Multiple sequence alignment - TraesCS4A01G031700

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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 TraesCS4A01G031700 chr4A 100.000 3172 0 0 1 3172 24761735 24764906 0.000000e+00 5858.0
1 TraesCS4A01G031700 chr4A 99.101 779 7 0 1 779 467532667 467531889 0.000000e+00 1400.0
2 TraesCS4A01G031700 chr4A 86.911 191 25 0 2526 2716 621564019 621564209 6.890000e-52 215.0
3 TraesCS4A01G031700 chr4A 90.323 62 6 0 776 837 175055760 175055821 7.290000e-12 82.4
4 TraesCS4A01G031700 chr4A 90.164 61 6 0 776 836 581475394 581475334 2.620000e-11 80.5
5 TraesCS4A01G031700 chr4B 89.707 2283 125 58 840 3069 552019569 552017344 0.000000e+00 2813.0
6 TraesCS4A01G031700 chr4B 91.379 58 5 0 776 833 562324311 562324368 2.620000e-11 80.5
7 TraesCS4A01G031700 chr4D 88.605 2387 133 69 852 3169 442900548 442898232 0.000000e+00 2772.0
8 TraesCS4A01G031700 chr6B 99.101 779 7 0 1 779 18914197 18914975 0.000000e+00 1400.0
9 TraesCS4A01G031700 chr5B 99.101 779 7 0 1 779 391230279 391229501 0.000000e+00 1400.0
10 TraesCS4A01G031700 chr5B 99.101 779 7 0 1 779 407129982 407130760 0.000000e+00 1400.0
11 TraesCS4A01G031700 chr5B 85.638 188 27 0 2529 2716 690909509 690909322 6.940000e-47 198.0
12 TraesCS4A01G031700 chr3B 99.101 779 7 0 1 779 454717948 454717170 0.000000e+00 1400.0
13 TraesCS4A01G031700 chr3B 93.103 58 4 0 776 833 773428201 773428258 5.640000e-13 86.1
14 TraesCS4A01G031700 chr3B 90.164 61 6 0 776 836 696703275 696703215 2.620000e-11 80.5
15 TraesCS4A01G031700 chr3A 99.101 779 7 0 1 779 11868304 11867526 0.000000e+00 1400.0
16 TraesCS4A01G031700 chr3A 90.164 61 6 0 776 836 547933364 547933304 2.620000e-11 80.5
17 TraesCS4A01G031700 chr2B 99.101 779 7 0 1 779 46598494 46599272 0.000000e+00 1400.0
18 TraesCS4A01G031700 chr2B 99.101 779 7 0 1 779 178705512 178706290 0.000000e+00 1400.0
19 TraesCS4A01G031700 chr2B 91.379 58 5 0 779 836 662485353 662485296 2.620000e-11 80.5
20 TraesCS4A01G031700 chr1B 99.101 779 7 0 1 779 393263066 393263844 0.000000e+00 1400.0
21 TraesCS4A01G031700 chr5D 86.911 191 25 0 2526 2716 547607257 547607447 6.890000e-52 215.0
22 TraesCS4A01G031700 chrUn 86.387 191 26 0 2526 2716 68495166 68495356 3.210000e-50 209.0
23 TraesCS4A01G031700 chr5A 93.443 61 4 0 776 836 661222758 661222698 1.210000e-14 91.6
24 TraesCS4A01G031700 chr5A 90.625 64 6 0 776 839 586310161 586310098 5.640000e-13 86.1


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 TraesCS4A01G031700 chr4A 24761735 24764906 3171 False 5858 5858 100.000 1 3172 1 chr4A.!!$F1 3171
1 TraesCS4A01G031700 chr4A 467531889 467532667 778 True 1400 1400 99.101 1 779 1 chr4A.!!$R1 778
2 TraesCS4A01G031700 chr4B 552017344 552019569 2225 True 2813 2813 89.707 840 3069 1 chr4B.!!$R1 2229
3 TraesCS4A01G031700 chr4D 442898232 442900548 2316 True 2772 2772 88.605 852 3169 1 chr4D.!!$R1 2317
4 TraesCS4A01G031700 chr6B 18914197 18914975 778 False 1400 1400 99.101 1 779 1 chr6B.!!$F1 778
5 TraesCS4A01G031700 chr5B 391229501 391230279 778 True 1400 1400 99.101 1 779 1 chr5B.!!$R1 778
6 TraesCS4A01G031700 chr5B 407129982 407130760 778 False 1400 1400 99.101 1 779 1 chr5B.!!$F1 778
7 TraesCS4A01G031700 chr3B 454717170 454717948 778 True 1400 1400 99.101 1 779 1 chr3B.!!$R1 778
8 TraesCS4A01G031700 chr3A 11867526 11868304 778 True 1400 1400 99.101 1 779 1 chr3A.!!$R1 778
9 TraesCS4A01G031700 chr2B 46598494 46599272 778 False 1400 1400 99.101 1 779 1 chr2B.!!$F1 778
10 TraesCS4A01G031700 chr2B 178705512 178706290 778 False 1400 1400 99.101 1 779 1 chr2B.!!$F2 778
11 TraesCS4A01G031700 chr1B 393263066 393263844 778 False 1400 1400 99.101 1 779 1 chr1B.!!$F1 778

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
947 957 0.106967 CAAGGGGAAGGAAGCTAGGC 60.107 60.0 0.0 0.0 0.00 3.93 F
948 958 0.253394 AAGGGGAAGGAAGCTAGGCT 60.253 55.0 0.0 0.0 42.56 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 1977 1.134995 TCAGTGAGCAAAGCGATCGAT 60.135 47.619 21.57 10.64 0.00 3.59 R
2497 2570 1.329292 TGCTTACCGCGATTATGTTGC 59.671 47.619 8.23 5.50 43.27 4.17 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
315 316 0.609131 CGACCCCTTGCTTCACCAAT 60.609 55.000 0.00 0.00 0.00 3.16
408 409 4.083590 GCGTCTGAAGCAATCTTTCTTCTT 60.084 41.667 10.72 0.00 39.41 2.52
532 533 2.569059 CAAGTCGCCATCTTCATCCAT 58.431 47.619 0.00 0.00 0.00 3.41
582 583 1.228190 GGGCCCTCCTTAAATACCCA 58.772 55.000 17.04 0.00 35.84 4.51
639 640 1.135083 CCACCACTTCGTTCTAGCGAT 60.135 52.381 0.00 0.00 40.76 4.58
779 780 4.229304 TCTTCTCTTCTCGAGAGGATGT 57.771 45.455 25.43 0.00 46.34 3.06
780 781 5.360649 TCTTCTCTTCTCGAGAGGATGTA 57.639 43.478 25.43 12.73 46.34 2.29
781 782 5.935945 TCTTCTCTTCTCGAGAGGATGTAT 58.064 41.667 25.43 0.00 46.34 2.29
782 783 6.361433 TCTTCTCTTCTCGAGAGGATGTATT 58.639 40.000 25.43 0.00 46.34 1.89
783 784 6.831353 TCTTCTCTTCTCGAGAGGATGTATTT 59.169 38.462 25.43 0.00 46.34 1.40
784 785 7.340743 TCTTCTCTTCTCGAGAGGATGTATTTT 59.659 37.037 25.43 0.00 46.34 1.82
787 788 7.883391 TCTTCTCGAGAGGATGTATTTTAGT 57.117 36.000 22.11 0.00 0.00 2.24
788 789 8.294954 TCTTCTCGAGAGGATGTATTTTAGTT 57.705 34.615 22.11 0.00 0.00 2.24
789 790 8.407064 TCTTCTCGAGAGGATGTATTTTAGTTC 58.593 37.037 22.11 0.00 0.00 3.01
790 791 7.883391 TCTCGAGAGGATGTATTTTAGTTCT 57.117 36.000 12.08 0.00 0.00 3.01
791 792 8.975663 TCTCGAGAGGATGTATTTTAGTTCTA 57.024 34.615 12.08 0.00 0.00 2.10
792 793 9.404848 TCTCGAGAGGATGTATTTTAGTTCTAA 57.595 33.333 12.08 0.00 0.00 2.10
827 828 6.019779 TCCAAGACAAATAATTTGGAACGG 57.980 37.500 2.52 0.00 44.38 4.44
828 829 5.770663 TCCAAGACAAATAATTTGGAACGGA 59.229 36.000 2.52 0.00 44.38 4.69
829 830 6.072175 TCCAAGACAAATAATTTGGAACGGAG 60.072 38.462 2.52 0.00 44.38 4.63
830 831 5.897377 AGACAAATAATTTGGAACGGAGG 57.103 39.130 0.00 0.00 44.81 4.30
831 832 4.705023 AGACAAATAATTTGGAACGGAGGG 59.295 41.667 0.00 0.00 44.81 4.30
832 833 4.668636 ACAAATAATTTGGAACGGAGGGA 58.331 39.130 0.00 0.00 44.81 4.20
833 834 5.081032 ACAAATAATTTGGAACGGAGGGAA 58.919 37.500 0.00 0.00 44.81 3.97
834 835 5.719563 ACAAATAATTTGGAACGGAGGGAAT 59.280 36.000 0.00 0.00 44.81 3.01
835 836 6.893005 ACAAATAATTTGGAACGGAGGGAATA 59.107 34.615 0.00 0.00 44.81 1.75
836 837 6.954487 AATAATTTGGAACGGAGGGAATAC 57.046 37.500 0.00 0.00 0.00 1.89
837 838 2.793288 TTTGGAACGGAGGGAATACC 57.207 50.000 0.00 0.00 40.67 2.73
850 851 3.734463 GGGAATACCTAGCAAAGAGAGC 58.266 50.000 0.00 0.00 35.85 4.09
854 855 4.826274 ATACCTAGCAAAGAGAGCACAA 57.174 40.909 0.00 0.00 0.00 3.33
859 860 0.514691 GCAAAGAGAGCACAAGGACG 59.485 55.000 0.00 0.00 0.00 4.79
886 892 1.227674 CCACCTATCCTCAAGCCGC 60.228 63.158 0.00 0.00 0.00 6.53
902 908 2.025969 CGCTGGATATGAGGCTGCG 61.026 63.158 0.00 0.00 36.19 5.18
939 949 0.408309 TCGAGTCTCAAGGGGAAGGA 59.592 55.000 0.00 0.00 0.00 3.36
941 951 1.205893 CGAGTCTCAAGGGGAAGGAAG 59.794 57.143 0.00 0.00 0.00 3.46
942 952 0.988063 AGTCTCAAGGGGAAGGAAGC 59.012 55.000 0.00 0.00 0.00 3.86
943 953 0.988063 GTCTCAAGGGGAAGGAAGCT 59.012 55.000 0.00 0.00 0.00 3.74
944 954 2.188817 GTCTCAAGGGGAAGGAAGCTA 58.811 52.381 0.00 0.00 0.00 3.32
945 955 2.169561 GTCTCAAGGGGAAGGAAGCTAG 59.830 54.545 0.00 0.00 0.00 3.42
946 956 1.488393 CTCAAGGGGAAGGAAGCTAGG 59.512 57.143 0.00 0.00 0.00 3.02
947 957 0.106967 CAAGGGGAAGGAAGCTAGGC 60.107 60.000 0.00 0.00 0.00 3.93
948 958 0.253394 AAGGGGAAGGAAGCTAGGCT 60.253 55.000 0.00 0.00 42.56 4.58
992 1002 0.741326 TATCACTCACTCCAGCGCTC 59.259 55.000 7.13 0.00 0.00 5.03
993 1003 1.954362 ATCACTCACTCCAGCGCTCC 61.954 60.000 7.13 0.00 0.00 4.70
1131 1147 3.443925 TCGCAGCTGGAGGAGACG 61.444 66.667 17.12 8.60 0.00 4.18
1371 1387 2.750637 GAGGCCTCCTCGTCGTCA 60.751 66.667 23.19 0.00 41.08 4.35
1799 1836 2.290577 ACACCATCCTCAAGAAGAAGGC 60.291 50.000 0.00 0.00 0.00 4.35
1895 1932 0.316204 ATCGACCAGGTTCGTTCGTT 59.684 50.000 0.00 0.00 40.07 3.85
1909 1951 2.728846 CGTTCGTTTCTTGGGATGCATG 60.729 50.000 2.46 0.00 0.00 4.06
1912 1954 1.067706 CGTTTCTTGGGATGCATGCAA 60.068 47.619 26.68 5.71 0.00 4.08
1913 1955 2.417651 CGTTTCTTGGGATGCATGCAAT 60.418 45.455 26.68 13.38 0.00 3.56
1934 1977 9.558396 TGCAATGTACTGTATGATAATCATTCA 57.442 29.630 0.00 0.00 38.26 2.57
1943 1986 7.260603 TGTATGATAATCATTCATCGATCGCT 58.739 34.615 11.09 0.00 38.26 4.93
1956 1999 2.099098 TCGATCGCTTTGCTCACTGATA 59.901 45.455 11.09 0.00 0.00 2.15
1961 2004 6.128715 CGATCGCTTTGCTCACTGATAATATT 60.129 38.462 0.26 0.00 0.00 1.28
1965 2008 6.238456 CGCTTTGCTCACTGATAATATTTGGA 60.238 38.462 0.00 0.00 0.00 3.53
1966 2009 6.914757 GCTTTGCTCACTGATAATATTTGGAC 59.085 38.462 0.00 0.00 0.00 4.02
1971 2014 6.017605 GCTCACTGATAATATTTGGACTGTGG 60.018 42.308 0.00 0.00 0.00 4.17
1973 2016 6.823182 TCACTGATAATATTTGGACTGTGGTG 59.177 38.462 0.00 0.00 0.00 4.17
2175 2226 1.597663 AGCACGACAACTTGTAACTGC 59.402 47.619 0.00 2.62 0.00 4.40
2248 2307 6.157820 TCACATGGGGATGAATCTTGTAACTA 59.842 38.462 0.00 0.00 0.00 2.24
2264 2323 5.919755 TGTAACTACCCATTGCGATCAATA 58.080 37.500 0.00 0.00 40.74 1.90
2276 2335 4.125703 TGCGATCAATATGTACACATGCA 58.874 39.130 0.00 0.00 37.15 3.96
2280 2339 6.400409 GCGATCAATATGTACACATGCAGTAG 60.400 42.308 0.00 0.00 37.15 2.57
2282 2341 7.543520 CGATCAATATGTACACATGCAGTAGAT 59.456 37.037 0.00 11.58 37.15 1.98
2289 2348 5.580691 TGTACACATGCAGTAGATTACTTGC 59.419 40.000 0.00 0.00 36.76 4.01
2290 2349 3.941483 ACACATGCAGTAGATTACTTGCC 59.059 43.478 0.00 0.00 36.76 4.52
2291 2350 3.313526 CACATGCAGTAGATTACTTGCCC 59.686 47.826 0.00 0.00 36.76 5.36
2292 2351 3.054434 ACATGCAGTAGATTACTTGCCCA 60.054 43.478 0.00 0.00 36.76 5.36
2293 2352 3.931907 TGCAGTAGATTACTTGCCCAT 57.068 42.857 0.00 0.00 36.76 4.00
2295 2354 3.455910 TGCAGTAGATTACTTGCCCATCT 59.544 43.478 0.00 0.00 36.76 2.90
2296 2355 4.061596 GCAGTAGATTACTTGCCCATCTC 58.938 47.826 0.00 0.00 36.76 2.75
2298 2357 3.961408 AGTAGATTACTTGCCCATCTCGT 59.039 43.478 0.00 0.00 34.86 4.18
2299 2358 5.009710 CAGTAGATTACTTGCCCATCTCGTA 59.990 44.000 0.00 0.00 36.76 3.43
2300 2359 5.597182 AGTAGATTACTTGCCCATCTCGTAA 59.403 40.000 0.00 0.00 34.86 3.18
2301 2360 4.694339 AGATTACTTGCCCATCTCGTAAC 58.306 43.478 0.00 0.00 0.00 2.50
2366 2426 5.943416 TGTGAAGAAGACTTGAAAACCTCAA 59.057 36.000 0.00 0.00 41.93 3.02
2367 2427 6.432783 TGTGAAGAAGACTTGAAAACCTCAAA 59.567 34.615 0.00 0.00 43.54 2.69
2368 2428 6.969473 GTGAAGAAGACTTGAAAACCTCAAAG 59.031 38.462 0.00 0.00 43.54 2.77
2369 2429 6.095440 TGAAGAAGACTTGAAAACCTCAAAGG 59.905 38.462 0.00 0.00 43.54 3.11
2370 2430 5.755849 AGAAGACTTGAAAACCTCAAAGGA 58.244 37.500 0.00 0.00 43.54 3.36
2371 2431 6.187682 AGAAGACTTGAAAACCTCAAAGGAA 58.812 36.000 0.00 0.00 43.54 3.36
2372 2432 6.319911 AGAAGACTTGAAAACCTCAAAGGAAG 59.680 38.462 0.00 0.00 43.54 3.46
2373 2433 5.510430 AGACTTGAAAACCTCAAAGGAAGT 58.490 37.500 0.00 0.00 43.54 3.01
2374 2434 5.952347 AGACTTGAAAACCTCAAAGGAAGTT 59.048 36.000 0.00 0.00 43.54 2.66
2375 2435 7.116736 AGACTTGAAAACCTCAAAGGAAGTTA 58.883 34.615 0.00 0.00 43.54 2.24
2376 2436 7.780271 AGACTTGAAAACCTCAAAGGAAGTTAT 59.220 33.333 0.00 0.00 43.54 1.89
2377 2437 7.716612 ACTTGAAAACCTCAAAGGAAGTTATG 58.283 34.615 0.00 0.00 43.54 1.90
2378 2438 6.084326 TGAAAACCTCAAAGGAAGTTATGC 57.916 37.500 0.00 0.00 37.67 3.14
2379 2439 5.833131 TGAAAACCTCAAAGGAAGTTATGCT 59.167 36.000 0.00 0.00 37.67 3.79
2380 2440 6.323739 TGAAAACCTCAAAGGAAGTTATGCTT 59.676 34.615 0.00 0.00 42.14 3.91
2392 2452 8.189119 AGGAAGTTATGCTTTGGAAAATAACA 57.811 30.769 7.05 0.00 37.76 2.41
2401 2462 8.309163 TGCTTTGGAAAATAACAAGCATAAAG 57.691 30.769 0.81 0.00 31.10 1.85
2402 2463 7.930865 TGCTTTGGAAAATAACAAGCATAAAGT 59.069 29.630 0.81 0.00 31.10 2.66
2426 2489 4.162320 TGGACACTCCCTCATAGAATTCAC 59.838 45.833 8.44 0.00 35.03 3.18
2427 2490 4.407296 GGACACTCCCTCATAGAATTCACT 59.593 45.833 8.44 0.00 0.00 3.41
2429 2492 4.780021 ACACTCCCTCATAGAATTCACTGT 59.220 41.667 8.44 0.00 0.00 3.55
2448 2511 6.051074 CACTGTATCAGCTCAACATAATCCA 58.949 40.000 0.00 0.00 34.37 3.41
2449 2512 6.018425 CACTGTATCAGCTCAACATAATCCAC 60.018 42.308 0.00 0.00 34.37 4.02
2450 2513 5.988287 TGTATCAGCTCAACATAATCCACA 58.012 37.500 0.00 0.00 0.00 4.17
2451 2514 6.594744 TGTATCAGCTCAACATAATCCACAT 58.405 36.000 0.00 0.00 0.00 3.21
2452 2515 7.734942 TGTATCAGCTCAACATAATCCACATA 58.265 34.615 0.00 0.00 0.00 2.29
2466 2534 4.908601 TCCACATAACTCCAGACACAAT 57.091 40.909 0.00 0.00 0.00 2.71
2489 2562 4.518970 TCATCTGGTACAAAAGAACCAAGC 59.481 41.667 0.00 0.00 44.92 4.01
2512 2585 4.627788 TGGCAACATAATCGCGGT 57.372 50.000 6.13 0.00 46.17 5.68
2514 2587 2.025589 TGGCAACATAATCGCGGTAA 57.974 45.000 6.13 0.00 46.17 2.85
2515 2588 1.937223 TGGCAACATAATCGCGGTAAG 59.063 47.619 6.13 0.00 46.17 2.34
2516 2589 1.333791 GGCAACATAATCGCGGTAAGC 60.334 52.381 6.13 3.85 43.95 3.09
2531 2615 3.369052 CGGTAAGCACCACCTATTTCTGA 60.369 47.826 0.00 0.00 46.14 3.27
2532 2616 4.192317 GGTAAGCACCACCTATTTCTGAG 58.808 47.826 0.00 0.00 45.04 3.35
2534 2618 4.640771 AAGCACCACCTATTTCTGAGAA 57.359 40.909 0.00 0.00 0.00 2.87
2562 2651 2.420022 CTCAAGTAAACCCGCATCCTTG 59.580 50.000 0.00 0.00 0.00 3.61
2742 2832 6.090088 CACAAGATAAGCACTCTACTCAACAC 59.910 42.308 0.00 0.00 0.00 3.32
2743 2833 5.984695 AGATAAGCACTCTACTCAACACA 57.015 39.130 0.00 0.00 0.00 3.72
2772 2862 7.174107 AGCTGATAAACTGGCATAACAAAAT 57.826 32.000 0.00 0.00 0.00 1.82
2773 2863 7.037438 AGCTGATAAACTGGCATAACAAAATG 58.963 34.615 0.00 0.00 0.00 2.32
2785 2880 9.330063 TGGCATAACAAAATGTATGTTTCAAAA 57.670 25.926 0.00 0.00 41.11 2.44
2811 2906 9.811995 ATGATAAATCATGAACACAATCAAAGG 57.188 29.630 0.00 0.00 45.27 3.11
2824 2919 7.729116 ACACAATCAAAGGAAATCAATTGACT 58.271 30.769 11.07 0.00 34.88 3.41
2830 2925 6.772233 TCAAAGGAAATCAATTGACTGTCTCA 59.228 34.615 11.07 0.00 0.00 3.27
2854 2949 8.378565 TCAAGAAATAGGAGATCACAACTTCTT 58.621 33.333 0.00 0.00 32.34 2.52
2890 2985 1.335872 GGAACAAACAACATGAGGCCG 60.336 52.381 0.00 0.00 0.00 6.13
2971 3070 8.593945 AAAATCCTATTGCAAAATCCTACTCA 57.406 30.769 1.71 0.00 0.00 3.41
2995 3094 0.468226 AGACTGGTTCTGCCGACAAA 59.532 50.000 0.00 0.00 41.21 2.83
3059 3158 4.600012 ATGTAGCGTGTTTGCTTATCAC 57.400 40.909 0.00 0.00 44.46 3.06
3085 3185 6.889177 TGATAACAGGTTCAATCTGCCATTAA 59.111 34.615 0.00 0.00 35.78 1.40
3086 3186 5.391312 AACAGGTTCAATCTGCCATTAAC 57.609 39.130 0.00 0.00 35.78 2.01
3108 3208 5.147767 ACCCCAAGCCATTTAATTCCTATC 58.852 41.667 0.00 0.00 0.00 2.08
3115 3215 6.194235 AGCCATTTAATTCCTATCAACACCA 58.806 36.000 0.00 0.00 0.00 4.17
3116 3216 6.840705 AGCCATTTAATTCCTATCAACACCAT 59.159 34.615 0.00 0.00 0.00 3.55
3117 3217 7.345392 AGCCATTTAATTCCTATCAACACCATT 59.655 33.333 0.00 0.00 0.00 3.16
3126 3226 6.957631 TCCTATCAACACCATTAATGTCTGT 58.042 36.000 14.25 11.46 0.00 3.41
3130 3230 5.372373 TCAACACCATTAATGTCTGTCACA 58.628 37.500 14.25 1.37 40.18 3.58
3132 3232 3.753272 ACACCATTAATGTCTGTCACAGC 59.247 43.478 14.25 0.00 38.85 4.40
3147 3247 3.603770 GTCACAGCGTTGACAAAATATGC 59.396 43.478 6.16 0.00 44.62 3.14
3148 3248 3.501828 TCACAGCGTTGACAAAATATGCT 59.498 39.130 6.16 0.00 0.00 3.79
3153 3253 5.855925 CAGCGTTGACAAAATATGCTTACAA 59.144 36.000 0.00 0.00 0.00 2.41
3169 3269 8.607441 ATGCTTACAATGGTGTATGTACATAG 57.393 34.615 15.93 5.29 39.96 2.23
3170 3270 7.787028 TGCTTACAATGGTGTATGTACATAGA 58.213 34.615 15.93 12.18 39.96 1.98
3171 3271 7.709182 TGCTTACAATGGTGTATGTACATAGAC 59.291 37.037 27.02 27.02 39.96 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
408 409 2.264005 TGTCCAGAAGGCGCTTAAAA 57.736 45.000 7.64 0.00 33.74 1.52
532 533 0.468226 GAGGGGATGCGGACAATGTA 59.532 55.000 0.00 0.00 0.00 2.29
582 583 1.428869 AGCTCAGGTGTTCAAGGAGT 58.571 50.000 0.00 0.00 0.00 3.85
639 640 1.153449 CGGGATAAGCGTGCCAAGA 60.153 57.895 0.00 0.00 0.00 3.02
804 805 5.770663 TCCGTTCCAAATTATTTGTCTTGGA 59.229 36.000 15.40 13.44 44.32 3.53
805 806 6.019779 TCCGTTCCAAATTATTTGTCTTGG 57.980 37.500 15.40 11.70 38.98 3.61
806 807 6.092748 CCTCCGTTCCAAATTATTTGTCTTG 58.907 40.000 15.40 1.88 38.98 3.02
807 808 5.185056 CCCTCCGTTCCAAATTATTTGTCTT 59.815 40.000 15.40 0.00 38.98 3.01
808 809 4.705023 CCCTCCGTTCCAAATTATTTGTCT 59.295 41.667 15.40 0.00 38.98 3.41
809 810 4.703093 TCCCTCCGTTCCAAATTATTTGTC 59.297 41.667 15.40 5.99 38.98 3.18
810 811 4.668636 TCCCTCCGTTCCAAATTATTTGT 58.331 39.130 15.40 0.00 38.98 2.83
811 812 5.652994 TTCCCTCCGTTCCAAATTATTTG 57.347 39.130 10.46 10.46 40.32 2.32
812 813 6.322969 GGTATTCCCTCCGTTCCAAATTATTT 59.677 38.462 0.00 0.00 0.00 1.40
813 814 5.831525 GGTATTCCCTCCGTTCCAAATTATT 59.168 40.000 0.00 0.00 0.00 1.40
814 815 5.133830 AGGTATTCCCTCCGTTCCAAATTAT 59.866 40.000 0.00 0.00 40.71 1.28
815 816 4.475747 AGGTATTCCCTCCGTTCCAAATTA 59.524 41.667 0.00 0.00 40.71 1.40
816 817 3.268595 AGGTATTCCCTCCGTTCCAAATT 59.731 43.478 0.00 0.00 40.71 1.82
817 818 2.850568 AGGTATTCCCTCCGTTCCAAAT 59.149 45.455 0.00 0.00 40.71 2.32
818 819 2.271777 AGGTATTCCCTCCGTTCCAAA 58.728 47.619 0.00 0.00 40.71 3.28
819 820 1.961133 AGGTATTCCCTCCGTTCCAA 58.039 50.000 0.00 0.00 40.71 3.53
820 821 2.674420 CTAGGTATTCCCTCCGTTCCA 58.326 52.381 0.00 0.00 44.81 3.53
821 822 1.343789 GCTAGGTATTCCCTCCGTTCC 59.656 57.143 0.00 0.00 44.81 3.62
822 823 2.037144 TGCTAGGTATTCCCTCCGTTC 58.963 52.381 0.00 0.00 44.81 3.95
823 824 2.170012 TGCTAGGTATTCCCTCCGTT 57.830 50.000 0.00 0.00 44.81 4.44
824 825 2.170012 TTGCTAGGTATTCCCTCCGT 57.830 50.000 0.00 0.00 44.81 4.69
825 826 2.698797 TCTTTGCTAGGTATTCCCTCCG 59.301 50.000 0.00 0.00 44.81 4.63
826 827 3.967987 TCTCTTTGCTAGGTATTCCCTCC 59.032 47.826 0.00 0.00 44.81 4.30
827 828 4.502431 GCTCTCTTTGCTAGGTATTCCCTC 60.502 50.000 0.00 0.00 44.81 4.30
829 830 3.134804 TGCTCTCTTTGCTAGGTATTCCC 59.865 47.826 0.00 0.00 0.00 3.97
830 831 4.123506 GTGCTCTCTTTGCTAGGTATTCC 58.876 47.826 0.00 0.00 0.00 3.01
831 832 4.759782 TGTGCTCTCTTTGCTAGGTATTC 58.240 43.478 0.00 0.00 0.00 1.75
832 833 4.826274 TGTGCTCTCTTTGCTAGGTATT 57.174 40.909 0.00 0.00 0.00 1.89
833 834 4.383552 CCTTGTGCTCTCTTTGCTAGGTAT 60.384 45.833 0.00 0.00 0.00 2.73
834 835 3.055819 CCTTGTGCTCTCTTTGCTAGGTA 60.056 47.826 0.00 0.00 0.00 3.08
835 836 2.289945 CCTTGTGCTCTCTTTGCTAGGT 60.290 50.000 0.00 0.00 0.00 3.08
836 837 2.027745 TCCTTGTGCTCTCTTTGCTAGG 60.028 50.000 0.00 0.00 0.00 3.02
837 838 2.999355 GTCCTTGTGCTCTCTTTGCTAG 59.001 50.000 0.00 0.00 0.00 3.42
838 839 2.610479 CGTCCTTGTGCTCTCTTTGCTA 60.610 50.000 0.00 0.00 0.00 3.49
844 845 0.251386 TCCTCGTCCTTGTGCTCTCT 60.251 55.000 0.00 0.00 0.00 3.10
850 851 1.070134 TGGTTTCTCCTCGTCCTTGTG 59.930 52.381 0.00 0.00 37.07 3.33
854 855 0.178929 AGGTGGTTTCTCCTCGTCCT 60.179 55.000 0.00 0.00 31.77 3.85
886 892 0.602106 CACCGCAGCCTCATATCCAG 60.602 60.000 0.00 0.00 0.00 3.86
902 908 2.750237 GGCCGATTGGGTGTCACC 60.750 66.667 14.13 14.13 38.44 4.02
942 952 0.399233 AGGGGAAGGTGCTAGCCTAG 60.399 60.000 13.29 0.00 38.03 3.02
943 953 0.044244 AAGGGGAAGGTGCTAGCCTA 59.956 55.000 13.29 0.00 38.03 3.93
944 954 1.229984 AAGGGGAAGGTGCTAGCCT 60.230 57.895 13.29 0.00 41.41 4.58
945 955 1.224870 GAAGGGGAAGGTGCTAGCC 59.775 63.158 13.29 3.27 0.00 3.93
946 956 0.179234 GAGAAGGGGAAGGTGCTAGC 59.821 60.000 8.10 8.10 0.00 3.42
947 957 0.833949 GGAGAAGGGGAAGGTGCTAG 59.166 60.000 0.00 0.00 0.00 3.42
948 958 0.976073 CGGAGAAGGGGAAGGTGCTA 60.976 60.000 0.00 0.00 0.00 3.49
1009 1022 2.770475 GAGGGGGAGGAAGGAGGC 60.770 72.222 0.00 0.00 0.00 4.70
1365 1381 2.951745 CCGAGCAGCGATGACGAC 60.952 66.667 18.76 0.00 44.57 4.34
1398 1426 4.736896 GAGTCCACGTCCGCCACC 62.737 72.222 0.00 0.00 0.00 4.61
1629 1666 3.009115 TGGGAGCAGTAGGGGCAC 61.009 66.667 0.00 0.00 0.00 5.01
1895 1932 2.181125 ACATTGCATGCATCCCAAGAA 58.819 42.857 23.37 3.69 0.00 2.52
1916 1958 7.221645 GCGATCGATGAATGATTATCATACAGT 59.778 37.037 21.57 0.00 35.76 3.55
1918 1960 7.260603 AGCGATCGATGAATGATTATCATACA 58.739 34.615 21.57 0.00 35.76 2.29
1919 1961 7.691430 AGCGATCGATGAATGATTATCATAC 57.309 36.000 21.57 0.87 35.76 2.39
1920 1962 8.598075 CAAAGCGATCGATGAATGATTATCATA 58.402 33.333 21.57 0.00 35.76 2.15
1926 1969 3.562973 AGCAAAGCGATCGATGAATGATT 59.437 39.130 21.57 0.00 0.00 2.57
1934 1977 1.134995 TCAGTGAGCAAAGCGATCGAT 60.135 47.619 21.57 10.64 0.00 3.59
1937 1980 6.718454 ATATTATCAGTGAGCAAAGCGATC 57.282 37.500 0.00 0.00 0.00 3.69
1938 1981 7.358066 CAAATATTATCAGTGAGCAAAGCGAT 58.642 34.615 0.00 0.00 0.00 4.58
1943 1986 7.611467 ACAGTCCAAATATTATCAGTGAGCAAA 59.389 33.333 0.00 0.00 0.00 3.68
1971 2014 2.510238 CAGCCCGCTAGACTGCAC 60.510 66.667 0.00 0.00 0.00 4.57
1973 2016 4.537433 CCCAGCCCGCTAGACTGC 62.537 72.222 0.00 0.00 0.00 4.40
2046 2097 1.719780 GTTGCCGAACTTCTCGTACAG 59.280 52.381 0.00 0.00 46.65 2.74
2144 2195 3.681473 TCGTGCTCGATGACCTGT 58.319 55.556 6.80 0.00 41.35 4.00
2248 2307 4.515191 GTGTACATATTGATCGCAATGGGT 59.485 41.667 0.00 0.00 44.18 4.51
2264 2323 6.258727 GCAAGTAATCTACTGCATGTGTACAT 59.741 38.462 0.00 0.00 39.39 2.29
2276 2335 3.961408 ACGAGATGGGCAAGTAATCTACT 59.039 43.478 0.00 0.00 41.73 2.57
2280 2339 4.694339 AGTTACGAGATGGGCAAGTAATC 58.306 43.478 0.00 0.00 31.24 1.75
2282 2341 5.047164 TGTTAGTTACGAGATGGGCAAGTAA 60.047 40.000 0.00 0.00 0.00 2.24
2287 2346 4.403113 TGTATGTTAGTTACGAGATGGGCA 59.597 41.667 0.00 0.00 0.00 5.36
2289 2348 7.709182 TCATTTGTATGTTAGTTACGAGATGGG 59.291 37.037 0.00 0.00 33.34 4.00
2290 2349 8.642908 TCATTTGTATGTTAGTTACGAGATGG 57.357 34.615 0.00 0.00 33.34 3.51
2325 2384 5.529430 TCTTCACACGTGACCATGTAATTTT 59.471 36.000 25.01 0.00 39.66 1.82
2337 2397 3.793797 TCAAGTCTTCTTCACACGTGA 57.206 42.857 25.01 0.00 37.91 4.35
2339 2399 4.094442 GGTTTTCAAGTCTTCTTCACACGT 59.906 41.667 0.00 0.00 0.00 4.49
2340 2400 4.332819 AGGTTTTCAAGTCTTCTTCACACG 59.667 41.667 0.00 0.00 0.00 4.49
2366 2426 8.646900 TGTTATTTTCCAAAGCATAACTTCCTT 58.353 29.630 0.00 0.00 37.75 3.36
2367 2427 8.189119 TGTTATTTTCCAAAGCATAACTTCCT 57.811 30.769 0.00 0.00 37.75 3.36
2368 2428 8.825667 TTGTTATTTTCCAAAGCATAACTTCC 57.174 30.769 0.00 0.00 37.75 3.46
2369 2429 8.435430 GCTTGTTATTTTCCAAAGCATAACTTC 58.565 33.333 0.00 0.00 37.75 3.01
2370 2430 7.930865 TGCTTGTTATTTTCCAAAGCATAACTT 59.069 29.630 4.39 0.00 41.70 2.66
2371 2431 7.441017 TGCTTGTTATTTTCCAAAGCATAACT 58.559 30.769 4.39 0.00 34.50 2.24
2372 2432 7.650834 TGCTTGTTATTTTCCAAAGCATAAC 57.349 32.000 4.39 0.00 34.15 1.89
2373 2433 9.935241 TTATGCTTGTTATTTTCCAAAGCATAA 57.065 25.926 25.64 25.64 40.41 1.90
2374 2434 9.935241 TTTATGCTTGTTATTTTCCAAAGCATA 57.065 25.926 19.20 19.20 37.05 3.14
2375 2435 8.845413 TTTATGCTTGTTATTTTCCAAAGCAT 57.155 26.923 20.87 20.87 38.17 3.79
2376 2436 7.930865 ACTTTATGCTTGTTATTTTCCAAAGCA 59.069 29.630 10.45 10.45 32.99 3.91
2377 2437 8.310406 ACTTTATGCTTGTTATTTTCCAAAGC 57.690 30.769 0.00 0.00 0.00 3.51
2379 2439 9.050601 CCAACTTTATGCTTGTTATTTTCCAAA 57.949 29.630 0.00 0.00 0.00 3.28
2380 2440 8.424918 TCCAACTTTATGCTTGTTATTTTCCAA 58.575 29.630 0.00 0.00 0.00 3.53
2381 2441 7.870445 GTCCAACTTTATGCTTGTTATTTTCCA 59.130 33.333 0.00 0.00 0.00 3.53
2382 2442 7.870445 TGTCCAACTTTATGCTTGTTATTTTCC 59.130 33.333 0.00 0.00 0.00 3.13
2383 2443 8.699749 GTGTCCAACTTTATGCTTGTTATTTTC 58.300 33.333 0.00 0.00 0.00 2.29
2384 2444 8.421002 AGTGTCCAACTTTATGCTTGTTATTTT 58.579 29.630 0.00 0.00 34.57 1.82
2387 2447 6.151144 GGAGTGTCCAACTTTATGCTTGTTAT 59.849 38.462 0.00 0.00 40.07 1.89
2388 2448 5.472137 GGAGTGTCCAACTTTATGCTTGTTA 59.528 40.000 0.00 0.00 40.07 2.41
2392 2452 3.074538 AGGGAGTGTCCAACTTTATGCTT 59.925 43.478 0.00 0.00 40.07 3.91
2401 2462 4.762289 ATTCTATGAGGGAGTGTCCAAC 57.238 45.455 0.00 0.00 38.64 3.77
2402 2463 4.782691 TGAATTCTATGAGGGAGTGTCCAA 59.217 41.667 7.05 0.00 38.64 3.53
2426 2489 6.051074 TGTGGATTATGTTGAGCTGATACAG 58.949 40.000 0.00 0.00 34.12 2.74
2427 2490 5.988287 TGTGGATTATGTTGAGCTGATACA 58.012 37.500 0.00 0.00 0.00 2.29
2429 2492 8.432013 AGTTATGTGGATTATGTTGAGCTGATA 58.568 33.333 0.00 0.00 0.00 2.15
2448 2511 6.111382 CAGATGATTGTGTCTGGAGTTATGT 58.889 40.000 0.00 0.00 38.50 2.29
2449 2512 6.600246 CAGATGATTGTGTCTGGAGTTATG 57.400 41.667 0.00 0.00 38.50 1.90
2497 2570 1.329292 TGCTTACCGCGATTATGTTGC 59.671 47.619 8.23 5.50 43.27 4.17
2508 2581 1.669265 GAAATAGGTGGTGCTTACCGC 59.331 52.381 1.50 1.50 43.06 5.68
2509 2582 2.936498 CAGAAATAGGTGGTGCTTACCG 59.064 50.000 0.00 0.00 43.06 4.02
2510 2583 4.081087 TCTCAGAAATAGGTGGTGCTTACC 60.081 45.833 0.00 0.00 38.52 2.85
2511 2584 5.086104 TCTCAGAAATAGGTGGTGCTTAC 57.914 43.478 0.00 0.00 0.00 2.34
2512 2585 5.755409 TTCTCAGAAATAGGTGGTGCTTA 57.245 39.130 0.00 0.00 0.00 3.09
2514 2587 4.018960 ACATTCTCAGAAATAGGTGGTGCT 60.019 41.667 0.00 0.00 0.00 4.40
2515 2588 4.265073 ACATTCTCAGAAATAGGTGGTGC 58.735 43.478 0.00 0.00 0.00 5.01
2516 2589 6.824305 AAACATTCTCAGAAATAGGTGGTG 57.176 37.500 0.00 0.00 0.00 4.17
2517 2590 7.690256 AGTAAACATTCTCAGAAATAGGTGGT 58.310 34.615 0.00 0.00 0.00 4.16
2562 2651 4.322567 AGGACAATTTTGAGACTGCTCTC 58.677 43.478 0.00 0.00 43.17 3.20
2742 2832 7.227314 TGTTATGCCAGTTTATCAGCTAATCTG 59.773 37.037 0.00 0.00 44.21 2.90
2743 2833 7.282585 TGTTATGCCAGTTTATCAGCTAATCT 58.717 34.615 0.00 0.00 0.00 2.40
2800 2895 7.654520 ACAGTCAATTGATTTCCTTTGATTGTG 59.345 33.333 12.12 0.00 43.18 3.33
2824 2919 6.857437 TGTGATCTCCTATTTCTTGAGACA 57.143 37.500 0.00 0.00 37.92 3.41
2864 2959 5.988561 GCCTCATGTTGTTTGTTCCATTTAA 59.011 36.000 0.00 0.00 0.00 1.52
2865 2960 5.510520 GGCCTCATGTTGTTTGTTCCATTTA 60.511 40.000 0.00 0.00 0.00 1.40
2866 2961 4.379652 GCCTCATGTTGTTTGTTCCATTT 58.620 39.130 0.00 0.00 0.00 2.32
2867 2962 3.244181 GGCCTCATGTTGTTTGTTCCATT 60.244 43.478 0.00 0.00 0.00 3.16
2869 2964 1.686052 GGCCTCATGTTGTTTGTTCCA 59.314 47.619 0.00 0.00 0.00 3.53
2870 2965 1.335872 CGGCCTCATGTTGTTTGTTCC 60.336 52.381 0.00 0.00 0.00 3.62
2871 2966 1.606668 TCGGCCTCATGTTGTTTGTTC 59.393 47.619 0.00 0.00 0.00 3.18
2872 2967 1.686355 TCGGCCTCATGTTGTTTGTT 58.314 45.000 0.00 0.00 0.00 2.83
2873 2968 1.909700 ATCGGCCTCATGTTGTTTGT 58.090 45.000 0.00 0.00 0.00 2.83
2874 2969 4.096231 TGATTATCGGCCTCATGTTGTTTG 59.904 41.667 0.00 0.00 0.00 2.93
2876 2971 3.884895 TGATTATCGGCCTCATGTTGTT 58.115 40.909 0.00 0.00 0.00 2.83
2878 2973 3.627123 TGTTGATTATCGGCCTCATGTTG 59.373 43.478 0.00 0.00 0.00 3.33
2890 2985 8.028354 TGATGTGACCATTGTTTGTTGATTATC 58.972 33.333 0.00 0.00 0.00 1.75
2941 3040 7.850193 AGGATTTTGCAATAGGATTTTTAGCA 58.150 30.769 0.00 0.00 0.00 3.49
2971 3070 0.034059 CGGCAGAACCAGTCTTCTGT 59.966 55.000 9.95 0.00 46.18 3.41
2995 3094 6.721318 TGTTTGTCCTAGCCTAAGATTGAAT 58.279 36.000 0.00 0.00 0.00 2.57
3059 3158 4.264253 TGGCAGATTGAACCTGTTATCAG 58.736 43.478 0.00 0.00 41.01 2.90
3079 3179 5.628797 ATTAAATGGCTTGGGGTTAATGG 57.371 39.130 0.00 0.00 0.00 3.16
3085 3185 3.490060 AGGAATTAAATGGCTTGGGGT 57.510 42.857 0.00 0.00 0.00 4.95
3086 3186 5.147032 TGATAGGAATTAAATGGCTTGGGG 58.853 41.667 0.00 0.00 0.00 4.96
3108 3208 5.687770 TGTGACAGACATTAATGGTGTTG 57.312 39.130 20.55 14.40 31.68 3.33
3115 3215 4.152402 GTCAACGCTGTGACAGACATTAAT 59.848 41.667 18.18 0.00 46.00 1.40
3116 3216 3.493129 GTCAACGCTGTGACAGACATTAA 59.507 43.478 18.18 0.00 46.00 1.40
3117 3217 3.057019 GTCAACGCTGTGACAGACATTA 58.943 45.455 18.18 0.00 46.00 1.90
3119 3219 1.502231 GTCAACGCTGTGACAGACAT 58.498 50.000 18.18 0.00 46.00 3.06
3126 3226 3.501828 AGCATATTTTGTCAACGCTGTGA 59.498 39.130 0.00 0.00 0.00 3.58
3130 3230 5.621197 TGTAAGCATATTTTGTCAACGCT 57.379 34.783 0.00 0.00 0.00 5.07
3132 3232 6.806249 ACCATTGTAAGCATATTTTGTCAACG 59.194 34.615 0.00 0.00 0.00 4.10
3143 3243 9.705290 CTATGTACATACACCATTGTAAGCATA 57.295 33.333 11.62 0.00 41.64 3.14
3144 3244 8.428852 TCTATGTACATACACCATTGTAAGCAT 58.571 33.333 11.62 0.00 41.64 3.79
3145 3245 7.709182 GTCTATGTACATACACCATTGTAAGCA 59.291 37.037 11.62 0.00 41.64 3.91
3146 3246 8.073355 GTCTATGTACATACACCATTGTAAGC 57.927 38.462 11.62 0.00 41.64 3.09


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

AutoCloner maintained by Alex Coulton.