Multiple sequence alignment - TraesCS3B01G173300

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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 TraesCS3B01G173300 chr3B 100.000 4141 0 0 1 4141 173388436 173384296 0.000000e+00 7648.0
1 TraesCS3B01G173300 chr3B 91.549 71 2 1 590 656 661782218 661782288 1.230000e-15 95.3
2 TraesCS3B01G173300 chr3B 89.552 67 6 1 526 592 753519205 753519140 2.650000e-12 84.2
3 TraesCS3B01G173300 chr3B 89.062 64 6 1 650 713 695558955 695558893 1.230000e-10 78.7
4 TraesCS3B01G173300 chr3A 94.040 3087 106 24 698 3733 128160714 128157655 0.000000e+00 4610.0
5 TraesCS3B01G173300 chr3A 90.168 417 32 7 3729 4141 128157625 128157214 6.090000e-148 534.0
6 TraesCS3B01G173300 chr3A 86.882 465 38 8 1 460 128161195 128160749 2.220000e-137 499.0
7 TraesCS3B01G173300 chr3A 83.582 134 18 4 2888 3019 127966030 127965899 5.620000e-24 122.0
8 TraesCS3B01G173300 chr3A 93.939 66 1 1 590 652 138479064 138479129 3.410000e-16 97.1
9 TraesCS3B01G173300 chr3A 97.959 49 1 0 544 592 514899162 514899114 7.380000e-13 86.1
10 TraesCS3B01G173300 chr3D 93.410 3035 99 28 725 3715 121963378 121960401 0.000000e+00 4403.0
11 TraesCS3B01G173300 chr3D 89.004 482 32 7 1 479 121965527 121965064 9.980000e-161 577.0
12 TraesCS3B01G173300 chr3D 89.952 418 32 8 3729 4141 121945302 121944890 7.880000e-147 531.0
13 TraesCS3B01G173300 chr3D 92.958 71 5 0 475 545 71512911 71512841 2.040000e-18 104.0
14 TraesCS3B01G173300 chr3D 90.789 76 7 0 3109 3184 121534731 121534656 7.320000e-18 102.0
15 TraesCS3B01G173300 chr3D 85.915 71 6 3 654 720 448433659 448433729 5.740000e-09 73.1
16 TraesCS3B01G173300 chr4D 85.834 2746 252 56 1456 4138 22580035 22582706 0.000000e+00 2789.0
17 TraesCS3B01G173300 chr4D 84.118 340 28 13 821 1145 22579585 22579913 5.200000e-79 305.0
18 TraesCS3B01G173300 chr4D 95.588 68 3 0 478 545 496282362 496282429 4.380000e-20 110.0
19 TraesCS3B01G173300 chr4D 91.071 56 3 2 652 707 478034014 478033961 1.600000e-09 75.0
20 TraesCS3B01G173300 chr4A 82.037 913 109 28 3251 4138 579525776 579524894 0.000000e+00 726.0
21 TraesCS3B01G173300 chr4A 90.308 227 14 4 3038 3257 579526075 579525850 1.460000e-74 291.0
22 TraesCS3B01G173300 chr4A 86.585 82 7 1 590 667 343481106 343481025 2.050000e-13 87.9
23 TraesCS3B01G173300 chr4A 90.000 60 4 2 644 703 133061446 133061389 4.440000e-10 76.8
24 TraesCS3B01G173300 chr4B 85.196 716 53 23 2103 2811 34567845 34568514 0.000000e+00 686.0
25 TraesCS3B01G173300 chr4B 86.111 648 70 11 1456 2100 34565530 34566160 0.000000e+00 680.0
26 TraesCS3B01G173300 chr4B 90.226 399 34 5 2768 3161 34568530 34568928 2.210000e-142 516.0
27 TraesCS3B01G173300 chr4B 84.709 412 31 10 3199 3601 34568923 34569311 2.340000e-102 383.0
28 TraesCS3B01G173300 chr4B 90.323 124 12 0 3729 3852 34569318 34569441 3.310000e-36 163.0
29 TraesCS3B01G173300 chr4B 91.549 71 5 1 475 545 642167076 642167145 3.410000e-16 97.1
30 TraesCS3B01G173300 chr4B 91.549 71 2 1 590 656 434049955 434049885 1.230000e-15 95.3
31 TraesCS3B01G173300 chr4B 88.462 78 4 2 590 663 308540772 308540696 5.700000e-14 89.8
32 TraesCS3B01G173300 chr2A 92.958 71 4 1 476 546 587158359 587158290 7.320000e-18 102.0
33 TraesCS3B01G173300 chr2A 98.039 51 1 0 542 592 283154845 283154795 5.700000e-14 89.8
34 TraesCS3B01G173300 chr2A 97.959 49 1 0 544 592 92786298 92786346 7.380000e-13 86.1
35 TraesCS3B01G173300 chr2A 93.617 47 1 2 654 699 564265034 564264989 7.430000e-08 69.4
36 TraesCS3B01G173300 chr7A 91.781 73 5 1 474 545 112786353 112786281 2.630000e-17 100.0
37 TraesCS3B01G173300 chr7A 97.959 49 1 0 544 592 366101751 366101703 7.380000e-13 86.1
38 TraesCS3B01G173300 chr7A 92.308 52 3 1 648 699 516148354 516148304 5.740000e-09 73.1
39 TraesCS3B01G173300 chr6D 92.754 69 5 0 477 545 292393181 292393249 2.630000e-17 100.0
40 TraesCS3B01G173300 chr6D 96.226 53 1 1 541 592 28210803 28210855 7.380000e-13 86.1
41 TraesCS3B01G173300 chr6A 92.754 69 5 0 477 545 57899068 57899000 2.630000e-17 100.0
42 TraesCS3B01G173300 chr7B 92.754 69 1 1 590 654 441595498 441595430 3.410000e-16 97.1
43 TraesCS3B01G173300 chr5A 86.957 92 4 4 590 674 393621116 393621206 3.410000e-16 97.1
44 TraesCS3B01G173300 chr5A 92.754 69 1 1 590 654 415491966 415491898 3.410000e-16 97.1
45 TraesCS3B01G173300 chr5A 91.429 70 5 1 472 541 471947880 471947948 1.230000e-15 95.3
46 TraesCS3B01G173300 chr5A 100.000 29 0 0 113 141 9513754 9513782 2.000000e-03 54.7
47 TraesCS3B01G173300 chr1B 92.754 69 1 1 589 653 274383075 274383143 3.410000e-16 97.1
48 TraesCS3B01G173300 chr1B 84.848 66 6 4 645 707 285341789 285341725 3.460000e-06 63.9
49 TraesCS3B01G173300 chr1A 90.541 74 5 2 473 546 264217592 264217521 3.410000e-16 97.1
50 TraesCS3B01G173300 chr1A 98.039 51 1 0 542 592 386998004 386998054 5.700000e-14 89.8
51 TraesCS3B01G173300 chr1A 97.959 49 1 0 544 592 527223011 527223059 7.380000e-13 86.1
52 TraesCS3B01G173300 chr1D 97.959 49 1 0 544 592 371674965 371674917 7.380000e-13 86.1
53 TraesCS3B01G173300 chr1D 79.439 107 12 6 45 141 359640767 359640873 2.670000e-07 67.6
54 TraesCS3B01G173300 chr2D 92.982 57 4 0 654 710 464519475 464519419 2.650000e-12 84.2
55 TraesCS3B01G173300 chr2D 91.525 59 3 2 646 703 473096419 473096362 3.430000e-11 80.5
56 TraesCS3B01G173300 chr2D 86.957 69 5 4 656 721 190586307 190586374 1.600000e-09 75.0
57 TraesCS3B01G173300 chr2D 86.957 69 5 4 656 721 190596421 190596488 1.600000e-09 75.0
58 TraesCS3B01G173300 chr2D 90.566 53 4 1 647 699 75097635 75097686 7.430000e-08 69.4
59 TraesCS3B01G173300 chr2D 85.714 56 5 2 113 168 139002879 139002931 5.780000e-04 56.5
60 TraesCS3B01G173300 chr5D 91.525 59 3 2 654 711 369429179 369429236 3.430000e-11 80.5
61 TraesCS3B01G173300 chr5B 88.889 63 5 2 644 705 315893395 315893334 4.440000e-10 76.8
62 TraesCS3B01G173300 chr6B 92.157 51 3 1 654 704 452186045 452185996 2.070000e-08 71.3


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 TraesCS3B01G173300 chr3B 173384296 173388436 4140 True 7648.0 7648 100.000000 1 4141 1 chr3B.!!$R1 4140
1 TraesCS3B01G173300 chr3A 128157214 128161195 3981 True 1881.0 4610 90.363333 1 4141 3 chr3A.!!$R3 4140
2 TraesCS3B01G173300 chr3D 121960401 121965527 5126 True 2490.0 4403 91.207000 1 3715 2 chr3D.!!$R4 3714
3 TraesCS3B01G173300 chr4D 22579585 22582706 3121 False 1547.0 2789 84.976000 821 4138 2 chr4D.!!$F2 3317
4 TraesCS3B01G173300 chr4A 579524894 579526075 1181 True 508.5 726 86.172500 3038 4138 2 chr4A.!!$R3 1100
5 TraesCS3B01G173300 chr4B 34565530 34569441 3911 False 485.6 686 87.313000 1456 3852 5 chr4B.!!$F2 2396

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
612 635 0.104356 TTGAACCTAGGTGGGTGGGA 60.104 55.0 17.14 0.0 39.85 4.37 F
613 636 0.104356 TGAACCTAGGTGGGTGGGAA 60.104 55.0 17.14 0.0 39.85 3.97 F
1094 2790 0.325765 GACCTGGAGGCTAGGGTCTT 60.326 60.0 19.30 0.0 43.30 3.01 F
1452 3148 0.461961 GAGACCATGGGAGAGTTCGG 59.538 60.0 18.09 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1620 3319 0.392706 TGTCACTGACTCCACGCAAT 59.607 50.000 10.54 0.0 33.15 3.56 R
2018 3720 0.935196 CCTTTTGCCGCGTATCCTAC 59.065 55.000 4.92 0.0 0.00 3.18 R
3045 6534 3.578282 TGACAGAACTCAAGAGCATACCA 59.422 43.478 0.00 0.0 0.00 3.25 R
3312 6894 2.889512 ACATAGACCCTGTCAGACACA 58.110 47.619 0.00 0.0 34.60 3.72 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
42 43 6.601613 TGGCCGAATTTAACTACATCATTCTT 59.398 34.615 0.00 0.00 0.00 2.52
66 67 2.434336 TCGGATCTCACGGGATTCAATT 59.566 45.455 0.00 0.00 0.00 2.32
81 82 3.694043 TCAATTGGTGATGGTCTTCGA 57.306 42.857 5.42 0.00 0.00 3.71
96 97 5.221441 TGGTCTTCGATGGATCAATTCGTAT 60.221 40.000 9.91 0.00 34.60 3.06
103 104 8.056407 TCGATGGATCAATTCGTATCTAATCT 57.944 34.615 9.91 0.00 34.60 2.40
135 136 4.825085 GTGTTTACAGGTTTGATCCTTCCA 59.175 41.667 0.00 0.00 35.37 3.53
153 154 7.057894 TCCTTCCAATCTAGAACTCTCTCTAC 58.942 42.308 0.00 0.00 32.70 2.59
155 156 6.328782 TCCAATCTAGAACTCTCTCTACCA 57.671 41.667 0.00 0.00 32.70 3.25
177 178 5.702670 CCAGTGATGATTGTTACTCTGTTGT 59.297 40.000 0.00 0.00 0.00 3.32
181 182 6.368791 GTGATGATTGTTACTCTGTTGTGCTA 59.631 38.462 0.00 0.00 0.00 3.49
214 219 1.021202 CACAAGTTTTGCTCGGTCCA 58.979 50.000 0.00 0.00 0.00 4.02
220 225 0.889186 TTTTGCTCGGTCCAAGAGGC 60.889 55.000 0.00 0.00 36.31 4.70
237 242 2.409870 GCAGGGACAATGAAGGCGG 61.410 63.158 0.00 0.00 0.00 6.13
240 245 1.976474 GGGACAATGAAGGCGGCAA 60.976 57.895 13.08 0.00 0.00 4.52
241 246 1.531739 GGGACAATGAAGGCGGCAAA 61.532 55.000 13.08 0.00 0.00 3.68
255 260 0.729690 GGCAAACCTTCATCTCGCTC 59.270 55.000 0.00 0.00 0.00 5.03
270 275 2.315246 GCTCTAGCGCAATGAAGGG 58.685 57.895 11.47 0.00 0.00 3.95
271 276 0.179073 GCTCTAGCGCAATGAAGGGA 60.179 55.000 11.47 0.00 0.00 4.20
273 278 0.901827 TCTAGCGCAATGAAGGGACA 59.098 50.000 11.47 0.00 0.00 4.02
274 279 1.277842 TCTAGCGCAATGAAGGGACAA 59.722 47.619 11.47 0.00 0.00 3.18
275 280 2.092968 TCTAGCGCAATGAAGGGACAAT 60.093 45.455 11.47 0.00 0.00 2.71
276 281 0.813184 AGCGCAATGAAGGGACAATG 59.187 50.000 11.47 0.00 0.00 2.82
277 282 0.810648 GCGCAATGAAGGGACAATGA 59.189 50.000 0.30 0.00 0.00 2.57
278 283 1.202114 GCGCAATGAAGGGACAATGAA 59.798 47.619 0.30 0.00 0.00 2.57
279 284 2.733227 GCGCAATGAAGGGACAATGAAG 60.733 50.000 0.30 0.00 0.00 3.02
280 285 2.159338 CGCAATGAAGGGACAATGAAGG 60.159 50.000 0.00 0.00 0.00 3.46
281 286 2.167075 GCAATGAAGGGACAATGAAGGG 59.833 50.000 0.00 0.00 0.00 3.95
282 287 3.700538 CAATGAAGGGACAATGAAGGGA 58.299 45.455 0.00 0.00 0.00 4.20
283 288 2.879103 TGAAGGGACAATGAAGGGAC 57.121 50.000 0.00 0.00 0.00 4.46
284 289 2.061848 TGAAGGGACAATGAAGGGACA 58.938 47.619 0.00 0.00 0.00 4.02
285 290 2.445145 TGAAGGGACAATGAAGGGACAA 59.555 45.455 0.00 0.00 0.00 3.18
286 291 2.887151 AGGGACAATGAAGGGACAAG 57.113 50.000 0.00 0.00 0.00 3.16
287 292 2.065799 AGGGACAATGAAGGGACAAGT 58.934 47.619 0.00 0.00 0.00 3.16
288 293 2.447047 AGGGACAATGAAGGGACAAGTT 59.553 45.455 0.00 0.00 0.00 2.66
289 294 3.117131 AGGGACAATGAAGGGACAAGTTT 60.117 43.478 0.00 0.00 0.00 2.66
290 295 3.641436 GGGACAATGAAGGGACAAGTTTT 59.359 43.478 0.00 0.00 0.00 2.43
291 296 4.501400 GGGACAATGAAGGGACAAGTTTTG 60.501 45.833 0.00 0.00 0.00 2.44
292 297 4.051237 GACAATGAAGGGACAAGTTTTGC 58.949 43.478 0.00 0.00 0.00 3.68
303 308 5.393461 GGGACAAGTTTTGCTAGATGATTGG 60.393 44.000 0.00 0.00 0.00 3.16
318 323 2.226200 TGATTGGTGAACATGCTTGTCG 59.774 45.455 5.61 0.00 34.06 4.35
451 456 7.946655 TTTAGTGGAGCAATATGACTTATCG 57.053 36.000 0.00 0.00 0.00 2.92
483 506 8.379457 AGGCAAATCCGTTTTTATATACTCTC 57.621 34.615 0.00 0.00 40.77 3.20
484 507 8.211629 AGGCAAATCCGTTTTTATATACTCTCT 58.788 33.333 0.00 0.00 40.77 3.10
485 508 8.496751 GGCAAATCCGTTTTTATATACTCTCTC 58.503 37.037 0.00 0.00 0.00 3.20
486 509 8.496751 GCAAATCCGTTTTTATATACTCTCTCC 58.503 37.037 0.00 0.00 0.00 3.71
487 510 9.542462 CAAATCCGTTTTTATATACTCTCTCCA 57.458 33.333 0.00 0.00 0.00 3.86
489 512 9.930693 AATCCGTTTTTATATACTCTCTCCATC 57.069 33.333 0.00 0.00 0.00 3.51
490 513 7.893658 TCCGTTTTTATATACTCTCTCCATCC 58.106 38.462 0.00 0.00 0.00 3.51
491 514 7.728981 TCCGTTTTTATATACTCTCTCCATCCT 59.271 37.037 0.00 0.00 0.00 3.24
492 515 9.021807 CCGTTTTTATATACTCTCTCCATCCTA 57.978 37.037 0.00 0.00 0.00 2.94
502 525 7.741554 ACTCTCTCCATCCTAAAATAAGTGT 57.258 36.000 0.00 0.00 0.00 3.55
503 526 7.787028 ACTCTCTCCATCCTAAAATAAGTGTC 58.213 38.462 0.00 0.00 0.00 3.67
504 527 7.621683 ACTCTCTCCATCCTAAAATAAGTGTCT 59.378 37.037 0.00 0.00 0.00 3.41
505 528 8.380742 TCTCTCCATCCTAAAATAAGTGTCTT 57.619 34.615 0.00 0.00 0.00 3.01
506 529 9.488762 TCTCTCCATCCTAAAATAAGTGTCTTA 57.511 33.333 0.00 0.00 0.00 2.10
508 531 9.886132 TCTCCATCCTAAAATAAGTGTCTTAAC 57.114 33.333 0.00 0.00 0.00 2.01
509 532 9.892130 CTCCATCCTAAAATAAGTGTCTTAACT 57.108 33.333 0.00 0.00 0.00 2.24
573 596 3.676093 CAGAAAGACTGTAAGGGAACCC 58.324 50.000 0.94 0.94 45.84 4.11
574 597 3.559384 CAGAAAGACTGTAAGGGAACCCC 60.559 52.174 6.23 0.00 45.84 4.95
576 599 6.517826 CAGAAAGACTGTAAGGGAACCCCTA 61.518 48.000 4.76 0.00 46.34 3.53
577 600 8.476810 CAGAAAGACTGTAAGGGAACCCCTAC 62.477 50.000 4.76 10.72 46.34 3.18
590 613 6.894339 GGAACCCCTACATTATAATTGGTG 57.106 41.667 0.00 0.00 0.00 4.17
591 614 5.243060 GGAACCCCTACATTATAATTGGTGC 59.757 44.000 0.00 0.00 0.00 5.01
592 615 4.736473 ACCCCTACATTATAATTGGTGCC 58.264 43.478 0.00 0.00 0.00 5.01
593 616 4.418863 ACCCCTACATTATAATTGGTGCCT 59.581 41.667 0.00 0.00 0.00 4.75
594 617 5.103258 ACCCCTACATTATAATTGGTGCCTT 60.103 40.000 0.00 0.00 0.00 4.35
595 618 5.243730 CCCCTACATTATAATTGGTGCCTTG 59.756 44.000 0.00 0.00 0.00 3.61
596 619 6.068010 CCCTACATTATAATTGGTGCCTTGA 58.932 40.000 0.00 0.00 0.00 3.02
597 620 6.549364 CCCTACATTATAATTGGTGCCTTGAA 59.451 38.462 0.00 0.00 0.00 2.69
598 621 7.425606 CCTACATTATAATTGGTGCCTTGAAC 58.574 38.462 0.00 0.00 0.00 3.18
599 622 6.220726 ACATTATAATTGGTGCCTTGAACC 57.779 37.500 0.00 0.00 38.26 3.62
600 623 5.957774 ACATTATAATTGGTGCCTTGAACCT 59.042 36.000 0.00 0.00 38.60 3.50
601 624 7.122715 ACATTATAATTGGTGCCTTGAACCTA 58.877 34.615 0.00 0.00 38.60 3.08
602 625 7.285401 ACATTATAATTGGTGCCTTGAACCTAG 59.715 37.037 0.00 0.00 38.60 3.02
603 626 2.514458 ATTGGTGCCTTGAACCTAGG 57.486 50.000 7.41 7.41 38.60 3.02
604 627 1.145571 TTGGTGCCTTGAACCTAGGT 58.854 50.000 9.21 9.21 38.60 3.08
605 628 0.400213 TGGTGCCTTGAACCTAGGTG 59.600 55.000 17.14 3.15 38.60 4.00
606 629 0.322546 GGTGCCTTGAACCTAGGTGG 60.323 60.000 17.14 13.53 42.93 4.61
607 630 0.322546 GTGCCTTGAACCTAGGTGGG 60.323 60.000 17.14 15.86 41.11 4.61
608 631 0.770557 TGCCTTGAACCTAGGTGGGT 60.771 55.000 17.14 0.00 42.05 4.51
609 632 0.322546 GCCTTGAACCTAGGTGGGTG 60.323 60.000 17.14 6.72 39.85 4.61
610 633 0.328258 CCTTGAACCTAGGTGGGTGG 59.672 60.000 17.14 12.14 39.85 4.61
611 634 0.328258 CTTGAACCTAGGTGGGTGGG 59.672 60.000 17.14 0.33 39.85 4.61
612 635 0.104356 TTGAACCTAGGTGGGTGGGA 60.104 55.000 17.14 0.00 39.85 4.37
613 636 0.104356 TGAACCTAGGTGGGTGGGAA 60.104 55.000 17.14 0.00 39.85 3.97
614 637 0.618981 GAACCTAGGTGGGTGGGAAG 59.381 60.000 17.14 0.00 39.85 3.46
615 638 0.845102 AACCTAGGTGGGTGGGAAGG 60.845 60.000 17.14 0.00 39.85 3.46
616 639 2.680370 CCTAGGTGGGTGGGAAGGC 61.680 68.421 0.00 0.00 0.00 4.35
617 640 1.923395 CTAGGTGGGTGGGAAGGCA 60.923 63.158 0.00 0.00 0.00 4.75
618 641 1.230149 TAGGTGGGTGGGAAGGCAT 60.230 57.895 0.00 0.00 0.00 4.40
619 642 1.279025 TAGGTGGGTGGGAAGGCATC 61.279 60.000 0.00 0.00 0.00 3.91
630 653 4.526102 AGGCATCCCTTCCCATCA 57.474 55.556 0.00 0.00 38.74 3.07
631 654 1.925888 AGGCATCCCTTCCCATCAC 59.074 57.895 0.00 0.00 38.74 3.06
632 655 0.625683 AGGCATCCCTTCCCATCACT 60.626 55.000 0.00 0.00 38.74 3.41
633 656 1.140312 GGCATCCCTTCCCATCACTA 58.860 55.000 0.00 0.00 0.00 2.74
634 657 1.072965 GGCATCCCTTCCCATCACTAG 59.927 57.143 0.00 0.00 0.00 2.57
635 658 1.072965 GCATCCCTTCCCATCACTAGG 59.927 57.143 0.00 0.00 0.00 3.02
636 659 1.072965 CATCCCTTCCCATCACTAGGC 59.927 57.143 0.00 0.00 0.00 3.93
637 660 0.343372 TCCCTTCCCATCACTAGGCT 59.657 55.000 0.00 0.00 0.00 4.58
638 661 1.578703 TCCCTTCCCATCACTAGGCTA 59.421 52.381 0.00 0.00 0.00 3.93
639 662 2.182312 TCCCTTCCCATCACTAGGCTAT 59.818 50.000 0.00 0.00 0.00 2.97
640 663 2.304180 CCCTTCCCATCACTAGGCTATG 59.696 54.545 0.00 0.00 0.00 2.23
641 664 2.289945 CCTTCCCATCACTAGGCTATGC 60.290 54.545 0.00 0.00 0.00 3.14
653 676 2.332063 GGCTATGCCTTAGTCTGCAA 57.668 50.000 0.73 0.00 46.69 4.08
654 677 2.643551 GGCTATGCCTTAGTCTGCAAA 58.356 47.619 0.73 0.00 46.69 3.68
655 678 3.016736 GGCTATGCCTTAGTCTGCAAAA 58.983 45.455 0.73 0.00 46.69 2.44
656 679 3.065925 GGCTATGCCTTAGTCTGCAAAAG 59.934 47.826 0.73 0.00 46.69 2.27
657 680 3.691609 GCTATGCCTTAGTCTGCAAAAGT 59.308 43.478 0.00 0.00 41.50 2.66
658 681 4.156739 GCTATGCCTTAGTCTGCAAAAGTT 59.843 41.667 0.00 0.00 41.50 2.66
659 682 5.354234 GCTATGCCTTAGTCTGCAAAAGTTA 59.646 40.000 0.00 0.00 41.50 2.24
660 683 6.038714 GCTATGCCTTAGTCTGCAAAAGTTAT 59.961 38.462 0.00 0.00 41.50 1.89
661 684 7.226720 GCTATGCCTTAGTCTGCAAAAGTTATA 59.773 37.037 0.00 0.00 41.50 0.98
662 685 6.737254 TGCCTTAGTCTGCAAAAGTTATAC 57.263 37.500 0.00 0.00 33.87 1.47
663 686 6.472887 TGCCTTAGTCTGCAAAAGTTATACT 58.527 36.000 0.00 0.00 33.87 2.12
664 687 7.617225 TGCCTTAGTCTGCAAAAGTTATACTA 58.383 34.615 0.00 0.00 33.87 1.82
665 688 8.098286 TGCCTTAGTCTGCAAAAGTTATACTAA 58.902 33.333 0.00 0.00 33.87 2.24
666 689 9.110502 GCCTTAGTCTGCAAAAGTTATACTAAT 57.889 33.333 0.00 0.00 30.17 1.73
671 694 9.502091 AGTCTGCAAAAGTTATACTAATGTTGA 57.498 29.630 0.00 0.00 0.00 3.18
672 695 9.760660 GTCTGCAAAAGTTATACTAATGTTGAG 57.239 33.333 0.00 0.00 0.00 3.02
673 696 9.719355 TCTGCAAAAGTTATACTAATGTTGAGA 57.281 29.630 0.00 0.00 0.00 3.27
674 697 9.760660 CTGCAAAAGTTATACTAATGTTGAGAC 57.239 33.333 0.00 0.00 0.00 3.36
675 698 9.278978 TGCAAAAGTTATACTAATGTTGAGACA 57.721 29.630 0.00 0.00 40.71 3.41
676 699 9.543018 GCAAAAGTTATACTAATGTTGAGACAC 57.457 33.333 0.00 0.00 38.91 3.67
686 709 8.110860 ACTAATGTTGAGACACTTATTTTGGG 57.889 34.615 0.00 0.00 38.91 4.12
687 710 7.942341 ACTAATGTTGAGACACTTATTTTGGGA 59.058 33.333 0.00 0.00 38.91 4.37
688 711 6.575162 ATGTTGAGACACTTATTTTGGGAC 57.425 37.500 0.00 0.00 38.91 4.46
689 712 4.513692 TGTTGAGACACTTATTTTGGGACG 59.486 41.667 0.00 0.00 0.00 4.79
690 713 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
691 714 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
692 715 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
693 716 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
694 717 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
695 718 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
696 719 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
697 720 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
698 721 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
699 722 1.732117 TTTTGGGACGGAGGGAGTAA 58.268 50.000 0.00 0.00 0.00 2.24
700 723 1.961133 TTTGGGACGGAGGGAGTAAT 58.039 50.000 0.00 0.00 0.00 1.89
701 724 2.852714 TTGGGACGGAGGGAGTAATA 57.147 50.000 0.00 0.00 0.00 0.98
702 725 3.339713 TTGGGACGGAGGGAGTAATAT 57.660 47.619 0.00 0.00 0.00 1.28
703 726 4.474303 TTGGGACGGAGGGAGTAATATA 57.526 45.455 0.00 0.00 0.00 0.86
707 730 4.946772 GGGACGGAGGGAGTAATATAGTAC 59.053 50.000 2.07 2.07 0.00 2.73
764 2445 4.067972 ACTATTTGACACCACGTCTTGT 57.932 40.909 0.00 0.00 45.60 3.16
1094 2790 0.325765 GACCTGGAGGCTAGGGTCTT 60.326 60.000 19.30 0.00 43.30 3.01
1150 2846 0.742281 CATGTCTGAGGGAGTTGCGG 60.742 60.000 0.00 0.00 0.00 5.69
1212 2908 2.660802 GAGGGTCTCGGCGGAAAA 59.339 61.111 7.21 0.00 0.00 2.29
1235 2931 1.148310 CAAAAGTCAGGCGACATCGT 58.852 50.000 11.04 0.00 45.23 3.73
1301 2997 2.276309 GAAGAGGGGATGGCTGTGGG 62.276 65.000 0.00 0.00 0.00 4.61
1446 3142 0.970937 GTGGACGAGACCATGGGAGA 60.971 60.000 18.09 0.00 42.17 3.71
1452 3148 0.461961 GAGACCATGGGAGAGTTCGG 59.538 60.000 18.09 0.00 0.00 4.30
1465 3161 1.812571 GAGTTCGGTGTGATGGCAATT 59.187 47.619 0.00 0.00 0.00 2.32
1493 3189 4.049869 CTGGATGACGATGATGTTCTGAG 58.950 47.826 0.00 0.00 0.00 3.35
1584 3283 1.002069 ATGGTCAAGGGCATGGAGAA 58.998 50.000 0.00 0.00 0.00 2.87
1594 3293 1.225704 CATGGAGAAGGGGAGGTGC 59.774 63.158 0.00 0.00 0.00 5.01
1620 3319 1.823470 AAGCAGCAGGAAACGTGCA 60.823 52.632 16.44 0.00 43.82 4.57
1702 3401 7.654022 AATCAAAAACCTGTTTCACCTCTAA 57.346 32.000 0.00 0.00 31.45 2.10
1706 3405 9.362151 TCAAAAACCTGTTTCACCTCTAATTAT 57.638 29.630 0.00 0.00 31.45 1.28
1815 3517 7.360946 CGGTTAACTAAAGGTCAATCAAAGAGG 60.361 40.741 5.42 0.00 0.00 3.69
2018 3720 9.209175 CGAGGAAACTTATAAAGATCTTATGGG 57.791 37.037 8.75 1.55 44.43 4.00
2333 5729 7.252708 TGTATCACCATTTACGTACTACAGTG 58.747 38.462 0.00 0.22 0.00 3.66
2378 5779 6.040729 TGACATCATTTGGACTGTTCATTGTT 59.959 34.615 0.00 0.00 0.00 2.83
2425 5854 2.242043 CTTGGCCTTGTCCTCAACAAT 58.758 47.619 3.32 0.00 46.53 2.71
2505 5935 7.995488 GGGAAGAAGAGATTTTCTATCATTGGA 59.005 37.037 0.00 0.00 36.42 3.53
2620 6050 4.407296 CAGGGCTTCTCAGACTAATAGGTT 59.593 45.833 0.00 0.00 0.00 3.50
2697 6127 5.533528 GGGTGTAGGTTTAACTGTCAACATT 59.466 40.000 0.00 0.00 0.00 2.71
2718 6148 8.409358 ACATTTCAAGCTCAGTTTTTAGGTAT 57.591 30.769 0.00 0.00 0.00 2.73
2758 6188 9.249457 GCTCAAGTTTAGCTTTTGTTCTATTTT 57.751 29.630 1.66 0.00 37.01 1.82
3045 6534 5.277828 GCACAAGACTTGGAAAAGTACGATT 60.278 40.000 19.16 0.00 32.22 3.34
3268 6846 8.979534 CCTTCTTAAGTAATCTGTAGTTAGGGT 58.020 37.037 1.63 0.00 0.00 4.34
3374 6959 2.551071 GCTCCCTGTAATATCCCTGCAC 60.551 54.545 0.00 0.00 0.00 4.57
3504 7089 5.973565 CGCTTCAATAATGAATGGAAGGTTC 59.026 40.000 4.69 0.00 43.46 3.62
3636 7221 4.090761 TCTGAAGCCACAAGAGTTTGAT 57.909 40.909 0.00 0.00 37.73 2.57
3810 7439 2.772568 TTGTCGTGCATGTTTCCTTG 57.227 45.000 5.68 0.00 0.00 3.61
3818 7447 2.499289 TGCATGTTTCCTTGGTTGTTGT 59.501 40.909 0.00 0.00 0.00 3.32
3852 7482 3.197766 GTGAGATCATTGTGTCACCCCTA 59.802 47.826 0.00 0.00 36.65 3.53
3853 7483 4.040047 TGAGATCATTGTGTCACCCCTAT 58.960 43.478 0.00 0.00 0.00 2.57
3854 7484 4.141642 TGAGATCATTGTGTCACCCCTATG 60.142 45.833 0.00 0.05 0.00 2.23
3856 7486 4.968719 AGATCATTGTGTCACCCCTATGTA 59.031 41.667 0.00 0.00 0.00 2.29
3858 7488 5.290493 TCATTGTGTCACCCCTATGTATC 57.710 43.478 0.00 0.00 0.00 2.24
3860 7490 3.123392 TGTGTCACCCCTATGTATCCA 57.877 47.619 0.00 0.00 0.00 3.41
3861 7491 2.769663 TGTGTCACCCCTATGTATCCAC 59.230 50.000 0.00 0.00 0.00 4.02
3863 7493 4.220724 GTGTCACCCCTATGTATCCACTA 58.779 47.826 0.00 0.00 0.00 2.74
3864 7494 4.838986 GTGTCACCCCTATGTATCCACTAT 59.161 45.833 0.00 0.00 0.00 2.12
3865 7495 4.838423 TGTCACCCCTATGTATCCACTATG 59.162 45.833 0.00 0.00 0.00 2.23
3866 7496 4.838986 GTCACCCCTATGTATCCACTATGT 59.161 45.833 0.00 0.00 0.00 2.29
3867 7497 6.014647 GTCACCCCTATGTATCCACTATGTA 58.985 44.000 0.00 0.00 0.00 2.29
3869 7499 7.837689 GTCACCCCTATGTATCCACTATGTATA 59.162 40.741 0.00 0.00 0.00 1.47
3871 7501 7.839705 CACCCCTATGTATCCACTATGTATACT 59.160 40.741 4.17 0.00 0.00 2.12
3874 7504 9.702253 CCCTATGTATCCACTATGTATACTCTT 57.298 37.037 4.17 0.00 0.00 2.85
3914 7544 0.028505 TCGTGTATCGACGCTTAGGC 59.971 55.000 0.00 0.00 44.01 3.93
4014 7644 5.643777 GCAGCTTCTCCTACAACTCAAATAA 59.356 40.000 0.00 0.00 0.00 1.40
4060 7690 4.188247 TGTATCGTCTTCCTTCCACTTG 57.812 45.455 0.00 0.00 0.00 3.16
4106 7736 6.848069 TCTAATTCCTTTCAAGACTTTGGGA 58.152 36.000 0.00 0.00 34.97 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 1.136305 GAATCCCGTGAGATCCGACAA 59.864 52.381 0.00 0.00 0.00 3.18
66 67 1.567357 TCCATCGAAGACCATCACCA 58.433 50.000 0.00 0.00 42.51 4.17
96 97 9.219603 CCTGTAAACACAAGAATGAAGATTAGA 57.780 33.333 0.00 0.00 0.00 2.10
103 104 7.397892 TCAAACCTGTAAACACAAGAATGAA 57.602 32.000 0.00 0.00 0.00 2.57
135 136 6.964464 TCACTGGTAGAGAGAGTTCTAGATT 58.036 40.000 0.00 0.00 32.53 2.40
153 154 5.702670 ACAACAGAGTAACAATCATCACTGG 59.297 40.000 0.00 0.00 0.00 4.00
155 156 5.180117 GCACAACAGAGTAACAATCATCACT 59.820 40.000 0.00 0.00 0.00 3.41
177 178 1.825474 GTGCTTAGACCAGGACTAGCA 59.175 52.381 14.46 14.46 32.55 3.49
181 182 2.330216 ACTTGTGCTTAGACCAGGACT 58.670 47.619 0.00 0.00 36.15 3.85
207 212 3.003173 CCCTGCCTCTTGGACCGA 61.003 66.667 0.00 0.00 34.57 4.69
208 213 3.003173 TCCCTGCCTCTTGGACCG 61.003 66.667 0.00 0.00 34.57 4.79
214 219 1.005215 CCTTCATTGTCCCTGCCTCTT 59.995 52.381 0.00 0.00 0.00 2.85
220 225 2.409870 GCCGCCTTCATTGTCCCTG 61.410 63.158 0.00 0.00 0.00 4.45
237 242 1.731720 AGAGCGAGATGAAGGTTTGC 58.268 50.000 0.00 0.00 0.00 3.68
240 245 2.880963 GCTAGAGCGAGATGAAGGTT 57.119 50.000 0.00 0.00 0.00 3.50
255 260 1.737838 TTGTCCCTTCATTGCGCTAG 58.262 50.000 9.73 0.00 0.00 3.42
262 267 3.075882 TGTCCCTTCATTGTCCCTTCATT 59.924 43.478 0.00 0.00 0.00 2.57
263 268 2.649312 TGTCCCTTCATTGTCCCTTCAT 59.351 45.455 0.00 0.00 0.00 2.57
264 269 2.061848 TGTCCCTTCATTGTCCCTTCA 58.938 47.619 0.00 0.00 0.00 3.02
265 270 2.879103 TGTCCCTTCATTGTCCCTTC 57.121 50.000 0.00 0.00 0.00 3.46
267 272 2.065799 ACTTGTCCCTTCATTGTCCCT 58.934 47.619 0.00 0.00 0.00 4.20
268 273 2.586648 ACTTGTCCCTTCATTGTCCC 57.413 50.000 0.00 0.00 0.00 4.46
269 274 4.620982 CAAAACTTGTCCCTTCATTGTCC 58.379 43.478 0.00 0.00 0.00 4.02
270 275 4.051237 GCAAAACTTGTCCCTTCATTGTC 58.949 43.478 0.00 0.00 0.00 3.18
271 276 3.706086 AGCAAAACTTGTCCCTTCATTGT 59.294 39.130 0.00 0.00 0.00 2.71
273 278 5.385198 TCTAGCAAAACTTGTCCCTTCATT 58.615 37.500 0.00 0.00 0.00 2.57
274 279 4.985538 TCTAGCAAAACTTGTCCCTTCAT 58.014 39.130 0.00 0.00 0.00 2.57
275 280 4.431416 TCTAGCAAAACTTGTCCCTTCA 57.569 40.909 0.00 0.00 0.00 3.02
276 281 5.003804 TCATCTAGCAAAACTTGTCCCTTC 58.996 41.667 0.00 0.00 0.00 3.46
277 282 4.985538 TCATCTAGCAAAACTTGTCCCTT 58.014 39.130 0.00 0.00 0.00 3.95
278 283 4.640771 TCATCTAGCAAAACTTGTCCCT 57.359 40.909 0.00 0.00 0.00 4.20
279 284 5.393461 CCAATCATCTAGCAAAACTTGTCCC 60.393 44.000 0.00 0.00 0.00 4.46
280 285 5.183904 ACCAATCATCTAGCAAAACTTGTCC 59.816 40.000 0.00 0.00 0.00 4.02
281 286 6.072508 TCACCAATCATCTAGCAAAACTTGTC 60.073 38.462 0.00 0.00 0.00 3.18
282 287 5.769662 TCACCAATCATCTAGCAAAACTTGT 59.230 36.000 0.00 0.00 0.00 3.16
283 288 6.258230 TCACCAATCATCTAGCAAAACTTG 57.742 37.500 0.00 0.00 0.00 3.16
284 289 6.265196 TGTTCACCAATCATCTAGCAAAACTT 59.735 34.615 0.00 0.00 0.00 2.66
285 290 5.769662 TGTTCACCAATCATCTAGCAAAACT 59.230 36.000 0.00 0.00 0.00 2.66
286 291 6.012658 TGTTCACCAATCATCTAGCAAAAC 57.987 37.500 0.00 0.00 0.00 2.43
287 292 6.623486 CATGTTCACCAATCATCTAGCAAAA 58.377 36.000 0.00 0.00 0.00 2.44
288 293 5.393352 GCATGTTCACCAATCATCTAGCAAA 60.393 40.000 0.00 0.00 0.00 3.68
289 294 4.096833 GCATGTTCACCAATCATCTAGCAA 59.903 41.667 0.00 0.00 0.00 3.91
290 295 3.628942 GCATGTTCACCAATCATCTAGCA 59.371 43.478 0.00 0.00 0.00 3.49
291 296 3.881688 AGCATGTTCACCAATCATCTAGC 59.118 43.478 0.00 0.00 0.00 3.42
292 297 5.356190 ACAAGCATGTTCACCAATCATCTAG 59.644 40.000 0.00 0.00 35.91 2.43
303 308 3.857093 ACAAAAACGACAAGCATGTTCAC 59.143 39.130 0.00 0.00 40.74 3.18
318 323 7.012421 ACAGAGAACATCAGAGGTAACAAAAAC 59.988 37.037 0.00 0.00 41.41 2.43
479 502 8.017418 AGACACTTATTTTAGGATGGAGAGAG 57.983 38.462 0.00 0.00 0.00 3.20
483 506 9.892130 AGTTAAGACACTTATTTTAGGATGGAG 57.108 33.333 0.00 0.00 0.00 3.86
550 573 7.771544 GGGGTTCCCTTACAGTCTTTCTGTC 62.772 52.000 7.87 0.00 46.24 3.51
552 575 3.559384 GGGGTTCCCTTACAGTCTTTCTG 60.559 52.174 7.87 0.00 44.11 3.02
553 576 2.643304 GGGGTTCCCTTACAGTCTTTCT 59.357 50.000 7.87 0.00 41.34 2.52
554 577 3.069079 GGGGTTCCCTTACAGTCTTTC 57.931 52.381 7.87 0.00 41.34 2.62
566 589 5.773176 CACCAATTATAATGTAGGGGTTCCC 59.227 44.000 13.41 0.00 45.90 3.97
567 590 5.243060 GCACCAATTATAATGTAGGGGTTCC 59.757 44.000 12.90 0.00 0.00 3.62
568 591 5.243060 GGCACCAATTATAATGTAGGGGTTC 59.757 44.000 12.90 5.73 0.00 3.62
569 592 5.103258 AGGCACCAATTATAATGTAGGGGTT 60.103 40.000 12.90 3.33 0.00 4.11
570 593 4.418863 AGGCACCAATTATAATGTAGGGGT 59.581 41.667 12.90 7.62 0.00 4.95
571 594 4.998051 AGGCACCAATTATAATGTAGGGG 58.002 43.478 13.41 11.24 0.00 4.79
572 595 6.068010 TCAAGGCACCAATTATAATGTAGGG 58.932 40.000 13.41 9.27 0.00 3.53
573 596 7.425606 GTTCAAGGCACCAATTATAATGTAGG 58.574 38.462 0.00 4.73 0.00 3.18
574 597 7.285401 AGGTTCAAGGCACCAATTATAATGTAG 59.715 37.037 0.00 0.00 36.67 2.74
575 598 7.122715 AGGTTCAAGGCACCAATTATAATGTA 58.877 34.615 0.00 0.00 36.67 2.29
576 599 5.957774 AGGTTCAAGGCACCAATTATAATGT 59.042 36.000 0.00 0.00 36.67 2.71
577 600 6.469782 AGGTTCAAGGCACCAATTATAATG 57.530 37.500 0.00 0.00 36.67 1.90
578 601 6.777580 CCTAGGTTCAAGGCACCAATTATAAT 59.222 38.462 0.00 0.00 36.67 1.28
579 602 6.126409 CCTAGGTTCAAGGCACCAATTATAA 58.874 40.000 0.00 0.00 36.67 0.98
580 603 5.192923 ACCTAGGTTCAAGGCACCAATTATA 59.807 40.000 9.21 0.00 37.67 0.98
581 604 4.017499 ACCTAGGTTCAAGGCACCAATTAT 60.017 41.667 9.21 0.00 37.67 1.28
582 605 3.332485 ACCTAGGTTCAAGGCACCAATTA 59.668 43.478 9.21 0.00 37.67 1.40
583 606 2.110011 ACCTAGGTTCAAGGCACCAATT 59.890 45.455 9.21 0.00 37.67 2.32
584 607 1.710809 ACCTAGGTTCAAGGCACCAAT 59.289 47.619 9.21 0.00 37.67 3.16
585 608 1.145571 ACCTAGGTTCAAGGCACCAA 58.854 50.000 9.21 0.00 37.67 3.67
586 609 0.400213 CACCTAGGTTCAAGGCACCA 59.600 55.000 13.15 0.00 37.67 4.17
587 610 0.322546 CCACCTAGGTTCAAGGCACC 60.323 60.000 13.15 0.00 37.67 5.01
588 611 0.322546 CCCACCTAGGTTCAAGGCAC 60.323 60.000 13.15 0.00 37.67 5.01
589 612 0.770557 ACCCACCTAGGTTCAAGGCA 60.771 55.000 13.15 0.00 36.44 4.75
590 613 0.322546 CACCCACCTAGGTTCAAGGC 60.323 60.000 13.15 0.00 38.39 4.35
591 614 0.328258 CCACCCACCTAGGTTCAAGG 59.672 60.000 13.15 13.20 38.39 3.61
592 615 0.328258 CCCACCCACCTAGGTTCAAG 59.672 60.000 13.15 0.00 38.39 3.02
593 616 0.104356 TCCCACCCACCTAGGTTCAA 60.104 55.000 13.15 0.00 38.39 2.69
594 617 0.104356 TTCCCACCCACCTAGGTTCA 60.104 55.000 13.15 0.00 38.39 3.18
595 618 0.618981 CTTCCCACCCACCTAGGTTC 59.381 60.000 13.15 0.00 38.39 3.62
596 619 0.845102 CCTTCCCACCCACCTAGGTT 60.845 60.000 13.15 0.00 38.39 3.50
597 620 1.229853 CCTTCCCACCCACCTAGGT 60.230 63.158 9.21 9.21 42.40 3.08
598 621 2.680370 GCCTTCCCACCCACCTAGG 61.680 68.421 7.41 7.41 37.03 3.02
599 622 1.281925 ATGCCTTCCCACCCACCTAG 61.282 60.000 0.00 0.00 0.00 3.02
600 623 1.230149 ATGCCTTCCCACCCACCTA 60.230 57.895 0.00 0.00 0.00 3.08
601 624 2.535317 ATGCCTTCCCACCCACCT 60.535 61.111 0.00 0.00 0.00 4.00
602 625 2.043953 GATGCCTTCCCACCCACC 60.044 66.667 0.00 0.00 0.00 4.61
603 626 2.043953 GGATGCCTTCCCACCCAC 60.044 66.667 0.00 0.00 38.75 4.61
611 634 0.552848 TGATGGGAAGGGATGCCTTC 59.447 55.000 32.03 32.03 42.13 3.46
612 635 0.259938 GTGATGGGAAGGGATGCCTT 59.740 55.000 19.76 19.76 40.93 4.35
613 636 0.625683 AGTGATGGGAAGGGATGCCT 60.626 55.000 0.00 0.00 40.93 4.75
614 637 1.072965 CTAGTGATGGGAAGGGATGCC 59.927 57.143 0.00 0.00 40.67 4.40
615 638 1.072965 CCTAGTGATGGGAAGGGATGC 59.927 57.143 0.00 0.00 0.00 3.91
616 639 1.072965 GCCTAGTGATGGGAAGGGATG 59.927 57.143 0.00 0.00 0.00 3.51
617 640 1.061033 AGCCTAGTGATGGGAAGGGAT 60.061 52.381 0.00 0.00 0.00 3.85
618 641 0.343372 AGCCTAGTGATGGGAAGGGA 59.657 55.000 0.00 0.00 0.00 4.20
619 642 2.103153 TAGCCTAGTGATGGGAAGGG 57.897 55.000 0.00 0.00 0.00 3.95
620 643 2.289945 GCATAGCCTAGTGATGGGAAGG 60.290 54.545 0.00 0.00 0.00 3.46
621 644 2.289945 GGCATAGCCTAGTGATGGGAAG 60.290 54.545 0.00 0.00 46.69 3.46
622 645 1.699634 GGCATAGCCTAGTGATGGGAA 59.300 52.381 0.00 0.00 46.69 3.97
623 646 1.352083 GGCATAGCCTAGTGATGGGA 58.648 55.000 0.00 0.00 46.69 4.37
624 647 3.944476 GGCATAGCCTAGTGATGGG 57.056 57.895 0.00 0.00 46.69 4.00
635 658 3.691609 ACTTTTGCAGACTAAGGCATAGC 59.308 43.478 0.00 0.00 40.17 2.97
636 659 5.886960 AACTTTTGCAGACTAAGGCATAG 57.113 39.130 0.00 0.00 40.17 2.23
637 660 8.265055 AGTATAACTTTTGCAGACTAAGGCATA 58.735 33.333 0.00 0.00 40.17 3.14
638 661 7.112779 AGTATAACTTTTGCAGACTAAGGCAT 58.887 34.615 0.00 0.00 40.17 4.40
639 662 6.472887 AGTATAACTTTTGCAGACTAAGGCA 58.527 36.000 0.00 0.00 38.46 4.75
640 663 6.986904 AGTATAACTTTTGCAGACTAAGGC 57.013 37.500 0.00 0.00 0.00 4.35
645 668 9.502091 TCAACATTAGTATAACTTTTGCAGACT 57.498 29.630 0.00 0.00 0.00 3.24
646 669 9.760660 CTCAACATTAGTATAACTTTTGCAGAC 57.239 33.333 0.00 0.00 0.00 3.51
647 670 9.719355 TCTCAACATTAGTATAACTTTTGCAGA 57.281 29.630 0.00 0.00 0.00 4.26
648 671 9.760660 GTCTCAACATTAGTATAACTTTTGCAG 57.239 33.333 0.00 0.00 0.00 4.41
649 672 9.278978 TGTCTCAACATTAGTATAACTTTTGCA 57.721 29.630 0.00 0.00 0.00 4.08
650 673 9.543018 GTGTCTCAACATTAGTATAACTTTTGC 57.457 33.333 0.00 0.00 37.81 3.68
660 683 9.226606 CCCAAAATAAGTGTCTCAACATTAGTA 57.773 33.333 0.00 0.00 37.81 1.82
661 684 7.942341 TCCCAAAATAAGTGTCTCAACATTAGT 59.058 33.333 0.00 0.00 37.81 2.24
662 685 8.237267 GTCCCAAAATAAGTGTCTCAACATTAG 58.763 37.037 0.00 0.00 37.81 1.73
663 686 7.094975 CGTCCCAAAATAAGTGTCTCAACATTA 60.095 37.037 0.00 0.00 37.81 1.90
664 687 6.293955 CGTCCCAAAATAAGTGTCTCAACATT 60.294 38.462 0.00 0.00 37.81 2.71
665 688 5.181245 CGTCCCAAAATAAGTGTCTCAACAT 59.819 40.000 0.00 0.00 37.81 2.71
666 689 4.513692 CGTCCCAAAATAAGTGTCTCAACA 59.486 41.667 0.00 0.00 0.00 3.33
667 690 4.083484 CCGTCCCAAAATAAGTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
668 691 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
669 692 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
670 693 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
671 694 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
672 695 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
673 696 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
674 697 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
675 698 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
676 699 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
677 700 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
678 701 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
679 702 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
680 703 1.732117 TTACTCCCTCCGTCCCAAAA 58.268 50.000 0.00 0.00 0.00 2.44
681 704 1.961133 ATTACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
682 705 2.852714 TATTACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
683 706 3.400322 ACTATATTACTCCCTCCGTCCCA 59.600 47.826 0.00 0.00 0.00 4.37
684 707 4.044946 ACTATATTACTCCCTCCGTCCC 57.955 50.000 0.00 0.00 0.00 4.46
685 708 5.814481 AGTACTATATTACTCCCTCCGTCC 58.186 45.833 0.00 0.00 0.00 4.79
686 709 7.757941 AAAGTACTATATTACTCCCTCCGTC 57.242 40.000 0.00 0.00 30.65 4.79
687 710 9.294614 CTAAAAGTACTATATTACTCCCTCCGT 57.705 37.037 0.00 0.00 30.65 4.69
688 711 9.512588 TCTAAAAGTACTATATTACTCCCTCCG 57.487 37.037 0.00 0.00 30.65 4.63
722 745 1.069765 CTGCCGCCGGATAAGTCAT 59.930 57.895 7.68 0.00 0.00 3.06
723 746 1.038681 TACTGCCGCCGGATAAGTCA 61.039 55.000 7.68 0.00 0.00 3.41
764 2445 1.533625 CTTTGGGCCGAAGACATCAA 58.466 50.000 26.70 0.00 0.00 2.57
859 2540 0.689412 GGGGTGAGGGGAAGAGAGAG 60.689 65.000 0.00 0.00 0.00 3.20
860 2541 1.392534 GGGGTGAGGGGAAGAGAGA 59.607 63.158 0.00 0.00 0.00 3.10
1150 2846 2.225727 CCTTTTTGCCTCTACGGTTCAC 59.774 50.000 0.00 0.00 34.25 3.18
1212 2908 1.388547 TGTCGCCTGACTTTTGCTTT 58.611 45.000 0.00 0.00 45.70 3.51
1226 2922 3.195698 GCCCTCCAACGATGTCGC 61.196 66.667 1.77 0.00 44.43 5.19
1235 2931 0.106569 ATTCATCGCATGCCCTCCAA 60.107 50.000 13.15 0.00 0.00 3.53
1301 2997 1.228657 GCTCTCCCCGTTGTTGACAC 61.229 60.000 0.00 0.00 0.00 3.67
1341 3037 0.039911 ACTTGCTAGGAGTCGGGACT 59.960 55.000 0.00 0.00 45.84 3.85
1381 3077 1.228367 CTGCAACACCCCTCTTGCT 60.228 57.895 4.19 0.00 42.77 3.91
1446 3142 1.909700 AATTGCCATCACACCGAACT 58.090 45.000 0.00 0.00 0.00 3.01
1452 3148 4.082081 TCCAGAATCAAATTGCCATCACAC 60.082 41.667 0.00 0.00 0.00 3.82
1465 3161 5.027293 ACATCATCGTCATCCAGAATCAA 57.973 39.130 0.00 0.00 0.00 2.57
1584 3283 1.412453 TTGTAACACGCACCTCCCCT 61.412 55.000 0.00 0.00 0.00 4.79
1594 3293 1.225855 TTCCTGCTGCTTGTAACACG 58.774 50.000 0.00 0.00 0.00 4.49
1620 3319 0.392706 TGTCACTGACTCCACGCAAT 59.607 50.000 10.54 0.00 33.15 3.56
1702 3401 5.071519 CCTCACTCTCAATCCCTGTCATAAT 59.928 44.000 0.00 0.00 0.00 1.28
1706 3405 2.182827 CCTCACTCTCAATCCCTGTCA 58.817 52.381 0.00 0.00 0.00 3.58
1785 3487 3.323751 TGACCTTTAGTTAACCGAGCC 57.676 47.619 0.88 0.00 0.00 4.70
1860 3562 1.068281 TCATCCTCGCTCTCTTCATGC 59.932 52.381 0.00 0.00 0.00 4.06
2018 3720 0.935196 CCTTTTGCCGCGTATCCTAC 59.065 55.000 4.92 0.00 0.00 3.18
2333 5729 6.908825 TGTCAGGACAAAATAGCAAATGTAC 58.091 36.000 0.00 0.00 38.56 2.90
2378 5779 7.150640 TGTCATACAAACAAAATGCTATGCAA 58.849 30.769 0.00 0.00 43.62 4.08
2505 5935 6.093219 GTCAAGTCAATGCAGTATCTGTCAAT 59.907 38.462 0.00 0.00 33.43 2.57
2620 6050 9.959721 AGAGAGGTATTTTGCAAATAGAACTAA 57.040 29.630 13.65 0.00 0.00 2.24
2697 6127 6.228258 ACGATACCTAAAAACTGAGCTTGAA 58.772 36.000 0.00 0.00 0.00 2.69
2855 6341 7.341805 ACTGAAGTAATATGCTGAAGAATGGT 58.658 34.615 0.00 0.00 0.00 3.55
2856 6342 7.496920 TGACTGAAGTAATATGCTGAAGAATGG 59.503 37.037 0.00 0.00 0.00 3.16
2861 6347 8.429493 TCAATGACTGAAGTAATATGCTGAAG 57.571 34.615 0.00 0.00 0.00 3.02
3045 6534 3.578282 TGACAGAACTCAAGAGCATACCA 59.422 43.478 0.00 0.00 0.00 3.25
3242 6740 8.979534 ACCCTAACTACAGATTACTTAAGAAGG 58.020 37.037 10.09 0.00 0.00 3.46
3312 6894 2.889512 ACATAGACCCTGTCAGACACA 58.110 47.619 0.00 0.00 34.60 3.72
3504 7089 1.673760 CACAATTTCCACTTCGTGCG 58.326 50.000 0.00 0.00 31.34 5.34
3615 7200 3.558931 TCAAACTCTTGTGGCTTCAGA 57.441 42.857 0.00 0.00 33.94 3.27
3636 7221 2.362503 AGTGCCTCGACCCGATCA 60.363 61.111 0.00 0.00 34.61 2.92
3657 7242 3.071479 GTTCTCCACGTGATTGCCTAAA 58.929 45.455 19.30 0.00 0.00 1.85
3810 7439 2.094234 ACCAACAAAGCTCACAACAACC 60.094 45.455 0.00 0.00 0.00 3.77
3818 7447 3.490439 TGATCTCACCAACAAAGCTCA 57.510 42.857 0.00 0.00 0.00 4.26
3866 7496 7.354751 TGTGCACCATGTATACAAGAGTATA 57.645 36.000 15.69 0.00 41.15 1.47
3867 7497 6.233905 TGTGCACCATGTATACAAGAGTAT 57.766 37.500 15.69 0.00 43.23 2.12
3869 7499 4.551702 TGTGCACCATGTATACAAGAGT 57.448 40.909 15.69 4.89 0.00 3.24
3871 7501 6.832520 AATTTGTGCACCATGTATACAAGA 57.167 33.333 15.69 0.00 33.39 3.02
3874 7504 5.182190 ACGAAATTTGTGCACCATGTATACA 59.818 36.000 15.69 8.27 0.00 2.29
3879 7509 2.100584 ACACGAAATTTGTGCACCATGT 59.899 40.909 15.69 0.90 41.03 3.21
3881 7511 4.671508 CGATACACGAAATTTGTGCACCAT 60.672 41.667 15.69 3.32 45.77 3.55
4060 7690 0.110486 TGGAGACCTTCCCAAGCAAC 59.890 55.000 0.00 0.00 46.19 4.17
4082 7712 6.715264 GTCCCAAAGTCTTGAAAGGAATTAGA 59.285 38.462 0.00 0.00 34.14 2.10


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

AutoCloner maintained by Alex Coulton.