Multiple sequence alignment - TraesCS5B01G112100

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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 TraesCS5B01G112100 chr5B 100.000 9041 0 0 1 9041 172632177 172623137 0.000000e+00 16696.0
1 TraesCS5B01G112100 chr5B 96.063 1854 53 10 1255 3097 570952010 570953854 0.000000e+00 3001.0
2 TraesCS5B01G112100 chr5B 97.872 47 1 0 1228 1274 570951780 570951826 2.090000e-11 82.4
3 TraesCS5B01G112100 chr5A 96.026 5436 154 36 42 5452 165336429 165331031 0.000000e+00 8785.0
4 TraesCS5B01G112100 chr5A 95.896 3070 96 17 5449 8500 165330433 165327376 0.000000e+00 4944.0
5 TraesCS5B01G112100 chr5A 100.000 35 0 0 3776 3810 165332832 165332798 2.110000e-06 65.8
6 TraesCS5B01G112100 chr5D 95.903 4930 141 35 1 4909 175757945 175762834 0.000000e+00 7928.0
7 TraesCS5B01G112100 chr5D 95.659 3087 71 25 5449 8500 175767572 175770630 0.000000e+00 4900.0
8 TraesCS5B01G112100 chr5D 92.509 534 40 0 8508 9041 242128824 242128291 0.000000e+00 765.0
9 TraesCS5B01G112100 chr5D 91.963 535 41 2 8508 9041 254515834 254516367 0.000000e+00 749.0
10 TraesCS5B01G112100 chr5D 92.205 526 41 0 8516 9041 220439939 220439414 0.000000e+00 745.0
11 TraesCS5B01G112100 chr5D 91.760 534 44 0 8508 9041 337719019 337719552 0.000000e+00 743.0
12 TraesCS5B01G112100 chr5D 95.599 409 14 3 4906 5312 175766869 175767275 0.000000e+00 652.0
13 TraesCS5B01G112100 chr5D 100.000 35 0 0 3776 3810 175761575 175761609 2.110000e-06 65.8
14 TraesCS5B01G112100 chr2B 94.798 2076 83 13 1035 3097 300325814 300327877 0.000000e+00 3212.0
15 TraesCS5B01G112100 chr2B 96.006 651 15 4 2456 3097 798304444 798305092 0.000000e+00 1048.0
16 TraesCS5B01G112100 chr2B 77.849 465 82 12 3919 4379 511276320 511276767 1.500000e-67 268.0
17 TraesCS5B01G112100 chr2B 80.800 125 22 2 5478 5602 508955240 508955118 7.470000e-16 97.1
18 TraesCS5B01G112100 chr3B 95.983 1892 59 10 1228 3105 279517710 279515822 0.000000e+00 3057.0
19 TraesCS5B01G112100 chr3B 87.984 258 25 4 5822 6078 819739795 819739543 5.310000e-77 300.0
20 TraesCS5B01G112100 chr3B 90.909 154 10 1 6841 6990 528176190 528176343 4.280000e-48 204.0
21 TraesCS5B01G112100 chr6B 95.503 1868 63 12 1228 3091 369658898 369657048 0.000000e+00 2964.0
22 TraesCS5B01G112100 chr7B 95.622 1713 53 11 1396 3097 423438575 423436874 0.000000e+00 2728.0
23 TraesCS5B01G112100 chr7B 94.376 729 20 3 1035 1763 732523148 732523855 0.000000e+00 1099.0
24 TraesCS5B01G112100 chr7B 76.000 300 60 12 4716 5010 296343599 296343307 2.630000e-30 145.0
25 TraesCS5B01G112100 chr4A 94.658 730 20 2 1035 1763 284249084 284248373 0.000000e+00 1114.0
26 TraesCS5B01G112100 chr2A 97.235 651 17 1 1036 1686 300215718 300215069 0.000000e+00 1101.0
27 TraesCS5B01G112100 chr2A 98.077 624 11 1 1060 1683 361488681 361489303 0.000000e+00 1085.0
28 TraesCS5B01G112100 chr2A 92.015 526 42 0 8516 9041 290200445 290199920 0.000000e+00 739.0
29 TraesCS5B01G112100 chr2A 77.925 453 83 9 3929 4379 553487072 553486635 5.380000e-67 267.0
30 TraesCS5B01G112100 chr2A 96.591 88 3 0 1035 1122 361488595 361488682 7.310000e-31 147.0
31 TraesCS5B01G112100 chr7A 96.933 652 17 3 1035 1686 240670604 240669956 0.000000e+00 1090.0
32 TraesCS5B01G112100 chr7A 88.000 250 27 2 5825 6074 540899264 540899510 8.880000e-75 292.0
33 TraesCS5B01G112100 chr7A 87.402 254 29 3 5828 6081 567679203 567678953 1.150000e-73 289.0
34 TraesCS5B01G112100 chr7A 90.968 155 9 2 6840 6989 579808373 579808527 4.280000e-48 204.0
35 TraesCS5B01G112100 chr7A 86.667 90 8 4 4923 5010 375886374 375886287 7.470000e-16 97.1
36 TraesCS5B01G112100 chr2D 91.948 534 43 0 8508 9041 538917935 538917402 0.000000e+00 749.0
37 TraesCS5B01G112100 chr2D 91.760 534 44 0 8508 9041 562880566 562880033 0.000000e+00 743.0
38 TraesCS5B01G112100 chr2D 91.199 534 46 1 8508 9041 318129778 318129246 0.000000e+00 725.0
39 TraesCS5B01G112100 chr2D 91.463 246 18 2 5830 6075 535222517 535222759 1.450000e-87 335.0
40 TraesCS5B01G112100 chr2D 77.851 456 84 9 3926 4379 433506446 433506886 5.380000e-67 267.0
41 TraesCS5B01G112100 chr2D 91.379 58 5 0 5536 5593 430621093 430621036 7.520000e-11 80.5
42 TraesCS5B01G112100 chr6D 91.573 534 44 1 8508 9041 65488500 65487968 0.000000e+00 736.0
43 TraesCS5B01G112100 chr6D 83.077 130 9 7 3430 3559 461651643 461651527 1.240000e-18 106.0
44 TraesCS5B01G112100 chr1A 89.328 253 22 4 5825 6076 531221190 531220942 6.820000e-81 313.0
45 TraesCS5B01G112100 chr1A 87.500 256 27 3 5822 6075 507545652 507545904 3.190000e-74 291.0
46 TraesCS5B01G112100 chr4D 88.583 254 25 3 5822 6075 506872086 506872335 1.140000e-78 305.0
47 TraesCS5B01G112100 chr4D 90.506 158 10 2 6840 6992 74079350 74079507 4.280000e-48 204.0
48 TraesCS5B01G112100 chr4D 86.207 58 8 0 5536 5593 463462593 463462650 7.580000e-06 63.9
49 TraesCS5B01G112100 chr4B 90.476 168 11 2 6840 7003 146469215 146469381 5.500000e-52 217.0
50 TraesCS5B01G112100 chr4B 76.009 446 85 17 3926 4366 132854587 132854159 2.560000e-50 211.0
51 TraesCS5B01G112100 chr4B 90.000 160 10 3 6835 6989 438375175 438375333 1.540000e-47 202.0
52 TraesCS5B01G112100 chr7D 90.683 161 11 1 6835 6991 34757024 34756864 2.560000e-50 211.0
53 TraesCS5B01G112100 chr7D 88.623 167 15 3 6829 6991 34373306 34373472 5.540000e-47 200.0
54 TraesCS5B01G112100 chr7D 80.882 136 19 7 4879 5010 311874974 311875106 5.780000e-17 100.0
55 TraesCS5B01G112100 chr7D 86.598 97 4 1 3317 3404 546101984 546102080 2.080000e-16 99.0
56 TraesCS5B01G112100 chrUn 76.898 303 58 12 4702 4999 10136987 10137282 2.610000e-35 161.0
57 TraesCS5B01G112100 chr1B 77.674 215 21 10 3105 3317 601830335 601830146 1.240000e-18 106.0
58 TraesCS5B01G112100 chr6A 80.000 130 12 8 3430 3559 608365662 608365547 5.820000e-12 84.2


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 TraesCS5B01G112100 chr5B 172623137 172632177 9040 True 16696.000000 16696 100.000000 1 9041 1 chr5B.!!$R1 9040
1 TraesCS5B01G112100 chr5B 570951780 570953854 2074 False 1541.700000 3001 96.967500 1228 3097 2 chr5B.!!$F1 1869
2 TraesCS5B01G112100 chr5A 165327376 165336429 9053 True 4598.266667 8785 97.307333 42 8500 3 chr5A.!!$R1 8458
3 TraesCS5B01G112100 chr5D 175757945 175762834 4889 False 3996.900000 7928 97.951500 1 4909 2 chr5D.!!$F3 4908
4 TraesCS5B01G112100 chr5D 175766869 175770630 3761 False 2776.000000 4900 95.629000 4906 8500 2 chr5D.!!$F4 3594
5 TraesCS5B01G112100 chr5D 242128291 242128824 533 True 765.000000 765 92.509000 8508 9041 1 chr5D.!!$R2 533
6 TraesCS5B01G112100 chr5D 254515834 254516367 533 False 749.000000 749 91.963000 8508 9041 1 chr5D.!!$F1 533
7 TraesCS5B01G112100 chr5D 220439414 220439939 525 True 745.000000 745 92.205000 8516 9041 1 chr5D.!!$R1 525
8 TraesCS5B01G112100 chr5D 337719019 337719552 533 False 743.000000 743 91.760000 8508 9041 1 chr5D.!!$F2 533
9 TraesCS5B01G112100 chr2B 300325814 300327877 2063 False 3212.000000 3212 94.798000 1035 3097 1 chr2B.!!$F1 2062
10 TraesCS5B01G112100 chr2B 798304444 798305092 648 False 1048.000000 1048 96.006000 2456 3097 1 chr2B.!!$F3 641
11 TraesCS5B01G112100 chr3B 279515822 279517710 1888 True 3057.000000 3057 95.983000 1228 3105 1 chr3B.!!$R1 1877
12 TraesCS5B01G112100 chr6B 369657048 369658898 1850 True 2964.000000 2964 95.503000 1228 3091 1 chr6B.!!$R1 1863
13 TraesCS5B01G112100 chr7B 423436874 423438575 1701 True 2728.000000 2728 95.622000 1396 3097 1 chr7B.!!$R2 1701
14 TraesCS5B01G112100 chr7B 732523148 732523855 707 False 1099.000000 1099 94.376000 1035 1763 1 chr7B.!!$F1 728
15 TraesCS5B01G112100 chr4A 284248373 284249084 711 True 1114.000000 1114 94.658000 1035 1763 1 chr4A.!!$R1 728
16 TraesCS5B01G112100 chr2A 300215069 300215718 649 True 1101.000000 1101 97.235000 1036 1686 1 chr2A.!!$R2 650
17 TraesCS5B01G112100 chr2A 290199920 290200445 525 True 739.000000 739 92.015000 8516 9041 1 chr2A.!!$R1 525
18 TraesCS5B01G112100 chr2A 361488595 361489303 708 False 616.000000 1085 97.334000 1035 1683 2 chr2A.!!$F1 648
19 TraesCS5B01G112100 chr7A 240669956 240670604 648 True 1090.000000 1090 96.933000 1035 1686 1 chr7A.!!$R1 651
20 TraesCS5B01G112100 chr2D 538917402 538917935 533 True 749.000000 749 91.948000 8508 9041 1 chr2D.!!$R3 533
21 TraesCS5B01G112100 chr2D 562880033 562880566 533 True 743.000000 743 91.760000 8508 9041 1 chr2D.!!$R4 533
22 TraesCS5B01G112100 chr2D 318129246 318129778 532 True 725.000000 725 91.199000 8508 9041 1 chr2D.!!$R1 533
23 TraesCS5B01G112100 chr6D 65487968 65488500 532 True 736.000000 736 91.573000 8508 9041 1 chr6D.!!$R1 533

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
238 239 0.184933 CAGGGTCAGGGTTTGGAACA 59.815 55.000 0.00 0.00 0.00 3.18 F
1792 2065 0.316204 ATGCCACAACTCTTTGCTGC 59.684 50.000 0.00 0.00 36.00 5.25 F
3443 3738 2.756760 GCCTCTGAGATCCATTTTTGCA 59.243 45.455 6.17 0.00 0.00 4.08 F
3703 3998 0.890542 TTCTGTGGTCTGGTGCATGC 60.891 55.000 11.82 11.82 0.00 4.06 F
5445 5760 0.032267 GAATCTCGACCCCCATCGTC 59.968 60.000 0.00 0.00 42.80 4.20 F
5526 6444 0.832135 TCTCGAACCCCTCACTTGCT 60.832 55.000 0.00 0.00 0.00 3.91 F
6063 6986 0.948678 GCGCGCCTTATATTTTGGGA 59.051 50.000 23.24 0.00 0.00 4.37 F
7223 8154 1.215647 CCAACTCGGAGGAACCTCG 59.784 63.158 10.23 9.70 43.59 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2159 2436 2.223135 GCTTCAGCGCCAACTTCTATTC 60.223 50.000 2.29 0.0 0.00 1.75 R
3681 3976 0.764271 TGCACCAGACCACAGAATGA 59.236 50.000 0.00 0.0 39.69 2.57 R
5359 5674 0.401395 AGAGGGTCAAGTGGGGTTCA 60.401 55.000 0.00 0.0 0.00 3.18 R
5634 6552 1.148273 GACTGGCTGGTTGGTGTCA 59.852 57.895 0.00 0.0 0.00 3.58 R
7350 8281 0.813184 CATGGCCACCATTGTCACTC 59.187 55.000 8.16 0.0 42.23 3.51 R
7352 8283 1.255882 TTCATGGCCACCATTGTCAC 58.744 50.000 8.16 0.0 42.23 3.67 R
7453 8384 1.535444 TGGGCCTGGAACTTCTCGA 60.535 57.895 4.53 0.0 0.00 4.04 R
8925 9883 1.062886 ACCTCATCCTCCGAGAATGGA 60.063 52.381 0.00 0.0 36.37 3.41 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
23 24 3.007635 GGTTCAGATTACGGTTTGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
25 26 2.262637 TCAGATTACGGTTTGGAGGGT 58.737 47.619 0.00 0.00 0.00 4.34
88 89 3.942130 ATAACAACTTGCTGGGCTTTC 57.058 42.857 0.00 0.00 0.00 2.62
238 239 0.184933 CAGGGTCAGGGTTTGGAACA 59.815 55.000 0.00 0.00 0.00 3.18
317 320 3.763671 CCAGTGGCAGGTTGGAAC 58.236 61.111 0.00 0.00 33.76 3.62
339 342 4.039609 ACAAAGGAAGCAGGAAAATCAAGG 59.960 41.667 0.00 0.00 0.00 3.61
346 349 2.765699 GCAGGAAAATCAAGGGGCAATA 59.234 45.455 0.00 0.00 0.00 1.90
361 364 6.249951 AGGGGCAATAGTTATTTGTGTGTAA 58.750 36.000 0.00 0.00 0.00 2.41
362 365 6.722129 AGGGGCAATAGTTATTTGTGTGTAAA 59.278 34.615 0.00 0.00 0.00 2.01
363 366 6.809689 GGGGCAATAGTTATTTGTGTGTAAAC 59.190 38.462 0.00 0.00 0.00 2.01
377 380 5.065859 TGTGTGTAAACAACAGGTCATTCAG 59.934 40.000 0.00 0.00 39.29 3.02
389 392 2.019984 GTCATTCAGGGATTCACCAGC 58.980 52.381 0.00 0.00 41.20 4.85
518 522 1.074248 CCCCTACTGTTTGGCCGTT 59.926 57.895 0.00 0.00 0.00 4.44
710 714 9.334693 CTAAACTGCTTATTTTCTGAATGTCAC 57.665 33.333 0.00 0.00 0.00 3.67
907 911 3.561725 GGCAACAGGACTATGCTTATCAC 59.438 47.826 8.54 0.00 39.94 3.06
1344 1615 3.178046 TGCTACTTACCCAACCAGATGA 58.822 45.455 0.00 0.00 0.00 2.92
1455 1726 6.377996 TGGTCCAGAGATATTCAATTGTTTGG 59.622 38.462 5.13 0.25 33.44 3.28
1722 1995 8.039603 TCACATCTTTAATAGTTTGCAATCGT 57.960 30.769 0.00 0.00 0.00 3.73
1750 2023 4.346734 AATTGCTGTGCTCGTATCTTTG 57.653 40.909 0.00 0.00 0.00 2.77
1787 2060 4.922206 TGGAGATAATGCCACAACTCTTT 58.078 39.130 0.00 0.00 0.00 2.52
1792 2065 0.316204 ATGCCACAACTCTTTGCTGC 59.684 50.000 0.00 0.00 36.00 5.25
1802 2075 7.086376 CACAACTCTTTGCTGCAATTATACTT 58.914 34.615 16.77 0.84 36.00 2.24
2159 2436 3.978687 ACACTTTGTACTTCTCCAGTCG 58.021 45.455 0.00 0.00 36.88 4.18
2516 2797 7.546250 AATCACCCTATCCATGAAGTAGTAG 57.454 40.000 0.00 0.00 0.00 2.57
2548 2829 7.333423 GTGTTTACTGAAATAGGAGTGCATGTA 59.667 37.037 0.00 0.00 0.00 2.29
2893 3176 4.454728 TTGCTATGGATTGTTCTTTGGC 57.545 40.909 0.00 0.00 0.00 4.52
3123 3418 9.224267 CAGCTATATATTTTACAATCTGCACCT 57.776 33.333 0.00 0.00 0.00 4.00
3199 3494 6.850752 TTATATCCTCGTATGATCTTGCCA 57.149 37.500 0.00 0.00 0.00 4.92
3321 3616 9.656040 AAAATAATTTTGCTCTATGATGTGCAA 57.344 25.926 0.00 0.00 42.28 4.08
3443 3738 2.756760 GCCTCTGAGATCCATTTTTGCA 59.243 45.455 6.17 0.00 0.00 4.08
3604 3899 4.869297 CCATTTTCAGTTTGTGCTTGTTCA 59.131 37.500 0.00 0.00 0.00 3.18
3691 3986 6.633500 TTCTTTTGGTAGTTCATTCTGTGG 57.367 37.500 0.00 0.00 0.00 4.17
3692 3987 5.690865 TCTTTTGGTAGTTCATTCTGTGGT 58.309 37.500 0.00 0.00 0.00 4.16
3693 3988 5.763204 TCTTTTGGTAGTTCATTCTGTGGTC 59.237 40.000 0.00 0.00 0.00 4.02
3694 3989 4.974645 TTGGTAGTTCATTCTGTGGTCT 57.025 40.909 0.00 0.00 0.00 3.85
3698 3993 3.131709 AGTTCATTCTGTGGTCTGGTG 57.868 47.619 0.00 0.00 0.00 4.17
3702 3997 1.471287 CATTCTGTGGTCTGGTGCATG 59.529 52.381 0.00 0.00 0.00 4.06
3703 3998 0.890542 TTCTGTGGTCTGGTGCATGC 60.891 55.000 11.82 11.82 0.00 4.06
3717 4012 1.305219 GCATGCTTGCGTAGGTTCCA 61.305 55.000 11.37 0.00 39.49 3.53
3859 4162 3.445450 TGTAGATCTTCTCTGCACCAGTC 59.555 47.826 0.00 0.00 41.10 3.51
3868 4171 4.290093 TCTCTGCACCAGTCCATAGTTAT 58.710 43.478 0.00 0.00 32.61 1.89
3922 4225 5.839621 TGAACAAACTGTCTACTACTGTCC 58.160 41.667 0.00 0.00 39.14 4.02
4383 4686 6.946340 TCCTCTATGCAAAGTCAGTAATTCA 58.054 36.000 0.00 0.00 0.00 2.57
4486 4789 2.965572 TATTTTACCACCGGGACTCG 57.034 50.000 6.32 0.00 38.05 4.18
4520 4823 0.890683 CCTGTGGCATCTGGGTTTTC 59.109 55.000 0.00 0.00 0.00 2.29
4595 4906 9.010366 GTGAAAATACTTCAAAGTGTGAAACTC 57.990 33.333 5.66 0.00 45.67 3.01
4607 4918 5.585390 AGTGTGAAACTCATCTTTTTGCAG 58.415 37.500 0.00 0.00 38.04 4.41
4632 4943 8.468399 AGGTACTATTCTTGTTGAGTAGCTAAC 58.532 37.037 10.07 0.00 46.20 2.34
4724 5036 1.293062 ATGATTCTGCACTCCTGGGT 58.707 50.000 0.00 0.00 0.00 4.51
4784 5096 7.456902 TCAGTCCATTATACTACCCCTTTATCC 59.543 40.741 0.00 0.00 0.00 2.59
4836 5148 7.201609 CCAGATAGCGCAAAGTGAGTTAAATAA 60.202 37.037 11.47 0.00 0.00 1.40
4892 5204 2.543777 TGCTCGTAGACTGCCTTTTT 57.456 45.000 0.00 0.00 0.00 1.94
4904 5216 6.665465 AGACTGCCTTTTTGTACGTAAAATC 58.335 36.000 0.00 0.00 30.39 2.17
4950 5263 9.565213 GGTTCTGATGATGTTCTTTTTATGAAG 57.435 33.333 0.00 0.00 0.00 3.02
5054 5367 2.168326 TGAGCGCAGAAAATCAGTCA 57.832 45.000 11.47 0.00 0.00 3.41
5060 5373 7.378181 TGAGCGCAGAAAATCAGTCATATATA 58.622 34.615 11.47 0.00 0.00 0.86
5061 5374 8.037166 TGAGCGCAGAAAATCAGTCATATATAT 58.963 33.333 11.47 0.00 0.00 0.86
5215 5529 4.094887 GTCACAAGTAATGCAATCGTGGAT 59.905 41.667 0.00 0.00 37.41 3.41
5291 5605 6.992715 ACAGTTACAAGTAATGCTTTGAGTCT 59.007 34.615 0.00 0.00 34.69 3.24
5301 5615 1.884067 GCTTTGAGTCTTGACCCCCAG 60.884 57.143 0.00 0.00 0.00 4.45
5359 5674 5.536161 ACAAGTAATGCAATTGTGGAGTCTT 59.464 36.000 7.40 3.26 36.99 3.01
5364 5679 2.622942 TGCAATTGTGGAGTCTTGAACC 59.377 45.455 7.40 0.00 0.00 3.62
5428 5743 5.866335 AAAATTACAGGTAATGCGTCGAA 57.134 34.783 5.51 0.00 36.04 3.71
5444 5759 1.735376 CGAATCTCGACCCCCATCGT 61.735 60.000 0.00 0.00 43.74 3.73
5445 5760 0.032267 GAATCTCGACCCCCATCGTC 59.968 60.000 0.00 0.00 42.80 4.20
5447 5762 2.299727 ATCTCGACCCCCATCGTCCT 62.300 60.000 0.00 0.00 42.80 3.85
5459 6377 3.370527 CCCATCGTCCTCTTATGGTTTGT 60.371 47.826 0.00 0.00 38.83 2.83
5463 6381 4.312443 TCGTCCTCTTATGGTTTGTGAAC 58.688 43.478 0.00 0.00 34.96 3.18
5526 6444 0.832135 TCTCGAACCCCTCACTTGCT 60.832 55.000 0.00 0.00 0.00 3.91
5598 6516 9.657419 GTTTTGAATGGGAAAGTATTTGATCAT 57.343 29.630 0.00 0.00 39.27 2.45
5634 6552 8.967664 TGGTAGTACACAATTTCTTTTACTGT 57.032 30.769 2.06 0.00 0.00 3.55
5699 6617 2.378522 CCCTCCTCCCCATTCCCT 59.621 66.667 0.00 0.00 0.00 4.20
5729 6647 1.074699 ACCCCTCCTCCGTAATCCC 60.075 63.158 0.00 0.00 0.00 3.85
5779 6697 3.888930 TCCAGCGATGACATGTACTATGA 59.111 43.478 0.06 0.00 0.00 2.15
5781 6699 4.261783 CCAGCGATGACATGTACTATGACT 60.262 45.833 0.06 0.00 0.00 3.41
5856 6777 1.489824 GCGCGCGTTGACTTTTCTA 59.510 52.632 32.35 0.00 0.00 2.10
5871 6792 4.926238 ACTTTTCTAGTCTTCATCGCACAG 59.074 41.667 0.00 0.00 28.23 3.66
6046 6969 1.082756 GACCGTGCAAAGTCAAGCG 60.083 57.895 11.50 0.00 33.08 4.68
6063 6986 0.948678 GCGCGCCTTATATTTTGGGA 59.051 50.000 23.24 0.00 0.00 4.37
6121 7045 4.082841 TGCATTGGTTGTTGTATGCTACTG 60.083 41.667 0.00 0.00 42.85 2.74
6182 7106 2.663602 CGCGATCATTATGCTAGTGGTC 59.336 50.000 0.00 0.00 0.00 4.02
6233 7157 4.710528 GTGTAGTTGCTGTACACAGTTC 57.289 45.455 10.87 2.75 46.42 3.01
6284 7208 3.931578 TCCAGCTCTGACTTTTTCTAGC 58.068 45.455 0.00 0.00 35.36 3.42
6406 7330 9.189156 TCCATAATAAAGATTATAAGGGCATGC 57.811 33.333 9.90 9.90 36.31 4.06
6768 7693 5.726980 TTGATGGTTCCAGAAAATCCTTG 57.273 39.130 0.00 0.00 0.00 3.61
6781 7706 6.004574 AGAAAATCCTTGGGTCTTGTAGAAC 58.995 40.000 0.00 0.00 0.00 3.01
6795 7720 4.336889 TGTAGAACCTGGTCTGTTTCAG 57.663 45.455 0.00 0.00 0.00 3.02
7017 7948 8.784043 AGTTAATTTGTAGTTGAGCTTTGGTAG 58.216 33.333 0.00 0.00 0.00 3.18
7212 8143 2.411547 CGTAAAAGCAGAAGCCAACTCG 60.412 50.000 0.00 0.00 43.56 4.18
7223 8154 1.215647 CCAACTCGGAGGAACCTCG 59.784 63.158 10.23 9.70 43.59 4.63
7252 8183 1.466856 TCATCCAGCATCCAAACAGC 58.533 50.000 0.00 0.00 0.00 4.40
7266 8197 2.149973 AACAGCCAGATTCCAATCCC 57.850 50.000 0.00 0.00 36.04 3.85
7350 8281 4.008074 TGGTAGCCAGAAAAGTCTTCAG 57.992 45.455 0.00 0.00 28.78 3.02
7352 8283 4.249661 GGTAGCCAGAAAAGTCTTCAGAG 58.750 47.826 0.00 0.00 28.78 3.35
7527 8458 1.524355 CTTCCATCGCATGCTAGTTCG 59.476 52.381 17.13 0.00 0.00 3.95
7535 8466 2.604914 CGCATGCTAGTTCGAGTGAATT 59.395 45.455 17.13 0.00 36.29 2.17
7827 8758 0.968405 ATGGCGTTGCAGAAAATGGT 59.032 45.000 0.00 0.00 0.00 3.55
7863 8794 2.634453 TCAGAATGTTCCAGAGACTGCA 59.366 45.455 0.00 0.00 37.40 4.41
8141 9076 4.142071 GCTCTGGACTGTTGATGAGACATA 60.142 45.833 0.00 0.00 0.00 2.29
8142 9077 5.453057 GCTCTGGACTGTTGATGAGACATAT 60.453 44.000 0.00 0.00 0.00 1.78
8232 9167 0.106819 GGTCTCTACCAGGGCGAGTA 60.107 60.000 7.04 0.00 45.98 2.59
8236 9171 3.132467 GTCTCTACCAGGGCGAGTATTTT 59.868 47.826 7.04 0.00 0.00 1.82
8346 9286 6.826231 TGCGGAATTTAAGACTTGATTGGATA 59.174 34.615 0.00 0.00 0.00 2.59
8398 9356 3.502211 TGTTCCGAGCTTTTCATTCTTCC 59.498 43.478 0.00 0.00 0.00 3.46
8426 9384 9.032624 AGTCAAGATCTCATCCAATTTTCAATT 57.967 29.630 0.00 0.00 0.00 2.32
8438 9396 6.201806 TCCAATTTTCAATTCGCGTTTCAAAT 59.798 30.769 5.77 5.85 0.00 2.32
8466 9424 3.492102 AGGCTATATTTGTGGTCGCAT 57.508 42.857 0.00 0.00 0.00 4.73
8497 9455 3.012518 AGCAATGAATCTAGTGCCACAC 58.987 45.455 0.00 0.00 42.18 3.82
8498 9456 2.223112 GCAATGAATCTAGTGCCACACG 60.223 50.000 0.00 0.00 39.64 4.49
8500 9458 0.973632 TGAATCTAGTGCCACACGGT 59.026 50.000 0.00 0.00 39.64 4.83
8501 9459 1.067142 TGAATCTAGTGCCACACGGTC 60.067 52.381 0.00 0.00 39.64 4.79
8502 9460 0.108804 AATCTAGTGCCACACGGTCG 60.109 55.000 0.00 0.00 39.64 4.79
8503 9461 1.945354 ATCTAGTGCCACACGGTCGG 61.945 60.000 0.00 0.00 39.64 4.79
8633 9591 5.215069 AGACCAACTCTCCATCATCTACAT 58.785 41.667 0.00 0.00 0.00 2.29
8661 9619 3.118454 GCTTACTGGCGCTTGCGA 61.118 61.111 19.55 0.00 40.46 5.10
8706 9664 1.154205 GCGATGCGAACACTGCCTAT 61.154 55.000 0.00 0.00 0.00 2.57
8725 9683 5.376625 CCTATTTTCAGGCCATAGCTAACA 58.623 41.667 5.01 0.00 39.73 2.41
8727 9685 4.301072 TTTTCAGGCCATAGCTAACAGT 57.699 40.909 5.01 0.00 39.73 3.55
8788 9746 3.322466 CCCTTCTGCAGTCCCCGT 61.322 66.667 14.67 0.00 0.00 5.28
8802 9760 1.515954 CCCGTGCGACATTAGGACT 59.484 57.895 0.00 0.00 0.00 3.85
8814 9772 2.118313 TTAGGACTCATGTCGACGGA 57.882 50.000 11.62 10.18 43.79 4.69
8871 9829 2.716017 CCTGTCTCTGGCCCTCGAC 61.716 68.421 0.00 4.23 0.00 4.20
8898 9856 2.255172 CGGCCGCCAGTGTGTTTTA 61.255 57.895 14.67 0.00 0.00 1.52
8946 9904 2.177016 TCCATTCTCGGAGGATGAGGTA 59.823 50.000 24.83 7.07 34.19 3.08
8951 9909 2.380249 TCTCGGAGGATGAGGTATGGAT 59.620 50.000 4.96 0.00 34.19 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.007635 CCCTCCAAACCGTAATCTGAAC 58.992 50.000 0.00 0.00 0.00 3.18
23 24 7.041372 TGCAGTAAGTGAAACAGATCTAAAACC 60.041 37.037 0.00 0.00 41.43 3.27
25 26 8.506437 CATGCAGTAAGTGAAACAGATCTAAAA 58.494 33.333 0.00 0.00 41.43 1.52
88 89 3.243068 GCTATTGTGGTATCAAAAGCCCG 60.243 47.826 0.00 0.00 0.00 6.13
238 239 6.822667 TGCAGAAACTGACATTCACATATT 57.177 33.333 2.81 0.00 32.44 1.28
241 242 5.518848 TTTGCAGAAACTGACATTCACAT 57.481 34.783 2.81 0.00 32.44 3.21
309 310 1.341209 CCTGCTTCCTTTGTTCCAACC 59.659 52.381 0.00 0.00 0.00 3.77
317 320 4.562143 CCCTTGATTTTCCTGCTTCCTTTG 60.562 45.833 0.00 0.00 0.00 2.77
328 331 6.731292 ATAACTATTGCCCCTTGATTTTCC 57.269 37.500 0.00 0.00 0.00 3.13
339 342 7.371936 TGTTTACACACAAATAACTATTGCCC 58.628 34.615 0.00 0.00 0.00 5.36
346 349 7.121463 TGACCTGTTGTTTACACACAAATAACT 59.879 33.333 8.84 0.00 39.13 2.24
361 364 3.814504 ATCCCTGAATGACCTGTTGTT 57.185 42.857 0.00 0.00 0.00 2.83
362 365 3.074390 TGAATCCCTGAATGACCTGTTGT 59.926 43.478 0.00 0.00 0.00 3.32
363 366 3.441572 GTGAATCCCTGAATGACCTGTTG 59.558 47.826 0.00 0.00 0.00 3.33
377 380 0.615331 TCTGTGAGCTGGTGAATCCC 59.385 55.000 0.00 0.00 34.77 3.85
526 530 5.762218 GTCTAGGATAACAATCATGCTGCTT 59.238 40.000 0.00 0.00 0.00 3.91
710 714 2.918712 ATTCGATGGGCTAGGACAAG 57.081 50.000 0.00 0.00 0.00 3.16
742 746 3.993081 CGAATGTATGCAGGGAAGAGATC 59.007 47.826 0.00 0.00 0.00 2.75
971 975 2.884012 CCCAACTACATTCAGCACACAA 59.116 45.455 0.00 0.00 0.00 3.33
1722 1995 4.764679 ACGAGCACAGCAATTTTTATCA 57.235 36.364 0.00 0.00 0.00 2.15
1750 2023 6.730960 TTATCTCCACGTGTCATAAAAACC 57.269 37.500 15.65 0.00 0.00 3.27
1787 2060 7.701924 GCATAAGTTGAAAGTATAATTGCAGCA 59.298 33.333 9.96 0.00 0.00 4.41
2159 2436 2.223135 GCTTCAGCGCCAACTTCTATTC 60.223 50.000 2.29 0.00 0.00 1.75
2372 2652 2.958355 CCTCAACCCCGCATAATTGATT 59.042 45.455 0.00 0.00 31.00 2.57
2516 2797 4.153475 TCCTATTTCAGTAAACACGCTTGC 59.847 41.667 0.00 0.00 0.00 4.01
2548 2829 6.016024 TGCTGCAGATAAGAACACAAGAAATT 60.016 34.615 20.43 0.00 0.00 1.82
2893 3176 6.334989 ACTTTTGTAAAGGGAAAAAGGTTCG 58.665 36.000 10.76 0.00 42.52 3.95
3117 3412 1.255882 CCAAACATTAGCCAGGTGCA 58.744 50.000 0.00 0.00 44.83 4.57
3123 3418 4.985538 AGAGAAGAACCAAACATTAGCCA 58.014 39.130 0.00 0.00 0.00 4.75
3321 3616 7.448469 ACAGCATCTACCAGAAAATACTTTGTT 59.552 33.333 0.00 0.00 0.00 2.83
3394 3689 6.851330 GCATTACAAAACTGAGAAGTACACAC 59.149 38.462 0.00 0.00 0.00 3.82
3443 3738 6.048732 ACCTCAAAAGTCACAAAAACCAAT 57.951 33.333 0.00 0.00 0.00 3.16
3666 3961 7.287696 ACCACAGAATGAACTACCAAAAGAATT 59.712 33.333 0.00 0.00 39.69 2.17
3667 3962 6.777580 ACCACAGAATGAACTACCAAAAGAAT 59.222 34.615 0.00 0.00 39.69 2.40
3668 3963 6.126409 ACCACAGAATGAACTACCAAAAGAA 58.874 36.000 0.00 0.00 39.69 2.52
3669 3964 5.690865 ACCACAGAATGAACTACCAAAAGA 58.309 37.500 0.00 0.00 39.69 2.52
3670 3965 5.765182 AGACCACAGAATGAACTACCAAAAG 59.235 40.000 0.00 0.00 39.69 2.27
3671 3966 5.530915 CAGACCACAGAATGAACTACCAAAA 59.469 40.000 0.00 0.00 39.69 2.44
3672 3967 5.063204 CAGACCACAGAATGAACTACCAAA 58.937 41.667 0.00 0.00 39.69 3.28
3675 3970 3.008049 ACCAGACCACAGAATGAACTACC 59.992 47.826 0.00 0.00 39.69 3.18
3676 3971 3.997021 CACCAGACCACAGAATGAACTAC 59.003 47.826 0.00 0.00 39.69 2.73
3677 3972 3.557054 GCACCAGACCACAGAATGAACTA 60.557 47.826 0.00 0.00 39.69 2.24
3678 3973 2.811873 GCACCAGACCACAGAATGAACT 60.812 50.000 0.00 0.00 39.69 3.01
3679 3974 1.537202 GCACCAGACCACAGAATGAAC 59.463 52.381 0.00 0.00 39.69 3.18
3680 3975 1.142667 TGCACCAGACCACAGAATGAA 59.857 47.619 0.00 0.00 39.69 2.57
3681 3976 0.764271 TGCACCAGACCACAGAATGA 59.236 50.000 0.00 0.00 39.69 2.57
3682 3977 1.471287 CATGCACCAGACCACAGAATG 59.529 52.381 0.00 0.00 46.00 2.67
3683 3978 1.830279 CATGCACCAGACCACAGAAT 58.170 50.000 0.00 0.00 0.00 2.40
3685 3980 1.302752 GCATGCACCAGACCACAGA 60.303 57.895 14.21 0.00 0.00 3.41
3686 3981 0.892358 AAGCATGCACCAGACCACAG 60.892 55.000 21.98 0.00 0.00 3.66
3687 3982 1.151221 AAGCATGCACCAGACCACA 59.849 52.632 21.98 0.00 0.00 4.17
3688 3983 1.582968 CAAGCATGCACCAGACCAC 59.417 57.895 21.98 0.00 0.00 4.16
3689 3984 4.084265 CAAGCATGCACCAGACCA 57.916 55.556 21.98 0.00 0.00 4.02
3702 3997 1.448985 TGAATGGAACCTACGCAAGC 58.551 50.000 0.00 0.00 45.62 4.01
3707 4002 4.503007 CGATACAGTTGAATGGAACCTACG 59.497 45.833 0.00 0.00 0.00 3.51
3868 4171 5.060427 TCCCAGAGGAAATCACTTTGAAA 57.940 39.130 0.00 0.00 40.08 2.69
3922 4225 8.837788 TTGTTGATCATATACTTCCTGCATAG 57.162 34.615 0.00 0.00 0.00 2.23
3943 4246 7.768582 CCCCAAGTAAAATGAGTTCTTTTTGTT 59.231 33.333 13.08 6.48 35.63 2.83
3944 4247 7.125053 TCCCCAAGTAAAATGAGTTCTTTTTGT 59.875 33.333 13.08 2.10 35.63 2.83
4383 4686 6.179756 ACCAAACAAAGCAGAAGGAAATTTT 58.820 32.000 0.00 0.00 0.00 1.82
4486 4789 3.860754 GCCACAGGAACACATAAAAAGGC 60.861 47.826 0.00 0.00 0.00 4.35
4520 4823 7.668525 ACTTTAGTTCTTTCTTTGTATCCCG 57.331 36.000 0.00 0.00 0.00 5.14
4595 4906 7.820648 ACAAGAATAGTACCTGCAAAAAGATG 58.179 34.615 0.00 0.00 0.00 2.90
4607 4918 8.248945 TGTTAGCTACTCAACAAGAATAGTACC 58.751 37.037 0.00 0.00 31.93 3.34
5215 5529 1.477685 GGTCCAGTGGGGTTCGAGAA 61.478 60.000 9.92 0.00 38.11 2.87
5301 5615 1.792949 CATAAACCATAGAGCGTCCGC 59.207 52.381 2.94 2.94 42.33 5.54
5334 5649 6.237901 AGACTCCACAATTGCATTACTTGTA 58.762 36.000 5.05 0.00 32.14 2.41
5359 5674 0.401395 AGAGGGTCAAGTGGGGTTCA 60.401 55.000 0.00 0.00 0.00 3.18
5364 5679 3.790089 AACTAAAGAGGGTCAAGTGGG 57.210 47.619 0.00 0.00 0.00 4.61
5400 5715 6.977213 ACGCATTACCTGTAATTTTTCTGTT 58.023 32.000 0.00 0.00 33.79 3.16
5428 5743 1.833049 GGACGATGGGGGTCGAGAT 60.833 63.158 3.09 0.00 44.06 2.75
5444 5759 6.303054 TCATTGTTCACAAACCATAAGAGGA 58.697 36.000 0.00 0.00 39.55 3.71
5445 5760 6.573664 TCATTGTTCACAAACCATAAGAGG 57.426 37.500 0.00 0.00 39.55 3.69
5447 5762 7.757941 TGATCATTGTTCACAAACCATAAGA 57.242 32.000 0.00 0.00 39.55 2.10
5526 6444 7.224753 GCTAGTTTGATTAAGCTGTGTATAGCA 59.775 37.037 3.48 0.00 46.07 3.49
5634 6552 1.148273 GACTGGCTGGTTGGTGTCA 59.852 57.895 0.00 0.00 0.00 3.58
5763 6681 9.015367 ACCATAGTAGTCATAGTACATGTCATC 57.985 37.037 0.00 0.00 0.00 2.92
5818 6736 5.061179 GCGCCTTATATTTTGAGGGAGTAA 58.939 41.667 0.00 0.00 0.00 2.24
5856 6777 1.802960 CAAAGCTGTGCGATGAAGACT 59.197 47.619 0.00 0.00 0.00 3.24
6046 6969 3.219281 TCCTTCCCAAAATATAAGGCGC 58.781 45.455 0.00 0.00 38.70 6.53
6063 6986 7.272144 ACATCATAAAAAGTACTCCCTCCTT 57.728 36.000 0.00 0.00 0.00 3.36
6284 7208 4.887748 AGTCCCATATGAAGCAATAGTCG 58.112 43.478 3.65 0.00 0.00 4.18
6406 7330 1.205417 GGCTGAAATCACCCCATTGTG 59.795 52.381 0.00 0.00 37.59 3.33
6715 7640 4.038282 AGCAACTGACTGAAAATCATGCAA 59.962 37.500 0.00 0.00 35.47 4.08
6768 7693 2.028020 CAGACCAGGTTCTACAAGACCC 60.028 54.545 0.00 0.00 0.00 4.46
6781 7706 1.597742 CACCACTGAAACAGACCAGG 58.402 55.000 5.76 4.76 35.18 4.45
6920 7851 4.369182 GGACTACATACGGACTGAAATGG 58.631 47.826 0.00 0.00 0.00 3.16
7116 8047 1.666700 GTTGGTTGCGACTGTACAACA 59.333 47.619 20.92 9.70 46.31 3.33
7212 8143 1.228657 GCACAACACGAGGTTCCTCC 61.229 60.000 12.54 0.00 37.72 4.30
7223 8154 0.883153 TGCTGGATGATGCACAACAC 59.117 50.000 0.00 0.00 33.94 3.32
7252 8183 4.349048 TGATGTAGAGGGATTGGAATCTGG 59.651 45.833 0.00 0.00 35.73 3.86
7266 8197 4.271696 TGGAACACCTGTTGATGTAGAG 57.728 45.455 0.00 0.00 38.56 2.43
7350 8281 0.813184 CATGGCCACCATTGTCACTC 59.187 55.000 8.16 0.00 42.23 3.51
7352 8283 1.255882 TTCATGGCCACCATTGTCAC 58.744 50.000 8.16 0.00 42.23 3.67
7453 8384 1.535444 TGGGCCTGGAACTTCTCGA 60.535 57.895 4.53 0.00 0.00 4.04
7827 8758 5.072055 ACATTCTGATCACCATTGTTGTCA 58.928 37.500 0.00 0.00 0.00 3.58
7863 8794 3.217626 CACCAGAACTTCAGCCTCTTTT 58.782 45.455 0.00 0.00 0.00 2.27
8141 9076 5.014755 TGGGTACAAACATTAAGACCTGGAT 59.985 40.000 0.00 0.00 0.00 3.41
8142 9077 4.351407 TGGGTACAAACATTAAGACCTGGA 59.649 41.667 0.00 0.00 0.00 3.86
8236 9171 9.288576 TCAGATGCTTCTATCAGAAAAGAAAAA 57.711 29.630 1.16 0.00 33.19 1.94
8241 9176 7.789273 ACATCAGATGCTTCTATCAGAAAAG 57.211 36.000 10.59 0.00 33.19 2.27
8242 9177 8.571461 AAACATCAGATGCTTCTATCAGAAAA 57.429 30.769 10.59 0.00 33.19 2.29
8243 9178 8.456471 CAAAACATCAGATGCTTCTATCAGAAA 58.544 33.333 10.59 0.00 33.19 2.52
8244 9179 7.825761 TCAAAACATCAGATGCTTCTATCAGAA 59.174 33.333 10.59 0.00 32.50 3.02
8245 9180 7.333323 TCAAAACATCAGATGCTTCTATCAGA 58.667 34.615 10.59 0.00 0.00 3.27
8382 9340 4.074970 TGACTGGGAAGAATGAAAAGCTC 58.925 43.478 0.00 0.00 0.00 4.09
8398 9356 6.376299 TGAAAATTGGATGAGATCTTGACTGG 59.624 38.462 0.00 0.00 0.00 4.00
8426 9384 4.260011 GCCTTTTGAAAATTTGAAACGCGA 60.260 37.500 15.93 0.00 0.00 5.87
8438 9396 7.087639 CGACCACAAATATAGCCTTTTGAAAA 58.912 34.615 4.03 0.00 36.54 2.29
8466 9424 8.400947 GCACTAGATTCATTGCTAGAAAATCAA 58.599 33.333 0.00 0.00 37.96 2.57
8500 9458 3.829048 TTTTTGTTCGCAGGCCGA 58.171 50.000 0.00 0.00 45.77 5.54
8559 9517 4.131088 GAGAGGCCGACCGTGTCC 62.131 72.222 0.00 0.00 42.76 4.02
8633 9591 1.749634 GCCAGTAAGCTTCCTCGTCTA 59.250 52.381 0.00 0.00 0.00 2.59
8706 9664 4.261801 GACTGTTAGCTATGGCCTGAAAA 58.738 43.478 3.32 0.00 39.73 2.29
8725 9683 4.719369 GTTGCGTCTCCGGCGACT 62.719 66.667 21.54 0.00 40.80 4.18
8788 9746 3.165058 GACATGAGTCCTAATGTCGCA 57.835 47.619 8.66 0.00 40.52 5.10
8802 9760 1.332686 CGGTAGAATCCGTCGACATGA 59.667 52.381 17.16 11.73 44.77 3.07
8814 9772 4.443598 GCAGAGAAAAGGGATCGGTAGAAT 60.444 45.833 0.00 0.00 0.00 2.40
8890 9848 3.126858 GCATTCTCCGCATCTAAAACACA 59.873 43.478 0.00 0.00 0.00 3.72
8895 9853 1.581934 CGGCATTCTCCGCATCTAAA 58.418 50.000 0.00 0.00 43.18 1.85
8925 9883 1.062886 ACCTCATCCTCCGAGAATGGA 60.063 52.381 0.00 0.00 36.37 3.41


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

AutoCloner maintained by Alex Coulton.