Multiple sequence alignment - TraesCS6A01G369600

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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 TraesCS6A01G369600 chr6A 100.000 6503 0 0 1 6503 594991860 594985358 0.000000e+00 12009.0
1 TraesCS6A01G369600 chr6A 88.571 665 70 4 1229 1889 595161664 595162326 0.000000e+00 802.0
2 TraesCS6A01G369600 chr6A 78.346 1076 164 37 3669 4710 101297407 101298447 3.310000e-177 632.0
3 TraesCS6A01G369600 chr6A 85.054 368 32 7 6121 6486 595164701 595165047 2.880000e-93 353.0
4 TraesCS6A01G369600 chr6A 79.077 325 40 14 6151 6472 602749640 602749341 1.430000e-46 198.0
5 TraesCS6A01G369600 chr6A 86.364 66 9 0 3413 3478 22813487 22813422 9.040000e-09 73.1
6 TraesCS6A01G369600 chr6A 100.000 36 0 0 5089 5124 594986725 594986690 4.210000e-07 67.6
7 TraesCS6A01G369600 chr6A 100.000 36 0 0 5136 5171 594986772 594986737 4.210000e-07 67.6
8 TraesCS6A01G369600 chrUn 92.193 4637 234 36 1341 5913 214051271 214046699 0.000000e+00 6440.0
9 TraesCS6A01G369600 chrUn 92.193 4637 234 36 1341 5913 240293814 240298386 0.000000e+00 6440.0
10 TraesCS6A01G369600 chrUn 89.578 1967 175 14 1643 3605 263804628 263806568 0.000000e+00 2470.0
11 TraesCS6A01G369600 chrUn 89.613 1964 174 14 1646 3605 289985332 289983395 0.000000e+00 2470.0
12 TraesCS6A01G369600 chrUn 89.032 1012 67 12 1 988 79442054 79443045 0.000000e+00 1214.0
13 TraesCS6A01G369600 chrUn 90.497 926 67 11 1341 2251 79443411 79444330 0.000000e+00 1203.0
14 TraesCS6A01G369600 chrUn 91.226 832 51 4 339 1166 263803143 263803956 0.000000e+00 1112.0
15 TraesCS6A01G369600 chrUn 91.226 832 51 4 339 1166 320556150 320556963 0.000000e+00 1112.0
16 TraesCS6A01G369600 chrUn 92.409 606 29 5 5912 6503 214046633 214046031 0.000000e+00 848.0
17 TraesCS6A01G369600 chrUn 92.409 606 29 5 5912 6503 240298452 240299054 0.000000e+00 848.0
18 TraesCS6A01G369600 chrUn 90.364 467 24 6 1164 1611 263804170 263804634 1.560000e-165 593.0
19 TraesCS6A01G369600 chrUn 87.393 349 16 10 1 343 219089044 219088718 6.160000e-100 375.0
20 TraesCS6A01G369600 chrUn 87.393 349 16 10 1 343 227608264 227607938 6.160000e-100 375.0
21 TraesCS6A01G369600 chrUn 87.393 349 16 10 1 343 279062580 279062254 6.160000e-100 375.0
22 TraesCS6A01G369600 chrUn 89.677 155 12 2 1460 1611 289985482 289985329 1.850000e-45 195.0
23 TraesCS6A01G369600 chrUn 97.727 44 1 0 5136 5179 214047503 214047460 6.990000e-10 76.8
24 TraesCS6A01G369600 chrUn 97.727 44 1 0 5136 5179 240297582 240297625 6.990000e-10 76.8
25 TraesCS6A01G369600 chrUn 93.333 45 3 0 5089 5133 214047456 214047412 4.210000e-07 67.6
26 TraesCS6A01G369600 chrUn 93.333 45 3 0 5089 5133 240297629 240297673 4.210000e-07 67.6
27 TraesCS6A01G369600 chr6B 92.101 4355 265 26 1603 5913 680931267 680935586 0.000000e+00 6063.0
28 TraesCS6A01G369600 chr6B 91.285 2249 151 20 1341 3571 680737608 680735387 0.000000e+00 3025.0
29 TraesCS6A01G369600 chr6B 83.992 2074 235 40 1229 3271 680988411 680990418 0.000000e+00 1901.0
30 TraesCS6A01G369600 chr6B 88.354 1185 90 12 1 1165 680741422 680740266 0.000000e+00 1380.0
31 TraesCS6A01G369600 chr6B 94.088 592 27 2 5912 6502 680935652 680936236 0.000000e+00 893.0
32 TraesCS6A01G369600 chr6B 83.276 867 96 23 3668 4508 680735366 680734523 0.000000e+00 752.0
33 TraesCS6A01G369600 chr6B 91.142 508 34 5 1 499 680916839 680917344 0.000000e+00 678.0
34 TraesCS6A01G369600 chr6B 91.211 421 29 2 6084 6503 680732604 680732191 3.400000e-157 566.0
35 TraesCS6A01G369600 chr6B 83.800 500 52 4 493 980 680928692 680929174 1.290000e-121 448.0
36 TraesCS6A01G369600 chr6B 87.295 244 21 5 1239 1474 681371884 681372125 2.990000e-68 270.0
37 TraesCS6A01G369600 chr6B 76.571 525 73 27 5199 5693 680733583 680733079 6.510000e-60 243.0
38 TraesCS6A01G369600 chr6B 77.684 354 40 27 1162 1490 680929330 680929669 5.180000e-41 180.0
39 TraesCS6A01G369600 chr6B 81.148 122 21 1 4928 5047 204626826 204626947 5.370000e-16 97.1
40 TraesCS6A01G369600 chr6B 97.727 44 1 0 5136 5179 680934765 680934808 6.990000e-10 76.8
41 TraesCS6A01G369600 chr6D 93.146 2130 105 24 1164 3271 449145737 449143627 0.000000e+00 3086.0
42 TraesCS6A01G369600 chr6D 83.463 2062 280 40 1237 3271 449376277 449378304 0.000000e+00 1862.0
43 TraesCS6A01G369600 chr6D 91.241 1176 60 20 1 1166 449147169 449146027 0.000000e+00 1561.0
44 TraesCS6A01G369600 chr6D 93.878 980 42 4 4638 5603 448911020 448910045 0.000000e+00 1461.0
45 TraesCS6A01G369600 chr6D 92.746 579 28 3 5912 6483 448909422 448908851 0.000000e+00 824.0
46 TraesCS6A01G369600 chr6D 79.345 1099 160 31 3689 4759 84073291 84074350 0.000000e+00 710.0
47 TraesCS6A01G369600 chr6D 88.305 590 41 13 5926 6503 449108536 449107963 0.000000e+00 682.0
48 TraesCS6A01G369600 chr6D 90.293 443 32 7 1354 1789 449375342 449375780 2.630000e-158 569.0
49 TraesCS6A01G369600 chr6D 86.966 468 31 7 709 1165 448911499 448911051 3.500000e-137 499.0
50 TraesCS6A01G369600 chr6D 94.295 298 10 2 5623 5913 448909785 448909488 3.580000e-122 449.0
51 TraesCS6A01G369600 chr6D 80.662 574 93 15 275 832 449285676 449286247 4.660000e-116 429.0
52 TraesCS6A01G369600 chr6D 87.500 320 39 1 3717 4036 449130760 449130442 1.030000e-97 368.0
53 TraesCS6A01G369600 chr6D 91.469 211 15 3 494 704 448912195 448911988 2.970000e-73 287.0
54 TraesCS6A01G369600 chr6D 76.744 430 63 20 6084 6503 455999098 455998696 8.550000e-49 206.0
55 TraesCS6A01G369600 chr6D 82.305 243 36 2 597 832 449154498 449154256 3.070000e-48 204.0
56 TraesCS6A01G369600 chr6D 86.517 178 20 4 1182 1359 449366107 449366280 6.650000e-45 193.0
57 TraesCS6A01G369600 chr6D 86.000 100 13 1 3576 3674 343615805 343615706 8.920000e-19 106.0
58 TraesCS6A01G369600 chr6D 86.585 82 10 1 6269 6350 449159461 449159381 8.980000e-14 89.8
59 TraesCS6A01G369600 chr6D 81.308 107 18 1 4928 5032 115328786 115328892 1.160000e-12 86.1
60 TraesCS6A01G369600 chr6D 97.727 44 1 0 5136 5179 448910561 448910518 6.990000e-10 76.8
61 TraesCS6A01G369600 chr1D 77.446 1104 169 47 3665 4711 406638500 406639580 2.610000e-163 586.0
62 TraesCS6A01G369600 chr1D 79.241 448 74 10 3717 4158 449332717 449332283 1.770000e-75 294.0
63 TraesCS6A01G369600 chr1D 81.461 178 29 3 3410 3585 449332965 449332790 6.800000e-30 143.0
64 TraesCS6A01G369600 chr4D 78.768 763 102 25 3751 4474 75505027 75505768 2.140000e-124 457.0
65 TraesCS6A01G369600 chr2D 75.185 1084 197 42 3669 4693 470218308 470219378 4.630000e-121 446.0
66 TraesCS6A01G369600 chr2D 78.797 665 93 21 4133 4758 318328050 318327395 2.820000e-108 403.0
67 TraesCS6A01G369600 chr2B 79.257 646 82 29 4151 4756 386305266 386304633 2.820000e-108 403.0
68 TraesCS6A01G369600 chr2B 82.090 335 45 11 4388 4715 549040672 549040998 8.310000e-69 272.0
69 TraesCS6A01G369600 chr2B 78.302 212 43 3 3923 4132 4881123 4880913 4.090000e-27 134.0
70 TraesCS6A01G369600 chr2B 91.209 91 7 1 3581 3670 519663404 519663494 8.850000e-24 122.0
71 TraesCS6A01G369600 chr2B 80.189 106 20 1 4214 4318 442340398 442340503 1.940000e-10 78.7
72 TraesCS6A01G369600 chr3B 76.351 296 52 15 3669 3957 463193363 463193079 6.800000e-30 143.0
73 TraesCS6A01G369600 chr3B 75.676 296 54 15 3669 3957 463185076 463184792 1.470000e-26 132.0
74 TraesCS6A01G369600 chr3A 75.758 297 52 17 3669 3957 477690943 477690659 1.470000e-26 132.0
75 TraesCS6A01G369600 chr3A 91.765 85 7 0 3582 3666 465824190 465824274 1.150000e-22 119.0
76 TraesCS6A01G369600 chr7B 75.172 290 64 5 3674 3958 53245626 53245912 5.290000e-26 130.0
77 TraesCS6A01G369600 chr7B 91.111 90 8 0 3585 3674 471435368 471435457 8.850000e-24 122.0
78 TraesCS6A01G369600 chr3D 75.427 293 54 16 3669 3954 355326599 355326880 6.850000e-25 126.0
79 TraesCS6A01G369600 chr3D 91.765 85 7 0 3582 3666 338932243 338932159 1.150000e-22 119.0
80 TraesCS6A01G369600 chr1A 89.796 98 8 2 3576 3673 80687849 80687944 2.460000e-24 124.0
81 TraesCS6A01G369600 chr4B 78.090 178 30 9 3411 3583 666597416 666597243 3.210000e-18 104.0
82 TraesCS6A01G369600 chr7D 92.000 50 4 0 3531 3580 488791451 488791500 3.250000e-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 TraesCS6A01G369600 chr6A 594985358 594991860 6502 True 12009.000000 12009 100.000000 1 6503 1 chr6A.!!$R2 6502
1 TraesCS6A01G369600 chr6A 101297407 101298447 1040 False 632.000000 632 78.346000 3669 4710 1 chr6A.!!$F1 1041
2 TraesCS6A01G369600 chr6A 595161664 595165047 3383 False 577.500000 802 86.812500 1229 6486 2 chr6A.!!$F2 5257
3 TraesCS6A01G369600 chrUn 214046031 214051271 5240 True 1858.100000 6440 93.915500 1341 6503 4 chrUn.!!$R4 5162
4 TraesCS6A01G369600 chrUn 240293814 240299054 5240 False 1858.100000 6440 93.915500 1341 6503 4 chrUn.!!$F3 5162
5 TraesCS6A01G369600 chrUn 263803143 263806568 3425 False 1391.666667 2470 90.389333 339 3605 3 chrUn.!!$F4 3266
6 TraesCS6A01G369600 chrUn 289983395 289985482 2087 True 1332.500000 2470 89.645000 1460 3605 2 chrUn.!!$R5 2145
7 TraesCS6A01G369600 chrUn 79442054 79444330 2276 False 1208.500000 1214 89.764500 1 2251 2 chrUn.!!$F2 2250
8 TraesCS6A01G369600 chrUn 320556150 320556963 813 False 1112.000000 1112 91.226000 339 1166 1 chrUn.!!$F1 827
9 TraesCS6A01G369600 chr6B 680988411 680990418 2007 False 1901.000000 1901 83.992000 1229 3271 1 chr6B.!!$F3 2042
10 TraesCS6A01G369600 chr6B 680928692 680936236 7544 False 1532.160000 6063 89.080000 493 6502 5 chr6B.!!$F5 6009
11 TraesCS6A01G369600 chr6B 680732191 680741422 9231 True 1193.200000 3025 86.139400 1 6503 5 chr6B.!!$R1 6502
12 TraesCS6A01G369600 chr6B 680916839 680917344 505 False 678.000000 678 91.142000 1 499 1 chr6B.!!$F2 498
13 TraesCS6A01G369600 chr6D 449143627 449147169 3542 True 2323.500000 3086 92.193500 1 3271 2 chr6D.!!$R8 3270
14 TraesCS6A01G369600 chr6D 449375342 449378304 2962 False 1215.500000 1862 86.878000 1237 3271 2 chr6D.!!$F5 2034
15 TraesCS6A01G369600 chr6D 84073291 84074350 1059 False 710.000000 710 79.345000 3689 4759 1 chr6D.!!$F1 1070
16 TraesCS6A01G369600 chr6D 449107963 449108536 573 True 682.000000 682 88.305000 5926 6503 1 chr6D.!!$R2 577
17 TraesCS6A01G369600 chr6D 448908851 448912195 3344 True 599.466667 1461 92.846833 494 6483 6 chr6D.!!$R7 5989
18 TraesCS6A01G369600 chr6D 449285676 449286247 571 False 429.000000 429 80.662000 275 832 1 chr6D.!!$F3 557
19 TraesCS6A01G369600 chr1D 406638500 406639580 1080 False 586.000000 586 77.446000 3665 4711 1 chr1D.!!$F1 1046
20 TraesCS6A01G369600 chr1D 449332283 449332965 682 True 218.500000 294 80.351000 3410 4158 2 chr1D.!!$R1 748
21 TraesCS6A01G369600 chr4D 75505027 75505768 741 False 457.000000 457 78.768000 3751 4474 1 chr4D.!!$F1 723
22 TraesCS6A01G369600 chr2D 470218308 470219378 1070 False 446.000000 446 75.185000 3669 4693 1 chr2D.!!$F1 1024
23 TraesCS6A01G369600 chr2D 318327395 318328050 655 True 403.000000 403 78.797000 4133 4758 1 chr2D.!!$R1 625
24 TraesCS6A01G369600 chr2B 386304633 386305266 633 True 403.000000 403 79.257000 4151 4756 1 chr2B.!!$R2 605

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
768 1278 0.804989 GCCGTTGGATGAAAGGACAG 59.195 55.000 0.00 0.0 35.30 3.51 F
1175 2970 0.471022 GAGGATGGTCTCTCCCCTCC 60.471 65.000 0.00 0.0 38.15 4.30 F
1923 7588 0.613292 AGCTGGTCATCTGTCTCCGT 60.613 55.000 0.00 0.0 0.00 4.69 F
2072 7737 0.371645 GCAGCTCACATTCAGTACGC 59.628 55.000 0.00 0.0 0.00 4.42 F
2149 7814 0.771127 CCTTGAAGGGGTCAACCTCA 59.229 55.000 2.50 0.0 41.47 3.86 F
2262 8252 1.066502 TCACTAAAGCGCCTGTGCATA 60.067 47.619 2.29 0.0 37.32 3.14 F
2328 8318 1.497161 CCCCGGGTCTTATCTCACTT 58.503 55.000 21.85 0.0 0.00 3.16 F
3961 10034 2.287103 CCACACTCATGCTCAATGATCG 59.713 50.000 0.00 0.0 44.40 3.69 F
4812 11684 1.000396 GCACAATTCCCCCTCTGCT 60.000 57.895 0.00 0.0 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1961 7626 0.102120 CTCAGGCTCATCGTCAGGAC 59.898 60.000 0.00 0.00 0.00 3.85 R
2059 7724 1.206132 TGGTAGGGCGTACTGAATGTG 59.794 52.381 16.07 0.00 0.00 3.21 R
3886 9950 0.107165 GGAAGGGTAGTGCATCCACC 60.107 60.000 5.92 5.92 43.09 4.61 R
3961 10034 1.430632 CCATGATCTTGCACGGCAC 59.569 57.895 3.07 0.00 38.71 5.01 R
4257 10336 3.436704 CACCGATCAACACTATTTGCACT 59.563 43.478 0.00 0.00 0.00 4.40 R
4352 10464 0.463654 TGCCATGCGAAGGATACCAC 60.464 55.000 0.00 0.00 35.32 4.16 R
4419 10548 1.065126 GGTTCCAGGTATGCTCAGCTT 60.065 52.381 0.00 0.00 0.00 3.74 R
5172 12058 0.098200 CGAGCTACATCGACCGAACA 59.902 55.000 0.00 0.00 45.56 3.18 R
6179 13722 1.261480 GAGTCAGGACTGCTTGAGGA 58.739 55.000 6.68 0.00 42.66 3.71 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
66 67 2.472488 CGCTTGTGGCAATTTTTCTGAC 59.528 45.455 0.00 0.00 41.91 3.51
86 87 5.674525 TGACCCTCAAAGTCATAAGCATAG 58.325 41.667 0.00 0.00 39.29 2.23
91 92 6.294473 CCTCAAAGTCATAAGCATAGGATGT 58.706 40.000 0.00 0.00 0.00 3.06
156 157 3.495729 CCACCCCTAGTTGTGGCT 58.504 61.111 13.25 0.00 44.98 4.75
178 179 5.183904 GCTCAAGGTTCAAATGGAAGTACAT 59.816 40.000 0.00 0.00 35.82 2.29
484 494 1.134220 ACGACAAGTTGCCTCTTTCCA 60.134 47.619 1.81 0.00 0.00 3.53
495 506 2.618816 GCCTCTTTCCATGTGTCCATCA 60.619 50.000 0.00 0.00 0.00 3.07
503 515 6.806668 TTCCATGTGTCCATCACTATCTTA 57.193 37.500 0.00 0.00 46.27 2.10
513 525 9.429109 TGTCCATCACTATCTTATTAGTGGTTA 57.571 33.333 10.72 0.00 45.95 2.85
535 547 2.367567 TCATCGTAGGTTAAGGCCATCC 59.632 50.000 5.01 0.93 0.00 3.51
569 581 3.310435 CCTACCCTTAACCCTGACCTAGT 60.310 52.174 0.00 0.00 0.00 2.57
668 681 8.786710 TTTGTAGGCCATAGTACCTCTTATTA 57.213 34.615 5.01 0.00 37.50 0.98
768 1278 0.804989 GCCGTTGGATGAAAGGACAG 59.195 55.000 0.00 0.00 35.30 3.51
783 1293 4.810191 AGGACAGGTGATAGTTCTTGTC 57.190 45.455 0.00 0.00 0.00 3.18
861 1390 7.885922 TGCTGTTTGTAGAGGGTAAATATTCAA 59.114 33.333 0.00 0.00 0.00 2.69
927 1457 9.537192 TTTAGTGTTTTTCTTATCTCGAGTTGA 57.463 29.630 13.13 0.00 0.00 3.18
970 1500 3.056107 CAGTCAATTTGGAGACGACCCTA 60.056 47.826 0.00 0.00 39.67 3.53
1073 1603 0.813184 CCGGCTGCAAAATCACTGAT 59.187 50.000 0.50 0.00 0.00 2.90
1170 2965 2.321719 GGGTTAGAGGATGGTCTCTCC 58.678 57.143 0.00 0.00 42.57 3.71
1173 2968 1.928480 TAGAGGATGGTCTCTCCCCT 58.072 55.000 0.00 0.00 42.57 4.79
1175 2970 0.471022 GAGGATGGTCTCTCCCCTCC 60.471 65.000 0.00 0.00 38.15 4.30
1178 2973 1.949449 ATGGTCTCTCCCCTCCCCT 60.949 63.158 0.00 0.00 34.77 4.79
1329 4410 4.504916 CCTCTGCTCCGGTGCTCG 62.505 72.222 27.24 18.37 38.88 5.03
1557 6135 1.092348 TCCGACTGTCACGAATCGAT 58.908 50.000 10.55 0.00 36.70 3.59
1579 6157 4.766375 TGTGATTTCCCGTCTCTTTATCC 58.234 43.478 0.00 0.00 0.00 2.59
1581 6159 4.037927 TGATTTCCCGTCTCTTTATCCCT 58.962 43.478 0.00 0.00 0.00 4.20
1591 6169 7.328737 CCGTCTCTTTATCCCTTTAGAGAAAA 58.671 38.462 0.00 0.00 43.28 2.29
1599 6180 9.681062 TTTATCCCTTTAGAGAAAACTACATGG 57.319 33.333 0.00 0.00 0.00 3.66
1627 6246 4.317359 TGGTGATGCCACATTCGG 57.683 55.556 0.00 0.00 43.61 4.30
1746 7411 0.968393 GAGACCTCCCTGACGAGCTT 60.968 60.000 0.00 0.00 0.00 3.74
1771 7436 1.069765 CGTGTGCTGTCCTTCCTGT 59.930 57.895 0.00 0.00 0.00 4.00
1775 7440 1.837051 TGCTGTCCTTCCTGTCGGT 60.837 57.895 0.00 0.00 0.00 4.69
1821 7486 4.467084 AACACCCGATGGCGCGAT 62.467 61.111 12.10 3.93 35.83 4.58
1842 7507 3.241530 TGGAGGCGCTTGACCAGT 61.242 61.111 7.64 0.00 0.00 4.00
1846 7511 1.152963 AGGCGCTTGACCAGTTTGT 60.153 52.632 7.64 0.00 0.00 2.83
1858 7523 4.936411 TGACCAGTTTGTTGTTCGTCTTTA 59.064 37.500 0.00 0.00 0.00 1.85
1869 7534 2.554893 GTTCGTCTTTAATGGGCCAACA 59.445 45.455 11.89 0.00 0.00 3.33
1923 7588 0.613292 AGCTGGTCATCTGTCTCCGT 60.613 55.000 0.00 0.00 0.00 4.69
1961 7626 1.953138 GGTGCGAGATCGATGCCTG 60.953 63.158 0.54 0.00 43.02 4.85
1977 7642 1.326213 CCTGTCCTGACGATGAGCCT 61.326 60.000 0.00 0.00 0.00 4.58
2059 7724 3.487879 GGAACTCGTAGTAAGAGCAGCTC 60.488 52.174 15.25 15.25 39.23 4.09
2072 7737 0.371645 GCAGCTCACATTCAGTACGC 59.628 55.000 0.00 0.00 0.00 4.42
2085 7750 1.001633 CAGTACGCCCTACCAGTGTTT 59.998 52.381 0.00 0.00 0.00 2.83
2106 7771 2.836372 TGATGTGCCTCTGAGTCTCATT 59.164 45.455 2.22 0.00 0.00 2.57
2149 7814 0.771127 CCTTGAAGGGGTCAACCTCA 59.229 55.000 2.50 0.00 41.47 3.86
2262 8252 1.066502 TCACTAAAGCGCCTGTGCATA 60.067 47.619 2.29 0.00 37.32 3.14
2314 8304 2.360600 TTCGGATTTGTGCCCCGG 60.361 61.111 0.00 0.00 43.16 5.73
2328 8318 1.497161 CCCCGGGTCTTATCTCACTT 58.503 55.000 21.85 0.00 0.00 3.16
2652 8651 6.875948 TTGTTAGAACTGCAGATAAGCAAA 57.124 33.333 23.35 4.38 45.13 3.68
2745 8745 9.747898 ATAACATAGTGTCTTGGTTGGATAAAA 57.252 29.630 0.00 0.00 0.00 1.52
2751 8751 8.281212 AGTGTCTTGGTTGGATAAAATATGAC 57.719 34.615 0.00 0.00 0.00 3.06
2755 8755 9.520204 GTCTTGGTTGGATAAAATATGACATTG 57.480 33.333 0.00 0.00 0.00 2.82
2773 8773 4.706476 ACATTGCAGGTTGTTATAGCACAT 59.294 37.500 0.00 0.00 34.56 3.21
2988 8989 5.304614 AGCTTGATAACACCGAGGTATATGT 59.695 40.000 0.00 0.00 27.68 2.29
3121 9125 9.054922 CCCAAGAAACAATAACACAATCATTTT 57.945 29.630 0.00 0.00 0.00 1.82
3316 9320 7.933396 TCATTGCCAATTAGAATGTATGACAG 58.067 34.615 0.00 0.00 0.00 3.51
3335 9339 3.261137 ACAGCCCTTCCTACTTGTTCTAC 59.739 47.826 0.00 0.00 0.00 2.59
3487 9493 8.510505 CAAAAACTGGAGACCAAAAATTTCAAA 58.489 29.630 0.00 0.00 30.80 2.69
3850 9914 4.512657 CGCATCTCGAATTTCTTGATGAC 58.487 43.478 21.78 15.33 41.67 3.06
3886 9950 3.055385 TCGGATGTGGTTTTCCCTTCTAG 60.055 47.826 0.00 0.00 39.73 2.43
3917 9987 5.105064 GCACTACCCTTCCTGTTAAGTCATA 60.105 44.000 0.00 0.00 0.00 2.15
3918 9988 6.574350 CACTACCCTTCCTGTTAAGTCATAG 58.426 44.000 0.00 0.00 0.00 2.23
3919 9989 6.380274 CACTACCCTTCCTGTTAAGTCATAGA 59.620 42.308 0.00 0.00 0.00 1.98
3961 10034 2.287103 CCACACTCATGCTCAATGATCG 59.713 50.000 0.00 0.00 44.40 3.69
4257 10336 5.192927 GTGGTGATTCCTCATTGGATAACA 58.807 41.667 0.00 0.00 45.68 2.41
4352 10464 5.591472 TGATCTACAATGGCTTCAAGAATGG 59.409 40.000 0.00 0.00 0.00 3.16
4419 10548 1.163420 CCAGTGCGTGCAACCAACTA 61.163 55.000 0.00 0.00 0.00 2.24
4442 10578 1.279025 TGAGCATACCTGGAACCCCC 61.279 60.000 0.00 0.00 0.00 5.40
4480 10623 2.154462 CATCTCCAAAAGCCGAGTGTT 58.846 47.619 0.00 0.00 0.00 3.32
4734 11606 1.666553 GACGGTGTCGGCAACATGA 60.667 57.895 5.62 0.00 45.37 3.07
4760 11632 3.600388 ACAAGTTCGGAGCCATTCTTAG 58.400 45.455 0.00 0.00 0.00 2.18
4793 11665 5.808366 AAGTGTTGTGTCCAAGATCTCTA 57.192 39.130 0.00 0.00 0.00 2.43
4812 11684 1.000396 GCACAATTCCCCCTCTGCT 60.000 57.895 0.00 0.00 0.00 4.24
4876 11759 1.818674 GAGCCATTTTGGATCGGTGTT 59.181 47.619 0.00 0.00 43.58 3.32
4883 11766 4.993029 TTTTGGATCGGTGTTGAAAGTT 57.007 36.364 0.00 0.00 0.00 2.66
4892 11775 2.354821 GGTGTTGAAAGTTTCGCTCTGT 59.645 45.455 10.92 0.00 0.00 3.41
4980 11863 1.614996 TCAACGTGGTCATGGCAATT 58.385 45.000 0.00 0.00 0.00 2.32
4982 11865 3.149981 TCAACGTGGTCATGGCAATTTA 58.850 40.909 0.00 0.00 0.00 1.40
5017 11900 5.104360 TCCCACTCATATTCCTCTTTGAAGG 60.104 44.000 0.00 0.00 37.81 3.46
5044 11927 3.520696 TCATCATACGGGGAGGATTCAT 58.479 45.455 0.00 0.00 0.00 2.57
5053 11936 2.941480 GGGAGGATTCATGCTCACAAT 58.059 47.619 10.16 0.00 46.51 2.71
5078 11961 7.202526 TGTATGACAAGAAAAGGCAAGAAAAG 58.797 34.615 0.00 0.00 0.00 2.27
5129 12015 2.048127 GGCACCGAGCTCGAGTTT 60.048 61.111 36.59 15.07 44.79 2.66
5201 12087 4.752879 GTAGCTCGTTGGGCGGCA 62.753 66.667 12.47 0.00 41.72 5.69
5397 12297 1.401018 GGCAGGAAAACGGTCGAAATG 60.401 52.381 0.00 0.00 0.00 2.32
5421 12321 4.920112 TTCGGGCGGTGGTGTGTG 62.920 66.667 0.00 0.00 0.00 3.82
5431 12331 0.179045 GTGGTGTGTGGAGCTTCTGT 60.179 55.000 0.00 0.00 0.00 3.41
5438 12338 4.400961 GGAGCTTCTGTGGCGGCT 62.401 66.667 11.43 0.00 37.77 5.52
5708 12865 2.024414 GTTTTGGTCTGCTGTTGGAGT 58.976 47.619 0.00 0.00 33.13 3.85
5737 12899 5.659440 TTGGCCTCAAAGACCATAAAATC 57.341 39.130 3.32 0.00 32.39 2.17
5797 12961 7.619302 TCTGCTATTGGGGATGTTTTTAGAATT 59.381 33.333 0.00 0.00 0.00 2.17
6006 13421 5.877012 AGTGTGTGATGAAAATAGTAGCTGG 59.123 40.000 0.00 0.00 0.00 4.85
6142 13684 7.482654 TGTTGTCAGTTTGATTAACAGAGAG 57.517 36.000 7.37 0.00 39.30 3.20
6162 13705 5.766222 AGAGTGAAAGTCAAATTGCATGTC 58.234 37.500 0.00 0.00 39.29 3.06
6179 13722 5.301551 TGCATGTCTTCCACACTTGTTTAAT 59.698 36.000 0.00 0.00 38.04 1.40
6398 13952 1.393603 TCCGCTGATAGTGACTCCAG 58.606 55.000 9.64 9.64 0.00 3.86
6405 13959 4.582656 GCTGATAGTGACTCCAGTGATAGT 59.417 45.833 13.82 0.00 0.00 2.12
6423 13977 5.714806 TGATAGTGACTAAGATGTGTGGTCA 59.285 40.000 0.00 0.00 35.04 4.02
6474 14028 5.824904 TTCTCTAAAGAATCTGCAATGGC 57.175 39.130 0.00 0.00 36.59 4.40
6486 14040 1.153784 CAATGGCGGCCATGTGTTC 60.154 57.895 33.56 0.00 44.40 3.18
6495 14049 0.447801 GCCATGTGTTCGCTGTTAGG 59.552 55.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 5.296151 TCCTATGCTTATGACTTTGAGGG 57.704 43.478 0.00 0.00 0.00 4.30
107 108 1.069973 TGCACATTCGCTTCTTCGTTG 60.070 47.619 0.00 0.00 0.00 4.10
156 157 7.942341 ACTTATGTACTTCCATTTGAACCTTGA 59.058 33.333 0.00 0.00 0.00 3.02
503 515 8.365647 CCTTAACCTACGATGATAACCACTAAT 58.634 37.037 0.00 0.00 0.00 1.73
513 525 3.008049 GGATGGCCTTAACCTACGATGAT 59.992 47.826 3.32 0.00 0.00 2.45
535 547 8.946248 AGGGTTAAGGGTAGGAATATTTAGAAG 58.054 37.037 0.00 0.00 0.00 2.85
536 548 8.720537 CAGGGTTAAGGGTAGGAATATTTAGAA 58.279 37.037 0.00 0.00 0.00 2.10
569 581 1.595109 CAGGCGTCAACAGTGAGCA 60.595 57.895 0.00 0.00 33.27 4.26
768 1278 1.135199 TCCGCGACAAGAACTATCACC 60.135 52.381 8.23 0.00 0.00 4.02
783 1293 3.059597 CAGTAGCAATCCTTTTATCCGCG 60.060 47.826 0.00 0.00 0.00 6.46
885 1414 6.422776 ACACTAAATTATCCGCAACAAGAG 57.577 37.500 0.00 0.00 0.00 2.85
970 1500 1.130054 TCTCTGGCTTGGTGCTCCTT 61.130 55.000 6.34 0.00 42.39 3.36
1019 1549 3.209812 CCGGCTCGTCCTCGATGA 61.210 66.667 0.00 0.00 45.21 2.92
1073 1603 2.562738 TCAATGCTCGGACTTCTCTTCA 59.437 45.455 0.00 0.00 0.00 3.02
1208 3008 1.227263 CTAATCGGCCGTGACCCTG 60.227 63.158 27.15 6.44 0.00 4.45
1210 3010 2.588034 GCTAATCGGCCGTGACCC 60.588 66.667 27.15 8.57 0.00 4.46
1329 4410 3.119096 GCGTCGGAGTTGGAAGGC 61.119 66.667 0.00 0.00 0.00 4.35
1557 6135 4.383770 GGGATAAAGAGACGGGAAATCACA 60.384 45.833 0.00 0.00 0.00 3.58
1579 6157 7.379098 GGAACCATGTAGTTTTCTCTAAAGG 57.621 40.000 0.00 0.00 0.00 3.11
1599 6180 1.478105 GGCATCACCAAATCAGGGAAC 59.522 52.381 0.00 0.00 38.86 3.62
1746 7411 1.218047 GGACAGCACACGCCATAGA 59.782 57.895 0.00 0.00 39.83 1.98
1771 7436 3.083349 CAGGGCATCCTCCACCGA 61.083 66.667 0.00 0.00 42.67 4.69
1775 7440 2.285592 TCTGCAGGGCATCCTCCA 60.286 61.111 15.13 0.00 42.67 3.86
1812 7477 2.733301 CTCCAGAGATCGCGCCAT 59.267 61.111 0.00 0.00 0.00 4.40
1821 7486 2.650116 GGTCAAGCGCCTCCAGAGA 61.650 63.158 2.29 0.00 0.00 3.10
1842 7507 4.500035 GGCCCATTAAAGACGAACAACAAA 60.500 41.667 0.00 0.00 0.00 2.83
1846 7511 2.865079 TGGCCCATTAAAGACGAACAA 58.135 42.857 0.00 0.00 0.00 2.83
1858 7523 1.596408 GCGGAAATGTTGGCCCATT 59.404 52.632 0.00 0.00 36.62 3.16
1869 7534 1.729284 AACGGTTGTATCGCGGAAAT 58.271 45.000 6.13 0.00 0.00 2.17
1923 7588 1.758514 GATGAGAGGCGAGTCCCCA 60.759 63.158 0.00 0.00 34.51 4.96
1961 7626 0.102120 CTCAGGCTCATCGTCAGGAC 59.898 60.000 0.00 0.00 0.00 3.85
1977 7642 2.417239 GGTGTTTGTGAACGTGTTCTCA 59.583 45.455 13.40 12.71 40.12 3.27
2059 7724 1.206132 TGGTAGGGCGTACTGAATGTG 59.794 52.381 16.07 0.00 0.00 3.21
2072 7737 1.812571 GCACATCAAACACTGGTAGGG 59.187 52.381 0.00 0.00 0.00 3.53
2085 7750 1.928868 TGAGACTCAGAGGCACATCA 58.071 50.000 5.91 0.00 0.00 3.07
2106 7771 1.850345 AGGGTCTTCAAGTGTTGGGAA 59.150 47.619 0.00 0.00 0.00 3.97
2149 7814 3.879892 GAGAACTTCAAAGCAGAGTGGTT 59.120 43.478 0.00 0.00 40.14 3.67
2262 8252 2.026075 AGGTAGAGAACAGTAGTCGGCT 60.026 50.000 0.00 0.00 0.00 5.52
2314 8304 5.009610 CCTCTAGCTGAAGTGAGATAAGACC 59.990 48.000 0.00 0.00 0.00 3.85
2328 8318 3.370953 GGCCTTCAAAATCCTCTAGCTGA 60.371 47.826 0.00 0.00 0.00 4.26
2668 8667 6.828785 AGGAAGATAAAGTACCAAAATGCGAT 59.171 34.615 0.00 0.00 0.00 4.58
2745 8745 6.772233 TGCTATAACAACCTGCAATGTCATAT 59.228 34.615 0.50 0.19 0.00 1.78
2751 8751 4.700268 TGTGCTATAACAACCTGCAATG 57.300 40.909 0.00 0.00 35.34 2.82
2755 8755 9.398170 CAAATAATATGTGCTATAACAACCTGC 57.602 33.333 0.00 0.00 32.81 4.85
2826 8827 4.935205 TCAAATCCCATCTGTACAGAAACG 59.065 41.667 28.43 18.81 41.36 3.60
2988 8989 5.842907 ACAGCAACATCGCTATCTATACAA 58.157 37.500 0.00 0.00 41.38 2.41
3121 9125 2.285756 CGAACTTTAGGCGTTCACACAA 59.714 45.455 0.00 0.00 40.50 3.33
3251 9255 6.360370 AAGCTAACTTACAATCTGAGTCCA 57.640 37.500 0.00 0.00 33.13 4.02
3316 9320 2.570302 TGGTAGAACAAGTAGGAAGGGC 59.430 50.000 0.00 0.00 0.00 5.19
3402 9406 4.067944 ACCTTCTCTCTCCACACCTAAT 57.932 45.455 0.00 0.00 0.00 1.73
3487 9493 5.417580 ACAAATATGTGTGGCGGAAGTAAAT 59.582 36.000 0.00 0.00 38.69 1.40
3639 9646 7.928873 ACTTCCTCTGTCCCAAATTATAAGAA 58.071 34.615 0.00 0.00 0.00 2.52
3648 9662 6.697641 ATAAAGTACTTCCTCTGTCCCAAA 57.302 37.500 8.95 0.00 0.00 3.28
3649 9663 6.697641 AATAAAGTACTTCCTCTGTCCCAA 57.302 37.500 8.95 0.00 0.00 4.12
3650 9664 6.727231 TGTAATAAAGTACTTCCTCTGTCCCA 59.273 38.462 8.95 0.00 0.00 4.37
3651 9665 7.179076 TGTAATAAAGTACTTCCTCTGTCCC 57.821 40.000 8.95 0.00 0.00 4.46
3652 9666 9.968870 CTATGTAATAAAGTACTTCCTCTGTCC 57.031 37.037 8.95 0.00 0.00 4.02
3687 9704 3.708631 TGTGTTGAATTTGGGATTGTGGT 59.291 39.130 0.00 0.00 0.00 4.16
3694 9711 6.968263 TGAATAAGTGTGTTGAATTTGGGA 57.032 33.333 0.00 0.00 0.00 4.37
3745 9805 6.481434 ACAAGACCACTAGTTCTACACTTT 57.519 37.500 0.00 0.00 36.88 2.66
3850 9914 3.187227 CACATCCGACAGTTTCTTCAAGG 59.813 47.826 0.00 0.00 0.00 3.61
3886 9950 0.107165 GGAAGGGTAGTGCATCCACC 60.107 60.000 5.92 5.92 43.09 4.61
3961 10034 1.430632 CCATGATCTTGCACGGCAC 59.569 57.895 3.07 0.00 38.71 5.01
4257 10336 3.436704 CACCGATCAACACTATTTGCACT 59.563 43.478 0.00 0.00 0.00 4.40
4352 10464 0.463654 TGCCATGCGAAGGATACCAC 60.464 55.000 0.00 0.00 35.32 4.16
4419 10548 1.065126 GGTTCCAGGTATGCTCAGCTT 60.065 52.381 0.00 0.00 0.00 3.74
4442 10578 1.559368 TGAACAAAGCATGGGGATGG 58.441 50.000 0.00 0.00 0.00 3.51
4444 10580 3.294214 GAGATGAACAAAGCATGGGGAT 58.706 45.455 0.00 0.00 0.00 3.85
4445 10581 2.621407 GGAGATGAACAAAGCATGGGGA 60.621 50.000 0.00 0.00 0.00 4.81
4734 11606 0.472471 TGGCTCCGAACTTGTTCCTT 59.528 50.000 7.78 0.00 0.00 3.36
4760 11632 0.375803 ACAACACTTTTGACGCCGAC 59.624 50.000 0.00 0.00 0.00 4.79
4793 11665 1.000396 GCAGAGGGGGAATTGTGCT 60.000 57.895 0.00 0.00 0.00 4.40
4812 11684 3.616956 AGAGCATGACCAATTCTTCGA 57.383 42.857 0.00 0.00 0.00 3.71
4876 11759 3.186409 GTGCATACAGAGCGAAACTTTCA 59.814 43.478 0.00 0.00 33.85 2.69
4883 11766 1.153647 CCGGTGCATACAGAGCGAA 60.154 57.895 0.00 0.00 35.10 4.70
4980 11863 9.730705 GAATATGAGTGGGATGAAGATGATTAA 57.269 33.333 0.00 0.00 0.00 1.40
4982 11865 7.018349 AGGAATATGAGTGGGATGAAGATGATT 59.982 37.037 0.00 0.00 0.00 2.57
5017 11900 2.234908 CCTCCCCGTATGATGATTCCTC 59.765 54.545 0.00 0.00 0.00 3.71
5044 11927 6.294120 CCTTTTCTTGTCATACATTGTGAGCA 60.294 38.462 0.00 0.00 0.00 4.26
5053 11936 6.707440 TTTCTTGCCTTTTCTTGTCATACA 57.293 33.333 0.00 0.00 0.00 2.29
5078 11961 7.597743 TGTTCGATGGAAGTTCTCTAAGTTAAC 59.402 37.037 2.25 0.00 31.49 2.01
5124 12007 4.093556 CGATGGAAGTTCTTAGCCAAACTC 59.906 45.833 2.25 0.00 34.71 3.01
5129 12015 3.007506 TGTTCGATGGAAGTTCTTAGCCA 59.992 43.478 2.25 0.00 31.49 4.75
5172 12058 0.098200 CGAGCTACATCGACCGAACA 59.902 55.000 0.00 0.00 45.56 3.18
5179 12065 1.141019 GCCCAACGAGCTACATCGA 59.859 57.895 2.78 0.00 45.56 3.59
5201 12087 3.069729 GTCCATCCTGACGCCTTTACTAT 59.930 47.826 0.00 0.00 0.00 2.12
5244 12131 1.595093 CGAAGTTGGTTGCATCCCCC 61.595 60.000 11.33 1.88 0.00 5.40
5354 12254 1.404717 GCCGATGGATGATATGCTCGT 60.405 52.381 0.00 0.00 0.00 4.18
5413 12313 0.179048 CACAGAAGCTCCACACACCA 60.179 55.000 0.00 0.00 0.00 4.17
5421 12321 4.400961 AGCCGCCACAGAAGCTCC 62.401 66.667 0.00 0.00 0.00 4.70
5468 12368 1.142688 AGCCCTGACACCCATTCCTT 61.143 55.000 0.00 0.00 0.00 3.36
5797 12961 2.622977 GGATTTGGAGGGTGTGCCATAA 60.623 50.000 0.00 0.00 36.17 1.90
6006 13421 8.329203 ACCTAAACTGAATTTCAAGATGAGAC 57.671 34.615 0.01 0.00 0.00 3.36
6142 13684 5.403466 GGAAGACATGCAATTTGACTTTCAC 59.597 40.000 0.00 0.00 31.02 3.18
6162 13705 6.633500 TTGAGGATTAAACAAGTGTGGAAG 57.367 37.500 0.00 0.00 0.00 3.46
6179 13722 1.261480 GAGTCAGGACTGCTTGAGGA 58.739 55.000 6.68 0.00 42.66 3.71
6398 13952 5.967088 ACCACACATCTTAGTCACTATCAC 58.033 41.667 0.00 0.00 0.00 3.06
6405 13959 3.895041 TGACTGACCACACATCTTAGTCA 59.105 43.478 0.00 0.00 40.26 3.41
6423 13977 5.862845 AGTCTTCAGATGAACAACATGACT 58.137 37.500 0.00 6.94 39.56 3.41
6474 14028 1.295357 TAACAGCGAACACATGGCCG 61.295 55.000 0.00 0.00 32.32 6.13


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

AutoCloner maintained by Alex Coulton.