Multiple sequence alignment - TraesCS3A01G442000

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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 TraesCS3A01G442000 chr3A 100.000 5814 0 0 1001 6814 684040773 684046586 0.000000e+00 10737
1 TraesCS3A01G442000 chr3A 80.183 2735 383 88 1186 3840 688693498 688690843 0.000000e+00 1901
2 TraesCS3A01G442000 chr3A 100.000 464 0 0 1 464 684039773 684040236 0.000000e+00 857
3 TraesCS3A01G442000 chr3A 90.347 404 31 5 1011 1411 433768343 433767945 2.180000e-144 523
4 TraesCS3A01G442000 chr3A 81.801 522 79 8 3843 4363 688690798 688690292 2.270000e-114 424
5 TraesCS3A01G442000 chr3A 81.670 491 63 18 4608 5094 688689942 688689475 3.860000e-102 383
6 TraesCS3A01G442000 chr3B 94.306 4830 218 32 1003 5805 724737564 724742363 0.000000e+00 7343
7 TraesCS3A01G442000 chr3B 79.775 2759 372 103 1186 3840 732619327 732616651 0.000000e+00 1832
8 TraesCS3A01G442000 chr3B 91.174 1031 42 22 5800 6811 724742395 724743395 0.000000e+00 1354
9 TraesCS3A01G442000 chr3B 90.249 482 13 12 1 464 724736929 724737394 3.520000e-167 599
10 TraesCS3A01G442000 chr3B 82.765 528 75 9 3843 4369 732616606 732616094 2.240000e-124 457
11 TraesCS3A01G442000 chr3B 82.822 489 61 16 4608 5094 732615735 732615268 3.800000e-112 416
12 TraesCS3A01G442000 chr3B 78.361 305 53 9 4822 5122 175096909 175096614 1.170000e-42 185
13 TraesCS3A01G442000 chr3D 96.081 3419 103 15 1001 4404 547298157 547301559 0.000000e+00 5542
14 TraesCS3A01G442000 chr3D 92.488 2343 107 35 4510 6814 547301664 547303975 0.000000e+00 3288
15 TraesCS3A01G442000 chr3D 80.394 2744 364 93 1186 3840 552003086 552000428 0.000000e+00 1927
16 TraesCS3A01G442000 chr3D 87.734 481 7 12 5 464 547297544 547297993 1.310000e-141 514
17 TraesCS3A01G442000 chr3D 82.331 532 78 8 3843 4373 552000383 551999867 1.350000e-121 448
18 TraesCS3A01G442000 chr3D 82.245 490 62 19 4608 5094 551999468 551999001 3.830000e-107 399
19 TraesCS3A01G442000 chr7D 91.844 564 39 5 4709 5268 12707764 12707204 0.000000e+00 780
20 TraesCS3A01G442000 chr7D 93.766 401 21 3 1011 1411 85519670 85520066 3.520000e-167 599
21 TraesCS3A01G442000 chr6D 92.658 395 25 3 1017 1411 32521945 32521555 3.570000e-157 566
22 TraesCS3A01G442000 chr6D 92.020 401 22 6 1011 1411 65145476 65145866 7.720000e-154 555
23 TraesCS3A01G442000 chr2B 91.022 401 33 2 1011 1411 765132716 765132319 7.780000e-149 538
24 TraesCS3A01G442000 chrUn 91.022 401 31 4 1011 1411 31512450 31512055 2.800000e-148 536
25 TraesCS3A01G442000 chr1A 90.274 401 35 3 1011 1411 287042325 287041929 7.830000e-144 521
26 TraesCS3A01G442000 chr1A 81.319 273 43 5 4607 4879 22935702 22935966 1.490000e-51 215
27 TraesCS3A01G442000 chr1A 78.723 282 47 9 4822 5099 244562253 244561981 7.020000e-40 176
28 TraesCS3A01G442000 chr2A 80.370 270 45 5 4610 4879 536571021 536570760 1.500000e-46 198
29 TraesCS3A01G442000 chr4B 78.361 305 53 9 4822 5122 489161469 489161764 1.170000e-42 185
30 TraesCS3A01G442000 chr4B 77.855 289 40 18 2168 2446 17357155 17357429 2.540000e-34 158
31 TraesCS3A01G442000 chr7B 78.033 305 54 9 4822 5122 665368557 665368262 5.430000e-41 180


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 TraesCS3A01G442000 chr3A 684039773 684046586 6813 False 5797.000000 10737 100.000000 1 6814 2 chr3A.!!$F1 6813
1 TraesCS3A01G442000 chr3A 688689475 688693498 4023 True 902.666667 1901 81.218000 1186 5094 3 chr3A.!!$R2 3908
2 TraesCS3A01G442000 chr3B 724736929 724743395 6466 False 3098.666667 7343 91.909667 1 6811 3 chr3B.!!$F1 6810
3 TraesCS3A01G442000 chr3B 732615268 732619327 4059 True 901.666667 1832 81.787333 1186 5094 3 chr3B.!!$R2 3908
4 TraesCS3A01G442000 chr3D 547297544 547303975 6431 False 3114.666667 5542 92.101000 5 6814 3 chr3D.!!$F1 6809
5 TraesCS3A01G442000 chr3D 551999001 552003086 4085 True 924.666667 1927 81.656667 1186 5094 3 chr3D.!!$R1 3908
6 TraesCS3A01G442000 chr7D 12707204 12707764 560 True 780.000000 780 91.844000 4709 5268 1 chr7D.!!$R1 559

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
338 365 0.875908 CACCACCACAGTCACAGTCG 60.876 60.000 0.00 0.0 0.00 4.18 F
444 471 1.145162 CTTTGTGTTTGTGCGTGGGC 61.145 55.000 0.00 0.0 40.52 5.36 F
1168 1204 2.220133 CCTCGTTGGTTACTGACGTTTG 59.780 50.000 9.78 0.0 37.95 2.93 F
1812 1881 0.107459 AATTTCCCTCCGCTCTCTGC 60.107 55.000 0.00 0.0 38.57 4.26 F
2193 2282 0.252479 CCTTGCTCTGATCTGTGGCT 59.748 55.000 15.98 0.0 0.00 4.75 F
3862 4072 0.252479 AAGATGCAGACAGAGGCCAG 59.748 55.000 5.01 0.0 0.00 4.85 F
3896 4106 1.279558 TGGAATAGCCAAAGCACCGTA 59.720 47.619 0.00 0.0 45.87 4.02 F
5535 6017 0.322456 TATCCGCTGGTTTGCTTGCT 60.322 50.000 0.00 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1551 1604 0.179225 CATGAGAAACGGGCGAAACG 60.179 55.000 0.00 0.00 37.36 3.60 R
1552 1605 0.454452 GCATGAGAAACGGGCGAAAC 60.454 55.000 0.00 0.00 0.00 2.78 R
2210 2300 1.467342 CAGATCACACACACTGGCATG 59.533 52.381 0.00 0.00 0.00 4.06 R
3292 3427 2.011122 TGACCCGAGAAAGAGGAAGT 57.989 50.000 0.00 0.00 0.00 3.01 R
3972 4185 0.107831 TGTTCAACCGGGGAGAACTG 59.892 55.000 25.82 6.62 41.56 3.16 R
5280 5751 0.030101 GCTTAACGCAACCTGCACAA 59.970 50.000 0.00 0.00 45.36 3.33 R
5728 6215 0.459237 CTCCGGAACAGCTACTGCAG 60.459 60.000 13.48 13.48 42.74 4.41 R
6578 7139 0.338120 CTCCCACCCCTCTCTCTCTT 59.662 60.000 0.00 0.00 0.00 2.85 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
330 357 4.935495 CGCCAGCACCACCACAGT 62.935 66.667 0.00 0.00 0.00 3.55
336 363 1.153168 GCACCACCACAGTCACAGT 60.153 57.895 0.00 0.00 0.00 3.55
337 364 1.160329 GCACCACCACAGTCACAGTC 61.160 60.000 0.00 0.00 0.00 3.51
338 365 0.875908 CACCACCACAGTCACAGTCG 60.876 60.000 0.00 0.00 0.00 4.18
339 366 1.300931 CCACCACAGTCACAGTCGG 60.301 63.158 0.00 0.00 0.00 4.79
340 367 1.956170 CACCACAGTCACAGTCGGC 60.956 63.158 0.00 0.00 0.00 5.54
341 368 2.134287 ACCACAGTCACAGTCGGCT 61.134 57.895 0.00 0.00 0.00 5.52
342 369 1.373497 CCACAGTCACAGTCGGCTC 60.373 63.158 0.00 0.00 0.00 4.70
343 370 1.730902 CACAGTCACAGTCGGCTCG 60.731 63.158 0.00 0.00 0.00 5.03
344 371 2.126307 CAGTCACAGTCGGCTCGG 60.126 66.667 0.00 0.00 0.00 4.63
345 372 4.057428 AGTCACAGTCGGCTCGGC 62.057 66.667 0.00 0.00 0.00 5.54
444 471 1.145162 CTTTGTGTTTGTGCGTGGGC 61.145 55.000 0.00 0.00 40.52 5.36
1168 1204 2.220133 CCTCGTTGGTTACTGACGTTTG 59.780 50.000 9.78 0.00 37.95 2.93
1342 1386 3.462021 CTCCCTTCCTCGCTTAATTCTG 58.538 50.000 0.00 0.00 0.00 3.02
1455 1508 2.300996 GAGGCCTCCATGAACCAGA 58.699 57.895 23.19 0.00 0.00 3.86
1554 1607 2.285894 CTTACCCCCTCCCCCGTT 60.286 66.667 0.00 0.00 0.00 4.44
1566 1619 2.667199 CCCGTTTCGCCCGTTTCT 60.667 61.111 0.00 0.00 0.00 2.52
1568 1621 1.957186 CCGTTTCGCCCGTTTCTCA 60.957 57.895 0.00 0.00 0.00 3.27
1699 1758 2.177531 GACGAGGTCTACGCGCAA 59.822 61.111 5.73 0.00 46.87 4.85
1763 1823 1.150536 GCTGGGTTCACACTTGGGA 59.849 57.895 0.00 0.00 0.00 4.37
1808 1877 1.134371 GTGCTAATTTCCCTCCGCTCT 60.134 52.381 0.00 0.00 0.00 4.09
1812 1881 0.107459 AATTTCCCTCCGCTCTCTGC 60.107 55.000 0.00 0.00 38.57 4.26
1828 1897 4.863491 TCTCTGCAATTTCTCAGCAAAAC 58.137 39.130 0.00 0.00 37.89 2.43
2193 2282 0.252479 CCTTGCTCTGATCTGTGGCT 59.748 55.000 15.98 0.00 0.00 4.75
2210 2300 1.268743 GGCTCTTTTACATCGCCATGC 60.269 52.381 0.00 0.00 40.41 4.06
2296 2386 2.028130 GTGACACCCCAACACATCAAA 58.972 47.619 0.00 0.00 35.06 2.69
2302 2392 2.632512 ACCCCAACACATCAAAACATCC 59.367 45.455 0.00 0.00 0.00 3.51
2320 2410 9.807649 AAAACATCCAATCTGTCTATAAATTGC 57.192 29.630 0.00 0.00 0.00 3.56
2478 2570 1.556451 GCTGGGGATGCCTTCATTTTT 59.444 47.619 2.19 0.00 31.96 1.94
2502 2594 3.135712 TCAGGTCTGTTGCTGTTTCCTTA 59.864 43.478 0.00 0.00 0.00 2.69
2543 2650 1.989706 AACCCGGTGCTAAATGTGTT 58.010 45.000 0.00 0.00 0.00 3.32
2743 2857 7.400339 ACCTAGGTATATGAACATGTCTATGGG 59.600 40.741 14.41 0.00 38.66 4.00
2754 2868 8.933653 TGAACATGTCTATGGGAATCATACTTA 58.066 33.333 0.00 0.00 38.66 2.24
2792 2915 2.022195 CCCATTGGCTCATTCTGAGTG 58.978 52.381 6.06 0.00 45.94 3.51
2972 3104 6.151144 GTGACTGTTGTATTTGCTTTCCCTAT 59.849 38.462 0.00 0.00 0.00 2.57
3127 3260 5.823570 TCGAACTGGAGATCTCTTAAGGTAG 59.176 44.000 21.81 15.01 0.00 3.18
3138 3271 5.651530 TCTCTTAAGGTAGCTGTTTGATCG 58.348 41.667 1.85 0.00 0.00 3.69
3292 3427 2.626785 TCATCACCTCCTGTTAACCCA 58.373 47.619 2.48 0.00 0.00 4.51
3447 3588 1.792949 GTGACGCTCTTGAAATGTCGT 59.207 47.619 0.00 0.00 32.32 4.34
3590 3731 3.252701 CCAGCAATGAATCTGATGCTACC 59.747 47.826 2.67 0.00 46.75 3.18
3773 3941 3.198853 AGACCTTTGATGAGGCTCCTAAC 59.801 47.826 12.86 1.42 40.65 2.34
3862 4072 0.252479 AAGATGCAGACAGAGGCCAG 59.748 55.000 5.01 0.00 0.00 4.85
3896 4106 1.279558 TGGAATAGCCAAAGCACCGTA 59.720 47.619 0.00 0.00 45.87 4.02
3972 4185 1.526575 TTGGTTAAGGCAGCAGCAGC 61.527 55.000 2.65 0.00 44.61 5.25
3973 4186 1.973281 GGTTAAGGCAGCAGCAGCA 60.973 57.895 12.41 0.00 45.49 4.41
3974 4187 1.505353 GTTAAGGCAGCAGCAGCAG 59.495 57.895 12.41 0.00 45.49 4.24
4013 4226 2.502492 CCGAGTGATCCGGCCTCAT 61.502 63.158 0.00 0.00 40.54 2.90
4082 4295 7.768582 AGTGGTTTCAAGATTTTTGGGTTTAAG 59.231 33.333 0.00 0.00 0.00 1.85
4386 4600 9.453572 CCATATGCTGGTCAATATACTTACAAT 57.546 33.333 0.00 0.00 40.49 2.71
4443 4681 7.283127 ACTTTGTCATAAATCTGTTGACTGTGT 59.717 33.333 4.19 0.00 40.29 3.72
4551 5017 3.430895 GGTTGCTGAATTCAATTGCACTG 59.569 43.478 17.60 2.14 33.13 3.66
4568 5034 3.866066 GCACTGTCCTGTCTGCTTAATCA 60.866 47.826 0.00 0.00 0.00 2.57
4578 5044 8.049117 TCCTGTCTGCTTAATCATGTATTCTTT 58.951 33.333 0.00 0.00 0.00 2.52
4596 5062 9.673454 GTATTCTTTCGTTATTTGTTTGGTCTT 57.327 29.630 0.00 0.00 0.00 3.01
4693 5159 3.128349 TCTGTCAAAGTTTGGCGACTAC 58.872 45.455 15.10 5.91 38.34 2.73
4759 5225 5.066375 TGGTGAACTGATGTCTTCAAACAAG 59.934 40.000 0.00 0.00 32.78 3.16
4786 5252 3.990469 GGCAGATTGTGTATACTGATCCG 59.010 47.826 4.17 0.00 32.90 4.18
4843 5309 3.093814 GGAGTAAGCCCTCTATCTAGCC 58.906 54.545 0.00 0.00 0.00 3.93
4861 5327 1.753073 GCCTGGTGCTTGCTTTGATAT 59.247 47.619 0.00 0.00 36.87 1.63
4874 5340 3.181530 GCTTTGATATACGTATGCCGCAG 60.182 47.826 18.37 9.38 41.42 5.18
4985 5451 3.194542 AGGTCCAGAAGATGAACTCGAAG 59.805 47.826 0.00 0.00 0.00 3.79
5050 5516 1.657751 GCAAACGAGAAGGCCCATCC 61.658 60.000 0.00 0.00 0.00 3.51
5124 5591 5.008712 CCGAATCCTTTCTATTGGTTAAGCC 59.991 44.000 1.51 0.00 37.90 4.35
5151 5618 2.158449 CGTTCCAGTGCATCAAGTTCTC 59.842 50.000 0.00 0.00 0.00 2.87
5220 5691 4.036262 TCACAGGATATTATTGTTTGCGCC 59.964 41.667 4.18 0.00 0.00 6.53
5280 5751 2.489275 CGTTGTTGGCCTTGGTGCT 61.489 57.895 3.32 0.00 0.00 4.40
5281 5752 1.822615 GTTGTTGGCCTTGGTGCTT 59.177 52.632 3.32 0.00 0.00 3.91
5282 5753 0.530431 GTTGTTGGCCTTGGTGCTTG 60.530 55.000 3.32 0.00 0.00 4.01
5533 6015 2.030363 TGTTTATCCGCTGGTTTGCTTG 60.030 45.455 0.00 0.00 0.00 4.01
5534 6016 0.525761 TTATCCGCTGGTTTGCTTGC 59.474 50.000 0.00 0.00 0.00 4.01
5535 6017 0.322456 TATCCGCTGGTTTGCTTGCT 60.322 50.000 0.00 0.00 0.00 3.91
5536 6018 1.181098 ATCCGCTGGTTTGCTTGCTT 61.181 50.000 0.00 0.00 0.00 3.91
5681 6164 6.885952 TTATCTACCTTGCTCTAGCTAGTG 57.114 41.667 20.10 18.34 41.24 2.74
5682 6165 4.237976 TCTACCTTGCTCTAGCTAGTGT 57.762 45.455 20.10 11.01 41.24 3.55
5683 6166 4.601084 TCTACCTTGCTCTAGCTAGTGTT 58.399 43.478 20.10 4.89 41.24 3.32
5684 6167 5.752650 TCTACCTTGCTCTAGCTAGTGTTA 58.247 41.667 20.10 8.83 41.24 2.41
5685 6168 4.993029 ACCTTGCTCTAGCTAGTGTTAG 57.007 45.455 20.10 16.55 41.24 2.34
5686 6169 4.345854 ACCTTGCTCTAGCTAGTGTTAGT 58.654 43.478 20.10 11.13 41.24 2.24
5687 6170 4.158764 ACCTTGCTCTAGCTAGTGTTAGTG 59.841 45.833 20.10 13.47 41.24 2.74
5725 6212 4.696455 ACCCTGTATTATTTAACCGACCG 58.304 43.478 0.00 0.00 0.00 4.79
5726 6213 4.405358 ACCCTGTATTATTTAACCGACCGA 59.595 41.667 0.00 0.00 0.00 4.69
5727 6214 4.746611 CCCTGTATTATTTAACCGACCGAC 59.253 45.833 0.00 0.00 0.00 4.79
5728 6215 4.746611 CCTGTATTATTTAACCGACCGACC 59.253 45.833 0.00 0.00 0.00 4.79
5729 6216 5.452356 CCTGTATTATTTAACCGACCGACCT 60.452 44.000 0.00 0.00 0.00 3.85
5746 6233 1.591703 CTGCAGTAGCTGTTCCGGA 59.408 57.895 5.25 0.00 42.74 5.14
5747 6234 0.459237 CTGCAGTAGCTGTTCCGGAG 60.459 60.000 3.34 0.00 42.74 4.63
5748 6235 1.185618 TGCAGTAGCTGTTCCGGAGT 61.186 55.000 3.34 0.00 42.74 3.85
5749 6236 0.815734 GCAGTAGCTGTTCCGGAGTA 59.184 55.000 3.34 0.00 37.91 2.59
5831 6357 3.031736 GGCTATAGAGTGTGAGTGGGAA 58.968 50.000 3.21 0.00 0.00 3.97
5951 6486 2.482374 GCACAACTGATCCGCTGC 59.518 61.111 0.00 0.00 0.00 5.25
6105 6644 0.970937 TTGGCCGAGTGGGAGACTAG 60.971 60.000 0.00 0.00 38.47 2.57
6106 6645 1.076923 GGCCGAGTGGGAGACTAGA 60.077 63.158 0.00 0.00 38.47 2.43
6107 6646 1.385756 GGCCGAGTGGGAGACTAGAC 61.386 65.000 0.00 0.00 38.47 2.59
6108 6647 0.394625 GCCGAGTGGGAGACTAGACT 60.395 60.000 0.00 0.00 38.47 3.24
6109 6648 1.134159 GCCGAGTGGGAGACTAGACTA 60.134 57.143 0.00 0.00 38.47 2.59
6180 6719 2.322830 GGTCCACGAAAGGAACGGC 61.323 63.158 0.00 0.00 39.92 5.68
6251 6790 2.492010 GGTAGGAAGGGGGCAAAGAAAA 60.492 50.000 0.00 0.00 0.00 2.29
6452 6993 1.304217 AGATGAGGTCGACGGTGGT 60.304 57.895 9.92 0.00 0.00 4.16
6529 7077 1.068250 GTATCTGTCTCGGCTGGCC 59.932 63.158 0.00 0.00 0.00 5.36
6566 7117 4.182433 TGCTGTTGGTCCACGCCA 62.182 61.111 0.00 0.00 36.62 5.69
6574 7125 2.112297 GTCCACGCCACTGGGAAA 59.888 61.111 0.00 0.00 35.59 3.13
6578 7139 0.821711 CCACGCCACTGGGAAAAGAA 60.822 55.000 0.00 0.00 35.59 2.52
6587 7148 4.040952 CCACTGGGAAAAGAAAGAGAGAGA 59.959 45.833 0.00 0.00 35.59 3.10
6588 7149 5.237048 CACTGGGAAAAGAAAGAGAGAGAG 58.763 45.833 0.00 0.00 0.00 3.20
6591 7152 3.054728 GGGAAAAGAAAGAGAGAGAGGGG 60.055 52.174 0.00 0.00 0.00 4.79
6592 7153 3.585289 GGAAAAGAAAGAGAGAGAGGGGT 59.415 47.826 0.00 0.00 0.00 4.95
6600 7161 2.284995 AGAGAGGGGTGGGAGTGC 60.285 66.667 0.00 0.00 0.00 4.40
6601 7162 2.607750 GAGAGGGGTGGGAGTGCA 60.608 66.667 0.00 0.00 0.00 4.57
6603 7164 1.542375 AGAGGGGTGGGAGTGCAAT 60.542 57.895 0.00 0.00 0.00 3.56
6699 7263 1.203313 GCAAGTCCCGTTCGTTTCG 59.797 57.895 0.00 0.00 0.00 3.46
6704 7268 2.029369 CCCGTTCGTTTCGTCCCA 59.971 61.111 0.00 0.00 0.00 4.37
6803 7368 2.227626 CGTATGGACCATGCAAACAACA 59.772 45.455 20.83 0.00 0.00 3.33
6805 7370 2.593346 TGGACCATGCAAACAACAAC 57.407 45.000 0.00 0.00 0.00 3.32
6806 7371 1.827344 TGGACCATGCAAACAACAACA 59.173 42.857 0.00 0.00 0.00 3.33
6807 7372 2.159128 TGGACCATGCAAACAACAACAG 60.159 45.455 0.00 0.00 0.00 3.16
6808 7373 2.100584 GGACCATGCAAACAACAACAGA 59.899 45.455 0.00 0.00 0.00 3.41
6810 7375 3.784338 ACCATGCAAACAACAACAGAAG 58.216 40.909 0.00 0.00 0.00 2.85
6813 7378 1.134848 TGCAAACAACAACAGAAGGGC 60.135 47.619 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
328 355 4.057428 GCCGAGCCGACTGTGACT 62.057 66.667 0.00 0.00 0.00 3.41
329 356 3.973267 GAGCCGAGCCGACTGTGAC 62.973 68.421 0.00 0.00 0.00 3.67
330 357 3.749064 GAGCCGAGCCGACTGTGA 61.749 66.667 0.00 0.00 0.00 3.58
1258 1297 2.725637 GGGAAGTAGAAGACGAGGTCT 58.274 52.381 0.00 0.00 45.64 3.85
1310 1349 3.626596 AAGGGAGGGAGGGAGGCA 61.627 66.667 0.00 0.00 0.00 4.75
1455 1508 2.514592 CATCTGGTTGCCGGCGAT 60.515 61.111 21.90 14.00 0.00 4.58
1551 1604 0.179225 CATGAGAAACGGGCGAAACG 60.179 55.000 0.00 0.00 37.36 3.60
1552 1605 0.454452 GCATGAGAAACGGGCGAAAC 60.454 55.000 0.00 0.00 0.00 2.78
1554 1607 1.003839 AGCATGAGAAACGGGCGAA 60.004 52.632 0.00 0.00 0.00 4.70
1562 1615 2.679837 GAGCGGAATTGAGCATGAGAAA 59.320 45.455 0.00 0.00 35.48 2.52
1566 1619 0.811219 CGGAGCGGAATTGAGCATGA 60.811 55.000 0.00 0.00 35.48 3.07
1568 1621 4.131376 CGGAGCGGAATTGAGCAT 57.869 55.556 4.79 0.00 35.48 3.79
1657 1710 4.056125 GCCTCCGCCTGCCAAAAC 62.056 66.667 0.00 0.00 0.00 2.43
1699 1758 1.145598 CTCCGGCATGAGCATGACT 59.854 57.895 14.27 0.00 44.62 3.41
1763 1823 2.573915 AGGCGGAAGAGGAAGAAAATCT 59.426 45.455 0.00 0.00 0.00 2.40
1808 1877 3.314913 TCGTTTTGCTGAGAAATTGCAGA 59.685 39.130 7.25 0.00 38.01 4.26
1812 1881 4.855388 CCATCTCGTTTTGCTGAGAAATTG 59.145 41.667 0.00 0.00 43.89 2.32
1828 1897 1.811266 CTTGTCCACCGCCATCTCG 60.811 63.158 0.00 0.00 0.00 4.04
2193 2282 2.223548 GCATGCATGGCGATGTAAAAGA 60.224 45.455 27.34 0.00 31.50 2.52
2210 2300 1.467342 CAGATCACACACACTGGCATG 59.533 52.381 0.00 0.00 0.00 4.06
2296 2386 8.523915 TGCAATTTATAGACAGATTGGATGTT 57.476 30.769 0.00 0.00 31.78 2.71
2302 2392 7.338800 ACCCTTGCAATTTATAGACAGATTG 57.661 36.000 0.00 0.00 33.71 2.67
2331 2422 7.926674 TGACATCAACATCATCAAGTACAAT 57.073 32.000 0.00 0.00 0.00 2.71
2478 2570 2.485479 GGAAACAGCAACAGACCTGAGA 60.485 50.000 3.76 0.00 33.40 3.27
2502 2594 6.151144 GGTTAAGAATTGTTATGCTGGTGAGT 59.849 38.462 0.00 0.00 0.00 3.41
2754 2868 7.336931 GCCAATGGGAACGAATTACATATAGAT 59.663 37.037 0.00 0.00 35.59 1.98
2792 2915 5.215160 CAAAGATTGGACACAAGTGTAAGC 58.785 41.667 5.74 1.13 45.05 3.09
2972 3104 6.072728 GGATCATGCACACAAAACTACACTTA 60.073 38.462 0.00 0.00 0.00 2.24
3105 3238 5.596772 AGCTACCTTAAGAGATCTCCAGTTC 59.403 44.000 19.30 5.83 0.00 3.01
3127 3260 7.798052 ACAAAATAAAAATTGCGATCAAACAGC 59.202 29.630 0.00 0.00 35.56 4.40
3292 3427 2.011122 TGACCCGAGAAAGAGGAAGT 57.989 50.000 0.00 0.00 0.00 3.01
3460 3601 7.174426 CAGAATCCATATCAATCTTAGCTGCAA 59.826 37.037 1.02 0.00 0.00 4.08
3465 3606 6.877855 TGAGCAGAATCCATATCAATCTTAGC 59.122 38.462 0.00 0.00 0.00 3.09
3590 3731 2.868583 CCACATCATAGGCTTCTGAACG 59.131 50.000 0.00 0.00 0.00 3.95
3773 3941 2.028420 TCTTGAATGAGCCATGACGG 57.972 50.000 0.00 0.00 38.11 4.79
3862 4072 5.415701 TGGCTATTCCAGAAATGAAACTCAC 59.584 40.000 0.00 0.00 40.72 3.51
3896 4106 5.833667 TGACTGATCTCTTGGATTACCGTAT 59.166 40.000 0.00 0.00 39.42 3.06
3972 4185 0.107831 TGTTCAACCGGGGAGAACTG 59.892 55.000 25.82 6.62 41.56 3.16
3973 4186 0.841289 TTGTTCAACCGGGGAGAACT 59.159 50.000 25.82 0.00 41.56 3.01
3974 4187 0.949397 GTTGTTCAACCGGGGAGAAC 59.051 55.000 21.73 21.73 41.42 3.01
4013 4226 3.054875 AGTCAACAGGAGCTATTGATGCA 60.055 43.478 4.09 0.00 34.98 3.96
4082 4295 0.532196 GGGCGCTGGTAGTATCAACC 60.532 60.000 7.64 0.00 37.53 3.77
4157 4370 2.620115 AGTTAATGATGCGGATGCTTGG 59.380 45.455 0.00 0.00 43.34 3.61
4262 4475 1.040646 TCGAACTGTGAGGAGCTTGT 58.959 50.000 0.00 0.00 0.00 3.16
4409 4644 6.488006 ACAGATTTATGACAAAGTGCTCAAGT 59.512 34.615 0.00 0.00 0.00 3.16
4484 4914 2.670479 CGCAGACATAGTATCCTGCTG 58.330 52.381 22.05 15.48 46.99 4.41
4500 4950 5.221891 ACAGTATTTAAGAATGTGCGCAG 57.778 39.130 12.22 0.00 0.00 5.18
4551 5017 6.989169 AGAATACATGATTAAGCAGACAGGAC 59.011 38.462 0.00 0.00 0.00 3.85
4568 5034 9.620660 GACCAAACAAATAACGAAAGAATACAT 57.379 29.630 0.00 0.00 0.00 2.29
4596 5062 9.478238 TGGTGAGTAACATATAAGTAAGTGGTA 57.522 33.333 0.00 0.00 0.00 3.25
4608 5074 6.179756 TGCAAGAACATGGTGAGTAACATAT 58.820 36.000 0.00 0.00 0.00 1.78
4613 5079 3.181445 ACCTGCAAGAACATGGTGAGTAA 60.181 43.478 0.00 0.00 34.07 2.24
4619 5085 2.363306 TGAACCTGCAAGAACATGGT 57.637 45.000 0.00 0.00 34.07 3.55
4693 5159 2.718220 CTCAGCTGTGAGTTCGTCG 58.282 57.895 14.67 0.00 44.72 5.12
4759 5225 5.368145 TCAGTATACACAATCTGCCAATCC 58.632 41.667 5.50 0.00 0.00 3.01
4786 5252 0.465097 CCAGCATCATGTCACCCTCC 60.465 60.000 0.00 0.00 0.00 4.30
4841 5307 1.176527 TATCAAAGCAAGCACCAGGC 58.823 50.000 0.00 0.00 45.30 4.85
4843 5309 3.623060 ACGTATATCAAAGCAAGCACCAG 59.377 43.478 0.00 0.00 0.00 4.00
4861 5327 1.860676 GGATTTCTGCGGCATACGTA 58.139 50.000 1.75 0.00 46.52 3.57
4874 5340 0.177373 AGTAACGGGAGGCGGATTTC 59.823 55.000 0.00 0.00 0.00 2.17
4985 5451 2.362717 CTCCTTTCTCGGGGTAGATGAC 59.637 54.545 0.00 0.00 0.00 3.06
5050 5516 1.302383 TAAATGGCTTGACGTGGCGG 61.302 55.000 0.00 0.00 0.00 6.13
5124 5591 0.647410 GATGCACTGGAACGACATCG 59.353 55.000 0.00 0.00 46.33 3.84
5151 5618 1.207329 CCGAGGGAGTTAAGGTCAAGG 59.793 57.143 0.00 0.00 0.00 3.61
5220 5691 3.928375 TCGGTGATGCGAATCATATCATG 59.072 43.478 9.89 0.00 35.05 3.07
5280 5751 0.030101 GCTTAACGCAACCTGCACAA 59.970 50.000 0.00 0.00 45.36 3.33
5281 5752 1.652012 GCTTAACGCAACCTGCACA 59.348 52.632 0.00 0.00 45.36 4.57
5282 5753 1.081442 GGCTTAACGCAACCTGCAC 60.081 57.895 0.00 0.00 45.36 4.57
5549 6031 9.707957 TCATAAATCTTGGCCCTAAAAATCTTA 57.292 29.630 0.00 0.00 0.00 2.10
5551 6033 8.788238 ATCATAAATCTTGGCCCTAAAAATCT 57.212 30.769 0.00 0.00 0.00 2.40
5555 6037 8.792633 CGATAATCATAAATCTTGGCCCTAAAA 58.207 33.333 0.00 0.00 0.00 1.52
5672 6155 8.124199 GCTTACTTACTCACTAACACTAGCTAG 58.876 40.741 19.44 19.44 0.00 3.42
5673 6156 7.609146 TGCTTACTTACTCACTAACACTAGCTA 59.391 37.037 0.00 0.00 0.00 3.32
5674 6157 6.433404 TGCTTACTTACTCACTAACACTAGCT 59.567 38.462 0.00 0.00 0.00 3.32
5675 6158 6.618811 TGCTTACTTACTCACTAACACTAGC 58.381 40.000 0.00 0.00 0.00 3.42
5676 6159 8.298140 ACTTGCTTACTTACTCACTAACACTAG 58.702 37.037 0.00 0.00 0.00 2.57
5677 6160 8.174733 ACTTGCTTACTTACTCACTAACACTA 57.825 34.615 0.00 0.00 0.00 2.74
5678 6161 7.052142 ACTTGCTTACTTACTCACTAACACT 57.948 36.000 0.00 0.00 0.00 3.55
5681 6164 6.810676 GGGTACTTGCTTACTTACTCACTAAC 59.189 42.308 0.00 0.00 0.00 2.34
5682 6165 6.723052 AGGGTACTTGCTTACTTACTCACTAA 59.277 38.462 0.00 0.00 0.00 2.24
5683 6166 6.152323 CAGGGTACTTGCTTACTTACTCACTA 59.848 42.308 0.00 0.00 0.00 2.74
5684 6167 5.047235 CAGGGTACTTGCTTACTTACTCACT 60.047 44.000 0.00 0.00 0.00 3.41
5685 6168 5.169295 CAGGGTACTTGCTTACTTACTCAC 58.831 45.833 0.00 0.00 0.00 3.51
5686 6169 4.836736 ACAGGGTACTTGCTTACTTACTCA 59.163 41.667 0.00 0.00 0.00 3.41
5687 6170 5.402997 ACAGGGTACTTGCTTACTTACTC 57.597 43.478 0.00 0.00 0.00 2.59
5725 6212 0.737715 CGGAACAGCTACTGCAGGTC 60.738 60.000 19.93 6.34 41.00 3.85
5726 6213 1.293498 CGGAACAGCTACTGCAGGT 59.707 57.895 19.93 2.28 42.74 4.00
5727 6214 1.448540 CCGGAACAGCTACTGCAGG 60.449 63.158 19.93 1.57 42.74 4.85
5728 6215 0.459237 CTCCGGAACAGCTACTGCAG 60.459 60.000 13.48 13.48 42.74 4.41
5729 6216 1.185618 ACTCCGGAACAGCTACTGCA 61.186 55.000 5.23 0.00 42.74 4.41
5746 6233 3.560068 CGTCTTTGCCAGTGTTTCTTACT 59.440 43.478 0.00 0.00 0.00 2.24
5747 6234 3.558418 TCGTCTTTGCCAGTGTTTCTTAC 59.442 43.478 0.00 0.00 0.00 2.34
5748 6235 3.799366 TCGTCTTTGCCAGTGTTTCTTA 58.201 40.909 0.00 0.00 0.00 2.10
5749 6236 2.639065 TCGTCTTTGCCAGTGTTTCTT 58.361 42.857 0.00 0.00 0.00 2.52
5951 6486 0.950836 TAAATCAATCATGCCGCCCG 59.049 50.000 0.00 0.00 0.00 6.13
6123 6662 4.415150 ACACCAGCGGCCTCCATG 62.415 66.667 0.00 0.00 0.00 3.66
6134 6673 2.815211 CCGATGCGTCCACACCAG 60.815 66.667 0.00 0.00 0.00 4.00
6166 6705 3.295228 CTGCGCCGTTCCTTTCGTG 62.295 63.158 4.18 0.00 0.00 4.35
6197 6736 3.051479 GTACCAACCAACCCGGCG 61.051 66.667 0.00 0.00 39.03 6.46
6290 6831 2.266055 CCGAGACAAGGGAGGCAC 59.734 66.667 0.00 0.00 0.00 5.01
6566 7117 4.285775 CCTCTCTCTCTTTCTTTTCCCAGT 59.714 45.833 0.00 0.00 0.00 4.00
6574 7125 2.545810 CCACCCCTCTCTCTCTTTCTT 58.454 52.381 0.00 0.00 0.00 2.52
6578 7139 0.338120 CTCCCACCCCTCTCTCTCTT 59.662 60.000 0.00 0.00 0.00 2.85
6587 7148 2.765969 CATTGCACTCCCACCCCT 59.234 61.111 0.00 0.00 0.00 4.79
6588 7149 3.070576 GCATTGCACTCCCACCCC 61.071 66.667 3.15 0.00 0.00 4.95
6591 7152 1.303561 TCCAGCATTGCACTCCCAC 60.304 57.895 11.91 0.00 0.00 4.61
6592 7153 1.001764 CTCCAGCATTGCACTCCCA 60.002 57.895 11.91 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.