Multiple sequence alignment - TraesCS6A01G299000

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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 TraesCS6A01G299000 chr6A 100.000 6916 0 0 1 6916 532312882 532319797 0.000000e+00 12772.0
1 TraesCS6A01G299000 chr6A 85.718 4138 433 71 1954 6007 532158739 532162802 0.000000e+00 4222.0
2 TraesCS6A01G299000 chr6A 94.331 635 32 2 6286 6916 558836343 558835709 0.000000e+00 970.0
3 TraesCS6A01G299000 chr6A 87.204 719 81 9 870 1583 532157944 532158656 0.000000e+00 808.0
4 TraesCS6A01G299000 chr6A 97.959 49 1 0 6234 6282 137273587 137273635 1.240000e-12 86.1
5 TraesCS6A01G299000 chr6D 94.994 6292 152 55 13 6238 387037703 387043897 0.000000e+00 9723.0
6 TraesCS6A01G299000 chr6D 86.268 4078 420 87 2004 6007 386946961 386950972 0.000000e+00 4300.0
7 TraesCS6A01G299000 chr6D 84.719 962 118 23 641 1586 386945898 386946846 0.000000e+00 935.0
8 TraesCS6A01G299000 chr6B 92.830 4714 201 46 13 4675 578395551 578400178 0.000000e+00 6706.0
9 TraesCS6A01G299000 chr6B 95.678 4049 132 14 2142 6179 578298384 578302400 0.000000e+00 6468.0
10 TraesCS6A01G299000 chr6B 85.509 4113 435 83 1931 5957 578209683 578213720 0.000000e+00 4145.0
11 TraesCS6A01G299000 chr6B 92.664 2113 87 28 13 2103 578292994 578295060 0.000000e+00 2981.0
12 TraesCS6A01G299000 chr6B 90.479 1607 84 27 4662 6238 578400199 578401766 0.000000e+00 2056.0
13 TraesCS6A01G299000 chr6B 93.701 635 37 1 6285 6916 114073566 114072932 0.000000e+00 948.0
14 TraesCS6A01G299000 chr6B 84.395 942 105 24 658 1586 578208706 578209618 0.000000e+00 887.0
15 TraesCS6A01G299000 chr6B 92.000 200 7 3 13 211 578395119 578395310 8.840000e-69 272.0
16 TraesCS6A01G299000 chr2A 95.591 635 25 1 6285 6916 721588046 721587412 0.000000e+00 1014.0
17 TraesCS6A01G299000 chr7A 94.803 635 30 1 6285 6916 704263869 704263235 0.000000e+00 987.0
18 TraesCS6A01G299000 chr3A 94.488 635 32 1 6285 6916 721553474 721552840 0.000000e+00 976.0
19 TraesCS6A01G299000 chr3A 94.173 635 34 1 6285 6916 741166908 741167542 0.000000e+00 965.0
20 TraesCS6A01G299000 chr5A 94.016 635 35 1 6285 6916 617372091 617371457 0.000000e+00 959.0
21 TraesCS6A01G299000 chr5A 86.610 351 44 3 1080 1428 458141108 458140759 1.090000e-102 385.0
22 TraesCS6A01G299000 chr3B 93.858 635 36 1 6285 6916 11915158 11914524 0.000000e+00 953.0
23 TraesCS6A01G299000 chr1B 93.594 640 37 2 6281 6916 61990128 61989489 0.000000e+00 952.0
24 TraesCS6A01G299000 chr1B 84.485 709 77 21 1332 2020 635135516 635136211 0.000000e+00 669.0
25 TraesCS6A01G299000 chr1B 84.485 709 77 21 1332 2020 667632399 667633094 0.000000e+00 669.0
26 TraesCS6A01G299000 chr7D 89.028 319 35 0 1080 1398 611161674 611161356 5.030000e-106 396.0
27 TraesCS6A01G299000 chrUn 91.453 117 10 0 1080 1196 297388624 297388508 2.000000e-35 161.0
28 TraesCS6A01G299000 chr4A 97.959 49 1 0 6234 6282 647219871 647219919 1.240000e-12 86.1
29 TraesCS6A01G299000 chr3D 97.959 49 1 0 6234 6282 526827417 526827465 1.240000e-12 86.1
30 TraesCS6A01G299000 chr7B 94.444 54 3 0 6229 6282 105954108 105954161 4.450000e-12 84.2
31 TraesCS6A01G299000 chr5B 94.545 55 1 2 6228 6282 661230302 661230250 4.450000e-12 84.2
32 TraesCS6A01G299000 chr5B 91.667 60 4 1 6223 6282 476008033 476007975 1.600000e-11 82.4
33 TraesCS6A01G299000 chr5D 94.340 53 3 0 6230 6282 180739340 180739392 1.600000e-11 82.4
34 TraesCS6A01G299000 chr5D 92.727 55 4 0 6228 6282 310766924 310766870 5.750000e-11 80.5
35 TraesCS6A01G299000 chr5D 86.957 69 6 3 6217 6282 458893953 458893885 2.680000e-09 75.0


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 TraesCS6A01G299000 chr6A 532312882 532319797 6915 False 12772.000000 12772 100.000000 1 6916 1 chr6A.!!$F2 6915
1 TraesCS6A01G299000 chr6A 532157944 532162802 4858 False 2515.000000 4222 86.461000 870 6007 2 chr6A.!!$F3 5137
2 TraesCS6A01G299000 chr6A 558835709 558836343 634 True 970.000000 970 94.331000 6286 6916 1 chr6A.!!$R1 630
3 TraesCS6A01G299000 chr6D 387037703 387043897 6194 False 9723.000000 9723 94.994000 13 6238 1 chr6D.!!$F1 6225
4 TraesCS6A01G299000 chr6D 386945898 386950972 5074 False 2617.500000 4300 85.493500 641 6007 2 chr6D.!!$F2 5366
5 TraesCS6A01G299000 chr6B 578292994 578302400 9406 False 4724.500000 6468 94.171000 13 6179 2 chr6B.!!$F2 6166
6 TraesCS6A01G299000 chr6B 578395119 578401766 6647 False 3011.333333 6706 91.769667 13 6238 3 chr6B.!!$F3 6225
7 TraesCS6A01G299000 chr6B 578208706 578213720 5014 False 2516.000000 4145 84.952000 658 5957 2 chr6B.!!$F1 5299
8 TraesCS6A01G299000 chr6B 114072932 114073566 634 True 948.000000 948 93.701000 6285 6916 1 chr6B.!!$R1 631
9 TraesCS6A01G299000 chr2A 721587412 721588046 634 True 1014.000000 1014 95.591000 6285 6916 1 chr2A.!!$R1 631
10 TraesCS6A01G299000 chr7A 704263235 704263869 634 True 987.000000 987 94.803000 6285 6916 1 chr7A.!!$R1 631
11 TraesCS6A01G299000 chr3A 721552840 721553474 634 True 976.000000 976 94.488000 6285 6916 1 chr3A.!!$R1 631
12 TraesCS6A01G299000 chr3A 741166908 741167542 634 False 965.000000 965 94.173000 6285 6916 1 chr3A.!!$F1 631
13 TraesCS6A01G299000 chr5A 617371457 617372091 634 True 959.000000 959 94.016000 6285 6916 1 chr5A.!!$R2 631
14 TraesCS6A01G299000 chr3B 11914524 11915158 634 True 953.000000 953 93.858000 6285 6916 1 chr3B.!!$R1 631
15 TraesCS6A01G299000 chr1B 61989489 61990128 639 True 952.000000 952 93.594000 6281 6916 1 chr1B.!!$R1 635
16 TraesCS6A01G299000 chr1B 635135516 635136211 695 False 669.000000 669 84.485000 1332 2020 1 chr1B.!!$F1 688
17 TraesCS6A01G299000 chr1B 667632399 667633094 695 False 669.000000 669 84.485000 1332 2020 1 chr1B.!!$F2 688

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
97 99 0.615331 CCTTCCTTCTGCTGCTGGTA 59.385 55.000 6.69 0.0 0.00 3.25 F
1281 1786 1.194547 CGTGACATTGTTCCAAGACCG 59.805 52.381 0.00 0.0 0.00 4.79 F
2494 6340 0.532573 GACGTCTTCCATCTCCAGCA 59.467 55.000 8.70 0.0 0.00 4.41 F
3905 7758 0.690762 AAACCCGCACACTGGAGTAT 59.309 50.000 0.00 0.0 0.00 2.12 F
4044 7897 3.217626 CAGGCTGTTCAAAGTCCTCTTT 58.782 45.455 6.28 0.0 43.66 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1865 2393 0.610232 ATTCAAGTGCACCTCCAGGC 60.610 55.000 14.63 0.0 39.32 4.85 R
3152 7005 0.035439 CACTGGCAGATAACCCCGTT 60.035 55.000 23.66 0.0 0.00 4.44 R
4044 7897 1.133325 ACAGTTAACCATGTGGCCCAA 60.133 47.619 0.00 0.0 39.32 4.12 R
4765 8686 0.480690 TTGGCATGTTACCACCACCT 59.519 50.000 0.00 0.0 36.76 4.00 R
6038 10020 0.450983 GCAGTACTTCGTAGGCTCGT 59.549 55.000 0.00 0.0 0.00 4.18 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
40 41 2.084610 GCAGACAAAAAGCCATTCCC 57.915 50.000 0.00 0.00 0.00 3.97
94 96 0.676151 GTCCCTTCCTTCTGCTGCTG 60.676 60.000 0.00 0.00 0.00 4.41
95 97 1.378250 CCCTTCCTTCTGCTGCTGG 60.378 63.158 6.69 1.48 0.00 4.85
96 98 1.377994 CCTTCCTTCTGCTGCTGGT 59.622 57.895 6.69 0.00 0.00 4.00
97 99 0.615331 CCTTCCTTCTGCTGCTGGTA 59.385 55.000 6.69 0.00 0.00 3.25
153 157 2.244382 CGAGCGCGTTTCGTTGTT 59.756 55.556 21.47 0.00 41.07 2.83
355 795 3.712881 GTTCGAGCGCGGCTTGTT 61.713 61.111 10.69 0.00 39.88 2.83
374 815 3.133003 TGTTTTCCTGAATTTTGCGGGAA 59.867 39.130 0.00 0.00 46.31 3.97
434 882 1.807142 GCTTCGCCAATAATAGAGGGC 59.193 52.381 0.00 0.00 42.98 5.19
556 1004 4.691326 TTTTTGGGGTTCGCCTATTTTT 57.309 36.364 7.39 0.00 37.45 1.94
594 1044 1.681538 TGCCGTTGACCTTTTTAGCA 58.318 45.000 0.00 0.00 0.00 3.49
654 1104 1.637553 AGTGCCTGATGAAGTGGGATT 59.362 47.619 0.00 0.00 0.00 3.01
942 1445 3.616956 TCTGTCTATGCTTTCCAGTGG 57.383 47.619 1.40 1.40 0.00 4.00
1075 1580 4.653341 ACCATGTCAAGGATTTGTTGGAAA 59.347 37.500 0.00 0.00 35.66 3.13
1173 1678 2.158623 TGCCATTGTTCAGTTCCAGTCT 60.159 45.455 0.00 0.00 0.00 3.24
1281 1786 1.194547 CGTGACATTGTTCCAAGACCG 59.805 52.381 0.00 0.00 0.00 4.79
1535 2044 6.176183 AGTTCCTTCTGATTCAGGTATGTTG 58.824 40.000 13.59 0.00 31.51 3.33
1563 2073 8.956533 TGTACAACACATGTATATGTATGCTT 57.043 30.769 16.09 0.00 45.53 3.91
1635 2145 2.622942 TCCTTTTCTGTTGCTGCGAATT 59.377 40.909 0.00 0.00 0.00 2.17
1677 2189 8.682710 AGTACATTACTGTGTTCACATTGTTTT 58.317 29.630 6.09 0.00 37.69 2.43
1809 2336 7.479980 TGTGCCAGAAACAATATAATTGCTAC 58.520 34.615 0.00 0.00 0.00 3.58
1850 2378 6.587206 TTTGGTCATTGATCATTTGCTGTA 57.413 33.333 0.00 0.00 0.00 2.74
1860 2388 6.044046 TGATCATTTGCTGTATTTGGAATGC 58.956 36.000 0.00 0.00 0.00 3.56
1861 2389 5.664294 TCATTTGCTGTATTTGGAATGCT 57.336 34.783 0.00 0.00 0.00 3.79
1862 2390 5.412640 TCATTTGCTGTATTTGGAATGCTG 58.587 37.500 0.00 0.00 0.00 4.41
1863 2391 3.872511 TTGCTGTATTTGGAATGCTGG 57.127 42.857 0.00 0.00 0.00 4.85
1864 2392 3.084536 TGCTGTATTTGGAATGCTGGA 57.915 42.857 0.00 0.00 0.00 3.86
1865 2393 3.018856 TGCTGTATTTGGAATGCTGGAG 58.981 45.455 0.00 0.00 0.00 3.86
1866 2394 2.223665 GCTGTATTTGGAATGCTGGAGC 60.224 50.000 0.00 0.00 42.50 4.70
1900 2428 6.145535 CACTTGAATTTTGTAGAGTTCAGCC 58.854 40.000 0.00 0.00 32.76 4.85
1904 2432 4.773323 ATTTTGTAGAGTTCAGCCTTGC 57.227 40.909 0.00 0.00 0.00 4.01
2103 2651 8.632679 CACCAATTGCTATAATACAGTTTCCAT 58.367 33.333 0.00 0.00 0.00 3.41
2209 6054 9.468532 GTTTATTGAAAGCTCAGAGATTTTTGT 57.531 29.630 14.80 6.71 33.48 2.83
2494 6340 0.532573 GACGTCTTCCATCTCCAGCA 59.467 55.000 8.70 0.00 0.00 4.41
3152 7005 1.739466 GCATGGATGTTTGCTTCTCGA 59.261 47.619 0.00 0.00 35.95 4.04
3153 7006 2.162208 GCATGGATGTTTGCTTCTCGAA 59.838 45.455 0.00 0.00 35.95 3.71
3239 7092 1.140375 GTATGCTGCAAGGCTTGGC 59.860 57.895 27.25 22.27 0.00 4.52
3419 7272 1.073284 TGCTTTACTCCCTCCGCTTTT 59.927 47.619 0.00 0.00 0.00 2.27
3497 7350 8.290325 CGCTGGAAACTATCTTTAAGAAAAAGT 58.710 33.333 0.00 0.76 0.00 2.66
3860 7713 5.022787 TCAAGGATATTTGTCCCAAAAGGG 58.977 41.667 0.00 0.00 39.17 3.95
3900 7753 1.586154 GGATGAAACCCGCACACTGG 61.586 60.000 0.00 0.00 0.00 4.00
3905 7758 0.690762 AAACCCGCACACTGGAGTAT 59.309 50.000 0.00 0.00 0.00 2.12
3925 7778 7.200434 AGTATGGACAGGTATTCATTCAAGT 57.800 36.000 0.00 0.00 0.00 3.16
4044 7897 3.217626 CAGGCTGTTCAAAGTCCTCTTT 58.782 45.455 6.28 0.00 43.66 2.52
4765 8686 6.590234 TTAGAGTTGAGCACATGAACTAGA 57.410 37.500 0.00 0.00 0.00 2.43
4831 8777 4.041567 TGCTCTCTGTTCCTTCCAATACAA 59.958 41.667 0.00 0.00 0.00 2.41
4860 8807 6.763610 GTGCTACAGTATAGGCTCAATTCTTT 59.236 38.462 0.00 0.00 0.00 2.52
4952 8906 9.143631 CATTTTGGATGGAATTGAAAAGACTAC 57.856 33.333 0.00 0.00 0.00 2.73
5340 9310 3.572682 CGACAGGGCTAACTATGTATCCA 59.427 47.826 0.00 0.00 0.00 3.41
5426 9396 3.134127 GATGTGGCAAGGCGGTCC 61.134 66.667 0.00 0.00 0.00 4.46
5621 9591 1.730902 CGACGCCGATGCTATCAGG 60.731 63.158 0.00 0.00 38.22 3.86
5874 9856 3.777106 ACTTTGTCAGGAAGATGCTCA 57.223 42.857 0.00 0.00 0.00 4.26
5996 9978 0.461548 AGAATGATCGCCGAAGAGCA 59.538 50.000 0.00 0.95 41.01 4.26
6023 10005 8.669946 TTGTAATTGTTGACTCAGATGTGTTA 57.330 30.769 0.00 0.00 0.00 2.41
6037 10019 5.355071 CAGATGTGTTAATGTACATGTGGCT 59.645 40.000 9.63 0.00 41.92 4.75
6038 10020 6.538381 CAGATGTGTTAATGTACATGTGGCTA 59.462 38.462 9.63 0.00 41.92 3.93
6039 10021 6.538742 AGATGTGTTAATGTACATGTGGCTAC 59.461 38.462 9.63 0.00 37.63 3.58
6041 10023 4.865925 GTGTTAATGTACATGTGGCTACGA 59.134 41.667 9.63 0.00 0.00 3.43
6042 10024 5.005394 GTGTTAATGTACATGTGGCTACGAG 59.995 44.000 9.63 0.00 0.00 4.18
6043 10025 2.225068 ATGTACATGTGGCTACGAGC 57.775 50.000 7.78 0.00 41.46 5.03
6072 10054 2.124109 TGCGAACCTTGTGGGCAA 60.124 55.556 0.00 0.00 39.10 4.52
6080 10062 2.724520 CTTGTGGGCAAGCAGAAGT 58.275 52.632 0.00 0.00 44.54 3.01
6081 10063 0.313043 CTTGTGGGCAAGCAGAAGTG 59.687 55.000 0.00 0.00 44.54 3.16
6082 10064 0.395586 TTGTGGGCAAGCAGAAGTGT 60.396 50.000 0.00 0.00 0.00 3.55
6083 10065 1.102809 TGTGGGCAAGCAGAAGTGTG 61.103 55.000 0.00 0.00 0.00 3.82
6084 10066 1.103398 GTGGGCAAGCAGAAGTGTGT 61.103 55.000 0.00 0.00 0.00 3.72
6085 10067 1.102809 TGGGCAAGCAGAAGTGTGTG 61.103 55.000 0.00 0.00 0.00 3.82
6086 10068 1.656441 GGCAAGCAGAAGTGTGTGG 59.344 57.895 0.00 0.00 0.00 4.17
6087 10069 1.656441 GCAAGCAGAAGTGTGTGGG 59.344 57.895 0.00 0.00 0.00 4.61
6088 10070 1.656441 CAAGCAGAAGTGTGTGGGC 59.344 57.895 0.00 0.00 0.00 5.36
6089 10071 1.102809 CAAGCAGAAGTGTGTGGGCA 61.103 55.000 0.00 0.00 0.00 5.36
6136 10118 9.167311 GTATTTCTGTGGTTTGATCTGTAATCT 57.833 33.333 0.00 0.00 0.00 2.40
6141 10123 6.177610 TGTGGTTTGATCTGTAATCTTACCC 58.822 40.000 0.00 0.00 32.72 3.69
6182 10187 3.362986 GGTCATATTCGTACTGCATTGCG 60.363 47.826 8.22 8.22 0.00 4.85
6233 10238 5.181811 CCAACTTCAGCTTGATTGTATGACA 59.818 40.000 0.00 0.00 0.00 3.58
6238 10243 6.968131 TCAGCTTGATTGTATGACAAGTAC 57.032 37.500 0.00 0.00 41.94 2.73
6239 10244 6.701340 TCAGCTTGATTGTATGACAAGTACT 58.299 36.000 0.00 0.00 41.94 2.73
6240 10245 6.813649 TCAGCTTGATTGTATGACAAGTACTC 59.186 38.462 0.00 0.00 41.94 2.59
6241 10246 6.036517 CAGCTTGATTGTATGACAAGTACTCC 59.963 42.308 0.00 0.00 41.94 3.85
6242 10247 5.294552 GCTTGATTGTATGACAAGTACTCCC 59.705 44.000 0.00 0.00 41.94 4.30
6243 10248 6.620877 TTGATTGTATGACAAGTACTCCCT 57.379 37.500 0.00 0.00 41.94 4.20
6244 10249 6.222038 TGATTGTATGACAAGTACTCCCTC 57.778 41.667 0.00 0.00 41.94 4.30
6245 10250 5.128827 TGATTGTATGACAAGTACTCCCTCC 59.871 44.000 0.00 0.00 41.94 4.30
6246 10251 3.021695 TGTATGACAAGTACTCCCTCCG 58.978 50.000 0.00 0.00 0.00 4.63
6247 10252 2.233305 ATGACAAGTACTCCCTCCGT 57.767 50.000 0.00 0.00 0.00 4.69
6248 10253 1.542492 TGACAAGTACTCCCTCCGTC 58.458 55.000 0.00 0.00 0.00 4.79
6249 10254 0.816373 GACAAGTACTCCCTCCGTCC 59.184 60.000 0.00 0.00 0.00 4.79
6250 10255 0.614134 ACAAGTACTCCCTCCGTCCC 60.614 60.000 0.00 0.00 0.00 4.46
6251 10256 0.613853 CAAGTACTCCCTCCGTCCCA 60.614 60.000 0.00 0.00 0.00 4.37
6252 10257 0.115745 AAGTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
6253 10258 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
6254 10259 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
6255 10260 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
6256 10261 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
6257 10262 2.488836 ACTCCCTCCGTCCCAAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
6258 10263 3.660959 ACTCCCTCCGTCCCAAAATATA 58.339 45.455 0.00 0.00 0.00 0.86
6259 10264 4.042174 ACTCCCTCCGTCCCAAAATATAA 58.958 43.478 0.00 0.00 0.00 0.98
6260 10265 4.102681 ACTCCCTCCGTCCCAAAATATAAG 59.897 45.833 0.00 0.00 0.00 1.73
6261 10266 4.300345 TCCCTCCGTCCCAAAATATAAGA 58.700 43.478 0.00 0.00 0.00 2.10
6262 10267 4.722781 TCCCTCCGTCCCAAAATATAAGAA 59.277 41.667 0.00 0.00 0.00 2.52
6263 10268 4.820173 CCCTCCGTCCCAAAATATAAGAAC 59.180 45.833 0.00 0.00 0.00 3.01
6264 10269 4.510340 CCTCCGTCCCAAAATATAAGAACG 59.490 45.833 0.00 0.00 0.00 3.95
6265 10270 5.088680 TCCGTCCCAAAATATAAGAACGT 57.911 39.130 0.00 0.00 0.00 3.99
6266 10271 5.490159 TCCGTCCCAAAATATAAGAACGTT 58.510 37.500 0.00 0.00 0.00 3.99
6267 10272 5.939296 TCCGTCCCAAAATATAAGAACGTTT 59.061 36.000 0.46 0.00 0.00 3.60
6268 10273 6.430616 TCCGTCCCAAAATATAAGAACGTTTT 59.569 34.615 0.46 0.00 0.00 2.43
6269 10274 7.040548 TCCGTCCCAAAATATAAGAACGTTTTT 60.041 33.333 9.22 9.22 0.00 1.94
6270 10275 8.235905 CCGTCCCAAAATATAAGAACGTTTTTA 58.764 33.333 13.02 13.02 0.00 1.52
6271 10276 9.609950 CGTCCCAAAATATAAGAACGTTTTTAA 57.390 29.630 14.41 5.85 0.00 1.52
6279 10284 9.953697 AATATAAGAACGTTTTTAACACAAGCA 57.046 25.926 14.41 0.00 0.00 3.91
6283 10288 7.851822 AGAACGTTTTTAACACAAGCATATG 57.148 32.000 0.46 0.00 0.00 1.78
6353 10358 4.247258 ACAACGTGGTCGCTAATCATTTA 58.753 39.130 0.00 0.00 41.18 1.40
6380 10386 1.434555 CACCGCGGATTCAGTAACAA 58.565 50.000 35.90 0.00 0.00 2.83
6386 10392 4.472286 CGCGGATTCAGTAACAATTTTGT 58.528 39.130 0.00 0.00 44.72 2.83
6388 10394 6.081049 CGCGGATTCAGTAACAATTTTGTAA 58.919 36.000 0.00 0.00 41.31 2.41
6642 10648 4.115199 GCCGGTGGGGATGCTCTT 62.115 66.667 1.90 0.00 38.47 2.85
6719 10725 4.035102 GCCTCTTCCCCAACCGCT 62.035 66.667 0.00 0.00 0.00 5.52
6723 10729 2.111999 CTCTTCCCCAACCGCTGTCA 62.112 60.000 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 96 2.964464 GAGCTAGGGTTCCTTACCTACC 59.036 54.545 0.00 0.00 46.86 3.18
95 97 2.622470 CGAGCTAGGGTTCCTTACCTAC 59.378 54.545 0.00 0.00 46.86 3.18
96 98 2.511218 TCGAGCTAGGGTTCCTTACCTA 59.489 50.000 0.00 0.00 46.86 3.08
97 99 1.287146 TCGAGCTAGGGTTCCTTACCT 59.713 52.381 0.00 0.00 46.86 3.08
153 157 1.549950 GCAAAGATGGAAGAACCCCCA 60.550 52.381 0.00 0.00 38.00 4.96
269 708 4.430908 ACGAAGTAAACTCCGATTGATCC 58.569 43.478 0.00 0.00 41.94 3.36
355 795 3.056179 GGATTCCCGCAAAATTCAGGAAA 60.056 43.478 0.00 0.00 39.89 3.13
374 815 2.493875 GGGTTTGGGGGTTTAGTTGGAT 60.494 50.000 0.00 0.00 0.00 3.41
434 882 2.400408 CGTTCCGAAAAGAAATGCAACG 59.600 45.455 0.00 0.00 0.00 4.10
553 1001 3.372660 AAAATAGGCGAACGGCAAAAA 57.627 38.095 21.28 5.73 46.16 1.94
554 1002 3.372660 AAAAATAGGCGAACGGCAAAA 57.627 38.095 21.28 8.00 46.16 2.44
594 1044 4.341235 GGGTAAAGCAAGAAACCAAGAACT 59.659 41.667 0.00 0.00 33.46 3.01
654 1104 2.948979 ACATGCCGACAAAAGAACAGAA 59.051 40.909 0.00 0.00 0.00 3.02
717 1167 4.356289 CAACGGTTTCACCCAAAACTAAG 58.644 43.478 0.00 0.00 38.81 2.18
970 1475 4.096382 GGTGCATACCAAAACTACATGAGG 59.904 45.833 0.00 0.00 46.71 3.86
1075 1580 3.131400 ACGTTGCCAGTACCAACAATTTT 59.869 39.130 12.16 0.00 41.94 1.82
1281 1786 9.798994 TCCTGTAGATTAAAAATCGTAGTTCTC 57.201 33.333 0.00 0.00 0.00 2.87
1535 2044 8.067784 GCATACATATACATGTGTTGTACAACC 58.932 37.037 30.68 22.74 45.17 3.77
1757 2279 5.122519 TGACAAGCAGAAGAAACATGTGTA 58.877 37.500 0.00 0.00 0.00 2.90
1759 2281 4.556942 TGACAAGCAGAAGAAACATGTG 57.443 40.909 0.00 0.00 0.00 3.21
1763 2285 4.458989 ACAAGTTGACAAGCAGAAGAAACA 59.541 37.500 10.54 0.00 0.00 2.83
1764 2286 4.795278 CACAAGTTGACAAGCAGAAGAAAC 59.205 41.667 10.54 0.00 0.00 2.78
1809 2336 4.635324 ACCAAAAGGCAACAAAGTGAAATG 59.365 37.500 0.00 0.00 41.41 2.32
1816 2343 4.440880 TCAATGACCAAAAGGCAACAAAG 58.559 39.130 0.00 0.00 41.41 2.77
1850 2378 1.481871 CAGGCTCCAGCATTCCAAAT 58.518 50.000 0.03 0.00 44.36 2.32
1860 2388 3.324930 TGCACCTCCAGGCTCCAG 61.325 66.667 0.00 0.00 39.32 3.86
1861 2389 3.640407 GTGCACCTCCAGGCTCCA 61.640 66.667 5.22 0.00 39.32 3.86
1862 2390 2.900106 AAGTGCACCTCCAGGCTCC 61.900 63.158 14.63 0.00 39.32 4.70
1863 2391 1.673665 CAAGTGCACCTCCAGGCTC 60.674 63.158 14.63 0.00 39.32 4.70
1864 2392 1.708993 TTCAAGTGCACCTCCAGGCT 61.709 55.000 14.63 0.00 39.32 4.58
1865 2393 0.610232 ATTCAAGTGCACCTCCAGGC 60.610 55.000 14.63 0.00 39.32 4.85
1866 2394 1.915141 AATTCAAGTGCACCTCCAGG 58.085 50.000 14.63 0.00 42.17 4.45
1900 2428 4.558538 AAGAGCAAACACTAACAGCAAG 57.441 40.909 0.00 0.00 0.00 4.01
1904 2432 6.363577 TCAAGAAAGAGCAAACACTAACAG 57.636 37.500 0.00 0.00 0.00 3.16
2103 2651 4.222366 TGCATGCAACCATTGAGGAAATAA 59.778 37.500 20.30 0.00 41.22 1.40
2209 6054 7.110155 GGATACATTTCTCCAACTGAGGTTAA 58.890 38.462 0.00 0.00 41.76 2.01
2323 6169 5.047448 CACTGGTCATCTGTATCATCCCTAG 60.047 48.000 0.00 0.00 0.00 3.02
2369 6215 2.131709 CCCAATGCTGGCTGATGGG 61.132 63.158 13.20 13.20 44.38 4.00
2494 6340 8.701908 AGTATTGCTTGAATATGAATGTCCAT 57.298 30.769 0.00 0.00 0.00 3.41
2768 6614 7.414098 GGTGATTTTAACATGTAGCGTGATCTT 60.414 37.037 0.00 0.00 0.00 2.40
3152 7005 0.035439 CACTGGCAGATAACCCCGTT 60.035 55.000 23.66 0.00 0.00 4.44
3153 7006 0.907704 TCACTGGCAGATAACCCCGT 60.908 55.000 23.66 0.00 0.00 5.28
3239 7092 5.611374 TCTGTTGAGGAACTAAAAGACTGG 58.389 41.667 0.00 0.00 41.55 4.00
3419 7272 7.832187 CCTTTGTAACCTCCATACCTTATTTGA 59.168 37.037 0.00 0.00 0.00 2.69
3497 7350 8.275015 TGTTTTCTGACTGAAACTTTGACATA 57.725 30.769 6.98 0.00 43.55 2.29
3860 7713 1.285023 GCATCCCATCATTGCTCGC 59.715 57.895 0.00 0.00 33.61 5.03
3900 7753 7.275920 ACTTGAATGAATACCTGTCCATACTC 58.724 38.462 0.00 0.00 0.00 2.59
3905 7758 6.542821 AGAAACTTGAATGAATACCTGTCCA 58.457 36.000 0.00 0.00 0.00 4.02
3925 7778 6.046593 CCACGGTTATCTGCACTATTAGAAA 58.953 40.000 0.00 0.00 0.00 2.52
4044 7897 1.133325 ACAGTTAACCATGTGGCCCAA 60.133 47.619 0.00 0.00 39.32 4.12
4282 8145 9.307121 CAAGAGTAGTACATCCAAGAAATAGTG 57.693 37.037 2.52 0.00 0.00 2.74
4765 8686 0.480690 TTGGCATGTTACCACCACCT 59.519 50.000 0.00 0.00 36.76 4.00
4831 8777 6.978674 TTGAGCCTATACTGTAGCACTTAT 57.021 37.500 0.00 0.00 0.00 1.73
4860 8807 3.737559 AGCCCCACATTAGTTTCATCA 57.262 42.857 0.00 0.00 0.00 3.07
4952 8906 2.671396 CGATCCAAAACGTAGGTCCTTG 59.329 50.000 0.00 0.00 0.00 3.61
5340 9310 4.288324 AGAGCTTCCCTATTACTCCCTT 57.712 45.455 0.00 0.00 0.00 3.95
5426 9396 8.771766 CCATCAACTATCAAATCAGTGTCATAG 58.228 37.037 0.00 0.00 0.00 2.23
5621 9591 0.733909 GCAAAGATTTCACCGCCAGC 60.734 55.000 0.00 0.00 0.00 4.85
5874 9856 4.396478 TCGTCTCATTCTGTTCTCGAGATT 59.604 41.667 17.44 0.00 35.35 2.40
5996 9978 8.169977 ACACATCTGAGTCAACAATTACAATT 57.830 30.769 0.00 0.00 0.00 2.32
6023 10005 2.550978 GCTCGTAGCCACATGTACATT 58.449 47.619 5.37 0.00 34.48 2.71
6037 10019 1.667724 GCAGTACTTCGTAGGCTCGTA 59.332 52.381 0.00 0.00 0.00 3.43
6038 10020 0.450983 GCAGTACTTCGTAGGCTCGT 59.549 55.000 0.00 0.00 0.00 4.18
6039 10021 0.589229 CGCAGTACTTCGTAGGCTCG 60.589 60.000 6.77 0.00 0.00 5.03
6041 10023 1.135460 GTTCGCAGTACTTCGTAGGCT 60.135 52.381 14.48 0.00 0.00 4.58
6042 10024 1.266466 GTTCGCAGTACTTCGTAGGC 58.734 55.000 14.48 2.77 0.00 3.93
6043 10025 1.471684 AGGTTCGCAGTACTTCGTAGG 59.528 52.381 14.48 0.00 0.00 3.18
6072 10054 0.178981 AATGCCCACACACTTCTGCT 60.179 50.000 0.00 0.00 0.00 4.24
6073 10055 0.675633 AAATGCCCACACACTTCTGC 59.324 50.000 0.00 0.00 0.00 4.26
6074 10056 1.000060 CCAAATGCCCACACACTTCTG 60.000 52.381 0.00 0.00 0.00 3.02
6075 10057 1.133513 TCCAAATGCCCACACACTTCT 60.134 47.619 0.00 0.00 0.00 2.85
6076 10058 1.327303 TCCAAATGCCCACACACTTC 58.673 50.000 0.00 0.00 0.00 3.01
6077 10059 1.619827 CATCCAAATGCCCACACACTT 59.380 47.619 0.00 0.00 0.00 3.16
6078 10060 1.259609 CATCCAAATGCCCACACACT 58.740 50.000 0.00 0.00 0.00 3.55
6079 10061 3.818586 CATCCAAATGCCCACACAC 57.181 52.632 0.00 0.00 0.00 3.82
6088 10070 0.801872 TCAACGACGGCATCCAAATG 59.198 50.000 0.00 0.00 35.87 2.32
6089 10071 1.529226 TTCAACGACGGCATCCAAAT 58.471 45.000 0.00 0.00 0.00 2.32
6099 10081 4.151689 ACCACAGAAATACATTCAACGACG 59.848 41.667 0.00 0.00 40.72 5.12
6233 10238 0.115745 TTGGGACGGAGGGAGTACTT 59.884 55.000 0.00 0.00 0.00 2.24
6238 10243 4.347000 TCTTATATTTTGGGACGGAGGGAG 59.653 45.833 0.00 0.00 0.00 4.30
6239 10244 4.300345 TCTTATATTTTGGGACGGAGGGA 58.700 43.478 0.00 0.00 0.00 4.20
6240 10245 4.699925 TCTTATATTTTGGGACGGAGGG 57.300 45.455 0.00 0.00 0.00 4.30
6241 10246 4.510340 CGTTCTTATATTTTGGGACGGAGG 59.490 45.833 0.00 0.00 0.00 4.30
6242 10247 5.114081 ACGTTCTTATATTTTGGGACGGAG 58.886 41.667 0.00 0.00 0.00 4.63
6243 10248 5.088680 ACGTTCTTATATTTTGGGACGGA 57.911 39.130 0.00 0.00 0.00 4.69
6244 10249 5.806366 AACGTTCTTATATTTTGGGACGG 57.194 39.130 0.00 0.00 0.00 4.79
6245 10250 9.609950 TTAAAAACGTTCTTATATTTTGGGACG 57.390 29.630 0.00 0.00 0.00 4.79
6253 10258 9.953697 TGCTTGTGTTAAAAACGTTCTTATATT 57.046 25.926 0.00 0.00 0.00 1.28
6257 10262 9.388346 CATATGCTTGTGTTAAAAACGTTCTTA 57.612 29.630 0.00 0.00 0.00 2.10
6258 10263 7.381139 CCATATGCTTGTGTTAAAAACGTTCTT 59.619 33.333 0.00 0.00 0.00 2.52
6259 10264 6.861055 CCATATGCTTGTGTTAAAAACGTTCT 59.139 34.615 0.00 0.00 0.00 3.01
6260 10265 6.858993 TCCATATGCTTGTGTTAAAAACGTTC 59.141 34.615 0.00 0.00 0.00 3.95
6261 10266 6.740110 TCCATATGCTTGTGTTAAAAACGTT 58.260 32.000 0.00 0.00 0.00 3.99
6262 10267 6.016610 ACTCCATATGCTTGTGTTAAAAACGT 60.017 34.615 0.00 0.00 0.00 3.99
6263 10268 6.305399 CACTCCATATGCTTGTGTTAAAAACG 59.695 38.462 0.00 0.00 0.00 3.60
6264 10269 7.367285 TCACTCCATATGCTTGTGTTAAAAAC 58.633 34.615 15.52 0.00 0.00 2.43
6265 10270 7.517614 TCACTCCATATGCTTGTGTTAAAAA 57.482 32.000 15.52 0.34 0.00 1.94
6266 10271 7.517614 TTCACTCCATATGCTTGTGTTAAAA 57.482 32.000 15.52 5.46 0.00 1.52
6267 10272 7.701539 ATTCACTCCATATGCTTGTGTTAAA 57.298 32.000 15.52 7.75 0.00 1.52
6268 10273 7.537715 CAATTCACTCCATATGCTTGTGTTAA 58.462 34.615 15.52 8.22 0.00 2.01
6269 10274 6.404623 GCAATTCACTCCATATGCTTGTGTTA 60.405 38.462 15.52 9.18 0.00 2.41
6270 10275 5.622914 GCAATTCACTCCATATGCTTGTGTT 60.623 40.000 15.52 6.18 0.00 3.32
6271 10276 4.142315 GCAATTCACTCCATATGCTTGTGT 60.142 41.667 15.52 1.76 0.00 3.72
6272 10277 4.142337 TGCAATTCACTCCATATGCTTGTG 60.142 41.667 12.00 12.00 34.97 3.33
6273 10278 4.018490 TGCAATTCACTCCATATGCTTGT 58.982 39.130 0.00 0.00 34.97 3.16
6274 10279 4.642445 TGCAATTCACTCCATATGCTTG 57.358 40.909 0.00 0.00 34.97 4.01
6275 10280 4.951715 TCTTGCAATTCACTCCATATGCTT 59.048 37.500 0.00 0.00 34.97 3.91
6276 10281 4.529897 TCTTGCAATTCACTCCATATGCT 58.470 39.130 0.00 0.00 34.97 3.79
6277 10282 4.906065 TCTTGCAATTCACTCCATATGC 57.094 40.909 0.00 0.00 0.00 3.14
6278 10283 6.038356 GGTTTCTTGCAATTCACTCCATATG 58.962 40.000 0.00 0.00 0.00 1.78
6279 10284 5.716228 TGGTTTCTTGCAATTCACTCCATAT 59.284 36.000 0.00 0.00 0.00 1.78
6280 10285 5.076182 TGGTTTCTTGCAATTCACTCCATA 58.924 37.500 0.00 0.00 0.00 2.74
6281 10286 3.896888 TGGTTTCTTGCAATTCACTCCAT 59.103 39.130 0.00 0.00 0.00 3.41
6282 10287 3.295093 TGGTTTCTTGCAATTCACTCCA 58.705 40.909 0.00 1.97 0.00 3.86
6283 10288 4.022068 TGATGGTTTCTTGCAATTCACTCC 60.022 41.667 0.00 0.00 0.00 3.85
6353 10358 1.862602 GAATCCGCGGTGGCTTTTGT 61.863 55.000 27.15 0.38 37.80 2.83
6386 10392 7.009999 GCGGAATTACATGTTCAATGCAATTTA 59.990 33.333 2.30 0.00 31.22 1.40
6388 10394 5.291614 GCGGAATTACATGTTCAATGCAATT 59.708 36.000 2.30 1.56 36.63 2.32
6395 10401 1.201976 CGCGCGGAATTACATGTTCAA 60.202 47.619 24.84 0.00 0.00 2.69
6484 10490 4.242475 TCGACAAGATGTACGCTCAAATT 58.758 39.130 0.00 0.00 0.00 1.82
6719 10725 3.141522 AACGACTTCGGCGGTGACA 62.142 57.895 7.21 0.00 44.95 3.58
6723 10729 2.444700 ATTCCAACGACTTCGGCGGT 62.445 55.000 7.21 0.00 44.95 5.68


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

AutoCloner maintained by Alex Coulton.