Multiple sequence alignment - TraesCS1D01G218700

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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 TraesCS1D01G218700 chr1D 100.000 5997 0 0 1 5997 305591786 305585790 0.000000e+00 11075.0
1 TraesCS1D01G218700 chr1A 97.803 2822 40 6 2780 5582 384334450 384331632 0.000000e+00 4848.0
2 TraesCS1D01G218700 chr1A 96.338 2130 49 14 669 2782 384336670 384334554 0.000000e+00 3474.0
3 TraesCS1D01G218700 chr1A 89.050 484 46 7 1763 2241 534273027 534272546 1.440000e-165 593.0
4 TraesCS1D01G218700 chr1A 94.839 155 0 1 5851 5997 384329657 384329503 1.000000e-57 235.0
5 TraesCS1D01G218700 chr1A 98.230 113 2 0 5747 5859 384329874 384329762 1.320000e-46 198.0
6 TraesCS1D01G218700 chr1A 97.561 82 2 0 1 82 384336817 384336736 2.250000e-29 141.0
7 TraesCS1D01G218700 chr1A 95.062 81 1 1 550 630 384336739 384336662 2.270000e-24 124.0
8 TraesCS1D01G218700 chr1A 98.000 50 1 0 2697 2746 104946104 104946055 2.980000e-13 87.9
9 TraesCS1D01G218700 chr1A 96.154 52 1 1 3472 3523 343398366 343398416 3.850000e-12 84.2
10 TraesCS1D01G218700 chr1B 94.181 1306 34 14 2262 3541 412898866 412897577 0.000000e+00 1953.0
11 TraesCS1D01G218700 chr1B 90.867 1281 62 26 4324 5583 412896433 412895187 0.000000e+00 1666.0
12 TraesCS1D01G218700 chr1B 94.719 871 18 14 752 1618 412900034 412899188 0.000000e+00 1328.0
13 TraesCS1D01G218700 chr1B 97.017 771 17 4 3540 4304 412897414 412896644 0.000000e+00 1291.0
14 TraesCS1D01G218700 chr1B 87.723 505 50 11 1763 2262 637548636 637549133 4.030000e-161 579.0
15 TraesCS1D01G218700 chr1B 86.341 205 17 7 550 748 412900290 412900091 4.710000e-51 213.0
16 TraesCS1D01G218700 chr1B 94.697 132 7 0 1633 1764 412898997 412898866 7.880000e-49 206.0
17 TraesCS1D01G218700 chrUn 100.000 389 0 0 4007 4395 480223431 480223819 0.000000e+00 719.0
18 TraesCS1D01G218700 chr3A 94.080 473 25 1 79 551 575543307 575543776 0.000000e+00 715.0
19 TraesCS1D01G218700 chr3A 95.349 43 2 0 3352 3394 509993906 509993948 1.080000e-07 69.4
20 TraesCS1D01G218700 chr7B 88.235 510 52 7 1763 2269 393179000 393178496 2.390000e-168 603.0
21 TraesCS1D01G218700 chr7B 86.200 471 38 7 79 549 52690578 52691021 9.040000e-133 484.0
22 TraesCS1D01G218700 chr7B 93.407 91 6 0 5579 5669 661996480 661996390 1.050000e-27 135.0
23 TraesCS1D01G218700 chr7B 100.000 45 0 0 3472 3516 255075444 255075400 3.850000e-12 84.2
24 TraesCS1D01G218700 chr5B 88.095 504 51 6 1763 2263 495125314 495125811 1.860000e-164 590.0
25 TraesCS1D01G218700 chr5B 87.640 89 7 3 2658 2746 525815051 525814967 3.820000e-17 100.0
26 TraesCS1D01G218700 chr3B 87.945 506 49 11 1763 2263 671671787 671671289 2.410000e-163 586.0
27 TraesCS1D01G218700 chr3B 87.897 504 53 7 1763 2263 764104113 764103615 2.410000e-163 586.0
28 TraesCS1D01G218700 chr3B 93.103 87 6 0 5581 5667 109876046 109875960 1.750000e-25 128.0
29 TraesCS1D01G218700 chr3B 92.135 89 7 0 5578 5666 802705063 802705151 6.310000e-25 126.0
30 TraesCS1D01G218700 chr3B 92.045 88 7 0 5581 5668 642815847 642815934 2.270000e-24 124.0
31 TraesCS1D01G218700 chr3B 88.776 98 8 3 5570 5667 551052602 551052696 3.800000e-22 117.0
32 TraesCS1D01G218700 chr3B 90.141 71 5 1 2539 2609 19389891 19389959 2.300000e-14 91.6
33 TraesCS1D01G218700 chr2B 87.184 515 56 9 1763 2273 631335976 631336484 1.450000e-160 577.0
34 TraesCS1D01G218700 chr2B 87.255 510 57 7 1763 2269 721244860 721245364 5.210000e-160 575.0
35 TraesCS1D01G218700 chr2B 96.078 51 0 2 3474 3523 651362573 651362524 1.390000e-11 82.4
36 TraesCS1D01G218700 chr2B 97.826 46 1 0 3472 3517 134045500 134045455 4.980000e-11 80.5
37 TraesCS1D01G218700 chr2B 97.222 36 1 0 2658 2693 139801474 139801509 1.800000e-05 62.1
38 TraesCS1D01G218700 chr2D 87.525 505 52 10 1763 2263 90901665 90902162 1.870000e-159 573.0
39 TraesCS1D01G218700 chr2D 83.607 122 15 5 5573 5692 649068709 649068591 6.350000e-20 110.0
40 TraesCS1D01G218700 chr2D 88.462 78 3 2 2656 2732 619562573 619562501 8.280000e-14 89.8
41 TraesCS1D01G218700 chr2D 97.826 46 1 0 3471 3516 83967087 83967042 4.980000e-11 80.5
42 TraesCS1D01G218700 chr2D 92.593 54 3 1 3469 3522 489410906 489410854 6.450000e-10 76.8
43 TraesCS1D01G218700 chr4B 92.963 270 16 2 287 553 641261889 641262158 2.030000e-104 390.0
44 TraesCS1D01G218700 chr4B 85.135 222 17 4 79 300 641261659 641261864 4.710000e-51 213.0
45 TraesCS1D01G218700 chr4B 91.398 93 8 0 5581 5673 180553956 180553864 1.750000e-25 128.0
46 TraesCS1D01G218700 chr4D 92.937 269 16 2 287 553 498890959 498891226 7.290000e-104 388.0
47 TraesCS1D01G218700 chr4D 89.640 222 19 4 79 300 498890716 498890933 4.580000e-71 279.0
48 TraesCS1D01G218700 chr4D 87.912 91 5 2 2660 2744 119751837 119751927 1.060000e-17 102.0
49 TraesCS1D01G218700 chr6A 90.526 95 9 0 5581 5675 15768149 15768243 6.310000e-25 126.0
50 TraesCS1D01G218700 chr6A 97.872 47 1 0 3471 3517 427446051 427446097 1.390000e-11 82.4
51 TraesCS1D01G218700 chr6A 95.918 49 2 0 80 128 609088770 609088722 4.980000e-11 80.5
52 TraesCS1D01G218700 chr5D 88.000 100 12 0 5582 5681 538166857 538166758 1.060000e-22 119.0
53 TraesCS1D01G218700 chr5D 86.517 89 8 1 2658 2746 432876206 432876122 1.780000e-15 95.3
54 TraesCS1D01G218700 chr5D 86.207 87 8 2 2657 2743 432876122 432876204 2.300000e-14 91.6
55 TraesCS1D01G218700 chr4A 89.773 88 5 1 2660 2743 389242323 389242236 6.350000e-20 110.0
56 TraesCS1D01G218700 chr4A 97.143 35 1 0 3380 3414 704166602 704166636 6.490000e-05 60.2
57 TraesCS1D01G218700 chr4A 100.000 30 0 0 2492 2521 159483072 159483043 8.400000e-04 56.5
58 TraesCS1D01G218700 chr3D 92.958 71 5 0 2539 2609 13419448 13419518 2.960000e-18 104.0


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 TraesCS1D01G218700 chr1D 305585790 305591786 5996 True 11075.000000 11075 100.000000 1 5997 1 chr1D.!!$R1 5996
1 TraesCS1D01G218700 chr1A 384329503 384336817 7314 True 1503.333333 4848 96.638833 1 5997 6 chr1A.!!$R3 5996
2 TraesCS1D01G218700 chr1B 412895187 412900290 5103 True 1109.500000 1953 92.970333 550 5583 6 chr1B.!!$R1 5033
3 TraesCS1D01G218700 chr7B 393178496 393179000 504 True 603.000000 603 88.235000 1763 2269 1 chr7B.!!$R2 506
4 TraesCS1D01G218700 chr2B 631335976 631336484 508 False 577.000000 577 87.184000 1763 2273 1 chr2B.!!$F2 510
5 TraesCS1D01G218700 chr2B 721244860 721245364 504 False 575.000000 575 87.255000 1763 2269 1 chr2B.!!$F3 506
6 TraesCS1D01G218700 chr4D 498890716 498891226 510 False 333.500000 388 91.288500 79 553 2 chr4D.!!$F2 474

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
325 367 0.167470 CGTCTCACAGCATGCTTTGG 59.833 55.000 28.64 20.35 42.53 3.28 F
363 405 0.533755 CCTTTCCTATGGCTGCCTCG 60.534 60.000 21.03 7.78 0.00 4.63 F
1585 1690 0.694444 TAAGGGGATGTGGGAGGCTC 60.694 60.000 5.78 5.78 0.00 4.70 F
2250 2535 1.072391 AAATGTGCATTGCATGTGCG 58.928 45.000 15.49 0.00 45.37 5.34 F
2698 2989 8.892723 CCATATTAATTGTCACTCAAACTGCTA 58.107 33.333 0.00 0.00 39.62 3.49 F
3262 3660 0.038744 ATGTCCCTCCCAGCACAAAG 59.961 55.000 0.00 0.00 0.00 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1315 1419 0.106918 TGACAGGAAAGGGCAAACGT 60.107 50.000 0.00 0.00 0.00 3.99 R
1592 1697 1.737236 TCAATTTGGTTCGATGCCTCG 59.263 47.619 4.89 4.89 46.41 4.63 R
3230 3628 1.134098 AGGGACATGGAACGCCTAATG 60.134 52.381 0.00 0.00 34.31 1.90 R
3237 3635 1.221840 CTGGGAGGGACATGGAACG 59.778 63.158 0.00 0.00 0.00 3.95 R
4395 5186 4.075763 GTGATGCACACTGAAGATGAAC 57.924 45.455 10.87 0.00 45.13 3.18 R
5229 6022 1.909700 ACACATTCCTTTCGGCACAT 58.090 45.000 0.00 0.00 0.00 3.21 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
27 28 9.031360 TGAATACTTTTATATGAGTTGAGACGC 57.969 33.333 0.00 0.00 0.00 5.19
97 98 2.823959 TCTTAGGCCCCGTTCTCTTTA 58.176 47.619 0.00 0.00 0.00 1.85
102 103 1.460504 GCCCCGTTCTCTTTAAAGGG 58.539 55.000 15.13 12.21 44.95 3.95
128 129 9.573133 GTTCTGAACCATAGGAATGTAAAAATG 57.427 33.333 9.38 0.00 0.00 2.32
133 134 6.866480 ACCATAGGAATGTAAAAATGTGCAG 58.134 36.000 0.00 0.00 0.00 4.41
137 138 6.610075 AGGAATGTAAAAATGTGCAGGAAT 57.390 33.333 0.00 0.00 0.00 3.01
149 150 3.266772 TGTGCAGGAATAGGGAATGAGTT 59.733 43.478 0.00 0.00 0.00 3.01
152 153 4.133078 GCAGGAATAGGGAATGAGTTCAG 58.867 47.826 0.00 0.00 36.01 3.02
176 177 6.822073 GTACAACACCAAGGAATTGAAAAC 57.178 37.500 12.00 5.70 0.00 2.43
177 178 5.413309 ACAACACCAAGGAATTGAAAACA 57.587 34.783 12.00 0.00 0.00 2.83
179 180 6.234177 ACAACACCAAGGAATTGAAAACAAA 58.766 32.000 12.00 0.00 0.00 2.83
181 182 6.293004 ACACCAAGGAATTGAAAACAAAGA 57.707 33.333 0.00 0.00 0.00 2.52
182 183 6.706295 ACACCAAGGAATTGAAAACAAAGAA 58.294 32.000 0.00 0.00 0.00 2.52
190 191 9.447157 AGGAATTGAAAACAAAGAAAATGAACA 57.553 25.926 0.00 0.00 0.00 3.18
197 198 9.745323 GAAAACAAAGAAAATGAACAAAGACTG 57.255 29.630 0.00 0.00 0.00 3.51
198 199 8.831715 AAACAAAGAAAATGAACAAAGACTGT 57.168 26.923 0.00 0.00 41.27 3.55
199 200 7.816945 ACAAAGAAAATGAACAAAGACTGTG 57.183 32.000 0.00 0.00 38.67 3.66
200 201 7.378181 ACAAAGAAAATGAACAAAGACTGTGT 58.622 30.769 0.00 0.00 38.67 3.72
223 224 2.446341 GGTGGACGAAGAAAGAGCG 58.554 57.895 0.00 0.00 0.00 5.03
251 252 1.977854 TCCCACTGCTAATCACACACT 59.022 47.619 0.00 0.00 0.00 3.55
302 303 7.897575 TTCATTTCAGCTAGTTCTTCTTCTC 57.102 36.000 0.00 0.00 0.00 2.87
303 304 7.238486 TCATTTCAGCTAGTTCTTCTTCTCT 57.762 36.000 0.00 0.00 0.00 3.10
305 306 6.656632 TTTCAGCTAGTTCTTCTTCTCTCA 57.343 37.500 0.00 0.00 0.00 3.27
306 307 5.637006 TCAGCTAGTTCTTCTTCTCTCAC 57.363 43.478 0.00 0.00 0.00 3.51
307 308 4.155099 TCAGCTAGTTCTTCTTCTCTCACG 59.845 45.833 0.00 0.00 0.00 4.35
325 367 0.167470 CGTCTCACAGCATGCTTTGG 59.833 55.000 28.64 20.35 42.53 3.28
335 377 6.929049 TCACAGCATGCTTTGGTATAGTATAC 59.071 38.462 28.64 11.29 42.53 1.47
363 405 0.533755 CCTTTCCTATGGCTGCCTCG 60.534 60.000 21.03 7.78 0.00 4.63
399 441 1.426251 AAGTGGTCAGGGTGGATGCA 61.426 55.000 0.00 0.00 0.00 3.96
423 465 5.661056 AGATTCCTGTGAAATCGACACTA 57.339 39.130 6.26 0.00 38.81 2.74
467 509 7.398047 TGGTATACTGTAGCTAGTTCCTTTGAA 59.602 37.037 2.25 0.00 32.19 2.69
475 517 3.246936 GCTAGTTCCTTTGAAACGAACGT 59.753 43.478 12.00 0.00 40.62 3.99
509 551 7.797121 AAAATAACCTGTGGAATTGAGGATT 57.203 32.000 0.00 0.00 0.00 3.01
779 879 1.296715 CGGCAGGAGCTGGTAAAGT 59.703 57.895 0.00 0.00 43.60 2.66
780 880 1.021390 CGGCAGGAGCTGGTAAAGTG 61.021 60.000 0.00 0.00 43.60 3.16
878 982 4.207019 CGTGAGAAATCAAACCAGCAAAAC 59.793 41.667 0.00 0.00 0.00 2.43
907 1011 2.022240 GATCTCGTGCACCTCCTCCC 62.022 65.000 12.15 0.00 0.00 4.30
1049 1153 4.619227 CGCCACGGAGGTTGGTGT 62.619 66.667 0.00 0.00 40.61 4.16
1230 1334 2.283254 GCTCATCAAGCGTCTCGTC 58.717 57.895 0.00 0.00 42.21 4.20
1315 1419 5.993441 GTGAGTACCCACAAACTTTAGCTAA 59.007 40.000 0.86 0.86 37.04 3.09
1355 1459 5.978322 GTCAGGAATCCGTTATTGACTAGTC 59.022 44.000 16.32 16.32 32.37 2.59
1377 1481 2.893489 GGGGATTGAAATACCTGATGGC 59.107 50.000 4.29 0.00 39.51 4.40
1407 1512 6.397272 TGATTGGCACTTTGGAATTACAATC 58.603 36.000 3.35 0.00 41.79 2.67
1585 1690 0.694444 TAAGGGGATGTGGGAGGCTC 60.694 60.000 5.78 5.78 0.00 4.70
1586 1691 3.866582 GGGGATGTGGGAGGCTCG 61.867 72.222 8.69 0.00 0.00 5.03
1587 1692 2.764128 GGGATGTGGGAGGCTCGA 60.764 66.667 8.69 0.00 0.00 4.04
1588 1693 2.801631 GGGATGTGGGAGGCTCGAG 61.802 68.421 8.45 8.45 0.00 4.04
1589 1694 2.801631 GGATGTGGGAGGCTCGAGG 61.802 68.421 15.58 0.00 0.00 4.63
1590 1695 3.453070 GATGTGGGAGGCTCGAGGC 62.453 68.421 30.15 30.15 41.43 4.70
1663 1944 8.147793 CACGTCAATTTCATCTAATATACGACG 58.852 37.037 0.00 0.00 44.88 5.12
1667 1948 8.139350 TCAATTTCATCTAATATACGACGGTGT 58.861 33.333 0.00 0.00 0.00 4.16
1677 1958 4.789095 ATACGACGGTGTCATTTATTGC 57.211 40.909 0.00 0.00 32.09 3.56
1956 2240 1.302907 ACTGATTCCTCTTGGGCCAT 58.697 50.000 7.26 0.00 34.39 4.40
2022 2306 2.324541 TGGTTTTGGGGGAGAAACATG 58.675 47.619 0.00 0.00 37.46 3.21
2117 2401 6.403866 TTGTGGGGATTGCATATGTTAATC 57.596 37.500 18.67 18.67 0.00 1.75
2250 2535 1.072391 AAATGTGCATTGCATGTGCG 58.928 45.000 15.49 0.00 45.37 5.34
2427 2714 9.720769 CTTAGGAAGTTTGACCAAGTTTATAGA 57.279 33.333 0.00 0.00 0.00 1.98
2698 2989 8.892723 CCATATTAATTGTCACTCAAACTGCTA 58.107 33.333 0.00 0.00 39.62 3.49
3262 3660 0.038744 ATGTCCCTCCCAGCACAAAG 59.961 55.000 0.00 0.00 0.00 2.77
3283 3681 9.739276 ACAAAGAGAAATGTTTATCATACTCCA 57.261 29.630 3.33 0.00 39.00 3.86
3430 3849 6.161855 TGTATCTGGGTTCATGATGTAGAC 57.838 41.667 0.00 0.00 0.00 2.59
3987 4576 6.851330 GCTTCGCCATATTGTTTCTAATACAC 59.149 38.462 0.00 0.00 0.00 2.90
4395 5186 1.341531 AGTCAGAGTGTCCAACTTCCG 59.658 52.381 0.00 0.00 40.07 4.30
4401 5192 2.737252 GAGTGTCCAACTTCCGTTCATC 59.263 50.000 0.00 0.00 40.07 2.92
4430 5221 5.297527 GTGTGCATCACATCCATCAATCTAA 59.702 40.000 12.63 0.00 46.32 2.10
4731 5522 6.554982 ACAGCTTATCCAGGTAATAGACATCA 59.445 38.462 0.00 0.00 0.00 3.07
4854 5646 0.900647 AGGAGCAGTTACGCAGGAGT 60.901 55.000 2.64 0.00 0.00 3.85
5201 5994 5.760743 AGGAAGTCTGTTCTAGTCTTTTTGC 59.239 40.000 0.00 0.00 35.38 3.68
5206 5999 2.289547 TGTTCTAGTCTTTTTGCGTGCC 59.710 45.455 0.00 0.00 0.00 5.01
5229 6022 5.467735 CCGACTGATTTGATGATAATCTGCA 59.532 40.000 0.00 0.00 35.55 4.41
5369 6162 8.673711 GTGGCTTGATACAACAATAATCACTTA 58.326 33.333 0.00 0.00 29.64 2.24
5403 6212 3.527533 CCAGGATTGAATTGCACATTGG 58.472 45.455 0.00 0.00 0.00 3.16
5475 6287 9.708222 CTAACTCCATTTCAAGTCATAATTTCG 57.292 33.333 0.00 0.00 0.00 3.46
5587 6401 9.593134 GATTCACATCATATCTTATGTACTCCC 57.407 37.037 0.00 0.00 34.61 4.30
5588 6402 8.727100 TTCACATCATATCTTATGTACTCCCT 57.273 34.615 0.00 0.00 34.61 4.20
5590 6404 8.807118 TCACATCATATCTTATGTACTCCCTTC 58.193 37.037 0.00 0.00 34.61 3.46
5591 6405 8.588472 CACATCATATCTTATGTACTCCCTTCA 58.412 37.037 0.00 0.00 34.61 3.02
5592 6406 9.331466 ACATCATATCTTATGTACTCCCTTCAT 57.669 33.333 0.00 0.00 34.61 2.57
5593 6407 9.814899 CATCATATCTTATGTACTCCCTTCATC 57.185 37.037 0.00 0.00 0.00 2.92
5594 6408 8.367660 TCATATCTTATGTACTCCCTTCATCC 57.632 38.462 0.00 0.00 0.00 3.51
5595 6409 7.400339 TCATATCTTATGTACTCCCTTCATCCC 59.600 40.741 0.00 0.00 0.00 3.85
5596 6410 4.890988 TCTTATGTACTCCCTTCATCCCA 58.109 43.478 0.00 0.00 0.00 4.37
5597 6411 5.476983 TCTTATGTACTCCCTTCATCCCAT 58.523 41.667 0.00 0.00 0.00 4.00
5598 6412 6.630131 TCTTATGTACTCCCTTCATCCCATA 58.370 40.000 0.00 0.00 0.00 2.74
5599 6413 7.079700 TCTTATGTACTCCCTTCATCCCATAA 58.920 38.462 0.00 0.00 0.00 1.90
5600 6414 7.739444 TCTTATGTACTCCCTTCATCCCATAAT 59.261 37.037 0.00 0.00 0.00 1.28
5601 6415 5.567037 TGTACTCCCTTCATCCCATAATG 57.433 43.478 0.00 0.00 0.00 1.90
5602 6416 4.975147 TGTACTCCCTTCATCCCATAATGT 59.025 41.667 0.00 0.00 0.00 2.71
5603 6417 6.147473 TGTACTCCCTTCATCCCATAATGTA 58.853 40.000 0.00 0.00 0.00 2.29
5604 6418 6.617784 TGTACTCCCTTCATCCCATAATGTAA 59.382 38.462 0.00 0.00 0.00 2.41
5605 6419 6.786843 ACTCCCTTCATCCCATAATGTAAT 57.213 37.500 0.00 0.00 0.00 1.89
5606 6420 7.888514 ACTCCCTTCATCCCATAATGTAATA 57.111 36.000 0.00 0.00 0.00 0.98
5607 6421 7.690256 ACTCCCTTCATCCCATAATGTAATAC 58.310 38.462 0.00 0.00 0.00 1.89
5608 6422 6.707290 TCCCTTCATCCCATAATGTAATACG 58.293 40.000 0.00 0.00 0.00 3.06
5609 6423 6.271391 TCCCTTCATCCCATAATGTAATACGT 59.729 38.462 0.00 0.00 0.00 3.57
5610 6424 6.940298 CCCTTCATCCCATAATGTAATACGTT 59.060 38.462 0.00 3.19 0.00 3.99
5611 6425 7.447238 CCCTTCATCCCATAATGTAATACGTTT 59.553 37.037 2.96 0.00 0.00 3.60
5612 6426 8.846211 CCTTCATCCCATAATGTAATACGTTTT 58.154 33.333 2.96 0.00 0.00 2.43
5654 6468 9.967451 TGTCAAAAAGTGTCTTATATTATGGGA 57.033 29.630 0.00 0.00 0.00 4.37
5656 6470 9.104965 TCAAAAAGTGTCTTATATTATGGGACG 57.895 33.333 0.00 0.00 0.00 4.79
5657 6471 8.342634 CAAAAAGTGTCTTATATTATGGGACGG 58.657 37.037 0.00 0.00 0.00 4.79
5658 6472 6.989155 AAGTGTCTTATATTATGGGACGGA 57.011 37.500 0.00 0.00 0.00 4.69
5659 6473 6.591750 AGTGTCTTATATTATGGGACGGAG 57.408 41.667 0.00 0.00 0.00 4.63
5660 6474 5.480772 AGTGTCTTATATTATGGGACGGAGG 59.519 44.000 0.00 0.00 0.00 4.30
5661 6475 4.775780 TGTCTTATATTATGGGACGGAGGG 59.224 45.833 0.00 0.00 0.00 4.30
5662 6476 5.021458 GTCTTATATTATGGGACGGAGGGA 58.979 45.833 0.00 0.00 0.00 4.20
5663 6477 5.127356 GTCTTATATTATGGGACGGAGGGAG 59.873 48.000 0.00 0.00 0.00 4.30
5664 6478 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
5665 6479 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
5666 6480 2.376695 TTATGGGACGGAGGGAGTAG 57.623 55.000 0.00 0.00 0.00 2.57
5667 6481 1.229131 TATGGGACGGAGGGAGTAGT 58.771 55.000 0.00 0.00 0.00 2.73
5668 6482 1.229131 ATGGGACGGAGGGAGTAGTA 58.771 55.000 0.00 0.00 0.00 1.82
5669 6483 1.229131 TGGGACGGAGGGAGTAGTAT 58.771 55.000 0.00 0.00 0.00 2.12
5670 6484 2.421725 TGGGACGGAGGGAGTAGTATA 58.578 52.381 0.00 0.00 0.00 1.47
5671 6485 2.785269 TGGGACGGAGGGAGTAGTATAA 59.215 50.000 0.00 0.00 0.00 0.98
5672 6486 3.400322 TGGGACGGAGGGAGTAGTATAAT 59.600 47.826 0.00 0.00 0.00 1.28
5673 6487 4.603171 TGGGACGGAGGGAGTAGTATAATA 59.397 45.833 0.00 0.00 0.00 0.98
5674 6488 5.074929 TGGGACGGAGGGAGTAGTATAATAA 59.925 44.000 0.00 0.00 0.00 1.40
5695 6509 5.405935 AAGTTTGGTCAAAGCTTTGTCTT 57.594 34.783 32.46 23.24 39.18 3.01
5699 6513 4.545823 TGGTCAAAGCTTTGTCTTAACG 57.454 40.909 32.46 10.34 39.18 3.18
5722 6544 5.570206 CGAACATATTACACCGCATACGTAT 59.430 40.000 1.14 1.14 37.70 3.06
5776 8266 3.688694 TTAAGAATGGTGGCAGTACGT 57.311 42.857 0.00 0.00 0.00 3.57
5782 8272 3.795623 ATGGTGGCAGTACGTACTTAG 57.204 47.619 25.35 16.11 33.46 2.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 9.573133 CATTTTTACATTCCTATGGTTCAGAAC 57.427 33.333 4.52 4.52 36.01 3.01
127 128 2.846206 ACTCATTCCCTATTCCTGCACA 59.154 45.455 0.00 0.00 0.00 4.57
128 129 3.567478 ACTCATTCCCTATTCCTGCAC 57.433 47.619 0.00 0.00 0.00 4.57
133 134 4.779993 ACCTGAACTCATTCCCTATTCC 57.220 45.455 0.00 0.00 33.49 3.01
137 138 4.841813 TGTTGTACCTGAACTCATTCCCTA 59.158 41.667 0.00 0.00 33.49 3.53
152 153 8.059120 TTGTTTTCAATTCCTTGGTGTTGTACC 61.059 37.037 0.00 0.00 41.38 3.34
176 177 7.329226 ACACACAGTCTTTGTTCATTTTCTTTG 59.671 33.333 0.00 0.00 38.16 2.77
177 178 7.378181 ACACACAGTCTTTGTTCATTTTCTTT 58.622 30.769 0.00 0.00 38.16 2.52
179 180 6.515272 ACACACAGTCTTTGTTCATTTTCT 57.485 33.333 0.00 0.00 38.16 2.52
181 182 5.799936 CGAACACACAGTCTTTGTTCATTTT 59.200 36.000 15.11 0.00 46.29 1.82
182 183 5.331902 CGAACACACAGTCTTTGTTCATTT 58.668 37.500 15.11 0.00 46.29 2.32
190 191 1.208535 TCCACCGAACACACAGTCTTT 59.791 47.619 0.00 0.00 0.00 2.52
284 285 4.155099 CGTGAGAGAAGAAGAACTAGCTGA 59.845 45.833 0.00 0.00 0.00 4.26
300 301 1.626747 CATGCTGTGAGACGTGAGAG 58.373 55.000 0.00 0.00 0.00 3.20
301 302 0.389037 GCATGCTGTGAGACGTGAGA 60.389 55.000 11.37 0.00 0.00 3.27
302 303 0.389556 AGCATGCTGTGAGACGTGAG 60.390 55.000 21.98 0.00 0.00 3.51
303 304 0.033920 AAGCATGCTGTGAGACGTGA 59.966 50.000 23.48 0.00 0.00 4.35
305 306 0.870393 CAAAGCATGCTGTGAGACGT 59.130 50.000 30.73 5.13 33.20 4.34
306 307 0.167470 CCAAAGCATGCTGTGAGACG 59.833 55.000 34.90 17.02 33.20 4.18
307 308 1.242076 ACCAAAGCATGCTGTGAGAC 58.758 50.000 34.90 0.00 33.20 3.36
335 377 5.221126 GCAGCCATAGGAAAGGTGAATAAAG 60.221 44.000 0.00 0.00 0.00 1.85
399 441 5.308825 AGTGTCGATTTCACAGGAATCTTT 58.691 37.500 7.32 0.00 38.16 2.52
423 465 1.915769 AGAGGAAAGGCTCGCCAGT 60.916 57.895 11.02 0.00 38.92 4.00
576 618 9.311916 CCATTTCTAACAAAAGTTCATGTCAAA 57.688 29.630 0.00 0.00 0.00 2.69
577 619 8.474025 ACCATTTCTAACAAAAGTTCATGTCAA 58.526 29.630 0.00 0.00 0.00 3.18
718 764 5.158494 GGCCGGTTTGTTAGTATTTTGAAG 58.842 41.667 1.90 0.00 0.00 3.02
779 879 3.534554 CACCTGTGCTGATATAACTGCA 58.465 45.455 9.95 9.95 41.07 4.41
780 880 2.874701 CCACCTGTGCTGATATAACTGC 59.125 50.000 5.11 5.11 35.76 4.40
878 982 1.807165 CACGAGATCTGGGTGTGCG 60.807 63.158 9.72 3.04 0.00 5.34
907 1011 1.002857 AAGTGGAAGGAAGGGGATGG 58.997 55.000 0.00 0.00 0.00 3.51
1230 1334 2.581354 CTGGCCTTGGTCTCCTCG 59.419 66.667 3.32 0.00 0.00 4.63
1315 1419 0.106918 TGACAGGAAAGGGCAAACGT 60.107 50.000 0.00 0.00 0.00 3.99
1355 1459 3.149196 CCATCAGGTATTTCAATCCCCG 58.851 50.000 0.00 0.00 0.00 5.73
1377 1481 5.902613 TTCCAAAGTGCCAATCAATCTAG 57.097 39.130 0.00 0.00 0.00 2.43
1407 1512 6.093219 CCAATTGGACATGTAGAACAGAGAAG 59.907 42.308 20.50 0.00 37.39 2.85
1592 1697 1.737236 TCAATTTGGTTCGATGCCTCG 59.263 47.619 4.89 4.89 46.41 4.63
1663 1944 3.498082 GTTCACCGCAATAAATGACACC 58.502 45.455 0.00 0.00 0.00 4.16
1956 2240 2.492881 CAACCATAAGCTGCAACATGGA 59.507 45.455 24.76 0.00 40.37 3.41
2173 2457 9.046296 ACATAAACTTGCTAATAGATTCGAAGG 57.954 33.333 3.35 0.00 0.00 3.46
2250 2535 8.473219 GGGCCACCTATAAATACTAGTATGTAC 58.527 40.741 16.11 1.84 0.00 2.90
2698 2989 2.165641 TGACGCTCAAACGGATGTATCT 59.834 45.455 0.00 0.00 37.37 1.98
3230 3628 1.134098 AGGGACATGGAACGCCTAATG 60.134 52.381 0.00 0.00 34.31 1.90
3237 3635 1.221840 CTGGGAGGGACATGGAACG 59.778 63.158 0.00 0.00 0.00 3.95
3587 4170 4.142093 ACCTTCACCATTTCTATGCAATGC 60.142 41.667 0.00 0.00 31.26 3.56
4395 5186 4.075763 GTGATGCACACTGAAGATGAAC 57.924 45.455 10.87 0.00 45.13 3.18
4430 5221 8.650490 ACTCATTGTGTTATTTCCCAAAAAGAT 58.350 29.630 0.00 0.00 0.00 2.40
4854 5646 8.280084 AGCTGGACCTATATAACGGATCTAATA 58.720 37.037 0.00 0.00 0.00 0.98
5201 5994 5.613360 GATTATCATCAAATCAGTCGGCACG 60.613 44.000 0.00 0.00 42.16 5.34
5206 5999 6.535274 TGCAGATTATCATCAAATCAGTCG 57.465 37.500 0.00 0.00 36.09 4.18
5229 6022 1.909700 ACACATTCCTTTCGGCACAT 58.090 45.000 0.00 0.00 0.00 3.21
5247 6040 5.845953 CACAGATGAACACACGTTGAATTAC 59.154 40.000 5.01 0.00 34.75 1.89
5248 6041 5.049749 CCACAGATGAACACACGTTGAATTA 60.050 40.000 5.01 0.00 34.75 1.40
5369 6162 4.369872 TCAATCCTGGGGGCAATTTAAAT 58.630 39.130 0.00 0.00 0.00 1.40
5475 6287 4.036852 GCCTTGTCTTAGCCAACCATAATC 59.963 45.833 0.00 0.00 0.00 1.75
5582 6396 6.786843 ATTACATTATGGGATGAAGGGAGT 57.213 37.500 0.00 0.00 0.00 3.85
5583 6397 6.818644 CGTATTACATTATGGGATGAAGGGAG 59.181 42.308 0.00 0.00 0.00 4.30
5585 6399 6.472887 ACGTATTACATTATGGGATGAAGGG 58.527 40.000 0.00 0.00 0.00 3.95
5586 6400 7.979444 AACGTATTACATTATGGGATGAAGG 57.021 36.000 0.00 0.00 0.00 3.46
5614 6428 9.772973 ACACTTTTTGACATTAGTGTAGTATCA 57.227 29.630 13.13 0.00 46.72 2.15
5628 6442 9.967451 TCCCATAATATAAGACACTTTTTGACA 57.033 29.630 0.00 0.00 0.00 3.58
5630 6444 9.104965 CGTCCCATAATATAAGACACTTTTTGA 57.895 33.333 0.00 0.00 0.00 2.69
5631 6445 8.342634 CCGTCCCATAATATAAGACACTTTTTG 58.657 37.037 0.00 0.00 0.00 2.44
5632 6446 8.269317 TCCGTCCCATAATATAAGACACTTTTT 58.731 33.333 0.00 0.00 0.00 1.94
5633 6447 7.798071 TCCGTCCCATAATATAAGACACTTTT 58.202 34.615 0.00 0.00 0.00 2.27
5634 6448 7.369551 TCCGTCCCATAATATAAGACACTTT 57.630 36.000 0.00 0.00 0.00 2.66
5635 6449 6.014499 CCTCCGTCCCATAATATAAGACACTT 60.014 42.308 0.00 0.00 0.00 3.16
5636 6450 5.480772 CCTCCGTCCCATAATATAAGACACT 59.519 44.000 0.00 0.00 0.00 3.55
5637 6451 5.337330 CCCTCCGTCCCATAATATAAGACAC 60.337 48.000 0.00 0.00 0.00 3.67
5638 6452 4.775780 CCCTCCGTCCCATAATATAAGACA 59.224 45.833 0.00 0.00 0.00 3.41
5639 6453 5.021458 TCCCTCCGTCCCATAATATAAGAC 58.979 45.833 0.00 0.00 0.00 3.01
5640 6454 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
5641 6455 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
5642 6456 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
5643 6457 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
5644 6458 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
5645 6459 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
5646 6460 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
5647 6461 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
5648 6462 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
5649 6463 1.229131 TACTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
5650 6464 1.229131 ATACTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
5651 6465 3.515602 TTATACTACTCCCTCCGTCCC 57.484 52.381 0.00 0.00 0.00 4.46
5652 6466 6.244654 ACTTATTATACTACTCCCTCCGTCC 58.755 44.000 0.00 0.00 0.00 4.79
5653 6467 7.757941 AACTTATTATACTACTCCCTCCGTC 57.242 40.000 0.00 0.00 0.00 4.79
5654 6468 7.015001 CCAAACTTATTATACTACTCCCTCCGT 59.985 40.741 0.00 0.00 0.00 4.69
5655 6469 7.015001 ACCAAACTTATTATACTACTCCCTCCG 59.985 40.741 0.00 0.00 0.00 4.63
5656 6470 8.260099 ACCAAACTTATTATACTACTCCCTCC 57.740 38.462 0.00 0.00 0.00 4.30
5657 6471 8.921205 TGACCAAACTTATTATACTACTCCCTC 58.079 37.037 0.00 0.00 0.00 4.30
5658 6472 8.849543 TGACCAAACTTATTATACTACTCCCT 57.150 34.615 0.00 0.00 0.00 4.20
5659 6473 9.895138 TTTGACCAAACTTATTATACTACTCCC 57.105 33.333 0.00 0.00 0.00 4.30
5666 6480 9.908152 ACAAAGCTTTGACCAAACTTATTATAC 57.092 29.630 38.78 0.00 40.55 1.47
5668 6482 8.860088 AGACAAAGCTTTGACCAAACTTATTAT 58.140 29.630 38.78 16.06 40.55 1.28
5669 6483 8.232913 AGACAAAGCTTTGACCAAACTTATTA 57.767 30.769 38.78 0.00 40.55 0.98
5670 6484 7.112452 AGACAAAGCTTTGACCAAACTTATT 57.888 32.000 38.78 16.67 40.55 1.40
5671 6485 6.715347 AGACAAAGCTTTGACCAAACTTAT 57.285 33.333 38.78 17.16 40.55 1.73
5672 6486 6.524101 AAGACAAAGCTTTGACCAAACTTA 57.476 33.333 38.78 0.00 40.55 2.24
5673 6487 5.405935 AAGACAAAGCTTTGACCAAACTT 57.594 34.783 38.78 26.78 40.55 2.66
5674 6488 6.330278 GTTAAGACAAAGCTTTGACCAAACT 58.670 36.000 38.78 23.80 40.55 2.66
5695 6509 5.399006 CGTATGCGGTGTAATATGTTCGTTA 59.601 40.000 0.00 0.00 0.00 3.18
5699 6513 6.939551 ATACGTATGCGGTGTAATATGTTC 57.060 37.500 7.41 0.00 43.45 3.18
5776 8266 8.891985 ATTCTCTCTCATATCCATGCTAAGTA 57.108 34.615 0.00 0.00 31.73 2.24
5782 8272 6.040209 ACTGATTCTCTCTCATATCCATGC 57.960 41.667 0.00 0.00 31.73 4.06


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

AutoCloner maintained by Alex Coulton.