Multiple sequence alignment - TraesCS7A01G359200

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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 TraesCS7A01G359200 chr7A 100.000 2696 0 0 1 2696 533322163 533324858 0.000000e+00 4979.0
1 TraesCS7A01G359200 chr7A 96.866 1978 38 15 1 1958 532955737 532953764 0.000000e+00 3288.0
2 TraesCS7A01G359200 chr7A 92.081 1427 62 18 1 1397 533005300 533003895 0.000000e+00 1962.0
3 TraesCS7A01G359200 chr7A 92.577 485 36 0 1212 1696 533035740 533035256 0.000000e+00 697.0
4 TraesCS7A01G359200 chr7A 90.645 310 29 0 1387 1696 533003101 533002792 1.930000e-111 412.0
5 TraesCS7A01G359200 chr7A 100.000 29 0 0 553 581 715763717 715763689 1.000000e-03 54.7
6 TraesCS7A01G359200 chr7B 92.134 928 50 6 793 1699 491116454 491117379 0.000000e+00 1288.0
7 TraesCS7A01G359200 chr7B 92.459 862 50 4 903 1750 490950313 490949453 0.000000e+00 1218.0
8 TraesCS7A01G359200 chr7B 89.316 833 42 22 905 1699 490896643 490895820 0.000000e+00 1002.0
9 TraesCS7A01G359200 chr7B 81.175 834 67 39 145 913 490899511 490898703 2.990000e-164 588.0
10 TraesCS7A01G359200 chr7B 83.957 561 63 15 264 808 490952141 490951592 1.850000e-141 512.0
11 TraesCS7A01G359200 chr7B 81.050 686 71 19 143 808 491115794 491116440 2.410000e-135 492.0
12 TraesCS7A01G359200 chr7B 90.572 297 27 1 2299 2594 490892903 490892607 2.520000e-105 392.0
13 TraesCS7A01G359200 chr7B 80.597 268 34 11 2029 2288 490895311 490895054 9.850000e-45 191.0
14 TraesCS7A01G359200 chr7B 82.738 168 20 5 1960 2120 491120755 491120920 1.010000e-29 141.0
15 TraesCS7A01G359200 chr7B 87.850 107 7 3 905 1010 490897306 490897205 1.310000e-23 121.0
16 TraesCS7A01G359200 chr7B 97.436 39 1 0 972 1010 490896804 490896766 1.730000e-07 67.6
17 TraesCS7A01G359200 chr7B 100.000 32 0 0 739 770 325992552 325992583 2.900000e-05 60.2
18 TraesCS7A01G359200 chr7D 88.866 979 50 24 919 1859 467682517 467683474 0.000000e+00 1149.0
19 TraesCS7A01G359200 chr5D 78.082 219 39 5 2199 2409 505539799 505539582 2.180000e-26 130.0
20 TraesCS7A01G359200 chr6B 100.000 29 0 0 739 767 500600779 500600751 1.000000e-03 54.7
21 TraesCS7A01G359200 chr3A 88.636 44 5 0 368 411 625406822 625406865 1.000000e-03 54.7


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 TraesCS7A01G359200 chr7A 533322163 533324858 2695 False 4979.000000 4979 100.000000 1 2696 1 chr7A.!!$F1 2695
1 TraesCS7A01G359200 chr7A 532953764 532955737 1973 True 3288.000000 3288 96.866000 1 1958 1 chr7A.!!$R1 1957
2 TraesCS7A01G359200 chr7A 533002792 533005300 2508 True 1187.000000 1962 91.363000 1 1696 2 chr7A.!!$R4 1695
3 TraesCS7A01G359200 chr7B 490949453 490952141 2688 True 865.000000 1218 88.208000 264 1750 2 chr7B.!!$R2 1486
4 TraesCS7A01G359200 chr7B 491115794 491120920 5126 False 640.333333 1288 85.307333 143 2120 3 chr7B.!!$F2 1977
5 TraesCS7A01G359200 chr7B 490892607 490899511 6904 True 393.600000 1002 87.824333 145 2594 6 chr7B.!!$R1 2449
6 TraesCS7A01G359200 chr7D 467682517 467683474 957 False 1149.000000 1149 88.866000 919 1859 1 chr7D.!!$F1 940

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
108 109 0.399091 TGGCTATGGAGAGTCCCTGG 60.399 60.000 0.00 0.00 35.03 4.45 F
970 3663 1.523711 GAATCGGCGAGCCCAATGA 60.524 57.895 17.22 0.05 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1138 3875 0.250901 GACTTGAGGAAGGCCAGCAA 60.251 55.0 5.01 0.31 36.29 3.91 R
2611 11686 0.029567 CTCATCACCGACGCCTAGTC 59.970 60.0 0.00 0.00 46.16 2.59 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
33 34 1.312815 GAGCCTCGGGATTCCAATTG 58.687 55.000 4.80 0.00 0.00 2.32
108 109 0.399091 TGGCTATGGAGAGTCCCTGG 60.399 60.000 0.00 0.00 35.03 4.45
124 125 3.655777 TCCCTGGTATCATTTGTATCCCC 59.344 47.826 0.00 0.00 0.00 4.81
707 801 2.831526 ACAGAACAGGCAAAACTGGTTT 59.168 40.909 0.00 0.00 38.83 3.27
970 3663 1.523711 GAATCGGCGAGCCCAATGA 60.524 57.895 17.22 0.05 0.00 2.57
1613 5154 6.103997 TCAACGATATCTTTGACTACAACCC 58.896 40.000 17.98 0.00 35.63 4.11
1730 5271 1.137086 GAAACAGCTAGCCTCATCCGA 59.863 52.381 12.13 0.00 0.00 4.55
1860 8451 6.892658 ACCTTATGATTTGTTTGTAGCACA 57.107 33.333 0.00 0.00 0.00 4.57
1880 8471 5.277974 GCACAAAACAAGTTGATGAGCTAGA 60.278 40.000 10.54 0.00 32.59 2.43
1958 8775 5.051039 TGTCTTCGAATTCTGAAAGTTCACG 60.051 40.000 0.00 0.00 32.90 4.35
1964 8885 6.866770 TCGAATTCTGAAAGTTCACGAGTAAT 59.133 34.615 3.52 0.00 32.90 1.89
1969 8890 6.687604 TCTGAAAGTTCACGAGTAATGATCA 58.312 36.000 0.00 0.00 32.90 2.92
1979 8900 3.063997 CGAGTAATGATCAGTGGTTTGCC 59.936 47.826 5.80 0.00 0.00 4.52
2001 8926 1.330655 TGGAGAGGATCGGCCAAGAC 61.331 60.000 2.24 0.00 40.55 3.01
2005 8930 0.537188 GAGGATCGGCCAAGACAAGA 59.463 55.000 2.24 0.00 40.02 3.02
2006 8931 1.139853 GAGGATCGGCCAAGACAAGAT 59.860 52.381 2.24 0.00 40.02 2.40
2009 8934 0.254178 ATCGGCCAAGACAAGATGCT 59.746 50.000 2.24 0.00 0.00 3.79
2015 8940 2.353406 GCCAAGACAAGATGCTGCAATT 60.353 45.455 6.36 1.57 0.00 2.32
2019 8944 5.107220 CCAAGACAAGATGCTGCAATTTTTC 60.107 40.000 6.36 6.95 0.00 2.29
2021 8946 5.850614 AGACAAGATGCTGCAATTTTTCTT 58.149 33.333 6.36 8.05 0.00 2.52
2022 8947 5.924825 AGACAAGATGCTGCAATTTTTCTTC 59.075 36.000 6.36 0.31 0.00 2.87
2023 8948 5.850614 ACAAGATGCTGCAATTTTTCTTCT 58.149 33.333 6.36 0.00 0.00 2.85
2025 8950 7.436118 ACAAGATGCTGCAATTTTTCTTCTTA 58.564 30.769 6.36 0.00 0.00 2.10
2026 8951 7.927629 ACAAGATGCTGCAATTTTTCTTCTTAA 59.072 29.630 6.36 0.00 0.00 1.85
2063 8988 4.150451 GCAATGCAAAACGCTAGAACAATT 59.850 37.500 0.00 0.00 43.06 2.32
2124 9051 9.786105 AAAGAAAAACTGTATTTGCAAATTTGG 57.214 25.926 28.45 19.26 0.00 3.28
2125 9052 8.729805 AGAAAAACTGTATTTGCAAATTTGGA 57.270 26.923 28.45 14.42 0.00 3.53
2163 9090 9.492973 AAAACTATATGCATTTGAAATATGGCC 57.507 29.630 3.54 0.00 0.00 5.36
2164 9091 8.426569 AACTATATGCATTTGAAATATGGCCT 57.573 30.769 3.54 0.00 0.00 5.19
2165 9092 8.426569 ACTATATGCATTTGAAATATGGCCTT 57.573 30.769 3.54 0.00 0.00 4.35
2166 9093 8.308931 ACTATATGCATTTGAAATATGGCCTTG 58.691 33.333 3.54 0.00 0.00 3.61
2168 9095 5.417754 TGCATTTGAAATATGGCCTTGAA 57.582 34.783 3.32 0.00 0.00 2.69
2169 9096 5.177326 TGCATTTGAAATATGGCCTTGAAC 58.823 37.500 3.32 0.00 0.00 3.18
2178 9106 0.882927 TGGCCTTGAACGGAAAGTCG 60.883 55.000 3.32 0.00 0.00 4.18
2179 9107 1.574702 GGCCTTGAACGGAAAGTCGG 61.575 60.000 0.00 0.00 0.00 4.79
2180 9108 0.601841 GCCTTGAACGGAAAGTCGGA 60.602 55.000 0.00 0.00 0.00 4.55
2190 9118 5.952526 ACGGAAAGTCGGAACATTAAAAT 57.047 34.783 0.00 0.00 0.00 1.82
2191 9119 7.172875 TGAACGGAAAGTCGGAACATTAAAATA 59.827 33.333 0.00 0.00 0.00 1.40
2238 9172 2.723273 GGAATCACCCAATTCCGAGTT 58.277 47.619 0.22 0.00 43.86 3.01
2241 9175 0.682852 TCACCCAATTCCGAGTTCGT 59.317 50.000 0.48 0.00 37.74 3.85
2245 9179 3.800506 CACCCAATTCCGAGTTCGTATAC 59.199 47.826 0.48 0.00 37.74 1.47
2246 9180 3.047796 CCCAATTCCGAGTTCGTATACG 58.952 50.000 19.23 19.23 41.45 3.06
2247 9181 3.489738 CCCAATTCCGAGTTCGTATACGT 60.490 47.826 23.67 5.86 40.80 3.57
2251 9185 1.935873 TCCGAGTTCGTATACGTCCTG 59.064 52.381 23.67 11.55 40.80 3.86
2252 9186 1.003116 CCGAGTTCGTATACGTCCTGG 60.003 57.143 23.67 19.10 40.80 4.45
2277 9211 4.100344 GGTCCAAACCACAAAAACTACCAT 59.900 41.667 0.00 0.00 45.68 3.55
2279 9213 6.110033 GTCCAAACCACAAAAACTACCATTT 58.890 36.000 0.00 0.00 0.00 2.32
2283 9217 7.982354 CCAAACCACAAAAACTACCATTTTAGA 59.018 33.333 0.00 0.00 31.50 2.10
2294 9228 9.758651 AAACTACCATTTTAGAAAATCCAACAC 57.241 29.630 0.00 0.00 36.52 3.32
2295 9229 8.472007 ACTACCATTTTAGAAAATCCAACACA 57.528 30.769 0.00 0.00 36.52 3.72
2296 9230 8.576442 ACTACCATTTTAGAAAATCCAACACAG 58.424 33.333 0.00 0.00 36.52 3.66
2323 11397 1.749634 ACGGGATTGACTCTAACTCCG 59.250 52.381 0.00 0.00 41.65 4.63
2330 11404 4.884668 TTGACTCTAACTCCGTCCAAAT 57.115 40.909 0.00 0.00 0.00 2.32
2346 11420 5.920193 TCCAAATTTGATGGATCTCAACC 57.080 39.130 19.86 0.00 41.98 3.77
2359 11433 4.164221 GGATCTCAACCTGGTTTGATCCTA 59.836 45.833 35.37 14.58 42.75 2.94
2364 11438 3.933861 ACCTGGTTTGATCCTATGGAC 57.066 47.619 0.00 0.00 32.98 4.02
2384 11458 4.158025 GGACTCACAAGAAGATACGGAAGA 59.842 45.833 0.00 0.00 0.00 2.87
2389 11463 7.332182 ACTCACAAGAAGATACGGAAGATTTTC 59.668 37.037 0.00 0.00 0.00 2.29
2397 11471 1.350019 ACGGAAGATTTTCGAGGGGTT 59.650 47.619 0.00 0.00 33.98 4.11
2398 11472 1.737793 CGGAAGATTTTCGAGGGGTTG 59.262 52.381 0.00 0.00 33.98 3.77
2405 11480 0.111446 TTTCGAGGGGTTGGCAATGA 59.889 50.000 1.92 0.00 0.00 2.57
2440 11515 1.836391 CAATGCCCTATGGGTCGGA 59.164 57.895 4.42 0.00 46.51 4.55
2443 11518 0.473694 ATGCCCTATGGGTCGGATGA 60.474 55.000 4.42 0.00 46.51 2.92
2462 11537 5.642063 GGATGACCGAAATTTGAAGACTACA 59.358 40.000 0.00 0.00 0.00 2.74
2467 11542 6.708285 ACCGAAATTTGAAGACTACACCTAT 58.292 36.000 0.00 0.00 0.00 2.57
2492 11567 4.904253 TTGACGGAAAACCCTACTTTTG 57.096 40.909 0.00 0.00 0.00 2.44
2494 11569 3.628487 TGACGGAAAACCCTACTTTTGTG 59.372 43.478 0.00 0.00 0.00 3.33
2521 11596 2.216940 CACTTGTGTGCGAAAATTGCAG 59.783 45.455 0.00 0.00 44.21 4.41
2522 11597 1.190763 CTTGTGTGCGAAAATTGCAGC 59.809 47.619 0.00 0.00 44.21 5.25
2536 11611 4.275508 CAGCCCCATAGCCGCCAT 62.276 66.667 0.00 0.00 0.00 4.40
2538 11613 3.297620 GCCCCATAGCCGCCATTG 61.298 66.667 0.00 0.00 0.00 2.82
2541 11616 2.126596 CCCATAGCCGCCATTGCAA 61.127 57.895 0.00 0.00 37.32 4.08
2558 11633 6.207417 CCATTGCAAAGGAGAAAACTCTTCTA 59.793 38.462 15.69 0.00 0.00 2.10
2574 11649 7.592885 ACTCTTCTACAACCAACACTACTAA 57.407 36.000 0.00 0.00 0.00 2.24
2576 11651 7.924947 ACTCTTCTACAACCAACACTACTAAAC 59.075 37.037 0.00 0.00 0.00 2.01
2594 11669 9.764363 CTACTAAACATAGGAATAGCATTGACA 57.236 33.333 0.00 0.00 0.00 3.58
2596 11671 9.277783 ACTAAACATAGGAATAGCATTGACATC 57.722 33.333 0.00 0.00 0.00 3.06
2597 11672 9.276590 CTAAACATAGGAATAGCATTGACATCA 57.723 33.333 0.00 0.00 0.00 3.07
2598 11673 7.502120 AACATAGGAATAGCATTGACATCAC 57.498 36.000 0.00 0.00 0.00 3.06
2599 11674 6.835174 ACATAGGAATAGCATTGACATCACT 58.165 36.000 0.00 0.00 0.00 3.41
2600 11675 6.709397 ACATAGGAATAGCATTGACATCACTG 59.291 38.462 0.00 0.00 0.00 3.66
2601 11676 5.363562 AGGAATAGCATTGACATCACTGA 57.636 39.130 3.59 0.00 0.00 3.41
2602 11677 5.121811 AGGAATAGCATTGACATCACTGAC 58.878 41.667 3.59 0.00 0.00 3.51
2603 11678 5.104610 AGGAATAGCATTGACATCACTGACT 60.105 40.000 3.59 3.36 0.00 3.41
2604 11679 5.007430 GGAATAGCATTGACATCACTGACTG 59.993 44.000 3.59 0.00 0.00 3.51
2605 11680 2.708051 AGCATTGACATCACTGACTGG 58.292 47.619 3.59 0.00 0.00 4.00
2606 11681 1.131883 GCATTGACATCACTGACTGGC 59.868 52.381 3.59 0.00 0.00 4.85
2607 11682 1.741706 CATTGACATCACTGACTGGCC 59.258 52.381 0.00 0.00 0.00 5.36
2608 11683 1.059098 TTGACATCACTGACTGGCCT 58.941 50.000 3.32 0.00 0.00 5.19
2609 11684 1.059098 TGACATCACTGACTGGCCTT 58.941 50.000 3.32 0.00 0.00 4.35
2610 11685 1.271001 TGACATCACTGACTGGCCTTG 60.271 52.381 3.32 0.00 0.00 3.61
2611 11686 0.037303 ACATCACTGACTGGCCTTGG 59.963 55.000 3.32 0.00 0.00 3.61
2612 11687 0.325933 CATCACTGACTGGCCTTGGA 59.674 55.000 3.32 0.00 0.00 3.53
2613 11688 0.326264 ATCACTGACTGGCCTTGGAC 59.674 55.000 3.32 0.00 0.00 4.02
2614 11689 0.764369 TCACTGACTGGCCTTGGACT 60.764 55.000 3.32 0.00 0.00 3.85
2615 11690 0.976641 CACTGACTGGCCTTGGACTA 59.023 55.000 3.32 0.00 0.00 2.59
2616 11691 1.066573 CACTGACTGGCCTTGGACTAG 60.067 57.143 3.32 0.00 0.00 2.57
2617 11692 0.539051 CTGACTGGCCTTGGACTAGG 59.461 60.000 3.32 0.00 38.40 3.02
2623 11698 2.494918 CCTTGGACTAGGCGTCGG 59.505 66.667 0.00 0.00 43.79 4.79
2624 11699 2.348888 CCTTGGACTAGGCGTCGGT 61.349 63.158 0.00 0.00 43.79 4.69
2625 11700 1.153823 CTTGGACTAGGCGTCGGTG 60.154 63.158 0.00 0.00 43.79 4.94
2626 11701 1.592400 CTTGGACTAGGCGTCGGTGA 61.592 60.000 0.00 0.00 43.79 4.02
2627 11702 0.968901 TTGGACTAGGCGTCGGTGAT 60.969 55.000 0.00 0.00 43.79 3.06
2628 11703 1.065928 GGACTAGGCGTCGGTGATG 59.934 63.158 0.00 0.00 43.79 3.07
2629 11704 1.381928 GGACTAGGCGTCGGTGATGA 61.382 60.000 0.00 0.00 43.79 2.92
2630 11705 0.029567 GACTAGGCGTCGGTGATGAG 59.970 60.000 0.00 0.00 32.04 2.90
2631 11706 1.299468 CTAGGCGTCGGTGATGAGC 60.299 63.158 0.00 0.00 0.00 4.26
2633 11708 4.451150 GGCGTCGGTGATGAGCCA 62.451 66.667 0.00 0.00 46.48 4.75
2634 11709 2.202932 GCGTCGGTGATGAGCCAT 60.203 61.111 0.00 0.00 0.00 4.40
2635 11710 1.067416 GCGTCGGTGATGAGCCATA 59.933 57.895 0.00 0.00 0.00 2.74
2636 11711 0.941463 GCGTCGGTGATGAGCCATAG 60.941 60.000 0.00 0.00 0.00 2.23
2637 11712 0.941463 CGTCGGTGATGAGCCATAGC 60.941 60.000 0.00 0.00 40.32 2.97
2638 11713 0.104855 GTCGGTGATGAGCCATAGCA 59.895 55.000 0.00 0.00 43.56 3.49
2639 11714 1.051008 TCGGTGATGAGCCATAGCAT 58.949 50.000 0.00 0.00 43.56 3.79
2640 11715 1.417517 TCGGTGATGAGCCATAGCATT 59.582 47.619 0.00 0.00 43.56 3.56
2641 11716 1.534163 CGGTGATGAGCCATAGCATTG 59.466 52.381 0.00 0.00 43.56 2.82
2642 11717 2.807837 CGGTGATGAGCCATAGCATTGA 60.808 50.000 0.00 0.00 43.56 2.57
2643 11718 2.551459 GGTGATGAGCCATAGCATTGAC 59.449 50.000 0.00 0.00 43.56 3.18
2644 11719 2.551459 GTGATGAGCCATAGCATTGACC 59.449 50.000 0.00 0.00 43.56 4.02
2645 11720 2.173143 TGATGAGCCATAGCATTGACCA 59.827 45.455 0.00 0.00 43.56 4.02
2646 11721 2.336945 TGAGCCATAGCATTGACCAG 57.663 50.000 0.00 0.00 43.56 4.00
2647 11722 0.950116 GAGCCATAGCATTGACCAGC 59.050 55.000 0.00 0.00 43.56 4.85
2648 11723 0.816825 AGCCATAGCATTGACCAGCG 60.817 55.000 0.00 0.00 43.56 5.18
2649 11724 1.097547 GCCATAGCATTGACCAGCGT 61.098 55.000 0.00 0.00 39.53 5.07
2650 11725 1.382522 CCATAGCATTGACCAGCGTT 58.617 50.000 0.00 0.00 35.48 4.84
2651 11726 1.331756 CCATAGCATTGACCAGCGTTC 59.668 52.381 0.00 0.00 35.48 3.95
2652 11727 2.283298 CATAGCATTGACCAGCGTTCT 58.717 47.619 0.00 0.00 35.48 3.01
2653 11728 3.457234 CATAGCATTGACCAGCGTTCTA 58.543 45.455 0.00 0.00 35.48 2.10
2654 11729 2.015736 AGCATTGACCAGCGTTCTAG 57.984 50.000 0.00 0.00 35.48 2.43
2655 11730 0.375106 GCATTGACCAGCGTTCTAGC 59.625 55.000 0.00 0.00 37.41 3.42
2656 11731 1.725641 CATTGACCAGCGTTCTAGCA 58.274 50.000 0.00 0.00 40.15 3.49
2657 11732 1.394917 CATTGACCAGCGTTCTAGCAC 59.605 52.381 0.00 0.00 40.15 4.40
2658 11733 0.666274 TTGACCAGCGTTCTAGCACG 60.666 55.000 10.73 10.73 43.36 5.34
2664 11739 3.238241 CGTTCTAGCACGCGTCCG 61.238 66.667 9.86 0.00 41.14 4.79
2677 11752 2.523015 CGCGTCCGTAATATGTATCCC 58.477 52.381 0.00 0.00 0.00 3.85
2678 11753 2.163010 CGCGTCCGTAATATGTATCCCT 59.837 50.000 0.00 0.00 0.00 4.20
2679 11754 3.374988 CGCGTCCGTAATATGTATCCCTA 59.625 47.826 0.00 0.00 0.00 3.53
2680 11755 4.495349 CGCGTCCGTAATATGTATCCCTAG 60.495 50.000 0.00 0.00 0.00 3.02
2681 11756 4.397417 GCGTCCGTAATATGTATCCCTAGT 59.603 45.833 0.00 0.00 0.00 2.57
2682 11757 5.448360 GCGTCCGTAATATGTATCCCTAGTC 60.448 48.000 0.00 0.00 0.00 2.59
2683 11758 5.879223 CGTCCGTAATATGTATCCCTAGTCT 59.121 44.000 0.00 0.00 0.00 3.24
2684 11759 6.036953 CGTCCGTAATATGTATCCCTAGTCTC 59.963 46.154 0.00 0.00 0.00 3.36
2685 11760 6.036953 GTCCGTAATATGTATCCCTAGTCTCG 59.963 46.154 0.00 0.00 0.00 4.04
2686 11761 5.296283 CCGTAATATGTATCCCTAGTCTCGG 59.704 48.000 0.00 0.00 0.00 4.63
2687 11762 5.220815 CGTAATATGTATCCCTAGTCTCGGC 60.221 48.000 0.00 0.00 0.00 5.54
2688 11763 2.982339 ATGTATCCCTAGTCTCGGCT 57.018 50.000 0.00 0.00 0.00 5.52
2689 11764 2.750141 TGTATCCCTAGTCTCGGCTT 57.250 50.000 0.00 0.00 0.00 4.35
2690 11765 2.307768 TGTATCCCTAGTCTCGGCTTG 58.692 52.381 0.00 0.00 0.00 4.01
2691 11766 2.092049 TGTATCCCTAGTCTCGGCTTGA 60.092 50.000 0.00 0.00 0.00 3.02
2692 11767 1.698506 ATCCCTAGTCTCGGCTTGAG 58.301 55.000 0.70 0.70 46.72 3.02
2693 11768 0.395862 TCCCTAGTCTCGGCTTGAGG 60.396 60.000 6.66 0.00 45.32 3.86
2694 11769 1.395826 CCCTAGTCTCGGCTTGAGGG 61.396 65.000 6.66 0.00 45.32 4.30
2695 11770 1.439644 CTAGTCTCGGCTTGAGGGC 59.560 63.158 6.66 1.81 45.32 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 4.092383 CCTTTGCAAACATATGAGCTTTGC 59.908 41.667 24.62 24.62 46.56 3.68
53 54 1.099879 GCAAGAGATGATGCGGCCTT 61.100 55.000 0.00 0.00 0.00 4.35
108 109 9.403583 TCAAAGTAAAGGGGATACAAATGATAC 57.596 33.333 0.00 0.00 39.74 2.24
400 441 4.992688 ACTCGCTGTTTCAAAATGTTCAA 58.007 34.783 0.00 0.00 0.00 2.69
970 3663 5.779771 TCTTCTGGGGTGCTTTTATTGATTT 59.220 36.000 0.00 0.00 0.00 2.17
1138 3875 0.250901 GACTTGAGGAAGGCCAGCAA 60.251 55.000 5.01 0.31 36.29 3.91
1613 5154 4.161295 TCCCCCTCATGAAGCGCG 62.161 66.667 0.00 0.00 0.00 6.86
1860 8451 7.420800 CACTTTCTAGCTCATCAACTTGTTTT 58.579 34.615 0.00 0.00 0.00 2.43
1880 8471 4.836125 AACTTTCATCGTCATGCACTTT 57.164 36.364 0.00 0.00 0.00 2.66
1958 8775 4.265073 AGGCAAACCACTGATCATTACTC 58.735 43.478 0.00 0.00 39.06 2.59
1969 8890 0.689623 CTCTCCAGAGGCAAACCACT 59.310 55.000 0.00 0.00 37.35 4.00
1979 8900 1.045350 TTGGCCGATCCTCTCCAGAG 61.045 60.000 0.00 0.00 41.71 3.35
1983 8908 1.330655 TGTCTTGGCCGATCCTCTCC 61.331 60.000 0.00 0.00 35.26 3.71
1984 8909 0.537188 TTGTCTTGGCCGATCCTCTC 59.463 55.000 0.00 0.00 35.26 3.20
1993 8918 1.246056 TGCAGCATCTTGTCTTGGCC 61.246 55.000 0.00 0.00 0.00 5.36
2001 8926 6.780706 AAGAAGAAAAATTGCAGCATCTTG 57.219 33.333 12.05 0.00 0.00 3.02
2006 8931 9.979578 TTCTTATTAAGAAGAAAAATTGCAGCA 57.020 25.926 20.12 0.00 42.31 4.41
2021 8946 4.518278 TGCAGCCCCATTCTTATTAAGA 57.482 40.909 1.90 1.90 35.26 2.10
2022 8947 5.535333 CATTGCAGCCCCATTCTTATTAAG 58.465 41.667 0.00 0.00 0.00 1.85
2023 8948 4.202243 GCATTGCAGCCCCATTCTTATTAA 60.202 41.667 3.15 0.00 0.00 1.40
2025 8950 2.103601 GCATTGCAGCCCCATTCTTATT 59.896 45.455 3.15 0.00 0.00 1.40
2026 8951 1.690352 GCATTGCAGCCCCATTCTTAT 59.310 47.619 3.15 0.00 0.00 1.73
2063 8988 7.571025 AGAAAGTGAGTAAACTAGAACCCAAA 58.429 34.615 0.00 0.00 0.00 3.28
2100 9025 8.729805 TCCAAATTTGCAAATACAGTTTTTCT 57.270 26.923 24.35 2.55 0.00 2.52
2101 9026 9.780413 TTTCCAAATTTGCAAATACAGTTTTTC 57.220 25.926 24.35 0.00 0.00 2.29
2144 9071 6.728089 TCAAGGCCATATTTCAAATGCATA 57.272 33.333 5.01 0.00 0.00 3.14
2146 9073 5.177326 GTTCAAGGCCATATTTCAAATGCA 58.823 37.500 5.01 0.00 0.00 3.96
2156 9083 3.279434 GACTTTCCGTTCAAGGCCATAT 58.721 45.455 5.01 0.00 0.00 1.78
2157 9084 2.706890 GACTTTCCGTTCAAGGCCATA 58.293 47.619 5.01 0.00 0.00 2.74
2158 9085 1.534729 GACTTTCCGTTCAAGGCCAT 58.465 50.000 5.01 0.00 0.00 4.40
2159 9086 0.882927 CGACTTTCCGTTCAAGGCCA 60.883 55.000 5.01 0.00 0.00 5.36
2161 9088 0.601841 TCCGACTTTCCGTTCAAGGC 60.602 55.000 0.00 0.00 0.00 4.35
2163 9090 2.206750 TGTTCCGACTTTCCGTTCAAG 58.793 47.619 0.00 0.00 0.00 3.02
2164 9091 2.312722 TGTTCCGACTTTCCGTTCAA 57.687 45.000 0.00 0.00 0.00 2.69
2165 9092 2.536761 ATGTTCCGACTTTCCGTTCA 57.463 45.000 0.00 0.00 0.00 3.18
2166 9093 4.996062 TTAATGTTCCGACTTTCCGTTC 57.004 40.909 0.00 0.00 0.00 3.95
2168 9095 5.952526 ATTTTAATGTTCCGACTTTCCGT 57.047 34.783 0.00 0.00 0.00 4.69
2169 9096 8.730970 TTTTATTTTAATGTTCCGACTTTCCG 57.269 30.769 0.00 0.00 0.00 4.30
2207 9141 2.983192 TGGGTGATTCCAAGTCCTACAA 59.017 45.455 0.00 0.00 38.11 2.41
2208 9142 2.626785 TGGGTGATTCCAAGTCCTACA 58.373 47.619 0.00 0.00 38.11 2.74
2209 9143 3.713826 TTGGGTGATTCCAAGTCCTAC 57.286 47.619 0.00 0.00 41.44 3.18
2233 9167 1.935873 TCCAGGACGTATACGAACTCG 59.064 52.381 30.77 18.93 43.02 4.18
2238 9172 1.475751 GGACCTCCAGGACGTATACGA 60.476 57.143 30.77 7.09 39.76 3.43
2251 9185 2.764010 AGTTTTTGTGGTTTGGACCTCC 59.236 45.455 0.00 0.00 46.66 4.30
2252 9186 4.202080 GGTAGTTTTTGTGGTTTGGACCTC 60.202 45.833 0.00 0.00 46.66 3.85
2277 9211 5.596361 TGCCTCTGTGTTGGATTTTCTAAAA 59.404 36.000 0.00 0.00 0.00 1.52
2279 9213 4.724399 TGCCTCTGTGTTGGATTTTCTAA 58.276 39.130 0.00 0.00 0.00 2.10
2283 9217 2.887152 GTCTGCCTCTGTGTTGGATTTT 59.113 45.455 0.00 0.00 0.00 1.82
2288 9222 1.669115 CCGTCTGCCTCTGTGTTGG 60.669 63.158 0.00 0.00 0.00 3.77
2290 9224 1.194781 ATCCCGTCTGCCTCTGTGTT 61.195 55.000 0.00 0.00 0.00 3.32
2292 9226 0.742281 CAATCCCGTCTGCCTCTGTG 60.742 60.000 0.00 0.00 0.00 3.66
2293 9227 0.904865 TCAATCCCGTCTGCCTCTGT 60.905 55.000 0.00 0.00 0.00 3.41
2294 9228 0.460987 GTCAATCCCGTCTGCCTCTG 60.461 60.000 0.00 0.00 0.00 3.35
2295 9229 0.616111 AGTCAATCCCGTCTGCCTCT 60.616 55.000 0.00 0.00 0.00 3.69
2296 9230 0.179097 GAGTCAATCCCGTCTGCCTC 60.179 60.000 0.00 0.00 0.00 4.70
2323 11397 5.420104 AGGTTGAGATCCATCAAATTTGGAC 59.580 40.000 17.90 4.24 45.71 4.02
2330 11404 4.387026 AACCAGGTTGAGATCCATCAAA 57.613 40.909 3.18 0.00 40.72 2.69
2344 11418 3.456277 GAGTCCATAGGATCAAACCAGGT 59.544 47.826 0.00 0.00 32.73 4.00
2346 11420 4.080919 TGTGAGTCCATAGGATCAAACCAG 60.081 45.833 0.00 0.00 32.73 4.00
2359 11433 4.023980 TCCGTATCTTCTTGTGAGTCCAT 58.976 43.478 0.00 0.00 0.00 3.41
2364 11438 7.463383 CGAAAATCTTCCGTATCTTCTTGTGAG 60.463 40.741 0.00 0.00 0.00 3.51
2384 11458 1.550072 CATTGCCAACCCCTCGAAAAT 59.450 47.619 0.00 0.00 0.00 1.82
2389 11463 2.046285 GGTCATTGCCAACCCCTCG 61.046 63.158 0.00 0.00 0.00 4.63
2397 11471 2.283821 GGCCCTTGGTCATTGCCA 60.284 61.111 0.00 0.00 41.76 4.92
2398 11472 3.076916 GGGCCCTTGGTCATTGCC 61.077 66.667 17.04 0.00 41.42 4.52
2410 11485 3.464494 GCATTGCTCCAAGGGCCC 61.464 66.667 16.46 16.46 0.00 5.80
2440 11515 5.411669 GGTGTAGTCTTCAAATTTCGGTCAT 59.588 40.000 0.00 0.00 0.00 3.06
2443 11518 4.969484 AGGTGTAGTCTTCAAATTTCGGT 58.031 39.130 0.00 0.00 0.00 4.69
2462 11537 6.758806 AGGGTTTTCCGTCAATATATAGGT 57.241 37.500 0.00 0.00 41.82 3.08
2467 11542 7.884354 ACAAAAGTAGGGTTTTCCGTCAATATA 59.116 33.333 0.00 0.00 41.82 0.86
2492 11567 3.749981 CACACAAGTGCCCCTCAC 58.250 61.111 0.00 0.00 45.98 3.51
2510 11585 1.536709 GCTATGGGGCTGCAATTTTCG 60.537 52.381 0.50 0.00 0.00 3.46
2521 11596 3.297620 CAATGGCGGCTATGGGGC 61.298 66.667 11.43 0.00 37.12 5.80
2522 11597 3.297620 GCAATGGCGGCTATGGGG 61.298 66.667 11.43 0.00 0.00 4.96
2558 11633 7.069877 TCCTATGTTTAGTAGTGTTGGTTGT 57.930 36.000 0.00 0.00 0.00 3.32
2574 11649 7.228108 CAGTGATGTCAATGCTATTCCTATGTT 59.772 37.037 0.00 0.00 35.12 2.71
2576 11651 6.932960 TCAGTGATGTCAATGCTATTCCTATG 59.067 38.462 5.64 0.00 41.24 2.23
2594 11669 0.326264 GTCCAAGGCCAGTCAGTGAT 59.674 55.000 5.01 0.00 0.00 3.06
2595 11670 0.764369 AGTCCAAGGCCAGTCAGTGA 60.764 55.000 5.01 0.00 0.00 3.41
2596 11671 0.976641 TAGTCCAAGGCCAGTCAGTG 59.023 55.000 5.01 0.00 0.00 3.66
2597 11672 1.270907 CTAGTCCAAGGCCAGTCAGT 58.729 55.000 5.01 0.00 0.00 3.41
2598 11673 0.539051 CCTAGTCCAAGGCCAGTCAG 59.461 60.000 5.01 0.00 0.00 3.51
2599 11674 2.683916 CCTAGTCCAAGGCCAGTCA 58.316 57.895 5.01 0.00 0.00 3.41
2606 11681 2.348888 ACCGACGCCTAGTCCAAGG 61.349 63.158 0.00 0.00 46.92 3.61
2607 11682 1.153823 CACCGACGCCTAGTCCAAG 60.154 63.158 0.00 0.00 46.92 3.61
2608 11683 0.968901 ATCACCGACGCCTAGTCCAA 60.969 55.000 0.00 0.00 46.92 3.53
2609 11684 1.379443 ATCACCGACGCCTAGTCCA 60.379 57.895 0.00 0.00 46.92 4.02
2610 11685 1.065928 CATCACCGACGCCTAGTCC 59.934 63.158 0.00 0.00 46.92 3.85
2611 11686 0.029567 CTCATCACCGACGCCTAGTC 59.970 60.000 0.00 0.00 46.16 2.59
2612 11687 2.005960 GCTCATCACCGACGCCTAGT 62.006 60.000 0.00 0.00 0.00 2.57
2613 11688 1.299468 GCTCATCACCGACGCCTAG 60.299 63.158 0.00 0.00 0.00 3.02
2614 11689 2.782222 GGCTCATCACCGACGCCTA 61.782 63.158 0.00 0.00 37.76 3.93
2615 11690 4.148825 GGCTCATCACCGACGCCT 62.149 66.667 0.00 0.00 37.76 5.52
2616 11691 2.363711 TATGGCTCATCACCGACGCC 62.364 60.000 0.00 0.00 41.06 5.68
2617 11692 0.941463 CTATGGCTCATCACCGACGC 60.941 60.000 0.00 0.00 0.00 5.19
2618 11693 0.941463 GCTATGGCTCATCACCGACG 60.941 60.000 0.00 0.00 35.22 5.12
2619 11694 0.104855 TGCTATGGCTCATCACCGAC 59.895 55.000 1.68 0.00 39.59 4.79
2620 11695 1.051008 ATGCTATGGCTCATCACCGA 58.949 50.000 1.68 0.00 39.59 4.69
2621 11696 1.534163 CAATGCTATGGCTCATCACCG 59.466 52.381 1.68 0.00 39.59 4.94
2622 11697 2.551459 GTCAATGCTATGGCTCATCACC 59.449 50.000 1.68 0.00 39.59 4.02
2623 11698 2.551459 GGTCAATGCTATGGCTCATCAC 59.449 50.000 1.68 0.00 39.59 3.06
2624 11699 2.173143 TGGTCAATGCTATGGCTCATCA 59.827 45.455 1.68 0.00 39.59 3.07
2625 11700 2.812591 CTGGTCAATGCTATGGCTCATC 59.187 50.000 1.68 0.00 39.59 2.92
2626 11701 2.860009 CTGGTCAATGCTATGGCTCAT 58.140 47.619 1.68 0.00 39.59 2.90
2627 11702 1.748244 GCTGGTCAATGCTATGGCTCA 60.748 52.381 1.68 0.00 39.59 4.26
2628 11703 0.950116 GCTGGTCAATGCTATGGCTC 59.050 55.000 1.68 0.00 39.59 4.70
2629 11704 0.816825 CGCTGGTCAATGCTATGGCT 60.817 55.000 1.68 0.00 39.59 4.75
2630 11705 1.097547 ACGCTGGTCAATGCTATGGC 61.098 55.000 0.00 0.00 39.26 4.40
2631 11706 1.331756 GAACGCTGGTCAATGCTATGG 59.668 52.381 0.00 0.00 0.00 2.74
2632 11707 2.283298 AGAACGCTGGTCAATGCTATG 58.717 47.619 0.00 0.00 0.00 2.23
2633 11708 2.698855 AGAACGCTGGTCAATGCTAT 57.301 45.000 0.00 0.00 0.00 2.97
2634 11709 2.738643 GCTAGAACGCTGGTCAATGCTA 60.739 50.000 0.00 0.00 0.00 3.49
2635 11710 2.009042 GCTAGAACGCTGGTCAATGCT 61.009 52.381 0.00 0.00 0.00 3.79
2636 11711 0.375106 GCTAGAACGCTGGTCAATGC 59.625 55.000 0.00 0.00 0.00 3.56
2637 11712 1.394917 GTGCTAGAACGCTGGTCAATG 59.605 52.381 0.00 0.00 0.00 2.82
2638 11713 1.726853 GTGCTAGAACGCTGGTCAAT 58.273 50.000 0.00 0.00 0.00 2.57
2639 11714 0.666274 CGTGCTAGAACGCTGGTCAA 60.666 55.000 11.04 0.00 36.65 3.18
2640 11715 1.080772 CGTGCTAGAACGCTGGTCA 60.081 57.895 11.04 0.00 36.65 4.02
2641 11716 3.768632 CGTGCTAGAACGCTGGTC 58.231 61.111 11.04 0.00 36.65 4.02
2647 11722 2.567470 TACGGACGCGTGCTAGAACG 62.567 60.000 28.07 19.46 46.30 3.95
2648 11723 0.454957 TTACGGACGCGTGCTAGAAC 60.455 55.000 28.07 6.23 0.00 3.01
2649 11724 0.452987 ATTACGGACGCGTGCTAGAA 59.547 50.000 28.07 18.32 0.00 2.10
2650 11725 1.298602 TATTACGGACGCGTGCTAGA 58.701 50.000 28.07 13.60 0.00 2.43
2651 11726 1.976728 CATATTACGGACGCGTGCTAG 59.023 52.381 28.07 16.14 0.00 3.42
2652 11727 1.334556 ACATATTACGGACGCGTGCTA 59.665 47.619 28.07 16.10 0.00 3.49
2653 11728 0.101759 ACATATTACGGACGCGTGCT 59.898 50.000 28.07 17.10 0.00 4.40
2654 11729 1.757574 TACATATTACGGACGCGTGC 58.242 50.000 20.70 21.34 0.00 5.34
2655 11730 2.912967 GGATACATATTACGGACGCGTG 59.087 50.000 20.70 5.54 0.00 5.34
2656 11731 2.095059 GGGATACATATTACGGACGCGT 60.095 50.000 13.85 13.85 39.74 6.01
2657 11732 2.163010 AGGGATACATATTACGGACGCG 59.837 50.000 3.53 3.53 39.74 6.01
2658 11733 3.863142 AGGGATACATATTACGGACGC 57.137 47.619 0.00 0.00 39.74 5.19
2659 11734 5.879223 AGACTAGGGATACATATTACGGACG 59.121 44.000 0.00 0.00 39.74 4.79
2660 11735 6.036953 CGAGACTAGGGATACATATTACGGAC 59.963 46.154 0.00 0.00 39.74 4.79
2661 11736 6.111382 CGAGACTAGGGATACATATTACGGA 58.889 44.000 0.00 0.00 39.74 4.69
2662 11737 5.296283 CCGAGACTAGGGATACATATTACGG 59.704 48.000 0.00 0.00 32.80 4.02
2663 11738 5.220815 GCCGAGACTAGGGATACATATTACG 60.221 48.000 3.58 0.00 39.74 3.18
2664 11739 5.887035 AGCCGAGACTAGGGATACATATTAC 59.113 44.000 3.58 0.00 39.74 1.89
2665 11740 6.075949 AGCCGAGACTAGGGATACATATTA 57.924 41.667 3.58 0.00 39.74 0.98
2666 11741 4.936802 AGCCGAGACTAGGGATACATATT 58.063 43.478 3.58 0.00 39.74 1.28
2667 11742 4.594675 AGCCGAGACTAGGGATACATAT 57.405 45.455 3.58 0.00 39.74 1.78
2668 11743 4.079970 CAAGCCGAGACTAGGGATACATA 58.920 47.826 3.58 0.00 39.74 2.29
2669 11744 2.894126 CAAGCCGAGACTAGGGATACAT 59.106 50.000 3.58 0.00 39.74 2.29
2670 11745 2.092049 TCAAGCCGAGACTAGGGATACA 60.092 50.000 3.58 0.00 39.74 2.29
2671 11746 2.554893 CTCAAGCCGAGACTAGGGATAC 59.445 54.545 3.58 0.00 45.45 2.24
2672 11747 2.489255 CCTCAAGCCGAGACTAGGGATA 60.489 54.545 3.58 0.00 45.45 2.59
2673 11748 1.698506 CTCAAGCCGAGACTAGGGAT 58.301 55.000 3.58 0.00 45.45 3.85
2674 11749 0.395862 CCTCAAGCCGAGACTAGGGA 60.396 60.000 3.58 0.00 45.45 4.20
2675 11750 1.395826 CCCTCAAGCCGAGACTAGGG 61.396 65.000 3.58 0.00 45.45 3.53
2676 11751 2.022240 GCCCTCAAGCCGAGACTAGG 62.022 65.000 2.33 0.00 45.45 3.02
2677 11752 1.439644 GCCCTCAAGCCGAGACTAG 59.560 63.158 2.33 0.00 45.45 2.57
2678 11753 3.617368 GCCCTCAAGCCGAGACTA 58.383 61.111 2.33 0.00 45.45 2.59


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

AutoCloner maintained by Alex Coulton.