Multiple sequence alignment - TraesCS7A01G556100

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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 TraesCS7A01G556100 chr7A 100.000 2465 0 0 1 2465 727709478 727711942 0.000000e+00 4553.0
1 TraesCS7A01G556100 chr7A 93.485 1320 79 5 1148 2463 727597236 727598552 0.000000e+00 1954.0
2 TraesCS7A01G556100 chr7A 88.333 600 58 8 908 1495 727580853 727581452 0.000000e+00 710.0
3 TraesCS7A01G556100 chr7A 86.167 600 68 9 908 1495 727583760 727584356 3.460000e-178 634.0
4 TraesCS7A01G556100 chr7A 75.517 629 115 27 985 1581 727721913 727722534 3.120000e-69 272.0
5 TraesCS7A01G556100 chr7A 74.954 539 85 29 985 1478 727532650 727533183 4.160000e-48 202.0
6 TraesCS7A01G556100 chr7A 87.931 174 17 2 622 791 727580303 727580476 4.160000e-48 202.0
7 TraesCS7A01G556100 chr7A 88.690 168 16 1 622 786 727583406 727583573 4.160000e-48 202.0
8 TraesCS7A01G556100 chr7A 88.690 168 16 1 622 786 727586611 727586778 4.160000e-48 202.0
9 TraesCS7A01G556100 chr7A 91.837 49 4 0 624 672 727532045 727532093 4.400000e-08 69.4
10 TraesCS7A01G556100 chr7D 93.414 1579 82 11 908 2465 638344151 638342574 0.000000e+00 2320.0
11 TraesCS7A01G556100 chr7D 87.734 481 59 0 991 1471 638354484 638354004 1.660000e-156 562.0
12 TraesCS7A01G556100 chr7D 83.176 529 58 12 2 510 638345043 638344526 2.890000e-124 455.0
13 TraesCS7A01G556100 chr7D 82.637 455 52 8 1611 2049 638352367 638351924 6.430000e-101 377.0
14 TraesCS7A01G556100 chr7D 89.850 266 25 2 2047 2311 638351813 638351549 8.440000e-90 340.0
15 TraesCS7A01G556100 chr7D 90.431 209 9 7 622 822 638344529 638344324 5.230000e-67 265.0
16 TraesCS7A01G556100 chr7D 77.243 457 77 18 985 1417 638288391 638287938 2.450000e-60 243.0
17 TraesCS7A01G556100 chr7D 90.598 117 9 2 1512 1626 638354007 638353891 1.180000e-33 154.0
18 TraesCS7A01G556100 chr7B 92.826 460 33 0 1590 2049 734366925 734367384 0.000000e+00 667.0
19 TraesCS7A01G556100 chr7B 94.258 418 23 1 2049 2465 734368491 734368908 2.670000e-179 638.0
20 TraesCS7A01G556100 chr7B 91.739 230 18 1 622 851 734365790 734366018 3.960000e-83 318.0
21 TraesCS7A01G556100 chr7B 77.778 522 85 22 985 1479 734379557 734380074 2.400000e-75 292.0
22 TraesCS7A01G556100 chr7B 88.281 128 14 1 503 629 78550154 78550027 4.250000e-33 152.0
23 TraesCS7A01G556100 chr3B 89.516 124 13 0 507 630 483569773 483569896 9.130000e-35 158.0
24 TraesCS7A01G556100 chr3B 88.462 130 13 2 507 634 755249038 755248909 3.280000e-34 156.0
25 TraesCS7A01G556100 chr2B 88.372 129 15 0 502 630 767419767 767419895 3.280000e-34 156.0
26 TraesCS7A01G556100 chr2B 88.618 123 13 1 507 629 113275275 113275154 5.490000e-32 148.0
27 TraesCS7A01G556100 chr6B 87.218 133 16 1 498 630 631288170 631288301 1.530000e-32 150.0
28 TraesCS7A01G556100 chr5D 88.618 123 14 0 507 629 439217629 439217751 1.530000e-32 150.0
29 TraesCS7A01G556100 chr5D 87.597 129 14 2 507 634 498400300 498400427 5.490000e-32 148.0
30 TraesCS7A01G556100 chr4A 87.302 126 16 0 507 632 658949231 658949106 7.100000e-31 145.0


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 TraesCS7A01G556100 chr7A 727709478 727711942 2464 False 4553.000000 4553 100.00000 1 2465 1 chr7A.!!$F2 2464
1 TraesCS7A01G556100 chr7A 727597236 727598552 1316 False 1954.000000 1954 93.48500 1148 2463 1 chr7A.!!$F1 1315
2 TraesCS7A01G556100 chr7A 727580303 727586778 6475 False 390.000000 710 87.96220 622 1495 5 chr7A.!!$F5 873
3 TraesCS7A01G556100 chr7A 727721913 727722534 621 False 272.000000 272 75.51700 985 1581 1 chr7A.!!$F3 596
4 TraesCS7A01G556100 chr7D 638342574 638345043 2469 True 1013.333333 2320 89.00700 2 2465 3 chr7D.!!$R2 2463
5 TraesCS7A01G556100 chr7D 638351549 638354484 2935 True 358.250000 562 87.70475 991 2311 4 chr7D.!!$R3 1320
6 TraesCS7A01G556100 chr7B 734365790 734368908 3118 False 541.000000 667 92.94100 622 2465 3 chr7B.!!$F2 1843
7 TraesCS7A01G556100 chr7B 734379557 734380074 517 False 292.000000 292 77.77800 985 1479 1 chr7B.!!$F1 494

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
619 642 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.20 F
861 927 0.108756 GCTACCACCGTCTGAACTCC 60.109 60.0 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1428 1810 0.982852 TATCTCCACCACCAGCCAGG 60.983 60.0 0.0 0.0 45.67 4.45 R
2095 9442 1.087501 GTTCCACTCCTGCGAATTCC 58.912 55.0 0.0 0.0 0.00 3.01 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
26 27 2.341257 AGCAAAGTACACAGAGCATCG 58.659 47.619 0.00 0.00 42.67 3.84
27 28 1.394917 GCAAAGTACACAGAGCATCGG 59.605 52.381 0.00 0.00 42.67 4.18
49 50 3.797039 CAATCGGACTTGCCTAATCTGA 58.203 45.455 0.00 0.00 32.42 3.27
51 52 2.457598 TCGGACTTGCCTAATCTGACT 58.542 47.619 0.00 0.00 0.00 3.41
64 65 6.511416 CCTAATCTGACTCCTTACATGTCTG 58.489 44.000 0.00 0.00 0.00 3.51
67 68 3.194329 TCTGACTCCTTACATGTCTGCAG 59.806 47.826 7.63 7.63 32.30 4.41
81 82 0.249868 CTGCAGAGACAACCGGACAA 60.250 55.000 9.46 0.00 0.00 3.18
82 83 0.531974 TGCAGAGACAACCGGACAAC 60.532 55.000 9.46 0.00 0.00 3.32
109 110 3.081061 GCATGTACACATTGAACCCTCA 58.919 45.455 0.00 0.00 33.61 3.86
120 121 4.916983 TTGAACCCTCATTTGTCTGTTG 57.083 40.909 0.00 0.00 0.00 3.33
124 125 3.424703 ACCCTCATTTGTCTGTTGATGG 58.575 45.455 0.00 0.00 33.09 3.51
129 130 5.335426 CCTCATTTGTCTGTTGATGGAGTTG 60.335 44.000 0.00 0.00 0.00 3.16
130 131 3.988379 TTTGTCTGTTGATGGAGTTGC 57.012 42.857 0.00 0.00 0.00 4.17
131 132 2.636647 TGTCTGTTGATGGAGTTGCA 57.363 45.000 0.00 0.00 0.00 4.08
134 135 2.421424 GTCTGTTGATGGAGTTGCATCC 59.579 50.000 10.53 0.00 40.03 3.51
138 139 0.178767 TGATGGAGTTGCATCCCTCG 59.821 55.000 10.53 0.00 36.94 4.63
175 176 5.602145 ACAAACATATAATTGGTGGGGATGG 59.398 40.000 5.07 0.00 0.00 3.51
217 240 5.690997 AAAAAGAAGACGATTTGGGAGAC 57.309 39.130 0.00 0.00 0.00 3.36
245 268 2.044793 ACACCCTCATTTCCTCCTCA 57.955 50.000 0.00 0.00 0.00 3.86
252 275 4.070716 CCTCATTTCCTCCTCACATATGC 58.929 47.826 1.58 0.00 0.00 3.14
255 278 0.829990 TTCCTCCTCACATATGCGCA 59.170 50.000 14.96 14.96 0.00 6.09
267 290 1.939974 TATGCGCAGACATCCTGAAC 58.060 50.000 18.32 0.00 45.78 3.18
269 292 0.036105 TGCGCAGACATCCTGAACAT 60.036 50.000 5.66 0.00 45.78 2.71
293 316 0.250513 AGACGATTTGGGAGTCTGGC 59.749 55.000 0.00 0.00 42.87 4.85
323 346 0.601558 TTTTCCTCTCTCGTGTCCCG 59.398 55.000 0.00 0.00 38.13 5.14
329 352 2.915659 TCTCGTGTCCCGGCACTT 60.916 61.111 10.04 0.00 37.24 3.16
330 353 2.738521 CTCGTGTCCCGGCACTTG 60.739 66.667 10.04 0.00 37.24 3.16
345 368 2.282816 TTGCCGGGGTTGTCCATG 60.283 61.111 2.18 0.00 37.22 3.66
350 373 1.077501 CGGGGTTGTCCATGCAGAT 60.078 57.895 0.00 0.00 37.22 2.90
378 401 4.159693 GGAAAGGATTTAATGTTCCCGCTT 59.840 41.667 0.00 0.00 39.27 4.68
380 403 3.023832 AGGATTTAATGTTCCCGCTTGG 58.976 45.455 0.00 0.00 32.05 3.61
381 404 2.481276 GGATTTAATGTTCCCGCTTGGC 60.481 50.000 0.00 0.00 0.00 4.52
408 431 5.631992 GCTCTTAGCACCACAATTTAGTTC 58.368 41.667 0.00 0.00 41.89 3.01
409 432 5.412904 GCTCTTAGCACCACAATTTAGTTCT 59.587 40.000 0.00 0.00 41.89 3.01
410 433 6.072452 GCTCTTAGCACCACAATTTAGTTCTT 60.072 38.462 0.00 0.00 41.89 2.52
411 434 7.522236 GCTCTTAGCACCACAATTTAGTTCTTT 60.522 37.037 0.00 0.00 41.89 2.52
412 435 8.232913 TCTTAGCACCACAATTTAGTTCTTTT 57.767 30.769 0.00 0.00 0.00 2.27
413 436 8.691797 TCTTAGCACCACAATTTAGTTCTTTTT 58.308 29.630 0.00 0.00 0.00 1.94
457 480 4.890088 AGTGGTAAAGCGTGTTTCATCTA 58.110 39.130 0.00 0.00 0.00 1.98
461 484 5.935206 TGGTAAAGCGTGTTTCATCTATTCA 59.065 36.000 0.00 0.00 0.00 2.57
469 492 6.036083 GCGTGTTTCATCTATTCACACATACT 59.964 38.462 0.00 0.00 38.10 2.12
490 513 2.708861 TGTGGTTCAGTGGTTGGTCTAT 59.291 45.455 0.00 0.00 0.00 1.98
520 543 7.540299 AGACTTTTATTTACTCTCTCAGTCCG 58.460 38.462 0.00 0.00 36.43 4.79
521 544 6.631962 ACTTTTATTTACTCTCTCAGTCCGG 58.368 40.000 0.00 0.00 36.43 5.14
522 545 6.436532 ACTTTTATTTACTCTCTCAGTCCGGA 59.563 38.462 0.00 0.00 36.43 5.14
523 546 6.845758 TTTATTTACTCTCTCAGTCCGGAA 57.154 37.500 5.23 0.00 36.43 4.30
524 547 6.845758 TTATTTACTCTCTCAGTCCGGAAA 57.154 37.500 5.23 0.00 36.43 3.13
525 548 5.941555 ATTTACTCTCTCAGTCCGGAAAT 57.058 39.130 5.23 0.00 36.43 2.17
526 549 8.529424 TTATTTACTCTCTCAGTCCGGAAATA 57.471 34.615 5.23 0.00 36.43 1.40
527 550 5.831702 TTACTCTCTCAGTCCGGAAATAC 57.168 43.478 5.23 0.00 36.43 1.89
528 551 3.698289 ACTCTCTCAGTCCGGAAATACA 58.302 45.455 5.23 0.00 0.00 2.29
529 552 4.282496 ACTCTCTCAGTCCGGAAATACAT 58.718 43.478 5.23 0.00 0.00 2.29
530 553 5.446860 ACTCTCTCAGTCCGGAAATACATA 58.553 41.667 5.23 0.00 0.00 2.29
531 554 6.071984 ACTCTCTCAGTCCGGAAATACATAT 58.928 40.000 5.23 0.00 0.00 1.78
532 555 6.207810 ACTCTCTCAGTCCGGAAATACATATC 59.792 42.308 5.23 0.00 0.00 1.63
533 556 5.181433 TCTCTCAGTCCGGAAATACATATCG 59.819 44.000 5.23 0.00 0.00 2.92
534 557 5.067954 TCTCAGTCCGGAAATACATATCGA 58.932 41.667 5.23 0.00 0.00 3.59
535 558 5.533528 TCTCAGTCCGGAAATACATATCGAA 59.466 40.000 5.23 0.00 0.00 3.71
536 559 5.769367 TCAGTCCGGAAATACATATCGAAG 58.231 41.667 5.23 0.00 0.00 3.79
537 560 5.533528 TCAGTCCGGAAATACATATCGAAGA 59.466 40.000 5.23 0.00 45.75 2.87
538 561 6.040054 TCAGTCCGGAAATACATATCGAAGAA 59.960 38.462 5.23 0.00 43.58 2.52
539 562 6.700081 CAGTCCGGAAATACATATCGAAGAAA 59.300 38.462 5.23 0.00 43.58 2.52
540 563 7.385205 CAGTCCGGAAATACATATCGAAGAAAT 59.615 37.037 5.23 0.00 43.58 2.17
541 564 7.385205 AGTCCGGAAATACATATCGAAGAAATG 59.615 37.037 5.23 0.00 43.58 2.32
542 565 6.649141 TCCGGAAATACATATCGAAGAAATGG 59.351 38.462 0.00 0.00 43.58 3.16
543 566 6.649141 CCGGAAATACATATCGAAGAAATGGA 59.351 38.462 0.00 0.00 43.58 3.41
544 567 7.360101 CCGGAAATACATATCGAAGAAATGGAC 60.360 40.741 0.00 0.00 43.58 4.02
545 568 7.170828 CGGAAATACATATCGAAGAAATGGACA 59.829 37.037 0.00 0.00 43.58 4.02
546 569 9.003658 GGAAATACATATCGAAGAAATGGACAT 57.996 33.333 0.00 0.00 43.58 3.06
552 575 9.559732 ACATATCGAAGAAATGGACATAAATGA 57.440 29.630 0.00 0.00 43.58 2.57
556 579 8.279970 TCGAAGAAATGGACATAAATGAATGT 57.720 30.769 0.00 0.00 42.75 2.71
557 580 9.389755 TCGAAGAAATGGACATAAATGAATGTA 57.610 29.630 0.00 0.00 40.17 2.29
597 620 8.595362 ACATCTATATACATTCATTCCTCGGA 57.405 34.615 0.00 0.00 0.00 4.55
598 621 8.470805 ACATCTATATACATTCATTCCTCGGAC 58.529 37.037 0.00 0.00 0.00 4.79
599 622 8.470002 CATCTATATACATTCATTCCTCGGACA 58.530 37.037 0.00 0.00 0.00 4.02
600 623 8.417273 TCTATATACATTCATTCCTCGGACAA 57.583 34.615 0.00 0.00 0.00 3.18
601 624 8.523658 TCTATATACATTCATTCCTCGGACAAG 58.476 37.037 0.00 0.00 0.00 3.16
602 625 3.703001 ACATTCATTCCTCGGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
603 626 4.819105 ACATTCATTCCTCGGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
604 627 5.359194 ACATTCATTCCTCGGACAAGTAT 57.641 39.130 0.00 0.00 0.00 2.12
605 628 5.745227 ACATTCATTCCTCGGACAAGTATT 58.255 37.500 0.00 0.00 0.00 1.89
606 629 6.180472 ACATTCATTCCTCGGACAAGTATTT 58.820 36.000 0.00 0.00 0.00 1.40
607 630 6.316390 ACATTCATTCCTCGGACAAGTATTTC 59.684 38.462 0.00 0.00 0.00 2.17
608 631 4.766375 TCATTCCTCGGACAAGTATTTCC 58.234 43.478 0.00 0.00 0.00 3.13
614 637 1.648504 GGACAAGTATTTCCGGACGG 58.351 55.000 1.83 3.96 0.00 4.79
615 638 1.205417 GGACAAGTATTTCCGGACGGA 59.795 52.381 1.83 9.76 43.52 4.69
616 639 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
617 640 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
618 641 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
619 642 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
620 643 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
631 654 3.243334 GGACGGAGGGAGTACTATTTTCG 60.243 52.174 0.00 0.54 0.00 3.46
725 757 7.013846 CCATGTACCAAACCAAACGGATAATAT 59.986 37.037 0.00 0.00 0.00 1.28
768 800 3.817647 GTGCATGGAGAAATATCCTGGAC 59.182 47.826 0.00 0.31 40.29 4.02
771 803 4.202398 GCATGGAGAAATATCCTGGACTGA 60.202 45.833 0.00 0.00 40.29 3.41
844 876 3.322466 CCCACTGGTCCTTCCGCT 61.322 66.667 0.00 0.00 39.52 5.52
851 883 2.183555 GTCCTTCCGCTACCACCG 59.816 66.667 0.00 0.00 0.00 4.94
852 884 2.283388 TCCTTCCGCTACCACCGT 60.283 61.111 0.00 0.00 0.00 4.83
853 885 2.183555 CCTTCCGCTACCACCGTC 59.816 66.667 0.00 0.00 0.00 4.79
854 886 2.348888 CCTTCCGCTACCACCGTCT 61.349 63.158 0.00 0.00 0.00 4.18
855 887 1.153823 CTTCCGCTACCACCGTCTG 60.154 63.158 0.00 0.00 0.00 3.51
856 888 1.592400 CTTCCGCTACCACCGTCTGA 61.592 60.000 0.00 0.00 0.00 3.27
861 927 0.108756 GCTACCACCGTCTGAACTCC 60.109 60.000 0.00 0.00 0.00 3.85
864 930 1.080705 CCACCGTCTGAACTCCGAC 60.081 63.158 0.00 0.00 0.00 4.79
868 934 1.507174 CGTCTGAACTCCGACCTCC 59.493 63.158 0.00 0.00 0.00 4.30
870 936 1.074423 TCTGAACTCCGACCTCCGT 59.926 57.895 0.00 0.00 36.31 4.69
881 947 0.736325 GACCTCCGTCCAACACATCG 60.736 60.000 0.00 0.00 32.40 3.84
882 948 1.183030 ACCTCCGTCCAACACATCGA 61.183 55.000 0.00 0.00 0.00 3.59
884 950 0.736325 CTCCGTCCAACACATCGACC 60.736 60.000 0.00 0.00 0.00 4.79
885 951 1.005512 CCGTCCAACACATCGACCA 60.006 57.895 0.00 0.00 0.00 4.02
886 952 0.601576 CCGTCCAACACATCGACCAA 60.602 55.000 0.00 0.00 0.00 3.67
887 953 0.511221 CGTCCAACACATCGACCAAC 59.489 55.000 0.00 0.00 0.00 3.77
888 954 1.588674 GTCCAACACATCGACCAACA 58.411 50.000 0.00 0.00 0.00 3.33
889 955 1.263217 GTCCAACACATCGACCAACAC 59.737 52.381 0.00 0.00 0.00 3.32
890 956 1.134371 TCCAACACATCGACCAACACA 60.134 47.619 0.00 0.00 0.00 3.72
891 957 1.879380 CCAACACATCGACCAACACAT 59.121 47.619 0.00 0.00 0.00 3.21
892 958 2.095768 CCAACACATCGACCAACACATC 60.096 50.000 0.00 0.00 0.00 3.06
893 959 2.807967 CAACACATCGACCAACACATCT 59.192 45.455 0.00 0.00 0.00 2.90
895 961 4.471904 ACACATCGACCAACACATCTAT 57.528 40.909 0.00 0.00 0.00 1.98
896 962 5.592104 ACACATCGACCAACACATCTATA 57.408 39.130 0.00 0.00 0.00 1.31
898 964 6.403049 ACACATCGACCAACACATCTATAAA 58.597 36.000 0.00 0.00 0.00 1.40
899 965 6.876789 ACACATCGACCAACACATCTATAAAA 59.123 34.615 0.00 0.00 0.00 1.52
900 966 7.064609 ACACATCGACCAACACATCTATAAAAG 59.935 37.037 0.00 0.00 0.00 2.27
901 967 7.277760 CACATCGACCAACACATCTATAAAAGA 59.722 37.037 0.00 0.00 39.02 2.52
902 968 7.822334 ACATCGACCAACACATCTATAAAAGAA 59.178 33.333 0.00 0.00 37.89 2.52
903 969 7.591006 TCGACCAACACATCTATAAAAGAAC 57.409 36.000 0.00 0.00 37.89 3.01
904 970 6.592607 TCGACCAACACATCTATAAAAGAACC 59.407 38.462 0.00 0.00 37.89 3.62
905 971 6.594159 CGACCAACACATCTATAAAAGAACCT 59.406 38.462 0.00 0.00 37.89 3.50
906 972 7.762615 CGACCAACACATCTATAAAAGAACCTA 59.237 37.037 0.00 0.00 37.89 3.08
913 1065 3.707611 TCTATAAAAGAACCTAGCGGCCA 59.292 43.478 2.24 0.00 0.00 5.36
978 1324 1.599518 CTTACCACAGCAACCGCCA 60.600 57.895 0.00 0.00 39.83 5.69
1012 1370 2.499289 GACTCAGACATGGTGGTCATCT 59.501 50.000 0.00 0.00 40.29 2.90
1015 1373 1.741706 CAGACATGGTGGTCATCTTGC 59.258 52.381 0.00 0.00 40.29 4.01
1020 1378 1.745489 GGTGGTCATCTTGCCGTCC 60.745 63.158 0.00 0.00 0.00 4.79
1117 1478 0.995024 CAGTTCCTCCTCCAACCCAT 59.005 55.000 0.00 0.00 0.00 4.00
1118 1479 1.355720 CAGTTCCTCCTCCAACCCATT 59.644 52.381 0.00 0.00 0.00 3.16
1224 1594 1.524621 GTGTGCGATATGCCTGGCT 60.525 57.895 21.03 8.02 45.60 4.75
1232 1602 0.833287 ATATGCCTGGCTGAGTTCGT 59.167 50.000 21.03 0.00 0.00 3.85
1244 1614 2.606826 GTTCGTGGAGGGGGAGGT 60.607 66.667 0.00 0.00 0.00 3.85
1294 1664 2.295885 CCTTCCATGTTCTCTGCATCC 58.704 52.381 0.00 0.00 0.00 3.51
1332 1702 3.971702 GCCACCTGCCCCTCTTGT 61.972 66.667 0.00 0.00 0.00 3.16
1523 2066 3.131396 CGGTTTGCTAGTTAGGCTATGG 58.869 50.000 0.00 0.00 0.00 2.74
1677 3855 4.822036 TGTTTGGTAAATGAGTCGTTGG 57.178 40.909 0.00 0.00 0.00 3.77
1738 3930 7.438564 AGTGCATAATATACGATACAACCACA 58.561 34.615 0.00 0.00 0.00 4.17
1883 4075 1.347378 TCTGTGTGAGTGGCAGCAATA 59.653 47.619 0.00 0.00 0.00 1.90
1892 4084 3.141398 AGTGGCAGCAATATATTGTCGG 58.859 45.455 23.14 17.04 39.88 4.79
2020 6888 1.389609 GGCTCGACCGGTGGAGATTA 61.390 60.000 40.63 12.33 37.59 1.75
2027 6895 2.928116 GACCGGTGGAGATTAAACGAAG 59.072 50.000 14.63 0.00 0.00 3.79
2057 9404 6.097412 GCAAGGACAAATCATAGGGAAGAATT 59.903 38.462 0.00 0.00 0.00 2.17
2072 9419 5.163612 GGGAAGAATTATTTCTGCAGGACAC 60.164 44.000 15.13 0.00 41.42 3.67
2095 9442 4.190001 CAATCCACTGGATCAGAAGTCAG 58.810 47.826 11.20 0.00 42.27 3.51
2100 9447 4.324099 CCACTGGATCAGAAGTCAGGAATT 60.324 45.833 1.59 0.00 35.18 2.17
2328 9705 8.877864 TTTTTATCCATAGTGTTCCACATCTT 57.122 30.769 0.00 0.00 36.74 2.40
2360 9737 2.285368 TCATGGAGGCGGGAGGTT 60.285 61.111 0.00 0.00 0.00 3.50
2438 9815 5.437060 ACTCAGTGTGACTATTTGTTTGGT 58.563 37.500 0.00 0.00 0.00 3.67
2455 9832 7.320443 TGTTTGGTCATAGAATGAGTAATGC 57.680 36.000 0.00 0.00 40.53 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.000891 TGCTCTGTGTACTTTGCTTATTTG 57.999 37.500 0.00 0.00 0.00 2.32
8 9 1.394917 GCCGATGCTCTGTGTACTTTG 59.605 52.381 0.00 0.00 33.53 2.77
19 20 0.811616 AAGTCCGATTGCCGATGCTC 60.812 55.000 0.00 0.00 41.76 4.26
20 21 1.091771 CAAGTCCGATTGCCGATGCT 61.092 55.000 0.00 0.00 41.76 3.79
21 22 1.353103 CAAGTCCGATTGCCGATGC 59.647 57.895 0.00 0.00 41.76 3.91
49 50 3.435275 TCTCTGCAGACATGTAAGGAGT 58.565 45.455 13.74 0.00 0.00 3.85
64 65 1.557443 CGTTGTCCGGTTGTCTCTGC 61.557 60.000 0.00 0.00 0.00 4.26
67 68 1.292992 AAACGTTGTCCGGTTGTCTC 58.707 50.000 0.00 0.00 46.79 3.36
75 76 0.869068 TACATGCCAAACGTTGTCCG 59.131 50.000 0.00 0.00 44.03 4.79
77 78 2.032302 TGTGTACATGCCAAACGTTGTC 59.968 45.455 0.00 0.00 0.00 3.18
81 82 2.881513 TCAATGTGTACATGCCAAACGT 59.118 40.909 0.00 0.00 36.56 3.99
82 83 3.550950 TCAATGTGTACATGCCAAACG 57.449 42.857 0.00 0.00 36.56 3.60
109 110 3.890756 TGCAACTCCATCAACAGACAAAT 59.109 39.130 0.00 0.00 0.00 2.32
120 121 0.465705 TCGAGGGATGCAACTCCATC 59.534 55.000 10.35 10.35 41.60 3.51
124 125 2.352960 GACAATTCGAGGGATGCAACTC 59.647 50.000 0.00 0.00 0.00 3.01
129 130 1.134401 TCTGGACAATTCGAGGGATGC 60.134 52.381 0.00 0.00 0.00 3.91
130 131 2.093500 TGTCTGGACAATTCGAGGGATG 60.093 50.000 0.51 0.00 38.56 3.51
131 132 2.093447 GTGTCTGGACAATTCGAGGGAT 60.093 50.000 4.92 0.00 43.77 3.85
134 135 2.455674 TGTGTCTGGACAATTCGAGG 57.544 50.000 4.92 0.00 43.77 4.63
205 206 0.460284 CGGACAGGTCTCCCAAATCG 60.460 60.000 0.00 0.00 0.00 3.34
208 209 0.395312 GTTCGGACAGGTCTCCCAAA 59.605 55.000 0.00 0.00 0.00 3.28
209 210 0.761323 TGTTCGGACAGGTCTCCCAA 60.761 55.000 0.00 0.00 0.00 4.12
210 211 1.152419 TGTTCGGACAGGTCTCCCA 60.152 57.895 0.00 0.00 0.00 4.37
214 237 1.152312 AGGGTGTTCGGACAGGTCT 60.152 57.895 0.00 0.00 36.20 3.85
217 240 0.324943 AATGAGGGTGTTCGGACAGG 59.675 55.000 0.00 0.00 36.20 4.00
228 251 2.044793 TGTGAGGAGGAAATGAGGGT 57.955 50.000 0.00 0.00 0.00 4.34
245 268 1.413812 TCAGGATGTCTGCGCATATGT 59.586 47.619 12.24 0.00 43.06 2.29
252 275 3.721035 TCATATGTTCAGGATGTCTGCG 58.279 45.455 1.90 0.00 43.06 5.18
255 278 5.360999 TCGTCTTCATATGTTCAGGATGTCT 59.639 40.000 1.90 0.00 37.40 3.41
267 290 5.464722 CAGACTCCCAAATCGTCTTCATATG 59.535 44.000 0.00 0.00 35.95 1.78
269 292 4.141937 CCAGACTCCCAAATCGTCTTCATA 60.142 45.833 0.00 0.00 35.95 2.15
350 373 7.175990 GCGGGAACATTAAATCCTTTCCATATA 59.824 37.037 0.00 0.00 37.98 0.86
385 408 5.412904 AGAACTAAATTGTGGTGCTAAGAGC 59.587 40.000 0.00 0.00 42.82 4.09
410 433 3.405689 TGGTGCTACGCTCCAAAAA 57.594 47.368 7.13 0.00 46.95 1.94
415 438 2.596904 TTTAGATGGTGCTACGCTCC 57.403 50.000 0.28 0.28 41.88 4.70
426 449 4.454504 ACACGCTTTACCACTTTTAGATGG 59.545 41.667 0.00 0.00 42.13 3.51
427 450 5.607119 ACACGCTTTACCACTTTTAGATG 57.393 39.130 0.00 0.00 0.00 2.90
431 454 5.814764 TGAAACACGCTTTACCACTTTTA 57.185 34.783 0.00 0.00 0.00 1.52
439 462 6.736853 GTGTGAATAGATGAAACACGCTTTAC 59.263 38.462 0.00 0.00 38.42 2.01
469 492 0.916086 AGACCAACCACTGAACCACA 59.084 50.000 0.00 0.00 0.00 4.17
502 525 7.558807 TGTATTTCCGGACTGAGAGAGTAAATA 59.441 37.037 1.83 0.00 33.83 1.40
504 527 5.713389 TGTATTTCCGGACTGAGAGAGTAAA 59.287 40.000 1.83 0.00 33.83 2.01
506 529 4.851843 TGTATTTCCGGACTGAGAGAGTA 58.148 43.478 1.83 0.00 33.83 2.59
507 530 3.698289 TGTATTTCCGGACTGAGAGAGT 58.302 45.455 1.83 0.00 37.76 3.24
508 531 4.927978 ATGTATTTCCGGACTGAGAGAG 57.072 45.455 1.83 0.00 0.00 3.20
509 532 5.181433 CGATATGTATTTCCGGACTGAGAGA 59.819 44.000 1.83 0.00 0.00 3.10
510 533 5.181433 TCGATATGTATTTCCGGACTGAGAG 59.819 44.000 1.83 0.00 0.00 3.20
511 534 5.067954 TCGATATGTATTTCCGGACTGAGA 58.932 41.667 1.83 0.00 0.00 3.27
512 535 5.372547 TCGATATGTATTTCCGGACTGAG 57.627 43.478 1.83 0.00 0.00 3.35
513 536 5.533528 TCTTCGATATGTATTTCCGGACTGA 59.466 40.000 1.83 0.00 0.00 3.41
514 537 5.769367 TCTTCGATATGTATTTCCGGACTG 58.231 41.667 1.83 0.00 0.00 3.51
515 538 6.401047 TTCTTCGATATGTATTTCCGGACT 57.599 37.500 1.83 0.00 0.00 3.85
516 539 7.360101 CCATTTCTTCGATATGTATTTCCGGAC 60.360 40.741 1.83 0.00 0.00 4.79
517 540 6.649141 CCATTTCTTCGATATGTATTTCCGGA 59.351 38.462 0.00 0.00 0.00 5.14
518 541 6.649141 TCCATTTCTTCGATATGTATTTCCGG 59.351 38.462 0.00 0.00 0.00 5.14
519 542 7.170828 TGTCCATTTCTTCGATATGTATTTCCG 59.829 37.037 0.00 0.00 0.00 4.30
520 543 8.378172 TGTCCATTTCTTCGATATGTATTTCC 57.622 34.615 0.00 0.00 0.00 3.13
526 549 9.559732 TCATTTATGTCCATTTCTTCGATATGT 57.440 29.630 0.00 0.00 0.00 2.29
530 553 8.906867 ACATTCATTTATGTCCATTTCTTCGAT 58.093 29.630 0.00 0.00 33.58 3.59
531 554 8.279970 ACATTCATTTATGTCCATTTCTTCGA 57.720 30.769 0.00 0.00 33.58 3.71
571 594 9.695155 TCCGAGGAATGAATGTATATAGATGTA 57.305 33.333 0.00 0.00 0.00 2.29
572 595 8.470805 GTCCGAGGAATGAATGTATATAGATGT 58.529 37.037 0.00 0.00 0.00 3.06
573 596 8.470002 TGTCCGAGGAATGAATGTATATAGATG 58.530 37.037 0.00 0.00 0.00 2.90
574 597 8.595362 TGTCCGAGGAATGAATGTATATAGAT 57.405 34.615 0.00 0.00 0.00 1.98
575 598 8.417273 TTGTCCGAGGAATGAATGTATATAGA 57.583 34.615 0.00 0.00 0.00 1.98
576 599 8.307483 ACTTGTCCGAGGAATGAATGTATATAG 58.693 37.037 0.00 0.00 0.00 1.31
577 600 8.190326 ACTTGTCCGAGGAATGAATGTATATA 57.810 34.615 0.00 0.00 0.00 0.86
578 601 7.067496 ACTTGTCCGAGGAATGAATGTATAT 57.933 36.000 0.00 0.00 0.00 0.86
579 602 6.479972 ACTTGTCCGAGGAATGAATGTATA 57.520 37.500 0.00 0.00 0.00 1.47
580 603 5.359194 ACTTGTCCGAGGAATGAATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
581 604 4.819105 ACTTGTCCGAGGAATGAATGTA 57.181 40.909 0.00 0.00 0.00 2.29
582 605 3.703001 ACTTGTCCGAGGAATGAATGT 57.297 42.857 0.00 0.00 0.00 2.71
583 606 6.238484 GGAAATACTTGTCCGAGGAATGAATG 60.238 42.308 0.00 0.00 0.00 2.67
584 607 5.823045 GGAAATACTTGTCCGAGGAATGAAT 59.177 40.000 0.00 0.00 0.00 2.57
585 608 5.183228 GGAAATACTTGTCCGAGGAATGAA 58.817 41.667 0.00 0.00 0.00 2.57
586 609 4.766375 GGAAATACTTGTCCGAGGAATGA 58.234 43.478 0.00 0.00 0.00 2.57
595 618 1.205417 TCCGTCCGGAAATACTTGTCC 59.795 52.381 5.23 0.00 42.05 4.02
596 619 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
597 620 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
598 621 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
599 622 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
600 623 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
601 624 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
602 625 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
603 626 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
604 627 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
605 628 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
606 629 0.982852 TAGTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
607 630 0.110104 ATAGTACTCCCTCCGTCCGG 59.890 60.000 0.00 0.00 0.00 5.14
608 631 1.978454 AATAGTACTCCCTCCGTCCG 58.022 55.000 0.00 0.00 0.00 4.79
609 632 3.243334 CGAAAATAGTACTCCCTCCGTCC 60.243 52.174 0.00 0.00 0.00 4.79
610 633 3.794812 GCGAAAATAGTACTCCCTCCGTC 60.795 52.174 0.00 0.00 0.00 4.79
611 634 2.100418 GCGAAAATAGTACTCCCTCCGT 59.900 50.000 0.00 0.00 0.00 4.69
612 635 2.545322 GGCGAAAATAGTACTCCCTCCG 60.545 54.545 0.00 0.43 0.00 4.63
613 636 2.433239 TGGCGAAAATAGTACTCCCTCC 59.567 50.000 0.00 0.00 0.00 4.30
614 637 3.132467 AGTGGCGAAAATAGTACTCCCTC 59.868 47.826 0.00 0.00 0.00 4.30
615 638 3.105283 AGTGGCGAAAATAGTACTCCCT 58.895 45.455 0.00 0.00 0.00 4.20
616 639 3.118884 TCAGTGGCGAAAATAGTACTCCC 60.119 47.826 0.00 0.00 0.00 4.30
617 640 4.119442 TCAGTGGCGAAAATAGTACTCC 57.881 45.455 0.00 0.00 0.00 3.85
618 641 5.232414 GTGATCAGTGGCGAAAATAGTACTC 59.768 44.000 0.00 0.00 0.00 2.59
619 642 5.105310 AGTGATCAGTGGCGAAAATAGTACT 60.105 40.000 1.14 0.00 0.00 2.73
620 643 5.109903 AGTGATCAGTGGCGAAAATAGTAC 58.890 41.667 1.14 0.00 0.00 2.73
631 654 1.550524 TGAGTGGTAGTGATCAGTGGC 59.449 52.381 13.54 5.92 0.00 5.01
725 757 1.268133 GCGTGGCAACTTCGTTTGTAA 60.268 47.619 0.00 0.00 37.08 2.41
768 800 0.177836 TACGGGTCCATGCATGTCAG 59.822 55.000 24.58 15.77 0.00 3.51
771 803 0.393808 GGTTACGGGTCCATGCATGT 60.394 55.000 24.58 8.14 0.00 3.21
844 876 0.250858 TCGGAGTTCAGACGGTGGTA 60.251 55.000 0.00 0.00 0.00 3.25
851 883 1.242665 ACGGAGGTCGGAGTTCAGAC 61.243 60.000 4.15 4.15 44.45 3.51
852 884 0.959372 GACGGAGGTCGGAGTTCAGA 60.959 60.000 0.00 0.00 44.45 3.27
853 885 1.507174 GACGGAGGTCGGAGTTCAG 59.493 63.158 0.00 0.00 44.45 3.02
854 886 1.975407 GGACGGAGGTCGGAGTTCA 60.975 63.158 0.00 0.00 44.39 3.18
855 887 1.530013 TTGGACGGAGGTCGGAGTTC 61.530 60.000 0.00 0.00 44.39 3.01
856 888 1.532316 TTGGACGGAGGTCGGAGTT 60.532 57.895 0.00 0.00 44.39 3.01
861 927 0.736325 GATGTGTTGGACGGAGGTCG 60.736 60.000 0.00 0.00 44.39 4.79
864 930 0.736325 GTCGATGTGTTGGACGGAGG 60.736 60.000 0.00 0.00 0.00 4.30
868 934 0.511221 GTTGGTCGATGTGTTGGACG 59.489 55.000 0.00 0.00 0.00 4.79
870 936 1.134371 TGTGTTGGTCGATGTGTTGGA 60.134 47.619 0.00 0.00 0.00 3.53
881 947 7.923414 AGGTTCTTTTATAGATGTGTTGGTC 57.077 36.000 0.00 0.00 31.54 4.02
882 948 7.553044 GCTAGGTTCTTTTATAGATGTGTTGGT 59.447 37.037 0.00 0.00 31.54 3.67
884 950 7.254455 CCGCTAGGTTCTTTTATAGATGTGTTG 60.254 40.741 0.00 0.00 31.54 3.33
885 951 6.761714 CCGCTAGGTTCTTTTATAGATGTGTT 59.238 38.462 0.00 0.00 31.54 3.32
886 952 6.281405 CCGCTAGGTTCTTTTATAGATGTGT 58.719 40.000 0.00 0.00 31.54 3.72
887 953 5.177696 GCCGCTAGGTTCTTTTATAGATGTG 59.822 44.000 0.00 0.00 40.50 3.21
888 954 5.298347 GCCGCTAGGTTCTTTTATAGATGT 58.702 41.667 0.00 0.00 40.50 3.06
889 955 4.691216 GGCCGCTAGGTTCTTTTATAGATG 59.309 45.833 0.00 0.00 40.50 2.90
890 956 4.347000 TGGCCGCTAGGTTCTTTTATAGAT 59.653 41.667 0.00 0.00 40.50 1.98
891 957 3.707611 TGGCCGCTAGGTTCTTTTATAGA 59.292 43.478 0.00 0.00 40.50 1.98
892 958 3.808174 GTGGCCGCTAGGTTCTTTTATAG 59.192 47.826 9.68 0.00 40.50 1.31
893 959 3.432608 GGTGGCCGCTAGGTTCTTTTATA 60.433 47.826 17.49 0.00 40.50 0.98
895 961 1.339342 GGTGGCCGCTAGGTTCTTTTA 60.339 52.381 17.49 0.00 40.50 1.52
896 962 0.608308 GGTGGCCGCTAGGTTCTTTT 60.608 55.000 17.49 0.00 40.50 2.27
898 964 2.669240 GGTGGCCGCTAGGTTCTT 59.331 61.111 17.49 0.00 40.50 2.52
899 965 3.400054 GGGTGGCCGCTAGGTTCT 61.400 66.667 17.49 0.00 40.50 3.01
900 966 3.387225 GAGGGTGGCCGCTAGGTTC 62.387 68.421 17.49 3.49 40.50 3.62
901 967 3.400054 GAGGGTGGCCGCTAGGTT 61.400 66.667 17.49 0.00 40.50 3.50
951 1297 1.448540 CTGTGGTAAGGCAGGCGAG 60.449 63.158 0.00 0.00 0.00 5.03
962 1308 2.031919 CTGGCGGTTGCTGTGGTA 59.968 61.111 0.00 0.00 42.25 3.25
989 1347 0.108615 GACCACCATGTCTGAGTCCG 60.109 60.000 0.00 0.00 32.39 4.79
1012 1370 2.112928 ACACAGCATGGACGGCAA 59.887 55.556 0.00 0.00 43.62 4.52
1015 1373 3.792047 CGCACACAGCATGGACGG 61.792 66.667 0.00 0.00 46.13 4.79
1020 1378 2.448153 AAACGAGCGCACACAGCATG 62.448 55.000 11.47 0.00 46.13 4.06
1088 1446 1.920835 GAGGAACTGGGGCTGGAGT 60.921 63.158 0.00 0.00 41.55 3.85
1096 1454 1.685820 GGTTGGAGGAGGAACTGGG 59.314 63.158 0.00 0.00 41.55 4.45
1224 1594 1.609501 CTCCCCCTCCACGAACTCA 60.610 63.158 0.00 0.00 0.00 3.41
1263 1633 3.925630 ATGGAAGGTGTGGCCGCAG 62.926 63.158 21.93 0.00 43.70 5.18
1428 1810 0.982852 TATCTCCACCACCAGCCAGG 60.983 60.000 0.00 0.00 45.67 4.45
1430 1812 1.626356 GCTATCTCCACCACCAGCCA 61.626 60.000 0.00 0.00 0.00 4.75
1615 3792 8.579682 AAGAAAATGAAGCACAAGAACAATAC 57.420 30.769 0.00 0.00 0.00 1.89
1677 3855 2.674796 AAACTAGCTGGGTCGACATC 57.325 50.000 18.91 9.49 0.00 3.06
1738 3930 5.850614 AGTTCACACTTTAGTTCACCGTAT 58.149 37.500 0.00 0.00 0.00 3.06
1775 3967 5.702670 AGAAGAGATTTGATGTCGCAGAAAA 59.297 36.000 0.00 0.00 39.69 2.29
1809 4001 3.583806 TGCCCAATAATTTGTTCAAGCG 58.416 40.909 0.00 0.00 0.00 4.68
1883 4075 9.921637 AACAAAACAAATTGATACCGACAATAT 57.078 25.926 0.00 0.00 37.04 1.28
2020 6888 2.639065 TGTCCTTGCACTTCTTCGTTT 58.361 42.857 0.00 0.00 0.00 3.60
2027 6895 4.096984 CCCTATGATTTGTCCTTGCACTTC 59.903 45.833 0.00 0.00 0.00 3.01
2057 9404 3.010027 TGGATTGGTGTCCTGCAGAAATA 59.990 43.478 17.39 0.00 39.12 1.40
2072 9419 3.054875 TGACTTCTGATCCAGTGGATTGG 60.055 47.826 25.55 19.50 43.27 3.16
2095 9442 1.087501 GTTCCACTCCTGCGAATTCC 58.912 55.000 0.00 0.00 0.00 3.01
2100 9447 1.621317 TGTTATGTTCCACTCCTGCGA 59.379 47.619 0.00 0.00 0.00 5.10
2328 9705 1.770658 CCATGAGCCCTCCTAACATCA 59.229 52.381 0.00 0.00 0.00 3.07
2360 9737 2.992124 TTCGTGAGTGTTTCTTGGGA 57.008 45.000 0.00 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.