Multiple sequence alignment - TraesCS4D01G054600

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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 TraesCS4D01G054600 chr4D 100.000 5569 0 0 1 5569 30274503 30280071 0.000000e+00 10285.0
1 TraesCS4D01G054600 chr4D 91.579 95 8 0 5475 5569 133736206 133736112 1.260000e-26 132.0
2 TraesCS4D01G054600 chr4D 91.579 95 8 0 5475 5569 487405367 487405273 1.260000e-26 132.0
3 TraesCS4D01G054600 chr4A 94.063 3015 70 37 2166 5101 572704515 572701531 0.000000e+00 4475.0
4 TraesCS4D01G054600 chr4A 96.197 1157 23 9 999 2146 572705854 572704710 0.000000e+00 1873.0
5 TraesCS4D01G054600 chr4A 92.577 714 36 10 2728 3428 516543601 516542892 0.000000e+00 1009.0
6 TraesCS4D01G054600 chr4A 91.509 318 21 2 446 757 572706547 572706230 3.080000e-117 433.0
7 TraesCS4D01G054600 chr4A 86.553 409 25 10 5097 5475 572701383 572700975 1.850000e-114 424.0
8 TraesCS4D01G054600 chr4A 89.489 333 21 8 19 339 572711249 572710919 5.190000e-110 409.0
9 TraesCS4D01G054600 chr4A 87.143 350 28 7 2 339 572707797 572707453 1.130000e-101 381.0
10 TraesCS4D01G054600 chr4A 88.976 254 26 2 446 697 572707329 572707076 4.190000e-81 313.0
11 TraesCS4D01G054600 chr4A 88.646 229 12 8 2728 2943 470121258 470121485 3.310000e-67 267.0
12 TraesCS4D01G054600 chr4A 92.667 150 8 2 774 920 572706162 572706013 4.370000e-51 213.0
13 TraesCS4D01G054600 chr4A 90.909 154 12 1 757 908 572706902 572706749 7.310000e-49 206.0
14 TraesCS4D01G054600 chr4A 92.000 100 7 1 339 437 55803010 55802911 7.520000e-29 139.0
15 TraesCS4D01G054600 chr4A 89.109 101 8 2 5469 5569 599620261 599620164 7.580000e-24 122.0
16 TraesCS4D01G054600 chr4A 91.304 69 2 1 906 970 572705989 572705921 2.140000e-14 91.6
17 TraesCS4D01G054600 chr4B 92.125 2400 98 26 818 3153 43172606 43174978 0.000000e+00 3301.0
18 TraesCS4D01G054600 chr4B 91.482 857 60 9 3917 4768 43175688 43176536 0.000000e+00 1166.0
19 TraesCS4D01G054600 chr4B 84.286 350 15 12 5097 5423 43176911 43177243 7.010000e-79 305.0
20 TraesCS4D01G054600 chr4B 83.459 266 8 8 4866 5101 43176535 43176794 1.220000e-51 215.0
21 TraesCS4D01G054600 chr4B 90.816 98 8 1 339 435 526138842 526138939 4.530000e-26 130.0
22 TraesCS4D01G054600 chr4B 89.474 95 8 2 5475 5569 520209363 520209271 9.800000e-23 119.0
23 TraesCS4D01G054600 chr7A 92.395 973 55 12 2470 3428 676176406 676177373 0.000000e+00 1369.0
24 TraesCS4D01G054600 chr5B 92.857 714 34 11 2728 3428 632166063 632165354 0.000000e+00 1020.0
25 TraesCS4D01G054600 chr5B 88.235 170 16 2 3750 3915 4857360 4857191 3.400000e-47 200.0
26 TraesCS4D01G054600 chr5B 87.755 98 12 0 5472 5569 419498385 419498482 1.270000e-21 115.0
27 TraesCS4D01G054600 chr2D 92.577 714 36 11 2728 3428 87644147 87644856 0.000000e+00 1009.0
28 TraesCS4D01G054600 chr2D 92.437 714 37 11 2728 3428 160960774 160960065 0.000000e+00 1003.0
29 TraesCS4D01G054600 chr7D 92.437 714 38 10 2728 3428 489710226 489709516 0.000000e+00 1005.0
30 TraesCS4D01G054600 chr7D 92.929 99 7 0 339 437 104199700 104199798 1.620000e-30 145.0
31 TraesCS4D01G054600 chr7D 91.753 97 7 1 339 434 167556269 167556365 3.500000e-27 134.0
32 TraesCS4D01G054600 chr7D 90.196 102 8 1 5468 5569 83752123 83752024 1.260000e-26 132.0
33 TraesCS4D01G054600 chr7D 90.816 98 7 2 5473 5569 36453213 36453117 4.530000e-26 130.0
34 TraesCS4D01G054600 chr5D 92.546 711 36 11 2731 3428 187525377 187524671 0.000000e+00 1003.0
35 TraesCS4D01G054600 chr5D 92.437 714 37 11 2728 3428 503682732 503682023 0.000000e+00 1003.0
36 TraesCS4D01G054600 chr5D 92.168 715 37 13 2728 3428 430561140 430560431 0.000000e+00 992.0
37 TraesCS4D01G054600 chrUn 92.297 714 38 10 2728 3428 105817971 105817262 0.000000e+00 998.0
38 TraesCS4D01G054600 chrUn 92.297 714 37 12 2728 3428 106339224 106338516 0.000000e+00 998.0
39 TraesCS4D01G054600 chr3A 91.877 714 40 11 2728 3428 703077193 703077901 0.000000e+00 981.0
40 TraesCS4D01G054600 chr3A 91.753 97 7 1 339 434 494235437 494235341 3.500000e-27 134.0
41 TraesCS4D01G054600 chr1D 94.231 156 4 3 2728 2879 61572916 61573070 3.350000e-57 233.0
42 TraesCS4D01G054600 chr6B 87.574 169 21 0 3749 3917 590448419 590448587 4.400000e-46 196.0
43 TraesCS4D01G054600 chr6B 85.799 169 23 1 3752 3920 545253920 545254087 1.590000e-40 178.0
44 TraesCS4D01G054600 chr3D 87.574 169 21 0 3749 3917 213682821 213682989 4.400000e-46 196.0
45 TraesCS4D01G054600 chr3D 91.667 96 8 0 339 434 202477136 202477231 3.500000e-27 134.0
46 TraesCS4D01G054600 chr1A 86.861 137 14 1 3777 3913 30128111 30128243 3.480000e-32 150.0
47 TraesCS4D01G054600 chr3B 93.000 100 7 0 339 438 242671261 242671162 4.500000e-31 147.0
48 TraesCS4D01G054600 chr3B 92.929 99 7 0 339 437 545889210 545889308 1.620000e-30 145.0
49 TraesCS4D01G054600 chr1B 92.000 100 6 2 337 436 189712194 189712291 7.520000e-29 139.0
50 TraesCS4D01G054600 chr1B 82.166 157 28 0 3751 3907 242744170 242744326 9.730000e-28 135.0
51 TraesCS4D01G054600 chr6D 91.398 93 6 2 5473 5564 83177242 83177151 5.860000e-25 126.0
52 TraesCS4D01G054600 chr2B 87.879 99 8 4 5473 5569 25707065 25707161 4.560000e-21 113.0


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 TraesCS4D01G054600 chr4D 30274503 30280071 5568 False 10285.00 10285 100.000 1 5569 1 chr4D.!!$F1 5568
1 TraesCS4D01G054600 chr4A 516542892 516543601 709 True 1009.00 1009 92.577 2728 3428 1 chr4A.!!$R2 700
2 TraesCS4D01G054600 chr4A 572700975 572711249 10274 True 881.86 4475 90.881 2 5475 10 chr4A.!!$R4 5473
3 TraesCS4D01G054600 chr4B 43172606 43177243 4637 False 1246.75 3301 87.838 818 5423 4 chr4B.!!$F2 4605
4 TraesCS4D01G054600 chr7A 676176406 676177373 967 False 1369.00 1369 92.395 2470 3428 1 chr7A.!!$F1 958
5 TraesCS4D01G054600 chr5B 632165354 632166063 709 True 1020.00 1020 92.857 2728 3428 1 chr5B.!!$R2 700
6 TraesCS4D01G054600 chr2D 87644147 87644856 709 False 1009.00 1009 92.577 2728 3428 1 chr2D.!!$F1 700
7 TraesCS4D01G054600 chr2D 160960065 160960774 709 True 1003.00 1003 92.437 2728 3428 1 chr2D.!!$R1 700
8 TraesCS4D01G054600 chr7D 489709516 489710226 710 True 1005.00 1005 92.437 2728 3428 1 chr7D.!!$R3 700
9 TraesCS4D01G054600 chr5D 187524671 187525377 706 True 1003.00 1003 92.546 2731 3428 1 chr5D.!!$R1 697
10 TraesCS4D01G054600 chr5D 503682023 503682732 709 True 1003.00 1003 92.437 2728 3428 1 chr5D.!!$R3 700
11 TraesCS4D01G054600 chr5D 430560431 430561140 709 True 992.00 992 92.168 2728 3428 1 chr5D.!!$R2 700
12 TraesCS4D01G054600 chrUn 105817262 105817971 709 True 998.00 998 92.297 2728 3428 1 chrUn.!!$R1 700
13 TraesCS4D01G054600 chrUn 106338516 106339224 708 True 998.00 998 92.297 2728 3428 1 chrUn.!!$R2 700
14 TraesCS4D01G054600 chr3A 703077193 703077901 708 False 981.00 981 91.877 2728 3428 1 chr3A.!!$F1 700

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
940 5316 0.319083 ATTAACCGACGCACTCCACA 59.681 50.000 0.00 0.0 0.00 4.17 F
1947 6383 2.106166 GCTCATTGAGAGGATGGTGGAT 59.894 50.000 17.87 0.0 44.86 3.41 F
2094 6530 1.744368 CAGATGCACGCTCAGGCTT 60.744 57.895 0.00 0.0 36.09 4.35 F
3586 8360 0.179076 TCCACATGCTATCTGGTGCG 60.179 55.000 0.00 0.0 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2025 6461 0.176449 TCCTCCACATGTCAGCATCG 59.824 55.0 0.0 0.0 31.99 3.84 R
3586 8360 0.745468 AGAGCCCCGAACGACTAATC 59.255 55.0 0.0 0.0 0.00 1.75 R
3964 8756 2.424956 GCAGGTGGTGGAATGAAAGATC 59.575 50.0 0.0 0.0 0.00 2.75 R
5142 10142 0.109086 AGCATCACTCTTCACCGACG 60.109 55.0 0.0 0.0 0.00 5.12 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
81 82 7.051690 GTCATTGGACATCGTGTGGAACAAT 62.052 44.000 0.00 0.00 46.61 2.71
140 153 4.279922 TCACTGTCTTTATGTCGTCTGGAA 59.720 41.667 0.00 0.00 0.00 3.53
177 190 7.801716 AATGATAAATTTAGACTGCGCCTTA 57.198 32.000 4.18 0.00 0.00 2.69
260 3739 4.965119 ATTTCCCTGTGCTACGAAATTC 57.035 40.909 0.00 0.00 32.40 2.17
273 3752 9.669353 GTGCTACGAAATTCAAAATCATATGAT 57.331 29.630 12.62 12.62 36.07 2.45
303 3782 8.842358 TTCTACCAAACTACCTTTTCATACAG 57.158 34.615 0.00 0.00 0.00 2.74
320 3799 6.121590 TCATACAGTGTCAACATGCCAATAT 58.878 36.000 0.00 0.00 0.00 1.28
339 3818 7.575365 CCAATATTTTTCTTTGGCAAAGACAC 58.425 34.615 35.46 0.00 46.53 3.67
340 3819 7.226325 CCAATATTTTTCTTTGGCAAAGACACA 59.774 33.333 35.46 25.08 46.53 3.72
341 3820 8.610896 CAATATTTTTCTTTGGCAAAGACACAA 58.389 29.630 35.46 27.29 46.53 3.33
342 3821 8.729805 ATATTTTTCTTTGGCAAAGACACAAA 57.270 26.923 35.46 30.42 46.53 2.83
343 3822 6.867662 TTTTTCTTTGGCAAAGACACAAAA 57.132 29.167 35.46 31.86 46.53 2.44
344 3823 6.867662 TTTTCTTTGGCAAAGACACAAAAA 57.132 29.167 35.46 28.48 46.53 1.94
345 3824 7.446001 TTTTCTTTGGCAAAGACACAAAAAT 57.554 28.000 35.46 0.00 46.53 1.82
346 3825 6.660887 TTCTTTGGCAAAGACACAAAAATC 57.339 33.333 35.46 0.00 46.53 2.17
348 3827 5.580297 TCTTTGGCAAAGACACAAAAATCAC 59.420 36.000 32.85 0.00 42.31 3.06
349 3828 4.734398 TGGCAAAGACACAAAAATCACT 57.266 36.364 0.00 0.00 0.00 3.41
350 3829 5.083533 TGGCAAAGACACAAAAATCACTT 57.916 34.783 0.00 0.00 0.00 3.16
351 3830 5.486526 TGGCAAAGACACAAAAATCACTTT 58.513 33.333 0.00 0.00 0.00 2.66
353 3832 6.756074 TGGCAAAGACACAAAAATCACTTTAG 59.244 34.615 0.00 0.00 0.00 1.85
354 3833 6.200854 GGCAAAGACACAAAAATCACTTTAGG 59.799 38.462 0.00 0.00 0.00 2.69
355 3834 6.756542 GCAAAGACACAAAAATCACTTTAGGT 59.243 34.615 0.00 0.00 0.00 3.08
356 3835 7.254084 GCAAAGACACAAAAATCACTTTAGGTG 60.254 37.037 0.00 0.00 46.60 4.00
357 3836 7.404671 AAGACACAAAAATCACTTTAGGTGT 57.595 32.000 0.00 0.00 43.17 4.16
359 3838 6.767524 ACACAAAAATCACTTTAGGTGTCA 57.232 33.333 0.00 0.00 45.50 3.58
360 3839 7.164230 ACACAAAAATCACTTTAGGTGTCAA 57.836 32.000 0.00 0.00 45.50 3.18
361 3840 7.607250 ACACAAAAATCACTTTAGGTGTCAAA 58.393 30.769 0.00 0.00 45.50 2.69
362 3841 8.257306 ACACAAAAATCACTTTAGGTGTCAAAT 58.743 29.630 0.00 0.00 45.50 2.32
364 3843 9.965824 ACAAAAATCACTTTAGGTGTCAAATAG 57.034 29.630 0.00 0.00 45.50 1.73
367 3846 6.636454 ATCACTTTAGGTGTCAAATAGGGA 57.364 37.500 0.00 0.00 45.50 4.20
368 3847 6.442541 TCACTTTAGGTGTCAAATAGGGAA 57.557 37.500 0.00 0.00 45.50 3.97
370 4381 6.271391 TCACTTTAGGTGTCAAATAGGGAAGA 59.729 38.462 0.00 0.00 45.50 2.87
376 4387 7.855784 AGGTGTCAAATAGGGAAGAAATTTT 57.144 32.000 0.00 0.00 0.00 1.82
398 4409 8.956533 TTTTATTTTATGCCAAATAGGGAAGC 57.043 30.769 0.00 0.00 42.99 3.86
400 4411 6.558488 ATTTTATGCCAAATAGGGAAGCAA 57.442 33.333 0.00 0.00 42.99 3.91
403 4414 6.558488 TTATGCCAAATAGGGAAGCAAATT 57.442 33.333 0.00 0.00 42.99 1.82
406 4417 6.365970 TGCCAAATAGGGAAGCAAATTTTA 57.634 33.333 0.00 0.00 38.09 1.52
407 4418 6.773638 TGCCAAATAGGGAAGCAAATTTTAA 58.226 32.000 0.00 0.00 38.09 1.52
408 4419 7.227156 TGCCAAATAGGGAAGCAAATTTTAAA 58.773 30.769 0.00 0.00 38.09 1.52
409 4420 7.721399 TGCCAAATAGGGAAGCAAATTTTAAAA 59.279 29.630 2.51 2.51 38.09 1.52
410 4421 8.572185 GCCAAATAGGGAAGCAAATTTTAAAAA 58.428 29.630 4.44 0.00 38.09 1.94
430 4441 6.702449 AAAAAGGGCCAAATAAGGAATTCT 57.298 33.333 6.18 0.00 0.00 2.40
431 4442 5.939764 AAAGGGCCAAATAAGGAATTCTC 57.060 39.130 6.18 0.00 0.00 2.87
433 4444 4.797743 AGGGCCAAATAAGGAATTCTCTC 58.202 43.478 6.18 0.00 0.00 3.20
435 4446 4.956075 GGGCCAAATAAGGAATTCTCTCAA 59.044 41.667 4.39 0.00 0.00 3.02
436 4447 5.600069 GGGCCAAATAAGGAATTCTCTCAAT 59.400 40.000 4.39 0.00 0.00 2.57
437 4448 6.098838 GGGCCAAATAAGGAATTCTCTCAATT 59.901 38.462 4.39 2.98 0.00 2.32
438 4449 7.365028 GGGCCAAATAAGGAATTCTCTCAATTT 60.365 37.037 4.39 7.93 0.00 1.82
439 4450 8.043113 GGCCAAATAAGGAATTCTCTCAATTTT 58.957 33.333 5.23 0.00 0.00 1.82
440 4451 9.091784 GCCAAATAAGGAATTCTCTCAATTTTC 57.908 33.333 5.23 3.33 0.00 2.29
459 4737 5.698741 TTTCTTCCATCCATGAAGAGCTA 57.301 39.130 0.00 0.00 36.48 3.32
468 4746 5.344743 TCCATGAAGAGCTACGAGATTTT 57.655 39.130 0.00 0.00 0.00 1.82
512 4790 2.035783 GTTTGGGTGCCCTCTCCC 59.964 66.667 8.91 0.00 44.43 4.30
519 4797 1.575447 GGTGCCCTCTCCCCTCAAAT 61.575 60.000 0.00 0.00 0.00 2.32
596 4876 8.593945 AATTAGGTCATTATGGACACAATTGT 57.406 30.769 4.92 4.92 39.59 2.71
600 4880 7.175104 AGGTCATTATGGACACAATTGTAAGT 58.825 34.615 11.53 5.98 39.59 2.24
603 4883 9.769093 GTCATTATGGACACAATTGTAAGTAAC 57.231 33.333 11.53 3.90 35.47 2.50
666 4950 7.452501 TGGAAACAAGATCTTGAGGATTGAAAT 59.547 33.333 36.15 11.62 42.93 2.17
697 4981 9.912634 TGAAAATACTTAGAAAAATCTTGCAGG 57.087 29.630 0.00 0.00 0.00 4.85
703 4987 2.827921 AGAAAAATCTTGCAGGCCGAAT 59.172 40.909 0.00 0.00 0.00 3.34
757 5041 7.404671 ACTTTCAAAAGTTATCAGTGTGGTT 57.595 32.000 2.30 0.00 46.52 3.67
758 5042 7.257722 ACTTTCAAAAGTTATCAGTGTGGTTG 58.742 34.615 2.30 0.00 46.52 3.77
759 5043 7.122055 ACTTTCAAAAGTTATCAGTGTGGTTGA 59.878 33.333 2.30 0.00 46.52 3.18
762 5046 7.424803 TCAAAAGTTATCAGTGTGGTTGATTG 58.575 34.615 0.00 0.00 36.68 2.67
763 5047 7.284261 TCAAAAGTTATCAGTGTGGTTGATTGA 59.716 33.333 0.00 0.00 36.68 2.57
766 5050 7.149569 AGTTATCAGTGTGGTTGATTGATTG 57.850 36.000 0.00 0.00 36.68 2.67
767 5051 6.151648 AGTTATCAGTGTGGTTGATTGATTGG 59.848 38.462 0.00 0.00 36.68 3.16
768 5052 3.156293 TCAGTGTGGTTGATTGATTGGG 58.844 45.455 0.00 0.00 0.00 4.12
769 5053 2.892852 CAGTGTGGTTGATTGATTGGGT 59.107 45.455 0.00 0.00 0.00 4.51
770 5054 2.892852 AGTGTGGTTGATTGATTGGGTG 59.107 45.455 0.00 0.00 0.00 4.61
771 5055 2.627699 GTGTGGTTGATTGATTGGGTGT 59.372 45.455 0.00 0.00 0.00 4.16
772 5056 3.069443 GTGTGGTTGATTGATTGGGTGTT 59.931 43.478 0.00 0.00 0.00 3.32
773 5057 3.708631 TGTGGTTGATTGATTGGGTGTTT 59.291 39.130 0.00 0.00 0.00 2.83
775 5059 5.122519 GTGGTTGATTGATTGGGTGTTTTT 58.877 37.500 0.00 0.00 0.00 1.94
776 5060 6.127054 TGTGGTTGATTGATTGGGTGTTTTTA 60.127 34.615 0.00 0.00 0.00 1.52
780 5116 8.845227 GGTTGATTGATTGGGTGTTTTTATTTT 58.155 29.630 0.00 0.00 0.00 1.82
811 5147 9.298774 GCAAAAGAAAAAGAGATATTGATGGAG 57.701 33.333 0.00 0.00 0.00 3.86
819 5157 6.896021 AGAGATATTGATGGAGCATTTTGG 57.104 37.500 0.00 0.00 0.00 3.28
940 5316 0.319083 ATTAACCGACGCACTCCACA 59.681 50.000 0.00 0.00 0.00 4.17
1187 5617 4.052229 CGACGTCAAGCCCGACCT 62.052 66.667 17.16 0.00 31.91 3.85
1206 5636 4.821589 GCCGCCTTCCTCGACCTG 62.822 72.222 0.00 0.00 0.00 4.00
1947 6383 2.106166 GCTCATTGAGAGGATGGTGGAT 59.894 50.000 17.87 0.00 44.86 3.41
1992 6428 2.394563 GCTTTGGAGCGAGCAGGTC 61.395 63.158 0.00 3.24 46.08 3.85
2094 6530 1.744368 CAGATGCACGCTCAGGCTT 60.744 57.895 0.00 0.00 36.09 4.35
2271 6890 8.246871 AGTTATCCATATGTGACATCAGATACG 58.753 37.037 0.00 0.00 35.36 3.06
2524 7147 9.672673 AGCACAAAATATCAATAAGTGTACTCT 57.327 29.630 0.00 0.00 0.00 3.24
2581 7207 6.014156 GGATATGACATAAGGCTGTAGGTTCT 60.014 42.308 0.00 0.00 0.00 3.01
3222 7984 4.220602 GCAAATGGTTAGGATGAGTGGTTT 59.779 41.667 0.00 0.00 0.00 3.27
3586 8360 0.179076 TCCACATGCTATCTGGTGCG 60.179 55.000 0.00 0.00 0.00 5.34
3642 8428 6.354362 GTGCACAATGTTCGTGATATAATTCG 59.646 38.462 13.17 0.00 36.43 3.34
3663 8449 3.374058 CGCTGTAAAATCGATCCTTGGTT 59.626 43.478 0.00 0.00 0.00 3.67
3746 8533 1.664321 CCTGCCTGAGCCTGCAATTC 61.664 60.000 0.00 0.00 36.98 2.17
3749 8536 0.893447 GCCTGAGCCTGCAATTCTTT 59.107 50.000 0.00 0.00 0.00 2.52
3964 8756 3.241322 GCTAATTAATTGCTTGCTGTGCG 59.759 43.478 11.05 0.00 0.00 5.34
4211 9003 5.715070 ACTCTTAGACTGTACTGCATCAAC 58.285 41.667 0.00 0.00 0.00 3.18
4246 9038 5.312895 AGCATTGTTGTTGTATACCACTGA 58.687 37.500 8.42 0.00 0.00 3.41
4247 9039 5.767665 AGCATTGTTGTTGTATACCACTGAA 59.232 36.000 8.42 0.16 0.00 3.02
4258 9050 2.683211 ACCACTGAATTTGGGCTCTT 57.317 45.000 0.00 0.00 38.59 2.85
4264 9056 2.023673 TGAATTTGGGCTCTTATGCGG 58.976 47.619 0.00 0.00 0.00 5.69
4267 9059 0.395586 TTTGGGCTCTTATGCGGCAT 60.396 50.000 20.57 20.57 0.00 4.40
4352 9144 0.183492 ACATCGCCCAACCTATGCAT 59.817 50.000 3.79 3.79 0.00 3.96
4556 9348 0.251341 ATCCACAAGGTCCACAAGGC 60.251 55.000 0.00 0.00 35.89 4.35
4570 9362 1.229209 AAGGCGGGGAAGACTGAGA 60.229 57.895 0.00 0.00 0.00 3.27
4636 9428 5.520288 CCTCATTGTACAATCGAACCTGTAG 59.480 44.000 18.25 3.77 0.00 2.74
4649 9441 4.608951 GAACCTGTAGTTATCTGTAGGCG 58.391 47.826 0.00 0.00 39.40 5.52
4655 9447 5.439721 TGTAGTTATCTGTAGGCGTCCTTA 58.560 41.667 3.71 0.00 34.61 2.69
4741 9533 7.715265 TTATGCACTAAGCTAAGCTATTCAC 57.285 36.000 0.00 0.00 45.94 3.18
4773 9565 4.579869 AGATACTAACTGCCACTGGTTTG 58.420 43.478 0.00 0.00 0.00 2.93
4774 9566 2.729028 ACTAACTGCCACTGGTTTGT 57.271 45.000 0.00 0.00 0.00 2.83
4775 9567 3.849563 ACTAACTGCCACTGGTTTGTA 57.150 42.857 0.00 0.00 31.90 2.41
4777 9569 2.428544 AACTGCCACTGGTTTGTACA 57.571 45.000 0.00 0.00 0.00 2.90
4778 9570 2.656947 ACTGCCACTGGTTTGTACAT 57.343 45.000 0.00 0.00 0.00 2.29
4779 9571 3.780804 ACTGCCACTGGTTTGTACATA 57.219 42.857 0.00 0.00 0.00 2.29
4780 9572 4.301072 ACTGCCACTGGTTTGTACATAT 57.699 40.909 0.00 0.00 0.00 1.78
4782 9574 4.260985 CTGCCACTGGTTTGTACATATCA 58.739 43.478 0.00 0.00 0.00 2.15
4783 9575 4.854173 TGCCACTGGTTTGTACATATCAT 58.146 39.130 0.00 0.00 0.00 2.45
4784 9576 4.881273 TGCCACTGGTTTGTACATATCATC 59.119 41.667 0.00 0.00 0.00 2.92
4785 9577 4.275936 GCCACTGGTTTGTACATATCATCC 59.724 45.833 0.00 0.00 0.00 3.51
4786 9578 4.821805 CCACTGGTTTGTACATATCATCCC 59.178 45.833 0.00 0.00 0.00 3.85
4787 9579 4.821805 CACTGGTTTGTACATATCATCCCC 59.178 45.833 0.00 0.00 0.00 4.81
4788 9580 4.476846 ACTGGTTTGTACATATCATCCCCA 59.523 41.667 0.00 0.00 0.00 4.96
4878 9671 1.665916 CTGTGCTCTGTCGTGTGGG 60.666 63.158 0.00 0.00 0.00 4.61
4927 9747 6.229733 ACTCTACCGTACCACAGTAGATATC 58.770 44.000 9.07 0.00 37.45 1.63
4935 9780 8.476447 CCGTACCACAGTAGATATCTATCTAGA 58.524 40.741 15.43 0.00 43.73 2.43
5021 9866 8.633075 AAAAATATTTTACATGAGTGATGGCG 57.367 30.769 13.68 0.00 36.23 5.69
5039 9884 2.419574 GGCGTCTGTTAAAGCCTGGATA 60.420 50.000 0.00 0.00 45.67 2.59
5103 10103 4.404394 TGAACCTAGAACTGTGTGAGTCAA 59.596 41.667 0.00 0.00 31.73 3.18
5142 10142 4.505191 TGCTGTTTTCGCTAATATACCGTC 59.495 41.667 0.00 0.00 0.00 4.79
5163 10163 1.728971 GTCGGTGAAGAGTGATGCTTG 59.271 52.381 0.00 0.00 0.00 4.01
5165 10165 2.560981 TCGGTGAAGAGTGATGCTTGTA 59.439 45.455 0.00 0.00 0.00 2.41
5166 10166 3.195610 TCGGTGAAGAGTGATGCTTGTAT 59.804 43.478 0.00 0.00 0.00 2.29
5167 10167 3.553511 CGGTGAAGAGTGATGCTTGTATC 59.446 47.826 0.00 0.00 0.00 2.24
5168 10168 3.873952 GGTGAAGAGTGATGCTTGTATCC 59.126 47.826 0.00 0.00 0.00 2.59
5186 10209 1.008538 CGCAGCAAACTTGACACCC 60.009 57.895 0.00 0.00 0.00 4.61
5212 10235 0.250467 TCTGCTTGAAGTGGTGAGGC 60.250 55.000 0.00 0.00 0.00 4.70
5296 10319 8.257602 TGCAAGTGTAATCCAAGACCTATATA 57.742 34.615 0.00 0.00 0.00 0.86
5312 10339 9.482175 AGACCTATATATGTATTCCCTGAGTTC 57.518 37.037 0.00 0.00 0.00 3.01
5349 10376 1.672356 CAGGCAGGGTTCGTGAAGG 60.672 63.158 0.00 0.00 0.00 3.46
5361 10388 3.269538 TCGTGAAGGTCTTGTTTGGAA 57.730 42.857 0.00 0.00 0.00 3.53
5371 10398 2.627699 TCTTGTTTGGAACCTGAATGCC 59.372 45.455 0.00 0.00 0.00 4.40
5395 10422 4.568760 GCTAGCATCAACTGTAGTTTCCTC 59.431 45.833 10.63 0.00 35.83 3.71
5417 10444 0.550914 TGAAGTTGCCTTGTCCCTGT 59.449 50.000 0.00 0.00 0.00 4.00
5436 10466 1.198637 GTGAGTCATTGTGAGCCTTGC 59.801 52.381 0.00 0.00 0.00 4.01
5440 10470 2.295349 AGTCATTGTGAGCCTTGCTTTG 59.705 45.455 0.00 0.00 39.88 2.77
5445 10475 1.251251 GTGAGCCTTGCTTTGGTGAT 58.749 50.000 0.00 0.00 39.88 3.06
5462 10492 3.244561 GGTGATGTTTCCTGAAGAGTGGA 60.245 47.826 0.00 0.00 0.00 4.02
5464 10494 2.550830 TGTTTCCTGAAGAGTGGAGC 57.449 50.000 0.00 0.00 33.46 4.70
5466 10496 0.693049 TTTCCTGAAGAGTGGAGCCC 59.307 55.000 0.00 0.00 33.46 5.19
5475 10505 2.192263 AGAGTGGAGCCCCTTTCTAAG 58.808 52.381 0.00 0.00 0.00 2.18
5476 10506 2.188817 GAGTGGAGCCCCTTTCTAAGA 58.811 52.381 0.00 0.00 0.00 2.10
5477 10507 2.169561 GAGTGGAGCCCCTTTCTAAGAG 59.830 54.545 0.00 0.00 0.00 2.85
5478 10508 0.912486 TGGAGCCCCTTTCTAAGAGC 59.088 55.000 0.00 0.00 0.00 4.09
5479 10509 0.912486 GGAGCCCCTTTCTAAGAGCA 59.088 55.000 0.00 0.00 32.20 4.26
5480 10510 1.492599 GGAGCCCCTTTCTAAGAGCAT 59.507 52.381 0.00 0.00 32.20 3.79
5481 10511 2.486370 GGAGCCCCTTTCTAAGAGCATC 60.486 54.545 0.00 0.00 32.20 3.91
5494 10524 0.445436 GAGCATCTTCAACAGCCACG 59.555 55.000 0.00 0.00 0.00 4.94
5495 10525 1.154150 GCATCTTCAACAGCCACGC 60.154 57.895 0.00 0.00 0.00 5.34
5496 10526 1.580845 GCATCTTCAACAGCCACGCT 61.581 55.000 0.00 0.00 40.77 5.07
5497 10527 1.725641 CATCTTCAACAGCCACGCTA 58.274 50.000 0.00 0.00 36.40 4.26
5498 10528 2.076100 CATCTTCAACAGCCACGCTAA 58.924 47.619 0.00 0.00 36.40 3.09
5499 10529 2.248280 TCTTCAACAGCCACGCTAAA 57.752 45.000 0.00 0.00 36.40 1.85
5500 10530 2.778299 TCTTCAACAGCCACGCTAAAT 58.222 42.857 0.00 0.00 36.40 1.40
5501 10531 3.932822 TCTTCAACAGCCACGCTAAATA 58.067 40.909 0.00 0.00 36.40 1.40
5502 10532 4.320023 TCTTCAACAGCCACGCTAAATAA 58.680 39.130 0.00 0.00 36.40 1.40
5503 10533 4.391830 TCTTCAACAGCCACGCTAAATAAG 59.608 41.667 0.00 0.00 36.40 1.73
5521 10551 3.829975 CGCTGCGCCGCAAATTTG 61.830 61.111 23.66 14.03 38.41 2.32
5534 10564 3.959609 CAAATTTGCTCTGTTTAGCGC 57.040 42.857 5.01 0.00 45.85 5.92
5535 10565 3.307674 CAAATTTGCTCTGTTTAGCGCA 58.692 40.909 11.47 0.00 45.85 6.09
5536 10566 2.619013 ATTTGCTCTGTTTAGCGCAC 57.381 45.000 11.47 0.00 43.74 5.34
5537 10567 0.234625 TTTGCTCTGTTTAGCGCACG 59.765 50.000 11.47 0.00 43.74 5.34
5538 10568 2.096594 GCTCTGTTTAGCGCACGC 59.903 61.111 11.47 6.99 42.33 5.34
5549 10579 4.265630 CGCACGCGCAATCGGTAG 62.266 66.667 5.73 0.00 38.40 3.18
5550 10580 2.883730 GCACGCGCAATCGGTAGA 60.884 61.111 5.73 0.00 38.36 2.59
5551 10581 2.860628 GCACGCGCAATCGGTAGAG 61.861 63.158 5.73 0.00 38.36 2.43
5552 10582 2.104331 ACGCGCAATCGGTAGAGG 59.896 61.111 5.73 0.00 35.95 3.69
5553 10583 2.658593 CGCGCAATCGGTAGAGGG 60.659 66.667 8.75 0.00 35.95 4.30
5554 10584 2.280186 GCGCAATCGGTAGAGGGG 60.280 66.667 0.30 0.00 35.95 4.79
5555 10585 2.280186 CGCAATCGGTAGAGGGGC 60.280 66.667 0.00 0.00 0.00 5.80
5556 10586 2.797278 CGCAATCGGTAGAGGGGCT 61.797 63.158 0.00 0.00 0.00 5.19
5557 10587 1.069935 GCAATCGGTAGAGGGGCTC 59.930 63.158 0.00 0.00 0.00 4.70
5558 10588 1.749033 CAATCGGTAGAGGGGCTCC 59.251 63.158 0.00 0.00 0.00 4.70
5559 10589 1.048724 CAATCGGTAGAGGGGCTCCA 61.049 60.000 4.79 0.00 34.83 3.86
5560 10590 0.760945 AATCGGTAGAGGGGCTCCAG 60.761 60.000 4.79 0.00 34.83 3.86
5561 10591 3.541713 CGGTAGAGGGGCTCCAGC 61.542 72.222 4.79 0.00 41.14 4.85
5562 10592 3.541713 GGTAGAGGGGCTCCAGCG 61.542 72.222 4.79 0.00 43.26 5.18
5563 10593 3.541713 GTAGAGGGGCTCCAGCGG 61.542 72.222 4.79 0.00 43.26 5.52
5564 10594 3.751018 TAGAGGGGCTCCAGCGGA 61.751 66.667 4.79 0.00 43.26 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 9.528018 GTCAGGATTTAGATTTTCAACAACAAA 57.472 29.630 0.00 0.00 0.00 2.83
21 22 8.912988 AGTCAGGATTTAGATTTTCAACAACAA 58.087 29.630 0.00 0.00 0.00 2.83
22 23 8.463930 AGTCAGGATTTAGATTTTCAACAACA 57.536 30.769 0.00 0.00 0.00 3.33
52 53 4.034394 CCACACGATGTCCAATGACTATTG 59.966 45.833 0.00 0.00 42.28 1.90
81 82 6.265422 GTCTCAAGAGGATTTTCAAAGGGAAA 59.735 38.462 0.00 0.00 43.59 3.13
118 119 4.174411 TCCAGACGACATAAAGACAGTG 57.826 45.455 0.00 0.00 0.00 3.66
120 121 8.969267 GTATAATTCCAGACGACATAAAGACAG 58.031 37.037 0.00 0.00 0.00 3.51
168 181 8.970691 ATATTATTAAAGCAATTAAGGCGCAG 57.029 30.769 10.83 0.00 36.94 5.18
289 3768 6.072728 GCATGTTGACACTGTATGAAAAGGTA 60.073 38.462 0.00 0.00 0.00 3.08
296 3775 3.415457 TGGCATGTTGACACTGTATGA 57.585 42.857 0.00 0.00 24.43 2.15
297 3776 4.707030 ATTGGCATGTTGACACTGTATG 57.293 40.909 0.00 0.00 33.32 2.39
298 3777 7.408756 AAATATTGGCATGTTGACACTGTAT 57.591 32.000 0.00 0.00 33.32 2.29
299 3778 6.832520 AAATATTGGCATGTTGACACTGTA 57.167 33.333 0.00 0.00 33.32 2.74
300 3779 5.726980 AAATATTGGCATGTTGACACTGT 57.273 34.783 0.00 0.00 33.32 3.55
301 3780 6.869913 AGAAAAATATTGGCATGTTGACACTG 59.130 34.615 0.00 0.00 33.32 3.66
303 3782 7.656707 AAGAAAAATATTGGCATGTTGACAC 57.343 32.000 0.00 0.00 33.32 3.67
348 3827 7.996098 TTTCTTCCCTATTTGACACCTAAAG 57.004 36.000 0.00 0.00 0.00 1.85
349 3828 8.950007 AATTTCTTCCCTATTTGACACCTAAA 57.050 30.769 0.00 0.00 0.00 1.85
350 3829 8.950007 AAATTTCTTCCCTATTTGACACCTAA 57.050 30.769 0.00 0.00 0.00 2.69
351 3830 8.950007 AAAATTTCTTCCCTATTTGACACCTA 57.050 30.769 0.00 0.00 0.00 3.08
376 4387 7.667575 TTGCTTCCCTATTTGGCATAAAATA 57.332 32.000 0.00 0.00 32.16 1.40
381 4392 6.558488 AAATTTGCTTCCCTATTTGGCATA 57.442 33.333 0.00 0.00 32.87 3.14
384 4395 7.680442 TTTAAAATTTGCTTCCCTATTTGGC 57.320 32.000 0.00 0.00 0.00 4.52
407 4418 6.501805 AGAGAATTCCTTATTTGGCCCTTTTT 59.498 34.615 0.00 0.00 0.00 1.94
408 4419 6.025539 AGAGAATTCCTTATTTGGCCCTTTT 58.974 36.000 0.00 0.00 0.00 2.27
409 4420 5.593786 AGAGAATTCCTTATTTGGCCCTTT 58.406 37.500 0.00 0.00 0.00 3.11
410 4421 5.204292 GAGAGAATTCCTTATTTGGCCCTT 58.796 41.667 0.00 0.00 0.00 3.95
412 4423 4.536765 TGAGAGAATTCCTTATTTGGCCC 58.463 43.478 0.00 0.00 0.00 5.80
413 4424 6.721704 ATTGAGAGAATTCCTTATTTGGCC 57.278 37.500 0.65 0.00 0.00 5.36
414 4425 9.091784 GAAAATTGAGAGAATTCCTTATTTGGC 57.908 33.333 0.65 3.75 0.00 4.52
419 4430 9.759473 TGGAAGAAAATTGAGAGAATTCCTTAT 57.241 29.630 0.65 0.00 36.69 1.73
421 4432 8.661752 ATGGAAGAAAATTGAGAGAATTCCTT 57.338 30.769 0.65 0.00 36.69 3.36
422 4433 7.341512 GGATGGAAGAAAATTGAGAGAATTCCT 59.658 37.037 0.65 0.00 36.69 3.36
423 4434 7.123247 TGGATGGAAGAAAATTGAGAGAATTCC 59.877 37.037 0.65 0.00 36.37 3.01
425 4436 8.475639 CATGGATGGAAGAAAATTGAGAGAATT 58.524 33.333 0.00 0.00 0.00 2.17
427 4438 7.177184 TCATGGATGGAAGAAAATTGAGAGAA 58.823 34.615 0.00 0.00 0.00 2.87
428 4439 6.724351 TCATGGATGGAAGAAAATTGAGAGA 58.276 36.000 0.00 0.00 0.00 3.10
429 4440 7.338703 TCTTCATGGATGGAAGAAAATTGAGAG 59.661 37.037 2.59 0.00 45.62 3.20
430 4441 7.177184 TCTTCATGGATGGAAGAAAATTGAGA 58.823 34.615 2.59 0.00 45.62 3.27
431 4442 7.400599 TCTTCATGGATGGAAGAAAATTGAG 57.599 36.000 2.59 0.00 45.62 3.02
439 4450 3.068732 CGTAGCTCTTCATGGATGGAAGA 59.931 47.826 0.00 4.93 46.21 2.87
440 4451 3.068732 TCGTAGCTCTTCATGGATGGAAG 59.931 47.826 0.00 0.00 42.42 3.46
441 4452 3.031013 TCGTAGCTCTTCATGGATGGAA 58.969 45.455 0.00 0.00 0.00 3.53
444 4455 3.998099 TCTCGTAGCTCTTCATGGATG 57.002 47.619 0.00 0.00 0.00 3.51
534 4814 5.211973 AGCATTAGGTGAGGAGACTTCATA 58.788 41.667 0.00 0.00 44.43 2.15
581 4861 7.232188 TGGGTTACTTACAATTGTGTCCATAA 58.768 34.615 21.42 9.32 39.30 1.90
596 4876 6.449956 AGGAATGGAGATACTGGGTTACTTA 58.550 40.000 0.00 0.00 0.00 2.24
600 4880 6.630131 TCATAGGAATGGAGATACTGGGTTA 58.370 40.000 0.00 0.00 33.61 2.85
603 4883 6.183361 TGTTTCATAGGAATGGAGATACTGGG 60.183 42.308 0.00 0.00 33.61 4.45
673 4957 7.819415 GGCCTGCAAGATTTTTCTAAGTATTTT 59.181 33.333 0.00 0.00 34.07 1.82
678 4962 3.191371 CGGCCTGCAAGATTTTTCTAAGT 59.809 43.478 0.00 0.00 34.07 2.24
697 4981 1.896220 TCAATATGGGCTCATTCGGC 58.104 50.000 3.29 0.00 34.96 5.54
741 5025 7.309377 CCAATCAATCAACCACACTGATAACTT 60.309 37.037 0.00 0.00 33.13 2.66
750 5034 2.627699 ACACCCAATCAATCAACCACAC 59.372 45.455 0.00 0.00 0.00 3.82
806 5142 3.967467 ATCTCCTCCAAAATGCTCCAT 57.033 42.857 0.00 0.00 0.00 3.41
811 5147 6.071165 CCCCATTAATATCTCCTCCAAAATGC 60.071 42.308 0.00 0.00 0.00 3.56
819 5157 5.825593 TGACACCCCATTAATATCTCCTC 57.174 43.478 0.00 0.00 0.00 3.71
1947 6383 0.677288 CGTTATCGGCCACCCTCATA 59.323 55.000 2.24 0.00 0.00 2.15
2025 6461 0.176449 TCCTCCACATGTCAGCATCG 59.824 55.000 0.00 0.00 31.99 3.84
2271 6890 4.635223 TCATCTAGCATGACAATACCAGC 58.365 43.478 0.00 0.00 0.00 4.85
2524 7147 9.330063 CAAGTCATGGCTCAAGTATAAAGAATA 57.670 33.333 0.00 0.00 0.00 1.75
2581 7207 2.507886 ACCACCATGATTACGGGAATGA 59.492 45.455 0.00 0.00 0.00 2.57
3190 7952 8.593945 TCATCCTAACCATTTGCTCTAAAAAT 57.406 30.769 0.00 0.00 0.00 1.82
3195 7957 5.396772 CCACTCATCCTAACCATTTGCTCTA 60.397 44.000 0.00 0.00 0.00 2.43
3222 7984 7.174946 CCATTGTAAAGCTAAACAGGAAAGAGA 59.825 37.037 0.00 0.00 0.00 3.10
3586 8360 0.745468 AGAGCCCCGAACGACTAATC 59.255 55.000 0.00 0.00 0.00 1.75
3642 8428 4.965119 AACCAAGGATCGATTTTACAGC 57.035 40.909 0.00 0.00 0.00 4.40
3746 8533 4.770010 TGGTAATCCAAACAAGGCCTAAAG 59.230 41.667 5.16 1.10 41.25 1.85
3964 8756 2.424956 GCAGGTGGTGGAATGAAAGATC 59.575 50.000 0.00 0.00 0.00 2.75
4246 9038 0.746659 GCCGCATAAGAGCCCAAATT 59.253 50.000 0.00 0.00 0.00 1.82
4247 9039 0.395586 TGCCGCATAAGAGCCCAAAT 60.396 50.000 0.00 0.00 0.00 2.32
4258 9050 4.322273 CCTGAGAAATAGAGATGCCGCATA 60.322 45.833 5.67 0.00 0.00 3.14
4264 9056 4.343526 TCCTCACCTGAGAAATAGAGATGC 59.656 45.833 3.73 0.00 44.74 3.91
4267 9059 5.770919 TCATCCTCACCTGAGAAATAGAGA 58.229 41.667 3.73 0.00 44.74 3.10
4352 9144 5.350365 GCAGTTCGACAATTTGTATCCACTA 59.650 40.000 1.15 0.00 0.00 2.74
4366 9158 0.601046 CAGCTCTTGGCAGTTCGACA 60.601 55.000 0.00 0.00 44.79 4.35
4556 9348 0.749649 CCATCTCTCAGTCTTCCCCG 59.250 60.000 0.00 0.00 0.00 5.73
4570 9362 2.279582 CGTTAGCGTCAGTTCCATCT 57.720 50.000 0.00 0.00 0.00 2.90
4608 9400 2.267426 TCGATTGTACAATGAGGCACG 58.733 47.619 25.42 19.53 0.00 5.34
4636 9428 4.523558 AGGATAAGGACGCCTACAGATAAC 59.476 45.833 0.00 0.00 31.13 1.89
4649 9441 7.662897 ACTTCAGATTATTCGAGGATAAGGAC 58.337 38.462 0.00 0.00 0.00 3.85
4655 9447 8.567285 AAACAAACTTCAGATTATTCGAGGAT 57.433 30.769 0.00 0.00 0.00 3.24
4741 9533 4.442192 GGCAGTTAGTATCTCAGAAGGTGG 60.442 50.000 0.00 0.00 0.00 4.61
4773 9565 4.220821 ACATCGAGTGGGGATGATATGTAC 59.779 45.833 8.62 0.00 43.07 2.90
4774 9566 4.416516 ACATCGAGTGGGGATGATATGTA 58.583 43.478 8.62 0.00 43.07 2.29
4775 9567 3.242867 ACATCGAGTGGGGATGATATGT 58.757 45.455 8.62 0.00 43.07 2.29
4777 9569 3.510459 TGACATCGAGTGGGGATGATAT 58.490 45.455 8.62 0.00 43.07 1.63
4778 9570 2.957474 TGACATCGAGTGGGGATGATA 58.043 47.619 8.62 0.00 43.07 2.15
4779 9571 1.793414 TGACATCGAGTGGGGATGAT 58.207 50.000 8.62 0.00 43.07 2.45
4780 9572 1.567357 TTGACATCGAGTGGGGATGA 58.433 50.000 8.62 0.00 43.07 2.92
4782 9574 1.628340 TGTTTGACATCGAGTGGGGAT 59.372 47.619 0.00 0.00 0.00 3.85
4783 9575 1.001974 CTGTTTGACATCGAGTGGGGA 59.998 52.381 0.00 0.00 0.00 4.81
4784 9576 1.001974 TCTGTTTGACATCGAGTGGGG 59.998 52.381 0.00 0.00 0.00 4.96
4785 9577 2.069273 GTCTGTTTGACATCGAGTGGG 58.931 52.381 0.00 0.00 44.73 4.61
4878 9671 7.389053 GTCCCAGACACATAAATAAGATGGATC 59.611 40.741 0.00 0.00 32.09 3.36
4927 9747 5.959583 AAGGGGAAAAGGTGTCTAGATAG 57.040 43.478 0.00 0.00 0.00 2.08
4935 9780 6.157123 TGTTCAAAATAAAGGGGAAAAGGTGT 59.843 34.615 0.00 0.00 0.00 4.16
5021 9866 4.200092 CCCTTATCCAGGCTTTAACAGAC 58.800 47.826 0.00 0.00 42.29 3.51
5039 9884 2.978278 CTCTGATAGGCATTCTCCCCTT 59.022 50.000 0.00 0.00 32.65 3.95
5045 9890 3.387962 TGTTCCCTCTGATAGGCATTCT 58.612 45.455 0.00 0.00 45.03 2.40
5103 10103 2.359967 GCAGCGGTAAGGTCTCCCT 61.360 63.158 0.00 0.00 45.63 4.20
5142 10142 0.109086 AGCATCACTCTTCACCGACG 60.109 55.000 0.00 0.00 0.00 5.12
5163 10163 1.804151 TGTCAAGTTTGCTGCGGATAC 59.196 47.619 0.00 0.00 0.00 2.24
5165 10165 0.593128 GTGTCAAGTTTGCTGCGGAT 59.407 50.000 0.00 0.00 0.00 4.18
5166 10166 1.444119 GGTGTCAAGTTTGCTGCGGA 61.444 55.000 0.00 0.00 0.00 5.54
5167 10167 1.008538 GGTGTCAAGTTTGCTGCGG 60.009 57.895 0.00 0.00 0.00 5.69
5168 10168 1.008538 GGGTGTCAAGTTTGCTGCG 60.009 57.895 0.00 0.00 0.00 5.18
5231 10254 3.696051 GCAGGATGGAAGCTACAATTTCA 59.304 43.478 0.00 0.00 35.86 2.69
5296 10319 5.163152 GGGAATGAGAACTCAGGGAATACAT 60.163 44.000 10.26 0.00 43.61 2.29
5301 10324 1.916181 GGGGAATGAGAACTCAGGGAA 59.084 52.381 10.26 0.00 43.61 3.97
5303 10326 1.289160 TGGGGAATGAGAACTCAGGG 58.711 55.000 10.26 0.00 43.61 4.45
5312 10339 2.364324 CTGGCATGAAATGGGGAATGAG 59.636 50.000 0.00 0.00 46.86 2.90
5349 10376 3.552890 GGCATTCAGGTTCCAAACAAGAC 60.553 47.826 0.00 0.00 0.00 3.01
5371 10398 3.307242 GGAAACTACAGTTGATGCTAGCG 59.693 47.826 10.77 0.00 38.44 4.26
5417 10444 1.072806 AGCAAGGCTCACAATGACTCA 59.927 47.619 0.00 0.00 30.62 3.41
5436 10466 4.823989 ACTCTTCAGGAAACATCACCAAAG 59.176 41.667 0.00 0.00 0.00 2.77
5440 10470 3.077359 CCACTCTTCAGGAAACATCACC 58.923 50.000 0.00 0.00 0.00 4.02
5445 10475 1.072331 GGCTCCACTCTTCAGGAAACA 59.928 52.381 0.00 0.00 32.57 2.83
5462 10492 2.486716 AGATGCTCTTAGAAAGGGGCT 58.513 47.619 0.00 0.00 0.00 5.19
5464 10494 4.494091 TGAAGATGCTCTTAGAAAGGGG 57.506 45.455 0.00 0.00 36.73 4.79
5466 10496 5.163774 GCTGTTGAAGATGCTCTTAGAAAGG 60.164 44.000 0.00 0.00 36.73 3.11
5475 10505 0.445436 CGTGGCTGTTGAAGATGCTC 59.555 55.000 0.00 0.00 0.00 4.26
5476 10506 1.580845 GCGTGGCTGTTGAAGATGCT 61.581 55.000 0.00 0.00 0.00 3.79
5477 10507 1.154150 GCGTGGCTGTTGAAGATGC 60.154 57.895 0.00 0.00 0.00 3.91
5478 10508 1.725641 TAGCGTGGCTGTTGAAGATG 58.274 50.000 0.00 0.00 40.10 2.90
5479 10509 2.472695 TTAGCGTGGCTGTTGAAGAT 57.527 45.000 0.00 0.00 40.10 2.40
5480 10510 2.248280 TTTAGCGTGGCTGTTGAAGA 57.752 45.000 0.00 0.00 40.10 2.87
5481 10511 4.651994 CTTATTTAGCGTGGCTGTTGAAG 58.348 43.478 0.00 0.00 40.10 3.02
5482 10512 3.119990 GCTTATTTAGCGTGGCTGTTGAA 60.120 43.478 0.00 0.00 40.71 2.69
5483 10513 2.418628 GCTTATTTAGCGTGGCTGTTGA 59.581 45.455 0.00 0.00 40.71 3.18
5484 10514 2.785679 GCTTATTTAGCGTGGCTGTTG 58.214 47.619 0.00 0.00 40.71 3.33
5514 10544 3.120121 GTGCGCTAAACAGAGCAAATTTG 59.880 43.478 14.03 14.03 45.38 2.32
5515 10545 3.308530 GTGCGCTAAACAGAGCAAATTT 58.691 40.909 9.73 0.00 45.38 1.82
5516 10546 2.665519 CGTGCGCTAAACAGAGCAAATT 60.666 45.455 9.73 0.00 45.38 1.82
5517 10547 1.135972 CGTGCGCTAAACAGAGCAAAT 60.136 47.619 9.73 0.00 45.38 2.32
5518 10548 0.234625 CGTGCGCTAAACAGAGCAAA 59.765 50.000 9.73 0.00 45.38 3.68
5519 10549 1.859398 CGTGCGCTAAACAGAGCAA 59.141 52.632 9.73 0.00 45.38 3.91
5520 10550 2.667318 GCGTGCGCTAAACAGAGCA 61.667 57.895 9.73 0.00 42.99 4.26
5521 10551 2.096594 GCGTGCGCTAAACAGAGC 59.903 61.111 9.73 0.00 39.20 4.09
5522 10552 2.391821 CGCGTGCGCTAAACAGAG 59.608 61.111 9.73 0.00 39.32 3.35
5533 10563 2.860628 CTCTACCGATTGCGCGTGC 61.861 63.158 15.48 15.48 43.20 5.34
5534 10564 2.230940 CCTCTACCGATTGCGCGTG 61.231 63.158 8.43 0.00 35.83 5.34
5535 10565 2.104331 CCTCTACCGATTGCGCGT 59.896 61.111 8.43 0.00 35.83 6.01
5536 10566 2.658593 CCCTCTACCGATTGCGCG 60.659 66.667 0.00 0.00 35.83 6.86
5537 10567 2.280186 CCCCTCTACCGATTGCGC 60.280 66.667 0.00 0.00 35.83 6.09
5538 10568 2.280186 GCCCCTCTACCGATTGCG 60.280 66.667 0.00 0.00 37.24 4.85
5539 10569 1.069935 GAGCCCCTCTACCGATTGC 59.930 63.158 0.00 0.00 0.00 3.56
5540 10570 1.048724 TGGAGCCCCTCTACCGATTG 61.049 60.000 0.00 0.00 0.00 2.67
5541 10571 0.760945 CTGGAGCCCCTCTACCGATT 60.761 60.000 0.00 0.00 0.00 3.34
5542 10572 1.152440 CTGGAGCCCCTCTACCGAT 60.152 63.158 0.00 0.00 0.00 4.18
5543 10573 2.279073 CTGGAGCCCCTCTACCGA 59.721 66.667 0.00 0.00 0.00 4.69
5544 10574 3.541713 GCTGGAGCCCCTCTACCG 61.542 72.222 0.00 0.00 34.31 4.02
5545 10575 3.541713 CGCTGGAGCCCCTCTACC 61.542 72.222 0.00 0.00 37.91 3.18
5546 10576 3.541713 CCGCTGGAGCCCCTCTAC 61.542 72.222 0.00 0.00 37.91 2.59
5547 10577 3.751018 TCCGCTGGAGCCCCTCTA 61.751 66.667 0.00 0.00 37.91 2.43


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

AutoCloner maintained by Alex Coulton.