Multiple sequence alignment - TraesCS5D01G139700

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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 TraesCS5D01G139700 chr5D 100.000 4582 0 0 1 4582 223228484 223233065 0.000000e+00 8462.0
1 TraesCS5D01G139700 chr5A 92.973 1423 60 21 869 2262 295586660 295588071 0.000000e+00 2037.0
2 TraesCS5D01G139700 chr5A 91.651 1066 47 10 3518 4582 295615684 295616708 0.000000e+00 1437.0
3 TraesCS5D01G139700 chr5A 92.077 732 51 6 1 728 295585940 295586668 0.000000e+00 1024.0
4 TraesCS5D01G139700 chr5A 95.087 631 29 1 2259 2887 295588344 295588974 0.000000e+00 992.0
5 TraesCS5D01G139700 chr5A 97.842 556 11 1 2967 3522 295588970 295589524 0.000000e+00 959.0
6 TraesCS5D01G139700 chr5A 80.189 530 94 10 4060 4582 597731041 597730516 2.000000e-103 387.0
7 TraesCS5D01G139700 chr5A 75.216 347 60 11 75 396 647608287 647607942 1.720000e-29 141.0
8 TraesCS5D01G139700 chr5B 97.548 938 20 3 2967 3902 249712801 249711865 0.000000e+00 1602.0
9 TraesCS5D01G139700 chr5B 92.132 788 33 11 1410 2184 249714072 249713301 0.000000e+00 1085.0
10 TraesCS5D01G139700 chr5B 92.804 667 40 6 3901 4561 249711569 249710905 0.000000e+00 959.0
11 TraesCS5D01G139700 chr5B 97.699 478 11 0 869 1346 249714672 249714195 0.000000e+00 822.0
12 TraesCS5D01G139700 chr5B 95.472 508 23 0 2373 2880 249713308 249712801 0.000000e+00 811.0
13 TraesCS5D01G139700 chr5B 93.007 429 22 6 305 728 249715089 249714664 1.810000e-173 619.0
14 TraesCS5D01G139700 chr5B 94.792 96 4 1 2886 2980 26770499 26770404 1.030000e-31 148.0
15 TraesCS5D01G139700 chr5B 85.263 95 12 2 305 397 709230648 709230742 3.770000e-16 97.1
16 TraesCS5D01G139700 chr1A 82.548 573 89 10 4014 4582 300579954 300580519 1.150000e-135 494.0
17 TraesCS5D01G139700 chr1A 91.071 112 6 3 2882 2993 575557358 575557251 1.030000e-31 148.0
18 TraesCS5D01G139700 chr1A 93.000 100 5 2 2871 2970 69995982 69995885 1.330000e-30 145.0
19 TraesCS5D01G139700 chr7D 80.822 584 102 9 4005 4582 65899477 65898898 2.510000e-122 449.0
20 TraesCS5D01G139700 chr7D 96.774 93 3 0 2886 2978 94261311 94261219 6.140000e-34 156.0
21 TraesCS5D01G139700 chr7D 79.888 179 32 4 4334 4512 621653336 621653162 1.340000e-25 128.0
22 TraesCS5D01G139700 chr7D 92.157 51 2 2 348 396 123202101 123202151 2.290000e-08 71.3
23 TraesCS5D01G139700 chr3A 81.090 587 84 19 4005 4581 71234570 71234001 1.170000e-120 444.0
24 TraesCS5D01G139700 chr3A 76.577 333 52 15 86 395 456717013 456717342 4.740000e-35 159.0
25 TraesCS5D01G139700 chr6A 81.328 482 74 12 4005 4480 22195547 22195076 1.200000e-100 377.0
26 TraesCS5D01G139700 chr6A 90.196 51 2 3 348 395 477135776 477135726 3.830000e-06 63.9
27 TraesCS5D01G139700 chr6B 81.148 488 65 16 4006 4485 37831489 37831021 2.600000e-97 366.0
28 TraesCS5D01G139700 chr6B 78.425 584 93 22 4005 4581 695129886 695130443 2.620000e-92 350.0
29 TraesCS5D01G139700 chr7A 85.433 254 33 4 4197 4448 15250907 15250656 1.260000e-65 261.0
30 TraesCS5D01G139700 chr7A 91.837 147 11 1 729 874 732909260 732909406 2.160000e-48 204.0
31 TraesCS5D01G139700 chr7A 75.000 428 75 16 4 402 539328391 539327967 7.880000e-38 169.0
32 TraesCS5D01G139700 chr3D 95.775 142 6 0 729 870 571857174 571857033 3.570000e-56 230.0
33 TraesCS5D01G139700 chr3D 94.286 140 8 0 729 868 576210567 576210706 9.980000e-52 215.0
34 TraesCS5D01G139700 chr3D 92.857 140 6 2 729 868 170555470 170555605 2.800000e-47 200.0
35 TraesCS5D01G139700 chr3D 96.739 92 2 1 2885 2975 497727998 497727907 7.940000e-33 152.0
36 TraesCS5D01G139700 chr3D 93.939 99 4 2 2876 2973 400749705 400749608 1.030000e-31 148.0
37 TraesCS5D01G139700 chr2D 95.714 140 6 0 729 868 563800992 563801131 4.610000e-55 226.0
38 TraesCS5D01G139700 chr2D 95.588 136 6 0 729 864 136830594 136830729 7.720000e-53 219.0
39 TraesCS5D01G139700 chr2D 96.552 116 2 2 753 868 89199410 89199297 1.680000e-44 191.0
40 TraesCS5D01G139700 chr2D 91.509 106 6 3 2868 2971 434352431 434352535 4.780000e-30 143.0
41 TraesCS5D01G139700 chr2D 75.221 339 56 14 87 400 2508184 2507849 8.000000e-28 135.0
42 TraesCS5D01G139700 chr6D 89.308 159 17 0 717 875 32365265 32365107 2.800000e-47 200.0
43 TraesCS5D01G139700 chr1B 90.845 142 13 0 729 870 677279026 677279167 1.680000e-44 191.0
44 TraesCS5D01G139700 chr1B 88.679 53 3 3 352 401 550370678 550370626 1.380000e-05 62.1
45 TraesCS5D01G139700 chr1D 77.059 340 53 13 86 402 208513471 208513808 6.090000e-39 172.0
46 TraesCS5D01G139700 chr1D 76.119 335 52 14 86 396 18988370 18988700 2.860000e-32 150.0
47 TraesCS5D01G139700 chr1D 93.269 104 4 3 2877 2979 460866495 460866596 2.860000e-32 150.0
48 TraesCS5D01G139700 chr2B 96.703 91 3 0 2883 2973 546125889 546125979 7.940000e-33 152.0
49 TraesCS5D01G139700 chr2B 73.639 349 65 18 74 399 151101953 151102297 4.850000e-20 110.0
50 TraesCS5D01G139700 chr2B 81.818 99 17 1 72 170 673053020 673053117 1.060000e-11 82.4
51 TraesCS5D01G139700 chr4B 73.994 323 61 10 78 377 478572984 478573306 4.850000e-20 110.0
52 TraesCS5D01G139700 chr4B 80.612 98 16 2 299 396 4606170 4606076 6.360000e-09 73.1
53 TraesCS5D01G139700 chr7B 93.023 43 2 1 357 398 597315105 597315063 1.380000e-05 62.1


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 TraesCS5D01G139700 chr5D 223228484 223233065 4581 False 8462 8462 100.00000 1 4582 1 chr5D.!!$F1 4581
1 TraesCS5D01G139700 chr5A 295615684 295616708 1024 False 1437 1437 91.65100 3518 4582 1 chr5A.!!$F1 1064
2 TraesCS5D01G139700 chr5A 295585940 295589524 3584 False 1253 2037 94.49475 1 3522 4 chr5A.!!$F2 3521
3 TraesCS5D01G139700 chr5A 597730516 597731041 525 True 387 387 80.18900 4060 4582 1 chr5A.!!$R1 522
4 TraesCS5D01G139700 chr5B 249710905 249715089 4184 True 983 1602 94.77700 305 4561 6 chr5B.!!$R2 4256
5 TraesCS5D01G139700 chr1A 300579954 300580519 565 False 494 494 82.54800 4014 4582 1 chr1A.!!$F1 568
6 TraesCS5D01G139700 chr7D 65898898 65899477 579 True 449 449 80.82200 4005 4582 1 chr7D.!!$R1 577
7 TraesCS5D01G139700 chr3A 71234001 71234570 569 True 444 444 81.09000 4005 4581 1 chr3A.!!$R1 576
8 TraesCS5D01G139700 chr6B 695129886 695130443 557 False 350 350 78.42500 4005 4581 1 chr6B.!!$F1 576

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
824 832 0.028242 GACGAGCGAGATCATGTCGT 59.972 55.0 6.02 10.89 46.02 4.34 F
1008 1019 0.177836 TCGCGACCATGATGACCATT 59.822 50.0 3.71 0.00 31.94 3.16 F
2175 2268 0.030908 CGAGAATGTAGGGGACGAGC 59.969 60.0 0.00 0.00 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2156 2249 0.030908 GCTCGTCCCCTACATTCTCG 59.969 60.0 0.0 0.0 0.00 4.04 R
2749 3123 0.744771 GAACTGAAGGGGATGGCGTC 60.745 60.0 0.0 0.0 0.00 5.19 R
3958 4637 1.089112 TGTGCCAAGATGAAGCATCG 58.911 50.0 0.0 0.0 44.67 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
33 34 2.027625 GGTCACTTTCGTCCTGGCG 61.028 63.158 4.48 4.48 0.00 5.69
35 36 3.423154 CACTTTCGTCCTGGCGGC 61.423 66.667 0.00 0.00 0.00 6.53
76 77 0.815095 TGCCGAGCGAAAGACTATGA 59.185 50.000 0.00 0.00 0.00 2.15
84 85 3.255888 AGCGAAAGACTATGAGTGTCACA 59.744 43.478 5.62 0.00 36.94 3.58
132 133 2.145397 TCTCTTCGTGTCAGGGCTAT 57.855 50.000 0.00 0.00 0.00 2.97
133 134 3.292492 TCTCTTCGTGTCAGGGCTATA 57.708 47.619 0.00 0.00 0.00 1.31
164 165 0.531974 TTGTCAACTGTGGACTCGGC 60.532 55.000 15.90 0.00 36.26 5.54
181 183 2.046892 CAGTGGTCTCTTGGGGCG 60.047 66.667 0.00 0.00 0.00 6.13
187 189 1.070786 GTCTCTTGGGGCGTTGTCA 59.929 57.895 0.00 0.00 0.00 3.58
198 200 2.158957 GGGCGTTGTCATGGATCTTAGA 60.159 50.000 0.00 0.00 0.00 2.10
213 215 4.837896 TCTTAGATGTGCTAGGTCATCG 57.162 45.455 0.00 0.00 43.34 3.84
229 231 3.276091 CGCGTGGGCTGTGTTCAA 61.276 61.111 0.00 0.00 36.88 2.69
235 237 2.034558 CGTGGGCTGTGTTCAAATCTTT 59.965 45.455 0.00 0.00 0.00 2.52
241 243 4.423732 GCTGTGTTCAAATCTTTGTGTGT 58.576 39.130 2.82 0.00 39.18 3.72
248 250 7.116233 GTGTTCAAATCTTTGTGTGTTCTTTGT 59.884 33.333 2.82 0.00 39.18 2.83
249 251 7.655328 TGTTCAAATCTTTGTGTGTTCTTTGTT 59.345 29.630 2.82 0.00 39.18 2.83
256 258 3.348119 TGTGTGTTCTTTGTTGGTAGCA 58.652 40.909 0.00 0.00 0.00 3.49
263 265 4.530710 TCTTTGTTGGTAGCATAGTCGT 57.469 40.909 0.00 0.00 0.00 4.34
267 269 2.559231 TGTTGGTAGCATAGTCGTGTGA 59.441 45.455 0.00 0.00 0.00 3.58
273 275 4.334759 GGTAGCATAGTCGTGTGAGTTCTA 59.665 45.833 0.00 0.00 0.00 2.10
275 277 3.756963 AGCATAGTCGTGTGAGTTCTACA 59.243 43.478 0.00 0.00 0.00 2.74
277 279 4.500837 GCATAGTCGTGTGAGTTCTACATG 59.499 45.833 0.00 0.00 36.60 3.21
285 287 6.038985 CGTGTGAGTTCTACATGATCTGATT 58.961 40.000 0.00 0.00 37.26 2.57
303 305 2.051334 TTATCATGGGACCGGCTTTG 57.949 50.000 0.00 0.00 0.00 2.77
307 309 1.074084 TCATGGGACCGGCTTTGTAAA 59.926 47.619 0.00 0.00 0.00 2.01
342 344 2.087501 TCTTGCATCGTTCGCCTTTA 57.912 45.000 0.00 0.00 0.00 1.85
420 423 8.884124 AAAGATTTGAAGGTGAGGATTCATTA 57.116 30.769 0.00 0.00 35.47 1.90
421 424 7.872113 AGATTTGAAGGTGAGGATTCATTAC 57.128 36.000 0.00 0.00 35.47 1.89
424 429 3.517901 TGAAGGTGAGGATTCATTACGGT 59.482 43.478 0.00 0.00 35.39 4.83
446 451 3.181429 TGAGCTTTCCAACCTCAGGATTT 60.181 43.478 0.00 0.00 34.56 2.17
449 454 5.393866 AGCTTTCCAACCTCAGGATTTAAA 58.606 37.500 0.00 0.00 34.56 1.52
610 615 3.717294 GTCCGTCCCACCTGCCAT 61.717 66.667 0.00 0.00 0.00 4.40
611 616 2.933287 TCCGTCCCACCTGCCATT 60.933 61.111 0.00 0.00 0.00 3.16
645 650 1.525384 CGAAAGACGACGAGACGAGAG 60.525 57.143 0.00 0.00 45.77 3.20
658 663 0.969917 ACGAGAGCAGAGCACCAGAT 60.970 55.000 0.00 0.00 0.00 2.90
661 666 2.035704 CGAGAGCAGAGCACCAGATATT 59.964 50.000 0.00 0.00 0.00 1.28
672 680 6.035368 AGCACCAGATATTCTATACTGCAG 57.965 41.667 13.48 13.48 0.00 4.41
696 704 2.322422 CGAGTACGACGCGTAGGG 59.678 66.667 23.21 13.06 43.06 3.53
727 735 4.137543 CTCATCCCTTCCCTTTAAATCCG 58.862 47.826 0.00 0.00 0.00 4.18
728 736 3.117663 TCATCCCTTCCCTTTAAATCCGG 60.118 47.826 0.00 0.00 0.00 5.14
729 737 2.564518 TCCCTTCCCTTTAAATCCGGA 58.435 47.619 6.61 6.61 0.00 5.14
730 738 2.508300 TCCCTTCCCTTTAAATCCGGAG 59.492 50.000 11.34 0.00 0.00 4.63
731 739 2.508300 CCCTTCCCTTTAAATCCGGAGA 59.492 50.000 11.34 0.00 0.00 3.71
732 740 3.053917 CCCTTCCCTTTAAATCCGGAGAA 60.054 47.826 11.34 4.24 0.00 2.87
733 741 3.945921 CCTTCCCTTTAAATCCGGAGAAC 59.054 47.826 11.34 0.00 0.00 3.01
734 742 4.324331 CCTTCCCTTTAAATCCGGAGAACT 60.324 45.833 11.34 0.00 0.00 3.01
735 743 4.216411 TCCCTTTAAATCCGGAGAACTG 57.784 45.455 11.34 0.00 0.00 3.16
736 744 2.683362 CCCTTTAAATCCGGAGAACTGC 59.317 50.000 11.34 0.00 0.00 4.40
737 745 3.610911 CCTTTAAATCCGGAGAACTGCT 58.389 45.455 11.34 0.00 0.00 4.24
738 746 4.383770 CCCTTTAAATCCGGAGAACTGCTA 60.384 45.833 11.34 0.00 0.00 3.49
739 747 4.571176 CCTTTAAATCCGGAGAACTGCTAC 59.429 45.833 11.34 0.00 0.00 3.58
740 748 4.811969 TTAAATCCGGAGAACTGCTACA 57.188 40.909 11.34 0.00 0.00 2.74
741 749 2.674796 AATCCGGAGAACTGCTACAC 57.325 50.000 11.34 0.00 0.00 2.90
742 750 0.824759 ATCCGGAGAACTGCTACACC 59.175 55.000 11.34 0.00 0.00 4.16
743 751 0.251653 TCCGGAGAACTGCTACACCT 60.252 55.000 0.00 0.00 0.00 4.00
744 752 1.005097 TCCGGAGAACTGCTACACCTA 59.995 52.381 0.00 0.00 0.00 3.08
745 753 1.134560 CCGGAGAACTGCTACACCTAC 59.865 57.143 0.00 0.00 0.00 3.18
746 754 1.202154 CGGAGAACTGCTACACCTACG 60.202 57.143 0.00 0.00 0.00 3.51
747 755 2.089980 GGAGAACTGCTACACCTACGA 58.910 52.381 0.00 0.00 0.00 3.43
748 756 2.159407 GGAGAACTGCTACACCTACGAC 60.159 54.545 0.00 0.00 0.00 4.34
749 757 2.748532 GAGAACTGCTACACCTACGACT 59.251 50.000 0.00 0.00 0.00 4.18
750 758 3.937706 GAGAACTGCTACACCTACGACTA 59.062 47.826 0.00 0.00 0.00 2.59
751 759 4.330250 AGAACTGCTACACCTACGACTAA 58.670 43.478 0.00 0.00 0.00 2.24
752 760 4.948621 AGAACTGCTACACCTACGACTAAT 59.051 41.667 0.00 0.00 0.00 1.73
753 761 5.418209 AGAACTGCTACACCTACGACTAATT 59.582 40.000 0.00 0.00 0.00 1.40
754 762 5.656213 ACTGCTACACCTACGACTAATTT 57.344 39.130 0.00 0.00 0.00 1.82
755 763 5.648572 ACTGCTACACCTACGACTAATTTC 58.351 41.667 0.00 0.00 0.00 2.17
756 764 4.665212 TGCTACACCTACGACTAATTTCG 58.335 43.478 0.00 0.00 44.87 3.46
767 775 5.443101 CGACTAATTTCGTACGATGTACG 57.557 43.478 20.27 20.16 41.79 3.67
779 787 2.789208 CGATGTACGTACGACAATGGT 58.211 47.619 24.41 6.81 37.22 3.55
780 788 2.780014 CGATGTACGTACGACAATGGTC 59.220 50.000 24.41 13.73 37.68 4.02
781 789 3.728566 CGATGTACGTACGACAATGGTCA 60.729 47.826 24.41 8.73 39.43 4.02
782 790 3.206034 TGTACGTACGACAATGGTCAG 57.794 47.619 24.41 0.00 44.54 3.51
783 791 1.916000 GTACGTACGACAATGGTCAGC 59.084 52.381 24.41 0.00 44.54 4.26
784 792 0.315886 ACGTACGACAATGGTCAGCA 59.684 50.000 24.41 0.00 44.54 4.41
785 793 0.992072 CGTACGACAATGGTCAGCAG 59.008 55.000 10.44 0.00 44.54 4.24
786 794 0.721718 GTACGACAATGGTCAGCAGC 59.278 55.000 0.13 0.00 44.54 5.25
787 795 0.391130 TACGACAATGGTCAGCAGCC 60.391 55.000 0.13 0.00 44.54 4.85
788 796 2.743752 CGACAATGGTCAGCAGCCG 61.744 63.158 0.13 0.00 44.54 5.52
789 797 2.360350 ACAATGGTCAGCAGCCGG 60.360 61.111 0.00 0.00 0.00 6.13
790 798 2.360350 CAATGGTCAGCAGCCGGT 60.360 61.111 1.90 0.00 0.00 5.28
791 799 2.045926 AATGGTCAGCAGCCGGTC 60.046 61.111 1.90 0.00 0.00 4.79
792 800 3.958147 AATGGTCAGCAGCCGGTCG 62.958 63.158 1.90 0.00 0.00 4.79
794 802 4.148825 GGTCAGCAGCCGGTCGAT 62.149 66.667 1.90 0.00 0.00 3.59
795 803 2.583593 GTCAGCAGCCGGTCGATC 60.584 66.667 1.90 0.00 0.00 3.69
796 804 4.193334 TCAGCAGCCGGTCGATCG 62.193 66.667 12.09 12.09 0.00 3.69
803 811 2.812499 CCGGTCGATCGGTTGGAT 59.188 61.111 28.99 0.00 44.60 3.41
804 812 1.591594 CCGGTCGATCGGTTGGATG 60.592 63.158 28.99 0.88 44.60 3.51
805 813 1.591594 CGGTCGATCGGTTGGATGG 60.592 63.158 16.41 0.00 34.82 3.51
806 814 1.820581 GGTCGATCGGTTGGATGGA 59.179 57.895 16.41 0.00 37.52 3.41
808 816 0.870307 GTCGATCGGTTGGATGGACG 60.870 60.000 16.41 0.00 46.38 4.79
809 817 1.033202 TCGATCGGTTGGATGGACGA 61.033 55.000 16.41 0.00 35.28 4.20
810 818 0.595053 CGATCGGTTGGATGGACGAG 60.595 60.000 7.38 0.00 38.85 4.18
811 819 0.876342 GATCGGTTGGATGGACGAGC 60.876 60.000 0.00 0.00 38.85 5.03
812 820 2.629050 ATCGGTTGGATGGACGAGCG 62.629 60.000 0.00 0.00 44.71 5.03
813 821 2.577059 GGTTGGATGGACGAGCGA 59.423 61.111 0.00 0.00 0.00 4.93
814 822 1.519455 GGTTGGATGGACGAGCGAG 60.519 63.158 0.00 0.00 0.00 5.03
815 823 1.511305 GTTGGATGGACGAGCGAGA 59.489 57.895 0.00 0.00 0.00 4.04
816 824 0.103208 GTTGGATGGACGAGCGAGAT 59.897 55.000 0.00 0.00 0.00 2.75
817 825 0.385751 TTGGATGGACGAGCGAGATC 59.614 55.000 0.00 0.00 0.00 2.75
818 826 0.751643 TGGATGGACGAGCGAGATCA 60.752 55.000 0.00 0.00 0.00 2.92
819 827 0.600557 GGATGGACGAGCGAGATCAT 59.399 55.000 0.00 0.00 0.00 2.45
820 828 1.668337 GGATGGACGAGCGAGATCATG 60.668 57.143 0.00 0.00 0.00 3.07
821 829 1.000827 GATGGACGAGCGAGATCATGT 60.001 52.381 0.00 0.00 0.00 3.21
822 830 0.382158 TGGACGAGCGAGATCATGTC 59.618 55.000 0.00 0.00 0.00 3.06
823 831 0.658829 GGACGAGCGAGATCATGTCG 60.659 60.000 0.00 0.00 40.50 4.35
824 832 0.028242 GACGAGCGAGATCATGTCGT 59.972 55.000 6.02 10.89 46.02 4.34
825 833 1.260825 GACGAGCGAGATCATGTCGTA 59.739 52.381 6.02 0.00 43.55 3.43
826 834 1.003759 ACGAGCGAGATCATGTCGTAC 60.004 52.381 6.02 0.00 41.82 3.67
827 835 1.664629 GAGCGAGATCATGTCGTACG 58.335 55.000 9.53 9.53 39.69 3.67
828 836 1.260825 GAGCGAGATCATGTCGTACGA 59.739 52.381 15.28 15.28 39.69 3.43
829 837 1.669265 AGCGAGATCATGTCGTACGAA 59.331 47.619 21.39 10.90 39.69 3.85
830 838 2.096980 AGCGAGATCATGTCGTACGAAA 59.903 45.455 21.39 16.34 39.69 3.46
831 839 2.850060 GCGAGATCATGTCGTACGAAAA 59.150 45.455 21.39 12.05 39.69 2.29
832 840 3.486108 GCGAGATCATGTCGTACGAAAAT 59.514 43.478 21.39 13.93 39.69 1.82
833 841 4.026804 GCGAGATCATGTCGTACGAAAATT 60.027 41.667 21.39 3.59 39.69 1.82
834 842 5.415366 CGAGATCATGTCGTACGAAAATTG 58.585 41.667 21.39 11.14 32.62 2.32
835 843 5.004440 CGAGATCATGTCGTACGAAAATTGT 59.996 40.000 21.39 7.54 32.62 2.71
836 844 6.195798 CGAGATCATGTCGTACGAAAATTGTA 59.804 38.462 21.39 5.51 32.62 2.41
837 845 7.218145 AGATCATGTCGTACGAAAATTGTAC 57.782 36.000 21.39 6.01 39.01 2.90
844 852 4.379374 GTACGAAAATTGTACGCACTGT 57.621 40.909 0.00 0.00 33.57 3.55
845 853 3.955771 ACGAAAATTGTACGCACTGTT 57.044 38.095 0.00 0.00 0.00 3.16
846 854 3.868835 ACGAAAATTGTACGCACTGTTC 58.131 40.909 0.00 0.00 0.00 3.18
847 855 3.310227 ACGAAAATTGTACGCACTGTTCA 59.690 39.130 0.00 0.00 0.00 3.18
848 856 4.024387 ACGAAAATTGTACGCACTGTTCAT 60.024 37.500 0.00 0.00 0.00 2.57
849 857 4.549599 CGAAAATTGTACGCACTGTTCATC 59.450 41.667 0.00 0.00 0.00 2.92
850 858 3.722555 AATTGTACGCACTGTTCATCG 57.277 42.857 0.00 0.00 0.00 3.84
851 859 2.143008 TTGTACGCACTGTTCATCGT 57.857 45.000 0.00 0.00 38.75 3.73
852 860 2.993449 TGTACGCACTGTTCATCGTA 57.007 45.000 0.00 0.00 36.50 3.43
853 861 3.497297 TGTACGCACTGTTCATCGTAT 57.503 42.857 0.00 0.00 39.21 3.06
854 862 3.175929 TGTACGCACTGTTCATCGTATG 58.824 45.455 0.00 0.00 39.21 2.39
855 863 0.999406 ACGCACTGTTCATCGTATGC 59.001 50.000 0.00 0.00 33.02 3.14
856 864 0.998669 CGCACTGTTCATCGTATGCA 59.001 50.000 0.00 0.00 33.27 3.96
857 865 1.267038 CGCACTGTTCATCGTATGCAC 60.267 52.381 0.00 0.00 33.27 4.57
858 866 1.731709 GCACTGTTCATCGTATGCACA 59.268 47.619 0.00 0.00 35.24 4.57
860 868 2.726555 CTGTTCATCGTATGCACAGC 57.273 50.000 11.98 0.00 44.88 4.40
861 869 2.001872 CTGTTCATCGTATGCACAGCA 58.998 47.619 11.98 0.00 44.88 4.41
862 870 2.416202 CTGTTCATCGTATGCACAGCAA 59.584 45.455 11.98 0.00 44.88 3.91
863 871 3.009026 TGTTCATCGTATGCACAGCAAT 58.991 40.909 0.00 0.00 43.62 3.56
864 872 3.439825 TGTTCATCGTATGCACAGCAATT 59.560 39.130 0.00 0.00 43.62 2.32
865 873 4.082841 TGTTCATCGTATGCACAGCAATTT 60.083 37.500 0.00 0.00 43.62 1.82
866 874 4.277257 TCATCGTATGCACAGCAATTTC 57.723 40.909 0.00 0.00 43.62 2.17
867 875 2.804421 TCGTATGCACAGCAATTTCG 57.196 45.000 0.00 0.00 43.62 3.46
868 876 2.073056 TCGTATGCACAGCAATTTCGT 58.927 42.857 0.00 0.00 43.62 3.85
869 877 2.482336 TCGTATGCACAGCAATTTCGTT 59.518 40.909 0.00 0.00 43.62 3.85
870 878 3.680458 TCGTATGCACAGCAATTTCGTTA 59.320 39.130 0.00 0.00 43.62 3.18
871 879 4.152580 TCGTATGCACAGCAATTTCGTTAA 59.847 37.500 0.00 0.00 43.62 2.01
872 880 4.848841 CGTATGCACAGCAATTTCGTTAAA 59.151 37.500 0.00 0.00 43.62 1.52
873 881 5.511377 CGTATGCACAGCAATTTCGTTAAAT 59.489 36.000 0.00 0.00 43.62 1.40
874 882 6.290540 CGTATGCACAGCAATTTCGTTAAATC 60.291 38.462 0.00 0.00 43.62 2.17
875 883 4.233789 TGCACAGCAATTTCGTTAAATCC 58.766 39.130 0.00 0.00 34.76 3.01
1008 1019 0.177836 TCGCGACCATGATGACCATT 59.822 50.000 3.71 0.00 31.94 3.16
1381 1447 4.883083 AGACGAATTAGCAGTTCAGTGAA 58.117 39.130 0.08 0.08 0.00 3.18
1398 1464 2.886512 GAAGGTGCTTTGCGCGATCG 62.887 60.000 12.10 11.69 43.27 3.69
1409 1487 1.062873 GCGCGATCGATCAGTAGAGC 61.063 60.000 24.40 16.63 38.10 4.09
1410 1488 0.235926 CGCGATCGATCAGTAGAGCA 59.764 55.000 24.40 0.00 38.10 4.26
1413 1491 2.287308 GCGATCGATCAGTAGAGCAGTT 60.287 50.000 24.40 0.00 0.00 3.16
1509 1587 3.794646 CGTACTACTACGGCGACTG 57.205 57.895 16.62 5.38 41.84 3.51
1725 1804 1.390125 CCCTCCCTGTCCTGTCTCT 59.610 63.158 0.00 0.00 0.00 3.10
1850 1930 6.917217 TGCGAATTTTCTTTCAAAAATGGT 57.083 29.167 0.00 0.00 38.51 3.55
1853 1933 6.238347 GCGAATTTTCTTTCAAAAATGGTGGT 60.238 34.615 0.00 0.00 38.51 4.16
1867 1947 4.927267 ATGGTGGTCAGAGGTGATTAAA 57.073 40.909 0.00 0.00 34.36 1.52
1894 1974 5.423610 AGATACACAGAGAATTGTACCTGCT 59.576 40.000 0.00 0.00 31.09 4.24
1918 2006 7.867403 GCTGTGAATCCATTTCTAACAAGAAAA 59.133 33.333 4.80 0.00 40.60 2.29
1950 2042 6.683974 AACGATCACATCCCTTGAAAATAG 57.316 37.500 0.00 0.00 0.00 1.73
2105 2197 7.013274 ACTGGTAGAACAACAAAGTACTACGTA 59.987 37.037 0.00 0.00 33.42 3.57
2106 2198 7.138736 TGGTAGAACAACAAAGTACTACGTAC 58.861 38.462 0.00 0.00 39.10 3.67
2108 2200 7.535599 GGTAGAACAACAAAGTACTACGTACTC 59.464 40.741 7.09 0.00 46.96 2.59
2109 2201 6.442112 AGAACAACAAAGTACTACGTACTCC 58.558 40.000 7.09 0.00 46.96 3.85
2156 2249 2.784380 GTCTGATACGTCGCATTCTGAC 59.216 50.000 0.00 11.24 32.45 3.51
2175 2268 0.030908 CGAGAATGTAGGGGACGAGC 59.969 60.000 0.00 0.00 0.00 5.03
2180 2273 0.537188 ATGTAGGGGACGAGCAACAG 59.463 55.000 0.00 0.00 0.00 3.16
2182 2275 3.001902 TAGGGGACGAGCAACAGCG 62.002 63.158 0.00 0.00 0.00 5.18
2196 2289 0.673644 ACAGCGCGACAGCCTTTAAT 60.674 50.000 12.10 0.00 41.18 1.40
2199 2292 1.135689 AGCGCGACAGCCTTTAATTTG 60.136 47.619 12.10 0.00 41.18 2.32
2232 2325 0.034059 ACTTGCAACCGTCAGAGAGG 59.966 55.000 0.00 0.00 0.00 3.69
2268 2640 2.093075 TCAGAGAGGGACTACTACACGG 60.093 54.545 0.00 0.00 41.55 4.94
2271 2643 3.202595 AGAGAGGGACTACTACACGGATT 59.797 47.826 0.00 0.00 41.55 3.01
2293 2665 9.362539 GGATTAACTTTGACATCTTAACTACGA 57.637 33.333 0.00 0.00 0.00 3.43
2406 2780 7.498900 TGAGTATCAACATCATCCACATTTACC 59.501 37.037 0.00 0.00 45.97 2.85
2446 2820 3.619038 AGCTAACGCTAAGCATCTTTGAC 59.381 43.478 6.96 0.00 46.79 3.18
2474 2848 6.849502 ACTAAAGCTGATCAATTGTGTGATG 58.150 36.000 5.13 0.00 38.38 3.07
2558 2932 1.338020 CTGGGCCTCAAGTTCAACAAC 59.662 52.381 4.53 0.00 0.00 3.32
2660 3034 2.284921 CCTGGACAGCCTGGGAGA 60.285 66.667 0.00 0.00 46.54 3.71
2741 3115 1.374758 GACCAGCACGAGGTTCCAG 60.375 63.158 0.00 0.00 40.09 3.86
2749 3123 0.969894 ACGAGGTTCCAGAGAAGGTG 59.030 55.000 0.00 0.00 30.91 4.00
2800 3174 4.892934 ACTTTGGTGAAGTTTTAGGCATGA 59.107 37.500 0.00 0.00 46.34 3.07
2810 3184 5.640732 AGTTTTAGGCATGATTTAAGTGCG 58.359 37.500 0.00 0.00 39.69 5.34
2819 3193 5.561499 GCATGATTTAAGTGCGTGAATATCG 59.439 40.000 0.00 0.00 0.00 2.92
2823 3197 1.732941 AAGTGCGTGAATATCGGCAA 58.267 45.000 0.00 0.00 0.00 4.52
2839 3213 4.584874 TCGGCAAGAATCAGGACAAATTA 58.415 39.130 0.00 0.00 0.00 1.40
2877 3254 7.148639 ACACACAAGCATCGTTATTTGTACTAG 60.149 37.037 0.00 0.00 32.86 2.57
2880 3257 8.318876 CACAAGCATCGTTATTTGTACTAGTAC 58.681 37.037 23.58 23.58 32.86 2.73
2882 3259 9.726232 CAAGCATCGTTATTTGTACTAGTACTA 57.274 33.333 28.56 20.97 37.00 1.82
2883 3260 9.947669 AAGCATCGTTATTTGTACTAGTACTAG 57.052 33.333 28.56 25.30 37.00 2.57
2885 3262 9.727627 GCATCGTTATTTGTACTAGTACTAGTT 57.272 33.333 34.30 21.19 43.35 2.24
2893 3270 9.625747 ATTTGTACTAGTACTAGTTACTCCCTC 57.374 37.037 34.30 17.16 43.35 4.30
2894 3271 7.986553 TGTACTAGTACTAGTTACTCCCTCT 57.013 40.000 34.30 12.87 43.35 3.69
2895 3272 7.790027 TGTACTAGTACTAGTTACTCCCTCTG 58.210 42.308 34.30 7.94 43.35 3.35
2896 3273 6.889595 ACTAGTACTAGTTACTCCCTCTGT 57.110 41.667 26.61 3.55 43.35 3.41
2897 3274 7.986553 ACTAGTACTAGTTACTCCCTCTGTA 57.013 40.000 26.61 0.00 43.35 2.74
2898 3275 8.386012 ACTAGTACTAGTTACTCCCTCTGTAA 57.614 38.462 26.61 0.00 43.35 2.41
2899 3276 8.830741 ACTAGTACTAGTTACTCCCTCTGTAAA 58.169 37.037 26.61 0.00 43.35 2.01
2900 3277 7.936496 AGTACTAGTTACTCCCTCTGTAAAC 57.064 40.000 0.00 0.00 36.09 2.01
2901 3278 7.697946 AGTACTAGTTACTCCCTCTGTAAACT 58.302 38.462 0.00 0.00 36.09 2.66
2902 3279 8.830741 AGTACTAGTTACTCCCTCTGTAAACTA 58.169 37.037 0.00 0.00 36.09 2.24
2903 3280 9.454859 GTACTAGTTACTCCCTCTGTAAACTAA 57.545 37.037 0.00 0.00 32.58 2.24
2912 3289 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2913 3290 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2914 3291 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2915 3292 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
2916 3293 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2933 3310 9.654663 AAGAGCGTTTAGATCATTAAAGTAGTT 57.345 29.630 0.00 0.00 37.82 2.24
2966 3343 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
2968 3345 9.939424 ACTCTTATATTAGTTTACAGAGGGAGT 57.061 33.333 0.00 0.00 32.21 3.85
2987 3364 5.128919 GGAGTATAACCTAACGAGTGAGGA 58.871 45.833 13.44 0.00 36.61 3.71
3167 3544 2.432628 CTCGCCGAGACCACAACC 60.433 66.667 8.82 0.00 0.00 3.77
3172 3549 1.003355 CCGAGACCACAACCTGCAT 60.003 57.895 0.00 0.00 0.00 3.96
3528 3905 3.327404 TGGAGGAAAGGGACGGGC 61.327 66.667 0.00 0.00 0.00 6.13
3958 4637 4.036352 CCTTAGTAAAGACTCGCATCGTC 58.964 47.826 0.00 0.00 37.10 4.20
4178 4865 7.928103 AGCACAAACATTATTTGAAAATGCAA 58.072 26.923 6.40 0.00 37.77 4.08
4211 4898 2.211806 CACAAAAACTTGGCATGGTGG 58.788 47.619 5.31 0.00 0.00 4.61
4212 4899 1.836802 ACAAAAACTTGGCATGGTGGT 59.163 42.857 5.31 0.00 0.00 4.16
4389 5078 9.252962 ACATTGTTCTCAAATTCATGAACTTTC 57.747 29.630 11.07 2.27 39.38 2.62
4531 5230 2.994699 CCCGGCCCAACAGATACA 59.005 61.111 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 2.349627 CGACGACGTCTTCAAGAAGAGT 60.350 50.000 24.36 12.12 46.93 3.24
150 151 1.069765 CACTGCCGAGTCCACAGTT 59.930 57.895 9.43 0.00 42.59 3.16
164 165 2.046892 CGCCCCAAGAGACCACTG 60.047 66.667 0.00 0.00 0.00 3.66
181 183 5.121811 AGCACATCTAAGATCCATGACAAC 58.878 41.667 0.00 0.00 0.00 3.32
187 189 5.150715 TGACCTAGCACATCTAAGATCCAT 58.849 41.667 0.00 0.00 0.00 3.41
198 200 0.528466 CACGCGATGACCTAGCACAT 60.528 55.000 15.93 0.61 0.00 3.21
213 215 0.387239 GATTTGAACACAGCCCACGC 60.387 55.000 0.00 0.00 0.00 5.34
229 231 6.036577 ACCAACAAAGAACACACAAAGATT 57.963 33.333 0.00 0.00 0.00 2.40
235 237 3.348119 TGCTACCAACAAAGAACACACA 58.652 40.909 0.00 0.00 0.00 3.72
241 243 4.688879 CACGACTATGCTACCAACAAAGAA 59.311 41.667 0.00 0.00 0.00 2.52
248 250 2.823747 ACTCACACGACTATGCTACCAA 59.176 45.455 0.00 0.00 0.00 3.67
249 251 2.443416 ACTCACACGACTATGCTACCA 58.557 47.619 0.00 0.00 0.00 3.25
256 258 6.544197 AGATCATGTAGAACTCACACGACTAT 59.456 38.462 0.00 0.00 0.00 2.12
263 265 8.917088 TGATAATCAGATCATGTAGAACTCACA 58.083 33.333 0.00 0.00 30.75 3.58
275 277 4.080695 CCGGTCCCATGATAATCAGATCAT 60.081 45.833 0.00 0.00 45.51 2.45
277 279 3.866651 CCGGTCCCATGATAATCAGATC 58.133 50.000 0.00 0.00 0.00 2.75
285 287 0.916086 ACAAAGCCGGTCCCATGATA 59.084 50.000 1.90 0.00 0.00 2.15
295 297 2.745821 GGTAGTCCTTTTACAAAGCCGG 59.254 50.000 0.00 0.00 0.00 6.13
303 305 6.258947 GCAAGATGATGAGGTAGTCCTTTTAC 59.741 42.308 0.00 0.00 45.24 2.01
307 309 3.776969 TGCAAGATGATGAGGTAGTCCTT 59.223 43.478 0.00 0.00 45.24 3.36
379 382 7.752695 TCAAATCTTTCTCGAAATAGGCTTTC 58.247 34.615 0.00 0.00 0.00 2.62
395 398 7.787623 AATGAATCCTCACCTTCAAATCTTT 57.212 32.000 0.00 0.00 35.20 2.52
396 399 7.066284 CGTAATGAATCCTCACCTTCAAATCTT 59.934 37.037 0.00 0.00 35.20 2.40
420 423 4.475527 GGTTGGAAAGCTCACCGT 57.524 55.556 0.00 0.00 42.05 4.83
446 451 7.386573 TCGTGCAATTGAGTAAAGTCTGATTTA 59.613 33.333 10.34 0.00 0.00 1.40
449 454 5.237815 TCGTGCAATTGAGTAAAGTCTGAT 58.762 37.500 10.34 0.00 0.00 2.90
645 650 6.098679 CAGTATAGAATATCTGGTGCTCTGC 58.901 44.000 0.00 0.00 0.00 4.26
658 663 4.512571 TCGTACACGCTGCAGTATAGAATA 59.487 41.667 16.64 0.00 39.60 1.75
661 666 2.282407 TCGTACACGCTGCAGTATAGA 58.718 47.619 16.64 3.61 39.60 1.98
672 680 2.204555 GCGTCGTACTCGTACACGC 61.205 63.158 25.46 25.46 46.96 5.34
696 704 0.467804 GAAGGGATGAGACCTGGAGC 59.532 60.000 0.00 0.00 38.63 4.70
727 735 2.089980 TCGTAGGTGTAGCAGTTCTCC 58.910 52.381 0.00 0.00 0.00 3.71
728 736 2.748532 AGTCGTAGGTGTAGCAGTTCTC 59.251 50.000 0.00 0.00 0.00 2.87
729 737 2.792878 AGTCGTAGGTGTAGCAGTTCT 58.207 47.619 0.00 0.00 0.00 3.01
730 738 4.691860 TTAGTCGTAGGTGTAGCAGTTC 57.308 45.455 0.00 0.00 0.00 3.01
731 739 5.656213 AATTAGTCGTAGGTGTAGCAGTT 57.344 39.130 0.00 0.00 0.00 3.16
732 740 5.648572 GAAATTAGTCGTAGGTGTAGCAGT 58.351 41.667 0.00 0.00 0.00 4.40
733 741 4.733887 CGAAATTAGTCGTAGGTGTAGCAG 59.266 45.833 0.00 0.00 36.26 4.24
734 742 4.665212 CGAAATTAGTCGTAGGTGTAGCA 58.335 43.478 0.00 0.00 36.26 3.49
745 753 5.443101 CGTACATCGTACGAAATTAGTCG 57.557 43.478 23.56 15.56 42.94 4.18
757 765 6.868774 TGACCATTGTCGTACGTACATCGTA 61.869 44.000 24.50 6.74 46.88 3.43
759 767 2.780014 GACCATTGTCGTACGTACATCG 59.220 50.000 24.50 11.75 46.00 3.84
760 768 3.761657 TGACCATTGTCGTACGTACATC 58.238 45.455 24.50 16.25 44.86 3.06
761 769 3.766151 CTGACCATTGTCGTACGTACAT 58.234 45.455 24.50 8.36 44.86 2.29
762 770 2.669113 GCTGACCATTGTCGTACGTACA 60.669 50.000 24.50 14.80 44.86 2.90
763 771 1.916000 GCTGACCATTGTCGTACGTAC 59.084 52.381 15.90 15.90 44.86 3.67
764 772 1.540707 TGCTGACCATTGTCGTACGTA 59.459 47.619 16.05 2.87 44.86 3.57
765 773 0.315886 TGCTGACCATTGTCGTACGT 59.684 50.000 16.05 0.00 44.86 3.57
766 774 0.992072 CTGCTGACCATTGTCGTACG 59.008 55.000 9.53 9.53 44.86 3.67
767 775 0.721718 GCTGCTGACCATTGTCGTAC 59.278 55.000 0.00 0.00 44.86 3.67
768 776 0.391130 GGCTGCTGACCATTGTCGTA 60.391 55.000 0.00 0.00 44.86 3.43
769 777 1.672356 GGCTGCTGACCATTGTCGT 60.672 57.895 0.00 0.00 44.86 4.34
770 778 2.743752 CGGCTGCTGACCATTGTCG 61.744 63.158 1.17 0.00 44.86 4.35
771 779 2.401766 CCGGCTGCTGACCATTGTC 61.402 63.158 10.70 0.00 42.12 3.18
772 780 2.360350 CCGGCTGCTGACCATTGT 60.360 61.111 10.70 0.00 0.00 2.71
773 781 2.360350 ACCGGCTGCTGACCATTG 60.360 61.111 10.70 0.00 0.00 2.82
774 782 2.045926 GACCGGCTGCTGACCATT 60.046 61.111 10.70 0.00 0.00 3.16
775 783 4.457496 CGACCGGCTGCTGACCAT 62.457 66.667 10.70 0.00 0.00 3.55
777 785 4.148825 ATCGACCGGCTGCTGACC 62.149 66.667 10.70 0.00 0.00 4.02
778 786 2.583593 GATCGACCGGCTGCTGAC 60.584 66.667 10.70 2.89 0.00 3.51
779 787 4.193334 CGATCGACCGGCTGCTGA 62.193 66.667 10.26 0.00 0.00 4.26
787 795 1.591594 CCATCCAACCGATCGACCG 60.592 63.158 18.66 1.96 0.00 4.79
788 796 0.529992 GTCCATCCAACCGATCGACC 60.530 60.000 18.66 0.00 34.12 4.79
789 797 0.870307 CGTCCATCCAACCGATCGAC 60.870 60.000 18.66 1.95 36.17 4.20
790 798 1.033202 TCGTCCATCCAACCGATCGA 61.033 55.000 18.66 0.00 0.00 3.59
791 799 0.595053 CTCGTCCATCCAACCGATCG 60.595 60.000 8.51 8.51 0.00 3.69
792 800 0.876342 GCTCGTCCATCCAACCGATC 60.876 60.000 0.00 0.00 0.00 3.69
793 801 1.144057 GCTCGTCCATCCAACCGAT 59.856 57.895 0.00 0.00 0.00 4.18
794 802 2.577059 GCTCGTCCATCCAACCGA 59.423 61.111 0.00 0.00 0.00 4.69
795 803 2.885644 CGCTCGTCCATCCAACCG 60.886 66.667 0.00 0.00 0.00 4.44
796 804 1.519455 CTCGCTCGTCCATCCAACC 60.519 63.158 0.00 0.00 0.00 3.77
797 805 0.103208 ATCTCGCTCGTCCATCCAAC 59.897 55.000 0.00 0.00 0.00 3.77
798 806 0.385751 GATCTCGCTCGTCCATCCAA 59.614 55.000 0.00 0.00 0.00 3.53
799 807 0.751643 TGATCTCGCTCGTCCATCCA 60.752 55.000 0.00 0.00 0.00 3.41
800 808 0.600557 ATGATCTCGCTCGTCCATCC 59.399 55.000 0.00 0.00 0.00 3.51
801 809 1.000827 ACATGATCTCGCTCGTCCATC 60.001 52.381 0.00 0.00 0.00 3.51
802 810 1.000827 GACATGATCTCGCTCGTCCAT 60.001 52.381 0.00 0.00 0.00 3.41
803 811 0.382158 GACATGATCTCGCTCGTCCA 59.618 55.000 0.00 0.00 0.00 4.02
804 812 0.658829 CGACATGATCTCGCTCGTCC 60.659 60.000 0.00 0.00 0.00 4.79
805 813 0.028242 ACGACATGATCTCGCTCGTC 59.972 55.000 0.00 0.00 32.22 4.20
806 814 1.003759 GTACGACATGATCTCGCTCGT 60.004 52.381 0.00 5.02 40.51 4.18
807 815 1.664629 GTACGACATGATCTCGCTCG 58.335 55.000 0.00 0.00 34.34 5.03
808 816 1.260825 TCGTACGACATGATCTCGCTC 59.739 52.381 15.28 0.00 34.34 5.03
809 817 1.296727 TCGTACGACATGATCTCGCT 58.703 50.000 15.28 0.00 34.34 4.93
810 818 2.101053 TTCGTACGACATGATCTCGC 57.899 50.000 19.36 0.00 34.34 5.03
811 819 5.004440 ACAATTTTCGTACGACATGATCTCG 59.996 40.000 19.36 0.28 37.17 4.04
812 820 6.332504 ACAATTTTCGTACGACATGATCTC 57.667 37.500 19.36 0.00 0.00 2.75
813 821 7.218145 GTACAATTTTCGTACGACATGATCT 57.782 36.000 19.36 0.67 30.72 2.75
823 831 4.379374 ACAGTGCGTACAATTTTCGTAC 57.621 40.909 6.38 6.74 39.60 3.67
824 832 4.507021 TGAACAGTGCGTACAATTTTCGTA 59.493 37.500 6.38 0.00 34.21 3.43
825 833 3.310227 TGAACAGTGCGTACAATTTTCGT 59.690 39.130 6.38 0.00 34.21 3.85
826 834 3.867665 TGAACAGTGCGTACAATTTTCG 58.132 40.909 6.38 0.00 34.21 3.46
827 835 4.549599 CGATGAACAGTGCGTACAATTTTC 59.450 41.667 6.38 3.35 32.60 2.29
828 836 4.024387 ACGATGAACAGTGCGTACAATTTT 60.024 37.500 6.38 0.00 34.93 1.82
829 837 3.496884 ACGATGAACAGTGCGTACAATTT 59.503 39.130 6.38 0.00 34.93 1.82
830 838 3.064207 ACGATGAACAGTGCGTACAATT 58.936 40.909 6.38 0.00 34.93 2.32
831 839 2.683968 ACGATGAACAGTGCGTACAAT 58.316 42.857 6.38 0.00 34.93 2.71
832 840 2.143008 ACGATGAACAGTGCGTACAA 57.857 45.000 6.38 0.00 34.93 2.41
833 841 2.993449 TACGATGAACAGTGCGTACA 57.007 45.000 6.38 0.00 38.09 2.90
834 842 2.034842 GCATACGATGAACAGTGCGTAC 60.035 50.000 0.00 0.00 41.29 3.67
835 843 2.190161 GCATACGATGAACAGTGCGTA 58.810 47.619 0.00 0.00 42.44 4.42
836 844 0.999406 GCATACGATGAACAGTGCGT 59.001 50.000 0.00 0.00 40.42 5.24
837 845 0.998669 TGCATACGATGAACAGTGCG 59.001 50.000 0.00 0.00 35.46 5.34
838 846 1.731709 TGTGCATACGATGAACAGTGC 59.268 47.619 4.99 0.00 43.79 4.40
842 850 2.091852 TGCTGTGCATACGATGAACA 57.908 45.000 7.98 7.98 46.41 3.18
843 851 3.680642 ATTGCTGTGCATACGATGAAC 57.319 42.857 0.00 0.00 38.76 3.18
844 852 4.661125 GAAATTGCTGTGCATACGATGAA 58.339 39.130 0.00 0.00 38.76 2.57
845 853 3.242381 CGAAATTGCTGTGCATACGATGA 60.242 43.478 0.00 0.00 38.76 2.92
846 854 3.031126 CGAAATTGCTGTGCATACGATG 58.969 45.455 0.00 0.00 38.76 3.84
847 855 2.677836 ACGAAATTGCTGTGCATACGAT 59.322 40.909 0.00 0.00 38.76 3.73
848 856 2.073056 ACGAAATTGCTGTGCATACGA 58.927 42.857 0.00 0.00 38.76 3.43
849 857 2.525750 ACGAAATTGCTGTGCATACG 57.474 45.000 0.00 0.00 38.76 3.06
850 858 6.020678 GGATTTAACGAAATTGCTGTGCATAC 60.021 38.462 0.00 0.00 38.76 2.39
851 859 6.033341 GGATTTAACGAAATTGCTGTGCATA 58.967 36.000 0.00 0.00 38.76 3.14
852 860 4.864247 GGATTTAACGAAATTGCTGTGCAT 59.136 37.500 0.00 0.00 38.76 3.96
853 861 4.233789 GGATTTAACGAAATTGCTGTGCA 58.766 39.130 0.00 0.00 35.33 4.57
854 862 3.300590 CGGATTTAACGAAATTGCTGTGC 59.699 43.478 0.00 0.00 35.33 4.57
855 863 4.472286 ACGGATTTAACGAAATTGCTGTG 58.528 39.130 0.00 0.00 35.33 3.66
856 864 4.759516 ACGGATTTAACGAAATTGCTGT 57.240 36.364 0.00 0.00 35.33 4.40
857 865 5.150683 TGAACGGATTTAACGAAATTGCTG 58.849 37.500 0.00 0.00 35.33 4.41
858 866 5.365403 TGAACGGATTTAACGAAATTGCT 57.635 34.783 0.00 0.00 35.33 3.91
859 867 6.143278 AGTTTGAACGGATTTAACGAAATTGC 59.857 34.615 0.00 0.00 35.33 3.56
860 868 7.617533 AGTTTGAACGGATTTAACGAAATTG 57.382 32.000 0.00 0.00 35.33 2.32
861 869 7.536281 GCTAGTTTGAACGGATTTAACGAAATT 59.464 33.333 0.00 0.00 35.33 1.82
862 870 7.019418 GCTAGTTTGAACGGATTTAACGAAAT 58.981 34.615 0.00 0.00 38.00 2.17
863 871 6.365050 GCTAGTTTGAACGGATTTAACGAAA 58.635 36.000 0.00 0.00 34.93 3.46
864 872 5.388682 CGCTAGTTTGAACGGATTTAACGAA 60.389 40.000 0.00 0.00 34.93 3.85
865 873 4.090354 CGCTAGTTTGAACGGATTTAACGA 59.910 41.667 0.00 0.00 34.93 3.85
866 874 4.143263 ACGCTAGTTTGAACGGATTTAACG 60.143 41.667 0.00 0.00 37.36 3.18
867 875 5.077424 CACGCTAGTTTGAACGGATTTAAC 58.923 41.667 0.00 0.00 0.00 2.01
868 876 4.152759 CCACGCTAGTTTGAACGGATTTAA 59.847 41.667 0.00 0.00 0.00 1.52
869 877 3.680937 CCACGCTAGTTTGAACGGATTTA 59.319 43.478 0.00 0.00 0.00 1.40
870 878 2.482721 CCACGCTAGTTTGAACGGATTT 59.517 45.455 0.00 0.00 0.00 2.17
871 879 2.073816 CCACGCTAGTTTGAACGGATT 58.926 47.619 0.00 0.00 0.00 3.01
872 880 1.674817 CCCACGCTAGTTTGAACGGAT 60.675 52.381 0.00 0.00 0.00 4.18
873 881 0.320073 CCCACGCTAGTTTGAACGGA 60.320 55.000 0.00 0.00 0.00 4.69
874 882 1.908066 GCCCACGCTAGTTTGAACGG 61.908 60.000 0.00 0.00 0.00 4.44
875 883 1.495951 GCCCACGCTAGTTTGAACG 59.504 57.895 0.00 0.00 0.00 3.95
981 990 4.796231 ATGGTCGCGAGCCACGTC 62.796 66.667 32.88 9.01 44.60 4.34
1292 1303 0.034059 AGAAGCAAGGAGACACGGTG 59.966 55.000 6.58 6.58 0.00 4.94
1398 1464 6.699642 GGAATGAACTAACTGCTCTACTGATC 59.300 42.308 0.00 0.00 0.00 2.92
1409 1487 9.751542 ATTATAGTCGAAGGAATGAACTAACTG 57.248 33.333 0.00 0.00 0.00 3.16
1509 1587 5.813080 AACCAGCGGTTCTAATTAATCAC 57.187 39.130 7.08 0.00 43.05 3.06
1637 1716 1.067516 ACAACAGTGCAGCATTTGGTC 59.932 47.619 15.23 0.00 0.00 4.02
1725 1804 0.533308 GTAGTTTGCCACGGGTGTCA 60.533 55.000 0.00 0.00 0.00 3.58
1780 1859 7.221450 AGTATCTATCTGTCCTGTCAGTAGTC 58.779 42.308 0.00 0.00 36.85 2.59
1781 1860 7.144234 AGTATCTATCTGTCCTGTCAGTAGT 57.856 40.000 0.00 0.00 36.85 2.73
1782 1861 6.653320 GGAGTATCTATCTGTCCTGTCAGTAG 59.347 46.154 0.00 0.00 34.47 2.57
1783 1862 6.330514 AGGAGTATCTATCTGTCCTGTCAGTA 59.669 42.308 0.00 0.00 36.24 2.74
1850 1930 7.618117 TGTATCTACTTTAATCACCTCTGACCA 59.382 37.037 0.00 0.00 0.00 4.02
1853 1933 8.589701 TGTGTATCTACTTTAATCACCTCTGA 57.410 34.615 0.00 0.00 0.00 3.27
1867 1947 7.416890 GCAGGTACAATTCTCTGTGTATCTACT 60.417 40.741 0.00 0.00 39.19 2.57
1894 1974 8.690884 TGTTTTCTTGTTAGAAATGGATTCACA 58.309 29.630 1.58 0.00 46.73 3.58
1918 2006 4.340950 AGGGATGTGATCGTTTGTTTTTGT 59.659 37.500 0.00 0.00 0.00 2.83
1950 2042 3.703001 TCCCAATTCAGGAGAAGTGTC 57.297 47.619 5.18 0.00 45.64 3.67
2105 2197 2.522185 ACACACGTGGTACATAGGAGT 58.478 47.619 21.57 0.00 44.52 3.85
2106 2198 3.693085 ACTACACACGTGGTACATAGGAG 59.307 47.826 21.57 9.34 44.52 3.69
2107 2199 3.689347 ACTACACACGTGGTACATAGGA 58.311 45.455 21.57 0.00 44.52 2.94
2156 2249 0.030908 GCTCGTCCCCTACATTCTCG 59.969 60.000 0.00 0.00 0.00 4.04
2175 2268 1.565156 TAAAGGCTGTCGCGCTGTTG 61.565 55.000 5.56 0.00 36.88 3.33
2180 2273 1.259316 CAAATTAAAGGCTGTCGCGC 58.741 50.000 0.00 0.00 36.88 6.86
2182 2275 2.253603 CTGCAAATTAAAGGCTGTCGC 58.746 47.619 0.00 0.00 0.00 5.19
2188 2281 4.388773 GCAACTAACCTGCAAATTAAAGGC 59.611 41.667 0.00 0.00 39.69 4.35
2199 2292 1.770957 GCAAGTTGCAACTAACCTGC 58.229 50.000 31.31 29.72 44.26 4.85
2241 2337 3.858135 AGTAGTCCCTCTCTGACCAAAA 58.142 45.455 0.00 0.00 33.09 2.44
2245 2341 3.281158 GTGTAGTAGTCCCTCTCTGACC 58.719 54.545 0.00 0.00 33.09 4.02
2252 2348 4.886489 AGTTAATCCGTGTAGTAGTCCCTC 59.114 45.833 0.00 0.00 0.00 4.30
2406 2780 4.250116 AGCTATCTCGCCTTGATGTTAG 57.750 45.455 0.00 0.00 0.00 2.34
2446 2820 6.800408 CACACAATTGATCAGCTTTAGTCAAG 59.200 38.462 13.59 0.00 34.45 3.02
2474 2848 3.273434 TCTGCAACTATCCAATCTGCAC 58.727 45.455 0.00 0.00 38.06 4.57
2558 2932 2.546789 GACGTACAACTCCCCAGTTTTG 59.453 50.000 0.00 0.00 41.24 2.44
2741 3115 1.153349 GGGATGGCGTCACCTTCTC 60.153 63.158 9.27 0.00 41.40 2.87
2749 3123 0.744771 GAACTGAAGGGGATGGCGTC 60.745 60.000 0.00 0.00 0.00 5.19
2800 3174 3.874543 TGCCGATATTCACGCACTTAAAT 59.125 39.130 0.00 0.00 0.00 1.40
2810 3184 4.212214 GTCCTGATTCTTGCCGATATTCAC 59.788 45.833 0.00 0.00 0.00 3.18
2819 3193 6.127647 TGTGATAATTTGTCCTGATTCTTGCC 60.128 38.462 0.00 0.00 0.00 4.52
2823 3197 7.835682 TGGAATGTGATAATTTGTCCTGATTCT 59.164 33.333 0.00 0.00 0.00 2.40
2839 3213 3.384146 TGCTTGTGTGTTTGGAATGTGAT 59.616 39.130 0.00 0.00 0.00 3.06
2877 3254 7.936496 AGTTTACAGAGGGAGTAACTAGTAC 57.064 40.000 0.00 0.00 31.67 2.73
2886 3263 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
2887 3264 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
2888 3265 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
2889 3266 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2890 3267 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
2907 3284 9.654663 AACTACTTTAATGATCTAAACGCTCTT 57.345 29.630 0.00 0.00 0.00 2.85
2940 3317 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
2942 3319 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
2951 3328 9.995594 TTAGGTTATACTCCCTCTGTAAACTAA 57.004 33.333 0.00 0.00 34.14 2.24
2952 3329 9.413734 GTTAGGTTATACTCCCTCTGTAAACTA 57.586 37.037 0.00 0.00 32.08 2.24
2953 3330 7.067981 CGTTAGGTTATACTCCCTCTGTAAACT 59.932 40.741 0.00 0.00 32.08 2.66
2954 3331 7.067494 TCGTTAGGTTATACTCCCTCTGTAAAC 59.933 40.741 0.00 0.00 32.08 2.01
2955 3332 7.118723 TCGTTAGGTTATACTCCCTCTGTAAA 58.881 38.462 0.00 0.00 32.08 2.01
2956 3333 6.662755 TCGTTAGGTTATACTCCCTCTGTAA 58.337 40.000 0.00 0.00 32.08 2.41
2957 3334 6.126652 ACTCGTTAGGTTATACTCCCTCTGTA 60.127 42.308 0.00 0.00 32.08 2.74
2958 3335 5.121380 TCGTTAGGTTATACTCCCTCTGT 57.879 43.478 0.00 0.00 32.08 3.41
2959 3336 5.008811 CACTCGTTAGGTTATACTCCCTCTG 59.991 48.000 0.00 0.00 32.08 3.35
2960 3337 5.104193 TCACTCGTTAGGTTATACTCCCTCT 60.104 44.000 0.00 0.00 32.08 3.69
2961 3338 5.128919 TCACTCGTTAGGTTATACTCCCTC 58.871 45.833 0.00 0.00 32.08 4.30
2962 3339 5.121380 TCACTCGTTAGGTTATACTCCCT 57.879 43.478 0.00 0.00 34.74 4.20
2963 3340 4.277921 CCTCACTCGTTAGGTTATACTCCC 59.722 50.000 0.00 0.00 0.00 4.30
2964 3341 5.128919 TCCTCACTCGTTAGGTTATACTCC 58.871 45.833 0.00 0.00 34.30 3.85
2965 3342 6.880942 ATCCTCACTCGTTAGGTTATACTC 57.119 41.667 0.00 0.00 34.30 2.59
2966 3343 6.606395 ACAATCCTCACTCGTTAGGTTATACT 59.394 38.462 0.00 0.00 34.30 2.12
2967 3344 6.803642 ACAATCCTCACTCGTTAGGTTATAC 58.196 40.000 0.00 0.00 34.30 1.47
2968 3345 8.701908 ATACAATCCTCACTCGTTAGGTTATA 57.298 34.615 0.00 0.00 34.30 0.98
2969 3346 5.934402 ACAATCCTCACTCGTTAGGTTAT 57.066 39.130 0.00 0.00 34.30 1.89
2987 3364 5.410355 ACTGCCTGCAAATGAAATACAAT 57.590 34.783 0.00 0.00 0.00 2.71
3133 3510 2.034048 GAGGAGAAGGTGGGATCCGC 62.034 65.000 5.45 0.61 36.91 5.54
3167 3544 2.410939 CAGTATCGGTGGATCATGCAG 58.589 52.381 0.00 0.00 34.00 4.41
3172 3549 3.223946 AGCCAGTATCGGTGGATCA 57.776 52.632 0.00 0.00 37.23 2.92
3528 3905 2.753966 CCGAGCCAATCCACAAGCG 61.754 63.158 0.00 0.00 0.00 4.68
3822 4201 5.030295 CGCACCATTAATGTTTGATCTGAC 58.970 41.667 14.25 0.00 0.00 3.51
3924 4601 9.538508 GAGTCTTTACTAAGGACAAAACACTTA 57.461 33.333 12.27 0.00 35.56 2.24
3958 4637 1.089112 TGTGCCAAGATGAAGCATCG 58.911 50.000 0.00 0.00 44.67 3.84
4138 4825 6.597614 TGTTTGTGCTTTCAAAATGTGTTTC 58.402 32.000 4.48 0.00 38.71 2.78
4185 4872 2.626840 TGCCAAGTTTTTGTGCTTTCC 58.373 42.857 0.00 0.00 33.98 3.13
4211 4898 3.119137 GGCCTTGTATCACCATTCCAAAC 60.119 47.826 0.00 0.00 0.00 2.93
4212 4899 3.096092 GGCCTTGTATCACCATTCCAAA 58.904 45.455 0.00 0.00 0.00 3.28
4347 5036 9.853921 GAGAACAATGTTTGCAAATTTAAGAAG 57.146 29.630 16.21 3.42 0.00 2.85
4389 5078 6.003950 TGAAAAGAGTTCCTGGGTATGAAAG 58.996 40.000 0.00 0.00 0.00 2.62
4495 5194 1.992233 GCCAAGCATTCGCCGATTCA 61.992 55.000 0.00 0.00 39.83 2.57
4531 5230 1.268589 CGACTGTATCGCTTCCATCGT 60.269 52.381 0.00 0.00 45.52 3.73


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

AutoCloner maintained by Alex Coulton.