Multiple sequence alignment - TraesCS3B01G404600

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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 TraesCS3B01G404600 chr3B 100.000 3501 0 0 1 3501 639753240 639756740 0.000000e+00 6466.0
1 TraesCS3B01G404600 chr3B 90.992 2531 171 27 198 2679 639148588 639151110 0.000000e+00 3358.0
2 TraesCS3B01G404600 chr3B 90.747 2464 178 22 261 2679 639552876 639555334 0.000000e+00 3241.0
3 TraesCS3B01G404600 chr3B 90.644 2469 165 23 261 2679 639398421 639400873 0.000000e+00 3219.0
4 TraesCS3B01G404600 chr3B 89.417 2504 197 40 235 2679 638959697 638962191 0.000000e+00 3094.0
5 TraesCS3B01G404600 chr3B 89.674 1317 110 10 1513 2805 639772243 639773557 0.000000e+00 1655.0
6 TraesCS3B01G404600 chr3B 81.652 1259 164 43 1473 2680 639892681 639893923 0.000000e+00 983.0
7 TraesCS3B01G404600 chr3B 80.447 1253 182 37 1473 2679 639854830 639856065 0.000000e+00 898.0
8 TraesCS3B01G404600 chr3B 81.722 1138 148 28 1582 2680 639658496 639659612 0.000000e+00 894.0
9 TraesCS3B01G404600 chr3B 99.578 237 1 0 1 237 639397752 639397988 1.930000e-117 433.0
10 TraesCS3B01G404600 chr3B 99.578 237 1 0 1 237 639552140 639552376 1.930000e-117 433.0
11 TraesCS3B01G404600 chr3B 81.336 584 58 17 2144 2677 639773556 639774138 8.980000e-116 427.0
12 TraesCS3B01G404600 chr3B 98.305 236 2 2 1 234 638959406 638959641 2.510000e-111 412.0
13 TraesCS3B01G404600 chr3B 97.653 213 4 1 1 213 639148361 639148572 7.140000e-97 364.0
14 TraesCS3B01G404600 chr3B 74.850 668 124 33 2870 3499 639771491 639772152 2.680000e-66 263.0
15 TraesCS3B01G404600 chr3B 82.308 260 28 10 3207 3448 639894388 639894647 3.540000e-50 209.0
16 TraesCS3B01G404600 chr3B 85.612 139 19 1 2870 3008 639152505 639152642 1.010000e-30 145.0
17 TraesCS3B01G404600 chr3B 84.892 139 21 0 2870 3008 639782204 639782342 1.310000e-29 141.0
18 TraesCS3B01G404600 chr3B 84.892 139 20 1 2870 3008 639556743 639556880 4.710000e-29 139.0
19 TraesCS3B01G404600 chr3B 84.173 139 22 0 2870 3008 639767137 639767275 6.100000e-28 135.0
20 TraesCS3B01G404600 chr3B 95.122 82 2 2 2763 2842 638963049 638963130 1.020000e-25 128.0
21 TraesCS3B01G404600 chr3B 93.976 83 5 0 2761 2843 639836073 639836155 3.670000e-25 126.0
22 TraesCS3B01G404600 chr3B 93.976 83 4 1 2761 2843 639774137 639774218 1.320000e-24 124.0
23 TraesCS3B01G404600 chr3B 93.902 82 5 0 2761 2842 639856062 639856143 1.320000e-24 124.0
24 TraesCS3B01G404600 chr3B 92.683 82 4 2 2763 2842 639556200 639556281 2.210000e-22 117.0
25 TraesCS3B01G404600 chr3B 90.805 87 5 3 2761 2844 639876832 639876918 2.860000e-21 113.0
26 TraesCS3B01G404600 chr3B 88.506 87 7 3 2761 2844 639857017 639857103 6.180000e-18 102.0
27 TraesCS3B01G404600 chr3B 89.610 77 7 1 3000 3076 638965050 638965125 2.880000e-16 97.1
28 TraesCS3B01G404600 chr3B 89.610 77 7 1 3000 3076 639403824 639403899 2.880000e-16 97.1
29 TraesCS3B01G404600 chr3B 89.610 77 7 1 3000 3076 639563397 639563472 2.880000e-16 97.1
30 TraesCS3B01G404600 chr3B 87.209 86 9 2 2761 2844 639862326 639862411 2.880000e-16 97.1
31 TraesCS3B01G404600 chr3B 86.047 86 10 2 2761 2844 639999344 639999429 1.340000e-14 91.6
32 TraesCS3B01G404600 chr3B 85.714 77 11 0 3000 3076 639778548 639778624 8.050000e-12 82.4
33 TraesCS3B01G404600 chr3B 86.957 69 9 0 2777 2845 639852208 639852276 1.040000e-10 78.7
34 TraesCS3B01G404600 chr3D 91.800 2744 145 35 1 2679 478737602 478740330 0.000000e+00 3747.0
35 TraesCS3B01G404600 chr3D 86.415 2488 242 42 260 2677 479449734 479452195 0.000000e+00 2634.0
36 TraesCS3B01G404600 chr3D 86.048 1240 129 18 1473 2672 479894800 479893565 0.000000e+00 1291.0
37 TraesCS3B01G404600 chr3D 82.788 825 82 30 1887 2679 479213666 479214462 0.000000e+00 682.0
38 TraesCS3B01G404600 chr3D 82.519 778 86 34 2761 3496 479452194 479452963 3.810000e-179 638.0
39 TraesCS3B01G404600 chr3D 85.461 564 51 14 260 812 479918904 479918361 3.050000e-155 558.0
40 TraesCS3B01G404600 chr3D 88.706 425 36 8 3085 3501 479893208 479892788 3.120000e-140 508.0
41 TraesCS3B01G404600 chr3D 87.783 442 38 13 3074 3501 479912626 479912187 1.450000e-138 503.0
42 TraesCS3B01G404600 chr3D 87.765 425 42 8 3082 3499 479214811 479215232 4.060000e-134 488.0
43 TraesCS3B01G404600 chr3D 86.667 435 47 11 3074 3499 479123009 479123441 4.090000e-129 472.0
44 TraesCS3B01G404600 chr3D 84.479 451 44 15 3074 3499 478740659 478741108 4.180000e-114 422.0
45 TraesCS3B01G404600 chr3D 77.095 537 84 31 2870 3380 479455861 479456384 1.240000e-69 274.0
46 TraesCS3B01G404600 chr3D 90.270 185 12 2 1 179 479116175 479116359 1.620000e-58 237.0
47 TraesCS3B01G404600 chr3D 82.418 273 26 8 2758 3008 479214456 479214728 5.880000e-53 219.0
48 TraesCS3B01G404600 chr3D 81.852 270 27 3 2761 3008 479961402 479961133 1.270000e-49 207.0
49 TraesCS3B01G404600 chr3D 79.290 338 21 7 2762 3077 479893560 479893250 1.280000e-44 191.0
50 TraesCS3B01G404600 chr3D 77.778 342 26 13 2761 3077 479122662 479122978 7.770000e-37 165.0
51 TraesCS3B01G404600 chr3D 87.786 131 15 1 2870 3000 478746003 478746132 6.050000e-33 152.0
52 TraesCS3B01G404600 chr3D 94.000 100 4 2 3401 3499 479464656 479464754 2.180000e-32 150.0
53 TraesCS3B01G404600 chr3D 92.857 84 4 2 2761 2842 478741251 478741334 1.710000e-23 121.0
54 TraesCS3B01G404600 chr3D 92.771 83 6 0 2761 2843 478752668 478752750 1.710000e-23 121.0
55 TraesCS3B01G404600 chr3D 90.698 86 6 2 2761 2844 479123581 479123666 2.860000e-21 113.0
56 TraesCS3B01G404600 chr3D 90.541 74 7 0 3001 3074 479005999 479006072 8.000000e-17 99.0
57 TraesCS3B01G404600 chr3D 87.013 77 10 0 3000 3076 479019195 479019271 1.730000e-13 87.9
58 TraesCS3B01G404600 chr3D 90.698 43 2 2 2698 2740 479153630 479153670 4.880000e-04 56.5
59 TraesCS3B01G404600 chr3D 89.130 46 3 2 2698 2743 479866526 479866483 4.880000e-04 56.5
60 TraesCS3B01G404600 chr3D 89.130 46 3 2 2698 2743 479897585 479897542 4.880000e-04 56.5
61 TraesCS3B01G404600 chr3A 87.720 2557 189 56 198 2679 622276752 622279258 0.000000e+00 2867.0
62 TraesCS3B01G404600 chr3A 85.620 1370 145 26 274 1614 622817695 622819041 0.000000e+00 1391.0
63 TraesCS3B01G404600 chr3A 85.412 1371 148 24 274 1614 622718008 622719356 0.000000e+00 1376.0
64 TraesCS3B01G404600 chr3A 85.207 1379 153 29 260 1614 622709283 622710634 0.000000e+00 1369.0
65 TraesCS3B01G404600 chr3A 84.538 1384 139 36 274 1614 622898907 622900258 0.000000e+00 1301.0
66 TraesCS3B01G404600 chr3A 84.920 1061 119 14 1659 2679 622719359 622720418 0.000000e+00 1035.0
67 TraesCS3B01G404600 chr3A 84.652 1062 123 17 1658 2679 622819043 622820104 0.000000e+00 1022.0
68 TraesCS3B01G404600 chr3A 84.608 1059 122 17 1661 2679 622900263 622901320 0.000000e+00 1014.0
69 TraesCS3B01G404600 chr3A 83.221 894 110 17 1826 2679 622891720 622892613 0.000000e+00 784.0
70 TraesCS3B01G404600 chr3A 82.662 894 114 17 1826 2679 622801595 622802487 0.000000e+00 754.0
71 TraesCS3B01G404600 chr3A 81.552 786 90 28 2761 3501 622892610 622893385 6.470000e-167 597.0
72 TraesCS3B01G404600 chr3A 81.319 728 80 37 2761 3443 622720415 622721131 1.110000e-149 540.0
73 TraesCS3B01G404600 chr3A 88.759 427 38 9 3082 3501 622811746 622812169 6.700000e-142 514.0
74 TraesCS3B01G404600 chr3A 84.564 447 48 10 3074 3499 622279550 622279996 1.160000e-114 424.0
75 TraesCS3B01G404600 chr3A 93.506 154 10 0 1 154 622276600 622276753 2.720000e-56 230.0


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 TraesCS3B01G404600 chr3B 639753240 639756740 3500 False 6466.000000 6466 100.000000 1 3501 1 chr3B.!!$F3 3500
1 TraesCS3B01G404600 chr3B 639148361 639152642 4281 False 1289.000000 3358 91.419000 1 3008 3 chr3B.!!$F10 3007
2 TraesCS3B01G404600 chr3B 639397752 639403899 6147 False 1249.700000 3219 93.277333 1 3076 3 chr3B.!!$F11 3075
3 TraesCS3B01G404600 chr3B 639552140 639556880 4740 False 982.500000 3241 91.975000 1 3008 4 chr3B.!!$F12 3007
4 TraesCS3B01G404600 chr3B 638959406 638965125 5719 False 932.775000 3094 93.113500 1 3076 4 chr3B.!!$F9 3075
5 TraesCS3B01G404600 chr3B 639658496 639659612 1116 False 894.000000 894 81.722000 1582 2680 1 chr3B.!!$F2 1098
6 TraesCS3B01G404600 chr3B 639771491 639774218 2727 False 617.250000 1655 84.959000 1513 3499 4 chr3B.!!$F13 1986
7 TraesCS3B01G404600 chr3B 639892681 639894647 1966 False 596.000000 983 81.980000 1473 3448 2 chr3B.!!$F16 1975
8 TraesCS3B01G404600 chr3B 639852208 639857103 4895 False 300.675000 898 87.453000 1473 2845 4 chr3B.!!$F15 1372
9 TraesCS3B01G404600 chr3D 478737602 478741334 3732 False 1430.000000 3747 89.712000 1 3499 3 chr3D.!!$F8 3498
10 TraesCS3B01G404600 chr3D 479449734 479456384 6650 False 1182.000000 2634 82.009667 260 3496 3 chr3D.!!$F11 3236
11 TraesCS3B01G404600 chr3D 479918361 479918904 543 True 558.000000 558 85.461000 260 812 1 chr3D.!!$R3 552
12 TraesCS3B01G404600 chr3D 479892788 479897585 4797 True 511.625000 1291 85.793500 1473 3501 4 chr3D.!!$R5 2028
13 TraesCS3B01G404600 chr3D 479213666 479215232 1566 False 463.000000 682 84.323667 1887 3499 3 chr3D.!!$F10 1612
14 TraesCS3B01G404600 chr3D 479122662 479123666 1004 False 250.000000 472 85.047667 2761 3499 3 chr3D.!!$F9 738
15 TraesCS3B01G404600 chr3A 622709283 622710634 1351 False 1369.000000 1369 85.207000 260 1614 1 chr3A.!!$F1 1354
16 TraesCS3B01G404600 chr3A 622817695 622820104 2409 False 1206.500000 1391 85.136000 274 2679 2 chr3A.!!$F6 2405
17 TraesCS3B01G404600 chr3A 622276600 622279996 3396 False 1173.666667 2867 88.596667 1 3499 3 chr3A.!!$F4 3498
18 TraesCS3B01G404600 chr3A 622898907 622901320 2413 False 1157.500000 1301 84.573000 274 2679 2 chr3A.!!$F8 2405
19 TraesCS3B01G404600 chr3A 622718008 622721131 3123 False 983.666667 1376 83.883667 274 3443 3 chr3A.!!$F5 3169
20 TraesCS3B01G404600 chr3A 622801595 622802487 892 False 754.000000 754 82.662000 1826 2679 1 chr3A.!!$F2 853
21 TraesCS3B01G404600 chr3A 622891720 622893385 1665 False 690.500000 784 82.386500 1826 3501 2 chr3A.!!$F7 1675

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
723 1271 1.427020 CCTCGGGTTCGTCTCGTAC 59.573 63.158 3.16 0.0 41.36 3.67 F
1230 1839 0.462759 GGAATGCCGAGGAGTTCCAG 60.463 60.000 16.17 0.0 39.86 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2137 4758 0.037882 CTCCTCAGCTTTCAGACGCA 60.038 55.0 0.0 0.0 0.0 5.24 R
2862 5705 0.603065 GCAAAGGCGAAGAACCCATT 59.397 50.0 0.0 0.0 0.0 3.16 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
513 1059 1.623973 GAAGAGCACCGTGCCGTAAC 61.624 60.000 19.96 6.96 46.52 2.50
515 1061 1.957186 GAGCACCGTGCCGTAACAA 60.957 57.895 19.96 0.00 46.52 2.83
651 1197 3.633094 CTCAGTCGTCGGGCAGTGG 62.633 68.421 0.00 0.00 0.00 4.00
693 1239 3.123804 CGTCGGCTAGCTATTGAACAAT 58.876 45.455 15.72 5.40 34.93 2.71
723 1271 1.427020 CCTCGGGTTCGTCTCGTAC 59.573 63.158 3.16 0.00 41.36 3.67
1230 1839 0.462759 GGAATGCCGAGGAGTTCCAG 60.463 60.000 16.17 0.00 39.86 3.86
1674 4275 4.946038 GCACCAGCCAACGGTATA 57.054 55.556 0.00 0.00 34.02 1.47
1767 4371 3.404773 CCTCCTCAAGGTGGGGTC 58.595 66.667 8.96 0.00 43.36 4.46
1844 4448 2.742372 GAACTGCATGGGCGACGT 60.742 61.111 0.00 0.00 45.35 4.34
2182 4803 3.617531 CGGAGCTACTGACCAGTGAAAAT 60.618 47.826 12.54 0.00 42.52 1.82
2183 4804 4.327680 GGAGCTACTGACCAGTGAAAATT 58.672 43.478 12.54 0.00 42.52 1.82
2341 4974 1.617850 CCACCACTTGCCAATTGCTTA 59.382 47.619 0.00 0.00 42.00 3.09
2397 5044 2.223782 TGCTGATGAAAACACCTTGTGC 60.224 45.455 0.00 0.00 36.98 4.57
2449 5114 2.833794 CAGTCCAAGGAGAACGTGAAA 58.166 47.619 0.00 0.00 0.00 2.69
2505 5170 0.694771 AGCTGCATCAGGTGAAAGGA 59.305 50.000 1.02 0.00 40.87 3.36
2632 5344 6.355588 ACCTAAAACCCATAAGGATCCAAT 57.644 37.500 15.82 3.97 39.89 3.16
2633 5345 6.136155 ACCTAAAACCCATAAGGATCCAATG 58.864 40.000 15.82 16.25 39.89 2.82
2634 5346 6.136155 CCTAAAACCCATAAGGATCCAATGT 58.864 40.000 15.82 3.83 39.89 2.71
2636 5348 4.879295 AACCCATAAGGATCCAATGTCA 57.121 40.909 15.82 0.00 39.89 3.58
2637 5349 4.443978 ACCCATAAGGATCCAATGTCAG 57.556 45.455 15.82 10.13 39.89 3.51
2638 5350 3.788142 ACCCATAAGGATCCAATGTCAGT 59.212 43.478 15.82 10.69 39.89 3.41
2639 5351 4.139786 CCCATAAGGATCCAATGTCAGTG 58.860 47.826 15.82 4.29 38.24 3.66
2640 5352 4.385643 CCCATAAGGATCCAATGTCAGTGT 60.386 45.833 15.82 0.00 38.24 3.55
2643 5355 6.828273 CCATAAGGATCCAATGTCAGTGTTTA 59.172 38.462 15.82 0.00 36.89 2.01
2645 5357 9.559732 CATAAGGATCCAATGTCAGTGTTTATA 57.440 33.333 15.82 0.00 0.00 0.98
2647 5359 8.455903 AAGGATCCAATGTCAGTGTTTATATG 57.544 34.615 15.82 0.00 0.00 1.78
2649 5361 6.772716 GGATCCAATGTCAGTGTTTATATGGT 59.227 38.462 6.95 0.00 0.00 3.55
2650 5362 7.041098 GGATCCAATGTCAGTGTTTATATGGTC 60.041 40.741 6.95 0.00 0.00 4.02
2651 5363 6.716284 TCCAATGTCAGTGTTTATATGGTCA 58.284 36.000 0.00 0.00 0.00 4.02
2653 5365 7.336679 TCCAATGTCAGTGTTTATATGGTCAAG 59.663 37.037 0.00 0.00 0.00 3.02
2654 5366 6.683974 ATGTCAGTGTTTATATGGTCAAGC 57.316 37.500 0.00 0.00 0.00 4.01
2655 5367 5.555966 TGTCAGTGTTTATATGGTCAAGCA 58.444 37.500 0.00 0.00 0.00 3.91
2657 5369 6.149308 TGTCAGTGTTTATATGGTCAAGCAAG 59.851 38.462 0.00 0.00 0.00 4.01
2658 5370 6.149474 GTCAGTGTTTATATGGTCAAGCAAGT 59.851 38.462 0.00 0.00 0.00 3.16
2659 5371 6.149308 TCAGTGTTTATATGGTCAAGCAAGTG 59.851 38.462 0.00 0.00 0.00 3.16
2662 5374 6.801862 GTGTTTATATGGTCAAGCAAGTGAAC 59.198 38.462 0.00 0.00 35.66 3.18
2663 5375 6.714810 TGTTTATATGGTCAAGCAAGTGAACT 59.285 34.615 2.36 0.00 36.13 3.01
2677 5389 4.852609 AGTGAACTTGTGTTGTCGTTAC 57.147 40.909 0.00 0.00 36.39 2.50
2680 5392 5.747197 AGTGAACTTGTGTTGTCGTTACTAG 59.253 40.000 0.00 0.00 36.39 2.57
2683 5395 5.252969 ACTTGTGTTGTCGTTACTAGTGA 57.747 39.130 5.39 0.00 31.14 3.41
2684 5396 5.653507 ACTTGTGTTGTCGTTACTAGTGAA 58.346 37.500 5.39 0.00 31.14 3.18
2685 5397 6.278363 ACTTGTGTTGTCGTTACTAGTGAAT 58.722 36.000 5.39 0.00 31.14 2.57
2686 5398 6.759827 ACTTGTGTTGTCGTTACTAGTGAATT 59.240 34.615 5.39 0.00 31.14 2.17
2687 5399 7.279313 ACTTGTGTTGTCGTTACTAGTGAATTT 59.721 33.333 5.39 0.00 31.14 1.82
2688 5400 6.939627 TGTGTTGTCGTTACTAGTGAATTTG 58.060 36.000 5.39 0.00 0.00 2.32
2689 5401 6.535865 TGTGTTGTCGTTACTAGTGAATTTGT 59.464 34.615 5.39 0.00 0.00 2.83
2691 5403 7.906527 GTGTTGTCGTTACTAGTGAATTTGTTT 59.093 33.333 5.39 0.00 0.00 2.83
2692 5404 7.906010 TGTTGTCGTTACTAGTGAATTTGTTTG 59.094 33.333 5.39 0.00 0.00 2.93
2694 5406 7.623770 TGTCGTTACTAGTGAATTTGTTTGTC 58.376 34.615 5.39 0.00 0.00 3.18
2696 5408 6.068931 CGTTACTAGTGAATTTGTTTGTCGG 58.931 40.000 5.39 0.00 0.00 4.79
2697 5409 6.292488 CGTTACTAGTGAATTTGTTTGTCGGT 60.292 38.462 5.39 0.00 0.00 4.69
2698 5410 5.418310 ACTAGTGAATTTGTTTGTCGGTG 57.582 39.130 0.00 0.00 0.00 4.94
2701 5413 4.200874 AGTGAATTTGTTTGTCGGTGGTA 58.799 39.130 0.00 0.00 0.00 3.25
2702 5414 4.825085 AGTGAATTTGTTTGTCGGTGGTAT 59.175 37.500 0.00 0.00 0.00 2.73
2703 5415 5.048991 AGTGAATTTGTTTGTCGGTGGTATC 60.049 40.000 0.00 0.00 0.00 2.24
2706 5418 6.655425 TGAATTTGTTTGTCGGTGGTATCATA 59.345 34.615 0.00 0.00 0.00 2.15
2709 5421 7.455641 TTTGTTTGTCGGTGGTATCATAATT 57.544 32.000 0.00 0.00 0.00 1.40
2710 5422 7.455641 TTGTTTGTCGGTGGTATCATAATTT 57.544 32.000 0.00 0.00 0.00 1.82
2711 5423 7.079182 TGTTTGTCGGTGGTATCATAATTTC 57.921 36.000 0.00 0.00 0.00 2.17
2713 5425 8.041919 TGTTTGTCGGTGGTATCATAATTTCTA 58.958 33.333 0.00 0.00 0.00 2.10
2717 5429 8.573885 TGTCGGTGGTATCATAATTTCTACTAG 58.426 37.037 0.00 0.00 0.00 2.57
2733 5445 7.865706 TTCTACTAGTAGTACCTAAAACCCG 57.134 40.000 25.58 0.43 34.84 5.28
2734 5446 6.958767 TCTACTAGTAGTACCTAAAACCCGT 58.041 40.000 25.58 0.00 34.84 5.28
2735 5447 8.086143 TCTACTAGTAGTACCTAAAACCCGTA 57.914 38.462 25.58 1.87 34.84 4.02
2736 5448 8.545472 TCTACTAGTAGTACCTAAAACCCGTAA 58.455 37.037 25.58 1.52 34.84 3.18
2737 5449 7.631717 ACTAGTAGTACCTAAAACCCGTAAG 57.368 40.000 0.00 0.00 0.00 2.34
2752 5464 3.821421 CGTAAGGATCCTTTACCAGCT 57.179 47.619 31.45 7.96 37.47 4.24
2754 5466 3.741388 CGTAAGGATCCTTTACCAGCTGG 60.741 52.174 31.45 31.60 37.47 4.85
2756 5468 3.199946 TAAGGATCCTTTACCAGCTGGTG 59.800 47.826 42.35 28.01 41.86 4.17
2854 5697 5.591067 TGATGTGTACTCGATATGTGTGGTA 59.409 40.000 0.00 0.00 0.00 3.25
2868 5755 5.249780 TGTGTGGTACATTTCTAATGGGT 57.750 39.130 0.00 0.00 44.52 4.51
2916 5805 4.199432 AGTGGAGATGACACATGAGTTC 57.801 45.455 0.00 0.00 41.21 3.01
2950 5839 2.050168 CGCACTTTGCCGCATTGT 60.050 55.556 0.00 0.00 41.12 2.71
3121 6060 1.375908 CGGCTAGCCTTCAGTTGCA 60.376 57.895 30.55 0.00 0.00 4.08
3139 6078 1.838913 CACTTTCTTGTTGGCCAACG 58.161 50.000 36.62 26.06 43.94 4.10
3214 6179 4.512484 GGGTGATCCTCTTTTTCTCAGAG 58.488 47.826 0.00 0.00 38.03 3.35
3241 6207 5.614324 TCCTCCTACACTTACCATCATTG 57.386 43.478 0.00 0.00 0.00 2.82
3372 6376 2.496899 AGGAGAATGTCAACGCCAAT 57.503 45.000 6.11 0.00 0.00 3.16
3420 6448 0.476771 ATTTGGTGAACGGTGACCCT 59.523 50.000 6.64 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
253 783 5.045869 GGCCTGTTAGAAGCCCACATATATA 60.046 44.000 0.00 0.00 41.00 0.86
258 788 0.034089 GGCCTGTTAGAAGCCCACAT 60.034 55.000 0.00 0.00 41.00 3.21
515 1061 3.462205 GGGGGTTGGATTAGTACAAGGAT 59.538 47.826 0.00 0.00 0.00 3.24
693 1239 2.831742 CCGAGGGGCGTGCTAGTA 60.832 66.667 0.00 0.00 38.67 1.82
723 1271 1.736645 CCACGAGTTACGCCTGGTG 60.737 63.158 5.54 5.54 46.94 4.17
1138 1747 2.068519 CTCGCACACAGAGTATTGCAA 58.931 47.619 0.00 0.00 34.49 4.08
1197 1806 3.752747 CGGCATTCCATATGTTGCTCATA 59.247 43.478 17.07 5.06 42.30 2.15
1767 4371 4.280494 CCGGGGCTCACGATACCG 62.280 72.222 0.00 0.00 43.89 4.02
1844 4448 3.181451 GCCACCATTCTCCATCATCACTA 60.181 47.826 0.00 0.00 0.00 2.74
2046 4665 1.609208 GGAGTGCAAGTGTCACCAAT 58.391 50.000 0.00 0.00 35.14 3.16
2137 4758 0.037882 CTCCTCAGCTTTCAGACGCA 60.038 55.000 0.00 0.00 0.00 5.24
2138 4759 0.739112 CCTCCTCAGCTTTCAGACGC 60.739 60.000 0.00 0.00 0.00 5.19
2201 4822 7.073342 ACGGTAAGAACTGAAAAGAATATGC 57.927 36.000 0.00 0.00 35.79 3.14
2495 5160 0.768221 TGGCAGGTCTCCTTTCACCT 60.768 55.000 0.00 0.00 44.42 4.00
2632 5344 5.555966 TGCTTGACCATATAAACACTGACA 58.444 37.500 0.00 0.00 0.00 3.58
2633 5345 6.149474 ACTTGCTTGACCATATAAACACTGAC 59.851 38.462 0.00 0.00 0.00 3.51
2634 5346 6.149308 CACTTGCTTGACCATATAAACACTGA 59.851 38.462 0.00 0.00 0.00 3.41
2636 5348 6.237901 TCACTTGCTTGACCATATAAACACT 58.762 36.000 0.00 0.00 0.00 3.55
2637 5349 6.494893 TCACTTGCTTGACCATATAAACAC 57.505 37.500 0.00 0.00 0.00 3.32
2638 5350 6.714810 AGTTCACTTGCTTGACCATATAAACA 59.285 34.615 0.00 0.00 0.00 2.83
2639 5351 7.145932 AGTTCACTTGCTTGACCATATAAAC 57.854 36.000 0.00 0.00 0.00 2.01
2640 5352 7.592938 CAAGTTCACTTGCTTGACCATATAAA 58.407 34.615 6.75 0.00 45.59 1.40
2643 5355 5.633830 CAAGTTCACTTGCTTGACCATAT 57.366 39.130 6.75 0.00 45.59 1.78
2645 5357 3.996150 CAAGTTCACTTGCTTGACCAT 57.004 42.857 6.75 0.00 45.59 3.55
2655 5367 4.933400 AGTAACGACAACACAAGTTCACTT 59.067 37.500 0.00 0.00 35.28 3.16
2657 5369 4.852609 AGTAACGACAACACAAGTTCAC 57.147 40.909 0.00 0.00 35.28 3.18
2658 5370 5.517411 CACTAGTAACGACAACACAAGTTCA 59.483 40.000 0.00 0.00 35.28 3.18
2659 5371 5.745294 TCACTAGTAACGACAACACAAGTTC 59.255 40.000 0.00 0.00 35.28 3.01
2662 5374 6.764877 ATTCACTAGTAACGACAACACAAG 57.235 37.500 0.00 0.00 0.00 3.16
2663 5375 7.064847 ACAAATTCACTAGTAACGACAACACAA 59.935 33.333 0.00 0.00 0.00 3.33
2665 5377 6.940714 ACAAATTCACTAGTAACGACAACAC 58.059 36.000 0.00 0.00 0.00 3.32
2667 5379 7.906527 ACAAACAAATTCACTAGTAACGACAAC 59.093 33.333 0.00 0.00 0.00 3.32
2668 5380 7.976826 ACAAACAAATTCACTAGTAACGACAA 58.023 30.769 0.00 0.00 0.00 3.18
2672 5384 6.068931 CCGACAAACAAATTCACTAGTAACG 58.931 40.000 0.00 0.00 0.00 3.18
2677 5389 4.274950 ACCACCGACAAACAAATTCACTAG 59.725 41.667 0.00 0.00 0.00 2.57
2680 5392 3.430333 ACCACCGACAAACAAATTCAC 57.570 42.857 0.00 0.00 0.00 3.18
2683 5395 5.975693 ATGATACCACCGACAAACAAATT 57.024 34.783 0.00 0.00 0.00 1.82
2684 5396 7.639113 ATTATGATACCACCGACAAACAAAT 57.361 32.000 0.00 0.00 0.00 2.32
2685 5397 7.455641 AATTATGATACCACCGACAAACAAA 57.544 32.000 0.00 0.00 0.00 2.83
2686 5398 7.392113 AGAAATTATGATACCACCGACAAACAA 59.608 33.333 0.00 0.00 0.00 2.83
2687 5399 6.882140 AGAAATTATGATACCACCGACAAACA 59.118 34.615 0.00 0.00 0.00 2.83
2688 5400 7.316544 AGAAATTATGATACCACCGACAAAC 57.683 36.000 0.00 0.00 0.00 2.93
2689 5401 8.262227 AGTAGAAATTATGATACCACCGACAAA 58.738 33.333 0.00 0.00 0.00 2.83
2691 5403 7.356089 AGTAGAAATTATGATACCACCGACA 57.644 36.000 0.00 0.00 0.00 4.35
2692 5404 8.574737 ACTAGTAGAAATTATGATACCACCGAC 58.425 37.037 3.59 0.00 0.00 4.79
2709 5421 7.402862 ACGGGTTTTAGGTACTACTAGTAGAA 58.597 38.462 31.93 15.23 42.67 2.10
2710 5422 6.958767 ACGGGTTTTAGGTACTACTAGTAGA 58.041 40.000 31.93 15.41 42.67 2.59
2711 5423 8.732746 TTACGGGTTTTAGGTACTACTAGTAG 57.267 38.462 25.30 25.30 42.67 2.57
2713 5425 6.603599 CCTTACGGGTTTTAGGTACTACTAGT 59.396 42.308 0.00 0.00 42.67 2.57
2717 5429 5.914898 TCCTTACGGGTTTTAGGTACTAC 57.085 43.478 0.00 0.00 37.18 2.73
2723 5435 4.498894 AAGGATCCTTACGGGTTTTAGG 57.501 45.455 25.99 0.00 34.05 2.69
2724 5436 5.819379 GGTAAAGGATCCTTACGGGTTTTAG 59.181 44.000 27.29 0.00 34.84 1.85
2725 5437 5.250313 TGGTAAAGGATCCTTACGGGTTTTA 59.750 40.000 27.29 10.52 34.84 1.52
2726 5438 4.043184 TGGTAAAGGATCCTTACGGGTTTT 59.957 41.667 27.29 11.55 34.84 2.43
2727 5439 3.588396 TGGTAAAGGATCCTTACGGGTTT 59.412 43.478 27.29 12.29 34.84 3.27
2728 5440 3.183801 TGGTAAAGGATCCTTACGGGTT 58.816 45.455 27.29 13.02 34.84 4.11
2730 5442 2.484947 GCTGGTAAAGGATCCTTACGGG 60.485 54.545 27.29 16.32 34.84 5.28
2731 5443 2.434702 AGCTGGTAAAGGATCCTTACGG 59.565 50.000 27.29 23.05 34.84 4.02
2732 5444 3.458189 CAGCTGGTAAAGGATCCTTACG 58.542 50.000 27.29 14.10 34.84 3.18
2733 5445 3.809905 CCAGCTGGTAAAGGATCCTTAC 58.190 50.000 27.29 21.89 34.84 2.34
2747 5459 0.687354 AACAGTACTCCACCAGCTGG 59.313 55.000 31.60 31.60 42.29 4.85
2748 5460 2.550830 AAACAGTACTCCACCAGCTG 57.449 50.000 6.78 6.78 0.00 4.24
2750 5462 4.161754 ACCTATAAACAGTACTCCACCAGC 59.838 45.833 0.00 0.00 0.00 4.85
2752 5464 9.085645 CATATACCTATAAACAGTACTCCACCA 57.914 37.037 0.00 0.00 0.00 4.17
2795 5510 9.323985 CTAATTTTCTTTTGTTCCATTTGTCCA 57.676 29.630 0.00 0.00 0.00 4.02
2854 5697 3.694566 GGCGAAGAACCCATTAGAAATGT 59.305 43.478 0.00 0.00 0.00 2.71
2862 5705 0.603065 GCAAAGGCGAAGAACCCATT 59.397 50.000 0.00 0.00 0.00 3.16
2916 5805 2.348666 GTGCGCCTATGTGACTAAACTG 59.651 50.000 4.18 0.00 0.00 3.16
2997 5901 9.333497 GCTCAAATTTCATTGGATTTAAAAAGC 57.667 29.630 0.00 0.00 0.00 3.51
3121 6060 1.757682 TCGTTGGCCAACAAGAAAGT 58.242 45.000 39.91 0.00 40.38 2.66
3214 6179 6.650120 TGATGGTAAGTGTAGGAGGATTTTC 58.350 40.000 0.00 0.00 0.00 2.29
3241 6207 1.150827 GGTTCTTGCAAGCAATTGCC 58.849 50.000 26.45 12.24 46.82 4.52
3350 6354 2.151202 TGGCGTTGACATTCTCCTTTC 58.849 47.619 0.00 0.00 0.00 2.62
3403 6431 1.448497 GAGGGTCACCGTTCACCAA 59.552 57.895 0.00 0.00 43.47 3.67
3420 6448 4.272489 CAAGGCTATGGAAGTTGAATGGA 58.728 43.478 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.