Multiple sequence alignment - TraesCS7D01G122800

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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 TraesCS7D01G122800 chr7D 100.000 4160 0 0 1 4160 76783258 76787417 0.000000e+00 7683.0
1 TraesCS7D01G122800 chr7D 85.536 3284 414 44 802 4064 76743450 76746693 0.000000e+00 3376.0
2 TraesCS7D01G122800 chr7D 85.484 3286 390 56 828 4077 76919223 76922457 0.000000e+00 3345.0
3 TraesCS7D01G122800 chr7D 85.266 2199 290 25 1900 4073 76973468 76975657 0.000000e+00 2235.0
4 TraesCS7D01G122800 chr7D 83.613 2325 346 25 1762 4059 76930733 76933049 0.000000e+00 2150.0
5 TraesCS7D01G122800 chr7D 86.540 1835 224 18 2238 4059 77045885 77047709 0.000000e+00 1999.0
6 TraesCS7D01G122800 chr7D 84.347 2038 265 25 2136 4160 76955733 76957729 0.000000e+00 1947.0
7 TraesCS7D01G122800 chr7D 81.616 1980 319 30 1738 3693 76624395 76622437 0.000000e+00 1598.0
8 TraesCS7D01G122800 chr7D 83.170 1634 254 16 981 2596 7548438 7550068 0.000000e+00 1474.0
9 TraesCS7D01G122800 chr7D 85.569 1081 85 26 542 1590 77038204 77039245 0.000000e+00 1066.0
10 TraesCS7D01G122800 chr7D 84.112 428 29 14 47 440 77037751 77038173 1.090000e-100 377.0
11 TraesCS7D01G122800 chr7D 87.705 244 10 5 1 234 76929177 76929410 2.470000e-67 267.0
12 TraesCS7D01G122800 chr7D 82.558 86 1 5 247 329 76929441 76929515 3.470000e-06 63.9
13 TraesCS7D01G122800 chr7B 87.225 3272 379 21 802 4059 23596595 23599841 0.000000e+00 3690.0
14 TraesCS7D01G122800 chr7B 88.037 3001 341 8 1091 4081 23958164 23961156 0.000000e+00 3537.0
15 TraesCS7D01G122800 chr7B 84.622 2315 317 24 1773 4059 23516992 23519295 0.000000e+00 2266.0
16 TraesCS7D01G122800 chr7B 82.819 2334 319 49 1762 4077 23934190 23936459 0.000000e+00 2013.0
17 TraesCS7D01G122800 chr7B 84.669 1859 241 22 833 2674 23582227 23584058 0.000000e+00 1814.0
18 TraesCS7D01G122800 chr7B 85.149 1313 183 11 2774 4081 23639655 23640960 0.000000e+00 1334.0
19 TraesCS7D01G122800 chr7A 85.803 3381 422 42 802 4160 80861875 80865219 0.000000e+00 3531.0
20 TraesCS7D01G122800 chr4A 82.380 1731 278 14 961 2674 731616812 731615092 0.000000e+00 1482.0
21 TraesCS7D01G122800 chr3B 82.937 1641 259 11 981 2603 741463218 741464855 0.000000e+00 1459.0
22 TraesCS7D01G122800 chr1B 94.074 270 13 2 24 290 136624547 136624816 1.390000e-109 407.0
23 TraesCS7D01G122800 chr5B 96.429 168 5 1 124 290 659982678 659982845 4.100000e-70 276.0


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 TraesCS7D01G122800 chr7D 76783258 76787417 4159 False 7683.000000 7683 100.000000 1 4160 1 chr7D.!!$F3 4159
1 TraesCS7D01G122800 chr7D 76743450 76746693 3243 False 3376.000000 3376 85.536000 802 4064 1 chr7D.!!$F2 3262
2 TraesCS7D01G122800 chr7D 76919223 76922457 3234 False 3345.000000 3345 85.484000 828 4077 1 chr7D.!!$F4 3249
3 TraesCS7D01G122800 chr7D 76973468 76975657 2189 False 2235.000000 2235 85.266000 1900 4073 1 chr7D.!!$F6 2173
4 TraesCS7D01G122800 chr7D 77045885 77047709 1824 False 1999.000000 1999 86.540000 2238 4059 1 chr7D.!!$F7 1821
5 TraesCS7D01G122800 chr7D 76955733 76957729 1996 False 1947.000000 1947 84.347000 2136 4160 1 chr7D.!!$F5 2024
6 TraesCS7D01G122800 chr7D 76622437 76624395 1958 True 1598.000000 1598 81.616000 1738 3693 1 chr7D.!!$R1 1955
7 TraesCS7D01G122800 chr7D 7548438 7550068 1630 False 1474.000000 1474 83.170000 981 2596 1 chr7D.!!$F1 1615
8 TraesCS7D01G122800 chr7D 76929177 76933049 3872 False 826.966667 2150 84.625333 1 4059 3 chr7D.!!$F8 4058
9 TraesCS7D01G122800 chr7D 77037751 77039245 1494 False 721.500000 1066 84.840500 47 1590 2 chr7D.!!$F9 1543
10 TraesCS7D01G122800 chr7B 23596595 23599841 3246 False 3690.000000 3690 87.225000 802 4059 1 chr7B.!!$F3 3257
11 TraesCS7D01G122800 chr7B 23958164 23961156 2992 False 3537.000000 3537 88.037000 1091 4081 1 chr7B.!!$F6 2990
12 TraesCS7D01G122800 chr7B 23516992 23519295 2303 False 2266.000000 2266 84.622000 1773 4059 1 chr7B.!!$F1 2286
13 TraesCS7D01G122800 chr7B 23934190 23936459 2269 False 2013.000000 2013 82.819000 1762 4077 1 chr7B.!!$F5 2315
14 TraesCS7D01G122800 chr7B 23582227 23584058 1831 False 1814.000000 1814 84.669000 833 2674 1 chr7B.!!$F2 1841
15 TraesCS7D01G122800 chr7B 23639655 23640960 1305 False 1334.000000 1334 85.149000 2774 4081 1 chr7B.!!$F4 1307
16 TraesCS7D01G122800 chr7A 80861875 80865219 3344 False 3531.000000 3531 85.803000 802 4160 1 chr7A.!!$F1 3358
17 TraesCS7D01G122800 chr4A 731615092 731616812 1720 True 1482.000000 1482 82.380000 961 2674 1 chr4A.!!$R1 1713
18 TraesCS7D01G122800 chr3B 741463218 741464855 1637 False 1459.000000 1459 82.937000 981 2603 1 chr3B.!!$F1 1622

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
765 813 0.188834 AGTAATCCCCTCCTCTCCCG 59.811 60.0 0.00 0.00 0.00 5.14 F
795 843 0.463833 CCGGACTTGGCAGTAATCCC 60.464 60.0 0.00 0.00 31.22 3.85 F
1329 1427 0.729116 GCTACATCACGCATTGCAGT 59.271 50.0 9.69 4.95 0.00 4.40 F
2684 2851 0.379669 GCTCCTTCATTGATGTGCCG 59.620 55.0 0.00 0.00 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2643 2810 0.981183 ACAAAGTGCGGGGAGATGTA 59.019 50.000 0.00 0.00 0.0 2.29 R
2684 2851 1.534163 GTGACAGCCGTTTAAACTCCC 59.466 52.381 16.01 4.54 0.0 4.30 R
2961 3135 1.086696 CAATGTTTCGAGGCATCCGT 58.913 50.000 0.00 0.00 0.0 4.69 R
3659 3844 0.250770 GGTCTTTGAGAACGGGGCTT 60.251 55.000 0.00 0.00 0.0 4.35 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
145 152 1.510480 GACAAGCACAGCACAGGGAC 61.510 60.000 0.00 0.00 0.00 4.46
227 238 1.275657 CGGTTCACGCTGTTCACAC 59.724 57.895 0.00 0.00 34.82 3.82
275 317 5.822519 GGTGTTGTCAGGATCAGCATTATTA 59.177 40.000 0.00 0.00 0.00 0.98
276 318 6.238484 GGTGTTGTCAGGATCAGCATTATTAC 60.238 42.308 0.00 0.00 0.00 1.89
277 319 5.822519 TGTTGTCAGGATCAGCATTATTACC 59.177 40.000 0.00 0.00 0.00 2.85
278 320 4.631131 TGTCAGGATCAGCATTATTACCG 58.369 43.478 0.00 0.00 0.00 4.02
279 321 3.433615 GTCAGGATCAGCATTATTACCGC 59.566 47.826 0.00 0.00 0.00 5.68
280 322 3.070878 TCAGGATCAGCATTATTACCGCA 59.929 43.478 0.00 0.00 0.00 5.69
281 323 3.434641 CAGGATCAGCATTATTACCGCAG 59.565 47.826 0.00 0.00 0.00 5.18
282 324 3.071602 AGGATCAGCATTATTACCGCAGT 59.928 43.478 0.00 0.00 0.00 4.40
283 325 3.187227 GGATCAGCATTATTACCGCAGTG 59.813 47.826 0.00 0.00 0.00 3.66
284 326 3.260475 TCAGCATTATTACCGCAGTGT 57.740 42.857 0.00 0.00 0.00 3.55
285 327 3.605634 TCAGCATTATTACCGCAGTGTT 58.394 40.909 0.00 0.00 0.00 3.32
286 328 4.006989 TCAGCATTATTACCGCAGTGTTT 58.993 39.130 0.00 0.00 0.00 2.83
289 331 4.094887 AGCATTATTACCGCAGTGTTTCAG 59.905 41.667 0.00 0.00 0.00 3.02
329 374 8.046708 TCCTAAGTGCAAGATTAGCAAGAAATA 58.953 33.333 8.42 0.00 44.64 1.40
402 450 9.635404 TTACTGGAAATTAGTCTCCTTCAAAAA 57.365 29.630 0.00 0.00 32.51 1.94
403 451 8.171164 ACTGGAAATTAGTCTCCTTCAAAAAG 57.829 34.615 0.00 0.00 32.51 2.27
442 490 7.611467 TCATGTTGCTAATACCATGACTTCTTT 59.389 33.333 0.00 0.00 38.90 2.52
444 492 8.177119 TGTTGCTAATACCATGACTTCTTTTT 57.823 30.769 0.00 0.00 0.00 1.94
470 518 8.561738 TGAAAAGAACATATTTAGTGAGGACC 57.438 34.615 0.00 0.00 0.00 4.46
471 519 7.610305 TGAAAAGAACATATTTAGTGAGGACCC 59.390 37.037 0.00 0.00 0.00 4.46
472 520 6.636454 AAGAACATATTTAGTGAGGACCCA 57.364 37.500 0.00 0.00 0.00 4.51
473 521 6.636454 AGAACATATTTAGTGAGGACCCAA 57.364 37.500 0.00 0.00 0.00 4.12
474 522 7.027874 AGAACATATTTAGTGAGGACCCAAA 57.972 36.000 0.00 0.00 0.00 3.28
475 523 7.466804 AGAACATATTTAGTGAGGACCCAAAA 58.533 34.615 0.00 0.00 0.00 2.44
476 524 7.947890 AGAACATATTTAGTGAGGACCCAAAAA 59.052 33.333 0.00 0.00 0.00 1.94
477 525 8.664669 AACATATTTAGTGAGGACCCAAAAAT 57.335 30.769 0.00 0.04 0.00 1.82
478 526 8.664669 ACATATTTAGTGAGGACCCAAAAATT 57.335 30.769 0.00 0.00 0.00 1.82
479 527 9.762381 ACATATTTAGTGAGGACCCAAAAATTA 57.238 29.630 0.00 0.00 0.00 1.40
484 532 9.990360 TTTAGTGAGGACCCAAAAATTAAATTC 57.010 29.630 0.00 0.00 0.00 2.17
485 533 7.610580 AGTGAGGACCCAAAAATTAAATTCA 57.389 32.000 0.00 0.00 0.00 2.57
486 534 7.670364 AGTGAGGACCCAAAAATTAAATTCAG 58.330 34.615 0.00 0.00 0.00 3.02
487 535 7.508977 AGTGAGGACCCAAAAATTAAATTCAGA 59.491 33.333 0.00 0.00 0.00 3.27
488 536 8.147704 GTGAGGACCCAAAAATTAAATTCAGAA 58.852 33.333 0.00 0.00 0.00 3.02
489 537 8.879227 TGAGGACCCAAAAATTAAATTCAGAAT 58.121 29.630 0.00 0.00 0.00 2.40
490 538 9.725019 GAGGACCCAAAAATTAAATTCAGAATT 57.275 29.630 2.20 2.20 0.00 2.17
491 539 9.506018 AGGACCCAAAAATTAAATTCAGAATTG 57.494 29.630 9.24 0.00 0.00 2.32
492 540 9.500785 GGACCCAAAAATTAAATTCAGAATTGA 57.499 29.630 9.24 0.00 0.00 2.57
526 574 8.729805 ACTGAGAAATCTATGAAACTGATTCC 57.270 34.615 0.00 0.00 37.22 3.01
528 576 9.170734 CTGAGAAATCTATGAAACTGATTCCAA 57.829 33.333 0.00 0.00 37.22 3.53
560 608 8.916628 TCATCATCATTATACAATTCGGGAAA 57.083 30.769 0.00 0.00 0.00 3.13
563 611 7.592938 TCATCATTATACAATTCGGGAAATGC 58.407 34.615 0.00 0.00 0.00 3.56
569 617 2.161609 ACAATTCGGGAAATGCGTCTTC 59.838 45.455 0.00 0.00 0.00 2.87
586 634 5.622856 GCGTCTTCTGTCAAAAATTGAGAAG 59.377 40.000 12.39 12.39 40.51 2.85
613 661 6.598753 ATTATACGAAATCCTGTGAAACCG 57.401 37.500 0.00 0.00 34.36 4.44
619 667 1.742761 ATCCTGTGAAACCGCTGATG 58.257 50.000 0.00 0.00 34.36 3.07
668 716 1.079987 AGAAGAGAGCAGGGGAGCA 59.920 57.895 0.00 0.00 36.85 4.26
681 729 0.603975 GGGAGCACGCTGAAGAGTTT 60.604 55.000 0.00 0.00 0.00 2.66
683 731 2.413837 GGAGCACGCTGAAGAGTTTAA 58.586 47.619 0.00 0.00 0.00 1.52
685 733 3.060602 GAGCACGCTGAAGAGTTTAACT 58.939 45.455 0.00 0.00 0.00 2.24
687 735 2.544267 GCACGCTGAAGAGTTTAACTGT 59.456 45.455 0.93 0.00 0.00 3.55
688 736 3.002348 GCACGCTGAAGAGTTTAACTGTT 59.998 43.478 7.22 7.22 34.11 3.16
690 738 5.277154 GCACGCTGAAGAGTTTAACTGTTTA 60.277 40.000 8.86 4.31 31.32 2.01
692 740 6.846283 CACGCTGAAGAGTTTAACTGTTTAAG 59.154 38.462 8.86 10.47 31.32 1.85
693 741 6.018180 ACGCTGAAGAGTTTAACTGTTTAAGG 60.018 38.462 8.86 2.94 31.32 2.69
694 742 6.143496 GCTGAAGAGTTTAACTGTTTAAGGC 58.857 40.000 8.86 7.51 31.32 4.35
695 743 6.295039 TGAAGAGTTTAACTGTTTAAGGCG 57.705 37.500 8.86 0.00 31.32 5.52
696 744 5.818857 TGAAGAGTTTAACTGTTTAAGGCGT 59.181 36.000 8.86 0.00 31.32 5.68
721 769 5.509670 CGGCAGAGTTATTATCTCCATGTCA 60.510 44.000 0.00 0.00 32.93 3.58
725 773 8.844244 GCAGAGTTATTATCTCCATGTCATTTT 58.156 33.333 0.00 0.00 32.93 1.82
765 813 0.188834 AGTAATCCCCTCCTCTCCCG 59.811 60.000 0.00 0.00 0.00 5.14
766 814 1.152312 TAATCCCCTCCTCTCCCGC 60.152 63.158 0.00 0.00 0.00 6.13
767 815 2.674672 TAATCCCCTCCTCTCCCGCC 62.675 65.000 0.00 0.00 0.00 6.13
795 843 0.463833 CCGGACTTGGCAGTAATCCC 60.464 60.000 0.00 0.00 31.22 3.85
796 844 0.463833 CGGACTTGGCAGTAATCCCC 60.464 60.000 0.00 0.00 31.22 4.81
797 845 0.919710 GGACTTGGCAGTAATCCCCT 59.080 55.000 0.00 0.00 31.22 4.79
798 846 1.134068 GGACTTGGCAGTAATCCCCTC 60.134 57.143 0.00 0.00 31.22 4.30
799 847 0.919710 ACTTGGCAGTAATCCCCTCC 59.080 55.000 0.00 0.00 0.00 4.30
800 848 1.216990 CTTGGCAGTAATCCCCTCCT 58.783 55.000 0.00 0.00 0.00 3.69
874 932 2.202987 GGTGCATGCTCTCCTCCG 60.203 66.667 20.33 0.00 0.00 4.63
907 985 7.823745 TCTTGGCTGTATTTCTTTCTTCTTT 57.176 32.000 0.00 0.00 0.00 2.52
936 1024 2.418471 CCTCTGTCAGTGCTGAATCCTC 60.418 54.545 3.19 0.00 41.85 3.71
1135 1227 2.501128 GCCATCTGCTAGCCGTCA 59.499 61.111 13.29 0.00 36.87 4.35
1150 1242 1.008538 GTCAAGTGCAAGTTGGCCG 60.009 57.895 4.75 0.00 45.88 6.13
1297 1395 1.079127 ATCGGCAAGTCCACTTCCG 60.079 57.895 17.35 17.35 42.48 4.30
1323 1421 1.029681 TACTCGGCTACATCACGCAT 58.970 50.000 0.00 0.00 0.00 4.73
1329 1427 0.729116 GCTACATCACGCATTGCAGT 59.271 50.000 9.69 4.95 0.00 4.40
1401 1499 3.795688 AAGATCAAGGAGCTGGTTGAA 57.204 42.857 10.58 0.00 36.31 2.69
1425 1523 3.896888 AGATGAACATGTTTGGCCTTGAA 59.103 39.130 13.36 0.00 0.00 2.69
1492 1590 1.341531 ACTCCAAACTGGACGAGTCTG 59.658 52.381 3.09 0.00 42.67 3.51
1533 1631 3.516586 TGATGACAAGAAGAGGGTGGTA 58.483 45.455 0.00 0.00 0.00 3.25
1534 1632 3.515502 TGATGACAAGAAGAGGGTGGTAG 59.484 47.826 0.00 0.00 0.00 3.18
1644 1742 5.441718 AGATGGTGTACAATGACCAAGAT 57.558 39.130 6.99 0.00 45.36 2.40
1675 1773 5.612725 ACATTTCCAGTTGAAAATGTGGT 57.387 34.783 8.40 0.00 45.67 4.16
1683 1781 4.212425 CAGTTGAAAATGTGGTACTGCGTA 59.788 41.667 0.00 0.00 0.00 4.42
1695 1793 4.868171 TGGTACTGCGTATCAGACAATTTC 59.132 41.667 0.00 0.00 45.72 2.17
1696 1794 4.868171 GGTACTGCGTATCAGACAATTTCA 59.132 41.667 0.00 0.00 45.72 2.69
1734 1832 5.046520 TGTGAAATCCATCATTGAATTGGCA 60.047 36.000 1.97 0.00 0.00 4.92
1801 1935 7.144000 GCAGAAGAAACTTGATGAAGTCATTT 58.856 34.615 0.00 0.00 41.87 2.32
1811 1948 2.151202 TGAAGTCATTTGCCGGAAGAC 58.849 47.619 5.05 0.00 0.00 3.01
1866 2003 4.186077 AGAGAAGACGATATGGGAGGAA 57.814 45.455 0.00 0.00 0.00 3.36
1869 2006 5.604650 AGAGAAGACGATATGGGAGGAAAAT 59.395 40.000 0.00 0.00 0.00 1.82
1910 2047 2.836154 TGGTGGACCAGGAAGTGC 59.164 61.111 0.00 0.00 42.01 4.40
1933 2070 1.139989 AGTTGTGACATGTCGAAGCG 58.860 50.000 20.54 0.00 0.00 4.68
1963 2100 4.097741 TGGCAACTATAATGTGCACCATTC 59.902 41.667 15.69 1.18 40.33 2.67
1977 2114 2.493278 CACCATTCAGCCCCTTAAGTTG 59.507 50.000 0.97 0.00 0.00 3.16
2082 2219 3.056393 TCACCATCGGAAGACGTATTGTT 60.056 43.478 0.00 0.00 46.97 2.83
2134 2271 3.004752 AGACAATGGGTGGATTGCTAC 57.995 47.619 0.00 0.00 36.89 3.58
2181 2318 3.433740 GGAAGGCCATCGAAGGAAGTAAT 60.434 47.826 11.67 0.00 0.00 1.89
2320 2457 6.260493 GGATTATGAGATGCAGAAGGATATGC 59.740 42.308 0.00 0.00 42.86 3.14
2425 2562 3.140144 TGAATTGGTTTGGAGGTCCTTCT 59.860 43.478 0.00 0.00 36.82 2.85
2561 2716 9.350357 CACCATAGAAGAATTGATTGAACAAAG 57.650 33.333 0.00 0.00 33.44 2.77
2684 2851 0.379669 GCTCCTTCATTGATGTGCCG 59.620 55.000 0.00 0.00 0.00 5.69
2688 2855 1.019673 CTTCATTGATGTGCCGGGAG 58.980 55.000 2.18 0.00 0.00 4.30
2811 2985 2.128035 CTCTCCAGTTGTGACGTCAAC 58.872 52.381 21.95 16.08 45.33 3.18
2837 3011 5.557576 AGATTGCTAGATTCAGTATGCCA 57.442 39.130 0.00 0.00 34.76 4.92
2878 3052 4.332543 CGTTGAGGCTGAATAATTGCACTA 59.667 41.667 0.00 0.00 0.00 2.74
2887 3061 6.258727 GCTGAATAATTGCACTAAGCTACAGA 59.741 38.462 0.00 0.00 45.94 3.41
2961 3135 5.250543 TCTTTCTGGATGTGATAAGTTGGGA 59.749 40.000 0.00 0.00 0.00 4.37
3150 3326 1.283347 AGCCAATCTCCAGCAGAAGA 58.717 50.000 0.00 0.00 33.62 2.87
3158 3334 6.600822 CCAATCTCCAGCAGAAGAAAAATCTA 59.399 38.462 0.00 0.00 33.62 1.98
3210 3395 3.963129 AGATTTGGCAGGACCGAAAATA 58.037 40.909 0.00 0.00 45.40 1.40
3266 3451 5.131642 TCAAGAACCTCATAGCAAGATCCAT 59.868 40.000 0.00 0.00 0.00 3.41
3268 3453 6.357579 AGAACCTCATAGCAAGATCCATAG 57.642 41.667 0.00 0.00 0.00 2.23
3273 3458 8.034313 ACCTCATAGCAAGATCCATAGTTTTA 57.966 34.615 0.00 0.00 0.00 1.52
3321 3506 1.852633 ACCACGATGGATGAGAGACA 58.147 50.000 10.46 0.00 40.96 3.41
3349 3534 8.031864 TCAAATGTTTCAGTGCTTAAGAAAACA 58.968 29.630 6.67 13.07 33.54 2.83
3367 3552 8.472007 AGAAAACACATAATTACCAACTGGAA 57.528 30.769 1.86 0.00 38.94 3.53
3413 3598 1.194781 GGCTCTCACCCTCACTGGAA 61.195 60.000 0.00 0.00 38.35 3.53
3440 3625 6.543465 TCTTATGCTTGATCAACATGGGTAAG 59.457 38.462 22.83 19.06 0.00 2.34
3461 3646 9.277783 GGTAAGCTGAAGACATTATGTGATAAT 57.722 33.333 1.24 0.00 35.92 1.28
3482 3667 2.239654 TCTTTGCATAGAAGGTGGAGGG 59.760 50.000 4.20 0.00 0.00 4.30
3593 3778 0.807667 GTGTGGCCACTGATAGCTCG 60.808 60.000 34.75 0.00 38.61 5.03
3659 3844 4.825085 CCTAAGGTTGCAAGTTTTCCACTA 59.175 41.667 0.00 0.00 32.94 2.74
3896 4104 0.108567 GCCTCACTTCTCTTCGGGAC 60.109 60.000 0.00 0.00 0.00 4.46
3900 4108 2.297597 CTCACTTCTCTTCGGGACTTGT 59.702 50.000 0.00 0.00 0.00 3.16
3906 4114 0.902531 TCTTCGGGACTTGTGGATCC 59.097 55.000 4.20 4.20 0.00 3.36
4011 4219 1.726791 CCGAGTTGGAAAGACGATGTG 59.273 52.381 0.00 0.00 42.00 3.21
4022 4230 0.608640 GACGATGTGGAGAAGGTGGT 59.391 55.000 0.00 0.00 0.00 4.16
4066 4274 3.315191 CCTATCCCAGTTAAACGCATTGG 59.685 47.826 0.00 0.00 0.00 3.16
4081 4289 3.374988 CGCATTGGAGCAGAGTCAAAATA 59.625 43.478 0.00 0.00 0.00 1.40
4082 4290 4.036027 CGCATTGGAGCAGAGTCAAAATAT 59.964 41.667 0.00 0.00 0.00 1.28
4091 4299 6.951971 AGCAGAGTCAAAATATAGAACTGGT 58.048 36.000 0.00 0.00 0.00 4.00
4125 4351 2.803030 AGCAGAAGCAGAATCCACAT 57.197 45.000 0.00 0.00 45.49 3.21
4133 4359 6.261603 CAGAAGCAGAATCCACATTTATAGCA 59.738 38.462 0.00 0.00 0.00 3.49
4134 4360 6.261826 AGAAGCAGAATCCACATTTATAGCAC 59.738 38.462 0.00 0.00 0.00 4.40
4135 4361 4.512944 AGCAGAATCCACATTTATAGCACG 59.487 41.667 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.338118 TGCTGGTTTTGAGGTGAAAGTAAG 59.662 41.667 0.00 0.00 0.00 2.34
10 11 2.942804 TGAATGCTGGTTTTGAGGTGA 58.057 42.857 0.00 0.00 0.00 4.02
11 12 3.581755 CATGAATGCTGGTTTTGAGGTG 58.418 45.455 0.00 0.00 0.00 4.00
12 13 3.947910 CATGAATGCTGGTTTTGAGGT 57.052 42.857 0.00 0.00 0.00 3.85
51 53 2.669133 CCACCGGGAAGATGCCTGA 61.669 63.158 6.32 0.00 36.35 3.86
145 152 0.900421 TCATCTCTCCAGCACCACTG 59.100 55.000 0.00 0.00 46.77 3.66
227 238 2.043411 CACGGTGTTTGCATCTTTTCG 58.957 47.619 0.00 0.00 0.00 3.46
275 317 1.001378 GAATTGCTGAAACACTGCGGT 60.001 47.619 0.00 0.00 44.53 5.68
276 318 1.267806 AGAATTGCTGAAACACTGCGG 59.732 47.619 0.00 0.00 44.53 5.69
277 319 2.693797 AGAATTGCTGAAACACTGCG 57.306 45.000 0.00 0.00 44.53 5.18
289 331 3.691609 CACTTAGGAGGGTTCAGAATTGC 59.308 47.826 0.00 0.00 0.00 3.56
298 340 4.626529 GCTAATCTTGCACTTAGGAGGGTT 60.627 45.833 10.34 0.00 0.00 4.11
333 378 8.560039 TCCCAAAACTAGTACTCCTATACAGTA 58.440 37.037 0.00 0.00 0.00 2.74
335 380 7.778853 TCTCCCAAAACTAGTACTCCTATACAG 59.221 40.741 0.00 0.00 0.00 2.74
336 381 7.645942 TCTCCCAAAACTAGTACTCCTATACA 58.354 38.462 0.00 0.00 0.00 2.29
337 382 8.709272 ATCTCCCAAAACTAGTACTCCTATAC 57.291 38.462 0.00 0.00 0.00 1.47
340 385 8.445361 AAAATCTCCCAAAACTAGTACTCCTA 57.555 34.615 0.00 0.00 0.00 2.94
341 386 6.954352 AAATCTCCCAAAACTAGTACTCCT 57.046 37.500 0.00 0.00 0.00 3.69
342 387 8.319881 ACTAAAATCTCCCAAAACTAGTACTCC 58.680 37.037 0.00 0.00 0.00 3.85
371 416 8.667592 AAGGAGACTAATTTCCAGTAACTAGT 57.332 34.615 0.00 0.00 42.68 2.57
379 427 8.171164 ACTTTTTGAAGGAGACTAATTTCCAG 57.829 34.615 0.00 0.00 42.68 3.86
444 492 9.010029 GGTCCTCACTAAATATGTTCTTTTCAA 57.990 33.333 0.00 0.00 0.00 2.69
446 494 7.610305 TGGGTCCTCACTAAATATGTTCTTTTC 59.390 37.037 0.00 0.00 0.00 2.29
449 497 6.636454 TGGGTCCTCACTAAATATGTTCTT 57.364 37.500 0.00 0.00 0.00 2.52
450 498 6.636454 TTGGGTCCTCACTAAATATGTTCT 57.364 37.500 0.00 0.00 0.00 3.01
451 499 7.696992 TTTTGGGTCCTCACTAAATATGTTC 57.303 36.000 0.00 0.00 0.00 3.18
453 501 8.664669 AATTTTTGGGTCCTCACTAAATATGT 57.335 30.769 0.00 0.00 0.00 2.29
458 506 9.990360 GAATTTAATTTTTGGGTCCTCACTAAA 57.010 29.630 0.00 0.00 0.00 1.85
459 507 9.148879 TGAATTTAATTTTTGGGTCCTCACTAA 57.851 29.630 0.00 0.00 0.00 2.24
460 508 8.713708 TGAATTTAATTTTTGGGTCCTCACTA 57.286 30.769 0.00 0.00 0.00 2.74
461 509 7.508977 TCTGAATTTAATTTTTGGGTCCTCACT 59.491 33.333 0.00 0.00 0.00 3.41
462 510 7.666623 TCTGAATTTAATTTTTGGGTCCTCAC 58.333 34.615 0.00 0.00 0.00 3.51
463 511 7.847711 TCTGAATTTAATTTTTGGGTCCTCA 57.152 32.000 0.00 0.00 0.00 3.86
464 512 9.725019 AATTCTGAATTTAATTTTTGGGTCCTC 57.275 29.630 9.76 0.00 0.00 3.71
465 513 9.506018 CAATTCTGAATTTAATTTTTGGGTCCT 57.494 29.630 12.74 0.00 0.00 3.85
466 514 9.500785 TCAATTCTGAATTTAATTTTTGGGTCC 57.499 29.630 12.74 0.00 0.00 4.46
500 548 9.171877 GGAATCAGTTTCATAGATTTCTCAGTT 57.828 33.333 0.00 0.00 35.94 3.16
501 549 8.324306 TGGAATCAGTTTCATAGATTTCTCAGT 58.676 33.333 0.00 0.00 35.94 3.41
502 550 8.728337 TGGAATCAGTTTCATAGATTTCTCAG 57.272 34.615 0.00 0.00 35.94 3.35
503 551 9.519191 TTTGGAATCAGTTTCATAGATTTCTCA 57.481 29.630 0.00 0.00 35.94 3.27
532 580 9.519191 TCCCGAATTGTATAATGATGATGAATT 57.481 29.630 0.00 0.00 0.00 2.17
533 581 9.519191 TTCCCGAATTGTATAATGATGATGAAT 57.481 29.630 0.00 0.00 0.00 2.57
535 583 8.916628 TTTCCCGAATTGTATAATGATGATGA 57.083 30.769 0.00 0.00 0.00 2.92
536 584 9.563898 CATTTCCCGAATTGTATAATGATGATG 57.436 33.333 0.00 0.00 0.00 3.07
537 585 8.246180 GCATTTCCCGAATTGTATAATGATGAT 58.754 33.333 0.00 0.00 0.00 2.45
539 587 6.524239 CGCATTTCCCGAATTGTATAATGATG 59.476 38.462 0.00 0.00 0.00 3.07
540 588 6.206634 ACGCATTTCCCGAATTGTATAATGAT 59.793 34.615 0.00 0.00 0.00 2.45
541 589 5.529430 ACGCATTTCCCGAATTGTATAATGA 59.471 36.000 0.00 0.00 0.00 2.57
543 591 5.763204 AGACGCATTTCCCGAATTGTATAAT 59.237 36.000 0.00 0.00 0.00 1.28
544 592 5.120399 AGACGCATTTCCCGAATTGTATAA 58.880 37.500 0.00 0.00 0.00 0.98
545 593 4.699637 AGACGCATTTCCCGAATTGTATA 58.300 39.130 0.00 0.00 0.00 1.47
546 594 3.541632 AGACGCATTTCCCGAATTGTAT 58.458 40.909 0.00 0.00 0.00 2.29
547 595 2.980568 AGACGCATTTCCCGAATTGTA 58.019 42.857 0.00 0.00 0.00 2.41
548 596 1.821216 AGACGCATTTCCCGAATTGT 58.179 45.000 0.00 0.00 0.00 2.71
549 597 2.420022 AGAAGACGCATTTCCCGAATTG 59.580 45.455 0.00 0.00 0.00 2.32
560 608 5.239306 TCTCAATTTTTGACAGAAGACGCAT 59.761 36.000 0.00 0.00 35.46 4.73
563 611 6.719365 ACTTCTCAATTTTTGACAGAAGACG 58.281 36.000 18.46 3.71 41.11 4.18
586 634 9.712359 GGTTTCACAGGATTTCGTATAATTAAC 57.288 33.333 0.00 0.00 0.00 2.01
590 638 5.007332 GCGGTTTCACAGGATTTCGTATAAT 59.993 40.000 0.00 0.00 0.00 1.28
603 651 3.354089 AAAACATCAGCGGTTTCACAG 57.646 42.857 0.00 0.00 37.47 3.66
604 652 3.791973 AAAAACATCAGCGGTTTCACA 57.208 38.095 0.00 0.00 37.47 3.58
643 691 2.183679 CCCTGCTCTCTTCTGTACCTT 58.816 52.381 0.00 0.00 0.00 3.50
668 716 6.018180 CCTTAAACAGTTAAACTCTTCAGCGT 60.018 38.462 0.00 0.00 0.00 5.07
681 729 1.270199 TGCCGACGCCTTAAACAGTTA 60.270 47.619 0.00 0.00 0.00 2.24
683 731 0.949105 CTGCCGACGCCTTAAACAGT 60.949 55.000 0.00 0.00 0.00 3.55
685 733 0.669318 CTCTGCCGACGCCTTAAACA 60.669 55.000 0.00 0.00 0.00 2.83
687 735 0.034337 AACTCTGCCGACGCCTTAAA 59.966 50.000 0.00 0.00 0.00 1.52
688 736 0.889994 TAACTCTGCCGACGCCTTAA 59.110 50.000 0.00 0.00 0.00 1.85
690 738 0.249398 AATAACTCTGCCGACGCCTT 59.751 50.000 0.00 0.00 0.00 4.35
692 740 2.059541 GATAATAACTCTGCCGACGCC 58.940 52.381 0.00 0.00 0.00 5.68
693 741 2.981140 GAGATAATAACTCTGCCGACGC 59.019 50.000 0.00 0.00 0.00 5.19
694 742 3.004419 TGGAGATAATAACTCTGCCGACG 59.996 47.826 0.00 0.00 35.10 5.12
695 743 4.585955 TGGAGATAATAACTCTGCCGAC 57.414 45.455 0.00 0.00 35.10 4.79
696 744 4.588951 ACATGGAGATAATAACTCTGCCGA 59.411 41.667 0.00 0.00 35.10 5.54
721 769 4.278419 CCGTTGGTGGAAAGAGAAGAAAAT 59.722 41.667 0.00 0.00 0.00 1.82
725 773 1.542547 GCCGTTGGTGGAAAGAGAAGA 60.543 52.381 0.00 0.00 0.00 2.87
765 813 3.406595 AAGTCCGGCTGCTATGGGC 62.407 63.158 0.00 0.84 42.22 5.36
766 814 1.524621 CAAGTCCGGCTGCTATGGG 60.525 63.158 0.00 0.00 0.00 4.00
767 815 1.524621 CCAAGTCCGGCTGCTATGG 60.525 63.158 0.00 0.00 0.00 2.74
787 835 0.568697 GGGGAGAGGAGGGGATTACT 59.431 60.000 0.00 0.00 0.00 2.24
788 836 0.267960 TGGGGAGAGGAGGGGATTAC 59.732 60.000 0.00 0.00 0.00 1.89
789 837 0.267960 GTGGGGAGAGGAGGGGATTA 59.732 60.000 0.00 0.00 0.00 1.75
791 839 2.263099 CTGTGGGGAGAGGAGGGGAT 62.263 65.000 0.00 0.00 0.00 3.85
792 840 2.874245 TGTGGGGAGAGGAGGGGA 60.874 66.667 0.00 0.00 0.00 4.81
793 841 2.366167 CTGTGGGGAGAGGAGGGG 60.366 72.222 0.00 0.00 0.00 4.79
795 843 3.086600 GCCTGTGGGGAGAGGAGG 61.087 72.222 0.00 0.00 37.23 4.30
796 844 3.465403 CGCCTGTGGGGAGAGGAG 61.465 72.222 0.00 0.00 37.91 3.69
797 845 3.992641 TCGCCTGTGGGGAGAGGA 61.993 66.667 0.00 0.00 39.75 3.71
874 932 7.150783 AGAAATACAGCCAAGAATCAAGAAC 57.849 36.000 0.00 0.00 0.00 3.01
907 985 1.475034 GCACTGACAGAGGAACAACCA 60.475 52.381 10.08 0.00 42.04 3.67
936 1024 2.939103 CAGCATACGAAAGAAGGGAAGG 59.061 50.000 0.00 0.00 0.00 3.46
1084 1176 3.735029 GTCGTCGTCGAGGCCACT 61.735 66.667 5.01 0.00 46.96 4.00
1135 1227 2.542907 CGTCGGCCAACTTGCACTT 61.543 57.895 2.24 0.00 0.00 3.16
1150 1242 2.509561 GCTCCTTTCCTCGGCGTC 60.510 66.667 6.85 0.00 0.00 5.19
1297 1395 0.464452 ATGTAGCCGAGTACCTTGCC 59.536 55.000 0.00 0.00 0.00 4.52
1329 1427 1.070786 AAAACGGAAGAGCAGCGGA 59.929 52.632 0.00 0.00 0.00 5.54
1401 1499 3.446442 AGGCCAAACATGTTCATCTCT 57.554 42.857 12.39 3.82 0.00 3.10
1425 1523 3.878778 CTCCTCCCGATTCACAGAATTT 58.121 45.455 0.00 0.00 0.00 1.82
1492 1590 2.386661 TCTCTTCCAAAGATGTCGGC 57.613 50.000 0.00 0.00 36.82 5.54
1558 1656 2.281761 CACCTGCACCTTCCGCTT 60.282 61.111 0.00 0.00 0.00 4.68
1644 1742 2.361757 CAACTGGAAATGTTGCTGGACA 59.638 45.455 0.00 0.00 38.36 4.02
1683 1781 7.458409 AGCAGTAACATTGAAATTGTCTGAT 57.542 32.000 0.00 0.00 0.00 2.90
1695 1793 7.537715 TGGATTTCACAATAGCAGTAACATTG 58.462 34.615 0.00 0.00 36.07 2.82
1696 1794 7.701539 TGGATTTCACAATAGCAGTAACATT 57.298 32.000 0.00 0.00 0.00 2.71
1734 1832 2.489329 CAGGTCGCATCTTCCATTTGTT 59.511 45.455 0.00 0.00 0.00 2.83
1801 1935 3.886505 ACAAGTAAAAATGTCTTCCGGCA 59.113 39.130 0.00 0.00 0.00 5.69
1866 2003 5.473039 GAGCATAACAGTGGCTTCAAATTT 58.527 37.500 0.00 0.00 38.15 1.82
1869 2006 2.819608 GGAGCATAACAGTGGCTTCAAA 59.180 45.455 0.00 0.00 38.15 2.69
1910 2047 4.205181 CGCTTCGACATGTCACAACTATAG 59.795 45.833 24.93 10.35 0.00 1.31
1933 2070 4.731773 GCACATTATAGTTGCCACTTGCTC 60.732 45.833 0.00 0.00 42.00 4.26
1977 2114 3.895232 TCTTCTTCACCTAGACATGCC 57.105 47.619 0.00 0.00 0.00 4.40
2042 2179 1.970640 TGACTAACTCTGCTTGCTCCA 59.029 47.619 0.00 0.00 0.00 3.86
2134 2271 3.745975 TCCTCTACATGTTGCTTTGAACG 59.254 43.478 2.30 0.00 0.00 3.95
2181 2318 5.607168 TGCCCACAATATTATCCCCAATA 57.393 39.130 0.00 0.00 0.00 1.90
2198 2335 1.548081 CATGACCTCATGTTTGCCCA 58.452 50.000 7.07 0.00 46.40 5.36
2641 2808 1.066143 CAAAGTGCGGGGAGATGTACT 60.066 52.381 0.00 0.00 32.14 2.73
2642 2809 1.338769 ACAAAGTGCGGGGAGATGTAC 60.339 52.381 0.00 0.00 0.00 2.90
2643 2810 0.981183 ACAAAGTGCGGGGAGATGTA 59.019 50.000 0.00 0.00 0.00 2.29
2684 2851 1.534163 GTGACAGCCGTTTAAACTCCC 59.466 52.381 16.01 4.54 0.00 4.30
2688 2855 2.287308 TGCATGTGACAGCCGTTTAAAC 60.287 45.455 8.35 8.35 0.00 2.01
2811 2985 5.288232 GCATACTGAATCTAGCAATCTAGCG 59.712 44.000 0.00 0.00 41.59 4.26
2837 3011 6.320494 TCAACGTTTGCAGGTTATACAATT 57.680 33.333 0.00 0.00 29.71 2.32
2878 3052 5.304614 TGTCTTCTGGTAACTTCTGTAGCTT 59.695 40.000 0.00 0.00 37.61 3.74
2887 3061 7.497249 GCTTATCATCATGTCTTCTGGTAACTT 59.503 37.037 0.00 0.00 37.61 2.66
2961 3135 1.086696 CAATGTTTCGAGGCATCCGT 58.913 50.000 0.00 0.00 0.00 4.69
3150 3326 8.739972 ACAGAACAACAACTCACTTAGATTTTT 58.260 29.630 0.00 0.00 0.00 1.94
3158 3334 3.443681 CCCAACAGAACAACAACTCACTT 59.556 43.478 0.00 0.00 0.00 3.16
3210 3395 5.954150 ACAATTCTTCCTCATTACATGCCTT 59.046 36.000 0.00 0.00 0.00 4.35
3231 3416 3.149196 GAGGTTCTTGATGCTGGAACAA 58.851 45.455 0.00 0.00 40.48 2.83
3244 3429 5.643421 ATGGATCTTGCTATGAGGTTCTT 57.357 39.130 0.00 0.00 0.00 2.52
3266 3451 7.068103 CCACCATATCCATGCAACTTAAAACTA 59.932 37.037 0.00 0.00 0.00 2.24
3268 3453 6.042143 CCACCATATCCATGCAACTTAAAAC 58.958 40.000 0.00 0.00 0.00 2.43
3273 3458 2.034124 GCCACCATATCCATGCAACTT 58.966 47.619 0.00 0.00 0.00 2.66
3321 3506 6.942532 TCTTAAGCACTGAAACATTTGAGT 57.057 33.333 0.00 0.00 34.94 3.41
3349 3534 6.780522 ACACCTTTTCCAGTTGGTAATTATGT 59.219 34.615 0.00 0.00 36.34 2.29
3413 3598 5.895534 ACCCATGTTGATCAAGCATAAGAAT 59.104 36.000 8.80 0.00 0.00 2.40
3440 3625 9.661187 CAAAGATTATCACATAATGTCTTCAGC 57.339 33.333 0.00 0.00 35.68 4.26
3461 3646 2.239654 CCCTCCACCTTCTATGCAAAGA 59.760 50.000 0.00 0.00 0.00 2.52
3482 3667 3.629142 AAATGTAGAGGGGTACTGTGC 57.371 47.619 0.00 0.00 0.00 4.57
3514 3699 3.024547 TCTACCAAGACCATCTCCTTCG 58.975 50.000 0.00 0.00 0.00 3.79
3593 3778 4.894784 TCTCAAGCATCGGGAATATTACC 58.105 43.478 6.65 6.65 0.00 2.85
3659 3844 0.250770 GGTCTTTGAGAACGGGGCTT 60.251 55.000 0.00 0.00 0.00 4.35
3896 4104 1.535462 GGACAACAACGGATCCACAAG 59.465 52.381 13.41 0.55 0.00 3.16
3900 4108 0.605319 GCTGGACAACAACGGATCCA 60.605 55.000 13.41 0.00 38.94 3.41
3906 4114 0.319211 TCTACCGCTGGACAACAACG 60.319 55.000 1.50 0.00 38.35 4.10
4011 4219 3.263425 TGGAAATACTCACCACCTTCTCC 59.737 47.826 0.00 0.00 0.00 3.71
4066 4274 7.010923 CACCAGTTCTATATTTTGACTCTGCTC 59.989 40.741 0.00 0.00 0.00 4.26
4091 4299 1.973515 TCTGCTTCTTCTTCTGGAGCA 59.026 47.619 0.00 0.00 0.00 4.26
4102 4328 3.080319 GTGGATTCTGCTTCTGCTTCTT 58.920 45.455 0.00 0.00 40.48 2.52
4125 4351 3.865745 GCTTCTGCTTCTCGTGCTATAAA 59.134 43.478 0.00 0.00 36.03 1.40
4133 4359 2.615869 GATTCTGCTTCTGCTTCTCGT 58.384 47.619 0.00 0.00 40.48 4.18
4134 4360 1.932511 GGATTCTGCTTCTGCTTCTCG 59.067 52.381 0.00 0.00 40.48 4.04
4135 4361 2.677337 GTGGATTCTGCTTCTGCTTCTC 59.323 50.000 0.00 0.00 40.48 2.87


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

AutoCloner maintained by Alex Coulton.