Multiple sequence alignment - TraesCS7D01G356200

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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 TraesCS7D01G356200 chr7D 100.000 5481 0 0 1 5481 459747676 459742196 0.000000e+00 10122.0
1 TraesCS7D01G356200 chr7D 80.136 1470 268 22 3057 4508 459464437 459462974 0.000000e+00 1075.0
2 TraesCS7D01G356200 chr7D 79.243 1479 273 22 3057 4512 459431609 459430142 0.000000e+00 1000.0
3 TraesCS7D01G356200 chr7D 95.683 278 6 5 4528 4804 270700087 270700359 5.040000e-120 442.0
4 TraesCS7D01G356200 chr7D 95.131 267 12 1 4538 4804 358198479 358198744 2.360000e-113 420.0
5 TraesCS7D01G356200 chr7A 96.415 3738 127 4 817 4550 539852828 539856562 0.000000e+00 6154.0
6 TraesCS7D01G356200 chr7A 87.994 3540 411 8 1019 4550 540202848 540206381 0.000000e+00 4170.0
7 TraesCS7D01G356200 chr7A 93.418 790 28 10 1 788 539852066 539852833 0.000000e+00 1149.0
8 TraesCS7D01G356200 chr7A 79.268 1476 271 22 3057 4509 540284390 540285853 0.000000e+00 998.0
9 TraesCS7D01G356200 chr7A 94.491 599 26 4 4802 5399 540207071 540207663 0.000000e+00 917.0
10 TraesCS7D01G356200 chr7A 83.425 181 21 7 13 187 540201920 540202097 5.680000e-35 159.0
11 TraesCS7D01G356200 chr7A 100.000 47 0 0 5416 5462 540207650 540207696 2.720000e-13 87.9
12 TraesCS7D01G356200 chr7B 90.718 3523 309 11 1035 4544 481668832 481665315 0.000000e+00 4678.0
13 TraesCS7D01G356200 chr7B 80.445 1483 256 27 3057 4516 481616062 481614591 0.000000e+00 1101.0
14 TraesCS7D01G356200 chr7B 90.123 81 5 1 2 82 481843797 481843720 9.710000e-18 102.0
15 TraesCS7D01G356200 chr5A 83.179 3573 542 33 1019 4546 680981209 680984767 0.000000e+00 3214.0
16 TraesCS7D01G356200 chr5A 82.728 3526 542 42 1019 4489 680921300 680924813 0.000000e+00 3075.0
17 TraesCS7D01G356200 chr4D 82.827 3657 556 40 941 4546 500300899 500304534 0.000000e+00 3208.0
18 TraesCS7D01G356200 chr4B 82.711 3644 555 44 940 4531 643629060 643632680 0.000000e+00 3169.0
19 TraesCS7D01G356200 chr4B 82.049 3582 579 41 1019 4546 643528201 643531772 0.000000e+00 2994.0
20 TraesCS7D01G356200 chrUn 82.867 3537 540 40 1019 4500 60417194 60413669 0.000000e+00 3114.0
21 TraesCS7D01G356200 chrUn 82.542 3580 565 36 1019 4546 16761166 16757595 0.000000e+00 3094.0
22 TraesCS7D01G356200 chrUn 83.066 2622 385 32 1973 4546 60473870 60471260 0.000000e+00 2327.0
23 TraesCS7D01G356200 chr5B 96.981 265 7 1 4541 4805 27825038 27825301 1.400000e-120 444.0
24 TraesCS7D01G356200 chr3A 95.896 268 9 2 4538 4804 23631277 23631543 3.030000e-117 433.0
25 TraesCS7D01G356200 chr2D 95.833 264 9 1 4541 4804 316662410 316662149 5.070000e-115 425.0
26 TraesCS7D01G356200 chr2B 95.506 267 11 1 4538 4804 384650626 384650891 5.070000e-115 425.0
27 TraesCS7D01G356200 chr1D 95.472 265 11 1 4541 4805 222025253 222025516 6.560000e-114 422.0
28 TraesCS7D01G356200 chr3D 95.131 267 12 1 4538 4804 231411412 231411677 2.360000e-113 420.0
29 TraesCS7D01G356200 chr1A 95.149 268 9 3 4538 4804 276244733 276244997 2.360000e-113 420.0


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 TraesCS7D01G356200 chr7D 459742196 459747676 5480 True 10122.000 10122 100.0000 1 5481 1 chr7D.!!$R3 5480
1 TraesCS7D01G356200 chr7D 459462974 459464437 1463 True 1075.000 1075 80.1360 3057 4508 1 chr7D.!!$R2 1451
2 TraesCS7D01G356200 chr7D 459430142 459431609 1467 True 1000.000 1000 79.2430 3057 4512 1 chr7D.!!$R1 1455
3 TraesCS7D01G356200 chr7A 539852066 539856562 4496 False 3651.500 6154 94.9165 1 4550 2 chr7A.!!$F2 4549
4 TraesCS7D01G356200 chr7A 540201920 540207696 5776 False 1333.475 4170 91.4775 13 5462 4 chr7A.!!$F3 5449
5 TraesCS7D01G356200 chr7A 540284390 540285853 1463 False 998.000 998 79.2680 3057 4509 1 chr7A.!!$F1 1452
6 TraesCS7D01G356200 chr7B 481665315 481668832 3517 True 4678.000 4678 90.7180 1035 4544 1 chr7B.!!$R2 3509
7 TraesCS7D01G356200 chr7B 481614591 481616062 1471 True 1101.000 1101 80.4450 3057 4516 1 chr7B.!!$R1 1459
8 TraesCS7D01G356200 chr5A 680981209 680984767 3558 False 3214.000 3214 83.1790 1019 4546 1 chr5A.!!$F2 3527
9 TraesCS7D01G356200 chr5A 680921300 680924813 3513 False 3075.000 3075 82.7280 1019 4489 1 chr5A.!!$F1 3470
10 TraesCS7D01G356200 chr4D 500300899 500304534 3635 False 3208.000 3208 82.8270 941 4546 1 chr4D.!!$F1 3605
11 TraesCS7D01G356200 chr4B 643629060 643632680 3620 False 3169.000 3169 82.7110 940 4531 1 chr4B.!!$F2 3591
12 TraesCS7D01G356200 chr4B 643528201 643531772 3571 False 2994.000 2994 82.0490 1019 4546 1 chr4B.!!$F1 3527
13 TraesCS7D01G356200 chrUn 60413669 60417194 3525 True 3114.000 3114 82.8670 1019 4500 1 chrUn.!!$R2 3481
14 TraesCS7D01G356200 chrUn 16757595 16761166 3571 True 3094.000 3094 82.5420 1019 4546 1 chrUn.!!$R1 3527
15 TraesCS7D01G356200 chrUn 60471260 60473870 2610 True 2327.000 2327 83.0660 1973 4546 1 chrUn.!!$R3 2573

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
689 829 0.105593 GAGCAGATTGGAGGCATCGA 59.894 55.0 0.00 0.0 0.00 3.59 F
802 942 0.178990 ACAAGTGGGGAGCTTGAACC 60.179 55.0 11.37 0.0 44.29 3.62 F
803 943 0.178992 CAAGTGGGGAGCTTGAACCA 60.179 55.0 0.00 0.0 44.29 3.67 F
879 1031 0.252330 TCCCAGTTCCCACCGTATCA 60.252 55.0 0.00 0.0 0.00 2.15 F
1581 1804 0.533951 GCATCCCTTCTGCTTTTGGG 59.466 55.0 0.00 0.0 40.95 4.12 F
2370 2593 1.341080 CAGGTGATTGGGGCTTTGTT 58.659 50.0 0.00 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1941 2164 0.036875 GAACCAGGGAGGACAGGTTG 59.963 60.000 0.00 0.00 43.94 3.77 R
2631 2854 2.341452 GGAAAGCCGGTTTTCTGCT 58.659 52.632 33.65 7.76 37.26 4.24 R
3212 3438 6.371548 TGGAAAGCTTGTACACAGATGATAAC 59.628 38.462 0.00 0.00 0.00 1.89 R
3232 3458 2.307686 GGGACATACCTCCTGTTGGAAA 59.692 50.000 0.00 0.00 42.66 3.13 R
3822 4117 6.366061 GGTTGTGAAGATAATCCAAAGCAAAC 59.634 38.462 0.00 0.00 0.00 2.93 R
4549 4865 1.070445 TGCGAACTAAAAAGGACCGGA 59.930 47.619 9.46 0.00 0.00 5.14 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
48 49 1.219124 GCTGAACGGCAGGATCAGA 59.781 57.895 20.42 0.00 45.03 3.27
132 139 2.360350 ATGTGGCTTCCTGTGCGG 60.360 61.111 0.00 0.00 0.00 5.69
197 204 3.428664 GTGCCATCCCCATCCCCA 61.429 66.667 0.00 0.00 0.00 4.96
203 210 1.078955 CATCCCCATCCCCATTAGCT 58.921 55.000 0.00 0.00 0.00 3.32
228 235 0.818296 AAGGAATGGAGACCGAGACG 59.182 55.000 0.00 0.00 0.00 4.18
332 339 5.179742 TGCATTTGGAAATCAGAAATGTTGC 59.820 36.000 13.95 0.00 38.69 4.17
334 341 6.293516 GCATTTGGAAATCAGAAATGTTGCAA 60.294 34.615 0.00 0.00 38.69 4.08
353 360 1.226717 GTCAACGAGGCGCCTAGAG 60.227 63.158 38.60 28.77 0.00 2.43
422 454 8.792633 CATCAAAGGTAGGAAAGTAAATGACAA 58.207 33.333 0.00 0.00 0.00 3.18
462 497 3.722147 CGTTCATACTTCAGCCAGCTAT 58.278 45.455 0.00 0.00 0.00 2.97
491 629 4.563184 CGTTCAGTCTAAGTTGCCTGTATC 59.437 45.833 0.00 0.00 0.00 2.24
492 630 5.622460 CGTTCAGTCTAAGTTGCCTGTATCT 60.622 44.000 0.00 0.00 0.00 1.98
495 633 5.949952 TCAGTCTAAGTTGCCTGTATCTGTA 59.050 40.000 0.00 0.00 0.00 2.74
496 634 6.607600 TCAGTCTAAGTTGCCTGTATCTGTAT 59.392 38.462 0.00 0.00 0.00 2.29
497 635 6.699204 CAGTCTAAGTTGCCTGTATCTGTATG 59.301 42.308 0.00 0.00 0.00 2.39
498 636 5.986135 GTCTAAGTTGCCTGTATCTGTATGG 59.014 44.000 0.00 0.00 0.00 2.74
499 637 3.845781 AGTTGCCTGTATCTGTATGGG 57.154 47.619 0.00 0.00 0.00 4.00
500 638 3.115390 AGTTGCCTGTATCTGTATGGGT 58.885 45.455 0.00 0.00 0.00 4.51
502 640 4.101119 AGTTGCCTGTATCTGTATGGGTAC 59.899 45.833 0.00 0.00 0.00 3.34
503 641 3.923648 TGCCTGTATCTGTATGGGTACT 58.076 45.455 0.00 0.00 0.00 2.73
504 642 5.069518 TGCCTGTATCTGTATGGGTACTA 57.930 43.478 0.00 0.00 0.00 1.82
548 686 1.135199 TGTCAAATCTCGCCGAGGTAC 60.135 52.381 15.08 2.86 0.00 3.34
549 687 0.458669 TCAAATCTCGCCGAGGTACC 59.541 55.000 15.08 2.73 0.00 3.34
670 808 1.673626 GGCTGGGACAATTGCAATGTG 60.674 52.381 13.82 14.95 38.70 3.21
676 816 2.229543 GGACAATTGCAATGTGAGCAGA 59.770 45.455 13.82 0.00 43.75 4.26
689 829 0.105593 GAGCAGATTGGAGGCATCGA 59.894 55.000 0.00 0.00 0.00 3.59
716 856 0.321122 GGCTGTCCCTGTCTGACAAG 60.321 60.000 12.16 5.66 41.85 3.16
745 885 4.023536 GGTCAAATCTGTTAGCGTCCAAAA 60.024 41.667 0.00 0.00 0.00 2.44
746 886 5.335661 GGTCAAATCTGTTAGCGTCCAAAAT 60.336 40.000 0.00 0.00 0.00 1.82
747 887 5.795441 GTCAAATCTGTTAGCGTCCAAAATC 59.205 40.000 0.00 0.00 0.00 2.17
748 888 4.965119 AATCTGTTAGCGTCCAAAATCC 57.035 40.909 0.00 0.00 0.00 3.01
749 889 3.410631 TCTGTTAGCGTCCAAAATCCA 57.589 42.857 0.00 0.00 0.00 3.41
750 890 3.334691 TCTGTTAGCGTCCAAAATCCAG 58.665 45.455 0.00 0.00 0.00 3.86
751 891 3.007506 TCTGTTAGCGTCCAAAATCCAGA 59.992 43.478 0.00 0.00 0.00 3.86
771 911 5.009310 CCAGATGCATGCACACAATATTAGT 59.991 40.000 25.37 1.30 0.00 2.24
773 913 7.295930 CAGATGCATGCACACAATATTAGTAG 58.704 38.462 25.37 0.00 0.00 2.57
776 916 8.675705 ATGCATGCACACAATATTAGTAGTAA 57.324 30.769 25.37 0.00 0.00 2.24
778 918 9.771534 TGCATGCACACAATATTAGTAGTAATA 57.228 29.630 18.46 11.56 35.90 0.98
793 933 9.940974 TTAGTAGTAATATTCTACAAGTGGGGA 57.059 33.333 18.85 0.00 39.86 4.81
794 934 8.480133 AGTAGTAATATTCTACAAGTGGGGAG 57.520 38.462 18.85 0.00 39.86 4.30
795 935 6.176014 AGTAATATTCTACAAGTGGGGAGC 57.824 41.667 0.00 0.00 0.00 4.70
796 936 5.905913 AGTAATATTCTACAAGTGGGGAGCT 59.094 40.000 0.00 0.00 0.00 4.09
797 937 5.717119 AATATTCTACAAGTGGGGAGCTT 57.283 39.130 0.00 0.00 0.00 3.74
798 938 2.859165 TTCTACAAGTGGGGAGCTTG 57.141 50.000 3.81 3.81 46.23 4.01
799 939 2.024176 TCTACAAGTGGGGAGCTTGA 57.976 50.000 11.37 0.00 44.29 3.02
800 940 2.334977 TCTACAAGTGGGGAGCTTGAA 58.665 47.619 11.37 0.00 44.29 2.69
801 941 2.038557 TCTACAAGTGGGGAGCTTGAAC 59.961 50.000 11.37 0.00 44.29 3.18
802 942 0.178990 ACAAGTGGGGAGCTTGAACC 60.179 55.000 11.37 0.00 44.29 3.62
803 943 0.178992 CAAGTGGGGAGCTTGAACCA 60.179 55.000 0.00 0.00 44.29 3.67
804 944 4.081050 GTGGGGAGCTTGAACCAC 57.919 61.111 12.28 12.28 45.56 4.16
805 945 4.002006 TGGGGAGCTTGAACCACT 57.998 55.556 0.00 0.00 0.00 4.00
806 946 3.173852 TGGGGAGCTTGAACCACTA 57.826 52.632 0.00 0.00 0.00 2.74
807 947 0.690762 TGGGGAGCTTGAACCACTAC 59.309 55.000 0.00 0.00 0.00 2.73
808 948 0.984995 GGGGAGCTTGAACCACTACT 59.015 55.000 0.00 0.00 0.00 2.57
809 949 1.351350 GGGGAGCTTGAACCACTACTT 59.649 52.381 0.00 0.00 0.00 2.24
810 950 2.570302 GGGGAGCTTGAACCACTACTTA 59.430 50.000 0.00 0.00 0.00 2.24
811 951 3.597255 GGGAGCTTGAACCACTACTTAC 58.403 50.000 0.00 0.00 0.00 2.34
812 952 3.007614 GGGAGCTTGAACCACTACTTACA 59.992 47.826 0.00 0.00 0.00 2.41
813 953 4.504340 GGGAGCTTGAACCACTACTTACAA 60.504 45.833 0.00 0.00 0.00 2.41
814 954 4.691216 GGAGCTTGAACCACTACTTACAAG 59.309 45.833 0.00 0.00 38.07 3.16
815 955 5.291905 AGCTTGAACCACTACTTACAAGT 57.708 39.130 0.00 0.00 42.91 3.16
821 961 8.789825 TTGAACCACTACTTACAAGTTACAAA 57.210 30.769 0.00 0.00 40.37 2.83
824 964 6.057533 ACCACTACTTACAAGTTACAAACCC 58.942 40.000 0.00 0.00 40.37 4.11
840 980 4.226168 ACAAACCCAAATCTGGTCCAAAAA 59.774 37.500 0.00 0.00 41.72 1.94
879 1031 0.252330 TCCCAGTTCCCACCGTATCA 60.252 55.000 0.00 0.00 0.00 2.15
883 1035 2.561569 CAGTTCCCACCGTATCAATCC 58.438 52.381 0.00 0.00 0.00 3.01
891 1043 1.217882 CCGTATCAATCCTTGACCGC 58.782 55.000 0.00 0.00 43.48 5.68
904 1056 3.432186 ACCGCAAAGTTGCTGTCC 58.568 55.556 13.75 0.00 46.41 4.02
919 1071 2.324541 CTGTCCAGAGGGCTTAGCTAT 58.675 52.381 3.59 0.00 0.00 2.97
1011 1219 5.063817 GCAAACAATAACAATGGCATCTTCC 59.936 40.000 0.00 0.00 0.00 3.46
1044 1255 4.464069 TCCAGGTTTTGTTTGGTTTCTG 57.536 40.909 0.00 0.00 33.65 3.02
1116 1333 5.755849 ACCGAAAATGATAGACAATCCCTT 58.244 37.500 0.00 0.00 33.22 3.95
1254 1477 0.955428 TGATTGCGCTGGACCTTGAC 60.955 55.000 9.73 0.00 0.00 3.18
1581 1804 0.533951 GCATCCCTTCTGCTTTTGGG 59.466 55.000 0.00 0.00 40.95 4.12
1941 2164 5.795972 GGAATAATACCTTCCTCACTAGGC 58.204 45.833 0.00 0.00 43.31 3.93
2370 2593 1.341080 CAGGTGATTGGGGCTTTGTT 58.659 50.000 0.00 0.00 0.00 2.83
2520 2743 5.393866 CAAATTTATGGGCCTATACCACCT 58.606 41.667 8.58 0.00 41.58 4.00
2558 2781 8.398665 CCTTAAGAGCCTCAATAATTTGTACAC 58.601 37.037 3.36 0.00 34.32 2.90
2565 2788 6.038936 GCCTCAATAATTTGTACACGGGTAAT 59.961 38.462 0.00 0.00 34.32 1.89
2631 2854 9.194972 CTGCATAGATTGGTCTATCTATCCTTA 57.805 37.037 10.46 1.16 44.06 2.69
3152 3378 6.908825 TCAATTTATCCTTCAACCAGTTTCG 58.091 36.000 0.00 0.00 0.00 3.46
3212 3438 6.258230 TGGTGCAGTATCAATTGAAAGAAG 57.742 37.500 13.09 3.30 0.00 2.85
3232 3458 6.940739 AGAAGTTATCATCTGTGTACAAGCT 58.059 36.000 0.00 0.00 0.00 3.74
3822 4117 2.533266 ATGTAGCCTTGGATGTAGCG 57.467 50.000 0.00 0.00 0.00 4.26
4162 4478 2.092429 TGGACAGATATCAACCAAGGGC 60.092 50.000 5.32 0.00 0.00 5.19
4255 4571 5.468072 CAGTGATGGTATAAGCCTTCATGAC 59.532 44.000 0.00 0.00 42.26 3.06
4497 4813 5.408356 CAGATGAAGCAAAGATTTGGAAGG 58.592 41.667 7.38 0.00 38.57 3.46
4504 4820 3.677976 GCAAAGATTTGGAAGGATGGCAG 60.678 47.826 7.38 0.00 38.57 4.85
4507 4823 2.511218 AGATTTGGAAGGATGGCAGCTA 59.489 45.455 1.50 0.00 0.00 3.32
4509 4825 1.289160 TTGGAAGGATGGCAGCTAGT 58.711 50.000 1.50 0.00 0.00 2.57
4512 4828 1.210478 GGAAGGATGGCAGCTAGTGAA 59.790 52.381 1.50 0.00 0.00 3.18
4516 4832 2.170187 AGGATGGCAGCTAGTGAAAGAG 59.830 50.000 1.50 0.00 0.00 2.85
4518 4834 1.352083 TGGCAGCTAGTGAAAGAGGT 58.648 50.000 0.00 0.00 0.00 3.85
4524 4840 2.093235 AGCTAGTGAAAGAGGTGCATCC 60.093 50.000 0.00 0.00 0.00 3.51
4532 4848 3.515602 AAGAGGTGCATCCAAAGAAGT 57.484 42.857 0.00 0.00 39.02 3.01
4539 4855 4.229876 GTGCATCCAAAGAAGTAAAGTGC 58.770 43.478 0.00 0.00 0.00 4.40
4544 4860 6.603095 CATCCAAAGAAGTAAAGTGCTGTAC 58.397 40.000 0.00 0.00 0.00 2.90
4545 4861 5.925509 TCCAAAGAAGTAAAGTGCTGTACT 58.074 37.500 0.00 0.00 42.89 2.73
4546 4862 5.989777 TCCAAAGAAGTAAAGTGCTGTACTC 59.010 40.000 0.00 0.00 39.18 2.59
4547 4863 5.179555 CCAAAGAAGTAAAGTGCTGTACTCC 59.820 44.000 0.00 0.00 39.18 3.85
4549 4865 4.161102 AGAAGTAAAGTGCTGTACTCCCT 58.839 43.478 0.00 1.87 39.18 4.20
4550 4866 4.221041 AGAAGTAAAGTGCTGTACTCCCTC 59.779 45.833 0.00 0.00 39.18 4.30
4551 4867 2.832733 AGTAAAGTGCTGTACTCCCTCC 59.167 50.000 0.00 0.00 39.18 4.30
4552 4868 0.608640 AAAGTGCTGTACTCCCTCCG 59.391 55.000 0.00 0.00 39.18 4.63
4553 4869 1.258445 AAGTGCTGTACTCCCTCCGG 61.258 60.000 0.00 0.00 39.18 5.14
4554 4870 1.982938 GTGCTGTACTCCCTCCGGT 60.983 63.158 0.00 0.00 0.00 5.28
4555 4871 1.681327 TGCTGTACTCCCTCCGGTC 60.681 63.158 0.00 0.00 0.00 4.79
4556 4872 2.424733 GCTGTACTCCCTCCGGTCC 61.425 68.421 0.00 0.00 0.00 4.46
4557 4873 1.306970 CTGTACTCCCTCCGGTCCT 59.693 63.158 0.00 0.00 0.00 3.85
4562 4878 2.034436 ACTCCCTCCGGTCCTTTTTA 57.966 50.000 0.00 0.00 0.00 1.52
4563 4879 1.907255 ACTCCCTCCGGTCCTTTTTAG 59.093 52.381 0.00 0.00 0.00 1.85
4566 4882 2.303890 TCCCTCCGGTCCTTTTTAGTTC 59.696 50.000 0.00 0.00 0.00 3.01
4567 4883 2.344025 CCTCCGGTCCTTTTTAGTTCG 58.656 52.381 0.00 0.00 0.00 3.95
4568 4884 1.730612 CTCCGGTCCTTTTTAGTTCGC 59.269 52.381 0.00 0.00 0.00 4.70
4569 4885 1.070445 TCCGGTCCTTTTTAGTTCGCA 59.930 47.619 0.00 0.00 0.00 5.10
4570 4886 2.081462 CCGGTCCTTTTTAGTTCGCAT 58.919 47.619 0.00 0.00 0.00 4.73
4573 4889 5.051816 CCGGTCCTTTTTAGTTCGCATATA 58.948 41.667 0.00 0.00 0.00 0.86
4574 4890 5.524646 CCGGTCCTTTTTAGTTCGCATATAA 59.475 40.000 0.00 0.00 0.00 0.98
4575 4891 6.292703 CCGGTCCTTTTTAGTTCGCATATAAG 60.293 42.308 0.00 0.00 0.00 1.73
4576 4892 6.477688 CGGTCCTTTTTAGTTCGCATATAAGA 59.522 38.462 0.00 0.00 0.00 2.10
4590 4906 9.594478 TTCGCATATAAGATTTGTCTAAAGTCA 57.406 29.630 0.00 0.00 0.00 3.41
4592 4908 9.855361 CGCATATAAGATTTGTCTAAAGTCAAG 57.145 33.333 0.00 0.00 0.00 3.02
4593 4909 9.657121 GCATATAAGATTTGTCTAAAGTCAAGC 57.343 33.333 0.00 0.00 0.00 4.01
4596 4912 6.809630 AAGATTTGTCTAAAGTCAAGCCTC 57.190 37.500 0.00 0.00 0.00 4.70
4597 4913 4.932200 AGATTTGTCTAAAGTCAAGCCTCG 59.068 41.667 0.00 0.00 0.00 4.63
4598 4914 3.746045 TTGTCTAAAGTCAAGCCTCGT 57.254 42.857 0.00 0.00 0.00 4.18
4600 4916 4.859304 TGTCTAAAGTCAAGCCTCGTAA 57.141 40.909 0.00 0.00 0.00 3.18
4601 4917 5.401531 TGTCTAAAGTCAAGCCTCGTAAT 57.598 39.130 0.00 0.00 0.00 1.89
4602 4918 5.168569 TGTCTAAAGTCAAGCCTCGTAATG 58.831 41.667 0.00 0.00 0.00 1.90
4604 4920 5.638234 GTCTAAAGTCAAGCCTCGTAATGTT 59.362 40.000 0.00 0.00 0.00 2.71
4606 4922 4.749245 AAGTCAAGCCTCGTAATGTTTG 57.251 40.909 0.00 0.00 0.00 2.93
4607 4923 4.002906 AGTCAAGCCTCGTAATGTTTGA 57.997 40.909 0.00 0.00 0.00 2.69
4608 4924 3.746492 AGTCAAGCCTCGTAATGTTTGAC 59.254 43.478 10.10 10.10 42.72 3.18
4609 4925 3.071479 TCAAGCCTCGTAATGTTTGACC 58.929 45.455 0.00 0.00 0.00 4.02
4610 4926 2.811431 CAAGCCTCGTAATGTTTGACCA 59.189 45.455 0.00 0.00 0.00 4.02
4611 4927 3.134574 AGCCTCGTAATGTTTGACCAA 57.865 42.857 0.00 0.00 0.00 3.67
4612 4928 2.812011 AGCCTCGTAATGTTTGACCAAC 59.188 45.455 0.00 0.00 35.71 3.77
4613 4929 2.812011 GCCTCGTAATGTTTGACCAACT 59.188 45.455 0.00 0.00 36.21 3.16
4614 4930 3.252458 GCCTCGTAATGTTTGACCAACTT 59.748 43.478 0.00 0.00 36.21 2.66
4615 4931 4.261447 GCCTCGTAATGTTTGACCAACTTT 60.261 41.667 0.00 0.00 36.81 2.66
4616 4932 5.049267 GCCTCGTAATGTTTGACCAACTTTA 60.049 40.000 0.00 0.00 35.11 1.85
4617 4933 6.349033 GCCTCGTAATGTTTGACCAACTTTAT 60.349 38.462 2.39 0.00 37.35 1.40
4618 4934 7.148373 GCCTCGTAATGTTTGACCAACTTTATA 60.148 37.037 2.39 0.00 37.35 0.98
4619 4935 8.388103 CCTCGTAATGTTTGACCAACTTTATAG 58.612 37.037 2.39 3.82 37.35 1.31
4621 4937 9.491675 TCGTAATGTTTGACCAACTTTATAGAA 57.508 29.630 2.39 0.00 37.35 2.10
4675 4991 8.242729 TCAATATCAGTAGATGTGTCATGACT 57.757 34.615 25.55 6.60 35.67 3.41
4676 4992 8.699130 TCAATATCAGTAGATGTGTCATGACTT 58.301 33.333 25.55 11.29 35.67 3.01
4681 4997 9.896645 ATCAGTAGATGTGTCATGACTTAAATT 57.103 29.630 25.55 10.21 31.91 1.82
4778 5588 9.495754 GTTTGACTTCAGACAATTCTTATATGC 57.504 33.333 0.00 0.00 31.96 3.14
4779 5589 8.791327 TTGACTTCAGACAATTCTTATATGCA 57.209 30.769 0.00 0.00 0.00 3.96
4780 5590 8.429493 TGACTTCAGACAATTCTTATATGCAG 57.571 34.615 0.00 0.00 0.00 4.41
4781 5591 8.260114 TGACTTCAGACAATTCTTATATGCAGA 58.740 33.333 0.00 0.00 0.00 4.26
4782 5592 8.659925 ACTTCAGACAATTCTTATATGCAGAG 57.340 34.615 0.00 0.00 0.00 3.35
4783 5593 8.263640 ACTTCAGACAATTCTTATATGCAGAGT 58.736 33.333 0.00 0.00 0.00 3.24
4784 5594 9.755804 CTTCAGACAATTCTTATATGCAGAGTA 57.244 33.333 0.00 0.00 0.00 2.59
4793 5603 8.732746 TTCTTATATGCAGAGTAAAAAGGACC 57.267 34.615 0.00 0.00 0.00 4.46
4794 5604 6.984474 TCTTATATGCAGAGTAAAAAGGACCG 59.016 38.462 0.00 0.00 0.00 4.79
4795 5605 2.178912 TGCAGAGTAAAAAGGACCGG 57.821 50.000 0.00 0.00 0.00 5.28
4796 5606 1.695242 TGCAGAGTAAAAAGGACCGGA 59.305 47.619 9.46 0.00 0.00 5.14
4797 5607 2.289444 TGCAGAGTAAAAAGGACCGGAG 60.289 50.000 9.46 0.00 0.00 4.63
4888 5698 5.123344 AGTTACTGGCATTTCCAAACGTATC 59.877 40.000 0.00 0.00 46.01 2.24
4938 5748 8.021396 GCATTTCGTGTAATTTTTCTCTAGGTT 58.979 33.333 0.00 0.00 0.00 3.50
4944 5754 8.339714 CGTGTAATTTTTCTCTAGGTTTGTTGA 58.660 33.333 0.00 0.00 0.00 3.18
4950 5760 8.433421 TTTTTCTCTAGGTTTGTTGAGTAGTG 57.567 34.615 0.00 0.00 0.00 2.74
4952 5762 4.021368 TCTCTAGGTTTGTTGAGTAGTGGC 60.021 45.833 0.00 0.00 0.00 5.01
4971 5781 2.216898 GCATCTCTGTAAGCACCATCC 58.783 52.381 0.00 0.00 0.00 3.51
4986 5796 1.337260 CCATCCGAGGGATAAAGCTCG 60.337 57.143 0.00 0.00 40.98 5.03
4988 5798 1.996798 TCCGAGGGATAAAGCTCGAT 58.003 50.000 0.00 0.00 41.24 3.59
5010 5820 4.297299 AGATTTGCATGCTTAATGTCCG 57.703 40.909 20.33 0.00 38.65 4.79
5076 5886 2.677836 CGAATGGGAATCAAAGCTCGAA 59.322 45.455 0.00 0.00 0.00 3.71
5158 5969 3.251004 GTCGATACAGATTGGATTTGCCC 59.749 47.826 0.00 0.00 34.97 5.36
5175 5986 0.536006 CCCAATCCCCGCAGAAGATC 60.536 60.000 0.00 0.00 0.00 2.75
5178 5989 1.672881 CAATCCCCGCAGAAGATCAAC 59.327 52.381 0.00 0.00 0.00 3.18
5181 5992 1.026718 CCCCGCAGAAGATCAACCAC 61.027 60.000 0.00 0.00 0.00 4.16
5334 6145 2.097038 CGCAAGACTGAAGGCTCCG 61.097 63.158 0.00 0.00 43.02 4.63
5336 6147 1.004560 CAAGACTGAAGGCTCCGCA 60.005 57.895 0.00 0.00 0.00 5.69
5392 6203 4.166011 GCGCGGTCCATTCAGCAC 62.166 66.667 8.83 0.00 0.00 4.40
5393 6204 3.499737 CGCGGTCCATTCAGCACC 61.500 66.667 0.00 0.00 0.00 5.01
5396 6207 2.438434 GGTCCATTCAGCACCGGG 60.438 66.667 6.32 0.00 0.00 5.73
5397 6208 3.134127 GTCCATTCAGCACCGGGC 61.134 66.667 6.32 6.61 45.30 6.13
5398 6209 4.424711 TCCATTCAGCACCGGGCC 62.425 66.667 6.32 0.00 46.50 5.80
5400 6211 4.431131 CATTCAGCACCGGGCCCT 62.431 66.667 22.43 0.00 46.50 5.19
5401 6212 3.661648 ATTCAGCACCGGGCCCTT 61.662 61.111 22.43 2.91 46.50 3.95
5402 6213 3.224007 ATTCAGCACCGGGCCCTTT 62.224 57.895 22.43 2.45 46.50 3.11
5403 6214 2.730129 ATTCAGCACCGGGCCCTTTT 62.730 55.000 22.43 0.00 46.50 2.27
5404 6215 2.917227 CAGCACCGGGCCCTTTTT 60.917 61.111 22.43 0.00 46.50 1.94
5470 6281 2.190756 GGGTCACGAGTAGTCCTGG 58.809 63.158 0.00 0.00 0.00 4.45
5471 6282 1.511768 GGTCACGAGTAGTCCTGGC 59.488 63.158 0.00 0.00 0.00 4.85
5472 6283 1.136984 GTCACGAGTAGTCCTGGCG 59.863 63.158 0.00 0.00 0.00 5.69
5473 6284 1.002990 TCACGAGTAGTCCTGGCGA 60.003 57.895 0.00 0.00 0.00 5.54
5474 6285 0.393944 TCACGAGTAGTCCTGGCGAT 60.394 55.000 0.00 0.00 0.00 4.58
5475 6286 0.248661 CACGAGTAGTCCTGGCGATG 60.249 60.000 0.00 0.00 0.00 3.84
5476 6287 1.360551 CGAGTAGTCCTGGCGATGG 59.639 63.158 0.00 0.00 0.00 3.51
5477 6288 1.742768 GAGTAGTCCTGGCGATGGG 59.257 63.158 0.00 0.00 0.00 4.00
5478 6289 2.109181 GTAGTCCTGGCGATGGGC 59.891 66.667 0.00 0.00 42.51 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 139 3.518998 CCCTGCTGCTGCTCATGC 61.519 66.667 17.00 1.02 40.48 4.06
197 204 4.413520 TCTCCATTCCTTTGCCTAGCTAAT 59.586 41.667 0.00 0.00 0.00 1.73
203 210 1.209504 CGGTCTCCATTCCTTTGCCTA 59.790 52.381 0.00 0.00 0.00 3.93
228 235 0.889306 ACGCAACCACTAGAGACTCC 59.111 55.000 0.00 0.00 0.00 3.85
235 242 2.333926 TCATTTCGACGCAACCACTAG 58.666 47.619 0.00 0.00 0.00 2.57
332 339 1.078759 CTAGGCGCCTCGTTGACTTG 61.079 60.000 36.73 3.22 0.00 3.16
334 341 1.658686 CTCTAGGCGCCTCGTTGACT 61.659 60.000 36.73 9.44 0.00 3.41
353 360 1.439543 ATCATTGGGAGAGGTAGCCC 58.560 55.000 0.00 0.00 44.93 5.19
432 467 2.984471 TGAAGTATGAACGCACGTCTTC 59.016 45.455 12.15 12.15 33.24 2.87
462 497 3.325870 CAACTTAGACTGAACGGCATGA 58.674 45.455 0.00 0.00 0.00 3.07
491 629 6.372659 GGAATGCATGAATAGTACCCATACAG 59.627 42.308 0.00 0.00 33.30 2.74
492 630 6.237901 GGAATGCATGAATAGTACCCATACA 58.762 40.000 0.00 0.00 33.30 2.29
495 633 4.041567 TCGGAATGCATGAATAGTACCCAT 59.958 41.667 0.00 0.00 0.00 4.00
496 634 3.389656 TCGGAATGCATGAATAGTACCCA 59.610 43.478 0.00 0.00 0.00 4.51
497 635 4.002906 TCGGAATGCATGAATAGTACCC 57.997 45.455 0.00 0.00 0.00 3.69
498 636 7.041721 TGATATCGGAATGCATGAATAGTACC 58.958 38.462 0.00 0.00 0.00 3.34
499 637 7.223582 CCTGATATCGGAATGCATGAATAGTAC 59.776 40.741 13.42 0.00 0.00 2.73
500 638 7.124147 TCCTGATATCGGAATGCATGAATAGTA 59.876 37.037 13.42 0.00 0.00 1.82
502 640 6.343703 TCCTGATATCGGAATGCATGAATAG 58.656 40.000 13.42 0.00 0.00 1.73
503 641 6.298441 TCCTGATATCGGAATGCATGAATA 57.702 37.500 13.42 0.00 0.00 1.75
504 642 5.169992 TCCTGATATCGGAATGCATGAAT 57.830 39.130 13.42 0.00 0.00 2.57
670 808 0.105593 TCGATGCCTCCAATCTGCTC 59.894 55.000 0.00 0.00 0.00 4.26
676 816 1.153086 GCAGGTCGATGCCTCCAAT 60.153 57.895 0.00 0.00 40.43 3.16
713 853 6.145535 GCTAACAGATTTGACCTTTCACTTG 58.854 40.000 0.00 0.00 0.00 3.16
716 856 4.213482 ACGCTAACAGATTTGACCTTTCAC 59.787 41.667 0.00 0.00 0.00 3.18
745 885 1.842052 TTGTGTGCATGCATCTGGAT 58.158 45.000 25.64 0.00 0.00 3.41
746 886 1.842052 ATTGTGTGCATGCATCTGGA 58.158 45.000 25.64 9.79 0.00 3.86
747 887 4.316205 AATATTGTGTGCATGCATCTGG 57.684 40.909 25.64 0.00 0.00 3.86
748 888 6.068473 ACTAATATTGTGTGCATGCATCTG 57.932 37.500 25.64 7.71 0.00 2.90
749 889 6.994496 ACTACTAATATTGTGTGCATGCATCT 59.006 34.615 25.64 9.42 0.00 2.90
750 890 7.194607 ACTACTAATATTGTGTGCATGCATC 57.805 36.000 25.64 19.65 0.00 3.91
751 891 8.675705 TTACTACTAATATTGTGTGCATGCAT 57.324 30.769 25.64 10.06 0.00 3.96
771 911 7.073854 AGCTCCCCACTTGTAGAATATTACTA 58.926 38.462 0.00 0.00 0.00 1.82
773 913 6.176014 AGCTCCCCACTTGTAGAATATTAC 57.824 41.667 0.00 0.00 0.00 1.89
776 916 4.721776 TCAAGCTCCCCACTTGTAGAATAT 59.278 41.667 3.67 0.00 43.97 1.28
778 918 2.912956 TCAAGCTCCCCACTTGTAGAAT 59.087 45.455 3.67 0.00 43.97 2.40
779 919 2.334977 TCAAGCTCCCCACTTGTAGAA 58.665 47.619 3.67 0.00 43.97 2.10
780 920 2.024176 TCAAGCTCCCCACTTGTAGA 57.976 50.000 3.67 0.00 43.97 2.59
781 921 2.427506 GTTCAAGCTCCCCACTTGTAG 58.572 52.381 3.67 0.00 43.97 2.74
782 922 1.073284 GGTTCAAGCTCCCCACTTGTA 59.927 52.381 3.67 0.00 43.97 2.41
783 923 0.178990 GGTTCAAGCTCCCCACTTGT 60.179 55.000 3.67 0.00 43.97 3.16
784 924 0.178992 TGGTTCAAGCTCCCCACTTG 60.179 55.000 0.00 0.00 44.76 3.16
785 925 0.178990 GTGGTTCAAGCTCCCCACTT 60.179 55.000 13.74 0.00 43.21 3.16
786 926 1.456287 GTGGTTCAAGCTCCCCACT 59.544 57.895 13.74 0.00 43.21 4.00
787 927 0.690762 TAGTGGTTCAAGCTCCCCAC 59.309 55.000 13.34 13.34 46.17 4.61
788 928 0.690762 GTAGTGGTTCAAGCTCCCCA 59.309 55.000 0.00 0.00 0.00 4.96
789 929 0.984995 AGTAGTGGTTCAAGCTCCCC 59.015 55.000 0.00 0.00 0.00 4.81
790 930 2.861147 AAGTAGTGGTTCAAGCTCCC 57.139 50.000 0.00 0.00 0.00 4.30
791 931 4.267349 TGTAAGTAGTGGTTCAAGCTCC 57.733 45.455 0.00 0.00 0.00 4.70
792 932 5.298347 ACTTGTAAGTAGTGGTTCAAGCTC 58.702 41.667 0.00 0.00 37.52 4.09
793 933 5.291905 ACTTGTAAGTAGTGGTTCAAGCT 57.708 39.130 0.00 0.00 37.52 3.74
794 934 6.480981 TGTAACTTGTAAGTAGTGGTTCAAGC 59.519 38.462 0.00 0.00 38.57 4.01
795 935 8.428186 TTGTAACTTGTAAGTAGTGGTTCAAG 57.572 34.615 0.00 0.00 38.57 3.02
796 936 8.667463 GTTTGTAACTTGTAAGTAGTGGTTCAA 58.333 33.333 0.00 0.00 38.57 2.69
797 937 7.280652 GGTTTGTAACTTGTAAGTAGTGGTTCA 59.719 37.037 0.00 0.00 38.57 3.18
798 938 7.254898 GGGTTTGTAACTTGTAAGTAGTGGTTC 60.255 40.741 0.00 0.00 38.57 3.62
799 939 6.543465 GGGTTTGTAACTTGTAAGTAGTGGTT 59.457 38.462 0.00 0.00 38.57 3.67
800 940 6.057533 GGGTTTGTAACTTGTAAGTAGTGGT 58.942 40.000 0.00 0.00 38.57 4.16
801 941 6.056884 TGGGTTTGTAACTTGTAAGTAGTGG 58.943 40.000 0.00 0.00 38.57 4.00
802 942 7.556733 TTGGGTTTGTAACTTGTAAGTAGTG 57.443 36.000 0.00 0.00 38.57 2.74
803 943 8.756486 ATTTGGGTTTGTAACTTGTAAGTAGT 57.244 30.769 0.00 0.00 38.57 2.73
804 944 9.063615 AGATTTGGGTTTGTAACTTGTAAGTAG 57.936 33.333 0.00 0.00 38.57 2.57
805 945 8.842280 CAGATTTGGGTTTGTAACTTGTAAGTA 58.158 33.333 0.00 0.00 38.57 2.24
806 946 7.201875 CCAGATTTGGGTTTGTAACTTGTAAGT 60.202 37.037 0.00 0.00 41.05 2.24
807 947 7.145323 CCAGATTTGGGTTTGTAACTTGTAAG 58.855 38.462 0.00 0.00 41.05 2.34
808 948 7.045126 CCAGATTTGGGTTTGTAACTTGTAA 57.955 36.000 0.00 0.00 41.05 2.41
809 949 6.642707 CCAGATTTGGGTTTGTAACTTGTA 57.357 37.500 0.00 0.00 41.05 2.41
810 950 5.529581 CCAGATTTGGGTTTGTAACTTGT 57.470 39.130 0.00 0.00 41.05 3.16
855 995 0.464373 CGGTGGGAACTGGGATGATG 60.464 60.000 0.00 0.00 0.00 3.07
879 1031 1.000274 GCAACTTTGCGGTCAAGGATT 60.000 47.619 0.00 0.00 45.11 3.01
891 1043 1.242076 CCCTCTGGACAGCAACTTTG 58.758 55.000 0.00 0.00 0.00 2.77
904 1056 4.100373 AGGGATAATAGCTAAGCCCTCTG 58.900 47.826 14.44 0.00 42.02 3.35
919 1071 6.923670 AGTACTCAACTATGGAGAGGGATAA 58.076 40.000 0.00 0.00 36.36 1.75
1011 1219 1.675552 AACCTGGAAACAAGACACCG 58.324 50.000 0.00 0.00 42.06 4.94
1116 1333 1.143684 AGCCAGGACTTGAAGCAAAGA 59.856 47.619 0.00 0.00 0.00 2.52
1149 1366 2.685388 GCTCCATGAAGCTAAAACTCCC 59.315 50.000 0.00 0.00 39.27 4.30
1254 1477 0.831966 AGCCTGAGATGCCTTCTGAG 59.168 55.000 0.00 0.00 35.63 3.35
1581 1804 4.434685 CGCAGCTCAGGGAGATTC 57.565 61.111 0.00 0.00 0.00 2.52
1941 2164 0.036875 GAACCAGGGAGGACAGGTTG 59.963 60.000 0.00 0.00 43.94 3.77
2370 2593 5.649395 CCTGGAGCAATTTGATAGTGAAGAA 59.351 40.000 0.00 0.00 0.00 2.52
2520 2743 3.347216 GCTCTTAAGGTTGCCAATCTCA 58.653 45.455 1.85 0.00 0.00 3.27
2558 2781 5.531122 TCCAGTGAGAAGATTATTACCCG 57.469 43.478 0.00 0.00 0.00 5.28
2565 2788 8.429641 GGTGGTATATTTCCAGTGAGAAGATTA 58.570 37.037 0.00 0.00 35.49 1.75
2610 2833 8.615705 TCTGCTAAGGATAGATAGACCAATCTA 58.384 37.037 0.00 0.00 41.50 1.98
2631 2854 2.341452 GGAAAGCCGGTTTTCTGCT 58.659 52.632 33.65 7.76 37.26 4.24
3212 3438 6.371548 TGGAAAGCTTGTACACAGATGATAAC 59.628 38.462 0.00 0.00 0.00 1.89
3232 3458 2.307686 GGGACATACCTCCTGTTGGAAA 59.692 50.000 0.00 0.00 42.66 3.13
3822 4117 6.366061 GGTTGTGAAGATAATCCAAAGCAAAC 59.634 38.462 0.00 0.00 0.00 2.93
4138 4454 4.194640 CCTTGGTTGATATCTGTCCACTG 58.805 47.826 3.98 5.75 0.00 3.66
4162 4478 2.742053 CACCCCAAAACTGTAGACATCG 59.258 50.000 0.00 0.00 0.00 3.84
4225 4541 6.949352 AGGCTTATACCATCACTGAATTTG 57.051 37.500 0.00 0.00 0.00 2.32
4255 4571 7.648142 TCTTTGTAAATGCTCTACCAACAAAG 58.352 34.615 15.39 15.39 46.88 2.77
4435 4751 3.381045 CGCGTGCTTGATTCTAAGGATA 58.619 45.455 0.00 0.00 30.62 2.59
4497 4813 2.093235 ACCTCTTTCACTAGCTGCCATC 60.093 50.000 0.00 0.00 0.00 3.51
4504 4820 2.284190 GGATGCACCTCTTTCACTAGC 58.716 52.381 0.00 0.00 35.41 3.42
4507 4823 2.957402 TTGGATGCACCTCTTTCACT 57.043 45.000 0.00 0.00 39.86 3.41
4509 4825 3.507162 TCTTTGGATGCACCTCTTTCA 57.493 42.857 0.00 0.00 39.86 2.69
4512 4828 3.515602 ACTTCTTTGGATGCACCTCTT 57.484 42.857 0.00 0.00 39.86 2.85
4516 4832 4.798574 CACTTTACTTCTTTGGATGCACC 58.201 43.478 0.00 0.00 39.54 5.01
4518 4834 4.022935 CAGCACTTTACTTCTTTGGATGCA 60.023 41.667 0.00 0.00 32.99 3.96
4524 4840 5.179555 GGGAGTACAGCACTTTACTTCTTTG 59.820 44.000 0.00 0.00 37.72 2.77
4532 4848 1.822990 CGGAGGGAGTACAGCACTTTA 59.177 52.381 0.00 0.00 37.72 1.85
4549 4865 1.070445 TGCGAACTAAAAAGGACCGGA 59.930 47.619 9.46 0.00 0.00 5.14
4550 4866 1.515081 TGCGAACTAAAAAGGACCGG 58.485 50.000 0.00 0.00 0.00 5.28
4551 4867 6.477688 TCTTATATGCGAACTAAAAAGGACCG 59.522 38.462 0.00 0.00 0.00 4.79
4552 4868 7.781548 TCTTATATGCGAACTAAAAAGGACC 57.218 36.000 0.00 0.00 0.00 4.46
4562 4878 9.601217 ACTTTAGACAAATCTTATATGCGAACT 57.399 29.630 0.00 0.00 36.29 3.01
4563 4879 9.851043 GACTTTAGACAAATCTTATATGCGAAC 57.149 33.333 0.00 0.00 36.29 3.95
4566 4882 9.855361 CTTGACTTTAGACAAATCTTATATGCG 57.145 33.333 0.00 0.00 36.29 4.73
4567 4883 9.657121 GCTTGACTTTAGACAAATCTTATATGC 57.343 33.333 0.00 0.00 36.29 3.14
4570 4886 9.601217 GAGGCTTGACTTTAGACAAATCTTATA 57.399 33.333 0.00 0.00 36.29 0.98
4573 4889 5.409826 CGAGGCTTGACTTTAGACAAATCTT 59.590 40.000 0.00 0.00 36.29 2.40
4574 4890 4.932200 CGAGGCTTGACTTTAGACAAATCT 59.068 41.667 0.00 0.00 39.15 2.40
4575 4891 4.691216 ACGAGGCTTGACTTTAGACAAATC 59.309 41.667 9.20 0.00 30.22 2.17
4576 4892 4.642429 ACGAGGCTTGACTTTAGACAAAT 58.358 39.130 9.20 0.00 30.22 2.32
4579 4895 4.859304 TTACGAGGCTTGACTTTAGACA 57.141 40.909 9.20 0.00 0.00 3.41
4580 4896 5.169295 ACATTACGAGGCTTGACTTTAGAC 58.831 41.667 9.20 0.00 0.00 2.59
4582 4898 6.147164 TCAAACATTACGAGGCTTGACTTTAG 59.853 38.462 9.20 0.00 0.00 1.85
4583 4899 5.992829 TCAAACATTACGAGGCTTGACTTTA 59.007 36.000 9.20 0.00 0.00 1.85
4584 4900 4.819630 TCAAACATTACGAGGCTTGACTTT 59.180 37.500 9.20 0.00 0.00 2.66
4586 4902 3.746492 GTCAAACATTACGAGGCTTGACT 59.254 43.478 9.20 0.00 39.54 3.41
4587 4903 3.120304 GGTCAAACATTACGAGGCTTGAC 60.120 47.826 9.20 5.19 41.09 3.18
4590 4906 3.134574 TGGTCAAACATTACGAGGCTT 57.865 42.857 0.00 0.00 0.00 4.35
4592 4908 2.812011 AGTTGGTCAAACATTACGAGGC 59.188 45.455 0.00 0.00 41.61 4.70
4593 4909 5.432885 AAAGTTGGTCAAACATTACGAGG 57.567 39.130 0.00 0.00 41.61 4.63
4595 4911 9.491675 TTCTATAAAGTTGGTCAAACATTACGA 57.508 29.630 0.00 0.00 41.61 3.43
4649 4965 8.868103 AGTCATGACACATCTACTGATATTGAT 58.132 33.333 27.02 0.00 0.00 2.57
4650 4966 8.242729 AGTCATGACACATCTACTGATATTGA 57.757 34.615 27.02 0.00 0.00 2.57
4651 4967 8.883954 AAGTCATGACACATCTACTGATATTG 57.116 34.615 27.02 0.00 0.00 1.90
4655 4971 9.896645 AATTTAAGTCATGACACATCTACTGAT 57.103 29.630 27.02 0.00 0.00 2.90
4752 5562 9.495754 GCATATAAGAATTGTCTGAAGTCAAAC 57.504 33.333 0.00 0.00 33.05 2.93
4753 5563 9.230122 TGCATATAAGAATTGTCTGAAGTCAAA 57.770 29.630 0.00 0.00 33.05 2.69
4754 5564 8.791327 TGCATATAAGAATTGTCTGAAGTCAA 57.209 30.769 0.00 0.00 33.05 3.18
4755 5565 8.260114 TCTGCATATAAGAATTGTCTGAAGTCA 58.740 33.333 0.00 0.00 33.05 3.41
4756 5566 8.654230 TCTGCATATAAGAATTGTCTGAAGTC 57.346 34.615 0.00 0.00 33.05 3.01
4757 5567 8.263640 ACTCTGCATATAAGAATTGTCTGAAGT 58.736 33.333 0.00 0.00 33.05 3.01
4758 5568 8.659925 ACTCTGCATATAAGAATTGTCTGAAG 57.340 34.615 0.00 0.00 33.05 3.02
4767 5577 9.343539 GGTCCTTTTTACTCTGCATATAAGAAT 57.656 33.333 0.00 0.00 0.00 2.40
4768 5578 7.494625 CGGTCCTTTTTACTCTGCATATAAGAA 59.505 37.037 0.00 0.00 0.00 2.52
4769 5579 6.984474 CGGTCCTTTTTACTCTGCATATAAGA 59.016 38.462 0.00 0.00 0.00 2.10
4770 5580 6.202954 CCGGTCCTTTTTACTCTGCATATAAG 59.797 42.308 0.00 0.00 0.00 1.73
4771 5581 6.053005 CCGGTCCTTTTTACTCTGCATATAA 58.947 40.000 0.00 0.00 0.00 0.98
4772 5582 5.364446 TCCGGTCCTTTTTACTCTGCATATA 59.636 40.000 0.00 0.00 0.00 0.86
4773 5583 4.163458 TCCGGTCCTTTTTACTCTGCATAT 59.837 41.667 0.00 0.00 0.00 1.78
4774 5584 3.516300 TCCGGTCCTTTTTACTCTGCATA 59.484 43.478 0.00 0.00 0.00 3.14
4775 5585 2.304761 TCCGGTCCTTTTTACTCTGCAT 59.695 45.455 0.00 0.00 0.00 3.96
4776 5586 1.695242 TCCGGTCCTTTTTACTCTGCA 59.305 47.619 0.00 0.00 0.00 4.41
4777 5587 2.347731 CTCCGGTCCTTTTTACTCTGC 58.652 52.381 0.00 0.00 0.00 4.26
4778 5588 2.354805 CCCTCCGGTCCTTTTTACTCTG 60.355 54.545 0.00 0.00 0.00 3.35
4779 5589 1.907255 CCCTCCGGTCCTTTTTACTCT 59.093 52.381 0.00 0.00 0.00 3.24
4780 5590 1.904537 TCCCTCCGGTCCTTTTTACTC 59.095 52.381 0.00 0.00 0.00 2.59
4781 5591 1.907255 CTCCCTCCGGTCCTTTTTACT 59.093 52.381 0.00 0.00 0.00 2.24
4782 5592 1.627329 ACTCCCTCCGGTCCTTTTTAC 59.373 52.381 0.00 0.00 0.00 2.01
4783 5593 2.034436 ACTCCCTCCGGTCCTTTTTA 57.966 50.000 0.00 0.00 0.00 1.52
4784 5594 2.034436 TACTCCCTCCGGTCCTTTTT 57.966 50.000 0.00 0.00 0.00 1.94
4785 5595 1.627329 GTTACTCCCTCCGGTCCTTTT 59.373 52.381 0.00 0.00 0.00 2.27
4786 5596 1.203275 AGTTACTCCCTCCGGTCCTTT 60.203 52.381 0.00 0.00 0.00 3.11
4787 5597 0.412640 AGTTACTCCCTCCGGTCCTT 59.587 55.000 0.00 0.00 0.00 3.36
4788 5598 1.064091 GTAGTTACTCCCTCCGGTCCT 60.064 57.143 0.00 0.00 0.00 3.85
4789 5599 1.397672 GTAGTTACTCCCTCCGGTCC 58.602 60.000 0.00 0.00 0.00 4.46
4790 5600 1.064091 AGGTAGTTACTCCCTCCGGTC 60.064 57.143 0.00 0.00 0.00 4.79
4791 5601 1.006020 AGGTAGTTACTCCCTCCGGT 58.994 55.000 0.00 0.00 0.00 5.28
4792 5602 2.156102 AAGGTAGTTACTCCCTCCGG 57.844 55.000 0.00 0.00 0.00 5.14
4834 5644 5.454613 CCAAAAGGAAACCACCAATAAGCTT 60.455 40.000 3.48 3.48 0.00 3.74
4835 5645 4.040339 CCAAAAGGAAACCACCAATAAGCT 59.960 41.667 0.00 0.00 0.00 3.74
4836 5646 4.039852 TCCAAAAGGAAACCACCAATAAGC 59.960 41.667 0.00 0.00 0.00 3.09
4871 5681 3.438781 TCAGTGATACGTTTGGAAATGCC 59.561 43.478 0.00 0.00 37.10 4.40
4888 5698 4.190001 ACTGCAGCAAGAGAATATCAGTG 58.810 43.478 15.27 0.00 32.96 3.66
4919 5729 9.665264 CTCAACAAACCTAGAGAAAAATTACAC 57.335 33.333 0.00 0.00 0.00 2.90
4938 5748 3.324846 ACAGAGATGCCACTACTCAACAA 59.675 43.478 0.00 0.00 33.69 2.83
4944 5754 3.099905 TGCTTACAGAGATGCCACTACT 58.900 45.455 0.00 0.00 0.00 2.57
4950 5760 2.216898 GATGGTGCTTACAGAGATGCC 58.783 52.381 0.00 0.00 0.00 4.40
4952 5762 2.101415 TCGGATGGTGCTTACAGAGATG 59.899 50.000 0.00 0.00 0.00 2.90
4986 5796 6.082338 CGGACATTAAGCATGCAAATCTATC 58.918 40.000 21.98 14.14 36.14 2.08
4988 5798 4.275689 CCGGACATTAAGCATGCAAATCTA 59.724 41.667 21.98 0.00 36.14 1.98
5010 5820 9.959749 TGTAAAAACATTTAACTCAATCTGACC 57.040 29.630 0.00 0.00 0.00 4.02
5038 5848 7.513856 TCCCATTCGGATCAAAAATCACTATA 58.486 34.615 0.00 0.00 34.86 1.31
5039 5849 6.364701 TCCCATTCGGATCAAAAATCACTAT 58.635 36.000 0.00 0.00 34.86 2.12
5040 5850 5.750524 TCCCATTCGGATCAAAAATCACTA 58.249 37.500 0.00 0.00 34.86 2.74
5052 5862 3.217626 GAGCTTTGATTCCCATTCGGAT 58.782 45.455 0.00 0.00 41.63 4.18
5076 5886 4.119136 TCGTGTCGAATTCATGTGCATAT 58.881 39.130 6.22 0.00 31.06 1.78
5094 5904 4.778904 TGTAGCGGATTTTCTTTTTCGTG 58.221 39.130 0.00 0.00 0.00 4.35
5103 5913 7.462462 CGAGTTACTACTTTGTAGCGGATTTTC 60.462 40.741 4.82 0.00 33.84 2.29
5138 5948 3.213506 TGGGCAAATCCAATCTGTATCG 58.786 45.455 0.00 0.00 36.21 2.92
5158 5969 1.672881 GTTGATCTTCTGCGGGGATTG 59.327 52.381 0.00 0.00 0.00 2.67
5175 5986 3.306973 CGTGTGCTATGTCTATGTGGTTG 59.693 47.826 0.00 0.00 0.00 3.77
5178 5989 1.860950 GCGTGTGCTATGTCTATGTGG 59.139 52.381 0.00 0.00 38.39 4.17
5181 5992 1.518515 CACGCGTGTGCTATGTCTATG 59.481 52.381 30.50 0.00 39.67 2.23
5373 6184 3.869272 GCTGAATGGACCGCGCTG 61.869 66.667 5.56 0.00 0.00 5.18
5384 6195 2.730129 AAAAGGGCCCGGTGCTGAAT 62.730 55.000 18.44 0.00 40.92 2.57
5403 6214 2.609984 CGGTGCTGAATCCATGCAAAAA 60.610 45.455 0.00 0.00 38.50 1.94
5404 6215 1.067706 CGGTGCTGAATCCATGCAAAA 60.068 47.619 0.00 0.00 38.50 2.44
5405 6216 0.527113 CGGTGCTGAATCCATGCAAA 59.473 50.000 0.00 0.00 38.50 3.68
5406 6217 1.314534 CCGGTGCTGAATCCATGCAA 61.315 55.000 0.00 0.00 38.50 4.08
5407 6218 1.750018 CCGGTGCTGAATCCATGCA 60.750 57.895 0.00 0.00 0.00 3.96
5408 6219 2.484062 CCCGGTGCTGAATCCATGC 61.484 63.158 0.00 0.00 0.00 4.06
5409 6220 2.484062 GCCCGGTGCTGAATCCATG 61.484 63.158 0.00 0.00 36.87 3.66
5410 6221 2.124151 GCCCGGTGCTGAATCCAT 60.124 61.111 0.00 0.00 36.87 3.41
5411 6222 4.424711 GGCCCGGTGCTGAATCCA 62.425 66.667 13.58 0.00 40.92 3.41
5412 6223 3.645268 AAGGCCCGGTGCTGAATCC 62.645 63.158 13.58 0.00 40.92 3.01
5413 6224 2.044946 AAGGCCCGGTGCTGAATC 60.045 61.111 13.58 0.00 40.92 2.52
5414 6225 2.044946 GAAGGCCCGGTGCTGAAT 60.045 61.111 13.58 0.00 40.92 2.57
5415 6226 4.697756 CGAAGGCCCGGTGCTGAA 62.698 66.667 13.58 0.00 40.92 3.02
5462 6273 2.364973 TGCCCATCGCCAGGACTA 60.365 61.111 0.00 0.00 36.24 2.59
5463 6274 3.790437 CTGCCCATCGCCAGGACT 61.790 66.667 0.00 0.00 36.24 3.85


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

AutoCloner maintained by Alex Coulton.