Multiple sequence alignment - TraesCS2B01G516800

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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 TraesCS2B01G516800 chr2B 100.000 4298 0 0 1 4298 711865847 711870144 0.000000e+00 7938.0
1 TraesCS2B01G516800 chr2B 83.083 1531 219 30 1494 3005 711726119 711727628 0.000000e+00 1356.0
2 TraesCS2B01G516800 chr2B 88.266 767 67 12 3534 4298 636761075 636761820 0.000000e+00 896.0
3 TraesCS2B01G516800 chr2B 79.978 894 141 30 1493 2370 711321093 711320222 3.650000e-175 625.0
4 TraesCS2B01G516800 chr2B 90.847 295 24 2 3529 3821 675368738 675369031 4.030000e-105 392.0
5 TraesCS2B01G516800 chr2B 85.714 392 30 7 3710 4078 675368964 675369352 1.450000e-104 390.0
6 TraesCS2B01G516800 chr2B 88.406 207 23 1 3040 3246 711727632 711727837 9.230000e-62 248.0
7 TraesCS2B01G516800 chr2B 77.901 362 55 21 3952 4295 507926430 507926784 7.290000e-48 202.0
8 TraesCS2B01G516800 chr2B 78.571 154 17 9 1027 1169 711718048 711718196 2.130000e-13 87.9
9 TraesCS2B01G516800 chr2B 92.157 51 4 0 1119 1169 711321548 711321498 5.960000e-09 73.1
10 TraesCS2B01G516800 chr2A 92.432 2973 145 30 1 2965 723060022 723062922 0.000000e+00 4170.0
11 TraesCS2B01G516800 chr2A 81.866 1533 229 39 1494 3004 722839861 722841366 0.000000e+00 1245.0
12 TraesCS2B01G516800 chr2A 76.303 1401 268 40 1495 2852 777836909 777835530 0.000000e+00 689.0
13 TraesCS2B01G516800 chr2A 88.398 543 42 8 3756 4298 678607159 678607680 6.060000e-178 634.0
14 TraesCS2B01G516800 chr2A 86.842 570 52 8 3710 4258 559619208 559619775 2.200000e-172 616.0
15 TraesCS2B01G516800 chr2A 79.754 894 141 28 1494 2370 722756484 722755614 2.840000e-171 612.0
16 TraesCS2B01G516800 chr2A 78.768 909 156 23 1495 2371 778799516 778800419 3.730000e-160 575.0
17 TraesCS2B01G516800 chr2A 94.208 259 14 1 3050 3308 723062976 723063233 1.120000e-105 394.0
18 TraesCS2B01G516800 chr2A 80.825 412 69 4 2448 2852 778803071 778803479 8.970000e-82 315.0
19 TraesCS2B01G516800 chr2A 80.720 389 70 4 2476 2860 722755596 722755209 9.040000e-77 298.0
20 TraesCS2B01G516800 chr2A 89.372 207 21 1 3040 3246 722841371 722841576 4.260000e-65 259.0
21 TraesCS2B01G516800 chr2A 79.787 188 15 14 998 1169 722830988 722831168 9.770000e-22 115.0
22 TraesCS2B01G516800 chr2A 82.075 106 15 4 1 106 769625815 769625714 2.130000e-13 87.9
23 TraesCS2B01G516800 chr2A 92.157 51 4 0 1119 1169 722756829 722756779 5.960000e-09 73.1
24 TraesCS2B01G516800 chr2D 95.518 1852 61 8 1460 3311 588435363 588437192 0.000000e+00 2940.0
25 TraesCS2B01G516800 chr2D 91.563 1363 93 12 1 1353 588433992 588435342 0.000000e+00 1860.0
26 TraesCS2B01G516800 chr2D 82.759 1537 213 39 1494 3005 588248461 588249970 0.000000e+00 1323.0
27 TraesCS2B01G516800 chr2D 79.836 853 140 24 1494 2330 588175583 588174747 1.030000e-165 593.0
28 TraesCS2B01G516800 chr2D 77.998 909 156 29 1490 2370 588453153 588454045 8.180000e-147 531.0
29 TraesCS2B01G516800 chr2D 85.787 394 36 4 3756 4147 535476918 535477293 2.410000e-107 399.0
30 TraesCS2B01G516800 chr2D 88.889 207 22 1 3040 3246 588249974 588250179 1.980000e-63 254.0
31 TraesCS2B01G516800 chr2D 83.962 106 14 3 1 106 644517784 644517682 9.840000e-17 99.0
32 TraesCS2B01G516800 chr2D 75.691 181 32 8 998 1169 588245670 588245847 3.560000e-11 80.5
33 TraesCS2B01G516800 chr2D 77.500 160 17 13 1027 1169 588235957 588236114 1.280000e-10 78.7
34 TraesCS2B01G516800 chr2D 92.157 51 4 0 1119 1169 588176033 588175983 5.960000e-09 73.1
35 TraesCS2B01G516800 chr1B 92.793 777 50 4 3522 4298 535691674 535692444 0.000000e+00 1120.0
36 TraesCS2B01G516800 chr1B 89.046 566 41 10 3744 4298 679725012 679725567 0.000000e+00 682.0
37 TraesCS2B01G516800 chr1B 84.667 150 11 3 3391 3528 535691474 535691623 5.800000e-29 139.0
38 TraesCS2B01G516800 chr6D 90.038 783 64 7 3525 4298 316320860 316320083 0.000000e+00 1002.0
39 TraesCS2B01G516800 chr3D 89.203 602 50 9 3710 4298 52819343 52818744 0.000000e+00 737.0
40 TraesCS2B01G516800 chr3D 91.694 301 22 3 3522 3821 52819574 52819276 8.600000e-112 414.0
41 TraesCS2B01G516800 chr3D 81.765 170 19 11 287 445 589796473 589796641 9.700000e-27 132.0
42 TraesCS2B01G516800 chr4D 93.165 278 18 1 3522 3799 441835244 441835520 1.440000e-109 407.0
43 TraesCS2B01G516800 chr4D 91.336 277 16 8 4025 4298 441835469 441835740 5.250000e-99 372.0
44 TraesCS2B01G516800 chr4D 92.478 226 15 2 3309 3532 441834970 441835195 5.360000e-84 322.0
45 TraesCS2B01G516800 chr4A 92.446 278 19 2 3522 3799 49206528 49206253 3.110000e-106 396.0
46 TraesCS2B01G516800 chr4A 90.654 214 18 1 3314 3525 49208670 49208457 2.530000e-72 283.0
47 TraesCS2B01G516800 chr7B 90.333 300 27 2 3522 3821 648279196 648279493 4.030000e-105 392.0
48 TraesCS2B01G516800 chr7B 80.851 188 18 15 287 461 621456137 621455955 9.700000e-27 132.0
49 TraesCS2B01G516800 chr4B 89.562 297 29 2 3525 3821 437095148 437094854 4.060000e-100 375.0
50 TraesCS2B01G516800 chr4B 84.574 188 17 11 283 461 606840819 606840635 4.420000e-40 176.0
51 TraesCS2B01G516800 chr4B 81.868 182 22 11 285 462 465007592 465007418 4.480000e-30 143.0
52 TraesCS2B01G516800 chr6B 90.749 227 15 1 3312 3532 79054630 79054856 9.040000e-77 298.0
53 TraesCS2B01G516800 chr6B 82.286 175 18 12 285 448 681209759 681209587 5.800000e-29 139.0
54 TraesCS2B01G516800 chr6B 82.927 123 12 8 459 577 355967830 355967947 7.600000e-18 102.0
55 TraesCS2B01G516800 chr6B 82.114 123 13 8 459 577 355976511 355976628 3.540000e-16 97.1
56 TraesCS2B01G516800 chrUn 83.158 190 19 11 285 461 294376823 294376634 1.240000e-35 161.0
57 TraesCS2B01G516800 chr3A 82.258 186 20 12 285 462 545908182 545908002 9.630000e-32 148.0
58 TraesCS2B01G516800 chr7D 84.466 103 16 0 1 103 511934656 511934554 7.600000e-18 102.0
59 TraesCS2B01G516800 chr7D 92.157 51 4 0 3312 3362 514346919 514346969 5.960000e-09 73.1
60 TraesCS2B01G516800 chr7D 83.333 78 12 1 1 78 159075160 159075236 2.140000e-08 71.3


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 TraesCS2B01G516800 chr2B 711865847 711870144 4297 False 7938.00 7938 100.000000 1 4298 1 chr2B.!!$F4 4297
1 TraesCS2B01G516800 chr2B 636761075 636761820 745 False 896.00 896 88.266000 3534 4298 1 chr2B.!!$F2 764
2 TraesCS2B01G516800 chr2B 711726119 711727837 1718 False 802.00 1356 85.744500 1494 3246 2 chr2B.!!$F6 1752
3 TraesCS2B01G516800 chr2B 675368738 675369352 614 False 391.00 392 88.280500 3529 4078 2 chr2B.!!$F5 549
4 TraesCS2B01G516800 chr2B 711320222 711321548 1326 True 349.05 625 86.067500 1119 2370 2 chr2B.!!$R1 1251
5 TraesCS2B01G516800 chr2A 723060022 723063233 3211 False 2282.00 4170 93.320000 1 3308 2 chr2A.!!$F5 3307
6 TraesCS2B01G516800 chr2A 722839861 722841576 1715 False 752.00 1245 85.619000 1494 3246 2 chr2A.!!$F4 1752
7 TraesCS2B01G516800 chr2A 777835530 777836909 1379 True 689.00 689 76.303000 1495 2852 1 chr2A.!!$R2 1357
8 TraesCS2B01G516800 chr2A 678607159 678607680 521 False 634.00 634 88.398000 3756 4298 1 chr2A.!!$F2 542
9 TraesCS2B01G516800 chr2A 559619208 559619775 567 False 616.00 616 86.842000 3710 4258 1 chr2A.!!$F1 548
10 TraesCS2B01G516800 chr2A 778799516 778803479 3963 False 445.00 575 79.796500 1495 2852 2 chr2A.!!$F6 1357
11 TraesCS2B01G516800 chr2A 722755209 722756829 1620 True 327.70 612 84.210333 1119 2860 3 chr2A.!!$R3 1741
12 TraesCS2B01G516800 chr2D 588433992 588437192 3200 False 2400.00 2940 93.540500 1 3311 2 chr2D.!!$F5 3310
13 TraesCS2B01G516800 chr2D 588245670 588250179 4509 False 552.50 1323 82.446333 998 3246 3 chr2D.!!$F4 2248
14 TraesCS2B01G516800 chr2D 588453153 588454045 892 False 531.00 531 77.998000 1490 2370 1 chr2D.!!$F3 880
15 TraesCS2B01G516800 chr2D 588174747 588176033 1286 True 333.05 593 85.996500 1119 2330 2 chr2D.!!$R2 1211
16 TraesCS2B01G516800 chr1B 679725012 679725567 555 False 682.00 682 89.046000 3744 4298 1 chr1B.!!$F1 554
17 TraesCS2B01G516800 chr1B 535691474 535692444 970 False 629.50 1120 88.730000 3391 4298 2 chr1B.!!$F2 907
18 TraesCS2B01G516800 chr6D 316320083 316320860 777 True 1002.00 1002 90.038000 3525 4298 1 chr6D.!!$R1 773
19 TraesCS2B01G516800 chr3D 52818744 52819574 830 True 575.50 737 90.448500 3522 4298 2 chr3D.!!$R1 776
20 TraesCS2B01G516800 chr4D 441834970 441835740 770 False 367.00 407 92.326333 3309 4298 3 chr4D.!!$F1 989
21 TraesCS2B01G516800 chr4A 49206253 49208670 2417 True 339.50 396 91.550000 3314 3799 2 chr4A.!!$R1 485

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
926 933 0.035630 CTGGAGACTTTGAGGGGCTG 60.036 60.0 0.00 0.0 0.00 4.85 F
996 1009 0.178533 TTTGGTCTCGTCCAACGGTT 59.821 50.0 8.44 0.0 45.60 4.44 F
1279 1329 0.314935 CGTGGTGGATTTTGCTGCTT 59.685 50.0 0.00 0.0 0.00 3.91 F
1456 3075 0.319083 GTCCCCGTCATGTGTACACA 59.681 55.0 29.70 29.7 46.44 3.72 F
2921 8286 0.892063 TCGTGGACATGGACATCGAA 59.108 50.0 0.00 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2183 4901 1.070105 CCGGTTCAAAGGTGTCCGA 59.930 57.895 0.00 0.00 41.84 4.55 R
2867 8232 1.677552 CTTGTACACCCCGGCTCTT 59.322 57.895 0.00 0.00 0.00 2.85 R
3273 8641 0.597568 CTTCACCTTTGCGCATGGAA 59.402 50.000 28.97 18.52 0.00 3.53 R
3284 8652 1.692519 ACACCTTCTACGCTTCACCTT 59.307 47.619 0.00 0.00 0.00 3.50 R
3772 11088 4.885907 TGAATGAGCCTCAATCCATCTTTC 59.114 41.667 7.30 0.99 0.00 2.62 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
90 91 6.372381 TGCCATATTACTGTCATGCATGTATC 59.628 38.462 25.43 16.83 0.00 2.24
110 111 2.906389 TCTGAAGTACAATGGTGAGGCT 59.094 45.455 0.00 0.00 0.00 4.58
162 163 5.612725 AGGTGGAAAATCAAGCAAAGAAA 57.387 34.783 0.00 0.00 0.00 2.52
204 205 2.771372 TCCACATAGTGCTAGATGGCAA 59.229 45.455 0.00 0.00 44.18 4.52
243 244 0.101759 TTGCCGATACCTAGCGTCAC 59.898 55.000 0.00 0.00 32.48 3.67
245 246 1.731433 GCCGATACCTAGCGTCACCA 61.731 60.000 0.00 0.00 32.48 4.17
258 259 2.224784 GCGTCACCAAGTAATTTTCCGT 59.775 45.455 0.00 0.00 0.00 4.69
306 307 2.490509 GGGGAAATACACTTTGGTTCCG 59.509 50.000 0.00 0.00 0.00 4.30
321 322 2.498885 GGTTCCGGGTTGTAGATACACT 59.501 50.000 0.00 0.00 35.64 3.55
463 466 6.966632 GGGCAAAGAAGACAAATTTGTTTTTC 59.033 34.615 24.02 25.37 42.43 2.29
464 467 7.361628 GGGCAAAGAAGACAAATTTGTTTTTCA 60.362 33.333 30.43 0.00 42.43 2.69
579 584 7.932120 TTGGGACATTTTGTTAAATTACACG 57.068 32.000 0.00 0.00 39.30 4.49
637 642 5.543790 AGCCTCACCTCCAAAAATAATTGTT 59.456 36.000 0.00 0.00 0.00 2.83
665 670 3.497262 CCGGAGTACTTTTGAAGGTCAAC 59.503 47.826 0.00 0.00 35.89 3.18
698 703 2.315386 GGTGTCCGGCTTGTCGTTC 61.315 63.158 0.00 0.00 0.00 3.95
712 717 3.810896 GTTCGGGCGGTGGCATTC 61.811 66.667 0.00 0.00 42.47 2.67
800 805 4.730966 AGAATAAGATCCTACAGCCTCGA 58.269 43.478 0.00 0.00 0.00 4.04
878 885 2.758089 GCAGAGAACATGGCGGCAG 61.758 63.158 19.29 12.11 0.00 4.85
917 924 2.695585 ACTTGGAGACCTGGAGACTTT 58.304 47.619 0.00 0.00 0.00 2.66
918 925 2.370189 ACTTGGAGACCTGGAGACTTTG 59.630 50.000 0.00 0.00 0.00 2.77
919 926 2.398754 TGGAGACCTGGAGACTTTGA 57.601 50.000 0.00 0.00 0.00 2.69
923 930 0.615850 GACCTGGAGACTTTGAGGGG 59.384 60.000 0.00 0.00 0.00 4.79
924 931 1.301293 CCTGGAGACTTTGAGGGGC 59.699 63.158 0.00 0.00 0.00 5.80
925 932 1.204113 CCTGGAGACTTTGAGGGGCT 61.204 60.000 0.00 0.00 0.00 5.19
926 933 0.035630 CTGGAGACTTTGAGGGGCTG 60.036 60.000 0.00 0.00 0.00 4.85
927 934 1.377856 GGAGACTTTGAGGGGCTGC 60.378 63.158 0.00 0.00 0.00 5.25
928 935 1.682257 GAGACTTTGAGGGGCTGCT 59.318 57.895 0.00 0.00 0.00 4.24
929 936 0.905357 GAGACTTTGAGGGGCTGCTA 59.095 55.000 0.00 0.00 0.00 3.49
930 937 0.615850 AGACTTTGAGGGGCTGCTAC 59.384 55.000 0.00 0.00 0.00 3.58
931 938 0.615850 GACTTTGAGGGGCTGCTACT 59.384 55.000 0.00 0.00 0.00 2.57
932 939 1.831736 GACTTTGAGGGGCTGCTACTA 59.168 52.381 0.00 0.00 0.00 1.82
933 940 2.236395 GACTTTGAGGGGCTGCTACTAA 59.764 50.000 0.00 0.00 0.00 2.24
974 987 1.600636 CAACCGGCAGAGGAAGCAA 60.601 57.895 0.00 0.00 34.73 3.91
996 1009 0.178533 TTTGGTCTCGTCCAACGGTT 59.821 50.000 8.44 0.00 45.60 4.44
1213 1238 3.427161 GCATTGTTGCTAGACCCAATC 57.573 47.619 0.00 0.00 45.77 2.67
1215 1240 3.382546 GCATTGTTGCTAGACCCAATCAT 59.617 43.478 0.00 0.00 45.77 2.45
1216 1241 4.735578 GCATTGTTGCTAGACCCAATCATG 60.736 45.833 0.00 0.00 45.77 3.07
1232 1257 5.547465 CAATCATGGGATGAATGGATTTGG 58.453 41.667 0.00 0.00 43.50 3.28
1233 1258 2.967201 TCATGGGATGAATGGATTTGGC 59.033 45.455 0.00 0.00 36.11 4.52
1234 1259 2.852714 TGGGATGAATGGATTTGGCT 57.147 45.000 0.00 0.00 0.00 4.75
1269 1319 3.031013 TGTATGTCTGATCGTGGTGGAT 58.969 45.455 0.00 0.00 0.00 3.41
1270 1320 3.450817 TGTATGTCTGATCGTGGTGGATT 59.549 43.478 0.00 0.00 0.00 3.01
1279 1329 0.314935 CGTGGTGGATTTTGCTGCTT 59.685 50.000 0.00 0.00 0.00 3.91
1326 1398 3.432252 CGAATGGTACGCTCTGTTTCTTT 59.568 43.478 0.00 0.00 0.00 2.52
1444 3063 0.463116 GACATTAATGGCGTCCCCGT 60.463 55.000 19.37 0.00 35.87 5.28
1445 3064 0.463116 ACATTAATGGCGTCCCCGTC 60.463 55.000 19.37 0.00 39.72 4.79
1451 3070 4.388499 GGCGTCCCCGTCATGTGT 62.388 66.667 0.00 0.00 38.92 3.72
1452 3071 2.574929 GCGTCCCCGTCATGTGTA 59.425 61.111 0.00 0.00 36.15 2.90
1453 3072 1.808390 GCGTCCCCGTCATGTGTAC 60.808 63.158 0.00 0.00 36.15 2.90
1455 3074 0.734942 CGTCCCCGTCATGTGTACAC 60.735 60.000 19.36 19.36 0.00 2.90
1456 3075 0.319083 GTCCCCGTCATGTGTACACA 59.681 55.000 29.70 29.70 46.44 3.72
2403 5152 2.833943 GCCATCCTCCAACCAAATTTCT 59.166 45.455 0.00 0.00 0.00 2.52
2404 5153 3.368739 GCCATCCTCCAACCAAATTTCTG 60.369 47.826 0.00 0.00 0.00 3.02
2406 5155 4.284234 CCATCCTCCAACCAAATTTCTGTT 59.716 41.667 0.00 0.00 0.00 3.16
2409 5158 5.669477 TCCTCCAACCAAATTTCTGTTTTG 58.331 37.500 0.88 0.00 34.55 2.44
2411 5160 5.523552 CCTCCAACCAAATTTCTGTTTTGTC 59.476 40.000 0.88 0.00 33.23 3.18
2441 5233 1.404391 CATGCTGACATGCTTTCCCTC 59.596 52.381 0.00 0.00 46.75 4.30
2448 5240 1.558756 ACATGCTTTCCCTCTCTCCTG 59.441 52.381 0.00 0.00 0.00 3.86
2526 7883 1.427809 ATGGCCAATCGAGGAGATCA 58.572 50.000 10.96 0.00 38.98 2.92
2921 8286 0.892063 TCGTGGACATGGACATCGAA 59.108 50.000 0.00 0.00 0.00 3.71
3007 8375 4.516698 TGAATCTTTTGCTCTGGTTCAGAC 59.483 41.667 0.00 0.00 35.39 3.51
3009 8377 4.156455 TCTTTTGCTCTGGTTCAGACTT 57.844 40.909 0.00 0.00 35.39 3.01
3012 8380 2.827800 TGCTCTGGTTCAGACTTCAG 57.172 50.000 0.00 0.00 35.39 3.02
3013 8381 2.319844 TGCTCTGGTTCAGACTTCAGA 58.680 47.619 0.00 0.00 35.39 3.27
3014 8382 2.902486 TGCTCTGGTTCAGACTTCAGAT 59.098 45.455 0.00 0.00 35.39 2.90
3015 8383 4.089361 TGCTCTGGTTCAGACTTCAGATA 58.911 43.478 0.00 0.00 35.39 1.98
3016 8384 4.528206 TGCTCTGGTTCAGACTTCAGATAA 59.472 41.667 0.00 0.00 35.39 1.75
3284 8652 3.430862 GCCGAGTTCCATGCGCAA 61.431 61.111 17.11 0.00 0.00 4.85
3389 8757 3.484229 CCGTTTCATCAAGATTCGTGCTC 60.484 47.826 0.00 0.00 0.00 4.26
3393 8761 4.192429 TCATCAAGATTCGTGCTCTCAA 57.808 40.909 0.00 0.00 0.00 3.02
3453 8821 1.870402 CGGTCAATACAACTGCACACA 59.130 47.619 0.00 0.00 0.00 3.72
3468 8844 3.443329 TGCACACATGAGACAAAACAGTT 59.557 39.130 0.00 0.00 0.00 3.16
3478 8854 4.331968 AGACAAAACAGTTCCTGACAACA 58.668 39.130 0.00 0.00 35.18 3.33
3489 8865 5.069516 AGTTCCTGACAACATTTTGCAGAAT 59.930 36.000 13.94 0.00 38.28 2.40
3525 8905 1.881709 CGAGAGATGTGCGCTGCAT 60.882 57.895 9.73 13.44 41.91 3.96
3527 8907 2.024305 GAGATGTGCGCTGCATGC 59.976 61.111 19.53 11.82 41.91 4.06
3531 8911 1.206745 GATGTGCGCTGCATGCATTC 61.207 55.000 22.97 14.95 45.34 2.67
3602 10914 3.744238 TCACGGTGACAAGATCTTCAA 57.256 42.857 6.76 0.00 0.00 2.69
3784 11100 6.845302 TCACTCATTTTCGAAAGATGGATTG 58.155 36.000 21.87 16.49 41.60 2.67
3867 11237 9.850628 ATTTCACTCATTTGATACAACTGATTG 57.149 29.630 12.32 12.32 41.98 2.67
4033 11427 8.816640 AAACAATTTCACTCGCTTCATAAAAT 57.183 26.923 0.00 0.00 0.00 1.82
4035 11429 9.906660 AACAATTTCACTCGCTTCATAAAATAA 57.093 25.926 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 9.927668 CTCCCACACAATAAATTCAACTATTTT 57.072 29.630 0.00 0.00 0.00 1.82
90 91 3.340814 AGCCTCACCATTGTACTTCAG 57.659 47.619 0.00 0.00 0.00 3.02
110 111 2.299013 TGTTTTCTCTTCAGCGGCTCTA 59.701 45.455 0.00 0.00 0.00 2.43
116 117 6.228273 TGTATTTCTGTTTTCTCTTCAGCG 57.772 37.500 0.00 0.00 0.00 5.18
162 163 7.096551 GTGGACCAAGTATTTTTGTATTGCAT 58.903 34.615 0.00 0.00 0.00 3.96
430 433 2.155279 GTCTTCTTTGCCCTGAAGTCC 58.845 52.381 0.00 0.00 40.20 3.85
463 466 7.212274 AGAAAATCCACCATTGACTTCTTTTG 58.788 34.615 0.00 0.00 0.00 2.44
464 467 7.365497 AGAAAATCCACCATTGACTTCTTTT 57.635 32.000 0.00 0.00 0.00 2.27
476 479 5.428184 AAACCACAAAAGAAAATCCACCA 57.572 34.783 0.00 0.00 0.00 4.17
557 562 5.921408 TGCGTGTAATTTAACAAAATGTCCC 59.079 36.000 0.00 0.00 0.00 4.46
558 563 6.088883 CCTGCGTGTAATTTAACAAAATGTCC 59.911 38.462 0.00 0.00 0.00 4.02
570 575 1.463444 GCGAGTTCCTGCGTGTAATTT 59.537 47.619 0.00 0.00 0.00 1.82
637 642 3.842007 TCAAAAGTACTCCGGGAAACA 57.158 42.857 0.00 0.00 0.00 2.83
665 670 0.815734 ACACCGGGTTATCAGAGACG 59.184 55.000 6.32 0.00 0.00 4.18
689 694 3.411351 CACCGCCCGAACGACAAG 61.411 66.667 0.00 0.00 34.06 3.16
698 703 4.776322 TCAGAATGCCACCGCCCG 62.776 66.667 0.00 0.00 34.76 6.13
712 717 4.758674 TGATCTGGAGCTTGTTTTTCTCAG 59.241 41.667 0.00 0.00 0.00 3.35
800 805 1.528824 CCTCGGGTGCTCATGGAAT 59.471 57.895 0.00 0.00 0.00 3.01
878 885 5.222631 CAAGTTCAATGCAAGTTTAGGACC 58.777 41.667 0.00 0.00 0.00 4.46
895 902 2.252714 AGTCTCCAGGTCTCCAAGTTC 58.747 52.381 0.00 0.00 0.00 3.01
917 924 4.284490 CAGATTATTAGTAGCAGCCCCTCA 59.716 45.833 0.00 0.00 0.00 3.86
918 925 4.323104 CCAGATTATTAGTAGCAGCCCCTC 60.323 50.000 0.00 0.00 0.00 4.30
919 926 3.584848 CCAGATTATTAGTAGCAGCCCCT 59.415 47.826 0.00 0.00 0.00 4.79
923 930 4.249661 GGCTCCAGATTATTAGTAGCAGC 58.750 47.826 0.00 0.00 0.00 5.25
924 931 4.619394 CGGGCTCCAGATTATTAGTAGCAG 60.619 50.000 0.00 0.00 0.00 4.24
925 932 3.258372 CGGGCTCCAGATTATTAGTAGCA 59.742 47.826 0.00 0.00 0.00 3.49
926 933 3.510360 TCGGGCTCCAGATTATTAGTAGC 59.490 47.826 0.00 0.00 0.00 3.58
927 934 5.715070 CTTCGGGCTCCAGATTATTAGTAG 58.285 45.833 0.00 0.00 0.00 2.57
928 935 4.021368 GCTTCGGGCTCCAGATTATTAGTA 60.021 45.833 0.00 0.00 38.06 1.82
929 936 3.244249 GCTTCGGGCTCCAGATTATTAGT 60.244 47.826 0.00 0.00 38.06 2.24
930 937 3.244215 TGCTTCGGGCTCCAGATTATTAG 60.244 47.826 3.33 0.00 42.39 1.73
931 938 2.703536 TGCTTCGGGCTCCAGATTATTA 59.296 45.455 3.33 0.00 42.39 0.98
932 939 1.490490 TGCTTCGGGCTCCAGATTATT 59.510 47.619 3.33 0.00 42.39 1.40
933 940 1.071385 CTGCTTCGGGCTCCAGATTAT 59.929 52.381 3.33 0.00 42.39 1.28
996 1009 0.826715 GAGAGAGTACAGCCATGGCA 59.173 55.000 37.18 15.78 44.88 4.92
1210 1235 4.041198 GCCAAATCCATTCATCCCATGATT 59.959 41.667 0.00 0.00 39.39 2.57
1213 1238 2.969950 AGCCAAATCCATTCATCCCATG 59.030 45.455 0.00 0.00 0.00 3.66
1215 1240 2.852714 AGCCAAATCCATTCATCCCA 57.147 45.000 0.00 0.00 0.00 4.37
1216 1241 5.047519 CAGATTAGCCAAATCCATTCATCCC 60.048 44.000 5.91 0.00 44.44 3.85
1218 1243 6.889301 TCAGATTAGCCAAATCCATTCATC 57.111 37.500 5.91 0.00 44.44 2.92
1219 1244 7.008332 TGATCAGATTAGCCAAATCCATTCAT 58.992 34.615 0.00 0.00 44.44 2.57
1220 1245 6.263842 GTGATCAGATTAGCCAAATCCATTCA 59.736 38.462 0.00 4.56 44.44 2.57
1221 1246 6.489361 AGTGATCAGATTAGCCAAATCCATTC 59.511 38.462 0.00 2.56 44.44 2.67
1222 1247 6.264744 CAGTGATCAGATTAGCCAAATCCATT 59.735 38.462 0.00 0.00 44.44 3.16
1223 1248 5.768662 CAGTGATCAGATTAGCCAAATCCAT 59.231 40.000 0.00 0.23 44.44 3.41
1224 1249 5.128205 CAGTGATCAGATTAGCCAAATCCA 58.872 41.667 0.00 0.00 44.44 3.41
1225 1250 5.008415 CACAGTGATCAGATTAGCCAAATCC 59.992 44.000 0.00 0.00 44.44 3.01
1226 1251 5.587844 ACACAGTGATCAGATTAGCCAAATC 59.412 40.000 7.81 1.94 43.81 2.17
1227 1252 5.503927 ACACAGTGATCAGATTAGCCAAAT 58.496 37.500 7.81 0.00 0.00 2.32
1228 1253 4.910195 ACACAGTGATCAGATTAGCCAAA 58.090 39.130 7.81 0.00 0.00 3.28
1229 1254 4.558226 ACACAGTGATCAGATTAGCCAA 57.442 40.909 7.81 0.00 0.00 4.52
1230 1255 5.129320 ACATACACAGTGATCAGATTAGCCA 59.871 40.000 7.81 0.00 0.00 4.75
1231 1256 5.605534 ACATACACAGTGATCAGATTAGCC 58.394 41.667 7.81 0.00 0.00 3.93
1232 1257 6.420306 CAGACATACACAGTGATCAGATTAGC 59.580 42.308 7.81 0.00 0.00 3.09
1233 1258 7.710896 TCAGACATACACAGTGATCAGATTAG 58.289 38.462 7.81 0.00 0.00 1.73
1234 1259 7.645058 TCAGACATACACAGTGATCAGATTA 57.355 36.000 7.81 0.00 0.00 1.75
1269 1319 1.541147 CATCCCGAAGAAGCAGCAAAA 59.459 47.619 0.00 0.00 0.00 2.44
1270 1320 1.167851 CATCCCGAAGAAGCAGCAAA 58.832 50.000 0.00 0.00 0.00 3.68
1326 1398 5.936686 CAGAATGCAGAGAAGAAACAAGA 57.063 39.130 0.00 0.00 0.00 3.02
1356 1428 5.355350 CCAGATGAAAATTCAGTCACCTACC 59.645 44.000 1.98 0.00 41.08 3.18
1445 3064 1.773410 TCCGTTCGTGTGTACACATG 58.227 50.000 33.23 33.23 46.75 3.21
1451 3070 1.597690 CGTCAGTTCCGTTCGTGTGTA 60.598 52.381 0.00 0.00 0.00 2.90
1452 3071 0.868602 CGTCAGTTCCGTTCGTGTGT 60.869 55.000 0.00 0.00 0.00 3.72
1453 3072 1.545614 CCGTCAGTTCCGTTCGTGTG 61.546 60.000 0.00 0.00 0.00 3.82
1455 3074 0.872881 AACCGTCAGTTCCGTTCGTG 60.873 55.000 0.00 0.00 30.99 4.35
1456 3075 0.872881 CAACCGTCAGTTCCGTTCGT 60.873 55.000 0.00 0.00 36.18 3.85
2116 4831 2.741598 GCGCTCAGCTTCAGCACT 60.742 61.111 13.64 0.00 45.16 4.40
2183 4901 1.070105 CCGGTTCAAAGGTGTCCGA 59.930 57.895 0.00 0.00 41.84 4.55
2403 5152 8.334263 TCAGCATGATAATAAGTGACAAAACA 57.666 30.769 0.00 0.00 42.56 2.83
2448 5240 2.124983 TGGGAAGATCTGCAGCGC 60.125 61.111 9.47 0.00 0.00 5.92
2867 8232 1.677552 CTTGTACACCCCGGCTCTT 59.322 57.895 0.00 0.00 0.00 2.85
2888 8253 3.305516 ACGAAAGCCCCGTACGGT 61.306 61.111 31.24 13.95 38.61 4.83
3007 8375 6.020599 CGATTTACAGTCGGTGTTATCTGAAG 60.021 42.308 0.00 0.00 40.94 3.02
3009 8377 5.124297 TCGATTTACAGTCGGTGTTATCTGA 59.876 40.000 0.00 0.00 40.94 3.27
3012 8380 5.338365 ACTCGATTTACAGTCGGTGTTATC 58.662 41.667 0.00 1.67 40.94 1.75
3013 8381 5.320549 ACTCGATTTACAGTCGGTGTTAT 57.679 39.130 0.00 0.00 40.94 1.89
3014 8382 4.771590 ACTCGATTTACAGTCGGTGTTA 57.228 40.909 0.00 0.00 40.94 2.41
3015 8383 3.655276 ACTCGATTTACAGTCGGTGTT 57.345 42.857 0.00 0.00 40.94 3.32
3016 8384 3.755378 AGTACTCGATTTACAGTCGGTGT 59.245 43.478 7.00 0.00 43.86 4.16
3273 8641 0.597568 CTTCACCTTTGCGCATGGAA 59.402 50.000 28.97 18.52 0.00 3.53
3284 8652 1.692519 ACACCTTCTACGCTTCACCTT 59.307 47.619 0.00 0.00 0.00 3.50
3368 8736 3.369147 AGAGCACGAATCTTGATGAAACG 59.631 43.478 0.00 0.00 35.00 3.60
3468 8844 6.003326 TCTATTCTGCAAAATGTTGTCAGGA 58.997 36.000 15.61 10.35 38.42 3.86
3478 8854 8.976353 TCTAACTCTCTCTCTATTCTGCAAAAT 58.024 33.333 0.00 0.00 0.00 1.82
3489 8865 7.591421 TCTCTCGATTCTAACTCTCTCTCTA 57.409 40.000 0.00 0.00 0.00 2.43
3575 10886 3.201353 TCTTGTCACCGTGATTCCAAA 57.799 42.857 4.13 0.00 0.00 3.28
3585 10897 4.811555 TGTTTTGAAGATCTTGTCACCG 57.188 40.909 14.00 0.00 0.00 4.94
3679 10994 6.382821 TCACAACGAAACAATTTTGTGTTC 57.617 33.333 14.78 3.35 45.89 3.18
3772 11088 4.885907 TGAATGAGCCTCAATCCATCTTTC 59.114 41.667 7.30 0.99 0.00 2.62
3784 11100 8.650714 GTGTGAAATAAATTTTGAATGAGCCTC 58.349 33.333 0.00 0.00 0.00 4.70
3867 11237 6.567769 TTTTCTTTCAATTCAAACGACTGC 57.432 33.333 0.00 0.00 0.00 4.40
4068 11462 7.111247 TCAGTGAATCCAGTGTTTTGAAATT 57.889 32.000 0.00 0.00 42.80 1.82
4165 11564 7.651808 TCTTCAGATGAGTGAAATTGGTTTTC 58.348 34.615 0.00 0.00 43.42 2.29


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

AutoCloner maintained by Alex Coulton.