Multiple sequence alignment - TraesCS6A01G110600

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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 TraesCS6A01G110600 chr6A 100.000 3281 0 0 1 3281 79816147 79812867 0.000000e+00 6059.0
1 TraesCS6A01G110600 chr6A 89.186 1831 109 41 586 2386 79704251 79702480 0.000000e+00 2202.0
2 TraesCS6A01G110600 chr6B 91.557 1895 89 32 525 2386 135997139 135995283 0.000000e+00 2547.0
3 TraesCS6A01G110600 chr6B 93.784 1657 76 14 743 2385 136101666 136100023 0.000000e+00 2464.0
4 TraesCS6A01G110600 chr6B 82.039 1069 152 28 1240 2278 199931539 199932597 0.000000e+00 874.0
5 TraesCS6A01G110600 chr6B 87.165 709 54 21 39 721 136102358 136101661 0.000000e+00 771.0
6 TraesCS6A01G110600 chr6B 82.397 534 49 23 18 534 135997667 135997162 1.090000e-114 424.0
7 TraesCS6A01G110600 chr6B 87.255 204 22 4 2391 2592 692336497 692336698 2.550000e-56 230.0
8 TraesCS6A01G110600 chr6B 74.684 237 50 6 147 376 655842107 655841874 2.690000e-16 97.1
9 TraesCS6A01G110600 chr6B 73.840 237 52 6 147 376 655847572 655847339 5.830000e-13 86.1
10 TraesCS6A01G110600 chr6D 90.948 1889 100 29 541 2386 62325965 62324105 0.000000e+00 2475.0
11 TraesCS6A01G110600 chr6D 94.634 1491 64 10 828 2303 62425494 62424005 0.000000e+00 2296.0
12 TraesCS6A01G110600 chr6D 83.067 1063 150 24 1235 2278 111018299 111019350 0.000000e+00 939.0
13 TraesCS6A01G110600 chr6D 89.744 195 17 3 3089 3280 406004945 406004751 2.530000e-61 246.0
14 TraesCS6A01G110600 chr6D 87.845 181 16 5 3101 3280 10688637 10688812 1.190000e-49 207.0
15 TraesCS6A01G110600 chr6D 89.583 144 6 5 547 687 62426205 62426068 1.210000e-39 174.0
16 TraesCS6A01G110600 chr6D 92.079 101 5 2 2625 2722 10688635 10688535 4.410000e-29 139.0
17 TraesCS6A01G110600 chr4A 87.222 1393 132 33 955 2327 677731794 677730428 0.000000e+00 1544.0
18 TraesCS6A01G110600 chr7B 87.320 1388 127 34 955 2324 2334144 2335500 0.000000e+00 1543.0
19 TraesCS6A01G110600 chr7B 86.869 1089 118 14 1310 2384 2329363 2328286 0.000000e+00 1195.0
20 TraesCS6A01G110600 chr7B 87.000 200 24 2 2390 2589 563656647 563656844 1.180000e-54 224.0
21 TraesCS6A01G110600 chr7A 88.200 1322 118 25 1085 2384 64210788 64209483 0.000000e+00 1543.0
22 TraesCS6A01G110600 chr7A 88.080 646 65 5 1628 2267 64212184 64211545 0.000000e+00 756.0
23 TraesCS6A01G110600 chr7A 89.180 305 23 5 2717 3011 653591143 653591447 4.000000e-99 372.0
24 TraesCS6A01G110600 chr7A 84.177 316 25 7 2724 3015 136290481 136290167 1.930000e-72 283.0
25 TraesCS6A01G110600 chr7A 88.571 140 15 1 3143 3281 482188 482049 5.630000e-38 169.0
26 TraesCS6A01G110600 chr4B 88.961 308 18 6 2718 3015 450930131 450929830 1.860000e-97 366.0
27 TraesCS6A01G110600 chr4B 89.796 245 21 4 3039 3280 450929505 450929262 8.840000e-81 311.0
28 TraesCS6A01G110600 chr4B 88.177 203 22 2 2390 2592 450930552 450930352 1.180000e-59 241.0
29 TraesCS6A01G110600 chr4B 91.089 101 6 2 2625 2722 450930341 450930241 2.050000e-27 134.0
30 TraesCS6A01G110600 chr5B 87.742 310 27 3 2718 3017 471080272 471080580 5.210000e-93 351.0
31 TraesCS6A01G110600 chr5B 86.592 179 20 4 3104 3280 646378849 646378673 9.290000e-46 195.0
32 TraesCS6A01G110600 chr3A 87.296 307 28 5 2717 3014 408035844 408035540 1.130000e-89 340.0
33 TraesCS6A01G110600 chr3A 89.098 266 23 5 3020 3280 408035237 408034973 3.160000e-85 326.0
34 TraesCS6A01G110600 chr3A 85.938 64 6 3 182 244 684709002 684708941 7.600000e-07 65.8
35 TraesCS6A01G110600 chr3D 86.731 309 26 7 2717 3015 384456527 384456830 2.440000e-86 329.0
36 TraesCS6A01G110600 chr3D 87.019 208 25 2 2386 2592 93826188 93826394 1.970000e-57 233.0
37 TraesCS6A01G110600 chr3D 83.607 244 21 9 3039 3280 384463923 384464149 9.220000e-51 211.0
38 TraesCS6A01G110600 chr3D 87.647 170 16 4 3114 3280 467841040 467841207 3.340000e-45 193.0
39 TraesCS6A01G110600 chr3D 79.724 217 25 9 2798 2996 594755420 594755635 4.410000e-29 139.0
40 TraesCS6A01G110600 chr5A 89.840 187 16 3 3096 3280 364348048 364347863 1.520000e-58 237.0
41 TraesCS6A01G110600 chr5A 92.199 141 11 0 2724 2864 704365291 704365431 2.000000e-47 200.0
42 TraesCS6A01G110600 chr5A 91.566 83 6 1 2914 2996 416166443 416166362 2.680000e-21 113.0
43 TraesCS6A01G110600 chr7D 87.192 203 25 1 2390 2592 567973709 567973508 2.550000e-56 230.0
44 TraesCS6A01G110600 chr7D 74.684 237 50 6 147 376 162826318 162826551 2.690000e-16 97.1
45 TraesCS6A01G110600 chr4D 86.321 212 25 4 2382 2592 30519905 30519697 9.160000e-56 228.0
46 TraesCS6A01G110600 chr4D 86.869 198 23 3 2386 2582 394149592 394149397 5.510000e-53 219.0
47 TraesCS6A01G110600 chr3B 82.332 283 23 13 3024 3280 14679014 14678733 1.530000e-53 220.0
48 TraesCS6A01G110600 chr3B 87.368 190 13 6 2838 3017 14679507 14679319 1.190000e-49 207.0
49 TraesCS6A01G110600 chr3B 88.660 97 8 2 2628 2721 14680521 14680425 7.440000e-22 115.0
50 TraesCS6A01G110600 chr1B 86.275 204 26 2 2390 2592 496073904 496073702 1.530000e-53 220.0
51 TraesCS6A01G110600 chr5D 88.108 185 20 2 3097 3280 539648466 539648649 5.510000e-53 219.0
52 TraesCS6A01G110600 chr1A 86.275 204 25 3 2390 2592 26308092 26307891 5.510000e-53 219.0
53 TraesCS6A01G110600 chr1A 91.566 83 6 1 2914 2996 56864529 56864448 2.680000e-21 113.0
54 TraesCS6A01G110600 chr2B 91.489 47 1 2 3024 3067 53996804 53996758 9.830000e-06 62.1
55 TraesCS6A01G110600 chr2A 91.489 47 1 2 3024 3067 35877191 35877145 9.830000e-06 62.1
56 TraesCS6A01G110600 chr2A 91.489 47 1 2 3024 3067 35916703 35916657 9.830000e-06 62.1
57 TraesCS6A01G110600 chrUn 87.037 54 4 2 3024 3074 24969340 24969287 1.270000e-04 58.4


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 TraesCS6A01G110600 chr6A 79812867 79816147 3280 True 6059.0 6059 100.00000 1 3281 1 chr6A.!!$R2 3280
1 TraesCS6A01G110600 chr6A 79702480 79704251 1771 True 2202.0 2202 89.18600 586 2386 1 chr6A.!!$R1 1800
2 TraesCS6A01G110600 chr6B 136100023 136102358 2335 True 1617.5 2464 90.47450 39 2385 2 chr6B.!!$R4 2346
3 TraesCS6A01G110600 chr6B 135995283 135997667 2384 True 1485.5 2547 86.97700 18 2386 2 chr6B.!!$R3 2368
4 TraesCS6A01G110600 chr6B 199931539 199932597 1058 False 874.0 874 82.03900 1240 2278 1 chr6B.!!$F1 1038
5 TraesCS6A01G110600 chr6D 62324105 62325965 1860 True 2475.0 2475 90.94800 541 2386 1 chr6D.!!$R2 1845
6 TraesCS6A01G110600 chr6D 62424005 62426205 2200 True 1235.0 2296 92.10850 547 2303 2 chr6D.!!$R4 1756
7 TraesCS6A01G110600 chr6D 111018299 111019350 1051 False 939.0 939 83.06700 1235 2278 1 chr6D.!!$F2 1043
8 TraesCS6A01G110600 chr4A 677730428 677731794 1366 True 1544.0 1544 87.22200 955 2327 1 chr4A.!!$R1 1372
9 TraesCS6A01G110600 chr7B 2334144 2335500 1356 False 1543.0 1543 87.32000 955 2324 1 chr7B.!!$F1 1369
10 TraesCS6A01G110600 chr7B 2328286 2329363 1077 True 1195.0 1195 86.86900 1310 2384 1 chr7B.!!$R1 1074
11 TraesCS6A01G110600 chr7A 64209483 64212184 2701 True 1149.5 1543 88.14000 1085 2384 2 chr7A.!!$R3 1299
12 TraesCS6A01G110600 chr4B 450929262 450930552 1290 True 263.0 366 89.50575 2390 3280 4 chr4B.!!$R1 890
13 TraesCS6A01G110600 chr3A 408034973 408035844 871 True 333.0 340 88.19700 2717 3280 2 chr3A.!!$R2 563

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
52 53 0.033781 GCATGCACTTGCCAAAGGAA 59.966 50.000 14.21 0.0 41.18 3.36 F
231 232 0.392998 GAGGCAAATGGCGAGAGGAA 60.393 55.000 0.98 0.0 46.16 3.36 F
274 276 0.531974 GTGTCTTTGACCGTGGCTGA 60.532 55.000 0.00 0.0 0.00 4.26 F
890 1451 1.565759 CCAATCCCACATCCCTCTTCA 59.434 52.381 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1767 2415 1.228154 GGTCCAGCCGTTGTTTCCT 60.228 57.895 0.00 0.0 0.00 3.36 R
1770 2418 1.528309 CTGGGTCCAGCCGTTGTTT 60.528 57.895 3.86 0.0 37.24 2.83 R
1848 2496 2.170187 CAGCTTGCCTACTCTCAGGAAT 59.830 50.000 0.00 0.0 38.00 3.01 R
2485 3163 0.184933 CCAGGGGGTGTTTTGTCTGA 59.815 55.000 0.00 0.0 0.00 3.27 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
29 30 3.259374 TGCCAAAGGGATTCGCATAAAAA 59.741 39.130 3.36 0.00 29.67 1.94
51 52 0.828762 AGCATGCACTTGCCAAAGGA 60.829 50.000 21.98 0.00 43.83 3.36
52 53 0.033781 GCATGCACTTGCCAAAGGAA 59.966 50.000 14.21 0.00 41.18 3.36
92 93 4.385405 GCTCACCGCACAGAGGCT 62.385 66.667 0.00 0.00 38.92 4.58
123 124 7.786178 AGTGTCAAATATAATTAGAAGCGCA 57.214 32.000 11.47 0.00 0.00 6.09
171 172 0.612174 TGAGACCTGCTCTACCGCTT 60.612 55.000 0.00 0.00 44.27 4.68
173 174 0.900647 AGACCTGCTCTACCGCTTGT 60.901 55.000 0.00 0.00 0.00 3.16
214 215 5.333492 GGATGAAGTAGACTACGATGACGAG 60.333 48.000 6.98 0.00 42.66 4.18
230 231 1.221840 GAGGCAAATGGCGAGAGGA 59.778 57.895 0.98 0.00 46.16 3.71
231 232 0.392998 GAGGCAAATGGCGAGAGGAA 60.393 55.000 0.98 0.00 46.16 3.36
272 274 1.594293 CGTGTCTTTGACCGTGGCT 60.594 57.895 0.00 0.00 0.00 4.75
274 276 0.531974 GTGTCTTTGACCGTGGCTGA 60.532 55.000 0.00 0.00 0.00 4.26
299 301 8.306313 ACAATGCCGTATATATAGGAGAATCA 57.694 34.615 12.92 4.67 36.25 2.57
331 333 2.068837 TCGCGATCACGGTTTAAACT 57.931 45.000 17.50 0.00 40.15 2.66
362 364 6.016860 GGTTTTCAACTCATAAACTTACCGGT 60.017 38.462 13.98 13.98 33.44 5.28
364 366 5.733620 TCAACTCATAAACTTACCGGTCT 57.266 39.130 12.40 0.00 0.00 3.85
406 408 3.703286 ACAAAAGAAAGTTGCGGTACC 57.297 42.857 0.16 0.16 0.00 3.34
433 437 7.094291 GCAAGGTCATAGACTAGATTATACGGT 60.094 40.741 0.00 0.00 32.47 4.83
443 447 2.561419 AGATTATACGGTGGACCATCGG 59.439 50.000 29.79 12.90 42.81 4.18
492 507 3.616721 AAGGTGAGGCGAGCGTGT 61.617 61.111 0.00 0.00 0.00 4.49
501 516 4.000557 CGAGCGTGTGTGTGTGGC 62.001 66.667 0.00 0.00 0.00 5.01
625 682 4.090761 ACATGGAGTGTGAGTGTGAATT 57.909 40.909 0.00 0.00 40.28 2.17
629 686 2.427506 GAGTGTGAGTGTGAATTCCCC 58.572 52.381 2.27 0.00 0.00 4.81
632 689 1.774254 TGTGAGTGTGAATTCCCCACT 59.226 47.619 21.36 21.36 41.90 4.00
633 690 2.154462 GTGAGTGTGAATTCCCCACTG 58.846 52.381 24.51 0.00 39.43 3.66
664 729 6.429385 GGCTTAAACTAATCCATCCATCTCTG 59.571 42.308 0.00 0.00 0.00 3.35
690 757 5.168569 CAGTTGCAGAAACGGTCTCTAATA 58.831 41.667 0.00 0.00 44.04 0.98
694 767 6.903883 TGCAGAAACGGTCTCTAATATTTC 57.096 37.500 0.00 0.00 32.70 2.17
890 1451 1.565759 CCAATCCCACATCCCTCTTCA 59.434 52.381 0.00 0.00 0.00 3.02
946 1515 1.878522 CCACTTCGATCGCCTTCGG 60.879 63.158 11.09 3.12 39.56 4.30
1068 1660 4.148825 CTCCCTTCCACCTCCGCG 62.149 72.222 0.00 0.00 0.00 6.46
1254 1861 2.512515 GAGAAGCTCCGCGCCATT 60.513 61.111 0.00 0.00 40.39 3.16
1600 2210 1.901948 AAGGACGACGTGCAGGAGA 60.902 57.895 21.84 0.00 0.00 3.71
1744 2392 2.224621 CCCAAGAGGTCAAAGAGCTTCA 60.225 50.000 0.00 0.00 40.67 3.02
1848 2496 2.347490 GCCAAGGACGAGCAGGAA 59.653 61.111 0.00 0.00 0.00 3.36
2282 2933 2.509569 TGCCGGCAAACTCTTTTGATA 58.490 42.857 30.74 0.00 44.38 2.15
2342 3016 4.820897 TGAACTCGTCAAATCTGCATAGT 58.179 39.130 0.00 0.00 31.51 2.12
2343 3017 5.961272 TGAACTCGTCAAATCTGCATAGTA 58.039 37.500 0.00 0.00 31.51 1.82
2344 3018 6.036470 TGAACTCGTCAAATCTGCATAGTAG 58.964 40.000 0.00 0.00 31.51 2.57
2345 3019 5.584253 ACTCGTCAAATCTGCATAGTAGT 57.416 39.130 0.00 0.00 0.00 2.73
2346 3020 5.967088 ACTCGTCAAATCTGCATAGTAGTT 58.033 37.500 0.00 0.00 0.00 2.24
2347 3021 6.037098 ACTCGTCAAATCTGCATAGTAGTTC 58.963 40.000 0.00 0.00 0.00 3.01
2348 3022 5.348986 TCGTCAAATCTGCATAGTAGTTCC 58.651 41.667 0.00 0.00 0.00 3.62
2349 3023 5.127194 TCGTCAAATCTGCATAGTAGTTCCT 59.873 40.000 0.00 0.00 0.00 3.36
2350 3024 5.233050 CGTCAAATCTGCATAGTAGTTCCTG 59.767 44.000 0.00 0.00 0.00 3.86
2351 3025 5.525378 GTCAAATCTGCATAGTAGTTCCTGG 59.475 44.000 0.00 0.00 0.00 4.45
2387 3065 9.675464 TTCTTTTGTAAGGTAGAAACTGAAAGA 57.325 29.630 0.00 0.00 32.65 2.52
2388 3066 9.675464 TCTTTTGTAAGGTAGAAACTGAAAGAA 57.325 29.630 0.00 0.00 32.65 2.52
2456 3134 8.487028 ACTTTATCTCCTGATCTATTTTTCGGT 58.513 33.333 0.00 0.00 34.32 4.69
2467 3145 9.292195 TGATCTATTTTTCGGTTTCTTTTACCT 57.708 29.630 0.00 0.00 33.35 3.08
2469 3147 8.913487 TCTATTTTTCGGTTTCTTTTACCTCT 57.087 30.769 0.00 0.00 33.35 3.69
2470 3148 9.346005 TCTATTTTTCGGTTTCTTTTACCTCTT 57.654 29.630 0.00 0.00 33.35 2.85
2475 3153 6.613755 TCGGTTTCTTTTACCTCTTCAAAG 57.386 37.500 0.00 0.00 33.35 2.77
2487 3165 8.746052 TTACCTCTTCAAAGAAACTCAAATCA 57.254 30.769 0.00 0.00 34.03 2.57
2525 3203 0.766131 TGGTTTTTCTCCACCCGCTA 59.234 50.000 0.00 0.00 31.24 4.26
2545 3223 3.045601 ACTGATGTGGCACTAGTCAAC 57.954 47.619 19.83 0.00 0.00 3.18
2550 3228 0.032952 GTGGCACTAGTCAACGGTGA 59.967 55.000 11.13 0.00 33.32 4.02
2582 3260 2.671682 GGGCTCCCTTGTCAGGTC 59.328 66.667 0.00 0.00 38.79 3.85
2592 3270 2.754552 CCTTGTCAGGTCTCTCTCTCTG 59.245 54.545 0.00 0.00 35.06 3.35
2594 3272 4.566697 CCTTGTCAGGTCTCTCTCTCTGTA 60.567 50.000 0.00 0.00 35.06 2.74
2596 3274 4.522114 TGTCAGGTCTCTCTCTCTGTATG 58.478 47.826 0.00 0.00 0.00 2.39
2598 3276 4.335315 GTCAGGTCTCTCTCTCTGTATGTG 59.665 50.000 0.00 0.00 0.00 3.21
2599 3277 4.018870 TCAGGTCTCTCTCTCTGTATGTGT 60.019 45.833 0.00 0.00 0.00 3.72
2600 3278 4.096231 CAGGTCTCTCTCTCTGTATGTGTG 59.904 50.000 0.00 0.00 0.00 3.82
2601 3279 4.013728 GGTCTCTCTCTCTGTATGTGTGT 58.986 47.826 0.00 0.00 0.00 3.72
2602 3280 4.142491 GGTCTCTCTCTCTGTATGTGTGTG 60.142 50.000 0.00 0.00 0.00 3.82
2603 3281 4.457603 GTCTCTCTCTCTGTATGTGTGTGT 59.542 45.833 0.00 0.00 0.00 3.72
2604 3282 4.457257 TCTCTCTCTCTGTATGTGTGTGTG 59.543 45.833 0.00 0.00 0.00 3.82
2605 3283 4.145052 TCTCTCTCTGTATGTGTGTGTGT 58.855 43.478 0.00 0.00 0.00 3.72
2606 3284 4.022849 TCTCTCTCTGTATGTGTGTGTGTG 60.023 45.833 0.00 0.00 0.00 3.82
2607 3285 3.636764 TCTCTCTGTATGTGTGTGTGTGT 59.363 43.478 0.00 0.00 0.00 3.72
2608 3286 3.716601 TCTCTGTATGTGTGTGTGTGTG 58.283 45.455 0.00 0.00 0.00 3.82
2609 3287 3.132111 TCTCTGTATGTGTGTGTGTGTGT 59.868 43.478 0.00 0.00 0.00 3.72
2610 3288 3.194062 TCTGTATGTGTGTGTGTGTGTG 58.806 45.455 0.00 0.00 0.00 3.82
2611 3289 2.935849 CTGTATGTGTGTGTGTGTGTGT 59.064 45.455 0.00 0.00 0.00 3.72
2612 3290 2.675348 TGTATGTGTGTGTGTGTGTGTG 59.325 45.455 0.00 0.00 0.00 3.82
2613 3291 0.451383 ATGTGTGTGTGTGTGTGTGC 59.549 50.000 0.00 0.00 0.00 4.57
2614 3292 1.225991 GTGTGTGTGTGTGTGTGCG 60.226 57.895 0.00 0.00 0.00 5.34
2615 3293 1.669437 TGTGTGTGTGTGTGTGCGT 60.669 52.632 0.00 0.00 0.00 5.24
2616 3294 1.225991 GTGTGTGTGTGTGTGCGTG 60.226 57.895 0.00 0.00 0.00 5.34
2617 3295 1.669437 TGTGTGTGTGTGTGCGTGT 60.669 52.632 0.00 0.00 0.00 4.49
2618 3296 1.225991 GTGTGTGTGTGTGCGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
2619 3297 1.669437 TGTGTGTGTGTGCGTGTGT 60.669 52.632 0.00 0.00 0.00 3.72
2620 3298 1.225991 GTGTGTGTGTGCGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
2621 3299 1.669437 TGTGTGTGTGCGTGTGTGT 60.669 52.632 0.00 0.00 0.00 3.72
2622 3300 1.225991 GTGTGTGTGCGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
2623 3301 1.669437 TGTGTGTGCGTGTGTGTGT 60.669 52.632 0.00 0.00 0.00 3.72
2638 3316 1.453015 GTGTGTCACAACAGCCCCA 60.453 57.895 7.38 0.00 35.64 4.96
2645 3323 4.305956 CAACAGCCCCAAGCCCCT 62.306 66.667 0.00 0.00 45.47 4.79
2662 3340 1.489481 CCTGACCTCCTCTATGCACA 58.511 55.000 0.00 0.00 0.00 4.57
2737 3532 3.610619 CTCACCAGCGATGCCACCA 62.611 63.158 0.00 0.00 0.00 4.17
2779 3574 2.345244 CAGAGGAGCTTGCACGGT 59.655 61.111 0.00 0.00 0.00 4.83
2791 3586 2.125713 CACGGTGGCGACTGCATA 60.126 61.111 7.70 0.00 45.35 3.14
2806 3601 6.611381 CGACTGCATATGAAGGAAAGAAAAA 58.389 36.000 15.46 0.00 0.00 1.94
2833 3628 8.258007 TGAGGAAGAACTCACGATTGTATTATT 58.742 33.333 0.00 0.00 42.26 1.40
2836 3631 9.745880 GGAAGAACTCACGATTGTATTATTCTA 57.254 33.333 0.00 0.00 0.00 2.10
2847 3642 9.653287 CGATTGTATTATTCTATGGGTGTACAT 57.347 33.333 0.00 0.00 34.90 2.29
2874 3669 1.269361 ACAGATAACACACGCACACGA 60.269 47.619 0.00 0.00 43.93 4.35
2893 3688 5.762218 ACACGACTAGACTAACTAACACAGT 59.238 40.000 0.00 0.00 40.05 3.55
2900 3695 8.582437 ACTAGACTAACTAACACAGTTATGCAA 58.418 33.333 0.00 0.00 46.27 4.08
2901 3696 7.891183 AGACTAACTAACACAGTTATGCAAG 57.109 36.000 0.00 0.00 46.27 4.01
3015 3820 2.443952 ATGTCCTCGCCGGATCCA 60.444 61.111 13.41 0.00 45.44 3.41
3022 4125 2.225791 CTCGCCGGATCCAACAGTGA 62.226 60.000 13.41 8.19 0.00 3.41
3102 4211 4.329638 ACCCAATGAGAGAGAGAGAGAA 57.670 45.455 0.00 0.00 0.00 2.87
3123 4232 5.365314 AGAAAGAGAGAGAAACCTGACAAGT 59.635 40.000 0.00 0.00 0.00 3.16
3131 4240 4.722700 CCTGACAAGTGGGCCCCG 62.723 72.222 22.27 7.78 0.00 5.73
3132 4241 3.953775 CTGACAAGTGGGCCCCGT 61.954 66.667 22.27 11.50 0.00 5.28
3134 4243 3.637273 GACAAGTGGGCCCCGTCT 61.637 66.667 22.27 12.56 0.00 4.18
3175 4284 4.019312 TGCCACATCAGCAGCGGA 62.019 61.111 0.00 0.00 34.69 5.54
3191 4300 0.447801 CGGATGGAGAAAAACCAGCG 59.552 55.000 0.00 0.00 43.64 5.18
3213 4323 0.825410 GGGGTGTTTTGTCCGGTTTT 59.175 50.000 0.00 0.00 0.00 2.43
3215 4325 1.477295 GGGTGTTTTGTCCGGTTTTGA 59.523 47.619 0.00 0.00 0.00 2.69
3271 4382 1.525175 TGGGGTAAAGTGAACCACCT 58.475 50.000 0.00 0.00 39.89 4.00
3273 4384 3.261962 TGGGGTAAAGTGAACCACCTAT 58.738 45.455 0.00 0.00 39.89 2.57
3280 4391 8.809066 GGGTAAAGTGAACCACCTATTTTATTT 58.191 33.333 0.00 0.00 38.87 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.109132 GCGAATCCCTTTGGCAAGTG 60.109 55.000 0.00 0.00 38.76 3.16
8 9 3.518634 TTTTATGCGAATCCCTTTGGC 57.481 42.857 0.00 0.00 39.31 4.52
29 30 2.093869 CCTTTGGCAAGTGCATGCTATT 60.094 45.455 20.33 10.63 45.68 1.73
52 53 8.007405 AGCTTTACATGTAGAAACACCTTTTT 57.993 30.769 5.56 0.00 38.78 1.94
112 113 2.985896 TGGTTTAGCTGCGCTTCTAAT 58.014 42.857 17.91 0.00 40.44 1.73
117 118 3.278574 TCATAATGGTTTAGCTGCGCTT 58.721 40.909 9.73 0.00 40.44 4.68
121 122 9.846248 CCTTATAAATCATAATGGTTTAGCTGC 57.154 33.333 0.00 0.00 36.50 5.25
144 145 0.980423 GAGCAGGTCTCAGGAACCTT 59.020 55.000 0.00 0.00 41.51 3.50
171 172 3.134792 AAACGCCGTGCACCAACA 61.135 55.556 12.15 0.00 0.00 3.33
173 174 3.893763 CCAAACGCCGTGCACCAA 61.894 61.111 12.15 0.00 0.00 3.67
214 215 1.997928 GCTTCCTCTCGCCATTTGCC 61.998 60.000 0.00 0.00 36.24 4.52
230 231 4.262592 CCAAATCAAGCTAGGGTTTTGCTT 60.263 41.667 0.00 0.00 46.38 3.91
231 232 3.259123 CCAAATCAAGCTAGGGTTTTGCT 59.741 43.478 0.00 0.00 38.87 3.91
272 274 7.712204 TTCTCCTATATATACGGCATTGTCA 57.288 36.000 0.00 0.00 0.00 3.58
274 276 8.306313 TGATTCTCCTATATATACGGCATTGT 57.694 34.615 0.00 0.00 0.00 2.71
299 301 2.257034 GATCGCGAAACTAGACCGTTT 58.743 47.619 15.24 0.00 39.63 3.60
406 408 6.962116 CGTATAATCTAGTCTATGACCTTGCG 59.038 42.308 0.00 0.00 32.18 4.85
422 426 2.561419 CCGATGGTCCACCGTATAATCT 59.439 50.000 4.55 0.00 39.43 2.40
475 490 3.616721 ACACGCTCGCCTCACCTT 61.617 61.111 0.00 0.00 0.00 3.50
492 507 1.134521 AGAAAGAGAACGCCACACACA 60.135 47.619 0.00 0.00 0.00 3.72
501 516 5.063186 CCAATGTGATGAGAGAAAGAGAACG 59.937 44.000 0.00 0.00 0.00 3.95
549 600 8.779303 ACACTTACACATCATTCGTTTATTTCA 58.221 29.630 0.00 0.00 0.00 2.69
555 606 5.295787 ACACACACTTACACATCATTCGTTT 59.704 36.000 0.00 0.00 0.00 3.60
625 682 2.032965 TAAGCCAAGTACAGTGGGGA 57.967 50.000 15.30 0.00 36.58 4.81
629 686 7.073342 GGATTAGTTTAAGCCAAGTACAGTG 57.927 40.000 0.00 0.00 43.52 3.66
664 729 0.586802 GACCGTTTCTGCAACTGTCC 59.413 55.000 4.01 0.00 41.47 4.02
690 757 6.868339 CCGTTTCTATTGCCTGAAAAAGAAAT 59.132 34.615 0.00 0.00 34.57 2.17
694 767 5.048713 AGACCGTTTCTATTGCCTGAAAAAG 60.049 40.000 0.00 0.00 34.52 2.27
700 773 3.190874 GAGAGACCGTTTCTATTGCCTG 58.809 50.000 0.00 0.00 33.22 4.85
816 901 0.671796 GGAAAAGTTTGACCGGGGTG 59.328 55.000 6.32 0.00 0.00 4.61
821 906 3.119495 GGATGATGGGAAAAGTTTGACCG 60.119 47.826 0.00 0.00 0.00 4.79
890 1451 1.135139 CGTCCGTGGAGATGAACTGAT 59.865 52.381 0.00 0.00 0.00 2.90
946 1515 4.459089 GGAGACTGGAGCGGGTGC 62.459 72.222 0.00 0.00 43.24 5.01
1574 2181 2.333938 CGTCGTCCTTGGTCGTGT 59.666 61.111 6.24 0.00 0.00 4.49
1600 2210 3.717294 GAGCACCCGGTCCATGGT 61.717 66.667 12.58 0.00 33.34 3.55
1767 2415 1.228154 GGTCCAGCCGTTGTTTCCT 60.228 57.895 0.00 0.00 0.00 3.36
1770 2418 1.528309 CTGGGTCCAGCCGTTGTTT 60.528 57.895 3.86 0.00 37.24 2.83
1848 2496 2.170187 CAGCTTGCCTACTCTCAGGAAT 59.830 50.000 0.00 0.00 38.00 3.01
2010 2661 3.515316 CTCCACCGTGTTCACCGCT 62.515 63.158 0.00 0.00 0.00 5.52
2282 2933 2.119495 AGTGAGTGAGTGAGTGGGTTT 58.881 47.619 0.00 0.00 0.00 3.27
2342 3016 8.802267 CAAAAGAATTAATGGAACCAGGAACTA 58.198 33.333 0.00 0.00 36.02 2.24
2343 3017 7.290014 ACAAAAGAATTAATGGAACCAGGAACT 59.710 33.333 0.00 0.00 43.88 3.01
2344 3018 7.441836 ACAAAAGAATTAATGGAACCAGGAAC 58.558 34.615 0.00 0.00 0.00 3.62
2345 3019 7.610580 ACAAAAGAATTAATGGAACCAGGAA 57.389 32.000 0.00 0.00 0.00 3.36
2346 3020 8.713708 TTACAAAAGAATTAATGGAACCAGGA 57.286 30.769 0.00 0.00 0.00 3.86
2347 3021 8.034804 CCTTACAAAAGAATTAATGGAACCAGG 58.965 37.037 0.00 0.00 34.37 4.45
2348 3022 8.585018 ACCTTACAAAAGAATTAATGGAACCAG 58.415 33.333 0.00 0.00 34.37 4.00
2349 3023 8.485578 ACCTTACAAAAGAATTAATGGAACCA 57.514 30.769 0.00 0.00 34.37 3.67
2419 3097 9.504708 GATCAGGAGATAAAGTGAATCATTCAT 57.495 33.333 2.67 0.00 36.95 2.57
2436 3114 6.947464 AGAAACCGAAAAATAGATCAGGAGA 58.053 36.000 0.00 0.00 0.00 3.71
2438 3116 7.996098 AAAGAAACCGAAAAATAGATCAGGA 57.004 32.000 0.00 0.00 0.00 3.86
2447 3125 8.002984 TGAAGAGGTAAAAGAAACCGAAAAAT 57.997 30.769 0.00 0.00 42.15 1.82
2449 3127 7.393841 TTGAAGAGGTAAAAGAAACCGAAAA 57.606 32.000 0.00 0.00 42.15 2.29
2467 3145 7.864108 TGTCTGATTTGAGTTTCTTTGAAGA 57.136 32.000 0.00 0.00 0.00 2.87
2469 3147 9.139174 GTTTTGTCTGATTTGAGTTTCTTTGAA 57.861 29.630 0.00 0.00 0.00 2.69
2470 3148 8.303156 TGTTTTGTCTGATTTGAGTTTCTTTGA 58.697 29.630 0.00 0.00 0.00 2.69
2475 3153 5.748630 GGGTGTTTTGTCTGATTTGAGTTTC 59.251 40.000 0.00 0.00 0.00 2.78
2480 3158 2.962421 GGGGGTGTTTTGTCTGATTTGA 59.038 45.455 0.00 0.00 0.00 2.69
2485 3163 0.184933 CCAGGGGGTGTTTTGTCTGA 59.815 55.000 0.00 0.00 0.00 3.27
2487 3165 1.152546 GCCAGGGGGTGTTTTGTCT 60.153 57.895 0.00 0.00 36.17 3.41
2525 3203 2.610479 CGTTGACTAGTGCCACATCAGT 60.610 50.000 0.00 0.00 0.00 3.41
2545 3223 1.302993 ACCCGGGTCAAAATCACCG 60.303 57.895 24.16 0.00 45.57 4.94
2582 3260 4.217334 ACACACACACATACAGAGAGAGAG 59.783 45.833 0.00 0.00 0.00 3.20
2592 3270 2.538737 GCACACACACACACACACATAC 60.539 50.000 0.00 0.00 0.00 2.39
2594 3272 0.451383 GCACACACACACACACACAT 59.549 50.000 0.00 0.00 0.00 3.21
2596 3274 1.225991 CGCACACACACACACACAC 60.226 57.895 0.00 0.00 0.00 3.82
2598 3276 1.225991 CACGCACACACACACACAC 60.226 57.895 0.00 0.00 0.00 3.82
2599 3277 1.669437 ACACGCACACACACACACA 60.669 52.632 0.00 0.00 0.00 3.72
2600 3278 1.225991 CACACGCACACACACACAC 60.226 57.895 0.00 0.00 0.00 3.82
2601 3279 1.669437 ACACACGCACACACACACA 60.669 52.632 0.00 0.00 0.00 3.72
2602 3280 1.225991 CACACACGCACACACACAC 60.226 57.895 0.00 0.00 0.00 3.82
2603 3281 1.669437 ACACACACGCACACACACA 60.669 52.632 0.00 0.00 0.00 3.72
2604 3282 1.225991 CACACACACGCACACACAC 60.226 57.895 0.00 0.00 0.00 3.82
2605 3283 1.669437 ACACACACACGCACACACA 60.669 52.632 0.00 0.00 0.00 3.72
2606 3284 1.225991 CACACACACACGCACACAC 60.226 57.895 0.00 0.00 0.00 3.82
2607 3285 1.631144 GACACACACACACGCACACA 61.631 55.000 0.00 0.00 0.00 3.72
2608 3286 1.060308 GACACACACACACGCACAC 59.940 57.895 0.00 0.00 0.00 3.82
2609 3287 1.374758 TGACACACACACACGCACA 60.375 52.632 0.00 0.00 0.00 4.57
2610 3288 3.480515 TGACACACACACACGCAC 58.519 55.556 0.00 0.00 0.00 5.34
2618 3296 1.724582 GGGGCTGTTGTGACACACAC 61.725 60.000 8.05 10.34 44.47 3.82
2619 3297 1.453015 GGGGCTGTTGTGACACACA 60.453 57.895 8.05 8.97 43.02 3.72
2620 3298 1.034838 TTGGGGCTGTTGTGACACAC 61.035 55.000 8.05 4.59 34.56 3.82
2621 3299 0.751277 CTTGGGGCTGTTGTGACACA 60.751 55.000 3.56 3.56 0.00 3.72
2622 3300 2.032981 CTTGGGGCTGTTGTGACAC 58.967 57.895 0.00 0.00 0.00 3.67
2623 3301 1.827789 GCTTGGGGCTGTTGTGACA 60.828 57.895 0.00 0.00 38.06 3.58
2638 3316 0.644937 ATAGAGGAGGTCAGGGGCTT 59.355 55.000 0.00 0.00 0.00 4.35
2645 3323 0.826715 GCTGTGCATAGAGGAGGTCA 59.173 55.000 15.47 0.00 0.00 4.02
2715 3396 2.265739 GCATCGCTGGTGAGGTCA 59.734 61.111 0.00 0.00 0.00 4.02
2720 3515 2.874648 GATGGTGGCATCGCTGGTGA 62.875 60.000 0.00 0.00 0.00 4.02
2779 3574 0.829990 TCCTTCATATGCAGTCGCCA 59.170 50.000 0.00 0.00 37.32 5.69
2791 3586 8.363390 GTTCTTCCTCATTTTTCTTTCCTTCAT 58.637 33.333 0.00 0.00 0.00 2.57
2806 3601 4.543590 ACAATCGTGAGTTCTTCCTCAT 57.456 40.909 0.00 0.00 43.03 2.90
2847 3642 5.927115 TGTGCGTGTGTTATCTGTGTATAAA 59.073 36.000 0.00 0.00 0.00 1.40
2893 3688 1.762708 GCTGGTTAGCCCTTGCATAA 58.237 50.000 0.00 0.00 44.33 1.90
2934 3738 0.041312 GTGTGTTGTTGCTACGCCAG 60.041 55.000 0.00 0.00 0.00 4.85
2940 3744 3.307512 CACTAACGTGTGTGTTGTTGCTA 59.692 43.478 11.58 0.00 36.39 3.49
2948 3752 0.586319 GCATGCACTAACGTGTGTGT 59.414 50.000 14.21 1.13 43.16 3.72
3015 3820 2.974698 GCTGCTGCCGTCACTGTT 60.975 61.111 3.85 0.00 0.00 3.16
3035 4138 3.327404 TCCCGCCCCTTCTTCCAC 61.327 66.667 0.00 0.00 0.00 4.02
3036 4139 3.009115 CTCCCGCCCCTTCTTCCA 61.009 66.667 0.00 0.00 0.00 3.53
3037 4140 4.491409 GCTCCCGCCCCTTCTTCC 62.491 72.222 0.00 0.00 0.00 3.46
3085 4194 6.962182 TCTCTCTTTCTCTCTCTCTCTCATT 58.038 40.000 0.00 0.00 0.00 2.57
3086 4195 6.385176 TCTCTCTCTTTCTCTCTCTCTCTCAT 59.615 42.308 0.00 0.00 0.00 2.90
3087 4196 5.721480 TCTCTCTCTTTCTCTCTCTCTCTCA 59.279 44.000 0.00 0.00 0.00 3.27
3102 4211 4.202305 CCACTTGTCAGGTTTCTCTCTCTT 60.202 45.833 0.00 0.00 0.00 2.85
3123 4232 3.549433 TTGACCTAGACGGGGCCCA 62.549 63.158 26.86 0.00 36.97 5.36
3131 4240 1.154197 GCGGTGGTTTTGACCTAGAC 58.846 55.000 0.00 0.00 0.00 2.59
3132 4241 1.053424 AGCGGTGGTTTTGACCTAGA 58.947 50.000 0.00 0.00 0.00 2.43
3134 4243 0.759959 TCAGCGGTGGTTTTGACCTA 59.240 50.000 15.67 0.00 0.00 3.08
3150 4259 1.066645 TGCTGATGTGGCACTAGTCAG 60.067 52.381 27.98 27.98 39.35 3.51
3175 4284 1.614317 CCCTCGCTGGTTTTTCTCCAT 60.614 52.381 0.00 0.00 34.26 3.41
3191 4300 1.602605 CCGGACAAAACACCCCCTC 60.603 63.158 0.00 0.00 0.00 4.30
3244 4355 5.123936 GGTTCACTTTACCCCATGATCTAC 58.876 45.833 0.00 0.00 0.00 2.59
3252 4363 1.525175 AGGTGGTTCACTTTACCCCA 58.475 50.000 0.00 0.00 34.66 4.96


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

AutoCloner maintained by Alex Coulton.