Multiple sequence alignment - TraesCS5B01G158000

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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 TraesCS5B01G158000 chr5B 100.000 4533 0 0 1 4533 291376979 291381511 0.000000e+00 8371.0
1 TraesCS5B01G158000 chr5B 89.863 365 30 5 3086 3446 456197680 456197319 3.190000e-126 462.0
2 TraesCS5B01G158000 chr5B 95.604 91 4 0 2844 2934 456197766 456197676 3.650000e-31 147.0
3 TraesCS5B01G158000 chr5D 95.325 3765 125 27 3 3746 257121833 257125567 0.000000e+00 5930.0
4 TraesCS5B01G158000 chr5D 90.016 621 44 8 187 803 257094894 257095500 0.000000e+00 787.0
5 TraesCS5B01G158000 chr5D 96.907 194 5 1 4116 4309 257126043 257126235 1.570000e-84 324.0
6 TraesCS5B01G158000 chr5D 93.158 190 11 2 796 984 257119127 257119315 1.240000e-70 278.0
7 TraesCS5B01G158000 chr5D 93.296 179 9 3 4357 4533 257126237 257126414 1.250000e-65 261.0
8 TraesCS5B01G158000 chr5D 94.690 113 3 1 3980 4089 257125839 257125951 6.030000e-39 172.0
9 TraesCS5B01G158000 chr5D 96.552 58 0 1 3925 3982 257125762 257125817 1.340000e-15 95.3
10 TraesCS5B01G158000 chr5A 94.264 3365 132 23 411 3746 341872194 341875526 0.000000e+00 5088.0
11 TraesCS5B01G158000 chr5A 90.676 547 45 6 1087 1631 419360558 419361100 0.000000e+00 723.0
12 TraesCS5B01G158000 chr5A 92.183 371 24 3 4116 4484 341876732 341877099 1.870000e-143 520.0
13 TraesCS5B01G158000 chr5A 91.977 349 23 3 3083 3428 680855432 680855778 6.820000e-133 484.0
14 TraesCS5B01G158000 chr5A 90.058 171 16 1 3 173 341866815 341866984 2.120000e-53 220.0
15 TraesCS5B01G158000 chr5A 95.604 91 4 0 2844 2934 680855349 680855439 3.650000e-31 147.0
16 TraesCS5B01G158000 chr7B 88.959 797 83 3 1128 1921 667441684 667440890 0.000000e+00 979.0
17 TraesCS5B01G158000 chr7B 81.788 604 63 26 2040 2614 667440900 667440315 3.190000e-126 462.0
18 TraesCS5B01G158000 chr7B 82.803 314 42 8 2425 2732 706385468 706385775 2.080000e-68 270.0
19 TraesCS5B01G158000 chr2A 92.844 559 35 3 2892 3447 734096131 734095575 0.000000e+00 806.0
20 TraesCS5B01G158000 chr2A 96.939 98 3 0 2978 3075 11804668 11804765 1.010000e-36 165.0
21 TraesCS5B01G158000 chr1B 89.871 543 48 5 1094 1631 676246096 676246636 0.000000e+00 691.0
22 TraesCS5B01G158000 chr1B 89.537 497 46 5 1087 1581 491545240 491545732 3.850000e-175 625.0
23 TraesCS5B01G158000 chr1B 92.526 388 26 1 2842 3226 618195192 618195579 1.840000e-153 553.0
24 TraesCS5B01G158000 chr1B 87.273 55 7 0 1577 1631 491697382 491697436 3.790000e-06 63.9
25 TraesCS5B01G158000 chr4B 92.802 389 24 3 2842 3227 94793539 94793926 1.100000e-155 560.0
26 TraesCS5B01G158000 chr1A 90.685 365 27 5 3086 3446 547386933 547386572 3.170000e-131 479.0
27 TraesCS5B01G158000 chr1A 96.703 91 3 0 2844 2934 547387019 547386929 7.850000e-33 152.0
28 TraesCS5B01G158000 chr3A 91.404 349 25 3 3083 3428 8157734 8158080 1.480000e-129 473.0
29 TraesCS5B01G158000 chr3A 96.703 91 3 0 2844 2934 8157651 8157741 7.850000e-33 152.0
30 TraesCS5B01G158000 chr6B 90.831 349 27 3 3083 3428 120668903 120669249 3.190000e-126 462.0
31 TraesCS5B01G158000 chr6A 90.831 349 27 3 3083 3428 539621825 539622171 3.190000e-126 462.0
32 TraesCS5B01G158000 chr6A 96.703 91 3 0 2844 2934 539621742 539621832 7.850000e-33 152.0
33 TraesCS5B01G158000 chr7D 81.470 313 46 8 2425 2731 614351270 614350964 3.500000e-61 246.0
34 TraesCS5B01G158000 chr7A 81.150 313 47 8 2425 2731 706398327 706398021 1.630000e-59 241.0
35 TraesCS5B01G158000 chr4A 91.096 146 12 1 1486 1631 541337122 541336978 3.580000e-46 196.0


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 TraesCS5B01G158000 chr5B 291376979 291381511 4532 False 8371.000000 8371 100.0000 1 4533 1 chr5B.!!$F1 4532
1 TraesCS5B01G158000 chr5D 257119127 257126414 7287 False 1176.716667 5930 94.9880 3 4533 6 chr5D.!!$F2 4530
2 TraesCS5B01G158000 chr5D 257094894 257095500 606 False 787.000000 787 90.0160 187 803 1 chr5D.!!$F1 616
3 TraesCS5B01G158000 chr5A 341872194 341877099 4905 False 2804.000000 5088 93.2235 411 4484 2 chr5A.!!$F3 4073
4 TraesCS5B01G158000 chr5A 419360558 419361100 542 False 723.000000 723 90.6760 1087 1631 1 chr5A.!!$F2 544
5 TraesCS5B01G158000 chr7B 667440315 667441684 1369 True 720.500000 979 85.3735 1128 2614 2 chr7B.!!$R1 1486
6 TraesCS5B01G158000 chr2A 734095575 734096131 556 True 806.000000 806 92.8440 2892 3447 1 chr2A.!!$R1 555
7 TraesCS5B01G158000 chr1B 676246096 676246636 540 False 691.000000 691 89.8710 1094 1631 1 chr1B.!!$F4 537

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
90 2795 0.249868 CACTCGTTCCTGCTCCAACA 60.250 55.000 0.0 0.0 0.00 3.33 F
291 3001 1.136197 CCGTTCGCTCGCTAGATAGAG 60.136 57.143 0.0 0.0 37.54 2.43 F
1098 3826 0.392060 TCACATGGCTGCTACTGCTG 60.392 55.000 0.0 0.0 40.48 4.41 F
2021 4756 0.674269 GCGATACCCAACAACCCGAA 60.674 55.000 0.0 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1078 3806 0.392193 AGCAGTAGCAGCCATGTGAC 60.392 55.000 0.00 0.0 45.49 3.67 R
1247 3979 1.817099 CAGAGGATGCCGTTCCAGC 60.817 63.158 0.89 0.0 38.32 4.85 R
2795 5568 0.515127 CGTAAGCAATGCACAACGGA 59.485 50.000 8.35 0.0 30.70 4.69 R
3802 6621 0.955905 TGATGAACTGGTGACGACGA 59.044 50.000 0.00 0.0 0.00 4.20 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 2729 1.277842 TGGCGATTTGGCTACTCTTCA 59.722 47.619 0.00 0.00 45.14 3.02
61 2766 3.181443 TGATGCCTCCTATGTCTACTCGA 60.181 47.826 0.00 0.00 0.00 4.04
72 2777 0.744281 TCTACTCGATCAATGGCGCA 59.256 50.000 10.83 0.00 0.00 6.09
90 2795 0.249868 CACTCGTTCCTGCTCCAACA 60.250 55.000 0.00 0.00 0.00 3.33
122 2827 7.549134 TGTTATATCTGCTCGACAACAGAAATT 59.451 33.333 10.98 0.49 45.49 1.82
123 2828 4.675190 ATCTGCTCGACAACAGAAATTG 57.325 40.909 10.98 0.00 45.49 2.32
127 2832 2.030805 GCTCGACAACAGAAATTGCCTT 60.031 45.455 0.00 0.00 32.47 4.35
128 2833 3.558505 CTCGACAACAGAAATTGCCTTG 58.441 45.455 0.00 0.00 32.47 3.61
175 2882 2.877335 CCTACCACGCTCACTAGTTTC 58.123 52.381 0.00 0.00 0.00 2.78
180 2887 3.808174 ACCACGCTCACTAGTTTCTTTTC 59.192 43.478 0.00 0.00 0.00 2.29
181 2888 4.058817 CCACGCTCACTAGTTTCTTTTCT 58.941 43.478 0.00 0.00 0.00 2.52
188 2895 8.426251 CGCTCACTAGTTTCTTTTCTAAGTTAC 58.574 37.037 0.00 0.00 32.98 2.50
202 2909 4.763793 TCTAAGTTACCACGCTCACTAGTT 59.236 41.667 0.00 0.00 0.00 2.24
208 2915 2.488545 ACCACGCTCACTAGTTAGTCTG 59.511 50.000 5.97 2.03 33.46 3.51
248 2955 4.625607 TTTTCTTCCTCTCCTCCAACTC 57.374 45.455 0.00 0.00 0.00 3.01
256 2963 2.495669 CTCTCCTCCAACTCCTTCTCAC 59.504 54.545 0.00 0.00 0.00 3.51
260 2970 1.738099 CCAACTCCTTCTCACGCGG 60.738 63.158 12.47 0.00 0.00 6.46
282 2992 3.332493 TAGTGGACCGTTCGCTCGC 62.332 63.158 0.00 0.00 0.00 5.03
291 3001 1.136197 CCGTTCGCTCGCTAGATAGAG 60.136 57.143 0.00 0.00 37.54 2.43
302 3013 4.579340 TCGCTAGATAGAGTCGGAAACATT 59.421 41.667 0.00 0.00 0.00 2.71
306 3017 5.091261 AGATAGAGTCGGAAACATTTGCT 57.909 39.130 0.00 0.00 0.00 3.91
311 3022 2.030805 AGTCGGAAACATTTGCTTCAGC 60.031 45.455 0.00 0.00 42.50 4.26
319 3030 1.541147 CATTTGCTTCAGCCTTTCCGA 59.459 47.619 0.00 0.00 41.18 4.55
377 3088 1.915141 ACAAGTTGCAAGATCCAGGG 58.085 50.000 0.00 0.00 0.00 4.45
394 3105 3.371917 CCAGGGCCAACATAGAAAGATGA 60.372 47.826 6.18 0.00 0.00 2.92
436 3147 2.723273 TCACAGCTCGATTGTCTAGGA 58.277 47.619 0.15 0.00 0.00 2.94
437 3148 2.685388 TCACAGCTCGATTGTCTAGGAG 59.315 50.000 0.15 0.00 0.00 3.69
438 3149 2.028130 ACAGCTCGATTGTCTAGGAGG 58.972 52.381 0.00 0.00 0.00 4.30
494 3205 7.934665 TGCTAGTACTTTTCACACAGGAATTAA 59.065 33.333 0.00 0.00 0.00 1.40
559 3270 4.790766 GCATGATTCGGCACTCCTATTTTG 60.791 45.833 0.00 0.00 0.00 2.44
581 3292 2.944129 TCTTTGTGAAAAGGGACCCTG 58.056 47.619 15.76 0.00 32.13 4.45
599 3311 4.684134 GCCCTGGGCCAAAGCAGA 62.684 66.667 27.77 0.00 44.06 4.26
600 3312 2.677875 CCCTGGGCCAAAGCAGAC 60.678 66.667 8.04 0.00 42.56 3.51
601 3313 2.437897 CCTGGGCCAAAGCAGACT 59.562 61.111 8.04 0.00 42.56 3.24
602 3314 1.676967 CCTGGGCCAAAGCAGACTC 60.677 63.158 8.04 0.00 42.56 3.36
603 3315 1.377994 CTGGGCCAAAGCAGACTCT 59.622 57.895 8.04 0.00 42.56 3.24
888 3610 4.911522 TCTCCCTCCTTCTTCAACCTTTAA 59.088 41.667 0.00 0.00 0.00 1.52
984 3706 1.210478 TGCTTCTTATGCCCTCTCCAC 59.790 52.381 0.00 0.00 0.00 4.02
1013 3735 1.265095 CTACGACATGCCATTGCCATC 59.735 52.381 0.00 0.00 36.33 3.51
1077 3805 4.168291 CGCCCTCTGCTTCTCCCC 62.168 72.222 0.00 0.00 38.05 4.81
1078 3806 4.168291 GCCCTCTGCTTCTCCCCG 62.168 72.222 0.00 0.00 36.87 5.73
1081 3809 1.984570 CCTCTGCTTCTCCCCGTCA 60.985 63.158 0.00 0.00 0.00 4.35
1083 3811 1.533033 TCTGCTTCTCCCCGTCACA 60.533 57.895 0.00 0.00 0.00 3.58
1091 3819 4.415150 CCCCGTCACATGGCTGCT 62.415 66.667 0.00 0.00 0.00 4.24
1092 3820 2.584064 CCCGTCACATGGCTGCTA 59.416 61.111 0.00 0.00 0.00 3.49
1098 3826 0.392060 TCACATGGCTGCTACTGCTG 60.392 55.000 0.00 0.00 40.48 4.41
1470 4202 4.263209 CGCATCCTCTCGCTCGCT 62.263 66.667 0.00 0.00 0.00 4.93
1588 4320 3.483587 GGAACCTCACCCTGCTCA 58.516 61.111 0.00 0.00 0.00 4.26
1755 4487 3.456277 GGTATGTCAACCTCTCCTCCAAT 59.544 47.826 0.00 0.00 36.53 3.16
1826 4558 1.471119 GTCACCATCGACCTGTCCTA 58.529 55.000 0.00 0.00 0.00 2.94
1833 4565 3.254060 CATCGACCTGTCCTACAACAAG 58.746 50.000 0.00 0.00 0.00 3.16
2021 4756 0.674269 GCGATACCCAACAACCCGAA 60.674 55.000 0.00 0.00 0.00 4.30
2094 4829 1.980772 GCTGAAGCTGGCCACCATT 60.981 57.895 0.00 0.00 38.21 3.16
2322 5060 2.050714 GACAGCGACGACACGGAA 60.051 61.111 0.00 0.00 0.00 4.30
2758 5527 2.017782 TGAAAAGTAAGCACGCAACCA 58.982 42.857 0.00 0.00 0.00 3.67
2794 5567 3.574614 GCGCCATTTCATTTAGTGTTGT 58.425 40.909 0.00 0.00 0.00 3.32
2795 5568 3.987220 GCGCCATTTCATTTAGTGTTGTT 59.013 39.130 0.00 0.00 0.00 2.83
2796 5569 4.089923 GCGCCATTTCATTTAGTGTTGTTC 59.910 41.667 0.00 0.00 0.00 3.18
2797 5570 4.621034 CGCCATTTCATTTAGTGTTGTTCC 59.379 41.667 0.00 0.00 0.00 3.62
2811 5584 0.743688 TGTTCCGTTGTGCATTGCTT 59.256 45.000 10.49 0.00 0.00 3.91
3519 6298 1.152271 TCCTTCCTCCAACTCCTCCTT 59.848 52.381 0.00 0.00 0.00 3.36
3548 6330 0.110328 GTGACAGTGACGACGTCGAT 60.110 55.000 41.52 26.13 43.02 3.59
3559 6341 0.838229 GACGTCGATTGTTCCGATCG 59.162 55.000 8.51 8.51 45.84 3.69
3561 6343 1.265568 CGTCGATTGTTCCGATCGTT 58.734 50.000 15.09 0.00 45.03 3.85
3572 6356 0.824759 CCGATCGTTCCTTCCTTCCT 59.175 55.000 15.09 0.00 0.00 3.36
3586 6370 0.914644 CTTCCTCTCCTCCATTGGCA 59.085 55.000 0.00 0.00 0.00 4.92
3728 6517 4.351131 GGATGTTGATGGTCCGTTTTAC 57.649 45.455 0.00 0.00 0.00 2.01
3730 6519 4.094442 GGATGTTGATGGTCCGTTTTACTC 59.906 45.833 0.00 0.00 0.00 2.59
3731 6520 4.074627 TGTTGATGGTCCGTTTTACTCA 57.925 40.909 0.00 0.00 0.00 3.41
3732 6521 3.810941 TGTTGATGGTCCGTTTTACTCAC 59.189 43.478 0.00 0.00 0.00 3.51
3733 6522 3.755112 TGATGGTCCGTTTTACTCACA 57.245 42.857 0.00 0.00 0.00 3.58
3783 6602 4.641396 TGTTCTAATCTCACACCAACCTG 58.359 43.478 0.00 0.00 0.00 4.00
3784 6603 3.334583 TCTAATCTCACACCAACCTGC 57.665 47.619 0.00 0.00 0.00 4.85
3793 6612 1.202557 ACACCAACCTGCAAAGCATTG 60.203 47.619 0.00 0.00 38.13 2.82
3806 6625 0.865769 AGCATTGGTTTGTCGTCGTC 59.134 50.000 0.00 0.00 0.00 4.20
3810 6629 0.179142 TTGGTTTGTCGTCGTCGTCA 60.179 50.000 1.33 0.00 38.33 4.35
3811 6630 0.866906 TGGTTTGTCGTCGTCGTCAC 60.867 55.000 1.40 0.00 35.26 3.67
3812 6631 1.543106 GGTTTGTCGTCGTCGTCACC 61.543 60.000 1.40 0.00 35.26 4.02
3813 6632 0.866906 GTTTGTCGTCGTCGTCACCA 60.867 55.000 1.40 0.00 35.26 4.17
3814 6633 0.593008 TTTGTCGTCGTCGTCACCAG 60.593 55.000 1.40 0.00 35.26 4.00
3816 6635 1.009222 GTCGTCGTCGTCACCAGTT 60.009 57.895 1.33 0.00 38.33 3.16
3817 6636 0.995731 GTCGTCGTCGTCACCAGTTC 60.996 60.000 1.33 0.00 38.33 3.01
3819 6638 0.386858 CGTCGTCGTCACCAGTTCAT 60.387 55.000 0.00 0.00 0.00 2.57
3820 6639 1.337821 GTCGTCGTCACCAGTTCATC 58.662 55.000 0.00 0.00 0.00 2.92
3821 6640 0.955905 TCGTCGTCACCAGTTCATCA 59.044 50.000 0.00 0.00 0.00 3.07
3822 6641 1.544246 TCGTCGTCACCAGTTCATCAT 59.456 47.619 0.00 0.00 0.00 2.45
3823 6642 1.920574 CGTCGTCACCAGTTCATCATC 59.079 52.381 0.00 0.00 0.00 2.92
3824 6643 2.671070 CGTCGTCACCAGTTCATCATCA 60.671 50.000 0.00 0.00 0.00 3.07
3825 6644 3.325870 GTCGTCACCAGTTCATCATCAA 58.674 45.455 0.00 0.00 0.00 2.57
3826 6645 3.745975 GTCGTCACCAGTTCATCATCAAA 59.254 43.478 0.00 0.00 0.00 2.69
3827 6646 3.996363 TCGTCACCAGTTCATCATCAAAG 59.004 43.478 0.00 0.00 0.00 2.77
3828 6647 3.425359 CGTCACCAGTTCATCATCAAAGC 60.425 47.826 0.00 0.00 0.00 3.51
3829 6648 3.084039 TCACCAGTTCATCATCAAAGCC 58.916 45.455 0.00 0.00 0.00 4.35
3830 6649 2.086869 ACCAGTTCATCATCAAAGCCG 58.913 47.619 0.00 0.00 0.00 5.52
3831 6650 2.086869 CCAGTTCATCATCAAAGCCGT 58.913 47.619 0.00 0.00 0.00 5.68
3832 6651 2.489329 CCAGTTCATCATCAAAGCCGTT 59.511 45.455 0.00 0.00 0.00 4.44
3833 6652 3.057315 CCAGTTCATCATCAAAGCCGTTT 60.057 43.478 0.00 0.00 0.00 3.60
3834 6653 3.916172 CAGTTCATCATCAAAGCCGTTTG 59.084 43.478 0.00 0.00 43.96 2.93
3835 6654 2.634982 TCATCATCAAAGCCGTTTGC 57.365 45.000 0.00 0.00 42.55 3.68
3836 6655 1.885233 TCATCATCAAAGCCGTTTGCA 59.115 42.857 0.00 0.00 42.55 4.08
3837 6656 2.492881 TCATCATCAAAGCCGTTTGCAT 59.507 40.909 0.00 0.00 42.55 3.96
3838 6657 3.056678 TCATCATCAAAGCCGTTTGCATT 60.057 39.130 0.00 0.00 42.55 3.56
3854 6673 0.522626 CATTGCATGCGTCTTGGTCA 59.477 50.000 14.09 0.00 0.00 4.02
3855 6674 1.068402 CATTGCATGCGTCTTGGTCAA 60.068 47.619 14.09 0.00 0.00 3.18
3856 6675 1.246649 TTGCATGCGTCTTGGTCAAT 58.753 45.000 14.09 0.00 0.00 2.57
3857 6676 1.246649 TGCATGCGTCTTGGTCAATT 58.753 45.000 14.09 0.00 0.00 2.32
3859 6678 2.161410 TGCATGCGTCTTGGTCAATTAC 59.839 45.455 14.09 0.00 0.00 1.89
3860 6679 2.787723 GCATGCGTCTTGGTCAATTACG 60.788 50.000 0.00 11.73 34.64 3.18
3861 6680 1.434555 TGCGTCTTGGTCAATTACGG 58.565 50.000 15.47 3.97 33.18 4.02
3862 6681 0.096454 GCGTCTTGGTCAATTACGGC 59.904 55.000 15.47 8.13 33.18 5.68
3863 6682 1.434555 CGTCTTGGTCAATTACGGCA 58.565 50.000 9.45 0.00 0.00 5.69
3884 6720 4.194640 CAACACAAGATCCATCTACAGGG 58.805 47.826 0.00 0.00 35.76 4.45
3885 6721 2.171448 ACACAAGATCCATCTACAGGGC 59.829 50.000 0.00 0.00 35.76 5.19
3886 6722 2.171237 CACAAGATCCATCTACAGGGCA 59.829 50.000 0.00 0.00 35.76 5.36
3887 6723 2.437281 ACAAGATCCATCTACAGGGCAG 59.563 50.000 0.00 0.00 35.76 4.85
3888 6724 1.727062 AGATCCATCTACAGGGCAGG 58.273 55.000 0.00 0.00 34.85 4.85
3889 6725 0.036022 GATCCATCTACAGGGCAGGC 59.964 60.000 0.00 0.00 0.00 4.85
3890 6726 0.695462 ATCCATCTACAGGGCAGGCA 60.695 55.000 0.00 0.00 0.00 4.75
3891 6727 1.147824 CCATCTACAGGGCAGGCAG 59.852 63.158 0.00 0.00 0.00 4.85
3892 6728 1.147824 CATCTACAGGGCAGGCAGG 59.852 63.158 0.00 0.00 0.00 4.85
3893 6729 2.074948 ATCTACAGGGCAGGCAGGG 61.075 63.158 0.00 0.00 0.00 4.45
3894 6730 3.801997 CTACAGGGCAGGCAGGGG 61.802 72.222 0.00 0.00 0.00 4.79
3895 6731 4.675303 TACAGGGCAGGCAGGGGT 62.675 66.667 0.00 0.00 0.00 4.95
3959 6795 1.538047 TCTGCATGGCCAAAACTCTC 58.462 50.000 10.96 0.00 0.00 3.20
3960 6796 1.074405 TCTGCATGGCCAAAACTCTCT 59.926 47.619 10.96 0.00 0.00 3.10
4018 6878 6.072452 GCTTCTTTATCCCATGTTGCTATACC 60.072 42.308 0.00 0.00 0.00 2.73
4042 6905 2.540383 AGTACTCCATGGAGCTGTTGA 58.460 47.619 36.78 15.57 45.54 3.18
4089 7724 0.107116 TGTTTTGGCGGGTGTGTACT 60.107 50.000 0.00 0.00 0.00 2.73
4090 7725 0.589708 GTTTTGGCGGGTGTGTACTC 59.410 55.000 0.00 0.00 0.00 2.59
4092 7727 1.697082 TTTGGCGGGTGTGTACTCCA 61.697 55.000 5.58 0.00 0.00 3.86
4093 7728 1.485294 TTGGCGGGTGTGTACTCCAT 61.485 55.000 5.58 0.00 0.00 3.41
4111 7790 2.441001 CCATGGAGCCTTCTTATCACCT 59.559 50.000 5.56 0.00 0.00 4.00
4112 7791 3.495806 CCATGGAGCCTTCTTATCACCTC 60.496 52.174 5.56 0.00 0.00 3.85
4114 7793 4.265856 TGGAGCCTTCTTATCACCTCTA 57.734 45.455 0.00 0.00 0.00 2.43
4126 7834 1.003118 TCACCTCTACCATGTTGCCAC 59.997 52.381 0.00 0.00 0.00 5.01
4162 7870 5.414454 CCTACATTCATTTCGTTTTCAGGGA 59.586 40.000 0.00 0.00 0.00 4.20
4239 7947 2.028476 TGTAGAACACCCGTGATCCTTG 60.028 50.000 0.96 0.00 33.49 3.61
4313 8021 3.214696 CTCCAAAGAGTGTTGGGACTT 57.785 47.619 4.22 0.00 46.89 3.01
4402 8110 3.060615 CCCACTCCTTGCTGCAGC 61.061 66.667 31.89 31.89 42.50 5.25
4407 8115 2.987547 TCCTTGCTGCAGCTTGCC 60.988 61.111 36.61 10.79 44.23 4.52
4459 8168 1.200020 GCTGGCTATGCGTTTTGTTCT 59.800 47.619 0.00 0.00 0.00 3.01
4488 8198 3.278987 TGGGTAAAACCTGTCCCTCTA 57.721 47.619 0.00 0.00 38.64 2.43
4512 8222 7.496346 AGATCTCTGTTTAGGTTACCATGAA 57.504 36.000 3.51 0.00 0.00 2.57
4521 8231 0.671163 GTTACCATGAACGGTCCGCA 60.671 55.000 12.28 2.07 40.67 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.003118 AGAGTAGCCAAATCGCCAACA 59.997 47.619 0.00 0.00 0.00 3.33
2 3 1.739067 AGAGTAGCCAAATCGCCAAC 58.261 50.000 0.00 0.00 0.00 3.77
3 4 2.290008 TGAAGAGTAGCCAAATCGCCAA 60.290 45.455 0.00 0.00 0.00 4.52
5 6 1.666189 GTGAAGAGTAGCCAAATCGCC 59.334 52.381 0.00 0.00 0.00 5.54
6 7 1.324736 CGTGAAGAGTAGCCAAATCGC 59.675 52.381 0.00 0.00 0.00 4.58
24 2729 1.867233 GCATCAATTATCGAGTGGCGT 59.133 47.619 0.00 0.00 41.80 5.68
61 2766 1.369091 GGAACGAGTGCGCCATTGAT 61.369 55.000 4.18 0.00 42.48 2.57
72 2777 0.249911 GTGTTGGAGCAGGAACGAGT 60.250 55.000 0.00 0.00 0.00 4.18
90 2795 4.099419 TGTCGAGCAGATATAACATGTGGT 59.901 41.667 0.00 0.00 0.00 4.16
109 2814 3.624326 TCAAGGCAATTTCTGTTGTCG 57.376 42.857 0.00 0.00 38.68 4.35
122 2827 1.531365 CCCAAGCACCTTCAAGGCA 60.531 57.895 2.20 0.00 39.63 4.75
123 2828 1.228552 TCCCAAGCACCTTCAAGGC 60.229 57.895 2.20 0.00 39.63 4.35
127 2832 1.761174 GGTCTCCCAAGCACCTTCA 59.239 57.895 0.00 0.00 0.00 3.02
128 2833 1.002011 GGGTCTCCCAAGCACCTTC 60.002 63.158 0.00 0.00 44.65 3.46
175 2882 4.989168 AGTGAGCGTGGTAACTTAGAAAAG 59.011 41.667 0.00 0.00 38.77 2.27
180 2887 4.698583 ACTAGTGAGCGTGGTAACTTAG 57.301 45.455 0.00 0.00 37.61 2.18
181 2888 5.707298 ACTAACTAGTGAGCGTGGTAACTTA 59.293 40.000 7.21 0.00 34.72 2.24
188 2895 2.732597 GCAGACTAACTAGTGAGCGTGG 60.733 54.545 7.21 0.00 36.50 4.94
202 2909 2.111384 GAGTTGGATGGAGGCAGACTA 58.889 52.381 0.00 0.00 0.00 2.59
208 2915 2.653234 ATCATGAGTTGGATGGAGGC 57.347 50.000 0.09 0.00 0.00 4.70
248 2955 4.124351 TACCGCCGCGTGAGAAGG 62.124 66.667 12.58 1.13 0.00 3.46
282 2992 6.276847 AGCAAATGTTTCCGACTCTATCTAG 58.723 40.000 0.00 0.00 0.00 2.43
291 3001 2.319472 GCTGAAGCAAATGTTTCCGAC 58.681 47.619 7.41 0.00 41.59 4.79
302 3013 1.909700 AATCGGAAAGGCTGAAGCAA 58.090 45.000 4.43 0.00 44.36 3.91
306 3017 6.834168 AAATTTCTAATCGGAAAGGCTGAA 57.166 33.333 0.00 0.00 38.38 3.02
311 3022 7.229506 AGCCATCTAAATTTCTAATCGGAAAGG 59.770 37.037 0.00 0.00 38.38 3.11
377 3088 4.646492 ACCCATTCATCTTTCTATGTTGGC 59.354 41.667 0.00 0.00 33.58 4.52
394 3105 7.147391 TGTGATGATACCACTATGTTACCCATT 60.147 37.037 0.00 0.00 35.66 3.16
436 3147 3.726557 TCCAGCTGTGATGATTTTCCT 57.273 42.857 13.81 0.00 0.00 3.36
437 3148 4.205587 AGATCCAGCTGTGATGATTTTCC 58.794 43.478 18.71 6.21 0.00 3.13
438 3149 5.579718 CAAGATCCAGCTGTGATGATTTTC 58.420 41.667 18.71 7.47 0.00 2.29
487 3198 9.289303 CATACATGCACAAAAGTAGTTAATTCC 57.711 33.333 0.00 0.00 0.00 3.01
494 3205 8.044309 TGGTATACATACATGCACAAAAGTAGT 58.956 33.333 5.01 0.00 34.98 2.73
559 3270 3.507622 CAGGGTCCCTTTTCACAAAGATC 59.492 47.826 8.08 0.00 41.97 2.75
596 3308 2.738213 AAAGGTGGCCGCAGAGTCTG 62.738 60.000 19.98 16.21 34.12 3.51
597 3309 2.056906 AAAAGGTGGCCGCAGAGTCT 62.057 55.000 19.98 1.91 0.00 3.24
598 3310 1.578206 GAAAAGGTGGCCGCAGAGTC 61.578 60.000 19.98 6.09 0.00 3.36
599 3311 1.600916 GAAAAGGTGGCCGCAGAGT 60.601 57.895 19.98 0.00 0.00 3.24
600 3312 1.600636 TGAAAAGGTGGCCGCAGAG 60.601 57.895 19.98 0.00 0.00 3.35
601 3313 1.896660 GTGAAAAGGTGGCCGCAGA 60.897 57.895 19.98 0.00 0.00 4.26
602 3314 2.644992 GTGAAAAGGTGGCCGCAG 59.355 61.111 19.98 0.00 0.00 5.18
603 3315 2.909965 GGTGAAAAGGTGGCCGCA 60.910 61.111 19.98 0.00 0.00 5.69
606 3318 1.001974 GGAATTGGTGAAAAGGTGGCC 59.998 52.381 0.00 0.00 0.00 5.36
827 3545 4.081972 GTGGAGTCAGAGCATAGTCAAGAA 60.082 45.833 0.00 0.00 0.00 2.52
888 3610 1.153329 TGGTTCACCGAAACTGCGT 60.153 52.632 0.00 0.00 39.43 5.24
910 3632 2.040278 CACTCCCTTGGATTGGTTGAGA 59.960 50.000 0.00 0.00 30.16 3.27
1025 3753 3.650298 ATGGATGCAGCAAGGCGGT 62.650 57.895 3.51 0.00 36.28 5.68
1077 3805 1.699656 GCAGTAGCAGCCATGTGACG 61.700 60.000 0.00 0.00 41.58 4.35
1078 3806 0.392193 AGCAGTAGCAGCCATGTGAC 60.392 55.000 0.00 0.00 45.49 3.67
1081 3809 1.748122 GCAGCAGTAGCAGCCATGT 60.748 57.895 0.00 0.00 46.35 3.21
1247 3979 1.817099 CAGAGGATGCCGTTCCAGC 60.817 63.158 0.89 0.00 38.32 4.85
1261 3993 2.123982 GGGGAAGGCCATGCAGAG 60.124 66.667 5.01 0.00 35.15 3.35
1470 4202 2.125310 CCCGTGATGCCGTTGCTA 60.125 61.111 0.00 0.00 38.71 3.49
1588 4320 2.156051 GAGACGGCGGTGAGGTTCTT 62.156 60.000 13.24 0.00 0.00 2.52
1781 4513 4.166011 GCAGGTGCGACGCCATTC 62.166 66.667 18.69 5.18 36.32 2.67
1826 4558 2.972505 CGCCGGTGAGCTTGTTGT 60.973 61.111 10.20 0.00 0.00 3.32
2094 4829 2.031919 CCGGCGGCAATGGCTATA 59.968 61.111 15.42 0.00 40.87 1.31
2322 5060 0.894184 ACGTGTCCGTCACATCCTCT 60.894 55.000 8.32 0.00 46.28 3.69
2758 5527 2.126734 CGCGTCTACGTCGGGTTT 60.127 61.111 0.00 0.00 42.22 3.27
2794 5567 1.069568 CGTAAGCAATGCACAACGGAA 60.070 47.619 8.35 0.00 30.70 4.30
2795 5568 0.515127 CGTAAGCAATGCACAACGGA 59.485 50.000 8.35 0.00 30.70 4.69
2796 5569 3.000164 CGTAAGCAATGCACAACGG 58.000 52.632 8.35 0.00 30.70 4.44
3519 6298 3.295273 ACTGTCACTGCGCGGAGA 61.295 61.111 34.91 19.00 0.00 3.71
3548 6330 1.621814 AGGAAGGAACGATCGGAACAA 59.378 47.619 20.98 0.00 0.00 2.83
3559 6341 1.834896 GGAGGAGAGGAAGGAAGGAAC 59.165 57.143 0.00 0.00 0.00 3.62
3561 6343 1.093408 TGGAGGAGAGGAAGGAAGGA 58.907 55.000 0.00 0.00 0.00 3.36
3592 6376 6.489361 AGAGAAGAAATCAACAAGCAGAACAT 59.511 34.615 0.00 0.00 0.00 2.71
3593 6377 5.824624 AGAGAAGAAATCAACAAGCAGAACA 59.175 36.000 0.00 0.00 0.00 3.18
3726 6515 2.753452 GTTCGGGAGAGATGTGTGAGTA 59.247 50.000 0.00 0.00 41.75 2.59
3727 6516 1.546476 GTTCGGGAGAGATGTGTGAGT 59.454 52.381 0.00 0.00 41.75 3.41
3728 6517 1.546029 TGTTCGGGAGAGATGTGTGAG 59.454 52.381 0.00 0.00 41.75 3.51
3730 6519 2.274437 CATGTTCGGGAGAGATGTGTG 58.726 52.381 0.00 0.00 41.75 3.82
3731 6520 1.902508 ACATGTTCGGGAGAGATGTGT 59.097 47.619 0.00 0.00 40.29 3.72
3732 6521 2.680312 ACATGTTCGGGAGAGATGTG 57.320 50.000 0.00 0.00 40.29 3.21
3733 6522 4.499865 CGATAACATGTTCGGGAGAGATGT 60.500 45.833 15.85 0.00 42.27 3.06
3783 6602 1.786579 GACGACAAACCAATGCTTTGC 59.213 47.619 6.81 0.00 32.71 3.68
3784 6603 2.043411 CGACGACAAACCAATGCTTTG 58.957 47.619 5.37 5.37 35.17 2.77
3793 6612 1.543106 GGTGACGACGACGACAAACC 61.543 60.000 15.32 8.80 44.04 3.27
3801 6620 1.335597 TGATGAACTGGTGACGACGAC 60.336 52.381 0.00 0.00 0.00 4.34
3802 6621 0.955905 TGATGAACTGGTGACGACGA 59.044 50.000 0.00 0.00 0.00 4.20
3806 6625 3.425359 GCTTTGATGATGAACTGGTGACG 60.425 47.826 0.00 0.00 0.00 4.35
3810 6629 2.086869 CGGCTTTGATGATGAACTGGT 58.913 47.619 0.00 0.00 0.00 4.00
3811 6630 2.086869 ACGGCTTTGATGATGAACTGG 58.913 47.619 0.00 0.00 0.00 4.00
3812 6631 3.837213 AACGGCTTTGATGATGAACTG 57.163 42.857 0.00 0.00 0.00 3.16
3813 6632 3.612479 GCAAACGGCTTTGATGATGAACT 60.612 43.478 11.81 0.00 39.43 3.01
3814 6633 2.663119 GCAAACGGCTTTGATGATGAAC 59.337 45.455 11.81 0.00 39.43 3.18
3816 6635 1.885233 TGCAAACGGCTTTGATGATGA 59.115 42.857 11.81 0.00 45.15 2.92
3817 6636 2.350899 TGCAAACGGCTTTGATGATG 57.649 45.000 11.81 0.00 45.15 3.07
3824 6643 1.149987 CATGCAATGCAAACGGCTTT 58.850 45.000 13.45 0.00 43.62 3.51
3825 6644 2.830264 CATGCAATGCAAACGGCTT 58.170 47.368 13.45 0.00 43.62 4.35
3826 6645 4.582760 CATGCAATGCAAACGGCT 57.417 50.000 13.45 0.00 43.62 5.52
3836 6655 1.246649 TTGACCAAGACGCATGCAAT 58.753 45.000 19.57 4.56 0.00 3.56
3837 6656 1.246649 ATTGACCAAGACGCATGCAA 58.753 45.000 19.57 0.70 0.00 4.08
3838 6657 1.246649 AATTGACCAAGACGCATGCA 58.753 45.000 19.57 0.00 0.00 3.96
3854 6673 3.417101 TGGATCTTGTGTTGCCGTAATT 58.583 40.909 0.00 0.00 0.00 1.40
3855 6674 3.066291 TGGATCTTGTGTTGCCGTAAT 57.934 42.857 0.00 0.00 0.00 1.89
3856 6675 2.552599 TGGATCTTGTGTTGCCGTAA 57.447 45.000 0.00 0.00 0.00 3.18
3857 6676 2.236146 AGATGGATCTTGTGTTGCCGTA 59.764 45.455 0.00 0.00 31.97 4.02
3859 6678 1.742761 AGATGGATCTTGTGTTGCCG 58.257 50.000 0.00 0.00 31.97 5.69
3860 6679 3.609853 TGTAGATGGATCTTGTGTTGCC 58.390 45.455 0.00 0.00 38.32 4.52
3861 6680 3.624861 CCTGTAGATGGATCTTGTGTTGC 59.375 47.826 0.00 0.00 38.32 4.17
3862 6681 4.194640 CCCTGTAGATGGATCTTGTGTTG 58.805 47.826 0.00 0.00 38.32 3.33
3863 6682 3.370953 GCCCTGTAGATGGATCTTGTGTT 60.371 47.826 0.00 0.00 38.32 3.32
3893 6729 0.979187 TGTATCCAAGGGACCCGACC 60.979 60.000 4.40 0.00 32.98 4.79
3894 6730 1.129058 ATGTATCCAAGGGACCCGAC 58.871 55.000 4.40 0.00 32.98 4.79
3895 6731 2.322658 GTATGTATCCAAGGGACCCGA 58.677 52.381 4.40 0.00 32.98 5.14
3896 6732 2.043992 TGTATGTATCCAAGGGACCCG 58.956 52.381 4.40 0.00 32.98 5.28
3897 6733 4.351111 AGAATGTATGTATCCAAGGGACCC 59.649 45.833 0.59 0.59 32.98 4.46
3898 6734 5.308825 CAGAATGTATGTATCCAAGGGACC 58.691 45.833 0.00 0.00 32.98 4.46
3917 6753 1.367346 TACCCCATGCAGAACCAGAA 58.633 50.000 0.00 0.00 0.00 3.02
3918 6754 1.595311 ATACCCCATGCAGAACCAGA 58.405 50.000 0.00 0.00 0.00 3.86
3920 6756 3.721575 AGAATATACCCCATGCAGAACCA 59.278 43.478 0.00 0.00 0.00 3.67
3921 6757 4.074970 CAGAATATACCCCATGCAGAACC 58.925 47.826 0.00 0.00 0.00 3.62
3922 6758 3.503748 GCAGAATATACCCCATGCAGAAC 59.496 47.826 0.00 0.00 33.92 3.01
3923 6759 3.138098 TGCAGAATATACCCCATGCAGAA 59.862 43.478 0.00 0.00 38.64 3.02
4018 6878 3.027412 ACAGCTCCATGGAGTACTACAG 58.973 50.000 36.32 21.18 43.70 2.74
4089 7724 2.439507 GGTGATAAGAAGGCTCCATGGA 59.560 50.000 15.27 15.27 0.00 3.41
4090 7725 2.441001 AGGTGATAAGAAGGCTCCATGG 59.559 50.000 4.97 4.97 0.00 3.66
4092 7727 3.663198 AGAGGTGATAAGAAGGCTCCAT 58.337 45.455 0.00 0.00 0.00 3.41
4093 7728 3.121929 AGAGGTGATAAGAAGGCTCCA 57.878 47.619 0.00 0.00 0.00 3.86
4126 7834 3.845178 TGAATGTAGGTTGCTACGAGTG 58.155 45.455 0.00 0.00 32.80 3.51
4162 7870 2.871633 CCGCCAAAACAAAGCAAATCTT 59.128 40.909 0.00 0.00 36.34 2.40
4239 7947 1.964373 ATGTTTGTGTCGTCGCCCC 60.964 57.895 0.00 0.00 0.00 5.80
4313 8021 2.690510 TCGCATGTCCATCCCCCA 60.691 61.111 0.00 0.00 0.00 4.96
4407 8115 4.497006 GCAGTAAGATAATGTTGCAGCAGG 60.497 45.833 9.71 0.00 0.00 4.85
4459 8168 1.497286 AGGTTTTACCCAACAGCTCCA 59.503 47.619 0.00 0.00 39.75 3.86
4488 8198 7.331791 GTTCATGGTAACCTAAACAGAGATCT 58.668 38.462 0.00 0.00 0.00 2.75
4512 8222 2.029073 CTTGACAGTGCGGACCGT 59.971 61.111 16.73 0.00 0.00 4.83


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

AutoCloner maintained by Alex Coulton.