Multiple sequence alignment - TraesCS6B01G412900

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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 TraesCS6B01G412900 chr6B 100.000 3328 0 0 1 3328 686362793 686366120 0.000000e+00 6146.0
1 TraesCS6B01G412900 chr6B 95.876 97 4 0 527 623 152102367 152102463 1.240000e-34 158.0
2 TraesCS6B01G412900 chr6D 92.716 1716 103 16 624 2330 451893711 451895413 0.000000e+00 2457.0
3 TraesCS6B01G412900 chr6D 95.178 871 25 8 2466 3328 451895517 451896378 0.000000e+00 1360.0
4 TraesCS6B01G412900 chr6D 90.196 51 5 0 2399 2449 438897012 438896962 2.140000e-07 67.6
5 TraesCS6B01G412900 chr6A 94.386 1425 52 5 914 2330 597788372 597789776 0.000000e+00 2163.0
6 TraesCS6B01G412900 chr6A 94.470 868 20 8 2476 3328 597789871 597790725 0.000000e+00 1312.0
7 TraesCS6B01G412900 chr7B 84.127 1386 187 16 958 2330 679359641 679361006 0.000000e+00 1310.0
8 TraesCS6B01G412900 chr7B 90.560 625 55 4 1 623 719643403 719644025 0.000000e+00 824.0
9 TraesCS6B01G412900 chr7B 94.667 525 27 1 1 524 337464441 337464965 0.000000e+00 813.0
10 TraesCS6B01G412900 chr2A 79.349 1322 238 26 1001 2304 724018456 724017152 0.000000e+00 896.0
11 TraesCS6B01G412900 chr2A 79.775 1246 230 15 1075 2304 723625413 723626652 0.000000e+00 885.0
12 TraesCS6B01G412900 chr2D 79.904 1249 223 19 1075 2304 589282371 589283610 0.000000e+00 891.0
13 TraesCS6B01G412900 chr2D 94.497 527 28 1 1 526 369384173 369384699 0.000000e+00 811.0
14 TraesCS6B01G412900 chr7D 94.877 527 26 1 1 526 500645042 500644516 0.000000e+00 822.0
15 TraesCS6B01G412900 chr7D 88.498 626 66 5 1 623 224501743 224501121 0.000000e+00 752.0
16 TraesCS6B01G412900 chr7D 94.231 104 5 1 527 630 635679033 635678931 1.240000e-34 158.0
17 TraesCS6B01G412900 chr4B 94.687 527 27 1 1 526 80840707 80841233 0.000000e+00 817.0
18 TraesCS6B01G412900 chr4B 94.497 527 28 1 1 526 232094658 232094132 0.000000e+00 811.0
19 TraesCS6B01G412900 chr4B 94.497 527 26 3 1 526 454653991 454654515 0.000000e+00 809.0
20 TraesCS6B01G412900 chr2B 94.687 527 27 1 1 526 221403953 221404479 0.000000e+00 817.0
21 TraesCS6B01G412900 chr2B 73.707 1179 249 39 1145 2292 785950499 785951647 1.440000e-108 403.0
22 TraesCS6B01G412900 chr2B 96.842 95 3 0 527 621 497871651 497871745 3.440000e-35 159.0
23 TraesCS6B01G412900 chr2B 95.876 97 4 0 527 623 677884241 677884145 1.240000e-34 158.0
24 TraesCS6B01G412900 chr2B 95.789 95 4 0 527 621 239684449 239684543 1.600000e-33 154.0
25 TraesCS6B01G412900 chr2B 95.652 46 2 0 2399 2444 28424610 28424565 1.280000e-09 75.0
26 TraesCS6B01G412900 chr2B 95.556 45 2 0 2399 2443 28424637 28424681 4.610000e-09 73.1
27 TraesCS6B01G412900 chrUn 74.382 1335 269 43 1001 2304 15345580 15346872 1.380000e-138 503.0
28 TraesCS6B01G412900 chrUn 74.382 1335 269 42 1001 2304 272744086 272742794 1.380000e-138 503.0
29 TraesCS6B01G412900 chrUn 95.652 46 2 0 2399 2444 288298383 288298338 1.280000e-09 75.0
30 TraesCS6B01G412900 chrUn 95.652 46 2 0 2399 2444 293843200 293843155 1.280000e-09 75.0
31 TraesCS6B01G412900 chr4D 96.907 97 3 0 527 623 295378061 295378157 2.660000e-36 163.0
32 TraesCS6B01G412900 chr4D 92.593 54 2 2 2391 2443 379335729 379335677 3.560000e-10 76.8
33 TraesCS6B01G412900 chr3D 89.076 119 8 5 527 645 163900088 163899975 3.460000e-30 143.0
34 TraesCS6B01G412900 chr3D 96.875 32 0 1 1654 1685 454670490 454670460 6.000000e-03 52.8
35 TraesCS6B01G412900 chr5B 90.741 54 3 2 2391 2443 57496856 57496908 1.660000e-08 71.3
36 TraesCS6B01G412900 chr3B 92.000 50 4 0 2394 2443 20026576 20026625 1.660000e-08 71.3
37 TraesCS6B01G412900 chr1D 88.679 53 6 0 2391 2443 452260409 452260461 7.710000e-07 65.8


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 TraesCS6B01G412900 chr6B 686362793 686366120 3327 False 6146.0 6146 100.000 1 3328 1 chr6B.!!$F2 3327
1 TraesCS6B01G412900 chr6D 451893711 451896378 2667 False 1908.5 2457 93.947 624 3328 2 chr6D.!!$F1 2704
2 TraesCS6B01G412900 chr6A 597788372 597790725 2353 False 1737.5 2163 94.428 914 3328 2 chr6A.!!$F1 2414
3 TraesCS6B01G412900 chr7B 679359641 679361006 1365 False 1310.0 1310 84.127 958 2330 1 chr7B.!!$F2 1372
4 TraesCS6B01G412900 chr7B 719643403 719644025 622 False 824.0 824 90.560 1 623 1 chr7B.!!$F3 622
5 TraesCS6B01G412900 chr7B 337464441 337464965 524 False 813.0 813 94.667 1 524 1 chr7B.!!$F1 523
6 TraesCS6B01G412900 chr2A 724017152 724018456 1304 True 896.0 896 79.349 1001 2304 1 chr2A.!!$R1 1303
7 TraesCS6B01G412900 chr2A 723625413 723626652 1239 False 885.0 885 79.775 1075 2304 1 chr2A.!!$F1 1229
8 TraesCS6B01G412900 chr2D 589282371 589283610 1239 False 891.0 891 79.904 1075 2304 1 chr2D.!!$F2 1229
9 TraesCS6B01G412900 chr2D 369384173 369384699 526 False 811.0 811 94.497 1 526 1 chr2D.!!$F1 525
10 TraesCS6B01G412900 chr7D 500644516 500645042 526 True 822.0 822 94.877 1 526 1 chr7D.!!$R2 525
11 TraesCS6B01G412900 chr7D 224501121 224501743 622 True 752.0 752 88.498 1 623 1 chr7D.!!$R1 622
12 TraesCS6B01G412900 chr4B 80840707 80841233 526 False 817.0 817 94.687 1 526 1 chr4B.!!$F1 525
13 TraesCS6B01G412900 chr4B 232094132 232094658 526 True 811.0 811 94.497 1 526 1 chr4B.!!$R1 525
14 TraesCS6B01G412900 chr4B 454653991 454654515 524 False 809.0 809 94.497 1 526 1 chr4B.!!$F2 525
15 TraesCS6B01G412900 chr2B 221403953 221404479 526 False 817.0 817 94.687 1 526 1 chr2B.!!$F2 525
16 TraesCS6B01G412900 chr2B 785950499 785951647 1148 False 403.0 403 73.707 1145 2292 1 chr2B.!!$F5 1147
17 TraesCS6B01G412900 chrUn 15345580 15346872 1292 False 503.0 503 74.382 1001 2304 1 chrUn.!!$F1 1303
18 TraesCS6B01G412900 chrUn 272742794 272744086 1292 True 503.0 503 74.382 1001 2304 1 chrUn.!!$R1 1303

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
784 792 0.182537 TTTGGACTGGATATGGGCCG 59.817 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2617 2731 0.392336 TGTGTTTGGATGCAAAGCCC 59.608 50.0 13.15 2.3 0.0 5.19 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
48 49 6.832384 TCATACCTAGTTCAATCTCGTTACCT 59.168 38.462 0.00 0.00 0.00 3.08
73 74 7.093354 TGCAAGTCTCTTTACTCATTCTGTAG 58.907 38.462 0.00 0.00 0.00 2.74
80 81 8.613482 TCTCTTTACTCATTCTGTAGTACATCG 58.387 37.037 2.82 0.00 0.00 3.84
121 122 1.481772 TCACTTTGCTTGCAAGGCTTT 59.518 42.857 27.10 4.06 0.00 3.51
221 223 1.341187 ACCCAACAAACACCTTCGGAA 60.341 47.619 0.00 0.00 0.00 4.30
228 230 4.070009 ACAAACACCTTCGGAAATACCTC 58.930 43.478 0.00 0.00 36.31 3.85
293 295 0.321564 CACACAAGGCATTCCTCCGA 60.322 55.000 0.00 0.00 43.40 4.55
326 328 7.043961 AGTTGCATAATCTCATAGTCGAAGA 57.956 36.000 0.00 0.00 0.00 2.87
395 397 9.224267 ACGATCATAATGCTAAGCTAATGAATT 57.776 29.630 0.00 0.00 30.51 2.17
411 413 3.073678 TGAATTGGTCTTGTCCATCACG 58.926 45.455 0.00 0.00 37.33 4.35
428 430 6.493458 TCCATCACGTCATTCTCCTAATGATA 59.507 38.462 3.93 0.00 38.71 2.15
510 512 5.595257 TCAACGAGCTAGTCTAGTAGAGA 57.405 43.478 8.68 0.00 30.15 3.10
546 550 7.906160 ACACGTAATACAATTCTAGCATGAAC 58.094 34.615 0.00 0.00 0.00 3.18
645 649 4.357947 GCGGCGAGACTGACACCA 62.358 66.667 12.98 0.00 0.00 4.17
647 651 2.430921 GGCGAGACTGACACCACG 60.431 66.667 0.00 0.00 0.00 4.94
694 701 1.043673 ATCTGGTAGGGTGAGACGGC 61.044 60.000 0.00 0.00 0.00 5.68
714 721 3.429272 GGCGGATTTGATGCAATTTGAGA 60.429 43.478 0.00 0.00 0.00 3.27
726 733 3.429410 GCAATTTGAGATGTTGTAGGGCC 60.429 47.826 0.00 0.00 0.00 5.80
727 734 3.737559 ATTTGAGATGTTGTAGGGCCA 57.262 42.857 6.18 0.00 0.00 5.36
735 742 1.306654 TTGTAGGGCCATCGGGTCT 60.307 57.895 6.18 0.00 39.39 3.85
736 743 1.622607 TTGTAGGGCCATCGGGTCTG 61.623 60.000 6.18 0.00 39.39 3.51
755 763 4.700365 CGTGGCGACGTGCTCAGA 62.700 66.667 13.58 0.00 45.43 3.27
769 777 1.597742 CTCAGACGCCCCATATTTGG 58.402 55.000 0.00 0.00 43.23 3.28
770 778 1.140852 CTCAGACGCCCCATATTTGGA 59.859 52.381 3.41 0.00 46.92 3.53
780 788 4.603131 CCCCATATTTGGACTGGATATGG 58.397 47.826 3.41 12.49 46.92 2.74
783 791 2.683211 ATTTGGACTGGATATGGGCC 57.317 50.000 0.00 0.00 0.00 5.80
784 792 0.182537 TTTGGACTGGATATGGGCCG 59.817 55.000 0.00 0.00 0.00 6.13
801 809 2.507944 GTGCCGATCAGCCCAGAT 59.492 61.111 0.00 0.00 0.00 2.90
814 822 0.606401 CCCAGATGTTTGTGGCGTCT 60.606 55.000 0.00 0.00 34.92 4.18
815 823 0.518636 CCAGATGTTTGTGGCGTCTG 59.481 55.000 7.36 7.36 44.98 3.51
821 829 0.248866 GTTTGTGGCGTCTGTTTGGG 60.249 55.000 0.00 0.00 0.00 4.12
824 832 2.280524 TGGCGTCTGTTTGGGTCG 60.281 61.111 0.00 0.00 0.00 4.79
835 843 6.566942 CGTCTGTTTGGGTCGAATTTTTATGA 60.567 38.462 0.00 0.00 0.00 2.15
850 858 0.613572 TATGACTGGCCAGTGACCGA 60.614 55.000 42.40 20.31 42.66 4.69
852 860 3.941657 GACTGGCCAGTGACCGAGC 62.942 68.421 42.40 22.13 42.66 5.03
853 861 4.767255 CTGGCCAGTGACCGAGCC 62.767 72.222 25.53 1.55 45.96 4.70
879 894 1.905843 CGGACATTGGTTTGGGGCA 60.906 57.895 0.00 0.00 0.00 5.36
880 895 1.671166 GGACATTGGTTTGGGGCAC 59.329 57.895 0.00 0.00 0.00 5.01
883 898 1.006337 CATTGGTTTGGGGCACGTG 60.006 57.895 12.28 12.28 0.00 4.49
884 899 2.206536 ATTGGTTTGGGGCACGTGG 61.207 57.895 18.88 0.00 0.00 4.94
887 902 3.977244 GTTTGGGGCACGTGGCTG 61.977 66.667 36.61 4.00 44.01 4.85
888 903 4.514585 TTTGGGGCACGTGGCTGT 62.515 61.111 36.61 0.00 44.01 4.40
889 904 3.121406 TTTGGGGCACGTGGCTGTA 62.121 57.895 36.61 22.18 44.01 2.74
890 905 3.545124 TTGGGGCACGTGGCTGTAG 62.545 63.158 36.61 1.87 44.01 2.74
891 906 3.702048 GGGGCACGTGGCTGTAGA 61.702 66.667 36.61 0.00 44.01 2.59
892 907 2.584608 GGGCACGTGGCTGTAGAT 59.415 61.111 36.61 0.00 44.01 1.98
915 930 3.969117 TGCTCTTATATTTGCTTGCGG 57.031 42.857 0.00 0.00 0.00 5.69
981 998 5.115622 GTGCAACATTTTTCTTAGCTTCGTC 59.884 40.000 0.00 0.00 36.32 4.20
983 1000 5.757886 CAACATTTTTCTTAGCTTCGTCCA 58.242 37.500 0.00 0.00 0.00 4.02
992 1009 2.301577 AGCTTCGTCCATTGAGCTAC 57.698 50.000 0.00 0.00 0.00 3.58
2292 2373 2.537560 CGCGACATGGATGCCTTCC 61.538 63.158 0.00 0.00 45.69 3.46
2304 2385 3.121030 CCTTCCGGAACTGCTGCG 61.121 66.667 14.35 1.06 38.86 5.18
2330 2411 3.452474 CGGCCTCTCAAAACTCTAGATG 58.548 50.000 0.00 0.00 0.00 2.90
2332 2413 4.438148 GGCCTCTCAAAACTCTAGATGTC 58.562 47.826 0.00 0.00 0.00 3.06
2336 2417 5.047021 CCTCTCAAAACTCTAGATGTCACCA 60.047 44.000 0.00 0.00 0.00 4.17
2346 2453 3.795688 AGATGTCACCAATGTTCCAGT 57.204 42.857 0.00 0.00 0.00 4.00
2351 2458 5.042463 TGTCACCAATGTTCCAGTTCTTA 57.958 39.130 0.00 0.00 0.00 2.10
2365 2473 5.932303 TCCAGTTCTTATTTCCTCAGTTTCG 59.068 40.000 0.00 0.00 0.00 3.46
2380 2488 4.444388 TCAGTTTCGAGTCTTGTTTCATCG 59.556 41.667 0.00 0.00 34.80 3.84
2387 2495 4.321217 CGAGTCTTGTTTCATCGAGTACAC 59.679 45.833 0.00 0.00 35.47 2.90
2390 2498 6.223852 AGTCTTGTTTCATCGAGTACACATT 58.776 36.000 0.00 0.00 0.00 2.71
2391 2499 7.375834 AGTCTTGTTTCATCGAGTACACATTA 58.624 34.615 0.00 0.00 0.00 1.90
2392 2500 7.328737 AGTCTTGTTTCATCGAGTACACATTAC 59.671 37.037 0.00 0.00 0.00 1.89
2395 2503 6.097356 TGTTTCATCGAGTACACATTACTCC 58.903 40.000 5.98 0.00 40.48 3.85
2396 2504 4.913335 TCATCGAGTACACATTACTCCC 57.087 45.455 5.98 0.00 40.48 4.30
2398 2506 5.687780 TCATCGAGTACACATTACTCCCTA 58.312 41.667 5.98 0.00 40.48 3.53
2401 2509 7.287005 TCATCGAGTACACATTACTCCCTAATT 59.713 37.037 5.98 0.00 40.48 1.40
2402 2510 7.414222 TCGAGTACACATTACTCCCTAATTT 57.586 36.000 5.98 0.00 40.48 1.82
2403 2511 7.262772 TCGAGTACACATTACTCCCTAATTTG 58.737 38.462 5.98 0.00 40.48 2.32
2406 2514 8.788325 AGTACACATTACTCCCTAATTTGAAC 57.212 34.615 0.00 0.00 30.11 3.18
2408 2516 9.880157 GTACACATTACTCCCTAATTTGAACTA 57.120 33.333 0.00 0.00 30.11 2.24
2410 2518 9.802039 ACACATTACTCCCTAATTTGAACTAAA 57.198 29.630 0.00 0.00 30.11 1.85
2414 2522 9.816787 ATTACTCCCTAATTTGAACTAAAACCA 57.183 29.630 0.00 0.00 0.00 3.67
2415 2523 7.520451 ACTCCCTAATTTGAACTAAAACCAC 57.480 36.000 0.00 0.00 0.00 4.16
2416 2524 6.206048 ACTCCCTAATTTGAACTAAAACCACG 59.794 38.462 0.00 0.00 0.00 4.94
2417 2525 6.297582 TCCCTAATTTGAACTAAAACCACGA 58.702 36.000 0.00 0.00 0.00 4.35
2418 2526 6.205270 TCCCTAATTTGAACTAAAACCACGAC 59.795 38.462 0.00 0.00 0.00 4.34
2419 2527 6.016943 CCCTAATTTGAACTAAAACCACGACA 60.017 38.462 0.00 0.00 0.00 4.35
2420 2528 7.419204 CCTAATTTGAACTAAAACCACGACAA 58.581 34.615 0.00 0.00 0.00 3.18
2421 2529 8.079809 CCTAATTTGAACTAAAACCACGACAAT 58.920 33.333 0.00 0.00 0.00 2.71
2424 2532 9.974980 AATTTGAACTAAAACCACGACAATAAT 57.025 25.926 0.00 0.00 0.00 1.28
2425 2533 9.974980 ATTTGAACTAAAACCACGACAATAATT 57.025 25.926 0.00 0.00 0.00 1.40
2426 2534 9.804758 TTTGAACTAAAACCACGACAATAATTT 57.195 25.926 0.00 0.00 0.00 1.82
2427 2535 9.804758 TTGAACTAAAACCACGACAATAATTTT 57.195 25.926 0.00 0.00 0.00 1.82
2428 2536 9.239002 TGAACTAAAACCACGACAATAATTTTG 57.761 29.630 0.00 0.00 0.00 2.44
2429 2537 9.453325 GAACTAAAACCACGACAATAATTTTGA 57.547 29.630 0.00 0.00 0.00 2.69
2430 2538 9.804758 AACTAAAACCACGACAATAATTTTGAA 57.195 25.926 0.00 0.00 0.00 2.69
2431 2539 9.804758 ACTAAAACCACGACAATAATTTTGAAA 57.195 25.926 0.00 0.00 0.00 2.69
2433 2541 6.741448 AACCACGACAATAATTTTGAAACG 57.259 33.333 0.00 0.00 0.00 3.60
2434 2542 5.216648 ACCACGACAATAATTTTGAAACGG 58.783 37.500 0.00 0.00 0.00 4.44
2435 2543 5.008811 ACCACGACAATAATTTTGAAACGGA 59.991 36.000 0.00 0.00 0.00 4.69
2436 2544 5.567534 CCACGACAATAATTTTGAAACGGAG 59.432 40.000 0.00 0.00 0.00 4.63
2437 2545 5.567534 CACGACAATAATTTTGAAACGGAGG 59.432 40.000 0.00 0.00 0.00 4.30
2438 2546 5.092781 CGACAATAATTTTGAAACGGAGGG 58.907 41.667 7.18 0.00 0.00 4.30
2439 2547 5.106475 CGACAATAATTTTGAAACGGAGGGA 60.106 40.000 7.18 0.00 0.00 4.20
2440 2548 6.267496 ACAATAATTTTGAAACGGAGGGAG 57.733 37.500 7.18 0.00 0.00 4.30
2441 2549 5.773176 ACAATAATTTTGAAACGGAGGGAGT 59.227 36.000 7.18 0.00 0.00 3.85
2442 2550 6.943718 ACAATAATTTTGAAACGGAGGGAGTA 59.056 34.615 7.18 0.00 0.00 2.59
2443 2551 6.997239 ATAATTTTGAAACGGAGGGAGTAC 57.003 37.500 0.00 0.00 0.00 2.73
2444 2552 2.845363 TTTGAAACGGAGGGAGTACC 57.155 50.000 0.00 0.00 40.67 3.34
2445 2553 1.719529 TTGAAACGGAGGGAGTACCA 58.280 50.000 0.00 0.00 43.89 3.25
2446 2554 1.719529 TGAAACGGAGGGAGTACCAA 58.280 50.000 0.00 0.00 43.89 3.67
2447 2555 2.262637 TGAAACGGAGGGAGTACCAAT 58.737 47.619 0.00 0.00 43.89 3.16
2448 2556 2.235402 TGAAACGGAGGGAGTACCAATC 59.765 50.000 0.00 0.00 43.89 2.67
2449 2557 2.249309 AACGGAGGGAGTACCAATCT 57.751 50.000 0.00 0.00 43.89 2.40
2450 2558 1.486211 ACGGAGGGAGTACCAATCTG 58.514 55.000 0.00 0.00 43.89 2.90
2451 2559 1.273098 ACGGAGGGAGTACCAATCTGT 60.273 52.381 0.00 0.00 43.89 3.41
2452 2560 1.137086 CGGAGGGAGTACCAATCTGTG 59.863 57.143 0.00 0.00 43.89 3.66
2453 2561 2.188817 GGAGGGAGTACCAATCTGTGT 58.811 52.381 0.00 0.00 43.89 3.72
2454 2562 3.371965 GGAGGGAGTACCAATCTGTGTA 58.628 50.000 0.00 0.00 43.89 2.90
2455 2563 3.967987 GGAGGGAGTACCAATCTGTGTAT 59.032 47.826 0.00 0.00 43.89 2.29
2456 2564 4.202264 GGAGGGAGTACCAATCTGTGTATG 60.202 50.000 0.00 0.00 43.89 2.39
2457 2565 3.134804 AGGGAGTACCAATCTGTGTATGC 59.865 47.826 0.00 0.00 43.89 3.14
2458 2566 3.134804 GGGAGTACCAATCTGTGTATGCT 59.865 47.826 0.00 0.00 39.85 3.79
2459 2567 4.344102 GGGAGTACCAATCTGTGTATGCTA 59.656 45.833 0.00 0.00 39.85 3.49
2460 2568 5.163343 GGGAGTACCAATCTGTGTATGCTAA 60.163 44.000 0.00 0.00 39.85 3.09
2461 2569 6.464465 GGGAGTACCAATCTGTGTATGCTAAT 60.464 42.308 0.00 0.00 39.85 1.73
2462 2570 6.647067 GGAGTACCAATCTGTGTATGCTAATC 59.353 42.308 0.00 0.00 35.97 1.75
2463 2571 7.124573 AGTACCAATCTGTGTATGCTAATCA 57.875 36.000 0.00 0.00 0.00 2.57
2464 2572 7.564793 AGTACCAATCTGTGTATGCTAATCAA 58.435 34.615 0.00 0.00 0.00 2.57
2489 2603 3.210227 TGGAGCGAACAGAAATTCAACA 58.790 40.909 0.00 0.00 0.00 3.33
2617 2731 6.127647 ACCAACCAAGCTTGTAATATCATGTG 60.128 38.462 24.35 7.46 0.00 3.21
2698 2812 9.025041 TCAGTAGATACAGTATATCCAACATGG 57.975 37.037 0.00 0.00 39.43 3.66
2908 3031 4.715523 TGGTTGTAGCCAGCGCCC 62.716 66.667 2.29 0.00 33.97 6.13
3058 3181 1.534717 CCCCATGCCCATTCCCATC 60.535 63.158 0.00 0.00 0.00 3.51
3059 3182 1.545211 CCCATGCCCATTCCCATCT 59.455 57.895 0.00 0.00 0.00 2.90
3089 3212 3.721370 ATCCCCATCGGTTGCTGGC 62.721 63.158 0.00 0.00 29.69 4.85
3105 3228 3.195632 GCCCATCCCCATCCCCAT 61.196 66.667 0.00 0.00 0.00 4.00
3148 3277 0.265553 CCATTCCCATCCCCATTGGT 59.734 55.000 1.20 0.00 34.77 3.67
3180 3309 0.106719 ATTCCGCCACCATAACCAGG 60.107 55.000 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 5.858381 ACAGAATGAGTAAAGAGACTTGCA 58.142 37.500 0.00 0.00 39.69 4.08
73 74 3.846360 AGTTAGTTGCAGGACGATGTAC 58.154 45.455 0.00 0.00 0.00 2.90
121 122 6.740401 GCCCTCTCGGTAATACACATCATAAA 60.740 42.308 0.00 0.00 0.00 1.40
228 230 9.979578 AACTGAGTGATTATAAAGATGCTCTAG 57.020 33.333 0.00 0.00 0.00 2.43
261 263 3.067106 CCTTGTGTGCTATCAAACGTCT 58.933 45.455 0.00 0.00 33.01 4.18
293 295 4.532126 TGAGATTATGCAACTCCCGGATAT 59.468 41.667 0.73 0.00 0.00 1.63
395 397 1.044611 TGACGTGATGGACAAGACCA 58.955 50.000 0.00 0.00 44.41 4.02
411 413 6.983307 CGGGATCATATCATTAGGAGAATGAC 59.017 42.308 2.24 0.00 39.22 3.06
428 430 6.376864 TGTTGTCATTTGATAAACGGGATCAT 59.623 34.615 0.00 0.00 33.41 2.45
463 465 9.232473 GATCAAAGATGGTTAAGTTTCCTAACT 57.768 33.333 0.00 0.00 46.44 2.24
510 512 7.651027 ATTGTATTACGTGTCCCTAGTAAGT 57.349 36.000 0.00 0.00 34.39 2.24
645 649 0.605589 CTGCTGTCTTCTTCCTCCGT 59.394 55.000 0.00 0.00 0.00 4.69
647 651 2.175202 TCTCTGCTGTCTTCTTCCTCC 58.825 52.381 0.00 0.00 0.00 4.30
694 701 5.345702 ACATCTCAAATTGCATCAAATCCG 58.654 37.500 0.00 0.00 0.00 4.18
714 721 1.279025 ACCCGATGGCCCTACAACAT 61.279 55.000 0.00 0.00 33.59 2.71
726 733 2.509336 GCCACGTCAGACCCGATG 60.509 66.667 0.00 0.00 0.00 3.84
727 734 4.129737 CGCCACGTCAGACCCGAT 62.130 66.667 0.00 0.00 0.00 4.18
748 756 0.546122 AAATATGGGGCGTCTGAGCA 59.454 50.000 0.00 0.00 39.27 4.26
751 759 3.798794 CCAAATATGGGGCGTCTGA 57.201 52.632 0.00 0.00 43.51 3.27
769 777 1.598130 GCACGGCCCATATCCAGTC 60.598 63.158 0.00 0.00 0.00 3.51
770 778 2.510906 GCACGGCCCATATCCAGT 59.489 61.111 0.00 0.00 0.00 4.00
784 792 1.890979 CATCTGGGCTGATCGGCAC 60.891 63.158 27.26 24.99 40.61 5.01
790 798 1.843368 CCACAAACATCTGGGCTGAT 58.157 50.000 0.00 0.00 0.00 2.90
796 804 0.518636 CAGACGCCACAAACATCTGG 59.481 55.000 0.00 0.00 34.43 3.86
798 806 1.967319 AACAGACGCCACAAACATCT 58.033 45.000 0.00 0.00 0.00 2.90
801 809 0.453793 CCAAACAGACGCCACAAACA 59.546 50.000 0.00 0.00 0.00 2.83
814 822 6.442952 CAGTCATAAAAATTCGACCCAAACA 58.557 36.000 0.00 0.00 0.00 2.83
815 823 5.861787 CCAGTCATAAAAATTCGACCCAAAC 59.138 40.000 0.00 0.00 0.00 2.93
821 829 4.156008 ACTGGCCAGTCATAAAAATTCGAC 59.844 41.667 33.20 0.00 36.92 4.20
824 832 5.402398 GTCACTGGCCAGTCATAAAAATTC 58.598 41.667 35.79 4.50 40.20 2.17
835 843 4.008933 GCTCGGTCACTGGCCAGT 62.009 66.667 33.20 33.20 43.61 4.00
856 864 1.531739 CCAAACCAATGTCCGGGTGG 61.532 60.000 0.00 7.24 37.50 4.61
863 871 1.288752 CGTGCCCCAAACCAATGTC 59.711 57.895 0.00 0.00 0.00 3.06
866 874 2.206536 CCACGTGCCCCAAACCAAT 61.207 57.895 10.91 0.00 0.00 3.16
879 894 0.826715 AGCATCATCTACAGCCACGT 59.173 50.000 0.00 0.00 0.00 4.49
880 895 1.068281 AGAGCATCATCTACAGCCACG 59.932 52.381 0.00 0.00 37.82 4.94
883 898 7.413877 GCAAATATAAGAGCATCATCTACAGCC 60.414 40.741 0.00 0.00 37.82 4.85
884 899 7.333921 AGCAAATATAAGAGCATCATCTACAGC 59.666 37.037 0.00 0.00 37.82 4.40
885 900 8.774890 AGCAAATATAAGAGCATCATCTACAG 57.225 34.615 0.00 0.00 37.82 2.74
886 901 8.996271 CAAGCAAATATAAGAGCATCATCTACA 58.004 33.333 0.00 0.00 37.82 2.74
887 902 7.961827 GCAAGCAAATATAAGAGCATCATCTAC 59.038 37.037 0.00 0.00 37.82 2.59
888 903 7.148523 CGCAAGCAAATATAAGAGCATCATCTA 60.149 37.037 0.00 0.00 37.82 1.98
889 904 6.348295 CGCAAGCAAATATAAGAGCATCATCT 60.348 38.462 0.00 0.00 37.82 2.90
890 905 5.793952 CGCAAGCAAATATAAGAGCATCATC 59.206 40.000 0.00 0.00 37.82 2.92
891 906 5.335426 CCGCAAGCAAATATAAGAGCATCAT 60.335 40.000 0.00 0.00 37.82 2.45
892 907 4.023792 CCGCAAGCAAATATAAGAGCATCA 60.024 41.667 0.00 0.00 37.82 3.07
915 930 2.474032 GGATGAACAAAACTAGCGCGAC 60.474 50.000 12.10 0.04 0.00 5.19
992 1009 1.846648 GTGATCTTCATACGGCGCG 59.153 57.895 6.90 0.00 0.00 6.86
1470 1517 1.707427 AGGATGAAGTTGCAGAACCCT 59.293 47.619 0.00 0.00 31.81 4.34
1655 1706 4.507916 TCCTCCTCCTCCTCGCCG 62.508 72.222 0.00 0.00 0.00 6.46
2304 2385 0.678048 AGTTTTGAGAGGCCGGATGC 60.678 55.000 5.05 0.00 40.16 3.91
2330 2411 6.575162 AATAAGAACTGGAACATTGGTGAC 57.425 37.500 0.00 0.00 38.20 3.67
2332 2413 6.209391 AGGAAATAAGAACTGGAACATTGGTG 59.791 38.462 0.00 0.00 38.20 4.17
2336 2417 7.234355 ACTGAGGAAATAAGAACTGGAACATT 58.766 34.615 0.00 0.00 38.20 2.71
2346 2453 6.994221 AGACTCGAAACTGAGGAAATAAGAA 58.006 36.000 0.00 0.00 40.39 2.52
2351 2458 4.962155 ACAAGACTCGAAACTGAGGAAAT 58.038 39.130 0.00 0.00 40.39 2.17
2365 2473 5.220381 TGTGTACTCGATGAAACAAGACTC 58.780 41.667 0.00 0.00 0.00 3.36
2380 2488 8.880750 GTTCAAATTAGGGAGTAATGTGTACTC 58.119 37.037 5.16 5.16 37.54 2.59
2390 2498 7.388500 CGTGGTTTTAGTTCAAATTAGGGAGTA 59.612 37.037 0.00 0.00 0.00 2.59
2391 2499 6.206048 CGTGGTTTTAGTTCAAATTAGGGAGT 59.794 38.462 0.00 0.00 0.00 3.85
2392 2500 6.428771 TCGTGGTTTTAGTTCAAATTAGGGAG 59.571 38.462 0.00 0.00 0.00 4.30
2395 2503 6.961576 TGTCGTGGTTTTAGTTCAAATTAGG 58.038 36.000 0.00 0.00 0.00 2.69
2398 2506 9.974980 ATTATTGTCGTGGTTTTAGTTCAAATT 57.025 25.926 0.00 0.00 0.00 1.82
2401 2509 9.804758 AAAATTATTGTCGTGGTTTTAGTTCAA 57.195 25.926 0.00 0.00 0.00 2.69
2402 2510 9.239002 CAAAATTATTGTCGTGGTTTTAGTTCA 57.761 29.630 0.00 0.00 0.00 3.18
2403 2511 9.453325 TCAAAATTATTGTCGTGGTTTTAGTTC 57.547 29.630 0.00 0.00 0.00 3.01
2408 2516 7.254151 CCGTTTCAAAATTATTGTCGTGGTTTT 60.254 33.333 0.00 0.00 0.00 2.43
2409 2517 6.199342 CCGTTTCAAAATTATTGTCGTGGTTT 59.801 34.615 0.00 0.00 0.00 3.27
2410 2518 5.688176 CCGTTTCAAAATTATTGTCGTGGTT 59.312 36.000 0.00 0.00 0.00 3.67
2413 2521 5.567534 CCTCCGTTTCAAAATTATTGTCGTG 59.432 40.000 0.00 0.00 0.00 4.35
2414 2522 5.335348 CCCTCCGTTTCAAAATTATTGTCGT 60.335 40.000 0.00 0.00 0.00 4.34
2415 2523 5.092781 CCCTCCGTTTCAAAATTATTGTCG 58.907 41.667 0.00 0.00 0.00 4.35
2416 2524 6.072119 ACTCCCTCCGTTTCAAAATTATTGTC 60.072 38.462 0.00 0.00 0.00 3.18
2417 2525 5.773176 ACTCCCTCCGTTTCAAAATTATTGT 59.227 36.000 0.00 0.00 0.00 2.71
2418 2526 6.267496 ACTCCCTCCGTTTCAAAATTATTG 57.733 37.500 0.00 0.00 0.00 1.90
2419 2527 6.376299 GGTACTCCCTCCGTTTCAAAATTATT 59.624 38.462 0.00 0.00 0.00 1.40
2420 2528 5.884232 GGTACTCCCTCCGTTTCAAAATTAT 59.116 40.000 0.00 0.00 0.00 1.28
2421 2529 5.221884 TGGTACTCCCTCCGTTTCAAAATTA 60.222 40.000 0.00 0.00 0.00 1.40
2422 2530 4.077108 GGTACTCCCTCCGTTTCAAAATT 58.923 43.478 0.00 0.00 0.00 1.82
2423 2531 3.073356 TGGTACTCCCTCCGTTTCAAAAT 59.927 43.478 0.00 0.00 0.00 1.82
2424 2532 2.438763 TGGTACTCCCTCCGTTTCAAAA 59.561 45.455 0.00 0.00 0.00 2.44
2425 2533 2.048601 TGGTACTCCCTCCGTTTCAAA 58.951 47.619 0.00 0.00 0.00 2.69
2426 2534 1.719529 TGGTACTCCCTCCGTTTCAA 58.280 50.000 0.00 0.00 0.00 2.69
2427 2535 1.719529 TTGGTACTCCCTCCGTTTCA 58.280 50.000 0.00 0.00 0.00 2.69
2428 2536 2.500504 AGATTGGTACTCCCTCCGTTTC 59.499 50.000 0.00 0.00 0.00 2.78
2429 2537 2.236395 CAGATTGGTACTCCCTCCGTTT 59.764 50.000 0.00 0.00 0.00 3.60
2430 2538 1.831736 CAGATTGGTACTCCCTCCGTT 59.168 52.381 0.00 0.00 0.00 4.44
2431 2539 1.273098 ACAGATTGGTACTCCCTCCGT 60.273 52.381 0.00 0.00 0.00 4.69
2432 2540 1.137086 CACAGATTGGTACTCCCTCCG 59.863 57.143 0.00 0.00 0.00 4.63
2433 2541 2.188817 ACACAGATTGGTACTCCCTCC 58.811 52.381 0.00 0.00 0.00 4.30
2434 2542 4.740934 GCATACACAGATTGGTACTCCCTC 60.741 50.000 0.00 0.00 0.00 4.30
2435 2543 3.134804 GCATACACAGATTGGTACTCCCT 59.865 47.826 0.00 0.00 0.00 4.20
2436 2544 3.134804 AGCATACACAGATTGGTACTCCC 59.865 47.826 0.00 0.00 0.00 4.30
2437 2545 4.408182 AGCATACACAGATTGGTACTCC 57.592 45.455 0.00 0.00 0.00 3.85
2438 2546 7.210174 TGATTAGCATACACAGATTGGTACTC 58.790 38.462 0.00 0.00 0.00 2.59
2439 2547 7.124573 TGATTAGCATACACAGATTGGTACT 57.875 36.000 0.00 0.00 0.00 2.73
2440 2548 7.786178 TTGATTAGCATACACAGATTGGTAC 57.214 36.000 0.00 0.00 0.00 3.34
2441 2549 8.800370 TTTTGATTAGCATACACAGATTGGTA 57.200 30.769 0.00 0.00 0.00 3.25
2442 2550 7.701539 TTTTGATTAGCATACACAGATTGGT 57.298 32.000 0.00 0.00 0.00 3.67
2443 2551 9.027129 CATTTTTGATTAGCATACACAGATTGG 57.973 33.333 0.00 0.00 0.00 3.16
2444 2552 9.027129 CCATTTTTGATTAGCATACACAGATTG 57.973 33.333 0.00 0.00 0.00 2.67
2445 2553 8.970020 TCCATTTTTGATTAGCATACACAGATT 58.030 29.630 0.00 0.00 0.00 2.40
2446 2554 8.523915 TCCATTTTTGATTAGCATACACAGAT 57.476 30.769 0.00 0.00 0.00 2.90
2447 2555 7.415541 GCTCCATTTTTGATTAGCATACACAGA 60.416 37.037 0.00 0.00 0.00 3.41
2448 2556 6.694411 GCTCCATTTTTGATTAGCATACACAG 59.306 38.462 0.00 0.00 0.00 3.66
2449 2557 6.563422 GCTCCATTTTTGATTAGCATACACA 58.437 36.000 0.00 0.00 0.00 3.72
2450 2558 5.682862 CGCTCCATTTTTGATTAGCATACAC 59.317 40.000 0.00 0.00 0.00 2.90
2451 2559 5.588246 TCGCTCCATTTTTGATTAGCATACA 59.412 36.000 0.00 0.00 0.00 2.29
2452 2560 6.060028 TCGCTCCATTTTTGATTAGCATAC 57.940 37.500 0.00 0.00 0.00 2.39
2453 2561 6.094742 TGTTCGCTCCATTTTTGATTAGCATA 59.905 34.615 0.00 0.00 0.00 3.14
2454 2562 5.105797 TGTTCGCTCCATTTTTGATTAGCAT 60.106 36.000 0.00 0.00 0.00 3.79
2455 2563 4.217334 TGTTCGCTCCATTTTTGATTAGCA 59.783 37.500 0.00 0.00 0.00 3.49
2456 2564 4.732784 TGTTCGCTCCATTTTTGATTAGC 58.267 39.130 0.00 0.00 0.00 3.09
2457 2565 6.182039 TCTGTTCGCTCCATTTTTGATTAG 57.818 37.500 0.00 0.00 0.00 1.73
2458 2566 6.567687 TTCTGTTCGCTCCATTTTTGATTA 57.432 33.333 0.00 0.00 0.00 1.75
2459 2567 5.452078 TTCTGTTCGCTCCATTTTTGATT 57.548 34.783 0.00 0.00 0.00 2.57
2460 2568 5.452078 TTTCTGTTCGCTCCATTTTTGAT 57.548 34.783 0.00 0.00 0.00 2.57
2461 2569 4.909696 TTTCTGTTCGCTCCATTTTTGA 57.090 36.364 0.00 0.00 0.00 2.69
2462 2570 5.691305 TGAATTTCTGTTCGCTCCATTTTTG 59.309 36.000 0.00 0.00 0.00 2.44
2463 2571 5.841810 TGAATTTCTGTTCGCTCCATTTTT 58.158 33.333 0.00 0.00 0.00 1.94
2464 2572 5.452078 TGAATTTCTGTTCGCTCCATTTT 57.548 34.783 0.00 0.00 0.00 1.82
2489 2603 9.869757 GCAATAAAAGGATGTACTACCATTTTT 57.130 29.630 13.75 12.14 0.00 1.94
2617 2731 0.392336 TGTGTTTGGATGCAAAGCCC 59.608 50.000 13.15 2.30 0.00 5.19
2698 2812 9.007901 CACTATTCTTTTTCCTATCCATCCATC 57.992 37.037 0.00 0.00 0.00 3.51
2699 2813 8.727149 TCACTATTCTTTTTCCTATCCATCCAT 58.273 33.333 0.00 0.00 0.00 3.41
2700 2814 8.101309 TCACTATTCTTTTTCCTATCCATCCA 57.899 34.615 0.00 0.00 0.00 3.41
2884 3007 1.302949 TGGCTACAACCAGATGGGC 59.697 57.895 3.48 0.00 42.05 5.36
3058 3181 1.993956 TGGGGATGAACCAACAACAG 58.006 50.000 0.00 0.00 41.20 3.16
3059 3182 2.524306 GATGGGGATGAACCAACAACA 58.476 47.619 0.00 0.00 42.17 3.33
3089 3212 1.466526 GAATGGGGATGGGGATGGG 59.533 63.158 0.00 0.00 0.00 4.00
3090 3213 1.466526 GGAATGGGGATGGGGATGG 59.533 63.158 0.00 0.00 0.00 3.51
3105 3228 1.062886 TGAACCAACAACCCATGGGAA 60.063 47.619 38.07 6.13 41.17 3.97
3148 3277 0.746563 GCGGAATGGGAATGAACCGA 60.747 55.000 0.00 0.00 42.40 4.69
3180 3309 0.392060 GGGTGTCGGTATTGGTGGTC 60.392 60.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.