Multiple sequence alignment - TraesCS1B01G056700

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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 TraesCS1B01G056700 chr1B 100.000 4282 0 0 1 4282 39576552 39580833 0.000000e+00 7908.0
1 TraesCS1B01G056700 chr1B 92.529 174 11 2 570 742 606841323 606841151 9.190000e-62 248.0
2 TraesCS1B01G056700 chr1D 92.359 2722 125 33 688 3365 23004183 23006865 0.000000e+00 3797.0
3 TraesCS1B01G056700 chr1D 91.582 594 43 6 4 596 23003447 23004034 0.000000e+00 813.0
4 TraesCS1B01G056700 chr1D 93.671 237 11 3 3589 3822 23007542 23007777 6.810000e-93 351.0
5 TraesCS1B01G056700 chr1D 92.070 227 16 1 4056 4282 23008277 23008501 6.910000e-83 318.0
6 TraesCS1B01G056700 chr1D 88.285 239 4 5 3821 4035 23007881 23008119 9.130000e-67 265.0
7 TraesCS1B01G056700 chr1D 96.324 136 4 1 3374 3509 23007411 23007545 5.570000e-54 222.0
8 TraesCS1B01G056700 chr1D 77.457 346 68 5 114 449 458152288 458151943 9.390000e-47 198.0
9 TraesCS1B01G056700 chr1D 84.416 77 7 2 409 480 113829632 113829708 2.140000e-08 71.3
10 TraesCS1B01G056700 chr1A 90.556 2806 155 43 736 3494 24318935 24321677 0.000000e+00 3613.0
11 TraesCS1B01G056700 chr1A 93.056 288 10 3 3589 3866 24321687 24321974 3.080000e-111 412.0
12 TraesCS1B01G056700 chr1A 93.392 227 13 2 4056 4281 24322634 24322859 6.860000e-88 335.0
13 TraesCS1B01G056700 chr1A 88.750 80 5 3 3956 4033 39405192 39405115 1.270000e-15 95.3
14 TraesCS1B01G056700 chr4A 79.404 403 75 8 49 450 67259377 67258982 1.170000e-70 278.0
15 TraesCS1B01G056700 chr7A 94.545 165 9 0 575 739 347249351 347249515 5.490000e-64 255.0
16 TraesCS1B01G056700 chrUn 93.023 172 12 0 575 746 280766298 280766127 7.110000e-63 252.0
17 TraesCS1B01G056700 chr2A 93.023 172 12 0 574 745 378016077 378015906 7.110000e-63 252.0
18 TraesCS1B01G056700 chr2A 97.802 91 2 0 3502 3592 678161261 678161351 1.590000e-34 158.0
19 TraesCS1B01G056700 chr2A 82.781 151 22 4 114 263 32381593 32381446 9.660000e-27 132.0
20 TraesCS1B01G056700 chr2A 73.790 248 41 8 256 479 26932795 26933042 4.590000e-10 76.8
21 TraesCS1B01G056700 chr5A 91.620 179 13 1 564 742 290391688 290391864 3.310000e-61 246.0
22 TraesCS1B01G056700 chr5A 91.573 178 15 0 567 744 687682577 687682754 3.310000e-61 246.0
23 TraesCS1B01G056700 chr3D 91.620 179 14 1 570 748 6181337 6181160 3.310000e-61 246.0
24 TraesCS1B01G056700 chr3D 79.429 175 25 6 114 280 613752916 613752745 3.500000e-21 113.0
25 TraesCS1B01G056700 chr7B 82.517 286 42 7 488 768 591379296 591379578 1.190000e-60 244.0
26 TraesCS1B01G056700 chr7B 77.739 283 57 5 49 331 528254592 528254868 7.360000e-38 169.0
27 TraesCS1B01G056700 chr7B 77.966 118 23 3 335 450 618545007 618544891 2.140000e-08 71.3
28 TraesCS1B01G056700 chr4B 91.011 178 16 0 565 742 575778147 575778324 1.540000e-59 241.0
29 TraesCS1B01G056700 chr4B 82.160 213 32 6 534 741 53483864 53484075 1.220000e-40 178.0
30 TraesCS1B01G056700 chr4B 97.826 92 1 1 3501 3592 413719567 413719657 1.590000e-34 158.0
31 TraesCS1B01G056700 chr4B 91.228 114 7 3 3491 3601 497489227 497489114 7.420000e-33 152.0
32 TraesCS1B01G056700 chr4D 82.143 252 36 7 507 754 7595503 7595749 1.560000e-49 207.0
33 TraesCS1B01G056700 chr4D 78.233 317 66 3 99 414 487357349 487357035 2.610000e-47 200.0
34 TraesCS1B01G056700 chr6D 83.408 223 31 5 527 743 25787406 25787628 7.260000e-48 202.0
35 TraesCS1B01G056700 chr5D 77.812 329 55 11 135 450 260681162 260680839 2.030000e-43 187.0
36 TraesCS1B01G056700 chr5D 97.826 92 1 1 3502 3593 322375744 322375834 1.590000e-34 158.0
37 TraesCS1B01G056700 chr5D 94.949 99 4 1 3506 3604 343797652 343797555 2.060000e-33 154.0
38 TraesCS1B01G056700 chr5D 74.922 319 55 16 109 414 45661869 45662175 5.810000e-24 122.0
39 TraesCS1B01G056700 chr3A 78.358 268 50 5 72 339 476399063 476399322 2.650000e-37 167.0
40 TraesCS1B01G056700 chr3A 96.809 94 3 0 3503 3596 437858540 437858447 1.590000e-34 158.0
41 TraesCS1B01G056700 chr3B 98.889 90 0 1 3503 3592 142864142 142864054 4.430000e-35 159.0
42 TraesCS1B01G056700 chr3B 95.918 98 3 1 3496 3593 21406337 21406241 1.590000e-34 158.0
43 TraesCS1B01G056700 chr3B 85.714 77 6 2 409 480 800980817 800980893 4.590000e-10 76.8
44 TraesCS1B01G056700 chr6A 92.593 108 6 2 3494 3601 563128007 563127902 2.060000e-33 154.0
45 TraesCS1B01G056700 chr7D 82.353 170 25 4 113 279 590915556 590915389 4.460000e-30 143.0
46 TraesCS1B01G056700 chr7D 74.373 359 59 19 140 480 104362933 104363276 5.810000e-24 122.0
47 TraesCS1B01G056700 chr2B 77.308 260 42 8 140 388 514707953 514707700 2.080000e-28 137.0
48 TraesCS1B01G056700 chr5B 85.526 76 6 1 409 479 626490995 626490920 1.650000e-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 TraesCS1B01G056700 chr1B 39576552 39580833 4281 False 7908.000000 7908 100.000000 1 4282 1 chr1B.!!$F1 4281
1 TraesCS1B01G056700 chr1D 23003447 23008501 5054 False 961.000000 3797 92.381833 4 4282 6 chr1D.!!$F2 4278
2 TraesCS1B01G056700 chr1A 24318935 24322859 3924 False 1453.333333 3613 92.334667 736 4281 3 chr1A.!!$F1 3545

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
235 236 0.611200 CACTGTTCCGGTGATGGGTA 59.389 55.000 0.00 0.0 42.79 3.69 F
429 430 0.714439 GCCTTAGCACGACGACTTTC 59.286 55.000 0.00 0.0 39.53 2.62 F
438 439 0.728466 CGACGACTTTCCGACTGTCC 60.728 60.000 1.55 0.0 0.00 4.02 F
1178 1252 1.111116 CCCCGTACCGAGATAGGCAA 61.111 60.000 0.00 0.0 33.69 4.52 F
1292 1366 0.038166 AAGCCGCTCCTTGATTTGGA 59.962 50.000 0.00 0.0 0.00 3.53 F
2199 2299 1.078143 AAGAATGTCGGCAGGGCTC 60.078 57.895 0.00 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1196 1270 0.035056 AAATCAAGGGGCGACAGGAG 60.035 55.0 0.00 0.0 0.00 3.69 R
1273 1347 0.038166 TCCAAATCAAGGAGCGGCTT 59.962 50.0 2.97 0.0 0.00 4.35 R
1274 1348 0.393537 CTCCAAATCAAGGAGCGGCT 60.394 55.0 0.00 0.0 45.51 5.52 R
2456 2556 0.251297 TGCTGTTGGGTGGGATCTTG 60.251 55.0 0.00 0.0 0.00 3.02 R
3017 3124 0.965439 TTTGAATCGGCCTGTTTGGG 59.035 50.0 0.00 0.0 36.00 4.12 R
4045 4842 0.036732 TTGTTGGCTGCCACCTCTAG 59.963 55.0 23.30 0.0 30.78 2.43 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 167 2.036475 TCTGTGTCTTGCTCAGGAAGAC 59.964 50.000 27.56 27.56 46.45 3.01
176 177 2.282958 AGGAAGACGAGGCGGTGA 60.283 61.111 0.00 0.00 0.00 4.02
206 207 6.101881 CCCCTAAAGATGGAATAAGGTTCTCT 59.898 42.308 0.00 0.00 0.00 3.10
235 236 0.611200 CACTGTTCCGGTGATGGGTA 59.389 55.000 0.00 0.00 42.79 3.69
243 244 1.623311 CCGGTGATGGGTATAGCATCA 59.377 52.381 4.02 8.28 33.50 3.07
295 296 0.747255 ATCTCGTGGGATTCAGTCGG 59.253 55.000 0.00 0.00 0.00 4.79
299 300 1.901085 GTGGGATTCAGTCGGAGCT 59.099 57.895 0.00 0.00 0.00 4.09
306 307 1.048601 TTCAGTCGGAGCTGGTCTTT 58.951 50.000 6.83 0.00 37.12 2.52
314 315 1.680249 GGAGCTGGTCTTTGGTGGATC 60.680 57.143 6.83 0.00 0.00 3.36
317 318 1.457346 CTGGTCTTTGGTGGATCTGC 58.543 55.000 0.00 0.00 0.00 4.26
323 324 1.734465 CTTTGGTGGATCTGCTTCGAC 59.266 52.381 0.00 0.00 0.00 4.20
345 346 2.557056 CCAGTCTTCCTTCGTGTGTCTA 59.443 50.000 0.00 0.00 0.00 2.59
348 349 3.827302 AGTCTTCCTTCGTGTGTCTACAT 59.173 43.478 0.00 0.00 39.39 2.29
359 360 2.708861 TGTGTCTACATGTTGGACCCTT 59.291 45.455 21.05 0.00 0.00 3.95
360 361 3.137544 TGTGTCTACATGTTGGACCCTTT 59.862 43.478 21.05 0.00 0.00 3.11
361 362 3.751698 GTGTCTACATGTTGGACCCTTTC 59.248 47.826 21.05 9.02 0.00 2.62
362 363 3.392947 TGTCTACATGTTGGACCCTTTCA 59.607 43.478 21.05 6.31 0.00 2.69
375 376 7.510675 TGGACCCTTTCAATCTATACTTCTT 57.489 36.000 0.00 0.00 0.00 2.52
379 380 8.809468 ACCCTTTCAATCTATACTTCTTTTCC 57.191 34.615 0.00 0.00 0.00 3.13
383 384 9.587772 CTTTCAATCTATACTTCTTTTCCTCGA 57.412 33.333 0.00 0.00 0.00 4.04
429 430 0.714439 GCCTTAGCACGACGACTTTC 59.286 55.000 0.00 0.00 39.53 2.62
438 439 0.728466 CGACGACTTTCCGACTGTCC 60.728 60.000 1.55 0.00 0.00 4.02
448 449 2.033372 TCCGACTGTCCACTACAACAA 58.967 47.619 1.55 0.00 37.74 2.83
457 458 1.302511 ACTACAACAAGCCCGGCTG 60.303 57.895 14.19 9.90 39.62 4.85
458 459 1.302511 CTACAACAAGCCCGGCTGT 60.303 57.895 14.19 10.03 39.62 4.40
460 461 4.347453 CAACAAGCCCGGCTGTGC 62.347 66.667 14.19 0.00 39.62 4.57
471 472 3.005539 GCTGTGCTGAGGGAGGGA 61.006 66.667 0.00 0.00 0.00 4.20
485 486 2.880890 GGGAGGGATGATGACAAAATCG 59.119 50.000 0.00 0.00 0.00 3.34
497 498 2.139917 ACAAAATCGCGCTTGTAGTCA 58.860 42.857 16.17 0.00 34.04 3.41
502 503 2.158330 CGCGCTTGTAGTCATCGCA 61.158 57.895 5.56 0.00 41.95 5.10
515 516 2.927477 GTCATCGCAAAATGGTCTACGA 59.073 45.455 0.00 0.00 0.00 3.43
524 525 5.512788 GCAAAATGGTCTACGAACATGAATG 59.487 40.000 0.00 0.00 39.25 2.67
528 529 4.323417 TGGTCTACGAACATGAATGCTTT 58.677 39.130 0.00 0.00 0.00 3.51
564 565 9.723601 ATTTTTGTGTTTTTCATACTGCCATAT 57.276 25.926 0.00 0.00 0.00 1.78
587 650 6.494666 TCATGATAAATACTCCCTCCGTTT 57.505 37.500 0.00 0.00 0.00 3.60
597 660 9.916360 AAATACTCCCTCCGTTTCTAAATATTT 57.084 29.630 5.89 5.89 0.00 1.40
604 667 9.169592 CCCTCCGTTTCTAAATATTTGTCTTTA 57.830 33.333 11.05 0.00 0.00 1.85
633 696 7.375834 AGATTTCAACAAGTGACTACATACGA 58.624 34.615 0.00 0.00 35.39 3.43
635 698 7.402811 TTTCAACAAGTGACTACATACGAAG 57.597 36.000 0.00 0.00 35.39 3.79
636 699 4.921515 TCAACAAGTGACTACATACGAAGC 59.078 41.667 0.00 0.00 0.00 3.86
637 700 4.514781 ACAAGTGACTACATACGAAGCA 57.485 40.909 0.00 0.00 0.00 3.91
639 702 5.294356 ACAAGTGACTACATACGAAGCAAA 58.706 37.500 0.00 0.00 0.00 3.68
642 705 6.408858 AGTGACTACATACGAAGCAAAATG 57.591 37.500 0.00 0.00 0.00 2.32
643 706 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
644 707 6.311445 AGTGACTACATACGAAGCAAAATGAG 59.689 38.462 0.00 0.00 0.00 2.90
647 710 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
650 713 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
652 715 7.549134 ACATACGAAGCAAAATGAGTGAATCTA 59.451 33.333 0.00 0.00 0.00 1.98
653 716 6.170675 ACGAAGCAAAATGAGTGAATCTAC 57.829 37.500 0.00 0.00 0.00 2.59
655 718 6.017933 CGAAGCAAAATGAGTGAATCTACAC 58.982 40.000 0.00 0.00 40.60 2.90
698 761 9.905713 ATACATCTGTATGTGGTAGTTCATTTT 57.094 29.630 2.10 0.00 45.99 1.82
699 762 8.044060 ACATCTGTATGTGGTAGTTCATTTTG 57.956 34.615 0.00 0.00 44.79 2.44
703 766 9.295825 TCTGTATGTGGTAGTTCATTTTGAATT 57.704 29.630 0.00 0.00 38.79 2.17
745 808 4.993029 AAAACAGAGGGAGTAGATCGAG 57.007 45.455 0.00 0.00 0.00 4.04
820 886 2.747989 CCCGAGCTAGGAAAAAGGAAAC 59.252 50.000 15.38 0.00 0.00 2.78
831 899 4.568760 GGAAAAAGGAAACACGCAAATGAA 59.431 37.500 0.00 0.00 0.00 2.57
851 919 6.090483 TGAAAACGGAAATGGAAAGCATTA 57.910 33.333 0.00 0.00 0.00 1.90
880 948 6.466812 CCGTCTTCAACATTAATGACGTTAG 58.533 40.000 22.16 11.41 43.56 2.34
1036 1110 4.573900 CCTGGATCCGAGATTATTCCTTG 58.426 47.826 7.39 0.00 0.00 3.61
1167 1241 3.782443 CTGGTGAGCCCCCGTACC 61.782 72.222 0.00 0.00 0.00 3.34
1176 1250 2.273912 CCCCCGTACCGAGATAGGC 61.274 68.421 0.00 0.00 33.69 3.93
1178 1252 1.111116 CCCCGTACCGAGATAGGCAA 61.111 60.000 0.00 0.00 33.69 4.52
1182 1256 3.057734 CCGTACCGAGATAGGCAATTTC 58.942 50.000 0.00 0.00 33.69 2.17
1185 1259 1.843851 ACCGAGATAGGCAATTTCCCA 59.156 47.619 0.00 0.00 33.69 4.37
1188 1262 3.433598 CCGAGATAGGCAATTTCCCAAGA 60.434 47.826 0.00 0.00 0.00 3.02
1196 1270 4.021104 AGGCAATTTCCCAAGAAAAGTAGC 60.021 41.667 0.00 0.00 44.91 3.58
1199 1273 5.714047 CAATTTCCCAAGAAAAGTAGCTCC 58.286 41.667 0.00 0.00 44.91 4.70
1210 1284 2.038975 TAGCTCCTGTCGCCCCTT 59.961 61.111 0.00 0.00 0.00 3.95
1273 1347 8.713708 CTTCCAAGGAAGGTATCTCTAGATAA 57.286 38.462 18.98 0.00 45.60 1.75
1274 1348 9.148879 CTTCCAAGGAAGGTATCTCTAGATAAA 57.851 37.037 18.98 0.00 45.60 1.40
1292 1366 0.038166 AAGCCGCTCCTTGATTTGGA 59.962 50.000 0.00 0.00 0.00 3.53
1305 1379 7.661040 TCCTTGATTTGGAGAATTTTCTGTTC 58.339 34.615 0.00 0.00 37.73 3.18
1401 1477 7.118101 AGCAATTATAGTTTAACGGACGTTTCA 59.882 33.333 15.64 0.40 39.31 2.69
1402 1478 7.745594 GCAATTATAGTTTAACGGACGTTTCAA 59.254 33.333 15.64 6.61 39.31 2.69
1449 1527 4.610605 TTAGGGTGTCTGTTCATCGAAA 57.389 40.909 0.00 0.00 0.00 3.46
1475 1553 1.304134 ATTGGCCTGACGGGTTTCC 60.304 57.895 3.32 0.00 37.43 3.13
1508 1586 5.944013 TGATTTGTTGTTCTGTCAAACGAA 58.056 33.333 0.00 0.00 34.63 3.85
1527 1606 5.464168 ACGAAAGAGGATTTTGATTTGCAG 58.536 37.500 0.00 0.00 0.00 4.41
1529 1608 3.498927 AGAGGATTTTGATTTGCAGCG 57.501 42.857 0.00 0.00 0.00 5.18
1535 1614 4.500477 GGATTTTGATTTGCAGCGTATCAC 59.500 41.667 8.38 0.00 0.00 3.06
1542 1621 3.312504 CAGCGTATCACGTCGGCG 61.313 66.667 8.42 8.42 44.73 6.46
1552 1631 2.795973 CGTCGGCGTATGTCAGGA 59.204 61.111 6.85 0.00 0.00 3.86
1584 1675 6.507023 AGTGGAATGCTCTGTTTAGTTTTTG 58.493 36.000 0.00 0.00 0.00 2.44
1739 1835 1.300971 CCCTCAACAGCGTGGACATG 61.301 60.000 0.00 0.00 0.00 3.21
1795 1891 1.378250 GCACCTTGGAGCAGCTGAT 60.378 57.895 20.43 12.64 0.00 2.90
1856 1952 5.149054 CGGAGCAATTCATCTTCACTTAC 57.851 43.478 0.00 0.00 0.00 2.34
1985 2081 3.192844 TCGGCGAGGATAATATGAACCTC 59.807 47.826 4.99 6.35 43.58 3.85
2072 2172 7.992754 ATGATTCTCTAGTTGTTTGCTCTTT 57.007 32.000 0.00 0.00 0.00 2.52
2073 2173 7.807977 TGATTCTCTAGTTGTTTGCTCTTTT 57.192 32.000 0.00 0.00 0.00 2.27
2078 2178 7.047891 TCTCTAGTTGTTTGCTCTTTTCTTGA 58.952 34.615 0.00 0.00 0.00 3.02
2098 2198 9.445786 TTCTTGATGTCTGTTTCGTTAAAATTC 57.554 29.630 0.00 0.00 0.00 2.17
2199 2299 1.078143 AAGAATGTCGGCAGGGCTC 60.078 57.895 0.00 0.00 0.00 4.70
2259 2359 1.615651 GGTTGGGTATGGCATGACACA 60.616 52.381 1.45 8.91 0.00 3.72
2261 2361 2.055684 TGGGTATGGCATGACACATG 57.944 50.000 1.45 7.29 0.00 3.21
2413 2513 7.823799 TCATGTGCAATATTACTTTCTGTCTCA 59.176 33.333 0.00 0.00 0.00 3.27
2501 2601 4.344968 AGAAGTTTTTGGGGAGGTGATTTG 59.655 41.667 0.00 0.00 0.00 2.32
2527 2627 5.221925 TGTCCCTTTTTCTGCTGTATTCTCT 60.222 40.000 0.00 0.00 0.00 3.10
2531 2631 5.495640 CTTTTTCTGCTGTATTCTCTCCCT 58.504 41.667 0.00 0.00 0.00 4.20
2543 2643 2.852449 TCTCTCCCTCAGTATGCTACG 58.148 52.381 0.00 0.00 34.76 3.51
2563 2663 3.194755 ACGCTTTCCACTTTTCCAGTTTT 59.805 39.130 0.00 0.00 30.92 2.43
2803 2904 1.202394 GGTTTGTCACACAGCAATGCA 60.202 47.619 8.35 0.00 0.00 3.96
2816 2917 2.674852 AGCAATGCACTCTCATGTTACG 59.325 45.455 8.35 0.00 0.00 3.18
2843 2944 9.467258 CAATTTTGCCACATATTTCACCTATAG 57.533 33.333 0.00 0.00 0.00 1.31
2884 2985 6.018832 CCTTGCAGTTTTTACCTTTCACATTG 60.019 38.462 0.00 0.00 0.00 2.82
2885 2986 5.971763 TGCAGTTTTTACCTTTCACATTGT 58.028 33.333 0.00 0.00 0.00 2.71
2886 2987 7.101652 TGCAGTTTTTACCTTTCACATTGTA 57.898 32.000 0.00 0.00 0.00 2.41
2887 2988 7.721402 TGCAGTTTTTACCTTTCACATTGTAT 58.279 30.769 0.00 0.00 0.00 2.29
2888 2989 7.865385 TGCAGTTTTTACCTTTCACATTGTATC 59.135 33.333 0.00 0.00 0.00 2.24
2889 2990 7.865385 GCAGTTTTTACCTTTCACATTGTATCA 59.135 33.333 0.00 0.00 0.00 2.15
2899 3006 9.226606 CCTTTCACATTGTATCAGTAAACCTTA 57.773 33.333 0.00 0.00 0.00 2.69
2960 3067 3.368427 CCTTTCCTAGCGAACAGACATCA 60.368 47.826 0.00 0.00 0.00 3.07
2993 3100 6.183360 CGACAATTCATCGACCTAATTCAACA 60.183 38.462 3.03 0.00 42.25 3.33
3017 3124 0.318120 CCATCACCAAACCAACTGGC 59.682 55.000 0.00 0.00 37.48 4.85
3020 3127 1.760086 CACCAAACCAACTGGCCCA 60.760 57.895 0.00 0.00 37.48 5.36
3096 3203 1.131126 GACATCATGCTTTGTGACCGG 59.869 52.381 0.00 0.00 0.00 5.28
3150 3257 0.664761 CTGTGGACAAGTTGGCACTG 59.335 55.000 11.70 7.32 31.60 3.66
3217 3324 4.666253 TTGCCCCAGCTGAGCACC 62.666 66.667 25.28 6.83 40.80 5.01
3226 3333 2.548875 CAGCTGAGCACCTGTATCTTC 58.451 52.381 8.42 0.00 0.00 2.87
3227 3334 1.484240 AGCTGAGCACCTGTATCTTCC 59.516 52.381 7.39 0.00 0.00 3.46
3229 3336 2.093235 GCTGAGCACCTGTATCTTCCTT 60.093 50.000 0.00 0.00 0.00 3.36
3230 3337 3.791245 CTGAGCACCTGTATCTTCCTTC 58.209 50.000 0.00 0.00 0.00 3.46
3321 3437 7.691463 GTCGAAAAATTGTGATTCTGATGAGAG 59.309 37.037 0.00 0.00 0.00 3.20
3383 4036 1.323412 GCCATCTCGAGCTCTCCTTA 58.677 55.000 12.85 0.00 0.00 2.69
3386 4039 2.293122 CCATCTCGAGCTCTCCTTACAG 59.707 54.545 12.85 0.00 0.00 2.74
3516 4174 9.710818 TTGTAAGTCAAATATAGTACTCCCTCT 57.289 33.333 0.00 0.00 32.64 3.69
3517 4175 9.132923 TGTAAGTCAAATATAGTACTCCCTCTG 57.867 37.037 0.00 0.00 0.00 3.35
3518 4176 9.134055 GTAAGTCAAATATAGTACTCCCTCTGT 57.866 37.037 0.00 0.00 0.00 3.41
3520 4178 9.710818 AAGTCAAATATAGTACTCCCTCTGTAA 57.289 33.333 0.00 0.00 0.00 2.41
3521 4179 9.710818 AGTCAAATATAGTACTCCCTCTGTAAA 57.289 33.333 0.00 0.00 0.00 2.01
3522 4180 9.747293 GTCAAATATAGTACTCCCTCTGTAAAC 57.253 37.037 0.00 0.00 0.00 2.01
3523 4181 9.710818 TCAAATATAGTACTCCCTCTGTAAACT 57.289 33.333 0.00 0.00 0.00 2.66
3534 4192 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
3536 4194 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
3586 4244 9.813446 AAACACTCTTATATTAGTTTACGGAGG 57.187 33.333 0.00 0.00 0.00 4.30
3587 4245 7.949434 ACACTCTTATATTAGTTTACGGAGGG 58.051 38.462 0.00 0.00 0.00 4.30
3598 4256 3.657398 TTACGGAGGGAGTATCTGACA 57.343 47.619 0.00 0.00 33.73 3.58
3758 4419 2.251409 TCAAGATAGCTGCAGCCATC 57.749 50.000 31.98 31.98 43.38 3.51
3837 4609 4.082679 GCATATTAGAGTAGAGGGTGGTCG 60.083 50.000 0.00 0.00 0.00 4.79
3900 4674 0.461163 CTTGTCACACCACACGGTCA 60.461 55.000 0.00 0.00 44.71 4.02
3925 4699 2.029288 CGACATGGCACGCTGTCTT 61.029 57.895 15.48 0.00 40.14 3.01
3968 4765 2.163010 CCTGCAAGAGGTTTGCTATGTG 59.837 50.000 12.45 0.05 45.13 3.21
4035 4832 3.698029 TGCTGCTTCTTTTGTCTGAAC 57.302 42.857 0.00 0.00 0.00 3.18
4038 4835 3.563390 GCTGCTTCTTTTGTCTGAACTCT 59.437 43.478 0.00 0.00 0.00 3.24
4039 4836 4.554330 GCTGCTTCTTTTGTCTGAACTCTG 60.554 45.833 0.00 0.00 0.00 3.35
4041 4838 5.185454 TGCTTCTTTTGTCTGAACTCTGAA 58.815 37.500 0.00 0.00 0.00 3.02
4042 4839 5.295292 TGCTTCTTTTGTCTGAACTCTGAAG 59.705 40.000 0.00 0.00 33.66 3.02
4043 4840 5.295540 GCTTCTTTTGTCTGAACTCTGAAGT 59.704 40.000 0.00 0.00 37.32 3.01
4044 4841 6.510960 GCTTCTTTTGTCTGAACTCTGAAGTC 60.511 42.308 0.00 0.00 33.48 3.01
4045 4842 5.360591 TCTTTTGTCTGAACTCTGAAGTCC 58.639 41.667 0.00 0.00 33.48 3.85
4046 4843 5.129485 TCTTTTGTCTGAACTCTGAAGTCCT 59.871 40.000 0.00 0.00 33.48 3.85
4047 4844 6.323996 TCTTTTGTCTGAACTCTGAAGTCCTA 59.676 38.462 0.00 0.00 33.48 2.94
4048 4845 5.713792 TTGTCTGAACTCTGAAGTCCTAG 57.286 43.478 0.00 0.00 33.48 3.02
4051 4848 4.398044 GTCTGAACTCTGAAGTCCTAGAGG 59.602 50.000 0.00 0.00 43.65 3.69
4054 4851 3.094484 ACTCTGAAGTCCTAGAGGTGG 57.906 52.381 0.00 0.00 43.65 4.61
4059 5554 1.268283 AAGTCCTAGAGGTGGCAGCC 61.268 60.000 13.95 3.66 36.34 4.85
4086 5581 7.997482 ACAAACTTTTCTTCTCCCTAAAAGAC 58.003 34.615 12.32 0.00 40.87 3.01
4091 5586 3.152341 TCTTCTCCCTAAAAGACGACGT 58.848 45.455 0.00 0.00 0.00 4.34
4149 5644 6.638610 TGCAATTCCATAATAGGGTTTTGTG 58.361 36.000 9.15 0.00 0.00 3.33
4187 5682 6.206438 TCATCTGGATTCGAAAAATGTTCACA 59.794 34.615 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.730680 CATGTTAACTCCTTACTAAATGCTTGT 58.269 33.333 7.22 0.00 0.00 3.16
1 2 8.946085 TCATGTTAACTCCTTACTAAATGCTTG 58.054 33.333 7.22 0.00 0.00 4.01
2 3 8.947115 GTCATGTTAACTCCTTACTAAATGCTT 58.053 33.333 7.22 0.00 0.00 3.91
57 58 1.226974 CACCACGTCTCCATAGCCG 60.227 63.158 0.00 0.00 0.00 5.52
58 59 1.144057 CCACCACGTCTCCATAGCC 59.856 63.158 0.00 0.00 0.00 3.93
95 96 1.304464 CAAAGCAAGGTCCCTCCCC 60.304 63.158 0.00 0.00 36.75 4.81
104 105 6.735678 AAAACACCTAAAAACAAAGCAAGG 57.264 33.333 0.00 0.00 0.00 3.61
136 137 2.438021 AGCAAGACACAGACCCTAAACA 59.562 45.455 0.00 0.00 0.00 2.83
176 177 5.075067 CCTTATTCCATCTTTAGGGGGTCAT 59.925 44.000 0.00 0.00 0.00 3.06
206 207 2.656069 GGAACAGTGGCTAGGCGGA 61.656 63.158 12.19 0.00 0.00 5.54
235 236 0.742281 GCGCCATCCGATGATGCTAT 60.742 55.000 10.12 0.00 45.86 2.97
243 244 4.592192 CTCCACGCGCCATCCGAT 62.592 66.667 5.73 0.00 40.02 4.18
254 255 0.527817 GCCGAAGACATACCTCCACG 60.528 60.000 0.00 0.00 0.00 4.94
295 296 1.280421 AGATCCACCAAAGACCAGCTC 59.720 52.381 0.00 0.00 0.00 4.09
299 300 1.067295 AGCAGATCCACCAAAGACCA 58.933 50.000 0.00 0.00 0.00 4.02
306 307 1.596934 GGTCGAAGCAGATCCACCA 59.403 57.895 0.00 0.00 0.00 4.17
314 315 0.390472 GGAAGACTGGGTCGAAGCAG 60.390 60.000 0.00 0.00 37.67 4.24
317 318 1.402984 CGAAGGAAGACTGGGTCGAAG 60.403 57.143 0.00 0.00 37.67 3.79
323 324 0.393077 ACACACGAAGGAAGACTGGG 59.607 55.000 0.00 0.00 0.00 4.45
345 346 4.118168 AGATTGAAAGGGTCCAACATGT 57.882 40.909 0.00 0.00 0.00 3.21
348 349 6.636454 AGTATAGATTGAAAGGGTCCAACA 57.364 37.500 0.00 0.00 0.00 3.33
359 360 8.528643 TGTCGAGGAAAAGAAGTATAGATTGAA 58.471 33.333 0.00 0.00 0.00 2.69
360 361 8.063200 TGTCGAGGAAAAGAAGTATAGATTGA 57.937 34.615 0.00 0.00 0.00 2.57
361 362 8.596380 GTTGTCGAGGAAAAGAAGTATAGATTG 58.404 37.037 0.00 0.00 0.00 2.67
362 363 8.311836 TGTTGTCGAGGAAAAGAAGTATAGATT 58.688 33.333 0.00 0.00 0.00 2.40
375 376 3.869065 ACAAGAACTGTTGTCGAGGAAA 58.131 40.909 0.00 0.00 35.71 3.13
429 430 2.404215 CTTGTTGTAGTGGACAGTCGG 58.596 52.381 0.00 0.00 39.88 4.79
438 439 1.302511 AGCCGGGCTTGTTGTAGTG 60.303 57.895 17.69 0.00 33.89 2.74
457 458 0.108207 CATCATCCCTCCCTCAGCAC 59.892 60.000 0.00 0.00 0.00 4.40
458 459 0.030807 TCATCATCCCTCCCTCAGCA 60.031 55.000 0.00 0.00 0.00 4.41
460 461 1.798626 TGTCATCATCCCTCCCTCAG 58.201 55.000 0.00 0.00 0.00 3.35
471 472 2.162208 ACAAGCGCGATTTTGTCATCAT 59.838 40.909 12.10 0.00 32.32 2.45
485 486 0.442310 TTTGCGATGACTACAAGCGC 59.558 50.000 0.00 0.00 46.22 5.92
497 498 3.331150 TGTTCGTAGACCATTTTGCGAT 58.669 40.909 0.00 0.00 34.32 4.58
502 503 5.415701 AGCATTCATGTTCGTAGACCATTTT 59.584 36.000 0.00 0.00 35.71 1.82
542 543 7.459795 TGATATGGCAGTATGAAAAACACAA 57.540 32.000 0.00 0.00 39.69 3.33
564 565 6.326583 AGAAACGGAGGGAGTATTTATCATGA 59.673 38.462 0.00 0.00 0.00 3.07
573 574 8.491958 ACAAATATTTAGAAACGGAGGGAGTAT 58.508 33.333 0.00 0.00 0.00 2.12
597 660 9.996554 TCACTTGTTGAAATCTCTATAAAGACA 57.003 29.630 0.00 0.00 0.00 3.41
613 676 4.921515 GCTTCGTATGTAGTCACTTGTTGA 59.078 41.667 0.00 0.00 0.00 3.18
616 679 4.514781 TGCTTCGTATGTAGTCACTTGT 57.485 40.909 0.00 0.00 0.00 3.16
617 680 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
619 682 6.163476 TCATTTTGCTTCGTATGTAGTCACT 58.837 36.000 0.00 0.00 0.00 3.41
620 683 6.090898 ACTCATTTTGCTTCGTATGTAGTCAC 59.909 38.462 0.00 0.00 0.00 3.67
621 684 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
622 685 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
625 688 7.549134 AGATTCACTCATTTTGCTTCGTATGTA 59.451 33.333 0.00 0.00 0.00 2.29
672 735 9.905713 AAAATGAACTACCACATACAGATGTAT 57.094 29.630 0.00 0.00 44.82 2.29
676 739 8.862325 TTCAAAATGAACTACCACATACAGAT 57.138 30.769 0.00 0.00 30.26 2.90
677 740 8.862325 ATTCAAAATGAACTACCACATACAGA 57.138 30.769 0.00 0.00 39.45 3.41
679 742 9.906660 GAAATTCAAAATGAACTACCACATACA 57.093 29.630 0.00 0.00 39.45 2.29
683 746 9.567776 TCTAGAAATTCAAAATGAACTACCACA 57.432 29.630 0.00 0.00 39.45 4.17
718 781 8.974238 TCGATCTACTCCCTCTGTTTTTAAATA 58.026 33.333 0.00 0.00 0.00 1.40
724 787 4.601084 TCTCGATCTACTCCCTCTGTTTT 58.399 43.478 0.00 0.00 0.00 2.43
725 788 4.237976 TCTCGATCTACTCCCTCTGTTT 57.762 45.455 0.00 0.00 0.00 2.83
729 792 4.830600 GGAAATTCTCGATCTACTCCCTCT 59.169 45.833 0.00 0.00 0.00 3.69
745 808 6.073058 GGCCATGTTTTTCTTTGAGGAAATTC 60.073 38.462 0.00 0.00 35.51 2.17
786 850 2.360852 TCGGGGACTCGAGGTGAC 60.361 66.667 18.41 3.77 34.82 3.67
820 886 3.121058 CCATTTCCGTTTTCATTTGCGTG 60.121 43.478 0.00 0.00 0.00 5.34
831 899 5.975693 TCTAATGCTTTCCATTTCCGTTT 57.024 34.783 0.00 0.00 41.29 3.60
1036 1110 4.933064 CGATCGAGGCGACAGGGC 62.933 72.222 10.26 0.00 39.18 5.19
1167 1241 3.808728 TCTTGGGAAATTGCCTATCTCG 58.191 45.455 4.89 0.00 0.00 4.04
1168 1242 6.153510 ACTTTTCTTGGGAAATTGCCTATCTC 59.846 38.462 4.89 0.00 40.57 2.75
1176 1250 5.478332 AGGAGCTACTTTTCTTGGGAAATTG 59.522 40.000 0.00 0.00 40.57 2.32
1178 1252 5.012893 CAGGAGCTACTTTTCTTGGGAAAT 58.987 41.667 0.00 0.00 40.57 2.17
1182 1256 3.339141 GACAGGAGCTACTTTTCTTGGG 58.661 50.000 0.00 0.00 0.00 4.12
1185 1259 2.613223 GGCGACAGGAGCTACTTTTCTT 60.613 50.000 0.00 0.00 34.52 2.52
1188 1262 0.036294 GGGCGACAGGAGCTACTTTT 60.036 55.000 0.00 0.00 34.52 2.27
1196 1270 0.035056 AAATCAAGGGGCGACAGGAG 60.035 55.000 0.00 0.00 0.00 3.69
1199 1273 1.937546 GCCAAATCAAGGGGCGACAG 61.938 60.000 0.00 0.00 38.04 3.51
1210 1284 3.210227 TGAACAGAAACTCGCCAAATCA 58.790 40.909 0.00 0.00 0.00 2.57
1263 1337 3.231207 AGGAGCGGCTTTATCTAGAGA 57.769 47.619 2.97 0.00 0.00 3.10
1269 1343 3.243201 CCAAATCAAGGAGCGGCTTTATC 60.243 47.826 2.97 0.00 0.00 1.75
1270 1344 2.689983 CCAAATCAAGGAGCGGCTTTAT 59.310 45.455 2.97 0.00 0.00 1.40
1271 1345 2.091541 CCAAATCAAGGAGCGGCTTTA 58.908 47.619 2.97 0.00 0.00 1.85
1272 1346 0.890683 CCAAATCAAGGAGCGGCTTT 59.109 50.000 2.97 0.00 0.00 3.51
1273 1347 0.038166 TCCAAATCAAGGAGCGGCTT 59.962 50.000 2.97 0.00 0.00 4.35
1274 1348 0.393537 CTCCAAATCAAGGAGCGGCT 60.394 55.000 0.00 0.00 45.51 5.52
1305 1379 7.094420 GGAAAGGAAGGAGAAGAAAGAAATCTG 60.094 40.741 0.00 0.00 0.00 2.90
1409 1485 5.346522 CCTAATCGCTCCGTTAAACTACTT 58.653 41.667 0.00 0.00 0.00 2.24
1410 1486 4.202090 CCCTAATCGCTCCGTTAAACTACT 60.202 45.833 0.00 0.00 0.00 2.57
1475 1553 5.123502 CAGAACAACAAATCATCTCTCCAGG 59.876 44.000 0.00 0.00 0.00 4.45
1508 1586 3.256631 ACGCTGCAAATCAAAATCCTCTT 59.743 39.130 0.00 0.00 0.00 2.85
1542 1621 7.681939 TTCCACTAACAATTTCCTGACATAC 57.318 36.000 0.00 0.00 0.00 2.39
1546 1625 5.183904 AGCATTCCACTAACAATTTCCTGAC 59.816 40.000 0.00 0.00 0.00 3.51
1548 1627 5.416952 AGAGCATTCCACTAACAATTTCCTG 59.583 40.000 0.00 0.00 0.00 3.86
1549 1628 5.416952 CAGAGCATTCCACTAACAATTTCCT 59.583 40.000 0.00 0.00 0.00 3.36
1550 1629 5.183904 ACAGAGCATTCCACTAACAATTTCC 59.816 40.000 0.00 0.00 0.00 3.13
1552 1631 6.655078 AACAGAGCATTCCACTAACAATTT 57.345 33.333 0.00 0.00 0.00 1.82
1603 1696 6.656270 ACTCAATGCTTATCACAGAAATCACA 59.344 34.615 0.00 0.00 0.00 3.58
1739 1835 4.385405 AGCAGCTCGTCAGGCACC 62.385 66.667 0.00 0.00 0.00 5.01
1795 1891 2.632512 TGTGTGCAACTCTCTATGTGGA 59.367 45.455 0.00 0.00 38.04 4.02
1856 1952 4.958509 ACACATCCTGATAGATCTGCAAG 58.041 43.478 5.18 0.00 0.00 4.01
1985 2081 2.871022 CTCCTTCATTCTCTTGATGGCG 59.129 50.000 2.41 0.00 39.57 5.69
2072 2172 9.445786 GAATTTTAACGAAACAGACATCAAGAA 57.554 29.630 0.00 0.00 0.00 2.52
2073 2173 8.616942 TGAATTTTAACGAAACAGACATCAAGA 58.383 29.630 0.00 0.00 0.00 3.02
2078 2178 8.967218 CAACATGAATTTTAACGAAACAGACAT 58.033 29.630 0.00 0.00 0.00 3.06
2098 2198 8.712285 ATTATTTCAAGAATGAAGGCAACATG 57.288 30.769 0.00 0.00 45.82 3.21
2199 2299 6.570789 CGTTTGCTGCTTGATATTTGTTTTTG 59.429 34.615 0.00 0.00 0.00 2.44
2413 2513 5.537188 TGCTTTGTTTCGCTGGATAAAAAT 58.463 33.333 0.00 0.00 0.00 1.82
2456 2556 0.251297 TGCTGTTGGGTGGGATCTTG 60.251 55.000 0.00 0.00 0.00 3.02
2501 2601 1.322442 ACAGCAGAAAAAGGGACAGC 58.678 50.000 0.00 0.00 0.00 4.40
2543 2643 5.175127 TCAAAAACTGGAAAAGTGGAAAGC 58.825 37.500 0.00 0.00 39.81 3.51
2563 2663 6.885918 TCCTGTCAAGATTTGCATCTTATCAA 59.114 34.615 2.30 0.00 46.44 2.57
2803 2904 4.475944 GCAAAATTGCGTAACATGAGAGT 58.524 39.130 0.00 0.00 45.11 3.24
2843 2944 3.572255 TGCAAGGGATTTAAGGAACACAC 59.428 43.478 0.00 0.00 0.00 3.82
2884 2985 8.950208 AATTCAGAGCTAAGGTTTACTGATAC 57.050 34.615 0.00 0.00 35.00 2.24
2886 2987 9.384764 GTAAATTCAGAGCTAAGGTTTACTGAT 57.615 33.333 0.00 0.00 35.00 2.90
2887 2988 8.372459 TGTAAATTCAGAGCTAAGGTTTACTGA 58.628 33.333 15.87 7.67 33.82 3.41
2888 2989 8.547967 TGTAAATTCAGAGCTAAGGTTTACTG 57.452 34.615 15.87 5.89 33.82 2.74
2889 2990 7.824779 CCTGTAAATTCAGAGCTAAGGTTTACT 59.175 37.037 15.87 0.00 37.61 2.24
2899 3006 5.181748 GTGATGACCTGTAAATTCAGAGCT 58.818 41.667 0.00 0.00 37.61 4.09
2993 3100 4.283212 CCAGTTGGTTTGGTGATGGTTATT 59.717 41.667 0.00 0.00 0.00 1.40
3017 3124 0.965439 TTTGAATCGGCCTGTTTGGG 59.035 50.000 0.00 0.00 36.00 4.12
3020 3127 1.686052 TGCTTTTGAATCGGCCTGTTT 59.314 42.857 0.00 0.00 0.00 2.83
3086 3193 1.070105 CGAACTCCCCGGTCACAAA 59.930 57.895 0.00 0.00 0.00 2.83
3096 3203 1.729881 GCAATCATGGCGAACTCCC 59.270 57.895 0.00 0.00 0.00 4.30
3150 3257 1.251251 AGACTTGGTGAATGGCAAGC 58.749 50.000 0.00 0.00 0.00 4.01
3217 3324 2.103941 GCTCCCCTGAAGGAAGATACAG 59.896 54.545 0.00 0.00 38.24 2.74
3226 3333 1.928868 ATTGTTTGCTCCCCTGAAGG 58.071 50.000 0.00 0.00 0.00 3.46
3227 3334 4.337555 CAGATATTGTTTGCTCCCCTGAAG 59.662 45.833 0.00 0.00 0.00 3.02
3229 3336 3.889815 CAGATATTGTTTGCTCCCCTGA 58.110 45.455 0.00 0.00 0.00 3.86
3230 3337 2.360165 GCAGATATTGTTTGCTCCCCTG 59.640 50.000 0.00 0.00 35.05 4.45
3296 3404 7.603784 TCTCTCATCAGAATCACAATTTTTCGA 59.396 33.333 0.00 0.00 0.00 3.71
3297 3405 7.745972 TCTCTCATCAGAATCACAATTTTTCG 58.254 34.615 0.00 0.00 0.00 3.46
3321 3437 5.106948 CGTCATGTGCCATTATTACTGGATC 60.107 44.000 4.34 0.00 35.70 3.36
3383 4036 7.715657 TGAATTGTTCTTGCAGAATTAACTGT 58.284 30.769 0.00 0.00 36.50 3.55
3386 4039 8.579682 AACTGAATTGTTCTTGCAGAATTAAC 57.420 30.769 0.00 0.00 36.50 2.01
3419 4072 1.625315 AGAGTATCAGCTGGCAACACA 59.375 47.619 15.13 0.00 39.36 3.72
3508 4166 9.939424 ACTCTTATATTAGTTTACAGAGGGAGT 57.061 33.333 0.00 0.00 32.21 3.85
3510 4168 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
3560 4218 9.813446 CCTCCGTAAACTAATATAAGAGTGTTT 57.187 33.333 0.00 0.00 0.00 2.83
3561 4219 8.419442 CCCTCCGTAAACTAATATAAGAGTGTT 58.581 37.037 0.00 0.00 0.00 3.32
3562 4220 7.781693 TCCCTCCGTAAACTAATATAAGAGTGT 59.218 37.037 0.00 0.00 0.00 3.55
3563 4221 8.174733 TCCCTCCGTAAACTAATATAAGAGTG 57.825 38.462 0.00 0.00 0.00 3.51
3564 4222 8.003629 ACTCCCTCCGTAAACTAATATAAGAGT 58.996 37.037 0.00 0.00 0.00 3.24
3565 4223 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
3569 4227 9.458727 CAGATACTCCCTCCGTAAACTAATATA 57.541 37.037 0.00 0.00 0.00 0.86
3570 4228 8.168725 TCAGATACTCCCTCCGTAAACTAATAT 58.831 37.037 0.00 0.00 0.00 1.28
3571 4229 7.446625 GTCAGATACTCCCTCCGTAAACTAATA 59.553 40.741 0.00 0.00 0.00 0.98
3572 4230 6.264970 GTCAGATACTCCCTCCGTAAACTAAT 59.735 42.308 0.00 0.00 0.00 1.73
3573 4231 5.591877 GTCAGATACTCCCTCCGTAAACTAA 59.408 44.000 0.00 0.00 0.00 2.24
3574 4232 5.128919 GTCAGATACTCCCTCCGTAAACTA 58.871 45.833 0.00 0.00 0.00 2.24
3575 4233 3.952967 GTCAGATACTCCCTCCGTAAACT 59.047 47.826 0.00 0.00 0.00 2.66
3576 4234 3.698040 TGTCAGATACTCCCTCCGTAAAC 59.302 47.826 0.00 0.00 0.00 2.01
3577 4235 3.972133 TGTCAGATACTCCCTCCGTAAA 58.028 45.455 0.00 0.00 0.00 2.01
3578 4236 3.657398 TGTCAGATACTCCCTCCGTAA 57.343 47.619 0.00 0.00 0.00 3.18
3579 4237 3.657398 TTGTCAGATACTCCCTCCGTA 57.343 47.619 0.00 0.00 0.00 4.02
3580 4238 2.526888 TTGTCAGATACTCCCTCCGT 57.473 50.000 0.00 0.00 0.00 4.69
3581 4239 4.408182 AATTTGTCAGATACTCCCTCCG 57.592 45.455 0.00 0.00 0.00 4.63
3582 4240 6.890293 ACTTAATTTGTCAGATACTCCCTCC 58.110 40.000 0.00 0.00 0.00 4.30
3583 4241 7.787028 AGACTTAATTTGTCAGATACTCCCTC 58.213 38.462 11.95 0.00 36.94 4.30
3584 4242 7.147637 GGAGACTTAATTTGTCAGATACTCCCT 60.148 40.741 11.95 0.00 36.94 4.20
3585 4243 6.987404 GGAGACTTAATTTGTCAGATACTCCC 59.013 42.308 11.95 0.00 36.94 4.30
3586 4244 7.556844 TGGAGACTTAATTTGTCAGATACTCC 58.443 38.462 0.00 0.00 39.27 3.85
3587 4245 9.255304 GATGGAGACTTAATTTGTCAGATACTC 57.745 37.037 11.95 0.00 36.94 2.59
3758 4419 1.045350 TGGACTAGCTAGCTGGGCAG 61.045 60.000 32.25 21.21 33.88 4.85
3837 4609 5.821470 TCCATCAGAATTCAGAAAGAGCATC 59.179 40.000 8.44 0.00 0.00 3.91
3870 4643 3.072915 TGGTGTGACAAGGTCATCTTCAT 59.927 43.478 2.02 0.00 44.63 2.57
3900 4674 1.291877 GCGTGCCATGTCGAGTTCTT 61.292 55.000 6.41 0.00 0.00 2.52
3925 4699 1.017177 GTGCAATCGACAGGCGGTTA 61.017 55.000 0.00 0.00 42.45 2.85
3968 4765 7.656707 AAATTTGTTCTGCCATGATGTTAAC 57.343 32.000 0.00 0.00 0.00 2.01
4035 4832 1.754226 GCCACCTCTAGGACTTCAGAG 59.246 57.143 2.23 0.00 38.42 3.35
4038 4835 1.561643 CTGCCACCTCTAGGACTTCA 58.438 55.000 2.23 0.00 38.94 3.02
4039 4836 0.176910 GCTGCCACCTCTAGGACTTC 59.823 60.000 2.23 0.00 38.94 3.01
4041 4838 1.687493 GGCTGCCACCTCTAGGACT 60.687 63.158 15.17 0.00 38.94 3.85
4042 4839 1.553690 TTGGCTGCCACCTCTAGGAC 61.554 60.000 23.30 0.00 38.94 3.85
4043 4840 1.229496 TTGGCTGCCACCTCTAGGA 60.229 57.895 23.30 0.09 38.94 2.94
4044 4841 1.078143 GTTGGCTGCCACCTCTAGG 60.078 63.158 23.30 0.00 42.17 3.02
4045 4842 0.036732 TTGTTGGCTGCCACCTCTAG 59.963 55.000 23.30 0.00 30.78 2.43
4046 4843 0.476338 TTTGTTGGCTGCCACCTCTA 59.524 50.000 23.30 2.76 30.78 2.43
4047 4844 1.109323 GTTTGTTGGCTGCCACCTCT 61.109 55.000 23.30 0.00 30.78 3.69
4048 4845 1.109323 AGTTTGTTGGCTGCCACCTC 61.109 55.000 23.30 15.03 30.78 3.85
4051 4848 1.933181 GAAAAGTTTGTTGGCTGCCAC 59.067 47.619 23.30 16.71 30.78 5.01
4054 4851 3.785486 AGAAGAAAAGTTTGTTGGCTGC 58.215 40.909 0.00 0.00 0.00 5.25
4059 5554 8.466798 TCTTTTAGGGAGAAGAAAAGTTTGTTG 58.533 33.333 6.31 0.00 39.87 3.33
4086 5581 6.866179 AGTTTCAGTTAGCTAATTACGTCG 57.134 37.500 9.88 0.00 0.00 5.12
4222 5717 3.625764 CGGGAACTTTTTCTGAACTCACA 59.374 43.478 0.00 0.00 31.71 3.58


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

AutoCloner maintained by Alex Coulton.