Multiple sequence alignment - TraesCS7B01G011200

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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 TraesCS7B01G011200 chr7B 100.000 3005 0 0 1 3005 7039371 7036367 0.000000e+00 5550.0
1 TraesCS7B01G011200 chr7D 93.090 2547 117 25 1 2515 65436318 65438837 0.000000e+00 3674.0
2 TraesCS7B01G011200 chr7D 95.823 407 14 3 2598 3004 65438836 65439239 0.000000e+00 654.0
3 TraesCS7B01G011200 chr7D 84.158 606 56 18 1597 2192 65627000 65626425 4.380000e-153 551.0
4 TraesCS7B01G011200 chr7D 85.455 110 11 3 2242 2348 65626190 65626083 3.170000e-20 110.0
5 TraesCS7B01G011200 chr7D 89.610 77 8 0 1094 1170 65666803 65666727 6.860000e-17 99.0
6 TraesCS7B01G011200 chr7A 94.802 1212 52 2 866 2077 69568139 69569339 0.000000e+00 1879.0
7 TraesCS7B01G011200 chr7A 94.637 1212 54 2 866 2077 69618534 69619734 0.000000e+00 1868.0
8 TraesCS7B01G011200 chr7A 93.888 409 23 2 2598 3005 69620251 69620658 1.530000e-172 616.0
9 TraesCS7B01G011200 chr7A 93.643 409 22 4 2598 3005 69569856 69570261 2.560000e-170 608.0
10 TraesCS7B01G011200 chr7A 79.686 827 119 31 3 812 69617607 69618401 4.380000e-153 551.0
11 TraesCS7B01G011200 chr7A 80.513 390 56 12 3 376 69567255 69567640 6.340000e-72 281.0
12 TraesCS7B01G011200 chr7A 84.483 290 29 12 2233 2515 69569577 69569857 3.820000e-69 272.0
13 TraesCS7B01G011200 chr7A 84.483 290 29 12 2233 2515 69619972 69620252 3.820000e-69 272.0
14 TraesCS7B01G011200 chr7A 92.806 139 7 3 2075 2211 69569459 69569596 6.570000e-47 198.0
15 TraesCS7B01G011200 chr7A 92.806 139 7 3 2075 2211 69619854 69619991 6.570000e-47 198.0
16 TraesCS7B01G011200 chr2B 88.641 986 91 8 1072 2044 110417466 110416489 0.000000e+00 1181.0
17 TraesCS7B01G011200 chr2B 77.983 813 139 32 1181 1985 111035647 111034867 9.750000e-130 473.0
18 TraesCS7B01G011200 chr2B 96.703 91 3 0 2514 2604 160407613 160407523 5.190000e-33 152.0
19 TraesCS7B01G011200 chr2D 87.167 1052 97 16 1072 2093 73009969 73008926 0.000000e+00 1160.0
20 TraesCS7B01G011200 chr2D 79.162 811 133 28 1181 1985 73316904 73317684 2.050000e-146 529.0
21 TraesCS7B01G011200 chr2A 86.819 1047 107 16 1072 2092 71614034 71612993 0.000000e+00 1140.0
22 TraesCS7B01G011200 chr2A 78.202 812 139 27 1181 1985 72697318 72696538 4.500000e-133 484.0
23 TraesCS7B01G011200 chr2A 94.737 95 5 0 2513 2607 630090994 630090900 6.710000e-32 148.0
24 TraesCS7B01G011200 chr5A 97.753 89 2 0 2514 2602 298806913 298806825 1.440000e-33 154.0
25 TraesCS7B01G011200 chr3D 97.727 88 2 0 2514 2601 355714691 355714604 5.190000e-33 152.0
26 TraesCS7B01G011200 chr1D 97.727 88 2 0 2514 2601 195609658 195609571 5.190000e-33 152.0
27 TraesCS7B01G011200 chr1B 96.667 90 3 0 2514 2603 618002463 618002552 1.870000e-32 150.0
28 TraesCS7B01G011200 chr1B 93.069 101 6 1 2501 2601 618002560 618002461 2.410000e-31 147.0
29 TraesCS7B01G011200 chr6B 93.939 99 4 2 2512 2609 339371327 339371424 6.710000e-32 148.0
30 TraesCS7B01G011200 chr6B 91.346 104 9 0 2496 2599 423189494 423189597 3.120000e-30 143.0
31 TraesCS7B01G011200 chr6D 97.059 34 1 0 343 376 20103299 20103332 1.160000e-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 TraesCS7B01G011200 chr7B 7036367 7039371 3004 True 5550.0 5550 100.0000 1 3005 1 chr7B.!!$R1 3004
1 TraesCS7B01G011200 chr7D 65436318 65439239 2921 False 2164.0 3674 94.4565 1 3004 2 chr7D.!!$F1 3003
2 TraesCS7B01G011200 chr7D 65626083 65627000 917 True 330.5 551 84.8065 1597 2348 2 chr7D.!!$R2 751
3 TraesCS7B01G011200 chr7A 69617607 69620658 3051 False 701.0 1868 89.1000 3 3005 5 chr7A.!!$F2 3002
4 TraesCS7B01G011200 chr7A 69567255 69570261 3006 False 647.6 1879 89.2494 3 3005 5 chr7A.!!$F1 3002
5 TraesCS7B01G011200 chr2B 110416489 110417466 977 True 1181.0 1181 88.6410 1072 2044 1 chr2B.!!$R1 972
6 TraesCS7B01G011200 chr2B 111034867 111035647 780 True 473.0 473 77.9830 1181 1985 1 chr2B.!!$R2 804
7 TraesCS7B01G011200 chr2D 73008926 73009969 1043 True 1160.0 1160 87.1670 1072 2093 1 chr2D.!!$R1 1021
8 TraesCS7B01G011200 chr2D 73316904 73317684 780 False 529.0 529 79.1620 1181 1985 1 chr2D.!!$F1 804
9 TraesCS7B01G011200 chr2A 71612993 71614034 1041 True 1140.0 1140 86.8190 1072 2092 1 chr2A.!!$R1 1020
10 TraesCS7B01G011200 chr2A 72696538 72697318 780 True 484.0 484 78.2020 1181 1985 1 chr2A.!!$R2 804

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
770 800 1.002792 GTTTTCACCACTTCACTCGCC 60.003 52.381 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2007 2175 0.179073 CCATTCTCGCCGTCCTCAAT 60.179 55.0 0.0 0.0 0.0 2.57 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
50 51 6.692486 CAGAGTAAGACAAGGATACAACAGT 58.308 40.000 0.00 0.00 41.41 3.55
53 54 7.179338 AGAGTAAGACAAGGATACAACAGTGAT 59.821 37.037 0.00 0.00 41.41 3.06
55 56 5.489792 AGACAAGGATACAACAGTGATGT 57.510 39.130 11.10 11.10 41.41 3.06
170 172 6.238211 GCATGATTTTATTAGTCTGCTCGTGT 60.238 38.462 0.00 0.00 0.00 4.49
217 224 4.576879 TCGCCGACAGTCTATCATATAGT 58.423 43.478 0.00 0.00 0.00 2.12
218 225 5.727434 TCGCCGACAGTCTATCATATAGTA 58.273 41.667 0.00 0.00 0.00 1.82
219 226 6.168389 TCGCCGACAGTCTATCATATAGTAA 58.832 40.000 0.00 0.00 0.00 2.24
220 227 6.822170 TCGCCGACAGTCTATCATATAGTAAT 59.178 38.462 0.00 0.00 0.00 1.89
221 228 7.983484 TCGCCGACAGTCTATCATATAGTAATA 59.017 37.037 0.00 0.00 0.00 0.98
222 229 8.063038 CGCCGACAGTCTATCATATAGTAATAC 58.937 40.741 0.00 0.00 0.00 1.89
251 277 3.773418 TTCCACTGATTCCACCGTTAA 57.227 42.857 0.00 0.00 0.00 2.01
271 297 6.448852 GTTAACTAAAAATTCTTTCGCCCCA 58.551 36.000 0.00 0.00 0.00 4.96
289 315 5.641636 CGCCCCACTTTTTAAATAAAGCAAT 59.358 36.000 0.46 0.00 38.42 3.56
308 334 6.212955 AGCAATTACGCAAACATACAAAGTT 58.787 32.000 0.00 0.00 0.00 2.66
317 343 6.086765 CGCAAACATACAAAGTTTAGAAGCAG 59.913 38.462 0.00 0.00 37.10 4.24
326 352 8.000780 ACAAAGTTTAGAAGCAGAAGTCAAAT 57.999 30.769 0.00 0.00 0.00 2.32
327 353 9.120538 ACAAAGTTTAGAAGCAGAAGTCAAATA 57.879 29.630 0.00 0.00 0.00 1.40
328 354 9.387123 CAAAGTTTAGAAGCAGAAGTCAAATAC 57.613 33.333 0.00 0.00 0.00 1.89
329 355 8.677148 AAGTTTAGAAGCAGAAGTCAAATACA 57.323 30.769 0.00 0.00 0.00 2.29
330 356 8.677148 AGTTTAGAAGCAGAAGTCAAATACAA 57.323 30.769 0.00 0.00 0.00 2.41
377 403 4.499040 CACAACTCAACAAGCCTAAAAACG 59.501 41.667 0.00 0.00 0.00 3.60
380 406 4.916870 ACTCAACAAGCCTAAAAACGTTC 58.083 39.130 0.00 0.00 0.00 3.95
537 566 2.138320 GATGATGTCATCGATGGCGTT 58.862 47.619 24.61 14.90 42.66 4.84
539 568 2.469826 TGATGTCATCGATGGCGTTAC 58.530 47.619 24.61 15.38 38.98 2.50
548 577 2.561549 GATGGCGTTACGTTCCCGGA 62.562 60.000 0.73 0.00 38.78 5.14
567 596 2.203070 CGGCTAAGCGGCTTCCAT 60.203 61.111 20.06 0.00 35.72 3.41
618 648 1.961394 GTATCAGTAGGTCGGCCATCA 59.039 52.381 9.71 0.00 37.19 3.07
673 703 1.613437 CCAAAGCGTTCACCAAAGGAT 59.387 47.619 0.00 0.00 0.00 3.24
685 715 2.225343 ACCAAAGGATCTCAATGCCCAA 60.225 45.455 0.00 0.00 0.00 4.12
693 723 4.464008 GATCTCAATGCCCAACCATCTAA 58.536 43.478 0.00 0.00 0.00 2.10
700 730 2.024414 GCCCAACCATCTAATGTGACC 58.976 52.381 0.00 0.00 0.00 4.02
770 800 1.002792 GTTTTCACCACTTCACTCGCC 60.003 52.381 0.00 0.00 0.00 5.54
835 970 5.483811 TGTTGCTCAAACGGACATATCTAA 58.516 37.500 0.00 0.00 42.10 2.10
836 971 5.350365 TGTTGCTCAAACGGACATATCTAAC 59.650 40.000 0.00 0.00 42.10 2.34
838 973 4.868171 TGCTCAAACGGACATATCTAACAC 59.132 41.667 0.00 0.00 0.00 3.32
943 1080 3.562557 TGTTTGGAGCCTTCGTTAAGTTC 59.437 43.478 0.00 0.00 0.00 3.01
1016 1153 1.739466 GAAGATGTTCCGAGCAATGCA 59.261 47.619 8.35 0.00 0.00 3.96
1739 1882 2.813908 GAACGCCATCTCGCCGTT 60.814 61.111 0.00 0.00 46.44 4.44
1989 2154 2.044946 GTGGGGAAGCCGCTCAAT 60.045 61.111 0.00 0.00 37.37 2.57
1994 2159 1.377202 GGAAGCCGCTCAATGTCCA 60.377 57.895 3.56 0.00 0.00 4.02
2005 2173 0.883833 CAATGTCCAGGCCTGTTGAC 59.116 55.000 30.63 28.31 0.00 3.18
2006 2174 0.773644 AATGTCCAGGCCTGTTGACT 59.226 50.000 30.43 19.10 0.00 3.41
2007 2175 1.656587 ATGTCCAGGCCTGTTGACTA 58.343 50.000 30.43 21.44 0.00 2.59
2008 2176 1.656587 TGTCCAGGCCTGTTGACTAT 58.343 50.000 30.43 0.00 0.00 2.12
2009 2177 1.985159 TGTCCAGGCCTGTTGACTATT 59.015 47.619 30.43 0.00 0.00 1.73
2010 2178 2.290260 TGTCCAGGCCTGTTGACTATTG 60.290 50.000 30.43 15.82 0.00 1.90
2011 2179 2.027192 GTCCAGGCCTGTTGACTATTGA 60.027 50.000 30.63 14.63 0.00 2.57
2025 2193 2.223829 ACTATTGAGGACGGCGAGAATG 60.224 50.000 16.62 0.00 0.00 2.67
2031 2199 4.778143 ACGGCGAGAATGGTGCCC 62.778 66.667 16.62 0.00 46.12 5.36
2036 2204 1.674322 CGAGAATGGTGCCCGGTTT 60.674 57.895 0.00 0.00 0.00 3.27
2116 2425 0.390340 TCAGAGCTCCGTGTGCATTC 60.390 55.000 10.93 0.00 0.00 2.67
2381 2902 9.150028 TGGATCACAATTCCATCATGAATATTT 57.850 29.630 0.00 0.00 38.35 1.40
2429 2950 3.717576 TCATCCCAACCAAATGGCATAA 58.282 40.909 0.00 0.00 39.26 1.90
2432 2953 3.717576 TCCCAACCAAATGGCATAATCA 58.282 40.909 0.00 0.00 39.26 2.57
2513 3034 4.581309 ATCTCATGGTTCTGGAACACAT 57.419 40.909 14.25 11.73 42.85 3.21
2514 3035 5.698741 ATCTCATGGTTCTGGAACACATA 57.301 39.130 14.25 3.39 42.85 2.29
2515 3036 4.832248 TCTCATGGTTCTGGAACACATAC 58.168 43.478 14.25 0.00 42.85 2.39
2516 3037 4.532126 TCTCATGGTTCTGGAACACATACT 59.468 41.667 14.25 0.00 42.85 2.12
2517 3038 4.832248 TCATGGTTCTGGAACACATACTC 58.168 43.478 14.25 0.00 42.85 2.59
2518 3039 3.695830 TGGTTCTGGAACACATACTCC 57.304 47.619 14.25 0.00 42.85 3.85
2519 3040 2.304761 TGGTTCTGGAACACATACTCCC 59.695 50.000 14.25 0.00 42.85 4.30
2520 3041 2.572104 GGTTCTGGAACACATACTCCCT 59.428 50.000 14.25 0.00 42.85 4.20
2521 3042 3.369576 GGTTCTGGAACACATACTCCCTC 60.370 52.174 14.25 0.00 42.85 4.30
2522 3043 2.467880 TCTGGAACACATACTCCCTCC 58.532 52.381 0.00 0.00 0.00 4.30
2523 3044 1.137086 CTGGAACACATACTCCCTCCG 59.863 57.143 0.00 0.00 0.00 4.63
2524 3045 1.192428 GGAACACATACTCCCTCCGT 58.808 55.000 0.00 0.00 0.00 4.69
2525 3046 1.553704 GGAACACATACTCCCTCCGTT 59.446 52.381 0.00 0.00 0.00 4.44
2526 3047 2.027469 GGAACACATACTCCCTCCGTTT 60.027 50.000 0.00 0.00 0.00 3.60
2527 3048 3.259902 GAACACATACTCCCTCCGTTTC 58.740 50.000 0.00 0.00 0.00 2.78
2528 3049 2.253610 ACACATACTCCCTCCGTTTCA 58.746 47.619 0.00 0.00 0.00 2.69
2529 3050 2.635915 ACACATACTCCCTCCGTTTCAA 59.364 45.455 0.00 0.00 0.00 2.69
2530 3051 3.071892 ACACATACTCCCTCCGTTTCAAA 59.928 43.478 0.00 0.00 0.00 2.69
2531 3052 4.261801 CACATACTCCCTCCGTTTCAAAT 58.738 43.478 0.00 0.00 0.00 2.32
2532 3053 4.700213 CACATACTCCCTCCGTTTCAAATT 59.300 41.667 0.00 0.00 0.00 1.82
2533 3054 5.878116 CACATACTCCCTCCGTTTCAAATTA 59.122 40.000 0.00 0.00 0.00 1.40
2534 3055 5.878669 ACATACTCCCTCCGTTTCAAATTAC 59.121 40.000 0.00 0.00 0.00 1.89
2535 3056 4.635699 ACTCCCTCCGTTTCAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
2536 3057 4.576879 ACTCCCTCCGTTTCAAATTACTC 58.423 43.478 0.00 0.00 0.00 2.59
2537 3058 3.592059 TCCCTCCGTTTCAAATTACTCG 58.408 45.455 0.00 0.00 0.00 4.18
2538 3059 3.007182 TCCCTCCGTTTCAAATTACTCGT 59.993 43.478 0.00 0.00 0.00 4.18
2539 3060 3.370061 CCCTCCGTTTCAAATTACTCGTC 59.630 47.826 0.00 0.00 0.00 4.20
2540 3061 3.060363 CCTCCGTTTCAAATTACTCGTCG 59.940 47.826 0.00 0.00 0.00 5.12
2541 3062 3.641648 TCCGTTTCAAATTACTCGTCGT 58.358 40.909 0.00 0.00 0.00 4.34
2542 3063 3.426191 TCCGTTTCAAATTACTCGTCGTG 59.574 43.478 0.00 0.00 0.00 4.35
2543 3064 3.422603 CCGTTTCAAATTACTCGTCGTGG 60.423 47.826 0.00 0.00 0.00 4.94
2544 3065 3.182972 CGTTTCAAATTACTCGTCGTGGT 59.817 43.478 0.00 0.00 0.00 4.16
2545 3066 4.318263 CGTTTCAAATTACTCGTCGTGGTT 60.318 41.667 0.00 0.00 0.00 3.67
2546 3067 5.504392 GTTTCAAATTACTCGTCGTGGTTT 58.496 37.500 0.00 0.00 0.00 3.27
2547 3068 5.738118 TTCAAATTACTCGTCGTGGTTTT 57.262 34.783 0.00 0.00 0.00 2.43
2548 3069 6.841443 TTCAAATTACTCGTCGTGGTTTTA 57.159 33.333 0.00 0.00 0.00 1.52
2549 3070 6.456447 TCAAATTACTCGTCGTGGTTTTAG 57.544 37.500 0.00 0.00 0.00 1.85
2550 3071 5.984926 TCAAATTACTCGTCGTGGTTTTAGT 59.015 36.000 0.00 0.00 0.00 2.24
2551 3072 6.479660 TCAAATTACTCGTCGTGGTTTTAGTT 59.520 34.615 0.00 0.00 0.00 2.24
2552 3073 6.457851 AATTACTCGTCGTGGTTTTAGTTC 57.542 37.500 0.00 0.00 0.00 3.01
2553 3074 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
2554 3075 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
2555 3076 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
2556 3077 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
2557 3078 5.295045 ACTCGTCGTGGTTTTAGTTCAAATT 59.705 36.000 0.00 0.00 0.00 1.82
2558 3079 6.121613 TCGTCGTGGTTTTAGTTCAAATTT 57.878 33.333 0.00 0.00 0.00 1.82
2559 3080 7.011295 ACTCGTCGTGGTTTTAGTTCAAATTTA 59.989 33.333 0.00 0.00 0.00 1.40
2560 3081 7.692088 TCGTCGTGGTTTTAGTTCAAATTTAA 58.308 30.769 0.00 0.00 0.00 1.52
2561 3082 8.180267 TCGTCGTGGTTTTAGTTCAAATTTAAA 58.820 29.630 0.00 0.00 0.00 1.52
2562 3083 8.254470 CGTCGTGGTTTTAGTTCAAATTTAAAC 58.746 33.333 0.00 0.00 0.00 2.01
2563 3084 9.292846 GTCGTGGTTTTAGTTCAAATTTAAACT 57.707 29.630 11.45 11.45 39.07 2.66
2574 3095 9.292846 AGTTCAAATTTAAACTAAAACCACGAC 57.707 29.630 4.83 0.00 34.05 4.34
2575 3096 7.895582 TCAAATTTAAACTAAAACCACGACG 57.104 32.000 0.00 0.00 0.00 5.12
2576 3097 7.692088 TCAAATTTAAACTAAAACCACGACGA 58.308 30.769 0.00 0.00 0.00 4.20
2577 3098 7.851963 TCAAATTTAAACTAAAACCACGACGAG 59.148 33.333 0.00 0.00 0.00 4.18
2578 3099 4.713854 TTAAACTAAAACCACGACGAGC 57.286 40.909 0.00 0.00 0.00 5.03
2579 3100 2.228138 AACTAAAACCACGACGAGCA 57.772 45.000 0.00 0.00 0.00 4.26
2580 3101 2.228138 ACTAAAACCACGACGAGCAA 57.772 45.000 0.00 0.00 0.00 3.91
2581 3102 2.762745 ACTAAAACCACGACGAGCAAT 58.237 42.857 0.00 0.00 0.00 3.56
2582 3103 3.135994 ACTAAAACCACGACGAGCAATT 58.864 40.909 0.00 0.00 0.00 2.32
2583 3104 3.562557 ACTAAAACCACGACGAGCAATTT 59.437 39.130 0.00 0.00 0.00 1.82
2584 3105 2.399396 AAACCACGACGAGCAATTTG 57.601 45.000 0.00 0.00 0.00 2.32
2585 3106 0.591170 AACCACGACGAGCAATTTGG 59.409 50.000 0.00 0.00 0.00 3.28
2586 3107 0.250124 ACCACGACGAGCAATTTGGA 60.250 50.000 0.00 0.00 0.00 3.53
2587 3108 0.871722 CCACGACGAGCAATTTGGAA 59.128 50.000 0.00 0.00 0.00 3.53
2588 3109 1.399727 CCACGACGAGCAATTTGGAAC 60.400 52.381 0.00 0.00 0.00 3.62
2589 3110 0.511221 ACGACGAGCAATTTGGAACG 59.489 50.000 0.00 0.00 0.00 3.95
2590 3111 0.179225 CGACGAGCAATTTGGAACGG 60.179 55.000 0.00 0.00 0.00 4.44
2591 3112 1.153353 GACGAGCAATTTGGAACGGA 58.847 50.000 0.00 0.00 0.00 4.69
2592 3113 1.128692 GACGAGCAATTTGGAACGGAG 59.871 52.381 0.00 0.00 0.00 4.63
2593 3114 0.447801 CGAGCAATTTGGAACGGAGG 59.552 55.000 0.00 0.00 0.00 4.30
2594 3115 0.811281 GAGCAATTTGGAACGGAGGG 59.189 55.000 0.00 0.00 0.00 4.30
2595 3116 0.404040 AGCAATTTGGAACGGAGGGA 59.596 50.000 0.00 0.00 0.00 4.20
2596 3117 0.811281 GCAATTTGGAACGGAGGGAG 59.189 55.000 0.00 0.00 0.00 4.30
2603 3124 1.621814 TGGAACGGAGGGAGTAGTTTG 59.378 52.381 0.00 0.00 0.00 2.93
2676 3197 8.696374 TGTCAACTTTGAATTGGGTTGTAATTA 58.304 29.630 0.00 0.00 39.21 1.40
2685 3206 9.132923 TGAATTGGGTTGTAATTACTTAACACA 57.867 29.630 15.97 15.97 34.89 3.72
2866 3388 9.606631 AACATCTGAGTTAGAAAATCATACTCC 57.393 33.333 0.00 0.00 39.30 3.85
2909 3431 8.877864 ATCCTACTCTAGAAATCTCTATGGTG 57.122 38.462 0.00 0.00 33.59 4.17
2938 3460 9.970395 TGTTAAACTCCATATACTATAACACCG 57.030 33.333 0.00 0.00 29.79 4.94
2949 3471 2.118313 ATAACACCGGGCCAAGTTAC 57.882 50.000 6.32 0.00 30.19 2.50
2975 3497 8.836413 CCTAAAATCACTAAAGAAGACACACAA 58.164 33.333 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.402793 TGTATCCTTGTCTTACTCTGCCTC 59.597 45.833 0.00 0.00 0.00 4.70
27 28 6.493802 TCACTGTTGTATCCTTGTCTTACTCT 59.506 38.462 0.00 0.00 0.00 3.24
50 51 4.256110 CTGATTAGTGGTTGAGCACATCA 58.744 43.478 14.86 13.60 35.62 3.07
53 54 2.371841 ACCTGATTAGTGGTTGAGCACA 59.628 45.455 14.86 0.00 31.62 4.57
55 56 3.838317 AGTACCTGATTAGTGGTTGAGCA 59.162 43.478 0.00 0.00 37.74 4.26
170 172 4.368808 GAGCTTGCGCGCGTTTCA 62.369 61.111 32.35 18.39 42.32 2.69
197 201 8.063038 CGTATTACTATATGATAGACTGTCGGC 58.937 40.741 1.52 0.00 0.00 5.54
217 224 9.378551 GGAATCAGTGGAAATATATGCGTATTA 57.621 33.333 3.23 0.00 0.00 0.98
218 225 7.882791 TGGAATCAGTGGAAATATATGCGTATT 59.117 33.333 3.23 0.00 0.00 1.89
219 226 7.334421 GTGGAATCAGTGGAAATATATGCGTAT 59.666 37.037 3.47 3.47 0.00 3.06
220 227 6.649141 GTGGAATCAGTGGAAATATATGCGTA 59.351 38.462 0.00 0.00 0.00 4.42
221 228 5.470098 GTGGAATCAGTGGAAATATATGCGT 59.530 40.000 0.00 0.00 0.00 5.24
222 229 5.106555 GGTGGAATCAGTGGAAATATATGCG 60.107 44.000 0.00 0.00 0.00 4.73
227 234 4.503714 ACGGTGGAATCAGTGGAAATAT 57.496 40.909 0.00 0.00 0.00 1.28
251 277 4.149598 AGTGGGGCGAAAGAATTTTTAGT 58.850 39.130 0.00 0.00 39.27 2.24
289 315 7.588488 GCTTCTAAACTTTGTATGTTTGCGTAA 59.412 33.333 0.00 0.00 38.02 3.18
308 334 8.902540 TCTTTGTATTTGACTTCTGCTTCTAA 57.097 30.769 0.00 0.00 0.00 2.10
351 377 0.395586 AGGCTTGTTGAGTTGTGCCA 60.396 50.000 0.00 0.00 42.46 4.92
356 382 4.668289 ACGTTTTTAGGCTTGTTGAGTTG 58.332 39.130 0.00 0.00 0.00 3.16
391 420 8.793592 GCCCTTTCTTTTCTCATTTTAGACTTA 58.206 33.333 0.00 0.00 0.00 2.24
395 424 6.074648 TGGCCCTTTCTTTTCTCATTTTAGA 58.925 36.000 0.00 0.00 0.00 2.10
402 431 3.025322 TGTTGGCCCTTTCTTTTCTCA 57.975 42.857 0.00 0.00 0.00 3.27
436 465 2.877866 CCGGACTATGGGTCTGTATCT 58.122 52.381 0.00 0.00 46.85 1.98
548 577 2.436115 GGAAGCCGCTTAGCCGTT 60.436 61.111 5.38 0.00 0.00 4.44
567 596 1.391157 GGTGTGGTTTTCTGCAGCCA 61.391 55.000 9.47 7.86 0.00 4.75
643 673 3.060363 GTGAACGCTTTGGACTATACGTG 59.940 47.826 0.00 0.00 33.48 4.49
645 675 2.601763 GGTGAACGCTTTGGACTATACG 59.398 50.000 0.00 0.00 0.00 3.06
673 703 4.209538 CATTAGATGGTTGGGCATTGAGA 58.790 43.478 0.00 0.00 0.00 3.27
685 715 3.513912 TCGTTCTGGTCACATTAGATGGT 59.486 43.478 0.00 0.00 33.60 3.55
693 723 1.079819 CGCCTCGTTCTGGTCACAT 60.080 57.895 0.00 0.00 0.00 3.21
700 730 2.507992 CCTGCTCGCCTCGTTCTG 60.508 66.667 0.00 0.00 0.00 3.02
744 774 2.032924 GTGAAGTGGTGAAAACCTTCCG 59.967 50.000 0.00 0.00 33.91 4.30
754 784 1.740332 TTCGGCGAGTGAAGTGGTGA 61.740 55.000 10.46 0.00 0.00 4.02
770 800 8.302438 AGGGAGTAATAATTTATACGGAGTTCG 58.698 37.037 0.00 0.00 37.78 3.95
876 1013 2.632996 TCTTTATACTCCCTGCCATCCG 59.367 50.000 0.00 0.00 0.00 4.18
910 1047 6.238484 CGAAGGCTCCAAACATCTTTATAAGG 60.238 42.308 0.00 0.00 0.00 2.69
943 1080 2.604914 CACAACGATAGCTAGGCAACTG 59.395 50.000 0.00 0.00 46.88 3.16
1016 1153 2.288640 CCTTCGTACCTGAAAAGGACGT 60.289 50.000 12.92 0.00 40.63 4.34
1591 1734 2.433318 GCTGGACGTGCAGAGGAC 60.433 66.667 37.18 17.80 0.00 3.85
1902 2067 2.915659 TCGGACGCCAGGAACACT 60.916 61.111 0.00 0.00 0.00 3.55
1926 2091 5.155161 AGATTATGCCCAGTGATGTACCTA 58.845 41.667 0.00 0.00 0.00 3.08
1989 2154 1.656587 ATAGTCAACAGGCCTGGACA 58.343 50.000 35.42 21.85 32.79 4.02
1994 2159 2.237392 GTCCTCAATAGTCAACAGGCCT 59.763 50.000 0.00 0.00 0.00 5.19
2005 2173 2.398498 CATTCTCGCCGTCCTCAATAG 58.602 52.381 0.00 0.00 0.00 1.73
2006 2174 1.068588 CCATTCTCGCCGTCCTCAATA 59.931 52.381 0.00 0.00 0.00 1.90
2007 2175 0.179073 CCATTCTCGCCGTCCTCAAT 60.179 55.000 0.00 0.00 0.00 2.57
2008 2176 1.218047 CCATTCTCGCCGTCCTCAA 59.782 57.895 0.00 0.00 0.00 3.02
2009 2177 1.982395 ACCATTCTCGCCGTCCTCA 60.982 57.895 0.00 0.00 0.00 3.86
2010 2178 1.519455 CACCATTCTCGCCGTCCTC 60.519 63.158 0.00 0.00 0.00 3.71
2011 2179 2.579201 CACCATTCTCGCCGTCCT 59.421 61.111 0.00 0.00 0.00 3.85
2025 2193 8.838081 TGTTTAATTTCTTGAAACCGGGCACC 62.838 42.308 6.32 0.00 36.72 5.01
2283 2789 5.626543 CCAAAACATCTTGATCGAAACACTG 59.373 40.000 0.00 0.00 0.00 3.66
2381 2902 6.652205 AACAAAGTTAGGAGGAATATCCCA 57.348 37.500 0.00 0.00 40.53 4.37
2513 3034 5.622914 CGAGTAATTTGAAACGGAGGGAGTA 60.623 44.000 0.00 0.00 0.00 2.59
2514 3035 4.576879 GAGTAATTTGAAACGGAGGGAGT 58.423 43.478 0.00 0.00 0.00 3.85
2515 3036 3.617263 CGAGTAATTTGAAACGGAGGGAG 59.383 47.826 0.00 0.00 0.00 4.30
2516 3037 3.007182 ACGAGTAATTTGAAACGGAGGGA 59.993 43.478 0.00 0.00 0.00 4.20
2517 3038 3.332034 ACGAGTAATTTGAAACGGAGGG 58.668 45.455 0.00 0.00 0.00 4.30
2518 3039 3.060363 CGACGAGTAATTTGAAACGGAGG 59.940 47.826 0.00 0.00 0.00 4.30
2519 3040 3.671928 ACGACGAGTAATTTGAAACGGAG 59.328 43.478 0.00 0.00 0.00 4.63
2520 3041 3.426191 CACGACGAGTAATTTGAAACGGA 59.574 43.478 0.00 0.00 0.00 4.69
2521 3042 3.422603 CCACGACGAGTAATTTGAAACGG 60.423 47.826 0.00 0.00 0.00 4.44
2522 3043 3.182972 ACCACGACGAGTAATTTGAAACG 59.817 43.478 0.00 0.00 0.00 3.60
2523 3044 4.720530 ACCACGACGAGTAATTTGAAAC 57.279 40.909 0.00 0.00 0.00 2.78
2524 3045 5.738118 AAACCACGACGAGTAATTTGAAA 57.262 34.783 0.00 0.00 0.00 2.69
2525 3046 5.738118 AAAACCACGACGAGTAATTTGAA 57.262 34.783 0.00 0.00 0.00 2.69
2526 3047 5.984926 ACTAAAACCACGACGAGTAATTTGA 59.015 36.000 0.00 0.00 0.00 2.69
2527 3048 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
2528 3049 6.479660 TGAACTAAAACCACGACGAGTAATTT 59.520 34.615 0.00 0.34 0.00 1.82
2529 3050 5.984926 TGAACTAAAACCACGACGAGTAATT 59.015 36.000 0.00 1.08 0.00 1.40
2530 3051 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
2531 3052 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
2532 3053 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
2533 3054 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
2534 3055 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
2535 3056 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
2536 3057 7.895582 TTAAATTTGAACTAAAACCACGACG 57.104 32.000 0.00 0.00 0.00 5.12
2537 3058 9.292846 AGTTTAAATTTGAACTAAAACCACGAC 57.707 29.630 22.70 0.00 35.55 4.34
2548 3069 9.292846 GTCGTGGTTTTAGTTTAAATTTGAACT 57.707 29.630 25.84 25.84 39.80 3.01
2549 3070 8.254470 CGTCGTGGTTTTAGTTTAAATTTGAAC 58.746 33.333 15.93 15.93 0.00 3.18
2550 3071 8.180267 TCGTCGTGGTTTTAGTTTAAATTTGAA 58.820 29.630 0.00 0.00 0.00 2.69
2551 3072 7.692088 TCGTCGTGGTTTTAGTTTAAATTTGA 58.308 30.769 0.00 0.00 0.00 2.69
2552 3073 7.356962 GCTCGTCGTGGTTTTAGTTTAAATTTG 60.357 37.037 0.00 0.00 0.00 2.32
2553 3074 6.634035 GCTCGTCGTGGTTTTAGTTTAAATTT 59.366 34.615 0.00 0.00 0.00 1.82
2554 3075 6.138088 GCTCGTCGTGGTTTTAGTTTAAATT 58.862 36.000 0.00 0.00 0.00 1.82
2555 3076 5.236911 TGCTCGTCGTGGTTTTAGTTTAAAT 59.763 36.000 0.00 0.00 0.00 1.40
2556 3077 4.569966 TGCTCGTCGTGGTTTTAGTTTAAA 59.430 37.500 0.00 0.00 0.00 1.52
2557 3078 4.118410 TGCTCGTCGTGGTTTTAGTTTAA 58.882 39.130 0.00 0.00 0.00 1.52
2558 3079 3.715495 TGCTCGTCGTGGTTTTAGTTTA 58.285 40.909 0.00 0.00 0.00 2.01
2559 3080 2.553086 TGCTCGTCGTGGTTTTAGTTT 58.447 42.857 0.00 0.00 0.00 2.66
2560 3081 2.228138 TGCTCGTCGTGGTTTTAGTT 57.772 45.000 0.00 0.00 0.00 2.24
2561 3082 2.228138 TTGCTCGTCGTGGTTTTAGT 57.772 45.000 0.00 0.00 0.00 2.24
2562 3083 3.806316 AATTGCTCGTCGTGGTTTTAG 57.194 42.857 0.00 0.00 0.00 1.85
2563 3084 3.304123 CCAAATTGCTCGTCGTGGTTTTA 60.304 43.478 0.00 0.00 0.00 1.52
2564 3085 2.542824 CCAAATTGCTCGTCGTGGTTTT 60.543 45.455 0.00 0.00 0.00 2.43
2565 3086 1.001815 CCAAATTGCTCGTCGTGGTTT 60.002 47.619 0.00 0.00 0.00 3.27
2566 3087 0.591170 CCAAATTGCTCGTCGTGGTT 59.409 50.000 0.00 0.00 0.00 3.67
2567 3088 0.250124 TCCAAATTGCTCGTCGTGGT 60.250 50.000 0.00 0.00 0.00 4.16
2568 3089 0.871722 TTCCAAATTGCTCGTCGTGG 59.128 50.000 0.00 0.00 0.00 4.94
2569 3090 1.721489 CGTTCCAAATTGCTCGTCGTG 60.721 52.381 0.00 0.00 0.00 4.35
2570 3091 0.511221 CGTTCCAAATTGCTCGTCGT 59.489 50.000 0.00 0.00 0.00 4.34
2571 3092 0.179225 CCGTTCCAAATTGCTCGTCG 60.179 55.000 0.00 0.00 0.00 5.12
2572 3093 1.128692 CTCCGTTCCAAATTGCTCGTC 59.871 52.381 0.00 0.00 0.00 4.20
2573 3094 1.156736 CTCCGTTCCAAATTGCTCGT 58.843 50.000 0.00 0.00 0.00 4.18
2574 3095 0.447801 CCTCCGTTCCAAATTGCTCG 59.552 55.000 0.00 0.00 0.00 5.03
2575 3096 0.811281 CCCTCCGTTCCAAATTGCTC 59.189 55.000 0.00 0.00 0.00 4.26
2576 3097 0.404040 TCCCTCCGTTCCAAATTGCT 59.596 50.000 0.00 0.00 0.00 3.91
2577 3098 0.811281 CTCCCTCCGTTCCAAATTGC 59.189 55.000 0.00 0.00 0.00 3.56
2578 3099 2.200373 ACTCCCTCCGTTCCAAATTG 57.800 50.000 0.00 0.00 0.00 2.32
2579 3100 2.910977 ACTACTCCCTCCGTTCCAAATT 59.089 45.455 0.00 0.00 0.00 1.82
2580 3101 2.547990 ACTACTCCCTCCGTTCCAAAT 58.452 47.619 0.00 0.00 0.00 2.32
2581 3102 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
2582 3103 2.019807 AACTACTCCCTCCGTTCCAA 57.980 50.000 0.00 0.00 0.00 3.53
2583 3104 1.621814 CAAACTACTCCCTCCGTTCCA 59.378 52.381 0.00 0.00 0.00 3.53
2584 3105 1.675116 GCAAACTACTCCCTCCGTTCC 60.675 57.143 0.00 0.00 0.00 3.62
2585 3106 1.001633 TGCAAACTACTCCCTCCGTTC 59.998 52.381 0.00 0.00 0.00 3.95
2586 3107 1.053424 TGCAAACTACTCCCTCCGTT 58.947 50.000 0.00 0.00 0.00 4.44
2587 3108 1.066143 CATGCAAACTACTCCCTCCGT 60.066 52.381 0.00 0.00 0.00 4.69
2588 3109 1.066143 ACATGCAAACTACTCCCTCCG 60.066 52.381 0.00 0.00 0.00 4.63
2589 3110 2.633488 GACATGCAAACTACTCCCTCC 58.367 52.381 0.00 0.00 0.00 4.30
2590 3111 2.271800 CGACATGCAAACTACTCCCTC 58.728 52.381 0.00 0.00 0.00 4.30
2591 3112 1.623811 ACGACATGCAAACTACTCCCT 59.376 47.619 0.00 0.00 0.00 4.20
2592 3113 2.094762 ACGACATGCAAACTACTCCC 57.905 50.000 0.00 0.00 0.00 4.30
2593 3114 5.178809 AGTTTAACGACATGCAAACTACTCC 59.821 40.000 0.00 0.00 38.96 3.85
2594 3115 6.071463 CAGTTTAACGACATGCAAACTACTC 58.929 40.000 0.00 0.00 38.75 2.59
2595 3116 5.756347 TCAGTTTAACGACATGCAAACTACT 59.244 36.000 0.00 0.00 38.75 2.57
2596 3117 5.981174 TCAGTTTAACGACATGCAAACTAC 58.019 37.500 0.00 0.00 38.75 2.73
2603 3124 3.063997 CCTCCATCAGTTTAACGACATGC 59.936 47.826 0.00 0.00 0.00 4.06
2676 3197 3.464111 AGTGGTAAGCGTGTGTTAAGT 57.536 42.857 0.00 0.00 0.00 2.24
2685 3206 6.548622 TGTCCTTAAGATATAGTGGTAAGCGT 59.451 38.462 3.36 0.00 0.00 5.07
2831 3353 6.041423 TCTAACTCAGATGTTGCAGAATGA 57.959 37.500 0.00 0.00 39.69 2.57
2928 3450 2.413310 AACTTGGCCCGGTGTTATAG 57.587 50.000 0.00 0.00 0.00 1.31
2949 3471 8.378172 TGTGTGTCTTCTTTAGTGATTTTAGG 57.622 34.615 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.