Multiple sequence alignment - TraesCS7D01G404100

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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 TraesCS7D01G404100 chr7D 100.000 6305 0 0 1 6305 520943695 520949999 0.000000e+00 11644.0
1 TraesCS7D01G404100 chr7D 89.087 4087 313 48 1777 5783 520877092 520881125 0.000000e+00 4953.0
2 TraesCS7D01G404100 chr7D 89.511 2679 145 44 244 2835 521707168 521709797 0.000000e+00 3265.0
3 TraesCS7D01G404100 chr7D 90.859 1630 106 11 1202 2802 521571550 521573165 0.000000e+00 2145.0
4 TraesCS7D01G404100 chr7D 87.357 1313 115 20 3954 5247 521709821 521711101 0.000000e+00 1458.0
5 TraesCS7D01G404100 chr7D 87.774 1186 88 19 2798 3947 521576050 521577214 0.000000e+00 1334.0
6 TraesCS7D01G404100 chr7D 85.577 1144 116 17 4133 5247 521577298 521578421 0.000000e+00 1153.0
7 TraesCS7D01G404100 chr7D 81.633 1372 195 26 4427 5780 521593702 521595034 0.000000e+00 1085.0
8 TraesCS7D01G404100 chr7D 91.667 432 19 11 515 935 520875747 520876172 3.480000e-162 582.0
9 TraesCS7D01G404100 chr7D 89.303 402 27 8 514 904 521570991 521571387 2.170000e-134 490.0
10 TraesCS7D01G404100 chr7D 94.821 251 10 2 1 250 521557599 521557847 8.150000e-104 388.0
11 TraesCS7D01G404100 chr7D 94.800 250 10 2 1 250 521706879 521707125 2.930000e-103 387.0
12 TraesCS7D01G404100 chr7D 93.173 249 15 1 2 250 520875225 520875471 1.370000e-96 364.0
13 TraesCS7D01G404100 chr7D 82.673 404 57 12 5912 6305 521512003 521512403 4.970000e-91 346.0
14 TraesCS7D01G404100 chr7D 80.149 403 65 13 5912 6305 521587133 521587529 3.060000e-73 287.0
15 TraesCS7D01G404100 chr7D 85.662 272 33 4 6018 6284 521579230 521579500 1.420000e-71 281.0
16 TraesCS7D01G404100 chr7D 100.000 104 0 0 6598 6701 520950292 520950395 6.860000e-45 193.0
17 TraesCS7D01G404100 chr7D 98.276 58 1 0 5912 5969 520881279 520881336 1.190000e-17 102.0
18 TraesCS7D01G404100 chr7D 97.297 37 0 1 479 515 521570929 521570964 2.020000e-05 62.1
19 TraesCS7D01G404100 chr7B 95.379 6102 154 28 244 6302 554777507 554783523 0.000000e+00 9588.0
20 TraesCS7D01G404100 chr7B 88.519 5348 400 68 514 5754 554359512 554364752 0.000000e+00 6277.0
21 TraesCS7D01G404100 chr7B 89.788 2781 201 36 1202 3947 555216914 555219646 0.000000e+00 3485.0
22 TraesCS7D01G404100 chr7B 91.935 1674 103 13 1187 2835 555417643 555419309 0.000000e+00 2314.0
23 TraesCS7D01G404100 chr7B 88.119 1313 127 13 3954 5247 555419369 555420671 0.000000e+00 1533.0
24 TraesCS7D01G404100 chr7B 84.896 1152 116 19 4133 5247 555219730 555220860 0.000000e+00 1110.0
25 TraesCS7D01G404100 chr7B 79.942 1371 218 27 4427 5780 555308259 555309589 0.000000e+00 955.0
26 TraesCS7D01G404100 chr7B 84.992 613 40 14 338 907 555216151 555216754 5.830000e-160 575.0
27 TraesCS7D01G404100 chr7B 86.160 513 38 14 244 725 555416565 555417075 2.140000e-144 523.0
28 TraesCS7D01G404100 chr7B 87.500 440 48 5 5333 5771 555420880 555421313 1.000000e-137 501.0
29 TraesCS7D01G404100 chr7B 86.245 458 26 9 727 1184 555417192 555417612 4.730000e-126 462.0
30 TraesCS7D01G404100 chr7B 94.400 250 11 2 1 250 555416276 555416522 1.360000e-101 381.0
31 TraesCS7D01G404100 chr7B 93.625 251 13 2 1 250 555215602 555215850 8.210000e-99 372.0
32 TraesCS7D01G404100 chr7B 91.481 270 21 1 248 515 595527214 595526945 2.950000e-98 370.0
33 TraesCS7D01G404100 chr7B 93.694 222 11 3 954 1174 595521067 595520848 5.010000e-86 329.0
34 TraesCS7D01G404100 chr7B 85.069 288 37 6 6020 6305 555164260 555164543 8.500000e-74 289.0
35 TraesCS7D01G404100 chr7B 84.247 292 40 5 6018 6305 555225622 555225911 5.120000e-71 279.0
36 TraesCS7D01G404100 chr7B 88.940 217 14 3 727 942 595521259 595521052 6.670000e-65 259.0
37 TraesCS7D01G404100 chr7B 82.877 292 44 5 6018 6305 555221604 555221893 2.400000e-64 257.0
38 TraesCS7D01G404100 chr7B 92.079 101 7 1 244 344 554359283 554359382 2.520000e-29 141.0
39 TraesCS7D01G404100 chr7B 98.276 58 1 0 5912 5969 554364941 554364998 1.190000e-17 102.0
40 TraesCS7D01G404100 chr7A 96.110 4216 114 9 1556 5754 600552789 600556971 0.000000e+00 6831.0
41 TraesCS7D01G404100 chr7A 88.722 4664 391 54 1187 5779 599500170 599504769 0.000000e+00 5574.0
42 TraesCS7D01G404100 chr7A 88.569 4654 377 60 1187 5754 598950441 598955025 0.000000e+00 5504.0
43 TraesCS7D01G404100 chr7A 89.566 2789 205 36 1202 3947 601466781 601469526 0.000000e+00 3459.0
44 TraesCS7D01G404100 chr7A 90.265 2301 129 30 583 2835 602020415 602022668 0.000000e+00 2920.0
45 TraesCS7D01G404100 chr7A 95.414 1330 36 8 244 1572 600550673 600551978 0.000000e+00 2095.0
46 TraesCS7D01G404100 chr7A 87.615 1300 111 18 3954 5232 602022728 602023998 0.000000e+00 1463.0
47 TraesCS7D01G404100 chr7A 85.652 1150 110 25 4133 5251 601469610 601470735 0.000000e+00 1158.0
48 TraesCS7D01G404100 chr7A 88.752 649 36 10 536 1181 599499511 599500125 0.000000e+00 760.0
49 TraesCS7D01G404100 chr7A 87.665 681 35 17 514 1181 598949752 598950396 0.000000e+00 747.0
50 TraesCS7D01G404100 chr7A 85.761 611 38 12 338 907 601466019 601466621 9.620000e-168 601.0
51 TraesCS7D01G404100 chr7A 82.318 673 83 24 5119 5783 602023927 602024571 9.820000e-153 551.0
52 TraesCS7D01G404100 chr7A 97.200 250 4 2 1 250 600550384 600550630 2.890000e-113 420.0
53 TraesCS7D01G404100 chr7A 95.200 250 9 2 1 250 602019707 602019953 6.300000e-105 392.0
54 TraesCS7D01G404100 chr7A 92.701 274 17 2 244 515 602019996 602020268 6.300000e-105 392.0
55 TraesCS7D01G404100 chr7A 93.208 265 15 1 6038 6302 600557512 600557773 2.930000e-103 387.0
56 TraesCS7D01G404100 chr7A 93.625 251 13 2 1 250 601465470 601465718 8.210000e-99 372.0
57 TraesCS7D01G404100 chr7A 92.771 249 16 1 2 250 598949234 598949480 6.390000e-95 359.0
58 TraesCS7D01G404100 chr7A 82.673 404 46 13 5912 6305 601471290 601471679 2.990000e-88 337.0
59 TraesCS7D01G404100 chr7A 86.154 195 13 8 5778 5969 598955119 598955302 1.470000e-46 198.0
60 TraesCS7D01G404100 chr7A 86.224 196 11 9 5778 5969 599504832 599505015 1.470000e-46 198.0
61 TraesCS7D01G404100 chr7A 93.069 101 6 1 244 344 598949523 598949622 5.420000e-31 147.0
62 TraesCS7D01G404100 chr7A 93.069 101 6 1 244 344 599499252 599499351 5.420000e-31 147.0
63 TraesCS7D01G404100 chr7A 81.967 122 11 3 5778 5898 600557065 600557176 7.160000e-15 93.5
64 TraesCS7D01G404100 chr7A 97.778 45 1 0 5921 5965 600557175 600557219 2.000000e-10 78.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G404100 chr7D 520943695 520950395 6700 False 5918.500000 11644 100.000000 1 6701 2 chr7D.!!$F6 6700
1 TraesCS7D01G404100 chr7D 521706879 521711101 4222 False 1703.333333 3265 90.556000 1 5247 3 chr7D.!!$F8 5246
2 TraesCS7D01G404100 chr7D 520875225 520881336 6111 False 1500.250000 4953 93.050750 2 5969 4 chr7D.!!$F5 5967
3 TraesCS7D01G404100 chr7D 521593702 521595034 1332 False 1085.000000 1085 81.633000 4427 5780 1 chr7D.!!$F4 1353
4 TraesCS7D01G404100 chr7D 521570929 521579500 8571 False 910.850000 2145 89.412000 479 6284 6 chr7D.!!$F7 5805
5 TraesCS7D01G404100 chr7B 554777507 554783523 6016 False 9588.000000 9588 95.379000 244 6302 1 chr7B.!!$F1 6058
6 TraesCS7D01G404100 chr7B 554359283 554364998 5715 False 2173.333333 6277 92.958000 244 5969 3 chr7B.!!$F4 5725
7 TraesCS7D01G404100 chr7B 555215602 555225911 10309 False 1013.000000 3485 86.737500 1 6305 6 chr7B.!!$F5 6304
8 TraesCS7D01G404100 chr7B 555308259 555309589 1330 False 955.000000 955 79.942000 4427 5780 1 chr7B.!!$F3 1353
9 TraesCS7D01G404100 chr7B 555416276 555421313 5037 False 952.333333 2314 89.059833 1 5771 6 chr7B.!!$F6 5770
10 TraesCS7D01G404100 chr7A 599499252 599505015 5763 False 1669.750000 5574 89.191750 244 5969 4 chr7A.!!$F2 5725
11 TraesCS7D01G404100 chr7A 600550384 600557773 7389 False 1650.866667 6831 93.612833 1 6302 6 chr7A.!!$F3 6301
12 TraesCS7D01G404100 chr7A 598949234 598955302 6068 False 1391.000000 5504 89.645600 2 5969 5 chr7A.!!$F1 5967
13 TraesCS7D01G404100 chr7A 601465470 601471679 6209 False 1185.400000 3459 87.455400 1 6305 5 chr7A.!!$F4 6304
14 TraesCS7D01G404100 chr7A 602019707 602024571 4864 False 1143.600000 2920 89.619800 1 5783 5 chr7A.!!$F5 5782

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
467 688 0.958091 CGAAATGCAGGTTGGGTCAA 59.042 50.000 0.0 0.0 0.00 3.18 F
1376 1905 1.272760 TGGCGGGAATTTTGGGTGTAT 60.273 47.619 0.0 0.0 0.00 2.29 F
2033 3521 1.414158 CGGAAGAGGCCCTAGATTCA 58.586 55.000 0.0 0.0 0.00 2.57 F
2271 3761 1.869767 GCAGCTATGTGTGCCTATGAC 59.130 52.381 0.0 0.0 33.29 3.06 F
2343 3833 2.752903 GCCGTTGGATACTGAAACCATT 59.247 45.455 0.0 0.0 33.56 3.16 F
3825 8305 5.003804 CCCAGTAAAAGCTCACACAGTTAT 58.996 41.667 0.0 0.0 0.00 1.89 F
4911 9461 1.272147 GGCCCACCTTCTGTTCTGATT 60.272 52.381 0.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1379 1908 0.102120 CCAAACTTCACGCCAAGCAA 59.898 50.000 0.00 0.00 0.00 3.91 R
2288 3778 1.428912 ACCATGTTCCAAGGGTCATGT 59.571 47.619 16.62 7.82 35.90 3.21 R
3825 8305 0.038021 TTAGCATGTGAGCTTGCCCA 59.962 50.000 4.49 0.00 43.70 5.36 R
3949 8429 5.126545 ACTGACGCAGGTATAAGACATAACA 59.873 40.000 10.80 0.00 35.51 2.41 R
3950 8430 5.589192 ACTGACGCAGGTATAAGACATAAC 58.411 41.667 10.80 0.00 35.51 1.89 R
5352 10070 0.607489 AAGGCTCAGACTGCGCATTT 60.607 50.000 18.55 9.63 26.81 2.32 R
6628 15627 0.387929 TTGATCTATCACCGGACGGC 59.612 55.000 9.46 0.00 39.32 5.68 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
106 108 3.604875 ATGAAGCTGGCCAAGAAATTG 57.395 42.857 7.01 0.00 0.00 2.32
245 296 7.144722 TCTAATGGTTGCAACTGAAGTATTG 57.855 36.000 27.64 10.31 0.00 1.90
467 688 0.958091 CGAAATGCAGGTTGGGTCAA 59.042 50.000 0.00 0.00 0.00 3.18
529 778 7.400339 AGAACAGATAACCTTCTTAGACCATGA 59.600 37.037 0.00 0.00 0.00 3.07
569 854 7.324375 GGTGCTTAGTAAAATAAACCGTGTTTC 59.676 37.037 5.46 0.00 0.00 2.78
605 945 2.290323 GCTTATGTCTGTGACAGGGGTT 60.290 50.000 13.33 0.00 46.04 4.11
1135 1616 7.616528 TCTCCATTTCAAATTTTCCCTTTCT 57.383 32.000 0.00 0.00 0.00 2.52
1185 1705 7.230913 CGAGGGAGAATGAAAGATAGTAGGTAA 59.769 40.741 0.00 0.00 0.00 2.85
1216 1736 6.829985 TGCATATTCATGGGGCTACTATAT 57.170 37.500 0.00 0.00 32.36 0.86
1376 1905 1.272760 TGGCGGGAATTTTGGGTGTAT 60.273 47.619 0.00 0.00 0.00 2.29
1379 1908 2.452505 CGGGAATTTTGGGTGTATGGT 58.547 47.619 0.00 0.00 0.00 3.55
2033 3521 1.414158 CGGAAGAGGCCCTAGATTCA 58.586 55.000 0.00 0.00 0.00 2.57
2153 3642 5.939883 CCACATCCTGAATGAACTTGAAGTA 59.060 40.000 0.00 0.00 38.83 2.24
2227 3717 5.116084 TCCTTCCATCCCAAACTCATAAG 57.884 43.478 0.00 0.00 0.00 1.73
2271 3761 1.869767 GCAGCTATGTGTGCCTATGAC 59.130 52.381 0.00 0.00 33.29 3.06
2343 3833 2.752903 GCCGTTGGATACTGAAACCATT 59.247 45.455 0.00 0.00 33.56 3.16
2901 7293 6.317893 TGAGCCTTATATTTTTCTTTCGTCCC 59.682 38.462 0.00 0.00 0.00 4.46
2930 7332 5.861787 ACTTTCCTGAACGAAACTTTTTGTG 59.138 36.000 0.00 0.00 35.06 3.33
3632 8100 8.353684 TCTTAGTGCGAAAAATAAAACATTCCA 58.646 29.630 0.00 0.00 0.00 3.53
3825 8305 5.003804 CCCAGTAAAAGCTCACACAGTTAT 58.996 41.667 0.00 0.00 0.00 1.89
3947 8427 9.387397 TCCCCTTTGTTATTTCTTTATTTTCCT 57.613 29.630 0.00 0.00 0.00 3.36
4350 8868 3.817709 TTGGCTTCTTTTTGTCCTTGG 57.182 42.857 0.00 0.00 0.00 3.61
4846 9396 2.265904 GGAAAGCCGTGGGGACAAC 61.266 63.158 0.00 0.00 46.06 3.32
4911 9461 1.272147 GGCCCACCTTCTGTTCTGATT 60.272 52.381 0.00 0.00 0.00 2.57
4989 9539 2.227865 GAGCCTGGCAAATAAACGTGAA 59.772 45.455 22.65 0.00 0.00 3.18
5014 9564 1.677576 TGCCTGTGAAGAGCAAAACAG 59.322 47.619 0.00 0.00 39.78 3.16
5015 9565 1.601412 GCCTGTGAAGAGCAAAACAGC 60.601 52.381 0.00 0.00 38.95 4.40
5352 10070 0.766674 ACTACCACCCCAGTGCAGAA 60.767 55.000 0.00 0.00 43.09 3.02
5628 10355 0.317160 ACGATTCTGCGAACCAGTCA 59.683 50.000 0.00 0.00 42.38 3.41
5652 10382 2.235016 CGCCGACAACGTGTTCTGT 61.235 57.895 0.00 0.00 37.88 3.41
5673 10407 3.506743 TGGAGCCCCCAGTTTGCA 61.507 61.111 0.00 0.00 40.82 4.08
5691 10426 1.338105 GCAGGCGATGACTATGGCATA 60.338 52.381 7.06 7.06 39.50 3.14
5835 10722 7.825331 TTCCAGACTTCTAGGAGTACATATG 57.175 40.000 2.82 0.00 32.11 1.78
5850 10737 8.956426 GGAGTACATATGATCTTCCTCTCTAAG 58.044 40.741 10.38 0.00 0.00 2.18
6006 10981 3.181443 ACACTTCGGTTTTCAGGATTCCT 60.181 43.478 0.00 0.00 0.00 3.36
6008 10983 4.278419 CACTTCGGTTTTCAGGATTCCTTT 59.722 41.667 1.28 0.00 0.00 3.11
6009 10984 4.893524 ACTTCGGTTTTCAGGATTCCTTTT 59.106 37.500 1.28 0.00 0.00 2.27
6010 10985 5.362717 ACTTCGGTTTTCAGGATTCCTTTTT 59.637 36.000 1.28 0.00 0.00 1.94
6042 11017 1.428912 TCTGGATTCCTTTTGCCAGGT 59.571 47.619 3.95 0.00 46.14 4.00
6150 15146 9.385902 CATCGCGTGATTTTAATTCATAGAAAT 57.614 29.630 9.17 0.00 30.49 2.17
6264 15263 8.106247 TCATTGGTACTGAAGTTTTTACATCC 57.894 34.615 0.00 0.00 0.00 3.51
6294 15293 8.682936 AGATGTACTGGAATCAATATGGTTTC 57.317 34.615 0.00 0.00 0.00 2.78
6629 15628 1.063166 GCACGCATGCCTTCTAAGC 59.937 57.895 13.15 2.09 46.97 3.09
6630 15629 1.723870 CACGCATGCCTTCTAAGCC 59.276 57.895 13.15 0.00 0.00 4.35
6631 15630 1.815421 ACGCATGCCTTCTAAGCCG 60.815 57.895 13.15 0.00 0.00 5.52
6632 15631 1.815421 CGCATGCCTTCTAAGCCGT 60.815 57.895 13.15 0.00 0.00 5.68
6633 15632 1.766143 CGCATGCCTTCTAAGCCGTC 61.766 60.000 13.15 0.00 0.00 4.79
6634 15633 1.440145 GCATGCCTTCTAAGCCGTCC 61.440 60.000 6.36 0.00 0.00 4.79
6635 15634 1.144057 ATGCCTTCTAAGCCGTCCG 59.856 57.895 0.00 0.00 0.00 4.79
6636 15635 2.202892 GCCTTCTAAGCCGTCCGG 60.203 66.667 0.24 0.24 38.57 5.14
6637 15636 3.015312 GCCTTCTAAGCCGTCCGGT 62.015 63.158 7.66 0.00 37.65 5.28
6638 15637 1.153628 CCTTCTAAGCCGTCCGGTG 60.154 63.158 7.66 0.00 37.65 4.94
6639 15638 1.601419 CCTTCTAAGCCGTCCGGTGA 61.601 60.000 7.66 0.00 37.65 4.02
6640 15639 0.460311 CTTCTAAGCCGTCCGGTGAT 59.540 55.000 7.66 0.00 37.65 3.06
6641 15640 1.679680 CTTCTAAGCCGTCCGGTGATA 59.320 52.381 7.66 0.00 37.65 2.15
6642 15641 1.315690 TCTAAGCCGTCCGGTGATAG 58.684 55.000 7.66 7.69 37.65 2.08
6643 15642 1.134007 TCTAAGCCGTCCGGTGATAGA 60.134 52.381 7.66 9.66 37.65 1.98
6644 15643 1.887198 CTAAGCCGTCCGGTGATAGAT 59.113 52.381 7.66 0.00 37.65 1.98
6645 15644 0.674534 AAGCCGTCCGGTGATAGATC 59.325 55.000 7.66 0.00 37.65 2.75
6646 15645 0.467474 AGCCGTCCGGTGATAGATCA 60.467 55.000 7.66 0.00 37.65 2.92
6647 15646 0.387929 GCCGTCCGGTGATAGATCAA 59.612 55.000 7.66 0.00 38.75 2.57
6648 15647 1.000955 GCCGTCCGGTGATAGATCAAT 59.999 52.381 7.66 0.00 38.75 2.57
6649 15648 2.548067 GCCGTCCGGTGATAGATCAATT 60.548 50.000 7.66 0.00 38.75 2.32
6650 15649 3.728845 CCGTCCGGTGATAGATCAATTT 58.271 45.455 0.00 0.00 38.75 1.82
6651 15650 4.127171 CCGTCCGGTGATAGATCAATTTT 58.873 43.478 0.00 0.00 38.75 1.82
6652 15651 5.294356 CCGTCCGGTGATAGATCAATTTTA 58.706 41.667 0.00 0.00 38.75 1.52
6653 15652 5.756347 CCGTCCGGTGATAGATCAATTTTAA 59.244 40.000 0.00 0.00 38.75 1.52
6654 15653 6.292703 CCGTCCGGTGATAGATCAATTTTAAC 60.293 42.308 0.00 0.00 38.75 2.01
6655 15654 6.292703 CGTCCGGTGATAGATCAATTTTAACC 60.293 42.308 0.00 0.00 38.75 2.85
6656 15655 5.756347 TCCGGTGATAGATCAATTTTAACCG 59.244 40.000 0.00 11.82 38.75 4.44
6657 15656 5.526111 CCGGTGATAGATCAATTTTAACCGT 59.474 40.000 15.37 0.00 38.75 4.83
6658 15657 6.037830 CCGGTGATAGATCAATTTTAACCGTT 59.962 38.462 15.37 0.00 38.75 4.44
6659 15658 7.414762 CCGGTGATAGATCAATTTTAACCGTTT 60.415 37.037 15.37 0.00 38.75 3.60
6660 15659 7.428183 CGGTGATAGATCAATTTTAACCGTTTG 59.572 37.037 11.01 0.00 38.75 2.93
6661 15660 8.455682 GGTGATAGATCAATTTTAACCGTTTGA 58.544 33.333 0.00 0.00 38.75 2.69
6667 15666 9.191995 AGATCAATTTTAACCGTTTGATTTCAC 57.808 29.630 0.00 0.00 38.55 3.18
6668 15667 9.191995 GATCAATTTTAACCGTTTGATTTCACT 57.808 29.630 0.00 0.00 38.55 3.41
6669 15668 8.346476 TCAATTTTAACCGTTTGATTTCACTG 57.654 30.769 0.00 0.00 0.00 3.66
6670 15669 7.976734 TCAATTTTAACCGTTTGATTTCACTGT 59.023 29.630 0.00 0.00 0.00 3.55
6671 15670 7.924103 ATTTTAACCGTTTGATTTCACTGTC 57.076 32.000 0.00 0.00 0.00 3.51
6672 15671 3.982576 AACCGTTTGATTTCACTGTCC 57.017 42.857 0.00 0.00 0.00 4.02
6673 15672 3.208747 ACCGTTTGATTTCACTGTCCT 57.791 42.857 0.00 0.00 0.00 3.85
6674 15673 2.878406 ACCGTTTGATTTCACTGTCCTG 59.122 45.455 0.00 0.00 0.00 3.86
6675 15674 2.350772 CCGTTTGATTTCACTGTCCTGC 60.351 50.000 0.00 0.00 0.00 4.85
6676 15675 2.662791 CGTTTGATTTCACTGTCCTGCG 60.663 50.000 0.00 0.00 0.00 5.18
6677 15676 1.522668 TTGATTTCACTGTCCTGCGG 58.477 50.000 0.00 0.00 0.00 5.69
6678 15677 0.396435 TGATTTCACTGTCCTGCGGT 59.604 50.000 0.00 0.00 37.11 5.68
6679 15678 1.621317 TGATTTCACTGTCCTGCGGTA 59.379 47.619 0.00 0.00 34.32 4.02
6680 15679 2.271800 GATTTCACTGTCCTGCGGTAG 58.728 52.381 0.00 0.00 34.32 3.18
6681 15680 1.334160 TTTCACTGTCCTGCGGTAGA 58.666 50.000 0.00 0.00 34.32 2.59
6682 15681 1.557099 TTCACTGTCCTGCGGTAGAT 58.443 50.000 0.00 0.00 34.32 1.98
6683 15682 1.557099 TCACTGTCCTGCGGTAGATT 58.443 50.000 0.00 0.00 34.32 2.40
6684 15683 1.899814 TCACTGTCCTGCGGTAGATTT 59.100 47.619 0.00 0.00 34.32 2.17
6685 15684 2.301870 TCACTGTCCTGCGGTAGATTTT 59.698 45.455 0.00 0.00 34.32 1.82
6686 15685 2.416547 CACTGTCCTGCGGTAGATTTTG 59.583 50.000 0.00 0.00 34.32 2.44
6687 15686 2.038557 ACTGTCCTGCGGTAGATTTTGT 59.961 45.455 0.00 0.00 34.32 2.83
6688 15687 2.416547 CTGTCCTGCGGTAGATTTTGTG 59.583 50.000 0.00 0.00 0.00 3.33
6689 15688 2.037902 TGTCCTGCGGTAGATTTTGTGA 59.962 45.455 0.00 0.00 0.00 3.58
6690 15689 2.415512 GTCCTGCGGTAGATTTTGTGAC 59.584 50.000 0.00 0.00 0.00 3.67
6691 15690 2.037902 TCCTGCGGTAGATTTTGTGACA 59.962 45.455 0.00 0.00 0.00 3.58
6692 15691 2.159627 CCTGCGGTAGATTTTGTGACAC 59.840 50.000 0.00 0.00 0.00 3.67
6693 15692 3.067106 CTGCGGTAGATTTTGTGACACT 58.933 45.455 7.20 0.00 0.00 3.55
6694 15693 2.805671 TGCGGTAGATTTTGTGACACTG 59.194 45.455 7.20 0.00 0.00 3.66
6695 15694 3.064207 GCGGTAGATTTTGTGACACTGA 58.936 45.455 7.20 0.00 0.00 3.41
6696 15695 3.496884 GCGGTAGATTTTGTGACACTGAA 59.503 43.478 7.20 2.10 0.00 3.02
6697 15696 4.154195 GCGGTAGATTTTGTGACACTGAAT 59.846 41.667 7.20 6.89 0.00 2.57
6698 15697 5.334879 GCGGTAGATTTTGTGACACTGAATT 60.335 40.000 7.20 0.00 0.00 2.17
6699 15698 6.307155 CGGTAGATTTTGTGACACTGAATTC 58.693 40.000 7.20 0.00 0.00 2.17
6700 15699 6.147821 CGGTAGATTTTGTGACACTGAATTCT 59.852 38.462 7.20 13.45 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 18 7.928706 GTCATGCATACCAAGAATTCTACTACT 59.071 37.037 8.75 0.00 0.00 2.57
106 108 7.148222 GGAAAAAGTCTGGAGAGTAAATAAGGC 60.148 40.741 0.00 0.00 0.00 4.35
438 659 4.946784 ACCTGCATTTCGAATAGTCAAC 57.053 40.909 0.00 0.00 0.00 3.18
467 688 2.485302 GCTTTTGGCACACCCTTTGATT 60.485 45.455 0.00 0.00 39.29 2.57
529 778 6.613153 ACTAAGCACCTCTCTAAGATTGTT 57.387 37.500 0.00 0.00 0.00 2.83
802 1263 8.896722 AAGGACAAGAACTTAAGGAGTATAGA 57.103 34.615 7.53 0.00 37.72 1.98
1135 1616 5.476091 AACACAACTTCCTTTTTGGACAA 57.524 34.783 0.00 0.00 46.14 3.18
1185 1705 5.131475 AGCCCCATGAATATGCAAAATCTTT 59.869 36.000 0.00 0.00 32.79 2.52
1376 1905 1.034838 AACTTCACGCCAAGCAACCA 61.035 50.000 0.00 0.00 0.00 3.67
1379 1908 0.102120 CCAAACTTCACGCCAAGCAA 59.898 50.000 0.00 0.00 0.00 3.91
1958 3429 8.098912 ACTTTGGAGAGTAAACACCGTATTATT 58.901 33.333 0.00 0.00 0.00 1.40
1963 3434 4.942761 ACTTTGGAGAGTAAACACCGTA 57.057 40.909 0.00 0.00 0.00 4.02
2060 3549 4.342378 TCCGCTACTATCAAATCAAGCTCT 59.658 41.667 0.00 0.00 0.00 4.09
2153 3642 5.171339 ACAAATGCTTACTGATGAGAGGT 57.829 39.130 0.00 0.00 0.00 3.85
2206 3696 4.860022 ACTTATGAGTTTGGGATGGAAGG 58.140 43.478 0.00 0.00 29.87 3.46
2227 3717 3.498777 GCCAAGAAACAACACTCCTAGAC 59.501 47.826 0.00 0.00 0.00 2.59
2288 3778 1.428912 ACCATGTTCCAAGGGTCATGT 59.571 47.619 16.62 7.82 35.90 3.21
2307 3797 3.305110 CAACGGCTTAACCACATTGAAC 58.695 45.455 0.00 0.00 39.03 3.18
2343 3833 6.111382 CAGTGCTCTCATCCTCAGAAAATTA 58.889 40.000 0.00 0.00 0.00 1.40
2901 7293 3.003689 AGTTTCGTTCAGGAAAGTGCATG 59.996 43.478 0.00 0.00 37.97 4.06
3825 8305 0.038021 TTAGCATGTGAGCTTGCCCA 59.962 50.000 4.49 0.00 43.70 5.36
3947 8427 6.399743 TGACGCAGGTATAAGACATAACAAA 58.600 36.000 0.00 0.00 0.00 2.83
3948 8428 5.968254 TGACGCAGGTATAAGACATAACAA 58.032 37.500 0.00 0.00 0.00 2.83
3949 8429 5.126545 ACTGACGCAGGTATAAGACATAACA 59.873 40.000 10.80 0.00 35.51 2.41
3950 8430 5.589192 ACTGACGCAGGTATAAGACATAAC 58.411 41.667 10.80 0.00 35.51 1.89
3951 8431 5.847111 ACTGACGCAGGTATAAGACATAA 57.153 39.130 10.80 0.00 35.51 1.90
3952 8432 6.060136 AGTACTGACGCAGGTATAAGACATA 58.940 40.000 10.80 0.00 35.51 2.29
4268 8776 6.731292 ATAAGGCCCCAATTTAACAGAATC 57.269 37.500 0.00 0.00 0.00 2.52
4350 8868 5.986004 AGAGTACAAACAAACACTAGCAC 57.014 39.130 0.00 0.00 0.00 4.40
4599 9134 5.529289 TGATAACCCTGAGATAACCTCTGT 58.471 41.667 0.00 0.00 42.44 3.41
4846 9396 3.787001 GGCCGAACTCTCCCCCAG 61.787 72.222 0.00 0.00 0.00 4.45
4911 9461 3.563261 CCCAAATGGACTTGGTACCATGA 60.563 47.826 29.21 10.26 44.79 3.07
4989 9539 1.302351 GCTCTTCACAGGCAGCACT 60.302 57.895 0.00 0.00 0.00 4.40
5014 9564 3.653344 TCTTGCGTCCATATACATCAGC 58.347 45.455 0.00 0.00 0.00 4.26
5015 9565 6.791887 AAATCTTGCGTCCATATACATCAG 57.208 37.500 0.00 0.00 0.00 2.90
5214 9807 3.188786 GCGTGCACCTCGTCCATC 61.189 66.667 12.15 0.00 0.00 3.51
5352 10070 0.607489 AAGGCTCAGACTGCGCATTT 60.607 50.000 18.55 9.63 26.81 2.32
5376 10094 0.747255 ACTCATCCCAATCCGAGTCG 59.253 55.000 5.29 5.29 33.49 4.18
5614 10341 2.343758 GCCTGACTGGTTCGCAGA 59.656 61.111 0.00 0.00 38.35 4.26
5673 10407 1.276421 GGTATGCCATAGTCATCGCCT 59.724 52.381 0.00 0.00 34.09 5.52
5903 10792 3.085443 AGAACTGACACACTTCACTCG 57.915 47.619 0.00 0.00 0.00 4.18
5905 10794 6.349777 GCTAGATAGAACTGACACACTTCACT 60.350 42.308 0.00 0.00 0.00 3.41
5907 10796 5.105716 GGCTAGATAGAACTGACACACTTCA 60.106 44.000 0.00 0.00 0.00 3.02
6008 10983 5.599242 AGGAATCCAGAAAACCCGTTAAAAA 59.401 36.000 0.61 0.00 0.00 1.94
6009 10984 5.141910 AGGAATCCAGAAAACCCGTTAAAA 58.858 37.500 0.61 0.00 0.00 1.52
6010 10985 4.732065 AGGAATCCAGAAAACCCGTTAAA 58.268 39.130 0.61 0.00 0.00 1.52
6011 10986 4.376225 AGGAATCCAGAAAACCCGTTAA 57.624 40.909 0.61 0.00 0.00 2.01
6012 10987 4.376225 AAGGAATCCAGAAAACCCGTTA 57.624 40.909 0.61 0.00 0.00 3.18
6013 10988 2.971901 AGGAATCCAGAAAACCCGTT 57.028 45.000 0.61 0.00 0.00 4.44
6014 10989 2.971901 AAGGAATCCAGAAAACCCGT 57.028 45.000 0.61 0.00 0.00 5.28
6015 10990 3.860754 GCAAAAGGAATCCAGAAAACCCG 60.861 47.826 0.61 0.00 0.00 5.28
6016 10991 3.557054 GGCAAAAGGAATCCAGAAAACCC 60.557 47.826 0.61 0.00 0.00 4.11
6024 10999 2.397044 AACCTGGCAAAAGGAATCCA 57.603 45.000 0.61 0.00 40.02 3.41
6150 15146 8.587608 AGAGTGCAAATAAATCCTCATTGAAAA 58.412 29.630 0.00 0.00 0.00 2.29
6264 15263 9.212641 CCATATTGATTCCAGTACATCTTACAG 57.787 37.037 0.00 0.00 0.00 2.74
6620 15619 1.153628 CACCGGACGGCTTAGAAGG 60.154 63.158 9.46 0.00 39.32 3.46
6621 15620 0.460311 ATCACCGGACGGCTTAGAAG 59.540 55.000 9.46 0.00 39.32 2.85
6622 15621 1.679680 CTATCACCGGACGGCTTAGAA 59.320 52.381 9.46 0.00 39.32 2.10
6623 15622 1.134007 TCTATCACCGGACGGCTTAGA 60.134 52.381 9.46 11.37 39.32 2.10
6624 15623 1.315690 TCTATCACCGGACGGCTTAG 58.684 55.000 9.46 9.33 39.32 2.18
6625 15624 1.884579 GATCTATCACCGGACGGCTTA 59.115 52.381 9.46 0.00 39.32 3.09
6626 15625 0.674534 GATCTATCACCGGACGGCTT 59.325 55.000 9.46 0.00 39.32 4.35
6627 15626 0.467474 TGATCTATCACCGGACGGCT 60.467 55.000 9.46 0.00 39.32 5.52
6628 15627 0.387929 TTGATCTATCACCGGACGGC 59.612 55.000 9.46 0.00 39.32 5.68
6629 15628 3.386768 AATTGATCTATCACCGGACGG 57.613 47.619 9.46 9.56 36.36 4.79
6630 15629 6.292703 GGTTAAAATTGATCTATCACCGGACG 60.293 42.308 9.46 0.00 36.36 4.79
6631 15630 6.292703 CGGTTAAAATTGATCTATCACCGGAC 60.293 42.308 9.46 0.00 36.36 4.79
6632 15631 5.756347 CGGTTAAAATTGATCTATCACCGGA 59.244 40.000 9.46 0.00 36.36 5.14
6633 15632 5.526111 ACGGTTAAAATTGATCTATCACCGG 59.474 40.000 22.05 0.00 39.38 5.28
6634 15633 6.598753 ACGGTTAAAATTGATCTATCACCG 57.401 37.500 19.18 19.18 40.27 4.94
6635 15634 8.455682 TCAAACGGTTAAAATTGATCTATCACC 58.544 33.333 0.00 0.00 36.36 4.02
6641 15640 9.191995 GTGAAATCAAACGGTTAAAATTGATCT 57.808 29.630 5.69 0.00 40.58 2.75
6642 15641 9.191995 AGTGAAATCAAACGGTTAAAATTGATC 57.808 29.630 5.69 0.00 40.58 2.92
6643 15642 8.977505 CAGTGAAATCAAACGGTTAAAATTGAT 58.022 29.630 0.00 0.00 42.61 2.57
6644 15643 7.976734 ACAGTGAAATCAAACGGTTAAAATTGA 59.023 29.630 0.00 0.00 36.35 2.57
6645 15644 8.125728 ACAGTGAAATCAAACGGTTAAAATTG 57.874 30.769 0.00 0.00 0.00 2.32
6646 15645 7.436970 GGACAGTGAAATCAAACGGTTAAAATT 59.563 33.333 0.00 0.00 0.00 1.82
6647 15646 6.921307 GGACAGTGAAATCAAACGGTTAAAAT 59.079 34.615 0.00 0.00 0.00 1.82
6648 15647 6.095720 AGGACAGTGAAATCAAACGGTTAAAA 59.904 34.615 0.00 0.00 0.00 1.52
6649 15648 5.591067 AGGACAGTGAAATCAAACGGTTAAA 59.409 36.000 0.00 0.00 0.00 1.52
6650 15649 5.008217 CAGGACAGTGAAATCAAACGGTTAA 59.992 40.000 0.00 0.00 0.00 2.01
6651 15650 4.513692 CAGGACAGTGAAATCAAACGGTTA 59.486 41.667 0.00 0.00 0.00 2.85
6652 15651 3.315191 CAGGACAGTGAAATCAAACGGTT 59.685 43.478 0.00 0.00 0.00 4.44
6653 15652 2.878406 CAGGACAGTGAAATCAAACGGT 59.122 45.455 0.00 0.00 0.00 4.83
6654 15653 2.350772 GCAGGACAGTGAAATCAAACGG 60.351 50.000 0.00 0.00 0.00 4.44
6655 15654 2.662791 CGCAGGACAGTGAAATCAAACG 60.663 50.000 0.00 0.00 0.00 3.60
6656 15655 2.921126 CGCAGGACAGTGAAATCAAAC 58.079 47.619 0.00 0.00 0.00 2.93
6672 15671 3.067106 AGTGTCACAAAATCTACCGCAG 58.933 45.455 5.62 0.00 0.00 5.18
6673 15672 2.805671 CAGTGTCACAAAATCTACCGCA 59.194 45.455 5.62 0.00 0.00 5.69
6674 15673 3.064207 TCAGTGTCACAAAATCTACCGC 58.936 45.455 5.62 0.00 0.00 5.68
6675 15674 5.862924 ATTCAGTGTCACAAAATCTACCG 57.137 39.130 5.62 0.00 0.00 4.02
6676 15675 7.440523 AGAATTCAGTGTCACAAAATCTACC 57.559 36.000 8.44 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.