Multiple sequence alignment - TraesCS7B01G473200

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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 TraesCS7B01G473200 chr7B 100.000 4536 0 0 1 4536 730021797 730026332 0.000000e+00 8377.0
1 TraesCS7B01G473200 chr7B 89.402 1538 131 19 2 1518 729677940 729679466 0.000000e+00 1908.0
2 TraesCS7B01G473200 chr7B 97.595 499 12 0 4038 4536 730033639 730034137 0.000000e+00 856.0
3 TraesCS7B01G473200 chr7B 90.180 499 47 1 4038 4536 231058818 231059314 0.000000e+00 649.0
4 TraesCS7B01G473200 chr7B 95.266 169 8 0 2 170 729642173 729642341 7.480000e-68 268.0
5 TraesCS7B01G473200 chr7B 97.143 140 4 0 31 170 729598614 729598753 2.110000e-58 237.0
6 TraesCS7B01G473200 chr7B 97.101 138 4 0 33 170 729605393 729605530 2.730000e-57 233.0
7 TraesCS7B01G473200 chr7A 91.013 3839 282 35 2 3806 723956301 723960110 0.000000e+00 5120.0
8 TraesCS7B01G473200 chr7A 83.678 870 113 15 2 859 723862187 723863039 0.000000e+00 793.0
9 TraesCS7B01G473200 chr7A 87.459 606 54 13 860 1449 723915096 723915695 0.000000e+00 678.0
10 TraesCS7B01G473200 chr7A 90.741 216 20 0 2 217 723740069 723740284 5.740000e-74 289.0
11 TraesCS7B01G473200 chr7D 92.373 3081 172 35 784 3835 628131326 628134372 0.000000e+00 4329.0
12 TraesCS7B01G473200 chr7D 86.676 743 85 8 4 736 628130595 628131333 0.000000e+00 811.0
13 TraesCS7B01G473200 chr7D 76.961 204 46 1 560 762 26809846 26810049 1.030000e-21 115.0
14 TraesCS7B01G473200 chr7D 91.489 47 3 1 3845 3890 628134348 628134394 3.790000e-06 63.9
15 TraesCS7B01G473200 chr3B 90.656 503 42 4 4038 4536 437929854 437930355 0.000000e+00 664.0
16 TraesCS7B01G473200 chr3B 90.020 501 48 1 4038 4536 437983940 437984440 0.000000e+00 647.0
17 TraesCS7B01G473200 chr3B 90.000 500 46 3 4038 4536 283298439 283297943 1.060000e-180 643.0
18 TraesCS7B01G473200 chr5B 90.400 500 42 5 4038 4536 588993273 588993767 0.000000e+00 652.0
19 TraesCS7B01G473200 chr5B 89.800 500 48 2 4038 4536 588952375 588952872 4.950000e-179 638.0
20 TraesCS7B01G473200 chr2B 90.180 499 47 1 4038 4536 642693632 642694128 0.000000e+00 649.0
21 TraesCS7B01G473200 chrUn 95.750 400 11 2 2014 2413 479428876 479429269 1.380000e-179 640.0
22 TraesCS7B01G473200 chrUn 89.243 502 47 5 4038 4536 76994985 76994488 4.980000e-174 621.0
23 TraesCS7B01G473200 chr1D 73.529 544 107 26 220 732 295132820 295133357 6.030000e-39 172.0
24 TraesCS7B01G473200 chr1D 72.706 436 99 17 307 729 483106790 483106362 1.320000e-25 128.0
25 TraesCS7B01G473200 chr1A 82.286 175 29 2 589 762 410441546 410441719 2.830000e-32 150.0
26 TraesCS7B01G473200 chr2D 76.265 257 49 10 575 828 590083073 590082826 4.760000e-25 126.0
27 TraesCS7B01G473200 chr2A 76.147 218 49 3 568 783 503630243 503630027 1.330000e-20 111.0
28 TraesCS7B01G473200 chr5A 77.596 183 37 4 574 754 537261401 537261581 1.730000e-19 108.0
29 TraesCS7B01G473200 chr4D 92.593 54 4 0 2050 2103 97381287 97381340 1.350000e-10 78.7


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 TraesCS7B01G473200 chr7B 730021797 730026332 4535 False 8377.000000 8377 100.000000 1 4536 1 chr7B.!!$F6 4535
1 TraesCS7B01G473200 chr7B 729677940 729679466 1526 False 1908.000000 1908 89.402000 2 1518 1 chr7B.!!$F5 1516
2 TraesCS7B01G473200 chr7A 723956301 723960110 3809 False 5120.000000 5120 91.013000 2 3806 1 chr7A.!!$F4 3804
3 TraesCS7B01G473200 chr7A 723862187 723863039 852 False 793.000000 793 83.678000 2 859 1 chr7A.!!$F2 857
4 TraesCS7B01G473200 chr7A 723915096 723915695 599 False 678.000000 678 87.459000 860 1449 1 chr7A.!!$F3 589
5 TraesCS7B01G473200 chr7D 628130595 628134394 3799 False 1734.633333 4329 90.179333 4 3890 3 chr7D.!!$F2 3886
6 TraesCS7B01G473200 chr3B 437929854 437930355 501 False 664.000000 664 90.656000 4038 4536 1 chr3B.!!$F1 498
7 TraesCS7B01G473200 chr3B 437983940 437984440 500 False 647.000000 647 90.020000 4038 4536 1 chr3B.!!$F2 498

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
190 192 0.393077 GCGCCTCTAGGGAAATAGCA 59.607 55.0 0.00 0.0 37.23 3.49 F
541 556 0.730265 TTGTTTGTGTGTCGACAGGC 59.270 50.0 20.73 15.0 30.74 4.85 F
1982 2052 0.254178 AGGAAGTTGCTGGCATCGAT 59.746 50.0 0.00 0.0 0.00 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1502 1570 0.098200 TGATCTTCTCGTACACGGCG 59.902 55.0 4.80 4.8 40.29 6.46 R
2491 2561 0.036388 GTGTCCGGATCTTCTTGGCA 60.036 55.0 7.81 0.0 0.00 4.92 R
3715 3804 0.036952 CTGACATGCCACTTCGACCT 60.037 55.0 0.00 0.0 0.00 3.85 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
40 41 4.465305 AGCACCTAACGTGTAAGACCTATT 59.535 41.667 0.00 0.00 44.97 1.73
166 167 3.118519 ACTCAAAAGGTGTACACGGTCTT 60.119 43.478 19.41 13.92 0.00 3.01
190 192 0.393077 GCGCCTCTAGGGAAATAGCA 59.607 55.000 0.00 0.00 37.23 3.49
242 246 4.021925 GCCCCTGTCTGCCTCGTT 62.022 66.667 0.00 0.00 0.00 3.85
281 285 2.264480 CAAGCGTGGTCGATCCCA 59.736 61.111 0.00 0.00 39.71 4.37
384 397 3.074412 GGTGGCTCTCGAAAGATGAAAA 58.926 45.455 0.00 0.00 40.84 2.29
406 419 4.870021 AAGATTCTTCCCACCTAGCATT 57.130 40.909 0.00 0.00 0.00 3.56
416 430 2.159382 CACCTAGCATTCCGTTTGGTT 58.841 47.619 0.00 0.00 31.84 3.67
449 463 4.321899 GCATAGTTGAAGGGCATGTGAAAA 60.322 41.667 0.00 0.00 0.00 2.29
520 535 4.578105 GGATCCACATGAATCTGGTCTTTC 59.422 45.833 6.95 0.00 0.00 2.62
521 536 3.955471 TCCACATGAATCTGGTCTTTCC 58.045 45.455 0.00 0.00 0.00 3.13
522 537 3.588842 TCCACATGAATCTGGTCTTTCCT 59.411 43.478 0.00 0.00 37.07 3.36
523 538 4.043310 TCCACATGAATCTGGTCTTTCCTT 59.957 41.667 0.00 0.00 37.07 3.36
527 542 5.835280 ACATGAATCTGGTCTTTCCTTGTTT 59.165 36.000 0.00 0.00 37.07 2.83
541 556 0.730265 TTGTTTGTGTGTCGACAGGC 59.270 50.000 20.73 15.00 30.74 4.85
566 585 1.927174 CCCGTCTACGCATCTTTTCAG 59.073 52.381 0.00 0.00 38.18 3.02
586 606 1.065109 GGTCGCGGTTGCTGTTTTT 59.935 52.632 6.13 0.00 39.65 1.94
605 626 2.656947 TGGCATTGGTCCTATAAGGC 57.343 50.000 0.00 0.00 34.61 4.35
606 627 1.849692 TGGCATTGGTCCTATAAGGCA 59.150 47.619 0.00 0.00 35.49 4.75
610 631 5.076873 GGCATTGGTCCTATAAGGCATTAA 58.923 41.667 0.00 0.00 35.49 1.40
625 646 3.003897 GGCATTAACACAACGACTTTCCA 59.996 43.478 0.00 0.00 0.00 3.53
634 655 4.025979 CACAACGACTTTCCAACTGTCTAC 60.026 45.833 0.00 0.00 0.00 2.59
660 681 1.796459 CAAGTTTTGCCAAGCATCAGC 59.204 47.619 0.00 0.00 38.76 4.26
778 799 7.894376 ATTTCTGGCATTCATTTTACTGTTG 57.106 32.000 0.00 0.00 0.00 3.33
779 800 6.647334 TTCTGGCATTCATTTTACTGTTGA 57.353 33.333 0.00 0.00 0.00 3.18
803 824 9.010029 TGATTGTGATTGATGATGATGAATAGG 57.990 33.333 0.00 0.00 0.00 2.57
1413 1477 1.153628 CCGCCGATTCCGTCTCTTT 60.154 57.895 0.00 0.00 0.00 2.52
1559 1627 2.125961 GCCCTACTCGGACATCGGT 61.126 63.158 0.00 0.00 39.77 4.69
1594 1663 4.512571 GGTCAAGGAGCAAGTACGTTTTTA 59.487 41.667 0.00 0.00 0.00 1.52
1635 1705 5.221185 CGATCAAATGCCTCCAAGAAATCAT 60.221 40.000 0.00 0.00 0.00 2.45
1637 1707 7.309012 CGATCAAATGCCTCCAAGAAATCATAT 60.309 37.037 0.00 0.00 0.00 1.78
1644 1714 5.452356 GCCTCCAAGAAATCATATTTGTGGG 60.452 44.000 9.92 4.86 0.00 4.61
1671 1741 2.926778 ATGCTGCCTCTGATCTAACC 57.073 50.000 0.00 0.00 0.00 2.85
1979 2049 1.471684 CTCAAGGAAGTTGCTGGCATC 59.528 52.381 0.00 0.00 35.94 3.91
1982 2052 0.254178 AGGAAGTTGCTGGCATCGAT 59.746 50.000 0.00 0.00 0.00 3.59
2136 2206 2.093973 CGGGTCTGTGCTTCTCATTACT 60.094 50.000 0.00 0.00 0.00 2.24
2147 2217 8.855110 TGTGCTTCTCATTACTGGAAATTTTAA 58.145 29.630 0.00 0.00 0.00 1.52
2169 2239 6.446659 AATTTTAGTAACACACAATTGCGC 57.553 33.333 5.05 0.00 0.00 6.09
2261 2331 2.107204 AGAAGCATCCAGAAGTGGTTGT 59.893 45.455 4.78 0.00 45.28 3.32
2323 2393 4.519437 CATCTCTCGCTGGCGCCA 62.519 66.667 30.59 30.59 39.59 5.69
2391 2461 3.707316 AGGTAGAGATGCAGACAAGAGT 58.293 45.455 0.00 0.00 0.00 3.24
2509 2579 0.250234 CTGCCAAGAAGATCCGGACA 59.750 55.000 6.12 0.00 0.00 4.02
2538 2608 3.474570 GAGCCCAGAGGACCGCAT 61.475 66.667 0.00 0.00 33.47 4.73
2584 2654 3.081409 GCCCTTGTCGGCCTCCTA 61.081 66.667 0.00 0.00 43.66 2.94
2617 2687 0.976641 AGAAGATCCAGGACAACGCA 59.023 50.000 0.00 0.00 0.00 5.24
2698 2768 0.107214 ACGCCATCCCGTTGATCATT 60.107 50.000 0.00 0.00 38.47 2.57
2810 2880 3.890926 GGGCCCTGGGAGGTATGC 61.891 72.222 19.27 0.00 31.93 3.14
2935 3005 4.162690 GAGGCCGGCATCGTTCCT 62.163 66.667 30.85 14.42 39.16 3.36
2962 3032 3.625313 TGCTCAAAATTCTCGACAACACA 59.375 39.130 0.00 0.00 0.00 3.72
2968 3038 4.474226 AATTCTCGACAACACAAAGCTC 57.526 40.909 0.00 0.00 0.00 4.09
2984 3054 0.745845 GCTCGGCATGGTTGATGAGT 60.746 55.000 0.00 0.00 33.31 3.41
2985 3055 1.012086 CTCGGCATGGTTGATGAGTG 58.988 55.000 0.00 0.00 33.31 3.51
3020 3090 0.984230 CCTGCTTGGGTCCAACTCTA 59.016 55.000 0.00 0.00 0.00 2.43
3031 3101 1.369091 CCAACTCTACATGCCGTGGC 61.369 60.000 3.30 3.30 42.35 5.01
3258 3328 0.107993 TCTCTGATTCAGCTTGCCCG 60.108 55.000 8.89 0.00 0.00 6.13
3277 3347 1.582502 CGGAAGTGCGAATCGTAGAAC 59.417 52.381 4.07 0.00 43.58 3.01
3307 3377 2.483877 TGCACTGTGGAATTAAAGCTCG 59.516 45.455 10.21 0.00 0.00 5.03
3308 3390 2.159517 GCACTGTGGAATTAAAGCTCGG 60.160 50.000 10.21 0.00 0.00 4.63
3330 3412 5.448632 CGGTCCATACTAAAGCAATGGTTTC 60.449 44.000 14.02 0.00 40.88 2.78
3382 3464 6.552725 AGATGGATAAGAGCAATGTAGACTGA 59.447 38.462 0.00 0.00 0.00 3.41
3509 3591 5.942236 TCATTGATTGAGGAACTGGAAGAAG 59.058 40.000 0.00 0.00 41.55 2.85
3528 3610 6.889595 AGAAGGAGAGAAATGAAGGAGATT 57.110 37.500 0.00 0.00 0.00 2.40
3553 3635 9.567776 TTTACTCTACTTCATTCATTTGTTGGA 57.432 29.630 0.00 0.00 0.00 3.53
3576 3658 7.757624 TGGAACTGAAATTTTGTTGTAAGTGAC 59.242 33.333 12.98 0.54 0.00 3.67
3577 3659 7.044314 GGAACTGAAATTTTGTTGTAAGTGACG 60.044 37.037 12.98 0.00 0.00 4.35
3715 3804 4.953940 AACAGGCCATTTCTTGCTTTAA 57.046 36.364 5.01 0.00 0.00 1.52
3730 3819 2.159517 GCTTTAAGGTCGAAGTGGCATG 60.160 50.000 0.00 0.00 0.00 4.06
3837 3927 9.435688 AAAAAGAACTTACAACAGATGCTTTTT 57.564 25.926 0.00 0.00 37.87 1.94
3890 3980 2.107378 TCTGTGATGGCCCTGTTTTACA 59.893 45.455 0.00 0.00 0.00 2.41
3891 3981 3.091545 CTGTGATGGCCCTGTTTTACAT 58.908 45.455 0.00 0.00 0.00 2.29
3892 3982 3.505386 TGTGATGGCCCTGTTTTACATT 58.495 40.909 0.00 0.00 0.00 2.71
3893 3983 3.257873 TGTGATGGCCCTGTTTTACATTG 59.742 43.478 0.00 0.00 0.00 2.82
3894 3984 3.258123 GTGATGGCCCTGTTTTACATTGT 59.742 43.478 0.00 0.00 0.00 2.71
3895 3985 3.257873 TGATGGCCCTGTTTTACATTGTG 59.742 43.478 0.00 0.00 0.00 3.33
3896 3986 2.672098 TGGCCCTGTTTTACATTGTGT 58.328 42.857 0.00 0.00 0.00 3.72
3897 3987 3.034635 TGGCCCTGTTTTACATTGTGTT 58.965 40.909 0.00 0.00 0.00 3.32
3898 3988 4.215908 TGGCCCTGTTTTACATTGTGTTA 58.784 39.130 0.00 0.00 0.00 2.41
3899 3989 4.038162 TGGCCCTGTTTTACATTGTGTTAC 59.962 41.667 0.00 0.00 0.00 2.50
3900 3990 4.038162 GGCCCTGTTTTACATTGTGTTACA 59.962 41.667 0.00 0.20 0.00 2.41
3901 3991 5.279256 GGCCCTGTTTTACATTGTGTTACAT 60.279 40.000 0.00 0.00 0.00 2.29
3902 3992 5.633182 GCCCTGTTTTACATTGTGTTACATG 59.367 40.000 0.00 0.00 0.00 3.21
3903 3993 6.155827 CCCTGTTTTACATTGTGTTACATGG 58.844 40.000 0.00 3.83 0.00 3.66
3904 3994 6.015856 CCCTGTTTTACATTGTGTTACATGGA 60.016 38.462 0.00 0.00 30.35 3.41
3905 3995 7.429633 CCTGTTTTACATTGTGTTACATGGAA 58.570 34.615 0.00 0.00 0.00 3.53
3906 3996 7.923344 CCTGTTTTACATTGTGTTACATGGAAA 59.077 33.333 0.00 0.00 0.00 3.13
3907 3997 9.307121 CTGTTTTACATTGTGTTACATGGAAAA 57.693 29.630 4.10 4.10 32.40 2.29
3908 3998 9.823647 TGTTTTACATTGTGTTACATGGAAAAT 57.176 25.926 9.79 0.00 34.81 1.82
3935 4025 8.870075 AATACAACAGATTTTAGAAGGAAGCT 57.130 30.769 0.00 0.00 0.00 3.74
3936 4026 8.870075 ATACAACAGATTTTAGAAGGAAGCTT 57.130 30.769 0.00 0.00 0.00 3.74
3937 4027 7.208225 ACAACAGATTTTAGAAGGAAGCTTC 57.792 36.000 18.54 18.54 0.00 3.86
3950 4040 1.457346 AAGCTTCCTTGATGCTTCCG 58.543 50.000 10.40 0.00 45.51 4.30
3951 4041 0.393537 AGCTTCCTTGATGCTTCCGG 60.394 55.000 0.00 0.00 39.48 5.14
3952 4042 1.379642 GCTTCCTTGATGCTTCCGGG 61.380 60.000 0.00 0.00 31.35 5.73
3953 4043 1.378514 TTCCTTGATGCTTCCGGGC 60.379 57.895 0.00 0.00 0.00 6.13
3954 4044 2.830370 CCTTGATGCTTCCGGGCC 60.830 66.667 0.00 0.00 0.00 5.80
3955 4045 2.830370 CTTGATGCTTCCGGGCCC 60.830 66.667 13.57 13.57 0.00 5.80
3956 4046 3.338250 TTGATGCTTCCGGGCCCT 61.338 61.111 22.43 0.00 0.00 5.19
3957 4047 1.983119 CTTGATGCTTCCGGGCCCTA 61.983 60.000 22.43 4.58 0.00 3.53
3958 4048 2.111251 GATGCTTCCGGGCCCTAC 59.889 66.667 22.43 4.74 0.00 3.18
3959 4049 2.690881 ATGCTTCCGGGCCCTACA 60.691 61.111 22.43 10.87 0.00 2.74
3960 4050 2.056906 GATGCTTCCGGGCCCTACAT 62.057 60.000 22.43 15.33 0.00 2.29
3961 4051 2.056906 ATGCTTCCGGGCCCTACATC 62.057 60.000 22.43 6.74 0.00 3.06
3962 4052 2.829592 CTTCCGGGCCCTACATCC 59.170 66.667 22.43 0.00 0.00 3.51
3963 4053 2.770904 TTCCGGGCCCTACATCCC 60.771 66.667 22.43 0.00 39.17 3.85
3964 4054 3.644465 TTCCGGGCCCTACATCCCA 62.644 63.158 22.43 0.00 42.75 4.37
3965 4055 3.093835 CCGGGCCCTACATCCCAA 61.094 66.667 22.43 0.00 42.75 4.12
3966 4056 2.685534 CCGGGCCCTACATCCCAAA 61.686 63.158 22.43 0.00 42.75 3.28
3967 4057 1.453197 CGGGCCCTACATCCCAAAC 60.453 63.158 22.43 0.00 42.75 2.93
3968 4058 1.453197 GGGCCCTACATCCCAAACG 60.453 63.158 17.04 0.00 42.18 3.60
3969 4059 2.119029 GGCCCTACATCCCAAACGC 61.119 63.158 0.00 0.00 0.00 4.84
3970 4060 2.119029 GCCCTACATCCCAAACGCC 61.119 63.158 0.00 0.00 0.00 5.68
3971 4061 1.453197 CCCTACATCCCAAACGCCC 60.453 63.158 0.00 0.00 0.00 6.13
3972 4062 1.301623 CCTACATCCCAAACGCCCA 59.698 57.895 0.00 0.00 0.00 5.36
3973 4063 0.322997 CCTACATCCCAAACGCCCAA 60.323 55.000 0.00 0.00 0.00 4.12
3974 4064 0.808755 CTACATCCCAAACGCCCAAC 59.191 55.000 0.00 0.00 0.00 3.77
3975 4065 0.110678 TACATCCCAAACGCCCAACA 59.889 50.000 0.00 0.00 0.00 3.33
3976 4066 0.757188 ACATCCCAAACGCCCAACAA 60.757 50.000 0.00 0.00 0.00 2.83
3977 4067 0.319469 CATCCCAAACGCCCAACAAC 60.319 55.000 0.00 0.00 0.00 3.32
3978 4068 0.469144 ATCCCAAACGCCCAACAACT 60.469 50.000 0.00 0.00 0.00 3.16
3979 4069 1.067250 CCCAAACGCCCAACAACTG 59.933 57.895 0.00 0.00 0.00 3.16
3980 4070 1.388065 CCCAAACGCCCAACAACTGA 61.388 55.000 0.00 0.00 0.00 3.41
3981 4071 0.457851 CCAAACGCCCAACAACTGAA 59.542 50.000 0.00 0.00 0.00 3.02
3982 4072 1.555477 CAAACGCCCAACAACTGAAC 58.445 50.000 0.00 0.00 0.00 3.18
3983 4073 1.134175 CAAACGCCCAACAACTGAACT 59.866 47.619 0.00 0.00 0.00 3.01
3984 4074 2.335316 AACGCCCAACAACTGAACTA 57.665 45.000 0.00 0.00 0.00 2.24
3985 4075 2.335316 ACGCCCAACAACTGAACTAA 57.665 45.000 0.00 0.00 0.00 2.24
3986 4076 1.944709 ACGCCCAACAACTGAACTAAC 59.055 47.619 0.00 0.00 0.00 2.34
3987 4077 1.944024 CGCCCAACAACTGAACTAACA 59.056 47.619 0.00 0.00 0.00 2.41
3988 4078 2.286772 CGCCCAACAACTGAACTAACAC 60.287 50.000 0.00 0.00 0.00 3.32
3989 4079 2.685897 GCCCAACAACTGAACTAACACA 59.314 45.455 0.00 0.00 0.00 3.72
3990 4080 3.488553 GCCCAACAACTGAACTAACACAC 60.489 47.826 0.00 0.00 0.00 3.82
3991 4081 3.692101 CCCAACAACTGAACTAACACACA 59.308 43.478 0.00 0.00 0.00 3.72
3992 4082 4.338118 CCCAACAACTGAACTAACACACAT 59.662 41.667 0.00 0.00 0.00 3.21
3993 4083 5.505654 CCCAACAACTGAACTAACACACATC 60.506 44.000 0.00 0.00 0.00 3.06
3994 4084 5.296780 CCAACAACTGAACTAACACACATCT 59.703 40.000 0.00 0.00 0.00 2.90
3995 4085 6.183360 CCAACAACTGAACTAACACACATCTT 60.183 38.462 0.00 0.00 0.00 2.40
3996 4086 6.363577 ACAACTGAACTAACACACATCTTG 57.636 37.500 0.00 0.00 0.00 3.02
3997 4087 6.112734 ACAACTGAACTAACACACATCTTGA 58.887 36.000 0.00 0.00 0.00 3.02
3998 4088 6.258727 ACAACTGAACTAACACACATCTTGAG 59.741 38.462 0.00 0.00 0.00 3.02
3999 4089 4.752101 ACTGAACTAACACACATCTTGAGC 59.248 41.667 0.00 0.00 0.00 4.26
4000 4090 4.702831 TGAACTAACACACATCTTGAGCA 58.297 39.130 0.00 0.00 0.00 4.26
4001 4091 5.308014 TGAACTAACACACATCTTGAGCAT 58.692 37.500 0.00 0.00 0.00 3.79
4002 4092 6.463360 TGAACTAACACACATCTTGAGCATA 58.537 36.000 0.00 0.00 0.00 3.14
4003 4093 6.934083 TGAACTAACACACATCTTGAGCATAA 59.066 34.615 0.00 0.00 0.00 1.90
4004 4094 6.974932 ACTAACACACATCTTGAGCATAAG 57.025 37.500 0.00 0.00 0.00 1.73
4005 4095 4.691860 AACACACATCTTGAGCATAAGC 57.308 40.909 0.00 0.00 42.56 3.09
4006 4096 3.678289 ACACACATCTTGAGCATAAGCA 58.322 40.909 0.00 0.00 45.49 3.91
4007 4097 4.267536 ACACACATCTTGAGCATAAGCAT 58.732 39.130 0.00 0.00 45.49 3.79
4008 4098 5.430886 ACACACATCTTGAGCATAAGCATA 58.569 37.500 0.00 0.00 45.49 3.14
4009 4099 6.060136 ACACACATCTTGAGCATAAGCATAT 58.940 36.000 0.00 0.00 45.49 1.78
4010 4100 6.204301 ACACACATCTTGAGCATAAGCATATC 59.796 38.462 0.00 0.00 45.49 1.63
4011 4101 6.427242 CACACATCTTGAGCATAAGCATATCT 59.573 38.462 0.00 0.00 45.49 1.98
4012 4102 6.649973 ACACATCTTGAGCATAAGCATATCTC 59.350 38.462 0.00 0.00 45.49 2.75
4013 4103 6.092396 CACATCTTGAGCATAAGCATATCTCC 59.908 42.308 0.00 0.00 45.49 3.71
4014 4104 5.813513 TCTTGAGCATAAGCATATCTCCA 57.186 39.130 0.00 0.00 45.49 3.86
4015 4105 6.178607 TCTTGAGCATAAGCATATCTCCAA 57.821 37.500 0.00 0.00 45.49 3.53
4016 4106 5.994054 TCTTGAGCATAAGCATATCTCCAAC 59.006 40.000 0.00 0.00 45.49 3.77
4017 4107 5.557576 TGAGCATAAGCATATCTCCAACT 57.442 39.130 0.00 0.00 45.49 3.16
4018 4108 6.670695 TGAGCATAAGCATATCTCCAACTA 57.329 37.500 0.00 0.00 45.49 2.24
4019 4109 6.459066 TGAGCATAAGCATATCTCCAACTAC 58.541 40.000 0.00 0.00 45.49 2.73
4020 4110 5.473931 AGCATAAGCATATCTCCAACTACG 58.526 41.667 0.00 0.00 45.49 3.51
4021 4111 5.011125 AGCATAAGCATATCTCCAACTACGT 59.989 40.000 0.00 0.00 45.49 3.57
4022 4112 5.696724 GCATAAGCATATCTCCAACTACGTT 59.303 40.000 0.00 0.00 41.58 3.99
4023 4113 6.202954 GCATAAGCATATCTCCAACTACGTTT 59.797 38.462 0.00 0.00 41.58 3.60
4024 4114 7.567571 CATAAGCATATCTCCAACTACGTTTG 58.432 38.462 0.00 0.00 0.00 2.93
4025 4115 5.086104 AGCATATCTCCAACTACGTTTGT 57.914 39.130 0.00 0.00 0.00 2.83
4026 4116 5.488341 AGCATATCTCCAACTACGTTTGTT 58.512 37.500 0.00 0.00 0.00 2.83
4027 4117 5.938125 AGCATATCTCCAACTACGTTTGTTT 59.062 36.000 0.00 0.00 0.00 2.83
4028 4118 6.021596 GCATATCTCCAACTACGTTTGTTTG 58.978 40.000 0.00 0.00 0.00 2.93
4029 4119 6.348213 GCATATCTCCAACTACGTTTGTTTGT 60.348 38.462 0.00 0.00 0.00 2.83
4030 4120 7.581476 CATATCTCCAACTACGTTTGTTTGTT 58.419 34.615 0.00 0.00 0.00 2.83
4031 4121 5.883503 TCTCCAACTACGTTTGTTTGTTT 57.116 34.783 0.00 0.00 0.00 2.83
4032 4122 5.632959 TCTCCAACTACGTTTGTTTGTTTG 58.367 37.500 0.00 0.00 0.00 2.93
4033 4123 4.167268 TCCAACTACGTTTGTTTGTTTGC 58.833 39.130 0.00 0.00 0.00 3.68
4034 4124 4.082679 TCCAACTACGTTTGTTTGTTTGCT 60.083 37.500 0.00 0.00 0.00 3.91
4035 4125 4.264380 CCAACTACGTTTGTTTGTTTGCTC 59.736 41.667 0.00 0.00 0.00 4.26
4036 4126 4.957759 ACTACGTTTGTTTGTTTGCTCT 57.042 36.364 0.00 0.00 0.00 4.09
4041 4131 3.002149 CGTTTGTTTGTTTGCTCTTGTCG 60.002 43.478 0.00 0.00 0.00 4.35
4050 4140 0.882927 TGCTCTTGTCGGGGAAAACG 60.883 55.000 0.00 0.00 0.00 3.60
4092 4182 2.703798 CCCTTCTACGTTCGGCGGA 61.704 63.158 7.21 0.00 46.52 5.54
4099 4189 0.664761 TACGTTCGGCGGAGGATTAG 59.335 55.000 15.74 0.00 46.52 1.73
4100 4190 1.318158 ACGTTCGGCGGAGGATTAGT 61.318 55.000 15.74 0.00 46.52 2.24
4101 4191 0.594284 CGTTCGGCGGAGGATTAGTC 60.594 60.000 7.21 0.00 36.85 2.59
4118 4208 2.049156 CGCACGAAGAGCAGGTCA 60.049 61.111 1.66 0.00 46.65 4.02
4128 4218 0.037232 GAGCAGGTCAAGCCGTTAGT 60.037 55.000 0.00 0.00 43.70 2.24
4142 4232 4.708421 AGCCGTTAGTACACAGAGGATTTA 59.292 41.667 0.00 0.00 0.00 1.40
4143 4233 4.802563 GCCGTTAGTACACAGAGGATTTAC 59.197 45.833 0.00 0.00 0.00 2.01
4201 4293 5.661312 AGTCCTGCTTGTCTGGTTATATGTA 59.339 40.000 0.00 0.00 35.49 2.29
4237 4329 2.582498 CTAGCTACGGTGCGTGCC 60.582 66.667 0.00 0.00 41.39 5.01
4251 4343 0.310854 CGTGCCTTGTCCAAAAGTCC 59.689 55.000 0.00 0.00 0.00 3.85
4263 4355 3.583086 TCCAAAAGTCCGAATCCTCTCTT 59.417 43.478 0.00 0.00 0.00 2.85
4268 4360 4.722361 AGTCCGAATCCTCTCTTTGTAC 57.278 45.455 0.00 0.00 0.00 2.90
4288 4380 1.114627 GCCTTGGGCCTCCTTTTATG 58.885 55.000 4.53 0.00 44.06 1.90
4295 4387 1.067213 GGCCTCCTTTTATGCGCAAAA 60.067 47.619 17.11 11.00 0.00 2.44
4296 4388 2.611722 GGCCTCCTTTTATGCGCAAAAA 60.612 45.455 17.11 19.85 0.00 1.94
4305 4397 0.879839 ATGCGCAAAAAGGTTGCCAC 60.880 50.000 17.11 0.00 42.10 5.01
4308 4400 1.489881 CGCAAAAAGGTTGCCACAGC 61.490 55.000 5.53 0.00 42.10 4.40
4400 4492 0.618458 TGTTGCCTATGTGTCCTCCC 59.382 55.000 0.00 0.00 0.00 4.30
4462 4554 1.391157 GCTCCTCCTCGCTCTGACAT 61.391 60.000 0.00 0.00 0.00 3.06
4465 4557 1.514553 CTCCTCGCTCTGACATGCA 59.485 57.895 0.00 0.00 0.00 3.96
4470 4562 0.466963 TCGCTCTGACATGCATCCAT 59.533 50.000 0.00 0.00 0.00 3.41
4506 4598 1.000145 GTGCCAAGCTCGCTAACTAC 59.000 55.000 7.22 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.597217 TTTGCACTTCGGGCCTGG 60.597 61.111 12.87 0.00 0.00 4.45
24 25 9.538508 GTATCCAAATAATAGGTCTTACACGTT 57.461 33.333 0.00 0.00 0.00 3.99
166 167 2.815684 TTTCCCTAGAGGCGCCAGGA 62.816 60.000 31.54 22.11 34.51 3.86
228 231 1.151668 CAGAAAACGAGGCAGACAGG 58.848 55.000 0.00 0.00 0.00 4.00
242 246 4.261801 GCATAGCCCTAAGTTCACAGAAA 58.738 43.478 0.00 0.00 0.00 2.52
274 278 2.768492 GCTGCAAAGGCTGGGATCG 61.768 63.158 0.00 0.00 41.91 3.69
281 285 4.729918 CCTCCCGCTGCAAAGGCT 62.730 66.667 0.00 0.00 41.91 4.58
384 397 4.870021 ATGCTAGGTGGGAAGAATCTTT 57.130 40.909 0.00 0.00 0.00 2.52
397 410 2.159382 CAACCAAACGGAATGCTAGGT 58.841 47.619 0.00 0.00 0.00 3.08
406 419 2.489971 CTAGAAGCACAACCAAACGGA 58.510 47.619 0.00 0.00 0.00 4.69
435 449 4.961438 AGACAAATTTTCACATGCCCTT 57.039 36.364 0.00 0.00 0.00 3.95
449 463 1.068741 GCGAGATCCCCGTAGACAAAT 59.931 52.381 6.92 0.00 0.00 2.32
520 535 1.330521 CCTGTCGACACACAAACAAGG 59.669 52.381 15.76 7.24 0.00 3.61
521 536 1.268032 GCCTGTCGACACACAAACAAG 60.268 52.381 15.76 1.06 0.00 3.16
522 537 0.730265 GCCTGTCGACACACAAACAA 59.270 50.000 15.76 0.00 0.00 2.83
523 538 0.107897 AGCCTGTCGACACACAAACA 60.108 50.000 15.76 0.00 0.00 2.83
527 542 0.529773 GAACAGCCTGTCGACACACA 60.530 55.000 15.76 0.00 0.00 3.72
541 556 0.456221 AGATGCGTAGACGGGAACAG 59.544 55.000 3.97 0.00 40.23 3.16
570 589 1.064946 CCAAAAACAGCAACCGCGA 59.935 52.632 8.23 0.00 45.49 5.87
571 590 2.584967 GCCAAAAACAGCAACCGCG 61.585 57.895 0.00 0.00 45.49 6.46
586 606 1.849692 TGCCTTATAGGACCAATGCCA 59.150 47.619 0.00 0.00 37.67 4.92
605 626 5.681105 CAGTTGGAAAGTCGTTGTGTTAATG 59.319 40.000 0.00 0.00 0.00 1.90
606 627 5.355910 ACAGTTGGAAAGTCGTTGTGTTAAT 59.644 36.000 0.00 0.00 0.00 1.40
610 631 2.676342 GACAGTTGGAAAGTCGTTGTGT 59.324 45.455 0.00 0.00 0.00 3.72
651 672 1.457346 CCCTTTCTTCGCTGATGCTT 58.543 50.000 0.00 0.00 36.97 3.91
660 681 0.457853 TCGTCATCGCCCTTTCTTCG 60.458 55.000 0.00 0.00 36.96 3.79
665 686 1.819632 GCCATCGTCATCGCCCTTT 60.820 57.895 0.00 0.00 36.96 3.11
667 688 4.592192 CGCCATCGTCATCGCCCT 62.592 66.667 0.00 0.00 36.96 5.19
760 781 6.867816 TCACAATCAACAGTAAAATGAATGCC 59.132 34.615 0.00 0.00 29.15 4.40
761 782 7.872163 TCACAATCAACAGTAAAATGAATGC 57.128 32.000 0.00 0.00 29.15 3.56
770 791 8.564509 TCATCATCAATCACAATCAACAGTAA 57.435 30.769 0.00 0.00 0.00 2.24
777 798 9.010029 CCTATTCATCATCATCAATCACAATCA 57.990 33.333 0.00 0.00 0.00 2.57
778 799 9.011095 ACCTATTCATCATCATCAATCACAATC 57.989 33.333 0.00 0.00 0.00 2.67
779 800 8.935614 ACCTATTCATCATCATCAATCACAAT 57.064 30.769 0.00 0.00 0.00 2.71
851 883 1.061253 GAGAAGCGAGGAGACGTCG 59.939 63.158 10.46 9.02 40.50 5.12
1403 1467 0.601558 CCTTGACGGAAAGAGACGGA 59.398 55.000 1.26 0.00 33.16 4.69
1404 1468 0.389948 CCCTTGACGGAAAGAGACGG 60.390 60.000 1.26 0.00 33.16 4.79
1413 1477 2.483547 TCCCATTAATCCCTTGACGGA 58.516 47.619 0.00 0.00 36.02 4.69
1484 1552 4.641645 CGGAACCTGCCCTGCACA 62.642 66.667 0.00 0.00 33.79 4.57
1493 1561 4.728102 TACACGGCGCGGAACCTG 62.728 66.667 22.76 11.61 0.00 4.00
1502 1570 0.098200 TGATCTTCTCGTACACGGCG 59.902 55.000 4.80 4.80 40.29 6.46
1559 1627 1.211212 TCCTTGACCTCGTCGGAGATA 59.789 52.381 0.00 0.00 43.27 1.98
1635 1705 4.157656 GCAGCATTAACAGACCCACAAATA 59.842 41.667 0.00 0.00 0.00 1.40
1637 1707 2.295909 GCAGCATTAACAGACCCACAAA 59.704 45.455 0.00 0.00 0.00 2.83
1644 1714 2.977914 TCAGAGGCAGCATTAACAGAC 58.022 47.619 0.00 0.00 0.00 3.51
1671 1741 1.272423 GCACGCTTTTGCCGTTTTG 59.728 52.632 0.00 0.00 43.93 2.44
1850 1920 4.154347 CGGAGGTCAGCCAGGCTC 62.154 72.222 12.53 0.13 36.40 4.70
1979 2049 2.030946 GCCGAGGATGTTTTTCTCATCG 59.969 50.000 0.00 0.18 43.19 3.84
1982 2052 1.001520 TCGCCGAGGATGTTTTTCTCA 59.998 47.619 0.00 0.00 0.00 3.27
2147 2217 4.615121 CGCGCAATTGTGTGTTACTAAAAT 59.385 37.500 21.58 0.00 37.58 1.82
2149 2219 3.546617 CGCGCAATTGTGTGTTACTAAA 58.453 40.909 21.58 0.00 37.58 1.85
2150 2220 2.096169 CCGCGCAATTGTGTGTTACTAA 60.096 45.455 26.08 0.00 37.58 2.24
2151 2221 1.461512 CCGCGCAATTGTGTGTTACTA 59.538 47.619 26.08 0.00 37.58 1.82
2152 2222 0.237235 CCGCGCAATTGTGTGTTACT 59.763 50.000 26.08 0.00 37.58 2.24
2153 2223 0.727793 CCCGCGCAATTGTGTGTTAC 60.728 55.000 26.08 7.49 37.58 2.50
2154 2224 0.885150 TCCCGCGCAATTGTGTGTTA 60.885 50.000 26.08 13.93 37.58 2.41
2155 2225 1.729470 TTCCCGCGCAATTGTGTGTT 61.729 50.000 26.08 0.00 37.58 3.32
2156 2226 1.729470 TTTCCCGCGCAATTGTGTGT 61.729 50.000 26.08 0.00 37.58 3.72
2169 2239 5.005779 CACTAAGATGAAGACGAATTTCCCG 59.994 44.000 0.00 0.00 0.00 5.14
2212 2282 7.600065 TCTCGTAAGTCTGCAAATAGTAGTTT 58.400 34.615 0.00 0.00 39.48 2.66
2218 2288 5.066634 TCTCCTCTCGTAAGTCTGCAAATAG 59.933 44.000 0.00 0.00 39.48 1.73
2311 2381 1.080569 AAAATTTGGCGCCAGCGAG 60.081 52.632 30.75 0.00 46.35 5.03
2323 2393 7.949434 AGATCAAGTTCTTGAGAGCAAAATTT 58.051 30.769 18.03 0.80 34.02 1.82
2348 2418 2.288666 GTTCTTCTCACACCACTGCAA 58.711 47.619 0.00 0.00 0.00 4.08
2391 2461 2.526304 CTCAACAGGAGGTTCGTCAA 57.474 50.000 0.00 0.00 40.13 3.18
2491 2561 0.036388 GTGTCCGGATCTTCTTGGCA 60.036 55.000 7.81 0.00 0.00 4.92
2509 2579 0.695347 CTGGGCTCTCCTTGGAAAGT 59.305 55.000 0.00 0.00 44.25 2.66
2538 2608 3.676049 GCCATCACTGTCAACGATGAGTA 60.676 47.826 11.14 0.00 39.09 2.59
2584 2654 2.005370 TCTTCTTGTCCGGGTACTGT 57.995 50.000 0.00 0.00 0.00 3.55
2617 2687 0.874607 GGTTGAGCAACGACGTGACT 60.875 55.000 0.00 1.28 42.02 3.41
2689 2759 6.606768 GTTCTTGAGGACTTCAATGATCAAC 58.393 40.000 0.00 0.00 44.48 3.18
2698 2768 0.756294 TGCCGTTCTTGAGGACTTCA 59.244 50.000 0.00 0.00 0.00 3.02
2752 2822 3.181465 CGTCTACCATGGACAGGCTAAAT 60.181 47.826 21.47 0.00 33.73 1.40
2810 2880 0.995024 AGGAGGTCAACCAATGGAGG 59.005 55.000 6.16 0.00 38.89 4.30
2935 3005 2.224079 GTCGAGAATTTTGAGCAGCACA 59.776 45.455 0.00 0.00 0.00 4.57
2962 3032 0.813184 CATCAACCATGCCGAGCTTT 59.187 50.000 0.00 0.00 0.00 3.51
2968 3038 1.430632 GCACTCATCAACCATGCCG 59.569 57.895 0.00 0.00 31.70 5.69
2984 3054 0.341258 AGGAGGAAGATGGAGAGGCA 59.659 55.000 0.00 0.00 0.00 4.75
2985 3055 0.758123 CAGGAGGAAGATGGAGAGGC 59.242 60.000 0.00 0.00 0.00 4.70
3031 3101 1.064946 GCTCTCTGTCCCGATCGTG 59.935 63.158 15.09 1.95 0.00 4.35
3214 3284 0.324285 CCTTCCTCTGTGCTCTGCTT 59.676 55.000 0.00 0.00 0.00 3.91
3258 3328 2.602878 TGTTCTACGATTCGCACTTCC 58.397 47.619 5.86 0.00 0.00 3.46
3277 3347 8.984891 TTTAATTCCACAGTGCATAATTCTTG 57.015 30.769 9.01 0.00 0.00 3.02
3307 3377 5.448632 CGAAACCATTGCTTTAGTATGGACC 60.449 44.000 15.38 0.00 41.05 4.46
3308 3390 5.569413 CGAAACCATTGCTTTAGTATGGAC 58.431 41.667 15.38 8.44 41.05 4.02
3330 3412 3.568538 CAAGACCAAGGAAATTCAAGCG 58.431 45.455 0.00 0.00 0.00 4.68
3356 3438 7.725844 TCAGTCTACATTGCTCTTATCCATCTA 59.274 37.037 0.00 0.00 0.00 1.98
3382 3464 7.828223 GCCATCTATGTAGATTCTCATTCCATT 59.172 37.037 0.00 0.00 40.91 3.16
3481 3563 5.005740 TCCAGTTCCTCAATCAATGAACAG 58.994 41.667 0.00 0.00 39.57 3.16
3509 3591 7.791029 AGAGTAAATCTCCTTCATTTCTCTCC 58.209 38.462 0.00 0.00 43.71 3.71
3528 3610 9.567776 TTCCAACAAATGAATGAAGTAGAGTAA 57.432 29.630 0.00 0.00 0.00 2.24
3553 3635 7.309920 ACGTCACTTACAACAAAATTTCAGTT 58.690 30.769 0.00 0.00 0.00 3.16
3643 3729 1.877443 CCACTGTCCGGACGAAAATTT 59.123 47.619 28.70 5.41 0.00 1.82
3706 3795 2.095718 GCCACTTCGACCTTAAAGCAAG 60.096 50.000 0.00 0.00 0.00 4.01
3715 3804 0.036952 CTGACATGCCACTTCGACCT 60.037 55.000 0.00 0.00 0.00 3.85
3730 3819 3.412237 TGCCTAGTAAACCAACCTGAC 57.588 47.619 0.00 0.00 0.00 3.51
3839 3929 7.008810 GCATCTGTTGTACGTTTTCTTCAAAAA 59.991 33.333 0.00 0.00 33.17 1.94
3840 3930 6.470877 GCATCTGTTGTACGTTTTCTTCAAAA 59.529 34.615 0.00 0.00 0.00 2.44
3841 3931 5.968848 GCATCTGTTGTACGTTTTCTTCAAA 59.031 36.000 0.00 0.00 0.00 2.69
3842 3932 5.295787 AGCATCTGTTGTACGTTTTCTTCAA 59.704 36.000 0.00 0.00 0.00 2.69
3843 3933 4.814234 AGCATCTGTTGTACGTTTTCTTCA 59.186 37.500 0.00 0.00 0.00 3.02
3844 3934 5.344207 AGCATCTGTTGTACGTTTTCTTC 57.656 39.130 0.00 0.00 0.00 2.87
3845 3935 5.751243 AAGCATCTGTTGTACGTTTTCTT 57.249 34.783 0.00 0.00 0.00 2.52
3846 3936 6.874134 AGATAAGCATCTGTTGTACGTTTTCT 59.126 34.615 0.00 0.00 40.15 2.52
3847 3937 7.061752 AGATAAGCATCTGTTGTACGTTTTC 57.938 36.000 0.00 0.00 40.15 2.29
3909 3999 9.301897 AGCTTCCTTCTAAAATCTGTTGTATTT 57.698 29.630 0.00 0.00 0.00 1.40
3910 4000 8.870075 AGCTTCCTTCTAAAATCTGTTGTATT 57.130 30.769 0.00 0.00 0.00 1.89
3911 4001 8.870075 AAGCTTCCTTCTAAAATCTGTTGTAT 57.130 30.769 0.00 0.00 0.00 2.29
3912 4002 7.390718 GGAAGCTTCCTTCTAAAATCTGTTGTA 59.609 37.037 33.98 0.00 45.44 2.41
3913 4003 6.207614 GGAAGCTTCCTTCTAAAATCTGTTGT 59.792 38.462 33.98 0.00 45.44 3.32
3914 4004 6.616017 GGAAGCTTCCTTCTAAAATCTGTTG 58.384 40.000 33.98 0.00 45.44 3.33
3915 4005 6.825944 GGAAGCTTCCTTCTAAAATCTGTT 57.174 37.500 33.98 0.00 45.44 3.16
3931 4021 1.457346 CGGAAGCATCAAGGAAGCTT 58.543 50.000 8.26 8.26 46.83 3.74
3932 4022 0.393537 CCGGAAGCATCAAGGAAGCT 60.394 55.000 0.00 0.00 38.27 3.74
3933 4023 1.379642 CCCGGAAGCATCAAGGAAGC 61.380 60.000 0.73 0.00 0.00 3.86
3934 4024 1.379642 GCCCGGAAGCATCAAGGAAG 61.380 60.000 0.73 0.00 0.00 3.46
3935 4025 1.378514 GCCCGGAAGCATCAAGGAA 60.379 57.895 0.73 0.00 0.00 3.36
3936 4026 2.272146 GCCCGGAAGCATCAAGGA 59.728 61.111 0.73 0.00 0.00 3.36
3937 4027 2.830370 GGCCCGGAAGCATCAAGG 60.830 66.667 0.73 0.00 0.00 3.61
3938 4028 1.983119 TAGGGCCCGGAAGCATCAAG 61.983 60.000 18.44 0.00 0.00 3.02
3939 4029 1.998438 TAGGGCCCGGAAGCATCAA 60.998 57.895 18.44 0.00 0.00 2.57
3940 4030 2.366301 TAGGGCCCGGAAGCATCA 60.366 61.111 18.44 0.00 0.00 3.07
3941 4031 2.056906 ATGTAGGGCCCGGAAGCATC 62.057 60.000 18.44 2.48 0.00 3.91
3942 4032 2.056906 GATGTAGGGCCCGGAAGCAT 62.057 60.000 18.44 16.74 0.00 3.79
3943 4033 2.690881 ATGTAGGGCCCGGAAGCA 60.691 61.111 18.44 12.50 0.00 3.91
3944 4034 2.111251 GATGTAGGGCCCGGAAGC 59.889 66.667 18.44 4.39 0.00 3.86
3945 4035 2.819284 GGGATGTAGGGCCCGGAAG 61.819 68.421 18.44 0.00 34.00 3.46
3946 4036 2.770904 GGGATGTAGGGCCCGGAA 60.771 66.667 18.44 5.87 34.00 4.30
3950 4040 1.453197 CGTTTGGGATGTAGGGCCC 60.453 63.158 16.46 16.46 44.93 5.80
3951 4041 2.119029 GCGTTTGGGATGTAGGGCC 61.119 63.158 0.00 0.00 0.00 5.80
3952 4042 2.119029 GGCGTTTGGGATGTAGGGC 61.119 63.158 0.00 0.00 0.00 5.19
3953 4043 1.453197 GGGCGTTTGGGATGTAGGG 60.453 63.158 0.00 0.00 0.00 3.53
3954 4044 0.322997 TTGGGCGTTTGGGATGTAGG 60.323 55.000 0.00 0.00 0.00 3.18
3955 4045 0.808755 GTTGGGCGTTTGGGATGTAG 59.191 55.000 0.00 0.00 0.00 2.74
3956 4046 0.110678 TGTTGGGCGTTTGGGATGTA 59.889 50.000 0.00 0.00 0.00 2.29
3957 4047 0.757188 TTGTTGGGCGTTTGGGATGT 60.757 50.000 0.00 0.00 0.00 3.06
3958 4048 0.319469 GTTGTTGGGCGTTTGGGATG 60.319 55.000 0.00 0.00 0.00 3.51
3959 4049 0.469144 AGTTGTTGGGCGTTTGGGAT 60.469 50.000 0.00 0.00 0.00 3.85
3960 4050 1.076632 AGTTGTTGGGCGTTTGGGA 60.077 52.632 0.00 0.00 0.00 4.37
3961 4051 1.067250 CAGTTGTTGGGCGTTTGGG 59.933 57.895 0.00 0.00 0.00 4.12
3962 4052 0.457851 TTCAGTTGTTGGGCGTTTGG 59.542 50.000 0.00 0.00 0.00 3.28
3963 4053 1.134175 AGTTCAGTTGTTGGGCGTTTG 59.866 47.619 0.00 0.00 0.00 2.93
3964 4054 1.470051 AGTTCAGTTGTTGGGCGTTT 58.530 45.000 0.00 0.00 0.00 3.60
3965 4055 2.335316 TAGTTCAGTTGTTGGGCGTT 57.665 45.000 0.00 0.00 0.00 4.84
3966 4056 1.944709 GTTAGTTCAGTTGTTGGGCGT 59.055 47.619 0.00 0.00 0.00 5.68
3967 4057 1.944024 TGTTAGTTCAGTTGTTGGGCG 59.056 47.619 0.00 0.00 0.00 6.13
3968 4058 2.685897 TGTGTTAGTTCAGTTGTTGGGC 59.314 45.455 0.00 0.00 0.00 5.36
3969 4059 3.692101 TGTGTGTTAGTTCAGTTGTTGGG 59.308 43.478 0.00 0.00 0.00 4.12
3970 4060 4.955925 TGTGTGTTAGTTCAGTTGTTGG 57.044 40.909 0.00 0.00 0.00 3.77
3971 4061 6.363577 AGATGTGTGTTAGTTCAGTTGTTG 57.636 37.500 0.00 0.00 0.00 3.33
3972 4062 6.597672 TCAAGATGTGTGTTAGTTCAGTTGTT 59.402 34.615 0.00 0.00 0.00 2.83
3973 4063 6.112734 TCAAGATGTGTGTTAGTTCAGTTGT 58.887 36.000 0.00 0.00 0.00 3.32
3974 4064 6.603237 TCAAGATGTGTGTTAGTTCAGTTG 57.397 37.500 0.00 0.00 0.00 3.16
3975 4065 5.237344 GCTCAAGATGTGTGTTAGTTCAGTT 59.763 40.000 0.00 0.00 0.00 3.16
3976 4066 4.752101 GCTCAAGATGTGTGTTAGTTCAGT 59.248 41.667 0.00 0.00 0.00 3.41
3977 4067 4.751600 TGCTCAAGATGTGTGTTAGTTCAG 59.248 41.667 0.00 0.00 0.00 3.02
3978 4068 4.702831 TGCTCAAGATGTGTGTTAGTTCA 58.297 39.130 0.00 0.00 0.00 3.18
3979 4069 5.869753 ATGCTCAAGATGTGTGTTAGTTC 57.130 39.130 0.00 0.00 0.00 3.01
3980 4070 6.128172 GCTTATGCTCAAGATGTGTGTTAGTT 60.128 38.462 2.50 0.00 36.03 2.24
3981 4071 5.352569 GCTTATGCTCAAGATGTGTGTTAGT 59.647 40.000 2.50 0.00 36.03 2.24
3982 4072 5.352293 TGCTTATGCTCAAGATGTGTGTTAG 59.648 40.000 1.96 0.00 40.48 2.34
3983 4073 5.244755 TGCTTATGCTCAAGATGTGTGTTA 58.755 37.500 1.96 0.00 40.48 2.41
3984 4074 4.074259 TGCTTATGCTCAAGATGTGTGTT 58.926 39.130 1.96 0.00 40.48 3.32
3985 4075 3.678289 TGCTTATGCTCAAGATGTGTGT 58.322 40.909 1.96 0.00 40.48 3.72
3986 4076 4.895224 ATGCTTATGCTCAAGATGTGTG 57.105 40.909 1.96 0.00 40.48 3.82
3987 4077 6.531923 AGATATGCTTATGCTCAAGATGTGT 58.468 36.000 1.96 0.00 40.48 3.72
3988 4078 6.092396 GGAGATATGCTTATGCTCAAGATGTG 59.908 42.308 14.86 0.00 40.48 3.21
3989 4079 6.171921 GGAGATATGCTTATGCTCAAGATGT 58.828 40.000 14.86 0.00 40.48 3.06
3990 4080 6.171213 TGGAGATATGCTTATGCTCAAGATG 58.829 40.000 14.86 0.00 40.48 2.90
3991 4081 6.370186 TGGAGATATGCTTATGCTCAAGAT 57.630 37.500 14.86 0.00 40.48 2.40
3992 4082 5.813513 TGGAGATATGCTTATGCTCAAGA 57.186 39.130 14.86 0.00 40.48 3.02
3993 4083 5.996513 AGTTGGAGATATGCTTATGCTCAAG 59.003 40.000 14.86 0.00 40.48 3.02
3994 4084 5.933617 AGTTGGAGATATGCTTATGCTCAA 58.066 37.500 14.86 6.68 40.48 3.02
3995 4085 5.557576 AGTTGGAGATATGCTTATGCTCA 57.442 39.130 14.86 0.00 40.48 4.26
3996 4086 5.574830 CGTAGTTGGAGATATGCTTATGCTC 59.425 44.000 1.96 4.28 40.48 4.26
3997 4087 5.011125 ACGTAGTTGGAGATATGCTTATGCT 59.989 40.000 1.96 0.00 37.78 3.79
3998 4088 5.230942 ACGTAGTTGGAGATATGCTTATGC 58.769 41.667 0.00 0.00 37.78 3.14
4016 4106 5.092781 ACAAGAGCAAACAAACAAACGTAG 58.907 37.500 0.00 0.00 0.00 3.51
4017 4107 5.049398 ACAAGAGCAAACAAACAAACGTA 57.951 34.783 0.00 0.00 0.00 3.57
4018 4108 3.908213 ACAAGAGCAAACAAACAAACGT 58.092 36.364 0.00 0.00 0.00 3.99
4019 4109 3.002149 CGACAAGAGCAAACAAACAAACG 60.002 43.478 0.00 0.00 0.00 3.60
4020 4110 3.303229 CCGACAAGAGCAAACAAACAAAC 59.697 43.478 0.00 0.00 0.00 2.93
4021 4111 3.506810 CCGACAAGAGCAAACAAACAAA 58.493 40.909 0.00 0.00 0.00 2.83
4022 4112 2.159310 CCCGACAAGAGCAAACAAACAA 60.159 45.455 0.00 0.00 0.00 2.83
4023 4113 1.403679 CCCGACAAGAGCAAACAAACA 59.596 47.619 0.00 0.00 0.00 2.83
4024 4114 1.269051 CCCCGACAAGAGCAAACAAAC 60.269 52.381 0.00 0.00 0.00 2.93
4025 4115 1.028905 CCCCGACAAGAGCAAACAAA 58.971 50.000 0.00 0.00 0.00 2.83
4026 4116 0.181587 TCCCCGACAAGAGCAAACAA 59.818 50.000 0.00 0.00 0.00 2.83
4027 4117 0.181587 TTCCCCGACAAGAGCAAACA 59.818 50.000 0.00 0.00 0.00 2.83
4028 4118 1.314730 TTTCCCCGACAAGAGCAAAC 58.685 50.000 0.00 0.00 0.00 2.93
4029 4119 1.679153 GTTTTCCCCGACAAGAGCAAA 59.321 47.619 0.00 0.00 0.00 3.68
4030 4120 1.314730 GTTTTCCCCGACAAGAGCAA 58.685 50.000 0.00 0.00 0.00 3.91
4031 4121 0.882927 CGTTTTCCCCGACAAGAGCA 60.883 55.000 0.00 0.00 0.00 4.26
4032 4122 0.601841 TCGTTTTCCCCGACAAGAGC 60.602 55.000 0.00 0.00 0.00 4.09
4033 4123 1.529865 GTTCGTTTTCCCCGACAAGAG 59.470 52.381 0.00 0.00 33.41 2.85
4034 4124 1.134461 TGTTCGTTTTCCCCGACAAGA 60.134 47.619 0.00 0.00 33.41 3.02
4035 4125 1.003223 GTGTTCGTTTTCCCCGACAAG 60.003 52.381 0.00 0.00 33.41 3.16
4036 4126 1.015868 GTGTTCGTTTTCCCCGACAA 58.984 50.000 0.00 0.00 33.41 3.18
4041 4131 2.089201 CCATAGGTGTTCGTTTTCCCC 58.911 52.381 0.00 0.00 0.00 4.81
4092 4182 1.202313 GCTCTTCGTGCGACTAATCCT 60.202 52.381 0.00 0.00 0.00 3.24
4099 4189 2.049063 ACCTGCTCTTCGTGCGAC 60.049 61.111 0.00 0.00 0.00 5.19
4100 4190 2.082629 TTGACCTGCTCTTCGTGCGA 62.083 55.000 0.00 0.00 0.00 5.10
4101 4191 1.621301 CTTGACCTGCTCTTCGTGCG 61.621 60.000 0.00 0.00 0.00 5.34
4104 4194 1.004440 GGCTTGACCTGCTCTTCGT 60.004 57.895 0.00 0.00 34.51 3.85
4118 4208 2.522185 TCCTCTGTGTACTAACGGCTT 58.478 47.619 0.00 0.00 0.00 4.35
4128 4218 3.798515 ACCTGGGTAAATCCTCTGTGTA 58.201 45.455 0.00 0.00 36.25 2.90
4201 4293 5.767168 AGCTAGTTCAAAAGCTCAAGAACAT 59.233 36.000 20.34 11.79 45.92 2.71
4237 4329 3.412386 AGGATTCGGACTTTTGGACAAG 58.588 45.455 0.00 0.00 0.00 3.16
4251 4343 2.159226 AGGCGTACAAAGAGAGGATTCG 60.159 50.000 0.00 0.00 0.00 3.34
4288 4380 1.489881 CTGTGGCAACCTTTTTGCGC 61.490 55.000 0.00 0.00 45.78 6.09
4305 4397 4.320456 ACCTCCTGTGTGCCGCTG 62.320 66.667 0.00 0.00 0.00 5.18
4360 4452 5.219633 ACACATTGAATGCGTTTTTCCTAC 58.780 37.500 4.84 0.00 0.00 3.18
4366 4458 2.543430 GGCAACACATTGAATGCGTTTT 59.457 40.909 8.69 0.00 38.15 2.43
4376 4468 3.084039 AGGACACATAGGCAACACATTG 58.916 45.455 0.00 0.00 38.99 2.82
4400 4492 1.676006 GTTGCCATCCCCGATAAAGTG 59.324 52.381 0.00 0.00 0.00 3.16
4422 4514 1.078426 CGAAGGACGGGATGGCTTT 60.078 57.895 0.00 0.00 38.46 3.51
4470 4562 1.228337 ACTGCATGCCTTGTCAGCA 60.228 52.632 16.68 0.00 45.94 4.41
4493 4585 0.457851 CAGCAGGTAGTTAGCGAGCT 59.542 55.000 2.25 2.25 39.31 4.09
4497 4589 1.726791 CAACACAGCAGGTAGTTAGCG 59.273 52.381 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.