Multiple sequence alignment - TraesCS5B01G169200

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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 TraesCS5B01G169200 chr5B 100.000 2693 0 0 1 2693 313312630 313309938 0.000000e+00 4974.0
1 TraesCS5B01G169200 chr5B 90.074 544 38 4 1 528 321464135 321464678 0.000000e+00 691.0
2 TraesCS5B01G169200 chr5B 89.725 545 40 4 1 529 320687911 320688455 0.000000e+00 682.0
3 TraesCS5B01G169200 chr5B 89.725 545 40 4 1 529 321441619 321442163 0.000000e+00 682.0
4 TraesCS5B01G169200 chr5B 89.834 541 39 4 4 528 691829738 691829198 0.000000e+00 680.0
5 TraesCS5B01G169200 chr5B 88.068 528 59 1 1 524 325397631 325397104 8.190000e-175 623.0
6 TraesCS5B01G169200 chr5B 85.816 564 35 20 1410 1930 313349945 313349384 8.420000e-155 556.0
7 TraesCS5B01G169200 chr5B 84.091 484 55 15 702 1178 313350638 313350170 5.290000e-122 448.0
8 TraesCS5B01G169200 chr5B 93.689 206 10 2 1271 1476 313350174 313349972 3.370000e-79 305.0
9 TraesCS5B01G169200 chr5B 91.045 67 3 2 1410 1476 313349990 313349927 1.330000e-13 87.9
10 TraesCS5B01G169200 chr5D 94.937 1422 46 9 528 1930 276547475 276546061 0.000000e+00 2204.0
11 TraesCS5B01G169200 chr5D 85.237 569 44 13 1399 1935 276553536 276552976 1.410000e-152 549.0
12 TraesCS5B01G169200 chr5D 82.840 507 56 19 684 1178 276554192 276553705 2.480000e-115 425.0
13 TraesCS5B01G169200 chr5D 78.694 582 84 26 1052 1627 276468045 276467498 4.270000e-93 351.0
14 TraesCS5B01G169200 chr5D 94.581 203 8 2 1271 1473 276553709 276553510 7.240000e-81 311.0
15 TraesCS5B01G169200 chr5D 86.957 207 25 2 2489 2693 276545613 276545407 5.800000e-57 231.0
16 TraesCS5B01G169200 chr5D 79.872 313 42 17 2128 2427 276545920 276545616 2.720000e-50 209.0
17 TraesCS5B01G169200 chr5A 88.994 1581 85 34 524 2077 364971041 364969523 0.000000e+00 1873.0
18 TraesCS5B01G169200 chr5A 87.544 562 32 14 1399 1930 364978374 364977821 1.370000e-172 616.0
19 TraesCS5B01G169200 chr5A 77.508 658 82 36 1054 1692 364962123 364961513 4.300000e-88 335.0
20 TraesCS5B01G169200 chr5A 91.102 236 17 3 946 1178 364978777 364978543 1.560000e-82 316.0
21 TraesCS5B01G169200 chr5A 93.103 203 11 2 1274 1476 364978544 364978345 7.290000e-76 294.0
22 TraesCS5B01G169200 chr5A 87.917 240 22 5 684 922 364979005 364978772 2.640000e-70 276.0
23 TraesCS5B01G169200 chr4B 90.110 546 38 4 1 530 100233571 100234116 0.000000e+00 695.0
24 TraesCS5B01G169200 chr4B 89.377 546 41 5 1 529 100220557 100221102 0.000000e+00 671.0
25 TraesCS5B01G169200 chr4B 87.209 86 8 3 2500 2582 582119133 582119048 7.940000e-16 95.3
26 TraesCS5B01G169200 chr7B 88.679 530 58 2 1 529 288462927 288462399 0.000000e+00 645.0
27 TraesCS5B01G169200 chr7B 82.443 131 22 1 2504 2634 734350118 734350247 2.190000e-21 113.0
28 TraesCS5B01G169200 chr4A 86.654 532 65 5 1 528 669627603 669628132 3.860000e-163 584.0
29 TraesCS5B01G169200 chr4D 85.841 113 12 4 2498 2606 465363714 465363602 1.690000e-22 117.0
30 TraesCS5B01G169200 chr4D 91.489 47 4 0 2381 2427 11004162 11004116 6.220000e-07 65.8
31 TraesCS5B01G169200 chr2D 80.672 119 20 3 2521 2637 340537947 340537830 3.690000e-14 89.8
32 TraesCS5B01G169200 chr6D 94.595 37 2 0 493 529 367412999 367413035 1.040000e-04 58.4


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 TraesCS5B01G169200 chr5B 313309938 313312630 2692 True 4974.000000 4974 100.000000 1 2693 1 chr5B.!!$R1 2692
1 TraesCS5B01G169200 chr5B 321464135 321464678 543 False 691.000000 691 90.074000 1 528 1 chr5B.!!$F3 527
2 TraesCS5B01G169200 chr5B 320687911 320688455 544 False 682.000000 682 89.725000 1 529 1 chr5B.!!$F1 528
3 TraesCS5B01G169200 chr5B 321441619 321442163 544 False 682.000000 682 89.725000 1 529 1 chr5B.!!$F2 528
4 TraesCS5B01G169200 chr5B 691829198 691829738 540 True 680.000000 680 89.834000 4 528 1 chr5B.!!$R3 524
5 TraesCS5B01G169200 chr5B 325397104 325397631 527 True 623.000000 623 88.068000 1 524 1 chr5B.!!$R2 523
6 TraesCS5B01G169200 chr5B 313349384 313350638 1254 True 349.225000 556 88.660250 702 1930 4 chr5B.!!$R4 1228
7 TraesCS5B01G169200 chr5D 276545407 276547475 2068 True 881.333333 2204 87.255333 528 2693 3 chr5D.!!$R2 2165
8 TraesCS5B01G169200 chr5D 276552976 276554192 1216 True 428.333333 549 87.552667 684 1935 3 chr5D.!!$R3 1251
9 TraesCS5B01G169200 chr5D 276467498 276468045 547 True 351.000000 351 78.694000 1052 1627 1 chr5D.!!$R1 575
10 TraesCS5B01G169200 chr5A 364969523 364971041 1518 True 1873.000000 1873 88.994000 524 2077 1 chr5A.!!$R2 1553
11 TraesCS5B01G169200 chr5A 364977821 364979005 1184 True 375.500000 616 89.916500 684 1930 4 chr5A.!!$R3 1246
12 TraesCS5B01G169200 chr5A 364961513 364962123 610 True 335.000000 335 77.508000 1054 1692 1 chr5A.!!$R1 638
13 TraesCS5B01G169200 chr4B 100233571 100234116 545 False 695.000000 695 90.110000 1 530 1 chr4B.!!$F2 529
14 TraesCS5B01G169200 chr4B 100220557 100221102 545 False 671.000000 671 89.377000 1 529 1 chr4B.!!$F1 528
15 TraesCS5B01G169200 chr7B 288462399 288462927 528 True 645.000000 645 88.679000 1 529 1 chr7B.!!$R1 528
16 TraesCS5B01G169200 chr4A 669627603 669628132 529 False 584.000000 584 86.654000 1 528 1 chr4A.!!$F1 527

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
399 401 0.038892 GAGCGTCGTTGTCTTGGGTA 60.039 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 2390 0.036875 GACCTTTCCTGGGTCCACAG 59.963 60.0 1.8 0.0 45.31 3.66 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
72 73 1.080705 CGAACTTCCGCCGTCTTCT 60.081 57.895 0.00 0.00 0.00 2.85
147 148 3.319198 GGGGAACAGGACTCCGCA 61.319 66.667 1.39 0.00 43.59 5.69
172 173 2.028130 AGGAGCAACGTGAGGATAGAG 58.972 52.381 0.00 0.00 0.00 2.43
389 391 4.719369 GCCACTCGGAGCGTCGTT 62.719 66.667 4.58 0.00 0.00 3.85
399 401 0.038892 GAGCGTCGTTGTCTTGGGTA 60.039 55.000 0.00 0.00 0.00 3.69
453 471 0.603975 GTTTCGGCTTGAGGCTCAGT 60.604 55.000 17.91 0.00 41.46 3.41
457 475 0.247736 CGGCTTGAGGCTCAGTTAGT 59.752 55.000 17.91 0.00 41.46 2.24
467 486 1.178276 CTCAGTTAGTCGGAGCTGGT 58.822 55.000 0.00 0.00 32.34 4.00
469 488 1.178276 CAGTTAGTCGGAGCTGGTCT 58.822 55.000 6.83 0.00 0.00 3.85
496 515 8.608844 AAGTCTTGATAAATTTTGAGTCTCGT 57.391 30.769 0.00 0.00 0.00 4.18
512 531 2.632544 CGTGTGAGCCTACCCGTGA 61.633 63.158 0.00 0.00 0.00 4.35
514 533 1.228769 TGTGAGCCTACCCGTGACT 60.229 57.895 0.00 0.00 0.00 3.41
535 554 2.946329 TCATTACTCCGACAGAGAGAGC 59.054 50.000 0.00 0.00 46.50 4.09
718 737 9.197694 GCGTCAATAATTCAGTATAGAGAATGT 57.802 33.333 1.48 0.00 34.86 2.71
739 758 6.494893 TGTACTGTTTGATTGGCTGATTAC 57.505 37.500 0.00 0.00 0.00 1.89
743 762 5.536161 ACTGTTTGATTGGCTGATTACTTGT 59.464 36.000 0.00 0.00 0.00 3.16
806 829 1.671901 CTGCTTCCCTCGTCCCTCTC 61.672 65.000 0.00 0.00 0.00 3.20
807 830 1.380650 GCTTCCCTCGTCCCTCTCT 60.381 63.158 0.00 0.00 0.00 3.10
842 865 2.622064 ATAAATGGCCAGGACGTCTC 57.378 50.000 13.05 5.70 0.00 3.36
848 871 2.948720 GCCAGGACGTCTCCTTGCT 61.949 63.158 16.46 0.00 45.77 3.91
849 872 1.079543 CCAGGACGTCTCCTTGCTG 60.080 63.158 16.46 12.38 45.77 4.41
850 873 1.739562 CAGGACGTCTCCTTGCTGC 60.740 63.158 16.46 0.00 45.77 5.25
1269 1338 3.359950 AGGAGGTGCTCAATTCAATTCC 58.640 45.455 0.00 0.00 31.08 3.01
1323 1392 1.930251 AGATCATCATCGTCGGGGAT 58.070 50.000 0.00 0.00 33.75 3.85
1339 1408 2.833582 ATGGCGTCGACCCGATCT 60.834 61.111 10.58 0.00 38.42 2.75
1565 1784 1.420312 GCTACTCTCAAAACGCGGC 59.580 57.895 12.47 0.00 0.00 6.53
1674 1893 2.842496 TCAGCATCAAGAACAGGATCCT 59.158 45.455 9.02 9.02 0.00 3.24
1724 1965 8.367660 AGTTGTTAGTTAAGGAGAGATGATGA 57.632 34.615 0.00 0.00 0.00 2.92
1887 2158 1.529226 CAATGGTGGTTTGGAGCGTA 58.471 50.000 0.00 0.00 0.00 4.42
1932 2203 7.614192 GGAATGAATAAAAGGAAACTCAGGGTA 59.386 37.037 0.00 0.00 42.68 3.69
1934 2205 8.753497 ATGAATAAAAGGAAACTCAGGGTATC 57.247 34.615 0.00 0.00 42.68 2.24
2035 2310 4.261741 GCATCAAAATCATGACGGGCTTAT 60.262 41.667 0.00 0.00 30.82 1.73
2036 2311 5.048782 GCATCAAAATCATGACGGGCTTATA 60.049 40.000 0.00 0.00 30.82 0.98
2049 2324 6.046290 ACGGGCTTATAACTGACTAAAAGT 57.954 37.500 0.00 0.00 0.00 2.66
2077 2352 0.617249 TGGCAGCCCTATTTTTGGGG 60.617 55.000 9.64 0.00 44.71 4.96
2095 2370 1.428869 GGGGTAGGATCATCTGCAGT 58.571 55.000 14.67 0.00 0.00 4.40
2097 2372 3.177228 GGGGTAGGATCATCTGCAGTAT 58.823 50.000 14.67 6.15 0.00 2.12
2118 2393 2.479566 CAGTACAATCACTGCCCTGT 57.520 50.000 0.00 0.00 39.54 4.00
2119 2394 2.079158 CAGTACAATCACTGCCCTGTG 58.921 52.381 0.00 0.00 39.54 3.66
2120 2395 1.003580 AGTACAATCACTGCCCTGTGG 59.996 52.381 0.00 0.00 38.40 4.17
2121 2396 1.003118 GTACAATCACTGCCCTGTGGA 59.997 52.381 5.63 0.00 38.40 4.02
2122 2397 0.250901 ACAATCACTGCCCTGTGGAC 60.251 55.000 5.63 0.00 38.40 4.02
2123 2398 0.962356 CAATCACTGCCCTGTGGACC 60.962 60.000 5.63 0.00 38.40 4.46
2124 2399 2.142292 AATCACTGCCCTGTGGACCC 62.142 60.000 5.63 0.00 38.40 4.46
2125 2400 3.569210 CACTGCCCTGTGGACCCA 61.569 66.667 0.00 0.00 34.56 4.51
2126 2401 3.252284 ACTGCCCTGTGGACCCAG 61.252 66.667 3.62 3.62 0.00 4.45
2133 2408 2.155065 CTGTGGACCCAGGAAAGGT 58.845 57.895 0.00 0.00 41.50 3.50
2155 2430 1.043022 AAAAAGGCCTCCAACAGCTG 58.957 50.000 13.48 13.48 0.00 4.24
2156 2431 1.466851 AAAAGGCCTCCAACAGCTGC 61.467 55.000 15.27 0.00 0.00 5.25
2158 2433 4.666253 GGCCTCCAACAGCTGCCA 62.666 66.667 15.27 0.00 41.76 4.92
2164 2439 1.891150 CTCCAACAGCTGCCAAATCTT 59.109 47.619 15.27 0.00 0.00 2.40
2169 2444 5.011943 TCCAACAGCTGCCAAATCTTAAAAT 59.988 36.000 15.27 0.00 0.00 1.82
2170 2445 6.210385 TCCAACAGCTGCCAAATCTTAAAATA 59.790 34.615 15.27 0.00 0.00 1.40
2171 2446 6.873076 CCAACAGCTGCCAAATCTTAAAATAA 59.127 34.615 15.27 0.00 0.00 1.40
2172 2447 7.387397 CCAACAGCTGCCAAATCTTAAAATAAA 59.613 33.333 15.27 0.00 0.00 1.40
2173 2448 8.772705 CAACAGCTGCCAAATCTTAAAATAAAA 58.227 29.630 15.27 0.00 0.00 1.52
2174 2449 9.506018 AACAGCTGCCAAATCTTAAAATAAAAT 57.494 25.926 15.27 0.00 0.00 1.82
2222 2503 3.127533 GCTCCTCGTGCGGCAAAT 61.128 61.111 3.23 0.00 0.00 2.32
2225 2506 0.454957 CTCCTCGTGCGGCAAATTTG 60.455 55.000 14.03 14.03 0.00 2.32
2226 2507 1.444212 CCTCGTGCGGCAAATTTGG 60.444 57.895 19.47 5.27 0.00 3.28
2228 2509 1.861542 CTCGTGCGGCAAATTTGGGA 61.862 55.000 19.47 2.54 0.00 4.37
2237 2518 1.934849 GCAAATTTGGGACACTTCGGC 60.935 52.381 19.47 0.00 39.29 5.54
2243 2524 3.195698 GGACACTTCGGCGGATGC 61.196 66.667 7.21 0.07 41.71 3.91
2264 2545 1.202405 CCAAAAACGTGAGGCTGCTTT 60.202 47.619 0.00 0.00 0.00 3.51
2265 2546 2.119457 CAAAAACGTGAGGCTGCTTTC 58.881 47.619 0.00 0.00 0.00 2.62
2275 2556 3.793144 CTGCTTTCGGACGCCTGC 61.793 66.667 0.00 0.00 0.00 4.85
2295 2576 4.430765 GCGGCCGGAAACTCTCGA 62.431 66.667 29.38 0.00 0.00 4.04
2306 2587 4.951963 CTCTCGAATCCGCCCGCC 62.952 72.222 0.00 0.00 35.37 6.13
2338 2619 2.969238 CATCATGGCCGGCTCGTC 60.969 66.667 28.56 10.32 0.00 4.20
2363 2644 3.560278 GCCGCCGACACCAATACG 61.560 66.667 0.00 0.00 0.00 3.06
2367 2648 2.171725 GCCGACACCAATACGCTCC 61.172 63.158 0.00 0.00 0.00 4.70
2368 2649 1.216977 CCGACACCAATACGCTCCA 59.783 57.895 0.00 0.00 0.00 3.86
2369 2650 0.179084 CCGACACCAATACGCTCCAT 60.179 55.000 0.00 0.00 0.00 3.41
2376 2657 1.595382 AATACGCTCCATGCCGCTC 60.595 57.895 0.00 0.00 38.78 5.03
2377 2658 2.310327 AATACGCTCCATGCCGCTCA 62.310 55.000 0.00 0.00 38.78 4.26
2378 2659 2.978452 ATACGCTCCATGCCGCTCAC 62.978 60.000 0.00 0.00 38.78 3.51
2426 2707 4.242475 GCAGTTTTGCCCTATTTTGTACC 58.758 43.478 0.00 0.00 44.74 3.34
2427 2708 4.481463 CAGTTTTGCCCTATTTTGTACCG 58.519 43.478 0.00 0.00 0.00 4.02
2428 2709 3.057104 AGTTTTGCCCTATTTTGTACCGC 60.057 43.478 0.00 0.00 0.00 5.68
2429 2710 1.465794 TTGCCCTATTTTGTACCGCC 58.534 50.000 0.00 0.00 0.00 6.13
2430 2711 0.621609 TGCCCTATTTTGTACCGCCT 59.378 50.000 0.00 0.00 0.00 5.52
2431 2712 1.004979 TGCCCTATTTTGTACCGCCTT 59.995 47.619 0.00 0.00 0.00 4.35
2432 2713 2.097036 GCCCTATTTTGTACCGCCTTT 58.903 47.619 0.00 0.00 0.00 3.11
2433 2714 2.494471 GCCCTATTTTGTACCGCCTTTT 59.506 45.455 0.00 0.00 0.00 2.27
2434 2715 3.674955 GCCCTATTTTGTACCGCCTTTTG 60.675 47.826 0.00 0.00 0.00 2.44
2435 2716 3.508402 CCCTATTTTGTACCGCCTTTTGT 59.492 43.478 0.00 0.00 0.00 2.83
2436 2717 4.481463 CCTATTTTGTACCGCCTTTTGTG 58.519 43.478 0.00 0.00 0.00 3.33
2437 2718 2.211353 TTTTGTACCGCCTTTTGTGC 57.789 45.000 0.00 0.00 0.00 4.57
2438 2719 1.394618 TTTGTACCGCCTTTTGTGCT 58.605 45.000 0.00 0.00 0.00 4.40
2439 2720 1.394618 TTGTACCGCCTTTTGTGCTT 58.605 45.000 0.00 0.00 0.00 3.91
2440 2721 1.394618 TGTACCGCCTTTTGTGCTTT 58.605 45.000 0.00 0.00 0.00 3.51
2441 2722 2.573369 TGTACCGCCTTTTGTGCTTTA 58.427 42.857 0.00 0.00 0.00 1.85
2442 2723 3.150767 TGTACCGCCTTTTGTGCTTTAT 58.849 40.909 0.00 0.00 0.00 1.40
2443 2724 3.570550 TGTACCGCCTTTTGTGCTTTATT 59.429 39.130 0.00 0.00 0.00 1.40
2444 2725 4.760715 TGTACCGCCTTTTGTGCTTTATTA 59.239 37.500 0.00 0.00 0.00 0.98
2445 2726 5.416326 TGTACCGCCTTTTGTGCTTTATTAT 59.584 36.000 0.00 0.00 0.00 1.28
2446 2727 6.598457 TGTACCGCCTTTTGTGCTTTATTATA 59.402 34.615 0.00 0.00 0.00 0.98
2447 2728 6.131544 ACCGCCTTTTGTGCTTTATTATAG 57.868 37.500 0.00 0.00 0.00 1.31
2448 2729 5.067283 ACCGCCTTTTGTGCTTTATTATAGG 59.933 40.000 0.00 0.00 0.00 2.57
2449 2730 5.507315 CCGCCTTTTGTGCTTTATTATAGGG 60.507 44.000 0.00 0.00 0.00 3.53
2450 2731 5.067283 CGCCTTTTGTGCTTTATTATAGGGT 59.933 40.000 0.00 0.00 0.00 4.34
2451 2732 6.405397 CGCCTTTTGTGCTTTATTATAGGGTT 60.405 38.462 0.00 0.00 0.00 4.11
2452 2733 6.756542 GCCTTTTGTGCTTTATTATAGGGTTG 59.243 38.462 0.00 0.00 0.00 3.77
2453 2734 7.363443 GCCTTTTGTGCTTTATTATAGGGTTGA 60.363 37.037 0.00 0.00 0.00 3.18
2454 2735 8.695456 CCTTTTGTGCTTTATTATAGGGTTGAT 58.305 33.333 0.00 0.00 0.00 2.57
2455 2736 9.520204 CTTTTGTGCTTTATTATAGGGTTGATG 57.480 33.333 0.00 0.00 0.00 3.07
2456 2737 8.588290 TTTGTGCTTTATTATAGGGTTGATGT 57.412 30.769 0.00 0.00 0.00 3.06
2457 2738 8.588290 TTGTGCTTTATTATAGGGTTGATGTT 57.412 30.769 0.00 0.00 0.00 2.71
2458 2739 7.995289 TGTGCTTTATTATAGGGTTGATGTTG 58.005 34.615 0.00 0.00 0.00 3.33
2459 2740 7.613801 TGTGCTTTATTATAGGGTTGATGTTGT 59.386 33.333 0.00 0.00 0.00 3.32
2460 2741 9.116067 GTGCTTTATTATAGGGTTGATGTTGTA 57.884 33.333 0.00 0.00 0.00 2.41
2461 2742 9.337396 TGCTTTATTATAGGGTTGATGTTGTAG 57.663 33.333 0.00 0.00 0.00 2.74
2462 2743 9.555727 GCTTTATTATAGGGTTGATGTTGTAGA 57.444 33.333 0.00 0.00 0.00 2.59
2466 2747 5.975988 ATAGGGTTGATGTTGTAGATGGT 57.024 39.130 0.00 0.00 0.00 3.55
2467 2748 3.955471 AGGGTTGATGTTGTAGATGGTG 58.045 45.455 0.00 0.00 0.00 4.17
2468 2749 2.423538 GGGTTGATGTTGTAGATGGTGC 59.576 50.000 0.00 0.00 0.00 5.01
2469 2750 3.347216 GGTTGATGTTGTAGATGGTGCT 58.653 45.455 0.00 0.00 0.00 4.40
2470 2751 3.127548 GGTTGATGTTGTAGATGGTGCTG 59.872 47.826 0.00 0.00 0.00 4.41
2471 2752 2.358957 TGATGTTGTAGATGGTGCTGC 58.641 47.619 0.00 0.00 0.00 5.25
2479 2760 4.334118 ATGGTGCTGCTCGTGCCA 62.334 61.111 7.05 2.31 38.71 4.92
2514 2795 7.920160 AAAATGTTTTTGTGCCCTATTATGG 57.080 32.000 0.00 0.00 0.00 2.74
2526 2807 2.233271 CTATTATGGGGCTGCTGTTGG 58.767 52.381 0.00 0.00 0.00 3.77
2528 2809 0.034186 TTATGGGGCTGCTGTTGGAG 60.034 55.000 0.00 0.00 34.56 3.86
2643 2924 6.601741 GAGATGCTCTAAAGTCTCCATTTG 57.398 41.667 0.00 0.00 32.83 2.32
2657 2938 2.911636 TCCATTTGCCCACCATCAAAAT 59.088 40.909 0.00 0.00 36.02 1.82
2661 2942 0.887247 TGCCCACCATCAAAATCACG 59.113 50.000 0.00 0.00 0.00 4.35
2663 2944 1.135402 GCCCACCATCAAAATCACGAC 60.135 52.381 0.00 0.00 0.00 4.34
2665 2946 2.162208 CCCACCATCAAAATCACGACAG 59.838 50.000 0.00 0.00 0.00 3.51
2670 2951 6.128035 CCACCATCAAAATCACGACAGAATTA 60.128 38.462 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 1.553248 CTATCGGACAGTGACCCCAAA 59.447 52.381 6.04 0.00 0.00 3.28
163 164 1.066303 CACTGTGCCGTCTCTATCCTC 59.934 57.143 0.00 0.00 0.00 3.71
389 391 2.751688 GGCGGGTTACCCAAGACA 59.248 61.111 21.58 0.00 45.83 3.41
427 445 2.668212 CAAGCCGAAACTCCGCCA 60.668 61.111 0.00 0.00 0.00 5.69
445 463 2.194460 GCTCCGACTAACTGAGCCT 58.806 57.895 0.00 0.00 45.62 4.58
453 471 3.428532 ACTTTAGACCAGCTCCGACTAA 58.571 45.455 0.00 0.00 0.00 2.24
457 475 2.217510 AGACTTTAGACCAGCTCCGA 57.782 50.000 0.00 0.00 0.00 4.55
491 510 4.013702 GGGTAGGCTCACACGAGA 57.986 61.111 0.00 0.00 42.34 4.04
496 515 1.228769 AGTCACGGGTAGGCTCACA 60.229 57.895 0.00 0.00 0.00 3.58
512 531 4.196193 CTCTCTCTGTCGGAGTAATGAGT 58.804 47.826 8.56 0.00 42.40 3.41
514 533 2.946329 GCTCTCTCTGTCGGAGTAATGA 59.054 50.000 8.56 3.27 42.40 2.57
547 566 5.252547 TGCTCCAAATTATCACACAGCTAA 58.747 37.500 0.00 0.00 0.00 3.09
718 737 6.714810 ACAAGTAATCAGCCAATCAAACAGTA 59.285 34.615 0.00 0.00 0.00 2.74
806 829 4.679373 TTTATAGGCTGGCAGAGAGAAG 57.321 45.455 20.86 0.00 0.00 2.85
807 830 4.202398 CCATTTATAGGCTGGCAGAGAGAA 60.202 45.833 20.86 2.60 0.00 2.87
842 865 1.307097 GCCTCTTATGAGCAGCAAGG 58.693 55.000 0.00 0.00 38.93 3.61
848 871 1.443407 GAGCCGCCTCTTATGAGCA 59.557 57.895 0.02 0.00 38.93 4.26
849 872 1.663074 CGAGCCGCCTCTTATGAGC 60.663 63.158 0.02 0.00 38.93 4.26
850 873 0.318275 GACGAGCCGCCTCTTATGAG 60.318 60.000 0.00 0.00 39.92 2.90
1216 1273 4.043037 AGAAGATGGAACGACGGATTAC 57.957 45.455 0.00 0.00 0.00 1.89
1323 1392 3.515286 GAGATCGGGTCGACGCCA 61.515 66.667 24.89 14.69 39.18 5.69
1339 1408 2.100410 GAGCATCGTCGTCAGCGA 59.900 61.111 0.00 0.00 45.79 4.93
1445 1640 4.796231 TCTTCTTCTCGCCGGCGC 62.796 66.667 42.78 9.12 39.59 6.53
1446 1641 2.126071 TTCTTCTTCTCGCCGGCG 60.126 61.111 42.13 42.13 41.35 6.46
1447 1642 1.811679 CCTTCTTCTTCTCGCCGGC 60.812 63.158 19.07 19.07 0.00 6.13
1448 1643 0.458716 GTCCTTCTTCTTCTCGCCGG 60.459 60.000 0.00 0.00 0.00 6.13
1449 1644 0.798771 CGTCCTTCTTCTTCTCGCCG 60.799 60.000 0.00 0.00 0.00 6.46
1450 1645 0.458716 CCGTCCTTCTTCTTCTCGCC 60.459 60.000 0.00 0.00 0.00 5.54
1565 1784 2.954868 GGTACGTGATCGGCGCAG 60.955 66.667 10.83 5.07 41.85 5.18
1674 1893 2.715749 ACTACATAATGCTGCAGCCA 57.284 45.000 34.64 22.77 41.18 4.75
1724 1965 0.817634 CTCCTGATCTCTCGCCGACT 60.818 60.000 0.00 0.00 0.00 4.18
1840 2088 3.751175 CCAACCAACCTGTACTGTACATG 59.249 47.826 19.99 18.86 38.15 3.21
1887 2158 6.440647 TCATTCCTCCTGTACAATCTGTTACT 59.559 38.462 0.00 0.00 0.00 2.24
2035 2310 7.769044 GCCATTGGAGATACTTTTAGTCAGTTA 59.231 37.037 6.95 0.00 0.00 2.24
2036 2311 6.599638 GCCATTGGAGATACTTTTAGTCAGTT 59.400 38.462 6.95 0.00 0.00 3.16
2049 2324 2.116869 TAGGGCTGCCATTGGAGATA 57.883 50.000 22.05 0.00 0.00 1.98
2058 2333 0.617249 CCCCAAAAATAGGGCTGCCA 60.617 55.000 22.05 0.00 45.39 4.92
2059 2334 1.337384 CCCCCAAAAATAGGGCTGCC 61.337 60.000 11.05 11.05 45.39 4.85
2077 2352 3.618507 GCATACTGCAGATGATCCTACCC 60.619 52.174 23.35 1.34 44.26 3.69
2091 2366 4.526970 CAGTGATTGTACTGCATACTGC 57.473 45.455 0.00 0.00 45.29 4.40
2101 2376 1.003118 TCCACAGGGCAGTGATTGTAC 59.997 52.381 10.43 0.00 42.05 2.90
2102 2377 1.003118 GTCCACAGGGCAGTGATTGTA 59.997 52.381 10.43 0.00 42.05 2.41
2103 2378 0.250901 GTCCACAGGGCAGTGATTGT 60.251 55.000 10.43 0.00 42.05 2.71
2104 2379 0.962356 GGTCCACAGGGCAGTGATTG 60.962 60.000 10.43 0.00 42.05 2.67
2105 2380 1.380302 GGTCCACAGGGCAGTGATT 59.620 57.895 10.43 0.00 42.05 2.57
2107 2382 3.249189 GGGTCCACAGGGCAGTGA 61.249 66.667 10.43 0.00 42.05 3.41
2108 2383 3.557903 CTGGGTCCACAGGGCAGTG 62.558 68.421 2.68 2.68 39.21 3.66
2109 2384 3.252284 CTGGGTCCACAGGGCAGT 61.252 66.667 0.00 0.00 34.84 4.40
2115 2390 0.036875 GACCTTTCCTGGGTCCACAG 59.963 60.000 1.80 0.00 45.31 3.66
2116 2391 2.151369 GACCTTTCCTGGGTCCACA 58.849 57.895 1.80 0.00 45.31 4.17
2170 2445 9.559732 AATGCTGCCTAGTTTTTCTAAAATTTT 57.440 25.926 8.75 8.75 0.00 1.82
2176 2451 9.691362 CTTTTTAATGCTGCCTAGTTTTTCTAA 57.309 29.630 0.00 0.00 0.00 2.10
2177 2452 9.073475 TCTTTTTAATGCTGCCTAGTTTTTCTA 57.927 29.630 0.00 0.00 0.00 2.10
2178 2453 7.951591 TCTTTTTAATGCTGCCTAGTTTTTCT 58.048 30.769 0.00 0.00 0.00 2.52
2179 2454 7.329471 CCTCTTTTTAATGCTGCCTAGTTTTTC 59.671 37.037 0.00 0.00 0.00 2.29
2185 2460 3.950395 AGCCTCTTTTTAATGCTGCCTAG 59.050 43.478 0.00 0.00 0.00 3.02
2194 2475 3.010420 GCACGAGGAGCCTCTTTTTAAT 58.990 45.455 14.19 0.00 40.69 1.40
2195 2476 2.423577 GCACGAGGAGCCTCTTTTTAA 58.576 47.619 14.19 0.00 40.69 1.52
2200 2481 3.764466 CCGCACGAGGAGCCTCTT 61.764 66.667 14.19 2.28 40.69 2.85
2222 2503 2.119484 ATCCGCCGAAGTGTCCCAAA 62.119 55.000 0.00 0.00 0.00 3.28
2225 2506 2.511600 CATCCGCCGAAGTGTCCC 60.512 66.667 0.00 0.00 0.00 4.46
2226 2507 3.195698 GCATCCGCCGAAGTGTCC 61.196 66.667 0.00 0.00 0.00 4.02
2237 2518 0.109781 CTCACGTTTTTGGGCATCCG 60.110 55.000 0.00 0.00 35.24 4.18
2243 2524 1.007387 GCAGCCTCACGTTTTTGGG 60.007 57.895 0.00 0.00 0.00 4.12
2249 2530 1.961277 CCGAAAGCAGCCTCACGTT 60.961 57.895 0.00 0.00 0.00 3.99
2251 2532 2.048222 TCCGAAAGCAGCCTCACG 60.048 61.111 0.00 0.00 0.00 4.35
2272 2553 4.481112 GTTTCCGGCCGCATGCAG 62.481 66.667 22.85 7.69 43.89 4.41
2275 2556 2.436646 AGAGTTTCCGGCCGCATG 60.437 61.111 22.85 6.58 0.00 4.06
2280 2561 0.810426 GGATTCGAGAGTTTCCGGCC 60.810 60.000 0.00 0.00 0.00 6.13
2282 2563 2.959275 CGGATTCGAGAGTTTCCGG 58.041 57.895 0.00 0.00 45.79 5.14
2285 2566 1.146358 CGGGCGGATTCGAGAGTTTC 61.146 60.000 0.00 0.00 39.00 2.78
2310 2591 1.524393 CCATGATGCACGGCAGCTA 60.524 57.895 13.77 3.23 45.80 3.32
2311 2592 2.827190 CCATGATGCACGGCAGCT 60.827 61.111 13.77 0.00 45.80 4.24
2312 2593 4.564116 GCCATGATGCACGGCAGC 62.564 66.667 12.13 7.11 45.81 5.25
2318 2599 3.589881 GAGCCGGCCATGATGCAC 61.590 66.667 26.15 0.00 0.00 4.57
2349 2630 2.171725 GGAGCGTATTGGTGTCGGC 61.172 63.158 0.00 0.00 0.00 5.54
2363 2644 3.503363 GTGTGAGCGGCATGGAGC 61.503 66.667 1.45 0.00 44.65 4.70
2367 2648 0.464373 AATAGGGTGTGAGCGGCATG 60.464 55.000 1.45 0.00 0.00 4.06
2368 2649 0.255890 AAATAGGGTGTGAGCGGCAT 59.744 50.000 1.45 0.00 0.00 4.40
2369 2650 0.037590 AAAATAGGGTGTGAGCGGCA 59.962 50.000 1.45 0.00 0.00 5.69
2411 2692 0.621609 AGGCGGTACAAAATAGGGCA 59.378 50.000 0.00 0.00 0.00 5.36
2412 2693 1.758936 AAGGCGGTACAAAATAGGGC 58.241 50.000 0.00 0.00 0.00 5.19
2415 2696 3.917985 GCACAAAAGGCGGTACAAAATAG 59.082 43.478 0.00 0.00 0.00 1.73
2416 2697 3.570550 AGCACAAAAGGCGGTACAAAATA 59.429 39.130 0.00 0.00 36.08 1.40
2417 2698 2.364002 AGCACAAAAGGCGGTACAAAAT 59.636 40.909 0.00 0.00 36.08 1.82
2419 2700 1.394618 AGCACAAAAGGCGGTACAAA 58.605 45.000 0.00 0.00 36.08 2.83
2420 2701 1.394618 AAGCACAAAAGGCGGTACAA 58.605 45.000 0.00 0.00 36.08 2.41
2421 2702 1.394618 AAAGCACAAAAGGCGGTACA 58.605 45.000 0.00 0.00 36.08 2.90
2422 2703 3.842732 ATAAAGCACAAAAGGCGGTAC 57.157 42.857 0.00 0.00 36.08 3.34
2423 2704 6.261381 CCTATAATAAAGCACAAAAGGCGGTA 59.739 38.462 0.00 0.00 36.08 4.02
2424 2705 5.067283 CCTATAATAAAGCACAAAAGGCGGT 59.933 40.000 0.00 0.00 36.08 5.68
2425 2706 5.507315 CCCTATAATAAAGCACAAAAGGCGG 60.507 44.000 0.00 0.00 36.08 6.13
2426 2707 5.067283 ACCCTATAATAAAGCACAAAAGGCG 59.933 40.000 0.00 0.00 36.08 5.52
2427 2708 6.465439 ACCCTATAATAAAGCACAAAAGGC 57.535 37.500 0.00 0.00 0.00 4.35
2428 2709 8.062065 TCAACCCTATAATAAAGCACAAAAGG 57.938 34.615 0.00 0.00 0.00 3.11
2429 2710 9.520204 CATCAACCCTATAATAAAGCACAAAAG 57.480 33.333 0.00 0.00 0.00 2.27
2430 2711 9.030452 ACATCAACCCTATAATAAAGCACAAAA 57.970 29.630 0.00 0.00 0.00 2.44
2431 2712 8.588290 ACATCAACCCTATAATAAAGCACAAA 57.412 30.769 0.00 0.00 0.00 2.83
2432 2713 8.465999 CAACATCAACCCTATAATAAAGCACAA 58.534 33.333 0.00 0.00 0.00 3.33
2433 2714 7.613801 ACAACATCAACCCTATAATAAAGCACA 59.386 33.333 0.00 0.00 0.00 4.57
2434 2715 7.996385 ACAACATCAACCCTATAATAAAGCAC 58.004 34.615 0.00 0.00 0.00 4.40
2435 2716 9.337396 CTACAACATCAACCCTATAATAAAGCA 57.663 33.333 0.00 0.00 0.00 3.91
2436 2717 9.555727 TCTACAACATCAACCCTATAATAAAGC 57.444 33.333 0.00 0.00 0.00 3.51
2440 2721 9.166222 ACCATCTACAACATCAACCCTATAATA 57.834 33.333 0.00 0.00 0.00 0.98
2441 2722 7.939039 CACCATCTACAACATCAACCCTATAAT 59.061 37.037 0.00 0.00 0.00 1.28
2442 2723 7.279615 CACCATCTACAACATCAACCCTATAA 58.720 38.462 0.00 0.00 0.00 0.98
2443 2724 6.687901 GCACCATCTACAACATCAACCCTATA 60.688 42.308 0.00 0.00 0.00 1.31
2444 2725 5.684704 CACCATCTACAACATCAACCCTAT 58.315 41.667 0.00 0.00 0.00 2.57
2445 2726 4.625324 GCACCATCTACAACATCAACCCTA 60.625 45.833 0.00 0.00 0.00 3.53
2446 2727 3.873801 GCACCATCTACAACATCAACCCT 60.874 47.826 0.00 0.00 0.00 4.34
2447 2728 2.423538 GCACCATCTACAACATCAACCC 59.576 50.000 0.00 0.00 0.00 4.11
2448 2729 3.127548 CAGCACCATCTACAACATCAACC 59.872 47.826 0.00 0.00 0.00 3.77
2449 2730 3.426695 GCAGCACCATCTACAACATCAAC 60.427 47.826 0.00 0.00 0.00 3.18
2450 2731 2.749076 GCAGCACCATCTACAACATCAA 59.251 45.455 0.00 0.00 0.00 2.57
2451 2732 2.026915 AGCAGCACCATCTACAACATCA 60.027 45.455 0.00 0.00 0.00 3.07
2452 2733 2.611292 GAGCAGCACCATCTACAACATC 59.389 50.000 0.00 0.00 0.00 3.06
2453 2734 2.636830 GAGCAGCACCATCTACAACAT 58.363 47.619 0.00 0.00 0.00 2.71
2454 2735 1.672737 CGAGCAGCACCATCTACAACA 60.673 52.381 0.00 0.00 0.00 3.33
2455 2736 1.002366 CGAGCAGCACCATCTACAAC 58.998 55.000 0.00 0.00 0.00 3.32
2456 2737 0.608130 ACGAGCAGCACCATCTACAA 59.392 50.000 0.00 0.00 0.00 2.41
2457 2738 0.108662 CACGAGCAGCACCATCTACA 60.109 55.000 0.00 0.00 0.00 2.74
2458 2739 1.424493 GCACGAGCAGCACCATCTAC 61.424 60.000 0.00 0.00 41.58 2.59
2459 2740 1.153568 GCACGAGCAGCACCATCTA 60.154 57.895 0.00 0.00 41.58 1.98
2460 2741 2.435586 GCACGAGCAGCACCATCT 60.436 61.111 0.00 0.00 41.58 2.90
2461 2742 3.503363 GGCACGAGCAGCACCATC 61.503 66.667 7.26 0.00 44.61 3.51
2462 2743 3.848301 TTGGCACGAGCAGCACCAT 62.848 57.895 7.26 0.00 44.61 3.55
2463 2744 4.560743 TTGGCACGAGCAGCACCA 62.561 61.111 7.26 0.00 44.61 4.17
2464 2745 2.348605 TTTTTGGCACGAGCAGCACC 62.349 55.000 7.26 0.00 44.61 5.01
2465 2746 1.065600 TTTTTGGCACGAGCAGCAC 59.934 52.632 7.26 0.00 44.61 4.40
2466 2747 3.519202 TTTTTGGCACGAGCAGCA 58.481 50.000 7.26 0.00 44.61 4.41
2489 2770 7.392953 CCCATAATAGGGCACAAAAACATTTTT 59.607 33.333 0.00 0.00 43.10 1.94
2490 2771 6.883756 CCCATAATAGGGCACAAAAACATTTT 59.116 34.615 0.00 0.00 43.10 1.82
2491 2772 6.413892 CCCATAATAGGGCACAAAAACATTT 58.586 36.000 0.00 0.00 43.10 2.32
2492 2773 5.988287 CCCATAATAGGGCACAAAAACATT 58.012 37.500 0.00 0.00 43.10 2.71
2493 2774 5.612725 CCCATAATAGGGCACAAAAACAT 57.387 39.130 0.00 0.00 43.10 2.71
2511 2792 2.233566 TCTCCAACAGCAGCCCCAT 61.234 57.895 0.00 0.00 0.00 4.00
2513 2794 2.360475 GTCTCCAACAGCAGCCCC 60.360 66.667 0.00 0.00 0.00 5.80
2514 2795 2.743928 CGTCTCCAACAGCAGCCC 60.744 66.667 0.00 0.00 0.00 5.19
2520 2801 2.357517 AAGCGCCGTCTCCAACAG 60.358 61.111 2.29 0.00 0.00 3.16
2554 2835 2.636768 ATTTAGAGCACAAAAGCGCC 57.363 45.000 2.29 0.00 40.15 6.53
2574 2855 5.517054 GCACGAAAACATGGTGAAGTAAAAA 59.483 36.000 0.00 0.00 39.90 1.94
2582 2863 0.466372 TGGGCACGAAAACATGGTGA 60.466 50.000 0.00 0.00 39.90 4.02
2639 2920 3.617045 CGTGATTTTGATGGTGGGCAAAT 60.617 43.478 0.00 0.00 34.36 2.32
2643 2924 1.135402 GTCGTGATTTTGATGGTGGGC 60.135 52.381 0.00 0.00 0.00 5.36
2657 2938 3.660501 AGTGCAGTAATTCTGTCGTGA 57.339 42.857 0.00 0.00 45.23 4.35


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

AutoCloner maintained by Alex Coulton.