Multiple sequence alignment - TraesCS7D01G405500

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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 TraesCS7D01G405500 chr7D 100.000 5097 0 0 1 5097 523044580 523049676 0.000000e+00 9413.0
1 TraesCS7D01G405500 chr7B 91.871 2940 183 30 1787 4699 557058271 557061181 0.000000e+00 4054.0
2 TraesCS7D01G405500 chr7B 92.465 1128 54 14 663 1782 557057119 557058223 0.000000e+00 1583.0
3 TraesCS7D01G405500 chr7B 84.646 495 46 19 31 518 557056437 557056908 2.780000e-127 466.0
4 TraesCS7D01G405500 chr7B 82.759 435 70 5 1 433 694761815 694761384 2.880000e-102 383.0
5 TraesCS7D01G405500 chr7B 81.609 435 71 8 1 432 696572431 696572003 8.120000e-93 351.0
6 TraesCS7D01G405500 chr7A 95.488 1928 69 7 2339 4257 603293109 603295027 0.000000e+00 3062.0
7 TraesCS7D01G405500 chr7A 95.361 1660 57 13 707 2353 603291439 603293091 0.000000e+00 2621.0
8 TraesCS7D01G405500 chr7A 91.206 705 58 4 1 702 603290484 603291187 0.000000e+00 955.0
9 TraesCS7D01G405500 chr7A 86.311 431 44 9 4249 4677 603296365 603296782 6.020000e-124 455.0
10 TraesCS7D01G405500 chr7A 78.636 440 80 12 1 433 207528040 207527608 3.890000e-71 279.0
11 TraesCS7D01G405500 chr7A 88.182 110 10 3 1896 2003 299329397 299329289 1.490000e-25 128.0
12 TraesCS7D01G405500 chr1D 86.183 427 28 15 1722 2126 264340605 264341022 2.820000e-117 433.0
13 TraesCS7D01G405500 chr1D 79.952 414 71 8 1 408 270233335 270232928 1.390000e-75 294.0
14 TraesCS7D01G405500 chr5D 85.315 429 30 16 1722 2126 87100072 87100491 3.670000e-111 412.0
15 TraesCS7D01G405500 chr5D 85.082 429 32 15 1722 2126 448744699 448744279 4.750000e-110 409.0
16 TraesCS7D01G405500 chr5D 84.848 429 33 15 1722 2126 399569970 399570390 2.210000e-108 403.0
17 TraesCS7D01G405500 chr5D 84.848 429 33 17 1722 2126 551597944 551598364 2.210000e-108 403.0
18 TraesCS7D01G405500 chr5D 81.436 404 71 4 1 401 332788334 332787932 1.370000e-85 327.0
19 TraesCS7D01G405500 chr3D 85.082 429 32 18 1722 2126 141517478 141517898 4.750000e-110 409.0
20 TraesCS7D01G405500 chr4D 84.615 429 34 15 1722 2126 255797132 255797552 1.030000e-106 398.0
21 TraesCS7D01G405500 chr4A 84.434 424 40 10 1722 2126 560894827 560894411 1.330000e-105 394.0
22 TraesCS7D01G405500 chr3A 84.323 421 40 10 1722 2123 6660090 6660503 6.190000e-104 388.0
23 TraesCS7D01G405500 chr1A 82.339 436 71 6 1 433 419491316 419490884 1.730000e-99 374.0
24 TraesCS7D01G405500 chr1A 83.686 331 36 7 1747 2064 107934555 107934230 3.860000e-76 296.0
25 TraesCS7D01G405500 chr3B 90.345 290 19 3 1718 1998 52422565 52422276 6.230000e-99 372.0
26 TraesCS7D01G405500 chr4B 82.258 372 60 6 1 370 585666145 585666512 2.960000e-82 316.0
27 TraesCS7D01G405500 chr2A 81.698 377 64 4 4 378 490612176 490611803 4.960000e-80 309.0
28 TraesCS7D01G405500 chr2A 85.000 160 16 4 1881 2039 306139633 306139785 6.830000e-34 156.0
29 TraesCS7D01G405500 chr2B 83.090 343 32 11 1736 2066 725306340 725306668 6.460000e-74 289.0
30 TraesCS7D01G405500 chr6B 83.523 176 15 10 1929 2099 424466725 424466559 8.840000e-33 152.0
31 TraesCS7D01G405500 chr6B 89.908 109 7 4 1892 1998 266861203 266861309 2.470000e-28 137.0
32 TraesCS7D01G405500 chr6B 85.938 128 17 1 1872 1998 247030750 247030877 8.900000e-28 135.0
33 TraesCS7D01G405500 chr5B 95.161 62 3 0 1018 1079 658542614 658542675 1.170000e-16 99.0
34 TraesCS7D01G405500 chr1B 100.000 28 0 0 1168 1195 9261424 9261397 9.000000e-03 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 TraesCS7D01G405500 chr7D 523044580 523049676 5096 False 9413.000000 9413 100.000000 1 5097 1 chr7D.!!$F1 5096
1 TraesCS7D01G405500 chr7B 557056437 557061181 4744 False 2034.333333 4054 89.660667 31 4699 3 chr7B.!!$F1 4668
2 TraesCS7D01G405500 chr7A 603290484 603296782 6298 False 1773.250000 3062 92.091500 1 4677 4 chr7A.!!$F1 4676

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
573 613 0.663153 GCATACGACCTTGGATTGGC 59.337 55.0 0.0 0.0 0.00 4.52 F
1624 1956 0.179067 GGTGGTGGTTGAGTGACGAA 60.179 55.0 0.0 0.0 0.00 3.85 F
3355 3794 0.665835 CAAAGCAGGTAAACGGCACA 59.334 50.0 0.0 0.0 43.19 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2258 2662 1.067706 TCAAAACAGAATGCGCATGGG 60.068 47.619 26.09 18.24 42.53 4.00 R
3437 3876 0.035056 CCTGGGGACACAGTTCATCC 60.035 60.000 0.34 0.00 36.75 3.51 R
4694 6490 1.202188 GCAAGAACTATTTCAGGCGGC 60.202 52.381 0.00 0.00 33.72 6.53 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
70 71 2.037251 TGAAGCATATACCTCCGAAGCC 59.963 50.000 0.00 0.00 0.00 4.35
71 72 1.717032 AGCATATACCTCCGAAGCCA 58.283 50.000 0.00 0.00 0.00 4.75
72 73 1.344763 AGCATATACCTCCGAAGCCAC 59.655 52.381 0.00 0.00 0.00 5.01
200 202 1.605710 GGCGCTGACCGTAGACTAATA 59.394 52.381 7.64 0.00 39.71 0.98
333 336 6.519382 TCAAACAATGGTCAAAATGTATGCA 58.481 32.000 0.00 0.00 0.00 3.96
357 360 1.251527 ACGCTGGATGTCCGACTCTT 61.252 55.000 0.00 0.00 39.43 2.85
364 367 2.693591 GGATGTCCGACTCTTGTATCCA 59.306 50.000 7.96 0.00 34.27 3.41
369 372 2.693591 TCCGACTCTTGTATCCATGTCC 59.306 50.000 0.00 0.00 0.00 4.02
370 373 2.430694 CCGACTCTTGTATCCATGTCCA 59.569 50.000 0.00 0.00 0.00 4.02
383 386 2.603776 GTCCACGGACTGGTCCCT 60.604 66.667 13.41 0.18 46.96 4.20
443 446 3.496884 GCGTTGAAGATGTAGGTCAAACA 59.503 43.478 0.00 0.00 33.29 2.83
572 612 2.036958 TGCATACGACCTTGGATTGG 57.963 50.000 0.00 0.00 0.00 3.16
573 613 0.663153 GCATACGACCTTGGATTGGC 59.337 55.000 0.00 0.00 0.00 4.52
589 629 2.041251 TGGCAATGCGAGATGATGAA 57.959 45.000 0.00 0.00 0.00 2.57
608 649 6.756074 TGATGAAAAAGCAAAATTGTTCGTCT 59.244 30.769 11.09 0.00 33.92 4.18
613 654 7.820044 AAAAGCAAAATTGTTCGTCTTAACA 57.180 28.000 0.00 0.00 37.58 2.41
651 692 2.995939 TCATTGAGCACGTGTTCATCTC 59.004 45.455 31.46 21.21 35.26 2.75
813 1138 3.131709 TGCTGAAAAAGACCTCCTCTG 57.868 47.619 0.00 0.00 0.00 3.35
835 1160 3.428282 AGCGGCCGCCTTTTAACG 61.428 61.111 44.47 6.94 43.17 3.18
837 1162 3.428282 CGGCCGCCTTTTAACGCT 61.428 61.111 14.67 0.00 0.00 5.07
1347 1675 1.205055 TACCTCTCTCTCTCTCCGCA 58.795 55.000 0.00 0.00 0.00 5.69
1372 1700 3.576356 CCGCACATGGTCGATGCC 61.576 66.667 9.92 0.00 35.91 4.40
1542 1873 5.876357 TCTCTTAAATGTGGTTGTTAGGCT 58.124 37.500 0.00 0.00 0.00 4.58
1575 1906 8.408601 TCGTTGGATATTTGGTTAGAGTACTAC 58.591 37.037 0.00 0.00 0.00 2.73
1624 1956 0.179067 GGTGGTGGTTGAGTGACGAA 60.179 55.000 0.00 0.00 0.00 3.85
1646 1978 5.242795 ACACAGATAACCTACCTTGCTTT 57.757 39.130 0.00 0.00 0.00 3.51
1647 1979 5.003804 ACACAGATAACCTACCTTGCTTTG 58.996 41.667 0.00 0.00 0.00 2.77
1649 1981 5.122396 CACAGATAACCTACCTTGCTTTGTC 59.878 44.000 0.00 0.00 0.00 3.18
1659 1991 3.564225 ACCTTGCTTTGTCGTTTAAGGAG 59.436 43.478 7.73 0.00 38.38 3.69
1660 1992 3.564225 CCTTGCTTTGTCGTTTAAGGAGT 59.436 43.478 0.00 0.00 37.46 3.85
1661 1993 4.753107 CCTTGCTTTGTCGTTTAAGGAGTA 59.247 41.667 0.00 0.00 37.46 2.59
1664 1996 6.295039 TGCTTTGTCGTTTAAGGAGTAAAG 57.705 37.500 14.49 14.49 32.22 1.85
1665 1997 5.818857 TGCTTTGTCGTTTAAGGAGTAAAGT 59.181 36.000 17.46 0.00 32.22 2.66
1716 2051 1.821136 CCTGATCTTGGGAAAAGGTGC 59.179 52.381 0.00 0.00 0.00 5.01
1803 2181 3.907894 TTATCCTGTTGCGTTTTGACC 57.092 42.857 0.00 0.00 0.00 4.02
1954 2342 9.235537 CAGTATGATTTATATGAGAGAGATGCG 57.764 37.037 0.00 0.00 39.69 4.73
2233 2637 4.631813 GTGCTCTCCGAATGAAACAGTAAT 59.368 41.667 0.00 0.00 0.00 1.89
2299 2703 4.257731 GAGAAAAACATCTGGGAGTCCTC 58.742 47.826 9.58 0.00 0.00 3.71
2362 2798 8.851145 TCAAACTAAGTGGTATTTGCAACATAA 58.149 29.630 0.00 0.00 33.09 1.90
2364 2800 9.471084 AAACTAAGTGGTATTTGCAACATAAAC 57.529 29.630 0.00 3.75 0.00 2.01
2924 3362 7.610305 TCCACTTTTGTTGTTTCTTTAGACTCT 59.390 33.333 0.00 0.00 0.00 3.24
2925 3363 8.244113 CCACTTTTGTTGTTTCTTTAGACTCTT 58.756 33.333 0.00 0.00 0.00 2.85
2931 3369 6.315393 TGTTGTTTCTTTAGACTCTTGGACAC 59.685 38.462 0.00 0.00 0.00 3.67
3098 3537 3.822167 TCAGATTTGAGCATGAACAGCAA 59.178 39.130 0.00 0.00 0.00 3.91
3099 3538 4.461431 TCAGATTTGAGCATGAACAGCAAT 59.539 37.500 0.00 0.00 0.00 3.56
3100 3539 5.648960 TCAGATTTGAGCATGAACAGCAATA 59.351 36.000 0.00 0.00 0.00 1.90
3101 3540 5.742453 CAGATTTGAGCATGAACAGCAATAC 59.258 40.000 0.00 0.00 0.00 1.89
3102 3541 5.416639 AGATTTGAGCATGAACAGCAATACA 59.583 36.000 0.00 0.00 0.00 2.29
3103 3542 4.690184 TTGAGCATGAACAGCAATACAG 57.310 40.909 0.00 0.00 0.00 2.74
3104 3543 2.421073 TGAGCATGAACAGCAATACAGC 59.579 45.455 0.00 0.00 0.00 4.40
3105 3544 2.421073 GAGCATGAACAGCAATACAGCA 59.579 45.455 0.00 0.00 36.85 4.41
3165 3604 9.784531 CTAATGTTCTTTCATCCACCAGTATAT 57.215 33.333 0.00 0.00 0.00 0.86
3355 3794 0.665835 CAAAGCAGGTAAACGGCACA 59.334 50.000 0.00 0.00 43.19 4.57
3402 3841 6.949715 TCCAACCATATAAACCTAAACGAGT 58.050 36.000 0.00 0.00 0.00 4.18
3437 3876 5.234329 CGTGTAAGTTGTAAGCTGATATGGG 59.766 44.000 0.00 0.00 0.00 4.00
3447 3886 3.051581 AGCTGATATGGGGATGAACTGT 58.948 45.455 0.00 0.00 0.00 3.55
3499 3938 1.233019 GCGCTCATGGCTACATCATT 58.767 50.000 0.00 0.00 39.13 2.57
3505 3944 4.517832 GCTCATGGCTACATCATTGATCAA 59.482 41.667 11.26 11.26 34.35 2.57
3658 4097 4.530857 CCGGCCATCGACCACCTC 62.531 72.222 2.24 0.00 42.43 3.85
3901 4340 2.034532 TACACACGGGAGCTCGGA 59.965 61.111 7.83 0.00 0.00 4.55
4085 4524 0.039165 GTTCCTCGGCAAGCCAAAAG 60.039 55.000 12.19 5.15 35.37 2.27
4173 4612 1.148310 AAGGTCATATACGCGCATGC 58.852 50.000 5.73 7.91 37.91 4.06
4191 4630 1.338655 TGCAGTGTACACGAGTTAGCA 59.661 47.619 19.93 18.87 36.20 3.49
4225 4671 5.478407 GGTTTGTGAAATGTATTTGGAGGG 58.522 41.667 0.00 0.00 0.00 4.30
4274 6066 2.337879 TTTCACCAAGGCCTCTGCGT 62.338 55.000 5.23 4.68 38.85 5.24
4317 6110 7.113544 GCAGAGTTTTTATTTCGGTTCTTTCTG 59.886 37.037 0.00 0.00 0.00 3.02
4487 6282 8.141835 ACTCACAATACCTTTTTGAATTTTGC 57.858 30.769 0.00 0.00 0.00 3.68
4683 6479 0.249398 AGTACTGATGGTTGGGACGC 59.751 55.000 0.00 0.00 0.00 5.19
4684 6480 0.249398 GTACTGATGGTTGGGACGCT 59.751 55.000 0.00 0.00 0.00 5.07
4708 6504 2.890474 CGCGCCGCCTGAAATAGT 60.890 61.111 2.28 0.00 0.00 2.12
4709 6505 2.461110 CGCGCCGCCTGAAATAGTT 61.461 57.895 2.28 0.00 0.00 2.24
4710 6506 1.352056 GCGCCGCCTGAAATAGTTC 59.648 57.895 0.00 0.00 0.00 3.01
4711 6507 1.090052 GCGCCGCCTGAAATAGTTCT 61.090 55.000 0.00 0.00 34.60 3.01
4712 6508 1.369625 CGCCGCCTGAAATAGTTCTT 58.630 50.000 4.35 0.00 34.60 2.52
4713 6509 1.062587 CGCCGCCTGAAATAGTTCTTG 59.937 52.381 4.35 0.00 34.60 3.02
4714 6510 1.202188 GCCGCCTGAAATAGTTCTTGC 60.202 52.381 4.35 5.92 34.60 4.01
4715 6511 2.083774 CCGCCTGAAATAGTTCTTGCA 58.916 47.619 14.39 0.00 34.60 4.08
4716 6512 2.684881 CCGCCTGAAATAGTTCTTGCAT 59.315 45.455 14.39 0.00 34.60 3.96
4717 6513 3.242870 CCGCCTGAAATAGTTCTTGCATC 60.243 47.826 14.39 0.00 34.60 3.91
4718 6514 3.544834 CGCCTGAAATAGTTCTTGCATCG 60.545 47.826 14.39 3.43 34.60 3.84
4719 6515 3.375299 GCCTGAAATAGTTCTTGCATCGT 59.625 43.478 4.35 0.00 34.60 3.73
4720 6516 4.142600 GCCTGAAATAGTTCTTGCATCGTT 60.143 41.667 4.35 0.00 34.60 3.85
4721 6517 5.619981 GCCTGAAATAGTTCTTGCATCGTTT 60.620 40.000 4.35 0.00 34.60 3.60
4722 6518 6.381801 CCTGAAATAGTTCTTGCATCGTTTT 58.618 36.000 4.35 0.00 34.60 2.43
4723 6519 6.524586 CCTGAAATAGTTCTTGCATCGTTTTC 59.475 38.462 4.35 0.00 34.60 2.29
4724 6520 7.202016 TGAAATAGTTCTTGCATCGTTTTCT 57.798 32.000 4.35 0.00 34.60 2.52
4725 6521 7.648142 TGAAATAGTTCTTGCATCGTTTTCTT 58.352 30.769 4.35 0.00 34.60 2.52
4726 6522 8.779303 TGAAATAGTTCTTGCATCGTTTTCTTA 58.221 29.630 4.35 0.00 34.60 2.10
4727 6523 9.774742 GAAATAGTTCTTGCATCGTTTTCTTAT 57.225 29.630 0.00 0.00 0.00 1.73
4728 6524 9.774742 AAATAGTTCTTGCATCGTTTTCTTATC 57.225 29.630 0.00 0.00 0.00 1.75
4729 6525 8.723942 ATAGTTCTTGCATCGTTTTCTTATCT 57.276 30.769 0.00 0.00 0.00 1.98
4730 6526 9.817809 ATAGTTCTTGCATCGTTTTCTTATCTA 57.182 29.630 0.00 0.00 0.00 1.98
4731 6527 8.190888 AGTTCTTGCATCGTTTTCTTATCTAG 57.809 34.615 0.00 0.00 0.00 2.43
4732 6528 7.819900 AGTTCTTGCATCGTTTTCTTATCTAGT 59.180 33.333 0.00 0.00 0.00 2.57
4733 6529 8.443937 GTTCTTGCATCGTTTTCTTATCTAGTT 58.556 33.333 0.00 0.00 0.00 2.24
4734 6530 8.547967 TCTTGCATCGTTTTCTTATCTAGTTT 57.452 30.769 0.00 0.00 0.00 2.66
4735 6531 8.999431 TCTTGCATCGTTTTCTTATCTAGTTTT 58.001 29.630 0.00 0.00 0.00 2.43
4736 6532 9.267096 CTTGCATCGTTTTCTTATCTAGTTTTC 57.733 33.333 0.00 0.00 0.00 2.29
4737 6533 7.453034 TGCATCGTTTTCTTATCTAGTTTTCG 58.547 34.615 0.00 0.00 0.00 3.46
4738 6534 7.117236 TGCATCGTTTTCTTATCTAGTTTTCGT 59.883 33.333 0.00 0.00 0.00 3.85
4739 6535 7.422746 GCATCGTTTTCTTATCTAGTTTTCGTG 59.577 37.037 0.00 0.00 0.00 4.35
4740 6536 6.814343 TCGTTTTCTTATCTAGTTTTCGTGC 58.186 36.000 0.00 0.00 0.00 5.34
4741 6537 5.722141 CGTTTTCTTATCTAGTTTTCGTGCG 59.278 40.000 0.00 0.00 0.00 5.34
4742 6538 6.587651 GTTTTCTTATCTAGTTTTCGTGCGT 58.412 36.000 0.00 0.00 0.00 5.24
4743 6539 6.774354 TTTCTTATCTAGTTTTCGTGCGTT 57.226 33.333 0.00 0.00 0.00 4.84
4744 6540 6.385537 TTCTTATCTAGTTTTCGTGCGTTC 57.614 37.500 0.00 0.00 0.00 3.95
4745 6541 4.860907 TCTTATCTAGTTTTCGTGCGTTCC 59.139 41.667 0.00 0.00 0.00 3.62
4746 6542 1.411394 TCTAGTTTTCGTGCGTTCCG 58.589 50.000 0.00 0.00 0.00 4.30
4747 6543 1.134226 CTAGTTTTCGTGCGTTCCGT 58.866 50.000 0.00 0.00 0.00 4.69
4748 6544 0.854062 TAGTTTTCGTGCGTTCCGTG 59.146 50.000 0.00 0.00 0.00 4.94
4749 6545 1.085501 AGTTTTCGTGCGTTCCGTGT 61.086 50.000 0.00 0.00 0.00 4.49
4750 6546 0.247775 GTTTTCGTGCGTTCCGTGTT 60.248 50.000 0.00 0.00 0.00 3.32
4751 6547 0.447011 TTTTCGTGCGTTCCGTGTTT 59.553 45.000 0.00 0.00 0.00 2.83
4752 6548 0.447011 TTTCGTGCGTTCCGTGTTTT 59.553 45.000 0.00 0.00 0.00 2.43
4753 6549 0.447011 TTCGTGCGTTCCGTGTTTTT 59.553 45.000 0.00 0.00 0.00 1.94
4779 6575 9.839817 TTATCCGATTTTCATATGGTAGTTTCA 57.160 29.630 2.13 0.00 0.00 2.69
4780 6576 8.924511 ATCCGATTTTCATATGGTAGTTTCAT 57.075 30.769 2.13 0.00 0.00 2.57
4781 6577 8.746052 TCCGATTTTCATATGGTAGTTTCATT 57.254 30.769 2.13 0.00 0.00 2.57
4782 6578 9.184523 TCCGATTTTCATATGGTAGTTTCATTT 57.815 29.630 2.13 0.00 0.00 2.32
4783 6579 9.801873 CCGATTTTCATATGGTAGTTTCATTTT 57.198 29.630 2.13 0.00 0.00 1.82
4818 6614 9.890352 TTTTTGTGTTCAATTCCTTTTTCTTTG 57.110 25.926 0.00 0.00 33.32 2.77
4819 6615 8.614469 TTTGTGTTCAATTCCTTTTTCTTTGT 57.386 26.923 0.00 0.00 33.32 2.83
4820 6616 8.614469 TTGTGTTCAATTCCTTTTTCTTTGTT 57.386 26.923 0.00 0.00 0.00 2.83
4821 6617 9.712305 TTGTGTTCAATTCCTTTTTCTTTGTTA 57.288 25.926 0.00 0.00 0.00 2.41
4822 6618 9.883142 TGTGTTCAATTCCTTTTTCTTTGTTAT 57.117 25.926 0.00 0.00 0.00 1.89
4850 6646 9.794685 TTTTTGCTTTTCTTTTTGTTTGTTTCT 57.205 22.222 0.00 0.00 0.00 2.52
4851 6647 9.794685 TTTTGCTTTTCTTTTTGTTTGTTTCTT 57.205 22.222 0.00 0.00 0.00 2.52
4903 6699 9.764363 AATAAGTCAAACATTTTCTCTTTTCCC 57.236 29.630 0.00 0.00 0.00 3.97
4904 6700 7.423844 AAGTCAAACATTTTCTCTTTTCCCT 57.576 32.000 0.00 0.00 0.00 4.20
4905 6701 7.423844 AGTCAAACATTTTCTCTTTTCCCTT 57.576 32.000 0.00 0.00 0.00 3.95
4906 6702 7.851228 AGTCAAACATTTTCTCTTTTCCCTTT 58.149 30.769 0.00 0.00 0.00 3.11
4907 6703 8.321353 AGTCAAACATTTTCTCTTTTCCCTTTT 58.679 29.630 0.00 0.00 0.00 2.27
4908 6704 8.946085 GTCAAACATTTTCTCTTTTCCCTTTTT 58.054 29.630 0.00 0.00 0.00 1.94
4913 6709 9.778741 ACATTTTCTCTTTTCCCTTTTTATTCC 57.221 29.630 0.00 0.00 0.00 3.01
4954 6750 9.829507 AAAAGTATCCAAATGTCATTTCAACAA 57.170 25.926 7.87 0.00 0.00 2.83
4955 6751 8.816640 AAGTATCCAAATGTCATTTCAACAAC 57.183 30.769 7.87 4.11 0.00 3.32
4956 6752 7.950512 AGTATCCAAATGTCATTTCAACAACA 58.049 30.769 7.87 0.00 0.00 3.33
4957 6753 8.420222 AGTATCCAAATGTCATTTCAACAACAA 58.580 29.630 7.87 0.00 0.00 2.83
4958 6754 9.039870 GTATCCAAATGTCATTTCAACAACAAA 57.960 29.630 7.87 0.00 0.00 2.83
4959 6755 7.301068 TCCAAATGTCATTTCAACAACAAAC 57.699 32.000 7.87 0.00 0.00 2.93
4960 6756 6.875726 TCCAAATGTCATTTCAACAACAAACA 59.124 30.769 7.87 0.00 0.00 2.83
4961 6757 7.388776 TCCAAATGTCATTTCAACAACAAACAA 59.611 29.630 7.87 0.00 0.00 2.83
4962 6758 8.019669 CCAAATGTCATTTCAACAACAAACAAA 58.980 29.630 7.87 0.00 0.00 2.83
4963 6759 8.838961 CAAATGTCATTTCAACAACAAACAAAC 58.161 29.630 7.87 0.00 0.00 2.93
4964 6760 7.664082 ATGTCATTTCAACAACAAACAAACA 57.336 28.000 0.00 0.00 0.00 2.83
4965 6761 7.482654 TGTCATTTCAACAACAAACAAACAA 57.517 28.000 0.00 0.00 0.00 2.83
4966 6762 8.092521 TGTCATTTCAACAACAAACAAACAAT 57.907 26.923 0.00 0.00 0.00 2.71
4967 6763 8.562892 TGTCATTTCAACAACAAACAAACAATT 58.437 25.926 0.00 0.00 0.00 2.32
5074 6870 7.088589 AGTGCATCATACACTTTTTATGTCC 57.911 36.000 0.00 0.00 46.01 4.02
5075 6871 6.658816 AGTGCATCATACACTTTTTATGTCCA 59.341 34.615 0.00 0.00 46.01 4.02
5076 6872 7.340232 AGTGCATCATACACTTTTTATGTCCAT 59.660 33.333 0.00 0.00 46.01 3.41
5077 6873 7.975616 GTGCATCATACACTTTTTATGTCCATT 59.024 33.333 0.00 0.00 35.12 3.16
5078 6874 9.183368 TGCATCATACACTTTTTATGTCCATTA 57.817 29.630 0.00 0.00 0.00 1.90
5096 6892 9.429359 TGTCCATTAATAATTTTGAAAATGCGT 57.571 25.926 3.62 0.00 0.00 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.361104 TTCCCCATGTTCGGCAGC 60.361 61.111 0.00 0.00 0.00 5.25
19 20 2.115291 GGCTCGCTTCCCCATGTTC 61.115 63.158 0.00 0.00 0.00 3.18
70 71 3.490759 GCACATCGGACTGGCGTG 61.491 66.667 0.00 0.00 0.00 5.34
257 259 5.968848 CGGTGGATTTCATATAAACCAAACG 59.031 40.000 0.00 0.00 0.00 3.60
305 307 8.702438 CATACATTTTGACCATTGTTTGAACTC 58.298 33.333 0.00 0.00 0.00 3.01
321 323 3.605056 CAGCGTTGTCTGCATACATTTTG 59.395 43.478 5.68 0.00 33.85 2.44
333 336 1.079819 CGGACATCCAGCGTTGTCT 60.080 57.895 0.00 0.00 41.55 3.41
572 612 3.242248 GCTTTTTCATCATCTCGCATTGC 59.758 43.478 0.00 0.00 0.00 3.56
573 613 4.417506 TGCTTTTTCATCATCTCGCATTG 58.582 39.130 0.00 0.00 0.00 2.82
589 629 7.820044 TGTTAAGACGAACAATTTTGCTTTT 57.180 28.000 0.00 0.00 36.39 2.27
613 654 8.632679 TGCTCAATGATGAAAGTTTTTAGTCTT 58.367 29.630 0.00 0.00 34.49 3.01
621 662 4.036734 ACACGTGCTCAATGATGAAAGTTT 59.963 37.500 17.22 0.00 34.49 2.66
622 663 3.565482 ACACGTGCTCAATGATGAAAGTT 59.435 39.130 17.22 0.00 34.49 2.66
632 673 2.998670 CTGAGATGAACACGTGCTCAAT 59.001 45.455 24.08 16.10 35.43 2.57
682 758 7.369803 TCTTCAGCTATGTGAGTTGATTTTC 57.630 36.000 0.00 0.00 44.02 2.29
822 1147 2.483745 GGAGCGTTAAAAGGCGGC 59.516 61.111 0.00 0.00 43.99 6.53
835 1160 0.248094 GAATTAAAGCGCACGGGAGC 60.248 55.000 11.47 4.76 40.48 4.70
837 1162 0.671163 ACGAATTAAAGCGCACGGGA 60.671 50.000 11.47 0.00 0.00 5.14
1372 1700 3.257624 ACAGTAAACTAGTCCGAACAGGG 59.742 47.826 0.00 0.00 41.52 4.45
1542 1873 9.451002 TCTAACCAAATATCCAACGACAAAATA 57.549 29.630 0.00 0.00 0.00 1.40
1624 1956 4.910458 AAGCAAGGTAGGTTATCTGTGT 57.090 40.909 0.00 0.00 0.00 3.72
1628 1960 4.020485 ACGACAAAGCAAGGTAGGTTATCT 60.020 41.667 0.00 0.00 0.00 1.98
1631 1963 3.756933 ACGACAAAGCAAGGTAGGTTA 57.243 42.857 0.00 0.00 0.00 2.85
1646 1978 5.750067 GTCACACTTTACTCCTTAAACGACA 59.250 40.000 0.00 0.00 0.00 4.35
1647 1979 5.750067 TGTCACACTTTACTCCTTAAACGAC 59.250 40.000 0.00 0.00 0.00 4.34
1649 1981 6.780706 ATGTCACACTTTACTCCTTAAACG 57.219 37.500 0.00 0.00 0.00 3.60
1659 1991 4.630069 AGCCGAACATATGTCACACTTTAC 59.370 41.667 9.23 0.00 0.00 2.01
1660 1992 4.827692 AGCCGAACATATGTCACACTTTA 58.172 39.130 9.23 0.00 0.00 1.85
1661 1993 3.674997 AGCCGAACATATGTCACACTTT 58.325 40.909 9.23 0.00 0.00 2.66
1664 1996 2.742053 ACAAGCCGAACATATGTCACAC 59.258 45.455 9.23 0.00 0.00 3.82
1665 1997 2.741517 CACAAGCCGAACATATGTCACA 59.258 45.455 9.23 0.00 0.00 3.58
1732 2067 8.547967 AACCACAATTGACACACTTATAGTAG 57.452 34.615 13.59 0.00 0.00 2.57
1796 2174 4.105057 ACTGTGGGTACATTAGGGTCAAAA 59.895 41.667 0.00 0.00 35.97 2.44
1803 2181 3.118738 GGTCAGACTGTGGGTACATTAGG 60.119 52.174 1.59 0.00 35.97 2.69
1954 2342 6.077838 CACTAAAACTACTTGCGAATCCAAC 58.922 40.000 0.00 0.00 0.00 3.77
2066 2458 7.663043 ACTGGTCCCTTTTATTTTTGTTACA 57.337 32.000 0.00 0.00 0.00 2.41
2258 2662 1.067706 TCAAAACAGAATGCGCATGGG 60.068 47.619 26.09 18.24 42.53 4.00
2364 2800 8.868916 CCCTTGTTCAATATGTAAATTTTTCCG 58.131 33.333 0.00 0.00 0.00 4.30
2924 3362 7.390440 AGAAAACTATGAATCAATCGTGTCCAA 59.610 33.333 0.00 0.00 0.00 3.53
2925 3363 6.878923 AGAAAACTATGAATCAATCGTGTCCA 59.121 34.615 0.00 0.00 0.00 4.02
2976 3414 3.745975 TGCGGTCTTCTATGTTTTCACAG 59.254 43.478 0.00 0.00 35.94 3.66
3099 3538 9.786105 CAACAAATGATATGTTTACATGCTGTA 57.214 29.630 5.64 0.00 38.90 2.74
3100 3539 8.306038 ACAACAAATGATATGTTTACATGCTGT 58.694 29.630 5.64 0.00 38.90 4.40
3101 3540 8.692110 ACAACAAATGATATGTTTACATGCTG 57.308 30.769 5.64 0.00 38.90 4.41
3102 3541 8.742777 AGACAACAAATGATATGTTTACATGCT 58.257 29.630 5.64 0.00 38.90 3.79
3103 3542 8.915871 AGACAACAAATGATATGTTTACATGC 57.084 30.769 5.64 0.00 38.90 4.06
3104 3543 9.507280 GGAGACAACAAATGATATGTTTACATG 57.493 33.333 5.64 0.00 38.90 3.21
3105 3544 9.241919 TGGAGACAACAAATGATATGTTTACAT 57.758 29.630 0.53 0.53 38.90 2.29
3355 3794 6.705825 GGATGCAAAGGTTTGTGAATTTAAGT 59.294 34.615 4.45 0.00 40.24 2.24
3402 3841 0.752054 ACTTACACGGGTCGTTTCCA 59.248 50.000 0.00 0.00 38.32 3.53
3437 3876 0.035056 CCTGGGGACACAGTTCATCC 60.035 60.000 0.34 0.00 36.75 3.51
3447 3886 1.682849 CCATCGAAACCTGGGGACA 59.317 57.895 0.00 0.00 39.59 4.02
3658 4097 0.591741 GGTTCGAGTCATAGGCGTCG 60.592 60.000 0.00 0.00 0.00 5.12
3889 4328 4.361971 TCCAGTCCGAGCTCCCGT 62.362 66.667 8.47 0.00 0.00 5.28
3901 4340 2.681778 CTCTCCACCGCCTCCAGT 60.682 66.667 0.00 0.00 0.00 4.00
4054 4493 0.744414 CGAGGAACGGGTAGTCGGTA 60.744 60.000 0.00 0.00 38.46 4.02
4081 4520 0.110238 CACACTACATGCGCGCTTTT 60.110 50.000 33.29 21.40 0.00 2.27
4085 4524 1.343821 GTACACACTACATGCGCGC 59.656 57.895 27.26 27.26 0.00 6.86
4173 4612 4.324669 CAGATTGCTAACTCGTGTACACTG 59.675 45.833 23.01 17.14 0.00 3.66
4191 4630 5.776716 ACATTTCACAAACCCATCTCAGATT 59.223 36.000 0.00 0.00 0.00 2.40
4274 6066 2.342279 CTCACGGAGTTGGCGGAA 59.658 61.111 0.00 0.00 41.61 4.30
4287 6079 5.358298 ACCGAAATAAAAACTCTGCTCAC 57.642 39.130 0.00 0.00 0.00 3.51
4485 6280 6.380095 AAAAGTAGAAACCGTTATGTTGCA 57.620 33.333 0.00 0.00 0.00 4.08
4550 6345 4.086457 TGCTGAAAAAGGGGGAAATCTAC 58.914 43.478 0.00 0.00 0.00 2.59
4553 6348 4.558226 ATTGCTGAAAAAGGGGGAAATC 57.442 40.909 0.00 0.00 0.00 2.17
4610 6406 4.275689 CCTGCGCTCCATTTATTACAATGA 59.724 41.667 9.73 0.00 36.39 2.57
4616 6412 1.225855 CGCCTGCGCTCCATTTATTA 58.774 50.000 9.73 0.00 0.00 0.98
4645 6441 4.047627 ACTATAGCAAAGGGCCAAAGTT 57.952 40.909 6.18 0.00 46.50 2.66
4655 6451 5.760253 CCCAACCATCAGTACTATAGCAAAG 59.240 44.000 0.00 0.00 0.00 2.77
4694 6490 1.202188 GCAAGAACTATTTCAGGCGGC 60.202 52.381 0.00 0.00 33.72 6.53
4699 6495 7.301054 AGAAAACGATGCAAGAACTATTTCAG 58.699 34.615 0.00 0.00 33.72 3.02
4700 6496 7.202016 AGAAAACGATGCAAGAACTATTTCA 57.798 32.000 0.00 0.00 33.72 2.69
4701 6497 9.774742 ATAAGAAAACGATGCAAGAACTATTTC 57.225 29.630 0.00 0.00 0.00 2.17
4702 6498 9.774742 GATAAGAAAACGATGCAAGAACTATTT 57.225 29.630 0.00 0.00 0.00 1.40
4703 6499 9.167311 AGATAAGAAAACGATGCAAGAACTATT 57.833 29.630 0.00 0.00 0.00 1.73
4704 6500 8.723942 AGATAAGAAAACGATGCAAGAACTAT 57.276 30.769 0.00 0.00 0.00 2.12
4705 6501 9.302345 CTAGATAAGAAAACGATGCAAGAACTA 57.698 33.333 0.00 0.00 0.00 2.24
4706 6502 7.819900 ACTAGATAAGAAAACGATGCAAGAACT 59.180 33.333 0.00 0.00 0.00 3.01
4707 6503 7.965045 ACTAGATAAGAAAACGATGCAAGAAC 58.035 34.615 0.00 0.00 0.00 3.01
4708 6504 8.547967 AACTAGATAAGAAAACGATGCAAGAA 57.452 30.769 0.00 0.00 0.00 2.52
4709 6505 8.547967 AAACTAGATAAGAAAACGATGCAAGA 57.452 30.769 0.00 0.00 0.00 3.02
4710 6506 9.267096 GAAAACTAGATAAGAAAACGATGCAAG 57.733 33.333 0.00 0.00 0.00 4.01
4711 6507 7.955324 CGAAAACTAGATAAGAAAACGATGCAA 59.045 33.333 0.00 0.00 0.00 4.08
4712 6508 7.117236 ACGAAAACTAGATAAGAAAACGATGCA 59.883 33.333 0.00 0.00 0.00 3.96
4713 6509 7.422746 CACGAAAACTAGATAAGAAAACGATGC 59.577 37.037 0.00 0.00 0.00 3.91
4714 6510 7.422746 GCACGAAAACTAGATAAGAAAACGATG 59.577 37.037 0.00 0.00 0.00 3.84
4715 6511 7.453838 GCACGAAAACTAGATAAGAAAACGAT 58.546 34.615 0.00 0.00 0.00 3.73
4716 6512 6.399249 CGCACGAAAACTAGATAAGAAAACGA 60.399 38.462 0.00 0.00 0.00 3.85
4717 6513 5.722141 CGCACGAAAACTAGATAAGAAAACG 59.278 40.000 0.00 0.00 0.00 3.60
4718 6514 6.587651 ACGCACGAAAACTAGATAAGAAAAC 58.412 36.000 0.00 0.00 0.00 2.43
4719 6515 6.774354 ACGCACGAAAACTAGATAAGAAAA 57.226 33.333 0.00 0.00 0.00 2.29
4720 6516 6.128742 GGAACGCACGAAAACTAGATAAGAAA 60.129 38.462 0.00 0.00 0.00 2.52
4721 6517 5.346822 GGAACGCACGAAAACTAGATAAGAA 59.653 40.000 0.00 0.00 0.00 2.52
4722 6518 4.860907 GGAACGCACGAAAACTAGATAAGA 59.139 41.667 0.00 0.00 0.00 2.10
4723 6519 5.127371 GGAACGCACGAAAACTAGATAAG 57.873 43.478 0.00 0.00 0.00 1.73
4753 6549 9.839817 TGAAACTACCATATGAAAATCGGATAA 57.160 29.630 3.65 0.00 0.00 1.75
4755 6551 8.924511 ATGAAACTACCATATGAAAATCGGAT 57.075 30.769 3.65 0.00 0.00 4.18
4756 6552 8.746052 AATGAAACTACCATATGAAAATCGGA 57.254 30.769 3.65 0.00 0.00 4.55
4757 6553 9.801873 AAAATGAAACTACCATATGAAAATCGG 57.198 29.630 3.65 0.00 0.00 4.18
4792 6588 9.890352 CAAAGAAAAAGGAATTGAACACAAAAA 57.110 25.926 0.00 0.00 0.00 1.94
4793 6589 9.061435 ACAAAGAAAAAGGAATTGAACACAAAA 57.939 25.926 0.00 0.00 0.00 2.44
4794 6590 8.614469 ACAAAGAAAAAGGAATTGAACACAAA 57.386 26.923 0.00 0.00 0.00 2.83
4795 6591 8.614469 AACAAAGAAAAAGGAATTGAACACAA 57.386 26.923 0.00 0.00 0.00 3.33
4796 6592 9.883142 ATAACAAAGAAAAAGGAATTGAACACA 57.117 25.926 0.00 0.00 0.00 3.72
4824 6620 9.794685 AGAAACAAACAAAAAGAAAAGCAAAAA 57.205 22.222 0.00 0.00 0.00 1.94
4825 6621 9.794685 AAGAAACAAACAAAAAGAAAAGCAAAA 57.205 22.222 0.00 0.00 0.00 2.44
4877 6673 9.764363 GGGAAAAGAGAAAATGTTTGACTTATT 57.236 29.630 0.00 0.00 0.00 1.40
4878 6674 9.147732 AGGGAAAAGAGAAAATGTTTGACTTAT 57.852 29.630 0.00 0.00 0.00 1.73
4879 6675 8.533569 AGGGAAAAGAGAAAATGTTTGACTTA 57.466 30.769 0.00 0.00 0.00 2.24
4880 6676 7.423844 AGGGAAAAGAGAAAATGTTTGACTT 57.576 32.000 0.00 0.00 0.00 3.01
4881 6677 7.423844 AAGGGAAAAGAGAAAATGTTTGACT 57.576 32.000 0.00 0.00 0.00 3.41
4882 6678 8.492673 AAAAGGGAAAAGAGAAAATGTTTGAC 57.507 30.769 0.00 0.00 0.00 3.18
4887 6683 9.778741 GGAATAAAAAGGGAAAAGAGAAAATGT 57.221 29.630 0.00 0.00 0.00 2.71
4928 6724 9.829507 TTGTTGAAATGACATTTGGATACTTTT 57.170 25.926 18.00 0.00 31.47 2.27
4929 6725 9.260002 GTTGTTGAAATGACATTTGGATACTTT 57.740 29.630 18.00 0.00 31.47 2.66
4930 6726 8.420222 TGTTGTTGAAATGACATTTGGATACTT 58.580 29.630 18.00 0.00 31.47 2.24
4931 6727 7.950512 TGTTGTTGAAATGACATTTGGATACT 58.049 30.769 18.00 0.00 31.47 2.12
4932 6728 8.586570 TTGTTGTTGAAATGACATTTGGATAC 57.413 30.769 18.00 10.18 31.47 2.24
4933 6729 9.039870 GTTTGTTGTTGAAATGACATTTGGATA 57.960 29.630 18.00 2.40 31.47 2.59
4934 6730 7.551974 TGTTTGTTGTTGAAATGACATTTGGAT 59.448 29.630 18.00 0.00 31.47 3.41
4935 6731 6.875726 TGTTTGTTGTTGAAATGACATTTGGA 59.124 30.769 18.00 3.71 31.47 3.53
4936 6732 7.069852 TGTTTGTTGTTGAAATGACATTTGG 57.930 32.000 18.00 0.00 31.47 3.28
4937 6733 8.838961 GTTTGTTTGTTGTTGAAATGACATTTG 58.161 29.630 18.00 0.00 31.47 2.32
4938 6734 8.562892 TGTTTGTTTGTTGTTGAAATGACATTT 58.437 25.926 13.24 13.24 34.64 2.32
4939 6735 8.092521 TGTTTGTTTGTTGTTGAAATGACATT 57.907 26.923 0.00 0.00 0.00 2.71
4940 6736 7.664082 TGTTTGTTTGTTGTTGAAATGACAT 57.336 28.000 0.00 0.00 0.00 3.06
4941 6737 7.482654 TTGTTTGTTTGTTGTTGAAATGACA 57.517 28.000 0.00 0.00 0.00 3.58
4942 6738 8.947304 AATTGTTTGTTTGTTGTTGAAATGAC 57.053 26.923 0.00 0.00 0.00 3.06
5051 6847 6.851609 TGGACATAAAAAGTGTATGATGCAC 58.148 36.000 5.47 5.47 33.86 4.57
5052 6848 7.643569 ATGGACATAAAAAGTGTATGATGCA 57.356 32.000 0.00 0.00 33.86 3.96
5070 6866 9.429359 ACGCATTTTCAAAATTATTAATGGACA 57.571 25.926 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.