Multiple sequence alignment - TraesCS6A01G401800

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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 TraesCS6A01G401800 chr6A 100.000 3692 0 0 1 3692 610187197 610190888 0.000000e+00 6818.0
1 TraesCS6A01G401800 chr6A 98.036 662 13 0 1 662 16108088 16107427 0.000000e+00 1151.0
2 TraesCS6A01G401800 chr6A 85.969 449 36 15 2963 3388 610206259 610205815 4.350000e-124 455.0
3 TraesCS6A01G401800 chr6A 80.038 521 78 20 850 1354 610250919 610250409 2.710000e-96 363.0
4 TraesCS6A01G401800 chr6A 87.755 98 10 2 2812 2908 610206603 610206507 3.010000e-21 113.0
5 TraesCS6A01G401800 chr6A 86.139 101 7 1 727 827 609847178 609847085 6.520000e-18 102.0
6 TraesCS6A01G401800 chr6A 93.846 65 4 0 1448 1512 609058263 609058199 8.440000e-17 99.0
7 TraesCS6A01G401800 chr6A 92.857 42 3 0 2402 2443 610209744 610209703 1.110000e-05 62.1
8 TraesCS6A01G401800 chr6B 90.198 2632 172 48 984 3564 706898373 706900969 0.000000e+00 3352.0
9 TraesCS6A01G401800 chr6B 91.653 1857 123 17 984 2810 706915431 706913577 0.000000e+00 2542.0
10 TraesCS6A01G401800 chr6B 82.100 838 112 19 678 1506 706878302 706879110 0.000000e+00 682.0
11 TraesCS6A01G401800 chr6B 82.377 488 46 18 2934 3388 706913215 706912735 4.470000e-104 388.0
12 TraesCS6A01G401800 chr6B 84.252 127 20 0 2684 2810 706935577 706935451 1.390000e-24 124.0
13 TraesCS6A01G401800 chr6B 96.667 60 2 0 3633 3692 706900988 706901047 2.350000e-17 100.0
14 TraesCS6A01G401800 chr6B 95.000 60 3 0 2812 2871 706935410 706935351 1.090000e-15 95.3
15 TraesCS6A01G401800 chr6D 92.339 1971 97 22 988 2920 463544995 463546949 0.000000e+00 2754.0
16 TraesCS6A01G401800 chr6D 85.567 582 60 14 669 1244 463537197 463537760 4.110000e-164 588.0
17 TraesCS6A01G401800 chr6D 81.192 537 61 24 2951 3450 463618439 463617906 2.670000e-106 396.0
18 TraesCS6A01G401800 chr6D 76.403 606 103 22 942 1533 463617204 463616625 1.300000e-74 291.0
19 TraesCS6A01G401800 chr6D 93.056 72 5 0 2813 2884 463618762 463618691 5.040000e-19 106.0
20 TraesCS6A01G401800 chr7A 97.741 664 13 1 1 662 732421128 732420465 0.000000e+00 1142.0
21 TraesCS6A01G401800 chr7A 97.130 662 19 0 1 662 731085536 731086197 0.000000e+00 1118.0
22 TraesCS6A01G401800 chr2A 97.734 662 15 0 1 662 777996124 777996785 0.000000e+00 1140.0
23 TraesCS6A01G401800 chr2A 97.432 662 17 0 1 662 31653402 31652741 0.000000e+00 1129.0
24 TraesCS6A01G401800 chr2A 96.988 664 18 1 1 662 767490083 767489420 0.000000e+00 1114.0
25 TraesCS6A01G401800 chrUn 97.432 662 17 0 1 662 75286844 75286183 0.000000e+00 1129.0
26 TraesCS6A01G401800 chr1A 97.293 665 18 0 1 665 2701962 2701298 0.000000e+00 1129.0
27 TraesCS6A01G401800 chr1A 97.285 663 17 1 1 663 13485627 13486288 0.000000e+00 1123.0
28 TraesCS6A01G401800 chr4D 95.000 60 3 0 1448 1507 503623886 503623827 1.090000e-15 95.3
29 TraesCS6A01G401800 chr4D 89.062 64 7 0 1449 1512 503594594 503594531 3.060000e-11 80.5
30 TraesCS6A01G401800 chr5A 85.333 75 11 0 1448 1522 688144612 688144538 1.100000e-10 78.7
31 TraesCS6A01G401800 chr4A 76.301 173 26 12 1039 1199 600466757 600466588 1.100000e-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 TraesCS6A01G401800 chr6A 610187197 610190888 3691 False 6818.000000 6818 100.000000 1 3692 1 chr6A.!!$F1 3691
1 TraesCS6A01G401800 chr6A 16107427 16108088 661 True 1151.000000 1151 98.036000 1 662 1 chr6A.!!$R1 661
2 TraesCS6A01G401800 chr6A 610250409 610250919 510 True 363.000000 363 80.038000 850 1354 1 chr6A.!!$R4 504
3 TraesCS6A01G401800 chr6A 610205815 610209744 3929 True 210.033333 455 88.860333 2402 3388 3 chr6A.!!$R5 986
4 TraesCS6A01G401800 chr6B 706898373 706901047 2674 False 1726.000000 3352 93.432500 984 3692 2 chr6B.!!$F2 2708
5 TraesCS6A01G401800 chr6B 706912735 706915431 2696 True 1465.000000 2542 87.015000 984 3388 2 chr6B.!!$R1 2404
6 TraesCS6A01G401800 chr6B 706878302 706879110 808 False 682.000000 682 82.100000 678 1506 1 chr6B.!!$F1 828
7 TraesCS6A01G401800 chr6D 463544995 463546949 1954 False 2754.000000 2754 92.339000 988 2920 1 chr6D.!!$F2 1932
8 TraesCS6A01G401800 chr6D 463537197 463537760 563 False 588.000000 588 85.567000 669 1244 1 chr6D.!!$F1 575
9 TraesCS6A01G401800 chr6D 463616625 463618762 2137 True 264.333333 396 83.550333 942 3450 3 chr6D.!!$R1 2508
10 TraesCS6A01G401800 chr7A 732420465 732421128 663 True 1142.000000 1142 97.741000 1 662 1 chr7A.!!$R1 661
11 TraesCS6A01G401800 chr7A 731085536 731086197 661 False 1118.000000 1118 97.130000 1 662 1 chr7A.!!$F1 661
12 TraesCS6A01G401800 chr2A 777996124 777996785 661 False 1140.000000 1140 97.734000 1 662 1 chr2A.!!$F1 661
13 TraesCS6A01G401800 chr2A 31652741 31653402 661 True 1129.000000 1129 97.432000 1 662 1 chr2A.!!$R1 661
14 TraesCS6A01G401800 chr2A 767489420 767490083 663 True 1114.000000 1114 96.988000 1 662 1 chr2A.!!$R2 661
15 TraesCS6A01G401800 chrUn 75286183 75286844 661 True 1129.000000 1129 97.432000 1 662 1 chrUn.!!$R1 661
16 TraesCS6A01G401800 chr1A 2701298 2701962 664 True 1129.000000 1129 97.293000 1 665 1 chr1A.!!$R1 664
17 TraesCS6A01G401800 chr1A 13485627 13486288 661 False 1123.000000 1123 97.285000 1 663 1 chr1A.!!$F1 662

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
847 850 0.100146 CTAGACCCAACTACGGACGC 59.900 60.0 0.00 0.0 0.0 5.19 F
1258 1909 0.091344 CGCGCGTTCAGAACAACTAG 59.909 55.0 24.19 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2082 2736 0.462759 GGTGTGCTAGCATCCACTCC 60.463 60.0 27.77 18.66 38.12 3.85 R
3023 6650 0.679505 CACCTCCAGTTCGACTTCCA 59.320 55.0 0.00 0.00 0.00 3.53 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
460 463 1.624391 GGTACTAAAGGGGCTGGAGGA 60.624 57.143 0.00 0.00 0.00 3.71
484 487 3.087031 CCCATTCTGACAACATTCTGCT 58.913 45.455 0.00 0.00 0.00 4.24
486 489 4.885907 CCCATTCTGACAACATTCTGCTAT 59.114 41.667 0.00 0.00 0.00 2.97
764 767 4.456566 AGACACAAAACCAAAACACGTACT 59.543 37.500 0.00 0.00 0.00 2.73
765 768 5.642919 AGACACAAAACCAAAACACGTACTA 59.357 36.000 0.00 0.00 0.00 1.82
766 769 5.630061 ACACAAAACCAAAACACGTACTAC 58.370 37.500 0.00 0.00 0.00 2.73
819 822 2.688507 ACCGGATCGATATGCACAATC 58.311 47.619 9.46 0.00 0.00 2.67
834 837 6.441093 TGCACAATCAATTCAATCTAGACC 57.559 37.500 0.00 0.00 0.00 3.85
847 850 0.100146 CTAGACCCAACTACGGACGC 59.900 60.000 0.00 0.00 0.00 5.19
883 886 1.360162 ACCCAGCCACCAGTACTACTA 59.640 52.381 0.00 0.00 0.00 1.82
884 887 1.755380 CCCAGCCACCAGTACTACTAC 59.245 57.143 0.00 0.00 0.00 2.73
885 888 2.623502 CCCAGCCACCAGTACTACTACT 60.624 54.545 0.00 0.00 33.01 2.57
1059 1697 0.393944 ACGTGCTCCTCGACATCCTA 60.394 55.000 0.00 0.00 0.00 2.94
1258 1909 0.091344 CGCGCGTTCAGAACAACTAG 59.909 55.000 24.19 0.00 0.00 2.57
1437 2088 2.517959 CCATTGCCAGAGAAGGAAACA 58.482 47.619 0.00 0.00 0.00 2.83
1535 2186 2.050918 GGGAAAGATCCTACCAGAGGG 58.949 57.143 0.00 0.00 46.70 4.30
1538 2189 3.389656 GGAAAGATCCTACCAGAGGGAAG 59.610 52.174 0.00 0.00 46.70 3.46
1608 2259 6.321181 ACTTGCCTATGTTGTTTGAAGAAGAA 59.679 34.615 0.00 0.00 0.00 2.52
1638 2289 4.465660 TCTGAAGAAGACCAAGAGGAGATG 59.534 45.833 0.00 0.00 38.69 2.90
1795 2449 4.494091 AGGAAACTCTATGACATGGTGG 57.506 45.455 0.00 0.00 32.90 4.61
1902 2556 2.030893 CCTTTTGATCTTGCGCAACTCA 60.031 45.455 21.02 20.97 0.00 3.41
1934 2588 2.225242 ACAACATGGCCCAATTACCAGA 60.225 45.455 0.00 0.00 39.88 3.86
2059 2713 3.370527 CCAACTAAGGGTATGGACACTGG 60.371 52.174 0.00 0.00 38.88 4.00
2076 2730 4.780021 ACACTGGTAGAATCAGAAGATGGT 59.220 41.667 0.00 0.00 36.22 3.55
2082 2736 4.484537 AGAATCAGAAGATGGTCAGGTG 57.515 45.455 0.00 0.00 33.90 4.00
2211 2865 8.806146 AGCTTGTTTGAACCTTATAACATTGAT 58.194 29.630 0.00 0.00 31.30 2.57
2215 2869 8.739039 TGTTTGAACCTTATAACATTGATGAGG 58.261 33.333 0.00 0.00 36.40 3.86
2227 2905 1.478631 TGATGAGGAGAGCGACACAT 58.521 50.000 0.00 0.00 0.00 3.21
2266 2944 1.455786 ACGATGAAAACGACGAAGCAG 59.544 47.619 0.00 0.00 34.88 4.24
2270 2948 1.864711 TGAAAACGACGAAGCAGAAGG 59.135 47.619 0.00 0.00 0.00 3.46
2282 2960 0.106819 GCAGAAGGCATCCATGAGGT 60.107 55.000 0.00 0.00 43.97 3.85
2325 3003 4.451096 ACAACCAGTAATGTTGATGACGAC 59.549 41.667 9.86 0.00 44.57 4.34
2345 3023 2.365617 ACGGTCACAGTGAAGAAGATGT 59.634 45.455 4.32 0.00 0.00 3.06
2369 3047 3.305629 GCTCACGAAGATGAAGATGACAC 59.694 47.826 0.00 0.00 0.00 3.67
2394 3072 7.446625 ACATTCAAAAGTGTAGAGAGCTTTGAT 59.553 33.333 0.00 0.00 33.36 2.57
2430 3108 4.021104 TCAGACGAGGACAACTTCATTGAT 60.021 41.667 0.00 0.00 41.23 2.57
2445 3123 9.512588 AACTTCATTGATCTACATGAAAGTTCT 57.487 29.630 0.00 3.02 33.01 3.01
2549 3248 7.981789 CGTTACAGCATATCATATTAGGACCAT 59.018 37.037 0.00 0.00 0.00 3.55
2642 3341 2.202960 TTACCGCCCATGCTACGC 60.203 61.111 0.00 0.00 34.43 4.42
2705 3422 3.702048 GTGACCTGCCCCGTAGCA 61.702 66.667 0.00 0.00 41.46 3.49
2757 6133 1.425066 TGAAGATGGACCAAGGTTGCT 59.575 47.619 0.00 0.00 0.00 3.91
2889 6310 9.974980 AATATACACCACTTTTTACTTTGTTGG 57.025 29.630 0.00 0.00 0.00 3.77
2898 6319 9.360093 CACTTTTTACTTTGTTGGTTGTGATAA 57.640 29.630 0.00 0.00 0.00 1.75
2926 6398 6.036517 GCTACTCCAGAATGTACATGTTTCTG 59.963 42.308 23.29 23.29 43.75 3.02
2927 6399 4.697352 ACTCCAGAATGTACATGTTTCTGC 59.303 41.667 24.25 6.46 43.12 4.26
2928 6400 4.650734 TCCAGAATGTACATGTTTCTGCA 58.349 39.130 24.25 13.53 43.12 4.41
2929 6401 5.255687 TCCAGAATGTACATGTTTCTGCAT 58.744 37.500 24.25 11.42 43.12 3.96
2930 6402 6.413892 TCCAGAATGTACATGTTTCTGCATA 58.586 36.000 24.25 13.86 43.12 3.14
2932 6559 7.012610 TCCAGAATGTACATGTTTCTGCATATG 59.987 37.037 24.25 14.88 43.12 1.78
2937 6564 8.962884 ATGTACATGTTTCTGCATATGTTCTA 57.037 30.769 7.78 0.00 35.55 2.10
2948 6575 7.382898 TCTGCATATGTTCTACTGTTGTGTTA 58.617 34.615 4.29 0.00 0.00 2.41
3011 6638 1.002990 CAGGCTGATGCTGGTGACA 60.003 57.895 9.42 0.00 39.59 3.58
3023 6650 1.738099 GGTGACAATGAGCGTCGCT 60.738 57.895 21.92 21.92 42.29 4.93
3029 6657 1.016130 CAATGAGCGTCGCTGGAAGT 61.016 55.000 27.16 6.37 39.88 3.01
3045 6673 2.047179 GTCGAACTGGAGGTGGCC 60.047 66.667 0.00 0.00 0.00 5.36
3046 6674 2.525629 TCGAACTGGAGGTGGCCA 60.526 61.111 0.00 0.00 36.30 5.36
3066 6694 2.637872 CAAAGAAGGAGAGGGTGTACCA 59.362 50.000 3.11 0.00 43.89 3.25
3108 6737 1.291877 GCTCACGCACGATCAGGTTT 61.292 55.000 0.00 0.00 35.78 3.27
3115 6744 2.436646 CGATCAGGTTTGCCGCCT 60.437 61.111 0.00 0.00 40.50 5.52
3136 6765 1.529010 CCCAGCAGCAACAGGTTGA 60.529 57.895 15.88 0.00 42.93 3.18
3208 6853 4.530857 GGGAGATGACCGCCACCG 62.531 72.222 0.00 0.00 36.33 4.94
3245 6890 1.064060 GACTGCAACGAAGCACAAACT 59.936 47.619 2.57 0.00 40.11 2.66
3273 6935 2.158900 AGAGTCTGTCAGTTTGTGGTGG 60.159 50.000 0.00 0.00 0.00 4.61
3277 6939 1.140852 CTGTCAGTTTGTGGTGGAGGA 59.859 52.381 0.00 0.00 0.00 3.71
3294 6956 3.614092 GAGGAGATTTGGCATGTTCAGA 58.386 45.455 0.00 0.00 0.00 3.27
3317 6982 8.253810 CAGATGGTTCTGTTCTTCAGTAGAATA 58.746 37.037 0.00 0.00 44.39 1.75
3338 7003 8.854117 AGAATAAATGATTGGCCTATCTGAAAC 58.146 33.333 24.65 11.90 0.00 2.78
3345 7010 2.819608 TGGCCTATCTGAAACAAGTTGC 59.180 45.455 3.32 0.00 0.00 4.17
3348 7013 3.375299 GCCTATCTGAAACAAGTTGCGAT 59.625 43.478 1.81 0.81 0.00 4.58
3350 7015 4.872691 CCTATCTGAAACAAGTTGCGATCT 59.127 41.667 1.81 0.00 0.00 2.75
3351 7016 4.675190 ATCTGAAACAAGTTGCGATCTG 57.325 40.909 1.81 3.62 0.00 2.90
3352 7017 3.727726 TCTGAAACAAGTTGCGATCTGA 58.272 40.909 1.81 5.82 0.00 3.27
3353 7018 3.494626 TCTGAAACAAGTTGCGATCTGAC 59.505 43.478 1.81 0.00 0.00 3.51
3354 7019 3.202097 TGAAACAAGTTGCGATCTGACA 58.798 40.909 1.81 0.00 0.00 3.58
3355 7020 3.248363 TGAAACAAGTTGCGATCTGACAG 59.752 43.478 1.81 0.00 0.00 3.51
3356 7021 2.533266 ACAAGTTGCGATCTGACAGT 57.467 45.000 1.81 0.00 0.00 3.55
3357 7022 2.408050 ACAAGTTGCGATCTGACAGTC 58.592 47.619 1.81 0.00 0.00 3.51
3358 7023 2.036475 ACAAGTTGCGATCTGACAGTCT 59.964 45.455 1.81 0.00 0.00 3.24
3359 7024 2.360553 AGTTGCGATCTGACAGTCTG 57.639 50.000 1.59 1.11 0.00 3.51
3360 7025 1.067283 AGTTGCGATCTGACAGTCTGG 60.067 52.381 4.53 0.00 0.00 3.86
3361 7026 1.067565 GTTGCGATCTGACAGTCTGGA 60.068 52.381 4.53 3.82 0.00 3.86
3362 7027 1.478631 TGCGATCTGACAGTCTGGAT 58.521 50.000 4.53 8.15 0.00 3.41
3363 7028 2.654863 TGCGATCTGACAGTCTGGATA 58.345 47.619 4.53 0.00 0.00 2.59
3364 7029 2.620585 TGCGATCTGACAGTCTGGATAG 59.379 50.000 4.53 9.31 0.00 2.08
3365 7030 2.606795 GCGATCTGACAGTCTGGATAGC 60.607 54.545 18.25 18.25 32.00 2.97
3366 7031 2.620585 CGATCTGACAGTCTGGATAGCA 59.379 50.000 4.53 0.00 0.00 3.49
3376 7041 7.671398 TGACAGTCTGGATAGCATCATCTAATA 59.329 37.037 4.53 0.00 0.00 0.98
3391 7056 9.152595 CATCATCTAATACATTCAGACATCCAG 57.847 37.037 0.00 0.00 0.00 3.86
3428 7094 3.365969 CGTTTCATTTCCCAGGTTACTGC 60.366 47.826 0.00 0.00 43.53 4.40
3447 7115 9.793252 GTTACTGCATTCAGATTAATTGTGATT 57.207 29.630 0.00 0.00 42.95 2.57
3474 7142 5.136828 TGATGTTTTGGAAGCAACTAGGAA 58.863 37.500 0.00 0.00 0.00 3.36
3531 7201 7.370383 ACAAACTGGCTAACATCTAAAACATG 58.630 34.615 0.00 0.00 0.00 3.21
3535 7205 4.398988 TGGCTAACATCTAAAACATGCAGG 59.601 41.667 0.00 0.00 0.00 4.85
3542 7212 3.495331 TCTAAAACATGCAGGCTTCCAA 58.505 40.909 0.00 0.00 0.00 3.53
3560 7230 5.818136 TCCAAGCTGAATAATGCTAACAC 57.182 39.130 0.00 0.00 38.75 3.32
3561 7231 5.252547 TCCAAGCTGAATAATGCTAACACA 58.747 37.500 0.00 0.00 38.75 3.72
3562 7232 5.709631 TCCAAGCTGAATAATGCTAACACAA 59.290 36.000 0.00 0.00 38.75 3.33
3563 7233 6.208402 TCCAAGCTGAATAATGCTAACACAAA 59.792 34.615 0.00 0.00 38.75 2.83
3564 7234 6.308766 CCAAGCTGAATAATGCTAACACAAAC 59.691 38.462 0.00 0.00 38.75 2.93
3565 7235 6.824305 AGCTGAATAATGCTAACACAAACT 57.176 33.333 0.00 0.00 37.81 2.66
3566 7236 6.615088 AGCTGAATAATGCTAACACAAACTG 58.385 36.000 0.00 0.00 37.81 3.16
3567 7237 5.287035 GCTGAATAATGCTAACACAAACTGC 59.713 40.000 0.00 0.00 0.00 4.40
3568 7238 6.573664 TGAATAATGCTAACACAAACTGCT 57.426 33.333 0.00 0.00 0.00 4.24
3569 7239 6.980593 TGAATAATGCTAACACAAACTGCTT 58.019 32.000 0.00 0.00 0.00 3.91
3570 7240 7.083858 TGAATAATGCTAACACAAACTGCTTC 58.916 34.615 0.00 0.00 0.00 3.86
3571 7241 4.916983 AATGCTAACACAAACTGCTTCA 57.083 36.364 0.00 0.00 0.00 3.02
3572 7242 4.916983 ATGCTAACACAAACTGCTTCAA 57.083 36.364 0.00 0.00 0.00 2.69
3573 7243 4.291540 TGCTAACACAAACTGCTTCAAG 57.708 40.909 0.00 0.00 0.00 3.02
3574 7244 3.944650 TGCTAACACAAACTGCTTCAAGA 59.055 39.130 0.00 0.00 0.00 3.02
3575 7245 4.397730 TGCTAACACAAACTGCTTCAAGAA 59.602 37.500 0.00 0.00 0.00 2.52
3576 7246 4.735338 GCTAACACAAACTGCTTCAAGAAC 59.265 41.667 0.00 0.00 0.00 3.01
3577 7247 3.782889 ACACAAACTGCTTCAAGAACC 57.217 42.857 0.00 0.00 0.00 3.62
3578 7248 2.427095 ACACAAACTGCTTCAAGAACCC 59.573 45.455 0.00 0.00 0.00 4.11
3579 7249 2.426738 CACAAACTGCTTCAAGAACCCA 59.573 45.455 0.00 0.00 0.00 4.51
3580 7250 2.427095 ACAAACTGCTTCAAGAACCCAC 59.573 45.455 0.00 0.00 0.00 4.61
3581 7251 1.308998 AACTGCTTCAAGAACCCACG 58.691 50.000 0.00 0.00 0.00 4.94
3582 7252 0.468226 ACTGCTTCAAGAACCCACGA 59.532 50.000 0.00 0.00 0.00 4.35
3583 7253 0.868406 CTGCTTCAAGAACCCACGAC 59.132 55.000 0.00 0.00 0.00 4.34
3584 7254 0.179234 TGCTTCAAGAACCCACGACA 59.821 50.000 0.00 0.00 0.00 4.35
3585 7255 1.305201 GCTTCAAGAACCCACGACAA 58.695 50.000 0.00 0.00 0.00 3.18
3586 7256 1.002792 GCTTCAAGAACCCACGACAAC 60.003 52.381 0.00 0.00 0.00 3.32
3587 7257 2.285083 CTTCAAGAACCCACGACAACA 58.715 47.619 0.00 0.00 0.00 3.33
3588 7258 2.404923 TCAAGAACCCACGACAACAA 57.595 45.000 0.00 0.00 0.00 2.83
3589 7259 2.011222 TCAAGAACCCACGACAACAAC 58.989 47.619 0.00 0.00 0.00 3.32
3590 7260 2.014128 CAAGAACCCACGACAACAACT 58.986 47.619 0.00 0.00 0.00 3.16
3591 7261 3.118702 TCAAGAACCCACGACAACAACTA 60.119 43.478 0.00 0.00 0.00 2.24
3592 7262 3.547054 AGAACCCACGACAACAACTAA 57.453 42.857 0.00 0.00 0.00 2.24
3593 7263 3.463944 AGAACCCACGACAACAACTAAG 58.536 45.455 0.00 0.00 0.00 2.18
3594 7264 3.133362 AGAACCCACGACAACAACTAAGA 59.867 43.478 0.00 0.00 0.00 2.10
3595 7265 3.547054 ACCCACGACAACAACTAAGAA 57.453 42.857 0.00 0.00 0.00 2.52
3596 7266 3.463944 ACCCACGACAACAACTAAGAAG 58.536 45.455 0.00 0.00 0.00 2.85
3597 7267 2.806244 CCCACGACAACAACTAAGAAGG 59.194 50.000 0.00 0.00 0.00 3.46
3598 7268 3.493699 CCCACGACAACAACTAAGAAGGA 60.494 47.826 0.00 0.00 0.00 3.36
3599 7269 4.124238 CCACGACAACAACTAAGAAGGAA 58.876 43.478 0.00 0.00 0.00 3.36
3600 7270 4.573201 CCACGACAACAACTAAGAAGGAAA 59.427 41.667 0.00 0.00 0.00 3.13
3601 7271 5.499047 CACGACAACAACTAAGAAGGAAAC 58.501 41.667 0.00 0.00 0.00 2.78
3602 7272 5.064198 CACGACAACAACTAAGAAGGAAACA 59.936 40.000 0.00 0.00 0.00 2.83
3603 7273 5.293569 ACGACAACAACTAAGAAGGAAACAG 59.706 40.000 0.00 0.00 0.00 3.16
3604 7274 5.293569 CGACAACAACTAAGAAGGAAACAGT 59.706 40.000 0.00 0.00 0.00 3.55
3605 7275 6.183360 CGACAACAACTAAGAAGGAAACAGTT 60.183 38.462 0.00 0.00 0.00 3.16
3606 7276 7.462571 ACAACAACTAAGAAGGAAACAGTTT 57.537 32.000 0.00 0.00 0.00 2.66
3607 7277 7.312899 ACAACAACTAAGAAGGAAACAGTTTG 58.687 34.615 2.34 0.00 0.00 2.93
3608 7278 5.891451 ACAACTAAGAAGGAAACAGTTTGC 58.109 37.500 9.45 9.45 0.00 3.68
3609 7279 4.813296 ACTAAGAAGGAAACAGTTTGCG 57.187 40.909 11.50 0.00 35.99 4.85
3610 7280 4.196971 ACTAAGAAGGAAACAGTTTGCGT 58.803 39.130 11.50 8.70 35.99 5.24
3611 7281 3.692791 AAGAAGGAAACAGTTTGCGTC 57.307 42.857 20.78 20.78 39.13 5.19
3612 7282 1.947456 AGAAGGAAACAGTTTGCGTCC 59.053 47.619 23.38 10.85 39.52 4.79
3613 7283 1.001706 GAAGGAAACAGTTTGCGTCCC 60.002 52.381 18.60 7.27 34.46 4.46
3614 7284 0.182775 AGGAAACAGTTTGCGTCCCT 59.817 50.000 11.50 4.84 35.99 4.20
3615 7285 1.418637 AGGAAACAGTTTGCGTCCCTA 59.581 47.619 11.50 0.00 35.99 3.53
3616 7286 1.534163 GGAAACAGTTTGCGTCCCTAC 59.466 52.381 2.34 0.00 0.00 3.18
3677 7354 8.472413 AGTTGTACCACGTGTATATAACTCAAT 58.528 33.333 22.56 9.89 31.23 2.57
3682 7359 6.533723 ACCACGTGTATATAACTCAATGTGTG 59.466 38.462 15.65 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
229 232 6.239036 GGTTAGCAACTTTGTCCTTTCATCTT 60.239 38.462 0.00 0.00 0.00 2.40
460 463 2.042162 AGAATGTTGTCAGAATGGGGCT 59.958 45.455 0.00 0.00 36.16 5.19
484 487 5.237996 CGAACCGGTACTAATGAGAGTGATA 59.762 44.000 8.00 0.00 0.00 2.15
486 489 3.376234 CGAACCGGTACTAATGAGAGTGA 59.624 47.826 8.00 0.00 0.00 3.41
657 660 1.019673 CCGAGGATCAAATGGCACTG 58.980 55.000 0.00 0.00 33.17 3.66
666 669 1.628340 ACACCACATTCCGAGGATCAA 59.372 47.619 0.00 0.00 33.17 2.57
764 767 1.068125 CGAGTCCATGTCCAACACGTA 60.068 52.381 0.00 0.00 0.00 3.57
765 768 0.319555 CGAGTCCATGTCCAACACGT 60.320 55.000 0.00 0.00 0.00 4.49
766 769 1.014044 CCGAGTCCATGTCCAACACG 61.014 60.000 0.00 0.00 0.00 4.49
819 822 5.523916 CCGTAGTTGGGTCTAGATTGAATTG 59.476 44.000 0.00 0.00 0.00 2.32
834 837 1.800315 CGTCTGCGTCCGTAGTTGG 60.800 63.158 4.76 0.00 0.00 3.77
1258 1909 4.462280 CCCGTCGTAAGCCCCACC 62.462 72.222 0.00 0.00 37.18 4.61
1437 2088 1.754234 GCCCTCGACAAATGGCCAT 60.754 57.895 14.09 14.09 37.94 4.40
1535 2186 0.178990 AGTTTGTGGCTGGGTCCTTC 60.179 55.000 0.00 0.00 0.00 3.46
1538 2189 1.463553 CCAAGTTTGTGGCTGGGTCC 61.464 60.000 0.00 0.00 0.00 4.46
1608 2259 6.296145 CCTCTTGGTCTTCTTCAGATAGGTTT 60.296 42.308 0.00 0.00 32.60 3.27
1745 2399 2.435410 GCCCCGGTACAAACTCCG 60.435 66.667 0.00 0.00 45.42 4.63
1809 2463 4.000988 ACTTCCATATTTTGACGCGACTT 58.999 39.130 15.93 0.00 0.00 3.01
1814 2468 2.538939 GCCGACTTCCATATTTTGACGC 60.539 50.000 0.00 0.00 0.00 5.19
1902 2556 0.991920 CCATGTTGTACACCCCCTCT 59.008 55.000 0.00 0.00 0.00 3.69
2059 2713 5.355596 CACCTGACCATCTTCTGATTCTAC 58.644 45.833 0.00 0.00 0.00 2.59
2076 2730 1.489481 CTAGCATCCACTCCACCTGA 58.511 55.000 0.00 0.00 0.00 3.86
2082 2736 0.462759 GGTGTGCTAGCATCCACTCC 60.463 60.000 27.77 18.66 38.12 3.85
2211 2865 0.813821 CAGATGTGTCGCTCTCCTCA 59.186 55.000 0.00 0.00 0.00 3.86
2214 2868 1.406898 TCATCAGATGTGTCGCTCTCC 59.593 52.381 10.34 0.00 0.00 3.71
2215 2869 2.859526 TCATCAGATGTGTCGCTCTC 57.140 50.000 10.34 0.00 0.00 3.20
2227 2905 2.223805 CGTTCCCATCACGATCATCAGA 60.224 50.000 0.00 0.00 40.20 3.27
2282 2960 0.839277 ATCATCGAAGCCACCATCCA 59.161 50.000 0.00 0.00 0.00 3.41
2325 3003 3.032017 ACATCTTCTTCACTGTGACCG 57.968 47.619 10.56 5.01 0.00 4.79
2345 3023 3.928992 GTCATCTTCATCTTCGTGAGCAA 59.071 43.478 0.00 0.00 0.00 3.91
2369 3047 7.194607 TCAAAGCTCTCTACACTTTTGAATG 57.805 36.000 0.00 0.00 31.43 2.67
2430 3108 6.712095 ACATGCTTTCAGAACTTTCATGTAGA 59.288 34.615 13.11 0.00 40.54 2.59
2445 3123 4.650734 TGTAATCCTGTGACATGCTTTCA 58.349 39.130 0.00 0.00 0.00 2.69
2549 3248 7.391554 GGTCATAGCCTAAATATTGCATTCTCA 59.608 37.037 0.00 0.00 0.00 3.27
2619 3318 1.152756 GCATGGGCGGTAAGGGAAT 60.153 57.895 0.00 0.00 0.00 3.01
2705 3422 9.877178 CTTGTTCTTCCTTGTAGATAGTTACAT 57.123 33.333 0.00 0.00 33.81 2.29
2757 6133 3.929002 GCTCAATGCAGCCCATGA 58.071 55.556 0.00 0.00 42.31 3.07
2885 6306 4.392138 GGAGTAGCTGTTATCACAACCAAC 59.608 45.833 0.00 0.00 30.36 3.77
2889 6310 5.073311 TCTGGAGTAGCTGTTATCACAAC 57.927 43.478 0.00 0.00 30.36 3.32
2898 6319 4.467795 ACATGTACATTCTGGAGTAGCTGT 59.532 41.667 5.37 0.00 0.00 4.40
2926 6398 8.664798 TCATTAACACAACAGTAGAACATATGC 58.335 33.333 1.58 0.00 0.00 3.14
2929 6401 9.936759 TGATCATTAACACAACAGTAGAACATA 57.063 29.630 0.00 0.00 0.00 2.29
2930 6402 8.846943 TGATCATTAACACAACAGTAGAACAT 57.153 30.769 0.00 0.00 0.00 2.71
2932 6559 8.935844 TGATGATCATTAACACAACAGTAGAAC 58.064 33.333 10.14 0.00 0.00 3.01
2948 6575 9.623000 TGAACAACAGAGATATTGATGATCATT 57.377 29.630 10.14 0.00 29.63 2.57
2967 6594 4.781071 CTCATCAAGAGCAACTGAACAAC 58.219 43.478 0.00 0.00 37.59 3.32
2998 6625 1.456296 GCTCATTGTCACCAGCATCA 58.544 50.000 0.00 0.00 0.00 3.07
3011 6638 0.737715 GACTTCCAGCGACGCTCATT 60.738 55.000 21.67 2.26 36.40 2.57
3023 6650 0.679505 CACCTCCAGTTCGACTTCCA 59.320 55.000 0.00 0.00 0.00 3.53
3029 6657 1.701031 TTTGGCCACCTCCAGTTCGA 61.701 55.000 3.88 0.00 37.44 3.71
3045 6673 2.637872 TGGTACACCCTCTCCTTCTTTG 59.362 50.000 0.00 0.00 34.29 2.77
3046 6674 2.986050 TGGTACACCCTCTCCTTCTTT 58.014 47.619 0.00 0.00 34.29 2.52
3093 6722 2.325082 GGCAAACCTGATCGTGCGT 61.325 57.895 0.00 0.00 37.89 5.24
3095 6724 2.480555 CGGCAAACCTGATCGTGC 59.519 61.111 0.00 0.00 36.24 5.34
3115 6744 1.715019 AACCTGTTGCTGCTGGGGTA 61.715 55.000 0.00 0.00 32.57 3.69
3127 6756 2.203294 GGTGGCCGTCAACCTGTT 60.203 61.111 0.00 0.00 0.00 3.16
3245 6890 3.758755 AACTGACAGACTCTGCATTGA 57.241 42.857 10.08 0.00 34.37 2.57
3273 6935 3.614092 TCTGAACATGCCAAATCTCCTC 58.386 45.455 0.00 0.00 0.00 3.71
3277 6939 3.705051 ACCATCTGAACATGCCAAATCT 58.295 40.909 0.00 0.00 0.00 2.40
3294 6956 9.965902 ATTTATTCTACTGAAGAACAGAACCAT 57.034 29.630 0.00 0.00 46.90 3.55
3308 6973 8.944029 CAGATAGGCCAATCATTTATTCTACTG 58.056 37.037 5.01 0.00 0.00 2.74
3317 6982 6.438425 ACTTGTTTCAGATAGGCCAATCATTT 59.562 34.615 5.01 0.00 0.00 2.32
3338 7003 2.411069 CAGACTGTCAGATCGCAACTTG 59.589 50.000 10.88 0.00 0.00 3.16
3345 7010 2.620585 TGCTATCCAGACTGTCAGATCG 59.379 50.000 10.88 8.83 0.00 3.69
3348 7013 3.635591 TGATGCTATCCAGACTGTCAGA 58.364 45.455 10.88 6.79 0.00 3.27
3350 7015 4.221530 AGATGATGCTATCCAGACTGTCA 58.778 43.478 10.88 0.00 0.00 3.58
3351 7016 4.870123 AGATGATGCTATCCAGACTGTC 57.130 45.455 0.00 0.00 0.00 3.51
3352 7017 6.931790 ATTAGATGATGCTATCCAGACTGT 57.068 37.500 0.93 0.00 0.00 3.55
3353 7018 7.834803 TGTATTAGATGATGCTATCCAGACTG 58.165 38.462 0.00 0.00 0.00 3.51
3354 7019 8.606754 ATGTATTAGATGATGCTATCCAGACT 57.393 34.615 0.00 0.00 0.00 3.24
3355 7020 9.311916 GAATGTATTAGATGATGCTATCCAGAC 57.688 37.037 0.00 0.00 0.00 3.51
3356 7021 9.039165 TGAATGTATTAGATGATGCTATCCAGA 57.961 33.333 0.00 0.00 0.00 3.86
3357 7022 9.315525 CTGAATGTATTAGATGATGCTATCCAG 57.684 37.037 0.00 0.00 0.00 3.86
3358 7023 9.039165 TCTGAATGTATTAGATGATGCTATCCA 57.961 33.333 0.00 0.00 0.00 3.41
3359 7024 9.311916 GTCTGAATGTATTAGATGATGCTATCC 57.688 37.037 0.00 0.00 0.00 2.59
3360 7025 9.866798 TGTCTGAATGTATTAGATGATGCTATC 57.133 33.333 0.00 0.00 0.00 2.08
3362 7027 9.866798 GATGTCTGAATGTATTAGATGATGCTA 57.133 33.333 0.00 0.00 0.00 3.49
3363 7028 7.823310 GGATGTCTGAATGTATTAGATGATGCT 59.177 37.037 0.00 0.00 0.00 3.79
3364 7029 7.605309 TGGATGTCTGAATGTATTAGATGATGC 59.395 37.037 0.00 0.00 0.00 3.91
3365 7030 9.152595 CTGGATGTCTGAATGTATTAGATGATG 57.847 37.037 0.00 0.00 0.00 3.07
3366 7031 9.097946 TCTGGATGTCTGAATGTATTAGATGAT 57.902 33.333 0.00 0.00 0.00 2.45
3376 7041 4.040829 TGTTCAGTCTGGATGTCTGAATGT 59.959 41.667 9.46 0.00 46.52 2.71
3391 7056 2.483877 TGAAACGATGGCATGTTCAGTC 59.516 45.455 3.81 5.55 0.00 3.51
3447 7115 7.450014 TCCTAGTTGCTTCCAAAACATCATAAA 59.550 33.333 0.00 0.00 31.68 1.40
3452 7120 5.705609 TTCCTAGTTGCTTCCAAAACATC 57.294 39.130 0.00 0.00 31.68 3.06
3474 7142 7.202526 CCGGATGTTTTGTGCAAATCTAATAT 58.797 34.615 0.00 0.00 0.00 1.28
3542 7212 6.615088 CAGTTTGTGTTAGCATTATTCAGCT 58.385 36.000 0.00 0.00 44.55 4.24
3560 7230 2.541588 CGTGGGTTCTTGAAGCAGTTTG 60.542 50.000 13.44 0.00 0.00 2.93
3561 7231 1.676006 CGTGGGTTCTTGAAGCAGTTT 59.324 47.619 13.44 0.00 0.00 2.66
3562 7232 1.134220 TCGTGGGTTCTTGAAGCAGTT 60.134 47.619 13.44 0.00 0.00 3.16
3563 7233 0.468226 TCGTGGGTTCTTGAAGCAGT 59.532 50.000 13.44 0.00 0.00 4.40
3564 7234 0.868406 GTCGTGGGTTCTTGAAGCAG 59.132 55.000 13.44 5.56 0.00 4.24
3565 7235 0.179234 TGTCGTGGGTTCTTGAAGCA 59.821 50.000 13.44 0.00 0.00 3.91
3566 7236 1.002792 GTTGTCGTGGGTTCTTGAAGC 60.003 52.381 4.19 4.19 0.00 3.86
3567 7237 2.285083 TGTTGTCGTGGGTTCTTGAAG 58.715 47.619 0.00 0.00 0.00 3.02
3568 7238 2.404923 TGTTGTCGTGGGTTCTTGAA 57.595 45.000 0.00 0.00 0.00 2.69
3569 7239 2.011222 GTTGTTGTCGTGGGTTCTTGA 58.989 47.619 0.00 0.00 0.00 3.02
3570 7240 2.014128 AGTTGTTGTCGTGGGTTCTTG 58.986 47.619 0.00 0.00 0.00 3.02
3571 7241 2.413310 AGTTGTTGTCGTGGGTTCTT 57.587 45.000 0.00 0.00 0.00 2.52
3572 7242 3.133362 TCTTAGTTGTTGTCGTGGGTTCT 59.867 43.478 0.00 0.00 0.00 3.01
3573 7243 3.460103 TCTTAGTTGTTGTCGTGGGTTC 58.540 45.455 0.00 0.00 0.00 3.62
3574 7244 3.547054 TCTTAGTTGTTGTCGTGGGTT 57.453 42.857 0.00 0.00 0.00 4.11
3575 7245 3.463944 CTTCTTAGTTGTTGTCGTGGGT 58.536 45.455 0.00 0.00 0.00 4.51
3576 7246 2.806244 CCTTCTTAGTTGTTGTCGTGGG 59.194 50.000 0.00 0.00 0.00 4.61
3577 7247 3.724374 TCCTTCTTAGTTGTTGTCGTGG 58.276 45.455 0.00 0.00 0.00 4.94
3578 7248 5.064198 TGTTTCCTTCTTAGTTGTTGTCGTG 59.936 40.000 0.00 0.00 0.00 4.35
3579 7249 5.180271 TGTTTCCTTCTTAGTTGTTGTCGT 58.820 37.500 0.00 0.00 0.00 4.34
3580 7250 5.293569 ACTGTTTCCTTCTTAGTTGTTGTCG 59.706 40.000 0.00 0.00 0.00 4.35
3581 7251 6.679327 ACTGTTTCCTTCTTAGTTGTTGTC 57.321 37.500 0.00 0.00 0.00 3.18
3582 7252 7.312899 CAAACTGTTTCCTTCTTAGTTGTTGT 58.687 34.615 2.13 0.00 32.42 3.32
3583 7253 6.253512 GCAAACTGTTTCCTTCTTAGTTGTTG 59.746 38.462 2.13 0.00 32.42 3.33
3584 7254 6.330278 GCAAACTGTTTCCTTCTTAGTTGTT 58.670 36.000 2.13 0.00 32.42 2.83
3585 7255 5.448632 CGCAAACTGTTTCCTTCTTAGTTGT 60.449 40.000 2.13 0.00 32.42 3.32
3586 7256 4.970003 CGCAAACTGTTTCCTTCTTAGTTG 59.030 41.667 2.13 0.00 32.42 3.16
3587 7257 4.638865 ACGCAAACTGTTTCCTTCTTAGTT 59.361 37.500 2.13 0.00 33.36 2.24
3588 7258 4.196971 ACGCAAACTGTTTCCTTCTTAGT 58.803 39.130 2.13 0.00 0.00 2.24
3589 7259 4.319549 GGACGCAAACTGTTTCCTTCTTAG 60.320 45.833 2.13 0.00 0.00 2.18
3590 7260 3.562557 GGACGCAAACTGTTTCCTTCTTA 59.437 43.478 2.13 0.00 0.00 2.10
3591 7261 2.357952 GGACGCAAACTGTTTCCTTCTT 59.642 45.455 2.13 0.00 0.00 2.52
3592 7262 1.947456 GGACGCAAACTGTTTCCTTCT 59.053 47.619 2.13 0.00 0.00 2.85
3593 7263 1.001706 GGGACGCAAACTGTTTCCTTC 60.002 52.381 2.13 0.00 0.00 3.46
3594 7264 1.029681 GGGACGCAAACTGTTTCCTT 58.970 50.000 2.13 0.00 0.00 3.36
3595 7265 0.182775 AGGGACGCAAACTGTTTCCT 59.817 50.000 2.13 3.84 0.00 3.36
3596 7266 1.534163 GTAGGGACGCAAACTGTTTCC 59.466 52.381 2.13 1.60 0.00 3.13
3597 7267 1.534163 GGTAGGGACGCAAACTGTTTC 59.466 52.381 2.13 0.00 0.00 2.78
3598 7268 1.134037 TGGTAGGGACGCAAACTGTTT 60.134 47.619 0.00 0.00 0.00 2.83
3599 7269 0.470766 TGGTAGGGACGCAAACTGTT 59.529 50.000 0.00 0.00 0.00 3.16
3600 7270 0.470766 TTGGTAGGGACGCAAACTGT 59.529 50.000 0.00 0.00 0.00 3.55
3601 7271 1.600023 TTTGGTAGGGACGCAAACTG 58.400 50.000 0.00 0.00 0.00 3.16
3602 7272 2.579410 ATTTGGTAGGGACGCAAACT 57.421 45.000 0.00 0.00 32.27 2.66
3603 7273 2.554893 TGAATTTGGTAGGGACGCAAAC 59.445 45.455 0.00 0.00 32.27 2.93
3604 7274 2.554893 GTGAATTTGGTAGGGACGCAAA 59.445 45.455 0.00 0.00 33.28 3.68
3605 7275 2.156098 GTGAATTTGGTAGGGACGCAA 58.844 47.619 0.00 0.00 0.00 4.85
3606 7276 1.072489 TGTGAATTTGGTAGGGACGCA 59.928 47.619 0.00 0.00 0.00 5.24
3607 7277 1.816074 TGTGAATTTGGTAGGGACGC 58.184 50.000 0.00 0.00 0.00 5.19
3608 7278 4.024048 GCATATGTGAATTTGGTAGGGACG 60.024 45.833 4.29 0.00 0.00 4.79
3609 7279 5.009010 CAGCATATGTGAATTTGGTAGGGAC 59.991 44.000 4.29 0.00 0.00 4.46
3610 7280 5.132502 CAGCATATGTGAATTTGGTAGGGA 58.867 41.667 4.29 0.00 0.00 4.20
3611 7281 4.279169 CCAGCATATGTGAATTTGGTAGGG 59.721 45.833 4.29 0.00 0.00 3.53
3612 7282 5.009010 GTCCAGCATATGTGAATTTGGTAGG 59.991 44.000 4.29 0.00 0.00 3.18
3613 7283 5.589855 TGTCCAGCATATGTGAATTTGGTAG 59.410 40.000 4.29 0.00 0.00 3.18
3614 7284 5.504853 TGTCCAGCATATGTGAATTTGGTA 58.495 37.500 4.29 0.00 0.00 3.25
3615 7285 4.343231 TGTCCAGCATATGTGAATTTGGT 58.657 39.130 4.29 0.00 0.00 3.67
3616 7286 4.987408 TGTCCAGCATATGTGAATTTGG 57.013 40.909 4.29 3.88 0.00 3.28


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

AutoCloner maintained by Alex Coulton.