Multiple sequence alignment - TraesCS5A01G244800

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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 TraesCS5A01G244800 chr5A 100.000 4210 0 0 1 4210 458332439 458328230 0.000000e+00 7775.0
1 TraesCS5A01G244800 chr5A 80.063 1269 199 33 941 2188 458320565 458319330 0.000000e+00 893.0
2 TraesCS5A01G244800 chr5A 87.405 524 57 5 969 1485 458493655 458493134 1.010000e-165 593.0
3 TraesCS5A01G244800 chr5A 81.353 606 87 14 2672 3264 458318969 458318377 1.770000e-128 470.0
4 TraesCS5A01G244800 chr5A 80.060 662 99 19 1160 1815 458562216 458561582 1.070000e-125 460.0
5 TraesCS5A01G244800 chr5A 87.252 353 36 6 1154 1500 458525183 458524834 1.100000e-105 394.0
6 TraesCS5A01G244800 chr5A 89.347 291 31 0 1584 1874 458351861 458351571 2.390000e-97 366.0
7 TraesCS5A01G244800 chr5A 90.110 273 27 0 3491 3763 35994589 35994317 5.180000e-94 355.0
8 TraesCS5A01G244800 chr5A 81.579 228 34 6 1583 1808 458278611 458278390 9.300000e-42 182.0
9 TraesCS5A01G244800 chr5A 82.775 209 27 7 2561 2762 458341466 458341260 1.200000e-40 178.0
10 TraesCS5A01G244800 chr5A 81.313 198 33 2 2774 2971 458341210 458341017 1.570000e-34 158.0
11 TraesCS5A01G244800 chr5A 100.000 63 0 0 530 592 669894695 669894757 2.660000e-22 117.0
12 TraesCS5A01G244800 chr5D 92.496 3465 221 24 1 3451 357081625 357078186 0.000000e+00 4922.0
13 TraesCS5A01G244800 chr5D 81.872 1175 158 32 941 2100 357065637 357064503 0.000000e+00 939.0
14 TraesCS5A01G244800 chr5D 95.575 452 19 1 3759 4210 352416359 352416809 0.000000e+00 723.0
15 TraesCS5A01G244800 chr5D 79.909 662 98 22 1160 1815 357396692 357396060 1.780000e-123 453.0
16 TraesCS5A01G244800 chr5D 85.523 373 47 5 1133 1500 357159799 357159429 2.370000e-102 383.0
17 TraesCS5A01G244800 chr5D 91.481 270 23 0 3491 3760 352415935 352416204 5.140000e-99 372.0
18 TraesCS5A01G244800 chr5D 86.321 212 23 3 3015 3224 357063684 357063477 4.240000e-55 226.0
19 TraesCS5A01G244800 chr5D 75.630 357 83 3 4 357 341685136 341685491 1.560000e-39 174.0
20 TraesCS5A01G244800 chr5D 80.786 229 34 7 1583 1808 356838188 356837967 2.010000e-38 171.0
21 TraesCS5A01G244800 chr5D 81.667 120 20 2 1959 2077 357395944 357395826 9.630000e-17 99.0
22 TraesCS5A01G244800 chr5D 92.157 51 4 0 2009 2059 357370985 357370935 5.840000e-09 73.1
23 TraesCS5A01G244800 chr5B 90.261 2608 160 34 937 3492 421861844 421859279 0.000000e+00 3323.0
24 TraesCS5A01G244800 chr5B 85.987 892 96 16 1 886 421862725 421861857 0.000000e+00 928.0
25 TraesCS5A01G244800 chr5B 80.547 1244 177 38 943 2162 421838199 421836997 0.000000e+00 896.0
26 TraesCS5A01G244800 chr5B 80.132 755 107 32 2672 3411 421836603 421835877 1.340000e-144 523.0
27 TraesCS5A01G244800 chr5B 81.140 228 35 7 1583 1808 421717381 421717160 4.330000e-40 176.0
28 TraesCS5A01G244800 chr5B 89.344 122 13 0 1694 1815 422040220 422040099 2.030000e-33 154.0
29 TraesCS5A01G244800 chr5B 83.333 120 18 2 1959 2077 422039983 422039865 4.450000e-20 110.0
30 TraesCS5A01G244800 chr1A 95.354 452 20 1 3759 4210 56549951 56549501 0.000000e+00 717.0
31 TraesCS5A01G244800 chr1A 94.690 452 22 2 3759 4210 55414788 55415237 0.000000e+00 701.0
32 TraesCS5A01G244800 chr1A 94.139 273 16 0 3491 3763 56550375 56550103 2.340000e-112 416.0
33 TraesCS5A01G244800 chr1A 92.803 264 19 0 3491 3754 55414364 55414627 2.370000e-102 383.0
34 TraesCS5A01G244800 chr1A 91.575 273 21 2 3491 3763 137737072 137736802 3.970000e-100 375.0
35 TraesCS5A01G244800 chr4D 95.133 452 21 1 3759 4210 232707057 232706607 0.000000e+00 712.0
36 TraesCS5A01G244800 chr4D 94.469 452 24 1 3759 4210 461471906 461472356 0.000000e+00 695.0
37 TraesCS5A01G244800 chr4D 87.500 56 6 1 1998 2053 5573127 5573181 3.510000e-06 63.9
38 TraesCS5A01G244800 chr4D 78.641 103 16 4 1960 2059 5580111 5580210 3.510000e-06 63.9
39 TraesCS5A01G244800 chr2D 94.690 452 22 2 3759 4210 346147640 346147191 0.000000e+00 701.0
40 TraesCS5A01G244800 chr2D 93.773 273 16 1 3491 3763 346148063 346147792 3.920000e-110 409.0
41 TraesCS5A01G244800 chr2D 75.783 351 71 14 31 373 632298149 632297805 9.360000e-37 165.0
42 TraesCS5A01G244800 chr7A 94.678 451 23 1 3760 4210 67978940 67978491 0.000000e+00 699.0
43 TraesCS5A01G244800 chr7A 94.457 451 24 1 3760 4210 67599059 67599508 0.000000e+00 693.0
44 TraesCS5A01G244800 chr7A 91.011 267 24 0 3497 3763 67979359 67979093 1.110000e-95 361.0
45 TraesCS5A01G244800 chr7A 76.294 367 71 12 73 429 655549197 655549557 9.300000e-42 182.0
46 TraesCS5A01G244800 chr1D 94.260 453 24 2 3759 4210 5287472 5287923 0.000000e+00 691.0
47 TraesCS5A01G244800 chr1D 90.335 269 26 0 3491 3759 481271399 481271667 1.860000e-93 353.0
48 TraesCS5A01G244800 chrUn 90.741 270 25 0 3491 3760 100306910 100307179 1.110000e-95 361.0
49 TraesCS5A01G244800 chr3A 78.717 343 65 8 3 337 426868073 426867731 5.480000e-54 222.0
50 TraesCS5A01G244800 chr7D 78.571 336 68 4 74 405 568187395 568187730 7.090000e-53 219.0
51 TraesCS5A01G244800 chr6A 76.257 358 79 5 23 377 186523289 186522935 7.190000e-43 185.0
52 TraesCS5A01G244800 chr7B 79.200 250 48 3 88 333 21940230 21940479 2.010000e-38 171.0
53 TraesCS5A01G244800 chr6D 75.862 348 68 13 87 426 439612472 439612811 3.370000e-36 163.0
54 TraesCS5A01G244800 chr4A 79.612 103 15 5 1960 2059 597944961 597944862 7.550000e-08 69.4
55 TraesCS5A01G244800 chr4B 87.500 56 6 1 1998 2053 9695556 9695610 3.510000e-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 TraesCS5A01G244800 chr5A 458328230 458332439 4209 True 7775.0 7775 100.0000 1 4210 1 chr5A.!!$R3 4209
1 TraesCS5A01G244800 chr5A 458318377 458320565 2188 True 681.5 893 80.7080 941 3264 2 chr5A.!!$R8 2323
2 TraesCS5A01G244800 chr5A 458493134 458493655 521 True 593.0 593 87.4050 969 1485 1 chr5A.!!$R5 516
3 TraesCS5A01G244800 chr5A 458561582 458562216 634 True 460.0 460 80.0600 1160 1815 1 chr5A.!!$R7 655
4 TraesCS5A01G244800 chr5D 357078186 357081625 3439 True 4922.0 4922 92.4960 1 3451 1 chr5D.!!$R2 3450
5 TraesCS5A01G244800 chr5D 357063477 357065637 2160 True 582.5 939 84.0965 941 3224 2 chr5D.!!$R5 2283
6 TraesCS5A01G244800 chr5D 352415935 352416809 874 False 547.5 723 93.5280 3491 4210 2 chr5D.!!$F2 719
7 TraesCS5A01G244800 chr5D 357395826 357396692 866 True 276.0 453 80.7880 1160 2077 2 chr5D.!!$R6 917
8 TraesCS5A01G244800 chr5B 421859279 421862725 3446 True 2125.5 3323 88.1240 1 3492 2 chr5B.!!$R3 3491
9 TraesCS5A01G244800 chr5B 421835877 421838199 2322 True 709.5 896 80.3395 943 3411 2 chr5B.!!$R2 2468
10 TraesCS5A01G244800 chr1A 56549501 56550375 874 True 566.5 717 94.7465 3491 4210 2 chr1A.!!$R2 719
11 TraesCS5A01G244800 chr1A 55414364 55415237 873 False 542.0 701 93.7465 3491 4210 2 chr1A.!!$F1 719
12 TraesCS5A01G244800 chr2D 346147191 346148063 872 True 555.0 701 94.2315 3491 4210 2 chr2D.!!$R2 719
13 TraesCS5A01G244800 chr7A 67978491 67979359 868 True 530.0 699 92.8445 3497 4210 2 chr7A.!!$R1 713

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
366 369 0.179129 CATTGAATGGCTTCCACGGC 60.179 55.000 0.00 0.00 35.80 5.68 F
414 417 0.442699 GCGGTTTGAGAATCGGTGTC 59.557 55.000 0.00 0.00 39.73 3.67 F
415 418 0.713883 CGGTTTGAGAATCGGTGTCG 59.286 55.000 0.00 0.00 38.61 4.35 F
602 605 1.004044 CACATCTGGAAGCCTGGAACT 59.996 52.381 0.00 0.00 0.00 3.01 F
1029 1043 1.277557 ACTACCTTCTTCCTGCTGCTG 59.722 52.381 0.00 0.00 0.00 4.41 F
2614 2687 1.002900 TCTTTTCCTTTGAGCGCAACG 60.003 47.619 11.47 0.13 32.79 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1985 2020 0.036388 GCTCCCCTTGTCGTTCATGA 60.036 55.0 0.00 0.00 0.00 3.07 R
2080 2115 0.318699 CACTGCCAGTCGTCTTTCGA 60.319 55.0 0.00 0.00 46.83 3.71 R
2386 2458 1.406065 ATCGTAGCCAGCCAGCTGAT 61.406 55.0 21.01 11.27 46.30 2.90 R
2515 2587 0.110733 TTTTTGCGCGCGGTAAGTAC 60.111 50.0 33.06 13.41 0.00 2.73 R
2759 2849 0.892063 TGCTCAATGTGTGCATGCAT 59.108 45.0 25.64 4.32 41.27 3.96 R
3855 4201 1.265236 CTTAGCCCACCCATGCAAAA 58.735 50.0 0.00 0.00 0.00 2.44 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
26 27 3.666374 CGTCCTGTCTAGTAACACGTCAC 60.666 52.174 0.00 0.00 0.00 3.67
51 52 2.173758 TTGAATAGGCGCGGACACCA 62.174 55.000 8.83 0.00 0.00 4.17
83 84 3.823330 GCGACATCCTCGACCGGT 61.823 66.667 6.92 6.92 46.14 5.28
85 86 2.697761 CGACATCCTCGACCGGTGT 61.698 63.158 14.63 0.00 46.14 4.16
149 152 1.237285 GCCGTCTTCAATGTGCAGGT 61.237 55.000 0.00 0.00 0.00 4.00
163 166 1.080772 CAGGTGCGCTCTACAACGA 60.081 57.895 9.73 0.00 0.00 3.85
172 175 2.923655 CGCTCTACAACGACATGAATGT 59.076 45.455 0.00 0.00 45.16 2.71
178 181 1.473677 CAACGACATGAATGTGGGCAT 59.526 47.619 0.00 0.00 41.95 4.40
180 183 0.664761 CGACATGAATGTGGGCATCC 59.335 55.000 0.00 0.00 41.95 3.51
200 203 3.118454 CGCCAGACGGAAATGCGT 61.118 61.111 0.00 0.00 40.33 5.24
205 208 4.811761 GACGGAAATGCGTGCGGC 62.812 66.667 4.28 0.00 43.96 6.53
239 242 0.698198 TTTGGGTGGTCAGGGTGGTA 60.698 55.000 0.00 0.00 0.00 3.25
248 251 0.766131 TCAGGGTGGTAAAAAGCGGA 59.234 50.000 0.00 0.00 0.00 5.54
249 252 1.353022 TCAGGGTGGTAAAAAGCGGAT 59.647 47.619 0.00 0.00 0.00 4.18
252 255 1.890489 GGGTGGTAAAAAGCGGATGTT 59.110 47.619 0.00 0.00 0.00 2.71
262 265 1.267121 AGCGGATGTTGGTACTGTCT 58.733 50.000 0.00 0.00 0.00 3.41
271 274 2.280552 GGTACTGTCTGGACGCCCA 61.281 63.158 0.00 0.00 40.95 5.36
278 281 3.365265 CTGGACGCCCACAAAGCC 61.365 66.667 0.00 0.00 37.58 4.35
301 304 3.317993 CCCCACATTTTTCTCGAGTTTGT 59.682 43.478 13.13 7.38 0.00 2.83
320 323 2.342648 GGAGAAAGTGCGTCCGGT 59.657 61.111 0.00 0.00 0.00 5.28
348 351 0.813610 CGGATCAACATAAGCCCGCA 60.814 55.000 0.00 0.00 0.00 5.69
352 355 2.121291 TCAACATAAGCCCGCATTGA 57.879 45.000 0.00 0.00 0.00 2.57
356 359 1.682854 ACATAAGCCCGCATTGAATGG 59.317 47.619 7.35 0.00 0.00 3.16
366 369 0.179129 CATTGAATGGCTTCCACGGC 60.179 55.000 0.00 0.00 35.80 5.68
385 388 2.710902 CCGGACAGCGTGATCCAGA 61.711 63.158 0.00 0.00 34.35 3.86
406 409 1.448985 GTATGCAGGCGGTTTGAGAA 58.551 50.000 0.00 0.00 0.00 2.87
410 413 1.982073 GCAGGCGGTTTGAGAATCGG 61.982 60.000 0.00 0.00 39.73 4.18
411 414 0.673644 CAGGCGGTTTGAGAATCGGT 60.674 55.000 0.00 0.00 39.73 4.69
414 417 0.442699 GCGGTTTGAGAATCGGTGTC 59.557 55.000 0.00 0.00 39.73 3.67
415 418 0.713883 CGGTTTGAGAATCGGTGTCG 59.286 55.000 0.00 0.00 38.61 4.35
480 483 7.173907 TGAACTCCTCATTTTGCTCTTCTAAAG 59.826 37.037 0.00 0.00 0.00 1.85
491 494 8.451908 TTTGCTCTTCTAAAGATATTTAGGGC 57.548 34.615 17.50 15.79 36.82 5.19
561 564 2.752903 GGTATGCGTCCAAAGGAATGTT 59.247 45.455 0.00 0.00 31.38 2.71
582 585 3.991605 ATGACGTAATCAAGTGCGTTC 57.008 42.857 0.00 0.00 41.93 3.95
602 605 1.004044 CACATCTGGAAGCCTGGAACT 59.996 52.381 0.00 0.00 0.00 3.01
612 615 4.522789 GGAAGCCTGGAACTTAAAACATCA 59.477 41.667 0.00 0.00 0.00 3.07
667 670 8.842358 TCTTGGTCTTAATCGAAGTAAATTGT 57.158 30.769 0.00 0.00 36.45 2.71
701 704 3.385577 TGTGTTAAAATTTGCTTCCGCC 58.614 40.909 0.00 0.00 34.43 6.13
702 705 2.407026 GTGTTAAAATTTGCTTCCGCCG 59.593 45.455 0.00 0.00 34.43 6.46
761 768 2.548067 CCGATGTACTCCATGGTTAGCC 60.548 54.545 12.58 0.00 32.56 3.93
808 815 5.219951 CGCGCCATGTAAACTCAAAAATTAC 60.220 40.000 0.00 0.00 0.00 1.89
849 856 3.134458 GGCAAGTATAGCTAGCCAACAG 58.866 50.000 12.13 5.61 44.59 3.16
894 901 5.543714 TGCTTCTATTCAGACCGTTGTTTA 58.456 37.500 0.00 0.00 0.00 2.01
895 902 6.170506 TGCTTCTATTCAGACCGTTGTTTAT 58.829 36.000 0.00 0.00 0.00 1.40
897 904 6.508088 GCTTCTATTCAGACCGTTGTTTATCG 60.508 42.308 0.00 0.00 0.00 2.92
910 917 6.034591 CGTTGTTTATCGGATCTCAGTTACT 58.965 40.000 0.00 0.00 0.00 2.24
965 972 1.781786 ATACACCTCGACAGGCAGAT 58.218 50.000 0.00 0.00 45.05 2.90
999 1006 1.728971 GATCACAAAGTCACAGGCGAG 59.271 52.381 0.00 0.00 0.00 5.03
1029 1043 1.277557 ACTACCTTCTTCCTGCTGCTG 59.722 52.381 0.00 0.00 0.00 4.41
1134 1149 1.369625 CTTTAAGGGCCAGTAGTGCG 58.630 55.000 6.18 0.00 0.00 5.34
1556 1581 6.571344 GCGGAGTAGATATCACTGATCATTGT 60.571 42.308 12.29 0.00 0.00 2.71
1615 1642 1.924731 ACGTGATCTTCCTGGAGTCA 58.075 50.000 0.00 0.54 0.00 3.41
1664 1691 2.031508 AGCAACAACCCGAACAATAACG 60.032 45.455 0.00 0.00 0.00 3.18
1880 1907 4.360563 CGGCATCTTGGTAAGTACTAGTG 58.639 47.826 5.39 0.00 0.00 2.74
1925 1960 3.244284 TGTCCCGCAACTTATTACACACT 60.244 43.478 0.00 0.00 0.00 3.55
1926 1961 3.749609 GTCCCGCAACTTATTACACACTT 59.250 43.478 0.00 0.00 0.00 3.16
1985 2020 2.676342 GCAATCCGTACCTTGACGATTT 59.324 45.455 0.00 0.00 45.82 2.17
2080 2115 2.024414 GTGAAAACTGCACCTTCACCT 58.976 47.619 15.31 0.00 41.94 4.00
2224 2265 2.416431 GGCTACGTAAGATCACACCGTT 60.416 50.000 0.00 0.00 43.62 4.44
2368 2440 4.304110 TCTTTGACCATTCACAGTACGTC 58.696 43.478 0.00 0.00 32.22 4.34
2373 2445 6.032956 TGACCATTCACAGTACGTCTTTAT 57.967 37.500 0.00 0.00 0.00 1.40
2515 2587 5.980116 CAGCTTGCAGGTAAGTACTGTATAG 59.020 44.000 0.00 0.00 38.22 1.31
2527 2599 3.615849 ACTGTATAGTACTTACCGCGC 57.384 47.619 0.00 0.00 34.74 6.86
2528 2600 2.032549 ACTGTATAGTACTTACCGCGCG 60.033 50.000 25.67 25.67 34.74 6.86
2614 2687 1.002900 TCTTTTCCTTTGAGCGCAACG 60.003 47.619 11.47 0.13 32.79 4.10
2660 2750 3.320626 GCAACTTCATTTCTTTCAGCCC 58.679 45.455 0.00 0.00 0.00 5.19
2772 2937 8.708378 AGGTACTATATATATGCATGCACACAT 58.292 33.333 25.37 18.26 36.02 3.21
2823 2988 5.221382 ACGCTTCAGGTTTCTAACTAGAACA 60.221 40.000 0.00 0.00 41.64 3.18
2939 3104 3.642503 CGCCCTTGGTACACCCCA 61.643 66.667 0.00 0.00 39.29 4.96
2956 3121 1.009829 CCAGACAGCGAGGTAATTGC 58.990 55.000 0.00 0.00 38.78 3.56
2979 3144 2.420022 GGGTGTTCAGAAATGGACATCG 59.580 50.000 0.00 0.00 0.00 3.84
2980 3145 3.334691 GGTGTTCAGAAATGGACATCGA 58.665 45.455 0.00 0.00 0.00 3.59
3040 3222 6.334378 TCCTGTGATGAAATTAATGGGGTA 57.666 37.500 0.00 0.00 0.00 3.69
3101 3284 0.874390 GAGGCTTCACGTTTGCATCA 59.126 50.000 12.03 0.00 37.44 3.07
3182 3365 1.640917 ACTCTTTCCTCAAGGGCGTA 58.359 50.000 0.00 0.00 36.23 4.42
3194 3378 4.468689 GGCGTACTCCCACCAGCC 62.469 72.222 0.00 0.00 37.61 4.85
3206 3390 0.893270 CACCAGCCGACATCCCAAAA 60.893 55.000 0.00 0.00 0.00 2.44
3227 3411 5.371115 AATGAGTTGTGTTATTTGGACGG 57.629 39.130 0.00 0.00 0.00 4.79
3229 3413 4.200874 TGAGTTGTGTTATTTGGACGGTT 58.799 39.130 0.00 0.00 0.00 4.44
3252 3440 8.349983 GGTTACTTGTTTATTGTGTGTTCTGAT 58.650 33.333 0.00 0.00 0.00 2.90
3408 3598 5.814764 AATGTTGTTTGCATTGAAAAGCA 57.185 30.435 0.00 0.00 39.32 3.91
3480 3670 6.238648 GCGTATTTCCCTTGTTAAGCATATGT 60.239 38.462 4.29 0.00 0.00 2.29
3484 3674 8.823220 ATTTCCCTTGTTAAGCATATGTTAGT 57.177 30.769 4.29 0.00 0.00 2.24
3520 3710 1.140052 TCAAACCAGAGTTCTTGGCGA 59.860 47.619 0.00 0.00 34.19 5.54
3555 3745 2.125350 GGCTCTGAGCAACTCCCG 60.125 66.667 28.95 0.00 44.75 5.14
3576 3766 2.008242 TTCTGGTTGGGGGTGATTTG 57.992 50.000 0.00 0.00 0.00 2.32
3647 3837 8.205131 GACAGGTGGTCGTTTATGTTTAATAT 57.795 34.615 0.00 0.00 36.65 1.28
3676 3866 4.098654 TCGAAAGCTTGGATCTAAGAGAGG 59.901 45.833 21.83 6.93 0.00 3.69
3694 3884 2.619646 GAGGTAGAGCTTTCGGGTAGAG 59.380 54.545 0.00 0.00 0.00 2.43
3735 3925 4.305769 CTTTGCCAAATCCGACATTTGAA 58.694 39.130 16.94 5.90 40.42 2.69
3738 3928 4.697514 TGCCAAATCCGACATTTGAAAAA 58.302 34.783 16.94 2.47 40.42 1.94
3769 4115 3.515901 AGTCCTAACGAGCTTCTTGGATT 59.484 43.478 0.00 0.00 0.00 3.01
3779 4125 3.026694 GCTTCTTGGATTTGGTAGCCAT 58.973 45.455 0.00 0.00 31.53 4.40
4037 4383 4.504858 TCTCCGTGAAGAGGAATTAAAGC 58.495 43.478 0.00 0.00 37.32 3.51
4093 4439 1.673626 GGGGACGCGAACACTCAATTA 60.674 52.381 15.93 0.00 0.00 1.40
4135 4481 4.022503 GGCAAGCACAGAAAGAAGAGAATT 60.023 41.667 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.365767 GGTGACGTGTTACTAGACAGGAC 60.366 52.174 10.29 5.79 38.44 3.85
26 27 1.280746 CGCGCCTATTCAATGCTGG 59.719 57.895 0.00 0.00 0.00 4.85
71 72 3.771160 GGCACACCGGTCGAGGAT 61.771 66.667 2.59 0.00 34.73 3.24
83 84 2.324330 CCGTCATTGAAGCGGCACA 61.324 57.895 1.45 0.00 38.99 4.57
85 86 1.298157 CTTCCGTCATTGAAGCGGCA 61.298 55.000 10.09 0.36 44.58 5.69
106 107 4.477975 CGGACGCGACCTCTCACC 62.478 72.222 24.38 7.87 0.00 4.02
149 152 0.242555 TCATGTCGTTGTAGAGCGCA 59.757 50.000 11.47 0.00 0.00 6.09
163 166 0.752743 CCGGATGCCCACATTCATGT 60.753 55.000 0.00 0.00 42.84 3.21
180 183 3.864686 CATTTCCGTCTGGCGCCG 61.865 66.667 23.90 16.91 39.71 6.46
187 190 3.118454 CCGCACGCATTTCCGTCT 61.118 61.111 0.00 0.00 39.83 4.18
193 196 4.054825 CCTTGGCCGCACGCATTT 62.055 61.111 0.00 0.00 40.31 2.32
205 208 3.979497 AAACCCCTCCGCCCTTGG 61.979 66.667 0.00 0.00 0.00 3.61
207 210 3.979497 CCAAACCCCTCCGCCCTT 61.979 66.667 0.00 0.00 0.00 3.95
212 215 3.562732 GACCACCCAAACCCCTCCG 62.563 68.421 0.00 0.00 0.00 4.63
221 224 0.698198 TTACCACCCTGACCACCCAA 60.698 55.000 0.00 0.00 0.00 4.12
239 242 3.219281 ACAGTACCAACATCCGCTTTTT 58.781 40.909 0.00 0.00 0.00 1.94
248 251 1.337823 GCGTCCAGACAGTACCAACAT 60.338 52.381 0.00 0.00 0.00 2.71
249 252 0.032952 GCGTCCAGACAGTACCAACA 59.967 55.000 0.00 0.00 0.00 3.33
252 255 2.280552 GGGCGTCCAGACAGTACCA 61.281 63.158 0.00 0.00 0.00 3.25
262 265 4.966787 GGGCTTTGTGGGCGTCCA 62.967 66.667 3.51 3.51 41.58 4.02
278 281 2.200373 ACTCGAGAAAAATGTGGGGG 57.800 50.000 21.68 0.00 0.00 5.40
285 288 4.714632 TCTCCCACAAACTCGAGAAAAAT 58.285 39.130 21.68 0.00 0.00 1.82
289 292 3.134081 ACTTTCTCCCACAAACTCGAGAA 59.866 43.478 21.68 0.00 39.09 2.87
294 297 1.264288 CGCACTTTCTCCCACAAACTC 59.736 52.381 0.00 0.00 0.00 3.01
301 304 2.342279 CGGACGCACTTTCTCCCA 59.658 61.111 0.00 0.00 0.00 4.37
339 342 2.114638 GCCATTCAATGCGGGCTTA 58.885 52.632 0.00 0.00 43.09 3.09
348 351 2.192605 GCCGTGGAAGCCATTCAAT 58.807 52.632 0.00 0.00 37.15 2.57
366 369 3.723235 CTGGATCACGCTGTCCGGG 62.723 68.421 0.00 0.00 43.23 5.73
385 388 1.004320 TCAAACCGCCTGCATACGT 60.004 52.632 7.61 0.00 0.00 3.57
406 409 2.068834 AGGGTATCTTCGACACCGAT 57.931 50.000 0.00 0.00 45.10 4.18
410 413 6.592607 TCAAATGTTTAGGGTATCTTCGACAC 59.407 38.462 0.00 0.00 0.00 3.67
411 414 6.703319 TCAAATGTTTAGGGTATCTTCGACA 58.297 36.000 0.00 0.00 0.00 4.35
414 417 7.042335 ACTCTCAAATGTTTAGGGTATCTTCG 58.958 38.462 0.00 0.00 0.00 3.79
415 418 8.794335 AACTCTCAAATGTTTAGGGTATCTTC 57.206 34.615 0.00 0.00 0.00 2.87
421 424 4.324267 CCGAACTCTCAAATGTTTAGGGT 58.676 43.478 0.00 0.00 0.00 4.34
480 483 8.125448 GCATTTCTAATCGATGCCCTAAATATC 58.875 37.037 0.00 0.00 40.10 1.63
500 503 8.950208 AAGAGTAGGTATGTTTAGAGCATTTC 57.050 34.615 0.00 0.00 0.00 2.17
511 514 4.803098 AACTGCGAAGAGTAGGTATGTT 57.197 40.909 0.00 0.00 36.85 2.71
513 516 3.865745 CCAAACTGCGAAGAGTAGGTATG 59.134 47.826 0.00 0.00 36.85 2.39
514 517 3.679083 GCCAAACTGCGAAGAGTAGGTAT 60.679 47.826 0.00 0.00 36.85 2.73
515 518 2.353406 GCCAAACTGCGAAGAGTAGGTA 60.353 50.000 0.00 0.00 36.85 3.08
516 519 1.608283 GCCAAACTGCGAAGAGTAGGT 60.608 52.381 0.00 0.00 36.85 3.08
517 520 1.079503 GCCAAACTGCGAAGAGTAGG 58.920 55.000 0.00 0.00 36.85 3.18
518 521 2.086054 AGCCAAACTGCGAAGAGTAG 57.914 50.000 0.00 0.00 38.61 2.57
561 564 4.325204 GTGAACGCACTTGATTACGTCATA 59.675 41.667 0.00 0.00 41.84 2.15
582 585 1.004044 AGTTCCAGGCTTCCAGATGTG 59.996 52.381 0.00 0.00 0.00 3.21
602 605 9.737427 TGTTCGCTTAGAAAAATGATGTTTTAA 57.263 25.926 0.00 0.00 41.10 1.52
612 615 9.705290 AAATGGTAAATGTTCGCTTAGAAAAAT 57.295 25.926 0.00 0.00 41.10 1.82
667 670 6.909550 ATTTTAACACAATGGGCTTACTGA 57.090 33.333 0.00 0.00 0.00 3.41
701 704 2.478033 GGGTTAAGAATGCCGGCCG 61.478 63.158 26.77 21.04 0.00 6.13
702 705 1.379309 TGGGTTAAGAATGCCGGCC 60.379 57.895 26.77 8.84 0.00 6.13
761 768 1.534805 CGGTCAGGTGAGACGATGATG 60.535 57.143 0.00 0.00 39.42 3.07
808 815 0.755327 GGGTTTGGATTCCCCGATGG 60.755 60.000 0.00 0.00 37.89 3.51
849 856 0.813210 CAGCTCGGATTCTCCAAGGC 60.813 60.000 0.00 0.00 35.91 4.35
894 901 3.904717 AGGTGAGTAACTGAGATCCGAT 58.095 45.455 0.00 0.00 0.00 4.18
895 902 3.367646 AGGTGAGTAACTGAGATCCGA 57.632 47.619 0.00 0.00 0.00 4.55
897 904 4.794334 TCCTAGGTGAGTAACTGAGATCC 58.206 47.826 9.08 0.00 0.00 3.36
899 906 5.459982 ACTCCTAGGTGAGTAACTGAGAT 57.540 43.478 17.66 0.00 43.65 2.75
910 917 7.072454 AGGAAAATGCATATTACTCCTAGGTGA 59.928 37.037 17.66 0.00 37.16 4.02
999 1006 3.370633 GGAAGAAGGTAGTCCCAACCATC 60.371 52.174 0.00 0.00 39.64 3.51
1050 1064 2.285592 TCCTGGGAGGCATCTGCA 60.286 61.111 4.33 0.00 44.36 4.41
1071 1085 3.008330 CAAGATGAACTTCCTGAGCTGG 58.992 50.000 0.00 0.00 36.61 4.85
1118 1133 0.248289 GTTCGCACTACTGGCCCTTA 59.752 55.000 0.00 0.00 0.00 2.69
1134 1149 2.322830 GGTTTCCTCGGGCACGTTC 61.323 63.158 8.89 0.00 41.85 3.95
1664 1691 3.708734 CGGGTCGCCAACGTTGTC 61.709 66.667 25.63 13.65 41.18 3.18
1880 1907 3.636153 AGGAGGTGAATCAAACTAGGC 57.364 47.619 0.00 0.00 0.00 3.93
1985 2020 0.036388 GCTCCCCTTGTCGTTCATGA 60.036 55.000 0.00 0.00 0.00 3.07
2080 2115 0.318699 CACTGCCAGTCGTCTTTCGA 60.319 55.000 0.00 0.00 46.83 3.71
2181 2222 2.646719 GAGTGGTACGTGCCGTCA 59.353 61.111 18.26 0.00 41.54 4.35
2256 2298 7.548780 TGCTGCCCATAGAAATGTTTTATTTTC 59.451 33.333 0.00 0.00 33.08 2.29
2352 2424 9.444600 AATTTATAAAGACGTACTGTGAATGGT 57.555 29.630 3.94 0.00 0.00 3.55
2373 2445 6.265196 CCAGCCAGCTGATAAACCATAATTTA 59.735 38.462 21.01 0.00 46.30 1.40
2382 2454 1.943340 GTAGCCAGCCAGCTGATAAAC 59.057 52.381 21.01 9.38 46.30 2.01
2386 2458 1.406065 ATCGTAGCCAGCCAGCTGAT 61.406 55.000 21.01 11.27 46.30 2.90
2515 2587 0.110733 TTTTTGCGCGCGGTAAGTAC 60.111 50.000 33.06 13.41 0.00 2.73
2614 2687 2.096980 GTGCAAATTAGTTAGACCGGGC 59.903 50.000 6.32 0.52 0.00 6.13
2660 2750 3.692576 CCGTCGTTATAGTCCAAGTCTG 58.307 50.000 0.00 0.00 0.00 3.51
2759 2849 0.892063 TGCTCAATGTGTGCATGCAT 59.108 45.000 25.64 4.32 41.27 3.96
2772 2937 6.183360 GCTACTTTATTCTGCTCAATGCTCAA 60.183 38.462 0.00 0.00 43.37 3.02
2823 2988 2.504367 CCCACTGAAGAAATCGTGGTT 58.496 47.619 14.00 0.00 44.33 3.67
2939 3104 2.015736 CAGCAATTACCTCGCTGTCT 57.984 50.000 6.56 0.00 46.36 3.41
2956 3121 2.862541 TGTCCATTTCTGAACACCCAG 58.137 47.619 0.00 0.00 35.55 4.45
2957 3122 3.420893 GATGTCCATTTCTGAACACCCA 58.579 45.455 0.00 0.00 0.00 4.51
2996 3165 4.751600 GGATCAAGCACACATCATATCGAA 59.248 41.667 0.00 0.00 0.00 3.71
2998 3167 4.151867 CAGGATCAAGCACACATCATATCG 59.848 45.833 0.00 0.00 0.00 2.92
3040 3222 2.308866 CCTCCAACCTAAATCCACCACT 59.691 50.000 0.00 0.00 0.00 4.00
3182 3365 2.607750 ATGTCGGCTGGTGGGAGT 60.608 61.111 0.00 0.00 0.00 3.85
3194 3378 3.253188 ACACAACTCATTTTGGGATGTCG 59.747 43.478 0.00 0.00 33.76 4.35
3206 3390 4.394729 ACCGTCCAAATAACACAACTCAT 58.605 39.130 0.00 0.00 0.00 2.90
3227 3411 9.730420 AATCAGAACACACAATAAACAAGTAAC 57.270 29.630 0.00 0.00 0.00 2.50
3408 3598 5.941948 GCTTATCCGGTACAAGCATTTAT 57.058 39.130 23.33 1.75 43.29 1.40
3420 3610 3.845781 ATTCAGACATGCTTATCCGGT 57.154 42.857 0.00 0.00 0.00 5.28
3451 3641 5.883673 TGCTTAACAAGGGAAATACGCTAAT 59.116 36.000 0.00 0.00 40.92 1.73
3452 3642 5.247084 TGCTTAACAAGGGAAATACGCTAA 58.753 37.500 0.00 0.00 40.92 3.09
3453 3643 4.834534 TGCTTAACAAGGGAAATACGCTA 58.165 39.130 0.00 0.00 40.92 4.26
3454 3644 3.681593 TGCTTAACAAGGGAAATACGCT 58.318 40.909 0.00 0.00 43.65 5.07
3455 3645 4.632538 ATGCTTAACAAGGGAAATACGC 57.367 40.909 0.00 0.00 0.00 4.42
3456 3646 7.259290 ACATATGCTTAACAAGGGAAATACG 57.741 36.000 1.58 0.00 0.00 3.06
3458 3648 9.914834 ACTAACATATGCTTAACAAGGGAAATA 57.085 29.630 1.58 0.00 0.00 1.40
3459 3649 8.823220 ACTAACATATGCTTAACAAGGGAAAT 57.177 30.769 1.58 0.00 0.00 2.17
3462 3652 9.914834 ATAAACTAACATATGCTTAACAAGGGA 57.085 29.630 1.58 0.00 0.00 4.20
3520 3710 2.171448 AGCCGCAGATCCTAACAAGATT 59.829 45.455 0.00 0.00 0.00 2.40
3555 3745 2.497273 CAAATCACCCCCAACCAGAATC 59.503 50.000 0.00 0.00 0.00 2.52
3576 3766 8.429237 TTTCCTCTCTCCTCCTAATGATATTC 57.571 38.462 0.00 0.00 0.00 1.75
3647 3837 7.726216 TCTTAGATCCAAGCTTTCGATAATGA 58.274 34.615 0.00 0.00 0.00 2.57
3676 3866 4.922471 ATTCTCTACCCGAAAGCTCTAC 57.078 45.455 0.00 0.00 0.00 2.59
3694 3884 5.291858 GCAAAGCATTAGCCCAAGTAAATTC 59.708 40.000 0.00 0.00 43.56 2.17
3754 3944 2.568623 ACCAAATCCAAGAAGCTCGT 57.431 45.000 0.00 0.00 0.00 4.18
3779 4125 2.358090 CCTGCATCCTTAACCCATTCCA 60.358 50.000 0.00 0.00 0.00 3.53
3788 4134 3.039011 GTCCTACCTCCTGCATCCTTAA 58.961 50.000 0.00 0.00 0.00 1.85
3855 4201 1.265236 CTTAGCCCACCCATGCAAAA 58.735 50.000 0.00 0.00 0.00 2.44
4093 4439 4.558538 GCCATTAGCGATCAAGTGAAAT 57.441 40.909 0.00 0.00 0.00 2.17
4135 4481 6.698008 TCTTCATCTTGTTCAAGCTGAAAA 57.302 33.333 22.84 13.74 38.22 2.29
4158 4504 6.718294 AGGTTATCCTGTCCTAAAATCGTTT 58.282 36.000 0.00 0.00 43.33 3.60


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

AutoCloner maintained by Alex Coulton.