Multiple sequence alignment - TraesCS4A01G229700

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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 TraesCS4A01G229700 chr4A 100.000 3515 0 0 1 3515 538907763 538904249 0.000000e+00 6492.0
1 TraesCS4A01G229700 chr4A 98.113 53 0 1 3463 3515 376817039 376817090 1.340000e-14 91.6
2 TraesCS4A01G229700 chr4A 94.828 58 1 2 3460 3515 596723138 596723195 4.830000e-14 89.8
3 TraesCS4A01G229700 chr4A 93.182 44 2 1 639 681 669634927 669634970 2.930000e-06 63.9
4 TraesCS4A01G229700 chr4B 91.410 2107 125 26 669 2753 86358959 86361031 0.000000e+00 2837.0
5 TraesCS4A01G229700 chr4B 95.617 616 27 0 1 616 385962908 385963523 0.000000e+00 989.0
6 TraesCS4A01G229700 chr4B 89.246 716 57 7 2758 3470 86361129 86361827 0.000000e+00 878.0
7 TraesCS4A01G229700 chr4B 95.161 62 2 1 615 676 193494747 193494687 2.890000e-16 97.1
8 TraesCS4A01G229700 chr3D 83.405 1621 194 37 996 2598 597265937 597264374 0.000000e+00 1434.0
9 TraesCS4A01G229700 chr3D 86.923 1170 119 20 997 2150 596993917 596995068 0.000000e+00 1282.0
10 TraesCS4A01G229700 chr3D 89.057 265 29 0 2254 2518 596995131 596995395 2.620000e-86 329.0
11 TraesCS4A01G229700 chr3B 83.323 1589 195 32 1012 2585 804113440 804111907 0.000000e+00 1402.0
12 TraesCS4A01G229700 chr3B 87.680 625 62 10 1532 2150 803334572 803333957 0.000000e+00 713.0
13 TraesCS4A01G229700 chr3B 87.319 623 64 9 1532 2148 803415329 803414716 0.000000e+00 699.0
14 TraesCS4A01G229700 chr3B 86.097 597 66 10 1 594 481255523 481256105 8.280000e-176 627.0
15 TraesCS4A01G229700 chr3B 88.213 263 31 0 2254 2516 803333895 803333633 7.320000e-82 315.0
16 TraesCS4A01G229700 chr3B 88.213 263 31 0 2254 2516 803461524 803461262 7.320000e-82 315.0
17 TraesCS4A01G229700 chr3B 100.000 30 0 0 643 672 195873977 195873948 4.900000e-04 56.5
18 TraesCS4A01G229700 chr3A 83.585 1523 193 35 1015 2518 727180666 727182150 0.000000e+00 1375.0
19 TraesCS4A01G229700 chr3A 85.697 804 99 11 1060 1856 727365436 727366230 0.000000e+00 833.0
20 TraesCS4A01G229700 chr3A 96.552 58 2 0 615 672 83211955 83212012 2.890000e-16 97.1
21 TraesCS4A01G229700 chr3A 96.364 55 1 1 3461 3515 636235043 636235096 4.830000e-14 89.8
22 TraesCS4A01G229700 chr2A 82.568 1612 216 32 997 2598 605310930 605312486 0.000000e+00 1360.0
23 TraesCS4A01G229700 chr2A 98.148 54 0 1 3460 3512 729183133 729183186 3.740000e-15 93.5
24 TraesCS4A01G229700 chr2A 88.235 51 5 1 638 687 33280831 33280881 3.790000e-05 60.2
25 TraesCS4A01G229700 chr2A 88.000 50 2 4 633 681 736538113 736538067 4.900000e-04 56.5
26 TraesCS4A01G229700 chr2B 96.596 617 20 1 1 616 17219031 17218415 0.000000e+00 1022.0
27 TraesCS4A01G229700 chr2B 95.631 618 25 1 1 616 414954135 414954752 0.000000e+00 990.0
28 TraesCS4A01G229700 chr2B 95.455 616 28 0 1 616 127203798 127204413 0.000000e+00 983.0
29 TraesCS4A01G229700 chr2B 94.595 37 1 1 638 673 51204214 51204178 4.900000e-04 56.5
30 TraesCS4A01G229700 chr2B 96.875 32 0 1 643 673 186939722 186939691 6.000000e-03 52.8
31 TraesCS4A01G229700 chrUn 83.152 1104 137 34 1533 2624 277309201 277308135 0.000000e+00 963.0
32 TraesCS4A01G229700 chrUn 87.680 625 62 10 1532 2150 291468981 291469596 0.000000e+00 713.0
33 TraesCS4A01G229700 chrUn 87.680 625 62 10 1532 2150 303788933 303789548 0.000000e+00 713.0
34 TraesCS4A01G229700 chrUn 87.680 625 62 10 1532 2150 308985238 308985853 0.000000e+00 713.0
35 TraesCS4A01G229700 chrUn 88.213 263 31 0 2254 2516 303789610 303789872 7.320000e-82 315.0
36 TraesCS4A01G229700 chrUn 88.213 263 31 0 2254 2516 308985915 308986177 7.320000e-82 315.0
37 TraesCS4A01G229700 chrUn 98.113 53 0 1 3463 3515 120141093 120141042 1.340000e-14 91.6
38 TraesCS4A01G229700 chr1B 90.090 111 10 1 1 110 686994534 686994424 3.660000e-30 143.0
39 TraesCS4A01G229700 chr5D 96.552 58 2 0 615 672 476466304 476466247 2.890000e-16 97.1
40 TraesCS4A01G229700 chr7B 100.000 49 0 0 3467 3515 679597346 679597298 1.340000e-14 91.6
41 TraesCS4A01G229700 chr7A 98.113 53 0 1 3463 3515 463707875 463707824 1.340000e-14 91.6
42 TraesCS4A01G229700 chr1A 98.113 53 0 1 3463 3515 107407961 107407910 1.340000e-14 91.6
43 TraesCS4A01G229700 chr5B 98.077 52 0 1 3465 3515 677132879 677132828 4.830000e-14 89.8
44 TraesCS4A01G229700 chr2D 90.244 41 4 0 632 672 147956218 147956258 2.000000e-03 54.7
45 TraesCS4A01G229700 chr2D 100.000 29 0 0 643 671 231594132 231594160 2.000000e-03 54.7


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G229700 chr4A 538904249 538907763 3514 True 6492.0 6492 100.0000 1 3515 1 chr4A.!!$R1 3514
1 TraesCS4A01G229700 chr4B 86358959 86361827 2868 False 1857.5 2837 90.3280 669 3470 2 chr4B.!!$F2 2801
2 TraesCS4A01G229700 chr4B 385962908 385963523 615 False 989.0 989 95.6170 1 616 1 chr4B.!!$F1 615
3 TraesCS4A01G229700 chr3D 597264374 597265937 1563 True 1434.0 1434 83.4050 996 2598 1 chr3D.!!$R1 1602
4 TraesCS4A01G229700 chr3D 596993917 596995395 1478 False 805.5 1282 87.9900 997 2518 2 chr3D.!!$F1 1521
5 TraesCS4A01G229700 chr3B 804111907 804113440 1533 True 1402.0 1402 83.3230 1012 2585 1 chr3B.!!$R4 1573
6 TraesCS4A01G229700 chr3B 803414716 803415329 613 True 699.0 699 87.3190 1532 2148 1 chr3B.!!$R2 616
7 TraesCS4A01G229700 chr3B 481255523 481256105 582 False 627.0 627 86.0970 1 594 1 chr3B.!!$F1 593
8 TraesCS4A01G229700 chr3B 803333633 803334572 939 True 514.0 713 87.9465 1532 2516 2 chr3B.!!$R5 984
9 TraesCS4A01G229700 chr3A 727180666 727182150 1484 False 1375.0 1375 83.5850 1015 2518 1 chr3A.!!$F3 1503
10 TraesCS4A01G229700 chr3A 727365436 727366230 794 False 833.0 833 85.6970 1060 1856 1 chr3A.!!$F4 796
11 TraesCS4A01G229700 chr2A 605310930 605312486 1556 False 1360.0 1360 82.5680 997 2598 1 chr2A.!!$F2 1601
12 TraesCS4A01G229700 chr2B 17218415 17219031 616 True 1022.0 1022 96.5960 1 616 1 chr2B.!!$R1 615
13 TraesCS4A01G229700 chr2B 414954135 414954752 617 False 990.0 990 95.6310 1 616 1 chr2B.!!$F2 615
14 TraesCS4A01G229700 chr2B 127203798 127204413 615 False 983.0 983 95.4550 1 616 1 chr2B.!!$F1 615
15 TraesCS4A01G229700 chrUn 277308135 277309201 1066 True 963.0 963 83.1520 1533 2624 1 chrUn.!!$R2 1091
16 TraesCS4A01G229700 chrUn 291468981 291469596 615 False 713.0 713 87.6800 1532 2150 1 chrUn.!!$F1 618
17 TraesCS4A01G229700 chrUn 303788933 303789872 939 False 514.0 713 87.9465 1532 2516 2 chrUn.!!$F2 984
18 TraesCS4A01G229700 chrUn 308985238 308986177 939 False 514.0 713 87.9465 1532 2516 2 chrUn.!!$F3 984

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
537 543 0.252881 TCAATGCCACCCTCCTCTCT 60.253 55.0 0.0 0.0 0.0 3.10 F
1734 1785 0.034896 GACCATCCTCAACACCACGT 59.965 55.0 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2203 2258 0.163360 GATGAAGATCGATGCTGCGC 59.837 55.0 0.54 0.0 0.0 6.09 R
3428 3602 0.038801 GCAAAGCTGTCTTCCCAAGC 60.039 55.0 0.00 0.0 0.0 4.01 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
135 139 3.967332 TCGGTCCGGACTTCTTATTTT 57.033 42.857 32.52 0.00 0.00 1.82
136 140 4.276058 TCGGTCCGGACTTCTTATTTTT 57.724 40.909 32.52 0.00 0.00 1.94
164 168 2.962421 CTGAAAACAAACTGGGGGCTTA 59.038 45.455 0.00 0.00 0.00 3.09
165 169 3.578282 CTGAAAACAAACTGGGGGCTTAT 59.422 43.478 0.00 0.00 0.00 1.73
285 291 1.601903 GCTCAGATCGACGACTCTCAT 59.398 52.381 0.00 0.00 0.00 2.90
339 345 3.452264 CACTGACATCCCAATAGAGGACA 59.548 47.826 0.00 0.00 35.85 4.02
398 404 3.918270 TCCATGTGGATATCATCATGGGT 59.082 43.478 33.34 9.78 45.06 4.51
423 429 1.645034 CCATGCTCACTACACCGAAG 58.355 55.000 0.00 0.00 0.00 3.79
509 515 0.758734 CCCAATAGAGGATGCGACCA 59.241 55.000 2.00 0.00 0.00 4.02
537 543 0.252881 TCAATGCCACCCTCCTCTCT 60.253 55.000 0.00 0.00 0.00 3.10
565 571 2.443632 TGTGGGTTTCACCATGGACTAA 59.556 45.455 21.47 6.41 45.48 2.24
616 622 2.034221 GAGCGGGAGGCCTTGTTT 59.966 61.111 6.77 0.00 45.17 2.83
617 623 2.282462 AGCGGGAGGCCTTGTTTG 60.282 61.111 6.77 0.00 45.17 2.93
618 624 2.282180 GCGGGAGGCCTTGTTTGA 60.282 61.111 6.77 0.00 34.80 2.69
619 625 1.901464 GCGGGAGGCCTTGTTTGAA 60.901 57.895 6.77 0.00 34.80 2.69
620 626 1.250840 GCGGGAGGCCTTGTTTGAAT 61.251 55.000 6.77 0.00 34.80 2.57
621 627 1.953311 GCGGGAGGCCTTGTTTGAATA 60.953 52.381 6.77 0.00 34.80 1.75
622 628 2.654863 CGGGAGGCCTTGTTTGAATAT 58.345 47.619 6.77 0.00 0.00 1.28
623 629 3.815809 CGGGAGGCCTTGTTTGAATATA 58.184 45.455 6.77 0.00 0.00 0.86
624 630 4.398319 CGGGAGGCCTTGTTTGAATATAT 58.602 43.478 6.77 0.00 0.00 0.86
625 631 5.556915 CGGGAGGCCTTGTTTGAATATATA 58.443 41.667 6.77 0.00 0.00 0.86
626 632 6.001460 CGGGAGGCCTTGTTTGAATATATAA 58.999 40.000 6.77 0.00 0.00 0.98
627 633 6.072673 CGGGAGGCCTTGTTTGAATATATAAC 60.073 42.308 6.77 0.00 0.00 1.89
628 634 7.004691 GGGAGGCCTTGTTTGAATATATAACT 58.995 38.462 6.77 0.00 0.00 2.24
629 635 8.161425 GGGAGGCCTTGTTTGAATATATAACTA 58.839 37.037 6.77 0.00 0.00 2.24
630 636 9.740710 GGAGGCCTTGTTTGAATATATAACTAT 57.259 33.333 6.77 0.00 0.00 2.12
648 654 5.830000 ACTATTTATTTTCTCCCCGTTGC 57.170 39.130 0.00 0.00 0.00 4.17
649 655 5.258051 ACTATTTATTTTCTCCCCGTTGCA 58.742 37.500 0.00 0.00 0.00 4.08
650 656 5.712917 ACTATTTATTTTCTCCCCGTTGCAA 59.287 36.000 0.00 0.00 0.00 4.08
651 657 3.926821 TTATTTTCTCCCCGTTGCAAC 57.073 42.857 19.89 19.89 0.00 4.17
665 671 3.659092 CAACGCACGGGCACATGT 61.659 61.111 11.77 0.00 41.24 3.21
666 672 3.659092 AACGCACGGGCACATGTG 61.659 61.111 21.83 21.83 41.24 3.21
742 748 3.329386 TGATCTTCCAAGAGTCAAAGCG 58.671 45.455 0.00 0.00 38.66 4.68
774 781 2.030091 GCTGGTTTATCCTCGCGTTTAC 59.970 50.000 5.77 0.00 37.07 2.01
836 848 5.359716 TTTGCCGTGACGTAATTAAACAT 57.640 34.783 3.64 0.00 0.00 2.71
837 849 4.587211 TGCCGTGACGTAATTAAACATC 57.413 40.909 3.64 0.00 0.00 3.06
841 853 5.617308 GCCGTGACGTAATTAAACATCCAAA 60.617 40.000 3.64 0.00 0.00 3.28
933 945 3.245443 TGCAATACCACAATTACCCACCT 60.245 43.478 0.00 0.00 0.00 4.00
939 951 2.093181 CCACAATTACCCACCTGATCGA 60.093 50.000 0.00 0.00 0.00 3.59
940 952 3.198068 CACAATTACCCACCTGATCGAG 58.802 50.000 0.00 0.00 0.00 4.04
941 953 2.838202 ACAATTACCCACCTGATCGAGT 59.162 45.455 0.00 0.00 0.00 4.18
960 974 9.288124 GATCGAGTATCATCATCATAAACTCAG 57.712 37.037 0.00 0.00 34.46 3.35
961 975 7.597386 TCGAGTATCATCATCATAAACTCAGG 58.403 38.462 0.00 0.00 33.19 3.86
962 976 6.810676 CGAGTATCATCATCATAAACTCAGGG 59.189 42.308 0.00 0.00 33.19 4.45
970 984 7.487822 TCATCATAAACTCAGGGAGATATCC 57.512 40.000 0.00 0.00 33.32 2.59
991 1005 1.268352 TCCAATCGCCGAAACAAAAGG 59.732 47.619 0.00 0.00 0.00 3.11
992 1006 1.059942 CAATCGCCGAAACAAAAGGC 58.940 50.000 0.00 0.00 46.88 4.35
1010 1024 4.637489 CGAGAGGATGAGCGGCGG 62.637 72.222 9.78 0.00 0.00 6.13
1032 1046 1.807573 GCTGTCGCTACTGCTGGTC 60.808 63.158 12.19 0.00 44.61 4.02
1038 1052 0.109458 CGCTACTGCTGGTCGTGTTA 60.109 55.000 0.00 0.00 36.97 2.41
1051 1065 1.424403 CGTGTTAACGGCACTGATGA 58.576 50.000 0.26 0.00 46.25 2.92
1071 1085 2.029964 TTGACGACGGTGAAGGCC 59.970 61.111 0.00 0.00 0.00 5.19
1101 1115 3.807538 GTGGACTACGGCGCGAGA 61.808 66.667 12.10 0.00 0.00 4.04
1102 1116 3.057548 TGGACTACGGCGCGAGAA 61.058 61.111 12.10 0.00 0.00 2.87
1411 1425 0.602905 GTACTGGGCGTGCAAGAAGT 60.603 55.000 2.99 6.10 0.00 3.01
1447 1472 4.326227 AGGGCCCCACGGTGAGTA 62.326 66.667 21.43 0.00 0.00 2.59
1458 1483 2.598637 CACGGTGAGTAATGACATGACG 59.401 50.000 0.74 0.00 0.00 4.35
1516 1559 2.035237 TTTCCTTGTGACGGACGCCT 62.035 55.000 0.00 0.00 0.00 5.52
1518 1565 2.317609 CCTTGTGACGGACGCCTTG 61.318 63.158 0.00 0.00 0.00 3.61
1530 1581 2.485122 GCCTTGCGTACATGCACC 59.515 61.111 0.00 0.00 46.25 5.01
1734 1785 0.034896 GACCATCCTCAACACCACGT 59.965 55.000 0.00 0.00 0.00 4.49
1851 1902 2.030540 CACCTTCAGTTGCCAGTTCATG 60.031 50.000 0.00 0.00 0.00 3.07
1852 1903 1.068055 CCTTCAGTTGCCAGTTCATGC 60.068 52.381 0.00 0.00 0.00 4.06
1853 1904 1.610038 CTTCAGTTGCCAGTTCATGCA 59.390 47.619 0.00 0.00 35.27 3.96
1854 1905 1.913778 TCAGTTGCCAGTTCATGCAT 58.086 45.000 0.00 0.00 37.33 3.96
1858 1909 2.426024 AGTTGCCAGTTCATGCATCATC 59.574 45.455 0.00 0.00 37.33 2.92
1859 1910 1.395635 TGCCAGTTCATGCATCATCC 58.604 50.000 0.00 0.00 31.31 3.51
1866 1917 6.071784 GCCAGTTCATGCATCATCCATTATTA 60.072 38.462 0.00 0.00 0.00 0.98
1884 1935 8.533965 CCATTATTATGTTTGCTTGTGATTTCG 58.466 33.333 0.00 0.00 0.00 3.46
1885 1936 9.075519 CATTATTATGTTTGCTTGTGATTTCGT 57.924 29.630 0.00 0.00 0.00 3.85
1886 1937 9.638239 ATTATTATGTTTGCTTGTGATTTCGTT 57.362 25.926 0.00 0.00 0.00 3.85
1887 1938 7.945033 ATTATGTTTGCTTGTGATTTCGTTT 57.055 28.000 0.00 0.00 0.00 3.60
1963 2018 4.891037 GGAGCATGGGAGGGCAGC 62.891 72.222 0.00 0.00 0.00 5.25
2104 2159 3.842126 CGCAGGTCACGATGCACG 61.842 66.667 4.66 7.07 42.68 5.34
2127 2182 2.511600 GCGAACCCCATCCTCGTG 60.512 66.667 0.00 0.00 35.06 4.35
2163 2218 3.490759 CGCAGCCGCAAAGTCGAT 61.491 61.111 0.00 0.00 38.40 3.59
2203 2258 2.092212 ACCCTAAGAGATGCCACCATTG 60.092 50.000 0.00 0.00 0.00 2.82
2206 2261 1.660560 AAGAGATGCCACCATTGCGC 61.661 55.000 0.00 0.00 0.00 6.09
2228 2283 3.184783 CAGCATCGATCTTCATCTCAAGC 59.815 47.826 0.00 0.00 0.00 4.01
2236 2293 2.097629 TCTTCATCTCAAGCTCCGTACG 59.902 50.000 8.69 8.69 0.00 3.67
2285 2349 4.109766 CACGAACTCTGTTGTTGTCTGTA 58.890 43.478 0.00 0.00 0.00 2.74
2430 2494 2.223595 CGAGAACATCAGGCTGACGTAT 60.224 50.000 21.37 10.28 0.00 3.06
2588 2662 8.673711 CCTCGATTCATTGGTTTCTGTAAATAA 58.326 33.333 0.00 0.00 0.00 1.40
2637 2712 3.991367 ACTACTAACACCTTGCACAGTC 58.009 45.455 0.00 0.00 0.00 3.51
2668 2745 1.474077 GCAGTGCTACCAAATCCAAGG 59.526 52.381 8.18 0.00 0.00 3.61
2732 2810 2.939103 GCTTGGTGTATCTCAAAGCGAT 59.061 45.455 0.00 0.00 0.00 4.58
2753 2831 5.452776 CGATCCTTACATGTAGCCCAAAGTA 60.453 44.000 5.56 0.00 0.00 2.24
2754 2832 5.353394 TCCTTACATGTAGCCCAAAGTAG 57.647 43.478 5.56 0.00 0.00 2.57
2755 2833 4.781087 TCCTTACATGTAGCCCAAAGTAGT 59.219 41.667 5.56 0.00 0.00 2.73
2756 2834 4.876107 CCTTACATGTAGCCCAAAGTAGTG 59.124 45.833 5.56 0.00 0.00 2.74
2769 2940 7.886446 AGCCCAAAGTAGTGCTTAGTAATTTTA 59.114 33.333 0.00 0.00 36.17 1.52
2943 3115 2.327200 ATTTGTAAGCGTAGAGGGGC 57.673 50.000 0.00 0.00 0.00 5.80
2966 3138 2.083774 CAAGAAGCAACCGGAATAGCA 58.916 47.619 9.46 0.00 0.00 3.49
2981 3153 5.918011 CGGAATAGCAAGCTAGTTCTTCTAG 59.082 44.000 7.91 0.00 46.39 2.43
3003 3175 5.772521 AGTGCATTTCACAAATACCTTGTC 58.227 37.500 0.00 0.00 45.50 3.18
3054 3226 4.789012 AATCCACAAACACCAAGCTATG 57.211 40.909 0.00 0.00 0.00 2.23
3061 3233 6.086222 CACAAACACCAAGCTATGTAATGTC 58.914 40.000 11.18 0.00 30.73 3.06
3071 3245 4.700213 AGCTATGTAATGTCCACCAACAAC 59.300 41.667 0.00 0.00 31.81 3.32
3078 3252 2.214347 TGTCCACCAACAACATACACG 58.786 47.619 0.00 0.00 0.00 4.49
3079 3253 1.069500 GTCCACCAACAACATACACGC 60.069 52.381 0.00 0.00 0.00 5.34
3109 3283 4.220602 AGCTCACAAAAACATCAATACCCC 59.779 41.667 0.00 0.00 0.00 4.95
3117 3291 8.432805 ACAAAAACATCAATACCCCAACATAAA 58.567 29.630 0.00 0.00 0.00 1.40
3118 3292 8.716909 CAAAAACATCAATACCCCAACATAAAC 58.283 33.333 0.00 0.00 0.00 2.01
3126 3300 3.492337 ACCCCAACATAAACGTCAATGT 58.508 40.909 9.31 9.31 37.94 2.71
3184 3358 6.785076 TCAACCCAATCAAACTATACTGGAA 58.215 36.000 0.00 0.00 0.00 3.53
3190 3364 7.122650 CCCAATCAAACTATACTGGAACAACAT 59.877 37.037 0.00 0.00 38.70 2.71
3191 3365 7.970061 CCAATCAAACTATACTGGAACAACATG 59.030 37.037 0.00 0.00 38.70 3.21
3192 3366 8.514594 CAATCAAACTATACTGGAACAACATGT 58.485 33.333 0.00 0.00 38.70 3.21
3204 3378 4.083003 GGAACAACATGTCCGAATAGCAAA 60.083 41.667 0.00 0.00 0.00 3.68
3214 3388 4.153475 GTCCGAATAGCAAACAAGCACTTA 59.847 41.667 0.00 0.00 36.85 2.24
3220 3394 7.167468 CGAATAGCAAACAAGCACTTAAAAAGT 59.833 33.333 0.00 0.00 44.06 2.66
3225 3399 6.311690 GCAAACAAGCACTTAAAAAGTAACCA 59.688 34.615 0.00 0.00 40.46 3.67
3255 3429 6.706295 ACAAAAGAAACACCAAATCAAAGGA 58.294 32.000 0.00 0.00 0.00 3.36
3256 3430 7.337938 ACAAAAGAAACACCAAATCAAAGGAT 58.662 30.769 0.00 0.00 34.43 3.24
3257 3431 8.482128 ACAAAAGAAACACCAAATCAAAGGATA 58.518 29.630 0.00 0.00 32.09 2.59
3259 3433 8.477419 AAAGAAACACCAAATCAAAGGATAGA 57.523 30.769 0.00 0.00 32.09 1.98
3261 3435 7.004086 AGAAACACCAAATCAAAGGATAGACA 58.996 34.615 0.00 0.00 32.09 3.41
3262 3436 6.824305 AACACCAAATCAAAGGATAGACAG 57.176 37.500 0.00 0.00 32.09 3.51
3263 3437 4.702131 ACACCAAATCAAAGGATAGACAGC 59.298 41.667 0.00 0.00 32.09 4.40
3264 3438 3.941483 ACCAAATCAAAGGATAGACAGCG 59.059 43.478 0.00 0.00 32.09 5.18
3265 3439 4.191544 CCAAATCAAAGGATAGACAGCGA 58.808 43.478 0.00 0.00 32.09 4.93
3266 3440 4.272018 CCAAATCAAAGGATAGACAGCGAG 59.728 45.833 0.00 0.00 32.09 5.03
3267 3441 2.586258 TCAAAGGATAGACAGCGAGC 57.414 50.000 0.00 0.00 0.00 5.03
3279 3453 2.743928 GCGAGCAACCCTCCACTG 60.744 66.667 0.00 0.00 37.27 3.66
3391 3565 6.012333 ACTTCTCTCCCTACTCTAGAAACTCA 60.012 42.308 0.00 0.00 0.00 3.41
3392 3566 6.390048 TCTCTCCCTACTCTAGAAACTCAA 57.610 41.667 0.00 0.00 0.00 3.02
3395 3569 5.823570 TCTCCCTACTCTAGAAACTCAATCG 59.176 44.000 0.00 0.00 0.00 3.34
3400 3574 7.013846 CCCTACTCTAGAAACTCAATCGAGAAT 59.986 40.741 0.00 0.00 42.34 2.40
3428 3602 4.946478 ACTCCAAATCTCTATTCCCGAG 57.054 45.455 0.00 0.00 0.00 4.63
3433 3607 3.760580 AATCTCTATTCCCGAGCTTGG 57.239 47.619 13.75 13.75 0.00 3.61
3442 3616 1.743252 CCGAGCTTGGGAAGACAGC 60.743 63.158 12.81 0.00 0.00 4.40
3446 3620 1.538950 GAGCTTGGGAAGACAGCTTTG 59.461 52.381 0.00 0.00 35.83 2.77
3459 3633 3.763671 CTTTGCCGAAAGCCACCT 58.236 55.556 0.00 0.00 42.71 4.00
3470 3644 2.191128 AAGCCACCTCAACTTGCTAG 57.809 50.000 0.00 0.00 0.00 3.42
3471 3645 1.059913 AGCCACCTCAACTTGCTAGT 58.940 50.000 0.00 0.00 35.68 2.57
3472 3646 2.257207 AGCCACCTCAACTTGCTAGTA 58.743 47.619 0.00 0.00 33.17 1.82
3473 3647 2.028020 AGCCACCTCAACTTGCTAGTAC 60.028 50.000 0.00 0.00 33.17 2.73
3474 3648 2.028020 GCCACCTCAACTTGCTAGTACT 60.028 50.000 0.00 0.00 33.17 2.73
3475 3649 3.851098 CCACCTCAACTTGCTAGTACTC 58.149 50.000 0.00 0.00 33.17 2.59
3476 3650 3.368531 CCACCTCAACTTGCTAGTACTCC 60.369 52.174 0.00 0.00 33.17 3.85
3477 3651 2.832733 ACCTCAACTTGCTAGTACTCCC 59.167 50.000 0.00 0.00 33.17 4.30
3478 3652 3.100671 CCTCAACTTGCTAGTACTCCCT 58.899 50.000 0.00 0.00 33.17 4.20
3479 3653 3.131400 CCTCAACTTGCTAGTACTCCCTC 59.869 52.174 0.00 0.00 33.17 4.30
3480 3654 3.097614 TCAACTTGCTAGTACTCCCTCC 58.902 50.000 0.00 0.00 33.17 4.30
3481 3655 1.765230 ACTTGCTAGTACTCCCTCCG 58.235 55.000 0.00 0.00 31.21 4.63
3482 3656 1.033574 CTTGCTAGTACTCCCTCCGG 58.966 60.000 0.00 0.00 0.00 5.14
3483 3657 0.333993 TTGCTAGTACTCCCTCCGGT 59.666 55.000 0.00 0.00 0.00 5.28
3484 3658 0.106819 TGCTAGTACTCCCTCCGGTC 60.107 60.000 0.00 0.00 0.00 4.79
3485 3659 0.822944 GCTAGTACTCCCTCCGGTCC 60.823 65.000 0.00 0.00 0.00 4.46
3486 3660 0.845337 CTAGTACTCCCTCCGGTCCT 59.155 60.000 0.00 0.00 0.00 3.85
3487 3661 1.214923 CTAGTACTCCCTCCGGTCCTT 59.785 57.143 0.00 0.00 0.00 3.36
3488 3662 0.412640 AGTACTCCCTCCGGTCCTTT 59.587 55.000 0.00 0.00 0.00 3.11
3489 3663 1.203275 AGTACTCCCTCCGGTCCTTTT 60.203 52.381 0.00 0.00 0.00 2.27
3490 3664 1.627329 GTACTCCCTCCGGTCCTTTTT 59.373 52.381 0.00 0.00 0.00 1.94
3491 3665 2.034436 ACTCCCTCCGGTCCTTTTTA 57.966 50.000 0.00 0.00 0.00 1.52
3492 3666 1.627329 ACTCCCTCCGGTCCTTTTTAC 59.373 52.381 0.00 0.00 0.00 2.01
3493 3667 1.907255 CTCCCTCCGGTCCTTTTTACT 59.093 52.381 0.00 0.00 0.00 2.24
3494 3668 1.904537 TCCCTCCGGTCCTTTTTACTC 59.095 52.381 0.00 0.00 0.00 2.59
3495 3669 1.907255 CCCTCCGGTCCTTTTTACTCT 59.093 52.381 0.00 0.00 0.00 3.24
3496 3670 2.354805 CCCTCCGGTCCTTTTTACTCTG 60.355 54.545 0.00 0.00 0.00 3.35
3497 3671 2.347731 CTCCGGTCCTTTTTACTCTGC 58.652 52.381 0.00 0.00 0.00 4.26
3498 3672 1.695242 TCCGGTCCTTTTTACTCTGCA 59.305 47.619 0.00 0.00 0.00 4.41
3499 3673 2.304761 TCCGGTCCTTTTTACTCTGCAT 59.695 45.455 0.00 0.00 0.00 3.96
3500 3674 3.516300 TCCGGTCCTTTTTACTCTGCATA 59.484 43.478 0.00 0.00 0.00 3.14
3501 3675 4.163458 TCCGGTCCTTTTTACTCTGCATAT 59.837 41.667 0.00 0.00 0.00 1.78
3502 3676 4.881850 CCGGTCCTTTTTACTCTGCATATT 59.118 41.667 0.00 0.00 0.00 1.28
3503 3677 6.053005 CCGGTCCTTTTTACTCTGCATATTA 58.947 40.000 0.00 0.00 0.00 0.98
3504 3678 6.202954 CCGGTCCTTTTTACTCTGCATATTAG 59.797 42.308 0.00 0.00 0.00 1.73
3505 3679 6.202954 CGGTCCTTTTTACTCTGCATATTAGG 59.797 42.308 0.00 0.00 0.00 2.69
3506 3680 7.054751 GGTCCTTTTTACTCTGCATATTAGGT 58.945 38.462 0.00 0.00 0.00 3.08
3507 3681 7.556635 GGTCCTTTTTACTCTGCATATTAGGTT 59.443 37.037 0.00 0.00 0.00 3.50
3508 3682 8.957466 GTCCTTTTTACTCTGCATATTAGGTTT 58.043 33.333 0.00 0.00 0.00 3.27
3509 3683 8.956426 TCCTTTTTACTCTGCATATTAGGTTTG 58.044 33.333 0.00 0.00 0.00 2.93
3510 3684 8.739972 CCTTTTTACTCTGCATATTAGGTTTGT 58.260 33.333 0.00 0.00 0.00 2.83
3511 3685 9.774742 CTTTTTACTCTGCATATTAGGTTTGTC 57.225 33.333 0.00 0.00 0.00 3.18
3512 3686 7.859325 TTTACTCTGCATATTAGGTTTGTCC 57.141 36.000 0.00 0.00 0.00 4.02
3513 3687 4.442706 ACTCTGCATATTAGGTTTGTCCG 58.557 43.478 0.00 0.00 41.99 4.79
3514 3688 4.161565 ACTCTGCATATTAGGTTTGTCCGA 59.838 41.667 0.00 0.00 41.99 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 139 4.358851 CCAGTTTGTTTTCAGATTGCGAA 58.641 39.130 0.00 0.00 0.00 4.70
136 140 3.243367 CCCAGTTTGTTTTCAGATTGCGA 60.243 43.478 0.00 0.00 0.00 5.10
164 168 0.530650 CAGCAATCCGTACGCCTGAT 60.531 55.000 10.49 4.63 0.00 2.90
165 169 1.153647 CAGCAATCCGTACGCCTGA 60.154 57.895 10.49 2.00 0.00 3.86
285 291 2.086869 GCTTCAATGCTAGAGTGCCAA 58.913 47.619 0.00 0.00 0.00 4.52
314 320 2.101415 CTCTATTGGGATGTCAGTGCGA 59.899 50.000 0.00 0.00 0.00 5.10
339 345 0.809385 ATCGACTCGTCATCGGTTGT 59.191 50.000 0.00 0.00 40.05 3.32
398 404 1.209504 GTGTAGTGAGCATGGGCCTAA 59.790 52.381 4.53 0.00 42.56 2.69
509 515 1.453155 GGTGGCATTGACTCGTCATT 58.547 50.000 0.00 0.00 39.64 2.57
537 543 3.430473 GTGAAACCCACATGGACCA 57.570 52.632 0.00 0.00 45.03 4.02
565 571 2.036256 GTGAAGTGGGCATGGGCT 59.964 61.111 0.00 0.00 40.87 5.19
622 628 9.059260 GCAACGGGGAGAAAATAAATAGTTATA 57.941 33.333 0.00 0.00 29.41 0.98
623 629 7.558444 TGCAACGGGGAGAAAATAAATAGTTAT 59.442 33.333 0.00 0.00 0.00 1.89
624 630 6.885376 TGCAACGGGGAGAAAATAAATAGTTA 59.115 34.615 0.00 0.00 0.00 2.24
625 631 5.712917 TGCAACGGGGAGAAAATAAATAGTT 59.287 36.000 0.00 0.00 0.00 2.24
626 632 5.258051 TGCAACGGGGAGAAAATAAATAGT 58.742 37.500 0.00 0.00 0.00 2.12
627 633 5.828299 TGCAACGGGGAGAAAATAAATAG 57.172 39.130 0.00 0.00 0.00 1.73
628 634 5.956642 GTTGCAACGGGGAGAAAATAAATA 58.043 37.500 14.90 0.00 0.00 1.40
629 635 4.816392 GTTGCAACGGGGAGAAAATAAAT 58.184 39.130 14.90 0.00 0.00 1.40
630 636 4.245845 GTTGCAACGGGGAGAAAATAAA 57.754 40.909 14.90 0.00 0.00 1.40
631 637 3.926821 GTTGCAACGGGGAGAAAATAA 57.073 42.857 14.90 0.00 0.00 1.40
648 654 3.659092 ACATGTGCCCGTGCGTTG 61.659 61.111 0.00 0.00 41.78 4.10
649 655 3.659092 CACATGTGCCCGTGCGTT 61.659 61.111 13.94 0.00 41.78 4.84
709 715 9.206690 ACTCTTGGAAGATCAATCAATAGACTA 57.793 33.333 0.00 0.00 33.93 2.59
710 716 8.088463 ACTCTTGGAAGATCAATCAATAGACT 57.912 34.615 0.00 0.00 33.93 3.24
711 717 7.984050 TGACTCTTGGAAGATCAATCAATAGAC 59.016 37.037 0.00 0.44 33.93 2.59
712 718 8.082672 TGACTCTTGGAAGATCAATCAATAGA 57.917 34.615 0.00 0.00 33.93 1.98
726 732 0.179032 TGCCGCTTTGACTCTTGGAA 60.179 50.000 0.00 0.00 0.00 3.53
742 748 0.673437 TAAACCAGCTGCAGTTTGCC 59.327 50.000 23.39 0.00 44.23 4.52
756 763 1.589779 CGGTAAACGCGAGGATAAACC 59.410 52.381 15.93 9.15 35.53 3.27
774 781 3.820590 TGTCCTGCAACACAACGG 58.179 55.556 0.00 0.00 0.00 4.44
806 818 0.030101 CGTCACGGCAAAACACCATT 59.970 50.000 0.00 0.00 0.00 3.16
836 848 2.675844 CGTTGCTAATCGTGGATTTGGA 59.324 45.455 0.00 0.00 33.95 3.53
837 849 2.418628 ACGTTGCTAATCGTGGATTTGG 59.581 45.455 0.00 0.00 38.85 3.28
841 853 2.429610 AGGTACGTTGCTAATCGTGGAT 59.570 45.455 0.00 0.00 40.50 3.41
939 951 7.732140 TCTCCCTGAGTTTATGATGATGATACT 59.268 37.037 0.00 0.00 0.00 2.12
940 952 7.901029 TCTCCCTGAGTTTATGATGATGATAC 58.099 38.462 0.00 0.00 0.00 2.24
941 953 8.676397 ATCTCCCTGAGTTTATGATGATGATA 57.324 34.615 0.00 0.00 0.00 2.15
962 976 1.819288 TCGGCGATTGGAGGATATCTC 59.181 52.381 4.99 0.00 41.71 2.75
970 984 2.584791 CTTTTGTTTCGGCGATTGGAG 58.415 47.619 11.76 0.66 0.00 3.86
992 1006 4.637489 CGCCGCTCATCCTCTCGG 62.637 72.222 0.00 0.00 44.29 4.63
994 1008 2.136196 CTACCGCCGCTCATCCTCTC 62.136 65.000 0.00 0.00 0.00 3.20
1009 1023 1.227002 GCAGTAGCGACAGCCTACC 60.227 63.158 2.86 0.00 46.67 3.18
1010 1024 4.403976 GCAGTAGCGACAGCCTAC 57.596 61.111 2.86 0.00 46.67 3.18
1032 1046 1.126113 GTCATCAGTGCCGTTAACACG 59.874 52.381 6.39 0.00 46.71 4.49
1038 1052 0.249699 TCAACGTCATCAGTGCCGTT 60.250 50.000 0.00 0.00 43.58 4.44
1066 1080 0.606604 ACGACATTGTACTCGGCCTT 59.393 50.000 0.00 0.00 34.07 4.35
1071 1085 2.631418 AGTCCACGACATTGTACTCG 57.369 50.000 0.00 1.11 34.60 4.18
1368 1382 4.636435 CCCTGCCCGTCCAACGTT 62.636 66.667 0.00 0.00 40.58 3.99
1447 1472 5.514274 AACCAAGAAAACGTCATGTCATT 57.486 34.783 0.00 0.00 0.00 2.57
1458 1483 6.720012 TTGCAAAGAGAAAACCAAGAAAAC 57.280 33.333 0.00 0.00 0.00 2.43
1516 1559 3.262936 GCAGGTGCATGTACGCAA 58.737 55.556 7.89 0.00 45.14 4.85
1530 1581 1.284657 CTAATGTCCAGCGTCTGCAG 58.715 55.000 7.63 7.63 46.23 4.41
1565 1616 1.417592 CGTTAGCTGCTTCACGCTG 59.582 57.895 17.54 0.00 40.11 5.18
1670 1721 2.994699 CCATCGGTGTTGGGGCTA 59.005 61.111 0.00 0.00 0.00 3.93
1717 1768 1.156736 GAACGTGGTGTTGAGGATGG 58.843 55.000 0.00 0.00 42.09 3.51
1851 1902 7.654520 ACAAGCAAACATAATAATGGATGATGC 59.345 33.333 0.00 0.00 38.51 3.91
1852 1903 8.974408 CACAAGCAAACATAATAATGGATGATG 58.026 33.333 0.00 0.00 37.43 3.07
1853 1904 8.916062 TCACAAGCAAACATAATAATGGATGAT 58.084 29.630 0.00 0.00 37.43 2.45
1854 1905 8.291191 TCACAAGCAAACATAATAATGGATGA 57.709 30.769 0.00 0.00 37.43 2.92
1858 1909 8.533965 CGAAATCACAAGCAAACATAATAATGG 58.466 33.333 0.00 0.00 37.43 3.16
1859 1910 9.075519 ACGAAATCACAAGCAAACATAATAATG 57.924 29.630 0.00 0.00 39.17 1.90
1866 1917 4.025813 GCAAACGAAATCACAAGCAAACAT 60.026 37.500 0.00 0.00 0.00 2.71
1884 1935 1.250476 CTATCAAACGCTGCGCAAAC 58.750 50.000 23.51 5.67 0.00 2.93
1885 1936 0.454285 GCTATCAAACGCTGCGCAAA 60.454 50.000 23.51 5.68 0.00 3.68
1886 1937 1.134487 GCTATCAAACGCTGCGCAA 59.866 52.632 23.51 5.29 0.00 4.85
1887 1938 1.368345 ATGCTATCAAACGCTGCGCA 61.368 50.000 23.51 10.98 0.00 6.09
2127 2182 1.602771 GGGGCAGTAGTTCTGGTCC 59.397 63.158 0.00 0.00 43.78 4.46
2203 2258 0.163360 GATGAAGATCGATGCTGCGC 59.837 55.000 0.54 0.00 0.00 6.09
2206 2261 3.184783 GCTTGAGATGAAGATCGATGCTG 59.815 47.826 0.54 0.00 33.34 4.41
2213 2268 3.451141 ACGGAGCTTGAGATGAAGATC 57.549 47.619 0.00 0.00 37.59 2.75
2214 2269 3.243234 CGTACGGAGCTTGAGATGAAGAT 60.243 47.826 7.57 0.00 0.00 2.40
2215 2270 2.097629 CGTACGGAGCTTGAGATGAAGA 59.902 50.000 7.57 0.00 0.00 2.87
2216 2271 2.455032 CGTACGGAGCTTGAGATGAAG 58.545 52.381 7.57 0.00 0.00 3.02
2228 2283 2.879462 GGCTTCACGCGTACGGAG 60.879 66.667 13.44 5.87 46.04 4.63
2285 2349 3.790437 CCCCCGAGCTCTGCATGT 61.790 66.667 12.85 0.00 0.00 3.21
2361 2425 1.488957 GCTGCAGTCGAACTTCACG 59.511 57.895 16.64 0.00 0.00 4.35
2410 2474 2.941453 TACGTCAGCCTGATGTTCTC 57.059 50.000 23.63 0.00 43.56 2.87
2588 2662 4.074970 ACGAACCAATCAAGCAAGAGAAT 58.925 39.130 0.00 0.00 0.00 2.40
2702 2779 7.936496 TTGAGATACACCAAGCAATGATTAA 57.064 32.000 0.00 0.00 0.00 1.40
2732 2810 4.781087 ACTACTTTGGGCTACATGTAAGGA 59.219 41.667 7.06 0.00 0.00 3.36
2753 2831 7.472543 CAAATCCGCTAAAATTACTAAGCACT 58.527 34.615 0.00 0.00 34.60 4.40
2754 2832 6.196538 GCAAATCCGCTAAAATTACTAAGCAC 59.803 38.462 0.00 0.00 34.60 4.40
2755 2833 6.094881 AGCAAATCCGCTAAAATTACTAAGCA 59.905 34.615 0.00 0.00 41.55 3.91
2756 2834 6.495706 AGCAAATCCGCTAAAATTACTAAGC 58.504 36.000 0.00 0.00 41.55 3.09
2813 2984 6.040616 ACCACGGGAAATTGTTGTGTTAATTA 59.959 34.615 0.00 0.00 0.00 1.40
2821 2992 2.104170 ACAACCACGGGAAATTGTTGT 58.896 42.857 3.87 3.87 43.26 3.32
2822 2993 2.880963 ACAACCACGGGAAATTGTTG 57.119 45.000 2.67 2.67 41.47 3.33
2823 2994 3.028130 AGAACAACCACGGGAAATTGTT 58.972 40.909 12.58 12.58 45.47 2.83
2825 2996 3.181480 ACAAGAACAACCACGGGAAATTG 60.181 43.478 0.00 0.00 0.00 2.32
2826 2997 3.028130 ACAAGAACAACCACGGGAAATT 58.972 40.909 0.00 0.00 0.00 1.82
2828 2999 1.746220 CACAAGAACAACCACGGGAAA 59.254 47.619 0.00 0.00 0.00 3.13
2831 3002 0.464735 TCCACAAGAACAACCACGGG 60.465 55.000 0.00 0.00 0.00 5.28
2832 3003 1.604604 ATCCACAAGAACAACCACGG 58.395 50.000 0.00 0.00 0.00 4.94
2879 3051 9.611284 CACAAAGATTCGATATCTCAAAACAAA 57.389 29.630 9.54 0.00 0.00 2.83
2894 3066 7.461107 ACCGTATGATTTTACACAAAGATTCG 58.539 34.615 0.00 0.00 0.00 3.34
2908 3080 9.872757 CGCTTACAAATTATAACCGTATGATTT 57.127 29.630 0.00 0.00 36.72 2.17
2909 3081 9.048446 ACGCTTACAAATTATAACCGTATGATT 57.952 29.630 0.00 0.00 29.51 2.57
2910 3082 8.597662 ACGCTTACAAATTATAACCGTATGAT 57.402 30.769 0.00 0.00 0.00 2.45
2911 3083 9.184062 CTACGCTTACAAATTATAACCGTATGA 57.816 33.333 8.98 0.00 30.06 2.15
2912 3084 9.184062 TCTACGCTTACAAATTATAACCGTATG 57.816 33.333 8.98 0.00 30.06 2.39
2913 3085 9.403110 CTCTACGCTTACAAATTATAACCGTAT 57.597 33.333 8.98 0.00 30.06 3.06
2914 3086 7.862372 CCTCTACGCTTACAAATTATAACCGTA 59.138 37.037 8.52 8.52 29.30 4.02
2915 3087 6.698766 CCTCTACGCTTACAAATTATAACCGT 59.301 38.462 7.50 7.50 30.95 4.83
2916 3088 6.145048 CCCTCTACGCTTACAAATTATAACCG 59.855 42.308 0.00 0.00 0.00 4.44
2943 3115 1.586154 ATTCCGGTTGCTTCTTGCCG 61.586 55.000 0.00 0.00 43.40 5.69
2947 3119 2.489938 TGCTATTCCGGTTGCTTCTT 57.510 45.000 0.00 0.00 0.00 2.52
2948 3120 2.359900 CTTGCTATTCCGGTTGCTTCT 58.640 47.619 0.00 0.00 0.00 2.85
2954 3126 3.197983 AGAACTAGCTTGCTATTCCGGTT 59.802 43.478 0.00 3.76 0.00 4.44
3003 3175 2.490509 TGGTTCAGATTTCTGCATGCAG 59.509 45.455 36.80 36.80 43.46 4.41
3054 3226 5.615984 CGTGTATGTTGTTGGTGGACATTAC 60.616 44.000 0.00 0.00 35.72 1.89
3061 3233 0.110419 CGCGTGTATGTTGTTGGTGG 60.110 55.000 0.00 0.00 0.00 4.61
3071 3245 1.205485 GAGCTGCTCTCGCGTGTATG 61.205 60.000 21.93 0.16 39.65 2.39
3079 3253 1.599071 TGTTTTTGTGAGCTGCTCTCG 59.401 47.619 28.04 0.00 44.86 4.04
3090 3264 5.605534 TGTTGGGGTATTGATGTTTTTGTG 58.394 37.500 0.00 0.00 0.00 3.33
3095 3269 6.209788 ACGTTTATGTTGGGGTATTGATGTTT 59.790 34.615 0.00 0.00 0.00 2.83
3142 3316 4.022589 GGTTGATATTGGAGGCATGACATG 60.023 45.833 11.27 11.27 0.00 3.21
3145 3319 2.887152 GGGTTGATATTGGAGGCATGAC 59.113 50.000 0.00 0.00 0.00 3.06
3181 3355 3.006940 TGCTATTCGGACATGTTGTTCC 58.993 45.455 0.00 0.00 0.00 3.62
3184 3358 3.818210 TGTTTGCTATTCGGACATGTTGT 59.182 39.130 0.00 0.00 0.00 3.32
3190 3364 2.225491 GTGCTTGTTTGCTATTCGGACA 59.775 45.455 0.00 0.00 0.00 4.02
3191 3365 2.484264 AGTGCTTGTTTGCTATTCGGAC 59.516 45.455 0.00 0.00 0.00 4.79
3192 3366 2.778299 AGTGCTTGTTTGCTATTCGGA 58.222 42.857 0.00 0.00 0.00 4.55
3204 3378 9.691362 CATATTGGTTACTTTTTAAGTGCTTGT 57.309 29.630 2.45 0.00 42.84 3.16
3220 3394 8.239038 TGGTGTTTCTTTTGTCATATTGGTTA 57.761 30.769 0.00 0.00 0.00 2.85
3225 3399 9.829507 TTGATTTGGTGTTTCTTTTGTCATATT 57.170 25.926 0.00 0.00 0.00 1.28
3255 3429 0.461961 GAGGGTTGCTCGCTGTCTAT 59.538 55.000 4.14 0.00 39.46 1.98
3256 3430 1.605058 GGAGGGTTGCTCGCTGTCTA 61.605 60.000 4.14 0.00 39.46 2.59
3257 3431 2.659610 GAGGGTTGCTCGCTGTCT 59.340 61.111 4.14 0.00 39.46 3.41
3259 3433 3.241530 TGGAGGGTTGCTCGCTGT 61.242 61.111 4.14 0.00 39.46 4.40
3261 3435 2.925170 AGTGGAGGGTTGCTCGCT 60.925 61.111 0.00 0.00 42.09 4.93
3262 3436 2.167398 TACAGTGGAGGGTTGCTCGC 62.167 60.000 0.00 0.00 0.00 5.03
3263 3437 0.108615 CTACAGTGGAGGGTTGCTCG 60.109 60.000 0.00 0.00 0.00 5.03
3264 3438 0.391793 GCTACAGTGGAGGGTTGCTC 60.392 60.000 4.06 0.00 33.86 4.26
3265 3439 1.679898 GCTACAGTGGAGGGTTGCT 59.320 57.895 4.06 0.00 33.86 3.91
3266 3440 1.741770 CGCTACAGTGGAGGGTTGC 60.742 63.158 11.28 0.00 33.42 4.17
3267 3441 0.537188 ATCGCTACAGTGGAGGGTTG 59.463 55.000 18.29 0.00 0.00 3.77
3279 3453 4.025647 GCCTTGTACTTGATTCATCGCTAC 60.026 45.833 0.00 0.00 0.00 3.58
3343 3517 7.349598 AGTGAGGCCTTTTGATCTACAAATAT 58.650 34.615 6.77 0.00 45.99 1.28
3349 3523 4.837972 AGAAGTGAGGCCTTTTGATCTAC 58.162 43.478 6.77 0.00 0.00 2.59
3391 3565 9.454859 AGATTTGGAGTTTTTCTATTCTCGATT 57.545 29.630 0.00 0.00 0.00 3.34
3392 3566 9.103861 GAGATTTGGAGTTTTTCTATTCTCGAT 57.896 33.333 0.00 0.00 0.00 3.59
3400 3574 7.769044 CGGGAATAGAGATTTGGAGTTTTTCTA 59.231 37.037 0.00 0.00 0.00 2.10
3428 3602 0.038801 GCAAAGCTGTCTTCCCAAGC 60.039 55.000 0.00 0.00 0.00 4.01
3433 3607 0.951558 TTTCGGCAAAGCTGTCTTCC 59.048 50.000 0.00 0.00 36.18 3.46
3446 3620 1.172812 AAGTTGAGGTGGCTTTCGGC 61.173 55.000 0.00 0.00 40.90 5.54
3456 3630 2.832733 GGGAGTACTAGCAAGTTGAGGT 59.167 50.000 7.16 4.21 37.15 3.85
3459 3633 3.097614 GGAGGGAGTACTAGCAAGTTGA 58.902 50.000 7.16 0.00 37.15 3.18
3477 3651 2.289444 TGCAGAGTAAAAAGGACCGGAG 60.289 50.000 9.46 0.00 0.00 4.63
3478 3652 1.695242 TGCAGAGTAAAAAGGACCGGA 59.305 47.619 9.46 0.00 0.00 5.14
3479 3653 2.178912 TGCAGAGTAAAAAGGACCGG 57.821 50.000 0.00 0.00 0.00 5.28
3480 3654 6.202954 CCTAATATGCAGAGTAAAAAGGACCG 59.797 42.308 0.00 0.00 0.00 4.79
3481 3655 7.054751 ACCTAATATGCAGAGTAAAAAGGACC 58.945 38.462 2.56 0.00 0.00 4.46
3482 3656 8.507524 AACCTAATATGCAGAGTAAAAAGGAC 57.492 34.615 2.56 0.00 0.00 3.85
3483 3657 8.956426 CAAACCTAATATGCAGAGTAAAAAGGA 58.044 33.333 2.56 0.00 0.00 3.36
3484 3658 8.739972 ACAAACCTAATATGCAGAGTAAAAAGG 58.260 33.333 0.00 0.00 0.00 3.11
3485 3659 9.774742 GACAAACCTAATATGCAGAGTAAAAAG 57.225 33.333 0.00 0.00 0.00 2.27
3486 3660 8.736244 GGACAAACCTAATATGCAGAGTAAAAA 58.264 33.333 0.00 0.00 35.41 1.94
3487 3661 7.065324 CGGACAAACCTAATATGCAGAGTAAAA 59.935 37.037 0.00 0.00 36.31 1.52
3488 3662 6.537301 CGGACAAACCTAATATGCAGAGTAAA 59.463 38.462 0.00 0.00 36.31 2.01
3489 3663 6.046593 CGGACAAACCTAATATGCAGAGTAA 58.953 40.000 0.00 0.00 36.31 2.24
3490 3664 5.361571 TCGGACAAACCTAATATGCAGAGTA 59.638 40.000 0.00 0.00 36.31 2.59
3491 3665 4.161565 TCGGACAAACCTAATATGCAGAGT 59.838 41.667 0.00 0.00 36.31 3.24
3492 3666 4.693283 TCGGACAAACCTAATATGCAGAG 58.307 43.478 0.00 0.00 36.31 3.35
3493 3667 4.746535 TCGGACAAACCTAATATGCAGA 57.253 40.909 0.00 0.00 36.31 4.26


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

AutoCloner maintained by Alex Coulton.