Multiple sequence alignment - TraesCS3B01G422600

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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 TraesCS3B01G422600 chr3B 100.000 4211 0 0 2796 7006 659574356 659578566 0.000000e+00 7777.0
1 TraesCS3B01G422600 chr3B 100.000 2406 0 0 1 2406 659571561 659573966 0.000000e+00 4444.0
2 TraesCS3B01G422600 chr3B 94.086 186 8 3 5957 6142 659582648 659582466 5.350000e-71 279.0
3 TraesCS3B01G422600 chr3D 94.734 1975 62 15 4019 5956 498871605 498873574 0.000000e+00 3033.0
4 TraesCS3B01G422600 chr3D 95.493 1553 43 6 834 2385 498866890 498868416 0.000000e+00 2455.0
5 TraesCS3B01G422600 chr3D 95.200 1125 19 5 2796 3885 498868615 498869739 0.000000e+00 1746.0
6 TraesCS3B01G422600 chr3D 93.719 796 38 6 52 839 498865845 498866636 0.000000e+00 1182.0
7 TraesCS3B01G422600 chr3A 93.766 1540 74 8 860 2389 638978329 638979856 0.000000e+00 2292.0
8 TraesCS3B01G422600 chr3A 92.549 1020 45 8 4961 5956 638982536 638983548 0.000000e+00 1434.0
9 TraesCS3B01G422600 chr3A 91.207 1069 63 11 3911 4963 638981380 638982433 0.000000e+00 1424.0
10 TraesCS3B01G422600 chr3A 93.189 925 32 13 2796 3693 638979931 638980851 0.000000e+00 1330.0
11 TraesCS3B01G422600 chr3A 86.525 141 13 3 3721 3858 638980848 638980985 4.380000e-32 150.0
12 TraesCS3B01G422600 chr3A 85.714 119 6 7 813 929 638976167 638976276 1.600000e-21 115.0
13 TraesCS3B01G422600 chr7A 89.038 1040 66 20 5977 7006 42745906 42746907 0.000000e+00 1245.0
14 TraesCS3B01G422600 chr7A 88.843 242 20 4 5957 6198 42790710 42790476 2.470000e-74 291.0
15 TraesCS3B01G422600 chr7A 94.643 56 3 0 6194 6249 42790506 42790451 3.480000e-13 87.9
16 TraesCS3B01G422600 chr7D 88.582 1051 80 18 5957 7006 80720701 80721712 0.000000e+00 1240.0
17 TraesCS3B01G422600 chr7D 89.796 196 20 0 5957 6152 80724668 80724473 1.170000e-62 252.0
18 TraesCS3B01G422600 chr5D 88.224 1053 82 24 5957 7006 211816647 211815634 0.000000e+00 1219.0
19 TraesCS3B01G422600 chr5D 90.909 198 18 0 5955 6152 211812672 211812869 4.170000e-67 267.0
20 TraesCS3B01G422600 chr7B 96.386 166 6 0 5988 6153 552555326 552555161 2.490000e-69 274.0
21 TraesCS3B01G422600 chr6B 84.615 221 29 2 5957 6172 314788803 314788583 1.530000e-51 215.0


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 TraesCS3B01G422600 chr3B 659571561 659578566 7005 False 6110.500000 7777 100.000000 1 7006 2 chr3B.!!$F1 7005
1 TraesCS3B01G422600 chr3D 498865845 498873574 7729 False 2104.000000 3033 94.786500 52 5956 4 chr3D.!!$F1 5904
2 TraesCS3B01G422600 chr3A 638976167 638983548 7381 False 1124.166667 2292 90.491667 813 5956 6 chr3A.!!$F1 5143
3 TraesCS3B01G422600 chr7A 42745906 42746907 1001 False 1245.000000 1245 89.038000 5977 7006 1 chr7A.!!$F1 1029
4 TraesCS3B01G422600 chr7D 80720701 80721712 1011 False 1240.000000 1240 88.582000 5957 7006 1 chr7D.!!$F1 1049
5 TraesCS3B01G422600 chr5D 211815634 211816647 1013 True 1219.000000 1219 88.224000 5957 7006 1 chr5D.!!$R1 1049

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
318 319 0.040157 GCGAGTGAAAGTTGCATGCA 60.040 50.000 18.46 18.46 46.27 3.96 F
1310 3691 0.250209 CTGACTGTGCTGGACTGCTT 60.250 55.000 6.12 0.00 0.00 3.91 F
1938 4327 1.755179 CCACCGGAGAATGAGCATTT 58.245 50.000 9.46 0.00 0.00 2.32 F
3077 5486 0.035458 GTTCACCCTGTCCAGAGTGG 59.965 60.000 8.79 0.00 37.69 4.00 F
3517 5955 0.530744 GTGGTACTGTCGATGCAGGA 59.469 55.000 7.82 0.00 40.59 3.86 F
4242 8421 0.391228 TGCCGAACACTGAAGCTACA 59.609 50.000 0.00 0.00 0.00 2.74 F
5674 9986 1.001406 CTGGAGCTTCGAACAGGAAGT 59.999 52.381 0.00 0.00 44.17 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1430 3811 0.979709 TGGCAGGATCACTCTCCCAG 60.980 60.000 0.00 0.0 35.79 4.45 R
2256 4647 2.775911 CTGGCAGATTTCAGGAGTCA 57.224 50.000 9.42 0.0 0.00 3.41 R
3893 6339 0.107459 GACTTCATGCACCTCCCCTC 60.107 60.000 0.00 0.0 0.00 4.30 R
3977 6765 0.179207 CATCATGTCACAGCACACGC 60.179 55.000 0.00 0.0 38.99 5.34 R
5244 9556 0.181114 ACAGCCATCGGTGCATACAT 59.819 50.000 0.00 0.0 41.36 2.29 R
5683 9995 0.036388 TCCAGATCCGAGGTTTGCAC 60.036 55.000 0.00 0.0 0.00 4.57 R
6536 10871 1.748591 GCACAATTTGGCCCAAAACCA 60.749 47.619 13.87 0.0 36.90 3.67 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
24 25 7.823745 ACCCAAATACATTATTGTCTCATCC 57.176 36.000 0.00 0.00 37.28 3.51
25 26 6.777580 ACCCAAATACATTATTGTCTCATCCC 59.222 38.462 0.00 0.00 37.28 3.85
26 27 6.072508 CCCAAATACATTATTGTCTCATCCCG 60.073 42.308 0.00 0.00 37.28 5.14
27 28 6.710295 CCAAATACATTATTGTCTCATCCCGA 59.290 38.462 0.00 0.00 37.28 5.14
28 29 7.307989 CCAAATACATTATTGTCTCATCCCGAC 60.308 40.741 0.00 0.00 37.28 4.79
29 30 4.753516 ACATTATTGTCTCATCCCGACA 57.246 40.909 0.00 0.00 39.45 4.35
34 35 3.694043 TTGTCTCATCCCGACAAATGA 57.306 42.857 3.38 0.00 45.39 2.57
35 36 2.972625 TGTCTCATCCCGACAAATGAC 58.027 47.619 0.00 0.00 38.36 3.06
36 37 2.301583 TGTCTCATCCCGACAAATGACA 59.698 45.455 0.00 0.00 38.36 3.58
37 38 3.244387 TGTCTCATCCCGACAAATGACAA 60.244 43.478 0.00 0.00 38.36 3.18
38 39 3.125316 GTCTCATCCCGACAAATGACAAC 59.875 47.826 0.00 0.00 0.00 3.32
39 40 3.073678 CTCATCCCGACAAATGACAACA 58.926 45.455 0.00 0.00 0.00 3.33
40 41 3.481453 TCATCCCGACAAATGACAACAA 58.519 40.909 0.00 0.00 0.00 2.83
41 42 4.078537 TCATCCCGACAAATGACAACAAT 58.921 39.130 0.00 0.00 0.00 2.71
42 43 5.249420 TCATCCCGACAAATGACAACAATA 58.751 37.500 0.00 0.00 0.00 1.90
43 44 5.353956 TCATCCCGACAAATGACAACAATAG 59.646 40.000 0.00 0.00 0.00 1.73
44 45 4.647611 TCCCGACAAATGACAACAATAGT 58.352 39.130 0.00 0.00 0.00 2.12
45 46 5.067273 TCCCGACAAATGACAACAATAGTT 58.933 37.500 0.00 0.00 38.88 2.24
46 47 5.180492 TCCCGACAAATGACAACAATAGTTC 59.820 40.000 0.00 0.00 35.28 3.01
47 48 5.390613 CCGACAAATGACAACAATAGTTCC 58.609 41.667 0.00 0.00 35.28 3.62
48 49 5.390613 CGACAAATGACAACAATAGTTCCC 58.609 41.667 0.00 0.00 35.28 3.97
49 50 5.619086 CGACAAATGACAACAATAGTTCCCC 60.619 44.000 0.00 0.00 35.28 4.81
50 51 5.393866 ACAAATGACAACAATAGTTCCCCT 58.606 37.500 0.00 0.00 35.28 4.79
71 72 5.163499 CCCTTTCACTCGCTCTAGATACTTT 60.163 44.000 0.00 0.00 0.00 2.66
74 75 3.066900 TCACTCGCTCTAGATACTTTGGC 59.933 47.826 0.00 0.00 0.00 4.52
75 76 3.024547 ACTCGCTCTAGATACTTTGGCA 58.975 45.455 0.00 0.00 0.00 4.92
77 78 2.100916 TCGCTCTAGATACTTTGGCACC 59.899 50.000 0.00 0.00 0.00 5.01
78 79 2.159099 CGCTCTAGATACTTTGGCACCA 60.159 50.000 0.00 0.00 0.00 4.17
79 80 3.493350 CGCTCTAGATACTTTGGCACCAT 60.493 47.826 0.00 0.00 0.00 3.55
80 81 4.061596 GCTCTAGATACTTTGGCACCATC 58.938 47.826 0.00 0.00 0.00 3.51
81 82 4.443457 GCTCTAGATACTTTGGCACCATCA 60.443 45.833 0.00 0.00 0.00 3.07
125 126 1.630878 GGAATCCACCTCCTGTTCAGT 59.369 52.381 0.00 0.00 0.00 3.41
140 141 3.327757 TGTTCAGTTGAGCAGTAATCCCT 59.672 43.478 0.00 0.00 31.61 4.20
187 188 6.568271 CGTTGGAAGTGATTCATGTGATCAAA 60.568 38.462 13.50 0.00 0.00 2.69
233 234 6.897966 TGAATAGATGGGTAGACAGAGTTCTT 59.102 38.462 0.00 0.00 0.00 2.52
242 243 6.473758 GGTAGACAGAGTTCTTTAATGGGTT 58.526 40.000 0.00 0.00 0.00 4.11
251 252 5.183140 AGTTCTTTAATGGGTTCGTTCATGG 59.817 40.000 0.00 0.00 0.00 3.66
280 281 1.448985 TGCCTTGTCGACCAAATAGC 58.551 50.000 14.12 8.01 31.20 2.97
292 293 5.810587 TCGACCAAATAGCTGATTGAGTAAC 59.189 40.000 13.19 1.65 0.00 2.50
318 319 0.040157 GCGAGTGAAAGTTGCATGCA 60.040 50.000 18.46 18.46 46.27 3.96
340 341 1.813513 AACACTTTCCCTCATGCGAG 58.186 50.000 0.00 0.00 39.16 5.03
356 357 1.532868 GCGAGTGAAAGTGCAACAGAT 59.467 47.619 0.00 0.00 41.43 2.90
425 426 3.514309 ACACTATAGCACCGAAGACCTTT 59.486 43.478 0.00 0.00 0.00 3.11
434 435 1.593196 CGAAGACCTTTGCTCCACAA 58.407 50.000 0.00 0.00 36.13 3.33
474 475 7.416964 TTTAAACACCCCATCCTTCATATTG 57.583 36.000 0.00 0.00 0.00 1.90
485 486 4.002982 TCCTTCATATTGCACATATCCGC 58.997 43.478 0.00 0.00 0.00 5.54
572 573 9.817809 GTATACCTCTTCATTGATGTTGTTAGA 57.182 33.333 0.00 0.00 0.00 2.10
583 584 6.299805 TGATGTTGTTAGAGCAACTCCTAT 57.700 37.500 10.10 0.00 46.33 2.57
637 645 7.609960 TGACCTGAAGCATTTGCATAAAAATA 58.390 30.769 5.20 0.00 45.16 1.40
638 646 8.093307 TGACCTGAAGCATTTGCATAAAAATAA 58.907 29.630 5.20 0.00 45.16 1.40
639 647 8.255394 ACCTGAAGCATTTGCATAAAAATAAC 57.745 30.769 5.20 0.00 45.16 1.89
641 649 8.719648 CCTGAAGCATTTGCATAAAAATAACAA 58.280 29.630 5.20 0.00 45.16 2.83
935 3316 1.979693 AGTCTCACTCGGCCCACTC 60.980 63.158 0.00 0.00 0.00 3.51
999 3380 2.362503 ATCGACCCACAGGCGAGA 60.363 61.111 0.00 0.00 42.31 4.04
1000 3381 2.418910 ATCGACCCACAGGCGAGAG 61.419 63.158 0.00 0.00 42.31 3.20
1025 3406 1.669779 ACATCTCGTCGCTACTGTACC 59.330 52.381 0.00 0.00 0.00 3.34
1127 3508 1.368950 GCAGAGGGCGATGATGCTA 59.631 57.895 0.00 0.00 34.10 3.49
1282 3663 4.817464 CACTAGGTACGAGCATAGAGTTCT 59.183 45.833 8.94 0.00 33.18 3.01
1310 3691 0.250209 CTGACTGTGCTGGACTGCTT 60.250 55.000 6.12 0.00 0.00 3.91
1613 4002 5.412904 GCACTAGATGGCCTTTAATATCACC 59.587 44.000 3.32 0.00 0.00 4.02
1783 4172 1.770658 TGAGGGCATGCTAAGCAGTAT 59.229 47.619 18.92 0.00 43.65 2.12
1788 4177 3.077359 GGCATGCTAAGCAGTATAAGGG 58.923 50.000 18.92 0.00 43.65 3.95
1938 4327 1.755179 CCACCGGAGAATGAGCATTT 58.245 50.000 9.46 0.00 0.00 2.32
2049 4439 2.494059 TGCTTTGAGTGTAAGCTGGTC 58.506 47.619 8.78 0.00 46.30 4.02
2067 4457 4.750941 TGGTCATTTGAAGGGGAATTCTT 58.249 39.130 5.23 0.00 0.00 2.52
2068 4458 4.527816 TGGTCATTTGAAGGGGAATTCTTG 59.472 41.667 5.23 0.00 0.00 3.02
2087 4477 8.833231 ATTCTTGGTATGATTATGGTTACGAG 57.167 34.615 0.00 0.00 0.00 4.18
2097 4487 8.500753 TGATTATGGTTACGAGCTTAATGTTT 57.499 30.769 0.00 0.00 35.21 2.83
2389 4780 0.622136 ATGCTCAGGTTCATCAGCCA 59.378 50.000 0.00 0.00 0.00 4.75
2396 4805 0.961019 GGTTCATCAGCCAACTTGCA 59.039 50.000 0.00 0.00 0.00 4.08
2911 5320 3.138283 AGAGTTCAGTTGAATTGGACCCA 59.862 43.478 0.00 0.00 36.33 4.51
3077 5486 0.035458 GTTCACCCTGTCCAGAGTGG 59.965 60.000 8.79 0.00 37.69 4.00
3366 5778 4.185413 CGCAGGTACACGAGCAAT 57.815 55.556 0.00 0.00 31.84 3.56
3385 5797 4.439289 GCAATGTCTTTGGCATAGTCTTCC 60.439 45.833 4.86 0.00 35.75 3.46
3509 5947 2.181021 GGGCGAGTGGTACTGTCG 59.819 66.667 7.43 7.43 37.32 4.35
3517 5955 0.530744 GTGGTACTGTCGATGCAGGA 59.469 55.000 7.82 0.00 40.59 3.86
3519 5957 1.831106 TGGTACTGTCGATGCAGGATT 59.169 47.619 7.82 0.00 40.59 3.01
3648 6086 3.431673 TCACATGGCTGGTGAACATAA 57.568 42.857 8.92 0.00 41.96 1.90
3679 6117 0.872388 GGTGTTTGGAGCAGGTAACG 59.128 55.000 0.00 0.00 46.39 3.18
3681 6119 1.798813 GTGTTTGGAGCAGGTAACGAG 59.201 52.381 0.00 0.00 46.39 4.18
3796 6242 4.602340 ATCCTATAAGCACTTGGTACCG 57.398 45.455 7.57 0.00 0.00 4.02
3872 6318 2.223249 ACGTGTGTGAATTTCTGTGTGC 60.223 45.455 0.00 0.00 0.00 4.57
3907 6353 3.813724 GGGGAGGGGAGGTGCATG 61.814 72.222 0.00 0.00 0.00 4.06
3908 6354 2.692368 GGGAGGGGAGGTGCATGA 60.692 66.667 0.00 0.00 0.00 3.07
3909 6355 2.308722 GGGAGGGGAGGTGCATGAA 61.309 63.158 0.00 0.00 0.00 2.57
3915 6703 0.678048 GGGAGGTGCATGAAGTCCAC 60.678 60.000 0.00 0.00 0.00 4.02
3936 6724 4.806247 CACTGCTAAGAACACTACTATGGC 59.194 45.833 0.00 0.00 0.00 4.40
3963 6751 5.141182 TCCAAATAAACTGTGGCCTGTTTA 58.859 37.500 21.95 21.95 44.14 2.01
4002 6790 1.624813 TGCTGTGACATGATGTCCTGA 59.375 47.619 21.68 1.51 46.40 3.86
4006 6794 3.099141 TGTGACATGATGTCCTGAGCTA 58.901 45.455 21.68 0.00 46.40 3.32
4012 6800 6.777580 TGACATGATGTCCTGAGCTAGTTATA 59.222 38.462 21.68 0.00 46.40 0.98
4013 6801 7.452813 TGACATGATGTCCTGAGCTAGTTATAT 59.547 37.037 21.68 0.00 46.40 0.86
4017 6805 6.782494 TGATGTCCTGAGCTAGTTATATTGGA 59.218 38.462 0.00 0.00 0.00 3.53
4106 8284 7.042335 CCAACTGGTTTTATGTGGTTTAAACA 58.958 34.615 19.57 0.57 33.33 2.83
4147 8325 4.955811 TCACTGTGAGTTTGTGGTCTAT 57.044 40.909 6.36 0.00 33.04 1.98
4165 8343 9.132521 GTGGTCTATGAACTTCAATGAAATTTG 57.867 33.333 0.00 0.00 31.22 2.32
4242 8421 0.391228 TGCCGAACACTGAAGCTACA 59.609 50.000 0.00 0.00 0.00 2.74
4266 8445 7.383300 ACACAATACCGTGAAGTACTTACTTTC 59.617 37.037 8.42 0.00 45.84 2.62
4291 8477 5.773680 TGTTATGGTACTAGATAGTCCCAGC 59.226 44.000 9.77 4.39 44.09 4.85
4300 8489 4.323553 AGATAGTCCCAGCGTTACATTC 57.676 45.455 0.00 0.00 0.00 2.67
4357 8546 6.291377 TGGGCAAAGTAGATATCACATTCTC 58.709 40.000 5.32 0.00 0.00 2.87
4360 8549 7.041508 GGGCAAAGTAGATATCACATTCTCTTG 60.042 40.741 5.32 0.00 0.00 3.02
4452 8641 3.319405 ACCGTATCAGAGATGCTGTAAGG 59.681 47.826 0.00 0.00 45.14 2.69
4548 8737 1.207329 GTAGTTGATCTCCCGGTTGCT 59.793 52.381 0.00 0.00 0.00 3.91
4690 8879 2.647683 TGCAAACTATCACCACCACA 57.352 45.000 0.00 0.00 0.00 4.17
4986 9283 3.710209 ATCTTGAGTAAGCAAGCCAGT 57.290 42.857 0.00 0.00 43.78 4.00
4996 9293 6.472887 AGTAAGCAAGCCAGTAGAATGTTAA 58.527 36.000 0.00 0.00 0.00 2.01
4999 9296 6.442513 AGCAAGCCAGTAGAATGTTAATTC 57.557 37.500 0.00 0.00 42.26 2.17
5021 9318 5.301555 TCGTTATGTTTGTCAAGGTCATGA 58.698 37.500 0.00 0.00 0.00 3.07
5023 9320 6.023435 CGTTATGTTTGTCAAGGTCATGATG 58.977 40.000 0.00 0.00 0.00 3.07
5025 9322 5.633830 ATGTTTGTCAAGGTCATGATGTC 57.366 39.130 0.00 0.00 0.00 3.06
5026 9323 4.459330 TGTTTGTCAAGGTCATGATGTCA 58.541 39.130 0.00 0.00 0.00 3.58
5143 9455 4.078639 AGCAATGCTCTAAGTCATACCC 57.921 45.455 0.00 0.00 30.62 3.69
5187 9499 4.019141 ACCATAGTTGATTTACCGGAACCA 60.019 41.667 9.46 0.00 0.00 3.67
5211 9523 7.040201 CCACCAATCATTATCTGTAATTCCCTG 60.040 40.741 0.00 0.00 0.00 4.45
5424 9736 5.702865 TGTATGAACTTGCAAGAAAGATGC 58.297 37.500 32.50 19.31 44.08 3.91
5631 9943 5.781210 ATAGAGCAAGAGATGATGAACGA 57.219 39.130 0.00 0.00 0.00 3.85
5674 9986 1.001406 CTGGAGCTTCGAACAGGAAGT 59.999 52.381 0.00 0.00 44.17 3.01
5675 9987 1.416401 TGGAGCTTCGAACAGGAAGTT 59.584 47.619 0.00 0.00 44.17 2.66
5901 10235 3.737032 TGAACATGAACGACTGTACCA 57.263 42.857 0.00 0.00 0.00 3.25
5988 10322 1.594331 GTATCATCCCGGAACTTGCC 58.406 55.000 0.73 0.00 0.00 4.52
6009 10343 2.576832 TTCGGTCCAACTCGGTCCC 61.577 63.158 0.00 0.00 39.67 4.46
6011 10345 2.993264 GGTCCAACTCGGTCCCGA 60.993 66.667 8.34 8.34 46.87 5.14
6111 10445 1.137086 CTGGCTCTACACTTGGCGTAT 59.863 52.381 0.00 0.00 0.00 3.06
6129 10463 0.387929 ATGTACCACGTATCAGCCCG 59.612 55.000 0.00 0.00 0.00 6.13
6154 10488 4.873129 CGTCATCGCCGGTCCCAG 62.873 72.222 1.90 0.00 0.00 4.45
6163 10497 4.463879 CGGTCCCAGCAGGCAGAG 62.464 72.222 0.00 0.00 34.51 3.35
6164 10498 4.792804 GGTCCCAGCAGGCAGAGC 62.793 72.222 0.00 0.00 34.51 4.09
6168 10502 4.834453 CCAGCAGGCAGAGCGGAG 62.834 72.222 0.00 0.00 37.01 4.63
6250 10584 4.634133 TGCGTGACGTCGTGGTCC 62.634 66.667 11.62 0.00 36.07 4.46
6261 10595 1.657181 CGTGGTCCTTTTGCGTTGC 60.657 57.895 0.00 0.00 0.00 4.17
6262 10596 1.299850 GTGGTCCTTTTGCGTTGCC 60.300 57.895 0.00 0.00 0.00 4.52
6263 10597 2.338620 GGTCCTTTTGCGTTGCCC 59.661 61.111 0.00 0.00 0.00 5.36
6264 10598 2.338620 GTCCTTTTGCGTTGCCCC 59.661 61.111 0.00 0.00 0.00 5.80
6296 10630 1.614583 CCCGTCTCTCTGTCTCTCCAA 60.615 57.143 0.00 0.00 0.00 3.53
6317 10652 1.921049 TCTCCTTCTCTTCCCCGACTA 59.079 52.381 0.00 0.00 0.00 2.59
6475 10810 4.458829 ATGGAGGGCCCTCGACGA 62.459 66.667 39.47 25.56 43.59 4.20
6536 10871 1.202382 GCCGACGAACTACTTAGGCAT 60.202 52.381 0.00 0.00 42.37 4.40
6554 10889 2.861274 CATGGTTTTGGGCCAAATTGT 58.139 42.857 30.82 15.16 39.72 2.71
6561 10896 1.079612 GGGCCAAATTGTGCTGCTC 60.080 57.895 4.39 0.00 0.00 4.26
6563 10898 0.319405 GGCCAAATTGTGCTGCTCTT 59.681 50.000 0.00 0.00 0.00 2.85
6589 10924 3.640257 TAGGTCGTCTGCTCCGGCT 62.640 63.158 0.00 0.00 39.59 5.52
6657 11000 5.682659 TGCTAGGGTTTTGTTACTGTACAA 58.317 37.500 0.00 0.00 36.30 2.41
6716 11061 0.107831 GTGCAGTGGGTGGTTCACTA 59.892 55.000 0.00 0.00 42.87 2.74
6806 11151 8.486210 AGAAGGTTTGCTATGATTACTGTCATA 58.514 33.333 0.00 0.00 39.45 2.15
6828 11173 8.067488 TCATATGGAGAGGGCATATTACAGATA 58.933 37.037 2.13 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.072508 CGGGATGAGACAATAATGTATTTGGG 60.073 42.308 0.00 0.00 40.74 4.12
2 3 6.710295 TCGGGATGAGACAATAATGTATTTGG 59.290 38.462 0.00 0.00 40.74 3.28
3 4 7.226523 TGTCGGGATGAGACAATAATGTATTTG 59.773 37.037 0.00 0.00 44.56 2.32
6 7 6.419484 TGTCGGGATGAGACAATAATGTAT 57.581 37.500 0.00 0.00 44.56 2.29
7 8 5.862678 TGTCGGGATGAGACAATAATGTA 57.137 39.130 0.00 0.00 44.56 2.29
8 9 4.753516 TGTCGGGATGAGACAATAATGT 57.246 40.909 0.00 0.00 44.56 2.71
15 16 2.301583 TGTCATTTGTCGGGATGAGACA 59.698 45.455 0.00 0.00 45.68 3.41
16 17 2.972625 TGTCATTTGTCGGGATGAGAC 58.027 47.619 0.00 0.00 38.98 3.36
17 18 3.244387 TGTTGTCATTTGTCGGGATGAGA 60.244 43.478 0.00 0.00 33.27 3.27
18 19 3.073678 TGTTGTCATTTGTCGGGATGAG 58.926 45.455 0.00 0.00 33.27 2.90
19 20 3.133141 TGTTGTCATTTGTCGGGATGA 57.867 42.857 0.00 0.00 0.00 2.92
20 21 3.913548 TTGTTGTCATTTGTCGGGATG 57.086 42.857 0.00 0.00 0.00 3.51
21 22 5.253330 ACTATTGTTGTCATTTGTCGGGAT 58.747 37.500 0.00 0.00 0.00 3.85
22 23 4.647611 ACTATTGTTGTCATTTGTCGGGA 58.352 39.130 0.00 0.00 0.00 5.14
23 24 5.371115 AACTATTGTTGTCATTTGTCGGG 57.629 39.130 0.00 0.00 34.71 5.14
24 25 5.390613 GGAACTATTGTTGTCATTTGTCGG 58.609 41.667 0.00 0.00 36.39 4.79
25 26 5.390613 GGGAACTATTGTTGTCATTTGTCG 58.609 41.667 0.00 0.00 36.39 4.35
26 27 5.476945 AGGGGAACTATTGTTGTCATTTGTC 59.523 40.000 0.00 0.00 36.39 3.18
27 28 5.393866 AGGGGAACTATTGTTGTCATTTGT 58.606 37.500 0.00 0.00 36.39 2.83
28 29 5.982890 AGGGGAACTATTGTTGTCATTTG 57.017 39.130 0.00 0.00 36.39 2.32
29 30 6.553100 TGAAAGGGGAACTATTGTTGTCATTT 59.447 34.615 0.00 0.21 36.39 2.32
30 31 6.015434 GTGAAAGGGGAACTATTGTTGTCATT 60.015 38.462 0.00 0.00 36.39 2.57
31 32 5.476945 GTGAAAGGGGAACTATTGTTGTCAT 59.523 40.000 0.00 0.00 36.39 3.06
32 33 4.825085 GTGAAAGGGGAACTATTGTTGTCA 59.175 41.667 0.00 0.00 36.39 3.58
33 34 5.070685 AGTGAAAGGGGAACTATTGTTGTC 58.929 41.667 0.00 0.00 36.39 3.18
34 35 5.061721 AGTGAAAGGGGAACTATTGTTGT 57.938 39.130 0.00 0.00 36.39 3.32
35 36 4.154195 CGAGTGAAAGGGGAACTATTGTTG 59.846 45.833 0.00 0.00 36.39 3.33
36 37 4.324267 CGAGTGAAAGGGGAACTATTGTT 58.676 43.478 0.00 0.00 39.42 2.83
37 38 3.868754 GCGAGTGAAAGGGGAACTATTGT 60.869 47.826 0.00 0.00 0.00 2.71
38 39 2.678336 GCGAGTGAAAGGGGAACTATTG 59.322 50.000 0.00 0.00 0.00 1.90
39 40 2.572104 AGCGAGTGAAAGGGGAACTATT 59.428 45.455 0.00 0.00 0.00 1.73
40 41 2.168728 GAGCGAGTGAAAGGGGAACTAT 59.831 50.000 0.00 0.00 0.00 2.12
41 42 1.549170 GAGCGAGTGAAAGGGGAACTA 59.451 52.381 0.00 0.00 0.00 2.24
42 43 0.321996 GAGCGAGTGAAAGGGGAACT 59.678 55.000 0.00 0.00 0.00 3.01
43 44 0.321996 AGAGCGAGTGAAAGGGGAAC 59.678 55.000 0.00 0.00 0.00 3.62
44 45 1.825474 CTAGAGCGAGTGAAAGGGGAA 59.175 52.381 0.00 0.00 0.00 3.97
45 46 1.005569 TCTAGAGCGAGTGAAAGGGGA 59.994 52.381 0.00 0.00 0.00 4.81
46 47 1.475403 TCTAGAGCGAGTGAAAGGGG 58.525 55.000 0.00 0.00 0.00 4.79
47 48 3.886505 AGTATCTAGAGCGAGTGAAAGGG 59.113 47.826 0.00 0.00 0.00 3.95
48 49 5.508200 AAGTATCTAGAGCGAGTGAAAGG 57.492 43.478 0.00 0.00 0.00 3.11
49 50 5.746245 CCAAAGTATCTAGAGCGAGTGAAAG 59.254 44.000 0.00 0.00 0.00 2.62
50 51 5.651530 CCAAAGTATCTAGAGCGAGTGAAA 58.348 41.667 0.00 0.00 0.00 2.69
71 72 5.735285 TGTTAAATTCAATGATGGTGCCA 57.265 34.783 0.00 0.00 0.00 4.92
74 75 6.527722 CGGTCTTGTTAAATTCAATGATGGTG 59.472 38.462 0.00 0.00 0.00 4.17
75 76 6.350110 CCGGTCTTGTTAAATTCAATGATGGT 60.350 38.462 0.00 0.00 0.00 3.55
77 78 5.516339 GCCGGTCTTGTTAAATTCAATGATG 59.484 40.000 1.90 0.00 0.00 3.07
78 79 5.650543 GCCGGTCTTGTTAAATTCAATGAT 58.349 37.500 1.90 0.00 0.00 2.45
79 80 4.378978 CGCCGGTCTTGTTAAATTCAATGA 60.379 41.667 1.90 0.00 0.00 2.57
80 81 3.851403 CGCCGGTCTTGTTAAATTCAATG 59.149 43.478 1.90 0.00 0.00 2.82
81 82 3.119637 CCGCCGGTCTTGTTAAATTCAAT 60.120 43.478 1.90 0.00 0.00 2.57
125 126 7.582719 ACCATTTATTAGGGATTACTGCTCAA 58.417 34.615 0.00 0.00 0.00 3.02
135 136 8.386264 CCTCATGAGTAACCATTTATTAGGGAT 58.614 37.037 21.11 0.00 0.00 3.85
140 141 6.588204 ACGCCTCATGAGTAACCATTTATTA 58.412 36.000 21.11 0.00 0.00 0.98
205 206 6.619464 ACTCTGTCTACCCATCTATTCATCT 58.381 40.000 0.00 0.00 0.00 2.90
233 234 7.889873 ATTAATCCATGAACGAACCCATTAA 57.110 32.000 0.00 0.00 0.00 1.40
242 243 6.279513 AGGCAAAAATTAATCCATGAACGA 57.720 33.333 0.00 0.00 0.00 3.85
251 252 5.465935 TGGTCGACAAGGCAAAAATTAATC 58.534 37.500 18.91 0.00 0.00 1.75
280 281 3.130516 TCGCCTGGTAGTTACTCAATCAG 59.869 47.826 0.00 0.00 0.00 2.90
292 293 2.069273 CAACTTTCACTCGCCTGGTAG 58.931 52.381 0.00 0.00 0.00 3.18
318 319 3.941483 CTCGCATGAGGGAAAGTGTTATT 59.059 43.478 0.00 0.00 38.65 1.40
340 341 7.324616 GTCTTGATTAATCTGTTGCACTTTCAC 59.675 37.037 16.24 0.00 0.00 3.18
356 357 5.875224 TGTTGGGAGATGTGTCTTGATTAA 58.125 37.500 0.00 0.00 33.97 1.40
397 398 0.179084 CGGTGCTATAGTGTGGGTGG 60.179 60.000 0.84 0.00 0.00 4.61
405 406 3.679083 GCAAAGGTCTTCGGTGCTATAGT 60.679 47.826 0.84 0.00 32.43 2.12
425 426 4.574674 ATCAAAGATAGGTTGTGGAGCA 57.425 40.909 0.00 0.00 0.00 4.26
471 472 0.179032 TTCCGGCGGATATGTGCAAT 60.179 50.000 31.59 0.00 0.00 3.56
472 473 0.179032 ATTCCGGCGGATATGTGCAA 60.179 50.000 31.59 12.82 0.00 4.08
474 475 1.868997 CATTCCGGCGGATATGTGC 59.131 57.895 31.59 0.00 0.00 4.57
485 486 1.065418 AGAAGTACCTTGGCATTCCGG 60.065 52.381 0.00 0.00 34.14 5.14
546 547 9.817809 TCTAACAACATCAATGAAGAGGTATAC 57.182 33.333 0.00 0.00 31.49 1.47
572 573 2.769095 GTCCTCTTCCATAGGAGTTGCT 59.231 50.000 0.00 0.00 43.81 3.91
604 612 6.152492 TGCAAATGCTTCAGGTCAATGTATAA 59.848 34.615 6.97 0.00 42.66 0.98
662 670 0.179103 AAAAGCAATGCGGGCATAGC 60.179 50.000 6.57 0.00 35.31 2.97
706 714 0.452184 TGTTTTCCAAAGCAACGCGA 59.548 45.000 15.93 0.00 0.00 5.87
766 775 5.121454 TGCCTTTTTCATTTGTTGTTCACAC 59.879 36.000 0.00 0.00 33.98 3.82
866 1134 4.537433 GGCAGGCCCAGCTACTCG 62.537 72.222 16.44 0.00 0.00 4.18
935 3316 4.111016 TCGCCGTGGACTGCGTAG 62.111 66.667 14.03 0.00 46.95 3.51
999 3380 0.180642 TAGCGACGAGATGTCCTCCT 59.819 55.000 0.00 0.00 45.23 3.69
1000 3381 0.308376 GTAGCGACGAGATGTCCTCC 59.692 60.000 0.00 0.00 45.23 4.30
1109 3490 0.669932 CTAGCATCATCGCCCTCTGC 60.670 60.000 0.00 0.00 0.00 4.26
1111 3492 1.670590 GCTAGCATCATCGCCCTCT 59.329 57.895 10.63 0.00 0.00 3.69
1282 3663 3.447229 TCCAGCACAGTCAGATCGAATTA 59.553 43.478 0.00 0.00 0.00 1.40
1333 3714 3.859386 GCCCAATTCGAAACTATTTGCAG 59.141 43.478 0.00 0.00 0.00 4.41
1430 3811 0.979709 TGGCAGGATCACTCTCCCAG 60.980 60.000 0.00 0.00 35.79 4.45
1613 4002 2.514458 ACCAGGAAATTACCAGGCAG 57.486 50.000 0.00 0.00 39.73 4.85
1700 4089 2.607038 GCTTTTTGCCAAACTACCCTCG 60.607 50.000 0.00 0.00 35.15 4.63
1783 4172 7.340743 TCAATTCACAACAGAAAACTTCCCTTA 59.659 33.333 0.00 0.00 0.00 2.69
1788 4177 9.736023 AGTAATCAATTCACAACAGAAAACTTC 57.264 29.630 0.00 0.00 0.00 3.01
1820 4209 3.122613 GCTCGACATCTGTTCACAAAGAG 59.877 47.826 0.00 0.00 0.00 2.85
2049 4439 6.380846 TCATACCAAGAATTCCCCTTCAAATG 59.619 38.462 0.65 0.00 0.00 2.32
2067 4457 5.801531 AGCTCGTAACCATAATCATACCA 57.198 39.130 0.00 0.00 0.00 3.25
2068 4458 8.656849 CATTAAGCTCGTAACCATAATCATACC 58.343 37.037 0.00 0.00 0.00 2.73
2087 4477 3.392882 AGCCTGCAAACAAACATTAAGC 58.607 40.909 0.00 0.00 0.00 3.09
2097 4487 2.356665 TTTACCAGAGCCTGCAAACA 57.643 45.000 0.00 0.00 0.00 2.83
2256 4647 2.775911 CTGGCAGATTTCAGGAGTCA 57.224 50.000 9.42 0.00 0.00 3.41
3366 5778 2.912956 AGGGAAGACTATGCCAAAGACA 59.087 45.455 0.00 0.00 32.31 3.41
3423 5861 8.608598 TCCACTCATCCAAATATCATGATACAT 58.391 33.333 17.60 7.25 0.00 2.29
3517 5955 6.606395 AGGCTTCTTTCTGATGCAGATAAAAT 59.394 34.615 0.00 0.00 44.64 1.82
3519 5957 5.503927 AGGCTTCTTTCTGATGCAGATAAA 58.496 37.500 0.00 0.00 44.64 1.40
3648 6086 5.104982 TGCTCCAAACACCTCTTTGAATTTT 60.105 36.000 0.00 0.00 33.61 1.82
3890 6336 3.813724 CATGCACCTCCCCTCCCC 61.814 72.222 0.00 0.00 0.00 4.81
3891 6337 2.276309 CTTCATGCACCTCCCCTCCC 62.276 65.000 0.00 0.00 0.00 4.30
3892 6338 1.225704 CTTCATGCACCTCCCCTCC 59.774 63.158 0.00 0.00 0.00 4.30
3893 6339 0.107459 GACTTCATGCACCTCCCCTC 60.107 60.000 0.00 0.00 0.00 4.30
3894 6340 1.566298 GGACTTCATGCACCTCCCCT 61.566 60.000 0.00 0.00 0.00 4.79
3895 6341 1.077429 GGACTTCATGCACCTCCCC 60.077 63.158 0.00 0.00 0.00 4.81
3896 6342 0.678048 GTGGACTTCATGCACCTCCC 60.678 60.000 0.00 0.00 43.60 4.30
3897 6343 2.859992 GTGGACTTCATGCACCTCC 58.140 57.895 0.00 0.00 43.60 4.30
3902 6348 2.302733 TCTTAGCAGTGGACTTCATGCA 59.697 45.455 0.00 0.00 41.14 3.96
3903 6349 2.977914 TCTTAGCAGTGGACTTCATGC 58.022 47.619 0.00 0.00 38.97 4.06
3904 6350 4.153117 GTGTTCTTAGCAGTGGACTTCATG 59.847 45.833 0.00 0.00 0.00 3.07
3905 6351 4.040952 AGTGTTCTTAGCAGTGGACTTCAT 59.959 41.667 0.00 0.00 0.00 2.57
3906 6352 3.388024 AGTGTTCTTAGCAGTGGACTTCA 59.612 43.478 0.00 0.00 0.00 3.02
3907 6353 3.996480 AGTGTTCTTAGCAGTGGACTTC 58.004 45.455 0.00 0.00 0.00 3.01
3908 6354 4.589374 AGTAGTGTTCTTAGCAGTGGACTT 59.411 41.667 0.00 0.00 0.00 3.01
3909 6355 4.153411 AGTAGTGTTCTTAGCAGTGGACT 58.847 43.478 0.00 0.00 0.00 3.85
3915 6703 5.163509 TGAGCCATAGTAGTGTTCTTAGCAG 60.164 44.000 0.00 0.00 0.00 4.24
3936 6724 4.019174 AGGCCACAGTTTATTTGGATGAG 58.981 43.478 5.01 0.00 31.39 2.90
3977 6765 0.179207 CATCATGTCACAGCACACGC 60.179 55.000 0.00 0.00 38.99 5.34
4012 6800 6.768381 GCCAAGAACTAGCTAATAACTCCAAT 59.232 38.462 0.00 0.00 0.00 3.16
4013 6801 6.113411 GCCAAGAACTAGCTAATAACTCCAA 58.887 40.000 0.00 0.00 0.00 3.53
4017 6805 4.120589 GCGCCAAGAACTAGCTAATAACT 58.879 43.478 0.00 0.00 0.00 2.24
4106 8284 1.656587 TAACACAGCCAGGATCCACT 58.343 50.000 15.82 5.26 0.00 4.00
4186 8364 2.039084 GGAGATTGACTGGTGGACAAGT 59.961 50.000 0.00 0.00 0.00 3.16
4242 8421 7.597743 CAGAAAGTAAGTACTTCACGGTATTGT 59.402 37.037 12.39 0.00 45.17 2.71
4291 8477 2.668250 TCGTCACAGTGGAATGTAACG 58.332 47.619 0.00 1.48 44.49 3.18
4300 8489 0.583438 CAGCAACTTCGTCACAGTGG 59.417 55.000 0.00 0.00 0.00 4.00
4548 8737 4.629958 ATTGCCAACCCCGCCCAA 62.630 61.111 0.00 0.00 0.00 4.12
4654 8843 2.017782 TGCAAACGTCACCTGCTTTAA 58.982 42.857 11.57 0.00 37.00 1.52
4690 8879 4.038271 TCAGGATGAAGTGAATGGCTTT 57.962 40.909 0.00 0.00 45.97 3.51
4778 8970 0.449388 CTCTTGGATTGCCTGCGAAC 59.551 55.000 0.00 0.00 34.31 3.95
4996 9293 6.429692 TCATGACCTTGACAAACATAACGAAT 59.570 34.615 0.00 0.00 0.00 3.34
4999 9296 5.605564 TCATGACCTTGACAAACATAACG 57.394 39.130 0.00 0.00 0.00 3.18
5143 9455 2.230660 GGTGAAGTTCCTTTGTCCAGG 58.769 52.381 0.00 0.00 34.86 4.45
5187 9499 7.815383 TCAGGGAATTACAGATAATGATTGGT 58.185 34.615 0.00 0.00 31.07 3.67
5244 9556 0.181114 ACAGCCATCGGTGCATACAT 59.819 50.000 0.00 0.00 41.36 2.29
5339 9651 1.517832 GTACGACTGCTGGCTGGAT 59.482 57.895 0.00 0.00 0.00 3.41
5424 9736 6.127619 GGACAAATTTCCAAAGACCTGGATAG 60.128 42.308 0.00 0.00 45.03 2.08
5631 9943 3.376234 CGCAATGTCTGAAAGGTCATCAT 59.624 43.478 0.00 0.00 32.91 2.45
5674 9986 0.534203 GAGGTTTGCACGGACAGGAA 60.534 55.000 0.00 0.00 0.00 3.36
5675 9987 1.070786 GAGGTTTGCACGGACAGGA 59.929 57.895 0.00 0.00 0.00 3.86
5683 9995 0.036388 TCCAGATCCGAGGTTTGCAC 60.036 55.000 0.00 0.00 0.00 4.57
5765 10078 2.515523 GGCTGATCCGCTGCACAT 60.516 61.111 9.11 0.00 42.62 3.21
5901 10235 4.680407 TGAGGTGTTATGTACAGGGTACT 58.320 43.478 0.33 0.00 37.45 2.73
5988 10322 2.431942 CCGAGTTGGACCGAACCG 60.432 66.667 0.00 1.35 42.00 4.44
5991 10325 3.053828 GGACCGAGTTGGACCGAA 58.946 61.111 2.42 0.00 42.76 4.30
6009 10343 7.267318 CGTATTGAATCGATACTCAACTTTCG 58.733 38.462 13.36 11.55 34.52 3.46
6011 10345 7.039882 ACCGTATTGAATCGATACTCAACTTT 58.960 34.615 13.36 3.05 34.52 2.66
6111 10445 1.811195 CGGGCTGATACGTGGTACA 59.189 57.895 0.00 0.00 0.00 2.90
6177 10511 4.834453 CTCCGCTCTGCCTGCTGG 62.834 72.222 5.03 5.03 0.00 4.85
6237 10571 1.155424 GCAAAAGGACCACGACGTCA 61.155 55.000 17.16 0.00 34.24 4.35
6242 10576 2.018544 CAACGCAAAAGGACCACGA 58.981 52.632 0.00 0.00 0.00 4.35
6243 10577 1.657181 GCAACGCAAAAGGACCACG 60.657 57.895 0.00 0.00 0.00 4.94
6296 10630 1.289530 AGTCGGGGAAGAGAAGGAGAT 59.710 52.381 0.00 0.00 0.00 2.75
6317 10652 2.039613 CTCTGCTCCCTCCTCTGTTTTT 59.960 50.000 0.00 0.00 0.00 1.94
6381 10716 1.041447 AGGAACTACCATCGGACGGG 61.041 60.000 0.00 0.00 42.04 5.28
6443 10778 2.358957 CTCCATCACCGCAGAAATCAA 58.641 47.619 0.00 0.00 0.00 2.57
6536 10871 1.748591 GCACAATTTGGCCCAAAACCA 60.749 47.619 13.87 0.00 36.90 3.67
6554 10889 3.674997 ACCTAATCGAAAAAGAGCAGCA 58.325 40.909 0.00 0.00 0.00 4.41
6589 10924 5.981088 ATGTTCTAACACAAATGATGGCA 57.019 34.783 0.00 0.00 42.51 4.92
6593 10928 8.143193 TGCAGAAAATGTTCTAACACAAATGAT 58.857 29.630 0.00 0.00 42.45 2.45
6716 11061 5.393068 AATCCACCATGTATCACCTCAAT 57.607 39.130 0.00 0.00 0.00 2.57
6806 11151 7.761981 AATATCTGTAATATGCCCTCTCCAT 57.238 36.000 0.00 0.00 0.00 3.41
6828 11173 5.625150 AGTGCTCTACCAACTCTTCAAAAT 58.375 37.500 0.00 0.00 0.00 1.82
6841 11187 3.906720 TCATAACCCAAGTGCTCTACC 57.093 47.619 0.00 0.00 0.00 3.18
6939 11285 5.236282 ACATAGCATCTATGTCTGCATCAC 58.764 41.667 12.31 0.00 40.88 3.06


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

AutoCloner maintained by Alex Coulton.