 59.442 45.455 19.20 0.00 0.00 1.94
2679 3270 1.139654 TCATCCCTACATGAGCAGTGC 59.860 52.381 7.13 7.13 0.00 4.40
2680 3271 3.109044 CTCATCCCTACATGAGCAGTG 57.891 52.381 0.00 0.00 42.58 3.66
2687 3278 7.011763 CACAGTTTATCAACTCATCCCTACATG 59.988 40.741 0.00 0.00 41.69 3.21
2688 3279 7.050377 CACAGTTTATCAACTCATCCCTACAT 58.950 38.462 0.00 0.00 41.69 2.29
2740 4740 8.447833 GGAACATCACGTCAAACAAAATAGATA 58.552 33.333 0.00 0.00 0.00 1.98
2741 4741 7.305474 GGAACATCACGTCAAACAAAATAGAT 58.695 34.615 0.00 0.00 0.00 1.98
2746 4896 3.697045 AGGGAACATCACGTCAAACAAAA 59.303 39.130 0.00 0.00 0.00 2.44
2754 4904 4.138487 AGGAATAAGGGAACATCACGTC 57.862 45.455 0.00 0.00 0.00 4.34
2756 4906 5.897377 AAAAGGAATAAGGGAACATCACG 57.103 39.130 0.00 0.00 0.00 4.35
2770 4920 6.199393 GCGCTCGTGAATATTTAAAAGGAAT 58.801 36.000 0.00 0.00 0.00 3.01
2846 6637 2.050442 GGGCCGACAAGCAAAACG 60.050 61.111 0.00 0.00 0.00 3.60
2915 6706 2.439507 ACTGCAGGAGAAGAAAGGAACA 59.560 45.455 19.93 0.00 0.00 3.18
3306 7097 5.587388 CATTACAAGAGAAATGCATGGGT 57.413 39.130 0.00 0.00 0.00 4.51
3394 7187 4.024048 CACATCGTCTGCTTTTAACACCTT 60.024 41.667 0.00 0.00 0.00 3.50
3852 7648 2.154798 CTTGGCTCAGGTCGGACGAA 62.155 60.000 1.43 0.00 0.00 3.85
4179 8005 0.307760 GTGTTTGCTGTGGAACCTCG 59.692 55.000 0.00 0.00 34.36 4.63
4326 8152 4.320608 AAACGGCATGCTAATTAATGGG 57.679 40.909 18.92 0.00 0.00 4.00
4395 8250 8.074972 CCCAACTAGCTAAATTACTAGAGTACG 58.925 40.741 13.96 0.00 38.53 3.67
4483 8343 1.526917 CGGATCCCCTGCCATGAAC 60.527 63.158 6.06 0.00 0.00 3.18
4538 8398 9.265901 ACGATCAAATGATAAGAGGTCTAATTG 57.734 33.333 0.00 0.00 34.37 2.32
4569 8429 0.572590 GACACACATACGAGATGCGC 59.427 55.000 0.00 0.00 46.04 6.09
4576 8436 2.647529 AGATTGCGACACACATACGA 57.352 45.000 0.00 0.00 0.00 3.43
4577 8437 2.222796 CCAAGATTGCGACACACATACG 60.223 50.000 0.00 0.00 0.00 3.06
4578 8438 3.000041 TCCAAGATTGCGACACACATAC 59.000 45.455 0.00 0.00 0.00 2.39
4579 8439 3.326836 TCCAAGATTGCGACACACATA 57.673 42.857 0.00 0.00 0.00 2.29
4580 8440 2.183478 TCCAAGATTGCGACACACAT 57.817 45.000 0.00 0.00 0.00 3.21
4581 8441 2.183478 ATCCAAGATTGCGACACACA 57.817 45.000 0.00 0.00 0.00 3.72
4582 8442 3.684788 ACTTATCCAAGATTGCGACACAC 59.315 43.478 0.00 0.00 35.60 3.82
4583 8443 3.937814 ACTTATCCAAGATTGCGACACA 58.062 40.909 0.00 0.00 35.60 3.72
4584 8444 4.154195 ACAACTTATCCAAGATTGCGACAC 59.846 41.667 0.00 0.00 35.60 3.67
4612 8472 5.160641 GTCTAAACCGTTGTATAACCGACA 58.839 41.667 0.00 0.00 33.12 4.35
4624 8484 1.043022 AGGTGGACGTCTAAACCGTT 58.957 50.000 16.46 3.88 38.92 4.44
4625 8485 1.043022 AAGGTGGACGTCTAAACCGT 58.957 50.000 16.46 15.29 42.06 4.83
4637 8497 0.817634 CACGGCAAGAACAAGGTGGA 60.818 55.000 0.00 0.00 0.00 4.02
4640 8500 2.193536 GCCACGGCAAGAACAAGGT 61.194 57.895 2.36 0.00 41.49 3.50
4653 8514 2.660490 ACATCGAAAAATGTTGCCACG 58.340 42.857 0.00 0.00 36.47 4.94
4662 8523 6.744112 TGGTGAGCTTTTAACATCGAAAAAT 58.256 32.000 0.00 0.00 0.00 1.82
4788 8654 6.516739 TGTCAAAGGTAAAAACATCACACA 57.483 33.333 0.00 0.00 0.00 3.72
4857 8726 1.756430 TGTTGTTGCACACTAGCCAA 58.244 45.000 0.00 0.00 0.00 4.52
4901 8770 2.033801 GCCGGTTCTCCATTCATTCATG 59.966 50.000 1.90 0.00 0.00 3.07
4915 8784 3.202706 GGCCTCGAATGCCGGTTC 61.203 66.667 9.64 0.00 39.48 3.62
5000 8870 5.103473 AGTGGGATCTATGTAGGTCTCTCAA 60.103 44.000 2.14 0.00 34.94 3.02
5006 8876 6.153680 CCAGATAAGTGGGATCTATGTAGGTC 59.846 46.154 0.00 0.00 32.27 3.85
5007 8877 6.019748 CCAGATAAGTGGGATCTATGTAGGT 58.980 44.000 0.00 0.00 32.27 3.08
5008 8878 5.105146 GCCAGATAAGTGGGATCTATGTAGG 60.105 48.000 0.00 0.00 38.14 3.18
5009 8879 5.481824 TGCCAGATAAGTGGGATCTATGTAG 59.518 44.000 0.00 0.00 38.14 2.74
5012 8882 4.564406 GGTGCCAGATAAGTGGGATCTATG 60.564 50.000 0.00 0.00 40.50 2.23
5018 8888 0.548926 TGGGTGCCAGATAAGTGGGA 60.549 55.000 0.00 0.00 38.14 4.37
5019 8889 0.394352 GTGGGTGCCAGATAAGTGGG 60.394 60.000 0.00 0.00 38.14 4.61
5020 8890 0.327924 TGTGGGTGCCAGATAAGTGG 59.672 55.000 0.00 0.00 41.01 4.00
5021 8891 2.425143 ATGTGGGTGCCAGATAAGTG 57.575 50.000 0.00 0.00 35.67 3.16
5023 8893 4.630644 ATCTATGTGGGTGCCAGATAAG 57.369 45.455 0.00 0.00 38.90 1.73
5024 8894 6.272090 TGATTATCTATGTGGGTGCCAGATAA 59.728 38.462 9.12 9.12 38.90 1.75
5123 9013 3.365969 GGTACTGTTGTTAACATGGCTGC 60.366 47.826 9.56 0.00 41.26 5.25
5124 9014 3.120338 CGGTACTGTTGTTAACATGGCTG 60.120 47.826 9.56 9.30 41.26 4.85
5125 9015 3.071479 CGGTACTGTTGTTAACATGGCT 58.929 45.455 9.56 0.00 41.26 4.75
5126 9016 2.413634 GCGGTACTGTTGTTAACATGGC 60.414 50.000 9.56 3.94 41.26 4.40
5127 9017 2.809119 TGCGGTACTGTTGTTAACATGG 59.191 45.455 9.56 5.40 41.26 3.66
5129 9019 3.468770 TGTGCGGTACTGTTGTTAACAT 58.531 40.909 9.56 0.00 41.26 2.71
5130 9020 2.867368 CTGTGCGGTACTGTTGTTAACA 59.133 45.455 3.59 3.59 39.52 2.41
5131 9021 3.060070 GTCTGTGCGGTACTGTTGTTAAC 60.060 47.826 3.10 0.00 0.00 2.01
5154 9053 2.350498 AGTTGTTCACAAGGTTCGAACG 59.650 45.455 21.34 10.81 41.52 3.95
5156 9055 6.687081 ATAAAGTTGTTCACAAGGTTCGAA 57.313 33.333 0.00 0.00 36.39 3.71
5185 9086 8.571461 AGCTATCTCAAAATCAATCAAACTCA 57.429 30.769 0.00 0.00 0.00 3.41
5187 9088 8.897752 GGTAGCTATCTCAAAATCAATCAAACT 58.102 33.333 0.00 0.00 0.00 2.66
5188 9089 8.131731 GGGTAGCTATCTCAAAATCAATCAAAC 58.868 37.037 3.53 0.00 0.00 2.93
5189 9090 7.012327 CGGGTAGCTATCTCAAAATCAATCAAA 59.988 37.037 3.53 0.00 0.00 2.69
5213 9114 1.667212 GGTACCGTTTGGAATAAGCGG 59.333 52.381 12.32 12.32 46.83 5.52
5222 9123 2.290464 TGTTCACAAGGTACCGTTTGG 58.710 47.619 16.03 7.21 42.84 3.28
5226 9127 2.093341 ACAGTTGTTCACAAGGTACCGT 60.093 45.455 6.18 0.00 36.39 4.83
5227 9128 2.557317 ACAGTTGTTCACAAGGTACCG 58.443 47.619 6.18 0.00 36.39 4.02
5237 9138 1.315981 TGCGGCCAAACAGTTGTTCA 61.316 50.000 2.24 0.00 37.25 3.18
5266 9167 6.105397 TGCTGATATGAGCTGTATGATCAA 57.895 37.500 15.43 0.00 44.77 2.57
5273 9174 8.316214 TCATATGAATTGCTGATATGAGCTGTA 58.684 33.333 15.43 1.62 39.90 2.74
5297 9198 1.710244 AGACCACCCACCAATGATTCA 59.290 47.619 0.00 0.00 0.00 2.57
5385 9291 7.232534 ACATCTACTTCATAAGGCCAAACAAAA 59.767 33.333 5.01 0.00 0.00 2.44
5386 9292 6.719370 ACATCTACTTCATAAGGCCAAACAAA 59.281 34.615 5.01 0.00 0.00 2.83
5387 9293 6.150976 CACATCTACTTCATAAGGCCAAACAA 59.849 38.462 5.01 0.00 0.00 2.83
5388 9294 5.647658 CACATCTACTTCATAAGGCCAAACA 59.352 40.000 5.01 0.00 0.00 2.83
5389 9295 5.648092 ACACATCTACTTCATAAGGCCAAAC 59.352 40.000 5.01 0.00 0.00 2.93
5390 9296 5.815581 ACACATCTACTTCATAAGGCCAAA 58.184 37.500 5.01 0.00 0.00 3.28
5391 9297 5.045942 TGACACATCTACTTCATAAGGCCAA 60.046 40.000 5.01 0.00 0.00 4.52
5392 9298 4.469586 TGACACATCTACTTCATAAGGCCA 59.530 41.667 5.01 0.00 0.00 5.36
5393 9299 5.023533 TGACACATCTACTTCATAAGGCC 57.976 43.478 0.00 0.00 0.00 5.19
5427 9333 9.418045 GGCTTATGTAGTCTATCAATCTCTTTC 57.582 37.037 0.00 0.00 0.00 2.62
5437 9343 8.451908 AACCATTTTGGCTTATGTAGTCTATC 57.548 34.615 0.00 0.00 42.67 2.08
5486 9392 8.843262 ACGGCTTACTTAGTAAAAACAAAGATT 58.157 29.630 6.29 0.00 0.00 2.40
5487 9393 8.387190 ACGGCTTACTTAGTAAAAACAAAGAT 57.613 30.769 6.29 0.00 0.00 2.40
5533 9439 1.993370 GCGCATAATCCGATAGTCCAC 59.007 52.381 0.30 0.00 0.00 4.02
5555 9461 0.103208 ACTTCATCCTCGACGCCATC 59.897 55.000 0.00 0.00 0.00 3.51
5569 9475 9.040259 CCTCTAGGATATATTTCCATCACTTCA 57.960 37.037 13.88 0.00 38.32 3.02


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

AutoCloner maintained by Alex Coulton.