Multiple sequence alignment - TraesCS3D01G198500

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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 TraesCS3D01G198500 chr3D 100.000 5989 0 0 1 5989 213677298 213683286 0.000000e+00 11060.0
1 TraesCS3D01G198500 chr3D 90.116 172 15 2 5524 5695 239876898 239876729 7.810000e-54 222.0
2 TraesCS3D01G198500 chr3D 95.960 99 4 0 5406 5504 462197413 462197511 1.730000e-35 161.0
3 TraesCS3D01G198500 chr3D 88.660 97 10 1 3981 4077 477907447 477907352 3.790000e-22 117.0
4 TraesCS3D01G198500 chr3B 98.022 4650 74 7 763 5410 286889646 286894279 0.000000e+00 8061.0
5 TraesCS3D01G198500 chr3B 92.126 127 4 2 5834 5959 286894798 286894919 2.220000e-39 174.0
6 TraesCS3D01G198500 chr3B 95.652 92 3 1 5687 5777 286894297 286894388 4.840000e-31 147.0
7 TraesCS3D01G198500 chr3B 88.660 97 10 1 3981 4077 637089785 637089690 3.790000e-22 117.0
8 TraesCS3D01G198500 chr3B 97.872 47 1 0 5802 5848 286894389 286894435 1.380000e-11 82.4
9 TraesCS3D01G198500 chr3A 98.716 3815 47 2 763 4576 278739644 278735831 0.000000e+00 6772.0
10 TraesCS3D01G198500 chr3A 98.393 809 13 0 4602 5410 278735837 278735029 0.000000e+00 1423.0
11 TraesCS3D01G198500 chr3A 93.642 755 47 1 1 755 352451855 352452608 0.000000e+00 1127.0
12 TraesCS3D01G198500 chr3A 96.377 276 3 3 5687 5959 278735011 278734740 1.180000e-121 448.0
13 TraesCS3D01G198500 chr3A 95.960 99 4 0 5407 5505 572598542 572598444 1.730000e-35 161.0
14 TraesCS3D01G198500 chr4A 93.664 726 44 2 1 726 492894633 492895356 0.000000e+00 1085.0
15 TraesCS3D01G198500 chr4A 87.574 169 21 0 5524 5692 572702928 572702760 4.740000e-46 196.0
16 TraesCS3D01G198500 chr4A 95.192 104 3 2 5407 5509 650040978 650040876 4.800000e-36 163.0
17 TraesCS3D01G198500 chr4A 89.362 94 9 1 3985 4078 27643526 27643618 3.790000e-22 117.0
18 TraesCS3D01G198500 chr2D 89.619 761 73 6 1 758 148973012 148973769 0.000000e+00 963.0
19 TraesCS3D01G198500 chr2D 85.635 724 100 4 27 750 352188686 352187967 0.000000e+00 758.0
20 TraesCS3D01G198500 chr2D 91.011 89 7 1 3985 4073 86080997 86080910 1.050000e-22 119.0
21 TraesCS3D01G198500 chr2D 91.228 57 1 4 3684 3737 47631359 47631304 2.310000e-09 75.0
22 TraesCS3D01G198500 chr2A 88.421 760 83 4 1 758 152598617 152597861 0.000000e+00 911.0
23 TraesCS3D01G198500 chr2A 92.135 89 6 1 3985 4073 86440627 86440540 2.270000e-24 124.0
24 TraesCS3D01G198500 chr2A 91.304 46 0 4 3692 3733 468290441 468290396 6.480000e-05 60.2
25 TraesCS3D01G198500 chr1D 86.490 755 101 1 1 755 286396355 286395602 0.000000e+00 828.0
26 TraesCS3D01G198500 chr7D 85.526 760 108 2 1 758 472803343 472804102 0.000000e+00 793.0
27 TraesCS3D01G198500 chr7D 84.946 744 109 3 1 743 509254167 509254908 0.000000e+00 750.0
28 TraesCS3D01G198500 chr7D 88.660 97 8 3 3974 4070 59711387 59711294 1.360000e-21 115.0
29 TraesCS3D01G198500 chr7D 94.444 36 1 1 3696 3730 499888752 499888717 3.000000e-03 54.7
30 TraesCS3D01G198500 chr2B 84.494 761 109 8 1 758 361967081 361966327 0.000000e+00 743.0
31 TraesCS3D01G198500 chr2B 91.818 110 9 0 5407 5516 668189781 668189672 2.890000e-33 154.0
32 TraesCS3D01G198500 chr6B 94.152 171 10 0 5522 5692 590448417 590448587 1.660000e-65 261.0
33 TraesCS3D01G198500 chr6B 92.308 169 13 0 5527 5695 545253920 545254088 2.160000e-59 241.0
34 TraesCS3D01G198500 chr6B 91.818 110 8 1 5407 5516 95757364 95757256 1.040000e-32 152.0
35 TraesCS3D01G198500 chr6B 85.507 69 9 1 3666 3733 431160255 431160187 2.990000e-08 71.3
36 TraesCS3D01G198500 chr6B 85.507 69 9 1 3666 3733 431204133 431204065 2.990000e-08 71.3
37 TraesCS3D01G198500 chr4B 92.262 168 13 0 5523 5690 179776701 179776868 7.760000e-59 239.0
38 TraesCS3D01G198500 chr4B 90.476 168 15 1 5524 5691 552841671 552841505 2.810000e-53 220.0
39 TraesCS3D01G198500 chr4B 95.098 102 4 1 5407 5507 658978260 658978361 6.210000e-35 159.0
40 TraesCS3D01G198500 chr4B 92.593 108 6 2 5406 5512 246455415 246455309 2.890000e-33 154.0
41 TraesCS3D01G198500 chr4B 91.954 87 6 1 3984 4070 41531416 41531501 2.930000e-23 121.0
42 TraesCS3D01G198500 chr1B 89.571 163 17 0 5526 5688 242744170 242744332 2.190000e-49 207.0
43 TraesCS3D01G198500 chr4D 87.574 169 21 0 5524 5692 30278251 30278419 4.740000e-46 196.0
44 TraesCS3D01G198500 chr5B 87.647 170 17 2 5525 5690 4857360 4857191 1.700000e-45 195.0
45 TraesCS3D01G198500 chr5D 95.238 105 4 1 5406 5510 379575719 379575616 1.340000e-36 165.0
46 TraesCS3D01G198500 chr7A 93.578 109 5 2 5402 5508 222500975 222500867 1.730000e-35 161.0
47 TraesCS3D01G198500 chr6A 90.196 51 2 3 3686 3733 115345506 115345456 5.010000e-06 63.9


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 TraesCS3D01G198500 chr3D 213677298 213683286 5988 False 11060.0 11060 100.000000 1 5989 1 chr3D.!!$F1 5988
1 TraesCS3D01G198500 chr3B 286889646 286894919 5273 False 2116.1 8061 95.918000 763 5959 4 chr3B.!!$F1 5196
2 TraesCS3D01G198500 chr3A 278734740 278739644 4904 True 2881.0 6772 97.828667 763 5959 3 chr3A.!!$R2 5196
3 TraesCS3D01G198500 chr3A 352451855 352452608 753 False 1127.0 1127 93.642000 1 755 1 chr3A.!!$F1 754
4 TraesCS3D01G198500 chr4A 492894633 492895356 723 False 1085.0 1085 93.664000 1 726 1 chr4A.!!$F2 725
5 TraesCS3D01G198500 chr2D 148973012 148973769 757 False 963.0 963 89.619000 1 758 1 chr2D.!!$F1 757
6 TraesCS3D01G198500 chr2D 352187967 352188686 719 True 758.0 758 85.635000 27 750 1 chr2D.!!$R3 723
7 TraesCS3D01G198500 chr2A 152597861 152598617 756 True 911.0 911 88.421000 1 758 1 chr2A.!!$R2 757
8 TraesCS3D01G198500 chr1D 286395602 286396355 753 True 828.0 828 86.490000 1 755 1 chr1D.!!$R1 754
9 TraesCS3D01G198500 chr7D 472803343 472804102 759 False 793.0 793 85.526000 1 758 1 chr7D.!!$F1 757
10 TraesCS3D01G198500 chr7D 509254167 509254908 741 False 750.0 750 84.946000 1 743 1 chr7D.!!$F2 742
11 TraesCS3D01G198500 chr2B 361966327 361967081 754 True 743.0 743 84.494000 1 758 1 chr2B.!!$R1 757

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
776 782 0.817013 TACCGGTGGCCTACTTTACG 59.183 55.000 19.93 0.0 0.00 3.18 F
1684 1692 0.031111 CACCAGGGAGGGAGGTATCA 60.031 60.000 0.00 0.0 43.89 2.15 F
2264 2272 3.107601 TCCCTGAGACCCTATCAGTTTG 58.892 50.000 2.60 0.0 42.18 2.93 F
3065 3073 3.036429 GCCAGGACTGCCTCCGATT 62.036 63.158 0.00 0.0 44.80 3.34 F
4265 4276 2.034685 GCAACCCAAGAAGGACAAACTC 59.965 50.000 0.00 0.0 41.22 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2264 2272 0.527817 CTCGATACTTCCGCCACACC 60.528 60.000 0.00 0.0 0.00 4.16 R
3065 3073 2.250924 TGTGAGCCTCATGTCAAGAGA 58.749 47.619 6.65 0.0 35.09 3.10 R
3674 3682 3.625853 TGGAAATGTCAAACCTCACACA 58.374 40.909 0.00 0.0 0.00 3.72 R
4598 4610 0.179020 CTTCCTGCACCAGAACACCA 60.179 55.000 0.00 0.0 32.44 4.17 R
5590 5602 0.035598 TCCAGCCGGAATCAAAACGA 59.964 50.000 5.05 0.0 38.83 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
121 123 7.825709 ACTTCCATATCTTATTCCAAATGGGA 58.174 34.615 0.00 0.00 46.61 4.37
158 160 4.455606 CCCCATTCCATTAGAGTGTCTTC 58.544 47.826 0.00 0.00 30.39 2.87
226 229 5.086058 CGAACCGAGAACATACCATTTTTG 58.914 41.667 0.00 0.00 0.00 2.44
287 290 4.393062 GCGAGAGTGGAATTGAAAGAATCA 59.607 41.667 0.00 0.00 35.85 2.57
388 393 5.842874 ACCTACCTTAGTTAACAGTTGTCCT 59.157 40.000 8.61 0.00 0.00 3.85
538 543 9.860898 ATAATGCTTTTCCAAGTAAAAGATGAC 57.139 29.630 12.06 0.00 45.33 3.06
573 578 6.014840 AGCTTGGAGTTCAACAAATCATCATT 60.015 34.615 0.00 0.00 0.00 2.57
685 690 6.967199 GGTTGAAAGAATGAATATCACGGAAC 59.033 38.462 0.00 0.00 0.00 3.62
707 713 5.804639 ACCCCATTCCTCTTTAATTTTTGC 58.195 37.500 0.00 0.00 0.00 3.68
738 744 6.321945 CACATTTTCCATGAGGACATCCAATA 59.678 38.462 0.00 0.00 45.73 1.90
743 749 4.909695 TCCATGAGGACATCCAATACATCT 59.090 41.667 0.00 0.00 39.61 2.90
745 751 6.558394 TCCATGAGGACATCCAATACATCTTA 59.442 38.462 0.00 0.00 39.61 2.10
755 761 9.512588 ACATCCAATACATCTTATTCTGATTCC 57.487 33.333 0.00 0.00 0.00 3.01
757 763 8.280258 TCCAATACATCTTATTCTGATTCCCT 57.720 34.615 0.00 0.00 0.00 4.20
758 764 9.392506 TCCAATACATCTTATTCTGATTCCCTA 57.607 33.333 0.00 0.00 0.00 3.53
759 765 9.442047 CCAATACATCTTATTCTGATTCCCTAC 57.558 37.037 0.00 0.00 0.00 3.18
760 766 9.442047 CAATACATCTTATTCTGATTCCCTACC 57.558 37.037 0.00 0.00 0.00 3.18
761 767 6.102897 ACATCTTATTCTGATTCCCTACCG 57.897 41.667 0.00 0.00 0.00 4.02
776 782 0.817013 TACCGGTGGCCTACTTTACG 59.183 55.000 19.93 0.00 0.00 3.18
801 809 1.715931 AGATGACCCATGTTCCCCAAA 59.284 47.619 0.00 0.00 0.00 3.28
849 857 1.006102 AATAGGAAGCCGCGATCCG 60.006 57.895 8.23 0.00 40.78 4.18
1684 1692 0.031111 CACCAGGGAGGGAGGTATCA 60.031 60.000 0.00 0.00 43.89 2.15
2264 2272 3.107601 TCCCTGAGACCCTATCAGTTTG 58.892 50.000 2.60 0.00 42.18 2.93
3065 3073 3.036429 GCCAGGACTGCCTCCGATT 62.036 63.158 0.00 0.00 44.80 3.34
3574 3582 6.589907 ACCTTTGTTTTCAACATTCTTGACAC 59.410 34.615 0.00 0.00 41.79 3.67
3673 3681 5.769662 TGTTCTTGATTGCTACTGGTCAAAT 59.230 36.000 0.00 0.00 30.96 2.32
3674 3682 6.265196 TGTTCTTGATTGCTACTGGTCAAATT 59.735 34.615 0.00 0.00 30.96 1.82
3894 3904 6.986231 GTGAATGGAGTTTGAAAGGTGAATTT 59.014 34.615 0.00 0.00 0.00 1.82
3998 4008 6.596309 TGATGCTAATACTCCCTCTGTATG 57.404 41.667 0.00 0.00 31.76 2.39
3999 4009 6.314917 TGATGCTAATACTCCCTCTGTATGA 58.685 40.000 0.00 0.00 31.76 2.15
4265 4276 2.034685 GCAACCCAAGAAGGACAAACTC 59.965 50.000 0.00 0.00 41.22 3.01
4266 4277 3.287222 CAACCCAAGAAGGACAAACTCA 58.713 45.455 0.00 0.00 41.22 3.41
4571 4583 4.141959 ACTTGCACAAGGTAAATGCTTTGT 60.142 37.500 14.51 0.00 42.53 2.83
4724 4736 3.438087 CCTTAGCAGTGACATTCTGGTTG 59.562 47.826 3.44 0.00 42.41 3.77
4744 4756 0.179009 GCCTGCATTCATCCCTGCTA 60.179 55.000 0.00 0.00 39.16 3.49
4768 4780 6.357367 AGGTTATTTCGCTGATGGTTCTTAT 58.643 36.000 0.00 0.00 0.00 1.73
5248 5260 5.973651 TTAGACAATTAGAGCATCGCTTG 57.026 39.130 0.00 0.00 39.88 4.01
5292 5304 9.383519 AGAGTTTGTTGTATGTCACATAATAGG 57.616 33.333 0.00 0.00 36.90 2.57
5411 5423 9.646427 GTCCATTTATACAATCAGAGATACTCC 57.354 37.037 0.00 0.00 0.00 3.85
5412 5424 8.816894 TCCATTTATACAATCAGAGATACTCCC 58.183 37.037 0.00 0.00 0.00 4.30
5413 5425 8.820831 CCATTTATACAATCAGAGATACTCCCT 58.179 37.037 0.00 0.00 0.00 4.20
5414 5426 9.868277 CATTTATACAATCAGAGATACTCCCTC 57.132 37.037 0.00 0.00 0.00 4.30
5415 5427 8.423906 TTTATACAATCAGAGATACTCCCTCC 57.576 38.462 0.00 0.00 0.00 4.30
5416 5428 3.226777 ACAATCAGAGATACTCCCTCCG 58.773 50.000 0.00 0.00 0.00 4.63
5417 5429 3.226777 CAATCAGAGATACTCCCTCCGT 58.773 50.000 0.00 0.00 0.00 4.69
5418 5430 3.603965 ATCAGAGATACTCCCTCCGTT 57.396 47.619 0.00 0.00 0.00 4.44
5419 5431 2.933573 TCAGAGATACTCCCTCCGTTC 58.066 52.381 0.00 0.00 0.00 3.95
5420 5432 2.510382 TCAGAGATACTCCCTCCGTTCT 59.490 50.000 0.00 0.00 0.00 3.01
5421 5433 3.715315 TCAGAGATACTCCCTCCGTTCTA 59.285 47.826 0.00 0.00 0.00 2.10
5422 5434 4.165565 TCAGAGATACTCCCTCCGTTCTAA 59.834 45.833 0.00 0.00 0.00 2.10
5423 5435 4.888239 CAGAGATACTCCCTCCGTTCTAAA 59.112 45.833 0.00 0.00 0.00 1.85
5424 5436 5.360144 CAGAGATACTCCCTCCGTTCTAAAA 59.640 44.000 0.00 0.00 0.00 1.52
5425 5437 6.041069 CAGAGATACTCCCTCCGTTCTAAAAT 59.959 42.308 0.00 0.00 0.00 1.82
5426 5438 7.230913 CAGAGATACTCCCTCCGTTCTAAAATA 59.769 40.741 0.00 0.00 0.00 1.40
5427 5439 7.449086 AGAGATACTCCCTCCGTTCTAAAATAG 59.551 40.741 0.00 0.00 0.00 1.73
5428 5440 7.296098 AGATACTCCCTCCGTTCTAAAATAGA 58.704 38.462 0.00 0.00 0.00 1.98
5429 5441 5.595257 ACTCCCTCCGTTCTAAAATAGAC 57.405 43.478 0.00 0.00 33.84 2.59
5430 5442 4.097589 ACTCCCTCCGTTCTAAAATAGACG 59.902 45.833 0.00 0.00 33.84 4.18
5431 5443 3.382546 TCCCTCCGTTCTAAAATAGACGG 59.617 47.826 15.83 15.83 43.94 4.79
5432 5444 3.382546 CCCTCCGTTCTAAAATAGACGGA 59.617 47.826 19.90 19.90 46.27 4.69
5433 5445 4.357996 CCTCCGTTCTAAAATAGACGGAC 58.642 47.826 18.47 3.61 45.01 4.79
5434 5446 4.357996 CTCCGTTCTAAAATAGACGGACC 58.642 47.826 18.47 0.00 45.01 4.46
5435 5447 3.763360 TCCGTTCTAAAATAGACGGACCA 59.237 43.478 18.47 5.99 45.01 4.02
5436 5448 4.220382 TCCGTTCTAAAATAGACGGACCAA 59.780 41.667 18.47 5.76 45.01 3.67
5437 5449 4.328169 CCGTTCTAAAATAGACGGACCAAC 59.672 45.833 16.47 0.27 44.63 3.77
5438 5450 5.166398 CGTTCTAAAATAGACGGACCAACT 58.834 41.667 0.00 0.00 33.84 3.16
5439 5451 5.636543 CGTTCTAAAATAGACGGACCAACTT 59.363 40.000 0.00 0.00 33.84 2.66
5440 5452 6.146673 CGTTCTAAAATAGACGGACCAACTTT 59.853 38.462 0.00 0.00 33.84 2.66
5441 5453 7.329226 CGTTCTAAAATAGACGGACCAACTTTA 59.671 37.037 0.00 0.00 33.84 1.85
5442 5454 9.159364 GTTCTAAAATAGACGGACCAACTTTAT 57.841 33.333 0.00 0.00 33.84 1.40
5444 5456 9.807649 TCTAAAATAGACGGACCAACTTTATAC 57.192 33.333 0.00 0.00 0.00 1.47
5445 5457 9.813446 CTAAAATAGACGGACCAACTTTATACT 57.187 33.333 0.00 0.00 0.00 2.12
5448 5460 9.591792 AAATAGACGGACCAACTTTATACTAAC 57.408 33.333 0.00 0.00 0.00 2.34
5449 5461 6.847421 AGACGGACCAACTTTATACTAACT 57.153 37.500 0.00 0.00 0.00 2.24
5450 5462 7.237209 AGACGGACCAACTTTATACTAACTT 57.763 36.000 0.00 0.00 0.00 2.66
5451 5463 7.674120 AGACGGACCAACTTTATACTAACTTT 58.326 34.615 0.00 0.00 0.00 2.66
5452 5464 7.601508 AGACGGACCAACTTTATACTAACTTTG 59.398 37.037 0.00 0.00 0.00 2.77
5453 5465 7.219322 ACGGACCAACTTTATACTAACTTTGT 58.781 34.615 0.00 0.00 0.00 2.83
5454 5466 8.367156 ACGGACCAACTTTATACTAACTTTGTA 58.633 33.333 0.00 0.00 0.00 2.41
5455 5467 8.650714 CGGACCAACTTTATACTAACTTTGTAC 58.349 37.037 0.00 0.00 0.00 2.90
5456 5468 9.716531 GGACCAACTTTATACTAACTTTGTACT 57.283 33.333 0.00 0.00 0.00 2.73
5489 5501 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
5490 5502 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
5491 5503 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
5492 5504 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
5493 5505 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
5494 5506 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
5495 5507 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
5496 5508 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
5497 5509 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
5498 5510 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
5499 5511 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
5500 5512 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
5501 5513 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
5502 5514 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
5503 5515 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
5504 5516 2.019807 TTTGGAACGGAGGGAGTACT 57.980 50.000 0.00 0.00 0.00 2.73
5527 5539 5.186996 ACATTTCAACAGTGTTGCTTAGG 57.813 39.130 27.74 18.74 0.00 2.69
5528 5540 3.708563 TTTCAACAGTGTTGCTTAGGC 57.291 42.857 27.74 0.00 39.26 3.93
5529 5541 2.638480 TCAACAGTGTTGCTTAGGCT 57.362 45.000 27.74 0.00 39.59 4.58
5530 5542 2.930950 TCAACAGTGTTGCTTAGGCTT 58.069 42.857 27.74 0.00 39.59 4.35
5531 5543 3.287222 TCAACAGTGTTGCTTAGGCTTT 58.713 40.909 27.74 0.00 39.59 3.51
5532 5544 3.066621 TCAACAGTGTTGCTTAGGCTTTG 59.933 43.478 27.74 4.12 39.59 2.77
5533 5545 2.654863 ACAGTGTTGCTTAGGCTTTGT 58.345 42.857 0.00 0.00 39.59 2.83
5534 5546 3.023832 ACAGTGTTGCTTAGGCTTTGTT 58.976 40.909 0.00 0.00 39.59 2.83
5535 5547 3.447229 ACAGTGTTGCTTAGGCTTTGTTT 59.553 39.130 0.00 0.00 39.59 2.83
5536 5548 3.798337 CAGTGTTGCTTAGGCTTTGTTTG 59.202 43.478 0.00 0.00 39.59 2.93
5537 5549 3.123050 GTGTTGCTTAGGCTTTGTTTGG 58.877 45.455 0.00 0.00 39.59 3.28
5538 5550 3.027412 TGTTGCTTAGGCTTTGTTTGGA 58.973 40.909 0.00 0.00 39.59 3.53
5539 5551 3.449018 TGTTGCTTAGGCTTTGTTTGGAA 59.551 39.130 0.00 0.00 39.59 3.53
5540 5552 4.100808 TGTTGCTTAGGCTTTGTTTGGAAT 59.899 37.500 0.00 0.00 39.59 3.01
5541 5553 4.255833 TGCTTAGGCTTTGTTTGGAATG 57.744 40.909 0.00 0.00 39.59 2.67
5542 5554 3.640967 TGCTTAGGCTTTGTTTGGAATGT 59.359 39.130 0.00 0.00 39.59 2.71
5543 5555 4.100808 TGCTTAGGCTTTGTTTGGAATGTT 59.899 37.500 0.00 0.00 39.59 2.71
5544 5556 4.448732 GCTTAGGCTTTGTTTGGAATGTTG 59.551 41.667 0.00 0.00 35.22 3.33
5545 5557 5.600696 CTTAGGCTTTGTTTGGAATGTTGT 58.399 37.500 0.00 0.00 0.00 3.32
5546 5558 4.486125 AGGCTTTGTTTGGAATGTTGTT 57.514 36.364 0.00 0.00 0.00 2.83
5547 5559 4.842574 AGGCTTTGTTTGGAATGTTGTTT 58.157 34.783 0.00 0.00 0.00 2.83
5548 5560 4.875536 AGGCTTTGTTTGGAATGTTGTTTC 59.124 37.500 0.00 0.00 0.00 2.78
5549 5561 4.260172 GGCTTTGTTTGGAATGTTGTTTCG 60.260 41.667 0.00 0.00 0.00 3.46
5550 5562 4.328712 GCTTTGTTTGGAATGTTGTTTCGT 59.671 37.500 0.00 0.00 0.00 3.85
5551 5563 5.500131 GCTTTGTTTGGAATGTTGTTTCGTC 60.500 40.000 0.00 0.00 0.00 4.20
5552 5564 4.974368 TGTTTGGAATGTTGTTTCGTCT 57.026 36.364 0.00 0.00 0.00 4.18
5553 5565 4.915704 TGTTTGGAATGTTGTTTCGTCTC 58.084 39.130 0.00 0.00 0.00 3.36
5554 5566 4.396478 TGTTTGGAATGTTGTTTCGTCTCA 59.604 37.500 0.00 0.00 0.00 3.27
5555 5567 5.106118 TGTTTGGAATGTTGTTTCGTCTCAA 60.106 36.000 0.00 0.00 0.00 3.02
5556 5568 5.568685 TTGGAATGTTGTTTCGTCTCAAA 57.431 34.783 0.00 0.00 0.00 2.69
5557 5569 5.766150 TGGAATGTTGTTTCGTCTCAAAT 57.234 34.783 0.00 0.00 0.00 2.32
5558 5570 6.869315 TGGAATGTTGTTTCGTCTCAAATA 57.131 33.333 0.00 0.00 0.00 1.40
5559 5571 6.664515 TGGAATGTTGTTTCGTCTCAAATAC 58.335 36.000 0.00 0.00 0.00 1.89
5560 5572 6.261158 TGGAATGTTGTTTCGTCTCAAATACA 59.739 34.615 0.00 0.00 0.00 2.29
5561 5573 6.577427 GGAATGTTGTTTCGTCTCAAATACAC 59.423 38.462 0.00 0.00 0.00 2.90
5562 5574 6.861065 ATGTTGTTTCGTCTCAAATACACT 57.139 33.333 0.00 0.00 0.00 3.55
5563 5575 6.671614 TGTTGTTTCGTCTCAAATACACTT 57.328 33.333 0.00 0.00 0.00 3.16
5564 5576 6.482835 TGTTGTTTCGTCTCAAATACACTTG 58.517 36.000 0.00 0.00 0.00 3.16
5565 5577 6.092944 TGTTGTTTCGTCTCAAATACACTTGT 59.907 34.615 0.00 0.00 0.00 3.16
5566 5578 7.278203 TGTTGTTTCGTCTCAAATACACTTGTA 59.722 33.333 0.00 0.00 34.67 2.41
5567 5579 7.402811 TGTTTCGTCTCAAATACACTTGTAG 57.597 36.000 0.00 0.00 33.52 2.74
5568 5580 7.204604 TGTTTCGTCTCAAATACACTTGTAGA 58.795 34.615 0.00 0.00 33.52 2.59
5569 5581 7.707464 TGTTTCGTCTCAAATACACTTGTAGAA 59.293 33.333 0.00 0.00 33.52 2.10
5570 5582 8.545420 GTTTCGTCTCAAATACACTTGTAGAAA 58.455 33.333 0.00 0.00 33.52 2.52
5571 5583 8.651391 TTCGTCTCAAATACACTTGTAGAAAA 57.349 30.769 0.00 0.00 33.52 2.29
5572 5584 8.294341 TCGTCTCAAATACACTTGTAGAAAAG 57.706 34.615 0.00 0.00 33.52 2.27
5573 5585 8.139350 TCGTCTCAAATACACTTGTAGAAAAGA 58.861 33.333 0.00 0.00 33.52 2.52
5574 5586 8.926710 CGTCTCAAATACACTTGTAGAAAAGAT 58.073 33.333 0.00 0.00 33.52 2.40
5584 5596 8.254508 ACACTTGTAGAAAAGATACAGATCTCC 58.745 37.037 0.00 0.00 41.87 3.71
5585 5597 7.433719 CACTTGTAGAAAAGATACAGATCTCCG 59.566 40.741 0.00 0.00 41.87 4.63
5586 5598 5.833082 TGTAGAAAAGATACAGATCTCCGC 58.167 41.667 0.00 0.00 41.87 5.54
5587 5599 5.594725 TGTAGAAAAGATACAGATCTCCGCT 59.405 40.000 0.00 0.00 41.87 5.52
5588 5600 5.195001 AGAAAAGATACAGATCTCCGCTC 57.805 43.478 0.00 0.00 41.87 5.03
5589 5601 4.646945 AGAAAAGATACAGATCTCCGCTCA 59.353 41.667 0.00 0.00 41.87 4.26
5590 5602 5.304101 AGAAAAGATACAGATCTCCGCTCAT 59.696 40.000 0.00 0.00 41.87 2.90
5591 5603 4.782019 AAGATACAGATCTCCGCTCATC 57.218 45.455 0.00 0.00 41.87 2.92
5592 5604 2.746904 AGATACAGATCTCCGCTCATCG 59.253 50.000 0.00 0.00 38.01 3.84
5593 5605 1.968704 TACAGATCTCCGCTCATCGT 58.031 50.000 0.00 0.00 36.19 3.73
5594 5606 1.107114 ACAGATCTCCGCTCATCGTT 58.893 50.000 0.00 0.00 36.19 3.85
5595 5607 1.478510 ACAGATCTCCGCTCATCGTTT 59.521 47.619 0.00 0.00 36.19 3.60
5596 5608 2.093973 ACAGATCTCCGCTCATCGTTTT 60.094 45.455 0.00 0.00 36.19 2.43
5597 5609 2.283617 CAGATCTCCGCTCATCGTTTTG 59.716 50.000 0.00 0.00 36.19 2.44
5598 5610 2.166459 AGATCTCCGCTCATCGTTTTGA 59.834 45.455 0.00 0.00 36.19 2.69
5599 5611 2.672961 TCTCCGCTCATCGTTTTGAT 57.327 45.000 0.00 0.00 38.01 2.57
5600 5612 2.972625 TCTCCGCTCATCGTTTTGATT 58.027 42.857 0.00 0.00 34.13 2.57
5601 5613 2.930040 TCTCCGCTCATCGTTTTGATTC 59.070 45.455 0.00 0.00 34.13 2.52
5602 5614 2.006888 TCCGCTCATCGTTTTGATTCC 58.993 47.619 0.00 0.00 34.13 3.01
5603 5615 1.267532 CCGCTCATCGTTTTGATTCCG 60.268 52.381 0.00 0.00 34.13 4.30
5604 5616 1.267532 CGCTCATCGTTTTGATTCCGG 60.268 52.381 0.00 0.00 34.13 5.14
5605 5617 1.531883 GCTCATCGTTTTGATTCCGGC 60.532 52.381 0.00 0.00 34.13 6.13
5606 5618 2.009774 CTCATCGTTTTGATTCCGGCT 58.990 47.619 0.00 0.00 34.13 5.52
5607 5619 1.737236 TCATCGTTTTGATTCCGGCTG 59.263 47.619 0.00 0.00 34.13 4.85
5608 5620 1.094785 ATCGTTTTGATTCCGGCTGG 58.905 50.000 4.71 4.71 31.57 4.85
5609 5621 0.035598 TCGTTTTGATTCCGGCTGGA 59.964 50.000 11.27 11.27 44.61 3.86
5619 5631 2.054232 TCCGGCTGGAACTCTACTAG 57.946 55.000 13.31 0.00 42.85 2.57
5620 5632 1.284198 TCCGGCTGGAACTCTACTAGT 59.716 52.381 13.31 0.00 42.85 2.57
5621 5633 1.405821 CCGGCTGGAACTCTACTAGTG 59.594 57.143 5.28 0.00 38.88 2.74
5622 5634 1.405821 CGGCTGGAACTCTACTAGTGG 59.594 57.143 5.39 1.87 38.88 4.00
5623 5635 1.137282 GGCTGGAACTCTACTAGTGGC 59.863 57.143 5.39 0.00 38.88 5.01
5624 5636 1.137282 GCTGGAACTCTACTAGTGGCC 59.863 57.143 5.39 0.00 38.88 5.36
5625 5637 1.405821 CTGGAACTCTACTAGTGGCCG 59.594 57.143 5.39 0.00 38.88 6.13
5626 5638 0.745468 GGAACTCTACTAGTGGCCGG 59.255 60.000 5.39 0.00 38.88 6.13
5627 5639 1.472188 GAACTCTACTAGTGGCCGGT 58.528 55.000 5.39 0.00 38.88 5.28
5628 5640 2.648059 GAACTCTACTAGTGGCCGGTA 58.352 52.381 5.39 0.00 38.88 4.02
5629 5641 2.814805 ACTCTACTAGTGGCCGGTAA 57.185 50.000 5.39 0.00 36.93 2.85
5630 5642 2.652590 ACTCTACTAGTGGCCGGTAAG 58.347 52.381 5.39 0.00 36.93 2.34
5631 5643 2.240667 ACTCTACTAGTGGCCGGTAAGA 59.759 50.000 5.39 0.00 36.93 2.10
5632 5644 3.117587 ACTCTACTAGTGGCCGGTAAGAT 60.118 47.826 5.39 0.00 36.93 2.40
5633 5645 4.103785 ACTCTACTAGTGGCCGGTAAGATA 59.896 45.833 5.39 0.00 36.93 1.98
5634 5646 5.222089 ACTCTACTAGTGGCCGGTAAGATAT 60.222 44.000 5.39 0.00 36.93 1.63
5635 5647 6.013032 ACTCTACTAGTGGCCGGTAAGATATA 60.013 42.308 5.39 0.00 36.93 0.86
5636 5648 6.176183 TCTACTAGTGGCCGGTAAGATATAC 58.824 44.000 5.39 0.00 0.00 1.47
5637 5649 3.755378 ACTAGTGGCCGGTAAGATATACG 59.245 47.826 1.90 0.00 0.00 3.06
5638 5650 2.590821 AGTGGCCGGTAAGATATACGT 58.409 47.619 1.90 0.00 0.00 3.57
5639 5651 2.295349 AGTGGCCGGTAAGATATACGTG 59.705 50.000 1.90 0.00 0.00 4.49
5640 5652 2.035066 GTGGCCGGTAAGATATACGTGT 59.965 50.000 1.90 0.00 0.00 4.49
5641 5653 3.253188 GTGGCCGGTAAGATATACGTGTA 59.747 47.826 1.90 0.00 0.00 2.90
5642 5654 3.888323 TGGCCGGTAAGATATACGTGTAA 59.112 43.478 1.90 0.00 0.00 2.41
5643 5655 4.340666 TGGCCGGTAAGATATACGTGTAAA 59.659 41.667 1.90 0.00 0.00 2.01
5644 5656 4.681483 GGCCGGTAAGATATACGTGTAAAC 59.319 45.833 1.90 0.00 0.00 2.01
5645 5657 5.507985 GGCCGGTAAGATATACGTGTAAACT 60.508 44.000 1.90 0.00 0.00 2.66
5646 5658 6.293955 GGCCGGTAAGATATACGTGTAAACTA 60.294 42.308 1.90 0.00 0.00 2.24
5647 5659 7.138736 GCCGGTAAGATATACGTGTAAACTAA 58.861 38.462 1.90 0.00 0.00 2.24
5648 5660 7.647715 GCCGGTAAGATATACGTGTAAACTAAA 59.352 37.037 1.90 0.00 0.00 1.85
5649 5661 9.683069 CCGGTAAGATATACGTGTAAACTAAAT 57.317 33.333 0.00 0.00 0.00 1.40
5671 5683 7.459394 AATACGTCTGTATTTGATTACACCG 57.541 36.000 0.00 0.00 46.61 4.94
5672 5684 3.615496 ACGTCTGTATTTGATTACACCGC 59.385 43.478 0.00 0.00 30.36 5.68
5673 5685 3.615056 CGTCTGTATTTGATTACACCGCA 59.385 43.478 0.00 0.00 0.00 5.69
5674 5686 4.270084 CGTCTGTATTTGATTACACCGCAT 59.730 41.667 0.00 0.00 0.00 4.73
5675 5687 5.556382 CGTCTGTATTTGATTACACCGCATC 60.556 44.000 0.00 0.00 0.00 3.91
5676 5688 4.814234 TCTGTATTTGATTACACCGCATCC 59.186 41.667 0.00 0.00 0.00 3.51
5677 5689 4.518249 TGTATTTGATTACACCGCATCCA 58.482 39.130 0.00 0.00 0.00 3.41
5678 5690 4.944317 TGTATTTGATTACACCGCATCCAA 59.056 37.500 0.00 0.00 0.00 3.53
5679 5691 4.637483 ATTTGATTACACCGCATCCAAG 57.363 40.909 0.00 0.00 0.00 3.61
5680 5692 1.378531 TGATTACACCGCATCCAAGC 58.621 50.000 0.00 0.00 0.00 4.01
5689 5701 2.513666 CATCCAAGCGCGGCCTTA 60.514 61.111 8.83 0.00 0.00 2.69
5690 5702 2.203070 ATCCAAGCGCGGCCTTAG 60.203 61.111 8.83 0.00 0.00 2.18
5959 6352 1.446016 GGGGGTCTTAGGGCATGTAT 58.554 55.000 0.00 0.00 0.00 2.29
5960 6353 1.073923 GGGGGTCTTAGGGCATGTATG 59.926 57.143 0.00 0.00 0.00 2.39
5970 6363 3.289834 CATGTATGCTGCCCGGGC 61.290 66.667 39.40 39.40 42.35 6.13
5971 6364 4.586235 ATGTATGCTGCCCGGGCC 62.586 66.667 41.75 27.90 41.09 5.80
5973 6366 4.586235 GTATGCTGCCCGGGCCAT 62.586 66.667 41.75 35.92 41.09 4.40
5974 6367 4.269523 TATGCTGCCCGGGCCATC 62.270 66.667 41.75 28.89 41.09 3.51
5980 6373 3.884774 GCCCGGGCCATCCACATA 61.885 66.667 36.64 0.00 34.36 2.29
5981 6374 2.431683 CCCGGGCCATCCACATAG 59.568 66.667 8.08 0.00 34.36 2.23
5982 6375 2.146724 CCCGGGCCATCCACATAGA 61.147 63.158 8.08 0.00 34.36 1.98
5983 6376 1.492133 CCCGGGCCATCCACATAGAT 61.492 60.000 8.08 0.00 34.36 1.98
5984 6377 1.275666 CCGGGCCATCCACATAGATA 58.724 55.000 4.39 0.00 34.36 1.98
5985 6378 1.628340 CCGGGCCATCCACATAGATAA 59.372 52.381 4.39 0.00 34.36 1.75
5986 6379 2.039746 CCGGGCCATCCACATAGATAAA 59.960 50.000 4.39 0.00 34.36 1.40
5987 6380 3.308402 CCGGGCCATCCACATAGATAAAT 60.308 47.826 4.39 0.00 34.36 1.40
5988 6381 4.335416 CGGGCCATCCACATAGATAAATT 58.665 43.478 4.39 0.00 34.36 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.163923 GGGTTACACTCGCTAACAAACATAC 60.164 44.000 0.00 0.00 0.00 2.39
46 47 0.462375 TATGGCGTACGCTTCATGGT 59.538 50.000 36.24 16.26 41.60 3.55
121 123 3.259592 GGGGCGAACCACAGTTAAT 57.740 52.632 0.00 0.00 40.19 1.40
226 229 7.420800 CAGATTTCATTGCTTGGAGTTATACC 58.579 38.462 0.00 0.00 0.00 2.73
287 290 2.297701 GTGGCCCATCGATGTACAATT 58.702 47.619 23.27 0.00 0.00 2.32
408 413 1.185315 CCCAAGTTGTGCCAATAGGG 58.815 55.000 1.45 0.00 40.85 3.53
538 543 1.290134 ACTCCAAGCTAAGGAAGGGG 58.710 55.000 8.95 1.04 34.08 4.79
573 578 2.955200 AAGGGCTAAGTACTACCCCA 57.045 50.000 19.89 0.00 43.96 4.96
685 690 4.869861 CGCAAAAATTAAAGAGGAATGGGG 59.130 41.667 0.00 0.00 0.00 4.96
707 713 2.223021 CCTCATGGAAAATGTGCGTACG 60.223 50.000 11.84 11.84 34.57 3.67
738 744 5.012148 CCGGTAGGGAATCAGAATAAGATGT 59.988 44.000 0.00 0.00 38.47 3.06
743 749 3.389983 CCACCGGTAGGGAATCAGAATAA 59.610 47.826 6.87 0.00 43.47 1.40
745 751 1.768870 CCACCGGTAGGGAATCAGAAT 59.231 52.381 6.87 0.00 43.47 2.40
755 761 1.137675 GTAAAGTAGGCCACCGGTAGG 59.862 57.143 6.87 12.99 45.13 3.18
757 763 0.817013 CGTAAAGTAGGCCACCGGTA 59.183 55.000 6.87 0.00 0.00 4.02
758 764 1.187567 ACGTAAAGTAGGCCACCGGT 61.188 55.000 5.01 0.00 0.00 5.28
759 765 0.037046 AACGTAAAGTAGGCCACCGG 60.037 55.000 5.01 0.00 0.00 5.28
760 766 1.073177 CAACGTAAAGTAGGCCACCG 58.927 55.000 5.01 3.05 0.00 4.94
761 767 1.002315 TCCAACGTAAAGTAGGCCACC 59.998 52.381 5.01 0.00 0.00 4.61
776 782 2.369394 GGAACATGGGTCATCTCCAAC 58.631 52.381 0.00 0.00 37.87 3.77
801 809 1.548582 CCTTCCACAATGGCAACTCCT 60.549 52.381 0.00 0.00 37.47 3.69
824 832 1.224592 CGGCTTCCTATTGGCTGGT 59.775 57.895 0.00 0.00 0.00 4.00
849 857 4.630894 TTTTGTCGATGTCATATTGGCC 57.369 40.909 0.00 0.00 0.00 5.36
881 889 1.068816 GTGTGTTTATCGGGGTTGTGC 60.069 52.381 0.00 0.00 0.00 4.57
886 894 3.713826 AATCTGTGTGTTTATCGGGGT 57.286 42.857 0.00 0.00 0.00 4.95
1197 1205 1.542175 CTGAGGGGAGATCGGGGTA 59.458 63.158 0.00 0.00 0.00 3.69
1684 1692 2.529389 AAGGCTTCGGGACCTGGT 60.529 61.111 0.00 0.00 36.07 4.00
2264 2272 0.527817 CTCGATACTTCCGCCACACC 60.528 60.000 0.00 0.00 0.00 4.16
3065 3073 2.250924 TGTGAGCCTCATGTCAAGAGA 58.749 47.619 6.65 0.00 35.09 3.10
3673 3681 4.019858 TGGAAATGTCAAACCTCACACAA 58.980 39.130 0.00 0.00 0.00 3.33
3674 3682 3.625853 TGGAAATGTCAAACCTCACACA 58.374 40.909 0.00 0.00 0.00 3.72
3998 4008 8.493547 AGCTTACAAACACGTCTTATAGTTTTC 58.506 33.333 0.00 0.00 32.34 2.29
3999 4009 8.374327 AGCTTACAAACACGTCTTATAGTTTT 57.626 30.769 0.00 0.00 32.34 2.43
4413 4424 6.327934 GCATGAGCACAAAAGTTGATAAGAT 58.672 36.000 0.00 0.00 41.58 2.40
4425 4436 1.042229 AGCAAAGGCATGAGCACAAA 58.958 45.000 0.00 0.00 44.61 2.83
4428 4439 2.019249 TGATAGCAAAGGCATGAGCAC 58.981 47.619 0.00 0.00 44.61 4.40
4593 4605 2.551912 GCACCAGAACACCAACGGG 61.552 63.158 0.00 0.00 41.29 5.28
4596 4608 0.465460 TCCTGCACCAGAACACCAAC 60.465 55.000 0.00 0.00 32.44 3.77
4598 4610 0.179020 CTTCCTGCACCAGAACACCA 60.179 55.000 0.00 0.00 32.44 4.17
4724 4736 2.496291 GCAGGGATGAATGCAGGCC 61.496 63.158 0.00 0.00 42.11 5.19
4744 4756 4.222124 AGAACCATCAGCGAAATAACCT 57.778 40.909 0.00 0.00 0.00 3.50
4768 4780 1.839354 TGACCATGAATCTAGCTGCCA 59.161 47.619 0.00 0.00 0.00 4.92
4843 4855 2.924290 GGAAATCTCGACTCCTGAAACG 59.076 50.000 0.00 0.00 0.00 3.60
5248 5260 2.810852 CTCTTCAAAGGCAGGAGAACAC 59.189 50.000 0.00 0.00 0.00 3.32
5292 5304 0.615331 TGAATGGCCAGGACAGACTC 59.385 55.000 13.05 0.00 0.00 3.36
5410 5422 3.382546 TCCGTCTATTTTAGAACGGAGGG 59.617 47.826 11.11 0.00 45.01 4.30
5411 5423 4.644103 TCCGTCTATTTTAGAACGGAGG 57.356 45.455 11.11 5.30 45.01 4.30
5413 5425 3.763360 TGGTCCGTCTATTTTAGAACGGA 59.237 43.478 11.11 11.11 46.27 4.69
5414 5426 4.114058 TGGTCCGTCTATTTTAGAACGG 57.886 45.455 6.45 6.45 43.94 4.44
5415 5427 5.166398 AGTTGGTCCGTCTATTTTAGAACG 58.834 41.667 0.00 0.00 36.40 3.95
5416 5428 7.430992 AAAGTTGGTCCGTCTATTTTAGAAC 57.569 36.000 0.00 0.00 36.40 3.01
5418 5430 9.807649 GTATAAAGTTGGTCCGTCTATTTTAGA 57.192 33.333 0.00 0.00 0.00 2.10
5419 5431 9.813446 AGTATAAAGTTGGTCCGTCTATTTTAG 57.187 33.333 0.00 0.00 0.00 1.85
5422 5434 9.591792 GTTAGTATAAAGTTGGTCCGTCTATTT 57.408 33.333 0.00 0.00 0.00 1.40
5423 5435 8.975295 AGTTAGTATAAAGTTGGTCCGTCTATT 58.025 33.333 0.00 0.00 0.00 1.73
5424 5436 8.530804 AGTTAGTATAAAGTTGGTCCGTCTAT 57.469 34.615 0.00 0.00 0.00 1.98
5425 5437 7.944729 AGTTAGTATAAAGTTGGTCCGTCTA 57.055 36.000 0.00 0.00 0.00 2.59
5426 5438 6.847421 AGTTAGTATAAAGTTGGTCCGTCT 57.153 37.500 0.00 0.00 0.00 4.18
5427 5439 7.386025 ACAAAGTTAGTATAAAGTTGGTCCGTC 59.614 37.037 0.00 0.00 0.00 4.79
5428 5440 7.219322 ACAAAGTTAGTATAAAGTTGGTCCGT 58.781 34.615 0.00 0.00 0.00 4.69
5429 5441 7.662604 ACAAAGTTAGTATAAAGTTGGTCCG 57.337 36.000 0.00 0.00 0.00 4.79
5430 5442 9.716531 AGTACAAAGTTAGTATAAAGTTGGTCC 57.283 33.333 0.00 0.00 30.33 4.46
5463 5475 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
5464 5476 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
5465 5477 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
5466 5478 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
5467 5479 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
5468 5480 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
5469 5481 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
5470 5482 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
5471 5483 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
5472 5484 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
5473 5485 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
5474 5486 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
5475 5487 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
5476 5488 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
5477 5489 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
5478 5490 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
5479 5491 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
5480 5492 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
5481 5493 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
5482 5494 4.098894 AGTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
5483 5495 2.910977 AGTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
5484 5496 2.332117 AGTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
5485 5497 2.019807 AGTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
5486 5498 2.225091 TGTAGTACTCCCTCCGTTCCAA 60.225 50.000 0.00 0.00 0.00 3.53
5487 5499 1.355381 TGTAGTACTCCCTCCGTTCCA 59.645 52.381 0.00 0.00 0.00 3.53
5488 5500 2.134789 TGTAGTACTCCCTCCGTTCC 57.865 55.000 0.00 0.00 0.00 3.62
5489 5501 4.159135 TGAAATGTAGTACTCCCTCCGTTC 59.841 45.833 0.00 0.00 0.00 3.95
5490 5502 4.091549 TGAAATGTAGTACTCCCTCCGTT 58.908 43.478 0.00 0.00 0.00 4.44
5491 5503 3.705051 TGAAATGTAGTACTCCCTCCGT 58.295 45.455 0.00 0.00 0.00 4.69
5492 5504 4.081862 TGTTGAAATGTAGTACTCCCTCCG 60.082 45.833 0.00 0.00 0.00 4.63
5493 5505 5.046520 ACTGTTGAAATGTAGTACTCCCTCC 60.047 44.000 0.00 0.00 0.00 4.30
5494 5506 5.869888 CACTGTTGAAATGTAGTACTCCCTC 59.130 44.000 0.00 0.00 0.00 4.30
5495 5507 5.307196 ACACTGTTGAAATGTAGTACTCCCT 59.693 40.000 0.00 0.00 0.00 4.20
5496 5508 5.548406 ACACTGTTGAAATGTAGTACTCCC 58.452 41.667 0.00 0.00 0.00 4.30
5497 5509 6.565999 GCAACACTGTTGAAATGTAGTACTCC 60.566 42.308 23.49 0.00 0.00 3.85
5498 5510 6.202954 AGCAACACTGTTGAAATGTAGTACTC 59.797 38.462 23.49 3.27 0.00 2.59
5499 5511 6.055588 AGCAACACTGTTGAAATGTAGTACT 58.944 36.000 23.49 0.00 0.00 2.73
5500 5512 6.300354 AGCAACACTGTTGAAATGTAGTAC 57.700 37.500 23.49 3.90 0.00 2.73
5501 5513 6.935741 AAGCAACACTGTTGAAATGTAGTA 57.064 33.333 23.49 0.00 0.00 1.82
5502 5514 5.835113 AAGCAACACTGTTGAAATGTAGT 57.165 34.783 23.49 0.00 0.00 2.73
5503 5515 6.373779 CCTAAGCAACACTGTTGAAATGTAG 58.626 40.000 23.49 14.71 0.00 2.74
5504 5516 5.278266 GCCTAAGCAACACTGTTGAAATGTA 60.278 40.000 23.49 7.78 39.53 2.29
5527 5539 4.328712 ACGAAACAACATTCCAAACAAAGC 59.671 37.500 0.00 0.00 0.00 3.51
5528 5540 5.804979 AGACGAAACAACATTCCAAACAAAG 59.195 36.000 0.00 0.00 0.00 2.77
5529 5541 5.715070 AGACGAAACAACATTCCAAACAAA 58.285 33.333 0.00 0.00 0.00 2.83
5530 5542 5.106118 TGAGACGAAACAACATTCCAAACAA 60.106 36.000 0.00 0.00 0.00 2.83
5531 5543 4.396478 TGAGACGAAACAACATTCCAAACA 59.604 37.500 0.00 0.00 0.00 2.83
5532 5544 4.915704 TGAGACGAAACAACATTCCAAAC 58.084 39.130 0.00 0.00 0.00 2.93
5533 5545 5.568685 TTGAGACGAAACAACATTCCAAA 57.431 34.783 0.00 0.00 0.00 3.28
5534 5546 5.568685 TTTGAGACGAAACAACATTCCAA 57.431 34.783 0.00 0.00 0.00 3.53
5535 5547 5.766150 ATTTGAGACGAAACAACATTCCA 57.234 34.783 0.00 0.00 0.00 3.53
5536 5548 6.577427 GTGTATTTGAGACGAAACAACATTCC 59.423 38.462 0.00 0.00 0.00 3.01
5537 5549 7.352739 AGTGTATTTGAGACGAAACAACATTC 58.647 34.615 0.00 0.00 0.00 2.67
5538 5550 7.259290 AGTGTATTTGAGACGAAACAACATT 57.741 32.000 0.00 0.00 0.00 2.71
5539 5551 6.861065 AGTGTATTTGAGACGAAACAACAT 57.139 33.333 0.00 0.00 0.00 2.71
5540 5552 6.092944 ACAAGTGTATTTGAGACGAAACAACA 59.907 34.615 0.00 0.00 0.00 3.33
5541 5553 6.483687 ACAAGTGTATTTGAGACGAAACAAC 58.516 36.000 0.00 0.00 0.00 3.32
5542 5554 6.671614 ACAAGTGTATTTGAGACGAAACAA 57.328 33.333 0.00 0.00 0.00 2.83
5543 5555 7.204604 TCTACAAGTGTATTTGAGACGAAACA 58.795 34.615 0.00 0.00 0.00 2.83
5544 5556 7.633361 TCTACAAGTGTATTTGAGACGAAAC 57.367 36.000 0.00 0.00 0.00 2.78
5545 5557 8.651391 TTTCTACAAGTGTATTTGAGACGAAA 57.349 30.769 0.00 0.00 0.00 3.46
5546 5558 8.651391 TTTTCTACAAGTGTATTTGAGACGAA 57.349 30.769 0.00 0.00 0.00 3.85
5547 5559 8.139350 TCTTTTCTACAAGTGTATTTGAGACGA 58.861 33.333 0.00 0.00 0.00 4.20
5548 5560 8.294341 TCTTTTCTACAAGTGTATTTGAGACG 57.706 34.615 0.00 0.00 0.00 4.18
5558 5570 8.254508 GGAGATCTGTATCTTTTCTACAAGTGT 58.745 37.037 0.00 0.00 42.73 3.55
5559 5571 7.433719 CGGAGATCTGTATCTTTTCTACAAGTG 59.566 40.741 0.00 0.00 42.73 3.16
5560 5572 7.484975 CGGAGATCTGTATCTTTTCTACAAGT 58.515 38.462 0.00 0.00 42.73 3.16
5561 5573 6.419413 GCGGAGATCTGTATCTTTTCTACAAG 59.581 42.308 0.00 0.00 42.73 3.16
5562 5574 6.096987 AGCGGAGATCTGTATCTTTTCTACAA 59.903 38.462 0.00 0.00 42.73 2.41
5563 5575 5.594725 AGCGGAGATCTGTATCTTTTCTACA 59.405 40.000 0.00 0.00 42.73 2.74
5564 5576 6.079424 AGCGGAGATCTGTATCTTTTCTAC 57.921 41.667 0.00 0.00 42.73 2.59
5565 5577 5.828328 TGAGCGGAGATCTGTATCTTTTCTA 59.172 40.000 0.00 0.00 46.78 2.10
5566 5578 4.646945 TGAGCGGAGATCTGTATCTTTTCT 59.353 41.667 0.00 0.00 46.78 2.52
5567 5579 4.938080 TGAGCGGAGATCTGTATCTTTTC 58.062 43.478 0.00 0.00 46.78 2.29
5568 5580 5.537188 GATGAGCGGAGATCTGTATCTTTT 58.463 41.667 0.00 0.00 46.78 2.27
5569 5581 4.320861 CGATGAGCGGAGATCTGTATCTTT 60.321 45.833 0.00 0.00 46.78 2.52
5570 5582 3.190327 CGATGAGCGGAGATCTGTATCTT 59.810 47.826 0.00 0.00 46.78 2.40
5571 5583 2.746904 CGATGAGCGGAGATCTGTATCT 59.253 50.000 0.00 0.00 46.78 1.98
5572 5584 2.486203 ACGATGAGCGGAGATCTGTATC 59.514 50.000 0.00 0.00 46.78 2.24
5573 5585 2.509569 ACGATGAGCGGAGATCTGTAT 58.490 47.619 0.00 0.00 46.78 2.29
5574 5586 1.968704 ACGATGAGCGGAGATCTGTA 58.031 50.000 0.00 0.00 46.78 2.74
5575 5587 1.107114 AACGATGAGCGGAGATCTGT 58.893 50.000 0.00 0.00 46.78 3.41
5576 5588 2.215907 AAACGATGAGCGGAGATCTG 57.784 50.000 0.00 0.00 46.78 2.90
5577 5589 2.166459 TCAAAACGATGAGCGGAGATCT 59.834 45.455 0.00 0.00 46.78 2.75
5578 5590 2.540515 TCAAAACGATGAGCGGAGATC 58.459 47.619 0.00 0.00 46.88 2.75
5579 5591 2.672961 TCAAAACGATGAGCGGAGAT 57.327 45.000 0.00 0.00 46.49 2.75
5580 5592 2.672961 ATCAAAACGATGAGCGGAGA 57.327 45.000 0.00 0.00 46.49 3.71
5581 5593 2.030946 GGAATCAAAACGATGAGCGGAG 59.969 50.000 0.00 0.00 46.49 4.63
5582 5594 2.006888 GGAATCAAAACGATGAGCGGA 58.993 47.619 0.00 0.00 46.49 5.54
5583 5595 1.267532 CGGAATCAAAACGATGAGCGG 60.268 52.381 0.00 0.00 46.49 5.52
5585 5597 1.531883 GCCGGAATCAAAACGATGAGC 60.532 52.381 5.05 0.00 33.40 4.26
5586 5598 2.009774 AGCCGGAATCAAAACGATGAG 58.990 47.619 5.05 0.00 33.40 2.90
5587 5599 1.737236 CAGCCGGAATCAAAACGATGA 59.263 47.619 5.05 0.00 33.40 2.92
5588 5600 1.202177 CCAGCCGGAATCAAAACGATG 60.202 52.381 5.05 0.00 33.40 3.84
5589 5601 1.094785 CCAGCCGGAATCAAAACGAT 58.905 50.000 5.05 0.00 35.12 3.73
5590 5602 0.035598 TCCAGCCGGAATCAAAACGA 59.964 50.000 5.05 0.00 38.83 3.85
5591 5603 0.878416 TTCCAGCCGGAATCAAAACG 59.122 50.000 5.05 0.00 46.79 3.60
5600 5612 1.284198 ACTAGTAGAGTTCCAGCCGGA 59.716 52.381 5.05 0.00 40.60 5.14
5601 5613 1.405821 CACTAGTAGAGTTCCAGCCGG 59.594 57.143 3.59 0.00 35.64 6.13
5602 5614 1.405821 CCACTAGTAGAGTTCCAGCCG 59.594 57.143 3.59 0.00 35.64 5.52
5603 5615 1.137282 GCCACTAGTAGAGTTCCAGCC 59.863 57.143 3.59 0.00 35.64 4.85
5604 5616 1.137282 GGCCACTAGTAGAGTTCCAGC 59.863 57.143 3.59 0.00 35.64 4.85
5605 5617 1.405821 CGGCCACTAGTAGAGTTCCAG 59.594 57.143 2.24 0.00 35.64 3.86
5606 5618 1.471119 CGGCCACTAGTAGAGTTCCA 58.529 55.000 2.24 0.00 35.64 3.53
5607 5619 0.745468 CCGGCCACTAGTAGAGTTCC 59.255 60.000 2.24 0.00 35.64 3.62
5608 5620 1.472188 ACCGGCCACTAGTAGAGTTC 58.528 55.000 0.00 0.00 35.64 3.01
5609 5621 2.814805 TACCGGCCACTAGTAGAGTT 57.185 50.000 0.00 0.00 35.64 3.01
5610 5622 2.240667 TCTTACCGGCCACTAGTAGAGT 59.759 50.000 0.00 0.00 39.82 3.24
5611 5623 2.928334 TCTTACCGGCCACTAGTAGAG 58.072 52.381 0.00 0.00 0.00 2.43
5612 5624 3.589951 ATCTTACCGGCCACTAGTAGA 57.410 47.619 0.00 0.00 0.00 2.59
5613 5625 5.064452 CGTATATCTTACCGGCCACTAGTAG 59.936 48.000 0.00 0.00 0.00 2.57
5614 5626 4.937620 CGTATATCTTACCGGCCACTAGTA 59.062 45.833 0.00 0.00 0.00 1.82
5615 5627 3.755378 CGTATATCTTACCGGCCACTAGT 59.245 47.826 0.00 0.00 0.00 2.57
5616 5628 3.755378 ACGTATATCTTACCGGCCACTAG 59.245 47.826 0.00 0.00 0.00 2.57
5617 5629 3.503363 CACGTATATCTTACCGGCCACTA 59.497 47.826 0.00 0.00 0.00 2.74
5618 5630 2.295349 CACGTATATCTTACCGGCCACT 59.705 50.000 0.00 0.00 0.00 4.00
5619 5631 2.035066 ACACGTATATCTTACCGGCCAC 59.965 50.000 0.00 0.00 0.00 5.01
5620 5632 2.309613 ACACGTATATCTTACCGGCCA 58.690 47.619 0.00 0.00 0.00 5.36
5621 5633 4.503741 TTACACGTATATCTTACCGGCC 57.496 45.455 0.00 0.00 0.00 6.13
5622 5634 5.523369 AGTTTACACGTATATCTTACCGGC 58.477 41.667 0.00 0.00 0.00 6.13
5623 5635 9.683069 ATTTAGTTTACACGTATATCTTACCGG 57.317 33.333 0.00 0.00 0.00 5.28
5635 5647 8.970691 AATACAGACGTATTTAGTTTACACGT 57.029 30.769 0.00 0.00 44.27 4.49
5648 5660 5.461078 GCGGTGTAATCAAATACAGACGTAT 59.539 40.000 0.00 0.00 40.15 3.06
5649 5661 4.799949 GCGGTGTAATCAAATACAGACGTA 59.200 41.667 0.00 0.00 38.53 3.57
5650 5662 3.615496 GCGGTGTAATCAAATACAGACGT 59.385 43.478 0.00 0.00 38.53 4.34
5651 5663 3.615056 TGCGGTGTAATCAAATACAGACG 59.385 43.478 0.00 0.00 38.93 4.18
5652 5664 5.277345 GGATGCGGTGTAATCAAATACAGAC 60.277 44.000 0.00 0.00 36.51 3.51
5653 5665 4.814234 GGATGCGGTGTAATCAAATACAGA 59.186 41.667 0.00 0.00 36.51 3.41
5654 5666 4.574421 TGGATGCGGTGTAATCAAATACAG 59.426 41.667 0.00 0.00 36.51 2.74
5655 5667 4.518249 TGGATGCGGTGTAATCAAATACA 58.482 39.130 0.00 0.00 33.52 2.29
5656 5668 5.493133 TTGGATGCGGTGTAATCAAATAC 57.507 39.130 0.00 0.00 0.00 1.89
5657 5669 4.036262 GCTTGGATGCGGTGTAATCAAATA 59.964 41.667 0.00 0.00 0.00 1.40
5658 5670 3.181487 GCTTGGATGCGGTGTAATCAAAT 60.181 43.478 0.00 0.00 0.00 2.32
5659 5671 2.163412 GCTTGGATGCGGTGTAATCAAA 59.837 45.455 0.00 0.00 0.00 2.69
5660 5672 1.742831 GCTTGGATGCGGTGTAATCAA 59.257 47.619 0.00 0.00 0.00 2.57
5661 5673 1.378531 GCTTGGATGCGGTGTAATCA 58.621 50.000 0.00 0.00 0.00 2.57
5672 5684 2.513666 TAAGGCCGCGCTTGGATG 60.514 61.111 5.56 0.00 0.00 3.51
5673 5685 2.203070 CTAAGGCCGCGCTTGGAT 60.203 61.111 5.56 0.00 0.00 3.41
5674 5686 3.702048 ACTAAGGCCGCGCTTGGA 61.702 61.111 14.81 0.00 0.00 3.53
5675 5687 3.499737 CACTAAGGCCGCGCTTGG 61.500 66.667 5.56 4.25 0.00 3.61
5676 5688 1.852067 AAACACTAAGGCCGCGCTTG 61.852 55.000 5.56 0.00 0.00 4.01
5677 5689 0.320946 TAAACACTAAGGCCGCGCTT 60.321 50.000 5.56 1.72 0.00 4.68
5678 5690 1.017701 GTAAACACTAAGGCCGCGCT 61.018 55.000 5.56 0.00 0.00 5.92
5679 5691 1.293267 TGTAAACACTAAGGCCGCGC 61.293 55.000 0.00 0.00 0.00 6.86
5680 5692 0.719465 CTGTAAACACTAAGGCCGCG 59.281 55.000 0.00 0.00 0.00 6.46
5681 5693 0.446616 GCTGTAAACACTAAGGCCGC 59.553 55.000 0.00 0.00 0.00 6.53
5682 5694 1.803334 TGCTGTAAACACTAAGGCCG 58.197 50.000 0.00 0.00 0.00 6.13
5683 5695 4.258543 TGTATGCTGTAAACACTAAGGCC 58.741 43.478 0.00 0.00 0.00 5.19
5684 5696 6.436843 AATGTATGCTGTAAACACTAAGGC 57.563 37.500 0.00 0.00 0.00 4.35
5685 5697 7.816640 ACAAATGTATGCTGTAAACACTAAGG 58.183 34.615 0.00 0.00 0.00 2.69
5686 5698 9.329913 GAACAAATGTATGCTGTAAACACTAAG 57.670 33.333 0.00 0.00 0.00 2.18
5687 5699 9.062524 AGAACAAATGTATGCTGTAAACACTAA 57.937 29.630 0.00 0.00 0.00 2.24
5688 5700 8.615878 AGAACAAATGTATGCTGTAAACACTA 57.384 30.769 0.00 0.00 0.00 2.74
5689 5701 7.510549 AGAACAAATGTATGCTGTAAACACT 57.489 32.000 0.00 0.00 0.00 3.55
5690 5702 7.860373 TCAAGAACAAATGTATGCTGTAAACAC 59.140 33.333 0.00 0.00 0.00 3.32
5963 6356 3.850098 CTATGTGGATGGCCCGGGC 62.850 68.421 38.57 38.57 37.93 6.13
5964 6357 1.492133 ATCTATGTGGATGGCCCGGG 61.492 60.000 19.09 19.09 37.93 5.73
5965 6358 1.275666 TATCTATGTGGATGGCCCGG 58.724 55.000 0.00 0.00 37.93 5.73
5966 6359 3.417069 TTTATCTATGTGGATGGCCCG 57.583 47.619 0.00 0.00 37.93 6.13


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

AutoCloner maintained by Alex Coulton.