Multiple sequence alignment - TraesCS7A01G270200

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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 TraesCS7A01G270200 chr7A 100.000 4581 0 0 1 4581 277449022 277444442 0.000000e+00 8460.0
1 TraesCS7A01G270200 chr7A 97.514 362 9 0 2479 2840 17840619 17840980 1.810000e-173 619.0
2 TraesCS7A01G270200 chr7A 96.694 363 12 0 2478 2840 17842733 17843095 5.070000e-169 604.0
3 TraesCS7A01G270200 chr7D 94.327 1745 45 21 749 2476 257712802 257714509 0.000000e+00 2625.0
4 TraesCS7A01G270200 chr7D 97.073 1435 29 2 2841 4274 257714507 257715929 0.000000e+00 2405.0
5 TraesCS7A01G270200 chr7D 87.312 465 35 11 277 730 532376225 532376676 1.140000e-140 510.0
6 TraesCS7A01G270200 chr7D 92.282 298 15 2 4291 4580 257715915 257716212 2.550000e-112 416.0
7 TraesCS7A01G270200 chr7B 97.024 672 19 1 831 1501 237239095 237239766 0.000000e+00 1129.0
8 TraesCS7A01G270200 chr7B 95.299 234 10 1 4042 4274 237241156 237241389 2.010000e-98 370.0
9 TraesCS7A01G270200 chr7B 93.548 155 8 2 3871 4023 237241017 237241171 3.560000e-56 230.0
10 TraesCS7A01G270200 chr7B 98.276 116 2 0 4291 4406 237241375 237241490 2.160000e-48 204.0
11 TraesCS7A01G270200 chr7B 94.643 112 6 0 4408 4519 237241822 237241933 1.690000e-39 174.0
12 TraesCS7A01G270200 chr7B 88.235 119 12 2 4291 4408 237241840 237241957 1.720000e-29 141.0
13 TraesCS7A01G270200 chr2A 90.463 734 46 9 1 730 4175154 4175867 0.000000e+00 946.0
14 TraesCS7A01G270200 chr2A 97.245 363 8 2 2479 2840 388679176 388679537 8.420000e-172 614.0
15 TraesCS7A01G270200 chr6D 89.341 713 46 12 32 730 4398468 4399164 0.000000e+00 869.0
16 TraesCS7A01G270200 chr1A 87.705 732 67 8 1 729 541322286 541322997 0.000000e+00 832.0
17 TraesCS7A01G270200 chr1A 97.521 363 9 0 2478 2840 103630429 103630791 5.030000e-174 621.0
18 TraesCS7A01G270200 chr1A 97.514 362 9 0 2479 2840 548467104 548467465 1.810000e-173 619.0
19 TraesCS7A01G270200 chr1A 97.238 362 10 0 2479 2840 63751684 63752045 8.420000e-172 614.0
20 TraesCS7A01G270200 chr1A 96.961 362 7 4 2479 2840 103628323 103628680 5.070000e-169 604.0
21 TraesCS7A01G270200 chr6A 97.790 362 8 0 2479 2840 585487768 585488129 3.890000e-175 625.0
22 TraesCS7A01G270200 chr3A 97.790 362 8 0 2479 2840 697504672 697504311 3.890000e-175 625.0
23 TraesCS7A01G270200 chr6B 92.615 325 18 6 1 324 171421433 171421114 3.230000e-126 462.0
24 TraesCS7A01G270200 chr6B 89.809 314 30 2 427 738 171807619 171807306 7.140000e-108 401.0
25 TraesCS7A01G270200 chr2B 94.690 113 5 1 213 324 268009950 268009838 1.690000e-39 174.0
26 TraesCS7A01G270200 chr5D 85.714 63 7 1 4520 4580 530015224 530015162 1.060000e-06 65.8
27 TraesCS7A01G270200 chrUn 100.000 29 0 0 4552 4580 360475018 360474990 2.000000e-03 54.7
28 TraesCS7A01G270200 chr5A 100.000 29 0 0 4552 4580 52263371 52263343 2.000000e-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 TraesCS7A01G270200 chr7A 277444442 277449022 4580 True 8460.000000 8460 100.000000 1 4581 1 chr7A.!!$R1 4580
1 TraesCS7A01G270200 chr7A 17840619 17843095 2476 False 611.500000 619 97.104000 2478 2840 2 chr7A.!!$F1 362
2 TraesCS7A01G270200 chr7D 257712802 257716212 3410 False 1815.333333 2625 94.560667 749 4580 3 chr7D.!!$F2 3831
3 TraesCS7A01G270200 chr7B 237239095 237241957 2862 False 374.666667 1129 94.504167 831 4519 6 chr7B.!!$F1 3688
4 TraesCS7A01G270200 chr2A 4175154 4175867 713 False 946.000000 946 90.463000 1 730 1 chr2A.!!$F1 729
5 TraesCS7A01G270200 chr6D 4398468 4399164 696 False 869.000000 869 89.341000 32 730 1 chr6D.!!$F1 698
6 TraesCS7A01G270200 chr1A 541322286 541322997 711 False 832.000000 832 87.705000 1 729 1 chr1A.!!$F2 728
7 TraesCS7A01G270200 chr1A 103628323 103630791 2468 False 612.500000 621 97.241000 2478 2840 2 chr1A.!!$F4 362

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
554 573 0.242825 TTTGAGGTCTACAGTCGGCG 59.757 55.000 0.00 0.00 0.00 6.46 F
743 762 0.532573 TGCCCTTTTTGCAAACGTCA 59.467 45.000 12.39 3.23 35.40 4.35 F
818 845 0.814812 ACTCGCTAGGGTCGCTACTC 60.815 60.000 6.70 0.00 0.00 2.59 F
822 849 0.883814 GCTAGGGTCGCTACTCGCTA 60.884 60.000 0.00 0.00 38.27 4.26 F
1690 1949 1.225376 TTTGAGCGGTGGCAGTAACG 61.225 55.000 0.00 0.00 43.41 3.18 F
2540 2808 1.383386 GGGAAGGAGGGAGGAGGTC 60.383 68.421 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1677 1705 0.391597 ATATCCCGTTACTGCCACCG 59.608 55.000 0.00 0.0 0.00 4.94 R
2607 2875 1.209747 CTAAACCCTAGCCGCCTCTTT 59.790 52.381 0.00 0.0 0.00 2.52 R
3065 5725 9.337396 ACATACAGAAAGAAAAATGTGAGTACA 57.663 29.630 0.00 0.0 41.89 2.90 R
3068 5728 8.450578 TGACATACAGAAAGAAAAATGTGAGT 57.549 30.769 0.00 0.0 0.00 3.41 R
3154 5814 0.320247 CATAGTCATCCGCAGCTCCC 60.320 60.000 0.00 0.0 0.00 4.30 R
4513 7510 0.251916 CCAGTGGATGAGGCGGTTTA 59.748 55.000 1.68 0.0 0.00 2.01 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
34 35 6.603940 AGCATGCCCAATTTTACTCTTTTA 57.396 33.333 15.66 0.00 0.00 1.52
146 150 1.273327 GCATTTTTGCTACCACAGGCT 59.727 47.619 0.00 0.00 0.00 4.58
236 241 6.597262 ACGTCCATTTTTCCAATTTTTGAC 57.403 33.333 0.00 0.00 0.00 3.18
257 262 1.208259 CCAGCGTTTTCAAGTTTGCC 58.792 50.000 0.00 0.00 0.00 4.52
363 379 3.325753 GGAGAGGGCAGCACCAGT 61.326 66.667 0.00 0.00 42.05 4.00
368 384 3.640407 GGGCAGCACCAGTGAGGA 61.640 66.667 0.99 0.00 42.05 3.71
375 391 2.601666 ACCAGTGAGGAGCGAGCA 60.602 61.111 0.00 0.00 41.22 4.26
483 501 4.687215 ACGACCGACGACGAGGGA 62.687 66.667 9.28 0.00 45.77 4.20
488 506 2.633509 CCGACGACGAGGGAAAGGT 61.634 63.158 9.28 0.00 42.66 3.50
505 523 4.371590 TGCCTAACTGCGCTGCGA 62.372 61.111 28.07 10.07 0.00 5.10
551 570 4.358494 CCTACTTTGAGGTCTACAGTCG 57.642 50.000 0.00 0.00 0.00 4.18
552 571 3.128938 CCTACTTTGAGGTCTACAGTCGG 59.871 52.174 0.00 0.00 0.00 4.79
553 572 1.272769 ACTTTGAGGTCTACAGTCGGC 59.727 52.381 0.00 0.00 0.00 5.54
554 573 0.242825 TTTGAGGTCTACAGTCGGCG 59.757 55.000 0.00 0.00 0.00 6.46
555 574 1.592400 TTGAGGTCTACAGTCGGCGG 61.592 60.000 7.21 0.00 0.00 6.13
556 575 2.754658 AGGTCTACAGTCGGCGGG 60.755 66.667 7.21 0.00 0.00 6.13
557 576 3.834799 GGTCTACAGTCGGCGGGG 61.835 72.222 7.21 0.00 0.00 5.73
558 577 4.509737 GTCTACAGTCGGCGGGGC 62.510 72.222 7.21 0.00 0.00 5.80
559 578 4.753662 TCTACAGTCGGCGGGGCT 62.754 66.667 7.21 0.00 0.00 5.19
654 673 1.234615 GCTGGCAAAACAGACGGCTA 61.235 55.000 0.00 0.00 45.69 3.93
730 749 2.190578 GCGCCTATCAGTGCCCTT 59.809 61.111 0.00 0.00 37.29 3.95
731 750 1.452108 GCGCCTATCAGTGCCCTTT 60.452 57.895 0.00 0.00 37.29 3.11
732 751 1.032114 GCGCCTATCAGTGCCCTTTT 61.032 55.000 0.00 0.00 37.29 2.27
733 752 1.463674 CGCCTATCAGTGCCCTTTTT 58.536 50.000 0.00 0.00 0.00 1.94
734 753 1.133025 CGCCTATCAGTGCCCTTTTTG 59.867 52.381 0.00 0.00 0.00 2.44
735 754 1.134995 GCCTATCAGTGCCCTTTTTGC 60.135 52.381 0.00 0.00 0.00 3.68
736 755 2.170166 CCTATCAGTGCCCTTTTTGCA 58.830 47.619 0.00 0.00 36.12 4.08
737 756 2.562298 CCTATCAGTGCCCTTTTTGCAA 59.438 45.455 0.00 0.00 41.06 4.08
738 757 3.006752 CCTATCAGTGCCCTTTTTGCAAA 59.993 43.478 8.05 8.05 41.06 3.68
739 758 2.307934 TCAGTGCCCTTTTTGCAAAC 57.692 45.000 12.39 0.08 41.06 2.93
740 759 0.929615 CAGTGCCCTTTTTGCAAACG 59.070 50.000 12.39 6.03 41.06 3.60
741 760 0.534873 AGTGCCCTTTTTGCAAACGT 59.465 45.000 12.39 0.00 41.06 3.99
742 761 0.927537 GTGCCCTTTTTGCAAACGTC 59.072 50.000 12.39 0.54 41.06 4.34
743 762 0.532573 TGCCCTTTTTGCAAACGTCA 59.467 45.000 12.39 3.23 35.40 4.35
744 763 1.137872 TGCCCTTTTTGCAAACGTCAT 59.862 42.857 12.39 0.00 35.40 3.06
745 764 1.792367 GCCCTTTTTGCAAACGTCATC 59.208 47.619 12.39 0.00 0.00 2.92
746 765 2.545742 GCCCTTTTTGCAAACGTCATCT 60.546 45.455 12.39 0.00 0.00 2.90
747 766 3.052036 CCCTTTTTGCAAACGTCATCTG 58.948 45.455 12.39 0.00 0.00 2.90
762 781 4.976224 TCATCTGGATGATTTGTTGCAG 57.024 40.909 8.96 0.00 42.42 4.41
802 829 0.892063 AAAGAGCTCGGACTCCACTC 59.108 55.000 8.37 0.00 37.39 3.51
816 843 1.355916 CACTCGCTAGGGTCGCTAC 59.644 63.158 6.70 0.00 0.00 3.58
817 844 1.096386 CACTCGCTAGGGTCGCTACT 61.096 60.000 6.70 0.00 0.00 2.57
818 845 0.814812 ACTCGCTAGGGTCGCTACTC 60.815 60.000 6.70 0.00 0.00 2.59
819 846 1.833434 CTCGCTAGGGTCGCTACTCG 61.833 65.000 6.70 7.23 40.15 4.18
820 847 2.332159 GCTAGGGTCGCTACTCGC 59.668 66.667 0.00 0.00 38.27 5.03
821 848 2.188161 GCTAGGGTCGCTACTCGCT 61.188 63.158 0.00 0.00 38.27 4.93
822 849 0.883814 GCTAGGGTCGCTACTCGCTA 60.884 60.000 0.00 0.00 38.27 4.26
1137 1164 1.694150 CTATCCTCTTCCCCATCGCAA 59.306 52.381 0.00 0.00 0.00 4.85
1314 1341 1.934463 CGCTTTCACAGTCGTGCTT 59.066 52.632 0.00 0.00 43.28 3.91
1548 1576 4.096003 CCCAAGGACCACGCGGAT 62.096 66.667 12.47 0.00 35.59 4.18
1632 1660 3.970842 TGAACTTACTGTTGGGTGGTTT 58.029 40.909 0.00 0.00 39.30 3.27
1663 1691 1.877443 ACAAACGGAAATGGGACTTCG 59.123 47.619 0.00 0.00 0.00 3.79
1672 1700 5.368989 GGAAATGGGACTTCGATGACTATT 58.631 41.667 5.16 4.79 0.00 1.73
1673 1701 5.823045 GGAAATGGGACTTCGATGACTATTT 59.177 40.000 15.45 15.45 0.00 1.40
1674 1702 6.238484 GGAAATGGGACTTCGATGACTATTTG 60.238 42.308 18.17 0.00 0.00 2.32
1675 1703 5.614324 ATGGGACTTCGATGACTATTTGA 57.386 39.130 5.16 0.00 0.00 2.69
1676 1704 5.011090 TGGGACTTCGATGACTATTTGAG 57.989 43.478 5.16 0.00 0.00 3.02
1677 1705 3.804873 GGGACTTCGATGACTATTTGAGC 59.195 47.826 5.16 0.00 0.00 4.26
1678 1706 3.487574 GGACTTCGATGACTATTTGAGCG 59.512 47.826 5.16 0.00 0.00 5.03
1679 1707 3.448686 ACTTCGATGACTATTTGAGCGG 58.551 45.455 5.16 0.00 0.00 5.52
1681 1709 2.809446 TCGATGACTATTTGAGCGGTG 58.191 47.619 0.00 0.00 0.00 4.94
1682 1710 1.860950 CGATGACTATTTGAGCGGTGG 59.139 52.381 0.00 0.00 0.00 4.61
1690 1949 1.225376 TTTGAGCGGTGGCAGTAACG 61.225 55.000 0.00 0.00 43.41 3.18
1743 2002 4.697828 TGCTATTATTTGCGTTCTGTTGGA 59.302 37.500 0.00 0.00 0.00 3.53
1780 2039 4.509616 TGGTTACGGTTCTGTTGATATGG 58.490 43.478 0.00 0.00 0.00 2.74
1783 2042 3.713826 ACGGTTCTGTTGATATGGGTT 57.286 42.857 0.00 0.00 0.00 4.11
1894 2154 2.715758 GCACATGCACATTGTCACG 58.284 52.632 0.00 0.00 41.59 4.35
1906 2166 6.580416 TGCACATTGTCACGTTATTGTAATTG 59.420 34.615 0.00 0.00 0.00 2.32
1918 2178 9.439500 ACGTTATTGTAATTGTAGTGGTGTATT 57.561 29.630 0.00 0.00 0.00 1.89
1926 2186 9.403110 GTAATTGTAGTGGTGTATTATCCTACG 57.597 37.037 0.00 0.00 0.00 3.51
1927 2187 6.395426 TTGTAGTGGTGTATTATCCTACGG 57.605 41.667 0.00 0.00 0.00 4.02
1928 2188 5.448654 TGTAGTGGTGTATTATCCTACGGT 58.551 41.667 0.00 0.00 0.00 4.83
1929 2189 4.931661 AGTGGTGTATTATCCTACGGTG 57.068 45.455 0.00 0.00 0.00 4.94
1930 2190 4.539726 AGTGGTGTATTATCCTACGGTGA 58.460 43.478 0.00 0.00 0.00 4.02
1971 2231 5.833082 ACTTCCGTCAGCTACTACATAATG 58.167 41.667 0.00 0.00 0.00 1.90
2015 2278 6.657875 AGAGAGCTGAATTATGCCTTTAGTT 58.342 36.000 0.00 0.00 0.00 2.24
2238 2506 1.403679 CTGGAGCGGTCTAGAACTGAG 59.596 57.143 21.94 0.00 36.22 3.35
2275 2543 9.897744 TTTGATCACTCAGATTTATGTTTGTTC 57.102 29.630 0.00 0.00 37.00 3.18
2282 2550 7.174946 ACTCAGATTTATGTTTGTTCGATGGTT 59.825 33.333 0.00 0.00 0.00 3.67
2309 2577 4.788075 TCTATGGGGAAAGAATTGAGGTGA 59.212 41.667 0.00 0.00 0.00 4.02
2339 2607 7.141363 GCATTCTTATAGGTTACATTTGGCAG 58.859 38.462 0.00 0.00 0.00 4.85
2415 2683 4.620609 CGAATTGAGAGAGAGAGTTGTGTG 59.379 45.833 0.00 0.00 0.00 3.82
2480 2748 7.334844 TCAGTATGAGTATGTAGTCTGTTGG 57.665 40.000 0.00 0.00 42.56 3.77
2481 2749 6.890268 TCAGTATGAGTATGTAGTCTGTTGGT 59.110 38.462 0.00 0.00 42.56 3.67
2482 2750 8.050930 TCAGTATGAGTATGTAGTCTGTTGGTA 58.949 37.037 0.00 0.00 42.56 3.25
2498 2766 6.210185 TCTGTTGGTAGAAACTAGGGTTCTAC 59.790 42.308 25.90 25.90 36.50 2.59
2539 2807 1.465189 AAGGGAAGGAGGGAGGAGGT 61.465 60.000 0.00 0.00 0.00 3.85
2540 2808 1.383386 GGGAAGGAGGGAGGAGGTC 60.383 68.421 0.00 0.00 0.00 3.85
2554 2822 1.668101 GAGGTCGGAGGAGATTGCGT 61.668 60.000 0.00 0.00 33.36 5.24
2592 2860 4.988598 CGTCCTTGCGGCTGGTGT 62.989 66.667 0.00 0.00 0.00 4.16
2596 2864 3.357079 CTTGCGGCTGGTGTGACC 61.357 66.667 0.00 0.00 39.22 4.02
2840 5500 5.807721 GCCCCTAATATGCTGGTCATAACAT 60.808 44.000 0.00 0.00 40.73 2.71
2841 5501 5.882557 CCCCTAATATGCTGGTCATAACATC 59.117 44.000 0.00 0.00 40.73 3.06
2842 5502 6.296662 CCCCTAATATGCTGGTCATAACATCT 60.297 42.308 0.00 0.00 40.73 2.90
2843 5503 6.596888 CCCTAATATGCTGGTCATAACATCTG 59.403 42.308 0.00 0.00 40.73 2.90
2844 5504 7.164122 CCTAATATGCTGGTCATAACATCTGT 58.836 38.462 0.00 0.00 40.73 3.41
2845 5505 7.663081 CCTAATATGCTGGTCATAACATCTGTT 59.337 37.037 0.69 0.69 40.73 3.16
2846 5506 7.502120 AATATGCTGGTCATAACATCTGTTC 57.498 36.000 0.00 0.00 40.73 3.18
2847 5507 4.558226 TGCTGGTCATAACATCTGTTCT 57.442 40.909 0.00 0.00 39.31 3.01
2848 5508 5.675684 TGCTGGTCATAACATCTGTTCTA 57.324 39.130 0.00 0.00 39.31 2.10
2849 5509 6.239217 TGCTGGTCATAACATCTGTTCTAT 57.761 37.500 0.00 0.00 39.31 1.98
2850 5510 7.360113 TGCTGGTCATAACATCTGTTCTATA 57.640 36.000 0.00 0.00 39.31 1.31
2851 5511 7.210174 TGCTGGTCATAACATCTGTTCTATAC 58.790 38.462 0.00 0.00 39.31 1.47
2896 5556 6.621316 AAAACCACACGTCATATTTGTACA 57.379 33.333 0.00 0.00 0.00 2.90
2938 5598 9.624697 AACTTTGCTACATGTGTTACATAAATG 57.375 29.630 9.11 0.00 36.53 2.32
3059 5719 5.344743 TCTCCATTGACAGGATTGTACTC 57.655 43.478 0.00 0.00 37.76 2.59
3060 5720 4.777366 TCTCCATTGACAGGATTGTACTCA 59.223 41.667 0.00 0.00 37.76 3.41
3061 5721 4.832248 TCCATTGACAGGATTGTACTCAC 58.168 43.478 0.00 0.00 37.76 3.51
3062 5722 4.285775 TCCATTGACAGGATTGTACTCACA 59.714 41.667 0.00 0.00 37.76 3.58
3063 5723 5.045651 TCCATTGACAGGATTGTACTCACAT 60.046 40.000 0.00 0.00 37.76 3.21
3064 5724 5.649395 CCATTGACAGGATTGTACTCACATT 59.351 40.000 0.00 0.00 37.76 2.71
3065 5725 6.151648 CCATTGACAGGATTGTACTCACATTT 59.848 38.462 0.00 0.00 37.76 2.32
3066 5726 6.558771 TTGACAGGATTGTACTCACATTTG 57.441 37.500 0.00 0.00 37.76 2.32
3067 5727 5.620206 TGACAGGATTGTACTCACATTTGT 58.380 37.500 0.00 0.00 37.76 2.83
3068 5728 6.764379 TGACAGGATTGTACTCACATTTGTA 58.236 36.000 0.00 0.00 37.76 2.41
3069 5729 6.649141 TGACAGGATTGTACTCACATTTGTAC 59.351 38.462 0.00 0.00 37.76 2.90
3070 5730 6.769512 ACAGGATTGTACTCACATTTGTACT 58.230 36.000 0.00 0.00 39.57 2.73
3086 5746 9.520204 ACATTTGTACTCACATTTTTCTTTCTG 57.480 29.630 0.00 0.00 33.76 3.02
3154 5814 1.730501 ATGATGCACTGTCGGTTGAG 58.269 50.000 0.00 0.00 0.00 3.02
3406 6066 2.691409 TCCCTGTGATCAATTCGTCC 57.309 50.000 0.00 0.00 0.00 4.79
3471 6131 1.123655 GTTCACAAAGCGCTTTCAGC 58.876 50.000 31.63 16.50 38.02 4.26
3599 6259 7.118971 GGATCTGAAGCCTGTTATGCTATAAAG 59.881 40.741 0.00 0.00 38.34 1.85
3707 6367 5.220043 GCATATAGTAGAGCGTAAATGTGCG 60.220 44.000 0.00 0.00 35.87 5.34
3862 6522 4.178956 TCTTTGGACTAAGGTTGCCTTT 57.821 40.909 5.69 0.00 41.69 3.11
3928 6588 3.281727 TTGCTGTTATCCCATCTGTCC 57.718 47.619 0.00 0.00 0.00 4.02
3948 6608 4.397417 GTCCACTCCTTCCATTTCAATGAG 59.603 45.833 0.81 0.00 38.70 2.90
3952 6612 6.434028 CCACTCCTTCCATTTCAATGAGTAAA 59.566 38.462 0.81 0.00 38.70 2.01
4014 6675 6.801575 TGCTTTTTAAAATCCAACTTCGACT 58.198 32.000 0.55 0.00 0.00 4.18
4171 6832 9.868277 TTCAAAGTTGAAATTTAGAATGTGTGT 57.132 25.926 4.00 0.00 43.62 3.72
4222 6883 4.024387 TGCATTTTTGGTTCTCAGTCGTAC 60.024 41.667 0.00 0.00 0.00 3.67
4260 6921 4.274147 AGATCCACGTTCTCAGATGTAGT 58.726 43.478 0.00 0.00 0.00 2.73
4261 6922 4.707448 AGATCCACGTTCTCAGATGTAGTT 59.293 41.667 0.00 0.00 0.00 2.24
4262 6923 4.436242 TCCACGTTCTCAGATGTAGTTC 57.564 45.455 0.00 0.00 0.00 3.01
4263 6924 3.824443 TCCACGTTCTCAGATGTAGTTCA 59.176 43.478 0.00 0.00 0.00 3.18
4264 6925 4.082733 TCCACGTTCTCAGATGTAGTTCAG 60.083 45.833 0.00 0.00 0.00 3.02
4265 6926 4.169508 CACGTTCTCAGATGTAGTTCAGG 58.830 47.826 0.00 0.00 0.00 3.86
4266 6927 3.827302 ACGTTCTCAGATGTAGTTCAGGT 59.173 43.478 0.00 0.00 0.00 4.00
4267 6928 4.281182 ACGTTCTCAGATGTAGTTCAGGTT 59.719 41.667 0.00 0.00 0.00 3.50
4268 6929 4.623167 CGTTCTCAGATGTAGTTCAGGTTG 59.377 45.833 0.00 0.00 0.00 3.77
4269 6930 5.564848 CGTTCTCAGATGTAGTTCAGGTTGA 60.565 44.000 0.00 0.00 0.00 3.18
4270 6931 6.223852 GTTCTCAGATGTAGTTCAGGTTGAA 58.776 40.000 0.00 0.00 33.32 2.69
4473 7464 6.017934 GTGATGCATTCCGTAACACATTCTAT 60.018 38.462 0.00 0.00 0.00 1.98
4509 7506 6.160576 AGGCATTTTGTGACAACAGTTTAT 57.839 33.333 0.00 0.00 38.81 1.40
4510 7507 6.581712 AGGCATTTTGTGACAACAGTTTATT 58.418 32.000 0.00 0.00 38.81 1.40
4512 7509 7.552330 AGGCATTTTGTGACAACAGTTTATTTT 59.448 29.630 0.00 0.00 38.81 1.82
4513 7510 8.180920 GGCATTTTGTGACAACAGTTTATTTTT 58.819 29.630 0.00 0.00 37.67 1.94
4551 7556 3.412386 TGGCTAGGCAAAAGAGAGTTTC 58.588 45.455 17.92 0.00 0.00 2.78
4574 7579 4.618067 CAGTTAATTAACGAAAAACCGGGC 59.382 41.667 19.92 0.00 40.96 6.13
4580 7585 2.605837 ACGAAAAACCGGGCAAAAAT 57.394 40.000 6.32 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.129287 AGAGTAAAATTGGGCATGCTTCG 59.871 43.478 18.92 0.00 0.00 3.79
121 125 4.756135 CCTGTGGTAGCAAAAATGCAAAAT 59.244 37.500 0.00 0.00 37.25 1.82
146 150 3.068024 AGCTCGTTCCAGCAAATCAAAAA 59.932 39.130 0.00 0.00 42.40 1.94
236 241 1.587946 GCAAACTTGAAAACGCTGGTG 59.412 47.619 0.00 0.00 0.00 4.17
348 364 2.527624 TCACTGGTGCTGCCCTCT 60.528 61.111 0.00 0.00 36.04 3.69
349 365 2.046507 CTCACTGGTGCTGCCCTC 60.047 66.667 0.00 0.00 36.04 4.30
350 366 3.644606 CCTCACTGGTGCTGCCCT 61.645 66.667 0.00 0.00 36.04 5.19
363 379 1.361632 CATCGATGCTCGCTCCTCA 59.638 57.895 13.37 0.00 40.21 3.86
368 384 0.105593 AATCACCATCGATGCTCGCT 59.894 50.000 20.25 0.92 40.21 4.93
375 391 1.536072 CCGTCGACAATCACCATCGAT 60.536 52.381 17.16 0.00 45.72 3.59
379 395 1.809619 CGCCGTCGACAATCACCAT 60.810 57.895 17.16 0.00 38.10 3.55
402 418 2.594013 TCCATGTTGTGCAGCGCA 60.594 55.556 11.47 3.96 35.60 6.09
473 491 2.342648 GCACCTTTCCCTCGTCGT 59.657 61.111 0.00 0.00 0.00 4.34
483 501 1.073199 AGCGCAGTTAGGCACCTTT 59.927 52.632 11.47 0.00 0.00 3.11
488 506 4.371590 TCGCAGCGCAGTTAGGCA 62.372 61.111 10.87 0.00 0.00 4.75
596 615 2.104111 TGACTTCGTCTTCCAACACCAT 59.896 45.455 0.00 0.00 33.15 3.55
597 616 1.483004 TGACTTCGTCTTCCAACACCA 59.517 47.619 0.00 0.00 33.15 4.17
654 673 1.081556 TGCACGATTAGCGCGTCATT 61.082 50.000 8.43 0.00 46.04 2.57
730 749 3.567585 TCATCCAGATGACGTTTGCAAAA 59.432 39.130 14.67 0.00 42.42 2.44
731 750 3.145286 TCATCCAGATGACGTTTGCAAA 58.855 40.909 8.05 8.05 42.42 3.68
732 751 2.777094 TCATCCAGATGACGTTTGCAA 58.223 42.857 6.24 0.00 42.42 4.08
733 752 2.470983 TCATCCAGATGACGTTTGCA 57.529 45.000 6.24 0.00 42.42 4.08
742 761 4.421058 CACTGCAACAAATCATCCAGATG 58.579 43.478 0.98 0.98 36.96 2.90
743 762 3.446161 CCACTGCAACAAATCATCCAGAT 59.554 43.478 0.00 0.00 39.09 2.90
744 763 2.821378 CCACTGCAACAAATCATCCAGA 59.179 45.455 0.00 0.00 0.00 3.86
745 764 2.673043 GCCACTGCAACAAATCATCCAG 60.673 50.000 0.00 0.00 37.47 3.86
746 765 1.273048 GCCACTGCAACAAATCATCCA 59.727 47.619 0.00 0.00 37.47 3.41
747 766 1.273048 TGCCACTGCAACAAATCATCC 59.727 47.619 0.00 0.00 46.66 3.51
785 804 1.747367 CGAGTGGAGTCCGAGCTCT 60.747 63.158 12.85 7.98 35.89 4.09
786 805 2.795297 CGAGTGGAGTCCGAGCTC 59.205 66.667 2.73 2.73 34.89 4.09
787 806 2.538512 TAGCGAGTGGAGTCCGAGCT 62.539 60.000 19.48 19.48 37.27 4.09
788 807 2.054140 CTAGCGAGTGGAGTCCGAGC 62.054 65.000 4.30 7.24 0.00 5.03
789 808 1.440938 CCTAGCGAGTGGAGTCCGAG 61.441 65.000 4.30 0.00 0.00 4.63
790 809 1.451567 CCTAGCGAGTGGAGTCCGA 60.452 63.158 4.30 0.00 0.00 4.55
802 829 2.632541 CGAGTAGCGACCCTAGCG 59.367 66.667 0.00 0.00 44.57 4.26
820 847 0.388649 GCCTCCGGTGATATGCGTAG 60.389 60.000 4.76 0.00 0.00 3.51
821 848 1.663739 GCCTCCGGTGATATGCGTA 59.336 57.895 4.76 0.00 0.00 4.42
822 849 2.421739 GCCTCCGGTGATATGCGT 59.578 61.111 4.76 0.00 0.00 5.24
1068 1095 2.035632 GTCGTCAGGATCCTGGAAGAT 58.964 52.381 35.95 1.30 43.75 2.40
1314 1341 2.759973 ATGAGAGAGCCGCCGGAA 60.760 61.111 7.68 0.00 0.00 4.30
1444 1472 2.355108 GCTCAGCCAGTTTCCTGTGATA 60.355 50.000 0.00 0.00 36.95 2.15
1548 1576 6.116711 TCCATGGCAAGTTTGTAGTTACTA 57.883 37.500 6.96 0.00 0.00 1.82
1632 1660 5.416326 CCATTTCCGTTTGTACCCATCTTTA 59.584 40.000 0.00 0.00 0.00 1.85
1663 1691 1.599542 GCCACCGCTCAAATAGTCATC 59.400 52.381 0.00 0.00 0.00 2.92
1672 1700 1.666553 CGTTACTGCCACCGCTCAA 60.667 57.895 0.00 0.00 35.36 3.02
1673 1701 2.048597 CGTTACTGCCACCGCTCA 60.049 61.111 0.00 0.00 35.36 4.26
1674 1702 2.813908 CCGTTACTGCCACCGCTC 60.814 66.667 0.00 0.00 35.36 5.03
1675 1703 4.388499 CCCGTTACTGCCACCGCT 62.388 66.667 0.00 0.00 35.36 5.52
1676 1704 2.300850 TATCCCGTTACTGCCACCGC 62.301 60.000 0.00 0.00 0.00 5.68
1677 1705 0.391597 ATATCCCGTTACTGCCACCG 59.608 55.000 0.00 0.00 0.00 4.94
1678 1706 2.104281 AGAATATCCCGTTACTGCCACC 59.896 50.000 0.00 0.00 0.00 4.61
1679 1707 3.131396 CAGAATATCCCGTTACTGCCAC 58.869 50.000 0.00 0.00 0.00 5.01
1681 1709 3.746045 TCAGAATATCCCGTTACTGCC 57.254 47.619 0.00 0.00 0.00 4.85
1682 1710 4.632153 ACATCAGAATATCCCGTTACTGC 58.368 43.478 0.00 0.00 0.00 4.40
1690 1949 8.682936 ATCTACACAAAACATCAGAATATCCC 57.317 34.615 0.00 0.00 0.00 3.85
1743 2002 8.570068 AACCGTAACCATAAATAATGACAAGT 57.430 30.769 0.00 0.00 37.86 3.16
1827 2086 5.853572 TGGGTTCAAATCCTAGTAAACCT 57.146 39.130 0.00 0.00 37.05 3.50
1971 2231 6.601332 TCTCTAATTTATGTCCACAATCCCC 58.399 40.000 0.00 0.00 0.00 4.81
2015 2278 7.984422 TCTTTGCTTATTCACTGAGATTTCA 57.016 32.000 0.00 0.00 0.00 2.69
2071 2334 2.744202 GACAATGGTCAGTGGATGTGAC 59.256 50.000 0.00 0.00 43.73 3.67
2220 2488 1.752683 TCTCAGTTCTAGACCGCTCC 58.247 55.000 0.00 0.00 0.00 4.70
2264 2532 7.447374 AGAATCAACCATCGAACAAACATAA 57.553 32.000 0.00 0.00 0.00 1.90
2266 2534 5.964958 AGAATCAACCATCGAACAAACAT 57.035 34.783 0.00 0.00 0.00 2.71
2268 2536 6.258160 CCATAGAATCAACCATCGAACAAAC 58.742 40.000 0.00 0.00 0.00 2.93
2270 2538 4.881273 CCCATAGAATCAACCATCGAACAA 59.119 41.667 0.00 0.00 0.00 2.83
2272 2540 3.815401 CCCCATAGAATCAACCATCGAAC 59.185 47.826 0.00 0.00 0.00 3.95
2273 2541 3.714280 TCCCCATAGAATCAACCATCGAA 59.286 43.478 0.00 0.00 0.00 3.71
2274 2542 3.313791 TCCCCATAGAATCAACCATCGA 58.686 45.455 0.00 0.00 0.00 3.59
2275 2543 3.769739 TCCCCATAGAATCAACCATCG 57.230 47.619 0.00 0.00 0.00 3.84
2282 2550 6.068853 ACCTCAATTCTTTCCCCATAGAATCA 60.069 38.462 0.00 0.00 39.53 2.57
2309 2577 8.632679 CAAATGTAACCTATAAGAATGCCATGT 58.367 33.333 0.00 0.00 0.00 3.21
2339 2607 9.988815 TCTTATCTTCTAAATATGAGAGCCAAC 57.011 33.333 0.00 0.00 0.00 3.77
2395 2663 3.306641 GGCACACAACTCTCTCTCTCAAT 60.307 47.826 0.00 0.00 0.00 2.57
2398 2666 1.892474 AGGCACACAACTCTCTCTCTC 59.108 52.381 0.00 0.00 0.00 3.20
2399 2667 1.617850 CAGGCACACAACTCTCTCTCT 59.382 52.381 0.00 0.00 0.00 3.10
2415 2683 2.288825 GCTAACAAAGAAAACCCCAGGC 60.289 50.000 0.00 0.00 0.00 4.85
2457 2725 7.101652 ACCAACAGACTACATACTCATACTG 57.898 40.000 0.00 0.00 0.00 2.74
2476 2744 5.728471 GGTAGAACCCTAGTTTCTACCAAC 58.272 45.833 32.40 18.60 45.01 3.77
2539 2807 2.892640 CCACGCAATCTCCTCCGA 59.107 61.111 0.00 0.00 0.00 4.55
2540 2808 2.892425 GCCACGCAATCTCCTCCG 60.892 66.667 0.00 0.00 0.00 4.63
2607 2875 1.209747 CTAAACCCTAGCCGCCTCTTT 59.790 52.381 0.00 0.00 0.00 2.52
3059 5719 9.520204 AGAAAGAAAAATGTGAGTACAAATGTG 57.480 29.630 0.00 0.00 40.84 3.21
3060 5720 9.520204 CAGAAAGAAAAATGTGAGTACAAATGT 57.480 29.630 0.00 0.00 40.84 2.71
3061 5721 9.520204 ACAGAAAGAAAAATGTGAGTACAAATG 57.480 29.630 0.00 0.00 40.84 2.32
3065 5725 9.337396 ACATACAGAAAGAAAAATGTGAGTACA 57.663 29.630 0.00 0.00 41.89 2.90
3066 5726 9.813080 GACATACAGAAAGAAAAATGTGAGTAC 57.187 33.333 0.00 0.00 0.00 2.73
3067 5727 9.554395 TGACATACAGAAAGAAAAATGTGAGTA 57.446 29.630 0.00 0.00 0.00 2.59
3068 5728 8.450578 TGACATACAGAAAGAAAAATGTGAGT 57.549 30.769 0.00 0.00 0.00 3.41
3069 5729 9.734620 TTTGACATACAGAAAGAAAAATGTGAG 57.265 29.630 0.00 0.00 0.00 3.51
3086 5746 4.638304 ACCGGCACCTATATTTGACATAC 58.362 43.478 0.00 0.00 0.00 2.39
3154 5814 0.320247 CATAGTCATCCGCAGCTCCC 60.320 60.000 0.00 0.00 0.00 4.30
3406 6066 2.135139 ACCATAAGTGCGATATGTGCG 58.865 47.619 0.00 0.00 34.24 5.34
3599 6259 3.551846 TCCTGAAGGTGGAAGTTTCAAC 58.448 45.455 0.00 0.00 36.34 3.18
3668 6328 8.023706 TCTACTATATGCTACAAAATCAGCTCG 58.976 37.037 0.00 0.00 38.63 5.03
3750 6410 5.246656 ACCCGACGAACATATATCCCATAAA 59.753 40.000 0.00 0.00 0.00 1.40
3826 6486 4.695928 GTCCAAAGAACATTCTGGGTAGAC 59.304 45.833 10.68 4.57 37.65 2.59
3928 6588 7.452880 TTTACTCATTGAAATGGAAGGAGTG 57.547 36.000 9.42 0.00 42.68 3.51
3948 6608 2.514902 TGAATTTCATGCGCGCTTTAC 58.485 42.857 33.29 14.80 0.00 2.01
3952 6612 1.534595 GGAATGAATTTCATGCGCGCT 60.535 47.619 33.29 15.19 37.15 5.92
4064 6725 9.898152 TTGAATTTGTATTGAAAGGGAGTTTTT 57.102 25.926 0.00 0.00 0.00 1.94
4171 6832 6.377996 CCCTCCATTCAAATGAATAAGACACA 59.622 38.462 8.24 0.00 42.41 3.72
4244 6905 3.827302 ACCTGAACTACATCTGAGAACGT 59.173 43.478 0.00 0.00 0.00 3.99
4309 6970 3.909662 GCGGAATGCATGACAGGT 58.090 55.556 0.00 0.00 45.45 4.00
4473 7464 7.280876 GTCACAAAATGCCTAATCATCTAGTCA 59.719 37.037 0.00 0.00 0.00 3.41
4509 7506 3.254657 CAGTGGATGAGGCGGTTTAAAAA 59.745 43.478 0.00 0.00 0.00 1.94
4510 7507 2.817258 CAGTGGATGAGGCGGTTTAAAA 59.183 45.455 0.00 0.00 0.00 1.52
4512 7509 1.339631 CCAGTGGATGAGGCGGTTTAA 60.340 52.381 1.68 0.00 0.00 1.52
4513 7510 0.251916 CCAGTGGATGAGGCGGTTTA 59.748 55.000 1.68 0.00 0.00 2.01
4515 7512 2.671070 CCAGTGGATGAGGCGGTT 59.329 61.111 1.68 0.00 0.00 4.44
4516 7513 4.101448 GCCAGTGGATGAGGCGGT 62.101 66.667 15.20 0.00 38.86 5.68
4551 7556 4.618067 GCCCGGTTTTTCGTTAATTAACTG 59.382 41.667 22.57 16.63 34.12 3.16


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

AutoCloner maintained by Alex Coulton.