Multiple sequence alignment - TraesCS6D01G101900

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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 TraesCS6D01G101900 chr6D 100.000 4032 0 0 1 4032 65344414 65340383 0.000000e+00 7446.0
1 TraesCS6D01G101900 chr6D 84.879 1693 175 33 793 2432 65361281 65359617 0.000000e+00 1633.0
2 TraesCS6D01G101900 chr6D 85.599 1486 182 21 893 2355 65095256 65093780 0.000000e+00 1530.0
3 TraesCS6D01G101900 chr6D 84.369 1625 174 27 859 2432 65051507 65053102 0.000000e+00 1520.0
4 TraesCS6D01G101900 chr6D 82.982 617 53 16 2735 3328 65053918 65054505 1.000000e-140 510.0
5 TraesCS6D01G101900 chr6D 83.737 578 52 16 2738 3291 65358779 65358220 3.600000e-140 508.0
6 TraesCS6D01G101900 chr6D 91.358 81 4 3 1 80 55391686 55391764 1.530000e-19 108.0
7 TraesCS6D01G101900 chr6D 91.358 81 4 3 1 80 129506363 129506285 1.530000e-19 108.0
8 TraesCS6D01G101900 chr6D 91.358 81 4 3 1 80 276378177 276378255 1.530000e-19 108.0
9 TraesCS6D01G101900 chr6D 91.358 81 4 3 1 80 386462031 386461953 1.530000e-19 108.0
10 TraesCS6D01G101900 chr6D 91.358 81 4 3 1 80 461774453 461774375 1.530000e-19 108.0
11 TraesCS6D01G101900 chr6D 85.455 55 8 0 552 606 388558440 388558386 1.570000e-04 58.4
12 TraesCS6D01G101900 chr6B 95.873 2399 66 13 793 3184 140333686 140331314 0.000000e+00 3851.0
13 TraesCS6D01G101900 chr6B 85.792 1661 154 25 829 2432 140367455 140365820 0.000000e+00 1685.0
14 TraesCS6D01G101900 chr6B 85.202 1507 161 27 956 2432 139883741 139885215 0.000000e+00 1491.0
15 TraesCS6D01G101900 chr6B 85.818 1382 152 27 893 2249 140097521 140096159 0.000000e+00 1426.0
16 TraesCS6D01G101900 chr6B 94.046 739 23 6 56 777 140339318 140338584 0.000000e+00 1101.0
17 TraesCS6D01G101900 chr6B 85.822 663 52 19 2964 3617 140363640 140363011 0.000000e+00 665.0
18 TraesCS6D01G101900 chr6B 82.820 617 54 19 2735 3328 139886030 139886617 4.650000e-139 505.0
19 TraesCS6D01G101900 chr6B 84.974 386 34 11 3238 3616 140331211 140330843 1.770000e-98 370.0
20 TraesCS6D01G101900 chr6B 87.448 239 19 5 3795 4032 140329838 140329610 8.590000e-67 265.0
21 TraesCS6D01G101900 chr6B 86.726 226 12 4 566 776 140333892 140333670 6.740000e-58 235.0
22 TraesCS6D01G101900 chr6B 93.902 82 5 0 793 874 140338601 140338520 1.520000e-24 124.0
23 TraesCS6D01G101900 chr6A 95.155 2126 81 4 793 2906 83599318 83601433 0.000000e+00 3336.0
24 TraesCS6D01G101900 chr6A 83.873 2071 264 42 893 2903 83644443 83646503 0.000000e+00 1910.0
25 TraesCS6D01G101900 chr6A 85.110 1726 180 30 793 2471 83434848 83436543 0.000000e+00 1692.0
26 TraesCS6D01G101900 chr6A 80.056 1790 270 49 999 2761 81191957 81190228 0.000000e+00 1247.0
27 TraesCS6D01G101900 chr6A 88.071 679 54 12 2949 3617 83439331 83439992 0.000000e+00 780.0
28 TraesCS6D01G101900 chr6A 94.949 396 16 4 45 436 83588730 83589125 5.730000e-173 617.0
29 TraesCS6D01G101900 chr6A 84.039 614 51 19 2735 3328 83437474 83438060 7.620000e-152 547.0
30 TraesCS6D01G101900 chr6A 95.638 298 13 0 2735 3032 83601343 83601640 2.820000e-131 479.0
31 TraesCS6D01G101900 chr6A 89.071 366 21 6 427 777 83598974 83599335 1.720000e-118 436.0
32 TraesCS6D01G101900 chr6A 86.162 383 28 11 3238 3617 83601810 83602170 1.360000e-104 390.0
33 TraesCS6D01G101900 chr6A 100.000 28 0 0 3157 3184 83601692 83601719 7.000000e-03 52.8
34 TraesCS6D01G101900 chr5B 82.146 1053 170 11 1856 2902 261675967 261674927 0.000000e+00 887.0
35 TraesCS6D01G101900 chr5B 81.377 494 77 8 2738 3230 261675010 261674531 4.890000e-104 388.0
36 TraesCS6D01G101900 chrUn 82.975 558 85 6 2351 2902 388715107 388714554 2.800000e-136 496.0
37 TraesCS6D01G101900 chrUn 81.892 613 60 18 2738 3326 388714637 388714052 1.700000e-128 470.0
38 TraesCS6D01G101900 chr1B 82.963 135 21 2 85 218 643307474 643307607 1.970000e-23 121.0
39 TraesCS6D01G101900 chr7D 95.890 73 3 0 1 73 29784658 29784586 7.080000e-23 119.0
40 TraesCS6D01G101900 chr7D 94.444 54 3 0 85 138 627737851 627737798 2.580000e-12 84.2
41 TraesCS6D01G101900 chr7D 94.444 54 3 0 85 138 627856089 627856036 2.580000e-12 84.2
42 TraesCS6D01G101900 chr7D 94.444 54 3 0 85 138 628011617 628011564 2.580000e-12 84.2
43 TraesCS6D01G101900 chr7D 88.889 63 7 0 76 138 627678088 627678026 1.200000e-10 78.7
44 TraesCS6D01G101900 chr7D 92.593 54 4 0 85 138 627935957 627935904 1.200000e-10 78.7
45 TraesCS6D01G101900 chr4B 91.358 81 4 3 1 80 352256561 352256639 1.530000e-19 108.0
46 TraesCS6D01G101900 chr1D 91.358 81 4 3 1 80 173414857 173414935 1.530000e-19 108.0
47 TraesCS6D01G101900 chr1D 91.358 81 4 3 1 80 374100863 374100941 1.530000e-19 108.0
48 TraesCS6D01G101900 chr7A 77.976 168 32 5 367 532 657674373 657674537 2.560000e-17 100.0
49 TraesCS6D01G101900 chr7A 94.444 54 3 0 85 138 723804382 723804329 2.580000e-12 84.2
50 TraesCS6D01G101900 chr3B 100.000 29 0 0 575 603 644173463 644173491 2.000000e-03 54.7


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 TraesCS6D01G101900 chr6D 65340383 65344414 4031 True 7446.000000 7446 100.00000 1 4032 1 chr6D.!!$R2 4031
1 TraesCS6D01G101900 chr6D 65093780 65095256 1476 True 1530.000000 1530 85.59900 893 2355 1 chr6D.!!$R1 1462
2 TraesCS6D01G101900 chr6D 65358220 65361281 3061 True 1070.500000 1633 84.30800 793 3291 2 chr6D.!!$R7 2498
3 TraesCS6D01G101900 chr6D 65051507 65054505 2998 False 1015.000000 1520 83.67550 859 3328 2 chr6D.!!$F3 2469
4 TraesCS6D01G101900 chr6B 140096159 140097521 1362 True 1426.000000 1426 85.81800 893 2249 1 chr6B.!!$R1 1356
5 TraesCS6D01G101900 chr6B 140329610 140333892 4282 True 1180.250000 3851 88.75525 566 4032 4 chr6B.!!$R2 3466
6 TraesCS6D01G101900 chr6B 140363011 140367455 4444 True 1175.000000 1685 85.80700 829 3617 2 chr6B.!!$R4 2788
7 TraesCS6D01G101900 chr6B 139883741 139886617 2876 False 998.000000 1491 84.01100 956 3328 2 chr6B.!!$F1 2372
8 TraesCS6D01G101900 chr6B 140338520 140339318 798 True 612.500000 1101 93.97400 56 874 2 chr6B.!!$R3 818
9 TraesCS6D01G101900 chr6A 83644443 83646503 2060 False 1910.000000 1910 83.87300 893 2903 1 chr6A.!!$F2 2010
10 TraesCS6D01G101900 chr6A 81190228 81191957 1729 True 1247.000000 1247 80.05600 999 2761 1 chr6A.!!$R1 1762
11 TraesCS6D01G101900 chr6A 83434848 83439992 5144 False 1006.333333 1692 85.74000 793 3617 3 chr6A.!!$F3 2824
12 TraesCS6D01G101900 chr6A 83598974 83602170 3196 False 938.760000 3336 93.20520 427 3617 5 chr6A.!!$F4 3190
13 TraesCS6D01G101900 chr5B 261674531 261675967 1436 True 637.500000 887 81.76150 1856 3230 2 chr5B.!!$R1 1374
14 TraesCS6D01G101900 chrUn 388714052 388715107 1055 True 483.000000 496 82.43350 2351 3326 2 chrUn.!!$R1 975

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
269 271 1.005347 GTGGGTACGAAATGAATCGCG 60.005 52.381 0.0 0.0 46.51 5.87 F
1235 1311 0.395862 ACCTCCTCCGATGACGACAT 60.396 55.000 0.0 0.0 42.66 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1849 1952 0.527817 CTGATACGGAGGCGTGAACC 60.528 60.0 0.0 0.0 0.0 3.62 R
3231 6882 0.176680 CCACATCTCAGTCTTCCCGG 59.823 60.0 0.0 0.0 0.0 5.73 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
41 42 7.839680 AACCATTTTATTATTGCCTCTAGGG 57.160 36.000 0.00 0.00 35.18 3.53
54 55 4.437682 CCTCTAGGGCATATTTCCAACA 57.562 45.455 0.00 0.00 0.00 3.33
78 79 7.093333 ACACTAATCACATCATGGACTAAGTCA 60.093 37.037 0.00 0.00 33.68 3.41
201 202 3.243334 TGCACAAAATGAATGCGAAGTCA 60.243 39.130 0.00 0.00 42.44 3.41
243 245 2.297701 TCACCACAAAAGAAGACCAGC 58.702 47.619 0.00 0.00 0.00 4.85
269 271 1.005347 GTGGGTACGAAATGAATCGCG 60.005 52.381 0.00 0.00 46.51 5.87
302 304 3.441572 GCCACATATGCCCACATTAGATC 59.558 47.826 1.58 0.00 37.74 2.75
412 414 2.109181 GAGATACCCAGTGGCGCC 59.891 66.667 22.73 22.73 33.59 6.53
466 468 4.204799 GGTTTTGTTAGGACTTGTCCTGT 58.795 43.478 27.20 9.24 40.93 4.00
672 690 9.909365 ACAGGTAGACTATTATAAACCCCTAAT 57.091 33.333 0.00 0.00 0.00 1.73
708 726 9.734620 TCTGATTTTGACATACACAAGAAAAAG 57.265 29.630 0.00 0.00 0.00 2.27
771 789 7.783090 CTGTTCACAGCTGAATATATCTGTT 57.217 36.000 23.35 0.00 38.69 3.16
772 790 8.206325 CTGTTCACAGCTGAATATATCTGTTT 57.794 34.615 23.35 0.00 38.69 2.83
773 791 7.977904 TGTTCACAGCTGAATATATCTGTTTG 58.022 34.615 23.35 3.01 38.69 2.93
774 792 7.823799 TGTTCACAGCTGAATATATCTGTTTGA 59.176 33.333 23.35 5.68 38.69 2.69
775 793 8.834465 GTTCACAGCTGAATATATCTGTTTGAT 58.166 33.333 23.35 0.00 38.69 2.57
776 794 8.969260 TCACAGCTGAATATATCTGTTTGATT 57.031 30.769 23.35 0.00 37.66 2.57
777 795 9.399797 TCACAGCTGAATATATCTGTTTGATTT 57.600 29.630 23.35 0.00 37.66 2.17
1235 1311 0.395862 ACCTCCTCCGATGACGACAT 60.396 55.000 0.00 0.00 42.66 3.06
1432 1514 3.785499 CGCTCCTCGTCGACGACA 61.785 66.667 34.97 22.87 44.22 4.35
1711 1814 2.743928 GGCGCTTCCCAGACACTG 60.744 66.667 7.64 0.00 0.00 3.66
2099 2205 3.181454 ACTGGGTCTTGTAACTTCTGTGG 60.181 47.826 0.00 0.00 0.00 4.17
2328 2448 2.219080 TCACGTCATGGTAGTACCCA 57.781 50.000 16.91 5.47 37.50 4.51
2427 2577 6.639632 ATTCAAGTGCTAGTTGTTCATTGT 57.360 33.333 0.00 0.00 30.75 2.71
2432 2582 9.278978 TCAAGTGCTAGTTGTTCATTGTTATAA 57.721 29.630 0.00 0.00 30.75 0.98
2841 4045 2.238646 GTGATGGTGTGGTAATGGAGGA 59.761 50.000 0.00 0.00 0.00 3.71
3040 6556 5.105106 TCGAGTTATGGCATGAGAGGTTTTA 60.105 40.000 10.98 0.00 0.00 1.52
3215 6854 5.298347 AGTTTTACTAGTCTGTTGCACTCC 58.702 41.667 0.00 0.00 0.00 3.85
3218 6857 5.546621 TTACTAGTCTGTTGCACTCCTTT 57.453 39.130 0.00 0.00 0.00 3.11
3224 6875 3.378427 GTCTGTTGCACTCCTTTTTGAGT 59.622 43.478 0.00 0.00 46.35 3.41
3225 6876 4.016444 TCTGTTGCACTCCTTTTTGAGTT 58.984 39.130 0.00 0.00 42.92 3.01
3226 6877 4.096382 TCTGTTGCACTCCTTTTTGAGTTC 59.904 41.667 0.00 0.00 42.92 3.01
3227 6878 4.016444 TGTTGCACTCCTTTTTGAGTTCT 58.984 39.130 0.00 0.00 42.92 3.01
3228 6879 4.096382 TGTTGCACTCCTTTTTGAGTTCTC 59.904 41.667 0.00 0.00 42.92 2.87
3229 6880 4.156455 TGCACTCCTTTTTGAGTTCTCT 57.844 40.909 1.53 0.00 42.92 3.10
3230 6881 5.290493 TGCACTCCTTTTTGAGTTCTCTA 57.710 39.130 1.53 0.00 42.92 2.43
3231 6882 5.057149 TGCACTCCTTTTTGAGTTCTCTAC 58.943 41.667 1.53 0.00 42.92 2.59
3232 6883 4.452795 GCACTCCTTTTTGAGTTCTCTACC 59.547 45.833 1.53 0.00 42.92 3.18
3233 6884 4.686554 CACTCCTTTTTGAGTTCTCTACCG 59.313 45.833 1.53 0.00 42.92 4.02
3234 6885 4.246458 CTCCTTTTTGAGTTCTCTACCGG 58.754 47.826 0.00 0.00 0.00 5.28
3235 6886 3.007614 TCCTTTTTGAGTTCTCTACCGGG 59.992 47.826 6.32 0.00 0.00 5.73
3236 6887 3.007614 CCTTTTTGAGTTCTCTACCGGGA 59.992 47.826 6.32 0.00 0.00 5.14
3278 6941 4.020307 ACCCTGGCTGAATATTGTTTTTGG 60.020 41.667 0.00 0.00 0.00 3.28
3280 6943 3.934579 CTGGCTGAATATTGTTTTTGGCC 59.065 43.478 0.00 0.00 37.77 5.36
3281 6944 3.582208 TGGCTGAATATTGTTTTTGGCCT 59.418 39.130 3.32 0.00 38.07 5.19
3282 6945 4.041444 TGGCTGAATATTGTTTTTGGCCTT 59.959 37.500 3.32 0.00 38.07 4.35
3283 6946 5.003160 GGCTGAATATTGTTTTTGGCCTTT 58.997 37.500 3.32 0.00 34.86 3.11
3284 6947 5.473162 GGCTGAATATTGTTTTTGGCCTTTT 59.527 36.000 3.32 0.00 34.86 2.27
3285 6948 6.016360 GGCTGAATATTGTTTTTGGCCTTTTT 60.016 34.615 3.32 0.00 34.86 1.94
3313 6976 5.523438 TTTTGGCTTGTAAAAGTACCCTG 57.477 39.130 0.00 0.00 0.00 4.45
3328 6996 1.140452 ACCCTGCTATCAGATGCACAG 59.860 52.381 0.00 0.00 42.95 3.66
3329 6997 1.140452 CCCTGCTATCAGATGCACAGT 59.860 52.381 0.00 0.00 42.95 3.55
3330 6998 2.481854 CCTGCTATCAGATGCACAGTC 58.518 52.381 0.00 0.00 42.95 3.51
3331 6999 2.159000 CCTGCTATCAGATGCACAGTCA 60.159 50.000 0.00 0.00 42.95 3.41
3332 7000 3.124560 CTGCTATCAGATGCACAGTCAG 58.875 50.000 0.00 0.00 42.95 3.51
3333 7001 2.762327 TGCTATCAGATGCACAGTCAGA 59.238 45.455 0.00 0.00 33.94 3.27
3429 7101 3.437049 CGTGACAGACAGTACAGATGAGA 59.563 47.826 0.00 0.00 0.00 3.27
3438 7110 7.866898 CAGACAGTACAGATGAGATATTTCTGG 59.133 40.741 0.00 0.00 40.92 3.86
3500 7172 4.305769 CATTTTCATGCCGGTTTCAGAAA 58.694 39.130 1.90 4.53 0.00 2.52
3511 7183 4.226761 CGGTTTCAGAAATTGCAGTTACC 58.773 43.478 0.00 0.00 0.00 2.85
3513 7185 4.038642 GGTTTCAGAAATTGCAGTTACCCA 59.961 41.667 0.00 0.00 0.00 4.51
3519 7193 6.211184 TCAGAAATTGCAGTTACCCATTGATT 59.789 34.615 0.00 0.00 0.00 2.57
3535 7209 7.986889 ACCCATTGATTACCAAAATTATGCTTC 59.013 33.333 0.00 0.00 38.43 3.86
3546 7220 6.532657 CCAAAATTATGCTTCCATTCACAGTC 59.467 38.462 0.00 0.00 32.85 3.51
3547 7221 5.841957 AATTATGCTTCCATTCACAGTCC 57.158 39.130 0.00 0.00 32.85 3.85
3552 7232 3.274288 GCTTCCATTCACAGTCCTAAGG 58.726 50.000 0.00 0.00 0.00 2.69
3559 7239 5.711976 CCATTCACAGTCCTAAGGAACAAAT 59.288 40.000 0.00 0.00 31.38 2.32
3567 7248 5.652452 AGTCCTAAGGAACAAATAATGGTGC 59.348 40.000 0.00 0.00 37.33 5.01
3609 7290 8.816640 ATTTTATTCTGTTGTTAAAGGCACTG 57.183 30.769 0.00 0.00 40.86 3.66
3611 7292 4.630894 TTCTGTTGTTAAAGGCACTGTG 57.369 40.909 2.76 2.76 40.86 3.66
3617 7298 6.062749 TGTTGTTAAAGGCACTGTGGTATAA 58.937 36.000 10.21 0.00 40.86 0.98
3618 7299 6.016943 TGTTGTTAAAGGCACTGTGGTATAAC 60.017 38.462 10.21 0.00 40.86 1.89
3619 7300 5.871834 TGTTAAAGGCACTGTGGTATAACT 58.128 37.500 10.21 0.00 40.86 2.24
3620 7301 7.006865 TGTTAAAGGCACTGTGGTATAACTA 57.993 36.000 10.21 0.00 40.86 2.24
3642 7357 7.752695 ACTAGTAAATAAGTTGCTGAACATGC 58.247 34.615 0.00 0.00 33.71 4.06
3643 7358 6.824305 AGTAAATAAGTTGCTGAACATGCT 57.176 33.333 0.00 0.00 34.17 3.79
3644 7359 7.921786 AGTAAATAAGTTGCTGAACATGCTA 57.078 32.000 0.00 0.00 34.17 3.49
3645 7360 8.335532 AGTAAATAAGTTGCTGAACATGCTAA 57.664 30.769 0.00 0.00 34.17 3.09
3646 7361 8.454106 AGTAAATAAGTTGCTGAACATGCTAAG 58.546 33.333 0.00 0.00 34.17 2.18
3647 7362 3.565905 AAGTTGCTGAACATGCTAAGC 57.434 42.857 0.00 0.00 34.17 3.09
3648 7363 2.507484 AGTTGCTGAACATGCTAAGCA 58.493 42.857 3.88 3.88 43.60 3.91
3649 7364 2.486982 AGTTGCTGAACATGCTAAGCAG 59.513 45.455 8.17 2.97 45.68 4.24
3650 7365 2.477845 TGCTGAACATGCTAAGCAGA 57.522 45.000 3.88 0.00 43.65 4.26
3651 7366 2.995283 TGCTGAACATGCTAAGCAGAT 58.005 42.857 3.88 0.00 43.65 2.90
3652 7367 4.141233 TGCTGAACATGCTAAGCAGATA 57.859 40.909 3.88 0.00 43.65 1.98
3656 7371 5.008415 GCTGAACATGCTAAGCAGATATTGT 59.992 40.000 0.17 0.00 43.65 2.71
3662 7377 5.801350 TGCTAAGCAGATATTGTGTGTTC 57.199 39.130 0.00 0.00 33.32 3.18
3678 7393 1.760029 TGTTCTGTGGTGCTGACACTA 59.240 47.619 7.34 0.00 46.57 2.74
3682 7397 1.069204 CTGTGGTGCTGACACTAGTGT 59.931 52.381 28.27 28.27 46.57 3.55
3692 7407 3.606886 CACTAGTGTGGCGAAACCT 57.393 52.632 15.06 0.00 40.33 3.50
3696 7429 4.110482 CACTAGTGTGGCGAAACCTATAC 58.890 47.826 15.06 0.00 40.33 1.47
3698 7431 1.547372 AGTGTGGCGAAACCTATACGT 59.453 47.619 0.00 0.00 40.22 3.57
3701 7434 2.159254 TGTGGCGAAACCTATACGTACC 60.159 50.000 0.00 0.00 40.22 3.34
3706 7439 2.603173 CGAAACCTATACGTACCGGAGC 60.603 54.545 9.46 0.00 0.00 4.70
3713 7446 1.651240 TACGTACCGGAGCTCACAGC 61.651 60.000 17.19 0.00 42.84 4.40
3743 8229 1.105457 GTAGCAAATGCCCATCTGCA 58.895 50.000 9.03 0.00 46.94 4.41
3748 8234 1.094785 AAATGCCCATCTGCACGTAC 58.905 50.000 0.00 0.00 45.48 3.67
3767 8253 3.356529 ACAACCTGAGCAGAATTAGGG 57.643 47.619 0.00 0.00 34.60 3.53
3772 8258 3.844211 ACCTGAGCAGAATTAGGGTGTAA 59.156 43.478 0.00 0.00 34.60 2.41
3773 8259 4.475016 ACCTGAGCAGAATTAGGGTGTAAT 59.525 41.667 0.00 0.00 34.60 1.89
3774 8260 5.665812 ACCTGAGCAGAATTAGGGTGTAATA 59.334 40.000 0.00 0.00 34.60 0.98
3782 8268 7.556635 GCAGAATTAGGGTGTAATAAAGAACCT 59.443 37.037 0.00 0.00 33.02 3.50
3800 8322 8.567285 AAGAACCTATTACAGATCAAAACCAG 57.433 34.615 0.00 0.00 0.00 4.00
3806 8328 2.404215 ACAGATCAAAACCAGTCGTCG 58.596 47.619 0.00 0.00 0.00 5.12
3814 8336 2.509336 CCAGTCGTCGGTGGATGC 60.509 66.667 8.44 0.00 35.67 3.91
3817 8339 1.679305 AGTCGTCGGTGGATGCTCT 60.679 57.895 0.00 0.00 0.00 4.09
3826 8348 1.661341 GTGGATGCTCTTGCTACAGG 58.339 55.000 0.00 0.00 40.48 4.00
3886 8409 0.173708 GCCTCTCGACCTCAACGAAT 59.826 55.000 0.00 0.00 39.23 3.34
3896 8419 2.676342 ACCTCAACGAATAAACCATCGC 59.324 45.455 0.00 0.00 42.61 4.58
3899 8422 2.092995 TCAACGAATAAACCATCGCACG 59.907 45.455 0.00 0.00 42.61 5.34
3900 8423 1.717194 ACGAATAAACCATCGCACGT 58.283 45.000 0.00 0.00 42.61 4.49
3901 8424 1.657094 ACGAATAAACCATCGCACGTC 59.343 47.619 0.00 0.00 42.61 4.34
3902 8425 1.924524 CGAATAAACCATCGCACGTCT 59.075 47.619 0.00 0.00 31.71 4.18
3903 8426 3.110358 CGAATAAACCATCGCACGTCTA 58.890 45.455 0.00 0.00 31.71 2.59
3904 8427 3.179795 CGAATAAACCATCGCACGTCTAG 59.820 47.826 0.00 0.00 31.71 2.43
3942 8465 3.399181 CGTGCTGCCTTCCCCCTA 61.399 66.667 0.00 0.00 0.00 3.53
3943 8466 2.746375 CGTGCTGCCTTCCCCCTAT 61.746 63.158 0.00 0.00 0.00 2.57
3977 8500 5.104776 TCCTTGCTACTTCTACCTCGTACTA 60.105 44.000 0.00 0.00 0.00 1.82
4002 8525 6.040842 AGTGCTTTCAGGTGTGTTGAATATTT 59.959 34.615 0.00 0.00 34.76 1.40
4021 8544 9.698617 GAATATTTGAGCAATTTTTCATCAAGC 57.301 29.630 0.00 0.00 32.00 4.01
4023 8546 7.739498 ATTTGAGCAATTTTTCATCAAGCTT 57.261 28.000 0.00 0.00 32.00 3.74
4028 8551 8.928733 TGAGCAATTTTTCATCAAGCTTAATTC 58.071 29.630 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 9.533831 CCCTAGAGGCAATAATAAAATGGTTAT 57.466 33.333 0.00 0.00 0.00 1.89
16 17 8.934023 CCCTAGAGGCAATAATAAAATGGTTA 57.066 34.615 0.00 0.00 0.00 2.85
17 18 7.839680 CCCTAGAGGCAATAATAAAATGGTT 57.160 36.000 0.00 0.00 0.00 3.67
33 34 4.137543 GTGTTGGAAATATGCCCTAGAGG 58.862 47.826 0.00 0.00 39.47 3.69
34 35 5.041191 AGTGTTGGAAATATGCCCTAGAG 57.959 43.478 0.00 0.00 0.00 2.43
35 36 6.569127 TTAGTGTTGGAAATATGCCCTAGA 57.431 37.500 0.00 0.00 0.00 2.43
36 37 6.998074 TGATTAGTGTTGGAAATATGCCCTAG 59.002 38.462 0.00 0.00 0.00 3.02
37 38 6.770785 GTGATTAGTGTTGGAAATATGCCCTA 59.229 38.462 0.00 0.00 0.00 3.53
38 39 5.594317 GTGATTAGTGTTGGAAATATGCCCT 59.406 40.000 0.00 0.00 0.00 5.19
39 40 5.359576 TGTGATTAGTGTTGGAAATATGCCC 59.640 40.000 0.00 0.00 0.00 5.36
40 41 6.449635 TGTGATTAGTGTTGGAAATATGCC 57.550 37.500 0.00 0.00 0.00 4.40
41 42 7.706159 TGATGTGATTAGTGTTGGAAATATGC 58.294 34.615 0.00 0.00 0.00 3.14
42 43 9.673454 CATGATGTGATTAGTGTTGGAAATATG 57.327 33.333 0.00 0.00 0.00 1.78
43 44 8.853126 CCATGATGTGATTAGTGTTGGAAATAT 58.147 33.333 0.00 0.00 0.00 1.28
44 45 8.052141 TCCATGATGTGATTAGTGTTGGAAATA 58.948 33.333 0.00 0.00 0.00 1.40
45 46 6.891361 TCCATGATGTGATTAGTGTTGGAAAT 59.109 34.615 0.00 0.00 0.00 2.17
46 47 6.150976 GTCCATGATGTGATTAGTGTTGGAAA 59.849 38.462 0.00 0.00 32.90 3.13
47 48 5.647658 GTCCATGATGTGATTAGTGTTGGAA 59.352 40.000 0.00 0.00 32.90 3.53
48 49 5.045651 AGTCCATGATGTGATTAGTGTTGGA 60.046 40.000 0.00 0.00 0.00 3.53
49 50 5.188434 AGTCCATGATGTGATTAGTGTTGG 58.812 41.667 0.00 0.00 0.00 3.77
50 51 7.550551 ACTTAGTCCATGATGTGATTAGTGTTG 59.449 37.037 0.00 0.00 0.00 3.33
51 52 7.624549 ACTTAGTCCATGATGTGATTAGTGTT 58.375 34.615 0.00 0.00 0.00 3.32
52 53 7.093333 TGACTTAGTCCATGATGTGATTAGTGT 60.093 37.037 10.10 0.00 0.00 3.55
53 54 7.267857 TGACTTAGTCCATGATGTGATTAGTG 58.732 38.462 10.10 0.00 0.00 2.74
54 55 7.423844 TGACTTAGTCCATGATGTGATTAGT 57.576 36.000 10.10 0.00 0.00 2.24
173 174 2.156891 GCATTCATTTTGTGCAGTGCAG 59.843 45.455 20.42 5.67 40.08 4.41
243 245 2.717390 TCATTTCGTACCCACCAATGG 58.283 47.619 0.00 0.00 46.81 3.16
269 271 3.383761 GCATATGTGGCCAATAACTTGC 58.616 45.455 7.24 9.01 0.00 4.01
466 468 5.300539 TCCAACTTTTCATTCAAATCACCGA 59.699 36.000 0.00 0.00 0.00 4.69
520 522 7.616528 TTTTCAAAAATGAAGGAAGGGAGAT 57.383 32.000 0.00 0.00 0.00 2.75
714 732 9.979270 CACAACTACTATTGACAGATGATTTTC 57.021 33.333 0.00 0.00 33.57 2.29
715 733 9.507329 ACACAACTACTATTGACAGATGATTTT 57.493 29.630 0.00 0.00 33.57 1.82
716 734 9.155975 GACACAACTACTATTGACAGATGATTT 57.844 33.333 0.00 0.00 33.57 2.17
717 735 8.314021 TGACACAACTACTATTGACAGATGATT 58.686 33.333 0.00 0.00 33.57 2.57
718 736 7.761704 GTGACACAACTACTATTGACAGATGAT 59.238 37.037 0.00 0.00 33.57 2.45
722 740 6.399639 TGTGACACAACTACTATTGACAGA 57.600 37.500 5.62 0.00 33.57 3.41
790 808 8.929746 GCAGATCAATCAAACAGATATATTCGA 58.070 33.333 0.00 0.00 35.39 3.71
791 809 8.715088 TGCAGATCAATCAAACAGATATATTCG 58.285 33.333 0.00 0.00 35.39 3.34
1526 1620 3.637273 GCCGGTGGAAGGAGGTGT 61.637 66.667 1.90 0.00 0.00 4.16
1849 1952 0.527817 CTGATACGGAGGCGTGAACC 60.528 60.000 0.00 0.00 0.00 3.62
2038 2144 1.589993 CAATCTCGAGCGCGTGGAT 60.590 57.895 10.30 11.85 38.98 3.41
2099 2205 5.120830 CACCTAATGAGTGTTAAGTGCAGAC 59.879 44.000 0.00 0.00 0.00 3.51
2328 2448 6.404844 GGGACGAACAGATATCGATATGACAT 60.405 42.308 22.37 6.39 42.76 3.06
2525 3558 4.394920 TCGAATGGACTGGATAGCAAAAAC 59.605 41.667 0.00 0.00 0.00 2.43
2841 4045 1.265454 GGATCCTGACACCGGACCTT 61.265 60.000 9.46 0.00 32.41 3.50
3040 6556 5.948162 AGCATCAGTACCATGATCAAAAACT 59.052 36.000 0.00 0.00 37.84 2.66
3215 6854 4.267349 TCCCGGTAGAGAACTCAAAAAG 57.733 45.455 0.00 0.00 0.00 2.27
3218 6857 3.257624 GTCTTCCCGGTAGAGAACTCAAA 59.742 47.826 0.00 0.00 0.00 2.69
3224 6875 2.307980 TCTCAGTCTTCCCGGTAGAGAA 59.692 50.000 0.00 0.00 0.00 2.87
3225 6876 1.914108 TCTCAGTCTTCCCGGTAGAGA 59.086 52.381 0.00 0.00 0.00 3.10
3226 6877 2.421751 TCTCAGTCTTCCCGGTAGAG 57.578 55.000 0.00 0.00 0.00 2.43
3227 6878 2.025226 ACATCTCAGTCTTCCCGGTAGA 60.025 50.000 0.00 0.00 0.00 2.59
3228 6879 2.099921 CACATCTCAGTCTTCCCGGTAG 59.900 54.545 0.00 0.00 0.00 3.18
3229 6880 2.100197 CACATCTCAGTCTTCCCGGTA 58.900 52.381 0.00 0.00 0.00 4.02
3230 6881 0.898320 CACATCTCAGTCTTCCCGGT 59.102 55.000 0.00 0.00 0.00 5.28
3231 6882 0.176680 CCACATCTCAGTCTTCCCGG 59.823 60.000 0.00 0.00 0.00 5.73
3232 6883 1.186200 TCCACATCTCAGTCTTCCCG 58.814 55.000 0.00 0.00 0.00 5.14
3233 6884 2.569404 ACTTCCACATCTCAGTCTTCCC 59.431 50.000 0.00 0.00 0.00 3.97
3234 6885 3.971245 ACTTCCACATCTCAGTCTTCC 57.029 47.619 0.00 0.00 0.00 3.46
3235 6886 4.382147 GGGTACTTCCACATCTCAGTCTTC 60.382 50.000 0.00 0.00 38.11 2.87
3236 6887 3.515901 GGGTACTTCCACATCTCAGTCTT 59.484 47.826 0.00 0.00 38.11 3.01
3313 6976 3.122297 GTCTGACTGTGCATCTGATAGC 58.878 50.000 0.00 0.00 0.00 2.97
3328 6996 9.409312 CACATCTCAGAATCATATTAGTCTGAC 57.591 37.037 11.91 0.00 43.51 3.51
3329 6997 8.583296 CCACATCTCAGAATCATATTAGTCTGA 58.417 37.037 14.46 14.46 45.47 3.27
3330 6998 8.583296 TCCACATCTCAGAATCATATTAGTCTG 58.417 37.037 7.83 7.83 41.70 3.51
3331 6999 8.718158 TCCACATCTCAGAATCATATTAGTCT 57.282 34.615 0.00 0.00 0.00 3.24
3332 7000 9.941325 ATTCCACATCTCAGAATCATATTAGTC 57.059 33.333 0.00 0.00 0.00 2.59
3333 7001 9.722184 CATTCCACATCTCAGAATCATATTAGT 57.278 33.333 0.00 0.00 0.00 2.24
3418 7090 8.607459 CAACAACCAGAAATATCTCATCTGTAC 58.393 37.037 0.00 0.00 39.10 2.90
3429 7101 7.038799 AGCTTCCAAATCAACAACCAGAAATAT 60.039 33.333 0.00 0.00 0.00 1.28
3438 7110 8.850156 ACCATATATAGCTTCCAAATCAACAAC 58.150 33.333 0.00 0.00 0.00 3.32
3492 7164 6.041409 TCAATGGGTAACTGCAATTTCTGAAA 59.959 34.615 5.15 5.15 0.00 2.69
3500 7172 5.268387 TGGTAATCAATGGGTAACTGCAAT 58.732 37.500 0.00 0.00 0.00 3.56
3511 7183 7.986320 TGGAAGCATAATTTTGGTAATCAATGG 59.014 33.333 0.93 0.00 34.98 3.16
3519 7193 7.178274 ACTGTGAATGGAAGCATAATTTTGGTA 59.822 33.333 0.93 0.00 0.00 3.25
3535 7209 4.286297 TGTTCCTTAGGACTGTGAATGG 57.714 45.455 0.00 0.00 0.00 3.16
3546 7220 4.733523 GCGCACCATTATTTGTTCCTTAGG 60.734 45.833 0.30 0.00 0.00 2.69
3547 7221 4.096382 AGCGCACCATTATTTGTTCCTTAG 59.904 41.667 11.47 0.00 0.00 2.18
3552 7232 2.345341 GCAAGCGCACCATTATTTGTTC 59.655 45.455 11.47 0.00 38.36 3.18
3559 7239 0.893270 AACAGGCAAGCGCACCATTA 60.893 50.000 11.47 0.00 41.24 1.90
3567 7248 7.542130 AGAATAAAATTTTAGAACAGGCAAGCG 59.458 33.333 15.45 0.00 0.00 4.68
3617 7298 7.607991 AGCATGTTCAGCAACTTATTTACTAGT 59.392 33.333 0.00 0.00 33.17 2.57
3618 7299 7.978982 AGCATGTTCAGCAACTTATTTACTAG 58.021 34.615 0.00 0.00 33.17 2.57
3619 7300 7.921786 AGCATGTTCAGCAACTTATTTACTA 57.078 32.000 0.00 0.00 33.17 1.82
3620 7301 6.824305 AGCATGTTCAGCAACTTATTTACT 57.176 33.333 0.00 0.00 33.17 2.24
3632 7347 5.008415 ACAATATCTGCTTAGCATGTTCAGC 59.992 40.000 7.58 8.64 38.13 4.26
3634 7349 5.882000 ACACAATATCTGCTTAGCATGTTCA 59.118 36.000 7.58 0.00 38.13 3.18
3635 7350 6.183360 ACACACAATATCTGCTTAGCATGTTC 60.183 38.462 7.58 0.00 38.13 3.18
3641 7356 5.352569 ACAGAACACACAATATCTGCTTAGC 59.647 40.000 0.00 0.00 42.34 3.09
3642 7357 6.183360 CCACAGAACACACAATATCTGCTTAG 60.183 42.308 1.77 0.00 42.34 2.18
3643 7358 5.643348 CCACAGAACACACAATATCTGCTTA 59.357 40.000 1.77 0.00 42.34 3.09
3644 7359 4.456911 CCACAGAACACACAATATCTGCTT 59.543 41.667 1.77 0.00 42.34 3.91
3645 7360 4.005650 CCACAGAACACACAATATCTGCT 58.994 43.478 1.77 0.00 42.34 4.24
3646 7361 3.753272 ACCACAGAACACACAATATCTGC 59.247 43.478 1.77 0.00 42.34 4.26
3647 7362 4.378770 GCACCACAGAACACACAATATCTG 60.379 45.833 0.00 0.00 43.79 2.90
3648 7363 3.753272 GCACCACAGAACACACAATATCT 59.247 43.478 0.00 0.00 0.00 1.98
3649 7364 3.753272 AGCACCACAGAACACACAATATC 59.247 43.478 0.00 0.00 0.00 1.63
3650 7365 3.503363 CAGCACCACAGAACACACAATAT 59.497 43.478 0.00 0.00 0.00 1.28
3651 7366 2.877786 CAGCACCACAGAACACACAATA 59.122 45.455 0.00 0.00 0.00 1.90
3652 7367 1.677576 CAGCACCACAGAACACACAAT 59.322 47.619 0.00 0.00 0.00 2.71
3656 7371 0.251634 TGTCAGCACCACAGAACACA 59.748 50.000 0.00 0.00 0.00 3.72
3662 7377 1.069204 ACACTAGTGTCAGCACCACAG 59.931 52.381 22.95 0.00 46.35 3.66
3678 7393 1.547372 ACGTATAGGTTTCGCCACACT 59.453 47.619 0.00 0.00 40.61 3.55
3682 7397 2.869233 GGTACGTATAGGTTTCGCCA 57.131 50.000 2.98 0.00 40.61 5.69
3692 7407 3.637860 GCTGTGAGCTCCGGTACGTATA 61.638 54.545 12.15 0.00 45.17 1.47
3696 7429 2.202623 GCTGTGAGCTCCGGTACG 60.203 66.667 12.15 0.89 45.88 3.67
3698 7431 1.185618 AGTTGCTGTGAGCTCCGGTA 61.186 55.000 12.15 4.51 42.97 4.02
3701 7434 0.244994 AGTAGTTGCTGTGAGCTCCG 59.755 55.000 12.15 0.52 42.97 4.63
3731 8217 0.035534 TTGTACGTGCAGATGGGCAT 60.036 50.000 6.41 0.00 46.92 4.40
3743 8229 3.402628 AATTCTGCTCAGGTTGTACGT 57.597 42.857 0.00 0.00 0.00 3.57
3748 8234 3.012518 CACCCTAATTCTGCTCAGGTTG 58.987 50.000 0.00 0.00 0.00 3.77
3774 8260 8.934023 TGGTTTTGATCTGTAATAGGTTCTTT 57.066 30.769 0.00 0.00 0.00 2.52
3782 8268 5.803461 CGACGACTGGTTTTGATCTGTAATA 59.197 40.000 0.00 0.00 0.00 0.98
3792 8278 0.531090 TCCACCGACGACTGGTTTTG 60.531 55.000 10.32 0.00 37.72 2.44
3798 8320 1.517257 GAGCATCCACCGACGACTG 60.517 63.158 0.00 0.00 0.00 3.51
3800 8322 1.078759 CAAGAGCATCCACCGACGAC 61.079 60.000 0.00 0.00 33.66 4.34
3806 8328 1.661341 CTGTAGCAAGAGCATCCACC 58.339 55.000 0.00 0.00 45.49 4.61
3814 8336 0.461693 GGCTCAGCCTGTAGCAAGAG 60.462 60.000 9.09 6.89 46.69 2.85
3859 8382 0.105760 AGGTCGAGAGGCATCAGGAT 60.106 55.000 0.00 0.00 37.54 3.24
3870 8393 3.256383 TGGTTTATTCGTTGAGGTCGAGA 59.744 43.478 0.00 0.00 38.52 4.04
3875 8398 2.676342 GCGATGGTTTATTCGTTGAGGT 59.324 45.455 0.00 0.00 0.00 3.85
3886 8409 2.093890 TCCTAGACGTGCGATGGTTTA 58.906 47.619 0.00 0.00 0.00 2.01
3899 8422 2.286872 TCACTCGGATTCGTCCTAGAC 58.713 52.381 0.00 0.00 37.69 2.59
3900 8423 2.169978 TCTCACTCGGATTCGTCCTAGA 59.830 50.000 0.00 0.00 37.69 2.43
3901 8424 2.288458 GTCTCACTCGGATTCGTCCTAG 59.712 54.545 0.00 0.00 37.69 3.02
3902 8425 2.286872 GTCTCACTCGGATTCGTCCTA 58.713 52.381 0.00 0.00 37.69 2.94
3903 8426 1.096416 GTCTCACTCGGATTCGTCCT 58.904 55.000 0.00 0.00 37.69 3.85
3904 8427 0.248134 CGTCTCACTCGGATTCGTCC 60.248 60.000 0.00 0.00 37.69 4.79
3909 8432 2.341101 ACGGCGTCTCACTCGGATT 61.341 57.895 6.77 0.00 0.00 3.01
3935 8458 1.713297 GAAAGCGTAGGATAGGGGGA 58.287 55.000 0.00 0.00 0.00 4.81
3937 8460 1.718280 AGGAAAGCGTAGGATAGGGG 58.282 55.000 0.00 0.00 0.00 4.79
3938 8461 2.807108 GCAAGGAAAGCGTAGGATAGGG 60.807 54.545 0.00 0.00 0.00 3.53
3940 8463 3.460857 AGCAAGGAAAGCGTAGGATAG 57.539 47.619 0.00 0.00 37.01 2.08
3941 8464 3.958798 AGTAGCAAGGAAAGCGTAGGATA 59.041 43.478 0.00 0.00 37.01 2.59
3942 8465 2.766828 AGTAGCAAGGAAAGCGTAGGAT 59.233 45.455 0.00 0.00 37.01 3.24
3943 8466 2.176889 AGTAGCAAGGAAAGCGTAGGA 58.823 47.619 0.00 0.00 37.01 2.94
3977 8500 2.418368 TCAACACACCTGAAAGCACT 57.582 45.000 0.00 0.00 0.00 4.40
4002 8525 8.836268 AATTAAGCTTGATGAAAAATTGCTCA 57.164 26.923 9.86 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.