Multiple sequence alignment - TraesCS1B01G218300

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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 TraesCS1B01G218300 chr1B 100.000 3092 0 0 1 3092 395751355 395754446 0.000000e+00 5710.0
1 TraesCS1B01G218300 chr1D 96.206 1766 41 12 615 2370 294131214 294132963 0.000000e+00 2867.0
2 TraesCS1B01G218300 chr1D 92.120 368 17 11 2418 2782 294132966 294133324 2.750000e-140 508.0
3 TraesCS1B01G218300 chr1D 88.732 355 34 5 2741 3092 294133326 294133677 2.200000e-116 429.0
4 TraesCS1B01G218300 chr1A 96.626 1630 31 7 770 2395 366543046 366544655 0.000000e+00 2684.0
5 TraesCS1B01G218300 chr1A 95.652 92 4 0 2557 2648 366544840 366544931 6.910000e-32 148.0
6 TraesCS1B01G218300 chr1A 94.286 70 4 0 2651 2720 366546745 366546814 1.170000e-19 108.0
7 TraesCS1B01G218300 chr4D 88.364 1100 117 11 1001 2093 487631864 487632959 0.000000e+00 1312.0
8 TraesCS1B01G218300 chr4B 88.091 1100 120 11 1001 2093 623163618 623164713 0.000000e+00 1295.0
9 TraesCS1B01G218300 chr5A 87.579 1103 123 13 1001 2093 669564673 669565771 0.000000e+00 1266.0
10 TraesCS1B01G218300 chr5B 91.220 615 53 1 1 614 614435939 614436553 0.000000e+00 835.0
11 TraesCS1B01G218300 chr5B 90.600 617 54 3 1 614 281855582 281856197 0.000000e+00 815.0
12 TraesCS1B01G218300 chr3B 90.806 620 54 3 1 618 524410268 524410886 0.000000e+00 826.0
13 TraesCS1B01G218300 chr3B 90.747 616 56 1 1 615 439014874 439015489 0.000000e+00 821.0
14 TraesCS1B01G218300 chr3B 90.762 617 52 3 1 614 605319307 605318693 0.000000e+00 819.0
15 TraesCS1B01G218300 chr7B 90.747 616 56 1 1 615 141155910 141155295 0.000000e+00 821.0
16 TraesCS1B01G218300 chr7B 90.732 615 55 2 1 614 298110260 298110873 0.000000e+00 819.0
17 TraesCS1B01G218300 chr7B 90.569 615 57 1 1 614 293855318 293855932 0.000000e+00 813.0
18 TraesCS1B01G218300 chr6B 90.422 616 58 1 1 615 600281347 600281962 0.000000e+00 809.0
19 TraesCS1B01G218300 chr6B 94.286 35 1 1 2750 2783 41702175 41702141 6.000000e-03 52.8


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 TraesCS1B01G218300 chr1B 395751355 395754446 3091 False 5710 5710 100.000000 1 3092 1 chr1B.!!$F1 3091
1 TraesCS1B01G218300 chr1D 294131214 294133677 2463 False 1268 2867 92.352667 615 3092 3 chr1D.!!$F1 2477
2 TraesCS1B01G218300 chr1A 366543046 366546814 3768 False 980 2684 95.521333 770 2720 3 chr1A.!!$F1 1950
3 TraesCS1B01G218300 chr4D 487631864 487632959 1095 False 1312 1312 88.364000 1001 2093 1 chr4D.!!$F1 1092
4 TraesCS1B01G218300 chr4B 623163618 623164713 1095 False 1295 1295 88.091000 1001 2093 1 chr4B.!!$F1 1092
5 TraesCS1B01G218300 chr5A 669564673 669565771 1098 False 1266 1266 87.579000 1001 2093 1 chr5A.!!$F1 1092
6 TraesCS1B01G218300 chr5B 614435939 614436553 614 False 835 835 91.220000 1 614 1 chr5B.!!$F2 613
7 TraesCS1B01G218300 chr5B 281855582 281856197 615 False 815 815 90.600000 1 614 1 chr5B.!!$F1 613
8 TraesCS1B01G218300 chr3B 524410268 524410886 618 False 826 826 90.806000 1 618 1 chr3B.!!$F2 617
9 TraesCS1B01G218300 chr3B 439014874 439015489 615 False 821 821 90.747000 1 615 1 chr3B.!!$F1 614
10 TraesCS1B01G218300 chr3B 605318693 605319307 614 True 819 819 90.762000 1 614 1 chr3B.!!$R1 613
11 TraesCS1B01G218300 chr7B 141155295 141155910 615 True 821 821 90.747000 1 615 1 chr7B.!!$R1 614
12 TraesCS1B01G218300 chr7B 298110260 298110873 613 False 819 819 90.732000 1 614 1 chr7B.!!$F2 613
13 TraesCS1B01G218300 chr7B 293855318 293855932 614 False 813 813 90.569000 1 614 1 chr7B.!!$F1 613
14 TraesCS1B01G218300 chr6B 600281347 600281962 615 False 809 809 90.422000 1 615 1 chr6B.!!$F1 614

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
604 609 0.177141 CCCGAGATCTGCCGGTTTTA 59.823 55.0 18.55 0.0 43.93 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2409 2432 0.462789 ACGAAACAGACGGTGAGGTT 59.537 50.0 0.0 0.0 34.93 3.5 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
87 89 2.573340 GAACCCGCCTTGCAATGG 59.427 61.111 0.00 5.03 0.00 3.16
88 90 2.203625 AACCCGCCTTGCAATGGT 60.204 55.556 0.00 1.73 32.80 3.55
115 117 4.883083 ACAATCTATGCGTCGGATACATT 58.117 39.130 1.90 2.08 0.00 2.71
152 154 0.618968 CAGGGGCTACTGAGGGAGTT 60.619 60.000 4.11 0.00 40.97 3.01
158 160 2.393646 GCTACTGAGGGAGTTCTGGAT 58.606 52.381 0.00 0.00 35.96 3.41
194 196 2.029020 GCGTCCAGGCTATGTGATATGA 60.029 50.000 0.00 0.00 0.00 2.15
251 254 1.264749 CCTTCCCCGTGTCTGGATGA 61.265 60.000 0.00 0.00 0.00 2.92
300 303 1.287730 GCGGTCGGATCATGCATCTC 61.288 60.000 0.00 0.00 0.00 2.75
360 363 4.831155 CCCTCCGGTGTCTATATAAACTGA 59.169 45.833 0.00 0.00 0.00 3.41
363 366 6.264744 CCTCCGGTGTCTATATAAACTGAAGA 59.735 42.308 0.00 0.00 0.00 2.87
417 422 4.722279 AGGCTAGACATTTAGGGTTTAGCT 59.278 41.667 12.75 0.00 44.15 3.32
501 506 5.246429 CAGGAAGTAGGGTATTACCTCCATC 59.754 48.000 16.39 8.41 42.09 3.51
504 509 6.100714 GGAAGTAGGGTATTACCTCCATCAAA 59.899 42.308 12.54 0.00 42.09 2.69
509 514 4.079385 GGGTATTACCTCCATCAAAAGGGT 60.079 45.833 12.54 0.00 38.64 4.34
531 536 2.094078 CCGAACCTGGGTAAACATCGTA 60.094 50.000 0.00 0.00 0.00 3.43
604 609 0.177141 CCCGAGATCTGCCGGTTTTA 59.823 55.000 18.55 0.00 43.93 1.52
622 627 5.121298 GGTTTTAACACCGACAGTAGATTCC 59.879 44.000 0.00 0.00 0.00 3.01
646 651 1.373497 CAGTGAGGAGTGGCGTGAC 60.373 63.158 0.00 0.00 0.00 3.67
648 653 1.115930 AGTGAGGAGTGGCGTGACTT 61.116 55.000 0.00 0.00 0.00 3.01
658 663 1.803519 GCGTGACTTGCCTCGAGAG 60.804 63.158 15.71 5.99 0.00 3.20
667 672 3.511934 ACTTGCCTCGAGAGTGTATCTTT 59.488 43.478 15.71 0.00 38.84 2.52
690 695 1.884579 TGTAATAGCGGACGAGATCCC 59.115 52.381 0.00 0.00 46.04 3.85
699 704 3.592059 CGGACGAGATCCCAAACTTTAA 58.408 45.455 0.00 0.00 46.04 1.52
707 712 7.886446 ACGAGATCCCAAACTTTAATTAAGGAA 59.114 33.333 13.73 0.00 38.23 3.36
723 728 8.574251 AATTAAGGAATAAAATGTTTTGCCCC 57.426 30.769 1.16 0.34 0.00 5.80
724 729 5.841267 AAGGAATAAAATGTTTTGCCCCT 57.159 34.783 1.16 2.32 0.00 4.79
766 771 2.485795 GGTCCAAGCCGTGTGCAAA 61.486 57.895 0.00 0.00 44.83 3.68
774 779 0.730494 GCCGTGTGCAAAAGCTGATC 60.730 55.000 0.00 0.00 40.77 2.92
842 847 1.817099 CCAGCAACGGCATCCTCTC 60.817 63.158 0.00 0.00 44.61 3.20
843 848 1.220206 CAGCAACGGCATCCTCTCT 59.780 57.895 0.00 0.00 44.61 3.10
844 849 1.088340 CAGCAACGGCATCCTCTCTG 61.088 60.000 0.00 0.00 44.61 3.35
845 850 2.467826 GCAACGGCATCCTCTCTGC 61.468 63.158 0.00 0.00 40.72 4.26
850 855 2.107953 GCATCCTCTCTGCCGTCC 59.892 66.667 0.00 0.00 33.44 4.79
851 856 2.430610 GCATCCTCTCTGCCGTCCT 61.431 63.158 0.00 0.00 33.44 3.85
932 949 0.397816 AATCTCAGGACTCCTCCCCG 60.398 60.000 0.00 0.00 37.25 5.73
955 972 3.304251 GGAGCCGCTTTCTCCTCT 58.696 61.111 0.00 0.00 45.13 3.69
977 994 3.256136 TCGAGTCAAACCTTTCTCTCCTC 59.744 47.826 0.00 0.00 0.00 3.71
978 995 3.615351 CGAGTCAAACCTTTCTCTCCTCC 60.615 52.174 0.00 0.00 0.00 4.30
979 996 3.580895 GAGTCAAACCTTTCTCTCCTCCT 59.419 47.826 0.00 0.00 0.00 3.69
980 997 3.580895 AGTCAAACCTTTCTCTCCTCCTC 59.419 47.826 0.00 0.00 0.00 3.71
981 998 2.907042 TCAAACCTTTCTCTCCTCCTCC 59.093 50.000 0.00 0.00 0.00 4.30
982 999 1.959710 AACCTTTCTCTCCTCCTCCC 58.040 55.000 0.00 0.00 0.00 4.30
983 1000 1.097722 ACCTTTCTCTCCTCCTCCCT 58.902 55.000 0.00 0.00 0.00 4.20
984 1001 1.007842 ACCTTTCTCTCCTCCTCCCTC 59.992 57.143 0.00 0.00 0.00 4.30
985 1002 1.691163 CCTTTCTCTCCTCCTCCCTCC 60.691 61.905 0.00 0.00 0.00 4.30
1251 1271 2.673833 GTCGACACCTTCTACAACCTG 58.326 52.381 11.55 0.00 0.00 4.00
2171 2191 0.394488 AGGAGCGGAATCAGACGAGA 60.394 55.000 0.00 0.00 0.00 4.04
2266 2286 6.051179 ACTGAGACTGGTTAATTAGTTCCC 57.949 41.667 0.00 0.00 0.00 3.97
2270 2290 2.240414 ACTGGTTAATTAGTTCCCGGGG 59.760 50.000 23.50 6.77 0.00 5.73
2271 2291 2.506644 CTGGTTAATTAGTTCCCGGGGA 59.493 50.000 23.50 12.99 0.00 4.81
2301 2321 3.010808 TCACCCGAAATCCCCACTTTATT 59.989 43.478 0.00 0.00 0.00 1.40
2305 2325 5.046878 ACCCGAAATCCCCACTTTATTTTTC 60.047 40.000 0.00 0.00 0.00 2.29
2309 2329 3.193395 TCCCCACTTTATTTTTCCCCC 57.807 47.619 0.00 0.00 0.00 5.40
2370 2393 4.081406 CAAACATTGGATTGGAGGACTCA 58.919 43.478 1.32 0.00 0.00 3.41
2382 2405 1.908483 GGACTCATCCCTCACCACC 59.092 63.158 0.00 0.00 39.39 4.61
2383 2406 0.618968 GGACTCATCCCTCACCACCT 60.619 60.000 0.00 0.00 39.39 4.00
2384 2407 0.827368 GACTCATCCCTCACCACCTC 59.173 60.000 0.00 0.00 0.00 3.85
2385 2408 0.117140 ACTCATCCCTCACCACCTCA 59.883 55.000 0.00 0.00 0.00 3.86
2386 2409 0.539051 CTCATCCCTCACCACCTCAC 59.461 60.000 0.00 0.00 0.00 3.51
2387 2410 0.909610 TCATCCCTCACCACCTCACC 60.910 60.000 0.00 0.00 0.00 4.02
2388 2411 1.990060 ATCCCTCACCACCTCACCG 60.990 63.158 0.00 0.00 0.00 4.94
2389 2412 2.748641 ATCCCTCACCACCTCACCGT 62.749 60.000 0.00 0.00 0.00 4.83
2390 2413 2.657237 CCTCACCACCTCACCGTC 59.343 66.667 0.00 0.00 0.00 4.79
2391 2414 1.908793 CCTCACCACCTCACCGTCT 60.909 63.158 0.00 0.00 0.00 4.18
2392 2415 1.290324 CTCACCACCTCACCGTCTG 59.710 63.158 0.00 0.00 0.00 3.51
2393 2416 2.357517 CACCACCTCACCGTCTGC 60.358 66.667 0.00 0.00 0.00 4.26
2394 2417 2.524394 ACCACCTCACCGTCTGCT 60.524 61.111 0.00 0.00 0.00 4.24
2395 2418 2.140792 ACCACCTCACCGTCTGCTT 61.141 57.895 0.00 0.00 0.00 3.91
2396 2419 1.374758 CCACCTCACCGTCTGCTTC 60.375 63.158 0.00 0.00 0.00 3.86
2397 2420 1.668294 CACCTCACCGTCTGCTTCT 59.332 57.895 0.00 0.00 0.00 2.85
2398 2421 0.034059 CACCTCACCGTCTGCTTCTT 59.966 55.000 0.00 0.00 0.00 2.52
2399 2422 0.759346 ACCTCACCGTCTGCTTCTTT 59.241 50.000 0.00 0.00 0.00 2.52
2400 2423 1.141053 ACCTCACCGTCTGCTTCTTTT 59.859 47.619 0.00 0.00 0.00 2.27
2401 2424 2.222027 CCTCACCGTCTGCTTCTTTTT 58.778 47.619 0.00 0.00 0.00 1.94
2402 2425 2.224314 CCTCACCGTCTGCTTCTTTTTC 59.776 50.000 0.00 0.00 0.00 2.29
2403 2426 2.872245 CTCACCGTCTGCTTCTTTTTCA 59.128 45.455 0.00 0.00 0.00 2.69
2404 2427 3.275143 TCACCGTCTGCTTCTTTTTCAA 58.725 40.909 0.00 0.00 0.00 2.69
2405 2428 3.312421 TCACCGTCTGCTTCTTTTTCAAG 59.688 43.478 0.00 0.00 0.00 3.02
2406 2429 3.312421 CACCGTCTGCTTCTTTTTCAAGA 59.688 43.478 0.00 0.00 37.24 3.02
2407 2430 3.945285 ACCGTCTGCTTCTTTTTCAAGAA 59.055 39.130 0.00 0.00 45.20 2.52
2408 2431 4.201920 ACCGTCTGCTTCTTTTTCAAGAAC 60.202 41.667 0.00 0.00 42.99 3.01
2409 2432 4.201910 CCGTCTGCTTCTTTTTCAAGAACA 60.202 41.667 0.00 0.00 42.99 3.18
2410 2433 5.331902 CGTCTGCTTCTTTTTCAAGAACAA 58.668 37.500 0.00 0.00 42.99 2.83
2411 2434 5.228012 CGTCTGCTTCTTTTTCAAGAACAAC 59.772 40.000 0.00 0.98 42.99 3.32
2423 2446 1.120530 AGAACAACCTCACCGTCTGT 58.879 50.000 0.00 0.00 0.00 3.41
2425 2448 2.093128 AGAACAACCTCACCGTCTGTTT 60.093 45.455 0.00 0.00 30.62 2.83
2427 2450 0.859232 CAACCTCACCGTCTGTTTCG 59.141 55.000 0.00 0.00 0.00 3.46
2430 2453 1.134610 ACCTCACCGTCTGTTTCGTTT 60.135 47.619 0.00 0.00 0.00 3.60
2446 2469 1.300080 TTTTGGCTTTGCTGCGAGC 60.300 52.632 16.54 16.54 42.82 5.03
2447 2470 3.541093 TTTGGCTTTGCTGCGAGCG 62.541 57.895 17.71 3.48 46.26 5.03
2466 2489 1.120437 GCGTTGTGTTTTACTGCAGC 58.880 50.000 15.27 0.00 0.00 5.25
2476 2499 1.438651 TTACTGCAGCGATTGTGTCC 58.561 50.000 15.27 0.00 0.00 4.02
2479 2502 1.690283 CTGCAGCGATTGTGTCCGAG 61.690 60.000 0.00 0.00 0.00 4.63
2502 2534 3.276846 GTGTGGGCGTGGTGTGTC 61.277 66.667 0.00 0.00 0.00 3.67
2587 2664 7.093858 GGATCTGTGGTTCAGTTACTTACTAGT 60.094 40.741 0.00 0.00 43.97 2.57
2761 4649 5.438761 ACACTTTCAAAGCATCTACAACC 57.561 39.130 0.00 0.00 0.00 3.77
2768 4656 7.701539 TTCAAAGCATCTACAACCACAATAT 57.298 32.000 0.00 0.00 0.00 1.28
2782 4670 5.445964 ACCACAATATACAAATCTGGACCC 58.554 41.667 0.00 0.00 0.00 4.46
2783 4671 5.193728 ACCACAATATACAAATCTGGACCCT 59.806 40.000 0.00 0.00 0.00 4.34
2784 4672 5.765182 CCACAATATACAAATCTGGACCCTC 59.235 44.000 0.00 0.00 0.00 4.30
2785 4673 5.466728 CACAATATACAAATCTGGACCCTCG 59.533 44.000 0.00 0.00 0.00 4.63
2786 4674 5.365605 ACAATATACAAATCTGGACCCTCGA 59.634 40.000 0.00 0.00 0.00 4.04
2787 4675 6.126883 ACAATATACAAATCTGGACCCTCGAA 60.127 38.462 0.00 0.00 0.00 3.71
2788 4676 2.474410 ACAAATCTGGACCCTCGAAC 57.526 50.000 0.00 0.00 0.00 3.95
2789 4677 1.337823 ACAAATCTGGACCCTCGAACG 60.338 52.381 0.00 0.00 0.00 3.95
2790 4678 0.974383 AAATCTGGACCCTCGAACGT 59.026 50.000 0.00 0.00 0.00 3.99
2791 4679 0.974383 AATCTGGACCCTCGAACGTT 59.026 50.000 0.00 0.00 0.00 3.99
2792 4680 0.531200 ATCTGGACCCTCGAACGTTC 59.469 55.000 18.47 18.47 0.00 3.95
2801 4734 2.027897 CGAACGTTCGTGGACCCA 59.972 61.111 35.92 0.00 45.09 4.51
2832 4765 2.426522 TCGCTTTGATCCCTCACTTTG 58.573 47.619 0.00 0.00 0.00 2.77
2833 4766 2.154462 CGCTTTGATCCCTCACTTTGT 58.846 47.619 0.00 0.00 0.00 2.83
2834 4767 3.007506 TCGCTTTGATCCCTCACTTTGTA 59.992 43.478 0.00 0.00 0.00 2.41
2842 4776 6.542821 TGATCCCTCACTTTGTAGACAAATT 58.457 36.000 8.22 0.51 43.92 1.82
2844 4778 8.160765 TGATCCCTCACTTTGTAGACAAATTTA 58.839 33.333 8.22 0.00 43.92 1.40
2855 4789 6.161381 TGTAGACAAATTTAGACCCTCGAAC 58.839 40.000 0.00 0.00 0.00 3.95
2860 4794 3.947910 ATTTAGACCCTCGAACGTTCA 57.052 42.857 26.71 13.46 0.00 3.18
2862 4796 2.933495 TAGACCCTCGAACGTTCATG 57.067 50.000 26.71 17.62 0.00 3.07
2866 4800 1.343465 ACCCTCGAACGTTCATGAACT 59.657 47.619 30.45 16.96 39.08 3.01
2874 4808 2.346803 ACGTTCATGAACTCATTCGGG 58.653 47.619 30.45 17.50 39.08 5.14
2876 4810 1.062587 GTTCATGAACTCATTCGGGCG 59.937 52.381 27.66 0.00 37.69 6.13
2881 4815 1.129326 GAACTCATTCGGGCGTATCG 58.871 55.000 0.00 0.00 0.00 2.92
2902 4836 5.305585 TCGCTTTGATACCTCACTTTTTCT 58.694 37.500 0.00 0.00 0.00 2.52
2912 4846 1.112459 CACTTTTTCTCGCGCACAAC 58.888 50.000 8.75 0.00 0.00 3.32
2917 4851 0.856641 TTTCTCGCGCACAACTACAC 59.143 50.000 8.75 0.00 0.00 2.90
2923 4857 0.319555 GCGCACAACTACACTCCTCA 60.320 55.000 0.30 0.00 0.00 3.86
2924 4858 1.419374 CGCACAACTACACTCCTCAC 58.581 55.000 0.00 0.00 0.00 3.51
2926 4860 2.545952 CGCACAACTACACTCCTCACTT 60.546 50.000 0.00 0.00 0.00 3.16
2928 4862 3.248602 GCACAACTACACTCCTCACTTTG 59.751 47.826 0.00 0.00 0.00 2.77
2929 4863 4.693283 CACAACTACACTCCTCACTTTGA 58.307 43.478 0.00 0.00 0.00 2.69
2930 4864 5.116180 CACAACTACACTCCTCACTTTGAA 58.884 41.667 0.00 0.00 0.00 2.69
2932 4866 4.338379 ACTACACTCCTCACTTTGAACC 57.662 45.455 0.00 0.00 0.00 3.62
2933 4867 2.640316 ACACTCCTCACTTTGAACCC 57.360 50.000 0.00 0.00 0.00 4.11
2934 4868 2.127708 ACACTCCTCACTTTGAACCCT 58.872 47.619 0.00 0.00 0.00 4.34
2948 4882 6.151144 ACTTTGAACCCTCATTTATCCTTTCG 59.849 38.462 0.00 0.00 0.00 3.46
2973 4907 7.637519 CGATGTCAGATATTTCATCAAACACAC 59.362 37.037 0.00 0.00 37.21 3.82
2975 4909 9.671279 ATGTCAGATATTTCATCAAACACACTA 57.329 29.630 0.00 0.00 0.00 2.74
2992 4926 5.611919 CACACTATGTGCATCATATAACGC 58.388 41.667 8.72 0.00 41.89 4.84
3011 4945 2.679996 GCCCCGCAACCCAATCTT 60.680 61.111 0.00 0.00 0.00 2.40
3014 4948 0.322997 CCCCGCAACCCAATCTTGTA 60.323 55.000 0.00 0.00 0.00 2.41
3019 4953 2.615493 CGCAACCCAATCTTGTAGGAGT 60.615 50.000 0.00 0.00 0.00 3.85
3088 5022 1.346395 GGGTTGGGTGAAAATTGGACC 59.654 52.381 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 89 4.357142 TCCGACGCATAGATTGTCTTTAC 58.643 43.478 0.00 0.00 0.00 2.01
88 90 4.642445 TCCGACGCATAGATTGTCTTTA 57.358 40.909 0.00 0.00 0.00 1.85
115 117 0.109532 TGAACCGGGCTTCAATGACA 59.890 50.000 6.32 0.00 0.00 3.58
152 154 1.691482 CCGAGGACCCCTTAATCCAGA 60.691 57.143 0.00 0.00 37.47 3.86
158 160 3.078836 CGCCCGAGGACCCCTTAA 61.079 66.667 0.00 0.00 31.76 1.85
194 196 3.861797 CGGCCCATTAGTCCGGCT 61.862 66.667 0.00 0.00 42.58 5.52
251 254 1.066573 CATCCACGCAAAGGAGAGTCT 60.067 52.381 0.00 0.00 38.83 3.24
284 287 0.683973 AGGGAGATGCATGATCCGAC 59.316 55.000 17.35 8.03 33.68 4.79
300 303 3.258622 AGAGTCGGTTTACAGAGAAAGGG 59.741 47.826 0.00 0.00 0.00 3.95
360 363 2.817665 AGCCCTACGGACTAAACTCTT 58.182 47.619 0.00 0.00 0.00 2.85
363 366 3.659183 TCTAGCCCTACGGACTAAACT 57.341 47.619 0.00 0.00 0.00 2.66
393 398 5.903589 AGCTAAACCCTAAATGTCTAGCCTA 59.096 40.000 0.00 0.00 32.53 3.93
405 410 6.712095 TCGAGATCGTAATAGCTAAACCCTAA 59.288 38.462 0.00 0.00 40.80 2.69
509 514 1.066716 CGATGTTTACCCAGGTTCGGA 60.067 52.381 0.00 0.00 0.00 4.55
531 536 1.008938 AGGTAACAGGAGGCAGAGGAT 59.991 52.381 0.00 0.00 41.41 3.24
604 609 2.163815 CTCGGAATCTACTGTCGGTGTT 59.836 50.000 0.00 0.00 0.00 3.32
618 623 1.272760 ACTCCTCACTGGTCTCGGAAT 60.273 52.381 0.00 0.00 37.07 3.01
622 627 1.886585 CCACTCCTCACTGGTCTCG 59.113 63.158 0.00 0.00 37.07 4.04
646 651 3.791973 AAGATACACTCTCGAGGCAAG 57.208 47.619 13.56 5.26 31.03 4.01
648 653 3.089284 TGAAAGATACACTCTCGAGGCA 58.911 45.455 13.56 0.00 31.03 4.75
654 659 7.327275 CCGCTATTACATGAAAGATACACTCTC 59.673 40.741 0.00 0.00 31.03 3.20
658 663 6.129168 CGTCCGCTATTACATGAAAGATACAC 60.129 42.308 0.00 0.00 0.00 2.90
667 672 3.190744 GGATCTCGTCCGCTATTACATGA 59.809 47.826 0.00 0.00 37.23 3.07
699 704 7.927788 AGGGGCAAAACATTTTATTCCTTAAT 58.072 30.769 0.00 0.00 0.00 1.40
731 736 1.138069 GACCTGGGCTAGAAGCTCTTC 59.862 57.143 0.00 1.52 43.70 2.87
734 739 0.978146 TGGACCTGGGCTAGAAGCTC 60.978 60.000 0.00 0.00 43.59 4.09
735 740 0.547712 TTGGACCTGGGCTAGAAGCT 60.548 55.000 0.00 0.00 41.99 3.74
736 741 0.107459 CTTGGACCTGGGCTAGAAGC 60.107 60.000 0.00 0.00 41.46 3.86
741 746 3.399181 CGGCTTGGACCTGGGCTA 61.399 66.667 0.00 0.00 0.00 3.93
766 771 2.031682 GTGTTTGCACTTCGATCAGCTT 60.032 45.455 0.00 0.00 42.13 3.74
774 779 1.278637 GTCCCGTGTTTGCACTTCG 59.721 57.895 0.00 0.00 43.16 3.79
791 796 1.378646 TCTGCTCATCTCGACCCGT 60.379 57.895 0.00 0.00 0.00 5.28
801 806 3.029483 TCAGATCTGGACTCTGCTCAT 57.971 47.619 22.42 0.00 39.98 2.90
847 852 1.641577 CTGGATTCGAAACGGAGGAC 58.358 55.000 0.00 0.00 0.00 3.85
848 853 0.108329 GCTGGATTCGAAACGGAGGA 60.108 55.000 14.18 0.00 0.00 3.71
849 854 0.108138 AGCTGGATTCGAAACGGAGG 60.108 55.000 14.18 0.44 0.00 4.30
850 855 1.002366 CAGCTGGATTCGAAACGGAG 58.998 55.000 5.57 7.29 0.00 4.63
851 856 0.391130 CCAGCTGGATTCGAAACGGA 60.391 55.000 29.88 0.00 37.39 4.69
932 949 1.435408 GAGAAAGCGGCTCCAGATGC 61.435 60.000 1.45 0.00 0.00 3.91
955 972 3.231818 AGGAGAGAAAGGTTTGACTCGA 58.768 45.455 0.00 0.00 34.98 4.04
977 994 1.077625 CCGATCTAGGGGAGGGAGG 59.922 68.421 0.00 0.00 0.00 4.30
978 995 4.854587 CCGATCTAGGGGAGGGAG 57.145 66.667 0.00 0.00 0.00 4.30
1251 1271 1.093159 ACTCGTAGATGTCGGTGACC 58.907 55.000 0.00 0.00 33.89 4.02
1467 1487 2.756760 GACCTGGTACTCGTTGATGGTA 59.243 50.000 0.00 0.00 0.00 3.25
1789 1809 3.532155 GGCGATCTCGTCCTGCCT 61.532 66.667 1.14 0.00 42.44 4.75
2040 2060 3.279646 CACCATGTGCATTGGGGTA 57.720 52.632 19.39 0.00 0.00 3.69
2171 2191 4.405116 TCAAAACCAAGAGCTGCATTTT 57.595 36.364 1.02 0.00 0.00 1.82
2266 2286 2.496291 GGGTGATACCGAGTCCCCG 61.496 68.421 0.00 0.00 39.83 5.73
2301 2321 4.931914 TCCACATATTAAACGGGGGAAAA 58.068 39.130 0.00 0.00 0.00 2.29
2305 2325 4.159244 TCTTCCACATATTAAACGGGGG 57.841 45.455 0.00 0.00 0.00 5.40
2309 2329 8.217115 CAGATCGATTCTTCCACATATTAAACG 58.783 37.037 0.00 0.00 29.93 3.60
2370 2393 1.990060 CGGTGAGGTGGTGAGGGAT 60.990 63.158 0.00 0.00 0.00 3.85
2380 2403 0.759346 AAAGAAGCAGACGGTGAGGT 59.241 50.000 0.00 0.00 0.00 3.85
2381 2404 1.884235 AAAAGAAGCAGACGGTGAGG 58.116 50.000 0.00 0.00 0.00 3.86
2382 2405 2.872245 TGAAAAAGAAGCAGACGGTGAG 59.128 45.455 0.00 0.00 0.00 3.51
2383 2406 2.912771 TGAAAAAGAAGCAGACGGTGA 58.087 42.857 0.00 0.00 0.00 4.02
2384 2407 3.312421 TCTTGAAAAAGAAGCAGACGGTG 59.688 43.478 0.00 0.00 0.00 4.94
2385 2408 3.541632 TCTTGAAAAAGAAGCAGACGGT 58.458 40.909 0.00 0.00 0.00 4.83
2386 2409 4.201910 TGTTCTTGAAAAAGAAGCAGACGG 60.202 41.667 1.25 0.00 39.26 4.79
2387 2410 4.908736 TGTTCTTGAAAAAGAAGCAGACG 58.091 39.130 1.25 0.00 39.26 4.18
2388 2411 5.516696 GGTTGTTCTTGAAAAAGAAGCAGAC 59.483 40.000 1.25 0.00 39.26 3.51
2389 2412 5.418840 AGGTTGTTCTTGAAAAAGAAGCAGA 59.581 36.000 1.25 0.00 39.26 4.26
2390 2413 5.654497 AGGTTGTTCTTGAAAAAGAAGCAG 58.346 37.500 1.25 0.00 39.26 4.24
2391 2414 5.184864 TGAGGTTGTTCTTGAAAAAGAAGCA 59.815 36.000 1.25 1.58 39.26 3.91
2392 2415 5.516696 GTGAGGTTGTTCTTGAAAAAGAAGC 59.483 40.000 1.25 0.00 39.26 3.86
2393 2416 6.036470 GGTGAGGTTGTTCTTGAAAAAGAAG 58.964 40.000 1.25 0.00 39.26 2.85
2394 2417 5.392595 CGGTGAGGTTGTTCTTGAAAAAGAA 60.393 40.000 0.00 0.00 36.52 2.52
2395 2418 4.095782 CGGTGAGGTTGTTCTTGAAAAAGA 59.904 41.667 0.00 0.00 0.00 2.52
2396 2419 4.142469 ACGGTGAGGTTGTTCTTGAAAAAG 60.142 41.667 0.00 0.00 0.00 2.27
2397 2420 3.759618 ACGGTGAGGTTGTTCTTGAAAAA 59.240 39.130 0.00 0.00 0.00 1.94
2398 2421 3.349022 ACGGTGAGGTTGTTCTTGAAAA 58.651 40.909 0.00 0.00 0.00 2.29
2399 2422 2.940410 GACGGTGAGGTTGTTCTTGAAA 59.060 45.455 0.00 0.00 0.00 2.69
2400 2423 2.169769 AGACGGTGAGGTTGTTCTTGAA 59.830 45.455 0.00 0.00 0.00 2.69
2401 2424 1.760613 AGACGGTGAGGTTGTTCTTGA 59.239 47.619 0.00 0.00 0.00 3.02
2402 2425 1.867233 CAGACGGTGAGGTTGTTCTTG 59.133 52.381 0.00 0.00 0.00 3.02
2403 2426 1.485066 ACAGACGGTGAGGTTGTTCTT 59.515 47.619 0.00 0.00 0.00 2.52
2404 2427 1.120530 ACAGACGGTGAGGTTGTTCT 58.879 50.000 0.00 0.00 0.00 3.01
2405 2428 1.949465 AACAGACGGTGAGGTTGTTC 58.051 50.000 0.00 0.00 0.00 3.18
2406 2429 2.285977 GAAACAGACGGTGAGGTTGTT 58.714 47.619 0.00 0.00 33.73 2.83
2407 2430 1.805120 CGAAACAGACGGTGAGGTTGT 60.805 52.381 0.00 0.00 0.00 3.32
2408 2431 0.859232 CGAAACAGACGGTGAGGTTG 59.141 55.000 0.00 0.00 0.00 3.77
2409 2432 0.462789 ACGAAACAGACGGTGAGGTT 59.537 50.000 0.00 0.00 34.93 3.50
2410 2433 0.462789 AACGAAACAGACGGTGAGGT 59.537 50.000 0.00 0.00 34.93 3.85
2411 2434 1.578583 AAACGAAACAGACGGTGAGG 58.421 50.000 0.00 0.00 34.93 3.86
2423 2446 1.285578 GCAGCAAAGCCAAAACGAAA 58.714 45.000 0.00 0.00 0.00 3.46
2425 2448 1.299014 CGCAGCAAAGCCAAAACGA 60.299 52.632 0.00 0.00 0.00 3.85
2427 2450 1.551503 GCTCGCAGCAAAGCCAAAAC 61.552 55.000 5.61 0.00 41.89 2.43
2430 2453 4.029186 CGCTCGCAGCAAAGCCAA 62.029 61.111 10.44 0.00 42.58 4.52
2446 2469 1.385038 CTGCAGTAAAACACAACGCG 58.615 50.000 3.53 3.53 0.00 6.01
2447 2470 1.120437 GCTGCAGTAAAACACAACGC 58.880 50.000 16.64 0.00 0.00 4.84
2455 2478 2.225491 GGACACAATCGCTGCAGTAAAA 59.775 45.455 16.64 0.00 0.00 1.52
2466 2489 3.554692 GGCGCTCGGACACAATCG 61.555 66.667 7.64 0.00 0.00 3.34
2499 2531 2.129146 AAGACCCACCGTGTCGACA 61.129 57.895 15.76 15.76 37.80 4.35
2500 2532 1.663702 CAAGACCCACCGTGTCGAC 60.664 63.158 9.11 9.11 37.80 4.20
2502 2534 2.167398 ATCCAAGACCCACCGTGTCG 62.167 60.000 0.00 0.00 37.80 4.35
2568 2645 8.469309 AGTACAACTAGTAAGTAACTGAACCA 57.531 34.615 9.05 0.00 39.39 3.67
2587 2664 4.808895 CCTGCACGCAGAAATATAGTACAA 59.191 41.667 20.42 0.00 46.30 2.41
2761 4649 5.466728 CGAGGGTCCAGATTTGTATATTGTG 59.533 44.000 0.00 0.00 0.00 3.33
2768 4656 2.094390 CGTTCGAGGGTCCAGATTTGTA 60.094 50.000 0.00 0.00 0.00 2.41
2785 4673 0.794473 GAATGGGTCCACGAACGTTC 59.206 55.000 18.47 18.47 0.00 3.95
2786 4674 0.947180 CGAATGGGTCCACGAACGTT 60.947 55.000 0.00 0.00 0.00 3.99
2787 4675 1.373748 CGAATGGGTCCACGAACGT 60.374 57.895 0.00 0.00 0.00 3.99
2788 4676 2.098233 CCGAATGGGTCCACGAACG 61.098 63.158 0.00 0.00 0.00 3.95
2789 4677 3.884900 CCGAATGGGTCCACGAAC 58.115 61.111 0.00 0.00 0.00 3.95
2801 4734 2.572191 TCAAAGCGATACGACCGAAT 57.428 45.000 0.00 0.00 0.00 3.34
2814 4747 4.393371 GTCTACAAAGTGAGGGATCAAAGC 59.607 45.833 0.00 0.00 0.00 3.51
2832 4765 5.287992 CGTTCGAGGGTCTAAATTTGTCTAC 59.712 44.000 0.00 0.00 0.00 2.59
2833 4766 5.047802 ACGTTCGAGGGTCTAAATTTGTCTA 60.048 40.000 0.00 0.00 0.00 2.59
2834 4767 4.243270 CGTTCGAGGGTCTAAATTTGTCT 58.757 43.478 0.00 0.00 0.00 3.41
2842 4776 2.821378 TCATGAACGTTCGAGGGTCTAA 59.179 45.455 22.48 2.77 0.00 2.10
2844 4778 1.254026 TCATGAACGTTCGAGGGTCT 58.746 50.000 22.48 0.00 0.00 3.85
2855 4789 1.062587 GCCCGAATGAGTTCATGAACG 59.937 52.381 28.18 17.44 45.50 3.95
2860 4794 2.755650 GATACGCCCGAATGAGTTCAT 58.244 47.619 0.00 0.00 38.41 2.57
2862 4796 1.129326 CGATACGCCCGAATGAGTTC 58.871 55.000 0.00 0.00 0.00 3.01
2881 4815 5.622378 CGAGAAAAAGTGAGGTATCAAAGC 58.378 41.667 0.00 0.00 37.14 3.51
2902 4836 1.372499 GGAGTGTAGTTGTGCGCGA 60.372 57.895 12.10 0.00 0.00 5.87
2912 4846 3.325135 AGGGTTCAAAGTGAGGAGTGTAG 59.675 47.826 0.00 0.00 0.00 2.74
2917 4851 3.710209 ATGAGGGTTCAAAGTGAGGAG 57.290 47.619 0.00 0.00 36.78 3.69
2923 4857 6.151144 CGAAAGGATAAATGAGGGTTCAAAGT 59.849 38.462 0.00 0.00 36.78 2.66
2924 4858 6.374333 TCGAAAGGATAAATGAGGGTTCAAAG 59.626 38.462 0.00 0.00 36.78 2.77
2926 4860 5.811190 TCGAAAGGATAAATGAGGGTTCAA 58.189 37.500 0.00 0.00 36.78 2.69
2928 4862 5.823045 ACATCGAAAGGATAAATGAGGGTTC 59.177 40.000 0.00 0.00 32.85 3.62
2929 4863 5.755849 ACATCGAAAGGATAAATGAGGGTT 58.244 37.500 0.00 0.00 32.85 4.11
2930 4864 5.104527 TGACATCGAAAGGATAAATGAGGGT 60.105 40.000 0.00 0.00 32.85 4.34
2932 4866 6.283694 TCTGACATCGAAAGGATAAATGAGG 58.716 40.000 0.00 0.00 32.85 3.86
2933 4867 7.959689 ATCTGACATCGAAAGGATAAATGAG 57.040 36.000 0.00 0.00 32.85 2.90
2948 4882 8.671921 AGTGTGTTTGATGAAATATCTGACATC 58.328 33.333 0.00 0.00 39.35 3.06
2973 4907 3.242091 GCCGCGTTATATGATGCACATAG 60.242 47.826 11.77 0.00 43.48 2.23
2975 4909 1.464608 GCCGCGTTATATGATGCACAT 59.535 47.619 11.77 0.00 42.39 3.21
3011 4945 4.363573 TCTCTCTCCACTCTACTCCTACA 58.636 47.826 0.00 0.00 0.00 2.74
3014 4948 4.108570 TCTTCTCTCTCCACTCTACTCCT 58.891 47.826 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.