Multiple sequence alignment - TraesCS7D01G369900

Loading Multiple Alignment...

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 TraesCS7D01G369900 chr7D 100.000 3174 0 0 1 3174 478573602 478570429 0.000000e+00 5862.0
1 TraesCS7D01G369900 chr7D 87.123 2089 159 68 394 2389 478326916 478328987 0.000000e+00 2266.0
2 TraesCS7D01G369900 chr7D 88.235 782 86 5 2392 3171 442798642 442797865 0.000000e+00 929.0
3 TraesCS7D01G369900 chr7D 77.755 481 85 20 1644 2110 579099707 579099235 3.120000e-70 276.0
4 TraesCS7D01G369900 chr7D 88.038 209 21 4 2969 3174 442797990 442797783 8.790000e-61 244.0
5 TraesCS7D01G369900 chr7D 88.950 181 18 1 2069 2249 478532693 478532515 4.120000e-54 222.0
6 TraesCS7D01G369900 chr7D 74.606 508 101 21 1620 2110 75948190 75948686 6.940000e-47 198.0
7 TraesCS7D01G369900 chr7D 75.854 410 75 21 1114 1514 478370385 478370779 1.500000e-43 187.0
8 TraesCS7D01G369900 chr7D 92.079 101 5 1 1 101 388125214 388125311 4.270000e-29 139.0
9 TraesCS7D01G369900 chr7D 90.099 101 7 1 1 101 393037855 393037758 9.240000e-26 128.0
10 TraesCS7D01G369900 chr7D 86.179 123 12 2 275 392 478326755 478326877 9.240000e-26 128.0
11 TraesCS7D01G369900 chr7A 88.014 2261 165 54 198 2391 516999040 516996819 0.000000e+00 2577.0
12 TraesCS7D01G369900 chr7A 84.608 2105 176 72 326 2337 517415525 517413476 0.000000e+00 1956.0
13 TraesCS7D01G369900 chr7A 86.667 285 38 0 2392 2676 714860394 714860678 1.840000e-82 316.0
14 TraesCS7D01G369900 chr7A 77.559 508 90 20 1618 2110 670946630 670946132 5.180000e-73 285.0
15 TraesCS7D01G369900 chr7A 87.879 132 13 3 193 323 517416568 517416439 5.480000e-33 152.0
16 TraesCS7D01G369900 chr7A 93.056 72 3 1 103 172 517416774 517416703 1.560000e-18 104.0
17 TraesCS7D01G369900 chr7A 79.730 148 15 7 3041 3174 714861615 714861761 3.370000e-15 93.5
18 TraesCS7D01G369900 chr7A 77.358 159 33 3 1074 1231 516873294 516873138 1.210000e-14 91.6
19 TraesCS7D01G369900 chr7A 88.060 67 6 2 2326 2391 517413259 517413194 9.440000e-11 78.7
20 TraesCS7D01G369900 chr7B 90.893 1120 65 20 1305 2389 503472862 503473979 0.000000e+00 1469.0
21 TraesCS7D01G369900 chr7B 92.773 678 36 7 1305 1969 504244335 504243658 0.000000e+00 968.0
22 TraesCS7D01G369900 chr7B 83.010 877 85 30 394 1230 503471898 503472750 0.000000e+00 736.0
23 TraesCS7D01G369900 chr7B 83.069 821 45 46 446 1230 504245210 504244448 0.000000e+00 660.0
24 TraesCS7D01G369900 chr7B 94.000 350 17 3 1965 2314 504237787 504237442 7.800000e-146 527.0
25 TraesCS7D01G369900 chr7B 87.714 350 27 4 103 448 504246424 504246087 8.250000e-106 394.0
26 TraesCS7D01G369900 chr7B 77.708 480 87 18 1644 2110 643292135 643291663 3.120000e-70 276.0
27 TraesCS7D01G369900 chr7B 77.014 509 87 25 1618 2110 643462863 643463357 6.750000e-67 265.0
28 TraesCS7D01G369900 chr7B 82.237 304 18 15 103 405 503471612 503471880 2.460000e-56 230.0
29 TraesCS7D01G369900 chr7B 93.617 47 0 3 2348 2391 375543305 375543351 2.040000e-07 67.6
30 TraesCS7D01G369900 chr1B 88.539 794 74 9 2392 3173 28497823 28498611 0.000000e+00 946.0
31 TraesCS7D01G369900 chr1B 89.147 129 13 1 3046 3174 28498400 28498527 3.280000e-35 159.0
32 TraesCS7D01G369900 chr4B 79.732 597 100 14 2410 2991 12438449 12439039 2.280000e-111 412.0
33 TraesCS7D01G369900 chr4B 88.889 108 10 1 2286 2391 283206984 283207091 7.140000e-27 132.0
34 TraesCS7D01G369900 chr6B 86.667 345 43 3 2391 2734 692021809 692021467 2.310000e-101 379.0
35 TraesCS7D01G369900 chr6B 83.700 227 36 1 2392 2618 41564536 41564761 2.480000e-51 213.0
36 TraesCS7D01G369900 chr6B 75.940 399 69 20 1123 1514 173391805 173392183 2.520000e-41 180.0
37 TraesCS7D01G369900 chr6B 92.079 101 5 1 1 101 39059055 39058958 4.270000e-29 139.0
38 TraesCS7D01G369900 chr6B 88.889 108 10 1 2286 2391 591329477 591329584 7.140000e-27 132.0
39 TraesCS7D01G369900 chr6B 90.099 101 7 2 1 101 32582266 32582363 9.240000e-26 128.0
40 TraesCS7D01G369900 chr5B 84.503 342 33 3 2392 2733 419767712 419767391 1.420000e-83 320.0
41 TraesCS7D01G369900 chr5B 91.057 123 11 0 3052 3174 419767397 419767275 1.960000e-37 167.0
42 TraesCS7D01G369900 chr5B 93.000 100 7 0 1 100 701795690 701795591 2.550000e-31 147.0
43 TraesCS7D01G369900 chr5B 91.089 101 6 1 1 101 439957794 439957697 1.990000e-27 134.0
44 TraesCS7D01G369900 chr5B 93.617 47 0 1 2348 2391 381102308 381102354 2.040000e-07 67.6
45 TraesCS7D01G369900 chr6D 76.078 510 90 25 1620 2110 25804450 25803954 1.470000e-58 237.0
46 TraesCS7D01G369900 chr6D 82.828 198 34 0 1317 1514 90922940 90923137 9.050000e-41 178.0
47 TraesCS7D01G369900 chr6D 83.333 102 17 0 1123 1224 90922746 90922847 9.370000e-16 95.3
48 TraesCS7D01G369900 chrUn 85.022 227 33 1 2392 2618 22824623 22824398 2.460000e-56 230.0
49 TraesCS7D01G369900 chr2A 84.141 227 36 0 2392 2618 723886745 723886519 1.480000e-53 220.0
50 TraesCS7D01G369900 chr4A 83.691 233 37 1 2386 2618 714073431 714073200 5.330000e-53 219.0
51 TraesCS7D01G369900 chr4A 92.157 102 5 1 1 102 701570706 701570608 1.190000e-29 141.0
52 TraesCS7D01G369900 chr3A 83.654 208 34 0 1317 1524 113922265 113922058 2.500000e-46 196.0
53 TraesCS7D01G369900 chr6A 82.828 198 34 0 1317 1514 109135962 109136159 9.050000e-41 178.0
54 TraesCS7D01G369900 chr6A 82.353 102 18 0 1123 1224 109135768 109135869 4.360000e-14 89.8
55 TraesCS7D01G369900 chr3D 93.069 101 7 0 1 101 367411367 367411467 7.090000e-32 148.0
56 TraesCS7D01G369900 chr2B 91.089 101 6 1 1 101 762068121 762068218 1.990000e-27 134.0


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 TraesCS7D01G369900 chr7D 478570429 478573602 3173 True 5862.000000 5862 100.00000 1 3174 1 chr7D.!!$R3 3173
1 TraesCS7D01G369900 chr7D 478326755 478328987 2232 False 1197.000000 2266 86.65100 275 2389 2 chr7D.!!$F4 2114
2 TraesCS7D01G369900 chr7D 442797783 442798642 859 True 586.500000 929 88.13650 2392 3174 2 chr7D.!!$R5 782
3 TraesCS7D01G369900 chr7A 516996819 516999040 2221 True 2577.000000 2577 88.01400 198 2391 1 chr7A.!!$R2 2193
4 TraesCS7D01G369900 chr7A 517413194 517416774 3580 True 572.675000 1956 88.40075 103 2391 4 chr7A.!!$R4 2288
5 TraesCS7D01G369900 chr7A 714860394 714861761 1367 False 204.750000 316 83.19850 2392 3174 2 chr7A.!!$F1 782
6 TraesCS7D01G369900 chr7B 503471612 503473979 2367 False 811.666667 1469 85.38000 103 2389 3 chr7B.!!$F3 2286
7 TraesCS7D01G369900 chr7B 504243658 504246424 2766 True 674.000000 968 87.85200 103 1969 3 chr7B.!!$R3 1866
8 TraesCS7D01G369900 chr1B 28497823 28498611 788 False 552.500000 946 88.84300 2392 3174 2 chr1B.!!$F1 782
9 TraesCS7D01G369900 chr4B 12438449 12439039 590 False 412.000000 412 79.73200 2410 2991 1 chr4B.!!$F1 581

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
694 2773 0.107654 AATAGTTCAGGGGAGTGCGC 60.108 55.0 0.0 0.0 0.00 6.09 F
1846 4050 0.793861 GCAACCGCATCTACAACGAA 59.206 50.0 0.0 0.0 38.36 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2155 4359 0.480690 TTTAGTTGGGCCTCCTGCAA 59.519 50.0 4.53 0.0 43.89 4.08 R
2849 6137 0.610174 TGCGTGGATCAGCTCTCTTT 59.390 50.0 8.21 0.0 0.00 2.52 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
70 71 2.274432 GGGTTTCCCCCGATCCAC 59.726 66.667 0.00 0.00 45.80 4.02
71 72 2.608550 GGGTTTCCCCCGATCCACA 61.609 63.158 0.00 0.00 45.80 4.17
72 73 1.381076 GGTTTCCCCCGATCCACAA 59.619 57.895 0.00 0.00 0.00 3.33
73 74 0.963856 GGTTTCCCCCGATCCACAAC 60.964 60.000 0.00 0.00 0.00 3.32
74 75 0.963856 GTTTCCCCCGATCCACAACC 60.964 60.000 0.00 0.00 0.00 3.77
75 76 1.427895 TTTCCCCCGATCCACAACCA 61.428 55.000 0.00 0.00 0.00 3.67
76 77 2.045340 CCCCCGATCCACAACCAC 60.045 66.667 0.00 0.00 0.00 4.16
77 78 2.045340 CCCCGATCCACAACCACC 60.045 66.667 0.00 0.00 0.00 4.61
78 79 2.753701 CCCGATCCACAACCACCA 59.246 61.111 0.00 0.00 0.00 4.17
79 80 1.674322 CCCGATCCACAACCACCAC 60.674 63.158 0.00 0.00 0.00 4.16
80 81 1.674322 CCGATCCACAACCACCACC 60.674 63.158 0.00 0.00 0.00 4.61
81 82 1.072332 CGATCCACAACCACCACCA 59.928 57.895 0.00 0.00 0.00 4.17
82 83 1.234615 CGATCCACAACCACCACCAC 61.235 60.000 0.00 0.00 0.00 4.16
83 84 0.893727 GATCCACAACCACCACCACC 60.894 60.000 0.00 0.00 0.00 4.61
84 85 1.650242 ATCCACAACCACCACCACCA 61.650 55.000 0.00 0.00 0.00 4.17
85 86 2.124693 CCACAACCACCACCACCAC 61.125 63.158 0.00 0.00 0.00 4.16
86 87 2.124693 CACAACCACCACCACCACC 61.125 63.158 0.00 0.00 0.00 4.61
87 88 2.277072 CAACCACCACCACCACCA 59.723 61.111 0.00 0.00 0.00 4.17
88 89 2.124693 CAACCACCACCACCACCAC 61.125 63.158 0.00 0.00 0.00 4.16
89 90 3.367907 AACCACCACCACCACCACC 62.368 63.158 0.00 0.00 0.00 4.61
90 91 3.498071 CCACCACCACCACCACCT 61.498 66.667 0.00 0.00 0.00 4.00
91 92 2.113139 CACCACCACCACCACCTC 59.887 66.667 0.00 0.00 0.00 3.85
92 93 2.367648 ACCACCACCACCACCTCA 60.368 61.111 0.00 0.00 0.00 3.86
93 94 2.113139 CCACCACCACCACCTCAC 59.887 66.667 0.00 0.00 0.00 3.51
94 95 2.280797 CACCACCACCACCTCACG 60.281 66.667 0.00 0.00 0.00 4.35
95 96 4.250305 ACCACCACCACCTCACGC 62.250 66.667 0.00 0.00 0.00 5.34
96 97 4.248842 CCACCACCACCTCACGCA 62.249 66.667 0.00 0.00 0.00 5.24
97 98 2.032528 CACCACCACCTCACGCAT 59.967 61.111 0.00 0.00 0.00 4.73
98 99 1.600636 CACCACCACCTCACGCATT 60.601 57.895 0.00 0.00 0.00 3.56
99 100 1.150536 ACCACCACCTCACGCATTT 59.849 52.632 0.00 0.00 0.00 2.32
100 101 0.889186 ACCACCACCTCACGCATTTC 60.889 55.000 0.00 0.00 0.00 2.17
101 102 0.888736 CCACCACCTCACGCATTTCA 60.889 55.000 0.00 0.00 0.00 2.69
116 117 3.572255 GCATTTCACCAACCTTTCCACTA 59.428 43.478 0.00 0.00 0.00 2.74
181 184 6.920569 AGGGTAGCGAAATACAATAGTTTG 57.079 37.500 0.00 0.00 38.86 2.93
214 331 4.657436 ATTGTCGTCCTATCTCCAGAAC 57.343 45.455 0.00 0.00 0.00 3.01
215 332 2.014857 TGTCGTCCTATCTCCAGAACG 58.985 52.381 0.00 0.00 0.00 3.95
266 383 3.204827 GCGATGCAATGCCGTCCT 61.205 61.111 1.53 0.00 0.00 3.85
267 384 2.711311 CGATGCAATGCCGTCCTG 59.289 61.111 1.53 0.00 0.00 3.86
268 385 1.815003 CGATGCAATGCCGTCCTGA 60.815 57.895 1.53 0.00 0.00 3.86
269 386 1.723870 GATGCAATGCCGTCCTGAC 59.276 57.895 1.53 0.00 0.00 3.51
295 424 3.444703 ACTCTACGATCAGTTGATGCC 57.555 47.619 0.00 0.00 34.33 4.40
303 432 1.953559 TCAGTTGATGCCGGATTAGC 58.046 50.000 5.05 0.00 0.00 3.09
304 433 1.209261 TCAGTTGATGCCGGATTAGCA 59.791 47.619 5.05 0.00 45.94 3.49
312 442 2.571212 TGCCGGATTAGCATACCTTTG 58.429 47.619 5.05 0.00 34.69 2.77
346 1387 0.183492 TGATTCATGGGCCAGCCTAC 59.817 55.000 13.78 4.10 36.10 3.18
405 1485 8.850156 ACAATAAAATATAGAATGAGTGGTGCC 58.150 33.333 0.00 0.00 0.00 5.01
489 2495 3.056458 TGCACCGTGGTGGAGTAG 58.944 61.111 20.00 0.00 45.49 2.57
523 2529 0.684535 TCAGCAACATTCGGTCCTCA 59.315 50.000 0.00 0.00 0.00 3.86
534 2544 1.729470 CGGTCCTCATCCTCAGTCCG 61.729 65.000 0.00 0.00 0.00 4.79
540 2550 0.606096 TCATCCTCAGTCCGCGAAAA 59.394 50.000 8.23 0.00 0.00 2.29
568 2584 2.507324 GCGCCGACTCAGAGGAAC 60.507 66.667 1.53 0.00 0.00 3.62
609 2635 0.526954 CTATACCCGTGACGTGCACC 60.527 60.000 12.15 0.00 44.85 5.01
642 2672 6.309251 GTCTCTGCGCTCTTATAATATTCCAC 59.691 42.308 9.73 0.00 0.00 4.02
693 2772 1.656652 CAATAGTTCAGGGGAGTGCG 58.343 55.000 0.00 0.00 0.00 5.34
694 2773 0.107654 AATAGTTCAGGGGAGTGCGC 60.108 55.000 0.00 0.00 0.00 6.09
695 2774 1.264749 ATAGTTCAGGGGAGTGCGCA 61.265 55.000 5.66 5.66 0.00 6.09
696 2775 1.264749 TAGTTCAGGGGAGTGCGCAT 61.265 55.000 15.91 1.95 0.00 4.73
754 2837 4.227134 ATGCCGGAGCGAGCGATT 62.227 61.111 5.05 0.00 44.31 3.34
890 2985 2.507992 CCTGCTTCCACGAGCTCG 60.508 66.667 33.45 33.45 43.11 5.03
891 2986 2.568612 CTGCTTCCACGAGCTCGA 59.431 61.111 40.58 17.82 43.11 4.04
962 3087 3.742882 TCGAGCTCACATCAAAAGAGTTG 59.257 43.478 15.40 0.00 0.00 3.16
980 3105 4.537751 AGTTGCCTCTAGCTAGTCACATA 58.462 43.478 20.10 0.00 44.23 2.29
1065 3192 2.807045 GTGCTCTGTGTCCTCGCG 60.807 66.667 0.00 0.00 0.00 5.87
1236 3388 3.365220 GCTTCGTCAATGTGAGTACTGTC 59.635 47.826 0.00 0.00 0.00 3.51
1247 3422 3.554324 GTGAGTACTGTCGTTTGCTTTGA 59.446 43.478 0.00 0.00 0.00 2.69
1275 3451 3.611766 AGCTGCTGGATTTTACGTACT 57.388 42.857 0.00 0.00 0.00 2.73
1276 3452 4.730949 AGCTGCTGGATTTTACGTACTA 57.269 40.909 0.00 0.00 0.00 1.82
1277 3453 4.430908 AGCTGCTGGATTTTACGTACTAC 58.569 43.478 0.00 0.00 0.00 2.73
1291 3467 4.268767 CGTACTACGTGCTGAGTAATGA 57.731 45.455 0.00 0.00 36.74 2.57
1292 3468 4.272480 CGTACTACGTGCTGAGTAATGAG 58.728 47.826 0.00 0.00 36.74 2.90
1295 3471 5.487153 ACTACGTGCTGAGTAATGAGTAG 57.513 43.478 0.00 0.00 37.09 2.57
1296 3472 5.183969 ACTACGTGCTGAGTAATGAGTAGA 58.816 41.667 0.00 0.00 35.59 2.59
1298 3474 4.011023 ACGTGCTGAGTAATGAGTAGAGT 58.989 43.478 0.00 0.00 0.00 3.24
1299 3475 5.183969 ACGTGCTGAGTAATGAGTAGAGTA 58.816 41.667 0.00 0.00 0.00 2.59
1300 3476 5.064962 ACGTGCTGAGTAATGAGTAGAGTAC 59.935 44.000 0.00 0.00 0.00 2.73
1302 3478 6.479331 CGTGCTGAGTAATGAGTAGAGTACTA 59.521 42.308 0.00 0.00 39.59 1.82
1303 3479 7.011202 CGTGCTGAGTAATGAGTAGAGTACTAA 59.989 40.741 0.00 0.00 39.59 2.24
1540 3724 2.517450 GCGCGCGACTAGCTTCAAT 61.517 57.895 37.18 0.00 45.59 2.57
1586 3777 6.702329 ACTACTACTTCTGCACTTATTTGCT 58.298 36.000 0.00 0.00 43.41 3.91
1589 3789 9.319143 CTACTACTTCTGCACTTATTTGCTATT 57.681 33.333 0.00 0.00 43.41 1.73
1590 3790 8.567285 ACTACTTCTGCACTTATTTGCTATTT 57.433 30.769 0.00 0.00 43.41 1.40
1595 3795 7.880160 TCTGCACTTATTTGCTATTTATGGT 57.120 32.000 0.00 0.00 43.41 3.55
1636 3840 3.036429 GCAGCTCGGAGGTCCCAAT 62.036 63.158 6.76 0.00 34.14 3.16
1846 4050 0.793861 GCAACCGCATCTACAACGAA 59.206 50.000 0.00 0.00 38.36 3.85
2005 4209 3.474570 GGCCTCCTGCACTCGGAT 61.475 66.667 0.00 0.00 43.89 4.18
2110 4314 1.228228 GGCCATGCTGAAGATGGGA 59.772 57.895 0.00 0.00 40.80 4.37
2155 4359 0.616111 AGACGGAGGTCAGGCTGAAT 60.616 55.000 20.62 11.21 45.92 2.57
2225 4431 5.486735 AATGATTGATGCCTTGGAAAACA 57.513 34.783 0.00 0.00 0.00 2.83
2254 4460 2.864343 GGTCAGGTTCACGTATGTATGC 59.136 50.000 0.00 0.00 0.00 3.14
2260 4466 5.522097 CAGGTTCACGTATGTATGCATGTAA 59.478 40.000 10.16 0.00 36.58 2.41
2261 4467 6.202762 CAGGTTCACGTATGTATGCATGTAAT 59.797 38.462 10.16 2.66 36.58 1.89
2316 4534 3.353836 CCGGGGTGAACGTGCAAG 61.354 66.667 0.00 0.00 0.00 4.01
2319 4537 2.639286 GGGTGAACGTGCAAGCTG 59.361 61.111 0.00 0.00 0.00 4.24
2359 4811 5.535842 CGTTGGTCGTAAGTGTATTATCG 57.464 43.478 0.00 0.00 39.48 2.92
2412 4864 9.208022 GGTACGAGTATTTAACCAAAAACTACT 57.792 33.333 0.00 0.00 0.00 2.57
2442 4894 6.849085 TGTTAATTCATGCCCACAAACTAT 57.151 33.333 0.00 0.00 0.00 2.12
2450 4902 6.862209 TCATGCCCACAAACTATCATTTTAC 58.138 36.000 0.00 0.00 0.00 2.01
2510 4962 7.724305 TCTGTGACTAAAAACTAACATGTCC 57.276 36.000 0.00 0.00 0.00 4.02
2529 4981 3.368843 GTCCGTAAATCAACCGATTCGTT 59.631 43.478 5.20 0.00 41.12 3.85
2548 5000 5.016985 TCGTTCATTTTAAACGCGCTTATC 58.983 37.500 5.73 0.00 46.78 1.75
2590 5042 1.737236 GTGCTGACATGGCATCGTAAA 59.263 47.619 0.00 0.00 41.86 2.01
2596 5048 4.006319 TGACATGGCATCGTAAATCAACA 58.994 39.130 0.00 0.00 0.00 3.33
2599 5051 2.784347 TGGCATCGTAAATCAACACCA 58.216 42.857 0.00 0.00 0.00 4.17
2624 5076 2.731451 GGTTGACCGTTAAGTTCGTACC 59.269 50.000 0.00 0.00 0.00 3.34
2625 5077 3.380142 GTTGACCGTTAAGTTCGTACCA 58.620 45.455 0.00 0.00 0.00 3.25
2806 6092 2.021584 CTAGTGCTGCGTGCGTTGA 61.022 57.895 0.00 0.00 46.63 3.18
2816 6104 0.042708 CGTGCGTTGATGCTGCTATC 60.043 55.000 0.00 3.32 35.36 2.08
2839 6127 2.491022 GGAGAGCGCCTGGACGTAT 61.491 63.158 2.29 0.00 34.88 3.06
2920 6219 1.041447 GGAGAAGCTACCACCGCCTA 61.041 60.000 0.00 0.00 0.00 3.93
2971 6270 2.666862 CCAACCAACGTAGCGGCA 60.667 61.111 1.45 0.00 0.00 5.69
3131 6526 3.997397 TTAGCGTGGTGGCGAGCA 61.997 61.111 0.00 0.00 38.18 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 4.660938 AACCCCTGTCGGCTTGGC 62.661 66.667 0.00 0.00 0.00 4.52
41 42 1.971695 GAAACCCCTGTCGGCTTGG 60.972 63.158 0.00 0.00 0.00 3.61
42 43 1.971695 GGAAACCCCTGTCGGCTTG 60.972 63.158 0.00 0.00 0.00 4.01
43 44 2.434774 GGAAACCCCTGTCGGCTT 59.565 61.111 0.00 0.00 0.00 4.35
55 56 0.963856 GGTTGTGGATCGGGGGAAAC 60.964 60.000 0.00 0.00 0.00 2.78
56 57 1.381076 GGTTGTGGATCGGGGGAAA 59.619 57.895 0.00 0.00 0.00 3.13
57 58 1.848431 TGGTTGTGGATCGGGGGAA 60.848 57.895 0.00 0.00 0.00 3.97
58 59 2.204013 TGGTTGTGGATCGGGGGA 60.204 61.111 0.00 0.00 0.00 4.81
59 60 2.045340 GTGGTTGTGGATCGGGGG 60.045 66.667 0.00 0.00 0.00 5.40
60 61 2.045340 GGTGGTTGTGGATCGGGG 60.045 66.667 0.00 0.00 0.00 5.73
61 62 1.674322 GTGGTGGTTGTGGATCGGG 60.674 63.158 0.00 0.00 0.00 5.14
62 63 1.674322 GGTGGTGGTTGTGGATCGG 60.674 63.158 0.00 0.00 0.00 4.18
63 64 1.072332 TGGTGGTGGTTGTGGATCG 59.928 57.895 0.00 0.00 0.00 3.69
64 65 0.893727 GGTGGTGGTGGTTGTGGATC 60.894 60.000 0.00 0.00 0.00 3.36
65 66 1.152830 GGTGGTGGTGGTTGTGGAT 59.847 57.895 0.00 0.00 0.00 3.41
66 67 2.309504 TGGTGGTGGTGGTTGTGGA 61.310 57.895 0.00 0.00 0.00 4.02
67 68 2.124693 GTGGTGGTGGTGGTTGTGG 61.125 63.158 0.00 0.00 0.00 4.17
68 69 2.124693 GGTGGTGGTGGTGGTTGTG 61.125 63.158 0.00 0.00 0.00 3.33
69 70 2.277404 GGTGGTGGTGGTGGTTGT 59.723 61.111 0.00 0.00 0.00 3.32
70 71 2.124693 GTGGTGGTGGTGGTGGTTG 61.125 63.158 0.00 0.00 0.00 3.77
71 72 2.277404 GTGGTGGTGGTGGTGGTT 59.723 61.111 0.00 0.00 0.00 3.67
72 73 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
73 74 3.491598 GAGGTGGTGGTGGTGGTGG 62.492 68.421 0.00 0.00 0.00 4.61
74 75 2.113139 GAGGTGGTGGTGGTGGTG 59.887 66.667 0.00 0.00 0.00 4.17
75 76 2.367648 TGAGGTGGTGGTGGTGGT 60.368 61.111 0.00 0.00 0.00 4.16
76 77 2.113139 GTGAGGTGGTGGTGGTGG 59.887 66.667 0.00 0.00 0.00 4.61
77 78 2.280797 CGTGAGGTGGTGGTGGTG 60.281 66.667 0.00 0.00 0.00 4.17
78 79 4.250305 GCGTGAGGTGGTGGTGGT 62.250 66.667 0.00 0.00 0.00 4.16
79 80 3.551496 ATGCGTGAGGTGGTGGTGG 62.551 63.158 0.00 0.00 0.00 4.61
80 81 1.172180 AAATGCGTGAGGTGGTGGTG 61.172 55.000 0.00 0.00 0.00 4.17
81 82 0.889186 GAAATGCGTGAGGTGGTGGT 60.889 55.000 0.00 0.00 0.00 4.16
82 83 0.888736 TGAAATGCGTGAGGTGGTGG 60.889 55.000 0.00 0.00 0.00 4.61
83 84 0.238289 GTGAAATGCGTGAGGTGGTG 59.762 55.000 0.00 0.00 0.00 4.17
84 85 0.889186 GGTGAAATGCGTGAGGTGGT 60.889 55.000 0.00 0.00 0.00 4.16
85 86 0.888736 TGGTGAAATGCGTGAGGTGG 60.889 55.000 0.00 0.00 0.00 4.61
86 87 0.950836 TTGGTGAAATGCGTGAGGTG 59.049 50.000 0.00 0.00 0.00 4.00
87 88 0.951558 GTTGGTGAAATGCGTGAGGT 59.048 50.000 0.00 0.00 0.00 3.85
88 89 0.240945 GGTTGGTGAAATGCGTGAGG 59.759 55.000 0.00 0.00 0.00 3.86
89 90 1.238439 AGGTTGGTGAAATGCGTGAG 58.762 50.000 0.00 0.00 0.00 3.51
90 91 1.686355 AAGGTTGGTGAAATGCGTGA 58.314 45.000 0.00 0.00 0.00 4.35
91 92 2.393764 GAAAGGTTGGTGAAATGCGTG 58.606 47.619 0.00 0.00 0.00 5.34
92 93 1.339929 GGAAAGGTTGGTGAAATGCGT 59.660 47.619 0.00 0.00 0.00 5.24
93 94 1.339610 TGGAAAGGTTGGTGAAATGCG 59.660 47.619 0.00 0.00 0.00 4.73
94 95 2.365293 AGTGGAAAGGTTGGTGAAATGC 59.635 45.455 0.00 0.00 0.00 3.56
95 96 5.105756 GGATAGTGGAAAGGTTGGTGAAATG 60.106 44.000 0.00 0.00 0.00 2.32
96 97 5.016831 GGATAGTGGAAAGGTTGGTGAAAT 58.983 41.667 0.00 0.00 0.00 2.17
97 98 4.105697 AGGATAGTGGAAAGGTTGGTGAAA 59.894 41.667 0.00 0.00 0.00 2.69
98 99 3.655777 AGGATAGTGGAAAGGTTGGTGAA 59.344 43.478 0.00 0.00 0.00 3.18
99 100 3.256704 AGGATAGTGGAAAGGTTGGTGA 58.743 45.455 0.00 0.00 0.00 4.02
100 101 3.721087 AGGATAGTGGAAAGGTTGGTG 57.279 47.619 0.00 0.00 0.00 4.17
101 102 3.197116 CGTAGGATAGTGGAAAGGTTGGT 59.803 47.826 0.00 0.00 0.00 3.67
116 117 8.258007 TGTAAAGATCAATCACTTTCGTAGGAT 58.742 33.333 0.00 0.00 37.49 3.24
181 184 8.625651 AGATAGGACGACAATATGCAGTATATC 58.374 37.037 0.00 0.00 30.65 1.63
189 192 4.218635 TCTGGAGATAGGACGACAATATGC 59.781 45.833 0.00 0.00 0.00 3.14
214 331 4.637968 CATGTCGAGGTCAAACAATTACG 58.362 43.478 0.00 0.00 0.00 3.18
215 332 4.083537 TGCATGTCGAGGTCAAACAATTAC 60.084 41.667 0.00 0.00 0.00 1.89
266 383 3.999001 ACTGATCGTAGAGTTGTACGTCA 59.001 43.478 8.41 9.86 44.94 4.35
267 384 4.596801 ACTGATCGTAGAGTTGTACGTC 57.403 45.455 8.41 6.60 44.94 4.34
268 385 4.453478 TCAACTGATCGTAGAGTTGTACGT 59.547 41.667 18.14 0.00 46.14 3.57
269 386 4.966249 TCAACTGATCGTAGAGTTGTACG 58.034 43.478 18.14 2.76 46.14 3.67
270 387 5.230306 GCATCAACTGATCGTAGAGTTGTAC 59.770 44.000 18.14 9.16 46.14 2.90
271 388 5.340803 GCATCAACTGATCGTAGAGTTGTA 58.659 41.667 18.14 9.43 46.14 2.41
272 389 4.177026 GCATCAACTGATCGTAGAGTTGT 58.823 43.478 18.14 7.70 46.14 3.32
295 424 6.208644 CCATTTTCAAAGGTATGCTAATCCG 58.791 40.000 0.00 0.00 0.00 4.18
303 432 2.757868 TCGGGCCATTTTCAAAGGTATG 59.242 45.455 4.39 0.00 0.00 2.39
304 433 3.023832 CTCGGGCCATTTTCAAAGGTAT 58.976 45.455 4.39 0.00 0.00 2.73
312 442 1.066152 GAATCAGCTCGGGCCATTTTC 59.934 52.381 2.00 0.00 39.73 2.29
405 1485 5.104776 TGGATAACTCCAGGTTCAATCAGAG 60.105 44.000 0.00 0.00 46.95 3.35
489 2495 1.149964 GCTGATACCGTTACGTGCCC 61.150 60.000 3.52 0.00 0.00 5.36
523 2529 2.280628 GAATTTTCGCGGACTGAGGAT 58.719 47.619 6.13 0.00 0.00 3.24
534 2544 1.462791 CGCATTACCGGAATTTTCGC 58.537 50.000 9.46 2.79 0.00 4.70
568 2584 3.716195 TGCATGGGTCAGTCCGGG 61.716 66.667 0.00 0.00 37.00 5.73
657 2692 9.008965 TGAACTATTGCATGTGTTAGTTATTGT 57.991 29.630 12.98 0.00 35.58 2.71
658 2693 9.494479 CTGAACTATTGCATGTGTTAGTTATTG 57.506 33.333 12.98 6.28 35.58 1.90
678 2733 2.596851 ATGCGCACTCCCCTGAACT 61.597 57.895 14.90 0.00 0.00 3.01
784 2867 0.250770 AAGGTTCTTGGCCGAACTCC 60.251 55.000 19.15 9.96 42.20 3.85
801 2887 5.090757 TCACGTACGAAATGCTACTACAAG 58.909 41.667 24.41 0.00 0.00 3.16
875 2970 2.568612 CTCGAGCTCGTGGAAGCA 59.431 61.111 33.33 13.31 45.00 3.91
890 2985 2.898729 TTATAGTGCTCCAGCTGCTC 57.101 50.000 8.66 0.00 42.66 4.26
891 2986 3.853355 ATTTATAGTGCTCCAGCTGCT 57.147 42.857 8.66 0.00 42.66 4.24
962 3087 3.504520 GGTCTATGTGACTAGCTAGAGGC 59.495 52.174 27.45 13.67 44.74 4.70
980 3105 0.108585 TGCTTCTTCGGCTTTGGTCT 59.891 50.000 0.00 0.00 0.00 3.85
1236 3388 3.983344 AGCTAGCAAAATCAAAGCAAACG 59.017 39.130 18.83 0.00 35.63 3.60
1275 3451 5.183969 ACTCTACTCATTACTCAGCACGTA 58.816 41.667 0.00 0.00 0.00 3.57
1276 3452 4.011023 ACTCTACTCATTACTCAGCACGT 58.989 43.478 0.00 0.00 0.00 4.49
1277 3453 4.624336 ACTCTACTCATTACTCAGCACG 57.376 45.455 0.00 0.00 0.00 5.34
1278 3454 6.687081 AGTACTCTACTCATTACTCAGCAC 57.313 41.667 0.00 0.00 32.47 4.40
1279 3455 8.841300 CATTAGTACTCTACTCATTACTCAGCA 58.159 37.037 0.00 0.00 40.14 4.41
1281 3457 9.062524 AGCATTAGTACTCTACTCATTACTCAG 57.937 37.037 0.00 0.00 40.14 3.35
1282 3458 8.982091 AGCATTAGTACTCTACTCATTACTCA 57.018 34.615 0.00 0.00 40.14 3.41
1289 3465 9.152595 CGATACATAGCATTAGTACTCTACTCA 57.847 37.037 0.00 0.00 40.14 3.41
1291 3467 7.066043 GCCGATACATAGCATTAGTACTCTACT 59.934 40.741 0.00 0.00 42.68 2.57
1292 3468 7.148289 TGCCGATACATAGCATTAGTACTCTAC 60.148 40.741 0.00 0.00 0.00 2.59
1295 3471 5.950883 TGCCGATACATAGCATTAGTACTC 58.049 41.667 0.00 0.00 0.00 2.59
1296 3472 5.105716 CCTGCCGATACATAGCATTAGTACT 60.106 44.000 0.00 0.00 35.64 2.73
1298 3474 4.159693 CCCTGCCGATACATAGCATTAGTA 59.840 45.833 0.00 0.00 35.64 1.82
1299 3475 3.055819 CCCTGCCGATACATAGCATTAGT 60.056 47.826 0.00 0.00 35.64 2.24
1300 3476 3.525537 CCCTGCCGATACATAGCATTAG 58.474 50.000 0.00 0.00 35.64 1.73
1302 3478 1.003580 CCCCTGCCGATACATAGCATT 59.996 52.381 0.00 0.00 35.64 3.56
1303 3479 0.615331 CCCCTGCCGATACATAGCAT 59.385 55.000 0.00 0.00 35.64 3.79
1586 3777 4.746535 TCAGCCGAGTCAACCATAAATA 57.253 40.909 0.00 0.00 0.00 1.40
1589 3789 2.301870 AGTTCAGCCGAGTCAACCATAA 59.698 45.455 0.00 0.00 0.00 1.90
1590 3790 1.899814 AGTTCAGCCGAGTCAACCATA 59.100 47.619 0.00 0.00 0.00 2.74
1595 3795 1.581934 CAACAGTTCAGCCGAGTCAA 58.418 50.000 0.00 0.00 0.00 3.18
1846 4050 0.823356 AGCTGGCGTTGATGTTGGTT 60.823 50.000 0.00 0.00 0.00 3.67
2005 4209 1.293498 GCCGTTGAAGAGCTCCTGA 59.707 57.895 10.93 0.00 0.00 3.86
2155 4359 0.480690 TTTAGTTGGGCCTCCTGCAA 59.519 50.000 4.53 0.00 43.89 4.08
2199 4405 7.765360 TGTTTTCCAAGGCATCAATCATTATTC 59.235 33.333 0.00 0.00 0.00 1.75
2225 4431 1.620822 GTGAACCTGACCAATGCCTT 58.379 50.000 0.00 0.00 0.00 4.35
2254 4460 6.160664 ACGTTCGGTGTTCTTTATTACATG 57.839 37.500 0.00 0.00 0.00 3.21
2260 4466 4.445385 GTGTGTACGTTCGGTGTTCTTTAT 59.555 41.667 0.00 0.00 0.00 1.40
2261 4467 3.796178 GTGTGTACGTTCGGTGTTCTTTA 59.204 43.478 0.00 0.00 0.00 1.85
2316 4534 4.201685 ACGTACATTTTGATACTTCGCAGC 60.202 41.667 0.00 0.00 0.00 5.25
2319 4537 5.019498 CCAACGTACATTTTGATACTTCGC 58.981 41.667 0.00 0.00 0.00 4.70
2321 4539 6.238508 CGACCAACGTACATTTTGATACTTC 58.761 40.000 0.00 0.00 37.22 3.01
2349 4796 9.626045 TCTGTATTGATGATGACGATAATACAC 57.374 33.333 0.00 0.00 36.59 2.90
2359 4811 6.543465 TCCCATTGTTCTGTATTGATGATGAC 59.457 38.462 0.00 0.00 0.00 3.06
2412 4864 6.997655 TGTGGGCATGAATTAACAAAATGTA 58.002 32.000 0.00 0.00 0.00 2.29
2426 4878 5.999205 AAAATGATAGTTTGTGGGCATGA 57.001 34.783 0.00 0.00 0.00 3.07
2503 4955 3.322211 TCGGTTGATTTACGGACATGT 57.678 42.857 0.00 0.00 0.00 3.21
2510 4962 4.571375 TGAACGAATCGGTTGATTTACG 57.429 40.909 7.80 0.00 44.79 3.18
2529 4981 5.284428 TGTGATAAGCGCGTTTAAAATGA 57.716 34.783 19.29 0.00 0.00 2.57
2599 5051 3.878699 ACGAACTTAACGGTCAACCAAAT 59.121 39.130 0.00 0.00 35.14 2.32
2641 5093 0.532573 GGACTTGGAGCAGATGTCGA 59.467 55.000 0.00 0.00 0.00 4.20
2787 6073 2.029073 AACGCACGCAGCACTAGT 59.971 55.556 0.00 0.00 46.13 2.57
2806 6092 2.161855 CTCTCCTCTCGATAGCAGCAT 58.838 52.381 0.00 0.00 0.00 3.79
2816 6104 3.898509 CCAGGCGCTCTCCTCTCG 61.899 72.222 7.64 0.00 33.25 4.04
2839 6127 2.126463 CTCTCTTTGTCGCCGCGA 60.126 61.111 12.39 12.39 0.00 5.87
2849 6137 0.610174 TGCGTGGATCAGCTCTCTTT 59.390 50.000 8.21 0.00 0.00 2.52
2898 6197 1.324005 GCGGTGGTAGCTTCTCCTCT 61.324 60.000 0.00 0.00 0.00 3.69
2951 6250 3.784412 CGCTACGTTGGTTGGCCG 61.784 66.667 0.00 0.00 37.67 6.13
3114 6500 3.997397 TGCTCGCCACCACGCTAA 61.997 61.111 0.00 0.00 0.00 3.09


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

AutoCloner maintained by Alex Coulton.