Multiple sequence alignment - TraesCS7B01G333600

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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 TraesCS7B01G333600 chr7B 100.000 3803 0 0 1 3803 588879885 588876083 0.000000e+00 7023.0
1 TraesCS7B01G333600 chr7B 95.231 1887 48 9 1577 3430 589735254 589737131 0.000000e+00 2948.0
2 TraesCS7B01G333600 chr7B 95.267 1817 29 17 1618 3406 589696286 589694499 0.000000e+00 2826.0
3 TraesCS7B01G333600 chr7B 93.650 1874 53 20 1467 3296 589919754 589921605 0.000000e+00 2741.0
4 TraesCS7B01G333600 chr7B 99.248 133 1 0 1259 1391 589919489 589919621 1.370000e-59 241.0
5 TraesCS7B01G333600 chr7B 87.821 156 8 2 1447 1602 498300237 498300093 5.050000e-39 172.0
6 TraesCS7B01G333600 chr7B 83.420 193 17 8 3462 3640 589897395 589897586 8.450000e-37 165.0
7 TraesCS7B01G333600 chr7B 80.000 210 11 10 3459 3668 589737453 589737631 3.990000e-25 126.0
8 TraesCS7B01G333600 chr7B 93.939 66 4 0 3673 3738 537746130 537746065 2.420000e-17 100.0
9 TraesCS7B01G333600 chr7B 100.000 39 0 0 1568 1606 589735140 589735178 5.270000e-09 73.1
10 TraesCS7B01G333600 chr7B 100.000 28 0 0 1259 1286 589934822 589934849 7.000000e-03 52.8
11 TraesCS7B01G333600 chr1B 94.164 2039 51 14 1430 3430 133124348 133122340 0.000000e+00 3044.0
12 TraesCS7B01G333600 chr1B 91.908 1693 54 23 1773 3430 133111350 133109706 0.000000e+00 2290.0
13 TraesCS7B01G333600 chr1B 91.617 1694 55 29 1773 3430 426481939 426480297 0.000000e+00 2261.0
14 TraesCS7B01G333600 chr1B 95.009 1062 45 3 333 1391 133125528 133124472 0.000000e+00 1661.0
15 TraesCS7B01G333600 chr1B 95.681 764 13 1 2553 3296 398964394 398965157 0.000000e+00 1210.0
16 TraesCS7B01G333600 chr1B 90.351 912 60 23 4 896 426498482 426497580 0.000000e+00 1171.0
17 TraesCS7B01G333600 chr1B 91.029 836 50 15 1677 2504 426496947 426496129 0.000000e+00 1105.0
18 TraesCS7B01G333600 chr1B 89.162 895 77 17 2 884 133112880 133111994 0.000000e+00 1098.0
19 TraesCS7B01G333600 chr1B 94.309 123 7 0 3681 3803 133121881 133121759 5.020000e-44 189.0
20 TraesCS7B01G333600 chr1B 93.701 127 4 2 3681 3803 133109479 133109353 1.800000e-43 187.0
21 TraesCS7B01G333600 chr1B 93.701 127 4 2 3681 3803 426494963 426494837 1.800000e-43 187.0
22 TraesCS7B01G333600 chr1B 92.126 127 6 2 3681 3803 426480070 426479944 3.900000e-40 176.0
23 TraesCS7B01G333600 chr1B 95.238 84 4 0 3588 3671 133109666 133109583 2.380000e-27 134.0
24 TraesCS7B01G333600 chr1B 94.048 84 5 0 3588 3671 426480257 426480174 1.110000e-25 128.0
25 TraesCS7B01G333600 chr7A 93.303 1732 66 17 1661 3361 627008678 627006966 0.000000e+00 2510.0
26 TraesCS7B01G333600 chr7A 91.486 1844 89 26 1619 3430 628385905 628384098 0.000000e+00 2473.0
27 TraesCS7B01G333600 chr7A 91.320 1659 68 19 1734 3330 627232462 627230818 0.000000e+00 2196.0
28 TraesCS7B01G333600 chr7A 94.472 814 15 9 2496 3281 628646394 628647205 0.000000e+00 1227.0
29 TraesCS7B01G333600 chr7A 89.479 922 73 21 2 909 627046731 627045820 0.000000e+00 1144.0
30 TraesCS7B01G333600 chr7A 91.940 670 48 4 2 666 580505706 580505038 0.000000e+00 933.0
31 TraesCS7B01G333600 chr7A 91.870 123 10 0 3681 3803 628383632 628383510 5.050000e-39 172.0
32 TraesCS7B01G333600 chr7A 88.889 144 9 5 1018 1161 628386313 628386177 1.820000e-38 171.0
33 TraesCS7B01G333600 chr7A 96.970 99 2 1 1248 1346 627234228 627234131 8.450000e-37 165.0
34 TraesCS7B01G333600 chr7A 97.500 80 2 0 1532 1611 628386020 628385941 1.840000e-28 137.0
35 TraesCS7B01G333600 chr7A 78.125 224 23 15 3473 3671 627006919 627006697 6.670000e-23 119.0
36 TraesCS7B01G333600 chr7A 92.647 68 5 0 3678 3745 580503502 580503435 8.690000e-17 99.0
37 TraesCS7B01G333600 chr7A 80.000 100 11 6 1194 1288 580504702 580504607 8.820000e-07 65.8
38 TraesCS7B01G333600 chr7A 97.222 36 1 0 1372 1407 627234156 627234121 1.140000e-05 62.1
39 TraesCS7B01G333600 chr7A 97.143 35 1 0 1577 1611 627008772 627008738 4.100000e-05 60.2
40 TraesCS7B01G333600 chr7A 96.970 33 1 0 1501 1533 627232648 627232616 5.310000e-04 56.5
41 TraesCS7B01G333600 chr5D 92.851 1119 57 9 335 1441 289356690 289355583 0.000000e+00 1602.0
42 TraesCS7B01G333600 chr5D 95.124 964 18 9 2496 3430 289354420 289353457 0.000000e+00 1493.0
43 TraesCS7B01G333600 chr5D 95.163 951 17 9 2496 3417 289420227 289419277 0.000000e+00 1474.0
44 TraesCS7B01G333600 chr5D 90.918 1068 63 15 1451 2504 289355493 289354446 0.000000e+00 1404.0
45 TraesCS7B01G333600 chr5D 94.269 855 34 5 1663 2504 289421105 289420253 0.000000e+00 1293.0
46 TraesCS7B01G333600 chr5D 90.493 831 57 11 2 820 289422360 289421540 0.000000e+00 1077.0
47 TraesCS7B01G333600 chr5D 91.141 745 52 10 4 737 289728462 289727721 0.000000e+00 998.0
48 TraesCS7B01G333600 chr5D 88.338 746 68 11 1766 2504 331837849 331838582 0.000000e+00 878.0
49 TraesCS7B01G333600 chr5D 96.604 530 9 7 2496 3017 289726496 289725968 0.000000e+00 870.0
50 TraesCS7B01G333600 chr5D 95.775 71 2 1 3673 3742 30056762 30056832 3.100000e-21 113.0
51 TraesCS7B01G333600 chr5D 84.553 123 6 3 3681 3803 289352996 289352887 4.020000e-20 110.0
52 TraesCS7B01G333600 chr5D 89.655 87 3 2 3462 3548 289354488 289354408 5.200000e-19 106.0
53 TraesCS7B01G333600 chr5D 91.026 78 7 0 3459 3536 331838537 331838614 5.200000e-19 106.0
54 TraesCS7B01G333600 chr6A 94.427 951 23 10 2496 3417 107265268 107266217 0.000000e+00 1435.0
55 TraesCS7B01G333600 chr6A 90.144 903 70 12 2 898 107262929 107263818 0.000000e+00 1157.0
56 TraesCS7B01G333600 chr6A 86.667 1020 69 17 1520 2504 107264255 107265242 0.000000e+00 1068.0
57 TraesCS7B01G333600 chr6A 100.000 32 0 0 1249 1280 107264075 107264106 4.100000e-05 60.2
58 TraesCS7B01G333600 chr7D 95.193 853 13 4 2496 3320 545266201 545265349 0.000000e+00 1323.0
59 TraesCS7B01G333600 chr7D 88.185 821 75 10 1625 2430 545650456 545651269 0.000000e+00 959.0
60 TraesCS7B01G333600 chr7D 84.783 184 19 5 980 1154 509580053 509579870 3.900000e-40 176.0
61 TraesCS7B01G333600 chr7D 87.218 133 13 4 3542 3671 509597948 509597817 8.510000e-32 148.0
62 TraesCS7B01G333600 chr7D 81.122 196 16 9 3459 3640 518767022 518767210 1.840000e-28 137.0
63 TraesCS7B01G333600 chr7D 85.185 81 9 2 1194 1272 509599036 509598957 3.150000e-11 80.5
64 TraesCS7B01G333600 chr7D 97.674 43 1 0 3626 3668 545652594 545652636 1.470000e-09 75.0
65 TraesCS7B01G333600 chr7D 96.875 32 0 1 1041 1071 545254722 545254753 7.000000e-03 52.8
66 TraesCS7B01G333600 chr2B 89.940 835 71 11 1 830 182135133 182134307 0.000000e+00 1064.0
67 TraesCS7B01G333600 chr2B 87.737 897 74 17 1561 2450 135512529 135513396 0.000000e+00 1014.0
68 TraesCS7B01G333600 chr2B 91.720 157 6 4 1192 1346 135512325 135512476 1.070000e-50 211.0
69 TraesCS7B01G333600 chr2B 92.233 103 2 1 3473 3575 136637786 136637690 1.420000e-29 141.0
70 TraesCS7B01G333600 chr2B 92.233 103 2 1 3473 3575 136813954 136813858 1.420000e-29 141.0
71 TraesCS7B01G333600 chr2B 90.385 104 3 2 3473 3575 137621303 137621206 3.080000e-26 130.0
72 TraesCS7B01G333600 chr2B 91.304 92 2 1 3459 3550 135466428 135466513 1.860000e-23 121.0
73 TraesCS7B01G333600 chr2B 89.474 95 4 1 3459 3553 182131223 182131135 8.630000e-22 115.0
74 TraesCS7B01G333600 chr2B 93.750 48 3 0 1481 1528 135512479 135512526 5.270000e-09 73.1
75 TraesCS7B01G333600 chr2D 93.642 173 5 1 3473 3645 84779224 84779058 1.750000e-63 254.0
76 TraesCS7B01G333600 chr2D 93.642 173 5 1 3473 3645 84936800 84936634 1.750000e-63 254.0
77 TraesCS7B01G333600 chr2D 93.064 173 6 1 3473 3645 85407597 85407431 8.160000e-62 248.0
78 TraesCS7B01G333600 chr6D 78.199 211 16 16 3476 3668 122990403 122990601 1.440000e-19 108.0
79 TraesCS7B01G333600 chr2A 97.297 37 0 1 3394 3430 85809098 85809063 1.140000e-05 62.1


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 TraesCS7B01G333600 chr7B 588876083 588879885 3802 True 7023.000000 7023 100.000000 1 3803 1 chr7B.!!$R3 3802
1 TraesCS7B01G333600 chr7B 589694499 589696286 1787 True 2826.000000 2826 95.267000 1618 3406 1 chr7B.!!$R4 1788
2 TraesCS7B01G333600 chr7B 589919489 589921605 2116 False 1491.000000 2741 96.449000 1259 3296 2 chr7B.!!$F4 2037
3 TraesCS7B01G333600 chr7B 589735140 589737631 2491 False 1049.033333 2948 91.743667 1568 3668 3 chr7B.!!$F3 2100
4 TraesCS7B01G333600 chr1B 133121759 133125528 3769 True 1631.333333 3044 94.494000 333 3803 3 chr1B.!!$R2 3470
5 TraesCS7B01G333600 chr1B 398964394 398965157 763 False 1210.000000 1210 95.681000 2553 3296 1 chr1B.!!$F1 743
6 TraesCS7B01G333600 chr1B 133109353 133112880 3527 True 927.250000 2290 92.502250 2 3803 4 chr1B.!!$R1 3801
7 TraesCS7B01G333600 chr1B 426479944 426481939 1995 True 855.000000 2261 92.597000 1773 3803 3 chr1B.!!$R3 2030
8 TraesCS7B01G333600 chr1B 426494837 426498482 3645 True 821.000000 1171 91.693667 4 3803 3 chr1B.!!$R4 3799
9 TraesCS7B01G333600 chr7A 628646394 628647205 811 False 1227.000000 1227 94.472000 2496 3281 1 chr7A.!!$F1 785
10 TraesCS7B01G333600 chr7A 627045820 627046731 911 True 1144.000000 1144 89.479000 2 909 1 chr7A.!!$R1 907
11 TraesCS7B01G333600 chr7A 627006697 627008772 2075 True 896.400000 2510 89.523667 1577 3671 3 chr7A.!!$R3 2094
12 TraesCS7B01G333600 chr7A 628383510 628386313 2803 True 738.250000 2473 92.436250 1018 3803 4 chr7A.!!$R5 2785
13 TraesCS7B01G333600 chr7A 627230818 627234228 3410 True 619.900000 2196 95.620500 1248 3330 4 chr7A.!!$R4 2082
14 TraesCS7B01G333600 chr7A 580503435 580505706 2271 True 365.933333 933 88.195667 2 3745 3 chr7A.!!$R2 3743
15 TraesCS7B01G333600 chr5D 289419277 289422360 3083 True 1281.333333 1474 93.308333 2 3417 3 chr5D.!!$R2 3415
16 TraesCS7B01G333600 chr5D 289352887 289356690 3803 True 943.000000 1602 90.620200 335 3803 5 chr5D.!!$R1 3468
17 TraesCS7B01G333600 chr5D 289725968 289728462 2494 True 934.000000 998 93.872500 4 3017 2 chr5D.!!$R3 3013
18 TraesCS7B01G333600 chr5D 331837849 331838614 765 False 492.000000 878 89.682000 1766 3536 2 chr5D.!!$F2 1770
19 TraesCS7B01G333600 chr6A 107262929 107266217 3288 False 930.050000 1435 92.809500 2 3417 4 chr6A.!!$F1 3415
20 TraesCS7B01G333600 chr7D 545265349 545266201 852 True 1323.000000 1323 95.193000 2496 3320 1 chr7D.!!$R2 824
21 TraesCS7B01G333600 chr7D 545650456 545652636 2180 False 517.000000 959 92.929500 1625 3668 2 chr7D.!!$F3 2043
22 TraesCS7B01G333600 chr2B 182131135 182135133 3998 True 589.500000 1064 89.707000 1 3553 2 chr2B.!!$R4 3552
23 TraesCS7B01G333600 chr2B 135512325 135513396 1071 False 432.700000 1014 91.069000 1192 2450 3 chr2B.!!$F2 1258

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
357 370 0.630673 AGGCCTGGCATATGTGGAAA 59.369 50.000 22.05 0.0 0.00 3.13 F
765 821 2.949177 TGGGCTTTTTACTGCTCAGA 57.051 45.000 3.60 0.0 34.40 3.27 F
1629 3608 2.879646 AGTCTCAGAACGACTTCGACTT 59.120 45.455 5.47 0.0 38.52 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1529 3344 0.526096 CGGATTCAAATTGCCTGCCG 60.526 55.0 0.0 0.0 0.0 5.69 R
2514 4706 0.884514 GGTTCCTTTGCTTCCTCTGC 59.115 55.0 0.0 0.0 0.0 4.26 R
3569 6961 0.106521 GATTCCTCTGCTCCCTCTGC 59.893 60.0 0.0 0.0 0.0 4.26 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
93 99 3.860536 GCATCTCGAGGAGTTTACTCAAC 59.139 47.826 13.56 4.37 44.60 3.18
156 162 7.390718 GGTGATTATTAGTGGCCGAAAGAATAT 59.609 37.037 0.00 0.00 0.00 1.28
202 208 4.038763 ACTGTTGGTGATCTTGTACGAGAA 59.961 41.667 16.82 0.00 0.00 2.87
217 223 4.592485 ACGAGAAGTGAGTGAACTGAAT 57.408 40.909 0.00 0.00 0.00 2.57
222 228 7.918033 ACGAGAAGTGAGTGAACTGAATATATG 59.082 37.037 0.00 0.00 0.00 1.78
224 230 9.243637 GAGAAGTGAGTGAACTGAATATATGTC 57.756 37.037 0.00 0.00 0.00 3.06
316 328 1.403914 CGCTGCAGTTCTCTCATGTCT 60.404 52.381 16.64 0.00 0.00 3.41
357 370 0.630673 AGGCCTGGCATATGTGGAAA 59.369 50.000 22.05 0.00 0.00 3.13
758 814 6.079712 AGTGAGGATTATGGGCTTTTTACT 57.920 37.500 0.00 0.00 0.00 2.24
765 821 2.949177 TGGGCTTTTTACTGCTCAGA 57.051 45.000 3.60 0.00 34.40 3.27
828 888 5.830912 AGTGAAATAAACATGTGTGTGTGG 58.169 37.500 0.00 0.00 38.92 4.17
829 889 5.359576 AGTGAAATAAACATGTGTGTGTGGT 59.640 36.000 0.00 0.00 38.92 4.16
830 890 6.039616 GTGAAATAAACATGTGTGTGTGGTT 58.960 36.000 0.00 0.00 38.92 3.67
831 891 6.019961 GTGAAATAAACATGTGTGTGTGGTTG 60.020 38.462 0.00 0.00 38.92 3.77
874 948 6.463995 TTTTCCATGGGCTACATTGTAATC 57.536 37.500 13.02 0.00 37.84 1.75
898 1003 7.081349 TCCAAACGTATGATGTTTCATGTTTC 58.919 34.615 0.00 0.00 42.60 2.78
972 1087 8.142994 ACAGTTATTCGCATGTCCTTTTATAG 57.857 34.615 0.00 0.00 0.00 1.31
1437 1699 7.020827 TCTGAGGAGTTACAATCCAAGAATT 57.979 36.000 0.00 0.00 39.47 2.17
1613 3532 5.875359 ACTCGGATTCAAAAACCATAGTCTC 59.125 40.000 0.00 0.00 0.00 3.36
1614 3533 5.800296 TCGGATTCAAAAACCATAGTCTCA 58.200 37.500 0.00 0.00 0.00 3.27
1616 3535 5.874810 CGGATTCAAAAACCATAGTCTCAGA 59.125 40.000 0.00 0.00 0.00 3.27
1629 3608 2.879646 AGTCTCAGAACGACTTCGACTT 59.120 45.455 5.47 0.00 38.52 3.01
2510 4702 4.439837 GGAAGAAATTGCATCAGAGGAAGC 60.440 45.833 0.00 0.00 38.21 3.86
2511 4703 3.693807 AGAAATTGCATCAGAGGAAGCA 58.306 40.909 0.00 0.00 45.17 3.91
2515 4707 1.171308 TGCATCAGAGGAAGCAAAGC 58.829 50.000 0.00 0.00 44.02 3.51
2516 4708 1.171308 GCATCAGAGGAAGCAAAGCA 58.829 50.000 0.00 0.00 37.67 3.91
2517 4709 1.132643 GCATCAGAGGAAGCAAAGCAG 59.867 52.381 0.00 0.00 37.67 4.24
2518 4710 2.708051 CATCAGAGGAAGCAAAGCAGA 58.292 47.619 0.00 0.00 0.00 4.26
2519 4711 2.469274 TCAGAGGAAGCAAAGCAGAG 57.531 50.000 0.00 0.00 0.00 3.35
2520 4712 1.002888 TCAGAGGAAGCAAAGCAGAGG 59.997 52.381 0.00 0.00 0.00 3.69
2521 4713 1.002888 CAGAGGAAGCAAAGCAGAGGA 59.997 52.381 0.00 0.00 0.00 3.71
2522 4714 1.701847 AGAGGAAGCAAAGCAGAGGAA 59.298 47.619 0.00 0.00 0.00 3.36
2523 4715 2.083002 GAGGAAGCAAAGCAGAGGAAG 58.917 52.381 0.00 0.00 0.00 3.46
2551 4743 5.035784 GAACCAATTCCTTTCTTGAGTCG 57.964 43.478 0.00 0.00 0.00 4.18
2867 5268 4.338879 AGGAAGCTCATGTACTGCAATTT 58.661 39.130 0.00 0.00 0.00 1.82
2871 5272 2.223340 GCTCATGTACTGCAATTTCGGG 60.223 50.000 0.00 0.00 0.00 5.14
2874 5275 1.816074 TGTACTGCAATTTCGGGACC 58.184 50.000 0.00 0.00 0.00 4.46
2969 5370 4.822026 AGGAGTAGAATTGAACTTGTCGG 58.178 43.478 0.00 0.00 0.00 4.79
3008 5409 2.811101 CTGCCTAGCGTCTGGAGG 59.189 66.667 0.00 0.00 0.00 4.30
3059 5480 0.949105 ATTGGCGTCGTGGTGAGTTC 60.949 55.000 0.00 0.00 0.00 3.01
3125 5546 4.058124 TGTGTATGTGTGAGTGAAGCTTC 58.942 43.478 19.89 19.89 0.00 3.86
3430 6276 6.357579 TGTGAAAAAGGTGGCATCATATTT 57.642 33.333 0.00 0.00 0.00 1.40
3434 6280 6.649973 TGAAAAAGGTGGCATCATATTTTGTG 59.350 34.615 11.86 0.00 0.00 3.33
3438 6284 4.081531 AGGTGGCATCATATTTTGTGTTGG 60.082 41.667 0.00 0.00 0.00 3.77
3441 6287 4.183101 GGCATCATATTTTGTGTTGGTGG 58.817 43.478 0.00 0.00 0.00 4.61
3444 6290 6.035843 GCATCATATTTTGTGTTGGTGGTAG 58.964 40.000 0.00 0.00 0.00 3.18
3455 6301 5.071250 TGTGTTGGTGGTAGTCTTTCTATGT 59.929 40.000 0.00 0.00 0.00 2.29
3468 6828 4.870426 TCTTTCTATGTTTCACGGATGAGC 59.130 41.667 0.00 0.00 35.83 4.26
3522 6887 0.318445 GCAGTGCAAGCTTCTTGGTG 60.318 55.000 11.09 0.00 0.00 4.17
3569 6961 2.447244 AGAGTCGGCAGTGAGAAAAG 57.553 50.000 0.00 0.00 0.00 2.27
3576 6968 1.163554 GCAGTGAGAAAAGCAGAGGG 58.836 55.000 0.00 0.00 0.00 4.30
3581 6973 1.002888 TGAGAAAAGCAGAGGGAGCAG 59.997 52.381 0.00 0.00 0.00 4.24
3586 6978 0.546267 AAGCAGAGGGAGCAGAGGAA 60.546 55.000 0.00 0.00 0.00 3.36
3587 6979 0.326427 AGCAGAGGGAGCAGAGGAAT 60.326 55.000 0.00 0.00 0.00 3.01
3588 6980 0.106521 GCAGAGGGAGCAGAGGAATC 59.893 60.000 0.00 0.00 0.00 2.52
3589 6981 1.792115 CAGAGGGAGCAGAGGAATCT 58.208 55.000 0.00 0.00 0.00 2.40
3595 6987 2.484594 GGGAGCAGAGGAATCTAGTTGC 60.485 54.545 0.00 0.00 0.00 4.17
3671 7066 4.789012 CTGGCATGTTTTCCAGTAATGT 57.211 40.909 8.51 0.00 43.66 2.71
3673 7068 6.455360 CTGGCATGTTTTCCAGTAATGTAT 57.545 37.500 8.51 0.00 43.66 2.29
3676 7169 6.042143 GGCATGTTTTCCAGTAATGTATTGG 58.958 40.000 0.00 0.00 36.94 3.16
3683 7177 8.616076 GTTTTCCAGTAATGTATTGGATCTGAG 58.384 37.037 0.88 0.00 43.06 3.35
3732 7234 8.103305 TGCCACTAGATCTCTTTCTATGTTTTT 58.897 33.333 0.00 0.00 0.00 1.94
3765 7267 6.479990 GTGTGCATCTGATGTATTTACAGCTA 59.520 38.462 18.19 0.00 42.66 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 7.605691 ACAAAAGATGTCAAGACTGAGATTAGG 59.394 37.037 1.53 0.00 37.96 2.69
22 25 8.464770 TGAAAAGTGAAACAAAAGATGTCAAG 57.535 30.769 0.00 0.00 42.99 3.02
93 99 2.681706 AGCTGAACACATCTGTCTTCG 58.318 47.619 0.00 0.00 0.00 3.79
202 208 8.298729 TCAGACATATATTCAGTTCACTCACT 57.701 34.615 0.00 0.00 0.00 3.41
222 228 9.155975 TGAACTATAAGAAATCTTGCTTCAGAC 57.844 33.333 5.93 0.00 37.40 3.51
224 230 8.939929 TGTGAACTATAAGAAATCTTGCTTCAG 58.060 33.333 5.93 0.00 37.40 3.02
357 370 0.035630 GCTCATGCAACCTCTGGTCT 60.036 55.000 0.00 0.00 39.41 3.85
363 376 0.524862 CCACAAGCTCATGCAACCTC 59.475 55.000 0.00 0.00 42.74 3.85
737 793 4.644685 GCAGTAAAAAGCCCATAATCCTCA 59.355 41.667 0.00 0.00 0.00 3.86
779 838 6.430925 CCACAAAACTGGTCTTTGATATCTCA 59.569 38.462 3.98 0.00 37.25 3.27
874 948 7.083858 AGAAACATGAAACATCATACGTTTGG 58.916 34.615 0.00 0.00 36.72 3.28
972 1087 3.550842 GCAAACAGTTGTTCTCATGTCCC 60.551 47.826 0.00 0.00 37.25 4.46
1445 1849 6.762187 CAGAAGAGCAAGATTAGACATGATGT 59.238 38.462 0.00 0.00 0.00 3.06
1454 1858 3.557228 AGCCCAGAAGAGCAAGATTAG 57.443 47.619 0.00 0.00 0.00 1.73
1529 3344 0.526096 CGGATTCAAATTGCCTGCCG 60.526 55.000 0.00 0.00 0.00 5.69
1613 3532 2.417339 TCCAAGTCGAAGTCGTTCTG 57.583 50.000 0.00 0.00 40.80 3.02
1614 3533 3.005472 TGAATCCAAGTCGAAGTCGTTCT 59.995 43.478 0.00 0.00 40.80 3.01
1616 3535 3.380479 TGAATCCAAGTCGAAGTCGTT 57.620 42.857 0.00 0.00 40.80 3.85
1629 3608 2.367030 CGGCAAGCAATTTGAATCCA 57.633 45.000 0.00 0.00 39.21 3.41
2510 4702 2.233271 TCCTTTGCTTCCTCTGCTTTG 58.767 47.619 0.00 0.00 0.00 2.77
2511 4703 2.625314 GTTCCTTTGCTTCCTCTGCTTT 59.375 45.455 0.00 0.00 0.00 3.51
2512 4704 2.234143 GTTCCTTTGCTTCCTCTGCTT 58.766 47.619 0.00 0.00 0.00 3.91
2513 4705 1.546548 GGTTCCTTTGCTTCCTCTGCT 60.547 52.381 0.00 0.00 0.00 4.24
2514 4706 0.884514 GGTTCCTTTGCTTCCTCTGC 59.115 55.000 0.00 0.00 0.00 4.26
2515 4707 2.276732 TGGTTCCTTTGCTTCCTCTG 57.723 50.000 0.00 0.00 0.00 3.35
2516 4708 3.532641 ATTGGTTCCTTTGCTTCCTCT 57.467 42.857 0.00 0.00 0.00 3.69
2517 4709 4.179926 GAATTGGTTCCTTTGCTTCCTC 57.820 45.455 0.00 0.00 0.00 3.71
2551 4743 2.302157 ACTAGCTTAACTCACCCACACC 59.698 50.000 0.00 0.00 0.00 4.16
2867 5268 2.473891 TACGCTCTGTCTGGTCCCGA 62.474 60.000 0.00 0.00 0.00 5.14
2871 5272 1.719780 CGTTTTACGCTCTGTCTGGTC 59.280 52.381 0.00 0.00 33.65 4.02
2969 5370 5.062683 CAGCTCACATGATTACTGTGTGTAC 59.937 44.000 0.00 0.00 43.53 2.90
3059 5480 2.609459 ACTCGTCAGAAACTGCAACTTG 59.391 45.455 0.00 0.00 0.00 3.16
3125 5546 2.370281 TCAAGGACTTGCTTAGCTCG 57.630 50.000 5.60 0.00 40.24 5.03
3430 6276 4.497291 AGAAAGACTACCACCAACACAA 57.503 40.909 0.00 0.00 0.00 3.33
3434 6280 6.708949 TGAAACATAGAAAGACTACCACCAAC 59.291 38.462 0.00 0.00 33.62 3.77
3438 6284 5.347907 CCGTGAAACATAGAAAGACTACCAC 59.652 44.000 0.00 0.00 35.74 4.16
3441 6287 7.033791 TCATCCGTGAAACATAGAAAGACTAC 58.966 38.462 0.00 0.00 35.74 2.73
3444 6290 5.220491 GCTCATCCGTGAAACATAGAAAGAC 60.220 44.000 0.00 0.00 35.74 3.01
3455 6301 1.805539 CGAGCGCTCATCCGTGAAA 60.806 57.895 34.69 0.00 33.05 2.69
3522 6887 5.401531 TCTGATGTAAGACTACCACCAAC 57.598 43.478 0.00 0.00 0.00 3.77
3569 6961 0.106521 GATTCCTCTGCTCCCTCTGC 59.893 60.000 0.00 0.00 0.00 4.26
3576 6968 3.533606 TGCAACTAGATTCCTCTGCTC 57.466 47.619 0.00 0.00 32.66 4.26
3581 6973 4.759782 TGTAGCTTGCAACTAGATTCCTC 58.240 43.478 0.00 0.00 0.00 3.71
3586 6978 5.308825 ACAACTTGTAGCTTGCAACTAGAT 58.691 37.500 0.00 0.00 0.00 1.98
3587 6979 4.703897 ACAACTTGTAGCTTGCAACTAGA 58.296 39.130 0.00 0.00 0.00 2.43
3588 6980 4.511454 TGACAACTTGTAGCTTGCAACTAG 59.489 41.667 0.00 0.00 0.00 2.57
3589 6981 4.447290 TGACAACTTGTAGCTTGCAACTA 58.553 39.130 0.00 0.00 0.00 2.24
3595 6987 6.545504 ACATAGTTGACAACTTGTAGCTTG 57.454 37.500 25.10 13.39 42.81 4.01
3671 7066 4.652881 ACATCAGACTGCTCAGATCCAATA 59.347 41.667 3.60 0.00 0.00 1.90
3673 7068 2.836372 ACATCAGACTGCTCAGATCCAA 59.164 45.455 3.60 0.00 0.00 3.53
3676 7169 3.989167 GCATACATCAGACTGCTCAGATC 59.011 47.826 3.60 0.00 0.00 2.75
3683 7177 2.011947 TGCTTGCATACATCAGACTGC 58.988 47.619 0.00 0.00 35.21 4.40
3765 7267 3.402628 AATTCGGACAGCAAGTACACT 57.597 42.857 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.