Multiple sequence alignment - TraesCS7A01G134900

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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 TraesCS7A01G134900 chr7A 100.000 2489 0 0 1 2489 87332964 87330476 0.000000e+00 4597
1 TraesCS7A01G134900 chr7A 89.937 159 14 2 508 665 14670565 14670722 1.170000e-48 204
2 TraesCS7A01G134900 chr7D 90.056 1619 108 31 706 2276 85932228 85930615 0.000000e+00 2049
3 TraesCS7A01G134900 chr6A 96.505 658 21 2 3 659 58032968 58033624 0.000000e+00 1086
4 TraesCS7A01G134900 chr7B 89.728 847 28 18 917 1722 35101487 35100659 0.000000e+00 1027
5 TraesCS7A01G134900 chr7B 87.398 492 54 4 1780 2263 35099533 35099042 2.160000e-155 558
6 TraesCS7A01G134900 chr7B 89.781 274 15 5 659 931 35103724 35103463 3.070000e-89 339
7 TraesCS7A01G134900 chr2B 91.667 672 52 3 1 669 175396805 175396135 0.000000e+00 928
8 TraesCS7A01G134900 chr3D 95.402 522 20 3 144 661 228947801 228947280 0.000000e+00 828
9 TraesCS7A01G134900 chrUn 92.083 581 40 5 1 579 6057548 6056972 0.000000e+00 813
10 TraesCS7A01G134900 chrUn 90.260 154 14 1 506 659 29905007 29904855 1.510000e-47 200
11 TraesCS7A01G134900 chr4A 96.544 434 12 2 2 432 132055166 132054733 0.000000e+00 715
12 TraesCS7A01G134900 chr4A 84.722 504 53 8 25 506 394925992 394926493 1.340000e-132 483
13 TraesCS7A01G134900 chr4A 95.455 242 11 0 419 660 132051715 132051474 1.080000e-103 387
14 TraesCS7A01G134900 chr4A 89.535 172 15 3 506 676 394926538 394926707 5.390000e-52 215
15 TraesCS7A01G134900 chr5A 86.056 502 48 6 27 506 200829587 200829086 1.020000e-143 520
16 TraesCS7A01G134900 chr5A 89.811 265 21 5 25 285 640074001 640074263 3.970000e-88 335
17 TraesCS7A01G134900 chr5A 88.584 219 22 2 291 506 640074313 640074531 1.900000e-66 263
18 TraesCS7A01G134900 chr5A 90.286 175 14 2 506 678 640074576 640074749 2.490000e-55 226
19 TraesCS7A01G134900 chr3B 86.157 484 45 7 45 506 733416807 733416324 1.030000e-138 503
20 TraesCS7A01G134900 chr1B 89.811 265 21 5 25 285 633695927 633695665 3.970000e-88 335
21 TraesCS7A01G134900 chr1B 89.041 219 21 2 291 506 633695614 633695396 4.080000e-68 268
22 TraesCS7A01G134900 chr6B 90.132 152 13 2 506 657 474505006 474505155 1.950000e-46 196


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 TraesCS7A01G134900 chr7A 87330476 87332964 2488 True 4597.000000 4597 100.000000 1 2489 1 chr7A.!!$R1 2488
1 TraesCS7A01G134900 chr7D 85930615 85932228 1613 True 2049.000000 2049 90.056000 706 2276 1 chr7D.!!$R1 1570
2 TraesCS7A01G134900 chr6A 58032968 58033624 656 False 1086.000000 1086 96.505000 3 659 1 chr6A.!!$F1 656
3 TraesCS7A01G134900 chr7B 35099042 35103724 4682 True 641.333333 1027 88.969000 659 2263 3 chr7B.!!$R1 1604
4 TraesCS7A01G134900 chr2B 175396135 175396805 670 True 928.000000 928 91.667000 1 669 1 chr2B.!!$R1 668
5 TraesCS7A01G134900 chr3D 228947280 228947801 521 True 828.000000 828 95.402000 144 661 1 chr3D.!!$R1 517
6 TraesCS7A01G134900 chrUn 6056972 6057548 576 True 813.000000 813 92.083000 1 579 1 chrUn.!!$R1 578
7 TraesCS7A01G134900 chr4A 132051474 132055166 3692 True 551.000000 715 95.999500 2 660 2 chr4A.!!$R1 658
8 TraesCS7A01G134900 chr4A 394925992 394926707 715 False 349.000000 483 87.128500 25 676 2 chr4A.!!$F1 651
9 TraesCS7A01G134900 chr5A 200829086 200829587 501 True 520.000000 520 86.056000 27 506 1 chr5A.!!$R1 479
10 TraesCS7A01G134900 chr5A 640074001 640074749 748 False 274.666667 335 89.560333 25 678 3 chr5A.!!$F1 653
11 TraesCS7A01G134900 chr1B 633695396 633695927 531 True 301.500000 335 89.426000 25 506 2 chr1B.!!$R1 481

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
852 4030 0.550914 TCAACTCCCAACTTGGTGCT 59.449 50.0 7.06 0.0 35.17 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2326 8680 0.396811 GCCGTCAGCCCACCTATTAT 59.603 55.0 0.0 0.0 34.35 1.28 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
99 100 9.650539 CAGTTATGGAATATGGAAGACATAGAG 57.349 37.037 0.00 0.00 44.79 2.43
492 3576 1.879380 GCATGCCAGTAGTTTCACACA 59.121 47.619 6.36 0.00 0.00 3.72
641 3817 0.741915 TTTTCTCCCGTTGCAACACC 59.258 50.000 28.01 2.77 0.00 4.16
760 3938 3.096092 AGTTTGCTCTAGTCTCCTCCAG 58.904 50.000 0.00 0.00 0.00 3.86
852 4030 0.550914 TCAACTCCCAACTTGGTGCT 59.449 50.000 7.06 0.00 35.17 4.40
864 4042 4.473477 ACTTGGTGCTCTTGACCTATAC 57.527 45.455 0.00 0.00 34.26 1.47
931 6105 5.803020 ACCAAAGATTTCGTATCTTGAGC 57.197 39.130 13.57 0.00 38.29 4.26
943 6123 6.320171 TCGTATCTTGAGCGCCTATAAATAC 58.680 40.000 2.29 5.14 0.00 1.89
957 6137 6.538742 GCCTATAAATACCATCGTATGTGCAT 59.461 38.462 0.00 0.00 35.29 3.96
1059 6246 0.322906 TGCACAGTCCACACCACAAA 60.323 50.000 0.00 0.00 0.00 2.83
1164 6351 2.049156 CGCTGCGGTCACTCTCAA 60.049 61.111 15.40 0.00 0.00 3.02
1285 6472 3.143515 TCGCCTCGATCTGCAGCT 61.144 61.111 9.47 0.00 0.00 4.24
1286 6473 2.657944 CGCCTCGATCTGCAGCTC 60.658 66.667 9.47 8.39 0.00 4.09
1496 6686 3.032609 CGATGAGTGATCCGCGCC 61.033 66.667 0.00 0.00 0.00 6.53
1499 6689 3.740128 ATGAGTGATCCGCGCCCAC 62.740 63.158 0.00 8.15 0.00 4.61
1598 6816 8.213518 AGATGCTGTGACAACGAATAAAATAT 57.786 30.769 0.00 0.00 0.00 1.28
1599 6817 9.325198 AGATGCTGTGACAACGAATAAAATATA 57.675 29.630 0.00 0.00 0.00 0.86
1600 6818 9.370126 GATGCTGTGACAACGAATAAAATATAC 57.630 33.333 0.00 0.00 0.00 1.47
1601 6819 8.257830 TGCTGTGACAACGAATAAAATATACA 57.742 30.769 0.00 0.00 0.00 2.29
1602 6820 8.387354 TGCTGTGACAACGAATAAAATATACAG 58.613 33.333 0.00 0.00 35.14 2.74
1603 6821 8.388103 GCTGTGACAACGAATAAAATATACAGT 58.612 33.333 0.00 0.00 34.67 3.55
1623 6844 5.463061 ACAGTACTTTACAAATGTAACGCGT 59.537 36.000 5.58 5.58 39.92 6.01
1699 6923 3.305881 GGCATCCGTTGTATACTCCTACC 60.306 52.174 4.17 0.00 0.00 3.18
1718 6942 5.243954 CCTACCTTCCTTTTCCTTTTCTTGG 59.756 44.000 0.00 0.00 0.00 3.61
1722 6946 3.219281 TCCTTTTCCTTTTCTTGGTCCG 58.781 45.455 0.00 0.00 0.00 4.79
1724 6948 3.243401 CCTTTTCCTTTTCTTGGTCCGTG 60.243 47.826 0.00 0.00 0.00 4.94
1726 6950 3.842007 TTCCTTTTCTTGGTCCGTGTA 57.158 42.857 0.00 0.00 0.00 2.90
1728 6952 2.701951 TCCTTTTCTTGGTCCGTGTACT 59.298 45.455 0.00 0.00 0.00 2.73
1732 6956 1.045407 TCTTGGTCCGTGTACTTGCT 58.955 50.000 0.00 0.00 0.00 3.91
1733 6957 1.148310 CTTGGTCCGTGTACTTGCTG 58.852 55.000 0.00 0.00 0.00 4.41
1734 6958 0.882927 TTGGTCCGTGTACTTGCTGC 60.883 55.000 0.00 0.00 0.00 5.25
1735 6959 2.380410 GGTCCGTGTACTTGCTGCG 61.380 63.158 0.00 0.00 0.00 5.18
1736 6960 2.048597 TCCGTGTACTTGCTGCGG 60.049 61.111 0.00 0.00 43.32 5.69
1757 6981 2.865669 GGTAGGCCAATGCGTTTGCG 62.866 60.000 5.01 0.00 38.26 4.85
1792 8125 4.213564 AGAGGAGCACTTGTTAATCCAG 57.786 45.455 0.00 0.00 32.21 3.86
1809 8142 5.796424 ATCCAGGGATAAATGACAATTGC 57.204 39.130 5.05 0.00 32.36 3.56
1904 8254 3.509575 GGAAACAATGCACCTCCATGTAA 59.490 43.478 0.00 0.00 0.00 2.41
1937 8287 7.612244 GGTACATAAGGACATCTCTAGCAGATA 59.388 40.741 0.00 0.00 40.20 1.98
2003 8355 6.382570 ACATCTAGCAGATCCCTTATATGACC 59.617 42.308 0.00 0.00 31.32 4.02
2007 8359 6.521527 AGCAGATCCCTTATATGACCTTTT 57.478 37.500 0.00 0.00 0.00 2.27
2022 8374 7.610580 ATGACCTTTTCACCCTTCAAAAATA 57.389 32.000 0.00 0.00 36.92 1.40
2043 8395 3.819564 ACCTTTTCTTGCAAAACCTCC 57.180 42.857 0.00 0.00 0.00 4.30
2047 8399 2.397044 TTCTTGCAAAACCTCCCCAT 57.603 45.000 0.00 0.00 0.00 4.00
2064 8416 6.155049 CCTCCCCATTCATTCACATTTAGTTT 59.845 38.462 0.00 0.00 0.00 2.66
2074 8427 3.518705 TCACATTTAGTTTAGCGGGGGTA 59.481 43.478 0.00 0.00 0.00 3.69
2077 8430 6.056884 CACATTTAGTTTAGCGGGGGTATTA 58.943 40.000 0.00 0.00 0.00 0.98
2079 8432 7.229907 CACATTTAGTTTAGCGGGGGTATTATT 59.770 37.037 0.00 0.00 0.00 1.40
2081 8434 9.457436 CATTTAGTTTAGCGGGGGTATTATTAT 57.543 33.333 0.00 0.00 0.00 1.28
2088 8441 4.765339 AGCGGGGGTATTATTATGAAAAGC 59.235 41.667 0.00 0.00 0.00 3.51
2113 8466 1.599797 CCGTCCACAACCCAACCTC 60.600 63.158 0.00 0.00 0.00 3.85
2124 8477 1.966451 CCAACCTCGTCAACTGGGC 60.966 63.158 0.00 0.00 0.00 5.36
2130 8483 2.281070 CGTCAACTGGGCTGTGCT 60.281 61.111 0.00 0.00 0.00 4.40
2137 8490 3.855503 CTGGGCTGTGCTTGGCAGA 62.856 63.158 0.00 0.00 40.08 4.26
2153 8506 2.214216 AGACCGGCCAGTTAGCACA 61.214 57.895 0.00 0.00 0.00 4.57
2154 8507 1.078426 GACCGGCCAGTTAGCACAT 60.078 57.895 0.00 0.00 0.00 3.21
2224 8578 4.838152 CGCACGTGGCCTGCCTAT 62.838 66.667 18.88 0.00 40.31 2.57
2263 8617 3.998672 CTGGGCACACGTACCGGT 61.999 66.667 13.98 13.98 0.00 5.28
2266 8620 2.639327 GGGCACACGTACCGGTACT 61.639 63.158 35.31 22.60 34.04 2.73
2268 8622 1.444895 GCACACGTACCGGTACTGG 60.445 63.158 35.31 28.84 34.04 4.00
2269 8623 1.444895 CACACGTACCGGTACTGGC 60.445 63.158 35.31 15.39 34.04 4.85
2271 8625 1.444895 CACGTACCGGTACTGGCAC 60.445 63.158 35.31 17.14 34.04 5.01
2272 8626 2.202518 CGTACCGGTACTGGCACG 60.203 66.667 35.31 27.60 41.92 5.34
2273 8627 3.277133 GTACCGGTACTGGCACGA 58.723 61.111 32.93 0.00 33.45 4.35
2274 8628 1.153958 GTACCGGTACTGGCACGAC 60.154 63.158 32.93 9.99 33.45 4.34
2275 8629 1.603171 TACCGGTACTGGCACGACA 60.603 57.895 21.25 0.00 0.00 4.35
2276 8630 1.177895 TACCGGTACTGGCACGACAA 61.178 55.000 21.25 0.00 0.00 3.18
2277 8631 1.736645 CCGGTACTGGCACGACAAG 60.737 63.158 8.07 0.00 0.00 3.16
2278 8632 1.287815 CGGTACTGGCACGACAAGA 59.712 57.895 0.00 0.00 0.00 3.02
2279 8633 0.108804 CGGTACTGGCACGACAAGAT 60.109 55.000 0.00 0.00 0.00 2.40
2280 8634 1.641577 GGTACTGGCACGACAAGATC 58.358 55.000 0.00 0.00 0.00 2.75
2281 8635 1.641577 GTACTGGCACGACAAGATCC 58.358 55.000 0.00 0.00 0.00 3.36
2282 8636 1.067142 GTACTGGCACGACAAGATCCA 60.067 52.381 0.00 0.00 0.00 3.41
2283 8637 0.615331 ACTGGCACGACAAGATCCAT 59.385 50.000 0.00 0.00 0.00 3.41
2284 8638 1.003580 ACTGGCACGACAAGATCCATT 59.996 47.619 0.00 0.00 0.00 3.16
2285 8639 2.086869 CTGGCACGACAAGATCCATTT 58.913 47.619 0.00 0.00 0.00 2.32
2286 8640 3.270027 CTGGCACGACAAGATCCATTTA 58.730 45.455 0.00 0.00 0.00 1.40
2287 8641 3.270027 TGGCACGACAAGATCCATTTAG 58.730 45.455 0.00 0.00 0.00 1.85
2288 8642 3.270877 GGCACGACAAGATCCATTTAGT 58.729 45.455 0.00 0.00 0.00 2.24
2289 8643 3.689649 GGCACGACAAGATCCATTTAGTT 59.310 43.478 0.00 0.00 0.00 2.24
2290 8644 4.156008 GGCACGACAAGATCCATTTAGTTT 59.844 41.667 0.00 0.00 0.00 2.66
2291 8645 5.335661 GGCACGACAAGATCCATTTAGTTTT 60.336 40.000 0.00 0.00 0.00 2.43
2292 8646 6.149633 GCACGACAAGATCCATTTAGTTTTT 58.850 36.000 0.00 0.00 0.00 1.94
2336 8690 7.138692 GCTCAATAGCTTGAATAATAGGTGG 57.861 40.000 0.00 0.00 45.85 4.61
2337 8691 6.150140 GCTCAATAGCTTGAATAATAGGTGGG 59.850 42.308 0.00 0.00 45.85 4.61
2338 8692 6.003950 TCAATAGCTTGAATAATAGGTGGGC 58.996 40.000 0.00 0.00 38.43 5.36
2339 8693 5.850046 ATAGCTTGAATAATAGGTGGGCT 57.150 39.130 0.00 0.00 0.00 5.19
2340 8694 3.825328 AGCTTGAATAATAGGTGGGCTG 58.175 45.455 0.00 0.00 0.00 4.85
2341 8695 3.459598 AGCTTGAATAATAGGTGGGCTGA 59.540 43.478 0.00 0.00 0.00 4.26
2342 8696 3.565902 GCTTGAATAATAGGTGGGCTGAC 59.434 47.826 0.00 0.00 0.00 3.51
2343 8697 3.469008 TGAATAATAGGTGGGCTGACG 57.531 47.619 0.00 0.00 0.00 4.35
2344 8698 2.104111 TGAATAATAGGTGGGCTGACGG 59.896 50.000 0.00 0.00 0.00 4.79
2345 8699 0.396811 ATAATAGGTGGGCTGACGGC 59.603 55.000 0.00 0.00 40.90 5.68
2346 8700 0.689745 TAATAGGTGGGCTGACGGCT 60.690 55.000 6.16 0.00 41.46 5.52
2347 8701 0.689745 AATAGGTGGGCTGACGGCTA 60.690 55.000 6.16 0.00 41.46 3.93
2348 8702 0.689745 ATAGGTGGGCTGACGGCTAA 60.690 55.000 6.16 0.00 41.46 3.09
2349 8703 0.905809 TAGGTGGGCTGACGGCTAAA 60.906 55.000 6.16 0.00 41.46 1.85
2350 8704 2.038837 GGTGGGCTGACGGCTAAAC 61.039 63.158 6.16 2.38 41.46 2.01
2351 8705 2.047655 TGGGCTGACGGCTAAACG 60.048 61.111 6.16 0.00 41.46 3.60
2377 8731 3.439440 GGCCCAGCCCCTTTAATAG 57.561 57.895 0.00 0.00 44.06 1.73
2378 8732 0.556258 GGCCCAGCCCCTTTAATAGT 59.444 55.000 0.00 0.00 44.06 2.12
2379 8733 1.778484 GGCCCAGCCCCTTTAATAGTA 59.222 52.381 0.00 0.00 44.06 1.82
2380 8734 2.378886 GGCCCAGCCCCTTTAATAGTAT 59.621 50.000 0.00 0.00 44.06 2.12
2381 8735 3.181422 GGCCCAGCCCCTTTAATAGTATT 60.181 47.826 0.17 0.17 44.06 1.89
2382 8736 4.480115 GCCCAGCCCCTTTAATAGTATTT 58.520 43.478 0.00 0.00 0.00 1.40
2383 8737 4.899457 GCCCAGCCCCTTTAATAGTATTTT 59.101 41.667 0.00 0.00 0.00 1.82
2384 8738 5.365605 GCCCAGCCCCTTTAATAGTATTTTT 59.634 40.000 0.00 0.00 0.00 1.94
2399 8753 3.717842 TTTTTGAGCGGTAGCCTGT 57.282 47.368 0.00 0.00 46.67 4.00
2400 8754 1.975660 TTTTTGAGCGGTAGCCTGTT 58.024 45.000 0.00 0.00 46.67 3.16
2401 8755 1.975660 TTTTGAGCGGTAGCCTGTTT 58.024 45.000 0.00 0.00 46.67 2.83
2402 8756 2.843401 TTTGAGCGGTAGCCTGTTTA 57.157 45.000 0.00 0.00 46.67 2.01
2403 8757 2.843401 TTGAGCGGTAGCCTGTTTAA 57.157 45.000 0.00 0.00 46.67 1.52
2404 8758 3.343941 TTGAGCGGTAGCCTGTTTAAT 57.656 42.857 0.00 0.00 46.67 1.40
2405 8759 4.475051 TTGAGCGGTAGCCTGTTTAATA 57.525 40.909 0.00 0.00 46.67 0.98
2406 8760 4.054780 TGAGCGGTAGCCTGTTTAATAG 57.945 45.455 0.00 0.00 46.67 1.73
2407 8761 3.449737 TGAGCGGTAGCCTGTTTAATAGT 59.550 43.478 0.00 0.00 46.67 2.12
2408 8762 4.646040 TGAGCGGTAGCCTGTTTAATAGTA 59.354 41.667 0.00 0.00 46.67 1.82
2409 8763 5.197682 AGCGGTAGCCTGTTTAATAGTAG 57.802 43.478 0.00 0.00 46.67 2.57
2410 8764 4.648307 AGCGGTAGCCTGTTTAATAGTAGT 59.352 41.667 0.00 0.00 46.67 2.73
2411 8765 4.743644 GCGGTAGCCTGTTTAATAGTAGTG 59.256 45.833 0.00 0.00 37.42 2.74
2412 8766 5.680665 GCGGTAGCCTGTTTAATAGTAGTGT 60.681 44.000 0.00 0.00 37.42 3.55
2413 8767 6.335777 CGGTAGCCTGTTTAATAGTAGTGTT 58.664 40.000 0.00 0.00 0.00 3.32
2414 8768 6.255020 CGGTAGCCTGTTTAATAGTAGTGTTG 59.745 42.308 0.00 0.00 0.00 3.33
2415 8769 7.101700 GGTAGCCTGTTTAATAGTAGTGTTGT 58.898 38.462 0.00 0.00 0.00 3.32
2416 8770 7.064253 GGTAGCCTGTTTAATAGTAGTGTTGTG 59.936 40.741 0.00 0.00 0.00 3.33
2417 8771 5.938125 AGCCTGTTTAATAGTAGTGTTGTGG 59.062 40.000 0.00 0.00 0.00 4.17
2418 8772 5.123344 GCCTGTTTAATAGTAGTGTTGTGGG 59.877 44.000 0.00 0.00 0.00 4.61
2419 8773 6.469410 CCTGTTTAATAGTAGTGTTGTGGGA 58.531 40.000 0.00 0.00 0.00 4.37
2420 8774 6.938030 CCTGTTTAATAGTAGTGTTGTGGGAA 59.062 38.462 0.00 0.00 0.00 3.97
2421 8775 7.119262 CCTGTTTAATAGTAGTGTTGTGGGAAG 59.881 40.741 0.00 0.00 0.00 3.46
2422 8776 6.428771 TGTTTAATAGTAGTGTTGTGGGAAGC 59.571 38.462 0.00 0.00 0.00 3.86
2423 8777 4.634012 AATAGTAGTGTTGTGGGAAGCA 57.366 40.909 0.00 0.00 0.00 3.91
2424 8778 4.634012 ATAGTAGTGTTGTGGGAAGCAA 57.366 40.909 0.00 0.00 0.00 3.91
2425 8779 2.572290 AGTAGTGTTGTGGGAAGCAAC 58.428 47.619 0.00 0.00 44.50 4.17
2426 8780 2.172717 AGTAGTGTTGTGGGAAGCAACT 59.827 45.455 9.16 0.00 44.54 3.16
2427 8781 3.389983 AGTAGTGTTGTGGGAAGCAACTA 59.610 43.478 9.16 0.00 44.54 2.24
2428 8782 3.290948 AGTGTTGTGGGAAGCAACTAA 57.709 42.857 9.16 0.00 44.54 2.24
2429 8783 3.832527 AGTGTTGTGGGAAGCAACTAAT 58.167 40.909 9.16 0.00 44.54 1.73
2430 8784 3.821033 AGTGTTGTGGGAAGCAACTAATC 59.179 43.478 9.16 0.00 44.54 1.75
2431 8785 3.568007 GTGTTGTGGGAAGCAACTAATCA 59.432 43.478 9.16 0.00 44.54 2.57
2432 8786 4.037446 GTGTTGTGGGAAGCAACTAATCAA 59.963 41.667 9.16 0.00 44.54 2.57
2433 8787 4.278170 TGTTGTGGGAAGCAACTAATCAAG 59.722 41.667 9.16 0.00 44.54 3.02
2434 8788 3.420893 TGTGGGAAGCAACTAATCAAGG 58.579 45.455 0.00 0.00 0.00 3.61
2435 8789 2.755103 GTGGGAAGCAACTAATCAAGGG 59.245 50.000 0.00 0.00 0.00 3.95
2436 8790 2.647299 TGGGAAGCAACTAATCAAGGGA 59.353 45.455 0.00 0.00 0.00 4.20
2437 8791 3.017442 GGGAAGCAACTAATCAAGGGAC 58.983 50.000 0.00 0.00 0.00 4.46
2438 8792 2.678336 GGAAGCAACTAATCAAGGGACG 59.322 50.000 0.00 0.00 0.00 4.79
2439 8793 1.739067 AGCAACTAATCAAGGGACGC 58.261 50.000 0.00 0.00 0.00 5.19
2440 8794 1.003118 AGCAACTAATCAAGGGACGCA 59.997 47.619 0.00 0.00 0.00 5.24
2441 8795 2.017049 GCAACTAATCAAGGGACGCAT 58.983 47.619 0.00 0.00 0.00 4.73
2442 8796 2.032178 GCAACTAATCAAGGGACGCATC 59.968 50.000 0.00 0.00 0.00 3.91
2443 8797 2.614057 CAACTAATCAAGGGACGCATCC 59.386 50.000 0.00 0.00 45.42 3.51
2481 8835 2.693267 AACTAATCAAGGGACGCTCC 57.307 50.000 0.00 0.00 35.23 4.70
2482 8836 1.867363 ACTAATCAAGGGACGCTCCT 58.133 50.000 0.00 0.00 36.57 3.69
2483 8837 1.757699 ACTAATCAAGGGACGCTCCTC 59.242 52.381 0.00 0.00 36.57 3.71
2484 8838 1.069358 CTAATCAAGGGACGCTCCTCC 59.931 57.143 0.00 0.00 36.57 4.30
2485 8839 0.909610 AATCAAGGGACGCTCCTCCA 60.910 55.000 0.00 0.00 36.57 3.86
2486 8840 1.333636 ATCAAGGGACGCTCCTCCAG 61.334 60.000 0.00 0.00 36.57 3.86
2487 8841 1.984570 CAAGGGACGCTCCTCCAGA 60.985 63.158 0.00 0.00 36.57 3.86
2488 8842 1.229209 AAGGGACGCTCCTCCAGAA 60.229 57.895 0.00 0.00 36.57 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 2.019156 GCTGCTATGAAACTGGGTCCC 61.019 57.143 0.00 0.00 0.00 4.46
492 3576 5.012664 AGTTTGTTTGGTCACCTTTCCTTTT 59.987 36.000 0.00 0.00 0.00 2.27
694 3870 1.743252 CTCGAGGGCTGCCTTGTTC 60.743 63.158 19.68 10.27 0.00 3.18
744 3921 2.438021 TCTCTCTGGAGGAGACTAGAGC 59.562 54.545 0.00 0.00 45.20 4.09
760 3938 1.936547 GCAATGTCGGTTGGATCTCTC 59.063 52.381 0.00 0.00 0.00 3.20
864 4042 8.873830 CCTGTCATGTAGTCTAAACTATTTGTG 58.126 37.037 0.00 0.00 40.08 3.33
879 4057 9.197694 GCTATTATAACTTGTCCTGTCATGTAG 57.802 37.037 0.00 0.00 0.00 2.74
931 6105 5.005394 GCACATACGATGGTATTTATAGGCG 59.995 44.000 0.00 0.00 37.24 5.52
943 6123 3.125829 GGCTTGATATGCACATACGATGG 59.874 47.826 0.00 0.00 33.60 3.51
957 6137 4.823442 GGAATGACATGTGATGGCTTGATA 59.177 41.667 1.15 0.00 39.69 2.15
1236 6423 1.802960 CAGTCTTTGCAGAGCATCGTT 59.197 47.619 0.00 0.00 42.67 3.85
1242 6429 2.324215 TGCACAGTCTTTGCAGAGC 58.676 52.632 9.63 0.00 45.06 4.09
1285 6472 2.586635 AACGCCGTTGCACGAAGA 60.587 55.556 0.00 0.00 46.05 2.87
1286 6473 2.425124 CAACGCCGTTGCACGAAG 60.425 61.111 17.84 0.00 46.05 3.79
1496 6686 1.153369 CTCCAGGGTACGCATGTGG 60.153 63.158 12.95 11.10 0.00 4.17
1499 6689 2.203070 GGCTCCAGGGTACGCATG 60.203 66.667 12.95 7.43 0.00 4.06
1598 6816 6.640499 ACGCGTTACATTTGTAAAGTACTGTA 59.360 34.615 5.58 0.00 41.58 2.74
1599 6817 5.463061 ACGCGTTACATTTGTAAAGTACTGT 59.537 36.000 5.58 0.00 41.58 3.55
1600 6818 5.781717 CACGCGTTACATTTGTAAAGTACTG 59.218 40.000 10.22 7.75 41.58 2.74
1601 6819 5.613142 GCACGCGTTACATTTGTAAAGTACT 60.613 40.000 10.22 0.00 41.58 2.73
1602 6820 4.546941 GCACGCGTTACATTTGTAAAGTAC 59.453 41.667 10.22 0.00 41.58 2.73
1603 6821 4.448395 AGCACGCGTTACATTTGTAAAGTA 59.552 37.500 10.22 0.00 41.58 2.24
1604 6822 3.249080 AGCACGCGTTACATTTGTAAAGT 59.751 39.130 10.22 8.91 41.58 2.66
1605 6823 3.805823 AGCACGCGTTACATTTGTAAAG 58.194 40.909 10.22 10.74 41.58 1.85
1606 6824 3.881780 AGCACGCGTTACATTTGTAAA 57.118 38.095 10.22 0.00 41.58 2.01
1699 6923 4.261614 CGGACCAAGAAAAGGAAAAGGAAG 60.262 45.833 0.00 0.00 0.00 3.46
1718 6942 2.380410 CCGCAGCAAGTACACGGAC 61.380 63.158 0.00 0.00 46.71 4.79
1722 6946 3.788766 CCGCCGCAGCAAGTACAC 61.789 66.667 0.00 0.00 39.83 2.90
1724 6948 2.125832 TACCGCCGCAGCAAGTAC 60.126 61.111 0.00 0.00 39.83 2.73
1726 6950 4.760047 CCTACCGCCGCAGCAAGT 62.760 66.667 0.00 0.00 39.83 3.16
1736 6960 2.696759 AAACGCATTGGCCTACCGC 61.697 57.895 3.32 1.88 39.70 5.68
1757 6981 2.352127 GCTCCTCTTGCCAATCAACAAC 60.352 50.000 0.00 0.00 0.00 3.32
1758 6982 1.888512 GCTCCTCTTGCCAATCAACAA 59.111 47.619 0.00 0.00 0.00 2.83
1759 6983 1.202915 TGCTCCTCTTGCCAATCAACA 60.203 47.619 0.00 0.00 0.00 3.33
1760 6984 1.200948 GTGCTCCTCTTGCCAATCAAC 59.799 52.381 0.00 0.00 0.00 3.18
1792 8125 5.976458 TCTTTGGCAATTGTCATTTATCCC 58.024 37.500 14.57 0.00 0.00 3.85
1809 8142 3.575687 ACTTGCAAGATTTCCCTCTTTGG 59.424 43.478 32.50 1.38 33.18 3.28
1826 8159 6.128634 GGCGTGTTCCTATTGTATATACTTGC 60.129 42.308 13.89 2.39 0.00 4.01
1842 8180 0.527565 ATGAATGCAAGGCGTGTTCC 59.472 50.000 1.69 0.00 0.00 3.62
1904 8254 7.633789 AGAGATGTCCTTATGTACCAACATTT 58.366 34.615 0.00 0.00 44.07 2.32
1957 8307 7.557719 AGATGTCCTTAATCATTTGAACCGAAT 59.442 33.333 0.00 0.00 0.00 3.34
1967 8317 7.393216 GGATCTGCTAGATGTCCTTAATCATT 58.607 38.462 0.00 0.00 34.53 2.57
2003 8355 8.731275 AAAGGTTATTTTTGAAGGGTGAAAAG 57.269 30.769 0.00 0.00 0.00 2.27
2007 8359 7.669089 AGAAAAGGTTATTTTTGAAGGGTGA 57.331 32.000 0.00 0.00 30.78 4.02
2022 8374 3.118408 GGGAGGTTTTGCAAGAAAAGGTT 60.118 43.478 0.00 0.00 0.00 3.50
2043 8395 6.692681 CGCTAAACTAAATGTGAATGAATGGG 59.307 38.462 0.00 0.00 0.00 4.00
2047 8399 5.124776 CCCCGCTAAACTAAATGTGAATGAA 59.875 40.000 0.00 0.00 0.00 2.57
2064 8416 5.941647 GCTTTTCATAATAATACCCCCGCTA 59.058 40.000 0.00 0.00 0.00 4.26
2074 8427 2.030274 GGGCGCGGCTTTTCATAATAAT 60.030 45.455 32.30 0.00 0.00 1.28
2077 8430 1.733526 GGGCGCGGCTTTTCATAAT 59.266 52.632 32.30 0.00 0.00 1.28
2079 8432 2.826738 GGGGCGCGGCTTTTCATA 60.827 61.111 32.30 0.00 0.00 2.15
2097 8450 0.883370 GACGAGGTTGGGTTGTGGAC 60.883 60.000 0.00 0.00 0.00 4.02
2107 8460 1.071471 AGCCCAGTTGACGAGGTTG 59.929 57.895 0.00 0.00 0.00 3.77
2113 8466 1.893808 AAGCACAGCCCAGTTGACG 60.894 57.895 0.00 0.00 0.00 4.35
2124 8477 3.052082 CCGGTCTGCCAAGCACAG 61.052 66.667 0.00 0.00 33.79 3.66
2137 8490 1.377202 CATGTGCTAACTGGCCGGT 60.377 57.895 12.85 12.85 0.00 5.28
2153 8506 1.455849 CATCATGGGCCGGGTACAT 59.544 57.895 2.18 0.00 0.00 2.29
2154 8507 2.751731 CCATCATGGGCCGGGTACA 61.752 63.158 2.18 0.00 32.67 2.90
2181 8535 1.223417 GACCCCGTTAACCACACGTG 61.223 60.000 15.48 15.48 35.81 4.49
2184 8538 3.955775 CGACCCCGTTAACCACAC 58.044 61.111 0.00 0.00 0.00 3.82
2207 8561 4.838152 ATAGGCAGGCCACGTGCG 62.838 66.667 10.91 4.74 44.77 5.34
2263 8617 1.262417 TGGATCTTGTCGTGCCAGTA 58.738 50.000 0.00 0.00 0.00 2.74
2266 8620 2.198827 AAATGGATCTTGTCGTGCCA 57.801 45.000 0.00 0.00 0.00 4.92
2268 8622 4.946784 AACTAAATGGATCTTGTCGTGC 57.053 40.909 0.00 0.00 0.00 5.34
2312 8666 6.150140 CCCACCTATTATTCAAGCTATTGAGC 59.850 42.308 0.00 0.00 45.89 4.26
2313 8667 6.150140 GCCCACCTATTATTCAAGCTATTGAG 59.850 42.308 0.00 0.00 45.89 3.02
2314 8668 6.003950 GCCCACCTATTATTCAAGCTATTGA 58.996 40.000 0.00 0.00 43.72 2.57
2315 8669 6.006449 AGCCCACCTATTATTCAAGCTATTG 58.994 40.000 0.00 0.00 37.80 1.90
2316 8670 6.006449 CAGCCCACCTATTATTCAAGCTATT 58.994 40.000 0.00 0.00 0.00 1.73
2317 8671 5.310594 TCAGCCCACCTATTATTCAAGCTAT 59.689 40.000 0.00 0.00 0.00 2.97
2318 8672 4.658435 TCAGCCCACCTATTATTCAAGCTA 59.342 41.667 0.00 0.00 0.00 3.32
2319 8673 3.459598 TCAGCCCACCTATTATTCAAGCT 59.540 43.478 0.00 0.00 0.00 3.74
2320 8674 3.565902 GTCAGCCCACCTATTATTCAAGC 59.434 47.826 0.00 0.00 0.00 4.01
2321 8675 3.809832 CGTCAGCCCACCTATTATTCAAG 59.190 47.826 0.00 0.00 0.00 3.02
2322 8676 3.433031 CCGTCAGCCCACCTATTATTCAA 60.433 47.826 0.00 0.00 0.00 2.69
2323 8677 2.104111 CCGTCAGCCCACCTATTATTCA 59.896 50.000 0.00 0.00 0.00 2.57
2324 8678 2.767505 CCGTCAGCCCACCTATTATTC 58.232 52.381 0.00 0.00 0.00 1.75
2325 8679 1.202770 GCCGTCAGCCCACCTATTATT 60.203 52.381 0.00 0.00 34.35 1.40
2326 8680 0.396811 GCCGTCAGCCCACCTATTAT 59.603 55.000 0.00 0.00 34.35 1.28
2327 8681 0.689745 AGCCGTCAGCCCACCTATTA 60.690 55.000 0.00 0.00 45.47 0.98
2328 8682 0.689745 TAGCCGTCAGCCCACCTATT 60.690 55.000 0.00 0.00 45.47 1.73
2329 8683 0.689745 TTAGCCGTCAGCCCACCTAT 60.690 55.000 0.00 0.00 45.47 2.57
2330 8684 0.905809 TTTAGCCGTCAGCCCACCTA 60.906 55.000 0.00 0.00 45.47 3.08
2331 8685 2.221299 TTTAGCCGTCAGCCCACCT 61.221 57.895 0.00 0.00 45.47 4.00
2332 8686 2.038837 GTTTAGCCGTCAGCCCACC 61.039 63.158 0.00 0.00 45.47 4.61
2333 8687 2.388232 CGTTTAGCCGTCAGCCCAC 61.388 63.158 0.00 0.00 45.47 4.61
2334 8688 2.047655 CGTTTAGCCGTCAGCCCA 60.048 61.111 0.00 0.00 45.47 5.36
2335 8689 2.047560 ACGTTTAGCCGTCAGCCC 60.048 61.111 0.00 0.00 45.47 5.19
2336 8690 3.023591 GCACGTTTAGCCGTCAGCC 62.024 63.158 0.00 0.00 45.47 4.85
2337 8691 2.474712 GCACGTTTAGCCGTCAGC 59.525 61.111 0.00 0.00 39.45 4.26
2338 8692 3.165498 GGCACGTTTAGCCGTCAG 58.835 61.111 0.00 0.00 43.15 3.51
2360 8714 3.808834 ATACTATTAAAGGGGCTGGGC 57.191 47.619 0.00 0.00 0.00 5.36
2381 8735 1.975660 AACAGGCTACCGCTCAAAAA 58.024 45.000 0.00 0.00 36.09 1.94
2382 8736 1.975660 AAACAGGCTACCGCTCAAAA 58.024 45.000 0.00 0.00 36.09 2.44
2383 8737 2.843401 TAAACAGGCTACCGCTCAAA 57.157 45.000 0.00 0.00 36.09 2.69
2384 8738 2.843401 TTAAACAGGCTACCGCTCAA 57.157 45.000 0.00 0.00 36.09 3.02
2385 8739 3.449737 ACTATTAAACAGGCTACCGCTCA 59.550 43.478 0.00 0.00 36.09 4.26
2386 8740 4.056092 ACTATTAAACAGGCTACCGCTC 57.944 45.455 0.00 0.00 36.09 5.03
2387 8741 4.648307 ACTACTATTAAACAGGCTACCGCT 59.352 41.667 0.00 0.00 36.09 5.52
2388 8742 4.743644 CACTACTATTAAACAGGCTACCGC 59.256 45.833 0.00 0.00 0.00 5.68
2389 8743 5.899299 ACACTACTATTAAACAGGCTACCG 58.101 41.667 0.00 0.00 0.00 4.02
2390 8744 7.064253 CACAACACTACTATTAAACAGGCTACC 59.936 40.741 0.00 0.00 0.00 3.18
2391 8745 7.064253 CCACAACACTACTATTAAACAGGCTAC 59.936 40.741 0.00 0.00 0.00 3.58
2392 8746 7.101054 CCACAACACTACTATTAAACAGGCTA 58.899 38.462 0.00 0.00 0.00 3.93
2393 8747 5.938125 CCACAACACTACTATTAAACAGGCT 59.062 40.000 0.00 0.00 0.00 4.58
2394 8748 5.123344 CCCACAACACTACTATTAAACAGGC 59.877 44.000 0.00 0.00 0.00 4.85
2395 8749 6.469410 TCCCACAACACTACTATTAAACAGG 58.531 40.000 0.00 0.00 0.00 4.00
2396 8750 7.360946 GCTTCCCACAACACTACTATTAAACAG 60.361 40.741 0.00 0.00 0.00 3.16
2397 8751 6.428771 GCTTCCCACAACACTACTATTAAACA 59.571 38.462 0.00 0.00 0.00 2.83
2398 8752 6.428771 TGCTTCCCACAACACTACTATTAAAC 59.571 38.462 0.00 0.00 0.00 2.01
2399 8753 6.535540 TGCTTCCCACAACACTACTATTAAA 58.464 36.000 0.00 0.00 0.00 1.52
2400 8754 6.116711 TGCTTCCCACAACACTACTATTAA 57.883 37.500 0.00 0.00 0.00 1.40
2401 8755 5.748670 TGCTTCCCACAACACTACTATTA 57.251 39.130 0.00 0.00 0.00 0.98
2402 8756 4.634012 TGCTTCCCACAACACTACTATT 57.366 40.909 0.00 0.00 0.00 1.73
2403 8757 4.324267 GTTGCTTCCCACAACACTACTAT 58.676 43.478 1.95 0.00 45.35 2.12
2404 8758 3.735591 GTTGCTTCCCACAACACTACTA 58.264 45.455 1.95 0.00 45.35 1.82
2405 8759 2.572290 GTTGCTTCCCACAACACTACT 58.428 47.619 1.95 0.00 45.35 2.57
2411 8765 4.321230 CCTTGATTAGTTGCTTCCCACAAC 60.321 45.833 0.00 0.00 46.18 3.32
2412 8766 3.826157 CCTTGATTAGTTGCTTCCCACAA 59.174 43.478 0.00 0.00 0.00 3.33
2413 8767 3.420893 CCTTGATTAGTTGCTTCCCACA 58.579 45.455 0.00 0.00 0.00 4.17
2414 8768 2.755103 CCCTTGATTAGTTGCTTCCCAC 59.245 50.000 0.00 0.00 0.00 4.61
2415 8769 2.647299 TCCCTTGATTAGTTGCTTCCCA 59.353 45.455 0.00 0.00 0.00 4.37
2416 8770 3.017442 GTCCCTTGATTAGTTGCTTCCC 58.983 50.000 0.00 0.00 0.00 3.97
2417 8771 2.678336 CGTCCCTTGATTAGTTGCTTCC 59.322 50.000 0.00 0.00 0.00 3.46
2418 8772 2.096013 GCGTCCCTTGATTAGTTGCTTC 59.904 50.000 0.00 0.00 0.00 3.86
2419 8773 2.084546 GCGTCCCTTGATTAGTTGCTT 58.915 47.619 0.00 0.00 0.00 3.91
2420 8774 1.003118 TGCGTCCCTTGATTAGTTGCT 59.997 47.619 0.00 0.00 0.00 3.91
2421 8775 1.448985 TGCGTCCCTTGATTAGTTGC 58.551 50.000 0.00 0.00 0.00 4.17
2422 8776 2.614057 GGATGCGTCCCTTGATTAGTTG 59.386 50.000 14.58 0.00 38.69 3.16
2423 8777 2.919228 GGATGCGTCCCTTGATTAGTT 58.081 47.619 14.58 0.00 38.69 2.24
2424 8778 2.622064 GGATGCGTCCCTTGATTAGT 57.378 50.000 14.58 0.00 38.69 2.24
2459 8813 3.756963 GGAGCGTCCCTTGATTAGTTTTT 59.243 43.478 0.00 0.00 0.00 1.94
2460 8814 3.009143 AGGAGCGTCCCTTGATTAGTTTT 59.991 43.478 1.06 0.00 37.19 2.43
2461 8815 2.572104 AGGAGCGTCCCTTGATTAGTTT 59.428 45.455 1.06 0.00 37.19 2.66
2462 8816 2.168728 GAGGAGCGTCCCTTGATTAGTT 59.831 50.000 0.00 0.00 37.19 2.24
2463 8817 1.757699 GAGGAGCGTCCCTTGATTAGT 59.242 52.381 0.00 0.00 37.19 2.24
2464 8818 1.069358 GGAGGAGCGTCCCTTGATTAG 59.931 57.143 0.00 0.00 37.19 1.73
2465 8819 1.120530 GGAGGAGCGTCCCTTGATTA 58.879 55.000 0.00 0.00 37.19 1.75
2466 8820 0.909610 TGGAGGAGCGTCCCTTGATT 60.910 55.000 6.75 0.00 37.19 2.57
2467 8821 1.306141 TGGAGGAGCGTCCCTTGAT 60.306 57.895 6.75 0.00 37.19 2.57
2468 8822 1.984570 CTGGAGGAGCGTCCCTTGA 60.985 63.158 6.75 0.00 37.19 3.02
2469 8823 1.544825 TTCTGGAGGAGCGTCCCTTG 61.545 60.000 6.75 0.00 37.19 3.61
2470 8824 1.229209 TTCTGGAGGAGCGTCCCTT 60.229 57.895 6.75 0.00 37.19 3.95
2471 8825 2.445614 TTCTGGAGGAGCGTCCCT 59.554 61.111 6.75 0.00 37.19 4.20


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

AutoCloner maintained by Alex Coulton.