Multiple sequence alignment - TraesCS7A01G459200

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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 TraesCS7A01G459200 chr7A 100.000 5121 0 0 1 5121 654208121 654203001 0.000000e+00 9457.0
1 TraesCS7A01G459200 chr7A 86.688 1863 210 25 1738 3568 46969060 46967204 0.000000e+00 2032.0
2 TraesCS7A01G459200 chr7A 84.375 640 58 31 962 1582 46969955 46969339 1.590000e-164 590.0
3 TraesCS7A01G459200 chr7A 92.208 77 1 3 525 597 290616137 290616062 2.520000e-18 104.0
4 TraesCS7A01G459200 chr7B 93.716 3708 167 34 708 4394 621476052 621472390 0.000000e+00 5496.0
5 TraesCS7A01G459200 chr7B 96.386 83 3 0 5039 5121 621472333 621472251 2.490000e-28 137.0
6 TraesCS7A01G459200 chr7D 93.750 2688 114 22 1729 4394 567659107 567656452 0.000000e+00 3984.0
7 TraesCS7A01G459200 chr7D 86.253 1884 214 30 1738 3585 44525152 44523278 0.000000e+00 2002.0
8 TraesCS7A01G459200 chr7D 91.830 1273 52 21 446 1699 567660335 567659096 0.000000e+00 1727.0
9 TraesCS7A01G459200 chr7D 84.300 707 54 39 962 1639 44525926 44525248 5.590000e-179 638.0
10 TraesCS7A01G459200 chr7D 91.791 402 22 9 1 395 567660722 567660325 2.700000e-152 549.0
11 TraesCS7A01G459200 chr7D 88.196 449 34 4 4400 4844 567656228 567655795 7.600000e-143 518.0
12 TraesCS7A01G459200 chr7D 85.263 285 22 10 4844 5121 567655745 567655474 5.050000e-70 276.0
13 TraesCS7A01G459200 chr4A 86.809 1880 209 27 1738 3584 655626533 655624660 0.000000e+00 2061.0
14 TraesCS7A01G459200 chr4A 83.689 656 68 30 967 1590 655627322 655626674 2.660000e-162 582.0
15 TraesCS7A01G459200 chr4A 92.000 75 2 4 524 597 625758222 625758293 9.070000e-18 102.0
16 TraesCS7A01G459200 chr1A 92.105 76 3 3 524 596 250197878 250197803 2.520000e-18 104.0
17 TraesCS7A01G459200 chr4B 91.781 73 1 3 529 597 364668404 364668475 4.220000e-16 97.1
18 TraesCS7A01G459200 chr6B 90.789 76 0 3 528 597 520230350 520230424 1.520000e-15 95.3
19 TraesCS7A01G459200 chr2A 90.667 75 2 4 528 601 391898706 391898776 1.520000e-15 95.3
20 TraesCS7A01G459200 chr1D 89.610 77 4 4 524 597 199068360 199068285 1.520000e-15 95.3
21 TraesCS7A01G459200 chr1B 90.541 74 4 3 526 597 131502937 131503009 1.520000e-15 95.3
22 TraesCS7A01G459200 chr2D 89.744 78 1 7 526 597 24451745 24451821 5.460000e-15 93.5


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 TraesCS7A01G459200 chr7A 654203001 654208121 5120 True 9457.0 9457 100.0000 1 5121 1 chr7A.!!$R2 5120
1 TraesCS7A01G459200 chr7A 46967204 46969955 2751 True 1311.0 2032 85.5315 962 3568 2 chr7A.!!$R3 2606
2 TraesCS7A01G459200 chr7B 621472251 621476052 3801 True 2816.5 5496 95.0510 708 5121 2 chr7B.!!$R1 4413
3 TraesCS7A01G459200 chr7D 567655474 567660722 5248 True 1410.8 3984 90.1660 1 5121 5 chr7D.!!$R2 5120
4 TraesCS7A01G459200 chr7D 44523278 44525926 2648 True 1320.0 2002 85.2765 962 3585 2 chr7D.!!$R1 2623
5 TraesCS7A01G459200 chr4A 655624660 655627322 2662 True 1321.5 2061 85.2490 967 3584 2 chr4A.!!$R1 2617

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
893 918 1.302033 CCAAAGTCAGGCTGCGTCT 60.302 57.895 10.34 5.28 0.00 4.18 F
1133 1189 0.462047 CTTCCCTCGGTCCAAATCGG 60.462 60.000 0.00 0.00 0.00 4.18 F
2059 2320 0.034059 CTTCTCAGTTGGACACGGCT 59.966 55.000 0.00 0.00 0.00 5.52 F
3309 3594 0.329261 CATTGACCAGGAAGCCCTCA 59.671 55.000 0.00 0.00 42.02 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1992 2253 0.323725 GCTTCCTGGAGCATTCCCAA 60.324 55.0 11.62 0.0 43.33 4.12 R
2427 2696 0.467384 ATGACGAATGGAGAGGGCAG 59.533 55.0 0.00 0.0 0.00 4.85 R
3931 4236 0.035534 ACACGCACCCATAAGCATCA 60.036 50.0 0.00 0.0 0.00 3.07 R
4599 5139 0.998928 TGGGAGGCATGTATGGTTGT 59.001 50.0 0.00 0.0 0.00 3.32 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
72 74 5.371115 ACATTTTTCAGATACACCGTTGG 57.629 39.130 0.00 0.00 0.00 3.77
98 100 8.766000 ACATTTTTCGAGTACACATACATGTA 57.234 30.769 8.27 8.27 39.39 2.29
103 105 8.766000 TTTCGAGTACACATACATGTAAATGT 57.234 30.769 22.06 22.06 39.39 2.71
402 409 8.715191 TGTCACAAACATATTTTTGAAAAGCT 57.285 26.923 18.78 0.00 36.51 3.74
403 410 9.160496 TGTCACAAACATATTTTTGAAAAGCTT 57.840 25.926 18.78 0.00 36.51 3.74
404 411 9.424659 GTCACAAACATATTTTTGAAAAGCTTG 57.575 29.630 18.78 6.86 36.51 4.01
405 412 9.376075 TCACAAACATATTTTTGAAAAGCTTGA 57.624 25.926 18.78 8.73 38.54 3.02
545 553 5.677567 GAAATATACTCCTCCGTCCCAAAA 58.322 41.667 0.00 0.00 0.00 2.44
547 555 7.383156 AAATATACTCCTCCGTCCCAAAATA 57.617 36.000 0.00 0.00 0.00 1.40
548 556 7.383156 AATATACTCCTCCGTCCCAAAATAA 57.617 36.000 0.00 0.00 0.00 1.40
549 557 3.629142 ACTCCTCCGTCCCAAAATAAG 57.371 47.619 0.00 0.00 0.00 1.73
551 559 3.270877 CTCCTCCGTCCCAAAATAAGTG 58.729 50.000 0.00 0.00 0.00 3.16
552 560 2.640826 TCCTCCGTCCCAAAATAAGTGT 59.359 45.455 0.00 0.00 0.00 3.55
554 562 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
555 563 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
556 564 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
557 565 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
558 566 4.083484 CCGTCCCAAAATAAGTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
559 567 4.755123 CGTCCCAAAATAAGTGTCTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
560 568 5.238650 CGTCCCAAAATAAGTGTCTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
561 569 6.238648 CGTCCCAAAATAAGTGTCTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
562 570 6.918022 GTCCCAAAATAAGTGTCTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
563 571 6.605594 TCCCAAAATAAGTGTCTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
564 572 7.776030 TCCCAAAATAAGTGTCTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
565 573 7.860872 CCCAAAATAAGTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
566 574 8.621286 CCAAAATAAGTGTCTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
604 621 7.923414 AGACACTTATTTTTGGGTATGTCTC 57.077 36.000 0.00 0.00 41.16 3.36
605 622 7.690256 AGACACTTATTTTTGGGTATGTCTCT 58.310 34.615 0.00 0.00 41.16 3.10
667 692 2.022129 GAACGTCAGGACAGCCGTG 61.022 63.158 0.00 0.00 39.96 4.94
669 694 4.662961 CGTCAGGACAGCCGTGCA 62.663 66.667 0.00 0.00 39.96 4.57
893 918 1.302033 CCAAAGTCAGGCTGCGTCT 60.302 57.895 10.34 5.28 0.00 4.18
902 927 4.767255 GCTGCGTCTGTCCCCCAG 62.767 72.222 0.00 0.00 42.97 4.45
941 966 2.499827 CCCTTCCTCCGGACCGATC 61.500 68.421 17.49 0.00 0.00 3.69
947 972 3.432051 CTCCGGACCGATCCAGCAC 62.432 68.421 17.49 0.00 46.67 4.40
952 977 3.391665 GACCGATCCAGCACCCCAG 62.392 68.421 0.00 0.00 0.00 4.45
1097 1151 4.580551 CTACCCGCCGTAAGCCCG 62.581 72.222 0.00 0.00 38.78 6.13
1123 1179 2.444895 CCCTCTCCCTTCCCTCGG 60.445 72.222 0.00 0.00 0.00 4.63
1133 1189 0.462047 CTTCCCTCGGTCCAAATCGG 60.462 60.000 0.00 0.00 0.00 4.18
1403 1459 1.144716 GCATCTCGGCCTCATGACA 59.855 57.895 0.00 0.00 0.00 3.58
1442 1506 3.627123 TGCGATGATGTTCCTGGTTATTG 59.373 43.478 0.00 0.00 0.00 1.90
1584 1665 2.588877 CAGCGCCTTCGGGTATGG 60.589 66.667 2.29 0.00 37.45 2.74
1702 1961 1.566018 AAGTAGTTCACGCTTGCCGC 61.566 55.000 0.00 0.00 41.76 6.53
1707 1966 4.617520 TCACGCTTGCCGCCTCAA 62.618 61.111 0.00 0.00 41.76 3.02
1712 1971 1.659794 GCTTGCCGCCTCAAAAAGA 59.340 52.632 0.00 0.00 0.00 2.52
1878 2137 2.795329 ACGGCTCATTGATCAGGTTTT 58.205 42.857 0.00 0.00 0.00 2.43
1879 2138 3.157087 ACGGCTCATTGATCAGGTTTTT 58.843 40.909 0.00 0.00 0.00 1.94
1914 2174 5.967674 GGAATTGTGAATTTCAGCTATCACG 59.032 40.000 0.00 0.00 43.91 4.35
1992 2253 2.373502 ACTGGAAAGTTAAGAGGCAGCT 59.626 45.455 0.00 0.00 0.00 4.24
2059 2320 0.034059 CTTCTCAGTTGGACACGGCT 59.966 55.000 0.00 0.00 0.00 5.52
2061 2322 1.112916 TCTCAGTTGGACACGGCTGA 61.113 55.000 0.00 0.00 36.65 4.26
2113 2374 1.405463 CCAATCGATCAGGACTCGTCA 59.595 52.381 10.51 0.00 37.40 4.35
2146 2407 5.298276 GTCTGTACAAATCCCACAAAAGTCA 59.702 40.000 0.00 0.00 0.00 3.41
2167 2428 0.951558 GCCGTTTCTTGAGCCTTCAA 59.048 50.000 0.00 0.00 40.92 2.69
2172 2433 4.261572 CCGTTTCTTGAGCCTTCAATTTCA 60.262 41.667 0.00 0.00 42.19 2.69
2248 2509 1.450531 GCACCACTTGTTCTGCAGCT 61.451 55.000 9.47 0.00 0.00 4.24
2373 2641 8.306038 TGTCTAAATGCTTTTGATTTACTGCAT 58.694 29.630 7.78 0.00 42.01 3.96
2559 2832 1.796459 GCGTCAACGTAACTGGAATGT 59.204 47.619 4.29 0.00 42.22 2.71
2837 3114 7.117236 GGGAGAAATATCGTAATATTGTTCGCA 59.883 37.037 0.00 0.00 37.96 5.10
3043 3324 8.171337 ACTGGGGTATCTAACTTCCTTTTTAT 57.829 34.615 0.00 0.00 0.00 1.40
3150 3435 3.906720 AGAGTTCCGCAGCCTATTTTA 57.093 42.857 0.00 0.00 0.00 1.52
3212 3497 6.360618 AGCCTAAATACAAATCTTCCAGGAG 58.639 40.000 0.00 0.00 0.00 3.69
3309 3594 0.329261 CATTGACCAGGAAGCCCTCA 59.671 55.000 0.00 0.00 42.02 3.86
3575 3879 3.184541 GTGATTGGCTGCAATGTTCATC 58.815 45.455 0.50 0.00 0.00 2.92
3625 3930 8.354426 AGTTTCTCTGACTAGTAGAAAGTGTTC 58.646 37.037 19.42 9.58 39.97 3.18
3702 4007 0.383231 GGATCTTTGCCATGCTTCCG 59.617 55.000 0.00 0.00 0.00 4.30
3753 4058 9.806448 AGATCTACTTCATCATGATAGTGTACT 57.194 33.333 17.76 10.47 0.00 2.73
3762 4067 5.594926 TCATGATAGTGTACTGAGCACATG 58.405 41.667 0.00 0.00 39.17 3.21
3915 4220 4.351054 GACACTGGGCCTGGTGGG 62.351 72.222 25.34 10.12 37.72 4.61
3931 4236 3.861797 GGGCACATCGACCCGGAT 61.862 66.667 0.73 0.00 36.07 4.18
4042 4347 1.349357 GAGGAGAAGTGCAGGTTCCTT 59.651 52.381 9.58 0.00 38.35 3.36
4132 4439 1.274728 ACCCGCTGAGATGATGATAGC 59.725 52.381 0.00 0.00 0.00 2.97
4143 4460 3.397849 TGATGATAGCAGTGCTGGATC 57.602 47.619 27.97 22.04 40.10 3.36
4145 4462 1.499368 TGATAGCAGTGCTGGATCCA 58.501 50.000 27.97 15.27 40.10 3.41
4225 4542 5.070001 AGCTGTTGTATTAAGGAAAGCACA 58.930 37.500 0.00 0.00 31.85 4.57
4261 4578 2.027377 AGCATCAGTGAGAAGGTTCCAG 60.027 50.000 0.00 0.00 0.00 3.86
4265 4582 4.543590 TCAGTGAGAAGGTTCCAGAATC 57.456 45.455 0.00 0.00 0.00 2.52
4307 4624 3.545703 CCTAAGGATAGTTTGTGGGCAG 58.454 50.000 0.00 0.00 0.00 4.85
4308 4625 2.514458 AAGGATAGTTTGTGGGCAGG 57.486 50.000 0.00 0.00 0.00 4.85
4333 4650 7.012989 GGTCAATCTGTTACAAGTTGGTACTTT 59.987 37.037 7.96 0.00 41.85 2.66
4394 4715 6.854892 GCACTGTATTCTCATACAATTGATGC 59.145 38.462 13.59 0.00 43.89 3.91
4395 4716 7.358066 CACTGTATTCTCATACAATTGATGCC 58.642 38.462 13.59 0.00 43.89 4.40
4396 4717 7.012610 CACTGTATTCTCATACAATTGATGCCA 59.987 37.037 13.59 0.00 43.89 4.92
4397 4718 7.722728 ACTGTATTCTCATACAATTGATGCCAT 59.277 33.333 13.59 6.88 43.89 4.40
4398 4719 8.102800 TGTATTCTCATACAATTGATGCCATC 57.897 34.615 13.59 0.00 42.01 3.51
4400 4721 9.440773 GTATTCTCATACAATTGATGCCATCTA 57.559 33.333 13.59 0.00 36.07 1.98
4504 5044 2.544903 CCTGGAAATTTTGGACGCGTTT 60.545 45.455 15.53 0.19 0.00 3.60
4505 5045 2.464865 TGGAAATTTTGGACGCGTTTG 58.535 42.857 15.53 0.00 0.00 2.93
4506 5046 1.191425 GGAAATTTTGGACGCGTTTGC 59.809 47.619 15.53 2.79 37.91 3.68
4543 5083 5.873179 TGCATTTCTTTAGGGAAACTACG 57.127 39.130 0.00 0.00 37.91 3.51
4560 5100 7.360946 GGAAACTACGTTGCTTTATTGATCAGT 60.361 37.037 0.00 0.00 0.00 3.41
4570 5110 8.058667 TGCTTTATTGATCAGTGATGTTCATT 57.941 30.769 11.20 2.85 0.00 2.57
4571 5111 8.186163 TGCTTTATTGATCAGTGATGTTCATTC 58.814 33.333 11.20 0.00 0.00 2.67
4593 5133 7.770801 TTCGAACTGTTACAATATCATGAGG 57.229 36.000 0.09 0.00 0.00 3.86
4594 5134 5.753438 TCGAACTGTTACAATATCATGAGGC 59.247 40.000 0.09 0.00 0.00 4.70
4595 5135 5.755375 CGAACTGTTACAATATCATGAGGCT 59.245 40.000 0.09 0.00 0.00 4.58
4596 5136 6.258727 CGAACTGTTACAATATCATGAGGCTT 59.741 38.462 0.09 0.00 0.00 4.35
4597 5137 7.201644 CGAACTGTTACAATATCATGAGGCTTT 60.202 37.037 0.09 0.00 0.00 3.51
4598 5138 9.109393 GAACTGTTACAATATCATGAGGCTTTA 57.891 33.333 0.09 0.00 0.00 1.85
4599 5139 9.461312 AACTGTTACAATATCATGAGGCTTTAA 57.539 29.630 0.09 0.00 0.00 1.52
4600 5140 8.893727 ACTGTTACAATATCATGAGGCTTTAAC 58.106 33.333 0.09 6.91 0.00 2.01
4601 5141 8.800370 TGTTACAATATCATGAGGCTTTAACA 57.200 30.769 13.77 13.77 0.00 2.41
4602 5142 9.237187 TGTTACAATATCATGAGGCTTTAACAA 57.763 29.630 14.76 4.67 0.00 2.83
4603 5143 9.503427 GTTACAATATCATGAGGCTTTAACAAC 57.497 33.333 0.09 0.00 0.00 3.32
4604 5144 7.100458 ACAATATCATGAGGCTTTAACAACC 57.900 36.000 0.09 0.00 0.00 3.77
4605 5145 6.663093 ACAATATCATGAGGCTTTAACAACCA 59.337 34.615 0.09 0.00 0.00 3.67
4606 5146 7.342799 ACAATATCATGAGGCTTTAACAACCAT 59.657 33.333 0.09 0.00 0.00 3.55
4607 5147 8.849168 CAATATCATGAGGCTTTAACAACCATA 58.151 33.333 0.09 0.00 0.00 2.74
4617 5157 2.143876 AACAACCATACATGCCTCCC 57.856 50.000 0.00 0.00 0.00 4.30
4618 5158 0.998928 ACAACCATACATGCCTCCCA 59.001 50.000 0.00 0.00 0.00 4.37
4667 5208 9.262358 AGCTAAACTATCATCCTCGAAATTAAC 57.738 33.333 0.00 0.00 0.00 2.01
4670 5211 6.494666 ACTATCATCCTCGAAATTAACCCA 57.505 37.500 0.00 0.00 0.00 4.51
4682 5223 8.972458 TCGAAATTAACCCATCTTGATTCATA 57.028 30.769 0.00 0.00 0.00 2.15
4715 5258 6.128282 TGACTCCTAAAAATCATCTTTGCGTC 60.128 38.462 0.00 0.00 0.00 5.19
4736 5279 5.459107 CGTCCTATGAGTTTTCTGATTACCG 59.541 44.000 0.00 0.00 0.00 4.02
4739 5282 2.343101 TGAGTTTTCTGATTACCGCCG 58.657 47.619 0.00 0.00 0.00 6.46
4740 5283 1.062148 GAGTTTTCTGATTACCGCCGC 59.938 52.381 0.00 0.00 0.00 6.53
4752 5295 4.474846 CGCCGCATTTTGACCCCG 62.475 66.667 0.00 0.00 0.00 5.73
4777 5320 2.866028 GGCACGCTCAAGCTCAAG 59.134 61.111 0.00 0.00 39.32 3.02
4785 5328 2.474359 CGCTCAAGCTCAAGAATATCCG 59.526 50.000 0.00 0.00 39.32 4.18
4791 5334 3.397482 AGCTCAAGAATATCCGTGATGC 58.603 45.455 0.00 0.00 0.00 3.91
4898 5491 3.877951 GAGGTAGAGTCCCTCACGA 57.122 57.895 9.83 0.00 46.46 4.35
4903 5496 3.025262 GGTAGAGTCCCTCACGATTTCT 58.975 50.000 0.00 0.00 32.06 2.52
4912 5505 3.525537 CCTCACGATTTCTGCATACTGT 58.474 45.455 0.00 0.00 0.00 3.55
4917 5510 2.279741 GATTTCTGCATACTGTCGCCA 58.720 47.619 0.00 0.00 0.00 5.69
4946 5539 0.748367 GCAGCCCCCTGTTTAGCTAC 60.748 60.000 0.00 0.00 41.26 3.58
4966 5559 4.182693 ACAACTGCATCCACATTGATTG 57.817 40.909 0.00 0.00 0.00 2.67
4967 5560 3.827876 ACAACTGCATCCACATTGATTGA 59.172 39.130 0.00 0.00 0.00 2.57
4968 5561 4.171005 CAACTGCATCCACATTGATTGAC 58.829 43.478 0.00 0.00 0.00 3.18
4971 5564 4.082408 ACTGCATCCACATTGATTGACTTG 60.082 41.667 0.00 0.00 0.00 3.16
4972 5565 3.184541 GCATCCACATTGATTGACTTGC 58.815 45.455 0.00 0.00 0.00 4.01
4973 5566 3.431856 CATCCACATTGATTGACTTGCG 58.568 45.455 0.00 0.00 0.00 4.85
4974 5567 1.199789 TCCACATTGATTGACTTGCGC 59.800 47.619 0.00 0.00 0.00 6.09
4976 5569 1.980844 CACATTGATTGACTTGCGCAC 59.019 47.619 11.12 0.00 0.00 5.34
4978 5571 2.034432 ACATTGATTGACTTGCGCACAA 59.966 40.909 11.12 12.59 0.00 3.33
4979 5572 2.859526 TTGATTGACTTGCGCACAAA 57.140 40.000 11.12 2.14 34.74 2.83
4980 5573 2.118228 TGATTGACTTGCGCACAAAC 57.882 45.000 11.12 11.11 34.74 2.93
4982 5575 1.001378 GATTGACTTGCGCACAAACCT 60.001 47.619 11.12 0.00 34.74 3.50
4984 5577 1.282875 GACTTGCGCACAAACCTCC 59.717 57.895 11.12 0.00 34.74 4.30
4985 5578 2.130073 GACTTGCGCACAAACCTCCC 62.130 60.000 11.12 0.00 34.74 4.30
4986 5579 1.898574 CTTGCGCACAAACCTCCCT 60.899 57.895 11.12 0.00 34.74 4.20
4987 5580 1.454847 TTGCGCACAAACCTCCCTT 60.455 52.632 11.12 0.00 31.21 3.95
4988 5581 0.179015 TTGCGCACAAACCTCCCTTA 60.179 50.000 11.12 0.00 31.21 2.69
4990 5583 1.279558 TGCGCACAAACCTCCCTTATA 59.720 47.619 5.66 0.00 0.00 0.98
4991 5584 1.940613 GCGCACAAACCTCCCTTATAG 59.059 52.381 0.30 0.00 0.00 1.31
4992 5585 2.561569 CGCACAAACCTCCCTTATAGG 58.438 52.381 0.00 0.00 40.20 2.57
5014 5607 4.000988 GGTAGCAAAGAGAAAACGGATCA 58.999 43.478 0.00 0.00 0.00 2.92
5025 5618 2.691409 AACGGATCACATGTACAGGG 57.309 50.000 12.79 4.11 0.00 4.45
5031 5624 0.037697 TCACATGTACAGGGCGTCAC 60.038 55.000 12.79 0.00 0.00 3.67
5072 5665 7.254185 CCAAATTTTGAATGGACAGCAATATCG 60.254 37.037 10.72 0.00 36.27 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 59 3.973206 AATGTCCAACGGTGTATCTGA 57.027 42.857 0.00 0.00 0.00 3.27
72 74 7.739295 ACATGTATGTGTACTCGAAAAATGTC 58.261 34.615 0.00 0.00 40.03 3.06
110 112 6.147985 ACTTAACAAATGTTTGGCACGTTTTT 59.852 30.769 3.85 0.00 41.13 1.94
118 120 7.489757 TGTTCTAACACTTAACAAATGTTTGGC 59.510 33.333 3.85 0.00 36.92 4.52
521 528 2.889045 TGGGACGGAGGAGTATATTTCG 59.111 50.000 0.00 0.00 0.00 3.46
547 555 8.472413 TGTAGTTAGTACAAAGTTGAGACACTT 58.528 33.333 0.00 0.00 38.78 3.16
548 556 8.004087 TGTAGTTAGTACAAAGTTGAGACACT 57.996 34.615 0.00 0.00 38.78 3.55
549 557 8.638685 TTGTAGTTAGTACAAAGTTGAGACAC 57.361 34.615 9.90 0.00 46.60 3.67
561 569 8.004087 AGTGTCTCAACTTTGTAGTTAGTACA 57.996 34.615 0.00 0.00 42.67 2.90
562 570 8.868635 AAGTGTCTCAACTTTGTAGTTAGTAC 57.131 34.615 0.00 0.00 42.67 2.73
645 670 1.523758 GGCTGTCCTGACGTTCATTT 58.476 50.000 0.00 0.00 0.00 2.32
667 692 0.442699 GGTTCGTTCGATGGAGTTGC 59.557 55.000 0.00 0.00 0.00 4.17
669 694 2.036733 TCTTGGTTCGTTCGATGGAGTT 59.963 45.455 0.00 0.00 0.00 3.01
869 894 3.376918 GCCTGACTTTGGGCTGGC 61.377 66.667 4.13 4.13 44.48 4.85
915 940 3.798511 GGAGGAAGGGGCCGGAAG 61.799 72.222 5.05 0.00 0.00 3.46
941 966 4.767255 GAGCGACTGGGGTGCTGG 62.767 72.222 0.00 0.00 39.49 4.85
952 977 2.650813 ATTGATGGGGAGCGAGCGAC 62.651 60.000 0.00 0.00 0.00 5.19
1097 1151 4.890306 GGGAGAGGGGAGGGGAGC 62.890 77.778 0.00 0.00 0.00 4.70
1099 1153 2.543637 AAGGGAGAGGGGAGGGGA 60.544 66.667 0.00 0.00 0.00 4.81
1110 1166 1.198759 TTTGGACCGAGGGAAGGGAG 61.199 60.000 0.00 0.00 0.00 4.30
1123 1179 1.648467 GGTGAGCAGCCGATTTGGAC 61.648 60.000 0.00 0.00 42.00 4.02
1340 1396 1.698506 GTGGAGATGAGGTCGAGGAT 58.301 55.000 0.00 0.00 0.00 3.24
1403 1459 3.211865 TCGCATCTAACATACGAGGTCT 58.788 45.455 0.00 0.00 0.00 3.85
1442 1506 3.290710 ACCTGCATTGTTATCCATCCAC 58.709 45.455 0.00 0.00 0.00 4.02
1584 1665 6.013842 AGTTTCTACTGCAAATTAACAGGC 57.986 37.500 11.21 0.00 38.25 4.85
1726 1985 5.708230 TGGTGTAAGTTCAAACTTCAACTGT 59.292 36.000 11.22 0.00 45.65 3.55
1732 1991 5.278315 GGTCCATGGTGTAAGTTCAAACTTC 60.278 44.000 12.58 5.14 45.65 3.01
1734 1993 4.142038 GGTCCATGGTGTAAGTTCAAACT 58.858 43.478 12.58 0.00 42.04 2.66
1752 2011 7.389053 CAGAACAGAGCATAATAATTAGGGTCC 59.611 40.741 0.00 0.00 43.23 4.46
1828 2087 0.676151 CTCCTTCTGGAACTGCTGCC 60.676 60.000 0.00 0.00 42.66 4.85
1878 2137 9.097257 GAAATTCACAATTCCTGAAACAAGAAA 57.903 29.630 0.29 0.00 31.48 2.52
1879 2138 8.256605 TGAAATTCACAATTCCTGAAACAAGAA 58.743 29.630 0.00 0.00 31.48 2.52
1992 2253 0.323725 GCTTCCTGGAGCATTCCCAA 60.324 55.000 11.62 0.00 43.33 4.12
2059 2320 1.143838 CGACAATCGGGGCATCTCA 59.856 57.895 0.00 0.00 36.00 3.27
2061 2322 1.144057 GACGACAATCGGGGCATCT 59.856 57.895 2.97 0.00 45.59 2.90
2132 2393 1.176527 CGGCATGACTTTTGTGGGAT 58.823 50.000 0.00 0.00 0.00 3.85
2146 2407 1.168714 GAAGGCTCAAGAAACGGCAT 58.831 50.000 0.00 0.00 0.00 4.40
2167 2428 2.173519 CTTGCACTGTCCCCATGAAAT 58.826 47.619 0.00 0.00 0.00 2.17
2172 2433 2.360350 CGCTTGCACTGTCCCCAT 60.360 61.111 0.00 0.00 0.00 4.00
2185 2446 2.033194 GTAGCTTTCCACGCCGCTT 61.033 57.895 0.00 0.00 34.14 4.68
2238 2499 2.223294 GCATCATCTTCAGCTGCAGAAC 60.223 50.000 20.00 0.00 33.13 3.01
2248 2509 1.780503 TCTCCGAGGCATCATCTTCA 58.219 50.000 0.00 0.00 0.00 3.02
2373 2641 5.601313 ACTCTAGTTGGTCAAAAGACAGGTA 59.399 40.000 0.00 0.00 0.00 3.08
2427 2696 0.467384 ATGACGAATGGAGAGGGCAG 59.533 55.000 0.00 0.00 0.00 4.85
3043 3324 1.358152 ACCCTGCTAACCTGCACTAA 58.642 50.000 0.00 0.00 38.12 2.24
3150 3435 2.653702 GTGAGTCGGTCAGCAGCT 59.346 61.111 0.00 0.00 35.13 4.24
3212 3497 4.508124 AGACAATCTTCGTGTTGAACTGTC 59.492 41.667 0.00 0.00 36.62 3.51
3309 3594 8.319057 TGTAACTGTTTATCAGATACCCATCT 57.681 34.615 0.00 0.00 45.60 2.90
3357 3642 0.108186 CCTGCTGCAGAACCATCGTA 60.108 55.000 30.10 0.00 32.44 3.43
3410 3699 9.998106 GGTAAACTAATCTAGCCATGATAGAAA 57.002 33.333 10.50 3.71 34.20 2.52
3625 3930 2.544685 CTGAAGCCATACTGGAACTCG 58.455 52.381 0.00 0.00 40.96 4.18
3652 3957 9.734984 ATGTATCATCATATGAATTCTCTGCAA 57.265 29.630 9.99 0.00 43.50 4.08
3753 4058 2.413310 ATGTGCAGATCATGTGCTCA 57.587 45.000 13.32 13.32 45.53 4.26
3915 4220 2.383245 ATCATCCGGGTCGATGTGCC 62.383 60.000 0.00 0.00 40.50 5.01
3920 4225 1.338107 TAAGCATCATCCGGGTCGAT 58.662 50.000 0.00 0.00 0.00 3.59
3931 4236 0.035534 ACACGCACCCATAAGCATCA 60.036 50.000 0.00 0.00 0.00 3.07
4015 4320 2.266055 CACTTCTCCTCCGCCCAC 59.734 66.667 0.00 0.00 0.00 4.61
4132 4439 4.334759 CAGTAAGAAATGGATCCAGCACTG 59.665 45.833 21.33 19.22 0.00 3.66
4143 4460 3.119884 TCAATGCGCACAGTAAGAAATGG 60.120 43.478 14.90 0.00 0.00 3.16
4145 4462 3.753272 AGTCAATGCGCACAGTAAGAAAT 59.247 39.130 14.90 0.00 0.00 2.17
4225 4542 4.402793 ACTGATGCTACCAACTAGTCGAAT 59.597 41.667 0.00 0.00 0.00 3.34
4307 4624 5.995897 AGTACCAACTTGTAACAGATTGACC 59.004 40.000 0.00 0.00 29.00 4.02
4308 4625 7.492352 AAGTACCAACTTGTAACAGATTGAC 57.508 36.000 0.00 0.00 44.40 3.18
4402 4723 9.260884 AGGGAGGGAGTCTCAGATATATTATAT 57.739 37.037 1.47 0.00 44.19 0.86
4407 4947 6.042586 AGTAGGGAGGGAGTCTCAGATATAT 58.957 44.000 1.47 0.00 44.19 0.86
4414 4954 1.619977 GCAAGTAGGGAGGGAGTCTCA 60.620 57.143 1.47 0.00 44.19 3.27
4468 5008 2.593026 TCCAGGAAGCCGAACAAATTT 58.407 42.857 0.00 0.00 0.00 1.82
4472 5012 2.286365 ATTTCCAGGAAGCCGAACAA 57.714 45.000 1.07 0.00 0.00 2.83
4477 5017 1.892474 TCCAAAATTTCCAGGAAGCCG 59.108 47.619 1.07 0.00 0.00 5.52
4504 5044 2.407268 CAATTATGCCGCCTGAGCA 58.593 52.632 0.00 0.00 45.94 4.26
4541 5081 5.412594 ACATCACTGATCAATAAAGCAACGT 59.587 36.000 0.00 0.00 0.00 3.99
4543 5083 7.307694 TGAACATCACTGATCAATAAAGCAAC 58.692 34.615 0.00 0.00 31.92 4.17
4570 5110 5.753438 GCCTCATGATATTGTAACAGTTCGA 59.247 40.000 0.00 0.00 0.00 3.71
4571 5111 5.755375 AGCCTCATGATATTGTAACAGTTCG 59.245 40.000 0.00 0.00 0.00 3.95
4575 5115 8.892723 TGTTAAAGCCTCATGATATTGTAACAG 58.107 33.333 13.30 0.00 0.00 3.16
4584 5124 7.342581 TGTATGGTTGTTAAAGCCTCATGATA 58.657 34.615 0.00 0.00 32.62 2.15
4593 5133 4.440112 GGAGGCATGTATGGTTGTTAAAGC 60.440 45.833 0.00 0.00 0.00 3.51
4594 5134 4.097892 GGGAGGCATGTATGGTTGTTAAAG 59.902 45.833 0.00 0.00 0.00 1.85
4595 5135 4.020543 GGGAGGCATGTATGGTTGTTAAA 58.979 43.478 0.00 0.00 0.00 1.52
4596 5136 3.010696 TGGGAGGCATGTATGGTTGTTAA 59.989 43.478 0.00 0.00 0.00 2.01
4597 5137 2.578480 TGGGAGGCATGTATGGTTGTTA 59.422 45.455 0.00 0.00 0.00 2.41
4598 5138 1.357420 TGGGAGGCATGTATGGTTGTT 59.643 47.619 0.00 0.00 0.00 2.83
4599 5139 0.998928 TGGGAGGCATGTATGGTTGT 59.001 50.000 0.00 0.00 0.00 3.32
4600 5140 2.142356 TTGGGAGGCATGTATGGTTG 57.858 50.000 0.00 0.00 0.00 3.77
4601 5141 2.042979 ACTTTGGGAGGCATGTATGGTT 59.957 45.455 0.00 0.00 0.00 3.67
4602 5142 1.640670 ACTTTGGGAGGCATGTATGGT 59.359 47.619 0.00 0.00 0.00 3.55
4603 5143 2.442236 ACTTTGGGAGGCATGTATGG 57.558 50.000 0.00 0.00 0.00 2.74
4604 5144 5.913137 TTAAACTTTGGGAGGCATGTATG 57.087 39.130 0.00 0.00 0.00 2.39
4605 5145 6.252995 TCTTTAAACTTTGGGAGGCATGTAT 58.747 36.000 0.00 0.00 0.00 2.29
4606 5146 5.636123 TCTTTAAACTTTGGGAGGCATGTA 58.364 37.500 0.00 0.00 0.00 2.29
4607 5147 4.479158 TCTTTAAACTTTGGGAGGCATGT 58.521 39.130 0.00 0.00 0.00 3.21
4665 5206 7.959658 TTTCATGTATGAATCAAGATGGGTT 57.040 32.000 8.02 0.00 45.30 4.11
4666 5207 7.781219 TCATTTCATGTATGAATCAAGATGGGT 59.219 33.333 8.02 0.00 45.30 4.51
4667 5208 8.080417 GTCATTTCATGTATGAATCAAGATGGG 58.920 37.037 8.02 0.00 45.30 4.00
4670 5211 9.064706 GGAGTCATTTCATGTATGAATCAAGAT 57.935 33.333 26.35 0.00 44.58 2.40
4682 5223 9.471702 AGATGATTTTTAGGAGTCATTTCATGT 57.528 29.630 0.00 0.00 31.86 3.21
4694 5235 5.253330 AGGACGCAAAGATGATTTTTAGGA 58.747 37.500 0.00 0.00 0.00 2.94
4715 5258 4.511826 GGCGGTAATCAGAAAACTCATAGG 59.488 45.833 0.00 0.00 0.00 2.57
4736 5279 4.128388 CCGGGGTCAAAATGCGGC 62.128 66.667 0.00 0.00 0.00 6.53
4739 5282 2.994417 TGCCCGGGGTCAAAATGC 60.994 61.111 25.28 4.35 0.00 3.56
4740 5283 3.005540 GCTGCCCGGGGTCAAAATG 62.006 63.158 25.28 1.51 0.00 2.32
4777 5320 2.996621 GCTACTGGCATCACGGATATTC 59.003 50.000 0.00 0.00 41.35 1.75
4791 5334 3.215151 TCTCTTCGGATAGTGCTACTGG 58.785 50.000 0.00 0.00 0.00 4.00
4837 5380 5.687780 TGAATCATATGAGTGGTGCATCTT 58.312 37.500 10.96 0.00 0.00 2.40
4898 5491 2.009774 GTGGCGACAGTATGCAGAAAT 58.990 47.619 0.00 0.00 44.46 2.17
4903 5496 4.596311 CTGTGGCGACAGTATGCA 57.404 55.556 19.70 0.00 44.15 3.96
4929 5522 1.004394 GTTGTAGCTAAACAGGGGGCT 59.996 52.381 0.00 0.00 38.62 5.19
4930 5523 1.004394 AGTTGTAGCTAAACAGGGGGC 59.996 52.381 16.14 0.00 0.00 5.80
4946 5539 4.082408 AGTCAATCAATGTGGATGCAGTTG 60.082 41.667 6.07 6.07 0.00 3.16
4966 5559 1.282875 GGAGGTTTGTGCGCAAGTC 59.717 57.895 14.00 10.96 41.68 3.01
4967 5560 2.193536 GGGAGGTTTGTGCGCAAGT 61.194 57.895 14.00 2.03 41.68 3.16
4968 5561 1.455383 AAGGGAGGTTTGTGCGCAAG 61.455 55.000 14.00 0.00 35.82 4.01
4971 5564 1.940613 CTATAAGGGAGGTTTGTGCGC 59.059 52.381 0.00 0.00 0.00 6.09
4972 5565 2.561569 CCTATAAGGGAGGTTTGTGCG 58.438 52.381 0.00 0.00 0.00 5.34
4984 5577 6.258068 CGTTTTCTCTTTGCTACCCTATAAGG 59.742 42.308 0.00 0.00 34.30 2.69
4985 5578 6.258068 CCGTTTTCTCTTTGCTACCCTATAAG 59.742 42.308 0.00 0.00 0.00 1.73
4986 5579 6.070653 TCCGTTTTCTCTTTGCTACCCTATAA 60.071 38.462 0.00 0.00 0.00 0.98
4987 5580 5.422970 TCCGTTTTCTCTTTGCTACCCTATA 59.577 40.000 0.00 0.00 0.00 1.31
4988 5581 4.224370 TCCGTTTTCTCTTTGCTACCCTAT 59.776 41.667 0.00 0.00 0.00 2.57
4990 5583 2.370849 TCCGTTTTCTCTTTGCTACCCT 59.629 45.455 0.00 0.00 0.00 4.34
4991 5584 2.774687 TCCGTTTTCTCTTTGCTACCC 58.225 47.619 0.00 0.00 0.00 3.69
4992 5585 4.000988 TGATCCGTTTTCTCTTTGCTACC 58.999 43.478 0.00 0.00 0.00 3.18
4993 5586 4.451096 TGTGATCCGTTTTCTCTTTGCTAC 59.549 41.667 0.00 0.00 0.00 3.58
4996 5589 3.896648 TGTGATCCGTTTTCTCTTTGC 57.103 42.857 0.00 0.00 0.00 3.68
4997 5590 5.362556 ACATGTGATCCGTTTTCTCTTTG 57.637 39.130 0.00 0.00 0.00 2.77
4998 5591 5.995282 TGTACATGTGATCCGTTTTCTCTTT 59.005 36.000 9.11 0.00 0.00 2.52
5000 5593 5.147330 TGTACATGTGATCCGTTTTCTCT 57.853 39.130 9.11 0.00 0.00 3.10
5014 5607 1.080093 CGTGACGCCCTGTACATGT 60.080 57.895 2.69 2.69 0.00 3.21
5025 5618 4.033129 TGGTTTTATATGCTAACGTGACGC 59.967 41.667 4.25 0.00 0.00 5.19
5063 5656 2.489073 GGAATGTTCCCCCGATATTGCT 60.489 50.000 0.09 0.00 41.62 3.91


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

AutoCloner maintained by Alex Coulton.