Multiple sequence alignment - TraesCS7D01G269000

Loading Multiple Alignment...

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 TraesCS7D01G269000 chr7D 100.000 5996 0 0 1 5996 253149355 253155350 0.000000e+00 11073
1 TraesCS7D01G269000 chr7B 93.568 3125 133 24 2870 5973 230210544 230213621 0.000000e+00 4595
2 TraesCS7D01G269000 chr7B 94.948 1049 46 6 1744 2789 230209501 230210545 0.000000e+00 1637
3 TraesCS7D01G269000 chr7B 95.383 823 24 7 692 1505 230208305 230209122 0.000000e+00 1297
4 TraesCS7D01G269000 chr7B 91.009 545 48 1 153 697 230206435 230206978 0.000000e+00 734
5 TraesCS7D01G269000 chr7B 94.477 344 17 1 1406 1747 230209131 230209474 4.120000e-146 529
6 TraesCS7D01G269000 chr7B 89.879 247 18 6 4413 4659 77187227 77187466 1.620000e-80 311
7 TraesCS7D01G269000 chr7B 85.654 237 34 0 4709 4945 77187465 77187701 3.590000e-62 250
8 TraesCS7D01G269000 chr7B 92.000 75 4 2 5046 5119 77187713 77187786 2.960000e-18 104
9 TraesCS7D01G269000 chr7A 95.186 2119 67 17 1747 3860 266980439 266978351 0.000000e+00 3315
10 TraesCS7D01G269000 chr7A 93.797 2144 99 17 3857 5982 266978318 266976191 0.000000e+00 3192
11 TraesCS7D01G269000 chr7A 92.813 1767 91 16 1 1747 266982219 266980469 0.000000e+00 2527
12 TraesCS7D01G269000 chr7A 87.931 290 28 6 3364 3651 697199464 697199180 9.630000e-88 335
13 TraesCS7D01G269000 chr7A 87.586 290 29 6 3364 3651 697176854 697176570 4.480000e-86 329
14 TraesCS7D01G269000 chr7A 92.105 114 5 2 5028 5140 27488178 27488288 2.240000e-34 158
15 TraesCS7D01G269000 chr4A 92.082 341 24 3 1 339 121510298 121510637 1.510000e-130 477
16 TraesCS7D01G269000 chr4A 94.059 101 4 2 5045 5144 703413136 703413235 1.040000e-32 152
17 TraesCS7D01G269000 chr6D 91.202 341 27 3 1 339 337237568 337237907 1.520000e-125 460
18 TraesCS7D01G269000 chr4B 90.698 344 26 6 1 340 426089321 426088980 2.550000e-123 453
19 TraesCS7D01G269000 chr4B 87.308 260 33 0 4687 4946 322656626 322656367 1.260000e-76 298
20 TraesCS7D01G269000 chr4B 91.525 118 5 2 5028 5144 322656372 322656259 2.240000e-34 158
21 TraesCS7D01G269000 chr4B 88.983 118 9 2 5028 5144 621863678 621863564 6.260000e-30 143
22 TraesCS7D01G269000 chr4D 90.643 342 28 4 1 340 126901006 126901345 9.160000e-123 451
23 TraesCS7D01G269000 chr4D 90.087 343 30 4 1 340 359207594 359207253 5.520000e-120 442
24 TraesCS7D01G269000 chr2B 90.643 342 29 3 1 340 478200522 478200862 9.160000e-123 451
25 TraesCS7D01G269000 chr5B 90.145 345 26 5 1 339 406069610 406069268 5.520000e-120 442
26 TraesCS7D01G269000 chr5B 87.372 293 31 5 3360 3651 534609912 534610199 1.250000e-86 331
27 TraesCS7D01G269000 chr1D 89.116 294 25 6 3360 3651 437805196 437805484 5.710000e-95 359
28 TraesCS7D01G269000 chr5A 90.517 232 16 5 4428 4659 37615290 37615515 9.770000e-78 302
29 TraesCS7D01G269000 chr5A 86.758 219 25 2 4709 4923 37615514 37615732 2.160000e-59 241
30 TraesCS7D01G269000 chr5A 90.533 169 14 2 4187 4353 37615092 37615260 7.820000e-54 222
31 TraesCS7D01G269000 chrUn 87.179 195 22 2 2436 2629 94388223 94388031 1.010000e-52 219
32 TraesCS7D01G269000 chrUn 87.113 194 22 2 2436 2628 94444903 94444712 3.640000e-52 217
33 TraesCS7D01G269000 chrUn 86.598 194 23 2 2436 2628 94309451 94309260 1.690000e-50 211
34 TraesCS7D01G269000 chrUn 86.598 194 23 2 2436 2628 94363574 94363383 1.690000e-50 211
35 TraesCS7D01G269000 chrUn 86.598 194 23 2 2436 2628 94412985 94412794 1.690000e-50 211
36 TraesCS7D01G269000 chrUn 86.577 149 18 1 2436 2584 470498388 470498242 4.810000e-36 163
37 TraesCS7D01G269000 chr3B 96.809 94 3 0 5561 5654 380513194 380513287 2.240000e-34 158
38 TraesCS7D01G269000 chr3B 91.089 101 7 2 5045 5144 573600358 573600457 1.050000e-27 135
39 TraesCS7D01G269000 chr6B 88.983 118 9 2 5028 5144 712640033 712640147 6.260000e-30 143


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 TraesCS7D01G269000 chr7D 253149355 253155350 5995 False 11073.000000 11073 100.000000 1 5996 1 chr7D.!!$F1 5995
1 TraesCS7D01G269000 chr7B 230206435 230213621 7186 False 1758.400000 4595 93.877000 153 5973 5 chr7B.!!$F2 5820
2 TraesCS7D01G269000 chr7B 77187227 77187786 559 False 221.666667 311 89.177667 4413 5119 3 chr7B.!!$F1 706
3 TraesCS7D01G269000 chr7A 266976191 266982219 6028 True 3011.333333 3315 93.932000 1 5982 3 chr7A.!!$R3 5981
4 TraesCS7D01G269000 chr5A 37615092 37615732 640 False 255.000000 302 89.269333 4187 4923 3 chr5A.!!$F1 736

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
385 391 0.654683 CTGGTTCAGCTTAGCATCGC 59.345 55.000 7.07 0.00 0.00 4.58 F
386 392 0.744414 TGGTTCAGCTTAGCATCGCC 60.744 55.000 7.07 4.04 0.00 5.54 F
1329 2680 1.001624 TTCAGTCGATTGCTGCGATG 58.998 50.000 7.20 0.34 40.19 3.84 F
1555 3020 4.736896 GACCGTGGGACGTCAGGC 62.737 72.222 18.91 5.18 40.58 4.85 F
2915 4412 0.108329 AGCTGCATGCCATTCTTTGC 60.108 50.000 16.68 6.58 44.23 3.68 F
4077 5625 0.174845 TATCCAGTCGTCCTTTGGCG 59.825 55.000 0.00 0.00 31.94 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1527 2992 2.431057 GTCCCACGGTCATCTCTATTGT 59.569 50.000 0.00 0.0 0.00 2.71 R
1982 3478 4.498894 TCTCTACGACTCTACCCAATCA 57.501 45.455 0.00 0.0 0.00 2.57 R
2784 4281 1.136305 GTGTCAATACTCTGCGGCCTA 59.864 52.381 0.00 0.0 0.00 3.93 R
3401 4905 0.811281 GCGTTTGGATCAGGGGAAAG 59.189 55.000 0.00 0.0 0.00 2.62 R
4845 6410 1.987807 ATGGAGGAGTGCCGATTGGG 61.988 60.000 0.00 0.0 39.96 4.12 R
5822 7398 0.817654 TTGCACGATCGACAGGAGAT 59.182 50.000 24.34 0.0 0.00 2.75 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
34 35 2.999185 ATGGAATGTGGGAAAGTGGT 57.001 45.000 0.00 0.00 0.00 4.16
48 49 2.067365 AGTGGTTGAGGGTTTTGGAC 57.933 50.000 0.00 0.00 0.00 4.02
66 67 4.517285 TGGACCAATATCTTCAAGCACTC 58.483 43.478 0.00 0.00 0.00 3.51
83 84 2.346847 CACTCGAGCAACTAAGTCATGC 59.653 50.000 13.61 0.00 40.34 4.06
249 251 3.795877 CCATGCCAACACTGAACTTTTT 58.204 40.909 0.00 0.00 0.00 1.94
278 280 9.771534 GAAATCTATCTTTGAGTAGGCATTAGT 57.228 33.333 0.00 0.00 0.00 2.24
321 327 5.862678 ATTAATTACCAAAACCATCCGGG 57.137 39.130 0.00 0.00 44.81 5.73
333 339 1.202927 CCATCCGGGGATTAGTTGCAT 60.203 52.381 0.00 0.00 31.62 3.96
360 366 3.049344 AGAAGTCAACACCCTTCTCCTT 58.951 45.455 0.00 0.00 42.86 3.36
377 383 3.790416 TTGCCGCCTGGTTCAGCTT 62.790 57.895 0.00 0.00 37.67 3.74
379 385 2.109126 GCCGCCTGGTTCAGCTTAG 61.109 63.158 0.00 0.00 37.67 2.18
385 391 0.654683 CTGGTTCAGCTTAGCATCGC 59.345 55.000 7.07 0.00 0.00 4.58
386 392 0.744414 TGGTTCAGCTTAGCATCGCC 60.744 55.000 7.07 4.04 0.00 5.54
402 408 1.593209 GCCGTTGTGGTTCTCGTCA 60.593 57.895 0.00 0.00 41.21 4.35
468 474 2.641559 GTAGATACCCGACGCCCG 59.358 66.667 0.00 0.00 38.18 6.13
535 541 2.110213 GCCGCCGACCCATTCATA 59.890 61.111 0.00 0.00 0.00 2.15
543 549 3.722147 CCGACCCATTCATAGTTCTCTG 58.278 50.000 0.00 0.00 0.00 3.35
559 565 6.763355 AGTTCTCTGTTCATCTCTTTTAGCA 58.237 36.000 0.00 0.00 0.00 3.49
565 571 7.563020 TCTGTTCATCTCTTTTAGCATGAGAT 58.437 34.615 0.00 0.00 43.90 2.75
629 635 4.733405 GTGCTAGGTTTTCTGTCAAAAACG 59.267 41.667 12.85 0.00 45.72 3.60
635 641 2.721425 TTCTGTCAAAAACGGGGTCT 57.279 45.000 0.00 0.00 34.76 3.85
650 656 2.496470 GGGGTCTAACGAGAATCAGTGT 59.504 50.000 0.00 0.00 31.96 3.55
662 669 4.748892 AGAATCAGTGTGATCTGTTACGG 58.251 43.478 0.00 0.00 35.76 4.02
665 672 1.066858 CAGTGTGATCTGTTACGGCCT 60.067 52.381 0.00 0.00 0.00 5.19
679 686 2.574018 GGCCTGCCCCAAACTCAAC 61.574 63.158 0.00 0.00 0.00 3.18
697 704 6.474630 ACTCAACAAATACCGGTACCAATTA 58.525 36.000 18.55 0.00 0.00 1.40
700 707 6.594937 TCAACAAATACCGGTACCAATTAGTC 59.405 38.462 18.55 0.00 0.00 2.59
716 2055 4.668138 TTAGTCAACCTAGCCCCAAATT 57.332 40.909 0.00 0.00 0.00 1.82
769 2108 8.752766 ACTACTTGAATTTCAGCATCATTTTG 57.247 30.769 0.00 0.00 0.00 2.44
770 2109 6.476243 ACTTGAATTTCAGCATCATTTTGC 57.524 33.333 0.00 0.00 43.09 3.68
856 2198 5.339477 TCACCCTAAGCTACTACTTTTCCT 58.661 41.667 0.00 0.00 0.00 3.36
857 2199 5.783875 TCACCCTAAGCTACTACTTTTCCTT 59.216 40.000 0.00 0.00 0.00 3.36
858 2200 6.271624 TCACCCTAAGCTACTACTTTTCCTTT 59.728 38.462 0.00 0.00 0.00 3.11
1304 2654 2.488545 TCGTCAAGCAGGTAGACTCTTC 59.511 50.000 0.00 0.00 0.00 2.87
1329 2680 1.001624 TTCAGTCGATTGCTGCGATG 58.998 50.000 7.20 0.34 40.19 3.84
1405 2760 5.600669 AAAGAAAGAGGTTTAGATGGGGT 57.399 39.130 0.00 0.00 0.00 4.95
1486 2949 7.890515 ACTTCATCACACATCGATCATAGTAT 58.109 34.615 0.00 0.00 0.00 2.12
1555 3020 4.736896 GACCGTGGGACGTCAGGC 62.737 72.222 18.91 5.18 40.58 4.85
1590 3055 9.048446 TCTTGAATATTTGTATACGGTTAAGCC 57.952 33.333 0.00 0.00 0.00 4.35
1767 3262 6.295067 GGTGGAGCAATGGTATTTTTGTAAGT 60.295 38.462 0.00 0.00 0.00 2.24
1772 3267 5.348451 GCAATGGTATTTTTGTAAGTGGCAG 59.652 40.000 0.00 0.00 0.00 4.85
1982 3478 7.496346 TCCTCCATTCAGTTTATCAGTTACT 57.504 36.000 0.00 0.00 0.00 2.24
2545 4042 9.589111 GGTGAGTTTAACCTGTTAAATTTGAAA 57.411 29.630 15.89 0.00 44.01 2.69
2576 4073 5.664457 TCGATCATGCTGTTTACTCTCATT 58.336 37.500 0.00 0.00 0.00 2.57
2596 4093 9.506018 TCTCATTTATGTTTCTTTCATCTGACA 57.494 29.630 0.00 0.00 0.00 3.58
2698 4195 7.833682 TGATACAGCCATAATTTTCTTCTTGGA 59.166 33.333 0.00 0.00 0.00 3.53
2784 4281 8.492415 TGGCAGGTAATCTTCTACTATATGTT 57.508 34.615 0.00 0.00 0.00 2.71
2789 4286 9.257428 AGGTAATCTTCTACTATATGTTAGGCC 57.743 37.037 0.00 0.00 0.00 5.19
2790 4287 8.189460 GGTAATCTTCTACTATATGTTAGGCCG 58.811 40.741 0.00 0.00 0.00 6.13
2791 4288 5.640189 TCTTCTACTATATGTTAGGCCGC 57.360 43.478 0.00 0.00 0.00 6.53
2792 4289 5.074804 TCTTCTACTATATGTTAGGCCGCA 58.925 41.667 0.00 0.00 0.00 5.69
2793 4290 5.183331 TCTTCTACTATATGTTAGGCCGCAG 59.817 44.000 0.00 0.00 0.00 5.18
2794 4291 4.659115 TCTACTATATGTTAGGCCGCAGA 58.341 43.478 0.00 0.00 0.00 4.26
2795 4292 3.944055 ACTATATGTTAGGCCGCAGAG 57.056 47.619 0.00 0.60 0.00 3.35
2843 4340 8.953507 AAAAATGTTGCTTTGAAACTTTGAAG 57.046 26.923 0.00 0.00 0.00 3.02
2863 4360 5.865013 TGAAGTATGAAATGTGCTTGCATTG 59.135 36.000 0.00 0.00 38.87 2.82
2915 4412 0.108329 AGCTGCATGCCATTCTTTGC 60.108 50.000 16.68 6.58 44.23 3.68
3169 4669 9.715121 TCGTCATATTTACCTGTTTACTCTTTT 57.285 29.630 0.00 0.00 0.00 2.27
3275 4776 4.251103 TGTGCTAGTTAGATCTGGGAGA 57.749 45.455 5.18 0.00 0.00 3.71
3345 4849 4.801164 TCTAGGAACCTGTACCATCCTAC 58.199 47.826 3.36 0.00 42.24 3.18
3346 4850 3.778622 AGGAACCTGTACCATCCTACT 57.221 47.619 4.56 0.00 40.47 2.57
3347 4851 3.375699 AGGAACCTGTACCATCCTACTG 58.624 50.000 4.56 0.00 40.47 2.74
3348 4852 3.012502 AGGAACCTGTACCATCCTACTGA 59.987 47.826 4.56 0.00 40.47 3.41
3349 4853 3.773119 GGAACCTGTACCATCCTACTGAA 59.227 47.826 0.00 0.00 0.00 3.02
3350 4854 4.224370 GGAACCTGTACCATCCTACTGAAA 59.776 45.833 0.00 0.00 0.00 2.69
3351 4855 4.820894 ACCTGTACCATCCTACTGAAAC 57.179 45.455 0.00 0.00 0.00 2.78
3352 4856 4.426704 ACCTGTACCATCCTACTGAAACT 58.573 43.478 0.00 0.00 0.00 2.66
3401 4905 1.865865 TCCGCACTCTCTTGTTCAAC 58.134 50.000 0.00 0.00 0.00 3.18
3419 4923 2.200373 ACTTTCCCCTGATCCAAACG 57.800 50.000 0.00 0.00 0.00 3.60
3428 4932 3.056607 CCCTGATCCAAACGCAAGAAATT 60.057 43.478 0.00 0.00 43.62 1.82
3454 4958 5.123936 AGTCTGTGTGGTTCTTTACTTTCC 58.876 41.667 0.00 0.00 0.00 3.13
3497 5001 3.132289 TCAGATGACGGGAAGATGGTTAC 59.868 47.826 0.00 0.00 0.00 2.50
3561 5069 3.131396 GGTTAGCATGTAATCCGTGGAG 58.869 50.000 0.00 0.00 0.00 3.86
3597 5105 6.314896 GCTATGTCATGCTTCTGAAACTTACT 59.685 38.462 0.00 0.00 0.00 2.24
3701 5209 2.158755 CCACTGTTGGGAGGTATGGATC 60.159 54.545 0.00 0.00 39.57 3.36
3719 5227 9.950496 GTATGGATCTCTGTTACCATGATTAAT 57.050 33.333 0.00 0.00 42.16 1.40
3779 5287 4.991687 TGCAGTGTGAAATCAATACGTACA 59.008 37.500 0.00 0.00 0.00 2.90
3851 5359 8.574251 TTGAGATGCTTTTTGCTAATAAGGTA 57.426 30.769 0.00 0.00 43.37 3.08
3855 5363 8.408601 AGATGCTTTTTGCTAATAAGGTATGTG 58.591 33.333 0.00 0.00 43.37 3.21
3893 5437 6.986817 ACCTCTATATGAATTCTCAACGTTGG 59.013 38.462 27.02 17.63 34.49 3.77
3903 5447 4.174411 TCTCAACGTTGGTGAGTCATAG 57.826 45.455 27.02 13.93 0.00 2.23
3967 5515 3.380004 TCACACCTGTTTGTTCCAATGTC 59.620 43.478 0.00 0.00 0.00 3.06
4077 5625 0.174845 TATCCAGTCGTCCTTTGGCG 59.825 55.000 0.00 0.00 31.94 5.69
4083 5631 1.959226 TCGTCCTTTGGCGCTTGTC 60.959 57.895 7.64 0.00 0.00 3.18
4084 5632 1.961277 CGTCCTTTGGCGCTTGTCT 60.961 57.895 7.64 0.00 0.00 3.41
4085 5633 1.507141 CGTCCTTTGGCGCTTGTCTT 61.507 55.000 7.64 0.00 0.00 3.01
4126 5674 6.547510 AGAATCTTTTCTGTTTACAGGTTGCT 59.452 34.615 9.82 0.00 43.91 3.91
4135 5683 4.274950 TGTTTACAGGTTGCTGAGTTTAGC 59.725 41.667 0.00 0.00 43.95 3.09
4318 5868 8.633075 CACAAAACTGTCATGTGTTTCTTATT 57.367 30.769 14.34 0.00 39.60 1.40
4507 6065 4.024893 CACCGTTATACCACATGCTTCATC 60.025 45.833 0.00 0.00 0.00 2.92
4676 6234 6.018589 TCTATCATGTACTACAGCATGCTC 57.981 41.667 19.68 6.00 42.53 4.26
4691 6249 4.346734 CATGCTCATGCGTTAGAAACTT 57.653 40.909 0.00 0.00 43.34 2.66
4692 6250 3.811722 TGCTCATGCGTTAGAAACTTG 57.188 42.857 0.00 0.00 43.34 3.16
4693 6251 3.398406 TGCTCATGCGTTAGAAACTTGA 58.602 40.909 0.00 0.00 43.34 3.02
4830 6395 1.153086 CCAGTACCATGGCCAGAGC 60.153 63.158 13.05 0.00 32.48 4.09
5285 6852 9.838975 TTTTGCAAACATATACTACATGTCAAG 57.161 29.630 12.39 0.00 35.58 3.02
5294 6861 6.985653 ATACTACATGTCAAGTGATAGGCT 57.014 37.500 0.00 0.00 0.00 4.58
5295 6862 5.269505 ACTACATGTCAAGTGATAGGCTC 57.730 43.478 0.00 0.00 0.00 4.70
5296 6863 3.170791 ACATGTCAAGTGATAGGCTCG 57.829 47.619 0.00 0.00 0.00 5.03
5299 6866 3.232213 TGTCAAGTGATAGGCTCGTTC 57.768 47.619 0.00 0.00 0.00 3.95
5353 6920 1.808945 CGCTCTTGCCATCTGTTCTTT 59.191 47.619 0.00 0.00 35.36 2.52
5364 6931 4.381292 CCATCTGTTCTTTGCATTCCCTTC 60.381 45.833 0.00 0.00 0.00 3.46
5388 6955 3.910490 GCGGTTTTGCTGGTGCCA 61.910 61.111 0.00 0.00 38.71 4.92
5463 7030 1.349688 CCCTTGGCCGGTATAGCATTA 59.650 52.381 1.90 0.00 0.00 1.90
5470 7037 2.678336 GCCGGTATAGCATTATTCCTGC 59.322 50.000 1.90 0.00 39.97 4.85
5492 7059 1.222936 CTACCTGCAGCTCCTTGGG 59.777 63.158 8.66 0.00 0.00 4.12
5655 7222 2.437895 GCCGTGTAAGGGGCTTCC 60.438 66.667 0.00 0.00 45.93 3.46
5676 7243 2.149803 CTGGCGTCTCCACCGTGTTA 62.150 60.000 0.00 0.00 40.72 2.41
5690 7257 2.404215 CGTGTTAGCTGTACTTGCACT 58.596 47.619 12.49 0.00 32.75 4.40
5691 7258 2.155732 CGTGTTAGCTGTACTTGCACTG 59.844 50.000 12.49 0.00 32.75 3.66
5731 7298 1.466950 GGCTTGCATTTGCGTAGTACA 59.533 47.619 0.38 0.00 45.83 2.90
5732 7299 2.095466 GGCTTGCATTTGCGTAGTACAA 60.095 45.455 0.38 0.00 45.83 2.41
5790 7357 3.548488 TTGGCTTTGGCAACTGGG 58.452 55.556 0.00 0.00 42.98 4.45
5798 7365 0.396974 TTGGCAACTGGGTTCTGCTT 60.397 50.000 0.00 0.00 36.32 3.91
5803 7370 0.538287 AACTGGGTTCTGCTTCCTGC 60.538 55.000 0.00 0.00 43.25 4.85
5918 7494 2.038814 TTGGTCGCCTCTGTCTTGCA 62.039 55.000 0.00 0.00 0.00 4.08
5949 7525 3.381590 GCCCTAGCCAAGATTTCGAAAAT 59.618 43.478 15.66 3.82 0.00 1.82
5951 7527 5.624509 GCCCTAGCCAAGATTTCGAAAATTT 60.625 40.000 15.66 9.35 0.00 1.82
5966 7542 8.527567 TTCGAAAATTTGTTCAACTTCAAACT 57.472 26.923 0.00 0.00 36.58 2.66
5982 7558 3.334691 CAAACTCAGTTTGCCGAGGATA 58.665 45.455 17.27 0.00 44.59 2.59
5983 7559 3.695830 AACTCAGTTTGCCGAGGATAA 57.304 42.857 0.00 0.00 33.36 1.75
5984 7560 3.252974 ACTCAGTTTGCCGAGGATAAG 57.747 47.619 0.00 0.00 33.36 1.73
5985 7561 2.093447 ACTCAGTTTGCCGAGGATAAGG 60.093 50.000 0.00 0.00 33.36 2.69
5986 7562 1.906574 TCAGTTTGCCGAGGATAAGGT 59.093 47.619 0.00 0.00 0.00 3.50
5987 7563 2.304761 TCAGTTTGCCGAGGATAAGGTT 59.695 45.455 0.00 0.00 0.00 3.50
5988 7564 3.081804 CAGTTTGCCGAGGATAAGGTTT 58.918 45.455 0.00 0.00 0.00 3.27
5989 7565 4.020039 TCAGTTTGCCGAGGATAAGGTTTA 60.020 41.667 0.00 0.00 0.00 2.01
5990 7566 4.332819 CAGTTTGCCGAGGATAAGGTTTAG 59.667 45.833 0.00 0.00 0.00 1.85
5991 7567 2.614829 TGCCGAGGATAAGGTTTAGC 57.385 50.000 0.00 0.00 0.00 3.09
5992 7568 1.202486 TGCCGAGGATAAGGTTTAGCG 60.202 52.381 0.00 0.00 0.00 4.26
5993 7569 1.068127 GCCGAGGATAAGGTTTAGCGA 59.932 52.381 0.00 0.00 0.00 4.93
5994 7570 2.288886 GCCGAGGATAAGGTTTAGCGAT 60.289 50.000 0.00 0.00 0.00 4.58
5995 7571 3.802675 GCCGAGGATAAGGTTTAGCGATT 60.803 47.826 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.987220 CCACATTCCATTTCGTCAAAACC 59.013 43.478 0.00 0.00 0.00 3.27
13 14 3.586429 ACCACTTTCCCACATTCCATTT 58.414 40.909 0.00 0.00 0.00 2.32
48 49 3.247173 GCTCGAGTGCTTGAAGATATTGG 59.753 47.826 15.13 0.00 0.00 3.16
66 67 5.530519 TTTTAGCATGACTTAGTTGCTCG 57.469 39.130 13.95 0.00 45.09 5.03
96 97 6.839134 AGGAAAGCCAATACTATTAAAAGGGG 59.161 38.462 0.00 0.00 36.29 4.79
125 126 5.731599 GTGATCCAAGATCACATTGAGTC 57.268 43.478 25.48 3.18 45.61 3.36
191 193 3.525609 TGTGGACCCCTCAAAATGCTATA 59.474 43.478 0.00 0.00 0.00 1.31
249 251 7.423844 TGCCTACTCAAAGATAGATTTCAGA 57.576 36.000 0.00 0.00 0.00 3.27
321 327 7.370383 TGACTTCTTGAAAATGCAACTAATCC 58.630 34.615 0.00 0.00 0.00 3.01
333 339 5.576447 GAAGGGTGTTGACTTCTTGAAAA 57.424 39.130 0.00 0.00 39.88 2.29
360 366 2.803155 CTAAGCTGAACCAGGCGGCA 62.803 60.000 13.08 0.00 40.08 5.69
377 383 1.004320 AACCACAACGGCGATGCTA 60.004 52.632 16.62 0.00 39.03 3.49
379 385 2.175811 GAACCACAACGGCGATGC 59.824 61.111 16.62 0.00 39.03 3.91
385 391 1.068474 GATGACGAGAACCACAACGG 58.932 55.000 0.00 0.00 42.50 4.44
386 392 0.708370 CGATGACGAGAACCACAACG 59.292 55.000 0.00 0.00 42.66 4.10
402 408 2.289002 GGTCTATACGTTCACCGACGAT 59.711 50.000 0.00 0.00 45.47 3.73
533 539 8.535335 TGCTAAAAGAGATGAACAGAGAACTAT 58.465 33.333 0.00 0.00 0.00 2.12
535 541 6.763355 TGCTAAAAGAGATGAACAGAGAACT 58.237 36.000 0.00 0.00 0.00 3.01
559 565 2.812836 TCCATGCCAACACATCTCAT 57.187 45.000 0.00 0.00 0.00 2.90
565 571 6.047870 GCAAATAAATATCCATGCCAACACA 58.952 36.000 0.00 0.00 0.00 3.72
629 635 2.496470 ACACTGATTCTCGTTAGACCCC 59.504 50.000 0.00 0.00 0.00 4.95
635 641 5.644977 ACAGATCACACTGATTCTCGTTA 57.355 39.130 0.00 0.00 37.20 3.18
650 656 1.220749 GGCAGGCCGTAACAGATCA 59.779 57.895 0.00 0.00 0.00 2.92
662 669 1.398958 TTGTTGAGTTTGGGGCAGGC 61.399 55.000 0.00 0.00 0.00 4.85
665 672 2.630580 GGTATTTGTTGAGTTTGGGGCA 59.369 45.455 0.00 0.00 0.00 5.36
679 686 6.183360 GGTTGACTAATTGGTACCGGTATTTG 60.183 42.308 19.19 12.14 0.00 2.32
697 704 3.542969 AAATTTGGGGCTAGGTTGACT 57.457 42.857 0.00 0.00 0.00 3.41
700 707 6.365520 AGATAGTAAATTTGGGGCTAGGTTG 58.634 40.000 0.00 0.00 0.00 3.77
716 2055 9.378551 ACGATTGAGTTAATTGCAAGATAGTAA 57.621 29.630 4.94 0.00 34.07 2.24
737 2076 7.667043 TGCTGAAATTCAAGTAGTTACGATT 57.333 32.000 0.00 0.00 0.00 3.34
755 2094 3.671433 GCTCTTCGCAAAATGATGCTGAA 60.671 43.478 1.99 6.00 44.21 3.02
768 2107 2.254546 TTTTCTTCAGGCTCTTCGCA 57.745 45.000 0.00 0.00 41.67 5.10
769 2108 2.096657 GGATTTTCTTCAGGCTCTTCGC 59.903 50.000 0.00 0.00 38.13 4.70
770 2109 2.349886 CGGATTTTCTTCAGGCTCTTCG 59.650 50.000 0.00 0.00 0.00 3.79
1329 2680 3.156334 CGTAGCAACGCAGTGGAC 58.844 61.111 0.00 0.00 45.00 4.02
1389 2744 5.074746 ACAAAAACCCCATCTAAACCTCT 57.925 39.130 0.00 0.00 0.00 3.69
1405 2760 3.563808 CCATCTCCACGTCTCAACAAAAA 59.436 43.478 0.00 0.00 0.00 1.94
1486 2949 3.932545 ACTAAATTTGCCAACGCATGA 57.067 38.095 0.00 0.00 46.67 3.07
1527 2992 2.431057 GTCCCACGGTCATCTCTATTGT 59.569 50.000 0.00 0.00 0.00 2.71
1555 3020 9.683069 GTATACAAATATTCAAGAAAGCCATGG 57.317 33.333 7.63 7.63 0.00 3.66
1772 3267 4.670227 AAAAAGTTGCAGATCTACGAGC 57.330 40.909 0.00 0.00 0.00 5.03
1923 3419 5.621422 CCAAATGTTGATGACTTGACGTAG 58.379 41.667 0.00 0.00 0.00 3.51
1982 3478 4.498894 TCTCTACGACTCTACCCAATCA 57.501 45.455 0.00 0.00 0.00 2.57
2292 3789 8.684520 GGTAAAGCTAGTACAGAGAGTCAATTA 58.315 37.037 9.13 0.00 0.00 1.40
2431 3928 6.207417 CACTGAAGTAAAATTCCACCTGTCAT 59.793 38.462 0.00 0.00 0.00 3.06
2576 4073 8.579006 AGCAAATGTCAGATGAAAGAAACATAA 58.421 29.630 0.00 0.00 0.00 1.90
2596 4093 7.521871 TTTTAATTGATTTTGGCCAGCAAAT 57.478 28.000 14.03 14.03 0.00 2.32
2784 4281 1.136305 GTGTCAATACTCTGCGGCCTA 59.864 52.381 0.00 0.00 0.00 3.93
2787 4284 1.656652 ATGTGTCAATACTCTGCGGC 58.343 50.000 0.00 0.00 0.00 6.53
2788 4285 2.282555 CGAATGTGTCAATACTCTGCGG 59.717 50.000 0.00 0.00 0.00 5.69
2789 4286 3.179048 TCGAATGTGTCAATACTCTGCG 58.821 45.455 0.00 0.00 0.00 5.18
2790 4287 5.530519 TTTCGAATGTGTCAATACTCTGC 57.469 39.130 0.00 0.00 0.00 4.26
2791 4288 6.963242 CCATTTTCGAATGTGTCAATACTCTG 59.037 38.462 0.00 0.00 0.00 3.35
2792 4289 6.878923 TCCATTTTCGAATGTGTCAATACTCT 59.121 34.615 0.00 0.00 0.00 3.24
2793 4290 7.072177 TCCATTTTCGAATGTGTCAATACTC 57.928 36.000 0.00 0.00 0.00 2.59
2794 4291 7.447374 TTCCATTTTCGAATGTGTCAATACT 57.553 32.000 0.00 0.00 0.00 2.12
2795 4292 8.514136 TTTTCCATTTTCGAATGTGTCAATAC 57.486 30.769 0.00 0.00 0.00 1.89
2834 4331 6.421801 GCAAGCACATTTCATACTTCAAAGTT 59.578 34.615 0.00 0.00 40.37 2.66
2843 4340 5.634439 TCAACAATGCAAGCACATTTCATAC 59.366 36.000 0.00 0.00 38.19 2.39
2915 4412 2.524569 ACCCAAATGGAAAAAGCACG 57.475 45.000 0.00 0.00 37.39 5.34
3169 4669 8.006298 ACGGAAAGAATATGCATATCCAAAAA 57.994 30.769 19.35 0.00 0.00 1.94
3316 4817 5.152934 TGGTACAGGTTCCTAGAAACTTCT 58.847 41.667 0.00 0.00 41.24 2.85
3317 4818 5.479124 TGGTACAGGTTCCTAGAAACTTC 57.521 43.478 0.00 0.00 0.00 3.01
3322 4826 4.348020 AGGATGGTACAGGTTCCTAGAA 57.652 45.455 0.00 0.00 42.88 2.10
3345 4849 5.811613 CAGGATAGCTCTTTCAGAGTTTCAG 59.188 44.000 0.00 0.00 44.12 3.02
3346 4850 5.247110 ACAGGATAGCTCTTTCAGAGTTTCA 59.753 40.000 0.00 0.00 44.12 2.69
3347 4851 5.580297 CACAGGATAGCTCTTTCAGAGTTTC 59.420 44.000 0.00 0.00 44.12 2.78
3348 4852 5.247110 TCACAGGATAGCTCTTTCAGAGTTT 59.753 40.000 0.00 0.00 44.12 2.66
3349 4853 4.774726 TCACAGGATAGCTCTTTCAGAGTT 59.225 41.667 0.00 0.00 44.12 3.01
3350 4854 4.348486 TCACAGGATAGCTCTTTCAGAGT 58.652 43.478 0.00 0.00 44.12 3.24
3351 4855 4.998671 TCACAGGATAGCTCTTTCAGAG 57.001 45.455 0.00 0.00 45.04 3.35
3352 4856 6.779539 TGATATCACAGGATAGCTCTTTCAGA 59.220 38.462 0.00 0.00 41.78 3.27
3392 4896 3.507622 GGATCAGGGGAAAGTTGAACAAG 59.492 47.826 0.00 0.00 0.00 3.16
3393 4897 3.117322 TGGATCAGGGGAAAGTTGAACAA 60.117 43.478 0.00 0.00 0.00 2.83
3401 4905 0.811281 GCGTTTGGATCAGGGGAAAG 59.189 55.000 0.00 0.00 0.00 2.62
3419 4923 6.743575 ACCACACAGACTATAATTTCTTGC 57.256 37.500 0.00 0.00 0.00 4.01
3428 4932 8.092687 GGAAAGTAAAGAACCACACAGACTATA 58.907 37.037 0.00 0.00 0.00 1.31
3497 5001 4.421479 AGAAGGGCACTCGTCGCG 62.421 66.667 0.00 0.00 0.00 5.87
3561 5069 6.857777 AGCATGACATAGCAAATAGAAGAC 57.142 37.500 0.00 0.00 0.00 3.01
3681 5189 2.774234 AGATCCATACCTCCCAACAGTG 59.226 50.000 0.00 0.00 0.00 3.66
3719 5227 4.218200 CAGTCTTCAACATTGCACCCATAA 59.782 41.667 0.00 0.00 0.00 1.90
3882 5426 3.614150 GCTATGACTCACCAACGTTGAGA 60.614 47.826 29.35 22.82 34.13 3.27
3885 5429 2.412870 TGCTATGACTCACCAACGTTG 58.587 47.619 21.47 21.47 0.00 4.10
3893 5437 4.987912 GGAAGAAGCTATGCTATGACTCAC 59.012 45.833 0.00 0.00 38.25 3.51
3930 5474 8.691661 AACAGGTGTGAAAATATCTTACAACT 57.308 30.769 0.00 0.00 39.70 3.16
3967 5515 3.120121 GCAAGCACAGCAAAATAGAAACG 59.880 43.478 0.00 0.00 0.00 3.60
4077 5625 9.319143 TCTTCTTTTATATGCTAGAAGACAAGC 57.681 33.333 15.53 0.00 44.50 4.01
4126 5674 2.434185 CTGCCGCCGCTAAACTCA 60.434 61.111 0.00 0.00 35.36 3.41
4135 5683 3.121030 CTCCAGTTTCTGCCGCCG 61.121 66.667 0.00 0.00 0.00 6.46
4283 5831 4.869215 TGACAGTTTTGTGTGCATTATGG 58.131 39.130 0.00 0.00 37.76 2.74
4316 5866 9.153479 AGATCTAGCCAGAATAGTAAGACAAAT 57.847 33.333 0.00 0.00 33.50 2.32
4318 5868 9.815306 ATAGATCTAGCCAGAATAGTAAGACAA 57.185 33.333 8.70 0.00 33.50 3.18
4425 5975 8.821147 TTTAAACGTAATCTTCACTAAGCAGA 57.179 30.769 0.00 0.00 32.36 4.26
4494 6052 3.785486 TCTTCTACGATGAAGCATGTGG 58.215 45.455 14.14 0.00 42.15 4.17
4507 6065 7.132213 TGTGAAAAAGAAAAGCATCTTCTACG 58.868 34.615 0.68 0.00 38.69 3.51
4676 6234 9.003112 CATTCTTAATCAAGTTTCTAACGCATG 57.997 33.333 0.00 0.00 36.23 4.06
4691 6249 8.281531 ACCCATTAGACAATCCATTCTTAATCA 58.718 33.333 0.00 0.00 0.00 2.57
4692 6250 8.697507 ACCCATTAGACAATCCATTCTTAATC 57.302 34.615 0.00 0.00 0.00 1.75
4693 6251 8.917088 CAACCCATTAGACAATCCATTCTTAAT 58.083 33.333 0.00 0.00 0.00 1.40
4845 6410 1.987807 ATGGAGGAGTGCCGATTGGG 61.988 60.000 0.00 0.00 39.96 4.12
4974 6539 0.959372 AAGCATCAGACAGCACTGCC 60.959 55.000 0.00 0.00 37.75 4.85
5191 6756 6.018669 AGACTTCTTTCTGTTGATTTGTCGAC 60.019 38.462 9.11 9.11 0.00 4.20
5258 6823 9.619316 TTGACATGTAGTATATGTTTGCAAAAC 57.381 29.630 14.67 8.16 38.78 2.43
5285 6852 3.860536 GTGAAGAAGAACGAGCCTATCAC 59.139 47.826 0.00 0.00 0.00 3.06
5294 6861 2.545952 GCAGACCAGTGAAGAAGAACGA 60.546 50.000 0.00 0.00 0.00 3.85
5295 6862 1.795286 GCAGACCAGTGAAGAAGAACG 59.205 52.381 0.00 0.00 0.00 3.95
5296 6863 2.838736 TGCAGACCAGTGAAGAAGAAC 58.161 47.619 0.00 0.00 0.00 3.01
5299 6866 2.291741 GGTTTGCAGACCAGTGAAGAAG 59.708 50.000 21.05 0.00 39.57 2.85
5335 6902 2.555325 TGCAAAGAACAGATGGCAAGAG 59.445 45.455 0.00 0.00 0.00 2.85
5353 6920 2.751436 GCCAGCGAAGGGAATGCA 60.751 61.111 0.00 0.00 0.00 3.96
5456 7023 4.846367 AGGTAGATGGCAGGAATAATGCTA 59.154 41.667 0.00 0.00 43.35 3.49
5463 7030 1.216064 TGCAGGTAGATGGCAGGAAT 58.784 50.000 0.00 0.00 32.95 3.01
5470 7037 0.835941 AAGGAGCTGCAGGTAGATGG 59.164 55.000 20.22 0.00 0.00 3.51
5676 7243 2.924185 CAGCAGTGCAAGTACAGCT 58.076 52.632 19.20 2.59 43.09 4.24
5731 7298 2.546494 GCAAGGCACACTCGCACTT 61.546 57.895 0.00 0.00 0.00 3.16
5732 7299 2.974698 GCAAGGCACACTCGCACT 60.975 61.111 0.00 0.00 0.00 4.40
5785 7352 1.073897 GCAGGAAGCAGAACCCAGT 59.926 57.895 0.00 0.00 44.79 4.00
5816 7392 1.069296 CGATCGACAGGAGATCAGCTC 60.069 57.143 10.26 0.00 43.35 4.09
5822 7398 0.817654 TTGCACGATCGACAGGAGAT 59.182 50.000 24.34 0.00 0.00 2.75
5833 7409 2.437359 GAGCCAGCCTTGCACGAT 60.437 61.111 0.00 0.00 0.00 3.73
5918 7494 2.041620 TCTTGGCTAGGGCAGTTCATTT 59.958 45.455 0.00 0.00 39.75 2.32
5966 7542 1.906574 ACCTTATCCTCGGCAAACTGA 59.093 47.619 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.