Multiple sequence alignment - TraesCS1D01G101300

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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 TraesCS1D01G101300 chr1D 100.000 5817 0 0 1 5817 89131849 89126033 0.000000e+00 10743.0
1 TraesCS1D01G101300 chr1A 93.282 5195 206 51 6 5119 85040736 85035604 0.000000e+00 7528.0
2 TraesCS1D01G101300 chr1A 95.640 711 24 5 5112 5817 85035355 85034647 0.000000e+00 1134.0
3 TraesCS1D01G101300 chr1A 90.000 70 7 0 5079 5148 543475078 543475009 2.230000e-14 91.6
4 TraesCS1D01G101300 chr1B 95.632 3205 94 14 904 4093 142321732 142318559 0.000000e+00 5101.0
5 TraesCS1D01G101300 chr1B 97.016 1106 33 0 4191 5296 142318548 142317443 0.000000e+00 1860.0
6 TraesCS1D01G101300 chr1B 95.076 528 13 3 5294 5817 142299259 142298741 0.000000e+00 819.0
7 TraesCS1D01G101300 chr1B 86.398 522 69 2 4179 4699 60056829 60057349 2.350000e-158 569.0
8 TraesCS1D01G101300 chr1B 82.439 410 50 15 334 731 142322524 142322125 7.220000e-89 339.0
9 TraesCS1D01G101300 chr1B 91.139 158 13 1 738 895 142321934 142321778 4.570000e-51 213.0
10 TraesCS1D01G101300 chr1B 83.575 207 26 6 4776 4980 60057354 60057554 2.770000e-43 187.0
11 TraesCS1D01G101300 chr1B 93.750 64 4 0 5079 5142 597156865 597156802 4.800000e-16 97.1
12 TraesCS1D01G101300 chr2D 86.817 531 67 3 4176 4704 86507902 86508431 1.810000e-164 590.0
13 TraesCS1D01G101300 chr2D 85.902 532 72 3 4176 4705 78675040 78675570 1.090000e-156 564.0
14 TraesCS1D01G101300 chr2D 87.445 454 35 4 3663 4114 86507470 86507903 2.420000e-138 503.0
15 TraesCS1D01G101300 chr2D 86.976 453 39 5 3663 4114 78674608 78675041 5.240000e-135 492.0
16 TraesCS1D01G101300 chr2D 84.475 219 26 6 4776 4992 78675573 78675785 5.910000e-50 209.0
17 TraesCS1D01G101300 chr2D 93.590 78 3 1 4090 4167 451974329 451974404 1.320000e-21 115.0
18 TraesCS1D01G101300 chr2D 82.707 133 16 5 4776 4906 86508432 86508559 1.710000e-20 111.0
19 TraesCS1D01G101300 chr2D 89.130 92 4 4 4089 4179 451974404 451974318 6.160000e-20 110.0
20 TraesCS1D01G101300 chr2D 82.946 129 10 10 83 208 407414459 407414578 7.970000e-19 106.0
21 TraesCS1D01G101300 chr2D 92.857 42 3 0 2643 2684 86507424 86507465 1.750000e-05 62.1
22 TraesCS1D01G101300 chr5A 86.353 447 58 3 4261 4705 691742209 691741764 8.760000e-133 484.0
23 TraesCS1D01G101300 chr5A 82.759 290 42 6 3368 3654 425457486 425457202 9.680000e-63 252.0
24 TraesCS1D01G101300 chr5A 92.857 42 3 0 2643 2684 691759247 691759206 1.750000e-05 62.1
25 TraesCS1D01G101300 chr3B 80.624 449 58 17 102 524 607218198 607217753 2.620000e-83 320.0
26 TraesCS1D01G101300 chr3B 90.000 70 7 0 5079 5148 8721953 8721884 2.230000e-14 91.6
27 TraesCS1D01G101300 chr7A 80.569 422 63 15 3238 3656 3785980 3785575 2.040000e-79 307.0
28 TraesCS1D01G101300 chr7A 82.182 275 46 1 3044 3318 2658549 2658278 3.500000e-57 233.0
29 TraesCS1D01G101300 chr7A 82.969 229 31 3 2486 2706 3786407 3786179 3.550000e-47 200.0
30 TraesCS1D01G101300 chr7A 76.205 332 55 14 129 445 569455068 569454746 2.810000e-33 154.0
31 TraesCS1D01G101300 chr7A 76.812 276 43 17 60 332 634790681 634790938 1.020000e-27 135.0
32 TraesCS1D01G101300 chr7A 86.667 120 16 0 3044 3163 2947301 2947420 3.660000e-27 134.0
33 TraesCS1D01G101300 chr7A 92.135 89 2 2 4086 4174 350571789 350571872 2.850000e-23 121.0
34 TraesCS1D01G101300 chr7A 93.750 80 2 1 4090 4169 350571866 350571790 3.680000e-22 117.0
35 TraesCS1D01G101300 chr7A 85.586 111 8 6 3614 3720 3589774 3589668 6.160000e-20 110.0
36 TraesCS1D01G101300 chr3A 89.744 195 16 3 3663 3856 699782440 699782631 4.500000e-61 246.0
37 TraesCS1D01G101300 chr3A 79.261 352 55 11 100 446 525295182 525295520 4.530000e-56 230.0
38 TraesCS1D01G101300 chr3A 90.476 42 4 0 2643 2684 699782394 699782435 8.140000e-04 56.5
39 TraesCS1D01G101300 chr6A 89.231 195 17 3 3663 3856 420595148 420594957 2.090000e-59 241.0
40 TraesCS1D01G101300 chr6A 89.231 195 17 3 3663 3856 595907273 595907464 2.090000e-59 241.0
41 TraesCS1D01G101300 chr6A 92.857 42 3 0 2643 2684 420595194 420595153 1.750000e-05 62.1
42 TraesCS1D01G101300 chr6A 92.857 42 3 0 2643 2684 595907227 595907268 1.750000e-05 62.1
43 TraesCS1D01G101300 chr7D 79.832 238 37 6 3028 3255 2882002 2881766 4.660000e-36 163.0
44 TraesCS1D01G101300 chr7D 80.269 223 29 3 3473 3694 3444570 3444362 2.810000e-33 154.0
45 TraesCS1D01G101300 chr7D 92.308 78 4 1 4090 4167 225203081 225203156 6.160000e-20 110.0
46 TraesCS1D01G101300 chr7D 88.889 90 4 5 4087 4174 135026245 135026330 7.970000e-19 106.0
47 TraesCS1D01G101300 chr4D 93.827 81 2 2 4089 4168 215459552 215459630 1.020000e-22 119.0
48 TraesCS1D01G101300 chr4D 88.506 87 4 5 124 208 328814809 328814727 3.710000e-17 100.0
49 TraesCS1D01G101300 chr6B 90.805 87 6 1 4090 4176 210282606 210282522 1.320000e-21 115.0
50 TraesCS1D01G101300 chr4A 79.730 148 18 9 3580 3720 741882504 741882646 4.800000e-16 97.1
51 TraesCS1D01G101300 chr2A 86.517 89 8 3 5079 5166 74145635 74145550 1.730000e-15 95.3
52 TraesCS1D01G101300 chr2A 90.541 74 3 4 5074 5145 182008983 182009054 1.730000e-15 95.3
53 TraesCS1D01G101300 chr2A 88.158 76 8 1 5079 5154 591280053 591279979 8.030000e-14 89.8


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 TraesCS1D01G101300 chr1D 89126033 89131849 5816 True 10743.000000 10743 100.000000 1 5817 1 chr1D.!!$R1 5816
1 TraesCS1D01G101300 chr1A 85034647 85040736 6089 True 4331.000000 7528 94.461000 6 5817 2 chr1A.!!$R2 5811
2 TraesCS1D01G101300 chr1B 142317443 142322524 5081 True 1878.250000 5101 91.556500 334 5296 4 chr1B.!!$R3 4962
3 TraesCS1D01G101300 chr1B 142298741 142299259 518 True 819.000000 819 95.076000 5294 5817 1 chr1B.!!$R1 523
4 TraesCS1D01G101300 chr1B 60056829 60057554 725 False 378.000000 569 84.986500 4179 4980 2 chr1B.!!$F1 801
5 TraesCS1D01G101300 chr2D 78674608 78675785 1177 False 421.666667 564 85.784333 3663 4992 3 chr2D.!!$F3 1329
6 TraesCS1D01G101300 chr2D 86507424 86508559 1135 False 316.525000 590 87.456500 2643 4906 4 chr2D.!!$F4 2263
7 TraesCS1D01G101300 chr7A 3785575 3786407 832 True 253.500000 307 81.769000 2486 3656 2 chr7A.!!$R5 1170

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
515 544 0.034089 CCAAGGCCCCTTTAGGAGTG 60.034 60.000 0.00 0.0 38.24 3.51 F
1680 1952 0.550914 TGCACAAGAAGGTGAGGGTT 59.449 50.000 0.00 0.0 41.32 4.11 F
2223 2495 1.001378 GCCGTTGCTTGTGTGAATTCT 60.001 47.619 7.05 0.0 33.53 2.40 F
3338 3642 0.038166 TGGTGAGCATCCAAACTCCC 59.962 55.000 0.00 0.0 31.65 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2004 2276 0.447406 TTTCAATCACAGCCATCGCG 59.553 50.000 0.0 0.00 41.18 5.87 R
2770 3057 2.099592 ACAAACCAGCACATGACAACTG 59.900 45.455 0.0 0.85 0.00 3.16 R
4082 4396 0.105039 GGCGGAGGAAGTACATGAGG 59.895 60.000 0.0 0.00 0.00 3.86 R
4843 5159 0.037697 GTATCGCCCAGTCACACACA 60.038 55.000 0.0 0.00 0.00 3.72 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.696187 GACCACTGGGCTAAAAACCAAA 59.304 45.455 0.00 0.00 36.09 3.28
33 34 4.165180 ACCACTGGGCTAAAAACCAAATTT 59.835 37.500 0.00 0.00 36.09 1.82
35 36 5.931724 CCACTGGGCTAAAAACCAAATTTAG 59.068 40.000 0.00 0.00 41.27 1.85
58 59 4.946160 AAATTGTTGGGATAGAGGGTGA 57.054 40.909 0.00 0.00 0.00 4.02
65 66 7.699709 TGTTGGGATAGAGGGTGATTTAATA 57.300 36.000 0.00 0.00 0.00 0.98
66 67 7.745717 TGTTGGGATAGAGGGTGATTTAATAG 58.254 38.462 0.00 0.00 0.00 1.73
72 73 8.826765 GGATAGAGGGTGATTTAATAGGAATGA 58.173 37.037 0.00 0.00 0.00 2.57
81 82 9.774742 GTGATTTAATAGGAATGAAAGTGACAC 57.225 33.333 0.00 0.00 0.00 3.67
106 107 5.367945 CCAACTTACCATGGTGTATAGGT 57.632 43.478 28.17 14.34 38.14 3.08
109 110 6.281405 CAACTTACCATGGTGTATAGGTCTC 58.719 44.000 28.17 0.00 35.62 3.36
116 117 5.540337 CCATGGTGTATAGGTCTCTGTGTAT 59.460 44.000 2.57 0.00 0.00 2.29
121 122 7.091443 GGTGTATAGGTCTCTGTGTATATTGC 58.909 42.308 0.00 0.00 0.00 3.56
133 134 9.709600 CTCTGTGTATATTGCTATAGTATGTCG 57.290 37.037 0.84 0.00 0.00 4.35
243 246 2.612567 GCACACGCGTCAAATGGGA 61.613 57.895 9.86 0.00 0.00 4.37
246 249 0.321210 ACACGCGTCAAATGGGATGA 60.321 50.000 9.86 0.00 0.00 2.92
311 315 9.613428 TTGATTTATGTATGAGTAGTGAAAGGG 57.387 33.333 0.00 0.00 0.00 3.95
320 325 6.248569 TGAGTAGTGAAAGGGAAGAAAGTT 57.751 37.500 0.00 0.00 0.00 2.66
322 327 7.798071 TGAGTAGTGAAAGGGAAGAAAGTTTA 58.202 34.615 0.00 0.00 0.00 2.01
323 328 7.931948 TGAGTAGTGAAAGGGAAGAAAGTTTAG 59.068 37.037 0.00 0.00 0.00 1.85
355 372 9.657419 GTTGAGATTGATTTGAATGGGTTAATT 57.343 29.630 0.00 0.00 0.00 1.40
360 377 8.967664 ATTGATTTGAATGGGTTAATTCATGG 57.032 30.769 0.80 0.00 44.04 3.66
376 393 2.562298 TCATGGCATTGTTTTGGGAGAC 59.438 45.455 0.00 0.00 0.00 3.36
388 405 2.479566 TGGGAGACTGCTGATTTGAC 57.520 50.000 0.00 0.00 0.00 3.18
403 420 4.754618 TGATTTGACTGAGTTAATGCACGT 59.245 37.500 0.00 0.00 0.00 4.49
411 428 5.699001 ACTGAGTTAATGCACGTGTCAAATA 59.301 36.000 18.38 10.21 0.00 1.40
413 430 5.929415 TGAGTTAATGCACGTGTCAAATAGA 59.071 36.000 18.38 0.28 0.00 1.98
428 445 5.652452 GTCAAATAGACCTGCCTAAATTGGT 59.348 40.000 0.00 0.00 41.56 3.67
462 479 2.810439 AGGACGCATCTAAGATGCTC 57.190 50.000 18.67 15.31 42.50 4.26
464 481 1.001268 GGACGCATCTAAGATGCTCGA 60.001 52.381 18.67 0.00 42.50 4.04
465 482 2.352225 GGACGCATCTAAGATGCTCGAT 60.352 50.000 18.67 0.00 42.50 3.59
471 499 6.749578 ACGCATCTAAGATGCTCGATATAAAG 59.250 38.462 18.67 7.29 42.50 1.85
480 508 3.199071 TGCTCGATATAAAGGTGTTGGGT 59.801 43.478 0.00 0.00 0.00 4.51
484 512 6.297080 TCGATATAAAGGTGTTGGGTTGTA 57.703 37.500 0.00 0.00 0.00 2.41
501 529 1.822990 TGTAAGGCGAGACTACCAAGG 59.177 52.381 0.00 0.00 0.00 3.61
515 544 0.034089 CCAAGGCCCCTTTAGGAGTG 60.034 60.000 0.00 0.00 38.24 3.51
520 549 1.512735 GCCCCTTTAGGAGTGGAGAT 58.487 55.000 0.00 0.00 38.24 2.75
521 550 1.141858 GCCCCTTTAGGAGTGGAGATG 59.858 57.143 0.00 0.00 38.24 2.90
523 552 3.321950 CCCCTTTAGGAGTGGAGATGAT 58.678 50.000 0.00 0.00 38.24 2.45
526 555 5.151454 CCCTTTAGGAGTGGAGATGATAGT 58.849 45.833 0.00 0.00 38.24 2.12
527 556 5.011533 CCCTTTAGGAGTGGAGATGATAGTG 59.988 48.000 0.00 0.00 38.24 2.74
529 558 6.015519 CCTTTAGGAGTGGAGATGATAGTGAG 60.016 46.154 0.00 0.00 37.39 3.51
530 559 3.843422 AGGAGTGGAGATGATAGTGAGG 58.157 50.000 0.00 0.00 0.00 3.86
639 669 7.003939 TCTCTTATTAACAATCACACGCATG 57.996 36.000 0.00 0.00 0.00 4.06
641 671 7.495606 TCTCTTATTAACAATCACACGCATGAT 59.504 33.333 0.00 0.00 41.20 2.45
649 679 7.961325 ACAATCACACGCATGATACATAATA 57.039 32.000 0.00 0.00 38.40 0.98
650 680 8.021955 ACAATCACACGCATGATACATAATAG 57.978 34.615 0.00 0.00 38.40 1.73
651 681 7.118245 ACAATCACACGCATGATACATAATAGG 59.882 37.037 0.00 0.00 38.40 2.57
765 979 9.206870 TCTGAATTTCCTGAAAATTGTTTATGC 57.793 29.630 0.78 0.00 45.47 3.14
804 1018 6.039270 TGGTCTTACCTTTTGACAATTCTGTG 59.961 38.462 0.00 0.00 39.58 3.66
925 1191 4.466828 CTCGTAGACATGCTTGTTTTTGG 58.533 43.478 6.70 0.00 35.79 3.28
994 1260 3.054065 CCTCTTGCTCTAGGGTTTTCCAT 60.054 47.826 0.00 0.00 42.91 3.41
1239 1511 2.697654 CTTCTCAACAAGCTCCTCCTG 58.302 52.381 0.00 0.00 0.00 3.86
1260 1532 1.443828 GGCGAATGACTCCTCCTCC 59.556 63.158 0.00 0.00 0.00 4.30
1263 1535 1.066587 GAATGACTCCTCCTCCGCG 59.933 63.158 0.00 0.00 0.00 6.46
1557 1829 1.731160 GGCGCTGATATCAAGATGCTC 59.269 52.381 7.64 1.72 0.00 4.26
1592 1864 1.534476 TAGTGGGCAACGGTGGAGA 60.534 57.895 0.90 0.00 37.60 3.71
1650 1922 2.826738 GGAGCTCTCCGCGAGTCT 60.827 66.667 14.64 5.37 45.59 3.24
1680 1952 0.550914 TGCACAAGAAGGTGAGGGTT 59.449 50.000 0.00 0.00 41.32 4.11
1686 1958 1.439543 AGAAGGTGAGGGTTGAGCTT 58.560 50.000 0.00 0.00 32.68 3.74
1749 2021 3.157949 GAGGGGAAGGAGGAGGCG 61.158 72.222 0.00 0.00 0.00 5.52
1776 2048 2.376228 TACTGGCGACACAGCTTGCA 62.376 55.000 0.00 0.00 42.21 4.08
1949 2221 2.580276 GGTGTCGGTATTGCGGGA 59.420 61.111 0.00 0.00 0.00 5.14
2004 2276 2.827642 GCATGGGAGGCAGCTGTC 60.828 66.667 11.28 11.28 0.00 3.51
2209 2481 2.159517 GCTACAGATGGAAAAGCCGTTG 60.160 50.000 0.00 0.00 40.66 4.10
2223 2495 1.001378 GCCGTTGCTTGTGTGAATTCT 60.001 47.619 7.05 0.00 33.53 2.40
2289 2561 1.824852 CCTAAGTGCCCCAAATTGGAC 59.175 52.381 14.62 3.79 40.96 4.02
2334 2606 5.423015 GAGATTGTGGAGAGCAATGAAGTA 58.577 41.667 0.00 0.00 36.77 2.24
2383 2655 9.723601 AGGTAATTATCATTTTGTTTGCACATT 57.276 25.926 0.00 0.00 31.06 2.71
2564 2838 1.109323 AAATGGCCATAAGGGAGCGC 61.109 55.000 21.15 0.00 40.01 5.92
2672 2953 2.952310 GGGCAAATATGGTGAAGACTCC 59.048 50.000 0.00 0.00 0.00 3.85
2775 3062 5.613358 GGATACCAGAACTTGTTCAGTTG 57.387 43.478 14.80 5.52 46.53 3.16
3050 3354 6.555360 CCAAAGTATACAGGAGAGATAACCCT 59.445 42.308 5.50 0.00 0.00 4.34
3236 3540 2.644299 TGGAATGTTGGAGATCTGTGGT 59.356 45.455 0.00 0.00 0.00 4.16
3336 3640 2.191128 ACTGGTGAGCATCCAAACTC 57.809 50.000 0.00 0.00 34.35 3.01
3338 3642 0.038166 TGGTGAGCATCCAAACTCCC 59.962 55.000 0.00 0.00 31.65 4.30
3780 4091 9.752961 TCATTTGTTTGCAATCATATTCCTATG 57.247 29.630 10.87 6.93 36.79 2.23
3872 4183 3.595173 TGGTTTCTGACATGTACCATCG 58.405 45.455 12.46 0.00 34.13 3.84
3873 4184 2.351726 GGTTTCTGACATGTACCATCGC 59.648 50.000 9.44 0.00 0.00 4.58
4123 4437 5.221441 GCCCCAAAATAAGTGTCTCAACTTT 60.221 40.000 0.00 0.00 40.77 2.66
4124 4438 6.215845 CCCCAAAATAAGTGTCTCAACTTTG 58.784 40.000 0.00 0.00 40.77 2.77
4125 4439 6.183360 CCCCAAAATAAGTGTCTCAACTTTGT 60.183 38.462 0.00 0.00 40.77 2.83
4126 4440 7.013846 CCCCAAAATAAGTGTCTCAACTTTGTA 59.986 37.037 0.00 0.00 40.77 2.41
4127 4441 7.860872 CCCAAAATAAGTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
4128 4442 8.402472 CCAAAATAAGTGTCTCAACTTTGTACA 58.598 33.333 0.00 0.00 40.77 2.90
4129 4443 9.221775 CAAAATAAGTGTCTCAACTTTGTACAC 57.778 33.333 16.12 16.12 40.77 2.90
4131 4445 9.826574 AAATAAGTGTCTCAACTTTGTACACTA 57.173 29.630 21.97 15.09 45.93 2.74
4132 4446 9.826574 AATAAGTGTCTCAACTTTGTACACTAA 57.173 29.630 21.97 0.00 45.93 2.24
4133 4447 9.826574 ATAAGTGTCTCAACTTTGTACACTAAA 57.173 29.630 21.97 16.86 45.93 1.85
4134 4448 7.772332 AGTGTCTCAACTTTGTACACTAAAG 57.228 36.000 21.08 0.00 45.41 1.85
4135 4449 7.822822 AAGTGTCTCAACTTTGTACACTAAAGT 59.177 33.333 21.97 5.74 45.93 2.66
4170 4484 1.288633 TGGGACGGAGGGAGTACATTA 59.711 52.381 0.00 0.00 0.00 1.90
4404 4720 6.517362 GCCTTGGAATAGAAAGAGTTTTTGCT 60.517 38.462 0.00 0.00 0.00 3.91
4467 4783 5.542635 TCTTAATGCCCCTATCATTACGTCT 59.457 40.000 0.00 0.00 36.47 4.18
4879 5196 5.277601 CGATACATCGTTGTTGGTTTTCT 57.722 39.130 4.14 0.00 44.74 2.52
4976 5293 5.122082 ACAAATTGTTTGAACTGTTGCCTTG 59.878 36.000 9.21 0.00 43.26 3.61
5143 5717 5.811796 TTTTGGTACAGAGGCAGTAGTAA 57.188 39.130 0.00 0.00 42.39 2.24
5152 5726 4.003648 AGAGGCAGTAGTAATGTTTGCAC 58.996 43.478 0.00 0.00 36.53 4.57
5196 5770 5.583457 GCGTCTTATATTTTGGTACAGTGGT 59.417 40.000 0.00 0.00 42.39 4.16
5265 5839 4.771114 TTCATTTGGGACATCGGATACT 57.229 40.909 0.00 0.00 39.30 2.12
5299 5873 0.895559 CAGCCCTTCTTCAACCCCAC 60.896 60.000 0.00 0.00 0.00 4.61
5329 5906 3.697747 CCCCAGCCGAACGTACCA 61.698 66.667 0.00 0.00 0.00 3.25
5428 6005 0.512952 CGTGGTTTCTTCAGGCTTCG 59.487 55.000 0.00 0.00 0.00 3.79
5468 6045 2.359230 GGTGCTCAGAGGCCACAC 60.359 66.667 5.01 2.91 0.00 3.82
5514 6091 3.760035 GCTTCGTCCCTGCCTCGA 61.760 66.667 0.00 0.00 0.00 4.04
5538 6115 1.731433 GGCGACTGCGTATGTAGGGA 61.731 60.000 4.98 0.00 44.10 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.752359 AGCCCAGTGGTCTACTTACTA 57.248 47.619 8.74 0.00 37.60 1.82
1 2 2.625282 AGCCCAGTGGTCTACTTACT 57.375 50.000 8.74 0.00 37.60 2.24
2 3 4.813750 TTTAGCCCAGTGGTCTACTTAC 57.186 45.455 8.74 0.00 37.60 2.34
4 5 4.395625 GTTTTTAGCCCAGTGGTCTACTT 58.604 43.478 8.74 0.00 37.60 2.24
11 12 4.350368 AATTTGGTTTTTAGCCCAGTGG 57.650 40.909 0.63 0.63 31.04 4.00
14 15 9.719355 ATTTACTAAATTTGGTTTTTAGCCCAG 57.281 29.630 12.75 0.00 39.29 4.45
30 31 8.566109 ACCCTCTATCCCAACAATTTACTAAAT 58.434 33.333 0.00 0.00 0.00 1.40
33 34 6.674861 TCACCCTCTATCCCAACAATTTACTA 59.325 38.462 0.00 0.00 0.00 1.82
35 36 5.751586 TCACCCTCTATCCCAACAATTTAC 58.248 41.667 0.00 0.00 0.00 2.01
65 66 4.974645 TGGTAGTGTCACTTTCATTCCT 57.025 40.909 11.54 0.00 0.00 3.36
66 67 5.063880 AGTTGGTAGTGTCACTTTCATTCC 58.936 41.667 11.54 5.63 0.00 3.01
72 73 5.362105 TGGTAAGTTGGTAGTGTCACTTT 57.638 39.130 11.54 0.59 0.00 2.66
81 82 6.099269 ACCTATACACCATGGTAAGTTGGTAG 59.901 42.308 19.28 13.82 44.38 3.18
109 110 9.709600 CTCGACATACTATAGCAATATACACAG 57.290 37.037 0.00 0.00 0.00 3.66
116 117 6.569179 TGTGCTCGACATACTATAGCAATA 57.431 37.500 0.00 0.00 44.16 1.90
131 132 5.250200 ACCAACCTATTATTTTGTGCTCGA 58.750 37.500 0.00 0.00 0.00 4.04
133 134 6.509418 TGACCAACCTATTATTTTGTGCTC 57.491 37.500 0.00 0.00 0.00 4.26
204 207 8.682895 GTGTGCGTGTTTTTGTTTTTAATTTTT 58.317 25.926 0.00 0.00 0.00 1.94
205 208 7.058467 CGTGTGCGTGTTTTTGTTTTTAATTTT 59.942 29.630 0.00 0.00 0.00 1.82
206 209 6.516695 CGTGTGCGTGTTTTTGTTTTTAATTT 59.483 30.769 0.00 0.00 0.00 1.82
207 210 6.010074 CGTGTGCGTGTTTTTGTTTTTAATT 58.990 32.000 0.00 0.00 0.00 1.40
208 211 5.542813 CGTGTGCGTGTTTTTGTTTTTAAT 58.457 33.333 0.00 0.00 0.00 1.40
209 212 4.663389 GCGTGTGCGTGTTTTTGTTTTTAA 60.663 37.500 0.00 0.00 40.81 1.52
233 236 4.280677 TCAAAGTTGGTCATCCCATTTGAC 59.719 41.667 6.19 0.00 42.90 3.18
238 241 7.586349 ACTATAATCAAAGTTGGTCATCCCAT 58.414 34.615 0.00 0.00 44.74 4.00
300 304 8.850007 ATCTAAACTTTCTTCCCTTTCACTAC 57.150 34.615 0.00 0.00 0.00 2.73
323 328 9.525409 CCCATTCAAATCAATCTCAACTAAATC 57.475 33.333 0.00 0.00 0.00 2.17
348 365 5.123661 CCCAAAACAATGCCATGAATTAACC 59.876 40.000 0.00 0.00 0.00 2.85
355 372 2.562298 GTCTCCCAAAACAATGCCATGA 59.438 45.455 0.00 0.00 0.00 3.07
360 377 1.615392 AGCAGTCTCCCAAAACAATGC 59.385 47.619 0.00 0.00 0.00 3.56
376 393 5.106436 TGCATTAACTCAGTCAAATCAGCAG 60.106 40.000 0.00 0.00 0.00 4.24
388 405 4.466567 TTTGACACGTGCATTAACTCAG 57.533 40.909 17.22 0.00 0.00 3.35
411 428 2.171003 GCAACCAATTTAGGCAGGTCT 58.829 47.619 0.00 0.00 32.05 3.85
413 430 0.887933 CGCAACCAATTTAGGCAGGT 59.112 50.000 0.00 0.00 35.47 4.00
416 433 0.965439 AAGCGCAACCAATTTAGGCA 59.035 45.000 11.47 0.00 0.00 4.75
418 435 2.867429 CTCAAGCGCAACCAATTTAGG 58.133 47.619 11.47 0.00 0.00 2.69
458 475 3.199071 ACCCAACACCTTTATATCGAGCA 59.801 43.478 0.00 0.00 0.00 4.26
462 479 6.037830 CCTTACAACCCAACACCTTTATATCG 59.962 42.308 0.00 0.00 0.00 2.92
464 481 5.655090 GCCTTACAACCCAACACCTTTATAT 59.345 40.000 0.00 0.00 0.00 0.86
465 482 5.011586 GCCTTACAACCCAACACCTTTATA 58.988 41.667 0.00 0.00 0.00 0.98
471 499 0.535553 TCGCCTTACAACCCAACACC 60.536 55.000 0.00 0.00 0.00 4.16
480 508 2.232941 CCTTGGTAGTCTCGCCTTACAA 59.767 50.000 0.00 0.00 0.00 2.41
484 512 1.597461 GCCTTGGTAGTCTCGCCTT 59.403 57.895 0.00 0.00 0.00 4.35
515 544 5.133941 TGTCACTACCTCACTATCATCTCC 58.866 45.833 0.00 0.00 0.00 3.71
520 549 7.898014 ATACAATGTCACTACCTCACTATCA 57.102 36.000 0.00 0.00 0.00 2.15
527 556 9.836076 GGTTTTTAAATACAATGTCACTACCTC 57.164 33.333 10.38 0.00 0.00 3.85
529 558 7.751793 CCGGTTTTTAAATACAATGTCACTACC 59.248 37.037 10.38 0.00 0.00 3.18
530 559 8.505625 TCCGGTTTTTAAATACAATGTCACTAC 58.494 33.333 0.00 0.00 0.00 2.73
586 615 8.977505 ACAAAGGTAAATGATGTTGAAAAATCG 58.022 29.630 0.00 0.00 0.00 3.34
620 649 7.778470 TGTATCATGCGTGTGATTGTTAATA 57.222 32.000 5.68 0.00 39.45 0.98
634 663 5.007039 GGCACATCCTATTATGTATCATGCG 59.993 44.000 0.00 0.00 38.01 4.73
639 669 4.568359 CGCTGGCACATCCTATTATGTATC 59.432 45.833 0.00 0.00 38.01 2.24
641 671 3.576550 TCGCTGGCACATCCTATTATGTA 59.423 43.478 0.00 0.00 38.01 2.29
649 679 0.035152 TGAAATCGCTGGCACATCCT 60.035 50.000 0.00 0.00 38.20 3.24
650 680 1.027357 ATGAAATCGCTGGCACATCC 58.973 50.000 0.00 0.00 38.20 3.51
651 681 1.672363 TCATGAAATCGCTGGCACATC 59.328 47.619 0.00 0.00 38.20 3.06
788 1002 4.827284 AGGGGTACACAGAATTGTCAAAAG 59.173 41.667 0.00 0.00 34.62 2.27
804 1018 1.375523 CCAAGACACGCAGGGGTAC 60.376 63.158 0.00 0.00 0.00 3.34
892 1121 4.571919 CATGTCTACGAGGGGTACAAAAA 58.428 43.478 0.00 0.00 0.00 1.94
895 1124 1.479323 GCATGTCTACGAGGGGTACAA 59.521 52.381 0.00 0.00 0.00 2.41
896 1125 1.108776 GCATGTCTACGAGGGGTACA 58.891 55.000 0.00 0.00 0.00 2.90
898 1127 1.754803 CAAGCATGTCTACGAGGGGTA 59.245 52.381 0.00 0.00 0.00 3.69
899 1128 0.537188 CAAGCATGTCTACGAGGGGT 59.463 55.000 0.00 0.00 0.00 4.95
900 1129 0.537188 ACAAGCATGTCTACGAGGGG 59.463 55.000 0.00 0.00 33.41 4.79
902 1131 4.466828 CAAAAACAAGCATGTCTACGAGG 58.533 43.478 0.00 0.00 39.40 4.63
903 1132 4.466828 CCAAAAACAAGCATGTCTACGAG 58.533 43.478 0.00 0.00 39.40 4.18
904 1133 3.252215 CCCAAAAACAAGCATGTCTACGA 59.748 43.478 0.00 0.00 39.40 3.43
905 1134 3.004315 ACCCAAAAACAAGCATGTCTACG 59.996 43.478 0.00 0.00 39.40 3.51
906 1135 4.584327 ACCCAAAAACAAGCATGTCTAC 57.416 40.909 0.00 0.00 39.40 2.59
908 1137 4.486125 AAACCCAAAAACAAGCATGTCT 57.514 36.364 0.00 0.00 39.40 3.41
909 1138 4.633565 TCAAAACCCAAAAACAAGCATGTC 59.366 37.500 0.00 0.00 39.40 3.06
910 1139 4.583871 TCAAAACCCAAAAACAAGCATGT 58.416 34.783 0.00 0.00 43.14 3.21
925 1191 3.730715 CGTGCTTGAGTCAAATCAAAACC 59.269 43.478 7.06 0.00 38.66 3.27
994 1260 2.434843 CGGGAGTAGCCATGGCAGA 61.435 63.158 37.18 22.58 44.88 4.26
1164 1436 3.758133 ATCCAGGTCCCGGAGCGAT 62.758 63.158 0.73 6.14 35.56 4.58
1239 1511 1.227002 GGAGGAGTCATTCGCCGTC 60.227 63.158 0.00 0.00 40.97 4.79
1557 1829 3.545703 CACTAGCTTGGACCCCAATAAG 58.454 50.000 0.00 0.87 43.07 1.73
1749 2021 1.070105 TGTCGCCAGTACCACCAAC 59.930 57.895 0.00 0.00 0.00 3.77
1776 2048 2.607771 GCACATTGCATTCAACGACCTT 60.608 45.455 0.00 0.00 44.26 3.50
1949 2221 4.632153 CTTGAGCAAGTAGTTGTACACCT 58.368 43.478 11.85 0.00 35.92 4.00
2004 2276 0.447406 TTTCAATCACAGCCATCGCG 59.553 50.000 0.00 0.00 41.18 5.87
2209 2481 2.046313 CAACGCAGAATTCACACAAGC 58.954 47.619 8.44 1.13 0.00 4.01
2223 2495 0.527113 CCCAATCTGCAATCAACGCA 59.473 50.000 0.00 0.00 37.88 5.24
2305 2577 2.027745 TGCTCTCCACAATCTCCTTGAC 60.028 50.000 0.00 0.00 38.29 3.18
2334 2606 4.946646 TGGGAATTTTAGGCAATCTTCCT 58.053 39.130 0.00 0.00 37.72 3.36
2383 2655 7.176515 ACAAGACAACATAAATGTAGCATCCAA 59.823 33.333 0.00 0.00 40.80 3.53
2564 2838 6.904954 ACACTTGTAATTATTGAAAACGCG 57.095 33.333 3.53 3.53 0.00 6.01
2770 3057 2.099592 ACAAACCAGCACATGACAACTG 59.900 45.455 0.00 0.85 0.00 3.16
2775 3062 9.801873 AATTTATATAACAAACCAGCACATGAC 57.198 29.630 0.00 0.00 0.00 3.06
2847 3147 4.439057 GAATATACTGCGACAAAGGACCA 58.561 43.478 0.00 0.00 0.00 4.02
2898 3198 8.141909 CAGGTTATTCGATGGTAAGACTTCATA 58.858 37.037 0.00 0.00 0.00 2.15
3050 3354 7.796054 AGAATTCTCGATATCTTCCCTTTGAA 58.204 34.615 0.88 0.00 0.00 2.69
3236 3540 2.156917 CTGAATTTCTCAGCAGGCACA 58.843 47.619 0.00 0.00 45.11 4.57
3780 4091 5.499047 GCAATACAAAACGATGCCTAGTAC 58.501 41.667 0.00 0.00 0.00 2.73
3900 4211 5.296035 AGTGTTACAGCAGACAAAAGGTAAC 59.704 40.000 0.00 0.00 40.37 2.50
3973 4284 7.117667 CACTGGATTATAAAACAAAGCCCAAAC 59.882 37.037 0.00 0.00 29.93 2.93
3992 4304 4.159135 GGTGATTGATTGAAAGCACTGGAT 59.841 41.667 5.44 0.00 44.06 3.41
4082 4396 0.105039 GGCGGAGGAAGTACATGAGG 59.895 60.000 0.00 0.00 0.00 3.86
4123 4437 9.826574 AAATAAGTGTCTCAACTTTAGTGTACA 57.173 29.630 0.00 0.00 40.77 2.90
4126 4440 8.621286 CCAAAATAAGTGTCTCAACTTTAGTGT 58.379 33.333 0.00 0.00 40.77 3.55
4127 4441 8.076178 CCCAAAATAAGTGTCTCAACTTTAGTG 58.924 37.037 0.00 0.00 40.77 2.74
4128 4442 7.996644 TCCCAAAATAAGTGTCTCAACTTTAGT 59.003 33.333 0.00 0.00 40.77 2.24
4129 4443 8.290325 GTCCCAAAATAAGTGTCTCAACTTTAG 58.710 37.037 0.00 0.00 40.77 1.85
4130 4444 7.041644 CGTCCCAAAATAAGTGTCTCAACTTTA 60.042 37.037 0.00 0.00 40.77 1.85
4131 4445 6.238648 CGTCCCAAAATAAGTGTCTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
4132 4446 5.238650 CGTCCCAAAATAAGTGTCTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
4133 4447 4.755123 CGTCCCAAAATAAGTGTCTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
4134 4448 4.083484 CCGTCCCAAAATAAGTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
4135 4449 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
4404 4720 4.471025 TCTTTCTCCTGTTGCTCCATGATA 59.529 41.667 0.00 0.00 0.00 2.15
4467 4783 3.449528 TTGCTACATTGCTGCAACAAA 57.550 38.095 18.51 4.78 41.06 2.83
4829 5145 5.635280 AGTCACACACATTCTACATCTTTCG 59.365 40.000 0.00 0.00 0.00 3.46
4843 5159 0.037697 GTATCGCCCAGTCACACACA 60.038 55.000 0.00 0.00 0.00 3.72
4879 5196 3.591023 CATCAGCAAAATGGATGCACAA 58.409 40.909 0.00 0.00 46.22 3.33
4976 5293 2.778299 TCCACCAAGCACTCAACATAC 58.222 47.619 0.00 0.00 0.00 2.39
5112 5429 6.953101 TGCCTCTGTACCAAAATATAAGACA 58.047 36.000 0.00 0.00 0.00 3.41
5143 5717 8.715191 TTCAGTTCAATTTAAAGTGCAAACAT 57.285 26.923 17.24 5.36 0.00 2.71
5152 5726 8.340230 AGACGCTTTTTCAGTTCAATTTAAAG 57.660 30.769 0.00 0.00 0.00 1.85
5196 5770 7.801104 TCAATCAATTTACCTGTAGCCTATCA 58.199 34.615 0.00 0.00 0.00 2.15
5265 5839 1.375908 GCTGCTGACCGTTGGATCA 60.376 57.895 0.00 0.00 0.00 2.92
5299 5873 1.895798 GGCTGGGGAAAAAGAAGAAGG 59.104 52.381 0.00 0.00 0.00 3.46
5428 6005 1.789078 CTGCTCAGCAACCACACACC 61.789 60.000 0.00 0.00 38.41 4.16
5468 6045 3.376859 AGATGCGCTCGAGATAGAATAGG 59.623 47.826 18.75 0.00 0.00 2.57
5472 6049 1.268079 CCAGATGCGCTCGAGATAGAA 59.732 52.381 18.75 0.79 0.00 2.10
5514 6091 4.129737 ATACGCAGTCGCCGCTGT 62.130 61.111 9.59 0.00 43.93 4.40
5538 6115 3.368571 GCTTTGGCTGGCGCTCTT 61.369 61.111 7.64 0.00 36.09 2.85


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

AutoCloner maintained by Alex Coulton.