Multiple sequence alignment - TraesCS6A01G115400

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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 TraesCS6A01G115400 chr6A 100.000 3114 0 0 1 3114 85260630 85263743 0.000000e+00 5751.0
1 TraesCS6A01G115400 chr6B 92.047 1182 55 20 855 2014 142612266 142613430 0.000000e+00 1626.0
2 TraesCS6A01G115400 chr6B 83.974 468 33 20 1 441 142611620 142612072 8.040000e-111 411.0
3 TraesCS6A01G115400 chr6B 82.569 218 31 7 2112 2327 142613490 142613702 5.300000e-43 185.0
4 TraesCS6A01G115400 chr6B 90.769 130 11 1 689 817 142612070 142612199 4.130000e-39 172.0
5 TraesCS6A01G115400 chr6D 89.163 1338 73 30 869 2182 67569015 67570304 0.000000e+00 1602.0
6 TraesCS6A01G115400 chr6D 85.052 669 93 6 2449 3114 81587559 81588223 0.000000e+00 675.0
7 TraesCS6A01G115400 chr6D 83.296 443 34 17 12 427 67568425 67568854 3.790000e-99 372.0
8 TraesCS6A01G115400 chr6D 82.090 335 58 2 2781 3114 137532168 137532501 5.080000e-73 285.0
9 TraesCS6A01G115400 chr6D 93.431 137 9 0 734 870 67568850 67568986 1.460000e-48 204.0
10 TraesCS6A01G115400 chr1B 92.504 667 47 3 2449 3114 61008404 61007740 0.000000e+00 952.0
11 TraesCS6A01G115400 chr7D 93.570 591 36 2 2449 3038 577319580 577320169 0.000000e+00 880.0
12 TraesCS6A01G115400 chr7D 80.941 404 74 3 1112 1515 612977377 612977777 1.800000e-82 316.0
13 TraesCS6A01G115400 chr7D 81.188 101 10 7 601 692 226157712 226157612 4.310000e-09 73.1
14 TraesCS6A01G115400 chr7D 92.000 50 3 1 643 692 34846366 34846318 5.570000e-08 69.4
15 TraesCS6A01G115400 chr2D 87.106 667 81 3 2449 3114 440628154 440628816 0.000000e+00 750.0
16 TraesCS6A01G115400 chr2D 84.817 191 26 3 455 644 576890719 576890531 4.100000e-44 189.0
17 TraesCS6A01G115400 chr2D 74.525 263 50 7 440 691 67195935 67196191 7.110000e-17 99.0
18 TraesCS6A01G115400 chr2D 73.432 271 57 7 434 694 534119014 534119279 1.540000e-13 87.9
19 TraesCS6A01G115400 chr2D 100.000 31 0 0 2339 2369 634570639 634570609 1.210000e-04 58.4
20 TraesCS6A01G115400 chr5A 85.174 661 91 4 2449 3109 548991161 548991814 0.000000e+00 671.0
21 TraesCS6A01G115400 chr5A 83.807 352 52 3 2449 2800 345768487 345768833 2.320000e-86 329.0
22 TraesCS6A01G115400 chr5A 87.619 105 13 0 539 643 7513963 7513859 4.220000e-24 122.0
23 TraesCS6A01G115400 chr5B 85.008 647 85 4 2449 3095 294079733 294080367 0.000000e+00 647.0
24 TraesCS6A01G115400 chr1D 89.960 498 48 2 2618 3114 367851473 367850977 2.620000e-180 641.0
25 TraesCS6A01G115400 chr1A 89.783 460 45 2 2651 3109 45504201 45503743 3.460000e-164 588.0
26 TraesCS6A01G115400 chr1A 83.051 118 14 4 531 644 582838576 582838691 5.490000e-18 102.0
27 TraesCS6A01G115400 chr2A 82.476 622 106 3 2454 3074 501324220 501323601 2.730000e-150 542.0
28 TraesCS6A01G115400 chr2A 73.993 273 51 12 440 697 771468433 771468700 3.310000e-15 93.5
29 TraesCS6A01G115400 chr4B 78.411 667 138 5 2449 3113 191094584 191095246 2.220000e-116 429.0
30 TraesCS6A01G115400 chr4B 80.787 432 80 2 1112 1543 640937 640509 4.980000e-88 335.0
31 TraesCS6A01G115400 chr7A 90.657 289 24 3 2828 3114 730885953 730885666 6.300000e-102 381.0
32 TraesCS6A01G115400 chr7A 82.469 405 66 5 1112 1515 704387759 704388159 1.780000e-92 350.0
33 TraesCS6A01G115400 chr7B 82.716 405 65 5 1112 1515 702535218 702535618 3.820000e-94 355.0
34 TraesCS6A01G115400 chr7B 81.572 407 66 6 1112 1515 702854453 702854053 8.330000e-86 327.0
35 TraesCS6A01G115400 chr4A 84.314 306 45 2 1112 1417 603534972 603534670 2.350000e-76 296.0
36 TraesCS6A01G115400 chr4A 86.170 188 26 0 455 642 742356860 742356673 1.460000e-48 204.0
37 TraesCS6A01G115400 chr4A 89.011 91 10 0 439 529 622441862 622441772 2.540000e-21 113.0
38 TraesCS6A01G115400 chr4A 89.011 91 10 0 439 529 622510929 622510839 2.540000e-21 113.0
39 TraesCS6A01G115400 chr4A 89.011 91 10 0 439 529 622559494 622559404 2.540000e-21 113.0
40 TraesCS6A01G115400 chr3A 81.579 266 39 5 438 694 526862517 526862781 8.750000e-51 211.0
41 TraesCS6A01G115400 chr3A 92.000 50 3 1 643 692 568577671 568577623 5.570000e-08 69.4
42 TraesCS6A01G115400 chr4D 81.648 267 36 8 436 691 40582144 40582408 3.150000e-50 209.0
43 TraesCS6A01G115400 chr2B 82.243 214 33 2 436 644 760863932 760864145 2.470000e-41 180.0
44 TraesCS6A01G115400 chr3D 81.776 214 34 5 434 644 8337914 8338125 1.150000e-39 174.0
45 TraesCS6A01G115400 chr3D 74.242 264 53 6 440 691 481916466 481916206 2.560000e-16 97.1
46 TraesCS6A01G115400 chr3B 92.157 51 3 1 643 693 525792354 525792403 1.550000e-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 TraesCS6A01G115400 chr6A 85260630 85263743 3113 False 5751.0 5751 100.00000 1 3114 1 chr6A.!!$F1 3113
1 TraesCS6A01G115400 chr6B 142611620 142613702 2082 False 598.5 1626 87.33975 1 2327 4 chr6B.!!$F1 2326
2 TraesCS6A01G115400 chr6D 67568425 67570304 1879 False 726.0 1602 88.63000 12 2182 3 chr6D.!!$F3 2170
3 TraesCS6A01G115400 chr6D 81587559 81588223 664 False 675.0 675 85.05200 2449 3114 1 chr6D.!!$F1 665
4 TraesCS6A01G115400 chr1B 61007740 61008404 664 True 952.0 952 92.50400 2449 3114 1 chr1B.!!$R1 665
5 TraesCS6A01G115400 chr7D 577319580 577320169 589 False 880.0 880 93.57000 2449 3038 1 chr7D.!!$F1 589
6 TraesCS6A01G115400 chr2D 440628154 440628816 662 False 750.0 750 87.10600 2449 3114 1 chr2D.!!$F2 665
7 TraesCS6A01G115400 chr5A 548991161 548991814 653 False 671.0 671 85.17400 2449 3109 1 chr5A.!!$F2 660
8 TraesCS6A01G115400 chr5B 294079733 294080367 634 False 647.0 647 85.00800 2449 3095 1 chr5B.!!$F1 646
9 TraesCS6A01G115400 chr2A 501323601 501324220 619 True 542.0 542 82.47600 2454 3074 1 chr2A.!!$R1 620
10 TraesCS6A01G115400 chr4B 191094584 191095246 662 False 429.0 429 78.41100 2449 3113 1 chr4B.!!$F1 664

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
47 48 0.034863 AAACCGTGTGTTGGTCAGGT 60.035 50.0 0.00 0.0 39.29 4.00 F
683 721 0.037046 GCGGACTAAAAAGGACCGGA 60.037 55.0 9.46 0.0 43.15 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1062 1147 0.181114 CAATGGAGGAGGCGAATGGA 59.819 55.0 0.00 0.0 0.00 3.41 R
2385 2507 0.029834 CAGCAGCTGTTTGAAAGCGT 59.970 50.0 16.64 0.0 45.59 5.07 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
44 45 0.035343 TCCAAACCGTGTGTTGGTCA 60.035 50.000 2.58 0.00 39.29 4.02
45 46 0.380378 CCAAACCGTGTGTTGGTCAG 59.620 55.000 0.00 0.00 39.29 3.51
46 47 0.380378 CAAACCGTGTGTTGGTCAGG 59.620 55.000 0.00 0.00 39.29 3.86
47 48 0.034863 AAACCGTGTGTTGGTCAGGT 60.035 50.000 0.00 0.00 39.29 4.00
48 49 0.463116 AACCGTGTGTTGGTCAGGTC 60.463 55.000 0.00 0.00 39.29 3.85
71 72 1.600916 GCCTCCTGTGGAACGCTTT 60.601 57.895 0.00 0.00 42.39 3.51
72 73 1.578206 GCCTCCTGTGGAACGCTTTC 61.578 60.000 0.00 0.00 42.39 2.62
73 74 0.250295 CCTCCTGTGGAACGCTTTCA 60.250 55.000 5.21 0.00 42.39 2.69
74 75 1.151668 CTCCTGTGGAACGCTTTCAG 58.848 55.000 5.21 0.00 42.39 3.02
94 98 3.574396 CAGTTCCCGCCTCATCTTATCTA 59.426 47.826 0.00 0.00 0.00 1.98
95 99 3.829601 AGTTCCCGCCTCATCTTATCTAG 59.170 47.826 0.00 0.00 0.00 2.43
96 100 3.527507 TCCCGCCTCATCTTATCTAGT 57.472 47.619 0.00 0.00 0.00 2.57
97 101 4.652679 TCCCGCCTCATCTTATCTAGTA 57.347 45.455 0.00 0.00 0.00 1.82
118 122 4.084888 CGGGTCGCTTTCCGTTGC 62.085 66.667 0.00 0.00 41.23 4.17
119 123 3.733960 GGGTCGCTTTCCGTTGCC 61.734 66.667 0.00 0.00 38.35 4.52
146 150 3.390521 CGGTGTAGCAGAGGCCCA 61.391 66.667 0.00 0.00 42.56 5.36
153 157 2.874648 TAGCAGAGGCCCATGTTGCG 62.875 60.000 0.00 0.00 42.56 4.85
154 158 3.818787 CAGAGGCCCATGTTGCGC 61.819 66.667 0.00 0.00 0.00 6.09
171 176 2.475466 GCGGCTGTGGACCATGATG 61.475 63.158 0.00 0.00 0.00 3.07
191 202 2.105128 CATCGGGAGAGACGTGCC 59.895 66.667 0.00 0.00 45.48 5.01
192 203 2.362503 ATCGGGAGAGACGTGCCA 60.363 61.111 0.00 0.00 45.48 4.92
228 239 2.046700 TTGGGTTCCATCGGTCGC 60.047 61.111 0.00 0.00 31.53 5.19
271 282 2.174969 TCAAACTCGCACGCCGTTT 61.175 52.632 0.00 5.03 38.35 3.60
273 284 1.885850 AAACTCGCACGCCGTTTCT 60.886 52.632 0.00 0.00 38.35 2.52
274 285 1.433837 AAACTCGCACGCCGTTTCTT 61.434 50.000 0.00 0.00 38.35 2.52
275 286 0.598158 AACTCGCACGCCGTTTCTTA 60.598 50.000 0.00 0.00 38.35 2.10
276 287 0.389426 ACTCGCACGCCGTTTCTTAT 60.389 50.000 0.00 0.00 38.35 1.73
291 306 9.789029 GCCGTTTCTTATTATTCGTTCTTATAC 57.211 33.333 0.00 0.00 0.00 1.47
321 354 4.159377 TCCATCGCAAATCACAAAGAAC 57.841 40.909 0.00 0.00 0.00 3.01
331 364 6.855914 GCAAATCACAAAGAACAGATAAACGA 59.144 34.615 0.00 0.00 0.00 3.85
332 365 7.378461 GCAAATCACAAAGAACAGATAAACGAA 59.622 33.333 0.00 0.00 0.00 3.85
343 376 6.182039 ACAGATAAACGAATGGTGTGATTG 57.818 37.500 0.00 0.00 0.00 2.67
349 382 5.545658 AACGAATGGTGTGATTGTATGTC 57.454 39.130 0.00 0.00 0.00 3.06
378 415 4.434520 GTGCTAGGATGTTCCAGTTCTAC 58.565 47.826 0.00 0.00 39.61 2.59
401 439 7.616698 ACACGCATGTCATACGAACAAATCG 62.617 44.000 12.38 0.00 46.74 3.34
442 480 8.947055 AAAAAGCAAATCAAGAAACATGTACT 57.053 26.923 0.00 0.00 0.00 2.73
443 481 8.579682 AAAAGCAAATCAAGAAACATGTACTC 57.420 30.769 0.00 0.00 0.00 2.59
444 482 6.259550 AGCAAATCAAGAAACATGTACTCC 57.740 37.500 0.00 0.00 0.00 3.85
445 483 5.183904 AGCAAATCAAGAAACATGTACTCCC 59.816 40.000 0.00 0.00 0.00 4.30
446 484 5.183904 GCAAATCAAGAAACATGTACTCCCT 59.816 40.000 0.00 0.00 0.00 4.20
447 485 6.623767 GCAAATCAAGAAACATGTACTCCCTC 60.624 42.308 0.00 0.00 0.00 4.30
448 486 6.380079 AATCAAGAAACATGTACTCCCTCT 57.620 37.500 0.00 0.00 0.00 3.69
449 487 5.825593 TCAAGAAACATGTACTCCCTCTT 57.174 39.130 0.00 0.00 0.00 2.85
450 488 6.928348 TCAAGAAACATGTACTCCCTCTTA 57.072 37.500 0.00 0.00 0.00 2.10
451 489 7.496346 TCAAGAAACATGTACTCCCTCTTAT 57.504 36.000 0.00 0.00 0.00 1.73
452 490 7.556844 TCAAGAAACATGTACTCCCTCTTATC 58.443 38.462 0.00 0.00 0.00 1.75
453 491 7.400339 TCAAGAAACATGTACTCCCTCTTATCT 59.600 37.037 0.00 0.00 0.00 1.98
454 492 7.741554 AGAAACATGTACTCCCTCTTATCTT 57.258 36.000 0.00 0.00 0.00 2.40
455 493 8.152023 AGAAACATGTACTCCCTCTTATCTTT 57.848 34.615 0.00 0.00 0.00 2.52
456 494 8.606830 AGAAACATGTACTCCCTCTTATCTTTT 58.393 33.333 0.00 0.00 0.00 2.27
457 495 9.232473 GAAACATGTACTCCCTCTTATCTTTTT 57.768 33.333 0.00 0.00 0.00 1.94
485 523 9.547753 ACTTCGCATATTAGATTTATGTCAAGT 57.452 29.630 0.00 0.00 32.30 3.16
487 525 9.764363 TTCGCATATTAGATTTATGTCAAGTCT 57.236 29.630 0.00 0.00 31.13 3.24
543 581 8.902540 AAAAAGTATCGGCATCTACAATATCA 57.097 30.769 0.00 0.00 0.00 2.15
544 582 8.902540 AAAAGTATCGGCATCTACAATATCAA 57.097 30.769 0.00 0.00 0.00 2.57
545 583 8.902540 AAAGTATCGGCATCTACAATATCAAA 57.097 30.769 0.00 0.00 0.00 2.69
546 584 9.507329 AAAGTATCGGCATCTACAATATCAAAT 57.493 29.630 0.00 0.00 0.00 2.32
598 636 8.986477 AATGAGTCTAACAATGTTAATTTGGC 57.014 30.769 7.30 0.00 0.00 4.52
599 637 6.607689 TGAGTCTAACAATGTTAATTTGGCG 58.392 36.000 7.30 0.00 0.00 5.69
600 638 6.205853 TGAGTCTAACAATGTTAATTTGGCGT 59.794 34.615 7.30 0.00 0.00 5.68
601 639 6.977213 AGTCTAACAATGTTAATTTGGCGTT 58.023 32.000 7.30 0.00 0.00 4.84
602 640 6.861055 AGTCTAACAATGTTAATTTGGCGTTG 59.139 34.615 7.30 0.00 35.81 4.10
603 641 6.639279 GTCTAACAATGTTAATTTGGCGTTGT 59.361 34.615 7.30 7.78 42.13 3.32
604 642 5.649602 AACAATGTTAATTTGGCGTTGTG 57.350 34.783 0.00 0.00 40.24 3.33
605 643 4.938080 ACAATGTTAATTTGGCGTTGTGA 58.062 34.783 11.04 0.00 39.82 3.58
606 644 5.352284 ACAATGTTAATTTGGCGTTGTGAA 58.648 33.333 11.04 0.00 39.82 3.18
607 645 5.988561 ACAATGTTAATTTGGCGTTGTGAAT 59.011 32.000 11.04 0.00 39.82 2.57
608 646 6.073873 ACAATGTTAATTTGGCGTTGTGAATG 60.074 34.615 11.04 0.00 39.82 2.67
609 647 4.938080 TGTTAATTTGGCGTTGTGAATGT 58.062 34.783 0.00 0.00 0.00 2.71
610 648 5.352284 TGTTAATTTGGCGTTGTGAATGTT 58.648 33.333 0.00 0.00 0.00 2.71
611 649 6.504398 TGTTAATTTGGCGTTGTGAATGTTA 58.496 32.000 0.00 0.00 0.00 2.41
612 650 6.638873 TGTTAATTTGGCGTTGTGAATGTTAG 59.361 34.615 0.00 0.00 0.00 2.34
613 651 4.846779 ATTTGGCGTTGTGAATGTTAGT 57.153 36.364 0.00 0.00 0.00 2.24
614 652 5.950758 ATTTGGCGTTGTGAATGTTAGTA 57.049 34.783 0.00 0.00 0.00 1.82
615 653 4.735662 TTGGCGTTGTGAATGTTAGTAC 57.264 40.909 0.00 0.00 0.00 2.73
616 654 3.997762 TGGCGTTGTGAATGTTAGTACT 58.002 40.909 0.00 0.00 0.00 2.73
617 655 4.382291 TGGCGTTGTGAATGTTAGTACTT 58.618 39.130 0.00 0.00 0.00 2.24
618 656 4.449743 TGGCGTTGTGAATGTTAGTACTTC 59.550 41.667 0.00 0.00 0.00 3.01
619 657 4.689345 GGCGTTGTGAATGTTAGTACTTCT 59.311 41.667 0.00 0.00 0.00 2.85
620 658 5.178809 GGCGTTGTGAATGTTAGTACTTCTT 59.821 40.000 0.00 0.00 0.00 2.52
621 659 6.293244 GGCGTTGTGAATGTTAGTACTTCTTT 60.293 38.462 0.00 0.00 0.00 2.52
622 660 7.130269 GCGTTGTGAATGTTAGTACTTCTTTT 58.870 34.615 0.00 0.00 0.00 2.27
623 661 7.642586 GCGTTGTGAATGTTAGTACTTCTTTTT 59.357 33.333 0.00 0.00 0.00 1.94
650 688 9.793259 ATAAATTTGGTCAAAGTAGACTTCAGA 57.207 29.630 0.00 0.00 38.57 3.27
651 689 7.497925 AATTTGGTCAAAGTAGACTTCAGAC 57.502 36.000 14.74 14.74 38.80 3.51
652 690 5.607939 TTGGTCAAAGTAGACTTCAGACA 57.392 39.130 20.42 7.54 40.06 3.41
653 691 5.607939 TGGTCAAAGTAGACTTCAGACAA 57.392 39.130 20.42 12.42 40.06 3.18
654 692 5.357257 TGGTCAAAGTAGACTTCAGACAAC 58.643 41.667 20.42 10.83 40.06 3.32
655 693 5.128827 TGGTCAAAGTAGACTTCAGACAACT 59.871 40.000 20.42 0.00 40.06 3.16
656 694 6.049790 GGTCAAAGTAGACTTCAGACAACTT 58.950 40.000 20.42 0.00 40.06 2.66
657 695 7.147794 TGGTCAAAGTAGACTTCAGACAACTTA 60.148 37.037 20.42 6.92 40.06 2.24
658 696 7.873505 GGTCAAAGTAGACTTCAGACAACTTAT 59.126 37.037 20.42 0.00 40.06 1.73
659 697 9.262358 GTCAAAGTAGACTTCAGACAACTTATT 57.738 33.333 16.77 0.00 39.07 1.40
666 704 8.581057 AGACTTCAGACAACTTATTATATGCG 57.419 34.615 0.00 0.00 0.00 4.73
667 705 7.653713 AGACTTCAGACAACTTATTATATGCGG 59.346 37.037 0.00 0.00 0.00 5.69
668 706 7.497595 ACTTCAGACAACTTATTATATGCGGA 58.502 34.615 0.00 0.00 0.00 5.54
669 707 7.438459 ACTTCAGACAACTTATTATATGCGGAC 59.562 37.037 0.00 0.00 0.00 4.79
670 708 7.050970 TCAGACAACTTATTATATGCGGACT 57.949 36.000 0.00 0.00 0.00 3.85
671 709 8.173542 TCAGACAACTTATTATATGCGGACTA 57.826 34.615 0.00 0.00 0.00 2.59
672 710 8.635328 TCAGACAACTTATTATATGCGGACTAA 58.365 33.333 0.00 0.00 0.00 2.24
673 711 9.256477 CAGACAACTTATTATATGCGGACTAAA 57.744 33.333 0.00 0.00 0.00 1.85
674 712 9.826574 AGACAACTTATTATATGCGGACTAAAA 57.173 29.630 0.00 0.00 0.00 1.52
677 715 9.878599 CAACTTATTATATGCGGACTAAAAAGG 57.121 33.333 0.00 0.00 0.00 3.11
678 716 9.841295 AACTTATTATATGCGGACTAAAAAGGA 57.159 29.630 0.00 0.00 0.00 3.36
679 717 9.269453 ACTTATTATATGCGGACTAAAAAGGAC 57.731 33.333 0.00 0.00 0.00 3.85
680 718 8.611654 TTATTATATGCGGACTAAAAAGGACC 57.388 34.615 0.00 0.00 0.00 4.46
681 719 1.734163 ATGCGGACTAAAAAGGACCG 58.266 50.000 0.00 0.00 45.26 4.79
682 720 0.320946 TGCGGACTAAAAAGGACCGG 60.321 55.000 0.00 0.00 43.15 5.28
683 721 0.037046 GCGGACTAAAAAGGACCGGA 60.037 55.000 9.46 0.00 43.15 5.14
684 722 2.005560 GCGGACTAAAAAGGACCGGAG 61.006 57.143 9.46 0.00 43.15 4.63
726 765 2.679837 CAAGCAAAGCATAGATCCGTGT 59.320 45.455 0.00 0.00 0.00 4.49
731 770 2.802787 AGCATAGATCCGTGTAGTGC 57.197 50.000 0.00 0.00 0.00 4.40
736 775 1.218047 GATCCGTGTAGTGCTGCCA 59.782 57.895 0.00 0.00 0.00 4.92
744 783 1.920325 TAGTGCTGCCAAGGCTCCT 60.920 57.895 12.96 5.33 42.51 3.69
827 866 7.201435 GCAAAGAAAACCCATTAATCGTCATTC 60.201 37.037 0.00 0.00 0.00 2.67
853 894 4.799419 TCCTTCGTAACAAAGAAAACCG 57.201 40.909 0.00 0.00 0.00 4.44
864 905 4.218852 ACAAAGAAAACCGAAAGTGAACCA 59.781 37.500 0.00 0.00 0.00 3.67
884 955 3.317993 CCAGACGTTTTGGTGAAGGAAAT 59.682 43.478 10.89 0.00 0.00 2.17
928 1006 5.122711 ACTGAATTACATTTTACCCGTTCGG 59.877 40.000 4.08 4.08 37.81 4.30
1022 1107 0.468226 TTTATACCCTGCCCGCTCAG 59.532 55.000 0.00 0.00 0.00 3.35
1070 1165 0.737219 AAGCAGAGCATTCCATTCGC 59.263 50.000 0.00 0.00 0.00 4.70
1081 1176 0.181114 TCCATTCGCCTCCTCCATTG 59.819 55.000 0.00 0.00 0.00 2.82
1088 1183 2.825836 CTCCTCCATTGCACGGCC 60.826 66.667 0.00 0.00 0.00 6.13
1549 1647 0.464373 CTACTACGACCCCGCCTACA 60.464 60.000 0.00 0.00 39.95 2.74
1641 1739 3.841758 GGGTACGGGTACGGCCAG 61.842 72.222 2.24 0.00 46.48 4.85
1642 1740 4.519437 GGTACGGGTACGGCCAGC 62.519 72.222 2.24 0.00 46.48 4.85
1802 1900 3.448340 GTACGGTTCGGGCGGGTA 61.448 66.667 0.00 0.00 0.00 3.69
1803 1901 3.448340 TACGGTTCGGGCGGGTAC 61.448 66.667 0.00 0.00 0.00 3.34
1830 1946 3.680786 TCGGTGAGTGACCCTGCG 61.681 66.667 0.00 0.00 42.62 5.18
1832 1948 4.314440 GGTGAGTGACCCTGCGCA 62.314 66.667 10.98 10.98 39.10 6.09
2049 2170 3.808618 GCACCTCCTGAGAGATTGTTGTT 60.809 47.826 0.00 0.00 43.39 2.83
2050 2171 3.750130 CACCTCCTGAGAGATTGTTGTTG 59.250 47.826 0.00 0.00 43.39 3.33
2051 2172 3.392616 ACCTCCTGAGAGATTGTTGTTGT 59.607 43.478 0.00 0.00 43.39 3.32
2052 2173 4.593206 ACCTCCTGAGAGATTGTTGTTGTA 59.407 41.667 0.00 0.00 43.39 2.41
2053 2174 5.249393 ACCTCCTGAGAGATTGTTGTTGTAT 59.751 40.000 0.00 0.00 43.39 2.29
2054 2175 5.583854 CCTCCTGAGAGATTGTTGTTGTATG 59.416 44.000 0.00 0.00 43.39 2.39
2057 2178 3.684305 TGAGAGATTGTTGTTGTATGCGG 59.316 43.478 0.00 0.00 0.00 5.69
2061 2182 0.312416 TTGTTGTTGTATGCGGTGGC 59.688 50.000 0.00 0.00 40.52 5.01
2070 2191 2.349969 TATGCGGTGGCGCTGACTAG 62.350 60.000 11.86 4.76 44.10 2.57
2092 2213 3.793465 GCCGCCAATATCTTCTTTGCTTC 60.793 47.826 0.00 0.00 0.00 3.86
2100 2221 9.118300 CCAATATCTTCTTTGCTTCTATTCTGT 57.882 33.333 0.00 0.00 0.00 3.41
2119 2240 6.494893 TCTGTCCGGATTTGTTGAATAAAG 57.505 37.500 7.81 0.00 0.00 1.85
2120 2241 5.414454 TCTGTCCGGATTTGTTGAATAAAGG 59.586 40.000 7.81 0.00 0.00 3.11
2127 2248 2.892373 TGTTGAATAAAGGCGCGAAG 57.108 45.000 12.10 0.00 0.00 3.79
2128 2249 1.466950 TGTTGAATAAAGGCGCGAAGG 59.533 47.619 12.10 0.00 0.00 3.46
2139 2260 2.752903 AGGCGCGAAGGAAATTAACAAT 59.247 40.909 12.10 0.00 0.00 2.71
2151 2272 7.593825 AGGAAATTAACAATGAGTGTAGCAAC 58.406 34.615 0.00 0.00 40.60 4.17
2153 2274 7.538678 GGAAATTAACAATGAGTGTAGCAACAG 59.461 37.037 0.00 0.00 40.60 3.16
2157 2278 3.928992 ACAATGAGTGTAGCAACAGATCG 59.071 43.478 0.00 0.00 39.29 3.69
2162 2283 4.864806 TGAGTGTAGCAACAGATCGAATTC 59.135 41.667 0.00 0.00 35.91 2.17
2165 2286 5.120830 AGTGTAGCAACAGATCGAATTCAAC 59.879 40.000 6.22 0.00 35.91 3.18
2166 2287 4.391830 TGTAGCAACAGATCGAATTCAACC 59.608 41.667 6.22 0.00 0.00 3.77
2167 2288 3.679389 AGCAACAGATCGAATTCAACCT 58.321 40.909 6.22 0.00 0.00 3.50
2168 2289 4.074970 AGCAACAGATCGAATTCAACCTT 58.925 39.130 6.22 0.00 0.00 3.50
2193 2314 0.396974 TGTGCCTTCCTTTGGTGCTT 60.397 50.000 0.00 0.00 0.00 3.91
2196 2317 0.889186 GCCTTCCTTTGGTGCTTCGA 60.889 55.000 0.00 0.00 0.00 3.71
2197 2318 1.160137 CCTTCCTTTGGTGCTTCGAG 58.840 55.000 0.00 0.00 0.00 4.04
2198 2319 1.270839 CCTTCCTTTGGTGCTTCGAGA 60.271 52.381 0.00 0.00 0.00 4.04
2210 2331 3.023832 TGCTTCGAGATGATCTGGTGTA 58.976 45.455 0.00 0.00 0.00 2.90
2213 2334 3.298686 TCGAGATGATCTGGTGTAGGT 57.701 47.619 0.00 0.00 0.00 3.08
2214 2335 3.632333 TCGAGATGATCTGGTGTAGGTT 58.368 45.455 0.00 0.00 0.00 3.50
2216 2337 4.466370 TCGAGATGATCTGGTGTAGGTTTT 59.534 41.667 0.00 0.00 0.00 2.43
2217 2338 5.046591 TCGAGATGATCTGGTGTAGGTTTTT 60.047 40.000 0.00 0.00 0.00 1.94
2244 2365 2.157738 GGAGCTGTTCTGCTGTTGATT 58.842 47.619 8.78 0.00 44.17 2.57
2246 2367 1.802960 AGCTGTTCTGCTGTTGATTCG 59.197 47.619 3.55 0.00 42.33 3.34
2248 2369 0.874390 TGTTCTGCTGTTGATTCGCC 59.126 50.000 0.00 0.00 0.00 5.54
2262 2384 3.763360 TGATTCGCCCAGATTGATGTTTT 59.237 39.130 0.00 0.00 0.00 2.43
2292 2414 1.066605 GGTATGAGCCGTCACGTATGT 59.933 52.381 0.00 0.00 34.75 2.29
2324 2446 2.363680 CGCCTCTGGAGTCATTGATACT 59.636 50.000 0.00 0.00 0.00 2.12
2325 2447 3.551863 CGCCTCTGGAGTCATTGATACTC 60.552 52.174 0.00 0.00 42.19 2.59
2326 2448 3.640967 GCCTCTGGAGTCATTGATACTCT 59.359 47.826 0.00 0.00 42.48 3.24
2328 2450 5.396213 GCCTCTGGAGTCATTGATACTCTTT 60.396 44.000 0.00 0.00 42.48 2.52
2329 2451 6.648192 CCTCTGGAGTCATTGATACTCTTTT 58.352 40.000 0.00 0.00 42.48 2.27
2330 2452 7.108847 CCTCTGGAGTCATTGATACTCTTTTT 58.891 38.462 0.00 0.00 42.48 1.94
2387 2509 9.125906 GTAGTAATGTATTATGGAGCAAGTACG 57.874 37.037 0.00 0.00 0.00 3.67
2388 2510 5.924475 AATGTATTATGGAGCAAGTACGC 57.076 39.130 0.00 0.00 0.00 4.42
2390 2512 5.018539 TGTATTATGGAGCAAGTACGCTT 57.981 39.130 0.00 0.00 44.01 4.68
2391 2513 5.424757 TGTATTATGGAGCAAGTACGCTTT 58.575 37.500 0.00 0.00 44.01 3.51
2392 2514 5.522460 TGTATTATGGAGCAAGTACGCTTTC 59.478 40.000 0.00 0.00 44.01 2.62
2393 2515 2.472695 ATGGAGCAAGTACGCTTTCA 57.527 45.000 0.00 0.75 44.01 2.69
2394 2516 2.248280 TGGAGCAAGTACGCTTTCAA 57.752 45.000 0.00 0.00 44.01 2.69
2395 2517 2.566913 TGGAGCAAGTACGCTTTCAAA 58.433 42.857 0.00 0.00 44.01 2.69
2396 2518 2.289547 TGGAGCAAGTACGCTTTCAAAC 59.710 45.455 0.00 0.00 44.01 2.93
2397 2519 2.289547 GGAGCAAGTACGCTTTCAAACA 59.710 45.455 0.00 0.00 44.01 2.83
2398 2520 3.545633 GAGCAAGTACGCTTTCAAACAG 58.454 45.455 0.00 0.00 44.01 3.16
2399 2521 2.044135 GCAAGTACGCTTTCAAACAGC 58.956 47.619 0.00 0.00 31.49 4.40
2400 2522 2.287009 GCAAGTACGCTTTCAAACAGCT 60.287 45.455 0.00 0.00 34.88 4.24
2401 2523 3.291585 CAAGTACGCTTTCAAACAGCTG 58.708 45.455 13.48 13.48 34.88 4.24
2402 2524 1.264288 AGTACGCTTTCAAACAGCTGC 59.736 47.619 15.27 0.00 34.88 5.25
2403 2525 1.264288 GTACGCTTTCAAACAGCTGCT 59.736 47.619 15.27 0.00 34.88 4.24
2404 2526 0.029834 ACGCTTTCAAACAGCTGCTG 59.970 50.000 27.02 27.02 34.88 4.41
2405 2527 0.308684 CGCTTTCAAACAGCTGCTGA 59.691 50.000 34.28 14.30 34.88 4.26
2406 2528 1.068748 CGCTTTCAAACAGCTGCTGAT 60.069 47.619 34.28 21.55 34.88 2.90
2407 2529 2.325761 GCTTTCAAACAGCTGCTGATG 58.674 47.619 34.28 28.30 35.18 3.07
2408 2530 2.325761 CTTTCAAACAGCTGCTGATGC 58.674 47.619 34.28 0.00 35.18 3.91
2419 2541 1.905637 TGCTGATGCATCCATCCATC 58.094 50.000 23.67 1.87 45.86 3.51
2420 2542 1.423921 TGCTGATGCATCCATCCATCT 59.576 47.619 23.67 0.00 45.86 2.90
2421 2543 2.640826 TGCTGATGCATCCATCCATCTA 59.359 45.455 23.67 0.81 45.86 1.98
2422 2544 3.008330 GCTGATGCATCCATCCATCTAC 58.992 50.000 23.67 0.00 45.86 2.59
2423 2545 3.607741 CTGATGCATCCATCCATCTACC 58.392 50.000 23.67 0.00 45.86 3.18
2424 2546 3.254089 TGATGCATCCATCCATCTACCT 58.746 45.455 23.67 0.00 45.86 3.08
2425 2547 3.262660 TGATGCATCCATCCATCTACCTC 59.737 47.826 23.67 0.00 45.86 3.85
2426 2548 1.620323 TGCATCCATCCATCTACCTCG 59.380 52.381 0.00 0.00 0.00 4.63
2427 2549 1.066573 GCATCCATCCATCTACCTCGG 60.067 57.143 0.00 0.00 0.00 4.63
2428 2550 1.066573 CATCCATCCATCTACCTCGGC 60.067 57.143 0.00 0.00 0.00 5.54
2429 2551 1.179174 TCCATCCATCTACCTCGGCG 61.179 60.000 0.00 0.00 0.00 6.46
2430 2552 1.290324 CATCCATCTACCTCGGCGG 59.710 63.158 7.21 0.00 39.35 6.13
2432 2554 0.759436 ATCCATCTACCTCGGCGGTT 60.759 55.000 7.21 0.00 46.37 4.44
2433 2555 1.067582 CCATCTACCTCGGCGGTTC 59.932 63.158 7.21 0.00 46.37 3.62
2434 2556 1.672854 CCATCTACCTCGGCGGTTCA 61.673 60.000 7.21 0.00 46.37 3.18
2435 2557 0.174845 CATCTACCTCGGCGGTTCAA 59.825 55.000 7.21 0.00 46.37 2.69
2436 2558 0.899720 ATCTACCTCGGCGGTTCAAA 59.100 50.000 7.21 0.00 46.37 2.69
2437 2559 0.899720 TCTACCTCGGCGGTTCAAAT 59.100 50.000 7.21 0.00 46.37 2.32
2438 2560 1.134907 TCTACCTCGGCGGTTCAAATC 60.135 52.381 7.21 0.00 46.37 2.17
2439 2561 0.899720 TACCTCGGCGGTTCAAATCT 59.100 50.000 7.21 0.00 46.37 2.40
2440 2562 0.673644 ACCTCGGCGGTTCAAATCTG 60.674 55.000 7.21 0.00 46.37 2.90
2441 2563 0.391130 CCTCGGCGGTTCAAATCTGA 60.391 55.000 7.21 0.00 0.00 3.27
2442 2564 1.656652 CTCGGCGGTTCAAATCTGAT 58.343 50.000 7.21 0.00 0.00 2.90
2443 2565 1.594862 CTCGGCGGTTCAAATCTGATC 59.405 52.381 7.21 0.00 0.00 2.92
2444 2566 0.301687 CGGCGGTTCAAATCTGATCG 59.698 55.000 0.00 0.00 34.03 3.69
2445 2567 1.651987 GGCGGTTCAAATCTGATCGA 58.348 50.000 0.00 0.00 33.23 3.59
2446 2568 1.327764 GGCGGTTCAAATCTGATCGAC 59.672 52.381 0.00 0.00 33.23 4.20
2447 2569 2.271800 GCGGTTCAAATCTGATCGACT 58.728 47.619 0.00 0.00 33.23 4.18
2457 2579 0.824109 CTGATCGACTGGGCCAAGTA 59.176 55.000 14.50 0.00 0.00 2.24
2525 2648 9.682465 GGAATCTAGGTATCAAAAACCTACTTT 57.318 33.333 0.00 0.00 45.69 2.66
2585 2709 7.559897 TCAAACTTCTCCAAAAACCAGACTTAT 59.440 33.333 0.00 0.00 0.00 1.73
2636 2760 7.711339 ACAACTCTCTAGACTTCGAAAACAAAT 59.289 33.333 0.00 0.00 0.00 2.32
2637 2761 8.552034 CAACTCTCTAGACTTCGAAAACAAATT 58.448 33.333 0.00 0.00 0.00 1.82
2638 2762 8.077836 ACTCTCTAGACTTCGAAAACAAATTG 57.922 34.615 0.00 0.00 0.00 2.32
2649 2773 4.566360 CGAAAACAAATTGCACAGTCCTTT 59.434 37.500 0.00 0.00 0.00 3.11
2671 2795 8.368668 CCTTTCTACCTATGGAGAATCGTAAAT 58.631 37.037 0.00 0.00 34.37 1.40
2807 2937 0.038310 CCTTTTCTCCCACTCCACCC 59.962 60.000 0.00 0.00 0.00 4.61
2854 2984 3.563808 TCATGCATTATGGTTTACTCGCC 59.436 43.478 0.00 0.00 37.39 5.54
2920 3051 3.181511 CGTCTGTTTTGTCTCTGTTGCAA 60.182 43.478 0.00 0.00 0.00 4.08
3004 3135 2.027625 GTGCGCCTACTCGTTGCTT 61.028 57.895 4.18 0.00 0.00 3.91
3014 3145 0.038159 CTCGTTGCTTTCCTCCGACT 60.038 55.000 0.00 0.00 0.00 4.18
3023 3154 3.572255 GCTTTCCTCCGACTATGAGATCT 59.428 47.826 0.00 0.00 31.26 2.75
3063 3194 0.690762 TGGAGTTCCAAGGCACCTAC 59.309 55.000 0.00 0.00 44.35 3.18
3096 3227 1.195115 TTCGGCTGGCTTCTCTGTAT 58.805 50.000 0.00 0.00 0.00 2.29
3097 3228 0.461548 TCGGCTGGCTTCTCTGTATG 59.538 55.000 0.00 0.00 0.00 2.39
3098 3229 0.176680 CGGCTGGCTTCTCTGTATGT 59.823 55.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 4.767255 CACAGGAGGCAGCGGACC 62.767 72.222 0.00 0.00 0.00 4.46
46 47 4.767255 CCACAGGAGGCAGCGGAC 62.767 72.222 0.00 0.00 0.00 4.79
48 49 4.020617 TTCCACAGGAGGCAGCGG 62.021 66.667 0.00 0.00 31.21 5.52
71 72 1.860641 TAAGATGAGGCGGGAACTGA 58.139 50.000 0.00 0.00 36.31 3.41
72 73 2.366916 AGATAAGATGAGGCGGGAACTG 59.633 50.000 0.00 0.00 38.10 3.16
73 74 2.683768 AGATAAGATGAGGCGGGAACT 58.316 47.619 0.00 0.00 0.00 3.01
74 75 3.574826 ACTAGATAAGATGAGGCGGGAAC 59.425 47.826 0.00 0.00 0.00 3.62
94 98 1.602327 GGAAAGCGACCCGACCTACT 61.602 60.000 0.00 0.00 0.00 2.57
95 99 1.153686 GGAAAGCGACCCGACCTAC 60.154 63.158 0.00 0.00 0.00 3.18
96 100 3.291611 GGAAAGCGACCCGACCTA 58.708 61.111 0.00 0.00 0.00 3.08
153 157 2.124570 ATCATGGTCCACAGCCGC 60.125 61.111 0.00 0.00 0.00 6.53
154 158 2.475466 GCATCATGGTCCACAGCCG 61.475 63.158 0.00 0.00 0.00 5.52
155 159 2.475466 CGCATCATGGTCCACAGCC 61.475 63.158 0.00 0.00 0.00 4.85
171 176 4.194720 ACGTCTCTCCCGATGCGC 62.195 66.667 0.00 0.00 0.00 6.09
204 215 3.220447 GATGGAACCCAACGACGAA 57.780 52.632 0.00 0.00 36.95 3.85
291 306 4.449068 GTGATTTGCGATGGATACTGGTAG 59.551 45.833 0.00 0.00 37.61 3.18
293 308 3.206150 GTGATTTGCGATGGATACTGGT 58.794 45.455 0.00 0.00 37.61 4.00
294 309 3.205338 TGTGATTTGCGATGGATACTGG 58.795 45.455 0.00 0.00 37.61 4.00
321 354 6.182039 ACAATCACACCATTCGTTTATCTG 57.818 37.500 0.00 0.00 0.00 2.90
331 364 3.054728 TCCGGACATACAATCACACCATT 60.055 43.478 0.00 0.00 0.00 3.16
332 365 2.503765 TCCGGACATACAATCACACCAT 59.496 45.455 0.00 0.00 0.00 3.55
343 376 1.000955 CCTAGCACCATCCGGACATAC 59.999 57.143 6.12 0.00 35.59 2.39
349 382 0.469917 AACATCCTAGCACCATCCGG 59.530 55.000 0.00 0.00 38.77 5.14
378 415 3.447752 TTTGTTCGTATGACATGCGTG 57.552 42.857 22.57 3.82 39.45 5.34
459 497 9.547753 ACTTGACATAAATCTAATATGCGAAGT 57.452 29.630 0.00 0.00 34.21 3.01
461 499 9.764363 AGACTTGACATAAATCTAATATGCGAA 57.236 29.630 0.00 0.00 34.75 4.70
517 555 9.990360 TGATATTGTAGATGCCGATACTTTTTA 57.010 29.630 0.00 0.00 0.00 1.52
518 556 8.902540 TGATATTGTAGATGCCGATACTTTTT 57.097 30.769 0.00 0.00 0.00 1.94
519 557 8.902540 TTGATATTGTAGATGCCGATACTTTT 57.097 30.769 0.00 0.00 0.00 2.27
520 558 8.902540 TTTGATATTGTAGATGCCGATACTTT 57.097 30.769 0.00 0.00 0.00 2.66
573 611 7.754924 CGCCAAATTAACATTGTTAGACTCATT 59.245 33.333 9.10 4.04 0.00 2.57
574 612 7.094377 ACGCCAAATTAACATTGTTAGACTCAT 60.094 33.333 9.10 0.00 0.00 2.90
575 613 6.205853 ACGCCAAATTAACATTGTTAGACTCA 59.794 34.615 9.10 0.00 0.00 3.41
576 614 6.608610 ACGCCAAATTAACATTGTTAGACTC 58.391 36.000 9.10 0.00 0.00 3.36
577 615 6.569179 ACGCCAAATTAACATTGTTAGACT 57.431 33.333 9.10 0.00 0.00 3.24
578 616 6.639279 ACAACGCCAAATTAACATTGTTAGAC 59.361 34.615 9.10 0.00 0.00 2.59
579 617 6.638873 CACAACGCCAAATTAACATTGTTAGA 59.361 34.615 9.10 2.55 0.00 2.10
580 618 6.638873 TCACAACGCCAAATTAACATTGTTAG 59.361 34.615 9.10 0.00 0.00 2.34
581 619 6.504398 TCACAACGCCAAATTAACATTGTTA 58.496 32.000 5.14 5.14 0.00 2.41
582 620 5.352284 TCACAACGCCAAATTAACATTGTT 58.648 33.333 7.30 7.30 0.00 2.83
583 621 4.938080 TCACAACGCCAAATTAACATTGT 58.062 34.783 3.05 0.00 0.00 2.71
584 622 5.896922 TTCACAACGCCAAATTAACATTG 57.103 34.783 0.00 0.00 0.00 2.82
585 623 5.988561 ACATTCACAACGCCAAATTAACATT 59.011 32.000 0.00 0.00 0.00 2.71
586 624 5.537188 ACATTCACAACGCCAAATTAACAT 58.463 33.333 0.00 0.00 0.00 2.71
587 625 4.938080 ACATTCACAACGCCAAATTAACA 58.062 34.783 0.00 0.00 0.00 2.41
588 626 5.898630 AACATTCACAACGCCAAATTAAC 57.101 34.783 0.00 0.00 0.00 2.01
589 627 6.740110 ACTAACATTCACAACGCCAAATTAA 58.260 32.000 0.00 0.00 0.00 1.40
590 628 6.320494 ACTAACATTCACAACGCCAAATTA 57.680 33.333 0.00 0.00 0.00 1.40
591 629 5.195001 ACTAACATTCACAACGCCAAATT 57.805 34.783 0.00 0.00 0.00 1.82
592 630 4.846779 ACTAACATTCACAACGCCAAAT 57.153 36.364 0.00 0.00 0.00 2.32
593 631 4.817464 AGTACTAACATTCACAACGCCAAA 59.183 37.500 0.00 0.00 0.00 3.28
594 632 4.382291 AGTACTAACATTCACAACGCCAA 58.618 39.130 0.00 0.00 0.00 4.52
595 633 3.997762 AGTACTAACATTCACAACGCCA 58.002 40.909 0.00 0.00 0.00 5.69
596 634 4.689345 AGAAGTACTAACATTCACAACGCC 59.311 41.667 0.00 0.00 0.00 5.68
597 635 5.840940 AGAAGTACTAACATTCACAACGC 57.159 39.130 0.00 0.00 0.00 4.84
624 662 9.793259 TCTGAAGTCTACTTTGACCAAATTTAT 57.207 29.630 0.00 0.00 37.66 1.40
625 663 9.052759 GTCTGAAGTCTACTTTGACCAAATTTA 57.947 33.333 13.99 0.00 37.66 1.40
626 664 7.556275 TGTCTGAAGTCTACTTTGACCAAATTT 59.444 33.333 18.53 0.00 38.12 1.82
627 665 7.054124 TGTCTGAAGTCTACTTTGACCAAATT 58.946 34.615 18.53 0.00 38.12 1.82
628 666 6.591935 TGTCTGAAGTCTACTTTGACCAAAT 58.408 36.000 18.53 0.00 38.12 2.32
629 667 5.984725 TGTCTGAAGTCTACTTTGACCAAA 58.015 37.500 18.53 0.00 38.12 3.28
630 668 5.607939 TGTCTGAAGTCTACTTTGACCAA 57.392 39.130 18.53 6.65 38.12 3.67
631 669 5.128827 AGTTGTCTGAAGTCTACTTTGACCA 59.871 40.000 18.53 10.82 38.12 4.02
632 670 5.602628 AGTTGTCTGAAGTCTACTTTGACC 58.397 41.667 18.53 10.15 38.12 4.02
633 671 8.819643 ATAAGTTGTCTGAAGTCTACTTTGAC 57.180 34.615 16.31 16.31 38.72 3.18
640 678 9.678941 CGCATATAATAAGTTGTCTGAAGTCTA 57.321 33.333 0.00 0.00 0.00 2.59
641 679 7.653713 CCGCATATAATAAGTTGTCTGAAGTCT 59.346 37.037 0.00 0.00 0.00 3.24
642 680 7.652105 TCCGCATATAATAAGTTGTCTGAAGTC 59.348 37.037 0.00 0.00 0.00 3.01
643 681 7.438459 GTCCGCATATAATAAGTTGTCTGAAGT 59.562 37.037 0.00 0.00 0.00 3.01
644 682 7.653713 AGTCCGCATATAATAAGTTGTCTGAAG 59.346 37.037 0.00 0.00 0.00 3.02
645 683 7.497595 AGTCCGCATATAATAAGTTGTCTGAA 58.502 34.615 0.00 0.00 0.00 3.02
646 684 7.050970 AGTCCGCATATAATAAGTTGTCTGA 57.949 36.000 0.00 0.00 0.00 3.27
647 685 8.812147 TTAGTCCGCATATAATAAGTTGTCTG 57.188 34.615 0.00 0.00 0.00 3.51
648 686 9.826574 TTTTAGTCCGCATATAATAAGTTGTCT 57.173 29.630 0.00 0.00 0.00 3.41
651 689 9.878599 CCTTTTTAGTCCGCATATAATAAGTTG 57.121 33.333 0.00 0.00 0.00 3.16
652 690 9.841295 TCCTTTTTAGTCCGCATATAATAAGTT 57.159 29.630 0.00 0.00 0.00 2.66
653 691 9.269453 GTCCTTTTTAGTCCGCATATAATAAGT 57.731 33.333 0.00 0.00 0.00 2.24
654 692 8.718734 GGTCCTTTTTAGTCCGCATATAATAAG 58.281 37.037 0.00 0.00 0.00 1.73
655 693 7.385752 CGGTCCTTTTTAGTCCGCATATAATAA 59.614 37.037 0.00 0.00 35.01 1.40
656 694 6.869913 CGGTCCTTTTTAGTCCGCATATAATA 59.130 38.462 0.00 0.00 35.01 0.98
657 695 5.699458 CGGTCCTTTTTAGTCCGCATATAAT 59.301 40.000 0.00 0.00 35.01 1.28
658 696 5.051816 CGGTCCTTTTTAGTCCGCATATAA 58.948 41.667 0.00 0.00 35.01 0.98
659 697 4.501915 CCGGTCCTTTTTAGTCCGCATATA 60.502 45.833 0.00 0.00 39.87 0.86
660 698 3.463944 CGGTCCTTTTTAGTCCGCATAT 58.536 45.455 0.00 0.00 35.01 1.78
661 699 2.419021 CCGGTCCTTTTTAGTCCGCATA 60.419 50.000 0.00 0.00 39.87 3.14
662 700 1.677820 CCGGTCCTTTTTAGTCCGCAT 60.678 52.381 0.00 0.00 39.87 4.73
663 701 0.320946 CCGGTCCTTTTTAGTCCGCA 60.321 55.000 0.00 0.00 39.87 5.69
664 702 0.037046 TCCGGTCCTTTTTAGTCCGC 60.037 55.000 0.00 0.00 39.87 5.54
665 703 1.405121 CCTCCGGTCCTTTTTAGTCCG 60.405 57.143 0.00 0.00 40.72 4.79
666 704 1.904537 TCCTCCGGTCCTTTTTAGTCC 59.095 52.381 0.00 0.00 0.00 3.85
667 705 3.007723 ACTTCCTCCGGTCCTTTTTAGTC 59.992 47.826 0.00 0.00 0.00 2.59
668 706 2.977580 ACTTCCTCCGGTCCTTTTTAGT 59.022 45.455 0.00 0.00 0.00 2.24
669 707 3.697619 ACTTCCTCCGGTCCTTTTTAG 57.302 47.619 0.00 0.00 0.00 1.85
670 708 4.162651 AGTACTTCCTCCGGTCCTTTTTA 58.837 43.478 0.00 0.00 0.00 1.52
671 709 2.977580 AGTACTTCCTCCGGTCCTTTTT 59.022 45.455 0.00 0.00 0.00 1.94
672 710 2.617658 AGTACTTCCTCCGGTCCTTTT 58.382 47.619 0.00 0.00 0.00 2.27
673 711 2.322339 AGTACTTCCTCCGGTCCTTT 57.678 50.000 0.00 0.00 0.00 3.11
674 712 2.042162 TGTAGTACTTCCTCCGGTCCTT 59.958 50.000 0.00 0.00 0.00 3.36
675 713 1.637553 TGTAGTACTTCCTCCGGTCCT 59.362 52.381 0.00 0.00 0.00 3.85
676 714 2.022934 CTGTAGTACTTCCTCCGGTCC 58.977 57.143 0.00 0.00 0.00 4.46
677 715 2.720915 ACTGTAGTACTTCCTCCGGTC 58.279 52.381 0.00 0.00 0.00 4.79
678 716 2.895242 ACTGTAGTACTTCCTCCGGT 57.105 50.000 0.00 0.00 0.00 5.28
679 717 3.762823 AGAAACTGTAGTACTTCCTCCGG 59.237 47.826 0.00 0.00 0.00 5.14
680 718 4.734917 CAGAAACTGTAGTACTTCCTCCG 58.265 47.826 0.00 0.00 0.00 4.63
681 719 4.496360 GCAGAAACTGTAGTACTTCCTCC 58.504 47.826 0.00 0.00 33.43 4.30
682 720 4.167268 CGCAGAAACTGTAGTACTTCCTC 58.833 47.826 0.00 0.00 33.43 3.71
683 721 3.614390 GCGCAGAAACTGTAGTACTTCCT 60.614 47.826 0.30 0.00 33.43 3.36
684 722 2.666994 GCGCAGAAACTGTAGTACTTCC 59.333 50.000 0.30 0.00 33.43 3.46
685 723 3.314553 TGCGCAGAAACTGTAGTACTTC 58.685 45.455 5.66 0.00 33.43 3.01
686 724 3.380479 TGCGCAGAAACTGTAGTACTT 57.620 42.857 5.66 0.00 33.43 2.24
687 725 3.318017 CTTGCGCAGAAACTGTAGTACT 58.682 45.455 11.31 0.00 33.43 2.73
688 726 2.159827 GCTTGCGCAGAAACTGTAGTAC 60.160 50.000 11.31 0.00 33.43 2.73
689 727 2.066262 GCTTGCGCAGAAACTGTAGTA 58.934 47.619 11.31 0.00 33.43 1.82
690 728 0.868406 GCTTGCGCAGAAACTGTAGT 59.132 50.000 11.31 0.00 33.43 2.73
691 729 0.867746 TGCTTGCGCAGAAACTGTAG 59.132 50.000 11.31 3.25 42.25 2.74
713 751 2.398498 CAGCACTACACGGATCTATGC 58.602 52.381 0.00 0.00 0.00 3.14
726 765 0.617535 TAGGAGCCTTGGCAGCACTA 60.618 55.000 14.54 7.33 0.00 2.74
731 770 2.027385 GGATTTTAGGAGCCTTGGCAG 58.973 52.381 14.54 0.00 0.00 4.85
736 775 3.456380 TGCAAGGATTTTAGGAGCCTT 57.544 42.857 0.00 0.00 41.22 4.35
827 866 5.699097 TTTCTTTGTTACGAAGGAATGGG 57.301 39.130 11.96 0.00 0.00 4.00
853 894 3.128068 ACCAAAACGTCTGGTTCACTTTC 59.872 43.478 14.86 0.00 45.13 2.62
864 905 4.642885 TCAATTTCCTTCACCAAAACGTCT 59.357 37.500 0.00 0.00 0.00 4.18
910 982 2.083002 GGCCGAACGGGTAAAATGTAA 58.917 47.619 15.01 0.00 38.44 2.41
1022 1107 1.227674 GGGTGATGATGGAGGCGAC 60.228 63.158 0.00 0.00 0.00 5.19
1061 1146 0.918983 AATGGAGGAGGCGAATGGAA 59.081 50.000 0.00 0.00 0.00 3.53
1062 1147 0.181114 CAATGGAGGAGGCGAATGGA 59.819 55.000 0.00 0.00 0.00 3.41
1063 1148 1.450531 GCAATGGAGGAGGCGAATGG 61.451 60.000 0.00 0.00 0.00 3.16
1197 1292 3.984200 GACCCAGAGCACGGCGTAC 62.984 68.421 14.22 7.36 0.00 3.67
1249 1344 2.853914 GCTCTCGCCGTTGTCAAC 59.146 61.111 5.58 5.58 0.00 3.18
1805 1903 4.065281 CACTCACCGACCCCGACC 62.065 72.222 0.00 0.00 38.22 4.79
1806 1904 2.987547 TCACTCACCGACCCCGAC 60.988 66.667 0.00 0.00 38.22 4.79
1807 1905 2.987547 GTCACTCACCGACCCCGA 60.988 66.667 0.00 0.00 38.22 5.14
1808 1906 4.065281 GGTCACTCACCGACCCCG 62.065 72.222 0.00 0.00 46.12 5.73
1830 1946 1.409381 CCCATCCCCTTCTTCTTCTGC 60.409 57.143 0.00 0.00 0.00 4.26
1831 1947 1.213926 CCCCATCCCCTTCTTCTTCTG 59.786 57.143 0.00 0.00 0.00 3.02
1832 1948 1.082879 TCCCCATCCCCTTCTTCTTCT 59.917 52.381 0.00 0.00 0.00 2.85
1952 2068 4.148825 CCTCCACCTTCTCCGCCG 62.149 72.222 0.00 0.00 0.00 6.46
2070 2191 1.678101 AGCAAAGAAGATATTGGCGGC 59.322 47.619 0.00 0.00 0.00 6.53
2071 2192 3.629398 AGAAGCAAAGAAGATATTGGCGG 59.371 43.478 0.00 0.00 0.00 6.13
2077 2198 7.655328 CGGACAGAATAGAAGCAAAGAAGATAT 59.345 37.037 0.00 0.00 0.00 1.63
2092 2213 6.683974 ATTCAACAAATCCGGACAGAATAG 57.316 37.500 6.12 0.00 0.00 1.73
2100 2221 3.127895 CGCCTTTATTCAACAAATCCGGA 59.872 43.478 6.61 6.61 0.00 5.14
2119 2240 2.622546 TTGTTAATTTCCTTCGCGCC 57.377 45.000 0.00 0.00 0.00 6.53
2120 2241 3.753842 TCATTGTTAATTTCCTTCGCGC 58.246 40.909 0.00 0.00 0.00 6.86
2127 2248 7.367285 TGTTGCTACACTCATTGTTAATTTCC 58.633 34.615 0.00 0.00 39.91 3.13
2128 2249 8.289618 TCTGTTGCTACACTCATTGTTAATTTC 58.710 33.333 0.00 0.00 39.91 2.17
2139 2260 3.934457 TTCGATCTGTTGCTACACTCA 57.066 42.857 0.00 0.00 0.00 3.41
2168 2289 4.742138 GCACCAAAGGAAGGCACATAAAAA 60.742 41.667 0.00 0.00 0.00 1.94
2186 2307 1.137675 CCAGATCATCTCGAAGCACCA 59.862 52.381 0.00 0.00 0.00 4.17
2193 2314 3.298686 ACCTACACCAGATCATCTCGA 57.701 47.619 0.00 0.00 0.00 4.04
2220 2341 2.057137 ACAGCAGAACAGCTCCAAAA 57.943 45.000 0.00 0.00 44.54 2.44
2221 2342 1.677576 CAACAGCAGAACAGCTCCAAA 59.322 47.619 0.00 0.00 44.54 3.28
2230 2351 0.169009 GGGCGAATCAACAGCAGAAC 59.831 55.000 0.00 0.00 0.00 3.01
2236 2357 2.358957 TCAATCTGGGCGAATCAACAG 58.641 47.619 0.00 0.00 0.00 3.16
2262 2384 1.663695 GGCTCATACCGCTGCTAAAA 58.336 50.000 0.00 0.00 0.00 1.52
2275 2397 0.179111 CCACATACGTGACGGCTCAT 60.179 55.000 10.66 0.00 46.80 2.90
2292 2414 2.847234 AGAGGCGTCCACAACCCA 60.847 61.111 2.06 0.00 0.00 4.51
2361 2483 9.125906 CGTACTTGCTCCATAATACATTACTAC 57.874 37.037 0.00 0.00 0.00 2.73
2362 2484 7.811236 GCGTACTTGCTCCATAATACATTACTA 59.189 37.037 0.00 0.00 0.00 1.82
2363 2485 6.645415 GCGTACTTGCTCCATAATACATTACT 59.355 38.462 0.00 0.00 0.00 2.24
2364 2486 6.645415 AGCGTACTTGCTCCATAATACATTAC 59.355 38.462 0.00 0.00 42.95 1.89
2365 2487 6.755206 AGCGTACTTGCTCCATAATACATTA 58.245 36.000 0.00 0.00 42.95 1.90
2366 2488 5.611374 AGCGTACTTGCTCCATAATACATT 58.389 37.500 0.00 0.00 42.95 2.71
2367 2489 5.215252 AGCGTACTTGCTCCATAATACAT 57.785 39.130 0.00 0.00 42.95 2.29
2368 2490 4.665833 AGCGTACTTGCTCCATAATACA 57.334 40.909 0.00 0.00 42.95 2.29
2369 2491 5.522460 TGAAAGCGTACTTGCTCCATAATAC 59.478 40.000 0.00 0.00 46.60 1.89
2370 2492 5.666462 TGAAAGCGTACTTGCTCCATAATA 58.334 37.500 0.00 0.00 46.60 0.98
2371 2493 4.513442 TGAAAGCGTACTTGCTCCATAAT 58.487 39.130 0.00 0.00 46.60 1.28
2372 2494 3.932822 TGAAAGCGTACTTGCTCCATAA 58.067 40.909 0.00 0.00 46.60 1.90
2373 2495 3.603158 TGAAAGCGTACTTGCTCCATA 57.397 42.857 0.00 0.00 46.60 2.74
2374 2496 2.472695 TGAAAGCGTACTTGCTCCAT 57.527 45.000 0.00 0.00 46.60 3.41
2375 2497 2.248280 TTGAAAGCGTACTTGCTCCA 57.752 45.000 0.00 0.00 46.60 3.86
2376 2498 2.289547 TGTTTGAAAGCGTACTTGCTCC 59.710 45.455 0.00 0.00 46.60 4.70
2377 2499 3.545633 CTGTTTGAAAGCGTACTTGCTC 58.454 45.455 0.00 0.00 46.60 4.26
2379 2501 2.044135 GCTGTTTGAAAGCGTACTTGC 58.956 47.619 0.00 0.00 35.85 4.01
2380 2502 3.291585 CAGCTGTTTGAAAGCGTACTTG 58.708 45.455 5.25 0.00 45.59 3.16
2381 2503 2.287009 GCAGCTGTTTGAAAGCGTACTT 60.287 45.455 16.64 0.00 45.59 2.24
2382 2504 1.264288 GCAGCTGTTTGAAAGCGTACT 59.736 47.619 16.64 0.00 45.59 2.73
2383 2505 1.264288 AGCAGCTGTTTGAAAGCGTAC 59.736 47.619 16.64 0.00 45.59 3.67
2384 2506 1.264020 CAGCAGCTGTTTGAAAGCGTA 59.736 47.619 16.64 0.00 45.59 4.42
2385 2507 0.029834 CAGCAGCTGTTTGAAAGCGT 59.970 50.000 16.64 0.00 45.59 5.07
2386 2508 0.308684 TCAGCAGCTGTTTGAAAGCG 59.691 50.000 22.10 0.00 45.59 4.68
2387 2509 2.325761 CATCAGCAGCTGTTTGAAAGC 58.674 47.619 22.10 3.99 41.15 3.51
2388 2510 2.325761 GCATCAGCAGCTGTTTGAAAG 58.674 47.619 22.10 18.03 41.58 2.62
2389 2511 2.427232 GCATCAGCAGCTGTTTGAAA 57.573 45.000 22.10 1.68 41.58 2.69
2405 2527 2.235650 CGAGGTAGATGGATGGATGCAT 59.764 50.000 0.00 0.00 41.76 3.96
2406 2528 1.620323 CGAGGTAGATGGATGGATGCA 59.380 52.381 0.00 0.00 0.00 3.96
2407 2529 1.066573 CCGAGGTAGATGGATGGATGC 60.067 57.143 0.00 0.00 0.00 3.91
2408 2530 1.066573 GCCGAGGTAGATGGATGGATG 60.067 57.143 0.00 0.00 0.00 3.51
2409 2531 1.270907 GCCGAGGTAGATGGATGGAT 58.729 55.000 0.00 0.00 0.00 3.41
2410 2532 1.179174 CGCCGAGGTAGATGGATGGA 61.179 60.000 0.00 0.00 0.00 3.41
2411 2533 1.290324 CGCCGAGGTAGATGGATGG 59.710 63.158 0.00 0.00 0.00 3.51
2412 2534 1.290324 CCGCCGAGGTAGATGGATG 59.710 63.158 0.00 0.00 34.51 3.51
2413 2535 3.778955 CCGCCGAGGTAGATGGAT 58.221 61.111 0.00 0.00 34.51 3.41
2422 2544 1.743772 ATCAGATTTGAACCGCCGAGG 60.744 52.381 0.00 0.00 39.74 4.63
2423 2545 1.594862 GATCAGATTTGAACCGCCGAG 59.405 52.381 0.00 0.00 36.78 4.63
2424 2546 1.651987 GATCAGATTTGAACCGCCGA 58.348 50.000 0.00 0.00 36.78 5.54
2425 2547 0.301687 CGATCAGATTTGAACCGCCG 59.698 55.000 0.00 0.00 36.78 6.46
2426 2548 1.327764 GTCGATCAGATTTGAACCGCC 59.672 52.381 6.55 0.00 36.78 6.13
2427 2549 2.029728 CAGTCGATCAGATTTGAACCGC 59.970 50.000 6.55 3.58 36.78 5.68
2428 2550 2.604914 CCAGTCGATCAGATTTGAACCG 59.395 50.000 0.00 5.43 36.78 4.44
2429 2551 2.939103 CCCAGTCGATCAGATTTGAACC 59.061 50.000 0.00 0.00 36.78 3.62
2430 2552 2.352960 GCCCAGTCGATCAGATTTGAAC 59.647 50.000 0.00 0.00 36.78 3.18
2431 2553 2.632377 GCCCAGTCGATCAGATTTGAA 58.368 47.619 0.00 0.00 36.78 2.69
2432 2554 1.134401 GGCCCAGTCGATCAGATTTGA 60.134 52.381 0.00 0.00 37.81 2.69
2433 2555 1.303309 GGCCCAGTCGATCAGATTTG 58.697 55.000 0.00 0.00 0.00 2.32
2434 2556 0.911769 TGGCCCAGTCGATCAGATTT 59.088 50.000 0.00 0.00 0.00 2.17
2435 2557 0.911769 TTGGCCCAGTCGATCAGATT 59.088 50.000 0.00 0.00 0.00 2.40
2436 2558 0.467384 CTTGGCCCAGTCGATCAGAT 59.533 55.000 0.00 0.00 0.00 2.90
2437 2559 0.904865 ACTTGGCCCAGTCGATCAGA 60.905 55.000 2.99 0.00 0.00 3.27
2438 2560 0.824109 TACTTGGCCCAGTCGATCAG 59.176 55.000 13.76 0.00 0.00 2.90
2439 2561 0.535335 GTACTTGGCCCAGTCGATCA 59.465 55.000 13.76 0.00 0.00 2.92
2440 2562 0.179081 GGTACTTGGCCCAGTCGATC 60.179 60.000 13.76 3.14 0.00 3.69
2441 2563 0.617820 AGGTACTTGGCCCAGTCGAT 60.618 55.000 13.76 0.00 27.25 3.59
2442 2564 1.229082 AGGTACTTGGCCCAGTCGA 60.229 57.895 13.76 0.00 27.25 4.20
2443 2565 3.388841 AGGTACTTGGCCCAGTCG 58.611 61.111 13.76 0.00 27.25 4.18
2457 2579 6.818142 GCATACATTTTTCCAAGCAATAAGGT 59.182 34.615 0.00 0.00 0.00 3.50
2551 2674 7.308288 GGTTTTTGGAGAAGTTTGAAAGCAAAA 60.308 33.333 0.00 0.00 44.91 2.44
2605 2729 3.189495 CGAAGTCTAGAGAGTTGTGCTGA 59.811 47.826 4.33 0.00 37.79 4.26
2612 2736 8.552034 CAATTTGTTTTCGAAGTCTAGAGAGTT 58.448 33.333 0.00 0.00 40.17 3.01
2636 2760 4.323485 CCATAGGTAGAAAGGACTGTGCAA 60.323 45.833 1.24 0.00 0.00 4.08
2637 2761 3.197766 CCATAGGTAGAAAGGACTGTGCA 59.802 47.826 1.24 0.00 0.00 4.57
2638 2762 3.451178 TCCATAGGTAGAAAGGACTGTGC 59.549 47.826 0.00 0.00 0.00 4.57
2649 2773 8.358148 GTTCATTTACGATTCTCCATAGGTAGA 58.642 37.037 0.00 0.00 0.00 2.59
2671 2795 2.147958 CGGAGGGTTCGAATTTGTTCA 58.852 47.619 0.00 0.00 0.00 3.18
2807 2937 2.465055 GAAACCAGGACCGAGGGTGG 62.465 65.000 10.32 3.34 35.25 4.61
2879 3010 2.005451 CGCAAGCTCTACAGAAGCAAT 58.995 47.619 0.00 0.00 0.00 3.56
3004 3135 6.381498 AGATAGATCTCATAGTCGGAGGAA 57.619 41.667 0.00 0.00 33.18 3.36
3023 3154 4.825634 CCAGATGTACCCTACGTTGAGATA 59.174 45.833 0.00 0.00 0.00 1.98
3033 3164 3.769189 TGGAACTCCAGATGTACCCTA 57.231 47.619 0.00 0.00 42.01 3.53
3063 3194 2.095059 CAGCCGAAAATCTTGACCTTGG 60.095 50.000 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.