Multiple sequence alignment - TraesCS6A01G076900

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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 TraesCS6A01G076900 chr6A 100.000 4492 0 0 1 4492 46975807 46980298 0.000000e+00 8296.0
1 TraesCS6A01G076900 chr6A 84.906 265 27 9 1299 1554 608299796 608299536 5.770000e-64 255.0
2 TraesCS6A01G076900 chr6D 97.257 2880 65 4 1 2866 472101768 472098889 0.000000e+00 4868.0
3 TraesCS6A01G076900 chr6D 95.440 614 17 3 3189 3792 472098185 472097573 0.000000e+00 968.0
4 TraesCS6A01G076900 chr6D 91.646 395 30 3 1856 2248 438546424 438546817 1.100000e-150 544.0
5 TraesCS6A01G076900 chr6D 96.358 302 7 1 2898 3195 472098514 472098213 1.120000e-135 494.0
6 TraesCS6A01G076900 chr6D 87.578 322 16 9 1 299 300987872 300988192 7.150000e-93 351.0
7 TraesCS6A01G076900 chr6D 94.271 192 9 2 3854 4044 472097573 472097383 4.400000e-75 292.0
8 TraesCS6A01G076900 chr6D 90.751 173 6 7 1260 1424 301046882 301047052 5.850000e-54 222.0
9 TraesCS6A01G076900 chr1B 92.534 3228 168 30 1 3195 681552367 681549180 0.000000e+00 4558.0
10 TraesCS6A01G076900 chr1B 90.597 1021 60 10 2193 3195 681454989 681455991 0.000000e+00 1321.0
11 TraesCS6A01G076900 chr1B 93.712 652 26 6 3189 3826 681456019 681456669 0.000000e+00 963.0
12 TraesCS6A01G076900 chr1B 92.438 648 19 6 3199 3826 681549139 681548502 0.000000e+00 898.0
13 TraesCS6A01G076900 chr1B 93.434 198 13 0 3832 4029 681458491 681458688 1.220000e-75 294.0
14 TraesCS6A01G076900 chr1B 93.434 198 13 0 3832 4029 681530514 681530317 1.220000e-75 294.0
15 TraesCS6A01G076900 chr1B 87.795 254 20 5 3216 3459 456154991 456154739 2.040000e-73 287.0
16 TraesCS6A01G076900 chr1B 92.424 198 15 0 3832 4029 681528643 681528446 2.650000e-72 283.0
17 TraesCS6A01G076900 chr1B 91.414 198 17 0 3832 4029 681524952 681524755 5.730000e-69 272.0
18 TraesCS6A01G076900 chr1B 93.085 188 7 3 1664 1845 681454803 681454990 2.060000e-68 270.0
19 TraesCS6A01G076900 chr1B 90.909 198 18 0 3832 4029 681526796 681526599 2.660000e-67 267.0
20 TraesCS6A01G076900 chr1B 91.979 187 15 0 3843 4029 681532360 681532174 3.450000e-66 263.0
21 TraesCS6A01G076900 chr1B 87.179 156 16 2 2911 3062 456155525 456155370 1.660000e-39 174.0
22 TraesCS6A01G076900 chr1B 83.453 139 10 8 4336 4462 301264416 301264279 2.840000e-22 117.0
23 TraesCS6A01G076900 chr7B 88.965 2347 146 38 1 2257 94814244 94816567 0.000000e+00 2795.0
24 TraesCS6A01G076900 chr7B 88.155 878 58 16 1 851 16180850 16181708 0.000000e+00 1003.0
25 TraesCS6A01G076900 chr7B 90.994 533 44 3 3500 4029 94818422 94818953 0.000000e+00 715.0
26 TraesCS6A01G076900 chr7B 87.200 250 12 5 3197 3435 94818179 94818419 2.660000e-67 267.0
27 TraesCS6A01G076900 chr7B 93.064 173 12 0 3023 3195 94817954 94818126 2.070000e-63 254.0
28 TraesCS6A01G076900 chr3A 90.625 1792 101 22 1 1735 737371360 737369579 0.000000e+00 2316.0
29 TraesCS6A01G076900 chr3A 95.238 189 8 1 2069 2257 737369177 737368990 9.450000e-77 298.0
30 TraesCS6A01G076900 chr3A 79.706 340 53 13 4137 4466 57018569 57018236 9.720000e-57 231.0
31 TraesCS6A01G076900 chr3A 93.939 66 4 0 3033 3098 737367060 737366995 2.860000e-17 100.0
32 TraesCS6A01G076900 chr1A 89.746 1336 82 20 3 1308 556348503 556347193 0.000000e+00 1657.0
33 TraesCS6A01G076900 chr1A 90.585 393 36 1 1856 2248 426233486 426233877 1.850000e-143 520.0
34 TraesCS6A01G076900 chr1A 85.283 265 26 9 1299 1554 46238300 46238560 1.240000e-65 261.0
35 TraesCS6A01G076900 chr1A 82.298 322 30 8 328 646 46237856 46238153 2.070000e-63 254.0
36 TraesCS6A01G076900 chr1A 79.868 303 40 14 4174 4466 262833966 262834257 7.620000e-48 202.0
37 TraesCS6A01G076900 chr1A 88.514 148 13 2 2911 3054 426234544 426234691 4.620000e-40 176.0
38 TraesCS6A01G076900 chr1A 85.417 144 19 2 3210 3351 455026137 455026280 1.010000e-31 148.0
39 TraesCS6A01G076900 chr1D 93.376 785 43 4 530 1306 469532387 469531604 0.000000e+00 1153.0
40 TraesCS6A01G076900 chr1D 90.920 848 62 7 3197 4032 469519212 469518368 0.000000e+00 1125.0
41 TraesCS6A01G076900 chr1D 94.700 434 21 2 1825 2257 469530941 469530509 0.000000e+00 673.0
42 TraesCS6A01G076900 chr1D 88.081 495 31 7 2712 3195 469519742 469519265 3.030000e-156 562.0
43 TraesCS6A01G076900 chr1D 86.253 451 30 12 1304 1728 469531465 469531021 1.140000e-125 460.0
44 TraesCS6A01G076900 chr1D 94.268 157 9 0 2488 2644 469519908 469519752 1.610000e-59 241.0
45 TraesCS6A01G076900 chr1D 87.324 142 17 1 3210 3350 355168204 355168345 1.290000e-35 161.0
46 TraesCS6A01G076900 chr1D 75.783 351 47 24 4139 4463 52325504 52325842 4.680000e-30 143.0
47 TraesCS6A01G076900 chr6B 88.771 944 64 14 126 1031 650654070 650655009 0.000000e+00 1118.0
48 TraesCS6A01G076900 chr6B 92.199 423 27 4 4074 4491 80846419 80845998 1.080000e-165 593.0
49 TraesCS6A01G076900 chr6B 85.714 511 50 17 1046 1554 650654995 650655484 6.660000e-143 518.0
50 TraesCS6A01G076900 chr6B 90.213 235 17 3 4233 4466 80968657 80968428 7.300000e-78 302.0
51 TraesCS6A01G076900 chr6B 88.000 200 22 2 4046 4243 80969220 80969021 7.510000e-58 235.0
52 TraesCS6A01G076900 chr6B 94.444 126 7 0 1 126 650653910 650654035 1.270000e-45 195.0
53 TraesCS6A01G076900 chr5B 87.725 945 73 15 126 1031 433191323 433192263 0.000000e+00 1062.0
54 TraesCS6A01G076900 chr5B 87.066 518 51 14 1046 1554 433192249 433192759 5.040000e-159 571.0
55 TraesCS6A01G076900 chr5B 94.215 121 6 1 7 126 433191168 433191288 2.760000e-42 183.0
56 TraesCS6A01G076900 chrUn 91.832 404 30 3 4090 4491 27021733 27021331 1.090000e-155 560.0
57 TraesCS6A01G076900 chrUn 92.098 367 26 3 4090 4454 27158512 27158877 8.620000e-142 514.0
58 TraesCS6A01G076900 chr2A 83.912 547 61 17 2934 3459 14939104 14938564 8.680000e-137 497.0
59 TraesCS6A01G076900 chr2A 90.741 54 5 0 4210 4263 14976163 14976110 6.230000e-09 73.1
60 TraesCS6A01G076900 chr4B 89.059 393 37 2 1856 2248 527742007 527742393 2.430000e-132 483.0
61 TraesCS6A01G076900 chr4B 89.295 383 35 2 1856 2238 438149824 438149448 4.070000e-130 475.0
62 TraesCS6A01G076900 chr4B 90.785 293 25 2 1846 2138 8268524 8268814 1.520000e-104 390.0
63 TraesCS6A01G076900 chr4B 92.481 266 19 1 1983 2248 69296778 69296514 3.280000e-101 379.0
64 TraesCS6A01G076900 chr4B 83.854 384 27 14 1588 1939 527741642 527742022 2.590000e-87 333.0
65 TraesCS6A01G076900 chr4B 87.739 261 20 6 3216 3466 438147901 438147643 1.220000e-75 294.0
66 TraesCS6A01G076900 chr4B 87.739 261 20 7 3216 3466 527744285 527744543 1.220000e-75 294.0
67 TraesCS6A01G076900 chr4B 83.588 262 15 11 1588 1844 438150168 438149930 2.100000e-53 220.0
68 TraesCS6A01G076900 chr7A 83.882 304 32 11 1552 1844 506129274 506128977 1.590000e-69 274.0
69 TraesCS6A01G076900 chr7A 96.154 78 3 0 126 203 675065001 675064924 1.310000e-25 128.0
70 TraesCS6A01G076900 chr3B 82.716 324 29 11 326 646 682065185 682064886 3.450000e-66 263.0
71 TraesCS6A01G076900 chr3B 87.342 79 8 2 4386 4463 70572132 70572209 6.190000e-14 89.8
72 TraesCS6A01G076900 chr2B 84.962 266 24 12 1299 1554 335377458 335377717 5.770000e-64 255.0
73 TraesCS6A01G076900 chr7D 79.726 365 35 16 1619 1951 426850225 426850582 1.260000e-55 228.0
74 TraesCS6A01G076900 chr5A 82.707 266 28 13 1299 1554 465298351 465298608 2.100000e-53 220.0


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 TraesCS6A01G076900 chr6A 46975807 46980298 4491 False 8296.000000 8296 100.000000 1 4492 1 chr6A.!!$F1 4491
1 TraesCS6A01G076900 chr6D 472097383 472101768 4385 True 1655.500000 4868 95.831500 1 4044 4 chr6D.!!$R1 4043
2 TraesCS6A01G076900 chr1B 681548502 681552367 3865 True 2728.000000 4558 92.486000 1 3826 2 chr1B.!!$R4 3825
3 TraesCS6A01G076900 chr1B 681454803 681458688 3885 False 712.000000 1321 92.707000 1664 4029 4 chr1B.!!$F1 2365
4 TraesCS6A01G076900 chr1B 681524755 681532360 7605 True 275.800000 294 92.032000 3832 4029 5 chr1B.!!$R3 197
5 TraesCS6A01G076900 chr1B 456154739 456155525 786 True 230.500000 287 87.487000 2911 3459 2 chr1B.!!$R2 548
6 TraesCS6A01G076900 chr7B 94814244 94818953 4709 False 1007.750000 2795 90.055750 1 4029 4 chr7B.!!$F2 4028
7 TraesCS6A01G076900 chr7B 16180850 16181708 858 False 1003.000000 1003 88.155000 1 851 1 chr7B.!!$F1 850
8 TraesCS6A01G076900 chr3A 737366995 737371360 4365 True 904.666667 2316 93.267333 1 3098 3 chr3A.!!$R2 3097
9 TraesCS6A01G076900 chr1A 556347193 556348503 1310 True 1657.000000 1657 89.746000 3 1308 1 chr1A.!!$R1 1305
10 TraesCS6A01G076900 chr1A 426233486 426234691 1205 False 348.000000 520 89.549500 1856 3054 2 chr1A.!!$F4 1198
11 TraesCS6A01G076900 chr1A 46237856 46238560 704 False 257.500000 261 83.790500 328 1554 2 chr1A.!!$F3 1226
12 TraesCS6A01G076900 chr1D 469530509 469532387 1878 True 762.000000 1153 91.443000 530 2257 3 chr1D.!!$R2 1727
13 TraesCS6A01G076900 chr1D 469518368 469519908 1540 True 642.666667 1125 91.089667 2488 4032 3 chr1D.!!$R1 1544
14 TraesCS6A01G076900 chr6B 650653910 650655484 1574 False 610.333333 1118 89.643000 1 1554 3 chr6B.!!$F1 1553
15 TraesCS6A01G076900 chr6B 80968428 80969220 792 True 268.500000 302 89.106500 4046 4466 2 chr6B.!!$R2 420
16 TraesCS6A01G076900 chr5B 433191168 433192759 1591 False 605.333333 1062 89.668667 7 1554 3 chr5B.!!$F1 1547
17 TraesCS6A01G076900 chr2A 14938564 14939104 540 True 497.000000 497 83.912000 2934 3459 1 chr2A.!!$R1 525
18 TraesCS6A01G076900 chr4B 527741642 527744543 2901 False 370.000000 483 86.884000 1588 3466 3 chr4B.!!$F2 1878
19 TraesCS6A01G076900 chr4B 438147643 438150168 2525 True 329.666667 475 86.874000 1588 3466 3 chr4B.!!$R2 1878

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
308 370 3.161866 TGGCTTGGAAATTCCTGGTAAC 58.838 45.455 13.78 0.02 37.46 2.50 F
668 743 5.554822 TCGTCATTGCCATAACTTTTACC 57.445 39.130 0.00 0.00 0.00 2.85 F
1158 1312 3.584406 TGATGTGATCAGGTCTTGAAGGT 59.416 43.478 0.00 0.00 39.77 3.50 F
1639 1963 0.663688 TTGCTATCGCTCGTCTCTCC 59.336 55.000 0.00 0.00 36.97 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1158 1312 4.037923 GGCCAGAACTGAAAATCAAGAACA 59.962 41.667 0.0 0.0 0.00 3.18 R
1639 1963 5.026462 CGAGCATGAGCAAAAATCTACAAG 58.974 41.667 0.0 0.0 45.49 3.16 R
2896 5658 0.654683 CTAGACTGCAATCAAGGCGC 59.345 55.000 0.0 0.0 0.00 6.53 R
3612 7009 0.039180 TCCTGTCTAGAGGCGGTGAA 59.961 55.000 0.0 0.0 32.51 3.18 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
308 370 3.161866 TGGCTTGGAAATTCCTGGTAAC 58.838 45.455 13.78 0.02 37.46 2.50
326 388 6.020971 GGTAACTTTGGTTAACAATGAGGG 57.979 41.667 8.10 0.00 43.12 4.30
509 576 8.079809 GTGATCTACTTCTTATCTGTTCTAGGC 58.920 40.741 0.00 0.00 0.00 3.93
668 743 5.554822 TCGTCATTGCCATAACTTTTACC 57.445 39.130 0.00 0.00 0.00 2.85
794 883 9.765795 TTTCAGTTTTCCAGAAGTTTTTGTTAA 57.234 25.926 0.00 0.00 0.00 2.01
1124 1278 7.012421 GGGTAAGCAAGACTACAAATAGGAATG 59.988 40.741 0.00 0.00 32.08 2.67
1158 1312 3.584406 TGATGTGATCAGGTCTTGAAGGT 59.416 43.478 0.00 0.00 39.77 3.50
1215 1369 5.600484 AGAATCCCTAGGTCTGATGTTAGTG 59.400 44.000 8.29 0.00 0.00 2.74
1639 1963 0.663688 TTGCTATCGCTCGTCTCTCC 59.336 55.000 0.00 0.00 36.97 3.71
2595 5032 3.056107 CACGAGACCACTCCCTGAATTTA 60.056 47.826 0.00 0.00 39.76 1.40
2604 5041 7.801104 ACCACTCCCTGAATTTATTTGTTTTT 58.199 30.769 0.00 0.00 0.00 1.94
2867 5629 7.906192 TCCAATGGGTCCATCAATAGATAGATA 59.094 37.037 0.00 0.00 35.31 1.98
2873 5635 8.816894 GGGTCCATCAATAGATAGATACAGAAA 58.183 37.037 0.00 0.00 31.88 2.52
2884 5646 8.644374 AGATAGATACAGAAATCTGACTACCC 57.356 38.462 16.93 11.21 46.59 3.69
2886 5648 4.902448 AGATACAGAAATCTGACTACCCCC 59.098 45.833 16.93 0.00 46.59 5.40
2913 6039 2.393768 CGCGCCTTGATTGCAGTCT 61.394 57.895 10.82 0.00 0.00 3.24
2921 6047 3.120060 CCTTGATTGCAGTCTAGTGTTGC 60.120 47.826 16.87 8.31 38.30 4.17
3017 6148 5.103290 TGGTTATCGTTGTTTTCAGAAGC 57.897 39.130 0.00 0.00 0.00 3.86
3141 6454 3.460857 GGATTACCTCCTACACTGCAG 57.539 52.381 13.48 13.48 41.29 4.41
3195 6508 7.268199 TCCAGTAAGCATGAATTGAATGATC 57.732 36.000 0.00 0.00 0.00 2.92
3437 6829 9.916360 TCTAGATGTTTAGTCCATCAAGTACTA 57.084 33.333 0.00 0.00 40.93 1.82
3453 6846 8.213518 TCAAGTACTATGAATCATTTGGCTTC 57.786 34.615 0.00 0.00 0.00 3.86
3572 6969 3.097728 GTCGTGGAGTGCGTCGTG 61.098 66.667 0.00 0.00 0.00 4.35
3608 7005 8.084073 CCAATGTCTTCTTTATTTTGAGAAGCA 58.916 33.333 7.95 9.33 45.33 3.91
3612 7009 9.017509 TGTCTTCTTTATTTTGAGAAGCATCAT 57.982 29.630 7.95 0.00 45.33 2.45
3809 7217 4.651778 AGTTTAACCAACTATGCAGCTGA 58.348 39.130 20.43 2.70 44.56 4.26
3810 7218 5.256474 AGTTTAACCAACTATGCAGCTGAT 58.744 37.500 20.43 10.74 44.56 2.90
3811 7219 5.711976 AGTTTAACCAACTATGCAGCTGATT 59.288 36.000 20.43 5.93 44.56 2.57
3812 7220 5.565592 TTAACCAACTATGCAGCTGATTG 57.434 39.130 20.43 12.26 0.00 2.67
3813 7221 1.747355 ACCAACTATGCAGCTGATTGC 59.253 47.619 20.43 2.64 44.33 3.56
3814 7222 9.648832 GTTTAACCAACTATGCAGCTGATTGCT 62.649 40.741 20.43 5.74 41.81 3.91
3827 7235 4.918037 GCTGATTGCTACTTCTCCAAATG 58.082 43.478 0.00 0.00 38.95 2.32
3828 7236 4.637534 GCTGATTGCTACTTCTCCAAATGA 59.362 41.667 0.00 0.00 38.95 2.57
3829 7237 5.124457 GCTGATTGCTACTTCTCCAAATGAA 59.876 40.000 0.00 0.00 38.95 2.57
3830 7238 6.349611 GCTGATTGCTACTTCTCCAAATGAAA 60.350 38.462 0.00 0.00 38.95 2.69
3831 7239 6.913170 TGATTGCTACTTCTCCAAATGAAAC 58.087 36.000 0.00 0.00 0.00 2.78
3832 7240 5.705609 TTGCTACTTCTCCAAATGAAACC 57.294 39.130 0.00 0.00 0.00 3.27
3833 7241 4.985538 TGCTACTTCTCCAAATGAAACCT 58.014 39.130 0.00 0.00 0.00 3.50
3834 7242 4.761739 TGCTACTTCTCCAAATGAAACCTG 59.238 41.667 0.00 0.00 0.00 4.00
3835 7243 4.379918 GCTACTTCTCCAAATGAAACCTGC 60.380 45.833 0.00 0.00 0.00 4.85
3836 7244 3.837355 ACTTCTCCAAATGAAACCTGCT 58.163 40.909 0.00 0.00 0.00 4.24
3837 7245 4.218312 ACTTCTCCAAATGAAACCTGCTT 58.782 39.130 0.00 0.00 0.00 3.91
3838 7246 4.651045 ACTTCTCCAAATGAAACCTGCTTT 59.349 37.500 0.00 0.00 0.00 3.51
3839 7247 4.853924 TCTCCAAATGAAACCTGCTTTC 57.146 40.909 0.00 0.00 39.11 2.62
3849 7257 6.317789 TGAAACCTGCTTTCAACTCTAATG 57.682 37.500 0.00 0.00 44.42 1.90
3850 7258 6.061441 TGAAACCTGCTTTCAACTCTAATGA 58.939 36.000 0.00 0.00 44.42 2.57
3851 7259 6.716628 TGAAACCTGCTTTCAACTCTAATGAT 59.283 34.615 0.00 0.00 44.42 2.45
3852 7260 6.749923 AACCTGCTTTCAACTCTAATGATC 57.250 37.500 0.00 0.00 0.00 2.92
3927 10645 4.270245 TCTCAGTTGTACATGCATGTGA 57.730 40.909 36.72 24.18 41.89 3.58
4032 10750 2.629617 GGCGCCCCAACTACTAGTATAA 59.370 50.000 18.11 0.00 0.00 0.98
4033 10751 3.260128 GGCGCCCCAACTACTAGTATAAT 59.740 47.826 18.11 0.00 0.00 1.28
4035 10753 5.047092 GGCGCCCCAACTACTAGTATAATAA 60.047 44.000 18.11 0.00 0.00 1.40
4036 10754 5.866092 GCGCCCCAACTACTAGTATAATAAC 59.134 44.000 2.33 0.00 0.00 1.89
4037 10755 6.294955 GCGCCCCAACTACTAGTATAATAACT 60.295 42.308 2.33 0.00 0.00 2.24
4051 10769 7.897864 AGTATAATAACTACTGCTCCATGACC 58.102 38.462 0.00 0.00 0.00 4.02
4054 10772 5.700402 ATAACTACTGCTCCATGACCTTT 57.300 39.130 0.00 0.00 0.00 3.11
4087 13071 1.826709 GCCACTCTAAGGGCCTCTC 59.173 63.158 6.46 0.00 44.53 3.20
4090 13074 1.118838 CACTCTAAGGGCCTCTCAGG 58.881 60.000 6.46 0.00 38.80 3.86
4115 13099 6.926272 GTCATAGGATTGGAGAACTACATGAC 59.074 42.308 0.00 0.00 0.00 3.06
4117 13101 8.004801 TCATAGGATTGGAGAACTACATGACTA 58.995 37.037 0.00 0.00 0.00 2.59
4118 13102 6.723298 AGGATTGGAGAACTACATGACTAG 57.277 41.667 0.00 0.00 0.00 2.57
4135 13384 8.256605 ACATGACTAGATAATATCTCACATGCC 58.743 37.037 25.43 8.61 41.84 4.40
4137 13386 5.655488 ACTAGATAATATCTCACATGCCGC 58.345 41.667 5.98 0.00 40.76 6.53
4149 13398 0.458889 CATGCCGCTGTGGAAATTGG 60.459 55.000 12.29 0.00 42.00 3.16
4157 13406 3.613671 CGCTGTGGAAATTGGTTGCAATA 60.614 43.478 0.59 0.00 39.54 1.90
4163 13412 9.248291 CTGTGGAAATTGGTTGCAATATATTAC 57.752 33.333 0.59 0.00 39.54 1.89
4291 15584 4.304110 AGAAGCTGTGTTTTTCATGCATG 58.696 39.130 21.07 21.07 33.32 4.06
4299 15592 4.682860 GTGTTTTTCATGCATGTTGAGAGG 59.317 41.667 25.43 0.00 0.00 3.69
4301 15594 5.068855 TGTTTTTCATGCATGTTGAGAGGAA 59.931 36.000 25.43 7.77 0.00 3.36
4404 15697 8.335532 TGAGAGAAATAAAAATAGTGGTGTGG 57.664 34.615 0.00 0.00 0.00 4.17
4411 15704 2.717639 AATAGTGGTGTGGATGAGGC 57.282 50.000 0.00 0.00 0.00 4.70
4467 15787 6.529220 AGTGGGATCATCTACTTAAGCATTC 58.471 40.000 1.29 0.00 0.00 2.67
4468 15788 6.100279 AGTGGGATCATCTACTTAAGCATTCA 59.900 38.462 1.29 0.00 0.00 2.57
4469 15789 6.767902 GTGGGATCATCTACTTAAGCATTCAA 59.232 38.462 1.29 0.00 0.00 2.69
4470 15790 7.283127 GTGGGATCATCTACTTAAGCATTCAAA 59.717 37.037 1.29 0.00 0.00 2.69
4471 15791 7.833682 TGGGATCATCTACTTAAGCATTCAAAA 59.166 33.333 1.29 0.00 0.00 2.44
4477 15797 9.859427 CATCTACTTAAGCATTCAAAATTTGGA 57.141 29.630 5.83 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
251 313 3.848726 ACAAGAAAACACAAAGGCACAG 58.151 40.909 0.00 0.00 0.00 3.66
308 370 6.642707 TTGTACCCTCATTGTTAACCAAAG 57.357 37.500 2.48 0.00 36.44 2.77
326 388 9.769093 AAGCAAATTAATTGTAGTCGATTGTAC 57.231 29.630 0.39 0.00 41.32 2.90
509 576 1.198397 GCAAGTCACGACAACGACG 59.802 57.895 0.00 0.00 42.66 5.12
668 743 3.669023 GCAAGAACTTTGATGAGAAGCCG 60.669 47.826 0.00 0.00 0.00 5.52
794 883 4.338879 ACAAAGATAGAAGTGGCATGCTT 58.661 39.130 18.92 3.65 0.00 3.91
992 1110 0.262580 ATTGGTGGGCATACAGGCAT 59.737 50.000 0.00 0.00 46.44 4.40
995 1113 1.113788 CCAATTGGTGGGCATACAGG 58.886 55.000 16.90 0.00 44.64 4.00
1035 1186 0.039165 CCTTTCTGCCCTTTCGCAAC 60.039 55.000 0.00 0.00 38.56 4.17
1124 1278 5.064452 CCTGATCACATCACTTCAAGCTTAC 59.936 44.000 0.00 0.00 35.06 2.34
1158 1312 4.037923 GGCCAGAACTGAAAATCAAGAACA 59.962 41.667 0.00 0.00 0.00 3.18
1639 1963 5.026462 CGAGCATGAGCAAAAATCTACAAG 58.974 41.667 0.00 0.00 45.49 3.16
1771 2100 5.050490 GGTAAATGACGAGCTACACATGAT 58.950 41.667 0.00 0.00 0.00 2.45
2425 4860 6.830324 CCAATCTATTCCTGAGAATGGTCAAA 59.170 38.462 0.00 0.00 42.78 2.69
2895 5657 1.083806 TAGACTGCAATCAAGGCGCG 61.084 55.000 0.00 0.00 0.00 6.86
2896 5658 0.654683 CTAGACTGCAATCAAGGCGC 59.345 55.000 0.00 0.00 0.00 6.53
2913 6039 3.142951 ACTTACAATTGGCGCAACACTA 58.857 40.909 10.83 0.00 0.00 2.74
2921 6047 4.685169 ACAATGAGACTTACAATTGGCG 57.315 40.909 10.83 0.00 0.00 5.69
3017 6148 7.599171 AGAGTAAATTGTTAAACCAATTCCCG 58.401 34.615 4.93 0.00 42.63 5.14
3195 6508 2.871133 TCAAGTGGTATCGCTTACGTG 58.129 47.619 0.47 0.00 41.32 4.49
3437 6829 5.943349 TGAATGGAAGCCAAATGATTCAT 57.057 34.783 0.00 0.00 36.95 2.57
3572 6969 0.394352 AAGACATTGGCGATGACCCC 60.394 55.000 21.46 7.27 39.15 4.95
3608 7005 2.363680 CTGTCTAGAGGCGGTGAATGAT 59.636 50.000 0.00 0.00 0.00 2.45
3612 7009 0.039180 TCCTGTCTAGAGGCGGTGAA 59.961 55.000 0.00 0.00 32.51 3.18
3791 7199 3.378112 GCAATCAGCTGCATAGTTGGTTA 59.622 43.478 9.47 0.00 36.48 2.85
3792 7200 2.165030 GCAATCAGCTGCATAGTTGGTT 59.835 45.455 9.47 0.00 38.78 3.67
3793 7201 1.747355 GCAATCAGCTGCATAGTTGGT 59.253 47.619 9.47 0.00 42.17 3.67
3794 7202 2.486951 GCAATCAGCTGCATAGTTGG 57.513 50.000 9.47 0.00 42.17 3.77
3805 7213 4.637534 TCATTTGGAGAAGTAGCAATCAGC 59.362 41.667 0.00 0.00 46.19 4.26
3806 7214 6.748333 TTCATTTGGAGAAGTAGCAATCAG 57.252 37.500 0.00 0.00 0.00 2.90
3807 7215 6.071952 GGTTTCATTTGGAGAAGTAGCAATCA 60.072 38.462 0.00 0.00 0.00 2.57
3808 7216 6.151817 AGGTTTCATTTGGAGAAGTAGCAATC 59.848 38.462 0.00 0.00 0.00 2.67
3809 7217 6.012745 AGGTTTCATTTGGAGAAGTAGCAAT 58.987 36.000 0.00 0.00 0.00 3.56
3810 7218 5.241506 CAGGTTTCATTTGGAGAAGTAGCAA 59.758 40.000 0.00 0.00 0.00 3.91
3811 7219 4.761739 CAGGTTTCATTTGGAGAAGTAGCA 59.238 41.667 0.00 0.00 0.00 3.49
3812 7220 4.379918 GCAGGTTTCATTTGGAGAAGTAGC 60.380 45.833 0.00 0.00 0.00 3.58
3813 7221 5.006386 AGCAGGTTTCATTTGGAGAAGTAG 58.994 41.667 0.00 0.00 0.00 2.57
3814 7222 4.985538 AGCAGGTTTCATTTGGAGAAGTA 58.014 39.130 0.00 0.00 0.00 2.24
3815 7223 3.837355 AGCAGGTTTCATTTGGAGAAGT 58.163 40.909 0.00 0.00 0.00 3.01
3816 7224 4.861102 AAGCAGGTTTCATTTGGAGAAG 57.139 40.909 0.00 0.00 0.00 2.85
3817 7225 5.200368 GAAAGCAGGTTTCATTTGGAGAA 57.800 39.130 18.37 0.00 43.70 2.87
3818 7226 4.853924 GAAAGCAGGTTTCATTTGGAGA 57.146 40.909 18.37 0.00 43.70 3.71
3827 7235 6.560253 TCATTAGAGTTGAAAGCAGGTTTC 57.440 37.500 16.78 16.78 44.41 2.78
3828 7236 6.944862 AGATCATTAGAGTTGAAAGCAGGTTT 59.055 34.615 0.00 0.00 0.00 3.27
3829 7237 6.373774 CAGATCATTAGAGTTGAAAGCAGGTT 59.626 38.462 0.00 0.00 0.00 3.50
3830 7238 5.879223 CAGATCATTAGAGTTGAAAGCAGGT 59.121 40.000 0.00 0.00 0.00 4.00
3831 7239 5.296283 CCAGATCATTAGAGTTGAAAGCAGG 59.704 44.000 0.00 0.00 0.00 4.85
3832 7240 6.111382 TCCAGATCATTAGAGTTGAAAGCAG 58.889 40.000 0.00 0.00 0.00 4.24
3833 7241 6.053632 TCCAGATCATTAGAGTTGAAAGCA 57.946 37.500 0.00 0.00 0.00 3.91
3834 7242 7.565323 AATCCAGATCATTAGAGTTGAAAGC 57.435 36.000 0.00 0.00 0.00 3.51
3835 7243 9.829507 AGTAATCCAGATCATTAGAGTTGAAAG 57.170 33.333 0.00 0.00 0.00 2.62
3838 7246 9.647918 AGTAGTAATCCAGATCATTAGAGTTGA 57.352 33.333 0.00 0.00 0.00 3.18
3839 7247 9.906660 GAGTAGTAATCCAGATCATTAGAGTTG 57.093 37.037 0.00 0.00 0.00 3.16
3840 7248 9.647918 TGAGTAGTAATCCAGATCATTAGAGTT 57.352 33.333 0.00 0.00 0.00 3.01
3841 7249 9.647918 TTGAGTAGTAATCCAGATCATTAGAGT 57.352 33.333 0.00 0.00 0.00 3.24
3843 7251 9.083422 CCTTGAGTAGTAATCCAGATCATTAGA 57.917 37.037 0.55 0.00 0.00 2.10
3844 7252 8.310382 CCCTTGAGTAGTAATCCAGATCATTAG 58.690 40.741 0.55 0.00 0.00 1.73
3845 7253 8.010697 TCCCTTGAGTAGTAATCCAGATCATTA 58.989 37.037 0.55 0.00 0.00 1.90
3846 7254 6.846505 TCCCTTGAGTAGTAATCCAGATCATT 59.153 38.462 0.55 0.00 0.00 2.57
3847 7255 6.385443 TCCCTTGAGTAGTAATCCAGATCAT 58.615 40.000 0.55 0.00 0.00 2.45
3848 7256 5.777449 TCCCTTGAGTAGTAATCCAGATCA 58.223 41.667 0.55 0.00 0.00 2.92
3849 7257 6.926630 ATCCCTTGAGTAGTAATCCAGATC 57.073 41.667 0.55 0.00 0.00 2.75
3850 7258 7.420680 CCAAATCCCTTGAGTAGTAATCCAGAT 60.421 40.741 0.55 0.00 37.17 2.90
3851 7259 6.126768 CCAAATCCCTTGAGTAGTAATCCAGA 60.127 42.308 0.55 0.00 37.17 3.86
3852 7260 6.058183 CCAAATCCCTTGAGTAGTAATCCAG 58.942 44.000 0.00 0.00 37.17 3.86
3927 10645 5.133221 TGCTTCTTTCTTTTTCTACTGCCT 58.867 37.500 0.00 0.00 0.00 4.75
4032 10750 5.189736 TGAAAGGTCATGGAGCAGTAGTTAT 59.810 40.000 0.00 0.00 31.89 1.89
4033 10751 4.530553 TGAAAGGTCATGGAGCAGTAGTTA 59.469 41.667 0.00 0.00 31.89 2.24
4035 10753 2.906389 TGAAAGGTCATGGAGCAGTAGT 59.094 45.455 0.00 0.00 31.89 2.73
4036 10754 3.616956 TGAAAGGTCATGGAGCAGTAG 57.383 47.619 0.00 0.00 31.89 2.57
4037 10755 3.519107 TGATGAAAGGTCATGGAGCAGTA 59.481 43.478 0.00 0.00 44.83 2.74
4044 10762 3.944015 GTCCTCTTGATGAAAGGTCATGG 59.056 47.826 0.00 0.00 44.83 3.66
4051 10769 1.734465 GGCACGTCCTCTTGATGAAAG 59.266 52.381 0.00 0.00 37.22 2.62
4054 10772 0.037326 GTGGCACGTCCTCTTGATGA 60.037 55.000 0.00 0.00 33.92 2.92
4087 13071 5.363868 TGTAGTTCTCCAATCCTATGACCTG 59.636 44.000 0.00 0.00 0.00 4.00
4090 13074 6.926272 GTCATGTAGTTCTCCAATCCTATGAC 59.074 42.308 0.00 0.00 35.52 3.06
4115 13099 5.747675 CAGCGGCATGTGAGATATTATCTAG 59.252 44.000 6.17 0.00 40.38 2.43
4117 13101 4.020751 ACAGCGGCATGTGAGATATTATCT 60.021 41.667 5.88 5.88 43.70 1.98
4118 13102 4.248859 ACAGCGGCATGTGAGATATTATC 58.751 43.478 1.45 0.00 30.46 1.75
4134 13383 0.667184 GCAACCAATTTCCACAGCGG 60.667 55.000 0.00 0.00 0.00 5.52
4135 13384 0.031857 TGCAACCAATTTCCACAGCG 59.968 50.000 0.00 0.00 0.00 5.18
4137 13386 9.248291 GTAATATATTGCAACCAATTTCCACAG 57.752 33.333 0.00 0.00 41.68 3.66
4261 15554 9.844790 CATGAAAAACACAGCTTCTATATTCAA 57.155 29.630 0.00 0.00 0.00 2.69
4273 15566 3.803231 TCAACATGCATGAAAAACACAGC 59.197 39.130 32.75 0.00 34.74 4.40
4276 15569 4.682860 CCTCTCAACATGCATGAAAAACAC 59.317 41.667 32.75 0.00 0.00 3.32
4315 15608 1.284982 ACACATCGCACTTCGTCAGC 61.285 55.000 0.00 0.00 39.67 4.26
4320 15613 1.070821 ACATGACACATCGCACTTCG 58.929 50.000 0.00 0.00 40.15 3.79
4328 15621 7.840342 ACTATTTCTCTCAACATGACACATC 57.160 36.000 0.00 0.00 0.00 3.06
4400 15693 2.124612 CATGCCGCCTCATCCACA 60.125 61.111 0.00 0.00 0.00 4.17
4404 15697 3.104766 CACACATGCCGCCTCATC 58.895 61.111 0.00 0.00 0.00 2.92
4467 15787 3.255642 ACCACTCCGTCATCCAAATTTTG 59.744 43.478 1.99 1.99 0.00 2.44
4468 15788 3.496331 ACCACTCCGTCATCCAAATTTT 58.504 40.909 0.00 0.00 0.00 1.82
4469 15789 3.081804 GACCACTCCGTCATCCAAATTT 58.918 45.455 0.00 0.00 32.74 1.82
4470 15790 2.039746 TGACCACTCCGTCATCCAAATT 59.960 45.455 0.00 0.00 37.85 1.82
4471 15791 1.628340 TGACCACTCCGTCATCCAAAT 59.372 47.619 0.00 0.00 37.85 2.32
4474 15794 4.531351 TGACCACTCCGTCATCCA 57.469 55.556 0.00 0.00 37.85 3.41


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

AutoCloner maintained by Alex Coulton.