Multiple sequence alignment - TraesCS3D01G195600

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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 TraesCS3D01G195600 chr3D 100.000 7205 0 0 1 7205 190252647 190259851 0.000000e+00 13306.0
1 TraesCS3D01G195600 chr3D 90.587 2231 188 16 1027 3240 189452259 189454484 0.000000e+00 2937.0
2 TraesCS3D01G195600 chr3D 93.333 540 36 0 4082 4621 189455245 189455784 0.000000e+00 798.0
3 TraesCS3D01G195600 chr3D 91.628 215 18 0 5891 6105 189456512 189456726 1.520000e-76 298.0
4 TraesCS3D01G195600 chr3D 81.622 185 25 7 6535 6710 354278416 354278600 2.090000e-30 145.0
5 TraesCS3D01G195600 chr3D 92.593 54 4 0 6489 6542 557928500 557928553 2.160000e-10 78.7
6 TraesCS3D01G195600 chr3A 96.545 3415 89 12 3312 6710 261351521 261348120 0.000000e+00 5626.0
7 TraesCS3D01G195600 chr3A 98.223 2363 31 4 954 3309 261353915 261351557 0.000000e+00 4120.0
8 TraesCS3D01G195600 chr3A 91.702 2133 174 3 1110 3240 249860852 249858721 0.000000e+00 2955.0
9 TraesCS3D01G195600 chr3A 93.889 540 33 0 4082 4621 249858024 249857485 0.000000e+00 815.0
10 TraesCS3D01G195600 chr3A 85.954 477 43 8 6720 7178 261347494 261347024 8.400000e-134 488.0
11 TraesCS3D01G195600 chr3A 92.093 215 17 0 5891 6105 249854704 249854490 3.270000e-78 303.0
12 TraesCS3D01G195600 chr3A 100.000 29 0 0 886 914 645644094 645644122 4.000000e-03 54.7
13 TraesCS3D01G195600 chr3B 98.657 2382 28 3 932 3309 275345996 275343615 0.000000e+00 4218.0
14 TraesCS3D01G195600 chr3B 95.801 1929 58 8 4804 6710 275338804 275336877 0.000000e+00 3092.0
15 TraesCS3D01G195600 chr3B 90.722 2231 185 16 1027 3240 274521400 274519175 0.000000e+00 2953.0
16 TraesCS3D01G195600 chr3B 97.335 1501 25 8 3312 4812 275343579 275342094 0.000000e+00 2536.0
17 TraesCS3D01G195600 chr3B 89.231 910 59 8 3 886 275347120 275346224 0.000000e+00 1101.0
18 TraesCS3D01G195600 chr3B 93.333 540 36 0 4082 4621 274518415 274517876 0.000000e+00 798.0
19 TraesCS3D01G195600 chr3B 89.706 476 31 5 6720 7178 275336257 275335783 6.220000e-165 592.0
20 TraesCS3D01G195600 chr3B 77.512 627 124 11 1179 1792 794561527 794562149 1.910000e-95 361.0
21 TraesCS3D01G195600 chr3B 91.628 215 18 0 5891 6105 274517145 274516931 1.520000e-76 298.0
22 TraesCS3D01G195600 chr3B 77.253 233 28 8 6766 6975 190159985 190159755 5.910000e-21 113.0
23 TraesCS3D01G195600 chr1D 87.692 520 63 1 3 521 125583530 125584049 8.000000e-169 604.0
24 TraesCS3D01G195600 chr1D 89.286 56 5 1 6488 6542 397638820 397638765 1.300000e-07 69.4
25 TraesCS3D01G195600 chr7B 85.115 524 78 0 3 526 118223802 118223279 2.960000e-148 536.0
26 TraesCS3D01G195600 chr7B 80.083 241 33 6 6739 6966 653979289 653979051 1.610000e-36 165.0
27 TraesCS3D01G195600 chr7B 92.523 107 8 0 3838 3944 216938334 216938228 3.480000e-33 154.0
28 TraesCS3D01G195600 chr7B 92.308 52 4 0 6491 6542 161450137 161450086 2.790000e-09 75.0
29 TraesCS3D01G195600 chr4B 85.115 524 76 1 3 526 324889866 324890387 1.060000e-147 534.0
30 TraesCS3D01G195600 chr6D 85.009 527 73 5 3 526 194228328 194227805 1.380000e-146 531.0
31 TraesCS3D01G195600 chr6D 82.420 529 89 3 3 527 200399957 200399429 6.590000e-125 459.0
32 TraesCS3D01G195600 chr6A 84.440 527 78 4 3 526 268963286 268962761 3.850000e-142 516.0
33 TraesCS3D01G195600 chr6A 100.000 28 0 0 7178 7205 438738420 438738393 1.300000e-02 52.8
34 TraesCS3D01G195600 chr2B 84.325 504 78 1 24 527 328986012 328986514 6.490000e-135 492.0
35 TraesCS3D01G195600 chr7D 82.649 536 84 9 3 532 384402527 384401995 3.940000e-127 466.0
36 TraesCS3D01G195600 chr6B 87.719 171 20 1 6540 6710 687189422 687189591 1.590000e-46 198.0
37 TraesCS3D01G195600 chr6B 92.308 52 4 0 6490 6541 151611945 151611894 2.790000e-09 75.0
38 TraesCS3D01G195600 chr2A 83.636 220 27 4 6491 6710 138526137 138526347 1.590000e-46 198.0
39 TraesCS3D01G195600 chr2A 87.402 127 14 1 6586 6710 103146348 103146474 2.090000e-30 145.0
40 TraesCS3D01G195600 chr2D 84.663 163 21 3 6537 6696 585102213 585102052 7.480000e-35 159.0
41 TraesCS3D01G195600 chr5A 90.741 108 10 0 3839 3946 559809527 559809634 2.090000e-30 145.0
42 TraesCS3D01G195600 chr5A 83.234 167 17 7 6554 6710 678928906 678929071 7.530000e-30 143.0
43 TraesCS3D01G195600 chr5A 79.851 134 24 3 6875 7007 657101430 657101561 2.140000e-15 95.3
44 TraesCS3D01G195600 chr5A 100.000 30 0 0 914 943 230543119 230543090 1.000000e-03 56.5
45 TraesCS3D01G195600 chr1B 90.179 112 10 1 3839 3949 301273502 301273391 2.090000e-30 145.0
46 TraesCS3D01G195600 chr1B 84.615 143 15 6 6569 6707 352132249 352132388 1.260000e-27 135.0
47 TraesCS3D01G195600 chr1B 86.458 96 13 0 6875 6970 535325516 535325611 9.890000e-19 106.0
48 TraesCS3D01G195600 chr1B 85.714 77 10 1 6489 6565 487212505 487212580 5.990000e-11 80.5
49 TraesCS3D01G195600 chr1A 89.815 108 11 0 3839 3946 352174199 352174092 9.750000e-29 139.0
50 TraesCS3D01G195600 chr7A 90.385 104 10 0 3835 3938 554392258 554392361 3.510000e-28 137.0
51 TraesCS3D01G195600 chr7A 96.970 33 0 1 6842 6874 2713394 2713363 4.000000e-03 54.7
52 TraesCS3D01G195600 chr5B 90.291 103 10 0 3844 3946 501957055 501956953 1.260000e-27 135.0
53 TraesCS3D01G195600 chr5B 87.611 113 14 0 3837 3949 440275947 440275835 1.630000e-26 132.0
54 TraesCS3D01G195600 chr5B 86.842 114 12 3 6854 6966 417156197 417156086 2.730000e-24 124.0
55 TraesCS3D01G195600 chr4A 80.247 162 31 1 6875 7035 619406842 619407003 3.530000e-23 121.0
56 TraesCS3D01G195600 chr4A 83.929 112 13 4 6858 6966 516582656 516582765 1.280000e-17 102.0
57 TraesCS3D01G195600 chr4D 79.518 166 30 4 6846 7007 507873938 507874103 1.640000e-21 115.0
58 TraesCS3D01G195600 chr5D 94.545 55 3 0 6488 6542 218853936 218853990 1.290000e-12 86.1
59 TraesCS3D01G195600 chr5D 92.727 55 4 0 6490 6544 308026712 308026766 5.990000e-11 80.5
60 TraesCS3D01G195600 chr5D 100.000 28 0 0 7178 7205 95028293 95028266 1.300000e-02 52.8


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 TraesCS3D01G195600 chr3D 190252647 190259851 7204 False 13306.000000 13306 100.000000 1 7205 1 chr3D.!!$F1 7204
1 TraesCS3D01G195600 chr3D 189452259 189456726 4467 False 1344.333333 2937 91.849333 1027 6105 3 chr3D.!!$F4 5078
2 TraesCS3D01G195600 chr3A 261347024 261353915 6891 True 3411.333333 5626 93.574000 954 7178 3 chr3A.!!$R2 6224
3 TraesCS3D01G195600 chr3A 249854490 249860852 6362 True 1357.666667 2955 92.561333 1110 6105 3 chr3A.!!$R1 4995
4 TraesCS3D01G195600 chr3B 275335783 275347120 11337 True 2307.800000 4218 94.146000 3 7178 5 chr3B.!!$R3 7175
5 TraesCS3D01G195600 chr3B 274516931 274521400 4469 True 1349.666667 2953 91.894333 1027 6105 3 chr3B.!!$R2 5078
6 TraesCS3D01G195600 chr3B 794561527 794562149 622 False 361.000000 361 77.512000 1179 1792 1 chr3B.!!$F1 613
7 TraesCS3D01G195600 chr1D 125583530 125584049 519 False 604.000000 604 87.692000 3 521 1 chr1D.!!$F1 518
8 TraesCS3D01G195600 chr7B 118223279 118223802 523 True 536.000000 536 85.115000 3 526 1 chr7B.!!$R1 523
9 TraesCS3D01G195600 chr4B 324889866 324890387 521 False 534.000000 534 85.115000 3 526 1 chr4B.!!$F1 523
10 TraesCS3D01G195600 chr6D 194227805 194228328 523 True 531.000000 531 85.009000 3 526 1 chr6D.!!$R1 523
11 TraesCS3D01G195600 chr6D 200399429 200399957 528 True 459.000000 459 82.420000 3 527 1 chr6D.!!$R2 524
12 TraesCS3D01G195600 chr6A 268962761 268963286 525 True 516.000000 516 84.440000 3 526 1 chr6A.!!$R1 523
13 TraesCS3D01G195600 chr2B 328986012 328986514 502 False 492.000000 492 84.325000 24 527 1 chr2B.!!$F1 503
14 TraesCS3D01G195600 chr7D 384401995 384402527 532 True 466.000000 466 82.649000 3 532 1 chr7D.!!$R1 529

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
596 618 0.391793 GGTTGTCAGGGAGCAGTAGC 60.392 60.000 0.00 0.0 42.56 3.58 F
2157 2399 0.455410 GTGCTCGATCTGCTCACTCT 59.545 55.000 8.62 0.0 0.00 3.24 F
2258 2500 0.460284 GTACCGTCAGATGCTGGTGG 60.460 60.000 6.19 0.0 35.93 4.61 F
2597 2839 1.006519 TCTCAGAGGAAGGGGAGTCAG 59.993 57.143 0.00 0.0 0.00 3.51 F
3220 3465 1.494960 TTGCCCTATGGAAATTGCCC 58.505 50.000 0.00 0.0 0.00 5.36 F
3931 4332 3.432252 CGTTTGAGCGACAAGTATTTCCT 59.568 43.478 0.00 0.0 39.77 3.36 F
5458 11475 2.031258 TGGTACCAATATGTGTGCGG 57.969 50.000 13.60 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2594 2836 0.254178 GGCTTGGAGGAATCAGCTGA 59.746 55.000 20.79 20.79 0.0 4.26 R
3996 4397 1.331756 GTGGCAATTATGAGCTCACCG 59.668 52.381 20.97 6.93 0.0 4.94 R
4328 4730 2.243810 GAGGTCTCCCATGGTAGCTAG 58.756 57.143 11.73 0.14 0.0 3.42 R
4625 5027 1.546029 GTTTCCCAAGGACTCCATTGC 59.454 52.381 0.00 0.00 0.0 3.56 R
4935 8639 1.805869 CTTCAGCAACAGAGGTCAGG 58.194 55.000 0.00 0.00 0.0 3.86 R
5527 11544 2.726760 GCACTCACAACTGAAGTCTACG 59.273 50.000 0.00 0.00 0.0 3.51 R
6782 13456 0.460722 TCCGTTCGTCTGACCAAACA 59.539 50.000 16.31 1.24 0.0 2.83 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
134 150 1.067776 CCTTGACACGTCCACTAGACC 60.068 57.143 0.00 0.00 43.08 3.85
173 189 0.670239 TTCATGCGACGTGCTGACAT 60.670 50.000 0.00 0.00 46.63 3.06
390 408 1.899437 TTGATGACCTGTCGGGAGGC 61.899 60.000 4.16 0.00 36.46 4.70
395 413 3.787001 CCTGTCGGGAGGCCTTCC 61.787 72.222 21.86 21.86 46.00 3.46
417 435 5.186215 TCCTCACGGTCTTGTATGTTGAATA 59.814 40.000 0.00 0.00 0.00 1.75
551 573 1.130054 ATGGATGTAGCTCCGGCCAT 61.130 55.000 2.24 0.00 38.21 4.40
552 574 1.302033 GGATGTAGCTCCGGCCATG 60.302 63.158 2.24 0.00 39.73 3.66
559 581 2.593725 CTCCGGCCATGGATGCAG 60.594 66.667 18.40 0.00 37.41 4.41
565 587 1.065273 GCCATGGATGCAGCTTTCG 59.935 57.895 18.40 0.00 0.00 3.46
577 599 1.441016 GCTTTCGTTTGCAGCTCCG 60.441 57.895 0.00 0.00 0.00 4.63
582 604 2.542907 CGTTTGCAGCTCCGGTTGT 61.543 57.895 0.00 0.00 0.00 3.32
596 618 0.391793 GGTTGTCAGGGAGCAGTAGC 60.392 60.000 0.00 0.00 42.56 3.58
621 643 1.134848 GCAGCTGAGAGAGGAAATCGT 60.135 52.381 20.43 0.00 0.00 3.73
624 646 1.205893 GCTGAGAGAGGAAATCGTGGT 59.794 52.381 0.00 0.00 0.00 4.16
631 653 2.106683 GGAAATCGTGGTGAGGGCG 61.107 63.158 0.00 0.00 0.00 6.13
632 654 2.746277 AAATCGTGGTGAGGGCGC 60.746 61.111 0.00 0.00 0.00 6.53
633 655 3.254024 AAATCGTGGTGAGGGCGCT 62.254 57.895 7.64 1.38 0.00 5.92
634 656 3.958147 AATCGTGGTGAGGGCGCTG 62.958 63.158 8.56 0.00 0.00 5.18
663 685 4.043200 GGCTTTGTGGTGCTCGCC 62.043 66.667 0.00 0.00 0.00 5.54
667 689 4.680237 TTGTGGTGCTCGCCGGAG 62.680 66.667 5.05 0.00 43.46 4.63
702 724 2.165437 GAGAGAACACGAGGAGATTGCT 59.835 50.000 0.00 0.00 0.00 3.91
704 726 2.670414 GAGAACACGAGGAGATTGCTTG 59.330 50.000 0.00 0.00 0.00 4.01
743 765 5.729510 AGAAAGACTAGTGGATGAGAAAGC 58.270 41.667 0.00 0.00 0.00 3.51
772 794 7.334858 GGAGAAGATAAGAAAGAGGAACACAT 58.665 38.462 0.00 0.00 0.00 3.21
777 799 4.574599 AAGAAAGAGGAACACATGTTGC 57.425 40.909 8.09 8.09 45.14 4.17
808 840 5.639506 CACCAAAAACAGATACACGAGAGAT 59.360 40.000 0.00 0.00 0.00 2.75
812 844 4.662468 AACAGATACACGAGAGATGCAT 57.338 40.909 0.00 0.00 0.00 3.96
818 850 3.095102 ACACGAGAGATGCATGATCAG 57.905 47.619 2.46 3.42 32.86 2.90
822 854 3.132160 CGAGAGATGCATGATCAGCTTT 58.868 45.455 2.46 0.00 32.18 3.51
839 871 1.087202 TTTAATCGCTCGCACGCCAT 61.087 50.000 0.00 0.00 0.00 4.40
886 918 4.818546 CGTTTCTCTAATACTCCCTCCGTA 59.181 45.833 0.00 0.00 0.00 4.02
887 919 5.297776 CGTTTCTCTAATACTCCCTCCGTAA 59.702 44.000 0.00 0.00 0.00 3.18
888 920 6.183360 CGTTTCTCTAATACTCCCTCCGTAAA 60.183 42.308 0.00 0.00 0.00 2.01
892 924 9.597681 TTCTCTAATACTCCCTCCGTAAATAAT 57.402 33.333 0.00 0.00 0.00 1.28
900 932 8.953223 ACTCCCTCCGTAAATAATATAAGAGT 57.047 34.615 0.00 0.00 0.00 3.24
901 933 8.804204 ACTCCCTCCGTAAATAATATAAGAGTG 58.196 37.037 0.00 0.00 0.00 3.51
904 936 9.774413 CCCTCCGTAAATAATATAAGAGTGTTT 57.226 33.333 0.00 0.00 0.00 2.83
918 950 8.773404 ATAAGAGTGTTTAAATCACTACGCTT 57.227 30.769 17.66 17.44 44.68 4.68
919 951 7.492352 AAGAGTGTTTAAATCACTACGCTTT 57.508 32.000 17.66 9.06 44.68 3.51
920 952 7.492352 AGAGTGTTTAAATCACTACGCTTTT 57.508 32.000 17.66 1.39 44.68 2.27
921 953 8.597662 AGAGTGTTTAAATCACTACGCTTTTA 57.402 30.769 17.66 0.00 44.68 1.52
922 954 9.216117 AGAGTGTTTAAATCACTACGCTTTTAT 57.784 29.630 17.66 0.36 44.68 1.40
998 1212 4.909880 CGCGAAGTAAAAAGAAAGGAAAGG 59.090 41.667 0.00 0.00 0.00 3.11
1023 1241 4.866508 ATACGAACAACTCCACTCTTCA 57.133 40.909 0.00 0.00 0.00 3.02
2116 2358 0.457035 CCAGCCCGAATTTGGATGTG 59.543 55.000 13.85 7.06 37.58 3.21
2157 2399 0.455410 GTGCTCGATCTGCTCACTCT 59.545 55.000 8.62 0.00 0.00 3.24
2258 2500 0.460284 GTACCGTCAGATGCTGGTGG 60.460 60.000 6.19 0.00 35.93 4.61
2594 2836 2.862597 ACTATCTCAGAGGAAGGGGAGT 59.137 50.000 0.00 0.00 0.00 3.85
2597 2839 1.006519 TCTCAGAGGAAGGGGAGTCAG 59.993 57.143 0.00 0.00 0.00 3.51
2811 3056 2.027285 TCTTAGCTGCAGTTGTGGCATA 60.027 45.455 16.64 0.00 41.06 3.14
3055 3300 5.319139 CAATCATGTAGACAGAGTTTTGCG 58.681 41.667 0.00 0.00 0.00 4.85
3220 3465 1.494960 TTGCCCTATGGAAATTGCCC 58.505 50.000 0.00 0.00 0.00 5.36
3664 4046 8.093927 AGGTTTATGTGTGTTTATTGGATTTGG 58.906 33.333 0.00 0.00 0.00 3.28
3720 4109 7.672122 TTTCTAGGAGGATAGTTAGGAAACC 57.328 40.000 0.00 0.00 36.15 3.27
3827 4228 9.271828 CAATTGCTTCTAAACAAAAGGGTTTAT 57.728 29.630 0.00 0.00 41.09 1.40
3931 4332 3.432252 CGTTTGAGCGACAAGTATTTCCT 59.568 43.478 0.00 0.00 39.77 3.36
3996 4397 7.549134 TCTGTATCATTGTGTATTGTCTTGGAC 59.451 37.037 0.00 0.00 0.00 4.02
4328 4730 3.694566 ACTTCAGAACCTGTGTTTGGAAC 59.305 43.478 0.00 0.00 33.97 3.62
4625 5027 6.124088 AGGTAATATGCTTCTTTCTTTGCG 57.876 37.500 0.00 0.00 0.00 4.85
4750 5152 7.136822 TCATGTAGCCAAGATACCTGTAAAT 57.863 36.000 0.00 0.00 0.00 1.40
4867 8570 7.037586 GGTCATAGACTTATATCCCCCAAATCA 60.038 40.741 0.00 0.00 32.47 2.57
4935 8639 6.254281 TGAAATACTGTTGCCTTTTAGCTC 57.746 37.500 0.00 0.00 0.00 4.09
5110 8815 3.818961 ATGTTGTGCTCTGTCATTTCG 57.181 42.857 0.00 0.00 0.00 3.46
5124 8829 4.122776 GTCATTTCGTCTGGCTCATATGT 58.877 43.478 1.90 0.00 0.00 2.29
5134 11052 4.818005 TCTGGCTCATATGTAGTGCATTTG 59.182 41.667 0.00 2.05 38.94 2.32
5169 11186 4.279671 TGCCCCTTTGTATTGTGTTTACAG 59.720 41.667 0.00 0.00 38.23 2.74
5458 11475 2.031258 TGGTACCAATATGTGTGCGG 57.969 50.000 13.60 0.00 0.00 5.69
5520 11537 7.469260 ACGCATGTAGAATATGGTTTAAACAC 58.531 34.615 19.57 9.74 0.00 3.32
5634 11651 9.118300 ACTCAATGCTAAGATTCCTAATTTCTG 57.882 33.333 0.00 0.00 0.00 3.02
5778 11799 3.906846 TGGGGCATCAGTTTTGGTTATTT 59.093 39.130 0.00 0.00 0.00 1.40
6210 12254 6.258507 GGCACAATGGGATTGATTGAATTAAC 59.741 38.462 3.35 0.00 42.83 2.01
6278 12322 3.558033 AGAAGAGGATCGTAGGGAAGTC 58.442 50.000 0.00 0.00 42.67 3.01
6327 12371 1.927174 CACTTCCTTTCGCGATAGGTG 59.073 52.381 34.70 29.61 32.31 4.00
6331 12375 3.872511 TCCTTTCGCGATAGGTGTTTA 57.127 42.857 34.70 19.23 32.31 2.01
6357 12401 7.490962 TGATAAATGGCGTTGTAGAAATAGG 57.509 36.000 0.00 0.00 0.00 2.57
6425 12469 3.067742 ACTGTATTACCGACCTCCATTCG 59.932 47.826 0.00 0.00 36.20 3.34
6433 12477 7.707624 TTACCGACCTCCATTCGTATAATAT 57.292 36.000 0.00 0.00 34.56 1.28
6519 12566 1.339929 ACAACCGGACTTTGCAAATCC 59.660 47.619 21.35 21.35 0.00 3.01
6531 12578 1.272425 TGCAAATCCGACCCCTCAAAT 60.272 47.619 0.00 0.00 0.00 2.32
6532 12579 2.025793 TGCAAATCCGACCCCTCAAATA 60.026 45.455 0.00 0.00 0.00 1.40
6548 12606 1.188863 AATACCCGCGGACACTAACT 58.811 50.000 30.73 0.00 0.00 2.24
6552 12610 1.005394 CCGCGGACACTAACTGGTT 60.005 57.895 24.07 0.00 0.00 3.67
6602 12660 5.070446 TCGGACACCTCAATTAGCATATCTT 59.930 40.000 0.00 0.00 0.00 2.40
6603 12661 5.406780 CGGACACCTCAATTAGCATATCTTC 59.593 44.000 0.00 0.00 0.00 2.87
6649 12707 7.661968 ACTATGTAAATGATGCTACATCGTCT 58.338 34.615 2.93 0.00 39.08 4.18
6710 12768 0.482446 TTTGGCCATGGTGGAGAAGT 59.518 50.000 14.67 0.00 40.96 3.01
6712 12770 0.482446 TGGCCATGGTGGAGAAGTTT 59.518 50.000 14.67 0.00 40.96 2.66
6713 12771 1.177401 GGCCATGGTGGAGAAGTTTC 58.823 55.000 14.67 0.00 40.96 2.78
6714 12772 0.804989 GCCATGGTGGAGAAGTTTCG 59.195 55.000 14.67 0.00 40.96 3.46
6715 12773 1.610624 GCCATGGTGGAGAAGTTTCGA 60.611 52.381 14.67 0.00 40.96 3.71
6736 13410 1.067283 CATAGATGGCCGAAGATCGCT 60.067 52.381 0.00 0.00 38.82 4.93
6737 13411 1.905637 TAGATGGCCGAAGATCGCTA 58.094 50.000 0.00 0.00 38.82 4.26
6782 13456 4.323104 GGAGATTGAAGTGAAGTGGCTAGT 60.323 45.833 0.00 0.00 0.00 2.57
6791 13465 2.171659 TGAAGTGGCTAGTGTTTGGTCA 59.828 45.455 0.00 0.00 0.00 4.02
6802 13476 1.134759 TGTTTGGTCAGACGAACGGAA 60.135 47.619 0.00 0.00 37.52 4.30
6822 13496 2.921221 AGGGGATGAGTATATGTGGGG 58.079 52.381 0.00 0.00 0.00 4.96
6825 13499 2.572104 GGGATGAGTATATGTGGGGTCC 59.428 54.545 0.00 0.00 0.00 4.46
6911 13596 2.263895 TATAAGGGGTGCTGGTCAGT 57.736 50.000 0.00 0.00 0.00 3.41
6925 13610 0.391597 GTCAGTCCGGGTGTTTGAGA 59.608 55.000 0.00 0.00 0.00 3.27
6982 13667 1.429148 CCGATCACTAACAAGGCGGC 61.429 60.000 0.00 0.00 0.00 6.53
6983 13668 0.460284 CGATCACTAACAAGGCGGCT 60.460 55.000 5.25 5.25 0.00 5.52
7015 13700 1.209640 GAGACGAGTTCGAGGCGTT 59.790 57.895 8.72 2.43 43.02 4.84
7038 13723 4.402474 TCGAGTGGAGATGCTCTTATTCAA 59.598 41.667 0.00 0.00 0.00 2.69
7039 13724 5.105351 TCGAGTGGAGATGCTCTTATTCAAA 60.105 40.000 0.00 0.00 0.00 2.69
7072 13757 6.257423 TGAAAATGCATCACAAACGCTATAG 58.743 36.000 0.00 0.00 0.00 1.31
7133 13825 3.706373 TTGGAGGTGCCGAGAGCC 61.706 66.667 0.00 0.00 42.71 4.70
7178 13870 2.741092 GGCGGATCGGATGCCTAA 59.259 61.111 11.09 0.00 45.40 2.69
7179 13871 1.296715 GGCGGATCGGATGCCTAAT 59.703 57.895 11.09 0.00 45.40 1.73
7180 13872 1.021390 GGCGGATCGGATGCCTAATG 61.021 60.000 11.09 0.00 45.40 1.90
7181 13873 0.320771 GCGGATCGGATGCCTAATGT 60.321 55.000 4.16 0.00 0.00 2.71
7182 13874 1.067142 GCGGATCGGATGCCTAATGTA 60.067 52.381 4.16 0.00 0.00 2.29
7183 13875 2.611971 GCGGATCGGATGCCTAATGTAA 60.612 50.000 4.16 0.00 0.00 2.41
7184 13876 3.254060 CGGATCGGATGCCTAATGTAAG 58.746 50.000 3.79 0.00 0.00 2.34
7185 13877 3.600388 GGATCGGATGCCTAATGTAAGG 58.400 50.000 0.00 0.00 39.87 2.69
7186 13878 3.600388 GATCGGATGCCTAATGTAAGGG 58.400 50.000 0.00 0.00 37.11 3.95
7187 13879 1.071699 TCGGATGCCTAATGTAAGGGC 59.928 52.381 0.00 0.00 45.45 5.19
7197 13889 6.455647 GCCTAATGTAAGGGCATTTTTATCC 58.544 40.000 0.00 0.00 44.69 2.59
7198 13890 6.518369 GCCTAATGTAAGGGCATTTTTATCCC 60.518 42.308 0.00 0.00 44.69 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
155 171 1.079888 ATGTCAGCACGTCGCATGA 60.080 52.632 11.58 9.24 46.13 3.07
173 189 1.062364 GGGAGGATCATCAGGATGCA 58.938 55.000 9.94 0.00 45.99 3.96
372 390 2.359169 GCCTCCCGACAGGTCATCA 61.359 63.158 0.00 0.00 35.72 3.07
395 413 7.277760 TCAATATTCAACATACAAGACCGTGAG 59.722 37.037 0.00 0.00 0.00 3.51
417 435 7.285858 GGAGGACTACTACATACAAGACTCAAT 59.714 40.741 0.00 0.00 0.00 2.57
551 573 0.039256 GCAAACGAAAGCTGCATCCA 60.039 50.000 1.02 0.00 41.44 3.41
552 574 0.039256 TGCAAACGAAAGCTGCATCC 60.039 50.000 1.02 0.00 45.02 3.51
559 581 1.441016 CGGAGCTGCAAACGAAAGC 60.441 57.895 5.91 0.00 37.20 3.51
565 587 1.282875 GACAACCGGAGCTGCAAAC 59.717 57.895 9.46 0.00 0.00 2.93
577 599 0.391793 GCTACTGCTCCCTGACAACC 60.392 60.000 0.00 0.00 36.03 3.77
582 604 1.075970 ATCCGCTACTGCTCCCTGA 60.076 57.895 0.00 0.00 36.97 3.86
596 618 1.067749 CCTCTCTCAGCTGCATCCG 59.932 63.158 9.47 0.00 0.00 4.18
604 626 1.205893 ACCACGATTTCCTCTCTCAGC 59.794 52.381 0.00 0.00 0.00 4.26
632 654 2.720144 AAAGCCAACCCCTGAGCCAG 62.720 60.000 0.00 0.00 0.00 4.85
633 655 2.777960 AAAGCCAACCCCTGAGCCA 61.778 57.895 0.00 0.00 0.00 4.75
634 656 2.118294 AAAGCCAACCCCTGAGCC 59.882 61.111 0.00 0.00 0.00 4.70
635 657 1.531602 ACAAAGCCAACCCCTGAGC 60.532 57.895 0.00 0.00 0.00 4.26
636 658 1.181098 CCACAAAGCCAACCCCTGAG 61.181 60.000 0.00 0.00 0.00 3.35
637 659 1.152567 CCACAAAGCCAACCCCTGA 60.153 57.895 0.00 0.00 0.00 3.86
638 660 1.457455 ACCACAAAGCCAACCCCTG 60.457 57.895 0.00 0.00 0.00 4.45
639 661 1.457455 CACCACAAAGCCAACCCCT 60.457 57.895 0.00 0.00 0.00 4.79
640 662 3.137687 CACCACAAAGCCAACCCC 58.862 61.111 0.00 0.00 0.00 4.95
641 663 2.087462 GAGCACCACAAAGCCAACCC 62.087 60.000 0.00 0.00 0.00 4.11
642 664 1.363807 GAGCACCACAAAGCCAACC 59.636 57.895 0.00 0.00 0.00 3.77
663 685 3.550820 TCTCTCTTCATCTTCTCCTCCG 58.449 50.000 0.00 0.00 0.00 4.63
667 689 5.650543 GTGTTCTCTCTCTTCATCTTCTCC 58.349 45.833 0.00 0.00 0.00 3.71
702 724 0.537188 CTTCTTCCTCTAGCGCCCAA 59.463 55.000 2.29 0.00 0.00 4.12
704 726 0.824759 TTCTTCTTCCTCTAGCGCCC 59.175 55.000 2.29 0.00 0.00 6.13
743 765 4.098654 TCCTCTTTCTTATCTTCTCCGCAG 59.901 45.833 0.00 0.00 0.00 5.18
772 794 0.749818 TTTTGGTGAGCCTCGCAACA 60.750 50.000 7.68 0.00 35.27 3.33
777 799 1.593196 TCTGTTTTTGGTGAGCCTCG 58.407 50.000 0.00 0.00 35.27 4.63
779 801 3.821033 GTGTATCTGTTTTTGGTGAGCCT 59.179 43.478 0.00 0.00 35.27 4.58
808 840 3.208594 AGCGATTAAAGCTGATCATGCA 58.791 40.909 16.20 0.00 44.22 3.96
812 844 1.860950 GCGAGCGATTAAAGCTGATCA 59.139 47.619 12.66 0.00 46.13 2.92
818 850 1.648460 GCGTGCGAGCGATTAAAGC 60.648 57.895 3.30 0.00 0.00 3.51
822 854 2.106131 ATGGCGTGCGAGCGATTA 59.894 55.556 3.30 0.00 38.18 1.75
892 924 9.865321 AAGCGTAGTGATTTAAACACTCTTATA 57.135 29.630 19.79 6.52 45.58 0.98
893 925 8.773404 AAGCGTAGTGATTTAAACACTCTTAT 57.227 30.769 19.79 8.55 45.58 1.73
894 926 8.597662 AAAGCGTAGTGATTTAAACACTCTTA 57.402 30.769 19.79 7.04 45.58 2.10
895 927 7.492352 AAAGCGTAGTGATTTAAACACTCTT 57.508 32.000 19.79 15.70 45.58 2.85
896 928 7.492352 AAAAGCGTAGTGATTTAAACACTCT 57.508 32.000 19.79 12.43 45.58 3.24
913 945 8.952278 TCCATCTGTAAACAAATATAAAAGCGT 58.048 29.630 0.00 0.00 0.00 5.07
952 1166 8.304138 CGCGTATAAGAATTAAGCAAAGTTTTG 58.696 33.333 0.00 0.28 36.20 2.44
998 1212 5.564048 AGAGTGGAGTTGTTCGTATACTC 57.436 43.478 0.56 0.00 38.02 2.59
1016 1234 2.932234 CGGGTGGAGCGTGAAGAGT 61.932 63.158 0.00 0.00 0.00 3.24
2116 2358 2.751806 CAAATCCAGCACCTTCCTCTTC 59.248 50.000 0.00 0.00 0.00 2.87
2157 2399 1.553248 CCACCTCCTCCACATTACGAA 59.447 52.381 0.00 0.00 0.00 3.85
2258 2500 1.065102 AGCACATGCATGAATCGCTTC 59.935 47.619 32.75 11.31 45.16 3.86
2594 2836 0.254178 GGCTTGGAGGAATCAGCTGA 59.746 55.000 20.79 20.79 0.00 4.26
2597 2839 1.382692 GCTGGCTTGGAGGAATCAGC 61.383 60.000 0.00 0.00 40.30 4.26
3055 3300 2.828874 GCTTCTCAGCAAGCATCTTC 57.171 50.000 1.85 0.00 46.93 2.87
3220 3465 8.392612 CAATTAAGCATTAGCCAAAGAAAATGG 58.607 33.333 0.00 0.00 43.56 3.16
3309 3559 6.617782 AGAATACTCCATATGCTATGCAGT 57.382 37.500 0.00 5.47 43.65 4.40
3310 3560 9.258826 GATAAGAATACTCCATATGCTATGCAG 57.741 37.037 0.00 0.00 43.65 4.41
3664 4046 3.793559 ACCTGACATTTGGCGAGTATAC 58.206 45.455 0.00 0.00 0.00 1.47
3827 4228 2.097825 GGAGGGAGTACAACGCTAAGA 58.902 52.381 8.97 0.00 0.00 2.10
3931 4332 6.208797 AGCTTTGCTATATACTACATCCGTCA 59.791 38.462 0.00 0.00 36.99 4.35
3996 4397 1.331756 GTGGCAATTATGAGCTCACCG 59.668 52.381 20.97 6.93 0.00 4.94
4328 4730 2.243810 GAGGTCTCCCATGGTAGCTAG 58.756 57.143 11.73 0.14 0.00 3.42
4625 5027 1.546029 GTTTCCCAAGGACTCCATTGC 59.454 52.381 0.00 0.00 0.00 3.56
4772 5174 4.892934 ACCTAAAGCAATTGGTCAAGTCAA 59.107 37.500 11.16 0.00 0.00 3.18
4867 8570 5.693555 GCTTAAAGTTTCTCATTGCAGCTTT 59.306 36.000 0.00 0.00 0.00 3.51
4935 8639 1.805869 CTTCAGCAACAGAGGTCAGG 58.194 55.000 0.00 0.00 0.00 3.86
5110 8815 3.459232 TGCACTACATATGAGCCAGAC 57.541 47.619 10.38 0.91 0.00 3.51
5124 8829 5.634439 GCAACATGACAATTCAAATGCACTA 59.366 36.000 0.00 0.00 38.00 2.74
5134 11052 3.244181 ACAAAGGGGCAACATGACAATTC 60.244 43.478 0.00 0.00 39.74 2.17
5202 11219 9.613428 CCTGATAAAAGGACACATAAAGATGTA 57.387 33.333 0.00 0.00 41.05 2.29
5458 11475 6.828502 TTATTCACGCATCTGACTAATGAC 57.171 37.500 0.00 0.00 0.00 3.06
5497 11514 9.289303 CAAGTGTTTAAACCATATTCTACATGC 57.711 33.333 15.59 0.00 0.00 4.06
5520 11537 4.677378 CACAACTGAAGTCTACGTCTCAAG 59.323 45.833 0.00 0.00 0.00 3.02
5527 11544 2.726760 GCACTCACAACTGAAGTCTACG 59.273 50.000 0.00 0.00 0.00 3.51
5691 11709 4.626604 CGGTTTGTGCAATTTTATGCTCAT 59.373 37.500 5.07 0.00 45.78 2.90
5757 11778 4.551702 AAATAACCAAAACTGATGCCCC 57.448 40.909 0.00 0.00 0.00 5.80
5778 11799 6.809689 CAGCTGTCAAAATTCTAATGCATCAA 59.190 34.615 5.25 0.00 0.00 2.57
6210 12254 7.548196 TTCTGTACACAAAAACTTCCTGTAG 57.452 36.000 0.00 0.00 0.00 2.74
6278 12322 2.031682 CGTTTTTCAGCTCCCAAGACTG 60.032 50.000 0.00 0.00 0.00 3.51
6327 12371 9.562583 TTTCTACAACGCCATTTATCAATAAAC 57.437 29.630 0.00 0.00 35.31 2.01
6331 12375 8.567948 CCTATTTCTACAACGCCATTTATCAAT 58.432 33.333 0.00 0.00 0.00 2.57
6357 12401 6.156519 AGGGTCAAAAATAGAAATTTCACGC 58.843 36.000 19.99 13.63 34.12 5.34
6433 12477 6.707440 TCTCAAGATAAAAACAGGCAACAA 57.293 33.333 0.00 0.00 41.41 2.83
6494 12541 2.422597 TGCAAAGTCCGGTTGTAGATG 58.577 47.619 0.00 0.00 0.00 2.90
6519 12566 1.523032 GCGGGTATTTGAGGGGTCG 60.523 63.158 0.00 0.00 0.00 4.79
6531 12578 1.597797 CCAGTTAGTGTCCGCGGGTA 61.598 60.000 27.83 12.16 0.00 3.69
6532 12579 2.654877 CAGTTAGTGTCCGCGGGT 59.345 61.111 27.83 10.43 0.00 5.28
6548 12606 5.779771 AGATTGGAAATTTGAGGCTTAACCA 59.220 36.000 0.00 0.00 43.14 3.67
6552 12610 6.009589 TGTGAGATTGGAAATTTGAGGCTTA 58.990 36.000 0.00 0.00 0.00 3.09
6602 12660 3.706183 TGCATGGGTTTGTATGGATTGA 58.294 40.909 0.00 0.00 0.00 2.57
6603 12661 4.081531 AGTTGCATGGGTTTGTATGGATTG 60.082 41.667 0.00 0.00 0.00 2.67
6649 12707 3.243737 CCGATAGCATGTTGTAGTAGCCA 60.244 47.826 0.00 0.00 0.00 4.75
6697 12755 2.766313 TGTCGAAACTTCTCCACCATG 58.234 47.619 0.00 0.00 0.00 3.66
6710 12768 2.429250 TCTTCGGCCATCTATGTCGAAA 59.571 45.455 2.24 0.00 39.30 3.46
6712 12770 1.687563 TCTTCGGCCATCTATGTCGA 58.312 50.000 2.24 0.00 32.60 4.20
6713 12771 2.600731 GATCTTCGGCCATCTATGTCG 58.399 52.381 2.24 0.00 0.00 4.35
6714 12772 2.600731 CGATCTTCGGCCATCTATGTC 58.399 52.381 2.24 0.00 36.00 3.06
6715 12773 1.337260 GCGATCTTCGGCCATCTATGT 60.337 52.381 2.24 0.00 40.84 2.29
6736 13410 1.553690 GCCACCCAAGCTCCTGTCTA 61.554 60.000 0.00 0.00 0.00 2.59
6737 13411 2.900106 GCCACCCAAGCTCCTGTCT 61.900 63.158 0.00 0.00 0.00 3.41
6782 13456 0.460722 TCCGTTCGTCTGACCAAACA 59.539 50.000 16.31 1.24 0.00 2.83
6791 13465 0.613853 TCATCCCCTTCCGTTCGTCT 60.614 55.000 0.00 0.00 0.00 4.18
6802 13476 2.184565 ACCCCACATATACTCATCCCCT 59.815 50.000 0.00 0.00 0.00 4.79
6822 13496 4.025401 CACGCTTTGCCACCGGAC 62.025 66.667 9.46 0.00 0.00 4.79
6911 13596 3.153825 GGGTCTCAAACACCCGGA 58.846 61.111 0.73 0.00 44.42 5.14
6925 13610 4.675029 CGGTCGCCTCAAACGGGT 62.675 66.667 0.00 0.00 0.00 5.28
6966 13651 1.831736 ACTAGCCGCCTTGTTAGTGAT 59.168 47.619 0.00 0.00 0.00 3.06
6982 13667 1.526041 CGTCTCATACGTCCGGACTAG 59.474 57.143 30.92 19.37 46.72 2.57
6983 13668 1.575244 CGTCTCATACGTCCGGACTA 58.425 55.000 30.92 21.44 46.72 2.59
7048 13733 3.367992 AGCGTTTGTGATGCATTTTCA 57.632 38.095 0.00 0.00 42.96 2.69
7072 13757 1.819632 CCACCAATAGCGCACCCTC 60.820 63.158 11.47 0.00 0.00 4.30
7080 13768 1.440145 GCTCCGAAGCCACCAATAGC 61.440 60.000 0.00 0.00 43.10 2.97
7152 13844 1.376683 CCGATCCGCCAAACAGGAA 60.377 57.895 0.00 0.00 40.32 3.36


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

AutoCloner maintained by Alex Coulton.