Multiple sequence alignment - TraesCS2B01G453600

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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 TraesCS2B01G453600 chr2B 100.000 2198 0 0 1 2198 647450070 647452267 0.000000e+00 4060.0
1 TraesCS2B01G453600 chr2B 88.889 549 30 6 720 1256 647538813 647539342 0.000000e+00 647.0
2 TraesCS2B01G453600 chr2B 93.842 406 25 0 1 406 647538135 647538540 1.440000e-171 612.0
3 TraesCS2B01G453600 chr2B 86.364 484 23 13 1538 1992 647539689 647540158 2.540000e-134 488.0
4 TraesCS2B01G453600 chr2B 83.044 519 55 20 855 1347 647603732 647604243 7.200000e-120 440.0
5 TraesCS2B01G453600 chr2B 84.615 312 19 10 1283 1570 647539444 647539750 1.280000e-72 283.0
6 TraesCS2B01G453600 chr2B 82.400 125 11 5 1389 1502 647604328 647604452 4.990000e-17 99.0
7 TraesCS2B01G453600 chr2B 82.927 123 6 8 406 513 647538699 647538821 1.800000e-16 97.1
8 TraesCS2B01G453600 chr2D 90.035 853 49 19 721 1552 542543683 542544520 0.000000e+00 1072.0
9 TraesCS2B01G453600 chr2D 86.018 894 70 32 711 1579 542328519 542329382 0.000000e+00 907.0
10 TraesCS2B01G453600 chr2D 82.979 799 56 31 828 1579 542710386 542711151 0.000000e+00 649.0
11 TraesCS2B01G453600 chr2D 85.082 610 33 20 1538 2097 542329310 542329911 8.810000e-159 569.0
12 TraesCS2B01G453600 chr2D 84.815 540 37 19 1538 2053 542711078 542711596 3.260000e-138 501.0
13 TraesCS2B01G453600 chr2D 85.393 445 38 12 828 1251 542777834 542778272 9.320000e-119 436.0
14 TraesCS2B01G453600 chr2D 83.298 473 25 20 1564 2019 542544477 542544912 9.520000e-104 387.0
15 TraesCS2B01G453600 chr2D 89.326 178 10 6 1 173 542687480 542687653 4.750000e-52 215.0
16 TraesCS2B01G453600 chr2D 95.556 45 2 0 2098 2142 491373807 491373851 3.030000e-09 73.1
17 TraesCS2B01G453600 chr2A 86.104 806 55 27 720 1500 685373379 685374152 0.000000e+00 815.0
18 TraesCS2B01G453600 chr2A 85.135 666 51 23 801 1462 685380432 685381053 2.380000e-179 638.0
19 TraesCS2B01G453600 chr2A 82.505 503 62 17 855 1343 685626706 685627196 3.380000e-113 418.0
20 TraesCS2B01G453600 chr2A 82.833 466 43 18 1 456 685372859 685373297 1.230000e-102 383.0
21 TraesCS2B01G453600 chr2A 79.355 155 12 14 1899 2053 685381470 685381604 8.360000e-15 91.6
22 TraesCS2B01G453600 chr2A 100.000 42 0 0 720 761 685380372 685380413 6.510000e-11 78.7
23 TraesCS2B01G453600 chr6D 88.942 208 21 2 511 718 456277690 456277485 2.800000e-64 255.0
24 TraesCS2B01G453600 chr6B 87.383 214 23 2 508 717 50414366 50414153 2.180000e-60 243.0
25 TraesCS2B01G453600 chrUn 87.678 211 21 2 512 717 171112601 171112391 7.840000e-60 241.0
26 TraesCS2B01G453600 chrUn 87.619 210 21 2 512 717 138415666 138415874 2.820000e-59 239.0
27 TraesCS2B01G453600 chrUn 87.143 210 23 1 512 717 138271934 138272143 3.650000e-58 235.0
28 TraesCS2B01G453600 chrUn 87.143 210 23 1 512 717 138484730 138484939 3.650000e-58 235.0
29 TraesCS2B01G453600 chr6A 87.619 210 22 1 512 717 558457705 558457496 7.840000e-60 241.0
30 TraesCS2B01G453600 chr6A 87.619 210 22 1 512 717 558461025 558460816 7.840000e-60 241.0
31 TraesCS2B01G453600 chr6A 97.674 43 1 0 2100 2142 484498 484456 8.420000e-10 75.0
32 TraesCS2B01G453600 chr4A 86.854 213 24 1 512 720 733355898 733355686 3.650000e-58 235.0
33 TraesCS2B01G453600 chr7D 97.872 47 1 0 2098 2144 612880966 612881012 5.030000e-12 82.4
34 TraesCS2B01G453600 chr3B 97.727 44 1 0 2101 2144 412593471 412593428 2.340000e-10 76.8
35 TraesCS2B01G453600 chr3B 92.000 50 3 1 2093 2142 437506758 437506710 3.920000e-08 69.4
36 TraesCS2B01G453600 chr7B 97.674 43 1 0 2100 2142 195210318 195210276 8.420000e-10 75.0
37 TraesCS2B01G453600 chr1B 92.453 53 2 2 2092 2142 572303 572251 8.420000e-10 75.0
38 TraesCS2B01G453600 chr5D 95.556 45 2 0 2098 2142 380846924 380846968 3.030000e-09 73.1
39 TraesCS2B01G453600 chr1D 97.619 42 1 0 2101 2142 447257723 447257682 3.030000e-09 73.1


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 TraesCS2B01G453600 chr2B 647450070 647452267 2197 False 4060.000000 4060 100.000000 1 2198 1 chr2B.!!$F1 2197
1 TraesCS2B01G453600 chr2B 647538135 647540158 2023 False 425.420000 647 87.327400 1 1992 5 chr2B.!!$F2 1991
2 TraesCS2B01G453600 chr2B 647603732 647604452 720 False 269.500000 440 82.722000 855 1502 2 chr2B.!!$F3 647
3 TraesCS2B01G453600 chr2D 542328519 542329911 1392 False 738.000000 907 85.550000 711 2097 2 chr2D.!!$F4 1386
4 TraesCS2B01G453600 chr2D 542543683 542544912 1229 False 729.500000 1072 86.666500 721 2019 2 chr2D.!!$F5 1298
5 TraesCS2B01G453600 chr2D 542710386 542711596 1210 False 575.000000 649 83.897000 828 2053 2 chr2D.!!$F6 1225
6 TraesCS2B01G453600 chr2A 685372859 685374152 1293 False 599.000000 815 84.468500 1 1500 2 chr2A.!!$F2 1499
7 TraesCS2B01G453600 chr2A 685380372 685381604 1232 False 269.433333 638 88.163333 720 2053 3 chr2A.!!$F3 1333
8 TraesCS2B01G453600 chr6A 558457496 558461025 3529 True 241.000000 241 87.619000 512 717 2 chr6A.!!$R2 205

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
636 891 0.115745 TAAGGAGGTGGGACCGAACT 59.884 55.0 0.0 0.0 44.9 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1743 5073 0.601046 CAGCTCAGGTTGAACAGCGA 60.601 55.0 0.0 0.0 0.0 4.93 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
131 136 2.015736 TTTGGCACGTGCACATTTTT 57.984 40.000 38.60 0.00 44.36 1.94
139 144 4.025813 GCACGTGCACATTTTTCATTTTCT 60.026 37.500 34.52 0.00 41.59 2.52
166 171 9.109393 AGTATTGTTTGTAGGCAACATATACAG 57.891 33.333 14.97 0.00 38.10 2.74
232 240 9.614792 AACAACTATATCCAAACTAAGATGTCC 57.385 33.333 0.00 0.00 0.00 4.02
233 241 8.211629 ACAACTATATCCAAACTAAGATGTCCC 58.788 37.037 0.00 0.00 0.00 4.46
259 267 3.369385 CGTAGGTCTTATCGCGTTCATT 58.631 45.455 5.77 0.00 0.00 2.57
288 296 6.658849 AGCCCAAAAGACCAAAAACTTTATT 58.341 32.000 0.00 0.00 35.66 1.40
303 328 9.651913 AAAAACTTTATTTTATCATGGATGCGT 57.348 25.926 0.00 0.00 30.98 5.24
306 331 9.897744 AACTTTATTTTATCATGGATGCGTATG 57.102 29.630 0.00 0.00 0.00 2.39
307 332 9.283768 ACTTTATTTTATCATGGATGCGTATGA 57.716 29.630 0.00 0.00 37.68 2.15
311 336 5.611796 TTATCATGGATGCGTATGAAAGC 57.388 39.130 0.00 0.00 36.93 3.51
319 344 2.016318 TGCGTATGAAAGCAAGATGGG 58.984 47.619 0.00 0.00 40.78 4.00
320 345 2.288666 GCGTATGAAAGCAAGATGGGA 58.711 47.619 0.00 0.00 0.00 4.37
321 346 2.682856 GCGTATGAAAGCAAGATGGGAA 59.317 45.455 0.00 0.00 0.00 3.97
322 347 3.487544 GCGTATGAAAGCAAGATGGGAAC 60.488 47.826 0.00 0.00 0.00 3.62
391 416 9.144298 ACATATAGTAATGTACTGTACCAAGCT 57.856 33.333 14.91 10.35 38.31 3.74
407 432 5.539048 ACCAAGCTGTTTGTGTAGTACTAG 58.461 41.667 1.87 0.00 34.87 2.57
408 433 5.070047 ACCAAGCTGTTTGTGTAGTACTAGT 59.930 40.000 1.87 0.00 34.87 2.57
449 634 0.738412 GTCCACTAGCGCCGCTAAAA 60.738 55.000 20.50 0.00 40.82 1.52
516 767 1.592669 GGGAGACGCACATGGATCG 60.593 63.158 0.00 0.00 0.00 3.69
524 775 1.750018 CACATGGATCGGGCTTGCA 60.750 57.895 0.00 0.00 0.00 4.08
533 784 2.363406 GGGCTTGCATGCTCCCTT 60.363 61.111 25.81 0.00 35.87 3.95
546 797 2.276309 CTCCCTTCCCATGCTCCCAC 62.276 65.000 0.00 0.00 0.00 4.61
548 799 2.311854 CCTTCCCATGCTCCCACCT 61.312 63.158 0.00 0.00 0.00 4.00
555 806 1.922369 ATGCTCCCACCTGTGCTCT 60.922 57.895 0.00 0.00 0.00 4.09
556 807 1.495579 ATGCTCCCACCTGTGCTCTT 61.496 55.000 0.00 0.00 0.00 2.85
561 812 2.039084 CTCCCACCTGTGCTCTTACTTT 59.961 50.000 0.00 0.00 0.00 2.66
571 822 4.049869 GTGCTCTTACTTTATCCTACGGC 58.950 47.826 0.00 0.00 0.00 5.68
612 867 9.621239 ATTTCTAATCTAATCATCTCACCCCTA 57.379 33.333 0.00 0.00 0.00 3.53
622 877 6.901615 TCATCTCACCCCTAATTTTAAGGA 57.098 37.500 0.00 0.00 36.08 3.36
629 884 3.530149 CCCCTAATTTTAAGGAGGTGGGA 59.470 47.826 0.00 0.00 36.08 4.37
633 888 1.732117 TTTTAAGGAGGTGGGACCGA 58.268 50.000 0.00 0.00 44.90 4.69
636 891 0.115745 TAAGGAGGTGGGACCGAACT 59.884 55.000 0.00 0.00 44.90 3.01
684 939 1.153188 TACGCGGGAGTACGGATGA 60.153 57.895 12.47 0.00 0.00 2.92
685 940 0.747644 TACGCGGGAGTACGGATGAA 60.748 55.000 12.47 0.00 0.00 2.57
690 945 1.136305 CGGGAGTACGGATGAACACAT 59.864 52.381 0.00 0.00 0.00 3.21
693 948 2.616960 GAGTACGGATGAACACATGCA 58.383 47.619 0.00 0.00 33.11 3.96
717 972 2.435059 GCAGGCAAGTCTCGTCCC 60.435 66.667 0.00 0.00 0.00 4.46
718 973 3.059982 CAGGCAAGTCTCGTCCCA 58.940 61.111 0.00 0.00 0.00 4.37
925 4005 0.348370 ATCCCACCTCCCTCCAATCT 59.652 55.000 0.00 0.00 0.00 2.40
927 4007 0.327000 CCCACCTCCCTCCAATCTCT 60.327 60.000 0.00 0.00 0.00 3.10
936 4018 5.011943 CCTCCCTCCAATCTCTATCTTCTTG 59.988 48.000 0.00 0.00 0.00 3.02
980 4080 0.820482 CCATCGATGGCAGCAATGGA 60.820 55.000 30.53 0.00 41.75 3.41
1193 4293 1.154073 GCCTCGTCACCGTCTACAC 60.154 63.158 0.00 0.00 35.01 2.90
1233 4370 2.471815 ACTCCTACCGATCCATCCAA 57.528 50.000 0.00 0.00 0.00 3.53
1319 4562 4.179298 GGTTACGGTCCTAAAGTAGCTTG 58.821 47.826 0.00 0.00 0.00 4.01
1320 4563 2.381725 ACGGTCCTAAAGTAGCTTGC 57.618 50.000 0.00 0.00 0.00 4.01
1321 4564 1.900486 ACGGTCCTAAAGTAGCTTGCT 59.100 47.619 0.00 0.00 0.00 3.91
1322 4565 3.094572 ACGGTCCTAAAGTAGCTTGCTA 58.905 45.455 0.00 0.00 0.00 3.49
1370 4657 8.725148 CATTCATCTAATTTCCAGTAGCCATAC 58.275 37.037 0.00 0.00 0.00 2.39
1420 4716 1.406539 CAAAACTGGCACTCTGCTGTT 59.593 47.619 0.00 0.00 44.28 3.16
1551 4868 8.990163 TTTTGAGTAACCCTTCTTGATTAAGT 57.010 30.769 0.00 0.00 35.38 2.24
1552 4869 8.990163 TTTGAGTAACCCTTCTTGATTAAGTT 57.010 30.769 0.00 0.00 35.38 2.66
1553 4870 8.990163 TTGAGTAACCCTTCTTGATTAAGTTT 57.010 30.769 0.00 0.00 35.38 2.66
1554 4871 8.990163 TGAGTAACCCTTCTTGATTAAGTTTT 57.010 30.769 0.00 0.00 35.38 2.43
1555 4872 9.416284 TGAGTAACCCTTCTTGATTAAGTTTTT 57.584 29.630 0.00 0.00 35.38 1.94
1641 4960 0.034574 ATTAATGCACGGCTGGGACA 60.035 50.000 0.00 0.00 0.00 4.02
1671 4994 5.589855 TCATGGTGATCGATAAAATGCAGTT 59.410 36.000 0.00 0.00 0.00 3.16
1674 4997 4.335315 GGTGATCGATAAAATGCAGTTCCA 59.665 41.667 0.00 0.00 0.00 3.53
1682 5005 0.610232 AATGCAGTTCCAGCCCACTC 60.610 55.000 0.00 0.00 0.00 3.51
1708 5031 0.376502 GACTAGCGTACCCGTCTGTC 59.623 60.000 0.00 0.00 36.15 3.51
1709 5032 0.321919 ACTAGCGTACCCGTCTGTCA 60.322 55.000 0.00 0.00 36.15 3.58
1739 5069 3.939592 AGTACATTGACTCGTCTCGATCA 59.060 43.478 0.00 0.00 34.61 2.92
1743 5073 4.097135 ACATTGACTCGTCTCGATCAATCT 59.903 41.667 17.52 10.19 39.48 2.40
1994 5402 1.935199 GTAAAATCCCCGCGATTCGAA 59.065 47.619 8.23 0.00 40.47 3.71
2060 5479 1.267121 GAGCCAGACCCTGTTCAGTA 58.733 55.000 0.00 0.00 0.00 2.74
2069 5488 5.765182 CAGACCCTGTTCAGTATTCACTTTT 59.235 40.000 0.00 0.00 30.46 2.27
2076 5495 7.041644 CCTGTTCAGTATTCACTTTTTAACCGA 60.042 37.037 0.00 0.00 30.46 4.69
2105 5524 6.631016 TGTCATGACAGTTCATTAGTACTCC 58.369 40.000 24.56 0.00 40.79 3.85
2106 5525 6.043411 GTCATGACAGTTCATTAGTACTCCC 58.957 44.000 21.07 0.00 40.79 4.30
2107 5526 5.958380 TCATGACAGTTCATTAGTACTCCCT 59.042 40.000 0.00 0.00 40.79 4.20
2108 5527 5.916661 TGACAGTTCATTAGTACTCCCTC 57.083 43.478 0.00 0.00 0.00 4.30
2109 5528 4.710375 TGACAGTTCATTAGTACTCCCTCC 59.290 45.833 0.00 0.00 0.00 4.30
2110 5529 3.700038 ACAGTTCATTAGTACTCCCTCCG 59.300 47.826 0.00 0.00 0.00 4.63
2111 5530 3.700038 CAGTTCATTAGTACTCCCTCCGT 59.300 47.826 0.00 0.00 0.00 4.69
2112 5531 4.159879 CAGTTCATTAGTACTCCCTCCGTT 59.840 45.833 0.00 0.00 0.00 4.44
2113 5532 4.776308 AGTTCATTAGTACTCCCTCCGTTT 59.224 41.667 0.00 0.00 0.00 3.60
2114 5533 4.996788 TCATTAGTACTCCCTCCGTTTC 57.003 45.455 0.00 0.00 0.00 2.78
2115 5534 4.346730 TCATTAGTACTCCCTCCGTTTCA 58.653 43.478 0.00 0.00 0.00 2.69
2116 5535 4.773674 TCATTAGTACTCCCTCCGTTTCAA 59.226 41.667 0.00 0.00 0.00 2.69
2117 5536 5.246656 TCATTAGTACTCCCTCCGTTTCAAA 59.753 40.000 0.00 0.00 0.00 2.69
2118 5537 5.549742 TTAGTACTCCCTCCGTTTCAAAA 57.450 39.130 0.00 0.00 0.00 2.44
2119 5538 4.635699 AGTACTCCCTCCGTTTCAAAAT 57.364 40.909 0.00 0.00 0.00 1.82
2120 5539 5.750352 AGTACTCCCTCCGTTTCAAAATA 57.250 39.130 0.00 0.00 0.00 1.40
2121 5540 6.117975 AGTACTCCCTCCGTTTCAAAATAA 57.882 37.500 0.00 0.00 0.00 1.40
2122 5541 6.536447 AGTACTCCCTCCGTTTCAAAATAAA 58.464 36.000 0.00 0.00 0.00 1.40
2123 5542 7.173032 AGTACTCCCTCCGTTTCAAAATAAAT 58.827 34.615 0.00 0.00 0.00 1.40
2124 5543 6.267496 ACTCCCTCCGTTTCAAAATAAATG 57.733 37.500 0.00 0.00 0.00 2.32
2125 5544 6.007703 ACTCCCTCCGTTTCAAAATAAATGA 58.992 36.000 0.00 0.00 0.00 2.57
2126 5545 6.072119 ACTCCCTCCGTTTCAAAATAAATGAC 60.072 38.462 0.00 0.00 0.00 3.06
2127 5546 6.007703 TCCCTCCGTTTCAAAATAAATGACT 58.992 36.000 0.00 0.00 0.00 3.41
2128 5547 6.150474 TCCCTCCGTTTCAAAATAAATGACTC 59.850 38.462 0.00 0.00 0.00 3.36
2129 5548 6.072175 CCCTCCGTTTCAAAATAAATGACTCA 60.072 38.462 0.00 0.00 0.00 3.41
2130 5549 7.367285 CCTCCGTTTCAAAATAAATGACTCAA 58.633 34.615 0.00 0.00 0.00 3.02
2131 5550 7.326063 CCTCCGTTTCAAAATAAATGACTCAAC 59.674 37.037 0.00 0.00 0.00 3.18
2132 5551 7.936584 TCCGTTTCAAAATAAATGACTCAACT 58.063 30.769 0.00 0.00 0.00 3.16
2133 5552 8.410141 TCCGTTTCAAAATAAATGACTCAACTT 58.590 29.630 0.00 0.00 0.00 2.66
2134 5553 9.030301 CCGTTTCAAAATAAATGACTCAACTTT 57.970 29.630 0.00 0.00 0.00 2.66
2175 5594 9.823647 AGATTGTTATACTAAGATGTGTTCAGG 57.176 33.333 0.00 0.00 0.00 3.86
2176 5595 8.964476 ATTGTTATACTAAGATGTGTTCAGGG 57.036 34.615 0.00 0.00 0.00 4.45
2177 5596 7.490657 TGTTATACTAAGATGTGTTCAGGGT 57.509 36.000 0.00 0.00 0.00 4.34
2178 5597 7.913789 TGTTATACTAAGATGTGTTCAGGGTT 58.086 34.615 0.00 0.00 0.00 4.11
2179 5598 9.038072 TGTTATACTAAGATGTGTTCAGGGTTA 57.962 33.333 0.00 0.00 0.00 2.85
2180 5599 9.880157 GTTATACTAAGATGTGTTCAGGGTTAA 57.120 33.333 0.00 0.00 0.00 2.01
2181 5600 9.880157 TTATACTAAGATGTGTTCAGGGTTAAC 57.120 33.333 0.00 0.00 0.00 2.01
2182 5601 6.435292 ACTAAGATGTGTTCAGGGTTAACT 57.565 37.500 5.42 0.00 0.00 2.24
2183 5602 6.231211 ACTAAGATGTGTTCAGGGTTAACTG 58.769 40.000 5.42 0.00 39.84 3.16
2184 5603 4.706842 AGATGTGTTCAGGGTTAACTGT 57.293 40.909 5.42 0.00 39.48 3.55
2185 5604 5.818678 AGATGTGTTCAGGGTTAACTGTA 57.181 39.130 5.42 0.00 39.48 2.74
2186 5605 5.794894 AGATGTGTTCAGGGTTAACTGTAG 58.205 41.667 5.42 0.00 39.48 2.74
2187 5606 4.345859 TGTGTTCAGGGTTAACTGTAGG 57.654 45.455 5.42 0.00 39.48 3.18
2188 5607 3.968649 TGTGTTCAGGGTTAACTGTAGGA 59.031 43.478 5.42 0.00 39.48 2.94
2189 5608 4.595781 TGTGTTCAGGGTTAACTGTAGGAT 59.404 41.667 5.42 0.00 39.48 3.24
2190 5609 5.072600 TGTGTTCAGGGTTAACTGTAGGATT 59.927 40.000 5.42 0.00 39.48 3.01
2191 5610 6.270463 TGTGTTCAGGGTTAACTGTAGGATTA 59.730 38.462 5.42 0.00 39.48 1.75
2192 5611 7.037873 TGTGTTCAGGGTTAACTGTAGGATTAT 60.038 37.037 5.42 0.00 39.48 1.28
2193 5612 8.480501 GTGTTCAGGGTTAACTGTAGGATTATA 58.519 37.037 5.42 0.00 39.48 0.98
2194 5613 8.480501 TGTTCAGGGTTAACTGTAGGATTATAC 58.519 37.037 5.42 0.00 39.48 1.47
2195 5614 8.702819 GTTCAGGGTTAACTGTAGGATTATACT 58.297 37.037 5.42 0.00 39.48 2.12
2196 5615 8.474710 TCAGGGTTAACTGTAGGATTATACTC 57.525 38.462 5.42 0.00 39.48 2.59
2197 5616 7.508296 TCAGGGTTAACTGTAGGATTATACTCC 59.492 40.741 5.42 0.79 39.48 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.528018 TTTGATTTTTGCTAAAAAGAATCGACT 57.472 25.926 10.04 0.00 42.97 4.18
131 136 8.856153 TGCCTACAAACAATACTAGAAAATGA 57.144 30.769 0.00 0.00 0.00 2.57
232 240 1.537562 GCGATAAGACCTACGGTTGGG 60.538 57.143 13.10 6.00 35.25 4.12
233 241 1.849097 GCGATAAGACCTACGGTTGG 58.151 55.000 7.08 7.08 35.25 3.77
244 252 4.042398 GCTAGACAATGAACGCGATAAGA 58.958 43.478 15.93 0.00 0.00 2.10
259 267 3.586470 TTTGGTCTTTTGGGCTAGACA 57.414 42.857 0.00 0.00 41.99 3.41
288 296 5.530543 TGCTTTCATACGCATCCATGATAAA 59.469 36.000 0.00 0.00 31.50 1.40
301 326 3.689161 TGTTCCCATCTTGCTTTCATACG 59.311 43.478 0.00 0.00 0.00 3.06
303 328 3.689161 CGTGTTCCCATCTTGCTTTCATA 59.311 43.478 0.00 0.00 0.00 2.15
305 330 1.879380 CGTGTTCCCATCTTGCTTTCA 59.121 47.619 0.00 0.00 0.00 2.69
306 331 1.401539 GCGTGTTCCCATCTTGCTTTC 60.402 52.381 0.00 0.00 0.00 2.62
307 332 0.598065 GCGTGTTCCCATCTTGCTTT 59.402 50.000 0.00 0.00 0.00 3.51
308 333 0.537143 TGCGTGTTCCCATCTTGCTT 60.537 50.000 0.00 0.00 0.00 3.91
309 334 0.322816 ATGCGTGTTCCCATCTTGCT 60.323 50.000 0.00 0.00 0.00 3.91
310 335 0.179156 CATGCGTGTTCCCATCTTGC 60.179 55.000 0.00 0.00 0.00 4.01
311 336 0.179156 GCATGCGTGTTCCCATCTTG 60.179 55.000 0.00 0.00 0.00 3.02
312 337 0.608856 TGCATGCGTGTTCCCATCTT 60.609 50.000 14.09 0.00 0.00 2.40
313 338 0.394762 ATGCATGCGTGTTCCCATCT 60.395 50.000 12.68 0.00 0.00 2.90
314 339 1.308047 TATGCATGCGTGTTCCCATC 58.692 50.000 22.77 0.00 0.00 3.51
315 340 1.761449 TTATGCATGCGTGTTCCCAT 58.239 45.000 22.77 5.40 0.00 4.00
316 341 1.201181 GTTTATGCATGCGTGTTCCCA 59.799 47.619 22.77 0.00 0.00 4.37
317 342 1.472480 AGTTTATGCATGCGTGTTCCC 59.528 47.619 22.77 5.81 0.00 3.97
318 343 2.919666 AGTTTATGCATGCGTGTTCC 57.080 45.000 22.77 7.52 0.00 3.62
319 344 6.307800 ACATTAAAGTTTATGCATGCGTGTTC 59.692 34.615 22.77 11.50 0.00 3.18
320 345 6.155827 ACATTAAAGTTTATGCATGCGTGTT 58.844 32.000 22.77 10.42 0.00 3.32
321 346 5.708948 ACATTAAAGTTTATGCATGCGTGT 58.291 33.333 22.77 8.91 0.00 4.49
322 347 6.630676 AACATTAAAGTTTATGCATGCGTG 57.369 33.333 22.77 0.09 0.00 5.34
389 414 8.928270 AATCATACTAGTACTACACAAACAGC 57.072 34.615 4.31 0.00 0.00 4.40
432 617 0.459585 TCTTTTAGCGGCGCTAGTGG 60.460 55.000 36.13 27.98 42.34 4.00
503 754 3.329542 AAGCCCGATCCATGTGCGT 62.330 57.895 0.00 0.00 0.00 5.24
504 755 2.514592 AAGCCCGATCCATGTGCG 60.515 61.111 0.00 0.00 0.00 5.34
505 756 3.113745 CAAGCCCGATCCATGTGC 58.886 61.111 0.00 0.00 0.00 4.57
506 757 1.105167 ATGCAAGCCCGATCCATGTG 61.105 55.000 0.00 0.00 0.00 3.21
507 758 1.105167 CATGCAAGCCCGATCCATGT 61.105 55.000 0.00 0.00 0.00 3.21
508 759 1.658114 CATGCAAGCCCGATCCATG 59.342 57.895 0.00 0.00 0.00 3.66
509 760 2.198287 GCATGCAAGCCCGATCCAT 61.198 57.895 14.21 0.00 0.00 3.41
510 761 2.829914 GCATGCAAGCCCGATCCA 60.830 61.111 14.21 0.00 0.00 3.41
516 767 2.363406 AAGGGAGCATGCAAGCCC 60.363 61.111 26.80 26.80 41.00 5.19
524 775 1.535685 GAGCATGGGAAGGGAGCAT 59.464 57.895 0.00 0.00 0.00 3.79
533 784 2.204136 ACAGGTGGGAGCATGGGA 60.204 61.111 0.00 0.00 0.00 4.37
546 797 5.282510 CGTAGGATAAAGTAAGAGCACAGG 58.717 45.833 0.00 0.00 0.00 4.00
584 835 9.883142 GGGGTGAGATGATTAGATTAGAAATAG 57.117 37.037 0.00 0.00 0.00 1.73
585 836 9.621239 AGGGGTGAGATGATTAGATTAGAAATA 57.379 33.333 0.00 0.00 0.00 1.40
586 837 8.517323 AGGGGTGAGATGATTAGATTAGAAAT 57.483 34.615 0.00 0.00 0.00 2.17
606 861 3.271225 CCCACCTCCTTAAAATTAGGGGT 59.729 47.826 1.97 0.00 37.03 4.95
612 867 2.645797 TCGGTCCCACCTCCTTAAAATT 59.354 45.455 0.00 0.00 35.66 1.82
622 877 3.801307 AAATAAAGTTCGGTCCCACCT 57.199 42.857 0.00 0.00 35.66 4.00
629 884 7.519032 TGATTGGAAGAAAATAAAGTTCGGT 57.481 32.000 0.00 0.00 0.00 4.69
636 891 9.218440 GGCTTGATTTGATTGGAAGAAAATAAA 57.782 29.630 0.00 0.00 0.00 1.40
676 931 1.406751 CCCTGCATGTGTTCATCCGTA 60.407 52.381 0.00 0.00 31.15 4.02
684 939 2.036256 GCTCCCCCTGCATGTGTT 59.964 61.111 0.00 0.00 0.00 3.32
685 940 3.259314 TGCTCCCCCTGCATGTGT 61.259 61.111 0.00 0.00 35.31 3.72
693 948 3.334054 GACTTGCCTGCTCCCCCT 61.334 66.667 0.00 0.00 0.00 4.79
1193 4293 0.250081 GAGGCTTGGATTCGGCTAGG 60.250 60.000 0.00 0.00 36.05 3.02
1233 4370 1.802880 GCACGCTAGTTGATCGATGGT 60.803 52.381 0.54 0.00 0.00 3.55
1320 4563 4.873746 TTACATTAGCCAGGCTAGCTAG 57.126 45.455 20.85 16.84 43.39 3.42
1321 4564 5.306937 TGAATTACATTAGCCAGGCTAGCTA 59.693 40.000 20.85 10.70 42.34 3.32
1322 4565 4.103153 TGAATTACATTAGCCAGGCTAGCT 59.897 41.667 20.85 13.01 42.34 3.32
1370 4657 0.034059 CGCCCACCAGATTAGCTAGG 59.966 60.000 0.00 0.00 0.00 3.02
1420 4716 1.141657 ACAGAGAGGTTGCTGCAAGAA 59.858 47.619 16.53 0.00 34.07 2.52
1621 4940 0.663153 GTCCCAGCCGTGCATTAATC 59.337 55.000 0.00 0.00 0.00 1.75
1627 4946 3.555324 TTCTGTCCCAGCCGTGCA 61.555 61.111 0.00 0.00 0.00 4.57
1641 4960 7.521099 GCATTTTATCGATCACCATGATGTTCT 60.521 37.037 0.00 0.00 37.20 3.01
1644 4963 5.532032 TGCATTTTATCGATCACCATGATGT 59.468 36.000 0.00 0.00 37.20 3.06
1671 4994 4.270153 ACTGGGGAGTGGGCTGGA 62.270 66.667 0.00 0.00 0.00 3.86
1674 4997 2.106923 TAGTCACTGGGGAGTGGGCT 62.107 60.000 0.00 0.00 40.03 5.19
1682 5005 1.673808 GGGTACGCTAGTCACTGGGG 61.674 65.000 3.44 3.44 0.00 4.96
1739 5069 2.693069 CTCAGGTTGAACAGCGAGATT 58.307 47.619 0.00 0.00 0.00 2.40
1743 5073 0.601046 CAGCTCAGGTTGAACAGCGA 60.601 55.000 0.00 0.00 0.00 4.93
1796 5131 6.071334 ACTGCTTAAGTGCTTATCAGTACAGA 60.071 38.462 17.62 0.00 38.07 3.41
1807 5145 3.873952 GCTGCTATACTGCTTAAGTGCTT 59.126 43.478 4.02 0.00 40.26 3.91
1809 5147 2.545946 GGCTGCTATACTGCTTAAGTGC 59.454 50.000 4.02 0.00 42.51 4.40
1810 5148 3.557595 GTGGCTGCTATACTGCTTAAGTG 59.442 47.826 4.02 0.37 42.51 3.16
1811 5149 3.197766 TGTGGCTGCTATACTGCTTAAGT 59.802 43.478 4.02 0.00 42.51 2.24
1812 5150 3.797039 TGTGGCTGCTATACTGCTTAAG 58.203 45.455 0.00 0.00 42.51 1.85
1813 5151 3.450817 TCTGTGGCTGCTATACTGCTTAA 59.549 43.478 0.00 0.00 42.51 1.85
2060 5479 6.540914 TGACAGACTTCGGTTAAAAAGTGAAT 59.459 34.615 4.41 0.00 35.90 2.57
2069 5488 4.594123 TGTCATGACAGACTTCGGTTAA 57.406 40.909 24.56 0.00 39.27 2.01
2091 5510 4.732672 AACGGAGGGAGTACTAATGAAC 57.267 45.455 0.00 0.00 0.00 3.18
2097 5516 5.750352 ATTTTGAAACGGAGGGAGTACTA 57.250 39.130 0.00 0.00 0.00 1.82
2098 5517 4.635699 ATTTTGAAACGGAGGGAGTACT 57.364 40.909 0.00 0.00 0.00 2.73
2099 5518 6.806388 TTTATTTTGAAACGGAGGGAGTAC 57.194 37.500 0.00 0.00 0.00 2.73
2100 5519 7.120138 GTCATTTATTTTGAAACGGAGGGAGTA 59.880 37.037 0.00 0.00 0.00 2.59
2101 5520 6.007703 TCATTTATTTTGAAACGGAGGGAGT 58.992 36.000 0.00 0.00 0.00 3.85
2102 5521 6.151144 AGTCATTTATTTTGAAACGGAGGGAG 59.849 38.462 0.00 0.00 0.00 4.30
2103 5522 6.007703 AGTCATTTATTTTGAAACGGAGGGA 58.992 36.000 0.00 0.00 0.00 4.20
2104 5523 6.072175 TGAGTCATTTATTTTGAAACGGAGGG 60.072 38.462 0.00 0.00 0.00 4.30
2105 5524 6.908825 TGAGTCATTTATTTTGAAACGGAGG 58.091 36.000 0.00 0.00 0.00 4.30
2106 5525 8.076178 AGTTGAGTCATTTATTTTGAAACGGAG 58.924 33.333 0.00 0.00 0.00 4.63
2107 5526 7.936584 AGTTGAGTCATTTATTTTGAAACGGA 58.063 30.769 0.00 0.00 0.00 4.69
2108 5527 8.574196 AAGTTGAGTCATTTATTTTGAAACGG 57.426 30.769 0.00 0.00 0.00 4.44
2149 5568 9.823647 CCTGAACACATCTTAGTATAACAATCT 57.176 33.333 0.00 0.00 0.00 2.40
2150 5569 9.046296 CCCTGAACACATCTTAGTATAACAATC 57.954 37.037 0.00 0.00 0.00 2.67
2151 5570 8.548877 ACCCTGAACACATCTTAGTATAACAAT 58.451 33.333 0.00 0.00 0.00 2.71
2152 5571 7.913789 ACCCTGAACACATCTTAGTATAACAA 58.086 34.615 0.00 0.00 0.00 2.83
2153 5572 7.490657 ACCCTGAACACATCTTAGTATAACA 57.509 36.000 0.00 0.00 0.00 2.41
2154 5573 9.880157 TTAACCCTGAACACATCTTAGTATAAC 57.120 33.333 0.00 0.00 0.00 1.89
2155 5574 9.880157 GTTAACCCTGAACACATCTTAGTATAA 57.120 33.333 0.00 0.00 0.00 0.98
2156 5575 9.263446 AGTTAACCCTGAACACATCTTAGTATA 57.737 33.333 0.88 0.00 0.00 1.47
2157 5576 8.041323 CAGTTAACCCTGAACACATCTTAGTAT 58.959 37.037 0.88 0.00 34.23 2.12
2158 5577 7.015877 ACAGTTAACCCTGAACACATCTTAGTA 59.984 37.037 0.88 0.00 36.30 1.82
2159 5578 6.183361 ACAGTTAACCCTGAACACATCTTAGT 60.183 38.462 0.88 0.00 36.30 2.24
2160 5579 6.231211 ACAGTTAACCCTGAACACATCTTAG 58.769 40.000 0.88 0.00 36.30 2.18
2161 5580 6.182507 ACAGTTAACCCTGAACACATCTTA 57.817 37.500 0.88 0.00 36.30 2.10
2162 5581 5.048846 ACAGTTAACCCTGAACACATCTT 57.951 39.130 0.88 0.00 36.30 2.40
2163 5582 4.706842 ACAGTTAACCCTGAACACATCT 57.293 40.909 0.88 0.00 36.30 2.90
2164 5583 4.935808 CCTACAGTTAACCCTGAACACATC 59.064 45.833 0.88 0.00 36.30 3.06
2165 5584 4.595781 TCCTACAGTTAACCCTGAACACAT 59.404 41.667 0.88 0.00 36.30 3.21
2166 5585 3.968649 TCCTACAGTTAACCCTGAACACA 59.031 43.478 0.88 0.00 36.30 3.72
2167 5586 4.612264 TCCTACAGTTAACCCTGAACAC 57.388 45.455 0.88 0.00 36.30 3.32
2168 5587 5.836024 AATCCTACAGTTAACCCTGAACA 57.164 39.130 0.88 0.00 36.30 3.18
2169 5588 8.702819 AGTATAATCCTACAGTTAACCCTGAAC 58.297 37.037 0.88 0.00 36.30 3.18
2170 5589 8.849543 AGTATAATCCTACAGTTAACCCTGAA 57.150 34.615 0.88 0.00 36.30 3.02
2171 5590 7.508296 GGAGTATAATCCTACAGTTAACCCTGA 59.492 40.741 12.01 0.00 36.35 3.86
2172 5591 7.668492 GGAGTATAATCCTACAGTTAACCCTG 58.332 42.308 12.01 0.00 36.35 4.45
2173 5592 7.852550 GGAGTATAATCCTACAGTTAACCCT 57.147 40.000 12.01 0.00 36.35 4.34


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

AutoCloner maintained by Alex Coulton.