Multiple sequence alignment - TraesCS5A01G359600

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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 TraesCS5A01G359600 chr5A 100.000 5006 0 0 1 5006 561536007 561531002 0.000000e+00 9245.0
1 TraesCS5A01G359600 chr5A 93.564 637 34 5 1 633 382553284 382552651 0.000000e+00 942.0
2 TraesCS5A01G359600 chr5A 95.775 71 2 1 4439 4509 624782117 624782048 4.100000e-21 113.0
3 TraesCS5A01G359600 chr5A 80.576 139 17 8 4869 5005 561508441 561508311 1.150000e-16 99.0
4 TraesCS5A01G359600 chr5A 86.047 86 8 3 4923 5006 561518966 561518883 6.900000e-14 89.8
5 TraesCS5A01G359600 chr5D 95.706 3330 107 10 1120 4442 444550823 444547523 0.000000e+00 5325.0
6 TraesCS5A01G359600 chr5D 89.097 321 25 4 4553 4869 444547500 444547186 1.690000e-104 390.0
7 TraesCS5A01G359600 chr5D 85.852 311 13 9 748 1058 444551524 444551245 8.140000e-78 302.0
8 TraesCS5A01G359600 chr5D 79.679 187 19 6 3859 4044 444540924 444540756 3.170000e-22 117.0
9 TraesCS5A01G359600 chr5D 86.905 84 11 0 4923 5006 444538360 444538277 1.480000e-15 95.3
10 TraesCS5A01G359600 chr5D 86.667 90 5 4 4923 5006 444546908 444546820 5.340000e-15 93.5
11 TraesCS5A01G359600 chr5B 96.892 3153 94 3 1033 4182 541344723 541341572 0.000000e+00 5276.0
12 TraesCS5A01G359600 chr5B 95.979 572 18 4 67 634 29626124 29626694 0.000000e+00 924.0
13 TraesCS5A01G359600 chr5B 89.583 192 1 6 748 939 541345304 541345132 5.040000e-55 226.0
14 TraesCS5A01G359600 chr5B 89.262 149 12 4 3863 4010 541336119 541335974 3.080000e-42 183.0
15 TraesCS5A01G359600 chr5B 93.182 88 4 2 644 729 541345376 541345289 1.460000e-25 128.0
16 TraesCS5A01G359600 chr7A 99.051 632 4 2 1 631 46687695 46688325 0.000000e+00 1133.0
17 TraesCS5A01G359600 chr4B 98.571 630 6 3 1 629 217077214 217076587 0.000000e+00 1110.0
18 TraesCS5A01G359600 chr4B 98.413 630 9 1 1 630 347543120 347543748 0.000000e+00 1107.0
19 TraesCS5A01G359600 chr4B 92.500 80 3 3 4439 4518 95218803 95218879 1.470000e-20 111.0
20 TraesCS5A01G359600 chr6B 94.146 632 31 5 1 629 189215820 189215192 0.000000e+00 957.0
21 TraesCS5A01G359600 chr6B 91.250 80 7 0 4431 4510 113298953 113298874 5.300000e-20 110.0
22 TraesCS5A01G359600 chr3B 96.643 566 16 3 67 630 545178489 545177925 0.000000e+00 937.0
23 TraesCS5A01G359600 chr2A 92.056 642 43 7 1 638 49164485 49163848 0.000000e+00 896.0
24 TraesCS5A01G359600 chr2A 93.506 77 3 2 4434 4508 194716794 194716870 4.100000e-21 113.0
25 TraesCS5A01G359600 chr2A 89.247 93 4 2 4439 4526 704774820 704774911 1.470000e-20 111.0
26 TraesCS5A01G359600 chr6A 91.798 634 44 6 1 631 539370331 539369703 0.000000e+00 876.0
27 TraesCS5A01G359600 chr6A 93.333 75 2 1 4437 4508 114239044 114238970 1.910000e-19 108.0
28 TraesCS5A01G359600 chr4D 95.890 73 1 1 4439 4509 427262323 427262395 3.170000e-22 117.0
29 TraesCS5A01G359600 chr7B 95.652 69 2 1 4439 4507 196961105 196961038 5.300000e-20 110.0
30 TraesCS5A01G359600 chr2D 93.333 75 2 1 4436 4507 376701187 376701261 1.910000e-19 108.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G359600 chr5A 561531002 561536007 5005 True 9245.000000 9245 100.0000 1 5006 1 chr5A.!!$R4 5005
1 TraesCS5A01G359600 chr5A 382552651 382553284 633 True 942.000000 942 93.5640 1 633 1 chr5A.!!$R1 632
2 TraesCS5A01G359600 chr5D 444546820 444551524 4704 True 1527.625000 5325 89.3305 748 5006 4 chr5D.!!$R2 4258
3 TraesCS5A01G359600 chr5B 541341572 541345376 3804 True 1876.666667 5276 93.2190 644 4182 3 chr5B.!!$R2 3538
4 TraesCS5A01G359600 chr5B 29626124 29626694 570 False 924.000000 924 95.9790 67 634 1 chr5B.!!$F1 567
5 TraesCS5A01G359600 chr7A 46687695 46688325 630 False 1133.000000 1133 99.0510 1 631 1 chr7A.!!$F1 630
6 TraesCS5A01G359600 chr4B 217076587 217077214 627 True 1110.000000 1110 98.5710 1 629 1 chr4B.!!$R1 628
7 TraesCS5A01G359600 chr4B 347543120 347543748 628 False 1107.000000 1107 98.4130 1 630 1 chr4B.!!$F2 629
8 TraesCS5A01G359600 chr6B 189215192 189215820 628 True 957.000000 957 94.1460 1 629 1 chr6B.!!$R2 628
9 TraesCS5A01G359600 chr3B 545177925 545178489 564 True 937.000000 937 96.6430 67 630 1 chr3B.!!$R1 563
10 TraesCS5A01G359600 chr2A 49163848 49164485 637 True 896.000000 896 92.0560 1 638 1 chr2A.!!$R1 637
11 TraesCS5A01G359600 chr6A 539369703 539370331 628 True 876.000000 876 91.7980 1 631 1 chr6A.!!$R2 630

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
727 737 0.035458 ACTGACAGTTGTAGGGCTGC 59.965 55.0 1.07 0.0 36.26 5.25 F
962 972 0.410663 TCCTACTCTCCCGAACCCAA 59.589 55.0 0.00 0.0 0.00 4.12 F
1504 2211 0.679505 CGTCTCCAACTCCTCCAACA 59.320 55.0 0.00 0.0 0.00 3.33 F
2073 2780 0.034337 CGAGGGACGAAACCTTTGGA 59.966 55.0 0.00 0.0 45.77 3.53 F
2175 2882 0.617935 TCATTGCCGATGGGAAGACA 59.382 50.0 0.00 0.0 36.27 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1638 2345 0.806868 TGTAGTACTCGGAGCCAACG 59.193 55.000 4.58 0.00 0.00 4.10 R
1887 2594 1.006825 TGACGAAAGACACGCCATCG 61.007 55.000 0.00 0.00 42.43 3.84 R
3362 4069 0.900647 CTCCCAGAGGACACGGTTCT 60.901 60.000 0.00 0.00 37.19 3.01 R
3432 4139 1.269448 TGCTTCATTCCGGTGAAAAGC 59.731 47.619 20.03 20.03 41.52 3.51 R
4098 4813 0.809241 CTGTCCCTCGAATGCTCTGC 60.809 60.000 0.00 0.00 0.00 4.26 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
19 20 2.496899 GCAACTTTCCTCATCTCCCA 57.503 50.000 0.00 0.00 0.00 4.37
634 643 4.579753 CGGGTGTAAACACTTCCCTTTTTA 59.420 41.667 12.65 0.00 45.73 1.52
638 647 7.988599 GGGTGTAAACACTTCCCTTTTTATTTT 59.011 33.333 12.65 0.00 45.73 1.82
687 696 1.542187 GCCTCTCTAACACGTGGGGT 61.542 60.000 21.57 7.20 0.00 4.95
717 727 3.694364 CTGCCAGTGACTGACAGTT 57.306 52.632 19.04 0.00 37.24 3.16
718 728 1.224075 CTGCCAGTGACTGACAGTTG 58.776 55.000 19.04 4.15 37.24 3.16
719 729 0.541392 TGCCAGTGACTGACAGTTGT 59.459 50.000 15.33 0.00 32.44 3.32
720 730 1.760029 TGCCAGTGACTGACAGTTGTA 59.240 47.619 15.33 0.00 32.44 2.41
721 731 2.224042 TGCCAGTGACTGACAGTTGTAG 60.224 50.000 15.33 1.15 32.44 2.74
722 732 2.868044 GCCAGTGACTGACAGTTGTAGG 60.868 54.545 15.33 10.97 32.44 3.18
723 733 2.289072 CCAGTGACTGACAGTTGTAGGG 60.289 54.545 15.33 4.87 32.44 3.53
724 734 1.344763 AGTGACTGACAGTTGTAGGGC 59.655 52.381 10.01 0.00 0.00 5.19
725 735 1.344763 GTGACTGACAGTTGTAGGGCT 59.655 52.381 10.01 0.00 0.00 5.19
726 736 1.344438 TGACTGACAGTTGTAGGGCTG 59.656 52.381 10.01 0.00 38.58 4.85
727 737 0.035458 ACTGACAGTTGTAGGGCTGC 59.965 55.000 1.07 0.00 36.26 5.25
728 738 0.674895 CTGACAGTTGTAGGGCTGCC 60.675 60.000 11.05 11.05 36.26 4.85
729 739 1.377333 GACAGTTGTAGGGCTGCCC 60.377 63.158 30.57 30.57 45.90 5.36
739 749 3.302344 GGCTGCCCCGCTCAAAAA 61.302 61.111 7.66 0.00 0.00 1.94
860 870 3.797353 CATCCCCACCCCACCGAG 61.797 72.222 0.00 0.00 0.00 4.63
861 871 4.019513 ATCCCCACCCCACCGAGA 62.020 66.667 0.00 0.00 0.00 4.04
862 872 3.572715 ATCCCCACCCCACCGAGAA 62.573 63.158 0.00 0.00 0.00 2.87
863 873 4.029809 CCCCACCCCACCGAGAAC 62.030 72.222 0.00 0.00 0.00 3.01
864 874 4.029809 CCCACCCCACCGAGAACC 62.030 72.222 0.00 0.00 0.00 3.62
865 875 2.928396 CCACCCCACCGAGAACCT 60.928 66.667 0.00 0.00 0.00 3.50
866 876 2.663196 CACCCCACCGAGAACCTC 59.337 66.667 0.00 0.00 0.00 3.85
867 877 2.606826 ACCCCACCGAGAACCTCC 60.607 66.667 0.00 0.00 0.00 4.30
868 878 3.400054 CCCCACCGAGAACCTCCC 61.400 72.222 0.00 0.00 0.00 4.30
869 879 3.400054 CCCACCGAGAACCTCCCC 61.400 72.222 0.00 0.00 0.00 4.81
870 880 2.284699 CCACCGAGAACCTCCCCT 60.285 66.667 0.00 0.00 0.00 4.79
871 881 2.359967 CCACCGAGAACCTCCCCTC 61.360 68.421 0.00 0.00 0.00 4.30
962 972 0.410663 TCCTACTCTCCCGAACCCAA 59.589 55.000 0.00 0.00 0.00 4.12
964 974 1.558233 CTACTCTCCCGAACCCAACT 58.442 55.000 0.00 0.00 0.00 3.16
967 977 2.227089 CTCTCCCGAACCCAACTCCG 62.227 65.000 0.00 0.00 0.00 4.63
968 978 3.952628 CTCCCGAACCCAACTCCGC 62.953 68.421 0.00 0.00 0.00 5.54
969 979 4.016706 CCCGAACCCAACTCCGCT 62.017 66.667 0.00 0.00 0.00 5.52
972 982 2.747686 GAACCCAACTCCGCTCCA 59.252 61.111 0.00 0.00 0.00 3.86
974 984 0.955919 GAACCCAACTCCGCTCCAAG 60.956 60.000 0.00 0.00 0.00 3.61
981 991 1.738099 CTCCGCTCCAAGTCCAACG 60.738 63.158 0.00 0.00 0.00 4.10
985 995 1.070786 GCTCCAAGTCCAACGTCCA 59.929 57.895 0.00 0.00 0.00 4.02
1167 1874 4.947147 TGCCGGCACACCAACCTC 62.947 66.667 29.03 0.00 34.57 3.85
1479 2186 2.050350 CCTCGGCCACGTCTTCCTA 61.050 63.158 2.24 0.00 41.85 2.94
1487 2194 1.751927 ACGTCTTCCTATCCGCCGT 60.752 57.895 0.00 0.00 0.00 5.68
1504 2211 0.679505 CGTCTCCAACTCCTCCAACA 59.320 55.000 0.00 0.00 0.00 3.33
1518 2225 4.250305 AACACCACCGCCGCTCTT 62.250 61.111 0.00 0.00 0.00 2.85
1599 2306 1.448540 CCTTCGCTGGACGCTCAAT 60.449 57.895 0.00 0.00 43.23 2.57
1601 2308 1.005037 TTCGCTGGACGCTCAATGT 60.005 52.632 0.00 0.00 43.23 2.71
1662 2369 1.033574 GCTCCGAGTACTACATGGCT 58.966 55.000 0.00 0.00 0.00 4.75
1674 2381 4.759205 ATGGCTTTCGGGTGGGCC 62.759 66.667 0.00 0.00 44.31 5.80
1749 2456 1.146263 CACCGAGGAAGGTATGCCC 59.854 63.158 0.00 0.00 43.89 5.36
1782 2489 5.277731 GGACTACTACATTACCGACTACAGC 60.278 48.000 0.00 0.00 0.00 4.40
1818 2525 1.448540 GGATGACCTGCCAGTGTCG 60.449 63.158 8.25 0.00 34.18 4.35
1858 2565 2.158957 GCTTATGATGACGGGAGGAACA 60.159 50.000 0.00 0.00 0.00 3.18
1941 2648 6.254589 GGAAACTCGATAGTGAAGATGACAAG 59.745 42.308 0.00 0.00 35.62 3.16
1952 2659 4.877823 TGAAGATGACAAGTATGATGTGCC 59.122 41.667 0.00 0.00 0.00 5.01
1995 2702 4.489771 GTGGTCTGGGCCATCGGG 62.490 72.222 6.72 0.00 41.08 5.14
2034 2741 2.125512 CTGCGCCCACACTACCTC 60.126 66.667 4.18 0.00 0.00 3.85
2043 2750 0.389948 CACACTACCTCCCGCAGAAC 60.390 60.000 0.00 0.00 0.00 3.01
2073 2780 0.034337 CGAGGGACGAAACCTTTGGA 59.966 55.000 0.00 0.00 45.77 3.53
2083 2790 3.129287 CGAAACCTTTGGATTGATGAGGG 59.871 47.826 0.00 0.00 0.00 4.30
2099 2806 1.003233 GAGGGTCAATTTGTCCGAGGT 59.997 52.381 6.59 0.00 0.00 3.85
2130 2837 1.002134 CCTTGGACCGTTGGATGCT 60.002 57.895 0.00 0.00 0.00 3.79
2175 2882 0.617935 TCATTGCCGATGGGAAGACA 59.382 50.000 0.00 0.00 36.27 3.41
2178 2885 2.511600 GCCGATGGGAAGACACCG 60.512 66.667 0.00 0.00 34.06 4.94
2203 2910 1.153289 GTGACATCCGCTCCAGCAT 60.153 57.895 0.00 0.00 42.21 3.79
2229 2936 2.503382 CCCAAACCCACCAAACCCG 61.503 63.158 0.00 0.00 0.00 5.28
2241 2948 1.003812 CCAAACCCGGACAAGGTGATA 59.996 52.381 0.73 0.00 37.78 2.15
2277 2984 2.980233 GCGCCACTGCTGAAGGTT 60.980 61.111 0.00 0.00 34.43 3.50
2303 3010 0.818040 GGTGTGCCGGTGAAGTTCTT 60.818 55.000 1.90 0.00 0.00 2.52
2316 3023 1.059913 AGTTCTTAGTGCAGGCTGGT 58.940 50.000 17.64 0.00 0.00 4.00
2529 3236 1.422402 GGGTGGAAGGTTCAAGTGGTA 59.578 52.381 0.00 0.00 0.00 3.25
2544 3251 1.050988 TGGTAGATGGAGGCCTCAGC 61.051 60.000 33.29 21.61 38.76 4.26
2565 3272 5.575218 CAGCGACATGTACAATAACAGTGTA 59.425 40.000 0.00 0.00 31.70 2.90
2566 3273 6.255670 CAGCGACATGTACAATAACAGTGTAT 59.744 38.462 0.00 0.00 34.15 2.29
2622 3329 5.381757 ACTCTGTCCACTGACTCTATATCC 58.618 45.833 0.00 0.00 42.28 2.59
2880 3587 2.570302 GCCTTCCTGTACTGGAAAGGTA 59.430 50.000 29.27 15.73 44.49 3.08
3231 3938 1.656441 CGTCCTTTTTGCTGCAGCT 59.344 52.632 36.61 0.00 42.66 4.24
3252 3959 2.427453 TGAGCTCCGAGGTTTCTATGTC 59.573 50.000 12.15 0.00 0.00 3.06
3279 3986 1.917303 GTGCACGTCAAGTTTGGTTTG 59.083 47.619 0.00 0.00 0.00 2.93
3462 4169 2.223572 CGGAATGAAGCATTTAGGCCAC 60.224 50.000 5.01 0.00 33.90 5.01
3544 4251 3.508012 CGCCATAGTTATAGCTCTGTCCT 59.492 47.826 0.00 0.00 0.00 3.85
3546 4253 5.233988 GCCATAGTTATAGCTCTGTCCTTG 58.766 45.833 0.00 0.00 0.00 3.61
3880 4590 7.662604 AATTGAATTTCTCATGCTTGTTTCC 57.337 32.000 0.00 0.00 32.78 3.13
4207 4922 9.409312 TGTAATGTGCTTAGAATTTTGAACATG 57.591 29.630 0.00 0.00 0.00 3.21
4223 4938 5.977635 TGAACATGTCCATAACTACTGGAG 58.022 41.667 0.00 0.00 43.33 3.86
4236 4951 5.426689 ACTACTGGAGCATCTTCAATTCA 57.573 39.130 0.00 0.00 33.73 2.57
4244 4959 5.356190 GGAGCATCTTCAATTCATTGACTGA 59.644 40.000 1.52 4.70 45.63 3.41
4294 5009 7.721402 AGAATATCACTGATGAGTGGTAAGAC 58.279 38.462 9.45 4.57 46.63 3.01
4341 5056 4.023279 TGCGCCAATGTGATAATATTGTCC 60.023 41.667 4.18 2.61 33.52 4.02
4343 5058 4.518590 CGCCAATGTGATAATATTGTCCCA 59.481 41.667 9.44 4.93 33.52 4.37
4354 5069 8.805175 TGATAATATTGTCCCAATGCTATTTGG 58.195 33.333 9.44 6.66 44.82 3.28
4368 5083 8.776470 CAATGCTATTTGGAAGTTGAAAAATGT 58.224 29.630 0.00 0.00 0.00 2.71
4369 5084 7.712264 TGCTATTTGGAAGTTGAAAAATGTG 57.288 32.000 0.00 0.00 0.00 3.21
4370 5085 6.202570 TGCTATTTGGAAGTTGAAAAATGTGC 59.797 34.615 0.00 0.00 0.00 4.57
4371 5086 6.424812 GCTATTTGGAAGTTGAAAAATGTGCT 59.575 34.615 0.00 0.00 0.00 4.40
4372 5087 7.041848 GCTATTTGGAAGTTGAAAAATGTGCTT 60.042 33.333 0.00 0.00 0.00 3.91
4373 5088 6.419980 TTTGGAAGTTGAAAAATGTGCTTG 57.580 33.333 0.00 0.00 0.00 4.01
4374 5089 5.083533 TGGAAGTTGAAAAATGTGCTTGT 57.916 34.783 0.00 0.00 0.00 3.16
4375 5090 6.214191 TGGAAGTTGAAAAATGTGCTTGTA 57.786 33.333 0.00 0.00 0.00 2.41
4376 5091 6.039616 TGGAAGTTGAAAAATGTGCTTGTAC 58.960 36.000 0.00 0.00 0.00 2.90
4377 5092 5.173131 GGAAGTTGAAAAATGTGCTTGTACG 59.827 40.000 0.00 0.00 0.00 3.67
4378 5093 5.243426 AGTTGAAAAATGTGCTTGTACGT 57.757 34.783 0.00 0.00 0.00 3.57
4379 5094 6.366315 AGTTGAAAAATGTGCTTGTACGTA 57.634 33.333 0.00 0.00 0.00 3.57
4389 5104 5.694816 TGTGCTTGTACGTATGAAAAATGG 58.305 37.500 0.00 0.00 0.00 3.16
4413 5128 4.521146 AGAGTAATCTGCATTCAAGGGTG 58.479 43.478 0.00 0.00 0.00 4.61
4442 5158 8.367911 TGGATATGACCATGTACAGAAATACTC 58.632 37.037 0.33 0.00 34.77 2.59
4443 5159 7.819900 GGATATGACCATGTACAGAAATACTCC 59.180 40.741 0.33 0.00 0.00 3.85
4444 5160 5.353394 TGACCATGTACAGAAATACTCCC 57.647 43.478 0.33 0.00 0.00 4.30
4445 5161 5.030147 TGACCATGTACAGAAATACTCCCT 58.970 41.667 0.33 0.00 0.00 4.20
4446 5162 5.128827 TGACCATGTACAGAAATACTCCCTC 59.871 44.000 0.33 0.00 0.00 4.30
4447 5163 4.409247 ACCATGTACAGAAATACTCCCTCC 59.591 45.833 0.33 0.00 0.00 4.30
4448 5164 4.408921 CCATGTACAGAAATACTCCCTCCA 59.591 45.833 0.33 0.00 0.00 3.86
4449 5165 5.072329 CCATGTACAGAAATACTCCCTCCAT 59.928 44.000 0.33 0.00 0.00 3.41
4450 5166 6.270000 CCATGTACAGAAATACTCCCTCCATA 59.730 42.308 0.33 0.00 0.00 2.74
4451 5167 7.202093 CCATGTACAGAAATACTCCCTCCATAA 60.202 40.741 0.33 0.00 0.00 1.90
4452 5168 7.743116 TGTACAGAAATACTCCCTCCATAAA 57.257 36.000 0.00 0.00 0.00 1.40
4453 5169 7.792032 TGTACAGAAATACTCCCTCCATAAAG 58.208 38.462 0.00 0.00 0.00 1.85
4454 5170 7.622081 TGTACAGAAATACTCCCTCCATAAAGA 59.378 37.037 0.00 0.00 0.00 2.52
4455 5171 7.510675 ACAGAAATACTCCCTCCATAAAGAA 57.489 36.000 0.00 0.00 0.00 2.52
4456 5172 7.928873 ACAGAAATACTCCCTCCATAAAGAAA 58.071 34.615 0.00 0.00 0.00 2.52
4457 5173 8.560903 ACAGAAATACTCCCTCCATAAAGAAAT 58.439 33.333 0.00 0.00 0.00 2.17
4465 5181 8.379331 ACTCCCTCCATAAAGAAATATAAGAGC 58.621 37.037 0.00 0.00 0.00 4.09
4466 5182 8.511748 TCCCTCCATAAAGAAATATAAGAGCT 57.488 34.615 0.00 0.00 0.00 4.09
4467 5183 9.615660 TCCCTCCATAAAGAAATATAAGAGCTA 57.384 33.333 0.00 0.00 0.00 3.32
4468 5184 9.883142 CCCTCCATAAAGAAATATAAGAGCTAG 57.117 37.037 0.00 0.00 0.00 3.42
4480 5196 8.973835 AATATAAGAGCTAGTGATCTAAACGC 57.026 34.615 0.00 0.00 38.07 4.84
4481 5197 4.993029 AAGAGCTAGTGATCTAAACGCT 57.007 40.909 0.00 0.00 38.07 5.07
4482 5198 4.561735 AGAGCTAGTGATCTAAACGCTC 57.438 45.455 13.12 13.12 39.83 5.03
4483 5199 4.204012 AGAGCTAGTGATCTAAACGCTCT 58.796 43.478 16.04 16.04 42.32 4.09
4484 5200 4.642885 AGAGCTAGTGATCTAAACGCTCTT 59.357 41.667 16.04 6.24 43.43 2.85
4485 5201 5.823570 AGAGCTAGTGATCTAAACGCTCTTA 59.176 40.000 16.04 0.00 43.43 2.10
4486 5202 6.488683 AGAGCTAGTGATCTAAACGCTCTTAT 59.511 38.462 16.04 2.24 43.43 1.73
4487 5203 7.662258 AGAGCTAGTGATCTAAACGCTCTTATA 59.338 37.037 16.04 0.00 43.43 0.98
4488 5204 8.343168 AGCTAGTGATCTAAACGCTCTTATAT 57.657 34.615 0.00 0.00 0.00 0.86
4489 5205 8.798402 AGCTAGTGATCTAAACGCTCTTATATT 58.202 33.333 0.00 0.00 0.00 1.28
4490 5206 9.413048 GCTAGTGATCTAAACGCTCTTATATTT 57.587 33.333 0.00 0.00 0.00 1.40
4501 5217 8.649973 AACGCTCTTATATTTCTTTACAGAGG 57.350 34.615 0.00 0.00 0.00 3.69
4502 5218 7.210873 ACGCTCTTATATTTCTTTACAGAGGG 58.789 38.462 8.36 8.36 42.53 4.30
4503 5219 7.069578 ACGCTCTTATATTTCTTTACAGAGGGA 59.930 37.037 14.96 0.00 40.49 4.20
4504 5220 7.596995 CGCTCTTATATTTCTTTACAGAGGGAG 59.403 40.741 4.76 0.00 40.49 4.30
4505 5221 8.425703 GCTCTTATATTTCTTTACAGAGGGAGT 58.574 37.037 0.00 0.00 0.00 3.85
4517 5233 7.607615 TTACAGAGGGAGTACTAAGTTGTTT 57.392 36.000 0.00 0.00 0.00 2.83
4520 5236 5.179555 CAGAGGGAGTACTAAGTTGTTTTGC 59.820 44.000 0.00 0.00 0.00 3.68
4525 5241 5.472137 GGAGTACTAAGTTGTTTTGCATCCA 59.528 40.000 0.00 0.00 0.00 3.41
4531 5247 0.678395 TTGTTTTGCATCCACGGCAT 59.322 45.000 0.00 0.00 41.58 4.40
4532 5248 0.243365 TGTTTTGCATCCACGGCATC 59.757 50.000 0.00 0.00 41.58 3.91
4533 5249 0.243365 GTTTTGCATCCACGGCATCA 59.757 50.000 0.00 0.00 41.58 3.07
4534 5250 1.135024 GTTTTGCATCCACGGCATCAT 60.135 47.619 0.00 0.00 41.58 2.45
4535 5251 1.184431 TTTGCATCCACGGCATCATT 58.816 45.000 0.00 0.00 41.58 2.57
4536 5252 1.184431 TTGCATCCACGGCATCATTT 58.816 45.000 0.00 0.00 41.58 2.32
4537 5253 2.049888 TGCATCCACGGCATCATTTA 57.950 45.000 0.00 0.00 36.11 1.40
4538 5254 2.373224 TGCATCCACGGCATCATTTAA 58.627 42.857 0.00 0.00 36.11 1.52
4539 5255 2.098934 TGCATCCACGGCATCATTTAAC 59.901 45.455 0.00 0.00 36.11 2.01
4540 5256 2.543653 GCATCCACGGCATCATTTAACC 60.544 50.000 0.00 0.00 0.00 2.85
4541 5257 2.498644 TCCACGGCATCATTTAACCA 57.501 45.000 0.00 0.00 0.00 3.67
4542 5258 2.364632 TCCACGGCATCATTTAACCAG 58.635 47.619 0.00 0.00 0.00 4.00
4543 5259 2.091541 CCACGGCATCATTTAACCAGT 58.908 47.619 0.00 0.00 0.00 4.00
4544 5260 2.097466 CCACGGCATCATTTAACCAGTC 59.903 50.000 0.00 0.00 0.00 3.51
4545 5261 2.746904 CACGGCATCATTTAACCAGTCA 59.253 45.455 0.00 0.00 0.00 3.41
4546 5262 3.009723 ACGGCATCATTTAACCAGTCAG 58.990 45.455 0.00 0.00 0.00 3.51
4547 5263 3.270027 CGGCATCATTTAACCAGTCAGA 58.730 45.455 0.00 0.00 0.00 3.27
4548 5264 3.310774 CGGCATCATTTAACCAGTCAGAG 59.689 47.826 0.00 0.00 0.00 3.35
4549 5265 3.629398 GGCATCATTTAACCAGTCAGAGG 59.371 47.826 0.00 0.00 0.00 3.69
4550 5266 4.517285 GCATCATTTAACCAGTCAGAGGA 58.483 43.478 0.00 0.00 0.00 3.71
4551 5267 5.128919 GCATCATTTAACCAGTCAGAGGAT 58.871 41.667 0.00 0.00 0.00 3.24
4571 5287 5.184671 AGGATTCAAAGGAGAGAAATTGTGC 59.815 40.000 0.00 0.00 0.00 4.57
4590 5306 9.537852 AATTGTGCATCATAGTGGGATATTATT 57.462 29.630 0.00 0.00 0.00 1.40
4591 5307 8.565896 TTGTGCATCATAGTGGGATATTATTC 57.434 34.615 0.00 0.00 0.00 1.75
4594 5310 8.454106 GTGCATCATAGTGGGATATTATTCAAC 58.546 37.037 0.00 0.00 0.00 3.18
4616 5332 7.336679 TCAACATATTTGTTCCGAGAATGTGAT 59.663 33.333 0.00 0.00 44.24 3.06
4631 5347 7.352079 AGAATGTGATATAAAAGGCAAAGGG 57.648 36.000 0.00 0.00 0.00 3.95
4655 5371 6.418956 GTGTTGTACTGTCTGTTGTATGTTG 58.581 40.000 0.00 0.00 0.00 3.33
4680 5396 6.512415 GCCAGTGCTATAGCTCTTTAAACATG 60.512 42.308 23.32 12.27 42.25 3.21
4735 5451 8.868522 TTTACTGATCATTCCATGAAACTTCT 57.131 30.769 0.00 0.00 43.50 2.85
4742 5458 9.770097 GATCATTCCATGAAACTTCTACATAGA 57.230 33.333 0.00 0.00 43.50 1.98
4754 5470 8.438676 AACTTCTACATAGATACAACAATGGC 57.561 34.615 0.00 0.00 31.40 4.40
4767 5483 4.815846 ACAACAATGGCAAGATTGGTTTTC 59.184 37.500 11.23 0.00 37.60 2.29
4768 5484 4.006780 ACAATGGCAAGATTGGTTTTCC 57.993 40.909 4.51 0.00 37.60 3.13
4782 5498 5.467035 TGGTTTTCCATGTCAGATTTTCC 57.533 39.130 0.00 0.00 46.22 3.13
4783 5499 4.022416 TGGTTTTCCATGTCAGATTTTCCG 60.022 41.667 0.00 0.00 46.22 4.30
4801 5517 3.150767 TCCGTTTTTGGGTCGATGATTT 58.849 40.909 0.00 0.00 0.00 2.17
4802 5518 3.057876 TCCGTTTTTGGGTCGATGATTTG 60.058 43.478 0.00 0.00 0.00 2.32
4811 5527 0.179084 TCGATGATTTGTCTCCGCCC 60.179 55.000 0.00 0.00 0.00 6.13
4814 5530 2.484889 GATGATTTGTCTCCGCCCTAC 58.515 52.381 0.00 0.00 0.00 3.18
4843 5561 4.218417 AGTTGGGAAATGTGCTTGTATGAC 59.782 41.667 0.00 0.00 0.00 3.06
4846 5564 4.218200 TGGGAAATGTGCTTGTATGACTTG 59.782 41.667 0.00 0.00 0.00 3.16
4851 5569 6.683974 AATGTGCTTGTATGACTTGTATCC 57.316 37.500 0.00 0.00 0.00 2.59
4852 5570 4.513442 TGTGCTTGTATGACTTGTATCCC 58.487 43.478 0.00 0.00 0.00 3.85
4855 5574 5.065218 GTGCTTGTATGACTTGTATCCCTTG 59.935 44.000 0.00 0.00 0.00 3.61
4860 5579 5.897250 TGTATGACTTGTATCCCTTGAGCTA 59.103 40.000 0.00 0.00 0.00 3.32
4869 5588 2.481441 TCCCTTGAGCTATGGATGTGT 58.519 47.619 0.00 0.00 0.00 3.72
4870 5589 2.171237 TCCCTTGAGCTATGGATGTGTG 59.829 50.000 0.00 0.00 0.00 3.82
4871 5590 2.171237 CCCTTGAGCTATGGATGTGTGA 59.829 50.000 0.00 0.00 0.00 3.58
4872 5591 3.370846 CCCTTGAGCTATGGATGTGTGAA 60.371 47.826 0.00 0.00 0.00 3.18
4873 5592 4.458397 CCTTGAGCTATGGATGTGTGAAT 58.542 43.478 0.00 0.00 0.00 2.57
4874 5593 4.514441 CCTTGAGCTATGGATGTGTGAATC 59.486 45.833 0.00 0.00 0.00 2.52
4875 5594 4.758773 TGAGCTATGGATGTGTGAATCA 57.241 40.909 0.00 0.00 0.00 2.57
4876 5595 4.445453 TGAGCTATGGATGTGTGAATCAC 58.555 43.478 6.41 6.41 46.31 3.06
4889 5818 1.228245 AATCACACAACCAGCGCCT 60.228 52.632 2.29 0.00 0.00 5.52
4893 5822 0.673333 CACACAACCAGCGCCTATGA 60.673 55.000 2.29 0.00 0.00 2.15
4904 5833 3.024547 AGCGCCTATGACTGAGAGTTTA 58.975 45.455 2.29 0.00 0.00 2.01
4913 5842 4.579869 TGACTGAGAGTTTATTTCAGGGC 58.420 43.478 5.79 0.00 41.98 5.19
4921 5850 4.652822 AGTTTATTTCAGGGCGAACTCTT 58.347 39.130 0.00 0.00 31.73 2.85
4948 5891 2.224314 GCTGCTTATATGGGAGCGTTTC 59.776 50.000 7.88 0.00 41.75 2.78
4960 5903 3.253955 CGTTTCGCCCTGGAAGTG 58.746 61.111 0.00 0.00 0.00 3.16
4969 5917 0.599558 CCCTGGAAGTGCATGTTGTG 59.400 55.000 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.818060 TGACAACAAACAGCTGCAACT 59.182 42.857 15.27 0.00 0.00 3.16
527 534 1.814169 GGGAGACGCGATTTGGGAC 60.814 63.158 15.93 0.00 0.00 4.46
656 665 0.612174 AGAGAGGCAAGGACGTGCTA 60.612 55.000 10.98 0.00 44.31 3.49
658 667 0.246635 TTAGAGAGGCAAGGACGTGC 59.753 55.000 0.00 0.00 44.14 5.34
714 724 3.717294 CGGGGCAGCCCTACAACT 61.717 66.667 30.52 0.00 44.66 3.16
722 732 3.302344 TTTTTGAGCGGGGCAGCC 61.302 61.111 1.26 1.26 38.01 4.85
738 748 4.684242 GCAGCGCCTACAACTTTTATTTTT 59.316 37.500 2.29 0.00 0.00 1.94
739 749 4.234574 GCAGCGCCTACAACTTTTATTTT 58.765 39.130 2.29 0.00 0.00 1.82
740 750 3.366985 GGCAGCGCCTACAACTTTTATTT 60.367 43.478 2.29 0.00 46.69 1.40
741 751 2.163613 GGCAGCGCCTACAACTTTTATT 59.836 45.455 2.29 0.00 46.69 1.40
742 752 1.743394 GGCAGCGCCTACAACTTTTAT 59.257 47.619 2.29 0.00 46.69 1.40
743 753 1.161843 GGCAGCGCCTACAACTTTTA 58.838 50.000 2.29 0.00 46.69 1.52
744 754 1.956802 GGCAGCGCCTACAACTTTT 59.043 52.632 2.29 0.00 46.69 2.27
745 755 3.668386 GGCAGCGCCTACAACTTT 58.332 55.556 2.29 0.00 46.69 2.66
824 834 4.389576 GACCGCCGCAGTTTGCTG 62.390 66.667 0.00 0.00 42.25 4.41
858 868 1.758906 CGGAGGAGGGGAGGTTCTC 60.759 68.421 0.00 0.00 0.00 2.87
859 869 1.812113 TTCGGAGGAGGGGAGGTTCT 61.812 60.000 0.00 0.00 0.00 3.01
860 870 0.691413 ATTCGGAGGAGGGGAGGTTC 60.691 60.000 0.00 0.00 0.00 3.62
861 871 0.640495 TATTCGGAGGAGGGGAGGTT 59.360 55.000 0.00 0.00 0.00 3.50
862 872 0.868186 ATATTCGGAGGAGGGGAGGT 59.132 55.000 0.00 0.00 0.00 3.85
863 873 1.562783 GATATTCGGAGGAGGGGAGG 58.437 60.000 0.00 0.00 0.00 4.30
864 874 1.203187 TGGATATTCGGAGGAGGGGAG 60.203 57.143 0.00 0.00 0.00 4.30
865 875 0.864659 TGGATATTCGGAGGAGGGGA 59.135 55.000 0.00 0.00 0.00 4.81
866 876 0.977395 GTGGATATTCGGAGGAGGGG 59.023 60.000 0.00 0.00 0.00 4.79
867 877 0.977395 GGTGGATATTCGGAGGAGGG 59.023 60.000 0.00 0.00 0.00 4.30
868 878 0.603569 CGGTGGATATTCGGAGGAGG 59.396 60.000 0.00 0.00 0.00 4.30
869 879 0.038159 GCGGTGGATATTCGGAGGAG 60.038 60.000 0.00 0.00 0.00 3.69
870 880 1.469335 GGCGGTGGATATTCGGAGGA 61.469 60.000 0.00 0.00 0.00 3.71
871 881 1.004918 GGCGGTGGATATTCGGAGG 60.005 63.158 0.00 0.00 0.00 4.30
940 950 1.393487 GGTTCGGGAGAGTAGGAGGC 61.393 65.000 0.00 0.00 41.75 4.70
941 951 0.756070 GGGTTCGGGAGAGTAGGAGG 60.756 65.000 0.00 0.00 41.75 4.30
942 952 0.033405 TGGGTTCGGGAGAGTAGGAG 60.033 60.000 0.00 0.00 41.75 3.69
943 953 0.410663 TTGGGTTCGGGAGAGTAGGA 59.589 55.000 0.00 0.00 41.75 2.94
947 957 1.192803 GGAGTTGGGTTCGGGAGAGT 61.193 60.000 0.00 0.00 41.75 3.24
951 961 4.011517 GCGGAGTTGGGTTCGGGA 62.012 66.667 0.00 0.00 0.00 5.14
962 972 1.371558 GTTGGACTTGGAGCGGAGT 59.628 57.895 0.00 0.00 0.00 3.85
964 974 2.342279 CGTTGGACTTGGAGCGGA 59.658 61.111 0.00 0.00 0.00 5.54
967 977 1.070786 TGGACGTTGGACTTGGAGC 59.929 57.895 0.00 0.00 0.00 4.70
968 978 0.602905 GGTGGACGTTGGACTTGGAG 60.603 60.000 0.00 0.00 0.00 3.86
969 979 1.448497 GGTGGACGTTGGACTTGGA 59.552 57.895 0.00 0.00 0.00 3.53
972 982 2.052047 CTGGGGTGGACGTTGGACTT 62.052 60.000 0.00 0.00 0.00 3.01
974 984 1.838073 ATCTGGGGTGGACGTTGGAC 61.838 60.000 0.00 0.00 0.00 4.02
981 991 1.303282 GTTGGGATCTGGGGTGGAC 59.697 63.158 0.00 0.00 0.00 4.02
985 995 2.617215 GGGGTTGGGATCTGGGGT 60.617 66.667 0.00 0.00 0.00 4.95
1018 1028 2.256764 CGCGGATCGAGATCTGGG 59.743 66.667 19.74 19.74 46.13 4.45
1479 2186 2.722201 GGAGTTGGAGACGGCGGAT 61.722 63.158 13.24 0.00 0.00 4.18
1487 2194 1.056660 GGTGTTGGAGGAGTTGGAGA 58.943 55.000 0.00 0.00 0.00 3.71
1534 2241 3.799755 GTCGAACATGGTGGGCGC 61.800 66.667 0.00 0.00 0.00 6.53
1638 2345 0.806868 TGTAGTACTCGGAGCCAACG 59.193 55.000 4.58 0.00 0.00 4.10
1641 2348 1.399714 CCATGTAGTACTCGGAGCCA 58.600 55.000 4.58 0.00 0.00 4.75
1674 2381 2.359975 GAGTTGGCCTTGGGGTCG 60.360 66.667 3.32 0.00 40.80 4.79
1749 2456 4.640789 AATGTAGTAGTCCTCTGCGAAG 57.359 45.455 0.00 0.00 0.00 3.79
1755 2462 5.370875 AGTCGGTAATGTAGTAGTCCTCT 57.629 43.478 0.00 0.00 0.00 3.69
1782 2489 1.746615 CTTCCCCATGGTGCACTCG 60.747 63.158 17.98 5.27 0.00 4.18
1812 2519 3.626924 GGGCACACTCCCGACACT 61.627 66.667 0.00 0.00 36.38 3.55
1818 2525 4.394712 CTGTCCGGGCACACTCCC 62.395 72.222 3.51 0.00 43.02 4.30
1858 2565 2.750814 CCCATAAACCAGCCTGGAATT 58.249 47.619 19.90 14.15 40.96 2.17
1887 2594 1.006825 TGACGAAAGACACGCCATCG 61.007 55.000 0.00 0.00 42.43 3.84
1893 2600 2.410785 TGTACCTGACGAAAGACACG 57.589 50.000 0.00 0.00 0.00 4.49
1926 2633 6.758416 GCACATCATACTTGTCATCTTCACTA 59.242 38.462 0.00 0.00 0.00 2.74
1932 2639 4.080695 ACAGGCACATCATACTTGTCATCT 60.081 41.667 0.00 0.00 0.00 2.90
1941 2648 1.133025 GCACCAACAGGCACATCATAC 59.867 52.381 0.00 0.00 0.00 2.39
1952 2659 2.669569 CCTCCGTGGCACCAACAG 60.670 66.667 12.86 2.56 0.00 3.16
2016 2723 3.665675 GAGGTAGTGTGGGCGCAGG 62.666 68.421 10.83 0.00 0.00 4.85
2017 2724 2.125512 GAGGTAGTGTGGGCGCAG 60.126 66.667 10.83 0.00 0.00 5.18
2022 2729 3.000819 TGCGGGAGGTAGTGTGGG 61.001 66.667 0.00 0.00 0.00 4.61
2025 2732 1.542187 GGTTCTGCGGGAGGTAGTGT 61.542 60.000 0.00 0.00 0.00 3.55
2034 2741 4.820744 CCCCCATGGTTCTGCGGG 62.821 72.222 11.73 9.12 38.52 6.13
2052 2759 1.302271 AAAGGTTTCGTCCCTCGGC 60.302 57.895 0.00 0.00 40.32 5.54
2061 2768 3.129287 CCCTCATCAATCCAAAGGTTTCG 59.871 47.826 0.00 0.00 0.00 3.46
2083 2790 1.535462 CACCACCTCGGACAAATTGAC 59.465 52.381 0.00 0.00 38.63 3.18
2130 2837 3.072330 TGTCCTGGTCTTGCTTATTGTCA 59.928 43.478 0.00 0.00 0.00 3.58
2175 2882 1.302511 GGATGTCACAACCAGCGGT 60.303 57.895 0.00 0.00 37.65 5.68
2178 2885 1.639298 GAGCGGATGTCACAACCAGC 61.639 60.000 4.76 8.61 0.00 4.85
2203 2910 1.899534 GTGGGTTTGGGTAGCGCAA 60.900 57.895 11.47 0.00 34.59 4.85
2229 2936 7.047891 TCTTGTTGATGTATATCACCTTGTCC 58.952 38.462 1.03 0.00 42.79 4.02
2241 2948 3.535561 CGCCTCCTTCTTGTTGATGTAT 58.464 45.455 0.00 0.00 0.00 2.29
2277 2984 4.954118 ACCGGCACACCCCTCTCA 62.954 66.667 0.00 0.00 0.00 3.27
2303 3010 1.134310 CATCATGACCAGCCTGCACTA 60.134 52.381 0.00 0.00 0.00 2.74
2316 3023 3.055240 TGACATACAGTGCCACATCATGA 60.055 43.478 0.00 0.00 0.00 3.07
2371 3078 6.754209 GCATATATGACCTCAGTCTTATTCCG 59.246 42.308 17.10 0.00 43.91 4.30
2529 3236 2.042537 TCGCTGAGGCCTCCATCT 60.043 61.111 29.95 0.00 34.44 2.90
2544 3251 7.959733 ACAATACACTGTTATTGTACATGTCG 58.040 34.615 18.27 0.00 42.90 4.35
2565 3272 3.377253 ACCTGCTGATCATCCAACAAT 57.623 42.857 0.00 0.00 0.00 2.71
2566 3273 2.885135 ACCTGCTGATCATCCAACAA 57.115 45.000 0.00 0.00 0.00 2.83
2622 3329 1.028130 TCTCACCTCGAGCTGCTATG 58.972 55.000 6.99 0.00 41.98 2.23
2730 3437 4.020218 TCAATCCAGTAAGTCTTGACCCTG 60.020 45.833 0.00 2.29 0.00 4.45
2880 3587 8.844244 GTTGGATCAATAATATTCTTGCACTCT 58.156 33.333 8.35 0.00 0.00 3.24
3231 3938 2.427453 GACATAGAAACCTCGGAGCTCA 59.573 50.000 17.19 0.00 0.00 4.26
3252 3959 1.139989 ACTTGACGTGCACTGAATCG 58.860 50.000 16.19 2.55 0.00 3.34
3362 4069 0.900647 CTCCCAGAGGACACGGTTCT 60.901 60.000 0.00 0.00 37.19 3.01
3432 4139 1.269448 TGCTTCATTCCGGTGAAAAGC 59.731 47.619 20.03 20.03 41.52 3.51
3462 4169 6.536582 CCTCTACATTTTCACTGTCATACCTG 59.463 42.308 0.00 0.00 0.00 4.00
3544 4251 7.335924 CCTTCGTTTGACCTCTTTATATTCCAA 59.664 37.037 0.00 0.00 0.00 3.53
3546 4253 6.260271 CCCTTCGTTTGACCTCTTTATATTCC 59.740 42.308 0.00 0.00 0.00 3.01
3736 4444 8.503428 ACACTGGGAGATAAAGATTGATCTAT 57.497 34.615 0.00 0.00 35.76 1.98
3774 4484 4.950475 TGAAAACAGGAATTGGTGTGTGTA 59.050 37.500 0.00 0.00 0.00 2.90
3880 4590 3.134623 TGGTACCATTCTGCCATGTAGAG 59.865 47.826 11.60 0.00 0.00 2.43
4098 4813 0.809241 CTGTCCCTCGAATGCTCTGC 60.809 60.000 0.00 0.00 0.00 4.26
4173 4888 8.565896 AATTCTAAGCACATTACAACATCTGA 57.434 30.769 0.00 0.00 0.00 3.27
4207 4922 4.946478 AGATGCTCCAGTAGTTATGGAC 57.054 45.455 0.00 0.00 41.96 4.02
4236 4951 9.865321 CAAAGTTTAATGGAATGATCAGTCAAT 57.135 29.630 23.34 15.86 38.01 2.57
4244 4959 8.579850 TCTACTGCAAAGTTTAATGGAATGAT 57.420 30.769 0.00 0.00 0.00 2.45
4258 4973 7.924947 TCATCAGTGATATTCTCTACTGCAAAG 59.075 37.037 5.03 0.00 40.15 2.77
4343 5058 8.776470 CACATTTTTCAACTTCCAAATAGCATT 58.224 29.630 0.00 0.00 0.00 3.56
4354 5069 5.741982 ACGTACAAGCACATTTTTCAACTTC 59.258 36.000 0.00 0.00 0.00 3.01
4366 5081 5.239744 ACCATTTTTCATACGTACAAGCACA 59.760 36.000 0.00 0.00 0.00 4.57
4367 5082 5.695818 ACCATTTTTCATACGTACAAGCAC 58.304 37.500 0.00 0.00 0.00 4.40
4368 5083 5.950758 ACCATTTTTCATACGTACAAGCA 57.049 34.783 0.00 0.00 0.00 3.91
4369 5084 7.064253 ACTCTACCATTTTTCATACGTACAAGC 59.936 37.037 0.00 0.00 0.00 4.01
4370 5085 8.475331 ACTCTACCATTTTTCATACGTACAAG 57.525 34.615 0.00 0.00 0.00 3.16
4371 5086 9.926158 TTACTCTACCATTTTTCATACGTACAA 57.074 29.630 0.00 0.00 0.00 2.41
4375 5090 9.314321 CAGATTACTCTACCATTTTTCATACGT 57.686 33.333 0.00 0.00 0.00 3.57
4376 5091 8.276325 GCAGATTACTCTACCATTTTTCATACG 58.724 37.037 0.00 0.00 0.00 3.06
4377 5092 9.109393 TGCAGATTACTCTACCATTTTTCATAC 57.891 33.333 0.00 0.00 0.00 2.39
4378 5093 9.851686 ATGCAGATTACTCTACCATTTTTCATA 57.148 29.630 0.00 0.00 0.00 2.15
4379 5094 8.757982 ATGCAGATTACTCTACCATTTTTCAT 57.242 30.769 0.00 0.00 0.00 2.57
4389 5104 5.525378 CACCCTTGAATGCAGATTACTCTAC 59.475 44.000 0.00 0.00 0.00 2.59
4413 5128 5.791336 TCTGTACATGGTCATATCCAGAC 57.209 43.478 0.00 0.00 41.05 3.51
4442 5158 9.883142 CTAGCTCTTATATTTCTTTATGGAGGG 57.117 37.037 0.00 0.00 0.00 4.30
4454 5170 9.413048 GCGTTTAGATCACTAGCTCTTATATTT 57.587 33.333 0.00 0.00 0.00 1.40
4455 5171 8.798402 AGCGTTTAGATCACTAGCTCTTATATT 58.202 33.333 0.00 0.00 0.00 1.28
4456 5172 8.343168 AGCGTTTAGATCACTAGCTCTTATAT 57.657 34.615 0.00 0.00 0.00 0.86
4457 5173 7.662258 AGAGCGTTTAGATCACTAGCTCTTATA 59.338 37.037 19.75 0.00 44.65 0.98
4458 5174 6.488683 AGAGCGTTTAGATCACTAGCTCTTAT 59.511 38.462 19.75 6.04 44.65 1.73
4459 5175 5.823570 AGAGCGTTTAGATCACTAGCTCTTA 59.176 40.000 19.75 0.00 44.65 2.10
4460 5176 4.642885 AGAGCGTTTAGATCACTAGCTCTT 59.357 41.667 19.75 9.75 44.65 2.85
4461 5177 4.204012 AGAGCGTTTAGATCACTAGCTCT 58.796 43.478 19.75 19.75 43.47 4.09
4462 5178 4.561735 AGAGCGTTTAGATCACTAGCTC 57.438 45.455 16.91 16.91 41.03 4.09
4463 5179 4.993029 AAGAGCGTTTAGATCACTAGCT 57.007 40.909 0.00 0.00 37.82 3.32
4464 5180 8.973835 AATATAAGAGCGTTTAGATCACTAGC 57.026 34.615 0.00 0.00 37.82 3.42
4475 5191 9.099454 CCTCTGTAAAGAAATATAAGAGCGTTT 57.901 33.333 0.00 0.00 0.00 3.60
4476 5192 7.711339 CCCTCTGTAAAGAAATATAAGAGCGTT 59.289 37.037 0.00 0.00 0.00 4.84
4477 5193 7.069578 TCCCTCTGTAAAGAAATATAAGAGCGT 59.930 37.037 0.00 0.00 0.00 5.07
4478 5194 7.434492 TCCCTCTGTAAAGAAATATAAGAGCG 58.566 38.462 0.00 0.00 0.00 5.03
4479 5195 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
4486 5202 9.765295 ACTTAGTACTCCCTCTGTAAAGAAATA 57.235 33.333 0.00 0.00 0.00 1.40
4487 5203 8.667592 ACTTAGTACTCCCTCTGTAAAGAAAT 57.332 34.615 0.00 0.00 0.00 2.17
4488 5204 8.365647 CAACTTAGTACTCCCTCTGTAAAGAAA 58.634 37.037 0.00 0.00 0.00 2.52
4489 5205 7.508296 ACAACTTAGTACTCCCTCTGTAAAGAA 59.492 37.037 0.00 0.00 0.00 2.52
4490 5206 7.008941 ACAACTTAGTACTCCCTCTGTAAAGA 58.991 38.462 0.00 0.00 0.00 2.52
4491 5207 7.229581 ACAACTTAGTACTCCCTCTGTAAAG 57.770 40.000 0.00 0.00 0.00 1.85
4492 5208 7.607615 AACAACTTAGTACTCCCTCTGTAAA 57.392 36.000 0.00 0.00 0.00 2.01
4493 5209 7.607615 AAACAACTTAGTACTCCCTCTGTAA 57.392 36.000 0.00 0.00 0.00 2.41
4494 5210 7.439381 CAAAACAACTTAGTACTCCCTCTGTA 58.561 38.462 0.00 0.00 0.00 2.74
4495 5211 6.289064 CAAAACAACTTAGTACTCCCTCTGT 58.711 40.000 0.00 0.00 0.00 3.41
4496 5212 5.179555 GCAAAACAACTTAGTACTCCCTCTG 59.820 44.000 0.00 0.00 0.00 3.35
4497 5213 5.163237 TGCAAAACAACTTAGTACTCCCTCT 60.163 40.000 0.00 0.00 0.00 3.69
4498 5214 5.061179 TGCAAAACAACTTAGTACTCCCTC 58.939 41.667 0.00 0.00 0.00 4.30
4499 5215 5.043737 TGCAAAACAACTTAGTACTCCCT 57.956 39.130 0.00 0.00 0.00 4.20
4500 5216 5.106277 GGATGCAAAACAACTTAGTACTCCC 60.106 44.000 0.00 0.00 0.00 4.30
4501 5217 5.472137 TGGATGCAAAACAACTTAGTACTCC 59.528 40.000 0.00 0.00 0.00 3.85
4502 5218 6.371389 GTGGATGCAAAACAACTTAGTACTC 58.629 40.000 0.00 0.00 0.00 2.59
4503 5219 5.049680 CGTGGATGCAAAACAACTTAGTACT 60.050 40.000 0.00 0.00 0.00 2.73
4504 5220 5.144359 CGTGGATGCAAAACAACTTAGTAC 58.856 41.667 0.00 0.00 0.00 2.73
4505 5221 4.214545 CCGTGGATGCAAAACAACTTAGTA 59.785 41.667 0.00 0.00 0.00 1.82
4506 5222 3.004315 CCGTGGATGCAAAACAACTTAGT 59.996 43.478 0.00 0.00 0.00 2.24
4507 5223 3.564511 CCGTGGATGCAAAACAACTTAG 58.435 45.455 0.00 0.00 0.00 2.18
4508 5224 2.287909 GCCGTGGATGCAAAACAACTTA 60.288 45.455 0.00 0.00 0.00 2.24
4511 5227 0.249238 TGCCGTGGATGCAAAACAAC 60.249 50.000 0.00 0.00 35.40 3.32
4517 5233 1.184431 AAATGATGCCGTGGATGCAA 58.816 45.000 0.00 0.00 42.92 4.08
4520 5236 2.687425 TGGTTAAATGATGCCGTGGATG 59.313 45.455 0.00 0.00 0.00 3.51
4525 5241 3.009723 CTGACTGGTTAAATGATGCCGT 58.990 45.455 0.00 0.00 0.00 5.68
4531 5247 6.373005 TGAATCCTCTGACTGGTTAAATGA 57.627 37.500 0.00 0.00 0.00 2.57
4532 5248 7.362401 CCTTTGAATCCTCTGACTGGTTAAATG 60.362 40.741 0.00 0.00 0.00 2.32
4533 5249 6.660949 CCTTTGAATCCTCTGACTGGTTAAAT 59.339 38.462 0.00 0.00 0.00 1.40
4534 5250 6.003950 CCTTTGAATCCTCTGACTGGTTAAA 58.996 40.000 0.00 0.00 0.00 1.52
4535 5251 5.309543 TCCTTTGAATCCTCTGACTGGTTAA 59.690 40.000 0.00 0.00 0.00 2.01
4536 5252 4.844085 TCCTTTGAATCCTCTGACTGGTTA 59.156 41.667 0.00 0.00 0.00 2.85
4537 5253 3.652869 TCCTTTGAATCCTCTGACTGGTT 59.347 43.478 0.00 0.00 0.00 3.67
4538 5254 3.251484 TCCTTTGAATCCTCTGACTGGT 58.749 45.455 0.00 0.00 0.00 4.00
4539 5255 3.517100 TCTCCTTTGAATCCTCTGACTGG 59.483 47.826 0.00 0.00 0.00 4.00
4540 5256 4.465660 TCTCTCCTTTGAATCCTCTGACTG 59.534 45.833 0.00 0.00 0.00 3.51
4541 5257 4.682563 TCTCTCCTTTGAATCCTCTGACT 58.317 43.478 0.00 0.00 0.00 3.41
4542 5258 5.413309 TTCTCTCCTTTGAATCCTCTGAC 57.587 43.478 0.00 0.00 0.00 3.51
4543 5259 6.633325 ATTTCTCTCCTTTGAATCCTCTGA 57.367 37.500 0.00 0.00 0.00 3.27
4544 5260 6.658391 ACAATTTCTCTCCTTTGAATCCTCTG 59.342 38.462 0.00 0.00 0.00 3.35
4545 5261 6.658391 CACAATTTCTCTCCTTTGAATCCTCT 59.342 38.462 0.00 0.00 0.00 3.69
4546 5262 6.624642 GCACAATTTCTCTCCTTTGAATCCTC 60.625 42.308 0.00 0.00 0.00 3.71
4547 5263 5.184671 GCACAATTTCTCTCCTTTGAATCCT 59.815 40.000 0.00 0.00 0.00 3.24
4548 5264 5.047802 TGCACAATTTCTCTCCTTTGAATCC 60.048 40.000 0.00 0.00 0.00 3.01
4549 5265 6.017400 TGCACAATTTCTCTCCTTTGAATC 57.983 37.500 0.00 0.00 0.00 2.52
4550 5266 6.209986 TGATGCACAATTTCTCTCCTTTGAAT 59.790 34.615 0.00 0.00 0.00 2.57
4551 5267 5.535783 TGATGCACAATTTCTCTCCTTTGAA 59.464 36.000 0.00 0.00 0.00 2.69
4616 5332 6.207810 CAGTACAACACCCTTTGCCTTTTATA 59.792 38.462 0.00 0.00 0.00 0.98
4631 5347 6.418956 CAACATACAACAGACAGTACAACAC 58.581 40.000 0.00 0.00 0.00 3.32
4655 5371 4.876107 TGTTTAAAGAGCTATAGCACTGGC 59.124 41.667 26.07 13.69 41.01 4.85
4680 5396 6.115446 TGAAGATGTTCCAATAGACATGGAC 58.885 40.000 0.00 0.00 46.37 4.02
4734 5450 8.613060 ATCTTGCCATTGTTGTATCTATGTAG 57.387 34.615 0.00 0.00 0.00 2.74
4735 5451 8.839343 CAATCTTGCCATTGTTGTATCTATGTA 58.161 33.333 0.00 0.00 0.00 2.29
4742 5458 5.743636 AACCAATCTTGCCATTGTTGTAT 57.256 34.783 0.00 0.00 32.61 2.29
4750 5466 3.583966 ACATGGAAAACCAATCTTGCCAT 59.416 39.130 0.00 0.00 35.18 4.40
4754 5470 5.710513 TCTGACATGGAAAACCAATCTTG 57.289 39.130 0.00 0.00 0.00 3.02
4767 5483 4.685628 CCAAAAACGGAAAATCTGACATGG 59.314 41.667 0.00 0.00 0.00 3.66
4768 5484 4.685628 CCCAAAAACGGAAAATCTGACATG 59.314 41.667 0.00 0.00 0.00 3.21
4769 5485 4.343814 ACCCAAAAACGGAAAATCTGACAT 59.656 37.500 0.00 0.00 0.00 3.06
4770 5486 3.702045 ACCCAAAAACGGAAAATCTGACA 59.298 39.130 0.00 0.00 0.00 3.58
4771 5487 4.295870 GACCCAAAAACGGAAAATCTGAC 58.704 43.478 0.00 0.00 0.00 3.51
4772 5488 3.003897 CGACCCAAAAACGGAAAATCTGA 59.996 43.478 0.00 0.00 0.00 3.27
4773 5489 3.003897 TCGACCCAAAAACGGAAAATCTG 59.996 43.478 0.00 0.00 0.00 2.90
4774 5490 3.215975 TCGACCCAAAAACGGAAAATCT 58.784 40.909 0.00 0.00 0.00 2.40
4775 5491 3.629438 TCGACCCAAAAACGGAAAATC 57.371 42.857 0.00 0.00 0.00 2.17
4776 5492 3.570550 TCATCGACCCAAAAACGGAAAAT 59.429 39.130 0.00 0.00 0.00 1.82
4777 5493 2.950309 TCATCGACCCAAAAACGGAAAA 59.050 40.909 0.00 0.00 0.00 2.29
4779 5495 2.257691 TCATCGACCCAAAAACGGAA 57.742 45.000 0.00 0.00 0.00 4.30
4780 5496 2.483014 ATCATCGACCCAAAAACGGA 57.517 45.000 0.00 0.00 0.00 4.69
4781 5497 3.241701 CAAATCATCGACCCAAAAACGG 58.758 45.455 0.00 0.00 0.00 4.44
4782 5498 3.896122 ACAAATCATCGACCCAAAAACG 58.104 40.909 0.00 0.00 0.00 3.60
4783 5499 5.121221 AGACAAATCATCGACCCAAAAAC 57.879 39.130 0.00 0.00 0.00 2.43
4801 5517 1.476845 TTGCAAGTAGGGCGGAGACA 61.477 55.000 0.00 0.00 37.00 3.41
4802 5518 0.741221 CTTGCAAGTAGGGCGGAGAC 60.741 60.000 18.65 0.00 0.00 3.36
4811 5527 4.549458 CACATTTCCCAACTTGCAAGTAG 58.451 43.478 31.31 23.94 38.57 2.57
4814 5530 2.137523 GCACATTTCCCAACTTGCAAG 58.862 47.619 24.84 24.84 0.00 4.01
4843 5561 4.963318 TCCATAGCTCAAGGGATACAAG 57.037 45.455 0.00 0.00 39.74 3.16
4846 5564 4.040952 ACACATCCATAGCTCAAGGGATAC 59.959 45.833 2.44 0.00 38.05 2.24
4851 5569 3.548745 TCACACATCCATAGCTCAAGG 57.451 47.619 0.00 0.00 0.00 3.61
4852 5570 5.121105 TGATTCACACATCCATAGCTCAAG 58.879 41.667 0.00 0.00 0.00 3.02
4869 5588 1.514678 GGCGCTGGTTGTGTGATTCA 61.515 55.000 7.64 0.00 0.00 2.57
4870 5589 1.210155 GGCGCTGGTTGTGTGATTC 59.790 57.895 7.64 0.00 0.00 2.52
4871 5590 0.036164 TAGGCGCTGGTTGTGTGATT 59.964 50.000 7.64 0.00 0.00 2.57
4872 5591 0.253044 ATAGGCGCTGGTTGTGTGAT 59.747 50.000 7.64 0.00 0.00 3.06
4873 5592 0.673333 CATAGGCGCTGGTTGTGTGA 60.673 55.000 7.64 0.00 0.00 3.58
4874 5593 0.673333 TCATAGGCGCTGGTTGTGTG 60.673 55.000 7.64 0.00 0.00 3.82
4875 5594 0.673644 GTCATAGGCGCTGGTTGTGT 60.674 55.000 7.64 0.00 0.00 3.72
4876 5595 0.391661 AGTCATAGGCGCTGGTTGTG 60.392 55.000 7.64 0.00 0.00 3.33
4878 5597 0.108186 TCAGTCATAGGCGCTGGTTG 60.108 55.000 7.64 0.21 0.00 3.77
4879 5598 0.176680 CTCAGTCATAGGCGCTGGTT 59.823 55.000 7.64 0.00 0.00 3.67
4889 5818 6.349300 GCCCTGAAATAAACTCTCAGTCATA 58.651 40.000 0.00 0.00 35.78 2.15
4893 5822 3.260884 TCGCCCTGAAATAAACTCTCAGT 59.739 43.478 0.00 0.00 35.78 3.41
4904 5833 3.010420 GCTTAAGAGTTCGCCCTGAAAT 58.990 45.455 6.67 0.00 38.60 2.17
4957 5900 1.956477 GGAACTTCCACAACATGCACT 59.044 47.619 2.62 0.00 36.28 4.40
4959 5902 1.955778 CAGGAACTTCCACAACATGCA 59.044 47.619 10.57 0.00 39.61 3.96
4960 5903 1.956477 ACAGGAACTTCCACAACATGC 59.044 47.619 10.57 0.00 39.61 4.06


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

AutoCloner maintained by Alex Coulton.