Multiple sequence alignment - TraesCS1D01G333900

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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 TraesCS1D01G333900 chr1D 100.000 6278 0 0 2256 8533 423862283 423856006 0.000000e+00 11594.0
1 TraesCS1D01G333900 chr1D 100.000 2009 0 0 1 2009 423864538 423862530 0.000000e+00 3711.0
2 TraesCS1D01G333900 chr1D 85.271 258 31 5 2372 2628 403274880 403275131 8.500000e-65 259.0
3 TraesCS1D01G333900 chr1B 95.946 4267 119 29 2261 6479 573385803 573381543 0.000000e+00 6872.0
4 TraesCS1D01G333900 chr1B 96.906 1002 30 1 6482 7483 573381470 573380470 0.000000e+00 1677.0
5 TraesCS1D01G333900 chr1B 89.960 1265 82 30 760 2001 573387396 573386154 0.000000e+00 1591.0
6 TraesCS1D01G333900 chr1B 93.888 769 42 3 1 768 573388181 573387417 0.000000e+00 1155.0
7 TraesCS1D01G333900 chr1B 93.333 555 32 3 7722 8272 573371862 573371309 0.000000e+00 815.0
8 TraesCS1D01G333900 chr1B 96.311 244 9 0 7482 7725 573380377 573380134 1.330000e-107 401.0
9 TraesCS1D01G333900 chr1B 92.511 227 9 2 8271 8497 573371246 573371028 1.380000e-82 318.0
10 TraesCS1D01G333900 chr1B 85.714 238 30 4 2390 2626 542136634 542136868 1.840000e-61 248.0
11 TraesCS1D01G333900 chr1B 97.727 44 1 0 7568 7611 573380246 573380203 9.190000e-10 76.8
12 TraesCS1D01G333900 chr1A 96.526 3483 77 10 2393 5833 520343764 520340284 0.000000e+00 5722.0
13 TraesCS1D01G333900 chr1A 94.755 1182 41 8 6237 7415 520339280 520338117 0.000000e+00 1820.0
14 TraesCS1D01G333900 chr1A 89.315 1095 75 25 826 1887 520344867 520343782 0.000000e+00 1336.0
15 TraesCS1D01G333900 chr1A 97.115 416 11 1 5825 6239 520340099 520339684 0.000000e+00 701.0
16 TraesCS1D01G333900 chr1A 85.882 255 29 4 2372 2625 498534238 498534486 1.830000e-66 265.0
17 TraesCS1D01G333900 chr1A 86.413 184 23 2 649 831 53653021 53652839 5.220000e-47 200.0
18 TraesCS1D01G333900 chr1A 91.549 71 6 0 649 719 53653065 53652995 1.960000e-16 99.0
19 TraesCS1D01G333900 chr1A 89.855 69 6 1 651 719 53653106 53653039 4.240000e-13 87.9
20 TraesCS1D01G333900 chrUn 100.000 422 0 0 4850 5271 476756149 476755728 0.000000e+00 780.0
21 TraesCS1D01G333900 chr3D 85.551 263 29 6 2378 2634 168185651 168185910 5.080000e-67 267.0
22 TraesCS1D01G333900 chr7D 85.156 256 31 5 2380 2634 436499195 436498946 1.100000e-63 255.0
23 TraesCS1D01G333900 chr5A 84.047 257 34 6 2380 2634 130535261 130535512 3.080000e-59 241.0
24 TraesCS1D01G333900 chr6A 82.955 264 41 3 2371 2634 73666954 73667213 1.430000e-57 235.0
25 TraesCS1D01G333900 chr4B 87.640 89 8 3 642 729 399199882 399199968 5.450000e-17 100.0
26 TraesCS1D01G333900 chr4B 91.549 71 6 0 649 719 399199933 399200003 1.960000e-16 99.0
27 TraesCS1D01G333900 chr4D 88.000 75 9 0 645 719 321913383 321913309 1.180000e-13 89.8
28 TraesCS1D01G333900 chr3B 85.542 83 8 3 650 730 807429244 807429324 5.490000e-12 84.2
29 TraesCS1D01G333900 chr2B 86.486 74 8 2 648 719 36778647 36778574 7.100000e-11 80.5


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 TraesCS1D01G333900 chr1D 423856006 423864538 8532 True 7652.500000 11594 100.00000 1 8533 2 chr1D.!!$R1 8532
1 TraesCS1D01G333900 chr1B 573380134 573388181 8047 True 1962.133333 6872 95.12300 1 7725 6 chr1B.!!$R2 7724
2 TraesCS1D01G333900 chr1B 573371028 573371862 834 True 566.500000 815 92.92200 7722 8497 2 chr1B.!!$R1 775
3 TraesCS1D01G333900 chr1A 520338117 520344867 6750 True 2394.750000 5722 94.42775 826 7415 4 chr1A.!!$R2 6589

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
545 547 0.391793 CGTCTTTCCCTTCTCCAGGC 60.392 60.000 0.00 0.0 42.29 4.85 F
1198 1238 0.310232 CTACCGCGCTCCTAGGTTAC 59.690 60.000 9.08 0.0 39.31 2.50 F
1952 2033 0.107410 TGTCTTTGGCCAACGAGTGT 60.107 50.000 23.91 0.0 0.00 3.55 F
2730 2934 1.133199 TCAACCCCTGCATTCCAAGTT 60.133 47.619 0.00 0.0 0.00 2.66 F
3816 4024 1.756538 ACCAAAACCAAAGCTGACCAG 59.243 47.619 0.00 0.0 0.00 4.00 F
4406 4628 1.078528 CCCCAGGTTTTCCCCCTTC 59.921 63.158 0.00 0.0 41.86 3.46 F
5923 6344 2.431942 GTTCATGTCGGCGTCGGT 60.432 61.111 10.62 0.0 36.95 4.69 F
6764 7666 2.555227 GGGAAGGCTGATTGTGGAGAAA 60.555 50.000 0.00 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1636 1715 0.473501 AATGCTTGGGGCCTTCCAAA 60.474 50.000 13.72 1.87 45.13 3.28 R
2730 2934 1.200519 GGTACAGACACTATGGGCCA 58.799 55.000 9.61 9.61 0.00 5.36 R
3784 3992 2.968574 TGGTTTTGGTGCAACATATGGT 59.031 40.909 4.62 0.00 39.98 3.55 R
4388 4609 1.078528 GAAGGGGGAAAACCTGGGG 59.921 63.158 0.00 0.00 38.63 4.96 R
5493 5716 0.960861 CCTGTTTCTTCTTCCGCCCC 60.961 60.000 0.00 0.00 0.00 5.80 R
6194 6616 0.664224 ACCCTTTTTGCACGTAACCG 59.336 50.000 0.00 0.00 40.83 4.44 R
7518 8514 0.958822 ACTTTCCGATGTGCAAACCC 59.041 50.000 0.00 0.00 0.00 4.11 R
8137 9134 0.038599 TGATGTTGGGTCTGCTGCAT 59.961 50.000 1.31 0.00 0.00 3.96 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
136 137 4.941657 TCATGTGATCTAGTGCTAAGCAG 58.058 43.478 0.00 0.00 40.08 4.24
139 140 3.118992 TGTGATCTAGTGCTAAGCAGGTG 60.119 47.826 0.00 0.00 40.08 4.00
167 168 1.027357 CATTCACCATAGCAGCCACC 58.973 55.000 0.00 0.00 0.00 4.61
191 192 0.683973 ATCTATCTGGCTCTTGGGCG 59.316 55.000 0.00 0.00 44.11 6.13
192 193 1.596477 CTATCTGGCTCTTGGGCGC 60.596 63.158 0.00 0.00 44.11 6.53
285 286 2.103153 TACCCCCTCCATAAGAGCTG 57.897 55.000 0.00 0.00 41.74 4.24
331 332 1.337728 ACACCGCAGAATGAATCGACA 60.338 47.619 0.00 0.00 39.69 4.35
338 339 3.493877 GCAGAATGAATCGACAGGATGAG 59.506 47.826 0.00 0.00 36.43 2.90
354 355 0.612732 TGAGAAAGCAATGGCCCCTG 60.613 55.000 0.00 0.00 42.56 4.45
400 401 0.549950 CCTCCAGTGCCATCATCCTT 59.450 55.000 0.00 0.00 0.00 3.36
408 409 1.133699 TGCCATCATCCTTCATCCACC 60.134 52.381 0.00 0.00 0.00 4.61
421 422 2.257409 ATCCACCGCCCATCAGTGTC 62.257 60.000 0.00 0.00 0.00 3.67
424 425 2.124983 CCGCCCATCAGTGTCCAG 60.125 66.667 0.00 0.00 0.00 3.86
442 443 1.348064 AGTTTCACTGATCCCACCGA 58.652 50.000 0.00 0.00 0.00 4.69
445 446 1.884075 TTCACTGATCCCACCGACGG 61.884 60.000 13.61 13.61 0.00 4.79
462 463 3.706055 GGTGGTATCCATCGCACAT 57.294 52.632 0.00 0.00 35.28 3.21
470 471 2.702898 TCCATCGCACATGTGTTTTG 57.297 45.000 26.01 18.90 0.00 2.44
472 473 1.269174 CCATCGCACATGTGTTTTGGA 59.731 47.619 26.01 15.59 31.21 3.53
503 505 6.199393 GTTCCATGTGACTTCTGTTTTACAC 58.801 40.000 0.00 0.00 0.00 2.90
533 535 4.062991 ACAATAGACAACCACCGTCTTTC 58.937 43.478 0.00 0.00 40.89 2.62
545 547 0.391793 CGTCTTTCCCTTCTCCAGGC 60.392 60.000 0.00 0.00 42.29 4.85
552 554 2.438075 CTTCTCCAGGCCAGCAGC 60.438 66.667 5.01 0.00 42.60 5.25
577 579 2.309613 TGTTGCTGGATGCTCAAAAGT 58.690 42.857 0.00 0.00 43.37 2.66
595 597 4.755266 AAGTGTATCCATGTACCCACTC 57.245 45.455 5.99 0.00 0.00 3.51
600 602 2.335681 TCCATGTACCCACTCAGGAA 57.664 50.000 0.00 0.00 41.22 3.36
615 617 0.674895 AGGAAGCGGCATGACACTTC 60.675 55.000 19.24 19.24 38.22 3.01
620 622 1.421410 GCGGCATGACACTTCTACCG 61.421 60.000 0.00 0.00 41.97 4.02
621 623 0.806102 CGGCATGACACTTCTACCGG 60.806 60.000 0.00 0.00 35.63 5.28
622 624 1.090052 GGCATGACACTTCTACCGGC 61.090 60.000 0.00 0.00 0.00 6.13
742 744 9.448438 TTTGATATATGAGGGTGGATTTTATCG 57.552 33.333 0.00 0.00 0.00 2.92
745 747 2.483547 TGAGGGTGGATTTTATCGGGA 58.516 47.619 0.00 0.00 0.00 5.14
747 749 4.236195 TGAGGGTGGATTTTATCGGGATA 58.764 43.478 0.00 0.00 0.00 2.59
768 770 8.562892 GGGATATGATTAGTCACAACATTTGAG 58.437 37.037 0.00 0.00 37.14 3.02
769 771 9.330063 GGATATGATTAGTCACAACATTTGAGA 57.670 33.333 0.00 0.00 37.14 3.27
780 811 6.491062 TCACAACATTTGAGAGATTTGTGGAT 59.509 34.615 11.26 0.00 42.56 3.41
843 875 8.121305 AGAATTATGTGATTTTGTGGTAGCAA 57.879 30.769 0.00 0.00 0.00 3.91
868 903 2.789917 CTGCTGCAGATTCACGGC 59.210 61.111 24.88 0.00 39.97 5.68
948 987 0.808755 CTAACCCAATCCAACGGTGC 59.191 55.000 0.00 0.00 0.00 5.01
979 1019 1.396653 GACGGGTCGATAGGAAGGAA 58.603 55.000 0.00 0.00 0.00 3.36
997 1037 3.217743 CCGGACCTAGTCGCTCCC 61.218 72.222 0.00 0.00 32.65 4.30
1139 1179 1.151677 TACCCTGACCCCAAGCCTT 60.152 57.895 0.00 0.00 0.00 4.35
1143 1183 2.451493 TGACCCCAAGCCTTCCCA 60.451 61.111 0.00 0.00 0.00 4.37
1195 1235 3.217743 GCTACCGCGCTCCTAGGT 61.218 66.667 9.08 7.58 41.73 3.08
1196 1236 2.783288 GCTACCGCGCTCCTAGGTT 61.783 63.158 9.08 0.00 39.31 3.50
1197 1237 1.450531 GCTACCGCGCTCCTAGGTTA 61.451 60.000 9.08 0.00 39.31 2.85
1198 1238 0.310232 CTACCGCGCTCCTAGGTTAC 59.690 60.000 9.08 0.00 39.31 2.50
1199 1239 1.439353 TACCGCGCTCCTAGGTTACG 61.439 60.000 9.08 12.09 39.31 3.18
1200 1240 2.654404 CGCGCTCCTAGGTTACGC 60.654 66.667 25.53 25.53 45.72 4.42
1201 1241 2.654404 GCGCTCCTAGGTTACGCG 60.654 66.667 22.91 23.04 45.88 6.01
1202 1242 2.025727 CGCTCCTAGGTTACGCGG 59.974 66.667 21.17 9.43 40.11 6.46
1203 1243 2.279318 GCTCCTAGGTTACGCGGC 60.279 66.667 12.47 0.00 0.00 6.53
1306 1375 1.198759 TGCGGAGAAAGGTAGGGCTT 61.199 55.000 0.00 0.00 0.00 4.35
1427 1501 1.393539 CGGCACTAACAATTGGAGACG 59.606 52.381 10.83 4.67 0.00 4.18
1563 1637 2.286833 GTGTCGTACCGCAATTGCATAT 59.713 45.455 28.77 15.89 42.21 1.78
1567 1641 5.237561 TGTCGTACCGCAATTGCATATATTT 59.762 36.000 28.77 7.73 42.21 1.40
1570 1644 7.634817 GTCGTACCGCAATTGCATATATTTATC 59.365 37.037 28.77 7.08 42.21 1.75
1647 1726 3.552132 TTGTTTTTCTTTGGAAGGCCC 57.448 42.857 0.00 0.00 32.61 5.80
1689 1768 4.994734 CACTATTTGCGTGCTAAGTATCG 58.005 43.478 0.00 0.00 0.00 2.92
1773 1854 4.081752 CACCTCTGCCATAGTATCATCTCC 60.082 50.000 0.00 0.00 0.00 3.71
1777 1858 6.382282 CCTCTGCCATAGTATCATCTCCATAA 59.618 42.308 0.00 0.00 0.00 1.90
1802 1883 5.477510 TGTGAGTTTTGTGATGTTGCTTTT 58.522 33.333 0.00 0.00 0.00 2.27
1893 1974 1.803289 GCACCTCGCTTGGGATTTC 59.197 57.895 0.00 0.00 37.77 2.17
1912 1993 1.091771 CGTCCTCGCCTTGCATGAAT 61.092 55.000 0.00 0.00 0.00 2.57
1923 2004 3.763360 CCTTGCATGAATGGTTCAACCTA 59.237 43.478 8.40 0.00 43.95 3.08
1946 2027 2.092323 GGTCCTATGTCTTTGGCCAAC 58.908 52.381 20.35 8.65 0.00 3.77
1952 2033 0.107410 TGTCTTTGGCCAACGAGTGT 60.107 50.000 23.91 0.00 0.00 3.55
1957 2038 4.453136 GTCTTTGGCCAACGAGTGTTATAA 59.547 41.667 23.91 1.33 36.28 0.98
1959 2040 2.352388 TGGCCAACGAGTGTTATAAGC 58.648 47.619 0.61 0.00 36.28 3.09
1998 2079 4.543590 AACTGAGAATGTGGTAGGTCTG 57.456 45.455 0.00 0.00 0.00 3.51
2001 2082 4.463186 ACTGAGAATGTGGTAGGTCTGTAC 59.537 45.833 0.00 0.00 0.00 2.90
2002 2083 4.673968 TGAGAATGTGGTAGGTCTGTACT 58.326 43.478 0.00 0.00 0.00 2.73
2003 2084 5.823312 TGAGAATGTGGTAGGTCTGTACTA 58.177 41.667 0.00 0.00 0.00 1.82
2004 2085 6.250711 TGAGAATGTGGTAGGTCTGTACTAA 58.749 40.000 0.00 0.00 0.00 2.24
2006 2087 7.093902 TGAGAATGTGGTAGGTCTGTACTAAAG 60.094 40.741 0.00 0.00 0.00 1.85
2007 2088 5.934402 ATGTGGTAGGTCTGTACTAAAGG 57.066 43.478 0.00 0.00 0.00 3.11
2008 2089 4.091549 TGTGGTAGGTCTGTACTAAAGGG 58.908 47.826 0.00 0.00 0.00 3.95
2293 2466 9.923143 AGATGTAATGAATTTATGCATCAATGG 57.077 29.630 20.16 0.00 35.18 3.16
2294 2467 9.917129 GATGTAATGAATTTATGCATCAATGGA 57.083 29.630 0.19 0.00 33.56 3.41
2298 2471 7.667043 ATGAATTTATGCATCAATGGATTGC 57.333 32.000 0.19 0.00 39.62 3.56
2333 2506 3.559597 CCACAATGGCCAATGGAAAATGT 60.560 43.478 24.49 9.75 33.80 2.71
2370 2543 6.040278 TGTCCACTCAAATTGCACTTTAATCA 59.960 34.615 1.27 0.00 0.00 2.57
2615 2790 7.715657 ACTTCAGACAAATTTTACATGCAGAA 58.284 30.769 0.00 0.00 0.00 3.02
2715 2919 6.177610 TGTTCCTATTCCTGTGTATTCAACC 58.822 40.000 0.00 0.00 0.00 3.77
2730 2934 1.133199 TCAACCCCTGCATTCCAAGTT 60.133 47.619 0.00 0.00 0.00 2.66
2944 3148 2.961062 GGGCTATACTCGGTTCTTGGTA 59.039 50.000 0.00 0.00 0.00 3.25
3531 3737 9.917887 ATCTTTGTTTATCTCATCTTCTGGAAT 57.082 29.630 0.00 0.00 0.00 3.01
3570 3776 8.891671 TTTTAGTCGTTAAATGTAGGTCTTGT 57.108 30.769 0.00 0.00 31.57 3.16
3571 3777 8.891671 TTTAGTCGTTAAATGTAGGTCTTGTT 57.108 30.769 0.00 0.00 0.00 2.83
3784 3992 2.300152 CAGTCAACCTCCTGTAGAAGCA 59.700 50.000 0.00 0.00 0.00 3.91
3816 4024 1.756538 ACCAAAACCAAAGCTGACCAG 59.243 47.619 0.00 0.00 0.00 4.00
3999 4213 6.769512 AGCTAGTGGGTATGGTATGTATTTG 58.230 40.000 0.00 0.00 0.00 2.32
4030 4244 8.519799 TTCCTTTTGTGACTTCTATGTTTCTT 57.480 30.769 0.00 0.00 0.00 2.52
4112 4326 9.546428 TTTGTTGTATACCATGTCATATGAGAG 57.454 33.333 5.42 0.00 0.00 3.20
4145 4359 8.916062 TCATTGTGACAATGGCTATAAATTCAT 58.084 29.630 31.10 0.00 0.00 2.57
4370 4591 3.630312 TGTGCCTTGGTTTGTAGTCTTTC 59.370 43.478 0.00 0.00 0.00 2.62
4406 4628 1.078528 CCCCAGGTTTTCCCCCTTC 59.921 63.158 0.00 0.00 41.86 3.46
4426 4648 7.390027 CCCTTCCTGACCATATATTCACTAAG 58.610 42.308 0.00 0.00 0.00 2.18
4504 4727 7.026562 TCAAATTTTACATACGCTGATGTTGG 58.973 34.615 5.76 0.00 40.54 3.77
4509 4732 7.618502 TTTACATACGCTGATGTTGGTATTT 57.381 32.000 5.76 0.00 40.54 1.40
5394 5617 4.423625 AGTAACAGAGTCTGCAAAACCT 57.576 40.909 20.31 4.98 34.37 3.50
5902 6323 5.124936 ACCTTCTTTGTAGGTGTTTGTGAAC 59.875 40.000 0.00 0.00 44.25 3.18
5914 6335 4.262045 GTGTTTGTGAACGTTGTTCATGTC 59.738 41.667 5.00 4.18 38.65 3.06
5923 6344 2.431942 GTTCATGTCGGCGTCGGT 60.432 61.111 10.62 0.00 36.95 4.69
6194 6616 3.584733 AAATATGCCTTCTGGGACCTC 57.415 47.619 0.00 0.00 36.19 3.85
6409 7240 9.225436 GGACTTGAAATATGATAAGAGAATCCC 57.775 37.037 0.00 0.00 33.66 3.85
6699 7601 4.093743 TGACTTGACCATGCCTACTCTTA 58.906 43.478 0.00 0.00 0.00 2.10
6764 7666 2.555227 GGGAAGGCTGATTGTGGAGAAA 60.555 50.000 0.00 0.00 0.00 2.52
7204 8106 2.684881 CAGCCACTTGTTTGAACTGACT 59.315 45.455 0.00 0.00 0.00 3.41
7226 8128 4.242475 TGAAGTTTTGACGATGTAGCGAT 58.758 39.130 0.00 0.00 34.83 4.58
7384 8286 4.214332 GTGTGACATTTGAGAGAGGAAACC 59.786 45.833 0.00 0.00 0.00 3.27
7540 8536 3.071479 GGTTTGCACATCGGAAAGTAGA 58.929 45.455 0.00 0.00 35.36 2.59
7544 8540 2.094182 TGCACATCGGAAAGTAGAGGTC 60.094 50.000 0.00 0.00 0.00 3.85
7623 8619 2.762887 TCACCTTGCCACACAAAAATCA 59.237 40.909 0.00 0.00 37.96 2.57
7645 8641 3.623060 AGTGTATCATGTTTGGTGCGATC 59.377 43.478 0.00 0.00 0.00 3.69
7656 8652 1.723870 GTGCGATCATCACCTTGCC 59.276 57.895 4.26 0.00 0.00 4.52
7665 8661 2.093921 TCATCACCTTGCCATGCATTTG 60.094 45.455 0.00 0.00 38.76 2.32
7712 8708 3.535561 TCATCGGAAAAAGCCTCTCATC 58.464 45.455 0.00 0.00 0.00 2.92
7729 8725 6.199908 CCTCTCATCGAATGTGTCTTATTCAC 59.800 42.308 0.00 0.00 34.90 3.18
7736 8732 6.009474 CGAATGTGTCTTATTCACGAAACTG 58.991 40.000 0.00 0.00 38.48 3.16
7739 8735 6.466308 TGTGTCTTATTCACGAAACTGATG 57.534 37.500 0.00 0.00 38.48 3.07
7787 8784 8.854614 AGTATAGTTCAAATATGCAATCCTCC 57.145 34.615 0.00 0.00 0.00 4.30
7792 8789 6.608405 AGTTCAAATATGCAATCCTCCATGAA 59.392 34.615 0.00 0.00 0.00 2.57
7824 8821 8.644216 TGAATAATTTACCCGCTTAGAGATACA 58.356 33.333 0.00 0.00 0.00 2.29
7834 8831 4.621991 GCTTAGAGATACAATGGCTCGAA 58.378 43.478 0.00 0.00 33.98 3.71
7842 8839 6.093404 AGATACAATGGCTCGAACATATACG 58.907 40.000 3.02 0.00 0.00 3.06
7891 8888 9.103048 CGAATATTCACAAACTCAACAAAGTAC 57.897 33.333 15.57 0.00 0.00 2.73
7892 8889 9.944663 GAATATTCACAAACTCAACAAAGTACA 57.055 29.630 10.68 0.00 0.00 2.90
8046 9043 1.146041 GGCCACATACCGCTCATCA 59.854 57.895 0.00 0.00 0.00 3.07
8048 9045 1.151668 GCCACATACCGCTCATCATC 58.848 55.000 0.00 0.00 0.00 2.92
8055 9052 1.068753 CCGCTCATCATCGCCTCTT 59.931 57.895 0.00 0.00 0.00 2.85
8062 9059 2.057316 CATCATCGCCTCTTCGACATC 58.943 52.381 0.00 0.00 41.62 3.06
8063 9060 1.102978 TCATCGCCTCTTCGACATCA 58.897 50.000 0.00 0.00 41.62 3.07
8101 9098 4.158786 ACCATCATGTTTGAACATCCCAA 58.841 39.130 6.39 0.00 46.10 4.12
8123 9120 0.040067 CTTGCGCAAAGACAAGTCCC 60.040 55.000 25.01 0.00 38.75 4.46
8146 9143 3.204505 GCAAAGCAAATGCAGCAGA 57.795 47.368 8.28 0.00 45.16 4.26
8147 9144 0.788391 GCAAAGCAAATGCAGCAGAC 59.212 50.000 8.28 0.00 45.16 3.51
8148 9145 1.425412 CAAAGCAAATGCAGCAGACC 58.575 50.000 8.28 0.00 45.16 3.85
8149 9146 0.319405 AAAGCAAATGCAGCAGACCC 59.681 50.000 8.28 0.00 45.16 4.46
8151 9148 0.828762 AGCAAATGCAGCAGACCCAA 60.829 50.000 8.28 0.00 45.16 4.12
8158 9158 0.890542 GCAGCAGACCCAACATCACA 60.891 55.000 0.00 0.00 0.00 3.58
8166 9166 1.270625 ACCCAACATCACACACTACCG 60.271 52.381 0.00 0.00 0.00 4.02
8220 9220 1.625818 ACCAGTGTCAGTGGATCCTTC 59.374 52.381 29.84 6.36 41.28 3.46
8246 9246 4.717877 TGAATCACTCAGAAAAAGAGGCA 58.282 39.130 0.00 0.00 37.43 4.75
8249 9249 3.329386 TCACTCAGAAAAAGAGGCATCG 58.671 45.455 0.00 0.00 37.43 3.84
8315 9379 2.484889 GTGTCCTTCACTCACAGGTTC 58.515 52.381 0.00 0.00 43.13 3.62
8339 9403 2.351455 GGGCACTTTCTGCTTAGAGAC 58.649 52.381 0.00 0.00 46.25 3.36
8354 9418 1.145738 AGAGACTGGTTGGTGGCAAAT 59.854 47.619 0.00 0.00 0.00 2.32
8430 9494 9.120538 TCTCACATTATTTAGGTAAAGATTGGC 57.879 33.333 4.79 0.00 0.00 4.52
8476 9540 3.898482 TCTATCAAGTGGTGGATCTCGA 58.102 45.455 0.00 0.00 0.00 4.04
8490 9554 2.125552 TCGAGGCTTGCATCACCG 60.126 61.111 7.99 0.00 0.00 4.94
8497 9561 1.244019 GCTTGCATCACCGGAACCTT 61.244 55.000 9.46 0.00 0.00 3.50
8498 9562 1.247567 CTTGCATCACCGGAACCTTT 58.752 50.000 9.46 0.00 0.00 3.11
8499 9563 1.613437 CTTGCATCACCGGAACCTTTT 59.387 47.619 9.46 0.00 0.00 2.27
8500 9564 1.698506 TGCATCACCGGAACCTTTTT 58.301 45.000 9.46 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 112 6.351711 TGCTTAGCACTAGATCACATGAAAT 58.648 36.000 1.39 0.00 31.71 2.17
136 137 6.127758 TGCTATGGTGAATGACATTAAACACC 60.128 38.462 22.07 22.07 45.16 4.16
139 140 5.973565 GCTGCTATGGTGAATGACATTAAAC 59.026 40.000 0.00 0.00 0.00 2.01
167 168 1.274728 CAAGAGCCAGATAGATCCCCG 59.725 57.143 0.00 0.00 0.00 5.73
191 192 0.451383 TGGTTGCACGCATGATTAGC 59.549 50.000 0.00 0.00 0.00 3.09
192 193 2.355444 TGATGGTTGCACGCATGATTAG 59.645 45.455 0.00 0.00 0.00 1.73
207 208 4.442706 GTTGAGACGGATTGTATGATGGT 58.557 43.478 0.00 0.00 0.00 3.55
285 286 1.000060 TGCACTTGAAGCTGAAATGGC 60.000 47.619 0.00 0.00 0.00 4.40
318 319 5.604758 TTCTCATCCTGTCGATTCATTCT 57.395 39.130 0.00 0.00 0.00 2.40
331 332 1.687368 GGGCCATTGCTTTCTCATCCT 60.687 52.381 4.39 0.00 37.74 3.24
338 339 1.187567 ACACAGGGGCCATTGCTTTC 61.188 55.000 4.39 0.00 37.74 2.62
354 355 4.261656 CGGTATGATCCTTAGAGACCACAC 60.262 50.000 0.00 0.00 0.00 3.82
400 401 1.995066 ACTGATGGGCGGTGGATGA 60.995 57.895 0.00 0.00 33.94 2.92
408 409 0.606401 AAACTGGACACTGATGGGCG 60.606 55.000 0.00 0.00 0.00 6.13
424 425 1.439679 GTCGGTGGGATCAGTGAAAC 58.560 55.000 0.00 0.00 0.00 2.78
442 443 1.143183 GTGCGATGGATACCACCGT 59.857 57.895 6.42 0.00 35.80 4.83
445 446 1.599071 CACATGTGCGATGGATACCAC 59.401 52.381 13.94 0.00 35.80 4.16
462 463 2.030363 GGAACGATGCATCCAAAACACA 60.030 45.455 20.87 0.00 35.71 3.72
470 471 1.331756 GTCACATGGAACGATGCATCC 59.668 52.381 20.87 9.17 35.11 3.51
472 473 2.408271 AGTCACATGGAACGATGCAT 57.592 45.000 0.00 0.00 38.25 3.96
503 505 5.469479 GGTGGTTGTCTATTGTTCAAATGG 58.531 41.667 0.00 0.00 0.00 3.16
577 579 3.310288 TCCTGAGTGGGTACATGGATACA 60.310 47.826 0.00 0.00 44.68 2.29
595 597 0.957395 AAGTGTCATGCCGCTTCCTG 60.957 55.000 0.00 0.00 29.40 3.86
600 602 0.108138 GGTAGAAGTGTCATGCCGCT 60.108 55.000 0.00 0.00 0.00 5.52
615 617 3.894547 AAACCAGCACCGCCGGTAG 62.895 63.158 9.25 4.76 32.11 3.18
663 665 5.488262 AACTCAATTCAAAATTCCCCCTG 57.512 39.130 0.00 0.00 0.00 4.45
724 726 3.053077 TCCCGATAAAATCCACCCTCAT 58.947 45.455 0.00 0.00 0.00 2.90
728 730 5.174037 TCATATCCCGATAAAATCCACCC 57.826 43.478 0.00 0.00 0.00 4.61
730 732 9.099454 GACTAATCATATCCCGATAAAATCCAC 57.901 37.037 0.00 0.00 0.00 4.02
732 734 9.099454 GTGACTAATCATATCCCGATAAAATCC 57.901 37.037 0.00 0.00 37.14 3.01
735 737 9.268268 GTTGTGACTAATCATATCCCGATAAAA 57.732 33.333 0.00 0.00 37.14 1.52
742 744 8.450578 TCAAATGTTGTGACTAATCATATCCC 57.549 34.615 0.00 0.00 37.14 3.85
747 749 9.458727 AATCTCTCAAATGTTGTGACTAATCAT 57.541 29.630 0.00 0.00 37.14 2.45
815 846 8.408601 GCTACCACAAAATCACATAATTCTCAT 58.591 33.333 0.00 0.00 0.00 2.90
819 850 8.931385 ATTGCTACCACAAAATCACATAATTC 57.069 30.769 0.00 0.00 32.27 2.17
822 853 7.459795 TGATTGCTACCACAAAATCACATAA 57.540 32.000 0.00 0.00 34.86 1.90
868 903 1.374758 GTCCTGTCAAGTGGCTCCG 60.375 63.158 0.00 0.00 0.00 4.63
997 1037 2.621668 GGAGGTGGAGAATTTTCCCAGG 60.622 54.545 12.27 0.00 36.35 4.45
1052 1092 3.917760 GACGAGGAGGCGGGATGG 61.918 72.222 0.00 0.00 35.12 3.51
1090 1130 2.678934 CCAGGGAGGAACGGTCGA 60.679 66.667 0.00 0.00 41.22 4.20
1139 1179 4.467084 GGGAAGCGCGATGTGGGA 62.467 66.667 12.10 0.00 0.00 4.37
1143 1183 4.814294 GACCGGGAAGCGCGATGT 62.814 66.667 12.10 0.00 42.31 3.06
1291 1360 3.772572 AGAAGAGAAGCCCTACCTTTCTC 59.227 47.826 5.55 5.55 0.00 2.87
1306 1375 5.219343 TGCAACAGATTTCAGAGAAGAGA 57.781 39.130 0.00 0.00 0.00 3.10
1410 1484 6.523201 GCAAATTACGTCTCCAATTGTTAGTG 59.477 38.462 4.43 2.50 0.00 2.74
1427 1501 3.505680 TGTGTGGACATCCTGCAAATTAC 59.494 43.478 0.00 0.00 36.82 1.89
1520 1594 3.126343 CCAATTGAACTTACGTGGTAGCC 59.874 47.826 7.12 0.00 0.00 3.93
1563 1637 7.934665 TGGGCAATTAACGAGCTAAGATAAATA 59.065 33.333 0.00 0.00 0.00 1.40
1567 1641 5.284861 TGGGCAATTAACGAGCTAAGATA 57.715 39.130 0.00 0.00 0.00 1.98
1570 1644 3.181500 GGTTGGGCAATTAACGAGCTAAG 60.181 47.826 0.00 0.00 0.00 2.18
1586 1660 2.338577 TTGGCAAAACAATGGTTGGG 57.661 45.000 0.00 0.00 37.30 4.12
1636 1715 0.473501 AATGCTTGGGGCCTTCCAAA 60.474 50.000 13.72 1.87 45.13 3.28
1637 1716 1.158227 AATGCTTGGGGCCTTCCAA 59.842 52.632 12.37 12.37 43.82 3.53
1638 1717 1.610086 CAATGCTTGGGGCCTTCCA 60.610 57.895 0.84 0.00 40.92 3.53
1689 1768 3.554259 TCTATGTCGATGCCACGATAC 57.446 47.619 5.70 0.00 43.93 2.24
1773 1854 7.383029 AGCAACATCACAAAACTCACAATTATG 59.617 33.333 0.00 0.00 0.00 1.90
1777 1858 5.266733 AGCAACATCACAAAACTCACAAT 57.733 34.783 0.00 0.00 0.00 2.71
1802 1883 2.026262 GCAGGATGGTTACAGAGGGAAA 60.026 50.000 0.00 0.00 35.86 3.13
1893 1974 1.091771 ATTCATGCAAGGCGAGGACG 61.092 55.000 0.00 0.00 42.93 4.79
1923 2004 1.840635 GGCCAAAGACATAGGACCTCT 59.159 52.381 0.00 0.00 0.00 3.69
1935 2016 2.623878 TAACACTCGTTGGCCAAAGA 57.376 45.000 28.79 28.79 36.52 2.52
1946 2027 7.862648 TGATCTACACTAGCTTATAACACTCG 58.137 38.462 0.00 0.00 0.00 4.18
1957 2038 8.067751 TCAGTTTACATTGATCTACACTAGCT 57.932 34.615 0.00 0.00 0.00 3.32
2255 2336 8.674263 AATTCATTACATCTTCATCTCACTCC 57.326 34.615 0.00 0.00 0.00 3.85
2292 2465 3.084039 TGGATTCACAGTTCTGCAATCC 58.916 45.455 23.40 23.40 42.00 3.01
2293 2466 4.088823 GTGGATTCACAGTTCTGCAATC 57.911 45.455 0.00 12.74 43.13 2.67
2333 2506 9.166173 CAATTTGAGTGGACATTCTACAGATTA 57.834 33.333 0.00 0.00 29.47 1.75
2370 2543 6.408770 AAAAAGAAATGGAGGAGGGAGTAT 57.591 37.500 0.00 0.00 0.00 2.12
2459 2633 9.866655 ATAACCATAGTATTGTGGATGTTCATT 57.133 29.630 8.05 0.00 37.77 2.57
2615 2790 4.652679 AGGTCCCTCCGTTTCTTTTTAT 57.347 40.909 0.00 0.00 41.99 1.40
2715 2919 1.593265 GCCAACTTGGAATGCAGGG 59.407 57.895 12.37 0.00 40.96 4.45
2730 2934 1.200519 GGTACAGACACTATGGGCCA 58.799 55.000 9.61 9.61 0.00 5.36
3784 3992 2.968574 TGGTTTTGGTGCAACATATGGT 59.031 40.909 4.62 0.00 39.98 3.55
3816 4024 4.558538 ACAATTTTATCTGGCGCTGATC 57.441 40.909 16.95 0.00 0.00 2.92
3999 4213 9.220767 ACATAGAAGTCACAAAAGGAAGATTAC 57.779 33.333 0.00 0.00 0.00 1.89
4112 4326 6.683974 AGCCATTGTCACAATGAGTTATAC 57.316 37.500 28.87 10.68 0.00 1.47
4145 4359 3.499338 AGGTCAAATGCAACATCCAGAA 58.501 40.909 0.00 0.00 0.00 3.02
4370 4591 5.300286 CCTGGGGACAAAATAAGCATAGAAG 59.700 44.000 0.00 0.00 42.06 2.85
4388 4609 1.078528 GAAGGGGGAAAACCTGGGG 59.921 63.158 0.00 0.00 38.63 4.96
4406 4628 8.597167 TCCATTCTTAGTGAATATATGGTCAGG 58.403 37.037 0.00 0.00 43.00 3.86
5271 5494 5.416947 CCGGACTTAACTATAGTTGTTGCT 58.583 41.667 25.27 3.22 38.90 3.91
5329 5552 5.129485 GTGATCTAATTCTTCCCCACTCTGA 59.871 44.000 0.00 0.00 0.00 3.27
5394 5617 1.179152 CAATCTCAACAGGCATGGCA 58.821 50.000 22.64 0.00 0.00 4.92
5493 5716 0.960861 CCTGTTTCTTCTTCCGCCCC 60.961 60.000 0.00 0.00 0.00 5.80
5854 6275 6.252599 ACCATAGGCATGACTGAATCTAAA 57.747 37.500 12.69 0.00 33.67 1.85
5902 6323 1.129809 GACGCCGACATGAACAACG 59.870 57.895 0.00 0.00 0.00 4.10
5923 6344 5.729510 TCAATGTCATGTTCACTTATCGGA 58.270 37.500 0.00 0.00 0.00 4.55
5926 6347 7.637229 CCAGATCAATGTCATGTTCACTTATC 58.363 38.462 0.00 0.00 0.00 1.75
5927 6348 6.039047 GCCAGATCAATGTCATGTTCACTTAT 59.961 38.462 0.00 0.00 0.00 1.73
5965 6386 3.253230 GTTGAAACCAACTATGCATGCC 58.747 45.455 16.68 0.00 40.44 4.40
5987 6408 1.226974 CACTCGGTGGATCGCGAAT 60.227 57.895 15.24 0.93 0.00 3.34
6194 6616 0.664224 ACCCTTTTTGCACGTAACCG 59.336 50.000 0.00 0.00 40.83 4.44
6409 7240 6.314648 TCAAAATTGATCAGAGGTTGAGATCG 59.685 38.462 0.00 0.00 40.72 3.69
6535 7437 5.372363 TGTGGAACATATAGAATGGGACCAT 59.628 40.000 0.00 0.00 45.67 3.55
6699 7601 2.694628 TCACCTTGTGCAGCAAAATCTT 59.305 40.909 0.00 0.00 36.53 2.40
7204 8106 3.644823 TCGCTACATCGTCAAAACTTCA 58.355 40.909 0.00 0.00 0.00 3.02
7226 8128 4.792068 AGCATGCCAGCCTAGTTTTTATA 58.208 39.130 15.66 0.00 34.23 0.98
7384 8286 3.966154 ACTGCAAGAATATACGACTCCG 58.034 45.455 0.00 0.00 38.71 4.63
7518 8514 0.958822 ACTTTCCGATGTGCAAACCC 59.041 50.000 0.00 0.00 0.00 4.11
7540 8536 9.046296 CAAATATTAGCTTCTGAAATACGACCT 57.954 33.333 0.00 0.00 0.00 3.85
7544 8540 9.638300 GTGTCAAATATTAGCTTCTGAAATACG 57.362 33.333 0.00 0.00 0.00 3.06
7623 8619 3.052455 TCGCACCAAACATGATACACT 57.948 42.857 0.00 0.00 0.00 3.55
7645 8641 2.093921 TCAAATGCATGGCAAGGTGATG 60.094 45.455 0.00 0.00 43.62 3.07
7656 8652 5.647589 ACATTCTAGCAGTTCAAATGCATG 58.352 37.500 13.16 9.25 46.31 4.06
7665 8661 9.765795 ATATGTAAAGGTACATTCTAGCAGTTC 57.234 33.333 4.80 0.00 46.74 3.01
7712 8708 6.009474 CAGTTTCGTGAATAAGACACATTCG 58.991 40.000 0.00 0.00 38.04 3.34
7729 8725 3.558505 CTTGCCTTGTTCATCAGTTTCG 58.441 45.455 0.00 0.00 0.00 3.46
7736 8732 3.019564 AGGTATGCTTGCCTTGTTCATC 58.980 45.455 3.21 0.00 33.59 2.92
7739 8735 3.942130 AAAGGTATGCTTGCCTTGTTC 57.058 42.857 20.27 0.00 46.06 3.18
7787 8784 8.184192 GCGGGTAAATTATTCATATCCTTCATG 58.816 37.037 0.00 0.00 0.00 3.07
7792 8789 8.822805 TCTAAGCGGGTAAATTATTCATATCCT 58.177 33.333 0.00 0.00 0.00 3.24
7824 8821 5.113383 TGTTTCGTATATGTTCGAGCCATT 58.887 37.500 5.16 0.00 37.38 3.16
7842 8839 5.907391 CGTGACCTGTTGAACTAATTGTTTC 59.093 40.000 0.00 0.00 39.30 2.78
7860 8857 5.856126 TGAGTTTGTGAATATTCGTGACC 57.144 39.130 10.80 0.00 0.00 4.02
7924 8921 2.288666 AGACACGAACATGTTTGCTGT 58.711 42.857 23.25 23.10 31.24 4.40
8046 9043 1.107114 ACTGATGTCGAAGAGGCGAT 58.893 50.000 0.00 0.00 42.82 4.58
8048 9045 1.671328 TCTACTGATGTCGAAGAGGCG 59.329 52.381 0.00 0.00 36.95 5.52
8055 9052 5.648092 TCAATTCTGACTCTACTGATGTCGA 59.352 40.000 0.00 0.00 33.81 4.20
8090 9087 1.243342 CGCAAGGCTTGGGATGTTCA 61.243 55.000 33.34 0.00 45.47 3.18
8101 9098 1.103398 ACTTGTCTTTGCGCAAGGCT 61.103 50.000 25.85 4.58 44.45 4.58
8137 9134 0.038599 TGATGTTGGGTCTGCTGCAT 59.961 50.000 1.31 0.00 0.00 3.96
8141 9138 0.473755 TGTGTGATGTTGGGTCTGCT 59.526 50.000 0.00 0.00 0.00 4.24
8142 9139 0.593128 GTGTGTGATGTTGGGTCTGC 59.407 55.000 0.00 0.00 0.00 4.26
8143 9140 2.260844 AGTGTGTGATGTTGGGTCTG 57.739 50.000 0.00 0.00 0.00 3.51
8146 9143 1.270625 CGGTAGTGTGTGATGTTGGGT 60.271 52.381 0.00 0.00 0.00 4.51
8147 9144 1.438651 CGGTAGTGTGTGATGTTGGG 58.561 55.000 0.00 0.00 0.00 4.12
8148 9145 1.438651 CCGGTAGTGTGTGATGTTGG 58.561 55.000 0.00 0.00 0.00 3.77
8149 9146 1.001520 TCCCGGTAGTGTGTGATGTTG 59.998 52.381 0.00 0.00 0.00 3.33
8151 9148 1.480954 GATCCCGGTAGTGTGTGATGT 59.519 52.381 0.00 0.00 0.00 3.06
8166 9166 2.109126 GCAGCGGAACACTGATCCC 61.109 63.158 0.00 0.00 41.72 3.85
8194 9194 2.111878 ACTGACACTGGTGCAGCC 59.888 61.111 14.36 5.89 37.86 4.85
8383 9447 9.265901 GTGAGATCTTCTTGCATTAGCTATTTA 57.734 33.333 0.00 0.00 42.74 1.40
8384 9448 7.772292 TGTGAGATCTTCTTGCATTAGCTATTT 59.228 33.333 0.00 0.00 42.74 1.40
8385 9449 7.278135 TGTGAGATCTTCTTGCATTAGCTATT 58.722 34.615 0.00 0.00 42.74 1.73
8386 9450 6.824553 TGTGAGATCTTCTTGCATTAGCTAT 58.175 36.000 0.00 0.00 42.74 2.97
8387 9451 6.225981 TGTGAGATCTTCTTGCATTAGCTA 57.774 37.500 0.00 0.00 42.74 3.32
8388 9452 5.095145 TGTGAGATCTTCTTGCATTAGCT 57.905 39.130 0.00 0.00 42.74 3.32
8389 9453 6.374565 AATGTGAGATCTTCTTGCATTAGC 57.625 37.500 0.00 0.00 42.57 3.09
8417 9481 1.271926 ACTTGCCGCCAATCTTTACCT 60.272 47.619 0.00 0.00 0.00 3.08
8430 9494 3.059935 GCAATTGTACCAAAAACTTGCCG 60.060 43.478 7.40 0.00 33.26 5.69
8455 9519 3.885901 CTCGAGATCCACCACTTGATAGA 59.114 47.826 6.58 0.00 0.00 1.98
8476 9540 1.675641 GTTCCGGTGATGCAAGCCT 60.676 57.895 0.00 0.00 0.00 4.58


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

AutoCloner maintained by Alex Coulton.