Multiple sequence alignment - TraesCS7D01G145800

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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 TraesCS7D01G145800 chr7D 100.000 6270 0 0 1 6270 92866584 92860315 0.000000e+00 11579.0
1 TraesCS7D01G145800 chr7D 100.000 2270 0 0 6629 8898 92859956 92857687 0.000000e+00 4193.0
2 TraesCS7D01G145800 chr7D 91.301 1322 84 20 1037 2342 93021465 93020159 0.000000e+00 1775.0
3 TraesCS7D01G145800 chr7D 97.740 885 18 2 8015 8898 29929498 29928615 0.000000e+00 1522.0
4 TraesCS7D01G145800 chr7D 97.735 883 16 2 8020 8898 587870705 587869823 0.000000e+00 1517.0
5 TraesCS7D01G145800 chr7D 81.540 1636 208 52 4564 6169 184486117 184487688 0.000000e+00 1262.0
6 TraesCS7D01G145800 chr7D 96.472 652 23 0 3118 3769 93019593 93018942 0.000000e+00 1077.0
7 TraesCS7D01G145800 chr7D 89.351 601 47 13 1 587 93024408 93023811 0.000000e+00 739.0
8 TraesCS7D01G145800 chr7D 85.786 598 75 7 3967 4560 184485482 184486073 7.580000e-175 625.0
9 TraesCS7D01G145800 chr7D 80.419 812 112 24 4725 5515 75280623 75281408 7.750000e-160 575.0
10 TraesCS7D01G145800 chr7D 94.203 345 16 2 2705 3045 93019941 93019597 2.850000e-144 523.0
11 TraesCS7D01G145800 chr7D 94.624 279 12 3 2386 2662 93020202 93019925 6.380000e-116 429.0
12 TraesCS7D01G145800 chr7D 85.437 309 44 1 1688 1996 75278530 75278837 4.010000e-83 320.0
13 TraesCS7D01G145800 chr7D 80.655 336 41 12 1225 1542 184474392 184474721 1.150000e-58 239.0
14 TraesCS7D01G145800 chr7D 81.081 296 52 4 1746 2040 184475275 184475567 5.370000e-57 233.0
15 TraesCS7D01G145800 chr7D 95.327 107 4 1 3761 3867 93015832 93015727 1.540000e-37 169.0
16 TraesCS7D01G145800 chr7D 86.667 135 15 2 4563 4694 75280492 75280626 7.200000e-31 147.0
17 TraesCS7D01G145800 chr7D 100.000 35 0 0 7947 7981 92858600 92858566 2.070000e-06 65.8
18 TraesCS7D01G145800 chr7D 100.000 35 0 0 7985 8019 92858638 92858604 2.070000e-06 65.8
19 TraesCS7D01G145800 chr7B 96.481 6195 160 20 1 6172 45345661 45339502 0.000000e+00 10179.0
20 TraesCS7D01G145800 chr7B 94.745 2740 91 18 1661 4389 45454073 45451376 0.000000e+00 4213.0
21 TraesCS7D01G145800 chr7B 81.912 1642 191 61 4564 6169 153558033 153559604 0.000000e+00 1290.0
22 TraesCS7D01G145800 chr7B 97.544 733 12 3 6734 7465 45450749 45450022 0.000000e+00 1249.0
23 TraesCS7D01G145800 chr7B 83.096 1337 176 29 3251 4560 21186364 21185051 0.000000e+00 1171.0
24 TraesCS7D01G145800 chr7B 95.506 623 24 2 4362 4984 45451364 45450746 0.000000e+00 992.0
25 TraesCS7D01G145800 chr7B 96.075 535 11 4 7473 8004 45444494 45443967 0.000000e+00 863.0
26 TraesCS7D01G145800 chr7B 85.619 598 76 7 3967 4560 153557398 153557989 3.530000e-173 619.0
27 TraesCS7D01G145800 chr7B 80.077 778 102 24 4569 5329 21185011 21184270 6.120000e-146 529.0
28 TraesCS7D01G145800 chr7B 95.094 265 9 2 7505 7769 45328506 45328246 1.790000e-111 414.0
29 TraesCS7D01G145800 chr7B 93.050 259 12 3 6867 7124 45330254 45330001 3.030000e-99 374.0
30 TraesCS7D01G145800 chr7B 88.077 260 25 5 1394 1649 45455565 45455308 4.040000e-78 303.0
31 TraesCS7D01G145800 chr7B 89.024 246 17 2 6635 6872 45339377 45339134 6.750000e-76 296.0
32 TraesCS7D01G145800 chr7B 95.349 172 8 0 2592 2763 426540120 426539949 3.160000e-69 274.0
33 TraesCS7D01G145800 chr7B 83.168 303 29 9 6880 7180 21183839 21183557 3.190000e-64 257.0
34 TraesCS7D01G145800 chr7B 88.235 204 21 3 2985 3186 21190151 21189949 3.210000e-59 241.0
35 TraesCS7D01G145800 chr7B 79.798 297 55 5 1746 2040 153553401 153553694 2.520000e-50 211.0
36 TraesCS7D01G145800 chr7B 81.928 166 20 2 1174 1338 153552500 153552656 2.020000e-26 132.0
37 TraesCS7D01G145800 chr7B 80.124 161 14 6 1400 1542 153552682 153552842 4.390000e-18 104.0
38 TraesCS7D01G145800 chr7B 87.805 82 7 3 7819 7898 45328238 45328158 9.510000e-15 93.5
39 TraesCS7D01G145800 chr7B 90.769 65 2 1 6188 6248 45339518 45339454 5.720000e-12 84.2
40 TraesCS7D01G145800 chr3D 98.295 880 14 1 8020 8898 589498372 589499251 0.000000e+00 1541.0
41 TraesCS7D01G145800 chr3D 91.489 94 7 1 862 955 104277274 104277182 2.610000e-25 128.0
42 TraesCS7D01G145800 chr3D 84.746 118 11 4 715 831 131343100 131342989 2.630000e-20 111.0
43 TraesCS7D01G145800 chr3D 97.561 41 1 0 822 862 104277330 104277290 4.460000e-08 71.3
44 TraesCS7D01G145800 chr2D 97.860 888 12 4 8018 8898 578694632 578693745 0.000000e+00 1528.0
45 TraesCS7D01G145800 chr2D 97.846 882 14 3 8021 8898 56899046 56899926 0.000000e+00 1519.0
46 TraesCS7D01G145800 chr2D 97.841 880 18 1 8020 8898 589596095 589596974 0.000000e+00 1519.0
47 TraesCS7D01G145800 chr2D 88.690 168 17 1 2796 2961 434685228 434685395 4.210000e-48 204.0
48 TraesCS7D01G145800 chrUn 97.856 886 13 4 8018 8898 89913104 89912220 0.000000e+00 1526.0
49 TraesCS7D01G145800 chrUn 86.170 94 8 1 862 955 326758033 326757945 7.350000e-16 97.1
50 TraesCS7D01G145800 chrUn 86.170 94 8 1 862 955 381260392 381260480 7.350000e-16 97.1
51 TraesCS7D01G145800 chr6D 97.846 882 18 1 8018 8898 448153919 448154800 0.000000e+00 1522.0
52 TraesCS7D01G145800 chr6D 100.000 38 0 0 2705 2742 153184905 153184868 4.460000e-08 71.3
53 TraesCS7D01G145800 chr5D 97.848 883 15 2 8020 8898 219949727 219950609 0.000000e+00 1522.0
54 TraesCS7D01G145800 chr5D 86.096 748 78 16 2227 2949 424347949 424348695 0.000000e+00 782.0
55 TraesCS7D01G145800 chr5D 87.409 413 35 10 2366 2762 330703729 330703318 8.140000e-125 459.0
56 TraesCS7D01G145800 chr5D 86.022 93 13 0 862 954 457748938 457749030 5.680000e-17 100.0
57 TraesCS7D01G145800 chr5B 88.533 593 52 15 2381 2961 513598509 513599097 0.000000e+00 704.0
58 TraesCS7D01G145800 chr5B 88.660 388 37 6 2381 2763 383541528 383541913 4.870000e-127 466.0
59 TraesCS7D01G145800 chr5B 91.018 167 14 1 2796 2961 70912676 70912842 3.230000e-54 224.0
60 TraesCS7D01G145800 chr5B 78.571 224 29 9 714 924 349176645 349176428 7.250000e-26 130.0
61 TraesCS7D01G145800 chr5B 86.170 94 13 0 862 955 648738606 648738699 1.580000e-17 102.0
62 TraesCS7D01G145800 chr5B 84.615 78 8 2 2266 2342 383541501 383541575 3.450000e-09 75.0
63 TraesCS7D01G145800 chr5A 83.908 348 29 12 2366 2709 24394255 24394579 3.120000e-79 307.0
64 TraesCS7D01G145800 chr5A 82.812 192 21 7 2392 2573 533749115 533748926 2.570000e-35 161.0
65 TraesCS7D01G145800 chr5A 86.170 94 13 0 862 955 328545342 328545435 1.580000e-17 102.0
66 TraesCS7D01G145800 chr5A 82.828 99 9 6 2260 2350 533749170 533749072 2.060000e-11 82.4
67 TraesCS7D01G145800 chr7A 86.038 265 31 6 1735 1996 79556556 79556817 6.800000e-71 279.0
68 TraesCS7D01G145800 chr4D 90.303 165 15 1 2798 2961 287297209 287297373 1.950000e-51 215.0
69 TraesCS7D01G145800 chr4D 85.470 117 11 6 751 862 8774373 8774258 5.640000e-22 117.0
70 TraesCS7D01G145800 chr2A 89.222 167 17 1 2796 2961 552474730 552474564 3.260000e-49 207.0
71 TraesCS7D01G145800 chr1B 87.222 180 15 4 681 857 661629208 661629034 1.960000e-46 198.0
72 TraesCS7D01G145800 chr1B 78.595 299 37 11 678 950 200944713 200945010 1.190000e-38 172.0
73 TraesCS7D01G145800 chr1A 82.418 182 26 3 681 860 496316538 496316361 4.300000e-33 154.0
74 TraesCS7D01G145800 chr4B 80.788 203 23 11 2381 2573 237054507 237054703 2.590000e-30 145.0
75 TraesCS7D01G145800 chr1D 83.019 159 18 7 676 831 324338799 324338951 1.560000e-27 135.0
76 TraesCS7D01G145800 chr1D 76.449 276 31 11 711 955 365968782 365969054 1.570000e-22 119.0
77 TraesCS7D01G145800 chr6B 85.593 118 11 5 2260 2376 442427416 442427304 1.570000e-22 119.0
78 TraesCS7D01G145800 chr6A 83.200 125 18 3 709 831 500513074 500513197 2.630000e-20 111.0
79 TraesCS7D01G145800 chr6A 86.022 93 13 0 862 954 79169148 79169240 5.680000e-17 100.0


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 TraesCS7D01G145800 chr7D 92857687 92866584 8897 True 3975.900000 11579 100.000000 1 8898 4 chr7D.!!$R3 8897
1 TraesCS7D01G145800 chr7D 29928615 29929498 883 True 1522.000000 1522 97.740000 8015 8898 1 chr7D.!!$R1 883
2 TraesCS7D01G145800 chr7D 587869823 587870705 882 True 1517.000000 1517 97.735000 8020 8898 1 chr7D.!!$R2 878
3 TraesCS7D01G145800 chr7D 184485482 184487688 2206 False 943.500000 1262 83.663000 3967 6169 2 chr7D.!!$F3 2202
4 TraesCS7D01G145800 chr7D 93015727 93024408 8681 True 785.333333 1775 93.546333 1 3867 6 chr7D.!!$R4 3866
5 TraesCS7D01G145800 chr7D 75278530 75281408 2878 False 347.333333 575 84.174333 1688 5515 3 chr7D.!!$F1 3827
6 TraesCS7D01G145800 chr7D 184474392 184475567 1175 False 236.000000 239 80.868000 1225 2040 2 chr7D.!!$F2 815
7 TraesCS7D01G145800 chr7B 45339134 45345661 6527 True 3519.733333 10179 92.091333 1 6872 3 chr7B.!!$R5 6871
8 TraesCS7D01G145800 chr7B 45450022 45455565 5543 True 1689.250000 4213 93.968000 1394 7465 4 chr7B.!!$R6 6071
9 TraesCS7D01G145800 chr7B 45443967 45444494 527 True 863.000000 863 96.075000 7473 8004 1 chr7B.!!$R1 531
10 TraesCS7D01G145800 chr7B 21183557 21190151 6594 True 549.500000 1171 83.644000 2985 7180 4 chr7B.!!$R3 4195
11 TraesCS7D01G145800 chr7B 153552500 153559604 7104 False 471.200000 1290 81.876200 1174 6169 5 chr7B.!!$F1 4995
12 TraesCS7D01G145800 chr7B 45328158 45330254 2096 True 293.833333 414 91.983000 6867 7898 3 chr7B.!!$R4 1031
13 TraesCS7D01G145800 chr3D 589498372 589499251 879 False 1541.000000 1541 98.295000 8020 8898 1 chr3D.!!$F1 878
14 TraesCS7D01G145800 chr2D 578693745 578694632 887 True 1528.000000 1528 97.860000 8018 8898 1 chr2D.!!$R1 880
15 TraesCS7D01G145800 chr2D 56899046 56899926 880 False 1519.000000 1519 97.846000 8021 8898 1 chr2D.!!$F1 877
16 TraesCS7D01G145800 chr2D 589596095 589596974 879 False 1519.000000 1519 97.841000 8020 8898 1 chr2D.!!$F3 878
17 TraesCS7D01G145800 chrUn 89912220 89913104 884 True 1526.000000 1526 97.856000 8018 8898 1 chrUn.!!$R1 880
18 TraesCS7D01G145800 chr6D 448153919 448154800 881 False 1522.000000 1522 97.846000 8018 8898 1 chr6D.!!$F1 880
19 TraesCS7D01G145800 chr5D 219949727 219950609 882 False 1522.000000 1522 97.848000 8020 8898 1 chr5D.!!$F1 878
20 TraesCS7D01G145800 chr5D 424347949 424348695 746 False 782.000000 782 86.096000 2227 2949 1 chr5D.!!$F2 722
21 TraesCS7D01G145800 chr5B 513598509 513599097 588 False 704.000000 704 88.533000 2381 2961 1 chr5B.!!$F2 580

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
738 2951 0.251916 TGTCCTACCAAAGCCCGATG 59.748 55.000 0.00 0.00 0.00 3.84 F
1310 3535 0.320771 GAGGCAAGAGGAAAGCGTCA 60.321 55.000 0.00 0.00 41.37 4.35 F
1389 3614 1.075226 TCCGAGGGATCCAAGAGGG 60.075 63.158 15.23 7.13 34.83 4.30 F
1409 3637 2.398803 GAAGGGATCCAAGAAGCGC 58.601 57.895 15.23 0.00 0.00 5.92 F
2404 6031 2.401766 GCCGTTGCTGCTGCTACAT 61.402 57.895 24.55 0.00 43.29 2.29 F
3394 10579 8.240267 AGATTCCTAGGTTTAGTAGTGACATC 57.760 38.462 9.08 0.00 0.00 3.06 F
4878 18074 7.546250 TTCAAAGAGAAGAGATTACTGGACT 57.454 36.000 0.00 0.00 0.00 3.85 F
5624 18938 1.588674 TGGTAACAGCAGGAACAACG 58.411 50.000 0.00 0.00 46.17 4.10 F
6934 20294 0.541764 TCCCTTTTCACCACCATGCC 60.542 55.000 0.00 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2155 5723 2.493675 GCCATGTCCTCCCTTTTCTTTC 59.506 50.000 0.00 0.0 0.00 2.62 R
2425 6052 4.175337 TGCAGCGGGGGATGTAGC 62.175 66.667 0.00 0.0 0.00 3.58 R
2874 6507 6.349033 GGGGATACGGCAAATACATATGAAAC 60.349 42.308 10.38 0.0 37.60 2.78 R
3394 10579 6.045318 CACAAGTATCTCCTGACCATAGTTG 58.955 44.000 0.00 0.0 38.55 3.16 R
4337 17428 7.187824 AGTAGACCATAAACATGAGATGTGT 57.812 36.000 0.00 0.7 44.07 3.72 R
4923 18120 6.119144 TGCGAAAAAGGATAATAGCAAGAC 57.881 37.500 0.00 0.0 0.00 3.01 R
6633 19984 2.821969 GGACAATGCACCTTCAAGATGT 59.178 45.455 0.00 0.0 0.00 3.06 R
7325 20686 1.347707 GAACTGGTCATGGTGGTCAGA 59.652 52.381 0.00 0.0 0.00 3.27 R
7991 22716 1.001293 GCGACTGGATATGATGCTGGA 59.999 52.381 0.00 0.0 0.00 3.86 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
48 49 2.776072 CCGCGATGTTGGTTCGAC 59.224 61.111 8.23 0.00 38.88 4.20
56 57 1.885850 GTTGGTTCGACGCTGTGGT 60.886 57.895 0.00 0.00 0.00 4.16
74 75 0.526662 GTGACAGTGACCTCTACCGG 59.473 60.000 0.00 0.00 0.00 5.28
95 96 3.823330 GATCGGTCAGCGGTCGGT 61.823 66.667 0.00 0.00 0.00 4.69
108 109 1.887088 CGGTCGGTCTATGGCTAGGAT 60.887 57.143 0.00 0.00 0.00 3.24
230 231 5.932619 AGTAAAGTTTCTTGTTTTGCCCT 57.067 34.783 0.00 0.00 0.00 5.19
231 232 5.660460 AGTAAAGTTTCTTGTTTTGCCCTG 58.340 37.500 0.00 0.00 0.00 4.45
309 310 1.524002 CTCAGTCCCATCATGCGGT 59.476 57.895 0.00 0.00 0.00 5.68
310 311 0.812811 CTCAGTCCCATCATGCGGTG 60.813 60.000 0.00 0.00 0.00 4.94
525 542 3.891422 TTGTGGGCAATTTGATGATCC 57.109 42.857 0.00 0.00 0.00 3.36
576 593 2.668632 GTCTGACGGGCCATTCCA 59.331 61.111 4.39 0.00 36.21 3.53
590 1463 2.292267 CATTCCATTGCGTTCCTAGCT 58.708 47.619 0.00 0.00 35.28 3.32
653 2866 2.395360 GCGGCAGCGTGGAATACAA 61.395 57.895 0.00 0.00 0.00 2.41
685 2898 3.488363 GTCTCATCCCGTGGAGTATACT 58.512 50.000 4.68 4.68 34.05 2.12
698 2911 3.553096 GGAGTATACTTGGCCATCTGTCG 60.553 52.174 6.09 0.00 0.00 4.35
700 2913 1.204146 ATACTTGGCCATCTGTCGGT 58.796 50.000 6.09 0.00 0.00 4.69
732 2945 1.378646 GGGCCTGTCCTACCAAAGC 60.379 63.158 0.84 0.00 34.39 3.51
738 2951 0.251916 TGTCCTACCAAAGCCCGATG 59.748 55.000 0.00 0.00 0.00 3.84
840 3055 1.030488 GCCGGGCCTCTTCCTTAAAC 61.030 60.000 8.12 0.00 0.00 2.01
851 3066 5.389859 TCTTCCTTAAACGGTGAATACGA 57.610 39.130 0.00 0.00 34.93 3.43
881 3096 2.143876 GGCTCAAAATCTAGGCCCAA 57.856 50.000 0.00 0.00 37.12 4.12
886 3101 2.017049 CAAAATCTAGGCCCAAGTCCG 58.983 52.381 0.00 0.00 0.00 4.79
954 3175 2.193248 GCCCATGGCCAGGACTAC 59.807 66.667 21.32 0.65 44.06 2.73
955 3176 2.919043 CCCATGGCCAGGACTACC 59.081 66.667 21.32 0.00 0.00 3.18
956 3177 2.505982 CCATGGCCAGGACTACCG 59.494 66.667 21.32 0.00 41.83 4.02
957 3178 2.367202 CCATGGCCAGGACTACCGT 61.367 63.158 21.32 0.00 41.83 4.83
958 3179 1.144057 CATGGCCAGGACTACCGTC 59.856 63.158 13.35 0.00 41.83 4.79
959 3180 1.305802 ATGGCCAGGACTACCGTCA 60.306 57.895 13.05 0.00 42.05 4.35
960 3181 0.907704 ATGGCCAGGACTACCGTCAA 60.908 55.000 13.05 0.00 42.05 3.18
1007 3231 2.094130 CCTTGTCTTCCCGTCTTCTACC 60.094 54.545 0.00 0.00 0.00 3.18
1030 3254 0.752376 CCTCTCTACCCGTCCCTGTC 60.752 65.000 0.00 0.00 0.00 3.51
1145 3370 1.165270 CCAAACCCTAAGAAGCACGG 58.835 55.000 0.00 0.00 0.00 4.94
1307 3532 2.744768 GCGAGGCAAGAGGAAAGCG 61.745 63.158 0.00 0.00 0.00 4.68
1310 3535 0.320771 GAGGCAAGAGGAAAGCGTCA 60.321 55.000 0.00 0.00 41.37 4.35
1389 3614 1.075226 TCCGAGGGATCCAAGAGGG 60.075 63.158 15.23 7.13 34.83 4.30
1409 3637 2.398803 GAAGGGATCCAAGAAGCGC 58.601 57.895 15.23 0.00 0.00 5.92
1445 3673 2.434359 AAAGCCGCTACGAGCACC 60.434 61.111 0.00 0.00 42.58 5.01
1924 5477 7.811236 CGTGAGTCTACTACAAAAACAATCCTA 59.189 37.037 0.00 0.00 0.00 2.94
2115 5683 2.803817 GGGACACGCGGGGATACAT 61.804 63.158 15.46 0.00 39.74 2.29
2403 6030 3.049674 GCCGTTGCTGCTGCTACA 61.050 61.111 24.55 5.05 43.29 2.74
2404 6031 2.401766 GCCGTTGCTGCTGCTACAT 61.402 57.895 24.55 0.00 43.29 2.29
3394 10579 8.240267 AGATTCCTAGGTTTAGTAGTGACATC 57.760 38.462 9.08 0.00 0.00 3.06
4677 17867 8.762426 GTTCAGGTTAGTGTTTACTTACTCTTG 58.238 37.037 0.00 0.00 36.83 3.02
4878 18074 7.546250 TTCAAAGAGAAGAGATTACTGGACT 57.454 36.000 0.00 0.00 0.00 3.85
4923 18120 2.254459 CCAAATGTCTCTCGTGTCTCG 58.746 52.381 0.00 0.00 41.41 4.04
5595 18909 2.833338 CTGCCTTCATTTTCATTCCCCA 59.167 45.455 0.00 0.00 0.00 4.96
5624 18938 1.588674 TGGTAACAGCAGGAACAACG 58.411 50.000 0.00 0.00 46.17 4.10
5656 18970 9.167311 ACTAACCTATTGAGCTTGTGAAAATAG 57.833 33.333 0.00 0.00 32.85 1.73
5857 19176 8.761575 TTACAAATGATGATTTTCTTGCCTTC 57.238 30.769 0.00 0.00 28.65 3.46
5859 19178 4.644103 ATGATGATTTTCTTGCCTTCCG 57.356 40.909 0.00 0.00 0.00 4.30
5906 19225 1.796796 GGCGCAACAAGATCAGTCC 59.203 57.895 10.83 0.00 0.00 3.85
5949 19270 3.803340 TCTCCTGTCATAAACCTTCCCT 58.197 45.455 0.00 0.00 0.00 4.20
6125 19448 8.959548 TGTTCAGAAACAAGAACATATGCATAT 58.040 29.630 13.63 13.63 46.46 1.78
6162 19485 7.823745 GGTTGGATACCTGTGAATAATCAAT 57.176 36.000 0.00 0.00 44.10 2.57
6163 19486 7.651808 GGTTGGATACCTGTGAATAATCAATG 58.348 38.462 0.00 0.00 44.10 2.82
6164 19487 7.285401 GGTTGGATACCTGTGAATAATCAATGT 59.715 37.037 0.00 0.00 44.10 2.71
6165 19488 9.337396 GTTGGATACCTGTGAATAATCAATGTA 57.663 33.333 0.00 0.00 37.30 2.29
6166 19489 9.559732 TTGGATACCTGTGAATAATCAATGTAG 57.440 33.333 0.00 0.00 37.30 2.74
6167 19490 8.713971 TGGATACCTGTGAATAATCAATGTAGT 58.286 33.333 0.00 0.00 37.30 2.73
6168 19491 9.209175 GGATACCTGTGAATAATCAATGTAGTC 57.791 37.037 0.00 0.00 37.30 2.59
6169 19492 9.764363 GATACCTGTGAATAATCAATGTAGTCA 57.236 33.333 0.00 0.00 37.30 3.41
6171 19494 8.442632 ACCTGTGAATAATCAATGTAGTCATG 57.557 34.615 0.00 0.00 37.30 3.07
6172 19495 8.049117 ACCTGTGAATAATCAATGTAGTCATGT 58.951 33.333 0.00 0.00 37.30 3.21
6173 19496 8.896744 CCTGTGAATAATCAATGTAGTCATGTT 58.103 33.333 0.00 0.00 37.30 2.71
6174 19497 9.926751 CTGTGAATAATCAATGTAGTCATGTTC 57.073 33.333 0.00 0.00 37.30 3.18
6175 19498 9.447157 TGTGAATAATCAATGTAGTCATGTTCA 57.553 29.630 0.00 0.00 37.30 3.18
6176 19499 9.926751 GTGAATAATCAATGTAGTCATGTTCAG 57.073 33.333 0.00 0.00 37.30 3.02
6177 19500 9.889128 TGAATAATCAATGTAGTCATGTTCAGA 57.111 29.630 0.00 0.00 34.19 3.27
6219 19542 8.153479 TGTAGTCATGCCATCAATTTACATAC 57.847 34.615 0.00 0.00 0.00 2.39
6234 19561 8.721478 CAATTTACATACATATACCTGGCAGAC 58.279 37.037 17.94 0.00 0.00 3.51
6257 19608 3.054802 ACCAAGGCTTCTCCTAGTCAATG 60.055 47.826 0.00 0.00 46.94 2.82
6654 20005 2.821969 ACATCTTGAAGGTGCATTGTCC 59.178 45.455 5.16 0.00 0.00 4.02
6659 20010 4.041567 TCTTGAAGGTGCATTGTCCTTAGA 59.958 41.667 6.33 4.66 43.12 2.10
6692 20043 7.664552 AATCAAATAATGAGGAATCAAGCCA 57.335 32.000 0.00 0.00 42.53 4.75
6699 20050 8.945195 ATAATGAGGAATCAAGCCATTAATCA 57.055 30.769 0.00 0.00 34.60 2.57
6710 20061 6.156602 TCAAGCCATTAATCAACCCATCATTT 59.843 34.615 0.00 0.00 0.00 2.32
6724 20075 7.902920 ACCCATCATTTTGAGCTTATTGTAT 57.097 32.000 0.00 0.00 0.00 2.29
6776 20127 6.012771 ACTGCCTTACACCTTTATAACTCCTT 60.013 38.462 0.00 0.00 0.00 3.36
6931 20291 3.922375 TCTTTTCCCTTTTCACCACCAT 58.078 40.909 0.00 0.00 0.00 3.55
6932 20292 3.640967 TCTTTTCCCTTTTCACCACCATG 59.359 43.478 0.00 0.00 0.00 3.66
6933 20293 1.337118 TTCCCTTTTCACCACCATGC 58.663 50.000 0.00 0.00 0.00 4.06
6934 20294 0.541764 TCCCTTTTCACCACCATGCC 60.542 55.000 0.00 0.00 0.00 4.40
6937 20297 1.066716 CCTTTTCACCACCATGCCATG 60.067 52.381 0.00 0.00 0.00 3.66
7128 20488 1.198094 TGGATTTGGGGCTCGAGACA 61.198 55.000 22.31 10.68 0.00 3.41
7325 20686 4.856801 GCACCATCATCGGCGGGT 62.857 66.667 7.21 2.36 0.00 5.28
7898 22623 5.785243 TCATTCATACGTGTCTGTGGTTTA 58.215 37.500 0.00 0.00 0.00 2.01
7905 22630 3.994392 ACGTGTCTGTGGTTTAATGCTAG 59.006 43.478 0.00 0.00 0.00 3.42
7926 22651 0.599204 GACCGTGTGTGTGGTAGTGG 60.599 60.000 0.00 0.00 38.99 4.00
7958 22683 5.170748 CAAAAGTAAAACCATGGATCCAGC 58.829 41.667 21.47 3.83 0.00 4.85
7989 22714 3.249320 CAGTCGCATTAGACAATCCATGG 59.751 47.826 4.97 4.97 43.24 3.66
7991 22716 4.067896 GTCGCATTAGACAATCCATGGAT 58.932 43.478 22.15 22.15 40.65 3.41
7992 22717 4.153117 GTCGCATTAGACAATCCATGGATC 59.847 45.833 27.45 16.25 40.65 3.36
7993 22718 3.438087 CGCATTAGACAATCCATGGATCC 59.562 47.826 27.45 18.30 33.08 3.36
7994 22719 4.401022 GCATTAGACAATCCATGGATCCA 58.599 43.478 27.45 18.88 33.08 3.41
7995 22720 4.458295 GCATTAGACAATCCATGGATCCAG 59.542 45.833 27.45 20.85 33.08 3.86
7996 22721 2.653234 AGACAATCCATGGATCCAGC 57.347 50.000 27.45 16.28 33.08 4.85
7997 22722 1.848388 AGACAATCCATGGATCCAGCA 59.152 47.619 27.45 6.56 33.08 4.41
7998 22723 2.445905 AGACAATCCATGGATCCAGCAT 59.554 45.455 27.45 8.16 33.08 3.79
7999 22724 2.818432 GACAATCCATGGATCCAGCATC 59.182 50.000 27.45 14.10 33.08 3.91
8000 22725 2.176148 ACAATCCATGGATCCAGCATCA 59.824 45.455 27.45 2.36 33.08 3.07
8001 22726 3.181422 ACAATCCATGGATCCAGCATCAT 60.181 43.478 27.45 5.82 33.08 2.45
8002 22727 4.043686 ACAATCCATGGATCCAGCATCATA 59.956 41.667 27.45 1.54 33.08 2.15
8003 22728 5.201243 CAATCCATGGATCCAGCATCATAT 58.799 41.667 27.45 4.49 33.08 1.78
8004 22729 4.498894 TCCATGGATCCAGCATCATATC 57.501 45.455 21.33 0.00 32.33 1.63
8005 22730 3.201487 TCCATGGATCCAGCATCATATCC 59.799 47.826 21.33 0.00 38.71 2.59
8007 22732 3.994931 TGGATCCAGCATCATATCCAG 57.005 47.619 11.44 0.00 42.25 3.86
8008 22733 3.254089 TGGATCCAGCATCATATCCAGT 58.746 45.455 11.44 0.00 42.25 4.00
8009 22734 3.262660 TGGATCCAGCATCATATCCAGTC 59.737 47.826 11.44 0.00 42.25 3.51
8010 22735 3.519579 GATCCAGCATCATATCCAGTCG 58.480 50.000 0.00 0.00 0.00 4.18
8011 22736 1.001293 TCCAGCATCATATCCAGTCGC 59.999 52.381 0.00 0.00 0.00 5.19
8012 22737 1.270465 CCAGCATCATATCCAGTCGCA 60.270 52.381 0.00 0.00 0.00 5.10
8013 22738 2.614734 CCAGCATCATATCCAGTCGCAT 60.615 50.000 0.00 0.00 0.00 4.73
8014 22739 3.072211 CAGCATCATATCCAGTCGCATT 58.928 45.455 0.00 0.00 0.00 3.56
8015 22740 4.248058 CAGCATCATATCCAGTCGCATTA 58.752 43.478 0.00 0.00 0.00 1.90
8016 22741 4.329256 CAGCATCATATCCAGTCGCATTAG 59.671 45.833 0.00 0.00 0.00 1.73
8192 22923 8.627403 TCACCAACAACAGTATATACTAGCTAC 58.373 37.037 15.03 0.00 34.13 3.58
8193 22924 8.410912 CACCAACAACAGTATATACTAGCTACA 58.589 37.037 15.03 0.00 34.13 2.74
8420 23154 4.841443 TTCATCATATTGGAGCATGCAC 57.159 40.909 21.98 14.31 34.66 4.57
8423 23157 5.562635 TCATCATATTGGAGCATGCACATA 58.437 37.500 21.98 8.93 34.66 2.29
8571 23305 6.089249 CACTCATGTGCACTGTAGGATATA 57.911 41.667 19.41 0.00 37.38 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 1.885850 ACCACAGCGTCGAACCAAC 60.886 57.895 0.00 0.00 0.00 3.77
56 57 0.611062 CCCGGTAGAGGTCACTGTCA 60.611 60.000 0.00 0.00 0.00 3.58
74 75 1.300233 GACCGCTGACCGATCATCC 60.300 63.158 0.00 0.00 40.02 3.51
86 87 1.152819 TAGCCATAGACCGACCGCT 60.153 57.895 0.00 0.00 0.00 5.52
95 96 3.399305 TCTCACTCCATCCTAGCCATAGA 59.601 47.826 0.00 0.00 0.00 1.98
108 109 1.536073 CCGAGCACCTTCTCACTCCA 61.536 60.000 0.00 0.00 33.41 3.86
259 260 0.464373 CCACCCTCATTCATGTCGGG 60.464 60.000 12.53 12.53 41.79 5.14
294 295 0.908910 TTACACCGCATGATGGGACT 59.091 50.000 11.37 0.00 31.21 3.85
345 359 2.374170 TCCACCCAAAAACCTCTCTACC 59.626 50.000 0.00 0.00 0.00 3.18
487 504 4.895297 CCACAAATATCTGCAATAGGGGTT 59.105 41.667 0.00 0.00 0.00 4.11
525 542 1.156736 GGTCATGTCAACTCCAACGG 58.843 55.000 0.00 0.00 0.00 4.44
576 593 0.250234 TCAGCAGCTAGGAACGCAAT 59.750 50.000 0.00 0.00 0.00 3.56
590 1463 2.589157 CCCCACCGGTTACTCAGCA 61.589 63.158 2.97 0.00 0.00 4.41
653 2866 1.690219 GGATGAGACGGGCAGGACAT 61.690 60.000 0.00 0.00 0.00 3.06
685 2898 2.264480 CGACCGACAGATGGCCAA 59.736 61.111 10.96 0.00 0.00 4.52
719 2932 0.251916 CATCGGGCTTTGGTAGGACA 59.748 55.000 0.00 0.00 0.00 4.02
771 2984 0.538746 CTGGTTTTAGGCCCAACGGT 60.539 55.000 0.00 0.00 0.00 4.83
840 3055 2.584143 GGCCCGTCGTATTCACCG 60.584 66.667 0.00 0.00 0.00 4.94
863 3078 2.685388 GACTTGGGCCTAGATTTTGAGC 59.315 50.000 21.96 0.00 0.00 4.26
956 3177 1.495951 GGTTCGCCACGTGATTGAC 59.504 57.895 19.30 10.09 37.19 3.18
957 3178 2.024868 CGGTTCGCCACGTGATTGA 61.025 57.895 19.30 8.72 37.00 2.57
958 3179 2.024868 TCGGTTCGCCACGTGATTG 61.025 57.895 19.30 6.20 37.00 2.67
959 3180 2.025418 GTCGGTTCGCCACGTGATT 61.025 57.895 19.30 0.00 37.00 2.57
960 3181 2.431942 GTCGGTTCGCCACGTGAT 60.432 61.111 19.30 0.00 37.00 3.06
1007 3231 1.152715 GGACGGGTAGAGAGGGAGG 60.153 68.421 0.00 0.00 0.00 4.30
1389 3614 0.464554 CGCTTCTTGGATCCCTTCCC 60.465 60.000 9.90 0.00 44.77 3.97
1409 3637 2.276732 TCTTCTTGCCAGTTCCCTTG 57.723 50.000 0.00 0.00 0.00 3.61
2115 5683 5.438698 TTTGGAAAATACGGAGGGATACA 57.561 39.130 0.00 0.00 39.74 2.29
2155 5723 2.493675 GCCATGTCCTCCCTTTTCTTTC 59.506 50.000 0.00 0.00 0.00 2.62
2425 6052 4.175337 TGCAGCGGGGGATGTAGC 62.175 66.667 0.00 0.00 0.00 3.58
2684 6317 6.556495 AGCCACAGAGAAGATTATCCATTAGA 59.444 38.462 0.00 0.00 0.00 2.10
2874 6507 6.349033 GGGGATACGGCAAATACATATGAAAC 60.349 42.308 10.38 0.00 37.60 2.78
3394 10579 6.045318 CACAAGTATCTCCTGACCATAGTTG 58.955 44.000 0.00 0.00 38.55 3.16
4337 17428 7.187824 AGTAGACCATAAACATGAGATGTGT 57.812 36.000 0.00 0.70 44.07 3.72
4677 17867 8.622157 GGAAAAATGGACTCCTAGCTTAAATAC 58.378 37.037 0.00 0.00 0.00 1.89
4852 18046 8.601546 AGTCCAGTAATCTCTTCTCTTTGAATT 58.398 33.333 0.00 0.00 33.71 2.17
4853 18047 8.144862 AGTCCAGTAATCTCTTCTCTTTGAAT 57.855 34.615 0.00 0.00 33.71 2.57
4923 18120 6.119144 TGCGAAAAAGGATAATAGCAAGAC 57.881 37.500 0.00 0.00 0.00 3.01
5624 18938 5.112686 CAAGCTCAATAGGTTAGTCTGTCC 58.887 45.833 0.00 0.00 41.45 4.02
5656 18970 6.878389 TGCCCCAAAAGATAAACATGATTTTC 59.122 34.615 0.00 0.00 0.00 2.29
6119 19442 8.225863 TCCAACCTCCCTAATTATTATATGCA 57.774 34.615 0.00 0.00 0.00 3.96
6151 19474 9.889128 TCTGAACATGACTACATTGATTATTCA 57.111 29.630 0.00 0.00 34.15 2.57
6179 19502 9.807649 GGCATGACTACATTGATTATTCTTTTT 57.192 29.630 0.00 0.00 34.15 1.94
6180 19503 8.970020 TGGCATGACTACATTGATTATTCTTTT 58.030 29.630 0.00 0.00 34.15 2.27
6181 19504 8.523915 TGGCATGACTACATTGATTATTCTTT 57.476 30.769 0.00 0.00 34.15 2.52
6182 19505 8.701908 ATGGCATGACTACATTGATTATTCTT 57.298 30.769 0.00 0.00 34.15 2.52
6183 19506 7.940688 TGATGGCATGACTACATTGATTATTCT 59.059 33.333 3.81 0.00 34.15 2.40
6186 19509 8.645814 ATTGATGGCATGACTACATTGATTAT 57.354 30.769 3.81 0.00 34.15 1.28
6219 19542 3.470709 CTTGGTGTCTGCCAGGTATATG 58.529 50.000 0.00 0.00 40.01 1.78
6631 19982 3.755378 GACAATGCACCTTCAAGATGTCT 59.245 43.478 0.00 0.00 34.58 3.41
6633 19984 2.821969 GGACAATGCACCTTCAAGATGT 59.178 45.455 0.00 0.00 0.00 3.06
6677 20028 6.041296 GGTTGATTAATGGCTTGATTCCTCAT 59.959 38.462 0.00 0.00 0.00 2.90
6692 20043 7.427989 AGCTCAAAATGATGGGTTGATTAAT 57.572 32.000 0.00 0.00 31.21 1.40
6699 20050 6.610075 ACAATAAGCTCAAAATGATGGGTT 57.390 33.333 0.00 0.00 0.00 4.11
6710 20061 9.618890 AGCTAAAAGATGATACAATAAGCTCAA 57.381 29.630 0.00 0.00 31.24 3.02
6724 20075 8.993121 GCTGCTTGTATTATAGCTAAAAGATGA 58.007 33.333 0.00 0.00 38.22 2.92
6931 20291 6.206395 ACGATTCAAATGATAAACATGGCA 57.794 33.333 0.00 0.00 39.39 4.92
6932 20292 7.275341 TGAAACGATTCAAATGATAAACATGGC 59.725 33.333 5.55 0.00 42.47 4.40
6933 20293 8.686397 TGAAACGATTCAAATGATAAACATGG 57.314 30.769 5.55 0.00 42.47 3.66
7265 20626 5.221641 ACTCAAGGGGGAAAAGTTAAAATGC 60.222 40.000 0.00 0.00 0.00 3.56
7325 20686 1.347707 GAACTGGTCATGGTGGTCAGA 59.652 52.381 0.00 0.00 0.00 3.27
7722 22445 1.587054 CTCCGCTCCAAGAGAACGT 59.413 57.895 0.00 0.00 31.43 3.99
7773 22496 6.127535 GCTCCAAACTATGTACTGTACCACTA 60.128 42.308 14.91 4.20 0.00 2.74
7795 22518 2.047179 GTCTGTCCAACCCGGCTC 60.047 66.667 0.00 0.00 33.14 4.70
7841 22564 4.620982 TGCATCGAACATCACGAGAATAT 58.379 39.130 0.00 0.00 42.81 1.28
7898 22623 1.014044 CACACACGGTCGCTAGCATT 61.014 55.000 16.45 0.00 0.00 3.56
7905 22630 2.019951 CTACCACACACACGGTCGC 61.020 63.158 0.00 0.00 36.69 5.19
7926 22651 4.352887 TGGTTTTACTTTTGCGTTGTAGC 58.647 39.130 0.00 0.00 37.71 3.58
7958 22683 5.473039 TGTCTAATGCGACTGGATATGATG 58.527 41.667 0.00 0.00 35.00 3.07
7989 22714 3.519579 CGACTGGATATGATGCTGGATC 58.480 50.000 1.79 1.79 0.00 3.36
7991 22716 1.001293 GCGACTGGATATGATGCTGGA 59.999 52.381 0.00 0.00 0.00 3.86
7992 22717 1.270465 TGCGACTGGATATGATGCTGG 60.270 52.381 0.00 0.00 0.00 4.85
7993 22718 2.159327 TGCGACTGGATATGATGCTG 57.841 50.000 0.00 0.00 0.00 4.41
7994 22719 3.413846 AATGCGACTGGATATGATGCT 57.586 42.857 0.00 0.00 0.00 3.79
7995 22720 4.328440 GTCTAATGCGACTGGATATGATGC 59.672 45.833 0.00 0.00 0.00 3.91
7996 22721 5.718146 AGTCTAATGCGACTGGATATGATG 58.282 41.667 0.00 0.00 42.39 3.07
7997 22722 5.991933 AGTCTAATGCGACTGGATATGAT 57.008 39.130 0.00 0.00 42.39 2.45
7998 22723 6.004574 ACTAGTCTAATGCGACTGGATATGA 58.995 40.000 12.85 0.00 42.93 2.15
7999 22724 6.072452 TCACTAGTCTAATGCGACTGGATATG 60.072 42.308 12.85 3.99 42.93 1.78
8000 22725 6.004574 TCACTAGTCTAATGCGACTGGATAT 58.995 40.000 12.85 0.00 42.93 1.63
8001 22726 5.374071 TCACTAGTCTAATGCGACTGGATA 58.626 41.667 12.85 1.18 42.93 2.59
8002 22727 4.207955 TCACTAGTCTAATGCGACTGGAT 58.792 43.478 12.85 0.00 42.93 3.41
8003 22728 3.617284 TCACTAGTCTAATGCGACTGGA 58.383 45.455 12.85 4.23 42.93 3.86
8004 22729 4.277174 AGATCACTAGTCTAATGCGACTGG 59.723 45.833 0.00 6.87 43.68 4.00
8005 22730 5.431420 AGATCACTAGTCTAATGCGACTG 57.569 43.478 0.00 1.80 43.68 3.51
8006 22731 6.768861 ACTTAGATCACTAGTCTAATGCGACT 59.231 38.462 0.00 0.00 45.62 4.18
8007 22732 6.961576 ACTTAGATCACTAGTCTAATGCGAC 58.038 40.000 0.00 0.00 37.50 5.19
8008 22733 8.672823 TTACTTAGATCACTAGTCTAATGCGA 57.327 34.615 0.00 0.00 37.50 5.10
8155 22886 6.182627 ACTGTTGTTGGTGATGATATGATGT 58.817 36.000 0.00 0.00 0.00 3.06
8192 22923 7.854422 CCATGTTGAACTCGATGATATCTTTTG 59.146 37.037 3.98 0.00 0.00 2.44
8193 22924 7.554118 ACCATGTTGAACTCGATGATATCTTTT 59.446 33.333 3.98 0.00 0.00 2.27
8420 23154 5.050490 CCACGATTAGGAGACAGGTTTATG 58.950 45.833 0.00 0.00 0.00 1.90
8423 23157 2.236395 CCCACGATTAGGAGACAGGTTT 59.764 50.000 0.00 0.00 0.00 3.27
8571 23305 4.013728 TCAATTGTTAGCTTACGGCCAAT 58.986 39.130 2.24 0.00 43.05 3.16


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

AutoCloner maintained by Alex Coulton.