Multiple sequence alignment - TraesCS4B01G200100

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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 TraesCS4B01G200100 chr4B 100.000 3954 0 0 1 3954 428456935 428460888 0.000000e+00 7302.0
1 TraesCS4B01G200100 chr4B 76.437 348 55 17 2386 2718 428410823 428411158 3.160000e-36 163.0
2 TraesCS4B01G200100 chr4A 87.861 2595 141 76 1040 3521 117286352 117283819 0.000000e+00 2887.0
3 TraesCS4B01G200100 chr4A 86.772 378 15 5 3581 3954 117283803 117283457 4.790000e-104 388.0
4 TraesCS4B01G200100 chr4A 76.144 721 126 33 1969 2671 117334739 117334047 1.760000e-88 337.0
5 TraesCS4B01G200100 chr4A 78.169 284 44 12 1364 1633 117337877 117337598 8.790000e-37 165.0
6 TraesCS4B01G200100 chr4A 93.478 92 3 1 857 948 117286443 117286355 2.480000e-27 134.0
7 TraesCS4B01G200100 chr4D 91.225 1322 63 18 2133 3416 348302208 348303514 0.000000e+00 1749.0
8 TraesCS4B01G200100 chr4D 91.132 1263 53 24 871 2120 348300881 348302097 0.000000e+00 1657.0
9 TraesCS4B01G200100 chr4D 81.365 381 34 19 3581 3954 348303695 348304045 3.890000e-70 276.0
10 TraesCS4B01G200100 chr4D 76.301 346 59 17 2386 2718 348298892 348299227 3.160000e-36 163.0
11 TraesCS4B01G200100 chr4D 93.069 101 3 1 3451 3547 348303600 348303700 1.150000e-30 145.0
12 TraesCS4B01G200100 chr4D 100.000 37 0 0 3405 3441 348303536 348303572 7.090000e-08 69.4
13 TraesCS4B01G200100 chr7D 91.725 858 68 3 1 857 102760893 102761748 0.000000e+00 1188.0
14 TraesCS4B01G200100 chr7D 78.388 856 174 11 6 857 554518007 554518855 2.690000e-151 545.0
15 TraesCS4B01G200100 chr2D 91.345 855 72 2 2 856 86581805 86582657 0.000000e+00 1168.0
16 TraesCS4B01G200100 chr3D 91.578 843 69 2 1 843 133998925 133999765 0.000000e+00 1162.0
17 TraesCS4B01G200100 chr1A 88.304 855 98 2 1 855 387054263 387055115 0.000000e+00 1024.0
18 TraesCS4B01G200100 chr1A 83.856 861 127 10 1 857 572249722 572248870 0.000000e+00 809.0
19 TraesCS4B01G200100 chr5A 92.081 644 49 2 214 857 38123876 38124517 0.000000e+00 905.0
20 TraesCS4B01G200100 chr5B 85.380 855 123 2 2 856 700138058 700137206 0.000000e+00 885.0
21 TraesCS4B01G200100 chr5B 79.594 838 147 18 27 857 631621719 631620899 2.650000e-161 579.0


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 TraesCS4B01G200100 chr4B 428456935 428460888 3953 False 7302.000000 7302 100.000000 1 3954 1 chr4B.!!$F2 3953
1 TraesCS4B01G200100 chr4A 117283457 117286443 2986 True 1136.333333 2887 89.370333 857 3954 3 chr4A.!!$R1 3097
2 TraesCS4B01G200100 chr4A 117334047 117337877 3830 True 251.000000 337 77.156500 1364 2671 2 chr4A.!!$R2 1307
3 TraesCS4B01G200100 chr4D 348298892 348304045 5153 False 676.566667 1749 88.848667 871 3954 6 chr4D.!!$F1 3083
4 TraesCS4B01G200100 chr7D 102760893 102761748 855 False 1188.000000 1188 91.725000 1 857 1 chr7D.!!$F1 856
5 TraesCS4B01G200100 chr7D 554518007 554518855 848 False 545.000000 545 78.388000 6 857 1 chr7D.!!$F2 851
6 TraesCS4B01G200100 chr2D 86581805 86582657 852 False 1168.000000 1168 91.345000 2 856 1 chr2D.!!$F1 854
7 TraesCS4B01G200100 chr3D 133998925 133999765 840 False 1162.000000 1162 91.578000 1 843 1 chr3D.!!$F1 842
8 TraesCS4B01G200100 chr1A 387054263 387055115 852 False 1024.000000 1024 88.304000 1 855 1 chr1A.!!$F1 854
9 TraesCS4B01G200100 chr1A 572248870 572249722 852 True 809.000000 809 83.856000 1 857 1 chr1A.!!$R1 856
10 TraesCS4B01G200100 chr5A 38123876 38124517 641 False 905.000000 905 92.081000 214 857 1 chr5A.!!$F1 643
11 TraesCS4B01G200100 chr5B 700137206 700138058 852 True 885.000000 885 85.380000 2 856 1 chr5B.!!$R2 854
12 TraesCS4B01G200100 chr5B 631620899 631621719 820 True 579.000000 579 79.594000 27 857 1 chr5B.!!$R1 830

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
796 798 0.322277 CTGATCAGCAGCCTGTTGGT 60.322 55.0 10.38 0.46 40.09 3.67 F
1150 2279 1.063183 CCTCCTCCATCTCCCATTCC 58.937 60.0 0.00 0.00 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1606 2782 1.072331 CACTACCTTGCAGTTCCTGGT 59.928 52.381 0.00 0.0 35.05 4.00 R
3147 7065 0.178992 CACAACCCAGAAGGCCAGAA 60.179 55.000 5.01 0.0 40.58 3.02 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
31 32 4.645809 GAGGACCTCCAACATGCC 57.354 61.111 10.74 0.00 38.89 4.40
54 55 2.499693 TCATCCATTGTTCTCACGCCTA 59.500 45.455 0.00 0.00 0.00 3.93
74 75 0.976073 CCGGTTCTGGGAGGAAGCTA 60.976 60.000 0.00 0.00 40.32 3.32
79 80 3.967987 GGTTCTGGGAGGAAGCTAGATTA 59.032 47.826 0.00 0.00 39.65 1.75
88 89 6.261158 GGGAGGAAGCTAGATTATTGTTTGAC 59.739 42.308 0.00 0.00 0.00 3.18
262 263 2.822561 TCCTGCTAGTTCAGTGAGACAG 59.177 50.000 0.00 0.00 32.32 3.51
279 280 5.045213 TGAGACAGACCAGAGAAGATCTAGT 60.045 44.000 0.00 0.00 36.10 2.57
286 287 4.159506 ACCAGAGAAGATCTAGTGTTGCTC 59.840 45.833 0.00 0.00 36.10 4.26
287 288 4.159321 CCAGAGAAGATCTAGTGTTGCTCA 59.841 45.833 0.00 0.00 36.10 4.26
305 306 0.971386 CAAACTTCCCAGGCAGCATT 59.029 50.000 0.00 0.00 0.00 3.56
392 394 1.203287 CCTCGATCAACTCAGCTGACA 59.797 52.381 13.74 0.00 0.00 3.58
393 395 2.353109 CCTCGATCAACTCAGCTGACAA 60.353 50.000 13.74 0.00 0.00 3.18
426 428 1.274703 GGAGGGGTTGCCAGATCAGA 61.275 60.000 0.00 0.00 0.00 3.27
467 469 1.271001 GGTGTAAAGCCGTACTTGGGT 60.271 52.381 0.00 0.00 42.79 4.51
470 472 2.632028 TGTAAAGCCGTACTTGGGTGTA 59.368 45.455 0.00 0.00 40.27 2.90
605 607 2.535984 CTGGAACAATCGCTACGATGAC 59.464 50.000 2.87 0.00 46.30 3.06
796 798 0.322277 CTGATCAGCAGCCTGTTGGT 60.322 55.000 10.38 0.46 40.09 3.67
851 854 3.127721 GCTCTCTGAAATTCCCCGAAAAG 59.872 47.826 0.00 0.00 0.00 2.27
870 873 4.843220 AAGAAAAATCAGTCACCAGCAG 57.157 40.909 0.00 0.00 0.00 4.24
871 874 2.555757 AGAAAAATCAGTCACCAGCAGC 59.444 45.455 0.00 0.00 0.00 5.25
874 877 1.531423 AATCAGTCACCAGCAGCTTG 58.469 50.000 0.00 0.00 0.00 4.01
960 2080 2.664851 CGTTGAAGGAGTGCCGCA 60.665 61.111 0.00 0.00 39.96 5.69
961 2081 2.946762 GTTGAAGGAGTGCCGCAC 59.053 61.111 16.04 16.04 39.96 5.34
962 2082 2.664851 TTGAAGGAGTGCCGCACG 60.665 61.111 17.64 0.00 39.64 5.34
963 2083 4.680237 TGAAGGAGTGCCGCACGG 62.680 66.667 17.64 4.30 39.64 4.94
964 2084 4.373116 GAAGGAGTGCCGCACGGA 62.373 66.667 17.64 0.00 39.64 4.69
989 2109 3.645687 GGAAGGTTGAGATGAGCTCCTAT 59.354 47.826 12.15 0.00 43.26 2.57
990 2110 4.262420 GGAAGGTTGAGATGAGCTCCTATC 60.262 50.000 12.15 9.06 43.26 2.08
991 2111 3.238597 AGGTTGAGATGAGCTCCTATCC 58.761 50.000 12.15 4.91 43.26 2.59
992 2112 3.116784 AGGTTGAGATGAGCTCCTATCCT 60.117 47.826 12.15 7.10 43.26 3.24
993 2113 4.107149 AGGTTGAGATGAGCTCCTATCCTA 59.893 45.833 12.15 0.00 43.26 2.94
994 2114 4.219725 GGTTGAGATGAGCTCCTATCCTAC 59.780 50.000 12.15 8.95 43.26 3.18
995 2115 3.680490 TGAGATGAGCTCCTATCCTACG 58.320 50.000 12.15 0.00 43.26 3.51
996 2116 2.422127 GAGATGAGCTCCTATCCTACGC 59.578 54.545 12.15 0.00 37.69 4.42
1091 2211 2.095853 CCGTGAATAATTGCACTCGCTT 59.904 45.455 0.00 0.00 39.64 4.68
1092 2212 3.345714 CGTGAATAATTGCACTCGCTTC 58.654 45.455 0.00 0.00 39.64 3.86
1137 2266 3.160748 GCCTGCCTCCTCCTCCTC 61.161 72.222 0.00 0.00 0.00 3.71
1138 2267 2.445654 CCTGCCTCCTCCTCCTCC 60.446 72.222 0.00 0.00 0.00 4.30
1150 2279 1.063183 CCTCCTCCATCTCCCATTCC 58.937 60.000 0.00 0.00 0.00 3.01
1330 2475 7.681939 AAATTACTCGATTGTGCCTTTCTTA 57.318 32.000 0.00 0.00 0.00 2.10
1486 2631 1.444895 GAGGCCAAATTGCACTGCG 60.445 57.895 5.01 0.00 0.00 5.18
1488 2633 2.650196 GCCAAATTGCACTGCGGA 59.350 55.556 0.00 0.00 0.00 5.54
1491 2636 1.079875 CCAAATTGCACTGCGGATGC 61.080 55.000 0.00 6.33 43.68 3.91
1634 2813 1.073199 GCAAGGTAGTGCCAGTGGT 59.927 57.895 11.74 0.00 38.66 4.16
1635 2814 0.323629 GCAAGGTAGTGCCAGTGGTA 59.676 55.000 11.74 2.55 38.66 3.25
1636 2815 1.065418 GCAAGGTAGTGCCAGTGGTAT 60.065 52.381 11.74 0.00 38.66 2.73
1637 2816 2.906354 CAAGGTAGTGCCAGTGGTATC 58.094 52.381 11.74 1.40 40.61 2.24
1681 2860 2.928334 CAGCCCATACTTTCAGCTCAT 58.072 47.619 0.00 0.00 0.00 2.90
1684 2863 2.483714 GCCCATACTTTCAGCTCATCGA 60.484 50.000 0.00 0.00 0.00 3.59
1767 2946 9.155975 TGCTAAGTTGAATCTTCTTTCTGTATC 57.844 33.333 0.00 0.00 0.00 2.24
1788 2967 5.523438 TCATTTTGTCCAGGGTTTACAAC 57.477 39.130 0.00 0.00 33.10 3.32
1791 2970 1.956297 TGTCCAGGGTTTACAACACG 58.044 50.000 0.00 0.00 40.59 4.49
1805 2984 4.602340 ACAACACGAGATCAAGGTAGTT 57.398 40.909 0.00 0.00 0.00 2.24
1967 5707 4.570772 TGCACGCTTCCTTTATAATCTGAC 59.429 41.667 0.00 0.00 0.00 3.51
2027 5767 4.074970 GAGAGAGCTTGGATTTGGTCAAA 58.925 43.478 0.00 0.00 33.63 2.69
2121 5861 7.150640 TCATATGTGCAATGCTTGTAAAAACA 58.849 30.769 6.82 0.00 0.00 2.83
2147 5986 7.651704 AGTGCAAAATTTTGTCAGTGGTATTAC 59.348 33.333 27.13 12.73 40.24 1.89
2478 6317 2.228822 GGCCAGTTCAGTTTGGTATGTG 59.771 50.000 0.00 0.00 36.81 3.21
2708 6593 7.383572 ACGCTAGATGAGATTATTCACATTGTC 59.616 37.037 0.00 0.00 33.91 3.18
2711 6596 9.761504 CTAGATGAGATTATTCACATTGTCTGT 57.238 33.333 0.15 0.00 39.20 3.41
2743 6652 5.103643 ACATACCCCTAGTACACTCTGATGA 60.104 44.000 0.00 0.00 32.46 2.92
2817 6726 2.223409 GGTCGACGCATATACACAGACA 60.223 50.000 9.92 0.00 0.00 3.41
2829 6738 0.944386 CACAGACAAAACTGGACCCG 59.056 55.000 0.00 0.00 41.59 5.28
2872 6781 1.066136 GGAGAAGTTTGGCGTACGAC 58.934 55.000 21.65 18.90 0.00 4.34
2887 6796 5.924825 GGCGTACGACATTTCCTTATATCTT 59.075 40.000 21.65 0.00 0.00 2.40
3032 6948 2.203294 ACTCGGGGGTGTTGCAAC 60.203 61.111 22.83 22.83 0.00 4.17
3104 7022 6.483640 AGAATAAACAGACAGACAGACAAACC 59.516 38.462 0.00 0.00 0.00 3.27
3107 7025 1.068588 CAGACAGACAGACAAACCGGA 59.931 52.381 9.46 0.00 0.00 5.14
3160 7078 3.872459 AGGATTATTCTGGCCTTCTGG 57.128 47.619 3.32 0.00 0.00 3.86
3167 7085 1.151450 CTGGCCTTCTGGGTTGTGT 59.849 57.895 3.32 0.00 37.43 3.72
3182 7100 3.291585 GTTGTGTTGAATGCTCGTGAAG 58.708 45.455 0.00 0.00 0.00 3.02
3185 7106 3.242706 TGTGTTGAATGCTCGTGAAGTTG 60.243 43.478 0.00 0.00 0.00 3.16
3188 7109 4.142491 TGTTGAATGCTCGTGAAGTTGTTT 60.142 37.500 0.00 0.00 0.00 2.83
3198 7119 6.691388 GCTCGTGAAGTTGTTTTTAATGAACT 59.309 34.615 0.00 0.00 0.00 3.01
3215 7137 3.117888 TGAACTGGTGCTCCTTTCTTCTT 60.118 43.478 16.03 0.00 31.87 2.52
3223 7145 5.352846 GGTGCTCCTTTCTTCTTCTATCAAC 59.647 44.000 0.00 0.00 0.00 3.18
3242 7164 3.255969 ACTTTAGTTGTCCACACGTGT 57.744 42.857 17.22 17.22 0.00 4.49
3243 7165 4.389890 ACTTTAGTTGTCCACACGTGTA 57.610 40.909 22.90 3.45 0.00 2.90
3403 7337 0.735287 GTCGGTGCCTCGTAGTTTCC 60.735 60.000 0.00 0.00 0.00 3.13
3441 7415 3.119495 CCTAATTGGCTTGCTTGGTGTAC 60.119 47.826 0.00 0.00 0.00 2.90
3444 7418 0.182537 TGGCTTGCTTGGTGTACACT 59.817 50.000 24.55 0.00 0.00 3.55
3445 7419 1.418264 TGGCTTGCTTGGTGTACACTA 59.582 47.619 24.55 17.13 0.00 2.74
3446 7420 1.804748 GGCTTGCTTGGTGTACACTAC 59.195 52.381 24.55 10.37 0.00 2.73
3447 7421 1.459592 GCTTGCTTGGTGTACACTACG 59.540 52.381 24.55 17.62 0.00 3.51
3448 7422 2.750948 CTTGCTTGGTGTACACTACGT 58.249 47.619 24.55 0.00 0.00 3.57
3449 7423 2.894763 TGCTTGGTGTACACTACGTT 57.105 45.000 24.55 0.00 0.00 3.99
3488 7484 2.550978 AGTCACTGTCCAAACGAGTTG 58.449 47.619 0.00 0.00 36.94 3.16
3541 7537 2.182825 GACTACAACAGTACGATGCCG 58.817 52.381 0.00 0.00 37.72 5.69
3542 7538 0.921347 CTACAACAGTACGATGCCGC 59.079 55.000 0.00 0.00 39.95 6.53
3543 7539 0.458889 TACAACAGTACGATGCCGCC 60.459 55.000 0.00 0.00 39.95 6.13
3544 7540 1.447838 CAACAGTACGATGCCGCCT 60.448 57.895 0.00 0.00 39.95 5.52
3545 7541 0.179121 CAACAGTACGATGCCGCCTA 60.179 55.000 0.00 0.00 39.95 3.93
3546 7542 0.533491 AACAGTACGATGCCGCCTAA 59.467 50.000 0.00 0.00 39.95 2.69
3547 7543 0.533491 ACAGTACGATGCCGCCTAAA 59.467 50.000 0.00 0.00 39.95 1.85
3548 7544 1.209128 CAGTACGATGCCGCCTAAAG 58.791 55.000 0.00 0.00 39.95 1.85
3549 7545 1.108776 AGTACGATGCCGCCTAAAGA 58.891 50.000 0.00 0.00 39.95 2.52
3550 7546 1.202382 AGTACGATGCCGCCTAAAGAC 60.202 52.381 0.00 0.00 39.95 3.01
3551 7547 1.108776 TACGATGCCGCCTAAAGACT 58.891 50.000 0.00 0.00 39.95 3.24
3552 7548 1.108776 ACGATGCCGCCTAAAGACTA 58.891 50.000 0.00 0.00 39.95 2.59
3553 7549 1.479323 ACGATGCCGCCTAAAGACTAA 59.521 47.619 0.00 0.00 39.95 2.24
3554 7550 2.102588 ACGATGCCGCCTAAAGACTAAT 59.897 45.455 0.00 0.00 39.95 1.73
3555 7551 2.731976 CGATGCCGCCTAAAGACTAATC 59.268 50.000 0.00 0.00 0.00 1.75
3556 7552 2.218953 TGCCGCCTAAAGACTAATCG 57.781 50.000 0.00 0.00 0.00 3.34
3557 7553 1.479323 TGCCGCCTAAAGACTAATCGT 59.521 47.619 0.00 0.00 0.00 3.73
3558 7554 2.125685 GCCGCCTAAAGACTAATCGTC 58.874 52.381 0.00 0.00 43.17 4.20
3568 7564 3.622627 GACTAATCGTCTCCTTACCCG 57.377 52.381 0.00 0.00 39.61 5.28
3569 7565 2.292845 GACTAATCGTCTCCTTACCCGG 59.707 54.545 0.00 0.00 39.61 5.73
3570 7566 2.092212 ACTAATCGTCTCCTTACCCGGA 60.092 50.000 0.73 0.00 0.00 5.14
3571 7567 1.856629 AATCGTCTCCTTACCCGGAA 58.143 50.000 0.73 0.00 31.44 4.30
3572 7568 1.856629 ATCGTCTCCTTACCCGGAAA 58.143 50.000 0.73 0.00 31.44 3.13
3573 7569 1.631405 TCGTCTCCTTACCCGGAAAA 58.369 50.000 0.73 0.00 31.44 2.29
3574 7570 1.969923 TCGTCTCCTTACCCGGAAAAA 59.030 47.619 0.73 0.00 31.44 1.94
3614 7610 1.722011 GCGTATGTGCGGCCTATATT 58.278 50.000 0.00 0.00 0.00 1.28
3661 7657 1.078426 AGCCATTACCGCTCGCTTT 60.078 52.632 0.00 0.00 0.00 3.51
3662 7658 0.676782 AGCCATTACCGCTCGCTTTT 60.677 50.000 0.00 0.00 0.00 2.27
3663 7659 0.170339 GCCATTACCGCTCGCTTTTT 59.830 50.000 0.00 0.00 0.00 1.94
3664 7660 1.794076 GCCATTACCGCTCGCTTTTTC 60.794 52.381 0.00 0.00 0.00 2.29
3665 7661 1.737793 CCATTACCGCTCGCTTTTTCT 59.262 47.619 0.00 0.00 0.00 2.52
3666 7662 2.161609 CCATTACCGCTCGCTTTTTCTT 59.838 45.455 0.00 0.00 0.00 2.52
3667 7663 3.417185 CATTACCGCTCGCTTTTTCTTC 58.583 45.455 0.00 0.00 0.00 2.87
3668 7664 2.450609 TACCGCTCGCTTTTTCTTCT 57.549 45.000 0.00 0.00 0.00 2.85
3669 7665 1.594331 ACCGCTCGCTTTTTCTTCTT 58.406 45.000 0.00 0.00 0.00 2.52
3670 7666 1.531578 ACCGCTCGCTTTTTCTTCTTC 59.468 47.619 0.00 0.00 0.00 2.87
3671 7667 1.801178 CCGCTCGCTTTTTCTTCTTCT 59.199 47.619 0.00 0.00 0.00 2.85
3672 7668 2.224314 CCGCTCGCTTTTTCTTCTTCTT 59.776 45.455 0.00 0.00 0.00 2.52
3673 7669 3.474304 CGCTCGCTTTTTCTTCTTCTTC 58.526 45.455 0.00 0.00 0.00 2.87
3674 7670 3.185391 CGCTCGCTTTTTCTTCTTCTTCT 59.815 43.478 0.00 0.00 0.00 2.85
3675 7671 4.319118 CGCTCGCTTTTTCTTCTTCTTCTT 60.319 41.667 0.00 0.00 0.00 2.52
3697 7693 9.898152 TTCTTCTTCTTCTTCTTCTTCTTCTTT 57.102 29.630 0.00 0.00 0.00 2.52
3704 7700 4.747108 TCTTCTTCTTCTTCTTTCACGCTG 59.253 41.667 0.00 0.00 0.00 5.18
3911 7918 2.669569 GGCAGCGTCTCCAGCAAA 60.670 61.111 0.00 0.00 37.01 3.68
3919 7929 1.455786 CGTCTCCAGCAAACAAGTACG 59.544 52.381 0.00 0.00 0.00 3.67
3920 7930 2.480845 GTCTCCAGCAAACAAGTACGT 58.519 47.619 0.00 0.00 0.00 3.57
3921 7931 3.645884 GTCTCCAGCAAACAAGTACGTA 58.354 45.455 0.00 0.00 0.00 3.57
3922 7932 3.427863 GTCTCCAGCAAACAAGTACGTAC 59.572 47.826 18.10 18.10 0.00 3.67
3930 7940 1.779569 ACAAGTACGTACTGCACAGC 58.220 50.000 28.00 0.00 36.50 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.104967 ACAATGGATGAGGGCATGTTG 58.895 47.619 0.00 0.00 34.11 3.33
31 32 1.667724 GCGTGAGAACAATGGATGAGG 59.332 52.381 0.00 0.00 0.00 3.86
54 55 2.593956 GCTTCCTCCCAGAACCGGT 61.594 63.158 0.00 0.00 0.00 5.28
74 75 7.259161 GGTAGAGAGACGTCAAACAATAATCT 58.741 38.462 19.50 8.12 0.00 2.40
79 80 3.056035 GGGGTAGAGAGACGTCAAACAAT 60.056 47.826 19.50 0.00 0.00 2.71
88 89 0.814812 GGAGTCGGGGTAGAGAGACG 60.815 65.000 0.00 0.00 38.53 4.18
157 158 2.823196 TGATTATGGCGCGTTCTTTG 57.177 45.000 8.43 0.00 0.00 2.77
229 230 2.292016 ACTAGCAGGATCGATCTTCACG 59.708 50.000 23.96 7.13 0.00 4.35
262 263 4.159506 AGCAACACTAGATCTTCTCTGGTC 59.840 45.833 0.00 0.00 43.25 4.02
279 280 1.691196 CCTGGGAAGTTTGAGCAACA 58.309 50.000 0.00 0.00 37.93 3.33
286 287 0.971386 AATGCTGCCTGGGAAGTTTG 59.029 50.000 0.00 0.00 0.00 2.93
287 288 0.971386 CAATGCTGCCTGGGAAGTTT 59.029 50.000 0.00 0.00 0.00 2.66
305 306 3.118408 CCATAGCCTGGTAGTAAAGTGCA 60.118 47.826 0.00 0.00 40.49 4.57
343 345 6.497437 TGTATTGATTTTGATGATGCTTCCG 58.503 36.000 0.00 0.00 0.00 4.30
348 350 7.334574 GCATCTGTATTGATTTTGATGATGC 57.665 36.000 0.00 0.00 44.32 3.91
392 394 1.420138 CCCTCCAATACCCGCTATGTT 59.580 52.381 0.00 0.00 0.00 2.71
393 395 1.056660 CCCTCCAATACCCGCTATGT 58.943 55.000 0.00 0.00 0.00 2.29
426 428 0.251787 AGCTCCCAAAAAGGCCGAAT 60.252 50.000 0.00 0.00 35.39 3.34
467 469 2.769663 AGCAATTAGTGGGTCCGATACA 59.230 45.455 0.00 0.00 0.00 2.29
470 472 1.837439 TCAGCAATTAGTGGGTCCGAT 59.163 47.619 0.00 0.00 0.00 4.18
605 607 0.384309 TAGGTGCTACAATCGAGCGG 59.616 55.000 0.00 0.00 43.19 5.52
796 798 0.602638 AGCATTCGCCGAACAGTCAA 60.603 50.000 0.00 0.00 39.83 3.18
851 854 2.555757 AGCTGCTGGTGACTGATTTTTC 59.444 45.455 0.00 0.00 0.00 2.29
935 2055 2.538939 GCACTCCTTCAACGTGTTTCAC 60.539 50.000 0.00 0.00 0.00 3.18
960 2080 0.974383 ATCTCAACCTTCCGTTCCGT 59.026 50.000 0.00 0.00 29.93 4.69
961 2081 1.067142 TCATCTCAACCTTCCGTTCCG 60.067 52.381 0.00 0.00 29.93 4.30
962 2082 2.622436 CTCATCTCAACCTTCCGTTCC 58.378 52.381 0.00 0.00 29.93 3.62
963 2083 2.003301 GCTCATCTCAACCTTCCGTTC 58.997 52.381 0.00 0.00 29.93 3.95
964 2084 1.625818 AGCTCATCTCAACCTTCCGTT 59.374 47.619 0.00 0.00 33.90 4.44
989 2109 2.335011 CGATCATGGCGCGTAGGA 59.665 61.111 8.43 5.02 0.00 2.94
990 2110 3.406361 GCGATCATGGCGCGTAGG 61.406 66.667 15.87 0.00 45.27 3.18
1135 2264 0.475906 GGTGGGAATGGGAGATGGAG 59.524 60.000 0.00 0.00 0.00 3.86
1136 2265 0.046242 AGGTGGGAATGGGAGATGGA 59.954 55.000 0.00 0.00 0.00 3.41
1137 2266 0.929244 AAGGTGGGAATGGGAGATGG 59.071 55.000 0.00 0.00 0.00 3.51
1138 2267 1.133668 GGAAGGTGGGAATGGGAGATG 60.134 57.143 0.00 0.00 0.00 2.90
1344 2489 8.604035 GCTGCGCATATGTGTTTATAAGTATAT 58.396 33.333 12.24 0.00 0.00 0.86
1345 2490 7.817478 AGCTGCGCATATGTGTTTATAAGTATA 59.183 33.333 12.24 0.00 0.00 1.47
1346 2491 6.650807 AGCTGCGCATATGTGTTTATAAGTAT 59.349 34.615 12.24 0.00 0.00 2.12
1347 2492 5.989168 AGCTGCGCATATGTGTTTATAAGTA 59.011 36.000 12.24 0.00 0.00 2.24
1348 2493 4.816385 AGCTGCGCATATGTGTTTATAAGT 59.184 37.500 12.24 0.00 0.00 2.24
1349 2494 5.348418 AGCTGCGCATATGTGTTTATAAG 57.652 39.130 12.24 7.29 0.00 1.73
1350 2495 4.213270 GGAGCTGCGCATATGTGTTTATAA 59.787 41.667 12.24 0.00 0.00 0.98
1351 2496 3.745975 GGAGCTGCGCATATGTGTTTATA 59.254 43.478 12.24 0.00 0.00 0.98
1352 2497 2.549754 GGAGCTGCGCATATGTGTTTAT 59.450 45.455 12.24 2.47 0.00 1.40
1353 2498 1.939934 GGAGCTGCGCATATGTGTTTA 59.060 47.619 12.24 4.36 0.00 2.01
1354 2499 0.734889 GGAGCTGCGCATATGTGTTT 59.265 50.000 12.24 1.53 0.00 2.83
1355 2500 1.097547 GGGAGCTGCGCATATGTGTT 61.098 55.000 12.24 0.00 0.00 3.32
1356 2501 1.524621 GGGAGCTGCGCATATGTGT 60.525 57.895 12.24 0.00 0.00 3.72
1357 2502 2.256591 GGGGAGCTGCGCATATGTG 61.257 63.158 12.24 12.04 0.00 3.21
1497 2642 8.621532 TCTGTGCAGAATTGAAAAGTTATAGT 57.378 30.769 0.00 0.00 33.91 2.12
1498 2643 9.713740 GATCTGTGCAGAATTGAAAAGTTATAG 57.286 33.333 5.95 0.00 41.36 1.31
1499 2644 9.230122 TGATCTGTGCAGAATTGAAAAGTTATA 57.770 29.630 5.95 0.00 41.36 0.98
1606 2782 1.072331 CACTACCTTGCAGTTCCTGGT 59.928 52.381 0.00 0.00 35.05 4.00
1634 2813 6.586463 GTCTGTGAATCAAAGAACACTCGATA 59.414 38.462 4.43 0.00 28.61 2.92
1635 2814 5.406780 GTCTGTGAATCAAAGAACACTCGAT 59.593 40.000 4.43 0.00 28.61 3.59
1636 2815 4.745125 GTCTGTGAATCAAAGAACACTCGA 59.255 41.667 4.43 0.00 28.61 4.04
1637 2816 4.375405 CGTCTGTGAATCAAAGAACACTCG 60.375 45.833 4.43 0.49 28.61 4.18
1738 2917 9.507329 ACAGAAAGAAGATTCAACTTAGCATAA 57.493 29.630 0.00 0.00 0.00 1.90
1788 2967 2.271800 GGCAACTACCTTGATCTCGTG 58.728 52.381 0.00 0.00 30.42 4.35
1791 2970 5.537300 TCTATGGCAACTACCTTGATCTC 57.463 43.478 0.00 0.00 37.61 2.75
2027 5767 5.813672 GCCATCAAAATTGCTGTCAATGTAT 59.186 36.000 0.00 0.00 41.77 2.29
2121 5861 4.470334 ACCACTGACAAAATTTTGCACT 57.530 36.364 26.94 11.03 41.79 4.40
2147 5986 9.787532 CCTACCAATTTATATGAACACAAACTG 57.212 33.333 0.00 0.00 0.00 3.16
2478 6317 2.992593 GAAAGGATTCCAGGTGGAGTC 58.007 52.381 12.06 12.06 46.56 3.36
2683 6568 7.598118 AGACAATGTGAATAATCTCATCTAGCG 59.402 37.037 0.00 0.00 38.48 4.26
2711 6596 7.413446 AGTGTACTAGGGGTATGTTACACTAA 58.587 38.462 13.77 0.00 33.72 2.24
2743 6652 5.936956 GGAGAACTGACATGAGATTGAGTTT 59.063 40.000 0.00 0.00 0.00 2.66
2872 6781 6.055588 ACCGACACCAAGATATAAGGAAATG 58.944 40.000 0.00 0.00 0.00 2.32
2887 6796 2.529780 AATAACACGAACCGACACCA 57.470 45.000 0.00 0.00 0.00 4.17
3053 6969 1.033746 ATGGCCTATATGCATGGCGC 61.034 55.000 17.60 0.00 46.97 6.53
3054 6970 0.736636 CATGGCCTATATGCATGGCG 59.263 55.000 17.60 3.62 46.97 5.69
3133 7051 5.046288 AGGCCAGAATAATCCTTCTTCAG 57.954 43.478 5.01 0.00 33.18 3.02
3139 7057 3.117360 CCCAGAAGGCCAGAATAATCCTT 60.117 47.826 5.01 0.00 41.27 3.36
3145 7063 1.992557 ACAACCCAGAAGGCCAGAATA 59.007 47.619 5.01 0.00 40.58 1.75
3147 7065 0.178992 CACAACCCAGAAGGCCAGAA 60.179 55.000 5.01 0.00 40.58 3.02
3148 7066 1.352622 ACACAACCCAGAAGGCCAGA 61.353 55.000 5.01 0.00 40.58 3.86
3149 7067 0.468029 AACACAACCCAGAAGGCCAG 60.468 55.000 5.01 0.00 40.58 4.85
3150 7068 0.754957 CAACACAACCCAGAAGGCCA 60.755 55.000 5.01 0.00 40.58 5.36
3151 7069 0.467290 TCAACACAACCCAGAAGGCC 60.467 55.000 0.00 0.00 40.58 5.19
3152 7070 1.398692 TTCAACACAACCCAGAAGGC 58.601 50.000 0.00 0.00 40.58 4.35
3153 7071 2.288395 GCATTCAACACAACCCAGAAGG 60.288 50.000 0.00 0.00 43.78 3.46
3154 7072 2.624838 AGCATTCAACACAACCCAGAAG 59.375 45.455 0.00 0.00 0.00 2.85
3160 7078 1.601903 TCACGAGCATTCAACACAACC 59.398 47.619 0.00 0.00 0.00 3.77
3167 7085 4.630894 AAACAACTTCACGAGCATTCAA 57.369 36.364 0.00 0.00 0.00 2.69
3182 7100 5.462068 GGAGCACCAGTTCATTAAAAACAAC 59.538 40.000 0.00 0.00 35.97 3.32
3185 7106 5.453567 AGGAGCACCAGTTCATTAAAAAC 57.546 39.130 2.07 0.00 38.94 2.43
3188 7109 5.385198 AGAAAGGAGCACCAGTTCATTAAA 58.615 37.500 15.59 0.00 38.94 1.52
3198 7119 4.532126 TGATAGAAGAAGAAAGGAGCACCA 59.468 41.667 2.07 0.00 38.94 4.17
3223 7145 4.208460 CAGTACACGTGTGGACAACTAAAG 59.792 45.833 30.83 10.18 46.74 1.85
3239 7161 8.594550 ACCCCTTAATATGTATGATCAGTACAC 58.405 37.037 15.64 6.43 35.11 2.90
3240 7162 8.736097 ACCCCTTAATATGTATGATCAGTACA 57.264 34.615 15.65 15.65 36.58 2.90
3241 7163 9.436957 CAACCCCTTAATATGTATGATCAGTAC 57.563 37.037 0.09 5.12 0.00 2.73
3242 7164 8.100791 GCAACCCCTTAATATGTATGATCAGTA 58.899 37.037 0.09 0.00 0.00 2.74
3243 7165 6.942576 GCAACCCCTTAATATGTATGATCAGT 59.057 38.462 0.09 0.00 0.00 3.41
3354 7288 5.221048 GCGATTAAAGATAGGTTGTGGCATT 60.221 40.000 0.00 0.00 0.00 3.56
3364 7298 6.030849 CCGACATAGAGCGATTAAAGATAGG 58.969 44.000 0.00 0.00 0.00 2.57
3366 7300 6.379386 CACCGACATAGAGCGATTAAAGATA 58.621 40.000 0.00 0.00 0.00 1.98
3367 7301 5.223382 CACCGACATAGAGCGATTAAAGAT 58.777 41.667 0.00 0.00 0.00 2.40
3368 7302 4.607955 CACCGACATAGAGCGATTAAAGA 58.392 43.478 0.00 0.00 0.00 2.52
3369 7303 3.182572 GCACCGACATAGAGCGATTAAAG 59.817 47.826 0.00 0.00 0.00 1.85
3370 7304 3.120792 GCACCGACATAGAGCGATTAAA 58.879 45.455 0.00 0.00 0.00 1.52
3371 7305 2.545113 GGCACCGACATAGAGCGATTAA 60.545 50.000 0.00 0.00 0.00 1.40
3403 7337 0.107017 TAGGAACCTCGTACGGGGAG 60.107 60.000 39.87 17.97 38.23 4.30
3441 7415 2.915463 CGGTAGCTCTTTGAACGTAGTG 59.085 50.000 0.00 0.00 45.00 2.74
3444 7418 2.095059 GGTCGGTAGCTCTTTGAACGTA 60.095 50.000 0.00 0.00 0.00 3.57
3445 7419 1.336609 GGTCGGTAGCTCTTTGAACGT 60.337 52.381 0.00 0.00 0.00 3.99
3446 7420 1.336517 TGGTCGGTAGCTCTTTGAACG 60.337 52.381 0.00 0.00 0.00 3.95
3447 7421 2.450609 TGGTCGGTAGCTCTTTGAAC 57.549 50.000 0.00 0.00 0.00 3.18
3448 7422 3.181458 ACTTTGGTCGGTAGCTCTTTGAA 60.181 43.478 0.00 0.00 0.00 2.69
3449 7423 2.367567 ACTTTGGTCGGTAGCTCTTTGA 59.632 45.455 0.00 0.00 0.00 2.69
3488 7484 0.247736 ATGCCGAGGACACTGACTTC 59.752 55.000 0.00 0.00 0.00 3.01
3549 7545 2.092212 TCCGGGTAAGGAGACGATTAGT 60.092 50.000 0.00 0.00 34.92 2.24
3550 7546 2.579873 TCCGGGTAAGGAGACGATTAG 58.420 52.381 0.00 0.00 34.92 1.73
3551 7547 2.734755 TCCGGGTAAGGAGACGATTA 57.265 50.000 0.00 0.00 34.92 1.75
3552 7548 1.856629 TTCCGGGTAAGGAGACGATT 58.143 50.000 0.00 0.00 41.98 3.34
3553 7549 1.856629 TTTCCGGGTAAGGAGACGAT 58.143 50.000 0.00 0.00 41.98 3.73
3554 7550 1.631405 TTTTCCGGGTAAGGAGACGA 58.369 50.000 0.00 0.00 41.98 4.20
3555 7551 2.460757 TTTTTCCGGGTAAGGAGACG 57.539 50.000 0.00 0.00 41.98 4.18
3661 7657 9.898152 AAGAAGAAGAAGAAGAAGAAGAAGAAA 57.102 29.630 0.00 0.00 0.00 2.52
3662 7658 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
3663 7659 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
3664 7660 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
3665 7661 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
3666 7662 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
3667 7663 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
3668 7664 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
3669 7665 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
3670 7666 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
3671 7667 9.898152 AAAGAAGAAGAAGAAGAAGAAGAAGAA 57.102 29.630 0.00 0.00 0.00 2.52
3672 7668 9.541143 GAAAGAAGAAGAAGAAGAAGAAGAAGA 57.459 33.333 0.00 0.00 0.00 2.87
3673 7669 9.323985 TGAAAGAAGAAGAAGAAGAAGAAGAAG 57.676 33.333 0.00 0.00 0.00 2.85
3674 7670 9.103861 GTGAAAGAAGAAGAAGAAGAAGAAGAA 57.896 33.333 0.00 0.00 0.00 2.52
3675 7671 7.436673 CGTGAAAGAAGAAGAAGAAGAAGAAGA 59.563 37.037 0.00 0.00 0.00 2.87
3911 7918 1.340248 AGCTGTGCAGTACGTACTTGT 59.660 47.619 25.35 2.52 33.46 3.16
3919 7929 0.391793 GGGAAGGAGCTGTGCAGTAC 60.392 60.000 0.00 0.00 0.00 2.73
3920 7930 0.545309 AGGGAAGGAGCTGTGCAGTA 60.545 55.000 0.00 0.00 0.00 2.74
3921 7931 0.545309 TAGGGAAGGAGCTGTGCAGT 60.545 55.000 0.00 0.00 0.00 4.40
3922 7932 0.615331 TTAGGGAAGGAGCTGTGCAG 59.385 55.000 0.00 0.00 0.00 4.41
3930 7940 5.995446 AGCAGAGTAATTTTAGGGAAGGAG 58.005 41.667 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.