Multiple sequence alignment - TraesCS4B01G201500

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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 TraesCS4B01G201500 chr4B 100.000 7633 0 0 1 7633 431787850 431795482 0.000000e+00 14096.0
1 TraesCS4B01G201500 chr4B 100.000 38 0 0 4823 4860 431792630 431792667 3.820000e-08 71.3
2 TraesCS4B01G201500 chr4B 100.000 38 0 0 4781 4818 431792672 431792709 3.820000e-08 71.3
3 TraesCS4B01G201500 chr4D 95.933 4180 93 15 146 4306 349182598 349186719 0.000000e+00 6706.0
4 TraesCS4B01G201500 chr4D 94.219 1678 54 13 5971 7633 349188064 349189713 0.000000e+00 2521.0
5 TraesCS4B01G201500 chr4D 97.753 979 19 3 4823 5799 349187033 349188010 0.000000e+00 1683.0
6 TraesCS4B01G201500 chr4D 98.588 354 3 2 4466 4818 349186718 349187070 6.500000e-175 625.0
7 TraesCS4B01G201500 chr4D 95.000 60 1 1 31 88 349182187 349182246 8.160000e-15 93.5
8 TraesCS4B01G201500 chr4D 93.478 46 2 1 102 147 349182281 349182325 4.940000e-07 67.6
9 TraesCS4B01G201500 chr4A 95.033 4288 154 35 31 4306 115796289 115792049 0.000000e+00 6684.0
10 TraesCS4B01G201500 chr4A 94.030 2831 101 29 4840 7633 115791725 115788926 0.000000e+00 4229.0
11 TraesCS4B01G201500 chr4A 94.915 354 9 3 4466 4818 115792050 115791705 5.210000e-151 545.0
12 TraesCS4B01G201500 chr4A 100.000 33 0 0 1 33 115796345 115796313 2.300000e-05 62.1
13 TraesCS4B01G201500 chr6A 91.876 1157 63 8 3166 4306 222558382 222557241 0.000000e+00 1587.0
14 TraesCS4B01G201500 chr7B 91.757 643 29 5 3674 4306 706224762 706225390 0.000000e+00 872.0
15 TraesCS4B01G201500 chr7B 97.143 175 3 2 4301 4475 497576790 497576618 2.080000e-75 294.0
16 TraesCS4B01G201500 chr7B 98.171 164 3 0 4305 4468 249675052 249674889 3.490000e-73 287.0
17 TraesCS4B01G201500 chr7B 97.605 167 4 0 4301 4467 544113038 544113204 3.490000e-73 287.0
18 TraesCS4B01G201500 chr7B 95.429 175 6 2 4301 4475 155387657 155387829 2.100000e-70 278.0
19 TraesCS4B01G201500 chr6B 91.446 643 30 6 3674 4306 119107593 119106966 0.000000e+00 859.0
20 TraesCS4B01G201500 chr1B 77.432 1316 264 28 1135 2436 44072049 44070753 0.000000e+00 754.0
21 TraesCS4B01G201500 chr1B 80.465 215 40 2 1336 1548 371475558 371475772 6.130000e-36 163.0
22 TraesCS4B01G201500 chr1D 77.069 1317 267 30 1135 2436 27900278 27898982 0.000000e+00 726.0
23 TraesCS4B01G201500 chr1A 76.917 1291 265 28 1160 2436 28762227 28760956 0.000000e+00 702.0
24 TraesCS4B01G201500 chr3B 85.831 367 42 8 2074 2436 311115050 311115410 1.550000e-101 381.0
25 TraesCS4B01G201500 chr3B 76.642 411 91 5 1336 1743 769467584 769467992 9.970000e-54 222.0
26 TraesCS4B01G201500 chr3A 83.862 378 48 10 2063 2436 336858505 336858873 1.580000e-91 348.0
27 TraesCS4B01G201500 chr3A 81.633 245 39 4 1239 1483 692344733 692344971 1.680000e-46 198.0
28 TraesCS4B01G201500 chr5B 97.633 169 4 0 4299 4467 701551643 701551811 2.690000e-74 291.0
29 TraesCS4B01G201500 chr2B 98.773 163 2 0 4305 4467 664125038 664125200 2.690000e-74 291.0
30 TraesCS4B01G201500 chr2B 97.561 164 4 0 4305 4468 713695959 713695796 1.620000e-71 281.0
31 TraesCS4B01G201500 chr6D 98.182 165 3 0 4304 4468 24998359 24998195 9.690000e-74 289.0
32 TraesCS4B01G201500 chrUn 94.915 177 8 1 4292 4467 65435274 65435450 7.540000e-70 276.0
33 TraesCS4B01G201500 chr3D 86.638 232 24 5 2197 2426 216472760 216472534 4.570000e-62 250.0
34 TraesCS4B01G201500 chr5D 90.667 75 6 1 1336 1409 88351902 88351828 1.750000e-16 99.0


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 TraesCS4B01G201500 chr4B 431787850 431795482 7632 False 4746.200 14096 100.0000 1 7633 3 chr4B.!!$F1 7632
1 TraesCS4B01G201500 chr4D 349182187 349189713 7526 False 1949.350 6706 95.8285 31 7633 6 chr4D.!!$F1 7602
2 TraesCS4B01G201500 chr4A 115788926 115796345 7419 True 2880.025 6684 95.9945 1 7633 4 chr4A.!!$R1 7632
3 TraesCS4B01G201500 chr6A 222557241 222558382 1141 True 1587.000 1587 91.8760 3166 4306 1 chr6A.!!$R1 1140
4 TraesCS4B01G201500 chr7B 706224762 706225390 628 False 872.000 872 91.7570 3674 4306 1 chr7B.!!$F3 632
5 TraesCS4B01G201500 chr6B 119106966 119107593 627 True 859.000 859 91.4460 3674 4306 1 chr6B.!!$R1 632
6 TraesCS4B01G201500 chr1B 44070753 44072049 1296 True 754.000 754 77.4320 1135 2436 1 chr1B.!!$R1 1301
7 TraesCS4B01G201500 chr1D 27898982 27900278 1296 True 726.000 726 77.0690 1135 2436 1 chr1D.!!$R1 1301
8 TraesCS4B01G201500 chr1A 28760956 28762227 1271 True 702.000 702 76.9170 1160 2436 1 chr1A.!!$R1 1276

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
359 683 0.179187 CTCTCACTGCGTGTAGGTCG 60.179 60.000 8.22 0.00 34.79 4.79 F
963 1305 0.475044 CCCTAGGTAGGAGCGTCTCT 59.525 60.000 8.29 0.00 46.63 3.10 F
2031 2374 1.444895 GGCTGTTGCTGCAATTCCG 60.445 57.895 19.11 8.33 39.59 4.30 F
2313 2656 1.686052 TGGCCAACTTTGAACATGGAC 59.314 47.619 0.61 0.00 41.58 4.02 F
3069 3415 3.070748 CGTGTATTGTCATTGTCCACCA 58.929 45.455 0.00 0.00 0.00 4.17 F
4319 4691 1.639628 TCTTCTACTCCCTCCGTTCCT 59.360 52.381 0.00 0.00 0.00 3.36 F
4369 4741 0.036765 GTGGACCACATACGGAGCAA 60.037 55.000 20.14 0.00 34.08 3.91 F
4370 4742 0.687920 TGGACCACATACGGAGCAAA 59.312 50.000 0.00 0.00 0.00 3.68 F
4371 4743 1.072489 TGGACCACATACGGAGCAAAA 59.928 47.619 0.00 0.00 0.00 2.44 F
5951 6348 1.134007 TCCCAGCATAGCTTCCACATG 60.134 52.381 0.00 0.00 36.40 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2049 2392 1.004628 AGTGCCAAGCATGTGGTGATA 59.995 47.619 4.42 0.00 41.91 2.15 R
2777 3123 2.644676 TCGTTGTTCCACCATTGACAA 58.355 42.857 0.00 0.00 0.00 3.18 R
3389 3737 0.904649 AGAGCACAACGGATCCATCA 59.095 50.000 13.41 0.00 0.00 3.07 R
4101 4454 6.147821 CGACTGATTTAAAGAAGAGAAGGCAA 59.852 38.462 6.87 0.00 0.00 4.52 R
4350 4722 0.036765 TTGCTCCGTATGTGGTCCAC 60.037 55.000 15.64 15.64 34.56 4.02 R
5358 5733 1.603172 GCCGACGTGAGGAATATGGAG 60.603 57.143 10.56 0.00 0.00 3.86 R
5905 6280 2.286833 TCTTTTTCGCAAGTCCTCAACG 59.713 45.455 0.00 0.00 39.48 4.10 R
5924 6301 3.956848 GGAAGCTATGCTGGGAAAAATCT 59.043 43.478 0.00 0.00 39.62 2.40 R
5959 6356 5.774690 ACACAAATCAATAAGGCCAGAAGAA 59.225 36.000 5.01 0.00 0.00 2.52 R
6943 7353 0.396435 ATGTGAACAAGGCCGAGACA 59.604 50.000 0.00 0.00 0.00 3.41 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
162 486 2.762745 GATAAAATTAGGAGGCGCGGA 58.237 47.619 8.83 0.00 0.00 5.54
295 619 0.253327 GGAAAGATTCCTCGCACCCT 59.747 55.000 1.86 0.00 46.57 4.34
354 678 2.646175 GCCCCTCTCACTGCGTGTA 61.646 63.158 8.22 0.00 34.79 2.90
359 683 0.179187 CTCTCACTGCGTGTAGGTCG 60.179 60.000 8.22 0.00 34.79 4.79
406 730 1.451387 GCACATACCGTTGGAGGGG 60.451 63.158 0.00 0.00 35.02 4.79
686 1025 7.308049 GCTCACGAAGATTAATATTTCTTCCCC 60.308 40.741 18.11 2.44 43.12 4.81
707 1046 2.401017 TCGCGATCGATTTGGAGTAG 57.599 50.000 21.57 0.00 40.21 2.57
708 1047 1.674441 TCGCGATCGATTTGGAGTAGT 59.326 47.619 21.57 0.00 40.21 2.73
710 1049 3.059120 TCGCGATCGATTTGGAGTAGTAG 60.059 47.826 21.57 0.00 40.21 2.57
711 1050 3.303857 CGCGATCGATTTGGAGTAGTAGT 60.304 47.826 21.57 0.00 38.10 2.73
713 1052 5.559608 CGCGATCGATTTGGAGTAGTAGTAA 60.560 44.000 21.57 0.00 38.10 2.24
714 1053 5.852229 GCGATCGATTTGGAGTAGTAGTAAG 59.148 44.000 21.57 0.00 0.00 2.34
715 1054 6.293298 GCGATCGATTTGGAGTAGTAGTAAGA 60.293 42.308 21.57 0.00 0.00 2.10
716 1055 7.637229 CGATCGATTTGGAGTAGTAGTAAGAA 58.363 38.462 10.26 0.00 0.00 2.52
717 1056 8.127327 CGATCGATTTGGAGTAGTAGTAAGAAA 58.873 37.037 10.26 0.00 0.00 2.52
718 1057 9.798994 GATCGATTTGGAGTAGTAGTAAGAAAA 57.201 33.333 0.00 0.00 0.00 2.29
963 1305 0.475044 CCCTAGGTAGGAGCGTCTCT 59.525 60.000 8.29 0.00 46.63 3.10
1677 2019 3.766591 ACAAGATTCATCTCGAGGACACT 59.233 43.478 13.56 2.55 35.76 3.55
2031 2374 1.444895 GGCTGTTGCTGCAATTCCG 60.445 57.895 19.11 8.33 39.59 4.30
2049 2392 4.357279 GAGGGCCTGCCTGCTGTT 62.357 66.667 12.95 0.00 36.10 3.16
2313 2656 1.686052 TGGCCAACTTTGAACATGGAC 59.314 47.619 0.61 0.00 41.58 4.02
2436 2779 5.750067 GGCTGCATTAAAGGTATGATTTGTG 59.250 40.000 0.50 0.00 0.00 3.33
2439 2782 7.009540 GCTGCATTAAAGGTATGATTTGTGAAC 59.990 37.037 0.00 0.00 0.00 3.18
2440 2783 7.890515 TGCATTAAAGGTATGATTTGTGAACA 58.109 30.769 0.00 0.00 0.00 3.18
2511 2857 5.335897 GCCAATTCTACACTCTTTGAATGCA 60.336 40.000 0.00 0.00 30.67 3.96
2528 2874 6.094719 TGAATGCATTTTAAGATGACACTGC 58.905 36.000 14.33 0.00 0.00 4.40
2672 3018 6.844696 TCATCCGATTTGCTAAGTATGTTC 57.155 37.500 0.00 0.00 0.00 3.18
2777 3123 5.654650 TGTATCTTTGTTGTTTGAAGGGTGT 59.345 36.000 0.00 0.00 0.00 4.16
3069 3415 3.070748 CGTGTATTGTCATTGTCCACCA 58.929 45.455 0.00 0.00 0.00 4.17
3184 3531 8.721478 TGCATATTTACTTTCTTTCAGTCAGTC 58.279 33.333 0.00 0.00 0.00 3.51
3298 3645 4.371624 TCCAATGTTTCTGGTCATGTCT 57.628 40.909 0.00 0.00 35.30 3.41
3311 3659 4.838423 TGGTCATGTCTTTTCTCTCCTACA 59.162 41.667 0.00 0.00 0.00 2.74
3313 3661 5.872070 GGTCATGTCTTTTCTCTCCTACAAG 59.128 44.000 0.00 0.00 0.00 3.16
3389 3737 5.749462 AGAAGTGCCTATATTCAGTTGCTT 58.251 37.500 0.75 0.00 0.00 3.91
4283 4655 9.199982 CCTTACATATGCAATTGAATCCATTTC 57.800 33.333 10.34 0.00 34.72 2.17
4306 4678 6.609533 TCGTTAGTGTCTGATTGTCTTCTAC 58.390 40.000 0.00 0.00 0.00 2.59
4307 4679 6.430308 TCGTTAGTGTCTGATTGTCTTCTACT 59.570 38.462 0.00 0.00 0.00 2.57
4308 4680 6.743627 CGTTAGTGTCTGATTGTCTTCTACTC 59.256 42.308 0.00 0.00 0.00 2.59
4309 4681 5.652994 AGTGTCTGATTGTCTTCTACTCC 57.347 43.478 0.00 0.00 0.00 3.85
4310 4682 4.464597 AGTGTCTGATTGTCTTCTACTCCC 59.535 45.833 0.00 0.00 0.00 4.30
4311 4683 4.464597 GTGTCTGATTGTCTTCTACTCCCT 59.535 45.833 0.00 0.00 0.00 4.20
4312 4684 4.707448 TGTCTGATTGTCTTCTACTCCCTC 59.293 45.833 0.00 0.00 0.00 4.30
4313 4685 4.098807 GTCTGATTGTCTTCTACTCCCTCC 59.901 50.000 0.00 0.00 0.00 4.30
4314 4686 3.024547 TGATTGTCTTCTACTCCCTCCG 58.975 50.000 0.00 0.00 0.00 4.63
4315 4687 2.599408 TTGTCTTCTACTCCCTCCGT 57.401 50.000 0.00 0.00 0.00 4.69
4316 4688 2.599408 TGTCTTCTACTCCCTCCGTT 57.401 50.000 0.00 0.00 0.00 4.44
4317 4689 2.444421 TGTCTTCTACTCCCTCCGTTC 58.556 52.381 0.00 0.00 0.00 3.95
4318 4690 1.750206 GTCTTCTACTCCCTCCGTTCC 59.250 57.143 0.00 0.00 0.00 3.62
4319 4691 1.639628 TCTTCTACTCCCTCCGTTCCT 59.360 52.381 0.00 0.00 0.00 3.36
4320 4692 2.848694 TCTTCTACTCCCTCCGTTCCTA 59.151 50.000 0.00 0.00 0.00 2.94
4321 4693 3.267812 TCTTCTACTCCCTCCGTTCCTAA 59.732 47.826 0.00 0.00 0.00 2.69
4322 4694 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
4323 4695 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
4324 4696 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
4325 4697 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
4326 4698 7.095183 TCTACTCCCTCCGTTCCTAAATATA 57.905 40.000 0.00 0.00 0.00 0.86
4327 4699 7.529555 TCTACTCCCTCCGTTCCTAAATATAA 58.470 38.462 0.00 0.00 0.00 0.98
4328 4700 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
4329 4701 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
4330 4702 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
4331 4703 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
4332 4704 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
4333 4705 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
4334 4706 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
4335 4707 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
4350 4722 6.783708 AGTCTTTGTAGAGATTCCACTAGG 57.216 41.667 0.00 0.00 0.00 3.02
4351 4723 6.257586 AGTCTTTGTAGAGATTCCACTAGGT 58.742 40.000 0.00 0.00 35.89 3.08
4352 4724 6.153680 AGTCTTTGTAGAGATTCCACTAGGTG 59.846 42.308 0.00 0.00 35.89 4.00
4363 4735 2.579207 CACTAGGTGGACCACATACG 57.421 55.000 25.75 17.52 38.89 3.06
4364 4736 1.136305 CACTAGGTGGACCACATACGG 59.864 57.143 25.75 14.34 38.89 4.02
4365 4737 1.006281 ACTAGGTGGACCACATACGGA 59.994 52.381 25.75 3.07 38.89 4.69
4366 4738 1.681793 CTAGGTGGACCACATACGGAG 59.318 57.143 25.75 9.53 38.89 4.63
4367 4739 1.153429 GGTGGACCACATACGGAGC 60.153 63.158 25.75 2.24 35.86 4.70
4368 4740 1.594833 GTGGACCACATACGGAGCA 59.405 57.895 20.14 0.00 34.08 4.26
4369 4741 0.036765 GTGGACCACATACGGAGCAA 60.037 55.000 20.14 0.00 34.08 3.91
4370 4742 0.687920 TGGACCACATACGGAGCAAA 59.312 50.000 0.00 0.00 0.00 3.68
4371 4743 1.072489 TGGACCACATACGGAGCAAAA 59.928 47.619 0.00 0.00 0.00 2.44
4372 4744 2.290641 TGGACCACATACGGAGCAAAAT 60.291 45.455 0.00 0.00 0.00 1.82
4373 4745 2.097466 GGACCACATACGGAGCAAAATG 59.903 50.000 0.00 0.00 0.00 2.32
4374 4746 3.006940 GACCACATACGGAGCAAAATGA 58.993 45.455 0.00 0.00 0.00 2.57
4375 4747 3.417101 ACCACATACGGAGCAAAATGAA 58.583 40.909 0.00 0.00 0.00 2.57
4376 4748 4.016444 ACCACATACGGAGCAAAATGAAT 58.984 39.130 0.00 0.00 0.00 2.57
4377 4749 4.142403 ACCACATACGGAGCAAAATGAATG 60.142 41.667 0.00 0.00 0.00 2.67
4378 4750 4.096231 CCACATACGGAGCAAAATGAATGA 59.904 41.667 0.00 0.00 0.00 2.57
4379 4751 5.392919 CCACATACGGAGCAAAATGAATGAA 60.393 40.000 0.00 0.00 0.00 2.57
4380 4752 6.267817 CACATACGGAGCAAAATGAATGAAT 58.732 36.000 0.00 0.00 0.00 2.57
4381 4753 6.415867 CACATACGGAGCAAAATGAATGAATC 59.584 38.462 0.00 0.00 0.00 2.52
4382 4754 6.319658 ACATACGGAGCAAAATGAATGAATCT 59.680 34.615 0.00 0.00 0.00 2.40
4383 4755 7.498900 ACATACGGAGCAAAATGAATGAATCTA 59.501 33.333 0.00 0.00 0.00 1.98
4384 4756 6.757897 ACGGAGCAAAATGAATGAATCTAA 57.242 33.333 0.00 0.00 0.00 2.10
4385 4757 7.156876 ACGGAGCAAAATGAATGAATCTAAA 57.843 32.000 0.00 0.00 0.00 1.85
4386 4758 7.029563 ACGGAGCAAAATGAATGAATCTAAAC 58.970 34.615 0.00 0.00 0.00 2.01
4387 4759 7.094205 ACGGAGCAAAATGAATGAATCTAAACT 60.094 33.333 0.00 0.00 0.00 2.66
4388 4760 7.756722 CGGAGCAAAATGAATGAATCTAAACTT 59.243 33.333 0.00 0.00 0.00 2.66
4411 4783 9.944376 ACTTAAAATGCATCTATATACATCCGT 57.056 29.630 0.00 0.00 0.00 4.69
4415 4787 7.953158 AATGCATCTATATACATCCGTATGC 57.047 36.000 0.00 0.00 38.79 3.14
4416 4788 5.519722 TGCATCTATATACATCCGTATGCG 58.480 41.667 0.00 0.00 38.79 4.73
4432 4804 6.764877 CGTATGCGGTTTATAGTGAAATCT 57.235 37.500 0.00 0.00 0.00 2.40
4433 4805 6.808264 CGTATGCGGTTTATAGTGAAATCTC 58.192 40.000 0.00 0.00 0.00 2.75
4434 4806 6.641314 CGTATGCGGTTTATAGTGAAATCTCT 59.359 38.462 0.00 0.00 0.00 3.10
4435 4807 7.806487 CGTATGCGGTTTATAGTGAAATCTCTA 59.194 37.037 0.00 0.00 0.00 2.43
4436 4808 7.948278 ATGCGGTTTATAGTGAAATCTCTAC 57.052 36.000 0.00 0.00 0.00 2.59
4437 4809 6.869695 TGCGGTTTATAGTGAAATCTCTACA 58.130 36.000 0.00 0.00 0.00 2.74
4438 4810 7.324935 TGCGGTTTATAGTGAAATCTCTACAA 58.675 34.615 0.00 0.00 0.00 2.41
4439 4811 7.820386 TGCGGTTTATAGTGAAATCTCTACAAA 59.180 33.333 0.00 0.00 0.00 2.83
4440 4812 8.328864 GCGGTTTATAGTGAAATCTCTACAAAG 58.671 37.037 0.00 0.00 0.00 2.77
4441 4813 9.582431 CGGTTTATAGTGAAATCTCTACAAAGA 57.418 33.333 0.00 0.00 0.00 2.52
4456 4828 9.924650 TCTCTACAAAGACTTACATTTAGGAAC 57.075 33.333 0.00 0.00 0.00 3.62
4457 4829 8.752766 TCTACAAAGACTTACATTTAGGAACG 57.247 34.615 0.00 0.00 0.00 3.95
4458 4830 6.796705 ACAAAGACTTACATTTAGGAACGG 57.203 37.500 0.00 0.00 0.00 4.44
4459 4831 6.527423 ACAAAGACTTACATTTAGGAACGGA 58.473 36.000 0.00 0.00 0.00 4.69
4460 4832 6.649557 ACAAAGACTTACATTTAGGAACGGAG 59.350 38.462 0.00 0.00 0.00 4.63
4461 4833 5.340439 AGACTTACATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
4462 4834 4.161754 AGACTTACATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
4463 4835 4.098894 ACTTACATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
4464 4836 4.161754 ACTTACATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
4465 4837 2.547990 ACATTTAGGAACGGAGGGAGT 58.452 47.619 0.00 0.00 0.00 3.85
4466 4838 3.716431 ACATTTAGGAACGGAGGGAGTA 58.284 45.455 0.00 0.00 0.00 2.59
4610 4982 4.226168 AGGCTACTTTCCTGCTGAATAGTT 59.774 41.667 0.00 0.00 31.67 2.24
4691 5064 6.534475 TGCCTTCATTAGATTTTCATTGCT 57.466 33.333 0.00 0.00 0.00 3.91
4791 5165 2.508716 ACTCATGATGGCCTTCTGTGAT 59.491 45.455 18.67 2.14 0.00 3.06
4792 5166 3.139850 CTCATGATGGCCTTCTGTGATC 58.860 50.000 18.67 5.20 0.00 2.92
4793 5167 2.506644 TCATGATGGCCTTCTGTGATCA 59.493 45.455 18.67 10.73 0.00 2.92
4794 5168 3.054213 TCATGATGGCCTTCTGTGATCAA 60.054 43.478 18.67 0.00 0.00 2.57
4795 5169 3.438216 TGATGGCCTTCTGTGATCAAA 57.562 42.857 18.67 0.00 0.00 2.69
4796 5170 3.972133 TGATGGCCTTCTGTGATCAAAT 58.028 40.909 18.67 0.00 0.00 2.32
4797 5171 5.114764 TGATGGCCTTCTGTGATCAAATA 57.885 39.130 18.67 0.00 0.00 1.40
4798 5172 5.508567 TGATGGCCTTCTGTGATCAAATAA 58.491 37.500 18.67 0.00 0.00 1.40
4799 5173 6.131264 TGATGGCCTTCTGTGATCAAATAAT 58.869 36.000 18.67 0.00 0.00 1.28
4800 5174 5.840243 TGGCCTTCTGTGATCAAATAATG 57.160 39.130 3.32 0.00 0.00 1.90
4801 5175 4.098349 TGGCCTTCTGTGATCAAATAATGC 59.902 41.667 3.32 0.00 0.00 3.56
4802 5176 4.098349 GGCCTTCTGTGATCAAATAATGCA 59.902 41.667 11.58 0.00 0.00 3.96
4803 5177 5.221382 GGCCTTCTGTGATCAAATAATGCAT 60.221 40.000 11.58 0.00 0.00 3.96
4804 5178 5.690409 GCCTTCTGTGATCAAATAATGCATG 59.310 40.000 0.00 0.00 0.00 4.06
4805 5179 5.690409 CCTTCTGTGATCAAATAATGCATGC 59.310 40.000 11.82 11.82 0.00 4.06
4806 5180 6.459670 TTCTGTGATCAAATAATGCATGCT 57.540 33.333 20.33 1.26 0.00 3.79
4807 5181 7.255346 CCTTCTGTGATCAAATAATGCATGCTA 60.255 37.037 20.33 3.94 0.00 3.49
4808 5182 7.754851 TCTGTGATCAAATAATGCATGCTAT 57.245 32.000 20.33 10.10 0.00 2.97
4809 5183 7.590279 TCTGTGATCAAATAATGCATGCTATG 58.410 34.615 20.33 8.66 0.00 2.23
4810 5184 7.229907 TCTGTGATCAAATAATGCATGCTATGT 59.770 33.333 20.33 1.24 0.00 2.29
4811 5185 7.718525 TGTGATCAAATAATGCATGCTATGTT 58.281 30.769 20.33 9.18 0.00 2.71
4812 5186 8.198778 TGTGATCAAATAATGCATGCTATGTTT 58.801 29.630 20.33 14.43 0.00 2.83
4813 5187 8.484799 GTGATCAAATAATGCATGCTATGTTTG 58.515 33.333 25.13 25.13 0.00 2.93
4814 5188 8.198778 TGATCAAATAATGCATGCTATGTTTGT 58.801 29.630 27.36 20.44 0.00 2.83
4815 5189 8.951787 ATCAAATAATGCATGCTATGTTTGTT 57.048 26.923 27.36 21.82 0.00 2.83
4817 5191 9.866798 TCAAATAATGCATGCTATGTTTGTTAA 57.133 25.926 27.36 16.15 0.00 2.01
4823 5197 7.754069 TGCATGCTATGTTTGTTAAATAAGC 57.246 32.000 20.33 0.00 0.00 3.09
4824 5198 6.756074 TGCATGCTATGTTTGTTAAATAAGCC 59.244 34.615 20.33 0.00 0.00 4.35
4825 5199 6.980397 GCATGCTATGTTTGTTAAATAAGCCT 59.020 34.615 11.37 0.00 0.00 4.58
4826 5200 7.492344 GCATGCTATGTTTGTTAAATAAGCCTT 59.508 33.333 11.37 0.00 0.00 4.35
4827 5201 9.023967 CATGCTATGTTTGTTAAATAAGCCTTC 57.976 33.333 0.00 0.00 0.00 3.46
4828 5202 8.348285 TGCTATGTTTGTTAAATAAGCCTTCT 57.652 30.769 0.00 0.00 0.00 2.85
4829 5203 8.243426 TGCTATGTTTGTTAAATAAGCCTTCTG 58.757 33.333 0.00 0.00 0.00 3.02
4830 5204 8.244113 GCTATGTTTGTTAAATAAGCCTTCTGT 58.756 33.333 0.00 0.00 0.00 3.41
4831 5205 9.559958 CTATGTTTGTTAAATAAGCCTTCTGTG 57.440 33.333 0.00 0.00 0.00 3.66
4832 5206 7.575414 TGTTTGTTAAATAAGCCTTCTGTGA 57.425 32.000 0.00 0.00 0.00 3.58
5280 5655 9.522804 TTTCGTTTGCTAATTACTTGAAACATT 57.477 25.926 0.00 0.00 0.00 2.71
5358 5733 2.151202 TCGAACATTGGAGAAGTTGCC 58.849 47.619 0.00 0.00 0.00 4.52
5493 5868 7.631510 TCCACCAGATAAGGATATCATGAAA 57.368 36.000 0.00 0.00 40.41 2.69
5594 5969 3.617531 CGTGCACTTCCTCAAGTATCCTT 60.618 47.826 16.19 0.00 41.24 3.36
5600 5975 6.481644 GCACTTCCTCAAGTATCCTTATCTTG 59.518 42.308 0.00 0.00 41.24 3.02
5803 6178 4.096681 TCAACTGGGAGATGCTTCTCTAA 58.903 43.478 24.20 14.22 46.46 2.10
5816 6191 5.674525 TGCTTCTCTAAAGTGTCCCATATG 58.325 41.667 0.00 0.00 0.00 1.78
5818 6193 5.755861 GCTTCTCTAAAGTGTCCCATATGTC 59.244 44.000 1.24 0.00 0.00 3.06
5820 6195 7.496346 TTCTCTAAAGTGTCCCATATGTCTT 57.504 36.000 1.24 0.00 0.00 3.01
5821 6196 7.113658 TCTCTAAAGTGTCCCATATGTCTTC 57.886 40.000 1.24 0.00 0.00 2.87
5823 6198 8.059461 TCTCTAAAGTGTCCCATATGTCTTCTA 58.941 37.037 1.24 0.00 0.00 2.10
5824 6199 8.008513 TCTAAAGTGTCCCATATGTCTTCTAC 57.991 38.462 1.24 0.00 0.00 2.59
5825 6200 6.875972 AAAGTGTCCCATATGTCTTCTACT 57.124 37.500 1.24 0.00 0.00 2.57
5826 6201 6.472686 AAGTGTCCCATATGTCTTCTACTC 57.527 41.667 1.24 0.00 0.00 2.59
5827 6202 4.896482 AGTGTCCCATATGTCTTCTACTCC 59.104 45.833 1.24 0.00 0.00 3.85
5834 6209 7.671819 TCCCATATGTCTTCTACTCCTATCTTG 59.328 40.741 1.24 0.00 0.00 3.02
5839 6214 5.658634 TGTCTTCTACTCCTATCTTGCATGT 59.341 40.000 0.00 0.00 0.00 3.21
5840 6215 6.833933 TGTCTTCTACTCCTATCTTGCATGTA 59.166 38.462 0.00 0.00 0.00 2.29
5841 6216 7.013750 TGTCTTCTACTCCTATCTTGCATGTAG 59.986 40.741 0.00 0.00 0.00 2.74
5849 6224 6.711277 TCCTATCTTGCATGTAGAAACTGTT 58.289 36.000 0.00 0.00 0.00 3.16
5878 6253 9.693739 TTCTCATAAGATCTTCAGTCTTACTCT 57.306 33.333 12.24 0.00 40.03 3.24
5906 6281 8.937634 AGGTCCAATAGTAATAAAGTTGTACG 57.062 34.615 0.00 0.00 0.00 3.67
5917 6294 6.780706 ATAAAGTTGTACGTTGAGGACTTG 57.219 37.500 0.00 0.00 33.83 3.16
5924 6301 2.011222 ACGTTGAGGACTTGCGAAAAA 58.989 42.857 0.00 0.00 0.00 1.94
5951 6348 1.134007 TCCCAGCATAGCTTCCACATG 60.134 52.381 0.00 0.00 36.40 3.21
5959 6356 4.763793 GCATAGCTTCCACATGATTATGGT 59.236 41.667 0.00 0.00 38.66 3.55
6019 6425 8.931385 AATATTAATTTATGAATGGATGCCGC 57.069 30.769 0.00 0.00 0.00 6.53
6037 6443 4.457603 TGCCGCTGTACTTATGTTTGAAAT 59.542 37.500 0.00 0.00 0.00 2.17
6092 6498 1.467678 TTGGGATTGCAACGGTTGGG 61.468 55.000 21.37 0.00 0.00 4.12
6431 6837 2.935238 GCTTCTTCTGGCAATGTCGGTA 60.935 50.000 0.00 0.00 0.00 4.02
6575 6981 4.685924 TCGACGAGGTTCTTAAGTTTGTT 58.314 39.130 1.63 0.00 0.00 2.83
6614 7020 1.114627 GGGCCAGAAAGCAATTAGGG 58.885 55.000 4.39 0.00 0.00 3.53
6672 7078 1.615424 ATTGCCACGGGGGAGTAGT 60.615 57.895 5.47 0.00 40.01 2.73
6682 7088 1.321074 GGGGAGTAGTCGTCTGGTGG 61.321 65.000 0.00 0.00 0.00 4.61
6701 7107 4.965283 TGGGACCCCATTATTTTTCTCT 57.035 40.909 8.45 0.00 41.89 3.10
6712 7121 2.951229 TTTTTCTCTTCCGAGGGCTT 57.049 45.000 0.00 0.00 37.86 4.35
6865 7274 1.142870 TCTTGCCCACTTACTGCAGTT 59.857 47.619 27.06 3.70 36.21 3.16
6869 7278 2.571653 TGCCCACTTACTGCAGTTATCT 59.428 45.455 27.06 0.99 0.00 1.98
6878 7288 8.436200 CACTTACTGCAGTTATCTTTCACTTAC 58.564 37.037 27.06 0.00 0.00 2.34
6907 7317 6.762702 TGAATTATTCTGCTCTGAATGCAA 57.237 33.333 6.50 1.45 40.13 4.08
6908 7318 7.342769 TGAATTATTCTGCTCTGAATGCAAT 57.657 32.000 6.50 0.00 40.13 3.56
6909 7319 7.200455 TGAATTATTCTGCTCTGAATGCAATG 58.800 34.615 6.50 0.00 40.13 2.82
6910 7320 6.954487 ATTATTCTGCTCTGAATGCAATGA 57.046 33.333 10.87 0.00 40.13 2.57
6911 7321 4.634184 ATTCTGCTCTGAATGCAATGAC 57.366 40.909 0.00 0.00 40.13 3.06
6912 7322 2.004733 TCTGCTCTGAATGCAATGACG 58.995 47.619 0.00 0.00 40.13 4.35
6913 7323 1.736126 CTGCTCTGAATGCAATGACGT 59.264 47.619 0.00 0.00 40.13 4.34
6914 7324 1.465777 TGCTCTGAATGCAATGACGTG 59.534 47.619 0.00 0.00 37.51 4.49
6915 7325 1.733912 GCTCTGAATGCAATGACGTGA 59.266 47.619 0.00 0.00 0.00 4.35
6916 7326 2.475187 GCTCTGAATGCAATGACGTGAC 60.475 50.000 0.00 0.00 0.00 3.67
6976 7386 3.371898 TGTTCACATAGCGATTCTGCTTG 59.628 43.478 8.00 8.63 44.46 4.01
6999 7409 2.703007 ACTCATCCTGGAGTATTGAGCC 59.297 50.000 19.91 0.00 45.95 4.70
7000 7410 1.688735 TCATCCTGGAGTATTGAGCCG 59.311 52.381 1.52 0.00 0.00 5.52
7001 7411 0.394565 ATCCTGGAGTATTGAGCCGC 59.605 55.000 1.52 0.00 0.00 6.53
7002 7412 0.687757 TCCTGGAGTATTGAGCCGCT 60.688 55.000 0.00 0.00 0.00 5.52
7003 7413 0.531532 CCTGGAGTATTGAGCCGCTG 60.532 60.000 0.00 0.00 0.00 5.18
7004 7414 0.461548 CTGGAGTATTGAGCCGCTGA 59.538 55.000 0.00 0.00 0.00 4.26
7005 7415 0.461548 TGGAGTATTGAGCCGCTGAG 59.538 55.000 0.00 0.00 0.00 3.35
7006 7416 0.878086 GGAGTATTGAGCCGCTGAGC 60.878 60.000 0.00 0.00 0.00 4.26
7007 7417 0.878086 GAGTATTGAGCCGCTGAGCC 60.878 60.000 0.00 0.00 0.00 4.70
7008 7418 1.144936 GTATTGAGCCGCTGAGCCT 59.855 57.895 0.00 0.00 0.00 4.58
7009 7419 0.878086 GTATTGAGCCGCTGAGCCTC 60.878 60.000 0.00 0.83 0.00 4.70
7010 7420 1.045350 TATTGAGCCGCTGAGCCTCT 61.045 55.000 11.13 2.90 0.00 3.69
7011 7421 2.308968 ATTGAGCCGCTGAGCCTCTC 62.309 60.000 11.13 11.58 0.00 3.20
7012 7422 3.146913 GAGCCGCTGAGCCTCTCT 61.147 66.667 11.75 0.00 0.00 3.10
7013 7423 3.429080 GAGCCGCTGAGCCTCTCTG 62.429 68.421 11.75 0.00 33.52 3.35
7034 7444 5.064441 TGTCTCTGCCGATCATATACATG 57.936 43.478 0.00 0.00 0.00 3.21
7036 7446 5.710099 TGTCTCTGCCGATCATATACATGTA 59.290 40.000 8.27 8.27 33.57 2.29
7037 7447 6.030849 GTCTCTGCCGATCATATACATGTAC 58.969 44.000 7.96 0.00 33.57 2.90
7038 7448 5.946377 TCTCTGCCGATCATATACATGTACT 59.054 40.000 7.96 0.57 33.57 2.73
7039 7449 7.065923 GTCTCTGCCGATCATATACATGTACTA 59.934 40.741 7.96 2.87 33.57 1.82
7040 7450 7.281100 TCTCTGCCGATCATATACATGTACTAG 59.719 40.741 7.96 0.84 33.57 2.57
7041 7451 6.884836 TCTGCCGATCATATACATGTACTAGT 59.115 38.462 7.96 0.00 33.57 2.57
7042 7452 8.044908 TCTGCCGATCATATACATGTACTAGTA 58.955 37.037 7.96 0.00 33.57 1.82
7082 7492 6.564709 TTGTGAAATCAGGAGAATCTGTTG 57.435 37.500 0.00 0.00 36.25 3.33
7097 7507 5.700402 ATCTGTTGCTCCTTATTGGTACT 57.300 39.130 0.00 0.00 37.07 2.73
7165 7577 8.931775 TGTACATTGTTTGTCATGTACTACATC 58.068 33.333 18.49 0.00 45.58 3.06
7264 7679 2.788233 CTCGTCGCTCTTGATCATCTTG 59.212 50.000 0.00 0.00 0.00 3.02
7366 7784 1.517257 CAGGCTACGCTGAACCTCG 60.517 63.158 0.00 0.00 0.00 4.63
7406 7830 2.677003 GGCGTCAACATGGTGTCGG 61.677 63.158 27.20 12.14 31.89 4.79
7462 7886 3.112709 GCGAACTCGAGGCACCAC 61.113 66.667 18.41 0.00 43.02 4.16
7513 7937 1.805945 GTACTCGGCGAGGCACTTG 60.806 63.158 36.81 14.76 41.55 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 129 4.617762 GCAAAAGAGGAATTCTGGAAGCTG 60.618 45.833 5.23 0.00 35.91 4.24
136 186 3.075148 GCCTCCTAATTTTATCGGGCTC 58.925 50.000 0.00 0.00 35.92 4.70
150 474 1.822613 CTGTACTCCGCGCCTCCTA 60.823 63.158 0.00 0.00 0.00 2.94
326 650 4.400961 AGAGGGGCGTGCTGCTTC 62.401 66.667 0.00 0.00 45.43 3.86
516 840 2.946564 TCGATGATGATATGTGGCGAC 58.053 47.619 0.00 0.00 0.00 5.19
586 911 4.884257 CGCGTATGGGGTGGGACG 62.884 72.222 0.00 0.00 38.32 4.79
710 1049 9.615295 TTCTTTATGGCGTAAACATTTTCTTAC 57.385 29.630 7.80 0.00 0.00 2.34
713 1052 9.191995 CTTTTCTTTATGGCGTAAACATTTTCT 57.808 29.630 7.80 0.00 0.00 2.52
714 1053 7.949962 GCTTTTCTTTATGGCGTAAACATTTTC 59.050 33.333 7.80 0.00 0.00 2.29
715 1054 7.358848 CGCTTTTCTTTATGGCGTAAACATTTT 60.359 33.333 7.80 0.00 40.78 1.82
716 1055 6.088883 CGCTTTTCTTTATGGCGTAAACATTT 59.911 34.615 7.80 0.00 40.78 2.32
717 1056 5.571357 CGCTTTTCTTTATGGCGTAAACATT 59.429 36.000 7.80 0.00 40.78 2.71
718 1057 5.092781 CGCTTTTCTTTATGGCGTAAACAT 58.907 37.500 7.80 0.00 40.78 2.71
719 1058 4.468643 CGCTTTTCTTTATGGCGTAAACA 58.531 39.130 7.80 0.00 40.78 2.83
1677 2019 1.770658 CACTCCTTGCCCTGGATATCA 59.229 52.381 4.83 0.00 32.56 2.15
2049 2392 1.004628 AGTGCCAAGCATGTGGTGATA 59.995 47.619 4.42 0.00 41.91 2.15
2313 2656 2.733552 CGCAATCATCTGGAGGTTATCG 59.266 50.000 0.00 0.00 0.00 2.92
2511 2857 8.814038 AAATAGAGGCAGTGTCATCTTAAAAT 57.186 30.769 0.00 0.00 0.00 1.82
2749 3095 7.763985 ACCCTTCAAACAACAAAGATACAAAAG 59.236 33.333 0.00 0.00 0.00 2.27
2777 3123 2.644676 TCGTTGTTCCACCATTGACAA 58.355 42.857 0.00 0.00 0.00 3.18
3004 3350 7.907214 ACGAAGAATAAAATGTGAGTAAGCT 57.093 32.000 0.00 0.00 0.00 3.74
3184 3531 6.146184 CCACATTGTAGCTGAATCTATAACCG 59.854 42.308 0.00 0.00 0.00 4.44
3313 3661 9.983804 GCAAGAGTACACTTTTACCATAAATAC 57.016 33.333 2.49 0.00 0.00 1.89
3389 3737 0.904649 AGAGCACAACGGATCCATCA 59.095 50.000 13.41 0.00 0.00 3.07
4101 4454 6.147821 CGACTGATTTAAAGAAGAGAAGGCAA 59.852 38.462 6.87 0.00 0.00 4.52
4156 4516 6.737254 AACAATGAACTACACGAAATAGGG 57.263 37.500 0.00 0.00 0.00 3.53
4283 4655 6.613233 AGTAGAAGACAATCAGACACTAACG 58.387 40.000 0.00 0.00 0.00 3.18
4306 4678 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
4307 4679 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
4308 4680 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
4309 4681 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
4310 4682 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
4324 4696 8.919145 CCTAGTGGAATCTCTACAAAGACTTAT 58.081 37.037 0.00 0.00 34.57 1.73
4325 4697 7.894364 ACCTAGTGGAATCTCTACAAAGACTTA 59.106 37.037 0.00 0.00 37.04 2.24
4326 4698 6.726764 ACCTAGTGGAATCTCTACAAAGACTT 59.273 38.462 0.00 0.00 37.04 3.01
4327 4699 6.153680 CACCTAGTGGAATCTCTACAAAGACT 59.846 42.308 0.00 0.00 37.04 3.24
4328 4700 6.334202 CACCTAGTGGAATCTCTACAAAGAC 58.666 44.000 0.00 0.00 37.04 3.01
4329 4701 6.531503 CACCTAGTGGAATCTCTACAAAGA 57.468 41.667 0.00 0.00 37.04 2.52
4344 4716 1.136305 CCGTATGTGGTCCACCTAGTG 59.864 57.143 19.57 9.04 36.82 2.74
4345 4717 1.006281 TCCGTATGTGGTCCACCTAGT 59.994 52.381 19.57 5.65 36.82 2.57
4346 4718 1.681793 CTCCGTATGTGGTCCACCTAG 59.318 57.143 19.57 8.03 36.82 3.02
4347 4719 1.771565 CTCCGTATGTGGTCCACCTA 58.228 55.000 19.57 11.14 36.82 3.08
4348 4720 1.614241 GCTCCGTATGTGGTCCACCT 61.614 60.000 19.57 12.22 36.82 4.00
4349 4721 1.153429 GCTCCGTATGTGGTCCACC 60.153 63.158 19.57 3.13 32.73 4.61
4350 4722 0.036765 TTGCTCCGTATGTGGTCCAC 60.037 55.000 15.64 15.64 34.56 4.02
4351 4723 0.687920 TTTGCTCCGTATGTGGTCCA 59.312 50.000 0.00 0.00 0.00 4.02
4352 4724 1.816074 TTTTGCTCCGTATGTGGTCC 58.184 50.000 0.00 0.00 0.00 4.46
4353 4725 3.006940 TCATTTTGCTCCGTATGTGGTC 58.993 45.455 0.00 0.00 0.00 4.02
4354 4726 3.066291 TCATTTTGCTCCGTATGTGGT 57.934 42.857 0.00 0.00 0.00 4.16
4355 4727 4.096231 TCATTCATTTTGCTCCGTATGTGG 59.904 41.667 0.00 0.00 0.00 4.17
4356 4728 5.233957 TCATTCATTTTGCTCCGTATGTG 57.766 39.130 0.00 0.00 0.00 3.21
4357 4729 5.895636 TTCATTCATTTTGCTCCGTATGT 57.104 34.783 0.00 0.00 0.00 2.29
4358 4730 6.732154 AGATTCATTCATTTTGCTCCGTATG 58.268 36.000 0.00 0.00 0.00 2.39
4359 4731 6.949352 AGATTCATTCATTTTGCTCCGTAT 57.051 33.333 0.00 0.00 0.00 3.06
4360 4732 7.857734 TTAGATTCATTCATTTTGCTCCGTA 57.142 32.000 0.00 0.00 0.00 4.02
4361 4733 6.757897 TTAGATTCATTCATTTTGCTCCGT 57.242 33.333 0.00 0.00 0.00 4.69
4362 4734 7.253422 AGTTTAGATTCATTCATTTTGCTCCG 58.747 34.615 0.00 0.00 0.00 4.63
4363 4735 8.992835 AAGTTTAGATTCATTCATTTTGCTCC 57.007 30.769 0.00 0.00 0.00 4.70
4385 4757 9.944376 ACGGATGTATATAGATGCATTTTAAGT 57.056 29.630 11.19 0.00 38.38 2.24
4389 4761 8.830580 GCATACGGATGTATATAGATGCATTTT 58.169 33.333 9.90 0.00 38.38 1.82
4390 4762 7.169813 CGCATACGGATGTATATAGATGCATTT 59.830 37.037 9.90 0.00 38.38 2.32
4391 4763 6.642540 CGCATACGGATGTATATAGATGCATT 59.357 38.462 9.90 1.23 38.38 3.56
4392 4764 6.152379 CGCATACGGATGTATATAGATGCAT 58.848 40.000 9.90 0.00 40.68 3.96
4393 4765 5.519722 CGCATACGGATGTATATAGATGCA 58.480 41.667 9.90 0.00 39.28 3.96
4409 4781 6.641314 AGAGATTTCACTATAAACCGCATACG 59.359 38.462 0.00 0.00 39.67 3.06
4410 4782 7.948278 AGAGATTTCACTATAAACCGCATAC 57.052 36.000 0.00 0.00 0.00 2.39
4411 4783 8.635328 TGTAGAGATTTCACTATAAACCGCATA 58.365 33.333 0.00 0.00 0.00 3.14
4412 4784 7.497595 TGTAGAGATTTCACTATAAACCGCAT 58.502 34.615 0.00 0.00 0.00 4.73
4413 4785 6.869695 TGTAGAGATTTCACTATAAACCGCA 58.130 36.000 0.00 0.00 0.00 5.69
4414 4786 7.766219 TTGTAGAGATTTCACTATAAACCGC 57.234 36.000 0.00 0.00 0.00 5.68
4415 4787 9.582431 TCTTTGTAGAGATTTCACTATAAACCG 57.418 33.333 3.91 0.00 31.22 4.44
4430 4802 9.924650 GTTCCTAAATGTAAGTCTTTGTAGAGA 57.075 33.333 0.00 0.00 0.00 3.10
4431 4803 8.861101 CGTTCCTAAATGTAAGTCTTTGTAGAG 58.139 37.037 0.00 0.00 0.00 2.43
4432 4804 7.816031 CCGTTCCTAAATGTAAGTCTTTGTAGA 59.184 37.037 0.00 0.00 0.00 2.59
4433 4805 7.816031 TCCGTTCCTAAATGTAAGTCTTTGTAG 59.184 37.037 0.00 0.00 0.00 2.74
4434 4806 7.669427 TCCGTTCCTAAATGTAAGTCTTTGTA 58.331 34.615 0.00 0.00 0.00 2.41
4435 4807 6.527423 TCCGTTCCTAAATGTAAGTCTTTGT 58.473 36.000 0.00 0.00 0.00 2.83
4436 4808 6.092259 CCTCCGTTCCTAAATGTAAGTCTTTG 59.908 42.308 0.00 0.00 0.00 2.77
4437 4809 6.171213 CCTCCGTTCCTAAATGTAAGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
4438 4810 5.338137 CCCTCCGTTCCTAAATGTAAGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
4439 4811 4.161754 CCCTCCGTTCCTAAATGTAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
4440 4812 4.161001 TCCCTCCGTTCCTAAATGTAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
4441 4813 4.098894 TCCCTCCGTTCCTAAATGTAAGT 58.901 43.478 0.00 0.00 0.00 2.24
4442 4814 4.161754 ACTCCCTCCGTTCCTAAATGTAAG 59.838 45.833 0.00 0.00 0.00 2.34
4443 4815 4.098894 ACTCCCTCCGTTCCTAAATGTAA 58.901 43.478 0.00 0.00 0.00 2.41
4444 4816 3.716431 ACTCCCTCCGTTCCTAAATGTA 58.284 45.455 0.00 0.00 0.00 2.29
4445 4817 2.547990 ACTCCCTCCGTTCCTAAATGT 58.452 47.619 0.00 0.00 0.00 2.71
4446 4818 4.344102 TGATACTCCCTCCGTTCCTAAATG 59.656 45.833 0.00 0.00 0.00 2.32
4447 4819 4.344390 GTGATACTCCCTCCGTTCCTAAAT 59.656 45.833 0.00 0.00 0.00 1.40
4448 4820 3.703052 GTGATACTCCCTCCGTTCCTAAA 59.297 47.826 0.00 0.00 0.00 1.85
4449 4821 3.053095 AGTGATACTCCCTCCGTTCCTAA 60.053 47.826 0.00 0.00 0.00 2.69
4450 4822 2.512896 AGTGATACTCCCTCCGTTCCTA 59.487 50.000 0.00 0.00 0.00 2.94
4451 4823 1.288335 AGTGATACTCCCTCCGTTCCT 59.712 52.381 0.00 0.00 0.00 3.36
4452 4824 1.777941 AGTGATACTCCCTCCGTTCC 58.222 55.000 0.00 0.00 0.00 3.62
4453 4825 4.202131 CCTTAAGTGATACTCCCTCCGTTC 60.202 50.000 0.97 0.00 0.00 3.95
4454 4826 3.705072 CCTTAAGTGATACTCCCTCCGTT 59.295 47.826 0.97 0.00 0.00 4.44
4455 4827 3.297736 CCTTAAGTGATACTCCCTCCGT 58.702 50.000 0.97 0.00 0.00 4.69
4456 4828 3.297736 ACCTTAAGTGATACTCCCTCCG 58.702 50.000 0.97 0.00 0.00 4.63
4457 4829 6.863210 AAGCACCTTAAGTGATACTCCCTCC 61.863 48.000 0.97 0.00 46.71 4.30
4458 4830 4.162509 AAGCACCTTAAGTGATACTCCCTC 59.837 45.833 0.97 0.00 46.71 4.30
4459 4831 4.104831 AAGCACCTTAAGTGATACTCCCT 58.895 43.478 0.97 0.00 46.71 4.20
4460 4832 4.162509 AGAAGCACCTTAAGTGATACTCCC 59.837 45.833 0.97 0.00 46.71 4.30
4461 4833 5.346181 AGAAGCACCTTAAGTGATACTCC 57.654 43.478 0.97 0.00 46.71 3.85
4462 4834 7.102847 AGTAGAAGCACCTTAAGTGATACTC 57.897 40.000 0.97 0.00 46.71 2.59
4463 4835 7.324178 CAAGTAGAAGCACCTTAAGTGATACT 58.676 38.462 0.97 4.96 46.71 2.12
4464 4836 6.036191 GCAAGTAGAAGCACCTTAAGTGATAC 59.964 42.308 0.97 3.20 46.71 2.24
4465 4837 6.106673 GCAAGTAGAAGCACCTTAAGTGATA 58.893 40.000 0.97 0.00 46.71 2.15
4610 4982 7.093945 TGTGTATCTTGAGTGTTACTAGCATCA 60.094 37.037 0.00 0.00 0.00 3.07
4791 5165 9.866798 TTAACAAACATAGCATGCATTATTTGA 57.133 25.926 28.90 14.79 31.76 2.69
4797 5171 8.819974 GCTTATTTAACAAACATAGCATGCATT 58.180 29.630 21.98 3.12 0.00 3.56
4798 5172 7.439056 GGCTTATTTAACAAACATAGCATGCAT 59.561 33.333 21.98 8.63 0.00 3.96
4799 5173 6.756074 GGCTTATTTAACAAACATAGCATGCA 59.244 34.615 21.98 6.36 0.00 3.96
4800 5174 6.980397 AGGCTTATTTAACAAACATAGCATGC 59.020 34.615 10.51 10.51 0.00 4.06
4801 5175 8.931385 AAGGCTTATTTAACAAACATAGCATG 57.069 30.769 0.00 0.00 0.00 4.06
4802 5176 8.971073 AGAAGGCTTATTTAACAAACATAGCAT 58.029 29.630 0.00 0.00 0.00 3.79
4803 5177 8.243426 CAGAAGGCTTATTTAACAAACATAGCA 58.757 33.333 0.00 0.00 0.00 3.49
4804 5178 8.244113 ACAGAAGGCTTATTTAACAAACATAGC 58.756 33.333 0.00 0.00 0.00 2.97
4805 5179 9.559958 CACAGAAGGCTTATTTAACAAACATAG 57.440 33.333 0.00 0.00 0.00 2.23
4806 5180 9.290988 TCACAGAAGGCTTATTTAACAAACATA 57.709 29.630 0.00 0.00 0.00 2.29
4807 5181 8.177119 TCACAGAAGGCTTATTTAACAAACAT 57.823 30.769 0.00 0.00 0.00 2.71
4808 5182 7.575414 TCACAGAAGGCTTATTTAACAAACA 57.425 32.000 0.00 0.00 0.00 2.83
4809 5183 8.296713 TGATCACAGAAGGCTTATTTAACAAAC 58.703 33.333 0.00 0.00 0.00 2.93
4810 5184 8.402798 TGATCACAGAAGGCTTATTTAACAAA 57.597 30.769 0.00 0.00 0.00 2.83
4811 5185 7.994425 TGATCACAGAAGGCTTATTTAACAA 57.006 32.000 0.00 0.00 0.00 2.83
4812 5186 7.994425 TTGATCACAGAAGGCTTATTTAACA 57.006 32.000 0.00 0.00 0.00 2.41
4817 5191 8.139989 GCATTATTTGATCACAGAAGGCTTATT 58.860 33.333 16.19 0.00 0.00 1.40
4818 5192 7.286087 TGCATTATTTGATCACAGAAGGCTTAT 59.714 33.333 21.80 0.00 0.00 1.73
4819 5193 6.602803 TGCATTATTTGATCACAGAAGGCTTA 59.397 34.615 21.80 4.99 0.00 3.09
4820 5194 5.419788 TGCATTATTTGATCACAGAAGGCTT 59.580 36.000 21.80 0.00 0.00 4.35
4821 5195 4.951715 TGCATTATTTGATCACAGAAGGCT 59.048 37.500 21.80 0.00 0.00 4.58
4822 5196 5.252969 TGCATTATTTGATCACAGAAGGC 57.747 39.130 16.51 16.51 0.00 4.35
4823 5197 5.690409 GCATGCATTATTTGATCACAGAAGG 59.310 40.000 14.21 0.00 0.00 3.46
4824 5198 6.504398 AGCATGCATTATTTGATCACAGAAG 58.496 36.000 21.98 0.00 0.00 2.85
4825 5199 6.459670 AGCATGCATTATTTGATCACAGAA 57.540 33.333 21.98 0.00 0.00 3.02
4826 5200 7.229907 ACATAGCATGCATTATTTGATCACAGA 59.770 33.333 21.98 0.00 0.00 3.41
4827 5201 7.368059 ACATAGCATGCATTATTTGATCACAG 58.632 34.615 21.98 0.00 0.00 3.66
4828 5202 7.279750 ACATAGCATGCATTATTTGATCACA 57.720 32.000 21.98 0.00 0.00 3.58
4829 5203 8.484799 CAAACATAGCATGCATTATTTGATCAC 58.515 33.333 21.98 0.00 0.00 3.06
4830 5204 8.198778 ACAAACATAGCATGCATTATTTGATCA 58.801 29.630 28.90 0.00 31.76 2.92
4831 5205 8.583810 ACAAACATAGCATGCATTATTTGATC 57.416 30.769 28.90 0.00 31.76 2.92
4832 5206 8.951787 AACAAACATAGCATGCATTATTTGAT 57.048 26.923 28.90 20.74 31.76 2.57
5248 5623 8.138712 TCAAGTAATTAGCAAACGAAATGGTTT 58.861 29.630 0.00 0.00 40.59 3.27
5358 5733 1.603172 GCCGACGTGAGGAATATGGAG 60.603 57.143 10.56 0.00 0.00 3.86
5493 5868 6.688073 TCATCACTTCTTCTAGGAGGTTTT 57.312 37.500 0.00 0.00 0.00 2.43
5816 6191 6.155475 ACATGCAAGATAGGAGTAGAAGAC 57.845 41.667 0.00 0.00 0.00 3.01
5818 6193 7.517614 TCTACATGCAAGATAGGAGTAGAAG 57.482 40.000 0.00 0.00 35.06 2.85
5820 6195 7.561722 AGTTTCTACATGCAAGATAGGAGTAGA 59.438 37.037 0.00 0.00 35.88 2.59
5821 6196 7.651304 CAGTTTCTACATGCAAGATAGGAGTAG 59.349 40.741 0.00 0.00 0.00 2.57
5823 6198 6.070538 ACAGTTTCTACATGCAAGATAGGAGT 60.071 38.462 0.00 0.00 0.00 3.85
5824 6199 6.344500 ACAGTTTCTACATGCAAGATAGGAG 58.656 40.000 0.00 0.00 0.00 3.69
5825 6200 6.299805 ACAGTTTCTACATGCAAGATAGGA 57.700 37.500 0.00 0.00 0.00 2.94
5826 6201 6.992063 AACAGTTTCTACATGCAAGATAGG 57.008 37.500 0.00 0.00 0.00 2.57
5862 6237 6.954684 TGGACCTTTAGAGTAAGACTGAAGAT 59.045 38.462 0.00 0.00 34.40 2.40
5905 6280 2.286833 TCTTTTTCGCAAGTCCTCAACG 59.713 45.455 0.00 0.00 39.48 4.10
5906 6281 3.963383 TCTTTTTCGCAAGTCCTCAAC 57.037 42.857 0.00 0.00 39.48 3.18
5924 6301 3.956848 GGAAGCTATGCTGGGAAAAATCT 59.043 43.478 0.00 0.00 39.62 2.40
5951 6348 6.772716 TCAATAAGGCCAGAAGAACCATAATC 59.227 38.462 5.01 0.00 0.00 1.75
5959 6356 5.774690 ACACAAATCAATAAGGCCAGAAGAA 59.225 36.000 5.01 0.00 0.00 2.52
6092 6498 7.601886 CCATGAGTGTACCAGATGATAAAGATC 59.398 40.741 0.00 0.00 0.00 2.75
6614 7020 3.429684 CCTTCTACTCTTCCTTCCGCTTC 60.430 52.174 0.00 0.00 0.00 3.86
6656 7062 2.682494 GACTACTCCCCCGTGGCA 60.682 66.667 0.00 0.00 0.00 4.92
6672 7078 4.242586 TGGGGTCCCACCAGACGA 62.243 66.667 10.98 0.00 41.02 4.20
6682 7088 4.338400 CGGAAGAGAAAAATAATGGGGTCC 59.662 45.833 0.00 0.00 0.00 4.46
6701 7107 0.110486 AAAGAGCAAAGCCCTCGGAA 59.890 50.000 0.00 0.00 34.56 4.30
6878 7288 7.506328 TTCAGAGCAGAATAATTCATGGATG 57.494 36.000 0.00 0.00 0.00 3.51
6943 7353 0.396435 ATGTGAACAAGGCCGAGACA 59.604 50.000 0.00 0.00 0.00 3.41
6997 7407 3.714871 GACAGAGAGGCTCAGCGGC 62.715 68.421 18.26 1.89 38.75 6.53
6999 7409 3.602103 AGACAGAGAGGCTCAGCG 58.398 61.111 18.26 6.40 32.06 5.18
7004 7414 2.051518 CGGCAGAGACAGAGAGGCT 61.052 63.158 0.00 0.00 39.48 4.58
7005 7415 1.391157 ATCGGCAGAGACAGAGAGGC 61.391 60.000 0.00 0.00 0.00 4.70
7006 7416 0.667993 GATCGGCAGAGACAGAGAGG 59.332 60.000 0.00 0.00 0.00 3.69
7007 7417 1.387539 TGATCGGCAGAGACAGAGAG 58.612 55.000 0.00 0.00 0.00 3.20
7008 7418 2.064434 ATGATCGGCAGAGACAGAGA 57.936 50.000 0.00 0.00 0.00 3.10
7009 7419 4.457257 TGTATATGATCGGCAGAGACAGAG 59.543 45.833 0.00 0.00 35.26 3.35
7010 7420 4.398319 TGTATATGATCGGCAGAGACAGA 58.602 43.478 0.00 0.00 35.26 3.41
7011 7421 4.773323 TGTATATGATCGGCAGAGACAG 57.227 45.455 0.00 0.00 35.26 3.51
7012 7422 4.524328 ACATGTATATGATCGGCAGAGACA 59.476 41.667 6.45 4.34 43.18 3.41
7013 7423 5.065704 ACATGTATATGATCGGCAGAGAC 57.934 43.478 6.45 0.00 37.73 3.36
7034 7444 8.759481 AAAGTAACCTCCCTATGTACTAGTAC 57.241 38.462 23.58 23.58 36.63 2.73
7036 7446 7.677319 ACAAAAGTAACCTCCCTATGTACTAGT 59.323 37.037 0.00 0.00 0.00 2.57
7037 7447 7.980099 CACAAAAGTAACCTCCCTATGTACTAG 59.020 40.741 0.00 0.00 0.00 2.57
7038 7448 7.675195 TCACAAAAGTAACCTCCCTATGTACTA 59.325 37.037 0.00 0.00 0.00 1.82
7039 7449 6.499350 TCACAAAAGTAACCTCCCTATGTACT 59.501 38.462 0.00 0.00 0.00 2.73
7040 7450 6.704310 TCACAAAAGTAACCTCCCTATGTAC 58.296 40.000 0.00 0.00 0.00 2.90
7041 7451 6.938698 TCACAAAAGTAACCTCCCTATGTA 57.061 37.500 0.00 0.00 0.00 2.29
7042 7452 5.836024 TCACAAAAGTAACCTCCCTATGT 57.164 39.130 0.00 0.00 0.00 2.29
7048 7458 5.768164 TCCTGATTTCACAAAAGTAACCTCC 59.232 40.000 0.00 0.00 0.00 4.30
7082 7492 5.753921 GTGATGTACAGTACCAATAAGGAGC 59.246 44.000 8.30 0.00 41.22 4.70
7366 7784 4.337060 GTGCCCGTGAAAACGCCC 62.337 66.667 0.00 0.00 0.00 6.13
7392 7810 1.666553 GACGCCGACACCATGTTGA 60.667 57.895 0.00 0.00 33.58 3.18
7462 7886 4.033776 ACCATGGGGGACGTGCTG 62.034 66.667 18.09 0.00 41.15 4.41


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

AutoCloner maintained by Alex Coulton.