Multiple sequence alignment - TraesCS2A01G531000

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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 TraesCS2A01G531000 chr2A 100.000 7349 0 0 1 7349 748459280 748451932 0.000000e+00 13572.0
1 TraesCS2A01G531000 chr2A 98.912 3310 18 3 2416 5707 216533007 216529698 0.000000e+00 5897.0
2 TraesCS2A01G531000 chr2A 98.912 3310 18 3 2416 5707 676079637 676076328 0.000000e+00 5897.0
3 TraesCS2A01G531000 chr2A 91.598 1928 150 5 507 2423 746620151 746622077 0.000000e+00 2652.0
4 TraesCS2A01G531000 chr2A 91.033 1829 135 6 610 2423 748285016 748286830 0.000000e+00 2442.0
5 TraesCS2A01G531000 chr2A 92.107 1723 130 6 701 2423 748203990 748205706 0.000000e+00 2423.0
6 TraesCS2A01G531000 chr2A 91.901 1741 117 7 706 2423 748437501 748439240 0.000000e+00 2412.0
7 TraesCS2A01G531000 chr2A 91.003 1067 60 14 5700 6738 748439208 748440266 0.000000e+00 1406.0
8 TraesCS2A01G531000 chr2A 94.701 887 28 7 6480 7349 746622743 746623627 0.000000e+00 1360.0
9 TraesCS2A01G531000 chr2A 86.127 1074 111 15 5700 6738 748401594 748402664 0.000000e+00 1123.0
10 TraesCS2A01G531000 chr2A 87.300 937 94 14 617 1533 748389783 748390714 0.000000e+00 1048.0
11 TraesCS2A01G531000 chr2A 90.826 763 66 4 5700 6461 748286798 748287557 0.000000e+00 1018.0
12 TraesCS2A01G531000 chr2A 87.171 912 84 16 5700 6584 748221207 748222112 0.000000e+00 1005.0
13 TraesCS2A01G531000 chr2A 92.857 406 13 1 6481 6870 748464677 748464272 6.390000e-160 575.0
14 TraesCS2A01G531000 chr2A 88.260 477 32 9 6480 6940 748210310 748210778 3.880000e-152 549.0
15 TraesCS2A01G531000 chr2A 86.848 441 32 9 6911 7349 748464273 748463857 3.100000e-128 470.0
16 TraesCS2A01G531000 chr2A 89.045 356 22 7 7011 7349 748210783 748211138 6.810000e-115 425.0
17 TraesCS2A01G531000 chr2A 83.266 496 48 13 1 472 746625300 746625784 2.450000e-114 424.0
18 TraesCS2A01G531000 chr2A 91.096 292 10 1 5437 5712 307427955 307427664 1.500000e-101 381.0
19 TraesCS2A01G531000 chr2A 100.000 74 0 0 5638 5711 135278833 135278906 3.580000e-28 137.0
20 TraesCS2A01G531000 chr2A 92.941 85 5 1 2 85 746619588 746619672 1.000000e-23 122.0
21 TraesCS2A01G531000 chr2A 81.203 133 18 5 7184 7311 748288330 748288460 4.690000e-17 100.0
22 TraesCS2A01G531000 chr2A 87.209 86 10 1 532 617 748284849 748284933 6.070000e-16 97.1
23 TraesCS2A01G531000 chr2A 84.416 77 12 0 7251 7327 747677283 747677207 7.910000e-10 76.8
24 TraesCS2A01G531000 chr1A 99.125 3316 10 4 2413 5710 517045158 517048472 0.000000e+00 5945.0
25 TraesCS2A01G531000 chr1A 98.340 2109 18 2 3629 5720 447066039 447068147 0.000000e+00 3685.0
26 TraesCS2A01G531000 chr1A 98.508 1877 11 2 3852 5711 10078177 10080053 0.000000e+00 3295.0
27 TraesCS2A01G531000 chr1A 89.700 233 7 2 5496 5711 244810734 244810966 1.560000e-71 281.0
28 TraesCS2A01G531000 chr3B 98.944 3313 17 3 2416 5710 695915043 695918355 0.000000e+00 5908.0
29 TraesCS2A01G531000 chr3B 98.912 3310 19 2 2416 5708 332929091 332925782 0.000000e+00 5897.0
30 TraesCS2A01G531000 chr3B 98.581 3313 30 2 2418 5713 707474404 707477716 0.000000e+00 5842.0
31 TraesCS2A01G531000 chr6B 98.825 3320 20 4 2410 5710 339383028 339386347 0.000000e+00 5897.0
32 TraesCS2A01G531000 chr6B 98.560 3333 26 5 2416 5730 606303256 606299928 0.000000e+00 5869.0
33 TraesCS2A01G531000 chr5A 98.912 3310 19 2 2416 5708 259069716 259066407 0.000000e+00 5897.0
34 TraesCS2A01G531000 chr5B 98.912 3308 19 2 2416 5706 306402349 306399042 0.000000e+00 5893.0
35 TraesCS2A01G531000 chr2B 98.911 3305 14 4 2416 5701 46596971 46600272 0.000000e+00 5884.0
36 TraesCS2A01G531000 chr2B 94.014 1821 103 2 609 2423 753931435 753929615 0.000000e+00 2754.0
37 TraesCS2A01G531000 chr2B 92.713 1729 116 2 704 2423 753792770 753794497 0.000000e+00 2486.0
38 TraesCS2A01G531000 chr2B 86.761 1065 108 10 5705 6741 753806976 753805917 0.000000e+00 1155.0
39 TraesCS2A01G531000 chr2B 88.492 895 70 20 6483 7348 753928947 753928057 0.000000e+00 1051.0
40 TraesCS2A01G531000 chr2B 95.174 518 16 7 6480 6990 753934713 753934198 0.000000e+00 809.0
41 TraesCS2A01G531000 chr2B 86.747 498 33 10 6501 6976 753795177 753795663 2.350000e-144 523.0
42 TraesCS2A01G531000 chr2B 89.516 372 24 8 6982 7349 753795714 753796074 2.420000e-124 457.0
43 TraesCS2A01G531000 chr2B 93.130 262 15 3 6501 6760 753787984 753788244 1.500000e-101 381.0
44 TraesCS2A01G531000 chr2B 89.734 263 13 7 85 336 753932324 753932065 2.560000e-84 324.0
45 TraesCS2A01G531000 chr2B 92.308 52 4 0 349 400 753931718 753931667 2.840000e-09 75.0
46 TraesCS2A01G531000 chr2B 96.970 33 1 0 669 701 753792720 753792752 1.000000e-03 56.5
47 TraesCS2A01G531000 chr2D 96.991 3323 70 6 2421 5725 294542236 294545546 0.000000e+00 5555.0
48 TraesCS2A01G531000 chr2D 90.523 1836 149 8 610 2423 617546306 617548138 0.000000e+00 2403.0
49 TraesCS2A01G531000 chr2D 91.821 1724 132 6 701 2415 617909825 617908102 0.000000e+00 2394.0
50 TraesCS2A01G531000 chr2D 91.114 1733 143 5 701 2423 617538794 617540525 0.000000e+00 2337.0
51 TraesCS2A01G531000 chr2D 90.789 1737 137 6 701 2415 617887250 617888985 0.000000e+00 2300.0
52 TraesCS2A01G531000 chr2D 90.258 1745 147 6 701 2423 617633782 617635525 0.000000e+00 2259.0
53 TraesCS2A01G531000 chr2D 90.809 1643 137 5 701 2330 617730855 617732496 0.000000e+00 2185.0
54 TraesCS2A01G531000 chr2D 91.359 1354 115 2 1071 2423 617760443 617761795 0.000000e+00 1851.0
55 TraesCS2A01G531000 chr2D 89.118 1066 81 13 5700 6738 617888961 617890018 0.000000e+00 1293.0
56 TraesCS2A01G531000 chr2D 87.160 1067 96 17 5705 6738 617548111 617549169 0.000000e+00 1173.0
57 TraesCS2A01G531000 chr2D 87.017 1009 99 12 5700 6680 617732537 617733541 0.000000e+00 1109.0
58 TraesCS2A01G531000 chr2D 92.744 758 51 3 5700 6456 617908126 617907372 0.000000e+00 1092.0
59 TraesCS2A01G531000 chr2D 93.562 699 45 0 5700 6398 617540493 617541191 0.000000e+00 1042.0
60 TraesCS2A01G531000 chr2D 90.215 511 32 9 6480 6974 617636191 617636699 0.000000e+00 651.0
61 TraesCS2A01G531000 chr2D 89.184 527 39 4 6480 6990 617762461 617762985 6.220000e-180 641.0
62 TraesCS2A01G531000 chr2D 90.591 372 28 5 6982 7349 617763017 617763385 3.080000e-133 486.0
63 TraesCS2A01G531000 chr2D 90.028 361 26 5 6999 7349 617636896 617637256 6.720000e-125 459.0
64 TraesCS2A01G531000 chr2D 85.915 355 29 4 701 1034 617760090 617760444 7.010000e-95 359.0
65 TraesCS2A01G531000 chr2D 92.727 165 6 2 7185 7349 617902205 617902047 4.430000e-57 233.0
66 TraesCS2A01G531000 chr2D 76.923 273 37 11 7081 7327 617413295 617413023 1.660000e-26 132.0
67 TraesCS2A01G531000 chr7B 93.344 1833 91 10 609 2423 726150171 726151990 0.000000e+00 2680.0
68 TraesCS2A01G531000 chr7B 86.000 500 39 16 1 479 726149468 726149957 2.370000e-139 507.0
69 TraesCS2A01G531000 chr4B 89.091 165 2 1 5563 5711 29579923 29580087 2.710000e-44 191.0
70 TraesCS2A01G531000 chr1D 79.779 272 38 15 8 272 289492632 289492371 1.630000e-41 182.0


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 TraesCS2A01G531000 chr2A 748451932 748459280 7348 True 13572.000 13572 100.00000 1 7349 1 chr2A.!!$R5 7348
1 TraesCS2A01G531000 chr2A 216529698 216533007 3309 True 5897.000 5897 98.91200 2416 5707 1 chr2A.!!$R1 3291
2 TraesCS2A01G531000 chr2A 676076328 676079637 3309 True 5897.000 5897 98.91200 2416 5707 1 chr2A.!!$R3 3291
3 TraesCS2A01G531000 chr2A 748203990 748205706 1716 False 2423.000 2423 92.10700 701 2423 1 chr2A.!!$F2 1722
4 TraesCS2A01G531000 chr2A 748437501 748440266 2765 False 1909.000 2412 91.45200 706 6738 2 chr2A.!!$F9 6032
5 TraesCS2A01G531000 chr2A 746619588 746625784 6196 False 1139.500 2652 90.62650 1 7349 4 chr2A.!!$F6 7348
6 TraesCS2A01G531000 chr2A 748401594 748402664 1070 False 1123.000 1123 86.12700 5700 6738 1 chr2A.!!$F5 1038
7 TraesCS2A01G531000 chr2A 748389783 748390714 931 False 1048.000 1048 87.30000 617 1533 1 chr2A.!!$F4 916
8 TraesCS2A01G531000 chr2A 748221207 748222112 905 False 1005.000 1005 87.17100 5700 6584 1 chr2A.!!$F3 884
9 TraesCS2A01G531000 chr2A 748284849 748288460 3611 False 914.275 2442 87.56775 532 7311 4 chr2A.!!$F8 6779
10 TraesCS2A01G531000 chr2A 748463857 748464677 820 True 522.500 575 89.85250 6481 7349 2 chr2A.!!$R6 868
11 TraesCS2A01G531000 chr2A 748210310 748211138 828 False 487.000 549 88.65250 6480 7349 2 chr2A.!!$F7 869
12 TraesCS2A01G531000 chr1A 517045158 517048472 3314 False 5945.000 5945 99.12500 2413 5710 1 chr1A.!!$F4 3297
13 TraesCS2A01G531000 chr1A 447066039 447068147 2108 False 3685.000 3685 98.34000 3629 5720 1 chr1A.!!$F3 2091
14 TraesCS2A01G531000 chr1A 10078177 10080053 1876 False 3295.000 3295 98.50800 3852 5711 1 chr1A.!!$F1 1859
15 TraesCS2A01G531000 chr3B 695915043 695918355 3312 False 5908.000 5908 98.94400 2416 5710 1 chr3B.!!$F1 3294
16 TraesCS2A01G531000 chr3B 332925782 332929091 3309 True 5897.000 5897 98.91200 2416 5708 1 chr3B.!!$R1 3292
17 TraesCS2A01G531000 chr3B 707474404 707477716 3312 False 5842.000 5842 98.58100 2418 5713 1 chr3B.!!$F2 3295
18 TraesCS2A01G531000 chr6B 339383028 339386347 3319 False 5897.000 5897 98.82500 2410 5710 1 chr6B.!!$F1 3300
19 TraesCS2A01G531000 chr6B 606299928 606303256 3328 True 5869.000 5869 98.56000 2416 5730 1 chr6B.!!$R1 3314
20 TraesCS2A01G531000 chr5A 259066407 259069716 3309 True 5897.000 5897 98.91200 2416 5708 1 chr5A.!!$R1 3292
21 TraesCS2A01G531000 chr5B 306399042 306402349 3307 True 5893.000 5893 98.91200 2416 5706 1 chr5B.!!$R1 3290
22 TraesCS2A01G531000 chr2B 46596971 46600272 3301 False 5884.000 5884 98.91100 2416 5701 1 chr2B.!!$F1 3285
23 TraesCS2A01G531000 chr2B 753805917 753806976 1059 True 1155.000 1155 86.76100 5705 6741 1 chr2B.!!$R1 1036
24 TraesCS2A01G531000 chr2B 753928057 753934713 6656 True 1002.600 2754 91.94440 85 7348 5 chr2B.!!$R2 7263
25 TraesCS2A01G531000 chr2B 753792720 753796074 3354 False 880.625 2486 91.48650 669 7349 4 chr2B.!!$F3 6680
26 TraesCS2A01G531000 chr2D 294542236 294545546 3310 False 5555.000 5555 96.99100 2421 5725 1 chr2D.!!$F1 3304
27 TraesCS2A01G531000 chr2D 617887250 617890018 2768 False 1796.500 2300 89.95350 701 6738 2 chr2D.!!$F7 6037
28 TraesCS2A01G531000 chr2D 617546306 617549169 2863 False 1788.000 2403 88.84150 610 6738 2 chr2D.!!$F3 6128
29 TraesCS2A01G531000 chr2D 617907372 617909825 2453 True 1743.000 2394 92.28250 701 6456 2 chr2D.!!$R3 5755
30 TraesCS2A01G531000 chr2D 617538794 617541191 2397 False 1689.500 2337 92.33800 701 6398 2 chr2D.!!$F2 5697
31 TraesCS2A01G531000 chr2D 617730855 617733541 2686 False 1647.000 2185 88.91300 701 6680 2 chr2D.!!$F5 5979
32 TraesCS2A01G531000 chr2D 617633782 617637256 3474 False 1123.000 2259 90.16700 701 7349 3 chr2D.!!$F4 6648
33 TraesCS2A01G531000 chr2D 617760090 617763385 3295 False 834.250 1851 89.26225 701 7349 4 chr2D.!!$F6 6648
34 TraesCS2A01G531000 chr7B 726149468 726151990 2522 False 1593.500 2680 89.67200 1 2423 2 chr7B.!!$F1 2422

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
299 319 1.621107 CAAGTGCATGGAATTGACGC 58.379 50.000 20.94 0.0 0.00 5.19 F
1942 2277 0.250640 GGGTAGGATGGATGCTGCTG 60.251 60.000 0.00 0.0 31.88 4.41 F
2402 2750 0.035739 TCACTCAGCGGGGTTAAACC 59.964 55.000 0.00 0.0 37.60 3.27 F
4927 5287 0.329596 GTGGCCATTGAGGTCTCCTT 59.670 55.000 9.72 0.0 44.59 3.36 F
5247 5607 4.144297 CTCTCCATTTGGTTTCTTGGACA 58.856 43.478 0.00 0.0 34.62 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2145 2492 2.609459 GTCAAACATATCCTGTGCCTCG 59.391 50.000 0.00 0.0 38.39 4.63 R
4927 5287 5.946942 ATTGGTGAGAAGCTCTTCATAGA 57.053 39.130 11.69 0.0 41.84 1.98 R
5247 5607 4.785376 AGGAGAGGTGTTGATATCCTTTGT 59.215 41.667 0.00 0.0 33.37 2.83 R
6067 6444 0.250901 TCTGCCAGCAACCCTTCTTC 60.251 55.000 0.00 0.0 0.00 2.87 R
7112 13645 1.477740 CGGAGAGACCTAGGCATCTGA 60.478 57.143 18.61 0.0 36.31 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
93 95 6.674066 TGACTTATTTTCAAATCCGTGAACC 58.326 36.000 0.00 0.00 37.24 3.62
186 189 8.870160 ATTCATGAACTTTTTCGTCAAATTCA 57.130 26.923 11.07 0.00 34.04 2.57
262 267 9.340327 CAAATCGTCAACTTTTTGTTAAATTCG 57.660 29.630 0.00 0.00 37.07 3.34
264 269 7.425915 TCGTCAACTTTTTGTTAAATTCGTG 57.574 32.000 0.00 0.00 37.07 4.35
265 270 6.469595 TCGTCAACTTTTTGTTAAATTCGTGG 59.530 34.615 0.00 0.00 37.07 4.94
266 271 6.469595 CGTCAACTTTTTGTTAAATTCGTGGA 59.530 34.615 0.00 0.00 37.07 4.02
267 272 7.512426 CGTCAACTTTTTGTTAAATTCGTGGAC 60.512 37.037 0.00 0.00 37.07 4.02
299 319 1.621107 CAAGTGCATGGAATTGACGC 58.379 50.000 20.94 0.00 0.00 5.19
379 399 2.749621 ACCCGAGAAGAAAATGTGATGC 59.250 45.455 0.00 0.00 0.00 3.91
428 461 3.181425 CCCTGGGGATCAAGAAATAGCAT 60.181 47.826 4.27 0.00 37.50 3.79
480 524 4.111375 GAGCATTACTCGGAAAGACTCA 57.889 45.455 0.00 0.00 35.18 3.41
481 525 4.688021 GAGCATTACTCGGAAAGACTCAT 58.312 43.478 0.00 0.00 35.18 2.90
482 526 4.688021 AGCATTACTCGGAAAGACTCATC 58.312 43.478 0.00 0.00 0.00 2.92
484 528 4.505922 GCATTACTCGGAAAGACTCATCAG 59.494 45.833 0.00 0.00 0.00 2.90
486 530 5.977489 TTACTCGGAAAGACTCATCAGAA 57.023 39.130 0.00 0.00 0.00 3.02
490 534 5.872070 ACTCGGAAAGACTCATCAGAAAATC 59.128 40.000 0.00 0.00 0.00 2.17
492 536 6.409704 TCGGAAAGACTCATCAGAAAATCAT 58.590 36.000 0.00 0.00 0.00 2.45
493 537 6.536582 TCGGAAAGACTCATCAGAAAATCATC 59.463 38.462 0.00 0.00 0.00 2.92
494 538 6.314648 CGGAAAGACTCATCAGAAAATCATCA 59.685 38.462 0.00 0.00 0.00 3.07
495 539 7.148356 CGGAAAGACTCATCAGAAAATCATCAA 60.148 37.037 0.00 0.00 0.00 2.57
499 543 6.093771 AGACTCATCAGAAAATCATCAAGTGC 59.906 38.462 0.00 0.00 0.00 4.40
501 545 5.011586 TCATCAGAAAATCATCAAGTGCCA 58.988 37.500 0.00 0.00 0.00 4.92
502 546 5.655090 TCATCAGAAAATCATCAAGTGCCAT 59.345 36.000 0.00 0.00 0.00 4.40
503 547 5.988310 TCAGAAAATCATCAAGTGCCATT 57.012 34.783 0.00 0.00 0.00 3.16
587 707 4.717313 GGCAAGTCCACCGGTCCC 62.717 72.222 2.59 0.00 34.01 4.46
612 842 2.357034 GCGTTCACTTCCTCGGCA 60.357 61.111 0.00 0.00 0.00 5.69
659 897 2.279851 CGTCGCAGGTGACACCAA 60.280 61.111 26.30 6.18 41.95 3.67
871 1161 3.041940 CGCACCACCTGTTCGACC 61.042 66.667 0.00 0.00 35.51 4.79
1375 1710 6.045318 CCTAATGTGGTGATCTACAACTCAG 58.955 44.000 0.00 0.00 41.82 3.35
1942 2277 0.250640 GGGTAGGATGGATGCTGCTG 60.251 60.000 0.00 0.00 31.88 4.41
2052 2387 4.262592 GGTCATTTTGTGAAAGCCAAGGAT 60.263 41.667 0.00 0.00 38.90 3.24
2142 2489 5.497474 GACCTATGCAAAGAAGGAAAGGTA 58.503 41.667 13.00 0.00 36.26 3.08
2145 2492 6.208797 ACCTATGCAAAGAAGGAAAGGTAAAC 59.791 38.462 13.00 0.00 34.40 2.01
2259 2607 0.324943 GCAAGGTGGAGGAAGCACTA 59.675 55.000 0.00 0.00 0.00 2.74
2393 2741 0.036010 AGGGAAATGTCACTCAGCGG 60.036 55.000 0.00 0.00 28.08 5.52
2394 2742 1.026718 GGGAAATGTCACTCAGCGGG 61.027 60.000 0.00 0.00 0.00 6.13
2395 2743 1.026718 GGAAATGTCACTCAGCGGGG 61.027 60.000 0.00 0.00 0.00 5.73
2396 2744 0.321653 GAAATGTCACTCAGCGGGGT 60.322 55.000 0.00 0.00 0.00 4.95
2397 2745 0.110486 AAATGTCACTCAGCGGGGTT 59.890 50.000 0.00 0.00 0.00 4.11
2398 2746 0.981183 AATGTCACTCAGCGGGGTTA 59.019 50.000 0.00 0.00 0.00 2.85
2399 2747 0.981183 ATGTCACTCAGCGGGGTTAA 59.019 50.000 0.00 0.00 0.00 2.01
2400 2748 0.759959 TGTCACTCAGCGGGGTTAAA 59.240 50.000 0.00 0.00 0.00 1.52
2401 2749 1.154197 GTCACTCAGCGGGGTTAAAC 58.846 55.000 0.00 0.00 0.00 2.01
2402 2750 0.035739 TCACTCAGCGGGGTTAAACC 59.964 55.000 0.00 0.00 37.60 3.27
4927 5287 0.329596 GTGGCCATTGAGGTCTCCTT 59.670 55.000 9.72 0.00 44.59 3.36
5247 5607 4.144297 CTCTCCATTTGGTTTCTTGGACA 58.856 43.478 0.00 0.00 34.62 4.02
6016 6393 6.173427 TGTTTGCTACTATATCAGCCATCA 57.827 37.500 3.89 0.00 36.95 3.07
6067 6444 8.820933 ACAGTGTAATGATGACGAATTTCATAG 58.179 33.333 0.00 0.00 36.30 2.23
6413 6791 6.491714 AGTTGGTATTCACTCATAGCTGAT 57.508 37.500 0.00 0.00 0.00 2.90
6746 7207 8.739039 TCTGTTTAATAATTGTGAGATGGTTGG 58.261 33.333 0.00 0.00 0.00 3.77
6857 7334 5.746307 TGCTCTAGATTAAATGCTTGCAG 57.254 39.130 0.87 0.00 0.00 4.41
6932 13187 4.250464 TCCTGGTTACTTTCAGTTATGCG 58.750 43.478 0.00 0.00 0.00 4.73
6933 13188 3.181510 CCTGGTTACTTTCAGTTATGCGC 60.182 47.826 0.00 0.00 0.00 6.09
7112 13645 8.082242 GGAACTGCTGACTGTAAAAATACATTT 58.918 33.333 0.00 0.00 0.00 2.32
7169 13706 9.757227 TTTACCTTTATTCATTGTTTTGACTGG 57.243 29.630 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 9.853555 TCACGAATTTAAGCAAATGACAATAAT 57.146 25.926 0.00 0.00 34.53 1.28
72 73 9.855021 AAATAGGTTCACGGATTTGAAAATAAG 57.145 29.630 0.00 0.00 37.24 1.73
279 284 1.621107 CGTCAATTCCATGCACTTGC 58.379 50.000 0.00 0.00 42.50 4.01
281 286 0.527565 GGCGTCAATTCCATGCACTT 59.472 50.000 0.00 0.00 0.00 3.16
282 287 1.315257 GGGCGTCAATTCCATGCACT 61.315 55.000 0.00 0.00 0.00 4.40
379 399 2.094803 CGAAGATCGGATCAGAGGGATG 60.095 54.545 19.47 0.00 36.00 3.51
428 461 2.568956 AGGTGAGCTGCACTCTTATCAA 59.431 45.455 14.60 0.00 46.41 2.57
480 524 6.070995 ACAATGGCACTTGATGATTTTCTGAT 60.071 34.615 13.95 0.00 0.00 2.90
481 525 5.244402 ACAATGGCACTTGATGATTTTCTGA 59.756 36.000 13.95 0.00 0.00 3.27
482 526 5.475719 ACAATGGCACTTGATGATTTTCTG 58.524 37.500 13.95 0.00 0.00 3.02
484 528 5.807011 GGTACAATGGCACTTGATGATTTTC 59.193 40.000 13.95 0.00 0.00 2.29
486 530 4.160252 GGGTACAATGGCACTTGATGATTT 59.840 41.667 13.95 0.00 0.00 2.17
490 534 1.750778 GGGGTACAATGGCACTTGATG 59.249 52.381 13.95 1.76 0.00 3.07
492 536 0.774276 TGGGGTACAATGGCACTTGA 59.226 50.000 13.95 0.00 0.00 3.02
493 537 1.545582 CTTGGGGTACAATGGCACTTG 59.454 52.381 0.00 0.00 38.65 3.16
494 538 1.923356 CTTGGGGTACAATGGCACTT 58.077 50.000 0.00 0.00 38.65 3.16
495 539 0.611896 GCTTGGGGTACAATGGCACT 60.612 55.000 0.00 0.00 38.65 4.40
499 543 0.887933 GTGTGCTTGGGGTACAATGG 59.112 55.000 0.00 0.00 41.85 3.16
501 545 1.241315 GCGTGTGCTTGGGGTACAAT 61.241 55.000 0.00 0.00 41.85 2.71
502 546 1.894756 GCGTGTGCTTGGGGTACAA 60.895 57.895 0.00 0.00 41.85 2.41
503 547 2.281208 GCGTGTGCTTGGGGTACA 60.281 61.111 0.00 0.00 38.18 2.90
1099 1427 2.391389 GGCGACCGAAGAAGGCAAG 61.391 63.158 0.00 0.00 33.69 4.01
1375 1710 3.984018 TTTGCTTAGTGCGTCGATAAC 57.016 42.857 0.00 0.00 46.63 1.89
1580 1915 4.580167 TGCAAAGGGAATCGATTAATGAGG 59.420 41.667 11.38 1.51 0.00 3.86
1942 2277 7.156876 TGACCATCTGATTAAATTTGTCCAC 57.843 36.000 0.00 0.00 0.00 4.02
2052 2387 9.334947 CCTCTATTAATTGCTTCAGAGATCAAA 57.665 33.333 10.85 0.00 32.98 2.69
2142 2489 3.350219 AACATATCCTGTGCCTCGTTT 57.650 42.857 0.00 0.00 38.39 3.60
2145 2492 2.609459 GTCAAACATATCCTGTGCCTCG 59.391 50.000 0.00 0.00 38.39 4.63
2259 2607 7.264221 CAGACTTCATAGCATCAAGTACTCTT 58.736 38.462 0.00 0.00 30.32 2.85
2394 2742 5.945466 TGATAAAAGTCGTGGGTTTAACC 57.055 39.130 5.40 5.40 37.60 2.85
2395 2743 6.727215 TGTTGATAAAAGTCGTGGGTTTAAC 58.273 36.000 0.00 0.00 0.00 2.01
2396 2744 6.939132 TGTTGATAAAAGTCGTGGGTTTAA 57.061 33.333 0.00 0.00 0.00 1.52
2397 2745 6.318144 TGTTGTTGATAAAAGTCGTGGGTTTA 59.682 34.615 0.00 0.00 0.00 2.01
2398 2746 5.125739 TGTTGTTGATAAAAGTCGTGGGTTT 59.874 36.000 0.00 0.00 0.00 3.27
2399 2747 4.641094 TGTTGTTGATAAAAGTCGTGGGTT 59.359 37.500 0.00 0.00 0.00 4.11
2400 2748 4.200874 TGTTGTTGATAAAAGTCGTGGGT 58.799 39.130 0.00 0.00 0.00 4.51
2401 2749 4.822036 TGTTGTTGATAAAAGTCGTGGG 57.178 40.909 0.00 0.00 0.00 4.61
2402 2750 5.574082 TGTTGTTGTTGATAAAAGTCGTGG 58.426 37.500 0.00 0.00 0.00 4.94
2403 2751 6.524933 TGTTGTTGTTGTTGATAAAAGTCGTG 59.475 34.615 0.00 0.00 0.00 4.35
2404 2752 6.613233 TGTTGTTGTTGTTGATAAAAGTCGT 58.387 32.000 0.00 0.00 0.00 4.34
2405 2753 7.061210 TGTTGTTGTTGTTGTTGATAAAAGTCG 59.939 33.333 0.00 0.00 0.00 4.18
2406 2754 8.233692 TGTTGTTGTTGTTGTTGATAAAAGTC 57.766 30.769 0.00 0.00 0.00 3.01
2407 2755 8.491950 GTTGTTGTTGTTGTTGTTGATAAAAGT 58.508 29.630 0.00 0.00 0.00 2.66
2408 2756 8.491152 TGTTGTTGTTGTTGTTGTTGATAAAAG 58.509 29.630 0.00 0.00 0.00 2.27
2409 2757 8.365399 TGTTGTTGTTGTTGTTGTTGATAAAA 57.635 26.923 0.00 0.00 0.00 1.52
2410 2758 7.946655 TGTTGTTGTTGTTGTTGTTGATAAA 57.053 28.000 0.00 0.00 0.00 1.40
2411 2759 7.946655 TTGTTGTTGTTGTTGTTGTTGATAA 57.053 28.000 0.00 0.00 0.00 1.75
2412 2760 7.359598 GCTTTGTTGTTGTTGTTGTTGTTGATA 60.360 33.333 0.00 0.00 0.00 2.15
2413 2761 6.565623 GCTTTGTTGTTGTTGTTGTTGTTGAT 60.566 34.615 0.00 0.00 0.00 2.57
2414 2762 5.277058 GCTTTGTTGTTGTTGTTGTTGTTGA 60.277 36.000 0.00 0.00 0.00 3.18
4927 5287 5.946942 ATTGGTGAGAAGCTCTTCATAGA 57.053 39.130 11.69 0.00 41.84 1.98
5247 5607 4.785376 AGGAGAGGTGTTGATATCCTTTGT 59.215 41.667 0.00 0.00 33.37 2.83
5737 6113 0.881118 GAGCGAAACAGCCCATCAAA 59.119 50.000 0.00 0.00 38.01 2.69
5798 6174 2.086869 CCACTGGTATGCCACTTTCAG 58.913 52.381 0.00 0.00 40.46 3.02
6016 6393 2.158623 TCACAACAGAAGGCACCAATCT 60.159 45.455 0.00 0.00 0.00 2.40
6067 6444 0.250901 TCTGCCAGCAACCCTTCTTC 60.251 55.000 0.00 0.00 0.00 2.87
6746 7207 1.897560 AGAGGGCAAAAGTAGTGCAC 58.102 50.000 9.40 9.40 46.18 4.57
6932 13187 3.594603 TTAGCACTACTGTTGAGAGGC 57.405 47.619 0.00 0.00 0.00 4.70
6933 13188 7.440523 AAAAATTAGCACTACTGTTGAGAGG 57.559 36.000 0.00 0.00 0.00 3.69
6976 13234 8.040716 ACTAGATTTTAGATGAAAACAACCCG 57.959 34.615 0.00 0.00 39.83 5.28
7112 13645 1.477740 CGGAGAGACCTAGGCATCTGA 60.478 57.143 18.61 0.00 36.31 3.27
7169 13706 2.257894 CTCTGTTCGTGATCAGTCAGC 58.742 52.381 0.00 0.00 34.36 4.26


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

AutoCloner maintained by Alex Coulton.