Multiple sequence alignment - TraesCS7A01G474000

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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 TraesCS7A01G474000 chr7A 100.000 4303 0 0 1 4303 669555251 669550949 0.000000e+00 7947
1 TraesCS7A01G474000 chr7D 90.044 3606 171 75 1 3519 577325953 577322449 0.000000e+00 4497
2 TraesCS7A01G474000 chr7D 89.486 428 37 4 3528 3955 577322024 577321605 6.330000e-148 534
3 TraesCS7A01G474000 chr7D 93.966 232 11 3 4039 4268 577318178 577317948 8.860000e-92 348
4 TraesCS7A01G474000 chr7B 89.503 2715 138 50 652 3305 640778030 640775402 0.000000e+00 3299
5 TraesCS7A01G474000 chr7B 86.613 620 64 5 1 619 640778632 640778031 0.000000e+00 667
6 TraesCS7A01G474000 chr7B 89.796 245 21 3 4039 4281 640725249 640725007 1.160000e-80 311
7 TraesCS7A01G474000 chr7B 90.805 174 16 0 2930 3103 640734301 640734128 2.590000e-57 233
8 TraesCS7A01G474000 chr3D 80.062 321 60 4 8 327 21588245 21588562 7.190000e-58 235


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 TraesCS7A01G474000 chr7A 669550949 669555251 4302 True 7947 7947 100.000000 1 4303 1 chr7A.!!$R1 4302
1 TraesCS7A01G474000 chr7D 577317948 577325953 8005 True 1793 4497 91.165333 1 4268 3 chr7D.!!$R1 4267
2 TraesCS7A01G474000 chr7B 640775402 640778632 3230 True 1983 3299 88.058000 1 3305 2 chr7B.!!$R3 3304

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
892 911 0.181114 CATGGCTCGGATCCAAGGAA 59.819 55.0 13.41 0.00 37.13 3.36 F
2158 2255 0.250295 ACTGTAGTTGCATGCACGGT 60.250 50.0 22.58 17.02 0.00 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2201 2298 0.247419 GTCGAGATGTGCACGCATTG 60.247 55.0 13.13 4.19 0.0 2.82 R
3414 3543 0.388649 AGACGTTGCTGATCACGACC 60.389 55.0 10.08 2.55 0.0 4.79 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
49 50 3.389329 GGCTTCAGTGATTCCTATCCTCA 59.611 47.826 0.00 0.00 0.00 3.86
111 112 2.804697 TCATCACCTTCGTTCGACAA 57.195 45.000 0.00 0.00 0.00 3.18
116 117 1.038280 ACCTTCGTTCGACAACTCCT 58.962 50.000 0.00 0.00 0.00 3.69
157 158 0.729116 CTACAGGCGATGTTGCTTGG 59.271 55.000 8.90 0.00 45.33 3.61
161 162 2.126346 GCGATGTTGCTTGGGTGC 60.126 61.111 0.00 0.00 0.00 5.01
180 181 1.713932 GCTCGGTTTTTCGTTTCATGC 59.286 47.619 0.00 0.00 0.00 4.06
181 182 2.856720 GCTCGGTTTTTCGTTTCATGCA 60.857 45.455 0.00 0.00 0.00 3.96
227 228 3.950397 TGGTAACTTGGGCACTTAGATG 58.050 45.455 0.00 0.00 37.61 2.90
284 285 4.988716 ACACCCGTCGAGCCTGGA 62.989 66.667 0.00 0.00 0.00 3.86
320 321 4.680237 TTGTGGCGGCGGAGTCAG 62.680 66.667 9.78 0.00 0.00 3.51
361 362 0.971386 GGTCCTTTGGTGGTAGTCGA 59.029 55.000 0.00 0.00 0.00 4.20
394 395 1.852157 AATGGTGGTGCCCTCCTCA 60.852 57.895 11.92 2.80 37.97 3.86
460 462 2.023414 AACGGGTTGTGTGCTCTCGA 62.023 55.000 0.00 0.00 0.00 4.04
490 492 5.751990 ACACGTTACCTTTGAGTTGTTCTAG 59.248 40.000 0.00 0.00 0.00 2.43
491 493 5.751990 CACGTTACCTTTGAGTTGTTCTAGT 59.248 40.000 0.00 0.00 0.00 2.57
492 494 6.919662 CACGTTACCTTTGAGTTGTTCTAGTA 59.080 38.462 0.00 0.00 0.00 1.82
517 519 8.451908 ACTGAGCACTTTGTATCTTTACTTTT 57.548 30.769 0.00 0.00 0.00 2.27
536 538 7.044589 ACTTTTGCTTTTCGTTAAGTTGTTG 57.955 32.000 0.00 0.00 0.00 3.33
553 555 8.691661 AAGTTGTTGTTATGTAATTCTGACCT 57.308 30.769 0.00 0.00 0.00 3.85
573 575 7.648142 TGACCTGTTGATGACTTTGTTAATTC 58.352 34.615 0.00 0.00 0.00 2.17
582 584 9.695526 TGATGACTTTGTTAATTCAAAATCAGG 57.304 29.630 8.93 0.00 43.29 3.86
585 587 7.867403 TGACTTTGTTAATTCAAAATCAGGCTC 59.133 33.333 1.05 0.00 38.18 4.70
589 591 8.816640 TTGTTAATTCAAAATCAGGCTCTTTC 57.183 30.769 0.00 0.00 0.00 2.62
590 592 8.181904 TGTTAATTCAAAATCAGGCTCTTTCT 57.818 30.769 0.00 0.00 0.00 2.52
591 593 9.295825 TGTTAATTCAAAATCAGGCTCTTTCTA 57.704 29.630 0.00 0.00 0.00 2.10
612 614 6.193761 TCTAAGCCTTCGTTTAAAAACAACG 58.806 36.000 6.41 0.00 46.78 4.10
614 616 2.216940 GCCTTCGTTTAAAAACAACGGC 59.783 45.455 6.41 9.06 45.70 5.68
619 621 2.035259 CGTTTAAAAACAACGGCAGTGC 60.035 45.455 6.55 6.55 42.68 4.40
620 622 2.924290 GTTTAAAAACAACGGCAGTGCA 59.076 40.909 18.61 0.00 38.74 4.57
622 624 1.851658 AAAAACAACGGCAGTGCATC 58.148 45.000 18.61 0.00 0.00 3.91
632 634 2.419673 CGGCAGTGCATCTCATTACAAA 59.580 45.455 18.61 0.00 0.00 2.83
637 639 6.024049 GCAGTGCATCTCATTACAAAGTAAC 58.976 40.000 11.09 0.00 0.00 2.50
673 675 1.132453 GCCCGAGGTTCAAATACTTGC 59.868 52.381 0.00 0.00 32.14 4.01
675 677 1.396996 CCGAGGTTCAAATACTTGCGG 59.603 52.381 0.00 0.00 32.14 5.69
679 681 1.890489 GGTTCAAATACTTGCGGGGTT 59.110 47.619 0.00 0.00 32.14 4.11
681 683 1.540267 TCAAATACTTGCGGGGTTGG 58.460 50.000 0.00 0.00 32.14 3.77
698 700 1.080298 GGCGTTGCGTGTAGGTAGT 60.080 57.895 0.00 0.00 0.00 2.73
703 705 2.160219 CGTTGCGTGTAGGTAGTACAGA 59.840 50.000 2.06 0.00 42.56 3.41
704 706 3.365264 CGTTGCGTGTAGGTAGTACAGAA 60.365 47.826 2.06 0.00 42.56 3.02
705 707 4.164294 GTTGCGTGTAGGTAGTACAGAAG 58.836 47.826 2.06 0.00 42.56 2.85
720 722 3.153919 ACAGAAGAGAGAGGTCACTGAC 58.846 50.000 0.00 0.00 31.77 3.51
723 725 0.402504 AGAGAGAGGTCACTGACGGT 59.597 55.000 3.04 0.00 32.65 4.83
731 735 1.456892 TCACTGACGGTGGTGTCCT 60.457 57.895 14.44 0.00 45.38 3.85
892 911 0.181114 CATGGCTCGGATCCAAGGAA 59.819 55.000 13.41 0.00 37.13 3.36
893 912 0.918983 ATGGCTCGGATCCAAGGAAA 59.081 50.000 13.41 0.00 37.13 3.13
894 913 0.253044 TGGCTCGGATCCAAGGAAAG 59.747 55.000 13.41 0.03 0.00 2.62
895 914 0.464554 GGCTCGGATCCAAGGAAAGG 60.465 60.000 13.41 0.00 0.00 3.11
896 915 0.253327 GCTCGGATCCAAGGAAAGGT 59.747 55.000 13.41 0.00 0.00 3.50
897 916 1.485066 GCTCGGATCCAAGGAAAGGTA 59.515 52.381 13.41 0.00 0.00 3.08
898 917 2.742204 GCTCGGATCCAAGGAAAGGTAC 60.742 54.545 13.41 0.00 0.00 3.34
899 918 1.479323 TCGGATCCAAGGAAAGGTACG 59.521 52.381 13.41 0.00 0.00 3.67
900 919 1.206371 CGGATCCAAGGAAAGGTACGT 59.794 52.381 13.41 0.00 0.00 3.57
901 920 2.629051 GGATCCAAGGAAAGGTACGTG 58.371 52.381 6.95 0.00 0.00 4.49
902 921 2.235402 GGATCCAAGGAAAGGTACGTGA 59.765 50.000 6.95 0.00 0.00 4.35
903 922 3.522553 GATCCAAGGAAAGGTACGTGAG 58.477 50.000 0.00 0.00 0.00 3.51
1022 1052 2.324330 CGCACACGGCCATGAAGAA 61.324 57.895 5.45 0.00 40.31 2.52
1082 1115 2.015726 TCTCCCTCCTCCTCCTCCC 61.016 68.421 0.00 0.00 0.00 4.30
1226 1280 0.911525 CCCACACAGTCCCATCTCCT 60.912 60.000 0.00 0.00 0.00 3.69
1240 1294 4.080356 CCCATCTCCTATCACAACTTTCCA 60.080 45.833 0.00 0.00 0.00 3.53
1286 1340 2.894387 GAGCAGAGCATGGACGGC 60.894 66.667 0.00 0.00 0.00 5.68
1349 1403 2.592993 CCACCCGCTCCTCAGGAAA 61.593 63.158 0.00 0.00 0.00 3.13
1651 1719 3.411351 CAACGGCCACGAGGTTCG 61.411 66.667 2.24 13.01 46.93 3.95
1672 1740 7.065803 GGTTCGTCATTTCTTCTCCATCAATTA 59.934 37.037 0.00 0.00 0.00 1.40
1673 1741 7.539712 TCGTCATTTCTTCTCCATCAATTAC 57.460 36.000 0.00 0.00 0.00 1.89
1674 1742 6.255670 TCGTCATTTCTTCTCCATCAATTACG 59.744 38.462 0.00 0.00 0.00 3.18
1696 1764 1.001706 CCTTGCTCGGCATGAATGATG 60.002 52.381 0.00 0.00 38.76 3.07
1835 1930 3.485947 TGCCATTAATTTGCGTGAGTC 57.514 42.857 3.08 0.00 0.00 3.36
1889 1984 4.416738 GTGGGGCAGCAGGAGGTC 62.417 72.222 0.00 0.00 0.00 3.85
2034 2129 4.767255 GCTGGCAGGTCACTCCCG 62.767 72.222 17.64 0.00 36.75 5.14
2067 2164 6.595682 TCCCATTTCCATCTCAGATTCTTAC 58.404 40.000 0.00 0.00 0.00 2.34
2068 2165 5.767168 CCCATTTCCATCTCAGATTCTTACC 59.233 44.000 0.00 0.00 0.00 2.85
2077 2174 4.216472 TCTCAGATTCTTACCGATGATCCG 59.784 45.833 0.00 0.00 0.00 4.18
2102 2199 5.763204 TCTCACTTGACTTGTTCATTAACCC 59.237 40.000 0.00 0.00 34.49 4.11
2132 2229 7.381408 TACGTAGTAACTTATTGCATCTGCATC 59.619 37.037 5.58 0.00 45.99 3.91
2142 2239 3.620929 GCATCTGCATCCATGTAACTG 57.379 47.619 0.00 0.00 41.59 3.16
2143 2240 2.947652 GCATCTGCATCCATGTAACTGT 59.052 45.455 0.00 0.00 41.59 3.55
2144 2241 4.129380 GCATCTGCATCCATGTAACTGTA 58.871 43.478 0.00 0.00 41.59 2.74
2145 2242 4.212847 GCATCTGCATCCATGTAACTGTAG 59.787 45.833 0.00 0.00 41.59 2.74
2146 2243 5.363101 CATCTGCATCCATGTAACTGTAGT 58.637 41.667 0.00 0.00 0.00 2.73
2147 2244 5.420725 TCTGCATCCATGTAACTGTAGTT 57.579 39.130 2.51 2.51 41.73 2.24
2148 2245 5.178061 TCTGCATCCATGTAACTGTAGTTG 58.822 41.667 7.50 0.00 38.90 3.16
2149 2246 3.689161 TGCATCCATGTAACTGTAGTTGC 59.311 43.478 7.50 6.71 40.37 4.17
2156 2253 2.478514 TGTAACTGTAGTTGCATGCACG 59.521 45.455 22.58 7.95 43.77 5.34
2157 2254 0.874390 AACTGTAGTTGCATGCACGG 59.126 50.000 22.58 16.31 36.80 4.94
2158 2255 0.250295 ACTGTAGTTGCATGCACGGT 60.250 50.000 22.58 17.02 0.00 4.83
2159 2256 1.001520 ACTGTAGTTGCATGCACGGTA 59.998 47.619 22.58 9.33 0.00 4.02
2246 2344 3.160777 AGATCGATTCCGTTGTGTACC 57.839 47.619 0.00 0.00 37.05 3.34
2268 2368 1.653151 GGCCGCTAGTTTAACCTCTG 58.347 55.000 0.00 0.00 0.00 3.35
2327 2427 7.598759 AGTACCCCAACTTGATATAGTACTG 57.401 40.000 5.39 0.00 38.14 2.74
2332 2432 7.038941 ACCCCAACTTGATATAGTACTGCTATC 60.039 40.741 5.39 12.02 40.61 2.08
2361 2461 6.785337 ATCCATGCATGTGGGAAATATATG 57.215 37.500 24.58 5.28 39.80 1.78
2435 2549 2.056577 GCTGCAGTGCAAGACAAAATC 58.943 47.619 20.22 0.00 38.41 2.17
2445 2561 3.801594 GCAAGACAAAATCGCTCCAAAAA 59.198 39.130 0.00 0.00 0.00 1.94
2448 2564 5.452078 AGACAAAATCGCTCCAAAAATGA 57.548 34.783 0.00 0.00 0.00 2.57
2454 2570 7.278424 ACAAAATCGCTCCAAAAATGATAATGG 59.722 33.333 0.00 0.00 0.00 3.16
2466 2582 9.097257 CAAAAATGATAATGGGTTGTGGTAATC 57.903 33.333 0.00 0.00 0.00 1.75
2472 2588 1.416772 TGGGTTGTGGTAATCGACACA 59.583 47.619 2.71 2.71 45.06 3.72
2680 2800 6.234177 AGTCAAATCTCAAACGATTCTTCCT 58.766 36.000 0.00 0.00 32.69 3.36
2690 2810 5.437191 AACGATTCTTCCTTCCCACTAAT 57.563 39.130 0.00 0.00 0.00 1.73
2700 2821 4.962995 TCCTTCCCACTAATCCTTCTACTG 59.037 45.833 0.00 0.00 0.00 2.74
2701 2822 4.962995 CCTTCCCACTAATCCTTCTACTGA 59.037 45.833 0.00 0.00 0.00 3.41
2708 2829 8.651389 CCCACTAATCCTTCTACTGATCATAAA 58.349 37.037 0.00 0.00 0.00 1.40
2730 2857 1.081892 ATTAGCAACTGACAGCTGCG 58.918 50.000 21.76 5.09 41.85 5.18
2744 2871 1.154282 CTGCGTGCATGTTGCTCTG 60.154 57.895 7.93 0.00 45.31 3.35
2745 2872 1.571215 CTGCGTGCATGTTGCTCTGA 61.571 55.000 7.93 0.00 45.31 3.27
3143 3272 2.504244 CGCAACCTCGAGACGGTC 60.504 66.667 15.71 0.00 32.46 4.79
3221 3350 2.415843 GGCGGCTGCTACGACATA 59.584 61.111 18.85 0.00 39.67 2.29
3224 3353 1.003851 GCGGCTGCTACGACATAAAA 58.996 50.000 11.21 0.00 38.39 1.52
3242 3371 3.984200 AAAGGCCTACGACGAGCGC 62.984 63.158 5.16 0.00 46.04 5.92
3326 3455 0.734889 TAGCGTTAGCCGAGGTGTAC 59.265 55.000 0.00 0.00 46.67 2.90
3352 3481 1.127766 TCAACAACGACACGCATATGC 59.872 47.619 18.08 18.08 37.78 3.14
3353 3482 1.136113 CAACAACGACACGCATATGCA 60.136 47.619 26.52 0.00 42.21 3.96
3354 3483 1.368641 ACAACGACACGCATATGCAT 58.631 45.000 26.52 9.89 42.21 3.96
3355 3484 1.062440 ACAACGACACGCATATGCATG 59.938 47.619 26.52 24.03 40.48 4.06
3390 3519 4.357142 CATGCTCATGTACATTTTGCCTC 58.643 43.478 5.37 0.00 34.23 4.70
3400 3529 0.243636 ATTTTGCCTCGCTTTTCGGG 59.756 50.000 0.00 0.00 39.05 5.14
3414 3543 2.278857 CGGGGACTTGATCGCTCG 60.279 66.667 0.00 0.00 40.16 5.03
3415 3544 2.107141 GGGGACTTGATCGCTCGG 59.893 66.667 0.00 0.00 40.16 4.63
3427 3569 2.181777 GCTCGGTCGTGATCAGCA 59.818 61.111 0.00 0.00 0.00 4.41
3436 3578 1.139989 CGTGATCAGCAACGTCTTGT 58.860 50.000 0.00 0.00 0.00 3.16
3447 3589 4.865365 AGCAACGTCTTGTCTAATTCTAGC 59.135 41.667 0.00 0.00 0.00 3.42
3459 3601 8.048534 TGTCTAATTCTAGCGTTAGTTGTACT 57.951 34.615 6.18 0.00 31.47 2.73
3466 3608 1.385743 GCGTTAGTTGTACTCGCACAG 59.614 52.381 7.70 0.00 45.01 3.66
3471 3613 3.173668 AGTTGTACTCGCACAGAACAA 57.826 42.857 0.00 0.00 29.79 2.83
3478 3620 0.865111 TCGCACAGAACAACAATCGG 59.135 50.000 0.00 0.00 0.00 4.18
3489 3633 2.297033 ACAACAATCGGAATTGCAGCTT 59.703 40.909 0.00 0.00 45.16 3.74
3505 3649 3.751621 CAGCTTGAGCCTAATTTTGACG 58.248 45.455 0.00 0.00 43.38 4.35
3526 4086 2.312424 AGGAAGTTCCTTCTCGAGGT 57.688 50.000 19.27 0.00 46.91 3.85
3533 4093 7.038516 AGGAAGTTCCTTCTCGAGGTATAAAAA 60.039 37.037 19.27 0.00 46.91 1.94
3541 4101 7.148457 CCTTCTCGAGGTATAAAAACCAAAGAC 60.148 40.741 13.56 0.00 42.40 3.01
3546 4106 6.859508 CGAGGTATAAAAACCAAAGACCAAAC 59.140 38.462 0.00 0.00 42.40 2.93
3550 4110 3.793797 AAAACCAAAGACCAAACTCCG 57.206 42.857 0.00 0.00 0.00 4.63
3565 4125 4.837093 AACTCCGAATCCATAAAGACCA 57.163 40.909 0.00 0.00 0.00 4.02
3600 4160 7.262048 TGTTTATCAAAACTGGAAGACCAAAC 58.738 34.615 3.01 0.00 46.32 2.93
3603 4163 8.754991 TTATCAAAACTGGAAGACCAAACTAA 57.245 30.769 0.00 0.00 46.32 2.24
3606 4166 8.073467 TCAAAACTGGAAGACCAAACTAATTT 57.927 30.769 0.00 0.00 46.32 1.82
3607 4167 8.194769 TCAAAACTGGAAGACCAAACTAATTTC 58.805 33.333 0.00 0.00 46.32 2.17
3636 4196 5.221621 GGATTAGTCTTCTTCCCTGGATGAG 60.222 48.000 0.00 0.00 31.47 2.90
3651 4211 2.989840 GGATGAGCGAATAACCGAGATG 59.010 50.000 0.00 0.00 0.00 2.90
3653 4213 1.068588 TGAGCGAATAACCGAGATGGG 59.931 52.381 0.00 0.00 44.64 4.00
3657 4217 1.066605 CGAATAACCGAGATGGGTCGT 59.933 52.381 0.00 0.00 44.64 4.34
3664 4224 1.599667 CCGAGATGGGTCGTATTCGTG 60.600 57.143 0.00 0.00 38.32 4.35
3674 4234 4.088648 GGTCGTATTCGTGCAATTCTTTG 58.911 43.478 0.00 0.00 38.33 2.77
3678 4238 4.783036 CGTATTCGTGCAATTCTTTGTCTG 59.217 41.667 0.00 0.00 35.17 3.51
3691 4251 6.403866 TTCTTTGTCTGTTTGTGGCATAAT 57.596 33.333 0.00 0.00 0.00 1.28
3693 4253 7.517614 TCTTTGTCTGTTTGTGGCATAATTA 57.482 32.000 0.00 0.00 0.00 1.40
3696 4256 4.764308 TGTCTGTTTGTGGCATAATTAGCA 59.236 37.500 0.00 0.69 0.00 3.49
3768 4328 7.172654 TGAATACACGATATACACATGTTGC 57.827 36.000 0.00 0.00 0.00 4.17
3800 4360 3.749088 CGACTTTTGGTTGCATACACCTA 59.251 43.478 7.54 0.00 0.00 3.08
3805 4365 6.717540 ACTTTTGGTTGCATACACCTATTACA 59.282 34.615 7.54 0.00 0.00 2.41
3820 4380 9.197306 ACACCTATTACACATATCTGTTGTCTA 57.803 33.333 0.00 0.00 31.62 2.59
3831 4391 5.551760 ATCTGTTGTCTAAATTCGGCTTG 57.448 39.130 0.00 0.00 0.00 4.01
3846 4406 1.065102 GGCTTGCATGCATCACTACTG 59.935 52.381 23.37 5.76 34.04 2.74
3876 4436 6.053632 ACATGAATCTGAGTTGTACCATGA 57.946 37.500 0.00 0.00 35.47 3.07
3888 4448 3.085533 TGTACCATGAAATTTGGTCGGG 58.914 45.455 3.52 0.00 44.15 5.14
3902 4462 1.972752 TCGGGACCGAACACGATCA 60.973 57.895 11.57 0.00 46.01 2.92
3919 4479 9.469807 AACACGATCATATAAAGACTGAAGATC 57.530 33.333 0.00 0.00 0.00 2.75
3929 4489 3.406764 AGACTGAAGATCAAACAGTGGC 58.593 45.455 18.93 9.47 43.49 5.01
3932 4492 2.414481 CTGAAGATCAAACAGTGGCGAG 59.586 50.000 0.00 0.00 0.00 5.03
3934 4494 2.086054 AGATCAAACAGTGGCGAGTC 57.914 50.000 0.00 0.00 0.00 3.36
3936 4496 0.033504 ATCAAACAGTGGCGAGTCGT 59.966 50.000 15.08 0.00 0.00 4.34
3941 4501 1.734477 CAGTGGCGAGTCGTGAAGG 60.734 63.158 15.08 0.00 0.00 3.46
3981 7321 3.410958 GAAAAGATCGGGCCGAGC 58.589 61.111 35.04 35.04 42.87 5.03
3982 7322 1.449601 GAAAAGATCGGGCCGAGCA 60.450 57.895 40.91 17.96 45.07 4.26
3985 7325 1.305930 AAAGATCGGGCCGAGCAAAC 61.306 55.000 40.91 24.25 45.07 2.93
3993 7333 1.360911 GCCGAGCAAACCCGAAAAA 59.639 52.632 0.00 0.00 0.00 1.94
4015 7355 0.459585 CGAGCGCTTGGGCTTACTTA 60.460 55.000 17.45 0.00 44.93 2.24
4019 7360 1.308998 CGCTTGGGCTTACTTATGGG 58.691 55.000 0.00 0.00 36.09 4.00
4033 7374 7.362920 GCTTACTTATGGGATTCAAACATGTGT 60.363 37.037 0.00 0.00 0.00 3.72
4037 7378 2.109834 TGGGATTCAAACATGTGTCCCT 59.890 45.455 23.03 3.54 44.47 4.20
4043 7947 4.632327 TCAAACATGTGTCCCTGACATA 57.368 40.909 0.00 0.00 44.63 2.29
4150 8054 8.934507 TTTTCGACATTGTTCAAATTTAAGGT 57.065 26.923 0.00 0.00 0.00 3.50
4151 8055 7.922505 TTCGACATTGTTCAAATTTAAGGTG 57.077 32.000 0.00 0.00 0.00 4.00
4153 8057 5.633182 CGACATTGTTCAAATTTAAGGTGGG 59.367 40.000 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.976073 AGGCATACTACCGGCACTGT 60.976 55.000 0.00 0.00 0.00 3.55
7 8 0.178068 CAAGGCATACTACCGGCACT 59.822 55.000 0.00 0.00 0.00 4.40
79 80 2.105821 AGGTGATGAAACCACGGAGAAA 59.894 45.455 0.00 0.00 43.20 2.52
111 112 4.054359 AGGTAGAATGTCAGACAGGAGT 57.946 45.455 9.64 0.00 0.00 3.85
116 117 2.637382 TGGCAAGGTAGAATGTCAGACA 59.363 45.455 5.50 5.50 0.00 3.41
148 149 2.594303 CCGAGCACCCAAGCAACA 60.594 61.111 0.00 0.00 36.85 3.33
157 158 1.064357 TGAAACGAAAAACCGAGCACC 59.936 47.619 0.00 0.00 0.00 5.01
161 162 2.973224 CTGCATGAAACGAAAAACCGAG 59.027 45.455 0.00 0.00 0.00 4.63
181 182 0.972883 GAGACAACAGGAGCAGACCT 59.027 55.000 0.00 0.00 41.43 3.85
267 268 4.988716 TCCAGGCTCGACGGGTGT 62.989 66.667 0.00 0.00 0.00 4.16
271 272 1.084370 GTTTCATCCAGGCTCGACGG 61.084 60.000 0.00 0.00 0.00 4.79
306 307 1.399744 ATAATCTGACTCCGCCGCCA 61.400 55.000 0.00 0.00 0.00 5.69
333 334 3.230134 CCACCAAAGGACCAAAATCAGA 58.770 45.455 0.00 0.00 0.00 3.27
335 336 3.039252 ACCACCAAAGGACCAAAATCA 57.961 42.857 0.00 0.00 0.00 2.57
337 338 4.149598 GACTACCACCAAAGGACCAAAAT 58.850 43.478 0.00 0.00 0.00 1.82
361 362 5.357878 CACCACCATTCTTGTATTATGCTGT 59.642 40.000 0.00 0.00 0.00 4.40
460 462 0.658897 CAAAGGTAACGTGTTGCGGT 59.341 50.000 0.00 0.00 46.52 5.68
490 492 8.535690 AAGTAAAGATACAAAGTGCTCAGTAC 57.464 34.615 0.00 0.00 34.29 2.73
491 493 9.555727 AAAAGTAAAGATACAAAGTGCTCAGTA 57.444 29.630 0.00 0.00 34.29 2.74
492 494 8.345565 CAAAAGTAAAGATACAAAGTGCTCAGT 58.654 33.333 0.00 0.00 34.29 3.41
517 519 7.251994 ACATAACAACAACTTAACGAAAAGCA 58.748 30.769 0.00 0.00 0.00 3.91
536 538 8.391106 GTCATCAACAGGTCAGAATTACATAAC 58.609 37.037 0.00 0.00 0.00 1.89
582 584 5.857822 TTAAACGAAGGCTTAGAAAGAGC 57.142 39.130 14.51 0.00 39.41 4.09
585 587 8.529102 GTTGTTTTTAAACGAAGGCTTAGAAAG 58.471 33.333 14.51 0.00 41.74 2.62
599 601 2.924290 TGCACTGCCGTTGTTTTTAAAC 59.076 40.909 0.00 0.00 39.33 2.01
612 614 3.441572 ACTTTGTAATGAGATGCACTGCC 59.558 43.478 0.00 0.00 0.00 4.85
614 616 6.128553 ACGTTACTTTGTAATGAGATGCACTG 60.129 38.462 14.29 0.00 0.00 3.66
619 621 7.273188 TCGAACGTTACTTTGTAATGAGATG 57.727 36.000 0.00 4.26 0.00 2.90
620 622 6.530534 CCTCGAACGTTACTTTGTAATGAGAT 59.469 38.462 0.00 3.21 0.00 2.75
622 624 5.444218 GCCTCGAACGTTACTTTGTAATGAG 60.444 44.000 0.00 7.62 0.00 2.90
632 634 1.135083 CATCCTGCCTCGAACGTTACT 60.135 52.381 0.00 0.00 0.00 2.24
637 639 2.892425 GCCATCCTGCCTCGAACG 60.892 66.667 0.00 0.00 0.00 3.95
675 677 2.961669 CTACACGCAACGCCAACCC 61.962 63.158 0.00 0.00 0.00 4.11
679 681 1.080366 CTACCTACACGCAACGCCA 60.080 57.895 0.00 0.00 0.00 5.69
681 683 1.262882 GTACTACCTACACGCAACGC 58.737 55.000 0.00 0.00 0.00 4.84
698 700 4.328536 GTCAGTGACCTCTCTCTTCTGTA 58.671 47.826 12.54 0.00 0.00 2.74
703 705 1.202952 ACCGTCAGTGACCTCTCTCTT 60.203 52.381 17.57 0.00 0.00 2.85
704 706 0.402504 ACCGTCAGTGACCTCTCTCT 59.597 55.000 17.57 0.00 0.00 3.10
705 707 2.949826 ACCGTCAGTGACCTCTCTC 58.050 57.895 17.57 0.00 0.00 3.20
720 722 4.742201 CTCGGCAGGACACCACCG 62.742 72.222 13.47 13.47 43.68 4.94
755 759 2.800544 CGCACGAGTTTAATATCCCTGG 59.199 50.000 0.00 0.00 0.00 4.45
757 761 2.159014 TGCGCACGAGTTTAATATCCCT 60.159 45.455 5.66 0.00 0.00 4.20
892 911 2.304092 TGTCACTCACTCACGTACCTT 58.696 47.619 0.00 0.00 0.00 3.50
893 912 1.977056 TGTCACTCACTCACGTACCT 58.023 50.000 0.00 0.00 0.00 3.08
894 913 2.596452 CATGTCACTCACTCACGTACC 58.404 52.381 0.00 0.00 0.00 3.34
895 914 1.986378 GCATGTCACTCACTCACGTAC 59.014 52.381 0.00 0.00 0.00 3.67
896 915 1.886542 AGCATGTCACTCACTCACGTA 59.113 47.619 0.00 0.00 0.00 3.57
897 916 0.676184 AGCATGTCACTCACTCACGT 59.324 50.000 0.00 0.00 0.00 4.49
898 917 1.344458 GAGCATGTCACTCACTCACG 58.656 55.000 0.00 0.00 34.18 4.35
899 918 1.674221 GGGAGCATGTCACTCACTCAC 60.674 57.143 0.00 0.00 34.59 3.51
900 919 0.610174 GGGAGCATGTCACTCACTCA 59.390 55.000 0.00 0.00 34.59 3.41
901 920 0.610174 TGGGAGCATGTCACTCACTC 59.390 55.000 3.22 0.00 38.45 3.51
902 921 0.322975 GTGGGAGCATGTCACTCACT 59.677 55.000 9.23 0.00 38.45 3.41
903 922 0.322975 AGTGGGAGCATGTCACTCAC 59.677 55.000 8.69 8.69 37.16 3.51
904 923 2.764007 AGTGGGAGCATGTCACTCA 58.236 52.632 0.00 0.00 37.16 3.41
905 924 3.450028 GAGTGGGAGCATGTCACTC 57.550 57.895 17.71 17.71 46.66 3.51
906 925 1.557269 GGGAGTGGGAGCATGTCACT 61.557 60.000 11.04 11.04 43.50 3.41
911 930 0.465097 GATGTGGGAGTGGGAGCATG 60.465 60.000 0.00 0.00 0.00 4.06
1082 1115 2.363018 TGCAGTCGAGGAGGAGGG 60.363 66.667 0.00 0.00 0.00 4.30
1135 1168 4.044721 CAGATGCTGCTGGATCCG 57.955 61.111 19.15 7.60 41.22 4.18
1240 1294 7.801104 TCACCAGTTCACCACATACATATTAT 58.199 34.615 0.00 0.00 0.00 1.28
1349 1403 2.581354 GCGCTCTGGATCCTGTGT 59.419 61.111 14.23 0.00 0.00 3.72
1651 1719 7.402640 GTCGTAATTGATGGAGAAGAAATGAC 58.597 38.462 0.00 0.00 0.00 3.06
1672 1740 2.434884 CATGCCGAGCAAGGTCGT 60.435 61.111 18.66 0.00 43.62 4.34
1673 1741 1.091771 ATTCATGCCGAGCAAGGTCG 61.092 55.000 14.11 14.11 43.62 4.79
1674 1742 0.379669 CATTCATGCCGAGCAAGGTC 59.620 55.000 2.68 0.00 43.62 3.85
1740 1808 3.590466 ATTCACCACCCAGGGCAGC 62.590 63.158 4.91 0.00 43.89 5.25
1798 1889 1.274447 GGCAACGGACCAGTACTAGTT 59.726 52.381 0.00 0.00 0.00 2.24
1799 1890 0.893447 GGCAACGGACCAGTACTAGT 59.107 55.000 0.00 0.00 0.00 2.57
1835 1930 4.758251 TGCTGCACACCCGATCCG 62.758 66.667 0.00 0.00 0.00 4.18
2034 2129 2.442236 TGGAAATGGGATGGAAGAGC 57.558 50.000 0.00 0.00 0.00 4.09
2067 2164 1.405463 TCAAGTGAGACGGATCATCGG 59.595 52.381 0.00 0.00 0.00 4.18
2068 2165 2.098280 AGTCAAGTGAGACGGATCATCG 59.902 50.000 0.00 0.00 43.24 3.84
2077 2174 6.293462 GGGTTAATGAACAAGTCAAGTGAGAC 60.293 42.308 0.00 0.00 40.50 3.36
2102 2199 8.532341 CAGATGCAATAAGTTACTACGTACAAG 58.468 37.037 0.00 0.00 0.00 3.16
2134 2231 3.125146 CGTGCATGCAACTACAGTTACAT 59.875 43.478 24.58 2.57 41.34 2.29
2135 2232 2.478514 CGTGCATGCAACTACAGTTACA 59.521 45.455 24.58 0.00 35.94 2.41
2136 2233 2.159707 CCGTGCATGCAACTACAGTTAC 60.160 50.000 24.58 4.64 36.32 2.50
2137 2234 2.073056 CCGTGCATGCAACTACAGTTA 58.927 47.619 24.58 0.00 36.32 2.24
2138 2235 0.874390 CCGTGCATGCAACTACAGTT 59.126 50.000 24.58 0.00 39.12 3.16
2139 2236 0.250295 ACCGTGCATGCAACTACAGT 60.250 50.000 24.58 10.58 0.00 3.55
2140 2237 1.720805 TACCGTGCATGCAACTACAG 58.279 50.000 24.58 9.92 0.00 2.74
2141 2238 2.171341 TTACCGTGCATGCAACTACA 57.829 45.000 24.58 3.79 0.00 2.74
2142 2239 3.546002 TTTTACCGTGCATGCAACTAC 57.454 42.857 24.58 9.13 0.00 2.73
2201 2298 0.247419 GTCGAGATGTGCACGCATTG 60.247 55.000 13.13 4.19 0.00 2.82
2246 2344 0.390735 AGGTTAAACTAGCGGCCGTG 60.391 55.000 28.70 19.18 0.00 4.94
2268 2368 2.489722 GGGTTGACCTCAAATGAAGAGC 59.510 50.000 0.00 0.00 37.63 4.09
2327 2427 3.750130 ACATGCATGGATTCTTCGATAGC 59.250 43.478 29.41 0.00 0.00 2.97
2332 2432 1.335810 CCCACATGCATGGATTCTTCG 59.664 52.381 29.41 2.41 43.02 3.79
2361 2461 5.355910 TCCTTTTTCTGCGGGAATTACATAC 59.644 40.000 0.00 0.00 33.53 2.39
2370 2484 2.649531 TTTCTCCTTTTTCTGCGGGA 57.350 45.000 0.00 0.00 0.00 5.14
2400 2514 0.250295 GCAGCCAAGTGTACAGTCCA 60.250 55.000 3.07 0.00 0.00 4.02
2435 2549 4.654091 ACCCATTATCATTTTTGGAGCG 57.346 40.909 0.00 0.00 0.00 5.03
2445 2561 5.763204 GTCGATTACCACAACCCATTATCAT 59.237 40.000 0.00 0.00 0.00 2.45
2448 2564 4.879545 GTGTCGATTACCACAACCCATTAT 59.120 41.667 0.00 0.00 0.00 1.28
2454 2570 2.735134 GAGTGTGTCGATTACCACAACC 59.265 50.000 8.02 0.92 42.73 3.77
2466 2582 2.085262 CGCTGAGCTGAGTGTGTCG 61.085 63.158 5.49 0.00 0.00 4.35
2559 2675 4.510038 AAACTGTAAGCTTTCATGCAGG 57.490 40.909 3.20 0.00 37.60 4.85
2670 2790 4.101741 AGGATTAGTGGGAAGGAAGAATCG 59.898 45.833 0.00 0.00 0.00 3.34
2680 2800 6.202331 TGATCAGTAGAAGGATTAGTGGGAA 58.798 40.000 0.00 0.00 0.00 3.97
2708 2829 3.905784 GCAGCTGTCAGTTGCTAATTTT 58.094 40.909 28.46 0.00 46.91 1.82
2716 2843 1.848932 ATGCACGCAGCTGTCAGTTG 61.849 55.000 16.64 12.04 45.94 3.16
2744 2871 0.453615 CGTCGCTCTGTCAGTCAGTC 60.454 60.000 0.00 0.00 43.97 3.51
2745 2872 1.576920 CGTCGCTCTGTCAGTCAGT 59.423 57.895 0.00 0.00 43.97 3.41
3224 3353 2.181021 CGCTCGTCGTAGGCCTTT 59.819 61.111 12.58 0.00 0.00 3.11
3305 3434 0.964358 ACACCTCGGCTAACGCTAGT 60.964 55.000 0.00 0.00 43.86 2.57
3306 3435 1.019673 TACACCTCGGCTAACGCTAG 58.980 55.000 0.00 0.00 43.86 3.42
3307 3436 0.734889 GTACACCTCGGCTAACGCTA 59.265 55.000 0.00 0.00 43.86 4.26
3308 3437 1.246056 TGTACACCTCGGCTAACGCT 61.246 55.000 0.00 0.00 43.86 5.07
3309 3438 0.388907 TTGTACACCTCGGCTAACGC 60.389 55.000 0.00 0.00 43.86 4.84
3310 3439 1.336148 TGTTGTACACCTCGGCTAACG 60.336 52.381 0.00 0.00 46.11 3.18
3311 3440 2.443887 TGTTGTACACCTCGGCTAAC 57.556 50.000 0.00 0.00 0.00 2.34
3326 3455 1.772966 GCGTGTCGTTGTTGATTGTTG 59.227 47.619 0.00 0.00 0.00 3.33
3374 3503 3.492421 AAGCGAGGCAAAATGTACATG 57.508 42.857 9.63 0.00 0.00 3.21
3390 3519 0.727398 GATCAAGTCCCCGAAAAGCG 59.273 55.000 0.00 0.00 40.47 4.68
3400 3529 1.586564 CGACCGAGCGATCAAGTCC 60.587 63.158 13.38 0.00 0.00 3.85
3414 3543 0.388649 AGACGTTGCTGATCACGACC 60.389 55.000 10.08 2.55 0.00 4.79
3415 3544 1.125021 CAAGACGTTGCTGATCACGAC 59.875 52.381 10.08 7.73 0.00 4.34
3427 3569 5.056894 ACGCTAGAATTAGACAAGACGTT 57.943 39.130 0.00 0.00 0.00 3.99
3436 3578 7.404985 CGAGTACAACTAACGCTAGAATTAGA 58.595 38.462 16.31 0.00 33.44 2.10
3447 3589 2.924903 TCTGTGCGAGTACAACTAACG 58.075 47.619 0.00 0.00 0.00 3.18
3459 3601 0.865111 CCGATTGTTGTTCTGTGCGA 59.135 50.000 0.00 0.00 0.00 5.10
3466 3608 2.663119 GCTGCAATTCCGATTGTTGTTC 59.337 45.455 0.00 0.00 43.67 3.18
3471 3613 2.161855 TCAAGCTGCAATTCCGATTGT 58.838 42.857 1.02 0.00 43.67 2.71
3478 3620 4.382345 AATTAGGCTCAAGCTGCAATTC 57.618 40.909 1.02 0.00 41.70 2.17
3489 3633 4.280436 TCCTTCGTCAAAATTAGGCTCA 57.720 40.909 0.00 0.00 0.00 4.26
3519 3663 5.935789 TGGTCTTTGGTTTTTATACCTCGAG 59.064 40.000 5.13 5.13 39.04 4.04
3521 3665 6.563222 TTGGTCTTTGGTTTTTATACCTCG 57.437 37.500 0.00 0.00 39.04 4.63
3526 4086 6.771749 TCGGAGTTTGGTCTTTGGTTTTTATA 59.228 34.615 0.00 0.00 0.00 0.98
3533 4093 2.721425 TTCGGAGTTTGGTCTTTGGT 57.279 45.000 0.00 0.00 0.00 3.67
3541 4101 4.335594 GGTCTTTATGGATTCGGAGTTTGG 59.664 45.833 0.00 0.00 0.00 3.28
3546 4106 5.186198 AGTTTGGTCTTTATGGATTCGGAG 58.814 41.667 0.00 0.00 0.00 4.63
3577 4137 7.654022 AGTTTGGTCTTCCAGTTTTGATAAA 57.346 32.000 0.00 0.00 45.22 1.40
3586 4146 4.760204 CCGAAATTAGTTTGGTCTTCCAGT 59.240 41.667 0.00 0.00 45.22 4.00
3600 4160 8.494016 AAGAAGACTAATCCAACCGAAATTAG 57.506 34.615 0.00 0.00 38.41 1.73
3603 4163 5.880887 GGAAGAAGACTAATCCAACCGAAAT 59.119 40.000 0.00 0.00 32.08 2.17
3606 4166 3.197116 GGGAAGAAGACTAATCCAACCGA 59.803 47.826 0.00 0.00 33.48 4.69
3607 4167 3.197983 AGGGAAGAAGACTAATCCAACCG 59.802 47.826 0.00 0.00 33.48 4.44
3636 4196 1.499049 GACCCATCTCGGTTATTCGC 58.501 55.000 0.00 0.00 35.79 4.70
3651 4211 2.277084 AGAATTGCACGAATACGACCC 58.723 47.619 0.00 0.00 42.66 4.46
3653 4213 4.708601 ACAAAGAATTGCACGAATACGAC 58.291 39.130 0.00 0.00 40.34 4.34
3657 4217 5.940192 ACAGACAAAGAATTGCACGAATA 57.060 34.783 0.00 0.00 40.34 1.75
3664 4224 3.245990 GCCACAAACAGACAAAGAATTGC 59.754 43.478 0.00 0.00 40.34 3.56
3674 4234 5.095490 GTGCTAATTATGCCACAAACAGAC 58.905 41.667 6.31 0.00 0.00 3.51
3678 4238 5.519927 GGATTGTGCTAATTATGCCACAAAC 59.480 40.000 20.62 18.61 36.19 2.93
3691 4251 0.988832 AAGACCGGGGATTGTGCTAA 59.011 50.000 6.32 0.00 0.00 3.09
3693 4253 1.201429 AGAAGACCGGGGATTGTGCT 61.201 55.000 6.32 0.00 0.00 4.40
3696 4256 0.546747 TGGAGAAGACCGGGGATTGT 60.547 55.000 6.32 0.00 0.00 2.71
3752 4312 4.570369 TGTTCAGGCAACATGTGTATATCG 59.430 41.667 0.00 0.00 40.29 2.92
3768 4328 2.504367 ACCAAAAGTCGGATGTTCAGG 58.496 47.619 0.00 0.00 0.00 3.86
3778 4338 2.552315 AGGTGTATGCAACCAAAAGTCG 59.448 45.455 8.72 0.00 31.21 4.18
3805 4365 6.349300 AGCCGAATTTAGACAACAGATATGT 58.651 36.000 0.00 0.00 0.00 2.29
3820 4380 1.205179 TGATGCATGCAAGCCGAATTT 59.795 42.857 26.68 4.06 0.00 1.82
3826 4386 1.065102 CAGTAGTGATGCATGCAAGCC 59.935 52.381 26.68 16.86 0.00 4.35
3831 4391 7.889589 TGTATATTACAGTAGTGATGCATGC 57.110 36.000 11.82 11.82 34.06 4.06
3888 4448 6.142480 CAGTCTTTATATGATCGTGTTCGGTC 59.858 42.308 0.00 0.00 46.10 4.79
3902 4462 9.388506 CCACTGTTTGATCTTCAGTCTTTATAT 57.611 33.333 12.48 0.00 39.89 0.86
3919 4479 0.874175 TCACGACTCGCCACTGTTTG 60.874 55.000 0.00 0.00 0.00 2.93
3929 4489 1.156736 ATTTTGGCCTTCACGACTCG 58.843 50.000 3.32 0.00 0.00 4.18
3932 4492 6.779115 AAAAATTATTTTGGCCTTCACGAC 57.221 33.333 3.32 0.00 37.36 4.34
3965 7305 0.608035 TTTGCTCGGCCCGATCTTTT 60.608 50.000 6.16 0.00 34.61 2.27
3993 7333 3.248446 TAAGCCCAAGCGCTCGGTT 62.248 57.895 14.54 16.15 46.67 4.44
3999 7339 0.663153 CCATAAGTAAGCCCAAGCGC 59.337 55.000 0.00 0.00 46.67 5.92
4000 7340 1.134220 TCCCATAAGTAAGCCCAAGCG 60.134 52.381 0.00 0.00 46.67 4.68
4015 7355 3.099141 GGGACACATGTTTGAATCCCAT 58.901 45.455 17.89 0.00 43.94 4.00
4019 7360 3.820467 TGTCAGGGACACATGTTTGAATC 59.180 43.478 0.00 0.00 37.67 2.52
4033 7374 3.941573 GGTTAAAACCGTATGTCAGGGA 58.058 45.455 0.00 0.00 39.66 4.20
4072 7976 9.653287 TGATCGTTTGTAAATTAGACTGAATCT 57.347 29.630 0.00 0.00 41.95 2.40


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

AutoCloner maintained by Alex Coulton.