Multiple sequence alignment - TraesCS4A01G318100

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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 TraesCS4A01G318100 chr4A 100.000 2747 0 0 1 2747 607263061 607260315 0.000000e+00 5073.0
1 TraesCS4A01G318100 chr4A 90.947 486 32 6 1015 1500 607178283 607177810 0.000000e+00 643.0
2 TraesCS4A01G318100 chr4A 85.657 251 36 0 1498 1748 607177677 607177427 5.830000e-67 265.0
3 TraesCS4A01G318100 chr5D 92.602 1568 69 21 960 2503 565703150 565701606 0.000000e+00 2209.0
4 TraesCS4A01G318100 chr5D 90.612 490 32 9 1015 1500 565659720 565659241 2.980000e-179 638.0
5 TraesCS4A01G318100 chr5D 84.861 251 37 1 1498 1748 565659116 565658867 4.540000e-63 252.0
6 TraesCS4A01G318100 chr5D 83.158 95 10 6 1103 1194 435933353 435933444 6.300000e-12 82.4
7 TraesCS4A01G318100 chr5D 97.222 36 1 0 16 51 565659903 565659868 8.210000e-06 62.1
8 TraesCS4A01G318100 chr5B 91.125 1600 92 19 935 2503 707439912 707441492 0.000000e+00 2122.0
9 TraesCS4A01G318100 chr5B 90.593 489 34 8 1015 1500 707475983 707476462 2.980000e-179 638.0
10 TraesCS4A01G318100 chr5B 86.056 251 35 0 1498 1748 707476592 707476842 1.250000e-68 270.0
11 TraesCS4A01G318100 chr5B 93.007 143 4 3 1 143 707439781 707439917 1.290000e-48 204.0
12 TraesCS4A01G318100 chr5B 85.350 157 22 1 1342 1497 529988183 529988339 7.870000e-36 161.0
13 TraesCS4A01G318100 chr5B 84.564 149 22 1 1342 1489 529609311 529609459 2.200000e-31 147.0
14 TraesCS4A01G318100 chr5B 83.333 96 8 8 1103 1194 529987512 529987603 6.300000e-12 82.4
15 TraesCS4A01G318100 chr5B 97.222 36 1 0 16 51 707475795 707475830 8.210000e-06 62.1
16 TraesCS4A01G318100 chr6B 99.497 795 4 0 147 941 28222534 28223328 0.000000e+00 1447.0
17 TraesCS4A01G318100 chr2B 98.507 804 12 0 139 942 772346895 772347698 0.000000e+00 1419.0
18 TraesCS4A01G318100 chr2B 96.734 796 8 1 146 941 390366178 390366955 0.000000e+00 1310.0
19 TraesCS4A01G318100 chr2B 95.274 804 17 3 141 941 593646554 593647339 0.000000e+00 1254.0
20 TraesCS4A01G318100 chr2B 93.089 246 15 2 2502 2747 184540166 184539923 2.600000e-95 359.0
21 TraesCS4A01G318100 chr6D 95.375 800 16 3 145 941 345314902 345315683 0.000000e+00 1253.0
22 TraesCS4A01G318100 chr6D 95.369 799 16 3 146 941 68971479 68970699 0.000000e+00 1251.0
23 TraesCS4A01G318100 chr7B 86.757 808 70 16 145 941 720177282 720176501 0.000000e+00 865.0
24 TraesCS4A01G318100 chr2D 87.296 614 39 16 338 941 24939221 24939805 0.000000e+00 665.0
25 TraesCS4A01G318100 chr2A 84.065 615 64 22 144 734 74646157 74645553 1.850000e-156 562.0
26 TraesCS4A01G318100 chr2A 95.473 243 11 0 2505 2747 610184880 610184638 3.320000e-104 388.0
27 TraesCS4A01G318100 chr2A 79.006 624 83 33 336 941 515289479 515290072 1.540000e-102 383.0
28 TraesCS4A01G318100 chr2A 90.286 175 15 2 770 944 74645549 74645377 7.650000e-56 228.0
29 TraesCS4A01G318100 chr2A 91.228 114 10 0 167 280 767765674 767765561 3.660000e-34 156.0
30 TraesCS4A01G318100 chr2A 97.222 36 1 0 148 183 767766452 767766417 8.210000e-06 62.1
31 TraesCS4A01G318100 chr5A 95.062 243 12 0 2505 2747 470121965 470122207 1.540000e-102 383.0
32 TraesCS4A01G318100 chr5A 93.878 245 14 1 2504 2747 680987518 680987762 4.320000e-98 368.0
33 TraesCS4A01G318100 chr5A 93.443 244 16 0 2504 2747 612174288 612174531 2.010000e-96 363.0
34 TraesCS4A01G318100 chr5A 83.333 96 8 8 1103 1194 550249761 550249852 6.300000e-12 82.4
35 TraesCS4A01G318100 chr5A 82.105 95 11 6 1103 1194 549953274 549953365 2.930000e-10 76.8
36 TraesCS4A01G318100 chr3A 93.200 250 16 1 2498 2747 588518520 588518768 1.550000e-97 366.0
37 TraesCS4A01G318100 chrUn 93.802 242 14 1 2506 2747 266374182 266373942 2.010000e-96 363.0
38 TraesCS4A01G318100 chr6A 93.469 245 14 2 2503 2747 616960846 616961088 2.010000e-96 363.0
39 TraesCS4A01G318100 chr6A 92.400 250 18 1 2498 2747 53544910 53544662 3.360000e-94 355.0


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 TraesCS4A01G318100 chr4A 607260315 607263061 2746 True 5073.000000 5073 100.000000 1 2747 1 chr4A.!!$R1 2746
1 TraesCS4A01G318100 chr4A 607177427 607178283 856 True 454.000000 643 88.302000 1015 1748 2 chr4A.!!$R2 733
2 TraesCS4A01G318100 chr5D 565701606 565703150 1544 True 2209.000000 2209 92.602000 960 2503 1 chr5D.!!$R1 1543
3 TraesCS4A01G318100 chr5D 565658867 565659903 1036 True 317.366667 638 90.898333 16 1748 3 chr5D.!!$R2 1732
4 TraesCS4A01G318100 chr5B 707439781 707441492 1711 False 1163.000000 2122 92.066000 1 2503 2 chr5B.!!$F3 2502
5 TraesCS4A01G318100 chr5B 707475795 707476842 1047 False 323.366667 638 91.290333 16 1748 3 chr5B.!!$F4 1732
6 TraesCS4A01G318100 chr6B 28222534 28223328 794 False 1447.000000 1447 99.497000 147 941 1 chr6B.!!$F1 794
7 TraesCS4A01G318100 chr2B 772346895 772347698 803 False 1419.000000 1419 98.507000 139 942 1 chr2B.!!$F3 803
8 TraesCS4A01G318100 chr2B 390366178 390366955 777 False 1310.000000 1310 96.734000 146 941 1 chr2B.!!$F1 795
9 TraesCS4A01G318100 chr2B 593646554 593647339 785 False 1254.000000 1254 95.274000 141 941 1 chr2B.!!$F2 800
10 TraesCS4A01G318100 chr6D 345314902 345315683 781 False 1253.000000 1253 95.375000 145 941 1 chr6D.!!$F1 796
11 TraesCS4A01G318100 chr6D 68970699 68971479 780 True 1251.000000 1251 95.369000 146 941 1 chr6D.!!$R1 795
12 TraesCS4A01G318100 chr7B 720176501 720177282 781 True 865.000000 865 86.757000 145 941 1 chr7B.!!$R1 796
13 TraesCS4A01G318100 chr2D 24939221 24939805 584 False 665.000000 665 87.296000 338 941 1 chr2D.!!$F1 603
14 TraesCS4A01G318100 chr2A 74645377 74646157 780 True 395.000000 562 87.175500 144 944 2 chr2A.!!$R2 800
15 TraesCS4A01G318100 chr2A 515289479 515290072 593 False 383.000000 383 79.006000 336 941 1 chr2A.!!$F1 605

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
995 1050 0.179004 ATCGACCGAGAGAGGCAGAT 60.179 55.0 0.0 0.0 33.69 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2535 2760 0.032267 GCCGCTCTATTTAGGCGTCT 59.968 55.0 14.78 0.0 46.23 4.18 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
43 44 1.933765 AGCTAGGAGGAGGAGGAAGAA 59.066 52.381 0.00 0.00 0.00 2.52
62 63 1.157870 AGACCAAGACCAACGCAACG 61.158 55.000 0.00 0.00 0.00 4.10
67 68 2.640736 AAGACCAACGCAACGCAACG 62.641 55.000 0.00 0.00 0.00 4.10
128 129 1.152419 GCTACCTCTCCTCCCCCTC 60.152 68.421 0.00 0.00 0.00 4.30
311 313 4.946266 TCGTCGGCGCGGAAAACA 62.946 61.111 19.96 0.89 38.14 2.83
647 692 9.601810 ACCTTATAATCCCTTCTTTTTCTTTGT 57.398 29.630 0.00 0.00 0.00 2.83
780 833 6.000840 TGTTGCCATACATAAACTCAGTTGA 58.999 36.000 0.00 0.00 0.00 3.18
944 997 3.552068 GCTCAAACCAAACACACCCATAC 60.552 47.826 0.00 0.00 0.00 2.39
945 998 3.632333 TCAAACCAAACACACCCATACA 58.368 40.909 0.00 0.00 0.00 2.29
946 999 4.219115 TCAAACCAAACACACCCATACAT 58.781 39.130 0.00 0.00 0.00 2.29
947 1000 4.651503 TCAAACCAAACACACCCATACATT 59.348 37.500 0.00 0.00 0.00 2.71
948 1001 4.864704 AACCAAACACACCCATACATTC 57.135 40.909 0.00 0.00 0.00 2.67
949 1002 3.161866 ACCAAACACACCCATACATTCC 58.838 45.455 0.00 0.00 0.00 3.01
950 1003 2.495669 CCAAACACACCCATACATTCCC 59.504 50.000 0.00 0.00 0.00 3.97
951 1004 2.495669 CAAACACACCCATACATTCCCC 59.504 50.000 0.00 0.00 0.00 4.81
952 1005 1.681229 ACACACCCATACATTCCCCT 58.319 50.000 0.00 0.00 0.00 4.79
953 1006 2.853430 ACACACCCATACATTCCCCTA 58.147 47.619 0.00 0.00 0.00 3.53
954 1007 2.777692 ACACACCCATACATTCCCCTAG 59.222 50.000 0.00 0.00 0.00 3.02
966 1019 4.837860 ACATTCCCCTAGCTAGATTCTCTG 59.162 45.833 22.70 13.36 0.00 3.35
990 1043 1.823260 CGTCGATCGACCGAGAGAGG 61.823 65.000 35.48 19.11 41.76 3.69
991 1044 1.888172 TCGATCGACCGAGAGAGGC 60.888 63.158 15.15 0.00 34.19 4.70
995 1050 0.179004 ATCGACCGAGAGAGGCAGAT 60.179 55.000 0.00 0.00 33.69 2.90
1010 1065 1.070445 GCAGATAGACATGGAGCAGCT 59.930 52.381 0.00 0.00 0.00 4.24
1521 1721 2.743928 CTGCTGAACGTGGAGGGC 60.744 66.667 0.00 0.00 0.00 5.19
1648 1848 3.141488 CGGCGCTGGAGGACTACT 61.141 66.667 8.83 0.00 0.00 2.57
1740 1940 2.190578 CCCAAGCCGGACATCTCC 59.809 66.667 5.05 0.00 36.56 3.71
1812 2015 6.119144 AGATTAGTTGACAAACACACACAC 57.881 37.500 0.00 0.00 38.88 3.82
1813 2016 5.645929 AGATTAGTTGACAAACACACACACA 59.354 36.000 0.00 0.00 38.88 3.72
1814 2017 3.552604 AGTTGACAAACACACACACAC 57.447 42.857 0.00 0.00 38.88 3.82
1815 2018 2.881513 AGTTGACAAACACACACACACA 59.118 40.909 0.00 0.00 38.88 3.72
1816 2019 2.977169 GTTGACAAACACACACACACAC 59.023 45.455 0.00 0.00 36.24 3.82
1817 2020 2.222027 TGACAAACACACACACACACA 58.778 42.857 0.00 0.00 0.00 3.72
1818 2021 2.031595 TGACAAACACACACACACACAC 60.032 45.455 0.00 0.00 0.00 3.82
1832 2035 4.022762 ACACACACACATCAGACTCTAGAC 60.023 45.833 0.00 0.00 0.00 2.59
1933 2136 9.956640 ATCTTGGATGGATTAATCAACTAGATC 57.043 33.333 17.07 7.68 35.39 2.75
1936 2139 7.606349 TGGATGGATTAATCAACTAGATCTCG 58.394 38.462 17.07 0.00 35.39 4.04
1937 2140 7.233553 TGGATGGATTAATCAACTAGATCTCGT 59.766 37.037 17.07 0.00 35.39 4.18
1979 2182 3.961849 TGGCTGGAGTATGTATGCAAAA 58.038 40.909 0.00 0.00 0.00 2.44
1981 2184 4.955450 TGGCTGGAGTATGTATGCAAAAAT 59.045 37.500 0.00 0.00 0.00 1.82
1982 2185 6.125719 TGGCTGGAGTATGTATGCAAAAATA 58.874 36.000 0.00 0.00 0.00 1.40
1983 2186 6.039270 TGGCTGGAGTATGTATGCAAAAATAC 59.961 38.462 0.00 0.00 34.24 1.89
1984 2187 6.263168 GGCTGGAGTATGTATGCAAAAATACT 59.737 38.462 14.80 14.80 38.29 2.12
1999 2202 9.593134 TGCAAAAATACTTTTATGTTCTTGTGT 57.407 25.926 0.00 0.00 32.85 3.72
2044 2247 7.843490 TTCTACTTGTGCTGTTTATGTATCC 57.157 36.000 0.00 0.00 0.00 2.59
2093 2296 3.673902 CCATTTCCATTTGGGGTTTGAC 58.326 45.455 0.00 0.00 37.22 3.18
2100 2303 4.596643 TCCATTTGGGGTTTGACATGATTT 59.403 37.500 0.00 0.00 37.22 2.17
2116 2319 1.820519 GATTTGGATCCACAGCAGCAA 59.179 47.619 15.91 4.38 0.00 3.91
2119 2322 0.178995 TGGATCCACAGCAGCAACAA 60.179 50.000 11.44 0.00 0.00 2.83
2122 2325 1.337703 GATCCACAGCAGCAACAACAA 59.662 47.619 0.00 0.00 0.00 2.83
2142 2349 7.927092 ACAACAACAACATGATTGATTGATTGA 59.073 29.630 0.00 0.00 0.00 2.57
2156 2364 7.646446 TGATTGATTGAACTGCAAAAAGATG 57.354 32.000 0.00 0.00 40.48 2.90
2157 2365 7.435305 TGATTGATTGAACTGCAAAAAGATGA 58.565 30.769 0.00 0.00 40.48 2.92
2167 2390 5.182760 ACTGCAAAAAGATGAGAGGATTGAC 59.817 40.000 0.00 0.00 0.00 3.18
2180 2403 0.947244 GATTGACGATGGATGTGGCC 59.053 55.000 0.00 0.00 0.00 5.36
2233 2456 2.932614 CAAGTGAGGTCGATCCATTCAC 59.067 50.000 8.16 8.16 39.93 3.18
2386 2611 2.524394 GGAGGATAGGCCGGCAGA 60.524 66.667 30.85 16.20 43.43 4.26
2466 2691 1.550976 CTACTCAAGTCACCCTCACCC 59.449 57.143 0.00 0.00 0.00 4.61
2470 2695 1.780309 TCAAGTCACCCTCACCCATTT 59.220 47.619 0.00 0.00 0.00 2.32
2494 2719 9.685276 TTTTTCTCATCAATTATCCTCTTGCTA 57.315 29.630 0.00 0.00 0.00 3.49
2496 2721 7.002250 TCTCATCAATTATCCTCTTGCTAGG 57.998 40.000 0.00 0.00 38.06 3.02
2511 2736 1.546923 GCTAGGTAGCTAGCTAAGGGC 59.453 57.143 35.59 23.75 46.32 5.19
2512 2737 2.877866 CTAGGTAGCTAGCTAAGGGCA 58.122 52.381 27.71 11.44 44.79 5.36
2513 2738 2.407340 AGGTAGCTAGCTAAGGGCAT 57.593 50.000 25.74 8.66 44.79 4.40
2514 2739 2.252714 AGGTAGCTAGCTAAGGGCATC 58.747 52.381 25.74 11.42 44.79 3.91
2515 2740 2.158234 AGGTAGCTAGCTAAGGGCATCT 60.158 50.000 25.74 7.98 44.79 2.90
2516 2741 2.635427 GGTAGCTAGCTAAGGGCATCTT 59.365 50.000 25.74 0.00 44.79 2.40
2517 2742 3.306433 GGTAGCTAGCTAAGGGCATCTTC 60.306 52.174 25.74 9.30 44.79 2.87
2518 2743 2.402564 AGCTAGCTAAGGGCATCTTCA 58.597 47.619 17.69 0.00 44.79 3.02
2519 2744 2.368221 AGCTAGCTAAGGGCATCTTCAG 59.632 50.000 17.69 0.00 44.79 3.02
2520 2745 2.765122 CTAGCTAAGGGCATCTTCAGC 58.235 52.381 0.00 4.40 44.79 4.26
2526 2751 3.093278 GGCATCTTCAGCCGTTCG 58.907 61.111 0.00 0.00 43.15 3.95
2527 2752 2.464459 GGCATCTTCAGCCGTTCGG 61.464 63.158 6.90 6.90 43.15 4.30
2537 2762 3.702048 CCGTTCGGCCTCCCAAGA 61.702 66.667 0.00 0.00 0.00 3.02
2538 2763 2.434359 CGTTCGGCCTCCCAAGAC 60.434 66.667 0.00 0.00 0.00 3.01
2539 2764 2.434359 GTTCGGCCTCCCAAGACG 60.434 66.667 0.00 0.00 0.00 4.18
2540 2765 4.388499 TTCGGCCTCCCAAGACGC 62.388 66.667 0.00 0.00 0.00 5.19
2543 2768 3.081409 GGCCTCCCAAGACGCCTA 61.081 66.667 0.00 0.00 40.09 3.93
2544 2769 2.666098 GGCCTCCCAAGACGCCTAA 61.666 63.158 0.00 0.00 40.09 2.69
2545 2770 1.298667 GCCTCCCAAGACGCCTAAA 59.701 57.895 0.00 0.00 0.00 1.85
2546 2771 0.107165 GCCTCCCAAGACGCCTAAAT 60.107 55.000 0.00 0.00 0.00 1.40
2547 2772 1.140252 GCCTCCCAAGACGCCTAAATA 59.860 52.381 0.00 0.00 0.00 1.40
2548 2773 2.807108 GCCTCCCAAGACGCCTAAATAG 60.807 54.545 0.00 0.00 0.00 1.73
2549 2774 2.698797 CCTCCCAAGACGCCTAAATAGA 59.301 50.000 0.00 0.00 0.00 1.98
2550 2775 3.243907 CCTCCCAAGACGCCTAAATAGAG 60.244 52.174 0.00 0.00 0.00 2.43
2551 2776 2.102588 TCCCAAGACGCCTAAATAGAGC 59.897 50.000 0.00 0.00 0.00 4.09
2555 2780 3.952811 CGCCTAAATAGAGCGGCC 58.047 61.111 12.51 0.00 45.88 6.13
2556 2781 1.367840 CGCCTAAATAGAGCGGCCT 59.632 57.895 0.00 0.00 45.88 5.19
2557 2782 0.946221 CGCCTAAATAGAGCGGCCTG 60.946 60.000 0.00 0.00 45.88 4.85
2558 2783 0.603975 GCCTAAATAGAGCGGCCTGG 60.604 60.000 0.00 0.00 36.56 4.45
2559 2784 0.035458 CCTAAATAGAGCGGCCTGGG 59.965 60.000 0.00 0.00 0.00 4.45
2560 2785 0.035458 CTAAATAGAGCGGCCTGGGG 59.965 60.000 0.00 0.00 0.00 4.96
2561 2786 1.415672 TAAATAGAGCGGCCTGGGGG 61.416 60.000 0.00 0.00 0.00 5.40
2579 2804 3.545481 CGTGCAGGCGCTAGTTCG 61.545 66.667 7.64 3.83 39.64 3.95
2580 2805 3.188786 GTGCAGGCGCTAGTTCGG 61.189 66.667 7.64 0.00 39.64 4.30
2589 2814 4.530857 CTAGTTCGGCCCCTGCGG 62.531 72.222 0.00 0.00 38.85 5.69
2606 2831 2.760385 GGCGACCTAGCTCCCAGT 60.760 66.667 0.00 0.00 37.29 4.00
2607 2832 2.787567 GGCGACCTAGCTCCCAGTC 61.788 68.421 0.00 0.00 37.29 3.51
2608 2833 2.052690 GCGACCTAGCTCCCAGTCA 61.053 63.158 0.00 0.00 0.00 3.41
2609 2834 1.810532 CGACCTAGCTCCCAGTCAC 59.189 63.158 0.00 0.00 0.00 3.67
2610 2835 1.810532 GACCTAGCTCCCAGTCACG 59.189 63.158 0.00 0.00 0.00 4.35
2611 2836 2.286127 GACCTAGCTCCCAGTCACGC 62.286 65.000 0.00 0.00 0.00 5.34
2612 2837 2.496817 CTAGCTCCCAGTCACGCC 59.503 66.667 0.00 0.00 0.00 5.68
2613 2838 3.075005 TAGCTCCCAGTCACGCCC 61.075 66.667 0.00 0.00 0.00 6.13
2618 2843 4.722700 CCCAGTCACGCCCCCAAG 62.723 72.222 0.00 0.00 0.00 3.61
2648 2873 3.780902 CCAGGATGCGGGAAATTTAAAC 58.219 45.455 0.00 0.00 31.97 2.01
2649 2874 3.447229 CCAGGATGCGGGAAATTTAAACT 59.553 43.478 0.00 0.00 31.97 2.66
2650 2875 4.081697 CCAGGATGCGGGAAATTTAAACTT 60.082 41.667 0.00 0.00 31.97 2.66
2651 2876 4.864247 CAGGATGCGGGAAATTTAAACTTG 59.136 41.667 0.00 0.00 0.00 3.16
2652 2877 4.081697 AGGATGCGGGAAATTTAAACTTGG 60.082 41.667 0.00 0.00 0.00 3.61
2653 2878 4.322424 GGATGCGGGAAATTTAAACTTGGT 60.322 41.667 0.00 0.00 0.00 3.67
2654 2879 4.245845 TGCGGGAAATTTAAACTTGGTC 57.754 40.909 0.00 0.00 0.00 4.02
2655 2880 3.239254 GCGGGAAATTTAAACTTGGTCG 58.761 45.455 0.00 0.00 0.00 4.79
2656 2881 3.304861 GCGGGAAATTTAAACTTGGTCGT 60.305 43.478 0.00 0.00 0.00 4.34
2657 2882 4.793678 GCGGGAAATTTAAACTTGGTCGTT 60.794 41.667 0.00 0.00 0.00 3.85
2658 2883 4.913345 CGGGAAATTTAAACTTGGTCGTTC 59.087 41.667 0.00 0.00 0.00 3.95
2659 2884 5.224888 GGGAAATTTAAACTTGGTCGTTCC 58.775 41.667 0.00 0.00 32.88 3.62
2660 2885 5.224888 GGAAATTTAAACTTGGTCGTTCCC 58.775 41.667 0.00 0.00 34.77 3.97
2661 2886 4.492791 AATTTAAACTTGGTCGTTCCCG 57.507 40.909 0.00 0.00 34.77 5.14
2662 2887 1.228533 TTAAACTTGGTCGTTCCCGC 58.771 50.000 0.00 0.00 34.77 6.13
2663 2888 0.393820 TAAACTTGGTCGTTCCCGCT 59.606 50.000 0.00 0.00 34.77 5.52
2664 2889 0.883370 AAACTTGGTCGTTCCCGCTC 60.883 55.000 0.00 0.00 34.77 5.03
2665 2890 1.755393 AACTTGGTCGTTCCCGCTCT 61.755 55.000 0.00 0.00 34.77 4.09
2666 2891 1.446272 CTTGGTCGTTCCCGCTCTC 60.446 63.158 0.00 0.00 34.77 3.20
2667 2892 2.154798 CTTGGTCGTTCCCGCTCTCA 62.155 60.000 0.00 0.00 34.77 3.27
2668 2893 1.750341 TTGGTCGTTCCCGCTCTCAA 61.750 55.000 0.00 0.00 34.77 3.02
2669 2894 1.005394 GGTCGTTCCCGCTCTCAAA 60.005 57.895 0.00 0.00 0.00 2.69
2670 2895 0.601841 GGTCGTTCCCGCTCTCAAAA 60.602 55.000 0.00 0.00 0.00 2.44
2671 2896 0.790814 GTCGTTCCCGCTCTCAAAAG 59.209 55.000 0.00 0.00 0.00 2.27
2672 2897 0.677288 TCGTTCCCGCTCTCAAAAGA 59.323 50.000 0.00 0.00 0.00 2.52
2673 2898 1.275291 TCGTTCCCGCTCTCAAAAGAT 59.725 47.619 0.00 0.00 0.00 2.40
2674 2899 1.394917 CGTTCCCGCTCTCAAAAGATG 59.605 52.381 0.00 0.00 0.00 2.90
2675 2900 1.131315 GTTCCCGCTCTCAAAAGATGC 59.869 52.381 0.00 0.00 0.00 3.91
2676 2901 0.392998 TCCCGCTCTCAAAAGATGCC 60.393 55.000 0.00 0.00 0.00 4.40
2677 2902 0.677731 CCCGCTCTCAAAAGATGCCA 60.678 55.000 0.00 0.00 0.00 4.92
2678 2903 0.449388 CCGCTCTCAAAAGATGCCAC 59.551 55.000 0.00 0.00 0.00 5.01
2679 2904 1.159285 CGCTCTCAAAAGATGCCACA 58.841 50.000 0.00 0.00 0.00 4.17
2680 2905 1.536766 CGCTCTCAAAAGATGCCACAA 59.463 47.619 0.00 0.00 0.00 3.33
2681 2906 2.030893 CGCTCTCAAAAGATGCCACAAA 60.031 45.455 0.00 0.00 0.00 2.83
2682 2907 3.366679 CGCTCTCAAAAGATGCCACAAAT 60.367 43.478 0.00 0.00 0.00 2.32
2683 2908 4.171754 GCTCTCAAAAGATGCCACAAATC 58.828 43.478 0.00 0.00 0.00 2.17
2684 2909 4.741342 CTCTCAAAAGATGCCACAAATCC 58.259 43.478 0.00 0.00 0.00 3.01
2685 2910 3.191162 TCTCAAAAGATGCCACAAATCCG 59.809 43.478 0.00 0.00 0.00 4.18
2686 2911 2.230992 TCAAAAGATGCCACAAATCCGG 59.769 45.455 0.00 0.00 0.00 5.14
2693 2918 2.476772 CCACAAATCCGGCAATCGA 58.523 52.632 0.00 0.00 42.43 3.59
2694 2919 0.808125 CCACAAATCCGGCAATCGAA 59.192 50.000 0.00 0.00 42.43 3.71
2695 2920 1.467374 CCACAAATCCGGCAATCGAAC 60.467 52.381 0.00 0.00 42.43 3.95
2696 2921 0.446222 ACAAATCCGGCAATCGAACG 59.554 50.000 0.00 0.00 42.43 3.95
2697 2922 0.446222 CAAATCCGGCAATCGAACGT 59.554 50.000 0.00 0.00 42.43 3.99
2698 2923 1.661617 CAAATCCGGCAATCGAACGTA 59.338 47.619 0.00 0.00 42.43 3.57
2699 2924 1.567504 AATCCGGCAATCGAACGTAG 58.432 50.000 0.00 0.00 42.43 3.51
2700 2925 0.458669 ATCCGGCAATCGAACGTAGT 59.541 50.000 0.00 0.00 42.43 2.73
2701 2926 0.179156 TCCGGCAATCGAACGTAGTC 60.179 55.000 0.00 0.00 37.27 2.59
2702 2927 0.179145 CCGGCAATCGAACGTAGTCT 60.179 55.000 0.00 0.00 37.27 3.24
2703 2928 0.914551 CGGCAATCGAACGTAGTCTG 59.085 55.000 0.00 0.00 45.00 3.51
2704 2929 1.278238 GGCAATCGAACGTAGTCTGG 58.722 55.000 0.00 0.00 45.00 3.86
2705 2930 0.645868 GCAATCGAACGTAGTCTGGC 59.354 55.000 0.00 0.00 45.00 4.85
2706 2931 0.914551 CAATCGAACGTAGTCTGGCG 59.085 55.000 0.00 0.00 45.00 5.69
2707 2932 0.524862 AATCGAACGTAGTCTGGCGT 59.475 50.000 0.00 0.00 45.00 5.68
2713 2938 2.798976 ACGTAGTCTGGCGTTACAAA 57.201 45.000 0.00 0.00 29.74 2.83
2714 2939 3.096489 ACGTAGTCTGGCGTTACAAAA 57.904 42.857 0.00 0.00 29.74 2.44
2715 2940 3.456280 ACGTAGTCTGGCGTTACAAAAA 58.544 40.909 0.00 0.00 29.74 1.94
2731 2956 0.998669 AAAAATAAAGCGCCGCATGC 59.001 45.000 13.36 7.91 0.00 4.06
2732 2957 0.805711 AAAATAAAGCGCCGCATGCC 60.806 50.000 13.36 0.00 36.24 4.40
2733 2958 2.935122 AAATAAAGCGCCGCATGCCG 62.935 55.000 13.36 12.17 36.24 5.69
2741 2966 4.817063 CCGCATGCCGCAAGTTCG 62.817 66.667 13.15 0.00 42.60 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.509575 CCTCCTAGCTGCTTGGATAGTAG 59.490 52.174 28.39 17.93 35.14 2.57
11 12 3.140332 TCCTCCTAGCTGCTTGGATAGTA 59.860 47.826 28.39 14.11 35.14 1.82
12 13 2.091055 TCCTCCTAGCTGCTTGGATAGT 60.091 50.000 28.39 0.00 35.14 2.12
43 44 1.157870 CGTTGCGTTGGTCTTGGTCT 61.158 55.000 0.00 0.00 0.00 3.85
62 63 1.596954 CCTACTGTTGTGTTGCGTTGC 60.597 52.381 0.00 0.00 0.00 4.17
67 68 7.061905 CGTATATATAGCCTACTGTTGTGTTGC 59.938 40.741 0.00 0.00 0.00 4.17
128 129 2.047274 CTATATGTGCCGGCCGGG 60.047 66.667 43.31 26.06 39.58 5.73
292 293 4.946266 TTTTCCGCGCCGACGACA 62.946 61.111 0.00 0.00 43.93 4.35
647 692 0.912487 AAGGACTATGGGCCGTTCCA 60.912 55.000 16.93 0.00 41.60 3.53
780 833 2.294979 GACTTCCGTTTGGTTTGGAGT 58.705 47.619 0.00 0.00 36.30 3.85
990 1043 1.070445 AGCTGCTCCATGTCTATCTGC 59.930 52.381 0.00 0.00 0.00 4.26
991 1044 2.548280 CCAGCTGCTCCATGTCTATCTG 60.548 54.545 8.66 0.00 0.00 2.90
995 1050 1.117994 CTCCAGCTGCTCCATGTCTA 58.882 55.000 8.66 0.00 0.00 2.59
1072 1130 2.987282 TTCTTGCTGCCGTTGCTCGA 62.987 55.000 0.00 0.00 42.86 4.04
1521 1721 0.028242 CCAGCAGCGAGTCGTAGTAG 59.972 60.000 15.08 2.11 0.00 2.57
1667 1867 4.742201 TGAGCTTCACGCCTCCGC 62.742 66.667 0.00 0.00 40.39 5.54
1669 1869 2.817396 GCTGAGCTTCACGCCTCC 60.817 66.667 0.00 0.00 40.39 4.30
1670 1870 2.099431 CAGCTGAGCTTCACGCCTC 61.099 63.158 8.42 0.00 36.40 4.70
1671 1871 2.047465 CAGCTGAGCTTCACGCCT 60.047 61.111 8.42 0.00 36.40 5.52
1673 1873 3.123620 CCCAGCTGAGCTTCACGC 61.124 66.667 17.39 0.00 36.40 5.34
1812 2015 6.691754 ATAGTCTAGAGTCTGATGTGTGTG 57.308 41.667 2.53 0.00 0.00 3.82
1815 2018 9.899661 GGATATATAGTCTAGAGTCTGATGTGT 57.100 37.037 2.53 0.00 0.00 3.72
1816 2019 9.898152 TGGATATATAGTCTAGAGTCTGATGTG 57.102 37.037 2.53 0.00 0.00 3.21
1832 2035 9.973661 TTTGGTTGGATGGTAATGGATATATAG 57.026 33.333 0.00 0.00 0.00 1.31
1927 2130 7.192913 GCCACAGAATGATATACGAGATCTAG 58.807 42.308 0.00 0.00 39.69 2.43
1933 2136 3.589988 GGGCCACAGAATGATATACGAG 58.410 50.000 4.39 0.00 39.69 4.18
1936 2139 3.402628 ACGGGCCACAGAATGATATAC 57.597 47.619 4.39 0.00 39.69 1.47
1937 2140 4.081142 CCATACGGGCCACAGAATGATATA 60.081 45.833 4.39 0.00 39.69 0.86
1979 2182 7.589954 GCACGAACACAAGAACATAAAAGTATT 59.410 33.333 0.00 0.00 0.00 1.89
1981 2184 6.259167 AGCACGAACACAAGAACATAAAAGTA 59.741 34.615 0.00 0.00 0.00 2.24
1982 2185 5.065988 AGCACGAACACAAGAACATAAAAGT 59.934 36.000 0.00 0.00 0.00 2.66
1983 2186 5.510671 AGCACGAACACAAGAACATAAAAG 58.489 37.500 0.00 0.00 0.00 2.27
1984 2187 5.493133 AGCACGAACACAAGAACATAAAA 57.507 34.783 0.00 0.00 0.00 1.52
1999 2202 0.944386 GAAAGTCAGCCAAGCACGAA 59.056 50.000 0.00 0.00 0.00 3.85
2001 2204 0.877071 ATGAAAGTCAGCCAAGCACG 59.123 50.000 0.00 0.00 0.00 5.34
2066 2269 2.625695 CCAAATGGAAATGGGCATCC 57.374 50.000 0.00 0.00 37.39 3.51
2093 2296 2.223735 GCTGCTGTGGATCCAAATCATG 60.224 50.000 18.20 8.25 33.21 3.07
2100 2303 0.178995 TTGTTGCTGCTGTGGATCCA 60.179 50.000 11.44 11.44 0.00 3.41
2116 2319 7.927092 TCAATCAATCAATCATGTTGTTGTTGT 59.073 29.630 0.00 0.00 0.00 3.32
2119 2322 8.145767 AGTTCAATCAATCAATCATGTTGTTGT 58.854 29.630 0.00 0.00 0.00 3.32
2122 2325 6.588756 GCAGTTCAATCAATCAATCATGTTGT 59.411 34.615 0.00 0.00 0.00 3.32
2142 2349 5.771666 TCAATCCTCTCATCTTTTTGCAGTT 59.228 36.000 0.00 0.00 0.00 3.16
2156 2364 3.388308 CACATCCATCGTCAATCCTCTC 58.612 50.000 0.00 0.00 0.00 3.20
2157 2365 2.103771 CCACATCCATCGTCAATCCTCT 59.896 50.000 0.00 0.00 0.00 3.69
2167 2390 2.111878 GGGAGGCCACATCCATCG 59.888 66.667 5.01 0.00 38.70 3.84
2180 2403 1.271926 ACTTTTCCGATGGTTGGGGAG 60.272 52.381 0.00 0.00 0.00 4.30
2233 2456 2.704596 AGAGGACAGATGGACATGGATG 59.295 50.000 0.00 0.00 0.00 3.51
2277 2500 3.304721 GCACACCCATGCAGCCAA 61.305 61.111 0.00 0.00 45.39 4.52
2386 2611 5.313280 TGTGGATAGTACTTGGTTGGTTT 57.687 39.130 0.00 0.00 0.00 3.27
2466 2691 9.245962 GCAAGAGGATAATTGATGAGAAAAATG 57.754 33.333 0.00 0.00 0.00 2.32
2470 2695 7.935755 CCTAGCAAGAGGATAATTGATGAGAAA 59.064 37.037 0.00 0.00 39.15 2.52
2494 2719 2.158234 AGATGCCCTTAGCTAGCTACCT 60.158 50.000 24.09 5.81 44.23 3.08
2496 2721 3.322254 TGAAGATGCCCTTAGCTAGCTAC 59.678 47.826 24.09 12.98 44.23 3.58
2509 2734 2.464459 CCGAACGGCTGAAGATGCC 61.464 63.158 0.00 0.00 46.42 4.40
2510 2735 3.093278 CCGAACGGCTGAAGATGC 58.907 61.111 0.00 0.00 0.00 3.91
2520 2745 3.702048 TCTTGGGAGGCCGAACGG 61.702 66.667 9.00 9.00 38.57 4.44
2521 2746 2.434359 GTCTTGGGAGGCCGAACG 60.434 66.667 0.00 0.00 0.00 3.95
2522 2747 2.434359 CGTCTTGGGAGGCCGAAC 60.434 66.667 0.00 0.00 0.00 3.95
2523 2748 4.388499 GCGTCTTGGGAGGCCGAA 62.388 66.667 0.00 0.00 44.61 4.30
2528 2753 2.698797 TCTATTTAGGCGTCTTGGGAGG 59.301 50.000 0.00 0.00 0.00 4.30
2529 2754 3.800604 GCTCTATTTAGGCGTCTTGGGAG 60.801 52.174 0.00 0.00 0.00 4.30
2530 2755 2.102588 GCTCTATTTAGGCGTCTTGGGA 59.897 50.000 0.00 0.00 0.00 4.37
2531 2756 2.484889 GCTCTATTTAGGCGTCTTGGG 58.515 52.381 0.00 0.00 0.00 4.12
2532 2757 2.128035 CGCTCTATTTAGGCGTCTTGG 58.872 52.381 0.00 0.00 43.28 3.61
2533 2758 2.128035 CCGCTCTATTTAGGCGTCTTG 58.872 52.381 0.00 0.00 46.23 3.02
2534 2759 1.538419 GCCGCTCTATTTAGGCGTCTT 60.538 52.381 0.00 0.00 46.23 3.01
2535 2760 0.032267 GCCGCTCTATTTAGGCGTCT 59.968 55.000 14.78 0.00 46.23 4.18
2536 2761 2.518711 GCCGCTCTATTTAGGCGTC 58.481 57.895 14.78 3.87 46.23 5.19
2537 2762 4.752514 GCCGCTCTATTTAGGCGT 57.247 55.556 14.78 0.00 46.23 5.68
2540 2765 0.035458 CCCAGGCCGCTCTATTTAGG 59.965 60.000 0.00 0.00 0.00 2.69
2541 2766 0.035458 CCCCAGGCCGCTCTATTTAG 59.965 60.000 0.00 0.00 0.00 1.85
2542 2767 1.415672 CCCCCAGGCCGCTCTATTTA 61.416 60.000 0.00 0.00 0.00 1.40
2543 2768 2.757124 CCCCCAGGCCGCTCTATTT 61.757 63.158 0.00 0.00 0.00 1.40
2544 2769 3.171388 CCCCCAGGCCGCTCTATT 61.171 66.667 0.00 0.00 0.00 1.73
2562 2787 3.545481 CGAACTAGCGCCTGCACG 61.545 66.667 2.29 1.03 46.23 5.34
2563 2788 3.188786 CCGAACTAGCGCCTGCAC 61.189 66.667 2.29 0.00 46.23 4.57
2584 2809 4.577246 GAGCTAGGTCGCCCGCAG 62.577 72.222 6.12 0.00 35.12 5.18
2588 2813 3.541713 CTGGGAGCTAGGTCGCCC 61.542 72.222 29.34 20.74 45.10 6.13
2589 2814 2.760385 ACTGGGAGCTAGGTCGCC 60.760 66.667 29.34 23.22 0.00 5.54
2590 2815 2.052690 TGACTGGGAGCTAGGTCGC 61.053 63.158 26.90 26.90 0.00 5.19
2591 2816 1.810532 GTGACTGGGAGCTAGGTCG 59.189 63.158 15.43 4.94 0.00 4.79
2592 2817 1.810532 CGTGACTGGGAGCTAGGTC 59.189 63.158 13.67 13.67 0.00 3.85
2593 2818 2.352032 GCGTGACTGGGAGCTAGGT 61.352 63.158 0.00 0.00 0.00 3.08
2594 2819 2.496817 GCGTGACTGGGAGCTAGG 59.503 66.667 0.00 0.00 0.00 3.02
2595 2820 2.496817 GGCGTGACTGGGAGCTAG 59.503 66.667 0.00 0.00 0.00 3.42
2596 2821 3.075005 GGGCGTGACTGGGAGCTA 61.075 66.667 0.00 0.00 0.00 3.32
2601 2826 4.722700 CTTGGGGGCGTGACTGGG 62.723 72.222 0.00 0.00 0.00 4.45
2627 2852 3.447229 AGTTTAAATTTCCCGCATCCTGG 59.553 43.478 0.00 0.00 0.00 4.45
2628 2853 4.718940 AGTTTAAATTTCCCGCATCCTG 57.281 40.909 0.00 0.00 0.00 3.86
2629 2854 4.081697 CCAAGTTTAAATTTCCCGCATCCT 60.082 41.667 0.00 0.00 0.00 3.24
2630 2855 4.180817 CCAAGTTTAAATTTCCCGCATCC 58.819 43.478 0.00 0.00 0.00 3.51
2631 2856 4.816392 ACCAAGTTTAAATTTCCCGCATC 58.184 39.130 0.00 0.00 0.00 3.91
2632 2857 4.617298 CGACCAAGTTTAAATTTCCCGCAT 60.617 41.667 0.00 0.00 0.00 4.73
2633 2858 3.304794 CGACCAAGTTTAAATTTCCCGCA 60.305 43.478 0.00 0.00 0.00 5.69
2634 2859 3.239254 CGACCAAGTTTAAATTTCCCGC 58.761 45.455 0.00 0.00 0.00 6.13
2635 2860 4.492791 ACGACCAAGTTTAAATTTCCCG 57.507 40.909 0.00 0.00 0.00 5.14
2636 2861 5.224888 GGAACGACCAAGTTTAAATTTCCC 58.775 41.667 0.00 0.00 38.79 3.97
2637 2862 5.224888 GGGAACGACCAAGTTTAAATTTCC 58.775 41.667 0.00 0.00 41.20 3.13
2655 2880 1.131315 GCATCTTTTGAGAGCGGGAAC 59.869 52.381 0.00 0.00 0.00 3.62
2656 2881 1.453155 GCATCTTTTGAGAGCGGGAA 58.547 50.000 0.00 0.00 0.00 3.97
2657 2882 0.392998 GGCATCTTTTGAGAGCGGGA 60.393 55.000 0.00 0.00 35.20 5.14
2658 2883 0.677731 TGGCATCTTTTGAGAGCGGG 60.678 55.000 0.00 0.00 35.20 6.13
2659 2884 0.449388 GTGGCATCTTTTGAGAGCGG 59.551 55.000 0.00 0.00 35.20 5.52
2660 2885 1.159285 TGTGGCATCTTTTGAGAGCG 58.841 50.000 0.00 0.00 35.20 5.03
2661 2886 3.648339 TTTGTGGCATCTTTTGAGAGC 57.352 42.857 0.00 0.00 34.10 4.09
2662 2887 4.673580 CGGATTTGTGGCATCTTTTGAGAG 60.674 45.833 0.00 0.00 0.00 3.20
2663 2888 3.191162 CGGATTTGTGGCATCTTTTGAGA 59.809 43.478 0.00 0.00 0.00 3.27
2664 2889 3.504863 CGGATTTGTGGCATCTTTTGAG 58.495 45.455 0.00 0.00 0.00 3.02
2665 2890 2.230992 CCGGATTTGTGGCATCTTTTGA 59.769 45.455 0.00 0.00 0.00 2.69
2666 2891 2.609350 CCGGATTTGTGGCATCTTTTG 58.391 47.619 0.00 0.00 0.00 2.44
2675 2900 0.808125 TTCGATTGCCGGATTTGTGG 59.192 50.000 5.05 0.00 39.14 4.17
2676 2901 1.790123 CGTTCGATTGCCGGATTTGTG 60.790 52.381 5.05 0.00 39.14 3.33
2677 2902 0.446222 CGTTCGATTGCCGGATTTGT 59.554 50.000 5.05 0.00 39.14 2.83
2678 2903 0.446222 ACGTTCGATTGCCGGATTTG 59.554 50.000 5.05 0.00 39.14 2.32
2679 2904 1.931172 CTACGTTCGATTGCCGGATTT 59.069 47.619 5.05 0.00 39.14 2.17
2680 2905 1.134907 ACTACGTTCGATTGCCGGATT 60.135 47.619 5.05 0.00 39.14 3.01
2681 2906 0.458669 ACTACGTTCGATTGCCGGAT 59.541 50.000 5.05 0.00 39.14 4.18
2682 2907 0.179156 GACTACGTTCGATTGCCGGA 60.179 55.000 5.05 0.00 39.14 5.14
2683 2908 0.179145 AGACTACGTTCGATTGCCGG 60.179 55.000 0.00 0.00 39.14 6.13
2684 2909 0.914551 CAGACTACGTTCGATTGCCG 59.085 55.000 0.00 0.00 40.25 5.69
2685 2910 1.278238 CCAGACTACGTTCGATTGCC 58.722 55.000 0.00 0.00 0.00 4.52
2686 2911 0.645868 GCCAGACTACGTTCGATTGC 59.354 55.000 0.00 0.00 0.00 3.56
2687 2912 0.914551 CGCCAGACTACGTTCGATTG 59.085 55.000 0.00 0.00 0.00 2.67
2688 2913 0.524862 ACGCCAGACTACGTTCGATT 59.475 50.000 0.00 0.00 40.09 3.34
2689 2914 2.177950 ACGCCAGACTACGTTCGAT 58.822 52.632 0.00 0.00 40.09 3.59
2690 2915 3.659334 ACGCCAGACTACGTTCGA 58.341 55.556 0.00 0.00 40.09 3.71
2694 2919 2.798976 TTTGTAACGCCAGACTACGT 57.201 45.000 0.00 0.00 46.07 3.57
2712 2937 0.998669 GCATGCGGCGCTTTATTTTT 59.001 45.000 33.26 4.50 0.00 1.94
2713 2938 0.805711 GGCATGCGGCGCTTTATTTT 60.806 50.000 33.26 5.94 46.16 1.82
2714 2939 1.226945 GGCATGCGGCGCTTTATTT 60.227 52.632 33.26 7.77 46.16 1.40
2715 2940 2.412937 GGCATGCGGCGCTTTATT 59.587 55.556 33.26 9.63 46.16 1.40


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

AutoCloner maintained by Alex Coulton.