Multiple sequence alignment - TraesCS2A01G198700

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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 TraesCS2A01G198700 chr2A 100.000 3971 0 0 1 3971 171075835 171079805 0.000000e+00 7334.0
1 TraesCS2A01G198700 chr2A 92.614 176 7 4 3255 3427 171079001 171079173 8.520000e-62 248.0
2 TraesCS2A01G198700 chr2A 92.614 176 7 4 3167 3339 171079089 171079261 8.520000e-62 248.0
3 TraesCS2A01G198700 chr2A 76.359 368 66 13 607 972 158180466 158180118 1.130000e-40 178.0
4 TraesCS2A01G198700 chr2A 92.045 88 7 0 3340 3427 171079001 171079088 1.500000e-24 124.0
5 TraesCS2A01G198700 chr2A 92.045 88 7 0 3167 3254 171079174 171079261 1.500000e-24 124.0
6 TraesCS2A01G198700 chr2B 90.763 1678 104 31 1689 3339 216939803 216941456 0.000000e+00 2193.0
7 TraesCS2A01G198700 chr2B 88.595 982 89 16 1 974 216937827 216938793 0.000000e+00 1171.0
8 TraesCS2A01G198700 chr2B 93.268 713 39 6 3255 3963 216941281 216941988 0.000000e+00 1042.0
9 TraesCS2A01G198700 chr2B 92.543 523 22 7 1009 1525 216938893 216939404 0.000000e+00 734.0
10 TraesCS2A01G198700 chr2B 77.455 448 77 17 531 973 763375290 763375718 3.060000e-61 246.0
11 TraesCS2A01G198700 chr2B 85.380 171 14 3 1520 1688 216939597 216939758 2.450000e-37 167.0
12 TraesCS2A01G198700 chr2D 92.164 1123 51 14 2245 3339 159850687 159851800 0.000000e+00 1552.0
13 TraesCS2A01G198700 chr2D 92.329 717 33 9 3255 3964 159851630 159852331 0.000000e+00 1000.0
14 TraesCS2A01G198700 chr2D 91.763 692 31 10 1011 1688 159849202 159849881 0.000000e+00 939.0
15 TraesCS2A01G198700 chr2D 94.780 364 13 4 1689 2051 159849929 159850287 2.680000e-156 562.0
16 TraesCS2A01G198700 chr2D 94.388 196 11 0 2049 2244 159850448 159850643 6.450000e-78 302.0
17 TraesCS2A01G198700 chr2D 91.057 123 10 1 1 122 159709559 159709681 8.830000e-37 165.0
18 TraesCS2A01G198700 chr2D 94.318 88 5 0 3167 3254 159851713 159851800 6.920000e-28 135.0
19 TraesCS2A01G198700 chr2D 90.789 76 4 3 3340 3413 159851630 159851704 9.080000e-17 99.0
20 TraesCS2A01G198700 chr3D 83.370 457 69 5 517 972 90832186 90831736 2.210000e-112 416.0
21 TraesCS2A01G198700 chr7D 81.330 466 72 7 514 969 205145556 205146016 8.110000e-97 364.0
22 TraesCS2A01G198700 chr7D 88.889 45 5 0 1858 1902 363558964 363559008 5.540000e-04 56.5
23 TraesCS2A01G198700 chr3A 79.449 472 78 11 514 972 739402554 739403019 2.300000e-82 316.0
24 TraesCS2A01G198700 chr3A 75.262 477 91 19 514 976 95939985 95940448 6.730000e-48 202.0
25 TraesCS2A01G198700 chr3A 75.055 453 92 15 522 972 64085732 64085299 1.460000e-44 191.0
26 TraesCS2A01G198700 chr7A 79.167 456 73 19 529 972 608261306 608261751 3.000000e-76 296.0
27 TraesCS2A01G198700 chr7A 75.561 446 84 12 529 972 708815407 708814985 3.130000e-46 196.0
28 TraesCS2A01G198700 chr7A 96.970 33 1 0 1870 1902 393766451 393766419 5.540000e-04 56.5
29 TraesCS2A01G198700 chr4B 78.233 464 84 12 514 965 575045942 575046400 8.400000e-72 281.0
30 TraesCS2A01G198700 chr4B 77.162 451 73 20 531 973 580799088 580799516 6.630000e-58 235.0
31 TraesCS2A01G198700 chr4B 76.068 468 81 23 512 972 594365225 594365668 8.640000e-52 215.0
32 TraesCS2A01G198700 chr5D 75.216 464 91 18 514 966 438821568 438821118 8.700000e-47 198.0
33 TraesCS2A01G198700 chr5D 76.426 263 58 4 536 796 12162243 12162503 5.350000e-29 139.0
34 TraesCS2A01G198700 chrUn 83.249 197 30 3 537 732 405573339 405573533 1.130000e-40 178.0
35 TraesCS2A01G198700 chrUn 82.741 197 31 3 537 732 17042641 17042835 5.280000e-39 172.0
36 TraesCS2A01G198700 chr7B 96.970 33 1 0 1870 1902 323208546 323208578 5.540000e-04 56.5


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 TraesCS2A01G198700 chr2A 171075835 171079805 3970 False 1615.600000 7334 93.8636 1 3971 5 chr2A.!!$F1 3970
1 TraesCS2A01G198700 chr2B 216937827 216941988 4161 False 1061.400000 2193 90.1098 1 3963 5 chr2B.!!$F2 3962
2 TraesCS2A01G198700 chr2D 159849202 159852331 3129 False 655.571429 1552 92.9330 1011 3964 7 chr2D.!!$F2 2953

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
312 314 0.037605 ACCTCCATCCGAACAACGTC 60.038 55.0 0.00 0.00 40.78 4.34 F
801 807 0.179215 GCGGTTGCTGTTCTGATTCG 60.179 55.0 0.00 0.00 38.39 3.34 F
2234 2726 0.179000 CCAGGCAGCTTAGGTGTAGG 59.821 60.0 13.13 8.58 33.19 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1398 1475 0.239347 CGAACCCGTCTTCGTACTGT 59.761 55.000 4.07 0.00 38.58 3.55 R
2284 2825 1.002134 CATGTCAAAGGGGACGGCT 60.002 57.895 0.00 0.00 40.72 5.52 R
3717 4288 0.390860 GCCACAGTGCTCGAGGATAT 59.609 55.000 15.58 1.25 0.00 1.63 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
29 31 2.046700 GGGACGGTGCCAAATCGA 60.047 61.111 14.36 0.00 0.00 3.59
68 70 7.298854 TCGATTTATGTCGATAGTCAAGCTAG 58.701 38.462 0.00 0.00 44.87 3.42
69 71 7.041303 TCGATTTATGTCGATAGTCAAGCTAGT 60.041 37.037 0.00 0.00 44.87 2.57
75 77 3.377485 TCGATAGTCAAGCTAGTGTCACC 59.623 47.826 0.00 0.00 32.45 4.02
79 81 2.094659 CAAGCTAGTGTCACCGGCG 61.095 63.158 0.00 0.00 0.00 6.46
109 111 2.331805 CTAGTCCGTGATCGCCCG 59.668 66.667 0.00 0.00 35.54 6.13
148 150 0.729140 CAAAAGACGATGCCGCCAAC 60.729 55.000 0.00 0.00 39.95 3.77
149 151 2.182614 AAAAGACGATGCCGCCAACG 62.183 55.000 0.00 0.00 42.17 4.10
177 179 2.394930 AAAACCAAACCAACACCAGC 57.605 45.000 0.00 0.00 0.00 4.85
178 180 0.539518 AAACCAAACCAACACCAGCC 59.460 50.000 0.00 0.00 0.00 4.85
179 181 0.616111 AACCAAACCAACACCAGCCA 60.616 50.000 0.00 0.00 0.00 4.75
194 196 1.081242 GCCAATGTGGAAGCACACG 60.081 57.895 0.00 0.00 44.21 4.49
198 200 1.227999 AATGTGGAAGCACACGTCCG 61.228 55.000 0.00 0.00 46.47 4.79
242 244 4.748892 CTTCTAGACGTCATTGACCATGT 58.251 43.478 19.50 3.56 34.06 3.21
257 259 1.134098 CCATGTCGCCAAGATAGGGTT 60.134 52.381 0.00 0.00 37.19 4.11
264 266 2.019984 GCCAAGATAGGGTTGAAGCTG 58.980 52.381 0.00 0.00 0.00 4.24
267 269 1.216990 AGATAGGGTTGAAGCTGGGG 58.783 55.000 0.00 0.00 0.00 4.96
278 280 3.138128 GCTGGGGCGCCGTTATTT 61.138 61.111 22.54 0.00 0.00 1.40
302 304 0.673644 CAACGTCACCACCTCCATCC 60.674 60.000 0.00 0.00 0.00 3.51
310 312 1.019278 CCACCTCCATCCGAACAACG 61.019 60.000 0.00 0.00 42.18 4.10
311 313 0.320421 CACCTCCATCCGAACAACGT 60.320 55.000 0.00 0.00 40.78 3.99
312 314 0.037605 ACCTCCATCCGAACAACGTC 60.038 55.000 0.00 0.00 40.78 4.34
340 342 4.962995 TGGAACCAAAACCTAATCCAAACA 59.037 37.500 0.00 0.00 34.21 2.83
348 350 7.437748 CAAAACCTAATCCAAACAACATACCA 58.562 34.615 0.00 0.00 0.00 3.25
353 355 6.866248 CCTAATCCAAACAACATACCAAACAC 59.134 38.462 0.00 0.00 0.00 3.32
389 391 3.443925 CTCTCTCGCCGCTGGTGA 61.444 66.667 9.84 9.84 40.17 4.02
436 438 1.296715 CCTTGACAACGGGAGGAGG 59.703 63.158 0.00 0.00 0.00 4.30
444 446 2.292323 ACAACGGGAGGAGGTAGAGATT 60.292 50.000 0.00 0.00 0.00 2.40
494 496 3.027412 GCTAGGTGAGAGTTGAGATGGA 58.973 50.000 0.00 0.00 0.00 3.41
499 501 3.370315 GGTGAGAGTTGAGATGGATTGCT 60.370 47.826 0.00 0.00 0.00 3.91
508 510 1.845143 AGATGGATTGCTGCTCCTCTT 59.155 47.619 9.08 0.00 33.69 2.85
512 514 0.450983 GATTGCTGCTCCTCTTGTGC 59.549 55.000 0.00 0.00 0.00 4.57
525 528 4.826733 TCCTCTTGTGCTTTGATGCTTTTA 59.173 37.500 0.00 0.00 0.00 1.52
541 544 6.834168 TGCTTTTATGAGTTTTCTTAGGGG 57.166 37.500 0.00 0.00 0.00 4.79
543 546 6.780522 TGCTTTTATGAGTTTTCTTAGGGGTT 59.219 34.615 0.00 0.00 0.00 4.11
560 563 2.038557 GGGTTGTGTCCTGCTTAGAGAA 59.961 50.000 0.00 0.00 0.00 2.87
568 571 1.272781 CTGCTTAGAGAAACGAGGCG 58.727 55.000 0.00 0.00 0.00 5.52
571 574 1.402456 GCTTAGAGAAACGAGGCGACA 60.402 52.381 0.00 0.00 0.00 4.35
604 607 4.658901 TGAAGATGGAATAAGGTACTCCCC 59.341 45.833 0.00 0.00 38.49 4.81
622 625 3.541713 GCCTAGCTCCCGTCCCAG 61.542 72.222 0.00 0.00 0.00 4.45
648 651 1.735376 TTCTAGCGTCATCGGAGGGC 61.735 60.000 0.00 0.00 37.56 5.19
649 652 2.441348 TAGCGTCATCGGAGGGCA 60.441 61.111 0.00 0.00 37.56 5.36
655 660 1.995066 TCATCGGAGGGCATGTGGT 60.995 57.895 0.00 0.00 0.00 4.16
665 670 0.598065 GGCATGTGGTGGTTTGTCTC 59.402 55.000 0.00 0.00 0.00 3.36
669 674 1.147600 GTGGTGGTTTGTCTCCGGT 59.852 57.895 0.00 0.00 0.00 5.28
687 692 2.049063 GGATCTCGCGGGATTCGG 60.049 66.667 24.71 0.00 39.69 4.30
691 696 3.884350 CTCGCGGGATTCGGTCGA 61.884 66.667 0.00 0.00 39.69 4.20
693 698 4.485834 CGCGGGATTCGGTCGACA 62.486 66.667 18.91 0.00 39.69 4.35
710 716 3.193903 TCGACATTTGTCTTCGGTGGATA 59.806 43.478 8.91 0.00 42.66 2.59
732 738 5.975693 ACACATGGATTCGGTATTTGTTT 57.024 34.783 0.00 0.00 0.00 2.83
747 753 4.955925 TTTGTTTGTGTGTCTACAGGTG 57.044 40.909 0.00 0.00 37.52 4.00
749 755 2.502130 TGTTTGTGTGTCTACAGGTGGA 59.498 45.455 0.00 0.00 37.52 4.02
750 756 3.131396 GTTTGTGTGTCTACAGGTGGAG 58.869 50.000 0.00 0.00 37.52 3.86
754 760 1.147191 TGTGTCTACAGGTGGAGTCCT 59.853 52.381 11.33 0.00 38.51 3.85
756 762 2.231721 GTGTCTACAGGTGGAGTCCTTC 59.768 54.545 11.33 3.59 35.37 3.46
771 777 7.494298 GTGGAGTCCTTCTGATCTAAATTTCTC 59.506 40.741 11.33 0.00 0.00 2.87
779 785 7.834068 TCTGATCTAAATTTCTCTTCAACGG 57.166 36.000 0.00 0.00 0.00 4.44
797 803 2.664851 CGGCGGTTGCTGTTCTGA 60.665 61.111 0.00 0.00 42.79 3.27
799 805 1.577328 CGGCGGTTGCTGTTCTGATT 61.577 55.000 0.00 0.00 42.79 2.57
801 807 0.179215 GCGGTTGCTGTTCTGATTCG 60.179 55.000 0.00 0.00 38.39 3.34
808 814 1.674221 GCTGTTCTGATTCGCTGGTCT 60.674 52.381 0.00 0.00 0.00 3.85
811 817 4.437239 CTGTTCTGATTCGCTGGTCTTAT 58.563 43.478 0.00 0.00 0.00 1.73
815 821 4.470602 TCTGATTCGCTGGTCTTATAGGA 58.529 43.478 0.00 0.00 0.00 2.94
827 833 5.708877 GTCTTATAGGACCTTAGCACGAT 57.291 43.478 0.00 0.00 0.00 3.73
835 841 3.132467 GGACCTTAGCACGATAACTTCCT 59.868 47.826 0.00 0.00 0.00 3.36
848 854 6.539464 ACGATAACTTCCTGACTGTCTACTAG 59.461 42.308 9.51 4.54 0.00 2.57
849 855 6.539464 CGATAACTTCCTGACTGTCTACTAGT 59.461 42.308 9.51 0.00 0.00 2.57
850 856 7.710044 CGATAACTTCCTGACTGTCTACTAGTA 59.290 40.741 9.51 1.89 0.00 1.82
851 857 8.735692 ATAACTTCCTGACTGTCTACTAGTAC 57.264 38.462 9.51 0.00 0.00 2.73
852 858 6.124316 ACTTCCTGACTGTCTACTAGTACA 57.876 41.667 9.51 0.00 0.00 2.90
853 859 6.540995 ACTTCCTGACTGTCTACTAGTACAA 58.459 40.000 9.51 0.00 0.00 2.41
854 860 7.176490 ACTTCCTGACTGTCTACTAGTACAAT 58.824 38.462 9.51 0.00 0.00 2.71
865 871 8.591072 TGTCTACTAGTACAATAAGTTTTGCCT 58.409 33.333 0.00 0.00 0.00 4.75
879 885 0.252239 TTGCCTGGCTCTAGTGAGGA 60.252 55.000 21.03 0.00 40.53 3.71
881 887 0.463620 GCCTGGCTCTAGTGAGGAAG 59.536 60.000 12.43 0.00 40.53 3.46
882 888 1.118838 CCTGGCTCTAGTGAGGAAGG 58.881 60.000 0.00 0.00 40.53 3.46
888 894 0.683504 TCTAGTGAGGAAGGGGCGAC 60.684 60.000 0.00 0.00 0.00 5.19
911 917 0.524862 GACGGCGTTCCTCTAACTCA 59.475 55.000 16.19 0.00 35.81 3.41
920 926 5.393243 GCGTTCCTCTAACTCACTTCAGTAT 60.393 44.000 0.00 0.00 35.81 2.12
926 932 8.740906 TCCTCTAACTCACTTCAGTATTTGTAG 58.259 37.037 0.00 0.00 0.00 2.74
933 939 4.030306 CACTTCAGTATTTGTAGTCGTCGC 59.970 45.833 0.00 0.00 35.50 5.19
940 946 1.527034 TTGTAGTCGTCGCTAGGTGT 58.473 50.000 0.00 0.00 0.00 4.16
945 951 1.736681 AGTCGTCGCTAGGTGTTCTAC 59.263 52.381 0.00 0.00 0.00 2.59
947 953 0.247974 CGTCGCTAGGTGTTCTACGG 60.248 60.000 0.00 0.00 0.00 4.02
950 956 2.098770 GTCGCTAGGTGTTCTACGGATT 59.901 50.000 0.00 0.00 0.00 3.01
952 958 3.947196 TCGCTAGGTGTTCTACGGATTTA 59.053 43.478 0.00 0.00 0.00 1.40
1007 1079 8.813643 AAAAAGATTCTGCAGAAAATGAAGAG 57.186 30.769 31.55 0.00 44.85 2.85
1106 1180 3.036084 GTCACACGGACACGCCTG 61.036 66.667 0.00 0.00 46.19 4.85
1197 1274 1.880340 GAAGCATCTCGCCGTCCTG 60.880 63.158 0.00 0.00 44.04 3.86
1441 1518 1.981254 CGTGGAATTGGTACGTACGT 58.019 50.000 25.98 25.98 33.48 3.57
1442 1519 3.129852 CGTGGAATTGGTACGTACGTA 57.870 47.619 23.60 23.60 33.48 3.57
1464 1541 2.390599 TGCGCTTGAATGGTCGCTC 61.391 57.895 9.73 0.00 46.73 5.03
1465 1542 2.697425 CGCTTGAATGGTCGCTCG 59.303 61.111 0.00 0.00 0.00 5.03
1634 1912 0.461548 ATCCTCGAGAGCGCAATTGA 59.538 50.000 15.71 5.86 37.46 2.57
1637 1915 0.371645 CTCGAGAGCGCAATTGAACC 59.628 55.000 11.47 0.00 37.46 3.62
1652 1930 6.563422 CAATTGAACCTCTGAACTTGTTTCA 58.437 36.000 0.00 0.00 42.26 2.69
1654 1932 8.352201 CAATTGAACCTCTGAACTTGTTTCATA 58.648 33.333 0.00 0.00 43.54 2.15
1655 1933 8.641498 ATTGAACCTCTGAACTTGTTTCATAT 57.359 30.769 0.00 0.00 43.54 1.78
1656 1934 9.739276 ATTGAACCTCTGAACTTGTTTCATATA 57.261 29.630 0.00 0.00 43.54 0.86
1658 1936 9.739276 TGAACCTCTGAACTTGTTTCATATATT 57.261 29.630 0.00 0.00 43.54 1.28
1661 1939 9.388506 ACCTCTGAACTTGTTTCATATATTCTG 57.611 33.333 0.00 0.00 43.54 3.02
1662 1940 9.388506 CCTCTGAACTTGTTTCATATATTCTGT 57.611 33.333 0.00 0.00 43.54 3.41
1681 1960 2.250188 GTTTTTCGCGTGATTCCCATG 58.750 47.619 5.77 0.00 34.90 3.66
1833 2159 9.243105 ACTATTATAGTGCAGATTTTGGTTTGT 57.757 29.630 3.83 0.00 37.69 2.83
1834 2160 9.507280 CTATTATAGTGCAGATTTTGGTTTGTG 57.493 33.333 0.00 0.00 0.00 3.33
1903 2229 8.225603 TGATCCAAAGGCTTAGAAATATGAAC 57.774 34.615 0.00 0.00 0.00 3.18
1936 2262 9.892130 TTAAAAGATCCCAAGCAACTTTTAAAA 57.108 25.926 15.69 0.00 43.46 1.52
1937 2263 8.978874 AAAAGATCCCAAGCAACTTTTAAAAT 57.021 26.923 0.09 0.00 38.45 1.82
1941 2267 9.489084 AGATCCCAAGCAACTTTTAAAATTTAC 57.511 29.630 0.09 0.00 0.00 2.01
1943 2269 6.702282 TCCCAAGCAACTTTTAAAATTTACCG 59.298 34.615 0.09 0.00 0.00 4.02
1944 2270 6.702282 CCCAAGCAACTTTTAAAATTTACCGA 59.298 34.615 0.09 0.00 0.00 4.69
1945 2271 7.095816 CCCAAGCAACTTTTAAAATTTACCGAG 60.096 37.037 0.09 0.00 0.00 4.63
1946 2272 7.650104 CCAAGCAACTTTTAAAATTTACCGAGA 59.350 33.333 0.09 0.00 0.00 4.04
2061 2550 6.660521 TGCCAAAAATCATACAAGAGTGAGAT 59.339 34.615 0.00 0.00 0.00 2.75
2079 2568 8.588290 AGTGAGATACAGTCCATAGGAATATC 57.412 38.462 0.00 0.00 31.38 1.63
2096 2588 5.474876 GGAATATCGATGGCCTCATTTTCTT 59.525 40.000 8.54 0.00 32.98 2.52
2107 2599 5.582269 GGCCTCATTTTCTTATCCAAAAAGC 59.418 40.000 0.00 0.00 0.00 3.51
2163 2655 8.844244 CAAAATCCTACAAGATTCTTATGGGAG 58.156 37.037 14.19 2.47 35.40 4.30
2207 2699 4.008074 TCGAAAGATGGCTTGGATATCC 57.992 45.455 15.39 15.39 33.79 2.59
2224 2716 0.185901 TCCTTTCAAACCAGGCAGCT 59.814 50.000 0.00 0.00 0.00 4.24
2234 2726 0.179000 CCAGGCAGCTTAGGTGTAGG 59.821 60.000 13.13 8.58 33.19 3.18
2255 2790 1.818959 CGTCCCCTCCGTGGTTTGTA 61.819 60.000 0.00 0.00 0.00 2.41
2284 2825 8.301720 ACTATGTCTACGCCATATTTTTCGATA 58.698 33.333 0.00 0.00 0.00 2.92
2475 3016 4.951254 TGTTGGACAGTTCGAATACTTCA 58.049 39.130 0.00 0.00 0.00 3.02
2604 3145 3.081409 TTGCTCCCCGAGGCTACC 61.081 66.667 0.00 0.00 0.00 3.18
2609 3150 2.186125 CCCCGAGGCTACCGAAAC 59.814 66.667 0.00 0.00 0.00 2.78
2628 3169 5.902981 CGAAACGAAAAACGAGGAAATACAA 59.097 36.000 0.00 0.00 45.77 2.41
2824 3368 8.635765 TGCAGAAGAAAAATATTTACCTCTGT 57.364 30.769 21.51 9.86 34.35 3.41
2825 3369 9.077885 TGCAGAAGAAAAATATTTACCTCTGTT 57.922 29.630 21.51 7.05 34.35 3.16
2868 3421 6.260050 AGAAATGCGACCATACGAAAATGTAT 59.740 34.615 0.00 0.00 35.45 2.29
2881 3434 5.006746 ACGAAAATGTATGAGAGGATTTCGC 59.993 40.000 15.13 0.00 46.72 4.70
2980 3533 5.242434 ACAAGCAAGATTGACGGTTACATA 58.758 37.500 4.93 0.00 34.20 2.29
2993 3546 8.467963 TGACGGTTACATATTGAGTAGGATAA 57.532 34.615 0.00 0.00 0.00 1.75
2996 3549 8.574737 ACGGTTACATATTGAGTAGGATAAGAC 58.425 37.037 0.00 0.00 0.00 3.01
3026 3579 1.652124 CGACAATGTACTACACGTGGC 59.348 52.381 21.57 5.04 0.00 5.01
3058 3611 4.161333 GCAGATTTTGAGTGTCGATTTGG 58.839 43.478 0.00 0.00 0.00 3.28
3079 3632 9.707957 ATTTGGGTTACTCATTTGTGGATATAA 57.292 29.630 0.00 0.00 0.00 0.98
3080 3633 8.514330 TTGGGTTACTCATTTGTGGATATAAC 57.486 34.615 0.00 0.00 0.00 1.89
3084 3637 7.228706 GGTTACTCATTTGTGGATATAACCCTG 59.771 40.741 0.00 0.00 36.06 4.45
3085 3638 5.133221 ACTCATTTGTGGATATAACCCTGC 58.867 41.667 0.00 0.00 0.00 4.85
3098 3663 9.553064 GGATATAACCCTGCATGAATAGAATAG 57.447 37.037 0.00 0.00 0.00 1.73
3103 3668 4.262635 CCCTGCATGAATAGAATAGTCGGT 60.263 45.833 0.00 0.00 38.77 4.69
3113 3678 9.346005 TGAATAGAATAGTCGGTGTACATTCTA 57.654 33.333 12.75 12.75 38.77 2.10
3166 3731 4.878971 TGATTTTTGTCCTGTGAACTCGAA 59.121 37.500 0.00 0.00 0.00 3.71
3277 3844 5.545658 AAAAATATCAGAACGTGCGACAT 57.454 34.783 0.00 0.00 0.00 3.06
3278 3845 5.545658 AAAATATCAGAACGTGCGACATT 57.454 34.783 0.00 0.00 0.00 2.71
3279 3846 5.545658 AAATATCAGAACGTGCGACATTT 57.454 34.783 0.00 0.00 0.00 2.32
3280 3847 5.545658 AATATCAGAACGTGCGACATTTT 57.454 34.783 0.00 0.00 0.00 1.82
3281 3848 2.661504 TCAGAACGTGCGACATTTTG 57.338 45.000 0.00 0.00 0.00 2.44
3282 3849 1.937223 TCAGAACGTGCGACATTTTGT 59.063 42.857 0.00 0.00 0.00 2.83
3283 3850 2.353269 TCAGAACGTGCGACATTTTGTT 59.647 40.909 0.00 0.00 0.00 2.83
3284 3851 3.105203 CAGAACGTGCGACATTTTGTTT 58.895 40.909 0.00 0.00 0.00 2.83
3285 3852 3.061928 CAGAACGTGCGACATTTTGTTTG 60.062 43.478 0.00 0.00 0.00 2.93
3286 3853 1.196200 ACGTGCGACATTTTGTTTGC 58.804 45.000 0.00 0.00 34.15 3.68
3287 3854 1.202245 ACGTGCGACATTTTGTTTGCT 60.202 42.857 0.00 0.00 34.49 3.91
3288 3855 1.447938 CGTGCGACATTTTGTTTGCTC 59.552 47.619 0.00 3.82 34.49 4.26
3289 3856 2.458951 GTGCGACATTTTGTTTGCTCA 58.541 42.857 0.00 0.00 34.49 4.26
3290 3857 3.052036 GTGCGACATTTTGTTTGCTCAT 58.948 40.909 0.00 0.00 34.49 2.90
3291 3858 3.051327 TGCGACATTTTGTTTGCTCATG 58.949 40.909 0.00 0.00 34.49 3.07
3292 3859 3.052036 GCGACATTTTGTTTGCTCATGT 58.948 40.909 0.00 0.00 31.90 3.21
3293 3860 3.490526 GCGACATTTTGTTTGCTCATGTT 59.509 39.130 0.00 0.00 31.90 2.71
3294 3861 4.025813 GCGACATTTTGTTTGCTCATGTTT 60.026 37.500 0.00 0.00 31.90 2.83
3295 3862 5.425398 CGACATTTTGTTTGCTCATGTTTG 58.575 37.500 0.00 0.00 0.00 2.93
3296 3863 5.231779 CGACATTTTGTTTGCTCATGTTTGA 59.768 36.000 0.00 0.00 0.00 2.69
3297 3864 6.348621 ACATTTTGTTTGCTCATGTTTGAC 57.651 33.333 0.00 0.00 0.00 3.18
3298 3865 5.873712 ACATTTTGTTTGCTCATGTTTGACA 59.126 32.000 0.00 0.00 0.00 3.58
3299 3866 6.036300 ACATTTTGTTTGCTCATGTTTGACAG 59.964 34.615 0.00 0.00 0.00 3.51
3300 3867 4.717233 TTGTTTGCTCATGTTTGACAGT 57.283 36.364 0.00 0.00 0.00 3.55
3301 3868 4.031418 TGTTTGCTCATGTTTGACAGTG 57.969 40.909 0.00 0.00 0.00 3.66
3302 3869 2.780065 TTGCTCATGTTTGACAGTGC 57.220 45.000 0.00 0.00 0.00 4.40
3303 3870 0.953727 TGCTCATGTTTGACAGTGCC 59.046 50.000 0.00 0.00 0.00 5.01
3304 3871 1.242076 GCTCATGTTTGACAGTGCCT 58.758 50.000 0.00 0.00 0.00 4.75
3305 3872 1.068748 GCTCATGTTTGACAGTGCCTG 60.069 52.381 0.00 1.16 37.52 4.85
3307 3874 2.620115 CTCATGTTTGACAGTGCCTGTT 59.380 45.455 8.90 0.00 45.44 3.16
3308 3875 3.023119 TCATGTTTGACAGTGCCTGTTT 58.977 40.909 8.90 0.00 45.44 2.83
3309 3876 3.446873 TCATGTTTGACAGTGCCTGTTTT 59.553 39.130 8.90 0.00 45.44 2.43
3310 3877 3.502191 TGTTTGACAGTGCCTGTTTTC 57.498 42.857 8.90 0.00 45.44 2.29
3311 3878 3.088532 TGTTTGACAGTGCCTGTTTTCT 58.911 40.909 8.90 0.00 45.44 2.52
3312 3879 3.128589 TGTTTGACAGTGCCTGTTTTCTC 59.871 43.478 8.90 0.00 45.44 2.87
3313 3880 3.281727 TTGACAGTGCCTGTTTTCTCT 57.718 42.857 8.90 0.00 45.44 3.10
3314 3881 4.415881 TTGACAGTGCCTGTTTTCTCTA 57.584 40.909 8.90 0.00 45.44 2.43
3315 3882 4.623932 TGACAGTGCCTGTTTTCTCTAT 57.376 40.909 8.90 0.00 45.44 1.98
3316 3883 5.738619 TGACAGTGCCTGTTTTCTCTATA 57.261 39.130 8.90 0.00 45.44 1.31
3317 3884 5.479306 TGACAGTGCCTGTTTTCTCTATAC 58.521 41.667 8.90 0.00 45.44 1.47
3318 3885 5.246203 TGACAGTGCCTGTTTTCTCTATACT 59.754 40.000 8.90 0.00 45.44 2.12
3319 3886 6.436218 TGACAGTGCCTGTTTTCTCTATACTA 59.564 38.462 8.90 0.00 45.44 1.82
3320 3887 7.039293 TGACAGTGCCTGTTTTCTCTATACTAA 60.039 37.037 8.90 0.00 45.44 2.24
3321 3888 7.324178 ACAGTGCCTGTTTTCTCTATACTAAG 58.676 38.462 2.38 0.00 42.59 2.18
3322 3889 7.178628 ACAGTGCCTGTTTTCTCTATACTAAGA 59.821 37.037 2.38 0.00 42.59 2.10
3323 3890 8.200792 CAGTGCCTGTTTTCTCTATACTAAGAT 58.799 37.037 0.00 0.00 0.00 2.40
3324 3891 8.763601 AGTGCCTGTTTTCTCTATACTAAGATT 58.236 33.333 0.00 0.00 0.00 2.40
3325 3892 9.384764 GTGCCTGTTTTCTCTATACTAAGATTT 57.615 33.333 0.00 0.00 0.00 2.17
3326 3893 9.383519 TGCCTGTTTTCTCTATACTAAGATTTG 57.616 33.333 0.00 0.00 0.00 2.32
3327 3894 9.384764 GCCTGTTTTCTCTATACTAAGATTTGT 57.615 33.333 0.00 0.00 0.00 2.83
3361 3928 4.336532 AAAAATATCAGAACGTGCGGAC 57.663 40.909 0.00 0.00 0.00 4.79
3372 3939 0.502275 CGTGCGGACATTTTGTTTGC 59.498 50.000 8.11 0.00 33.32 3.68
3455 4022 4.488770 ACTGAACTTCCTTCTCTCTTCCT 58.511 43.478 0.00 0.00 0.00 3.36
3601 4170 1.275291 GAATGTCTGAACCCAGTCGGA 59.725 52.381 0.00 0.00 41.16 4.55
3615 4184 4.680237 CGGACGAAGCCTGCCACA 62.680 66.667 0.00 0.00 0.00 4.17
3616 4185 2.045926 GGACGAAGCCTGCCACAT 60.046 61.111 0.00 0.00 0.00 3.21
3716 4287 0.243636 GGAACAACATTTGGGCGGAG 59.756 55.000 0.00 0.00 34.12 4.63
3717 4288 1.243902 GAACAACATTTGGGCGGAGA 58.756 50.000 0.00 0.00 34.12 3.71
3723 4294 2.057922 ACATTTGGGCGGAGATATCCT 58.942 47.619 4.57 0.00 0.00 3.24
3729 4300 1.244697 GGCGGAGATATCCTCGAGCA 61.245 60.000 6.99 0.00 43.40 4.26
3731 4302 1.529226 CGGAGATATCCTCGAGCACT 58.471 55.000 6.99 0.92 42.89 4.40
3743 4314 0.886490 CGAGCACTGTGGCCTCTTTT 60.886 55.000 10.21 0.00 0.00 2.27
3745 4316 0.886490 AGCACTGTGGCCTCTTTTCG 60.886 55.000 10.21 0.00 0.00 3.46
3819 4390 2.347490 CCCGTCTCACCTGTTGGG 59.653 66.667 0.00 0.00 41.89 4.12
3828 4399 0.036010 CACCTGTTGGGAAGCTCGAT 60.036 55.000 0.00 0.00 38.76 3.59
3964 4535 2.953466 GCAGTATGACAACCCGAGTA 57.047 50.000 0.00 0.00 39.69 2.59
3965 4536 3.241067 GCAGTATGACAACCCGAGTAA 57.759 47.619 0.00 0.00 39.69 2.24
3966 4537 3.592059 GCAGTATGACAACCCGAGTAAA 58.408 45.455 0.00 0.00 39.69 2.01
3967 4538 3.998341 GCAGTATGACAACCCGAGTAAAA 59.002 43.478 0.00 0.00 39.69 1.52
3968 4539 4.634443 GCAGTATGACAACCCGAGTAAAAT 59.366 41.667 0.00 0.00 39.69 1.82
3969 4540 5.447279 GCAGTATGACAACCCGAGTAAAATG 60.447 44.000 0.00 0.00 39.69 2.32
3970 4541 4.634443 AGTATGACAACCCGAGTAAAATGC 59.366 41.667 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.666209 GATTTGGCACCGTCCCCATG 61.666 60.000 0.00 0.00 0.00 3.66
18 20 2.359478 ACCCCGTCGATTTGGCAC 60.359 61.111 0.00 0.00 0.00 5.01
61 63 2.094659 CGCCGGTGACACTAGCTTG 61.095 63.158 10.20 0.00 0.00 4.01
68 70 1.733399 GAGTTCTCGCCGGTGACAC 60.733 63.158 15.21 13.75 0.00 3.67
69 71 2.649034 GAGTTCTCGCCGGTGACA 59.351 61.111 15.21 0.00 0.00 3.58
75 77 1.642037 TAGGTCACGAGTTCTCGCCG 61.642 60.000 19.90 12.55 36.44 6.46
79 81 1.397692 CGGACTAGGTCACGAGTTCTC 59.602 57.143 0.00 0.00 32.39 2.87
109 111 1.299089 GCAAGTTGTTCCCACGCAC 60.299 57.895 4.48 0.00 0.00 5.34
112 114 0.453793 TTGTGCAAGTTGTTCCCACG 59.546 50.000 4.48 0.00 0.00 4.94
159 161 0.539518 GGCTGGTGTTGGTTTGGTTT 59.460 50.000 0.00 0.00 0.00 3.27
162 164 0.758123 ATTGGCTGGTGTTGGTTTGG 59.242 50.000 0.00 0.00 0.00 3.28
194 196 1.805945 GCCAGTGTCATCGTCGGAC 60.806 63.158 0.00 0.00 35.83 4.79
198 200 0.605319 TTTGGGCCAGTGTCATCGTC 60.605 55.000 6.23 0.00 0.00 4.20
222 224 3.181500 CGACATGGTCAATGACGTCTAGA 60.181 47.826 17.92 8.97 45.43 2.43
242 244 1.406887 GCTTCAACCCTATCTTGGCGA 60.407 52.381 0.00 0.00 0.00 5.54
264 266 0.248743 GCTTTAAATAACGGCGCCCC 60.249 55.000 23.46 0.00 0.00 5.80
267 269 1.575803 CGTTGCTTTAAATAACGGCGC 59.424 47.619 21.02 0.00 42.31 6.53
278 280 1.541670 GGAGGTGGTGACGTTGCTTTA 60.542 52.381 0.00 0.00 0.00 1.85
302 304 2.159707 GGTTCCATGATGACGTTGTTCG 60.160 50.000 0.00 0.00 46.00 3.95
310 312 5.975693 TTAGGTTTTGGTTCCATGATGAC 57.024 39.130 0.00 0.00 0.00 3.06
311 313 5.656416 GGATTAGGTTTTGGTTCCATGATGA 59.344 40.000 0.00 0.00 0.00 2.92
312 314 5.421693 TGGATTAGGTTTTGGTTCCATGATG 59.578 40.000 0.00 0.00 0.00 3.07
340 342 7.282901 ACCTTAGTTTTACGTGTTTGGTATGTT 59.717 33.333 0.00 0.00 0.00 2.71
384 386 1.008327 TCCCCTCTATCTGCTTCACCA 59.992 52.381 0.00 0.00 0.00 4.17
389 391 0.944999 TCCCTCCCCTCTATCTGCTT 59.055 55.000 0.00 0.00 0.00 3.91
396 398 0.253020 GGTGGTTTCCCTCCCCTCTA 60.253 60.000 0.00 0.00 38.28 2.43
400 402 2.931649 TCGGTGGTTTCCCTCCCC 60.932 66.667 0.00 0.00 40.68 4.81
436 438 2.510613 CTCCCCTCTCCGAATCTCTAC 58.489 57.143 0.00 0.00 0.00 2.59
444 446 0.691078 CAAATCCCTCCCCTCTCCGA 60.691 60.000 0.00 0.00 0.00 4.55
479 481 3.870274 CAGCAATCCATCTCAACTCTCA 58.130 45.455 0.00 0.00 0.00 3.27
494 496 0.037877 AGCACAAGAGGAGCAGCAAT 59.962 50.000 0.00 0.00 0.00 3.56
499 501 2.156917 CATCAAAGCACAAGAGGAGCA 58.843 47.619 0.00 0.00 0.00 4.26
508 510 5.710513 ACTCATAAAAGCATCAAAGCACA 57.289 34.783 0.00 0.00 36.85 4.57
525 528 5.061721 ACACAACCCCTAAGAAAACTCAT 57.938 39.130 0.00 0.00 0.00 2.90
541 544 3.184581 CGTTTCTCTAAGCAGGACACAAC 59.815 47.826 0.00 0.00 0.00 3.32
543 546 2.626266 TCGTTTCTCTAAGCAGGACACA 59.374 45.455 0.00 0.00 0.00 3.72
560 563 3.575351 GAGCCACTGTCGCCTCGTT 62.575 63.158 0.00 0.00 0.00 3.85
571 574 1.649321 TCCATCTTCACAGAGCCACT 58.351 50.000 0.00 0.00 30.36 4.00
622 625 1.281899 GATGACGCTAGAAGCACCAC 58.718 55.000 0.00 0.00 42.58 4.16
648 651 0.874390 CGGAGACAAACCACCACATG 59.126 55.000 0.00 0.00 0.00 3.21
649 652 0.250727 CCGGAGACAAACCACCACAT 60.251 55.000 0.00 0.00 0.00 3.21
655 660 0.323629 GATCCACCGGAGACAAACCA 59.676 55.000 9.46 0.00 34.05 3.67
669 674 2.728180 CGAATCCCGCGAGATCCA 59.272 61.111 8.23 0.00 0.00 3.41
691 696 4.000988 GTGTATCCACCGAAGACAAATGT 58.999 43.478 0.00 0.00 35.44 2.71
693 698 4.280436 TGTGTATCCACCGAAGACAAAT 57.720 40.909 0.00 0.00 41.09 2.32
710 716 5.242838 ACAAACAAATACCGAATCCATGTGT 59.757 36.000 0.00 0.00 0.00 3.72
713 719 5.572511 CACACAAACAAATACCGAATCCATG 59.427 40.000 0.00 0.00 0.00 3.66
732 738 1.961394 GACTCCACCTGTAGACACACA 59.039 52.381 0.00 0.00 0.00 3.72
747 753 7.791029 AGAGAAATTTAGATCAGAAGGACTCC 58.209 38.462 0.00 0.00 0.00 3.85
749 755 8.820831 TGAAGAGAAATTTAGATCAGAAGGACT 58.179 33.333 0.00 0.00 0.00 3.85
750 756 9.442047 TTGAAGAGAAATTTAGATCAGAAGGAC 57.558 33.333 0.00 0.00 0.00 3.85
754 760 7.148407 GCCGTTGAAGAGAAATTTAGATCAGAA 60.148 37.037 0.00 0.00 0.00 3.02
756 762 6.481984 GCCGTTGAAGAGAAATTTAGATCAG 58.518 40.000 0.00 0.00 0.00 2.90
771 777 4.383602 CAACCGCCGCCGTTGAAG 62.384 66.667 16.71 0.00 31.64 3.02
779 785 4.389576 CAGAACAGCAACCGCCGC 62.390 66.667 0.00 0.00 39.83 6.53
792 798 4.893524 TCCTATAAGACCAGCGAATCAGAA 59.106 41.667 0.00 0.00 0.00 3.02
808 814 7.255730 GGAAGTTATCGTGCTAAGGTCCTATAA 60.256 40.741 0.00 0.00 0.00 0.98
811 817 4.340381 GGAAGTTATCGTGCTAAGGTCCTA 59.660 45.833 0.00 0.00 0.00 2.94
815 821 3.767673 TCAGGAAGTTATCGTGCTAAGGT 59.232 43.478 0.00 0.00 42.37 3.50
824 830 5.821516 AGTAGACAGTCAGGAAGTTATCG 57.178 43.478 2.66 0.00 0.00 2.92
827 833 7.683578 TGTACTAGTAGACAGTCAGGAAGTTA 58.316 38.462 1.87 0.00 0.00 2.24
848 854 4.459337 AGAGCCAGGCAAAACTTATTGTAC 59.541 41.667 15.80 0.00 32.80 2.90
849 855 4.662278 AGAGCCAGGCAAAACTTATTGTA 58.338 39.130 15.80 0.00 32.80 2.41
850 856 3.500343 AGAGCCAGGCAAAACTTATTGT 58.500 40.909 15.80 0.00 32.80 2.71
851 857 4.702131 ACTAGAGCCAGGCAAAACTTATTG 59.298 41.667 15.80 0.00 0.00 1.90
852 858 4.702131 CACTAGAGCCAGGCAAAACTTATT 59.298 41.667 15.80 0.00 0.00 1.40
853 859 4.019321 TCACTAGAGCCAGGCAAAACTTAT 60.019 41.667 15.80 0.00 0.00 1.73
854 860 3.326588 TCACTAGAGCCAGGCAAAACTTA 59.673 43.478 15.80 0.00 0.00 2.24
865 871 0.325671 CCCCTTCCTCACTAGAGCCA 60.326 60.000 0.00 0.00 40.68 4.75
893 899 0.243095 GTGAGTTAGAGGAACGCCGT 59.757 55.000 0.00 0.00 43.37 5.68
899 905 7.963532 ACAAATACTGAAGTGAGTTAGAGGAA 58.036 34.615 0.00 0.00 0.00 3.36
900 906 7.540474 ACAAATACTGAAGTGAGTTAGAGGA 57.460 36.000 0.00 0.00 0.00 3.71
904 910 8.021973 ACGACTACAAATACTGAAGTGAGTTAG 58.978 37.037 0.00 0.00 0.00 2.34
905 911 7.879070 ACGACTACAAATACTGAAGTGAGTTA 58.121 34.615 0.00 0.00 0.00 2.24
906 912 6.746120 ACGACTACAAATACTGAAGTGAGTT 58.254 36.000 0.00 0.00 0.00 3.01
907 913 6.328641 ACGACTACAAATACTGAAGTGAGT 57.671 37.500 0.00 0.00 0.00 3.41
911 917 4.082895 AGCGACGACTACAAATACTGAAGT 60.083 41.667 0.00 0.00 0.00 3.01
920 926 1.881973 ACACCTAGCGACGACTACAAA 59.118 47.619 0.00 0.00 0.00 2.83
926 932 1.528603 CGTAGAACACCTAGCGACGAC 60.529 57.143 0.00 0.00 0.00 4.34
1103 1177 2.556840 ATTCGGATGGGTGGTGCAGG 62.557 60.000 0.00 0.00 0.00 4.85
1106 1180 1.823899 GGATTCGGATGGGTGGTGC 60.824 63.158 0.00 0.00 0.00 5.01
1163 1237 2.203140 CTTCTTGCGCAGTGACGACG 62.203 60.000 11.31 0.00 34.06 5.12
1197 1274 1.439365 CGCAGTCGCAGAAAGCAAC 60.439 57.895 0.00 0.00 46.13 4.17
1278 1355 3.620785 GGCCGCGGAGAGATGGAT 61.621 66.667 33.48 0.00 0.00 3.41
1398 1475 0.239347 CGAACCCGTCTTCGTACTGT 59.761 55.000 4.07 0.00 38.58 3.55
1441 1518 1.004320 ACCATTCAAGCGCACCGTA 60.004 52.632 11.47 0.00 0.00 4.02
1442 1519 2.281484 ACCATTCAAGCGCACCGT 60.281 55.556 11.47 0.00 0.00 4.83
1443 1520 2.480555 GACCATTCAAGCGCACCG 59.519 61.111 11.47 0.00 0.00 4.94
1444 1521 2.480555 CGACCATTCAAGCGCACC 59.519 61.111 11.47 0.00 0.00 5.01
1448 1525 1.805539 TCGAGCGACCATTCAAGCG 60.806 57.895 0.00 0.00 34.34 4.68
1449 1526 0.737715 AGTCGAGCGACCATTCAAGC 60.738 55.000 18.28 0.00 45.59 4.01
1450 1527 2.561733 TAGTCGAGCGACCATTCAAG 57.438 50.000 18.28 0.00 45.59 3.02
1451 1528 2.230508 AGTTAGTCGAGCGACCATTCAA 59.769 45.455 18.28 4.03 45.59 2.69
1464 1541 6.570692 ACTTAATGTGGATACCAGTTAGTCG 58.429 40.000 0.00 0.00 32.34 4.18
1465 1542 6.696148 CGACTTAATGTGGATACCAGTTAGTC 59.304 42.308 0.00 0.00 37.74 2.59
1569 1847 5.946377 AGAAAAAGGGGAGACACATGAATAC 59.054 40.000 0.00 0.00 34.58 1.89
1652 1930 7.352739 GGAATCACGCGAAAAACAGAATATAT 58.647 34.615 15.93 0.00 0.00 0.86
1654 1932 5.448632 GGGAATCACGCGAAAAACAGAATAT 60.449 40.000 15.93 0.00 0.00 1.28
1655 1933 4.142773 GGGAATCACGCGAAAAACAGAATA 60.143 41.667 15.93 0.00 0.00 1.75
1656 1934 3.365969 GGGAATCACGCGAAAAACAGAAT 60.366 43.478 15.93 0.00 0.00 2.40
1658 1936 1.533731 GGGAATCACGCGAAAAACAGA 59.466 47.619 15.93 0.00 0.00 3.41
1659 1937 1.265635 TGGGAATCACGCGAAAAACAG 59.734 47.619 15.93 0.00 0.00 3.16
1661 1939 2.095466 TCATGGGAATCACGCGAAAAAC 60.095 45.455 15.93 0.44 0.00 2.43
1662 1940 2.155279 TCATGGGAATCACGCGAAAAA 58.845 42.857 15.93 0.00 0.00 1.94
1664 1942 1.814793 TTCATGGGAATCACGCGAAA 58.185 45.000 15.93 0.00 0.00 3.46
1783 2109 6.913673 GTGCATGTTCAAAGATTGCAATTTTT 59.086 30.769 19.26 19.26 32.46 1.94
1833 2159 4.481368 AAGTCGCTTCATATGTAACCCA 57.519 40.909 1.90 0.00 0.00 4.51
1834 2160 4.035208 CCAAAGTCGCTTCATATGTAACCC 59.965 45.833 1.90 0.00 0.00 4.11
1903 2229 6.194796 TGCTTGGGATCTTTTAAAATCTCG 57.805 37.500 0.09 0.00 0.00 4.04
1940 2266 9.444600 TCTATTTATAAGTTGCTTTTTCTCGGT 57.555 29.630 0.00 0.00 0.00 4.69
1941 2267 9.704098 GTCTATTTATAAGTTGCTTTTTCTCGG 57.296 33.333 0.00 0.00 0.00 4.63
2061 2550 5.127194 GCCATCGATATTCCTATGGACTGTA 59.873 44.000 0.00 0.00 41.20 2.74
2065 2554 3.452627 AGGCCATCGATATTCCTATGGAC 59.547 47.826 5.01 0.00 46.25 4.02
2079 2568 4.136796 TGGATAAGAAAATGAGGCCATCG 58.863 43.478 5.01 0.00 31.40 3.84
2107 2599 9.726438 CACCCTACTTTCTTTTCCATATATAGG 57.274 37.037 0.00 0.00 0.00 2.57
2163 2655 5.248380 AGGGCCTATTTGGATCAGATAAC 57.752 43.478 2.82 0.00 38.35 1.89
2207 2699 2.229784 CCTAAGCTGCCTGGTTTGAAAG 59.770 50.000 0.00 0.00 37.56 2.62
2224 2716 1.686800 GGGGACGGCCTACACCTAA 60.687 63.158 7.57 0.00 0.00 2.69
2284 2825 1.002134 CATGTCAAAGGGGACGGCT 60.002 57.895 0.00 0.00 40.72 5.52
2415 2956 1.543358 GCAAGAGGCCAAGGAGAAAAG 59.457 52.381 5.01 0.00 36.11 2.27
2501 3042 4.989168 ACGACAAGATAACTGACAAAGGAC 59.011 41.667 0.00 0.00 0.00 3.85
2604 3145 5.433855 TGTATTTCCTCGTTTTTCGTTTCG 58.566 37.500 0.00 0.00 40.80 3.46
2609 3150 5.619607 CACTGTTGTATTTCCTCGTTTTTCG 59.380 40.000 0.00 0.00 41.41 3.46
2628 3169 2.479566 AATGATCAGGAACGCACTGT 57.520 45.000 0.09 0.00 37.25 3.55
2868 3421 3.196469 AGTTCTCATGCGAAATCCTCTCA 59.804 43.478 0.00 0.00 0.00 3.27
2980 3533 6.382570 AGTGAAGCAGTCTTATCCTACTCAAT 59.617 38.462 0.00 0.00 31.48 2.57
2993 3546 2.036475 ACATTGTCGAGTGAAGCAGTCT 59.964 45.455 0.00 0.00 32.17 3.24
2996 3549 3.579709 AGTACATTGTCGAGTGAAGCAG 58.420 45.455 0.00 0.00 0.00 4.24
3026 3579 4.015084 ACTCAAAATCTGCAGGGATTCTG 58.985 43.478 15.13 4.78 46.03 3.02
3040 3593 5.768164 AGTAACCCAAATCGACACTCAAAAT 59.232 36.000 0.00 0.00 0.00 1.82
3058 3611 7.228706 CAGGGTTATATCCACAAATGAGTAACC 59.771 40.741 2.29 0.00 36.81 2.85
3079 3632 4.262635 CCGACTATTCTATTCATGCAGGGT 60.263 45.833 0.00 0.00 0.00 4.34
3080 3633 4.248859 CCGACTATTCTATTCATGCAGGG 58.751 47.826 0.00 0.00 0.00 4.45
3084 3637 6.213677 TGTACACCGACTATTCTATTCATGC 58.786 40.000 0.00 0.00 0.00 4.06
3085 3638 8.818141 AATGTACACCGACTATTCTATTCATG 57.182 34.615 0.00 0.00 0.00 3.07
3098 3663 4.320057 CCCTACGATAGAATGTACACCGAC 60.320 50.000 0.00 0.00 41.38 4.79
3103 3668 5.422970 ACAAACCCCTACGATAGAATGTACA 59.577 40.000 0.00 0.00 41.38 2.90
3113 3678 3.244770 ACATTCACACAAACCCCTACGAT 60.245 43.478 0.00 0.00 0.00 3.73
3177 3744 7.889745 TGAACAAACAAAATTATCACACGTTG 58.110 30.769 0.00 0.00 0.00 4.10
3255 3822 5.545658 ATGTCGCACGTTCTGATATTTTT 57.454 34.783 0.00 0.00 0.00 1.94
3256 3823 5.545658 AATGTCGCACGTTCTGATATTTT 57.454 34.783 0.00 0.00 0.00 1.82
3257 3824 5.545658 AAATGTCGCACGTTCTGATATTT 57.454 34.783 9.11 9.11 31.33 1.40
3258 3825 5.106712 ACAAAATGTCGCACGTTCTGATATT 60.107 36.000 0.00 0.00 0.00 1.28
3259 3826 4.391830 ACAAAATGTCGCACGTTCTGATAT 59.608 37.500 0.00 0.00 0.00 1.63
3260 3827 3.743911 ACAAAATGTCGCACGTTCTGATA 59.256 39.130 0.00 0.00 0.00 2.15
3261 3828 2.548057 ACAAAATGTCGCACGTTCTGAT 59.452 40.909 0.00 0.00 0.00 2.90
3262 3829 1.937223 ACAAAATGTCGCACGTTCTGA 59.063 42.857 0.00 0.00 0.00 3.27
3263 3830 2.383298 ACAAAATGTCGCACGTTCTG 57.617 45.000 0.00 0.00 0.00 3.02
3264 3831 3.105203 CAAACAAAATGTCGCACGTTCT 58.895 40.909 0.00 0.00 0.00 3.01
3265 3832 2.346285 GCAAACAAAATGTCGCACGTTC 60.346 45.455 0.00 0.00 0.00 3.95
3266 3833 1.586123 GCAAACAAAATGTCGCACGTT 59.414 42.857 0.00 0.00 0.00 3.99
3267 3834 1.196200 GCAAACAAAATGTCGCACGT 58.804 45.000 0.00 0.00 0.00 4.49
3268 3835 1.447938 GAGCAAACAAAATGTCGCACG 59.552 47.619 7.36 0.00 0.00 5.34
3269 3836 2.458951 TGAGCAAACAAAATGTCGCAC 58.541 42.857 7.36 2.83 0.00 5.34
3270 3837 2.859526 TGAGCAAACAAAATGTCGCA 57.140 40.000 7.36 0.00 0.00 5.10
3271 3838 3.052036 ACATGAGCAAACAAAATGTCGC 58.948 40.909 0.00 0.00 0.00 5.19
3272 3839 5.231779 TCAAACATGAGCAAACAAAATGTCG 59.768 36.000 0.00 0.00 31.29 4.35
3273 3840 6.035866 TGTCAAACATGAGCAAACAAAATGTC 59.964 34.615 0.00 0.00 31.29 3.06
3274 3841 5.873712 TGTCAAACATGAGCAAACAAAATGT 59.126 32.000 0.00 0.00 32.99 2.71
3275 3842 6.036300 ACTGTCAAACATGAGCAAACAAAATG 59.964 34.615 0.00 0.00 0.00 2.32
3276 3843 6.036300 CACTGTCAAACATGAGCAAACAAAAT 59.964 34.615 0.00 0.00 0.00 1.82
3277 3844 5.348179 CACTGTCAAACATGAGCAAACAAAA 59.652 36.000 0.00 0.00 0.00 2.44
3278 3845 4.863689 CACTGTCAAACATGAGCAAACAAA 59.136 37.500 0.00 0.00 0.00 2.83
3279 3846 4.422840 CACTGTCAAACATGAGCAAACAA 58.577 39.130 0.00 0.00 0.00 2.83
3280 3847 3.734597 GCACTGTCAAACATGAGCAAACA 60.735 43.478 0.00 0.00 0.00 2.83
3281 3848 2.791004 GCACTGTCAAACATGAGCAAAC 59.209 45.455 0.00 0.00 0.00 2.93
3282 3849 2.223782 GGCACTGTCAAACATGAGCAAA 60.224 45.455 0.00 0.00 0.00 3.68
3283 3850 1.337703 GGCACTGTCAAACATGAGCAA 59.662 47.619 0.00 0.00 0.00 3.91
3284 3851 0.953727 GGCACTGTCAAACATGAGCA 59.046 50.000 0.00 0.00 0.00 4.26
3285 3852 1.242076 AGGCACTGTCAAACATGAGC 58.758 50.000 0.00 0.00 37.18 4.26
3298 3865 7.719871 TCTTAGTATAGAGAAAACAGGCACT 57.280 36.000 0.00 0.00 43.88 4.40
3299 3866 8.950208 AATCTTAGTATAGAGAAAACAGGCAC 57.050 34.615 0.00 0.00 0.00 5.01
3300 3867 9.383519 CAAATCTTAGTATAGAGAAAACAGGCA 57.616 33.333 0.00 0.00 0.00 4.75
3301 3868 9.384764 ACAAATCTTAGTATAGAGAAAACAGGC 57.615 33.333 0.00 0.00 0.00 4.85
3357 3924 3.641648 ACATGAGCAAACAAAATGTCCG 58.358 40.909 0.00 0.00 0.00 4.79
3359 3926 6.035866 TGTCAAACATGAGCAAACAAAATGTC 59.964 34.615 0.00 0.00 31.29 3.06
3360 3927 5.873712 TGTCAAACATGAGCAAACAAAATGT 59.126 32.000 0.00 0.00 32.99 2.71
3361 3928 6.036300 ACTGTCAAACATGAGCAAACAAAATG 59.964 34.615 0.00 0.00 0.00 2.32
3372 3939 2.031420 CAGGCACACTGTCAAACATGAG 60.031 50.000 0.00 0.00 42.42 2.90
3417 3984 3.410631 TCAGTAAACCCGAATGCTCAA 57.589 42.857 0.00 0.00 0.00 3.02
3464 4031 1.001764 TGCTGTGCATCCCCAAGAG 60.002 57.895 0.00 0.00 31.71 2.85
3601 4170 1.762957 AGTATATGTGGCAGGCTTCGT 59.237 47.619 0.00 0.00 0.00 3.85
3716 4287 1.604185 GCCACAGTGCTCGAGGATATC 60.604 57.143 15.58 0.00 0.00 1.63
3717 4288 0.390860 GCCACAGTGCTCGAGGATAT 59.609 55.000 15.58 1.25 0.00 1.63
3723 4294 1.758440 AAAGAGGCCACAGTGCTCGA 61.758 55.000 5.01 0.00 0.00 4.04
3729 4300 0.535102 CCACGAAAAGAGGCCACAGT 60.535 55.000 5.01 0.00 0.00 3.55
3731 4302 0.817634 CACCACGAAAAGAGGCCACA 60.818 55.000 5.01 0.00 33.55 4.17
3743 4314 2.902423 AAAAGCAGGCACCACCACGA 62.902 55.000 0.00 0.00 43.14 4.35
3745 4316 1.067916 CAAAAGCAGGCACCACCAC 59.932 57.895 0.00 0.00 43.14 4.16
3819 4390 8.847444 AAATAATGAACAATGAATCGAGCTTC 57.153 30.769 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.