Multiple sequence alignment - TraesCS5D01G228500

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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 TraesCS5D01G228500 chr5D 100.000 5859 0 0 1 5859 335869074 335874932 0.000000e+00 10820
1 TraesCS5D01G228500 chr5D 95.842 2020 74 9 2037 4050 62145465 62143450 0.000000e+00 3256
2 TraesCS5D01G228500 chr1D 94.805 2021 89 8 2046 4058 451869942 451871954 0.000000e+00 3136
3 TraesCS5D01G228500 chr7D 94.669 2026 95 8 2037 4056 566995218 566993200 0.000000e+00 3131
4 TraesCS5D01G228500 chr7D 94.477 2028 93 11 2037 4056 227751699 227753715 0.000000e+00 3107
5 TraesCS5D01G228500 chr7B 94.231 2028 100 10 2039 4058 650044338 650042320 0.000000e+00 3081
6 TraesCS5D01G228500 chr3D 93.261 2018 112 15 2036 4046 568836107 568834107 0.000000e+00 2952
7 TraesCS5D01G228500 chr5A 93.849 1967 105 11 2037 3999 531689511 531691465 0.000000e+00 2948
8 TraesCS5D01G228500 chr5A 87.323 1483 94 43 581 2037 437034662 437036076 0.000000e+00 1611
9 TraesCS5D01G228500 chr5A 93.640 912 43 11 4058 4965 437036076 437036976 0.000000e+00 1349
10 TraesCS5D01G228500 chr5A 87.128 940 54 26 4966 5859 437037153 437038071 0.000000e+00 1003
11 TraesCS5D01G228500 chr5A 86.237 465 47 6 1 453 437034075 437034534 6.820000e-134 488
12 TraesCS5D01G228500 chr6B 93.008 1845 113 11 2036 3870 1403896 1405734 0.000000e+00 2678
13 TraesCS5D01G228500 chr2B 94.035 1274 69 5 2037 3303 352977501 352976228 0.000000e+00 1925
14 TraesCS5D01G228500 chr5B 89.079 1520 99 21 4058 5523 393835144 393836650 0.000000e+00 1825
15 TraesCS5D01G228500 chr5B 89.591 1124 64 26 577 1668 393830584 393831686 0.000000e+00 1378
16 TraesCS5D01G228500 chr5B 89.420 586 44 6 1 572 393829958 393830539 0.000000e+00 723
17 TraesCS5D01G228500 chr5B 94.156 308 11 3 1731 2037 393834843 393835144 4.140000e-126 462
18 TraesCS5D01G228500 chr5B 87.945 365 27 2 5508 5859 393838425 393838785 1.170000e-111 414
19 TraesCS5D01G228500 chr5B 98.333 60 1 0 1681 1740 393832594 393832653 8.030000e-19 106
20 TraesCS5D01G228500 chr4A 93.657 804 40 6 3258 4059 42691332 42690538 0.000000e+00 1192
21 TraesCS5D01G228500 chr4A 93.035 804 44 9 3258 4059 49500601 49499808 0.000000e+00 1164


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 TraesCS5D01G228500 chr5D 335869074 335874932 5858 False 10820.00 10820 100.000000 1 5859 1 chr5D.!!$F1 5858
1 TraesCS5D01G228500 chr5D 62143450 62145465 2015 True 3256.00 3256 95.842000 2037 4050 1 chr5D.!!$R1 2013
2 TraesCS5D01G228500 chr1D 451869942 451871954 2012 False 3136.00 3136 94.805000 2046 4058 1 chr1D.!!$F1 2012
3 TraesCS5D01G228500 chr7D 566993200 566995218 2018 True 3131.00 3131 94.669000 2037 4056 1 chr7D.!!$R1 2019
4 TraesCS5D01G228500 chr7D 227751699 227753715 2016 False 3107.00 3107 94.477000 2037 4056 1 chr7D.!!$F1 2019
5 TraesCS5D01G228500 chr7B 650042320 650044338 2018 True 3081.00 3081 94.231000 2039 4058 1 chr7B.!!$R1 2019
6 TraesCS5D01G228500 chr3D 568834107 568836107 2000 True 2952.00 2952 93.261000 2036 4046 1 chr3D.!!$R1 2010
7 TraesCS5D01G228500 chr5A 531689511 531691465 1954 False 2948.00 2948 93.849000 2037 3999 1 chr5A.!!$F1 1962
8 TraesCS5D01G228500 chr5A 437034075 437038071 3996 False 1112.75 1611 88.582000 1 5859 4 chr5A.!!$F2 5858
9 TraesCS5D01G228500 chr6B 1403896 1405734 1838 False 2678.00 2678 93.008000 2036 3870 1 chr6B.!!$F1 1834
10 TraesCS5D01G228500 chr2B 352976228 352977501 1273 True 1925.00 1925 94.035000 2037 3303 1 chr2B.!!$R1 1266
11 TraesCS5D01G228500 chr5B 393829958 393838785 8827 False 818.00 1825 91.420667 1 5859 6 chr5B.!!$F1 5858
12 TraesCS5D01G228500 chr4A 42690538 42691332 794 True 1192.00 1192 93.657000 3258 4059 1 chr4A.!!$R1 801
13 TraesCS5D01G228500 chr4A 49499808 49500601 793 True 1164.00 1164 93.035000 3258 4059 1 chr4A.!!$R2 801

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
806 889 0.034186 ATTCCAAGCCTGGCGATTCA 60.034 50.000 13.96 0.00 43.17 2.57 F
1490 1616 0.033991 TACTCGCTCTGCTCCTCCTT 60.034 55.000 0.00 0.00 0.00 3.36 F
1668 1824 0.183014 TTGGGCTTGTGGGTTTCGTA 59.817 50.000 0.00 0.00 0.00 3.43 F
2199 5452 0.315568 ACCCGCGAGATCTTGATAGC 59.684 55.000 14.59 6.14 0.00 2.97 F
2247 5500 1.001181 CACCCAACTGATGCCCTTTTG 59.999 52.381 0.00 0.00 0.00 2.44 F
3750 7031 1.209019 CTCCCAGTGCAGCAGATAGTT 59.791 52.381 0.00 0.00 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1646 1802 0.105964 GAAACCCACAAGCCCAAACC 59.894 55.000 0.00 0.00 0.00 3.27 R
3060 6321 0.667993 ACACAGGTCATTTTGGTGCG 59.332 50.000 0.00 0.00 32.89 5.34 R
3112 6373 3.985008 TCTTTTCGATCGTTCAACCTGA 58.015 40.909 15.94 1.73 0.00 3.86 R
3817 7098 0.811616 CCCAGTGCGGCAGATAGTTC 60.812 60.000 1.18 0.00 0.00 3.01 R
4105 7386 1.816074 GGTACCTGAAAATGACCGCA 58.184 50.000 4.06 0.00 0.00 5.69 R
5189 8700 0.387929 TGTCGTCCCTTCTGTGTGAC 59.612 55.000 0.00 0.00 0.00 3.67 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
18 19 2.988684 TTGGGTGCATTGGCCGTC 60.989 61.111 0.00 0.00 40.13 4.79
36 37 2.125269 GTCGCCGGGCTGTACATT 60.125 61.111 18.34 0.00 0.00 2.71
42 43 0.960364 CCGGGCTGTACATTGTGCTT 60.960 55.000 6.45 0.00 0.00 3.91
57 58 3.062639 CTTTGGGGCAAAGCAGGG 58.937 61.111 0.00 0.00 43.07 4.45
68 69 2.142292 AAAGCAGGGGACGCCAAGAT 62.142 55.000 11.67 0.00 0.00 2.40
71 72 3.470888 AGGGGACGCCAAGATCCG 61.471 66.667 11.67 0.00 35.67 4.18
176 177 1.592400 CTCCTAGCGGACGACAACCA 61.592 60.000 0.00 0.00 34.92 3.67
190 191 3.440228 GACAACCAGATCGAGAAGTAGC 58.560 50.000 0.00 0.00 0.00 3.58
191 192 2.166664 ACAACCAGATCGAGAAGTAGCC 59.833 50.000 0.00 0.00 0.00 3.93
192 193 2.145397 ACCAGATCGAGAAGTAGCCA 57.855 50.000 0.00 0.00 0.00 4.75
193 194 2.028130 ACCAGATCGAGAAGTAGCCAG 58.972 52.381 0.00 0.00 0.00 4.85
194 195 1.339610 CCAGATCGAGAAGTAGCCAGG 59.660 57.143 0.00 0.00 0.00 4.45
214 215 4.026052 AGGGGCTCTACAATTTTGGAATG 58.974 43.478 0.00 0.00 0.00 2.67
229 230 2.027385 GGAATGGCCAGTGATCTTTCC 58.973 52.381 12.17 13.73 36.34 3.13
260 261 3.320826 GGTCCCATGTGTTTTTGTAGCTT 59.679 43.478 0.00 0.00 0.00 3.74
332 337 3.945434 GGCATCATGTCGCCGCTG 61.945 66.667 11.49 0.00 38.82 5.18
355 360 6.964908 TGATGTACAAAATATAATGCCCGTG 58.035 36.000 0.00 0.00 0.00 4.94
363 368 2.869233 ATAATGCCCGTGAATGTTGC 57.131 45.000 0.00 0.00 0.00 4.17
374 379 1.317613 GAATGTTGCTGTGTCCCACA 58.682 50.000 0.00 0.00 42.45 4.17
388 393 6.068010 TGTGTCCCACAAATTTAAGATGAGT 58.932 36.000 0.00 0.00 41.69 3.41
389 394 6.206634 TGTGTCCCACAAATTTAAGATGAGTC 59.793 38.462 0.00 0.00 41.69 3.36
417 432 2.226912 TGCTTACCAATTACGGCAACAC 59.773 45.455 0.00 0.00 0.00 3.32
449 470 1.934589 TCGGTGGCTACAATCAATCG 58.065 50.000 1.52 0.00 0.00 3.34
457 478 5.350365 GTGGCTACAATCAATCGTACTTTCA 59.650 40.000 0.00 0.00 0.00 2.69
469 490 2.073816 GTACTTTCACCGTGTCATGGG 58.926 52.381 15.69 3.79 0.00 4.00
500 521 2.578495 GCTTGATCACGCAGAAACTTG 58.422 47.619 18.52 0.00 0.00 3.16
524 545 0.729690 GCGAATCTGGCTTCTTGACC 59.270 55.000 0.00 0.00 0.00 4.02
572 597 2.936919 TGTGCATTTCAGTGAGGACT 57.063 45.000 0.00 0.00 0.00 3.85
573 598 4.350368 TTGTGCATTTCAGTGAGGACTA 57.650 40.909 0.00 0.00 0.00 2.59
574 599 4.350368 TGTGCATTTCAGTGAGGACTAA 57.650 40.909 0.00 0.00 0.00 2.24
575 600 4.065088 TGTGCATTTCAGTGAGGACTAAC 58.935 43.478 0.00 0.00 0.00 2.34
621 700 8.593492 ATGAAAATGAAAGGTGCTAAAGAAAC 57.407 30.769 0.00 0.00 0.00 2.78
623 702 7.706179 TGAAAATGAAAGGTGCTAAAGAAACAG 59.294 33.333 0.00 0.00 0.00 3.16
624 703 5.712152 ATGAAAGGTGCTAAAGAAACAGG 57.288 39.130 0.00 0.00 0.00 4.00
627 706 5.654650 TGAAAGGTGCTAAAGAAACAGGAAA 59.345 36.000 0.00 0.00 0.00 3.13
628 707 6.153680 TGAAAGGTGCTAAAGAAACAGGAAAA 59.846 34.615 0.00 0.00 0.00 2.29
629 708 6.538945 AAGGTGCTAAAGAAACAGGAAAAA 57.461 33.333 0.00 0.00 0.00 1.94
630 709 6.731292 AGGTGCTAAAGAAACAGGAAAAAT 57.269 33.333 0.00 0.00 0.00 1.82
631 710 7.833285 AGGTGCTAAAGAAACAGGAAAAATA 57.167 32.000 0.00 0.00 0.00 1.40
632 711 7.886338 AGGTGCTAAAGAAACAGGAAAAATAG 58.114 34.615 0.00 0.00 0.00 1.73
633 712 7.505923 AGGTGCTAAAGAAACAGGAAAAATAGT 59.494 33.333 0.00 0.00 0.00 2.12
638 717 3.057526 AGAAACAGGAAAAATAGTGCCGC 60.058 43.478 0.00 0.00 0.00 6.53
643 722 0.247537 GAAAAATAGTGCCGCCGACG 60.248 55.000 0.00 0.00 39.67 5.12
664 743 1.530419 ACGGTGCCAGCCAATTCAA 60.530 52.632 0.00 0.00 0.00 2.69
670 749 2.360165 GTGCCAGCCAATTCAAGATAGG 59.640 50.000 0.00 0.00 0.00 2.57
732 815 0.898320 AGAGGGGAACATGAGTCACG 59.102 55.000 0.00 0.00 0.00 4.35
734 817 0.544357 AGGGGAACATGAGTCACGGA 60.544 55.000 0.00 0.00 0.00 4.69
736 819 1.065418 GGGGAACATGAGTCACGGAAT 60.065 52.381 0.00 0.00 0.00 3.01
754 837 4.177783 GGAATCGAAGAGAAGGACAAGAC 58.822 47.826 0.00 0.00 43.63 3.01
804 887 1.560505 AAATTCCAAGCCTGGCGATT 58.439 45.000 13.96 0.00 43.17 3.34
805 888 1.106285 AATTCCAAGCCTGGCGATTC 58.894 50.000 13.96 0.00 43.17 2.52
806 889 0.034186 ATTCCAAGCCTGGCGATTCA 60.034 50.000 13.96 0.00 43.17 2.57
807 890 0.960364 TTCCAAGCCTGGCGATTCAC 60.960 55.000 13.96 0.00 43.17 3.18
855 944 1.269257 GCAGCCGGCAATTCTTTATCC 60.269 52.381 31.54 0.00 43.97 2.59
860 949 3.221771 CCGGCAATTCTTTATCCCATCA 58.778 45.455 0.00 0.00 0.00 3.07
861 950 3.636300 CCGGCAATTCTTTATCCCATCAA 59.364 43.478 0.00 0.00 0.00 2.57
868 960 7.147915 GCAATTCTTTATCCCATCAACTGGTAA 60.148 37.037 0.00 0.00 44.30 2.85
869 961 8.748412 CAATTCTTTATCCCATCAACTGGTAAA 58.252 33.333 0.00 0.00 44.30 2.01
875 967 3.081804 CCCATCAACTGGTAAACTGGTC 58.918 50.000 0.00 0.00 44.30 4.02
886 978 3.251004 GGTAAACTGGTCTGACTGCAAAG 59.749 47.826 7.85 1.43 0.00 2.77
956 1048 2.370189 ACATGGATGCTCCTACTTAGCC 59.630 50.000 0.00 0.00 39.30 3.93
959 1051 0.319986 GATGCTCCTACTTAGCCGGC 60.320 60.000 21.89 21.89 39.30 6.13
1290 1409 2.970324 GCAACCACGTCGCTTCCA 60.970 61.111 0.00 0.00 0.00 3.53
1296 1422 0.803768 CCACGTCGCTTCCATCTCTG 60.804 60.000 0.00 0.00 0.00 3.35
1303 1429 0.602372 GCTTCCATCTCTGATCCCGC 60.602 60.000 0.00 0.00 0.00 6.13
1321 1447 3.499737 CCGCATCCCTCGTGTTGC 61.500 66.667 0.00 0.00 0.00 4.17
1329 1455 1.751351 TCCCTCGTGTTGCTGATAGAG 59.249 52.381 0.00 0.00 0.00 2.43
1330 1456 1.478510 CCCTCGTGTTGCTGATAGAGT 59.521 52.381 0.00 0.00 0.00 3.24
1331 1457 2.688446 CCCTCGTGTTGCTGATAGAGTA 59.312 50.000 0.00 0.00 0.00 2.59
1395 1521 2.044650 TTCATGGGGCTGCAGCTC 60.045 61.111 35.82 33.64 41.88 4.09
1490 1616 0.033991 TACTCGCTCTGCTCCTCCTT 60.034 55.000 0.00 0.00 0.00 3.36
1513 1639 0.389817 TTTCTCCGCCTCACGTCATG 60.390 55.000 0.00 0.00 41.42 3.07
1565 1691 1.221021 GGCCGTCCGATTTCCTTCT 59.779 57.895 0.00 0.00 0.00 2.85
1566 1692 0.392595 GGCCGTCCGATTTCCTTCTT 60.393 55.000 0.00 0.00 0.00 2.52
1646 1802 0.469331 ATCAGGCCTGCCCATTGATG 60.469 55.000 28.91 0.73 36.58 3.07
1668 1824 0.183014 TTGGGCTTGTGGGTTTCGTA 59.817 50.000 0.00 0.00 0.00 3.43
1911 5162 1.589630 CGACCGATGACTGGGTGAA 59.410 57.895 0.00 0.00 36.46 3.18
1954 5205 3.596214 GAACGCCTTCTGTTTCTCCATA 58.404 45.455 0.00 0.00 0.00 2.74
2009 5260 3.205338 GCACCTTGGCTTGAAAACATTT 58.795 40.909 0.00 0.00 0.00 2.32
2019 5270 5.699001 GGCTTGAAAACATTTATCCCGTTTT 59.301 36.000 0.00 0.00 43.54 2.43
2021 5272 7.385478 GGCTTGAAAACATTTATCCCGTTTTTA 59.615 33.333 0.00 0.00 41.57 1.52
2098 5349 6.905067 AATATCTCAGCATTCCCCATATCT 57.095 37.500 0.00 0.00 0.00 1.98
2124 5376 1.341531 CACACTCTTCCACGTCCTCTT 59.658 52.381 0.00 0.00 0.00 2.85
2153 5405 5.116180 ACACAACACCCGATCTATATTGTG 58.884 41.667 17.79 17.79 46.80 3.33
2180 5433 1.159285 CTGCTTTCTGCCATCGTTGA 58.841 50.000 0.00 0.00 42.00 3.18
2199 5452 0.315568 ACCCGCGAGATCTTGATAGC 59.684 55.000 14.59 6.14 0.00 2.97
2247 5500 1.001181 CACCCAACTGATGCCCTTTTG 59.999 52.381 0.00 0.00 0.00 2.44
2392 5646 3.661758 ATTGCAGCGCATAAATTTTGC 57.338 38.095 11.47 8.81 38.76 3.68
2395 5649 2.667481 TGCAGCGCATAAATTTTGCTTC 59.333 40.909 11.47 9.16 37.96 3.86
2604 5860 6.813152 GTCTTTTATTGGCATGTGCAAGTTAT 59.187 34.615 7.36 0.00 44.36 1.89
2681 5937 5.042463 TCCTTATTGTCACACAACCTTCA 57.958 39.130 0.00 0.00 41.40 3.02
3085 6346 3.055530 ACCAAAATGACCTGTGTTTGCAA 60.056 39.130 0.00 0.00 31.11 4.08
3112 6373 7.415206 GGCACGACTAATAATCCAGAAAAATGT 60.415 37.037 0.00 0.00 0.00 2.71
3410 6680 6.531948 TGAACCTTTTATGAAAACACAAACGG 59.468 34.615 0.00 0.00 0.00 4.44
3413 6683 7.545489 ACCTTTTATGAAAACACAAACGGTTA 58.455 30.769 0.00 0.00 30.80 2.85
3663 6942 4.471548 TCCAAACATTTTAGGAAACGGGA 58.528 39.130 0.00 0.00 0.00 5.14
3750 7031 1.209019 CTCCCAGTGCAGCAGATAGTT 59.791 52.381 0.00 0.00 0.00 2.24
4098 7379 6.318396 TGCGATTGATTGGTTTCTGAATGATA 59.682 34.615 0.00 0.00 0.00 2.15
4140 7424 4.587684 CAGGTACCGGTCTGTAAATCCTAT 59.412 45.833 12.40 0.00 0.00 2.57
4143 7427 5.048154 GGTACCGGTCTGTAAATCCTATCTC 60.048 48.000 12.40 0.00 0.00 2.75
4320 7606 2.046120 TGCACGCATGGCATCAGA 60.046 55.556 0.00 0.00 36.11 3.27
4321 7607 2.110352 TGCACGCATGGCATCAGAG 61.110 57.895 0.00 0.00 36.11 3.35
4322 7608 2.713770 CACGCATGGCATCAGAGC 59.286 61.111 0.00 0.00 0.00 4.09
4346 7632 5.824904 ATCCACATGTTATTCTGAACTGC 57.175 39.130 0.00 0.00 0.00 4.40
4347 7633 3.684305 TCCACATGTTATTCTGAACTGCG 59.316 43.478 0.00 0.00 0.00 5.18
4348 7634 3.436704 CCACATGTTATTCTGAACTGCGT 59.563 43.478 0.00 0.00 0.00 5.24
4349 7635 4.083324 CCACATGTTATTCTGAACTGCGTT 60.083 41.667 0.00 0.00 0.00 4.84
4350 7636 4.847757 CACATGTTATTCTGAACTGCGTTG 59.152 41.667 0.00 0.00 0.00 4.10
4351 7637 4.754618 ACATGTTATTCTGAACTGCGTTGA 59.245 37.500 0.00 0.00 0.00 3.18
4352 7638 5.238432 ACATGTTATTCTGAACTGCGTTGAA 59.762 36.000 0.00 0.00 0.00 2.69
4360 7646 4.994217 TCTGAACTGCGTTGAATGTTGATA 59.006 37.500 0.00 0.00 0.00 2.15
4366 7659 9.370126 GAACTGCGTTGAATGTTGATATATAAC 57.630 33.333 0.00 0.00 0.00 1.89
4434 7727 1.059942 CATCGGGCGCAAACTTTTTC 58.940 50.000 10.83 0.00 0.00 2.29
4518 7811 3.001838 GCGCGGTCATCACAACAATATTA 59.998 43.478 8.83 0.00 0.00 0.98
4589 7905 4.825422 TGAACTTCCTATTCTGCTCAGTG 58.175 43.478 0.00 0.00 0.00 3.66
4628 7944 5.255596 CGTGGATGATGTTTACGATGAAAC 58.744 41.667 0.00 0.00 39.35 2.78
4681 7997 3.834813 TGATCATCCTAGGCCTGTATGTC 59.165 47.826 17.99 14.72 0.00 3.06
4768 8084 6.034683 CTGAAAGCATTTTAGAGCAAGATTGC 59.965 38.462 9.54 9.54 43.61 3.56
4896 8214 5.665459 GAATCAGCTTCTAGCCTTTGAGTA 58.335 41.667 0.00 0.00 43.77 2.59
4897 8215 5.885449 ATCAGCTTCTAGCCTTTGAGTAT 57.115 39.130 0.00 0.00 43.77 2.12
4908 8226 5.635120 AGCCTTTGAGTATTAATGATCCCC 58.365 41.667 0.00 0.00 0.00 4.81
5012 8512 6.256321 GGCCATGCTAAAATTATCAAACACAG 59.744 38.462 0.00 0.00 0.00 3.66
5013 8513 6.813152 GCCATGCTAAAATTATCAAACACAGT 59.187 34.615 0.00 0.00 0.00 3.55
5014 8514 7.009540 GCCATGCTAAAATTATCAAACACAGTC 59.990 37.037 0.00 0.00 0.00 3.51
5016 8516 9.069078 CATGCTAAAATTATCAAACACAGTCTG 57.931 33.333 0.00 0.00 0.00 3.51
5017 8517 8.389779 TGCTAAAATTATCAAACACAGTCTGA 57.610 30.769 6.91 0.00 0.00 3.27
5019 8519 9.118236 GCTAAAATTATCAAACACAGTCTGAAC 57.882 33.333 6.91 0.00 0.00 3.18
5021 8521 8.856490 AAAATTATCAAACACAGTCTGAACAC 57.144 30.769 6.91 0.00 0.00 3.32
5022 8522 7.566760 AATTATCAAACACAGTCTGAACACA 57.433 32.000 6.91 0.00 0.00 3.72
5057 8564 3.557054 GCCGAGCATATATTTGACCCAGA 60.557 47.826 0.00 0.00 0.00 3.86
5070 8577 0.104934 ACCCAGACAGTCAGGAACCT 60.105 55.000 13.59 0.00 0.00 3.50
5111 8618 4.459852 AGGATTAATCAGGGAACATGGG 57.540 45.455 17.07 0.00 0.00 4.00
5148 8655 0.673644 AATTGGCAAGGACCGAGACG 60.674 55.000 5.96 0.00 0.00 4.18
5257 8768 2.842208 TGCAAGTGAAAGTGAAACGG 57.158 45.000 0.00 0.00 45.86 4.44
5258 8769 1.403679 TGCAAGTGAAAGTGAAACGGG 59.596 47.619 0.00 0.00 45.86 5.28
5273 8784 2.312424 ACGGGGAGGATATCTCTTCC 57.688 55.000 2.05 6.36 44.88 3.46
5276 8787 3.243724 CGGGGAGGATATCTCTTCCTTT 58.756 50.000 14.71 0.00 44.95 3.11
5277 8788 3.007398 CGGGGAGGATATCTCTTCCTTTG 59.993 52.174 14.71 5.58 44.95 2.77
5280 8791 5.103898 GGGGAGGATATCTCTTCCTTTGTTT 60.104 44.000 14.71 0.00 44.95 2.83
5282 8793 6.058833 GGAGGATATCTCTTCCTTTGTTTCC 58.941 44.000 2.05 0.00 43.75 3.13
5283 8794 6.126623 GGAGGATATCTCTTCCTTTGTTTCCT 60.127 42.308 2.05 0.00 43.75 3.36
5284 8795 7.277405 AGGATATCTCTTCCTTTGTTTCCTT 57.723 36.000 2.05 0.00 40.84 3.36
5285 8796 7.115414 AGGATATCTCTTCCTTTGTTTCCTTG 58.885 38.462 2.05 0.00 40.84 3.61
5286 8797 6.183360 GGATATCTCTTCCTTTGTTTCCTTGC 60.183 42.308 2.05 0.00 0.00 4.01
5349 8872 1.972795 TGGGAGGTACGCACTAACTTT 59.027 47.619 0.00 0.00 36.54 2.66
5372 8895 5.983333 ATTCCTCATTAGGTCCACTGAAT 57.017 39.130 0.00 0.00 44.09 2.57
5373 8896 5.779241 TTCCTCATTAGGTCCACTGAATT 57.221 39.130 0.00 0.00 44.09 2.17
5376 8899 5.488919 TCCTCATTAGGTCCACTGAATTCTT 59.511 40.000 7.05 0.00 44.09 2.52
5377 8900 5.819901 CCTCATTAGGTCCACTGAATTCTTC 59.180 44.000 7.05 0.00 38.19 2.87
5410 8939 4.640201 TGGATAATAACTCTTTGCTGTGGC 59.360 41.667 0.00 0.00 39.26 5.01
5426 8955 3.138304 TGTGGCTGATGTTTACAGTGAC 58.862 45.455 0.00 0.00 37.64 3.67
5583 10916 2.845967 CCATTGTTATCTGAAAACGCGC 59.154 45.455 5.73 0.00 0.00 6.86
5606 10939 3.377485 ACGCTGATACTACTTCGACATGT 59.623 43.478 0.00 0.00 0.00 3.21
5613 10946 6.972901 TGATACTACTTCGACATGTCAATGAC 59.027 38.462 24.93 6.41 37.24 3.06
5682 11027 2.420687 GCTGTCTCCCATACTTCCTTGG 60.421 54.545 0.00 0.00 0.00 3.61
5765 11110 2.433318 GACACGGAGTCTGGCAGC 60.433 66.667 10.34 5.16 41.61 5.25
5786 11131 1.501169 TGCTGAACGCATATGATCCG 58.499 50.000 6.97 3.14 45.47 4.18
5788 11133 1.501169 CTGAACGCATATGATCCGCA 58.499 50.000 6.97 0.00 0.00 5.69
5816 11161 4.329545 GACCCAGGCAGCCACGAA 62.330 66.667 15.80 0.00 0.00 3.85
5818 11163 4.641645 CCCAGGCAGCCACGAACA 62.642 66.667 15.80 0.00 0.00 3.18
5839 11184 1.854743 CATCGCTGTCCGTCATTACTG 59.145 52.381 0.00 0.00 38.35 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 3.516512 TCCCCTGCTTTGCCCCAA 61.517 61.111 0.00 0.00 0.00 4.12
93 94 2.692557 CGACCATGTCTTCTCCAGATCT 59.307 50.000 0.00 0.00 32.60 2.75
176 177 1.698506 CCCTGGCTACTTCTCGATCT 58.301 55.000 0.00 0.00 0.00 2.75
190 191 2.102578 CCAAAATTGTAGAGCCCCTGG 58.897 52.381 0.00 0.00 0.00 4.45
191 192 3.085952 TCCAAAATTGTAGAGCCCCTG 57.914 47.619 0.00 0.00 0.00 4.45
192 193 3.825908 TTCCAAAATTGTAGAGCCCCT 57.174 42.857 0.00 0.00 0.00 4.79
193 194 3.132824 CCATTCCAAAATTGTAGAGCCCC 59.867 47.826 0.00 0.00 0.00 5.80
194 195 3.430790 GCCATTCCAAAATTGTAGAGCCC 60.431 47.826 0.00 0.00 0.00 5.19
214 215 1.034292 GCTGGGAAAGATCACTGGCC 61.034 60.000 0.00 0.00 0.00 5.36
332 337 7.197071 TCACGGGCATTATATTTTGTACATC 57.803 36.000 0.00 0.00 0.00 3.06
374 379 5.264395 CACCCCCTGACTCATCTTAAATTT 58.736 41.667 0.00 0.00 0.00 1.82
388 393 1.080638 AATTGGTAAGCACCCCCTGA 58.919 50.000 0.00 0.00 45.11 3.86
389 394 2.375146 GTAATTGGTAAGCACCCCCTG 58.625 52.381 0.00 0.00 45.11 4.45
417 432 1.197721 GCCACCGAATTGTGAAGACAG 59.802 52.381 0.00 0.00 38.55 3.51
449 470 2.073816 CCCATGACACGGTGAAAGTAC 58.926 52.381 16.29 0.00 0.00 2.73
457 478 2.286365 AATCAAACCCATGACACGGT 57.714 45.000 0.00 0.00 30.82 4.83
469 490 3.163594 CGTGATCAAGCGGAAATCAAAC 58.836 45.455 0.00 0.00 31.61 2.93
500 521 0.463620 AGAAGCCAGATTCGCCTCTC 59.536 55.000 0.00 0.00 34.27 3.20
621 700 0.098728 CGGCGGCACTATTTTTCCTG 59.901 55.000 10.53 0.00 0.00 3.86
623 702 0.098200 GTCGGCGGCACTATTTTTCC 59.902 55.000 6.63 0.00 0.00 3.13
624 703 0.247537 CGTCGGCGGCACTATTTTTC 60.248 55.000 13.62 0.00 0.00 2.29
627 706 1.808390 GTCGTCGGCGGCACTATTT 60.808 57.895 10.16 0.00 43.09 1.40
628 707 2.202703 GTCGTCGGCGGCACTATT 60.203 61.111 10.16 0.00 43.09 1.73
643 722 2.200170 GAATTGGCTGGCACCGTGTC 62.200 60.000 2.29 0.00 0.00 3.67
647 726 1.213537 CTTGAATTGGCTGGCACCG 59.786 57.895 2.29 0.00 0.00 4.94
664 743 2.107552 CCCGAGTTCTCCTCTCCTATCT 59.892 54.545 0.00 0.00 38.11 1.98
670 749 1.513622 GTGCCCGAGTTCTCCTCTC 59.486 63.158 0.00 0.00 38.11 3.20
732 815 4.177783 GTCTTGTCCTTCTCTTCGATTCC 58.822 47.826 0.00 0.00 0.00 3.01
734 817 4.873746 TGTCTTGTCCTTCTCTTCGATT 57.126 40.909 0.00 0.00 0.00 3.34
736 819 3.383505 TGTTGTCTTGTCCTTCTCTTCGA 59.616 43.478 0.00 0.00 0.00 3.71
754 837 5.556355 AAGTATGCACAGTGATCATGTTG 57.444 39.130 4.15 0.85 0.00 3.33
804 887 2.810887 GCGAGCATGCGTGAGTGA 60.811 61.111 13.01 0.00 0.00 3.41
805 888 3.857854 GGCGAGCATGCGTGAGTG 61.858 66.667 13.01 0.00 35.06 3.51
831 916 3.064324 GAATTGCCGGCTGCCTGT 61.064 61.111 29.70 6.67 40.16 4.00
860 949 3.744530 GCAGTCAGACCAGTTTACCAGTT 60.745 47.826 0.00 0.00 0.00 3.16
861 950 2.224305 GCAGTCAGACCAGTTTACCAGT 60.224 50.000 0.00 0.00 0.00 4.00
868 960 1.312815 GCTTTGCAGTCAGACCAGTT 58.687 50.000 0.00 0.00 0.00 3.16
869 961 0.536006 GGCTTTGCAGTCAGACCAGT 60.536 55.000 0.00 0.00 0.00 4.00
875 967 1.576421 GTTCGGGCTTTGCAGTCAG 59.424 57.895 0.00 0.00 0.00 3.51
886 978 4.565166 GCTAATTTTGTTTATGGTTCGGGC 59.435 41.667 0.00 0.00 0.00 6.13
1276 1395 1.215647 GAGATGGAAGCGACGTGGT 59.784 57.895 0.00 0.00 0.00 4.16
1280 1399 1.601663 GGATCAGAGATGGAAGCGACG 60.602 57.143 0.00 0.00 0.00 5.12
1286 1405 1.410850 GGGCGGGATCAGAGATGGAA 61.411 60.000 0.00 0.00 0.00 3.53
1287 1406 1.838846 GGGCGGGATCAGAGATGGA 60.839 63.158 0.00 0.00 0.00 3.41
1290 1409 3.620785 GCGGGCGGGATCAGAGAT 61.621 66.667 0.00 0.00 0.00 2.75
1303 1429 2.819595 CAACACGAGGGATGCGGG 60.820 66.667 0.00 0.00 38.32 6.13
1321 1447 4.702612 ACCGGCATGTATCTACTCTATCAG 59.297 45.833 0.00 0.00 0.00 2.90
1329 1455 2.030185 ACATCGACCGGCATGTATCTAC 60.030 50.000 11.59 0.00 31.20 2.59
1330 1456 2.235891 ACATCGACCGGCATGTATCTA 58.764 47.619 11.59 0.00 31.20 1.98
1331 1457 1.040646 ACATCGACCGGCATGTATCT 58.959 50.000 11.59 0.00 31.20 1.98
1414 1540 3.580319 GAGGTTGGTGGTGGCCCT 61.580 66.667 0.00 0.00 0.00 5.19
1490 1616 2.646175 CGTGAGGCGGAGAAAGGGA 61.646 63.158 0.00 0.00 36.85 4.20
1646 1802 0.105964 GAAACCCACAAGCCCAAACC 59.894 55.000 0.00 0.00 0.00 3.27
1911 5162 0.107456 CATGAGGTAGATGCCGCCTT 59.893 55.000 0.00 0.00 31.89 4.35
1954 5205 2.512692 TTGCCTGCAAGATGTACCAT 57.487 45.000 0.00 0.00 34.07 3.55
2098 5349 1.069090 GTGGAAGAGTGTGTGCGGA 59.931 57.895 0.00 0.00 0.00 5.54
2124 5376 1.944024 GATCGGGTGTTGTGTTCACAA 59.056 47.619 13.36 13.36 37.52 3.33
2180 5433 0.315568 GCTATCAAGATCTCGCGGGT 59.684 55.000 5.57 0.00 0.00 5.28
2392 5646 4.227512 TGCGCTAATTATGCCAATGAAG 57.772 40.909 9.73 0.00 0.00 3.02
2395 5649 4.858692 GGTTATGCGCTAATTATGCCAATG 59.141 41.667 9.73 0.00 0.00 2.82
2510 5766 7.540055 GCATGTGCTAATAAAAGAGAATATGCC 59.460 37.037 0.00 0.00 38.21 4.40
2604 5860 3.358111 TCCACAAATTATTGCCGGAGA 57.642 42.857 5.05 0.00 40.34 3.71
2681 5937 5.815581 TGTGCCTAAGTTGTCTGGAAATAT 58.184 37.500 0.00 0.00 0.00 1.28
2735 5992 4.416516 TGATAGGAACAGTCTCACCTTGA 58.583 43.478 0.00 0.00 34.42 3.02
3060 6321 0.667993 ACACAGGTCATTTTGGTGCG 59.332 50.000 0.00 0.00 32.89 5.34
3085 6346 5.353394 TTTCTGGATTATTAGTCGTGCCT 57.647 39.130 0.00 0.00 0.00 4.75
3112 6373 3.985008 TCTTTTCGATCGTTCAACCTGA 58.015 40.909 15.94 1.73 0.00 3.86
3410 6680 5.668558 AAGTCGGTCACAACTTCAATAAC 57.331 39.130 0.00 0.00 29.89 1.89
3413 6683 6.687081 TTAAAAGTCGGTCACAACTTCAAT 57.313 33.333 0.00 0.00 34.71 2.57
3773 7054 4.114997 GTGCCGGCCCATTTCGTG 62.115 66.667 26.77 0.00 0.00 4.35
3817 7098 0.811616 CCCAGTGCGGCAGATAGTTC 60.812 60.000 1.18 0.00 0.00 3.01
4068 7349 3.820467 AGAAACCAATCAATCGCACAGAA 59.180 39.130 0.00 0.00 0.00 3.02
4098 7379 4.021192 ACCTGAAAATGACCGCAAATCATT 60.021 37.500 2.13 2.13 46.40 2.57
4104 7385 2.156098 GGTACCTGAAAATGACCGCAA 58.844 47.619 4.06 0.00 0.00 4.85
4105 7386 1.816074 GGTACCTGAAAATGACCGCA 58.184 50.000 4.06 0.00 0.00 5.69
4140 7424 1.964223 GCCAAGGATAGTGGATCGAGA 59.036 52.381 0.00 0.00 38.54 4.04
4143 7427 2.213499 GTTGCCAAGGATAGTGGATCG 58.787 52.381 0.00 0.00 38.54 3.69
4221 7505 4.125703 GCTTCCAGATCTCCATGTAGTTG 58.874 47.826 0.00 0.00 0.00 3.16
4317 7603 5.587443 TCAGAATAACATGTGGATTGCTCTG 59.413 40.000 10.22 10.99 0.00 3.35
4318 7604 5.748402 TCAGAATAACATGTGGATTGCTCT 58.252 37.500 10.22 0.92 0.00 4.09
4319 7605 6.094603 AGTTCAGAATAACATGTGGATTGCTC 59.905 38.462 10.22 0.00 0.00 4.26
4320 7606 5.948162 AGTTCAGAATAACATGTGGATTGCT 59.052 36.000 10.22 5.78 0.00 3.91
4321 7607 6.032094 CAGTTCAGAATAACATGTGGATTGC 58.968 40.000 10.22 4.06 0.00 3.56
4322 7608 6.032094 GCAGTTCAGAATAACATGTGGATTG 58.968 40.000 10.22 2.10 0.00 2.67
4349 7635 8.556194 GCCAAACTCGTTATATATCAACATTCA 58.444 33.333 0.00 0.00 0.00 2.57
4350 7636 8.015658 GGCCAAACTCGTTATATATCAACATTC 58.984 37.037 0.00 0.00 0.00 2.67
4351 7637 7.500892 TGGCCAAACTCGTTATATATCAACATT 59.499 33.333 0.61 0.00 0.00 2.71
4352 7638 6.995686 TGGCCAAACTCGTTATATATCAACAT 59.004 34.615 0.61 0.00 0.00 2.71
4589 7905 1.867233 CCACGGTAGCAGTGATTATGC 59.133 52.381 15.28 0.00 41.83 3.14
4681 7997 1.302511 AGCTTTACCCCACAGCACG 60.303 57.895 0.00 0.00 35.88 5.34
4732 8048 9.234827 TCTAAAATGCTTTCAGAATCATCAGAA 57.765 29.630 0.43 0.00 30.16 3.02
4768 8084 4.216257 CCACTTTCTACTTTCACACCCATG 59.784 45.833 0.00 0.00 0.00 3.66
4777 8093 5.561679 AGATTGGTCCCACTTTCTACTTTC 58.438 41.667 0.00 0.00 0.00 2.62
4896 8214 9.579932 GAAGTATCAGAAAAGGGGATCATTAAT 57.420 33.333 0.00 0.00 0.00 1.40
4897 8215 8.781951 AGAAGTATCAGAAAAGGGGATCATTAA 58.218 33.333 0.00 0.00 0.00 1.40
4908 8226 5.936956 AGCAGTGGAAGAAGTATCAGAAAAG 59.063 40.000 0.00 0.00 0.00 2.27
5012 8512 5.117592 GCACATTAAGCATTTGTGTTCAGAC 59.882 40.000 7.71 0.00 42.11 3.51
5013 8513 5.221880 GCACATTAAGCATTTGTGTTCAGA 58.778 37.500 7.71 0.00 42.11 3.27
5014 8514 4.386652 GGCACATTAAGCATTTGTGTTCAG 59.613 41.667 7.71 0.00 42.11 3.02
5016 8516 3.364621 CGGCACATTAAGCATTTGTGTTC 59.635 43.478 7.71 1.68 42.11 3.18
5017 8517 3.005261 TCGGCACATTAAGCATTTGTGTT 59.995 39.130 7.71 0.00 42.11 3.32
5019 8519 3.173599 CTCGGCACATTAAGCATTTGTG 58.826 45.455 2.42 2.42 42.80 3.33
5020 8520 2.415893 GCTCGGCACATTAAGCATTTGT 60.416 45.455 0.00 0.00 34.86 2.83
5021 8521 2.187707 GCTCGGCACATTAAGCATTTG 58.812 47.619 0.00 0.00 34.86 2.32
5022 8522 1.818060 TGCTCGGCACATTAAGCATTT 59.182 42.857 0.00 0.00 39.69 2.32
5070 8577 4.526650 TCCTAATAATGCCAGACAGCGATA 59.473 41.667 0.00 0.00 34.65 2.92
5142 8649 7.408123 AGTAGTCATTCTTAACATACGTCTCG 58.592 38.462 0.00 0.00 0.00 4.04
5184 8695 2.243810 GTCCCTTCTGTGTGACTCTCT 58.756 52.381 0.00 0.00 0.00 3.10
5185 8696 1.068194 CGTCCCTTCTGTGTGACTCTC 60.068 57.143 0.00 0.00 0.00 3.20
5186 8697 0.962489 CGTCCCTTCTGTGTGACTCT 59.038 55.000 0.00 0.00 0.00 3.24
5187 8698 0.959553 TCGTCCCTTCTGTGTGACTC 59.040 55.000 0.00 0.00 0.00 3.36
5188 8699 0.674534 GTCGTCCCTTCTGTGTGACT 59.325 55.000 0.00 0.00 0.00 3.41
5189 8700 0.387929 TGTCGTCCCTTCTGTGTGAC 59.612 55.000 0.00 0.00 0.00 3.67
5190 8701 1.068588 CTTGTCGTCCCTTCTGTGTGA 59.931 52.381 0.00 0.00 0.00 3.58
5223 8734 4.695455 TCACTTGCAAGAATAGTTGTAGCC 59.305 41.667 32.50 0.00 0.00 3.93
5257 8768 5.638530 AACAAAGGAAGAGATATCCTCCC 57.361 43.478 1.19 1.55 46.65 4.30
5258 8769 6.058833 GGAAACAAAGGAAGAGATATCCTCC 58.941 44.000 0.00 0.00 46.65 4.30
5273 8784 6.526674 GGTAATATTGTCGCAAGGAAACAAAG 59.473 38.462 0.00 0.00 35.59 2.77
5276 8787 5.250200 AGGTAATATTGTCGCAAGGAAACA 58.750 37.500 0.00 0.00 38.47 2.83
5277 8788 5.813080 AGGTAATATTGTCGCAAGGAAAC 57.187 39.130 0.00 0.00 38.47 2.78
5280 8791 5.054477 GCTTAGGTAATATTGTCGCAAGGA 58.946 41.667 0.00 0.00 38.47 3.36
5282 8793 5.986135 AGAGCTTAGGTAATATTGTCGCAAG 59.014 40.000 0.00 1.83 0.00 4.01
5283 8794 5.914033 AGAGCTTAGGTAATATTGTCGCAA 58.086 37.500 0.00 0.00 0.00 4.85
5284 8795 5.531122 AGAGCTTAGGTAATATTGTCGCA 57.469 39.130 0.00 0.00 0.00 5.10
5285 8796 5.405873 GGAAGAGCTTAGGTAATATTGTCGC 59.594 44.000 0.00 0.00 0.00 5.19
5286 8797 6.750148 AGGAAGAGCTTAGGTAATATTGTCG 58.250 40.000 0.00 0.00 0.00 4.35
5372 8895 8.375506 AGTTATTATCCACTGAACACAGAAGAA 58.624 33.333 0.00 0.00 35.80 2.52
5373 8896 7.907389 AGTTATTATCCACTGAACACAGAAGA 58.093 34.615 0.00 0.00 35.80 2.87
5376 8899 7.482169 AGAGTTATTATCCACTGAACACAGA 57.518 36.000 0.00 0.00 35.80 3.41
5377 8900 8.446273 CAAAGAGTTATTATCCACTGAACACAG 58.554 37.037 0.00 0.00 37.63 3.66
5583 10916 3.400505 TGTCGAAGTAGTATCAGCGTG 57.599 47.619 0.00 0.00 0.00 5.34
5606 10939 7.977789 TTTTAGAGTAGTGCAATGTCATTGA 57.022 32.000 26.36 10.77 42.83 2.57
5613 10946 6.094603 AGGCTGATTTTTAGAGTAGTGCAATG 59.905 38.462 0.00 0.00 0.00 2.82
5724 11069 6.716173 TCTGATAATTTTAGCATGCATGGCTA 59.284 34.615 27.34 23.14 42.62 3.93
5785 11130 0.674581 TGGGTCAAATCTGCTCTGCG 60.675 55.000 0.00 0.00 0.00 5.18
5786 11131 1.093159 CTGGGTCAAATCTGCTCTGC 58.907 55.000 0.00 0.00 0.00 4.26
5788 11133 0.034670 GCCTGGGTCAAATCTGCTCT 60.035 55.000 0.00 0.00 0.00 4.09
5816 11161 0.037326 AATGACGGACAGCGATGTGT 60.037 50.000 12.87 3.07 0.00 3.72
5818 11163 1.476891 AGTAATGACGGACAGCGATGT 59.523 47.619 5.74 5.74 0.00 3.06
5839 11184 1.386533 CATGTTGGCTCAGTCATCCC 58.613 55.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.