Multiple sequence alignment - TraesCS4B01G063900

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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 TraesCS4B01G063900 chr4B 100.000 4211 0 0 1 4211 55926469 55922259 0.000000e+00 7777.0
1 TraesCS4B01G063900 chr4B 80.943 1952 344 19 1241 3168 55756175 55754228 0.000000e+00 1519.0
2 TraesCS4B01G063900 chr4B 97.761 134 2 1 433 565 106858593 106858460 3.270000e-56 230.0
3 TraesCS4B01G063900 chr4A 95.984 2988 75 16 561 3509 562404461 562407442 0.000000e+00 4811.0
4 TraesCS4B01G063900 chr4A 81.013 1954 345 15 1238 3168 562452434 562454384 0.000000e+00 1530.0
5 TraesCS4B01G063900 chr4A 93.166 439 26 4 1 438 562404032 562404467 3.550000e-180 641.0
6 TraesCS4B01G063900 chr4A 92.105 380 24 4 3837 4211 562408223 562408601 8.020000e-147 531.0
7 TraesCS4B01G063900 chr4D 96.340 2650 50 10 962 3589 38446068 38448692 0.000000e+00 4313.0
8 TraesCS4B01G063900 chr4D 81.352 1952 336 17 1241 3168 38354514 38352567 0.000000e+00 1563.0
9 TraesCS4B01G063900 chr4D 92.926 622 29 7 3594 4211 38449147 38449757 0.000000e+00 891.0
10 TraesCS4B01G063900 chr4D 87.444 446 30 5 1 438 38444832 38445259 1.360000e-134 490.0
11 TraesCS4B01G063900 chr4D 90.833 120 10 1 654 772 38445428 38445547 4.360000e-35 159.0
12 TraesCS4B01G063900 chr4D 90.435 115 11 0 850 964 38445688 38445802 7.290000e-33 152.0
13 TraesCS4B01G063900 chr4D 93.684 95 5 1 561 654 38445253 38445347 1.580000e-29 141.0
14 TraesCS4B01G063900 chr6A 82.799 1436 229 15 1313 2736 84970203 84968774 0.000000e+00 1267.0
15 TraesCS4B01G063900 chr6A 80.720 389 68 6 2787 3171 84968753 84968368 3.180000e-76 296.0
16 TraesCS4B01G063900 chr6D 82.742 1437 228 17 1313 2736 67392514 67391085 0.000000e+00 1262.0
17 TraesCS4B01G063900 chr6D 81.250 384 66 5 2787 3166 67391064 67390683 5.290000e-79 305.0
18 TraesCS4B01G063900 chrUn 99.223 386 3 0 1589 1974 480666151 480666536 0.000000e+00 697.0
19 TraesCS4B01G063900 chr6B 97.744 133 3 0 433 565 54403667 54403535 3.270000e-56 230.0
20 TraesCS4B01G063900 chr6B 95.139 144 6 1 429 572 707499514 707499656 4.240000e-55 226.0
21 TraesCS4B01G063900 chr6B 95.070 142 5 1 439 580 68120703 68120842 5.480000e-54 222.0
22 TraesCS4B01G063900 chr3D 97.037 135 3 1 439 572 84562736 84562602 4.240000e-55 226.0
23 TraesCS4B01G063900 chr5B 96.992 133 4 0 436 568 383524650 383524782 1.520000e-54 224.0
24 TraesCS4B01G063900 chr5B 91.772 158 8 5 430 583 345054166 345054322 9.170000e-52 215.0
25 TraesCS4B01G063900 chr1B 95.683 139 6 0 436 574 626226876 626227014 1.520000e-54 224.0
26 TraesCS4B01G063900 chr1A 91.824 159 8 5 409 566 187375239 187375085 2.550000e-52 217.0
27 TraesCS4B01G063900 chr2B 85.714 77 10 1 3593 3669 89543649 89543724 3.490000e-11 80.5


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 TraesCS4B01G063900 chr4B 55922259 55926469 4210 True 7777.000000 7777 100.000000 1 4211 1 chr4B.!!$R2 4210
1 TraesCS4B01G063900 chr4B 55754228 55756175 1947 True 1519.000000 1519 80.943000 1241 3168 1 chr4B.!!$R1 1927
2 TraesCS4B01G063900 chr4A 562404032 562408601 4569 False 1994.333333 4811 93.751667 1 4211 3 chr4A.!!$F2 4210
3 TraesCS4B01G063900 chr4A 562452434 562454384 1950 False 1530.000000 1530 81.013000 1238 3168 1 chr4A.!!$F1 1930
4 TraesCS4B01G063900 chr4D 38352567 38354514 1947 True 1563.000000 1563 81.352000 1241 3168 1 chr4D.!!$R1 1927
5 TraesCS4B01G063900 chr4D 38444832 38449757 4925 False 1024.333333 4313 91.943667 1 4211 6 chr4D.!!$F1 4210
6 TraesCS4B01G063900 chr6A 84968368 84970203 1835 True 781.500000 1267 81.759500 1313 3171 2 chr6A.!!$R1 1858
7 TraesCS4B01G063900 chr6D 67390683 67392514 1831 True 783.500000 1262 81.996000 1313 3166 2 chr6D.!!$R1 1853

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
457 467 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.0 44.66 2.17 F
460 470 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.0 44.66 2.12 F
566 576 0.251297 TTTCGGACGGAGGGAGTACA 60.251 55.000 0.00 0.0 0.00 2.90 F
1656 2145 1.295423 GCAGCCTCGTTTCAGGGTA 59.705 57.895 0.00 0.0 42.70 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1656 2145 3.446161 CCTCCATTGCATCAACATCAACT 59.554 43.478 0.00 0.00 0.00 3.16 R
2349 2838 3.795688 TTTTTCCAGTCCTCAGCTGAT 57.204 42.857 18.63 0.00 36.12 2.90 R
2752 3241 3.806949 TTTCCCTTGTTCAGCATAGGT 57.193 42.857 0.00 0.00 0.00 3.08 R
3457 3963 0.039617 TGGCACATTACGTTGCTTGC 60.040 50.000 9.61 6.63 0.00 4.01 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
28 29 2.936498 GCTTAGTGCTTTCTGCGGAATA 59.064 45.455 9.22 0.00 46.63 1.75
30 31 4.750098 GCTTAGTGCTTTCTGCGGAATATA 59.250 41.667 9.22 0.00 46.63 0.86
83 84 8.605947 AGCACATAGGCTAGATTTATTATTCCA 58.394 33.333 0.00 0.00 43.70 3.53
138 139 0.598680 GATCAGCTCGATTCGTGGGG 60.599 60.000 5.89 0.00 33.17 4.96
139 140 1.330655 ATCAGCTCGATTCGTGGGGT 61.331 55.000 5.89 1.25 0.00 4.95
180 181 2.972505 AGACGCCGTGCCTGTTTG 60.973 61.111 0.00 0.00 0.00 2.93
235 244 5.129815 AGCATGTGGAGCCATAAATTTTCAT 59.870 36.000 0.00 0.00 0.00 2.57
279 288 1.205893 CCTGTCTCTAGCCACTTCCAC 59.794 57.143 0.00 0.00 0.00 4.02
313 322 5.957842 TTGTGCTCCCATTAAACTTGTAG 57.042 39.130 0.00 0.00 0.00 2.74
414 424 5.938125 TCTCTGGAGCTGTTACCAATTTAAC 59.062 40.000 0.00 0.00 35.67 2.01
436 446 7.664552 AACTGAGACTAGACTACTAGAGCTA 57.335 40.000 10.60 0.00 46.34 3.32
437 447 7.047460 ACTGAGACTAGACTACTAGAGCTAC 57.953 44.000 10.60 0.00 46.34 3.58
438 448 6.837568 ACTGAGACTAGACTACTAGAGCTACT 59.162 42.308 10.60 0.00 46.34 2.57
439 449 8.000709 ACTGAGACTAGACTACTAGAGCTACTA 58.999 40.741 10.60 0.00 46.34 1.82
440 450 8.169977 TGAGACTAGACTACTAGAGCTACTAC 57.830 42.308 10.60 0.00 46.34 2.73
441 451 8.000709 TGAGACTAGACTACTAGAGCTACTACT 58.999 40.741 10.60 0.00 46.34 2.57
442 452 8.401490 AGACTAGACTACTAGAGCTACTACTC 57.599 42.308 10.60 0.00 46.34 2.59
443 453 7.449704 AGACTAGACTACTAGAGCTACTACTCC 59.550 44.444 10.60 0.00 46.34 3.85
444 454 5.813513 AGACTACTAGAGCTACTACTCCC 57.186 47.826 0.00 0.00 37.39 4.30
445 455 5.470501 AGACTACTAGAGCTACTACTCCCT 58.529 45.833 0.00 0.00 37.39 4.20
446 456 5.541484 AGACTACTAGAGCTACTACTCCCTC 59.459 48.000 0.00 0.00 37.39 4.30
447 457 4.594491 ACTACTAGAGCTACTACTCCCTCC 59.406 50.000 0.00 0.00 37.39 4.30
448 458 2.369532 ACTAGAGCTACTACTCCCTCCG 59.630 54.545 0.00 0.00 37.39 4.63
449 459 1.215140 AGAGCTACTACTCCCTCCGT 58.785 55.000 0.00 0.00 37.39 4.69
450 460 1.141455 AGAGCTACTACTCCCTCCGTC 59.859 57.143 0.00 0.00 37.39 4.79
451 461 0.183252 AGCTACTACTCCCTCCGTCC 59.817 60.000 0.00 0.00 0.00 4.79
452 462 1.165284 GCTACTACTCCCTCCGTCCG 61.165 65.000 0.00 0.00 0.00 4.79
453 463 0.534652 CTACTACTCCCTCCGTCCGG 60.535 65.000 0.00 0.00 0.00 5.14
454 464 0.982852 TACTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
455 465 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
456 466 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
457 467 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
458 468 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
459 469 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
460 470 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
461 471 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
462 472 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
463 473 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
464 474 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
465 475 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
466 476 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
467 477 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
468 478 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
469 479 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
470 480 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
471 481 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
472 482 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
473 483 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
474 484 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
475 485 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
476 486 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
484 494 8.096414 ACTTGTCATCAAAATGAATAAAAGGGG 58.904 33.333 0.00 0.00 43.42 4.79
485 495 7.789202 TGTCATCAAAATGAATAAAAGGGGA 57.211 32.000 0.00 0.00 43.42 4.81
486 496 8.378115 TGTCATCAAAATGAATAAAAGGGGAT 57.622 30.769 0.00 0.00 43.42 3.85
487 497 8.259411 TGTCATCAAAATGAATAAAAGGGGATG 58.741 33.333 0.00 0.00 43.42 3.51
488 498 8.260114 GTCATCAAAATGAATAAAAGGGGATGT 58.740 33.333 0.00 0.00 43.42 3.06
489 499 9.486123 TCATCAAAATGAATAAAAGGGGATGTA 57.514 29.630 0.00 0.00 38.97 2.29
492 502 9.713684 TCAAAATGAATAAAAGGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
497 507 8.561536 TGAATAAAAGGGGATGTATCTAGACA 57.438 34.615 0.00 0.00 0.00 3.41
498 508 9.170890 TGAATAAAAGGGGATGTATCTAGACAT 57.829 33.333 0.00 0.00 42.82 3.06
506 516 9.845214 AGGGGATGTATCTAGACATATTTTAGT 57.155 33.333 0.00 0.00 40.18 2.24
530 540 9.225682 AGTTCTAGATACATCCCTTTTTATCCA 57.774 33.333 0.00 0.00 0.00 3.41
536 546 9.713684 AGATACATCCCTTTTTATCCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
539 549 8.378115 ACATCCCTTTTTATCCATTTTGATGA 57.622 30.769 0.00 0.00 32.39 2.92
540 550 8.260114 ACATCCCTTTTTATCCATTTTGATGAC 58.740 33.333 0.00 0.00 32.39 3.06
541 551 7.789202 TCCCTTTTTATCCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
542 552 8.200024 TCCCTTTTTATCCATTTTGATGACAA 57.800 30.769 0.00 0.00 0.00 3.18
543 553 8.313292 TCCCTTTTTATCCATTTTGATGACAAG 58.687 33.333 0.00 0.00 37.32 3.16
544 554 8.096414 CCCTTTTTATCCATTTTGATGACAAGT 58.904 33.333 0.00 0.00 37.32 3.16
551 561 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
552 562 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
553 563 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
554 564 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
555 565 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
556 566 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
557 567 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
558 568 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
559 569 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
560 570 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
561 571 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
562 572 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
563 573 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
566 576 0.251297 TTTCGGACGGAGGGAGTACA 60.251 55.000 0.00 0.00 0.00 2.90
607 617 2.232941 TCCTGGAGTAACTTAACTGGCG 59.767 50.000 0.00 0.00 0.00 5.69
662 753 9.952030 TGAATGACAGTGGTTCATACTTAATAA 57.048 29.630 0.00 0.00 0.00 1.40
693 784 8.172484 GCTCAATACAAATTTGTGTATACGTCA 58.828 33.333 29.72 10.16 42.58 4.35
730 821 4.399395 TGAGGCAGGCCAGCGAAG 62.399 66.667 14.62 0.00 38.92 3.79
893 1081 6.513806 TCTTACTTGTTACATGCATGCAAT 57.486 33.333 26.68 18.32 0.00 3.56
904 1092 9.904647 GTTACATGCATGCAATTGTAAAATAAG 57.095 29.630 32.84 12.60 34.93 1.73
919 1107 5.874895 AAAATAAGCGTACCTGAAGAACC 57.125 39.130 0.00 0.00 0.00 3.62
1111 1585 2.743928 CAGTCCAAGGTGGCGAGC 60.744 66.667 0.00 0.00 37.47 5.03
1128 1602 2.266554 GAGCTGGTCGAAGTTGATGAG 58.733 52.381 0.00 0.00 0.00 2.90
1656 2145 1.295423 GCAGCCTCGTTTCAGGGTA 59.705 57.895 0.00 0.00 42.70 3.69
1830 2319 2.079925 GGGCAGTTCATTGACTCTGAC 58.920 52.381 17.08 14.97 35.45 3.51
2349 2838 3.814625 TGACAACTACAATGAAGCACCA 58.185 40.909 0.00 0.00 0.00 4.17
2752 3241 2.652095 CCGCTCCCCTTAACACCGA 61.652 63.158 0.00 0.00 0.00 4.69
2824 3316 1.610522 CCCAAGCAACTCAACCTTCAG 59.389 52.381 0.00 0.00 0.00 3.02
3123 3621 2.412323 CCGTCCGGAGATCGTGGAA 61.412 63.158 3.06 0.00 37.50 3.53
3168 3666 3.913573 CTGAATTCGACCGCCGCG 61.914 66.667 5.59 5.59 38.37 6.46
3251 3749 4.008330 AGCATGCATATATGTCTTCTGGC 58.992 43.478 21.98 8.51 0.00 4.85
3266 3764 4.008933 GGCGCCTGTGAGTGGTCT 62.009 66.667 22.15 0.00 0.00 3.85
3267 3765 2.031163 GCGCCTGTGAGTGGTCTT 59.969 61.111 0.00 0.00 0.00 3.01
3274 3772 3.883489 GCCTGTGAGTGGTCTTTTTAACT 59.117 43.478 0.00 0.00 0.00 2.24
3283 3781 5.751990 AGTGGTCTTTTTAACTGTAGTCGTG 59.248 40.000 0.00 0.00 0.00 4.35
3352 3852 6.767902 TGGATCTGTCCTAGAATGTAATTTGC 59.232 38.462 0.00 0.00 45.32 3.68
3441 3947 4.220821 ACCAGAGATGTTATCTGACGTTGT 59.779 41.667 4.57 0.00 45.80 3.32
3457 3963 3.252215 ACGTTGTTTGGGATGTGTATGTG 59.748 43.478 0.00 0.00 0.00 3.21
3473 3983 2.397777 TGTGCAAGCAACGTAATGTG 57.602 45.000 0.00 0.00 0.00 3.21
3507 4017 5.351189 GGATTGTGTTTGTGCTTCAGTTTTT 59.649 36.000 0.00 0.00 0.00 1.94
3576 4086 0.913451 AGCCTTGGTCATCCTCTGCT 60.913 55.000 0.00 0.00 34.23 4.24
3589 4143 2.577563 TCCTCTGCTTCAAATCCATGGA 59.422 45.455 18.88 18.88 0.00 3.41
3590 4144 3.010472 TCCTCTGCTTCAAATCCATGGAA 59.990 43.478 20.67 0.00 0.00 3.53
3591 4145 3.380637 CCTCTGCTTCAAATCCATGGAAG 59.619 47.826 20.67 12.39 40.69 3.46
3596 4150 4.634184 CTTCAAATCCATGGAAGCAGAG 57.366 45.455 20.67 10.66 32.54 3.35
3597 4151 4.267536 CTTCAAATCCATGGAAGCAGAGA 58.732 43.478 20.67 8.43 32.54 3.10
3598 4152 3.882444 TCAAATCCATGGAAGCAGAGAG 58.118 45.455 20.67 3.42 0.00 3.20
3615 4755 1.811359 AGAGCTTTCTGTTGCTGCATC 59.189 47.619 1.84 2.97 39.91 3.91
3694 4834 4.373116 TTGGAGCGGTGCCTCGAC 62.373 66.667 2.94 0.00 32.57 4.20
3748 4888 1.385743 GCATTACTCGACGTGTGTGAC 59.614 52.381 12.54 4.98 0.00 3.67
3749 4889 2.657184 CATTACTCGACGTGTGTGACA 58.343 47.619 12.54 0.00 0.00 3.58
3762 4902 4.612712 CGTGTGTGACACCCATATTTCAAC 60.613 45.833 13.85 0.00 45.93 3.18
3763 4903 4.277174 GTGTGTGACACCCATATTTCAACA 59.723 41.667 13.85 0.00 43.05 3.33
3764 4904 4.518590 TGTGTGACACCCATATTTCAACAG 59.481 41.667 13.85 0.00 32.73 3.16
3765 4905 4.518970 GTGTGACACCCATATTTCAACAGT 59.481 41.667 3.92 0.00 0.00 3.55
3766 4906 4.518590 TGTGACACCCATATTTCAACAGTG 59.481 41.667 2.45 0.00 0.00 3.66
3767 4907 4.518970 GTGACACCCATATTTCAACAGTGT 59.481 41.667 0.00 0.00 39.53 3.55
3768 4908 5.009610 GTGACACCCATATTTCAACAGTGTT 59.990 40.000 1.64 1.64 37.13 3.32
3769 4909 5.596361 TGACACCCATATTTCAACAGTGTTT 59.404 36.000 5.57 0.00 37.13 2.83
3770 4910 5.841810 ACACCCATATTTCAACAGTGTTTG 58.158 37.500 5.57 0.77 33.42 2.93
3771 4911 4.685628 CACCCATATTTCAACAGTGTTTGC 59.314 41.667 5.57 0.00 0.00 3.68
3772 4912 3.919804 CCCATATTTCAACAGTGTTTGCG 59.080 43.478 5.57 0.00 0.00 4.85
3773 4913 4.320861 CCCATATTTCAACAGTGTTTGCGA 60.321 41.667 5.57 0.00 0.00 5.10
3774 4914 4.616802 CCATATTTCAACAGTGTTTGCGAC 59.383 41.667 5.57 0.00 0.00 5.19
3825 4965 7.509141 TGATTCACTGAAATACTTTGAGCAA 57.491 32.000 0.00 0.00 0.00 3.91
3896 5049 2.479566 ACACTTCCGCATGTTCAGAT 57.520 45.000 0.00 0.00 0.00 2.90
3949 5102 8.341892 TCATTGTGTTATTTACATAGGCAACA 57.658 30.769 0.00 0.00 39.39 3.33
4010 5168 2.927477 CTGTCCATCAATGCAATGCAAC 59.073 45.455 13.45 4.36 43.62 4.17
4018 5176 6.183360 CCATCAATGCAATGCAACTCTAGTTA 60.183 38.462 13.45 0.00 43.62 2.24
4038 5196 0.041833 TGAGAGGAGTTGGCCTAGCT 59.958 55.000 3.32 0.00 38.73 3.32
4105 5263 9.709495 ATGTACACATATTGTTGCTGAAATTTT 57.291 25.926 0.00 0.00 39.91 1.82
4137 5295 9.278978 TGTGATAAGTTGTAATCTGCTAACAAA 57.721 29.630 0.00 0.00 35.08 2.83
4203 5361 3.126831 GTTTCGGCTGTGATCCTCATAG 58.873 50.000 0.00 0.00 38.45 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 7.801716 AAATATATTCCGCAGAAAGCACTAA 57.198 32.000 0.00 0.00 46.13 2.24
10 11 7.041372 GGAAAATATATTCCGCAGAAAGCACTA 60.041 37.037 0.00 0.00 46.13 2.74
28 29 5.300752 ACGAGATCGCTGAATGGAAAATAT 58.699 37.500 1.39 0.00 44.43 1.28
30 31 3.535561 ACGAGATCGCTGAATGGAAAAT 58.464 40.909 1.39 0.00 44.43 1.82
138 139 0.181350 CCTCCATGTAGCTCCCCAAC 59.819 60.000 0.00 0.00 0.00 3.77
139 140 1.635817 GCCTCCATGTAGCTCCCCAA 61.636 60.000 0.00 0.00 0.00 4.12
169 170 2.393764 GGATCAAAACAAACAGGCACG 58.606 47.619 0.00 0.00 0.00 5.34
180 181 5.516090 TCACAAAAGCTTACGGATCAAAAC 58.484 37.500 0.00 0.00 0.00 2.43
215 224 4.222366 TGCATGAAAATTTATGGCTCCACA 59.778 37.500 0.00 0.00 0.00 4.17
235 244 6.922957 GGACTTCAAGTTCACAAATTTATGCA 59.077 34.615 0.00 0.00 0.00 3.96
279 288 1.197721 GGAGCACAATCAAACTCACGG 59.802 52.381 0.00 0.00 0.00 4.94
376 386 3.664107 TCCAGAGAAGTTTGTTCATCCG 58.336 45.455 0.00 0.00 0.00 4.18
414 424 7.286215 AGTAGCTCTAGTAGTCTAGTCTCAG 57.714 44.000 0.00 0.00 42.88 3.35
436 446 1.856539 TTCCGGACGGAGGGAGTAGT 61.857 60.000 13.64 0.00 46.06 2.73
437 447 0.682209 TTTCCGGACGGAGGGAGTAG 60.682 60.000 13.64 0.00 46.06 2.57
438 448 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
439 449 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
440 450 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
441 451 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
442 452 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
443 453 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
444 454 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
445 455 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
446 456 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
447 457 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
448 458 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
449 459 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
450 460 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
451 461 8.915871 ATTCATTTTGATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 37.32 4.30
458 468 8.096414 CCCCTTTTATTCATTTTGATGACAAGT 58.904 33.333 0.00 0.00 37.32 3.16
459 469 8.313292 TCCCCTTTTATTCATTTTGATGACAAG 58.687 33.333 0.00 0.00 37.32 3.16
460 470 8.200024 TCCCCTTTTATTCATTTTGATGACAA 57.800 30.769 0.00 0.00 0.00 3.18
461 471 7.789202 TCCCCTTTTATTCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
462 472 8.260114 ACATCCCCTTTTATTCATTTTGATGAC 58.740 33.333 0.00 0.00 32.39 3.06
463 473 8.378115 ACATCCCCTTTTATTCATTTTGATGA 57.622 30.769 0.00 0.00 32.39 2.92
466 476 9.713684 AGATACATCCCCTTTTATTCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
471 481 9.170890 TGTCTAGATACATCCCCTTTTATTCAT 57.829 33.333 0.00 0.00 0.00 2.57
472 482 8.561536 TGTCTAGATACATCCCCTTTTATTCA 57.438 34.615 0.00 0.00 0.00 2.57
480 490 9.845214 ACTAAAATATGTCTAGATACATCCCCT 57.155 33.333 0.00 0.00 40.52 4.79
504 514 9.225682 TGGATAAAAAGGGATGTATCTAGAACT 57.774 33.333 0.00 0.00 0.00 3.01
510 520 9.713684 TCAAAATGGATAAAAAGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
513 523 9.486123 TCATCAAAATGGATAAAAAGGGATGTA 57.514 29.630 0.00 0.00 33.42 2.29
514 524 8.260114 GTCATCAAAATGGATAAAAAGGGATGT 58.740 33.333 0.00 0.00 33.42 3.06
515 525 8.259411 TGTCATCAAAATGGATAAAAAGGGATG 58.741 33.333 0.00 0.00 33.42 3.51
516 526 8.378115 TGTCATCAAAATGGATAAAAAGGGAT 57.622 30.769 0.00 0.00 33.42 3.85
517 527 7.789202 TGTCATCAAAATGGATAAAAAGGGA 57.211 32.000 0.00 0.00 33.42 4.20
518 528 8.096414 ACTTGTCATCAAAATGGATAAAAAGGG 58.904 33.333 0.00 0.00 33.42 3.95
526 536 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
527 537 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
528 538 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
529 539 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
530 540 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
531 541 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
532 542 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
533 543 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
534 544 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
535 545 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
536 546 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
537 547 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
538 548 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
539 549 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
540 550 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
541 551 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
542 552 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
543 553 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
544 554 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
545 555 1.479730 GTACTCCCTCCGTCCGAAAAT 59.520 52.381 0.00 0.00 0.00 1.82
546 556 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
547 557 0.251297 TGTACTCCCTCCGTCCGAAA 60.251 55.000 0.00 0.00 0.00 3.46
548 558 0.251297 TTGTACTCCCTCCGTCCGAA 60.251 55.000 0.00 0.00 0.00 4.30
549 559 0.033796 ATTGTACTCCCTCCGTCCGA 60.034 55.000 0.00 0.00 0.00 4.55
550 560 0.822164 AATTGTACTCCCTCCGTCCG 59.178 55.000 0.00 0.00 0.00 4.79
551 561 4.081254 AGTTAAATTGTACTCCCTCCGTCC 60.081 45.833 0.00 0.00 0.00 4.79
552 562 4.868734 CAGTTAAATTGTACTCCCTCCGTC 59.131 45.833 0.00 0.00 0.00 4.79
553 563 4.285260 ACAGTTAAATTGTACTCCCTCCGT 59.715 41.667 0.00 0.00 0.00 4.69
554 564 4.630069 CACAGTTAAATTGTACTCCCTCCG 59.370 45.833 0.00 0.00 0.00 4.63
555 565 5.557866 ACACAGTTAAATTGTACTCCCTCC 58.442 41.667 0.00 0.00 0.00 4.30
556 566 6.072673 CCAACACAGTTAAATTGTACTCCCTC 60.073 42.308 0.00 0.00 0.00 4.30
557 567 5.768164 CCAACACAGTTAAATTGTACTCCCT 59.232 40.000 0.00 0.00 0.00 4.20
558 568 5.766174 TCCAACACAGTTAAATTGTACTCCC 59.234 40.000 0.00 0.00 0.00 4.30
559 569 6.293790 GGTCCAACACAGTTAAATTGTACTCC 60.294 42.308 0.00 0.00 0.00 3.85
560 570 6.261381 TGGTCCAACACAGTTAAATTGTACTC 59.739 38.462 0.00 0.00 0.00 2.59
561 571 6.123651 TGGTCCAACACAGTTAAATTGTACT 58.876 36.000 0.00 0.00 0.00 2.73
562 572 6.380095 TGGTCCAACACAGTTAAATTGTAC 57.620 37.500 0.00 0.00 0.00 2.90
563 573 6.207810 GGATGGTCCAACACAGTTAAATTGTA 59.792 38.462 0.00 0.00 36.28 2.41
566 576 5.243730 CAGGATGGTCCAACACAGTTAAATT 59.756 40.000 0.00 0.00 39.61 1.82
607 617 2.511900 TGGGAAACGACACCCCAC 59.488 61.111 11.49 0.00 44.67 4.61
795 983 7.432869 CAAAGGGTTCTTTCAATGATGTAACA 58.567 34.615 0.00 0.00 40.92 2.41
865 1053 5.351233 TGCATGTAACAAGTAAGAAACGG 57.649 39.130 0.00 0.00 0.00 4.44
866 1054 5.283717 GCATGCATGTAACAAGTAAGAAACG 59.716 40.000 26.79 0.00 0.00 3.60
875 1063 6.947903 TTACAATTGCATGCATGTAACAAG 57.052 33.333 29.83 22.54 35.28 3.16
893 1081 7.095102 GGTTCTTCAGGTACGCTTATTTTACAA 60.095 37.037 0.00 0.00 0.00 2.41
904 1092 2.490903 TCTACAGGTTCTTCAGGTACGC 59.509 50.000 0.00 0.00 0.00 4.42
919 1107 7.121168 TGAGGCAAAATCCATAAACTTCTACAG 59.879 37.037 0.00 0.00 0.00 2.74
1111 1585 2.376808 AGCTCATCAACTTCGACCAG 57.623 50.000 0.00 0.00 0.00 4.00
1128 1602 2.935201 CAACTCATCACCTTGAGCTAGC 59.065 50.000 6.62 6.62 45.75 3.42
1491 1980 5.363005 ACCAGTATATCTGTAACGCCTCTTT 59.637 40.000 0.00 0.00 42.19 2.52
1656 2145 3.446161 CCTCCATTGCATCAACATCAACT 59.554 43.478 0.00 0.00 0.00 3.16
1830 2319 6.369059 AGCATTCTTCGATGTAATTTCCAG 57.631 37.500 0.00 0.00 0.00 3.86
2349 2838 3.795688 TTTTTCCAGTCCTCAGCTGAT 57.204 42.857 18.63 0.00 36.12 2.90
2752 3241 3.806949 TTTCCCTTGTTCAGCATAGGT 57.193 42.857 0.00 0.00 0.00 3.08
2824 3316 0.322816 TCTTGAAGGCCATCACCAGC 60.323 55.000 10.89 0.00 0.00 4.85
3045 3540 5.123936 GTTCCTGCGGAAAATATAGAGGTT 58.876 41.667 10.87 0.00 43.86 3.50
3114 3612 2.202623 ACGAGCGCTTCCACGATC 60.203 61.111 21.19 1.08 44.58 3.69
3242 3740 1.739562 CTCACAGGCGCCAGAAGAC 60.740 63.158 31.54 0.00 0.00 3.01
3251 3749 1.308998 AAAAAGACCACTCACAGGCG 58.691 50.000 0.00 0.00 0.00 5.52
3266 3764 7.065563 TGCCTAAAACACGACTACAGTTAAAAA 59.934 33.333 0.00 0.00 0.00 1.94
3267 3765 6.538021 TGCCTAAAACACGACTACAGTTAAAA 59.462 34.615 0.00 0.00 0.00 1.52
3274 3772 3.319972 ACTCTGCCTAAAACACGACTACA 59.680 43.478 0.00 0.00 0.00 2.74
3283 3781 3.883489 AGTCCACAAACTCTGCCTAAAAC 59.117 43.478 0.00 0.00 0.00 2.43
3352 3852 4.217983 AGGAGTTAACAGAGTTCTACACGG 59.782 45.833 8.61 0.00 0.00 4.94
3441 3947 2.230992 GCTTGCACATACACATCCCAAA 59.769 45.455 0.00 0.00 0.00 3.28
3457 3963 0.039617 TGGCACATTACGTTGCTTGC 60.040 50.000 9.61 6.63 0.00 4.01
3473 3983 3.443045 CACAATCCACCGGCTGGC 61.443 66.667 12.89 0.00 40.39 4.85
3561 4071 3.507162 TTTGAAGCAGAGGATGACCAA 57.493 42.857 0.00 0.00 38.94 3.67
3565 4075 4.204799 CATGGATTTGAAGCAGAGGATGA 58.795 43.478 0.00 0.00 0.00 2.92
3576 4086 4.267536 CTCTCTGCTTCCATGGATTTGAA 58.732 43.478 17.06 2.82 0.00 2.69
3591 4145 1.197264 CAGCAACAGAAAGCTCTCTGC 59.803 52.381 17.14 4.27 45.72 4.26
3593 4147 1.202734 TGCAGCAACAGAAAGCTCTCT 60.203 47.619 0.00 0.00 39.50 3.10
3594 4148 1.233019 TGCAGCAACAGAAAGCTCTC 58.767 50.000 0.00 0.00 39.50 3.20
3595 4149 1.811359 GATGCAGCAACAGAAAGCTCT 59.189 47.619 0.00 0.00 39.50 4.09
3596 4150 1.465354 CGATGCAGCAACAGAAAGCTC 60.465 52.381 1.53 0.00 39.50 4.09
3597 4151 0.520404 CGATGCAGCAACAGAAAGCT 59.480 50.000 1.53 0.00 42.94 3.74
3598 4152 0.518636 TCGATGCAGCAACAGAAAGC 59.481 50.000 1.53 0.00 0.00 3.51
3600 4154 3.567530 CATTTCGATGCAGCAACAGAAA 58.432 40.909 19.09 19.09 33.08 2.52
3602 4156 1.469703 CCATTTCGATGCAGCAACAGA 59.530 47.619 1.53 0.00 0.00 3.41
3615 4755 7.306749 CCTGTCTTTTCAAAATCAACCATTTCG 60.307 37.037 0.00 0.00 33.16 3.46
3748 4888 4.685628 GCAAACACTGTTGAAATATGGGTG 59.314 41.667 0.00 0.00 0.00 4.61
3749 4889 4.558496 CGCAAACACTGTTGAAATATGGGT 60.558 41.667 0.00 0.00 0.00 4.51
3762 4902 1.845809 GCCCTCTGTCGCAAACACTG 61.846 60.000 0.00 0.00 33.24 3.66
3763 4903 1.598130 GCCCTCTGTCGCAAACACT 60.598 57.895 0.00 0.00 33.24 3.55
3764 4904 2.946762 GCCCTCTGTCGCAAACAC 59.053 61.111 0.00 0.00 33.24 3.32
3765 4905 2.664851 CGCCCTCTGTCGCAAACA 60.665 61.111 0.00 0.00 36.18 2.83
3771 4911 2.584418 CATGAGCGCCCTCTGTCG 60.584 66.667 2.29 0.00 38.93 4.35
3772 4912 1.227205 CTCATGAGCGCCCTCTGTC 60.227 63.158 10.38 0.00 38.93 3.51
3773 4913 1.986757 ACTCATGAGCGCCCTCTGT 60.987 57.895 22.83 0.00 38.93 3.41
3774 4914 1.521010 CACTCATGAGCGCCCTCTG 60.521 63.158 22.83 7.70 38.93 3.35
3796 4936 6.486320 TCAAAGTATTTCAGTGAATCAGCACA 59.514 34.615 6.36 0.00 37.45 4.57
3797 4937 6.902341 TCAAAGTATTTCAGTGAATCAGCAC 58.098 36.000 6.36 1.18 35.03 4.40
4010 5168 4.038642 GGCCAACTCCTCTCATAACTAGAG 59.961 50.000 0.00 0.00 40.21 2.43
4018 5176 1.127343 GCTAGGCCAACTCCTCTCAT 58.873 55.000 5.01 0.00 37.66 2.90
4038 5196 1.401409 GCGCATGCAAAAGCAACTAGA 60.401 47.619 19.57 0.00 42.15 2.43
4105 5263 6.371548 GCAGATTACAACTTATCACACCAAGA 59.628 38.462 0.00 0.00 0.00 3.02
4160 5318 4.777896 ACAAGATCTTAGTACCAGGAGCAA 59.222 41.667 7.86 0.00 0.00 3.91
4174 5332 3.126001 TCACAGCCGAAACAAGATCTT 57.874 42.857 0.88 0.88 0.00 2.40


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

AutoCloner maintained by Alex Coulton.