Multiple sequence alignment - TraesCS5D01G158000

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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 TraesCS5D01G158000 chr5D 100.000 3884 0 0 1 3884 246012525 246008642 0.000000e+00 7173.0
1 TraesCS5D01G158000 chr5A 93.819 3608 183 16 1 3595 329994969 329991389 0.000000e+00 5391.0
2 TraesCS5D01G158000 chr5A 78.777 1946 377 27 157 2082 606352873 606350944 0.000000e+00 1273.0
3 TraesCS5D01G158000 chr5A 77.070 1993 404 46 136 2101 73828610 73826644 0.000000e+00 1099.0
4 TraesCS5D01G158000 chr5A 87.500 200 22 3 3576 3775 329991310 329991114 1.090000e-55 228.0
5 TraesCS5D01G158000 chr5B 94.959 2222 92 6 1 2217 280650279 280648073 0.000000e+00 3465.0
6 TraesCS5D01G158000 chr5B 92.004 938 67 4 2228 3161 280647979 280647046 0.000000e+00 1310.0
7 TraesCS5D01G158000 chr5B 78.112 1960 391 27 157 2089 596824493 596822545 0.000000e+00 1208.0
8 TraesCS5D01G158000 chr5B 78.091 1949 397 22 157 2089 596224155 596226089 0.000000e+00 1206.0
9 TraesCS5D01G158000 chr5B 77.766 1934 386 33 157 2071 596393863 596395771 0.000000e+00 1149.0
10 TraesCS5D01G158000 chr5B 76.393 1974 409 50 155 2101 86246899 86244956 0.000000e+00 1011.0
11 TraesCS5D01G158000 chr5B 80.727 633 113 9 1469 2098 85946160 85945534 5.830000e-133 484.0
12 TraesCS5D01G158000 chr5B 80.890 382 66 4 2513 2894 280603530 280603156 1.060000e-75 294.0
13 TraesCS5D01G158000 chr5B 86.512 215 22 1 3130 3344 280647041 280646834 3.020000e-56 230.0
14 TraesCS5D01G158000 chr7D 77.911 1924 396 26 154 2062 19050923 19052832 0.000000e+00 1171.0
15 TraesCS5D01G158000 chr7D 79.444 360 68 3 2541 2894 19052903 19053262 2.320000e-62 250.0
16 TraesCS5D01G158000 chr7D 97.531 81 2 0 3804 3884 93883392 93883472 5.230000e-29 139.0
17 TraesCS5D01G158000 chr4A 77.743 1923 395 28 157 2062 713505173 713503267 0.000000e+00 1149.0
18 TraesCS5D01G158000 chr4A 79.326 653 123 10 1280 1923 739711973 739711324 7.650000e-122 448.0
19 TraesCS5D01G158000 chr4A 78.834 652 126 10 1281 1923 742107464 742106816 2.770000e-116 429.0
20 TraesCS5D01G158000 chr4A 80.597 335 65 0 2541 2875 741162664 741162998 3.850000e-65 259.0
21 TraesCS5D01G158000 chr4A 79.444 360 68 3 2541 2894 713503196 713502837 2.320000e-62 250.0
22 TraesCS5D01G158000 chr4A 80.000 335 67 0 2541 2875 733993696 733994030 8.330000e-62 248.0
23 TraesCS5D01G158000 chr4A 88.415 164 18 1 3024 3187 514080008 514080170 3.060000e-46 196.0
24 TraesCS5D01G158000 chr7A 77.541 1928 396 34 154 2062 19517134 19519043 0.000000e+00 1127.0
25 TraesCS5D01G158000 chr7A 79.558 362 65 3 2541 2893 3141218 3141579 2.320000e-62 250.0
26 TraesCS5D01G158000 chr7A 79.444 360 68 4 2541 2894 19519114 19519473 2.320000e-62 250.0
27 TraesCS5D01G158000 chr1B 88.636 176 13 6 3005 3175 632020900 632021073 1.410000e-49 207.0
28 TraesCS5D01G158000 chr4D 90.000 160 15 1 3028 3187 296729394 296729552 5.090000e-49 206.0
29 TraesCS5D01G158000 chr1A 90.323 155 14 1 3028 3181 155857859 155857705 6.580000e-48 202.0
30 TraesCS5D01G158000 chr4B 89.809 157 14 2 3031 3185 146469365 146469209 2.370000e-47 200.0
31 TraesCS5D01G158000 chr3A 90.196 153 15 0 3028 3180 582283367 582283215 2.370000e-47 200.0
32 TraesCS5D01G158000 chr3A 97.531 81 2 0 3804 3884 687616129 687616209 5.230000e-29 139.0
33 TraesCS5D01G158000 chr3A 96.341 82 3 0 3803 3884 737387917 737387836 6.770000e-28 135.0
34 TraesCS5D01G158000 chr3A 96.296 81 3 0 3804 3884 716802988 716803068 2.430000e-27 134.0
35 TraesCS5D01G158000 chr3A 96.250 80 3 0 3803 3882 15314539 15314618 8.760000e-27 132.0
36 TraesCS5D01G158000 chr3D 88.485 165 17 2 3023 3186 322435448 322435285 8.510000e-47 198.0
37 TraesCS5D01G158000 chr1D 97.561 82 2 0 3803 3884 468747496 468747415 1.450000e-29 141.0
38 TraesCS5D01G158000 chr2A 97.531 81 2 0 3804 3884 594654360 594654280 5.230000e-29 139.0
39 TraesCS5D01G158000 chr2B 96.386 83 3 0 3802 3884 615332462 615332380 1.880000e-28 137.0
40 TraesCS5D01G158000 chr3B 96.341 82 3 0 3803 3884 507302846 507302927 6.770000e-28 135.0
41 TraesCS5D01G158000 chr6B 81.818 99 13 4 3664 3760 34087977 34088072 1.160000e-10 78.7


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 TraesCS5D01G158000 chr5D 246008642 246012525 3883 True 7173.000000 7173 100.000000 1 3884 1 chr5D.!!$R1 3883
1 TraesCS5D01G158000 chr5A 329991114 329994969 3855 True 2809.500000 5391 90.659500 1 3775 2 chr5A.!!$R3 3774
2 TraesCS5D01G158000 chr5A 606350944 606352873 1929 True 1273.000000 1273 78.777000 157 2082 1 chr5A.!!$R2 1925
3 TraesCS5D01G158000 chr5A 73826644 73828610 1966 True 1099.000000 1099 77.070000 136 2101 1 chr5A.!!$R1 1965
4 TraesCS5D01G158000 chr5B 280646834 280650279 3445 True 1668.333333 3465 91.158333 1 3344 3 chr5B.!!$R5 3343
5 TraesCS5D01G158000 chr5B 596822545 596824493 1948 True 1208.000000 1208 78.112000 157 2089 1 chr5B.!!$R4 1932
6 TraesCS5D01G158000 chr5B 596224155 596226089 1934 False 1206.000000 1206 78.091000 157 2089 1 chr5B.!!$F1 1932
7 TraesCS5D01G158000 chr5B 596393863 596395771 1908 False 1149.000000 1149 77.766000 157 2071 1 chr5B.!!$F2 1914
8 TraesCS5D01G158000 chr5B 86244956 86246899 1943 True 1011.000000 1011 76.393000 155 2101 1 chr5B.!!$R2 1946
9 TraesCS5D01G158000 chr5B 85945534 85946160 626 True 484.000000 484 80.727000 1469 2098 1 chr5B.!!$R1 629
10 TraesCS5D01G158000 chr7D 19050923 19053262 2339 False 710.500000 1171 78.677500 154 2894 2 chr7D.!!$F2 2740
11 TraesCS5D01G158000 chr4A 713502837 713505173 2336 True 699.500000 1149 78.593500 157 2894 2 chr4A.!!$R3 2737
12 TraesCS5D01G158000 chr4A 739711324 739711973 649 True 448.000000 448 79.326000 1280 1923 1 chr4A.!!$R1 643
13 TraesCS5D01G158000 chr4A 742106816 742107464 648 True 429.000000 429 78.834000 1281 1923 1 chr4A.!!$R2 642
14 TraesCS5D01G158000 chr7A 19517134 19519473 2339 False 688.500000 1127 78.492500 154 2894 2 chr7A.!!$F2 2740

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
446 447 0.608035 TGCCATCCGGTCTTTGTTCC 60.608 55.000 0.00 0.0 33.28 3.62 F
2200 2252 1.133482 CGAGGCCCAGGGGAATAAAAT 60.133 52.381 7.91 0.0 37.50 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2318 2453 1.660607 CGTGGCTAATGTGTACTGCAG 59.339 52.381 13.48 13.48 0.00 4.41 R
3853 4144 0.032130 CTCATACGCATGTACGGCCT 59.968 55.000 0.00 0.00 37.37 5.19 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
30 31 9.712359 GTTTAGGAAACTTAACACAGTTAACAG 57.288 33.333 8.61 1.86 46.47 3.16
133 134 2.490991 AGGACAGAACAAACTTACGGC 58.509 47.619 0.00 0.00 0.00 5.68
386 387 9.189723 CAAGAAATTGGAAACTTGAGAAATCTC 57.810 33.333 3.43 3.43 41.16 2.75
398 399 4.703897 TGAGAAATCTCGTTTGGTTGACT 58.296 39.130 5.99 0.00 45.72 3.41
423 424 4.254402 AGTTCTAACAAACTCTCCGGTC 57.746 45.455 0.00 0.00 34.37 4.79
446 447 0.608035 TGCCATCCGGTCTTTGTTCC 60.608 55.000 0.00 0.00 33.28 3.62
470 471 1.544246 GGCCGGCTACAAAATTTCACT 59.456 47.619 28.56 0.00 0.00 3.41
695 700 2.076100 TGCGTGCCTCAGAAAATAGTG 58.924 47.619 0.00 0.00 0.00 2.74
828 833 4.060205 ACATTGTTCAATTTGAGCCTTGC 58.940 39.130 10.28 0.00 0.00 4.01
1117 1130 3.928727 TGCTTGAAGCCTTGAATCTTG 57.071 42.857 15.43 0.00 41.51 3.02
1212 1225 5.821470 GTCTTATAACAAACTAGAAGGGCCC 59.179 44.000 16.46 16.46 0.00 5.80
1300 1313 3.214328 GGTGATGGTGTGAAAAGTCTGT 58.786 45.455 0.00 0.00 0.00 3.41
1822 1845 2.564062 ACTGCAATTGAGTTGGATTGGG 59.436 45.455 10.34 0.00 37.53 4.12
1909 1932 3.507622 TGCACCGATAGTCCATAGAGATG 59.492 47.826 0.00 0.00 0.00 2.90
1967 1990 6.888105 TCAGTGCCTGTATATCAGATTTTGA 58.112 36.000 0.00 0.00 46.27 2.69
1996 2019 5.007136 GCAAAAGTACTAGATGGAGATGCAC 59.993 44.000 0.00 0.00 0.00 4.57
2052 2081 7.093771 GGATATCTTGCCCCAGGTAAAATTATG 60.094 40.741 2.05 0.00 0.00 1.90
2053 2082 5.199982 TCTTGCCCCAGGTAAAATTATGA 57.800 39.130 0.00 0.00 0.00 2.15
2054 2083 5.200483 TCTTGCCCCAGGTAAAATTATGAG 58.800 41.667 0.00 0.00 0.00 2.90
2059 2088 6.102615 TGCCCCAGGTAAAATTATGAGTATCT 59.897 38.462 0.00 0.00 34.92 1.98
2060 2089 7.293771 TGCCCCAGGTAAAATTATGAGTATCTA 59.706 37.037 0.00 0.00 34.92 1.98
2109 2161 8.000285 TGTTTTCTCTATCTCGTAAACGTTTC 58.000 34.615 18.42 8.47 40.80 2.78
2112 2164 6.169419 TCTCTATCTCGTAAACGTTTCGAA 57.831 37.500 24.80 18.86 40.80 3.71
2187 2239 2.028112 TGCATCTATAATGACGAGGCCC 60.028 50.000 0.00 0.00 33.93 5.80
2200 2252 1.133482 CGAGGCCCAGGGGAATAAAAT 60.133 52.381 7.91 0.00 37.50 1.82
2208 2260 6.295859 GGCCCAGGGGAATAAAATATTTCATC 60.296 42.308 7.91 0.82 37.50 2.92
2290 2425 4.559153 AGAACAGTTTACCATGCATTTGC 58.441 39.130 0.00 0.00 42.50 3.68
2309 2444 5.682943 TTGCCTACAGTACACATTTTGTC 57.317 39.130 0.00 0.00 39.91 3.18
2318 2453 8.764524 ACAGTACACATTTTGTCTCTAATCTC 57.235 34.615 0.00 0.00 39.91 2.75
2323 2458 6.370994 ACACATTTTGTCTCTAATCTCTGCAG 59.629 38.462 7.63 7.63 29.79 4.41
2338 2473 1.660607 CTGCAGTACACATTAGCCACG 59.339 52.381 5.25 0.00 0.00 4.94
2347 2482 3.623060 ACACATTAGCCACGTCAATCATC 59.377 43.478 0.00 0.00 0.00 2.92
2371 2506 5.354234 CGAGCCCATTTGTTTCACTAACTAT 59.646 40.000 0.00 0.00 37.64 2.12
2373 2508 7.539034 AGCCCATTTGTTTCACTAACTATTT 57.461 32.000 0.00 0.00 37.64 1.40
2374 2509 7.378181 AGCCCATTTGTTTCACTAACTATTTG 58.622 34.615 0.00 0.00 37.64 2.32
2375 2510 6.090763 GCCCATTTGTTTCACTAACTATTTGC 59.909 38.462 0.00 0.00 37.64 3.68
2406 2544 6.762661 GCAATTTGTAATAATGGACATTGGCT 59.237 34.615 7.76 0.00 32.50 4.75
2411 2549 6.418946 TGTAATAATGGACATTGGCTGTGTA 58.581 36.000 7.76 0.00 38.54 2.90
2422 2560 1.321074 GGCTGTGTACGCCTCTAGGT 61.321 60.000 3.51 0.00 44.17 3.08
2457 2595 9.533253 AAGTGATTTCCATTTGTCTAAAAACAG 57.467 29.630 0.00 0.00 0.00 3.16
2463 2601 8.911918 TTCCATTTGTCTAAAAACAGTAGCTA 57.088 30.769 0.00 0.00 0.00 3.32
2665 2810 1.542915 CTTCCATGGCCAACAGAAGTG 59.457 52.381 24.36 12.41 30.68 3.16
2715 2860 2.555227 GCTCCCATTCCCTGAAACTGAA 60.555 50.000 0.00 0.00 0.00 3.02
2718 2863 5.509498 CTCCCATTCCCTGAAACTGAAATA 58.491 41.667 0.00 0.00 0.00 1.40
2882 3030 3.189606 ACATTGTCATCCCTTCCACCTA 58.810 45.455 0.00 0.00 0.00 3.08
2937 3088 9.737427 TTCATTTTAATTAGAGAACGTTTGCAA 57.263 25.926 0.46 0.00 0.00 4.08
3111 3262 6.266168 TCAAATGAGTGAACAAACACAGTT 57.734 33.333 0.00 0.00 42.45 3.16
3115 3266 9.086336 CAAATGAGTGAACAAACACAGTTAAAT 57.914 29.630 0.00 0.00 42.45 1.40
3177 3364 5.045432 ACCTTATATTTGTGAACGGAGGGAA 60.045 40.000 0.00 0.00 0.00 3.97
3186 3373 4.529377 TGTGAACGGAGGGAATACTAGTTT 59.471 41.667 0.00 0.00 0.00 2.66
3242 3429 5.847304 TGCTGTCTATCCTATGTGTGATTC 58.153 41.667 0.00 0.00 0.00 2.52
3289 3476 5.862323 TCTTACGAGTTTTCTCTACATGCAC 59.138 40.000 0.00 0.00 44.16 4.57
3375 3562 5.923684 GTGCTAGTGATAGGCTTCTCAATAC 59.076 44.000 0.00 0.00 0.00 1.89
3378 3565 6.644592 GCTAGTGATAGGCTTCTCAATACTTG 59.355 42.308 0.00 0.00 0.00 3.16
3381 3568 6.328672 AGTGATAGGCTTCTCAATACTTGGAT 59.671 38.462 0.00 0.00 0.00 3.41
3394 3581 9.927668 CTCAATACTTGGATTGGTTTTGTTTAT 57.072 29.630 5.81 0.00 37.41 1.40
3470 3663 4.082517 TGTTTGCAAACTTTGTACTCAGCA 60.083 37.500 35.09 13.66 39.59 4.41
3486 3679 9.938280 TGTACTCAGCAATGTAATAACTTAAGT 57.062 29.630 1.12 1.12 0.00 2.24
3526 3719 3.947834 GCAGAGAGCAGGGCTAATAAAAA 59.052 43.478 0.00 0.00 44.79 1.94
3621 3912 4.080356 TGGTTTCCAAGGGATACATGAGAG 60.080 45.833 0.00 0.00 35.79 3.20
3688 3979 4.689612 TTGCAGAAAAGTAGACAGGACT 57.310 40.909 0.00 0.00 0.00 3.85
3689 3980 4.689612 TGCAGAAAAGTAGACAGGACTT 57.310 40.909 0.00 0.00 38.81 3.01
3691 3982 3.187432 GCAGAAAAGTAGACAGGACTTGC 59.813 47.826 0.00 0.00 37.22 4.01
3699 3990 2.417719 AGACAGGACTTGCGATGTTTC 58.582 47.619 0.00 0.00 0.00 2.78
3719 4010 1.652124 CGTTAACGAGGTTCACCATCG 59.348 52.381 23.35 13.17 43.02 3.84
3730 4021 1.496060 TCACCATCGTGGCTAATCCT 58.504 50.000 4.23 0.00 42.67 3.24
3731 4022 1.138859 TCACCATCGTGGCTAATCCTG 59.861 52.381 4.23 0.00 42.67 3.86
3735 4026 1.688735 CATCGTGGCTAATCCTGAGGA 59.311 52.381 2.43 2.43 35.55 3.71
3739 4030 2.103094 CGTGGCTAATCCTGAGGAATGA 59.897 50.000 4.76 0.00 34.34 2.57
3743 4034 6.479884 GTGGCTAATCCTGAGGAATGATTAT 58.520 40.000 4.76 0.00 34.34 1.28
3754 4045 3.073650 AGGAATGATTATGGGCTCACCTC 59.926 47.826 0.00 0.00 41.11 3.85
3769 4060 3.197983 TCACCTCCCCATCTACCAAATT 58.802 45.455 0.00 0.00 0.00 1.82
3775 4066 6.566480 ACCTCCCCATCTACCAAATTACATAT 59.434 38.462 0.00 0.00 0.00 1.78
3776 4067 7.075009 ACCTCCCCATCTACCAAATTACATATT 59.925 37.037 0.00 0.00 0.00 1.28
3777 4068 7.611855 CCTCCCCATCTACCAAATTACATATTC 59.388 40.741 0.00 0.00 0.00 1.75
3778 4069 8.051468 TCCCCATCTACCAAATTACATATTCA 57.949 34.615 0.00 0.00 0.00 2.57
3779 4070 8.506921 TCCCCATCTACCAAATTACATATTCAA 58.493 33.333 0.00 0.00 0.00 2.69
3780 4071 8.576442 CCCCATCTACCAAATTACATATTCAAC 58.424 37.037 0.00 0.00 0.00 3.18
3781 4072 9.130661 CCCATCTACCAAATTACATATTCAACA 57.869 33.333 0.00 0.00 0.00 3.33
3782 4073 9.950680 CCATCTACCAAATTACATATTCAACAC 57.049 33.333 0.00 0.00 0.00 3.32
3800 4091 8.775220 TTCAACACAATTTTAACAGATACACG 57.225 30.769 0.00 0.00 0.00 4.49
3801 4092 7.356540 TCAACACAATTTTAACAGATACACGG 58.643 34.615 0.00 0.00 0.00 4.94
3802 4093 5.695818 ACACAATTTTAACAGATACACGGC 58.304 37.500 0.00 0.00 0.00 5.68
3803 4094 5.239744 ACACAATTTTAACAGATACACGGCA 59.760 36.000 0.00 0.00 0.00 5.69
3804 4095 6.072175 ACACAATTTTAACAGATACACGGCAT 60.072 34.615 0.00 0.00 0.00 4.40
3805 4096 6.251163 CACAATTTTAACAGATACACGGCATG 59.749 38.462 0.00 0.00 0.00 4.06
3806 4097 4.349663 TTTTAACAGATACACGGCATGC 57.650 40.909 9.90 9.90 0.00 4.06
3807 4098 2.979814 TAACAGATACACGGCATGCT 57.020 45.000 18.92 0.00 0.00 3.79
3808 4099 2.979814 AACAGATACACGGCATGCTA 57.020 45.000 18.92 1.76 0.00 3.49
3809 4100 3.475566 AACAGATACACGGCATGCTAT 57.524 42.857 18.92 7.29 0.00 2.97
3810 4101 2.759191 ACAGATACACGGCATGCTATG 58.241 47.619 18.92 17.74 0.00 2.23
3825 4116 5.750650 CATGCTATGCACACGATAAAATCA 58.249 37.500 0.00 0.00 43.04 2.57
3826 4117 5.408204 TGCTATGCACACGATAAAATCAG 57.592 39.130 0.00 0.00 31.71 2.90
3827 4118 4.273235 TGCTATGCACACGATAAAATCAGG 59.727 41.667 0.00 0.00 31.71 3.86
3828 4119 4.511454 GCTATGCACACGATAAAATCAGGA 59.489 41.667 0.00 0.00 0.00 3.86
3829 4120 4.882671 ATGCACACGATAAAATCAGGAC 57.117 40.909 0.00 0.00 0.00 3.85
3830 4121 2.670905 TGCACACGATAAAATCAGGACG 59.329 45.455 0.00 0.00 0.00 4.79
3831 4122 2.927477 GCACACGATAAAATCAGGACGA 59.073 45.455 0.00 0.00 0.00 4.20
3832 4123 3.555956 GCACACGATAAAATCAGGACGAT 59.444 43.478 0.00 0.00 35.12 3.73
3833 4124 4.034048 GCACACGATAAAATCAGGACGATT 59.966 41.667 0.00 0.00 46.70 3.34
3834 4125 5.728255 CACACGATAAAATCAGGACGATTC 58.272 41.667 0.00 0.00 43.83 2.52
3835 4126 5.290885 CACACGATAAAATCAGGACGATTCA 59.709 40.000 0.00 0.00 43.83 2.57
3836 4127 5.291128 ACACGATAAAATCAGGACGATTCAC 59.709 40.000 0.00 0.00 43.83 3.18
3837 4128 5.290885 CACGATAAAATCAGGACGATTCACA 59.709 40.000 0.00 0.00 43.83 3.58
3838 4129 5.520288 ACGATAAAATCAGGACGATTCACAG 59.480 40.000 0.00 0.00 43.83 3.66
3839 4130 5.748630 CGATAAAATCAGGACGATTCACAGA 59.251 40.000 0.00 0.00 43.83 3.41
3840 4131 6.291849 CGATAAAATCAGGACGATTCACAGAC 60.292 42.308 0.00 0.00 43.83 3.51
3841 4132 2.568696 ATCAGGACGATTCACAGACG 57.431 50.000 0.00 0.00 0.00 4.18
3842 4133 1.530323 TCAGGACGATTCACAGACGA 58.470 50.000 0.00 0.00 0.00 4.20
3843 4134 2.092323 TCAGGACGATTCACAGACGAT 58.908 47.619 0.00 0.00 0.00 3.73
3844 4135 2.159379 TCAGGACGATTCACAGACGATG 60.159 50.000 0.00 0.00 0.00 3.84
3845 4136 1.135139 AGGACGATTCACAGACGATGG 59.865 52.381 0.00 0.00 0.00 3.51
3846 4137 1.135083 GGACGATTCACAGACGATGGT 60.135 52.381 0.00 0.00 0.00 3.55
3847 4138 2.607187 GACGATTCACAGACGATGGTT 58.393 47.619 0.00 0.00 0.00 3.67
3848 4139 3.428452 GGACGATTCACAGACGATGGTTA 60.428 47.826 0.00 0.00 0.00 2.85
3849 4140 4.171005 GACGATTCACAGACGATGGTTAA 58.829 43.478 0.00 0.00 0.00 2.01
3850 4141 4.562082 ACGATTCACAGACGATGGTTAAA 58.438 39.130 0.00 0.00 0.00 1.52
3851 4142 5.175859 ACGATTCACAGACGATGGTTAAAT 58.824 37.500 0.00 0.00 0.00 1.40
3852 4143 5.291128 ACGATTCACAGACGATGGTTAAATC 59.709 40.000 0.00 0.00 0.00 2.17
3853 4144 5.290885 CGATTCACAGACGATGGTTAAATCA 59.709 40.000 0.00 0.00 0.00 2.57
3854 4145 6.508563 CGATTCACAGACGATGGTTAAATCAG 60.509 42.308 0.00 0.00 0.00 2.90
3855 4146 4.503910 TCACAGACGATGGTTAAATCAGG 58.496 43.478 0.00 0.00 0.00 3.86
3856 4147 3.063997 CACAGACGATGGTTAAATCAGGC 59.936 47.826 0.00 0.00 0.00 4.85
3857 4148 2.614057 CAGACGATGGTTAAATCAGGCC 59.386 50.000 0.00 0.00 0.00 5.19
3858 4149 1.597663 GACGATGGTTAAATCAGGCCG 59.402 52.381 0.00 0.00 0.00 6.13
3859 4150 1.065709 ACGATGGTTAAATCAGGCCGT 60.066 47.619 0.00 0.00 0.00 5.68
3860 4151 2.168936 ACGATGGTTAAATCAGGCCGTA 59.831 45.455 0.00 0.00 0.00 4.02
3861 4152 2.542595 CGATGGTTAAATCAGGCCGTAC 59.457 50.000 0.00 0.00 0.00 3.67
3862 4153 3.537580 GATGGTTAAATCAGGCCGTACA 58.462 45.455 0.00 0.00 0.00 2.90
3863 4154 3.637911 TGGTTAAATCAGGCCGTACAT 57.362 42.857 0.00 0.00 0.00 2.29
3864 4155 3.275143 TGGTTAAATCAGGCCGTACATG 58.725 45.455 0.00 0.00 0.00 3.21
3865 4156 2.032924 GGTTAAATCAGGCCGTACATGC 59.967 50.000 0.00 0.00 0.00 4.06
3866 4157 1.577468 TAAATCAGGCCGTACATGCG 58.423 50.000 0.00 0.00 0.00 4.73
3867 4158 0.392461 AAATCAGGCCGTACATGCGT 60.392 50.000 0.00 0.00 0.00 5.24
3868 4159 0.462375 AATCAGGCCGTACATGCGTA 59.538 50.000 0.00 0.00 0.00 4.42
3869 4160 0.679505 ATCAGGCCGTACATGCGTAT 59.320 50.000 0.00 0.00 0.00 3.06
3870 4161 0.249280 TCAGGCCGTACATGCGTATG 60.249 55.000 12.28 12.28 40.24 2.39
3871 4162 0.249280 CAGGCCGTACATGCGTATGA 60.249 55.000 20.86 1.06 36.84 2.15
3872 4163 0.032130 AGGCCGTACATGCGTATGAG 59.968 55.000 20.86 10.35 36.84 2.90
3873 4164 0.249322 GGCCGTACATGCGTATGAGT 60.249 55.000 20.86 0.90 36.84 3.41
3874 4165 0.852777 GCCGTACATGCGTATGAGTG 59.147 55.000 20.86 8.33 36.84 3.51
3875 4166 1.535226 GCCGTACATGCGTATGAGTGA 60.535 52.381 20.86 0.00 36.84 3.41
3876 4167 2.804647 CCGTACATGCGTATGAGTGAA 58.195 47.619 20.86 0.00 36.84 3.18
3877 4168 3.183754 CCGTACATGCGTATGAGTGAAA 58.816 45.455 20.86 0.00 36.84 2.69
3878 4169 3.000078 CCGTACATGCGTATGAGTGAAAC 60.000 47.826 20.86 7.04 36.84 2.78
3879 4170 3.610677 CGTACATGCGTATGAGTGAAACA 59.389 43.478 20.86 0.00 36.84 2.83
3880 4171 4.090786 CGTACATGCGTATGAGTGAAACAA 59.909 41.667 20.86 0.00 36.84 2.83
3881 4172 4.404507 ACATGCGTATGAGTGAAACAAC 57.595 40.909 20.86 0.00 37.19 3.32
3882 4173 3.812609 ACATGCGTATGAGTGAAACAACA 59.187 39.130 20.86 0.00 37.19 3.33
3883 4174 3.870723 TGCGTATGAGTGAAACAACAC 57.129 42.857 0.00 0.00 41.43 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 5.061721 TCCTTATTTCTTTAGGGATGGGC 57.938 43.478 0.00 0.00 0.00 5.36
133 134 1.806542 CCAGACTGTTTGGAATGGACG 59.193 52.381 11.74 0.00 37.96 4.79
386 387 6.477688 TGTTAGAACTTAGAGTCAACCAAACG 59.522 38.462 0.00 0.00 0.00 3.60
398 399 5.537674 ACCGGAGAGTTTGTTAGAACTTAGA 59.462 40.000 9.46 0.00 39.84 2.10
423 424 2.983879 AAAGACCGGATGGCAGGGG 61.984 63.158 9.46 3.72 39.70 4.79
470 471 5.536538 TCCAACCAACATGTTGTTATAAGCA 59.463 36.000 31.20 9.46 43.22 3.91
695 700 1.899814 TGGTGGTATGACTCCAGTGAC 59.100 52.381 0.00 0.00 35.49 3.67
828 833 0.178992 TCCCCTGAGCAAGTTGTTGG 60.179 55.000 4.48 0.00 33.87 3.77
1300 1313 2.035237 GACGTGTGGTCACAAGGGGA 62.035 60.000 18.15 0.00 45.36 4.81
1317 1330 7.941919 ACTTCCTTCCTTTTTGATAACTTGAC 58.058 34.615 0.00 0.00 0.00 3.18
1996 2019 1.956477 AGCAAGCCTTGTACAGTTTGG 59.044 47.619 6.28 7.54 0.00 3.28
2052 2081 9.530633 ACACAAAGATTTAACCGATAGATACTC 57.469 33.333 0.00 0.00 39.76 2.59
2053 2082 9.886132 AACACAAAGATTTAACCGATAGATACT 57.114 29.630 0.00 0.00 39.76 2.12
2054 2083 9.916397 CAACACAAAGATTTAACCGATAGATAC 57.084 33.333 0.00 0.00 39.76 2.24
2059 2088 7.731882 TGACAACACAAAGATTTAACCGATA 57.268 32.000 0.00 0.00 0.00 2.92
2060 2089 6.627395 TGACAACACAAAGATTTAACCGAT 57.373 33.333 0.00 0.00 0.00 4.18
2109 2161 3.194861 TCGCCAAATAATGACCTCTTCG 58.805 45.455 0.00 0.00 0.00 3.79
2112 2164 5.418840 ACAAATTCGCCAAATAATGACCTCT 59.581 36.000 0.00 0.00 0.00 3.69
2208 2260 9.901172 ACTAATAGGTGTTTAGGGTTTTAGATG 57.099 33.333 0.00 0.00 32.15 2.90
2217 2269 7.657023 AGTCAGTACTAATAGGTGTTTAGGG 57.343 40.000 0.00 0.00 32.84 3.53
2218 2270 9.367444 CAAAGTCAGTACTAATAGGTGTTTAGG 57.633 37.037 0.00 0.00 33.75 2.69
2224 2359 9.035607 CATAAGCAAAGTCAGTACTAATAGGTG 57.964 37.037 0.00 0.00 33.75 4.00
2226 2361 8.204836 ACCATAAGCAAAGTCAGTACTAATAGG 58.795 37.037 0.00 0.00 33.75 2.57
2290 2425 9.088512 GATTAGAGACAAAATGTGTACTGTAGG 57.911 37.037 0.00 0.00 41.96 3.18
2309 2444 6.640499 GCTAATGTGTACTGCAGAGATTAGAG 59.360 42.308 23.85 13.32 30.77 2.43
2318 2453 1.660607 CGTGGCTAATGTGTACTGCAG 59.339 52.381 13.48 13.48 0.00 4.41
2323 2458 3.930229 TGATTGACGTGGCTAATGTGTAC 59.070 43.478 0.00 0.00 0.00 2.90
2338 2473 2.684881 ACAAATGGGCTCGATGATTGAC 59.315 45.455 0.00 0.00 0.00 3.18
2347 2482 3.502211 AGTTAGTGAAACAAATGGGCTCG 59.498 43.478 0.00 0.00 41.43 5.03
2374 2509 7.973388 TGTCCATTATTACAAATTGCTAACAGC 59.027 33.333 0.00 0.00 42.82 4.40
2393 2531 2.083774 CGTACACAGCCAATGTCCATT 58.916 47.619 0.00 0.00 41.41 3.16
2406 2544 3.354948 TCTTACCTAGAGGCGTACACA 57.645 47.619 0.00 0.00 39.32 3.72
2411 2549 3.028094 TGGAATCTTACCTAGAGGCGT 57.972 47.619 0.00 0.00 39.32 5.68
2415 2553 7.713073 GGAAATCACTTGGAATCTTACCTAGAG 59.287 40.741 0.00 0.00 36.02 2.43
2422 2560 8.421249 ACAAATGGAAATCACTTGGAATCTTA 57.579 30.769 0.00 0.00 36.95 2.10
2517 2656 6.052360 TGCTATGCCAATATTGACGAGTTAA 58.948 36.000 17.23 0.00 0.00 2.01
2665 2810 2.288395 CCAACAAATCCTCAAGTGGTGC 60.288 50.000 0.00 0.00 0.00 5.01
2718 2863 7.094634 ACGATCACTTTGAATATTTCACTTGCT 60.095 33.333 0.00 0.00 39.87 3.91
2810 2955 4.681942 CAGGTCTTTCAGTTGTAGAGAACG 59.318 45.833 0.00 0.00 0.00 3.95
2852 3000 2.821969 GGGATGACAATGTCAGTTTGCT 59.178 45.455 21.23 3.36 46.04 3.91
2882 3030 2.224042 TGTCTTGAGCACATTCACGACT 60.224 45.455 12.01 0.00 43.13 4.18
3022 3173 2.635915 TGTGAACGGAGGGAGTAACAAT 59.364 45.455 0.00 0.00 0.00 2.71
3093 3244 7.026562 CACATTTAACTGTGTTTGTTCACTCA 58.973 34.615 15.75 0.00 41.29 3.41
3328 3515 4.637534 CACCACTCAAACTGAATCCTATGG 59.362 45.833 0.00 0.00 0.00 2.74
3375 3562 8.606040 AACATGATAAACAAAACCAATCCAAG 57.394 30.769 0.00 0.00 0.00 3.61
3378 3565 6.866248 ACGAACATGATAAACAAAACCAATCC 59.134 34.615 0.00 0.00 0.00 3.01
3381 3568 6.415280 CGAACGAACATGATAAACAAAACCAA 59.585 34.615 0.00 0.00 0.00 3.67
3394 3581 4.862350 TCAAACTACTCGAACGAACATGA 58.138 39.130 0.00 0.00 0.00 3.07
3434 3627 6.024656 GTTTGCAAACAATGGTCTTGCCAG 62.025 45.833 32.21 0.00 43.58 4.85
3531 3724 8.239038 TCCACCATTGTAAAAGTTGATAACAA 57.761 30.769 0.00 0.00 34.81 2.83
3532 3725 7.825331 TCCACCATTGTAAAAGTTGATAACA 57.175 32.000 0.00 0.00 0.00 2.41
3548 3741 3.053395 ACAGTGCTCCATATTCCACCATT 60.053 43.478 0.00 0.00 0.00 3.16
3656 3947 9.713740 GTCTACTTTTCTGCAATGATAGATTTG 57.286 33.333 0.00 0.00 0.00 2.32
3658 3949 9.107177 CTGTCTACTTTTCTGCAATGATAGATT 57.893 33.333 0.00 0.00 0.00 2.40
3659 3950 7.714377 CCTGTCTACTTTTCTGCAATGATAGAT 59.286 37.037 0.00 0.00 0.00 1.98
3661 3952 7.010923 GTCCTGTCTACTTTTCTGCAATGATAG 59.989 40.741 0.00 0.00 0.00 2.08
3662 3953 6.818644 GTCCTGTCTACTTTTCTGCAATGATA 59.181 38.462 0.00 0.00 0.00 2.15
3663 3954 5.645497 GTCCTGTCTACTTTTCTGCAATGAT 59.355 40.000 0.00 0.00 0.00 2.45
3699 3990 1.652124 CGATGGTGAACCTCGTTAACG 59.348 52.381 21.85 21.85 41.45 3.18
3714 4005 1.270518 CCTCAGGATTAGCCACGATGG 60.271 57.143 0.00 0.00 41.55 3.51
3716 4007 2.088104 TCCTCAGGATTAGCCACGAT 57.912 50.000 0.00 0.00 40.02 3.73
3719 4010 3.845781 TCATTCCTCAGGATTAGCCAC 57.154 47.619 0.00 0.00 40.02 5.01
3730 4021 3.181440 GGTGAGCCCATAATCATTCCTCA 60.181 47.826 0.00 0.00 0.00 3.86
3731 4022 3.073650 AGGTGAGCCCATAATCATTCCTC 59.926 47.826 0.00 0.00 34.66 3.71
3735 4026 2.108952 GGGAGGTGAGCCCATAATCATT 59.891 50.000 0.00 0.00 45.31 2.57
3754 4045 8.576442 GTTGAATATGTAATTTGGTAGATGGGG 58.424 37.037 0.00 0.00 0.00 4.96
3775 4066 7.858382 CCGTGTATCTGTTAAAATTGTGTTGAA 59.142 33.333 0.00 0.00 0.00 2.69
3776 4067 7.356540 CCGTGTATCTGTTAAAATTGTGTTGA 58.643 34.615 0.00 0.00 0.00 3.18
3777 4068 6.087555 GCCGTGTATCTGTTAAAATTGTGTTG 59.912 38.462 0.00 0.00 0.00 3.33
3778 4069 6.146898 GCCGTGTATCTGTTAAAATTGTGTT 58.853 36.000 0.00 0.00 0.00 3.32
3779 4070 5.239744 TGCCGTGTATCTGTTAAAATTGTGT 59.760 36.000 0.00 0.00 0.00 3.72
3780 4071 5.694816 TGCCGTGTATCTGTTAAAATTGTG 58.305 37.500 0.00 0.00 0.00 3.33
3781 4072 5.950758 TGCCGTGTATCTGTTAAAATTGT 57.049 34.783 0.00 0.00 0.00 2.71
3782 4073 5.229887 GCATGCCGTGTATCTGTTAAAATTG 59.770 40.000 6.36 0.00 0.00 2.32
3783 4074 5.125417 AGCATGCCGTGTATCTGTTAAAATT 59.875 36.000 15.66 0.00 0.00 1.82
3784 4075 4.640201 AGCATGCCGTGTATCTGTTAAAAT 59.360 37.500 15.66 0.00 0.00 1.82
3785 4076 4.006989 AGCATGCCGTGTATCTGTTAAAA 58.993 39.130 15.66 0.00 0.00 1.52
3786 4077 3.605634 AGCATGCCGTGTATCTGTTAAA 58.394 40.909 15.66 0.00 0.00 1.52
3787 4078 3.260475 AGCATGCCGTGTATCTGTTAA 57.740 42.857 15.66 0.00 0.00 2.01
3788 4079 2.979814 AGCATGCCGTGTATCTGTTA 57.020 45.000 15.66 0.00 0.00 2.41
3789 4080 2.979814 TAGCATGCCGTGTATCTGTT 57.020 45.000 15.66 0.00 0.00 3.16
3790 4081 2.759191 CATAGCATGCCGTGTATCTGT 58.241 47.619 15.66 0.00 0.00 3.41
3802 4093 5.750650 TGATTTTATCGTGTGCATAGCATG 58.249 37.500 0.00 0.00 41.91 4.06
3803 4094 5.049198 CCTGATTTTATCGTGTGCATAGCAT 60.049 40.000 0.00 0.00 41.91 3.79
3804 4095 4.273235 CCTGATTTTATCGTGTGCATAGCA 59.727 41.667 0.00 0.00 35.60 3.49
3805 4096 4.511454 TCCTGATTTTATCGTGTGCATAGC 59.489 41.667 0.00 0.00 0.00 2.97
3806 4097 5.332581 CGTCCTGATTTTATCGTGTGCATAG 60.333 44.000 0.00 0.00 0.00 2.23
3807 4098 4.506288 CGTCCTGATTTTATCGTGTGCATA 59.494 41.667 0.00 0.00 0.00 3.14
3808 4099 3.309682 CGTCCTGATTTTATCGTGTGCAT 59.690 43.478 0.00 0.00 0.00 3.96
3809 4100 2.670905 CGTCCTGATTTTATCGTGTGCA 59.329 45.455 0.00 0.00 0.00 4.57
3810 4101 2.927477 TCGTCCTGATTTTATCGTGTGC 59.073 45.455 0.00 0.00 0.00 4.57
3811 4102 5.718649 AATCGTCCTGATTTTATCGTGTG 57.281 39.130 0.00 0.00 45.06 3.82
3822 4113 2.092323 TCGTCTGTGAATCGTCCTGAT 58.908 47.619 0.00 0.00 39.67 2.90
3823 4114 1.530323 TCGTCTGTGAATCGTCCTGA 58.470 50.000 0.00 0.00 0.00 3.86
3824 4115 2.188524 CATCGTCTGTGAATCGTCCTG 58.811 52.381 0.00 0.00 0.00 3.86
3825 4116 1.135139 CCATCGTCTGTGAATCGTCCT 59.865 52.381 0.00 0.00 0.00 3.85
3826 4117 1.135083 ACCATCGTCTGTGAATCGTCC 60.135 52.381 0.00 0.00 0.00 4.79
3827 4118 2.279582 ACCATCGTCTGTGAATCGTC 57.720 50.000 0.00 0.00 0.00 4.20
3828 4119 2.743636 AACCATCGTCTGTGAATCGT 57.256 45.000 0.00 0.00 0.00 3.73
3829 4120 5.290885 TGATTTAACCATCGTCTGTGAATCG 59.709 40.000 0.00 0.00 0.00 3.34
3830 4121 6.238211 CCTGATTTAACCATCGTCTGTGAATC 60.238 42.308 0.00 0.00 0.00 2.52
3831 4122 5.586243 CCTGATTTAACCATCGTCTGTGAAT 59.414 40.000 0.00 0.00 0.00 2.57
3832 4123 4.935205 CCTGATTTAACCATCGTCTGTGAA 59.065 41.667 0.00 0.00 0.00 3.18
3833 4124 4.503910 CCTGATTTAACCATCGTCTGTGA 58.496 43.478 0.00 0.00 0.00 3.58
3834 4125 3.063997 GCCTGATTTAACCATCGTCTGTG 59.936 47.826 0.00 0.00 0.00 3.66
3835 4126 3.270877 GCCTGATTTAACCATCGTCTGT 58.729 45.455 0.00 0.00 0.00 3.41
3836 4127 2.614057 GGCCTGATTTAACCATCGTCTG 59.386 50.000 0.00 0.00 0.00 3.51
3837 4128 2.741878 CGGCCTGATTTAACCATCGTCT 60.742 50.000 0.00 0.00 0.00 4.18
3838 4129 1.597663 CGGCCTGATTTAACCATCGTC 59.402 52.381 0.00 0.00 0.00 4.20
3839 4130 1.065709 ACGGCCTGATTTAACCATCGT 60.066 47.619 0.00 0.00 0.00 3.73
3840 4131 1.663695 ACGGCCTGATTTAACCATCG 58.336 50.000 0.00 0.00 0.00 3.84
3841 4132 3.537580 TGTACGGCCTGATTTAACCATC 58.462 45.455 0.00 0.00 0.00 3.51
3842 4133 3.637911 TGTACGGCCTGATTTAACCAT 57.362 42.857 0.00 0.00 0.00 3.55
3843 4134 3.275143 CATGTACGGCCTGATTTAACCA 58.725 45.455 0.00 0.00 0.00 3.67
3844 4135 2.032924 GCATGTACGGCCTGATTTAACC 59.967 50.000 0.00 0.00 0.00 2.85
3845 4136 2.286184 CGCATGTACGGCCTGATTTAAC 60.286 50.000 0.00 0.00 0.00 2.01
3846 4137 1.937223 CGCATGTACGGCCTGATTTAA 59.063 47.619 0.00 0.00 0.00 1.52
3847 4138 1.134640 ACGCATGTACGGCCTGATTTA 60.135 47.619 0.00 0.00 37.37 1.40
3848 4139 0.392461 ACGCATGTACGGCCTGATTT 60.392 50.000 0.00 0.00 37.37 2.17
3849 4140 0.462375 TACGCATGTACGGCCTGATT 59.538 50.000 0.00 0.00 37.37 2.57
3850 4141 0.679505 ATACGCATGTACGGCCTGAT 59.320 50.000 0.00 0.00 37.37 2.90
3851 4142 0.249280 CATACGCATGTACGGCCTGA 60.249 55.000 0.00 0.00 37.37 3.86
3852 4143 0.249280 TCATACGCATGTACGGCCTG 60.249 55.000 0.00 0.00 37.37 4.85
3853 4144 0.032130 CTCATACGCATGTACGGCCT 59.968 55.000 0.00 0.00 37.37 5.19
3854 4145 0.249322 ACTCATACGCATGTACGGCC 60.249 55.000 0.00 0.00 37.37 6.13
3855 4146 0.852777 CACTCATACGCATGTACGGC 59.147 55.000 0.00 0.00 37.37 5.68
3856 4147 2.485266 TCACTCATACGCATGTACGG 57.515 50.000 0.00 0.00 37.37 4.02
3857 4148 3.610677 TGTTTCACTCATACGCATGTACG 59.389 43.478 0.00 0.00 39.50 3.67
3858 4149 5.107259 TGTTGTTTCACTCATACGCATGTAC 60.107 40.000 0.00 0.00 32.26 2.90
3859 4150 4.991687 TGTTGTTTCACTCATACGCATGTA 59.008 37.500 0.00 0.00 33.57 2.29
3860 4151 3.812609 TGTTGTTTCACTCATACGCATGT 59.187 39.130 0.00 0.00 33.57 3.21
3861 4152 4.151070 GTGTTGTTTCACTCATACGCATG 58.849 43.478 0.00 0.00 35.68 4.06
3862 4153 4.404507 GTGTTGTTTCACTCATACGCAT 57.595 40.909 0.00 0.00 35.68 4.73
3863 4154 3.870723 GTGTTGTTTCACTCATACGCA 57.129 42.857 0.00 0.00 35.68 5.24


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

AutoCloner maintained by Alex Coulton.