Multiple sequence alignment - TraesCS7A01G217700

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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 TraesCS7A01G217700 chr7A 100.000 5119 0 0 1 5119 184315230 184320348 0.000000e+00 9454.0
1 TraesCS7A01G217700 chr7A 88.940 1745 138 36 1089 2796 184326532 184328258 0.000000e+00 2102.0
2 TraesCS7A01G217700 chr7A 83.889 2098 258 60 781 2813 184169352 184171434 0.000000e+00 1929.0
3 TraesCS7A01G217700 chr7A 87.979 1306 129 21 2865 4165 184171519 184172801 0.000000e+00 1517.0
4 TraesCS7A01G217700 chr7A 93.841 828 48 1 3347 4174 184328896 184329720 0.000000e+00 1243.0
5 TraesCS7A01G217700 chr7A 87.571 700 62 14 4172 4855 184329851 184330541 0.000000e+00 787.0
6 TraesCS7A01G217700 chr7A 90.758 422 30 1 2864 3285 184328452 184328864 5.790000e-154 555.0
7 TraesCS7A01G217700 chr7A 84.096 415 50 8 4172 4576 184172941 184173349 2.240000e-103 387.0
8 TraesCS7A01G217700 chr7A 77.266 673 61 40 1 649 184168627 184169231 1.380000e-80 311.0
9 TraesCS7A01G217700 chr7A 88.583 254 15 8 697 941 184326056 184326304 3.880000e-76 296.0
10 TraesCS7A01G217700 chr7A 90.000 210 14 5 948 1155 184326362 184326566 1.090000e-66 265.0
11 TraesCS7A01G217700 chr7A 77.215 237 36 11 4856 5088 184330885 184331107 6.960000e-24 122.0
12 TraesCS7A01G217700 chr7A 83.471 121 7 7 1 121 184325791 184325898 3.260000e-17 100.0
13 TraesCS7A01G217700 chr7A 86.154 65 9 0 3570 3634 184171165 184171229 2.560000e-08 71.3
14 TraesCS7A01G217700 chr7D 95.618 3674 139 10 1118 4772 180014239 180017909 0.000000e+00 5873.0
15 TraesCS7A01G217700 chr7D 91.969 1021 74 5 1783 2796 180071703 180072722 0.000000e+00 1424.0
16 TraesCS7A01G217700 chr7D 94.807 828 43 0 3347 4174 180073376 180074203 0.000000e+00 1291.0
17 TraesCS7A01G217700 chr7D 93.269 624 35 5 973 1591 180070896 180071517 0.000000e+00 913.0
18 TraesCS7A01G217700 chr7D 90.042 713 51 11 4157 4855 180074321 180075027 0.000000e+00 905.0
19 TraesCS7A01G217700 chr7D 90.995 422 29 1 2864 3285 180072932 180073344 1.240000e-155 560.0
20 TraesCS7A01G217700 chr7D 82.340 470 65 14 697 1155 180013775 180014237 4.800000e-105 392.0
21 TraesCS7A01G217700 chr7D 89.247 279 23 5 4846 5119 180017904 180018180 4.910000e-90 342.0
22 TraesCS7A01G217700 chr7D 88.710 186 12 4 761 941 180070634 180070815 8.630000e-53 219.0
23 TraesCS7A01G217700 chr7D 75.560 491 42 31 193 657 180013412 180013850 2.450000e-38 171.0
24 TraesCS7A01G217700 chr7D 77.731 238 33 13 4856 5088 180075369 180075591 1.500000e-25 128.0
25 TraesCS7A01G217700 chr7D 84.956 113 5 6 1 113 180070160 180070260 2.520000e-18 104.0
26 TraesCS7A01G217700 chr7B 88.955 1838 150 30 990 2796 145964826 145966641 0.000000e+00 2220.0
27 TraesCS7A01G217700 chr7B 90.666 1307 92 15 2864 4170 145933799 145935075 0.000000e+00 1711.0
28 TraesCS7A01G217700 chr7B 87.701 1309 130 22 2865 4165 145825873 145827158 0.000000e+00 1496.0
29 TraesCS7A01G217700 chr7B 87.044 1289 110 33 2858 4130 145966826 145968073 0.000000e+00 1402.0
30 TraesCS7A01G217700 chr7B 90.000 1020 87 11 1783 2796 145932565 145933575 0.000000e+00 1304.0
31 TraesCS7A01G217700 chr7B 89.588 970 64 27 4172 5119 145935210 145936164 0.000000e+00 1197.0
32 TraesCS7A01G217700 chr7B 85.556 1080 125 21 1760 2813 145824714 145825788 0.000000e+00 1101.0
33 TraesCS7A01G217700 chr7B 88.556 935 41 25 1 916 145930682 145931569 0.000000e+00 1074.0
34 TraesCS7A01G217700 chr7B 85.451 921 110 20 765 1672 145823681 145824590 0.000000e+00 937.0
35 TraesCS7A01G217700 chr7B 86.333 739 58 18 947 1651 145931623 145932352 0.000000e+00 765.0
36 TraesCS7A01G217700 chr7B 94.076 422 22 3 4646 5065 145970369 145970789 5.590000e-179 638.0
37 TraesCS7A01G217700 chr7B 84.259 324 39 7 4172 4488 145827298 145827616 6.440000e-79 305.0
38 TraesCS7A01G217700 chr7B 84.568 162 25 0 4013 4174 145968073 145968234 1.480000e-35 161.0
39 TraesCS7A01G217700 chr7B 89.320 103 10 1 4281 4383 145968690 145968791 1.500000e-25 128.0
40 TraesCS7A01G217700 chr7B 86.111 108 3 6 1 108 145964033 145964128 7.010000e-19 106.0
41 TraesCS7A01G217700 chr4A 90.969 454 41 0 2343 2796 726121103 726120650 3.390000e-171 612.0
42 TraesCS7A01G217700 chr4A 87.302 189 15 3 3087 3275 726120143 726119964 1.870000e-49 207.0
43 TraesCS7A01G217700 chr4A 91.589 107 9 0 2871 2977 726120545 726120439 1.150000e-31 148.0
44 TraesCS7A01G217700 chrUn 88.722 399 33 9 1760 2149 477165654 477165259 1.290000e-130 477.0


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 TraesCS7A01G217700 chr7A 184315230 184320348 5118 False 9454.000000 9454 100.000000 1 5119 1 chr7A.!!$F1 5118
1 TraesCS7A01G217700 chr7A 184168627 184173349 4722 False 843.060000 1929 83.876800 1 4576 5 chr7A.!!$F2 4575
2 TraesCS7A01G217700 chr7A 184325791 184331107 5316 False 683.750000 2102 87.547375 1 5088 8 chr7A.!!$F3 5087
3 TraesCS7A01G217700 chr7D 180013412 180018180 4768 False 1694.500000 5873 85.691250 193 5119 4 chr7D.!!$F1 4926
4 TraesCS7A01G217700 chr7D 180070160 180075591 5431 False 693.000000 1424 89.059875 1 5088 8 chr7D.!!$F2 5087
5 TraesCS7A01G217700 chr7B 145930682 145936164 5482 False 1210.200000 1711 89.028600 1 5119 5 chr7B.!!$F2 5118
6 TraesCS7A01G217700 chr7B 145823681 145827616 3935 False 959.750000 1496 85.741750 765 4488 4 chr7B.!!$F1 3723
7 TraesCS7A01G217700 chr7B 145964033 145970789 6756 False 775.833333 2220 88.345667 1 5065 6 chr7B.!!$F3 5064
8 TraesCS7A01G217700 chr4A 726119964 726121103 1139 True 322.333333 612 89.953333 2343 3275 3 chr4A.!!$R1 932

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
964 1478 0.811915 GCAGAGACTAAGACCAGCGA 59.188 55.000 0.00 0.00 0.00 4.93 F
2552 3313 0.037326 CAGTCCCAAGCGCTACAAGA 60.037 55.000 12.05 2.27 0.00 3.02 F
3536 4708 1.698532 ACAAGGATGGCCATTTTGCAA 59.301 42.857 29.45 0.00 36.29 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2643 3404 0.871722 TGTTTGCAGTACATGACGCC 59.128 50.000 0.0 0.0 0.0 5.68 R
3838 5010 1.405661 CCCTTCTCCTTCACTAACCGC 60.406 57.143 0.0 0.0 0.0 5.68 R
4617 6364 1.135689 CGGTTGGCGGAATTTCTTCAG 60.136 52.381 0.0 0.0 32.7 3.02 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
24 25 7.194607 CTGGTACTTGAATGGCATTATACTG 57.805 40.000 13.65 4.87 0.00 2.74
25 26 6.658849 TGGTACTTGAATGGCATTATACTGT 58.341 36.000 13.65 10.18 0.00 3.55
26 27 7.797062 TGGTACTTGAATGGCATTATACTGTA 58.203 34.615 13.65 9.27 0.00 2.74
94 100 4.497507 CGATTCTCGCTGGATACTACACAA 60.498 45.833 0.00 0.00 31.14 3.33
108 114 1.825191 CACAAGCACAGGCACAGGT 60.825 57.895 0.00 0.00 44.61 4.00
140 146 1.528309 ACCCCAACAAACCTCTGCG 60.528 57.895 0.00 0.00 0.00 5.18
178 187 3.096092 ACTAGAAGAGCCAAGTCTCAGG 58.904 50.000 0.00 0.00 35.59 3.86
180 189 2.334023 AGAAGAGCCAAGTCTCAGGTT 58.666 47.619 0.00 0.00 35.59 3.50
316 327 9.197694 CGAGGTTCATTTAGTTATAAGATGAGG 57.802 37.037 0.00 0.00 0.00 3.86
338 349 7.092444 TGAGGAAGATAGATAGAAAGGGCAAAA 60.092 37.037 0.00 0.00 0.00 2.44
384 395 4.664688 AAGGGAACAAATGACTGATCCT 57.335 40.909 0.00 0.00 38.13 3.24
389 400 4.142513 GGAACAAATGACTGATCCTCTTGC 60.143 45.833 0.00 0.00 35.82 4.01
405 416 4.437930 CCTCTTGCAAAGCAACATACTAGC 60.438 45.833 0.00 0.00 45.70 3.42
440 459 7.171167 CAGATGGAAATACATGAGATGTCTGAC 59.829 40.741 0.00 0.00 43.67 3.51
481 504 4.300189 TGGATGTTTGTGCAAGTTGTAC 57.700 40.909 16.28 16.28 33.42 2.90
482 505 3.951037 TGGATGTTTGTGCAAGTTGTACT 59.049 39.130 22.27 4.28 33.97 2.73
483 506 5.126779 TGGATGTTTGTGCAAGTTGTACTA 58.873 37.500 22.27 13.87 33.97 1.82
484 507 5.008217 TGGATGTTTGTGCAAGTTGTACTAC 59.992 40.000 22.27 19.16 33.97 2.73
485 508 5.008217 GGATGTTTGTGCAAGTTGTACTACA 59.992 40.000 23.44 23.44 34.83 2.74
486 509 5.478233 TGTTTGTGCAAGTTGTACTACAG 57.522 39.130 22.27 3.31 33.97 2.74
501 529 5.420739 TGTACTACAGTATCATGGCTTGACA 59.579 40.000 5.09 0.00 37.11 3.58
502 530 5.016051 ACTACAGTATCATGGCTTGACAG 57.984 43.478 5.09 0.00 37.11 3.51
503 531 3.272574 ACAGTATCATGGCTTGACAGG 57.727 47.619 5.09 0.00 37.11 4.00
510 538 3.708451 TCATGGCTTGACAGGAGTACTA 58.292 45.455 0.00 0.00 0.00 1.82
527 555 9.810870 AGGAGTACTATACTAATACAAGAAGGG 57.189 37.037 0.00 0.00 39.59 3.95
553 581 9.944376 GAGTATATCCTATTGCAATTTGGTAGA 57.056 33.333 18.75 4.44 0.00 2.59
649 806 3.609853 TGTGCTGCTCCAAATTAGGTAG 58.390 45.455 0.00 0.00 0.00 3.18
650 807 2.945668 GTGCTGCTCCAAATTAGGTAGG 59.054 50.000 0.00 0.00 0.00 3.18
652 809 3.265737 TGCTGCTCCAAATTAGGTAGGAA 59.734 43.478 0.00 0.00 0.00 3.36
653 810 4.079787 TGCTGCTCCAAATTAGGTAGGAAT 60.080 41.667 0.00 0.00 0.00 3.01
656 813 6.569127 TGCTCCAAATTAGGTAGGAATGTA 57.431 37.500 0.00 0.00 0.00 2.29
657 814 6.354130 TGCTCCAAATTAGGTAGGAATGTAC 58.646 40.000 0.00 0.00 0.00 2.90
659 816 7.346175 TGCTCCAAATTAGGTAGGAATGTACTA 59.654 37.037 0.00 0.00 0.00 1.82
664 821 9.930693 CAAATTAGGTAGGAATGTACTATCTCC 57.069 37.037 0.00 0.00 34.01 3.71
665 822 7.941431 ATTAGGTAGGAATGTACTATCTCCG 57.059 40.000 0.00 0.00 34.01 4.63
667 824 5.315348 AGGTAGGAATGTACTATCTCCGTC 58.685 45.833 0.00 0.00 32.91 4.79
668 825 5.073417 AGGTAGGAATGTACTATCTCCGTCT 59.927 44.000 0.00 0.00 32.91 4.18
670 827 6.939163 GGTAGGAATGTACTATCTCCGTCTTA 59.061 42.308 0.00 0.00 32.91 2.10
671 828 7.446625 GGTAGGAATGTACTATCTCCGTCTTAA 59.553 40.741 0.00 0.00 32.91 1.85
672 829 7.893124 AGGAATGTACTATCTCCGTCTTAAA 57.107 36.000 0.00 0.00 32.91 1.52
674 831 8.925338 AGGAATGTACTATCTCCGTCTTAAAAT 58.075 33.333 0.00 0.00 32.91 1.82
675 832 8.979574 GGAATGTACTATCTCCGTCTTAAAATG 58.020 37.037 0.00 0.00 0.00 2.32
676 833 9.530633 GAATGTACTATCTCCGTCTTAAAATGT 57.469 33.333 0.00 0.00 0.00 2.71
680 837 8.966194 GTACTATCTCCGTCTTAAAATGTAAGC 58.034 37.037 0.00 0.00 0.00 3.09
684 841 6.228258 TCTCCGTCTTAAAATGTAAGCTGTT 58.772 36.000 0.00 0.00 0.00 3.16
686 843 6.894828 TCCGTCTTAAAATGTAAGCTGTTTC 58.105 36.000 0.00 0.00 0.00 2.78
688 845 7.227910 TCCGTCTTAAAATGTAAGCTGTTTCTT 59.772 33.333 0.00 0.00 0.00 2.52
690 847 9.872757 CGTCTTAAAATGTAAGCTGTTTCTTTA 57.127 29.630 0.00 0.00 0.00 1.85
693 850 9.129209 CTTAAAATGTAAGCTGTTTCTTTAGGC 57.871 33.333 0.00 0.00 0.00 3.93
694 851 6.901081 AAATGTAAGCTGTTTCTTTAGGCT 57.099 33.333 0.00 0.00 34.52 4.58
695 852 7.996098 AAATGTAAGCTGTTTCTTTAGGCTA 57.004 32.000 0.00 0.00 32.64 3.93
697 854 6.985188 TGTAAGCTGTTTCTTTAGGCTATG 57.015 37.500 0.00 0.00 32.64 2.23
698 855 6.472887 TGTAAGCTGTTTCTTTAGGCTATGT 58.527 36.000 0.00 0.00 32.64 2.29
699 856 7.617225 TGTAAGCTGTTTCTTTAGGCTATGTA 58.383 34.615 0.00 0.00 32.64 2.29
702 859 7.793927 AGCTGTTTCTTTAGGCTATGTAATC 57.206 36.000 0.00 0.00 0.00 1.75
706 863 9.553064 CTGTTTCTTTAGGCTATGTAATCTGAT 57.447 33.333 0.00 0.00 0.00 2.90
716 873 8.317679 AGGCTATGTAATCTGATTATCTGAACC 58.682 37.037 12.84 10.45 0.00 3.62
720 877 7.792374 TGTAATCTGATTATCTGAACCAAGC 57.208 36.000 12.84 0.00 0.00 4.01
721 878 7.337938 TGTAATCTGATTATCTGAACCAAGCA 58.662 34.615 12.84 0.26 0.00 3.91
722 879 6.690194 AATCTGATTATCTGAACCAAGCAC 57.310 37.500 0.00 0.00 0.00 4.40
724 881 5.748402 TCTGATTATCTGAACCAAGCACAT 58.252 37.500 0.00 0.00 0.00 3.21
725 882 6.888105 TCTGATTATCTGAACCAAGCACATA 58.112 36.000 0.00 0.00 0.00 2.29
728 885 8.523915 TGATTATCTGAACCAAGCACATATTT 57.476 30.769 0.00 0.00 0.00 1.40
730 887 9.241317 GATTATCTGAACCAAGCACATATTTTG 57.759 33.333 0.00 0.00 0.00 2.44
731 888 4.808558 TCTGAACCAAGCACATATTTTGC 58.191 39.130 0.00 0.00 40.52 3.68
732 889 3.924144 TGAACCAAGCACATATTTTGCC 58.076 40.909 2.94 0.00 41.18 4.52
735 892 2.028203 ACCAAGCACATATTTTGCCCAC 60.028 45.455 2.94 0.00 41.18 4.61
736 893 2.261345 CAAGCACATATTTTGCCCACG 58.739 47.619 2.94 0.00 41.18 4.94
738 895 2.717390 AGCACATATTTTGCCCACGTA 58.283 42.857 2.94 0.00 41.18 3.57
739 896 3.085533 AGCACATATTTTGCCCACGTAA 58.914 40.909 2.94 0.00 41.18 3.18
740 897 3.128589 AGCACATATTTTGCCCACGTAAG 59.871 43.478 2.94 0.00 41.18 2.34
741 898 3.119637 GCACATATTTTGCCCACGTAAGT 60.120 43.478 0.00 0.00 42.97 2.24
742 899 4.617298 GCACATATTTTGCCCACGTAAGTT 60.617 41.667 0.00 0.00 41.08 2.66
743 900 6.076032 GCACATATTTTGCCCACGTAAGTTT 61.076 40.000 0.00 0.00 41.08 2.66
744 901 6.842773 GCACATATTTTGCCCACGTAAGTTTA 60.843 38.462 0.00 0.00 41.08 2.01
756 913 4.264543 CGTAAGTTTATGCTGCTCCAAG 57.735 45.455 0.00 0.00 0.00 3.61
757 914 3.684788 CGTAAGTTTATGCTGCTCCAAGT 59.315 43.478 0.00 0.00 0.00 3.16
758 915 4.154195 CGTAAGTTTATGCTGCTCCAAGTT 59.846 41.667 0.00 2.84 0.00 2.66
759 916 5.334879 CGTAAGTTTATGCTGCTCCAAGTTT 60.335 40.000 0.00 0.00 0.00 2.66
803 999 1.208052 GCATGAAGCTAGGACTCACCA 59.792 52.381 0.00 0.00 39.95 4.17
804 1000 2.741228 GCATGAAGCTAGGACTCACCAG 60.741 54.545 0.00 0.00 39.95 4.00
805 1001 1.561643 TGAAGCTAGGACTCACCAGG 58.438 55.000 0.00 0.00 42.04 4.45
941 1401 3.234386 GCGATGTGGCTTTGAAGTTTAC 58.766 45.455 0.00 0.00 0.00 2.01
943 1403 4.712763 CGATGTGGCTTTGAAGTTTACTC 58.287 43.478 0.00 0.00 0.00 2.59
944 1404 4.213270 CGATGTGGCTTTGAAGTTTACTCA 59.787 41.667 0.00 0.00 0.00 3.41
945 1405 5.615544 CGATGTGGCTTTGAAGTTTACTCAG 60.616 44.000 0.00 0.00 0.00 3.35
953 1465 5.537300 TTGAAGTTTACTCAGCAGAGACT 57.463 39.130 13.73 3.14 44.98 3.24
964 1478 0.811915 GCAGAGACTAAGACCAGCGA 59.188 55.000 0.00 0.00 0.00 4.93
979 1493 3.057033 ACCAGCGACGTTTACTAGTTCAT 60.057 43.478 0.00 0.00 0.00 2.57
1111 1638 4.353437 GCAGCTGCAGGCAACACC 62.353 66.667 33.36 0.00 44.79 4.16
1175 1780 1.744741 GAGCTCCTGTGGAAGCTGC 60.745 63.158 0.87 0.00 36.72 5.25
1491 2096 3.217017 CTACGCCGCTGGGAGCTA 61.217 66.667 0.00 0.00 39.60 3.32
1503 2108 0.617820 GGGAGCTACAGGGAGGTGAA 60.618 60.000 0.00 0.00 0.00 3.18
1602 2207 1.528129 GCACCTAAGAAGCTGCAAGT 58.472 50.000 1.02 0.00 35.30 3.16
1743 2453 1.876156 CCTTGAAAGAAGTCGCAGCTT 59.124 47.619 0.00 0.00 0.00 3.74
1812 2546 3.598299 CTGCAAAGGAGAGAGAGGAAAG 58.402 50.000 0.00 0.00 0.00 2.62
1944 2681 1.068333 CAGTAACCACATTGCTGGTGC 60.068 52.381 10.42 7.79 44.32 5.01
1972 2709 1.681793 CTCCGAGACCATTATCCACGT 59.318 52.381 0.00 0.00 0.00 4.49
1990 2727 2.256174 CGTCGATTCAAGGCGTTCTTA 58.744 47.619 0.00 0.00 33.68 2.10
2071 2808 5.182950 TCAAACAGCGATGGATTATGTTGTT 59.817 36.000 5.32 0.00 34.50 2.83
2099 2836 1.887242 GCTCTGCGGTTGTGTGTGA 60.887 57.895 0.00 0.00 0.00 3.58
2231 2968 6.882610 TCATTCAGTGTATTGAACTTGCTT 57.117 33.333 0.00 0.00 39.68 3.91
2341 3081 1.270550 GCCTTGTTGGAACCTGACATG 59.729 52.381 0.00 0.00 38.35 3.21
2552 3313 0.037326 CAGTCCCAAGCGCTACAAGA 60.037 55.000 12.05 2.27 0.00 3.02
2606 3367 2.940158 CCTCTTTGGCCATCATCATCA 58.060 47.619 6.09 0.00 0.00 3.07
2643 3404 5.301045 AGTTGATTACCATTCATGCCATGAG 59.699 40.000 7.55 0.00 40.94 2.90
2843 3640 3.329225 GGAGAGCATAATAGGGGCTTCTT 59.671 47.826 0.00 0.00 38.15 2.52
2849 3646 5.247337 AGCATAATAGGGGCTTCTTCTAGAC 59.753 44.000 0.00 0.00 33.21 2.59
2978 3949 4.019174 AGGTGGCTTTTGGACTGATAATG 58.981 43.478 0.00 0.00 0.00 1.90
3157 4320 2.164663 GCTGCGTGCATGCGTACTA 61.165 57.895 25.05 7.05 42.31 1.82
3227 4390 8.721478 GCAGAAAAGTGTCAACATCTTTCTATA 58.279 33.333 15.97 0.00 37.44 1.31
3399 4571 3.433274 CACACGACAAGCACAAGTGATAT 59.567 43.478 4.04 0.00 36.71 1.63
3536 4708 1.698532 ACAAGGATGGCCATTTTGCAA 59.301 42.857 29.45 0.00 36.29 4.08
3571 4743 3.770388 TCCATGATACCAACCTAACACGA 59.230 43.478 0.00 0.00 0.00 4.35
3695 4867 3.747854 TTGCCATGAAAACAGCAATGA 57.252 38.095 0.00 0.00 40.13 2.57
3787 4959 2.859526 TTTTTGCACTCGTCATTGCA 57.140 40.000 0.00 0.00 46.93 4.08
4056 5359 6.855763 TTATTGTTTCTCAAGGCCATCATT 57.144 33.333 5.01 0.00 39.55 2.57
4129 5432 5.069119 TGACAACTGTGAGATGTGAAGTAGT 59.931 40.000 0.00 0.00 31.03 2.73
4267 5718 5.705441 TGTAATGTTCCAAAGTGAGGATGTC 59.295 40.000 0.00 0.00 34.56 3.06
4306 5979 6.860023 AGTCTCTTTGAAAATGAAGCAATTCG 59.140 34.615 0.00 0.00 28.96 3.34
4344 6017 4.443394 GGCGGTGTCACTAGTATTTTATCG 59.557 45.833 2.35 0.00 0.00 2.92
4351 6024 6.040878 GTCACTAGTATTTTATCGGCACAGT 58.959 40.000 0.00 0.00 0.00 3.55
4424 6099 6.156083 TGTGTAAATGATGTCCAGGTATGAGA 59.844 38.462 0.00 0.00 0.00 3.27
4538 6221 3.840078 TGTTCAAGGATGGAGAGACATGA 59.160 43.478 0.00 0.00 0.00 3.07
4539 6222 4.081254 TGTTCAAGGATGGAGAGACATGAG 60.081 45.833 0.00 0.00 0.00 2.90
4541 6224 4.356436 TCAAGGATGGAGAGACATGAGAA 58.644 43.478 0.00 0.00 0.00 2.87
4542 6225 4.967442 TCAAGGATGGAGAGACATGAGAAT 59.033 41.667 0.00 0.00 0.00 2.40
4546 6229 7.630005 AGGATGGAGAGACATGAGAATAAAT 57.370 36.000 0.00 0.00 0.00 1.40
4547 6230 7.678837 AGGATGGAGAGACATGAGAATAAATC 58.321 38.462 0.00 0.00 0.00 2.17
4551 6294 7.504403 TGGAGAGACATGAGAATAAATCTTCC 58.496 38.462 0.00 0.79 38.96 3.46
4554 6297 9.612066 GAGAGACATGAGAATAAATCTTCCTTT 57.388 33.333 0.00 0.00 38.96 3.11
4558 6301 9.794685 GACATGAGAATAAATCTTCCTTTTTCC 57.205 33.333 0.00 0.00 38.96 3.13
4563 6306 8.427902 AGAATAAATCTTCCTTTTTCCTTGCT 57.572 30.769 0.00 0.00 33.39 3.91
4617 6364 2.290387 GGAACTCCCTTCCTGGTTTCTC 60.290 54.545 0.00 0.00 44.90 2.87
4621 6368 2.639839 CTCCCTTCCTGGTTTCTCTGAA 59.360 50.000 0.00 0.00 0.00 3.02
4636 6383 2.159382 TCTGAAGAAATTCCGCCAACC 58.841 47.619 0.00 0.00 0.00 3.77
4695 7798 0.880718 TGTAACACGGCGCATCAACA 60.881 50.000 10.83 2.36 0.00 3.33
4729 7832 3.444742 TGCCAGGAGATTGCACAAATAAG 59.555 43.478 0.00 0.00 0.00 1.73
4817 7921 2.242196 GGGATGAGGACCTGATTTTGGA 59.758 50.000 0.00 0.00 0.00 3.53
4818 7922 3.117360 GGGATGAGGACCTGATTTTGGAT 60.117 47.826 0.00 0.00 0.00 3.41
4974 8422 2.292918 ACAGCCCAGTATAGGACCAAGA 60.293 50.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.286595 CGTGCATGGCAAGCTAATACAG 60.287 50.000 16.31 0.00 41.47 2.74
23 24 1.670295 CGTGCATGGCAAGCTAATACA 59.330 47.619 16.31 0.00 41.47 2.29
24 25 1.670811 ACGTGCATGGCAAGCTAATAC 59.329 47.619 16.31 4.62 41.40 1.89
25 26 1.670295 CACGTGCATGGCAAGCTAATA 59.330 47.619 16.31 0.00 41.40 0.98
26 27 0.452987 CACGTGCATGGCAAGCTAAT 59.547 50.000 16.31 0.00 41.40 1.73
94 100 1.372683 CTGTACCTGTGCCTGTGCT 59.627 57.895 0.00 0.00 38.71 4.40
108 114 0.471022 TGGGGTGCTCTGTGACTGTA 60.471 55.000 0.00 0.00 0.00 2.74
178 187 4.793216 GTGAAGTGTGTGTGAACATTGAAC 59.207 41.667 0.00 0.00 31.49 3.18
180 189 4.006319 TGTGAAGTGTGTGTGAACATTGA 58.994 39.130 0.00 0.00 31.49 2.57
244 254 3.349927 TCTTGGATTGTGATGCCTGAAG 58.650 45.455 0.00 0.00 0.00 3.02
307 318 9.540538 CCCTTTCTATCTATCTTCCTCATCTTA 57.459 37.037 0.00 0.00 0.00 2.10
308 319 7.038373 GCCCTTTCTATCTATCTTCCTCATCTT 60.038 40.741 0.00 0.00 0.00 2.40
316 327 7.283329 TCCTTTTGCCCTTTCTATCTATCTTC 58.717 38.462 0.00 0.00 0.00 2.87
338 349 4.825199 ACTCCTATCCTAGCTCTTTCCT 57.175 45.455 0.00 0.00 0.00 3.36
389 400 9.045223 TGAATATAGTGCTAGTATGTTGCTTTG 57.955 33.333 0.00 0.00 0.00 2.77
440 459 1.972872 AGACAGTGTTCCAAAGCCTG 58.027 50.000 0.00 0.00 0.00 4.85
481 504 4.100035 TCCTGTCAAGCCATGATACTGTAG 59.900 45.833 0.00 0.00 40.97 2.74
482 505 4.030216 TCCTGTCAAGCCATGATACTGTA 58.970 43.478 0.00 0.00 40.97 2.74
483 506 2.840038 TCCTGTCAAGCCATGATACTGT 59.160 45.455 0.00 0.00 40.97 3.55
484 507 3.118482 ACTCCTGTCAAGCCATGATACTG 60.118 47.826 0.00 0.00 40.97 2.74
485 508 3.110705 ACTCCTGTCAAGCCATGATACT 58.889 45.455 0.00 0.00 40.97 2.12
486 509 3.550437 ACTCCTGTCAAGCCATGATAC 57.450 47.619 0.00 0.00 40.97 2.24
501 529 9.810870 CCCTTCTTGTATTAGTATAGTACTCCT 57.189 37.037 0.00 0.00 40.14 3.69
502 530 9.804977 TCCCTTCTTGTATTAGTATAGTACTCC 57.195 37.037 0.00 0.00 40.14 3.85
523 551 7.671398 CCAAATTGCAATAGGATATACTCCCTT 59.329 37.037 20.68 1.93 46.27 3.95
524 552 7.177878 CCAAATTGCAATAGGATATACTCCCT 58.822 38.462 20.68 0.00 46.27 4.20
525 553 6.948309 ACCAAATTGCAATAGGATATACTCCC 59.052 38.462 28.13 0.00 46.27 4.30
527 555 9.944376 TCTACCAAATTGCAATAGGATATACTC 57.056 33.333 28.13 0.00 0.00 2.59
529 557 9.502091 TGTCTACCAAATTGCAATAGGATATAC 57.498 33.333 28.13 20.66 0.00 1.47
571 599 9.964303 CAGCCTAATCAGATTATAGCATACTAG 57.036 37.037 19.95 0.00 0.00 2.57
572 600 9.700831 TCAGCCTAATCAGATTATAGCATACTA 57.299 33.333 19.95 5.33 0.00 1.82
573 601 8.601047 TCAGCCTAATCAGATTATAGCATACT 57.399 34.615 19.95 4.54 0.00 2.12
574 602 9.092876 GTTCAGCCTAATCAGATTATAGCATAC 57.907 37.037 19.95 13.39 0.00 2.39
581 729 5.874093 CTGGGTTCAGCCTAATCAGATTAT 58.126 41.667 3.19 0.00 37.43 1.28
606 756 5.874261 ACAAACTTATGTGGGCAAAATATGC 59.126 36.000 0.00 0.00 42.54 3.14
649 806 8.979574 CATTTTAAGACGGAGATAGTACATTCC 58.020 37.037 0.00 0.00 0.00 3.01
650 807 9.530633 ACATTTTAAGACGGAGATAGTACATTC 57.469 33.333 0.00 0.00 0.00 2.67
656 813 7.707035 CAGCTTACATTTTAAGACGGAGATAGT 59.293 37.037 0.00 0.00 0.00 2.12
657 814 7.707035 ACAGCTTACATTTTAAGACGGAGATAG 59.293 37.037 0.00 0.00 0.00 2.08
659 816 6.407202 ACAGCTTACATTTTAAGACGGAGAT 58.593 36.000 0.00 0.00 0.00 2.75
664 821 8.782533 AAAGAAACAGCTTACATTTTAAGACG 57.217 30.769 0.00 0.00 0.00 4.18
667 824 9.129209 GCCTAAAGAAACAGCTTACATTTTAAG 57.871 33.333 0.00 0.00 0.00 1.85
668 825 8.856103 AGCCTAAAGAAACAGCTTACATTTTAA 58.144 29.630 0.00 0.00 0.00 1.52
670 827 7.290110 AGCCTAAAGAAACAGCTTACATTTT 57.710 32.000 0.00 0.00 0.00 1.82
671 828 6.901081 AGCCTAAAGAAACAGCTTACATTT 57.099 33.333 0.00 0.00 0.00 2.32
672 829 7.611855 ACATAGCCTAAAGAAACAGCTTACATT 59.388 33.333 0.00 0.00 35.03 2.71
674 831 6.472887 ACATAGCCTAAAGAAACAGCTTACA 58.527 36.000 0.00 0.00 35.03 2.41
675 832 6.986904 ACATAGCCTAAAGAAACAGCTTAC 57.013 37.500 0.00 0.00 35.03 2.34
676 833 9.326413 GATTACATAGCCTAAAGAAACAGCTTA 57.674 33.333 0.00 0.00 35.03 3.09
679 836 7.495934 TCAGATTACATAGCCTAAAGAAACAGC 59.504 37.037 0.00 0.00 0.00 4.40
680 837 8.948631 TCAGATTACATAGCCTAAAGAAACAG 57.051 34.615 0.00 0.00 0.00 3.16
690 847 8.317679 GGTTCAGATAATCAGATTACATAGCCT 58.682 37.037 4.91 0.00 0.00 4.58
691 848 8.097038 TGGTTCAGATAATCAGATTACATAGCC 58.903 37.037 4.91 5.16 0.00 3.93
692 849 9.494271 TTGGTTCAGATAATCAGATTACATAGC 57.506 33.333 4.91 1.28 0.00 2.97
694 851 9.494271 GCTTGGTTCAGATAATCAGATTACATA 57.506 33.333 4.91 0.00 0.00 2.29
695 852 7.994911 TGCTTGGTTCAGATAATCAGATTACAT 59.005 33.333 4.91 0.00 0.00 2.29
697 854 7.280876 TGTGCTTGGTTCAGATAATCAGATTAC 59.719 37.037 4.91 0.71 0.00 1.89
698 855 7.337938 TGTGCTTGGTTCAGATAATCAGATTA 58.662 34.615 5.29 5.29 0.00 1.75
699 856 6.182627 TGTGCTTGGTTCAGATAATCAGATT 58.817 36.000 0.20 0.20 0.00 2.40
702 859 7.741027 ATATGTGCTTGGTTCAGATAATCAG 57.259 36.000 0.00 0.00 0.00 2.90
706 863 7.035004 GCAAAATATGTGCTTGGTTCAGATAA 58.965 34.615 4.72 0.00 39.00 1.75
710 867 3.928375 GGCAAAATATGTGCTTGGTTCAG 59.072 43.478 10.55 0.00 41.88 3.02
712 869 3.261580 GGGCAAAATATGTGCTTGGTTC 58.738 45.455 10.55 0.00 41.88 3.62
713 870 2.636893 TGGGCAAAATATGTGCTTGGTT 59.363 40.909 10.55 0.00 41.88 3.67
714 871 2.028203 GTGGGCAAAATATGTGCTTGGT 60.028 45.455 10.55 0.00 41.88 3.67
716 873 2.261345 CGTGGGCAAAATATGTGCTTG 58.739 47.619 10.55 0.00 41.88 4.01
720 877 4.695217 ACTTACGTGGGCAAAATATGTG 57.305 40.909 0.00 0.00 0.00 3.21
721 878 5.715434 AAACTTACGTGGGCAAAATATGT 57.285 34.783 0.00 0.00 0.00 2.29
722 879 6.198216 GCATAAACTTACGTGGGCAAAATATG 59.802 38.462 0.00 0.00 0.00 1.78
724 881 5.416326 AGCATAAACTTACGTGGGCAAAATA 59.584 36.000 0.00 0.00 0.00 1.40
725 882 4.219725 AGCATAAACTTACGTGGGCAAAAT 59.780 37.500 0.00 0.00 0.00 1.82
728 885 2.486203 CAGCATAAACTTACGTGGGCAA 59.514 45.455 0.00 0.00 0.00 4.52
730 887 1.202143 GCAGCATAAACTTACGTGGGC 60.202 52.381 0.00 0.00 0.00 5.36
731 888 2.351726 GAGCAGCATAAACTTACGTGGG 59.648 50.000 0.00 0.00 0.00 4.61
732 889 2.351726 GGAGCAGCATAAACTTACGTGG 59.648 50.000 0.00 0.00 0.00 4.94
735 892 3.684788 ACTTGGAGCAGCATAAACTTACG 59.315 43.478 0.00 0.00 0.00 3.18
736 893 5.629079 AACTTGGAGCAGCATAAACTTAC 57.371 39.130 0.00 0.00 0.00 2.34
738 895 4.874970 CAAACTTGGAGCAGCATAAACTT 58.125 39.130 0.00 0.00 0.00 2.66
739 896 4.510038 CAAACTTGGAGCAGCATAAACT 57.490 40.909 0.00 0.00 0.00 2.66
753 910 9.886132 ATATTTACTACACTCCTACCAAACTTG 57.114 33.333 0.00 0.00 0.00 3.16
754 911 9.886132 CATATTTACTACACTCCTACCAAACTT 57.114 33.333 0.00 0.00 0.00 2.66
755 912 7.985752 GCATATTTACTACACTCCTACCAAACT 59.014 37.037 0.00 0.00 0.00 2.66
756 913 7.985752 AGCATATTTACTACACTCCTACCAAAC 59.014 37.037 0.00 0.00 0.00 2.93
757 914 7.985184 CAGCATATTTACTACACTCCTACCAAA 59.015 37.037 0.00 0.00 0.00 3.28
758 915 7.497595 CAGCATATTTACTACACTCCTACCAA 58.502 38.462 0.00 0.00 0.00 3.67
759 916 6.462487 GCAGCATATTTACTACACTCCTACCA 60.462 42.308 0.00 0.00 0.00 3.25
803 999 2.909504 TTCTGCAGTCTACTCCTCCT 57.090 50.000 14.67 0.00 0.00 3.69
804 1000 3.368948 CCTTTTCTGCAGTCTACTCCTCC 60.369 52.174 14.67 0.00 0.00 4.30
805 1001 3.511934 TCCTTTTCTGCAGTCTACTCCTC 59.488 47.826 14.67 0.00 0.00 3.71
884 1340 7.255942 CCACCAATAATATCCCATGGAGAAAAC 60.256 40.741 15.22 0.00 34.05 2.43
941 1401 2.159254 GCTGGTCTTAGTCTCTGCTGAG 60.159 54.545 14.07 14.07 41.51 3.35
943 1403 1.468908 CGCTGGTCTTAGTCTCTGCTG 60.469 57.143 0.00 0.00 0.00 4.41
944 1404 0.814457 CGCTGGTCTTAGTCTCTGCT 59.186 55.000 0.00 0.00 0.00 4.24
945 1405 0.811915 TCGCTGGTCTTAGTCTCTGC 59.188 55.000 0.00 0.00 0.00 4.26
953 1465 3.753272 ACTAGTAAACGTCGCTGGTCTTA 59.247 43.478 0.00 0.00 0.00 2.10
964 1478 6.821031 AGACTGAGATGAACTAGTAAACGT 57.179 37.500 0.00 0.00 0.00 3.99
979 1493 1.211703 TGTGGGTTTGCAAGACTGAGA 59.788 47.619 0.00 0.00 0.00 3.27
1046 1573 1.072159 CGGAATCCTCCATGGCTCC 59.928 63.158 6.96 6.72 42.58 4.70
1156 1761 1.078567 CAGCTTCCACAGGAGCTCC 60.079 63.158 26.22 26.22 35.28 4.70
1175 1780 0.537188 ATCAGCACCAGGTACTTCCG 59.463 55.000 0.00 0.00 41.99 4.30
1288 1893 1.478105 CTGGACCTCATCACGATGTCA 59.522 52.381 6.91 0.25 40.11 3.58
1503 2108 3.261897 CACCCAGATGTAAACAGAGGTCT 59.738 47.826 0.00 0.00 0.00 3.85
1696 2301 1.280421 ACTTCTTCCATCTGGACTGGC 59.720 52.381 0.00 0.00 45.39 4.85
1715 2320 4.858140 GCGACTTCTTTCAAGGTCTACTAC 59.142 45.833 0.00 0.00 0.00 2.73
1717 2322 3.321111 TGCGACTTCTTTCAAGGTCTACT 59.679 43.478 0.00 0.00 0.00 2.57
1718 2323 3.650139 TGCGACTTCTTTCAAGGTCTAC 58.350 45.455 0.00 0.00 0.00 2.59
1743 2453 4.356405 TCTTCTGCAAGATCAAGAACCA 57.644 40.909 0.00 0.00 46.36 3.67
1812 2546 5.469479 TGCGATTTCTTTCAAGATTTTCCC 58.531 37.500 0.00 0.00 34.49 3.97
1972 2709 4.566759 CAGATTAAGAACGCCTTGAATCGA 59.433 41.667 0.00 0.00 36.34 3.59
1990 2727 1.263356 AAGCAGTGGCATTGCAGATT 58.737 45.000 32.23 17.84 43.92 2.40
2071 2808 2.472695 ACCGCAGAGCATTTGACTTA 57.527 45.000 0.00 0.00 0.00 2.24
2099 2836 6.183361 CCCATAAGCCCAAAGAGACTAACTAT 60.183 42.308 0.00 0.00 0.00 2.12
2341 3081 2.663119 GCCGTTGTTTGATTGATCTTGC 59.337 45.455 0.00 0.00 0.00 4.01
2479 3240 3.801698 CCCATCACTGTTATCTGTCCAG 58.198 50.000 0.00 0.00 0.00 3.86
2552 3313 6.516194 GCTGTGGCATTGCAATAGAAGAATAT 60.516 38.462 12.53 0.00 38.54 1.28
2606 3367 4.101741 GGTAATCAACTGGCTCTGGAGTAT 59.898 45.833 0.00 0.00 0.00 2.12
2643 3404 0.871722 TGTTTGCAGTACATGACGCC 59.128 50.000 0.00 0.00 0.00 5.68
2807 3568 3.321039 TGCTCTCCCACCATATCTTGAT 58.679 45.455 0.00 0.00 0.00 2.57
2843 3640 3.459969 TCTGGAGTATCAGCAGGTCTAGA 59.540 47.826 0.00 0.00 36.25 2.43
2849 3646 2.762887 TGTCTTCTGGAGTATCAGCAGG 59.237 50.000 0.00 0.00 36.25 4.85
3227 4390 4.067896 ACTGCAAGAACAACGAGAATGAT 58.932 39.130 0.00 0.00 37.43 2.45
3235 4398 2.845967 GACAAACACTGCAAGAACAACG 59.154 45.455 0.00 0.00 37.43 4.10
3399 4571 4.461431 TGTGCTCCGTTCTCTTACTATCAA 59.539 41.667 0.00 0.00 0.00 2.57
3536 4708 1.971149 TCATGGAGGATTGGGTCACT 58.029 50.000 0.00 0.00 0.00 3.41
3571 4743 7.254795 GCGTTGCAATAGAAGAATACCTTGTAT 60.255 37.037 0.59 0.00 41.47 2.29
3695 4867 4.729868 AGTAAACCAAGCAAGTCCAAGAT 58.270 39.130 0.00 0.00 0.00 2.40
3787 4959 6.396829 TGAATGACGATGTAGATGATCACT 57.603 37.500 0.00 0.00 0.00 3.41
3838 5010 1.405661 CCCTTCTCCTTCACTAACCGC 60.406 57.143 0.00 0.00 0.00 5.68
3952 5135 6.490381 TCACAACTGAGACTACTCTTACACAT 59.510 38.462 0.00 0.00 42.99 3.21
4030 5333 7.243604 TGATGGCCTTGAGAAACAATAAAAT 57.756 32.000 3.32 0.00 37.88 1.82
4041 5344 9.866655 AAATAATACTAAATGATGGCCTTGAGA 57.133 29.630 3.32 0.00 0.00 3.27
4160 5466 2.430332 CTCCTCTCCACATCAGAAGGTC 59.570 54.545 0.00 0.00 0.00 3.85
4220 5671 6.597280 ACACCTATTTCTCTCTTTCATTCAGC 59.403 38.462 0.00 0.00 0.00 4.26
4306 5979 2.388232 CGCCCTGCAGTAAACGACC 61.388 63.158 13.81 0.00 0.00 4.79
4344 6017 3.611766 AGGTATCAGTGTTACTGTGCC 57.388 47.619 10.44 8.90 46.03 5.01
4515 6198 3.685139 TGTCTCTCCATCCTTGAACAC 57.315 47.619 0.00 0.00 0.00 3.32
4538 6221 8.427902 AGCAAGGAAAAAGGAAGATTTATTCT 57.572 30.769 0.00 0.00 35.70 2.40
4539 6222 9.794685 CTAGCAAGGAAAAAGGAAGATTTATTC 57.205 33.333 0.00 0.00 0.00 1.75
4541 6224 9.183368 CTCTAGCAAGGAAAAAGGAAGATTTAT 57.817 33.333 0.00 0.00 0.00 1.40
4542 6225 8.383175 TCTCTAGCAAGGAAAAAGGAAGATTTA 58.617 33.333 0.00 0.00 0.00 1.40
4546 6229 5.280215 CCTCTCTAGCAAGGAAAAAGGAAGA 60.280 44.000 4.64 0.00 34.35 2.87
4547 6230 4.940654 CCTCTCTAGCAAGGAAAAAGGAAG 59.059 45.833 4.64 0.00 34.35 3.46
4557 6300 2.745968 ACTCCTTCCTCTCTAGCAAGG 58.254 52.381 4.32 4.32 37.36 3.61
4558 6301 6.279882 CAAATACTCCTTCCTCTCTAGCAAG 58.720 44.000 0.00 0.00 0.00 4.01
4563 6306 3.637229 CGCCAAATACTCCTTCCTCTCTA 59.363 47.826 0.00 0.00 0.00 2.43
4617 6364 1.135689 CGGTTGGCGGAATTTCTTCAG 60.136 52.381 0.00 0.00 32.70 3.02
4621 6368 1.677633 CCCGGTTGGCGGAATTTCT 60.678 57.895 0.00 0.00 0.00 2.52
4631 6378 4.820744 CCTCATGGGCCCGGTTGG 62.821 72.222 19.37 13.30 37.09 3.77
4974 8422 8.331740 TCCTAGTCTTCCTTGAATGAATGAATT 58.668 33.333 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.