Multiple sequence alignment - TraesCS7A01G230800

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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 TraesCS7A01G230800 chr7A 100.000 2444 0 0 1 2444 201371384 201368941 0.000000e+00 4514.0
1 TraesCS7A01G230800 chr7A 96.373 193 6 1 565 756 402560752 402560560 1.410000e-82 316.0
2 TraesCS7A01G230800 chr7A 95.789 190 8 0 567 756 659095549 659095738 8.490000e-80 307.0
3 TraesCS7A01G230800 chrUn 97.603 1627 19 6 836 2444 93420587 93418963 0.000000e+00 2771.0
4 TraesCS7A01G230800 chrUn 97.360 1288 19 3 836 2108 383641523 383640236 0.000000e+00 2176.0
5 TraesCS7A01G230800 chrUn 96.686 1026 17 5 851 1860 449522460 449523484 0.000000e+00 1690.0
6 TraesCS7A01G230800 chrUn 97.053 509 7 1 836 1336 93421102 93420594 0.000000e+00 850.0
7 TraesCS7A01G230800 chrUn 98.246 57 1 0 2388 2444 278879873 278879817 1.550000e-17 100.0
8 TraesCS7A01G230800 chrUn 90.789 76 5 2 769 844 401329318 401329391 1.550000e-17 100.0
9 TraesCS7A01G230800 chr5D 97.417 1626 23 6 836 2444 560876231 560877854 0.000000e+00 2752.0
10 TraesCS7A01G230800 chr5D 97.296 1627 24 7 836 2444 503209670 503211294 0.000000e+00 2743.0
11 TraesCS7A01G230800 chr5D 96.431 1625 41 5 836 2444 329193714 329195337 0.000000e+00 2663.0
12 TraesCS7A01G230800 chr5D 97.354 567 15 0 1 567 519981500 519982066 0.000000e+00 965.0
13 TraesCS7A01G230800 chr5D 97.176 425 4 1 836 1252 6197542 6197118 0.000000e+00 712.0
14 TraesCS7A01G230800 chr5D 83.974 156 25 0 567 722 1331698 1331543 1.510000e-32 150.0
15 TraesCS7A01G230800 chr5D 94.286 70 2 2 769 838 551102784 551102717 3.320000e-19 106.0
16 TraesCS7A01G230800 chr5D 93.056 72 2 2 767 838 424056091 424056023 4.300000e-18 102.0
17 TraesCS7A01G230800 chr3B 97.352 1624 26 6 836 2444 201518440 201520061 0.000000e+00 2745.0
18 TraesCS7A01G230800 chr3B 94.286 70 2 1 769 838 711239965 711239898 3.320000e-19 106.0
19 TraesCS7A01G230800 chr4D 96.057 1623 47 7 836 2444 19920249 19921868 0.000000e+00 2627.0
20 TraesCS7A01G230800 chr4D 97.359 568 14 1 1 567 273794116 273793549 0.000000e+00 965.0
21 TraesCS7A01G230800 chr4D 91.781 73 5 1 767 838 135647249 135647321 1.550000e-17 100.0
22 TraesCS7A01G230800 chr4D 91.176 68 5 1 769 836 172339744 172339810 9.310000e-15 91.6
23 TraesCS7A01G230800 chr4D 95.000 40 2 0 797 836 162416314 162416275 2.030000e-06 63.9
24 TraesCS7A01G230800 chr4D 97.059 34 1 0 803 836 452000918 452000885 9.440000e-05 58.4
25 TraesCS7A01G230800 chr6A 95.998 1624 48 6 836 2444 260129014 260127393 0.000000e+00 2623.0
26 TraesCS7A01G230800 chr6A 95.812 191 7 1 567 756 370981194 370981384 8.490000e-80 307.0
27 TraesCS7A01G230800 chr1A 94.941 1621 48 9 836 2444 168446825 168445227 0.000000e+00 2508.0
28 TraesCS7A01G230800 chr1A 96.316 190 6 1 568 756 228387445 228387634 6.560000e-81 311.0
29 TraesCS7A01G230800 chr1A 95.789 190 8 0 567 756 161650480 161650291 8.490000e-80 307.0
30 TraesCS7A01G230800 chr1A 92.857 210 6 2 836 1037 352124754 352124546 1.840000e-76 296.0
31 TraesCS7A01G230800 chr1D 97.368 760 10 3 836 1585 206073602 206072843 0.000000e+00 1284.0
32 TraesCS7A01G230800 chr1D 96.117 618 16 1 836 1445 254501760 254502377 0.000000e+00 1002.0
33 TraesCS7A01G230800 chr1D 97.359 568 14 1 1 567 455428538 455427971 0.000000e+00 965.0
34 TraesCS7A01G230800 chr1D 97.183 568 15 1 1 567 58795366 58795933 0.000000e+00 959.0
35 TraesCS7A01G230800 chr1D 93.443 183 4 1 845 1019 16963145 16962963 5.180000e-67 265.0
36 TraesCS7A01G230800 chr1D 90.173 173 8 3 864 1027 349815919 349816091 1.470000e-52 217.0
37 TraesCS7A01G230800 chr1D 96.078 102 3 1 962 1063 422383382 422383482 5.410000e-37 165.0
38 TraesCS7A01G230800 chr1D 98.148 54 1 0 785 838 10122868 10122921 7.190000e-16 95.3
39 TraesCS7A01G230800 chr1D 97.059 34 1 0 803 836 448443843 448443810 9.440000e-05 58.4
40 TraesCS7A01G230800 chr6D 97.354 567 15 0 1 567 311440912 311440346 0.000000e+00 965.0
41 TraesCS7A01G230800 chr6D 97.183 568 15 1 1 567 366596540 366595973 0.000000e+00 959.0
42 TraesCS7A01G230800 chr6D 94.220 173 5 3 2069 2238 386750952 386750782 2.410000e-65 259.0
43 TraesCS7A01G230800 chr6D 98.333 120 2 0 2303 2422 429809470 429809589 6.850000e-51 211.0
44 TraesCS7A01G230800 chr6D 95.652 92 4 0 836 927 16308350 16308441 5.440000e-32 148.0
45 TraesCS7A01G230800 chr6D 94.286 70 1 2 769 838 442971461 442971395 1.200000e-18 104.0
46 TraesCS7A01G230800 chr6D 98.113 53 1 0 784 836 349694541 349694593 2.590000e-15 93.5
47 TraesCS7A01G230800 chr2D 97.359 568 14 1 1 567 145784855 145785422 0.000000e+00 965.0
48 TraesCS7A01G230800 chr2D 97.354 567 15 0 1 567 349987689 349988255 0.000000e+00 965.0
49 TraesCS7A01G230800 chr2A 97.359 568 13 2 1 567 156706664 156706098 0.000000e+00 965.0
50 TraesCS7A01G230800 chr2A 96.316 190 6 1 568 756 485513582 485513393 6.560000e-81 311.0
51 TraesCS7A01G230800 chr2A 95.789 190 8 0 567 756 621967329 621967140 8.490000e-80 307.0
52 TraesCS7A01G230800 chr2A 95.588 68 1 1 771 838 485513423 485513358 9.240000e-20 108.0
53 TraesCS7A01G230800 chr5A 96.373 193 7 0 564 756 39791501 39791693 3.920000e-83 318.0
54 TraesCS7A01G230800 chr5A 96.825 189 5 1 569 756 146594432 146594620 5.070000e-82 315.0
55 TraesCS7A01G230800 chr2B 95.833 72 1 2 767 838 746623733 746623664 5.520000e-22 115.0
56 TraesCS7A01G230800 chr1B 95.833 72 1 2 767 838 462927564 462927633 5.520000e-22 115.0
57 TraesCS7A01G230800 chr7B 95.714 70 1 1 769 838 66003232 66003165 7.140000e-21 111.0
58 TraesCS7A01G230800 chr7B 95.714 70 2 1 769 838 266246602 266246534 7.140000e-21 111.0
59 TraesCS7A01G230800 chr5B 95.714 70 2 1 769 838 545444037 545444105 7.140000e-21 111.0
60 TraesCS7A01G230800 chr4A 94.366 71 3 1 769 838 723980646 723980716 9.240000e-20 108.0
61 TraesCS7A01G230800 chr3D 92.105 76 4 2 769 844 596251552 596251479 3.320000e-19 106.0
62 TraesCS7A01G230800 chr3D 94.286 70 1 2 769 838 29085566 29085500 1.200000e-18 104.0
63 TraesCS7A01G230800 chr3D 93.056 72 2 2 767 838 268732247 268732179 4.300000e-18 102.0
64 TraesCS7A01G230800 chr3D 90.789 76 5 2 769 844 596246219 596246146 1.550000e-17 100.0
65 TraesCS7A01G230800 chr4B 94.118 68 4 0 769 836 269741954 269741887 1.200000e-18 104.0
66 TraesCS7A01G230800 chr4B 94.286 70 1 2 769 838 555295360 555295426 1.200000e-18 104.0
67 TraesCS7A01G230800 chr7D 96.491 57 2 0 780 836 69463848 69463904 7.190000e-16 95.3
68 TraesCS7A01G230800 chr7D 89.189 74 7 1 765 838 52125759 52125687 9.310000e-15 91.6


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 TraesCS7A01G230800 chr7A 201368941 201371384 2443 True 4514.0 4514 100.000 1 2444 1 chr7A.!!$R1 2443
1 TraesCS7A01G230800 chrUn 383640236 383641523 1287 True 2176.0 2176 97.360 836 2108 1 chrUn.!!$R2 1272
2 TraesCS7A01G230800 chrUn 93418963 93421102 2139 True 1810.5 2771 97.328 836 2444 2 chrUn.!!$R3 1608
3 TraesCS7A01G230800 chrUn 449522460 449523484 1024 False 1690.0 1690 96.686 851 1860 1 chrUn.!!$F2 1009
4 TraesCS7A01G230800 chr5D 560876231 560877854 1623 False 2752.0 2752 97.417 836 2444 1 chr5D.!!$F4 1608
5 TraesCS7A01G230800 chr5D 503209670 503211294 1624 False 2743.0 2743 97.296 836 2444 1 chr5D.!!$F2 1608
6 TraesCS7A01G230800 chr5D 329193714 329195337 1623 False 2663.0 2663 96.431 836 2444 1 chr5D.!!$F1 1608
7 TraesCS7A01G230800 chr5D 519981500 519982066 566 False 965.0 965 97.354 1 567 1 chr5D.!!$F3 566
8 TraesCS7A01G230800 chr3B 201518440 201520061 1621 False 2745.0 2745 97.352 836 2444 1 chr3B.!!$F1 1608
9 TraesCS7A01G230800 chr4D 19920249 19921868 1619 False 2627.0 2627 96.057 836 2444 1 chr4D.!!$F1 1608
10 TraesCS7A01G230800 chr4D 273793549 273794116 567 True 965.0 965 97.359 1 567 1 chr4D.!!$R2 566
11 TraesCS7A01G230800 chr6A 260127393 260129014 1621 True 2623.0 2623 95.998 836 2444 1 chr6A.!!$R1 1608
12 TraesCS7A01G230800 chr1A 168445227 168446825 1598 True 2508.0 2508 94.941 836 2444 1 chr1A.!!$R2 1608
13 TraesCS7A01G230800 chr1D 206072843 206073602 759 True 1284.0 1284 97.368 836 1585 1 chr1D.!!$R2 749
14 TraesCS7A01G230800 chr1D 254501760 254502377 617 False 1002.0 1002 96.117 836 1445 1 chr1D.!!$F3 609
15 TraesCS7A01G230800 chr1D 455427971 455428538 567 True 965.0 965 97.359 1 567 1 chr1D.!!$R4 566
16 TraesCS7A01G230800 chr1D 58795366 58795933 567 False 959.0 959 97.183 1 567 1 chr1D.!!$F2 566
17 TraesCS7A01G230800 chr6D 311440346 311440912 566 True 965.0 965 97.354 1 567 1 chr6D.!!$R1 566
18 TraesCS7A01G230800 chr6D 366595973 366596540 567 True 959.0 959 97.183 1 567 1 chr6D.!!$R2 566
19 TraesCS7A01G230800 chr2D 145784855 145785422 567 False 965.0 965 97.359 1 567 1 chr2D.!!$F1 566
20 TraesCS7A01G230800 chr2D 349987689 349988255 566 False 965.0 965 97.354 1 567 1 chr2D.!!$F2 566
21 TraesCS7A01G230800 chr2A 156706098 156706664 566 True 965.0 965 97.359 1 567 1 chr2A.!!$R1 566

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
717 719 0.035534 ACATCCACGCTGTGCCATTA 60.036 50.0 3.56 0.0 31.34 1.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2017 2550 0.10339 GAGGAAGAGGGCGCTAGTTC 59.897 60.0 7.64 9.89 0.0 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
120 121 4.256110 CTGTGATGTAGGTTGCATCTTGA 58.744 43.478 8.28 0.00 42.21 3.02
217 218 7.228108 AGAGTGATATTGGTTGCATGTTCATAG 59.772 37.037 0.00 0.00 0.00 2.23
269 270 4.584325 TGTTGAAATGCCTTCTGCTTACTT 59.416 37.500 0.00 0.00 42.00 2.24
363 365 2.190313 CCTATCCTGCGCTTGCCA 59.810 61.111 9.73 0.00 38.03 4.92
403 405 3.811497 CGTCTGTATCATGCATCAACCAT 59.189 43.478 0.00 0.00 0.00 3.55
509 511 1.208165 GGGATGTTGGTGGTCCTCCT 61.208 60.000 11.28 0.00 32.55 3.69
567 569 5.409826 ACTGCTACTGCTAATGAAGTTGAAC 59.590 40.000 0.00 0.00 40.48 3.18
568 570 5.304778 TGCTACTGCTAATGAAGTTGAACA 58.695 37.500 0.00 0.00 40.48 3.18
569 571 5.179368 TGCTACTGCTAATGAAGTTGAACAC 59.821 40.000 0.00 0.00 40.48 3.32
570 572 5.409826 GCTACTGCTAATGAAGTTGAACACT 59.590 40.000 0.00 0.00 33.29 3.55
571 573 6.590292 GCTACTGCTAATGAAGTTGAACACTA 59.410 38.462 0.00 0.00 33.29 2.74
572 574 6.787085 ACTGCTAATGAAGTTGAACACTAC 57.213 37.500 0.00 0.00 32.94 2.73
573 575 6.525629 ACTGCTAATGAAGTTGAACACTACT 58.474 36.000 0.00 0.00 32.94 2.57
574 576 7.667557 ACTGCTAATGAAGTTGAACACTACTA 58.332 34.615 0.00 0.00 32.94 1.82
575 577 7.815068 ACTGCTAATGAAGTTGAACACTACTAG 59.185 37.037 0.00 0.00 32.94 2.57
576 578 7.097192 TGCTAATGAAGTTGAACACTACTAGG 58.903 38.462 0.00 0.00 32.94 3.02
577 579 7.039293 TGCTAATGAAGTTGAACACTACTAGGA 60.039 37.037 0.00 0.00 32.94 2.94
578 580 7.817962 GCTAATGAAGTTGAACACTACTAGGAA 59.182 37.037 0.00 0.00 32.94 3.36
579 581 9.706691 CTAATGAAGTTGAACACTACTAGGAAA 57.293 33.333 0.00 0.00 32.94 3.13
580 582 8.974060 AATGAAGTTGAACACTACTAGGAAAA 57.026 30.769 0.00 0.00 32.94 2.29
581 583 8.974060 ATGAAGTTGAACACTACTAGGAAAAA 57.026 30.769 0.00 0.00 32.94 1.94
582 584 8.433421 TGAAGTTGAACACTACTAGGAAAAAG 57.567 34.615 0.00 0.00 32.94 2.27
583 585 7.497909 TGAAGTTGAACACTACTAGGAAAAAGG 59.502 37.037 0.00 0.00 32.94 3.11
584 586 6.896883 AGTTGAACACTACTAGGAAAAAGGT 58.103 36.000 0.00 0.00 31.97 3.50
585 587 7.344134 AGTTGAACACTACTAGGAAAAAGGTT 58.656 34.615 0.00 0.00 31.97 3.50
586 588 8.488668 AGTTGAACACTACTAGGAAAAAGGTTA 58.511 33.333 0.00 0.00 31.97 2.85
587 589 9.281371 GTTGAACACTACTAGGAAAAAGGTTAT 57.719 33.333 0.00 0.00 0.00 1.89
609 611 9.884465 GTTATAGATGAAATTGACACTAATGGC 57.116 33.333 0.00 0.00 0.00 4.40
610 612 5.490139 AGATGAAATTGACACTAATGGCG 57.510 39.130 0.00 0.00 36.14 5.69
611 613 3.485947 TGAAATTGACACTAATGGCGC 57.514 42.857 0.00 0.00 36.14 6.53
612 614 2.816672 TGAAATTGACACTAATGGCGCA 59.183 40.909 10.83 0.00 36.14 6.09
613 615 2.919666 AATTGACACTAATGGCGCAC 57.080 45.000 10.83 0.00 36.14 5.34
614 616 1.094785 ATTGACACTAATGGCGCACC 58.905 50.000 10.83 0.00 36.14 5.01
623 625 2.669229 TGGCGCACCAGACATGTG 60.669 61.111 10.83 0.00 42.67 3.21
624 626 3.434319 GGCGCACCAGACATGTGG 61.434 66.667 10.83 0.97 44.01 4.17
630 632 3.434319 CCAGACATGTGGTGCGCC 61.434 66.667 10.11 10.11 32.32 6.53
631 633 2.669229 CAGACATGTGGTGCGCCA 60.669 61.111 16.89 16.89 43.73 5.69
642 644 3.928727 TGGTGCGCCACTACTATATAC 57.071 47.619 16.89 0.00 40.46 1.47
643 645 3.493334 TGGTGCGCCACTACTATATACT 58.507 45.455 16.89 0.00 40.46 2.12
644 646 4.654915 TGGTGCGCCACTACTATATACTA 58.345 43.478 16.89 0.00 40.46 1.82
645 647 5.072055 TGGTGCGCCACTACTATATACTAA 58.928 41.667 16.89 0.00 40.46 2.24
646 648 5.713389 TGGTGCGCCACTACTATATACTAAT 59.287 40.000 16.89 0.00 40.46 1.73
647 649 6.034591 GGTGCGCCACTACTATATACTAATG 58.965 44.000 12.58 0.00 34.40 1.90
648 650 6.034591 GTGCGCCACTACTATATACTAATGG 58.965 44.000 4.18 0.00 0.00 3.16
649 651 5.041940 GCGCCACTACTATATACTAATGGC 58.958 45.833 10.25 10.25 46.34 4.40
651 653 5.041940 GCCACTACTATATACTAATGGCGC 58.958 45.833 0.00 0.00 41.74 6.53
652 654 5.393787 GCCACTACTATATACTAATGGCGCA 60.394 44.000 10.83 0.00 41.74 6.09
653 655 6.034591 CCACTACTATATACTAATGGCGCAC 58.965 44.000 10.83 0.00 0.00 5.34
654 656 6.034591 CACTACTATATACTAATGGCGCACC 58.965 44.000 10.83 0.00 0.00 5.01
670 672 3.293714 CCATGTGTTGGTGCGCCA 61.294 61.111 16.89 16.89 44.38 5.69
671 673 2.638354 CCATGTGTTGGTGCGCCAT 61.638 57.895 21.95 0.61 45.56 4.40
672 674 1.289694 CATGTGTTGGTGCGCCATT 59.710 52.632 21.95 0.00 45.56 3.16
673 675 0.525311 CATGTGTTGGTGCGCCATTA 59.475 50.000 21.95 9.48 45.56 1.90
674 676 0.810648 ATGTGTTGGTGCGCCATTAG 59.189 50.000 21.95 0.00 45.56 1.73
675 677 0.536233 TGTGTTGGTGCGCCATTAGT 60.536 50.000 21.95 0.00 45.56 2.24
676 678 0.109781 GTGTTGGTGCGCCATTAGTG 60.110 55.000 21.95 0.00 45.56 2.74
677 679 0.536233 TGTTGGTGCGCCATTAGTGT 60.536 50.000 21.95 0.00 45.56 3.55
678 680 0.168128 GTTGGTGCGCCATTAGTGTC 59.832 55.000 21.95 1.56 45.56 3.67
679 681 0.958382 TTGGTGCGCCATTAGTGTCC 60.958 55.000 21.95 0.00 45.56 4.02
680 682 1.376683 GGTGCGCCATTAGTGTCCA 60.377 57.895 12.58 0.00 34.09 4.02
681 683 0.958382 GGTGCGCCATTAGTGTCCAA 60.958 55.000 12.58 0.00 34.09 3.53
682 684 0.447801 GTGCGCCATTAGTGTCCAAG 59.552 55.000 4.18 0.00 0.00 3.61
683 685 0.036164 TGCGCCATTAGTGTCCAAGT 59.964 50.000 4.18 0.00 0.00 3.16
684 686 1.276705 TGCGCCATTAGTGTCCAAGTA 59.723 47.619 4.18 0.00 0.00 2.24
685 687 1.664151 GCGCCATTAGTGTCCAAGTAC 59.336 52.381 0.00 0.00 0.00 2.73
686 688 2.677037 GCGCCATTAGTGTCCAAGTACT 60.677 50.000 0.00 0.00 0.00 2.73
687 689 3.429822 GCGCCATTAGTGTCCAAGTACTA 60.430 47.826 0.00 0.00 0.00 1.82
688 690 4.751060 CGCCATTAGTGTCCAAGTACTAA 58.249 43.478 0.00 0.00 41.88 2.24
689 691 5.357257 CGCCATTAGTGTCCAAGTACTAAT 58.643 41.667 0.00 0.00 45.89 1.73
693 695 3.247006 AGTGTCCAAGTACTAATGGCG 57.753 47.619 8.52 0.00 36.62 5.69
694 696 1.664151 GTGTCCAAGTACTAATGGCGC 59.336 52.381 8.52 0.00 36.62 6.53
695 697 1.276705 TGTCCAAGTACTAATGGCGCA 59.723 47.619 10.83 7.42 36.62 6.09
696 698 1.664151 GTCCAAGTACTAATGGCGCAC 59.336 52.381 10.83 0.00 36.62 5.34
697 699 1.014352 CCAAGTACTAATGGCGCACC 58.986 55.000 10.83 0.00 0.00 5.01
709 711 3.792047 CGCACCACATCCACGCTG 61.792 66.667 0.00 0.00 0.00 5.18
710 712 2.669569 GCACCACATCCACGCTGT 60.670 61.111 0.00 0.00 0.00 4.40
711 713 2.969806 GCACCACATCCACGCTGTG 61.970 63.158 2.27 2.27 42.88 3.66
712 714 2.669569 ACCACATCCACGCTGTGC 60.670 61.111 3.56 0.00 42.10 4.57
713 715 3.434319 CCACATCCACGCTGTGCC 61.434 66.667 3.56 0.00 42.10 5.01
714 716 2.669229 CACATCCACGCTGTGCCA 60.669 61.111 3.56 0.00 37.76 4.92
715 717 2.042259 CACATCCACGCTGTGCCAT 61.042 57.895 3.56 0.00 37.76 4.40
716 718 1.303561 ACATCCACGCTGTGCCATT 60.304 52.632 3.56 0.00 31.34 3.16
717 719 0.035534 ACATCCACGCTGTGCCATTA 60.036 50.000 3.56 0.00 31.34 1.90
718 720 0.659427 CATCCACGCTGTGCCATTAG 59.341 55.000 3.56 0.00 31.34 1.73
719 721 0.253044 ATCCACGCTGTGCCATTAGT 59.747 50.000 3.56 0.00 31.34 2.24
720 722 0.899019 TCCACGCTGTGCCATTAGTA 59.101 50.000 3.56 0.00 31.34 1.82
721 723 1.276705 TCCACGCTGTGCCATTAGTAA 59.723 47.619 3.56 0.00 31.34 2.24
722 724 1.396996 CCACGCTGTGCCATTAGTAAC 59.603 52.381 3.56 0.00 31.34 2.50
723 725 2.073056 CACGCTGTGCCATTAGTAACA 58.927 47.619 0.00 0.00 0.00 2.41
724 726 2.482336 CACGCTGTGCCATTAGTAACAA 59.518 45.455 0.00 0.00 0.00 2.83
725 727 2.742053 ACGCTGTGCCATTAGTAACAAG 59.258 45.455 0.00 0.00 0.00 3.16
726 728 3.000041 CGCTGTGCCATTAGTAACAAGA 59.000 45.455 0.00 0.00 0.00 3.02
727 729 3.623060 CGCTGTGCCATTAGTAACAAGAT 59.377 43.478 0.00 0.00 0.00 2.40
728 730 4.094887 CGCTGTGCCATTAGTAACAAGATT 59.905 41.667 0.00 0.00 0.00 2.40
729 731 5.391950 CGCTGTGCCATTAGTAACAAGATTT 60.392 40.000 0.00 0.00 0.00 2.17
730 732 6.389906 GCTGTGCCATTAGTAACAAGATTTT 58.610 36.000 0.00 0.00 0.00 1.82
731 733 6.868339 GCTGTGCCATTAGTAACAAGATTTTT 59.132 34.615 0.00 0.00 0.00 1.94
810 812 6.484818 TTTCAAAACTAGTAATGGCGTACC 57.515 37.500 0.00 0.00 0.00 3.34
819 821 4.288234 TGGCGTACCAGGGGATAG 57.712 61.111 0.00 0.00 42.67 2.08
820 822 1.312092 TGGCGTACCAGGGGATAGT 59.688 57.895 0.00 0.00 42.67 2.12
821 823 1.046472 TGGCGTACCAGGGGATAGTG 61.046 60.000 0.00 0.00 42.67 2.74
822 824 1.069258 GCGTACCAGGGGATAGTGC 59.931 63.158 0.00 0.00 0.00 4.40
823 825 1.682451 GCGTACCAGGGGATAGTGCA 61.682 60.000 0.00 0.00 0.00 4.57
824 826 0.104304 CGTACCAGGGGATAGTGCAC 59.896 60.000 9.40 9.40 0.00 4.57
825 827 0.468648 GTACCAGGGGATAGTGCACC 59.531 60.000 14.63 0.00 0.00 5.01
826 828 0.043485 TACCAGGGGATAGTGCACCA 59.957 55.000 14.63 0.00 0.00 4.17
827 829 0.624500 ACCAGGGGATAGTGCACCAT 60.625 55.000 14.63 5.01 0.00 3.55
828 830 0.552848 CCAGGGGATAGTGCACCATT 59.447 55.000 14.63 0.00 0.00 3.16
829 831 1.774254 CCAGGGGATAGTGCACCATTA 59.226 52.381 14.63 0.00 0.00 1.90
830 832 2.487265 CCAGGGGATAGTGCACCATTAC 60.487 54.545 14.63 2.78 0.00 1.89
831 833 2.439507 CAGGGGATAGTGCACCATTACT 59.560 50.000 14.63 2.32 0.00 2.24
832 834 3.646162 CAGGGGATAGTGCACCATTACTA 59.354 47.826 14.63 0.00 34.23 1.82
833 835 3.904339 AGGGGATAGTGCACCATTACTAG 59.096 47.826 14.63 0.00 33.32 2.57
834 836 3.646637 GGGGATAGTGCACCATTACTAGT 59.353 47.826 14.63 0.00 33.32 2.57
891 893 4.454504 GGTGCAACTTCGGAAAAGAGAATA 59.545 41.667 0.00 0.00 36.74 1.75
1063 1073 7.013834 ACCTATCCCAATAACAAAGAAACCAA 58.986 34.615 0.00 0.00 0.00 3.67
1297 1822 3.628942 GTGGTACTTCTTTCCCGTGTTTT 59.371 43.478 0.00 0.00 0.00 2.43
1307 1832 6.297582 TCTTTCCCGTGTTTTAAATACTCCA 58.702 36.000 3.32 0.00 0.00 3.86
1417 1942 8.040132 TCAATAAATTCCAAAATCCATTTCGCT 58.960 29.630 0.00 0.00 0.00 4.93
1598 2125 5.167303 ACTTCCAAGTGAATCTTCCCTAC 57.833 43.478 0.00 0.00 37.98 3.18
1853 2386 5.938125 TCTTACTCAAAAGGTCCAATAGTGC 59.062 40.000 0.00 0.00 0.00 4.40
1871 2404 5.060427 AGTGCATGTATATTGGCCCTTTA 57.940 39.130 0.00 0.00 0.00 1.85
2017 2550 9.177304 GAGTAAACCTGTTTTTATTTTCTTCGG 57.823 33.333 0.00 0.00 34.23 4.30
2170 2707 6.491714 TTTTCATTTCCATTCCCACAAGAA 57.508 33.333 0.00 0.00 0.00 2.52
2171 2708 6.491714 TTTCATTTCCATTCCCACAAGAAA 57.508 33.333 0.00 0.00 0.00 2.52
2406 2943 7.632898 GCAGTTATGTATCTAGGACCTTTGACA 60.633 40.741 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.438336 CGCAGATGCAATTCAACAGAATCT 60.438 41.667 5.55 0.00 42.21 2.40
21 22 2.624316 ACGCAGATGCAATTCAACAG 57.376 45.000 5.55 0.00 42.21 3.16
120 121 5.799213 AGCAGTACAAGCTAGAAGACAATT 58.201 37.500 10.67 0.00 41.32 2.32
217 218 4.940654 AGAAGAAATGAAAGCTAGGCACTC 59.059 41.667 0.00 0.00 41.75 3.51
363 365 6.688578 ACAGACGAACACTACTTTGATGTAT 58.311 36.000 0.00 0.00 0.00 2.29
509 511 0.596600 GTCTCTGTTTGCGTCGGTGA 60.597 55.000 0.00 0.00 0.00 4.02
583 585 9.884465 GCCATTAGTGTCAATTTCATCTATAAC 57.116 33.333 0.00 0.00 0.00 1.89
584 586 8.773645 CGCCATTAGTGTCAATTTCATCTATAA 58.226 33.333 0.00 0.00 0.00 0.98
585 587 7.095229 GCGCCATTAGTGTCAATTTCATCTATA 60.095 37.037 0.00 0.00 0.00 1.31
586 588 6.293626 GCGCCATTAGTGTCAATTTCATCTAT 60.294 38.462 0.00 0.00 0.00 1.98
587 589 5.007626 GCGCCATTAGTGTCAATTTCATCTA 59.992 40.000 0.00 0.00 0.00 1.98
588 590 4.201950 GCGCCATTAGTGTCAATTTCATCT 60.202 41.667 0.00 0.00 0.00 2.90
589 591 4.037690 GCGCCATTAGTGTCAATTTCATC 58.962 43.478 0.00 0.00 0.00 2.92
590 592 3.443329 TGCGCCATTAGTGTCAATTTCAT 59.557 39.130 4.18 0.00 0.00 2.57
591 593 2.816672 TGCGCCATTAGTGTCAATTTCA 59.183 40.909 4.18 0.00 0.00 2.69
592 594 3.171277 GTGCGCCATTAGTGTCAATTTC 58.829 45.455 4.18 0.00 0.00 2.17
593 595 2.094752 GGTGCGCCATTAGTGTCAATTT 60.095 45.455 12.58 0.00 34.09 1.82
594 596 1.472480 GGTGCGCCATTAGTGTCAATT 59.528 47.619 12.58 0.00 34.09 2.32
595 597 1.094785 GGTGCGCCATTAGTGTCAAT 58.905 50.000 12.58 0.00 34.09 2.57
596 598 0.250510 TGGTGCGCCATTAGTGTCAA 60.251 50.000 16.89 0.00 40.46 3.18
597 599 0.673333 CTGGTGCGCCATTAGTGTCA 60.673 55.000 21.54 0.00 45.05 3.58
598 600 0.391130 TCTGGTGCGCCATTAGTGTC 60.391 55.000 21.54 0.00 45.05 3.67
599 601 0.673644 GTCTGGTGCGCCATTAGTGT 60.674 55.000 21.54 0.00 45.05 3.55
600 602 0.673333 TGTCTGGTGCGCCATTAGTG 60.673 55.000 21.54 7.89 45.05 2.74
601 603 0.253044 ATGTCTGGTGCGCCATTAGT 59.747 50.000 21.54 3.93 45.05 2.24
602 604 0.659427 CATGTCTGGTGCGCCATTAG 59.341 55.000 21.54 8.73 45.05 1.73
603 605 0.035534 ACATGTCTGGTGCGCCATTA 60.036 50.000 21.54 8.54 45.05 1.90
604 606 1.303561 ACATGTCTGGTGCGCCATT 60.304 52.632 21.54 2.22 45.05 3.16
605 607 2.042259 CACATGTCTGGTGCGCCAT 61.042 57.895 21.54 0.85 45.05 4.40
606 608 2.669229 CACATGTCTGGTGCGCCA 60.669 61.111 19.93 19.93 43.73 5.69
607 609 3.434319 CCACATGTCTGGTGCGCC 61.434 66.667 10.11 10.11 34.94 6.53
608 610 2.669569 ACCACATGTCTGGTGCGC 60.670 61.111 7.18 0.00 43.38 6.09
612 614 2.669569 GCGCACCACATGTCTGGT 60.670 61.111 0.30 2.18 46.18 4.00
613 615 3.434319 GGCGCACCACATGTCTGG 61.434 66.667 10.83 0.00 37.33 3.86
614 616 2.669229 TGGCGCACCACATGTCTG 60.669 61.111 10.83 0.00 42.67 3.51
622 624 3.493334 AGTATATAGTAGTGGCGCACCA 58.507 45.455 10.83 0.00 46.51 4.17
623 625 5.633830 TTAGTATATAGTAGTGGCGCACC 57.366 43.478 10.83 0.00 34.49 5.01
624 626 6.034591 CCATTAGTATATAGTAGTGGCGCAC 58.965 44.000 20.32 5.73 33.88 5.34
625 627 6.203808 CCATTAGTATATAGTAGTGGCGCA 57.796 41.667 20.32 0.00 33.88 6.09
629 631 6.034591 GTGCGCCATTAGTATATAGTAGTGG 58.965 44.000 24.81 24.81 40.19 4.00
630 632 6.034591 GGTGCGCCATTAGTATATAGTAGTG 58.965 44.000 12.58 11.39 34.09 2.74
631 633 5.713389 TGGTGCGCCATTAGTATATAGTAGT 59.287 40.000 16.89 0.00 40.46 2.73
632 634 6.203808 TGGTGCGCCATTAGTATATAGTAG 57.796 41.667 16.89 0.00 40.46 2.57
662 664 0.958382 TTGGACACTAATGGCGCACC 60.958 55.000 10.83 0.00 32.81 5.01
663 665 0.447801 CTTGGACACTAATGGCGCAC 59.552 55.000 10.83 0.00 32.81 5.34
664 666 0.036164 ACTTGGACACTAATGGCGCA 59.964 50.000 10.83 0.00 32.81 6.09
665 667 1.664151 GTACTTGGACACTAATGGCGC 59.336 52.381 0.00 0.00 32.81 6.53
666 668 3.247006 AGTACTTGGACACTAATGGCG 57.753 47.619 0.00 0.00 32.81 5.69
670 672 5.357257 CGCCATTAGTACTTGGACACTAAT 58.643 41.667 16.40 0.00 44.78 1.73
671 673 4.751060 CGCCATTAGTACTTGGACACTAA 58.249 43.478 16.40 0.00 40.50 2.24
672 674 3.429822 GCGCCATTAGTACTTGGACACTA 60.430 47.826 16.40 0.00 34.81 2.74
673 675 2.677037 GCGCCATTAGTACTTGGACACT 60.677 50.000 16.40 0.00 34.81 3.55
674 676 1.664151 GCGCCATTAGTACTTGGACAC 59.336 52.381 16.40 2.35 34.81 3.67
675 677 1.276705 TGCGCCATTAGTACTTGGACA 59.723 47.619 16.40 10.65 34.81 4.02
676 678 1.664151 GTGCGCCATTAGTACTTGGAC 59.336 52.381 16.40 8.48 34.81 4.02
677 679 1.406341 GGTGCGCCATTAGTACTTGGA 60.406 52.381 16.40 0.00 34.81 3.53
678 680 1.014352 GGTGCGCCATTAGTACTTGG 58.986 55.000 12.58 8.98 36.03 3.61
679 681 1.732941 TGGTGCGCCATTAGTACTTG 58.267 50.000 16.89 0.00 40.46 3.16
692 694 3.792047 CAGCGTGGATGTGGTGCG 61.792 66.667 0.00 0.00 0.00 5.34
693 695 2.669569 ACAGCGTGGATGTGGTGC 60.670 61.111 0.00 0.00 37.10 5.01
694 696 3.256936 CACAGCGTGGATGTGGTG 58.743 61.111 6.13 0.00 44.80 4.17
785 787 7.013083 TGGTACGCCATTACTAGTTTTGAAAAA 59.987 33.333 0.00 0.00 40.46 1.94
786 788 6.485984 TGGTACGCCATTACTAGTTTTGAAAA 59.514 34.615 0.00 0.00 40.46 2.29
787 789 5.996513 TGGTACGCCATTACTAGTTTTGAAA 59.003 36.000 0.00 0.00 40.46 2.69
788 790 5.549347 TGGTACGCCATTACTAGTTTTGAA 58.451 37.500 0.00 0.00 40.46 2.69
789 791 5.149973 TGGTACGCCATTACTAGTTTTGA 57.850 39.130 0.00 0.00 40.46 2.69
790 792 4.331717 CCTGGTACGCCATTACTAGTTTTG 59.668 45.833 0.00 0.00 45.05 2.44
791 793 4.510571 CCTGGTACGCCATTACTAGTTTT 58.489 43.478 0.00 0.00 45.05 2.43
792 794 3.118519 CCCTGGTACGCCATTACTAGTTT 60.119 47.826 0.00 0.00 45.05 2.66
793 795 2.433239 CCCTGGTACGCCATTACTAGTT 59.567 50.000 0.00 0.00 45.05 2.24
794 796 2.037144 CCCTGGTACGCCATTACTAGT 58.963 52.381 0.00 0.00 45.05 2.57
795 797 1.343465 CCCCTGGTACGCCATTACTAG 59.657 57.143 0.00 0.00 45.05 2.57
796 798 1.063038 TCCCCTGGTACGCCATTACTA 60.063 52.381 0.00 0.00 45.05 1.82
797 799 0.325860 TCCCCTGGTACGCCATTACT 60.326 55.000 0.00 0.00 45.05 2.24
798 800 0.763035 ATCCCCTGGTACGCCATTAC 59.237 55.000 0.00 0.00 45.05 1.89
799 801 2.253610 CTATCCCCTGGTACGCCATTA 58.746 52.381 0.00 0.00 45.05 1.90
800 802 1.056660 CTATCCCCTGGTACGCCATT 58.943 55.000 0.00 0.00 45.05 3.16
801 803 0.105142 ACTATCCCCTGGTACGCCAT 60.105 55.000 0.00 0.00 45.05 4.40
802 804 1.046472 CACTATCCCCTGGTACGCCA 61.046 60.000 0.00 0.00 43.73 5.69
803 805 1.746517 CACTATCCCCTGGTACGCC 59.253 63.158 0.00 0.00 0.00 5.68
804 806 1.069258 GCACTATCCCCTGGTACGC 59.931 63.158 0.00 0.00 0.00 4.42
805 807 0.104304 GTGCACTATCCCCTGGTACG 59.896 60.000 10.32 0.00 0.00 3.67
806 808 0.468648 GGTGCACTATCCCCTGGTAC 59.531 60.000 17.98 0.00 0.00 3.34
807 809 0.043485 TGGTGCACTATCCCCTGGTA 59.957 55.000 17.98 0.00 0.00 3.25
808 810 0.624500 ATGGTGCACTATCCCCTGGT 60.625 55.000 17.98 0.00 0.00 4.00
809 811 0.552848 AATGGTGCACTATCCCCTGG 59.447 55.000 16.73 0.00 0.00 4.45
810 812 2.439507 AGTAATGGTGCACTATCCCCTG 59.560 50.000 16.73 0.00 0.00 4.45
811 813 2.776665 AGTAATGGTGCACTATCCCCT 58.223 47.619 16.73 9.41 0.00 4.79
812 814 3.646637 ACTAGTAATGGTGCACTATCCCC 59.353 47.826 16.73 7.30 0.00 4.81
813 815 4.957684 ACTAGTAATGGTGCACTATCCC 57.042 45.455 16.73 9.74 0.00 3.85
814 816 7.723324 TCTTAACTAGTAATGGTGCACTATCC 58.277 38.462 16.73 10.09 0.00 2.59
815 817 9.765795 ATTCTTAACTAGTAATGGTGCACTATC 57.234 33.333 16.73 4.97 0.00 2.08
818 820 8.204836 CCTATTCTTAACTAGTAATGGTGCACT 58.795 37.037 17.98 0.00 0.00 4.40
819 821 8.202137 TCCTATTCTTAACTAGTAATGGTGCAC 58.798 37.037 8.80 8.80 0.00 4.57
820 822 8.313944 TCCTATTCTTAACTAGTAATGGTGCA 57.686 34.615 0.00 0.00 0.00 4.57
821 823 9.780186 AATCCTATTCTTAACTAGTAATGGTGC 57.220 33.333 0.00 0.00 0.00 5.01
891 893 7.115414 ACTCTAGGCAAGAAAAGCTTTATCAT 58.885 34.615 13.10 0.00 33.60 2.45
1252 1777 4.811498 TCGGGTAATATTTCCAGAGGAGA 58.189 43.478 12.61 0.67 31.21 3.71
1417 1942 1.189524 ACGGTTGTAGCTACTGGGCA 61.190 55.000 23.84 0.95 34.17 5.36
1853 2386 8.862325 TTGTCTATAAAGGGCCAATATACATG 57.138 34.615 6.18 0.00 0.00 3.21
1984 2517 1.525175 AACAGGTTTACTCCACCCCA 58.475 50.000 0.00 0.00 34.44 4.96
2017 2550 0.103390 GAGGAAGAGGGCGCTAGTTC 59.897 60.000 7.64 9.89 0.00 3.01
2238 2775 6.740110 TCAGACAGAACTCAGAAAGAACTAC 58.260 40.000 0.00 0.00 0.00 2.73
2406 2943 4.184629 GAGTTAGAGACGCATCCATTTGT 58.815 43.478 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.