Multiple sequence alignment - TraesCS7D01G243400

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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 TraesCS7D01G243400 chr7D 100.000 4895 0 0 1 4895 209790086 209794980 0.000000e+00 9040
1 TraesCS7D01G243400 chr7A 93.612 4023 161 54 35 4017 222496909 222500875 0.000000e+00 5917
2 TraesCS7D01G243400 chr7A 95.304 575 20 2 4015 4582 222500970 222501544 0.000000e+00 905
3 TraesCS7D01G243400 chr7B 93.092 2316 114 24 1 2283 191779601 191777299 0.000000e+00 3349
4 TraesCS7D01G243400 chr7B 96.167 1200 39 3 2282 3477 191777195 191775999 0.000000e+00 1954
5 TraesCS7D01G243400 chr7B 94.761 878 37 5 3462 4337 191775940 191775070 0.000000e+00 1358
6 TraesCS7D01G243400 chr7B 86.321 212 21 4 4516 4725 191774963 191774758 1.770000e-54 224
7 TraesCS7D01G243400 chr5A 93.902 328 17 3 1655 1981 256223250 256222925 4.400000e-135 492
8 TraesCS7D01G243400 chr5D 76.800 250 54 4 3527 3774 375191978 375191731 2.380000e-28 137


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 TraesCS7D01G243400 chr7D 209790086 209794980 4894 False 9040.00 9040 100.00000 1 4895 1 chr7D.!!$F1 4894
1 TraesCS7D01G243400 chr7A 222496909 222501544 4635 False 3411.00 5917 94.45800 35 4582 2 chr7A.!!$F1 4547
2 TraesCS7D01G243400 chr7B 191774758 191779601 4843 True 1721.25 3349 92.58525 1 4725 4 chr7B.!!$R1 4724

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
437 459 0.179037 TGCTGGTCTGCTATGCCATC 60.179 55.000 1.84 0.0 0.0 3.51 F
440 462 0.390492 TGGTCTGCTATGCCATCTCG 59.610 55.000 0.00 0.0 0.0 4.04 F
623 658 0.892755 ACATGGACGAGACGCCTAAA 59.107 50.000 0.00 0.0 0.0 1.85 F
2155 2196 1.131638 TGGCCGCATTAGAGAGGATT 58.868 50.000 0.00 0.0 0.0 3.01 F
2867 3025 1.064017 TCCAACTTTTGAGTGCACCCT 60.064 47.619 14.63 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2062 2100 0.680618 TTTGCTTGCCATTGGAGTGG 59.319 50.000 6.95 0.0 42.35 4.00 R
2063 2101 1.342174 AGTTTGCTTGCCATTGGAGTG 59.658 47.619 6.95 0.0 0.00 3.51 R
2475 2625 1.069227 GCAGCCTTCCACAAGTTAACG 60.069 52.381 0.00 0.0 0.00 3.18 R
3678 3917 0.419459 ACCCTCTCCTCTGGACCATT 59.581 55.000 0.00 0.0 0.00 3.16 R
4818 5186 0.107993 AGTGCATGAGACCACCGATG 60.108 55.000 0.00 0.0 32.48 3.84 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
86 91 0.953960 GGACTGGTGGTAGTTTGCGG 60.954 60.000 0.00 0.00 0.00 5.69
88 93 1.001181 GACTGGTGGTAGTTTGCGGTA 59.999 52.381 0.00 0.00 0.00 4.02
112 117 1.452145 TTCACGAGTTTTGCAGCCCC 61.452 55.000 0.00 0.00 0.00 5.80
126 131 2.667199 CCCCGTTGTTCCCGTGAC 60.667 66.667 0.00 0.00 0.00 3.67
238 243 9.760077 GACTTGAATAGTATTAGGAATTTCGGA 57.240 33.333 0.00 0.00 37.17 4.55
239 244 9.765795 ACTTGAATAGTATTAGGAATTTCGGAG 57.234 33.333 0.00 0.00 34.56 4.63
351 356 1.543802 GTTCGATGAACCAATTGGCCA 59.456 47.619 24.79 21.35 36.65 5.36
353 358 2.023673 TCGATGAACCAATTGGCCATC 58.976 47.619 31.18 31.18 41.31 3.51
354 359 1.750206 CGATGAACCAATTGGCCATCA 59.250 47.619 35.05 29.77 43.11 3.07
355 360 2.166050 CGATGAACCAATTGGCCATCAA 59.834 45.455 35.05 20.34 43.11 2.57
382 404 5.762045 CAATTACTGGAGTTGTTCTTGGTG 58.238 41.667 0.00 0.00 0.00 4.17
385 407 4.974645 ACTGGAGTTGTTCTTGGTGATA 57.025 40.909 0.00 0.00 0.00 2.15
386 408 5.304686 ACTGGAGTTGTTCTTGGTGATAA 57.695 39.130 0.00 0.00 0.00 1.75
387 409 5.880901 ACTGGAGTTGTTCTTGGTGATAAT 58.119 37.500 0.00 0.00 0.00 1.28
388 410 6.306987 ACTGGAGTTGTTCTTGGTGATAATT 58.693 36.000 0.00 0.00 0.00 1.40
389 411 6.207417 ACTGGAGTTGTTCTTGGTGATAATTG 59.793 38.462 0.00 0.00 0.00 2.32
390 412 6.068010 TGGAGTTGTTCTTGGTGATAATTGT 58.932 36.000 0.00 0.00 0.00 2.71
391 413 6.549364 TGGAGTTGTTCTTGGTGATAATTGTT 59.451 34.615 0.00 0.00 0.00 2.83
392 414 7.721842 TGGAGTTGTTCTTGGTGATAATTGTTA 59.278 33.333 0.00 0.00 0.00 2.41
393 415 8.237267 GGAGTTGTTCTTGGTGATAATTGTTAG 58.763 37.037 0.00 0.00 0.00 2.34
394 416 8.691661 AGTTGTTCTTGGTGATAATTGTTAGT 57.308 30.769 0.00 0.00 0.00 2.24
395 417 9.787435 AGTTGTTCTTGGTGATAATTGTTAGTA 57.213 29.630 0.00 0.00 0.00 1.82
423 445 2.159517 GGCAACGATTAAGACTTGCTGG 60.160 50.000 11.46 0.00 39.21 4.85
437 459 0.179037 TGCTGGTCTGCTATGCCATC 60.179 55.000 1.84 0.00 0.00 3.51
440 462 0.390492 TGGTCTGCTATGCCATCTCG 59.610 55.000 0.00 0.00 0.00 4.04
460 482 3.005472 TCGTGTGAAGTAGTTAAGCAGCT 59.995 43.478 0.00 0.00 0.00 4.24
464 486 6.090898 CGTGTGAAGTAGTTAAGCAGCTTATT 59.909 38.462 15.81 6.68 0.00 1.40
465 487 7.360101 CGTGTGAAGTAGTTAAGCAGCTTATTT 60.360 37.037 15.81 9.47 0.00 1.40
466 488 8.290325 GTGTGAAGTAGTTAAGCAGCTTATTTT 58.710 33.333 15.81 7.16 0.00 1.82
467 489 8.846211 TGTGAAGTAGTTAAGCAGCTTATTTTT 58.154 29.630 15.81 6.65 0.00 1.94
508 533 8.911918 TGAGAACTTGGCTGTATTTACTTTTA 57.088 30.769 0.00 0.00 0.00 1.52
561 588 1.380112 GTACTCCCGCTGTCCTCCT 60.380 63.158 0.00 0.00 0.00 3.69
564 591 2.680352 TCCCGCTGTCCTCCTCAC 60.680 66.667 0.00 0.00 0.00 3.51
571 598 2.034812 CGCTGTCCTCCTCACTATAACC 59.965 54.545 0.00 0.00 0.00 2.85
572 599 2.034812 GCTGTCCTCCTCACTATAACCG 59.965 54.545 0.00 0.00 0.00 4.44
583 610 6.097839 TCCTCACTATAACCGAGTAGCAAATT 59.902 38.462 0.00 0.00 0.00 1.82
587 614 8.447833 TCACTATAACCGAGTAGCAAATTTTTG 58.552 33.333 0.00 0.00 41.03 2.44
595 630 6.381801 CGAGTAGCAAATTTTTGGATGAAGT 58.618 36.000 5.28 0.00 38.57 3.01
596 631 6.863126 CGAGTAGCAAATTTTTGGATGAAGTT 59.137 34.615 5.28 0.00 38.57 2.66
613 648 9.268268 GGATGAAGTTAAATATAACATGGACGA 57.732 33.333 0.00 0.00 43.20 4.20
623 658 0.892755 ACATGGACGAGACGCCTAAA 59.107 50.000 0.00 0.00 0.00 1.85
680 715 6.073385 CCTTGATTTCGACATCACATCCTATG 60.073 42.308 13.66 0.00 32.68 2.23
762 798 2.607187 CACGTCTTGGAGGTGTGTATC 58.393 52.381 10.87 0.00 41.60 2.24
829 865 5.026038 TCTTCTTCCGACCTGTTTGTTTA 57.974 39.130 0.00 0.00 0.00 2.01
830 866 5.430007 TCTTCTTCCGACCTGTTTGTTTAA 58.570 37.500 0.00 0.00 0.00 1.52
832 868 6.544564 TCTTCTTCCGACCTGTTTGTTTAAAT 59.455 34.615 0.00 0.00 0.00 1.40
857 893 7.479352 TTCCTTTATGCCTGAATTTGAATGA 57.521 32.000 0.00 0.00 0.00 2.57
867 903 8.970020 TGCCTGAATTTGAATGATGTATTACTT 58.030 29.630 0.00 0.00 0.00 2.24
889 925 5.452078 TTTCTTCTGGCATCGACATTTTT 57.548 34.783 0.00 0.00 0.00 1.94
921 957 3.084786 AGTCTTATTTGGACAGGCTTGC 58.915 45.455 0.00 0.00 36.29 4.01
937 973 1.634702 TTGCTTTGCAAACGTGGTTC 58.365 45.000 8.05 0.00 45.96 3.62
955 991 7.874016 ACGTGGTTCTGTAATTATTTGTGTCTA 59.126 33.333 0.00 0.00 0.00 2.59
956 992 8.166706 CGTGGTTCTGTAATTATTTGTGTCTAC 58.833 37.037 0.00 0.00 0.00 2.59
1078 1115 4.389374 TGAACCATCCAGAGTTTCTGTTC 58.611 43.478 5.46 0.00 42.80 3.18
1227 1264 3.859386 GTCAAGTTCAAAACAAGGTGCAG 59.141 43.478 0.00 0.00 0.00 4.41
1431 1468 3.446516 GCAATGAAGAGGCCAAAGAGATT 59.553 43.478 5.01 0.00 0.00 2.40
1455 1492 2.059541 GTGTTAGACGAAGCTCCACAC 58.940 52.381 0.00 0.00 0.00 3.82
1479 1516 3.242804 GCGATCAGAGTACTGGTACTGAC 60.243 52.174 16.78 5.11 45.63 3.51
1988 2026 2.813754 CAATCAACTCCAACCATGACGT 59.186 45.455 0.00 0.00 0.00 4.34
2062 2100 1.514087 CATGCCAGTGCCATGGAAC 59.486 57.895 18.40 17.12 43.57 3.62
2063 2101 1.683365 ATGCCAGTGCCATGGAACC 60.683 57.895 20.15 4.89 43.57 3.62
2155 2196 1.131638 TGGCCGCATTAGAGAGGATT 58.868 50.000 0.00 0.00 0.00 3.01
2215 2256 4.709397 TGGTGGCAGGTAATATTTTCCTTG 59.291 41.667 8.55 6.73 0.00 3.61
2259 2304 4.373156 AACTGGTCTTGCATTCCTAGTT 57.627 40.909 0.00 0.00 0.00 2.24
2269 2314 3.745975 TGCATTCCTAGTTCAGTGTTTCG 59.254 43.478 0.00 0.00 0.00 3.46
2274 2319 3.807622 TCCTAGTTCAGTGTTTCGCAAAG 59.192 43.478 0.00 0.00 0.00 2.77
2288 2438 3.925379 TCGCAAAGAAATAGTCTGCAGA 58.075 40.909 13.74 13.74 36.40 4.26
2297 2447 7.422465 AGAAATAGTCTGCAGAGATTCTCTT 57.578 36.000 18.89 6.76 35.19 2.85
2299 2449 8.413229 AGAAATAGTCTGCAGAGATTCTCTTAC 58.587 37.037 18.89 9.56 35.19 2.34
2412 2562 2.657237 CCGGCAGAAGGTTCGTCT 59.343 61.111 0.00 0.00 0.00 4.18
2475 2625 2.338785 GCAGCAAGGCACCTTCTCC 61.339 63.158 0.00 0.00 33.42 3.71
2556 2706 3.446570 GGGCATGAGTGTGGCTGC 61.447 66.667 0.00 0.00 43.55 5.25
2597 2747 9.739276 AAAACTGGTATTCATTGACATCTCTAA 57.261 29.630 0.00 0.00 0.00 2.10
2647 2805 8.996988 TTCTAATTTGTGTATTTGACGTGTTC 57.003 30.769 0.00 0.00 0.00 3.18
2677 2835 1.471287 CAGGTGATGGAGCAATGTGTG 59.529 52.381 0.00 0.00 0.00 3.82
2867 3025 1.064017 TCCAACTTTTGAGTGCACCCT 60.064 47.619 14.63 0.00 0.00 4.34
2945 3103 6.033831 GTGGTTGAGATCAAAATTATTGTGCG 59.966 38.462 0.00 0.00 37.63 5.34
3072 3234 2.716424 TGACCCTGAGGATGAAGGTTTT 59.284 45.455 0.00 0.00 36.73 2.43
3093 3255 6.773976 TTTGACATAGGAAATGGGAATGAC 57.226 37.500 0.00 0.00 0.00 3.06
3130 3292 5.734503 GCAGCTGAAGCAAAGTCTTTTAAGT 60.735 40.000 20.43 0.00 45.16 2.24
3218 3380 3.490759 GGTCAGTGTCCGCGCATG 61.491 66.667 8.75 0.00 0.00 4.06
3235 3397 2.162408 GCATGGCTCCAGACAAGTTTAC 59.838 50.000 0.00 0.00 36.16 2.01
3264 3426 4.402155 TGTTTTCTGTTGGATTGAGCTGTT 59.598 37.500 0.00 0.00 0.00 3.16
3352 3514 1.138069 TGCAACTTCACTCCTGACGAA 59.862 47.619 0.00 0.00 0.00 3.85
3420 3582 7.732222 ATTCTGAGGTGTTATTTCTCTCTCT 57.268 36.000 0.00 0.00 0.00 3.10
3449 3611 9.965824 CCACAATGTTTTGGGATTATATAGTTC 57.034 33.333 0.00 0.00 38.63 3.01
3644 3883 2.169330 GGAGGAGAAAGTGTCGGTAGT 58.831 52.381 0.00 0.00 0.00 2.73
3678 3917 1.986757 GCTGGACAGGAGAGCCTCA 60.987 63.158 1.01 0.00 44.80 3.86
3711 3950 1.664321 GAGGGTACACCAGCGACGAT 61.664 60.000 0.00 0.00 43.89 3.73
3762 4001 2.383527 CCTGTTCGACAAGAGCGCC 61.384 63.158 2.29 0.00 32.25 6.53
3849 4088 0.108424 CGAGGTTTGAGCTCCTGAGG 60.108 60.000 12.15 0.00 39.44 3.86
3859 4098 4.728780 TCCTGAGGGAGGTATGGC 57.271 61.111 0.00 0.00 43.37 4.40
3860 4099 2.027802 TCCTGAGGGAGGTATGGCT 58.972 57.895 0.00 0.00 43.37 4.75
3970 4212 0.321653 CCCTGGAGAGGTGAAAACCG 60.322 60.000 0.00 0.00 37.73 4.44
4083 4422 8.777578 AGTAGTGTATAGGACATAAATGGACA 57.222 34.615 0.00 0.00 41.14 4.02
4444 4792 1.137282 TGTTTGGCACGAGTGTACAGA 59.863 47.619 0.00 0.00 0.00 3.41
4473 4826 7.177878 AGATCTGGTTGATGGTTTTGATACTT 58.822 34.615 0.00 0.00 35.14 2.24
4596 4949 2.032799 AGCGAGAACAAGATAGAGAGCG 59.967 50.000 0.00 0.00 0.00 5.03
4628 4996 2.106683 GTATCGGTGCCACTGCCAC 61.107 63.158 0.00 0.00 36.33 5.01
4644 5012 4.158394 ACTGCCACATCGCATTTTAGAAAT 59.842 37.500 0.00 0.00 38.30 2.17
4646 5014 5.820131 TGCCACATCGCATTTTAGAAATAG 58.180 37.500 0.00 0.00 32.62 1.73
4647 5015 4.676924 GCCACATCGCATTTTAGAAATAGC 59.323 41.667 0.00 0.00 0.00 2.97
4648 5016 4.905866 CCACATCGCATTTTAGAAATAGCG 59.094 41.667 16.55 16.55 40.52 4.26
4649 5017 5.501715 CACATCGCATTTTAGAAATAGCGT 58.498 37.500 19.33 10.99 40.25 5.07
4650 5018 5.965334 CACATCGCATTTTAGAAATAGCGTT 59.035 36.000 19.33 13.51 40.25 4.84
4651 5019 6.468956 CACATCGCATTTTAGAAATAGCGTTT 59.531 34.615 19.33 11.78 40.25 3.60
4652 5020 7.008266 CACATCGCATTTTAGAAATAGCGTTTT 59.992 33.333 19.33 9.67 40.25 2.43
4653 5021 7.218204 ACATCGCATTTTAGAAATAGCGTTTTC 59.782 33.333 19.33 6.36 40.25 2.29
4654 5022 6.025280 TCGCATTTTAGAAATAGCGTTTTCC 58.975 36.000 19.33 0.00 40.25 3.13
4655 5023 6.027749 CGCATTTTAGAAATAGCGTTTTCCT 58.972 36.000 15.41 0.00 36.47 3.36
4656 5024 6.526674 CGCATTTTAGAAATAGCGTTTTCCTT 59.473 34.615 15.41 0.00 36.47 3.36
4657 5025 7.694784 CGCATTTTAGAAATAGCGTTTTCCTTA 59.305 33.333 15.41 0.00 36.47 2.69
4658 5026 9.010366 GCATTTTAGAAATAGCGTTTTCCTTAG 57.990 33.333 9.82 0.48 36.47 2.18
4697 5065 2.426024 TCTATCGGTACTCAAGCCACAC 59.574 50.000 0.00 0.00 0.00 3.82
4699 5067 0.973632 TCGGTACTCAAGCCACACAT 59.026 50.000 0.00 0.00 0.00 3.21
4701 5069 2.563620 TCGGTACTCAAGCCACACATAA 59.436 45.455 0.00 0.00 0.00 1.90
4702 5070 3.007074 TCGGTACTCAAGCCACACATAAA 59.993 43.478 0.00 0.00 0.00 1.40
4703 5071 3.370978 CGGTACTCAAGCCACACATAAAG 59.629 47.826 0.00 0.00 0.00 1.85
4704 5072 3.127030 GGTACTCAAGCCACACATAAAGC 59.873 47.826 0.00 0.00 0.00 3.51
4705 5073 1.806542 ACTCAAGCCACACATAAAGCG 59.193 47.619 0.00 0.00 0.00 4.68
4711 5079 2.050691 GCCACACATAAAGCGTGTTTG 58.949 47.619 0.00 0.00 45.12 2.93
4725 5093 5.758924 AGCGTGTTTGAAGGATTTTTAGAC 58.241 37.500 0.00 0.00 0.00 2.59
4726 5094 4.915667 GCGTGTTTGAAGGATTTTTAGACC 59.084 41.667 0.00 0.00 0.00 3.85
4727 5095 5.144359 CGTGTTTGAAGGATTTTTAGACCG 58.856 41.667 0.00 0.00 0.00 4.79
4728 5096 5.049954 CGTGTTTGAAGGATTTTTAGACCGA 60.050 40.000 0.00 0.00 0.00 4.69
4729 5097 6.348213 CGTGTTTGAAGGATTTTTAGACCGAT 60.348 38.462 0.00 0.00 0.00 4.18
4730 5098 7.148540 CGTGTTTGAAGGATTTTTAGACCGATA 60.149 37.037 0.00 0.00 0.00 2.92
4731 5099 7.961283 GTGTTTGAAGGATTTTTAGACCGATAC 59.039 37.037 0.00 0.00 0.00 2.24
4732 5100 7.120138 TGTTTGAAGGATTTTTAGACCGATACC 59.880 37.037 0.00 0.00 0.00 2.73
4733 5101 6.555463 TGAAGGATTTTTAGACCGATACCT 57.445 37.500 0.00 0.00 0.00 3.08
4734 5102 6.579865 TGAAGGATTTTTAGACCGATACCTC 58.420 40.000 0.00 0.00 0.00 3.85
4735 5103 5.548181 AGGATTTTTAGACCGATACCTCC 57.452 43.478 0.00 0.00 0.00 4.30
4736 5104 5.217400 AGGATTTTTAGACCGATACCTCCT 58.783 41.667 0.00 0.00 0.00 3.69
4737 5105 5.304871 AGGATTTTTAGACCGATACCTCCTC 59.695 44.000 0.00 0.00 0.00 3.71
4738 5106 5.511031 GGATTTTTAGACCGATACCTCCTCC 60.511 48.000 0.00 0.00 0.00 4.30
4739 5107 2.267174 TTAGACCGATACCTCCTCCG 57.733 55.000 0.00 0.00 0.00 4.63
4740 5108 1.135094 TAGACCGATACCTCCTCCGT 58.865 55.000 0.00 0.00 0.00 4.69
4741 5109 0.179023 AGACCGATACCTCCTCCGTC 60.179 60.000 0.00 0.00 0.00 4.79
4742 5110 1.152798 ACCGATACCTCCTCCGTCC 60.153 63.158 0.00 0.00 0.00 4.79
4743 5111 1.902432 CCGATACCTCCTCCGTCCC 60.902 68.421 0.00 0.00 0.00 4.46
4744 5112 1.152819 CGATACCTCCTCCGTCCCA 60.153 63.158 0.00 0.00 0.00 4.37
4745 5113 0.539901 CGATACCTCCTCCGTCCCAT 60.540 60.000 0.00 0.00 0.00 4.00
4746 5114 1.271762 CGATACCTCCTCCGTCCCATA 60.272 57.143 0.00 0.00 0.00 2.74
4747 5115 2.816712 CGATACCTCCTCCGTCCCATAA 60.817 54.545 0.00 0.00 0.00 1.90
4748 5116 3.442076 GATACCTCCTCCGTCCCATAAT 58.558 50.000 0.00 0.00 0.00 1.28
4749 5117 4.607239 GATACCTCCTCCGTCCCATAATA 58.393 47.826 0.00 0.00 0.00 0.98
4750 5118 3.562108 ACCTCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
4751 5119 3.870559 ACCTCCTCCGTCCCATAATATT 58.129 45.455 0.00 0.00 0.00 1.28
4752 5120 4.240323 ACCTCCTCCGTCCCATAATATTT 58.760 43.478 0.00 0.00 0.00 1.40
4753 5121 5.408824 ACCTCCTCCGTCCCATAATATTTA 58.591 41.667 0.00 0.00 0.00 1.40
4754 5122 6.030082 ACCTCCTCCGTCCCATAATATTTAT 58.970 40.000 0.00 0.00 0.00 1.40
4755 5123 6.070194 ACCTCCTCCGTCCCATAATATTTATG 60.070 42.308 0.00 1.14 0.00 1.90
4756 5124 6.156256 CCTCCTCCGTCCCATAATATTTATGA 59.844 42.308 8.47 0.00 0.00 2.15
4757 5125 7.311046 CCTCCTCCGTCCCATAATATTTATGAA 60.311 40.741 8.47 0.00 0.00 2.57
4758 5126 8.158025 TCCTCCGTCCCATAATATTTATGAAT 57.842 34.615 8.47 0.00 0.00 2.57
4759 5127 8.611257 TCCTCCGTCCCATAATATTTATGAATT 58.389 33.333 8.47 0.00 0.00 2.17
4760 5128 9.899661 CCTCCGTCCCATAATATTTATGAATTA 57.100 33.333 8.47 0.00 0.00 1.40
4792 5160 8.958119 AAAACGCTCTTATGTTATAAGATGGA 57.042 30.769 10.68 3.44 33.61 3.41
4793 5161 8.958119 AAACGCTCTTATGTTATAAGATGGAA 57.042 30.769 10.68 0.00 33.61 3.53
4794 5162 8.594881 AACGCTCTTATGTTATAAGATGGAAG 57.405 34.615 10.68 2.74 33.61 3.46
4795 5163 7.952671 ACGCTCTTATGTTATAAGATGGAAGA 58.047 34.615 10.68 6.53 33.61 2.87
4796 5164 8.421784 ACGCTCTTATGTTATAAGATGGAAGAA 58.578 33.333 10.68 0.00 33.61 2.52
4797 5165 8.920665 CGCTCTTATGTTATAAGATGGAAGAAG 58.079 37.037 10.68 1.45 33.61 2.85
4798 5166 9.771534 GCTCTTATGTTATAAGATGGAAGAAGT 57.228 33.333 10.68 0.00 33.61 3.01
4833 5201 6.624352 AAAATTATCATCGGTGGTCTCATG 57.376 37.500 0.00 0.00 0.00 3.07
4834 5202 2.820059 TATCATCGGTGGTCTCATGC 57.180 50.000 0.00 0.00 0.00 4.06
4835 5203 0.832626 ATCATCGGTGGTCTCATGCA 59.167 50.000 0.00 0.00 0.00 3.96
4836 5204 0.108186 TCATCGGTGGTCTCATGCAC 60.108 55.000 0.00 0.00 0.00 4.57
4837 5205 0.107993 CATCGGTGGTCTCATGCACT 60.108 55.000 0.00 0.00 0.00 4.40
4838 5206 1.136891 CATCGGTGGTCTCATGCACTA 59.863 52.381 0.00 0.00 0.00 2.74
4839 5207 1.485124 TCGGTGGTCTCATGCACTAT 58.515 50.000 0.00 0.00 0.00 2.12
4840 5208 1.831106 TCGGTGGTCTCATGCACTATT 59.169 47.619 0.00 0.00 0.00 1.73
4841 5209 2.236146 TCGGTGGTCTCATGCACTATTT 59.764 45.455 0.00 0.00 0.00 1.40
4842 5210 3.009723 CGGTGGTCTCATGCACTATTTT 58.990 45.455 0.00 0.00 0.00 1.82
4843 5211 3.063997 CGGTGGTCTCATGCACTATTTTC 59.936 47.826 0.00 0.00 0.00 2.29
4844 5212 4.009675 GGTGGTCTCATGCACTATTTTCA 58.990 43.478 0.00 0.00 0.00 2.69
4845 5213 4.458989 GGTGGTCTCATGCACTATTTTCAA 59.541 41.667 0.00 0.00 0.00 2.69
4846 5214 5.392380 GGTGGTCTCATGCACTATTTTCAAG 60.392 44.000 0.00 0.00 0.00 3.02
4847 5215 5.412594 GTGGTCTCATGCACTATTTTCAAGA 59.587 40.000 0.00 0.00 0.00 3.02
4848 5216 6.003326 TGGTCTCATGCACTATTTTCAAGAA 58.997 36.000 0.00 0.00 0.00 2.52
4849 5217 6.489700 TGGTCTCATGCACTATTTTCAAGAAA 59.510 34.615 0.00 0.00 0.00 2.52
4850 5218 7.014134 TGGTCTCATGCACTATTTTCAAGAAAA 59.986 33.333 10.09 10.09 43.48 2.29
4851 5219 7.867403 GGTCTCATGCACTATTTTCAAGAAAAA 59.133 33.333 11.53 0.00 42.71 1.94
4852 5220 8.909671 GTCTCATGCACTATTTTCAAGAAAAAG 58.090 33.333 11.53 11.82 42.71 2.27
4853 5221 7.596248 TCTCATGCACTATTTTCAAGAAAAAGC 59.404 33.333 11.53 12.71 42.71 3.51
4854 5222 7.436118 TCATGCACTATTTTCAAGAAAAAGCT 58.564 30.769 11.53 0.00 42.71 3.74
4855 5223 7.927629 TCATGCACTATTTTCAAGAAAAAGCTT 59.072 29.630 11.53 0.00 42.71 3.74
4856 5224 8.553696 CATGCACTATTTTCAAGAAAAAGCTTT 58.446 29.630 5.69 5.69 42.71 3.51
4857 5225 8.130307 TGCACTATTTTCAAGAAAAAGCTTTC 57.870 30.769 13.10 0.36 42.71 2.62
4858 5226 7.763528 TGCACTATTTTCAAGAAAAAGCTTTCA 59.236 29.630 13.10 0.00 42.99 2.69
4859 5227 8.768019 GCACTATTTTCAAGAAAAAGCTTTCAT 58.232 29.630 13.10 4.55 42.99 2.57
4863 5231 7.538303 TTTTCAAGAAAAAGCTTTCATGACC 57.462 32.000 13.10 0.00 44.64 4.02
4864 5232 5.850557 TCAAGAAAAAGCTTTCATGACCA 57.149 34.783 13.10 0.00 41.79 4.02
4865 5233 6.409524 TCAAGAAAAAGCTTTCATGACCAT 57.590 33.333 13.10 0.00 41.79 3.55
4866 5234 6.819284 TCAAGAAAAAGCTTTCATGACCATT 58.181 32.000 13.10 0.00 41.79 3.16
4867 5235 6.925165 TCAAGAAAAAGCTTTCATGACCATTC 59.075 34.615 13.10 9.74 41.79 2.67
4868 5236 6.409524 AGAAAAAGCTTTCATGACCATTCA 57.590 33.333 13.10 0.00 42.99 2.57
4869 5237 6.218746 AGAAAAAGCTTTCATGACCATTCAC 58.781 36.000 13.10 0.00 42.99 3.18
4870 5238 5.534207 AAAAGCTTTCATGACCATTCACA 57.466 34.783 13.10 0.00 33.38 3.58
4871 5239 4.778534 AAGCTTTCATGACCATTCACAG 57.221 40.909 0.00 0.00 33.38 3.66
4872 5240 3.087031 AGCTTTCATGACCATTCACAGG 58.913 45.455 0.00 0.00 33.38 4.00
4873 5241 2.165030 GCTTTCATGACCATTCACAGGG 59.835 50.000 0.00 0.00 33.38 4.45
4874 5242 2.512692 TTCATGACCATTCACAGGGG 57.487 50.000 0.00 0.00 33.38 4.79
4875 5243 1.371467 TCATGACCATTCACAGGGGT 58.629 50.000 0.00 0.00 37.70 4.95
4876 5244 2.556766 TCATGACCATTCACAGGGGTA 58.443 47.619 0.00 0.00 34.39 3.69
4877 5245 2.916269 TCATGACCATTCACAGGGGTAA 59.084 45.455 0.00 0.00 34.39 2.85
4878 5246 2.871096 TGACCATTCACAGGGGTAAC 57.129 50.000 0.00 0.00 34.39 2.50
4879 5247 2.058705 TGACCATTCACAGGGGTAACA 58.941 47.619 0.00 0.00 34.39 2.41
4880 5248 2.443632 TGACCATTCACAGGGGTAACAA 59.556 45.455 0.00 0.00 34.39 2.83
4881 5249 3.117474 TGACCATTCACAGGGGTAACAAA 60.117 43.478 0.00 0.00 34.39 2.83
4882 5250 3.892588 GACCATTCACAGGGGTAACAAAA 59.107 43.478 0.00 0.00 34.39 2.44
4883 5251 4.290942 ACCATTCACAGGGGTAACAAAAA 58.709 39.130 0.00 0.00 39.74 1.94
4884 5252 4.904853 ACCATTCACAGGGGTAACAAAAAT 59.095 37.500 0.00 0.00 39.74 1.82
4885 5253 5.011635 ACCATTCACAGGGGTAACAAAAATC 59.988 40.000 0.00 0.00 39.74 2.17
4886 5254 5.245977 CCATTCACAGGGGTAACAAAAATCT 59.754 40.000 0.00 0.00 39.74 2.40
4887 5255 6.435904 CCATTCACAGGGGTAACAAAAATCTA 59.564 38.462 0.00 0.00 39.74 1.98
4888 5256 7.362920 CCATTCACAGGGGTAACAAAAATCTAG 60.363 40.741 0.00 0.00 39.74 2.43
4889 5257 5.566469 TCACAGGGGTAACAAAAATCTAGG 58.434 41.667 0.00 0.00 39.74 3.02
4890 5258 5.311121 TCACAGGGGTAACAAAAATCTAGGA 59.689 40.000 0.00 0.00 39.74 2.94
4891 5259 5.648092 CACAGGGGTAACAAAAATCTAGGAG 59.352 44.000 0.00 0.00 39.74 3.69
4892 5260 5.193679 CAGGGGTAACAAAAATCTAGGAGG 58.806 45.833 0.00 0.00 39.74 4.30
4893 5261 4.856182 AGGGGTAACAAAAATCTAGGAGGT 59.144 41.667 0.00 0.00 39.74 3.85
4894 5262 5.315109 AGGGGTAACAAAAATCTAGGAGGTT 59.685 40.000 0.00 0.00 39.74 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 5.011227 AGGAAAACAGAAGGTCAGTCTAGAC 59.989 44.000 15.41 15.41 37.80 2.59
16 17 4.073293 TCAGGAAAACAGAAGGTCAGTC 57.927 45.455 0.00 0.00 0.00 3.51
20 21 3.084786 CCCATCAGGAAAACAGAAGGTC 58.915 50.000 0.00 0.00 38.24 3.85
86 91 2.230864 GCAAAACTCGTGAATGCGTAC 58.769 47.619 0.00 0.00 0.00 3.67
88 93 0.660488 TGCAAAACTCGTGAATGCGT 59.340 45.000 0.00 0.00 39.81 5.24
112 117 0.812412 AAGTGGTCACGGGAACAACG 60.812 55.000 7.16 0.00 43.73 4.10
126 131 1.080569 GCACCGGCAAATCAAGTGG 60.081 57.895 0.00 0.00 40.72 4.00
153 158 1.574702 GGACGACAAGGAAAAGGCGG 61.575 60.000 0.00 0.00 0.00 6.13
154 159 0.882927 TGGACGACAAGGAAAAGGCG 60.883 55.000 0.00 0.00 0.00 5.52
238 243 3.601685 CCAAACCAAACCGCCGCT 61.602 61.111 0.00 0.00 0.00 5.52
239 244 3.433540 AACCAAACCAAACCGCCGC 62.434 57.895 0.00 0.00 0.00 6.53
351 356 5.072741 ACAACTCCAGTAATTGCTGTTGAT 58.927 37.500 23.04 9.80 39.05 2.57
353 358 4.836125 ACAACTCCAGTAATTGCTGTTG 57.164 40.909 20.28 18.90 40.76 3.33
354 359 5.133221 AGAACAACTCCAGTAATTGCTGTT 58.867 37.500 20.28 9.10 34.84 3.16
355 360 4.718961 AGAACAACTCCAGTAATTGCTGT 58.281 39.130 20.28 1.90 34.84 4.40
391 413 9.880157 AGTCTTAATCGTTGCCTAAAATTACTA 57.120 29.630 0.00 0.00 0.00 1.82
392 414 8.788325 AGTCTTAATCGTTGCCTAAAATTACT 57.212 30.769 0.00 0.00 0.00 2.24
393 415 9.274065 CAAGTCTTAATCGTTGCCTAAAATTAC 57.726 33.333 0.00 0.00 0.00 1.89
394 416 7.966204 GCAAGTCTTAATCGTTGCCTAAAATTA 59.034 33.333 5.05 0.00 39.52 1.40
395 417 6.806739 GCAAGTCTTAATCGTTGCCTAAAATT 59.193 34.615 5.05 0.00 39.52 1.82
396 418 6.151144 AGCAAGTCTTAATCGTTGCCTAAAAT 59.849 34.615 10.56 0.00 45.23 1.82
423 445 1.202463 ACACGAGATGGCATAGCAGAC 60.202 52.381 0.00 0.00 0.00 3.51
437 459 3.365220 GCTGCTTAACTACTTCACACGAG 59.635 47.826 0.00 0.00 0.00 4.18
440 462 6.969828 ATAAGCTGCTTAACTACTTCACAC 57.030 37.500 24.34 0.00 29.35 3.82
483 505 7.817418 AAAAGTAAATACAGCCAAGTTCTCA 57.183 32.000 0.00 0.00 0.00 3.27
541 566 1.668101 GGAGGACAGCGGGAGTACTG 61.668 65.000 0.00 0.00 39.86 2.74
547 574 1.859841 TAGTGAGGAGGACAGCGGGA 61.860 60.000 0.00 0.00 0.00 5.14
561 588 8.447833 CAAAAATTTGCTACTCGGTTATAGTGA 58.552 33.333 0.00 0.00 0.00 3.41
564 591 7.981142 TCCAAAAATTTGCTACTCGGTTATAG 58.019 34.615 0.29 0.00 36.86 1.31
571 598 6.381801 ACTTCATCCAAAAATTTGCTACTCG 58.618 36.000 0.29 0.00 36.86 4.18
572 599 9.691362 TTAACTTCATCCAAAAATTTGCTACTC 57.309 29.630 0.29 0.00 36.86 2.59
587 614 9.268268 TCGTCCATGTTATATTTAACTTCATCC 57.732 33.333 7.45 0.00 38.81 3.51
595 630 5.693104 GGCGTCTCGTCCATGTTATATTTAA 59.307 40.000 0.00 0.00 0.00 1.52
596 631 5.010314 AGGCGTCTCGTCCATGTTATATTTA 59.990 40.000 0.00 0.00 28.67 1.40
605 640 1.135083 ACTTTAGGCGTCTCGTCCATG 60.135 52.381 0.00 0.00 28.67 3.66
613 648 4.951094 ACTGATAAGAGACTTTAGGCGTCT 59.049 41.667 0.00 0.00 43.97 4.18
623 658 4.601406 AGGACTCCACTGATAAGAGACT 57.399 45.455 0.00 0.00 0.00 3.24
680 715 6.381801 ACCAAATCGTCATTCTCATTTTCAC 58.618 36.000 0.00 0.00 0.00 3.18
762 798 6.258068 GCTTATACTGGTTTGCAGTAGTAAGG 59.742 42.308 9.05 0.00 38.38 2.69
829 865 9.743581 ATTCAAATTCAGGCATAAAGGAAATTT 57.256 25.926 0.00 0.00 34.72 1.82
830 866 9.169592 CATTCAAATTCAGGCATAAAGGAAATT 57.830 29.630 0.00 0.00 0.00 1.82
832 868 7.905265 TCATTCAAATTCAGGCATAAAGGAAA 58.095 30.769 0.00 0.00 0.00 3.13
857 893 7.011482 GTCGATGCCAGAAGAAAAGTAATACAT 59.989 37.037 0.00 0.00 0.00 2.29
864 900 3.126001 TGTCGATGCCAGAAGAAAAGT 57.874 42.857 0.00 0.00 0.00 2.66
865 901 4.691860 AATGTCGATGCCAGAAGAAAAG 57.308 40.909 0.00 0.00 0.00 2.27
867 903 5.241506 AGAAAAATGTCGATGCCAGAAGAAA 59.758 36.000 0.00 0.00 0.00 2.52
889 925 8.690203 TGTCCAAATAAGACTGAAAAATGAGA 57.310 30.769 0.00 0.00 35.21 3.27
921 957 2.559998 ACAGAACCACGTTTGCAAAG 57.440 45.000 13.26 9.42 0.00 2.77
955 991 5.463051 AATCTGATTCCTGGAGAAATGGT 57.537 39.130 0.00 0.00 38.21 3.55
956 992 6.830324 TGTTAATCTGATTCCTGGAGAAATGG 59.170 38.462 6.10 0.00 38.21 3.16
1227 1264 1.926510 GTGTTGTTTGGTGCTTTCTGC 59.073 47.619 0.00 0.00 43.25 4.26
1332 1369 1.306141 TGATGGAGGGCGAGAAGGT 60.306 57.895 0.00 0.00 0.00 3.50
1431 1468 2.560981 TGGAGCTTCGTCTAACACATCA 59.439 45.455 0.00 0.00 0.00 3.07
1455 1492 2.946329 AGTACCAGTACTCTGATCGCAG 59.054 50.000 4.61 0.00 42.30 5.18
1479 1516 8.845942 TTTCTTCAATATCAGCAATTTCATCG 57.154 30.769 0.00 0.00 0.00 3.84
1509 1546 4.510038 AACTGCTTTGTCATCATCAACC 57.490 40.909 0.00 0.00 0.00 3.77
1677 1714 4.437239 CATGAGTGTACAGCCTAGAAAGG 58.563 47.826 0.00 0.00 46.76 3.11
1988 2026 6.183360 TGTGCACTGCCATTTAAGTTTTTAGA 60.183 34.615 19.41 0.00 0.00 2.10
2062 2100 0.680618 TTTGCTTGCCATTGGAGTGG 59.319 50.000 6.95 0.00 42.35 4.00
2063 2101 1.342174 AGTTTGCTTGCCATTGGAGTG 59.658 47.619 6.95 0.00 0.00 3.51
2071 2112 2.582728 CAAGTTCAGTTTGCTTGCCA 57.417 45.000 0.00 0.00 34.16 4.92
2155 2196 7.775093 ACAATCCGAGAAAATATCCAAGATTCA 59.225 33.333 0.00 0.00 0.00 2.57
2215 2256 2.621668 GGAGCAAGGGATTATATGGCCC 60.622 54.545 0.00 0.00 42.37 5.80
2259 2304 5.758296 AGACTATTTCTTTGCGAAACACTGA 59.242 36.000 0.00 0.00 43.90 3.41
2269 2314 6.315891 AGAATCTCTGCAGACTATTTCTTTGC 59.684 38.462 13.74 3.22 28.96 3.68
2297 2447 7.039504 ACAAATTTAGAGAACAGTAGGTCCGTA 60.040 37.037 0.00 0.00 0.00 4.02
2299 2449 6.164176 ACAAATTTAGAGAACAGTAGGTCCG 58.836 40.000 0.00 0.00 0.00 4.79
2412 2562 1.422402 ACTTTCCGAGCTTTTGGGGTA 59.578 47.619 0.00 0.00 0.00 3.69
2475 2625 1.069227 GCAGCCTTCCACAAGTTAACG 60.069 52.381 0.00 0.00 0.00 3.18
2647 2805 6.596309 TGCTCCATCACCTGATAATAGTAG 57.404 41.667 0.00 0.00 32.63 2.57
2677 2835 0.885196 TTGCAACATCTAAACGGGCC 59.115 50.000 0.00 0.00 0.00 5.80
3072 3234 4.163268 TCGTCATTCCCATTTCCTATGTCA 59.837 41.667 0.00 0.00 0.00 3.58
3093 3255 1.536766 TCAGCTGCACCAATTCTTTCG 59.463 47.619 9.47 0.00 0.00 3.46
3130 3292 5.877012 GGAGATCACTCAGTTCATTAAGCAA 59.123 40.000 0.00 0.00 44.22 3.91
3218 3380 1.270678 ACGGTAAACTTGTCTGGAGCC 60.271 52.381 0.00 0.00 0.00 4.70
3235 3397 4.513692 TCAATCCAACAGAAAACAGTACGG 59.486 41.667 0.00 0.00 0.00 4.02
3264 3426 5.762711 TGATAGACAGTGCAAAAGCTTAACA 59.237 36.000 0.00 0.00 0.00 2.41
3352 3514 1.700042 GGACAGGATCGGGGCAGAAT 61.700 60.000 0.00 0.00 0.00 2.40
3420 3582 7.969690 ATATAATCCCAAAACATTGTGGTGA 57.030 32.000 0.13 0.00 32.60 4.02
3474 3713 2.118228 TGTCTGTTGCGCAAATGTTC 57.882 45.000 26.87 12.78 0.00 3.18
3678 3917 0.419459 ACCCTCTCCTCTGGACCATT 59.581 55.000 0.00 0.00 0.00 3.16
3711 3950 3.437198 GGGAGTCCAGGTCATCTAGATCA 60.437 52.174 12.30 0.00 0.00 2.92
3762 4001 2.281208 TTTGACGGCGAAGGTGGG 60.281 61.111 16.62 0.00 0.00 4.61
3784 4023 1.598130 GAGCAGTGAAAGGCGTGGT 60.598 57.895 0.00 0.00 34.54 4.16
3849 4088 2.423446 CGCTCCAGCCATACCTCC 59.577 66.667 0.00 0.00 37.91 4.30
3970 4212 2.192624 TGCAAAAGCAACTTCTTTCGC 58.807 42.857 0.00 0.00 36.73 4.70
4083 4422 3.099170 CCAGGGGGCCATAGTGCT 61.099 66.667 4.39 0.00 0.00 4.40
4444 4792 6.962182 TCAAAACCATCAACCAGATCTCTAT 58.038 36.000 0.00 0.00 33.72 1.98
4473 4826 1.203038 TCCATTTGCAAGCCCAGAGAA 60.203 47.619 0.00 0.00 0.00 2.87
4596 4949 1.069258 GATACCTACCGCTGCCACC 59.931 63.158 0.00 0.00 0.00 4.61
4628 4996 7.305418 GGAAAACGCTATTTCTAAAATGCGATG 60.305 37.037 22.65 4.66 42.17 3.84
4644 5012 5.464389 GCCGATATTTCTAAGGAAAACGCTA 59.536 40.000 0.00 0.00 43.51 4.26
4646 5014 4.272748 AGCCGATATTTCTAAGGAAAACGC 59.727 41.667 0.00 0.00 43.51 4.84
4647 5015 5.986004 AGCCGATATTTCTAAGGAAAACG 57.014 39.130 0.00 0.00 43.51 3.60
4648 5016 6.972901 CCAAAGCCGATATTTCTAAGGAAAAC 59.027 38.462 0.00 0.00 43.51 2.43
4649 5017 6.887545 TCCAAAGCCGATATTTCTAAGGAAAA 59.112 34.615 0.00 0.00 43.51 2.29
4650 5018 6.419791 TCCAAAGCCGATATTTCTAAGGAAA 58.580 36.000 0.00 0.00 44.26 3.13
4651 5019 5.996644 TCCAAAGCCGATATTTCTAAGGAA 58.003 37.500 0.00 0.00 0.00 3.36
4652 5020 5.623956 TCCAAAGCCGATATTTCTAAGGA 57.376 39.130 0.00 0.00 0.00 3.36
4653 5021 6.712547 AGATTCCAAAGCCGATATTTCTAAGG 59.287 38.462 0.00 0.00 0.00 2.69
4654 5022 7.736447 AGATTCCAAAGCCGATATTTCTAAG 57.264 36.000 0.00 0.00 0.00 2.18
4655 5023 9.436957 GATAGATTCCAAAGCCGATATTTCTAA 57.563 33.333 0.00 0.00 0.00 2.10
4656 5024 7.759886 CGATAGATTCCAAAGCCGATATTTCTA 59.240 37.037 0.00 0.00 39.76 2.10
4657 5025 6.591834 CGATAGATTCCAAAGCCGATATTTCT 59.408 38.462 0.00 0.00 39.76 2.52
4658 5026 6.183360 CCGATAGATTCCAAAGCCGATATTTC 60.183 42.308 0.00 0.00 39.76 2.17
4659 5027 5.643777 CCGATAGATTCCAAAGCCGATATTT 59.356 40.000 0.00 0.00 39.76 1.40
4660 5028 5.178797 CCGATAGATTCCAAAGCCGATATT 58.821 41.667 0.00 0.00 39.76 1.28
4661 5029 4.223032 ACCGATAGATTCCAAAGCCGATAT 59.777 41.667 0.00 0.00 39.76 1.63
4662 5030 3.576982 ACCGATAGATTCCAAAGCCGATA 59.423 43.478 0.00 0.00 39.76 2.92
4663 5031 2.368875 ACCGATAGATTCCAAAGCCGAT 59.631 45.455 0.00 0.00 39.76 4.18
4664 5032 1.760613 ACCGATAGATTCCAAAGCCGA 59.239 47.619 0.00 0.00 39.76 5.54
4697 5065 7.406799 AAAAATCCTTCAAACACGCTTTATG 57.593 32.000 0.00 0.00 0.00 1.90
4699 5067 7.858879 GTCTAAAAATCCTTCAAACACGCTTTA 59.141 33.333 0.00 0.00 0.00 1.85
4701 5069 6.206498 GTCTAAAAATCCTTCAAACACGCTT 58.794 36.000 0.00 0.00 0.00 4.68
4702 5070 5.278315 GGTCTAAAAATCCTTCAAACACGCT 60.278 40.000 0.00 0.00 0.00 5.07
4703 5071 4.915667 GGTCTAAAAATCCTTCAAACACGC 59.084 41.667 0.00 0.00 0.00 5.34
4704 5072 5.049954 TCGGTCTAAAAATCCTTCAAACACG 60.050 40.000 0.00 0.00 0.00 4.49
4705 5073 6.308371 TCGGTCTAAAAATCCTTCAAACAC 57.692 37.500 0.00 0.00 0.00 3.32
4711 5079 5.990386 GGAGGTATCGGTCTAAAAATCCTTC 59.010 44.000 0.00 0.00 0.00 3.46
4725 5093 1.902432 GGGACGGAGGAGGTATCGG 60.902 68.421 0.00 0.00 0.00 4.18
4726 5094 0.539901 ATGGGACGGAGGAGGTATCG 60.540 60.000 0.00 0.00 0.00 2.92
4727 5095 2.599408 TATGGGACGGAGGAGGTATC 57.401 55.000 0.00 0.00 0.00 2.24
4728 5096 3.562108 ATTATGGGACGGAGGAGGTAT 57.438 47.619 0.00 0.00 0.00 2.73
4729 5097 4.687262 ATATTATGGGACGGAGGAGGTA 57.313 45.455 0.00 0.00 0.00 3.08
4730 5098 3.562108 ATATTATGGGACGGAGGAGGT 57.438 47.619 0.00 0.00 0.00 3.85
4731 5099 4.910458 AAATATTATGGGACGGAGGAGG 57.090 45.455 0.00 0.00 0.00 4.30
4732 5100 7.182817 TCATAAATATTATGGGACGGAGGAG 57.817 40.000 9.53 0.00 0.00 3.69
4733 5101 7.562259 TTCATAAATATTATGGGACGGAGGA 57.438 36.000 9.53 0.00 0.00 3.71
4734 5102 8.807948 AATTCATAAATATTATGGGACGGAGG 57.192 34.615 9.53 0.00 0.00 4.30
4754 5122 9.820229 CATAAGAGCGTTTTTAACACTAATTCA 57.180 29.630 0.00 0.00 0.00 2.57
4755 5123 9.821662 ACATAAGAGCGTTTTTAACACTAATTC 57.178 29.630 0.00 0.00 0.00 2.17
4766 5134 9.391006 TCCATCTTATAACATAAGAGCGTTTTT 57.609 29.630 12.69 0.00 37.04 1.94
4767 5135 8.958119 TCCATCTTATAACATAAGAGCGTTTT 57.042 30.769 12.69 0.00 37.04 2.43
4768 5136 8.958119 TTCCATCTTATAACATAAGAGCGTTT 57.042 30.769 12.69 0.00 37.04 3.60
4769 5137 8.421784 TCTTCCATCTTATAACATAAGAGCGTT 58.578 33.333 12.69 0.00 37.04 4.84
4770 5138 7.952671 TCTTCCATCTTATAACATAAGAGCGT 58.047 34.615 12.69 0.00 37.04 5.07
4771 5139 8.818141 TTCTTCCATCTTATAACATAAGAGCG 57.182 34.615 12.69 7.55 37.04 5.03
4772 5140 9.771534 ACTTCTTCCATCTTATAACATAAGAGC 57.228 33.333 12.69 0.00 37.04 4.09
4809 5177 6.460123 GCATGAGACCACCGATGATAATTTTT 60.460 38.462 0.00 0.00 0.00 1.94
4810 5178 5.009010 GCATGAGACCACCGATGATAATTTT 59.991 40.000 0.00 0.00 0.00 1.82
4811 5179 4.516698 GCATGAGACCACCGATGATAATTT 59.483 41.667 0.00 0.00 0.00 1.82
4812 5180 4.067896 GCATGAGACCACCGATGATAATT 58.932 43.478 0.00 0.00 0.00 1.40
4813 5181 3.071457 TGCATGAGACCACCGATGATAAT 59.929 43.478 0.00 0.00 0.00 1.28
4814 5182 2.433970 TGCATGAGACCACCGATGATAA 59.566 45.455 0.00 0.00 0.00 1.75
4815 5183 2.038659 TGCATGAGACCACCGATGATA 58.961 47.619 0.00 0.00 0.00 2.15
4816 5184 0.832626 TGCATGAGACCACCGATGAT 59.167 50.000 0.00 0.00 0.00 2.45
4817 5185 0.108186 GTGCATGAGACCACCGATGA 60.108 55.000 0.00 0.00 0.00 2.92
4818 5186 0.107993 AGTGCATGAGACCACCGATG 60.108 55.000 0.00 0.00 32.48 3.84
4819 5187 1.485124 TAGTGCATGAGACCACCGAT 58.515 50.000 0.00 0.00 32.48 4.18
4820 5188 1.485124 ATAGTGCATGAGACCACCGA 58.515 50.000 0.00 0.00 32.48 4.69
4821 5189 2.315925 AATAGTGCATGAGACCACCG 57.684 50.000 0.00 0.00 32.48 4.94
4822 5190 4.009675 TGAAAATAGTGCATGAGACCACC 58.990 43.478 0.00 0.00 32.48 4.61
4823 5191 5.412594 TCTTGAAAATAGTGCATGAGACCAC 59.587 40.000 0.00 0.00 0.00 4.16
4824 5192 5.559770 TCTTGAAAATAGTGCATGAGACCA 58.440 37.500 0.00 0.00 0.00 4.02
4825 5193 6.500684 TTCTTGAAAATAGTGCATGAGACC 57.499 37.500 0.00 0.00 0.00 3.85
4826 5194 8.801715 TTTTTCTTGAAAATAGTGCATGAGAC 57.198 30.769 9.02 0.00 32.44 3.36
4827 5195 7.596248 GCTTTTTCTTGAAAATAGTGCATGAGA 59.404 33.333 9.02 0.00 36.68 3.27
4828 5196 7.597743 AGCTTTTTCTTGAAAATAGTGCATGAG 59.402 33.333 9.02 2.82 36.68 2.90
4829 5197 7.436118 AGCTTTTTCTTGAAAATAGTGCATGA 58.564 30.769 9.02 0.00 36.68 3.07
4830 5198 7.647907 AGCTTTTTCTTGAAAATAGTGCATG 57.352 32.000 9.02 0.00 36.68 4.06
4831 5199 8.667076 AAAGCTTTTTCTTGAAAATAGTGCAT 57.333 26.923 5.69 3.65 36.68 3.96
4832 5200 7.763528 TGAAAGCTTTTTCTTGAAAATAGTGCA 59.236 29.630 14.05 0.00 36.68 4.57
4833 5201 8.130307 TGAAAGCTTTTTCTTGAAAATAGTGC 57.870 30.769 14.05 10.60 36.68 4.40
4837 5205 9.260002 GGTCATGAAAGCTTTTTCTTGAAAATA 57.740 29.630 14.05 1.58 42.67 1.40
4838 5206 7.769970 TGGTCATGAAAGCTTTTTCTTGAAAAT 59.230 29.630 14.05 0.00 42.67 1.82
4839 5207 7.102346 TGGTCATGAAAGCTTTTTCTTGAAAA 58.898 30.769 14.05 4.61 42.67 2.29
4840 5208 6.638610 TGGTCATGAAAGCTTTTTCTTGAAA 58.361 32.000 14.05 5.19 42.67 2.69
4841 5209 6.219417 TGGTCATGAAAGCTTTTTCTTGAA 57.781 33.333 14.05 0.00 42.67 2.69
4842 5210 5.850557 TGGTCATGAAAGCTTTTTCTTGA 57.149 34.783 14.05 12.15 40.50 3.02
4843 5211 6.702723 TGAATGGTCATGAAAGCTTTTTCTTG 59.297 34.615 14.05 10.04 37.41 3.02
4844 5212 6.703165 GTGAATGGTCATGAAAGCTTTTTCTT 59.297 34.615 14.05 0.00 35.80 2.52
4845 5213 6.183360 TGTGAATGGTCATGAAAGCTTTTTCT 60.183 34.615 14.05 0.00 35.80 2.52
4846 5214 5.984926 TGTGAATGGTCATGAAAGCTTTTTC 59.015 36.000 14.05 10.63 35.80 2.29
4847 5215 5.916318 TGTGAATGGTCATGAAAGCTTTTT 58.084 33.333 14.05 0.29 35.80 1.94
4848 5216 5.510179 CCTGTGAATGGTCATGAAAGCTTTT 60.510 40.000 14.05 0.00 35.80 2.27
4849 5217 4.021719 CCTGTGAATGGTCATGAAAGCTTT 60.022 41.667 12.53 12.53 35.80 3.51
4850 5218 3.508793 CCTGTGAATGGTCATGAAAGCTT 59.491 43.478 0.00 0.00 35.80 3.74
4851 5219 3.087031 CCTGTGAATGGTCATGAAAGCT 58.913 45.455 0.00 0.00 35.80 3.74
4852 5220 2.165030 CCCTGTGAATGGTCATGAAAGC 59.835 50.000 0.00 0.00 35.80 3.51
4853 5221 2.756760 CCCCTGTGAATGGTCATGAAAG 59.243 50.000 0.00 0.00 35.80 2.62
4854 5222 2.109834 ACCCCTGTGAATGGTCATGAAA 59.890 45.455 0.00 0.00 35.80 2.69
4855 5223 1.710244 ACCCCTGTGAATGGTCATGAA 59.290 47.619 0.00 0.00 35.80 2.57
4856 5224 1.371467 ACCCCTGTGAATGGTCATGA 58.629 50.000 0.00 0.00 35.80 3.07
4857 5225 3.016736 GTTACCCCTGTGAATGGTCATG 58.983 50.000 0.00 0.00 35.80 3.07
4858 5226 2.647299 TGTTACCCCTGTGAATGGTCAT 59.353 45.455 0.00 0.00 35.80 3.06
4859 5227 2.058705 TGTTACCCCTGTGAATGGTCA 58.941 47.619 0.00 0.00 33.55 4.02
4860 5228 2.871096 TGTTACCCCTGTGAATGGTC 57.129 50.000 0.00 0.00 33.55 4.02
4861 5229 3.603965 TTTGTTACCCCTGTGAATGGT 57.396 42.857 0.00 0.00 36.15 3.55
4862 5230 4.946478 TTTTTGTTACCCCTGTGAATGG 57.054 40.909 0.00 0.00 0.00 3.16
4863 5231 6.345096 AGATTTTTGTTACCCCTGTGAATG 57.655 37.500 0.00 0.00 0.00 2.67
4864 5232 6.663523 CCTAGATTTTTGTTACCCCTGTGAAT 59.336 38.462 0.00 0.00 0.00 2.57
4865 5233 6.007703 CCTAGATTTTTGTTACCCCTGTGAA 58.992 40.000 0.00 0.00 0.00 3.18
4866 5234 5.311121 TCCTAGATTTTTGTTACCCCTGTGA 59.689 40.000 0.00 0.00 0.00 3.58
4867 5235 5.566469 TCCTAGATTTTTGTTACCCCTGTG 58.434 41.667 0.00 0.00 0.00 3.66
4868 5236 5.281037 CCTCCTAGATTTTTGTTACCCCTGT 60.281 44.000 0.00 0.00 0.00 4.00
4869 5237 5.193679 CCTCCTAGATTTTTGTTACCCCTG 58.806 45.833 0.00 0.00 0.00 4.45
4870 5238 4.856182 ACCTCCTAGATTTTTGTTACCCCT 59.144 41.667 0.00 0.00 0.00 4.79
4871 5239 5.188988 ACCTCCTAGATTTTTGTTACCCC 57.811 43.478 0.00 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.