Multiple sequence alignment - TraesCS4D01G089900

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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 TraesCS4D01G089900 chr4D 100.000 8270 0 0 1 8270 65119793 65128062 0.000000e+00 15272.0
1 TraesCS4D01G089900 chr4B 96.193 5411 185 14 969 6364 95669886 95675290 0.000000e+00 8831.0
2 TraesCS4D01G089900 chr4B 96.752 1878 34 8 6361 8221 95675374 95677241 0.000000e+00 3105.0
3 TraesCS4D01G089900 chr4B 92.230 296 9 5 1 282 95664602 95664897 2.780000e-109 407.0
4 TraesCS4D01G089900 chr4B 80.000 175 25 7 606 774 95669687 95669857 4.050000e-23 121.0
5 TraesCS4D01G089900 chr4B 96.226 53 2 0 8218 8270 464164886 464164834 4.110000e-13 87.9
6 TraesCS4D01G089900 chr4B 80.851 94 14 3 773 863 414334399 414334307 4.140000e-08 71.3
7 TraesCS4D01G089900 chr4B 97.143 35 1 0 6590 6624 525844368 525844334 8.960000e-05 60.2
8 TraesCS4D01G089900 chr4A 92.824 4515 246 32 738 5223 531081602 531086067 0.000000e+00 6471.0
9 TraesCS4D01G089900 chr4A 91.087 920 58 13 5218 6124 531087194 531088102 0.000000e+00 1223.0
10 TraesCS4D01G089900 chr4A 83.689 797 28 31 1 749 531076822 531077564 0.000000e+00 658.0
11 TraesCS4D01G089900 chr4A 77.083 192 42 2 2568 2758 740765907 740765717 8.780000e-20 110.0
12 TraesCS4D01G089900 chr4A 94.444 54 2 1 8217 8270 603530158 603530106 1.910000e-11 82.4
13 TraesCS4D01G089900 chr4A 100.000 39 0 0 6587 6625 554704106 554704144 1.150000e-08 73.1
14 TraesCS4D01G089900 chr4A 86.154 65 9 0 6523 6587 60654156 60654220 4.140000e-08 71.3
15 TraesCS4D01G089900 chr2A 77.488 613 106 27 4681 5276 419651018 419650421 1.030000e-88 339.0
16 TraesCS4D01G089900 chr2A 85.455 110 16 0 7067 7176 419649512 419649403 1.890000e-21 115.0
17 TraesCS4D01G089900 chr2A 91.304 69 6 0 6519 6587 657517733 657517801 2.460000e-15 95.3
18 TraesCS4D01G089900 chr2A 87.719 57 7 0 6531 6587 58392344 58392288 5.360000e-07 67.6
19 TraesCS4D01G089900 chr7A 72.236 407 105 6 2562 2964 13237597 13237999 1.460000e-22 119.0
20 TraesCS4D01G089900 chr7A 96.774 62 2 0 6526 6587 532464060 532464121 4.080000e-18 104.0
21 TraesCS4D01G089900 chr2D 85.981 107 15 0 7067 7173 315417891 315417997 1.890000e-21 115.0
22 TraesCS4D01G089900 chr2B 85.981 107 15 0 7067 7173 383277080 383277186 1.890000e-21 115.0
23 TraesCS4D01G089900 chr2B 91.111 45 4 0 6587 6631 462889306 462889262 2.490000e-05 62.1
24 TraesCS4D01G089900 chr7D 80.147 136 27 0 2562 2697 2543043 2543178 1.470000e-17 102.0
25 TraesCS4D01G089900 chr7D 79.130 115 9 6 6523 6624 560910706 560910818 1.930000e-06 65.8
26 TraesCS4D01G089900 chr6A 92.424 66 5 0 6522 6587 539229956 539230021 2.460000e-15 95.3
27 TraesCS4D01G089900 chr6A 96.154 52 1 1 8220 8270 5223133 5223082 5.320000e-12 84.2
28 TraesCS4D01G089900 chr7B 98.077 52 1 0 8219 8270 609192616 609192667 3.180000e-14 91.6
29 TraesCS4D01G089900 chr7B 94.231 52 3 0 8214 8265 218545853 218545904 6.880000e-11 80.5
30 TraesCS4D01G089900 chr1B 93.443 61 2 2 8212 8270 277767117 277767057 1.140000e-13 89.8
31 TraesCS4D01G089900 chr5D 96.154 52 2 0 8219 8270 340967842 340967791 1.480000e-12 86.1
32 TraesCS4D01G089900 chr5D 94.231 52 3 0 8219 8270 493900722 493900671 6.880000e-11 80.5
33 TraesCS4D01G089900 chr5D 94.737 38 2 0 6587 6624 335230249 335230286 8.960000e-05 60.2
34 TraesCS4D01G089900 chr3D 91.803 61 5 0 6527 6587 420810457 420810517 1.480000e-12 86.1
35 TraesCS4D01G089900 chr3D 90.625 64 6 0 6524 6587 420810579 420810516 1.480000e-12 86.1
36 TraesCS4D01G089900 chr1A 89.706 68 5 2 6526 6593 481650102 481650037 1.480000e-12 86.1
37 TraesCS4D01G089900 chr3A 96.000 50 2 0 6570 6619 137607678 137607629 1.910000e-11 82.4
38 TraesCS4D01G089900 chr6B 92.727 55 4 0 8211 8265 204159129 204159183 6.880000e-11 80.5
39 TraesCS4D01G089900 chr3B 95.918 49 2 0 6571 6619 181317775 181317727 6.880000e-11 80.5


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 TraesCS4D01G089900 chr4D 65119793 65128062 8269 False 15272 15272 100.000000 1 8270 1 chr4D.!!$F1 8269
1 TraesCS4D01G089900 chr4B 95669687 95677241 7554 False 4019 8831 90.981667 606 8221 3 chr4B.!!$F2 7615
2 TraesCS4D01G089900 chr4A 531081602 531088102 6500 False 3847 6471 91.955500 738 6124 2 chr4A.!!$F4 5386
3 TraesCS4D01G089900 chr4A 531076822 531077564 742 False 658 658 83.689000 1 749 1 chr4A.!!$F2 748
4 TraesCS4D01G089900 chr2A 419649403 419651018 1615 True 227 339 81.471500 4681 7176 2 chr2A.!!$R2 2495

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
478 503 0.033781 GCATCAACCCAAGCAAGCAA 59.966 50.000 0.00 0.00 0.00 3.91 F
480 505 0.319405 ATCAACCCAAGCAAGCAAGC 59.681 50.000 0.00 0.00 0.00 4.01 F
2280 2352 0.108138 ACGGTGTAGCTCTGGAATGC 60.108 55.000 0.00 0.00 0.00 3.56 F
2288 2360 0.807496 GCTCTGGAATGCTGTGGTTC 59.193 55.000 0.00 0.00 0.00 3.62 F
3420 3492 1.001764 TGGCCTGATGAACCTGCAG 60.002 57.895 6.78 6.78 0.00 4.41 F
4253 4325 1.134491 GTTTGCTGATAGCGGGTAGGT 60.134 52.381 0.00 0.00 46.26 3.08 F
5346 6593 0.179073 CTGACGTGCCAAGGATAGGG 60.179 60.000 0.00 0.00 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1371 1443 0.035317 TTGTGCTCGGCTTCAGTGAT 59.965 50.0 0.0 0.0 0.00 3.06 R
2419 2491 0.104120 GGCAAACCACCACACTTTCC 59.896 55.0 0.0 0.0 35.26 3.13 R
3912 3984 0.037590 TGCGGGCATTGAAACCTAGT 59.962 50.0 0.0 0.0 0.00 2.57 R
4253 4325 2.225318 GGGTGGGGGTGTTGGTAAATAA 60.225 50.0 0.0 0.0 0.00 1.40 R
4750 4838 0.391793 GTACTCCAGGTGCCTTCAGC 60.392 60.0 0.0 0.0 44.14 4.26 R
5429 6676 1.039856 TTGGAAGCCAAGGCAAGAAC 58.960 50.0 14.4 0.0 44.88 3.01 R
7284 8720 0.991355 TGGTTCTTGTGGGGTGGAGT 60.991 55.0 0.0 0.0 0.00 3.85 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
192 193 4.271816 CCTCCATCGCCGTCTCCG 62.272 72.222 0.00 0.00 0.00 4.63
193 194 3.209812 CTCCATCGCCGTCTCCGA 61.210 66.667 0.00 0.00 39.24 4.55
194 195 3.187699 CTCCATCGCCGTCTCCGAG 62.188 68.421 0.00 0.00 38.20 4.63
195 196 4.933064 CCATCGCCGTCTCCGAGC 62.933 72.222 0.00 0.00 38.20 5.03
196 197 4.933064 CATCGCCGTCTCCGAGCC 62.933 72.222 0.00 0.00 38.20 4.70
229 230 3.710722 AGCACCCTGGCCGAGAAG 61.711 66.667 0.00 0.00 0.00 2.85
249 250 3.803162 GGGGAGGGAAGAGCAGCC 61.803 72.222 0.00 0.00 0.00 4.85
305 330 6.943899 AATGGAGAAAAGAGGACTAGACTT 57.056 37.500 0.00 0.00 0.00 3.01
306 331 9.716556 ATAATGGAGAAAAGAGGACTAGACTTA 57.283 33.333 0.00 0.00 0.00 2.24
370 395 2.236395 CCCAACCTTTCTATCGTGGACT 59.764 50.000 0.00 0.00 0.00 3.85
371 396 3.522553 CCAACCTTTCTATCGTGGACTC 58.477 50.000 0.00 0.00 0.00 3.36
372 397 3.179830 CAACCTTTCTATCGTGGACTCG 58.820 50.000 0.00 0.00 0.00 4.18
373 398 2.444421 ACCTTTCTATCGTGGACTCGT 58.556 47.619 0.00 0.00 0.00 4.18
374 399 2.824341 ACCTTTCTATCGTGGACTCGTT 59.176 45.455 0.00 0.00 0.00 3.85
375 400 3.119566 ACCTTTCTATCGTGGACTCGTTC 60.120 47.826 0.00 0.00 0.00 3.95
376 401 3.436496 CTTTCTATCGTGGACTCGTTCC 58.564 50.000 0.00 0.00 46.13 3.62
383 408 2.126580 GGACTCGTTCCGTCACCG 60.127 66.667 0.00 0.00 33.46 4.94
417 442 1.820481 CTCCTCCTCCTCCGTCGTC 60.820 68.421 0.00 0.00 0.00 4.20
455 480 3.522731 CTCCTCCTCTGTCCGGCG 61.523 72.222 0.00 0.00 0.00 6.46
470 495 3.053291 GCGACCGCATCAACCCAA 61.053 61.111 9.73 0.00 41.49 4.12
471 496 3.039202 GCGACCGCATCAACCCAAG 62.039 63.158 9.73 0.00 41.49 3.61
472 497 2.877691 GACCGCATCAACCCAAGC 59.122 61.111 0.00 0.00 0.00 4.01
473 498 1.971167 GACCGCATCAACCCAAGCA 60.971 57.895 0.00 0.00 0.00 3.91
474 499 1.523154 GACCGCATCAACCCAAGCAA 61.523 55.000 0.00 0.00 0.00 3.91
475 500 1.213537 CCGCATCAACCCAAGCAAG 59.786 57.895 0.00 0.00 0.00 4.01
476 501 1.444895 CGCATCAACCCAAGCAAGC 60.445 57.895 0.00 0.00 0.00 4.01
477 502 1.667151 GCATCAACCCAAGCAAGCA 59.333 52.632 0.00 0.00 0.00 3.91
478 503 0.033781 GCATCAACCCAAGCAAGCAA 59.966 50.000 0.00 0.00 0.00 3.91
479 504 1.938016 GCATCAACCCAAGCAAGCAAG 60.938 52.381 0.00 0.00 0.00 4.01
480 505 0.319405 ATCAACCCAAGCAAGCAAGC 59.681 50.000 0.00 0.00 0.00 4.01
546 571 4.101448 GCGCACCATCTCCACCCT 62.101 66.667 0.30 0.00 0.00 4.34
548 573 1.450312 CGCACCATCTCCACCCTTC 60.450 63.158 0.00 0.00 0.00 3.46
559 584 1.073722 CACCCTTCCAGAGCAGCAA 59.926 57.895 0.00 0.00 0.00 3.91
564 613 1.004560 TTCCAGAGCAGCAACCTCG 60.005 57.895 0.00 0.00 34.56 4.63
642 691 0.828343 GCCGGCTGTAGTCCCTATCT 60.828 60.000 22.15 0.00 0.00 1.98
681 733 4.402155 CGATTTGGGGATTTCTGAATTGGA 59.598 41.667 0.00 0.00 0.00 3.53
685 737 3.333381 TGGGGATTTCTGAATTGGAGTGA 59.667 43.478 0.00 0.00 0.00 3.41
809 865 2.685380 AGGCTCCTCCCTGGTTCG 60.685 66.667 0.00 0.00 37.07 3.95
814 870 1.202545 GCTCCTCCCTGGTTCGATTAC 60.203 57.143 0.00 0.00 37.07 1.89
927 995 2.479560 GCAGAACTGGTTTTGTGTGTCC 60.480 50.000 3.99 0.00 0.00 4.02
940 1008 5.975693 TTGTGTGTCCAGTTTTTCTCTTT 57.024 34.783 0.00 0.00 0.00 2.52
970 1038 4.199310 GCTCTTGCCCTTACATGTCATTA 58.801 43.478 0.00 0.00 0.00 1.90
1221 1293 2.493273 ATACCCCCAACCACAAGGCG 62.493 60.000 0.00 0.00 39.06 5.52
1358 1430 1.338973 GGTCAGTCGTGTCAAGGTGTA 59.661 52.381 0.00 0.00 0.00 2.90
1371 1443 4.023536 GTCAAGGTGTATCGGCTTTTCAAA 60.024 41.667 0.00 0.00 0.00 2.69
1374 1446 4.331968 AGGTGTATCGGCTTTTCAAATCA 58.668 39.130 0.00 0.00 0.00 2.57
1375 1447 4.156008 AGGTGTATCGGCTTTTCAAATCAC 59.844 41.667 0.00 0.00 0.00 3.06
1384 1456 3.304659 GCTTTTCAAATCACTGAAGCCGA 60.305 43.478 0.00 0.00 36.69 5.54
1405 1477 2.158475 AGCACAAGGGTTTCCAAGATCA 60.158 45.455 0.00 0.00 34.83 2.92
1443 1515 2.962569 CTGGAGGCGAGTGAACGA 59.037 61.111 0.00 0.00 35.09 3.85
1473 1545 4.408270 AGGTATCATCTTGATGACTGTGCT 59.592 41.667 14.58 2.18 37.70 4.40
1476 1548 4.276058 TCATCTTGATGACTGTGCTTCA 57.724 40.909 9.02 0.00 0.00 3.02
1477 1549 3.999001 TCATCTTGATGACTGTGCTTCAC 59.001 43.478 9.02 0.00 34.56 3.18
1487 1559 0.320421 TGTGCTTCACGTTCTAGCCC 60.320 55.000 9.94 1.01 37.14 5.19
1498 1570 2.230508 CGTTCTAGCCCTGTGTTCACTA 59.769 50.000 4.59 0.00 0.00 2.74
1508 1580 2.744202 CTGTGTTCACTAGGCACAATCC 59.256 50.000 11.04 0.00 41.73 3.01
1552 1624 2.785562 CCACGGATTTCCTTGTTGGTA 58.214 47.619 2.81 0.00 33.82 3.25
1775 1847 2.902486 ACATCCTCTCTCAAGTTCAGCA 59.098 45.455 0.00 0.00 0.00 4.41
1797 1869 5.452077 GCATTGTCGACTACCCTCTTATTCT 60.452 44.000 17.92 0.00 0.00 2.40
1829 1901 6.307318 GTGCAAAATCTCATTGACAATCTCAC 59.693 38.462 0.00 0.00 0.00 3.51
1830 1902 6.016108 TGCAAAATCTCATTGACAATCTCACA 60.016 34.615 0.00 0.00 0.00 3.58
1962 2034 2.618241 TGATTGTGCACAGTGGAGTTTC 59.382 45.455 20.57 3.84 0.00 2.78
2096 2168 9.435688 AGAAATAAAAATGCTAACCAACCATTC 57.564 29.630 0.00 0.00 0.00 2.67
2226 2298 3.004752 AGCGCTTTTCCAGATGGTAAT 57.995 42.857 2.64 0.00 36.34 1.89
2235 2307 7.862873 GCTTTTCCAGATGGTAATAATTACAGC 59.137 37.037 0.00 0.00 37.88 4.40
2259 2331 7.040478 AGCAGAATAATAACAACAGCAGAAACA 60.040 33.333 0.00 0.00 0.00 2.83
2263 2335 4.732285 ATAACAACAGCAGAAACAGACG 57.268 40.909 0.00 0.00 0.00 4.18
2280 2352 0.108138 ACGGTGTAGCTCTGGAATGC 60.108 55.000 0.00 0.00 0.00 3.56
2288 2360 0.807496 GCTCTGGAATGCTGTGGTTC 59.193 55.000 0.00 0.00 0.00 3.62
2363 2435 7.648908 TGCAGAATTGTTCTTCAGTATTGTTTG 59.351 33.333 0.00 0.00 38.11 2.93
2407 2479 6.950041 TCCTGATCAATTGAAGGAAGTTTCAT 59.050 34.615 21.58 0.00 36.97 2.57
2472 2544 3.543680 TGTATTGCTGGTCTCTTAGCC 57.456 47.619 0.00 0.00 39.15 3.93
2590 2662 8.419922 AGAAGTACTAAACCTTAGCTACAGTT 57.580 34.615 0.00 0.00 0.00 3.16
2599 2671 4.221041 ACCTTAGCTACAGTTGTCTTCCTC 59.779 45.833 0.00 0.00 0.00 3.71
2629 2701 4.393990 TGAAGACATGCTTGCTGTATCTTG 59.606 41.667 7.05 0.00 36.83 3.02
2640 2712 5.806654 TGCTGTATCTTGCTATGTATCCA 57.193 39.130 0.00 0.00 0.00 3.41
2648 2720 3.060479 TGCTATGTATCCAGAGGGGTT 57.940 47.619 0.00 0.00 38.11 4.11
2724 2796 4.098501 ACTGCAAAGGAAGAAAAAGAGGTG 59.901 41.667 0.00 0.00 0.00 4.00
2765 2837 7.885297 AGCTATTTTTATGAGCTTGTCAACAA 58.115 30.769 0.00 0.00 44.08 2.83
2796 2868 3.572255 TCCAACCTGAGCAAATTAACCAC 59.428 43.478 0.00 0.00 0.00 4.16
2821 2893 6.753913 ATGATGAGGTGTTATCCTGTACAT 57.246 37.500 0.00 0.00 38.02 2.29
2925 2997 7.014615 GCCATCACAGGAAATTCTAATATGGTT 59.985 37.037 12.61 0.00 34.09 3.67
2970 3042 2.094803 CAGTGCCAAATATGCGACCAAA 60.095 45.455 0.00 0.00 0.00 3.28
3048 3120 2.942804 TGTTTGCCTTCTGATGTGGAA 58.057 42.857 0.00 0.00 0.00 3.53
3066 3138 4.153475 GTGGAATTTAAGTTGCTGCGAGTA 59.847 41.667 3.98 0.00 0.00 2.59
3067 3139 4.941263 TGGAATTTAAGTTGCTGCGAGTAT 59.059 37.500 3.98 0.00 0.00 2.12
3069 3141 6.596106 TGGAATTTAAGTTGCTGCGAGTATTA 59.404 34.615 3.98 0.00 0.00 0.98
3071 3143 8.129211 GGAATTTAAGTTGCTGCGAGTATTAAT 58.871 33.333 0.00 0.00 0.00 1.40
3078 3150 4.119862 TGCTGCGAGTATTAATCCTTGAC 58.880 43.478 0.00 0.00 0.00 3.18
3183 3255 7.412137 TTCATGCGATATCATTGTAGAACTG 57.588 36.000 3.12 0.00 0.00 3.16
3197 3269 4.790962 ACTGCCAGCCCAGATGCG 62.791 66.667 0.00 0.00 36.67 4.73
3206 3278 1.676678 GCCCAGATGCGAGGACTACA 61.677 60.000 0.00 0.00 0.00 2.74
3238 3310 7.099120 GGAAACACTGGAAATAAATGCAAGAT 58.901 34.615 0.00 0.00 0.00 2.40
3239 3311 7.276438 GGAAACACTGGAAATAAATGCAAGATC 59.724 37.037 0.00 0.00 0.00 2.75
3244 3316 7.648112 CACTGGAAATAAATGCAAGATCATCTG 59.352 37.037 0.00 0.00 0.00 2.90
3261 3333 5.698104 TCATCTGCTGTTCCATTGGATATT 58.302 37.500 6.15 0.00 0.00 1.28
3265 3337 7.750229 TCTGCTGTTCCATTGGATATTATTC 57.250 36.000 6.15 0.00 0.00 1.75
3274 3346 6.443527 TCCATTGGATATTATTCATCTCCCGA 59.556 38.462 0.00 0.00 28.50 5.14
3288 3360 2.036475 TCTCCCGAGCTTATTGCATCTC 59.964 50.000 0.00 0.00 45.94 2.75
3336 3408 2.908940 GGGATTGGCCGCATCAGG 60.909 66.667 14.98 0.00 37.63 3.86
3376 3448 6.266558 ACAGTATTTTGACCTTGGCAATAACA 59.733 34.615 0.00 0.00 27.33 2.41
3399 3471 3.930336 TGAAGACAATGTACTGAGCCTG 58.070 45.455 0.00 0.00 0.00 4.85
3420 3492 1.001764 TGGCCTGATGAACCTGCAG 60.002 57.895 6.78 6.78 0.00 4.41
3480 3552 4.660168 AGCATCTGAAGAGAAACATGGTT 58.340 39.130 0.00 0.00 0.00 3.67
3484 3556 4.067896 TCTGAAGAGAAACATGGTTGCTC 58.932 43.478 0.00 7.74 0.00 4.26
3571 3643 3.067180 CACAGCCATTTACCATGATGTCC 59.933 47.826 0.00 0.00 0.00 4.02
3584 3656 1.275010 TGATGTCCTGAGCAGCGTTTA 59.725 47.619 0.00 0.00 0.00 2.01
3585 3657 2.093500 TGATGTCCTGAGCAGCGTTTAT 60.093 45.455 0.00 0.00 0.00 1.40
3597 3669 3.600388 CAGCGTTTATTCTCCTCCTGTT 58.400 45.455 0.00 0.00 0.00 3.16
3617 3689 5.505780 TGTTTTTCTTCAGGGTCTTCAGAA 58.494 37.500 0.00 0.00 0.00 3.02
3654 3726 3.496515 CCCCAATTTGCATGTTTTCCAGT 60.497 43.478 0.00 0.00 0.00 4.00
3655 3727 4.136051 CCCAATTTGCATGTTTTCCAGTT 58.864 39.130 0.00 0.00 0.00 3.16
3912 3984 2.760092 GCCCAATGTTCATAGGCTCAAA 59.240 45.455 15.19 0.00 40.57 2.69
4065 4137 2.376808 CAGAGTCTGCGTTCAAGGAT 57.623 50.000 7.33 0.00 0.00 3.24
4253 4325 1.134491 GTTTGCTGATAGCGGGTAGGT 60.134 52.381 0.00 0.00 46.26 3.08
4300 4380 6.853872 CCGCGCTAAAAGCAAATATTATGTTA 59.146 34.615 5.56 0.00 42.58 2.41
4336 4416 4.881273 TCTCACAAGTAAAATGTGCACACT 59.119 37.500 24.37 8.89 46.05 3.55
4405 4487 5.817296 TGATGCTTACATGTCTGATGGTTAC 59.183 40.000 0.00 0.00 36.35 2.50
4432 4514 3.943381 GGTGACAAATCAGATCATGCAGA 59.057 43.478 0.00 0.00 34.75 4.26
4618 4700 6.270463 AGCTCCATCATCTCATCACTCTTTAT 59.730 38.462 0.00 0.00 0.00 1.40
4750 4838 3.185188 CCCAGAAGATCATATTTCACGCG 59.815 47.826 3.53 3.53 0.00 6.01
5317 6564 0.179187 CCTACTGTCACGTGAGAGCG 60.179 60.000 35.02 26.64 38.85 5.03
5346 6593 0.179073 CTGACGTGCCAAGGATAGGG 60.179 60.000 0.00 0.00 0.00 3.53
5382 6629 3.501445 GCAGTTTGATCTTCAAGTCAGCT 59.499 43.478 0.00 0.00 37.70 4.24
5459 6706 5.163374 GCCTTGGCTTCCAATTTATCTCAAT 60.163 40.000 4.11 0.00 43.07 2.57
5520 6767 9.044150 TCAAATTTGCCAATAGAACAAGAAAAG 57.956 29.630 13.54 0.00 0.00 2.27
5725 6973 5.476254 TCTCCTCTGTGATGATGTATAGCAG 59.524 44.000 0.00 0.00 0.00 4.24
5809 7057 6.914757 GCCAATTTAAGCATGAGAACATAGTC 59.085 38.462 0.00 0.00 35.09 2.59
6009 7257 5.395325 AGCAATAACAGAATCGATTGTCG 57.605 39.130 16.96 9.02 42.10 4.35
6044 7292 4.755123 CACCATATTCTTAGGGGTTTAGCG 59.245 45.833 0.00 0.00 33.44 4.26
6125 7459 2.498078 AGTTCCTGCTAACTAGGTCAGC 59.502 50.000 0.00 0.00 37.93 4.26
6131 7465 2.029307 CTAACTAGGTCAGCGGGGCC 62.029 65.000 0.00 0.00 0.00 5.80
6221 7555 5.421056 AGCCCAGGTTTAGTTTTATTTAGGC 59.579 40.000 0.00 0.00 0.00 3.93
6222 7556 5.421056 GCCCAGGTTTAGTTTTATTTAGGCT 59.579 40.000 0.00 0.00 0.00 4.58
6249 7583 1.133915 ACTCGTCCATCTCTCTCCCTC 60.134 57.143 0.00 0.00 0.00 4.30
6252 7586 1.953686 CGTCCATCTCTCTCCCTCTTC 59.046 57.143 0.00 0.00 0.00 2.87
6336 7670 1.412079 TTGTCAAGCCAACATGCCTT 58.588 45.000 0.00 0.00 0.00 4.35
6533 7954 9.162764 GTTGCGTCCATAATCATATATTACCTT 57.837 33.333 0.00 0.00 0.00 3.50
6537 7958 9.234384 CGTCCATAATCATATATTACCTTCGTC 57.766 37.037 0.00 0.00 0.00 4.20
6910 8333 2.503356 CACTTAGCTGGGAGAGTGGATT 59.497 50.000 0.00 0.00 36.68 3.01
6939 8362 2.031683 CGACCACCTGTGTTCAAGTTTC 59.968 50.000 0.00 0.00 0.00 2.78
7042 8465 2.857186 TGCTGGTATTCACTTCTGCA 57.143 45.000 0.00 0.00 0.00 4.41
7102 8538 6.266131 ACAGGGATATCAAAGGAGCAAATA 57.734 37.500 4.83 0.00 0.00 1.40
7282 8718 4.437390 CGTCAAGATGATGCAAAACCCTAC 60.437 45.833 0.00 0.00 0.00 3.18
7284 8720 5.048083 GTCAAGATGATGCAAAACCCTACAA 60.048 40.000 0.00 0.00 0.00 2.41
7302 8738 0.185175 AACTCCACCCCACAAGAACC 59.815 55.000 0.00 0.00 0.00 3.62
7395 8832 4.434520 GGGTGATAGTCTAAACAGTGAGC 58.565 47.826 0.00 0.00 0.00 4.26
7405 8842 0.835543 AACAGTGAGCTCAGGAGGCT 60.836 55.000 18.89 7.37 43.26 4.58
7406 8843 0.835543 ACAGTGAGCTCAGGAGGCTT 60.836 55.000 18.89 0.00 40.40 4.35
7407 8844 0.324285 CAGTGAGCTCAGGAGGCTTT 59.676 55.000 18.89 0.00 40.40 3.51
7408 8845 0.324285 AGTGAGCTCAGGAGGCTTTG 59.676 55.000 18.89 0.00 40.40 2.77
7409 8846 0.036022 GTGAGCTCAGGAGGCTTTGT 59.964 55.000 18.89 0.00 40.40 2.83
7410 8847 1.276421 GTGAGCTCAGGAGGCTTTGTA 59.724 52.381 18.89 0.00 40.40 2.41
7411 8848 1.552337 TGAGCTCAGGAGGCTTTGTAG 59.448 52.381 13.74 0.00 40.40 2.74
7489 8926 1.919918 CCTCACATCGACTTCAGCTC 58.080 55.000 0.00 0.00 0.00 4.09
7527 8977 0.748005 ACCAGCGCTGAACAGTTTGT 60.748 50.000 38.06 21.19 0.00 2.83
7591 9041 5.091261 ACATCTGAATGGTGACTTAGGTC 57.909 43.478 0.00 0.00 38.77 3.85
7628 9078 0.240411 CAGCTTTTCTGCACCAGCTC 59.760 55.000 2.00 0.00 40.75 4.09
7679 9129 0.035056 GTCACTCTGTTGGATGGGGG 60.035 60.000 0.00 0.00 0.00 5.40
7737 9187 3.079578 CTCAAGAATGTGCATCTGGTGT 58.920 45.455 0.00 0.00 0.00 4.16
7808 9258 0.465824 GATGATGCAGGCCTCAGCTT 60.466 55.000 15.52 9.61 39.73 3.74
7981 9431 4.932146 AGTTTCTTGTGGAAATGGAAACG 58.068 39.130 0.00 0.00 45.65 3.60
7987 9437 2.227194 GTGGAAATGGAAACGGACAGT 58.773 47.619 0.00 0.00 0.00 3.55
8063 9513 8.937634 GGAAGTTTCCGTTTATCTATTGTCTA 57.062 34.615 0.00 0.00 37.65 2.59
8078 9528 2.827755 TGTCTATGTAGCCCACTCCAA 58.172 47.619 0.00 0.00 0.00 3.53
8102 9552 4.017958 TCCAACCCATATAGACTTTTGGCA 60.018 41.667 0.00 0.00 33.46 4.92
8229 9680 8.777578 TTACACATATACATTACTCCCTCTGT 57.222 34.615 0.00 0.00 0.00 3.41
8230 9681 7.676683 ACACATATACATTACTCCCTCTGTT 57.323 36.000 0.00 0.00 0.00 3.16
8231 9682 7.727181 ACACATATACATTACTCCCTCTGTTC 58.273 38.462 0.00 0.00 0.00 3.18
8232 9683 7.344612 ACACATATACATTACTCCCTCTGTTCA 59.655 37.037 0.00 0.00 0.00 3.18
8233 9684 7.653713 CACATATACATTACTCCCTCTGTTCAC 59.346 40.741 0.00 0.00 0.00 3.18
8234 9685 7.565398 ACATATACATTACTCCCTCTGTTCACT 59.435 37.037 0.00 0.00 0.00 3.41
8235 9686 6.875972 ATACATTACTCCCTCTGTTCACTT 57.124 37.500 0.00 0.00 0.00 3.16
8236 9687 5.568620 ACATTACTCCCTCTGTTCACTTT 57.431 39.130 0.00 0.00 0.00 2.66
8237 9688 5.941788 ACATTACTCCCTCTGTTCACTTTT 58.058 37.500 0.00 0.00 0.00 2.27
8238 9689 7.074653 ACATTACTCCCTCTGTTCACTTTTA 57.925 36.000 0.00 0.00 0.00 1.52
8239 9690 7.690256 ACATTACTCCCTCTGTTCACTTTTAT 58.310 34.615 0.00 0.00 0.00 1.40
8240 9691 8.822805 ACATTACTCCCTCTGTTCACTTTTATA 58.177 33.333 0.00 0.00 0.00 0.98
8241 9692 9.667107 CATTACTCCCTCTGTTCACTTTTATAA 57.333 33.333 0.00 0.00 0.00 0.98
8242 9693 9.892130 ATTACTCCCTCTGTTCACTTTTATAAG 57.108 33.333 0.00 0.00 37.40 1.73
8243 9694 6.712276 ACTCCCTCTGTTCACTTTTATAAGG 58.288 40.000 0.00 0.00 35.61 2.69
8244 9695 5.497474 TCCCTCTGTTCACTTTTATAAGGC 58.503 41.667 0.00 0.00 35.61 4.35
8245 9696 4.640647 CCCTCTGTTCACTTTTATAAGGCC 59.359 45.833 0.00 0.00 35.61 5.19
8246 9697 5.501156 CCTCTGTTCACTTTTATAAGGCCT 58.499 41.667 0.00 0.00 35.61 5.19
8247 9698 5.946377 CCTCTGTTCACTTTTATAAGGCCTT 59.054 40.000 24.18 24.18 35.61 4.35
8248 9699 6.127897 CCTCTGTTCACTTTTATAAGGCCTTG 60.128 42.308 28.77 12.48 35.61 3.61
8249 9700 6.303839 TCTGTTCACTTTTATAAGGCCTTGT 58.696 36.000 28.77 24.00 35.61 3.16
8250 9701 7.455058 TCTGTTCACTTTTATAAGGCCTTGTA 58.545 34.615 28.77 22.82 35.61 2.41
8251 9702 7.389607 TCTGTTCACTTTTATAAGGCCTTGTAC 59.610 37.037 28.77 13.67 35.61 2.90
8252 9703 6.999272 TGTTCACTTTTATAAGGCCTTGTACA 59.001 34.615 28.77 16.00 35.61 2.90
8253 9704 7.040961 TGTTCACTTTTATAAGGCCTTGTACAC 60.041 37.037 28.77 14.61 35.61 2.90
8254 9705 6.535540 TCACTTTTATAAGGCCTTGTACACA 58.464 36.000 28.77 7.10 35.61 3.72
8255 9706 7.172342 TCACTTTTATAAGGCCTTGTACACAT 58.828 34.615 28.77 14.50 35.61 3.21
8256 9707 7.668052 TCACTTTTATAAGGCCTTGTACACATT 59.332 33.333 28.77 6.06 35.61 2.71
8257 9708 8.303876 CACTTTTATAAGGCCTTGTACACATTT 58.696 33.333 28.77 5.03 35.61 2.32
8258 9709 8.520351 ACTTTTATAAGGCCTTGTACACATTTC 58.480 33.333 28.77 0.00 35.61 2.17
8259 9710 8.410673 TTTTATAAGGCCTTGTACACATTTCA 57.589 30.769 28.77 5.11 0.00 2.69
8260 9711 7.624360 TTATAAGGCCTTGTACACATTTCAG 57.376 36.000 28.77 0.00 0.00 3.02
8261 9712 3.788227 AGGCCTTGTACACATTTCAGA 57.212 42.857 0.00 0.00 0.00 3.27
8262 9713 3.412386 AGGCCTTGTACACATTTCAGAC 58.588 45.455 0.00 0.00 0.00 3.51
8263 9714 3.146066 GGCCTTGTACACATTTCAGACA 58.854 45.455 0.00 0.00 0.00 3.41
8264 9715 3.189287 GGCCTTGTACACATTTCAGACAG 59.811 47.826 0.00 0.00 0.00 3.51
8265 9716 3.365364 GCCTTGTACACATTTCAGACAGC 60.365 47.826 0.00 0.00 0.00 4.40
8266 9717 3.814842 CCTTGTACACATTTCAGACAGCA 59.185 43.478 0.00 0.00 0.00 4.41
8267 9718 4.456911 CCTTGTACACATTTCAGACAGCAT 59.543 41.667 0.00 0.00 0.00 3.79
8268 9719 5.361135 TTGTACACATTTCAGACAGCATG 57.639 39.130 0.00 0.00 46.00 4.06
8269 9720 3.189080 TGTACACATTTCAGACAGCATGC 59.811 43.478 10.51 10.51 42.53 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
200 201 4.767255 GGTGCTGGGTGGAGCGAG 62.767 72.222 0.00 0.00 42.32 5.03
203 204 4.729918 CAGGGTGCTGGGTGGAGC 62.730 72.222 0.00 0.00 39.62 4.70
204 205 4.039092 CCAGGGTGCTGGGTGGAG 62.039 72.222 0.00 0.00 40.68 3.86
215 216 3.322466 CACCTTCTCGGCCAGGGT 61.322 66.667 11.37 0.54 34.02 4.34
229 230 2.610859 TGCTCTTCCCTCCCCACC 60.611 66.667 0.00 0.00 0.00 4.61
249 250 2.700897 AGGATAATCTCCCCACAGTTCG 59.299 50.000 0.00 0.00 46.27 3.95
279 280 8.616799 AGTCTAGTCCTCTTTTCTCCATTATT 57.383 34.615 0.00 0.00 0.00 1.40
281 282 9.191479 CTAAGTCTAGTCCTCTTTTCTCCATTA 57.809 37.037 0.00 0.00 0.00 1.90
282 283 6.943899 AAGTCTAGTCCTCTTTTCTCCATT 57.056 37.500 0.00 0.00 0.00 3.16
283 284 6.609616 CCTAAGTCTAGTCCTCTTTTCTCCAT 59.390 42.308 0.00 0.00 0.00 3.41
284 285 5.952947 CCTAAGTCTAGTCCTCTTTTCTCCA 59.047 44.000 0.00 0.00 0.00 3.86
329 354 3.134458 GGAGATATTTTGGGCTGTCGAG 58.866 50.000 0.00 0.00 0.00 4.04
382 407 4.452733 GGAGAACCTCCGCCCACG 62.453 72.222 0.00 0.00 41.08 4.94
393 418 0.753848 CGGAGGAGGAGGAGGAGAAC 60.754 65.000 0.00 0.00 0.00 3.01
396 421 1.152839 GACGGAGGAGGAGGAGGAG 60.153 68.421 0.00 0.00 0.00 3.69
397 422 3.008408 GACGGAGGAGGAGGAGGA 58.992 66.667 0.00 0.00 0.00 3.71
398 423 2.517402 CGACGGAGGAGGAGGAGG 60.517 72.222 0.00 0.00 0.00 4.30
455 480 1.523154 TTGCTTGGGTTGATGCGGTC 61.523 55.000 0.00 0.00 0.00 4.79
480 505 2.961526 TCGGTTTGGAGCTAAGCTAG 57.038 50.000 0.00 0.00 39.88 3.42
530 555 1.450312 GAAGGGTGGAGATGGTGCG 60.450 63.158 0.00 0.00 0.00 5.34
534 559 0.835941 CTCTGGAAGGGTGGAGATGG 59.164 60.000 0.00 0.00 0.00 3.51
538 563 1.601171 CTGCTCTGGAAGGGTGGAG 59.399 63.158 0.00 0.00 36.17 3.86
546 571 1.004560 CGAGGTTGCTGCTCTGGAA 60.005 57.895 0.00 0.00 0.00 3.53
548 573 3.123620 GCGAGGTTGCTGCTCTGG 61.124 66.667 0.00 0.00 0.00 3.86
681 733 1.022903 ATCCCCTCTTCCTCCTCACT 58.977 55.000 0.00 0.00 0.00 3.41
685 737 1.501582 CGAAATCCCCTCTTCCTCCT 58.498 55.000 0.00 0.00 0.00 3.69
718 772 2.904178 AATAGCCTTTTCCCCGCCCG 62.904 60.000 0.00 0.00 0.00 6.13
725 779 2.289565 CCGGTCAGAATAGCCTTTTCC 58.710 52.381 0.00 0.00 0.00 3.13
814 870 0.907486 TGAGGCAGAGACCATTCTGG 59.093 55.000 5.30 0.00 43.80 3.86
850 917 2.028385 TCCTTTTACTGAACCGCTCCTC 60.028 50.000 0.00 0.00 0.00 3.71
852 919 2.028385 TCTCCTTTTACTGAACCGCTCC 60.028 50.000 0.00 0.00 0.00 4.70
927 995 6.976925 AGAGCAATGTGAAAAGAGAAAAACTG 59.023 34.615 0.00 0.00 0.00 3.16
940 1008 1.999648 AAGGGCAAGAGCAATGTGAA 58.000 45.000 0.00 0.00 44.61 3.18
970 1038 6.013984 ACCTGAAAAATCAAAGCATGGAGAAT 60.014 34.615 0.00 0.00 0.00 2.40
1221 1293 3.307059 GCACCTCATCCATCCAGTATACC 60.307 52.174 0.00 0.00 0.00 2.73
1308 1380 1.079750 GACGGCTCTGGTCTTGACC 60.080 63.158 12.54 12.54 0.00 4.02
1358 1430 4.616835 GCTTCAGTGATTTGAAAAGCCGAT 60.617 41.667 0.00 0.00 36.69 4.18
1371 1443 0.035317 TTGTGCTCGGCTTCAGTGAT 59.965 50.000 0.00 0.00 0.00 3.06
1374 1446 1.302033 CCTTGTGCTCGGCTTCAGT 60.302 57.895 0.00 0.00 0.00 3.41
1375 1447 2.037136 CCCTTGTGCTCGGCTTCAG 61.037 63.158 0.00 0.00 0.00 3.02
1384 1456 2.158475 TGATCTTGGAAACCCTTGTGCT 60.158 45.455 0.00 0.00 0.00 4.40
1405 1477 1.611851 CCAGGGTCCTGAGCTCTGT 60.612 63.158 17.91 0.00 46.30 3.41
1434 1506 0.592148 ACCTCTCACGTCGTTCACTC 59.408 55.000 0.00 0.00 0.00 3.51
1443 1515 4.889995 TCATCAAGATGATACCTCTCACGT 59.110 41.667 8.61 0.00 42.42 4.49
1473 1545 1.045407 ACACAGGGCTAGAACGTGAA 58.955 50.000 12.56 0.00 0.00 3.18
1476 1548 1.045407 TGAACACAGGGCTAGAACGT 58.955 50.000 0.00 0.00 0.00 3.99
1477 1549 1.000955 AGTGAACACAGGGCTAGAACG 59.999 52.381 7.68 0.00 0.00 3.95
1487 1559 2.744202 GGATTGTGCCTAGTGAACACAG 59.256 50.000 7.68 3.31 44.46 3.66
1498 1570 1.002134 CTGGAACCGGATTGTGCCT 60.002 57.895 9.46 0.00 34.70 4.75
1508 1580 1.002087 GTCCATATAGGCCTGGAACCG 59.998 57.143 17.99 0.00 42.99 4.44
1552 1624 5.543507 AGCTTAATCTTCAGGTCATCGAT 57.456 39.130 0.00 0.00 0.00 3.59
1727 1799 4.491234 AGTAGTCTCTTTGTGTCTGACG 57.509 45.455 2.98 0.00 33.40 4.35
1775 1847 6.574350 CAAGAATAAGAGGGTAGTCGACAAT 58.426 40.000 19.50 0.00 0.00 2.71
1829 1901 9.495572 GGTACCTCTTATCTTGGAGATATTTTG 57.504 37.037 4.06 0.00 37.09 2.44
1830 1902 9.453830 AGGTACCTCTTATCTTGGAGATATTTT 57.546 33.333 9.21 0.00 37.09 1.82
1962 2034 1.070821 ATCGACTGTGCACATTCACG 58.929 50.000 29.59 24.73 39.73 4.35
2235 2307 8.506437 TCTGTTTCTGCTGTTGTTATTATTCTG 58.494 33.333 0.00 0.00 0.00 3.02
2259 2331 1.478510 CATTCCAGAGCTACACCGTCT 59.521 52.381 0.00 0.00 0.00 4.18
2263 2335 1.065854 ACAGCATTCCAGAGCTACACC 60.066 52.381 0.00 0.00 39.50 4.16
2280 2352 8.954950 AAATATTATCAGACTGAGAACCACAG 57.045 34.615 14.47 0.00 40.68 3.66
2310 2382 1.607801 GGCTGCCAAGGGGTTTCATC 61.608 60.000 15.17 0.00 36.17 2.92
2363 2435 0.320771 ACACCGATGTTCAGAGCCAC 60.321 55.000 0.00 0.00 34.46 5.01
2407 2479 6.828273 CCACCACACTTTCCAATGAATCTATA 59.172 38.462 0.00 0.00 0.00 1.31
2413 2485 3.025322 ACCACCACACTTTCCAATGAA 57.975 42.857 0.00 0.00 0.00 2.57
2419 2491 0.104120 GGCAAACCACCACACTTTCC 59.896 55.000 0.00 0.00 35.26 3.13
2451 2523 3.263170 TGGCTAAGAGACCAGCAATACAA 59.737 43.478 0.00 0.00 39.63 2.41
2472 2544 1.609072 TCAGAGTTGTCCGTCTGACTG 59.391 52.381 6.21 0.00 43.41 3.51
2484 2556 3.189618 TGATGCCATAGCTCAGAGTTG 57.810 47.619 0.00 0.00 40.80 3.16
2529 2601 8.707449 TCTTCCAAAGTAGGACTTGTACTTAAA 58.293 33.333 0.00 0.00 39.34 1.52
2599 2671 6.097356 ACAGCAAGCATGTCTTCAAATAATG 58.903 36.000 0.00 0.00 31.27 1.90
2640 2712 0.544357 TCCACATCGTGAACCCCTCT 60.544 55.000 0.00 0.00 35.23 3.69
2648 2720 3.417069 AATCAACCTTCCACATCGTGA 57.583 42.857 0.00 0.00 35.23 4.35
2724 2796 6.890979 AAATAGCTATCTGCAATTTCCTCC 57.109 37.500 6.72 0.00 45.94 4.30
2765 2837 1.213926 GCTCAGGTTGGATCATTCCCT 59.786 52.381 0.00 0.00 41.83 4.20
2796 2868 6.348498 TGTACAGGATAACACCTCATCATTG 58.652 40.000 0.00 0.00 38.32 2.82
2810 2882 3.263170 AGTGTGGTGCAATGTACAGGATA 59.737 43.478 0.33 0.00 0.00 2.59
2811 2883 2.040278 AGTGTGGTGCAATGTACAGGAT 59.960 45.455 0.33 0.00 0.00 3.24
2821 2893 2.684128 CACGTACAGTGTGGTGCAA 58.316 52.632 5.88 0.00 45.51 4.08
2892 2964 4.796038 ATTTCCTGTGATGGCTTTTGAG 57.204 40.909 0.00 0.00 0.00 3.02
2925 2997 1.893544 AGTGGAGAGAAAGTCGACGA 58.106 50.000 10.46 0.00 0.00 4.20
3048 3120 7.499232 AGGATTAATACTCGCAGCAACTTAAAT 59.501 33.333 0.00 0.00 0.00 1.40
3066 3138 4.424842 TGCCCCAAAAGTCAAGGATTAAT 58.575 39.130 0.00 0.00 0.00 1.40
3067 3139 3.850752 TGCCCCAAAAGTCAAGGATTAA 58.149 40.909 0.00 0.00 0.00 1.40
3069 3141 2.368548 GTTGCCCCAAAAGTCAAGGATT 59.631 45.455 0.00 0.00 0.00 3.01
3071 3143 1.408969 GTTGCCCCAAAAGTCAAGGA 58.591 50.000 0.00 0.00 0.00 3.36
3171 3243 1.098050 GGGCTGGCAGTTCTACAATG 58.902 55.000 17.16 0.00 0.00 2.82
3197 3269 6.313905 CAGTGTTTCCATGTATTGTAGTCCTC 59.686 42.308 0.00 0.00 0.00 3.71
3206 3278 9.874205 CATTTATTTCCAGTGTTTCCATGTATT 57.126 29.630 0.00 0.00 0.00 1.89
3261 3333 4.040339 TGCAATAAGCTCGGGAGATGAATA 59.960 41.667 0.00 0.00 45.94 1.75
3265 3337 2.245159 TGCAATAAGCTCGGGAGATG 57.755 50.000 0.00 0.00 45.94 2.90
3274 3346 4.340666 TCGAAGAGAGAGATGCAATAAGCT 59.659 41.667 0.00 0.00 45.94 3.74
3305 3377 3.571401 GCCAATCCCATCAGGTAGATTTG 59.429 47.826 0.00 0.00 33.72 2.32
3336 3408 4.879104 ATACTGTAGTGTACGCAGAGAC 57.121 45.455 9.48 1.88 34.60 3.36
3376 3448 3.580458 AGGCTCAGTACATTGTCTTCAGT 59.420 43.478 0.00 0.00 0.00 3.41
3399 3471 1.379044 CAGGTTCATCAGGCCACCC 60.379 63.158 5.01 0.00 0.00 4.61
3406 3478 4.763073 TGAAGATACTGCAGGTTCATCAG 58.237 43.478 19.93 0.00 0.00 2.90
3420 3492 7.055667 TGTGGAATAGGTGAGATGAAGATAC 57.944 40.000 0.00 0.00 0.00 2.24
3480 3552 1.644509 TAACAGAAGAGGCCAGAGCA 58.355 50.000 5.01 0.00 42.56 4.26
3484 3556 2.941720 GCTTGATAACAGAAGAGGCCAG 59.058 50.000 5.01 0.00 0.00 4.85
3571 3643 2.863137 GAGGAGAATAAACGCTGCTCAG 59.137 50.000 0.00 0.00 45.46 3.35
3597 3669 5.755849 AGTTTCTGAAGACCCTGAAGAAAA 58.244 37.500 0.00 0.00 38.28 2.29
3617 3689 1.799933 TGGGGGCAACAAATCAAGTT 58.200 45.000 0.00 0.00 39.74 2.66
3654 3726 4.264352 ACTGCTCCAATATCCTTGGGAAAA 60.264 41.667 4.28 0.00 39.96 2.29
3655 3727 3.269381 ACTGCTCCAATATCCTTGGGAAA 59.731 43.478 4.28 0.00 39.96 3.13
3698 3770 3.314541 GTAGTTCACGGACCACAAGAT 57.685 47.619 0.00 0.00 0.00 2.40
3759 3831 5.181245 CCGGACATACAATGAAAGAACAGTT 59.819 40.000 0.00 0.00 0.00 3.16
3912 3984 0.037590 TGCGGGCATTGAAACCTAGT 59.962 50.000 0.00 0.00 0.00 2.57
4065 4137 4.406456 ACCTTGAATGCTTGTGAATGGTA 58.594 39.130 0.00 0.00 0.00 3.25
4253 4325 2.225318 GGGTGGGGGTGTTGGTAAATAA 60.225 50.000 0.00 0.00 0.00 1.40
4315 4395 4.397730 ACAGTGTGCACATTTTACTTGTGA 59.602 37.500 24.69 0.00 45.83 3.58
4336 4416 1.904287 AGGTTTGCTGGCGAAATACA 58.096 45.000 0.00 0.00 0.00 2.29
4405 4487 3.678289 TGATCTGATTTGTCACCCTGTG 58.322 45.455 0.00 0.00 34.45 3.66
4432 4514 5.579753 AAATCCATATGCTGAGGAGACAT 57.420 39.130 0.00 0.00 34.40 3.06
4463 4545 2.802816 GGCATAGTCAGCTTTGTATCGG 59.197 50.000 0.00 0.00 0.00 4.18
4618 4700 5.279960 CCGGATCCCATGTATATGTTTCAGA 60.280 44.000 6.06 0.00 32.21 3.27
4672 4754 1.070289 GGTATTCCTTGGCGTAGGAGG 59.930 57.143 8.02 0.00 44.82 4.30
4676 4764 2.550978 CACTGGTATTCCTTGGCGTAG 58.449 52.381 0.00 0.00 34.23 3.51
4750 4838 0.391793 GTACTCCAGGTGCCTTCAGC 60.392 60.000 0.00 0.00 44.14 4.26
5005 5095 6.905736 TCCAGTATGCCTACATTTAAATGGA 58.094 36.000 27.43 20.69 37.74 3.41
5133 5229 8.764287 GTTTGCAAAAGAACAGCTTGTAATTAT 58.236 29.630 14.67 0.00 36.80 1.28
5308 6555 3.250323 CGTGCATCCGCTCTCACG 61.250 66.667 0.00 0.00 44.62 4.35
5429 6676 1.039856 TTGGAAGCCAAGGCAAGAAC 58.960 50.000 14.40 0.00 44.88 3.01
5520 6767 6.572703 GCTGCTAGGGTTGGAGTATAATCTAC 60.573 46.154 0.00 0.00 0.00 2.59
5580 6827 7.591006 TTGGTTGACGAAGATTGTAAGTATC 57.409 36.000 0.00 0.00 0.00 2.24
5623 6870 3.008266 GGTGGTACAACTAGGGTGCTTTA 59.992 47.826 0.00 0.00 46.61 1.85
5725 6973 5.241728 AGTCAGCAAAGGTATCTTGAAAACC 59.758 40.000 0.00 0.00 32.75 3.27
5809 7057 5.357257 ACAGTTTCGCTACCATAATACTGG 58.643 41.667 0.00 0.00 42.35 4.00
6009 7257 4.265073 AGAATATGGTGAGTGAAGTTGCC 58.735 43.478 0.00 0.00 0.00 4.52
6044 7292 6.692249 GCATAATATTTTGGCCATGCAAAAAC 59.308 34.615 16.77 0.00 43.04 2.43
6125 7459 2.876550 GCAAATACTTAACTAGGCCCCG 59.123 50.000 0.00 0.00 0.00 5.73
6131 7465 4.887655 CCCAAGGGGCAAATACTTAACTAG 59.112 45.833 0.00 0.00 35.35 2.57
6249 7583 3.430218 AGCTTTTTGTGATCGAGACGAAG 59.570 43.478 0.00 0.00 39.99 3.79
6252 7586 4.903638 TTAGCTTTTTGTGATCGAGACG 57.096 40.909 0.00 0.00 0.00 4.18
6336 7670 4.742417 CTTGAAATGTTGTTGTGTGGACA 58.258 39.130 0.00 0.00 0.00 4.02
6533 7954 3.991773 CGAAGACAAGTAATTTGGGACGA 59.008 43.478 0.00 0.00 41.25 4.20
6537 7958 7.495934 AGACATATCGAAGACAAGTAATTTGGG 59.504 37.037 0.00 0.00 42.51 4.12
6714 8135 5.985530 ACCACATTCATATACATGTCTGACG 59.014 40.000 0.00 1.44 30.90 4.35
6910 8333 1.695242 ACACAGGTGGTCGGATTGTAA 59.305 47.619 4.24 0.00 34.19 2.41
6939 8362 2.222624 GAACTCAAATTCGTGTTCGCG 58.777 47.619 0.00 0.00 36.96 5.87
7102 8538 4.523083 ACACCGTTACCATCAATTAGCAT 58.477 39.130 0.00 0.00 0.00 3.79
7249 8685 4.749099 GCATCATCTTGACGCTCTTCTAAT 59.251 41.667 0.00 0.00 32.15 1.73
7257 8693 2.095059 GGTTTTGCATCATCTTGACGCT 60.095 45.455 0.00 0.00 36.42 5.07
7282 8718 1.318576 GTTCTTGTGGGGTGGAGTTG 58.681 55.000 0.00 0.00 0.00 3.16
7284 8720 0.991355 TGGTTCTTGTGGGGTGGAGT 60.991 55.000 0.00 0.00 0.00 3.85
7355 8791 1.159713 CCGAGTGCAGCACAGTTTGA 61.160 55.000 27.35 0.00 36.74 2.69
7357 8793 1.893808 CCCGAGTGCAGCACAGTTT 60.894 57.895 27.35 6.51 36.74 2.66
7395 8832 3.744660 ACAAACTACAAAGCCTCCTGAG 58.255 45.455 0.00 0.00 0.00 3.35
7405 8842 4.667573 TCCCATGGCATACAAACTACAAA 58.332 39.130 6.09 0.00 0.00 2.83
7406 8843 4.269183 CTCCCATGGCATACAAACTACAA 58.731 43.478 6.09 0.00 0.00 2.41
7407 8844 3.884895 CTCCCATGGCATACAAACTACA 58.115 45.455 6.09 0.00 0.00 2.74
7408 8845 2.618709 GCTCCCATGGCATACAAACTAC 59.381 50.000 6.09 0.00 0.00 2.73
7409 8846 2.422803 GGCTCCCATGGCATACAAACTA 60.423 50.000 6.09 0.00 0.00 2.24
7410 8847 1.686115 GGCTCCCATGGCATACAAACT 60.686 52.381 6.09 0.00 0.00 2.66
7411 8848 0.746659 GGCTCCCATGGCATACAAAC 59.253 55.000 6.09 0.00 0.00 2.93
7449 8886 0.887933 AAAACTATGGTTGCCAGCCG 59.112 50.000 0.00 0.00 36.75 5.52
7527 8977 1.754226 GTGTTTTCAGTGGGGCTTTGA 59.246 47.619 0.00 0.00 0.00 2.69
7679 9129 3.879892 CCTGCTCCCTAAAAGTTATCTGC 59.120 47.826 0.00 0.00 0.00 4.26
7737 9187 5.181811 CAGATGAAACAATCTTGCACCTACA 59.818 40.000 0.00 0.00 34.60 2.74
7808 9258 2.451990 CGCATGATTGACGTCGGCA 61.452 57.895 11.62 0.00 0.00 5.69
7809 9259 1.692148 TTCGCATGATTGACGTCGGC 61.692 55.000 11.62 6.57 0.00 5.54
7810 9260 0.718904 TTTCGCATGATTGACGTCGG 59.281 50.000 11.62 0.00 0.00 4.79
7811 9261 2.502280 TTTTCGCATGATTGACGTCG 57.498 45.000 11.62 0.00 0.00 5.12
7812 9262 5.108630 GCAATATTTTCGCATGATTGACGTC 60.109 40.000 9.11 9.11 30.62 4.34
7813 9263 4.734854 GCAATATTTTCGCATGATTGACGT 59.265 37.500 0.00 0.00 30.62 4.34
7814 9264 4.734370 TGCAATATTTTCGCATGATTGACG 59.266 37.500 0.00 0.00 30.62 4.35
7981 9431 3.067833 GCTCCACTAGAAAACACTGTCC 58.932 50.000 0.00 0.00 0.00 4.02
7987 9437 2.438021 ACTGGTGCTCCACTAGAAAACA 59.562 45.455 14.39 0.00 44.01 2.83
8060 9510 2.972713 GGATTGGAGTGGGCTACATAGA 59.027 50.000 3.15 0.00 35.09 1.98
8061 9511 2.705658 TGGATTGGAGTGGGCTACATAG 59.294 50.000 3.15 0.00 35.09 2.23
8063 9513 1.595311 TGGATTGGAGTGGGCTACAT 58.405 50.000 3.15 0.00 35.09 2.29
8078 9528 5.140454 GCCAAAAGTCTATATGGGTTGGAT 58.860 41.667 12.56 0.00 36.90 3.41
8221 9672 5.497474 GCCTTATAAAAGTGAACAGAGGGA 58.503 41.667 0.00 0.00 0.00 4.20
8222 9673 4.640647 GGCCTTATAAAAGTGAACAGAGGG 59.359 45.833 0.00 0.00 0.00 4.30
8223 9674 5.501156 AGGCCTTATAAAAGTGAACAGAGG 58.499 41.667 0.00 0.00 0.00 3.69
8224 9675 6.431234 ACAAGGCCTTATAAAAGTGAACAGAG 59.569 38.462 20.00 1.54 0.00 3.35
8225 9676 6.303839 ACAAGGCCTTATAAAAGTGAACAGA 58.696 36.000 20.00 0.00 0.00 3.41
8226 9677 6.575162 ACAAGGCCTTATAAAAGTGAACAG 57.425 37.500 20.00 2.68 0.00 3.16
8227 9678 6.999272 TGTACAAGGCCTTATAAAAGTGAACA 59.001 34.615 20.00 9.95 0.00 3.18
8228 9679 7.040961 TGTGTACAAGGCCTTATAAAAGTGAAC 60.041 37.037 20.00 13.04 0.00 3.18
8229 9680 6.999272 TGTGTACAAGGCCTTATAAAAGTGAA 59.001 34.615 20.00 0.95 0.00 3.18
8230 9681 6.535540 TGTGTACAAGGCCTTATAAAAGTGA 58.464 36.000 20.00 0.00 0.00 3.41
8231 9682 6.811253 TGTGTACAAGGCCTTATAAAAGTG 57.189 37.500 20.00 6.46 0.00 3.16
8232 9683 8.417273 AAATGTGTACAAGGCCTTATAAAAGT 57.583 30.769 20.00 13.37 0.00 2.66
8233 9684 8.519526 TGAAATGTGTACAAGGCCTTATAAAAG 58.480 33.333 20.00 7.24 0.00 2.27
8234 9685 8.410673 TGAAATGTGTACAAGGCCTTATAAAA 57.589 30.769 20.00 0.00 0.00 1.52
8235 9686 7.885922 TCTGAAATGTGTACAAGGCCTTATAAA 59.114 33.333 20.00 2.80 0.00 1.40
8236 9687 7.335924 GTCTGAAATGTGTACAAGGCCTTATAA 59.664 37.037 20.00 3.31 0.00 0.98
8237 9688 6.821665 GTCTGAAATGTGTACAAGGCCTTATA 59.178 38.462 20.00 9.01 0.00 0.98
8238 9689 5.648092 GTCTGAAATGTGTACAAGGCCTTAT 59.352 40.000 20.00 10.37 0.00 1.73
8239 9690 5.001232 GTCTGAAATGTGTACAAGGCCTTA 58.999 41.667 20.00 0.00 0.00 2.69
8240 9691 3.821033 GTCTGAAATGTGTACAAGGCCTT 59.179 43.478 13.78 13.78 0.00 4.35
8241 9692 3.181445 TGTCTGAAATGTGTACAAGGCCT 60.181 43.478 0.00 0.00 0.00 5.19
8242 9693 3.146066 TGTCTGAAATGTGTACAAGGCC 58.854 45.455 0.00 0.00 0.00 5.19
8243 9694 3.365364 GCTGTCTGAAATGTGTACAAGGC 60.365 47.826 0.00 0.00 0.00 4.35
8244 9695 3.814842 TGCTGTCTGAAATGTGTACAAGG 59.185 43.478 0.00 0.00 0.00 3.61
8245 9696 5.388111 CATGCTGTCTGAAATGTGTACAAG 58.612 41.667 0.00 0.00 0.00 3.16
8246 9697 4.320421 GCATGCTGTCTGAAATGTGTACAA 60.320 41.667 11.37 0.00 0.00 2.41
8247 9698 3.189080 GCATGCTGTCTGAAATGTGTACA 59.811 43.478 11.37 0.00 0.00 2.90
8248 9699 3.751621 GCATGCTGTCTGAAATGTGTAC 58.248 45.455 11.37 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.