Multiple sequence alignment - TraesCS2D01G388900

Loading Multiple Alignment...

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 TraesCS2D01G388900 chr2D 100.000 3616 0 0 1 3616 495103265 495099650 0.000000e+00 6678.0
1 TraesCS2D01G388900 chr2D 89.881 336 18 6 697 1022 495109860 495109531 5.580000e-113 418.0
2 TraesCS2D01G388900 chr2D 88.889 180 16 3 2981 3159 129947141 129947317 6.080000e-53 219.0
3 TraesCS2D01G388900 chr2D 92.079 101 8 0 2259 2359 129946662 129946762 3.760000e-30 143.0
4 TraesCS2D01G388900 chr2D 98.571 70 1 0 3162 3231 495100070 495100001 1.360000e-24 124.0
5 TraesCS2D01G388900 chr2D 98.571 70 1 0 3196 3265 495100104 495100035 1.360000e-24 124.0
6 TraesCS2D01G388900 chr2D 96.610 59 1 1 644 701 495118214 495118156 2.970000e-16 97.1
7 TraesCS2D01G388900 chr2D 97.436 39 0 1 3165 3202 495100033 495099995 8.380000e-07 65.8
8 TraesCS2D01G388900 chr2D 97.436 39 0 1 3233 3271 495100101 495100064 8.380000e-07 65.8
9 TraesCS2D01G388900 chr2A 94.612 2283 72 19 683 2950 638681444 638683690 0.000000e+00 3487.0
10 TraesCS2D01G388900 chr2A 94.574 387 8 2 3230 3616 638684342 638684715 1.450000e-163 586.0
11 TraesCS2D01G388900 chr2A 94.510 255 9 4 2949 3202 638684133 638684383 4.380000e-104 388.0
12 TraesCS2D01G388900 chr2A 93.725 255 11 4 2949 3202 638683798 638684048 9.480000e-101 377.0
13 TraesCS2D01G388900 chr2A 96.154 52 2 0 645 696 638606739 638606790 6.430000e-13 86.1
14 TraesCS2D01G388900 chr2A 94.231 52 3 0 3230 3281 638684007 638684058 2.990000e-11 80.5
15 TraesCS2D01G388900 chr2A 100.000 36 0 0 3196 3231 638684007 638684042 2.330000e-07 67.6
16 TraesCS2D01G388900 chr2A 100.000 36 0 0 3196 3231 638684342 638684377 2.330000e-07 67.6
17 TraesCS2D01G388900 chr2B 95.942 1380 50 4 1826 3202 582809164 582807788 0.000000e+00 2233.0
18 TraesCS2D01G388900 chr2B 89.221 1271 68 27 646 1872 582810414 582809169 0.000000e+00 1524.0
19 TraesCS2D01G388900 chr2B 99.478 383 2 0 3233 3615 582807826 582807444 0.000000e+00 697.0
20 TraesCS2D01G388900 chr2B 100.000 36 0 0 3196 3231 582807829 582807794 2.330000e-07 67.6
21 TraesCS2D01G388900 chr6D 97.050 644 18 1 1 643 443752488 443751845 0.000000e+00 1083.0
22 TraesCS2D01G388900 chr6D 95.356 646 26 4 1 644 81109150 81108507 0.000000e+00 1024.0
23 TraesCS2D01G388900 chr3A 96.579 643 20 2 1 641 700229557 700230199 0.000000e+00 1064.0
24 TraesCS2D01G388900 chr3A 96.820 629 18 2 17 643 700208447 700207819 0.000000e+00 1050.0
25 TraesCS2D01G388900 chr3A 87.403 643 71 7 10 643 57255715 57256356 0.000000e+00 730.0
26 TraesCS2D01G388900 chr1D 95.944 641 25 1 4 643 199670806 199670166 0.000000e+00 1038.0
27 TraesCS2D01G388900 chr1B 86.769 650 73 12 1 643 655060403 655061046 0.000000e+00 712.0
28 TraesCS2D01G388900 chr1B 86.574 648 70 14 1 641 677819843 677819206 0.000000e+00 699.0
29 TraesCS2D01G388900 chr5B 86.728 648 70 14 1 643 460028561 460027925 0.000000e+00 706.0
30 TraesCS2D01G388900 chr1A 88.000 225 22 4 2229 2451 403664005 403664226 9.960000e-66 261.0
31 TraesCS2D01G388900 chr1A 88.827 179 16 3 2981 3159 497217650 497217824 2.190000e-52 217.0
32 TraesCS2D01G388900 chr5D 89.017 173 15 3 2988 3159 361590874 361591043 1.020000e-50 211.0
33 TraesCS2D01G388900 chr5D 91.346 104 9 0 2254 2357 361590383 361590486 3.760000e-30 143.0


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 TraesCS2D01G388900 chr2D 495099650 495103265 3615 True 1411.520000 6678 98.402800 1 3616 5 chr2D.!!$R3 3615
1 TraesCS2D01G388900 chr2A 638681444 638684715 3271 False 721.957143 3487 95.950286 683 3616 7 chr2A.!!$F2 2933
2 TraesCS2D01G388900 chr2B 582807444 582810414 2970 True 1130.400000 2233 96.160250 646 3615 4 chr2B.!!$R1 2969
3 TraesCS2D01G388900 chr6D 443751845 443752488 643 True 1083.000000 1083 97.050000 1 643 1 chr6D.!!$R2 642
4 TraesCS2D01G388900 chr6D 81108507 81109150 643 True 1024.000000 1024 95.356000 1 644 1 chr6D.!!$R1 643
5 TraesCS2D01G388900 chr3A 700229557 700230199 642 False 1064.000000 1064 96.579000 1 641 1 chr3A.!!$F2 640
6 TraesCS2D01G388900 chr3A 700207819 700208447 628 True 1050.000000 1050 96.820000 17 643 1 chr3A.!!$R1 626
7 TraesCS2D01G388900 chr3A 57255715 57256356 641 False 730.000000 730 87.403000 10 643 1 chr3A.!!$F1 633
8 TraesCS2D01G388900 chr1D 199670166 199670806 640 True 1038.000000 1038 95.944000 4 643 1 chr1D.!!$R1 639
9 TraesCS2D01G388900 chr1B 655060403 655061046 643 False 712.000000 712 86.769000 1 643 1 chr1B.!!$F1 642
10 TraesCS2D01G388900 chr1B 677819206 677819843 637 True 699.000000 699 86.574000 1 641 1 chr1B.!!$R1 640
11 TraesCS2D01G388900 chr5B 460027925 460028561 636 True 706.000000 706 86.728000 1 643 1 chr5B.!!$R1 642

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
851 882 1.378646 GGCTTTCCTTTCCCCGGAG 60.379 63.158 0.73 0.0 0.00 4.63 F
1371 1415 0.026803 GATTAGCTCGCGCTTGGTTG 59.973 55.000 4.69 0.0 46.47 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2103 2219 0.249489 CCGCCATCTTCCTCCGTAAG 60.249 60.0 0.00 0.0 0.0 2.34 R
3187 3749 0.555769 TGCCCTGGGTTGTTCTTTCT 59.444 50.0 15.56 0.0 0.0 2.52 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
386 404 8.182881 GTGCGTTAAAAATGTATATTGGGTACA 58.817 33.333 0.00 0.00 36.58 2.90
554 573 7.580007 AGGTTTAAAATAGACCGGGATAACAT 58.420 34.615 6.32 0.00 38.48 2.71
620 639 1.523758 AGCTTTCGCCGACAAATTCT 58.476 45.000 0.00 0.00 36.60 2.40
644 663 6.121776 AGGTTTGTTTTGGACTTTTTCCTT 57.878 33.333 0.00 0.00 46.10 3.36
645 664 6.170506 AGGTTTGTTTTGGACTTTTTCCTTC 58.829 36.000 0.00 0.00 46.10 3.46
646 665 5.353123 GGTTTGTTTTGGACTTTTTCCTTCC 59.647 40.000 0.00 0.00 46.10 3.46
647 666 4.746535 TGTTTTGGACTTTTTCCTTCCC 57.253 40.909 0.00 0.00 46.10 3.97
648 667 4.097418 TGTTTTGGACTTTTTCCTTCCCA 58.903 39.130 0.00 0.00 46.10 4.37
649 668 4.532521 TGTTTTGGACTTTTTCCTTCCCAA 59.467 37.500 0.00 0.00 46.10 4.12
650 669 5.013183 TGTTTTGGACTTTTTCCTTCCCAAA 59.987 36.000 0.00 0.00 46.10 3.28
658 677 2.552093 TTCCTTCCCAAACCCAAACA 57.448 45.000 0.00 0.00 0.00 2.83
676 695 4.942761 AACAATGTCCTTGCTCAACAAT 57.057 36.364 0.00 0.00 38.50 2.71
697 716 6.038050 ACAATGCCAAACGTTTTGATGATTTT 59.962 30.769 15.68 1.81 0.00 1.82
699 718 7.721286 ATGCCAAACGTTTTGATGATTTTTA 57.279 28.000 15.68 0.00 0.00 1.52
700 719 7.721286 TGCCAAACGTTTTGATGATTTTTAT 57.279 28.000 15.68 0.00 0.00 1.40
702 721 8.066595 TGCCAAACGTTTTGATGATTTTTATTG 58.933 29.630 15.68 0.00 0.00 1.90
703 722 8.067189 GCCAAACGTTTTGATGATTTTTATTGT 58.933 29.630 15.68 0.00 0.00 2.71
807 837 2.028112 AGAGGCGAATCACTTACAGCAA 60.028 45.455 0.00 0.00 0.00 3.91
825 855 1.949525 CAAAGGGCAATATGGTCCGAG 59.050 52.381 0.00 0.00 37.71 4.63
851 882 1.378646 GGCTTTCCTTTCCCCGGAG 60.379 63.158 0.73 0.00 0.00 4.63
859 890 2.543067 CTTTCCCCGGAGCCCAGAAG 62.543 65.000 0.73 0.00 0.00 2.85
1126 1165 5.123227 CACCGTATTCATGGGTAATCACTT 58.877 41.667 0.00 0.00 34.82 3.16
1164 1203 0.471401 GCCTACCTATTCCTCCCCGT 60.471 60.000 0.00 0.00 0.00 5.28
1170 1209 5.072736 CCTACCTATTCCTCCCCGTTTATTT 59.927 44.000 0.00 0.00 0.00 1.40
1179 1218 3.688235 TCCCCGTTTATTTGGTCGATTT 58.312 40.909 0.00 0.00 0.00 2.17
1187 1226 7.277098 CCGTTTATTTGGTCGATTTTCTCTCTA 59.723 37.037 0.00 0.00 0.00 2.43
1189 1228 9.922305 GTTTATTTGGTCGATTTTCTCTCTATG 57.078 33.333 0.00 0.00 0.00 2.23
1272 1315 0.590195 CTAATTGAGCATCGCCAGCC 59.410 55.000 0.00 0.00 38.61 4.85
1348 1392 2.095053 GGAGAAATCGCTTGCTCTCAAC 59.905 50.000 6.93 0.00 36.78 3.18
1350 1394 1.131315 GAAATCGCTTGCTCTCAACCC 59.869 52.381 0.00 0.00 0.00 4.11
1351 1395 0.036732 AATCGCTTGCTCTCAACCCA 59.963 50.000 0.00 0.00 0.00 4.51
1353 1397 1.004560 CGCTTGCTCTCAACCCAGA 60.005 57.895 0.00 0.00 0.00 3.86
1355 1399 1.831580 GCTTGCTCTCAACCCAGATT 58.168 50.000 0.00 0.00 0.00 2.40
1356 1400 2.677902 CGCTTGCTCTCAACCCAGATTA 60.678 50.000 0.00 0.00 0.00 1.75
1357 1401 2.941720 GCTTGCTCTCAACCCAGATTAG 59.058 50.000 0.00 0.00 0.00 1.73
1358 1402 2.698855 TGCTCTCAACCCAGATTAGC 57.301 50.000 0.00 0.00 0.00 3.09
1359 1403 2.191400 TGCTCTCAACCCAGATTAGCT 58.809 47.619 0.00 0.00 31.39 3.32
1360 1404 2.169352 TGCTCTCAACCCAGATTAGCTC 59.831 50.000 0.00 0.00 31.39 4.09
1361 1405 2.801342 GCTCTCAACCCAGATTAGCTCG 60.801 54.545 0.00 0.00 0.00 5.03
1362 1406 1.137086 TCTCAACCCAGATTAGCTCGC 59.863 52.381 0.00 0.00 0.00 5.03
1363 1407 0.179111 TCAACCCAGATTAGCTCGCG 60.179 55.000 0.00 0.00 0.00 5.87
1364 1408 1.521681 AACCCAGATTAGCTCGCGC 60.522 57.895 0.00 0.00 0.00 6.86
1366 1410 1.227380 CCCAGATTAGCTCGCGCTT 60.227 57.895 4.69 0.00 46.47 4.68
1367 1411 1.493950 CCCAGATTAGCTCGCGCTTG 61.494 60.000 4.69 0.00 46.47 4.01
1368 1412 1.493950 CCAGATTAGCTCGCGCTTGG 61.494 60.000 4.69 2.92 46.47 3.61
1369 1413 0.807667 CAGATTAGCTCGCGCTTGGT 60.808 55.000 4.69 6.12 46.47 3.67
1370 1414 0.108138 AGATTAGCTCGCGCTTGGTT 60.108 50.000 4.69 0.00 46.47 3.67
1371 1415 0.026803 GATTAGCTCGCGCTTGGTTG 59.973 55.000 4.69 0.00 46.47 3.77
1667 1711 2.492090 GAGCTCGCACTCACCGAT 59.508 61.111 0.00 0.00 36.65 4.18
2103 2219 1.709147 CGGCTCTGGTGCAGCATTAC 61.709 60.000 20.52 11.06 38.77 1.89
2105 2221 1.457346 GCTCTGGTGCAGCATTACTT 58.543 50.000 20.52 0.00 36.82 2.24
2242 2358 0.436531 GCTGACGAAAACTCTGCTCG 59.563 55.000 0.00 0.00 38.53 5.03
2484 2600 1.135094 ACCCAATGAGGCTCGATCAT 58.865 50.000 10.42 0.00 39.06 2.45
2485 2601 1.492176 ACCCAATGAGGCTCGATCATT 59.508 47.619 10.42 6.87 45.88 2.57
2488 2604 3.070018 CCAATGAGGCTCGATCATTACC 58.930 50.000 10.42 0.00 43.74 2.85
2491 2607 0.038159 GAGGCTCGATCATTACCGGG 60.038 60.000 6.32 0.00 0.00 5.73
2558 2674 7.684317 TTATGATGAGGTACCAAATAGTCCA 57.316 36.000 15.94 1.93 0.00 4.02
2638 2754 1.035385 TGAAGCATGGCAGCTCATGG 61.035 55.000 19.53 7.18 45.89 3.66
2778 2896 3.117663 ACTTCAGCAGTTTTAGGGGTTGA 60.118 43.478 0.00 0.00 27.32 3.18
2855 2973 1.281419 ATACCACCATCCGTCCAACA 58.719 50.000 0.00 0.00 0.00 3.33
2876 2994 1.979155 GCCCTGAGGGTTTGCCTTC 60.979 63.158 20.64 0.00 46.51 3.46
2911 3029 2.262211 TGAATCTCGTCAGTTCATGCG 58.738 47.619 0.00 0.00 0.00 4.73
2995 3557 7.278646 TGAAACTCTCGATTACATGAATCTTGG 59.721 37.037 0.00 0.00 41.72 3.61
3141 3703 6.119536 TGAAGGTTTACAATCACACAGAACT 58.880 36.000 0.00 0.00 0.00 3.01
3142 3704 7.276658 TGAAGGTTTACAATCACACAGAACTA 58.723 34.615 0.00 0.00 0.00 2.24
3143 3705 7.441157 TGAAGGTTTACAATCACACAGAACTAG 59.559 37.037 0.00 0.00 0.00 2.57
3184 3746 3.598264 ACCCAGGGCAGATAATTAGCTA 58.402 45.455 4.91 0.00 0.00 3.32
3185 3747 3.980698 ACCCAGGGCAGATAATTAGCTAA 59.019 43.478 8.99 8.99 0.00 3.09
3186 3748 4.202472 ACCCAGGGCAGATAATTAGCTAAC 60.202 45.833 8.70 0.00 0.00 2.34
3187 3749 4.202461 CCCAGGGCAGATAATTAGCTAACA 60.202 45.833 8.70 0.00 0.00 2.41
3188 3750 4.999950 CCAGGGCAGATAATTAGCTAACAG 59.000 45.833 8.70 0.00 0.00 3.16
3189 3751 5.221722 CCAGGGCAGATAATTAGCTAACAGA 60.222 44.000 8.70 0.00 0.00 3.41
3190 3752 6.291377 CAGGGCAGATAATTAGCTAACAGAA 58.709 40.000 8.70 0.00 0.00 3.02
3191 3753 6.767902 CAGGGCAGATAATTAGCTAACAGAAA 59.232 38.462 8.70 0.00 0.00 2.52
3192 3754 6.995091 AGGGCAGATAATTAGCTAACAGAAAG 59.005 38.462 8.70 0.00 0.00 2.62
3193 3755 6.992715 GGGCAGATAATTAGCTAACAGAAAGA 59.007 38.462 8.70 0.00 0.00 2.52
3194 3756 7.499232 GGGCAGATAATTAGCTAACAGAAAGAA 59.501 37.037 8.70 0.00 0.00 2.52
3195 3757 8.338986 GGCAGATAATTAGCTAACAGAAAGAAC 58.661 37.037 8.70 0.00 0.00 3.01
3196 3758 8.883731 GCAGATAATTAGCTAACAGAAAGAACA 58.116 33.333 8.70 0.00 0.00 3.18
3199 3761 9.989869 GATAATTAGCTAACAGAAAGAACAACC 57.010 33.333 8.70 0.00 0.00 3.77
3200 3762 6.819397 ATTAGCTAACAGAAAGAACAACCC 57.181 37.500 8.70 0.00 0.00 4.11
3201 3763 4.164843 AGCTAACAGAAAGAACAACCCA 57.835 40.909 0.00 0.00 0.00 4.51
3202 3764 4.137543 AGCTAACAGAAAGAACAACCCAG 58.862 43.478 0.00 0.00 0.00 4.45
3203 3765 3.253432 GCTAACAGAAAGAACAACCCAGG 59.747 47.826 0.00 0.00 0.00 4.45
3204 3766 2.364972 ACAGAAAGAACAACCCAGGG 57.635 50.000 2.85 2.85 0.00 4.45
3205 3767 0.961753 CAGAAAGAACAACCCAGGGC 59.038 55.000 4.91 0.00 0.00 5.19
3206 3768 0.555769 AGAAAGAACAACCCAGGGCA 59.444 50.000 4.91 0.00 0.00 5.36
3207 3769 0.961753 GAAAGAACAACCCAGGGCAG 59.038 55.000 4.91 0.00 0.00 4.85
3208 3770 0.555769 AAAGAACAACCCAGGGCAGA 59.444 50.000 4.91 0.00 0.00 4.26
3209 3771 0.779997 AAGAACAACCCAGGGCAGAT 59.220 50.000 4.91 0.00 0.00 2.90
3210 3772 1.668826 AGAACAACCCAGGGCAGATA 58.331 50.000 4.91 0.00 0.00 1.98
3211 3773 1.992557 AGAACAACCCAGGGCAGATAA 59.007 47.619 4.91 0.00 0.00 1.75
3212 3774 2.582636 AGAACAACCCAGGGCAGATAAT 59.417 45.455 4.91 0.00 0.00 1.28
3213 3775 3.011708 AGAACAACCCAGGGCAGATAATT 59.988 43.478 4.91 0.00 0.00 1.40
3214 3776 4.229582 AGAACAACCCAGGGCAGATAATTA 59.770 41.667 4.91 0.00 0.00 1.40
3215 3777 4.170468 ACAACCCAGGGCAGATAATTAG 57.830 45.455 4.91 0.00 0.00 1.73
3216 3778 2.887152 CAACCCAGGGCAGATAATTAGC 59.113 50.000 4.91 0.00 0.00 3.09
3217 3779 2.422746 ACCCAGGGCAGATAATTAGCT 58.577 47.619 4.91 0.00 0.00 3.32
3218 3780 3.598264 ACCCAGGGCAGATAATTAGCTA 58.402 45.455 4.91 0.00 0.00 3.32
3219 3781 3.980698 ACCCAGGGCAGATAATTAGCTAA 59.019 43.478 8.99 8.99 0.00 3.09
3220 3782 4.202472 ACCCAGGGCAGATAATTAGCTAAC 60.202 45.833 8.70 0.00 0.00 2.34
3221 3783 4.202461 CCCAGGGCAGATAATTAGCTAACA 60.202 45.833 8.70 0.00 0.00 2.41
3222 3784 4.999950 CCAGGGCAGATAATTAGCTAACAG 59.000 45.833 8.70 0.00 0.00 3.16
3223 3785 5.221722 CCAGGGCAGATAATTAGCTAACAGA 60.222 44.000 8.70 0.00 0.00 3.41
3224 3786 6.291377 CAGGGCAGATAATTAGCTAACAGAA 58.709 40.000 8.70 0.00 0.00 3.02
3225 3787 6.767902 CAGGGCAGATAATTAGCTAACAGAAA 59.232 38.462 8.70 0.00 0.00 2.52
3226 3788 6.995091 AGGGCAGATAATTAGCTAACAGAAAG 59.005 38.462 8.70 0.00 0.00 2.62
3227 3789 6.992715 GGGCAGATAATTAGCTAACAGAAAGA 59.007 38.462 8.70 0.00 0.00 2.52
3228 3790 7.499232 GGGCAGATAATTAGCTAACAGAAAGAA 59.501 37.037 8.70 0.00 0.00 2.52
3229 3791 8.338986 GGCAGATAATTAGCTAACAGAAAGAAC 58.661 37.037 8.70 0.00 0.00 3.01
3230 3792 8.883731 GCAGATAATTAGCTAACAGAAAGAACA 58.116 33.333 8.70 0.00 0.00 3.18
3234 3796 7.631717 AATTAGCTAACAGAAAGAACATCCC 57.368 36.000 8.70 0.00 0.00 3.85
3235 3797 4.640771 AGCTAACAGAAAGAACATCCCA 57.359 40.909 0.00 0.00 0.00 4.37
3236 3798 4.583871 AGCTAACAGAAAGAACATCCCAG 58.416 43.478 0.00 0.00 0.00 4.45
3237 3799 3.691609 GCTAACAGAAAGAACATCCCAGG 59.308 47.826 0.00 0.00 0.00 4.45
3238 3800 2.887151 ACAGAAAGAACATCCCAGGG 57.113 50.000 0.00 0.00 0.00 4.45
3239 3801 1.272147 ACAGAAAGAACATCCCAGGGC 60.272 52.381 0.00 0.00 0.00 5.19
3240 3802 1.075601 AGAAAGAACATCCCAGGGCA 58.924 50.000 0.00 0.00 0.00 5.36
3241 3803 1.005215 AGAAAGAACATCCCAGGGCAG 59.995 52.381 0.00 0.00 0.00 4.85
3242 3804 1.004745 GAAAGAACATCCCAGGGCAGA 59.995 52.381 0.00 0.00 0.00 4.26
3243 3805 1.302907 AAGAACATCCCAGGGCAGAT 58.697 50.000 0.00 0.00 0.00 2.90
3244 3806 2.196742 AGAACATCCCAGGGCAGATA 57.803 50.000 0.00 0.00 0.00 1.98
3245 3807 2.492025 AGAACATCCCAGGGCAGATAA 58.508 47.619 0.00 0.00 0.00 1.75
3246 3808 3.059097 AGAACATCCCAGGGCAGATAAT 58.941 45.455 0.00 0.00 0.00 1.28
3247 3809 3.464833 AGAACATCCCAGGGCAGATAATT 59.535 43.478 0.00 0.00 0.00 1.40
3248 3810 4.665009 AGAACATCCCAGGGCAGATAATTA 59.335 41.667 0.00 0.00 0.00 1.40
3249 3811 4.647564 ACATCCCAGGGCAGATAATTAG 57.352 45.455 0.00 0.00 0.00 1.73
3250 3812 3.245052 ACATCCCAGGGCAGATAATTAGC 60.245 47.826 0.00 0.00 0.00 3.09
3251 3813 2.706350 TCCCAGGGCAGATAATTAGCT 58.294 47.619 0.00 0.00 0.00 3.32
3290 3852 4.100653 CCCATCATCTCTGTCATGTACACT 59.899 45.833 0.00 0.00 33.45 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 64 7.630470 TGTACACACAGTTTTGTTTGAAAAG 57.370 32.000 0.00 0.00 37.20 2.27
169 171 6.920758 TGGTTCAACATTTTCAAATTCGTAGG 59.079 34.615 0.00 0.00 0.00 3.18
554 573 4.278170 CCTTGAAATCAGCACACCAAACTA 59.722 41.667 0.00 0.00 0.00 2.24
644 663 2.043227 GGACATTGTTTGGGTTTGGGA 58.957 47.619 0.00 0.00 0.00 4.37
645 664 2.046292 AGGACATTGTTTGGGTTTGGG 58.954 47.619 0.00 0.00 0.00 4.12
646 665 3.465871 CAAGGACATTGTTTGGGTTTGG 58.534 45.455 0.00 0.00 33.95 3.28
647 666 2.871633 GCAAGGACATTGTTTGGGTTTG 59.128 45.455 1.33 0.00 41.29 2.93
648 667 2.771372 AGCAAGGACATTGTTTGGGTTT 59.229 40.909 1.33 0.00 41.29 3.27
649 668 2.365293 GAGCAAGGACATTGTTTGGGTT 59.635 45.455 1.33 0.00 41.29 4.11
650 669 1.963515 GAGCAAGGACATTGTTTGGGT 59.036 47.619 1.33 0.00 41.29 4.51
658 677 2.028748 GGCATTGTTGAGCAAGGACATT 60.029 45.455 0.00 0.00 45.51 2.71
676 695 7.721286 ATAAAAATCATCAAAACGTTTGGCA 57.279 28.000 15.46 1.63 0.00 4.92
697 716 7.334421 GCTCTTCCATTCAACAGAGTACAATAA 59.666 37.037 0.00 0.00 36.02 1.40
699 718 5.645497 GCTCTTCCATTCAACAGAGTACAAT 59.355 40.000 0.00 0.00 36.02 2.71
700 719 4.997395 GCTCTTCCATTCAACAGAGTACAA 59.003 41.667 0.00 0.00 36.02 2.41
702 721 3.935828 GGCTCTTCCATTCAACAGAGTAC 59.064 47.826 0.00 0.00 36.02 2.73
703 722 3.055094 GGGCTCTTCCATTCAACAGAGTA 60.055 47.826 0.00 0.00 36.02 2.59
704 723 2.290577 GGGCTCTTCCATTCAACAGAGT 60.291 50.000 0.00 0.00 36.02 3.24
706 725 1.704628 TGGGCTCTTCCATTCAACAGA 59.295 47.619 0.00 0.00 36.21 3.41
707 726 2.205022 TGGGCTCTTCCATTCAACAG 57.795 50.000 0.00 0.00 36.21 3.16
708 727 2.449464 CATGGGCTCTTCCATTCAACA 58.551 47.619 0.00 0.00 44.55 3.33
710 729 1.961435 GCCATGGGCTCTTCCATTCAA 60.961 52.381 15.13 0.00 44.55 2.69
807 837 1.141053 GTCTCGGACCATATTGCCCTT 59.859 52.381 0.00 0.00 0.00 3.95
825 855 1.296755 GAAAGGAAAGCCCGACCGTC 61.297 60.000 0.00 0.00 40.87 4.79
851 882 2.743928 CGTCTGGTGCTTCTGGGC 60.744 66.667 0.00 0.00 0.00 5.36
859 890 3.112709 GAGGAACGCGTCTGGTGC 61.113 66.667 14.44 1.02 0.00 5.01
1164 1203 9.109393 CCATAGAGAGAAAATCGACCAAATAAA 57.891 33.333 0.00 0.00 0.00 1.40
1170 1209 3.388024 CCCCATAGAGAGAAAATCGACCA 59.612 47.826 0.00 0.00 0.00 4.02
1179 1218 4.338795 ACTGTTCTCCCCATAGAGAGAA 57.661 45.455 0.00 0.00 44.72 2.87
1187 1226 3.434309 CAAATCCAACTGTTCTCCCCAT 58.566 45.455 0.00 0.00 0.00 4.00
1189 1228 1.546029 GCAAATCCAACTGTTCTCCCC 59.454 52.381 0.00 0.00 0.00 4.81
1272 1315 2.306341 ATCAACGAGGAGCATCTGTG 57.694 50.000 0.00 0.00 33.73 3.66
1358 1402 0.453282 CATTGACAACCAAGCGCGAG 60.453 55.000 12.10 0.00 38.31 5.03
1359 1403 1.573932 CATTGACAACCAAGCGCGA 59.426 52.632 12.10 0.00 38.31 5.87
1360 1404 1.442520 CCATTGACAACCAAGCGCG 60.443 57.895 0.00 0.00 38.31 6.86
1361 1405 1.734117 GCCATTGACAACCAAGCGC 60.734 57.895 0.00 0.00 38.31 5.92
1362 1406 0.031857 TTGCCATTGACAACCAAGCG 59.968 50.000 0.00 0.00 38.31 4.68
1363 1407 2.070783 CATTGCCATTGACAACCAAGC 58.929 47.619 0.00 0.00 38.31 4.01
1364 1408 2.613474 CCCATTGCCATTGACAACCAAG 60.613 50.000 0.00 0.00 38.31 3.61
1365 1409 1.347050 CCCATTGCCATTGACAACCAA 59.653 47.619 0.00 0.00 39.41 3.67
1366 1410 0.975135 CCCATTGCCATTGACAACCA 59.025 50.000 0.00 0.00 0.00 3.67
1367 1411 0.249955 CCCCATTGCCATTGACAACC 59.750 55.000 0.00 0.00 0.00 3.77
1368 1412 0.975887 ACCCCATTGCCATTGACAAC 59.024 50.000 0.00 0.00 0.00 3.32
1369 1413 1.727062 AACCCCATTGCCATTGACAA 58.273 45.000 0.00 0.00 0.00 3.18
1370 1414 1.347050 CAAACCCCATTGCCATTGACA 59.653 47.619 0.00 0.00 0.00 3.58
1371 1415 1.338960 CCAAACCCCATTGCCATTGAC 60.339 52.381 0.00 0.00 0.00 3.18
1731 1796 4.008933 GACCACCACCAGCGAGCT 62.009 66.667 0.00 0.00 0.00 4.09
1732 1797 3.825160 TTGACCACCACCAGCGAGC 62.825 63.158 0.00 0.00 0.00 5.03
2103 2219 0.249489 CCGCCATCTTCCTCCGTAAG 60.249 60.000 0.00 0.00 0.00 2.34
2105 2221 2.792947 GCCGCCATCTTCCTCCGTA 61.793 63.158 0.00 0.00 0.00 4.02
2222 2338 0.793250 GAGCAGAGTTTTCGTCAGCC 59.207 55.000 0.00 0.00 0.00 4.85
2456 2572 3.016736 AGCCTCATTGGGTGTAATTTCG 58.983 45.455 0.00 0.00 46.19 3.46
2558 2674 1.139058 AGTGCGAGGACACAGAACTTT 59.861 47.619 0.00 0.00 43.23 2.66
2638 2754 6.706055 TCTTTCAACTATGTGACGATGTTC 57.294 37.500 0.00 0.00 0.00 3.18
2742 2860 4.233789 TGCTGAAGTTCAACAACAACAAC 58.766 39.130 6.49 0.00 34.60 3.32
2876 2994 7.276438 TGACGAGATTCATACAAATTCAGTCTG 59.724 37.037 0.00 0.00 0.00 3.51
2911 3029 8.606602 AGAACAATTGCATCTGTTTTTCTTTTC 58.393 29.630 13.43 1.09 35.93 2.29
3093 3655 8.307483 TCAGAGTTGTTGAATGTTTACCAAAAA 58.693 29.630 0.00 0.00 0.00 1.94
3184 3746 2.666317 CCCTGGGTTGTTCTTTCTGTT 58.334 47.619 3.97 0.00 0.00 3.16
3185 3747 1.754201 GCCCTGGGTTGTTCTTTCTGT 60.754 52.381 15.56 0.00 0.00 3.41
3186 3748 0.961753 GCCCTGGGTTGTTCTTTCTG 59.038 55.000 15.56 0.00 0.00 3.02
3187 3749 0.555769 TGCCCTGGGTTGTTCTTTCT 59.444 50.000 15.56 0.00 0.00 2.52
3188 3750 0.961753 CTGCCCTGGGTTGTTCTTTC 59.038 55.000 15.56 0.00 0.00 2.62
3189 3751 0.555769 TCTGCCCTGGGTTGTTCTTT 59.444 50.000 15.56 0.00 0.00 2.52
3190 3752 0.779997 ATCTGCCCTGGGTTGTTCTT 59.220 50.000 15.56 0.00 0.00 2.52
3191 3753 1.668826 TATCTGCCCTGGGTTGTTCT 58.331 50.000 15.56 0.00 0.00 3.01
3192 3754 2.507407 TTATCTGCCCTGGGTTGTTC 57.493 50.000 15.56 0.00 0.00 3.18
3193 3755 3.473113 AATTATCTGCCCTGGGTTGTT 57.527 42.857 15.56 5.39 0.00 2.83
3194 3756 3.688414 GCTAATTATCTGCCCTGGGTTGT 60.688 47.826 15.56 1.00 0.00 3.32
3195 3757 2.887152 GCTAATTATCTGCCCTGGGTTG 59.113 50.000 15.56 7.67 0.00 3.77
3196 3758 2.785857 AGCTAATTATCTGCCCTGGGTT 59.214 45.455 15.56 0.90 0.00 4.11
3197 3759 2.422746 AGCTAATTATCTGCCCTGGGT 58.577 47.619 15.56 0.00 0.00 4.51
3198 3760 4.202461 TGTTAGCTAATTATCTGCCCTGGG 60.202 45.833 9.88 8.86 0.00 4.45
3199 3761 4.973168 TGTTAGCTAATTATCTGCCCTGG 58.027 43.478 9.88 0.00 0.00 4.45
3200 3762 5.858381 TCTGTTAGCTAATTATCTGCCCTG 58.142 41.667 9.88 0.00 0.00 4.45
3201 3763 6.500589 TTCTGTTAGCTAATTATCTGCCCT 57.499 37.500 9.88 0.00 0.00 5.19
3202 3764 6.992715 TCTTTCTGTTAGCTAATTATCTGCCC 59.007 38.462 9.88 0.00 0.00 5.36
3203 3765 8.338986 GTTCTTTCTGTTAGCTAATTATCTGCC 58.661 37.037 9.88 0.00 0.00 4.85
3204 3766 8.883731 TGTTCTTTCTGTTAGCTAATTATCTGC 58.116 33.333 9.88 0.00 0.00 4.26
3208 3770 9.343539 GGGATGTTCTTTCTGTTAGCTAATTAT 57.656 33.333 9.88 0.00 0.00 1.28
3209 3771 8.325787 TGGGATGTTCTTTCTGTTAGCTAATTA 58.674 33.333 9.88 1.43 0.00 1.40
3210 3772 7.175104 TGGGATGTTCTTTCTGTTAGCTAATT 58.825 34.615 9.88 0.00 0.00 1.40
3211 3773 6.721318 TGGGATGTTCTTTCTGTTAGCTAAT 58.279 36.000 9.88 0.00 0.00 1.73
3212 3774 6.121776 TGGGATGTTCTTTCTGTTAGCTAA 57.878 37.500 0.86 0.86 0.00 3.09
3213 3775 5.338381 CCTGGGATGTTCTTTCTGTTAGCTA 60.338 44.000 0.00 0.00 0.00 3.32
3214 3776 4.566488 CCTGGGATGTTCTTTCTGTTAGCT 60.566 45.833 0.00 0.00 0.00 3.32
3215 3777 3.691609 CCTGGGATGTTCTTTCTGTTAGC 59.308 47.826 0.00 0.00 0.00 3.09
3216 3778 4.265073 CCCTGGGATGTTCTTTCTGTTAG 58.735 47.826 7.01 0.00 0.00 2.34
3217 3779 3.561313 GCCCTGGGATGTTCTTTCTGTTA 60.561 47.826 19.27 0.00 0.00 2.41
3218 3780 2.819348 GCCCTGGGATGTTCTTTCTGTT 60.819 50.000 19.27 0.00 0.00 3.16
3219 3781 1.272147 GCCCTGGGATGTTCTTTCTGT 60.272 52.381 19.27 0.00 0.00 3.41
3220 3782 1.272092 TGCCCTGGGATGTTCTTTCTG 60.272 52.381 19.27 0.00 0.00 3.02
3221 3783 1.005215 CTGCCCTGGGATGTTCTTTCT 59.995 52.381 19.27 0.00 0.00 2.52
3222 3784 1.004745 TCTGCCCTGGGATGTTCTTTC 59.995 52.381 19.27 0.00 0.00 2.62
3223 3785 1.075601 TCTGCCCTGGGATGTTCTTT 58.924 50.000 19.27 0.00 0.00 2.52
3224 3786 1.302907 ATCTGCCCTGGGATGTTCTT 58.697 50.000 19.27 0.00 0.00 2.52
3225 3787 2.196742 TATCTGCCCTGGGATGTTCT 57.803 50.000 19.27 0.00 0.00 3.01
3226 3788 3.515602 ATTATCTGCCCTGGGATGTTC 57.484 47.619 19.27 0.00 0.00 3.18
3227 3789 3.979501 AATTATCTGCCCTGGGATGTT 57.020 42.857 19.27 5.61 0.00 2.71
3228 3790 3.245052 GCTAATTATCTGCCCTGGGATGT 60.245 47.826 19.27 0.97 0.00 3.06
3229 3791 3.009916 AGCTAATTATCTGCCCTGGGATG 59.990 47.826 19.27 8.06 0.00 3.51
3230 3792 3.263724 AGCTAATTATCTGCCCTGGGAT 58.736 45.455 19.27 3.46 0.00 3.85
3231 3793 2.706350 AGCTAATTATCTGCCCTGGGA 58.294 47.619 19.27 0.28 0.00 4.37
3232 3794 4.202461 TGTTAGCTAATTATCTGCCCTGGG 60.202 45.833 9.88 8.86 0.00 4.45
3233 3795 4.973168 TGTTAGCTAATTATCTGCCCTGG 58.027 43.478 9.88 0.00 0.00 4.45
3234 3796 5.858381 TCTGTTAGCTAATTATCTGCCCTG 58.142 41.667 9.88 0.00 0.00 4.45
3235 3797 6.500589 TTCTGTTAGCTAATTATCTGCCCT 57.499 37.500 9.88 0.00 0.00 5.19
3236 3798 6.992715 TCTTTCTGTTAGCTAATTATCTGCCC 59.007 38.462 9.88 0.00 0.00 5.36
3237 3799 8.338986 GTTCTTTCTGTTAGCTAATTATCTGCC 58.661 37.037 9.88 0.00 0.00 4.85
3238 3800 8.883731 TGTTCTTTCTGTTAGCTAATTATCTGC 58.116 33.333 9.88 0.00 0.00 4.26
3243 3805 8.789762 GGGTTTGTTCTTTCTGTTAGCTAATTA 58.210 33.333 9.88 1.43 0.00 1.40
3244 3806 7.286775 TGGGTTTGTTCTTTCTGTTAGCTAATT 59.713 33.333 9.88 0.00 0.00 1.40
3245 3807 6.775629 TGGGTTTGTTCTTTCTGTTAGCTAAT 59.224 34.615 9.88 0.00 0.00 1.73
3246 3808 6.123651 TGGGTTTGTTCTTTCTGTTAGCTAA 58.876 36.000 0.86 0.86 0.00 3.09
3247 3809 5.686753 TGGGTTTGTTCTTTCTGTTAGCTA 58.313 37.500 0.00 0.00 0.00 3.32
3248 3810 4.532834 TGGGTTTGTTCTTTCTGTTAGCT 58.467 39.130 0.00 0.00 0.00 3.32
3249 3811 4.911514 TGGGTTTGTTCTTTCTGTTAGC 57.088 40.909 0.00 0.00 0.00 3.09
3250 3812 6.633500 TGATGGGTTTGTTCTTTCTGTTAG 57.367 37.500 0.00 0.00 0.00 2.34
3251 3813 7.004086 AGATGATGGGTTTGTTCTTTCTGTTA 58.996 34.615 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.