Multiple sequence alignment - TraesCS6B01G439600

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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 TraesCS6B01G439600 chr6B 100.000 4549 0 0 1 4549 704970654 704975202 0.000000e+00 8401.0
1 TraesCS6B01G439600 chr6D 92.523 3932 187 49 663 4535 462484088 462487971 0.000000e+00 5533.0
2 TraesCS6B01G439600 chr6D 81.361 338 31 16 6 321 462483433 462483760 3.510000e-61 246.0
3 TraesCS6B01G439600 chr6D 94.915 59 3 0 2000 2058 157662034 157661976 4.850000e-15 93.5
4 TraesCS6B01G439600 chr6A 91.696 3950 197 45 691 4549 609285364 609289273 0.000000e+00 5356.0
5 TraesCS6B01G439600 chr6A 89.474 247 15 5 1 247 609284304 609284539 7.400000e-78 302.0
6 TraesCS6B01G439600 chr3D 92.836 684 44 5 1686 2366 537652793 537653474 0.000000e+00 987.0
7 TraesCS6B01G439600 chr3D 91.533 685 51 7 1686 2366 537647607 537648288 0.000000e+00 937.0
8 TraesCS6B01G439600 chr3D 96.610 59 2 0 2000 2058 105174646 105174704 1.040000e-16 99.0
9 TraesCS6B01G439600 chr3D 96.610 59 2 0 2000 2058 105252424 105252482 1.040000e-16 99.0
10 TraesCS6B01G439600 chr3D 96.610 59 2 0 2000 2058 105279850 105279908 1.040000e-16 99.0
11 TraesCS6B01G439600 chr1B 91.053 380 31 3 1990 2369 577993507 577993131 1.130000e-140 510.0
12 TraesCS6B01G439600 chr1B 90.299 134 11 2 1713 1844 577993688 577993555 1.680000e-39 174.0
13 TraesCS6B01G439600 chr2B 81.612 484 84 4 1250 1732 11076223 11076702 3.300000e-106 396.0
14 TraesCS6B01G439600 chr2D 80.228 526 93 9 1250 1771 273880 274398 7.140000e-103 385.0
15 TraesCS6B01G439600 chr2D 91.304 46 4 0 4489 4534 110909707 110909752 3.800000e-06 63.9
16 TraesCS6B01G439600 chr5A 83.624 287 20 15 1388 1673 338378695 338378955 1.260000e-60 244.0
17 TraesCS6B01G439600 chr5D 85.202 223 18 11 1388 1609 255368895 255369103 9.910000e-52 215.0
18 TraesCS6B01G439600 chr4B 84.753 223 17 12 1388 1609 43226101 43225895 1.660000e-49 207.0
19 TraesCS6B01G439600 chr5B 83.408 223 16 15 1388 1609 286876423 286876221 2.160000e-43 187.0
20 TraesCS6B01G439600 chr5B 100.000 28 0 0 4488 4515 241402225 241402252 8.000000e-03 52.8
21 TraesCS6B01G439600 chr3A 82.667 75 13 0 4461 4535 479136716 479136790 2.940000e-07 67.6


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 TraesCS6B01G439600 chr6B 704970654 704975202 4548 False 8401.0 8401 100.000 1 4549 1 chr6B.!!$F1 4548
1 TraesCS6B01G439600 chr6D 462483433 462487971 4538 False 2889.5 5533 86.942 6 4535 2 chr6D.!!$F1 4529
2 TraesCS6B01G439600 chr6A 609284304 609289273 4969 False 2829.0 5356 90.585 1 4549 2 chr6A.!!$F1 4548
3 TraesCS6B01G439600 chr3D 537652793 537653474 681 False 987.0 987 92.836 1686 2366 1 chr3D.!!$F5 680
4 TraesCS6B01G439600 chr3D 537647607 537648288 681 False 937.0 937 91.533 1686 2366 1 chr3D.!!$F4 680
5 TraesCS6B01G439600 chr1B 577993131 577993688 557 True 342.0 510 90.676 1713 2369 2 chr1B.!!$R1 656
6 TraesCS6B01G439600 chr2D 273880 274398 518 False 385.0 385 80.228 1250 1771 1 chr2D.!!$F1 521

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
773 1265 0.095935 CGTGCTTGCTCTGATTTCCG 59.904 55.0 0.00 0.0 0.00 4.30 F
982 1506 0.460284 CGCCAAGATTGTAGCGGACT 60.460 55.0 7.92 0.0 44.64 3.85 F
2415 2952 0.817654 TCGTCTCCACGCTCATCAAT 59.182 50.0 0.00 0.0 46.28 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2415 2952 0.455815 CCGACATCTCCATGACGTCA 59.544 55.000 22.48 22.48 43.83 4.35 R
2589 3126 1.285078 TGGAAGATCCTCCTCTCGTCA 59.715 52.381 11.69 0.00 37.46 4.35 R
3721 4284 0.954449 CAGAGCAGCACACAGGGAAG 60.954 60.000 0.00 0.00 0.00 3.46 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
46 48 7.194112 TGAAATAAAAATCATCCCTTTCCCC 57.806 36.000 0.00 0.00 0.00 4.81
52 54 0.909623 TCATCCCTTTCCCCGTCTTC 59.090 55.000 0.00 0.00 0.00 2.87
85 87 1.627879 CAGTCTTCGCTCAGCTTCTC 58.372 55.000 0.00 0.00 0.00 2.87
87 89 1.153939 TCTTCGCTCAGCTTCTCGC 60.154 57.895 0.00 0.00 39.57 5.03
130 166 6.353404 TGGTTGAAAATTAGTGGGAAATCC 57.647 37.500 0.00 0.00 0.00 3.01
153 189 3.411517 CCTCCCAATCCCACCGCT 61.412 66.667 0.00 0.00 0.00 5.52
201 237 1.521681 CGATGCTCCTCCGGTTTCC 60.522 63.158 0.00 0.00 0.00 3.13
221 258 3.195698 CGCGACTAAGCCAAGCCC 61.196 66.667 0.00 0.00 0.00 5.19
222 259 2.824489 GCGACTAAGCCAAGCCCC 60.824 66.667 0.00 0.00 0.00 5.80
247 284 2.289694 CCAGGTCCAATGTCTTCGTCTT 60.290 50.000 0.00 0.00 0.00 3.01
248 285 2.996621 CAGGTCCAATGTCTTCGTCTTC 59.003 50.000 0.00 0.00 0.00 2.87
249 286 1.993370 GGTCCAATGTCTTCGTCTTCG 59.007 52.381 0.00 0.00 38.55 3.79
250 287 2.609737 GGTCCAATGTCTTCGTCTTCGT 60.610 50.000 0.00 0.00 38.33 3.85
251 288 2.662156 GTCCAATGTCTTCGTCTTCGTC 59.338 50.000 0.00 0.00 38.33 4.20
252 289 2.557056 TCCAATGTCTTCGTCTTCGTCT 59.443 45.455 0.00 0.00 38.33 4.18
253 290 3.005472 TCCAATGTCTTCGTCTTCGTCTT 59.995 43.478 0.00 0.00 38.33 3.01
336 782 0.391793 CCTCCGCTCCTTCAACTTCC 60.392 60.000 0.00 0.00 0.00 3.46
341 787 1.404851 CGCTCCTTCAACTTCCTCTCC 60.405 57.143 0.00 0.00 0.00 3.71
342 788 1.404851 GCTCCTTCAACTTCCTCTCCG 60.405 57.143 0.00 0.00 0.00 4.63
344 790 0.391793 CCTTCAACTTCCTCTCCGCC 60.392 60.000 0.00 0.00 0.00 6.13
345 791 0.391793 CTTCAACTTCCTCTCCGCCC 60.392 60.000 0.00 0.00 0.00 6.13
346 792 1.125093 TTCAACTTCCTCTCCGCCCA 61.125 55.000 0.00 0.00 0.00 5.36
347 793 1.078848 CAACTTCCTCTCCGCCCAG 60.079 63.158 0.00 0.00 0.00 4.45
348 794 2.294078 AACTTCCTCTCCGCCCAGG 61.294 63.158 0.00 0.00 42.97 4.45
349 795 2.685380 CTTCCTCTCCGCCCAGGT 60.685 66.667 0.00 0.00 41.99 4.00
350 796 1.381327 CTTCCTCTCCGCCCAGGTA 60.381 63.158 0.00 0.00 41.99 3.08
351 797 1.677637 CTTCCTCTCCGCCCAGGTAC 61.678 65.000 0.00 0.00 41.99 3.34
352 798 3.528370 CCTCTCCGCCCAGGTACG 61.528 72.222 0.00 0.00 41.99 3.67
353 799 2.754658 CTCTCCGCCCAGGTACGT 60.755 66.667 0.00 0.00 41.99 3.57
355 801 2.183555 CTCCGCCCAGGTACGTTC 59.816 66.667 0.00 0.00 41.99 3.95
356 802 3.695022 CTCCGCCCAGGTACGTTCG 62.695 68.421 0.00 0.00 41.99 3.95
360 806 4.807039 CCCAGGTACGTTCGCCCG 62.807 72.222 0.00 0.00 0.00 6.13
361 807 4.807039 CCAGGTACGTTCGCCCGG 62.807 72.222 0.00 0.00 0.00 5.73
378 824 3.768922 GCAGCACGAGGCCTCTCT 61.769 66.667 29.73 19.90 46.50 3.10
380 826 3.768922 AGCACGAGGCCTCTCTGC 61.769 66.667 31.24 31.24 46.50 4.26
389 835 3.136750 CCTCTCTGCCTGATCGGG 58.863 66.667 16.98 16.98 0.00 5.14
400 846 1.541015 CCTGATCGGGCGATTCATTCA 60.541 52.381 7.89 0.00 34.60 2.57
401 847 1.528586 CTGATCGGGCGATTCATTCAC 59.471 52.381 0.00 0.00 34.60 3.18
406 852 2.703409 GCGATTCATTCACGCGCT 59.297 55.556 5.73 0.00 43.85 5.92
409 855 1.366961 GATTCATTCACGCGCTCGC 60.367 57.895 5.73 3.90 39.84 5.03
410 856 1.756375 GATTCATTCACGCGCTCGCT 61.756 55.000 5.73 0.00 39.84 4.93
412 858 3.918220 CATTCACGCGCTCGCTCC 61.918 66.667 5.73 0.00 39.84 4.70
420 866 3.586961 CGCTCGCTCCTGGATCGA 61.587 66.667 20.09 20.09 0.00 3.59
446 916 1.808234 GATCGATCCACGCGGTTTCG 61.808 60.000 14.76 13.54 42.26 3.46
457 927 4.426313 GGTTTCGGGCCCCTGGAG 62.426 72.222 18.66 0.58 0.00 3.86
478 948 2.821969 GTGACCAATCCATGTTCTTGCT 59.178 45.455 0.00 0.00 0.00 3.91
512 986 1.448013 CTTTCTTCTCCCGCGGGAC 60.448 63.158 42.66 0.00 39.76 4.46
579 1053 4.767633 CGAGGTAGTGTCTCGTGC 57.232 61.111 5.46 0.00 46.16 5.34
584 1058 1.136984 GTAGTGTCTCGTGCTCCCG 59.863 63.158 0.00 0.00 0.00 5.14
604 1095 0.981277 TCCGGATTCCCTCTGTTCCC 60.981 60.000 0.00 0.00 0.00 3.97
608 1099 1.626631 GGATTCCCTCTGTTCCCCTCT 60.627 57.143 0.00 0.00 0.00 3.69
610 1101 0.252742 TTCCCTCTGTTCCCCTCTCC 60.253 60.000 0.00 0.00 0.00 3.71
611 1102 1.156322 TCCCTCTGTTCCCCTCTCCT 61.156 60.000 0.00 0.00 0.00 3.69
612 1103 0.252927 CCCTCTGTTCCCCTCTCCTT 60.253 60.000 0.00 0.00 0.00 3.36
614 1105 1.553417 CCTCTGTTCCCCTCTCCTTCA 60.553 57.143 0.00 0.00 0.00 3.02
615 1106 1.552792 CTCTGTTCCCCTCTCCTTCAC 59.447 57.143 0.00 0.00 0.00 3.18
616 1107 0.247736 CTGTTCCCCTCTCCTTCACG 59.752 60.000 0.00 0.00 0.00 4.35
617 1108 1.192146 TGTTCCCCTCTCCTTCACGG 61.192 60.000 0.00 0.00 0.00 4.94
618 1109 1.612442 TTCCCCTCTCCTTCACGGG 60.612 63.158 0.00 0.00 36.42 5.28
619 1110 3.787001 CCCCTCTCCTTCACGGGC 61.787 72.222 0.00 0.00 35.29 6.13
623 1114 3.672295 CTCTCCTTCACGGGCTGGC 62.672 68.421 0.00 0.00 0.00 4.85
625 1116 3.672295 CTCCTTCACGGGCTGGCTC 62.672 68.421 0.00 0.00 0.00 4.70
631 1122 4.473520 ACGGGCTGGCTCGGATTG 62.474 66.667 19.04 0.00 45.45 2.67
633 1124 2.272146 GGGCTGGCTCGGATTGAA 59.728 61.111 0.00 0.00 0.00 2.69
638 1129 1.450531 CTGGCTCGGATTGAATGCCC 61.451 60.000 2.32 0.00 42.62 5.36
656 1147 4.637489 CCGAGATCGCCCGCTCTG 62.637 72.222 0.00 0.00 38.18 3.35
657 1148 3.893763 CGAGATCGCCCGCTCTGT 61.894 66.667 0.00 0.00 0.00 3.41
658 1149 2.026879 GAGATCGCCCGCTCTGTC 59.973 66.667 0.00 0.00 0.00 3.51
659 1150 2.441164 AGATCGCCCGCTCTGTCT 60.441 61.111 0.00 0.00 0.00 3.41
660 1151 2.279120 GATCGCCCGCTCTGTCTG 60.279 66.667 0.00 0.00 0.00 3.51
661 1152 3.069980 GATCGCCCGCTCTGTCTGT 62.070 63.158 0.00 0.00 0.00 3.41
680 1171 0.607762 TCTGTCTCTGCTCTGCTCGT 60.608 55.000 0.00 0.00 0.00 4.18
684 1175 0.678048 TCTCTGCTCTGCTCGTGCTA 60.678 55.000 11.19 0.00 40.48 3.49
753 1245 3.411517 CATCCCTGCCCCCTCGTT 61.412 66.667 0.00 0.00 0.00 3.85
762 1254 3.423154 CCCCTCGTTCGTGCTTGC 61.423 66.667 0.00 0.00 0.00 4.01
764 1256 2.383527 CCCTCGTTCGTGCTTGCTC 61.384 63.158 0.00 0.00 0.00 4.26
765 1257 1.373497 CCTCGTTCGTGCTTGCTCT 60.373 57.895 0.00 0.00 0.00 4.09
766 1258 1.621301 CCTCGTTCGTGCTTGCTCTG 61.621 60.000 0.00 0.00 0.00 3.35
767 1259 0.664466 CTCGTTCGTGCTTGCTCTGA 60.664 55.000 0.00 0.00 0.00 3.27
769 1261 0.792640 CGTTCGTGCTTGCTCTGATT 59.207 50.000 0.00 0.00 0.00 2.57
771 1263 2.723010 CGTTCGTGCTTGCTCTGATTTC 60.723 50.000 0.00 0.00 0.00 2.17
773 1265 0.095935 CGTGCTTGCTCTGATTTCCG 59.904 55.000 0.00 0.00 0.00 4.30
775 1267 1.308069 TGCTTGCTCTGATTTCCGGC 61.308 55.000 0.00 0.00 0.00 6.13
776 1268 1.308069 GCTTGCTCTGATTTCCGGCA 61.308 55.000 0.00 0.00 0.00 5.69
779 1271 2.464459 GCTCTGATTTCCGGCACCG 61.464 63.158 1.02 1.02 39.44 4.94
782 1281 1.218047 CTGATTTCCGGCACCGAGA 59.782 57.895 11.42 3.34 42.83 4.04
798 1298 2.668457 CCGAGAAACTGAAATCGTCTGG 59.332 50.000 0.00 0.00 33.43 3.86
807 1307 5.547465 ACTGAAATCGTCTGGTTGTTCATA 58.453 37.500 0.00 0.00 0.00 2.15
814 1314 3.554129 CGTCTGGTTGTTCATACAGGTGA 60.554 47.826 0.00 0.00 35.28 4.02
819 1319 1.368641 TGTTCATACAGGTGATGCGC 58.631 50.000 0.00 0.00 0.00 6.09
820 1320 1.066215 TGTTCATACAGGTGATGCGCT 60.066 47.619 9.73 0.00 0.00 5.92
821 1321 1.594862 GTTCATACAGGTGATGCGCTC 59.405 52.381 9.73 4.27 0.00 5.03
846 1357 2.464459 CCGCCGAGCTTGATTGGAC 61.464 63.158 1.22 0.00 0.00 4.02
851 1362 2.162681 CCGAGCTTGATTGGACCTTTT 58.837 47.619 1.22 0.00 0.00 2.27
856 1367 2.162408 GCTTGATTGGACCTTTTCTCCG 59.838 50.000 0.00 0.00 0.00 4.63
857 1368 3.412386 CTTGATTGGACCTTTTCTCCGT 58.588 45.455 0.00 0.00 0.00 4.69
865 1376 0.875059 CCTTTTCTCCGTTGGTCAGC 59.125 55.000 0.00 0.00 0.00 4.26
922 1446 3.991367 AGCGGCGCTAACTAATAATCTT 58.009 40.909 35.68 3.06 36.99 2.40
924 1448 3.988517 GCGGCGCTAACTAATAATCTTCT 59.011 43.478 26.86 0.00 0.00 2.85
980 1504 4.513519 CGCCAAGATTGTAGCGGA 57.486 55.556 7.92 0.00 44.64 5.54
982 1506 0.460284 CGCCAAGATTGTAGCGGACT 60.460 55.000 7.92 0.00 44.64 3.85
983 1507 1.739067 GCCAAGATTGTAGCGGACTT 58.261 50.000 0.00 0.00 0.00 3.01
984 1508 1.666189 GCCAAGATTGTAGCGGACTTC 59.334 52.381 0.00 0.00 0.00 3.01
985 1509 1.927174 CCAAGATTGTAGCGGACTTCG 59.073 52.381 0.00 0.00 42.76 3.79
986 1510 2.607187 CAAGATTGTAGCGGACTTCGT 58.393 47.619 0.00 0.00 41.72 3.85
1452 1989 2.202756 GCCTTCACCTACGAGCCG 60.203 66.667 0.00 0.00 0.00 5.52
2007 2544 1.375908 GCCGATGCTCAAGGTGTCA 60.376 57.895 0.00 0.00 33.53 3.58
2415 2952 0.817654 TCGTCTCCACGCTCATCAAT 59.182 50.000 0.00 0.00 46.28 2.57
2655 3192 1.137675 CTCATCAGCCGGATTGACTCA 59.862 52.381 5.05 0.00 32.57 3.41
2835 3372 2.281208 CCGGGGCAGTTCAAACGA 60.281 61.111 0.00 0.00 0.00 3.85
2920 3458 6.038997 AGGTACTGTCAACTGTCTATTTCC 57.961 41.667 0.00 0.00 37.18 3.13
2921 3459 5.542635 AGGTACTGTCAACTGTCTATTTCCA 59.457 40.000 0.00 0.00 37.18 3.53
2968 3530 9.151471 GTTCAAACTGAGAGCATATAAGTAACA 57.849 33.333 0.00 0.00 0.00 2.41
3059 3622 3.458163 CTCGACGGGCAAGGGCTA 61.458 66.667 0.00 0.00 40.87 3.93
3062 3625 3.712907 GACGGGCAAGGGCTACCA 61.713 66.667 0.00 0.00 40.87 3.25
3224 3787 2.029606 CGACGATGACATCAACATGGTG 59.970 50.000 15.58 3.69 36.97 4.17
3230 3793 0.036732 ACATCAACATGGTGGTCGCT 59.963 50.000 11.68 0.00 31.38 4.93
3251 3814 0.107752 GGAAGCTCCTGGAGAAGCTG 60.108 60.000 27.53 0.53 37.71 4.24
3254 3817 3.041469 GCTCCTGGAGAAGCTGGGG 62.041 68.421 27.53 0.00 0.00 4.96
3263 3826 4.643387 AAGCTGGGGTGCGTGGTC 62.643 66.667 0.00 0.00 38.13 4.02
3269 3832 4.083862 GGGTGCGTGGTCTCCTCC 62.084 72.222 0.00 0.00 0.00 4.30
3272 3835 1.681327 GTGCGTGGTCTCCTCCCTA 60.681 63.158 0.00 0.00 0.00 3.53
3278 3841 0.854039 TGGTCTCCTCCCTACCCTCA 60.854 60.000 0.00 0.00 31.97 3.86
3512 4075 2.512515 GTGGTCATGCTCGAGGCC 60.513 66.667 15.58 0.00 40.92 5.19
3551 4114 1.012086 TTCTTCAGAGCGCATGATGC 58.988 50.000 11.47 7.49 40.69 3.91
3650 4213 2.481471 GCTACCAAAGGGGCGATGC 61.481 63.158 0.00 0.00 42.05 3.91
3680 4243 1.275666 TCTTTGATCAGAAGGGCCGA 58.724 50.000 13.94 0.00 0.00 5.54
3809 4372 6.699204 CACTGTTCCACATATTCTAGCAGTAG 59.301 42.308 0.00 0.00 33.95 2.57
3810 4373 6.607600 ACTGTTCCACATATTCTAGCAGTAGA 59.392 38.462 0.00 0.00 33.60 2.59
3811 4374 7.288852 ACTGTTCCACATATTCTAGCAGTAGAT 59.711 37.037 0.00 0.00 35.12 1.98
3828 4391 3.567478 AGATGATGGGAGGTTACAAGC 57.433 47.619 0.00 0.00 0.00 4.01
3846 4409 2.069430 CAAGAGGGGGAGGAGCCTC 61.069 68.421 8.03 8.03 42.04 4.70
3847 4410 2.571816 AAGAGGGGGAGGAGCCTCA 61.572 63.158 17.68 0.00 44.40 3.86
3848 4411 2.766229 GAGGGGGAGGAGCCTCAC 60.766 72.222 17.68 14.27 45.26 3.51
3851 4414 3.086600 GGGGAGGAGCCTCACTGG 61.087 72.222 17.71 0.00 45.30 4.00
3854 4417 2.267324 GAGGAGCCTCACTGGTGC 59.733 66.667 11.58 0.00 42.31 5.01
3899 4462 5.226194 AGAGATCCAGGAGAAATACATGC 57.774 43.478 0.00 0.00 0.00 4.06
3904 4467 2.810274 CCAGGAGAAATACATGCGATGG 59.190 50.000 0.00 0.00 33.60 3.51
3950 4513 0.040351 TGTCTGACAGGAGAGGAGGG 59.960 60.000 6.36 0.00 0.00 4.30
4094 4657 4.201744 GCAACATTTTGTATTCAGGCATGC 60.202 41.667 9.90 9.90 34.90 4.06
4134 4698 4.443978 ACCATTCTTATGTCCCTCCATG 57.556 45.455 0.00 0.00 0.00 3.66
4140 4704 7.725397 CCATTCTTATGTCCCTCCATGATTTTA 59.275 37.037 0.00 0.00 0.00 1.52
4141 4705 9.135189 CATTCTTATGTCCCTCCATGATTTTAA 57.865 33.333 0.00 0.00 0.00 1.52
4143 4707 9.540538 TTCTTATGTCCCTCCATGATTTTAAAA 57.459 29.630 2.51 2.51 0.00 1.52
4144 4708 9.540538 TCTTATGTCCCTCCATGATTTTAAAAA 57.459 29.630 4.44 0.00 0.00 1.94
4183 4772 2.880268 TGTGGTGCATCTTCAGAAGTTG 59.120 45.455 14.67 14.67 0.00 3.16
4189 4778 3.004002 TGCATCTTCAGAAGTTGTGCAAG 59.996 43.478 24.90 1.31 38.47 4.01
4233 4822 4.685169 AGTAAACAAATGTCTGGATGCG 57.315 40.909 0.00 0.00 0.00 4.73
4273 4862 1.003580 TCCAGGAAGATCTTGTGGTGC 59.996 52.381 23.80 7.07 0.00 5.01
4277 4866 2.912956 AGGAAGATCTTGTGGTGCCTAA 59.087 45.455 14.00 0.00 0.00 2.69
4318 4907 5.221185 CCAAGATTAGCAGATGGTGAATTGG 60.221 44.000 8.65 8.65 31.20 3.16
4351 4941 2.390938 CTGCTGCAGTTCAAACATGTG 58.609 47.619 21.21 0.00 0.00 3.21
4444 5034 6.126409 TCTTGTGTACCTCTTCCATGTTTTT 58.874 36.000 0.00 0.00 0.00 1.94
4475 5075 1.552578 AAAAGACCCCAATAACGCCC 58.447 50.000 0.00 0.00 0.00 6.13
4480 5080 1.078001 CCCCAATAACGCCCGAACT 60.078 57.895 0.00 0.00 0.00 3.01
4505 5105 3.993081 CGCCTTTTTACCATTGCAAATCA 59.007 39.130 1.71 0.00 0.00 2.57
4516 5116 4.444468 CATTGCAAATCAAACGTTTTCGG 58.556 39.130 11.66 0.11 41.17 4.30
4535 5135 1.268352 GGTGGCAATTTTAGTGACGCA 59.732 47.619 0.00 0.00 36.15 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 54 4.742201 ACTGCTGTAGCCGCACGG 62.742 66.667 4.30 4.30 41.18 4.94
106 142 6.327626 TGGATTTCCCACTAATTTTCAACCAA 59.672 34.615 0.00 0.00 40.82 3.67
107 143 5.841237 TGGATTTCCCACTAATTTTCAACCA 59.159 36.000 0.00 0.00 40.82 3.67
108 144 6.353404 TGGATTTCCCACTAATTTTCAACC 57.647 37.500 0.00 0.00 40.82 3.77
130 166 0.106015 GTGGGATTGGGAGGGGATTG 60.106 60.000 0.00 0.00 0.00 2.67
136 172 3.411517 AGCGGTGGGATTGGGAGG 61.412 66.667 0.00 0.00 0.00 4.30
137 173 1.987807 ATCAGCGGTGGGATTGGGAG 61.988 60.000 15.67 0.00 0.00 4.30
138 174 1.983119 GATCAGCGGTGGGATTGGGA 61.983 60.000 15.67 0.00 0.00 4.37
139 175 1.526917 GATCAGCGGTGGGATTGGG 60.527 63.158 15.67 0.00 0.00 4.12
140 176 1.889105 CGATCAGCGGTGGGATTGG 60.889 63.158 15.67 0.00 36.03 3.16
201 237 2.167861 GCTTGGCTTAGTCGCGGAG 61.168 63.158 6.13 0.46 0.00 4.63
221 258 1.078426 GACATTGGACCTGGACCGG 60.078 63.158 10.56 0.00 0.00 5.28
222 259 0.324943 AAGACATTGGACCTGGACCG 59.675 55.000 10.56 0.00 0.00 4.79
314 351 2.203938 TTGAAGGAGCGGAGGGGT 60.204 61.111 0.00 0.00 0.00 4.95
325 771 0.391793 GGCGGAGAGGAAGTTGAAGG 60.392 60.000 0.00 0.00 0.00 3.46
336 782 2.280823 GAACGTACCTGGGCGGAGAG 62.281 65.000 15.29 0.00 36.31 3.20
344 790 4.807039 CCGGGCGAACGTACCTGG 62.807 72.222 13.87 13.87 45.95 4.45
361 807 3.768922 AGAGAGGCCTCGTGCTGC 61.769 66.667 26.95 12.87 44.08 5.25
362 808 2.183811 CAGAGAGGCCTCGTGCTG 59.816 66.667 27.30 27.30 44.08 4.41
363 809 3.768922 GCAGAGAGGCCTCGTGCT 61.769 66.667 36.98 28.01 44.08 4.40
371 817 2.420890 CCGATCAGGCAGAGAGGC 59.579 66.667 0.00 0.00 44.61 4.70
380 826 1.151668 GAATGAATCGCCCGATCAGG 58.848 55.000 3.41 0.00 40.63 3.86
389 835 1.366961 GAGCGCGTGAATGAATCGC 60.367 57.895 8.43 0.00 45.34 4.58
457 927 2.821969 AGCAAGAACATGGATTGGTCAC 59.178 45.455 0.00 0.00 45.12 3.67
462 932 2.876091 CAGCAGCAAGAACATGGATTG 58.124 47.619 0.00 0.00 0.00 2.67
487 957 0.391263 CGGGAGAAGAAAGAACCGGG 60.391 60.000 6.32 0.00 37.80 5.73
490 960 1.019805 CCGCGGGAGAAGAAAGAACC 61.020 60.000 20.10 0.00 0.00 3.62
492 962 1.189524 TCCCGCGGGAGAAGAAAGAA 61.190 55.000 42.66 17.45 39.76 2.52
494 964 1.448013 GTCCCGCGGGAGAAGAAAG 60.448 63.158 46.28 16.91 46.16 2.62
495 965 2.660802 GTCCCGCGGGAGAAGAAA 59.339 61.111 46.28 22.20 46.16 2.52
496 966 3.755628 CGTCCCGCGGGAGAAGAA 61.756 66.667 46.28 23.05 46.16 2.52
539 1013 3.764466 AGCCGGAGTTCCTCAGCG 61.764 66.667 5.05 0.00 36.73 5.18
545 1019 2.046217 GGGTTCAGCCGGAGTTCC 60.046 66.667 5.05 0.00 38.44 3.62
551 1025 3.072468 TACCTCGGGTTCAGCCGG 61.072 66.667 17.01 0.00 37.09 6.13
584 1058 0.178301 GGAACAGAGGGAATCCGGAC 59.822 60.000 6.12 0.00 38.33 4.79
604 1095 2.581354 CAGCCCGTGAAGGAGAGG 59.419 66.667 0.00 0.00 45.00 3.69
608 1099 3.706373 GAGCCAGCCCGTGAAGGA 61.706 66.667 0.00 0.00 45.00 3.36
614 1105 4.473520 CAATCCGAGCCAGCCCGT 62.474 66.667 0.00 0.00 0.00 5.28
615 1106 2.947938 ATTCAATCCGAGCCAGCCCG 62.948 60.000 0.00 0.00 0.00 6.13
616 1107 1.152881 ATTCAATCCGAGCCAGCCC 60.153 57.895 0.00 0.00 0.00 5.19
617 1108 2.028130 CATTCAATCCGAGCCAGCC 58.972 57.895 0.00 0.00 0.00 4.85
618 1109 1.358046 GCATTCAATCCGAGCCAGC 59.642 57.895 0.00 0.00 0.00 4.85
619 1110 1.450531 GGGCATTCAATCCGAGCCAG 61.451 60.000 0.00 0.00 46.96 4.85
623 1114 1.893808 CGGGGGCATTCAATCCGAG 60.894 63.158 0.00 0.00 42.94 4.63
625 1116 1.893808 CTCGGGGGCATTCAATCCG 60.894 63.158 0.00 0.00 41.80 4.18
631 1122 2.666526 GCGATCTCGGGGGCATTC 60.667 66.667 1.34 0.00 40.23 2.67
650 1141 1.135717 CAGAGACAGACAGACAGAGCG 60.136 57.143 0.00 0.00 0.00 5.03
651 1142 1.402720 GCAGAGACAGACAGACAGAGC 60.403 57.143 0.00 0.00 0.00 4.09
652 1143 2.161855 AGCAGAGACAGACAGACAGAG 58.838 52.381 0.00 0.00 0.00 3.35
654 1145 2.095110 CAGAGCAGAGACAGACAGACAG 60.095 54.545 0.00 0.00 0.00 3.51
655 1146 1.885233 CAGAGCAGAGACAGACAGACA 59.115 52.381 0.00 0.00 0.00 3.41
656 1147 1.402720 GCAGAGCAGAGACAGACAGAC 60.403 57.143 0.00 0.00 0.00 3.51
657 1148 0.887247 GCAGAGCAGAGACAGACAGA 59.113 55.000 0.00 0.00 0.00 3.41
658 1149 0.889994 AGCAGAGCAGAGACAGACAG 59.110 55.000 0.00 0.00 0.00 3.51
659 1150 0.887247 GAGCAGAGCAGAGACAGACA 59.113 55.000 0.00 0.00 0.00 3.41
660 1151 0.179166 CGAGCAGAGCAGAGACAGAC 60.179 60.000 0.00 0.00 0.00 3.51
661 1152 0.607762 ACGAGCAGAGCAGAGACAGA 60.608 55.000 0.00 0.00 0.00 3.41
680 1171 1.480212 CCTCCCACACCACACTAGCA 61.480 60.000 0.00 0.00 0.00 3.49
684 1175 0.986019 TTGTCCTCCCACACCACACT 60.986 55.000 0.00 0.00 0.00 3.55
751 1243 2.413371 GGAAATCAGAGCAAGCACGAAC 60.413 50.000 0.00 0.00 0.00 3.95
752 1244 1.806542 GGAAATCAGAGCAAGCACGAA 59.193 47.619 0.00 0.00 0.00 3.85
753 1245 1.442769 GGAAATCAGAGCAAGCACGA 58.557 50.000 0.00 0.00 0.00 4.35
755 1247 0.449388 CCGGAAATCAGAGCAAGCAC 59.551 55.000 0.00 0.00 0.00 4.40
758 1250 0.449388 GTGCCGGAAATCAGAGCAAG 59.551 55.000 5.05 0.00 34.79 4.01
759 1251 0.960364 GGTGCCGGAAATCAGAGCAA 60.960 55.000 5.05 0.00 34.79 3.91
762 1254 0.807667 CTCGGTGCCGGAAATCAGAG 60.808 60.000 5.05 3.54 40.25 3.35
764 1256 0.391130 TTCTCGGTGCCGGAAATCAG 60.391 55.000 5.05 0.00 40.25 2.90
765 1257 0.035598 TTTCTCGGTGCCGGAAATCA 59.964 50.000 5.05 0.00 40.25 2.57
766 1258 0.446616 GTTTCTCGGTGCCGGAAATC 59.553 55.000 21.02 14.58 39.12 2.17
767 1259 0.036306 AGTTTCTCGGTGCCGGAAAT 59.964 50.000 21.02 12.56 39.12 2.17
769 1261 1.301401 CAGTTTCTCGGTGCCGGAA 60.301 57.895 5.05 10.01 40.25 4.30
771 1263 0.882927 TTTCAGTTTCTCGGTGCCGG 60.883 55.000 10.94 0.00 40.25 6.13
773 1265 1.128692 CGATTTCAGTTTCTCGGTGCC 59.871 52.381 0.00 0.00 0.00 5.01
775 1267 3.121944 CAGACGATTTCAGTTTCTCGGTG 59.878 47.826 0.00 0.00 35.52 4.94
776 1268 3.318017 CAGACGATTTCAGTTTCTCGGT 58.682 45.455 0.00 0.00 35.52 4.69
779 1271 4.511826 ACAACCAGACGATTTCAGTTTCTC 59.488 41.667 0.00 0.00 0.00 2.87
782 1281 4.638421 TGAACAACCAGACGATTTCAGTTT 59.362 37.500 0.00 0.00 0.00 2.66
798 1298 2.476185 GCGCATCACCTGTATGAACAAC 60.476 50.000 0.30 0.00 34.49 3.32
807 1307 1.620739 ATCCAGAGCGCATCACCTGT 61.621 55.000 11.47 0.00 0.00 4.00
821 1321 4.845580 AAGCTCGGCGGCATCCAG 62.846 66.667 19.61 5.03 34.17 3.86
846 1357 0.875059 GCTGACCAACGGAGAAAAGG 59.125 55.000 0.00 0.00 0.00 3.11
890 1413 4.910585 CGCCGCTTAATCCGCCCT 62.911 66.667 0.00 0.00 0.00 5.19
922 1446 3.003173 CAGGTGGGGAAGCGGAGA 61.003 66.667 0.00 0.00 0.00 3.71
980 1504 6.434661 CCATGTGATGGTTAGGGACGAAGT 62.435 50.000 0.00 0.00 45.93 3.01
982 1506 2.093181 CCATGTGATGGTTAGGGACGAA 60.093 50.000 0.00 0.00 45.54 3.85
983 1507 1.484653 CCATGTGATGGTTAGGGACGA 59.515 52.381 0.00 0.00 45.54 4.20
984 1508 1.953559 CCATGTGATGGTTAGGGACG 58.046 55.000 0.00 0.00 45.54 4.79
1197 1724 2.234913 AATGCGGGTACTCCACGTCC 62.235 60.000 0.00 0.00 34.36 4.79
1458 1995 2.049063 AGCAGGACGAGCACGAAC 60.049 61.111 11.40 2.21 42.66 3.95
2007 2544 2.032681 GTGCCGCCCTTGAAGTCT 59.967 61.111 0.00 0.00 0.00 3.24
2226 2763 4.451150 GCCATGAGCGTGTCCCGA 62.451 66.667 0.00 0.00 39.56 5.14
2271 2808 1.917495 CATCCCCTGGCTCATGACA 59.083 57.895 0.00 0.00 0.00 3.58
2415 2952 0.455815 CCGACATCTCCATGACGTCA 59.544 55.000 22.48 22.48 43.83 4.35
2514 3051 3.575351 GAAGTCGCAGAGGCACCGT 62.575 63.158 0.00 0.00 41.24 4.83
2589 3126 1.285078 TGGAAGATCCTCCTCTCGTCA 59.715 52.381 11.69 0.00 37.46 4.35
2914 3452 9.206870 GAATTTGAAATGAGCTTGTTGGAAATA 57.793 29.630 0.00 0.00 0.00 1.40
2920 3458 7.223193 TGAACTGAATTTGAAATGAGCTTGTTG 59.777 33.333 0.00 0.00 0.00 3.33
2921 3459 7.267128 TGAACTGAATTTGAAATGAGCTTGTT 58.733 30.769 0.00 0.00 0.00 2.83
2997 3560 6.139048 CATCATCTGATGGCATTACAACAA 57.861 37.500 17.06 0.00 46.09 2.83
2998 3561 5.761165 CATCATCTGATGGCATTACAACA 57.239 39.130 17.06 0.00 46.09 3.33
3059 3622 1.270414 CCAGGGTCATGCTCTCTGGT 61.270 60.000 21.07 0.00 39.90 4.00
3062 3625 1.908340 GCACCAGGGTCATGCTCTCT 61.908 60.000 0.00 0.00 36.40 3.10
3110 3673 1.293498 GGTGCTGGACGACATGAGT 59.707 57.895 0.00 0.00 0.00 3.41
3179 3742 0.820226 TGAGCAGGATCTTCAGTCCG 59.180 55.000 0.00 0.00 40.76 4.79
3230 3793 1.608717 GCTTCTCCAGGAGCTTCCGA 61.609 60.000 12.26 0.00 42.75 4.55
3251 3814 4.083862 GAGGAGACCACGCACCCC 62.084 72.222 0.00 0.00 0.00 4.95
3254 3817 1.681327 TAGGGAGGAGACCACGCAC 60.681 63.158 0.00 0.00 0.00 5.34
3278 3841 2.206036 TTCAGGAACCCCGACCCT 59.794 61.111 0.00 0.00 37.58 4.34
3332 3895 2.338500 GTCATCTCGAGGTTCACCAAC 58.662 52.381 13.56 0.00 38.89 3.77
3333 3896 1.067846 CGTCATCTCGAGGTTCACCAA 60.068 52.381 13.56 0.00 38.89 3.67
3417 3980 1.227645 CCGACGTCATGGCCATCAT 60.228 57.895 17.61 0.54 36.31 2.45
3512 4075 2.581354 CGGGTGAGCTCCTCCTTG 59.419 66.667 19.72 11.82 0.00 3.61
3634 4197 2.274104 GGCATCGCCCCTTTGGTA 59.726 61.111 0.00 0.00 44.06 3.25
3650 4213 6.349944 CCTTCTGATCAAAGATTTCACAAGGG 60.350 42.308 15.13 0.00 34.05 3.95
3680 4243 2.737376 GTTTCTTCGCCGTCGCCT 60.737 61.111 0.00 0.00 35.26 5.52
3721 4284 0.954449 CAGAGCAGCACACAGGGAAG 60.954 60.000 0.00 0.00 0.00 3.46
3790 4353 7.093596 CCATCATCTACTGCTAGAATATGTGGA 60.094 40.741 0.00 0.00 32.49 4.02
3809 4372 3.281727 TGCTTGTAACCTCCCATCATC 57.718 47.619 0.00 0.00 0.00 2.92
3810 4373 3.266772 TCTTGCTTGTAACCTCCCATCAT 59.733 43.478 0.00 0.00 0.00 2.45
3811 4374 2.642311 TCTTGCTTGTAACCTCCCATCA 59.358 45.455 0.00 0.00 0.00 3.07
3828 4391 2.041928 AGGCTCCTCCCCCTCTTG 59.958 66.667 0.00 0.00 34.51 3.02
3846 4409 4.193865 TCAATGTATCATCAGCACCAGTG 58.806 43.478 0.00 0.00 0.00 3.66
3847 4410 4.492494 TCAATGTATCATCAGCACCAGT 57.508 40.909 0.00 0.00 0.00 4.00
3848 4411 5.763698 AGAATCAATGTATCATCAGCACCAG 59.236 40.000 0.00 0.00 0.00 4.00
3851 4414 7.255491 TCAAGAATCAATGTATCATCAGCAC 57.745 36.000 0.00 0.00 0.00 4.40
3904 4467 2.119801 ATTGCCACTGGTGATGAGAC 57.880 50.000 1.93 0.00 0.00 3.36
3950 4513 4.828072 AATACACTTCTGAACCTCTCCC 57.172 45.455 0.00 0.00 0.00 4.30
4027 4590 7.004086 ACAACTAGAATCCAATGTTCAAAGGA 58.996 34.615 0.00 0.00 34.12 3.36
4094 4657 4.445453 TGGTTCGATCCATTCTCATTGAG 58.555 43.478 11.25 7.38 31.96 3.02
4143 4707 4.501915 CCACATCTTCAGCAACCACATTTT 60.502 41.667 0.00 0.00 0.00 1.82
4144 4708 3.006110 CCACATCTTCAGCAACCACATTT 59.994 43.478 0.00 0.00 0.00 2.32
4146 4710 2.165167 CCACATCTTCAGCAACCACAT 58.835 47.619 0.00 0.00 0.00 3.21
4147 4711 1.133823 ACCACATCTTCAGCAACCACA 60.134 47.619 0.00 0.00 0.00 4.17
4148 4712 1.267806 CACCACATCTTCAGCAACCAC 59.732 52.381 0.00 0.00 0.00 4.16
4149 4713 1.608055 CACCACATCTTCAGCAACCA 58.392 50.000 0.00 0.00 0.00 3.67
4233 4822 3.416156 GATGCACCATATCTCCCCTTTC 58.584 50.000 0.00 0.00 0.00 2.62
4259 4848 4.080356 TGCTATTAGGCACCACAAGATCTT 60.080 41.667 0.88 0.88 37.29 2.40
4351 4941 4.866486 GGTTGTTCAATCCATTCTCATTGC 59.134 41.667 0.00 0.00 31.15 3.56
4459 5059 1.555477 TTCGGGCGTTATTGGGGTCT 61.555 55.000 0.00 0.00 0.00 3.85
4480 5080 3.735237 TGCAATGGTAAAAAGGCGAAA 57.265 38.095 0.00 0.00 0.00 3.46
4505 5105 2.588027 AATTGCCACCGAAAACGTTT 57.412 40.000 7.96 7.96 0.00 3.60
4516 5116 2.697431 TGCGTCACTAAAATTGCCAC 57.303 45.000 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.