Multiple sequence alignment - TraesCS7A01G009400

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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 TraesCS7A01G009400 chr7A 100.000 4994 0 0 1 4994 4071660 4066667 0.000000e+00 9223.0
1 TraesCS7A01G009400 chr7A 79.557 949 181 12 1690 2633 4254345 4253405 0.000000e+00 665.0
2 TraesCS7A01G009400 chr7A 79.433 953 179 17 1696 2638 29664668 29663723 0.000000e+00 658.0
3 TraesCS7A01G009400 chr7A 77.039 662 131 13 3291 3946 29662750 29662104 1.320000e-95 361.0
4 TraesCS7A01G009400 chr7A 94.737 114 5 1 4882 4994 4036942 4036829 5.140000e-40 176.0
5 TraesCS7A01G009400 chr7A 92.000 100 8 0 1303 1402 4254755 4254656 1.870000e-29 141.0
6 TraesCS7A01G009400 chr7A 90.000 100 10 0 1303 1402 29665099 29665000 4.060000e-26 130.0
7 TraesCS7A01G009400 chr4A 90.100 2010 127 38 683 2658 739272617 739274588 0.000000e+00 2543.0
8 TraesCS7A01G009400 chr4A 90.513 1560 108 17 2812 4350 739274997 739276537 0.000000e+00 2025.0
9 TraesCS7A01G009400 chr4A 92.453 636 33 9 1 621 739271944 739272579 0.000000e+00 894.0
10 TraesCS7A01G009400 chr4A 80.355 957 174 14 1684 2633 739130002 739130951 0.000000e+00 713.0
11 TraesCS7A01G009400 chr4A 81.024 859 150 11 1701 2555 738889299 738888450 0.000000e+00 671.0
12 TraesCS7A01G009400 chr4A 90.843 415 28 7 4449 4861 739276848 739277254 9.450000e-152 547.0
13 TraesCS7A01G009400 chr4A 76.538 878 180 14 1700 2556 739066047 739066919 1.640000e-124 457.0
14 TraesCS7A01G009400 chr4A 76.546 857 176 20 1713 2552 738961924 738962772 3.550000e-121 446.0
15 TraesCS7A01G009400 chr4A 90.071 141 8 3 4859 4994 739278400 739278539 1.430000e-40 178.0
16 TraesCS7A01G009400 chr4A 91.150 113 10 0 4026 4138 697763763 697763875 2.410000e-33 154.0
17 TraesCS7A01G009400 chr4A 91.262 103 8 1 1313 1415 739129605 739129706 6.740000e-29 139.0
18 TraesCS7A01G009400 chr4A 93.407 91 6 0 1310 1400 738961150 738961240 8.720000e-28 135.0
19 TraesCS7A01G009400 chr7D 92.771 1494 93 12 2812 4293 4290078 4288588 0.000000e+00 2146.0
20 TraesCS7A01G009400 chr7D 92.249 1316 61 18 117 1403 4293038 4291735 0.000000e+00 1827.0
21 TraesCS7A01G009400 chr7D 90.008 1261 98 14 3114 4367 29600033 29601272 0.000000e+00 1605.0
22 TraesCS7A01G009400 chr7D 90.596 1191 82 18 1489 2659 4291692 4290512 0.000000e+00 1552.0
23 TraesCS7A01G009400 chr7D 90.123 648 55 7 1684 2327 29581919 29582561 0.000000e+00 833.0
24 TraesCS7A01G009400 chr7D 81.002 858 152 9 1701 2555 4794077 4794926 0.000000e+00 671.0
25 TraesCS7A01G009400 chr7D 79.332 958 179 18 1684 2633 4425739 4424793 0.000000e+00 654.0
26 TraesCS7A01G009400 chr7D 79.307 923 172 14 1700 2613 4414107 4413195 3.280000e-176 628.0
27 TraesCS7A01G009400 chr7D 91.874 443 27 9 4438 4876 4287720 4287283 1.190000e-170 610.0
28 TraesCS7A01G009400 chr7D 92.262 336 19 4 4367 4701 29601311 29601640 2.100000e-128 470.0
29 TraesCS7A01G009400 chr7D 77.795 662 126 13 3291 3946 4424235 4423589 6.060000e-104 388.0
30 TraesCS7A01G009400 chr7D 77.238 659 135 10 3291 3946 29403470 29402824 6.110000e-99 372.0
31 TraesCS7A01G009400 chr7D 90.726 248 18 3 2812 3054 29599799 29600046 4.820000e-85 326.0
32 TraesCS7A01G009400 chr7D 93.333 105 4 1 4706 4810 29601567 29601668 8.660000e-33 152.0
33 TraesCS7A01G009400 chr7D 91.743 109 8 1 1 108 4293195 4293087 3.110000e-32 150.0
34 TraesCS7A01G009400 chr7D 90.099 101 10 0 4894 4994 29603599 29603699 1.130000e-26 132.0
35 TraesCS7A01G009400 chr7D 90.722 97 9 0 1310 1406 4654394 4654298 4.060000e-26 130.0
36 TraesCS7A01G009400 chr7D 89.000 100 11 0 1303 1402 4426139 4426040 1.890000e-24 124.0
37 TraesCS7A01G009400 chr7D 93.590 78 5 0 4366 4443 4288234 4288157 3.160000e-22 117.0
38 TraesCS7A01G009400 chr7D 94.521 73 4 0 4709 4781 4287532 4287460 4.090000e-21 113.0
39 TraesCS7A01G009400 chr7D 89.535 86 9 0 1318 1403 4518596 4518511 5.290000e-20 110.0
40 TraesCS7A01G009400 chr7D 100.000 28 0 0 2707 2734 29599442 29599469 9.000000e-03 52.8
41 TraesCS7A01G009400 chr6B 91.818 110 9 0 4026 4135 454457614 454457723 2.410000e-33 154.0
42 TraesCS7A01G009400 chr3B 91.818 110 9 0 4026 4135 241364649 241364758 2.410000e-33 154.0
43 TraesCS7A01G009400 chr3B 87.611 113 14 0 4026 4138 8107950 8107838 1.130000e-26 132.0
44 TraesCS7A01G009400 chr2B 91.150 113 10 0 4026 4138 588268162 588268050 2.410000e-33 154.0
45 TraesCS7A01G009400 chr6D 89.189 111 12 0 4026 4136 158213429 158213539 6.740000e-29 139.0
46 TraesCS7A01G009400 chr1B 78.767 146 25 5 4428 4571 478476485 478476344 5.320000e-15 93.5


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 TraesCS7A01G009400 chr7A 4066667 4071660 4993 True 9223.000000 9223 100.000000 1 4994 1 chr7A.!!$R2 4993
1 TraesCS7A01G009400 chr7A 4253405 4254755 1350 True 403.000000 665 85.778500 1303 2633 2 chr7A.!!$R3 1330
2 TraesCS7A01G009400 chr7A 29662104 29665099 2995 True 383.000000 658 82.157333 1303 3946 3 chr7A.!!$R4 2643
3 TraesCS7A01G009400 chr4A 739271944 739278539 6595 False 1237.400000 2543 90.796000 1 4994 5 chr4A.!!$F5 4993
4 TraesCS7A01G009400 chr4A 738888450 738889299 849 True 671.000000 671 81.024000 1701 2555 1 chr4A.!!$R1 854
5 TraesCS7A01G009400 chr4A 739066047 739066919 872 False 457.000000 457 76.538000 1700 2556 1 chr4A.!!$F2 856
6 TraesCS7A01G009400 chr4A 739129605 739130951 1346 False 426.000000 713 85.808500 1313 2633 2 chr4A.!!$F4 1320
7 TraesCS7A01G009400 chr4A 738961150 738962772 1622 False 290.500000 446 84.976500 1310 2552 2 chr4A.!!$F3 1242
8 TraesCS7A01G009400 chr7D 4287283 4293195 5912 True 930.714286 2146 92.477714 1 4876 7 chr7D.!!$R5 4875
9 TraesCS7A01G009400 chr7D 29581919 29582561 642 False 833.000000 833 90.123000 1684 2327 1 chr7D.!!$F2 643
10 TraesCS7A01G009400 chr7D 4794077 4794926 849 False 671.000000 671 81.002000 1701 2555 1 chr7D.!!$F1 854
11 TraesCS7A01G009400 chr7D 4413195 4414107 912 True 628.000000 628 79.307000 1700 2613 1 chr7D.!!$R1 913
12 TraesCS7A01G009400 chr7D 29599442 29603699 4257 False 456.300000 1605 92.738000 2707 4994 6 chr7D.!!$F3 2287
13 TraesCS7A01G009400 chr7D 4423589 4426139 2550 True 388.666667 654 82.042333 1303 3946 3 chr7D.!!$R6 2643
14 TraesCS7A01G009400 chr7D 29402824 29403470 646 True 372.000000 372 77.238000 3291 3946 1 chr7D.!!$R4 655

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
626 683 0.321122 GATGGAGGCCTCGCTTATGG 60.321 60.000 26.36 0.0 0.0 2.74 F
1293 1397 1.067060 CGAGCGGACCAGAACATCATA 59.933 52.381 0.00 0.0 0.0 2.15 F
2647 3367 1.043816 ATGCTCGTACTCCCTCCATG 58.956 55.000 0.00 0.0 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 1721 1.552578 TGGTACGTAGCCATGTCAGT 58.447 50.000 21.20 0.00 0.00 3.41 R
2786 4049 1.735018 TGGCATGCACGTGTATAACAC 59.265 47.619 19.02 9.84 45.26 3.32 R
4082 5406 0.040058 TGCAGATGACATTTGGGGCT 59.960 50.000 7.97 0.00 0.00 5.19 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
101 103 6.085121 TGTCGTTTAACATATTGTGTAGCG 57.915 37.500 0.00 0.00 41.14 4.26
199 245 5.023920 CACTCGTTGTCATGTATTTGCATC 58.976 41.667 0.00 0.00 0.00 3.91
259 305 6.183360 GGATGTTGTGATAAATGAGGTTGGAG 60.183 42.308 0.00 0.00 0.00 3.86
285 331 1.994507 GCTAGTCTTCAGCGGCGAGA 61.995 60.000 12.98 4.36 0.00 4.04
363 409 2.570098 TGTCTCCCTCTACCTACCTCA 58.430 52.381 0.00 0.00 0.00 3.86
366 412 1.854280 CTCCCTCTACCTACCTCACCT 59.146 57.143 0.00 0.00 0.00 4.00
378 424 3.544698 ACCTCACCTTCCTCTCTTGTA 57.455 47.619 0.00 0.00 0.00 2.41
379 425 3.436243 ACCTCACCTTCCTCTCTTGTAG 58.564 50.000 0.00 0.00 0.00 2.74
407 458 8.445588 TCTTCATCTCCCTTTACCTTTTTAACT 58.554 33.333 0.00 0.00 0.00 2.24
442 493 2.781667 AGGAGCCAGAACCCATTAGAT 58.218 47.619 0.00 0.00 0.00 1.98
447 498 3.459598 AGCCAGAACCCATTAGATAAGCA 59.540 43.478 0.00 0.00 0.00 3.91
449 500 4.217118 GCCAGAACCCATTAGATAAGCATG 59.783 45.833 0.00 0.00 0.00 4.06
451 502 5.471456 CCAGAACCCATTAGATAAGCATGAC 59.529 44.000 0.00 0.00 0.00 3.06
456 507 8.995027 AACCCATTAGATAAGCATGACAATAA 57.005 30.769 0.00 0.00 0.00 1.40
457 508 8.995027 ACCCATTAGATAAGCATGACAATAAA 57.005 30.769 0.00 0.00 0.00 1.40
508 560 1.160137 CTGCAACCTAGTCCAAGCAC 58.840 55.000 0.00 0.00 0.00 4.40
621 678 4.804420 TGGGATGGAGGCCTCGCT 62.804 66.667 26.36 15.84 0.00 4.93
622 679 3.483869 GGGATGGAGGCCTCGCTT 61.484 66.667 26.36 16.43 0.00 4.68
623 680 2.140792 GGGATGGAGGCCTCGCTTA 61.141 63.158 26.36 12.87 0.00 3.09
624 681 1.484444 GGGATGGAGGCCTCGCTTAT 61.484 60.000 26.36 16.90 0.00 1.73
626 683 0.321122 GATGGAGGCCTCGCTTATGG 60.321 60.000 26.36 0.00 0.00 2.74
727 808 1.855360 CGAAGTCGCTAGAAATGCCTC 59.145 52.381 0.00 0.00 0.00 4.70
775 864 1.971284 CGTCATTTTCGTCGTCACGTA 59.029 47.619 0.00 0.00 46.76 3.57
850 942 2.543777 TGCCGCTCTTGTTCTAAAGT 57.456 45.000 0.00 0.00 0.00 2.66
856 948 4.499183 CGCTCTTGTTCTAAAGTCTCCAT 58.501 43.478 0.00 0.00 0.00 3.41
1019 1123 3.760035 GGCTCCTCGAGACCGCAA 61.760 66.667 15.71 0.00 30.04 4.85
1053 1157 4.042062 TCAAAAGATTTCCTCCTGAGCTCA 59.958 41.667 17.19 17.19 0.00 4.26
1062 1166 2.659016 CTGAGCTCAGGAACGGCA 59.341 61.111 32.30 0.55 40.20 5.69
1213 1317 2.825836 CCATGGTGGCGCTCTTCC 60.826 66.667 7.64 5.56 0.00 3.46
1293 1397 1.067060 CGAGCGGACCAGAACATCATA 59.933 52.381 0.00 0.00 0.00 2.15
1297 1401 2.732366 CGGACCAGAACATCATAGTCG 58.268 52.381 0.00 0.00 0.00 4.18
1299 1403 2.101582 GGACCAGAACATCATAGTCGCT 59.898 50.000 0.00 0.00 0.00 4.93
1403 1507 6.698380 AGAAGAACTACATGAACGGTATGTT 58.302 36.000 0.00 0.00 45.61 2.71
1422 1527 8.832521 GGTATGTTACGGAATTCATTGTCATTA 58.167 33.333 7.93 0.00 0.00 1.90
1453 1558 7.452880 TCGAATTGTTGAATTTGGAGATTCT 57.547 32.000 0.00 0.00 37.04 2.40
1455 1560 8.668353 TCGAATTGTTGAATTTGGAGATTCTAG 58.332 33.333 0.00 0.00 37.04 2.43
1502 1680 1.522668 CTTGTTCCATGCACGGAGAA 58.477 50.000 0.01 0.00 36.12 2.87
1520 1698 3.809905 AGAAAGAAAGAAACTGACCGCT 58.190 40.909 0.00 0.00 0.00 5.52
1527 1705 1.602377 AGAAACTGACCGCTTTTTCCG 59.398 47.619 0.00 0.00 0.00 4.30
1536 1721 1.265635 CCGCTTTTTCCGTGTTGATGA 59.734 47.619 0.00 0.00 0.00 2.92
1635 1831 4.767255 CTGCCCAGCGGTCTGTCC 62.767 72.222 0.00 0.00 38.66 4.02
1647 1843 3.967203 GGTCTGTCCGTCTCTATGTAC 57.033 52.381 0.00 0.00 0.00 2.90
1648 1844 3.543665 GGTCTGTCCGTCTCTATGTACT 58.456 50.000 0.00 0.00 0.00 2.73
1649 1845 3.946558 GGTCTGTCCGTCTCTATGTACTT 59.053 47.826 0.00 0.00 0.00 2.24
1650 1846 5.121811 GGTCTGTCCGTCTCTATGTACTTA 58.878 45.833 0.00 0.00 0.00 2.24
1717 2417 3.413846 CATGCAGCTCCCATGTACTAT 57.586 47.619 13.33 0.00 36.26 2.12
1873 2576 2.158959 CGACATCCACGGCGTTCTC 61.159 63.158 11.19 0.00 0.00 2.87
2281 2996 1.508088 CGGCAGCAACAATTCCTCC 59.492 57.895 0.00 0.00 0.00 4.30
2350 3068 1.886313 CTACTACGCGCTCGGGAGA 60.886 63.158 5.73 0.26 40.69 3.71
2354 3072 1.338484 ACTACGCGCTCGGGAGATATA 60.338 52.381 5.73 0.00 40.69 0.86
2554 3274 2.288025 GGCTTCGGTCCAGGTACCA 61.288 63.158 15.94 0.00 39.71 3.25
2559 3279 3.528532 CTTCGGTCCAGGTACCATTAAC 58.471 50.000 15.94 6.44 39.71 2.01
2572 3292 7.763985 CAGGTACCATTAACATGCATCGATATA 59.236 37.037 15.94 0.00 0.00 0.86
2578 3298 8.676401 CCATTAACATGCATCGATATAATTCCA 58.324 33.333 0.00 0.00 0.00 3.53
2589 3309 9.559958 CATCGATATAATTCCATTTTACCTTGC 57.440 33.333 0.00 0.00 0.00 4.01
2616 3336 9.705290 GTTTACCATCAACCATTAGTTTCATTT 57.295 29.630 0.00 0.00 36.18 2.32
2647 3367 1.043816 ATGCTCGTACTCCCTCCATG 58.956 55.000 0.00 0.00 0.00 3.66
2650 3370 1.207329 GCTCGTACTCCCTCCATGTTT 59.793 52.381 0.00 0.00 0.00 2.83
2651 3371 2.893637 CTCGTACTCCCTCCATGTTTG 58.106 52.381 0.00 0.00 0.00 2.93
2654 3407 3.000727 CGTACTCCCTCCATGTTTGTTC 58.999 50.000 0.00 0.00 0.00 3.18
2656 3409 1.271379 ACTCCCTCCATGTTTGTTCGG 60.271 52.381 0.00 0.00 0.00 4.30
2690 3443 7.280876 AGCTTGAGTTATATTTCATCGAAAGCA 59.719 33.333 10.30 0.00 34.92 3.91
2691 3444 7.374491 GCTTGAGTTATATTTCATCGAAAGCAC 59.626 37.037 0.00 0.00 34.92 4.40
2738 3491 9.668497 ACAAAGTTTCTAAACATATACTCCCTC 57.332 33.333 8.21 0.00 41.30 4.30
2741 3494 8.840200 AGTTTCTAAACATATACTCCCTCTGA 57.160 34.615 8.21 0.00 41.30 3.27
2743 3496 9.699703 GTTTCTAAACATATACTCCCTCTGATC 57.300 37.037 0.74 0.00 38.74 2.92
2744 3497 8.423906 TTCTAAACATATACTCCCTCTGATCC 57.576 38.462 0.00 0.00 0.00 3.36
2747 3500 9.480861 CTAAACATATACTCCCTCTGATCCATA 57.519 37.037 0.00 0.00 0.00 2.74
2748 3501 8.742125 AAACATATACTCCCTCTGATCCATAA 57.258 34.615 0.00 0.00 0.00 1.90
2749 3502 8.923838 AACATATACTCCCTCTGATCCATAAT 57.076 34.615 0.00 0.00 0.00 1.28
2806 4069 1.735018 GTGTTATACACGTGCATGCCA 59.265 47.619 17.22 6.77 39.53 4.92
2807 4070 2.160615 GTGTTATACACGTGCATGCCAA 59.839 45.455 17.22 0.00 39.53 4.52
2808 4071 2.418280 TGTTATACACGTGCATGCCAAG 59.582 45.455 17.22 8.92 0.00 3.61
2809 4072 2.394930 TATACACGTGCATGCCAAGT 57.605 45.000 17.22 9.61 36.56 3.16
2810 4073 2.394930 ATACACGTGCATGCCAAGTA 57.605 45.000 17.22 12.85 34.30 2.24
2887 4151 6.737254 ATGTGTTGTAGGAAAATAGGTTCG 57.263 37.500 0.00 0.00 0.00 3.95
3023 4293 0.978151 TTGAGGCACGGGTTAGCTTA 59.022 50.000 0.00 0.00 0.00 3.09
3025 4295 1.557832 TGAGGCACGGGTTAGCTTAAT 59.442 47.619 0.00 0.00 0.00 1.40
3026 4296 2.026636 TGAGGCACGGGTTAGCTTAATT 60.027 45.455 0.00 0.00 0.00 1.40
3028 4298 2.752903 AGGCACGGGTTAGCTTAATTTG 59.247 45.455 0.00 0.00 0.00 2.32
3029 4299 2.490509 GGCACGGGTTAGCTTAATTTGT 59.509 45.455 0.00 0.00 0.00 2.83
3030 4300 3.427098 GGCACGGGTTAGCTTAATTTGTC 60.427 47.826 0.00 0.00 0.00 3.18
3034 4304 4.007659 CGGGTTAGCTTAATTTGTCCTGT 58.992 43.478 0.00 0.00 0.00 4.00
3036 4306 4.398358 GGGTTAGCTTAATTTGTCCTGTCC 59.602 45.833 0.00 0.00 0.00 4.02
3037 4307 4.094442 GGTTAGCTTAATTTGTCCTGTCCG 59.906 45.833 0.00 0.00 0.00 4.79
3091 4376 2.332063 ATGCATAGGTCGGAGGTTTG 57.668 50.000 0.00 0.00 0.00 2.93
3101 4386 2.879026 GTCGGAGGTTTGCTCTCTTTTT 59.121 45.455 0.00 0.00 0.00 1.94
3131 4418 4.580167 ACAAGCTAAGCACACAAAATCAGA 59.420 37.500 0.00 0.00 0.00 3.27
3133 4420 5.972107 AGCTAAGCACACAAAATCAGAAT 57.028 34.783 0.00 0.00 0.00 2.40
3134 4421 7.040478 ACAAGCTAAGCACACAAAATCAGAATA 60.040 33.333 0.00 0.00 0.00 1.75
3137 4424 7.972277 AGCTAAGCACACAAAATCAGAATATTG 59.028 33.333 0.00 0.00 0.00 1.90
3174 4463 6.720012 ATTTTGTTTGTGTGGTCACTTTTC 57.280 33.333 2.66 0.00 44.14 2.29
3178 4467 6.576662 TGTTTGTGTGGTCACTTTTCTTAA 57.423 33.333 2.66 0.00 44.14 1.85
3179 4468 7.164230 TGTTTGTGTGGTCACTTTTCTTAAT 57.836 32.000 2.66 0.00 44.14 1.40
3205 4496 3.438216 TCAATGGAGATTGCAAGACCA 57.562 42.857 19.23 19.23 39.16 4.02
3370 4693 1.238625 GCCGGTAGAGGAGATCGAGG 61.239 65.000 1.90 0.00 0.00 4.63
3690 5013 0.321564 CCCACTTCTGCCATGACGAA 60.322 55.000 0.00 0.00 0.00 3.85
3724 5047 2.564771 GGGCGAATGATGTCATGAAGA 58.435 47.619 0.00 0.00 36.56 2.87
3726 5049 3.461061 GGCGAATGATGTCATGAAGAGA 58.539 45.455 0.00 0.00 36.56 3.10
3862 5186 1.029947 GGTGTACCCAATGGAAGCCG 61.030 60.000 0.00 0.00 34.81 5.52
3903 5227 1.178276 ACCTTTTCAACAACGCCACA 58.822 45.000 0.00 0.00 0.00 4.17
4003 5327 3.415370 GACGACTCGTAGCTTCAGTAAC 58.585 50.000 3.53 0.00 41.37 2.50
4041 5365 2.897823 ATGGGGTTAGGATCCTCTGT 57.102 50.000 20.22 0.00 0.00 3.41
4043 5367 3.788116 TGGGGTTAGGATCCTCTGTAA 57.212 47.619 20.22 3.67 0.00 2.41
4082 5406 4.248842 CACTGCCGTGTGGACCCA 62.249 66.667 0.00 0.00 37.49 4.51
4089 5413 3.897122 GTGTGGACCCAGCCCCAA 61.897 66.667 0.00 0.00 33.69 4.12
4098 5422 0.032813 CCCAGCCCCAAATGTCATCT 60.033 55.000 0.00 0.00 0.00 2.90
4105 5429 3.559069 CCCCAAATGTCATCTGCACTAT 58.441 45.455 0.00 0.00 0.00 2.12
4121 5445 4.038763 TGCACTATAGCACCATACAGTACC 59.961 45.833 0.00 0.00 40.11 3.34
4227 5551 0.808453 GGAGTGTTATGCGCGCCTTA 60.808 55.000 30.77 17.72 43.04 2.69
4228 5552 1.217882 GAGTGTTATGCGCGCCTTAT 58.782 50.000 30.77 18.34 0.00 1.73
4261 5587 6.827586 TTTCTGTTAGGTGTGTTTGTCTTT 57.172 33.333 0.00 0.00 0.00 2.52
4332 5663 5.669477 TGGCTTGGTTATCATTTTATTGGC 58.331 37.500 0.00 0.00 0.00 4.52
4340 5671 6.424812 GGTTATCATTTTATTGGCTTGGATGC 59.575 38.462 0.00 0.00 0.00 3.91
4399 6011 4.615223 GCAAACATCATCATATGCAGCGAT 60.615 41.667 0.00 0.00 34.10 4.58
4567 6623 5.510861 GCGAGGGAGCATAGTATTAAAGGAA 60.511 44.000 0.00 0.00 37.05 3.36
4607 6663 6.593978 CACATCTAGAGTGTGTTAAGTTTGC 58.406 40.000 19.15 0.00 41.48 3.68
4635 6691 0.731514 TCGCTGCCTTCGTAAGTTCG 60.732 55.000 0.00 0.00 39.48 3.95
4641 6697 3.916761 TGCCTTCGTAAGTTCGTAATGT 58.083 40.909 0.00 0.00 39.48 2.71
4672 6728 6.533730 ACATAGAAAGGTCATCAAGTGTTGA 58.466 36.000 0.00 0.00 45.01 3.18
4704 6760 5.007234 GCCACACGTAATGTATAAATGCTGA 59.993 40.000 0.00 0.00 40.64 4.26
4705 6761 6.293407 GCCACACGTAATGTATAAATGCTGAT 60.293 38.462 0.00 0.00 40.64 2.90
4707 6763 7.587392 CCACACGTAATGTATAAATGCTGATTG 59.413 37.037 0.00 0.00 40.64 2.67
4769 6826 0.888285 TTGATGCATGTGCCACACGA 60.888 50.000 2.46 0.00 41.18 4.35
4820 6877 7.193595 ACATCGACTTTAAGTGTTTTTCCTTG 58.806 34.615 0.93 0.00 0.00 3.61
4876 8310 9.901724 CTCTGTATCACGTAAAACAATCATAAC 57.098 33.333 0.00 0.00 0.00 1.89
4892 8326 9.709495 ACAATCATAACACTTATTTTGCATGTT 57.291 25.926 5.09 5.09 37.30 2.71
4961 8907 6.500684 TGAAGAAAATGCTCACCTTGTATC 57.499 37.500 0.00 0.00 0.00 2.24
4985 8932 5.845103 TGAAAATGTTCAGTGTGCATTGAT 58.155 33.333 12.91 7.64 38.88 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 7.272978 GGACTACCTTAATCTCATGTAAAGCA 58.727 38.462 0.00 0.00 0.00 3.91
25 26 2.802816 GTCATCAATCCATGCGGACTAC 59.197 50.000 0.00 0.00 46.79 2.73
75 77 8.322428 CGCTACACAATATGTTAAACGACATAA 58.678 33.333 2.28 0.00 43.52 1.90
150 192 9.362151 GTATGAAATAGAGAGATATAGAGGGGG 57.638 40.741 0.00 0.00 0.00 5.40
199 245 5.741388 AAAGAGTACAACAAAGCTGACAG 57.259 39.130 0.00 0.00 0.00 3.51
259 305 0.804156 GCTGAAGACTAGCGAGTGGC 60.804 60.000 3.45 0.00 44.05 5.01
363 409 3.466395 AGAGCTACAAGAGAGGAAGGT 57.534 47.619 0.00 0.00 0.00 3.50
366 412 5.268387 AGATGAAGAGCTACAAGAGAGGAA 58.732 41.667 0.00 0.00 0.00 3.36
378 424 3.730269 AGGTAAAGGGAGATGAAGAGCT 58.270 45.455 0.00 0.00 0.00 4.09
379 425 4.495690 AAGGTAAAGGGAGATGAAGAGC 57.504 45.455 0.00 0.00 0.00 4.09
508 560 6.772605 TCATGATGATATGGGGTCTGTAAAG 58.227 40.000 0.00 0.00 0.00 1.85
621 678 0.107410 CCTGCAACCCTACGCCATAA 60.107 55.000 0.00 0.00 0.00 1.90
622 679 1.524961 CCTGCAACCCTACGCCATA 59.475 57.895 0.00 0.00 0.00 2.74
623 680 2.272146 CCTGCAACCCTACGCCAT 59.728 61.111 0.00 0.00 0.00 4.40
624 681 4.715523 GCCTGCAACCCTACGCCA 62.716 66.667 0.00 0.00 0.00 5.69
727 808 3.325201 GACCACGGCCAAGGTAGGG 62.325 68.421 15.61 0.52 38.50 3.53
775 864 8.136165 GGATTATCGATATTGACCGCTAATACT 58.864 37.037 5.84 0.00 30.45 2.12
936 1040 6.350629 ACGTTACCACTCTACCATTAAACT 57.649 37.500 0.00 0.00 0.00 2.66
937 1041 6.870439 AGAACGTTACCACTCTACCATTAAAC 59.130 38.462 0.00 0.00 0.00 2.01
1019 1123 2.969628 ATCTTTTGATCGGCTCGTCT 57.030 45.000 0.00 0.00 32.94 4.18
1025 1129 3.065925 CAGGAGGAAATCTTTTGATCGGC 59.934 47.826 0.00 0.00 38.40 5.54
1069 1173 3.414700 GCTGCGTGACTTCACCGG 61.415 66.667 0.00 0.00 43.66 5.28
1213 1317 4.803426 GAGGAGCGCGTGGGTGAG 62.803 72.222 8.43 0.00 0.00 3.51
1281 1385 1.863454 GCAGCGACTATGATGTTCTGG 59.137 52.381 0.00 0.00 0.00 3.86
1403 1507 9.559732 AATGAGATAATGACAATGAATTCCGTA 57.440 29.630 2.27 0.00 0.00 4.02
1422 1527 7.829725 TCCAAATTCAACAATTCGAATGAGAT 58.170 30.769 12.25 0.00 32.27 2.75
1423 1528 7.174772 TCTCCAAATTCAACAATTCGAATGAGA 59.825 33.333 12.25 11.19 32.27 3.27
1453 1558 5.048921 CGTGCCGGAGAAAGAAGATATACTA 60.049 44.000 5.05 0.00 0.00 1.82
1455 1560 3.982058 CGTGCCGGAGAAAGAAGATATAC 59.018 47.826 5.05 0.00 0.00 1.47
1457 1562 2.693591 TCGTGCCGGAGAAAGAAGATAT 59.306 45.455 5.05 0.00 0.00 1.63
1487 1603 2.559698 TTCTTTCTCCGTGCATGGAA 57.440 45.000 27.33 15.79 37.64 3.53
1502 1680 4.983671 AAAAGCGGTCAGTTTCTTTCTT 57.016 36.364 0.00 0.00 0.00 2.52
1520 1698 3.942115 TGTCAGTCATCAACACGGAAAAA 59.058 39.130 0.00 0.00 0.00 1.94
1527 1705 2.430465 AGCCATGTCAGTCATCAACAC 58.570 47.619 0.00 0.00 34.09 3.32
1536 1721 1.552578 TGGTACGTAGCCATGTCAGT 58.447 50.000 21.20 0.00 0.00 3.41
1607 1796 4.457496 TGGGCAGCGAGCTAGTGC 62.457 66.667 11.11 11.11 44.79 4.40
1627 1816 3.543665 AGTACATAGAGACGGACAGACC 58.456 50.000 0.00 0.00 0.00 3.85
1646 1842 7.514721 TGAGGAGGTGTTTCAGTTAATTAAGT 58.485 34.615 0.00 0.00 0.00 2.24
1647 1843 7.979444 TGAGGAGGTGTTTCAGTTAATTAAG 57.021 36.000 0.00 0.00 0.00 1.85
1648 1844 8.754991 TTTGAGGAGGTGTTTCAGTTAATTAA 57.245 30.769 0.00 0.00 0.00 1.40
1649 1845 8.754991 TTTTGAGGAGGTGTTTCAGTTAATTA 57.245 30.769 0.00 0.00 0.00 1.40
1650 1846 7.654022 TTTTGAGGAGGTGTTTCAGTTAATT 57.346 32.000 0.00 0.00 0.00 1.40
1676 2026 7.763528 TGCATGTTGTGTTTCAGTTAGAATTTT 59.236 29.630 0.00 0.00 35.83 1.82
1678 2028 6.804677 TGCATGTTGTGTTTCAGTTAGAATT 58.195 32.000 0.00 0.00 35.83 2.17
1682 2032 3.976942 GCTGCATGTTGTGTTTCAGTTAG 59.023 43.478 0.00 0.00 0.00 2.34
2350 3068 1.871039 GTGTTGGTCGCCGCATTATAT 59.129 47.619 0.00 0.00 0.00 0.86
2354 3072 3.722295 CGTGTTGGTCGCCGCATT 61.722 61.111 0.00 0.00 0.00 3.56
2542 3260 2.949644 GCATGTTAATGGTACCTGGACC 59.050 50.000 14.36 4.48 40.21 4.46
2559 3279 9.507280 GGTAAAATGGAATTATATCGATGCATG 57.493 33.333 2.46 0.00 33.67 4.06
2572 3292 6.160684 GGTAAACGCAAGGTAAAATGGAATT 58.839 36.000 0.00 0.00 46.39 2.17
2578 3298 5.968528 TGATGGTAAACGCAAGGTAAAAT 57.031 34.783 0.00 0.00 46.39 1.82
2589 3309 6.904498 TGAAACTAATGGTTGATGGTAAACG 58.096 36.000 0.00 0.00 38.29 3.60
2616 3336 2.988010 ACGAGCATGCCTAATGAAGA 57.012 45.000 15.66 0.00 38.72 2.87
2647 3367 2.613730 GCTTCCTTAGCCGAACAAAC 57.386 50.000 0.00 0.00 44.48 2.93
2668 3421 7.841915 TGTGCTTTCGATGAAATATAACTCA 57.158 32.000 0.00 0.00 30.85 3.41
2670 3423 8.437360 TGATGTGCTTTCGATGAAATATAACT 57.563 30.769 0.00 0.00 30.85 2.24
2678 3431 8.984891 AAATTAAATGATGTGCTTTCGATGAA 57.015 26.923 0.00 0.00 0.00 2.57
2786 4049 1.735018 TGGCATGCACGTGTATAACAC 59.265 47.619 19.02 9.84 45.26 3.32
2787 4050 2.100605 TGGCATGCACGTGTATAACA 57.899 45.000 19.02 16.73 0.00 2.41
2788 4051 2.418628 ACTTGGCATGCACGTGTATAAC 59.581 45.455 19.02 14.46 0.00 1.89
2791 4054 2.394930 TACTTGGCATGCACGTGTAT 57.605 45.000 21.36 16.07 0.00 2.29
2792 4055 2.171341 TTACTTGGCATGCACGTGTA 57.829 45.000 21.36 14.09 0.00 2.90
2796 4059 2.252747 CACATTTACTTGGCATGCACG 58.747 47.619 21.36 9.26 0.00 5.34
2797 4060 2.230992 TCCACATTTACTTGGCATGCAC 59.769 45.455 21.36 9.64 32.37 4.57
2798 4061 2.523245 TCCACATTTACTTGGCATGCA 58.477 42.857 21.36 2.54 32.37 3.96
2800 4063 3.257873 TGGTTCCACATTTACTTGGCATG 59.742 43.478 0.00 0.00 32.37 4.06
2801 4064 3.505386 TGGTTCCACATTTACTTGGCAT 58.495 40.909 0.00 0.00 32.37 4.40
2803 4066 3.763897 AGATGGTTCCACATTTACTTGGC 59.236 43.478 0.00 0.00 32.37 4.52
2804 4067 4.380867 GCAGATGGTTCCACATTTACTTGG 60.381 45.833 0.00 0.00 0.00 3.61
2806 4069 3.763897 GGCAGATGGTTCCACATTTACTT 59.236 43.478 0.00 0.00 0.00 2.24
2807 4070 3.010584 AGGCAGATGGTTCCACATTTACT 59.989 43.478 0.00 0.00 0.00 2.24
2808 4071 3.356290 AGGCAGATGGTTCCACATTTAC 58.644 45.455 0.00 0.00 0.00 2.01
2809 4072 3.737559 AGGCAGATGGTTCCACATTTA 57.262 42.857 0.00 0.00 0.00 1.40
2810 4073 2.610438 AGGCAGATGGTTCCACATTT 57.390 45.000 0.00 0.00 0.00 2.32
2879 4143 5.634020 CGACTTTCTCTGTTTTCGAACCTAT 59.366 40.000 0.00 0.00 0.00 2.57
2883 4147 3.554731 ACCGACTTTCTCTGTTTTCGAAC 59.445 43.478 0.00 0.00 0.00 3.95
2886 4150 4.531659 AAACCGACTTTCTCTGTTTTCG 57.468 40.909 0.00 0.00 33.77 3.46
2887 4151 7.012959 ACTTAAACCGACTTTCTCTGTTTTC 57.987 36.000 0.00 0.00 37.46 2.29
3023 4293 5.008316 GTGTTTAGTTCGGACAGGACAAATT 59.992 40.000 0.00 0.00 0.00 1.82
3025 4295 3.872771 GTGTTTAGTTCGGACAGGACAAA 59.127 43.478 0.00 0.00 0.00 2.83
3026 4296 3.118702 TGTGTTTAGTTCGGACAGGACAA 60.119 43.478 0.00 0.00 0.00 3.18
3028 4298 2.798847 GTGTGTTTAGTTCGGACAGGAC 59.201 50.000 0.00 0.00 0.00 3.85
3029 4299 2.224113 GGTGTGTTTAGTTCGGACAGGA 60.224 50.000 0.00 0.00 0.00 3.86
3030 4300 2.140717 GGTGTGTTTAGTTCGGACAGG 58.859 52.381 0.00 0.00 0.00 4.00
3034 4304 3.142951 CCATTGGTGTGTTTAGTTCGGA 58.857 45.455 0.00 0.00 0.00 4.55
3036 4306 3.363575 CGACCATTGGTGTGTTTAGTTCG 60.364 47.826 14.44 2.38 35.25 3.95
3037 4307 3.562557 ACGACCATTGGTGTGTTTAGTTC 59.437 43.478 14.44 0.00 35.25 3.01
3101 4386 6.443934 TTGTGTGCTTAGCTTGTTCTAAAA 57.556 33.333 5.60 0.00 0.00 1.52
3103 4388 6.443934 TTTTGTGTGCTTAGCTTGTTCTAA 57.556 33.333 5.60 0.00 0.00 2.10
3104 4389 6.262049 TGATTTTGTGTGCTTAGCTTGTTCTA 59.738 34.615 5.60 0.00 0.00 2.10
3106 4391 5.280945 TGATTTTGTGTGCTTAGCTTGTTC 58.719 37.500 5.60 0.00 0.00 3.18
3117 4404 7.872163 TGAACAATATTCTGATTTTGTGTGC 57.128 32.000 0.00 0.00 37.45 4.57
3137 4424 9.260002 ACACAAACAAAATAGGAATGAATGAAC 57.740 29.630 0.00 0.00 0.00 3.18
3174 4463 7.494211 TGCAATCTCCATTGATTTCCATTAAG 58.506 34.615 0.00 0.00 41.97 1.85
3178 4467 5.659525 TCTTGCAATCTCCATTGATTTCCAT 59.340 36.000 0.00 0.00 41.97 3.41
3179 4468 5.018149 TCTTGCAATCTCCATTGATTTCCA 58.982 37.500 0.00 0.00 41.97 3.53
3229 4520 8.417106 TGCACATTGATACCAAGAACTTAAAAA 58.583 29.630 0.00 0.00 35.48 1.94
3370 4693 3.435186 GCTGTTGAAGCGGAGGGC 61.435 66.667 0.00 0.00 43.45 5.19
3690 5013 1.736645 CGCCCGAGACGACAACAAT 60.737 57.895 0.00 0.00 0.00 2.71
3724 5047 4.320456 CGTGCTGCCCACCACTCT 62.320 66.667 0.00 0.00 41.53 3.24
3741 5064 2.821366 CCATCGAGCACTGGCACC 60.821 66.667 0.00 0.00 44.61 5.01
3903 5227 2.039624 ACGGTGATGGAGGAGCCT 59.960 61.111 0.00 0.00 37.63 4.58
4003 5327 8.855804 ACCCCATTACCAGATTAGTATATAGG 57.144 38.462 0.00 0.00 0.00 2.57
4041 5365 3.069016 CCGTACTGCATGGTGGACTATTA 59.931 47.826 0.00 0.00 0.00 0.98
4043 5367 1.412710 CCGTACTGCATGGTGGACTAT 59.587 52.381 0.00 0.00 0.00 2.12
4082 5406 0.040058 TGCAGATGACATTTGGGGCT 59.960 50.000 7.97 0.00 0.00 5.19
4089 5413 4.141642 TGGTGCTATAGTGCAGATGACATT 60.142 41.667 0.84 0.00 44.20 2.71
4098 5422 4.038763 GGTACTGTATGGTGCTATAGTGCA 59.961 45.833 0.84 0.00 41.05 4.57
4105 5429 1.407618 CTGCGGTACTGTATGGTGCTA 59.592 52.381 3.10 0.00 0.00 3.49
4121 5445 3.657956 GAGGTTGAGATCCTCTGCG 57.342 57.895 4.91 0.00 45.56 5.18
4138 5462 1.067295 AAGTGACCCTCATTGCCAGA 58.933 50.000 0.00 0.00 0.00 3.86
4227 5551 3.634910 ACCTAACAGAAAAACCGCACAAT 59.365 39.130 0.00 0.00 0.00 2.71
4228 5552 3.018149 ACCTAACAGAAAAACCGCACAA 58.982 40.909 0.00 0.00 0.00 3.33
4288 5619 6.041979 AGCCAACACAAATAGAGTCCAAAATT 59.958 34.615 0.00 0.00 0.00 1.82
4340 5671 1.298563 CCGCAGCGTTAATGCATGG 60.299 57.895 21.31 14.83 44.05 3.66
4342 5673 2.114670 AGCCGCAGCGTTAATGCAT 61.115 52.632 21.31 0.00 46.67 3.96
4346 5677 1.234615 ACAACAGCCGCAGCGTTAAT 61.235 50.000 15.05 0.00 46.67 1.40
4410 6022 1.064952 GGTGGGCATTGTTGTATACGC 59.935 52.381 0.00 0.00 0.00 4.42
4411 6023 1.673920 GGGTGGGCATTGTTGTATACG 59.326 52.381 0.00 0.00 0.00 3.06
4444 6056 1.073763 TCTTGGGTTCATCCACAGGTG 59.926 52.381 0.00 0.00 36.38 4.00
4597 6653 5.846473 CAGCGAGTTCTAAAGCAAACTTAAC 59.154 40.000 0.00 0.00 35.90 2.01
4598 6654 5.560183 GCAGCGAGTTCTAAAGCAAACTTAA 60.560 40.000 0.00 0.00 35.90 1.85
4599 6655 4.084013 GCAGCGAGTTCTAAAGCAAACTTA 60.084 41.667 0.00 0.00 35.90 2.24
4600 6656 3.304057 GCAGCGAGTTCTAAAGCAAACTT 60.304 43.478 0.00 0.00 35.90 2.66
4607 6663 1.656095 CGAAGGCAGCGAGTTCTAAAG 59.344 52.381 0.00 0.00 0.00 1.85
4672 6728 1.672363 CATTACGTGTGGCAGATGCAT 59.328 47.619 0.00 0.00 44.36 3.96
4678 6734 5.007626 AGCATTTATACATTACGTGTGGCAG 59.992 40.000 0.00 0.00 42.24 4.85
4884 8318 9.941325 ATGGACATTATTAAAAAGAACATGCAA 57.059 25.926 0.00 0.00 0.00 4.08
4886 8320 8.819974 CCATGGACATTATTAAAAAGAACATGC 58.180 33.333 5.56 0.00 31.95 4.06
4887 8321 9.874205 ACCATGGACATTATTAAAAAGAACATG 57.126 29.630 21.47 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.