Multiple sequence alignment - TraesCS7A01G485100

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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 TraesCS7A01G485100 chr7A 100.000 2573 0 0 1 2573 676057205 676059777 0.000000e+00 4752.0
1 TraesCS7A01G485100 chr7A 85.884 758 92 7 874 1622 676287851 676287100 0.000000e+00 793.0
2 TraesCS7A01G485100 chr7A 95.139 288 13 1 1648 1935 671787737 671787451 1.090000e-123 453.0
3 TraesCS7A01G485100 chr7A 91.892 222 16 2 2310 2529 671785590 671785369 2.490000e-80 309.0
4 TraesCS7A01G485100 chr3A 93.363 889 43 6 1649 2529 33137239 33136359 0.000000e+00 1301.0
5 TraesCS7A01G485100 chr3A 92.697 890 43 8 1648 2529 988141 989016 0.000000e+00 1264.0
6 TraesCS7A01G485100 chr3A 91.218 911 39 19 1648 2525 17439649 17438747 0.000000e+00 1201.0
7 TraesCS7A01G485100 chr3A 96.226 53 1 1 785 836 55775936 55775988 4.560000e-13 86.1
8 TraesCS7A01G485100 chr5A 92.697 890 49 5 1649 2530 576611590 576612471 0.000000e+00 1269.0
9 TraesCS7A01G485100 chr2A 92.584 890 50 5 1648 2529 726366154 726365273 0.000000e+00 1264.0
10 TraesCS7A01G485100 chr2A 87.872 907 61 30 1649 2525 757463631 757464518 0.000000e+00 1020.0
11 TraesCS7A01G485100 chr2A 90.016 621 37 11 1646 2242 36413459 36414078 0.000000e+00 780.0
12 TraesCS7A01G485100 chr2A 89.632 299 15 9 2240 2529 36414956 36415247 1.450000e-97 366.0
13 TraesCS7A01G485100 chr2A 80.000 145 28 1 508 651 667950120 667950264 3.500000e-19 106.0
14 TraesCS7A01G485100 chr7D 92.155 905 52 7 748 1648 585599015 585599904 0.000000e+00 1260.0
15 TraesCS7A01G485100 chr7D 79.853 407 54 14 367 749 585598485 585598887 3.260000e-69 272.0
16 TraesCS7A01G485100 chr7D 79.058 382 41 20 4 376 585598098 585598449 2.580000e-55 226.0
17 TraesCS7A01G485100 chr7D 90.000 50 5 0 604 653 75958920 75958969 5.940000e-07 65.8
18 TraesCS7A01G485100 chr6A 90.659 910 52 16 1648 2532 522207677 522206776 0.000000e+00 1179.0
19 TraesCS7A01G485100 chr7B 87.179 702 87 3 935 1635 655112154 655111455 0.000000e+00 795.0
20 TraesCS7A01G485100 chr7B 86.866 335 18 5 1314 1648 654981780 654982088 4.070000e-93 351.0
21 TraesCS7A01G485100 chr7B 97.674 43 1 0 613 655 22511040 22510998 9.870000e-10 75.0
22 TraesCS7A01G485100 chr3D 80.100 201 32 7 457 651 4407315 4407117 2.670000e-30 143.0
23 TraesCS7A01G485100 chr1A 83.562 146 21 1 192 334 497933447 497933302 1.610000e-27 134.0
24 TraesCS7A01G485100 chr6D 76.818 220 42 9 437 652 379064000 379063786 5.820000e-22 115.0
25 TraesCS7A01G485100 chr6D 76.577 222 39 12 437 652 379065181 379064967 2.710000e-20 110.0
26 TraesCS7A01G485100 chr6D 78.873 142 21 8 439 576 446136103 446135967 1.270000e-13 87.9
27 TraesCS7A01G485100 chr3B 98.113 53 0 1 785 836 68601915 68601967 9.800000e-15 91.6
28 TraesCS7A01G485100 chr1B 75.248 202 43 5 453 651 60258962 60259159 3.530000e-14 89.8
29 TraesCS7A01G485100 chr2D 78.462 130 25 3 508 635 647276508 647276380 5.900000e-12 82.4
30 TraesCS7A01G485100 chr5D 78.195 133 23 6 524 653 51269380 51269251 2.120000e-11 80.5
31 TraesCS7A01G485100 chr5B 76.316 152 32 4 439 590 555242743 555242596 7.630000e-11 78.7
32 TraesCS7A01G485100 chr4B 79.592 98 16 3 489 584 369489041 369489136 1.650000e-07 67.6


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 TraesCS7A01G485100 chr7A 676057205 676059777 2572 False 4752 4752 100.000000 1 2573 1 chr7A.!!$F1 2572
1 TraesCS7A01G485100 chr7A 676287100 676287851 751 True 793 793 85.884000 874 1622 1 chr7A.!!$R1 748
2 TraesCS7A01G485100 chr7A 671785369 671787737 2368 True 381 453 93.515500 1648 2529 2 chr7A.!!$R2 881
3 TraesCS7A01G485100 chr3A 33136359 33137239 880 True 1301 1301 93.363000 1649 2529 1 chr3A.!!$R2 880
4 TraesCS7A01G485100 chr3A 988141 989016 875 False 1264 1264 92.697000 1648 2529 1 chr3A.!!$F1 881
5 TraesCS7A01G485100 chr3A 17438747 17439649 902 True 1201 1201 91.218000 1648 2525 1 chr3A.!!$R1 877
6 TraesCS7A01G485100 chr5A 576611590 576612471 881 False 1269 1269 92.697000 1649 2530 1 chr5A.!!$F1 881
7 TraesCS7A01G485100 chr2A 726365273 726366154 881 True 1264 1264 92.584000 1648 2529 1 chr2A.!!$R1 881
8 TraesCS7A01G485100 chr2A 757463631 757464518 887 False 1020 1020 87.872000 1649 2525 1 chr2A.!!$F2 876
9 TraesCS7A01G485100 chr2A 36413459 36415247 1788 False 573 780 89.824000 1646 2529 2 chr2A.!!$F3 883
10 TraesCS7A01G485100 chr7D 585598098 585599904 1806 False 586 1260 83.688667 4 1648 3 chr7D.!!$F2 1644
11 TraesCS7A01G485100 chr6A 522206776 522207677 901 True 1179 1179 90.659000 1648 2532 1 chr6A.!!$R1 884
12 TraesCS7A01G485100 chr7B 655111455 655112154 699 True 795 795 87.179000 935 1635 1 chr7B.!!$R2 700

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
41 42 0.469331 TCGGAGCCCTCGACCATTAT 60.469 55.0 0.00 0.0 0.0 1.28 F
81 86 0.531090 CCTCACCCACGAACGTTTCA 60.531 55.0 0.46 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1119 1340 0.461870 ATATGAGCTTCGTGCCGCAA 60.462 50.0 0.0 0.0 44.23 4.85 R
1580 1801 0.467384 CGGACTGCCTCTTGATCCAT 59.533 55.0 0.0 0.0 0.00 3.41 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
18 19 3.376218 CCTCTCATCCTCAAAGGCG 57.624 57.895 0.00 0.00 34.61 5.52
23 24 2.125106 ATCCTCAAAGGCGCGGTC 60.125 61.111 8.83 0.00 34.61 4.79
40 41 1.076559 TCGGAGCCCTCGACCATTA 60.077 57.895 0.00 0.00 0.00 1.90
41 42 0.469331 TCGGAGCCCTCGACCATTAT 60.469 55.000 0.00 0.00 0.00 1.28
49 54 2.899900 CCCTCGACCATTATCATCCTCA 59.100 50.000 0.00 0.00 0.00 3.86
53 58 3.070018 CGACCATTATCATCCTCAAGCC 58.930 50.000 0.00 0.00 0.00 4.35
65 70 2.677875 CAAGCCCCTGTTGCCCTC 60.678 66.667 0.00 0.00 0.00 4.30
70 75 3.579302 CCCTGTTGCCCTCACCCA 61.579 66.667 0.00 0.00 0.00 4.51
71 76 2.282462 CCTGTTGCCCTCACCCAC 60.282 66.667 0.00 0.00 0.00 4.61
76 81 3.818121 TTGCCCTCACCCACGAACG 62.818 63.158 0.00 0.00 0.00 3.95
81 86 0.531090 CCTCACCCACGAACGTTTCA 60.531 55.000 0.46 0.00 0.00 2.69
92 97 2.774074 CGAACGTTTCAAAAACCGTCAG 59.226 45.455 0.46 0.00 32.30 3.51
108 113 1.137086 GTCAGCATGTGGACGTCCTAT 59.863 52.381 33.39 24.01 37.40 2.57
117 122 2.033550 GTGGACGTCCTATAGAGCACAG 59.966 54.545 33.39 0.00 36.82 3.66
118 123 2.299521 GGACGTCCTATAGAGCACAGT 58.700 52.381 27.64 0.00 0.00 3.55
119 124 2.291190 GGACGTCCTATAGAGCACAGTC 59.709 54.545 27.64 6.98 0.00 3.51
120 125 2.943690 GACGTCCTATAGAGCACAGTCA 59.056 50.000 3.51 0.00 0.00 3.41
121 126 3.556999 ACGTCCTATAGAGCACAGTCAT 58.443 45.455 0.00 0.00 0.00 3.06
127 134 6.207614 GTCCTATAGAGCACAGTCATCATACA 59.792 42.308 0.00 0.00 0.00 2.29
137 144 3.686241 CAGTCATCATACATATTGGCGGG 59.314 47.826 0.00 0.00 0.00 6.13
147 154 2.538512 TATTGGCGGGCGCTTGGTTA 62.539 55.000 7.64 0.00 41.60 2.85
154 161 1.602605 GGCGCTTGGTTACCCTTGT 60.603 57.895 7.64 0.00 0.00 3.16
161 168 1.291272 GGTTACCCTTGTCGCGAGT 59.709 57.895 10.24 6.04 0.00 4.18
163 170 1.373748 TTACCCTTGTCGCGAGTGC 60.374 57.895 10.24 0.00 37.91 4.40
164 171 2.089887 TTACCCTTGTCGCGAGTGCA 62.090 55.000 10.24 0.00 42.97 4.57
185 192 4.797471 CATAGTGGTTGTTGTCCATGTTG 58.203 43.478 0.00 0.00 37.30 3.33
197 204 0.752054 CCATGTTGGCAAGTGTTGGT 59.248 50.000 0.00 0.00 0.00 3.67
246 253 4.070552 GCCAACCTCGGCGAGAGT 62.071 66.667 36.47 27.51 45.44 3.24
247 254 2.182030 CCAACCTCGGCGAGAGTC 59.818 66.667 36.47 0.00 45.44 3.36
248 255 2.344203 CCAACCTCGGCGAGAGTCT 61.344 63.158 36.47 18.62 45.44 3.24
249 256 1.153939 CAACCTCGGCGAGAGTCTG 60.154 63.158 36.47 23.95 45.44 3.51
250 257 2.995872 AACCTCGGCGAGAGTCTGC 61.996 63.158 36.47 1.37 45.44 4.26
251 258 3.137459 CCTCGGCGAGAGTCTGCT 61.137 66.667 36.47 0.00 45.44 4.24
252 259 2.101965 CTCGGCGAGAGTCTGCTG 59.898 66.667 32.07 13.96 41.99 4.41
253 260 3.408501 CTCGGCGAGAGTCTGCTGG 62.409 68.421 32.07 0.34 41.99 4.85
255 262 3.768922 GGCGAGAGTCTGCTGGCT 61.769 66.667 0.00 0.00 39.27 4.75
256 263 2.508887 GCGAGAGTCTGCTGGCTG 60.509 66.667 1.04 0.00 36.78 4.85
262 269 1.534959 AGTCTGCTGGCTGTCCTCA 60.535 57.895 0.00 0.00 0.00 3.86
267 274 3.314331 CTGGCTGTCCTCACCCGT 61.314 66.667 0.00 0.00 0.00 5.28
268 275 1.982395 CTGGCTGTCCTCACCCGTA 60.982 63.158 0.00 0.00 0.00 4.02
290 297 1.321445 GCGCTTTCAAATTGATTCGGC 59.679 47.619 0.00 0.00 0.00 5.54
300 307 3.963383 ATTGATTCGGCGTGATTAACC 57.037 42.857 6.85 0.00 0.00 2.85
321 328 7.633193 AACCGTGTGCCTAATTAATTAATCA 57.367 32.000 11.08 7.05 0.00 2.57
324 331 7.284489 ACCGTGTGCCTAATTAATTAATCACAT 59.716 33.333 27.20 17.66 37.14 3.21
397 452 9.784531 AATTGTCTGTCTAATTATATGGGAGTG 57.215 33.333 0.00 0.00 0.00 3.51
405 460 9.857957 GTCTAATTATATGGGAGTGTAGTTAGC 57.142 37.037 0.00 0.00 0.00 3.09
413 468 4.645136 TGGGAGTGTAGTTAGCTGTCTATG 59.355 45.833 0.00 0.00 0.00 2.23
415 470 4.888239 GGAGTGTAGTTAGCTGTCTATGGA 59.112 45.833 0.00 0.00 0.00 3.41
418 473 6.660800 AGTGTAGTTAGCTGTCTATGGACTA 58.339 40.000 10.82 0.00 42.54 2.59
419 474 7.117397 AGTGTAGTTAGCTGTCTATGGACTAA 58.883 38.462 10.82 0.00 42.54 2.24
420 475 7.780745 AGTGTAGTTAGCTGTCTATGGACTAAT 59.219 37.037 10.82 0.00 42.54 1.73
421 476 8.414778 GTGTAGTTAGCTGTCTATGGACTAATT 58.585 37.037 10.82 1.23 42.54 1.40
422 477 9.636789 TGTAGTTAGCTGTCTATGGACTAATTA 57.363 33.333 10.82 0.36 42.54 1.40
425 480 9.594936 AGTTAGCTGTCTATGGACTAATTATCT 57.405 33.333 10.82 0.00 42.54 1.98
429 492 8.147058 AGCTGTCTATGGACTAATTATCTGTTG 58.853 37.037 10.82 0.00 42.54 3.33
430 493 7.386299 GCTGTCTATGGACTAATTATCTGTTGG 59.614 40.741 10.82 0.00 42.54 3.77
433 496 4.164843 TGGACTAATTATCTGTTGGCCC 57.835 45.455 0.00 0.00 0.00 5.80
435 498 3.883489 GGACTAATTATCTGTTGGCCCAC 59.117 47.826 0.00 0.00 0.00 4.61
447 510 4.826556 TGTTGGCCCACTTAATTAATTGC 58.173 39.130 11.05 4.35 0.00 3.56
459 522 7.439056 CACTTAATTAATTGCCTGCCTAATTGG 59.561 37.037 11.05 0.00 39.35 3.16
464 527 4.906747 ATTGCCTGCCTAATTGGAAAAA 57.093 36.364 0.00 0.00 38.35 1.94
486 549 8.897872 AAAAACCTCTCTTTCTAATTGTACGA 57.102 30.769 0.00 0.00 0.00 3.43
504 567 4.412796 ACGAGGGCTTAATTAACTACCC 57.587 45.455 14.49 14.49 37.63 3.69
553 617 8.189119 TGACTTGGTTTTAAATTGATTAGGCT 57.811 30.769 0.00 0.00 0.00 4.58
554 618 8.646900 TGACTTGGTTTTAAATTGATTAGGCTT 58.353 29.630 0.00 0.00 0.00 4.35
556 620 8.646900 ACTTGGTTTTAAATTGATTAGGCTTGA 58.353 29.630 0.00 0.00 0.00 3.02
559 623 9.838339 TGGTTTTAAATTGATTAGGCTTGAAAA 57.162 25.926 0.00 0.00 0.00 2.29
609 673 9.120538 ACTAATTCCGCACATAATTAATTGTCT 57.879 29.630 11.05 0.00 29.62 3.41
614 678 7.269316 TCCGCACATAATTAATTGTCTGACTA 58.731 34.615 11.05 1.38 0.00 2.59
616 680 7.850982 CCGCACATAATTAATTGTCTGACTAAC 59.149 37.037 11.05 0.00 0.00 2.34
631 695 9.665719 TGTCTGACTAACTAATTGCATTAATGA 57.334 29.630 19.73 0.00 0.00 2.57
686 763 6.130298 GCACTAATATATGTGTGCCAAACA 57.870 37.500 22.56 0.00 46.84 2.83
687 764 6.559810 GCACTAATATATGTGTGCCAAACAA 58.440 36.000 22.56 0.00 46.84 2.83
688 765 6.472163 GCACTAATATATGTGTGCCAAACAAC 59.528 38.462 22.56 3.78 46.84 3.32
690 767 8.026026 CACTAATATATGTGTGCCAAACAACAA 58.974 33.333 0.00 0.00 41.57 2.83
691 768 8.026607 ACTAATATATGTGTGCCAAACAACAAC 58.973 33.333 0.00 0.00 41.57 3.32
692 769 1.919918 ATGTGTGCCAAACAACAACG 58.080 45.000 0.00 0.00 41.57 4.10
699 778 2.094494 TGCCAAACAACAACGTGTCAAT 60.094 40.909 0.00 0.00 0.00 2.57
701 780 3.369451 GCCAAACAACAACGTGTCAATTT 59.631 39.130 0.00 0.00 0.00 1.82
807 1018 5.467035 TCTCACTTGTCATCATGTACACA 57.533 39.130 0.00 0.00 32.05 3.72
819 1030 4.263139 CATGTACACATGTTGACCATCG 57.737 45.455 13.13 0.00 46.40 3.84
973 1188 2.093500 AGCTCGGACAACAAGCATATCA 60.093 45.455 0.00 0.00 38.51 2.15
992 1207 2.742372 CCCACAAAGAGACGCGGG 60.742 66.667 12.47 0.00 0.00 6.13
1024 1239 2.224967 GCTATGGCCAAGATCATTCCCT 60.225 50.000 10.96 0.00 0.00 4.20
1035 1250 1.952621 TCATTCCCTTCCTCCTCGTT 58.047 50.000 0.00 0.00 0.00 3.85
1083 1304 2.359478 ACGGATTGCCCCAACGTC 60.359 61.111 0.00 0.00 31.39 4.34
1180 1401 4.465512 GCCAATGCGGTGCTGACG 62.466 66.667 0.00 0.00 36.97 4.35
1317 1538 3.011635 GCTCTCCGGCAAGCAGAGA 62.012 63.158 18.65 11.38 36.52 3.10
1326 1547 0.103937 GCAAGCAGAGAGACGCCTAT 59.896 55.000 0.00 0.00 0.00 2.57
1356 1577 4.729856 AACGACTACGCACCGGCC 62.730 66.667 0.00 0.00 43.96 6.13
1580 1801 4.222810 ACTGTTAGGCATATGAGTGTGTGA 59.777 41.667 6.97 0.00 0.00 3.58
1600 1821 1.144936 GGATCAAGAGGCAGTCCGG 59.855 63.158 0.00 0.00 37.47 5.14
1607 1828 3.302347 GAGGCAGTCCGGACACCAG 62.302 68.421 34.98 23.78 37.47 4.00
1627 1848 8.052748 ACACCAGAGAGCAAATAATAAATACCA 58.947 33.333 0.00 0.00 0.00 3.25
1628 1849 8.902806 CACCAGAGAGCAAATAATAAATACCAA 58.097 33.333 0.00 0.00 0.00 3.67
1710 1931 0.828022 TACAATGGGCCCTACAGTCG 59.172 55.000 25.70 6.85 0.00 4.18
1848 2082 9.344309 AGCAATTTGAAATTTGAACAAAAACAG 57.656 25.926 0.00 0.00 37.14 3.16
1907 2142 4.264172 ACAAGATAAACCCCCAGCAACATA 60.264 41.667 0.00 0.00 0.00 2.29
1913 2154 4.534647 AACCCCCAGCAACATATAATCA 57.465 40.909 0.00 0.00 0.00 2.57
1974 2216 7.642669 ACATGAAACAATTACTTGTGTGAGAG 58.357 34.615 0.00 0.00 44.83 3.20
1977 2219 7.693952 TGAAACAATTACTTGTGTGAGAGTTC 58.306 34.615 0.00 0.00 44.83 3.01
2073 2318 0.249398 GGACCGGTGCTAGTGTCAAT 59.751 55.000 20.19 0.00 0.00 2.57
2163 2408 1.544759 CCTTGTCGCCTTGGGTACTTT 60.545 52.381 0.00 0.00 0.00 2.66
2177 2507 7.093024 CCTTGGGTACTTTCAGAAGAACCTATA 60.093 40.741 9.38 0.00 36.69 1.31
2211 3088 4.276926 ACAGAACTCACTGGCAAAGAAATC 59.723 41.667 0.00 0.00 41.59 2.17
2231 3108 7.768120 AGAAATCAAGGAGATGATACAACTGAC 59.232 37.037 0.00 0.00 39.08 3.51
2258 4038 2.434884 ATGAGCGTCGCTTGGGTG 60.435 61.111 22.67 0.00 39.88 4.61
2365 4733 6.428465 TCACACAAAACGAAGCAATTAGGATA 59.572 34.615 0.00 0.00 0.00 2.59
2435 4816 8.885494 TCAGTTTATTTTTCCCTTCAAATGTG 57.115 30.769 0.00 0.00 0.00 3.21
2471 4852 0.983378 GAGAGTGTATGGTGGGCCCT 60.983 60.000 25.70 4.56 0.00 5.19
2542 4923 3.495670 GGCTCTGACCGCTATATAGTG 57.504 52.381 15.18 15.18 0.00 2.74
2543 4924 2.820787 GGCTCTGACCGCTATATAGTGT 59.179 50.000 19.41 13.00 32.08 3.55
2544 4925 3.256136 GGCTCTGACCGCTATATAGTGTT 59.744 47.826 19.41 7.74 32.08 3.32
2545 4926 4.458295 GGCTCTGACCGCTATATAGTGTTA 59.542 45.833 19.41 9.66 32.08 2.41
2546 4927 5.392286 GCTCTGACCGCTATATAGTGTTAC 58.608 45.833 19.41 11.67 32.08 2.50
2547 4928 5.048921 GCTCTGACCGCTATATAGTGTTACA 60.049 44.000 19.41 14.70 32.08 2.41
2548 4929 6.349445 GCTCTGACCGCTATATAGTGTTACAT 60.349 42.308 19.41 2.71 32.08 2.29
2549 4930 6.909909 TCTGACCGCTATATAGTGTTACATG 58.090 40.000 19.41 7.71 32.08 3.21
2550 4931 5.466819 TGACCGCTATATAGTGTTACATGC 58.533 41.667 19.41 0.00 32.08 4.06
2551 4932 5.010213 TGACCGCTATATAGTGTTACATGCA 59.990 40.000 19.41 0.00 32.08 3.96
2552 4933 6.037786 ACCGCTATATAGTGTTACATGCAT 57.962 37.500 19.41 0.00 32.08 3.96
2553 4934 5.869344 ACCGCTATATAGTGTTACATGCATG 59.131 40.000 25.09 25.09 32.08 4.06
2554 4935 6.099341 CCGCTATATAGTGTTACATGCATGA 58.901 40.000 32.75 13.72 32.08 3.07
2555 4936 6.758416 CCGCTATATAGTGTTACATGCATGAT 59.242 38.462 32.75 18.51 32.08 2.45
2556 4937 7.043125 CCGCTATATAGTGTTACATGCATGATC 60.043 40.741 32.75 20.21 32.08 2.92
2557 4938 7.704047 CGCTATATAGTGTTACATGCATGATCT 59.296 37.037 32.75 21.18 0.00 2.75
2563 4944 7.488187 AGTGTTACATGCATGATCTATTGTC 57.512 36.000 32.75 12.64 0.00 3.18
2564 4945 7.049754 AGTGTTACATGCATGATCTATTGTCA 58.950 34.615 32.75 13.90 0.00 3.58
2565 4946 7.226128 AGTGTTACATGCATGATCTATTGTCAG 59.774 37.037 32.75 1.77 0.00 3.51
2566 4947 6.484308 TGTTACATGCATGATCTATTGTCAGG 59.516 38.462 32.75 1.29 0.00 3.86
2567 4948 4.395625 ACATGCATGATCTATTGTCAGGG 58.604 43.478 32.75 0.59 0.00 4.45
2568 4949 3.497103 TGCATGATCTATTGTCAGGGG 57.503 47.619 0.00 0.00 0.00 4.79
2569 4950 2.779430 TGCATGATCTATTGTCAGGGGT 59.221 45.455 0.00 0.00 0.00 4.95
2570 4951 3.144506 GCATGATCTATTGTCAGGGGTG 58.855 50.000 0.00 0.00 0.00 4.61
2571 4952 3.748083 CATGATCTATTGTCAGGGGTGG 58.252 50.000 0.00 0.00 0.00 4.61
2572 4953 3.129262 TGATCTATTGTCAGGGGTGGA 57.871 47.619 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.813210 GCGCCTTTGAGGATGAGAGG 60.813 60.000 0.00 0.00 37.67 3.69
1 2 1.150567 CGCGCCTTTGAGGATGAGAG 61.151 60.000 0.00 0.00 37.67 3.20
2 3 1.153568 CGCGCCTTTGAGGATGAGA 60.154 57.895 0.00 0.00 37.67 3.27
23 24 0.038159 GATAATGGTCGAGGGCTCCG 60.038 60.000 0.00 0.00 0.00 4.63
37 38 3.059097 ACAGGGGCTTGAGGATGATAAT 58.941 45.455 0.00 0.00 0.00 1.28
40 41 1.064166 CAACAGGGGCTTGAGGATGAT 60.064 52.381 0.00 0.00 0.00 2.45
41 42 0.329261 CAACAGGGGCTTGAGGATGA 59.671 55.000 0.00 0.00 0.00 2.92
49 54 3.185203 TGAGGGCAACAGGGGCTT 61.185 61.111 0.00 0.00 39.74 4.35
53 58 3.579302 TGGGTGAGGGCAACAGGG 61.579 66.667 0.00 0.00 39.74 4.45
65 70 2.546195 TTTTGAAACGTTCGTGGGTG 57.454 45.000 0.00 0.00 0.00 4.61
70 75 2.159234 TGACGGTTTTTGAAACGTTCGT 59.841 40.909 0.00 3.93 39.95 3.85
71 76 2.771689 TGACGGTTTTTGAAACGTTCG 58.228 42.857 0.00 0.10 39.95 3.95
76 81 3.242712 CACATGCTGACGGTTTTTGAAAC 59.757 43.478 0.00 0.00 0.00 2.78
81 86 1.336755 GTCCACATGCTGACGGTTTTT 59.663 47.619 0.00 0.00 0.00 1.94
92 97 2.608261 GCTCTATAGGACGTCCACATGC 60.608 54.545 35.00 24.57 38.89 4.06
102 107 5.720371 ATGATGACTGTGCTCTATAGGAC 57.280 43.478 0.00 0.00 43.91 3.85
108 113 7.381323 CCAATATGTATGATGACTGTGCTCTA 58.619 38.462 0.00 0.00 0.00 2.43
117 122 2.420022 GCCCGCCAATATGTATGATGAC 59.580 50.000 0.00 0.00 0.00 3.06
118 123 2.710377 GCCCGCCAATATGTATGATGA 58.290 47.619 0.00 0.00 0.00 2.92
119 124 1.398041 CGCCCGCCAATATGTATGATG 59.602 52.381 0.00 0.00 0.00 3.07
120 125 1.737838 CGCCCGCCAATATGTATGAT 58.262 50.000 0.00 0.00 0.00 2.45
121 126 0.953471 GCGCCCGCCAATATGTATGA 60.953 55.000 0.00 0.00 34.56 2.15
127 134 2.906897 CCAAGCGCCCGCCAATAT 60.907 61.111 2.29 0.00 43.17 1.28
147 154 1.884075 TATGCACTCGCGACAAGGGT 61.884 55.000 3.71 0.00 42.97 4.34
154 161 0.735978 CAACCACTATGCACTCGCGA 60.736 55.000 9.26 9.26 42.97 5.87
161 168 2.647683 TGGACAACAACCACTATGCA 57.352 45.000 0.00 0.00 32.03 3.96
163 170 4.321156 CCAACATGGACAACAACCACTATG 60.321 45.833 0.00 0.00 40.96 2.23
164 171 3.826157 CCAACATGGACAACAACCACTAT 59.174 43.478 0.00 0.00 40.96 2.12
185 192 1.525077 TGGACGACCAACACTTGCC 60.525 57.895 3.49 0.00 43.91 4.52
197 204 0.390340 GCTCTCAGCAACATGGACGA 60.390 55.000 0.00 0.00 41.89 4.20
230 237 2.182030 GACTCTCGCCGAGGTTGG 59.818 66.667 15.08 5.16 44.33 3.77
231 238 1.153939 CAGACTCTCGCCGAGGTTG 60.154 63.158 15.08 7.62 44.33 3.77
232 239 2.995872 GCAGACTCTCGCCGAGGTT 61.996 63.158 15.08 0.69 44.33 3.50
233 240 3.444805 GCAGACTCTCGCCGAGGT 61.445 66.667 15.08 10.98 44.33 3.85
234 241 3.137459 AGCAGACTCTCGCCGAGG 61.137 66.667 15.08 7.64 44.33 4.63
235 242 2.101965 CAGCAGACTCTCGCCGAG 59.898 66.667 8.05 8.05 45.56 4.63
236 243 3.443925 CCAGCAGACTCTCGCCGA 61.444 66.667 0.00 0.00 0.00 5.54
238 245 3.768922 AGCCAGCAGACTCTCGCC 61.769 66.667 0.00 0.00 0.00 5.54
239 246 2.508887 CAGCCAGCAGACTCTCGC 60.509 66.667 0.00 0.00 0.00 5.03
240 247 1.153862 GACAGCCAGCAGACTCTCG 60.154 63.158 0.00 0.00 0.00 4.04
241 248 1.217779 GGACAGCCAGCAGACTCTC 59.782 63.158 0.00 0.00 0.00 3.20
242 249 1.229145 AGGACAGCCAGCAGACTCT 60.229 57.895 0.00 0.00 36.29 3.24
243 250 1.217779 GAGGACAGCCAGCAGACTC 59.782 63.158 0.00 0.00 36.29 3.36
244 251 1.534959 TGAGGACAGCCAGCAGACT 60.535 57.895 0.00 0.00 36.29 3.24
245 252 1.375268 GTGAGGACAGCCAGCAGAC 60.375 63.158 0.00 0.00 36.29 3.51
246 253 2.587247 GGTGAGGACAGCCAGCAGA 61.587 63.158 0.00 0.00 38.41 4.26
247 254 2.046507 GGTGAGGACAGCCAGCAG 60.047 66.667 0.00 0.00 38.41 4.24
253 260 1.448013 GCTTACGGGTGAGGACAGC 60.448 63.158 0.00 0.00 42.88 4.40
254 261 1.153823 CGCTTACGGGTGAGGACAG 60.154 63.158 0.00 0.00 34.97 3.51
255 262 2.967397 CGCTTACGGGTGAGGACA 59.033 61.111 0.00 0.00 34.97 4.02
256 263 2.502692 AAGCGCTTACGGGTGAGGAC 62.503 60.000 23.72 0.00 40.57 3.85
262 269 1.530323 ATTTGAAAGCGCTTACGGGT 58.470 45.000 25.33 7.11 40.57 5.28
267 274 4.411327 CCGAATCAATTTGAAAGCGCTTA 58.589 39.130 25.33 8.13 0.00 3.09
268 275 3.244976 CCGAATCAATTTGAAAGCGCTT 58.755 40.909 18.98 18.98 0.00 4.68
290 297 1.999048 TAGGCACACGGTTAATCACG 58.001 50.000 0.00 0.00 0.00 4.35
300 307 7.113404 GCATGTGATTAATTAATTAGGCACACG 59.887 37.037 28.53 25.02 39.06 4.49
379 434 9.857957 GCTAACTACACTCCCATATAATTAGAC 57.142 37.037 0.00 0.00 0.00 2.59
381 436 9.862371 CAGCTAACTACACTCCCATATAATTAG 57.138 37.037 0.00 0.00 0.00 1.73
389 444 3.714144 AGACAGCTAACTACACTCCCAT 58.286 45.455 0.00 0.00 0.00 4.00
392 447 4.888239 TCCATAGACAGCTAACTACACTCC 59.112 45.833 0.00 0.00 0.00 3.85
405 460 7.386299 GCCAACAGATAATTAGTCCATAGACAG 59.614 40.741 0.00 0.00 46.15 3.51
413 468 3.883489 GTGGGCCAACAGATAATTAGTCC 59.117 47.826 8.40 0.00 0.00 3.85
415 470 4.862641 AGTGGGCCAACAGATAATTAGT 57.137 40.909 14.26 0.00 0.00 2.24
418 473 8.602472 TTAATTAAGTGGGCCAACAGATAATT 57.398 30.769 22.18 22.18 32.08 1.40
419 474 8.782137 ATTAATTAAGTGGGCCAACAGATAAT 57.218 30.769 14.26 11.08 0.00 1.28
420 475 8.474025 CAATTAATTAAGTGGGCCAACAGATAA 58.526 33.333 14.26 9.19 0.00 1.75
421 476 7.417342 GCAATTAATTAAGTGGGCCAACAGATA 60.417 37.037 22.94 0.00 32.42 1.98
422 477 6.630188 GCAATTAATTAAGTGGGCCAACAGAT 60.630 38.462 22.94 0.26 32.42 2.90
423 478 5.337169 GCAATTAATTAAGTGGGCCAACAGA 60.337 40.000 22.94 0.00 32.42 3.41
425 480 4.323104 GGCAATTAATTAAGTGGGCCAACA 60.323 41.667 22.94 0.00 39.88 3.33
429 492 3.741075 GCAGGCAATTAATTAAGTGGGCC 60.741 47.826 22.94 19.10 40.41 5.80
430 493 3.457234 GCAGGCAATTAATTAAGTGGGC 58.543 45.455 22.94 16.49 32.42 5.36
433 496 7.439056 CCAATTAGGCAGGCAATTAATTAAGTG 59.561 37.037 18.83 18.83 34.67 3.16
435 498 7.725251 TCCAATTAGGCAGGCAATTAATTAAG 58.275 34.615 0.00 0.00 37.29 1.85
464 527 6.351117 CCCTCGTACAATTAGAAAGAGAGGTT 60.351 42.308 6.88 0.00 40.64 3.50
465 528 5.127356 CCCTCGTACAATTAGAAAGAGAGGT 59.873 44.000 6.88 0.00 40.64 3.85
466 529 5.593010 CCCTCGTACAATTAGAAAGAGAGG 58.407 45.833 0.00 1.03 41.58 3.69
467 530 5.044558 GCCCTCGTACAATTAGAAAGAGAG 58.955 45.833 0.00 0.00 0.00 3.20
484 547 3.387397 CGGGTAGTTAATTAAGCCCTCG 58.613 50.000 20.95 11.15 34.17 4.63
486 549 2.158711 GGCGGGTAGTTAATTAAGCCCT 60.159 50.000 20.95 10.00 37.54 5.19
533 596 9.838339 TTTTCAAGCCTAATCAATTTAAAACCA 57.162 25.926 0.00 0.00 0.00 3.67
577 641 7.492352 AATTATGTGCGGAATTAGTTAGGTC 57.508 36.000 0.00 0.00 0.00 3.85
578 642 8.967664 TTAATTATGTGCGGAATTAGTTAGGT 57.032 30.769 0.00 0.00 31.09 3.08
587 651 7.283127 AGTCAGACAATTAATTATGTGCGGAAT 59.717 33.333 2.66 0.00 0.00 3.01
590 654 6.363577 AGTCAGACAATTAATTATGTGCGG 57.636 37.500 2.66 0.00 0.00 5.69
666 743 7.218014 CGTTGTTGTTTGGCACACATATATTAG 59.782 37.037 7.38 0.00 39.29 1.73
671 748 3.067461 ACGTTGTTGTTTGGCACACATAT 59.933 39.130 7.38 0.00 39.29 1.78
673 750 1.203523 ACGTTGTTGTTTGGCACACAT 59.796 42.857 7.38 0.00 39.29 3.21
678 755 0.881796 TGACACGTTGTTGTTTGGCA 59.118 45.000 0.00 0.00 0.00 4.92
679 756 1.983972 TTGACACGTTGTTGTTTGGC 58.016 45.000 0.00 0.00 0.00 4.52
680 757 4.032331 GGAAATTGACACGTTGTTGTTTGG 59.968 41.667 0.00 0.00 0.00 3.28
681 758 4.032331 GGGAAATTGACACGTTGTTGTTTG 59.968 41.667 0.00 0.00 0.00 2.93
683 760 3.445805 AGGGAAATTGACACGTTGTTGTT 59.554 39.130 0.00 0.00 0.00 2.83
684 761 3.020984 AGGGAAATTGACACGTTGTTGT 58.979 40.909 0.00 0.00 0.00 3.32
685 762 3.708563 AGGGAAATTGACACGTTGTTG 57.291 42.857 0.00 0.00 0.00 3.33
686 763 4.729227 AAAGGGAAATTGACACGTTGTT 57.271 36.364 0.00 0.00 0.00 2.83
687 764 5.838531 TTAAAGGGAAATTGACACGTTGT 57.161 34.783 0.00 0.00 0.00 3.32
688 765 7.590279 ACTATTAAAGGGAAATTGACACGTTG 58.410 34.615 0.00 0.00 0.00 4.10
690 767 8.851541 TTACTATTAAAGGGAAATTGACACGT 57.148 30.769 0.00 0.00 0.00 4.49
691 768 9.769093 CTTTACTATTAAAGGGAAATTGACACG 57.231 33.333 4.98 0.00 40.39 4.49
773 981 6.106877 TGACAAGTGAGAAAAAGAAACGAG 57.893 37.500 0.00 0.00 0.00 4.18
775 983 6.486248 TGATGACAAGTGAGAAAAAGAAACG 58.514 36.000 0.00 0.00 0.00 3.60
776 984 7.917505 ACATGATGACAAGTGAGAAAAAGAAAC 59.082 33.333 0.00 0.00 0.00 2.78
780 991 7.800380 GTGTACATGATGACAAGTGAGAAAAAG 59.200 37.037 0.00 0.00 0.00 2.27
807 1018 1.339920 TGATGCACCGATGGTCAACAT 60.340 47.619 0.00 0.00 44.18 2.71
818 1029 1.259770 CGATGAAGATGTGATGCACCG 59.740 52.381 0.00 0.00 32.73 4.94
819 1030 2.283298 ACGATGAAGATGTGATGCACC 58.717 47.619 0.00 0.00 32.73 5.01
920 1132 9.203421 GCACAACATTGCACTATATGTAGTATA 57.797 33.333 1.36 0.00 42.49 1.47
973 1188 2.030562 CGCGTCTCTTTGTGGGGT 59.969 61.111 0.00 0.00 0.00 4.95
992 1207 3.239861 GCCATAGCCATAGAGCACC 57.760 57.895 0.00 0.00 34.23 5.01
1011 1226 3.494048 CGAGGAGGAAGGGAATGATCTTG 60.494 52.174 0.00 0.00 0.00 3.02
1022 1237 2.950975 GGTACTAGAACGAGGAGGAAGG 59.049 54.545 0.00 0.00 0.00 3.46
1024 1239 2.309755 TGGGTACTAGAACGAGGAGGAA 59.690 50.000 0.00 0.00 0.00 3.36
1035 1250 1.070134 GCCATGCGAATGGGTACTAGA 59.930 52.381 24.35 0.00 41.94 2.43
1119 1340 0.461870 ATATGAGCTTCGTGCCGCAA 60.462 50.000 0.00 0.00 44.23 4.85
1137 1358 1.364171 GCGGATGCAGAGGTCGTAT 59.636 57.895 0.00 0.00 42.15 3.06
1168 1389 4.961511 GGACACGTCAGCACCGCA 62.962 66.667 0.00 0.00 0.00 5.69
1172 1393 4.295119 ACGGGGACACGTCAGCAC 62.295 66.667 0.00 0.00 45.08 4.40
1290 1511 2.492090 CCGGAGAGCGAGGAGTTG 59.508 66.667 0.00 0.00 0.00 3.16
1317 1538 2.435693 GCACCCCTCATAGGCGTCT 61.436 63.158 0.00 0.00 32.73 4.18
1326 1547 1.003839 GTCGTTCATGCACCCCTCA 60.004 57.895 0.00 0.00 0.00 3.86
1356 1577 2.278206 CGGTCGATGGAGCTGTCG 60.278 66.667 5.37 0.00 38.53 4.35
1442 1663 4.024670 GTCCCTACACTTCTCCACACTAT 58.975 47.826 0.00 0.00 0.00 2.12
1580 1801 0.467384 CGGACTGCCTCTTGATCCAT 59.533 55.000 0.00 0.00 0.00 3.41
1600 1821 8.560374 GGTATTTATTATTTGCTCTCTGGTGTC 58.440 37.037 0.00 0.00 0.00 3.67
1607 1828 9.971922 AATGCTTGGTATTTATTATTTGCTCTC 57.028 29.630 0.00 0.00 0.00 3.20
1627 1848 2.618053 GTAGCGGTGTACTCAATGCTT 58.382 47.619 11.90 1.14 37.44 3.91
1628 1849 1.134788 GGTAGCGGTGTACTCAATGCT 60.135 52.381 0.00 11.53 38.91 3.79
1710 1931 2.609459 CGAACATGGAGATGTAAGGTGC 59.391 50.000 0.00 0.00 42.30 5.01
1848 2082 5.531287 ACTGTTCTTGTATGGAAGGTGTTTC 59.469 40.000 0.00 0.00 34.93 2.78
1907 2142 7.289310 TCACCACATTACCACATGATGATTAT 58.711 34.615 0.00 0.00 0.00 1.28
1913 2154 4.209538 CCATCACCACATTACCACATGAT 58.790 43.478 0.00 0.00 0.00 2.45
1974 2216 3.002791 TGACGATTCTCTTGCATGGAAC 58.997 45.455 0.00 0.00 0.00 3.62
1977 2219 2.349590 TGTGACGATTCTCTTGCATGG 58.650 47.619 0.00 0.00 0.00 3.66
2177 2507 6.543100 GCCAGTGAGTTCTGTACTAGTAGTAT 59.457 42.308 13.09 0.00 37.17 2.12
2211 3088 6.259608 GGATTGTCAGTTGTATCATCTCCTTG 59.740 42.308 0.00 0.00 0.00 3.61
2231 3108 1.333524 GCGACGCTCATGAATGGATTG 60.334 52.381 13.73 0.00 0.00 2.67
2272 4052 4.220382 TCTCCCAATTAATTGCACCAAGTG 59.780 41.667 20.67 6.31 36.48 3.16
2365 4733 1.149174 CGGTGGAGCCAGCCAATAT 59.851 57.895 12.65 0.00 40.20 1.28
2435 4816 4.092529 CACTCTCTGTGCACATGTATTGAC 59.907 45.833 22.00 0.00 40.06 3.18
2471 4852 1.925285 CTAGGGCCCAGCATGTCCAA 61.925 60.000 27.56 0.00 0.00 3.53
2525 4906 6.569801 GCATGTAACACTATATAGCGGTCAGA 60.570 42.308 9.78 0.00 0.00 3.27
2532 4913 8.939201 AGATCATGCATGTAACACTATATAGC 57.061 34.615 25.43 5.24 0.00 2.97
2537 4918 9.212641 GACAATAGATCATGCATGTAACACTAT 57.787 33.333 25.43 20.72 0.00 2.12
2538 4919 8.203485 TGACAATAGATCATGCATGTAACACTA 58.797 33.333 25.43 19.69 0.00 2.74
2539 4920 7.049754 TGACAATAGATCATGCATGTAACACT 58.950 34.615 25.43 18.45 0.00 3.55
2540 4921 7.250445 TGACAATAGATCATGCATGTAACAC 57.750 36.000 25.43 13.17 0.00 3.32
2541 4922 6.484308 CCTGACAATAGATCATGCATGTAACA 59.516 38.462 25.43 7.44 0.00 2.41
2542 4923 6.072838 CCCTGACAATAGATCATGCATGTAAC 60.073 42.308 25.43 16.93 0.00 2.50
2543 4924 5.999600 CCCTGACAATAGATCATGCATGTAA 59.000 40.000 25.43 8.61 0.00 2.41
2544 4925 5.513614 CCCCTGACAATAGATCATGCATGTA 60.514 44.000 25.43 11.89 0.00 2.29
2545 4926 4.395625 CCCTGACAATAGATCATGCATGT 58.604 43.478 25.43 13.42 0.00 3.21
2546 4927 3.756963 CCCCTGACAATAGATCATGCATG 59.243 47.826 21.07 21.07 0.00 4.06
2547 4928 3.396946 ACCCCTGACAATAGATCATGCAT 59.603 43.478 0.00 0.00 0.00 3.96
2548 4929 2.779430 ACCCCTGACAATAGATCATGCA 59.221 45.455 0.00 0.00 0.00 3.96
2549 4930 3.144506 CACCCCTGACAATAGATCATGC 58.855 50.000 0.00 0.00 0.00 4.06
2550 4931 3.392285 TCCACCCCTGACAATAGATCATG 59.608 47.826 0.00 0.00 0.00 3.07
2551 4932 3.668821 TCCACCCCTGACAATAGATCAT 58.331 45.455 0.00 0.00 0.00 2.45
2552 4933 3.129262 TCCACCCCTGACAATAGATCA 57.871 47.619 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.