Multiple sequence alignment - TraesCS5D01G529000

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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 TraesCS5D01G529000 chr5D 100.000 3530 0 0 1 3530 545920579 545924108 0.000000e+00 6519.0
1 TraesCS5D01G529000 chr5B 89.423 2619 166 48 590 3175 688840600 688843140 0.000000e+00 3199.0
2 TraesCS5D01G529000 chr5B 89.967 1834 153 14 590 2406 688719585 688721404 0.000000e+00 2338.0
3 TraesCS5D01G529000 chr5B 88.673 1695 152 23 897 2573 688926714 688928386 0.000000e+00 2030.0
4 TraesCS5D01G529000 chr5B 88.654 1701 146 25 897 2573 689026621 689028298 0.000000e+00 2028.0
5 TraesCS5D01G529000 chr5B 92.308 468 30 3 1 468 688718839 688719300 0.000000e+00 660.0
6 TraesCS5D01G529000 chr5B 85.304 313 35 7 3218 3530 688929216 688929517 2.650000e-81 313.0
7 TraesCS5D01G529000 chr5B 84.984 313 36 7 3218 3530 689029683 689029984 1.230000e-79 307.0
8 TraesCS5D01G529000 chr5B 88.660 194 20 1 590 781 688804901 688805094 5.890000e-58 235.0
9 TraesCS5D01G529000 chr5B 87.692 195 21 2 590 781 688926403 688926597 1.280000e-54 224.0
10 TraesCS5D01G529000 chr5B 87.692 195 21 2 590 781 689026310 689026504 1.280000e-54 224.0
11 TraesCS5D01G529000 chr4A 92.914 1877 85 24 590 2449 623725069 623723224 0.000000e+00 2686.0
12 TraesCS5D01G529000 chr4A 92.537 1876 79 25 590 2449 623681785 623679955 0.000000e+00 2632.0
13 TraesCS5D01G529000 chr4A 98.053 976 12 4 1 976 623691053 623690085 0.000000e+00 1690.0
14 TraesCS5D01G529000 chr4A 97.541 976 17 4 1 976 623750859 623749891 0.000000e+00 1663.0
15 TraesCS5D01G529000 chr4A 86.119 1376 164 14 1048 2411 623749892 623748532 0.000000e+00 1458.0
16 TraesCS5D01G529000 chr4A 85.034 1343 172 16 1082 2411 623741912 623740586 0.000000e+00 1339.0
17 TraesCS5D01G529000 chr4A 86.354 916 111 11 1048 1956 623690086 623689178 0.000000e+00 987.0
18 TraesCS5D01G529000 chr4A 99.160 357 3 0 750 1106 623743769 623743413 0.000000e+00 643.0
19 TraesCS5D01G529000 chr4A 81.754 707 79 27 2479 3174 623678042 623677375 2.400000e-151 545.0
20 TraesCS5D01G529000 chr4A 81.241 709 84 25 2479 3174 623721312 623720640 8.680000e-146 527.0
21 TraesCS5D01G529000 chr4A 86.000 450 48 4 1965 2411 623689011 623688574 5.340000e-128 468.0
22 TraesCS5D01G529000 chr1A 97.147 666 19 0 1784 2449 569763584 569762919 0.000000e+00 1125.0
23 TraesCS5D01G529000 chr1A 93.575 716 20 7 876 1587 569764274 569763581 0.000000e+00 1044.0
24 TraesCS5D01G529000 chr1A 81.690 710 79 27 2479 3174 569755626 569754954 8.620000e-151 544.0
25 TraesCS5D01G529000 chrUn 88.770 374 27 9 3170 3530 335286613 335286984 8.990000e-121 444.0
26 TraesCS5D01G529000 chrUn 88.770 374 27 9 3170 3530 335289317 335289688 8.990000e-121 444.0
27 TraesCS5D01G529000 chrUn 88.770 374 27 9 3170 3530 467682428 467682799 8.990000e-121 444.0
28 TraesCS5D01G529000 chrUn 84.984 313 36 7 3218 3530 402901389 402901088 1.230000e-79 307.0
29 TraesCS5D01G529000 chr3A 76.549 226 40 7 3227 3439 383646108 383645883 1.040000e-20 111.0
30 TraesCS5D01G529000 chr7A 84.270 89 11 3 2737 2823 34751687 34751774 2.260000e-12 84.2
31 TraesCS5D01G529000 chr7A 92.500 40 1 2 3216 3255 431001099 431001136 4.920000e-04 56.5
32 TraesCS5D01G529000 chr1D 82.353 85 11 4 3409 3491 377948730 377948648 1.760000e-08 71.3
33 TraesCS5D01G529000 chr3B 88.679 53 5 1 3286 3338 8005933 8005882 2.940000e-06 63.9


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 TraesCS5D01G529000 chr5D 545920579 545924108 3529 False 6519.000000 6519 100.000000 1 3530 1 chr5D.!!$F1 3529
1 TraesCS5D01G529000 chr5B 688840600 688843140 2540 False 3199.000000 3199 89.423000 590 3175 1 chr5B.!!$F2 2585
2 TraesCS5D01G529000 chr5B 688718839 688721404 2565 False 1499.000000 2338 91.137500 1 2406 2 chr5B.!!$F3 2405
3 TraesCS5D01G529000 chr5B 688926403 688929517 3114 False 855.666667 2030 87.223000 590 3530 3 chr5B.!!$F4 2940
4 TraesCS5D01G529000 chr5B 689026310 689029984 3674 False 853.000000 2028 87.110000 590 3530 3 chr5B.!!$F5 2940
5 TraesCS5D01G529000 chr4A 623720640 623725069 4429 True 1606.500000 2686 87.077500 590 3174 2 chr4A.!!$R3 2584
6 TraesCS5D01G529000 chr4A 623677375 623681785 4410 True 1588.500000 2632 87.145500 590 3174 2 chr4A.!!$R1 2584
7 TraesCS5D01G529000 chr4A 623748532 623750859 2327 True 1560.500000 1663 91.830000 1 2411 2 chr4A.!!$R5 2410
8 TraesCS5D01G529000 chr4A 623688574 623691053 2479 True 1048.333333 1690 90.135667 1 2411 3 chr4A.!!$R2 2410
9 TraesCS5D01G529000 chr4A 623740586 623743769 3183 True 991.000000 1339 92.097000 750 2411 2 chr4A.!!$R4 1661
10 TraesCS5D01G529000 chr1A 569762919 569764274 1355 True 1084.500000 1125 95.361000 876 2449 2 chr1A.!!$R2 1573
11 TraesCS5D01G529000 chr1A 569754954 569755626 672 True 544.000000 544 81.690000 2479 3174 1 chr1A.!!$R1 695
12 TraesCS5D01G529000 chrUn 335286613 335289688 3075 False 444.000000 444 88.770000 3170 3530 2 chrUn.!!$F2 360

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
431 434 2.668457 CGCTTACAGCAGTGGAGTTTAG 59.332 50.000 0.00 0.0 42.58 1.85 F
1219 3009 2.603247 GCACCATGCACGTCGACAA 61.603 57.895 17.16 0.0 44.26 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2366 4353 1.153147 GGGGGCGAAGTGGATCTTC 60.153 63.158 0.0 0.0 46.39 2.87 R
3211 8296 0.035458 AGTTTGCTCTGAAGGGACGG 59.965 55.000 0.0 0.0 0.00 4.79 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
88 89 5.549742 TTTCTACGGGTTCTAAGGTTTGA 57.450 39.130 0.00 0.00 0.00 2.69
202 203 4.666512 ACTAGTTAGGTTCGGTTAGGACA 58.333 43.478 0.00 0.00 0.00 4.02
204 205 3.504375 AGTTAGGTTCGGTTAGGACAGT 58.496 45.455 0.00 0.00 0.00 3.55
207 208 5.184671 AGTTAGGTTCGGTTAGGACAGTTAG 59.815 44.000 0.00 0.00 0.00 2.34
210 211 4.776308 AGGTTCGGTTAGGACAGTTAGATT 59.224 41.667 0.00 0.00 0.00 2.40
211 212 5.247792 AGGTTCGGTTAGGACAGTTAGATTT 59.752 40.000 0.00 0.00 0.00 2.17
213 214 7.125356 AGGTTCGGTTAGGACAGTTAGATTTAT 59.875 37.037 0.00 0.00 0.00 1.40
214 215 7.224167 GGTTCGGTTAGGACAGTTAGATTTATG 59.776 40.741 0.00 0.00 0.00 1.90
215 216 7.414222 TCGGTTAGGACAGTTAGATTTATGT 57.586 36.000 0.00 0.00 0.00 2.29
216 217 7.262772 TCGGTTAGGACAGTTAGATTTATGTG 58.737 38.462 0.00 0.00 0.00 3.21
431 434 2.668457 CGCTTACAGCAGTGGAGTTTAG 59.332 50.000 0.00 0.00 42.58 1.85
1218 3008 3.041351 GCACCATGCACGTCGACA 61.041 61.111 17.16 0.00 44.26 4.35
1219 3009 2.603247 GCACCATGCACGTCGACAA 61.603 57.895 17.16 0.00 44.26 3.18
1703 3504 3.327404 GTCCTCGGCCTGGGGAAA 61.327 66.667 16.44 0.00 0.00 3.13
2366 4353 0.752658 TCTATGACATCACAGCCGGG 59.247 55.000 2.18 0.00 0.00 5.73
2450 4437 2.963101 GTGGGCTTCAAGTAAACCCTTT 59.037 45.455 0.00 0.00 41.44 3.11
2456 4443 7.509659 TGGGCTTCAAGTAAACCCTTTTATTTA 59.490 33.333 0.00 0.00 41.44 1.40
2513 6384 9.734620 TTTTCTTGAATTAGATGTTGTCAACTG 57.265 29.630 16.45 0.00 0.00 3.16
2514 6385 8.675705 TTCTTGAATTAGATGTTGTCAACTGA 57.324 30.769 16.45 0.00 0.00 3.41
2515 6386 8.675705 TCTTGAATTAGATGTTGTCAACTGAA 57.324 30.769 16.45 6.06 0.00 3.02
2516 6387 9.288576 TCTTGAATTAGATGTTGTCAACTGAAT 57.711 29.630 16.45 2.19 0.00 2.57
2517 6388 9.338291 CTTGAATTAGATGTTGTCAACTGAATG 57.662 33.333 16.45 0.00 0.00 2.67
2553 6428 1.410882 GACTAGACATGTGGCTCTCCC 59.589 57.143 1.15 0.00 33.72 4.30
2586 6461 1.070758 TCCTTCATTAGCGCATCTCCC 59.929 52.381 11.47 0.00 0.00 4.30
2588 6463 2.564771 CTTCATTAGCGCATCTCCCAA 58.435 47.619 11.47 0.00 0.00 4.12
2589 6464 1.953559 TCATTAGCGCATCTCCCAAC 58.046 50.000 11.47 0.00 0.00 3.77
2590 6465 1.209261 TCATTAGCGCATCTCCCAACA 59.791 47.619 11.47 0.00 0.00 3.33
2591 6466 1.331756 CATTAGCGCATCTCCCAACAC 59.668 52.381 11.47 0.00 0.00 3.32
2595 6470 1.079819 CGCATCTCCCAACACGACT 60.080 57.895 0.00 0.00 0.00 4.18
2596 6471 0.172578 CGCATCTCCCAACACGACTA 59.827 55.000 0.00 0.00 0.00 2.59
2597 6472 1.641577 GCATCTCCCAACACGACTAC 58.358 55.000 0.00 0.00 0.00 2.73
2602 6477 2.295349 TCTCCCAACACGACTACTCAAC 59.705 50.000 0.00 0.00 0.00 3.18
2603 6478 2.296471 CTCCCAACACGACTACTCAACT 59.704 50.000 0.00 0.00 0.00 3.16
2605 6480 2.035449 CCCAACACGACTACTCAACTCA 59.965 50.000 0.00 0.00 0.00 3.41
2607 6482 3.490249 CCAACACGACTACTCAACTCACA 60.490 47.826 0.00 0.00 0.00 3.58
2609 6484 2.950309 ACACGACTACTCAACTCACAGT 59.050 45.455 0.00 0.00 0.00 3.55
2610 6485 4.132336 ACACGACTACTCAACTCACAGTA 58.868 43.478 0.00 0.00 0.00 2.74
2611 6486 4.760715 ACACGACTACTCAACTCACAGTAT 59.239 41.667 0.00 0.00 0.00 2.12
2612 6487 5.106634 ACACGACTACTCAACTCACAGTATC 60.107 44.000 0.00 0.00 0.00 2.24
2613 6488 5.122554 CACGACTACTCAACTCACAGTATCT 59.877 44.000 0.00 0.00 0.00 1.98
2614 6489 5.122554 ACGACTACTCAACTCACAGTATCTG 59.877 44.000 0.00 0.00 37.52 2.90
2615 6490 5.122554 CGACTACTCAACTCACAGTATCTGT 59.877 44.000 0.00 0.00 46.51 3.41
2616 6491 6.348622 CGACTACTCAACTCACAGTATCTGTT 60.349 42.308 0.00 0.00 42.59 3.16
2617 6492 6.915349 ACTACTCAACTCACAGTATCTGTTC 58.085 40.000 0.00 0.00 42.59 3.18
2618 6493 4.799678 ACTCAACTCACAGTATCTGTTCG 58.200 43.478 0.00 0.00 42.59 3.95
2619 6494 3.575630 TCAACTCACAGTATCTGTTCGC 58.424 45.455 0.00 0.00 42.59 4.70
2620 6495 2.264109 ACTCACAGTATCTGTTCGCG 57.736 50.000 0.00 0.00 42.59 5.87
2621 6496 1.135373 ACTCACAGTATCTGTTCGCGG 60.135 52.381 6.13 0.00 42.59 6.46
2622 6497 1.132453 CTCACAGTATCTGTTCGCGGA 59.868 52.381 6.13 0.00 42.59 5.54
2623 6498 1.135489 TCACAGTATCTGTTCGCGGAC 60.135 52.381 11.62 11.62 42.59 4.79
2624 6499 0.885879 ACAGTATCTGTTCGCGGACA 59.114 50.000 21.11 21.11 42.59 4.02
2625 6500 1.269166 CAGTATCTGTTCGCGGACAC 58.731 55.000 18.26 6.98 34.95 3.67
2626 6501 0.179171 AGTATCTGTTCGCGGACACG 60.179 55.000 18.26 13.14 35.19 4.49
2647 6742 1.809619 ATCCGTGGACGTGAATGCG 60.810 57.895 0.00 0.00 37.74 4.73
2663 6758 4.530857 CGGGAGCCGGTCATCCAC 62.531 72.222 19.84 10.92 44.15 4.02
2673 7751 3.295973 CCGGTCATCCACCCATTTAAAT 58.704 45.455 0.00 0.00 43.31 1.40
2727 7805 4.498513 CGGTGTTCATACTTCATAGCGGTA 60.499 45.833 0.00 0.00 0.00 4.02
2728 7806 4.743644 GGTGTTCATACTTCATAGCGGTAC 59.256 45.833 0.00 0.00 0.00 3.34
2734 7814 3.906720 ACTTCATAGCGGTACCACAAT 57.093 42.857 13.54 0.00 0.00 2.71
2741 7821 6.350103 TCATAGCGGTACCACAATCAAAATA 58.650 36.000 13.54 0.00 0.00 1.40
2747 7827 4.396790 GGTACCACAATCAAAATAAGGCGA 59.603 41.667 7.15 0.00 0.00 5.54
2772 7852 8.970691 AATGTTCATAGTTTTTACATGTGCTC 57.029 30.769 9.11 0.00 30.43 4.26
2773 7853 6.598525 TGTTCATAGTTTTTACATGTGCTCG 58.401 36.000 9.11 0.00 0.00 5.03
2792 7872 4.629200 GCTCGATCACAGAATTTTCAGTCT 59.371 41.667 0.00 0.00 0.00 3.24
2793 7873 5.121454 GCTCGATCACAGAATTTTCAGTCTT 59.879 40.000 0.00 0.00 0.00 3.01
2798 7878 6.005583 TCACAGAATTTTCAGTCTTGCATC 57.994 37.500 0.00 0.00 0.00 3.91
2800 7880 4.828939 ACAGAATTTTCAGTCTTGCATCCA 59.171 37.500 0.00 0.00 0.00 3.41
2801 7881 5.479375 ACAGAATTTTCAGTCTTGCATCCAT 59.521 36.000 0.00 0.00 0.00 3.41
2825 7909 3.467374 AAAAAGGAATTTTCGCCTGCA 57.533 38.095 0.00 0.00 36.49 4.41
2828 7912 1.327303 AGGAATTTTCGCCTGCACAA 58.673 45.000 0.00 0.00 32.06 3.33
2829 7913 1.000274 AGGAATTTTCGCCTGCACAAC 60.000 47.619 0.00 0.00 32.06 3.32
2833 7917 1.733402 TTTTCGCCTGCACAACCCAG 61.733 55.000 0.00 0.00 0.00 4.45
2850 7934 2.045524 CCAGATGTATGTGCCTCCTCT 58.954 52.381 0.00 0.00 0.00 3.69
2855 7939 4.586841 AGATGTATGTGCCTCCTCTCTAAC 59.413 45.833 0.00 0.00 0.00 2.34
2858 7942 1.853963 TGTGCCTCCTCTCTAACTCC 58.146 55.000 0.00 0.00 0.00 3.85
2861 7945 1.272536 TGCCTCCTCTCTAACTCCGTT 60.273 52.381 0.00 0.00 0.00 4.44
2865 7949 3.618351 CTCCTCTCTAACTCCGTTACCA 58.382 50.000 0.00 0.00 0.00 3.25
2872 7956 1.349067 AACTCCGTTACCAGCTCCTT 58.651 50.000 0.00 0.00 0.00 3.36
2874 7958 0.179134 CTCCGTTACCAGCTCCTTCG 60.179 60.000 0.00 0.00 0.00 3.79
2899 7983 2.427245 CCGCCTCGTTCTCCTCCAT 61.427 63.158 0.00 0.00 0.00 3.41
2900 7984 1.066587 CGCCTCGTTCTCCTCCATC 59.933 63.158 0.00 0.00 0.00 3.51
2902 7986 0.179097 GCCTCGTTCTCCTCCATCAC 60.179 60.000 0.00 0.00 0.00 3.06
2903 7987 0.461961 CCTCGTTCTCCTCCATCACC 59.538 60.000 0.00 0.00 0.00 4.02
2904 7988 0.101399 CTCGTTCTCCTCCATCACCG 59.899 60.000 0.00 0.00 0.00 4.94
2905 7989 1.141881 CGTTCTCCTCCATCACCGG 59.858 63.158 0.00 0.00 0.00 5.28
2906 7990 1.320344 CGTTCTCCTCCATCACCGGA 61.320 60.000 9.46 0.00 0.00 5.14
2907 7991 1.123928 GTTCTCCTCCATCACCGGAT 58.876 55.000 9.46 0.00 33.56 4.18
2908 7992 1.069358 GTTCTCCTCCATCACCGGATC 59.931 57.143 9.46 0.00 33.56 3.36
2909 7993 0.261696 TCTCCTCCATCACCGGATCA 59.738 55.000 9.46 0.00 33.56 2.92
2910 7994 1.123077 CTCCTCCATCACCGGATCAA 58.877 55.000 9.46 0.00 33.56 2.57
2911 7995 0.830648 TCCTCCATCACCGGATCAAC 59.169 55.000 9.46 0.00 33.56 3.18
2912 7996 0.179045 CCTCCATCACCGGATCAACC 60.179 60.000 9.46 0.00 33.56 3.77
2924 8008 0.598065 GATCAACCGCCAAGCACTTT 59.402 50.000 0.00 0.00 0.00 2.66
2938 8022 6.972901 GCCAAGCACTTTAATATTCTAACACC 59.027 38.462 0.00 0.00 0.00 4.16
2948 8032 3.655276 ATTCTAACACCGACGACTTGT 57.345 42.857 0.00 0.00 0.00 3.16
2949 8033 3.441496 TTCTAACACCGACGACTTGTT 57.559 42.857 12.19 12.19 37.27 2.83
2958 8042 0.165944 GACGACTTGTTGGCCGAATG 59.834 55.000 0.00 0.00 0.00 2.67
2990 8074 2.238395 ACAAAGGCCCAAAACACAACAT 59.762 40.909 0.00 0.00 0.00 2.71
2991 8075 2.871633 CAAAGGCCCAAAACACAACATC 59.128 45.455 0.00 0.00 0.00 3.06
2992 8076 1.786937 AGGCCCAAAACACAACATCA 58.213 45.000 0.00 0.00 0.00 3.07
2993 8077 2.114616 AGGCCCAAAACACAACATCAA 58.885 42.857 0.00 0.00 0.00 2.57
3001 8085 5.390356 CCAAAACACAACATCAACCACAAAC 60.390 40.000 0.00 0.00 0.00 2.93
3002 8086 4.527509 AACACAACATCAACCACAAACA 57.472 36.364 0.00 0.00 0.00 2.83
3025 8109 1.186917 TGAAAGCACAAGGGGCCATG 61.187 55.000 4.39 6.42 0.00 3.66
3026 8110 0.899717 GAAAGCACAAGGGGCCATGA 60.900 55.000 14.66 0.00 0.00 3.07
3045 8129 2.225242 TGAATGGCCCCACACACTTAAT 60.225 45.455 0.00 0.00 0.00 1.40
3056 8140 4.394920 CCACACACTTAATGAGCCGTTAAT 59.605 41.667 0.00 0.00 0.00 1.40
3081 8165 4.153256 GCCGAAAGTAACCACAATTTACG 58.847 43.478 0.00 0.00 35.05 3.18
3082 8166 4.083908 GCCGAAAGTAACCACAATTTACGA 60.084 41.667 0.00 0.00 35.05 3.43
3084 8168 5.068256 CGAAAGTAACCACAATTTACGACG 58.932 41.667 0.00 0.00 35.05 5.12
3085 8169 4.996062 AAGTAACCACAATTTACGACGG 57.004 40.909 0.00 0.00 35.05 4.79
3126 8211 2.029964 GGGCCGAAACTCGTCACA 59.970 61.111 0.00 0.00 38.40 3.58
3127 8212 1.595929 GGGCCGAAACTCGTCACAA 60.596 57.895 0.00 0.00 38.40 3.33
3157 8242 1.382146 CCCAAAGGCATCATGGGCT 60.382 57.895 9.01 1.63 46.77 5.19
3205 8290 1.448540 CACATGTGGCTCTCCGTCC 60.449 63.158 18.51 0.00 34.14 4.79
3261 11050 2.202171 GCATTTCGTCCGTGCGTG 60.202 61.111 0.00 0.00 0.00 5.34
3263 11052 3.419759 ATTTCGTCCGTGCGTGCC 61.420 61.111 0.00 0.00 0.00 5.01
3307 11096 4.015406 TCTGCCCAACGTGCCGAT 62.015 61.111 0.00 0.00 0.00 4.18
3313 11102 1.312371 CCCAACGTGCCGATCCAAAT 61.312 55.000 0.00 0.00 0.00 2.32
3338 11127 1.281656 GCGTCCACTTTTTGTCCGG 59.718 57.895 0.00 0.00 0.00 5.14
3340 11129 1.440938 CGTCCACTTTTTGTCCGGCA 61.441 55.000 0.00 0.00 0.00 5.69
3355 11144 0.893270 CGGCAGGTGACCCATTTCAA 60.893 55.000 0.00 0.00 0.00 2.69
3384 11173 1.364901 GGACCTCGTTTGTGTCGGA 59.635 57.895 0.00 0.00 0.00 4.55
3387 11187 1.300620 CCTCGTTTGTGTCGGAGCA 60.301 57.895 0.00 0.00 0.00 4.26
3412 11212 2.404995 CGACGTCCGCCTACTCCTT 61.405 63.158 10.58 0.00 0.00 3.36
3418 11218 1.232216 CCGCCTACTCCTTCCCCTA 59.768 63.158 0.00 0.00 0.00 3.53
3464 11264 2.324541 CCTTCTCTTCCTCCCATCGAT 58.675 52.381 0.00 0.00 0.00 3.59
3467 11267 3.162147 TCTCTTCCTCCCATCGATAGG 57.838 52.381 3.11 3.11 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 5.401531 TGTCGCTACAGAGAAAACCTAAT 57.598 39.130 0.00 0.00 0.00 1.73
202 203 6.958767 AGCAAGGTACCACATAAATCTAACT 58.041 36.000 15.94 0.00 0.00 2.24
204 205 7.172342 ACAAGCAAGGTACCACATAAATCTAA 58.828 34.615 15.94 0.00 0.00 2.10
207 208 5.897377 ACAAGCAAGGTACCACATAAATC 57.103 39.130 15.94 0.00 0.00 2.17
210 211 5.133941 TGAAACAAGCAAGGTACCACATAA 58.866 37.500 15.94 0.00 0.00 1.90
211 212 4.720046 TGAAACAAGCAAGGTACCACATA 58.280 39.130 15.94 0.00 0.00 2.29
213 214 2.948979 CTGAAACAAGCAAGGTACCACA 59.051 45.455 15.94 0.00 0.00 4.17
214 215 2.293399 CCTGAAACAAGCAAGGTACCAC 59.707 50.000 15.94 2.82 0.00 4.16
215 216 2.173782 TCCTGAAACAAGCAAGGTACCA 59.826 45.455 15.94 0.00 0.00 3.25
216 217 2.552743 GTCCTGAAACAAGCAAGGTACC 59.447 50.000 2.73 2.73 0.00 3.34
337 340 8.090250 TCTTGCGCTAAAATGTAAAGAAACTA 57.910 30.769 9.73 0.00 0.00 2.24
338 341 6.966021 TCTTGCGCTAAAATGTAAAGAAACT 58.034 32.000 9.73 0.00 0.00 2.66
347 350 8.810427 CATTTCAATTATCTTGCGCTAAAATGT 58.190 29.630 9.73 0.00 0.00 2.71
431 434 5.176958 GCAGGCATGAATTGAAGAATAATGC 59.823 40.000 0.62 0.00 39.18 3.56
1703 3504 1.408340 CAGATGAGAGACGGCATCAGT 59.592 52.381 0.00 0.00 42.52 3.41
2306 4293 3.047735 ATCGCGCCGATGATGGTA 58.952 55.556 12.73 0.00 45.24 3.25
2366 4353 1.153147 GGGGGCGAAGTGGATCTTC 60.153 63.158 0.00 0.00 46.39 2.87
2411 4398 2.571653 CCACATCCTAGTTCAGTTGGGA 59.428 50.000 0.00 0.00 0.00 4.37
2456 4443 8.974408 GCATTGATCTAAAACGGTAAACTTTTT 58.026 29.630 0.00 0.00 0.00 1.94
2472 4462 9.985730 AATTCAAGAAAAAGTTGCATTGATCTA 57.014 25.926 0.00 0.00 0.00 1.98
2473 4463 8.897872 AATTCAAGAAAAAGTTGCATTGATCT 57.102 26.923 0.00 0.00 0.00 2.75
2538 6409 1.524482 GGAGGGAGAGCCACATGTC 59.476 63.158 0.00 0.00 35.15 3.06
2553 6428 2.285442 AAGGAACGGGGAGGGGAG 60.285 66.667 0.00 0.00 0.00 4.30
2586 6461 3.702330 TGTGAGTTGAGTAGTCGTGTTG 58.298 45.455 0.00 0.00 0.00 3.33
2588 6463 2.950309 ACTGTGAGTTGAGTAGTCGTGT 59.050 45.455 0.00 0.00 0.00 4.49
2589 6464 3.627732 ACTGTGAGTTGAGTAGTCGTG 57.372 47.619 0.00 0.00 0.00 4.35
2590 6465 5.122554 CAGATACTGTGAGTTGAGTAGTCGT 59.877 44.000 0.00 0.00 0.00 4.34
2591 6466 5.122554 ACAGATACTGTGAGTTGAGTAGTCG 59.877 44.000 3.54 0.00 43.63 4.18
2595 6470 5.619309 GCGAACAGATACTGTGAGTTGAGTA 60.619 44.000 5.17 0.00 44.62 2.59
2596 6471 4.799678 CGAACAGATACTGTGAGTTGAGT 58.200 43.478 5.17 0.00 44.62 3.41
2597 6472 3.610242 GCGAACAGATACTGTGAGTTGAG 59.390 47.826 5.17 0.00 44.62 3.02
2602 6477 1.132453 TCCGCGAACAGATACTGTGAG 59.868 52.381 8.23 4.31 44.62 3.51
2603 6478 1.135489 GTCCGCGAACAGATACTGTGA 60.135 52.381 8.23 0.00 44.62 3.58
2607 6482 0.179171 CGTGTCCGCGAACAGATACT 60.179 55.000 8.23 0.00 0.00 2.12
2609 6484 4.777781 CGTGTCCGCGAACAGATA 57.222 55.556 8.23 0.00 0.00 1.98
2620 6495 4.077184 TCCACGGATGGCGTGTCC 62.077 66.667 0.00 0.00 46.80 4.02
2621 6496 2.813908 GTCCACGGATGGCGTGTC 60.814 66.667 0.00 0.00 46.80 3.67
2622 6497 4.735132 CGTCCACGGATGGCGTGT 62.735 66.667 0.00 0.00 46.80 4.49
2625 6500 3.925362 TTCACGTCCACGGATGGCG 62.925 63.158 10.03 1.92 46.80 5.69
2626 6501 1.449601 ATTCACGTCCACGGATGGC 60.450 57.895 10.03 0.00 46.80 4.40
2634 6509 2.264480 CTCCCGCATTCACGTCCA 59.736 61.111 0.00 0.00 0.00 4.02
2639 6514 4.778143 ACCGGCTCCCGCATTCAC 62.778 66.667 0.00 0.00 46.86 3.18
2642 6517 3.757248 GATGACCGGCTCCCGCATT 62.757 63.158 0.00 0.00 46.86 3.56
2647 6742 4.176752 GGTGGATGACCGGCTCCC 62.177 72.222 13.99 5.94 39.42 4.30
2655 6750 4.734398 TGCATTTAAATGGGTGGATGAC 57.266 40.909 25.61 9.31 36.90 3.06
2691 7769 4.902443 TGAACACCGCACTTTTAATTGA 57.098 36.364 0.00 0.00 0.00 2.57
2703 7781 2.218759 CGCTATGAAGTATGAACACCGC 59.781 50.000 0.00 0.00 0.00 5.68
2727 7805 5.047377 ACATTCGCCTTATTTTGATTGTGGT 60.047 36.000 0.00 0.00 0.00 4.16
2728 7806 5.410067 ACATTCGCCTTATTTTGATTGTGG 58.590 37.500 0.00 0.00 0.00 4.17
2734 7814 7.624360 ACTATGAACATTCGCCTTATTTTGA 57.376 32.000 0.00 0.00 0.00 2.69
2741 7821 7.209471 TGTAAAAACTATGAACATTCGCCTT 57.791 32.000 0.00 0.00 0.00 4.35
2747 7827 7.750458 CGAGCACATGTAAAAACTATGAACATT 59.250 33.333 0.00 0.00 0.00 2.71
2772 7852 5.084722 GCAAGACTGAAAATTCTGTGATCG 58.915 41.667 9.95 0.00 39.10 3.69
2773 7853 6.005583 TGCAAGACTGAAAATTCTGTGATC 57.994 37.500 9.95 0.00 39.10 2.92
2810 7890 1.418373 GTTGTGCAGGCGAAAATTCC 58.582 50.000 0.00 0.00 0.00 3.01
2822 7906 2.435422 CACATACATCTGGGTTGTGCA 58.565 47.619 0.00 0.00 32.24 4.57
2825 7909 1.635487 AGGCACATACATCTGGGTTGT 59.365 47.619 0.00 0.00 0.00 3.32
2828 7912 0.839946 GGAGGCACATACATCTGGGT 59.160 55.000 0.00 0.00 0.00 4.51
2829 7913 1.071385 GAGGAGGCACATACATCTGGG 59.929 57.143 0.00 0.00 0.00 4.45
2833 7917 4.586841 AGTTAGAGAGGAGGCACATACATC 59.413 45.833 0.00 0.00 0.00 3.06
2858 7942 0.460284 ATGCGAAGGAGCTGGTAACG 60.460 55.000 0.00 0.00 38.13 3.18
2861 7945 0.107703 CCAATGCGAAGGAGCTGGTA 60.108 55.000 0.00 0.00 38.13 3.25
2865 7949 2.439156 GGCCAATGCGAAGGAGCT 60.439 61.111 0.00 0.00 38.85 4.09
2874 7958 4.179579 GAACGAGGCGGCCAATGC 62.180 66.667 23.09 6.46 0.00 3.56
2888 7972 1.069358 GATCCGGTGATGGAGGAGAAC 59.931 57.143 0.00 0.00 42.45 3.01
2904 7988 1.244019 AAGTGCTTGGCGGTTGATCC 61.244 55.000 0.00 0.00 0.00 3.36
2905 7989 0.598065 AAAGTGCTTGGCGGTTGATC 59.402 50.000 0.00 0.00 0.00 2.92
2906 7990 1.904287 TAAAGTGCTTGGCGGTTGAT 58.096 45.000 0.00 0.00 0.00 2.57
2907 7991 1.681538 TTAAAGTGCTTGGCGGTTGA 58.318 45.000 0.00 0.00 0.00 3.18
2908 7992 2.723124 ATTAAAGTGCTTGGCGGTTG 57.277 45.000 0.00 0.00 0.00 3.77
2909 7993 4.705023 AGAATATTAAAGTGCTTGGCGGTT 59.295 37.500 0.00 0.00 0.00 4.44
2910 7994 4.270008 AGAATATTAAAGTGCTTGGCGGT 58.730 39.130 0.00 0.00 0.00 5.68
2911 7995 4.900635 AGAATATTAAAGTGCTTGGCGG 57.099 40.909 0.00 0.00 0.00 6.13
2912 7996 6.687105 GTGTTAGAATATTAAAGTGCTTGGCG 59.313 38.462 0.00 0.00 0.00 5.69
2913 7997 6.972901 GGTGTTAGAATATTAAAGTGCTTGGC 59.027 38.462 0.00 0.00 0.00 4.52
2914 7998 7.065324 TCGGTGTTAGAATATTAAAGTGCTTGG 59.935 37.037 0.00 0.00 0.00 3.61
2924 8008 6.855836 ACAAGTCGTCGGTGTTAGAATATTA 58.144 36.000 0.00 0.00 0.00 0.98
2938 8022 1.289109 ATTCGGCCAACAAGTCGTCG 61.289 55.000 2.24 0.00 0.00 5.12
2948 8032 0.609151 TTACGAGGTCATTCGGCCAA 59.391 50.000 2.24 0.00 44.57 4.52
2949 8033 0.609151 TTTACGAGGTCATTCGGCCA 59.391 50.000 2.24 0.00 44.57 5.36
2958 8042 1.538512 GGGCCTTTGTTTTACGAGGTC 59.461 52.381 0.84 0.00 30.68 3.85
2990 8074 2.136298 TTCAGCCTGTTTGTGGTTGA 57.864 45.000 0.00 0.00 41.80 3.18
2991 8075 2.813061 CTTTCAGCCTGTTTGTGGTTG 58.187 47.619 0.00 0.00 37.18 3.77
2992 8076 1.136891 GCTTTCAGCCTGTTTGTGGTT 59.863 47.619 0.00 0.00 34.48 3.67
2993 8077 0.746659 GCTTTCAGCCTGTTTGTGGT 59.253 50.000 0.00 0.00 34.48 4.16
3001 8085 1.530013 CCCCTTGTGCTTTCAGCCTG 61.530 60.000 0.00 0.00 41.51 4.85
3002 8086 1.228675 CCCCTTGTGCTTTCAGCCT 60.229 57.895 0.00 0.00 41.51 4.58
3025 8109 1.917872 TTAAGTGTGTGGGGCCATTC 58.082 50.000 4.39 0.00 0.00 2.67
3026 8110 2.178580 CATTAAGTGTGTGGGGCCATT 58.821 47.619 4.39 0.00 0.00 3.16
3045 8129 0.825410 TTCGGCCTATTAACGGCTCA 59.175 50.000 15.08 2.46 46.73 4.26
3056 8140 3.706600 ATTGTGGTTACTTTCGGCCTA 57.293 42.857 0.00 0.00 0.00 3.93
3067 8151 2.075338 GGCCGTCGTAAATTGTGGTTA 58.925 47.619 0.00 0.00 0.00 2.85
3081 8165 1.604693 CCGTTATGTCTATGGGCCGTC 60.605 57.143 0.00 0.00 0.00 4.79
3082 8166 0.391597 CCGTTATGTCTATGGGCCGT 59.608 55.000 2.58 2.58 0.00 5.68
3084 8168 2.567615 AGATCCGTTATGTCTATGGGCC 59.432 50.000 0.00 0.00 0.00 5.80
3085 8169 3.963428 AGATCCGTTATGTCTATGGGC 57.037 47.619 0.00 0.00 0.00 5.36
3126 8211 3.701205 CCTTTGGGCCATTTTAAGCTT 57.299 42.857 7.26 3.48 0.00 3.74
3175 8260 2.880890 GCCACATGTGTTGTCTTCTCTT 59.119 45.455 23.79 0.00 36.00 2.85
3176 8261 2.105477 AGCCACATGTGTTGTCTTCTCT 59.895 45.455 23.79 4.51 36.00 3.10
3177 8262 2.481952 GAGCCACATGTGTTGTCTTCTC 59.518 50.000 23.79 13.25 36.00 2.87
3205 8290 3.083997 CTGAAGGGACGGGGAGGG 61.084 72.222 0.00 0.00 0.00 4.30
3211 8296 0.035458 AGTTTGCTCTGAAGGGACGG 59.965 55.000 0.00 0.00 0.00 4.79
3215 8300 1.882623 GTTGGAGTTTGCTCTGAAGGG 59.117 52.381 0.00 0.00 41.38 3.95
3251 11040 3.361977 AAATGGGCACGCACGGAC 61.362 61.111 0.00 0.00 0.00 4.79
3254 11043 2.128853 AACTCAAATGGGCACGCACG 62.129 55.000 0.00 0.00 0.00 5.34
3255 11044 0.664166 CAACTCAAATGGGCACGCAC 60.664 55.000 0.00 0.00 0.00 5.34
3256 11045 0.821301 TCAACTCAAATGGGCACGCA 60.821 50.000 0.00 0.00 0.00 5.24
3257 11046 0.313672 TTCAACTCAAATGGGCACGC 59.686 50.000 0.00 0.00 0.00 5.34
3258 11047 2.393764 GTTTCAACTCAAATGGGCACG 58.606 47.619 0.00 0.00 0.00 5.34
3259 11048 2.034053 TCGTTTCAACTCAAATGGGCAC 59.966 45.455 0.00 0.00 0.00 5.01
3260 11049 2.302260 TCGTTTCAACTCAAATGGGCA 58.698 42.857 0.00 0.00 0.00 5.36
3261 11050 3.049912 GTTCGTTTCAACTCAAATGGGC 58.950 45.455 0.00 0.00 0.00 5.36
3263 11052 4.667262 TGTGTTCGTTTCAACTCAAATGG 58.333 39.130 0.00 0.00 29.13 3.16
3264 11053 6.624710 TTTGTGTTCGTTTCAACTCAAATG 57.375 33.333 9.52 0.00 41.42 2.32
3265 11054 6.866248 ACTTTTGTGTTCGTTTCAACTCAAAT 59.134 30.769 12.67 1.53 43.73 2.32
3307 11096 3.115892 GACGCGCGTCCATTTGGA 61.116 61.111 44.30 0.00 43.08 3.53
3338 11127 0.244721 GCTTGAAATGGGTCACCTGC 59.755 55.000 0.00 0.00 37.76 4.85
3340 11129 0.251787 GGGCTTGAAATGGGTCACCT 60.252 55.000 0.00 0.00 37.76 4.00
3395 11195 1.432657 GAAGGAGTAGGCGGACGTC 59.567 63.158 7.13 7.13 0.00 4.34
3399 11199 1.291459 TAGGGGAAGGAGTAGGCGGA 61.291 60.000 0.00 0.00 0.00 5.54
3445 11245 3.509575 CCTATCGATGGGAGGAAGAGAAG 59.490 52.174 22.56 0.00 31.45 2.85
3464 11264 2.443390 GGCCGGGAGTGCTACCTA 60.443 66.667 2.18 0.00 0.00 3.08
3495 11295 2.202570 CGGAACTAGGTGACGGCG 60.203 66.667 4.80 4.80 0.00 6.46


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

AutoCloner maintained by Alex Coulton.