Multiple sequence alignment - TraesCS6D01G112200

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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 TraesCS6D01G112200 chr6D 100.000 8006 0 0 1 8006 78757723 78765728 0.000000e+00 14785.0
1 TraesCS6D01G112200 chr6D 84.108 3593 386 89 3805 7311 78542155 78538662 0.000000e+00 3301.0
2 TraesCS6D01G112200 chr6D 88.467 1396 128 14 1213 2577 78544789 78543396 0.000000e+00 1655.0
3 TraesCS6D01G112200 chr6D 96.524 633 19 2 7374 8006 68725072 68725701 0.000000e+00 1044.0
4 TraesCS6D01G112200 chr6D 78.638 1278 162 57 5263 6481 78303942 78302717 0.000000e+00 745.0
5 TraesCS6D01G112200 chr6D 82.367 862 102 26 2989 3813 78543058 78542210 0.000000e+00 704.0
6 TraesCS6D01G112200 chr6D 80.121 825 97 28 34 799 78545979 78545163 3.260000e-153 553.0
7 TraesCS6D01G112200 chr6D 77.778 936 126 41 4235 5130 78500946 78500053 1.200000e-137 501.0
8 TraesCS6D01G112200 chr6D 90.476 189 18 0 997 1185 78544967 78544779 4.800000e-62 250.0
9 TraesCS6D01G112200 chr6D 81.319 273 44 7 4238 4509 78357785 78357519 1.750000e-51 215.0
10 TraesCS6D01G112200 chr6D 93.182 44 3 0 6557 6600 296824505 296824462 1.860000e-06 65.8
11 TraesCS6D01G112200 chr6B 94.323 4668 154 39 2742 7375 151380088 151384678 0.000000e+00 7049.0
12 TraesCS6D01G112200 chr6B 92.738 2644 79 34 1 2580 151377332 151379926 0.000000e+00 3714.0
13 TraesCS6D01G112200 chr6B 83.881 3592 381 95 3805 7311 151300782 151297304 0.000000e+00 3243.0
14 TraesCS6D01G112200 chr6B 87.758 1405 130 18 1213 2577 151303565 151302163 0.000000e+00 1604.0
15 TraesCS6D01G112200 chr6B 81.944 864 104 28 2989 3813 151301687 151300837 0.000000e+00 684.0
16 TraesCS6D01G112200 chr6B 79.556 856 96 42 1 799 151304747 151303914 9.140000e-149 538.0
17 TraesCS6D01G112200 chr6B 82.560 539 92 2 2032 2569 151154021 151153484 2.610000e-129 473.0
18 TraesCS6D01G112200 chr6B 86.779 416 53 2 6460 6874 151149284 151148870 5.660000e-126 462.0
19 TraesCS6D01G112200 chr6B 81.313 594 88 16 5263 5842 151151077 151150493 2.040000e-125 460.0
20 TraesCS6D01G112200 chr6B 80.364 494 48 25 5993 6474 151149802 151149346 5.990000e-86 329.0
21 TraesCS6D01G112200 chr6B 94.702 151 3 2 2602 2747 151379911 151380061 6.250000e-56 230.0
22 TraesCS6D01G112200 chr6A 84.053 3543 403 92 3833 7311 94200552 94197108 0.000000e+00 3264.0
23 TraesCS6D01G112200 chr6A 91.580 1817 100 18 807 2580 94232463 94234269 0.000000e+00 2459.0
24 TraesCS6D01G112200 chr6A 92.286 1439 79 14 5946 7378 94238698 94240110 0.000000e+00 2013.0
25 TraesCS6D01G112200 chr6A 88.613 1449 110 26 3533 4942 94235339 94236771 0.000000e+00 1711.0
26 TraesCS6D01G112200 chr6A 87.124 1398 136 21 1213 2580 94210871 94209488 0.000000e+00 1544.0
27 TraesCS6D01G112200 chr6A 94.347 796 31 10 2742 3533 94234431 94235216 0.000000e+00 1208.0
28 TraesCS6D01G112200 chr6A 88.338 686 46 14 4977 5637 94236770 94237446 0.000000e+00 793.0
29 TraesCS6D01G112200 chr6A 81.687 901 117 27 2952 3813 94207276 94206385 0.000000e+00 706.0
30 TraesCS6D01G112200 chr6A 84.277 477 43 20 1 467 94231745 94232199 3.430000e-118 436.0
31 TraesCS6D01G112200 chr6A 85.142 424 61 2 6460 6882 93890543 93890121 4.440000e-117 433.0
32 TraesCS6D01G112200 chr6A 79.448 652 82 31 5841 6474 93891227 93890610 1.610000e-111 414.0
33 TraesCS6D01G112200 chr6A 93.358 271 18 0 5629 5899 94238424 94238694 1.250000e-107 401.0
34 TraesCS6D01G112200 chr6A 81.659 458 58 16 5260 5698 94070343 94069893 2.750000e-94 357.0
35 TraesCS6D01G112200 chr6A 88.987 227 25 0 5263 5489 93891819 93891593 1.700000e-71 281.0
36 TraesCS6D01G112200 chr6A 78.218 505 56 29 1 470 94212150 94211665 2.850000e-69 274.0
37 TraesCS6D01G112200 chr6A 90.860 186 16 1 1000 1185 94211045 94210861 1.730000e-61 248.0
38 TraesCS6D01G112200 chr6A 92.617 149 6 3 2604 2747 94234256 94234404 8.140000e-50 209.0
39 TraesCS6D01G112200 chr6A 93.182 44 3 0 6557 6600 423533530 423533487 1.860000e-06 65.8
40 TraesCS6D01G112200 chr7D 97.781 631 14 0 7375 8005 618056962 618057592 0.000000e+00 1088.0
41 TraesCS6D01G112200 chr5D 97.781 631 14 0 7376 8006 543429286 543428656 0.000000e+00 1088.0
42 TraesCS6D01G112200 chr5D 96.651 627 19 2 7380 8006 5413792 5414416 0.000000e+00 1040.0
43 TraesCS6D01G112200 chr2D 97.306 631 17 0 7376 8006 535225490 535226120 0.000000e+00 1072.0
44 TraesCS6D01G112200 chr2D 96.672 631 21 0 7376 8006 526120178 526120808 0.000000e+00 1050.0
45 TraesCS6D01G112200 chr2D 96.667 630 19 1 7377 8006 73827508 73828135 0.000000e+00 1046.0
46 TraesCS6D01G112200 chr3D 97.156 633 15 2 7377 8006 571148828 571148196 0.000000e+00 1066.0
47 TraesCS6D01G112200 chr3D 95.419 633 27 2 7375 8006 360567094 360566463 0.000000e+00 1007.0


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 TraesCS6D01G112200 chr6D 78757723 78765728 8005 False 14785.000000 14785 100.000000 1 8006 1 chr6D.!!$F2 8005
1 TraesCS6D01G112200 chr6D 78538662 78545979 7317 True 1292.600000 3301 85.107800 34 7311 5 chr6D.!!$R5 7277
2 TraesCS6D01G112200 chr6D 68725072 68725701 629 False 1044.000000 1044 96.524000 7374 8006 1 chr6D.!!$F1 632
3 TraesCS6D01G112200 chr6D 78302717 78303942 1225 True 745.000000 745 78.638000 5263 6481 1 chr6D.!!$R1 1218
4 TraesCS6D01G112200 chr6D 78500053 78500946 893 True 501.000000 501 77.778000 4235 5130 1 chr6D.!!$R3 895
5 TraesCS6D01G112200 chr6B 151377332 151384678 7346 False 3664.333333 7049 93.921000 1 7375 3 chr6B.!!$F1 7374
6 TraesCS6D01G112200 chr6B 151297304 151304747 7443 True 1517.250000 3243 83.284750 1 7311 4 chr6B.!!$R2 7310
7 TraesCS6D01G112200 chr6B 151148870 151154021 5151 True 431.000000 473 82.754000 2032 6874 4 chr6B.!!$R1 4842
8 TraesCS6D01G112200 chr6A 94197108 94200552 3444 True 3264.000000 3264 84.053000 3833 7311 1 chr6A.!!$R2 3478
9 TraesCS6D01G112200 chr6A 94231745 94240110 8365 False 1153.750000 2459 90.677000 1 7378 8 chr6A.!!$F1 7377
10 TraesCS6D01G112200 chr6A 94206385 94212150 5765 True 693.000000 1544 84.472250 1 3813 4 chr6A.!!$R5 3812
11 TraesCS6D01G112200 chr6A 93890121 93891819 1698 True 376.000000 433 84.525667 5263 6882 3 chr6A.!!$R4 1619
12 TraesCS6D01G112200 chr7D 618056962 618057592 630 False 1088.000000 1088 97.781000 7375 8005 1 chr7D.!!$F1 630
13 TraesCS6D01G112200 chr5D 543428656 543429286 630 True 1088.000000 1088 97.781000 7376 8006 1 chr5D.!!$R1 630
14 TraesCS6D01G112200 chr5D 5413792 5414416 624 False 1040.000000 1040 96.651000 7380 8006 1 chr5D.!!$F1 626
15 TraesCS6D01G112200 chr2D 535225490 535226120 630 False 1072.000000 1072 97.306000 7376 8006 1 chr2D.!!$F3 630
16 TraesCS6D01G112200 chr2D 526120178 526120808 630 False 1050.000000 1050 96.672000 7376 8006 1 chr2D.!!$F2 630
17 TraesCS6D01G112200 chr2D 73827508 73828135 627 False 1046.000000 1046 96.667000 7377 8006 1 chr2D.!!$F1 629
18 TraesCS6D01G112200 chr3D 571148196 571148828 632 True 1066.000000 1066 97.156000 7377 8006 1 chr3D.!!$R2 629
19 TraesCS6D01G112200 chr3D 360566463 360567094 631 True 1007.000000 1007 95.419000 7375 8006 1 chr3D.!!$R1 631

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
31 34 0.112606 TGAGACCGAGGTCAAGGAGT 59.887 55.000 22.66 2.25 46.76 3.85 F
32 35 0.528470 GAGACCGAGGTCAAGGAGTG 59.472 60.000 22.66 0.00 46.76 3.51 F
952 1203 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72 F
2595 2896 0.402887 GGGTCCCCCTTTTCGAAAGA 59.597 55.000 10.98 1.64 41.34 2.52 F
3579 4149 0.110486 TTCTCCCCACCTGCTTTGTC 59.890 55.000 0.00 0.00 0.00 3.18 F
3581 4151 0.607489 CTCCCCACCTGCTTTGTCTG 60.607 60.000 0.00 0.00 0.00 3.51 F
4540 5510 1.570803 ATGCTTTGCTATTTGGGCCA 58.429 45.000 0.00 0.00 0.00 5.36 F
5030 6048 2.436417 GCAATGGTACTTCCTGCAGAA 58.564 47.619 17.39 6.85 37.35 3.02 F
5493 6558 3.476552 TCTGGCTGAGGTAAAAACTGTG 58.523 45.455 0.00 0.00 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1042 1297 0.543277 TCAGGCTGTCCATGGATCAC 59.457 55.000 19.62 9.94 33.74 3.06 R
1126 1382 1.155042 GCAACAGAGGTGCTTCTCAG 58.845 55.000 0.00 4.30 36.30 3.35 R
2730 3039 1.076332 CCCGAGGTTGTCAATCGAAC 58.924 55.000 9.61 0.00 38.72 3.95 R
4165 5067 4.261801 ACATTAGTGATGAAAGTTCCCCG 58.738 43.478 1.26 0.00 39.15 5.73 R
5030 6048 4.697352 CCCATTGATCTTCTTTCGAACTGT 59.303 41.667 0.00 0.00 0.00 3.55 R
5131 6155 5.506708 ACTGTGTTACCTTTTCCTTTGAGT 58.493 37.500 0.00 0.00 0.00 3.41 R
6004 8624 3.664107 TCTGGAAAACTTCATGGACTCG 58.336 45.455 0.00 0.00 0.00 4.18 R
6950 9678 0.528470 CCCACCGTGTTGTTGTTGTT 59.472 50.000 0.00 0.00 0.00 2.83 R
7194 9926 1.441732 GCTGTCCAAACCCGAACGTT 61.442 55.000 0.00 0.00 0.00 3.99 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
31 34 0.112606 TGAGACCGAGGTCAAGGAGT 59.887 55.000 22.66 2.25 46.76 3.85
32 35 0.528470 GAGACCGAGGTCAAGGAGTG 59.472 60.000 22.66 0.00 46.76 3.51
49 52 1.099689 GTGAAGGAGAGGAGACCGAG 58.900 60.000 0.00 0.00 0.00 4.63
355 393 7.212976 TCTGCAGTAATGCCAATTGTTAAAAA 58.787 30.769 14.67 0.00 0.00 1.94
470 528 9.582431 TTCGTTAGGATCATCTTGTTAGTTTAG 57.418 33.333 0.00 0.00 0.00 1.85
523 600 2.390599 CCACGGCCACAAGATCACG 61.391 63.158 2.24 0.00 0.00 4.35
570 701 1.212935 AGTTCCACACTGTTTCAGGCT 59.787 47.619 1.90 0.00 35.51 4.58
623 772 1.707989 TGAGCCATGGGGTTTACTTGA 59.292 47.619 15.13 0.00 36.17 3.02
688 851 5.003804 GGAGGACAGTCTTTTTCTAATGCA 58.996 41.667 0.00 0.00 0.00 3.96
700 863 7.656948 TCTTTTTCTAATGCAAACAAAGGGATG 59.343 33.333 0.00 0.00 0.00 3.51
720 883 7.070571 AGGGATGATAGAGTCAAGTCTAAAAGG 59.929 40.741 0.00 0.00 40.97 3.11
721 884 6.704050 GGATGATAGAGTCAAGTCTAAAAGGC 59.296 42.308 0.00 0.00 40.97 4.35
743 906 3.660813 CGCAATTATTTCGCAGCTGTATG 59.339 43.478 16.64 5.99 0.00 2.39
761 924 5.815581 TGTATGCTTTCTATTGGTGGAAGT 58.184 37.500 0.00 0.00 0.00 3.01
765 928 5.007682 TGCTTTCTATTGGTGGAAGTTACC 58.992 41.667 0.00 0.00 38.71 2.85
878 1093 2.337849 TGCTACTCCCATGGATATGCA 58.662 47.619 15.22 13.68 32.79 3.96
879 1094 2.914941 TGCTACTCCCATGGATATGCAT 59.085 45.455 15.22 3.79 32.79 3.96
899 1116 5.543507 CATATATATGCCAGTCTCTCCCC 57.456 47.826 9.75 0.00 0.00 4.81
935 1186 3.706594 TCCTCTCTCTCTCTCTCTCTCAC 59.293 52.174 0.00 0.00 0.00 3.51
936 1187 3.452264 CCTCTCTCTCTCTCTCTCTCACA 59.548 52.174 0.00 0.00 0.00 3.58
937 1188 4.437239 CTCTCTCTCTCTCTCTCTCACAC 58.563 52.174 0.00 0.00 0.00 3.82
938 1189 3.837731 TCTCTCTCTCTCTCTCTCACACA 59.162 47.826 0.00 0.00 0.00 3.72
939 1190 3.935203 CTCTCTCTCTCTCTCTCACACAC 59.065 52.174 0.00 0.00 0.00 3.82
940 1191 3.326297 TCTCTCTCTCTCTCTCACACACA 59.674 47.826 0.00 0.00 0.00 3.72
941 1192 3.407698 TCTCTCTCTCTCTCACACACAC 58.592 50.000 0.00 0.00 0.00 3.82
942 1193 3.145286 CTCTCTCTCTCTCACACACACA 58.855 50.000 0.00 0.00 0.00 3.72
943 1194 2.881513 TCTCTCTCTCTCACACACACAC 59.118 50.000 0.00 0.00 0.00 3.82
944 1195 2.620585 CTCTCTCTCTCACACACACACA 59.379 50.000 0.00 0.00 0.00 3.72
945 1196 2.359214 TCTCTCTCTCACACACACACAC 59.641 50.000 0.00 0.00 0.00 3.82
946 1197 2.099405 TCTCTCTCACACACACACACA 58.901 47.619 0.00 0.00 0.00 3.72
947 1198 2.159240 TCTCTCTCACACACACACACAC 60.159 50.000 0.00 0.00 0.00 3.82
948 1199 1.548269 TCTCTCACACACACACACACA 59.452 47.619 0.00 0.00 0.00 3.72
949 1200 1.660607 CTCTCACACACACACACACAC 59.339 52.381 0.00 0.00 0.00 3.82
950 1201 1.001406 TCTCACACACACACACACACA 59.999 47.619 0.00 0.00 0.00 3.72
951 1202 1.128507 CTCACACACACACACACACAC 59.871 52.381 0.00 0.00 0.00 3.82
952 1203 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
953 1204 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
954 1205 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
955 1206 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
956 1207 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
957 1208 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
958 1209 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
959 1210 1.468127 CACACACACACACACACACAT 59.532 47.619 0.00 0.00 0.00 3.21
1005 1260 7.750229 ACAAGAGTGAAGAATAAGCATGAAA 57.250 32.000 0.00 0.00 0.00 2.69
1042 1297 5.165961 TCTCCTTTTCTACATGTTCCAGG 57.834 43.478 2.30 3.34 0.00 4.45
1126 1382 5.581605 TCTTTCAGTTCAGAAAATGCACAC 58.418 37.500 0.00 0.00 37.09 3.82
1623 1879 3.523157 TGGATGGACATCATACTTGTGGT 59.477 43.478 13.72 0.00 37.59 4.16
1675 1931 4.334481 GTGAACAAAGGTATGGGTAATCCG 59.666 45.833 0.00 0.00 38.76 4.18
1708 1964 1.815003 CTGGATTTGAGGCCACTGAAC 59.185 52.381 5.01 0.00 0.00 3.18
1967 2242 5.561725 GCTGCTTTTAGCCTTATACTGCATC 60.562 44.000 0.00 0.00 41.51 3.91
2073 2374 1.080927 ACCCCTCGGATCCCCTAGAT 61.081 60.000 6.06 0.00 38.17 1.98
2358 2659 6.061441 TGTCAATAACAAGACATGGAACAGT 58.939 36.000 0.00 0.00 39.65 3.55
2531 2832 0.955428 GCGGTTGCAACTGATCCTGA 60.955 55.000 36.72 0.00 42.15 3.86
2556 2857 4.380531 ACGGTATGGATTTAGTGATGCAG 58.619 43.478 0.00 0.00 30.70 4.41
2580 2881 4.414337 TTAGTACGGACTAGAGAGGGTC 57.586 50.000 7.73 0.00 39.36 4.46
2581 2882 1.490069 AGTACGGACTAGAGAGGGTCC 59.510 57.143 0.00 0.00 46.00 4.46
2582 2883 0.842635 TACGGACTAGAGAGGGTCCC 59.157 60.000 0.00 0.00 46.56 4.46
2584 2885 1.233659 GGACTAGAGAGGGTCCCCC 59.766 68.421 3.51 0.00 44.35 5.40
2594 2895 2.957060 GGGTCCCCCTTTTCGAAAG 58.043 57.895 10.98 5.63 41.34 2.62
2595 2896 0.402887 GGGTCCCCCTTTTCGAAAGA 59.597 55.000 10.98 1.64 41.34 2.52
2668 2969 5.297029 GGTCCTGTCTAATTTGCAATAGACC 59.703 44.000 26.30 16.14 44.74 3.85
2730 3039 5.699097 TTCAACCCTGAATTCTAAAACCG 57.301 39.130 7.05 0.00 36.62 4.44
2773 3117 7.251994 GGTAGTCTCACTAGTGATTTAGTGTG 58.748 42.308 25.35 11.54 46.75 3.82
2787 3131 2.203126 TGTGACGTGCATGCCACA 60.203 55.556 22.28 22.28 44.91 4.17
2835 3179 1.369625 CCATGCCACTAAGTTCCGTC 58.630 55.000 0.00 0.00 0.00 4.79
2849 3193 6.969828 AAGTTCCGTCTATTGATCTGTTTC 57.030 37.500 0.00 0.00 0.00 2.78
2938 3282 9.296400 GAGCTTGTTTTAGATTGTTTGTTGTTA 57.704 29.630 0.00 0.00 0.00 2.41
3196 3638 3.370103 GGGTGATCCATGTACTCCGAAAA 60.370 47.826 0.00 0.00 35.00 2.29
3201 3643 5.642063 TGATCCATGTACTCCGAAAACTTTC 59.358 40.000 0.00 0.00 0.00 2.62
3243 3685 2.810274 CTCATATCCACCAGCAAATCCG 59.190 50.000 0.00 0.00 0.00 4.18
3321 3764 5.290493 ACCCATTCTCATACGCTGAATAA 57.710 39.130 0.00 0.00 32.14 1.40
3577 4147 2.806945 TATTCTCCCCACCTGCTTTG 57.193 50.000 0.00 0.00 0.00 2.77
3579 4149 0.110486 TTCTCCCCACCTGCTTTGTC 59.890 55.000 0.00 0.00 0.00 3.18
3581 4151 0.607489 CTCCCCACCTGCTTTGTCTG 60.607 60.000 0.00 0.00 0.00 3.51
3586 4157 2.086869 CCACCTGCTTTGTCTGGTATG 58.913 52.381 0.00 0.00 36.66 2.39
3609 4180 8.647256 ATGTGTAGGAACTAGTAGTGTACTTT 57.353 34.615 2.90 0.00 44.14 2.66
3684 4274 7.793427 CGCAGACATTTGAAAATTACCAAAAAG 59.207 33.333 8.59 7.52 36.10 2.27
3738 4328 3.077359 AGCTTGTTTACACATGGAGAGC 58.923 45.455 0.00 0.00 33.56 4.09
4074 4976 2.479656 TCCGAAAACGTTGTATTTCCCG 59.520 45.455 0.00 0.00 33.07 5.14
4102 5004 9.515226 TTTCCTTATTAGCTGTAATTCACAAGT 57.485 29.630 0.00 0.00 36.48 3.16
4540 5510 1.570803 ATGCTTTGCTATTTGGGCCA 58.429 45.000 0.00 0.00 0.00 5.36
4614 5586 7.011499 TGGTTAGCTGGAAAGATAAGTTACA 57.989 36.000 0.00 0.00 0.00 2.41
4696 5690 9.431887 GAATAGAATAATATGCTAACGGTTGGA 57.568 33.333 8.54 0.00 0.00 3.53
4772 5787 9.630098 TTTCATTTCTTCAAGAGCATTCATTAC 57.370 29.630 0.00 0.00 0.00 1.89
5030 6048 2.436417 GCAATGGTACTTCCTGCAGAA 58.564 47.619 17.39 6.85 37.35 3.02
5171 6198 4.641989 ACACAGTCAGATGGAAATAATGGC 59.358 41.667 0.00 0.00 0.00 4.40
5258 6312 3.932545 AAATGCTTGCCATTACGTTGA 57.067 38.095 0.00 0.00 43.22 3.18
5490 6555 4.793201 AGTTTCTGGCTGAGGTAAAAACT 58.207 39.130 2.28 2.28 32.31 2.66
5491 6556 4.580580 AGTTTCTGGCTGAGGTAAAAACTG 59.419 41.667 6.21 0.00 34.99 3.16
5492 6557 3.857157 TCTGGCTGAGGTAAAAACTGT 57.143 42.857 0.00 0.00 0.00 3.55
5493 6558 3.476552 TCTGGCTGAGGTAAAAACTGTG 58.523 45.455 0.00 0.00 0.00 3.66
5495 6560 3.882888 CTGGCTGAGGTAAAAACTGTGAA 59.117 43.478 0.00 0.00 0.00 3.18
5496 6561 4.469657 TGGCTGAGGTAAAAACTGTGAAT 58.530 39.130 0.00 0.00 0.00 2.57
6004 8624 7.713942 ACCTTCAATTATCCGTGATTACTAACC 59.286 37.037 0.00 0.00 0.00 2.85
6555 9283 3.618594 GCAGTTATCACATCAGCGAGAAA 59.381 43.478 0.00 0.00 0.00 2.52
6738 9466 4.649674 GGGGACTATGACATCAACTCTGTA 59.350 45.833 0.00 0.00 0.00 2.74
6819 9547 4.947147 GCGGAGGTGGTGGCACAA 62.947 66.667 20.82 4.91 44.16 3.33
6940 9668 5.637387 GCACTTGAGGTAGAAGAAGAAGAAG 59.363 44.000 0.00 0.00 0.00 2.85
6942 9670 7.437748 CACTTGAGGTAGAAGAAGAAGAAGAA 58.562 38.462 0.00 0.00 0.00 2.52
6943 9671 7.598493 CACTTGAGGTAGAAGAAGAAGAAGAAG 59.402 40.741 0.00 0.00 0.00 2.85
6944 9672 7.507616 ACTTGAGGTAGAAGAAGAAGAAGAAGA 59.492 37.037 0.00 0.00 0.00 2.87
6945 9673 7.841282 TGAGGTAGAAGAAGAAGAAGAAGAA 57.159 36.000 0.00 0.00 0.00 2.52
6946 9674 8.251383 TGAGGTAGAAGAAGAAGAAGAAGAAA 57.749 34.615 0.00 0.00 0.00 2.52
6947 9675 8.875168 TGAGGTAGAAGAAGAAGAAGAAGAAAT 58.125 33.333 0.00 0.00 0.00 2.17
6950 9678 9.930693 GGTAGAAGAAGAAGAAGAAGAAATACA 57.069 33.333 0.00 0.00 0.00 2.29
6971 9699 1.755008 AACAACAACACGGTGGGGG 60.755 57.895 13.48 3.87 0.00 5.40
7018 9746 8.283699 TGCAATGAGATGATAGTTTTGATGAA 57.716 30.769 0.00 0.00 0.00 2.57
7021 9749 9.932699 CAATGAGATGATAGTTTTGATGAACTC 57.067 33.333 0.00 0.00 40.24 3.01
7076 9807 6.175471 TCTTTACCTTTCGGATAAACCTTCC 58.825 40.000 0.00 0.00 36.31 3.46
7083 9814 2.569853 TCGGATAAACCTTCCTCTTGCA 59.430 45.455 0.00 0.00 36.31 4.08
7100 9831 5.591099 TCTTGCATTTCTTTGTGAAGTTCC 58.409 37.500 0.00 0.00 35.89 3.62
7194 9926 2.361119 CGAGTGGATCACCGGAGAATTA 59.639 50.000 9.46 0.00 39.42 1.40
7211 9943 2.322355 TTAACGTTCGGGTTTGGACA 57.678 45.000 2.82 0.00 0.00 4.02
7214 9946 1.890041 CGTTCGGGTTTGGACAGCA 60.890 57.895 0.00 0.00 0.00 4.41
7287 10022 3.745975 TGGCATCTTCGTCTTAGTTTGTG 59.254 43.478 0.00 0.00 0.00 3.33
7298 10033 4.854839 GTCTTAGTTTGTGCGTGTTTTTGT 59.145 37.500 0.00 0.00 0.00 2.83
7319 10054 2.851195 TGTTTCTCTCCTCTTGGCAAC 58.149 47.619 0.00 0.00 0.00 4.17
7457 10210 3.704566 AGGACTAGTTCAGAACACACACA 59.295 43.478 15.85 0.00 0.00 3.72
7458 10211 3.802685 GGACTAGTTCAGAACACACACAC 59.197 47.826 15.85 0.73 0.00 3.82
7733 11875 1.141053 AGACAGTTTGAAGAGGGCGTT 59.859 47.619 0.00 0.00 0.00 4.84
7750 11892 3.242543 GGCGTTAGTAGATCGTCGAAGAA 60.243 47.826 4.85 0.00 39.69 2.52
7756 11898 1.394618 AGATCGTCGAAGAAGGGAGG 58.605 55.000 4.85 0.00 39.69 4.30
7775 11917 3.549794 AGGGCTGAATCACAAGCTTATC 58.450 45.455 0.00 0.00 0.00 1.75
7968 12593 4.806247 CAGGAGAAGAATATGTGGTTCGAC 59.194 45.833 0.00 0.00 0.00 4.20
7989 12614 2.236395 CTCTTCGGGGGTATCACAAAGT 59.764 50.000 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 34 0.992695 TCTCGGTCTCCTCTCCTTCA 59.007 55.000 0.00 0.00 0.00 3.02
32 35 1.675552 CTCTCGGTCTCCTCTCCTTC 58.324 60.000 0.00 0.00 0.00 3.46
49 52 1.950909 CAGATAGTGGAGTCGTCCCTC 59.049 57.143 0.00 0.00 43.15 4.30
104 109 3.403057 CGTCAAGACACCACCGCG 61.403 66.667 0.00 0.00 0.00 6.46
236 256 2.182537 CGTACCGTACCTGGCCAC 59.817 66.667 0.00 0.00 0.00 5.01
523 600 4.142491 TGCATTCCAACCGATATTGTTGTC 60.142 41.667 14.38 3.73 41.13 3.18
657 819 1.078143 GACTGTCCTCCCATGTGGC 60.078 63.158 0.00 0.00 0.00 5.01
688 851 6.784031 ACTTGACTCTATCATCCCTTTGTTT 58.216 36.000 0.00 0.00 37.11 2.83
700 863 4.504826 GCGCCTTTTAGACTTGACTCTATC 59.495 45.833 0.00 0.00 0.00 2.08
721 884 2.178474 ACAGCTGCGAAATAATTGCG 57.822 45.000 15.27 0.00 0.00 4.85
743 906 5.562506 GGTAACTTCCACCAATAGAAAGC 57.437 43.478 0.00 0.00 36.01 3.51
761 924 7.327975 ACAGTTTCGTCATGATAATGAGGTAA 58.672 34.615 11.67 6.67 37.60 2.85
878 1093 4.561752 GGGGGAGAGACTGGCATATATAT 58.438 47.826 0.00 0.00 0.00 0.86
879 1094 3.995636 GGGGGAGAGACTGGCATATATA 58.004 50.000 0.00 0.00 0.00 0.86
899 1116 2.713167 AGAGAGGAGAGAGAGATGAGGG 59.287 54.545 0.00 0.00 0.00 4.30
901 1118 4.592351 AGAGAGAGAGGAGAGAGAGATGAG 59.408 50.000 0.00 0.00 0.00 2.90
902 1119 4.560739 AGAGAGAGAGGAGAGAGAGATGA 58.439 47.826 0.00 0.00 0.00 2.92
903 1120 4.592351 AGAGAGAGAGAGGAGAGAGAGATG 59.408 50.000 0.00 0.00 0.00 2.90
904 1121 4.825445 AGAGAGAGAGAGGAGAGAGAGAT 58.175 47.826 0.00 0.00 0.00 2.75
935 1186 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
936 1187 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
937 1188 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
938 1189 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
939 1190 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
940 1191 1.819928 ATGTGTGTGTGTGTGTGTGT 58.180 45.000 0.00 0.00 0.00 3.72
941 1192 4.987912 TCTATATGTGTGTGTGTGTGTGTG 59.012 41.667 0.00 0.00 0.00 3.82
942 1193 5.208463 TCTATATGTGTGTGTGTGTGTGT 57.792 39.130 0.00 0.00 0.00 3.72
943 1194 5.120674 CCTTCTATATGTGTGTGTGTGTGTG 59.879 44.000 0.00 0.00 0.00 3.82
944 1195 5.237815 CCTTCTATATGTGTGTGTGTGTGT 58.762 41.667 0.00 0.00 0.00 3.72
945 1196 4.093408 GCCTTCTATATGTGTGTGTGTGTG 59.907 45.833 0.00 0.00 0.00 3.82
946 1197 4.020218 AGCCTTCTATATGTGTGTGTGTGT 60.020 41.667 0.00 0.00 0.00 3.72
947 1198 4.507710 AGCCTTCTATATGTGTGTGTGTG 58.492 43.478 0.00 0.00 0.00 3.82
948 1199 4.467795 AGAGCCTTCTATATGTGTGTGTGT 59.532 41.667 0.00 0.00 0.00 3.72
949 1200 5.016051 AGAGCCTTCTATATGTGTGTGTG 57.984 43.478 0.00 0.00 0.00 3.82
950 1201 5.894393 ACTAGAGCCTTCTATATGTGTGTGT 59.106 40.000 0.00 0.00 35.43 3.72
951 1202 6.398234 ACTAGAGCCTTCTATATGTGTGTG 57.602 41.667 0.00 0.00 35.43 3.82
952 1203 7.268586 CAAACTAGAGCCTTCTATATGTGTGT 58.731 38.462 0.00 0.00 35.43 3.72
953 1204 6.201806 GCAAACTAGAGCCTTCTATATGTGTG 59.798 42.308 0.00 0.00 35.43 3.82
954 1205 6.098982 AGCAAACTAGAGCCTTCTATATGTGT 59.901 38.462 0.00 0.00 35.43 3.72
955 1206 6.520272 AGCAAACTAGAGCCTTCTATATGTG 58.480 40.000 0.00 0.00 35.43 3.21
956 1207 6.325028 TGAGCAAACTAGAGCCTTCTATATGT 59.675 38.462 0.00 0.00 35.43 2.29
957 1208 6.644592 GTGAGCAAACTAGAGCCTTCTATATG 59.355 42.308 0.00 0.00 35.43 1.78
958 1209 6.325028 TGTGAGCAAACTAGAGCCTTCTATAT 59.675 38.462 0.00 0.00 35.43 0.86
959 1210 5.656859 TGTGAGCAAACTAGAGCCTTCTATA 59.343 40.000 0.00 0.00 35.43 1.31
1005 1260 5.746990 AAAGGAGAACTGCTACACATAGT 57.253 39.130 0.00 0.00 0.00 2.12
1042 1297 0.543277 TCAGGCTGTCCATGGATCAC 59.457 55.000 19.62 9.94 33.74 3.06
1109 1365 4.454678 TCTCAGTGTGCATTTTCTGAACT 58.545 39.130 11.84 0.00 36.67 3.01
1126 1382 1.155042 GCAACAGAGGTGCTTCTCAG 58.845 55.000 0.00 4.30 36.30 3.35
1623 1879 6.770785 ACAAACTTGCAAGTAATCAGTAGGAA 59.229 34.615 31.31 0.00 38.57 3.36
1675 1931 5.394553 CCTCAAATCCAGCCCAGAAATAAAC 60.395 44.000 0.00 0.00 0.00 2.01
1708 1964 2.596776 CTCTGGGTAGAGGGTGGTG 58.403 63.158 0.00 0.00 45.47 4.17
1937 2205 2.420058 AGGCTAAAAGCAGCGGTTAT 57.580 45.000 0.78 0.00 44.75 1.89
1967 2242 8.816640 AAAAATACACCTTGCAGATAAAACTG 57.183 30.769 0.00 0.00 40.43 3.16
2073 2374 4.485163 CATTATATGTCGTCCAGATGCGA 58.515 43.478 0.00 0.00 34.54 5.10
2358 2659 1.114722 ACGTTGGGGTGTAAGGTCGA 61.115 55.000 0.00 0.00 0.00 4.20
2531 2832 5.057149 GCATCACTAAATCCATACCGTCTT 58.943 41.667 0.00 0.00 0.00 3.01
2556 2857 5.863965 ACCCTCTCTAGTCCGTACTAATAC 58.136 45.833 0.00 0.00 37.75 1.89
2597 2898 6.127225 GGTTATACCCTCTCTAGTCCGTTTTT 60.127 42.308 0.00 0.00 30.04 1.94
2599 2900 4.892345 GGTTATACCCTCTCTAGTCCGTTT 59.108 45.833 0.00 0.00 30.04 3.60
2600 2901 4.079558 TGGTTATACCCTCTCTAGTCCGTT 60.080 45.833 0.00 0.00 37.50 4.44
2609 2910 4.216708 ACTGTAGCTGGTTATACCCTCTC 58.783 47.826 0.00 0.00 37.50 3.20
2668 2969 4.199310 TCAGAGTTGGAAAGTGGACTTTG 58.801 43.478 9.49 0.00 45.37 2.77
2730 3039 1.076332 CCCGAGGTTGTCAATCGAAC 58.924 55.000 9.61 0.00 38.72 3.95
2773 3117 1.135315 GACATGTGGCATGCACGTC 59.865 57.895 21.36 13.35 0.00 4.34
2821 3165 5.980116 CAGATCAATAGACGGAACTTAGTGG 59.020 44.000 0.00 0.00 0.00 4.00
2938 3282 4.202141 CCATGAACAAACAGACACCACAAT 60.202 41.667 0.00 0.00 0.00 2.71
2940 3284 2.687425 CCATGAACAAACAGACACCACA 59.313 45.455 0.00 0.00 0.00 4.17
2941 3285 2.543653 GCCATGAACAAACAGACACCAC 60.544 50.000 0.00 0.00 0.00 4.16
2942 3286 1.680735 GCCATGAACAAACAGACACCA 59.319 47.619 0.00 0.00 0.00 4.17
2943 3287 1.956477 AGCCATGAACAAACAGACACC 59.044 47.619 0.00 0.00 0.00 4.16
3138 3580 4.039124 ACCACACCAAAATTGTCTTGGATC 59.961 41.667 13.22 0.00 45.31 3.36
3196 3638 7.500559 GCAGTTTAATCCTCTCCATATGAAAGT 59.499 37.037 3.65 0.00 0.00 2.66
3201 3643 6.528321 TGAGCAGTTTAATCCTCTCCATATG 58.472 40.000 0.00 0.00 0.00 1.78
3243 3685 7.923414 AACTTACAGTCCCATTATTTCAGAC 57.077 36.000 0.00 0.00 0.00 3.51
3332 3775 8.842280 TGTTCATTTGTCCTAAACGTTTCTTAT 58.158 29.630 18.42 0.00 0.00 1.73
3577 4147 6.827762 ACTACTAGTTCCTACACATACCAGAC 59.172 42.308 0.00 0.00 0.00 3.51
3579 4149 6.602406 ACACTACTAGTTCCTACACATACCAG 59.398 42.308 0.00 0.00 0.00 4.00
3581 4151 7.772757 AGTACACTACTAGTTCCTACACATACC 59.227 40.741 0.00 0.00 37.23 2.73
3613 4184 7.578852 AGCTTATACAAACCTTCGTGTTTTAC 58.421 34.615 0.00 0.00 36.33 2.01
3684 4274 8.677148 TTAAGAATATCAGTACAAGCATTCCC 57.323 34.615 0.00 0.00 0.00 3.97
3738 4328 9.825972 CTACTGTGTAAATTGTTTCAGGTAATG 57.174 33.333 0.00 0.00 0.00 1.90
3790 4391 8.570068 TTTAAGAAATGTACTGTTATCCACCC 57.430 34.615 0.00 0.00 0.00 4.61
4074 4976 7.985476 TGTGAATTACAGCTAATAAGGAAAGC 58.015 34.615 0.00 0.00 33.42 3.51
4165 5067 4.261801 ACATTAGTGATGAAAGTTCCCCG 58.738 43.478 1.26 0.00 39.15 5.73
4772 5787 7.136119 TGACACTATTTTTAAAGGTGCTTTCG 58.864 34.615 10.43 0.00 35.21 3.46
4962 5980 9.010029 CGACCCTGGCAATTATAAATATACTTT 57.990 33.333 0.00 0.00 0.00 2.66
4963 5981 7.610305 CCGACCCTGGCAATTATAAATATACTT 59.390 37.037 0.00 0.00 0.00 2.24
4964 5982 7.110155 CCGACCCTGGCAATTATAAATATACT 58.890 38.462 0.00 0.00 0.00 2.12
5030 6048 4.697352 CCCATTGATCTTCTTTCGAACTGT 59.303 41.667 0.00 0.00 0.00 3.55
5131 6155 5.506708 ACTGTGTTACCTTTTCCTTTGAGT 58.493 37.500 0.00 0.00 0.00 3.41
5490 6555 7.509141 AATTGTGACACATAGAACATTCACA 57.491 32.000 9.55 0.00 41.11 3.58
5491 6556 9.891828 TTTAATTGTGACACATAGAACATTCAC 57.108 29.630 9.55 0.00 35.08 3.18
5492 6557 9.891828 GTTTAATTGTGACACATAGAACATTCA 57.108 29.630 9.55 0.00 0.00 2.57
5922 8035 6.712998 TGTTTCTGTAATCCGATTTTCAGGAA 59.287 34.615 17.90 15.07 40.32 3.36
6004 8624 3.664107 TCTGGAAAACTTCATGGACTCG 58.336 45.455 0.00 0.00 0.00 4.18
6555 9283 1.350193 CGAAGCTGTACATGTCGCTT 58.650 50.000 22.30 22.30 44.61 4.68
6738 9466 1.542492 CCAAGTCAGCAGCTTTCCAT 58.458 50.000 0.00 0.00 0.00 3.41
6816 9544 3.744660 CTCCAAGCACTCCTTAAGTTGT 58.255 45.455 0.97 0.00 35.45 3.32
6819 9547 1.981495 AGCTCCAAGCACTCCTTAAGT 59.019 47.619 0.97 0.00 45.56 2.24
6849 9577 1.318886 TTCCTCTCCTCTCGCTGCAG 61.319 60.000 10.11 10.11 0.00 4.41
6940 9668 6.020995 CCGTGTTGTTGTTGTTGTATTTCTTC 60.021 38.462 0.00 0.00 0.00 2.87
6942 9670 5.106078 ACCGTGTTGTTGTTGTTGTATTTCT 60.106 36.000 0.00 0.00 0.00 2.52
6943 9671 5.003967 CACCGTGTTGTTGTTGTTGTATTTC 59.996 40.000 0.00 0.00 0.00 2.17
6944 9672 4.859798 CACCGTGTTGTTGTTGTTGTATTT 59.140 37.500 0.00 0.00 0.00 1.40
6945 9673 4.416620 CACCGTGTTGTTGTTGTTGTATT 58.583 39.130 0.00 0.00 0.00 1.89
6946 9674 3.181495 CCACCGTGTTGTTGTTGTTGTAT 60.181 43.478 0.00 0.00 0.00 2.29
6947 9675 2.161808 CCACCGTGTTGTTGTTGTTGTA 59.838 45.455 0.00 0.00 0.00 2.41
6948 9676 1.068194 CCACCGTGTTGTTGTTGTTGT 60.068 47.619 0.00 0.00 0.00 3.32
6949 9677 1.623359 CCACCGTGTTGTTGTTGTTG 58.377 50.000 0.00 0.00 0.00 3.33
6950 9678 0.528470 CCCACCGTGTTGTTGTTGTT 59.472 50.000 0.00 0.00 0.00 2.83
7018 9746 5.636903 ACCTCCAGCATTTATGTATGAGT 57.363 39.130 0.00 0.00 0.00 3.41
7021 9749 5.132502 TCCAACCTCCAGCATTTATGTATG 58.867 41.667 0.00 0.00 0.00 2.39
7076 9807 5.689068 GGAACTTCACAAAGAAATGCAAGAG 59.311 40.000 0.00 0.00 35.40 2.85
7155 9887 4.212004 CACTCGAGCTTCTTTCATCACAAA 59.788 41.667 13.61 0.00 0.00 2.83
7194 9926 1.441732 GCTGTCCAAACCCGAACGTT 61.442 55.000 0.00 0.00 0.00 3.99
7211 9943 1.927174 GAAACGTATCACTCGCATGCT 59.073 47.619 17.13 0.00 0.00 3.79
7214 9946 3.119459 ACTGAGAAACGTATCACTCGCAT 60.119 43.478 0.00 0.00 32.81 4.73
7271 10003 2.538449 ACACGCACAAACTAAGACGAAG 59.462 45.455 0.00 0.00 0.00 3.79
7287 10022 3.546271 GGAGAGAAACAACAAAAACACGC 59.454 43.478 0.00 0.00 0.00 5.34
7298 10033 3.214328 GTTGCCAAGAGGAGAGAAACAA 58.786 45.455 0.00 0.00 36.89 2.83
7457 10210 7.410174 TGGATTTATTATTGTGAGACTTGGGT 58.590 34.615 0.00 0.00 0.00 4.51
7458 10211 7.775093 TCTGGATTTATTATTGTGAGACTTGGG 59.225 37.037 0.00 0.00 0.00 4.12
7733 11875 4.378774 CTCCCTTCTTCGACGATCTACTA 58.621 47.826 0.00 0.00 0.00 1.82
7750 11892 0.622665 CTTGTGATTCAGCCCTCCCT 59.377 55.000 0.00 0.00 0.00 4.20
7756 11898 2.286654 GCGATAAGCTTGTGATTCAGCC 60.287 50.000 9.86 0.00 44.04 4.85
7968 12593 2.236395 ACTTTGTGATACCCCCGAAGAG 59.764 50.000 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.