Multiple sequence alignment - TraesCS1A01G189100

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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 TraesCS1A01G189100 chr1A 100.000 6312 0 0 1 6312 342386353 342392664 0.000000e+00 11657.0
1 TraesCS1A01G189100 chr1D 94.938 3793 106 38 484 4219 258582295 258578532 0.000000e+00 5862.0
2 TraesCS1A01G189100 chr1D 96.029 2065 51 8 4262 6312 258578533 258576486 0.000000e+00 3330.0
3 TraesCS1A01G189100 chr1D 94.277 332 12 7 1 328 258582667 258582339 9.450000e-138 501.0
4 TraesCS1A01G189100 chr1D 93.023 86 6 0 326 411 50949109 50949024 6.640000e-25 126.0
5 TraesCS1A01G189100 chr1B 94.481 2265 71 22 583 2823 354228022 354230256 0.000000e+00 3441.0
6 TraesCS1A01G189100 chr1B 96.286 1454 39 5 3964 5414 354231810 354233251 0.000000e+00 2372.0
7 TraesCS1A01G189100 chr1B 95.856 1086 39 5 2812 3895 354230322 354231403 0.000000e+00 1751.0
8 TraesCS1A01G189100 chr1B 97.112 831 23 1 5446 6276 354233459 354234288 0.000000e+00 1400.0
9 TraesCS1A01G189100 chr1B 91.705 217 5 8 1 211 354227342 354227551 8.010000e-74 289.0
10 TraesCS1A01G189100 chr1B 85.000 180 22 5 410 586 354227765 354227942 1.810000e-40 178.0
11 TraesCS1A01G189100 chr1B 96.512 86 1 1 3893 3978 354231563 354231646 2.370000e-29 141.0
12 TraesCS1A01G189100 chr1B 90.123 81 8 0 5365 5445 354929293 354929373 8.650000e-19 106.0
13 TraesCS1A01G189100 chr1B 100.000 40 0 0 6273 6312 354234396 354234435 2.440000e-09 75.0
14 TraesCS1A01G189100 chr5B 96.512 86 3 0 326 411 372164485 372164570 6.600000e-30 143.0
15 TraesCS1A01G189100 chr5B 92.045 88 6 1 324 411 641394184 641394098 8.590000e-24 122.0
16 TraesCS1A01G189100 chr5B 88.060 67 8 0 5379 5445 304270727 304270661 5.250000e-11 80.5
17 TraesCS1A01G189100 chr3B 92.222 90 7 0 326 415 58087651 58087740 1.850000e-25 128.0
18 TraesCS1A01G189100 chr3B 93.103 87 6 0 326 412 458191848 458191762 1.850000e-25 128.0
19 TraesCS1A01G189100 chr6A 93.023 86 6 0 326 411 104518772 104518687 6.640000e-25 126.0
20 TraesCS1A01G189100 chr4B 93.023 86 6 0 326 411 323790964 323791049 6.640000e-25 126.0
21 TraesCS1A01G189100 chr4B 90.625 96 7 2 317 411 595701711 595701805 6.640000e-25 126.0
22 TraesCS1A01G189100 chr4B 87.500 80 10 0 5366 5445 15429045 15428966 6.740000e-15 93.5
23 TraesCS1A01G189100 chr7D 88.350 103 9 2 309 411 30997899 30997998 3.090000e-23 121.0
24 TraesCS1A01G189100 chr5A 94.030 67 4 0 5379 5445 356137353 356137287 1.120000e-17 102.0
25 TraesCS1A01G189100 chr5A 85.246 61 8 1 5379 5439 311947309 311947250 1.900000e-05 62.1
26 TraesCS1A01G189100 chr5D 80.992 121 17 5 5367 5483 223642930 223643048 2.420000e-14 91.6
27 TraesCS1A01G189100 chr4A 100.000 29 0 0 5363 5391 565304095 565304123 3.000000e-03 54.7
28 TraesCS1A01G189100 chr2A 100.000 28 0 0 5390 5417 318377907 318377880 1.100000e-02 52.8


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 TraesCS1A01G189100 chr1A 342386353 342392664 6311 False 11657.000 11657 100.000000 1 6312 1 chr1A.!!$F1 6311
1 TraesCS1A01G189100 chr1D 258576486 258582667 6181 True 3231.000 5862 95.081333 1 6312 3 chr1D.!!$R2 6311
2 TraesCS1A01G189100 chr1B 354227342 354234435 7093 False 1205.875 3441 94.619000 1 6312 8 chr1B.!!$F2 6311

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
769 1093 1.003118 TCAGTAAGCACCATCACACCC 59.997 52.381 0.00 0.00 0.00 4.61 F
1387 1727 0.179119 ATTCTATATACGCGCCCGCC 60.179 55.000 5.73 0.00 38.22 6.13 F
1969 2314 1.069364 GCTGACTGCTGCTTCTGTTTC 60.069 52.381 0.00 0.00 38.95 2.78 F
3211 3639 1.956477 CACAAGGGTGCTAGCAGTTTT 59.044 47.619 20.03 9.62 38.37 2.43 F
3674 4102 1.189752 TTGTGCAGTTTGCCTGGAAA 58.810 45.000 0.00 0.00 43.76 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1969 2314 0.879090 GGTAACCTTCCAAGCAACCG 59.121 55.000 0.00 0.0 0.00 4.44 R
3021 3448 2.758089 GCTCATCAGTGGCAAGGCG 61.758 63.158 0.00 0.0 0.00 5.52 R
3485 3913 2.763249 GGTGTCTGAACAACAAGCAG 57.237 50.000 0.00 0.0 42.99 4.24 R
4230 5048 0.107456 AACTCACTCCACACAGGCAG 59.893 55.000 0.00 0.0 37.29 4.85 R
5570 6569 0.456824 CAGCGTCTGTGCGTACTGAT 60.457 55.000 15.58 0.0 40.67 2.90 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
88 89 5.456822 CGACCTGCTTTCTTTTCTTTTCTTG 59.543 40.000 0.00 0.00 0.00 3.02
153 154 3.683587 GATTTGCGAGCGCCCAACC 62.684 63.158 12.70 0.00 41.09 3.77
178 179 1.072505 CCGCCCGCCTACCATATTT 59.927 57.895 0.00 0.00 0.00 1.40
198 402 9.012161 CATATTTGACCCCATTTTTGTTTCATT 57.988 29.630 0.00 0.00 0.00 2.57
300 506 3.872459 TTGGCCCCATTTTTGTTTCAT 57.128 38.095 0.00 0.00 0.00 2.57
335 541 7.443259 TTTTTCTTAATGGTTACTTCCTCCG 57.557 36.000 0.00 0.00 0.00 4.63
336 542 5.750352 TTCTTAATGGTTACTTCCTCCGT 57.250 39.130 0.00 0.00 0.00 4.69
337 543 5.750352 TCTTAATGGTTACTTCCTCCGTT 57.250 39.130 0.00 0.00 35.14 4.44
338 544 5.727434 TCTTAATGGTTACTTCCTCCGTTC 58.273 41.667 0.00 0.00 33.32 3.95
339 545 5.482878 TCTTAATGGTTACTTCCTCCGTTCT 59.517 40.000 0.00 0.00 33.32 3.01
340 546 6.664816 TCTTAATGGTTACTTCCTCCGTTCTA 59.335 38.462 0.00 0.00 33.32 2.10
341 547 5.750352 AATGGTTACTTCCTCCGTTCTAA 57.250 39.130 0.00 0.00 0.00 2.10
342 548 5.750352 ATGGTTACTTCCTCCGTTCTAAA 57.250 39.130 0.00 0.00 0.00 1.85
343 549 5.549742 TGGTTACTTCCTCCGTTCTAAAA 57.450 39.130 0.00 0.00 0.00 1.52
344 550 6.117975 TGGTTACTTCCTCCGTTCTAAAAT 57.882 37.500 0.00 0.00 0.00 1.82
345 551 7.243604 TGGTTACTTCCTCCGTTCTAAAATA 57.756 36.000 0.00 0.00 0.00 1.40
346 552 7.325694 TGGTTACTTCCTCCGTTCTAAAATAG 58.674 38.462 0.00 0.00 0.00 1.73
347 553 7.178983 TGGTTACTTCCTCCGTTCTAAAATAGA 59.821 37.037 0.00 0.00 0.00 1.98
348 554 8.202811 GGTTACTTCCTCCGTTCTAAAATAGAT 58.797 37.037 0.00 0.00 34.22 1.98
349 555 9.032420 GTTACTTCCTCCGTTCTAAAATAGATG 57.968 37.037 0.00 0.00 34.22 2.90
350 556 7.419711 ACTTCCTCCGTTCTAAAATAGATGA 57.580 36.000 0.00 0.00 34.22 2.92
351 557 7.266400 ACTTCCTCCGTTCTAAAATAGATGAC 58.734 38.462 0.00 0.00 34.22 3.06
352 558 6.158023 TCCTCCGTTCTAAAATAGATGACC 57.842 41.667 0.00 0.00 34.22 4.02
353 559 5.070047 TCCTCCGTTCTAAAATAGATGACCC 59.930 44.000 0.00 0.00 34.22 4.46
354 560 5.163343 CCTCCGTTCTAAAATAGATGACCCA 60.163 44.000 0.00 0.00 34.22 4.51
355 561 6.302535 TCCGTTCTAAAATAGATGACCCAA 57.697 37.500 0.00 0.00 34.22 4.12
356 562 6.895782 TCCGTTCTAAAATAGATGACCCAAT 58.104 36.000 0.00 0.00 34.22 3.16
357 563 7.343357 TCCGTTCTAAAATAGATGACCCAATT 58.657 34.615 0.00 0.00 34.22 2.32
358 564 7.832187 TCCGTTCTAAAATAGATGACCCAATTT 59.168 33.333 0.00 0.00 34.22 1.82
359 565 8.466798 CCGTTCTAAAATAGATGACCCAATTTT 58.533 33.333 0.00 0.00 36.04 1.82
403 609 7.921786 ATTGAGTCATCTATTTTGAAACGGA 57.078 32.000 0.00 0.00 0.00 4.69
404 610 6.968131 TGAGTCATCTATTTTGAAACGGAG 57.032 37.500 0.00 0.00 0.00 4.63
405 611 5.874810 TGAGTCATCTATTTTGAAACGGAGG 59.125 40.000 0.00 0.00 0.00 4.30
406 612 6.049955 AGTCATCTATTTTGAAACGGAGGA 57.950 37.500 0.00 0.00 0.00 3.71
407 613 6.472887 AGTCATCTATTTTGAAACGGAGGAA 58.527 36.000 0.00 0.00 0.00 3.36
408 614 6.595716 AGTCATCTATTTTGAAACGGAGGAAG 59.404 38.462 0.00 0.00 0.00 3.46
409 615 6.371825 GTCATCTATTTTGAAACGGAGGAAGT 59.628 38.462 0.00 0.00 0.00 3.01
410 616 7.548075 GTCATCTATTTTGAAACGGAGGAAGTA 59.452 37.037 0.00 0.00 0.00 2.24
411 617 7.548075 TCATCTATTTTGAAACGGAGGAAGTAC 59.452 37.037 0.00 0.00 0.00 2.73
436 642 8.809066 ACAAGTGTATAATACAACTAGGACACA 58.191 33.333 0.00 0.00 40.93 3.72
437 643 9.084164 CAAGTGTATAATACAACTAGGACACAC 57.916 37.037 0.00 0.00 40.93 3.82
444 650 2.102588 ACAACTAGGACACACTGGACAC 59.897 50.000 0.00 0.00 0.00 3.67
447 653 1.902508 CTAGGACACACTGGACACCAT 59.097 52.381 0.00 0.00 30.82 3.55
454 660 3.264193 ACACACTGGACACCATCATACAT 59.736 43.478 0.00 0.00 30.82 2.29
455 661 3.624410 CACACTGGACACCATCATACATG 59.376 47.826 0.00 0.00 30.82 3.21
456 662 3.264193 ACACTGGACACCATCATACATGT 59.736 43.478 2.69 2.69 30.82 3.21
457 663 4.469586 ACACTGGACACCATCATACATGTA 59.530 41.667 8.27 8.27 30.82 2.29
458 664 5.130975 ACACTGGACACCATCATACATGTAT 59.869 40.000 12.75 12.75 30.82 2.29
459 665 5.467735 CACTGGACACCATCATACATGTATG 59.532 44.000 31.63 31.63 43.16 2.39
460 666 4.388485 TGGACACCATCATACATGTATGC 58.612 43.478 32.32 19.87 41.92 3.14
461 667 4.141528 TGGACACCATCATACATGTATGCA 60.142 41.667 32.32 23.42 41.92 3.96
462 668 5.005740 GGACACCATCATACATGTATGCAT 58.994 41.667 32.32 24.29 41.92 3.96
463 669 9.168131 CTGGACACCATCATACATGTATGCATG 62.168 44.444 32.32 30.24 44.43 4.06
480 686 9.012161 TGTATGCATGCATGTATTTATGTATGT 57.988 29.630 37.43 13.31 46.39 2.29
522 728 7.727578 TTCTAGGAATACTACACATCACCAA 57.272 36.000 0.00 0.00 0.00 3.67
525 731 5.978814 AGGAATACTACACATCACCAAGAC 58.021 41.667 0.00 0.00 0.00 3.01
610 902 1.352352 AGGTAGTGTTGCCAATCAGCT 59.648 47.619 0.00 0.00 0.00 4.24
627 919 5.818136 TCAGCTATGAATGGCAACTTTAC 57.182 39.130 0.00 0.00 36.66 2.01
684 1003 4.552166 ACAACAACTTGAAACTCATCCG 57.448 40.909 0.00 0.00 0.00 4.18
694 1013 2.270352 AACTCATCCGTCCAAGCAAA 57.730 45.000 0.00 0.00 0.00 3.68
701 1020 1.825474 TCCGTCCAAGCAAACCAAAAA 59.175 42.857 0.00 0.00 0.00 1.94
752 1076 5.152623 TCTAAACCAACTCCATCAGTCAG 57.847 43.478 0.00 0.00 32.30 3.51
760 1084 2.234908 ACTCCATCAGTCAGTAAGCACC 59.765 50.000 0.00 0.00 0.00 5.01
769 1093 1.003118 TCAGTAAGCACCATCACACCC 59.997 52.381 0.00 0.00 0.00 4.61
779 1103 1.228552 ATCACACCCCACACAAGCC 60.229 57.895 0.00 0.00 0.00 4.35
1040 1364 4.309950 AAGACGACCCACCACCGC 62.310 66.667 0.00 0.00 0.00 5.68
1387 1727 0.179119 ATTCTATATACGCGCCCGCC 60.179 55.000 5.73 0.00 38.22 6.13
1421 1761 2.222729 CGTTCGATTTGATTCACGGACC 60.223 50.000 0.00 0.00 31.59 4.46
1425 1765 1.396996 GATTTGATTCACGGACCGGTG 59.603 52.381 14.63 13.83 39.29 4.94
1653 1997 2.816087 CCTGATCTTTGCAATATCGGGG 59.184 50.000 27.60 20.68 40.89 5.73
1788 2133 7.965107 AGTCGAATCATTTAGCTGATTGTTTTC 59.035 33.333 3.83 6.32 44.00 2.29
1969 2314 1.069364 GCTGACTGCTGCTTCTGTTTC 60.069 52.381 0.00 0.00 38.95 2.78
2585 2935 3.256960 GGTGGGGGCAGTCTGGAA 61.257 66.667 1.14 0.00 0.00 3.53
2617 2967 7.364762 CCAGGTATGTTACTGTCATAAAGGAGT 60.365 40.741 0.00 0.00 32.90 3.85
2657 3007 2.858745 ACCATTTCACGCCTGTACTTT 58.141 42.857 0.00 0.00 0.00 2.66
2855 3282 5.864418 ATATTAACTTGACCGGCTCTACA 57.136 39.130 0.00 0.00 0.00 2.74
2989 3416 3.315191 ACTTTCTCCAAATTCACACACGG 59.685 43.478 0.00 0.00 0.00 4.94
3021 3448 4.023365 GCAATTCAGCCATCCAGTTATCTC 60.023 45.833 0.00 0.00 0.00 2.75
3089 3517 4.164843 ACACTCACCATACACCACTTTT 57.835 40.909 0.00 0.00 0.00 2.27
3169 3597 3.072211 TGAGTGCTGCTTGATTTCTGAG 58.928 45.455 0.00 0.00 0.00 3.35
3175 3603 6.045318 GTGCTGCTTGATTTCTGAGTCTATA 58.955 40.000 0.00 0.00 0.00 1.31
3202 3630 8.417124 TTTTTGAGAAAACACACAAGGGTGCT 62.417 38.462 1.66 0.00 42.55 4.40
3211 3639 1.956477 CACAAGGGTGCTAGCAGTTTT 59.044 47.619 20.03 9.62 38.37 2.43
3231 3659 6.604795 AGTTTTATTCTGCATACCAGCTGATT 59.395 34.615 17.39 3.91 41.20 2.57
3252 3680 9.252962 CTGATTTGGTTCTTATAATCAATTGGC 57.747 33.333 5.42 0.00 36.78 4.52
3485 3913 9.612620 CTTGACTTATTTCACCTTTGATACAAC 57.387 33.333 0.00 0.00 0.00 3.32
3492 3920 4.460263 TCACCTTTGATACAACTGCTTGT 58.540 39.130 0.00 0.00 43.39 3.16
3628 4056 2.765699 AGAATTTGGGTTGCAACACACT 59.234 40.909 33.41 23.35 43.07 3.55
3674 4102 1.189752 TTGTGCAGTTTGCCTGGAAA 58.810 45.000 0.00 0.00 43.76 3.13
3729 4162 3.968649 ACATGACACACTTTGCATGAAC 58.031 40.909 0.00 0.00 39.87 3.18
3730 4163 3.380954 ACATGACACACTTTGCATGAACA 59.619 39.130 0.00 0.00 39.87 3.18
3731 4164 4.038282 ACATGACACACTTTGCATGAACAT 59.962 37.500 0.00 0.00 39.87 2.71
3732 4165 4.652421 TGACACACTTTGCATGAACATT 57.348 36.364 0.00 0.00 0.00 2.71
3733 4166 4.361420 TGACACACTTTGCATGAACATTG 58.639 39.130 0.00 0.00 0.00 2.82
3828 4261 6.906157 AACAATTTGTCAAGAGATGGACAT 57.094 33.333 1.83 0.00 43.01 3.06
4058 4832 6.912203 TTTATCACAAACTCGAAACACTCA 57.088 33.333 0.00 0.00 0.00 3.41
4071 4845 2.969821 ACACTCAATAAGTTGGGGCA 57.030 45.000 0.00 0.00 40.26 5.36
4124 4898 6.528321 TGAGGCTCATATTTCTGTATCCTTG 58.472 40.000 14.43 0.00 0.00 3.61
4219 5037 6.367421 CAGAAACATGAAACCGAATACGAAA 58.633 36.000 0.00 0.00 42.66 3.46
4220 5038 7.021196 CAGAAACATGAAACCGAATACGAAAT 58.979 34.615 0.00 0.00 42.66 2.17
4221 5039 8.172484 CAGAAACATGAAACCGAATACGAAATA 58.828 33.333 0.00 0.00 42.66 1.40
4222 5040 8.723311 AGAAACATGAAACCGAATACGAAATAA 58.277 29.630 0.00 0.00 42.66 1.40
4223 5041 8.663771 AAACATGAAACCGAATACGAAATAAC 57.336 30.769 0.00 0.00 42.66 1.89
4224 5042 6.778108 ACATGAAACCGAATACGAAATAACC 58.222 36.000 0.00 0.00 42.66 2.85
4225 5043 6.596497 ACATGAAACCGAATACGAAATAACCT 59.404 34.615 0.00 0.00 42.66 3.50
4226 5044 6.411630 TGAAACCGAATACGAAATAACCTG 57.588 37.500 0.00 0.00 42.66 4.00
4227 5045 6.164876 TGAAACCGAATACGAAATAACCTGA 58.835 36.000 0.00 0.00 42.66 3.86
4228 5046 6.649973 TGAAACCGAATACGAAATAACCTGAA 59.350 34.615 0.00 0.00 42.66 3.02
4229 5047 6.413018 AACCGAATACGAAATAACCTGAAC 57.587 37.500 0.00 0.00 42.66 3.18
4230 5048 4.872124 ACCGAATACGAAATAACCTGAACC 59.128 41.667 0.00 0.00 42.66 3.62
4231 5049 5.114081 CCGAATACGAAATAACCTGAACCT 58.886 41.667 0.00 0.00 42.66 3.50
4232 5050 5.006358 CCGAATACGAAATAACCTGAACCTG 59.994 44.000 0.00 0.00 42.66 4.00
4233 5051 5.501897 CGAATACGAAATAACCTGAACCTGC 60.502 44.000 0.00 0.00 42.66 4.85
4234 5052 2.433436 ACGAAATAACCTGAACCTGCC 58.567 47.619 0.00 0.00 0.00 4.85
4235 5053 2.039879 ACGAAATAACCTGAACCTGCCT 59.960 45.455 0.00 0.00 0.00 4.75
4236 5054 2.420022 CGAAATAACCTGAACCTGCCTG 59.580 50.000 0.00 0.00 0.00 4.85
4237 5055 3.421844 GAAATAACCTGAACCTGCCTGT 58.578 45.455 0.00 0.00 0.00 4.00
4238 5056 2.496899 ATAACCTGAACCTGCCTGTG 57.503 50.000 0.00 0.00 0.00 3.66
4239 5057 1.136828 TAACCTGAACCTGCCTGTGT 58.863 50.000 0.00 0.00 0.00 3.72
4240 5058 0.466189 AACCTGAACCTGCCTGTGTG 60.466 55.000 0.00 0.00 0.00 3.82
4241 5059 1.601759 CCTGAACCTGCCTGTGTGG 60.602 63.158 0.00 0.00 39.35 4.17
4242 5060 1.451504 CTGAACCTGCCTGTGTGGA 59.548 57.895 0.00 0.00 38.35 4.02
4243 5061 0.604780 CTGAACCTGCCTGTGTGGAG 60.605 60.000 0.00 0.00 38.35 3.86
4244 5062 1.344953 TGAACCTGCCTGTGTGGAGT 61.345 55.000 0.00 0.00 38.35 3.85
4245 5063 0.886490 GAACCTGCCTGTGTGGAGTG 60.886 60.000 0.00 0.00 38.35 3.51
4246 5064 1.344953 AACCTGCCTGTGTGGAGTGA 61.345 55.000 0.00 0.00 38.35 3.41
4247 5065 1.004080 CCTGCCTGTGTGGAGTGAG 60.004 63.158 0.00 0.00 38.35 3.51
4248 5066 1.750930 CTGCCTGTGTGGAGTGAGT 59.249 57.895 0.00 0.00 38.35 3.41
4249 5067 0.107456 CTGCCTGTGTGGAGTGAGTT 59.893 55.000 0.00 0.00 38.35 3.01
4250 5068 0.546122 TGCCTGTGTGGAGTGAGTTT 59.454 50.000 0.00 0.00 38.35 2.66
4251 5069 1.765904 TGCCTGTGTGGAGTGAGTTTA 59.234 47.619 0.00 0.00 38.35 2.01
4252 5070 2.171659 TGCCTGTGTGGAGTGAGTTTAA 59.828 45.455 0.00 0.00 38.35 1.52
4253 5071 2.808543 GCCTGTGTGGAGTGAGTTTAAG 59.191 50.000 0.00 0.00 38.35 1.85
4254 5072 3.403038 CCTGTGTGGAGTGAGTTTAAGG 58.597 50.000 0.00 0.00 38.35 2.69
4255 5073 3.181454 CCTGTGTGGAGTGAGTTTAAGGT 60.181 47.826 0.00 0.00 38.35 3.50
4256 5074 4.451900 CTGTGTGGAGTGAGTTTAAGGTT 58.548 43.478 0.00 0.00 0.00 3.50
4257 5075 4.850680 TGTGTGGAGTGAGTTTAAGGTTT 58.149 39.130 0.00 0.00 0.00 3.27
4258 5076 5.991861 TGTGTGGAGTGAGTTTAAGGTTTA 58.008 37.500 0.00 0.00 0.00 2.01
4259 5077 6.597562 TGTGTGGAGTGAGTTTAAGGTTTAT 58.402 36.000 0.00 0.00 0.00 1.40
4260 5078 7.057894 TGTGTGGAGTGAGTTTAAGGTTTATT 58.942 34.615 0.00 0.00 0.00 1.40
4261 5079 8.212312 TGTGTGGAGTGAGTTTAAGGTTTATTA 58.788 33.333 0.00 0.00 0.00 0.98
4262 5080 9.059260 GTGTGGAGTGAGTTTAAGGTTTATTAA 57.941 33.333 0.00 0.00 0.00 1.40
4400 5218 3.187227 GTCACGAGTTCTGCATCAAATGT 59.813 43.478 0.00 0.00 0.00 2.71
4510 5328 7.438160 TGGAATAATGTCATTCACTAAGCTACG 59.562 37.037 0.07 0.00 36.77 3.51
4658 5476 1.746220 GCAGCTCTCTCTTCCGAGTTA 59.254 52.381 0.00 0.00 38.45 2.24
4952 5770 9.903682 CTGGTTGTGAATATATTTGGATTCATC 57.096 33.333 0.00 0.00 42.43 2.92
4959 5777 6.674694 ATATATTTGGATTCATCGCAGCTC 57.325 37.500 0.00 0.00 0.00 4.09
5056 5874 2.158559 TGGTGTTTTGGTGATCCATCG 58.841 47.619 0.00 0.00 43.91 3.84
5200 6020 7.554118 ACTGTTCTGTAGCTGCATGTAAATTAT 59.446 33.333 4.51 0.00 0.00 1.28
5261 6081 5.862323 CCCGGTGATAAGATTCTATGTAACG 59.138 44.000 0.00 0.00 0.00 3.18
5317 6137 6.500684 TTATGCCACAATCTCTTCAGTTTC 57.499 37.500 0.00 0.00 0.00 2.78
5341 6161 6.548622 TCTTTGTACAGTACAGTAGTGGTTCT 59.451 38.462 18.05 1.68 40.24 3.01
5426 6410 4.465632 ACGGACTACATACATGCTGAAA 57.534 40.909 3.07 0.00 0.00 2.69
5427 6411 5.023533 ACGGACTACATACATGCTGAAAT 57.976 39.130 3.07 0.00 0.00 2.17
5428 6412 6.156748 ACGGACTACATACATGCTGAAATA 57.843 37.500 3.07 0.00 0.00 1.40
5570 6569 3.824443 TCAGTCATCAGTCGTCTTTGGTA 59.176 43.478 0.00 0.00 0.00 3.25
5933 6932 2.227968 AAGCAAAGCGCACGATCGTC 62.228 55.000 19.84 12.31 46.13 4.20
5951 6950 2.654404 GCGTCAGGGTCGTATCGC 60.654 66.667 0.00 0.00 37.17 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 2.544267 GACACGGGACAAAGTTTCTGAG 59.456 50.000 0.00 0.00 0.00 3.35
88 89 0.249657 GTCCTCCGATGATGTCCAGC 60.250 60.000 0.00 0.00 0.00 4.85
237 442 6.744537 GGTATGCGTCCTACTTGTATTATACG 59.255 42.308 0.00 0.00 0.00 3.06
315 521 5.482878 AGAACGGAGGAAGTAACCATTAAGA 59.517 40.000 0.00 0.00 0.00 2.10
321 527 5.549742 TTTTAGAACGGAGGAAGTAACCA 57.450 39.130 0.00 0.00 0.00 3.67
328 534 6.407752 GGGTCATCTATTTTAGAACGGAGGAA 60.408 42.308 0.00 0.00 38.50 3.36
329 535 5.070047 GGGTCATCTATTTTAGAACGGAGGA 59.930 44.000 0.00 0.00 38.50 3.71
330 536 5.163343 TGGGTCATCTATTTTAGAACGGAGG 60.163 44.000 0.00 0.00 38.50 4.30
331 537 5.914033 TGGGTCATCTATTTTAGAACGGAG 58.086 41.667 0.00 0.00 38.50 4.63
332 538 5.943349 TGGGTCATCTATTTTAGAACGGA 57.057 39.130 0.00 0.00 38.50 4.69
333 539 7.568199 AATTGGGTCATCTATTTTAGAACGG 57.432 36.000 0.00 0.00 38.50 4.44
377 583 9.443323 TCCGTTTCAAAATAGATGACTCAATTA 57.557 29.630 0.00 0.00 0.00 1.40
378 584 8.335532 TCCGTTTCAAAATAGATGACTCAATT 57.664 30.769 0.00 0.00 0.00 2.32
379 585 7.066284 CCTCCGTTTCAAAATAGATGACTCAAT 59.934 37.037 0.00 0.00 0.00 2.57
380 586 6.371548 CCTCCGTTTCAAAATAGATGACTCAA 59.628 38.462 0.00 0.00 0.00 3.02
381 587 5.874810 CCTCCGTTTCAAAATAGATGACTCA 59.125 40.000 0.00 0.00 0.00 3.41
382 588 6.106673 TCCTCCGTTTCAAAATAGATGACTC 58.893 40.000 0.00 0.00 0.00 3.36
383 589 6.049955 TCCTCCGTTTCAAAATAGATGACT 57.950 37.500 0.00 0.00 0.00 3.41
384 590 6.371825 ACTTCCTCCGTTTCAAAATAGATGAC 59.628 38.462 0.00 0.00 0.00 3.06
385 591 6.472887 ACTTCCTCCGTTTCAAAATAGATGA 58.527 36.000 0.00 0.00 0.00 2.92
386 592 6.743575 ACTTCCTCCGTTTCAAAATAGATG 57.256 37.500 0.00 0.00 0.00 2.90
387 593 7.391620 TGTACTTCCTCCGTTTCAAAATAGAT 58.608 34.615 0.00 0.00 0.00 1.98
388 594 6.761312 TGTACTTCCTCCGTTTCAAAATAGA 58.239 36.000 0.00 0.00 0.00 1.98
389 595 7.172703 ACTTGTACTTCCTCCGTTTCAAAATAG 59.827 37.037 0.00 0.00 0.00 1.73
390 596 6.993902 ACTTGTACTTCCTCCGTTTCAAAATA 59.006 34.615 0.00 0.00 0.00 1.40
391 597 5.826208 ACTTGTACTTCCTCCGTTTCAAAAT 59.174 36.000 0.00 0.00 0.00 1.82
392 598 5.065474 CACTTGTACTTCCTCCGTTTCAAAA 59.935 40.000 0.00 0.00 0.00 2.44
393 599 4.573201 CACTTGTACTTCCTCCGTTTCAAA 59.427 41.667 0.00 0.00 0.00 2.69
394 600 4.124238 CACTTGTACTTCCTCCGTTTCAA 58.876 43.478 0.00 0.00 0.00 2.69
395 601 3.133362 ACACTTGTACTTCCTCCGTTTCA 59.867 43.478 0.00 0.00 0.00 2.69
396 602 3.725490 ACACTTGTACTTCCTCCGTTTC 58.275 45.455 0.00 0.00 0.00 2.78
397 603 3.832615 ACACTTGTACTTCCTCCGTTT 57.167 42.857 0.00 0.00 0.00 3.60
398 604 6.594788 TTATACACTTGTACTTCCTCCGTT 57.405 37.500 0.00 0.00 32.72 4.44
399 605 6.786967 ATTATACACTTGTACTTCCTCCGT 57.213 37.500 0.00 0.00 32.72 4.69
400 606 7.709947 TGTATTATACACTTGTACTTCCTCCG 58.290 38.462 0.29 0.00 32.89 4.63
401 607 9.310716 GTTGTATTATACACTTGTACTTCCTCC 57.689 37.037 4.35 0.00 38.63 4.30
410 616 8.809066 TGTGTCCTAGTTGTATTATACACTTGT 58.191 33.333 4.35 0.00 38.63 3.16
411 617 9.084164 GTGTGTCCTAGTTGTATTATACACTTG 57.916 37.037 4.35 6.90 38.63 3.16
436 642 5.614308 CATACATGTATGATGGTGTCCAGT 58.386 41.667 33.21 0.20 44.22 4.00
437 643 4.453478 GCATACATGTATGATGGTGTCCAG 59.547 45.833 38.21 15.84 44.22 3.86
454 660 9.012161 ACATACATAAATACATGCATGCATACA 57.988 29.630 31.73 21.98 34.35 2.29
458 664 9.012161 ACATACATACATAAATACATGCATGCA 57.988 29.630 26.53 25.04 34.35 3.96
499 705 7.068348 GTCTTGGTGATGTGTAGTATTCCTAGA 59.932 40.741 0.00 0.00 0.00 2.43
522 728 1.533469 CCGTCTCTTTCCCCACGTCT 61.533 60.000 0.00 0.00 0.00 4.18
525 731 0.250166 AAACCGTCTCTTTCCCCACG 60.250 55.000 0.00 0.00 0.00 4.94
610 902 3.283751 CCCGGTAAAGTTGCCATTCATA 58.716 45.455 0.00 0.00 32.69 2.15
627 919 2.511600 CGCCTTTAGTGAGCCCGG 60.512 66.667 0.00 0.00 0.00 5.73
701 1020 1.463553 CGGGCCAAGCTTTTTCACCT 61.464 55.000 4.39 0.00 0.00 4.00
752 1076 0.037590 TGGGGTGTGATGGTGCTTAC 59.962 55.000 0.00 0.00 0.00 2.34
760 1084 1.526575 GGCTTGTGTGGGGTGTGATG 61.527 60.000 0.00 0.00 0.00 3.07
779 1103 4.941325 TGAGTATAGATTAGTAGCCGCG 57.059 45.455 0.00 0.00 0.00 6.46
782 1106 7.363094 GGACCACATGAGTATAGATTAGTAGCC 60.363 44.444 0.00 0.00 0.00 3.93
907 1231 6.773976 ATTTCCATTTTCATCCTCGCTTTA 57.226 33.333 0.00 0.00 0.00 1.85
908 1232 5.665916 ATTTCCATTTTCATCCTCGCTTT 57.334 34.783 0.00 0.00 0.00 3.51
1653 1997 4.571984 ACAAGAATTCAGTTTTTGGCTTGC 59.428 37.500 8.44 0.00 36.50 4.01
1788 2133 1.949525 CATCCGCCCATCCAAGTAAAG 59.050 52.381 0.00 0.00 0.00 1.85
1835 2180 1.377725 CACCTCCCAGTGTCCATGC 60.378 63.158 0.00 0.00 32.89 4.06
1969 2314 0.879090 GGTAACCTTCCAAGCAACCG 59.121 55.000 0.00 0.00 0.00 4.44
2519 2867 4.081752 CCAGCTCCTGATCCATACAGATAC 60.082 50.000 0.00 0.00 37.54 2.24
2585 2935 7.799616 TTATGACAGTAACATACCTGGCAACAT 60.800 37.037 0.00 0.00 38.43 2.71
2617 2967 8.795842 AATGGTACTTGTCCAAAAATACGATA 57.204 30.769 0.00 0.00 38.52 2.92
2657 3007 9.634163 ATTAGAACGTATCAATACATATGCGAA 57.366 29.630 1.58 0.00 35.54 4.70
2855 3282 5.187186 ACAGGAAGATACACGTTAGGTTCAT 59.813 40.000 0.00 0.00 0.00 2.57
2989 3416 4.500375 GGATGGCTGAATTGCTGGAATAAC 60.500 45.833 0.00 0.00 0.00 1.89
3021 3448 2.758089 GCTCATCAGTGGCAAGGCG 61.758 63.158 0.00 0.00 0.00 5.52
3127 3555 8.131100 CACTCATTGTTGTTCATCAAAGTAACT 58.869 33.333 1.35 0.00 37.81 2.24
3136 3564 3.057736 AGCAGCACTCATTGTTGTTCATC 60.058 43.478 0.00 0.00 38.64 2.92
3169 3597 9.997482 TTGTGTGTTTTCTCAAAAAGTATAGAC 57.003 29.630 0.00 0.00 35.10 2.59
3175 3603 5.011635 ACCCTTGTGTGTTTTCTCAAAAAGT 59.988 36.000 0.00 0.00 35.10 2.66
3211 3639 4.823442 CCAAATCAGCTGGTATGCAGAATA 59.177 41.667 15.13 0.00 32.48 1.75
3231 3659 5.960811 TGGGCCAATTGATTATAAGAACCAA 59.039 36.000 2.13 0.00 0.00 3.67
3252 3680 3.804036 TCCGCAAGATACATAAACTGGG 58.196 45.455 0.00 0.00 43.02 4.45
3328 3756 3.620488 ACTCAAGAACAGACTTTGGCAA 58.380 40.909 0.00 0.00 0.00 4.52
3485 3913 2.763249 GGTGTCTGAACAACAAGCAG 57.237 50.000 0.00 0.00 42.99 4.24
3492 3920 7.392953 TGAAAGCATTATATGGTGTCTGAACAA 59.607 33.333 9.65 0.00 43.65 2.83
3759 4192 6.394809 TCGTTGAGCAGTCTGTAAAATATGA 58.605 36.000 0.93 0.00 0.00 2.15
4058 4832 5.025453 ACTGAATGATTGCCCCAACTTATT 58.975 37.500 0.00 0.00 0.00 1.40
4100 4874 6.528321 CAAGGATACAGAAATATGAGCCTCA 58.472 40.000 0.00 0.00 41.41 3.86
4124 4898 1.146041 TGGCATCATACGACCCTGC 59.854 57.895 0.00 0.00 0.00 4.85
4174 4948 9.679661 TTTCTGCCATTATCACTGTTTATTAGA 57.320 29.630 0.00 0.00 0.00 2.10
4219 5037 1.705186 ACACAGGCAGGTTCAGGTTAT 59.295 47.619 0.00 0.00 0.00 1.89
4220 5038 1.136828 ACACAGGCAGGTTCAGGTTA 58.863 50.000 0.00 0.00 0.00 2.85
4221 5039 0.466189 CACACAGGCAGGTTCAGGTT 60.466 55.000 0.00 0.00 0.00 3.50
4222 5040 1.149174 CACACAGGCAGGTTCAGGT 59.851 57.895 0.00 0.00 0.00 4.00
4223 5041 1.601759 CCACACAGGCAGGTTCAGG 60.602 63.158 0.00 0.00 0.00 3.86
4224 5042 0.604780 CTCCACACAGGCAGGTTCAG 60.605 60.000 0.00 0.00 37.29 3.02
4225 5043 1.344953 ACTCCACACAGGCAGGTTCA 61.345 55.000 0.00 0.00 37.29 3.18
4226 5044 0.886490 CACTCCACACAGGCAGGTTC 60.886 60.000 0.00 0.00 37.29 3.62
4227 5045 1.149174 CACTCCACACAGGCAGGTT 59.851 57.895 0.00 0.00 37.29 3.50
4228 5046 1.762522 CTCACTCCACACAGGCAGGT 61.763 60.000 0.00 0.00 37.29 4.00
4229 5047 1.004080 CTCACTCCACACAGGCAGG 60.004 63.158 0.00 0.00 37.29 4.85
4230 5048 0.107456 AACTCACTCCACACAGGCAG 59.893 55.000 0.00 0.00 37.29 4.85
4231 5049 0.546122 AAACTCACTCCACACAGGCA 59.454 50.000 0.00 0.00 37.29 4.75
4232 5050 2.543777 TAAACTCACTCCACACAGGC 57.456 50.000 0.00 0.00 37.29 4.85
4233 5051 3.181454 ACCTTAAACTCACTCCACACAGG 60.181 47.826 0.00 0.00 39.47 4.00
4234 5052 4.073293 ACCTTAAACTCACTCCACACAG 57.927 45.455 0.00 0.00 0.00 3.66
4235 5053 4.497291 AACCTTAAACTCACTCCACACA 57.503 40.909 0.00 0.00 0.00 3.72
4236 5054 7.506328 AATAAACCTTAAACTCACTCCACAC 57.494 36.000 0.00 0.00 0.00 3.82
4237 5055 9.280174 CTTAATAAACCTTAAACTCACTCCACA 57.720 33.333 0.00 0.00 0.00 4.17
4238 5056 9.281371 ACTTAATAAACCTTAAACTCACTCCAC 57.719 33.333 0.00 0.00 0.00 4.02
4239 5057 9.498176 GACTTAATAAACCTTAAACTCACTCCA 57.502 33.333 0.00 0.00 0.00 3.86
4240 5058 9.498176 TGACTTAATAAACCTTAAACTCACTCC 57.502 33.333 0.00 0.00 0.00 3.85
4400 5218 3.261643 TGGTTGAGCAAAGATAGAGAGCA 59.738 43.478 0.00 0.00 0.00 4.26
4463 5281 2.677289 CCTGCAGAGAGGGCATGGT 61.677 63.158 17.39 0.00 41.06 3.55
4510 5328 1.374758 CCTTCTGTCGGTGTGCTCC 60.375 63.158 0.00 0.00 0.00 4.70
4572 5390 2.233922 AGTCCACAGAACGGGTATTCAG 59.766 50.000 0.00 0.00 0.00 3.02
4658 5476 0.760567 TGCAGGTCAGTGGACAGACT 60.761 55.000 2.79 0.00 46.17 3.24
4920 5738 6.040842 CCAAATATATTCACAACCAGGAAGGG 59.959 42.308 0.00 0.00 43.89 3.95
4959 5777 0.873054 GCTGATCATCTCCCGCATTG 59.127 55.000 0.00 0.00 0.00 2.82
5200 6020 0.772384 ACAACCCCATCCAAACCGTA 59.228 50.000 0.00 0.00 0.00 4.02
5261 6081 3.963129 TCAGGGGGTAATTTGATGTCAC 58.037 45.455 0.00 0.00 0.00 3.67
5317 6137 6.641314 CAGAACCACTACTGTACTGTACAAAG 59.359 42.308 20.09 20.15 38.38 2.77
5341 6161 1.471287 GCATTTCATGTGAGCTCAGCA 59.529 47.619 18.89 18.00 0.00 4.41
5471 6469 5.239525 CCCTCCGTTCCAAATTCATAAGATC 59.760 44.000 0.00 0.00 0.00 2.75
5479 6477 4.594123 TTTTTCCCTCCGTTCCAAATTC 57.406 40.909 0.00 0.00 0.00 2.17
5481 6479 4.416516 AGATTTTTCCCTCCGTTCCAAAT 58.583 39.130 0.00 0.00 0.00 2.32
5570 6569 0.456824 CAGCGTCTGTGCGTACTGAT 60.457 55.000 15.58 0.00 40.67 2.90
5593 6592 3.367743 TAACAGCTCGACCGCCGT 61.368 61.111 0.00 0.00 39.75 5.68
5933 6932 2.352001 CGATACGACCCTGACGCG 60.352 66.667 3.53 3.53 0.00 6.01
5936 6935 2.025727 CGGCGATACGACCCTGAC 59.974 66.667 0.00 0.00 35.47 3.51
5951 6950 0.038709 GATCTCGATCCAAGCCTCGG 60.039 60.000 0.00 0.00 35.64 4.63


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

AutoCloner maintained by Alex Coulton.