Multiple sequence alignment - TraesCS7B01G065300

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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 TraesCS7B01G065300 chr7B 100.000 2624 0 0 1 2624 70819285 70816662 0.000000e+00 4846.0
1 TraesCS7B01G065300 chr7D 91.099 1775 126 16 1 1766 111084511 111082760 0.000000e+00 2374.0
2 TraesCS7B01G065300 chr7D 82.239 259 25 10 2000 2242 111082364 111082111 1.230000e-48 204.0
3 TraesCS7B01G065300 chr7D 88.387 155 15 1 2344 2495 111079421 111079267 1.600000e-42 183.0
4 TraesCS7B01G065300 chr7A 93.889 900 53 1 833 1732 116486703 116487600 0.000000e+00 1356.0
5 TraesCS7B01G065300 chr7A 91.053 760 40 14 1 735 116485861 116486617 0.000000e+00 1002.0
6 TraesCS7B01G065300 chr7A 78.373 467 67 16 2097 2543 116169154 116168702 3.330000e-69 272.0
7 TraesCS7B01G065300 chr7A 87.234 141 11 3 1511 1651 116600737 116600604 1.260000e-33 154.0
8 TraesCS7B01G065300 chr1D 87.041 926 85 12 834 1735 486387161 486388075 0.000000e+00 1013.0
9 TraesCS7B01G065300 chr1D 90.221 542 45 6 2 536 486382522 486383062 0.000000e+00 701.0
10 TraesCS7B01G065300 chr1B 86.233 908 90 14 830 1713 677322915 677323811 0.000000e+00 952.0
11 TraesCS7B01G065300 chr1B 90.926 540 41 6 2 534 677320010 677320548 0.000000e+00 719.0
12 TraesCS7B01G065300 chr1A 91.481 540 38 6 2 534 583996899 583997437 0.000000e+00 736.0
13 TraesCS7B01G065300 chr1A 89.855 69 3 2 1813 1877 536618467 536618535 4.650000e-13 86.1
14 TraesCS7B01G065300 chr2B 73.941 472 101 19 936 1390 793525632 793525166 1.250000e-38 171.0
15 TraesCS7B01G065300 chr5B 81.679 131 14 8 1780 1902 141580457 141580585 1.660000e-17 100.0
16 TraesCS7B01G065300 chr5D 80.952 84 10 4 1813 1891 92139969 92140051 7.840000e-06 62.1


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 TraesCS7B01G065300 chr7B 70816662 70819285 2623 True 4846.000000 4846 100.000000 1 2624 1 chr7B.!!$R1 2623
1 TraesCS7B01G065300 chr7D 111079267 111084511 5244 True 920.333333 2374 87.241667 1 2495 3 chr7D.!!$R1 2494
2 TraesCS7B01G065300 chr7A 116485861 116487600 1739 False 1179.000000 1356 92.471000 1 1732 2 chr7A.!!$F1 1731
3 TraesCS7B01G065300 chr1D 486387161 486388075 914 False 1013.000000 1013 87.041000 834 1735 1 chr1D.!!$F2 901
4 TraesCS7B01G065300 chr1D 486382522 486383062 540 False 701.000000 701 90.221000 2 536 1 chr1D.!!$F1 534
5 TraesCS7B01G065300 chr1B 677320010 677323811 3801 False 835.500000 952 88.579500 2 1713 2 chr1B.!!$F1 1711
6 TraesCS7B01G065300 chr1A 583996899 583997437 538 False 736.000000 736 91.481000 2 534 1 chr1A.!!$F2 532

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
987 3185 0.038435 TCGTCCACGGCGACATTAAA 60.038 50.0 16.62 0.0 40.29 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2259 4712 0.032815 TCGACTCCGTCAATGTGCAA 59.967 50.0 0.0 0.0 37.05 4.08 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
144 145 1.729470 CTCCGGACTCCCTCGACATG 61.729 65.000 0.00 0.00 0.00 3.21
153 154 1.226323 CCTCGACATGGACGACGAC 60.226 63.158 0.00 0.00 35.88 4.34
324 325 2.760374 GCCATCAAGGTATTCTCTCGG 58.240 52.381 0.00 0.00 40.61 4.63
381 382 0.545171 AGGTCACCATCATCAGCAGG 59.455 55.000 0.00 0.00 0.00 4.85
597 611 9.869757 TGATTTCGTATCTTGACTAAAATGAGA 57.130 29.630 2.85 0.00 0.00 3.27
614 628 8.697507 AAAATGAGACTAATTTTGGACTCACT 57.302 30.769 9.40 0.00 41.30 3.41
618 632 7.155328 TGAGACTAATTTTGGACTCACTCTTC 58.845 38.462 5.12 0.00 36.11 2.87
619 633 6.159988 AGACTAATTTTGGACTCACTCTTCG 58.840 40.000 0.00 0.00 0.00 3.79
623 637 6.969828 AATTTTGGACTCACTCTTCGTATC 57.030 37.500 0.00 0.00 0.00 2.24
624 638 5.462530 TTTTGGACTCACTCTTCGTATCA 57.537 39.130 0.00 0.00 0.00 2.15
625 639 5.661056 TTTGGACTCACTCTTCGTATCAT 57.339 39.130 0.00 0.00 0.00 2.45
626 640 5.661056 TTGGACTCACTCTTCGTATCATT 57.339 39.130 0.00 0.00 0.00 2.57
628 642 6.037786 TGGACTCACTCTTCGTATCATTTT 57.962 37.500 0.00 0.00 0.00 1.82
694 733 4.465632 ACAATGCATGATGAGCAACATT 57.534 36.364 0.00 0.00 46.27 2.71
703 742 2.084610 TGAGCAACATTCGACCTCTG 57.915 50.000 0.00 0.00 0.00 3.35
742 781 7.471721 CACGGAGCAAAATTCATATTAGTTGA 58.528 34.615 0.00 0.00 0.00 3.18
800 839 3.381949 GACCTAAATTCTCGGTCGATGG 58.618 50.000 0.00 0.00 38.00 3.51
812 851 1.080093 TCGATGGACAGTGGCGAAC 60.080 57.895 0.00 0.00 0.00 3.95
814 853 0.172578 CGATGGACAGTGGCGAACTA 59.827 55.000 0.00 0.00 36.83 2.24
817 856 0.888619 TGGACAGTGGCGAACTAGAG 59.111 55.000 0.00 0.00 36.83 2.43
855 3053 0.532573 TGAGTCGGAGTGCTTGGATC 59.467 55.000 0.00 0.00 0.00 3.36
881 3079 5.426689 TCTGATTCTACTTGATTGTGCCT 57.573 39.130 0.00 0.00 0.00 4.75
987 3185 0.038435 TCGTCCACGGCGACATTAAA 60.038 50.000 16.62 0.00 40.29 1.52
1003 3201 4.458989 ACATTAAACCGAGCAACATCATGT 59.541 37.500 0.00 0.00 0.00 3.21
1019 3217 5.646793 ACATCATGTTGGATGAGTTCTTCAG 59.353 40.000 9.90 0.00 46.00 3.02
1041 3239 1.215647 CAAGCTAGGCGACTTCGGT 59.784 57.895 0.00 0.00 43.67 4.69
1047 3245 0.747283 TAGGCGACTTCGGTCTCTCC 60.747 60.000 0.00 0.00 43.67 3.71
1288 3486 1.688311 CGTGGGACCTCTATGGAAGGA 60.688 57.143 0.00 0.00 39.71 3.36
1323 3521 2.049063 GCTGACGAGCGTCTTGGT 60.049 61.111 21.68 0.00 44.80 3.67
1350 3548 3.703127 GACCGGTGGGAGGTGGAC 61.703 72.222 14.63 0.00 43.01 4.02
1357 3555 4.035102 GGGAGGTGGACAGGGTGC 62.035 72.222 0.00 0.00 0.00 5.01
1686 3932 3.130340 TGTGGTGGACAAAGAAGAAAAGC 59.870 43.478 0.00 0.00 0.00 3.51
1707 3953 4.339814 AGCTTCGGTGGACAAAATTTGTAA 59.660 37.500 11.71 0.50 45.52 2.41
1750 3996 2.318908 TGCAGAGGAAAATGCCAAACT 58.681 42.857 0.00 0.00 41.85 2.66
1756 4003 3.081804 AGGAAAATGCCAAACTAGACCG 58.918 45.455 0.00 0.00 0.00 4.79
1757 4004 3.078837 GGAAAATGCCAAACTAGACCGA 58.921 45.455 0.00 0.00 0.00 4.69
1766 4013 3.368427 CCAAACTAGACCGAGCTTCATGA 60.368 47.826 0.00 0.00 0.00 3.07
1768 4015 3.791973 ACTAGACCGAGCTTCATGAAG 57.208 47.619 27.82 27.82 41.24 3.02
1771 4018 0.107945 GACCGAGCTTCATGAAGGCT 60.108 55.000 31.41 27.18 38.80 4.58
1772 4019 0.107945 ACCGAGCTTCATGAAGGCTC 60.108 55.000 31.41 30.66 38.80 4.70
1774 4021 1.569708 CGAGCTTCATGAAGGCTCTC 58.430 55.000 32.96 28.09 38.37 3.20
1775 4022 1.136695 CGAGCTTCATGAAGGCTCTCT 59.863 52.381 32.96 24.35 38.37 3.10
1776 4023 2.360483 CGAGCTTCATGAAGGCTCTCTA 59.640 50.000 32.96 7.69 38.37 2.43
1777 4024 3.550639 CGAGCTTCATGAAGGCTCTCTAG 60.551 52.174 32.96 23.29 38.37 2.43
1790 4185 7.388224 TGAAGGCTCTCTAGTATGTACTATTCG 59.612 40.741 0.69 0.00 38.06 3.34
1792 4187 7.225725 AGGCTCTCTAGTATGTACTATTCGTT 58.774 38.462 0.69 0.00 38.06 3.85
1795 4190 7.388500 GCTCTCTAGTATGTACTATTCGTTCCT 59.612 40.741 0.69 0.00 38.06 3.36
1802 4197 8.628280 AGTATGTACTATTCGTTCCTAAAGTCC 58.372 37.037 0.00 0.00 34.13 3.85
1811 4206 6.494893 TCGTTCCTAAAGTCCATGATTTTG 57.505 37.500 0.00 0.00 0.00 2.44
1844 4244 4.737054 CAGCTCGCAATTCAAGGTATTTT 58.263 39.130 0.00 0.00 0.00 1.82
1849 4249 7.067494 AGCTCGCAATTCAAGGTATTTTATTCT 59.933 33.333 0.00 0.00 0.00 2.40
1850 4250 7.166473 GCTCGCAATTCAAGGTATTTTATTCTG 59.834 37.037 0.00 0.00 0.00 3.02
1970 4371 1.129437 GCATTCGTGGAGCTTGTTCTC 59.871 52.381 0.00 0.00 0.00 2.87
1994 4395 0.179026 ATGCCCTACTCTGCATGCAG 60.179 55.000 36.80 36.80 45.96 4.41
1995 4396 2.185494 GCCCTACTCTGCATGCAGC 61.185 63.158 37.48 23.80 43.31 5.25
1996 4397 1.525535 CCCTACTCTGCATGCAGCC 60.526 63.158 37.48 1.58 44.83 4.85
1997 4398 1.525535 CCTACTCTGCATGCAGCCC 60.526 63.158 37.48 1.17 44.83 5.19
1998 4399 1.525923 CTACTCTGCATGCAGCCCT 59.474 57.895 37.48 24.58 44.83 5.19
2005 4432 1.105167 TGCATGCAGCCCTATCTTGC 61.105 55.000 18.46 0.00 44.83 4.01
2019 4446 6.505272 CCCTATCTTGCAACTGTACTAGTAC 58.495 44.000 23.58 23.58 39.18 2.73
2022 4449 7.863375 CCTATCTTGCAACTGTACTAGTACATC 59.137 40.741 30.78 20.78 44.15 3.06
2052 4479 1.514678 GACTGCGCAATTGGTGTGGA 61.515 55.000 13.05 0.00 38.25 4.02
2054 4481 0.244450 CTGCGCAATTGGTGTGGAAT 59.756 50.000 13.05 0.00 37.65 3.01
2055 4482 0.243365 TGCGCAATTGGTGTGGAATC 59.757 50.000 8.16 0.00 34.82 2.52
2056 4483 0.243365 GCGCAATTGGTGTGGAATCA 59.757 50.000 0.30 0.00 38.25 2.57
2057 4484 1.733389 GCGCAATTGGTGTGGAATCAG 60.733 52.381 0.30 0.00 38.25 2.90
2065 4508 4.822036 TGGTGTGGAATCAGTTAAAACG 57.178 40.909 0.00 0.00 0.00 3.60
2067 4510 4.035792 TGGTGTGGAATCAGTTAAAACGTG 59.964 41.667 0.00 0.00 0.00 4.49
2075 4518 7.660617 TGGAATCAGTTAAAACGTGGTTGTATA 59.339 33.333 0.00 0.00 0.00 1.47
2078 4521 5.409214 TCAGTTAAAACGTGGTTGTATAGCC 59.591 40.000 0.00 0.00 0.00 3.93
2079 4522 5.179742 CAGTTAAAACGTGGTTGTATAGCCA 59.820 40.000 0.00 0.00 34.49 4.75
2081 4524 6.262720 AGTTAAAACGTGGTTGTATAGCCAAA 59.737 34.615 0.00 0.00 39.03 3.28
2082 4525 5.517322 AAAACGTGGTTGTATAGCCAAAA 57.483 34.783 0.00 0.00 39.03 2.44
2243 4696 7.647907 GGATAATTTCCGTACATCGTTGTAT 57.352 36.000 9.43 0.00 36.36 2.29
2244 4697 7.507304 GGATAATTTCCGTACATCGTTGTATG 58.493 38.462 15.87 15.87 42.57 2.39
2245 4698 7.170320 GGATAATTTCCGTACATCGTTGTATGT 59.830 37.037 19.49 8.48 41.74 2.29
2246 4699 6.730960 AATTTCCGTACATCGTTGTATGTT 57.269 33.333 19.49 8.56 41.74 2.71
2247 4700 5.766702 TTTCCGTACATCGTTGTATGTTC 57.233 39.130 19.49 4.00 41.74 3.18
2248 4701 4.437772 TCCGTACATCGTTGTATGTTCA 57.562 40.909 19.49 5.60 41.74 3.18
2249 4702 4.417506 TCCGTACATCGTTGTATGTTCAG 58.582 43.478 19.49 8.51 41.74 3.02
2250 4703 3.550275 CCGTACATCGTTGTATGTTCAGG 59.450 47.826 19.49 9.48 41.74 3.86
2251 4704 4.171005 CGTACATCGTTGTATGTTCAGGT 58.829 43.478 14.95 0.00 40.35 4.00
2252 4705 5.334319 CGTACATCGTTGTATGTTCAGGTA 58.666 41.667 14.95 0.00 40.35 3.08
2253 4706 5.454554 CGTACATCGTTGTATGTTCAGGTAG 59.545 44.000 14.95 0.00 40.35 3.18
2254 4707 4.181578 ACATCGTTGTATGTTCAGGTAGC 58.818 43.478 0.00 0.00 36.71 3.58
2255 4708 3.945981 TCGTTGTATGTTCAGGTAGCA 57.054 42.857 0.00 0.00 0.00 3.49
2256 4709 4.465632 TCGTTGTATGTTCAGGTAGCAT 57.534 40.909 0.00 0.00 33.12 3.79
2257 4710 4.180817 TCGTTGTATGTTCAGGTAGCATG 58.819 43.478 0.00 0.00 30.77 4.06
2258 4711 3.932710 CGTTGTATGTTCAGGTAGCATGT 59.067 43.478 0.00 0.00 30.77 3.21
2259 4712 4.391830 CGTTGTATGTTCAGGTAGCATGTT 59.608 41.667 0.00 0.00 30.77 2.71
2260 4713 5.106712 CGTTGTATGTTCAGGTAGCATGTTT 60.107 40.000 0.00 0.00 30.77 2.83
2261 4714 5.878332 TGTATGTTCAGGTAGCATGTTTG 57.122 39.130 0.00 0.00 30.77 2.93
2273 4726 2.702898 CATGTTTGCACATTGACGGA 57.297 45.000 0.00 0.00 41.16 4.69
2274 4727 2.587956 CATGTTTGCACATTGACGGAG 58.412 47.619 0.00 0.00 41.16 4.63
2275 4728 2.030893 CATGTTTGCACATTGACGGAGT 60.031 45.455 0.00 0.00 43.02 3.85
2276 4729 2.226437 ATGTTTGCACATTGACGGAGTC 59.774 45.455 0.00 0.00 46.31 3.36
2304 4757 4.537751 TGTCTAAGGACATAGAGGAGGTG 58.462 47.826 0.00 0.00 46.19 4.00
2318 4771 8.705594 CATAGAGGAGGTGAATAGTCCTAAAAA 58.294 37.037 0.00 0.00 41.00 1.94
2391 7484 6.624526 GCAACAAATTATTTTGCATATGTCGC 59.375 34.615 4.29 0.00 45.01 5.19
2416 7509 1.445942 CCACCTTGACTGTGGTCGT 59.554 57.895 1.27 0.00 46.62 4.34
2427 7520 0.032952 TGTGGTCGTGCACTCTAACC 59.967 55.000 16.19 16.23 0.00 2.85
2431 7524 0.038159 GTCGTGCACTCTAACCTGCT 60.038 55.000 16.19 0.00 34.29 4.24
2432 7525 0.679505 TCGTGCACTCTAACCTGCTT 59.320 50.000 16.19 0.00 34.29 3.91
2450 7543 4.687215 GAGTGCCAGGCGTGCTCA 62.687 66.667 19.69 0.00 0.00 4.26
2487 7580 0.035915 GCACCTTCACCTCCCTTCTC 60.036 60.000 0.00 0.00 0.00 2.87
2488 7581 1.352083 CACCTTCACCTCCCTTCTCA 58.648 55.000 0.00 0.00 0.00 3.27
2489 7582 1.699634 CACCTTCACCTCCCTTCTCAA 59.300 52.381 0.00 0.00 0.00 3.02
2490 7583 1.981495 ACCTTCACCTCCCTTCTCAAG 59.019 52.381 0.00 0.00 0.00 3.02
2491 7584 1.339535 CCTTCACCTCCCTTCTCAAGC 60.340 57.143 0.00 0.00 0.00 4.01
2492 7585 1.627834 CTTCACCTCCCTTCTCAAGCT 59.372 52.381 0.00 0.00 0.00 3.74
2493 7586 1.270907 TCACCTCCCTTCTCAAGCTC 58.729 55.000 0.00 0.00 0.00 4.09
2494 7587 1.203237 TCACCTCCCTTCTCAAGCTCT 60.203 52.381 0.00 0.00 0.00 4.09
2495 7588 2.043115 TCACCTCCCTTCTCAAGCTCTA 59.957 50.000 0.00 0.00 0.00 2.43
2496 7589 2.167487 CACCTCCCTTCTCAAGCTCTAC 59.833 54.545 0.00 0.00 0.00 2.59
2497 7590 1.760029 CCTCCCTTCTCAAGCTCTACC 59.240 57.143 0.00 0.00 0.00 3.18
2498 7591 2.461695 CTCCCTTCTCAAGCTCTACCA 58.538 52.381 0.00 0.00 0.00 3.25
2499 7592 2.167487 CTCCCTTCTCAAGCTCTACCAC 59.833 54.545 0.00 0.00 0.00 4.16
2500 7593 1.208293 CCCTTCTCAAGCTCTACCACC 59.792 57.143 0.00 0.00 0.00 4.61
2501 7594 1.902508 CCTTCTCAAGCTCTACCACCA 59.097 52.381 0.00 0.00 0.00 4.17
2502 7595 2.303022 CCTTCTCAAGCTCTACCACCAA 59.697 50.000 0.00 0.00 0.00 3.67
2503 7596 3.054802 CCTTCTCAAGCTCTACCACCAAT 60.055 47.826 0.00 0.00 0.00 3.16
2504 7597 3.616956 TCTCAAGCTCTACCACCAATG 57.383 47.619 0.00 0.00 0.00 2.82
2505 7598 2.906389 TCTCAAGCTCTACCACCAATGT 59.094 45.455 0.00 0.00 0.00 2.71
2506 7599 3.005554 CTCAAGCTCTACCACCAATGTG 58.994 50.000 0.00 0.00 42.39 3.21
2516 7609 4.438255 CCAATGTGGTCATGCCCA 57.562 55.556 0.00 0.00 36.04 5.36
2517 7610 2.668612 CCAATGTGGTCATGCCCAA 58.331 52.632 0.00 0.00 35.92 4.12
2518 7611 1.196911 CCAATGTGGTCATGCCCAAT 58.803 50.000 0.00 0.00 35.92 3.16
2519 7612 1.555992 CCAATGTGGTCATGCCCAATT 59.444 47.619 0.00 0.00 35.92 2.32
2520 7613 2.623535 CAATGTGGTCATGCCCAATTG 58.376 47.619 0.00 6.66 35.92 2.32
2521 7614 0.538118 ATGTGGTCATGCCCAATTGC 59.462 50.000 0.00 0.00 35.92 3.56
2522 7615 0.830866 TGTGGTCATGCCCAATTGCA 60.831 50.000 0.00 0.00 46.94 4.08
2536 7629 2.924185 TTGCAGTGCAAGCTCTCTC 58.076 52.632 26.36 0.00 43.99 3.20
2537 7630 0.947660 TTGCAGTGCAAGCTCTCTCG 60.948 55.000 26.36 0.00 43.99 4.04
2538 7631 2.099431 GCAGTGCAAGCTCTCTCGG 61.099 63.158 11.09 0.00 0.00 4.63
2539 7632 2.099431 CAGTGCAAGCTCTCTCGGC 61.099 63.158 0.00 0.00 0.00 5.54
2540 7633 2.047844 GTGCAAGCTCTCTCGGCA 60.048 61.111 0.00 0.00 32.41 5.69
2541 7634 1.669115 GTGCAAGCTCTCTCGGCAA 60.669 57.895 0.00 0.00 35.32 4.52
2542 7635 1.669115 TGCAAGCTCTCTCGGCAAC 60.669 57.895 0.00 0.00 32.07 4.17
2543 7636 1.375268 GCAAGCTCTCTCGGCAACT 60.375 57.895 0.00 0.00 0.00 3.16
2544 7637 0.952984 GCAAGCTCTCTCGGCAACTT 60.953 55.000 0.00 0.00 0.00 2.66
2545 7638 1.074752 CAAGCTCTCTCGGCAACTTC 58.925 55.000 0.00 0.00 0.00 3.01
2546 7639 0.972883 AAGCTCTCTCGGCAACTTCT 59.027 50.000 0.00 0.00 0.00 2.85
2547 7640 0.530288 AGCTCTCTCGGCAACTTCTC 59.470 55.000 0.00 0.00 0.00 2.87
2548 7641 0.244994 GCTCTCTCGGCAACTTCTCA 59.755 55.000 0.00 0.00 0.00 3.27
2549 7642 1.337260 GCTCTCTCGGCAACTTCTCAA 60.337 52.381 0.00 0.00 0.00 3.02
2550 7643 2.868044 GCTCTCTCGGCAACTTCTCAAA 60.868 50.000 0.00 0.00 0.00 2.69
2551 7644 3.594134 CTCTCTCGGCAACTTCTCAAAT 58.406 45.455 0.00 0.00 0.00 2.32
2552 7645 3.999663 CTCTCTCGGCAACTTCTCAAATT 59.000 43.478 0.00 0.00 0.00 1.82
2553 7646 3.748048 TCTCTCGGCAACTTCTCAAATTG 59.252 43.478 0.00 0.00 0.00 2.32
2554 7647 3.738982 TCTCGGCAACTTCTCAAATTGA 58.261 40.909 0.00 0.00 0.00 2.57
2555 7648 4.133820 TCTCGGCAACTTCTCAAATTGAA 58.866 39.130 0.00 0.00 0.00 2.69
2556 7649 4.578516 TCTCGGCAACTTCTCAAATTGAAA 59.421 37.500 0.00 0.00 0.00 2.69
2557 7650 4.858935 TCGGCAACTTCTCAAATTGAAAG 58.141 39.130 12.80 12.80 0.00 2.62
2558 7651 3.426525 CGGCAACTTCTCAAATTGAAAGC 59.573 43.478 13.72 5.59 0.00 3.51
2559 7652 4.370917 GGCAACTTCTCAAATTGAAAGCA 58.629 39.130 13.72 0.00 0.00 3.91
2560 7653 4.810491 GGCAACTTCTCAAATTGAAAGCAA 59.190 37.500 13.72 0.00 38.60 3.91
2561 7654 5.467735 GGCAACTTCTCAAATTGAAAGCAAT 59.532 36.000 13.72 0.00 46.35 3.56
2562 7655 6.360329 GCAACTTCTCAAATTGAAAGCAATG 58.640 36.000 13.72 11.98 43.71 2.82
2563 7656 6.565247 GCAACTTCTCAAATTGAAAGCAATGG 60.565 38.462 13.72 0.00 43.71 3.16
2564 7657 5.544650 ACTTCTCAAATTGAAAGCAATGGG 58.455 37.500 13.72 0.00 43.71 4.00
2565 7658 3.929094 TCTCAAATTGAAAGCAATGGGC 58.071 40.909 0.00 0.00 43.71 5.36
2587 7680 5.523369 GCATAAGCCTAAACTAAGCATTGG 58.477 41.667 0.00 0.00 33.58 3.16
2588 7681 5.067805 GCATAAGCCTAAACTAAGCATTGGT 59.932 40.000 0.00 0.00 36.51 3.67
2589 7682 6.405842 GCATAAGCCTAAACTAAGCATTGGTT 60.406 38.462 6.33 6.33 42.87 3.67
2590 7683 7.201785 GCATAAGCCTAAACTAAGCATTGGTTA 60.202 37.037 7.97 7.97 41.25 2.85
2597 7690 4.355543 ACTAAGCATTGGTTATGTTGCG 57.644 40.909 8.64 0.00 35.77 4.85
2598 7691 3.756434 ACTAAGCATTGGTTATGTTGCGT 59.244 39.130 8.64 0.41 35.77 5.24
2599 7692 4.938832 ACTAAGCATTGGTTATGTTGCGTA 59.061 37.500 8.64 0.00 35.77 4.42
2600 7693 4.775058 AAGCATTGGTTATGTTGCGTAA 57.225 36.364 0.00 0.00 40.00 3.18
2601 7694 4.775058 AGCATTGGTTATGTTGCGTAAA 57.225 36.364 0.00 0.00 40.00 2.01
2602 7695 5.127693 AGCATTGGTTATGTTGCGTAAAA 57.872 34.783 0.00 0.00 40.00 1.52
2603 7696 5.533482 AGCATTGGTTATGTTGCGTAAAAA 58.467 33.333 0.00 0.00 40.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 1.004560 TCTGGCTGCCTGTTTCTCG 60.005 57.895 21.03 0.00 0.00 4.04
153 154 3.479269 GCGCTGGAACCGAACTCG 61.479 66.667 0.00 0.00 39.44 4.18
480 481 3.512680 CTCTTGTTTGCCGTAGAGGTAG 58.487 50.000 0.00 0.00 43.70 3.18
544 551 9.170734 AGTTAAGAATACGACTGACATGTACTA 57.829 33.333 0.00 0.00 0.00 1.82
545 552 8.053026 AGTTAAGAATACGACTGACATGTACT 57.947 34.615 0.00 0.00 0.00 2.73
597 611 5.855045 ACGAAGAGTGAGTCCAAAATTAGT 58.145 37.500 0.00 0.00 0.00 2.24
628 642 9.451002 TGTGTTAATAATATCGTCCTCCAAAAA 57.549 29.630 0.00 0.00 0.00 1.94
694 733 4.625028 CATCTTGATTATGCAGAGGTCGA 58.375 43.478 0.00 0.00 0.00 4.20
759 798 3.927142 GTCTCAATGGACTCAAAGGTACG 59.073 47.826 0.00 0.00 33.81 3.67
760 799 4.020128 AGGTCTCAATGGACTCAAAGGTAC 60.020 45.833 2.80 0.00 36.55 3.34
764 803 7.609532 AGAATTTAGGTCTCAATGGACTCAAAG 59.390 37.037 2.80 0.00 36.55 2.77
800 839 1.540267 TGTCTCTAGTTCGCCACTGTC 59.460 52.381 0.00 0.00 35.97 3.51
812 851 5.120519 AGTTTCGAACGACTAGTGTCTCTAG 59.879 44.000 0.00 7.29 42.77 2.43
814 853 3.814283 AGTTTCGAACGACTAGTGTCTCT 59.186 43.478 0.00 0.00 40.86 3.10
817 856 3.881795 TCAGTTTCGAACGACTAGTGTC 58.118 45.455 0.00 0.00 39.70 3.67
826 865 1.328439 CTCCGACTCAGTTTCGAACG 58.672 55.000 0.00 0.00 38.85 3.95
855 3053 6.971184 GGCACAATCAAGTAGAATCAGATTTG 59.029 38.462 0.00 0.00 0.00 2.32
1003 3201 2.106338 TGGTGCTGAAGAACTCATCCAA 59.894 45.455 0.00 0.00 32.14 3.53
1019 3217 1.362406 GAAGTCGCCTAGCTTGGTGC 61.362 60.000 21.18 16.01 43.29 5.01
1041 3239 1.824329 GTCGATGAGCCGGGAGAGA 60.824 63.158 2.18 0.00 0.00 3.10
1047 3245 4.873129 CCGTGGTCGATGAGCCGG 62.873 72.222 0.00 0.00 37.46 6.13
1255 3453 4.641645 CCACGCCCACTCCAGCAA 62.642 66.667 0.00 0.00 0.00 3.91
1323 3521 4.953868 CACCGGTCGAACACGCCA 62.954 66.667 2.59 0.00 0.00 5.69
1524 3722 0.393673 CAACAGTGGTGGTGGTGTCA 60.394 55.000 0.00 0.00 37.78 3.58
1557 3803 0.665068 ATTGCGTCGCTGTTGTACGA 60.665 50.000 19.50 0.00 38.89 3.43
1686 3932 6.212955 ACATTACAAATTTTGTCCACCGAAG 58.787 36.000 17.64 4.52 44.12 3.79
1707 3953 7.093333 TGCATTGATCCCTATATTACTCGACAT 60.093 37.037 0.00 0.00 0.00 3.06
1750 3996 1.137086 GCCTTCATGAAGCTCGGTCTA 59.863 52.381 27.01 0.00 37.11 2.59
1756 4003 2.985957 AGAGAGCCTTCATGAAGCTC 57.014 50.000 31.44 31.44 39.55 4.09
1757 4004 3.373830 ACTAGAGAGCCTTCATGAAGCT 58.626 45.455 27.01 25.11 37.11 3.74
1766 4013 7.225725 ACGAATAGTACATACTAGAGAGCCTT 58.774 38.462 0.00 0.00 41.62 4.35
1768 4015 7.361116 GGAACGAATAGTACATACTAGAGAGCC 60.361 44.444 0.00 0.00 41.62 4.70
1776 4023 8.628280 GGACTTTAGGAACGAATAGTACATACT 58.372 37.037 0.00 0.00 40.24 2.12
1777 4024 8.408601 TGGACTTTAGGAACGAATAGTACATAC 58.591 37.037 0.00 0.00 27.50 2.39
1790 4185 8.887036 AAAACAAAATCATGGACTTTAGGAAC 57.113 30.769 0.00 0.00 0.00 3.62
1849 4249 7.495606 GGATGTGATGTGTATGTGTAGATTTCA 59.504 37.037 0.00 0.00 0.00 2.69
1850 4250 7.712639 AGGATGTGATGTGTATGTGTAGATTTC 59.287 37.037 0.00 0.00 0.00 2.17
1855 4255 6.108687 ACAAGGATGTGATGTGTATGTGTAG 58.891 40.000 0.00 0.00 38.69 2.74
1940 4341 4.947388 AGCTCCACGAATGCCTTAATTTTA 59.053 37.500 0.00 0.00 0.00 1.52
1970 4371 1.838112 TGCAGAGTAGGGCATTTTGG 58.162 50.000 0.00 0.00 34.58 3.28
1994 4395 3.268023 AGTACAGTTGCAAGATAGGGC 57.732 47.619 0.00 0.00 0.00 5.19
1995 4396 5.599999 ACTAGTACAGTTGCAAGATAGGG 57.400 43.478 0.00 0.00 31.59 3.53
1996 4397 7.096884 TGTACTAGTACAGTTGCAAGATAGG 57.903 40.000 27.99 0.00 40.77 2.57
2019 4446 6.828502 TTGCGCAGTCTAGTTTATAAGATG 57.171 37.500 11.31 0.00 0.00 2.90
2022 4449 6.037172 ACCAATTGCGCAGTCTAGTTTATAAG 59.963 38.462 11.31 0.00 0.00 1.73
2035 4462 0.244450 ATTCCACACCAATTGCGCAG 59.756 50.000 11.31 0.42 0.00 5.18
2052 4479 7.361457 GGCTATACAACCACGTTTTAACTGATT 60.361 37.037 0.00 0.00 0.00 2.57
2054 4481 5.409214 GGCTATACAACCACGTTTTAACTGA 59.591 40.000 0.00 0.00 0.00 3.41
2055 4482 5.179742 TGGCTATACAACCACGTTTTAACTG 59.820 40.000 0.00 0.00 0.00 3.16
2056 4483 5.307204 TGGCTATACAACCACGTTTTAACT 58.693 37.500 0.00 0.00 0.00 2.24
2057 4484 5.610235 TGGCTATACAACCACGTTTTAAC 57.390 39.130 0.00 0.00 0.00 2.01
2176 4619 8.921670 AGTAAAATGTTTTGAATTCCATTACGC 58.078 29.630 2.27 0.51 0.00 4.42
2242 4695 3.057315 GTGCAAACATGCTACCTGAACAT 60.057 43.478 2.22 0.00 35.49 2.71
2243 4696 2.293122 GTGCAAACATGCTACCTGAACA 59.707 45.455 2.22 0.00 35.49 3.18
2244 4697 2.293122 TGTGCAAACATGCTACCTGAAC 59.707 45.455 2.22 0.00 35.49 3.18
2245 4698 2.580962 TGTGCAAACATGCTACCTGAA 58.419 42.857 2.22 0.00 35.49 3.02
2246 4699 2.268762 TGTGCAAACATGCTACCTGA 57.731 45.000 2.22 0.00 35.49 3.86
2247 4700 3.057386 TCAATGTGCAAACATGCTACCTG 60.057 43.478 2.22 1.16 35.49 4.00
2248 4701 3.057315 GTCAATGTGCAAACATGCTACCT 60.057 43.478 2.22 0.00 35.49 3.08
2249 4702 3.244976 GTCAATGTGCAAACATGCTACC 58.755 45.455 2.22 0.00 35.49 3.18
2250 4703 2.910482 CGTCAATGTGCAAACATGCTAC 59.090 45.455 2.22 0.36 35.49 3.58
2251 4704 2.095314 CCGTCAATGTGCAAACATGCTA 60.095 45.455 2.22 0.00 35.49 3.49
2252 4705 1.336148 CCGTCAATGTGCAAACATGCT 60.336 47.619 2.22 0.00 35.49 3.79
2253 4706 1.062258 CCGTCAATGTGCAAACATGC 58.938 50.000 0.00 0.00 0.00 4.06
2254 4707 2.030893 ACTCCGTCAATGTGCAAACATG 60.031 45.455 0.00 0.00 0.00 3.21
2255 4708 2.226437 GACTCCGTCAATGTGCAAACAT 59.774 45.455 0.00 0.00 32.09 2.71
2256 4709 1.601903 GACTCCGTCAATGTGCAAACA 59.398 47.619 0.00 0.00 32.09 2.83
2257 4710 1.398451 CGACTCCGTCAATGTGCAAAC 60.398 52.381 0.00 0.00 32.09 2.93
2258 4711 0.865111 CGACTCCGTCAATGTGCAAA 59.135 50.000 0.00 0.00 32.09 3.68
2259 4712 0.032815 TCGACTCCGTCAATGTGCAA 59.967 50.000 0.00 0.00 37.05 4.08
2260 4713 0.388520 CTCGACTCCGTCAATGTGCA 60.389 55.000 0.00 0.00 37.05 4.57
2261 4714 0.109272 TCTCGACTCCGTCAATGTGC 60.109 55.000 0.00 0.00 37.05 4.57
2262 4715 1.200252 ACTCTCGACTCCGTCAATGTG 59.800 52.381 0.00 0.00 37.05 3.21
2263 4716 1.200252 CACTCTCGACTCCGTCAATGT 59.800 52.381 0.00 0.00 37.05 2.71
2264 4717 1.200252 ACACTCTCGACTCCGTCAATG 59.800 52.381 0.00 0.00 37.05 2.82
2265 4718 1.469308 GACACTCTCGACTCCGTCAAT 59.531 52.381 0.00 0.00 37.05 2.57
2266 4719 0.873054 GACACTCTCGACTCCGTCAA 59.127 55.000 0.00 0.00 37.05 3.18
2267 4720 0.035036 AGACACTCTCGACTCCGTCA 59.965 55.000 0.00 0.00 37.05 4.35
2268 4721 2.007360 TAGACACTCTCGACTCCGTC 57.993 55.000 0.00 0.00 37.05 4.79
2269 4722 2.348660 CTTAGACACTCTCGACTCCGT 58.651 52.381 0.00 0.00 37.05 4.69
2270 4723 1.666700 CCTTAGACACTCTCGACTCCG 59.333 57.143 0.00 0.00 37.07 4.63
2271 4724 2.679336 GTCCTTAGACACTCTCGACTCC 59.321 54.545 0.00 0.00 42.99 3.85
2283 4736 4.794334 TCACCTCCTCTATGTCCTTAGAC 58.206 47.826 0.00 0.00 43.83 2.59
2284 4737 5.467668 TTCACCTCCTCTATGTCCTTAGA 57.532 43.478 0.00 0.00 0.00 2.10
2293 4746 8.855804 TTTTTAGGACTATTCACCTCCTCTAT 57.144 34.615 0.00 0.00 35.87 1.98
2374 7467 3.302805 CGGACGCGACATATGCAAAATAA 60.303 43.478 15.93 0.00 0.00 1.40
2377 7470 0.371989 CGGACGCGACATATGCAAAA 59.628 50.000 15.93 0.00 0.00 2.44
2384 7477 2.486504 GTGGTCGGACGCGACATA 59.513 61.111 15.93 0.00 40.34 2.29
2389 7482 4.351938 TCAAGGTGGTCGGACGCG 62.352 66.667 3.53 3.53 0.00 6.01
2391 7484 1.372997 CAGTCAAGGTGGTCGGACG 60.373 63.158 1.43 0.00 35.49 4.79
2416 7509 1.694150 ACTCAAGCAGGTTAGAGTGCA 59.306 47.619 13.38 0.00 42.47 4.57
2427 7520 3.429141 CGCCTGGCACTCAAGCAG 61.429 66.667 20.29 0.00 32.51 4.24
2431 7524 4.254709 AGCACGCCTGGCACTCAA 62.255 61.111 20.29 0.00 0.00 3.02
2432 7525 4.687215 GAGCACGCCTGGCACTCA 62.687 66.667 20.29 0.00 0.00 3.41
2444 7537 5.181748 GGAGGAATATATGATGGTGAGCAC 58.818 45.833 0.00 0.00 0.00 4.40
2450 7543 3.055094 GGTGCGGAGGAATATATGATGGT 60.055 47.826 0.00 0.00 0.00 3.55
2453 7546 4.532126 TGAAGGTGCGGAGGAATATATGAT 59.468 41.667 0.00 0.00 0.00 2.45
2454 7547 3.901222 TGAAGGTGCGGAGGAATATATGA 59.099 43.478 0.00 0.00 0.00 2.15
2499 7592 1.196911 ATTGGGCATGACCACATTGG 58.803 50.000 23.50 0.00 45.02 3.16
2500 7593 2.623535 CAATTGGGCATGACCACATTG 58.376 47.619 26.93 26.93 41.03 2.82
2501 7594 1.065998 GCAATTGGGCATGACCACATT 60.066 47.619 23.50 19.55 41.03 2.71
2502 7595 0.538118 GCAATTGGGCATGACCACAT 59.462 50.000 23.50 14.51 41.03 3.21
2503 7596 0.830866 TGCAATTGGGCATGACCACA 60.831 50.000 23.50 12.84 41.03 4.17
2504 7597 0.108520 CTGCAATTGGGCATGACCAC 60.109 55.000 23.50 9.77 43.97 4.16
2505 7598 0.542467 ACTGCAATTGGGCATGACCA 60.542 50.000 19.12 19.12 43.97 4.02
2506 7599 0.108520 CACTGCAATTGGGCATGACC 60.109 55.000 12.04 12.04 43.97 4.02
2507 7600 0.738412 GCACTGCAATTGGGCATGAC 60.738 55.000 7.72 0.00 43.97 3.06
2508 7601 1.186267 TGCACTGCAATTGGGCATGA 61.186 50.000 7.72 0.00 43.97 3.07
2509 7602 0.320858 TTGCACTGCAATTGGGCATG 60.321 50.000 12.59 2.47 43.99 4.06
2510 7603 2.059522 TTGCACTGCAATTGGGCAT 58.940 47.368 12.59 0.00 43.99 4.40
2511 7604 3.547247 TTGCACTGCAATTGGGCA 58.453 50.000 12.59 0.00 43.99 5.36
2518 7611 0.947660 CGAGAGAGCTTGCACTGCAA 60.948 55.000 15.63 15.63 46.80 4.08
2519 7612 1.373873 CGAGAGAGCTTGCACTGCA 60.374 57.895 12.59 0.00 36.47 4.41
2520 7613 2.099431 CCGAGAGAGCTTGCACTGC 61.099 63.158 2.91 2.91 0.00 4.40
2521 7614 2.099431 GCCGAGAGAGCTTGCACTG 61.099 63.158 0.00 0.00 0.00 3.66
2522 7615 2.104572 TTGCCGAGAGAGCTTGCACT 62.105 55.000 0.00 0.00 33.64 4.40
2534 7627 4.488126 TTCAATTTGAGAAGTTGCCGAG 57.512 40.909 0.00 0.00 0.00 4.63
2535 7628 4.792704 GCTTTCAATTTGAGAAGTTGCCGA 60.793 41.667 15.99 0.00 0.00 5.54
2536 7629 3.426525 GCTTTCAATTTGAGAAGTTGCCG 59.573 43.478 15.99 0.00 0.00 5.69
2537 7630 4.370917 TGCTTTCAATTTGAGAAGTTGCC 58.629 39.130 15.99 6.52 0.00 4.52
2538 7631 5.971895 TTGCTTTCAATTTGAGAAGTTGC 57.028 34.783 15.99 7.24 0.00 4.17
2539 7632 6.073440 CCCATTGCTTTCAATTTGAGAAGTTG 60.073 38.462 15.99 12.74 40.74 3.16
2540 7633 5.993441 CCCATTGCTTTCAATTTGAGAAGTT 59.007 36.000 15.99 0.00 40.74 2.66
2541 7634 5.544650 CCCATTGCTTTCAATTTGAGAAGT 58.455 37.500 15.99 2.67 40.74 3.01
2542 7635 4.390909 GCCCATTGCTTTCAATTTGAGAAG 59.609 41.667 12.86 12.86 40.74 2.85
2543 7636 4.202336 TGCCCATTGCTTTCAATTTGAGAA 60.202 37.500 0.00 0.00 40.74 2.87
2544 7637 3.324268 TGCCCATTGCTTTCAATTTGAGA 59.676 39.130 0.00 0.00 40.74 3.27
2545 7638 3.666274 TGCCCATTGCTTTCAATTTGAG 58.334 40.909 0.00 0.00 40.74 3.02
2546 7639 3.766068 TGCCCATTGCTTTCAATTTGA 57.234 38.095 0.00 0.00 40.74 2.69
2547 7640 5.448089 GCTTATGCCCATTGCTTTCAATTTG 60.448 40.000 0.00 0.00 40.74 2.32
2548 7641 4.637091 GCTTATGCCCATTGCTTTCAATTT 59.363 37.500 0.00 0.00 40.74 1.82
2549 7642 4.193865 GCTTATGCCCATTGCTTTCAATT 58.806 39.130 0.00 0.00 40.74 2.32
2550 7643 3.800531 GCTTATGCCCATTGCTTTCAAT 58.199 40.909 0.00 0.00 43.31 2.57
2551 7644 3.249986 GCTTATGCCCATTGCTTTCAA 57.750 42.857 0.00 0.00 42.00 2.69
2552 7645 2.965572 GCTTATGCCCATTGCTTTCA 57.034 45.000 0.00 0.00 42.00 2.69
2564 7657 5.067805 ACCAATGCTTAGTTTAGGCTTATGC 59.932 40.000 0.00 0.00 38.76 3.14
2565 7658 6.699575 ACCAATGCTTAGTTTAGGCTTATG 57.300 37.500 0.00 0.00 0.00 1.90
2566 7659 8.850156 CATAACCAATGCTTAGTTTAGGCTTAT 58.150 33.333 0.00 0.00 0.00 1.73
2567 7660 7.832187 ACATAACCAATGCTTAGTTTAGGCTTA 59.168 33.333 0.00 0.00 39.39 3.09
2568 7661 6.663523 ACATAACCAATGCTTAGTTTAGGCTT 59.336 34.615 0.00 0.00 39.39 4.35
2569 7662 6.187682 ACATAACCAATGCTTAGTTTAGGCT 58.812 36.000 0.00 0.00 39.39 4.58
2570 7663 6.451064 ACATAACCAATGCTTAGTTTAGGC 57.549 37.500 0.00 0.00 39.39 3.93
2571 7664 6.751888 GCAACATAACCAATGCTTAGTTTAGG 59.248 38.462 0.00 0.00 39.39 2.69
2572 7665 6.468956 CGCAACATAACCAATGCTTAGTTTAG 59.531 38.462 0.00 0.00 39.39 1.85
2573 7666 6.072397 ACGCAACATAACCAATGCTTAGTTTA 60.072 34.615 0.00 0.00 39.39 2.01
2574 7667 5.160641 CGCAACATAACCAATGCTTAGTTT 58.839 37.500 0.00 0.00 39.39 2.66
2575 7668 4.217550 ACGCAACATAACCAATGCTTAGTT 59.782 37.500 0.00 0.00 39.39 2.24
2576 7669 3.756434 ACGCAACATAACCAATGCTTAGT 59.244 39.130 0.00 0.00 39.39 2.24
2577 7670 4.355543 ACGCAACATAACCAATGCTTAG 57.644 40.909 0.00 0.00 39.39 2.18
2578 7671 5.881777 TTACGCAACATAACCAATGCTTA 57.118 34.783 0.00 0.00 39.39 3.09
2579 7672 4.775058 TTACGCAACATAACCAATGCTT 57.225 36.364 0.00 0.00 39.39 3.91
2580 7673 4.775058 TTTACGCAACATAACCAATGCT 57.225 36.364 0.00 0.00 39.39 3.79
2581 7674 5.830900 TTTTTACGCAACATAACCAATGC 57.169 34.783 0.00 0.00 39.39 3.56


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

AutoCloner maintained by Alex Coulton.