Multiple sequence alignment - TraesCS6A01G381400

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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 TraesCS6A01G381400 chr6A 100.000 3389 0 0 1 3389 601145836 601149224 0.000000e+00 6259.0
1 TraesCS6A01G381400 chr6A 83.642 1186 116 28 502 1659 600913880 600912745 0.000000e+00 1044.0
2 TraesCS6A01G381400 chr6A 81.694 1240 178 32 905 2125 601033203 601031994 0.000000e+00 987.0
3 TraesCS6A01G381400 chr6A 84.070 747 107 6 954 1688 600978225 600977479 0.000000e+00 710.0
4 TraesCS6A01G381400 chr6A 82.880 625 100 5 1771 2389 600977207 600976584 3.820000e-154 555.0
5 TraesCS6A01G381400 chr6A 94.025 318 12 2 800 1110 600963981 600963664 3.060000e-130 475.0
6 TraesCS6A01G381400 chr6A 82.727 440 46 16 2015 2434 601138017 601137588 6.910000e-97 364.0
7 TraesCS6A01G381400 chr6A 84.775 289 24 7 502 779 600964749 600964470 4.310000e-69 272.0
8 TraesCS6A01G381400 chr6A 90.576 191 16 1 996 1186 601138331 601138143 5.610000e-63 252.0
9 TraesCS6A01G381400 chr6A 85.567 194 17 6 450 638 601033451 601033264 3.450000e-45 193.0
10 TraesCS6A01G381400 chr6A 86.391 169 23 0 1794 1962 600960668 600960500 5.770000e-43 185.0
11 TraesCS6A01G381400 chr6A 89.583 144 14 1 2246 2389 601008608 601008466 7.470000e-42 182.0
12 TraesCS6A01G381400 chr6A 94.805 77 3 1 417 493 601146020 601146095 5.940000e-23 119.0
13 TraesCS6A01G381400 chr6A 94.805 77 3 1 185 260 601146252 601146328 5.940000e-23 119.0
14 TraesCS6A01G381400 chr6A 80.405 148 22 6 2531 2673 600965583 600965438 4.620000e-19 106.0
15 TraesCS6A01G381400 chr6D 85.137 2449 253 67 539 2938 454825424 454827810 0.000000e+00 2403.0
16 TraesCS6A01G381400 chr6D 82.882 2401 270 84 103 2449 454659842 454657529 0.000000e+00 2026.0
17 TraesCS6A01G381400 chr6D 82.569 1962 249 41 996 2942 454749509 454747626 0.000000e+00 1642.0
18 TraesCS6A01G381400 chr6D 95.792 499 19 1 1 497 454823817 454824315 0.000000e+00 804.0
19 TraesCS6A01G381400 chr6D 83.212 411 59 10 2966 3370 454747641 454747235 5.340000e-98 368.0
20 TraesCS6A01G381400 chr6D 92.571 175 13 0 996 1170 454662409 454662583 5.610000e-63 252.0
21 TraesCS6A01G381400 chr6D 89.262 149 13 3 257 404 298453713 298453567 2.080000e-42 183.0
22 TraesCS6A01G381400 chr6D 96.104 77 2 1 417 493 454824003 454824078 1.280000e-24 124.0
23 TraesCS6A01G381400 chr6B 83.410 1748 213 43 736 2453 691633689 691631989 0.000000e+00 1550.0
24 TraesCS6A01G381400 chr6B 82.949 1560 173 45 1849 3369 691788155 691789660 0.000000e+00 1321.0
25 TraesCS6A01G381400 chr6B 82.768 1445 188 42 987 2403 691783885 691782474 0.000000e+00 1232.0
26 TraesCS6A01G381400 chr6B 79.241 790 86 38 303 1064 691787414 691788153 2.370000e-131 479.0
27 TraesCS6A01G381400 chr6B 74.451 1092 218 36 1064 2120 692016791 692015726 6.770000e-112 414.0
28 TraesCS6A01G381400 chr6B 92.473 93 4 3 521 613 691633826 691633737 2.740000e-26 130.0
29 TraesCS6A01G381400 chr6B 89.062 64 5 2 198 260 691787545 691787607 1.010000e-10 78.7
30 TraesCS6A01G381400 chrUn 77.988 686 105 30 2690 3369 333016311 333016956 4.100000e-104 388.0
31 TraesCS6A01G381400 chrUn 77.988 686 105 30 2690 3369 333019097 333019742 4.100000e-104 388.0
32 TraesCS6A01G381400 chrUn 77.988 686 105 30 2690 3369 389609588 389610233 4.100000e-104 388.0
33 TraesCS6A01G381400 chrUn 78.107 676 104 28 2699 3369 410543299 410542663 4.100000e-104 388.0
34 TraesCS6A01G381400 chrUn 81.863 408 62 10 2966 3369 75867247 75867646 1.950000e-87 333.0
35 TraesCS6A01G381400 chrUn 81.618 408 63 10 2966 3369 294266349 294266748 9.070000e-86 327.0
36 TraesCS6A01G381400 chr2A 88.667 150 13 2 257 405 696850734 696850880 2.690000e-41 180.0
37 TraesCS6A01G381400 chr4A 90.370 135 12 1 257 391 75320438 75320571 3.480000e-40 176.0
38 TraesCS6A01G381400 chr4A 83.721 172 24 4 260 429 139870625 139870794 3.500000e-35 159.0
39 TraesCS6A01G381400 chr3D 88.356 146 16 1 257 402 87926017 87926161 1.250000e-39 174.0
40 TraesCS6A01G381400 chr2D 87.097 155 16 4 257 409 299891698 299891546 4.500000e-39 172.0
41 TraesCS6A01G381400 chr2D 86.928 153 18 2 254 406 373883449 373883599 1.620000e-38 171.0
42 TraesCS6A01G381400 chr2D 83.333 174 23 5 16 184 606636405 606636577 4.530000e-34 156.0
43 TraesCS6A01G381400 chr7D 86.538 156 19 2 257 411 14440318 14440472 1.620000e-38 171.0
44 TraesCS6A01G381400 chr7D 82.659 173 28 2 257 428 128144035 128143864 5.860000e-33 152.0
45 TraesCS6A01G381400 chr7D 78.857 175 28 8 257 426 507853743 507853573 3.580000e-20 110.0
46 TraesCS6A01G381400 chr4D 84.524 168 23 2 19 184 339065105 339064939 2.710000e-36 163.0
47 TraesCS6A01G381400 chr4D 78.836 189 26 13 257 436 318476255 318476438 7.680000e-22 115.0
48 TraesCS6A01G381400 chr5D 83.735 166 26 1 19 184 397198104 397198268 4.530000e-34 156.0
49 TraesCS6A01G381400 chr5D 83.735 166 24 3 19 184 397224534 397224696 1.630000e-33 154.0
50 TraesCS6A01G381400 chr5D 77.852 149 25 8 1250 1394 379229531 379229387 6.030000e-13 86.1
51 TraesCS6A01G381400 chr5D 76.821 151 30 5 1250 1398 379251200 379251053 2.800000e-11 80.5
52 TraesCS6A01G381400 chr1B 83.140 172 25 4 15 184 376615236 376615067 1.630000e-33 154.0
53 TraesCS6A01G381400 chr1B 82.840 169 24 5 18 184 578099062 578098897 2.730000e-31 147.0
54 TraesCS6A01G381400 chr1D 83.333 168 24 4 18 184 424477324 424477160 5.860000e-33 152.0
55 TraesCS6A01G381400 chr5B 82.941 170 25 3 16 184 491101752 491101586 2.110000e-32 150.0
56 TraesCS6A01G381400 chr5B 82.249 169 27 3 257 424 70793525 70793359 3.530000e-30 143.0
57 TraesCS6A01G381400 chr5B 77.703 148 27 6 1250 1394 455147593 455147449 6.030000e-13 86.1
58 TraesCS6A01G381400 chr4B 83.784 148 23 1 270 416 35522556 35522703 4.560000e-29 139.0
59 TraesCS6A01G381400 chr1A 80.110 181 32 4 257 437 584511797 584511621 7.630000e-27 132.0
60 TraesCS6A01G381400 chr1A 77.483 151 29 5 1250 1398 586720305 586720158 6.030000e-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 TraesCS6A01G381400 chr6A 601145836 601149224 3388 False 2165.666667 6259 96.536667 1 3389 3 chr6A.!!$F1 3388
1 TraesCS6A01G381400 chr6A 600912745 600913880 1135 True 1044.000000 1044 83.642000 502 1659 1 chr6A.!!$R1 1157
2 TraesCS6A01G381400 chr6A 600976584 600978225 1641 True 632.500000 710 83.475000 954 2389 2 chr6A.!!$R4 1435
3 TraesCS6A01G381400 chr6A 601031994 601033451 1457 True 590.000000 987 83.630500 450 2125 2 chr6A.!!$R5 1675
4 TraesCS6A01G381400 chr6A 601137588 601138331 743 True 308.000000 364 86.651500 996 2434 2 chr6A.!!$R6 1438
5 TraesCS6A01G381400 chr6A 600960500 600965583 5083 True 259.500000 475 86.399000 502 2673 4 chr6A.!!$R3 2171
6 TraesCS6A01G381400 chr6D 454657529 454659842 2313 True 2026.000000 2026 82.882000 103 2449 1 chr6D.!!$R2 2346
7 TraesCS6A01G381400 chr6D 454823817 454827810 3993 False 1110.333333 2403 92.344333 1 2938 3 chr6D.!!$F2 2937
8 TraesCS6A01G381400 chr6D 454747235 454749509 2274 True 1005.000000 1642 82.890500 996 3370 2 chr6D.!!$R3 2374
9 TraesCS6A01G381400 chr6B 691782474 691783885 1411 True 1232.000000 1232 82.768000 987 2403 1 chr6B.!!$R1 1416
10 TraesCS6A01G381400 chr6B 691631989 691633826 1837 True 840.000000 1550 87.941500 521 2453 2 chr6B.!!$R3 1932
11 TraesCS6A01G381400 chr6B 691787414 691789660 2246 False 626.233333 1321 83.750667 198 3369 3 chr6B.!!$F1 3171
12 TraesCS6A01G381400 chr6B 692015726 692016791 1065 True 414.000000 414 74.451000 1064 2120 1 chr6B.!!$R2 1056
13 TraesCS6A01G381400 chrUn 333016311 333019742 3431 False 388.000000 388 77.988000 2690 3369 2 chrUn.!!$F4 679
14 TraesCS6A01G381400 chrUn 389609588 389610233 645 False 388.000000 388 77.988000 2690 3369 1 chrUn.!!$F3 679
15 TraesCS6A01G381400 chrUn 410542663 410543299 636 True 388.000000 388 78.107000 2699 3369 1 chrUn.!!$R1 670

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
867 2726 0.596083 GCTCGACCCACTGATCATCG 60.596 60.0 8.95 8.95 0.00 3.84 F
1709 6022 0.104487 CTCTGCTCCATCGCATCTGT 59.896 55.0 0.00 0.00 39.52 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2156 6717 0.101040 TGAGCAAGCAAGCACAACAC 59.899 50.0 3.19 0.0 36.85 3.32 R
2950 10365 0.034059 GTGTGACTGTGTCCCCTCAG 59.966 60.0 0.00 0.0 38.01 3.35 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 32 4.628766 GCGAAACTTATACTCCTTCCGTTT 59.371 41.667 0.00 0.00 0.00 3.60
43 44 6.164176 ACTCCTTCCGTTTCTTAATGTAGTG 58.836 40.000 0.00 0.00 0.00 2.74
46 47 5.390567 CCTTCCGTTTCTTAATGTAGTGTGC 60.391 44.000 0.00 0.00 0.00 4.57
516 1562 4.789012 ACCAAGCATAGGTTTTGTCATG 57.211 40.909 0.00 0.00 35.33 3.07
517 1563 3.511146 ACCAAGCATAGGTTTTGTCATGG 59.489 43.478 0.00 0.00 35.33 3.66
518 1564 3.763360 CCAAGCATAGGTTTTGTCATGGA 59.237 43.478 0.00 0.00 0.00 3.41
519 1565 4.220382 CCAAGCATAGGTTTTGTCATGGAA 59.780 41.667 0.00 0.00 0.00 3.53
561 1903 2.032681 GACCTTTCCGTGGCAGCT 59.967 61.111 0.00 0.00 0.00 4.24
631 1980 2.683572 GCCCCAAACCCACCCATC 60.684 66.667 0.00 0.00 0.00 3.51
632 1981 2.038813 CCCCAAACCCACCCATCC 59.961 66.667 0.00 0.00 0.00 3.51
633 1982 2.362375 CCCAAACCCACCCATCCG 60.362 66.667 0.00 0.00 0.00 4.18
634 1983 2.362375 CCAAACCCACCCATCCGG 60.362 66.667 0.00 0.00 37.81 5.14
775 2143 2.031157 AGTATTGCACCGCAGTTTTGTC 60.031 45.455 0.00 0.00 40.61 3.18
805 2651 1.299316 CAACGGTGCCACTGCTTTG 60.299 57.895 2.90 0.00 38.71 2.77
854 2711 1.523095 GACAGAACACACAAGCTCGAC 59.477 52.381 0.00 0.00 0.00 4.20
867 2726 0.596083 GCTCGACCCACTGATCATCG 60.596 60.000 8.95 8.95 0.00 3.84
908 2781 4.134563 CAAAGGCAGTTTGGTACTACTGT 58.865 43.478 18.03 0.00 41.78 3.55
909 2782 5.302360 CAAAGGCAGTTTGGTACTACTGTA 58.698 41.667 18.03 0.00 41.78 2.74
910 2783 4.532314 AGGCAGTTTGGTACTACTGTAC 57.468 45.455 18.03 13.59 46.06 2.90
911 2784 4.158015 AGGCAGTTTGGTACTACTGTACT 58.842 43.478 18.03 14.88 46.04 2.73
912 2785 5.327732 AGGCAGTTTGGTACTACTGTACTA 58.672 41.667 18.03 0.00 46.04 1.82
913 2786 5.418209 AGGCAGTTTGGTACTACTGTACTAG 59.582 44.000 18.03 0.00 46.04 2.57
914 2787 5.100943 GCAGTTTGGTACTACTGTACTAGC 58.899 45.833 18.03 5.73 46.04 3.42
915 2788 5.105837 GCAGTTTGGTACTACTGTACTAGCT 60.106 44.000 18.03 0.00 46.04 3.32
1013 2894 1.934589 TTCACTATGCCGTCGATTGG 58.065 50.000 0.00 2.46 0.00 3.16
1191 5450 1.136446 CAGTTTACTTACACCGTGCGC 60.136 52.381 0.00 0.00 0.00 6.09
1230 5504 2.479049 CGCTGAATTTTGGGCTCATCTG 60.479 50.000 0.00 0.00 0.00 2.90
1247 5531 1.351017 TCTGATGGTGGAGTGGTTTCC 59.649 52.381 0.00 0.00 37.77 3.13
1277 5561 1.986575 GCAAGAACGCCCATCTGCTC 61.987 60.000 0.00 0.00 0.00 4.26
1313 5597 1.915769 GGAGAGGCTCACCCTGTGT 60.916 63.158 19.06 0.00 46.60 3.72
1334 5618 2.532256 CGCCGACGTCCTCGACTAT 61.532 63.158 16.20 0.00 46.14 2.12
1379 5663 3.329889 TGCCAGGGCGTCTTCCAT 61.330 61.111 5.74 0.00 45.51 3.41
1439 5724 2.098614 CCTCTGCTCTGCTCACTTCTA 58.901 52.381 0.00 0.00 0.00 2.10
1455 5748 7.064728 GCTCACTTCTATCGATTTTAACAAGGT 59.935 37.037 1.71 0.00 0.00 3.50
1478 5775 4.523943 TCCGTGTACTTACTTGCTTCCTAA 59.476 41.667 0.00 0.00 0.00 2.69
1487 5784 6.204882 ACTTACTTGCTTCCTAAATGTGTCAC 59.795 38.462 0.00 0.00 0.00 3.67
1488 5785 4.718961 ACTTGCTTCCTAAATGTGTCACT 58.281 39.130 4.27 0.00 0.00 3.41
1490 5787 6.296026 ACTTGCTTCCTAAATGTGTCACTAA 58.704 36.000 4.27 0.00 0.00 2.24
1509 5817 1.529010 CTTGCAGGACCTTGTGCCA 60.529 57.895 0.00 0.00 39.04 4.92
1671 5979 0.985549 GCGACTACGACTTCTGCAAG 59.014 55.000 0.00 0.00 42.66 4.01
1707 6020 1.697284 TACTCTGCTCCATCGCATCT 58.303 50.000 0.00 0.00 39.52 2.90
1709 6022 0.104487 CTCTGCTCCATCGCATCTGT 59.896 55.000 0.00 0.00 39.52 3.41
1711 6024 0.656259 CTGCTCCATCGCATCTGTTG 59.344 55.000 0.00 0.00 39.52 3.33
1728 6049 1.002792 GTTGTTTCTCGCTGGTGAACC 60.003 52.381 0.00 0.00 0.00 3.62
1730 6051 1.959226 TTTCTCGCTGGTGAACCGC 60.959 57.895 6.33 6.33 39.43 5.68
1739 6060 0.320858 TGGTGAACCGCGCTCATTTA 60.321 50.000 5.56 0.00 39.43 1.40
1740 6061 1.014352 GGTGAACCGCGCTCATTTAT 58.986 50.000 5.56 0.00 0.00 1.40
1746 6067 0.363512 CCGCGCTCATTTATCGATCG 59.636 55.000 9.36 9.36 0.00 3.69
1756 6077 0.458716 TTATCGATCGCCGTGTGCAA 60.459 50.000 11.09 0.00 41.33 4.08
1758 6082 0.249280 ATCGATCGCCGTGTGCAATA 60.249 50.000 11.09 0.00 41.33 1.90
1767 6091 1.732259 CCGTGTGCAATACAGAACCTC 59.268 52.381 0.00 0.00 40.69 3.85
1905 6420 2.089980 CTCAACTTTAGCAGCAGCCAT 58.910 47.619 0.00 0.00 43.56 4.40
1993 6508 4.617520 ATGTCGCCCGTGCACACA 62.618 61.111 18.64 13.43 37.32 3.72
2070 6588 1.295357 TACACCGCGCACATTTCCTG 61.295 55.000 8.75 0.00 0.00 3.86
2076 6594 1.154093 CGCACATTTCCTGCAGCTG 60.154 57.895 10.11 10.11 34.00 4.24
2109 6627 3.762288 TCTTCTCGCAGTACCACATAACT 59.238 43.478 0.00 0.00 0.00 2.24
2121 6644 3.071479 CCACATAACTGCCAAGTACGTT 58.929 45.455 0.00 0.00 34.77 3.99
2126 6649 0.672342 ACTGCCAAGTACGTTCGACT 59.328 50.000 0.00 0.00 33.79 4.18
2131 6692 5.058149 TGCCAAGTACGTTCGACTATAAA 57.942 39.130 0.00 0.00 0.00 1.40
2132 6693 5.468592 TGCCAAGTACGTTCGACTATAAAA 58.531 37.500 0.00 0.00 0.00 1.52
2133 6694 5.345741 TGCCAAGTACGTTCGACTATAAAAC 59.654 40.000 0.00 0.00 0.00 2.43
2136 6697 6.470235 CCAAGTACGTTCGACTATAAAACGAT 59.530 38.462 13.08 1.71 46.42 3.73
2138 6699 7.009568 AGTACGTTCGACTATAAAACGATCT 57.990 36.000 13.08 7.88 46.42 2.75
2140 6701 7.965107 AGTACGTTCGACTATAAAACGATCTTT 59.035 33.333 13.08 0.00 46.42 2.52
2141 6702 6.975126 ACGTTCGACTATAAAACGATCTTTG 58.025 36.000 13.08 0.00 46.42 2.77
2143 6704 6.887763 CGTTCGACTATAAAACGATCTTTGTG 59.112 38.462 0.89 0.00 46.42 3.33
2145 6706 7.502177 TCGACTATAAAACGATCTTTGTGTC 57.498 36.000 0.00 0.00 0.00 3.67
2146 6707 7.085746 TCGACTATAAAACGATCTTTGTGTCA 58.914 34.615 0.00 0.00 0.00 3.58
2155 6716 9.787532 AAAACGATCTTTGTGTCATTATTATGG 57.212 29.630 0.00 0.00 32.40 2.74
2156 6717 7.496529 ACGATCTTTGTGTCATTATTATGGG 57.503 36.000 0.00 0.00 32.40 4.00
2159 6720 7.012327 CGATCTTTGTGTCATTATTATGGGTGT 59.988 37.037 0.00 0.00 32.40 4.16
2160 6721 8.593945 ATCTTTGTGTCATTATTATGGGTGTT 57.406 30.769 0.00 0.00 32.40 3.32
2187 6751 0.305922 CTTGCTCATCGCGGATTTCC 59.694 55.000 6.13 0.00 43.27 3.13
2319 6883 4.330944 AAGTTTGTATGAGACGGTGACA 57.669 40.909 0.00 0.00 0.00 3.58
2398 6967 1.001633 CCTACTTGTAACAGGCCACGT 59.998 52.381 5.01 0.00 0.00 4.49
2409 6978 4.030452 GCCACGTGACAAGCCTGC 62.030 66.667 19.30 5.15 0.00 4.85
2468 7037 8.632906 AGAAGAAGATGAACAAGAAATCATGT 57.367 30.769 0.00 0.00 36.45 3.21
2650 7227 6.914665 TCAGGATTTTAGGGATTCATCATGT 58.085 36.000 0.00 0.00 29.79 3.21
2651 7228 8.044574 TCAGGATTTTAGGGATTCATCATGTA 57.955 34.615 0.00 0.00 29.79 2.29
2669 7246 4.614555 TGTAAATGGCGTATTTCTGCAG 57.385 40.909 7.63 7.63 39.61 4.41
2860 7467 6.978080 TGGCAAAGATACTGTTGTTTCTTTTC 59.022 34.615 10.35 7.25 45.42 2.29
2938 10353 7.785985 AGATGATCCAATCCCATACAATTTCAA 59.214 33.333 0.00 0.00 0.00 2.69
2939 10354 7.730672 TGATCCAATCCCATACAATTTCAAA 57.269 32.000 0.00 0.00 0.00 2.69
2940 10355 7.555087 TGATCCAATCCCATACAATTTCAAAC 58.445 34.615 0.00 0.00 0.00 2.93
2941 10356 7.399765 TGATCCAATCCCATACAATTTCAAACT 59.600 33.333 0.00 0.00 0.00 2.66
2971 10386 0.034059 GAGGGGACACAGTCACACAG 59.966 60.000 1.48 0.00 37.77 3.66
3047 10464 4.452455 ACAGTCCATGACATTCTCGAAAAC 59.548 41.667 0.00 0.00 34.60 2.43
3061 10479 5.060506 TCTCGAAAACAAAACAGCCTATGA 58.939 37.500 0.00 0.00 0.00 2.15
3072 10490 7.754924 ACAAAACAGCCTATGATAATTCAAACG 59.245 33.333 0.00 0.00 34.96 3.60
3076 10494 8.225603 ACAGCCTATGATAATTCAAACGAAAT 57.774 30.769 0.00 0.00 34.96 2.17
3112 10530 7.441760 TGCGTGGTAAATTCTTCACTAACTTAA 59.558 33.333 0.00 0.00 0.00 1.85
3129 10547 9.760077 ACTAACTTAATACCGATCATTTACCTG 57.240 33.333 0.00 0.00 0.00 4.00
3150 10568 5.104527 CCTGTTTATAGAAGATGACCCCACA 60.105 44.000 0.00 0.00 0.00 4.17
3164 10582 1.422781 CCCCACAGCCATAGACATGAT 59.577 52.381 0.00 0.00 33.67 2.45
3170 10588 3.649502 ACAGCCATAGACATGATCCATCA 59.350 43.478 0.00 0.00 41.70 3.07
3219 10641 5.426504 ACAAGCCTGATCTCTACTGAAATG 58.573 41.667 0.00 0.00 0.00 2.32
3253 10675 1.942776 TCTTCATGGACTCTGGCTGA 58.057 50.000 0.00 0.00 0.00 4.26
3254 10676 2.475155 TCTTCATGGACTCTGGCTGAT 58.525 47.619 0.00 0.00 0.00 2.90
3258 10680 2.169978 TCATGGACTCTGGCTGATTGAG 59.830 50.000 0.00 0.00 0.00 3.02
3269 10692 3.126831 GGCTGATTGAGAATACCTGTCG 58.873 50.000 0.00 0.00 0.00 4.35
3270 10693 2.541762 GCTGATTGAGAATACCTGTCGC 59.458 50.000 0.00 0.00 0.00 5.19
3279 10702 2.795175 ATACCTGTCGCGTATGAAGG 57.205 50.000 5.77 9.68 0.00 3.46
3369 10792 8.363390 GGAATGAAATAAGAAATCAGGATTCCC 58.637 37.037 0.00 0.00 29.54 3.97
3370 10793 9.140874 GAATGAAATAAGAAATCAGGATTCCCT 57.859 33.333 0.00 0.00 45.74 4.20
3386 10809 8.337118 AGGATTCCCTGATATAGAAAAAGACA 57.663 34.615 0.00 0.00 42.42 3.41
3387 10810 8.953665 AGGATTCCCTGATATAGAAAAAGACAT 58.046 33.333 0.00 0.00 42.42 3.06
3388 10811 9.225436 GGATTCCCTGATATAGAAAAAGACATC 57.775 37.037 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 3.694043 TTGGTCACAGTTAGCATAGCA 57.306 42.857 0.00 0.00 0.00 3.49
220 223 5.333566 TTTGACTTTCCCCTCTGGTAAAT 57.666 39.130 0.00 0.00 34.77 1.40
516 1562 2.799540 GCGCGTCATCGTTCCTTCC 61.800 63.158 8.43 0.00 39.49 3.46
517 1563 2.695646 GCGCGTCATCGTTCCTTC 59.304 61.111 8.43 0.00 39.49 3.46
518 1564 3.179265 CGCGCGTCATCGTTCCTT 61.179 61.111 24.19 0.00 39.49 3.36
519 1565 4.111016 TCGCGCGTCATCGTTCCT 62.111 61.111 30.98 0.00 39.49 3.36
635 1984 1.252215 TATTCAGGGGCGTGACACGA 61.252 55.000 31.08 8.97 46.05 4.35
638 1987 1.557371 TGAATATTCAGGGGCGTGACA 59.443 47.619 14.23 0.00 32.50 3.58
713 2076 2.367202 GGGAAGTCGATGGGAGGCA 61.367 63.158 0.00 0.00 0.00 4.75
775 2143 2.352229 CCGTTGCACAACAGCACG 60.352 61.111 13.52 0.00 45.61 5.34
805 2651 2.408704 CGCGCTCCACTATTTATACTGC 59.591 50.000 5.56 0.00 0.00 4.40
854 2711 0.176449 TGCTGACGATGATCAGTGGG 59.824 55.000 0.09 0.00 46.65 4.61
867 2726 0.456312 GCTTGATGCTTGCTGCTGAC 60.456 55.000 0.00 0.00 43.37 3.51
871 2730 1.068474 CTTTGCTTGATGCTTGCTGC 58.932 50.000 0.00 0.00 43.37 5.25
908 2781 0.395311 ACTGCACGGGCTAGCTAGTA 60.395 55.000 21.62 1.10 41.91 1.82
909 2782 1.258445 AACTGCACGGGCTAGCTAGT 61.258 55.000 21.62 12.02 41.91 2.57
910 2783 0.744874 TAACTGCACGGGCTAGCTAG 59.255 55.000 16.84 16.84 41.91 3.42
911 2784 0.744874 CTAACTGCACGGGCTAGCTA 59.255 55.000 12.74 1.59 41.91 3.32
912 2785 1.517832 CTAACTGCACGGGCTAGCT 59.482 57.895 12.74 0.27 41.91 3.32
913 2786 2.174319 GCTAACTGCACGGGCTAGC 61.174 63.158 12.74 12.83 42.31 3.42
914 2787 1.521681 GGCTAACTGCACGGGCTAG 60.522 63.158 12.74 9.54 45.15 3.42
915 2788 2.582436 GGCTAACTGCACGGGCTA 59.418 61.111 12.74 0.00 45.15 3.93
1013 2894 4.025401 CGTTGTCGGTGGCCTTGC 62.025 66.667 3.32 0.00 0.00 4.01
1191 5450 1.668337 GCGAGATCGATCATGGACTGG 60.668 57.143 26.47 7.83 43.02 4.00
1230 5504 1.305930 GCGGAAACCACTCCACCATC 61.306 60.000 0.00 0.00 34.91 3.51
1439 5724 4.320870 ACACGGACCTTGTTAAAATCGAT 58.679 39.130 0.00 0.00 0.00 3.59
1455 5748 2.895404 AGGAAGCAAGTAAGTACACGGA 59.105 45.455 0.00 0.00 0.00 4.69
1478 5775 3.815401 GTCCTGCAAGTTAGTGACACATT 59.185 43.478 8.59 0.00 0.00 2.71
1487 5784 1.537202 GCACAAGGTCCTGCAAGTTAG 59.463 52.381 0.00 0.00 33.31 2.34
1488 5785 1.604604 GCACAAGGTCCTGCAAGTTA 58.395 50.000 0.00 0.00 33.31 2.24
1490 5787 1.529244 GGCACAAGGTCCTGCAAGT 60.529 57.895 4.16 0.00 34.90 3.16
1509 5817 3.745803 GTTCCCTCGACGGCGACT 61.746 66.667 10.67 0.00 42.51 4.18
1594 5902 2.282180 GGGGTTCATGTGCACGGT 60.282 61.111 13.13 0.00 0.00 4.83
1671 5979 4.563184 CAGAGTATTCTTACGCCTGTGTTC 59.437 45.833 0.00 0.00 33.29 3.18
1707 6020 1.668751 GTTCACCAGCGAGAAACAACA 59.331 47.619 0.00 0.00 0.00 3.33
1709 6022 1.305201 GGTTCACCAGCGAGAAACAA 58.695 50.000 0.00 0.00 31.85 2.83
1728 6049 3.819275 CGATCGATAAATGAGCGCG 57.181 52.632 10.26 0.00 38.47 6.86
1739 6060 0.249280 TATTGCACACGGCGATCGAT 60.249 50.000 21.57 0.00 43.38 3.59
1740 6061 1.139947 TATTGCACACGGCGATCGA 59.860 52.632 21.57 0.00 43.38 3.59
1746 6067 0.168128 GGTTCTGTATTGCACACGGC 59.832 55.000 0.00 0.00 45.13 5.68
1756 6077 2.099921 CGCAGCAGTAGAGGTTCTGTAT 59.900 50.000 0.00 0.00 34.57 2.29
1758 6082 0.244994 CGCAGCAGTAGAGGTTCTGT 59.755 55.000 0.00 0.00 34.57 3.41
1893 6408 2.512286 GCGACATGGCTGCTGCTA 60.512 61.111 15.64 10.07 39.59 3.49
1905 6420 3.755628 GTGAGGTAGCGGGCGACA 61.756 66.667 6.27 0.00 0.00 4.35
2022 6537 3.083349 ATGCAGAGGTAGCGGCCA 61.083 61.111 2.24 0.00 33.85 5.36
2076 6594 2.103340 GAGAAGAGGTCGCCGAGC 59.897 66.667 8.49 8.49 0.00 5.03
2109 6627 4.700268 TTATAGTCGAACGTACTTGGCA 57.300 40.909 0.00 0.00 0.00 4.92
2121 6644 7.085746 TGACACAAAGATCGTTTTATAGTCGA 58.914 34.615 0.00 0.00 37.96 4.20
2131 6692 7.556275 ACCCATAATAATGACACAAAGATCGTT 59.444 33.333 0.00 0.00 34.84 3.85
2132 6693 7.012327 CACCCATAATAATGACACAAAGATCGT 59.988 37.037 0.00 0.00 34.84 3.73
2133 6694 7.012327 ACACCCATAATAATGACACAAAGATCG 59.988 37.037 0.00 0.00 34.84 3.69
2136 6697 7.450014 ACAACACCCATAATAATGACACAAAGA 59.550 33.333 0.00 0.00 34.84 2.52
2138 6699 7.374272 CACAACACCCATAATAATGACACAAA 58.626 34.615 0.00 0.00 34.84 2.83
2140 6701 5.105957 GCACAACACCCATAATAATGACACA 60.106 40.000 0.00 0.00 34.84 3.72
2141 6702 5.125417 AGCACAACACCCATAATAATGACAC 59.875 40.000 0.00 0.00 34.84 3.67
2143 6704 5.835113 AGCACAACACCCATAATAATGAC 57.165 39.130 0.00 0.00 34.84 3.06
2145 6706 4.805192 GCAAGCACAACACCCATAATAATG 59.195 41.667 0.00 0.00 0.00 1.90
2146 6707 4.711355 AGCAAGCACAACACCCATAATAAT 59.289 37.500 0.00 0.00 0.00 1.28
2153 6714 1.815196 CAAGCAAGCACAACACCCA 59.185 52.632 0.00 0.00 0.00 4.51
2154 6715 1.592400 GCAAGCAAGCACAACACCC 60.592 57.895 0.00 0.00 0.00 4.61
2155 6716 0.595825 GAGCAAGCAAGCACAACACC 60.596 55.000 3.19 0.00 36.85 4.16
2156 6717 0.101040 TGAGCAAGCAAGCACAACAC 59.899 50.000 3.19 0.00 36.85 3.32
2159 6720 0.239082 CGATGAGCAAGCAAGCACAA 59.761 50.000 4.82 0.00 38.54 3.33
2160 6721 1.871077 CGATGAGCAAGCAAGCACA 59.129 52.632 3.34 3.34 39.35 4.57
2319 6883 0.322648 GGCCCTTTTTCTGCAAGCAT 59.677 50.000 0.00 0.00 0.00 3.79
2343 6907 2.747686 GGAACAACGGGCAGAGGA 59.252 61.111 0.00 0.00 0.00 3.71
2398 6967 0.401356 TTCATCAGGCAGGCTTGTCA 59.599 50.000 2.31 0.00 0.00 3.58
2409 6978 5.803967 GCTTTGCTCTGTTTATTTCATCAGG 59.196 40.000 0.00 0.00 0.00 3.86
2468 7037 9.695526 CACAATTCCATGTTGAATCTTAGAAAA 57.304 29.630 1.85 0.00 33.91 2.29
2555 7128 7.819644 TGTTTATCATTGAACCAGAATGACAG 58.180 34.615 0.00 0.00 41.46 3.51
2650 7227 3.376859 CACCTGCAGAAATACGCCATTTA 59.623 43.478 17.39 0.00 36.96 1.40
2651 7228 2.164219 CACCTGCAGAAATACGCCATTT 59.836 45.455 17.39 0.00 39.63 2.32
2669 7246 6.677913 ACTTTTACATGTTACATTCTGCACC 58.322 36.000 2.30 0.00 0.00 5.01
2733 7313 3.963374 ACTCATTCTTCTCCATCGATCCA 59.037 43.478 0.00 0.00 0.00 3.41
2950 10365 0.034059 GTGTGACTGTGTCCCCTCAG 59.966 60.000 0.00 0.00 38.01 3.35
2958 10373 4.072131 AGTTTGAAACTGTGTGACTGTGT 58.928 39.130 10.18 0.00 41.01 3.72
2959 10374 4.685169 AGTTTGAAACTGTGTGACTGTG 57.315 40.909 10.18 0.00 41.01 3.66
2960 10375 4.518970 ACAAGTTTGAAACTGTGTGACTGT 59.481 37.500 11.83 7.36 41.91 3.55
2961 10376 5.046910 ACAAGTTTGAAACTGTGTGACTG 57.953 39.130 11.83 6.72 41.91 3.51
2962 10377 5.003804 AGACAAGTTTGAAACTGTGTGACT 58.996 37.500 21.63 14.92 41.91 3.41
2963 10378 5.122396 AGAGACAAGTTTGAAACTGTGTGAC 59.878 40.000 21.63 13.41 41.91 3.67
2964 10379 5.122239 CAGAGACAAGTTTGAAACTGTGTGA 59.878 40.000 21.63 0.00 41.91 3.58
2971 10386 6.494842 TGTTATGCAGAGACAAGTTTGAAAC 58.505 36.000 0.00 0.00 0.00 2.78
3000 10415 8.597167 TGTCTATATGCTTTGCCTCTATTGTAT 58.403 33.333 0.00 0.00 0.00 2.29
3010 10425 3.808728 TGGACTGTCTATATGCTTTGCC 58.191 45.455 7.85 0.00 0.00 4.52
3022 10437 3.092301 TCGAGAATGTCATGGACTGTCT 58.908 45.455 7.85 0.83 33.15 3.41
3047 10464 7.967854 TCGTTTGAATTATCATAGGCTGTTTTG 59.032 33.333 0.00 0.00 34.96 2.44
3061 10479 6.638610 TGGATGGCAATTTCGTTTGAATTAT 58.361 32.000 0.00 0.00 33.20 1.28
3072 10490 1.563111 CACGCATGGATGGCAATTTC 58.437 50.000 0.00 0.00 0.00 2.17
3129 10547 4.816925 GCTGTGGGGTCATCTTCTATAAAC 59.183 45.833 0.00 0.00 0.00 2.01
3150 10568 4.987963 TTGATGGATCATGTCTATGGCT 57.012 40.909 0.00 0.00 36.56 4.75
3219 10641 2.151202 TGAAGAAACGCTGAATGTCCC 58.849 47.619 0.00 0.00 0.00 4.46
3253 10675 2.961526 ACGCGACAGGTATTCTCAAT 57.038 45.000 15.93 0.00 0.00 2.57
3254 10676 3.379057 TCATACGCGACAGGTATTCTCAA 59.621 43.478 15.93 0.00 0.00 3.02
3258 10680 3.050619 CCTTCATACGCGACAGGTATTC 58.949 50.000 15.93 0.00 0.00 1.75
3279 10702 5.107259 TGTCAACGTTGTATGCTTGTATGAC 60.107 40.000 26.47 13.67 35.30 3.06
3339 10762 7.719483 TCCTGATTTCTTATTTCATTCCATGC 58.281 34.615 0.00 0.00 0.00 4.06


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

AutoCloner maintained by Alex Coulton.