Multiple sequence alignment - TraesCS2B01G353900

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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 TraesCS2B01G353900 chr2B 100.000 2983 0 0 1 2983 504747115 504750097 0.000000e+00 5509.0
1 TraesCS2B01G353900 chr2B 96.970 1056 23 5 884 1931 512372892 512371838 0.000000e+00 1764.0
2 TraesCS2B01G353900 chr2B 90.022 912 60 15 1 893 512374257 512373358 0.000000e+00 1151.0
3 TraesCS2B01G353900 chr2B 95.846 674 25 3 1929 2601 512371680 512371009 0.000000e+00 1086.0
4 TraesCS2B01G353900 chr2B 95.238 609 16 8 3 607 512398077 512397478 0.000000e+00 952.0
5 TraesCS2B01G353900 chr2B 98.315 356 5 1 2628 2983 110763446 110763092 9.080000e-175 623.0
6 TraesCS2B01G353900 chr2B 98.315 356 5 1 2628 2983 790496999 790497353 9.080000e-175 623.0
7 TraesCS2B01G353900 chr2B 98.050 359 3 2 2628 2983 161702035 161702392 3.270000e-174 621.0
8 TraesCS2B01G353900 chr2B 77.532 543 80 29 6 539 512366471 512365962 3.760000e-74 289.0
9 TraesCS2B01G353900 chr2B 91.667 168 14 0 2466 2633 512364239 512364072 1.790000e-57 233.0
10 TraesCS2B01G353900 chr2B 75.275 546 80 33 2 539 512360106 512359608 3.010000e-50 209.0
11 TraesCS2B01G353900 chr2D 91.283 2214 114 32 445 2627 427932067 427934232 0.000000e+00 2946.0
12 TraesCS2B01G353900 chr2D 93.518 1990 82 12 624 2601 427753036 427754990 0.000000e+00 2916.0
13 TraesCS2B01G353900 chr2D 90.683 2211 118 36 445 2627 427914590 427916740 0.000000e+00 2861.0
14 TraesCS2B01G353900 chr2D 92.924 1823 74 18 445 2249 427897470 427899255 0.000000e+00 2601.0
15 TraesCS2B01G353900 chr2D 84.852 878 88 23 817 1671 427925316 427926171 0.000000e+00 843.0
16 TraesCS2B01G353900 chr2D 84.642 879 88 24 817 1671 427909567 427910422 0.000000e+00 832.0
17 TraesCS2B01G353900 chr2D 90.973 565 28 13 1 547 427752151 427752710 0.000000e+00 739.0
18 TraesCS2B01G353900 chr2D 82.847 822 94 24 817 1615 427784419 427785216 0.000000e+00 693.0
19 TraesCS2B01G353900 chr2D 94.162 394 21 2 2234 2627 427899293 427899684 1.530000e-167 599.0
20 TraesCS2B01G353900 chr2D 88.152 422 34 9 2 415 427896984 427897397 3.460000e-134 488.0
21 TraesCS2B01G353900 chr2D 76.234 547 95 24 2 540 427923287 427923806 1.060000e-64 257.0
22 TraesCS2B01G353900 chr2D 75.868 547 96 25 2 540 427942518 427943036 2.300000e-61 246.0
23 TraesCS2B01G353900 chr2D 75.229 545 94 25 2 536 427903949 427904462 1.390000e-53 220.0
24 TraesCS2B01G353900 chr2D 78.889 270 35 17 272 536 427783426 427783678 2.380000e-36 163.0
25 TraesCS2B01G353900 chr2D 90.000 100 10 0 2101 2200 427785797 427785896 2.410000e-26 130.0
26 TraesCS2B01G353900 chr2D 84.762 105 10 3 1681 1785 427927975 427928073 1.890000e-17 100.0
27 TraesCS2B01G353900 chr2D 81.905 105 13 4 1681 1785 427910501 427910599 1.910000e-12 84.2
28 TraesCS2B01G353900 chr2A 92.092 1214 70 14 499 1701 559830347 559829149 0.000000e+00 1687.0
29 TraesCS2B01G353900 chr2A 93.188 1057 55 5 1035 2080 559749979 559748929 0.000000e+00 1537.0
30 TraesCS2B01G353900 chr2A 90.577 520 25 8 2128 2633 559748931 559748422 0.000000e+00 667.0
31 TraesCS2B01G353900 chr2A 92.663 368 27 0 2234 2601 559826548 559826181 5.660000e-147 531.0
32 TraesCS2B01G353900 chr2A 91.870 369 21 3 1689 2057 559827636 559827277 9.540000e-140 507.0
33 TraesCS2B01G353900 chr2A 87.978 366 36 5 2101 2463 559703416 559703056 2.750000e-115 425.0
34 TraesCS2B01G353900 chr2A 85.203 419 43 13 2 415 559830849 559830445 2.140000e-111 412.0
35 TraesCS2B01G353900 chr2A 83.971 418 46 11 5 415 559750490 559750087 6.030000e-102 381.0
36 TraesCS2B01G353900 chr2A 88.306 248 27 2 631 876 560210065 560209818 2.250000e-76 296.0
37 TraesCS2B01G353900 chr2A 75.774 549 90 26 2 539 559838902 559838386 1.380000e-58 237.0
38 TraesCS2B01G353900 chr2A 79.359 281 43 12 254 532 559779666 559779399 1.830000e-42 183.0
39 TraesCS2B01G353900 chr6B 98.596 356 4 1 2628 2983 361591321 361590967 1.950000e-176 628.0
40 TraesCS2B01G353900 chr7A 98.329 359 3 1 2628 2983 23420177 23420535 7.020000e-176 627.0
41 TraesCS2B01G353900 chr1B 98.315 356 5 1 2628 2983 457063206 457062852 9.080000e-175 623.0
42 TraesCS2B01G353900 chr1B 97.778 360 4 2 2627 2983 343954645 343955003 4.220000e-173 617.0
43 TraesCS2B01G353900 chr7B 98.050 359 3 2 2628 2983 23388178 23387821 3.270000e-174 621.0
44 TraesCS2B01G353900 chr7B 98.050 359 3 2 2628 2983 458854607 458854250 3.270000e-174 621.0


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 TraesCS2B01G353900 chr2B 504747115 504750097 2982 False 5509.000000 5509 100.000000 1 2983 1 chr2B.!!$F2 2982
1 TraesCS2B01G353900 chr2B 512371009 512374257 3248 True 1333.666667 1764 94.279333 1 2601 3 chr2B.!!$R4 2600
2 TraesCS2B01G353900 chr2B 512397478 512398077 599 True 952.000000 952 95.238000 3 607 1 chr2B.!!$R2 604
3 TraesCS2B01G353900 chr2B 512359608 512366471 6863 True 243.666667 289 81.491333 2 2633 3 chr2B.!!$R3 2631
4 TraesCS2B01G353900 chr2D 427752151 427754990 2839 False 1827.500000 2916 92.245500 1 2601 2 chr2D.!!$F3 2600
5 TraesCS2B01G353900 chr2D 427909567 427916740 7173 False 1259.066667 2861 85.743333 445 2627 3 chr2D.!!$F6 2182
6 TraesCS2B01G353900 chr2D 427896984 427899684 2700 False 1229.333333 2601 91.746000 2 2627 3 chr2D.!!$F5 2625
7 TraesCS2B01G353900 chr2D 427923287 427934232 10945 False 1036.500000 2946 84.282750 2 2627 4 chr2D.!!$F7 2625
8 TraesCS2B01G353900 chr2D 427783426 427785896 2470 False 328.666667 693 83.912000 272 2200 3 chr2D.!!$F4 1928
9 TraesCS2B01G353900 chr2D 427942518 427943036 518 False 246.000000 246 75.868000 2 540 1 chr2D.!!$F2 538
10 TraesCS2B01G353900 chr2D 427903949 427904462 513 False 220.000000 220 75.229000 2 536 1 chr2D.!!$F1 534
11 TraesCS2B01G353900 chr2A 559748422 559750490 2068 True 861.666667 1537 89.245333 5 2633 3 chr2A.!!$R5 2628
12 TraesCS2B01G353900 chr2A 559826181 559830849 4668 True 784.250000 1687 90.457000 2 2601 4 chr2A.!!$R6 2599
13 TraesCS2B01G353900 chr2A 559838386 559838902 516 True 237.000000 237 75.774000 2 539 1 chr2A.!!$R3 537

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
654 15469 0.400213 CTTAACCACAGGTGCCTCCA 59.6 55.0 0.0 0.0 35.34 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2605 20352 0.034059 CTCTTGGCAAGACGGTCTGT 59.966 55.0 25.38 0.0 33.12 3.41 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
308 9399 8.498575 TGTATGGTCTCACATGGGATAAAAATA 58.501 33.333 0.00 0.00 32.39 1.40
309 9400 9.520515 GTATGGTCTCACATGGGATAAAAATAT 57.479 33.333 0.00 0.00 32.39 1.28
310 9401 7.822161 TGGTCTCACATGGGATAAAAATATG 57.178 36.000 0.00 0.00 0.00 1.78
311 9402 6.777091 TGGTCTCACATGGGATAAAAATATGG 59.223 38.462 0.00 0.00 0.00 2.74
312 9403 7.004086 GGTCTCACATGGGATAAAAATATGGA 58.996 38.462 0.00 0.00 0.00 3.41
317 9408 7.285172 TCACATGGGATAAAAATATGGAGTGTG 59.715 37.037 0.00 0.00 33.86 3.82
457 15017 2.992817 ATTTGTCAAGCCACCGCCCA 62.993 55.000 0.00 0.00 34.57 5.36
586 15158 4.332543 AAGGCGTGGGAGGGAGGA 62.333 66.667 0.00 0.00 0.00 3.71
654 15469 0.400213 CTTAACCACAGGTGCCTCCA 59.600 55.000 0.00 0.00 35.34 3.86
665 15480 2.579860 AGGTGCCTCCATCAATTCTCTT 59.420 45.455 0.00 0.00 39.02 2.85
668 15483 4.205587 GTGCCTCCATCAATTCTCTTGAT 58.794 43.478 0.00 0.00 39.53 2.57
736 15552 2.296471 AGGTGTTCCGAAGCCTATATCG 59.704 50.000 3.07 0.00 39.05 2.92
751 15569 6.157994 AGCCTATATCGCCATCCCTTTTATAA 59.842 38.462 0.00 0.00 0.00 0.98
907 16246 6.553857 ACCGAATTAGACACCCTCTATCTAT 58.446 40.000 0.00 0.00 31.11 1.98
924 16263 8.023021 TCTATCTATTGTGCCATCTGTACTTT 57.977 34.615 0.00 0.00 0.00 2.66
1019 16377 1.417890 CCCAGGGCATAATCGAACTCT 59.582 52.381 0.00 0.00 0.00 3.24
1020 16378 2.548920 CCCAGGGCATAATCGAACTCTC 60.549 54.545 0.00 0.00 0.00 3.20
1021 16379 2.366916 CCAGGGCATAATCGAACTCTCT 59.633 50.000 0.00 0.00 0.00 3.10
1022 16380 3.553922 CCAGGGCATAATCGAACTCTCTC 60.554 52.174 0.00 0.00 0.00 3.20
1253 16618 2.528127 TCTTGTCCTTGCCCCCGA 60.528 61.111 0.00 0.00 0.00 5.14
2213 19740 4.154918 GCTGGACATAAGCACCATATTAGC 59.845 45.833 0.00 0.00 40.52 3.09
2214 19741 5.303259 TGGACATAAGCACCATATTAGCA 57.697 39.130 0.00 0.00 0.00 3.49
2215 19742 5.879763 TGGACATAAGCACCATATTAGCAT 58.120 37.500 0.00 0.00 0.00 3.79
2216 19743 7.014988 TGGACATAAGCACCATATTAGCATA 57.985 36.000 0.00 0.00 0.00 3.14
2242 19976 9.948964 ATATAAGCTGTAATGTTCATGCATCTA 57.051 29.630 0.00 0.00 0.00 1.98
2332 20076 4.213270 TGTTGTTGAAGCGACTTCTAATGG 59.787 41.667 16.76 0.00 40.73 3.16
2563 20310 2.961768 CAATTCTGGGCGCCGTTT 59.038 55.556 22.54 6.24 0.00 3.60
2596 20343 1.710013 TTCTTTGGCTCATCGTCGTC 58.290 50.000 0.00 0.00 0.00 4.20
2603 20350 1.471676 GGCTCATCGTCGTCTTTGGAT 60.472 52.381 0.00 0.00 0.00 3.41
2605 20352 2.735444 GCTCATCGTCGTCTTTGGATGA 60.735 50.000 2.97 2.97 42.02 2.92
2633 20380 2.038557 GTCTTGCCAAGAGGGTGTTAGA 59.961 50.000 7.55 0.00 38.41 2.10
2634 20381 2.038557 TCTTGCCAAGAGGGTGTTAGAC 59.961 50.000 2.24 0.00 39.65 2.59
2635 20382 1.729586 TGCCAAGAGGGTGTTAGACT 58.270 50.000 0.00 0.00 39.65 3.24
2636 20383 1.347707 TGCCAAGAGGGTGTTAGACTG 59.652 52.381 0.00 0.00 39.65 3.51
2639 20386 3.197983 GCCAAGAGGGTGTTAGACTGTAT 59.802 47.826 0.00 0.00 39.65 2.29
2641 20388 5.803470 GCCAAGAGGGTGTTAGACTGTATTT 60.803 44.000 0.00 0.00 39.65 1.40
2643 20390 6.817140 CCAAGAGGGTGTTAGACTGTATTTAC 59.183 42.308 0.00 0.00 0.00 2.01
2645 20392 7.735326 AGAGGGTGTTAGACTGTATTTACAT 57.265 36.000 0.00 0.00 35.36 2.29
2646 20393 7.556844 AGAGGGTGTTAGACTGTATTTACATG 58.443 38.462 0.00 0.00 35.36 3.21
2648 20395 7.103641 AGGGTGTTAGACTGTATTTACATGTG 58.896 38.462 9.11 0.00 35.36 3.21
2650 20397 8.036575 GGGTGTTAGACTGTATTTACATGTGTA 58.963 37.037 9.11 0.00 35.36 2.90
2651 20398 9.595823 GGTGTTAGACTGTATTTACATGTGTAT 57.404 33.333 9.11 4.21 35.36 2.29
2719 21192 2.291043 CCTAGAGGGTTGTGCCGGT 61.291 63.158 1.90 0.00 38.44 5.28
2720 21193 1.677552 CTAGAGGGTTGTGCCGGTT 59.322 57.895 1.90 0.00 38.44 4.44
2721 21194 0.391263 CTAGAGGGTTGTGCCGGTTC 60.391 60.000 1.90 0.00 38.44 3.62
2723 21196 4.280019 AGGGTTGTGCCGGTTCCC 62.280 66.667 1.90 8.32 38.44 3.97
2742 21215 2.532250 CCCCCAAAGCCTATTGTCTT 57.468 50.000 0.00 0.00 0.00 3.01
2743 21216 3.662759 CCCCCAAAGCCTATTGTCTTA 57.337 47.619 0.00 0.00 0.00 2.10
2744 21217 3.288092 CCCCCAAAGCCTATTGTCTTAC 58.712 50.000 0.00 0.00 0.00 2.34
2745 21218 3.308832 CCCCCAAAGCCTATTGTCTTACA 60.309 47.826 0.00 0.00 0.00 2.41
2746 21219 4.536765 CCCCAAAGCCTATTGTCTTACAT 58.463 43.478 0.00 0.00 0.00 2.29
2747 21220 4.339247 CCCCAAAGCCTATTGTCTTACATG 59.661 45.833 0.00 0.00 0.00 3.21
2748 21221 4.339247 CCCAAAGCCTATTGTCTTACATGG 59.661 45.833 0.00 0.00 0.00 3.66
2749 21222 4.949856 CCAAAGCCTATTGTCTTACATGGT 59.050 41.667 0.00 0.00 0.00 3.55
2750 21223 6.119536 CCAAAGCCTATTGTCTTACATGGTA 58.880 40.000 0.00 0.00 0.00 3.25
2751 21224 6.772716 CCAAAGCCTATTGTCTTACATGGTAT 59.227 38.462 0.00 0.00 0.00 2.73
2752 21225 7.041098 CCAAAGCCTATTGTCTTACATGGTATC 60.041 40.741 0.00 0.00 0.00 2.24
2756 21229 5.405571 CCTATTGTCTTACATGGTATCACGC 59.594 44.000 0.00 0.00 0.00 5.34
2758 21231 5.585820 TTGTCTTACATGGTATCACGCTA 57.414 39.130 0.00 0.00 0.00 4.26
2759 21232 5.183014 TGTCTTACATGGTATCACGCTAG 57.817 43.478 0.00 0.00 0.00 3.42
2760 21233 4.037565 TGTCTTACATGGTATCACGCTAGG 59.962 45.833 0.00 0.00 0.00 3.02
2761 21234 4.037684 GTCTTACATGGTATCACGCTAGGT 59.962 45.833 0.00 0.00 0.00 3.08
2762 21235 4.647853 TCTTACATGGTATCACGCTAGGTT 59.352 41.667 0.00 0.00 0.00 3.50
2763 21236 5.829391 TCTTACATGGTATCACGCTAGGTTA 59.171 40.000 0.00 0.00 0.00 2.85
2764 21237 4.317671 ACATGGTATCACGCTAGGTTAC 57.682 45.455 0.00 0.00 0.00 2.50
2765 21238 3.243301 ACATGGTATCACGCTAGGTTACG 60.243 47.826 0.00 0.00 0.00 3.18
2767 21240 2.355756 TGGTATCACGCTAGGTTACGTC 59.644 50.000 0.00 0.00 41.32 4.34
2769 21242 0.379669 ATCACGCTAGGTTACGTCCG 59.620 55.000 0.00 0.00 41.32 4.79
2770 21243 1.870901 CACGCTAGGTTACGTCCGC 60.871 63.158 0.00 0.00 41.32 5.54
2771 21244 2.042831 ACGCTAGGTTACGTCCGCT 61.043 57.895 0.00 0.00 38.28 5.52
2772 21245 1.138247 CGCTAGGTTACGTCCGCTT 59.862 57.895 0.00 0.00 0.00 4.68
2773 21246 0.864797 CGCTAGGTTACGTCCGCTTC 60.865 60.000 0.00 0.00 0.00 3.86
2774 21247 0.527169 GCTAGGTTACGTCCGCTTCC 60.527 60.000 0.00 0.00 0.00 3.46
2775 21248 0.248377 CTAGGTTACGTCCGCTTCCG 60.248 60.000 0.00 0.00 0.00 4.30
2776 21249 2.270297 TAGGTTACGTCCGCTTCCGC 62.270 60.000 0.00 0.00 0.00 5.54
2777 21250 3.184003 GTTACGTCCGCTTCCGCC 61.184 66.667 0.00 0.00 0.00 6.13
2778 21251 3.376078 TTACGTCCGCTTCCGCCT 61.376 61.111 0.00 0.00 0.00 5.52
2780 21253 1.594194 TTACGTCCGCTTCCGCCTAA 61.594 55.000 0.00 0.00 0.00 2.69
2782 21255 1.738830 CGTCCGCTTCCGCCTAAAA 60.739 57.895 0.00 0.00 0.00 1.52
2783 21256 1.293267 CGTCCGCTTCCGCCTAAAAA 61.293 55.000 0.00 0.00 0.00 1.94
2784 21257 0.167470 GTCCGCTTCCGCCTAAAAAC 59.833 55.000 0.00 0.00 0.00 2.43
2785 21258 0.956902 TCCGCTTCCGCCTAAAAACC 60.957 55.000 0.00 0.00 0.00 3.27
2788 21261 1.676615 CGCTTCCGCCTAAAAACCCTA 60.677 52.381 0.00 0.00 0.00 3.53
2789 21262 2.439409 GCTTCCGCCTAAAAACCCTAA 58.561 47.619 0.00 0.00 0.00 2.69
2790 21263 2.821378 GCTTCCGCCTAAAAACCCTAAA 59.179 45.455 0.00 0.00 0.00 1.85
2793 21266 1.469703 CCGCCTAAAAACCCTAAACCG 59.530 52.381 0.00 0.00 0.00 4.44
2794 21267 1.135603 CGCCTAAAAACCCTAAACCGC 60.136 52.381 0.00 0.00 0.00 5.68
2795 21268 1.203052 GCCTAAAAACCCTAAACCGCC 59.797 52.381 0.00 0.00 0.00 6.13
2796 21269 1.469703 CCTAAAAACCCTAAACCGCCG 59.530 52.381 0.00 0.00 0.00 6.46
2797 21270 0.880441 TAAAAACCCTAAACCGCCGC 59.120 50.000 0.00 0.00 0.00 6.53
2798 21271 1.808531 AAAAACCCTAAACCGCCGCC 61.809 55.000 0.00 0.00 0.00 6.13
2856 21329 3.900892 CCGTCGCCCGACTGCTAT 61.901 66.667 17.39 0.00 42.54 2.97
2857 21330 2.655364 CGTCGCCCGACTGCTATG 60.655 66.667 17.39 0.00 42.54 2.23
2858 21331 2.805546 GTCGCCCGACTGCTATGA 59.194 61.111 13.10 0.00 41.57 2.15
2859 21332 1.589196 GTCGCCCGACTGCTATGAC 60.589 63.158 13.10 0.00 41.57 3.06
2860 21333 2.655364 CGCCCGACTGCTATGACG 60.655 66.667 0.00 0.00 0.00 4.35
2861 21334 2.494918 GCCCGACTGCTATGACGT 59.505 61.111 0.00 0.00 0.00 4.34
2862 21335 1.589196 GCCCGACTGCTATGACGTC 60.589 63.158 9.11 9.11 0.00 4.34
2863 21336 1.065928 CCCGACTGCTATGACGTCC 59.934 63.158 14.12 0.00 0.00 4.79
2864 21337 1.298413 CCGACTGCTATGACGTCCG 60.298 63.158 14.12 6.35 0.00 4.79
2867 21340 2.655364 CTGCTATGACGTCCGCCG 60.655 66.667 14.12 5.90 44.03 6.46
2868 21341 4.865761 TGCTATGACGTCCGCCGC 62.866 66.667 14.12 10.82 41.42 6.53
2869 21342 4.570663 GCTATGACGTCCGCCGCT 62.571 66.667 14.12 0.00 41.42 5.52
2870 21343 2.655364 CTATGACGTCCGCCGCTG 60.655 66.667 14.12 0.00 41.42 5.18
2871 21344 4.865761 TATGACGTCCGCCGCTGC 62.866 66.667 14.12 0.00 41.42 5.25
2901 21374 4.038080 CGCCACCGGTTTTCTGCC 62.038 66.667 2.97 0.00 0.00 4.85
2908 21381 3.062466 GGTTTTCTGCCGGCCTCC 61.062 66.667 26.77 13.01 0.00 4.30
2909 21382 3.062466 GTTTTCTGCCGGCCTCCC 61.062 66.667 26.77 2.75 0.00 4.30
2926 22560 2.578178 CTCGCGGCACTTCTCTCG 60.578 66.667 6.13 0.00 0.00 4.04
2927 22561 3.040414 CTCGCGGCACTTCTCTCGA 62.040 63.158 6.13 0.00 0.00 4.04
2928 22562 2.578178 CGCGGCACTTCTCTCGAG 60.578 66.667 5.93 5.93 0.00 4.04
2929 22563 2.202676 GCGGCACTTCTCTCGAGG 60.203 66.667 13.56 3.44 0.00 4.63
2930 22564 2.202676 CGGCACTTCTCTCGAGGC 60.203 66.667 13.56 6.57 0.00 4.70
2931 22565 2.185608 GGCACTTCTCTCGAGGCC 59.814 66.667 13.56 12.42 0.00 5.19
2932 22566 2.202676 GCACTTCTCTCGAGGCCG 60.203 66.667 13.56 1.70 37.07 6.13
2935 22569 2.103934 CTTCTCTCGAGGCCGCTG 59.896 66.667 13.56 0.00 35.37 5.18
2936 22570 3.423162 CTTCTCTCGAGGCCGCTGG 62.423 68.421 13.56 0.00 35.37 4.85
2937 22571 3.938637 TTCTCTCGAGGCCGCTGGA 62.939 63.158 13.56 1.48 35.37 3.86
2938 22572 3.222855 CTCTCGAGGCCGCTGGAT 61.223 66.667 13.56 0.00 35.37 3.41
2939 22573 3.496875 CTCTCGAGGCCGCTGGATG 62.497 68.421 13.56 0.00 35.37 3.51
2950 22584 3.801997 CTGGATGCCGCCTCCCTT 61.802 66.667 11.73 0.00 31.32 3.95
2952 22586 3.797353 GGATGCCGCCTCCCTTCA 61.797 66.667 3.36 0.00 0.00 3.02
2953 22587 2.203126 GATGCCGCCTCCCTTCAG 60.203 66.667 0.00 0.00 0.00 3.02
2954 22588 3.764160 GATGCCGCCTCCCTTCAGG 62.764 68.421 0.00 0.00 36.50 3.86
2960 23183 3.068691 CCTCCCTTCAGGCGTCGA 61.069 66.667 0.00 0.00 34.51 4.20
2963 23186 2.278857 CCCTTCAGGCGTCGATCG 60.279 66.667 9.36 9.36 43.12 3.69
2965 23188 2.278857 CTTCAGGCGTCGATCGGG 60.279 66.667 16.41 8.98 40.26 5.14
2972 23195 3.502455 CGTCGATCGGGACACGGA 61.502 66.667 16.41 0.00 44.45 4.69
2975 23198 4.907034 CGATCGGGACACGGAGCG 62.907 72.222 7.38 0.00 46.36 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 8405 6.075918 CACTTTGTTTCAACGAGATCATCTG 58.924 40.000 0.00 0.00 0.00 2.90
267 8586 9.461312 TGAGACCATACATGCTAATTTTAAAGT 57.539 29.630 0.00 0.00 0.00 2.66
308 9399 3.211865 GCATGATCACATCACACTCCAT 58.788 45.455 0.00 0.00 43.01 3.41
309 9400 2.635714 GCATGATCACATCACACTCCA 58.364 47.619 0.00 0.00 43.01 3.86
310 9401 1.945394 GGCATGATCACATCACACTCC 59.055 52.381 0.00 0.00 43.01 3.85
311 9402 1.596260 CGGCATGATCACATCACACTC 59.404 52.381 0.00 0.00 43.01 3.51
312 9403 1.207811 TCGGCATGATCACATCACACT 59.792 47.619 0.00 0.00 43.01 3.55
317 9408 1.146637 GAGCTCGGCATGATCACATC 58.853 55.000 0.00 0.00 34.15 3.06
457 15017 4.159879 CAGAAGGAACGGAGTACCTTGTAT 59.840 45.833 0.00 0.00 45.00 2.29
665 15480 8.088365 TCAAGAGAAACGAGTCTCAAAATATCA 58.912 33.333 18.05 0.00 45.55 2.15
668 15483 8.657074 TTTCAAGAGAAACGAGTCTCAAAATA 57.343 30.769 18.05 3.06 45.55 1.40
1019 16377 3.779738 TCAGTGGATCTGAGAGAGAGAGA 59.220 47.826 0.00 0.00 46.77 3.10
1020 16378 4.155063 TCAGTGGATCTGAGAGAGAGAG 57.845 50.000 0.00 0.00 46.77 3.20
1733 18671 3.730715 CCACAACTGAAATGAAACGAAGC 59.269 43.478 0.00 0.00 0.00 3.86
2014 19122 8.974060 TTTGAAACTGAAACTGGAGTAGTAAT 57.026 30.769 0.00 0.00 39.18 1.89
2215 19742 9.948964 AGATGCATGAACATTACAGCTTATATA 57.051 29.630 2.46 0.00 0.00 0.86
2216 19743 8.859236 AGATGCATGAACATTACAGCTTATAT 57.141 30.769 2.46 0.00 0.00 0.86
2242 19976 9.802039 TGGTTTAAAATCTGTTAGGTAAGTCAT 57.198 29.630 0.00 0.00 0.00 3.06
2332 20076 6.489361 ACCATTGATATCTTTGATCCAAGCTC 59.511 38.462 3.98 0.56 0.00 4.09
2563 20310 6.820656 TGAGCCAAAGAAAAAGTTTGCATTTA 59.179 30.769 0.00 0.00 34.18 1.40
2605 20352 0.034059 CTCTTGGCAAGACGGTCTGT 59.966 55.000 25.38 0.00 33.12 3.41
2676 21149 9.333961 GGGGTGGCCTATCACATATATATATAA 57.666 37.037 3.32 0.00 39.27 0.98
2678 21151 7.557283 AGGGGTGGCCTATCACATATATATAT 58.443 38.462 3.32 0.00 39.27 0.86
2679 21152 6.945371 AGGGGTGGCCTATCACATATATATA 58.055 40.000 3.32 0.00 39.27 0.86
2688 21161 1.343069 CTCTAGGGGTGGCCTATCAC 58.657 60.000 3.32 0.00 36.95 3.06
2690 21163 3.074788 CCTCTAGGGGTGGCCTATC 57.925 63.158 3.32 0.00 0.00 2.08
2701 21174 1.838073 AACCGGCACAACCCTCTAGG 61.838 60.000 0.00 0.00 43.78 3.02
2703 21176 1.675219 GAACCGGCACAACCCTCTA 59.325 57.895 0.00 0.00 33.26 2.43
2705 21178 2.671963 GGAACCGGCACAACCCTC 60.672 66.667 0.00 0.00 33.26 4.30
2723 21196 2.532250 AAGACAATAGGCTTTGGGGG 57.468 50.000 0.00 0.00 0.00 5.40
2724 21197 3.963129 TGTAAGACAATAGGCTTTGGGG 58.037 45.455 0.00 0.00 0.00 4.96
2725 21198 4.339247 CCATGTAAGACAATAGGCTTTGGG 59.661 45.833 0.00 0.00 0.00 4.12
2726 21199 4.949856 ACCATGTAAGACAATAGGCTTTGG 59.050 41.667 0.00 0.00 0.00 3.28
2727 21200 7.498900 TGATACCATGTAAGACAATAGGCTTTG 59.501 37.037 0.00 0.00 0.00 2.77
2728 21201 7.499232 GTGATACCATGTAAGACAATAGGCTTT 59.501 37.037 0.00 0.00 0.00 3.51
2729 21202 6.992715 GTGATACCATGTAAGACAATAGGCTT 59.007 38.462 0.00 0.00 0.00 4.35
2730 21203 6.525629 GTGATACCATGTAAGACAATAGGCT 58.474 40.000 0.00 0.00 0.00 4.58
2731 21204 5.405571 CGTGATACCATGTAAGACAATAGGC 59.594 44.000 0.00 0.00 0.00 3.93
2732 21205 5.405571 GCGTGATACCATGTAAGACAATAGG 59.594 44.000 0.00 0.00 0.00 2.57
2733 21206 6.216569 AGCGTGATACCATGTAAGACAATAG 58.783 40.000 0.00 0.00 0.00 1.73
2734 21207 6.156748 AGCGTGATACCATGTAAGACAATA 57.843 37.500 0.00 0.00 0.00 1.90
2735 21208 5.023533 AGCGTGATACCATGTAAGACAAT 57.976 39.130 0.00 0.00 0.00 2.71
2736 21209 4.465632 AGCGTGATACCATGTAAGACAA 57.534 40.909 0.00 0.00 0.00 3.18
2737 21210 4.037565 CCTAGCGTGATACCATGTAAGACA 59.962 45.833 0.00 0.00 0.00 3.41
2738 21211 4.037684 ACCTAGCGTGATACCATGTAAGAC 59.962 45.833 0.00 0.00 0.00 3.01
2739 21212 4.212716 ACCTAGCGTGATACCATGTAAGA 58.787 43.478 0.00 0.00 0.00 2.10
2740 21213 4.585955 ACCTAGCGTGATACCATGTAAG 57.414 45.455 0.00 0.00 0.00 2.34
2741 21214 5.506151 CGTAACCTAGCGTGATACCATGTAA 60.506 44.000 0.00 0.00 0.00 2.41
2742 21215 4.023792 CGTAACCTAGCGTGATACCATGTA 60.024 45.833 0.00 0.00 0.00 2.29
2743 21216 3.243301 CGTAACCTAGCGTGATACCATGT 60.243 47.826 0.00 0.00 0.00 3.21
2744 21217 3.243301 ACGTAACCTAGCGTGATACCATG 60.243 47.826 0.00 0.00 40.03 3.66
2745 21218 2.954318 ACGTAACCTAGCGTGATACCAT 59.046 45.455 0.00 0.00 40.03 3.55
2746 21219 2.355756 GACGTAACCTAGCGTGATACCA 59.644 50.000 0.00 0.00 41.70 3.25
2747 21220 2.287248 GGACGTAACCTAGCGTGATACC 60.287 54.545 0.00 0.00 41.70 2.73
2748 21221 2.600792 CGGACGTAACCTAGCGTGATAC 60.601 54.545 0.00 0.00 41.70 2.24
2749 21222 1.599071 CGGACGTAACCTAGCGTGATA 59.401 52.381 0.00 0.00 41.70 2.15
2750 21223 0.379669 CGGACGTAACCTAGCGTGAT 59.620 55.000 0.00 0.00 41.70 3.06
2751 21224 1.796151 CGGACGTAACCTAGCGTGA 59.204 57.895 0.00 0.00 41.70 4.35
2752 21225 1.870901 GCGGACGTAACCTAGCGTG 60.871 63.158 0.00 0.00 41.70 5.34
2756 21229 0.248377 CGGAAGCGGACGTAACCTAG 60.248 60.000 0.00 0.00 0.00 3.02
2758 21231 2.570181 CGGAAGCGGACGTAACCT 59.430 61.111 0.00 0.00 0.00 3.50
2770 21243 3.192001 GGTTTAGGGTTTTTAGGCGGAAG 59.808 47.826 0.00 0.00 0.00 3.46
2771 21244 3.156293 GGTTTAGGGTTTTTAGGCGGAA 58.844 45.455 0.00 0.00 0.00 4.30
2772 21245 2.794103 GGTTTAGGGTTTTTAGGCGGA 58.206 47.619 0.00 0.00 0.00 5.54
2773 21246 1.469703 CGGTTTAGGGTTTTTAGGCGG 59.530 52.381 0.00 0.00 0.00 6.13
2774 21247 1.135603 GCGGTTTAGGGTTTTTAGGCG 60.136 52.381 0.00 0.00 0.00 5.52
2775 21248 1.203052 GGCGGTTTAGGGTTTTTAGGC 59.797 52.381 0.00 0.00 0.00 3.93
2776 21249 1.469703 CGGCGGTTTAGGGTTTTTAGG 59.530 52.381 0.00 0.00 0.00 2.69
2777 21250 1.135603 GCGGCGGTTTAGGGTTTTTAG 60.136 52.381 9.78 0.00 0.00 1.85
2778 21251 0.880441 GCGGCGGTTTAGGGTTTTTA 59.120 50.000 9.78 0.00 0.00 1.52
2780 21253 2.270257 GGCGGCGGTTTAGGGTTTT 61.270 57.895 9.78 0.00 0.00 2.43
2841 21314 1.589196 GTCATAGCAGTCGGGCGAC 60.589 63.158 0.00 0.00 44.86 5.19
2842 21315 2.805546 GTCATAGCAGTCGGGCGA 59.194 61.111 0.00 0.00 39.27 5.54
2844 21317 1.589196 GACGTCATAGCAGTCGGGC 60.589 63.158 11.55 0.00 0.00 6.13
2845 21318 1.065928 GGACGTCATAGCAGTCGGG 59.934 63.158 18.91 0.00 35.87 5.14
2846 21319 1.298413 CGGACGTCATAGCAGTCGG 60.298 63.158 18.91 0.00 35.87 4.79
2847 21320 1.939785 GCGGACGTCATAGCAGTCG 60.940 63.158 18.91 9.94 35.87 4.18
2848 21321 1.589196 GGCGGACGTCATAGCAGTC 60.589 63.158 24.14 9.45 0.00 3.51
2849 21322 2.494918 GGCGGACGTCATAGCAGT 59.505 61.111 24.14 0.00 0.00 4.40
2850 21323 2.655364 CGGCGGACGTCATAGCAG 60.655 66.667 24.14 18.86 37.93 4.24
2851 21324 4.865761 GCGGCGGACGTCATAGCA 62.866 66.667 24.14 0.00 46.52 3.49
2852 21325 4.570663 AGCGGCGGACGTCATAGC 62.571 66.667 18.91 18.23 46.52 2.97
2853 21326 2.655364 CAGCGGCGGACGTCATAG 60.655 66.667 18.91 9.16 46.52 2.23
2854 21327 4.865761 GCAGCGGCGGACGTCATA 62.866 66.667 18.91 0.00 46.52 2.15
2878 21351 4.636435 AAACCGGTGGCGGTGGAG 62.636 66.667 8.52 0.00 42.06 3.86
2879 21352 4.192453 AAAACCGGTGGCGGTGGA 62.192 61.111 8.52 0.00 42.06 4.02
2880 21353 3.666253 GAAAACCGGTGGCGGTGG 61.666 66.667 8.52 0.00 42.06 4.61
2881 21354 2.593436 AGAAAACCGGTGGCGGTG 60.593 61.111 8.52 0.00 42.06 4.94
2882 21355 2.593436 CAGAAAACCGGTGGCGGT 60.593 61.111 8.52 0.00 45.25 5.68
2883 21356 4.038080 GCAGAAAACCGGTGGCGG 62.038 66.667 8.52 2.28 0.00 6.13
2891 21364 3.062466 GGAGGCCGGCAGAAAACC 61.062 66.667 30.85 16.82 0.00 3.27
2894 21367 3.717294 GAGGGAGGCCGGCAGAAA 61.717 66.667 30.85 0.00 0.00 2.52
2909 21382 2.578178 CGAGAGAAGTGCCGCGAG 60.578 66.667 8.23 0.00 0.00 5.03
2912 22546 2.202676 CCTCGAGAGAAGTGCCGC 60.203 66.667 15.71 0.00 41.32 6.53
2914 22548 2.185608 GGCCTCGAGAGAAGTGCC 59.814 66.667 15.71 13.28 41.32 5.01
2935 22569 3.764160 CTGAAGGGAGGCGGCATCC 62.764 68.421 24.64 24.64 35.99 3.51
2936 22570 2.203126 CTGAAGGGAGGCGGCATC 60.203 66.667 13.08 6.01 0.00 3.91
2937 22571 3.801997 CCTGAAGGGAGGCGGCAT 61.802 66.667 13.08 0.00 37.23 4.40
2943 22577 2.356818 GATCGACGCCTGAAGGGAGG 62.357 65.000 0.00 0.00 39.30 4.30
2944 22578 1.066587 GATCGACGCCTGAAGGGAG 59.933 63.158 0.00 0.00 40.87 4.30
2945 22579 2.771639 CGATCGACGCCTGAAGGGA 61.772 63.158 10.26 0.00 37.23 4.20
2946 22580 2.278857 CGATCGACGCCTGAAGGG 60.279 66.667 10.26 0.00 35.18 3.95
2948 22582 2.278857 CCCGATCGACGCCTGAAG 60.279 66.667 18.66 0.00 41.07 3.02
2950 22584 3.515286 GTCCCGATCGACGCCTGA 61.515 66.667 18.66 0.09 41.07 3.86
2952 22586 3.823330 GTGTCCCGATCGACGCCT 61.823 66.667 18.66 0.00 41.07 5.52
2956 23179 2.408022 CTCCGTGTCCCGATCGAC 59.592 66.667 18.66 8.46 39.56 4.20
2958 23181 4.907034 CGCTCCGTGTCCCGATCG 62.907 72.222 8.51 8.51 39.56 3.69
2960 23183 3.823330 GACGCTCCGTGTCCCGAT 61.823 66.667 0.00 0.00 41.37 4.18


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

AutoCloner maintained by Alex Coulton.