Multiple sequence alignment - TraesCS2B01G404000

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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 TraesCS2B01G404000 chr2B 100.000 3610 0 0 1 3610 572180707 572177098 0.000000e+00 6667.0
1 TraesCS2B01G404000 chr2B 85.847 2268 213 53 1194 3392 572313757 572311529 0.000000e+00 2311.0
2 TraesCS2B01G404000 chr2B 83.514 1474 141 47 528 1937 571345478 571346913 0.000000e+00 1282.0
3 TraesCS2B01G404000 chr2B 83.500 1303 156 33 1925 3187 571346934 571348217 0.000000e+00 1160.0
4 TraesCS2B01G404000 chr2B 86.697 436 33 13 708 1120 572314292 572313859 9.130000e-126 460.0
5 TraesCS2B01G404000 chr2B 81.149 435 67 10 1413 1844 572324577 572324155 5.780000e-88 335.0
6 TraesCS2B01G404000 chr2B 88.889 180 15 5 150 327 37886387 37886563 2.180000e-52 217.0
7 TraesCS2B01G404000 chr2B 85.253 217 25 5 906 1120 572325283 572325072 2.180000e-52 217.0
8 TraesCS2B01G404000 chr2B 87.135 171 21 1 1177 1346 572324925 572324755 3.680000e-45 193.0
9 TraesCS2B01G404000 chr2B 87.662 154 10 6 3466 3610 572310901 572310748 1.720000e-38 171.0
10 TraesCS2B01G404000 chr2B 92.241 116 7 2 354 469 64555685 64555572 2.880000e-36 163.0
11 TraesCS2B01G404000 chr2D 92.436 2631 137 20 522 3121 487725399 487722800 0.000000e+00 3699.0
12 TraesCS2B01G404000 chr2D 89.762 2354 169 26 73 2382 487595079 487592754 0.000000e+00 2946.0
13 TraesCS2B01G404000 chr2D 84.278 2983 293 93 538 3392 487934903 487931969 0.000000e+00 2748.0
14 TraesCS2B01G404000 chr2D 85.010 2615 282 60 631 3187 486390421 486392983 0.000000e+00 2556.0
15 TraesCS2B01G404000 chr2D 91.365 498 40 2 3113 3610 487613877 487613383 0.000000e+00 678.0
16 TraesCS2B01G404000 chr2D 81.618 680 92 20 1171 1844 488058528 488057876 1.910000e-147 532.0
17 TraesCS2B01G404000 chr2D 87.805 205 19 4 924 1125 488058858 488058657 6.030000e-58 235.0
18 TraesCS2B01G404000 chr2D 90.964 166 13 2 163 327 87407362 87407526 4.690000e-54 222.0
19 TraesCS2B01G404000 chr2D 91.411 163 12 2 165 326 318257043 318256882 4.690000e-54 222.0
20 TraesCS2B01G404000 chr2D 84.821 224 27 2 637 860 488059497 488059281 6.070000e-53 219.0
21 TraesCS2B01G404000 chr2D 90.419 167 13 3 1 166 487725594 487725430 2.180000e-52 217.0
22 TraesCS2B01G404000 chr2D 92.373 118 7 1 351 468 11039640 11039755 2.230000e-37 167.0
23 TraesCS2B01G404000 chr2D 83.429 175 26 2 2039 2213 488057152 488056981 3.730000e-35 159.0
24 TraesCS2B01G404000 chr2D 88.660 97 6 2 3514 3610 487931409 487931318 2.950000e-21 113.0
25 TraesCS2B01G404000 chr2D 81.818 121 14 3 1881 2001 488057366 488057254 1.070000e-15 95.3
26 TraesCS2B01G404000 chr2A 82.941 2122 245 60 1190 3214 631855769 631857870 0.000000e+00 1805.0
27 TraesCS2B01G404000 chr2A 84.904 1570 171 34 1872 3401 632588116 632586573 0.000000e+00 1526.0
28 TraesCS2B01G404000 chr2A 88.921 695 55 14 1194 1872 632588884 632588196 0.000000e+00 837.0
29 TraesCS2B01G404000 chr2A 82.486 531 39 26 631 1122 631855156 631855671 2.010000e-112 416.0
30 TraesCS2B01G404000 chr2A 83.296 449 32 20 709 1120 632589430 632588988 1.220000e-99 374.0
31 TraesCS2B01G404000 chr2A 81.818 462 61 13 1413 1866 632594782 632594336 2.050000e-97 366.0
32 TraesCS2B01G404000 chr2A 87.281 228 24 5 636 861 632596352 632596128 4.630000e-64 255.0
33 TraesCS2B01G404000 chr2A 86.977 215 20 5 919 1131 632595506 632595298 6.030000e-58 235.0
34 TraesCS2B01G404000 chr7D 80.750 1626 189 54 1446 3017 446551621 446550066 0.000000e+00 1155.0
35 TraesCS2B01G404000 chr4B 81.613 1463 167 44 1443 2859 16786692 16788098 0.000000e+00 1118.0
36 TraesCS2B01G404000 chr4B 89.080 174 16 3 154 326 344463288 344463459 2.820000e-51 213.0
37 TraesCS2B01G404000 chr4B 88.268 179 17 4 152 327 135218034 135218211 1.020000e-50 211.0
38 TraesCS2B01G404000 chr4B 91.597 119 10 0 360 478 344463351 344463469 8.020000e-37 165.0
39 TraesCS2B01G404000 chr4B 93.636 110 7 0 360 469 453048614 453048505 8.020000e-37 165.0
40 TraesCS2B01G404000 chr7A 82.310 831 98 21 1909 2709 321636676 321635865 0.000000e+00 675.0
41 TraesCS2B01G404000 chr3D 80.916 917 113 30 2141 3014 16449271 16450168 0.000000e+00 667.0
42 TraesCS2B01G404000 chr3D 95.000 40 2 0 3400 3439 110337948 110337909 3.010000e-06 63.9
43 TraesCS2B01G404000 chr6B 81.555 759 93 17 1446 2200 247035819 247035104 1.870000e-162 582.0
44 TraesCS2B01G404000 chr6B 90.854 164 13 2 165 327 119526809 119526971 6.070000e-53 219.0
45 TraesCS2B01G404000 chrUn 83.478 575 76 12 2252 2808 195338034 195338607 5.340000e-143 518.0
46 TraesCS2B01G404000 chrUn 83.733 375 51 5 2252 2616 40175582 40175208 2.670000e-91 346.0
47 TraesCS2B01G404000 chrUn 84.925 199 27 2 2621 2817 40170469 40170272 7.910000e-47 198.0
48 TraesCS2B01G404000 chrUn 85.789 190 24 2 2621 2808 422925607 422925795 7.910000e-47 198.0
49 TraesCS2B01G404000 chrUn 95.192 104 5 0 366 469 141680848 141680745 8.020000e-37 165.0
50 TraesCS2B01G404000 chr4A 80.792 682 84 17 1446 2123 729645105 729644467 1.160000e-134 490.0
51 TraesCS2B01G404000 chr6A 79.138 441 49 21 2833 3240 226334905 226334475 7.690000e-67 265.0
52 TraesCS2B01G404000 chr7B 88.764 178 16 4 165 339 677889394 677889218 7.850000e-52 215.0
53 TraesCS2B01G404000 chr7B 93.636 110 7 0 360 469 114143378 114143487 8.020000e-37 165.0
54 TraesCS2B01G404000 chr7B 92.500 40 3 0 3400 3439 407388766 407388805 1.400000e-04 58.4
55 TraesCS2B01G404000 chr1B 93.636 110 7 0 360 469 139877903 139878012 8.020000e-37 165.0
56 TraesCS2B01G404000 chr1B 90.833 120 9 1 349 468 668064739 668064622 3.730000e-35 159.0
57 TraesCS2B01G404000 chr3B 84.337 83 8 4 12 91 68601786 68601706 3.870000e-10 76.8
58 TraesCS2B01G404000 chr3B 95.000 40 2 0 3400 3439 764119428 764119389 3.010000e-06 63.9
59 TraesCS2B01G404000 chr3A 81.928 83 11 4 12 91 55773242 55773161 2.330000e-07 67.6
60 TraesCS2B01G404000 chr1A 95.000 40 2 0 3400 3439 408688679 408688640 3.010000e-06 63.9


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 TraesCS2B01G404000 chr2B 572177098 572180707 3609 True 6667.000000 6667 100.000000 1 3610 1 chr2B.!!$R2 3609
1 TraesCS2B01G404000 chr2B 571345478 571348217 2739 False 1221.000000 1282 83.507000 528 3187 2 chr2B.!!$F2 2659
2 TraesCS2B01G404000 chr2B 572310748 572314292 3544 True 980.666667 2311 86.735333 708 3610 3 chr2B.!!$R3 2902
3 TraesCS2B01G404000 chr2B 572324155 572325283 1128 True 248.333333 335 84.512333 906 1844 3 chr2B.!!$R4 938
4 TraesCS2B01G404000 chr2D 487592754 487595079 2325 True 2946.000000 2946 89.762000 73 2382 1 chr2D.!!$R2 2309
5 TraesCS2B01G404000 chr2D 486390421 486392983 2562 False 2556.000000 2556 85.010000 631 3187 1 chr2D.!!$F3 2556
6 TraesCS2B01G404000 chr2D 487722800 487725594 2794 True 1958.000000 3699 91.427500 1 3121 2 chr2D.!!$R4 3120
7 TraesCS2B01G404000 chr2D 487931318 487934903 3585 True 1430.500000 2748 86.469000 538 3610 2 chr2D.!!$R5 3072
8 TraesCS2B01G404000 chr2D 488056981 488059497 2516 True 248.060000 532 83.898200 637 2213 5 chr2D.!!$R6 1576
9 TraesCS2B01G404000 chr2A 631855156 631857870 2714 False 1110.500000 1805 82.713500 631 3214 2 chr2A.!!$F1 2583
10 TraesCS2B01G404000 chr2A 632586573 632589430 2857 True 912.333333 1526 85.707000 709 3401 3 chr2A.!!$R1 2692
11 TraesCS2B01G404000 chr2A 632594336 632596352 2016 True 285.333333 366 85.358667 636 1866 3 chr2A.!!$R2 1230
12 TraesCS2B01G404000 chr7D 446550066 446551621 1555 True 1155.000000 1155 80.750000 1446 3017 1 chr7D.!!$R1 1571
13 TraesCS2B01G404000 chr4B 16786692 16788098 1406 False 1118.000000 1118 81.613000 1443 2859 1 chr4B.!!$F1 1416
14 TraesCS2B01G404000 chr7A 321635865 321636676 811 True 675.000000 675 82.310000 1909 2709 1 chr7A.!!$R1 800
15 TraesCS2B01G404000 chr3D 16449271 16450168 897 False 667.000000 667 80.916000 2141 3014 1 chr3D.!!$F1 873
16 TraesCS2B01G404000 chr6B 247035104 247035819 715 True 582.000000 582 81.555000 1446 2200 1 chr6B.!!$R1 754
17 TraesCS2B01G404000 chrUn 195338034 195338607 573 False 518.000000 518 83.478000 2252 2808 1 chrUn.!!$F1 556
18 TraesCS2B01G404000 chr4A 729644467 729645105 638 True 490.000000 490 80.792000 1446 2123 1 chr4A.!!$R1 677

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
21 22 1.077089 TCGTCGTTGTTCGCACACAA 61.077 50.0 0.00 0.00 39.67 3.33 F
133 134 1.370609 TCGCGCGGAATTAATTTGGA 58.629 45.0 31.69 1.65 0.00 3.53 F
470 495 1.600058 TAGGAACGGAGGGAGTAGGA 58.400 55.0 0.00 0.00 0.00 2.94 F
980 1680 1.731433 GCCACGCGTACCAGATCCTA 61.731 60.0 13.44 0.00 0.00 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1448 2448 0.108709 CATTTGGTCCGTTGGGCATG 60.109 55.000 0.00 0.0 0.00 4.06 R
2120 3757 3.876914 CAGCGGCCTATTTCTGATGTTTA 59.123 43.478 0.00 0.0 0.00 2.01 R
2217 3860 5.431765 AGACAAGTAATGCTAAGTGGGATG 58.568 41.667 0.00 0.0 0.00 3.51 R
2674 4393 0.320858 TTTGCGAACGCCCTCATGTA 60.321 50.000 16.27 0.0 41.09 2.29 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
17 18 4.698496 CATCGTCGTTGTTCGCAC 57.302 55.556 0.00 0.00 39.67 5.34
18 19 1.849973 CATCGTCGTTGTTCGCACA 59.150 52.632 0.00 0.00 39.67 4.57
21 22 1.077089 TCGTCGTTGTTCGCACACAA 61.077 50.000 0.00 0.00 39.67 3.33
39 40 7.706281 CACACAACCATTAGTGCAAAAATAA 57.294 32.000 0.00 0.00 39.30 1.40
133 134 1.370609 TCGCGCGGAATTAATTTGGA 58.629 45.000 31.69 1.65 0.00 3.53
138 140 3.674955 GCGCGGAATTAATTTGGAAACCT 60.675 43.478 8.83 0.00 0.00 3.50
174 176 5.730296 ATTCATTAGATGTACTCCCTCCG 57.270 43.478 0.00 0.00 0.00 4.63
184 186 3.449737 TGTACTCCCTCCGTTCCTAAATG 59.550 47.826 0.00 0.00 0.00 2.32
185 187 2.547990 ACTCCCTCCGTTCCTAAATGT 58.452 47.619 0.00 0.00 0.00 2.71
196 198 9.556030 CTCCGTTCCTAAATGTTAAATCTTTTC 57.444 33.333 0.00 0.00 0.00 2.29
239 264 5.415701 ACATACGGAGCAAAATGAGTGAATT 59.584 36.000 0.00 0.00 0.00 2.17
327 352 9.895138 TTTATATTTAGAAACACAGGGAGTACC 57.105 33.333 0.00 0.00 40.67 3.34
352 377 7.309621 CCTCTAATGAATTGCATTAATGAGGGG 60.310 40.741 19.73 9.27 46.15 4.79
361 386 6.634889 TGCATTAATGAGGGGCTACATATA 57.365 37.500 19.73 0.00 0.00 0.86
362 387 7.211897 TGCATTAATGAGGGGCTACATATAT 57.788 36.000 19.73 0.00 0.00 0.86
363 388 7.056006 TGCATTAATGAGGGGCTACATATATG 58.944 38.462 19.73 11.29 0.00 1.78
364 389 7.092489 TGCATTAATGAGGGGCTACATATATGA 60.092 37.037 19.73 2.59 0.00 2.15
375 400 7.039784 GGGGCTACATATATGAAGCAAAATGAA 60.040 37.037 19.63 0.00 0.00 2.57
377 402 9.350357 GGCTACATATATGAAGCAAAATGAATG 57.650 33.333 19.63 0.00 0.00 2.67
389 414 8.773033 AAGCAAAATGAATGAATCTATACCCT 57.227 30.769 0.00 0.00 0.00 4.34
458 483 9.490663 CTCTAAAAATACTTGCATTTAGGAACG 57.509 33.333 12.84 0.00 36.48 3.95
470 495 1.600058 TAGGAACGGAGGGAGTAGGA 58.400 55.000 0.00 0.00 0.00 2.94
515 540 5.707298 CCAATAGTCTGTGTGATCCACTTTT 59.293 40.000 13.32 2.96 44.81 2.27
516 541 6.128172 CCAATAGTCTGTGTGATCCACTTTTC 60.128 42.308 13.32 4.63 44.81 2.29
517 542 3.744660 AGTCTGTGTGATCCACTTTTCC 58.255 45.455 13.32 1.42 44.81 3.13
534 559 7.177392 CCACTTTTCCAATTATTCTTCACTCCT 59.823 37.037 0.00 0.00 0.00 3.69
598 623 2.035576 GGTACGGTCACACTTCACTCTT 59.964 50.000 0.00 0.00 0.00 2.85
732 807 4.147449 CCGCTGATCCGGCTGTCA 62.147 66.667 0.00 0.00 42.03 3.58
796 877 3.319198 GCGGAGGAAGGGGTGACA 61.319 66.667 0.00 0.00 0.00 3.58
936 1634 3.130869 ACTGTGTGTTGTTGTTGATGCAT 59.869 39.130 0.00 0.00 0.00 3.96
980 1680 1.731433 GCCACGCGTACCAGATCCTA 61.731 60.000 13.44 0.00 0.00 2.94
1088 1788 3.517901 TCGTCATCAACCATCCTAAAGGT 59.482 43.478 0.00 0.00 40.61 3.50
1147 1851 8.608598 ACTATTACCTAATTACTGGGTGTGTTT 58.391 33.333 5.38 0.00 34.86 2.83
1315 2145 5.929992 CAGCAAACCAAATGATCACATCTTT 59.070 36.000 0.00 0.00 35.50 2.52
1375 2205 4.391830 GGTACATGCATACATAATCCCACG 59.608 45.833 0.00 0.00 33.67 4.94
1385 2219 3.055963 ACATAATCCCACGTAAACGACCA 60.056 43.478 9.86 0.00 43.02 4.02
1404 2238 5.633830 ACCATGTAGTTCAGCTGATTTTG 57.366 39.130 19.04 9.51 0.00 2.44
1409 2243 7.095940 CCATGTAGTTCAGCTGATTTTGTTTTG 60.096 37.037 19.04 8.83 0.00 2.44
1439 2439 9.936759 ATATCTTAGCTAACCTTATCAAGCTTC 57.063 33.333 0.86 0.00 42.52 3.86
1448 2448 1.742761 TATCAAGCTTCTGTGCAGGC 58.257 50.000 0.00 0.00 34.99 4.85
1852 2894 5.456763 GGATGGAGGACAGGTAATAAGCATT 60.457 44.000 0.00 0.00 0.00 3.56
1938 3507 7.907389 TGCTATTCTAAACCATTCGATCCTAT 58.093 34.615 0.00 0.00 0.00 2.57
2120 3757 2.863809 AGGTTTCGATCCTGCAAAGTT 58.136 42.857 8.57 0.00 33.62 2.66
2217 3860 6.385649 TTCATGTGGAAGAAGGTAACAAAC 57.614 37.500 0.00 0.00 41.41 2.93
2233 3899 6.376018 GGTAACAAACATCCCACTTAGCATTA 59.624 38.462 0.00 0.00 0.00 1.90
2396 4090 3.130516 CCGTTCTACACAGGAAGCATCTA 59.869 47.826 0.00 0.00 0.00 1.98
2448 4142 3.154710 GTCTTTGGATTCGAAAAGGGGT 58.845 45.455 0.00 0.00 34.75 4.95
2477 4171 2.501610 GGGGCTGTTAGAGGCTCG 59.498 66.667 9.22 0.00 46.72 5.03
2516 4210 4.446371 ACGATTGGGATTGTCTGAAGATC 58.554 43.478 0.00 0.00 0.00 2.75
2520 4214 3.548770 TGGGATTGTCTGAAGATCATGC 58.451 45.455 0.00 0.00 0.00 4.06
2552 4247 7.011669 GCAACAATTCCTTATTTGAATCCCATG 59.988 37.037 0.00 0.00 31.39 3.66
2577 4282 0.954452 GCAACACCCTCCACTCTTTG 59.046 55.000 0.00 0.00 0.00 2.77
2584 4289 2.509964 ACCCTCCACTCTTTGTGTTTCT 59.490 45.455 0.00 0.00 44.81 2.52
2670 4389 4.202357 GGATCACTCACTTGGTATGGCATA 60.202 45.833 2.32 2.32 0.00 3.14
2674 4393 6.186957 TCACTCACTTGGTATGGCATAAAAT 58.813 36.000 9.14 0.00 0.00 1.82
2744 4463 2.025605 AGATGAAGGAGGCAAGCATCAA 60.026 45.455 9.04 0.00 38.19 2.57
2822 4549 2.551721 CCTGATCCACTGCACTCAAGTT 60.552 50.000 0.00 0.00 0.00 2.66
2927 4691 4.542697 ACAAGAAACAACCCAGTAATGGT 58.457 39.130 8.66 0.00 37.85 3.55
2928 4692 5.697067 ACAAGAAACAACCCAGTAATGGTA 58.303 37.500 8.66 0.00 34.15 3.25
2965 4730 4.262721 GGGTTAATCAGTAGTGTGTGGTCA 60.263 45.833 0.00 0.00 0.00 4.02
3057 4835 0.956633 CTTTGCATGACAGTGCCACT 59.043 50.000 0.00 0.00 44.43 4.00
3084 4873 3.273434 GAGAATGCTTGACTGTGCCATA 58.727 45.455 0.00 0.00 0.00 2.74
3086 4875 5.039920 AGAATGCTTGACTGTGCCATATA 57.960 39.130 0.00 0.00 0.00 0.86
3091 4880 6.135290 TGCTTGACTGTGCCATATAATTTC 57.865 37.500 0.00 0.00 0.00 2.17
3097 4886 9.549078 TTGACTGTGCCATATAATTTCGTAATA 57.451 29.630 0.00 0.00 0.00 0.98
3124 4919 2.338577 ACAGGTGAGCCATGATTAGC 57.661 50.000 0.00 0.00 37.19 3.09
3147 4942 4.340617 GGACCAAAACTGATGACCCATTA 58.659 43.478 0.00 0.00 0.00 1.90
3151 4946 5.594317 ACCAAAACTGATGACCCATTATAGC 59.406 40.000 0.00 0.00 0.00 2.97
3172 4967 3.034635 CAAGGTAGTGCTCCTCCTACAT 58.965 50.000 0.00 0.00 36.17 2.29
3174 4969 1.689273 GGTAGTGCTCCTCCTACATGG 59.311 57.143 0.00 0.00 36.17 3.66
3193 4988 2.023404 TGGAGCCCTACCAAGATCACTA 60.023 50.000 0.00 0.00 34.25 2.74
3255 5050 0.179936 AGCTCCCTTGATGCTAGTGC 59.820 55.000 0.00 0.00 35.05 4.40
3269 5064 2.417379 GCTAGTGCGGATCTGTCTTTCA 60.417 50.000 2.89 0.00 0.00 2.69
3273 5068 2.548057 GTGCGGATCTGTCTTTCACAAA 59.452 45.455 2.89 0.00 33.31 2.83
3367 5163 4.494091 AGCTAACCTGCATTCATACACT 57.506 40.909 0.00 0.00 34.99 3.55
3370 5166 5.129485 AGCTAACCTGCATTCATACACTAGT 59.871 40.000 0.00 0.00 34.99 2.57
3377 5173 7.230510 ACCTGCATTCATACACTAGTTTTTCAA 59.769 33.333 0.00 0.00 0.00 2.69
3378 5174 8.246180 CCTGCATTCATACACTAGTTTTTCAAT 58.754 33.333 0.00 0.00 0.00 2.57
3394 5190 8.837389 AGTTTTTCAATAGGTTAGTGACTTCAC 58.163 33.333 0.77 0.77 46.77 3.18
3401 5197 5.140747 AGGTTAGTGACTTCACACTCATC 57.859 43.478 11.85 0.00 46.36 2.92
3402 5198 4.835615 AGGTTAGTGACTTCACACTCATCT 59.164 41.667 11.85 0.00 46.36 2.90
3403 5199 6.010850 AGGTTAGTGACTTCACACTCATCTA 58.989 40.000 11.85 0.00 46.36 1.98
3405 5201 6.754209 GGTTAGTGACTTCACACTCATCTATG 59.246 42.308 11.85 0.00 46.36 2.23
3406 5202 4.753233 AGTGACTTCACACTCATCTATGC 58.247 43.478 11.85 0.00 46.36 3.14
3411 5207 8.138074 GTGACTTCACACTCATCTATGCTATTA 58.862 37.037 4.43 0.00 45.75 0.98
3412 5208 8.695456 TGACTTCACACTCATCTATGCTATTAA 58.305 33.333 0.00 0.00 0.00 1.40
3415 5211 8.893219 TTCACACTCATCTATGCTATTAAAGG 57.107 34.615 0.00 0.00 0.00 3.11
3417 5213 6.652481 CACACTCATCTATGCTATTAAAGGGG 59.348 42.308 0.00 0.00 0.00 4.79
3421 5217 8.325046 ACTCATCTATGCTATTAAAGGGGAATC 58.675 37.037 0.00 0.00 0.00 2.52
3422 5218 7.331026 TCATCTATGCTATTAAAGGGGAATCG 58.669 38.462 0.00 0.00 0.00 3.34
3424 5220 7.311092 TCTATGCTATTAAAGGGGAATCGAA 57.689 36.000 0.00 0.00 0.00 3.71
3425 5221 7.159372 TCTATGCTATTAAAGGGGAATCGAAC 58.841 38.462 0.00 0.00 0.00 3.95
3426 5222 4.124238 TGCTATTAAAGGGGAATCGAACG 58.876 43.478 0.00 0.00 0.00 3.95
3429 5225 2.282701 TAAAGGGGAATCGAACGTCG 57.717 50.000 0.00 0.00 42.10 5.12
3430 5226 0.319405 AAAGGGGAATCGAACGTCGT 59.681 50.000 0.00 0.00 41.35 4.34
3431 5227 0.389426 AAGGGGAATCGAACGTCGTG 60.389 55.000 0.00 0.00 41.35 4.35
3432 5228 1.213537 GGGGAATCGAACGTCGTGA 59.786 57.895 0.00 0.00 41.35 4.35
3438 5234 1.625616 ATCGAACGTCGTGATGGTTC 58.374 50.000 0.00 6.67 41.35 3.62
3439 5235 0.387622 TCGAACGTCGTGATGGTTCC 60.388 55.000 0.00 0.00 41.35 3.62
3440 5236 1.670971 CGAACGTCGTGATGGTTCCG 61.671 60.000 0.00 0.00 37.38 4.30
3442 5238 0.942410 AACGTCGTGATGGTTCCGTG 60.942 55.000 0.00 0.00 0.00 4.94
3444 5240 1.342082 CGTCGTGATGGTTCCGTGAC 61.342 60.000 0.00 0.00 0.00 3.67
3445 5241 0.319211 GTCGTGATGGTTCCGTGACA 60.319 55.000 2.09 0.00 0.00 3.58
3447 5243 1.289109 CGTGATGGTTCCGTGACACC 61.289 60.000 0.00 0.00 0.00 4.16
3448 5244 0.953960 GTGATGGTTCCGTGACACCC 60.954 60.000 0.00 0.00 31.24 4.61
3451 5247 1.125093 ATGGTTCCGTGACACCCTGA 61.125 55.000 0.00 0.00 31.24 3.86
3452 5248 1.125093 TGGTTCCGTGACACCCTGAT 61.125 55.000 0.00 0.00 31.24 2.90
3453 5249 0.036306 GGTTCCGTGACACCCTGATT 59.964 55.000 0.00 0.00 0.00 2.57
3454 5250 1.544759 GGTTCCGTGACACCCTGATTT 60.545 52.381 0.00 0.00 0.00 2.17
3456 5252 0.762418 TCCGTGACACCCTGATTTGT 59.238 50.000 0.00 0.00 0.00 2.83
3459 5255 2.287547 CCGTGACACCCTGATTTGTTTG 60.288 50.000 0.00 0.00 0.00 2.93
3460 5256 2.742774 GTGACACCCTGATTTGTTTGC 58.257 47.619 0.00 0.00 0.00 3.68
3462 5258 2.762887 TGACACCCTGATTTGTTTGCAA 59.237 40.909 0.00 0.00 0.00 4.08
3464 5260 4.141756 TGACACCCTGATTTGTTTGCAATT 60.142 37.500 0.00 0.00 34.18 2.32
3482 5839 4.321899 GCAATTGTGGCCATCAGAAAGTTA 60.322 41.667 9.72 0.00 32.20 2.24
3486 5843 7.716799 ATTGTGGCCATCAGAAAGTTATTTA 57.283 32.000 9.72 0.00 32.20 1.40
3487 5844 6.757897 TGTGGCCATCAGAAAGTTATTTAG 57.242 37.500 9.72 0.00 0.00 1.85
3511 5877 8.294954 AGACCTCTAGATCAAAAGTTCGAATA 57.705 34.615 0.00 0.00 0.00 1.75
3556 5954 3.133721 CCTTTGGTGTTTCATTGGACCAA 59.866 43.478 9.92 9.92 44.81 3.67
3560 5958 5.720371 TGGTGTTTCATTGGACCAAATAG 57.280 39.130 11.82 4.72 35.51 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.383026 GCACTAATGGTTGTGTGCG 57.617 52.632 0.00 0.00 44.60 5.34
51 52 9.339492 GACTTGATTTTCAAATTGATCTGTCTC 57.661 33.333 0.00 0.00 35.73 3.36
103 104 0.719465 TCCGCGCGAAAAGATTTCTC 59.281 50.000 34.63 0.00 0.00 2.87
196 198 7.382488 CCGTATGTAGTCCATAGTGAAAATCTG 59.618 40.741 0.00 0.00 36.71 2.90
200 202 6.682113 GCTCCGTATGTAGTCCATAGTGAAAA 60.682 42.308 0.00 0.00 36.71 2.29
201 203 5.221185 GCTCCGTATGTAGTCCATAGTGAAA 60.221 44.000 0.00 0.00 36.71 2.69
205 207 3.828921 TGCTCCGTATGTAGTCCATAGT 58.171 45.455 0.00 0.00 36.71 2.12
206 208 4.848562 TTGCTCCGTATGTAGTCCATAG 57.151 45.455 0.00 0.00 36.71 2.23
267 292 9.201989 AGAGATTCCACTACAAACTACATATGA 57.798 33.333 10.38 0.00 0.00 2.15
316 341 9.010300 ATGCAATTCATTAGAGGTACTCCCTGT 62.010 40.741 0.00 0.00 45.10 4.00
317 342 6.689946 ATGCAATTCATTAGAGGTACTCCCTG 60.690 42.308 0.00 0.00 45.10 4.45
327 352 7.600065 CCCCTCATTAATGCAATTCATTAGAG 58.400 38.462 10.76 13.17 45.42 2.43
362 387 8.632679 GGGTATAGATTCATTCATTTTGCTTCA 58.367 33.333 0.00 0.00 0.00 3.02
363 388 8.854117 AGGGTATAGATTCATTCATTTTGCTTC 58.146 33.333 0.00 0.00 0.00 3.86
364 389 8.773033 AGGGTATAGATTCATTCATTTTGCTT 57.227 30.769 0.00 0.00 0.00 3.91
422 447 9.905713 TGCAAGTATTTTTAGAGATTCCACTAT 57.094 29.630 0.00 0.00 0.00 2.12
441 466 3.370103 CCCTCCGTTCCTAAATGCAAGTA 60.370 47.826 0.00 0.00 0.00 2.24
446 471 1.209747 ACTCCCTCCGTTCCTAAATGC 59.790 52.381 0.00 0.00 0.00 3.56
470 495 5.265989 TGGCGGAAATAGGTAGGAAAAATT 58.734 37.500 0.00 0.00 0.00 1.82
479 504 4.652421 ACAGACTATTGGCGGAAATAGGTA 59.348 41.667 13.72 0.00 42.19 3.08
488 513 2.205074 GATCACACAGACTATTGGCGG 58.795 52.381 0.00 0.00 0.00 6.13
490 515 3.266510 TGGATCACACAGACTATTGGC 57.733 47.619 0.00 0.00 0.00 4.52
515 540 6.816640 CGTGTAAGGAGTGAAGAATAATTGGA 59.183 38.462 0.00 0.00 0.00 3.53
516 541 6.456988 GCGTGTAAGGAGTGAAGAATAATTGG 60.457 42.308 0.00 0.00 0.00 3.16
517 542 6.456988 GGCGTGTAAGGAGTGAAGAATAATTG 60.457 42.308 0.00 0.00 0.00 2.32
573 598 0.032952 GAAGTGTGACCGTACCAGCA 59.967 55.000 0.00 0.00 0.00 4.41
576 601 1.338973 GAGTGAAGTGTGACCGTACCA 59.661 52.381 0.00 0.00 0.00 3.25
583 608 1.140816 GGCGAAGAGTGAAGTGTGAC 58.859 55.000 0.00 0.00 0.00 3.67
598 623 2.925724 CTAGAGAGGAAGAGAAGGCGA 58.074 52.381 0.00 0.00 0.00 5.54
685 742 3.411517 CTTCGCCCCATCCCCAGT 61.412 66.667 0.00 0.00 0.00 4.00
732 807 1.153086 GCATGCCCATTCTCCGTCT 60.153 57.895 6.36 0.00 0.00 4.18
796 877 3.767630 AACGAGCACGGCCCACTTT 62.768 57.895 8.74 0.00 44.46 2.66
871 1517 9.996554 TCATATGGTGAATGATATACGAGTTTT 57.003 29.630 2.13 0.00 32.78 2.43
872 1518 9.996554 TTCATATGGTGAATGATATACGAGTTT 57.003 29.630 2.13 0.00 41.79 2.66
909 1593 1.006832 ACAACAACACACAGTCGCTC 58.993 50.000 0.00 0.00 0.00 5.03
936 1634 4.367023 GGCCTGTACGTCGTGCCA 62.367 66.667 17.04 8.98 41.76 4.92
980 1680 0.701147 CCTTGAGGCCTCCCTTCTTT 59.299 55.000 29.95 0.00 43.12 2.52
1088 1788 5.712917 GGGAACACCATGGTAAACATCTTTA 59.287 40.000 19.28 0.00 37.84 1.85
1147 1851 9.685828 CGTCAACCTTATTTGAATTAAAAAGGA 57.314 29.630 11.58 0.00 38.00 3.36
1168 1990 5.878332 ATGCATGTTAAGTTGATCGTCAA 57.122 34.783 0.00 0.00 33.32 3.18
1315 2145 4.994282 ACCCATGATCCGTGTAGTAGATA 58.006 43.478 0.00 0.00 0.00 1.98
1375 2205 4.091509 CAGCTGAACTACATGGTCGTTTAC 59.908 45.833 8.42 0.00 34.43 2.01
1385 2219 7.491682 ACAAAACAAAATCAGCTGAACTACAT 58.508 30.769 22.50 0.00 0.00 2.29
1448 2448 0.108709 CATTTGGTCCGTTGGGCATG 60.109 55.000 0.00 0.00 0.00 4.06
1575 2601 7.435068 AGCGTACATACTGTTTCAGATTTTT 57.565 32.000 3.70 0.00 35.18 1.94
1577 2603 7.172532 TCAAAGCGTACATACTGTTTCAGATTT 59.827 33.333 3.70 0.00 35.18 2.17
2120 3757 3.876914 CAGCGGCCTATTTCTGATGTTTA 59.123 43.478 0.00 0.00 0.00 2.01
2217 3860 5.431765 AGACAAGTAATGCTAAGTGGGATG 58.568 41.667 0.00 0.00 0.00 3.51
2233 3899 7.635648 ACTTAGTACTCCAGATCTAGACAAGT 58.364 38.462 0.00 0.00 0.00 3.16
2477 4171 1.523938 GTCGACTAATGGCTGGCCC 60.524 63.158 8.70 0.00 34.56 5.80
2520 4214 6.680810 TCAAATAAGGAATTGTTGCACTCAG 58.319 36.000 0.00 0.00 0.00 3.35
2552 4247 0.598065 GTGGAGGGTGTTGCATGTTC 59.402 55.000 0.00 0.00 0.00 3.18
2577 4282 7.093992 AGCAGAGTAAGTTCTATCAGAAACAC 58.906 38.462 0.00 0.00 35.75 3.32
2584 4289 9.800572 ATCAGTATAGCAGAGTAAGTTCTATCA 57.199 33.333 0.00 0.00 0.00 2.15
2643 4360 0.396435 ACCAAGTGAGTGATCCGCAA 59.604 50.000 0.00 0.00 0.00 4.85
2670 4389 1.400494 GCGAACGCCCTCATGTATTTT 59.600 47.619 8.03 0.00 34.56 1.82
2674 4393 0.320858 TTTGCGAACGCCCTCATGTA 60.321 50.000 16.27 0.00 41.09 2.29
2822 4549 2.646930 CATTTGCTACTGCTCCCATGA 58.353 47.619 0.00 0.00 40.48 3.07
2965 4730 6.872020 CAGTCAAATTTGATTTTCAGAGGCAT 59.128 34.615 23.05 0.00 39.73 4.40
3024 4802 7.304735 TGTCATGCAAAGATATTAACACACAC 58.695 34.615 0.00 0.00 0.00 3.82
3025 4803 7.174772 ACTGTCATGCAAAGATATTAACACACA 59.825 33.333 0.00 0.00 0.00 3.72
3091 4880 6.982141 TGGCTCACCTGTTTATTACTATTACG 59.018 38.462 0.00 0.00 36.63 3.18
3097 4886 5.435686 TCATGGCTCACCTGTTTATTACT 57.564 39.130 0.00 0.00 36.63 2.24
3124 4919 1.165270 GGGTCATCAGTTTTGGTCCG 58.835 55.000 0.00 0.00 0.00 4.79
3151 4946 2.457598 TGTAGGAGGAGCACTACCTTG 58.542 52.381 0.00 0.00 38.98 3.61
3172 4967 1.204146 GTGATCTTGGTAGGGCTCCA 58.796 55.000 0.00 0.00 0.00 3.86
3174 4969 3.451178 TGTTAGTGATCTTGGTAGGGCTC 59.549 47.826 0.00 0.00 0.00 4.70
3232 5027 2.573462 ACTAGCATCAAGGGAGCTTCAA 59.427 45.455 0.00 0.00 39.68 2.69
3255 5050 3.679980 ACGATTTGTGAAAGACAGATCCG 59.320 43.478 0.00 0.00 41.25 4.18
3269 5064 0.389426 CCCGAGACCGAACGATTTGT 60.389 55.000 0.00 0.00 38.22 2.83
3273 5068 3.834799 GGCCCGAGACCGAACGAT 61.835 66.667 0.00 0.00 38.22 3.73
3322 5118 7.255139 GCTAATTTAATTAGATTGCCTCACGGT 60.255 37.037 24.02 0.00 43.85 4.83
3347 5143 5.360591 ACTAGTGTATGAATGCAGGTTAGC 58.639 41.667 0.00 0.00 0.00 3.09
3348 5144 7.849804 AAACTAGTGTATGAATGCAGGTTAG 57.150 36.000 0.00 0.00 0.00 2.34
3370 5166 8.617809 GTGTGAAGTCACTAACCTATTGAAAAA 58.382 33.333 12.43 0.00 46.55 1.94
3377 5173 6.665680 AGATGAGTGTGAAGTCACTAACCTAT 59.334 38.462 12.43 1.90 46.81 2.57
3378 5174 6.010850 AGATGAGTGTGAAGTCACTAACCTA 58.989 40.000 12.43 0.00 46.81 3.08
3394 5190 7.009179 TCCCCTTTAATAGCATAGATGAGTG 57.991 40.000 0.00 0.00 0.00 3.51
3401 5197 6.090898 CGTTCGATTCCCCTTTAATAGCATAG 59.909 42.308 0.00 0.00 0.00 2.23
3402 5198 5.929992 CGTTCGATTCCCCTTTAATAGCATA 59.070 40.000 0.00 0.00 0.00 3.14
3403 5199 4.755123 CGTTCGATTCCCCTTTAATAGCAT 59.245 41.667 0.00 0.00 0.00 3.79
3405 5201 4.124970 ACGTTCGATTCCCCTTTAATAGC 58.875 43.478 0.00 0.00 0.00 2.97
3406 5202 4.443394 CGACGTTCGATTCCCCTTTAATAG 59.557 45.833 0.00 0.00 43.74 1.73
3411 5207 0.319405 ACGACGTTCGATTCCCCTTT 59.681 50.000 13.06 0.00 43.74 3.11
3412 5208 0.389426 CACGACGTTCGATTCCCCTT 60.389 55.000 13.06 0.00 43.74 3.95
3415 5211 0.921347 CATCACGACGTTCGATTCCC 59.079 55.000 13.06 0.00 43.74 3.97
3417 5213 1.625616 ACCATCACGACGTTCGATTC 58.374 50.000 13.06 0.00 43.74 2.52
3421 5217 1.670971 CGGAACCATCACGACGTTCG 61.671 60.000 0.00 0.00 46.93 3.95
3422 5218 0.665369 ACGGAACCATCACGACGTTC 60.665 55.000 0.00 0.00 36.08 3.95
3424 5220 1.372499 CACGGAACCATCACGACGT 60.372 57.895 0.00 0.00 34.61 4.34
3425 5221 1.081041 TCACGGAACCATCACGACG 60.081 57.895 0.00 0.00 0.00 5.12
3426 5222 0.319211 TGTCACGGAACCATCACGAC 60.319 55.000 0.00 0.00 0.00 4.34
3429 5225 0.953960 GGGTGTCACGGAACCATCAC 60.954 60.000 0.00 0.00 38.27 3.06
3430 5226 1.125093 AGGGTGTCACGGAACCATCA 61.125 55.000 0.00 0.00 38.27 3.07
3431 5227 0.673644 CAGGGTGTCACGGAACCATC 60.674 60.000 0.00 0.00 38.27 3.51
3432 5228 1.125093 TCAGGGTGTCACGGAACCAT 61.125 55.000 0.00 0.00 38.27 3.55
3438 5234 1.604604 AACAAATCAGGGTGTCACGG 58.395 50.000 0.00 0.00 0.00 4.94
3439 5235 2.858260 GCAAACAAATCAGGGTGTCACG 60.858 50.000 0.00 0.00 0.00 4.35
3440 5236 2.100584 TGCAAACAAATCAGGGTGTCAC 59.899 45.455 0.00 0.00 0.00 3.67
3442 5238 3.451141 TTGCAAACAAATCAGGGTGTC 57.549 42.857 0.00 0.00 31.21 3.67
3444 5240 4.024725 CACAATTGCAAACAAATCAGGGTG 60.025 41.667 1.71 0.00 39.77 4.61
3445 5241 4.128643 CACAATTGCAAACAAATCAGGGT 58.871 39.130 1.71 0.00 39.77 4.34
3447 5243 3.058777 GCCACAATTGCAAACAAATCAGG 60.059 43.478 1.71 0.00 39.77 3.86
3448 5244 3.058777 GGCCACAATTGCAAACAAATCAG 60.059 43.478 1.71 0.00 39.77 2.90
3451 5247 2.928334 TGGCCACAATTGCAAACAAAT 58.072 38.095 0.00 0.00 39.77 2.32
3452 5248 2.408271 TGGCCACAATTGCAAACAAA 57.592 40.000 0.00 0.00 39.77 2.83
3453 5249 2.158856 TGATGGCCACAATTGCAAACAA 60.159 40.909 8.16 0.00 40.87 2.83
3454 5250 1.415289 TGATGGCCACAATTGCAAACA 59.585 42.857 8.16 0.53 0.00 2.83
3456 5252 1.969208 TCTGATGGCCACAATTGCAAA 59.031 42.857 8.16 0.00 0.00 3.68
3459 5255 2.028748 ACTTTCTGATGGCCACAATTGC 60.029 45.455 8.16 0.00 0.00 3.56
3460 5256 3.947910 ACTTTCTGATGGCCACAATTG 57.052 42.857 8.16 3.24 0.00 2.32
3462 5258 6.610075 AAATAACTTTCTGATGGCCACAAT 57.390 33.333 8.16 0.00 0.00 2.71
3464 5260 6.374333 GTCTAAATAACTTTCTGATGGCCACA 59.626 38.462 8.16 7.81 0.00 4.17
3482 5839 8.750298 TCGAACTTTTGATCTAGAGGTCTAAAT 58.250 33.333 10.24 0.00 0.00 1.40
3486 5843 6.591750 TTCGAACTTTTGATCTAGAGGTCT 57.408 37.500 10.24 0.00 0.00 3.85
3511 5877 4.237724 CGACTGCCATCACGTTATCATAT 58.762 43.478 0.00 0.00 0.00 1.78
3556 5954 9.722184 CAAGTCATGATGATATGTTCTCCTATT 57.278 33.333 0.00 0.00 0.00 1.73
3558 5956 8.255111 ACAAGTCATGATGATATGTTCTCCTA 57.745 34.615 0.00 0.00 28.11 2.94
3559 5957 7.134362 ACAAGTCATGATGATATGTTCTCCT 57.866 36.000 0.00 0.00 28.11 3.69
3560 5958 7.496920 TCAACAAGTCATGATGATATGTTCTCC 59.503 37.037 19.34 0.00 36.53 3.71


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

AutoCloner maintained by Alex Coulton.