Multiple sequence alignment - TraesCS7D01G303800

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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 TraesCS7D01G303800 chr7D 100.000 3203 0 0 1 3203 385430681 385433883 0.000000e+00 5915.0
1 TraesCS7D01G303800 chr7D 83.361 601 77 6 2558 3135 58136354 58135754 4.700000e-148 534.0
2 TraesCS7D01G303800 chr7A 91.068 1377 62 27 1 1357 433375686 433377021 0.000000e+00 1805.0
3 TraesCS7D01G303800 chr7A 93.646 960 41 7 1357 2300 433377272 433378227 0.000000e+00 1417.0
4 TraesCS7D01G303800 chr7A 82.022 623 76 16 2540 3135 143185298 143185911 6.170000e-137 497.0
5 TraesCS7D01G303800 chr7A 82.903 503 56 9 2558 3032 719360322 719360822 2.950000e-115 425.0
6 TraesCS7D01G303800 chr7B 92.814 1155 59 14 1357 2499 379777266 379778408 0.000000e+00 1652.0
7 TraesCS7D01G303800 chr7B 89.244 595 28 14 779 1359 379776466 379777038 0.000000e+00 712.0
8 TraesCS7D01G303800 chr7B 87.480 623 55 12 75 685 379775665 379776276 0.000000e+00 697.0
9 TraesCS7D01G303800 chr7B 81.414 608 79 14 2558 3135 222311997 222312600 1.740000e-127 466.0
10 TraesCS7D01G303800 chr4A 85.510 628 65 9 2539 3141 578106736 578106110 1.620000e-177 632.0
11 TraesCS7D01G303800 chr4A 90.000 70 6 1 3066 3135 583896700 583896768 4.400000e-14 89.8
12 TraesCS7D01G303800 chr6A 83.518 631 67 8 2540 3135 608655993 608656621 3.610000e-154 555.0
13 TraesCS7D01G303800 chr6A 81.509 530 80 14 2620 3135 562468002 562468527 1.370000e-113 420.0
14 TraesCS7D01G303800 chr5D 84.000 600 70 11 2558 3135 295079780 295080375 1.300000e-153 553.0
15 TraesCS7D01G303800 chr4D 85.988 521 68 4 2620 3135 414044391 414043871 1.300000e-153 553.0
16 TraesCS7D01G303800 chr5B 81.761 636 75 11 2539 3141 679666806 679666179 7.980000e-136 494.0
17 TraesCS7D01G303800 chr3B 81.260 603 79 21 2558 3135 650063802 650063209 1.050000e-124 457.0
18 TraesCS7D01G303800 chr2D 81.054 607 81 18 2558 3135 61450848 61450247 1.350000e-123 453.0
19 TraesCS7D01G303800 chr2D 83.902 205 27 5 2934 3135 85859763 85859562 1.170000e-44 191.0
20 TraesCS7D01G303800 chr1A 83.058 484 70 8 2558 3032 509038249 509038729 2.280000e-116 429.0
21 TraesCS7D01G303800 chr3A 81.081 518 86 9 2620 3128 468613155 468612641 1.380000e-108 403.0
22 TraesCS7D01G303800 chr2B 75.545 413 60 16 2539 2928 495165560 495165954 7.110000e-37 165.0
23 TraesCS7D01G303800 chr3D 87.640 89 5 1 2539 2621 337317736 337317648 7.310000e-17 99.0


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 TraesCS7D01G303800 chr7D 385430681 385433883 3202 False 5915.000000 5915 100.000 1 3203 1 chr7D.!!$F1 3202
1 TraesCS7D01G303800 chr7D 58135754 58136354 600 True 534.000000 534 83.361 2558 3135 1 chr7D.!!$R1 577
2 TraesCS7D01G303800 chr7A 433375686 433378227 2541 False 1611.000000 1805 92.357 1 2300 2 chr7A.!!$F3 2299
3 TraesCS7D01G303800 chr7A 143185298 143185911 613 False 497.000000 497 82.022 2540 3135 1 chr7A.!!$F1 595
4 TraesCS7D01G303800 chr7A 719360322 719360822 500 False 425.000000 425 82.903 2558 3032 1 chr7A.!!$F2 474
5 TraesCS7D01G303800 chr7B 379775665 379778408 2743 False 1020.333333 1652 89.846 75 2499 3 chr7B.!!$F2 2424
6 TraesCS7D01G303800 chr7B 222311997 222312600 603 False 466.000000 466 81.414 2558 3135 1 chr7B.!!$F1 577
7 TraesCS7D01G303800 chr4A 578106110 578106736 626 True 632.000000 632 85.510 2539 3141 1 chr4A.!!$R1 602
8 TraesCS7D01G303800 chr6A 608655993 608656621 628 False 555.000000 555 83.518 2540 3135 1 chr6A.!!$F2 595
9 TraesCS7D01G303800 chr6A 562468002 562468527 525 False 420.000000 420 81.509 2620 3135 1 chr6A.!!$F1 515
10 TraesCS7D01G303800 chr5D 295079780 295080375 595 False 553.000000 553 84.000 2558 3135 1 chr5D.!!$F1 577
11 TraesCS7D01G303800 chr4D 414043871 414044391 520 True 553.000000 553 85.988 2620 3135 1 chr4D.!!$R1 515
12 TraesCS7D01G303800 chr5B 679666179 679666806 627 True 494.000000 494 81.761 2539 3141 1 chr5B.!!$R1 602
13 TraesCS7D01G303800 chr3B 650063209 650063802 593 True 457.000000 457 81.260 2558 3135 1 chr3B.!!$R1 577
14 TraesCS7D01G303800 chr2D 61450247 61450848 601 True 453.000000 453 81.054 2558 3135 1 chr2D.!!$R1 577
15 TraesCS7D01G303800 chr3A 468612641 468613155 514 True 403.000000 403 81.081 2620 3128 1 chr3A.!!$R1 508

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
939 1072 0.532417 GCATCTCGCTCATTCCTGCT 60.532 55.0 0.0 0.0 37.77 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2473 2896 0.241481 GGTATTTTTGGCCGCACGAA 59.759 50.0 0.0 0.0 0.0 3.85 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
67 68 9.513906 TGTTCAGACTTTGTCAATTATATCCAA 57.486 29.630 0.46 0.00 34.60 3.53
69 70 8.506168 TCAGACTTTGTCAATTATATCCAACC 57.494 34.615 0.46 0.00 34.60 3.77
119 128 4.379302 AAAGTCCCTCAGAAGCTCAAAT 57.621 40.909 0.00 0.00 0.00 2.32
120 129 4.379302 AAGTCCCTCAGAAGCTCAAATT 57.621 40.909 0.00 0.00 0.00 1.82
121 130 4.379302 AGTCCCTCAGAAGCTCAAATTT 57.621 40.909 0.00 0.00 0.00 1.82
122 131 4.734266 AGTCCCTCAGAAGCTCAAATTTT 58.266 39.130 0.00 0.00 0.00 1.82
123 132 5.143369 AGTCCCTCAGAAGCTCAAATTTTT 58.857 37.500 0.00 0.00 0.00 1.94
124 133 5.242615 AGTCCCTCAGAAGCTCAAATTTTTC 59.757 40.000 0.00 0.00 0.00 2.29
125 134 5.010012 GTCCCTCAGAAGCTCAAATTTTTCA 59.990 40.000 0.00 0.00 0.00 2.69
126 135 5.776716 TCCCTCAGAAGCTCAAATTTTTCAT 59.223 36.000 0.00 0.00 0.00 2.57
315 337 3.073946 CCACCCCACCCTAGTATTTATGG 59.926 52.174 0.00 0.00 0.00 2.74
433 455 6.647212 TTGCAACTCGTCTACAAGATAATG 57.353 37.500 0.00 0.00 0.00 1.90
439 461 9.516314 CAACTCGTCTACAAGATAATGTATTGA 57.484 33.333 0.00 0.00 35.37 2.57
595 617 4.803613 GCCTGTTTTCAGTTGGTTGTAAAG 59.196 41.667 0.00 0.00 45.68 1.85
699 721 6.088483 GTGTACGTCAATCGATGTAAAGAACA 59.912 38.462 0.00 0.00 43.58 3.18
939 1072 0.532417 GCATCTCGCTCATTCCTGCT 60.532 55.000 0.00 0.00 37.77 4.24
980 1121 5.757808 GCTAATCCAAGATCTCCAAGAACTC 59.242 44.000 0.00 0.00 0.00 3.01
1066 1208 1.810532 CCTTCCTTCCTCTCGGTCG 59.189 63.158 0.00 0.00 0.00 4.79
1082 1224 1.135402 GGTCGCACCCTTTATTTGCTG 60.135 52.381 0.00 0.00 33.90 4.41
1141 1283 2.661866 GCGCGGCGAGATTATGGT 60.662 61.111 28.54 0.00 0.00 3.55
1142 1284 2.244651 GCGCGGCGAGATTATGGTT 61.245 57.895 28.54 0.00 0.00 3.67
1143 1285 1.853319 CGCGGCGAGATTATGGTTC 59.147 57.895 19.16 0.00 0.00 3.62
1144 1286 0.597637 CGCGGCGAGATTATGGTTCT 60.598 55.000 19.16 0.00 0.00 3.01
1145 1287 1.583054 GCGGCGAGATTATGGTTCTT 58.417 50.000 12.98 0.00 0.00 2.52
1146 1288 2.750948 GCGGCGAGATTATGGTTCTTA 58.249 47.619 12.98 0.00 0.00 2.10
1147 1289 3.326747 GCGGCGAGATTATGGTTCTTAT 58.673 45.455 12.98 0.00 0.00 1.73
1148 1290 3.123621 GCGGCGAGATTATGGTTCTTATG 59.876 47.826 12.98 0.00 0.00 1.90
1149 1291 4.307432 CGGCGAGATTATGGTTCTTATGT 58.693 43.478 0.00 0.00 0.00 2.29
1188 1334 2.224917 TGGGCGATTTACTTTCTTGGGT 60.225 45.455 0.00 0.00 0.00 4.51
1245 1392 2.955614 ACATCGGAGTTGGTTAGTTCG 58.044 47.619 0.00 0.00 0.00 3.95
1246 1393 2.559668 ACATCGGAGTTGGTTAGTTCGA 59.440 45.455 0.00 0.00 41.33 3.71
1247 1394 2.712057 TCGGAGTTGGTTAGTTCGAC 57.288 50.000 0.00 0.00 32.18 4.20
1248 1395 2.233271 TCGGAGTTGGTTAGTTCGACT 58.767 47.619 0.00 0.00 32.18 4.18
1249 1396 2.624838 TCGGAGTTGGTTAGTTCGACTT 59.375 45.455 0.00 0.00 32.18 3.01
1250 1397 2.729882 CGGAGTTGGTTAGTTCGACTTG 59.270 50.000 0.00 0.00 28.94 3.16
1283 1430 0.107831 CTCCGTTGTTCTGTTCCCCA 59.892 55.000 0.00 0.00 0.00 4.96
1293 1440 2.142292 CTGTTCCCCAGGGGTTCAGG 62.142 65.000 28.78 17.70 44.74 3.86
1316 1463 4.440112 GCTTTCGAAACCAAATCATAGGGG 60.440 45.833 6.47 0.00 0.00 4.79
1322 1469 5.621329 CGAAACCAAATCATAGGGGAAACAC 60.621 44.000 0.00 0.00 0.00 3.32
1338 1486 1.717032 ACACCCAGAGTTGCTCACTA 58.283 50.000 0.00 0.00 35.01 2.74
1362 1761 1.265095 AGTGACTGTTTGCGCAAGATG 59.735 47.619 23.68 17.92 43.02 2.90
1438 1837 3.743584 GCCAAGCTAGCAGATGAGATTCA 60.744 47.826 18.83 0.00 0.00 2.57
1448 1847 3.068732 CAGATGAGATTCAGAAGGGCGTA 59.931 47.826 0.00 0.00 0.00 4.42
1463 1862 1.152383 GCGTATCTTCCGTCCAAGGC 61.152 60.000 0.00 0.00 0.00 4.35
1558 1963 8.845227 AGTATATTGAGATGATCTACCGCTATG 58.155 37.037 0.00 0.00 0.00 2.23
1629 2035 4.147321 CCCCATCCCAAACTCTGAATATG 58.853 47.826 0.00 0.00 0.00 1.78
1662 2068 2.246789 GAGACTCTTTCTGACGAAGCG 58.753 52.381 0.00 0.00 33.22 4.68
1665 2071 1.269831 ACTCTTTCTGACGAAGCGCTT 60.270 47.619 25.35 25.35 0.00 4.68
1737 2143 4.560856 GAGCTCGCCGACGCTGAT 62.561 66.667 14.20 0.00 39.84 2.90
1909 2315 2.005971 AGAAACCACCGCGTAAGATC 57.994 50.000 4.92 0.00 43.02 2.75
1921 2327 3.459145 GCGTAAGATCCCTTCTTCCTTC 58.541 50.000 0.00 0.00 43.75 3.46
1944 2350 8.909708 TTCGTTGATTTGTCATGGAAATTATC 57.090 30.769 0.00 0.00 0.00 1.75
2206 2628 1.486310 TCAAGGGTTCTCCATGATCGG 59.514 52.381 0.00 0.00 38.24 4.18
2220 2642 3.344137 ATCGGCGGCCACCAAGATT 62.344 57.895 20.71 0.00 0.00 2.40
2340 2762 2.028748 TCTGTGGCGACCTTAGGTTAAC 60.029 50.000 4.99 0.00 35.25 2.01
2368 2790 4.457466 GGACCAAGTACTTGAGGTTGAAA 58.543 43.478 32.50 0.00 42.93 2.69
2369 2791 4.885325 GGACCAAGTACTTGAGGTTGAAAA 59.115 41.667 32.50 0.00 42.93 2.29
2370 2792 5.220989 GGACCAAGTACTTGAGGTTGAAAAC 60.221 44.000 32.50 12.35 44.03 2.43
2372 2794 5.357032 ACCAAGTACTTGAGGTTGAAAACTG 59.643 40.000 32.50 15.46 44.13 3.16
2373 2795 5.357032 CCAAGTACTTGAGGTTGAAAACTGT 59.643 40.000 32.50 0.00 44.13 3.55
2376 2798 8.568472 CAAGTACTTGAGGTTGAAAACTGTTGC 61.568 40.741 28.17 0.00 44.13 4.17
2388 2810 8.479280 GTTGAAAACTGTTGCTGTTATAACATG 58.521 33.333 18.35 13.14 45.32 3.21
2397 2819 4.943093 TGCTGTTATAACATGTGCTGTCAT 59.057 37.500 18.35 0.00 36.98 3.06
2413 2835 4.095334 GCTGTCATGTCATGCACATTTCTA 59.905 41.667 8.03 0.00 43.89 2.10
2420 2842 7.283580 TCATGTCATGCACATTTCTATGATCAA 59.716 33.333 8.03 0.00 43.89 2.57
2448 2870 7.012799 GCAGAAAATCGGAAAAGAGATCCTAAT 59.987 37.037 0.00 0.00 34.66 1.73
2459 2882 5.289083 AGAGATCCTAATGAAACTCAGCC 57.711 43.478 0.00 0.00 0.00 4.85
2467 2890 5.642063 CCTAATGAAACTCAGCCGTTTTCTA 59.358 40.000 0.00 0.00 37.24 2.10
2473 2896 6.206634 TGAAACTCAGCCGTTTTCTATGAAAT 59.793 34.615 0.00 0.00 37.24 2.17
2482 2905 3.398954 TTTCTATGAAATTCGTGCGGC 57.601 42.857 0.00 0.00 0.00 6.53
2484 2907 1.013596 CTATGAAATTCGTGCGGCCA 58.986 50.000 2.24 0.00 0.00 5.36
2488 2911 1.202417 TGAAATTCGTGCGGCCAAAAA 60.202 42.857 2.24 0.00 0.00 1.94
2489 2912 2.065512 GAAATTCGTGCGGCCAAAAAT 58.934 42.857 2.24 0.00 0.00 1.82
2490 2913 3.246619 GAAATTCGTGCGGCCAAAAATA 58.753 40.909 2.24 0.00 0.00 1.40
2491 2914 2.271821 ATTCGTGCGGCCAAAAATAC 57.728 45.000 2.24 0.00 0.00 1.89
2492 2915 0.241481 TTCGTGCGGCCAAAAATACC 59.759 50.000 2.24 0.00 0.00 2.73
2494 2917 1.591504 CGTGCGGCCAAAAATACCCT 61.592 55.000 2.24 0.00 0.00 4.34
2496 2919 1.819903 GTGCGGCCAAAAATACCCTTA 59.180 47.619 2.24 0.00 0.00 2.69
2498 2921 3.100671 TGCGGCCAAAAATACCCTTAAT 58.899 40.909 2.24 0.00 0.00 1.40
2499 2922 3.131400 TGCGGCCAAAAATACCCTTAATC 59.869 43.478 2.24 0.00 0.00 1.75
2500 2923 3.131400 GCGGCCAAAAATACCCTTAATCA 59.869 43.478 2.24 0.00 0.00 2.57
2501 2924 4.678622 CGGCCAAAAATACCCTTAATCAC 58.321 43.478 2.24 0.00 0.00 3.06
2502 2925 4.401202 CGGCCAAAAATACCCTTAATCACT 59.599 41.667 2.24 0.00 0.00 3.41
2503 2926 5.105513 CGGCCAAAAATACCCTTAATCACTT 60.106 40.000 2.24 0.00 0.00 3.16
2504 2927 6.095720 CGGCCAAAAATACCCTTAATCACTTA 59.904 38.462 2.24 0.00 0.00 2.24
2505 2928 7.363094 CGGCCAAAAATACCCTTAATCACTTAA 60.363 37.037 2.24 0.00 0.00 1.85
2506 2929 7.762615 GGCCAAAAATACCCTTAATCACTTAAC 59.237 37.037 0.00 0.00 0.00 2.01
2507 2930 7.486870 GCCAAAAATACCCTTAATCACTTAACG 59.513 37.037 0.00 0.00 0.00 3.18
2508 2931 8.517056 CCAAAAATACCCTTAATCACTTAACGT 58.483 33.333 0.00 0.00 0.00 3.99
2509 2932 9.337091 CAAAAATACCCTTAATCACTTAACGTG 57.663 33.333 0.00 0.00 45.18 4.49
2510 2933 8.625786 AAAATACCCTTAATCACTTAACGTGT 57.374 30.769 0.00 0.00 44.16 4.49
2511 2934 7.838771 AATACCCTTAATCACTTAACGTGTC 57.161 36.000 0.00 0.00 44.16 3.67
2512 2935 4.572909 ACCCTTAATCACTTAACGTGTCC 58.427 43.478 0.00 0.00 44.16 4.02
2513 2936 3.615496 CCCTTAATCACTTAACGTGTCCG 59.385 47.826 0.00 0.00 44.16 4.79
2514 2937 3.061697 CCTTAATCACTTAACGTGTCCGC 59.938 47.826 0.00 0.00 44.16 5.54
2515 2938 2.157834 AATCACTTAACGTGTCCGCA 57.842 45.000 0.00 0.00 44.16 5.69
2516 2939 1.710013 ATCACTTAACGTGTCCGCAG 58.290 50.000 0.00 0.00 44.16 5.18
2517 2940 0.386476 TCACTTAACGTGTCCGCAGT 59.614 50.000 0.00 0.00 44.16 4.40
2518 2941 1.608109 TCACTTAACGTGTCCGCAGTA 59.392 47.619 0.00 0.00 44.16 2.74
2519 2942 2.034432 TCACTTAACGTGTCCGCAGTAA 59.966 45.455 0.00 0.00 44.16 2.24
2520 2943 2.796031 CACTTAACGTGTCCGCAGTAAA 59.204 45.455 0.00 0.00 38.84 2.01
2521 2944 3.054878 ACTTAACGTGTCCGCAGTAAAG 58.945 45.455 0.00 0.00 37.70 1.85
2522 2945 1.421382 TAACGTGTCCGCAGTAAAGC 58.579 50.000 0.00 0.00 37.70 3.51
2523 2946 0.531090 AACGTGTCCGCAGTAAAGCA 60.531 50.000 0.00 0.00 37.70 3.91
2524 2947 0.531090 ACGTGTCCGCAGTAAAGCAA 60.531 50.000 0.00 0.00 37.70 3.91
2525 2948 0.796312 CGTGTCCGCAGTAAAGCAAT 59.204 50.000 0.00 0.00 0.00 3.56
2526 2949 1.996898 CGTGTCCGCAGTAAAGCAATA 59.003 47.619 0.00 0.00 0.00 1.90
2527 2950 2.222729 CGTGTCCGCAGTAAAGCAATAC 60.223 50.000 0.00 0.00 0.00 1.89
2528 2951 3.000727 GTGTCCGCAGTAAAGCAATACT 58.999 45.455 0.00 0.00 36.57 2.12
2529 2952 3.435671 GTGTCCGCAGTAAAGCAATACTT 59.564 43.478 0.00 0.00 41.70 2.24
2636 3079 0.956633 TCCGACGACTACAAGCACTT 59.043 50.000 0.00 0.00 0.00 3.16
2637 3080 1.338973 TCCGACGACTACAAGCACTTT 59.661 47.619 0.00 0.00 0.00 2.66
2674 3122 4.222847 GCCGTCATCGTCCCTCCC 62.223 72.222 0.00 0.00 35.01 4.30
2700 3157 1.519408 GAGCCGAGCAAACCTTGTTA 58.481 50.000 0.00 0.00 0.00 2.41
2709 3167 5.235616 CGAGCAAACCTTGTTAAGTAGACAA 59.764 40.000 0.00 0.00 35.81 3.18
2759 3217 1.878656 GACCAGCGCACCAGAGTAGT 61.879 60.000 11.47 0.00 0.00 2.73
2765 3223 1.992170 CGCACCAGAGTAGTAACCAC 58.008 55.000 0.00 0.00 0.00 4.16
2769 3227 0.179145 CCAGAGTAGTAACCACCGCG 60.179 60.000 0.00 0.00 0.00 6.46
2811 3270 6.187727 TCAGAAGGATCAAACCTGTAAACT 57.812 37.500 0.00 0.00 40.49 2.66
2841 3345 4.021894 CGAAGACCGGATCCAAATAGATCT 60.022 45.833 9.46 0.00 42.02 2.75
2848 3352 5.105310 CCGGATCCAAATAGATCTACCGAAT 60.105 44.000 21.08 6.70 42.02 3.34
2879 3387 0.670706 CCGATCCTGCGAGATCTGAA 59.329 55.000 0.00 0.00 40.50 3.02
2902 3412 2.100879 GACACCTTCACACGCCCTCT 62.101 60.000 0.00 0.00 0.00 3.69
3016 3526 5.238650 CCAAGACGTTGAACCTAACAAGAAT 59.761 40.000 0.00 0.00 35.46 2.40
3027 3537 1.534729 AACAAGAATGAGAACGGGGC 58.465 50.000 0.00 0.00 0.00 5.80
3032 3542 2.211468 GAATGAGAACGGGGCCCCTT 62.211 60.000 38.17 28.39 0.00 3.95
3135 3666 3.070748 GCGAGGAGAAGAGCTTTTCTTT 58.929 45.455 19.59 11.78 46.12 2.52
3138 3669 5.179555 GCGAGGAGAAGAGCTTTTCTTTTAA 59.820 40.000 19.59 0.00 46.12 1.52
3141 3672 7.171678 CGAGGAGAAGAGCTTTTCTTTTAAAGA 59.828 37.037 19.59 2.94 46.12 2.52
3142 3673 8.753497 AGGAGAAGAGCTTTTCTTTTAAAGAA 57.247 30.769 19.59 15.24 46.12 2.52
3143 3674 9.360901 AGGAGAAGAGCTTTTCTTTTAAAGAAT 57.639 29.630 19.59 6.04 46.12 2.40
3162 3693 7.396540 AAGAATATACTTTCAGGTTGCTTGG 57.603 36.000 0.00 0.00 0.00 3.61
3163 3694 6.721318 AGAATATACTTTCAGGTTGCTTGGA 58.279 36.000 0.00 0.00 0.00 3.53
3164 3695 6.599638 AGAATATACTTTCAGGTTGCTTGGAC 59.400 38.462 0.00 0.00 0.00 4.02
3165 3696 2.435372 ACTTTCAGGTTGCTTGGACA 57.565 45.000 0.00 0.00 0.00 4.02
3166 3697 2.733956 ACTTTCAGGTTGCTTGGACAA 58.266 42.857 0.00 0.00 0.00 3.18
3167 3698 3.096092 ACTTTCAGGTTGCTTGGACAAA 58.904 40.909 0.00 0.00 0.00 2.83
3168 3699 3.119137 ACTTTCAGGTTGCTTGGACAAAC 60.119 43.478 0.00 0.00 37.52 2.93
3170 3701 3.569194 TCAGGTTGCTTGGACAAACTA 57.431 42.857 0.00 0.00 45.75 2.24
3171 3702 4.098914 TCAGGTTGCTTGGACAAACTAT 57.901 40.909 0.00 0.00 45.75 2.12
3172 3703 4.469657 TCAGGTTGCTTGGACAAACTATT 58.530 39.130 0.00 0.00 45.75 1.73
3173 3704 4.518970 TCAGGTTGCTTGGACAAACTATTC 59.481 41.667 0.00 0.00 45.75 1.75
3174 3705 4.278170 CAGGTTGCTTGGACAAACTATTCA 59.722 41.667 0.00 0.00 45.75 2.57
3175 3706 4.892934 AGGTTGCTTGGACAAACTATTCAA 59.107 37.500 0.00 0.00 45.66 2.69
3176 3707 4.982295 GGTTGCTTGGACAAACTATTCAAC 59.018 41.667 0.00 0.00 34.31 3.18
3177 3708 5.451242 GGTTGCTTGGACAAACTATTCAACA 60.451 40.000 0.00 0.00 34.31 3.33
3178 3709 5.437289 TGCTTGGACAAACTATTCAACAG 57.563 39.130 0.00 0.00 0.00 3.16
3179 3710 4.887071 TGCTTGGACAAACTATTCAACAGT 59.113 37.500 0.00 0.00 0.00 3.55
3180 3711 5.359576 TGCTTGGACAAACTATTCAACAGTT 59.640 36.000 0.00 0.00 37.85 3.16
3181 3712 6.127479 TGCTTGGACAAACTATTCAACAGTTT 60.127 34.615 0.00 0.00 44.91 2.66
3182 3713 6.756542 GCTTGGACAAACTATTCAACAGTTTT 59.243 34.615 0.00 0.00 42.18 2.43
3183 3714 7.277760 GCTTGGACAAACTATTCAACAGTTTTT 59.722 33.333 0.00 0.00 42.18 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 131 9.573166 CACCCTCCTATATAAATGTCAAATGAA 57.427 33.333 0.00 0.00 0.00 2.57
123 132 8.944138 TCACCCTCCTATATAAATGTCAAATGA 58.056 33.333 0.00 0.00 0.00 2.57
124 133 9.745018 ATCACCCTCCTATATAAATGTCAAATG 57.255 33.333 0.00 0.00 0.00 2.32
125 134 9.965902 GATCACCCTCCTATATAAATGTCAAAT 57.034 33.333 0.00 0.00 0.00 2.32
126 135 8.383175 GGATCACCCTCCTATATAAATGTCAAA 58.617 37.037 0.00 0.00 32.18 2.69
204 215 8.384718 TGAATTGATTCCTCATTTTTCCCAAAT 58.615 29.630 1.56 0.00 35.97 2.32
439 461 5.885912 ACGCAAAAAGGACCACATATAGATT 59.114 36.000 0.00 0.00 0.00 2.40
699 721 7.654022 TTCTTTTGATTGAGTAAACACCCTT 57.346 32.000 0.00 0.00 0.00 3.95
733 755 3.660501 ACACTTCATTCACGCTACTCA 57.339 42.857 0.00 0.00 0.00 3.41
876 1008 2.094100 TATGGGAGGGAGAGCTCTTG 57.906 55.000 19.36 0.00 0.00 3.02
939 1072 6.384015 TGGATTAGCTAGTTGAAGAAGATGGA 59.616 38.462 0.00 0.00 0.00 3.41
980 1121 2.787473 TGGTCAGCTTGGATACTTGG 57.213 50.000 0.00 0.00 37.61 3.61
1082 1224 0.306533 TCGAACAAGAAAGTTGCCGC 59.693 50.000 0.00 0.00 0.00 6.53
1141 1283 8.094798 AGTGCGTAATCAAAAAGACATAAGAA 57.905 30.769 0.00 0.00 0.00 2.52
1142 1284 7.667043 AGTGCGTAATCAAAAAGACATAAGA 57.333 32.000 0.00 0.00 0.00 2.10
1143 1285 7.271223 CCAAGTGCGTAATCAAAAAGACATAAG 59.729 37.037 0.00 0.00 0.00 1.73
1144 1286 7.081349 CCAAGTGCGTAATCAAAAAGACATAA 58.919 34.615 0.00 0.00 0.00 1.90
1145 1287 6.348950 CCCAAGTGCGTAATCAAAAAGACATA 60.349 38.462 0.00 0.00 0.00 2.29
1146 1288 5.460646 CCAAGTGCGTAATCAAAAAGACAT 58.539 37.500 0.00 0.00 0.00 3.06
1147 1289 4.261405 CCCAAGTGCGTAATCAAAAAGACA 60.261 41.667 0.00 0.00 0.00 3.41
1148 1290 4.226761 CCCAAGTGCGTAATCAAAAAGAC 58.773 43.478 0.00 0.00 0.00 3.01
1149 1291 3.305064 GCCCAAGTGCGTAATCAAAAAGA 60.305 43.478 0.00 0.00 0.00 2.52
1162 1304 2.488153 AGAAAGTAAATCGCCCAAGTGC 59.512 45.455 0.00 0.00 0.00 4.40
1188 1334 0.037326 GTCACTGCGTCAGGGATTCA 60.037 55.000 13.60 0.00 46.09 2.57
1201 1348 5.988462 ACACTTCCAAATGCAGTGTCACTG 61.988 45.833 25.83 25.83 46.61 3.66
1202 1349 2.620115 CACTTCCAAATGCAGTGTCACT 59.380 45.455 0.00 0.00 34.39 3.41
1205 1352 3.563808 TGTACACTTCCAAATGCAGTGTC 59.436 43.478 15.76 10.59 46.61 3.67
1207 1354 4.669965 CGATGTACACTTCCAAATGCAGTG 60.670 45.833 0.00 8.60 43.12 3.66
1217 1364 2.028385 ACCAACTCCGATGTACACTTCC 60.028 50.000 0.00 0.00 0.00 3.46
1219 1366 3.764237 AACCAACTCCGATGTACACTT 57.236 42.857 0.00 0.00 0.00 3.16
1245 1392 1.001860 AGCAACAGAGCTCTCCAAGTC 59.998 52.381 14.96 1.21 42.18 3.01
1246 1393 1.055040 AGCAACAGAGCTCTCCAAGT 58.945 50.000 14.96 5.87 42.18 3.16
1247 1394 3.931768 AGCAACAGAGCTCTCCAAG 57.068 52.632 14.96 5.12 42.18 3.61
1283 1430 0.476771 TTTCGAAAGCCTGAACCCCT 59.523 50.000 6.47 0.00 0.00 4.79
1293 1440 4.440112 CCCCTATGATTTGGTTTCGAAAGC 60.440 45.833 28.47 28.47 36.95 3.51
1316 1463 1.604278 GTGAGCAACTCTGGGTGTTTC 59.396 52.381 0.00 0.00 0.00 2.78
1322 1469 1.895798 TGAGTAGTGAGCAACTCTGGG 59.104 52.381 4.32 0.00 42.17 4.45
1338 1486 0.461870 TGCGCAAACAGTCACTGAGT 60.462 50.000 13.14 0.00 35.18 3.41
1438 1837 0.745468 GACGGAAGATACGCCCTTCT 59.255 55.000 10.50 0.00 39.80 2.85
1448 1847 1.079127 CACGCCTTGGACGGAAGAT 60.079 57.895 7.97 0.00 34.00 2.40
1463 1862 1.421410 GCCATAGCTTGACGTCCACG 61.421 60.000 14.12 2.17 39.90 4.94
1469 1868 0.108186 TCACCTGCCATAGCTTGACG 60.108 55.000 0.00 0.00 40.80 4.35
1629 2035 1.380112 AGTCTCCGGGACCTGTAGC 60.380 63.158 16.57 0.00 45.54 3.58
1662 2068 2.507769 GCGCCCATCTTTGCAAGC 60.508 61.111 0.00 0.00 0.00 4.01
1665 2071 2.751436 GGAGCGCCCATCTTTGCA 60.751 61.111 2.29 0.00 34.14 4.08
1683 2089 1.890894 CACGTCATCCCTCTTCGGT 59.109 57.895 0.00 0.00 0.00 4.69
1684 2090 1.519455 GCACGTCATCCCTCTTCGG 60.519 63.158 0.00 0.00 0.00 4.30
1737 2143 1.602237 GAACCCGAAGATGAGGCCA 59.398 57.895 5.01 0.00 0.00 5.36
1848 2254 2.470286 GAGAAGAACAACGCGGCG 59.530 61.111 22.36 22.36 0.00 6.46
1909 2315 3.821033 ACAAATCAACGAAGGAAGAAGGG 59.179 43.478 0.00 0.00 0.00 3.95
1921 2327 9.655769 CTAGATAATTTCCATGACAAATCAACG 57.344 33.333 0.00 0.00 38.69 4.10
1944 2350 7.426929 ACAAGATCAGCAACAAACTAACTAG 57.573 36.000 0.00 0.00 0.00 2.57
2178 2600 2.039084 TGGAGAACCCTTGAGCTTCTTC 59.961 50.000 0.00 0.00 35.38 2.87
2206 2628 2.200170 GACACAATCTTGGTGGCCGC 62.200 60.000 8.12 8.12 38.37 6.53
2220 2642 5.989168 ACTCAACTTTATTCATGTCGACACA 59.011 36.000 22.71 7.77 36.78 3.72
2340 2762 1.148310 CAAGTACTTGGTCCGCACAG 58.852 55.000 25.19 0.00 36.95 3.66
2368 2790 5.241506 AGCACATGTTATAACAGCAACAGTT 59.758 36.000 22.03 1.68 43.04 3.16
2369 2791 4.761739 AGCACATGTTATAACAGCAACAGT 59.238 37.500 22.03 11.15 43.04 3.55
2370 2792 5.090757 CAGCACATGTTATAACAGCAACAG 58.909 41.667 22.03 10.48 43.04 3.16
2372 2794 5.046910 ACAGCACATGTTATAACAGCAAC 57.953 39.130 22.03 12.38 39.96 4.17
2373 2795 4.759183 TGACAGCACATGTTATAACAGCAA 59.241 37.500 22.03 0.26 44.17 3.91
2397 2819 6.038936 CCTTGATCATAGAAATGTGCATGACA 59.961 38.462 0.00 0.00 39.53 3.58
2413 2835 3.889815 TCCGATTTTCTGCCTTGATCAT 58.110 40.909 0.00 0.00 0.00 2.45
2420 2842 4.021102 TCTCTTTTCCGATTTTCTGCCT 57.979 40.909 0.00 0.00 0.00 4.75
2448 2870 4.637276 TCATAGAAAACGGCTGAGTTTCA 58.363 39.130 20.83 11.83 42.81 2.69
2459 2882 3.778718 CCGCACGAATTTCATAGAAAACG 59.221 43.478 15.26 15.26 0.00 3.60
2467 2890 0.600557 TTTGGCCGCACGAATTTCAT 59.399 45.000 0.00 0.00 0.00 2.57
2473 2896 0.241481 GGTATTTTTGGCCGCACGAA 59.759 50.000 0.00 0.00 0.00 3.85
2482 2905 8.517056 ACGTTAAGTGATTAAGGGTATTTTTGG 58.483 33.333 5.69 0.00 0.00 3.28
2500 2923 2.798976 TTACTGCGGACACGTTAAGT 57.201 45.000 0.00 0.00 43.45 2.24
2501 2924 2.159881 GCTTTACTGCGGACACGTTAAG 60.160 50.000 0.00 0.00 43.45 1.85
2502 2925 1.794116 GCTTTACTGCGGACACGTTAA 59.206 47.619 0.00 0.00 43.45 2.01
2503 2926 1.269673 TGCTTTACTGCGGACACGTTA 60.270 47.619 0.00 0.00 43.45 3.18
2504 2927 0.531090 TGCTTTACTGCGGACACGTT 60.531 50.000 0.00 0.00 43.45 3.99
2505 2928 0.531090 TTGCTTTACTGCGGACACGT 60.531 50.000 0.00 0.00 43.45 4.49
2506 2929 0.796312 ATTGCTTTACTGCGGACACG 59.204 50.000 0.00 0.00 44.63 4.49
2507 2930 3.000727 AGTATTGCTTTACTGCGGACAC 58.999 45.455 0.00 0.00 31.25 3.67
2508 2931 3.328382 AGTATTGCTTTACTGCGGACA 57.672 42.857 0.00 0.00 31.25 4.02
2509 2932 4.153475 TCAAAGTATTGCTTTACTGCGGAC 59.847 41.667 0.00 0.00 44.95 4.79
2510 2933 4.320023 TCAAAGTATTGCTTTACTGCGGA 58.680 39.130 0.00 0.00 44.95 5.54
2511 2934 4.437390 CCTCAAAGTATTGCTTTACTGCGG 60.437 45.833 0.00 0.00 44.95 5.69
2512 2935 4.154195 ACCTCAAAGTATTGCTTTACTGCG 59.846 41.667 0.00 0.00 44.95 5.18
2513 2936 5.629079 ACCTCAAAGTATTGCTTTACTGC 57.371 39.130 0.00 0.00 44.95 4.40
2514 2937 5.858581 GCAACCTCAAAGTATTGCTTTACTG 59.141 40.000 0.00 0.00 44.95 2.74
2515 2938 6.013842 GCAACCTCAAAGTATTGCTTTACT 57.986 37.500 0.00 0.00 44.95 2.24
2674 3122 3.589654 TTTGCTCGGCTCCGGTGAG 62.590 63.158 7.92 9.29 41.84 3.51
2687 3141 6.073222 CGATTGTCTACTTAACAAGGTTTGCT 60.073 38.462 0.00 0.00 39.78 3.91
2700 3157 4.483311 GACGACTTTCCGATTGTCTACTT 58.517 43.478 0.00 0.00 0.00 2.24
2709 3167 0.806868 TAGCACGACGACTTTCCGAT 59.193 50.000 0.00 0.00 0.00 4.18
2759 3217 0.609151 TTCTTCATCCGCGGTGGTTA 59.391 50.000 27.15 5.24 39.52 2.85
2765 3223 0.736325 ACGACTTTCTTCATCCGCGG 60.736 55.000 22.12 22.12 0.00 6.46
2769 3227 7.596995 CCTTCTGATATACGACTTTCTTCATCC 59.403 40.741 0.00 0.00 0.00 3.51
2811 3270 0.248289 GATCCGGTCTTCGTTTGGGA 59.752 55.000 0.00 0.00 37.11 4.37
2841 3345 0.457035 GTCGGTGCTGGTATTCGGTA 59.543 55.000 0.00 0.00 0.00 4.02
2848 3352 2.420568 GGATCGGTCGGTGCTGGTA 61.421 63.158 0.00 0.00 0.00 3.25
2890 3400 1.977009 ATCGTCAGAGGGCGTGTGA 60.977 57.895 2.61 2.61 0.00 3.58
3016 3526 3.327404 GAAGGGGCCCCGTTCTCA 61.327 66.667 35.78 0.00 42.84 3.27
3044 3554 0.540830 AGGTGCAGAGGTTCTCGACT 60.541 55.000 0.00 0.00 35.36 4.18
3046 3556 1.251527 GGAGGTGCAGAGGTTCTCGA 61.252 60.000 0.00 0.00 35.36 4.04
3052 3577 2.976490 GCCATGGAGGTGCAGAGGT 61.976 63.158 18.40 0.00 40.61 3.85
3115 3645 6.787085 TTAAAAGAAAAGCTCTTCTCCTCG 57.213 37.500 2.00 0.00 44.00 4.63
3138 3669 7.121315 GTCCAAGCAACCTGAAAGTATATTCTT 59.879 37.037 0.00 0.00 0.00 2.52
3141 3672 6.245408 TGTCCAAGCAACCTGAAAGTATATT 58.755 36.000 0.00 0.00 0.00 1.28
3142 3673 5.815581 TGTCCAAGCAACCTGAAAGTATAT 58.184 37.500 0.00 0.00 0.00 0.86
3143 3674 5.235850 TGTCCAAGCAACCTGAAAGTATA 57.764 39.130 0.00 0.00 0.00 1.47
3144 3675 4.098914 TGTCCAAGCAACCTGAAAGTAT 57.901 40.909 0.00 0.00 0.00 2.12
3145 3676 3.569194 TGTCCAAGCAACCTGAAAGTA 57.431 42.857 0.00 0.00 0.00 2.24
3146 3677 2.435372 TGTCCAAGCAACCTGAAAGT 57.565 45.000 0.00 0.00 0.00 2.66
3147 3678 3.131046 AGTTTGTCCAAGCAACCTGAAAG 59.869 43.478 0.00 0.00 0.00 2.62
3148 3679 3.096092 AGTTTGTCCAAGCAACCTGAAA 58.904 40.909 0.00 0.00 0.00 2.69
3149 3680 2.733956 AGTTTGTCCAAGCAACCTGAA 58.266 42.857 0.00 0.00 0.00 3.02
3150 3681 2.435372 AGTTTGTCCAAGCAACCTGA 57.565 45.000 0.00 0.00 0.00 3.86
3151 3682 4.278170 TGAATAGTTTGTCCAAGCAACCTG 59.722 41.667 0.00 0.00 0.00 4.00
3152 3683 4.469657 TGAATAGTTTGTCCAAGCAACCT 58.530 39.130 0.00 0.00 0.00 3.50
3153 3684 4.846779 TGAATAGTTTGTCCAAGCAACC 57.153 40.909 0.00 0.00 0.00 3.77
3154 3685 5.587289 TGTTGAATAGTTTGTCCAAGCAAC 58.413 37.500 0.00 0.00 35.10 4.17
3155 3686 5.359576 ACTGTTGAATAGTTTGTCCAAGCAA 59.640 36.000 0.00 0.00 0.00 3.91
3156 3687 4.887071 ACTGTTGAATAGTTTGTCCAAGCA 59.113 37.500 0.00 0.00 0.00 3.91
3157 3688 5.438761 ACTGTTGAATAGTTTGTCCAAGC 57.561 39.130 0.00 0.00 0.00 4.01
3158 3689 8.702163 AAAAACTGTTGAATAGTTTGTCCAAG 57.298 30.769 18.54 0.00 44.98 3.61


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

AutoCloner maintained by Alex Coulton.