Multiple sequence alignment - TraesCS4A01G006400

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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 TraesCS4A01G006400 chr4A 100.000 5298 0 0 1 5298 4156880 4162177 0.000000e+00 9784.0
1 TraesCS4A01G006400 chr4A 92.013 1227 69 13 897 2096 4196474 4195250 0.000000e+00 1696.0
2 TraesCS4A01G006400 chr4A 89.816 1198 70 22 935 2120 4241466 4240309 0.000000e+00 1489.0
3 TraesCS4A01G006400 chr4A 86.877 1364 93 35 909 2255 4475273 4473979 0.000000e+00 1448.0
4 TraesCS4A01G006400 chr4A 93.853 846 37 6 3472 4305 4194158 4193316 0.000000e+00 1260.0
5 TraesCS4A01G006400 chr4A 91.943 844 56 6 3472 4305 4472823 4471982 0.000000e+00 1171.0
6 TraesCS4A01G006400 chr4A 91.346 832 53 7 3491 4305 4239104 4238275 0.000000e+00 1120.0
7 TraesCS4A01G006400 chr4A 90.997 311 25 2 2974 3283 4239542 4239234 2.950000e-112 416.0
8 TraesCS4A01G006400 chr4A 86.575 365 34 9 2985 3336 4473230 4472868 6.430000e-104 388.0
9 TraesCS4A01G006400 chr4A 88.026 309 22 10 3054 3347 4194493 4194185 8.440000e-93 351.0
10 TraesCS4A01G006400 chr4A 81.933 238 14 10 2709 2946 4473925 4473717 1.960000e-39 174.0
11 TraesCS4A01G006400 chr4A 87.097 93 12 0 4889 4981 4161676 4161768 7.260000e-19 106.0
12 TraesCS4A01G006400 chr4A 87.097 93 12 0 4797 4889 4161768 4161860 7.260000e-19 106.0
13 TraesCS4A01G006400 chr4D 91.326 2813 141 46 2530 5298 466729202 466726449 0.000000e+00 3747.0
14 TraesCS4A01G006400 chr4D 92.128 1753 82 24 456 2180 466731383 466729659 0.000000e+00 2422.0
15 TraesCS4A01G006400 chr4D 88.991 1408 88 33 797 2177 466292298 466293665 0.000000e+00 1679.0
16 TraesCS4A01G006400 chr4D 91.064 1231 57 18 975 2177 466334365 466335570 0.000000e+00 1615.0
17 TraesCS4A01G006400 chr4D 90.577 1231 60 19 975 2177 466403353 466404555 0.000000e+00 1580.0
18 TraesCS4A01G006400 chr4D 91.813 855 48 6 3472 4305 466405642 466406495 0.000000e+00 1171.0
19 TraesCS4A01G006400 chr4D 91.895 839 54 4 3478 4305 466294457 466295292 0.000000e+00 1160.0
20 TraesCS4A01G006400 chr4D 91.432 852 53 7 3472 4305 466336315 466337164 0.000000e+00 1151.0
21 TraesCS4A01G006400 chr4D 91.870 369 27 2 1 369 466732145 466731780 3.660000e-141 512.0
22 TraesCS4A01G006400 chr4D 93.312 314 20 1 2198 2511 466729604 466729292 3.740000e-126 462.0
23 TraesCS4A01G006400 chr4D 93.617 235 15 0 3049 3283 466294113 466294347 8.440000e-93 351.0
24 TraesCS4A01G006400 chr4D 87.960 299 24 7 3049 3335 466405299 466405597 5.080000e-90 342.0
25 TraesCS4A01G006400 chr4D 86.943 314 26 10 3049 3347 466335975 466336288 6.570000e-89 339.0
26 TraesCS4A01G006400 chr4D 88.811 143 13 3 2694 2836 466335732 466335871 7.050000e-39 172.0
27 TraesCS4A01G006400 chr4D 89.524 105 7 4 2722 2826 466405060 466405160 4.310000e-26 130.0
28 TraesCS4A01G006400 chr4D 88.889 99 11 0 4797 4895 466726853 466726755 7.210000e-24 122.0
29 TraesCS4A01G006400 chr4D 89.583 96 10 0 4892 4987 466726942 466726847 7.210000e-24 122.0
30 TraesCS4A01G006400 chr4B 92.282 2099 103 26 2520 4584 584528742 584526669 0.000000e+00 2924.0
31 TraesCS4A01G006400 chr4B 89.565 1332 77 24 886 2177 584125801 584127110 0.000000e+00 1633.0
32 TraesCS4A01G006400 chr4B 89.414 1332 80 23 886 2177 584054436 584055746 0.000000e+00 1622.0
33 TraesCS4A01G006400 chr4B 96.000 750 28 2 768 1516 584530076 584529328 0.000000e+00 1218.0
34 TraesCS4A01G006400 chr4B 90.437 847 58 8 3480 4305 583767761 583768605 0.000000e+00 1094.0
35 TraesCS4A01G006400 chr4B 89.651 860 61 14 3472 4305 584127872 584128729 0.000000e+00 1070.0
36 TraesCS4A01G006400 chr4B 89.186 860 65 14 3472 4305 584056513 584057370 0.000000e+00 1048.0
37 TraesCS4A01G006400 chr4B 95.789 380 13 1 1549 1928 584529238 584528862 1.260000e-170 610.0
38 TraesCS4A01G006400 chr4B 89.831 295 23 2 4580 4874 584506263 584505976 6.480000e-99 372.0
39 TraesCS4A01G006400 chr4B 88.581 289 30 2 2996 3283 583767356 583767642 1.090000e-91 348.0
40 TraesCS4A01G006400 chr4B 87.956 274 32 1 5025 5298 584505973 584505701 6.620000e-84 322.0
41 TraesCS4A01G006400 chr4B 85.859 297 17 8 476 747 584530742 584530446 5.190000e-75 292.0
42 TraesCS4A01G006400 chr4B 90.756 119 9 1 2694 2812 583766948 583767064 1.980000e-34 158.0
43 TraesCS4A01G006400 chr4B 91.964 112 6 3 2719 2830 584055917 584056025 2.560000e-33 154.0
44 TraesCS4A01G006400 chr4B 91.964 112 6 3 2719 2830 584127281 584127389 2.560000e-33 154.0
45 TraesCS4A01G006400 chrUn 93.401 394 17 2 1576 1969 479224296 479223912 4.600000e-160 575.0
46 TraesCS4A01G006400 chr2B 80.508 354 60 9 4902 5250 760881320 760881669 4.070000e-66 263.0
47 TraesCS4A01G006400 chr5A 100.000 30 0 0 605 634 63381581 63381552 7.410000e-04 56.5


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 TraesCS4A01G006400 chr4A 4156880 4162177 5297 False 3332.000000 9784 91.398000 1 5298 3 chr4A.!!$F1 5297
1 TraesCS4A01G006400 chr4A 4193316 4196474 3158 True 1102.333333 1696 91.297333 897 4305 3 chr4A.!!$R1 3408
2 TraesCS4A01G006400 chr4A 4238275 4241466 3191 True 1008.333333 1489 90.719667 935 4305 3 chr4A.!!$R2 3370
3 TraesCS4A01G006400 chr4A 4471982 4475273 3291 True 795.250000 1448 86.832000 909 4305 4 chr4A.!!$R3 3396
4 TraesCS4A01G006400 chr4D 466726449 466732145 5696 True 1231.166667 3747 91.184667 1 5298 6 chr4D.!!$R1 5297
5 TraesCS4A01G006400 chr4D 466292298 466295292 2994 False 1063.333333 1679 91.501000 797 4305 3 chr4D.!!$F1 3508
6 TraesCS4A01G006400 chr4D 466334365 466337164 2799 False 819.250000 1615 89.562500 975 4305 4 chr4D.!!$F2 3330
7 TraesCS4A01G006400 chr4D 466403353 466406495 3142 False 805.750000 1580 89.968500 975 4305 4 chr4D.!!$F3 3330
8 TraesCS4A01G006400 chr4B 584526669 584530742 4073 True 1261.000000 2924 92.482500 476 4584 4 chr4B.!!$R2 4108
9 TraesCS4A01G006400 chr4B 584125801 584128729 2928 False 952.333333 1633 90.393333 886 4305 3 chr4B.!!$F3 3419
10 TraesCS4A01G006400 chr4B 584054436 584057370 2934 False 941.333333 1622 90.188000 886 4305 3 chr4B.!!$F2 3419
11 TraesCS4A01G006400 chr4B 583766948 583768605 1657 False 533.333333 1094 89.924667 2694 4305 3 chr4B.!!$F1 1611
12 TraesCS4A01G006400 chr4B 584505701 584506263 562 True 347.000000 372 88.893500 4580 5298 2 chr4B.!!$R1 718

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
110 111 0.031585 AAGTTGTGTCGTAGCTCGCA 59.968 50.0 0.00 0.00 39.67 5.10 F
222 223 0.172578 CACTTATGTCGAGTCGGCCA 59.827 55.0 15.66 11.27 0.00 5.36 F
1334 2105 0.245266 TGGCGCTACATCTCGTTTGA 59.755 50.0 7.64 0.00 0.00 2.69 F
2140 3530 0.108329 GCGATTTGGGAGAGTCGGAA 60.108 55.0 0.00 0.00 34.85 4.30 F
2836 4771 0.247934 CGCACGCATCACTCGTAGTA 60.248 55.0 0.00 0.00 38.19 1.82 F
4095 6891 1.028330 TTCGAGCTACCGTCCGTGAT 61.028 55.0 0.00 0.00 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1699 2539 0.961358 CTCAACGGTCTCCTCCTCGT 60.961 60.000 0.00 0.00 37.45 4.18 R
2113 3229 1.000233 TCCCAAATCGCCAAGGCAT 60.000 52.632 12.19 1.27 42.06 4.40 R
2672 4486 0.106918 TGACCCCAACTGGTGTGTTC 60.107 55.000 0.00 0.00 39.24 3.18 R
3083 5811 0.936297 CTCGCCTGCAAACAAGCAAC 60.936 55.000 0.00 0.00 45.13 4.17 R
4231 7027 0.108329 CGATCCAGTTGCCCTTACGT 60.108 55.000 0.00 0.00 0.00 3.57 R
5246 8065 0.618458 TGTAGCTAGGCTGGTTTGGG 59.382 55.000 0.00 0.00 40.10 4.12 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
33 34 4.385358 AATTTTATCACCCGCACCATTC 57.615 40.909 0.00 0.00 0.00 2.67
35 36 2.325583 TTATCACCCGCACCATTCTC 57.674 50.000 0.00 0.00 0.00 2.87
39 40 1.675641 ACCCGCACCATTCTCAAGC 60.676 57.895 0.00 0.00 0.00 4.01
56 57 0.322975 AGCGAATGTTGTGCTCCTCT 59.677 50.000 0.00 0.00 32.44 3.69
57 58 1.160137 GCGAATGTTGTGCTCCTCTT 58.840 50.000 0.00 0.00 0.00 2.85
68 69 2.230266 GTGCTCCTCTTCTCTCTCGTTT 59.770 50.000 0.00 0.00 0.00 3.60
99 100 2.930826 ACCGAAGATGGAAGTTGTGT 57.069 45.000 0.00 0.00 0.00 3.72
101 102 1.726791 CCGAAGATGGAAGTTGTGTCG 59.273 52.381 0.00 0.00 0.00 4.35
110 111 0.031585 AAGTTGTGTCGTAGCTCGCA 59.968 50.000 0.00 0.00 39.67 5.10
131 132 5.614760 GCATTTGATTGCTTTGATGTGTTC 58.385 37.500 0.00 0.00 39.57 3.18
136 137 0.187117 TGCTTTGATGTGTTCCCCCA 59.813 50.000 0.00 0.00 0.00 4.96
138 139 1.691434 GCTTTGATGTGTTCCCCCAAA 59.309 47.619 0.00 0.00 0.00 3.28
140 141 2.461300 TTGATGTGTTCCCCCAAACA 57.539 45.000 0.00 0.00 36.82 2.83
147 148 2.041216 GTGTTCCCCCAAACATAGAGGT 59.959 50.000 0.00 0.00 40.96 3.85
155 156 2.524306 CAAACATAGAGGTGGGCCAAA 58.476 47.619 8.40 0.00 37.19 3.28
185 186 1.202348 GCCCAACAGTAATGACCAAGC 59.798 52.381 0.00 0.00 0.00 4.01
213 214 0.530650 AGGCGATGGCACTTATGTCG 60.531 55.000 1.01 1.77 42.47 4.35
222 223 0.172578 CACTTATGTCGAGTCGGCCA 59.827 55.000 15.66 11.27 0.00 5.36
243 244 1.153349 GCAAGGCTAACGGGAGGAG 60.153 63.158 0.00 0.00 0.00 3.69
250 251 1.673808 CTAACGGGAGGAGGGGAACG 61.674 65.000 0.00 0.00 0.00 3.95
253 254 1.152610 CGGGAGGAGGGGAACGATA 60.153 63.158 0.00 0.00 0.00 2.92
254 255 0.757935 CGGGAGGAGGGGAACGATAA 60.758 60.000 0.00 0.00 0.00 1.75
261 262 2.258726 GGGGAACGATAATGGCGGC 61.259 63.158 0.00 0.00 0.00 6.53
275 276 1.022451 GGCGGCGATACAAAGGTCAA 61.022 55.000 12.98 0.00 0.00 3.18
322 323 4.264373 AGGATAAAAAGGGCAGCCAATA 57.736 40.909 15.19 0.00 0.00 1.90
347 348 7.989826 AGACATATGAAATAACCTTGAAGTGC 58.010 34.615 10.38 0.00 29.06 4.40
363 364 6.942532 TGAAGTGCACCCATATTTAAGATC 57.057 37.500 14.63 0.00 0.00 2.75
364 365 6.422333 TGAAGTGCACCCATATTTAAGATCA 58.578 36.000 14.63 0.00 0.00 2.92
365 366 7.062322 TGAAGTGCACCCATATTTAAGATCAT 58.938 34.615 14.63 0.00 0.00 2.45
366 367 8.217111 TGAAGTGCACCCATATTTAAGATCATA 58.783 33.333 14.63 0.00 0.00 2.15
367 368 9.236006 GAAGTGCACCCATATTTAAGATCATAT 57.764 33.333 14.63 0.00 0.00 1.78
368 369 8.571461 AGTGCACCCATATTTAAGATCATATG 57.429 34.615 14.63 0.00 34.39 1.78
369 370 8.166061 AGTGCACCCATATTTAAGATCATATGT 58.834 33.333 14.63 0.00 33.22 2.29
370 371 9.448438 GTGCACCCATATTTAAGATCATATGTA 57.552 33.333 5.22 0.00 33.22 2.29
371 372 9.448438 TGCACCCATATTTAAGATCATATGTAC 57.552 33.333 1.90 0.00 33.22 2.90
372 373 8.893727 GCACCCATATTTAAGATCATATGTACC 58.106 37.037 1.90 0.00 33.22 3.34
373 374 9.396022 CACCCATATTTAAGATCATATGTACCC 57.604 37.037 1.90 0.00 33.22 3.69
374 375 8.265055 ACCCATATTTAAGATCATATGTACCCG 58.735 37.037 1.90 0.00 33.22 5.28
375 376 7.226720 CCCATATTTAAGATCATATGTACCCGC 59.773 40.741 1.90 0.00 33.22 6.13
376 377 7.768582 CCATATTTAAGATCATATGTACCCGCA 59.231 37.037 1.90 0.00 33.22 5.69
377 378 9.161629 CATATTTAAGATCATATGTACCCGCAA 57.838 33.333 1.90 0.00 31.29 4.85
378 379 9.733556 ATATTTAAGATCATATGTACCCGCAAA 57.266 29.630 1.90 0.00 0.00 3.68
379 380 7.867305 TTTAAGATCATATGTACCCGCAAAA 57.133 32.000 1.90 0.00 0.00 2.44
380 381 7.867305 TTAAGATCATATGTACCCGCAAAAA 57.133 32.000 1.90 0.00 0.00 1.94
417 418 8.899427 TTTAAGATCATATGAGAGGCAAAGAG 57.101 34.615 11.78 0.00 0.00 2.85
425 426 3.415212 TGAGAGGCAAAGAGAACAATGG 58.585 45.455 0.00 0.00 0.00 3.16
446 454 8.332464 CAATGGTAAACAATACGAATGTACGAT 58.668 33.333 0.00 0.00 37.03 3.73
447 455 7.224290 TGGTAAACAATACGAATGTACGATG 57.776 36.000 0.00 0.00 37.03 3.84
451 459 9.184062 GTAAACAATACGAATGTACGATGGATA 57.816 33.333 0.00 0.00 37.03 2.59
455 463 2.620115 ACGAATGTACGATGGATACGGT 59.380 45.455 0.00 0.00 36.75 4.83
458 466 4.615223 CGAATGTACGATGGATACGGTCAT 60.615 45.833 0.00 0.00 35.39 3.06
459 467 5.391203 CGAATGTACGATGGATACGGTCATA 60.391 44.000 0.00 0.00 35.39 2.15
460 468 4.754372 TGTACGATGGATACGGTCATAC 57.246 45.455 0.00 0.00 42.51 2.39
461 469 4.392047 TGTACGATGGATACGGTCATACT 58.608 43.478 0.00 0.00 42.51 2.12
462 470 4.823442 TGTACGATGGATACGGTCATACTT 59.177 41.667 0.00 0.00 42.51 2.24
473 821 7.861872 GGATACGGTCATACTTAGAAAGAAGAC 59.138 40.741 0.00 0.00 0.00 3.01
474 822 6.585695 ACGGTCATACTTAGAAAGAAGACA 57.414 37.500 0.00 0.00 32.77 3.41
505 853 4.781775 AGAGGAAGGAGACGATAGAAGA 57.218 45.455 0.00 0.00 41.38 2.87
506 854 5.118729 AGAGGAAGGAGACGATAGAAGAA 57.881 43.478 0.00 0.00 41.38 2.52
510 858 6.133356 AGGAAGGAGACGATAGAAGAAAGAT 58.867 40.000 0.00 0.00 41.38 2.40
528 876 8.804912 AGAAAGATAAAAGCAGATGACAGATT 57.195 30.769 0.00 0.00 0.00 2.40
556 904 1.069090 GCACTGTGAGGTGGAACGA 59.931 57.895 12.86 0.00 38.12 3.85
562 910 1.628340 TGTGAGGTGGAACGATTGGAT 59.372 47.619 0.00 0.00 38.12 3.41
570 918 1.332686 GGAACGATTGGATAAACGCCC 59.667 52.381 0.00 0.00 35.75 6.13
574 922 3.020984 ACGATTGGATAAACGCCCATTT 58.979 40.909 0.00 0.00 35.75 2.32
592 940 2.710096 TTTACCCAGTGGAGCTATGC 57.290 50.000 11.95 0.00 34.81 3.14
726 1100 1.340502 GGGCCTAGCTTGCTCTTTCTT 60.341 52.381 0.84 0.00 0.00 2.52
748 1122 4.486090 TCTCTAGCTACGTTTCAGCAAAG 58.514 43.478 11.19 7.91 41.66 2.77
832 1563 4.976224 ATAAATACGCCAACCCTTGTTC 57.024 40.909 0.00 0.00 30.42 3.18
873 1604 1.525995 ACAACACACAAGCCCTCCG 60.526 57.895 0.00 0.00 0.00 4.63
880 1611 3.752339 CAAGCCCTCCGCAAAGCC 61.752 66.667 0.00 0.00 41.38 4.35
963 1729 2.280797 GAGCACCTCGCCACACAA 60.281 61.111 0.00 0.00 44.04 3.33
1334 2105 0.245266 TGGCGCTACATCTCGTTTGA 59.755 50.000 7.64 0.00 0.00 2.69
1359 2130 3.306225 CCAAGGTGGTGGACATCAAATTG 60.306 47.826 4.77 4.77 41.65 2.32
1500 2271 9.778741 CAGGTACCAATATATACTTTGACATGT 57.221 33.333 15.94 0.00 0.00 3.21
1699 2539 1.609061 GCTGGACTACTGCAAGCTGAA 60.609 52.381 5.93 0.00 42.90 3.02
1851 2694 9.717942 CTAGCTATGCATAGGAAAGATTTAACT 57.282 33.333 30.14 17.73 0.00 2.24
2013 2862 1.068748 CAAGCATGTTCACACAGAGCC 60.069 52.381 0.00 0.00 38.19 4.70
2057 2912 9.543018 GGATACTAATAAATATTGTGAAAGCGC 57.457 33.333 0.00 0.00 0.00 5.92
2140 3530 0.108329 GCGATTTGGGAGAGTCGGAA 60.108 55.000 0.00 0.00 34.85 4.30
2172 3562 3.006537 CGGAAAAGGTCACTCTTGTCCTA 59.993 47.826 11.46 0.00 44.95 2.94
2177 3567 2.158143 AGGTCACTCTTGTCCTAACCCT 60.158 50.000 0.00 0.00 39.27 4.34
2180 3570 4.445879 GGTCACTCTTGTCCTAACCCTTTT 60.446 45.833 0.00 0.00 0.00 2.27
2181 3571 5.131067 GTCACTCTTGTCCTAACCCTTTTT 58.869 41.667 0.00 0.00 0.00 1.94
2233 3949 1.542492 AGGCAGGTCTCTTGCATTTG 58.458 50.000 6.23 0.00 0.00 2.32
2272 3988 6.920758 CACTAGACATAATTAGGACAGTGCTC 59.079 42.308 3.76 0.00 0.00 4.26
2289 4005 3.293337 TGCTCATGCATTGGCTCTTAAT 58.707 40.909 17.83 0.00 45.31 1.40
2301 4017 8.883731 GCATTGGCTCTTAATACGTTATCATAT 58.116 33.333 0.00 0.00 36.96 1.78
2314 4030 7.444629 ACGTTATCATATGTACGGTAGTGAT 57.555 36.000 22.03 9.03 38.26 3.06
2363 4079 5.402270 GCATTGTCTGTTAAATGTTGTGTCC 59.598 40.000 0.00 0.00 36.39 4.02
2414 4130 7.353525 TGGAACCATATTTACATGTCCATCTT 58.646 34.615 0.00 0.00 30.25 2.40
2417 4133 8.593945 AACCATATTTACATGTCCATCTTGTT 57.406 30.769 0.00 0.00 36.20 2.83
2422 4138 2.440409 ACATGTCCATCTTGTTGCCTC 58.560 47.619 0.00 0.00 31.71 4.70
2426 4142 2.037902 TGTCCATCTTGTTGCCTCGTTA 59.962 45.455 0.00 0.00 0.00 3.18
2439 4155 2.431057 GCCTCGTTATGGAGAGAAAGGA 59.569 50.000 0.00 0.00 36.65 3.36
2443 4159 5.086104 TCGTTATGGAGAGAAAGGAAAGG 57.914 43.478 0.00 0.00 0.00 3.11
2453 4169 8.228905 TGGAGAGAAAGGAAAGGGTAAAAATTA 58.771 33.333 0.00 0.00 0.00 1.40
2458 4174 9.442062 AGAAAGGAAAGGGTAAAAATTAGGAAA 57.558 29.630 0.00 0.00 0.00 3.13
2475 4191 9.533831 AATTAGGAAAATAAGTCACACCAGATT 57.466 29.630 0.00 0.00 0.00 2.40
2480 4196 7.201652 GGAAAATAAGTCACACCAGATTAGAGC 60.202 40.741 0.00 0.00 0.00 4.09
2491 4207 8.554528 CACACCAGATTAGAGCATTAATTACAG 58.445 37.037 0.00 0.00 0.00 2.74
2532 4274 9.239551 AGTTATTCTTCACTAACAAATAACCCC 57.760 33.333 10.89 0.00 40.87 4.95
2533 4275 8.464404 GTTATTCTTCACTAACAAATAACCCCC 58.536 37.037 0.00 0.00 37.06 5.40
2539 4281 5.189145 TCACTAACAAATAACCCCCTCTCTC 59.811 44.000 0.00 0.00 0.00 3.20
2541 4327 5.791141 ACTAACAAATAACCCCCTCTCTCTT 59.209 40.000 0.00 0.00 0.00 2.85
2542 4328 4.846168 ACAAATAACCCCCTCTCTCTTC 57.154 45.455 0.00 0.00 0.00 2.87
2609 4403 3.392616 AGACAAACATCAGGACTGTCCTT 59.607 43.478 26.37 10.95 46.91 3.36
2787 4722 3.342719 TGCAACAAAGATTATCTGCCGA 58.657 40.909 0.00 0.00 0.00 5.54
2821 4756 2.695359 TCCAAACTAGATTGTCCGCAC 58.305 47.619 11.34 0.00 0.00 5.34
2826 4761 0.855349 CTAGATTGTCCGCACGCATC 59.145 55.000 0.00 0.00 0.00 3.91
2835 4770 1.514228 CGCACGCATCACTCGTAGT 60.514 57.895 0.00 0.00 38.19 2.73
2836 4771 0.247934 CGCACGCATCACTCGTAGTA 60.248 55.000 0.00 0.00 38.19 1.82
2846 4781 5.333492 GCATCACTCGTAGTACTAGCTAGTG 60.333 48.000 32.21 22.07 37.10 2.74
2951 5184 2.992689 TGACGCTTGACCCGGCTA 60.993 61.111 0.00 0.00 34.10 3.93
3083 5811 2.094575 TCGATTAACCGATTGCGTTTGG 59.905 45.455 0.00 0.00 33.14 3.28
3403 6151 3.252974 ACATCGGGACTCAAGAACATC 57.747 47.619 0.00 0.00 0.00 3.06
3444 6195 2.674357 CGTACCCCTTAATTTGTCACCG 59.326 50.000 0.00 0.00 0.00 4.94
3764 6528 2.355363 CTCGACGACGGCACCAAA 60.355 61.111 7.55 0.00 40.21 3.28
3942 6732 3.568538 CATCGATCGATGCTGATGTACA 58.431 45.455 37.03 5.97 44.27 2.90
3947 6737 5.175673 TCGATCGATGCTGATGTACAAATTC 59.824 40.000 15.15 0.00 0.00 2.17
3948 6738 5.613360 CGATCGATGCTGATGTACAAATTCC 60.613 44.000 10.26 0.00 0.00 3.01
3953 6745 6.808212 CGATGCTGATGTACAAATTCCTTTTT 59.192 34.615 0.00 0.00 0.00 1.94
4095 6891 1.028330 TTCGAGCTACCGTCCGTGAT 61.028 55.000 0.00 0.00 0.00 3.06
4261 7057 1.142748 CTGGATCGCCGAGCTCTTT 59.857 57.895 12.85 0.00 36.79 2.52
4323 7125 8.260818 ACTCATACTGCAGTGTATAATTCAACT 58.739 33.333 29.57 0.00 32.48 3.16
4455 7259 7.264373 ACTTAACCAAGTCTCAAGTCAATTG 57.736 36.000 0.00 0.00 41.25 2.32
4456 7260 7.054124 ACTTAACCAAGTCTCAAGTCAATTGA 58.946 34.615 3.38 3.38 41.25 2.57
4457 7261 5.757850 AACCAAGTCTCAAGTCAATTGAC 57.242 39.130 27.69 27.69 43.09 3.18
4597 7412 4.216257 ACATCATCCAGACCAAAGAAAACG 59.784 41.667 0.00 0.00 0.00 3.60
4601 7416 5.358442 TCATCCAGACCAAAGAAAACGAAAA 59.642 36.000 0.00 0.00 0.00 2.29
4655 7474 7.281774 ACATTTTAATGCAAATCACCAACACAA 59.718 29.630 0.00 0.00 40.04 3.33
4672 7491 3.119990 ACACAACAAAGTTCAGACAACGG 60.120 43.478 0.00 0.00 0.00 4.44
4729 7548 3.679389 AGAGAACACAACATGGATGGAC 58.321 45.455 0.00 0.00 0.00 4.02
4752 7571 2.031682 CGTCTTCTTGAGGGTTTTGCTG 60.032 50.000 0.00 0.00 0.00 4.41
4773 7592 5.023533 TGCTGATATTCCAGTGTACTTCC 57.976 43.478 0.00 0.00 36.57 3.46
4775 7594 4.101741 GCTGATATTCCAGTGTACTTCCCT 59.898 45.833 0.00 0.00 36.57 4.20
4779 7598 2.391926 TCCAGTGTACTTCCCTCACA 57.608 50.000 0.00 0.00 34.94 3.58
4787 7606 1.237285 ACTTCCCTCACAATGCGCAC 61.237 55.000 14.90 0.00 0.00 5.34
4851 7670 9.113838 CCACATCTTATATTATATCAACCTGGC 57.886 37.037 0.00 0.00 0.00 4.85
4852 7671 9.896645 CACATCTTATATTATATCAACCTGGCT 57.103 33.333 0.00 0.00 0.00 4.75
4876 7695 1.885871 GCAAAAGGCGCCTTCAGAT 59.114 52.632 40.13 23.40 34.84 2.90
4890 7709 1.825090 TCAGATGCATCCACAACACC 58.175 50.000 23.06 0.00 0.00 4.16
4896 7715 0.602638 GCATCCACAACACCGTCTCA 60.603 55.000 0.00 0.00 0.00 3.27
4909 7728 2.236146 ACCGTCTCATTGCAGGATACAA 59.764 45.455 6.73 0.00 41.41 2.41
4926 7745 8.739039 CAGGATACAAATTCAAACCACATCTTA 58.261 33.333 0.00 0.00 41.41 2.10
4989 7808 1.545428 GCATCCACAACAGGGTCTGAA 60.545 52.381 1.59 0.00 35.18 3.02
5006 7825 2.626743 CTGAAATTCCATCAGATGCCCC 59.373 50.000 4.68 0.00 45.74 5.80
5008 7827 1.238615 AATTCCATCAGATGCCCCCT 58.761 50.000 4.68 0.00 0.00 4.79
5029 7848 5.123979 CCCTGTAAATCCTTGTACTGCTTTC 59.876 44.000 0.00 0.00 0.00 2.62
5101 7920 6.158695 AGAGATCCAGGAGCACCTATTAAAAA 59.841 38.462 7.64 0.00 45.94 1.94
5104 7923 5.826643 TCCAGGAGCACCTATTAAAAACAT 58.173 37.500 1.02 0.00 45.94 2.71
5113 7932 7.232534 AGCACCTATTAAAAACATTGGAGTTCA 59.767 33.333 0.00 0.00 0.00 3.18
5158 7977 7.657761 ACAGGACAACAGAAGAAACTACATTAG 59.342 37.037 0.00 0.00 0.00 1.73
5167 7986 8.821894 CAGAAGAAACTACATTAGGATGTAAGC 58.178 37.037 1.47 0.00 45.50 3.09
5199 8018 1.324134 CAAAGCCAGTGTTTTGCAACG 59.676 47.619 0.00 0.00 36.17 4.10
5231 8050 9.921637 AAAGTTATCAACAGAAACTTGAAACAA 57.078 25.926 0.85 0.00 41.36 2.83
5237 8056 8.655651 TCAACAGAAACTTGAAACAAACTTTT 57.344 26.923 0.00 0.00 0.00 2.27
5243 8062 7.759886 AGAAACTTGAAACAAACTTTTAGCCTC 59.240 33.333 0.00 0.00 0.00 4.70
5244 8063 6.775594 ACTTGAAACAAACTTTTAGCCTCT 57.224 33.333 0.00 0.00 0.00 3.69
5245 8064 6.564328 ACTTGAAACAAACTTTTAGCCTCTG 58.436 36.000 0.00 0.00 0.00 3.35
5246 8065 4.932146 TGAAACAAACTTTTAGCCTCTGC 58.068 39.130 0.00 0.00 37.95 4.26
5247 8066 4.202111 TGAAACAAACTTTTAGCCTCTGCC 60.202 41.667 0.00 0.00 38.69 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.675641 GCTTGAGAATGGTGCGGGT 60.676 57.895 0.00 0.00 0.00 5.28
22 23 2.753966 CGCTTGAGAATGGTGCGGG 61.754 63.158 0.00 0.00 42.46 6.13
24 25 0.729116 ATTCGCTTGAGAATGGTGCG 59.271 50.000 0.00 0.00 46.71 5.34
33 34 1.135859 GGAGCACAACATTCGCTTGAG 60.136 52.381 0.00 0.00 35.75 3.02
35 36 0.877071 AGGAGCACAACATTCGCTTG 59.123 50.000 0.00 0.00 35.75 4.01
39 40 2.670414 GAGAAGAGGAGCACAACATTCG 59.330 50.000 0.00 0.00 0.00 3.34
56 57 5.786264 AGGTCAAGTAAAACGAGAGAGAA 57.214 39.130 0.00 0.00 0.00 2.87
57 58 6.294397 GGTTAGGTCAAGTAAAACGAGAGAGA 60.294 42.308 0.00 0.00 0.00 3.10
68 69 4.773674 TCCATCTTCGGTTAGGTCAAGTAA 59.226 41.667 0.00 0.00 0.00 2.24
99 100 1.327460 GCAATCAAATGCGAGCTACGA 59.673 47.619 9.32 0.00 45.77 3.43
110 111 5.240121 GGGAACACATCAAAGCAATCAAAT 58.760 37.500 0.00 0.00 0.00 2.32
131 132 0.258774 CCCACCTCTATGTTTGGGGG 59.741 60.000 0.00 0.00 44.54 5.40
136 137 2.990740 TTTGGCCCACCTCTATGTTT 57.009 45.000 0.00 0.00 36.63 2.83
138 139 2.624029 CCATTTTGGCCCACCTCTATGT 60.624 50.000 0.00 0.00 36.63 2.29
140 141 2.459555 CCATTTTGGCCCACCTCTAT 57.540 50.000 0.00 0.00 36.63 1.98
165 166 1.202348 GCTTGGTCATTACTGTTGGGC 59.798 52.381 0.00 0.00 0.00 5.36
213 214 2.747855 CCTTGCCTTGGCCGACTC 60.748 66.667 9.35 0.00 0.00 3.36
222 223 1.299976 CTCCCGTTAGCCTTGCCTT 59.700 57.895 0.00 0.00 0.00 4.35
243 244 2.258726 GCCGCCATTATCGTTCCCC 61.259 63.158 0.00 0.00 0.00 4.81
250 251 2.159627 CCTTTGTATCGCCGCCATTATC 59.840 50.000 0.00 0.00 0.00 1.75
253 254 0.393808 ACCTTTGTATCGCCGCCATT 60.394 50.000 0.00 0.00 0.00 3.16
254 255 0.814010 GACCTTTGTATCGCCGCCAT 60.814 55.000 0.00 0.00 0.00 4.40
261 262 7.706607 TCTCTGTATTCATTGACCTTTGTATCG 59.293 37.037 0.00 0.00 0.00 2.92
322 323 7.611467 TGCACTTCAAGGTTATTTCATATGTCT 59.389 33.333 1.90 0.00 0.00 3.41
347 348 9.396022 GGGTACATATGATCTTAAATATGGGTG 57.604 37.037 10.38 0.12 39.87 4.61
391 392 9.504708 CTCTTTGCCTCTCATATGATCTTAAAT 57.495 33.333 5.72 0.00 0.00 1.40
392 393 8.708378 TCTCTTTGCCTCTCATATGATCTTAAA 58.292 33.333 5.72 4.44 0.00 1.52
393 394 8.255111 TCTCTTTGCCTCTCATATGATCTTAA 57.745 34.615 5.72 0.00 0.00 1.85
394 395 7.846101 TCTCTTTGCCTCTCATATGATCTTA 57.154 36.000 5.72 0.00 0.00 2.10
395 396 6.744175 TCTCTTTGCCTCTCATATGATCTT 57.256 37.500 5.72 0.00 0.00 2.40
396 397 6.099413 TGTTCTCTTTGCCTCTCATATGATCT 59.901 38.462 5.72 0.00 0.00 2.75
397 398 6.286758 TGTTCTCTTTGCCTCTCATATGATC 58.713 40.000 5.72 0.00 0.00 2.92
398 399 6.244552 TGTTCTCTTTGCCTCTCATATGAT 57.755 37.500 5.72 0.00 0.00 2.45
399 400 5.682234 TGTTCTCTTTGCCTCTCATATGA 57.318 39.130 5.07 5.07 0.00 2.15
417 418 9.269415 GTACATTCGTATTGTTTACCATTGTTC 57.731 33.333 0.00 0.00 0.00 3.18
425 426 7.453980 TCCATCGTACATTCGTATTGTTTAC 57.546 36.000 0.00 0.00 0.00 2.01
446 454 7.558807 TCTTCTTTCTAAGTATGACCGTATCCA 59.441 37.037 0.00 0.00 0.00 3.41
447 455 7.861872 GTCTTCTTTCTAAGTATGACCGTATCC 59.138 40.741 0.00 0.00 0.00 2.59
451 459 6.585695 TGTCTTCTTTCTAAGTATGACCGT 57.414 37.500 0.00 0.00 0.00 4.83
473 821 6.037098 CGTCTCCTTCCTCTAACTTATGTTG 58.963 44.000 4.33 0.00 37.59 3.33
474 822 5.950549 TCGTCTCCTTCCTCTAACTTATGTT 59.049 40.000 0.00 0.00 39.98 2.71
480 828 5.633655 TCTATCGTCTCCTTCCTCTAACT 57.366 43.478 0.00 0.00 0.00 2.24
505 853 8.571461 TCAATCTGTCATCTGCTTTTATCTTT 57.429 30.769 0.00 0.00 0.00 2.52
506 854 7.282675 CCTCAATCTGTCATCTGCTTTTATCTT 59.717 37.037 0.00 0.00 0.00 2.40
510 858 6.053632 TCCTCAATCTGTCATCTGCTTTTA 57.946 37.500 0.00 0.00 0.00 1.52
528 876 2.291865 ACCTCACAGTGCTCTATCCTCA 60.292 50.000 0.00 0.00 0.00 3.86
556 904 4.100344 GGGTAAAATGGGCGTTTATCCAAT 59.900 41.667 9.95 0.00 40.20 3.16
562 910 2.820787 CACTGGGTAAAATGGGCGTTTA 59.179 45.455 0.00 0.00 0.00 2.01
570 918 3.316308 GCATAGCTCCACTGGGTAAAATG 59.684 47.826 0.00 0.00 34.93 2.32
574 922 1.209504 GTGCATAGCTCCACTGGGTAA 59.790 52.381 0.00 0.00 34.93 2.85
645 1018 2.026356 TGCCATGCAGTATACCTGTGTT 60.026 45.455 0.00 0.00 43.55 3.32
647 1020 2.330440 TGCCATGCAGTATACCTGTG 57.670 50.000 0.00 0.00 43.55 3.66
669 1042 4.328712 CAGTACATACAAGCATACGCACAA 59.671 41.667 0.00 0.00 42.27 3.33
726 1100 4.217767 TCTTTGCTGAAACGTAGCTAGAGA 59.782 41.667 10.01 7.52 41.66 3.10
756 1135 3.619038 CCCACTGCGTCTCTTAGAAAATC 59.381 47.826 0.00 0.00 0.00 2.17
771 1496 2.031163 ACGTGAGCTTCCCACTGC 59.969 61.111 2.91 0.00 32.64 4.40
781 1506 3.163655 GCTCTTGAGCACGTGAGC 58.836 61.111 22.23 14.45 43.75 4.26
832 1563 1.121240 GTGTCTTGTGTGTCGACGAG 58.879 55.000 11.62 3.94 0.00 4.18
873 1604 0.523519 GAGGTGCTGTTAGGCTTTGC 59.476 55.000 0.00 0.00 0.00 3.68
880 1611 0.244994 AGAGCGTGAGGTGCTGTTAG 59.755 55.000 0.00 0.00 44.18 2.34
963 1729 0.964358 GCTGGATGAAGCTGGCTGTT 60.964 55.000 0.00 0.00 40.20 3.16
1500 2271 3.706802 TCTCGAAACAAGCATGCAAAA 57.293 38.095 21.98 0.00 0.00 2.44
1699 2539 0.961358 CTCAACGGTCTCCTCCTCGT 60.961 60.000 0.00 0.00 37.45 4.18
1820 2663 4.404185 TTCCTATGCATAGCTAGGAGGA 57.596 45.455 25.60 16.70 43.30 3.71
1821 2664 4.774726 TCTTTCCTATGCATAGCTAGGAGG 59.225 45.833 25.60 14.69 43.30 4.30
1822 2665 5.991933 TCTTTCCTATGCATAGCTAGGAG 57.008 43.478 25.60 17.25 43.30 3.69
2113 3229 1.000233 TCCCAAATCGCCAAGGCAT 60.000 52.632 12.19 1.27 42.06 4.40
2140 3530 2.171870 TGACCTTTTCCGGAACAGAGTT 59.828 45.455 28.09 13.83 0.00 3.01
2151 3541 3.493767 AGGACAAGAGTGACCTTTTCC 57.506 47.619 9.55 9.55 46.17 3.13
2180 3570 3.130340 GGCTGTTGAGACAAGGTCAAAAA 59.870 43.478 0.00 0.00 35.71 1.94
2181 3571 2.687935 GGCTGTTGAGACAAGGTCAAAA 59.312 45.455 0.00 0.00 35.71 2.44
2182 3572 2.092429 AGGCTGTTGAGACAAGGTCAAA 60.092 45.455 0.00 0.00 35.71 2.69
2184 3574 1.131638 AGGCTGTTGAGACAAGGTCA 58.868 50.000 0.00 0.00 34.85 4.02
2185 3575 3.526534 GATAGGCTGTTGAGACAAGGTC 58.473 50.000 0.00 0.00 34.85 3.85
2186 3576 2.237392 GGATAGGCTGTTGAGACAAGGT 59.763 50.000 0.00 0.00 34.85 3.50
2187 3577 2.503356 AGGATAGGCTGTTGAGACAAGG 59.497 50.000 0.00 0.00 34.85 3.61
2189 3579 3.133003 GCTAGGATAGGCTGTTGAGACAA 59.867 47.826 0.00 0.00 39.70 3.18
2191 3581 3.378911 GCTAGGATAGGCTGTTGAGAC 57.621 52.381 0.00 0.00 39.70 3.36
2233 3949 6.668541 ATGTCTAGTGTACATTGAACATGC 57.331 37.500 15.14 0.00 33.83 4.06
2272 3988 4.818534 ACGTATTAAGAGCCAATGCATG 57.181 40.909 0.00 0.00 41.13 4.06
2289 4005 7.961325 TCACTACCGTACATATGATAACGTA 57.039 36.000 10.38 9.68 33.63 3.57
2398 4114 5.018809 AGGCAACAAGATGGACATGTAAAT 58.981 37.500 0.00 0.00 41.41 1.40
2406 4122 1.523758 AACGAGGCAACAAGATGGAC 58.476 50.000 0.00 0.00 41.41 4.02
2414 4130 2.176045 TCTCTCCATAACGAGGCAACA 58.824 47.619 0.00 0.00 41.41 3.33
2417 4133 2.168521 CCTTTCTCTCCATAACGAGGCA 59.831 50.000 0.00 0.00 0.00 4.75
2422 4138 4.192317 CCCTTTCCTTTCTCTCCATAACG 58.808 47.826 0.00 0.00 0.00 3.18
2426 4142 5.860648 TTTACCCTTTCCTTTCTCTCCAT 57.139 39.130 0.00 0.00 0.00 3.41
2453 4169 7.918076 TCTAATCTGGTGTGACTTATTTTCCT 58.082 34.615 0.00 0.00 0.00 3.36
2458 4174 6.299805 TGCTCTAATCTGGTGTGACTTATT 57.700 37.500 0.00 0.00 0.00 1.40
2475 4191 8.956533 TTGCATGTACTGTAATTAATGCTCTA 57.043 30.769 15.15 3.03 40.74 2.43
2511 4227 6.045106 AGAGGGGGTTATTTGTTAGTGAAGAA 59.955 38.462 0.00 0.00 0.00 2.52
2512 4228 5.550403 AGAGGGGGTTATTTGTTAGTGAAGA 59.450 40.000 0.00 0.00 0.00 2.87
2513 4229 5.816682 AGAGGGGGTTATTTGTTAGTGAAG 58.183 41.667 0.00 0.00 0.00 3.02
2514 4230 5.550403 AGAGAGGGGGTTATTTGTTAGTGAA 59.450 40.000 0.00 0.00 0.00 3.18
2516 4232 5.189934 AGAGAGAGGGGGTTATTTGTTAGTG 59.810 44.000 0.00 0.00 0.00 2.74
2532 4274 8.825745 GCAATGTATTTAAAGAGAAGAGAGAGG 58.174 37.037 0.00 0.00 0.00 3.69
2533 4275 8.825745 GGCAATGTATTTAAAGAGAAGAGAGAG 58.174 37.037 0.00 0.00 0.00 3.20
2539 4281 7.093322 AGCTGGCAATGTATTTAAAGAGAAG 57.907 36.000 0.00 0.00 0.00 2.85
2541 4327 6.767902 CCTAGCTGGCAATGTATTTAAAGAGA 59.232 38.462 0.00 0.00 0.00 3.10
2542 4328 6.543831 ACCTAGCTGGCAATGTATTTAAAGAG 59.456 38.462 0.00 0.00 40.22 2.85
2581 4367 4.082408 CAGTCCTGATGTTTGTCTACGGTA 60.082 45.833 0.00 0.00 0.00 4.02
2582 4368 2.897969 AGTCCTGATGTTTGTCTACGGT 59.102 45.455 0.00 0.00 0.00 4.83
2609 4403 6.576185 AGGAACGTTGAAAAGTCAAGTAGTA 58.424 36.000 5.00 0.00 44.44 1.82
2665 4479 3.576982 CCCAACTGGTGTGTTCTAGTCTA 59.423 47.826 0.00 0.00 0.00 2.59
2666 4480 2.368875 CCCAACTGGTGTGTTCTAGTCT 59.631 50.000 0.00 0.00 0.00 3.24
2667 4481 2.550208 CCCCAACTGGTGTGTTCTAGTC 60.550 54.545 0.00 0.00 0.00 2.59
2668 4482 1.420138 CCCCAACTGGTGTGTTCTAGT 59.580 52.381 0.00 0.00 0.00 2.57
2669 4483 1.420138 ACCCCAACTGGTGTGTTCTAG 59.580 52.381 0.00 0.00 37.20 2.43
2670 4484 1.418637 GACCCCAACTGGTGTGTTCTA 59.581 52.381 0.00 0.00 39.24 2.10
2671 4485 0.182775 GACCCCAACTGGTGTGTTCT 59.817 55.000 0.00 0.00 39.24 3.01
2672 4486 0.106918 TGACCCCAACTGGTGTGTTC 60.107 55.000 0.00 0.00 39.24 3.18
2673 4487 0.333312 TTGACCCCAACTGGTGTGTT 59.667 50.000 0.00 0.00 39.24 3.32
2674 4488 0.333312 TTTGACCCCAACTGGTGTGT 59.667 50.000 0.00 0.00 39.24 3.72
2675 4489 1.032014 CTTTGACCCCAACTGGTGTG 58.968 55.000 0.00 0.00 39.24 3.82
2676 4490 0.923358 TCTTTGACCCCAACTGGTGT 59.077 50.000 0.00 0.00 39.24 4.16
2677 4491 2.065899 TTCTTTGACCCCAACTGGTG 57.934 50.000 0.00 0.00 39.24 4.17
2787 4722 3.562182 AGTTTGGAAGGTTCGTTTGGAT 58.438 40.909 0.00 0.00 0.00 3.41
2821 4756 2.544686 AGCTAGTACTACGAGTGATGCG 59.455 50.000 0.00 0.00 0.00 4.73
2826 4761 3.248125 GCCACTAGCTAGTACTACGAGTG 59.752 52.174 25.63 23.22 38.99 3.51
2835 4770 1.048601 GCCATGGCCACTAGCTAGTA 58.951 55.000 27.24 11.22 43.05 1.82
2836 4771 1.832912 GCCATGGCCACTAGCTAGT 59.167 57.895 27.24 20.95 43.05 2.57
2846 4781 2.895372 CGTTAGGACGCCATGGCC 60.895 66.667 30.79 17.56 43.03 5.36
2933 5166 2.890847 CTAGCCGGGTCAAGCGTCAG 62.891 65.000 10.79 0.00 0.00 3.51
3003 5729 2.099638 CGCGACGGAATCTCGACA 59.900 61.111 0.00 0.00 37.77 4.35
3083 5811 0.936297 CTCGCCTGCAAACAAGCAAC 60.936 55.000 0.00 0.00 45.13 4.17
3403 6151 2.733671 CTCGAGCATGCACACGTGG 61.734 63.158 21.98 10.05 33.09 4.94
3444 6195 4.025229 TCGTGCAGTAATGTTCTTGTTGAC 60.025 41.667 0.00 0.00 0.00 3.18
3589 6353 1.445582 GGCGTCAGACCGTACTTGG 60.446 63.158 0.00 0.00 0.00 3.61
3695 6459 1.594310 GGAGGCTCTCTTGAAGCGT 59.406 57.895 15.23 0.00 0.00 5.07
3764 6528 2.526873 ACAAGGTCCGCCTCCACT 60.527 61.111 0.00 0.00 46.33 4.00
3940 6730 3.205338 GCCACTGCAAAAAGGAATTTGT 58.795 40.909 0.00 0.00 41.34 2.83
3942 6732 3.557228 TGCCACTGCAAAAAGGAATTT 57.443 38.095 0.00 0.00 46.66 1.82
4231 7027 0.108329 CGATCCAGTTGCCCTTACGT 60.108 55.000 0.00 0.00 0.00 3.57
4261 7057 0.595588 CCTTGTTGTTGTATGGCGCA 59.404 50.000 10.83 0.00 0.00 6.09
4321 7123 1.005687 AGCTACAGGGGACGTAGAAGT 59.994 52.381 1.62 0.00 38.71 3.01
4323 7125 2.226962 AAGCTACAGGGGACGTAGAA 57.773 50.000 1.62 0.00 38.71 2.10
4536 7351 8.991275 TGATTTATTTCTTAATTGATTGGGGCT 58.009 29.630 0.00 0.00 0.00 5.19
4627 7446 6.988580 TGTTGGTGATTTGCATTAAAATGTGA 59.011 30.769 4.71 0.00 38.65 3.58
4655 7474 1.021968 GGCCGTTGTCTGAACTTTGT 58.978 50.000 0.00 0.00 0.00 2.83
4729 7548 2.224314 GCAAAACCCTCAAGAAGACGAG 59.776 50.000 0.00 0.00 0.00 4.18
4752 7571 4.101741 AGGGAAGTACACTGGAATATCAGC 59.898 45.833 0.00 0.00 38.26 4.26
4773 7592 0.244450 AAATGGTGCGCATTGTGAGG 59.756 50.000 15.91 0.00 0.00 3.86
4775 7594 1.339291 TGAAAATGGTGCGCATTGTGA 59.661 42.857 15.91 0.00 0.00 3.58
4779 7598 2.224018 ACAGTTGAAAATGGTGCGCATT 60.224 40.909 15.91 2.15 0.00 3.56
4787 7606 5.772825 TGGAAAGAGACAGTTGAAAATGG 57.227 39.130 0.00 0.00 0.00 3.16
4851 7670 2.744768 GGCGCCTTTTGCTCTCGAG 61.745 63.158 22.15 5.93 38.05 4.04
4852 7671 2.731691 AAGGCGCCTTTTGCTCTCGA 62.732 55.000 35.84 0.00 38.05 4.04
4876 7695 0.602638 GAGACGGTGTTGTGGATGCA 60.603 55.000 0.00 0.00 0.00 3.96
4890 7709 5.065090 TGAATTTGTATCCTGCAATGAGACG 59.935 40.000 6.28 0.00 0.00 4.18
4896 7715 6.165577 GTGGTTTGAATTTGTATCCTGCAAT 58.834 36.000 0.00 0.00 0.00 3.56
4926 7745 3.296854 TCGAGCCAGACTGGTATAATGT 58.703 45.455 22.58 0.00 40.46 2.71
4989 7808 1.133262 CAGGGGGCATCTGATGGAATT 60.133 52.381 18.60 0.00 34.36 2.17
5001 7820 1.080638 ACAAGGATTTACAGGGGGCA 58.919 50.000 0.00 0.00 0.00 5.36
5006 7825 5.940470 AGAAAGCAGTACAAGGATTTACAGG 59.060 40.000 0.00 0.00 0.00 4.00
5008 7827 5.938125 GGAGAAAGCAGTACAAGGATTTACA 59.062 40.000 0.00 0.00 0.00 2.41
5054 7873 2.942804 TGAAACATGTTCTTGGGCTGA 58.057 42.857 12.39 0.00 0.00 4.26
5061 7880 7.052873 CCTGGATCTCTATGAAACATGTTCTT 58.947 38.462 12.39 0.00 0.00 2.52
5101 7920 8.938906 GCAATGAAATTTTATGAACTCCAATGT 58.061 29.630 0.00 0.00 31.22 2.71
5104 7923 6.878389 GGGCAATGAAATTTTATGAACTCCAA 59.122 34.615 0.00 0.00 31.22 3.53
5113 7932 4.080413 CCTGTGGGGGCAATGAAATTTTAT 60.080 41.667 0.00 0.00 31.22 1.40
5121 7940 2.763215 GTCCTGTGGGGGCAATGA 59.237 61.111 0.00 0.00 40.02 2.57
5158 7977 7.025963 CTTTGTGAAAGAAGATGCTTACATCC 58.974 38.462 2.52 0.00 45.80 3.51
5167 7986 4.037208 ACACTGGCTTTGTGAAAGAAGATG 59.963 41.667 11.45 2.21 41.02 2.90
5199 8018 9.185192 CAAGTTTCTGTTGATAACTTTGAATCC 57.815 33.333 0.00 0.00 39.40 3.01
5231 8050 2.628178 GTTTGGGCAGAGGCTAAAAGTT 59.372 45.455 3.83 0.00 39.79 2.66
5237 8056 1.685224 CTGGTTTGGGCAGAGGCTA 59.315 57.895 0.00 0.00 40.87 3.93
5239 8058 3.376918 GCTGGTTTGGGCAGAGGC 61.377 66.667 0.00 0.00 40.13 4.70
5243 8062 2.048603 GCTAGGCTGGTTTGGGCAG 61.049 63.158 0.00 0.00 0.00 4.85
5244 8063 1.204786 TAGCTAGGCTGGTTTGGGCA 61.205 55.000 0.00 0.00 40.10 5.36
5245 8064 0.748367 GTAGCTAGGCTGGTTTGGGC 60.748 60.000 0.00 0.00 40.10 5.36
5246 8065 0.618458 TGTAGCTAGGCTGGTTTGGG 59.382 55.000 0.00 0.00 40.10 4.12
5247 8066 2.489938 TTGTAGCTAGGCTGGTTTGG 57.510 50.000 0.00 0.00 40.10 3.28


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

AutoCloner maintained by Alex Coulton.