Multiple sequence alignment - TraesCS3D01G487600

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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 TraesCS3D01G487600 chr3D 100.000 3209 0 0 1 3209 582878845 582882053 0.000000e+00 5927
1 TraesCS3D01G487600 chr3D 85.586 222 28 3 205 426 582849407 582849624 2.490000e-56 230
2 TraesCS3D01G487600 chr3B 95.305 1427 49 6 609 2017 778343312 778341886 0.000000e+00 2248
3 TraesCS3D01G487600 chr3B 95.417 1200 35 7 2019 3209 778341932 778340744 0.000000e+00 1893
4 TraesCS3D01G487600 chr3B 91.818 440 28 2 1 440 778343756 778343325 9.850000e-170 606
5 TraesCS3D01G487600 chr6B 89.286 1148 84 18 2019 3150 16339950 16341074 0.000000e+00 1402
6 TraesCS3D01G487600 chr6B 92.969 768 49 4 2384 3150 52979754 52978991 0.000000e+00 1114
7 TraesCS3D01G487600 chr6B 85.880 1034 137 3 983 2016 16237292 16238316 0.000000e+00 1092
8 TraesCS3D01G487600 chr6B 87.289 889 111 2 1130 2017 15715092 15714205 0.000000e+00 1014
9 TraesCS3D01G487600 chr6B 84.029 958 112 27 2019 2952 16238271 16239211 0.000000e+00 883
10 TraesCS3D01G487600 chr6B 87.776 769 48 22 2023 2759 15263332 15262578 0.000000e+00 857
11 TraesCS3D01G487600 chr6B 86.667 525 60 7 2633 3150 670590756 670590235 9.990000e-160 573
12 TraesCS3D01G487600 chr6B 80.577 762 104 19 2460 3209 16435082 16435811 6.050000e-152 547
13 TraesCS3D01G487600 chr6B 88.161 397 45 2 2019 2414 15233886 15233491 3.750000e-129 472
14 TraesCS3D01G487600 chr6B 87.657 397 46 3 2019 2414 16268334 16268728 2.920000e-125 459
15 TraesCS3D01G487600 chr6B 82.494 417 45 15 2028 2429 15215892 15215489 1.100000e-89 340
16 TraesCS3D01G487600 chr6B 76.482 523 70 24 2710 3209 90942001 90942493 5.350000e-58 235
17 TraesCS3D01G487600 chr6D 85.343 1078 130 20 947 2017 33894995 33896051 0.000000e+00 1090
18 TraesCS3D01G487600 chr6D 84.906 954 130 6 1058 2004 8578870 8577924 0.000000e+00 952
19 TraesCS3D01G487600 chr6D 81.866 761 100 17 2460 3209 8550862 8550129 9.850000e-170 606
20 TraesCS3D01G487600 chr6D 84.075 427 49 10 2019 2429 8551830 8551407 8.340000e-106 394
21 TraesCS3D01G487600 chr6A 84.215 1077 148 14 940 2004 30560630 30559564 0.000000e+00 1027
22 TraesCS3D01G487600 chr6A 87.402 889 111 1 1129 2017 9040185 9039298 0.000000e+00 1020
23 TraesCS3D01G487600 chr6A 82.665 698 88 19 2460 3150 9357028 9357699 3.570000e-164 588
24 TraesCS3D01G487600 chr6A 83.455 411 54 5 2799 3209 9475897 9476293 1.410000e-98 370
25 TraesCS3D01G487600 chr2B 84.653 1023 135 17 990 2004 89499946 89500954 0.000000e+00 1000
26 TraesCS3D01G487600 chr2B 83.365 1058 156 16 960 2004 89494577 89495627 0.000000e+00 961
27 TraesCS3D01G487600 chr2B 85.167 418 47 8 2023 2429 54015692 54015279 6.400000e-112 414
28 TraesCS3D01G487600 chr2B 84.689 418 49 8 2023 2429 54043044 54042631 1.390000e-108 403
29 TraesCS3D01G487600 chr5D 88.970 689 64 11 2460 3145 499863106 499862427 0.000000e+00 841
30 TraesCS3D01G487600 chr5D 86.250 400 43 7 2021 2409 42077023 42077421 1.060000e-114 424
31 TraesCS3D01G487600 chr5D 83.810 420 56 5 2021 2429 499864111 499863693 3.880000e-104 388
32 TraesCS3D01G487600 chr5A 87.826 690 71 12 2460 3145 624203854 624203174 0.000000e+00 797
33 TraesCS3D01G487600 chr5A 84.504 413 55 7 2021 2429 624204734 624204327 1.790000e-107 399
34 TraesCS3D01G487600 chr5B 88.431 631 57 14 2460 3085 621236410 621235791 0.000000e+00 747
35 TraesCS3D01G487600 chr5B 86.911 382 41 7 2460 2834 556624598 556624219 1.380000e-113 420
36 TraesCS3D01G487600 chr5B 83.803 426 51 9 2021 2429 621237309 621236885 3.880000e-104 388
37 TraesCS3D01G487600 chrUn 86.207 435 35 7 2796 3209 95439808 95440238 6.310000e-122 448
38 TraesCS3D01G487600 chr2A 86.301 219 26 3 2930 3145 12834687 12834904 5.350000e-58 235


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 TraesCS3D01G487600 chr3D 582878845 582882053 3208 False 5927.000000 5927 100.0000 1 3209 1 chr3D.!!$F2 3208
1 TraesCS3D01G487600 chr3B 778340744 778343756 3012 True 1582.333333 2248 94.1800 1 3209 3 chr3B.!!$R1 3208
2 TraesCS3D01G487600 chr6B 16339950 16341074 1124 False 1402.000000 1402 89.2860 2019 3150 1 chr6B.!!$F2 1131
3 TraesCS3D01G487600 chr6B 52978991 52979754 763 True 1114.000000 1114 92.9690 2384 3150 1 chr6B.!!$R5 766
4 TraesCS3D01G487600 chr6B 15714205 15715092 887 True 1014.000000 1014 87.2890 1130 2017 1 chr6B.!!$R4 887
5 TraesCS3D01G487600 chr6B 16237292 16239211 1919 False 987.500000 1092 84.9545 983 2952 2 chr6B.!!$F5 1969
6 TraesCS3D01G487600 chr6B 15262578 15263332 754 True 857.000000 857 87.7760 2023 2759 1 chr6B.!!$R3 736
7 TraesCS3D01G487600 chr6B 670590235 670590756 521 True 573.000000 573 86.6670 2633 3150 1 chr6B.!!$R6 517
8 TraesCS3D01G487600 chr6B 16435082 16435811 729 False 547.000000 547 80.5770 2460 3209 1 chr6B.!!$F3 749
9 TraesCS3D01G487600 chr6D 33894995 33896051 1056 False 1090.000000 1090 85.3430 947 2017 1 chr6D.!!$F1 1070
10 TraesCS3D01G487600 chr6D 8577924 8578870 946 True 952.000000 952 84.9060 1058 2004 1 chr6D.!!$R1 946
11 TraesCS3D01G487600 chr6D 8550129 8551830 1701 True 500.000000 606 82.9705 2019 3209 2 chr6D.!!$R2 1190
12 TraesCS3D01G487600 chr6A 30559564 30560630 1066 True 1027.000000 1027 84.2150 940 2004 1 chr6A.!!$R2 1064
13 TraesCS3D01G487600 chr6A 9039298 9040185 887 True 1020.000000 1020 87.4020 1129 2017 1 chr6A.!!$R1 888
14 TraesCS3D01G487600 chr6A 9357028 9357699 671 False 588.000000 588 82.6650 2460 3150 1 chr6A.!!$F1 690
15 TraesCS3D01G487600 chr2B 89499946 89500954 1008 False 1000.000000 1000 84.6530 990 2004 1 chr2B.!!$F2 1014
16 TraesCS3D01G487600 chr2B 89494577 89495627 1050 False 961.000000 961 83.3650 960 2004 1 chr2B.!!$F1 1044
17 TraesCS3D01G487600 chr5D 499862427 499864111 1684 True 614.500000 841 86.3900 2021 3145 2 chr5D.!!$R1 1124
18 TraesCS3D01G487600 chr5A 624203174 624204734 1560 True 598.000000 797 86.1650 2021 3145 2 chr5A.!!$R1 1124
19 TraesCS3D01G487600 chr5B 621235791 621237309 1518 True 567.500000 747 86.1170 2021 3085 2 chr5B.!!$R2 1064

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
472 473 0.037232 GGCAGCTGGTATCCGGTATC 60.037 60.0 17.12 0.0 31.34 2.24 F
689 690 0.165944 CATCGCCAAAGTTGTCGACC 59.834 55.0 14.12 0.0 33.59 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2074 2109 1.538950 CTCAGCCTCCTTGAAAACAGC 59.461 52.381 0.00 0.0 0.00 4.40 R
2424 2491 1.997874 GTGAGCCCTCCTCCATGGT 60.998 63.158 12.58 0.0 39.98 3.55 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
51 52 2.415608 GCAGATCTCCCCGACGACA 61.416 63.158 0.00 0.00 0.00 4.35
56 57 3.307906 CTCCCCGACGACACCCAA 61.308 66.667 0.00 0.00 0.00 4.12
147 148 3.726144 AGCTGCCCCTCCAGAAGC 61.726 66.667 0.00 0.00 34.77 3.86
169 170 3.679755 GGATCCCCTTGGCTCCAT 58.320 61.111 0.00 0.00 44.90 3.41
170 171 1.458045 GGATCCCCTTGGCTCCATC 59.542 63.158 0.00 0.00 44.90 3.51
171 172 1.355718 GGATCCCCTTGGCTCCATCA 61.356 60.000 0.00 0.00 44.90 3.07
172 173 0.179006 GATCCCCTTGGCTCCATCAC 60.179 60.000 0.00 0.00 0.00 3.06
173 174 0.920763 ATCCCCTTGGCTCCATCACA 60.921 55.000 0.00 0.00 0.00 3.58
174 175 1.139498 TCCCCTTGGCTCCATCACAA 61.139 55.000 0.00 0.00 0.00 3.33
204 205 2.202987 GCTCCTCGCCACCATCTG 60.203 66.667 0.00 0.00 0.00 2.90
228 229 1.697432 TCGACCAAAAGGACATCCAGT 59.303 47.619 0.00 0.00 38.89 4.00
257 258 3.635331 CTCAAACTGCAGGACAATGTTG 58.365 45.455 19.93 9.90 0.00 3.33
274 275 8.232913 ACAATGTTGAGTAACTAAAACCACAT 57.767 30.769 0.00 0.00 37.68 3.21
278 279 7.276658 TGTTGAGTAACTAAAACCACATGAGA 58.723 34.615 0.00 0.00 37.68 3.27
290 291 4.119862 ACCACATGAGAAAATACGATCGG 58.880 43.478 20.98 1.23 0.00 4.18
320 321 4.731773 GCTGGCTTTACCTTTTGATCGATG 60.732 45.833 0.54 0.00 40.22 3.84
330 331 3.616956 TTTGATCGATGAAGTGAGCCT 57.383 42.857 0.54 0.00 0.00 4.58
413 414 0.957395 TCCTCGTCCACGTACTCCAC 60.957 60.000 0.00 0.00 40.80 4.02
432 433 1.226435 GATGACGAGCGAGCGACTT 60.226 57.895 4.36 0.00 34.83 3.01
440 441 2.278857 CGAGCGACTTCGGGATGG 60.279 66.667 0.02 0.00 40.23 3.51
441 442 2.771639 CGAGCGACTTCGGGATGGA 61.772 63.158 0.02 0.00 40.23 3.41
444 445 0.757188 AGCGACTTCGGGATGGAGAT 60.757 55.000 0.02 0.00 40.23 2.75
445 446 0.105039 GCGACTTCGGGATGGAGATT 59.895 55.000 0.02 0.00 40.23 2.40
446 447 1.870167 GCGACTTCGGGATGGAGATTC 60.870 57.143 0.02 0.00 40.23 2.52
449 450 2.695666 GACTTCGGGATGGAGATTCAGA 59.304 50.000 0.00 0.00 0.00 3.27
452 453 4.164988 ACTTCGGGATGGAGATTCAGATTT 59.835 41.667 0.00 0.00 0.00 2.17
453 454 4.077300 TCGGGATGGAGATTCAGATTTG 57.923 45.455 0.00 0.00 0.00 2.32
454 455 3.144506 CGGGATGGAGATTCAGATTTGG 58.855 50.000 0.00 0.00 0.00 3.28
455 456 2.889678 GGGATGGAGATTCAGATTTGGC 59.110 50.000 0.00 0.00 0.00 4.52
456 457 3.559069 GGATGGAGATTCAGATTTGGCA 58.441 45.455 0.00 0.00 0.00 4.92
457 458 3.568853 GGATGGAGATTCAGATTTGGCAG 59.431 47.826 0.00 0.00 0.00 4.85
458 459 2.372264 TGGAGATTCAGATTTGGCAGC 58.628 47.619 0.00 0.00 0.00 5.25
459 460 2.025605 TGGAGATTCAGATTTGGCAGCT 60.026 45.455 0.00 0.00 0.00 4.24
460 461 2.358267 GGAGATTCAGATTTGGCAGCTG 59.642 50.000 10.11 10.11 0.00 4.24
461 462 2.358267 GAGATTCAGATTTGGCAGCTGG 59.642 50.000 17.12 0.00 0.00 4.85
462 463 2.097825 GATTCAGATTTGGCAGCTGGT 58.902 47.619 17.12 4.36 0.00 4.00
463 464 2.877097 TTCAGATTTGGCAGCTGGTA 57.123 45.000 17.12 0.00 0.00 3.25
464 465 3.370840 TTCAGATTTGGCAGCTGGTAT 57.629 42.857 17.12 0.00 0.00 2.73
465 466 2.923121 TCAGATTTGGCAGCTGGTATC 58.077 47.619 17.12 0.00 0.00 2.24
466 467 1.952296 CAGATTTGGCAGCTGGTATCC 59.048 52.381 17.12 8.57 0.00 2.59
467 468 0.947244 GATTTGGCAGCTGGTATCCG 59.053 55.000 17.12 0.00 0.00 4.18
468 469 0.466189 ATTTGGCAGCTGGTATCCGG 60.466 55.000 17.12 0.00 0.00 5.14
469 470 1.847798 TTTGGCAGCTGGTATCCGGT 61.848 55.000 17.12 0.00 31.34 5.28
470 471 0.978667 TTGGCAGCTGGTATCCGGTA 60.979 55.000 17.12 0.00 31.34 4.02
471 472 0.762842 TGGCAGCTGGTATCCGGTAT 60.763 55.000 17.12 0.00 31.34 2.73
472 473 0.037232 GGCAGCTGGTATCCGGTATC 60.037 60.000 17.12 0.00 31.34 2.24
473 474 0.969894 GCAGCTGGTATCCGGTATCT 59.030 55.000 17.12 0.00 31.34 1.98
474 475 1.344763 GCAGCTGGTATCCGGTATCTT 59.655 52.381 17.12 0.00 31.34 2.40
475 476 2.561419 GCAGCTGGTATCCGGTATCTTA 59.439 50.000 17.12 0.00 31.34 2.10
476 477 3.195825 GCAGCTGGTATCCGGTATCTTAT 59.804 47.826 17.12 0.00 31.34 1.73
477 478 4.748892 CAGCTGGTATCCGGTATCTTATG 58.251 47.826 5.57 0.00 31.34 1.90
478 479 4.462834 CAGCTGGTATCCGGTATCTTATGA 59.537 45.833 5.57 0.00 31.34 2.15
479 480 5.047306 CAGCTGGTATCCGGTATCTTATGAA 60.047 44.000 5.57 0.00 31.34 2.57
480 481 5.186021 AGCTGGTATCCGGTATCTTATGAAG 59.814 44.000 0.00 0.00 31.34 3.02
481 482 5.185249 GCTGGTATCCGGTATCTTATGAAGA 59.815 44.000 0.00 0.00 35.53 2.87
483 484 7.579723 GCTGGTATCCGGTATCTTATGAAGATT 60.580 40.741 0.00 0.00 46.77 2.40
484 485 7.837863 TGGTATCCGGTATCTTATGAAGATTC 58.162 38.462 0.00 2.67 45.75 2.52
485 486 7.453439 TGGTATCCGGTATCTTATGAAGATTCA 59.547 37.037 0.00 0.00 45.75 2.57
486 487 7.976734 GGTATCCGGTATCTTATGAAGATTCAG 59.023 40.741 0.00 3.63 45.75 3.02
487 488 7.782897 ATCCGGTATCTTATGAAGATTCAGA 57.217 36.000 0.00 4.33 45.75 3.27
488 489 7.782897 TCCGGTATCTTATGAAGATTCAGAT 57.217 36.000 0.00 2.05 45.75 2.90
489 490 8.195165 TCCGGTATCTTATGAAGATTCAGATT 57.805 34.615 0.00 0.00 45.75 2.40
490 491 8.651389 TCCGGTATCTTATGAAGATTCAGATTT 58.349 33.333 0.00 0.00 45.75 2.17
491 492 8.930760 CCGGTATCTTATGAAGATTCAGATTTC 58.069 37.037 7.01 0.00 45.75 2.17
492 493 9.481340 CGGTATCTTATGAAGATTCAGATTTCA 57.519 33.333 7.01 0.00 45.75 2.69
524 525 9.628500 ATTTTCAGAGAGTTAAGTAGTTTGGTT 57.372 29.630 0.00 0.00 0.00 3.67
525 526 9.457436 TTTTCAGAGAGTTAAGTAGTTTGGTTT 57.543 29.630 0.00 0.00 0.00 3.27
526 527 9.457436 TTTCAGAGAGTTAAGTAGTTTGGTTTT 57.543 29.630 0.00 0.00 0.00 2.43
527 528 9.457436 TTCAGAGAGTTAAGTAGTTTGGTTTTT 57.543 29.630 0.00 0.00 0.00 1.94
551 552 8.481974 TTTGGGAAAACTAAACTAAAAACTGC 57.518 30.769 0.00 0.00 0.00 4.40
552 553 7.412853 TGGGAAAACTAAACTAAAAACTGCT 57.587 32.000 0.00 0.00 0.00 4.24
553 554 7.842982 TGGGAAAACTAAACTAAAAACTGCTT 58.157 30.769 0.00 0.00 0.00 3.91
554 555 8.315482 TGGGAAAACTAAACTAAAAACTGCTTT 58.685 29.630 0.00 0.00 0.00 3.51
555 556 8.600625 GGGAAAACTAAACTAAAAACTGCTTTG 58.399 33.333 0.00 0.00 0.00 2.77
556 557 8.114290 GGAAAACTAAACTAAAAACTGCTTTGC 58.886 33.333 0.00 0.00 0.00 3.68
557 558 8.771920 AAAACTAAACTAAAAACTGCTTTGCT 57.228 26.923 0.00 0.00 0.00 3.91
558 559 8.771920 AAACTAAACTAAAAACTGCTTTGCTT 57.228 26.923 0.00 0.00 0.00 3.91
559 560 7.987268 ACTAAACTAAAAACTGCTTTGCTTC 57.013 32.000 0.00 0.00 0.00 3.86
560 561 6.978659 ACTAAACTAAAAACTGCTTTGCTTCC 59.021 34.615 0.00 0.00 0.00 3.46
561 562 5.598416 AACTAAAAACTGCTTTGCTTCCT 57.402 34.783 0.00 0.00 0.00 3.36
562 563 5.598416 ACTAAAAACTGCTTTGCTTCCTT 57.402 34.783 0.00 0.00 0.00 3.36
563 564 5.977635 ACTAAAAACTGCTTTGCTTCCTTT 58.022 33.333 0.00 0.00 0.00 3.11
564 565 6.042777 ACTAAAAACTGCTTTGCTTCCTTTC 58.957 36.000 0.00 0.00 0.00 2.62
565 566 4.743057 AAAACTGCTTTGCTTCCTTTCT 57.257 36.364 0.00 0.00 0.00 2.52
566 567 3.722728 AACTGCTTTGCTTCCTTTCTG 57.277 42.857 0.00 0.00 0.00 3.02
567 568 1.959282 ACTGCTTTGCTTCCTTTCTGG 59.041 47.619 0.00 0.00 37.10 3.86
568 569 2.233271 CTGCTTTGCTTCCTTTCTGGA 58.767 47.619 0.00 0.00 44.51 3.86
569 570 2.824341 CTGCTTTGCTTCCTTTCTGGAT 59.176 45.455 0.00 0.00 45.68 3.41
570 571 2.821969 TGCTTTGCTTCCTTTCTGGATC 59.178 45.455 0.00 0.00 45.68 3.36
571 572 2.165234 GCTTTGCTTCCTTTCTGGATCC 59.835 50.000 4.20 4.20 45.68 3.36
572 573 2.113860 TTGCTTCCTTTCTGGATCCG 57.886 50.000 7.39 2.06 45.68 4.18
573 574 0.253044 TGCTTCCTTTCTGGATCCGG 59.747 55.000 15.09 15.09 45.68 5.14
574 575 1.098129 GCTTCCTTTCTGGATCCGGC 61.098 60.000 16.48 0.00 45.68 6.13
575 576 0.811616 CTTCCTTTCTGGATCCGGCG 60.812 60.000 16.48 0.00 45.68 6.46
576 577 2.203070 CCTTTCTGGATCCGGCGG 60.203 66.667 22.51 22.51 38.35 6.13
577 578 2.897350 CTTTCTGGATCCGGCGGC 60.897 66.667 23.83 8.24 0.00 6.53
578 579 4.483243 TTTCTGGATCCGGCGGCC 62.483 66.667 23.83 18.72 0.00 6.13
593 594 4.344865 GCCTCCCCCTTGCGACAA 62.345 66.667 0.00 0.00 0.00 3.18
594 595 2.045926 CCTCCCCCTTGCGACAAG 60.046 66.667 11.23 11.23 0.00 3.16
604 605 3.056328 GCGACAAGCCCTCCCAAC 61.056 66.667 0.00 0.00 40.81 3.77
605 606 2.359975 CGACAAGCCCTCCCAACC 60.360 66.667 0.00 0.00 0.00 3.77
606 607 2.035783 GACAAGCCCTCCCAACCC 59.964 66.667 0.00 0.00 0.00 4.11
607 608 2.780924 ACAAGCCCTCCCAACCCA 60.781 61.111 0.00 0.00 0.00 4.51
613 614 2.757077 CCTCCCAACCCACTCCAC 59.243 66.667 0.00 0.00 0.00 4.02
639 640 2.279073 CCTCTCGGTGCCCCTCTA 59.721 66.667 0.00 0.00 0.00 2.43
645 646 1.819632 CGGTGCCCCTCTATGTTGC 60.820 63.158 0.00 0.00 0.00 4.17
685 686 2.076863 ACTAGCATCGCCAAAGTTGTC 58.923 47.619 0.00 0.00 0.00 3.18
689 690 0.165944 CATCGCCAAAGTTGTCGACC 59.834 55.000 14.12 0.00 33.59 4.79
722 723 1.417592 GACAGCGCGAACATCACAG 59.582 57.895 12.10 0.00 0.00 3.66
744 745 4.400109 GTGCACCGCGTCTCGAGA 62.400 66.667 12.08 12.08 41.67 4.04
758 759 5.332707 CGTCTCGAGAAAATGATGTCACTA 58.667 41.667 18.55 0.00 0.00 2.74
826 827 7.405292 TGTTTGATCTATGTTTGGGAGATCTT 58.595 34.615 11.30 0.00 43.96 2.40
879 880 3.720818 AAAACAAAAACGCAAGCACAG 57.279 38.095 0.00 0.00 45.62 3.66
880 881 2.362169 AACAAAAACGCAAGCACAGT 57.638 40.000 0.00 0.00 45.62 3.55
886 892 4.886247 AAAACGCAAGCACAGTAAGTAA 57.114 36.364 0.00 0.00 45.62 2.24
923 929 2.426842 CCCCCAGCTAAAAAGAGAGG 57.573 55.000 0.00 0.00 0.00 3.69
926 932 2.308866 CCCCAGCTAAAAAGAGAGGGAA 59.691 50.000 1.62 0.00 36.09 3.97
1038 1057 0.542938 CCATCCTCGCCCATCTCCTA 60.543 60.000 0.00 0.00 0.00 2.94
1039 1058 0.605589 CATCCTCGCCCATCTCCTAC 59.394 60.000 0.00 0.00 0.00 3.18
1066 1085 4.767255 CAGCCACCTCTCCCGCAC 62.767 72.222 0.00 0.00 0.00 5.34
1099 1118 0.324183 CCTCCTCTCTGTCTCTGCCA 60.324 60.000 0.00 0.00 0.00 4.92
1818 1853 1.344114 GAGGTGGGCATTGCTTTTTCA 59.656 47.619 8.82 0.00 0.00 2.69
1882 1917 1.186200 CAGGTCCGAGTTCCTCATCA 58.814 55.000 0.00 0.00 30.91 3.07
1883 1918 1.550524 CAGGTCCGAGTTCCTCATCAA 59.449 52.381 0.00 0.00 30.91 2.57
2054 2089 5.266788 TCTCAAGGAAAATGGATTGCTCAT 58.733 37.500 0.00 0.00 29.97 2.90
2074 2109 1.154016 CGTGACCCGAGCTACAGTG 60.154 63.158 0.00 0.00 39.56 3.66
2145 2180 0.178981 ACAAGGAAGCTGCACCACAT 60.179 50.000 15.83 2.20 0.00 3.21
2179 2214 2.877097 TGATGCTGCTTGTAAAGGGA 57.123 45.000 0.00 0.00 46.35 4.20
2185 2220 2.623416 GCTGCTTGTAAAGGGAAACTGT 59.377 45.455 0.00 0.00 46.35 3.55
2236 2283 1.559682 ACGGGCTATGATCTGGTTGTT 59.440 47.619 0.00 0.00 0.00 2.83
2424 2491 9.591792 CATATTGAAACTAAGTGTGAGATCAGA 57.408 33.333 0.00 0.00 0.00 3.27
2543 3332 8.052748 ACCTATGTGCCTCTGTTCATTTTTATA 58.947 33.333 0.00 0.00 0.00 0.98
2578 3367 4.067896 TCAAGACAATGGAGAAGCACTTC 58.932 43.478 2.04 2.04 39.78 3.01
2747 3598 2.831526 GTGGGTAATTCTTGGTGCCAAT 59.168 45.455 3.91 0.00 35.20 3.16
2959 3824 4.668636 CAGGTTCTTAATTACAACCCCCA 58.331 43.478 16.91 0.00 40.56 4.96
2984 3849 6.149633 AGTATTCTTGTTTGTTCGAAATGCC 58.850 36.000 0.00 0.00 0.00 4.40
2990 3855 2.574212 GTTCGAAATGCCGCGCAG 60.574 61.111 8.75 0.00 43.65 5.18
2996 3861 0.937304 GAAATGCCGCGCAGAATCTA 59.063 50.000 8.75 0.00 43.65 1.98
3168 4034 7.053316 TCACAACCATGTTTGATCTGAAAAT 57.947 32.000 10.27 0.00 37.82 1.82
3173 4039 9.258826 CAACCATGTTTGATCTGAAAATACAAA 57.741 29.630 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 3.209812 TCGTCGGGGAGATCTGCG 61.210 66.667 8.26 0.00 0.00 5.18
51 52 2.195683 CTGGTGCACTGGTTGGGT 59.804 61.111 17.98 0.00 0.00 4.51
80 81 0.839277 CATGGGCCTAGTGGACATCA 59.161 55.000 4.53 0.00 45.45 3.07
102 103 2.048127 AGGTTCTTCTGCGGCGAC 60.048 61.111 12.98 2.02 0.00 5.19
105 106 2.461416 GAAGAGGTTCTTCTGCGGC 58.539 57.895 10.72 0.00 46.98 6.53
123 124 2.588989 GAGGGGCAGCTGAAGAGG 59.411 66.667 20.43 0.00 0.00 3.69
125 126 2.203983 TGGAGGGGCAGCTGAAGA 60.204 61.111 20.43 0.00 0.00 2.87
147 148 2.123982 GCCAAGGGGATCCTGCTG 60.124 66.667 12.58 6.14 44.07 4.41
168 169 4.268359 GAGCAGAAGAAGGGATTTGTGAT 58.732 43.478 0.00 0.00 0.00 3.06
169 170 3.560025 GGAGCAGAAGAAGGGATTTGTGA 60.560 47.826 0.00 0.00 0.00 3.58
170 171 2.751806 GGAGCAGAAGAAGGGATTTGTG 59.248 50.000 0.00 0.00 0.00 3.33
171 172 2.646798 AGGAGCAGAAGAAGGGATTTGT 59.353 45.455 0.00 0.00 0.00 2.83
172 173 3.277715 GAGGAGCAGAAGAAGGGATTTG 58.722 50.000 0.00 0.00 0.00 2.32
173 174 2.093235 CGAGGAGCAGAAGAAGGGATTT 60.093 50.000 0.00 0.00 0.00 2.17
174 175 1.484240 CGAGGAGCAGAAGAAGGGATT 59.516 52.381 0.00 0.00 0.00 3.01
204 205 1.464997 GATGTCCTTTTGGTCGACTGC 59.535 52.381 16.46 0.00 41.38 4.40
228 229 3.353836 GCAGTTTGAGCGGCCGAA 61.354 61.111 33.48 12.33 0.00 4.30
290 291 0.037232 AGGTAAAGCCAGCAGACGAC 60.037 55.000 0.00 0.00 40.61 4.34
320 321 0.179097 CCGGCTTCTAGGCTCACTTC 60.179 60.000 0.00 0.00 38.85 3.01
380 381 3.236003 GAGGACTTGAACGGGCCGT 62.236 63.158 28.83 28.83 43.97 5.68
382 383 2.434359 CGAGGACTTGAACGGGCC 60.434 66.667 0.00 0.00 0.00 5.80
413 414 2.904747 AAGTCGCTCGCTCGTCATCG 62.905 60.000 0.00 0.00 38.55 3.84
432 433 3.181451 CCAAATCTGAATCTCCATCCCGA 60.181 47.826 0.00 0.00 0.00 5.14
440 441 2.358267 CCAGCTGCCAAATCTGAATCTC 59.642 50.000 8.66 0.00 0.00 2.75
441 442 2.291411 ACCAGCTGCCAAATCTGAATCT 60.291 45.455 8.66 0.00 0.00 2.40
444 445 2.877097 TACCAGCTGCCAAATCTGAA 57.123 45.000 8.66 0.00 0.00 3.02
445 446 2.421952 GGATACCAGCTGCCAAATCTGA 60.422 50.000 8.66 0.00 0.00 3.27
446 447 1.952296 GGATACCAGCTGCCAAATCTG 59.048 52.381 8.66 0.00 0.00 2.90
449 450 0.466189 CCGGATACCAGCTGCCAAAT 60.466 55.000 8.66 0.00 0.00 2.32
452 453 0.762842 ATACCGGATACCAGCTGCCA 60.763 55.000 9.46 0.00 0.00 4.92
453 454 0.037232 GATACCGGATACCAGCTGCC 60.037 60.000 9.46 2.74 0.00 4.85
454 455 0.969894 AGATACCGGATACCAGCTGC 59.030 55.000 9.46 0.00 0.00 5.25
455 456 4.462834 TCATAAGATACCGGATACCAGCTG 59.537 45.833 9.46 6.78 0.00 4.24
456 457 4.673968 TCATAAGATACCGGATACCAGCT 58.326 43.478 9.46 0.00 0.00 4.24
457 458 5.185249 TCTTCATAAGATACCGGATACCAGC 59.815 44.000 9.46 0.00 31.20 4.85
458 459 6.835819 TCTTCATAAGATACCGGATACCAG 57.164 41.667 9.46 0.00 31.20 4.00
498 499 9.628500 AACCAAACTACTTAACTCTCTGAAAAT 57.372 29.630 0.00 0.00 0.00 1.82
499 500 9.457436 AAACCAAACTACTTAACTCTCTGAAAA 57.543 29.630 0.00 0.00 0.00 2.29
500 501 9.457436 AAAACCAAACTACTTAACTCTCTGAAA 57.543 29.630 0.00 0.00 0.00 2.69
501 502 9.457436 AAAAACCAAACTACTTAACTCTCTGAA 57.543 29.630 0.00 0.00 0.00 3.02
525 526 8.937884 GCAGTTTTTAGTTTAGTTTTCCCAAAA 58.062 29.630 0.00 0.00 0.00 2.44
526 527 8.315482 AGCAGTTTTTAGTTTAGTTTTCCCAAA 58.685 29.630 0.00 0.00 0.00 3.28
527 528 7.842982 AGCAGTTTTTAGTTTAGTTTTCCCAA 58.157 30.769 0.00 0.00 0.00 4.12
528 529 7.412853 AGCAGTTTTTAGTTTAGTTTTCCCA 57.587 32.000 0.00 0.00 0.00 4.37
529 530 8.600625 CAAAGCAGTTTTTAGTTTAGTTTTCCC 58.399 33.333 0.00 0.00 0.00 3.97
530 531 8.114290 GCAAAGCAGTTTTTAGTTTAGTTTTCC 58.886 33.333 0.00 0.00 0.00 3.13
531 532 8.869897 AGCAAAGCAGTTTTTAGTTTAGTTTTC 58.130 29.630 0.00 0.00 0.00 2.29
532 533 8.771920 AGCAAAGCAGTTTTTAGTTTAGTTTT 57.228 26.923 0.00 0.00 0.00 2.43
533 534 8.771920 AAGCAAAGCAGTTTTTAGTTTAGTTT 57.228 26.923 0.00 0.00 0.00 2.66
534 535 7.491372 GGAAGCAAAGCAGTTTTTAGTTTAGTT 59.509 33.333 0.00 0.00 0.00 2.24
535 536 6.978659 GGAAGCAAAGCAGTTTTTAGTTTAGT 59.021 34.615 0.00 0.00 0.00 2.24
536 537 7.203218 AGGAAGCAAAGCAGTTTTTAGTTTAG 58.797 34.615 0.00 0.00 0.00 1.85
537 538 7.107639 AGGAAGCAAAGCAGTTTTTAGTTTA 57.892 32.000 0.00 0.00 0.00 2.01
538 539 5.977635 AGGAAGCAAAGCAGTTTTTAGTTT 58.022 33.333 0.00 0.00 0.00 2.66
539 540 5.598416 AGGAAGCAAAGCAGTTTTTAGTT 57.402 34.783 0.00 0.00 0.00 2.24
540 541 5.598416 AAGGAAGCAAAGCAGTTTTTAGT 57.402 34.783 0.00 0.00 0.00 2.24
541 542 6.199719 CAGAAAGGAAGCAAAGCAGTTTTTAG 59.800 38.462 0.00 0.00 0.00 1.85
542 543 6.042143 CAGAAAGGAAGCAAAGCAGTTTTTA 58.958 36.000 0.00 0.00 0.00 1.52
543 544 4.872124 CAGAAAGGAAGCAAAGCAGTTTTT 59.128 37.500 0.00 0.00 0.00 1.94
544 545 4.436332 CAGAAAGGAAGCAAAGCAGTTTT 58.564 39.130 0.00 0.00 0.00 2.43
545 546 3.181472 CCAGAAAGGAAGCAAAGCAGTTT 60.181 43.478 0.00 0.00 41.22 2.66
546 547 2.363359 CCAGAAAGGAAGCAAAGCAGTT 59.637 45.455 0.00 0.00 41.22 3.16
547 548 1.959282 CCAGAAAGGAAGCAAAGCAGT 59.041 47.619 0.00 0.00 41.22 4.40
548 549 2.233271 TCCAGAAAGGAAGCAAAGCAG 58.767 47.619 0.00 0.00 45.65 4.24
549 550 2.363306 TCCAGAAAGGAAGCAAAGCA 57.637 45.000 0.00 0.00 45.65 3.91
559 560 2.203070 CCGCCGGATCCAGAAAGG 60.203 66.667 13.41 5.34 39.47 3.11
560 561 2.897350 GCCGCCGGATCCAGAAAG 60.897 66.667 7.68 0.00 0.00 2.62
561 562 4.483243 GGCCGCCGGATCCAGAAA 62.483 66.667 7.68 0.00 0.00 2.52
576 577 4.344865 TTGTCGCAAGGGGGAGGC 62.345 66.667 0.00 0.00 36.56 4.70
577 578 2.045926 CTTGTCGCAAGGGGGAGG 60.046 66.667 10.56 0.00 36.56 4.30
578 579 2.747855 GCTTGTCGCAAGGGGGAG 60.748 66.667 17.36 0.00 36.56 4.30
579 580 4.344865 GGCTTGTCGCAAGGGGGA 62.345 66.667 17.36 0.00 41.67 4.81
581 582 4.351054 AGGGCTTGTCGCAAGGGG 62.351 66.667 17.36 0.00 41.67 4.79
582 583 2.747855 GAGGGCTTGTCGCAAGGG 60.748 66.667 17.36 0.00 41.67 3.95
583 584 2.747855 GGAGGGCTTGTCGCAAGG 60.748 66.667 17.36 4.19 41.67 3.61
584 585 2.747855 GGGAGGGCTTGTCGCAAG 60.748 66.667 13.18 13.18 41.67 4.01
585 586 3.126703 TTGGGAGGGCTTGTCGCAA 62.127 57.895 9.33 9.33 42.63 4.85
586 587 3.565214 TTGGGAGGGCTTGTCGCA 61.565 61.111 0.00 0.00 41.67 5.10
587 588 3.056328 GTTGGGAGGGCTTGTCGC 61.056 66.667 0.00 0.00 38.13 5.19
588 589 2.359975 GGTTGGGAGGGCTTGTCG 60.360 66.667 0.00 0.00 0.00 4.35
589 590 2.035783 GGGTTGGGAGGGCTTGTC 59.964 66.667 0.00 0.00 0.00 3.18
590 591 2.780924 TGGGTTGGGAGGGCTTGT 60.781 61.111 0.00 0.00 0.00 3.16
591 592 2.283173 GTGGGTTGGGAGGGCTTG 60.283 66.667 0.00 0.00 0.00 4.01
592 593 2.452491 AGTGGGTTGGGAGGGCTT 60.452 61.111 0.00 0.00 0.00 4.35
593 594 2.936032 GAGTGGGTTGGGAGGGCT 60.936 66.667 0.00 0.00 0.00 5.19
594 595 4.048470 GGAGTGGGTTGGGAGGGC 62.048 72.222 0.00 0.00 0.00 5.19
595 596 2.531685 TGGAGTGGGTTGGGAGGG 60.532 66.667 0.00 0.00 0.00 4.30
596 597 2.757077 GTGGAGTGGGTTGGGAGG 59.243 66.667 0.00 0.00 0.00 4.30
597 598 1.500783 ATGGTGGAGTGGGTTGGGAG 61.501 60.000 0.00 0.00 0.00 4.30
598 599 0.178858 TATGGTGGAGTGGGTTGGGA 60.179 55.000 0.00 0.00 0.00 4.37
599 600 0.926293 ATATGGTGGAGTGGGTTGGG 59.074 55.000 0.00 0.00 0.00 4.12
600 601 2.826674 AATATGGTGGAGTGGGTTGG 57.173 50.000 0.00 0.00 0.00 3.77
601 602 3.023832 GGAAATATGGTGGAGTGGGTTG 58.976 50.000 0.00 0.00 0.00 3.77
602 603 2.024369 GGGAAATATGGTGGAGTGGGTT 60.024 50.000 0.00 0.00 0.00 4.11
603 604 1.569072 GGGAAATATGGTGGAGTGGGT 59.431 52.381 0.00 0.00 0.00 4.51
604 605 1.852965 AGGGAAATATGGTGGAGTGGG 59.147 52.381 0.00 0.00 0.00 4.61
605 606 2.780010 AGAGGGAAATATGGTGGAGTGG 59.220 50.000 0.00 0.00 0.00 4.00
606 607 3.493350 CGAGAGGGAAATATGGTGGAGTG 60.493 52.174 0.00 0.00 0.00 3.51
607 608 2.700897 CGAGAGGGAAATATGGTGGAGT 59.299 50.000 0.00 0.00 0.00 3.85
639 640 1.141881 CCGCCGACTAGAGCAACAT 59.858 57.895 0.00 0.00 0.00 2.71
645 646 4.577246 GCAGGCCGCCGACTAGAG 62.577 72.222 3.05 0.00 32.94 2.43
664 665 1.806542 ACAACTTTGGCGATGCTAGTG 59.193 47.619 0.00 0.00 0.00 2.74
722 723 4.760047 AGACGCGGTGCACCATCC 62.760 66.667 34.16 20.32 35.14 3.51
727 728 3.891586 TTCTCGAGACGCGGTGCAC 62.892 63.158 16.36 8.80 41.33 4.57
799 800 8.717717 AGATCTCCCAAACATAGATCAAACATA 58.282 33.333 12.61 0.00 38.18 2.29
826 827 1.147473 CGTGATGTGCTGCAGTTACA 58.853 50.000 22.28 22.28 0.00 2.41
880 881 9.810870 GGGGAGAGAAGAGATTACTATTACTTA 57.189 37.037 0.00 0.00 0.00 2.24
1038 1057 0.474660 AGGTGGCTGGAGAAGAAGGT 60.475 55.000 0.00 0.00 0.00 3.50
1039 1058 0.251634 GAGGTGGCTGGAGAAGAAGG 59.748 60.000 0.00 0.00 0.00 3.46
1099 1118 2.031163 GGAGATTGCGGGCGCTAT 59.969 61.111 7.64 0.00 42.51 2.97
1747 1782 3.423154 CTCCACTTTGGCGGCGAC 61.423 66.667 12.98 9.31 37.47 5.19
1818 1853 1.968540 GAGCAACGCTGGAGCCTTT 60.969 57.895 0.00 0.00 39.88 3.11
1882 1917 2.193536 GTTGCAAGCCCACCTCGTT 61.194 57.895 0.00 0.00 0.00 3.85
1883 1918 2.594592 GTTGCAAGCCCACCTCGT 60.595 61.111 0.00 0.00 0.00 4.18
1969 2004 8.925161 TTTTCCTTGAGAAACTTTACAACATG 57.075 30.769 0.00 0.00 44.20 3.21
2017 2052 8.925161 TTTTCCTTGAGAAACTTTACAACATG 57.075 30.769 0.00 0.00 44.20 3.21
2054 2089 2.986979 TGTAGCTCGGGTCACGCA 60.987 61.111 0.00 0.00 43.86 5.24
2074 2109 1.538950 CTCAGCCTCCTTGAAAACAGC 59.461 52.381 0.00 0.00 0.00 4.40
2145 2180 4.498850 GCAGCATCATAGTCTTCTTCGAGA 60.499 45.833 0.00 0.00 0.00 4.04
2179 2214 7.441157 TGTGAATCTGAAATTAGTCGACAGTTT 59.559 33.333 19.50 14.52 0.00 2.66
2185 2220 6.256539 GCTCATGTGAATCTGAAATTAGTCGA 59.743 38.462 0.00 0.00 0.00 4.20
2236 2283 3.762288 ACCTAAGAGTCATACAACAGCGA 59.238 43.478 0.00 0.00 0.00 4.93
2424 2491 1.997874 GTGAGCCCTCCTCCATGGT 60.998 63.158 12.58 0.00 39.98 3.55
2522 3309 6.007076 TGGTATAAAAATGAACAGAGGCACA 58.993 36.000 0.00 0.00 0.00 4.57
2543 3332 7.402054 TCCATTGTCTTGATAACATTACTGGT 58.598 34.615 0.00 0.00 0.00 4.00
2578 3367 8.492673 TTTGTCTCAATAACATTACTAGCAGG 57.507 34.615 0.00 0.00 0.00 4.85
2959 3824 6.640907 GGCATTTCGAACAAACAAGAATACTT 59.359 34.615 0.00 0.00 36.73 2.24
2984 3849 4.492570 CCAAAAGTTAGTAGATTCTGCGCG 60.493 45.833 0.00 0.00 0.00 6.86
2990 3855 4.398358 GTGCCCCCAAAAGTTAGTAGATTC 59.602 45.833 0.00 0.00 0.00 2.52
2996 3861 2.694616 ATGTGCCCCCAAAAGTTAGT 57.305 45.000 0.00 0.00 0.00 2.24
3173 4039 7.376335 AGGTTAAAGAAAGTACTGGAGTTCT 57.624 36.000 0.00 0.00 31.69 3.01


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

AutoCloner maintained by Alex Coulton.