Multiple sequence alignment - TraesCS5A01G342500

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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 TraesCS5A01G342500 chr5A 100.000 2613 0 0 1 2613 547646467 547643855 0.000000e+00 4826.0
1 TraesCS5A01G342500 chr5A 87.443 438 41 8 2177 2613 547637314 547636890 2.340000e-135 492.0
2 TraesCS5A01G342500 chr5A 81.836 512 78 10 2102 2608 549156728 549157229 1.450000e-112 416.0
3 TraesCS5A01G342500 chr5A 83.086 337 57 0 1149 1485 548240247 548239911 9.080000e-80 307.0
4 TraesCS5A01G342500 chr5A 93.382 136 9 0 524 659 521007467 521007332 4.410000e-48 202.0
5 TraesCS5A01G342500 chr5D 94.774 1129 51 5 1484 2611 433020534 433019413 0.000000e+00 1751.0
6 TraesCS5A01G342500 chr5D 84.625 813 63 28 721 1495 433021582 433020794 0.000000e+00 752.0
7 TraesCS5A01G342500 chr5D 85.150 532 63 13 2087 2613 435247835 435248355 4.950000e-147 531.0
8 TraesCS5A01G342500 chr5D 87.586 435 40 8 2177 2610 433015724 433015303 2.340000e-135 492.0
9 TraesCS5A01G342500 chr5D 83.533 334 55 0 1149 1482 434323221 434323554 1.950000e-81 313.0
10 TraesCS5A01G342500 chr5D 90.991 222 20 0 20 241 433021835 433021614 1.520000e-77 300.0
11 TraesCS5A01G342500 chr5D 80.466 343 61 3 1149 1485 434402795 434402453 9.280000e-65 257.0
12 TraesCS5A01G342500 chr5B 92.985 613 39 4 1484 2093 526586755 526586144 0.000000e+00 891.0
13 TraesCS5A01G342500 chr5B 95.048 525 17 4 2090 2611 526586115 526585597 0.000000e+00 817.0
14 TraesCS5A01G342500 chr5B 88.172 651 48 11 851 1472 526587698 526587048 0.000000e+00 749.0
15 TraesCS5A01G342500 chr5B 84.860 535 62 12 2087 2613 527056954 527056431 2.980000e-144 521.0
16 TraesCS5A01G342500 chr5B 84.774 532 65 10 2087 2613 528540501 528541021 1.070000e-143 520.0
17 TraesCS5A01G342500 chr5B 87.900 438 39 8 2177 2613 526581696 526581272 1.080000e-138 503.0
18 TraesCS5A01G342500 chr5B 85.127 511 42 9 14 511 432957289 432956800 2.340000e-135 492.0
19 TraesCS5A01G342500 chr5B 84.149 511 47 9 14 511 82564004 82563515 5.090000e-127 464.0
20 TraesCS5A01G342500 chr5B 82.975 511 52 10 14 511 76672217 76672705 1.860000e-116 429.0
21 TraesCS5A01G342500 chr5B 83.807 457 40 9 14 457 645657386 645657821 1.130000e-108 403.0
22 TraesCS5A01G342500 chr5B 89.286 196 17 2 647 839 526587878 526587684 2.600000e-60 243.0
23 TraesCS5A01G342500 chr5B 93.007 143 9 1 517 659 304689553 304689412 9.480000e-50 207.0
24 TraesCS5A01G342500 chr5B 82.083 240 43 0 1149 1388 527064665 527064426 3.410000e-49 206.0
25 TraesCS5A01G342500 chr5B 93.985 133 8 0 521 653 327750235 327750367 4.410000e-48 202.0
26 TraesCS5A01G342500 chr5B 78.509 228 34 11 126 348 526588320 526588103 4.540000e-28 135.0
27 TraesCS5A01G342500 chr5B 100.000 34 0 0 339 372 526588088 526588055 2.170000e-06 63.9
28 TraesCS5A01G342500 chr5B 96.970 33 1 0 2060 2092 596385139 596385171 3.630000e-04 56.5
29 TraesCS5A01G342500 chr6D 91.646 395 28 5 1624 2013 218313920 218314314 2.290000e-150 542.0
30 TraesCS5A01G342500 chrUn 84.149 511 47 9 14 511 244631511 244631022 5.090000e-127 464.0
31 TraesCS5A01G342500 chr3A 84.149 511 47 9 14 511 24623831 24624320 5.090000e-127 464.0
32 TraesCS5A01G342500 chr2B 81.535 482 58 14 14 476 3365555 3366024 4.110000e-98 368.0
33 TraesCS5A01G342500 chr2B 96.063 127 5 0 524 650 677806504 677806378 9.480000e-50 207.0
34 TraesCS5A01G342500 chr2B 90.000 140 13 1 524 662 65089957 65089818 2.070000e-41 180.0
35 TraesCS5A01G342500 chr2B 93.333 60 0 2 649 708 720521277 720521332 4.630000e-13 86.1
36 TraesCS5A01G342500 chr7B 89.591 269 25 3 244 511 558945289 558945023 3.220000e-89 339.0
37 TraesCS5A01G342500 chr4D 96.899 129 4 0 523 651 311194978 311194850 1.570000e-52 217.0
38 TraesCS5A01G342500 chr3D 95.349 129 6 0 524 652 35819021 35819149 3.410000e-49 206.0
39 TraesCS5A01G342500 chr3D 94.697 132 6 1 524 654 335367446 335367315 1.230000e-48 204.0
40 TraesCS5A01G342500 chr6B 94.656 131 7 0 520 650 39758401 39758531 1.230000e-48 204.0
41 TraesCS5A01G342500 chr1B 93.939 132 8 0 520 651 453762624 453762755 1.590000e-47 200.0
42 TraesCS5A01G342500 chr1B 86.957 161 21 0 14 174 652544465 652544625 5.740000e-42 182.0
43 TraesCS5A01G342500 chr1B 86.335 161 22 0 14 174 592416194 592416354 2.670000e-40 176.0
44 TraesCS5A01G342500 chr3B 89.474 152 14 2 516 666 814799747 814799597 9.540000e-45 191.0
45 TraesCS5A01G342500 chr7A 92.481 133 9 1 518 650 132902376 132902507 3.430000e-44 189.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G342500 chr5A 547643855 547646467 2612 True 4826.000000 4826 100.000000 1 2613 1 chr5A.!!$R3 2612
1 TraesCS5A01G342500 chr5A 549156728 549157229 501 False 416.000000 416 81.836000 2102 2608 1 chr5A.!!$F1 506
2 TraesCS5A01G342500 chr5D 433015303 433021835 6532 True 823.750000 1751 89.494000 20 2611 4 chr5D.!!$R2 2591
3 TraesCS5A01G342500 chr5D 435247835 435248355 520 False 531.000000 531 85.150000 2087 2613 1 chr5D.!!$F2 526
4 TraesCS5A01G342500 chr5B 527056431 527056954 523 True 521.000000 521 84.860000 2087 2613 1 chr5B.!!$R4 526
5 TraesCS5A01G342500 chr5B 528540501 528541021 520 False 520.000000 520 84.774000 2087 2613 1 chr5B.!!$F3 526
6 TraesCS5A01G342500 chr5B 526581272 526588320 7048 True 485.985714 891 90.271429 126 2613 7 chr5B.!!$R6 2487

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
435 508 0.112412 TTGAAGGCCTTCCCTCAACC 59.888 55.0 36.75 15.38 45.62 3.77 F
1288 1405 0.028902 GCACAACGGTCTTTGGTGAC 59.971 55.0 0.00 0.00 36.31 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1461 1578 0.249120 TCCAACGGTAGGCATCACAG 59.751 55.000 0.00 0.0 0.00 3.66 R
2296 2740 2.047844 AGTGCTAGCTGTGTGGCG 60.048 61.111 17.23 0.0 37.29 5.69 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
31 32 5.032327 TGAGTAGATGCAGATCAATTGCT 57.968 39.130 0.00 0.00 42.02 3.91
35 36 7.006865 AGTAGATGCAGATCAATTGCTATCT 57.993 36.000 16.73 16.73 42.02 1.98
55 56 7.704472 GCTATCTGTTCTCTTGATTATATCCCG 59.296 40.741 0.00 0.00 0.00 5.14
93 94 3.198872 GAGAAAGTATGTAGTGCTGGCC 58.801 50.000 0.00 0.00 0.00 5.36
95 96 0.178068 AAGTATGTAGTGCTGGCCCG 59.822 55.000 0.00 0.00 0.00 6.13
101 102 1.685765 TAGTGCTGGCCCGTGAGAT 60.686 57.895 0.00 0.00 0.00 2.75
114 115 3.252215 CCCGTGAGATTGAGTAGAGCTAG 59.748 52.174 0.00 0.00 0.00 3.42
124 125 6.734502 TTGAGTAGAGCTAGCTAGTCTCTA 57.265 41.667 30.55 30.55 40.11 2.43
141 142 4.755123 GTCTCTACAAGCAACTTAAAGCCA 59.245 41.667 0.00 0.00 0.00 4.75
168 169 7.012327 CAGTCTTTAGTTGATGGTCTGTTTGAA 59.988 37.037 0.00 0.00 0.00 2.69
195 196 4.278170 TGCCTTCTTATTGTCAACAGGTTG 59.722 41.667 5.81 5.81 41.71 3.77
198 199 5.047802 CCTTCTTATTGTCAACAGGTTGCAT 60.048 40.000 7.28 2.77 40.24 3.96
200 201 6.494893 TCTTATTGTCAACAGGTTGCATAC 57.505 37.500 7.28 1.99 40.24 2.39
205 206 2.554032 GTCAACAGGTTGCATACAGCTT 59.446 45.455 7.28 0.00 45.94 3.74
249 266 3.323403 GCTGCCTCTACTGATATGAACCT 59.677 47.826 0.00 0.00 0.00 3.50
254 271 5.480073 GCCTCTACTGATATGAACCTCATCT 59.520 44.000 0.00 0.00 38.26 2.90
259 276 6.992664 ACTGATATGAACCTCATCTAGCTT 57.007 37.500 0.00 0.00 38.26 3.74
273 290 7.981789 CCTCATCTAGCTTACATAAAACTGTCA 59.018 37.037 0.00 0.00 0.00 3.58
292 309 4.570772 TGTCACTTGCTAGAACAAACTCAC 59.429 41.667 1.04 0.00 0.00 3.51
295 312 4.024556 CACTTGCTAGAACAAACTCACTGG 60.025 45.833 1.04 0.00 0.00 4.00
303 320 1.488812 ACAAACTCACTGGTGTGCCTA 59.511 47.619 0.53 0.00 43.49 3.93
305 322 1.717032 AACTCACTGGTGTGCCTAGA 58.283 50.000 0.00 0.00 43.49 2.43
306 323 1.717032 ACTCACTGGTGTGCCTAGAA 58.283 50.000 0.00 0.00 43.49 2.10
335 352 6.432783 CCACATAACCAAAACATGTCCTCTTA 59.567 38.462 0.00 0.00 30.59 2.10
379 452 2.644151 AGGGGTTACAGAAAGGTGGAT 58.356 47.619 0.00 0.00 0.00 3.41
384 457 5.190330 GGGGTTACAGAAAGGTGGATAACTA 59.810 44.000 0.00 0.00 0.00 2.24
385 458 6.296605 GGGGTTACAGAAAGGTGGATAACTAA 60.297 42.308 0.00 0.00 0.00 2.24
411 484 2.637382 TGAACATGTCCACAAGGAGCTA 59.363 45.455 0.00 0.00 46.92 3.32
412 485 3.072330 TGAACATGTCCACAAGGAGCTAA 59.928 43.478 0.00 0.00 46.92 3.09
415 488 0.324943 TGTCCACAAGGAGCTAAGCC 59.675 55.000 0.00 0.00 46.92 4.35
434 507 1.539157 CTTGAAGGCCTTCCCTCAAC 58.461 55.000 36.75 16.10 45.62 3.18
435 508 0.112412 TTGAAGGCCTTCCCTCAACC 59.888 55.000 36.75 15.38 45.62 3.77
436 509 0.772124 TGAAGGCCTTCCCTCAACCT 60.772 55.000 36.75 4.28 45.62 3.50
441 515 1.480498 GGCCTTCCCTCAACCTCAAAA 60.480 52.381 0.00 0.00 0.00 2.44
469 543 3.644966 TCCACAAGGAACTCAAACAGT 57.355 42.857 0.00 0.00 42.23 3.55
471 545 3.694072 TCCACAAGGAACTCAAACAGTTG 59.306 43.478 0.00 0.00 46.10 3.16
487 561 7.389330 TCAAACAGTTGTGTCTAAGAAACTCAA 59.611 33.333 0.00 0.00 35.08 3.02
491 565 6.260936 CAGTTGTGTCTAAGAAACTCAACCAT 59.739 38.462 14.15 0.00 45.42 3.55
492 566 7.441157 CAGTTGTGTCTAAGAAACTCAACCATA 59.559 37.037 14.15 0.00 45.42 2.74
513 587 2.301346 CCATAACTGGGAAGTCCATGC 58.699 52.381 0.00 0.00 46.01 4.06
514 588 2.301346 CATAACTGGGAAGTCCATGCC 58.699 52.381 0.00 0.00 46.01 4.40
518 592 2.361104 GGGAAGTCCATGCCGCAA 60.361 61.111 0.00 0.00 37.91 4.85
519 593 1.976474 GGGAAGTCCATGCCGCAAA 60.976 57.895 0.00 0.00 37.91 3.68
520 594 1.322538 GGGAAGTCCATGCCGCAAAT 61.323 55.000 0.00 0.00 37.91 2.32
521 595 1.388547 GGAAGTCCATGCCGCAAATA 58.611 50.000 0.00 0.00 35.64 1.40
522 596 1.065551 GGAAGTCCATGCCGCAAATAC 59.934 52.381 0.00 0.00 35.64 1.89
523 597 2.017049 GAAGTCCATGCCGCAAATACT 58.983 47.619 0.00 0.00 0.00 2.12
524 598 3.202906 GAAGTCCATGCCGCAAATACTA 58.797 45.455 0.00 0.00 0.00 1.82
525 599 2.561569 AGTCCATGCCGCAAATACTAC 58.438 47.619 0.00 0.00 0.00 2.73
526 600 2.170607 AGTCCATGCCGCAAATACTACT 59.829 45.455 0.00 0.00 0.00 2.57
527 601 2.544267 GTCCATGCCGCAAATACTACTC 59.456 50.000 0.00 0.00 0.00 2.59
528 602 1.873591 CCATGCCGCAAATACTACTCC 59.126 52.381 0.00 0.00 0.00 3.85
529 603 1.873591 CATGCCGCAAATACTACTCCC 59.126 52.381 0.00 0.00 0.00 4.30
530 604 1.200519 TGCCGCAAATACTACTCCCT 58.799 50.000 0.00 0.00 0.00 4.20
531 605 1.138266 TGCCGCAAATACTACTCCCTC 59.862 52.381 0.00 0.00 0.00 4.30
532 606 1.540580 GCCGCAAATACTACTCCCTCC 60.541 57.143 0.00 0.00 0.00 4.30
533 607 1.269621 CCGCAAATACTACTCCCTCCG 60.270 57.143 0.00 0.00 0.00 4.63
534 608 1.407979 CGCAAATACTACTCCCTCCGT 59.592 52.381 0.00 0.00 0.00 4.69
535 609 2.543238 CGCAAATACTACTCCCTCCGTC 60.543 54.545 0.00 0.00 0.00 4.79
536 610 2.223994 GCAAATACTACTCCCTCCGTCC 60.224 54.545 0.00 0.00 0.00 4.79
537 611 2.364647 CAAATACTACTCCCTCCGTCCC 59.635 54.545 0.00 0.00 0.00 4.46
538 612 1.229131 ATACTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
539 613 1.002069 TACTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
540 614 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
541 615 1.272807 CTACTCCCTCCGTCCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
542 616 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
543 617 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
544 618 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
545 619 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
546 620 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
547 621 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
548 622 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
549 623 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
550 624 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
551 625 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
552 626 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
553 627 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
554 628 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
555 629 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
556 630 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
557 631 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
558 632 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
559 633 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
560 634 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
561 635 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
605 679 8.642908 TCACATTTTAGTGTTAGATACATCCG 57.357 34.615 0.00 0.00 39.39 4.18
606 680 8.255206 TCACATTTTAGTGTTAGATACATCCGT 58.745 33.333 0.00 0.00 39.39 4.69
607 681 9.524106 CACATTTTAGTGTTAGATACATCCGTA 57.476 33.333 0.00 0.00 39.39 4.02
643 717 9.884465 ATTTAAGACAAGAATTTTGAGACGAAG 57.116 29.630 0.00 0.00 0.00 3.79
644 718 5.931441 AGACAAGAATTTTGAGACGAAGG 57.069 39.130 0.00 0.00 0.00 3.46
645 719 4.757149 AGACAAGAATTTTGAGACGAAGGG 59.243 41.667 0.00 0.00 0.00 3.95
649 723 5.740290 AGAATTTTGAGACGAAGGGAGTA 57.260 39.130 0.00 0.00 0.00 2.59
652 726 4.675976 TTTTGAGACGAAGGGAGTACAA 57.324 40.909 0.00 0.00 0.00 2.41
663 737 4.142609 AGGGAGTACAATACATGCACTG 57.857 45.455 0.00 0.00 35.72 3.66
666 740 4.513442 GGAGTACAATACATGCACTGGAA 58.487 43.478 0.00 0.00 35.72 3.53
672 746 4.340666 ACAATACATGCACTGGAACACAAA 59.659 37.500 0.00 0.00 0.00 2.83
676 750 1.832883 TGCACTGGAACACAAACAGT 58.167 45.000 0.00 0.00 45.62 3.55
678 752 1.742831 GCACTGGAACACAAACAGTCA 59.257 47.619 0.00 0.00 43.09 3.41
735 812 3.258123 ACATAACACAAGATGGGTTTGGC 59.742 43.478 2.99 0.00 42.12 4.52
768 845 4.160439 GTCAAGATATGGACTCCTGTCACA 59.840 45.833 0.00 0.00 44.61 3.58
793 870 4.550831 CGTGAGATGCCGAATATCAAACAC 60.551 45.833 0.00 0.00 38.22 3.32
797 874 3.942539 TGCCGAATATCAAACACATCG 57.057 42.857 0.00 0.00 0.00 3.84
835 912 3.457610 AGCTTTTCAACACCAACCATG 57.542 42.857 0.00 0.00 0.00 3.66
853 930 4.158394 ACCATGTGGAAGCAAATGATACAC 59.842 41.667 5.96 0.00 38.94 2.90
856 939 4.148079 TGTGGAAGCAAATGATACACCAA 58.852 39.130 0.00 0.00 0.00 3.67
889 972 1.940613 GCCGCGATCTAATCCAAACTT 59.059 47.619 8.23 0.00 0.00 2.66
894 977 5.119279 CCGCGATCTAATCCAAACTTATCAG 59.881 44.000 8.23 0.00 0.00 2.90
950 1038 3.545481 CTGCGCCGACACGATGAC 61.545 66.667 4.18 0.00 34.06 3.06
1015 1103 0.376152 CAACAGCATCACCTGATCGC 59.624 55.000 0.00 3.05 36.67 4.58
1021 1109 1.153568 ATCACCTGATCGCCACACG 60.154 57.895 0.00 0.00 45.62 4.49
1042 1130 2.475371 ATCCACCACCAGCTGAGCAC 62.475 60.000 17.39 0.00 0.00 4.40
1082 1170 0.317020 GCAGCACACGTTCTCCAAAC 60.317 55.000 0.00 0.00 0.00 2.93
1096 1184 2.555757 CTCCAAACCTCCAGCTGAAAAG 59.444 50.000 17.39 9.44 0.00 2.27
1142 1235 1.446907 CGCCAAGAGATTTGCTCAGT 58.553 50.000 0.00 0.00 46.45 3.41
1147 1240 1.831580 AGAGATTTGCTCAGTTGGCC 58.168 50.000 0.00 0.00 46.45 5.36
1285 1402 2.184167 CGGCACAACGGTCTTTGGT 61.184 57.895 0.00 0.00 0.00 3.67
1288 1405 0.028902 GCACAACGGTCTTTGGTGAC 59.971 55.000 0.00 0.00 36.31 3.67
1352 1469 0.108186 CAAGATCACGCTGCCCTGTA 60.108 55.000 0.00 0.00 0.00 2.74
1354 1471 0.833287 AGATCACGCTGCCCTGTAAT 59.167 50.000 0.00 0.00 0.00 1.89
1373 1490 2.889617 CCGCGGTGATGGAGTACA 59.110 61.111 19.50 0.00 0.00 2.90
1482 1605 0.462047 GTGATGCCTACCGTTGGAGG 60.462 60.000 2.88 0.00 35.78 4.30
1491 1893 3.181454 CCTACCGTTGGAGGCATCTAAAT 60.181 47.826 0.00 0.00 33.69 1.40
1498 1900 2.103094 TGGAGGCATCTAAATCAGGACG 59.897 50.000 0.00 0.00 0.00 4.79
1499 1901 2.139118 GAGGCATCTAAATCAGGACGC 58.861 52.381 0.00 0.00 0.00 5.19
1502 1904 3.006323 AGGCATCTAAATCAGGACGCTAG 59.994 47.826 0.00 0.00 0.00 3.42
1512 1914 4.736126 TCAGGACGCTAGAATGATCAAA 57.264 40.909 0.00 0.00 0.00 2.69
1515 1917 5.351465 TCAGGACGCTAGAATGATCAAAAAC 59.649 40.000 0.00 0.00 0.00 2.43
1532 1934 8.871686 ATCAAAAACTTGTGAATTAGTGAACC 57.128 30.769 0.00 0.00 0.00 3.62
1549 1951 4.096003 CGGCCAGGTGGTACAGGG 62.096 72.222 2.24 0.00 41.80 4.45
1650 2054 0.320771 AAAGCAGGCTGTACTCCACG 60.321 55.000 17.16 0.00 0.00 4.94
1652 2056 1.185618 AGCAGGCTGTACTCCACGAA 61.186 55.000 17.16 0.00 0.00 3.85
1653 2057 0.320421 GCAGGCTGTACTCCACGAAA 60.320 55.000 17.16 0.00 0.00 3.46
1690 2095 5.771165 GGGGGTAAAAGACACTGATGTTTAA 59.229 40.000 0.00 0.00 39.95 1.52
1762 2167 6.862090 GTGTCGACACAAGATTTAGTAGAAGT 59.138 38.462 37.16 0.00 45.75 3.01
1815 2220 4.009015 GCTGAAGGCCCAAAGGAG 57.991 61.111 0.00 0.00 33.47 3.69
1890 2295 8.144478 GCCATCAAGAACTAAGATATGACACTA 58.856 37.037 0.00 0.00 0.00 2.74
1894 2299 9.952188 TCAAGAACTAAGATATGACACTATTCG 57.048 33.333 0.00 0.00 0.00 3.34
1908 2313 8.047413 TGACACTATTCGACAAGTTATCTGTA 57.953 34.615 0.00 0.00 0.00 2.74
1957 2362 7.072177 TCGCACCTAATCAAAATGTTAAGAG 57.928 36.000 0.00 0.00 0.00 2.85
1958 2363 6.653320 TCGCACCTAATCAAAATGTTAAGAGT 59.347 34.615 0.00 0.00 0.00 3.24
1960 2365 8.612619 CGCACCTAATCAAAATGTTAAGAGTAT 58.387 33.333 0.00 0.00 0.00 2.12
1981 2386 4.495911 TGCATTCAAGTACAATCGCAAA 57.504 36.364 0.00 0.00 0.00 3.68
2075 2480 1.142060 TCTTCCCTCCGTCCCAAAAA 58.858 50.000 0.00 0.00 0.00 1.94
2277 2721 3.065510 CAGAGAGCAAATTGATGGCTGAG 59.934 47.826 0.00 0.00 38.15 3.35
2278 2722 3.015327 GAGAGCAAATTGATGGCTGAGT 58.985 45.455 0.00 0.00 38.15 3.41
2279 2723 4.080695 AGAGAGCAAATTGATGGCTGAGTA 60.081 41.667 0.00 0.00 38.15 2.59
2280 2724 3.944015 AGAGCAAATTGATGGCTGAGTAC 59.056 43.478 0.00 0.00 38.15 2.73
2281 2725 3.944015 GAGCAAATTGATGGCTGAGTACT 59.056 43.478 0.00 0.00 38.15 2.73
2296 2740 2.229302 GAGTACTAGTCCCATCGATGGC 59.771 54.545 34.77 23.43 46.70 4.40
2302 2746 4.854924 CCCATCGATGGCGCCACA 62.855 66.667 34.77 19.79 46.70 4.17
2600 3045 0.173935 AACCACAGACGACGTTGTGA 59.826 50.000 28.74 0.00 45.79 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.172875 GCAATTGATCTGCATCTACTCATAGTT 59.827 37.037 10.34 0.00 39.69 2.24
5 6 6.649973 GCAATTGATCTGCATCTACTCATAGT 59.350 38.462 10.34 0.00 39.69 2.12
6 7 6.874664 AGCAATTGATCTGCATCTACTCATAG 59.125 38.462 10.34 0.00 42.48 2.23
7 8 6.766429 AGCAATTGATCTGCATCTACTCATA 58.234 36.000 10.34 0.00 42.48 2.15
8 9 5.622180 AGCAATTGATCTGCATCTACTCAT 58.378 37.500 10.34 0.00 42.48 2.90
9 10 5.032327 AGCAATTGATCTGCATCTACTCA 57.968 39.130 10.34 0.00 42.48 3.41
10 11 7.063662 CAGATAGCAATTGATCTGCATCTACTC 59.936 40.741 18.83 5.90 41.84 2.59
11 12 6.874664 CAGATAGCAATTGATCTGCATCTACT 59.125 38.462 18.83 2.65 41.84 2.57
12 13 7.062906 CAGATAGCAATTGATCTGCATCTAC 57.937 40.000 18.83 0.00 41.84 2.59
31 32 7.674348 ACCGGGATATAATCAAGAGAACAGATA 59.326 37.037 6.32 0.00 0.00 1.98
35 36 7.606135 TTACCGGGATATAATCAAGAGAACA 57.394 36.000 6.32 0.00 0.00 3.18
74 75 2.289565 GGGCCAGCACTACATACTTTC 58.710 52.381 4.39 0.00 0.00 2.62
75 76 1.406887 CGGGCCAGCACTACATACTTT 60.407 52.381 4.39 0.00 0.00 2.66
93 94 3.304391 GCTAGCTCTACTCAATCTCACGG 60.304 52.174 7.70 0.00 0.00 4.94
95 96 5.763204 ACTAGCTAGCTCTACTCAATCTCAC 59.237 44.000 23.26 0.00 0.00 3.51
101 102 5.623956 AGAGACTAGCTAGCTCTACTCAA 57.376 43.478 30.18 12.31 36.08 3.02
124 125 3.023832 ACTGTGGCTTTAAGTTGCTTGT 58.976 40.909 0.00 0.00 0.00 3.16
141 142 5.552870 ACAGACCATCAACTAAAGACTGT 57.447 39.130 0.00 0.00 0.00 3.55
168 169 4.460263 TGTTGACAATAAGAAGGCACTGT 58.540 39.130 0.00 0.00 40.86 3.55
176 177 6.488344 TGTATGCAACCTGTTGACAATAAGAA 59.512 34.615 13.94 0.00 42.93 2.52
195 196 6.426025 TCTGATAATGATCACAAGCTGTATGC 59.574 38.462 0.00 0.00 37.15 3.14
198 199 7.729116 TCATCTGATAATGATCACAAGCTGTA 58.271 34.615 0.00 0.00 37.15 2.74
200 201 6.347806 GCTCATCTGATAATGATCACAAGCTG 60.348 42.308 0.00 0.00 37.15 4.24
205 206 4.995487 GCTGCTCATCTGATAATGATCACA 59.005 41.667 0.00 0.00 37.15 3.58
249 266 8.531982 AGTGACAGTTTTATGTAAGCTAGATGA 58.468 33.333 0.00 0.00 32.25 2.92
254 271 6.934645 AGCAAGTGACAGTTTTATGTAAGCTA 59.065 34.615 0.00 0.00 32.25 3.32
259 276 7.929245 TGTTCTAGCAAGTGACAGTTTTATGTA 59.071 33.333 0.00 0.00 32.25 2.29
273 290 4.130118 CCAGTGAGTTTGTTCTAGCAAGT 58.870 43.478 0.00 0.00 0.00 3.16
292 309 0.322546 GGGGTTTCTAGGCACACCAG 60.323 60.000 8.28 0.00 36.36 4.00
295 312 0.109723 TGTGGGGTTTCTAGGCACAC 59.890 55.000 0.00 0.00 0.00 3.82
303 320 4.290942 TGTTTTGGTTATGTGGGGTTTCT 58.709 39.130 0.00 0.00 0.00 2.52
305 322 4.410555 ACATGTTTTGGTTATGTGGGGTTT 59.589 37.500 0.00 0.00 34.04 3.27
306 323 3.970640 ACATGTTTTGGTTATGTGGGGTT 59.029 39.130 0.00 0.00 34.04 4.11
335 352 7.148069 CCTTTGGTTCTGAACTTGAAAGTAGTT 60.148 37.037 19.05 0.00 38.57 2.24
374 447 8.345565 GGACATGTTCATCATTTAGTTATCCAC 58.654 37.037 0.00 0.00 34.09 4.02
379 452 8.628630 TTGTGGACATGTTCATCATTTAGTTA 57.371 30.769 10.76 0.00 34.09 2.24
384 457 5.078949 TCCTTGTGGACATGTTCATCATTT 58.921 37.500 10.76 0.00 37.46 2.32
385 458 4.665451 TCCTTGTGGACATGTTCATCATT 58.335 39.130 10.76 0.00 37.46 2.57
451 525 4.082787 ACACAACTGTTTGAGTTCCTTGTG 60.083 41.667 0.00 0.00 43.52 3.33
460 534 7.064609 TGAGTTTCTTAGACACAACTGTTTGAG 59.935 37.037 2.90 0.00 36.48 3.02
462 536 7.072177 TGAGTTTCTTAGACACAACTGTTTG 57.928 36.000 2.90 0.00 38.83 2.93
464 538 6.093633 GGTTGAGTTTCTTAGACACAACTGTT 59.906 38.462 14.06 0.00 43.48 3.16
469 543 6.708949 GGTATGGTTGAGTTTCTTAGACACAA 59.291 38.462 1.23 0.00 0.00 3.33
470 544 6.183361 TGGTATGGTTGAGTTTCTTAGACACA 60.183 38.462 1.23 0.00 0.00 3.72
471 545 6.228258 TGGTATGGTTGAGTTTCTTAGACAC 58.772 40.000 0.00 0.00 0.00 3.67
487 561 3.458487 GGACTTCCCAGTTATGGTATGGT 59.542 47.826 0.00 0.00 46.10 3.55
509 583 1.873591 GGGAGTAGTATTTGCGGCATG 59.126 52.381 2.28 0.00 0.00 4.06
511 585 1.138266 GAGGGAGTAGTATTTGCGGCA 59.862 52.381 0.00 0.00 0.00 5.69
513 587 1.269621 CGGAGGGAGTAGTATTTGCGG 60.270 57.143 0.00 0.00 0.00 5.69
514 588 1.407979 ACGGAGGGAGTAGTATTTGCG 59.592 52.381 0.00 0.00 0.00 4.85
518 592 1.572415 TGGGACGGAGGGAGTAGTATT 59.428 52.381 0.00 0.00 0.00 1.89
519 593 1.229131 TGGGACGGAGGGAGTAGTAT 58.771 55.000 0.00 0.00 0.00 2.12
520 594 1.002069 TTGGGACGGAGGGAGTAGTA 58.998 55.000 0.00 0.00 0.00 1.82
521 595 0.115745 TTTGGGACGGAGGGAGTAGT 59.884 55.000 0.00 0.00 0.00 2.73
522 596 1.272807 TTTTGGGACGGAGGGAGTAG 58.727 55.000 0.00 0.00 0.00 2.57
523 597 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
524 598 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
525 599 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
526 600 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
527 601 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
528 602 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
529 603 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
530 604 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
531 605 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
532 606 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
533 607 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
534 608 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
535 609 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
579 653 9.093970 CGGATGTATCTAACACTAAAATGTGAA 57.906 33.333 1.47 0.00 42.09 3.18
580 654 8.255206 ACGGATGTATCTAACACTAAAATGTGA 58.745 33.333 1.47 0.00 42.09 3.58
581 655 8.420374 ACGGATGTATCTAACACTAAAATGTG 57.580 34.615 0.00 0.00 42.09 3.21
617 691 9.884465 CTTCGTCTCAAAATTCTTGTCTTAAAT 57.116 29.630 0.00 0.00 0.00 1.40
618 692 8.342634 CCTTCGTCTCAAAATTCTTGTCTTAAA 58.657 33.333 0.00 0.00 0.00 1.52
619 693 7.041372 CCCTTCGTCTCAAAATTCTTGTCTTAA 60.041 37.037 0.00 0.00 0.00 1.85
620 694 6.426937 CCCTTCGTCTCAAAATTCTTGTCTTA 59.573 38.462 0.00 0.00 0.00 2.10
621 695 5.239525 CCCTTCGTCTCAAAATTCTTGTCTT 59.760 40.000 0.00 0.00 0.00 3.01
622 696 4.757149 CCCTTCGTCTCAAAATTCTTGTCT 59.243 41.667 0.00 0.00 0.00 3.41
623 697 4.755123 TCCCTTCGTCTCAAAATTCTTGTC 59.245 41.667 0.00 0.00 0.00 3.18
624 698 4.714632 TCCCTTCGTCTCAAAATTCTTGT 58.285 39.130 0.00 0.00 0.00 3.16
625 699 4.757149 ACTCCCTTCGTCTCAAAATTCTTG 59.243 41.667 0.00 0.00 0.00 3.02
626 700 4.974399 ACTCCCTTCGTCTCAAAATTCTT 58.026 39.130 0.00 0.00 0.00 2.52
627 701 4.625607 ACTCCCTTCGTCTCAAAATTCT 57.374 40.909 0.00 0.00 0.00 2.40
628 702 5.235516 TGTACTCCCTTCGTCTCAAAATTC 58.764 41.667 0.00 0.00 0.00 2.17
629 703 5.223449 TGTACTCCCTTCGTCTCAAAATT 57.777 39.130 0.00 0.00 0.00 1.82
630 704 4.884668 TGTACTCCCTTCGTCTCAAAAT 57.115 40.909 0.00 0.00 0.00 1.82
631 705 4.675976 TTGTACTCCCTTCGTCTCAAAA 57.324 40.909 0.00 0.00 0.00 2.44
632 706 4.884668 ATTGTACTCCCTTCGTCTCAAA 57.115 40.909 0.00 0.00 0.00 2.69
633 707 4.768448 TGTATTGTACTCCCTTCGTCTCAA 59.232 41.667 0.00 0.00 0.00 3.02
634 708 4.338012 TGTATTGTACTCCCTTCGTCTCA 58.662 43.478 0.00 0.00 0.00 3.27
635 709 4.978083 TGTATTGTACTCCCTTCGTCTC 57.022 45.455 0.00 0.00 0.00 3.36
636 710 4.441634 GCATGTATTGTACTCCCTTCGTCT 60.442 45.833 0.00 0.00 0.00 4.18
637 711 3.802685 GCATGTATTGTACTCCCTTCGTC 59.197 47.826 0.00 0.00 0.00 4.20
638 712 3.196901 TGCATGTATTGTACTCCCTTCGT 59.803 43.478 0.00 0.00 0.00 3.85
639 713 3.555956 GTGCATGTATTGTACTCCCTTCG 59.444 47.826 0.00 0.00 37.89 3.79
640 714 4.572389 CAGTGCATGTATTGTACTCCCTTC 59.428 45.833 0.00 0.00 46.94 3.46
641 715 4.517285 CAGTGCATGTATTGTACTCCCTT 58.483 43.478 0.00 0.00 46.94 3.95
642 716 3.118261 CCAGTGCATGTATTGTACTCCCT 60.118 47.826 5.62 0.00 46.94 4.20
643 717 3.118408 TCCAGTGCATGTATTGTACTCCC 60.118 47.826 5.62 0.00 46.94 4.30
644 718 4.137116 TCCAGTGCATGTATTGTACTCC 57.863 45.455 5.62 0.00 46.94 3.85
645 719 4.935205 TGTTCCAGTGCATGTATTGTACTC 59.065 41.667 5.62 0.00 46.94 2.59
649 723 3.485394 TGTGTTCCAGTGCATGTATTGT 58.515 40.909 5.62 0.00 0.00 2.71
652 726 3.888323 TGTTTGTGTTCCAGTGCATGTAT 59.112 39.130 0.00 0.00 0.00 2.29
663 737 1.742831 TGTGCTGACTGTTTGTGTTCC 59.257 47.619 0.00 0.00 0.00 3.62
666 740 1.094785 GGTGTGCTGACTGTTTGTGT 58.905 50.000 0.00 0.00 0.00 3.72
672 746 0.744414 GTGTGTGGTGTGCTGACTGT 60.744 55.000 0.00 0.00 0.00 3.55
676 750 0.179936 TGATGTGTGTGGTGTGCTGA 59.820 50.000 0.00 0.00 0.00 4.26
678 752 0.469494 TCTGATGTGTGTGGTGTGCT 59.531 50.000 0.00 0.00 0.00 4.40
709 786 6.458206 CCAAACCCATCTTGTGTTATGTATCG 60.458 42.308 0.00 0.00 0.00 2.92
735 812 5.067936 AGTCCATATCTTGACTAGAACCACG 59.932 44.000 0.00 0.00 39.96 4.94
768 845 3.452755 TGATATTCGGCATCTCACGTT 57.547 42.857 0.00 0.00 0.00 3.99
793 870 2.263077 GTGCTGGTCTAGAACACGATG 58.737 52.381 6.32 0.00 34.80 3.84
797 874 1.801178 GCTTGTGCTGGTCTAGAACAC 59.199 52.381 6.32 7.83 44.85 3.32
835 912 4.782019 TTGGTGTATCATTTGCTTCCAC 57.218 40.909 0.00 0.00 0.00 4.02
950 1038 4.493747 GAGACGACGGGAAGGGCG 62.494 72.222 0.00 0.00 0.00 6.13
983 1071 1.905922 GCTGTTGAGCTGAGCCGTTC 61.906 60.000 0.00 0.00 42.52 3.95
1015 1103 0.391130 CTGGTGGTGGATACGTGTGG 60.391 60.000 0.00 0.00 42.51 4.17
1021 1109 0.462759 GCTCAGCTGGTGGTGGATAC 60.463 60.000 15.13 0.00 41.59 2.24
1072 1160 1.072331 TCAGCTGGAGGTTTGGAGAAC 59.928 52.381 15.13 0.00 0.00 3.01
1096 1184 0.323360 TGGTTCTGGCTGGGTATTGC 60.323 55.000 0.00 0.00 0.00 3.56
1133 1226 1.321474 CTCTTGGCCAACTGAGCAAA 58.679 50.000 16.05 0.00 0.00 3.68
1147 1240 1.734477 CGTCACGGTGAGCCTCTTG 60.734 63.158 11.83 0.00 0.00 3.02
1204 1321 1.743623 CATGACGCAACGGCCCTTA 60.744 57.895 0.00 0.00 31.60 2.69
1212 1329 1.131826 GCCGTGTACATGACGCAAC 59.868 57.895 16.87 0.00 38.57 4.17
1213 1330 2.030401 GGCCGTGTACATGACGCAA 61.030 57.895 16.87 0.00 38.57 4.85
1352 1469 1.966901 TACTCCATCACCGCGGCATT 61.967 55.000 28.58 6.80 0.00 3.56
1354 1471 3.071837 TACTCCATCACCGCGGCA 61.072 61.111 28.58 13.44 0.00 5.69
1373 1490 1.408405 CCTCCTCAGCAAGCACATGAT 60.408 52.381 0.00 0.00 0.00 2.45
1461 1578 0.249120 TCCAACGGTAGGCATCACAG 59.751 55.000 0.00 0.00 0.00 3.66
1482 1605 4.244425 TCTAGCGTCCTGATTTAGATGC 57.756 45.455 0.00 0.00 43.85 3.91
1491 1893 4.736126 TTTGATCATTCTAGCGTCCTGA 57.264 40.909 0.00 0.00 0.00 3.86
1498 1900 8.976986 ATTCACAAGTTTTTGATCATTCTAGC 57.023 30.769 0.00 0.00 37.73 3.42
1512 1914 4.261447 GCCGGTTCACTAATTCACAAGTTT 60.261 41.667 1.90 0.00 0.00 2.66
1515 1917 2.161609 GGCCGGTTCACTAATTCACAAG 59.838 50.000 1.90 0.00 0.00 3.16
1532 1934 4.096003 CCCTGTACCACCTGGCCG 62.096 72.222 0.00 0.00 39.32 6.13
1549 1951 3.960102 TGATGGTTCATCCTAAAATGGCC 59.040 43.478 0.00 0.00 39.87 5.36
1614 2018 6.738453 GCCTGCTTTCTCTTCCATTTTGTAAA 60.738 38.462 0.00 0.00 0.00 2.01
1690 2095 8.677148 ACAACATTCAGTAATTCAGTAACAGT 57.323 30.769 0.00 0.00 0.00 3.55
1704 2109 4.953579 AGTTTTGTGGGTACAACATTCAGT 59.046 37.500 0.00 0.00 45.91 3.41
1815 2220 3.194542 TCCTTAGCTCTTTCTCTGCACTC 59.805 47.826 0.00 0.00 0.00 3.51
1890 2295 5.720202 TGCAGTACAGATAACTTGTCGAAT 58.280 37.500 0.00 0.00 0.00 3.34
1894 2299 6.968131 TTGATGCAGTACAGATAACTTGTC 57.032 37.500 0.00 0.00 0.00 3.18
1902 2307 9.217278 GATGATCTTAATTGATGCAGTACAGAT 57.783 33.333 0.00 0.00 0.00 2.90
1908 2313 5.950023 AGGGATGATCTTAATTGATGCAGT 58.050 37.500 0.00 0.00 0.00 4.40
1926 2331 3.644966 TTGATTAGGTGCGAAAGGGAT 57.355 42.857 0.00 0.00 0.00 3.85
1957 2362 5.155509 TGCGATTGTACTTGAATGCATAC 57.844 39.130 0.00 0.00 0.00 2.39
1958 2363 5.809719 TTGCGATTGTACTTGAATGCATA 57.190 34.783 0.00 0.00 0.00 3.14
1960 2365 4.495911 TTTGCGATTGTACTTGAATGCA 57.504 36.364 0.00 0.00 0.00 3.96
1981 2386 5.489792 TGAGAAGCTGACTTAGTTGGAAT 57.510 39.130 0.00 0.00 35.82 3.01
2296 2740 2.047844 AGTGCTAGCTGTGTGGCG 60.048 61.111 17.23 0.00 37.29 5.69


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

AutoCloner maintained by Alex Coulton.