Multiple sequence alignment - TraesCS7A01G081600

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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 TraesCS7A01G081600 chr7A 100.000 2873 0 0 1 2873 46999846 47002718 0.000000e+00 5306
1 TraesCS7A01G081600 chr7A 77.377 1746 265 84 581 2277 47283032 47284696 0.000000e+00 917
2 TraesCS7A01G081600 chr7A 78.112 1430 221 57 564 1976 47007169 47008523 0.000000e+00 822
3 TraesCS7A01G081600 chr7A 78.093 1059 191 23 1229 2277 47017088 47018115 1.450000e-177 632
4 TraesCS7A01G081600 chr7A 73.960 1467 252 87 634 2035 47256427 47255026 9.320000e-130 473
5 TraesCS7A01G081600 chr7A 77.200 807 149 25 642 1439 47225350 47224570 3.400000e-119 438
6 TraesCS7A01G081600 chr7A 79.104 469 77 17 698 1159 47016594 47017048 1.290000e-78 303
7 TraesCS7A01G081600 chr7A 95.192 104 4 1 2421 2524 417602719 417602617 2.290000e-36 163
8 TraesCS7A01G081600 chr7D 94.389 2406 89 23 45 2419 44529874 44532264 0.000000e+00 3653
9 TraesCS7A01G081600 chr7D 79.091 1430 212 53 564 1976 44538184 44539543 0.000000e+00 904
10 TraesCS7A01G081600 chr7D 77.522 783 143 19 1231 2004 44551176 44551934 9.450000e-120 440
11 TraesCS7A01G081600 chr7D 93.976 166 9 1 2659 2824 44532498 44532662 1.710000e-62 250
12 TraesCS7A01G081600 chr7D 92.357 157 12 0 2503 2659 44532257 44532413 1.040000e-54 224
13 TraesCS7A01G081600 chr7D 81.111 180 30 2 980 1159 44550961 44551136 1.070000e-29 141
14 TraesCS7A01G081600 chr4A 94.085 727 40 3 1551 2275 655663943 655664668 0.000000e+00 1101
15 TraesCS7A01G081600 chr4A 77.569 1440 218 61 566 1976 656249655 656251018 0.000000e+00 773
16 TraesCS7A01G081600 chr4A 79.855 963 160 20 1221 2174 656498949 656498012 0.000000e+00 673
17 TraesCS7A01G081600 chr4A 76.905 1299 217 50 650 1933 656748882 656747652 0.000000e+00 660
18 TraesCS7A01G081600 chr4A 76.783 1318 217 56 635 1933 656550782 656552029 0.000000e+00 656
19 TraesCS7A01G081600 chr4A 77.851 1061 189 26 1229 2277 656480529 656481555 1.460000e-172 616
20 TraesCS7A01G081600 chr4A 78.926 968 159 30 1221 2174 656707926 656708862 1.460000e-172 616
21 TraesCS7A01G081600 chr4A 79.007 705 114 19 1217 1910 656030512 656031193 4.370000e-123 451
22 TraesCS7A01G081600 chr4A 94.554 202 9 2 2657 2858 655665044 655665243 7.730000e-81 311
23 TraesCS7A01G081600 chr4A 82.474 194 29 4 965 1157 655659094 655659283 6.370000e-37 165
24 TraesCS7A01G081600 chr4A 89.655 116 11 1 2303 2418 655664739 655664853 2.310000e-31 147
25 TraesCS7A01G081600 chr4A 79.739 153 31 0 721 873 655470342 655470494 8.410000e-21 111
26 TraesCS7A01G081600 chrUn 75.533 1688 291 73 631 2277 48990306 48991912 0.000000e+00 717
27 TraesCS7A01G081600 chrUn 77.734 1024 183 25 1235 2247 48866358 48865369 1.150000e-163 586
28 TraesCS7A01G081600 chrUn 79.104 469 75 16 698 1159 48866856 48866404 4.650000e-78 302
29 TraesCS7A01G081600 chrUn 93.233 133 7 2 2729 2861 45118371 45118501 8.120000e-46 195
30 TraesCS7A01G081600 chrUn 93.233 133 7 2 2729 2861 222666144 222666014 8.120000e-46 195
31 TraesCS7A01G081600 chrUn 93.233 133 7 2 2729 2861 423257337 423257207 8.120000e-46 195
32 TraesCS7A01G081600 chrUn 93.233 133 7 2 2729 2861 441343984 441344114 8.120000e-46 195
33 TraesCS7A01G081600 chrUn 82.258 124 22 0 677 800 282687890 282688013 1.090000e-19 108
34 TraesCS7A01G081600 chr3D 77.572 486 89 15 673 1147 9132093 9131617 2.820000e-70 276
35 TraesCS7A01G081600 chr3D 97.059 102 2 1 2421 2521 609956927 609956826 1.370000e-38 171
36 TraesCS7A01G081600 chr6A 93.233 133 7 2 2729 2861 84417057 84416927 8.120000e-46 195
37 TraesCS7A01G081600 chr6A 93.233 133 7 2 2729 2861 289139405 289139535 8.120000e-46 195
38 TraesCS7A01G081600 chr6A 94.495 109 4 2 2421 2528 218792615 218792722 1.770000e-37 167
39 TraesCS7A01G081600 chr4D 93.233 133 7 2 2729 2861 123309170 123309040 8.120000e-46 195
40 TraesCS7A01G081600 chr3B 74.779 452 88 15 711 1155 3205443 3205875 2.270000e-41 180
41 TraesCS7A01G081600 chr3A 74.494 494 88 27 673 1157 11865278 11865742 2.270000e-41 180
42 TraesCS7A01G081600 chr4B 98.947 95 1 0 2421 2515 199928613 199928707 1.370000e-38 171
43 TraesCS7A01G081600 chr2B 98.947 95 1 0 2421 2515 663367712 663367618 1.370000e-38 171
44 TraesCS7A01G081600 chr5B 97.959 98 1 1 2421 2518 138779413 138779317 4.920000e-38 169
45 TraesCS7A01G081600 chr5B 95.098 102 3 2 2421 2522 9655900 9655999 2.960000e-35 159
46 TraesCS7A01G081600 chr2D 96.117 103 2 2 2421 2523 442879180 442879080 1.770000e-37 167
47 TraesCS7A01G081600 chr2D 94.444 108 3 3 2421 2525 561840854 561840747 2.290000e-36 163
48 TraesCS7A01G081600 chr2D 77.889 199 42 2 677 874 19016129 19016326 3.890000e-24 122


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 TraesCS7A01G081600 chr7A 46999846 47002718 2872 False 5306.000000 5306 100.000000 1 2873 1 chr7A.!!$F1 2872
1 TraesCS7A01G081600 chr7A 47283032 47284696 1664 False 917.000000 917 77.377000 581 2277 1 chr7A.!!$F3 1696
2 TraesCS7A01G081600 chr7A 47007169 47008523 1354 False 822.000000 822 78.112000 564 1976 1 chr7A.!!$F2 1412
3 TraesCS7A01G081600 chr7A 47255026 47256427 1401 True 473.000000 473 73.960000 634 2035 1 chr7A.!!$R2 1401
4 TraesCS7A01G081600 chr7A 47016594 47018115 1521 False 467.500000 632 78.598500 698 2277 2 chr7A.!!$F4 1579
5 TraesCS7A01G081600 chr7A 47224570 47225350 780 True 438.000000 438 77.200000 642 1439 1 chr7A.!!$R1 797
6 TraesCS7A01G081600 chr7D 44529874 44532662 2788 False 1375.666667 3653 93.574000 45 2824 3 chr7D.!!$F2 2779
7 TraesCS7A01G081600 chr7D 44538184 44539543 1359 False 904.000000 904 79.091000 564 1976 1 chr7D.!!$F1 1412
8 TraesCS7A01G081600 chr7D 44550961 44551934 973 False 290.500000 440 79.316500 980 2004 2 chr7D.!!$F3 1024
9 TraesCS7A01G081600 chr4A 656249655 656251018 1363 False 773.000000 773 77.569000 566 1976 1 chr4A.!!$F4 1410
10 TraesCS7A01G081600 chr4A 656498012 656498949 937 True 673.000000 673 79.855000 1221 2174 1 chr4A.!!$R1 953
11 TraesCS7A01G081600 chr4A 656747652 656748882 1230 True 660.000000 660 76.905000 650 1933 1 chr4A.!!$R2 1283
12 TraesCS7A01G081600 chr4A 656550782 656552029 1247 False 656.000000 656 76.783000 635 1933 1 chr4A.!!$F6 1298
13 TraesCS7A01G081600 chr4A 656480529 656481555 1026 False 616.000000 616 77.851000 1229 2277 1 chr4A.!!$F5 1048
14 TraesCS7A01G081600 chr4A 656707926 656708862 936 False 616.000000 616 78.926000 1221 2174 1 chr4A.!!$F7 953
15 TraesCS7A01G081600 chr4A 655663943 655665243 1300 False 519.666667 1101 92.764667 1551 2858 3 chr4A.!!$F8 1307
16 TraesCS7A01G081600 chr4A 656030512 656031193 681 False 451.000000 451 79.007000 1217 1910 1 chr4A.!!$F3 693
17 TraesCS7A01G081600 chrUn 48990306 48991912 1606 False 717.000000 717 75.533000 631 2277 1 chrUn.!!$F2 1646
18 TraesCS7A01G081600 chrUn 48865369 48866856 1487 True 444.000000 586 78.419000 698 2247 2 chrUn.!!$R3 1549

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
440 465 0.467844 TGCCCCATTGCTCGCATATT 60.468 50.0 0.0 0.0 0.0 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2289 2480 0.179018 AGACACACAACCAGCTTCCC 60.179 55.0 0.0 0.0 0.0 3.97 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
22 23 5.920193 CCTCTCTCTCTCTTTCTGAACAT 57.080 43.478 0.00 0.00 0.00 2.71
23 24 6.284891 CCTCTCTCTCTCTTTCTGAACATT 57.715 41.667 0.00 0.00 0.00 2.71
24 25 7.403312 CCTCTCTCTCTCTTTCTGAACATTA 57.597 40.000 0.00 0.00 0.00 1.90
25 26 7.483307 CCTCTCTCTCTCTTTCTGAACATTAG 58.517 42.308 0.00 0.00 0.00 1.73
26 27 6.862209 TCTCTCTCTCTTTCTGAACATTAGC 58.138 40.000 0.00 0.00 0.00 3.09
27 28 5.971763 TCTCTCTCTTTCTGAACATTAGCC 58.028 41.667 0.00 0.00 0.00 3.93
28 29 4.748892 TCTCTCTTTCTGAACATTAGCCG 58.251 43.478 0.00 0.00 0.00 5.52
29 30 4.462834 TCTCTCTTTCTGAACATTAGCCGA 59.537 41.667 0.00 0.00 0.00 5.54
30 31 5.127845 TCTCTCTTTCTGAACATTAGCCGAT 59.872 40.000 0.00 0.00 0.00 4.18
31 32 6.321435 TCTCTCTTTCTGAACATTAGCCGATA 59.679 38.462 0.00 0.00 0.00 2.92
32 33 7.014711 TCTCTCTTTCTGAACATTAGCCGATAT 59.985 37.037 0.00 0.00 0.00 1.63
33 34 6.925718 TCTCTTTCTGAACATTAGCCGATATG 59.074 38.462 0.00 0.00 0.00 1.78
34 35 6.582636 TCTTTCTGAACATTAGCCGATATGT 58.417 36.000 0.00 0.00 36.58 2.29
35 36 7.722363 TCTTTCTGAACATTAGCCGATATGTA 58.278 34.615 0.00 0.00 34.04 2.29
36 37 8.367911 TCTTTCTGAACATTAGCCGATATGTAT 58.632 33.333 0.00 0.00 34.04 2.29
37 38 9.639601 CTTTCTGAACATTAGCCGATATGTATA 57.360 33.333 0.00 0.00 34.04 1.47
73 74 0.965866 GGCTACTGTTTCTTGCCCCC 60.966 60.000 0.00 0.00 37.81 5.40
105 106 1.484240 CGATCTGCCTTTCTCCTTCCT 59.516 52.381 0.00 0.00 0.00 3.36
138 139 4.376413 CGTCGAGTGATTTCTTGTTTCCTG 60.376 45.833 0.00 0.00 0.00 3.86
173 174 4.762289 AGGCCGAGATCTACATTTTCTT 57.238 40.909 0.00 0.00 0.00 2.52
188 189 3.753294 TTTCTTCTTCTTCTGGTCGCT 57.247 42.857 0.00 0.00 0.00 4.93
249 250 2.789491 GGGCTTTGAGCTCATTATGC 57.211 50.000 19.04 16.42 42.59 3.14
250 251 2.305009 GGGCTTTGAGCTCATTATGCT 58.695 47.619 19.04 0.00 42.59 3.79
263 285 8.774890 AGCTCATTATGCTCTAAGTGATATTG 57.225 34.615 0.00 0.00 35.67 1.90
440 465 0.467844 TGCCCCATTGCTCGCATATT 60.468 50.000 0.00 0.00 0.00 1.28
465 495 4.867047 CGATTATGACCATGCCTACAGATC 59.133 45.833 0.00 0.00 0.00 2.75
478 508 4.020751 GCCTACAGATCAATAGCTCCATGA 60.021 45.833 0.00 0.00 0.00 3.07
493 523 4.678574 GCTCCATGACAGCAAATGCAAATA 60.679 41.667 8.28 0.00 45.16 1.40
554 585 5.852282 TTTGTTTCCTCAGAAGAAAAGGG 57.148 39.130 0.00 0.00 35.13 3.95
560 591 6.901081 TTCCTCAGAAGAAAAGGGAATTTC 57.099 37.500 0.00 0.00 39.16 2.17
586 617 3.560068 ACAAAATCTCACACCGAGTGTTC 59.440 43.478 6.91 0.00 45.08 3.18
636 667 0.800012 ACGCGGCATCGTAATGTTTT 59.200 45.000 12.47 0.00 41.36 2.43
637 668 1.179332 CGCGGCATCGTAATGTTTTG 58.821 50.000 0.00 0.00 38.89 2.44
718 758 1.157870 CGTCTTTGACAACCTGCCGT 61.158 55.000 0.00 0.00 32.09 5.68
828 870 4.522789 GGTACTTCCACCAACACATTCATT 59.477 41.667 0.00 0.00 38.55 2.57
830 872 3.253188 ACTTCCACCAACACATTCATTCG 59.747 43.478 0.00 0.00 0.00 3.34
834 876 3.191162 CCACCAACACATTCATTCGTGAT 59.809 43.478 0.00 0.00 36.91 3.06
1239 1311 4.414852 CAATTGAGTTGCCCGATTACTTG 58.585 43.478 0.00 0.00 0.00 3.16
1927 2065 2.853542 TCTGCTGTGCCCTTGGGA 60.854 61.111 10.36 0.00 0.00 4.37
2229 2416 6.259608 TGGCATTTTAGTTGTTGAAATGGTTG 59.740 34.615 9.31 0.00 39.78 3.77
2277 2468 7.644157 GCTTAATATTTCGACCTTTCATGTTCC 59.356 37.037 0.00 0.00 0.00 3.62
2289 2480 5.341872 TTTCATGTTCCCTGGCATATTTG 57.658 39.130 0.00 0.00 0.00 2.32
2323 2556 4.036262 TGTGTGTCTGATTGTTGCTTAACC 59.964 41.667 0.00 0.00 0.00 2.85
2342 2575 7.201401 GCTTAACCGTTGTTAAAATATTGGCAG 60.201 37.037 0.00 0.00 44.18 4.85
2408 2641 7.362920 GCTTGACTGTTGGTTATTGTATCCAAT 60.363 37.037 0.00 0.00 42.10 3.16
2437 2670 3.896648 TTTTGAGTTGGTTGCGAGATC 57.103 42.857 0.00 0.00 0.00 2.75
2438 2671 2.839486 TTGAGTTGGTTGCGAGATCT 57.161 45.000 0.00 0.00 0.00 2.75
2439 2672 2.839486 TGAGTTGGTTGCGAGATCTT 57.161 45.000 0.00 0.00 0.00 2.40
2440 2673 3.953712 TGAGTTGGTTGCGAGATCTTA 57.046 42.857 0.00 0.00 0.00 2.10
2441 2674 4.471904 TGAGTTGGTTGCGAGATCTTAT 57.528 40.909 0.00 0.00 0.00 1.73
2442 2675 4.183865 TGAGTTGGTTGCGAGATCTTATG 58.816 43.478 0.00 0.00 0.00 1.90
2443 2676 3.535561 AGTTGGTTGCGAGATCTTATGG 58.464 45.455 0.00 0.00 0.00 2.74
2444 2677 2.614057 GTTGGTTGCGAGATCTTATGGG 59.386 50.000 0.00 0.00 0.00 4.00
2445 2678 1.837439 TGGTTGCGAGATCTTATGGGT 59.163 47.619 0.00 0.00 0.00 4.51
2446 2679 2.238646 TGGTTGCGAGATCTTATGGGTT 59.761 45.455 0.00 0.00 0.00 4.11
2447 2680 3.279434 GGTTGCGAGATCTTATGGGTTT 58.721 45.455 0.00 0.00 0.00 3.27
2448 2681 3.312697 GGTTGCGAGATCTTATGGGTTTC 59.687 47.826 0.00 0.00 0.00 2.78
2449 2682 3.904800 TGCGAGATCTTATGGGTTTCA 57.095 42.857 0.00 0.00 0.00 2.69
2450 2683 3.531538 TGCGAGATCTTATGGGTTTCAC 58.468 45.455 0.00 0.00 0.00 3.18
2451 2684 2.872858 GCGAGATCTTATGGGTTTCACC 59.127 50.000 0.00 0.00 37.60 4.02
2452 2685 3.432326 GCGAGATCTTATGGGTTTCACCT 60.432 47.826 0.00 0.00 38.64 4.00
2453 2686 4.372656 CGAGATCTTATGGGTTTCACCTC 58.627 47.826 0.00 0.00 38.64 3.85
2454 2687 4.100189 CGAGATCTTATGGGTTTCACCTCT 59.900 45.833 0.00 0.00 38.64 3.69
2455 2688 5.302059 CGAGATCTTATGGGTTTCACCTCTA 59.698 44.000 0.00 0.00 38.64 2.43
2456 2689 6.515862 CGAGATCTTATGGGTTTCACCTCTAG 60.516 46.154 0.00 0.00 38.64 2.43
2457 2690 4.755266 TCTTATGGGTTTCACCTCTAGC 57.245 45.455 0.00 0.00 38.64 3.42
2458 2691 3.454812 TCTTATGGGTTTCACCTCTAGCC 59.545 47.826 0.00 0.00 38.64 3.93
2459 2692 0.919710 ATGGGTTTCACCTCTAGCCC 59.080 55.000 0.00 0.00 38.64 5.19
2460 2693 0.474854 TGGGTTTCACCTCTAGCCCA 60.475 55.000 0.00 0.00 43.17 5.36
2461 2694 0.035343 GGGTTTCACCTCTAGCCCAC 60.035 60.000 0.00 0.00 38.64 4.61
2462 2695 0.035343 GGTTTCACCTCTAGCCCACC 60.035 60.000 0.00 0.00 34.73 4.61
2463 2696 0.035343 GTTTCACCTCTAGCCCACCC 60.035 60.000 0.00 0.00 0.00 4.61
2464 2697 1.205460 TTTCACCTCTAGCCCACCCC 61.205 60.000 0.00 0.00 0.00 4.95
2465 2698 2.285368 CACCTCTAGCCCACCCCA 60.285 66.667 0.00 0.00 0.00 4.96
2466 2699 1.923395 CACCTCTAGCCCACCCCAA 60.923 63.158 0.00 0.00 0.00 4.12
2467 2700 1.923909 ACCTCTAGCCCACCCCAAC 60.924 63.158 0.00 0.00 0.00 3.77
2468 2701 1.616628 CCTCTAGCCCACCCCAACT 60.617 63.158 0.00 0.00 0.00 3.16
2469 2702 1.208165 CCTCTAGCCCACCCCAACTT 61.208 60.000 0.00 0.00 0.00 2.66
2470 2703 0.035056 CTCTAGCCCACCCCAACTTG 60.035 60.000 0.00 0.00 0.00 3.16
2471 2704 0.770557 TCTAGCCCACCCCAACTTGT 60.771 55.000 0.00 0.00 0.00 3.16
2472 2705 0.112412 CTAGCCCACCCCAACTTGTT 59.888 55.000 0.00 0.00 0.00 2.83
2473 2706 0.558712 TAGCCCACCCCAACTTGTTT 59.441 50.000 0.00 0.00 0.00 2.83
2474 2707 1.048160 AGCCCACCCCAACTTGTTTG 61.048 55.000 0.00 0.00 34.63 2.93
2485 2718 3.977427 CAACTTGTTTGGGACTAAAGGC 58.023 45.455 0.00 0.00 0.00 4.35
2486 2719 3.595190 ACTTGTTTGGGACTAAAGGCT 57.405 42.857 0.00 0.00 0.00 4.58
2487 2720 3.910989 ACTTGTTTGGGACTAAAGGCTT 58.089 40.909 0.00 0.00 0.00 4.35
2488 2721 4.286707 ACTTGTTTGGGACTAAAGGCTTT 58.713 39.130 17.76 17.76 0.00 3.51
2489 2722 4.099419 ACTTGTTTGGGACTAAAGGCTTTG 59.901 41.667 22.32 13.97 0.00 2.77
2490 2723 3.637769 TGTTTGGGACTAAAGGCTTTGT 58.362 40.909 22.32 16.86 0.00 2.83
2491 2724 4.027437 TGTTTGGGACTAAAGGCTTTGTT 58.973 39.130 22.32 8.73 0.00 2.83
2492 2725 4.142049 TGTTTGGGACTAAAGGCTTTGTTG 60.142 41.667 22.32 13.85 0.00 3.33
2493 2726 3.306472 TGGGACTAAAGGCTTTGTTGT 57.694 42.857 22.32 16.69 0.00 3.32
2494 2727 3.637769 TGGGACTAAAGGCTTTGTTGTT 58.362 40.909 22.32 1.84 0.00 2.83
2495 2728 3.383185 TGGGACTAAAGGCTTTGTTGTTG 59.617 43.478 22.32 7.79 0.00 3.33
2496 2729 3.383505 GGGACTAAAGGCTTTGTTGTTGT 59.616 43.478 22.32 10.58 0.00 3.32
2497 2730 4.142026 GGGACTAAAGGCTTTGTTGTTGTT 60.142 41.667 22.32 0.00 0.00 2.83
2498 2731 4.803613 GGACTAAAGGCTTTGTTGTTGTTG 59.196 41.667 22.32 0.00 0.00 3.33
2499 2732 5.400066 ACTAAAGGCTTTGTTGTTGTTGT 57.600 34.783 22.32 0.00 0.00 3.32
2500 2733 5.789521 ACTAAAGGCTTTGTTGTTGTTGTT 58.210 33.333 22.32 0.00 0.00 2.83
2501 2734 5.637387 ACTAAAGGCTTTGTTGTTGTTGTTG 59.363 36.000 22.32 0.00 0.00 3.33
2502 2735 3.676291 AGGCTTTGTTGTTGTTGTTGT 57.324 38.095 0.00 0.00 0.00 3.32
2503 2736 4.001618 AGGCTTTGTTGTTGTTGTTGTT 57.998 36.364 0.00 0.00 0.00 2.83
2504 2737 3.745458 AGGCTTTGTTGTTGTTGTTGTTG 59.255 39.130 0.00 0.00 0.00 3.33
2505 2738 3.496507 GGCTTTGTTGTTGTTGTTGTTGT 59.503 39.130 0.00 0.00 0.00 3.32
2506 2739 4.024472 GGCTTTGTTGTTGTTGTTGTTGTT 60.024 37.500 0.00 0.00 0.00 2.83
2507 2740 4.903016 GCTTTGTTGTTGTTGTTGTTGTTG 59.097 37.500 0.00 0.00 0.00 3.33
2604 2839 4.319046 CGCTATGTTGATCAGCATGTTACC 60.319 45.833 29.05 14.24 37.40 2.85
2608 2843 2.309528 TGATCAGCATGTTACCGTCC 57.690 50.000 0.00 0.00 37.40 4.79
2609 2844 1.552792 TGATCAGCATGTTACCGTCCA 59.447 47.619 0.00 0.00 37.40 4.02
2612 2847 1.346395 TCAGCATGTTACCGTCCACTT 59.654 47.619 0.00 0.00 37.40 3.16
2613 2848 2.151202 CAGCATGTTACCGTCCACTTT 58.849 47.619 0.00 0.00 0.00 2.66
2737 3057 4.095483 CCACCTTCAGGAATCGATGAAAAG 59.905 45.833 0.00 0.00 35.14 2.27
2738 3058 3.691609 ACCTTCAGGAATCGATGAAAAGC 59.308 43.478 0.00 0.00 35.14 3.51
2830 3150 0.811616 CCAGCAGGAGCACGGTAATC 60.812 60.000 0.00 0.00 45.49 1.75
2845 3165 2.301346 GTAATCCCGGACGAGTAGGAA 58.699 52.381 0.73 0.00 30.71 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.920193 ATGTTCAGAAAGAGAGAGAGAGG 57.080 43.478 0.00 0.00 0.00 3.69
1 2 6.974622 GCTAATGTTCAGAAAGAGAGAGAGAG 59.025 42.308 0.00 0.00 0.00 3.20
3 4 6.042143 GGCTAATGTTCAGAAAGAGAGAGAG 58.958 44.000 0.00 0.00 0.00 3.20
4 5 5.393569 CGGCTAATGTTCAGAAAGAGAGAGA 60.394 44.000 0.00 0.00 0.00 3.10
5 6 4.803088 CGGCTAATGTTCAGAAAGAGAGAG 59.197 45.833 0.00 0.00 0.00 3.20
7 8 4.748892 TCGGCTAATGTTCAGAAAGAGAG 58.251 43.478 0.00 0.00 0.00 3.20
8 9 4.801330 TCGGCTAATGTTCAGAAAGAGA 57.199 40.909 0.00 0.00 0.00 3.10
9 10 6.703607 ACATATCGGCTAATGTTCAGAAAGAG 59.296 38.462 0.00 0.00 32.43 2.85
10 11 6.582636 ACATATCGGCTAATGTTCAGAAAGA 58.417 36.000 0.00 0.00 32.43 2.52
11 12 6.851222 ACATATCGGCTAATGTTCAGAAAG 57.149 37.500 0.00 0.00 32.43 2.62
26 27 7.535489 TCGGCGATCTATATATACATATCGG 57.465 40.000 4.99 10.39 37.34 4.18
27 28 7.636745 GCTTCGGCGATCTATATATACATATCG 59.363 40.741 11.76 16.14 39.26 2.92
28 29 8.829514 GCTTCGGCGATCTATATATACATATC 57.170 38.462 11.76 0.00 0.00 1.63
56 57 2.286365 TTGGGGGCAAGAAACAGTAG 57.714 50.000 0.00 0.00 0.00 2.57
73 74 4.609018 AGATCGGGCGGCGGATTG 62.609 66.667 28.45 5.58 0.00 2.67
83 84 0.543749 AAGGAGAAAGGCAGATCGGG 59.456 55.000 0.00 0.00 0.00 5.14
105 106 1.872388 TCACTCGACGCATGGAAAAA 58.128 45.000 0.00 0.00 0.00 1.94
173 174 0.244994 GCTCAGCGACCAGAAGAAGA 59.755 55.000 0.00 0.00 0.00 2.87
188 189 2.338620 CGTTCTGGTCCGTGCTCA 59.661 61.111 0.00 0.00 0.00 4.26
199 200 1.425428 GAGCGCCAAATCCGTTCTG 59.575 57.895 2.29 0.00 33.90 3.02
386 411 8.845413 ACATTTGTTTATTGCAACATGGTTAT 57.155 26.923 0.00 0.00 36.54 1.89
416 441 1.522092 CGAGCAATGGGGCACTCTA 59.478 57.895 0.00 0.00 35.83 2.43
419 444 2.269520 TATGCGAGCAATGGGGCACT 62.270 55.000 0.57 0.00 38.36 4.40
440 465 2.969262 TGTAGGCATGGTCATAATCGGA 59.031 45.455 0.00 0.00 0.00 4.55
465 495 4.607955 CATTTGCTGTCATGGAGCTATTG 58.392 43.478 15.84 11.76 37.35 1.90
530 560 6.439058 TCCCTTTTCTTCTGAGGAAACAAAAA 59.561 34.615 13.67 0.00 33.22 1.94
547 577 8.893219 AGATTTTGTGAAGAAATTCCCTTTTC 57.107 30.769 0.00 0.00 36.13 2.29
550 581 7.069826 TGTGAGATTTTGTGAAGAAATTCCCTT 59.930 33.333 0.00 0.00 0.00 3.95
554 585 6.360681 CGGTGTGAGATTTTGTGAAGAAATTC 59.639 38.462 0.00 0.00 0.00 2.17
560 591 8.104431 AACACTCGGTGTGAGATTTTGTGAAG 62.104 42.308 16.31 0.00 46.79 3.02
615 646 0.738063 AACATTACGATGCCGCGTGA 60.738 50.000 4.92 3.56 45.23 4.35
636 667 8.902806 TGATAAGAAGAAAAAGAACAAGAAGCA 58.097 29.630 0.00 0.00 0.00 3.91
637 668 9.392021 CTGATAAGAAGAAAAAGAACAAGAAGC 57.608 33.333 0.00 0.00 0.00 3.86
830 872 1.148157 CTGACGGCGGTGATGATCAC 61.148 60.000 16.95 16.95 46.23 3.06
834 876 4.451150 GGCTGACGGCGGTGATGA 62.451 66.667 13.24 0.00 42.94 2.92
1239 1311 2.901042 GATCCCACGGTGAGGACC 59.099 66.667 17.06 7.24 39.14 4.46
1927 2065 5.127845 CACATGGCTCGTAAGGGATAGATAT 59.872 44.000 0.00 0.00 44.69 1.63
2019 2180 7.747799 GCATAACAATCACGAATTGATGATAGG 59.252 37.037 17.85 10.04 44.86 2.57
2103 2277 1.692411 GGGGAACAGCAGAACACTTT 58.308 50.000 0.00 0.00 0.00 2.66
2174 2359 9.784680 CTTCTCATGAAGGAATTAACAATCAAG 57.215 33.333 0.00 0.00 44.33 3.02
2229 2416 1.280421 ACAGAAGGGAGCATCTGAACC 59.720 52.381 9.56 0.00 44.64 3.62
2277 2468 1.684983 CAGCTTCCCAAATATGCCAGG 59.315 52.381 0.00 0.00 0.00 4.45
2289 2480 0.179018 AGACACACAACCAGCTTCCC 60.179 55.000 0.00 0.00 0.00 3.97
2323 2556 4.326009 GCACCTGCCAATATTTTAACAACG 59.674 41.667 0.00 0.00 34.31 4.10
2342 2575 4.504097 GTGAAAGTCAATGAAACAAGCACC 59.496 41.667 0.00 0.00 0.00 5.01
2416 2649 3.882888 AGATCTCGCAACCAACTCAAAAA 59.117 39.130 0.00 0.00 0.00 1.94
2417 2650 3.476552 AGATCTCGCAACCAACTCAAAA 58.523 40.909 0.00 0.00 0.00 2.44
2418 2651 3.126001 AGATCTCGCAACCAACTCAAA 57.874 42.857 0.00 0.00 0.00 2.69
2419 2652 2.839486 AGATCTCGCAACCAACTCAA 57.161 45.000 0.00 0.00 0.00 3.02
2420 2653 2.839486 AAGATCTCGCAACCAACTCA 57.161 45.000 0.00 0.00 0.00 3.41
2421 2654 3.557595 CCATAAGATCTCGCAACCAACTC 59.442 47.826 0.00 0.00 0.00 3.01
2422 2655 3.535561 CCATAAGATCTCGCAACCAACT 58.464 45.455 0.00 0.00 0.00 3.16
2423 2656 2.614057 CCCATAAGATCTCGCAACCAAC 59.386 50.000 0.00 0.00 0.00 3.77
2424 2657 2.238646 ACCCATAAGATCTCGCAACCAA 59.761 45.455 0.00 0.00 0.00 3.67
2425 2658 1.837439 ACCCATAAGATCTCGCAACCA 59.163 47.619 0.00 0.00 0.00 3.67
2426 2659 2.622064 ACCCATAAGATCTCGCAACC 57.378 50.000 0.00 0.00 0.00 3.77
2427 2660 3.938963 TGAAACCCATAAGATCTCGCAAC 59.061 43.478 0.00 0.00 0.00 4.17
2428 2661 3.938963 GTGAAACCCATAAGATCTCGCAA 59.061 43.478 0.00 0.00 0.00 4.85
2429 2662 3.531538 GTGAAACCCATAAGATCTCGCA 58.468 45.455 0.00 0.00 0.00 5.10
2444 2677 0.035343 GGGTGGGCTAGAGGTGAAAC 60.035 60.000 0.00 0.00 0.00 2.78
2445 2678 1.205460 GGGGTGGGCTAGAGGTGAAA 61.205 60.000 0.00 0.00 0.00 2.69
2446 2679 1.615424 GGGGTGGGCTAGAGGTGAA 60.615 63.158 0.00 0.00 0.00 3.18
2447 2680 2.040606 GGGGTGGGCTAGAGGTGA 59.959 66.667 0.00 0.00 0.00 4.02
2448 2681 1.923395 TTGGGGTGGGCTAGAGGTG 60.923 63.158 0.00 0.00 0.00 4.00
2449 2682 1.923909 GTTGGGGTGGGCTAGAGGT 60.924 63.158 0.00 0.00 0.00 3.85
2450 2683 1.208165 AAGTTGGGGTGGGCTAGAGG 61.208 60.000 0.00 0.00 0.00 3.69
2451 2684 0.035056 CAAGTTGGGGTGGGCTAGAG 60.035 60.000 0.00 0.00 0.00 2.43
2452 2685 0.770557 ACAAGTTGGGGTGGGCTAGA 60.771 55.000 7.96 0.00 0.00 2.43
2453 2686 0.112412 AACAAGTTGGGGTGGGCTAG 59.888 55.000 7.96 0.00 0.00 3.42
2454 2687 0.558712 AAACAAGTTGGGGTGGGCTA 59.441 50.000 7.96 0.00 0.00 3.93
2455 2688 1.048160 CAAACAAGTTGGGGTGGGCT 61.048 55.000 7.96 0.00 33.18 5.19
2456 2689 1.445518 CAAACAAGTTGGGGTGGGC 59.554 57.895 7.96 0.00 33.18 5.36
2464 2697 3.636764 AGCCTTTAGTCCCAAACAAGTTG 59.363 43.478 0.00 0.00 36.94 3.16
2465 2698 3.910989 AGCCTTTAGTCCCAAACAAGTT 58.089 40.909 0.00 0.00 0.00 2.66
2466 2699 3.595190 AGCCTTTAGTCCCAAACAAGT 57.405 42.857 0.00 0.00 0.00 3.16
2467 2700 4.099419 ACAAAGCCTTTAGTCCCAAACAAG 59.901 41.667 0.00 0.00 0.00 3.16
2468 2701 4.027437 ACAAAGCCTTTAGTCCCAAACAA 58.973 39.130 0.00 0.00 0.00 2.83
2469 2702 3.637769 ACAAAGCCTTTAGTCCCAAACA 58.362 40.909 0.00 0.00 0.00 2.83
2470 2703 4.142026 ACAACAAAGCCTTTAGTCCCAAAC 60.142 41.667 0.00 0.00 0.00 2.93
2471 2704 4.027437 ACAACAAAGCCTTTAGTCCCAAA 58.973 39.130 0.00 0.00 0.00 3.28
2472 2705 3.637769 ACAACAAAGCCTTTAGTCCCAA 58.362 40.909 0.00 0.00 0.00 4.12
2473 2706 3.306472 ACAACAAAGCCTTTAGTCCCA 57.694 42.857 0.00 0.00 0.00 4.37
2474 2707 3.383505 ACAACAACAAAGCCTTTAGTCCC 59.616 43.478 0.00 0.00 0.00 4.46
2475 2708 4.649088 ACAACAACAAAGCCTTTAGTCC 57.351 40.909 0.00 0.00 0.00 3.85
2476 2709 5.407502 ACAACAACAACAAAGCCTTTAGTC 58.592 37.500 0.00 0.00 0.00 2.59
2477 2710 5.400066 ACAACAACAACAAAGCCTTTAGT 57.600 34.783 0.00 0.00 0.00 2.24
2478 2711 5.637387 ACAACAACAACAACAAAGCCTTTAG 59.363 36.000 0.00 0.00 0.00 1.85
2479 2712 5.542779 ACAACAACAACAACAAAGCCTTTA 58.457 33.333 0.00 0.00 0.00 1.85
2480 2713 4.384940 ACAACAACAACAACAAAGCCTTT 58.615 34.783 0.00 0.00 0.00 3.11
2481 2714 4.001618 ACAACAACAACAACAAAGCCTT 57.998 36.364 0.00 0.00 0.00 4.35
2482 2715 3.676291 ACAACAACAACAACAAAGCCT 57.324 38.095 0.00 0.00 0.00 4.58
2483 2716 3.496507 ACAACAACAACAACAACAAAGCC 59.503 39.130 0.00 0.00 0.00 4.35
2484 2717 4.723879 ACAACAACAACAACAACAAAGC 57.276 36.364 0.00 0.00 0.00 3.51
2485 2718 6.042144 ACAACAACAACAACAACAACAAAG 57.958 33.333 0.00 0.00 0.00 2.77
2486 2719 6.250819 CAACAACAACAACAACAACAACAAA 58.749 32.000 0.00 0.00 0.00 2.83
2487 2720 5.220662 CCAACAACAACAACAACAACAACAA 60.221 36.000 0.00 0.00 0.00 2.83
2488 2721 4.271049 CCAACAACAACAACAACAACAACA 59.729 37.500 0.00 0.00 0.00 3.33
2489 2722 4.271291 ACCAACAACAACAACAACAACAAC 59.729 37.500 0.00 0.00 0.00 3.32
2490 2723 4.442706 ACCAACAACAACAACAACAACAA 58.557 34.783 0.00 0.00 0.00 2.83
2491 2724 4.060038 ACCAACAACAACAACAACAACA 57.940 36.364 0.00 0.00 0.00 3.33
2492 2725 5.224135 ACTACCAACAACAACAACAACAAC 58.776 37.500 0.00 0.00 0.00 3.32
2493 2726 5.455056 ACTACCAACAACAACAACAACAA 57.545 34.783 0.00 0.00 0.00 2.83
2494 2727 6.016527 TGTTACTACCAACAACAACAACAACA 60.017 34.615 0.00 0.00 35.53 3.33
2495 2728 6.380190 TGTTACTACCAACAACAACAACAAC 58.620 36.000 0.00 0.00 35.53 3.32
2496 2729 6.570672 TGTTACTACCAACAACAACAACAA 57.429 33.333 0.00 0.00 35.53 2.83
2497 2730 6.207025 ACTTGTTACTACCAACAACAACAACA 59.793 34.615 0.00 0.00 42.08 3.33
2498 2731 6.614160 ACTTGTTACTACCAACAACAACAAC 58.386 36.000 0.00 0.00 42.08 3.32
2499 2732 6.821031 ACTTGTTACTACCAACAACAACAA 57.179 33.333 0.00 0.00 42.08 2.83
2500 2733 6.821031 AACTTGTTACTACCAACAACAACA 57.179 33.333 0.00 0.00 42.08 3.33
2501 2734 6.901357 CGTAACTTGTTACTACCAACAACAAC 59.099 38.462 17.90 0.00 42.08 3.32
2502 2735 6.815641 TCGTAACTTGTTACTACCAACAACAA 59.184 34.615 17.90 0.00 42.08 2.83
2503 2736 6.336566 TCGTAACTTGTTACTACCAACAACA 58.663 36.000 17.90 0.00 42.08 3.33
2504 2737 6.826893 TCGTAACTTGTTACTACCAACAAC 57.173 37.500 17.90 0.00 42.08 3.32
2505 2738 7.463913 CGTTTCGTAACTTGTTACTACCAACAA 60.464 37.037 17.90 1.87 44.10 2.83
2506 2739 6.019961 CGTTTCGTAACTTGTTACTACCAACA 60.020 38.462 17.90 0.00 36.65 3.33
2507 2740 6.347110 CGTTTCGTAACTTGTTACTACCAAC 58.653 40.000 17.90 13.67 31.89 3.77
2604 2839 2.328099 GCCAGCCTCAAAGTGGACG 61.328 63.158 0.00 0.00 32.60 4.79
2608 2843 1.447317 AACACGCCAGCCTCAAAGTG 61.447 55.000 0.00 0.00 35.89 3.16
2609 2844 0.107831 TAACACGCCAGCCTCAAAGT 59.892 50.000 0.00 0.00 0.00 2.66
2612 2847 1.904287 AAATAACACGCCAGCCTCAA 58.096 45.000 0.00 0.00 0.00 3.02
2613 2848 1.904287 AAAATAACACGCCAGCCTCA 58.096 45.000 0.00 0.00 0.00 3.86
2654 2889 0.866483 GCTAACAGTAGCGCCGAGAC 60.866 60.000 2.29 0.00 43.29 3.36
2737 3057 5.633601 TCGGAATCATGTAAATGTAGATCGC 59.366 40.000 0.00 0.00 0.00 4.58
2738 3058 7.084486 TCTCGGAATCATGTAAATGTAGATCG 58.916 38.462 0.00 0.00 0.00 3.69
2830 3150 1.664321 CTGGTTCCTACTCGTCCGGG 61.664 65.000 0.00 0.00 0.00 5.73
2833 3153 1.104630 CCTCTGGTTCCTACTCGTCC 58.895 60.000 0.00 0.00 0.00 4.79
2845 3165 1.974236 CAGTTCCTGAGTTCCTCTGGT 59.026 52.381 14.44 0.00 45.70 4.00


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

AutoCloner maintained by Alex Coulton.