Multiple sequence alignment - TraesCS2A01G085200

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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 TraesCS2A01G085200 chr2A 100.000 2801 0 0 1 2801 39306283 39309083 0.000000e+00 5173.0
1 TraesCS2A01G085200 chr2A 90.112 1972 132 18 693 2602 39414518 39412548 0.000000e+00 2503.0
2 TraesCS2A01G085200 chr2A 92.424 660 44 5 1 657 49328798 49329454 0.000000e+00 937.0
3 TraesCS2A01G085200 chr2D 91.763 1736 109 13 693 2397 35922868 35924600 0.000000e+00 2383.0
4 TraesCS2A01G085200 chr2D 82.099 324 34 15 383 701 381339403 381339099 3.580000e-64 255.0
5 TraesCS2A01G085200 chr2D 82.520 246 16 5 2506 2724 35924614 35924859 1.020000e-44 191.0
6 TraesCS2A01G085200 chr2B 85.714 1330 147 20 1001 2298 61300912 61299594 0.000000e+00 1363.0
7 TraesCS2A01G085200 chr2B 84.206 1146 126 23 955 2069 61495048 61493927 0.000000e+00 1062.0
8 TraesCS2A01G085200 chr2B 92.388 289 19 2 2112 2397 61493394 61493106 2.600000e-110 409.0
9 TraesCS2A01G085200 chr2B 81.793 368 59 8 332 694 300505 300869 4.530000e-78 302.0
10 TraesCS2A01G085200 chr2B 82.520 246 16 5 2506 2724 61493092 61492847 1.020000e-44 191.0
11 TraesCS2A01G085200 chr2B 94.792 96 5 0 2507 2602 61299559 61299464 1.740000e-32 150.0
12 TraesCS2A01G085200 chr3A 95.845 698 25 4 1 695 734244597 734243901 0.000000e+00 1125.0
13 TraesCS2A01G085200 chr6A 95.245 694 28 5 1 692 2032250 2032940 0.000000e+00 1094.0
14 TraesCS2A01G085200 chr6A 80.728 467 58 14 236 700 613407038 613406602 4.470000e-88 335.0
15 TraesCS2A01G085200 chr7A 94.460 704 31 7 1 699 635299750 635300450 0.000000e+00 1077.0
16 TraesCS2A01G085200 chr7A 92.075 694 38 4 1 692 636140790 636141468 0.000000e+00 961.0
17 TraesCS2A01G085200 chr7A 93.119 654 39 4 1 650 662168374 662169025 0.000000e+00 953.0
18 TraesCS2A01G085200 chr7A 91.367 695 50 5 1 692 695868176 695868863 0.000000e+00 942.0
19 TraesCS2A01G085200 chr7A 90.791 695 57 6 1 692 711451801 711452491 0.000000e+00 922.0
20 TraesCS2A01G085200 chr7A 94.621 409 21 1 294 701 2585964 2585556 1.420000e-177 632.0
21 TraesCS2A01G085200 chr4A 92.407 698 47 4 1 694 628316668 628317363 0.000000e+00 990.0
22 TraesCS2A01G085200 chr6B 82.955 704 107 13 3 700 63673443 63672747 8.520000e-175 623.0
23 TraesCS2A01G085200 chr5D 85.765 281 34 6 435 711 417869100 417869378 2.730000e-75 292.0
24 TraesCS2A01G085200 chr5D 81.369 263 24 17 453 710 370855464 370855222 1.020000e-44 191.0
25 TraesCS2A01G085200 chr1D 74.681 470 69 25 238 702 474348643 474349067 2.230000e-36 163.0
26 TraesCS2A01G085200 chr3D 83.673 98 15 1 595 692 586574268 586574364 1.070000e-14 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 TraesCS2A01G085200 chr2A 39306283 39309083 2800 False 5173.0 5173 100.000000 1 2801 1 chr2A.!!$F1 2800
1 TraesCS2A01G085200 chr2A 39412548 39414518 1970 True 2503.0 2503 90.112000 693 2602 1 chr2A.!!$R1 1909
2 TraesCS2A01G085200 chr2A 49328798 49329454 656 False 937.0 937 92.424000 1 657 1 chr2A.!!$F2 656
3 TraesCS2A01G085200 chr2D 35922868 35924859 1991 False 1287.0 2383 87.141500 693 2724 2 chr2D.!!$F1 2031
4 TraesCS2A01G085200 chr2B 61299464 61300912 1448 True 756.5 1363 90.253000 1001 2602 2 chr2B.!!$R1 1601
5 TraesCS2A01G085200 chr2B 61492847 61495048 2201 True 554.0 1062 86.371333 955 2724 3 chr2B.!!$R2 1769
6 TraesCS2A01G085200 chr3A 734243901 734244597 696 True 1125.0 1125 95.845000 1 695 1 chr3A.!!$R1 694
7 TraesCS2A01G085200 chr6A 2032250 2032940 690 False 1094.0 1094 95.245000 1 692 1 chr6A.!!$F1 691
8 TraesCS2A01G085200 chr7A 635299750 635300450 700 False 1077.0 1077 94.460000 1 699 1 chr7A.!!$F1 698
9 TraesCS2A01G085200 chr7A 636140790 636141468 678 False 961.0 961 92.075000 1 692 1 chr7A.!!$F2 691
10 TraesCS2A01G085200 chr7A 662168374 662169025 651 False 953.0 953 93.119000 1 650 1 chr7A.!!$F3 649
11 TraesCS2A01G085200 chr7A 695868176 695868863 687 False 942.0 942 91.367000 1 692 1 chr7A.!!$F4 691
12 TraesCS2A01G085200 chr7A 711451801 711452491 690 False 922.0 922 90.791000 1 692 1 chr7A.!!$F5 691
13 TraesCS2A01G085200 chr4A 628316668 628317363 695 False 990.0 990 92.407000 1 694 1 chr4A.!!$F1 693
14 TraesCS2A01G085200 chr6B 63672747 63673443 696 True 623.0 623 82.955000 3 700 1 chr6B.!!$R1 697

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
942 950 0.612229 CTCATCACAGGCACCTGAGT 59.388 55.0 23.3 5.65 46.3 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2003 2039 0.249031 GTTCAAACACAGCACCAGGC 60.249 55.0 0.0 0.0 45.3 4.85 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
168 174 2.098117 GCCTAGCCGTCGACTTAGTTTA 59.902 50.000 14.70 0.00 0.00 2.01
281 288 6.557110 GCCGTTGGCTTAGTTTCAAATTATA 58.443 36.000 0.00 0.00 46.69 0.98
288 295 6.256321 GGCTTAGTTTCAAATTATACCGACGA 59.744 38.462 0.00 0.00 0.00 4.20
701 709 4.620567 CGATTCTGGTAGTGATGACACCAA 60.621 45.833 7.70 0.00 46.99 3.67
706 714 2.549992 GGTAGTGATGACACCAACAGCA 60.550 50.000 0.00 0.00 46.99 4.41
865 873 1.877443 GCAAGTCAACGGGCTCTAAAA 59.123 47.619 0.00 0.00 0.00 1.52
894 902 3.056465 AGTGTAGTGCTAGGAACAAGCTC 60.056 47.826 0.00 0.00 40.73 4.09
901 909 2.613223 GCTAGGAACAAGCTCGGAGTTT 60.613 50.000 6.90 3.86 37.01 2.66
919 927 5.459536 AGTTTCAAGGAGGCTGAATTTTC 57.540 39.130 0.00 0.00 32.98 2.29
922 930 5.649782 TTCAAGGAGGCTGAATTTTCATC 57.350 39.130 0.00 0.00 36.46 2.92
942 950 0.612229 CTCATCACAGGCACCTGAGT 59.388 55.000 23.30 5.65 46.30 3.41
967 975 1.202348 CGGCAGAGATCGAAGACACAT 60.202 52.381 0.00 0.00 42.51 3.21
1060 1068 2.360483 CTGAGCTGCGAAGAAGGATCTA 59.640 50.000 0.00 0.00 33.77 1.98
1113 1121 2.464682 GCTTCGCAGCAGAGTGATT 58.535 52.632 0.97 0.00 46.49 2.57
1390 1398 2.022129 CAGGGAGTGAACGCGTGTC 61.022 63.158 14.98 13.38 0.00 3.67
1431 1439 2.107031 CCATATTGACCTGATGGAGCCA 59.893 50.000 0.00 0.00 42.41 4.75
1444 1452 4.845796 TGATGGAGCCATATCAAGGATACA 59.154 41.667 1.21 0.00 40.18 2.29
1512 1520 2.762887 CACTGGTGGAGAAGATCTGCTA 59.237 50.000 2.13 0.00 35.71 3.49
1518 1526 4.161377 GGTGGAGAAGATCTGCTAAACTCT 59.839 45.833 2.13 0.00 35.71 3.24
1519 1527 5.348164 GTGGAGAAGATCTGCTAAACTCTC 58.652 45.833 2.13 6.50 35.71 3.20
1546 1554 5.073144 GGACATTACAGGGGATGGAAATCTA 59.927 44.000 0.00 0.00 34.61 1.98
1548 1556 6.605119 ACATTACAGGGGATGGAAATCTAAG 58.395 40.000 0.00 0.00 34.61 2.18
1572 1580 3.676646 GCCTGCAATGTTCATTTCTTCAC 59.323 43.478 0.00 0.00 0.00 3.18
1579 1587 6.968904 GCAATGTTCATTTCTTCACGATACAT 59.031 34.615 0.00 0.00 0.00 2.29
1583 1591 7.518161 TGTTCATTTCTTCACGATACATTGAC 58.482 34.615 0.00 0.00 0.00 3.18
1593 1601 4.023107 CACGATACATTGACCTACGAGGAT 60.023 45.833 7.76 0.00 37.67 3.24
1596 1604 5.278315 CGATACATTGACCTACGAGGATGAA 60.278 44.000 7.76 0.00 37.67 2.57
1598 1606 2.961526 TTGACCTACGAGGATGAAGC 57.038 50.000 7.76 0.00 37.67 3.86
1635 1643 7.607615 TGAATATGAAGATGACATCAGAGGA 57.392 36.000 17.57 0.53 0.00 3.71
1718 1726 7.700234 CGCTATCTACCTGATTATGAATGAGTC 59.300 40.741 0.00 0.00 36.65 3.36
1749 1757 2.005451 CTGTCTGATCTTCAAAGGGCG 58.995 52.381 0.00 0.00 0.00 6.13
1750 1758 0.729690 GTCTGATCTTCAAAGGGCGC 59.270 55.000 0.00 0.00 0.00 6.53
1779 1787 2.027469 GGGTGGTTACCTTAGTCACCTG 60.027 54.545 2.07 0.00 46.66 4.00
1824 1832 8.486210 TGAAAGCATCCTACATTATACTTCTGT 58.514 33.333 0.00 0.00 0.00 3.41
1825 1833 8.668510 AAAGCATCCTACATTATACTTCTGTG 57.331 34.615 0.00 0.00 0.00 3.66
1833 1841 8.144478 CCTACATTATACTTCTGTGCACAGTAT 58.856 37.037 38.41 30.90 44.12 2.12
1849 1857 3.181482 ACAGTATGCTTCCGTCATCTGAG 60.181 47.826 0.00 0.00 42.53 3.35
1858 1866 2.095461 CCGTCATCTGAGAGAAGACCA 58.905 52.381 3.97 0.00 39.14 4.02
1864 1872 1.474478 TCTGAGAGAAGACCATCGCAC 59.526 52.381 0.00 0.00 0.00 5.34
1865 1873 1.476085 CTGAGAGAAGACCATCGCACT 59.524 52.381 0.00 0.00 0.00 4.40
1881 1889 3.119814 TCGCACTCTCTGTACATCAACTC 60.120 47.826 0.00 0.00 0.00 3.01
1889 1897 4.993905 TCTGTACATCAACTCGTGTATGG 58.006 43.478 0.00 0.00 33.78 2.74
1891 1899 2.760634 ACATCAACTCGTGTATGGCA 57.239 45.000 0.00 0.00 0.00 4.92
1906 1914 1.179152 TGGCAGCACATGATTCAAGG 58.821 50.000 0.00 0.00 0.00 3.61
1913 1921 2.359848 GCACATGATTCAAGGCATGCTA 59.640 45.455 18.92 0.00 44.30 3.49
1947 1955 3.442996 GCCTTAGCTCTTCTGCGAA 57.557 52.632 0.00 0.00 38.13 4.70
1975 2011 3.889815 TCCATTTCATCATGGACAGGTC 58.110 45.455 0.00 0.00 46.67 3.85
1976 2012 3.524789 TCCATTTCATCATGGACAGGTCT 59.475 43.478 0.00 0.00 46.67 3.85
1988 2024 4.264253 TGGACAGGTCTAATGCAATGAAG 58.736 43.478 0.00 0.00 0.00 3.02
2119 2647 4.565652 GCCCTTCTTTGAGATGTCCTTGTA 60.566 45.833 0.00 0.00 0.00 2.41
2160 2688 3.262420 GTGTGATGACTGGTGTATGTCC 58.738 50.000 0.00 0.00 32.67 4.02
2281 2811 2.124570 GATGCTGGCGTGGTGGAT 60.125 61.111 0.00 0.00 0.00 3.41
2302 2832 3.027412 TCTCTAGACCCTCTTGACATGC 58.973 50.000 0.00 0.00 0.00 4.06
2331 2861 8.086522 GCATTTTACTCTGCATTGGAATATCAT 58.913 33.333 0.00 0.00 38.28 2.45
2421 2953 6.600427 TGATTGATTCATGTCAGTTATGCACT 59.400 34.615 0.00 0.00 35.35 4.40
2435 2967 5.475719 GTTATGCACTGGAGTGTACAACTA 58.524 41.667 10.63 0.00 42.21 2.24
2445 2977 6.237313 GGAGTGTACAACTACAAAATCACC 57.763 41.667 0.00 0.00 39.87 4.02
2453 2985 4.974645 ACTACAAAATCACCTCCTGTCA 57.025 40.909 0.00 0.00 0.00 3.58
2464 2996 4.220413 CCTGTCATCTGCAGCAGG 57.780 61.111 22.62 19.63 41.89 4.85
2479 3018 8.297470 TCTGCAGCAGGATAAATTATCTTTTT 57.703 30.769 22.62 0.00 35.52 1.94
2497 3036 5.189342 TCTTTTTGGCAGATCATCTCTCTCT 59.811 40.000 0.00 0.00 29.16 3.10
2639 3224 0.543883 TGCTCAGCACCTCCTCTCTT 60.544 55.000 0.00 0.00 31.71 2.85
2650 3235 4.040461 CACCTCCTCTCTTCTTGTACCAAA 59.960 45.833 0.00 0.00 0.00 3.28
2659 3244 8.924511 TCTCTTCTTGTACCAAAATTCAGATT 57.075 30.769 0.00 0.00 0.00 2.40
2668 3253 8.196771 TGTACCAAAATTCAGATTGATAATGGC 58.803 33.333 0.00 0.00 0.00 4.40
2677 3262 4.023450 CAGATTGATAATGGCGAGCATGTT 60.023 41.667 0.00 0.00 0.00 2.71
2680 3265 2.618241 TGATAATGGCGAGCATGTTTCC 59.382 45.455 0.00 0.00 0.00 3.13
2684 3269 1.327303 TGGCGAGCATGTTTCCTTTT 58.673 45.000 0.00 0.00 0.00 2.27
2724 3313 2.633488 GAGCCCTCGTAGATTTTGCTT 58.367 47.619 0.00 0.00 33.89 3.91
2725 3314 3.431766 GGAGCCCTCGTAGATTTTGCTTA 60.432 47.826 0.00 0.00 33.89 3.09
2726 3315 4.381411 GAGCCCTCGTAGATTTTGCTTAT 58.619 43.478 0.00 0.00 33.89 1.73
2727 3316 4.781934 AGCCCTCGTAGATTTTGCTTATT 58.218 39.130 0.00 0.00 33.89 1.40
2728 3317 5.193679 AGCCCTCGTAGATTTTGCTTATTT 58.806 37.500 0.00 0.00 33.89 1.40
2729 3318 5.297029 AGCCCTCGTAGATTTTGCTTATTTC 59.703 40.000 0.00 0.00 33.89 2.17
2730 3319 5.505819 GCCCTCGTAGATTTTGCTTATTTCC 60.506 44.000 0.00 0.00 33.89 3.13
2731 3320 5.823045 CCCTCGTAGATTTTGCTTATTTCCT 59.177 40.000 0.00 0.00 33.89 3.36
2732 3321 6.017852 CCCTCGTAGATTTTGCTTATTTCCTC 60.018 42.308 0.00 0.00 33.89 3.71
2733 3322 6.763610 CCTCGTAGATTTTGCTTATTTCCTCT 59.236 38.462 0.00 0.00 33.89 3.69
2734 3323 7.042389 CCTCGTAGATTTTGCTTATTTCCTCTC 60.042 40.741 0.00 0.00 33.89 3.20
2735 3324 6.761714 TCGTAGATTTTGCTTATTTCCTCTCC 59.238 38.462 0.00 0.00 0.00 3.71
2736 3325 6.763610 CGTAGATTTTGCTTATTTCCTCTCCT 59.236 38.462 0.00 0.00 0.00 3.69
2737 3326 7.042389 CGTAGATTTTGCTTATTTCCTCTCCTC 60.042 40.741 0.00 0.00 0.00 3.71
2738 3327 6.967897 AGATTTTGCTTATTTCCTCTCCTCT 58.032 36.000 0.00 0.00 0.00 3.69
2739 3328 7.409358 AGATTTTGCTTATTTCCTCTCCTCTT 58.591 34.615 0.00 0.00 0.00 2.85
2740 3329 8.552296 AGATTTTGCTTATTTCCTCTCCTCTTA 58.448 33.333 0.00 0.00 0.00 2.10
2741 3330 8.744568 ATTTTGCTTATTTCCTCTCCTCTTAG 57.255 34.615 0.00 0.00 0.00 2.18
2742 3331 5.878406 TGCTTATTTCCTCTCCTCTTAGG 57.122 43.478 0.00 0.00 36.46 2.69
2743 3332 5.529289 TGCTTATTTCCTCTCCTCTTAGGA 58.471 41.667 0.00 0.00 43.43 2.94
2744 3333 6.146760 TGCTTATTTCCTCTCCTCTTAGGAT 58.853 40.000 0.00 0.00 44.81 3.24
2745 3334 6.268847 TGCTTATTTCCTCTCCTCTTAGGATC 59.731 42.308 0.00 0.00 44.81 3.36
2746 3335 6.268847 GCTTATTTCCTCTCCTCTTAGGATCA 59.731 42.308 0.00 0.00 44.81 2.92
2747 3336 7.525360 GCTTATTTCCTCTCCTCTTAGGATCAG 60.525 44.444 0.00 0.00 44.81 2.90
2748 3337 5.473849 TTTCCTCTCCTCTTAGGATCAGA 57.526 43.478 0.00 0.00 44.81 3.27
2749 3338 5.678142 TTCCTCTCCTCTTAGGATCAGAT 57.322 43.478 0.00 0.00 44.81 2.90
2750 3339 4.996793 TCCTCTCCTCTTAGGATCAGATG 58.003 47.826 0.00 0.00 44.81 2.90
2751 3340 4.088634 CCTCTCCTCTTAGGATCAGATGG 58.911 52.174 0.00 0.00 44.81 3.51
2752 3341 4.202663 CCTCTCCTCTTAGGATCAGATGGA 60.203 50.000 0.00 0.00 44.81 3.41
2753 3342 5.518904 CCTCTCCTCTTAGGATCAGATGGAT 60.519 48.000 0.00 0.00 44.81 3.41
2754 3343 6.297536 CCTCTCCTCTTAGGATCAGATGGATA 60.298 46.154 0.00 0.00 44.81 2.59
2755 3344 7.295999 TCTCCTCTTAGGATCAGATGGATAT 57.704 40.000 0.00 0.00 44.81 1.63
2756 3345 7.353525 TCTCCTCTTAGGATCAGATGGATATC 58.646 42.308 0.00 0.00 44.81 1.63
2757 3346 7.186225 TCTCCTCTTAGGATCAGATGGATATCT 59.814 40.741 2.05 0.00 44.81 1.98
2758 3347 7.717451 TCCTCTTAGGATCAGATGGATATCTT 58.283 38.462 2.05 0.00 40.06 2.40
2759 3348 7.838696 TCCTCTTAGGATCAGATGGATATCTTC 59.161 40.741 2.05 0.68 40.06 2.87
2760 3349 7.618907 CCTCTTAGGATCAGATGGATATCTTCA 59.381 40.741 2.05 0.00 38.49 3.02
2761 3350 9.204337 CTCTTAGGATCAGATGGATATCTTCAT 57.796 37.037 2.05 0.00 41.71 2.57
2762 3351 9.199645 TCTTAGGATCAGATGGATATCTTCATC 57.800 37.037 11.85 11.85 41.71 2.92
2763 3352 8.906238 TTAGGATCAGATGGATATCTTCATCA 57.094 34.615 18.52 3.60 41.71 3.07
2764 3353 7.185318 AGGATCAGATGGATATCTTCATCAC 57.815 40.000 18.52 10.04 41.71 3.06
2765 3354 6.729569 AGGATCAGATGGATATCTTCATCACA 59.270 38.462 18.52 8.87 41.71 3.58
2766 3355 7.237055 AGGATCAGATGGATATCTTCATCACAA 59.763 37.037 18.52 8.20 41.71 3.33
2767 3356 7.333921 GGATCAGATGGATATCTTCATCACAAC 59.666 40.741 18.52 10.27 41.71 3.32
2768 3357 7.370905 TCAGATGGATATCTTCATCACAACT 57.629 36.000 18.52 3.37 41.71 3.16
2769 3358 7.799081 TCAGATGGATATCTTCATCACAACTT 58.201 34.615 18.52 1.20 41.71 2.66
2770 3359 7.713942 TCAGATGGATATCTTCATCACAACTTG 59.286 37.037 18.52 10.36 41.71 3.16
2771 3360 6.996879 AGATGGATATCTTCATCACAACTTGG 59.003 38.462 18.52 0.00 40.79 3.61
2772 3361 6.312141 TGGATATCTTCATCACAACTTGGA 57.688 37.500 2.05 0.00 0.00 3.53
2773 3362 6.903516 TGGATATCTTCATCACAACTTGGAT 58.096 36.000 2.05 0.00 0.00 3.41
2774 3363 7.348815 TGGATATCTTCATCACAACTTGGATT 58.651 34.615 2.05 0.00 0.00 3.01
2775 3364 7.500227 TGGATATCTTCATCACAACTTGGATTC 59.500 37.037 2.05 0.00 0.00 2.52
2776 3365 7.718753 GGATATCTTCATCACAACTTGGATTCT 59.281 37.037 2.05 0.00 0.00 2.40
2777 3366 6.754702 ATCTTCATCACAACTTGGATTCTG 57.245 37.500 0.00 0.00 0.00 3.02
2778 3367 5.005740 TCTTCATCACAACTTGGATTCTGG 58.994 41.667 0.00 0.00 0.00 3.86
2779 3368 4.371624 TCATCACAACTTGGATTCTGGT 57.628 40.909 0.00 0.00 0.00 4.00
2780 3369 4.728772 TCATCACAACTTGGATTCTGGTT 58.271 39.130 0.00 0.00 0.00 3.67
2781 3370 4.761739 TCATCACAACTTGGATTCTGGTTC 59.238 41.667 0.00 0.00 0.00 3.62
2782 3371 3.138304 TCACAACTTGGATTCTGGTTCG 58.862 45.455 0.00 0.00 0.00 3.95
2783 3372 3.138304 CACAACTTGGATTCTGGTTCGA 58.862 45.455 0.00 0.00 0.00 3.71
2784 3373 3.563808 CACAACTTGGATTCTGGTTCGAA 59.436 43.478 0.00 0.00 0.00 3.71
2785 3374 4.036262 CACAACTTGGATTCTGGTTCGAAA 59.964 41.667 0.00 0.00 0.00 3.46
2786 3375 4.827284 ACAACTTGGATTCTGGTTCGAAAT 59.173 37.500 0.00 0.00 0.00 2.17
2787 3376 5.048713 ACAACTTGGATTCTGGTTCGAAATC 60.049 40.000 0.00 0.00 0.00 2.17
2788 3377 4.911390 ACTTGGATTCTGGTTCGAAATCT 58.089 39.130 0.00 0.00 0.00 2.40
2789 3378 5.316987 ACTTGGATTCTGGTTCGAAATCTT 58.683 37.500 0.00 0.00 0.00 2.40
2790 3379 5.182001 ACTTGGATTCTGGTTCGAAATCTTG 59.818 40.000 0.00 0.00 0.00 3.02
2791 3380 4.651778 TGGATTCTGGTTCGAAATCTTGT 58.348 39.130 0.00 0.00 0.00 3.16
2792 3381 4.455533 TGGATTCTGGTTCGAAATCTTGTG 59.544 41.667 0.00 0.00 0.00 3.33
2793 3382 3.896648 TTCTGGTTCGAAATCTTGTGC 57.103 42.857 0.00 0.00 0.00 4.57
2794 3383 3.126001 TCTGGTTCGAAATCTTGTGCT 57.874 42.857 0.00 0.00 0.00 4.40
2795 3384 3.476552 TCTGGTTCGAAATCTTGTGCTT 58.523 40.909 0.00 0.00 0.00 3.91
2796 3385 3.250762 TCTGGTTCGAAATCTTGTGCTTG 59.749 43.478 0.00 0.00 0.00 4.01
2797 3386 3.210227 TGGTTCGAAATCTTGTGCTTGA 58.790 40.909 0.00 0.00 0.00 3.02
2798 3387 3.250762 TGGTTCGAAATCTTGTGCTTGAG 59.749 43.478 0.00 0.00 0.00 3.02
2799 3388 3.365364 GGTTCGAAATCTTGTGCTTGAGG 60.365 47.826 0.00 0.00 0.00 3.86
2800 3389 3.401033 TCGAAATCTTGTGCTTGAGGA 57.599 42.857 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 89 1.300697 GCCCTATGCCGACGGTTAG 60.301 63.158 16.73 15.80 0.00 2.34
84 90 0.467844 TAGCCCTATGCCGACGGTTA 60.468 55.000 16.73 5.55 42.71 2.85
86 92 2.123597 TAGCCCTATGCCGACGGT 60.124 61.111 16.73 0.00 42.71 4.83
196 203 3.659089 GACACGTGGGCGCCTATGT 62.659 63.158 29.92 29.92 42.83 2.29
516 523 1.135603 GTCGGCATATACGATACGCCA 60.136 52.381 10.89 0.00 43.13 5.69
701 709 0.846693 ACAGGGGACTTCTTTGCTGT 59.153 50.000 0.00 0.00 40.21 4.40
706 714 4.227527 CCATACCTTACAGGGGACTTCTTT 59.772 45.833 0.00 0.00 40.58 2.52
865 873 3.982516 TCCTAGCACTACACTTCAGGAT 58.017 45.455 0.00 0.00 0.00 3.24
894 902 0.321671 TCAGCCTCCTTGAAACTCCG 59.678 55.000 0.00 0.00 0.00 4.63
919 927 0.545171 AGGTGCCTGTGATGAGGATG 59.455 55.000 0.00 0.00 34.69 3.51
922 930 0.107800 CTCAGGTGCCTGTGATGAGG 60.108 60.000 16.85 0.00 43.96 3.86
939 947 1.416813 CGATCTCTGCCGCACAACTC 61.417 60.000 0.00 0.00 0.00 3.01
942 950 0.737367 CTTCGATCTCTGCCGCACAA 60.737 55.000 0.00 0.00 0.00 3.33
950 958 5.749596 ACTCTATGTGTCTTCGATCTCTG 57.250 43.478 0.00 0.00 0.00 3.35
1034 1042 0.037882 TTCTTCGCAGCTCAGGACAG 60.038 55.000 0.00 0.00 0.00 3.51
1060 1068 7.818997 TCAGAGTAGTCGGTATCATTATGTT 57.181 36.000 0.00 0.00 0.00 2.71
1113 1121 7.276658 ACAACTTTGTTAAATGAACGCATCAAA 59.723 29.630 0.00 0.00 38.96 2.69
1410 1418 2.107031 TGGCTCCATCAGGTCAATATGG 59.893 50.000 0.00 0.00 41.33 2.74
1431 1439 9.606631 GAGACAAAGTTTCTGTATCCTTGATAT 57.393 33.333 0.00 0.00 30.47 1.63
1444 1452 6.096001 AGCTGAAACAATGAGACAAAGTTTCT 59.904 34.615 20.93 0.00 44.94 2.52
1509 1517 5.086104 TGTAATGTCCCAGAGAGTTTAGC 57.914 43.478 0.00 0.00 0.00 3.09
1512 1520 3.264450 CCCTGTAATGTCCCAGAGAGTTT 59.736 47.826 0.00 0.00 0.00 2.66
1518 1526 2.126882 CATCCCCTGTAATGTCCCAGA 58.873 52.381 0.00 0.00 0.00 3.86
1519 1527 1.143684 CCATCCCCTGTAATGTCCCAG 59.856 57.143 0.00 0.00 0.00 4.45
1546 1554 1.648116 AATGAACATTGCAGGCCCTT 58.352 45.000 0.00 0.00 0.00 3.95
1548 1556 1.551883 AGAAATGAACATTGCAGGCCC 59.448 47.619 0.00 0.00 0.00 5.80
1572 1580 4.215613 TCATCCTCGTAGGTCAATGTATCG 59.784 45.833 1.60 0.00 36.53 2.92
1579 1587 2.166459 CAGCTTCATCCTCGTAGGTCAA 59.834 50.000 0.00 0.00 36.53 3.18
1583 1591 0.249657 GCCAGCTTCATCCTCGTAGG 60.250 60.000 0.00 0.00 36.46 3.18
1593 1601 3.650281 TCAAATCTATGGCCAGCTTCA 57.350 42.857 13.05 0.00 0.00 3.02
1596 1604 5.884322 TCATATTCAAATCTATGGCCAGCT 58.116 37.500 13.05 0.00 0.00 4.24
1598 1606 7.991084 TCTTCATATTCAAATCTATGGCCAG 57.009 36.000 13.05 0.00 0.00 4.85
1635 1643 8.088463 AGGAGTTCATCAATAATCTCAGAAGT 57.912 34.615 0.00 0.00 0.00 3.01
1644 1652 5.817816 GTGACGGAAGGAGTTCATCAATAAT 59.182 40.000 0.00 0.00 33.44 1.28
1647 1655 3.261897 AGTGACGGAAGGAGTTCATCAAT 59.738 43.478 0.00 0.00 33.44 2.57
1764 1772 4.476297 TCACAGACAGGTGACTAAGGTAA 58.524 43.478 0.00 0.00 42.56 2.85
1797 1805 8.768955 CAGAAGTATAATGTAGGATGCTTTCAC 58.231 37.037 0.00 0.00 29.45 3.18
1833 1841 1.839424 TCTCTCAGATGACGGAAGCA 58.161 50.000 0.00 0.00 0.00 3.91
1835 1843 3.181491 GGTCTTCTCTCAGATGACGGAAG 60.181 52.174 11.41 11.04 45.22 3.46
1849 1857 1.748493 AGAGAGTGCGATGGTCTTCTC 59.252 52.381 0.00 0.00 0.00 2.87
1858 1866 3.445450 AGTTGATGTACAGAGAGTGCGAT 59.555 43.478 0.33 0.00 35.35 4.58
1864 1872 4.427096 ACACGAGTTGATGTACAGAGAG 57.573 45.455 0.33 0.00 0.00 3.20
1865 1873 5.163652 CCATACACGAGTTGATGTACAGAGA 60.164 44.000 0.33 0.00 34.24 3.10
1881 1889 1.302366 ATCATGTGCTGCCATACACG 58.698 50.000 0.00 0.00 39.71 4.49
1889 1897 0.528924 TGCCTTGAATCATGTGCTGC 59.471 50.000 0.00 0.00 0.00 5.25
1891 1899 1.136305 GCATGCCTTGAATCATGTGCT 59.864 47.619 6.36 0.00 41.44 4.40
1975 2011 3.490419 GCCTTCAGCCTTCATTGCATTAG 60.490 47.826 0.00 0.00 34.35 1.73
1976 2012 2.428171 GCCTTCAGCCTTCATTGCATTA 59.572 45.455 0.00 0.00 34.35 1.90
2003 2039 0.249031 GTTCAAACACAGCACCAGGC 60.249 55.000 0.00 0.00 45.30 4.85
2119 2647 3.031736 ACACAAGTGTAGAGTGTCCACT 58.968 45.455 3.64 0.00 42.36 4.00
2160 2688 4.034048 CACTGCATACTAAAGGGCGTAAAG 59.966 45.833 0.00 0.00 0.00 1.85
2281 2811 3.027412 GCATGTCAAGAGGGTCTAGAGA 58.973 50.000 0.00 0.00 0.00 3.10
2366 2897 9.842775 AGACAATAGGTATATCATGGCATTATG 57.157 33.333 0.00 0.00 0.00 1.90
2386 2918 8.288689 TGACATGAATCAATCATCAAGACAAT 57.711 30.769 0.00 0.00 45.91 2.71
2421 2953 5.761234 GGTGATTTTGTAGTTGTACACTCCA 59.239 40.000 0.00 0.00 38.95 3.86
2435 2967 4.330250 CAGATGACAGGAGGTGATTTTGT 58.670 43.478 0.00 0.00 0.00 2.83
2445 2977 3.067074 CTGCTGCAGATGACAGGAG 57.933 57.895 24.88 9.86 45.32 3.69
2453 2985 8.474710 AAAAGATAATTTATCCTGCTGCAGAT 57.525 30.769 30.10 21.45 35.79 2.90
2479 3018 3.138839 AGAGAGAGAGAGATGATCTGCCA 59.861 47.826 0.00 0.00 38.84 4.92
2497 3036 6.950842 TCATAGCTTTTCCATTTGAGAGAGA 58.049 36.000 0.00 0.00 0.00 3.10
2650 3235 4.823442 TGCTCGCCATTATCAATCTGAATT 59.177 37.500 0.00 0.00 0.00 2.17
2659 3244 2.618241 GGAAACATGCTCGCCATTATCA 59.382 45.455 0.00 0.00 29.71 2.15
2667 3252 1.669795 CCCAAAAGGAAACATGCTCGC 60.670 52.381 0.00 0.00 38.24 5.03
2668 3253 1.669795 GCCCAAAAGGAAACATGCTCG 60.670 52.381 0.00 0.00 38.24 5.03
2677 3262 0.251121 TGATCGCAGCCCAAAAGGAA 60.251 50.000 0.00 0.00 38.24 3.36
2680 3265 0.449388 GTCTGATCGCAGCCCAAAAG 59.551 55.000 0.00 0.00 42.01 2.27
2684 3269 3.381983 ACGTCTGATCGCAGCCCA 61.382 61.111 0.00 0.00 42.01 5.36
2713 3302 8.095452 AGAGGAGAGGAAATAAGCAAAATCTA 57.905 34.615 0.00 0.00 0.00 1.98
2731 3320 7.186225 AGATATCCATCTGATCCTAAGAGGAGA 59.814 40.741 0.00 0.00 43.09 3.71
2732 3321 7.356680 AGATATCCATCTGATCCTAAGAGGAG 58.643 42.308 0.00 0.00 43.09 3.69
2733 3322 7.295999 AGATATCCATCTGATCCTAAGAGGA 57.704 40.000 0.00 0.00 43.58 3.71
2734 3323 7.618907 TGAAGATATCCATCTGATCCTAAGAGG 59.381 40.741 0.00 0.00 40.81 3.69
2735 3324 8.592529 TGAAGATATCCATCTGATCCTAAGAG 57.407 38.462 0.00 0.00 40.81 2.85
2736 3325 9.199645 GATGAAGATATCCATCTGATCCTAAGA 57.800 37.037 12.30 0.00 40.81 2.10
2737 3326 8.979534 TGATGAAGATATCCATCTGATCCTAAG 58.020 37.037 17.58 0.00 40.81 2.18
2738 3327 8.756927 GTGATGAAGATATCCATCTGATCCTAA 58.243 37.037 17.58 0.00 40.81 2.69
2739 3328 7.897565 TGTGATGAAGATATCCATCTGATCCTA 59.102 37.037 17.58 0.28 40.81 2.94
2740 3329 6.729569 TGTGATGAAGATATCCATCTGATCCT 59.270 38.462 17.58 0.00 40.81 3.24
2741 3330 6.944096 TGTGATGAAGATATCCATCTGATCC 58.056 40.000 17.58 6.46 40.81 3.36
2742 3331 8.095792 AGTTGTGATGAAGATATCCATCTGATC 58.904 37.037 17.58 9.76 40.81 2.92
2743 3332 7.975608 AGTTGTGATGAAGATATCCATCTGAT 58.024 34.615 17.58 2.60 40.81 2.90
2744 3333 7.370905 AGTTGTGATGAAGATATCCATCTGA 57.629 36.000 17.58 6.51 40.81 3.27
2745 3334 7.041303 CCAAGTTGTGATGAAGATATCCATCTG 60.041 40.741 17.58 9.73 40.81 2.90
2746 3335 6.996879 CCAAGTTGTGATGAAGATATCCATCT 59.003 38.462 17.58 3.35 43.67 2.90
2747 3336 6.994496 TCCAAGTTGTGATGAAGATATCCATC 59.006 38.462 12.55 12.55 39.55 3.51
2748 3337 6.903516 TCCAAGTTGTGATGAAGATATCCAT 58.096 36.000 1.45 0.00 0.00 3.41
2749 3338 6.312141 TCCAAGTTGTGATGAAGATATCCA 57.688 37.500 1.45 0.00 0.00 3.41
2750 3339 7.718753 AGAATCCAAGTTGTGATGAAGATATCC 59.281 37.037 1.45 0.00 0.00 2.59
2751 3340 8.557864 CAGAATCCAAGTTGTGATGAAGATATC 58.442 37.037 1.45 0.00 0.00 1.63
2752 3341 7.501559 CCAGAATCCAAGTTGTGATGAAGATAT 59.498 37.037 1.45 0.00 0.00 1.63
2753 3342 6.825213 CCAGAATCCAAGTTGTGATGAAGATA 59.175 38.462 1.45 0.00 0.00 1.98
2754 3343 5.651139 CCAGAATCCAAGTTGTGATGAAGAT 59.349 40.000 1.45 0.00 0.00 2.40
2755 3344 5.005740 CCAGAATCCAAGTTGTGATGAAGA 58.994 41.667 1.45 0.00 0.00 2.87
2756 3345 4.763793 ACCAGAATCCAAGTTGTGATGAAG 59.236 41.667 1.45 0.00 0.00 3.02
2757 3346 4.728772 ACCAGAATCCAAGTTGTGATGAA 58.271 39.130 1.45 0.00 0.00 2.57
2758 3347 4.371624 ACCAGAATCCAAGTTGTGATGA 57.628 40.909 1.45 0.00 0.00 2.92
2759 3348 4.378770 CGAACCAGAATCCAAGTTGTGATG 60.379 45.833 1.45 0.00 0.00 3.07
2760 3349 3.753272 CGAACCAGAATCCAAGTTGTGAT 59.247 43.478 1.45 1.85 0.00 3.06
2761 3350 3.138304 CGAACCAGAATCCAAGTTGTGA 58.862 45.455 1.45 0.00 0.00 3.58
2762 3351 3.138304 TCGAACCAGAATCCAAGTTGTG 58.862 45.455 1.45 0.00 0.00 3.33
2763 3352 3.485463 TCGAACCAGAATCCAAGTTGT 57.515 42.857 1.45 0.00 0.00 3.32
2764 3353 4.829064 TTTCGAACCAGAATCCAAGTTG 57.171 40.909 0.00 0.00 0.00 3.16
2765 3354 5.316987 AGATTTCGAACCAGAATCCAAGTT 58.683 37.500 0.00 0.00 0.00 2.66
2766 3355 4.911390 AGATTTCGAACCAGAATCCAAGT 58.089 39.130 0.00 0.00 0.00 3.16
2767 3356 5.182001 ACAAGATTTCGAACCAGAATCCAAG 59.818 40.000 0.00 0.00 0.00 3.61
2768 3357 5.048782 CACAAGATTTCGAACCAGAATCCAA 60.049 40.000 0.00 0.00 0.00 3.53
2769 3358 4.455533 CACAAGATTTCGAACCAGAATCCA 59.544 41.667 0.00 0.00 0.00 3.41
2770 3359 4.672801 GCACAAGATTTCGAACCAGAATCC 60.673 45.833 0.00 0.00 0.00 3.01
2771 3360 4.154918 AGCACAAGATTTCGAACCAGAATC 59.845 41.667 0.00 0.00 0.00 2.52
2772 3361 4.074970 AGCACAAGATTTCGAACCAGAAT 58.925 39.130 0.00 0.00 0.00 2.40
2773 3362 3.476552 AGCACAAGATTTCGAACCAGAA 58.523 40.909 0.00 0.00 0.00 3.02
2774 3363 3.126001 AGCACAAGATTTCGAACCAGA 57.874 42.857 0.00 0.00 0.00 3.86
2775 3364 3.250762 TCAAGCACAAGATTTCGAACCAG 59.749 43.478 0.00 0.00 0.00 4.00
2776 3365 3.210227 TCAAGCACAAGATTTCGAACCA 58.790 40.909 0.00 0.00 0.00 3.67
2777 3366 3.365364 CCTCAAGCACAAGATTTCGAACC 60.365 47.826 0.00 0.00 0.00 3.62
2778 3367 3.498397 TCCTCAAGCACAAGATTTCGAAC 59.502 43.478 0.00 0.00 0.00 3.95
2779 3368 3.738982 TCCTCAAGCACAAGATTTCGAA 58.261 40.909 0.00 0.00 0.00 3.71
2780 3369 3.401033 TCCTCAAGCACAAGATTTCGA 57.599 42.857 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.