Multiple sequence alignment - TraesCS4B01G353000

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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 TraesCS4B01G353000 chr4B 100.000 4233 0 0 1 4233 644790016 644785784 0.000000e+00 7817.0
1 TraesCS4B01G353000 chr4B 85.870 92 9 3 591 680 40078832 40078921 1.250000e-15 95.3
2 TraesCS4B01G353000 chr4B 93.617 47 3 0 2691 2737 644787275 644787229 2.110000e-08 71.3
3 TraesCS4B01G353000 chr4B 93.617 47 3 0 2742 2788 644787326 644787280 2.110000e-08 71.3
4 TraesCS4B01G353000 chr5A 94.223 3358 144 27 893 4231 683349052 683352378 0.000000e+00 5081.0
5 TraesCS4B01G353000 chr5A 86.207 377 30 14 3 369 683343991 683344355 5.130000e-104 388.0
6 TraesCS4B01G353000 chr5A 80.567 247 33 7 588 824 553462926 553463167 4.350000e-40 176.0
7 TraesCS4B01G353000 chr5A 94.231 52 3 0 2688 2739 683350890 683350941 3.510000e-11 80.5
8 TraesCS4B01G353000 chr4D 93.380 2009 86 17 1717 3687 500822210 500820211 0.000000e+00 2929.0
9 TraesCS4B01G353000 chr4D 91.562 1114 54 19 553 1655 500823536 500822452 0.000000e+00 1500.0
10 TraesCS4B01G353000 chr4D 96.175 366 10 4 3749 4111 500820207 500819843 2.820000e-166 595.0
11 TraesCS4B01G353000 chr4D 89.633 463 22 15 3 455 500823969 500823523 2.210000e-157 566.0
12 TraesCS4B01G353000 chr4D 96.319 163 6 0 4069 4231 500819844 500819682 6.980000e-68 268.0
13 TraesCS4B01G353000 chr4D 80.784 255 36 6 589 833 394302093 394301842 2.010000e-43 187.0
14 TraesCS4B01G353000 chr4D 90.789 76 7 0 478 553 500823544 500823469 7.490000e-18 102.0
15 TraesCS4B01G353000 chr4D 95.238 63 3 0 1655 1717 500822305 500822243 2.690000e-17 100.0
16 TraesCS4B01G353000 chr4D 95.918 49 2 0 2691 2739 500821164 500821116 3.510000e-11 80.5
17 TraesCS4B01G353000 chr3A 83.607 244 27 6 591 824 63180775 63180535 2.560000e-52 217.0
18 TraesCS4B01G353000 chr1B 79.767 257 36 8 588 832 433422809 433423061 5.630000e-39 172.0
19 TraesCS4B01G353000 chr5B 79.498 239 28 7 587 824 23394927 23394709 2.640000e-32 150.0
20 TraesCS4B01G353000 chr5B 78.661 239 30 6 587 824 23364685 23364467 5.710000e-29 139.0
21 TraesCS4B01G353000 chr3D 78.261 230 33 8 598 816 313602411 313602188 9.550000e-27 132.0
22 TraesCS4B01G353000 chr6A 100.000 37 0 0 2945 2981 617624893 617624857 7.590000e-08 69.4
23 TraesCS4B01G353000 chr6B 97.297 37 1 0 2945 2981 720746621 720746657 3.530000e-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 TraesCS4B01G353000 chr4B 644785784 644790016 4232 True 2653.2000 7817 95.744667 1 4233 3 chr4B.!!$R1 4232
1 TraesCS4B01G353000 chr5A 683349052 683352378 3326 False 2580.7500 5081 94.227000 893 4231 2 chr5A.!!$F3 3338
2 TraesCS4B01G353000 chr4D 500819682 500823969 4287 True 767.5625 2929 93.626750 3 4231 8 chr4D.!!$R2 4228

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
212 221 0.035820 TTACCGGCAGGCTTAAGGTG 60.036 55.0 0.00 0.0 42.76 4.00 F
799 818 0.099436 GCCATGCTGCTTAAAGTCCG 59.901 55.0 0.00 0.0 0.00 4.79 F
1568 1590 0.246635 CACCGCTGCTAGTACTGGTT 59.753 55.0 5.39 0.0 0.00 3.67 F
2833 3071 0.252467 ACCTAGGTGAGCTTGAGCCT 60.252 55.0 15.42 0.0 43.38 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1545 1567 0.033796 AGTACTAGCAGCGGTGGGTA 60.034 55.0 17.54 6.3 0.0 3.69 R
2788 3026 0.037605 AGAGGCGTTTTACCAGACCG 60.038 55.0 0.00 0.0 0.0 4.79 R
2851 3089 0.109132 CTTGTTCCTTTGCCATCGCC 60.109 55.0 0.00 0.0 0.0 5.54 R
3954 4202 0.319555 TACTGCACACCGACTTCAGC 60.320 55.0 0.00 0.0 0.0 4.26 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
32 33 0.777446 TTGAAAGGGAAGGGTGGAGG 59.223 55.000 0.00 0.00 0.00 4.30
97 100 1.945387 AGATAGTGCTGCCATTGTCG 58.055 50.000 0.00 0.00 0.00 4.35
98 101 1.208052 AGATAGTGCTGCCATTGTCGT 59.792 47.619 0.00 0.00 0.00 4.34
99 102 2.430694 AGATAGTGCTGCCATTGTCGTA 59.569 45.455 0.00 0.00 0.00 3.43
101 104 2.113860 AGTGCTGCCATTGTCGTAAT 57.886 45.000 0.00 0.00 0.00 1.89
102 105 1.739466 AGTGCTGCCATTGTCGTAATG 59.261 47.619 0.00 7.78 0.00 1.90
103 106 0.451383 TGCTGCCATTGTCGTAATGC 59.549 50.000 0.00 6.29 0.00 3.56
105 108 1.382522 CTGCCATTGTCGTAATGCCT 58.617 50.000 8.86 0.00 0.00 4.75
111 114 3.440173 CCATTGTCGTAATGCCTTTGTCT 59.560 43.478 8.86 0.00 0.00 3.41
139 142 4.640771 ATTCTTGGCTCTGTAGTGGAAA 57.359 40.909 0.00 0.00 0.00 3.13
140 143 4.431416 TTCTTGGCTCTGTAGTGGAAAA 57.569 40.909 0.00 0.00 0.00 2.29
212 221 0.035820 TTACCGGCAGGCTTAAGGTG 60.036 55.000 0.00 0.00 42.76 4.00
214 223 3.499737 CGGCAGGCTTAAGGTGCG 61.500 66.667 4.29 0.00 38.13 5.34
215 224 2.359975 GGCAGGCTTAAGGTGCGT 60.360 61.111 4.29 0.00 38.13 5.24
216 225 2.690778 GGCAGGCTTAAGGTGCGTG 61.691 63.158 4.29 4.18 45.53 5.34
217 226 2.870372 CAGGCTTAAGGTGCGTGC 59.130 61.111 4.29 0.00 39.00 5.34
218 227 2.742372 AGGCTTAAGGTGCGTGCG 60.742 61.111 4.29 0.00 0.00 5.34
242 251 3.341823 AGTTGTGACAAGAGGCATGATC 58.658 45.455 0.00 0.00 0.00 2.92
244 253 1.293924 GTGACAAGAGGCATGATCGG 58.706 55.000 0.00 0.00 0.00 4.18
265 274 2.419057 GCTTCTGTGTGCCAGGTTT 58.581 52.632 0.00 0.00 41.83 3.27
278 287 5.716228 TGTGCCAGGTTTAGATGAAAATGAT 59.284 36.000 0.00 0.00 0.00 2.45
279 288 6.038356 GTGCCAGGTTTAGATGAAAATGATG 58.962 40.000 0.00 0.00 0.00 3.07
280 289 5.951148 TGCCAGGTTTAGATGAAAATGATGA 59.049 36.000 0.00 0.00 0.00 2.92
281 290 6.436847 TGCCAGGTTTAGATGAAAATGATGAA 59.563 34.615 0.00 0.00 0.00 2.57
282 291 7.124599 TGCCAGGTTTAGATGAAAATGATGAAT 59.875 33.333 0.00 0.00 0.00 2.57
283 292 7.437267 GCCAGGTTTAGATGAAAATGATGAATG 59.563 37.037 0.00 0.00 0.00 2.67
285 294 9.297586 CAGGTTTAGATGAAAATGATGAATGTG 57.702 33.333 0.00 0.00 0.00 3.21
286 295 9.028284 AGGTTTAGATGAAAATGATGAATGTGT 57.972 29.630 0.00 0.00 0.00 3.72
287 296 9.643693 GGTTTAGATGAAAATGATGAATGTGTT 57.356 29.630 0.00 0.00 0.00 3.32
318 327 7.722949 AAAAGGAGATGAAAATGAAGGCATA 57.277 32.000 0.00 0.00 33.44 3.14
320 329 7.909485 AAGGAGATGAAAATGAAGGCATAAT 57.091 32.000 0.00 0.00 33.44 1.28
321 330 7.521871 AGGAGATGAAAATGAAGGCATAATC 57.478 36.000 0.00 0.00 33.44 1.75
322 331 6.206243 AGGAGATGAAAATGAAGGCATAATCG 59.794 38.462 0.00 0.00 33.44 3.34
411 420 6.174049 GGTTAGTTTCTGCTCTGTCCTTTAT 58.826 40.000 0.00 0.00 0.00 1.40
417 426 2.799412 CTGCTCTGTCCTTTATCGCATC 59.201 50.000 0.00 0.00 0.00 3.91
438 447 3.378112 TCGATGGATTCAATTTCAGTGGC 59.622 43.478 0.00 0.00 0.00 5.01
441 450 2.562298 TGGATTCAATTTCAGTGGCCAC 59.438 45.455 29.22 29.22 0.00 5.01
451 460 1.281577 TCAGTGGCCACATGCAGATTA 59.718 47.619 36.39 12.22 43.89 1.75
452 461 2.092267 TCAGTGGCCACATGCAGATTAT 60.092 45.455 36.39 10.00 43.89 1.28
453 462 2.691526 CAGTGGCCACATGCAGATTATT 59.308 45.455 36.39 9.43 43.89 1.40
454 463 3.131577 CAGTGGCCACATGCAGATTATTT 59.868 43.478 36.39 9.21 43.89 1.40
455 464 3.382546 AGTGGCCACATGCAGATTATTTC 59.617 43.478 36.39 4.59 43.89 2.17
456 465 2.358582 TGGCCACATGCAGATTATTTCG 59.641 45.455 0.00 0.00 43.89 3.46
457 466 2.388121 GCCACATGCAGATTATTTCGC 58.612 47.619 0.00 0.00 40.77 4.70
458 467 2.223548 GCCACATGCAGATTATTTCGCA 60.224 45.455 0.00 0.00 40.77 5.10
459 468 3.734597 GCCACATGCAGATTATTTCGCAA 60.735 43.478 0.00 0.00 40.77 4.85
460 469 4.422840 CCACATGCAGATTATTTCGCAAA 58.577 39.130 0.00 0.00 37.40 3.68
461 470 4.863689 CCACATGCAGATTATTTCGCAAAA 59.136 37.500 0.00 0.00 37.40 2.44
462 471 5.348179 CCACATGCAGATTATTTCGCAAAAA 59.652 36.000 0.00 0.00 37.40 1.94
536 545 7.160547 TGAAAAATAAAGGACCCCGATAAAC 57.839 36.000 0.00 0.00 0.00 2.01
538 547 3.870538 ATAAAGGACCCCGATAAACCC 57.129 47.619 0.00 0.00 0.00 4.11
539 548 0.627451 AAAGGACCCCGATAAACCCC 59.373 55.000 0.00 0.00 0.00 4.95
544 553 1.522130 CCCCGATAAACCCCGAACG 60.522 63.158 0.00 0.00 0.00 3.95
545 554 2.175621 CCCGATAAACCCCGAACGC 61.176 63.158 0.00 0.00 0.00 4.84
546 555 1.153509 CCGATAAACCCCGAACGCT 60.154 57.895 0.00 0.00 0.00 5.07
547 556 0.741927 CCGATAAACCCCGAACGCTT 60.742 55.000 0.00 0.00 0.00 4.68
548 557 0.372334 CGATAAACCCCGAACGCTTG 59.628 55.000 0.00 0.00 0.00 4.01
549 558 0.730840 GATAAACCCCGAACGCTTGG 59.269 55.000 0.00 0.00 0.00 3.61
550 559 0.325602 ATAAACCCCGAACGCTTGGA 59.674 50.000 0.00 0.00 0.00 3.53
551 560 0.325602 TAAACCCCGAACGCTTGGAT 59.674 50.000 0.00 0.00 0.00 3.41
552 561 0.538746 AAACCCCGAACGCTTGGATT 60.539 50.000 0.00 0.00 0.00 3.01
553 562 0.325602 AACCCCGAACGCTTGGATTA 59.674 50.000 0.00 0.00 0.00 1.75
554 563 0.544697 ACCCCGAACGCTTGGATTAT 59.455 50.000 0.00 0.00 0.00 1.28
555 564 0.944386 CCCCGAACGCTTGGATTATG 59.056 55.000 0.00 0.00 0.00 1.90
556 565 0.307760 CCCGAACGCTTGGATTATGC 59.692 55.000 0.00 0.00 0.00 3.14
557 566 1.013596 CCGAACGCTTGGATTATGCA 58.986 50.000 0.00 0.00 0.00 3.96
558 567 1.003545 CCGAACGCTTGGATTATGCAG 60.004 52.381 0.00 0.00 0.00 4.41
559 568 1.933181 CGAACGCTTGGATTATGCAGA 59.067 47.619 0.00 0.00 0.00 4.26
560 569 2.545526 CGAACGCTTGGATTATGCAGAT 59.454 45.455 0.00 0.00 0.00 2.90
561 570 3.002656 CGAACGCTTGGATTATGCAGATT 59.997 43.478 0.00 0.00 0.00 2.40
562 571 4.531332 GAACGCTTGGATTATGCAGATTC 58.469 43.478 0.00 0.00 0.00 2.52
563 572 3.813443 ACGCTTGGATTATGCAGATTCT 58.187 40.909 3.50 0.00 0.00 2.40
564 573 4.960938 ACGCTTGGATTATGCAGATTCTA 58.039 39.130 3.50 0.00 0.00 2.10
565 574 5.555017 ACGCTTGGATTATGCAGATTCTAT 58.445 37.500 3.50 0.00 0.00 1.98
566 575 6.701340 ACGCTTGGATTATGCAGATTCTATA 58.299 36.000 3.50 0.00 0.00 1.31
567 576 7.161404 ACGCTTGGATTATGCAGATTCTATAA 58.839 34.615 3.50 0.00 0.00 0.98
568 577 7.118390 ACGCTTGGATTATGCAGATTCTATAAC 59.882 37.037 3.50 0.00 0.00 1.89
569 578 7.413438 CGCTTGGATTATGCAGATTCTATAACC 60.413 40.741 3.50 0.00 0.00 2.85
570 579 7.148171 GCTTGGATTATGCAGATTCTATAACCC 60.148 40.741 3.50 0.00 0.00 4.11
571 580 6.721318 TGGATTATGCAGATTCTATAACCCC 58.279 40.000 3.50 2.10 0.00 4.95
572 581 6.505344 TGGATTATGCAGATTCTATAACCCCT 59.495 38.462 3.50 0.00 0.00 4.79
573 582 7.682459 TGGATTATGCAGATTCTATAACCCCTA 59.318 37.037 3.50 0.00 0.00 3.53
574 583 8.718656 GGATTATGCAGATTCTATAACCCCTAT 58.281 37.037 3.50 0.00 0.00 2.57
579 588 8.917414 TGCAGATTCTATAACCCCTATTATCT 57.083 34.615 0.00 0.00 0.00 1.98
594 603 9.961264 CCCCTATTATCTAAGAAATAAAGGACC 57.039 37.037 0.00 0.00 0.00 4.46
595 604 9.961264 CCCTATTATCTAAGAAATAAAGGACCC 57.039 37.037 0.00 0.00 0.00 4.46
596 605 9.961264 CCTATTATCTAAGAAATAAAGGACCCC 57.039 37.037 0.00 0.00 0.00 4.95
597 606 9.654663 CTATTATCTAAGAAATAAAGGACCCCG 57.345 37.037 0.00 0.00 0.00 5.73
598 607 7.679732 TTATCTAAGAAATAAAGGACCCCGA 57.320 36.000 0.00 0.00 0.00 5.14
599 608 6.765355 ATCTAAGAAATAAAGGACCCCGAT 57.235 37.500 0.00 0.00 0.00 4.18
600 609 7.867160 ATCTAAGAAATAAAGGACCCCGATA 57.133 36.000 0.00 0.00 0.00 2.92
601 610 7.679732 TCTAAGAAATAAAGGACCCCGATAA 57.320 36.000 0.00 0.00 0.00 1.75
602 611 8.093118 TCTAAGAAATAAAGGACCCCGATAAA 57.907 34.615 0.00 0.00 0.00 1.40
603 612 8.720537 TCTAAGAAATAAAGGACCCCGATAAAT 58.279 33.333 0.00 0.00 0.00 1.40
604 613 7.818997 AAGAAATAAAGGACCCCGATAAATC 57.181 36.000 0.00 0.00 0.00 2.17
605 614 6.304624 AGAAATAAAGGACCCCGATAAATCC 58.695 40.000 0.00 0.00 0.00 3.01
606 615 4.652679 ATAAAGGACCCCGATAAATCCC 57.347 45.455 0.00 0.00 30.99 3.85
607 616 1.901648 AAGGACCCCGATAAATCCCA 58.098 50.000 0.00 0.00 30.99 4.37
608 617 1.901648 AGGACCCCGATAAATCCCAA 58.098 50.000 0.00 0.00 30.99 4.12
609 618 2.210644 AGGACCCCGATAAATCCCAAA 58.789 47.619 0.00 0.00 30.99 3.28
610 619 2.789399 AGGACCCCGATAAATCCCAAAT 59.211 45.455 0.00 0.00 30.99 2.32
645 655 2.351350 GCATGTCATCCCGAACGTTTTT 60.351 45.455 0.46 0.00 0.00 1.94
676 686 5.234466 ACTTTAGTTGACTTGAGATGGCT 57.766 39.130 0.00 0.00 0.00 4.75
683 702 4.737855 TGACTTGAGATGGCTACTAACC 57.262 45.455 0.00 0.00 0.00 2.85
711 730 2.093890 ACTTTGTCCCGGTTCGTTTTT 58.906 42.857 0.00 0.00 0.00 1.94
735 754 4.545610 TCGACAGAAAATTGCCATGTTTC 58.454 39.130 0.00 0.00 0.00 2.78
740 759 5.005094 CAGAAAATTGCCATGTTTCCCAAT 58.995 37.500 2.96 0.00 32.74 3.16
756 775 4.004314 TCCCAATCTCGCGTGAAATAAAA 58.996 39.130 15.50 0.00 0.00 1.52
761 780 3.412654 TCTCGCGTGAAATAAAATTGCG 58.587 40.909 8.66 0.00 44.90 4.85
769 788 6.674090 GCGTGAAATAAAATTGCGATGAAAAG 59.326 34.615 0.00 0.00 0.00 2.27
788 807 2.568090 GTTCGGGTTGCCATGCTG 59.432 61.111 0.00 0.00 0.00 4.41
789 808 3.372730 TTCGGGTTGCCATGCTGC 61.373 61.111 0.00 0.00 0.00 5.25
790 809 3.866379 TTCGGGTTGCCATGCTGCT 62.866 57.895 0.00 0.00 0.00 4.24
791 810 3.376078 CGGGTTGCCATGCTGCTT 61.376 61.111 0.00 0.00 0.00 3.91
793 812 1.594194 CGGGTTGCCATGCTGCTTAA 61.594 55.000 0.00 0.00 0.00 1.85
794 813 0.607620 GGGTTGCCATGCTGCTTAAA 59.392 50.000 0.00 0.00 0.00 1.52
795 814 1.404583 GGGTTGCCATGCTGCTTAAAG 60.405 52.381 0.00 0.00 0.00 1.85
796 815 1.273327 GGTTGCCATGCTGCTTAAAGT 59.727 47.619 0.00 0.00 0.00 2.66
797 816 2.599659 GTTGCCATGCTGCTTAAAGTC 58.400 47.619 0.00 0.00 0.00 3.01
798 817 1.176527 TGCCATGCTGCTTAAAGTCC 58.823 50.000 0.00 0.00 0.00 3.85
799 818 0.099436 GCCATGCTGCTTAAAGTCCG 59.901 55.000 0.00 0.00 0.00 4.79
800 819 1.737838 CCATGCTGCTTAAAGTCCGA 58.262 50.000 0.00 0.00 0.00 4.55
801 820 2.083774 CCATGCTGCTTAAAGTCCGAA 58.916 47.619 0.00 0.00 0.00 4.30
802 821 2.684881 CCATGCTGCTTAAAGTCCGAAT 59.315 45.455 0.00 0.00 0.00 3.34
803 822 3.129287 CCATGCTGCTTAAAGTCCGAATT 59.871 43.478 0.00 0.00 0.00 2.17
868 888 2.568090 GCCCTGTGCATTTCCGTG 59.432 61.111 0.00 0.00 40.77 4.94
869 889 2.568090 CCCTGTGCATTTCCGTGC 59.432 61.111 0.00 0.00 45.25 5.34
875 895 2.126888 GCATTTCCGTGCGTGTGG 60.127 61.111 0.00 0.00 35.10 4.17
889 909 1.002773 CGTGTGGGGGTTAAAGTAGCT 59.997 52.381 0.00 0.00 0.00 3.32
890 910 2.551504 CGTGTGGGGGTTAAAGTAGCTT 60.552 50.000 0.00 0.00 0.00 3.74
958 979 1.761667 CTCCCTCTCCAGCCTCCAG 60.762 68.421 0.00 0.00 0.00 3.86
961 982 3.847602 CTCTCCAGCCTCCAGCCG 61.848 72.222 0.00 0.00 45.47 5.52
1473 1495 3.844090 GGCAGGGTCGAGGAGCTC 61.844 72.222 4.71 4.71 0.00 4.09
1545 1567 4.457496 CGATGTGAGCCCACGCCT 62.457 66.667 0.00 0.00 46.06 5.52
1546 1568 2.900273 GATGTGAGCCCACGCCTA 59.100 61.111 0.00 0.00 46.06 3.93
1547 1569 1.521681 GATGTGAGCCCACGCCTAC 60.522 63.158 0.00 0.00 46.06 3.18
1548 1570 2.925162 GATGTGAGCCCACGCCTACC 62.925 65.000 0.00 0.00 46.06 3.18
1549 1571 4.468689 GTGAGCCCACGCCTACCC 62.469 72.222 0.00 0.00 34.57 3.69
1559 1581 3.467226 GCCTACCCACCGCTGCTA 61.467 66.667 0.00 0.00 0.00 3.49
1563 1585 0.384669 CTACCCACCGCTGCTAGTAC 59.615 60.000 0.00 0.00 0.00 2.73
1567 1589 1.605058 CCACCGCTGCTAGTACTGGT 61.605 60.000 5.39 0.00 0.00 4.00
1568 1590 0.246635 CACCGCTGCTAGTACTGGTT 59.753 55.000 5.39 0.00 0.00 3.67
1630 1653 3.120060 GCCTAGATGTGCAACTGTTTCAG 60.120 47.826 0.00 0.00 38.04 3.02
1649 1672 3.569277 TCAGAGCTGCATTTGCTTTACAA 59.431 39.130 1.02 0.00 41.30 2.41
1686 1856 3.181480 TGGGTTGCTTAAGCTGTTTGTTC 60.181 43.478 26.90 9.78 42.66 3.18
1760 1963 6.849588 ATTGAAAGATTTGGCAAAGTGTTC 57.150 33.333 18.61 18.36 0.00 3.18
1766 1969 6.899393 AGATTTGGCAAAGTGTTCAATAGA 57.101 33.333 18.61 0.00 0.00 1.98
1767 1970 7.472334 AGATTTGGCAAAGTGTTCAATAGAT 57.528 32.000 18.61 0.00 0.00 1.98
1768 1971 7.542025 AGATTTGGCAAAGTGTTCAATAGATC 58.458 34.615 18.61 6.09 0.00 2.75
1769 1972 6.647334 TTTGGCAAAGTGTTCAATAGATCA 57.353 33.333 8.93 0.00 0.00 2.92
1770 1973 5.885230 TGGCAAAGTGTTCAATAGATCAG 57.115 39.130 0.00 0.00 0.00 2.90
1771 1974 4.156556 TGGCAAAGTGTTCAATAGATCAGC 59.843 41.667 0.00 0.00 0.00 4.26
1772 1975 4.397417 GGCAAAGTGTTCAATAGATCAGCT 59.603 41.667 0.00 0.00 0.00 4.24
1773 1976 5.448360 GGCAAAGTGTTCAATAGATCAGCTC 60.448 44.000 0.00 0.00 0.00 4.09
1879 2082 1.630126 ATGGACTCGGCCTTGCTCAT 61.630 55.000 0.00 0.00 0.00 2.90
1940 2143 9.615295 TTTGCTATTTAGTGAAATACGGTTTTC 57.385 29.630 5.63 5.63 36.62 2.29
1942 2145 6.903479 GCTATTTAGTGAAATACGGTTTTCGG 59.097 38.462 7.54 0.00 38.53 4.30
1943 2146 6.806388 ATTTAGTGAAATACGGTTTTCGGT 57.194 33.333 7.54 1.61 44.45 4.69
1956 2160 5.148568 CGGTTTTCGGTAACTTTGGTTATG 58.851 41.667 0.00 0.00 39.67 1.90
2059 2263 3.368321 CGTGGTGTCATACGTTTGATG 57.632 47.619 11.90 1.07 35.70 3.07
2080 2284 6.368791 TGATGTGTTGCTGAAGTATTAGTCAC 59.631 38.462 0.00 0.00 0.00 3.67
2125 2331 9.293404 TGTTACTATGTGTTAAGTGTAGAGTCT 57.707 33.333 0.00 0.00 0.00 3.24
2199 2405 2.160822 TCTTGCTGCTCTGTGACTTC 57.839 50.000 0.00 0.00 0.00 3.01
2204 2410 1.975837 CTGCTCTGTGACTTCTCGAC 58.024 55.000 0.00 0.00 0.00 4.20
2217 2423 4.745649 ACTTCTCGACTGTTATGGTTAGC 58.254 43.478 0.00 0.00 0.00 3.09
2449 2663 1.283029 ACTGATGGTGGTGAATCTGGG 59.717 52.381 0.00 0.00 0.00 4.45
2450 2664 0.625316 TGATGGTGGTGAATCTGGGG 59.375 55.000 0.00 0.00 0.00 4.96
2613 2827 1.520342 CTTGCCGAGGTAGCTCTGC 60.520 63.158 25.78 25.78 34.78 4.26
2614 2828 1.954362 CTTGCCGAGGTAGCTCTGCT 61.954 60.000 30.06 0.00 43.41 4.24
2627 2841 1.544314 GCTCTGCTCTTCCAACTGGTT 60.544 52.381 0.00 0.00 36.34 3.67
2628 2842 2.149578 CTCTGCTCTTCCAACTGGTTG 58.850 52.381 6.50 6.50 40.13 3.77
2666 2880 5.703130 GTCCTTGGATATTCATTAGTGCTCC 59.297 44.000 0.00 0.00 0.00 4.70
2727 2965 1.486310 TGAAGCACCTGTTGACTCACT 59.514 47.619 0.00 0.00 0.00 3.41
2788 3026 0.819259 TTGACTCACTGTTGCAGGCC 60.819 55.000 0.00 0.00 35.51 5.19
2794 3032 3.052082 CTGTTGCAGGCCGGTCTG 61.052 66.667 31.91 31.91 37.79 3.51
2833 3071 0.252467 ACCTAGGTGAGCTTGAGCCT 60.252 55.000 15.42 0.00 43.38 4.58
2851 3089 3.054802 AGCCTCCAAGTACAATCAGGAAG 60.055 47.826 0.00 0.00 0.00 3.46
2887 3125 0.034670 AAGGAGATCAACAGCCAGCC 60.035 55.000 0.00 0.00 0.00 4.85
2888 3126 1.452833 GGAGATCAACAGCCAGCCC 60.453 63.158 0.00 0.00 0.00 5.19
3001 3239 2.284190 GATGAGGTTAGGCAGCTGAAC 58.716 52.381 20.43 13.08 31.44 3.18
3081 3319 1.260538 TGGGGTCTGCTAGCTGTGAG 61.261 60.000 17.23 4.76 0.00 3.51
3215 3453 4.343814 ACAAGAAAACGGGTCATCCAAAAT 59.656 37.500 0.00 0.00 34.36 1.82
3288 3526 3.506096 CTGCATCTGCCTGTGCCG 61.506 66.667 0.00 0.00 40.56 5.69
3350 3590 6.976934 AGTTGGTTCACATAGTTTCCAAAT 57.023 33.333 0.00 0.00 36.84 2.32
3426 3666 6.293955 GCTGTCTAAATTTGTGCTTGTCCTAA 60.294 38.462 0.00 0.00 0.00 2.69
3522 3763 8.079211 TGATGAAGGTACTGCTCTTTAGTAAT 57.921 34.615 0.00 0.00 40.86 1.89
3554 3795 3.581024 TTGTGGCAATCTTGAATGCTC 57.419 42.857 10.03 5.44 42.20 4.26
3576 3822 3.096489 TGCTTTGAAATGTGAACTGGC 57.904 42.857 0.00 0.00 0.00 4.85
3585 3831 1.774110 TGTGAACTGGCCACATTTGT 58.226 45.000 0.00 0.00 39.36 2.83
3632 3878 3.069443 TGCAGATTTTTCACTTTGGTCCC 59.931 43.478 0.00 0.00 0.00 4.46
3640 3886 2.359975 CTTTGGTCCCGCCCTGTC 60.360 66.667 0.00 0.00 36.04 3.51
3665 3911 5.163385 TGAGACGAAAACCAGGAGAAACTTA 60.163 40.000 0.00 0.00 0.00 2.24
3687 3933 1.139853 GCTGGTCATGGTTCCTCTAGG 59.860 57.143 0.00 0.00 0.00 3.02
3712 3958 6.350445 GCATCAGTGGGAGAAATGTAAATGTT 60.350 38.462 0.00 0.00 0.00 2.71
3809 4056 4.926860 GCAATGTCTGCCATTTTAAACC 57.073 40.909 0.00 0.00 46.13 3.27
3860 4107 8.109705 TCAAACATTTTATGCAGTGTAGACAT 57.890 30.769 0.00 0.00 0.00 3.06
3954 4202 4.269603 TGATTGCCGTTTCATGTTTTGTTG 59.730 37.500 0.00 0.00 0.00 3.33
3986 4234 5.105752 GGTGTGCAGTAAAACAACATGAAA 58.894 37.500 0.00 0.00 34.05 2.69
4032 4281 4.881920 ACAGTCACTGCTTGTTTTGTTTT 58.118 34.783 4.13 0.00 34.37 2.43
4119 4409 2.435059 GACCTGCTTCTGGACGCC 60.435 66.667 0.00 0.00 0.00 5.68
4168 4458 3.181474 GCGGTAGAAGCTCCAAACTAGAT 60.181 47.826 0.00 0.00 0.00 1.98
4231 4521 7.117956 GTGGAGGACAAAGTAGAGTAAAACATC 59.882 40.741 0.00 0.00 0.00 3.06
4232 4522 7.016268 TGGAGGACAAAGTAGAGTAAAACATCT 59.984 37.037 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.550869 CCTTTCAATTCCCTGCCAGGT 60.551 52.381 10.47 0.00 31.93 4.00
1 2 1.188863 CCTTTCAATTCCCTGCCAGG 58.811 55.000 2.91 2.91 34.30 4.45
13 14 0.777446 CCTCCACCCTTCCCTTTCAA 59.223 55.000 0.00 0.00 0.00 2.69
14 15 0.402861 ACCTCCACCCTTCCCTTTCA 60.403 55.000 0.00 0.00 0.00 2.69
16 17 0.482887 CAACCTCCACCCTTCCCTTT 59.517 55.000 0.00 0.00 0.00 3.11
97 100 5.886960 ATTCTCACAGACAAAGGCATTAC 57.113 39.130 0.00 0.00 0.00 1.89
98 101 6.240894 AGAATTCTCACAGACAAAGGCATTA 58.759 36.000 0.88 0.00 0.00 1.90
99 102 5.075493 AGAATTCTCACAGACAAAGGCATT 58.925 37.500 0.88 0.00 0.00 3.56
101 104 4.090761 AGAATTCTCACAGACAAAGGCA 57.909 40.909 0.88 0.00 0.00 4.75
102 105 4.320788 CCAAGAATTCTCACAGACAAAGGC 60.321 45.833 8.78 0.00 0.00 4.35
103 106 4.320788 GCCAAGAATTCTCACAGACAAAGG 60.321 45.833 8.78 0.32 0.00 3.11
105 108 4.464008 AGCCAAGAATTCTCACAGACAAA 58.536 39.130 8.78 0.00 0.00 2.83
111 114 3.777106 ACAGAGCCAAGAATTCTCACA 57.223 42.857 8.78 0.00 0.00 3.58
139 142 0.250901 AACCCAGCAGAGCACGAATT 60.251 50.000 0.00 0.00 0.00 2.17
140 143 0.957395 CAACCCAGCAGAGCACGAAT 60.957 55.000 0.00 0.00 0.00 3.34
169 178 8.664211 AATTCGGAGGATTATTCAGAACTTAC 57.336 34.615 0.00 0.00 32.91 2.34
170 179 9.760077 GTAATTCGGAGGATTATTCAGAACTTA 57.240 33.333 0.00 0.00 32.91 2.24
171 180 7.715686 GGTAATTCGGAGGATTATTCAGAACTT 59.284 37.037 0.00 0.00 32.91 2.66
172 181 7.217906 GGTAATTCGGAGGATTATTCAGAACT 58.782 38.462 0.00 0.00 32.91 3.01
173 182 6.145696 CGGTAATTCGGAGGATTATTCAGAAC 59.854 42.308 0.00 0.00 32.91 3.01
204 213 0.944311 ACTCACGCACGCACCTTAAG 60.944 55.000 0.00 0.00 0.00 1.85
212 221 2.031044 TTGTCACAACTCACGCACGC 62.031 55.000 0.00 0.00 0.00 5.34
214 223 1.258982 CTCTTGTCACAACTCACGCAC 59.741 52.381 0.00 0.00 0.00 5.34
215 224 1.570813 CTCTTGTCACAACTCACGCA 58.429 50.000 0.00 0.00 0.00 5.24
216 225 0.861837 CCTCTTGTCACAACTCACGC 59.138 55.000 0.00 0.00 0.00 5.34
217 226 0.861837 GCCTCTTGTCACAACTCACG 59.138 55.000 0.00 0.00 0.00 4.35
218 227 1.953559 TGCCTCTTGTCACAACTCAC 58.046 50.000 0.00 0.00 0.00 3.51
278 287 9.748708 CATCTCCTTTTTCTTTTAACACATTCA 57.251 29.630 0.00 0.00 0.00 2.57
279 288 9.965824 TCATCTCCTTTTTCTTTTAACACATTC 57.034 29.630 0.00 0.00 0.00 2.67
288 297 9.551734 CCTTCATTTTCATCTCCTTTTTCTTTT 57.448 29.630 0.00 0.00 0.00 2.27
289 298 7.658982 GCCTTCATTTTCATCTCCTTTTTCTTT 59.341 33.333 0.00 0.00 0.00 2.52
290 299 7.157347 GCCTTCATTTTCATCTCCTTTTTCTT 58.843 34.615 0.00 0.00 0.00 2.52
291 300 6.268387 TGCCTTCATTTTCATCTCCTTTTTCT 59.732 34.615 0.00 0.00 0.00 2.52
292 301 6.458210 TGCCTTCATTTTCATCTCCTTTTTC 58.542 36.000 0.00 0.00 0.00 2.29
297 306 6.206243 CGATTATGCCTTCATTTTCATCTCCT 59.794 38.462 0.00 0.00 34.22 3.69
298 307 6.376978 CGATTATGCCTTCATTTTCATCTCC 58.623 40.000 0.00 0.00 34.22 3.71
311 320 5.355910 ACATTACGAAAACCGATTATGCCTT 59.644 36.000 0.00 0.00 41.76 4.35
318 327 6.799925 CAGCTAAAACATTACGAAAACCGATT 59.200 34.615 0.00 0.00 41.76 3.34
320 329 5.681880 CAGCTAAAACATTACGAAAACCGA 58.318 37.500 0.00 0.00 41.76 4.69
321 330 4.319901 GCAGCTAAAACATTACGAAAACCG 59.680 41.667 0.00 0.00 45.44 4.44
322 331 5.216648 TGCAGCTAAAACATTACGAAAACC 58.783 37.500 0.00 0.00 0.00 3.27
382 391 5.241728 GGACAGAGCAGAAACTAACCAAAAT 59.758 40.000 0.00 0.00 0.00 1.82
383 392 4.578928 GGACAGAGCAGAAACTAACCAAAA 59.421 41.667 0.00 0.00 0.00 2.44
411 420 3.876320 TGAAATTGAATCCATCGATGCGA 59.124 39.130 20.25 17.68 41.13 5.10
417 426 3.489738 GGCCACTGAAATTGAATCCATCG 60.490 47.826 0.00 0.00 0.00 3.84
438 447 3.696281 TGCGAAATAATCTGCATGTGG 57.304 42.857 0.00 0.00 34.31 4.17
473 482 4.713321 AGAATCTGCATATGGCCACTTTTT 59.287 37.500 8.16 0.00 43.89 1.94
474 483 4.284178 AGAATCTGCATATGGCCACTTTT 58.716 39.130 8.16 0.00 43.89 2.27
475 484 3.907221 AGAATCTGCATATGGCCACTTT 58.093 40.909 8.16 0.00 43.89 2.66
476 485 3.589951 AGAATCTGCATATGGCCACTT 57.410 42.857 8.16 0.00 43.89 3.16
477 486 3.589951 AAGAATCTGCATATGGCCACT 57.410 42.857 8.16 0.00 43.89 4.00
478 487 5.507985 GGTTAAAGAATCTGCATATGGCCAC 60.508 44.000 8.16 0.00 43.89 5.01
479 488 4.584325 GGTTAAAGAATCTGCATATGGCCA 59.416 41.667 8.56 8.56 43.89 5.36
480 489 4.021981 GGGTTAAAGAATCTGCATATGGCC 60.022 45.833 4.56 0.00 43.89 5.36
481 490 4.021981 GGGGTTAAAGAATCTGCATATGGC 60.022 45.833 4.56 0.00 45.13 4.40
482 491 5.388654 AGGGGTTAAAGAATCTGCATATGG 58.611 41.667 4.56 0.00 0.00 2.74
483 492 8.641498 AATAGGGGTTAAAGAATCTGCATATG 57.359 34.615 0.00 0.00 0.00 1.78
486 495 9.660544 AAATAATAGGGGTTAAAGAATCTGCAT 57.339 29.630 0.00 0.00 0.00 3.96
487 496 8.912988 CAAATAATAGGGGTTAAAGAATCTGCA 58.087 33.333 0.00 0.00 0.00 4.41
488 497 9.131791 TCAAATAATAGGGGTTAAAGAATCTGC 57.868 33.333 0.00 0.00 0.00 4.26
511 520 7.309928 GGTTTATCGGGGTCCTTTATTTTTCAA 60.310 37.037 0.00 0.00 0.00 2.69
520 529 0.627451 GGGGTTTATCGGGGTCCTTT 59.373 55.000 0.00 0.00 0.00 3.11
529 538 0.372334 CAAGCGTTCGGGGTTTATCG 59.628 55.000 0.00 0.00 0.00 2.92
536 545 0.944386 CATAATCCAAGCGTTCGGGG 59.056 55.000 0.00 0.00 0.00 5.73
538 547 1.003545 CTGCATAATCCAAGCGTTCGG 60.004 52.381 0.00 0.00 0.00 4.30
539 548 1.933181 TCTGCATAATCCAAGCGTTCG 59.067 47.619 0.00 0.00 0.00 3.95
544 553 7.148171 GGGTTATAGAATCTGCATAATCCAAGC 60.148 40.741 9.23 0.00 36.05 4.01
545 554 7.337942 GGGGTTATAGAATCTGCATAATCCAAG 59.662 40.741 13.99 0.00 37.21 3.61
546 555 7.018550 AGGGGTTATAGAATCTGCATAATCCAA 59.981 37.037 13.99 0.00 37.21 3.53
547 556 6.505344 AGGGGTTATAGAATCTGCATAATCCA 59.495 38.462 13.99 0.00 37.21 3.41
548 557 6.963322 AGGGGTTATAGAATCTGCATAATCC 58.037 40.000 6.55 6.55 35.51 3.01
553 562 9.512748 AGATAATAGGGGTTATAGAATCTGCAT 57.487 33.333 0.00 0.00 0.00 3.96
554 563 8.917414 AGATAATAGGGGTTATAGAATCTGCA 57.083 34.615 0.00 0.00 0.00 4.41
568 577 9.961264 GGTCCTTTATTTCTTAGATAATAGGGG 57.039 37.037 0.00 0.00 0.00 4.79
569 578 9.961264 GGGTCCTTTATTTCTTAGATAATAGGG 57.039 37.037 0.00 0.00 0.00 3.53
570 579 9.961264 GGGGTCCTTTATTTCTTAGATAATAGG 57.039 37.037 0.00 0.00 0.00 2.57
571 580 9.654663 CGGGGTCCTTTATTTCTTAGATAATAG 57.345 37.037 0.00 0.00 0.00 1.73
572 581 9.383578 TCGGGGTCCTTTATTTCTTAGATAATA 57.616 33.333 0.00 0.00 0.00 0.98
573 582 8.271398 TCGGGGTCCTTTATTTCTTAGATAAT 57.729 34.615 0.00 0.00 0.00 1.28
574 583 7.679732 TCGGGGTCCTTTATTTCTTAGATAA 57.320 36.000 0.00 0.00 0.00 1.75
575 584 7.867160 ATCGGGGTCCTTTATTTCTTAGATA 57.133 36.000 0.00 0.00 0.00 1.98
576 585 6.765355 ATCGGGGTCCTTTATTTCTTAGAT 57.235 37.500 0.00 0.00 0.00 1.98
577 586 7.679732 TTATCGGGGTCCTTTATTTCTTAGA 57.320 36.000 0.00 0.00 0.00 2.10
578 587 8.919777 ATTTATCGGGGTCCTTTATTTCTTAG 57.080 34.615 0.00 0.00 0.00 2.18
579 588 7.940688 GGATTTATCGGGGTCCTTTATTTCTTA 59.059 37.037 0.00 0.00 0.00 2.10
580 589 6.776116 GGATTTATCGGGGTCCTTTATTTCTT 59.224 38.462 0.00 0.00 0.00 2.52
581 590 6.304624 GGATTTATCGGGGTCCTTTATTTCT 58.695 40.000 0.00 0.00 0.00 2.52
582 591 5.475909 GGGATTTATCGGGGTCCTTTATTTC 59.524 44.000 0.00 0.00 0.00 2.17
583 592 5.103430 TGGGATTTATCGGGGTCCTTTATTT 60.103 40.000 0.00 0.00 0.00 1.40
584 593 4.417518 TGGGATTTATCGGGGTCCTTTATT 59.582 41.667 0.00 0.00 0.00 1.40
585 594 3.984770 TGGGATTTATCGGGGTCCTTTAT 59.015 43.478 0.00 0.00 0.00 1.40
586 595 3.395604 TGGGATTTATCGGGGTCCTTTA 58.604 45.455 0.00 0.00 0.00 1.85
587 596 2.210644 TGGGATTTATCGGGGTCCTTT 58.789 47.619 0.00 0.00 0.00 3.11
588 597 1.901648 TGGGATTTATCGGGGTCCTT 58.098 50.000 0.00 0.00 0.00 3.36
589 598 1.901648 TTGGGATTTATCGGGGTCCT 58.098 50.000 0.00 0.00 0.00 3.85
590 599 2.740506 TTTGGGATTTATCGGGGTCC 57.259 50.000 0.00 0.00 0.00 4.46
591 600 2.296190 GCATTTGGGATTTATCGGGGTC 59.704 50.000 0.00 0.00 0.00 4.46
592 601 2.091333 AGCATTTGGGATTTATCGGGGT 60.091 45.455 0.00 0.00 0.00 4.95
593 602 2.597455 AGCATTTGGGATTTATCGGGG 58.403 47.619 0.00 0.00 0.00 5.73
594 603 3.981211 CAAGCATTTGGGATTTATCGGG 58.019 45.455 0.00 0.00 0.00 5.14
711 730 4.582701 ACATGGCAATTTTCTGTCGAAA 57.417 36.364 0.00 0.00 37.36 3.46
717 736 4.005487 TGGGAAACATGGCAATTTTCTG 57.995 40.909 18.32 3.57 31.21 3.02
735 754 4.349663 TTTTATTTCACGCGAGATTGGG 57.650 40.909 15.93 0.00 0.00 4.12
740 759 3.123790 TCGCAATTTTATTTCACGCGAGA 59.876 39.130 15.93 7.99 44.49 4.04
756 775 1.465689 CCGAACGCTTTTCATCGCAAT 60.466 47.619 0.00 0.00 34.13 3.56
761 780 1.963747 CAACCCGAACGCTTTTCATC 58.036 50.000 0.00 0.00 0.00 2.92
769 788 4.776647 GCATGGCAACCCGAACGC 62.777 66.667 0.00 0.00 0.00 4.84
799 818 7.422399 TCGGAAATGATAAATCCCGAAAATTC 58.578 34.615 0.00 0.00 42.31 2.17
800 819 7.341445 TCGGAAATGATAAATCCCGAAAATT 57.659 32.000 0.00 0.00 42.31 1.82
801 820 6.952773 TCGGAAATGATAAATCCCGAAAAT 57.047 33.333 0.00 0.00 42.31 1.82
857 877 2.636462 CACACGCACGGAAATGCA 59.364 55.556 0.00 0.00 46.47 3.96
859 879 2.560861 CCCACACGCACGGAAATG 59.439 61.111 0.00 0.00 0.00 2.32
860 880 2.671619 CCCCACACGCACGGAAAT 60.672 61.111 0.00 0.00 0.00 2.17
861 881 4.939368 CCCCCACACGCACGGAAA 62.939 66.667 0.00 0.00 0.00 3.13
864 884 3.828694 TTAACCCCCACACGCACGG 62.829 63.158 0.00 0.00 0.00 4.94
865 885 1.847890 CTTTAACCCCCACACGCACG 61.848 60.000 0.00 0.00 0.00 5.34
866 886 0.820482 ACTTTAACCCCCACACGCAC 60.820 55.000 0.00 0.00 0.00 5.34
867 887 0.763652 TACTTTAACCCCCACACGCA 59.236 50.000 0.00 0.00 0.00 5.24
868 888 1.445871 CTACTTTAACCCCCACACGC 58.554 55.000 0.00 0.00 0.00 5.34
869 889 1.002773 AGCTACTTTAACCCCCACACG 59.997 52.381 0.00 0.00 0.00 4.49
870 890 2.873094 AGCTACTTTAACCCCCACAC 57.127 50.000 0.00 0.00 0.00 3.82
871 891 3.117436 ACAAAGCTACTTTAACCCCCACA 60.117 43.478 0.00 0.00 31.96 4.17
872 892 3.493334 ACAAAGCTACTTTAACCCCCAC 58.507 45.455 0.00 0.00 31.96 4.61
873 893 3.887916 ACAAAGCTACTTTAACCCCCA 57.112 42.857 0.00 0.00 31.96 4.96
874 894 3.693085 GCTACAAAGCTACTTTAACCCCC 59.307 47.826 0.00 0.00 45.85 5.40
875 895 4.959596 GCTACAAAGCTACTTTAACCCC 57.040 45.455 0.00 0.00 45.85 4.95
889 909 2.215196 GTCAAGTCGGTTGGCTACAAA 58.785 47.619 0.80 0.00 37.81 2.83
890 910 1.541670 GGTCAAGTCGGTTGGCTACAA 60.542 52.381 0.80 0.00 40.92 2.41
1458 1480 3.074999 GCAGAGCTCCTCGACCCTG 62.075 68.421 10.93 0.01 35.36 4.45
1473 1495 2.593978 CCCAGGTCCTCATGGCAG 59.406 66.667 0.00 0.00 43.29 4.85
1545 1567 0.033796 AGTACTAGCAGCGGTGGGTA 60.034 55.000 17.54 6.30 0.00 3.69
1546 1568 1.305046 AGTACTAGCAGCGGTGGGT 60.305 57.895 17.54 5.41 0.00 4.51
1547 1569 1.141881 CAGTACTAGCAGCGGTGGG 59.858 63.158 17.54 0.00 0.00 4.61
1548 1570 1.141881 CCAGTACTAGCAGCGGTGG 59.858 63.158 17.54 1.98 0.00 4.61
1549 1571 0.246635 AACCAGTACTAGCAGCGGTG 59.753 55.000 10.98 10.98 0.00 4.94
1550 1572 0.974383 AAACCAGTACTAGCAGCGGT 59.026 50.000 0.00 0.00 0.00 5.68
1559 1581 5.219633 CGCAAAAGCATAAAAACCAGTACT 58.780 37.500 0.00 0.00 0.00 2.73
1563 1585 3.801594 ACACGCAAAAGCATAAAAACCAG 59.198 39.130 0.00 0.00 0.00 4.00
1567 1589 4.684193 CGAACACGCAAAAGCATAAAAA 57.316 36.364 0.00 0.00 0.00 1.94
1588 1611 0.108207 ATCTAGCAGCAGACATGGGC 59.892 55.000 0.00 0.00 0.00 5.36
1649 1672 4.041691 AGCAACCCACACTTCTACTACATT 59.958 41.667 0.00 0.00 0.00 2.71
1760 1963 5.050023 CAGTTGCTGATGAGCTGATCTATTG 60.050 44.000 14.50 3.72 46.39 1.90
1766 1969 2.783609 ACAGTTGCTGATGAGCTGAT 57.216 45.000 5.57 0.00 46.39 2.90
1767 1970 2.827921 TCTACAGTTGCTGATGAGCTGA 59.172 45.455 5.57 0.00 46.39 4.26
1768 1971 2.928757 GTCTACAGTTGCTGATGAGCTG 59.071 50.000 5.57 0.00 46.39 4.24
1769 1972 2.564504 TGTCTACAGTTGCTGATGAGCT 59.435 45.455 5.57 0.00 46.39 4.09
1770 1973 2.928757 CTGTCTACAGTTGCTGATGAGC 59.071 50.000 0.00 0.00 41.18 4.26
1771 1974 3.194329 TCCTGTCTACAGTTGCTGATGAG 59.806 47.826 9.17 0.00 42.27 2.90
1772 1975 3.165071 TCCTGTCTACAGTTGCTGATGA 58.835 45.455 9.17 0.00 42.27 2.92
1773 1976 3.599730 TCCTGTCTACAGTTGCTGATG 57.400 47.619 9.17 0.00 42.27 3.07
1868 2071 1.544724 TACAACCAATGAGCAAGGCC 58.455 50.000 0.00 0.00 0.00 5.19
1879 2082 7.276658 TCTAACTGTGAACTCATTACAACCAA 58.723 34.615 0.00 0.00 0.00 3.67
1940 2143 4.153475 CAGGTGACATAACCAAAGTTACCG 59.847 45.833 0.00 0.00 44.07 4.02
1942 2145 6.565247 CGAACAGGTGACATAACCAAAGTTAC 60.565 42.308 0.00 0.00 43.20 2.50
1943 2146 5.467399 CGAACAGGTGACATAACCAAAGTTA 59.533 40.000 0.00 0.00 43.20 2.24
1956 2160 2.011222 TGAACCAAACGAACAGGTGAC 58.989 47.619 0.00 0.00 35.42 3.67
2000 2204 1.597854 TTGCAACAGGTCGAGCAGG 60.598 57.895 18.15 10.94 38.35 4.85
2039 2243 2.734606 ACATCAAACGTATGACACCACG 59.265 45.455 3.85 9.29 43.63 4.94
2051 2255 3.338818 ACTTCAGCAACACATCAAACG 57.661 42.857 0.00 0.00 0.00 3.60
2059 2263 6.593978 CAAGTGACTAATACTTCAGCAACAC 58.406 40.000 0.00 0.00 36.29 3.32
2080 2284 5.695851 AACAGTTCCAACTATCAAGCAAG 57.304 39.130 0.00 0.00 37.08 4.01
2125 2331 7.721399 TCTGATAGTATCTCACATGTAAGCTCA 59.279 37.037 11.40 0.00 0.00 4.26
2181 2387 2.067766 GAGAAGTCACAGAGCAGCAAG 58.932 52.381 0.00 0.00 0.00 4.01
2187 2393 1.268352 ACAGTCGAGAAGTCACAGAGC 59.732 52.381 0.00 0.00 0.00 4.09
2188 2394 3.634568 AACAGTCGAGAAGTCACAGAG 57.365 47.619 0.00 0.00 0.00 3.35
2199 2405 6.481954 AAAAAGCTAACCATAACAGTCGAG 57.518 37.500 0.00 0.00 0.00 4.04
2226 2440 4.398673 GTGACCGACTACATCCTAAGAAGT 59.601 45.833 0.00 0.00 0.00 3.01
2288 2502 3.290948 TGTGCAAAGTAACCAAGGAGT 57.709 42.857 0.00 0.00 0.00 3.85
2449 2663 1.340017 TGCTTAGCACTGAACCCATCC 60.340 52.381 1.39 0.00 31.71 3.51
2450 2664 2.113860 TGCTTAGCACTGAACCCATC 57.886 50.000 1.39 0.00 31.71 3.51
2627 2841 1.002069 AGGACATCAATTCCAGGGCA 58.998 50.000 0.00 0.00 35.33 5.36
2628 2842 1.753073 CAAGGACATCAATTCCAGGGC 59.247 52.381 0.00 0.00 35.33 5.19
2666 2880 2.947652 CCCAAGCACATATGTCCTTCAG 59.052 50.000 9.15 4.36 0.00 3.02
2746 2984 0.460987 GTGCTTCAGTCCCCGATGAG 60.461 60.000 0.00 0.00 0.00 2.90
2788 3026 0.037605 AGAGGCGTTTTACCAGACCG 60.038 55.000 0.00 0.00 0.00 4.79
2794 3032 6.748333 AGGTATTTTAAGAGGCGTTTTACC 57.252 37.500 0.00 0.00 0.00 2.85
2833 3071 2.354704 CGCCTTCCTGATTGTACTTGGA 60.355 50.000 0.00 0.00 0.00 3.53
2851 3089 0.109132 CTTGTTCCTTTGCCATCGCC 60.109 55.000 0.00 0.00 0.00 5.54
3001 3239 1.472082 TGCAACAGCAACATAATCCCG 59.528 47.619 0.00 0.00 34.85 5.14
3081 3319 6.842163 TCCTCGTTTTCTTCAAGCAAATATC 58.158 36.000 0.00 0.00 0.00 1.63
3215 3453 5.512942 TTACATCAGGAGGAATTGACCAA 57.487 39.130 0.00 0.00 0.00 3.67
3274 3512 3.807538 GTGCGGCACAGGCAGATG 61.808 66.667 27.10 0.00 41.83 2.90
3426 3666 5.822132 ATACAAGATAGGAGCTGCAGAAT 57.178 39.130 20.43 4.39 0.00 2.40
3522 3763 7.122501 TCAAGATTGCCACAAAGATTTATAGCA 59.877 33.333 0.00 0.00 0.00 3.49
3537 3778 2.159156 GCATGAGCATTCAAGATTGCCA 60.159 45.455 11.94 10.34 41.58 4.92
3538 3779 2.100916 AGCATGAGCATTCAAGATTGCC 59.899 45.455 11.94 6.10 45.49 4.52
3554 3795 3.430895 GCCAGTTCACATTTCAAAGCATG 59.569 43.478 0.00 0.00 0.00 4.06
3585 3831 7.473735 AAATCAGACAGTCTCTCAGATAACA 57.526 36.000 0.00 0.00 0.00 2.41
3632 3878 0.319555 TTTTCGTCTCAGACAGGGCG 60.320 55.000 5.45 0.00 32.09 6.13
3640 3886 3.386768 TTCTCCTGGTTTTCGTCTCAG 57.613 47.619 0.00 0.00 0.00 3.35
3665 3911 1.194781 AGAGGAACCATGACCAGCGT 61.195 55.000 0.00 0.00 0.00 5.07
3687 3933 5.126061 ACATTTACATTTCTCCCACTGATGC 59.874 40.000 0.00 0.00 0.00 3.91
3728 3974 5.554350 TGAGAATATAACCCCTATTTCCCCC 59.446 44.000 0.00 0.00 0.00 5.40
3798 4045 2.336667 CAGCGCAAGGGTTTAAAATGG 58.663 47.619 11.47 0.00 38.28 3.16
3809 4056 0.820891 AATCATAGCCCAGCGCAAGG 60.821 55.000 11.47 11.28 41.38 3.61
3849 4096 8.542132 CCAAAAACATTTCAAATGTCTACACTG 58.458 33.333 16.21 8.07 0.00 3.66
3860 4107 5.755861 GGTTCGGATCCAAAAACATTTCAAA 59.244 36.000 13.41 0.00 0.00 2.69
3954 4202 0.319555 TACTGCACACCGACTTCAGC 60.320 55.000 0.00 0.00 0.00 4.26
3986 4234 7.031372 GTCAATGCATACACAATGAAAGACAT 58.969 34.615 0.00 0.00 41.45 3.06
3994 4242 5.090757 GTGACTGTCAATGCATACACAATG 58.909 41.667 12.81 0.00 38.74 2.82
4032 4281 1.213182 TGTCCAACACCAAAGTAGCCA 59.787 47.619 0.00 0.00 0.00 4.75
4129 4419 2.990479 CCTCCGTCCTTTCCTGGG 59.010 66.667 0.00 0.00 0.00 4.45
4141 4431 2.413765 GAGCTTCTACCGCCTCCG 59.586 66.667 0.00 0.00 0.00 4.63
4168 4458 3.960102 ACCTGCAAAAGTTGAATCCTGAA 59.040 39.130 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.