Multiple sequence alignment - TraesCS5A01G277900

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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 TraesCS5A01G277900 chr5A 100.000 2599 0 0 1 2599 487782860 487785458 0.000000e+00 4800
1 TraesCS5A01G277900 chr5D 87.770 1619 87 49 1020 2599 385781826 385783372 0.000000e+00 1790
2 TraesCS5A01G277900 chr5D 95.561 428 15 3 1 427 385780232 385780656 0.000000e+00 682
3 TraesCS5A01G277900 chr5D 92.325 456 22 7 577 1021 385781272 385781725 1.010000e-178 636
4 TraesCS5A01G277900 chr5B 87.189 1288 71 46 1020 2278 463220267 463221489 0.000000e+00 1378
5 TraesCS5A01G277900 chr5B 88.811 429 31 8 595 1021 463219759 463220172 6.420000e-141 510
6 TraesCS5A01G277900 chr5B 94.928 138 7 0 1 138 463217979 463218116 1.570000e-52 217
7 TraesCS5A01G277900 chr5B 83.019 265 17 14 2359 2599 463221529 463221789 5.630000e-52 215


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 TraesCS5A01G277900 chr5A 487782860 487785458 2598 False 4800 4800 100.000000 1 2599 1 chr5A.!!$F1 2598
1 TraesCS5A01G277900 chr5D 385780232 385783372 3140 False 1036 1790 91.885333 1 2599 3 chr5D.!!$F1 2598
2 TraesCS5A01G277900 chr5B 463217979 463221789 3810 False 580 1378 88.486750 1 2599 4 chr5B.!!$F1 2598

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
92 94 0.818296 CCCCACACTCTAGTTCCTCG 59.182 60.0 0.0 0.0 0.0 4.63 F
1014 2221 0.118144 AGCCCCAACCTCTCTCTCTT 59.882 55.0 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1056 2363 0.685131 TCTTGATCGGCGGTAGGGAA 60.685 55.0 7.21 0.0 0.0 3.97 R
2426 3770 0.034337 TACTCCACCGGCAACTTCAC 59.966 55.0 0.00 0.0 0.0 3.18 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
92 94 0.818296 CCCCACACTCTAGTTCCTCG 59.182 60.000 0.00 0.00 0.00 4.63
146 551 5.373812 ACCTCCGACCTTTTTCATGATAT 57.626 39.130 0.00 0.00 0.00 1.63
147 552 5.755849 ACCTCCGACCTTTTTCATGATATT 58.244 37.500 0.00 0.00 0.00 1.28
148 553 6.895782 ACCTCCGACCTTTTTCATGATATTA 58.104 36.000 0.00 0.00 0.00 0.98
164 569 5.653507 TGATATTACGTACTGGTTGTCACC 58.346 41.667 0.00 0.00 44.56 4.02
188 593 4.215613 GCCCGTTAAGAACAATTCAGAACT 59.784 41.667 0.00 0.00 0.00 3.01
266 910 5.227908 TGCTACTCTAACCTTTCAACTTCG 58.772 41.667 0.00 0.00 0.00 3.79
291 935 3.855689 AAGAATTGCAATGTTCTCCCG 57.144 42.857 13.82 0.00 33.76 5.14
331 975 4.277174 CACCGCATATATCTAGGAGCTAGG 59.723 50.000 0.00 0.00 35.03 3.02
433 1079 3.061322 ACGTGCGCTAAAACACTATCAA 58.939 40.909 9.73 0.00 34.58 2.57
440 1086 7.749126 GTGCGCTAAAACACTATCAAAAATAGT 59.251 33.333 9.73 0.00 35.39 2.12
464 1110 2.207478 GGGGGAGGGGGAGGATAC 59.793 72.222 0.00 0.00 0.00 2.24
481 1127 5.986004 GGATACTTACTTGGATTCGTTGG 57.014 43.478 0.00 0.00 0.00 3.77
482 1128 5.667466 GGATACTTACTTGGATTCGTTGGA 58.333 41.667 0.00 0.00 0.00 3.53
483 1129 5.753921 GGATACTTACTTGGATTCGTTGGAG 59.246 44.000 0.00 0.00 0.00 3.86
484 1130 3.939066 ACTTACTTGGATTCGTTGGAGG 58.061 45.455 0.00 0.00 0.00 4.30
485 1131 3.326880 ACTTACTTGGATTCGTTGGAGGT 59.673 43.478 0.00 0.00 0.00 3.85
486 1132 2.951229 ACTTGGATTCGTTGGAGGTT 57.049 45.000 0.00 0.00 0.00 3.50
487 1133 2.779506 ACTTGGATTCGTTGGAGGTTC 58.220 47.619 0.00 0.00 0.00 3.62
488 1134 2.105821 ACTTGGATTCGTTGGAGGTTCA 59.894 45.455 0.00 0.00 0.00 3.18
489 1135 3.244911 ACTTGGATTCGTTGGAGGTTCAT 60.245 43.478 0.00 0.00 0.00 2.57
490 1136 4.019681 ACTTGGATTCGTTGGAGGTTCATA 60.020 41.667 0.00 0.00 0.00 2.15
491 1137 3.869065 TGGATTCGTTGGAGGTTCATAC 58.131 45.455 0.00 0.00 0.00 2.39
492 1138 3.262151 TGGATTCGTTGGAGGTTCATACA 59.738 43.478 0.00 0.00 0.00 2.29
493 1139 4.080582 TGGATTCGTTGGAGGTTCATACAT 60.081 41.667 0.00 0.00 0.00 2.29
494 1140 4.273480 GGATTCGTTGGAGGTTCATACATG 59.727 45.833 0.00 0.00 0.00 3.21
495 1141 3.973206 TCGTTGGAGGTTCATACATGT 57.027 42.857 2.69 2.69 0.00 3.21
524 1331 3.894782 TGTGTACATGTTGTGTCATGC 57.105 42.857 2.30 0.00 46.15 4.06
536 1343 7.595311 TGTTGTGTCATGCTAGTAATAGTTG 57.405 36.000 0.00 0.00 0.00 3.16
550 1357 6.540083 AGTAATAGTTGGGGGTGCATTATAC 58.460 40.000 0.00 0.00 0.00 1.47
558 1365 6.308015 TGGGGGTGCATTATACAGATATAC 57.692 41.667 0.00 0.00 0.00 1.47
559 1366 6.029431 TGGGGGTGCATTATACAGATATACT 58.971 40.000 0.00 0.00 0.00 2.12
561 1368 7.680739 TGGGGGTGCATTATACAGATATACTTA 59.319 37.037 0.00 0.00 0.00 2.24
562 1369 8.714906 GGGGGTGCATTATACAGATATACTTAT 58.285 37.037 0.00 0.00 0.00 1.73
584 1696 9.613428 CTTATATGTTTTTGGTACTGAGATGGA 57.387 33.333 0.00 0.00 0.00 3.41
624 1816 2.199236 GCTCTATTTTACGACACCCGG 58.801 52.381 0.00 0.00 43.93 5.73
677 1869 8.660968 AGAAAGAATTCTTTATTTTTCTCGCG 57.339 30.769 28.83 0.00 43.43 5.87
678 1870 8.504005 AGAAAGAATTCTTTATTTTTCTCGCGA 58.496 29.630 28.83 9.26 43.43 5.87
679 1871 9.278734 GAAAGAATTCTTTATTTTTCTCGCGAT 57.721 29.630 28.83 5.61 45.37 4.58
701 1904 8.005466 GCGATAATTTTGATACAAATTGCATGG 58.995 33.333 0.00 0.00 31.73 3.66
711 1914 4.370917 ACAAATTGCATGGTTCAAGTGTC 58.629 39.130 0.00 0.00 0.00 3.67
773 1976 3.711190 AGGATCCATTTGTAAAATGCCCC 59.289 43.478 15.82 7.36 0.00 5.80
794 1997 1.574263 AAGTCTTGCCTCCTCCTACC 58.426 55.000 0.00 0.00 0.00 3.18
798 2001 1.644337 TCTTGCCTCCTCCTACCACTA 59.356 52.381 0.00 0.00 0.00 2.74
814 2017 7.816031 TCCTACCACTAAAGTAAAATTCACTCG 59.184 37.037 0.00 0.00 0.00 4.18
910 2113 5.138125 AGTTTGCAATTACACCCTTCATG 57.862 39.130 0.00 0.00 0.00 3.07
926 2129 5.279607 CCCTTCATGAATGCCTTTCTTTTCA 60.280 40.000 8.96 0.00 35.23 2.69
974 2177 1.519758 CGGTGCCGCTACTATTTAACG 59.480 52.381 0.00 0.00 0.00 3.18
1012 2219 0.907230 ACAGCCCCAACCTCTCTCTC 60.907 60.000 0.00 0.00 0.00 3.20
1014 2221 0.118144 AGCCCCAACCTCTCTCTCTT 59.882 55.000 0.00 0.00 0.00 2.85
1015 2222 0.988063 GCCCCAACCTCTCTCTCTTT 59.012 55.000 0.00 0.00 0.00 2.52
1016 2223 1.065782 GCCCCAACCTCTCTCTCTTTC 60.066 57.143 0.00 0.00 0.00 2.62
1018 2225 2.545810 CCCAACCTCTCTCTCTTTCCT 58.454 52.381 0.00 0.00 0.00 3.36
1020 2227 2.165437 CCAACCTCTCTCTCTTTCCTCG 59.835 54.545 0.00 0.00 0.00 4.63
1021 2228 2.137810 ACCTCTCTCTCTTTCCTCGG 57.862 55.000 0.00 0.00 0.00 4.63
1059 2366 2.579738 GACGAGTCCCTGCCTTCC 59.420 66.667 0.00 0.00 0.00 3.46
1062 2369 1.381327 CGAGTCCCTGCCTTCCCTA 60.381 63.158 0.00 0.00 0.00 3.53
1225 2538 2.432628 CGACGTCCAAGGAGTGCC 60.433 66.667 10.58 0.00 0.00 5.01
1429 2742 4.570663 GGATCCGGGCGTCGTGAG 62.571 72.222 0.00 0.00 37.11 3.51
1477 2794 2.202837 CCCCGGTTCGGTCGATTC 60.203 66.667 0.00 0.00 46.80 2.52
1484 2801 1.538419 GGTTCGGTCGATTCATCTCCC 60.538 57.143 0.00 0.00 0.00 4.30
1517 2835 1.462670 CAGTCGCTTGCTTCTTTCTCC 59.537 52.381 0.00 0.00 0.00 3.71
1532 2850 2.587060 TCTCCTCTCCTCTCCTCTCT 57.413 55.000 0.00 0.00 0.00 3.10
1537 2855 0.633921 TCTCCTCTCCTCTCTTGGGG 59.366 60.000 0.00 0.00 0.00 4.96
1543 2861 0.900647 CTCCTCTCTTGGGGTCGTGT 60.901 60.000 0.00 0.00 0.00 4.49
1563 2881 5.051039 CGTGTCCATGGTAAATTATGAGTCG 60.051 44.000 12.58 0.00 0.00 4.18
1564 2882 5.815740 GTGTCCATGGTAAATTATGAGTCGT 59.184 40.000 12.58 0.00 0.00 4.34
1565 2883 6.018994 GTGTCCATGGTAAATTATGAGTCGTC 60.019 42.308 12.58 0.00 0.00 4.20
1567 2885 6.421202 GTCCATGGTAAATTATGAGTCGTCTC 59.579 42.308 12.58 2.47 40.79 3.36
1574 2892 4.757799 ATTATGAGTCGTCTCCTCATCG 57.242 45.455 7.21 0.00 44.35 3.84
1623 2941 3.508845 AGTGGTATGTGTGCTTCCTTT 57.491 42.857 0.00 0.00 0.00 3.11
1624 2942 3.412386 AGTGGTATGTGTGCTTCCTTTC 58.588 45.455 0.00 0.00 0.00 2.62
1625 2943 2.159627 GTGGTATGTGTGCTTCCTTTCG 59.840 50.000 0.00 0.00 0.00 3.46
1626 2944 1.130561 GGTATGTGTGCTTCCTTTCGC 59.869 52.381 0.00 0.00 0.00 4.70
1627 2945 1.130561 GTATGTGTGCTTCCTTTCGCC 59.869 52.381 0.00 0.00 0.00 5.54
1628 2946 0.537143 ATGTGTGCTTCCTTTCGCCA 60.537 50.000 0.00 0.00 0.00 5.69
1629 2947 0.537143 TGTGTGCTTCCTTTCGCCAT 60.537 50.000 0.00 0.00 0.00 4.40
1630 2948 0.169009 GTGTGCTTCCTTTCGCCATC 59.831 55.000 0.00 0.00 0.00 3.51
1665 2983 5.091431 GTGAAATTCTCATGCAAGCTGTAC 58.909 41.667 0.00 0.00 36.14 2.90
1677 2995 3.312697 GCAAGCTGTACAATAAGGTAGGC 59.687 47.826 0.00 0.00 0.00 3.93
1718 3036 1.030488 GGTTAAGGGCGGAAGAAGGC 61.030 60.000 0.00 0.00 0.00 4.35
1742 3060 6.259829 GCTGTAAGAAAATTCAGAGAGATCCC 59.740 42.308 0.00 0.00 34.07 3.85
1747 3065 5.425539 AGAAAATTCAGAGAGATCCCGGTAA 59.574 40.000 0.00 0.00 0.00 2.85
1748 3066 5.896073 AAATTCAGAGAGATCCCGGTAAT 57.104 39.130 0.00 0.00 0.00 1.89
1753 3071 6.591750 TCAGAGAGATCCCGGTAATTAATC 57.408 41.667 0.00 0.00 0.00 1.75
1757 3075 7.547370 CAGAGAGATCCCGGTAATTAATCAATC 59.453 40.741 0.00 0.00 0.00 2.67
1801 3130 6.699575 ACTACCAGAATTGTGCAATTATCC 57.300 37.500 9.78 0.00 40.77 2.59
1839 3169 3.631227 CCAATTCAGCCAGAATCCTCTTC 59.369 47.826 2.81 0.00 46.09 2.87
1854 3184 5.830000 TCCTCTTCTTGTTAATCGATCGA 57.170 39.130 21.86 21.86 0.00 3.59
1855 3185 6.392625 TCCTCTTCTTGTTAATCGATCGAT 57.607 37.500 24.60 24.60 36.23 3.59
1856 3186 6.439599 TCCTCTTCTTGTTAATCGATCGATC 58.560 40.000 29.48 18.06 33.08 3.69
1867 3197 1.441849 GATCGATCGCCGCTCAGAG 60.442 63.158 11.09 0.00 38.37 3.35
1945 3275 3.301706 GAGACGAGGCGACTAATCAATC 58.698 50.000 0.00 0.00 44.43 2.67
1981 3312 4.569162 TCCACCGTTCTCGCTAATTAATTG 59.431 41.667 11.05 2.59 35.54 2.32
1996 3327 0.033208 AATTGGGATGCCATGTCCGT 60.033 50.000 6.84 0.00 36.58 4.69
1997 3328 0.466189 ATTGGGATGCCATGTCCGTC 60.466 55.000 6.84 0.00 36.58 4.79
1998 3329 2.203209 GGGATGCCATGTCCGTCC 60.203 66.667 0.00 11.55 36.58 4.79
1999 3330 2.588877 GGATGCCATGTCCGTCCG 60.589 66.667 6.21 0.00 0.00 4.79
2000 3331 2.588877 GATGCCATGTCCGTCCGG 60.589 66.667 0.00 0.00 0.00 5.14
2001 3332 4.856801 ATGCCATGTCCGTCCGGC 62.857 66.667 0.00 0.00 45.11 6.13
2020 3351 2.669781 GCAATCCATGGAGATTTGGGA 58.330 47.619 21.33 0.00 34.19 4.37
2026 3358 0.988145 ATGGAGATTTGGGAGGGCGA 60.988 55.000 0.00 0.00 0.00 5.54
2036 3368 1.600916 GGAGGGCGAGTGTGCTTTT 60.601 57.895 0.00 0.00 34.52 2.27
2037 3369 1.578206 GGAGGGCGAGTGTGCTTTTC 61.578 60.000 0.00 0.00 34.52 2.29
2116 3448 2.418746 GCTAATCGGGACATGACACAGT 60.419 50.000 0.00 0.00 0.00 3.55
2117 3449 2.386661 AATCGGGACATGACACAGTC 57.613 50.000 0.00 2.08 0.00 3.51
2149 3482 1.077334 TCTCCTTTTCTCCTCTCCGGT 59.923 52.381 0.00 0.00 0.00 5.28
2151 3484 0.537653 CCTTTTCTCCTCTCCGGTCC 59.462 60.000 0.00 0.00 0.00 4.46
2152 3485 1.267121 CTTTTCTCCTCTCCGGTCCA 58.733 55.000 0.00 0.00 0.00 4.02
2153 3486 1.205893 CTTTTCTCCTCTCCGGTCCAG 59.794 57.143 0.00 0.00 0.00 3.86
2154 3487 0.114560 TTTCTCCTCTCCGGTCCAGT 59.885 55.000 0.00 0.00 0.00 4.00
2155 3488 0.323542 TTCTCCTCTCCGGTCCAGTC 60.324 60.000 0.00 0.00 0.00 3.51
2175 3508 6.209391 CCAGTCTCCAGTGGTGAATTATTTTT 59.791 38.462 15.36 0.00 38.24 1.94
2176 3509 7.308435 CAGTCTCCAGTGGTGAATTATTTTTC 58.692 38.462 15.36 0.63 0.00 2.29
2177 3510 7.175641 CAGTCTCCAGTGGTGAATTATTTTTCT 59.824 37.037 15.36 2.89 0.00 2.52
2178 3511 7.391833 AGTCTCCAGTGGTGAATTATTTTTCTC 59.608 37.037 15.36 0.00 0.00 2.87
2179 3512 7.391833 GTCTCCAGTGGTGAATTATTTTTCTCT 59.608 37.037 15.36 0.00 0.00 3.10
2183 3516 8.025445 CCAGTGGTGAATTATTTTTCTCTTCTG 58.975 37.037 0.00 0.00 0.00 3.02
2184 3517 8.786898 CAGTGGTGAATTATTTTTCTCTTCTGA 58.213 33.333 0.00 0.00 30.90 3.27
2209 3542 5.129485 TGAAGATCCTGATTTGTCTCTACCC 59.871 44.000 0.00 0.00 0.00 3.69
2215 3548 5.964477 TCCTGATTTGTCTCTACCCTAACAT 59.036 40.000 0.00 0.00 0.00 2.71
2219 3552 7.130099 TGATTTGTCTCTACCCTAACATCCTA 58.870 38.462 0.00 0.00 0.00 2.94
2223 3556 4.583907 GTCTCTACCCTAACATCCTACACC 59.416 50.000 0.00 0.00 0.00 4.16
2248 3592 1.032114 CCTCCAAAATCCGGCAGTCC 61.032 60.000 0.00 0.00 0.00 3.85
2261 3605 2.369394 GGCAGTCCTAATTTGTCCCTG 58.631 52.381 0.00 0.00 0.00 4.45
2263 3607 2.619074 GCAGTCCTAATTTGTCCCTGCT 60.619 50.000 12.16 0.00 40.39 4.24
2272 3616 2.254546 TTGTCCCTGCTGTAACAGTG 57.745 50.000 0.00 0.00 35.83 3.66
2273 3617 1.128200 TGTCCCTGCTGTAACAGTGT 58.872 50.000 0.00 0.00 35.83 3.55
2274 3618 2.321719 TGTCCCTGCTGTAACAGTGTA 58.678 47.619 0.00 0.00 35.83 2.90
2289 3633 8.456471 TGTAACAGTGTAGTACATGATGTAGTC 58.544 37.037 15.67 8.92 37.62 2.59
2290 3634 6.120378 ACAGTGTAGTACATGATGTAGTCG 57.880 41.667 15.67 4.70 37.62 4.18
2291 3635 5.646793 ACAGTGTAGTACATGATGTAGTCGT 59.353 40.000 15.67 5.24 37.62 4.34
2292 3636 6.820152 ACAGTGTAGTACATGATGTAGTCGTA 59.180 38.462 15.67 2.37 37.62 3.43
2293 3637 7.011202 ACAGTGTAGTACATGATGTAGTCGTAG 59.989 40.741 15.67 7.09 37.62 3.51
2294 3638 7.011202 CAGTGTAGTACATGATGTAGTCGTAGT 59.989 40.741 15.67 5.01 37.62 2.73
2295 3639 7.011202 AGTGTAGTACATGATGTAGTCGTAGTG 59.989 40.741 15.67 0.00 37.62 2.74
2296 3640 6.820152 TGTAGTACATGATGTAGTCGTAGTGT 59.180 38.462 15.67 0.00 37.62 3.55
2297 3641 6.754702 AGTACATGATGTAGTCGTAGTGTT 57.245 37.500 5.37 0.00 31.20 3.32
2300 3644 9.551734 AGTACATGATGTAGTCGTAGTGTTATA 57.448 33.333 5.37 0.00 31.20 0.98
2343 3687 0.322322 TGTGTAGCTGGTTAACCCCG 59.678 55.000 21.97 13.64 34.29 5.73
2348 3692 1.602605 GCTGGTTAACCCCGCTGTT 60.603 57.895 21.97 0.00 34.29 3.16
2349 3693 1.862602 GCTGGTTAACCCCGCTGTTG 61.863 60.000 21.97 3.49 34.29 3.33
2351 3695 0.183014 TGGTTAACCCCGCTGTTGAA 59.817 50.000 21.97 0.00 34.29 2.69
2401 3745 7.698836 AAATTCATTCAGTTGTGTTGTTAGC 57.301 32.000 0.00 0.00 0.00 3.09
2403 3747 3.568007 TCATTCAGTTGTGTTGTTAGCCC 59.432 43.478 0.00 0.00 0.00 5.19
2404 3748 1.975660 TCAGTTGTGTTGTTAGCCCC 58.024 50.000 0.00 0.00 0.00 5.80
2405 3749 0.958822 CAGTTGTGTTGTTAGCCCCC 59.041 55.000 0.00 0.00 0.00 5.40
2421 3765 4.399395 CCCTGGCTCTCTGCGCAA 62.399 66.667 13.05 1.37 44.05 4.85
2422 3766 3.123620 CCTGGCTCTCTGCGCAAC 61.124 66.667 13.05 0.00 44.05 4.17
2423 3767 2.047465 CTGGCTCTCTGCGCAACT 60.047 61.111 13.05 0.00 44.05 3.16
2424 3768 2.357881 TGGCTCTCTGCGCAACTG 60.358 61.111 13.05 4.43 44.05 3.16
2425 3769 2.047844 GGCTCTCTGCGCAACTGA 60.048 61.111 13.05 8.99 44.05 3.41
2426 3770 2.099431 GGCTCTCTGCGCAACTGAG 61.099 63.158 21.91 21.91 43.73 3.35
2447 3807 1.338674 TGAAGTTGCCGGTGGAGTATG 60.339 52.381 1.90 0.00 0.00 2.39
2452 3812 1.518572 GCCGGTGGAGTATGTGACG 60.519 63.158 1.90 0.00 0.00 4.35
2493 3857 1.162698 CCAGTCGTAGGAACAGACGA 58.837 55.000 0.00 0.00 44.43 4.20
2524 3901 1.326213 ATCGTCCAGAGTCTGCCCTG 61.326 60.000 15.10 1.11 0.00 4.45
2546 3923 2.626780 GGCCTTTTGTCCGGTGCTC 61.627 63.158 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 6.766944 TGTTCTAAATTGTTCTTAACCGGTGA 59.233 34.615 8.52 0.00 0.00 4.02
164 569 2.739913 TCTGAATTGTTCTTAACGGGCG 59.260 45.455 0.00 0.00 0.00 6.13
188 593 4.658435 TCACTGGCAGGGATTAATAGCTAA 59.342 41.667 17.16 0.00 0.00 3.09
331 975 1.620413 GCCTGCACTGAATTTTGCGC 61.620 55.000 0.00 0.00 41.96 6.09
433 1079 4.629779 CCCCCGCGACACTATTTT 57.370 55.556 8.23 0.00 0.00 1.82
452 1098 2.595380 TCCAAGTAAGTATCCTCCCCCT 59.405 50.000 0.00 0.00 0.00 4.79
453 1099 3.056201 TCCAAGTAAGTATCCTCCCCC 57.944 52.381 0.00 0.00 0.00 5.40
454 1100 4.262506 CGAATCCAAGTAAGTATCCTCCCC 60.263 50.000 0.00 0.00 0.00 4.81
455 1101 4.344390 ACGAATCCAAGTAAGTATCCTCCC 59.656 45.833 0.00 0.00 0.00 4.30
456 1102 5.532664 ACGAATCCAAGTAAGTATCCTCC 57.467 43.478 0.00 0.00 0.00 4.30
457 1103 5.753921 CCAACGAATCCAAGTAAGTATCCTC 59.246 44.000 0.00 0.00 0.00 3.71
458 1104 5.424252 TCCAACGAATCCAAGTAAGTATCCT 59.576 40.000 0.00 0.00 0.00 3.24
459 1105 5.667466 TCCAACGAATCCAAGTAAGTATCC 58.333 41.667 0.00 0.00 0.00 2.59
460 1106 5.753921 CCTCCAACGAATCCAAGTAAGTATC 59.246 44.000 0.00 0.00 0.00 2.24
461 1107 5.189145 ACCTCCAACGAATCCAAGTAAGTAT 59.811 40.000 0.00 0.00 0.00 2.12
462 1108 4.529377 ACCTCCAACGAATCCAAGTAAGTA 59.471 41.667 0.00 0.00 0.00 2.24
463 1109 3.326880 ACCTCCAACGAATCCAAGTAAGT 59.673 43.478 0.00 0.00 0.00 2.24
464 1110 3.939066 ACCTCCAACGAATCCAAGTAAG 58.061 45.455 0.00 0.00 0.00 2.34
465 1111 4.202377 TGAACCTCCAACGAATCCAAGTAA 60.202 41.667 0.00 0.00 0.00 2.24
466 1112 3.325425 TGAACCTCCAACGAATCCAAGTA 59.675 43.478 0.00 0.00 0.00 2.24
467 1113 2.105821 TGAACCTCCAACGAATCCAAGT 59.894 45.455 0.00 0.00 0.00 3.16
468 1114 2.778299 TGAACCTCCAACGAATCCAAG 58.222 47.619 0.00 0.00 0.00 3.61
469 1115 2.940994 TGAACCTCCAACGAATCCAA 57.059 45.000 0.00 0.00 0.00 3.53
470 1116 3.262151 TGTATGAACCTCCAACGAATCCA 59.738 43.478 0.00 0.00 0.00 3.41
471 1117 3.869065 TGTATGAACCTCCAACGAATCC 58.131 45.455 0.00 0.00 0.00 3.01
472 1118 4.876107 ACATGTATGAACCTCCAACGAATC 59.124 41.667 0.00 0.00 0.00 2.52
473 1119 4.843728 ACATGTATGAACCTCCAACGAAT 58.156 39.130 0.00 0.00 0.00 3.34
474 1120 4.280436 ACATGTATGAACCTCCAACGAA 57.720 40.909 0.00 0.00 0.00 3.85
475 1121 3.973206 ACATGTATGAACCTCCAACGA 57.027 42.857 0.00 0.00 0.00 3.85
476 1122 7.151976 TGATATACATGTATGAACCTCCAACG 58.848 38.462 25.48 0.00 0.00 4.10
477 1123 8.902540 TTGATATACATGTATGAACCTCCAAC 57.097 34.615 25.48 5.23 0.00 3.77
479 1125 9.506018 CATTTGATATACATGTATGAACCTCCA 57.494 33.333 25.48 5.95 0.00 3.86
480 1126 9.507329 ACATTTGATATACATGTATGAACCTCC 57.493 33.333 25.48 8.97 0.00 4.30
482 1128 9.851686 ACACATTTGATATACATGTATGAACCT 57.148 29.630 25.48 4.26 0.00 3.50
493 1139 9.225436 ACACAACATGTACACATTTGATATACA 57.775 29.630 16.10 0.00 40.88 2.29
494 1140 9.702726 GACACAACATGTACACATTTGATATAC 57.297 33.333 16.10 3.86 43.56 1.47
495 1141 9.442047 TGACACAACATGTACACATTTGATATA 57.558 29.630 16.10 2.36 43.56 0.86
510 1317 7.776933 ACTATTACTAGCATGACACAACATG 57.223 36.000 0.00 0.00 46.96 3.21
524 1331 4.706842 ATGCACCCCCAACTATTACTAG 57.293 45.455 0.00 0.00 0.00 2.57
536 1343 6.561519 AGTATATCTGTATAATGCACCCCC 57.438 41.667 0.00 0.00 0.00 5.40
558 1365 9.613428 TCCATCTCAGTACCAAAAACATATAAG 57.387 33.333 0.00 0.00 0.00 1.73
559 1366 9.967451 TTCCATCTCAGTACCAAAAACATATAA 57.033 29.630 0.00 0.00 0.00 0.98
561 1368 7.557719 CCTTCCATCTCAGTACCAAAAACATAT 59.442 37.037 0.00 0.00 0.00 1.78
562 1369 6.884295 CCTTCCATCTCAGTACCAAAAACATA 59.116 38.462 0.00 0.00 0.00 2.29
563 1370 5.711976 CCTTCCATCTCAGTACCAAAAACAT 59.288 40.000 0.00 0.00 0.00 2.71
564 1371 5.070001 CCTTCCATCTCAGTACCAAAAACA 58.930 41.667 0.00 0.00 0.00 2.83
567 1374 5.073144 ACTTCCTTCCATCTCAGTACCAAAA 59.927 40.000 0.00 0.00 0.00 2.44
569 1376 4.168101 ACTTCCTTCCATCTCAGTACCAA 58.832 43.478 0.00 0.00 0.00 3.67
570 1377 3.791320 ACTTCCTTCCATCTCAGTACCA 58.209 45.455 0.00 0.00 0.00 3.25
571 1378 5.395435 GGTTACTTCCTTCCATCTCAGTACC 60.395 48.000 0.00 0.00 0.00 3.34
573 1380 4.401519 CGGTTACTTCCTTCCATCTCAGTA 59.598 45.833 0.00 0.00 0.00 2.74
575 1382 3.447586 TCGGTTACTTCCTTCCATCTCAG 59.552 47.826 0.00 0.00 0.00 3.35
584 1696 2.809299 GCACAACCTCGGTTACTTCCTT 60.809 50.000 0.21 0.00 36.46 3.36
672 1864 7.165647 TGCAATTTGTATCAAAATTATCGCGAG 59.834 33.333 16.66 0.00 37.59 5.03
673 1865 6.969473 TGCAATTTGTATCAAAATTATCGCGA 59.031 30.769 13.09 13.09 37.59 5.87
674 1866 7.147550 TGCAATTTGTATCAAAATTATCGCG 57.852 32.000 0.00 0.00 37.59 5.87
675 1867 8.005466 CCATGCAATTTGTATCAAAATTATCGC 58.995 33.333 0.00 0.00 37.59 4.58
676 1868 9.033481 ACCATGCAATTTGTATCAAAATTATCG 57.967 29.630 0.00 0.00 37.59 2.92
679 1871 9.716531 TGAACCATGCAATTTGTATCAAAATTA 57.283 25.926 0.00 0.00 37.59 1.40
680 1872 8.618702 TGAACCATGCAATTTGTATCAAAATT 57.381 26.923 0.00 0.00 39.71 1.82
681 1873 8.618702 TTGAACCATGCAATTTGTATCAAAAT 57.381 26.923 0.00 0.00 0.00 1.82
682 1874 7.714377 ACTTGAACCATGCAATTTGTATCAAAA 59.286 29.630 0.00 0.00 0.00 2.44
711 1914 6.971527 ATTTGGTTTGCAATGTCACATATG 57.028 33.333 0.00 0.00 0.00 1.78
771 1974 0.322906 GGAGGAGGCAAGACTTTGGG 60.323 60.000 0.00 0.00 34.79 4.12
773 1976 2.355209 GGTAGGAGGAGGCAAGACTTTG 60.355 54.545 0.00 0.00 37.36 2.77
814 2017 4.708601 CGAGTGGTGCTGTTTATTACAAC 58.291 43.478 0.00 0.00 36.02 3.32
910 2113 3.614176 GGCGAATGAAAAGAAAGGCATTC 59.386 43.478 0.00 0.00 41.79 2.67
926 2129 2.066999 GGGAGACAGGGAGGCGAAT 61.067 63.158 0.00 0.00 0.00 3.34
1012 2219 1.805254 CCATTGCTGCCGAGGAAAG 59.195 57.895 0.00 0.00 32.62 2.62
1014 2221 2.751436 GCCATTGCTGCCGAGGAA 60.751 61.111 0.00 0.00 33.52 3.36
1015 2222 4.802051 GGCCATTGCTGCCGAGGA 62.802 66.667 0.00 0.00 39.48 3.71
1021 2228 2.832201 GGAGGAGGCCATTGCTGC 60.832 66.667 5.01 0.00 37.74 5.25
1056 2363 0.685131 TCTTGATCGGCGGTAGGGAA 60.685 55.000 7.21 0.00 0.00 3.97
1059 2366 1.299165 CGTCTTGATCGGCGGTAGG 60.299 63.158 7.21 0.00 0.00 3.18
1215 2528 1.153289 CAGGATCCGGCACTCCTTG 60.153 63.158 15.10 8.94 39.95 3.61
1225 2538 4.598894 CTCGGGCAGCAGGATCCG 62.599 72.222 5.98 2.47 43.42 4.18
1429 2742 2.887568 CGACCAGATCGCAGCACC 60.888 66.667 0.00 0.00 45.52 5.01
1517 2835 1.411501 CCCCAAGAGAGGAGAGGAGAG 60.412 61.905 0.00 0.00 0.00 3.20
1532 2850 0.836830 TACCATGGACACGACCCCAA 60.837 55.000 21.47 0.00 35.85 4.12
1537 2855 5.815740 ACTCATAATTTACCATGGACACGAC 59.184 40.000 21.47 0.00 0.00 4.34
1543 2861 6.462487 GGAGACGACTCATAATTTACCATGGA 60.462 42.308 21.47 0.00 44.22 3.41
1563 2881 9.790389 CCTTATTTATGTATACGATGAGGAGAC 57.210 37.037 10.86 0.00 0.00 3.36
1564 2882 9.529823 ACCTTATTTATGTATACGATGAGGAGA 57.470 33.333 17.94 0.00 30.51 3.71
1565 2883 9.574458 CACCTTATTTATGTATACGATGAGGAG 57.426 37.037 17.94 11.07 30.51 3.69
1567 2885 9.706691 AACACCTTATTTATGTATACGATGAGG 57.293 33.333 13.11 13.11 31.77 3.86
1600 2918 3.173965 AGGAAGCACACATACCACTACT 58.826 45.455 0.00 0.00 0.00 2.57
1606 2924 1.130561 GCGAAAGGAAGCACACATACC 59.869 52.381 0.00 0.00 0.00 2.73
1641 2959 3.168963 CAGCTTGCATGAGAATTTCACG 58.831 45.455 3.33 0.00 38.99 4.35
1665 2983 7.228706 CCCAGTAATTAACAGCCTACCTTATTG 59.771 40.741 0.00 0.00 0.00 1.90
1677 2995 3.374058 CACTTCCGCCCAGTAATTAACAG 59.626 47.826 0.00 0.00 0.00 3.16
1718 3036 6.478344 CGGGATCTCTCTGAATTTTCTTACAG 59.522 42.308 0.00 0.00 0.00 2.74
1776 3094 7.716998 AGGATAATTGCACAATTCTGGTAGTAG 59.283 37.037 11.69 0.00 40.99 2.57
1777 3095 7.573710 AGGATAATTGCACAATTCTGGTAGTA 58.426 34.615 11.69 0.00 40.99 1.82
1778 3096 6.426587 AGGATAATTGCACAATTCTGGTAGT 58.573 36.000 11.69 0.00 40.99 2.73
1779 3097 6.543465 TGAGGATAATTGCACAATTCTGGTAG 59.457 38.462 11.69 0.00 40.99 3.18
1812 3141 3.129988 GGATTCTGGCTGAATTGGAACAG 59.870 47.826 18.88 0.00 44.70 3.16
1854 3184 2.028778 GATGCTCTGAGCGGCGAT 59.971 61.111 23.35 2.76 46.26 4.58
1855 3185 4.212913 GGATGCTCTGAGCGGCGA 62.213 66.667 23.35 7.50 46.26 5.54
1856 3186 3.804153 ATGGATGCTCTGAGCGGCG 62.804 63.158 23.35 0.51 46.26 6.46
1857 3187 2.110627 ATGGATGCTCTGAGCGGC 59.889 61.111 23.35 17.11 46.26 6.53
1858 3188 1.597302 CCATGGATGCTCTGAGCGG 60.597 63.158 23.35 13.85 46.26 5.52
1909 3239 1.086634 GTCTCGTCCTTCATGCAGCC 61.087 60.000 0.00 0.00 0.00 4.85
1981 3312 2.203209 GGACGGACATGGCATCCC 60.203 66.667 9.54 0.71 31.99 3.85
1996 3327 0.846015 AATCTCCATGGATTGCCGGA 59.154 50.000 16.63 8.32 34.99 5.14
1997 3328 1.338973 CAAATCTCCATGGATTGCCGG 59.661 52.381 16.63 2.02 36.24 6.13
1998 3329 1.338973 CCAAATCTCCATGGATTGCCG 59.661 52.381 16.63 2.86 39.12 5.69
1999 3330 1.690352 CCCAAATCTCCATGGATTGCC 59.310 52.381 16.63 0.00 39.12 4.52
2000 3331 2.626743 CTCCCAAATCTCCATGGATTGC 59.373 50.000 16.63 0.00 39.12 3.56
2001 3332 3.228453 CCTCCCAAATCTCCATGGATTG 58.772 50.000 16.63 16.59 39.12 2.67
2020 3351 1.961277 CGAAAAGCACACTCGCCCT 60.961 57.895 0.00 0.00 0.00 5.19
2026 3358 2.542907 CGCCACCGAAAAGCACACT 61.543 57.895 0.00 0.00 36.29 3.55
2059 3391 1.895798 TGTCTGTTCTCTCTCGGCATT 59.104 47.619 0.00 0.00 0.00 3.56
2141 3474 1.000771 TGGAGACTGGACCGGAGAG 60.001 63.158 9.46 2.58 0.00 3.20
2149 3482 2.030027 ATTCACCACTGGAGACTGGA 57.970 50.000 0.71 0.00 30.45 3.86
2151 3484 6.824305 AAAATAATTCACCACTGGAGACTG 57.176 37.500 0.71 0.00 0.00 3.51
2152 3485 7.234355 AGAAAAATAATTCACCACTGGAGACT 58.766 34.615 0.71 0.00 0.00 3.24
2153 3486 7.391833 AGAGAAAAATAATTCACCACTGGAGAC 59.608 37.037 0.71 0.00 0.00 3.36
2154 3487 7.461749 AGAGAAAAATAATTCACCACTGGAGA 58.538 34.615 0.71 0.00 0.00 3.71
2155 3488 7.693969 AGAGAAAAATAATTCACCACTGGAG 57.306 36.000 0.71 0.00 0.00 3.86
2179 3512 6.955364 AGACAAATCAGGATCTTCATCAGAA 58.045 36.000 0.00 0.00 34.16 3.02
2183 3516 6.928492 GGTAGAGACAAATCAGGATCTTCATC 59.072 42.308 0.00 0.00 0.00 2.92
2184 3517 6.183361 GGGTAGAGACAAATCAGGATCTTCAT 60.183 42.308 0.00 0.00 0.00 2.57
2193 3526 6.098982 AGGATGTTAGGGTAGAGACAAATCAG 59.901 42.308 0.00 0.00 0.00 2.90
2209 3542 1.206745 CGCGCGGTGTAGGATGTTAG 61.207 60.000 24.84 0.00 0.00 2.34
2223 3556 4.536687 GGATTTTGGAGGCGCGCG 62.537 66.667 28.44 28.44 0.00 6.86
2248 3592 5.003804 ACTGTTACAGCAGGGACAAATTAG 58.996 41.667 12.80 0.00 40.59 1.73
2261 3605 6.100004 ACATCATGTACTACACTGTTACAGC 58.900 40.000 12.80 0.00 34.37 4.40
2263 3607 8.344446 ACTACATCATGTACTACACTGTTACA 57.656 34.615 0.00 0.00 0.00 2.41
2272 3616 7.244166 ACACTACGACTACATCATGTACTAC 57.756 40.000 0.00 0.00 0.00 2.73
2273 3617 7.854557 AACACTACGACTACATCATGTACTA 57.145 36.000 0.00 0.00 0.00 1.82
2274 3618 6.754702 AACACTACGACTACATCATGTACT 57.245 37.500 0.00 0.00 0.00 2.73
2310 3654 6.014499 ACCAGCTACACAGTAGAATTTACAGT 60.014 38.462 8.29 0.00 0.00 3.55
2313 3657 8.654215 GTTAACCAGCTACACAGTAGAATTTAC 58.346 37.037 8.29 0.00 0.00 2.01
2314 3658 7.820872 GGTTAACCAGCTACACAGTAGAATTTA 59.179 37.037 20.12 0.00 35.64 1.40
2343 3687 2.349817 CGTGTGGATGAACTTCAACAGC 60.350 50.000 0.00 0.00 0.00 4.40
2348 3692 1.225855 GTGCGTGTGGATGAACTTCA 58.774 50.000 0.00 0.00 0.00 3.02
2349 3693 1.195448 CTGTGCGTGTGGATGAACTTC 59.805 52.381 0.00 0.00 0.00 3.01
2351 3695 0.392706 TCTGTGCGTGTGGATGAACT 59.607 50.000 0.00 0.00 0.00 3.01
2378 3722 6.215845 GGCTAACAACACAACTGAATGAATT 58.784 36.000 0.00 0.00 0.00 2.17
2381 3725 3.568007 GGGCTAACAACACAACTGAATGA 59.432 43.478 0.00 0.00 0.00 2.57
2404 3748 4.399395 TTGCGCAGAGAGCCAGGG 62.399 66.667 11.31 0.00 41.38 4.45
2405 3749 3.123620 GTTGCGCAGAGAGCCAGG 61.124 66.667 11.31 0.00 41.38 4.45
2406 3750 2.047465 AGTTGCGCAGAGAGCCAG 60.047 61.111 11.31 0.00 41.38 4.85
2408 3752 2.047844 TCAGTTGCGCAGAGAGCC 60.048 61.111 11.31 0.00 41.38 4.70
2409 3753 1.373999 ACTCAGTTGCGCAGAGAGC 60.374 57.895 26.36 10.20 35.10 4.09
2411 3755 0.389025 TTCACTCAGTTGCGCAGAGA 59.611 50.000 26.36 17.38 35.10 3.10
2412 3756 0.788995 CTTCACTCAGTTGCGCAGAG 59.211 55.000 20.09 20.09 36.86 3.35
2413 3757 0.104855 ACTTCACTCAGTTGCGCAGA 59.895 50.000 11.31 3.53 0.00 4.26
2414 3758 0.940126 AACTTCACTCAGTTGCGCAG 59.060 50.000 11.31 0.00 35.57 5.18
2415 3759 0.657312 CAACTTCACTCAGTTGCGCA 59.343 50.000 5.66 5.66 45.43 6.09
2416 3760 3.444657 CAACTTCACTCAGTTGCGC 57.555 52.632 0.00 0.00 45.43 6.09
2420 3764 0.180406 ACCGGCAACTTCACTCAGTT 59.820 50.000 0.00 0.00 37.49 3.16
2421 3765 0.532862 CACCGGCAACTTCACTCAGT 60.533 55.000 0.00 0.00 0.00 3.41
2422 3766 1.230635 CCACCGGCAACTTCACTCAG 61.231 60.000 0.00 0.00 0.00 3.35
2423 3767 1.227823 CCACCGGCAACTTCACTCA 60.228 57.895 0.00 0.00 0.00 3.41
2424 3768 0.951040 CTCCACCGGCAACTTCACTC 60.951 60.000 0.00 0.00 0.00 3.51
2425 3769 1.071471 CTCCACCGGCAACTTCACT 59.929 57.895 0.00 0.00 0.00 3.41
2426 3770 0.034337 TACTCCACCGGCAACTTCAC 59.966 55.000 0.00 0.00 0.00 3.18
2447 3807 5.220491 GCTCTGGATTTATTTCACTCGTCAC 60.220 44.000 0.00 0.00 0.00 3.67
2452 3812 5.882557 TGGAAGCTCTGGATTTATTTCACTC 59.117 40.000 0.00 0.00 0.00 3.51
2493 3857 2.124570 GACGATGGCCCTGCATGT 60.125 61.111 0.00 0.00 0.00 3.21
2524 3901 2.361230 CCGGACAAAAGGCCCCTC 60.361 66.667 0.00 0.00 0.00 4.30
2531 3908 1.247567 AATGGAGCACCGGACAAAAG 58.752 50.000 9.46 0.00 39.42 2.27
2546 3923 1.178534 AAGCCGTGGTGACCAAATGG 61.179 55.000 5.57 10.27 42.17 3.16


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

AutoCloner maintained by Alex Coulton.