Multiple sequence alignment - TraesCS7D01G010200

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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 TraesCS7D01G010200 chr7D 100.000 3779 0 0 1 3779 4876186 4879964 0.000000e+00 6979.0
1 TraesCS7D01G010200 chr7D 82.287 446 70 7 2861 3300 33750690 33750248 9.910000e-101 377.0
2 TraesCS7D01G010200 chr7D 79.493 434 65 12 3290 3718 33750216 33749802 1.720000e-73 287.0
3 TraesCS7D01G010200 chr7A 92.762 2017 102 20 872 2853 4687950 4685943 0.000000e+00 2876.0
4 TraesCS7D01G010200 chr7A 88.294 504 31 17 1 498 4689136 4688655 2.530000e-161 579.0
5 TraesCS7D01G010200 chr4A 95.493 1753 59 13 1053 2792 738815283 738817028 0.000000e+00 2782.0
6 TraesCS7D01G010200 chr4A 94.585 277 13 2 597 873 666834764 666834490 9.700000e-116 427.0
7 TraesCS7D01G010200 chr4A 94.224 277 14 2 597 873 666827800 666827526 4.510000e-114 422.0
8 TraesCS7D01G010200 chr4A 94.224 277 14 2 597 873 666841749 666841475 4.510000e-114 422.0
9 TraesCS7D01G010200 chr4A 94.224 277 14 2 597 873 666845242 666844968 4.510000e-114 422.0
10 TraesCS7D01G010200 chr4A 94.505 273 13 2 610 881 542612489 542612218 1.620000e-113 420.0
11 TraesCS7D01G010200 chr4A 93.863 277 15 2 597 873 666838257 666837983 2.100000e-112 416.0
12 TraesCS7D01G010200 chr4A 82.394 426 64 9 2857 3274 595649840 595650262 9.980000e-96 361.0
13 TraesCS7D01G010200 chr4A 98.824 85 1 0 1 85 738814841 738814925 6.540000e-33 152.0
14 TraesCS7D01G010200 chr1D 94.769 497 23 3 3285 3779 253061633 253061138 0.000000e+00 771.0
15 TraesCS7D01G010200 chr1D 94.824 425 21 1 2863 3286 253062098 253061674 0.000000e+00 662.0
16 TraesCS7D01G010200 chr1D 81.481 189 26 5 100 284 471119833 471119650 3.040000e-31 147.0
17 TraesCS7D01G010200 chr4D 91.849 503 33 3 3285 3779 497238027 497238529 0.000000e+00 695.0
18 TraesCS7D01G010200 chr4D 92.056 428 32 2 2861 3287 497237561 497237987 5.400000e-168 601.0
19 TraesCS7D01G010200 chr4D 89.489 352 21 6 3430 3779 497238556 497238893 7.500000e-117 431.0
20 TraesCS7D01G010200 chr6D 91.348 497 40 3 3285 3779 5188110 5187615 0.000000e+00 676.0
21 TraesCS7D01G010200 chr6D 97.388 268 6 1 610 877 434447425 434447159 4.450000e-124 455.0
22 TraesCS7D01G010200 chr6D 80.930 430 71 10 2865 3287 98198601 98198176 2.810000e-86 329.0
23 TraesCS7D01G010200 chr6D 94.483 145 7 1 3143 3287 5188293 5188150 4.910000e-54 222.0
24 TraesCS7D01G010200 chr5B 75.766 1370 278 37 1199 2547 9417141 9418477 3.180000e-180 641.0
25 TraesCS7D01G010200 chr5B 73.910 1353 293 38 1198 2532 9334334 9333024 4.390000e-134 488.0
26 TraesCS7D01G010200 chr5D 75.494 1367 287 33 1199 2547 9471220 9472556 3.200000e-175 625.0
27 TraesCS7D01G010200 chr5D 74.453 1370 285 42 1200 2547 9387039 9385713 7.190000e-147 531.0
28 TraesCS7D01G010200 chr5D 86.667 435 50 7 3290 3720 64259344 64258914 3.420000e-130 475.0
29 TraesCS7D01G010200 chr5D 96.212 264 9 1 610 873 119267843 119267581 7.500000e-117 431.0
30 TraesCS7D01G010200 chr5D 84.055 439 58 11 2857 3287 64259823 64259389 2.720000e-111 412.0
31 TraesCS7D01G010200 chr5A 75.455 1373 286 35 1199 2547 7506165 7504820 4.150000e-174 621.0
32 TraesCS7D01G010200 chr5A 75.292 1372 295 33 1192 2547 7619461 7620804 1.930000e-172 616.0
33 TraesCS7D01G010200 chr5A 96.241 266 9 1 608 873 463746732 463746468 5.800000e-118 435.0
34 TraesCS7D01G010200 chr5A 84.839 310 35 10 2859 3160 666128150 666127845 6.130000e-78 302.0
35 TraesCS7D01G010200 chr3B 85.781 429 54 6 2862 3287 825996512 825996088 7.450000e-122 448.0
36 TraesCS7D01G010200 chr3B 88.889 324 33 1 3285 3608 825996047 825995727 2.740000e-106 396.0
37 TraesCS7D01G010200 chr1B 83.095 420 66 2 2871 3287 490762734 490763151 9.910000e-101 377.0
38 TraesCS7D01G010200 chr1B 88.845 251 26 2 3285 3535 490763191 490763439 1.320000e-79 307.0
39 TraesCS7D01G010200 chr7B 78.811 387 77 3 1288 1669 140156141 140156527 4.840000e-64 255.0
40 TraesCS7D01G010200 chr7B 82.432 148 15 5 140 284 71134857 71134996 6.630000e-23 119.0
41 TraesCS7D01G010200 chr2B 84.507 213 27 5 74 284 759057798 759058006 4.950000e-49 206.0
42 TraesCS7D01G010200 chr6B 79.931 289 48 8 1 284 269078329 269078046 1.780000e-48 204.0
43 TraesCS7D01G010200 chr1A 77.083 144 31 2 1252 1394 579288550 579288408 8.700000e-12 82.4
44 TraesCS7D01G010200 chr1A 82.927 82 10 3 189 267 357187833 357187753 1.880000e-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 TraesCS7D01G010200 chr7D 4876186 4879964 3778 False 6979.000000 6979 100.000000 1 3779 1 chr7D.!!$F1 3778
1 TraesCS7D01G010200 chr7D 33749802 33750690 888 True 332.000000 377 80.890000 2861 3718 2 chr7D.!!$R1 857
2 TraesCS7D01G010200 chr7A 4685943 4689136 3193 True 1727.500000 2876 90.528000 1 2853 2 chr7A.!!$R1 2852
3 TraesCS7D01G010200 chr4A 738814841 738817028 2187 False 1467.000000 2782 97.158500 1 2792 2 chr4A.!!$F2 2791
4 TraesCS7D01G010200 chr4A 666834490 666845242 10752 True 421.750000 427 94.224000 597 873 4 chr4A.!!$R3 276
5 TraesCS7D01G010200 chr1D 253061138 253062098 960 True 716.500000 771 94.796500 2863 3779 2 chr1D.!!$R2 916
6 TraesCS7D01G010200 chr4D 497237561 497238893 1332 False 575.666667 695 91.131333 2861 3779 3 chr4D.!!$F1 918
7 TraesCS7D01G010200 chr6D 5187615 5188293 678 True 449.000000 676 92.915500 3143 3779 2 chr6D.!!$R3 636
8 TraesCS7D01G010200 chr5B 9417141 9418477 1336 False 641.000000 641 75.766000 1199 2547 1 chr5B.!!$F1 1348
9 TraesCS7D01G010200 chr5B 9333024 9334334 1310 True 488.000000 488 73.910000 1198 2532 1 chr5B.!!$R1 1334
10 TraesCS7D01G010200 chr5D 9471220 9472556 1336 False 625.000000 625 75.494000 1199 2547 1 chr5D.!!$F1 1348
11 TraesCS7D01G010200 chr5D 9385713 9387039 1326 True 531.000000 531 74.453000 1200 2547 1 chr5D.!!$R1 1347
12 TraesCS7D01G010200 chr5D 64258914 64259823 909 True 443.500000 475 85.361000 2857 3720 2 chr5D.!!$R3 863
13 TraesCS7D01G010200 chr5A 7504820 7506165 1345 True 621.000000 621 75.455000 1199 2547 1 chr5A.!!$R1 1348
14 TraesCS7D01G010200 chr5A 7619461 7620804 1343 False 616.000000 616 75.292000 1192 2547 1 chr5A.!!$F1 1355
15 TraesCS7D01G010200 chr3B 825995727 825996512 785 True 422.000000 448 87.335000 2862 3608 2 chr3B.!!$R1 746
16 TraesCS7D01G010200 chr1B 490762734 490763439 705 False 342.000000 377 85.970000 2871 3535 2 chr1B.!!$F1 664

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
489 510 0.030297 AGAGGAGGCCTGGATCACAT 60.030 55.0 12.00 0.0 31.76 3.21 F
1227 9038 0.037326 TGGTAGAGCTCAAAGCCACG 60.037 55.0 17.77 0.0 43.77 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2129 11547 4.864334 CCATCTCCGCCAGCACCC 62.864 72.222 0.0 0.0 0.0 4.61 R
2825 12636 0.965363 GCGAATGGTGAATGGGTGGT 60.965 55.000 0.0 0.0 0.0 4.16 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
44 45 7.014702 GGTGGAATTTTTGCATAAACAATTCG 58.985 34.615 4.36 0.00 36.09 3.34
85 86 3.070302 GTGGCAATGGTTTACCCTTGAAA 59.930 43.478 17.64 5.03 42.08 2.69
88 89 5.163152 TGGCAATGGTTTACCCTTGAAAAAT 60.163 36.000 17.64 0.00 42.08 1.82
140 141 7.595819 TCAAAATAAGGAACAACCAATCTGT 57.404 32.000 0.00 0.00 42.04 3.41
141 142 8.698973 TCAAAATAAGGAACAACCAATCTGTA 57.301 30.769 0.00 0.00 42.04 2.74
143 144 6.759497 AATAAGGAACAACCAATCTGTAGC 57.241 37.500 0.00 0.00 42.04 3.58
144 145 3.788227 AGGAACAACCAATCTGTAGCA 57.212 42.857 0.00 0.00 42.04 3.49
145 146 4.098914 AGGAACAACCAATCTGTAGCAA 57.901 40.909 0.00 0.00 42.04 3.91
146 147 4.666512 AGGAACAACCAATCTGTAGCAAT 58.333 39.130 0.00 0.00 42.04 3.56
147 148 5.815581 AGGAACAACCAATCTGTAGCAATA 58.184 37.500 0.00 0.00 42.04 1.90
148 149 5.882557 AGGAACAACCAATCTGTAGCAATAG 59.117 40.000 0.00 0.00 42.04 1.73
149 150 5.648092 GGAACAACCAATCTGTAGCAATAGT 59.352 40.000 0.00 0.00 38.79 2.12
150 151 6.821665 GGAACAACCAATCTGTAGCAATAGTA 59.178 38.462 0.00 0.00 38.79 1.82
151 152 7.499232 GGAACAACCAATCTGTAGCAATAGTAT 59.501 37.037 0.00 0.00 38.79 2.12
152 153 9.542462 GAACAACCAATCTGTAGCAATAGTATA 57.458 33.333 0.00 0.00 0.00 1.47
153 154 8.888579 ACAACCAATCTGTAGCAATAGTATAC 57.111 34.615 0.00 0.00 0.00 1.47
228 243 7.992180 AACTTCACTCTAAATTGCACTTTTG 57.008 32.000 7.39 6.03 0.00 2.44
244 259 7.835822 TGCACTTTTGGTAGTATGCAAATAAT 58.164 30.769 0.00 0.00 27.91 1.28
289 304 7.930513 TTCTCACATATTGCATAGTTACTCG 57.069 36.000 0.00 0.00 0.00 4.18
296 311 3.371102 TGCATAGTTACTCGCTCCATC 57.629 47.619 7.94 0.00 0.00 3.51
306 321 3.480470 ACTCGCTCCATCCCAAAATATG 58.520 45.455 0.00 0.00 0.00 1.78
313 328 5.950549 GCTCCATCCCAAAATATGAGATCAT 59.049 40.000 0.31 0.31 40.22 2.45
333 348 4.536090 TCATTTTGACACTATCAGGAGGGT 59.464 41.667 0.00 0.00 38.99 4.34
340 355 6.199376 TGACACTATCAGGAGGGTGTATTTA 58.801 40.000 9.09 0.00 42.01 1.40
478 499 0.178990 GAGGGAGAGAGAGAGGAGGC 60.179 65.000 0.00 0.00 0.00 4.70
480 501 1.655114 GGGAGAGAGAGAGGAGGCCT 61.655 65.000 3.86 3.86 36.03 5.19
481 502 0.468029 GGAGAGAGAGAGGAGGCCTG 60.468 65.000 12.00 0.00 31.76 4.85
482 503 0.468029 GAGAGAGAGAGGAGGCCTGG 60.468 65.000 12.00 0.00 31.76 4.45
489 510 0.030297 AGAGGAGGCCTGGATCACAT 60.030 55.000 12.00 0.00 31.76 3.21
498 519 6.365970 AGGCCTGGATCACATAGTTAATAG 57.634 41.667 3.11 0.00 0.00 1.73
500 521 4.938226 GCCTGGATCACATAGTTAATAGGC 59.062 45.833 0.00 0.00 39.98 3.93
501 522 5.280215 GCCTGGATCACATAGTTAATAGGCT 60.280 44.000 0.00 0.00 42.66 4.58
502 523 6.745474 GCCTGGATCACATAGTTAATAGGCTT 60.745 42.308 0.00 0.00 42.66 4.35
503 524 6.876257 CCTGGATCACATAGTTAATAGGCTTC 59.124 42.308 0.00 0.00 0.00 3.86
504 525 6.455647 TGGATCACATAGTTAATAGGCTTCG 58.544 40.000 0.00 0.00 0.00 3.79
505 526 5.869888 GGATCACATAGTTAATAGGCTTCGG 59.130 44.000 0.00 0.00 0.00 4.30
506 527 4.628074 TCACATAGTTAATAGGCTTCGGC 58.372 43.478 0.00 0.00 40.88 5.54
517 538 3.646715 CTTCGGCCCAACCCAGGA 61.647 66.667 0.00 0.00 33.26 3.86
518 539 3.179339 TTCGGCCCAACCCAGGAA 61.179 61.111 0.00 0.00 33.26 3.36
521 542 4.280019 GGCCCAACCCAGGAACGT 62.280 66.667 0.00 0.00 0.00 3.99
522 543 2.983592 GCCCAACCCAGGAACGTG 60.984 66.667 0.00 0.00 0.00 4.49
523 544 2.833227 CCCAACCCAGGAACGTGA 59.167 61.111 0.00 0.00 0.00 4.35
524 545 1.302511 CCCAACCCAGGAACGTGAG 60.303 63.158 0.00 0.00 0.00 3.51
525 546 1.302511 CCAACCCAGGAACGTGAGG 60.303 63.158 0.00 0.00 0.00 3.86
526 547 1.752198 CAACCCAGGAACGTGAGGA 59.248 57.895 0.00 0.00 0.00 3.71
527 548 0.320771 CAACCCAGGAACGTGAGGAG 60.321 60.000 0.00 0.00 0.00 3.69
528 549 2.113243 AACCCAGGAACGTGAGGAGC 62.113 60.000 0.00 0.00 0.00 4.70
529 550 2.286523 CCCAGGAACGTGAGGAGCT 61.287 63.158 0.00 0.00 0.00 4.09
531 552 1.216710 CAGGAACGTGAGGAGCTCC 59.783 63.158 26.22 26.22 0.00 4.70
542 563 1.747444 AGGAGCTCCTTCAGGGAAAA 58.253 50.000 30.40 0.00 46.09 2.29
543 564 2.282900 AGGAGCTCCTTCAGGGAAAAT 58.717 47.619 30.40 2.81 46.09 1.82
544 565 2.240921 AGGAGCTCCTTCAGGGAAAATC 59.759 50.000 30.40 0.00 46.09 2.17
545 566 2.025887 GGAGCTCCTTCAGGGAAAATCA 60.026 50.000 26.25 0.00 44.58 2.57
546 567 3.562176 GGAGCTCCTTCAGGGAAAATCAA 60.562 47.826 26.25 0.00 44.58 2.57
547 568 3.693578 GAGCTCCTTCAGGGAAAATCAAG 59.306 47.826 0.87 0.00 44.58 3.02
548 569 2.165234 GCTCCTTCAGGGAAAATCAAGC 59.835 50.000 0.00 0.00 44.58 4.01
564 1096 4.818534 TCAAGCAGCTAAAGTGTTCTTG 57.181 40.909 0.00 0.00 33.79 3.02
576 1108 6.469782 AAAGTGTTCTTGGAAATGTGATGT 57.530 33.333 0.00 0.00 33.79 3.06
595 1127 8.770828 TGTGATGTTTTACTTTTCTGTACTAGC 58.229 33.333 0.00 0.00 0.00 3.42
596 1128 8.989980 GTGATGTTTTACTTTTCTGTACTAGCT 58.010 33.333 0.00 0.00 0.00 3.32
623 1155 0.822164 AAATGTACTCCCTCCGTCCG 59.178 55.000 0.00 0.00 0.00 4.79
624 1156 0.324091 AATGTACTCCCTCCGTCCGT 60.324 55.000 0.00 0.00 0.00 4.69
661 1193 6.182507 TCTAGCTTTTGTCCTAGGTCAAAA 57.817 37.500 31.58 31.58 39.44 2.44
712 1244 9.686683 AGGAAAAAGTACTAGCATTTATGACAT 57.313 29.630 0.00 0.00 0.00 3.06
947 8463 7.803279 AAATTAGTTTCAGAACGAAGAACCT 57.197 32.000 0.00 0.00 40.75 3.50
951 8467 1.878953 TCAGAACGAAGAACCTTGCC 58.121 50.000 0.00 0.00 0.00 4.52
967 8496 1.492764 TGCCAGCTAGGTTAGGGTAC 58.507 55.000 0.00 0.00 40.61 3.34
1019 8548 3.206150 ACACACGAGAAACAGAAGCAAT 58.794 40.909 0.00 0.00 0.00 3.56
1045 8576 1.097547 GCTGCTTGGTGTGTGAGTGT 61.098 55.000 0.00 0.00 0.00 3.55
1047 8578 0.251634 TGCTTGGTGTGTGAGTGTGA 59.748 50.000 0.00 0.00 0.00 3.58
1048 8579 0.940126 GCTTGGTGTGTGAGTGTGAG 59.060 55.000 0.00 0.00 0.00 3.51
1221 9032 1.295423 GGCGGTGGTAGAGCTCAAA 59.705 57.895 17.77 0.00 0.00 2.69
1227 9038 0.037326 TGGTAGAGCTCAAAGCCACG 60.037 55.000 17.77 0.00 43.77 4.94
1990 11399 2.049063 AGAGCACCTTGACGACGC 60.049 61.111 0.00 0.00 0.00 5.19
2030 11439 2.034066 GGCCCAGCACAGCTACAA 59.966 61.111 0.00 0.00 36.40 2.41
2040 11449 1.301716 CAGCTACAACGTGCAGGGT 60.302 57.895 11.67 0.00 0.00 4.34
2655 12438 2.363147 GCCCCGCCCACCAAATAA 60.363 61.111 0.00 0.00 0.00 1.40
2685 12481 7.642082 TCAACTCTCCATTTACTACTACTCC 57.358 40.000 0.00 0.00 0.00 3.85
2686 12482 7.179966 TCAACTCTCCATTTACTACTACTCCA 58.820 38.462 0.00 0.00 0.00 3.86
2690 12486 7.774625 ACTCTCCATTTACTACTACTCCACTAC 59.225 40.741 0.00 0.00 0.00 2.73
2704 12500 4.510340 ACTCCACTACGTTTGTTTCATCAC 59.490 41.667 0.00 0.00 0.00 3.06
2715 12511 7.442969 ACGTTTGTTTCATCACTCCATTTACTA 59.557 33.333 0.00 0.00 0.00 1.82
2723 12519 7.478322 TCATCACTCCATTTACTACTACGTTC 58.522 38.462 0.00 0.00 0.00 3.95
2724 12520 6.199937 TCACTCCATTTACTACTACGTTCC 57.800 41.667 0.00 0.00 0.00 3.62
2726 12522 5.018809 ACTCCATTTACTACTACGTTCCCA 58.981 41.667 0.00 0.00 0.00 4.37
2741 12541 6.834168 ACGTTCCCATTTTTATCTTCATGT 57.166 33.333 0.00 0.00 0.00 3.21
2781 12592 5.487433 TCGTGAGCTGAAATGAATAAAGGA 58.513 37.500 0.00 0.00 0.00 3.36
2800 12611 2.305052 GGAGCATCTCATCATCCATGGA 59.695 50.000 18.88 18.88 32.64 3.41
2801 12612 3.054287 GGAGCATCTCATCATCCATGGAT 60.054 47.826 22.15 22.15 32.64 3.41
2807 12618 6.473758 CATCTCATCATCCATGGATAGTGTT 58.526 40.000 26.87 9.10 32.93 3.32
2810 12621 8.211030 TCTCATCATCCATGGATAGTGTTTAT 57.789 34.615 26.87 9.06 32.93 1.40
2830 12641 7.612633 TGTTTATTTAATCTCACCCTTACCACC 59.387 37.037 0.00 0.00 0.00 4.61
2833 12644 2.286935 ATCTCACCCTTACCACCCAT 57.713 50.000 0.00 0.00 0.00 4.00
2835 12646 1.913419 TCTCACCCTTACCACCCATTC 59.087 52.381 0.00 0.00 0.00 2.67
2840 12651 1.287739 CCCTTACCACCCATTCACCAT 59.712 52.381 0.00 0.00 0.00 3.55
2844 12655 0.965363 ACCACCCATTCACCATTCGC 60.965 55.000 0.00 0.00 0.00 4.70
2849 12660 2.158900 ACCCATTCACCATTCGCTAGAG 60.159 50.000 0.00 0.00 0.00 2.43
2853 12664 2.988010 TCACCATTCGCTAGAGCAAT 57.012 45.000 1.89 0.00 42.21 3.56
2854 12665 2.554142 TCACCATTCGCTAGAGCAATG 58.446 47.619 14.55 14.55 42.21 2.82
2856 12667 1.959042 CCATTCGCTAGAGCAATGGT 58.041 50.000 23.54 0.00 44.78 3.55
2857 12668 1.869767 CCATTCGCTAGAGCAATGGTC 59.130 52.381 23.54 3.97 44.78 4.02
2858 12669 2.484417 CCATTCGCTAGAGCAATGGTCT 60.484 50.000 19.28 19.28 44.78 3.85
2859 12670 3.243873 CCATTCGCTAGAGCAATGGTCTA 60.244 47.826 19.45 19.45 44.78 2.59
2860 12671 4.562347 CCATTCGCTAGAGCAATGGTCTAT 60.562 45.833 20.64 5.81 44.78 1.98
2903 12714 6.314152 CAGGAGAGCTGCTATATTCATTGATG 59.686 42.308 0.15 0.00 0.00 3.07
2921 12733 9.519191 TCATTGATGAGAGAGAAATGGTAAAAA 57.481 29.630 0.00 0.00 32.11 1.94
2960 12773 8.715190 AATTAAGGAAAACTAGGCTAAAACCA 57.285 30.769 0.00 0.00 0.00 3.67
3004 12818 3.660865 CAAAACTAGGTCTAAGCACCGT 58.339 45.455 0.00 0.00 41.90 4.83
3038 12852 3.134127 GCCAAAGGCCAGCTACCG 61.134 66.667 5.01 0.00 44.06 4.02
3131 12954 3.562557 GTCTTCAAAGTAACGCCTCCAAA 59.437 43.478 0.00 0.00 0.00 3.28
3198 13021 3.576550 GCCAAATCTTAGGTTTTCACCCA 59.423 43.478 0.00 0.00 45.63 4.51
3452 13703 1.280457 CAGGAACTAGCAAGGACCCT 58.720 55.000 0.00 0.00 36.02 4.34
3538 13790 4.414956 TGGATCTGGCCGGGACCT 62.415 66.667 22.10 3.62 0.00 3.85
3553 13805 0.108804 GACCTCGCCGAAATCAGACA 60.109 55.000 0.00 0.00 0.00 3.41
3609 13861 1.001641 CACCAAAGCTAGCAGGCCT 60.002 57.895 18.83 0.00 0.00 5.19
3642 13897 1.439228 CAGATCGGCGAGGATGTGT 59.561 57.895 17.22 0.00 34.11 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 117 7.595819 ACAGATTGGTTGTTCCTTATTTTGA 57.404 32.000 0.00 0.00 37.07 2.69
193 208 6.509418 TTAGAGTGAAGTTTTGTGCAAGTT 57.491 33.333 0.00 0.00 0.00 2.66
268 283 5.842907 AGCGAGTAACTATGCAATATGTGA 58.157 37.500 0.00 0.00 0.00 3.58
284 299 4.346709 TCATATTTTGGGATGGAGCGAGTA 59.653 41.667 0.00 0.00 0.00 2.59
285 300 3.136443 TCATATTTTGGGATGGAGCGAGT 59.864 43.478 0.00 0.00 0.00 4.18
286 301 3.743521 TCATATTTTGGGATGGAGCGAG 58.256 45.455 0.00 0.00 0.00 5.03
287 302 3.390967 TCTCATATTTTGGGATGGAGCGA 59.609 43.478 0.00 0.00 26.46 4.93
289 304 5.319453 TGATCTCATATTTTGGGATGGAGC 58.681 41.667 0.00 0.00 45.96 4.70
296 311 8.472413 AGTGTCAAAATGATCTCATATTTTGGG 58.528 33.333 20.34 5.24 46.51 4.12
306 321 6.705381 CCTCCTGATAGTGTCAAAATGATCTC 59.295 42.308 0.00 0.00 36.14 2.75
313 328 3.650942 ACACCCTCCTGATAGTGTCAAAA 59.349 43.478 0.00 0.00 39.14 2.44
354 369 5.738619 ATTTTGGGATGTTGGGTTAGTTC 57.261 39.130 0.00 0.00 0.00 3.01
449 470 6.663523 CCTCTCTCTCTCCCTCTATTTATTCC 59.336 46.154 0.00 0.00 0.00 3.01
462 483 0.468029 CAGGCCTCCTCTCTCTCTCC 60.468 65.000 0.00 0.00 0.00 3.71
463 484 0.468029 CCAGGCCTCCTCTCTCTCTC 60.468 65.000 0.00 0.00 0.00 3.20
466 487 0.188342 GATCCAGGCCTCCTCTCTCT 59.812 60.000 0.00 0.00 0.00 3.10
478 499 6.365970 AGCCTATTAACTATGTGATCCAGG 57.634 41.667 0.00 0.00 0.00 4.45
480 501 6.455647 CGAAGCCTATTAACTATGTGATCCA 58.544 40.000 0.00 0.00 0.00 3.41
481 502 5.869888 CCGAAGCCTATTAACTATGTGATCC 59.130 44.000 0.00 0.00 0.00 3.36
482 503 5.348997 GCCGAAGCCTATTAACTATGTGATC 59.651 44.000 0.00 0.00 0.00 2.92
500 521 3.204467 TTCCTGGGTTGGGCCGAAG 62.204 63.158 0.00 0.00 38.44 3.79
501 522 3.179339 TTCCTGGGTTGGGCCGAA 61.179 61.111 0.00 0.00 38.44 4.30
502 523 3.961414 GTTCCTGGGTTGGGCCGA 61.961 66.667 0.00 0.00 38.44 5.54
504 525 4.280019 ACGTTCCTGGGTTGGGCC 62.280 66.667 0.00 0.00 0.00 5.80
505 526 2.983592 CACGTTCCTGGGTTGGGC 60.984 66.667 0.00 0.00 0.00 5.36
506 527 1.302511 CTCACGTTCCTGGGTTGGG 60.303 63.158 0.00 0.00 0.00 4.12
507 528 1.302511 CCTCACGTTCCTGGGTTGG 60.303 63.158 0.00 0.00 0.00 3.77
509 530 2.058675 CTCCTCACGTTCCTGGGTT 58.941 57.895 0.00 0.00 0.00 4.11
510 531 2.584391 GCTCCTCACGTTCCTGGGT 61.584 63.158 0.00 0.00 0.00 4.51
514 535 1.077625 AGGAGCTCCTCACGTTCCT 59.922 57.895 30.40 4.26 44.77 3.36
515 536 3.701454 AGGAGCTCCTCACGTTCC 58.299 61.111 30.40 1.47 44.77 3.62
529 550 3.424703 CTGCTTGATTTTCCCTGAAGGA 58.575 45.455 0.00 0.00 45.68 3.36
531 552 2.824341 AGCTGCTTGATTTTCCCTGAAG 59.176 45.455 0.00 0.00 0.00 3.02
532 553 2.880443 AGCTGCTTGATTTTCCCTGAA 58.120 42.857 0.00 0.00 0.00 3.02
533 554 2.592102 AGCTGCTTGATTTTCCCTGA 57.408 45.000 0.00 0.00 0.00 3.86
535 556 4.219288 CACTTTAGCTGCTTGATTTTCCCT 59.781 41.667 7.79 0.00 0.00 4.20
536 557 4.021981 ACACTTTAGCTGCTTGATTTTCCC 60.022 41.667 7.79 0.00 0.00 3.97
537 558 5.126396 ACACTTTAGCTGCTTGATTTTCC 57.874 39.130 7.79 0.00 0.00 3.13
538 559 6.442112 AGAACACTTTAGCTGCTTGATTTTC 58.558 36.000 7.79 4.63 0.00 2.29
539 560 6.396829 AGAACACTTTAGCTGCTTGATTTT 57.603 33.333 7.79 0.00 0.00 1.82
542 563 4.217118 CCAAGAACACTTTAGCTGCTTGAT 59.783 41.667 7.79 0.00 34.71 2.57
543 564 3.565482 CCAAGAACACTTTAGCTGCTTGA 59.435 43.478 7.79 0.00 34.71 3.02
544 565 3.565482 TCCAAGAACACTTTAGCTGCTTG 59.435 43.478 7.79 1.94 0.00 4.01
545 566 3.820557 TCCAAGAACACTTTAGCTGCTT 58.179 40.909 7.79 0.00 0.00 3.91
546 567 3.492102 TCCAAGAACACTTTAGCTGCT 57.508 42.857 7.57 7.57 0.00 4.24
547 568 4.568152 TTTCCAAGAACACTTTAGCTGC 57.432 40.909 0.00 0.00 0.00 5.25
548 569 5.916883 CACATTTCCAAGAACACTTTAGCTG 59.083 40.000 0.00 0.00 0.00 4.24
564 1096 8.871686 ACAGAAAAGTAAAACATCACATTTCC 57.128 30.769 0.00 0.00 34.51 3.13
594 1126 6.514705 CGGAGGGAGTACATTTTACTACTAGC 60.515 46.154 0.00 0.00 0.00 3.42
595 1127 6.545298 ACGGAGGGAGTACATTTTACTACTAG 59.455 42.308 0.00 0.00 0.00 2.57
596 1128 6.426587 ACGGAGGGAGTACATTTTACTACTA 58.573 40.000 0.00 0.00 0.00 1.82
597 1129 5.267587 ACGGAGGGAGTACATTTTACTACT 58.732 41.667 0.00 0.00 0.00 2.57
598 1130 5.451103 GGACGGAGGGAGTACATTTTACTAC 60.451 48.000 0.00 0.00 0.00 2.73
599 1131 4.646492 GGACGGAGGGAGTACATTTTACTA 59.354 45.833 0.00 0.00 0.00 1.82
600 1132 3.450096 GGACGGAGGGAGTACATTTTACT 59.550 47.826 0.00 0.00 0.00 2.24
601 1133 3.736126 CGGACGGAGGGAGTACATTTTAC 60.736 52.174 0.00 0.00 0.00 2.01
604 1136 0.822164 CGGACGGAGGGAGTACATTT 59.178 55.000 0.00 0.00 0.00 2.32
607 1139 1.676635 CACGGACGGAGGGAGTACA 60.677 63.158 0.00 0.00 0.00 2.90
623 1155 8.989980 ACAAAAGCTAGAAGTACACTTATTCAC 58.010 33.333 0.00 0.00 36.11 3.18
624 1156 9.204570 GACAAAAGCTAGAAGTACACTTATTCA 57.795 33.333 0.00 0.00 36.11 2.57
947 8463 1.835531 GTACCCTAACCTAGCTGGCAA 59.164 52.381 0.00 0.00 40.22 4.52
951 8467 9.436957 CATTTTATATGTACCCTAACCTAGCTG 57.563 37.037 0.00 0.00 0.00 4.24
967 8496 3.426191 GCGCATGCACACCATTTTATATG 59.574 43.478 19.57 0.00 42.15 1.78
2129 11547 4.864334 CCATCTCCGCCAGCACCC 62.864 72.222 0.00 0.00 0.00 4.61
2529 12312 1.144936 CATCTCCTCCTTGGCGTCC 59.855 63.158 0.00 0.00 35.26 4.79
2664 12460 6.733509 AGTGGAGTAGTAGTAAATGGAGAGT 58.266 40.000 0.00 0.00 0.00 3.24
2666 12462 6.765036 CGTAGTGGAGTAGTAGTAAATGGAGA 59.235 42.308 0.00 0.00 0.00 3.71
2670 12466 8.025445 ACAAACGTAGTGGAGTAGTAGTAAATG 58.975 37.037 0.00 0.00 45.00 2.32
2673 12469 7.510549 AACAAACGTAGTGGAGTAGTAGTAA 57.489 36.000 0.00 0.00 45.00 2.24
2678 12474 5.266733 TGAAACAAACGTAGTGGAGTAGT 57.733 39.130 0.00 0.00 45.00 2.73
2684 12480 4.084013 GGAGTGATGAAACAAACGTAGTGG 60.084 45.833 0.00 0.00 45.00 4.00
2685 12481 4.509970 TGGAGTGATGAAACAAACGTAGTG 59.490 41.667 0.00 0.00 45.00 2.74
2690 12486 6.668323 AGTAAATGGAGTGATGAAACAAACG 58.332 36.000 0.00 0.00 0.00 3.60
2704 12500 5.587388 TGGGAACGTAGTAGTAAATGGAG 57.413 43.478 0.00 0.00 45.00 3.86
2723 12519 9.603921 ATTAAGCAACATGAAGATAAAAATGGG 57.396 29.630 0.00 0.00 0.00 4.00
2741 12541 6.371548 AGCTCACGATGAAGTAAATTAAGCAA 59.628 34.615 0.00 0.00 0.00 3.91
2781 12592 4.783763 ACTATCCATGGATGATGAGATGCT 59.216 41.667 33.41 9.26 36.17 3.79
2801 12612 9.895138 GGTAAGGGTGAGATTAAATAAACACTA 57.105 33.333 0.00 0.00 0.00 2.74
2807 12618 6.217900 TGGGTGGTAAGGGTGAGATTAAATAA 59.782 38.462 0.00 0.00 0.00 1.40
2810 12621 3.917629 TGGGTGGTAAGGGTGAGATTAAA 59.082 43.478 0.00 0.00 0.00 1.52
2814 12625 2.286935 ATGGGTGGTAAGGGTGAGAT 57.713 50.000 0.00 0.00 0.00 2.75
2821 12632 2.826674 ATGGTGAATGGGTGGTAAGG 57.173 50.000 0.00 0.00 0.00 2.69
2825 12636 0.965363 GCGAATGGTGAATGGGTGGT 60.965 55.000 0.00 0.00 0.00 4.16
2830 12641 1.869767 GCTCTAGCGAATGGTGAATGG 59.130 52.381 0.00 0.00 0.00 3.16
2833 12644 2.760634 TTGCTCTAGCGAATGGTGAA 57.239 45.000 0.00 0.00 45.83 3.18
2835 12646 1.600957 CCATTGCTCTAGCGAATGGTG 59.399 52.381 23.66 9.43 44.78 4.17
2840 12651 4.672587 AATAGACCATTGCTCTAGCGAA 57.327 40.909 0.00 0.00 45.83 4.70
2869 12680 2.593346 CAGCTCTCCTGCTATCGTTT 57.407 50.000 0.00 0.00 41.98 3.60
2921 12733 7.593351 TTTCCTTAATTAACCTAGGGGTCTT 57.407 36.000 14.81 0.12 46.67 3.01
2927 12739 8.272889 AGCCTAGTTTTCCTTAATTAACCTAGG 58.727 37.037 7.41 7.41 34.03 3.02
2960 12773 3.975168 AGTGTTTAGCCCGTCTGTTAT 57.025 42.857 0.00 0.00 0.00 1.89
3004 12818 1.962306 GCCGGTGGTTTGCGACTTA 60.962 57.895 1.90 0.00 0.00 2.24
3038 12852 2.159268 GGTAGTTGTCTCGGAAGTAGCC 60.159 54.545 0.00 0.00 0.00 3.93
3045 12859 1.345415 GGTTTGGGTAGTTGTCTCGGA 59.655 52.381 0.00 0.00 0.00 4.55
3131 12954 2.300152 TGTCTCTGACATCGCTTCCTTT 59.700 45.455 0.00 0.00 37.67 3.11
3538 13790 1.447838 GCCTGTCTGATTTCGGCGA 60.448 57.895 4.99 4.99 0.00 5.54
3572 13824 4.011517 GTTCCCGCCCAGTTCCGA 62.012 66.667 0.00 0.00 0.00 4.55
3642 13897 1.805120 GCGCGGGCTAATCTGTTTCTA 60.805 52.381 18.33 0.00 35.83 2.10
3748 14006 2.936032 GGTGCTCCCCCTTCTGGT 60.936 66.667 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.