Multiple sequence alignment - TraesCS7B01G376500

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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 TraesCS7B01G376500 chr7B 100.000 2687 0 0 1 2687 641367957 641370643 0.000000e+00 4963.0
1 TraesCS7B01G376500 chr7B 91.320 1970 113 25 59 1989 641742986 641741036 0.000000e+00 2638.0
2 TraesCS7B01G376500 chr7B 82.662 571 91 6 1020 1586 642076924 642076358 1.440000e-137 499.0
3 TraesCS7B01G376500 chr7B 88.206 407 31 8 1997 2399 641741149 641740756 1.130000e-128 470.0
4 TraesCS7B01G376500 chr7B 79.685 571 96 11 1020 1586 642261311 642261865 6.970000e-106 394.0
5 TraesCS7B01G376500 chr7B 80.562 427 48 21 3 425 641459775 641460170 2.020000e-76 296.0
6 TraesCS7B01G376500 chr7B 93.548 93 5 1 2596 2687 646376648 646376556 1.300000e-28 137.0
7 TraesCS7B01G376500 chr7B 82.759 116 20 0 1322 1437 641554873 641554988 1.320000e-18 104.0
8 TraesCS7B01G376500 chr7B 98.214 56 1 0 1 56 641743021 641742966 6.120000e-17 99.0
9 TraesCS7B01G376500 chr7B 73.315 371 52 23 482 813 642077476 642077114 2.850000e-15 93.5
10 TraesCS7B01G376500 chr7A 89.587 2468 135 48 1 2399 670166429 670168843 0.000000e+00 3022.0
11 TraesCS7B01G376500 chr7A 81.993 572 89 8 1024 1586 670342225 670341659 8.710000e-130 473.0
12 TraesCS7B01G376500 chr7A 75.325 462 50 28 482 881 670342841 670342382 2.140000e-36 163.0
13 TraesCS7B01G376500 chr7D 93.152 1840 71 16 1 1796 577920973 577922801 0.000000e+00 2649.0
14 TraesCS7B01G376500 chr7D 82.807 570 95 2 1020 1586 577963504 577964073 8.580000e-140 507.0
15 TraesCS7B01G376500 chr7D 77.542 895 103 48 3 838 577962437 577963292 1.470000e-122 449.0
16 TraesCS7B01G376500 chr7D 92.887 239 16 1 1835 2072 577922805 577923043 1.980000e-91 346.0
17 TraesCS7B01G376500 chr7D 88.559 236 20 4 156 391 577884852 577885080 2.040000e-71 279.0
18 TraesCS7B01G376500 chr7D 97.163 141 1 2 22 161 577882982 577883120 4.470000e-58 235.0
19 TraesCS7B01G376500 chr7D 89.308 159 8 7 275 427 578164334 578164179 9.820000e-45 191.0
20 TraesCS7B01G376500 chr7D 95.402 87 3 1 434 520 577885265 577885350 1.300000e-28 137.0
21 TraesCS7B01G376500 chr7D 96.104 77 3 0 2430 2506 577923644 577923720 2.810000e-25 126.0
22 TraesCS7B01G376500 chr7D 89.024 82 6 2 2322 2403 577923567 577923645 6.120000e-17 99.0
23 TraesCS7B01G376500 chr3D 92.888 1828 75 16 1 1796 55155502 55157306 0.000000e+00 2604.0
24 TraesCS7B01G376500 chr3D 87.772 597 56 9 1834 2429 55157309 55157889 0.000000e+00 682.0
25 TraesCS7B01G376500 chr3D 93.407 91 6 0 1994 2084 55157348 55157438 4.670000e-28 135.0
26 TraesCS7B01G376500 chr5B 93.407 91 5 1 2598 2687 26233986 26234076 1.680000e-27 134.0
27 TraesCS7B01G376500 chr5B 88.182 110 8 5 2579 2684 516457624 516457732 2.810000e-25 126.0
28 TraesCS7B01G376500 chr4B 93.407 91 5 1 2598 2687 579432400 579432310 1.680000e-27 134.0
29 TraesCS7B01G376500 chr3B 93.407 91 5 1 2598 2687 130052320 130052230 1.680000e-27 134.0
30 TraesCS7B01G376500 chr3B 91.753 97 7 1 2592 2687 807155646 807155550 1.680000e-27 134.0
31 TraesCS7B01G376500 chr3B 90.625 96 7 2 2593 2687 778005730 778005636 2.810000e-25 126.0
32 TraesCS7B01G376500 chr2A 92.308 91 6 1 2598 2687 68011272 68011182 7.810000e-26 128.0
33 TraesCS7B01G376500 chr2B 90.625 96 7 2 2593 2687 609150962 609151056 2.810000e-25 126.0


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 TraesCS7B01G376500 chr7B 641367957 641370643 2686 False 4963.000000 4963 100.000000 1 2687 1 chr7B.!!$F1 2686
1 TraesCS7B01G376500 chr7B 641740756 641743021 2265 True 1069.000000 2638 92.580000 1 2399 3 chr7B.!!$R2 2398
2 TraesCS7B01G376500 chr7B 642261311 642261865 554 False 394.000000 394 79.685000 1020 1586 1 chr7B.!!$F4 566
3 TraesCS7B01G376500 chr7B 642076358 642077476 1118 True 296.250000 499 77.988500 482 1586 2 chr7B.!!$R3 1104
4 TraesCS7B01G376500 chr7A 670166429 670168843 2414 False 3022.000000 3022 89.587000 1 2399 1 chr7A.!!$F1 2398
5 TraesCS7B01G376500 chr7A 670341659 670342841 1182 True 318.000000 473 78.659000 482 1586 2 chr7A.!!$R1 1104
6 TraesCS7B01G376500 chr7D 577920973 577923720 2747 False 805.000000 2649 92.791750 1 2506 4 chr7D.!!$F2 2505
7 TraesCS7B01G376500 chr7D 577962437 577964073 1636 False 478.000000 507 80.174500 3 1586 2 chr7D.!!$F3 1583
8 TraesCS7B01G376500 chr7D 577882982 577885350 2368 False 217.000000 279 93.708000 22 520 3 chr7D.!!$F1 498
9 TraesCS7B01G376500 chr3D 55155502 55157889 2387 False 1140.333333 2604 91.355667 1 2429 3 chr3D.!!$F1 2428

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
260 2000 0.038166 TGATCAGTTCCCACCCTTGC 59.962 55.0 0.0 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 3946 0.248458 CCACGACAACAGCAACCAAC 60.248 55.0 0.0 0.0 0.0 3.77 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
20 21 1.600663 CGAGTGCGGATGGTGATACTC 60.601 57.143 0.00 0.00 33.15 2.59
260 2000 0.038166 TGATCAGTTCCCACCCTTGC 59.962 55.000 0.00 0.00 0.00 4.01
262 2002 1.142688 ATCAGTTCCCACCCTTGCCT 61.143 55.000 0.00 0.00 0.00 4.75
397 2140 6.414732 CCTGGAGTTAGAAACCACATTATCA 58.585 40.000 0.00 0.00 0.00 2.15
398 2141 7.056635 CCTGGAGTTAGAAACCACATTATCAT 58.943 38.462 0.00 0.00 0.00 2.45
399 2142 7.227512 CCTGGAGTTAGAAACCACATTATCATC 59.772 40.741 0.00 0.00 0.00 2.92
585 2494 5.450550 GCCTTTGTAGCCAGATTTATTCCAC 60.451 44.000 0.00 0.00 0.00 4.02
734 2674 5.192927 TGATTTTGCGAGGATCCTAACAAT 58.807 37.500 23.02 13.56 0.00 2.71
844 2797 3.761897 ACCTAGAGGCTAGCACTATCTG 58.238 50.000 18.24 12.10 39.32 2.90
1008 3022 0.955428 AAGCAGTGCACATGGTACCG 60.955 55.000 21.04 0.00 31.67 4.02
1029 3120 1.344953 TGGGTGTTGTCACTCCTGCT 61.345 55.000 0.00 0.00 43.84 4.24
1046 3137 1.648720 CTGGTTCACAGCCAACACG 59.351 57.895 0.00 0.00 40.97 4.49
1185 3280 2.658538 CGAGCAACGGTCAGAGATG 58.341 57.895 0.00 0.00 38.46 2.90
1227 3322 3.252284 CACCCCCTGCCACTCACT 61.252 66.667 0.00 0.00 0.00 3.41
1350 3445 1.839994 ACGATGAGGTCATGGATGGTT 59.160 47.619 8.76 0.00 36.57 3.67
1353 3448 3.181466 CGATGAGGTCATGGATGGTTACA 60.181 47.826 0.00 0.00 36.57 2.41
1444 3539 5.942872 ACGACTTCTTGCTGGATTTATTTG 58.057 37.500 0.00 0.00 0.00 2.32
1464 3562 1.873903 GCCAGTGAAGAGACGAAGCAA 60.874 52.381 0.00 0.00 0.00 3.91
1648 3752 2.363276 ATCCGTCCGGCACCTACA 60.363 61.111 0.00 0.00 34.68 2.74
1674 3778 0.183492 AAGAGCCTCCACAACAGCAA 59.817 50.000 0.00 0.00 0.00 3.91
1691 3795 2.610519 AAGAGGGGCCCTGAAGCTG 61.611 63.158 34.51 0.00 31.76 4.24
1730 3834 3.334691 CTCGTTTCAGCCTGGACATTTA 58.665 45.455 0.00 0.00 0.00 1.40
1731 3835 3.745799 TCGTTTCAGCCTGGACATTTAA 58.254 40.909 0.00 0.00 0.00 1.52
1732 3836 4.138290 TCGTTTCAGCCTGGACATTTAAA 58.862 39.130 0.00 0.00 0.00 1.52
1796 3901 2.536761 ATTCGTCGGTTGAAACAGGA 57.463 45.000 0.00 0.00 0.00 3.86
1810 3915 2.777832 ACAGGAGGTTTCTGATCAGC 57.222 50.000 18.36 4.04 36.22 4.26
1830 3939 4.120723 GCAGAAGCTTAGGAGGTCCTCC 62.121 59.091 28.46 28.46 43.51 4.30
1865 3974 1.000884 TGTTGTCGTGGTGTCGTTTC 58.999 50.000 0.00 0.00 0.00 2.78
1879 3988 5.800941 GGTGTCGTTTCAGAAGTACTATGAG 59.199 44.000 9.83 1.74 0.00 2.90
1883 3992 8.570488 TGTCGTTTCAGAAGTACTATGAGTTTA 58.430 33.333 9.83 0.00 0.00 2.01
1930 4039 6.561519 TTTTACCATTCCAAACCCAAAAGA 57.438 33.333 0.00 0.00 0.00 2.52
1950 4059 2.514824 GCCTCCGGTGATGCCTTC 60.515 66.667 4.76 0.00 34.25 3.46
1964 4074 7.857885 CGGTGATGCCTTCTTTTTATTTCTATC 59.142 37.037 0.00 0.00 34.25 2.08
2019 4129 8.517878 ACCATGAATTTGTGATTTGAGACTAAG 58.482 33.333 0.00 0.00 0.00 2.18
2044 4154 5.105473 TGGTCAAATTTTACCGTTCCAAACA 60.105 36.000 15.15 0.00 38.70 2.83
2147 4576 5.065235 TGTCTTGCATGAAGTTTCAGATCA 58.935 37.500 3.51 0.00 41.08 2.92
2148 4577 5.708697 TGTCTTGCATGAAGTTTCAGATCAT 59.291 36.000 3.51 0.00 41.08 2.45
2230 4659 2.303022 ACAGTTGATGGTCGGTCATTCT 59.697 45.455 0.00 0.00 0.00 2.40
2235 4664 0.107508 ATGGTCGGTCATTCTGCTGG 60.108 55.000 0.00 0.00 0.00 4.85
2299 4730 5.793817 TGTAGAGCAGCATCAAGTCTTTTA 58.206 37.500 0.00 0.00 0.00 1.52
2300 4731 6.409704 TGTAGAGCAGCATCAAGTCTTTTAT 58.590 36.000 0.00 0.00 0.00 1.40
2301 4732 6.536582 TGTAGAGCAGCATCAAGTCTTTTATC 59.463 38.462 0.00 0.00 0.00 1.75
2316 4747 3.587797 TTTATCGACGACAGGAAAGCT 57.412 42.857 0.00 0.00 0.00 3.74
2317 4748 2.561733 TATCGACGACAGGAAAGCTG 57.438 50.000 0.00 0.00 0.00 4.24
2318 4749 0.108615 ATCGACGACAGGAAAGCTGG 60.109 55.000 0.00 0.00 0.00 4.85
2429 4883 0.166814 CCGTTTTGTGAGCAGCTAGC 59.833 55.000 6.62 6.62 46.19 3.42
2439 4893 2.233654 GCAGCTAGCGTGATGACCG 61.234 63.158 9.55 0.00 0.00 4.79
2447 4901 2.230940 CGTGATGACCGTCGATGCC 61.231 63.158 0.00 0.00 0.00 4.40
2506 4960 1.899814 TGTGTTTAGCCGAGACCAGAT 59.100 47.619 0.00 0.00 0.00 2.90
2507 4961 2.271800 GTGTTTAGCCGAGACCAGATG 58.728 52.381 0.00 0.00 0.00 2.90
2508 4962 1.899814 TGTTTAGCCGAGACCAGATGT 59.100 47.619 0.00 0.00 0.00 3.06
2509 4963 2.094182 TGTTTAGCCGAGACCAGATGTC 60.094 50.000 0.00 0.00 44.82 3.06
2518 4972 1.079503 GACCAGATGTCGTTCCAAGC 58.920 55.000 0.00 0.00 33.49 4.01
2519 4973 0.321653 ACCAGATGTCGTTCCAAGCC 60.322 55.000 0.00 0.00 0.00 4.35
2520 4974 1.026718 CCAGATGTCGTTCCAAGCCC 61.027 60.000 0.00 0.00 0.00 5.19
2521 4975 0.321564 CAGATGTCGTTCCAAGCCCA 60.322 55.000 0.00 0.00 0.00 5.36
2522 4976 0.036010 AGATGTCGTTCCAAGCCCAG 60.036 55.000 0.00 0.00 0.00 4.45
2523 4977 0.321653 GATGTCGTTCCAAGCCCAGT 60.322 55.000 0.00 0.00 0.00 4.00
2524 4978 0.110486 ATGTCGTTCCAAGCCCAGTT 59.890 50.000 0.00 0.00 0.00 3.16
2525 4979 0.106918 TGTCGTTCCAAGCCCAGTTT 60.107 50.000 0.00 0.00 0.00 2.66
2526 4980 1.141254 TGTCGTTCCAAGCCCAGTTTA 59.859 47.619 0.00 0.00 0.00 2.01
2527 4981 1.534163 GTCGTTCCAAGCCCAGTTTAC 59.466 52.381 0.00 0.00 0.00 2.01
2528 4982 1.141254 TCGTTCCAAGCCCAGTTTACA 59.859 47.619 0.00 0.00 0.00 2.41
2529 4983 1.265905 CGTTCCAAGCCCAGTTTACAC 59.734 52.381 0.00 0.00 0.00 2.90
2530 4984 1.611977 GTTCCAAGCCCAGTTTACACC 59.388 52.381 0.00 0.00 0.00 4.16
2531 4985 0.250553 TCCAAGCCCAGTTTACACCG 60.251 55.000 0.00 0.00 0.00 4.94
2532 4986 1.241315 CCAAGCCCAGTTTACACCGG 61.241 60.000 0.00 0.00 0.00 5.28
2533 4987 1.602605 AAGCCCAGTTTACACCGGC 60.603 57.895 0.00 0.42 38.60 6.13
2534 4988 2.281900 GCCCAGTTTACACCGGCA 60.282 61.111 0.00 0.00 38.31 5.69
2535 4989 2.622962 GCCCAGTTTACACCGGCAC 61.623 63.158 0.00 0.00 38.31 5.01
2536 4990 1.228003 CCCAGTTTACACCGGCACA 60.228 57.895 0.00 0.00 0.00 4.57
2537 4991 1.234615 CCCAGTTTACACCGGCACAG 61.235 60.000 0.00 0.00 0.00 3.66
2538 4992 0.534203 CCAGTTTACACCGGCACAGT 60.534 55.000 0.00 0.00 0.00 3.55
2539 4993 0.586319 CAGTTTACACCGGCACAGTG 59.414 55.000 0.00 0.00 41.15 3.66
2540 4994 1.164041 AGTTTACACCGGCACAGTGC 61.164 55.000 17.97 17.97 44.08 4.40
2556 5010 3.549467 GCATCACTTGCGACGTCA 58.451 55.556 17.16 0.00 42.54 4.35
2557 5011 1.130613 GCATCACTTGCGACGTCAC 59.869 57.895 17.16 6.48 42.54 3.67
2558 5012 1.556591 GCATCACTTGCGACGTCACA 61.557 55.000 17.16 9.64 42.54 3.58
2559 5013 0.858583 CATCACTTGCGACGTCACAA 59.141 50.000 17.38 17.38 0.00 3.33
2560 5014 1.260297 CATCACTTGCGACGTCACAAA 59.740 47.619 18.72 6.10 0.00 2.83
2561 5015 1.360820 TCACTTGCGACGTCACAAAA 58.639 45.000 18.72 6.13 0.00 2.44
2562 5016 1.326245 TCACTTGCGACGTCACAAAAG 59.674 47.619 18.72 15.18 0.00 2.27
2563 5017 1.326245 CACTTGCGACGTCACAAAAGA 59.674 47.619 18.72 0.00 0.00 2.52
2564 5018 1.593006 ACTTGCGACGTCACAAAAGAG 59.407 47.619 18.72 10.33 0.00 2.85
2565 5019 0.934496 TTGCGACGTCACAAAAGAGG 59.066 50.000 16.21 0.00 0.00 3.69
2566 5020 1.204312 GCGACGTCACAAAAGAGGC 59.796 57.895 17.16 3.35 0.00 4.70
2567 5021 1.222115 GCGACGTCACAAAAGAGGCT 61.222 55.000 17.16 0.00 0.00 4.58
2568 5022 1.217882 CGACGTCACAAAAGAGGCTT 58.782 50.000 17.16 0.00 0.00 4.35
2569 5023 1.192534 CGACGTCACAAAAGAGGCTTC 59.807 52.381 17.16 0.00 0.00 3.86
2570 5024 2.210116 GACGTCACAAAAGAGGCTTCA 58.790 47.619 11.55 0.00 0.00 3.02
2571 5025 2.808543 GACGTCACAAAAGAGGCTTCAT 59.191 45.455 11.55 0.00 0.00 2.57
2572 5026 2.808543 ACGTCACAAAAGAGGCTTCATC 59.191 45.455 0.00 0.00 0.00 2.92
2573 5027 2.807967 CGTCACAAAAGAGGCTTCATCA 59.192 45.455 0.00 0.00 0.00 3.07
2574 5028 3.364366 CGTCACAAAAGAGGCTTCATCAC 60.364 47.826 0.00 0.00 0.00 3.06
2575 5029 3.565482 GTCACAAAAGAGGCTTCATCACA 59.435 43.478 0.00 0.00 0.00 3.58
2576 5030 4.217118 GTCACAAAAGAGGCTTCATCACAT 59.783 41.667 0.00 0.00 0.00 3.21
2577 5031 4.828939 TCACAAAAGAGGCTTCATCACATT 59.171 37.500 0.00 0.00 0.00 2.71
2578 5032 6.003326 TCACAAAAGAGGCTTCATCACATTA 58.997 36.000 0.00 0.00 0.00 1.90
2579 5033 6.489700 TCACAAAAGAGGCTTCATCACATTAA 59.510 34.615 0.00 0.00 0.00 1.40
2580 5034 7.014134 TCACAAAAGAGGCTTCATCACATTAAA 59.986 33.333 0.00 0.00 0.00 1.52
2581 5035 7.652909 CACAAAAGAGGCTTCATCACATTAAAA 59.347 33.333 0.00 0.00 0.00 1.52
2582 5036 8.203485 ACAAAAGAGGCTTCATCACATTAAAAA 58.797 29.630 0.00 0.00 0.00 1.94
2601 5055 3.949842 AAAAAGAGCTTCATTCAGGCC 57.050 42.857 0.00 0.00 0.00 5.19
2602 5056 2.592102 AAAGAGCTTCATTCAGGCCA 57.408 45.000 5.01 0.00 0.00 5.36
2603 5057 2.592102 AAGAGCTTCATTCAGGCCAA 57.408 45.000 5.01 0.00 0.00 4.52
2604 5058 1.831580 AGAGCTTCATTCAGGCCAAC 58.168 50.000 5.01 0.00 0.00 3.77
2605 5059 1.353694 AGAGCTTCATTCAGGCCAACT 59.646 47.619 5.01 0.00 0.00 3.16
2606 5060 1.742268 GAGCTTCATTCAGGCCAACTC 59.258 52.381 5.01 0.00 0.00 3.01
2607 5061 0.813821 GCTTCATTCAGGCCAACTCC 59.186 55.000 5.01 0.00 0.00 3.85
2608 5062 1.887956 GCTTCATTCAGGCCAACTCCA 60.888 52.381 5.01 0.00 0.00 3.86
2609 5063 1.815003 CTTCATTCAGGCCAACTCCAC 59.185 52.381 5.01 0.00 0.00 4.02
2610 5064 0.038166 TCATTCAGGCCAACTCCACC 59.962 55.000 5.01 0.00 0.00 4.61
2611 5065 1.002134 ATTCAGGCCAACTCCACCG 60.002 57.895 5.01 0.00 0.00 4.94
2612 5066 3.842925 TTCAGGCCAACTCCACCGC 62.843 63.158 5.01 0.00 0.00 5.68
2613 5067 4.641645 CAGGCCAACTCCACCGCA 62.642 66.667 5.01 0.00 0.00 5.69
2614 5068 4.643387 AGGCCAACTCCACCGCAC 62.643 66.667 5.01 0.00 0.00 5.34
2616 5070 4.980805 GCCAACTCCACCGCACGA 62.981 66.667 0.00 0.00 0.00 4.35
2617 5071 3.041940 CCAACTCCACCGCACGAC 61.042 66.667 0.00 0.00 0.00 4.34
2618 5072 3.041940 CAACTCCACCGCACGACC 61.042 66.667 0.00 0.00 0.00 4.79
2619 5073 4.309950 AACTCCACCGCACGACCC 62.310 66.667 0.00 0.00 0.00 4.46
2623 5077 4.939368 CCACCGCACGACCCCAAA 62.939 66.667 0.00 0.00 0.00 3.28
2624 5078 3.656045 CACCGCACGACCCCAAAC 61.656 66.667 0.00 0.00 0.00 2.93
2627 5081 4.973055 CGCACGACCCCAAACGGA 62.973 66.667 0.00 0.00 0.00 4.69
2628 5082 2.359478 GCACGACCCCAAACGGAT 60.359 61.111 0.00 0.00 0.00 4.18
2629 5083 2.686816 GCACGACCCCAAACGGATG 61.687 63.158 0.00 0.00 0.00 3.51
2630 5084 1.302192 CACGACCCCAAACGGATGT 60.302 57.895 0.00 0.00 0.00 3.06
2631 5085 1.004200 ACGACCCCAAACGGATGTC 60.004 57.895 0.00 0.00 0.00 3.06
2632 5086 1.743995 CGACCCCAAACGGATGTCC 60.744 63.158 0.00 0.00 0.00 4.02
2652 5106 2.293677 GGATTGGCCGAATTTTGTCC 57.706 50.000 0.00 0.00 0.00 4.02
2653 5107 1.548269 GGATTGGCCGAATTTTGTCCA 59.452 47.619 0.00 0.00 0.00 4.02
2654 5108 2.168313 GGATTGGCCGAATTTTGTCCAT 59.832 45.455 0.00 0.00 0.00 3.41
2655 5109 3.369366 GGATTGGCCGAATTTTGTCCATT 60.369 43.478 0.00 0.00 0.00 3.16
2656 5110 3.760580 TTGGCCGAATTTTGTCCATTT 57.239 38.095 0.00 0.00 0.00 2.32
2657 5111 3.037431 TGGCCGAATTTTGTCCATTTG 57.963 42.857 0.00 0.00 0.00 2.32
2658 5112 2.289320 TGGCCGAATTTTGTCCATTTGG 60.289 45.455 0.00 0.00 38.00 3.28
2659 5113 2.345876 GCCGAATTTTGTCCATTTGGG 58.654 47.619 0.00 0.00 36.13 4.12
2660 5114 2.028567 GCCGAATTTTGTCCATTTGGGA 60.029 45.455 0.00 0.00 45.89 4.37
2667 5121 2.994699 TCCATTTGGGACGCCGAT 59.005 55.556 0.00 0.00 42.15 4.18
2668 5122 1.451207 TCCATTTGGGACGCCGATG 60.451 57.895 0.00 0.00 42.15 3.84
2669 5123 2.480610 CCATTTGGGACGCCGATGG 61.481 63.158 0.00 6.79 40.01 3.51
2670 5124 2.124320 ATTTGGGACGCCGATGGG 60.124 61.111 0.00 0.00 0.00 4.00
2671 5125 2.978946 ATTTGGGACGCCGATGGGT 61.979 57.895 0.00 0.00 40.88 4.51
2672 5126 2.493273 ATTTGGGACGCCGATGGGTT 62.493 55.000 0.00 0.00 37.85 4.11
2673 5127 3.615509 TTGGGACGCCGATGGGTTC 62.616 63.158 0.00 0.00 37.85 3.62
2674 5128 4.090588 GGGACGCCGATGGGTTCA 62.091 66.667 0.00 0.00 37.85 3.18
2675 5129 2.818274 GGACGCCGATGGGTTCAC 60.818 66.667 0.00 0.00 37.85 3.18
2676 5130 2.818274 GACGCCGATGGGTTCACC 60.818 66.667 0.00 0.00 37.85 4.02
2677 5131 4.752879 ACGCCGATGGGTTCACCG 62.753 66.667 0.00 0.00 44.64 4.94
2678 5132 4.752879 CGCCGATGGGTTCACCGT 62.753 66.667 0.00 0.00 44.64 4.83
2679 5133 3.124921 GCCGATGGGTTCACCGTG 61.125 66.667 0.00 0.00 44.64 4.94
2680 5134 2.345991 CCGATGGGTTCACCGTGT 59.654 61.111 0.00 0.00 44.64 4.49
2681 5135 1.740296 CCGATGGGTTCACCGTGTC 60.740 63.158 0.00 0.00 44.64 3.67
2682 5136 1.740296 CGATGGGTTCACCGTGTCC 60.740 63.158 0.00 3.05 44.64 4.02
2683 5137 1.740296 GATGGGTTCACCGTGTCCG 60.740 63.158 0.00 0.00 44.64 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
585 2494 5.924475 AGTAAACGGTTGACAAAGATCAG 57.076 39.130 10.90 0.00 0.00 2.90
734 2674 5.125257 TCAGTTTCAAACAGAGTGCATTTCA 59.875 36.000 2.41 0.00 0.00 2.69
1008 3022 1.813513 CAGGAGTGACAACACCCATC 58.186 55.000 0.00 0.00 46.99 3.51
1016 3030 0.836606 TGAACCAGCAGGAGTGACAA 59.163 50.000 0.35 0.00 38.69 3.18
1029 3120 1.092921 GTCGTGTTGGCTGTGAACCA 61.093 55.000 0.00 0.00 34.65 3.67
1185 3280 1.520342 GATGTCAGTCGCCTGCTCC 60.520 63.158 0.00 0.00 38.66 4.70
1227 3322 5.249393 GGCCTTCATGATCTTCCTTATCCTA 59.751 44.000 0.00 0.00 0.00 2.94
1350 3445 0.321298 GGCGCTTGTCCTCCTTTGTA 60.321 55.000 7.64 0.00 0.00 2.41
1353 3448 2.358737 CGGCGCTTGTCCTCCTTT 60.359 61.111 7.64 0.00 0.00 3.11
1444 3539 0.319900 TGCTTCGTCTCTTCACTGGC 60.320 55.000 0.00 0.00 0.00 4.85
1449 3544 1.048601 ACCCTTGCTTCGTCTCTTCA 58.951 50.000 0.00 0.00 0.00 3.02
1464 3562 1.064389 GCCATAGGAAGCAAGAACCCT 60.064 52.381 0.00 0.00 0.00 4.34
1665 3769 2.116125 GGCCCCTCTTGCTGTTGT 59.884 61.111 0.00 0.00 0.00 3.32
1674 3778 3.013932 CAGCTTCAGGGCCCCTCT 61.014 66.667 21.43 5.52 0.00 3.69
1691 3795 0.820871 AGGACTCTGAATCTGGCGAC 59.179 55.000 0.00 0.00 0.00 5.19
1746 3850 7.090808 TCATATTATGAAAGCTAACGCGAGAT 58.909 34.615 15.93 0.00 37.53 2.75
1748 3852 6.690704 TCATATTATGAAAGCTAACGCGAG 57.309 37.500 15.93 0.36 37.53 5.03
1821 3926 0.615850 CAACCTTCCAGGAGGACCTC 59.384 60.000 13.60 13.60 45.73 3.85
1822 3927 0.842467 CCAACCTTCCAGGAGGACCT 60.842 60.000 10.96 0.00 45.73 3.85
1823 3928 1.134438 ACCAACCTTCCAGGAGGACC 61.134 60.000 10.96 0.00 45.73 4.46
1830 3939 1.067516 CAACAGCAACCAACCTTCCAG 59.932 52.381 0.00 0.00 0.00 3.86
1837 3946 0.248458 CCACGACAACAGCAACCAAC 60.248 55.000 0.00 0.00 0.00 3.77
1879 3988 8.879759 TCGACCAATTAGTCTCAAATCATAAAC 58.120 33.333 2.54 0.00 34.46 2.01
1883 3992 8.511604 AATTCGACCAATTAGTCTCAAATCAT 57.488 30.769 2.54 0.00 32.48 2.45
1964 4074 6.578545 GCCACACGCAAACATATCATAAATAG 59.421 38.462 0.00 0.00 37.47 1.73
1991 4101 8.585471 AGTCTCAAATCACAAATTCATGGTAT 57.415 30.769 0.00 0.00 0.00 2.73
2019 4129 4.571372 TGGAACGGTAAAATTTGACCAC 57.429 40.909 22.35 13.23 35.26 4.16
2044 4154 1.064017 TCACCAGAGGCCAACTTTTGT 60.064 47.619 5.01 0.00 0.00 2.83
2169 4598 2.276201 TGCACATTCGGTTTCGGATAG 58.724 47.619 0.00 0.00 31.84 2.08
2235 4664 1.131883 CTGCTACTTGCCATGCTTCAC 59.868 52.381 0.00 0.00 42.00 3.18
2299 4730 0.108615 CCAGCTTTCCTGTCGTCGAT 60.109 55.000 0.00 0.00 40.06 3.59
2300 4731 1.289066 CCAGCTTTCCTGTCGTCGA 59.711 57.895 0.00 0.00 40.06 4.20
2301 4732 1.738099 CCCAGCTTTCCTGTCGTCG 60.738 63.158 0.00 0.00 40.06 5.12
2316 4747 2.128290 CTGCATCACCCAGTGACCCA 62.128 60.000 0.00 0.00 45.65 4.51
2317 4748 1.377725 CTGCATCACCCAGTGACCC 60.378 63.158 0.00 0.00 45.65 4.46
2318 4749 1.377725 CCTGCATCACCCAGTGACC 60.378 63.158 0.00 0.00 45.65 4.02
2387 4841 1.521681 GACCGGCCTGTGATAGCAC 60.522 63.158 3.79 3.61 45.35 4.40
2422 4876 0.867753 GACGGTCATCACGCTAGCTG 60.868 60.000 13.93 10.24 34.00 4.24
2429 4883 2.230940 GGCATCGACGGTCATCACG 61.231 63.158 9.10 0.00 37.36 4.35
2430 4884 2.230940 CGGCATCGACGGTCATCAC 61.231 63.158 9.10 0.00 39.00 3.06
2439 4893 2.736144 TAATGATACCCGGCATCGAC 57.264 50.000 0.00 0.00 39.00 4.20
2447 4901 4.268644 GTGATGCGATGATAATGATACCCG 59.731 45.833 0.00 0.00 0.00 5.28
2506 4960 0.106918 AAACTGGGCTTGGAACGACA 60.107 50.000 0.00 0.00 0.00 4.35
2507 4961 1.534163 GTAAACTGGGCTTGGAACGAC 59.466 52.381 0.00 0.00 0.00 4.34
2508 4962 1.141254 TGTAAACTGGGCTTGGAACGA 59.859 47.619 0.00 0.00 0.00 3.85
2509 4963 1.265905 GTGTAAACTGGGCTTGGAACG 59.734 52.381 0.00 0.00 0.00 3.95
2510 4964 1.611977 GGTGTAAACTGGGCTTGGAAC 59.388 52.381 0.00 0.00 0.00 3.62
2511 4965 1.816183 CGGTGTAAACTGGGCTTGGAA 60.816 52.381 0.00 0.00 0.00 3.53
2512 4966 0.250553 CGGTGTAAACTGGGCTTGGA 60.251 55.000 0.00 0.00 0.00 3.53
2513 4967 1.241315 CCGGTGTAAACTGGGCTTGG 61.241 60.000 2.47 0.00 32.56 3.61
2514 4968 1.862602 GCCGGTGTAAACTGGGCTTG 61.863 60.000 13.11 0.00 40.59 4.01
2515 4969 1.602605 GCCGGTGTAAACTGGGCTT 60.603 57.895 13.11 0.00 40.59 4.35
2516 4970 2.033602 GCCGGTGTAAACTGGGCT 59.966 61.111 13.11 0.00 40.59 5.19
2517 4971 2.281900 TGCCGGTGTAAACTGGGC 60.282 61.111 13.11 11.71 44.00 5.36
2518 4972 1.228003 TGTGCCGGTGTAAACTGGG 60.228 57.895 13.11 1.31 36.66 4.45
2519 4973 0.534203 ACTGTGCCGGTGTAAACTGG 60.534 55.000 6.53 6.53 39.14 4.00
2520 4974 0.586319 CACTGTGCCGGTGTAAACTG 59.414 55.000 1.90 1.35 36.14 3.16
2521 4975 1.164041 GCACTGTGCCGGTGTAAACT 61.164 55.000 21.78 0.00 42.21 2.66
2522 4976 1.281656 GCACTGTGCCGGTGTAAAC 59.718 57.895 21.78 0.00 42.21 2.01
2523 4977 0.536233 ATGCACTGTGCCGGTGTAAA 60.536 50.000 28.17 8.89 44.23 2.01
2524 4978 0.953471 GATGCACTGTGCCGGTGTAA 60.953 55.000 28.17 9.64 44.23 2.41
2525 4979 1.375396 GATGCACTGTGCCGGTGTA 60.375 57.895 28.17 10.38 44.23 2.90
2526 4980 2.669569 GATGCACTGTGCCGGTGT 60.670 61.111 28.17 10.35 44.23 4.16
2527 4981 2.669229 TGATGCACTGTGCCGGTG 60.669 61.111 28.17 9.15 44.23 4.94
2528 4982 2.669569 GTGATGCACTGTGCCGGT 60.670 61.111 28.17 15.19 44.23 5.28
2529 4983 1.968017 AAGTGATGCACTGTGCCGG 60.968 57.895 28.17 0.00 44.62 6.13
2530 4984 1.208358 CAAGTGATGCACTGTGCCG 59.792 57.895 28.17 5.88 44.62 5.69
2540 4994 0.858583 TTGTGACGTCGCAAGTGATG 59.141 50.000 34.19 1.51 40.93 3.07
2541 4995 1.577468 TTTGTGACGTCGCAAGTGAT 58.423 45.000 34.95 0.00 45.60 3.06
2542 4996 1.326245 CTTTTGTGACGTCGCAAGTGA 59.674 47.619 34.95 25.52 45.60 3.41
2543 4997 1.326245 TCTTTTGTGACGTCGCAAGTG 59.674 47.619 34.95 30.04 45.60 3.16
2544 4998 1.593006 CTCTTTTGTGACGTCGCAAGT 59.407 47.619 34.95 0.00 45.60 3.16
2545 4999 1.070577 CCTCTTTTGTGACGTCGCAAG 60.071 52.381 34.95 27.48 45.60 4.01
2546 5000 0.934496 CCTCTTTTGTGACGTCGCAA 59.066 50.000 34.19 34.19 43.70 4.85
2547 5001 1.495584 GCCTCTTTTGTGACGTCGCA 61.496 55.000 27.03 27.03 34.11 5.10
2548 5002 1.204312 GCCTCTTTTGTGACGTCGC 59.796 57.895 22.00 22.00 0.00 5.19
2549 5003 1.192534 GAAGCCTCTTTTGTGACGTCG 59.807 52.381 11.62 0.00 0.00 5.12
2550 5004 2.210116 TGAAGCCTCTTTTGTGACGTC 58.790 47.619 9.11 9.11 0.00 4.34
2551 5005 2.325583 TGAAGCCTCTTTTGTGACGT 57.674 45.000 0.00 0.00 0.00 4.34
2552 5006 2.807967 TGATGAAGCCTCTTTTGTGACG 59.192 45.455 0.00 0.00 0.00 4.35
2553 5007 3.565482 TGTGATGAAGCCTCTTTTGTGAC 59.435 43.478 0.00 0.00 0.00 3.67
2554 5008 3.819368 TGTGATGAAGCCTCTTTTGTGA 58.181 40.909 0.00 0.00 0.00 3.58
2555 5009 4.778534 ATGTGATGAAGCCTCTTTTGTG 57.221 40.909 0.00 0.00 0.00 3.33
2556 5010 6.899393 TTAATGTGATGAAGCCTCTTTTGT 57.101 33.333 0.00 0.00 0.00 2.83
2557 5011 8.592105 TTTTTAATGTGATGAAGCCTCTTTTG 57.408 30.769 0.00 0.00 0.00 2.44
2581 5035 3.233507 TGGCCTGAATGAAGCTCTTTTT 58.766 40.909 3.32 0.00 0.00 1.94
2582 5036 2.880443 TGGCCTGAATGAAGCTCTTTT 58.120 42.857 3.32 0.00 0.00 2.27
2583 5037 2.560105 GTTGGCCTGAATGAAGCTCTTT 59.440 45.455 3.32 0.00 0.00 2.52
2584 5038 2.165998 GTTGGCCTGAATGAAGCTCTT 58.834 47.619 3.32 0.00 0.00 2.85
2585 5039 1.353694 AGTTGGCCTGAATGAAGCTCT 59.646 47.619 3.32 0.00 0.00 4.09
2586 5040 1.742268 GAGTTGGCCTGAATGAAGCTC 59.258 52.381 3.32 0.00 0.00 4.09
2587 5041 1.615384 GGAGTTGGCCTGAATGAAGCT 60.615 52.381 3.32 0.00 0.00 3.74
2588 5042 0.813821 GGAGTTGGCCTGAATGAAGC 59.186 55.000 3.32 0.00 0.00 3.86
2589 5043 1.815003 GTGGAGTTGGCCTGAATGAAG 59.185 52.381 3.32 0.00 0.00 3.02
2590 5044 1.547675 GGTGGAGTTGGCCTGAATGAA 60.548 52.381 3.32 0.00 0.00 2.57
2591 5045 0.038166 GGTGGAGTTGGCCTGAATGA 59.962 55.000 3.32 0.00 0.00 2.57
2592 5046 1.308069 CGGTGGAGTTGGCCTGAATG 61.308 60.000 3.32 0.00 0.00 2.67
2593 5047 1.002134 CGGTGGAGTTGGCCTGAAT 60.002 57.895 3.32 0.00 0.00 2.57
2594 5048 2.429930 CGGTGGAGTTGGCCTGAA 59.570 61.111 3.32 0.00 0.00 3.02
2595 5049 4.329545 GCGGTGGAGTTGGCCTGA 62.330 66.667 3.32 0.00 0.00 3.86
2596 5050 4.641645 TGCGGTGGAGTTGGCCTG 62.642 66.667 3.32 0.00 0.00 4.85
2597 5051 4.643387 GTGCGGTGGAGTTGGCCT 62.643 66.667 3.32 0.00 0.00 5.19
2599 5053 4.980805 TCGTGCGGTGGAGTTGGC 62.981 66.667 0.00 0.00 0.00 4.52
2600 5054 3.041940 GTCGTGCGGTGGAGTTGG 61.042 66.667 0.00 0.00 0.00 3.77
2601 5055 3.041940 GGTCGTGCGGTGGAGTTG 61.042 66.667 0.00 0.00 0.00 3.16
2602 5056 4.309950 GGGTCGTGCGGTGGAGTT 62.310 66.667 0.00 0.00 0.00 3.01
2606 5060 4.939368 TTTGGGGTCGTGCGGTGG 62.939 66.667 0.00 0.00 0.00 4.61
2607 5061 3.656045 GTTTGGGGTCGTGCGGTG 61.656 66.667 0.00 0.00 0.00 4.94
2610 5064 4.973055 TCCGTTTGGGGTCGTGCG 62.973 66.667 0.00 0.00 36.01 5.34
2611 5065 2.359478 ATCCGTTTGGGGTCGTGC 60.359 61.111 0.00 0.00 36.01 5.34
2612 5066 1.296056 GACATCCGTTTGGGGTCGTG 61.296 60.000 0.00 0.00 36.01 4.35
2613 5067 1.004200 GACATCCGTTTGGGGTCGT 60.004 57.895 0.00 0.00 36.01 4.34
2614 5068 1.743995 GGACATCCGTTTGGGGTCG 60.744 63.158 0.00 0.00 39.44 4.79
2615 5069 4.313819 GGACATCCGTTTGGGGTC 57.686 61.111 0.00 0.00 38.48 4.46
2633 5087 1.548269 TGGACAAAATTCGGCCAATCC 59.452 47.619 2.24 0.90 0.00 3.01
2634 5088 3.525268 ATGGACAAAATTCGGCCAATC 57.475 42.857 2.24 0.00 31.53 2.67
2635 5089 3.979101 AATGGACAAAATTCGGCCAAT 57.021 38.095 2.24 0.00 31.53 3.16
2636 5090 3.397482 CAAATGGACAAAATTCGGCCAA 58.603 40.909 2.24 0.00 31.53 4.52
2637 5091 2.289320 CCAAATGGACAAAATTCGGCCA 60.289 45.455 2.24 4.92 37.39 5.36
2638 5092 2.345876 CCAAATGGACAAAATTCGGCC 58.654 47.619 0.00 0.00 37.39 6.13
2639 5093 2.028567 TCCCAAATGGACAAAATTCGGC 60.029 45.455 0.00 0.00 38.61 5.54
2640 5094 3.951775 TCCCAAATGGACAAAATTCGG 57.048 42.857 0.00 0.00 38.61 4.30
2650 5104 1.451207 CATCGGCGTCCCAAATGGA 60.451 57.895 6.85 0.00 42.41 3.41
2651 5105 2.480610 CCATCGGCGTCCCAAATGG 61.481 63.158 6.85 7.78 37.59 3.16
2652 5106 2.480610 CCCATCGGCGTCCCAAATG 61.481 63.158 6.85 1.47 0.00 2.32
2653 5107 2.124320 CCCATCGGCGTCCCAAAT 60.124 61.111 6.85 0.00 0.00 2.32
2654 5108 3.198953 AACCCATCGGCGTCCCAAA 62.199 57.895 6.85 0.00 0.00 3.28
2655 5109 3.615509 GAACCCATCGGCGTCCCAA 62.616 63.158 6.85 0.00 0.00 4.12
2656 5110 4.090588 GAACCCATCGGCGTCCCA 62.091 66.667 6.85 0.00 0.00 4.37
2657 5111 4.090588 TGAACCCATCGGCGTCCC 62.091 66.667 6.85 0.00 0.00 4.46
2658 5112 2.818274 GTGAACCCATCGGCGTCC 60.818 66.667 6.85 0.00 0.00 4.79
2659 5113 2.818274 GGTGAACCCATCGGCGTC 60.818 66.667 6.85 0.00 0.00 5.19
2660 5114 4.752879 CGGTGAACCCATCGGCGT 62.753 66.667 6.85 0.00 42.85 5.68
2665 5119 1.740296 CGGACACGGTGAACCCATC 60.740 63.158 16.29 0.10 36.18 3.51
2666 5120 2.345991 CGGACACGGTGAACCCAT 59.654 61.111 16.29 0.00 36.18 4.00


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

AutoCloner maintained by Alex Coulton.