Multiple sequence alignment - TraesCS4B01G290900

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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 TraesCS4B01G290900 chr4B 100.000 3698 0 0 1 3698 575769867 575773564 0.000000e+00 6830.0
1 TraesCS4B01G290900 chr4B 91.703 687 52 5 3016 3698 60079476 60080161 0.000000e+00 948.0
2 TraesCS4B01G290900 chr4B 90.698 86 8 0 61 146 260072666 260072751 8.390000e-22 115.0
3 TraesCS4B01G290900 chr4B 100.000 28 0 0 150 177 327862112 327862139 7.000000e-03 52.8
4 TraesCS4B01G290900 chr5D 90.901 2286 129 36 652 2886 28023782 28026039 0.000000e+00 2996.0
5 TraesCS4B01G290900 chr5D 91.058 1767 104 15 978 2719 27861701 27859964 0.000000e+00 2338.0
6 TraesCS4B01G290900 chr5D 88.000 225 7 10 169 373 27862697 27862473 7.930000e-62 248.0
7 TraesCS4B01G290900 chr5D 86.239 218 13 4 655 866 27862125 27861919 1.730000e-53 220.0
8 TraesCS4B01G290900 chr5D 89.535 86 9 0 61 146 433810401 433810486 3.900000e-20 110.0
9 TraesCS4B01G290900 chr5D 86.735 98 8 3 2832 2924 27859785 27859688 1.820000e-18 104.0
10 TraesCS4B01G290900 chr5D 87.368 95 7 3 2923 3012 28026107 28026201 1.820000e-18 104.0
11 TraesCS4B01G290900 chr5D 85.567 97 10 2 2832 2924 27857343 27857247 8.450000e-17 99.0
12 TraesCS4B01G290900 chr5A 90.792 2259 138 36 718 2924 19066954 19069194 0.000000e+00 2955.0
13 TraesCS4B01G290900 chr5A 84.615 494 37 18 203 684 19066491 19066957 4.350000e-124 455.0
14 TraesCS4B01G290900 chr5A 89.583 96 8 2 61 156 653299582 653299489 1.800000e-23 121.0
15 TraesCS4B01G290900 chr5A 88.636 88 9 1 61 147 482121669 482121582 5.050000e-19 106.0
16 TraesCS4B01G290900 chr3A 90.087 686 64 4 3016 3698 706840418 706839734 0.000000e+00 887.0
17 TraesCS4B01G290900 chr3A 84.211 114 12 3 37 147 746316851 746316741 5.050000e-19 106.0
18 TraesCS4B01G290900 chr2A 88.270 682 66 12 3016 3691 588260793 588261466 0.000000e+00 804.0
19 TraesCS4B01G290900 chr2A 86.026 687 75 15 3016 3691 72930934 72930258 0.000000e+00 717.0
20 TraesCS4B01G290900 chr2A 90.588 85 8 0 63 147 689199777 689199861 3.020000e-21 113.0
21 TraesCS4B01G290900 chr1A 87.883 685 71 8 3016 3691 494818890 494819571 0.000000e+00 795.0
22 TraesCS4B01G290900 chr1A 94.872 39 0 2 150 186 544726822 544726784 3.990000e-05 60.2
23 TraesCS4B01G290900 chr6A 86.696 684 78 12 3016 3691 432569423 432568745 0.000000e+00 747.0
24 TraesCS4B01G290900 chr3D 85.962 691 80 11 3016 3692 125023352 125022665 0.000000e+00 723.0
25 TraesCS4B01G290900 chr3D 85.944 683 85 9 3016 3691 509148676 509149354 0.000000e+00 719.0
26 TraesCS4B01G290900 chr7A 86.091 683 79 16 3016 3691 97875970 97875297 0.000000e+00 721.0
27 TraesCS4B01G290900 chr4A 79.719 641 100 22 1177 1808 597052603 597053222 1.580000e-118 436.0
28 TraesCS4B01G290900 chr4A 95.455 44 1 1 20 63 624607184 624607142 6.630000e-08 69.4
29 TraesCS4B01G290900 chr6D 91.954 87 7 0 61 147 428908357 428908443 5.020000e-24 122.0
30 TraesCS4B01G290900 chr7D 89.412 85 9 0 63 147 161541393 161541309 1.400000e-19 108.0
31 TraesCS4B01G290900 chr2D 88.235 85 10 0 62 146 616608428 616608512 6.530000e-18 102.0
32 TraesCS4B01G290900 chrUn 100.000 29 0 0 150 178 31220637 31220665 2.000000e-03 54.7
33 TraesCS4B01G290900 chr3B 100.000 29 0 0 149 177 32058686 32058714 2.000000e-03 54.7
34 TraesCS4B01G290900 chr3B 91.892 37 3 0 23 59 214569365 214569329 7.000000e-03 52.8
35 TraesCS4B01G290900 chr1D 100.000 29 0 0 150 178 168043439 168043411 2.000000e-03 54.7
36 TraesCS4B01G290900 chr4D 100.000 28 0 0 150 177 108967481 108967508 7.000000e-03 52.8


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 TraesCS4B01G290900 chr4B 575769867 575773564 3697 False 6830.0 6830 100.0000 1 3698 1 chr4B.!!$F4 3697
1 TraesCS4B01G290900 chr4B 60079476 60080161 685 False 948.0 948 91.7030 3016 3698 1 chr4B.!!$F1 682
2 TraesCS4B01G290900 chr5D 28023782 28026201 2419 False 1550.0 2996 89.1345 652 3012 2 chr5D.!!$F2 2360
3 TraesCS4B01G290900 chr5D 27857247 27862697 5450 True 601.8 2338 87.5198 169 2924 5 chr5D.!!$R1 2755
4 TraesCS4B01G290900 chr5A 19066491 19069194 2703 False 1705.0 2955 87.7035 203 2924 2 chr5A.!!$F1 2721
5 TraesCS4B01G290900 chr3A 706839734 706840418 684 True 887.0 887 90.0870 3016 3698 1 chr3A.!!$R1 682
6 TraesCS4B01G290900 chr2A 588260793 588261466 673 False 804.0 804 88.2700 3016 3691 1 chr2A.!!$F1 675
7 TraesCS4B01G290900 chr2A 72930258 72930934 676 True 717.0 717 86.0260 3016 3691 1 chr2A.!!$R1 675
8 TraesCS4B01G290900 chr1A 494818890 494819571 681 False 795.0 795 87.8830 3016 3691 1 chr1A.!!$F1 675
9 TraesCS4B01G290900 chr6A 432568745 432569423 678 True 747.0 747 86.6960 3016 3691 1 chr6A.!!$R1 675
10 TraesCS4B01G290900 chr3D 125022665 125023352 687 True 723.0 723 85.9620 3016 3692 1 chr3D.!!$R1 676
11 TraesCS4B01G290900 chr3D 509148676 509149354 678 False 719.0 719 85.9440 3016 3691 1 chr3D.!!$F1 675
12 TraesCS4B01G290900 chr7A 97875297 97875970 673 True 721.0 721 86.0910 3016 3691 1 chr7A.!!$R1 675
13 TraesCS4B01G290900 chr4A 597052603 597053222 619 False 436.0 436 79.7190 1177 1808 1 chr4A.!!$F1 631

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
930 1231 0.391927 GGCGCCACATTACTGTACCA 60.392 55.0 24.8 0.0 33.14 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2924 3346 0.031616 AGAGAGCTTCCACCCCTAGG 60.032 60.0 0.06 0.06 40.04 3.02 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
22 23 3.028094 ACTTCCTCGGCTCCTAATACA 57.972 47.619 0.00 0.00 0.00 2.29
23 24 3.577919 ACTTCCTCGGCTCCTAATACAT 58.422 45.455 0.00 0.00 0.00 2.29
24 25 4.737578 ACTTCCTCGGCTCCTAATACATA 58.262 43.478 0.00 0.00 0.00 2.29
25 26 5.145564 ACTTCCTCGGCTCCTAATACATAA 58.854 41.667 0.00 0.00 0.00 1.90
26 27 5.601313 ACTTCCTCGGCTCCTAATACATAAA 59.399 40.000 0.00 0.00 0.00 1.40
27 28 5.723672 TCCTCGGCTCCTAATACATAAAG 57.276 43.478 0.00 0.00 0.00 1.85
28 29 5.145564 TCCTCGGCTCCTAATACATAAAGT 58.854 41.667 0.00 0.00 0.00 2.66
29 30 5.601313 TCCTCGGCTCCTAATACATAAAGTT 59.399 40.000 0.00 0.00 0.00 2.66
30 31 5.696724 CCTCGGCTCCTAATACATAAAGTTG 59.303 44.000 0.00 0.00 0.00 3.16
31 32 6.462487 CCTCGGCTCCTAATACATAAAGTTGA 60.462 42.308 0.00 0.00 0.00 3.18
32 33 6.513180 TCGGCTCCTAATACATAAAGTTGAG 58.487 40.000 0.00 0.00 0.00 3.02
33 34 6.322969 TCGGCTCCTAATACATAAAGTTGAGA 59.677 38.462 0.00 0.00 0.00 3.27
34 35 6.421202 CGGCTCCTAATACATAAAGTTGAGAC 59.579 42.308 0.00 0.00 0.00 3.36
35 36 7.272978 GGCTCCTAATACATAAAGTTGAGACA 58.727 38.462 0.00 0.00 0.00 3.41
36 37 7.224949 GGCTCCTAATACATAAAGTTGAGACAC 59.775 40.741 0.00 0.00 0.00 3.67
37 38 7.982354 GCTCCTAATACATAAAGTTGAGACACT 59.018 37.037 0.00 0.00 0.00 3.55
38 39 9.877178 CTCCTAATACATAAAGTTGAGACACTT 57.123 33.333 0.00 0.00 38.74 3.16
52 53 9.915629 AGTTGAGACACTTATTTTAGTACAGAG 57.084 33.333 0.00 0.00 0.00 3.35
53 54 9.141400 GTTGAGACACTTATTTTAGTACAGAGG 57.859 37.037 0.00 0.00 0.00 3.69
54 55 7.837863 TGAGACACTTATTTTAGTACAGAGGG 58.162 38.462 0.00 0.00 0.00 4.30
55 56 7.672660 TGAGACACTTATTTTAGTACAGAGGGA 59.327 37.037 0.00 0.00 0.00 4.20
56 57 8.068892 AGACACTTATTTTAGTACAGAGGGAG 57.931 38.462 0.00 0.00 0.00 4.30
57 58 7.674772 AGACACTTATTTTAGTACAGAGGGAGT 59.325 37.037 0.00 0.00 0.00 3.85
58 59 8.890410 ACACTTATTTTAGTACAGAGGGAGTA 57.110 34.615 0.00 0.00 0.00 2.59
59 60 8.747471 ACACTTATTTTAGTACAGAGGGAGTAC 58.253 37.037 0.00 0.00 41.59 2.73
74 75 9.765795 CAGAGGGAGTACTATAAGTATTTTTGG 57.234 37.037 0.00 0.00 32.65 3.28
75 76 9.725206 AGAGGGAGTACTATAAGTATTTTTGGA 57.275 33.333 0.00 0.00 32.65 3.53
76 77 9.984190 GAGGGAGTACTATAAGTATTTTTGGAG 57.016 37.037 0.00 0.00 32.65 3.86
77 78 9.725206 AGGGAGTACTATAAGTATTTTTGGAGA 57.275 33.333 0.00 0.00 32.65 3.71
88 89 7.264373 AGTATTTTTGGAGATTCTAATGCGG 57.736 36.000 0.00 0.00 0.00 5.69
89 90 7.054124 AGTATTTTTGGAGATTCTAATGCGGA 58.946 34.615 0.00 0.00 0.00 5.54
90 91 5.560966 TTTTTGGAGATTCTAATGCGGAC 57.439 39.130 0.00 0.00 0.00 4.79
91 92 4.487714 TTTGGAGATTCTAATGCGGACT 57.512 40.909 0.00 0.00 0.00 3.85
92 93 5.607939 TTTGGAGATTCTAATGCGGACTA 57.392 39.130 0.00 0.00 0.00 2.59
93 94 4.585955 TGGAGATTCTAATGCGGACTAC 57.414 45.455 0.00 0.00 0.00 2.73
94 95 3.958147 TGGAGATTCTAATGCGGACTACA 59.042 43.478 0.00 0.00 0.00 2.74
95 96 4.588951 TGGAGATTCTAATGCGGACTACAT 59.411 41.667 0.00 0.00 0.00 2.29
96 97 4.926238 GGAGATTCTAATGCGGACTACATG 59.074 45.833 0.00 0.00 0.00 3.21
97 98 4.310769 AGATTCTAATGCGGACTACATGC 58.689 43.478 0.00 0.00 0.00 4.06
98 99 2.134201 TCTAATGCGGACTACATGCG 57.866 50.000 0.00 0.00 46.53 4.73
99 100 1.139989 CTAATGCGGACTACATGCGG 58.860 55.000 0.00 0.00 43.46 5.69
101 102 2.494445 TGCGGACTACATGCGGAG 59.506 61.111 0.00 0.00 43.46 4.63
135 136 9.236006 AGTGAATTTGCACTCTAAAATATGTCT 57.764 29.630 0.00 0.00 45.54 3.41
164 165 5.746990 ATCCGAGTATTTAGGAATGGAGG 57.253 43.478 0.00 0.00 37.62 4.30
165 166 3.901844 TCCGAGTATTTAGGAATGGAGGG 59.098 47.826 0.00 0.00 0.00 4.30
166 167 3.901844 CCGAGTATTTAGGAATGGAGGGA 59.098 47.826 0.00 0.00 0.00 4.20
167 168 4.021016 CCGAGTATTTAGGAATGGAGGGAG 60.021 50.000 0.00 0.00 0.00 4.30
238 239 4.262635 GGAAGTTGGTTGAGATCTCTGTCA 60.263 45.833 22.95 14.50 0.00 3.58
281 282 2.992543 GTTTTGTTGTTGCTGTTGCTGA 59.007 40.909 0.00 0.00 40.48 4.26
411 436 8.071368 TGGTCGACATTTTTCTTGTGTTATTAC 58.929 33.333 18.91 0.00 0.00 1.89
412 437 8.287503 GGTCGACATTTTTCTTGTGTTATTACT 58.712 33.333 18.91 0.00 0.00 2.24
413 438 9.659830 GTCGACATTTTTCTTGTGTTATTACTT 57.340 29.630 11.55 0.00 0.00 2.24
435 460 6.598064 ACTTATTAGGAAAGAAATGGTCCACG 59.402 38.462 0.00 0.00 33.57 4.94
503 554 1.336125 GCAGCAGGCTGATTAATCACC 59.664 52.381 24.46 18.18 46.30 4.02
504 555 2.646930 CAGCAGGCTGATTAATCACCA 58.353 47.619 25.73 7.28 46.30 4.17
520 571 2.905736 TCACCAGTGATCTGACATTGGA 59.094 45.455 20.22 4.85 46.08 3.53
521 572 3.520721 TCACCAGTGATCTGACATTGGAT 59.479 43.478 20.22 8.60 46.08 3.41
522 573 3.875727 CACCAGTGATCTGACATTGGATC 59.124 47.826 20.22 0.00 46.08 3.36
524 575 3.181472 CCAGTGATCTGACATTGGATCGA 60.181 47.826 12.89 0.00 46.08 3.59
526 577 2.791560 GTGATCTGACATTGGATCGACG 59.208 50.000 0.00 0.00 40.63 5.12
528 579 3.130340 TGATCTGACATTGGATCGACGAA 59.870 43.478 0.00 0.00 40.63 3.85
529 580 3.150848 TCTGACATTGGATCGACGAAG 57.849 47.619 0.00 0.00 0.00 3.79
532 583 2.425668 TGACATTGGATCGACGAAGCTA 59.574 45.455 0.00 0.00 0.00 3.32
533 584 3.119280 TGACATTGGATCGACGAAGCTAA 60.119 43.478 0.00 1.87 0.00 3.09
537 588 2.201732 TGGATCGACGAAGCTAATTGC 58.798 47.619 0.00 0.00 43.29 3.56
549 600 2.992242 GCTAATTGCTTCTCAATCGCC 58.008 47.619 0.00 0.00 44.23 5.54
551 602 2.927553 AATTGCTTCTCAATCGCCAC 57.072 45.000 0.00 0.00 44.23 5.01
553 604 2.760634 TTGCTTCTCAATCGCCACTA 57.239 45.000 0.00 0.00 0.00 2.74
554 605 2.760634 TGCTTCTCAATCGCCACTAA 57.239 45.000 0.00 0.00 0.00 2.24
571 622 5.449177 GCCACTAATTTGTCAGCTGATTACC 60.449 44.000 21.47 7.44 0.00 2.85
572 623 5.066505 CCACTAATTTGTCAGCTGATTACCC 59.933 44.000 21.47 7.03 0.00 3.69
573 624 5.647658 CACTAATTTGTCAGCTGATTACCCA 59.352 40.000 21.47 9.92 0.00 4.51
574 625 6.150976 CACTAATTTGTCAGCTGATTACCCAA 59.849 38.462 21.47 15.65 0.00 4.12
577 628 3.500448 TGTCAGCTGATTACCCAACAA 57.500 42.857 21.47 0.00 0.00 2.83
578 629 3.146066 TGTCAGCTGATTACCCAACAAC 58.854 45.455 21.47 3.13 0.00 3.32
583 684 2.095059 GCTGATTACCCAACAACAGCAG 60.095 50.000 0.00 0.00 46.30 4.24
590 691 1.504359 CCAACAACAGCAGCAAATGG 58.496 50.000 0.00 0.00 0.00 3.16
608 709 1.628340 TGGTGATGATGAGGTTTCGGT 59.372 47.619 0.00 0.00 0.00 4.69
617 733 0.511653 GAGGTTTCGGTTTGCGTCTC 59.488 55.000 0.00 0.00 0.00 3.36
621 737 1.458445 GTTTCGGTTTGCGTCTCCTAC 59.542 52.381 0.00 0.00 0.00 3.18
703 828 1.909700 TCCATCACTCCAAAAGCACC 58.090 50.000 0.00 0.00 0.00 5.01
704 829 1.425066 TCCATCACTCCAAAAGCACCT 59.575 47.619 0.00 0.00 0.00 4.00
705 830 2.642311 TCCATCACTCCAAAAGCACCTA 59.358 45.455 0.00 0.00 0.00 3.08
706 831 3.266772 TCCATCACTCCAAAAGCACCTAT 59.733 43.478 0.00 0.00 0.00 2.57
707 832 3.379372 CCATCACTCCAAAAGCACCTATG 59.621 47.826 0.00 0.00 0.00 2.23
830 970 5.353123 ACACAAAGTCACAAACGTACTCATT 59.647 36.000 0.00 0.00 0.00 2.57
930 1231 0.391927 GGCGCCACATTACTGTACCA 60.392 55.000 24.80 0.00 33.14 3.25
931 1232 1.006832 GCGCCACATTACTGTACCAG 58.993 55.000 0.00 0.00 37.52 4.00
937 1238 2.932614 CACATTACTGTACCAGAGCTGC 59.067 50.000 0.00 0.00 35.18 5.25
938 1239 2.834549 ACATTACTGTACCAGAGCTGCT 59.165 45.455 0.00 0.00 35.18 4.24
940 1241 1.475403 TACTGTACCAGAGCTGCTCC 58.525 55.000 25.09 10.64 35.18 4.70
941 1242 1.140589 CTGTACCAGAGCTGCTCCG 59.859 63.158 25.09 15.78 32.44 4.63
943 1244 3.461773 TACCAGAGCTGCTCCGCC 61.462 66.667 25.09 1.71 0.00 6.13
969 1270 4.259292 CGAGTCGTCCAAATTCGATTACAC 60.259 45.833 3.82 0.00 38.32 2.90
976 1277 4.570772 TCCAAATTCGATTACACTAGCTGC 59.429 41.667 0.00 0.00 0.00 5.25
1008 1316 2.299867 GGACATCAACACCATGGCTTTT 59.700 45.455 13.04 0.00 29.06 2.27
1024 1332 1.299014 TTTTTCAAGCGGCTGTGCG 60.299 52.632 1.81 0.00 40.67 5.34
1078 1386 0.831966 CATCTCCTTCCTGCTGCTCT 59.168 55.000 0.00 0.00 0.00 4.09
1096 1404 0.796870 CTTGCTCGTCGTCGTATGCA 60.797 55.000 13.01 13.01 37.22 3.96
1102 1410 1.135344 TCGTCGTCGTATGCATTTCCA 60.135 47.619 3.54 0.00 38.33 3.53
1134 1442 1.003718 CGGCGGGACCTTCTTCTTT 60.004 57.895 0.00 0.00 35.61 2.52
1320 1634 2.607750 GAGGGGCTCTGGTGGTCA 60.608 66.667 0.00 0.00 0.00 4.02
1374 1688 1.830477 CTGCTCCTGCTCTTCTACCTT 59.170 52.381 0.00 0.00 40.48 3.50
1620 1937 4.796231 GTGGTCGCCATCGTCGCT 62.796 66.667 1.90 0.00 35.28 4.93
1769 2089 2.905935 TTCCTCTCCCTCTACGCCGG 62.906 65.000 0.00 0.00 0.00 6.13
2091 2424 4.379243 CCAACCGTGCTCCTCGCT 62.379 66.667 0.00 0.00 40.11 4.93
2100 2433 3.710722 CTCCTCGCTGGCACCCTT 61.711 66.667 0.00 0.00 35.26 3.95
2325 2664 4.379243 CTCGCGTGGGGCAACTCT 62.379 66.667 5.77 0.00 43.84 3.24
2515 2854 1.154169 GTGGATGCGTCGACGTACA 60.154 57.895 35.48 26.67 42.22 2.90
2547 2892 4.028490 CTGGTGGCCGGGCTAACA 62.028 66.667 29.87 22.44 33.54 2.41
2604 2949 4.664677 GACGCCACACTCGGTGCT 62.665 66.667 4.23 0.00 46.50 4.40
2715 3060 3.054802 AGTGATTGAGGACTGTTGGATCC 60.055 47.826 4.20 4.20 34.98 3.36
2717 3062 3.054875 TGATTGAGGACTGTTGGATCCTG 60.055 47.826 14.23 3.33 45.74 3.86
2719 3064 2.182827 TGAGGACTGTTGGATCCTGAG 58.817 52.381 14.23 8.38 45.74 3.35
2720 3065 1.484240 GAGGACTGTTGGATCCTGAGG 59.516 57.143 14.23 0.00 45.74 3.86
2721 3066 0.107459 GGACTGTTGGATCCTGAGGC 60.107 60.000 14.23 7.88 31.75 4.70
2722 3067 0.908198 GACTGTTGGATCCTGAGGCT 59.092 55.000 14.23 0.00 0.00 4.58
2723 3068 2.111384 GACTGTTGGATCCTGAGGCTA 58.889 52.381 14.23 0.00 0.00 3.93
2724 3069 2.703007 GACTGTTGGATCCTGAGGCTAT 59.297 50.000 14.23 0.00 0.00 2.97
2725 3070 3.898123 GACTGTTGGATCCTGAGGCTATA 59.102 47.826 14.23 0.00 0.00 1.31
2726 3071 3.900601 ACTGTTGGATCCTGAGGCTATAG 59.099 47.826 14.23 0.00 0.00 1.31
2728 3073 3.116746 TGTTGGATCCTGAGGCTATAGGA 60.117 47.826 18.93 18.93 46.43 2.94
2729 3074 3.176924 TGGATCCTGAGGCTATAGGAC 57.823 52.381 19.00 13.52 45.30 3.85
2730 3075 2.450886 TGGATCCTGAGGCTATAGGACA 59.549 50.000 19.00 12.32 45.30 4.02
2731 3076 3.096092 GGATCCTGAGGCTATAGGACAG 58.904 54.545 19.00 6.86 45.30 3.51
2732 3077 2.002505 TCCTGAGGCTATAGGACAGC 57.997 55.000 14.21 0.00 38.15 4.40
2733 3078 1.217942 TCCTGAGGCTATAGGACAGCA 59.782 52.381 14.21 0.00 40.95 4.41
2735 3080 1.342819 CTGAGGCTATAGGACAGCACC 59.657 57.143 1.04 0.00 40.95 5.01
2736 3081 0.315568 GAGGCTATAGGACAGCACCG 59.684 60.000 1.04 0.00 40.95 4.94
2737 3082 0.106167 AGGCTATAGGACAGCACCGA 60.106 55.000 1.04 0.00 40.95 4.69
2738 3083 0.315568 GGCTATAGGACAGCACCGAG 59.684 60.000 1.04 0.00 40.95 4.63
2739 3084 0.319125 GCTATAGGACAGCACCGAGC 60.319 60.000 1.04 0.00 46.19 5.03
2806 3198 1.002379 CTGGCTTGGCTGCTTCTCT 60.002 57.895 0.00 0.00 0.00 3.10
2808 3200 1.299321 GGCTTGGCTGCTTCTCTCT 59.701 57.895 0.00 0.00 0.00 3.10
2814 3206 0.319728 GGCTGCTTCTCTCTCACACA 59.680 55.000 0.00 0.00 0.00 3.72
2817 3209 0.319040 TGCTTCTCTCTCACACACGC 60.319 55.000 0.00 0.00 0.00 5.34
2818 3210 0.038709 GCTTCTCTCTCACACACGCT 60.039 55.000 0.00 0.00 0.00 5.07
2819 3211 1.975837 CTTCTCTCTCACACACGCTC 58.024 55.000 0.00 0.00 0.00 5.03
2820 3212 0.238553 TTCTCTCTCACACACGCTCG 59.761 55.000 0.00 0.00 0.00 5.03
2899 3316 8.293867 TGTTGTCTGTTGTAAATTAAGTATGGC 58.706 33.333 0.00 0.00 0.00 4.40
2913 3335 3.566351 AGTATGGCATAGGAAAAAGGGC 58.434 45.455 7.61 0.00 0.00 5.19
2916 3338 2.831565 TGGCATAGGAAAAAGGGCATT 58.168 42.857 0.00 0.00 0.00 3.56
2924 3346 7.468768 GCATAGGAAAAAGGGCATTAAGTACTC 60.469 40.741 0.00 0.00 0.00 2.59
2925 3347 5.262009 AGGAAAAAGGGCATTAAGTACTCC 58.738 41.667 0.00 0.00 0.00 3.85
2929 3841 5.632034 AAAGGGCATTAAGTACTCCTAGG 57.368 43.478 0.82 0.82 0.00 3.02
2993 3909 4.142816 GGTCCACGATTTTGACTTGATCAG 60.143 45.833 0.00 0.00 38.99 2.90
2994 3910 4.452455 GTCCACGATTTTGACTTGATCAGT 59.548 41.667 0.00 0.00 38.99 3.41
2997 3913 3.189287 ACGATTTTGACTTGATCAGTGCC 59.811 43.478 0.00 0.00 38.99 5.01
3012 3929 1.750778 AGTGCCTTGTGTTTTGTGGAG 59.249 47.619 0.00 0.00 0.00 3.86
3014 3931 1.748493 TGCCTTGTGTTTTGTGGAGTC 59.252 47.619 0.00 0.00 0.00 3.36
3070 4056 2.875933 TGATTTCGTCCGCTTTTTGTCT 59.124 40.909 0.00 0.00 0.00 3.41
3163 4153 3.336715 GACCCATTTTGACGCGGCC 62.337 63.158 10.82 0.56 0.00 6.13
3261 4253 0.108992 GAGTCCACGCGTCCACATTA 60.109 55.000 9.86 0.00 0.00 1.90
3262 4254 0.535335 AGTCCACGCGTCCACATTAT 59.465 50.000 9.86 0.00 0.00 1.28
3263 4255 1.066430 AGTCCACGCGTCCACATTATT 60.066 47.619 9.86 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.737578 TGTATTAGGAGCCGAGGAAGTAT 58.262 43.478 0.00 0.00 0.00 2.12
1 2 4.174704 TGTATTAGGAGCCGAGGAAGTA 57.825 45.455 0.00 0.00 0.00 2.24
2 3 3.028094 TGTATTAGGAGCCGAGGAAGT 57.972 47.619 0.00 0.00 0.00 3.01
3 4 5.723672 TTATGTATTAGGAGCCGAGGAAG 57.276 43.478 0.00 0.00 0.00 3.46
4 5 5.601313 ACTTTATGTATTAGGAGCCGAGGAA 59.399 40.000 0.00 0.00 0.00 3.36
5 6 5.145564 ACTTTATGTATTAGGAGCCGAGGA 58.854 41.667 0.00 0.00 0.00 3.71
6 7 5.470047 ACTTTATGTATTAGGAGCCGAGG 57.530 43.478 0.00 0.00 0.00 4.63
7 8 6.513180 TCAACTTTATGTATTAGGAGCCGAG 58.487 40.000 0.00 0.00 0.00 4.63
8 9 6.322969 TCTCAACTTTATGTATTAGGAGCCGA 59.677 38.462 0.00 0.00 0.00 5.54
9 10 6.421202 GTCTCAACTTTATGTATTAGGAGCCG 59.579 42.308 0.00 0.00 0.00 5.52
10 11 7.224949 GTGTCTCAACTTTATGTATTAGGAGCC 59.775 40.741 0.00 0.00 0.00 4.70
11 12 7.982354 AGTGTCTCAACTTTATGTATTAGGAGC 59.018 37.037 0.00 0.00 0.00 4.70
12 13 9.877178 AAGTGTCTCAACTTTATGTATTAGGAG 57.123 33.333 0.00 0.00 37.05 3.69
26 27 9.915629 CTCTGTACTAAAATAAGTGTCTCAACT 57.084 33.333 0.00 0.00 0.00 3.16
27 28 9.141400 CCTCTGTACTAAAATAAGTGTCTCAAC 57.859 37.037 0.00 0.00 0.00 3.18
28 29 8.311836 CCCTCTGTACTAAAATAAGTGTCTCAA 58.688 37.037 0.00 0.00 0.00 3.02
29 30 7.672660 TCCCTCTGTACTAAAATAAGTGTCTCA 59.327 37.037 0.00 0.00 0.00 3.27
30 31 8.064336 TCCCTCTGTACTAAAATAAGTGTCTC 57.936 38.462 0.00 0.00 0.00 3.36
31 32 7.674772 ACTCCCTCTGTACTAAAATAAGTGTCT 59.325 37.037 0.00 0.00 0.00 3.41
32 33 7.838884 ACTCCCTCTGTACTAAAATAAGTGTC 58.161 38.462 0.00 0.00 0.00 3.67
33 34 7.793948 ACTCCCTCTGTACTAAAATAAGTGT 57.206 36.000 0.00 0.00 0.00 3.55
34 35 8.968969 AGTACTCCCTCTGTACTAAAATAAGTG 58.031 37.037 4.94 0.00 45.86 3.16
48 49 9.765795 CCAAAAATACTTATAGTACTCCCTCTG 57.234 37.037 0.00 0.00 32.84 3.35
49 50 9.725206 TCCAAAAATACTTATAGTACTCCCTCT 57.275 33.333 0.00 0.00 32.84 3.69
50 51 9.984190 CTCCAAAAATACTTATAGTACTCCCTC 57.016 37.037 0.00 0.00 32.84 4.30
51 52 9.725206 TCTCCAAAAATACTTATAGTACTCCCT 57.275 33.333 0.00 0.00 32.84 4.20
62 63 8.836413 CCGCATTAGAATCTCCAAAAATACTTA 58.164 33.333 0.00 0.00 0.00 2.24
63 64 7.556275 TCCGCATTAGAATCTCCAAAAATACTT 59.444 33.333 0.00 0.00 0.00 2.24
64 65 7.012421 GTCCGCATTAGAATCTCCAAAAATACT 59.988 37.037 0.00 0.00 0.00 2.12
65 66 7.012421 AGTCCGCATTAGAATCTCCAAAAATAC 59.988 37.037 0.00 0.00 0.00 1.89
66 67 7.054124 AGTCCGCATTAGAATCTCCAAAAATA 58.946 34.615 0.00 0.00 0.00 1.40
67 68 5.888161 AGTCCGCATTAGAATCTCCAAAAAT 59.112 36.000 0.00 0.00 0.00 1.82
68 69 5.253330 AGTCCGCATTAGAATCTCCAAAAA 58.747 37.500 0.00 0.00 0.00 1.94
69 70 4.843728 AGTCCGCATTAGAATCTCCAAAA 58.156 39.130 0.00 0.00 0.00 2.44
70 71 4.487714 AGTCCGCATTAGAATCTCCAAA 57.512 40.909 0.00 0.00 0.00 3.28
71 72 4.404394 TGTAGTCCGCATTAGAATCTCCAA 59.596 41.667 0.00 0.00 0.00 3.53
72 73 3.958147 TGTAGTCCGCATTAGAATCTCCA 59.042 43.478 0.00 0.00 0.00 3.86
73 74 4.585955 TGTAGTCCGCATTAGAATCTCC 57.414 45.455 0.00 0.00 0.00 3.71
74 75 4.387256 GCATGTAGTCCGCATTAGAATCTC 59.613 45.833 0.00 0.00 0.00 2.75
75 76 4.310769 GCATGTAGTCCGCATTAGAATCT 58.689 43.478 0.00 0.00 0.00 2.40
76 77 3.121944 CGCATGTAGTCCGCATTAGAATC 59.878 47.826 0.00 0.00 0.00 2.52
77 78 3.059884 CGCATGTAGTCCGCATTAGAAT 58.940 45.455 0.00 0.00 0.00 2.40
78 79 2.469826 CGCATGTAGTCCGCATTAGAA 58.530 47.619 0.00 0.00 0.00 2.10
79 80 1.269569 CCGCATGTAGTCCGCATTAGA 60.270 52.381 0.00 0.00 0.00 2.10
80 81 1.139989 CCGCATGTAGTCCGCATTAG 58.860 55.000 0.00 0.00 0.00 1.73
81 82 0.747852 TCCGCATGTAGTCCGCATTA 59.252 50.000 0.00 0.00 0.00 1.90
82 83 0.530650 CTCCGCATGTAGTCCGCATT 60.531 55.000 0.00 0.00 0.00 3.56
83 84 1.068083 CTCCGCATGTAGTCCGCAT 59.932 57.895 0.00 0.00 0.00 4.73
84 85 2.494445 CTCCGCATGTAGTCCGCA 59.506 61.111 0.00 0.00 0.00 5.69
85 86 2.962253 GCTCCGCATGTAGTCCGC 60.962 66.667 0.00 0.00 0.00 5.54
86 87 0.739462 TTTGCTCCGCATGTAGTCCG 60.739 55.000 0.00 0.00 38.76 4.79
87 88 1.448985 TTTTGCTCCGCATGTAGTCC 58.551 50.000 0.00 0.00 38.76 3.85
88 89 2.677836 TCATTTTGCTCCGCATGTAGTC 59.322 45.455 0.00 0.00 38.76 2.59
89 90 2.679837 CTCATTTTGCTCCGCATGTAGT 59.320 45.455 0.00 0.00 38.76 2.73
90 91 2.679837 ACTCATTTTGCTCCGCATGTAG 59.320 45.455 0.00 0.00 38.76 2.74
91 92 2.419673 CACTCATTTTGCTCCGCATGTA 59.580 45.455 0.00 0.00 38.76 2.29
92 93 1.200716 CACTCATTTTGCTCCGCATGT 59.799 47.619 0.00 0.00 38.76 3.21
93 94 1.469703 TCACTCATTTTGCTCCGCATG 59.530 47.619 0.00 0.00 38.76 4.06
94 95 1.825090 TCACTCATTTTGCTCCGCAT 58.175 45.000 0.00 0.00 38.76 4.73
95 96 1.603456 TTCACTCATTTTGCTCCGCA 58.397 45.000 0.00 0.00 36.47 5.69
96 97 2.927553 ATTCACTCATTTTGCTCCGC 57.072 45.000 0.00 0.00 0.00 5.54
138 139 9.148879 CCTCCATTCCTAAATACTCGGATATAT 57.851 37.037 0.00 0.00 0.00 0.86
139 140 7.563924 CCCTCCATTCCTAAATACTCGGATATA 59.436 40.741 0.00 0.00 0.00 0.86
140 141 6.384305 CCCTCCATTCCTAAATACTCGGATAT 59.616 42.308 0.00 0.00 0.00 1.63
141 142 5.720041 CCCTCCATTCCTAAATACTCGGATA 59.280 44.000 0.00 0.00 0.00 2.59
142 143 4.532521 CCCTCCATTCCTAAATACTCGGAT 59.467 45.833 0.00 0.00 0.00 4.18
143 144 3.901844 CCCTCCATTCCTAAATACTCGGA 59.098 47.826 0.00 0.00 0.00 4.55
144 145 3.901844 TCCCTCCATTCCTAAATACTCGG 59.098 47.826 0.00 0.00 0.00 4.63
145 146 4.589374 ACTCCCTCCATTCCTAAATACTCG 59.411 45.833 0.00 0.00 0.00 4.18
146 147 7.011382 TCTACTCCCTCCATTCCTAAATACTC 58.989 42.308 0.00 0.00 0.00 2.59
147 148 6.935036 TCTACTCCCTCCATTCCTAAATACT 58.065 40.000 0.00 0.00 0.00 2.12
148 149 7.509659 TCTTCTACTCCCTCCATTCCTAAATAC 59.490 40.741 0.00 0.00 0.00 1.89
149 150 7.601942 TCTTCTACTCCCTCCATTCCTAAATA 58.398 38.462 0.00 0.00 0.00 1.40
150 151 6.453476 TCTTCTACTCCCTCCATTCCTAAAT 58.547 40.000 0.00 0.00 0.00 1.40
151 152 5.850278 TCTTCTACTCCCTCCATTCCTAAA 58.150 41.667 0.00 0.00 0.00 1.85
152 153 5.483174 TCTTCTACTCCCTCCATTCCTAA 57.517 43.478 0.00 0.00 0.00 2.69
153 154 5.688220 ATCTTCTACTCCCTCCATTCCTA 57.312 43.478 0.00 0.00 0.00 2.94
154 155 4.567987 ATCTTCTACTCCCTCCATTCCT 57.432 45.455 0.00 0.00 0.00 3.36
155 156 6.943899 ATTATCTTCTACTCCCTCCATTCC 57.056 41.667 0.00 0.00 0.00 3.01
157 158 9.052365 GGAATATTATCTTCTACTCCCTCCATT 57.948 37.037 0.00 0.00 0.00 3.16
158 159 8.413821 AGGAATATTATCTTCTACTCCCTCCAT 58.586 37.037 0.00 0.00 0.00 3.41
159 160 7.780822 AGGAATATTATCTTCTACTCCCTCCA 58.219 38.462 0.00 0.00 0.00 3.86
160 161 9.192642 GTAGGAATATTATCTTCTACTCCCTCC 57.807 40.741 0.00 0.00 0.00 4.30
161 162 9.192642 GGTAGGAATATTATCTTCTACTCCCTC 57.807 40.741 0.00 0.00 0.00 4.30
162 163 8.689054 TGGTAGGAATATTATCTTCTACTCCCT 58.311 37.037 0.00 0.00 0.00 4.20
163 164 8.896722 TGGTAGGAATATTATCTTCTACTCCC 57.103 38.462 0.00 0.00 0.00 4.30
259 260 2.735663 CAGCAACAGCAACAACAAAACA 59.264 40.909 0.00 0.00 0.00 2.83
299 322 0.967380 GCCCAACCTGGTCCATTGAG 60.967 60.000 0.00 0.00 35.17 3.02
374 399 6.633500 AAAATGTCGACCATTCTTTTGAGA 57.367 33.333 14.12 0.00 43.04 3.27
411 436 6.598064 ACGTGGACCATTTCTTTCCTAATAAG 59.402 38.462 0.00 0.00 0.00 1.73
412 437 6.478129 ACGTGGACCATTTCTTTCCTAATAA 58.522 36.000 0.00 0.00 0.00 1.40
413 438 6.057321 ACGTGGACCATTTCTTTCCTAATA 57.943 37.500 0.00 0.00 0.00 0.98
414 439 4.918588 ACGTGGACCATTTCTTTCCTAAT 58.081 39.130 0.00 0.00 0.00 1.73
415 440 4.320870 GACGTGGACCATTTCTTTCCTAA 58.679 43.478 0.00 0.00 0.00 2.69
416 441 3.615592 CGACGTGGACCATTTCTTTCCTA 60.616 47.826 0.00 0.00 0.00 2.94
417 442 2.779506 GACGTGGACCATTTCTTTCCT 58.220 47.619 0.00 0.00 0.00 3.36
435 460 0.944386 AGCATGTGTGTTTGGTCGAC 59.056 50.000 7.13 7.13 0.00 4.20
462 512 3.857052 CTTAGATTAGGGCACAACGACA 58.143 45.455 0.00 0.00 0.00 4.35
503 554 3.801050 GTCGATCCAATGTCAGATCACTG 59.199 47.826 0.00 0.00 44.66 3.66
504 555 3.489908 CGTCGATCCAATGTCAGATCACT 60.490 47.826 0.00 0.00 39.09 3.41
529 580 2.355756 TGGCGATTGAGAAGCAATTAGC 59.644 45.455 0.00 0.00 46.90 3.09
532 583 2.440409 AGTGGCGATTGAGAAGCAATT 58.560 42.857 0.00 0.00 46.90 2.32
537 588 5.122239 TGACAAATTAGTGGCGATTGAGAAG 59.878 40.000 0.00 0.00 0.00 2.85
539 590 4.574892 TGACAAATTAGTGGCGATTGAGA 58.425 39.130 0.00 0.00 0.00 3.27
542 593 3.127548 AGCTGACAAATTAGTGGCGATTG 59.872 43.478 0.00 0.00 0.00 2.67
543 594 3.127548 CAGCTGACAAATTAGTGGCGATT 59.872 43.478 8.42 0.00 0.00 3.34
544 595 2.679837 CAGCTGACAAATTAGTGGCGAT 59.320 45.455 8.42 0.00 0.00 4.58
545 596 2.076100 CAGCTGACAAATTAGTGGCGA 58.924 47.619 8.42 0.00 0.00 5.54
546 597 2.076100 TCAGCTGACAAATTAGTGGCG 58.924 47.619 13.74 0.00 0.00 5.69
547 598 4.708726 AATCAGCTGACAAATTAGTGGC 57.291 40.909 20.97 0.00 0.00 5.01
549 600 5.647658 TGGGTAATCAGCTGACAAATTAGTG 59.352 40.000 20.97 0.00 0.00 2.74
551 602 6.150976 TGTTGGGTAATCAGCTGACAAATTAG 59.849 38.462 20.97 0.00 0.00 1.73
553 604 4.832266 TGTTGGGTAATCAGCTGACAAATT 59.168 37.500 20.97 12.12 0.00 1.82
554 605 4.406456 TGTTGGGTAATCAGCTGACAAAT 58.594 39.130 20.97 8.44 0.00 2.32
571 622 1.202557 ACCATTTGCTGCTGTTGTTGG 60.203 47.619 0.00 2.50 0.00 3.77
572 623 1.862201 CACCATTTGCTGCTGTTGTTG 59.138 47.619 0.00 0.00 0.00 3.33
573 624 1.755959 TCACCATTTGCTGCTGTTGTT 59.244 42.857 0.00 0.00 0.00 2.83
574 625 1.401761 TCACCATTTGCTGCTGTTGT 58.598 45.000 0.00 0.00 0.00 3.32
577 628 1.913778 TCATCACCATTTGCTGCTGT 58.086 45.000 0.00 0.00 0.00 4.40
578 629 2.425668 TCATCATCACCATTTGCTGCTG 59.574 45.455 0.00 0.00 0.00 4.41
583 684 4.427312 GAAACCTCATCATCACCATTTGC 58.573 43.478 0.00 0.00 0.00 3.68
590 691 3.670627 GCAAACCGAAACCTCATCATCAC 60.671 47.826 0.00 0.00 0.00 3.06
608 709 2.870435 GCAGAAAGGTAGGAGACGCAAA 60.870 50.000 0.00 0.00 0.00 3.68
617 733 0.329596 AGCTTGGGCAGAAAGGTAGG 59.670 55.000 0.00 0.00 41.70 3.18
621 737 1.101331 GATGAGCTTGGGCAGAAAGG 58.899 55.000 0.00 0.00 41.70 3.11
703 828 3.188667 CAGCCATGTCATAGCAAGCATAG 59.811 47.826 6.01 0.00 0.00 2.23
704 829 3.143728 CAGCCATGTCATAGCAAGCATA 58.856 45.455 6.01 0.00 0.00 3.14
705 830 1.954382 CAGCCATGTCATAGCAAGCAT 59.046 47.619 6.01 0.00 0.00 3.79
706 831 1.385528 CAGCCATGTCATAGCAAGCA 58.614 50.000 6.01 0.00 0.00 3.91
707 832 0.030369 GCAGCCATGTCATAGCAAGC 59.970 55.000 6.01 5.61 0.00 4.01
708 833 0.666913 GGCAGCCATGTCATAGCAAG 59.333 55.000 6.55 0.00 0.00 4.01
709 834 1.096967 CGGCAGCCATGTCATAGCAA 61.097 55.000 13.30 0.00 0.00 3.91
710 835 1.524393 CGGCAGCCATGTCATAGCA 60.524 57.895 13.30 0.00 0.00 3.49
711 836 2.901292 GCGGCAGCCATGTCATAGC 61.901 63.158 13.30 0.00 37.42 2.97
830 970 2.222007 ATTTGCTTTTGTCGCTGCAA 57.778 40.000 0.00 0.00 42.60 4.08
905 1199 2.120909 GTAATGTGGCGCCATGGCT 61.121 57.895 35.23 19.52 45.14 4.75
943 1244 1.708027 GAATTTGGACGACTCGGCG 59.292 57.895 0.00 0.00 34.63 6.46
944 1245 0.734942 TCGAATTTGGACGACTCGGC 60.735 55.000 2.98 0.00 33.62 5.54
945 1246 1.922570 ATCGAATTTGGACGACTCGG 58.077 50.000 2.98 0.00 41.17 4.63
946 1247 3.855379 TGTAATCGAATTTGGACGACTCG 59.145 43.478 0.00 0.00 41.17 4.18
947 1248 4.863131 AGTGTAATCGAATTTGGACGACTC 59.137 41.667 0.00 0.00 41.17 3.36
948 1249 4.817517 AGTGTAATCGAATTTGGACGACT 58.182 39.130 0.00 0.00 41.17 4.18
949 1250 5.276254 GCTAGTGTAATCGAATTTGGACGAC 60.276 44.000 0.00 0.00 41.17 4.34
950 1251 4.802039 GCTAGTGTAATCGAATTTGGACGA 59.198 41.667 0.00 0.00 42.49 4.20
953 1254 4.570772 GCAGCTAGTGTAATCGAATTTGGA 59.429 41.667 0.00 0.00 0.00 3.53
976 1277 2.279120 GATGTCCGGAGCTCAGCG 60.279 66.667 17.19 10.77 0.00 5.18
1008 1316 2.590291 TCGCACAGCCGCTTGAAA 60.590 55.556 0.00 0.00 0.00 2.69
1011 1319 3.485431 CTCTCGCACAGCCGCTTG 61.485 66.667 0.00 0.00 0.00 4.01
1050 1358 4.845580 AAGGAGATGCTGGCCGCG 62.846 66.667 13.55 0.00 43.27 6.46
1051 1359 2.899339 GAAGGAGATGCTGGCCGC 60.899 66.667 11.92 11.92 39.77 6.53
1053 1361 1.153005 CAGGAAGGAGATGCTGGCC 60.153 63.158 0.00 0.00 35.36 5.36
1060 1368 1.209990 CAAGAGCAGCAGGAAGGAGAT 59.790 52.381 0.00 0.00 0.00 2.75
1061 1369 0.612229 CAAGAGCAGCAGGAAGGAGA 59.388 55.000 0.00 0.00 0.00 3.71
1078 1386 0.179148 ATGCATACGACGACGAGCAA 60.179 50.000 22.49 11.80 43.18 3.91
1096 1404 4.178214 CCGCGTGCGCATGGAAAT 62.178 61.111 29.57 0.00 42.06 2.17
1251 1559 1.305930 GGTAGTCGACGTACCCGGTT 61.306 60.000 23.11 3.80 38.78 4.44
1392 1706 1.226717 CGAGGCGCAGAAGTACTCC 60.227 63.158 10.83 0.00 0.00 3.85
1743 2063 3.378399 GAGGGAGAGGAAGCACGCC 62.378 68.421 0.00 0.00 0.00 5.68
1769 2089 1.764180 CGAGACGAGGAGGACGTAGC 61.764 65.000 0.00 0.00 43.97 3.58
1823 2147 0.109781 CATTGTGTTGGTGCTACCGC 60.110 55.000 0.00 0.00 42.58 5.68
1827 2151 1.885887 GGCTTCATTGTGTTGGTGCTA 59.114 47.619 0.00 0.00 0.00 3.49
2025 2358 4.851214 AGAGGGGAGAGGAGCGCC 62.851 72.222 2.29 0.00 38.53 6.53
2035 2368 4.144727 GGCGAGGAGGAGAGGGGA 62.145 72.222 0.00 0.00 0.00 4.81
2091 2424 4.338710 GTGCCGGTAAGGGTGCCA 62.339 66.667 1.90 0.00 41.48 4.92
2418 2757 1.896660 CCCCACCACCGTGTTGAAG 60.897 63.158 0.00 0.00 38.41 3.02
2442 2781 2.202987 GCCAGTGCCATCGAGAGG 60.203 66.667 2.43 2.43 0.00 3.69
2472 2811 1.033746 TCTTGTACGGCTCCGGGTAG 61.034 60.000 13.31 0.00 44.69 3.18
2545 2890 2.597217 CACCACCAACGCCCATGT 60.597 61.111 0.00 0.00 0.00 3.21
2547 2892 4.284550 AGCACCACCAACGCCCAT 62.285 61.111 0.00 0.00 0.00 4.00
2676 3021 1.067000 CACTGTCTTGGCAGGAGAGAG 60.067 57.143 26.94 18.69 40.59 3.20
2715 3060 1.342819 GGTGCTGTCCTATAGCCTCAG 59.657 57.143 0.00 3.84 40.42 3.35
2716 3061 1.414158 GGTGCTGTCCTATAGCCTCA 58.586 55.000 0.00 0.00 40.42 3.86
2717 3062 0.315568 CGGTGCTGTCCTATAGCCTC 59.684 60.000 0.00 0.00 40.42 4.70
2719 3064 0.315568 CTCGGTGCTGTCCTATAGCC 59.684 60.000 0.00 0.00 40.42 3.93
2720 3065 0.319125 GCTCGGTGCTGTCCTATAGC 60.319 60.000 0.00 0.00 41.49 2.97
2721 3066 0.039978 CGCTCGGTGCTGTCCTATAG 60.040 60.000 0.23 0.00 40.11 1.31
2722 3067 0.464916 TCGCTCGGTGCTGTCCTATA 60.465 55.000 0.23 0.00 40.11 1.31
2723 3068 1.320344 TTCGCTCGGTGCTGTCCTAT 61.320 55.000 0.23 0.00 40.11 2.57
2724 3069 1.974875 TTCGCTCGGTGCTGTCCTA 60.975 57.895 0.23 0.00 40.11 2.94
2725 3070 3.303135 TTCGCTCGGTGCTGTCCT 61.303 61.111 0.23 0.00 40.11 3.85
2726 3071 3.112709 GTTCGCTCGGTGCTGTCC 61.113 66.667 0.23 0.00 40.11 4.02
2728 3073 3.865929 CTGGTTCGCTCGGTGCTGT 62.866 63.158 0.23 0.00 40.11 4.40
2729 3074 3.114616 CTGGTTCGCTCGGTGCTG 61.115 66.667 0.23 0.00 40.11 4.41
2731 3076 3.642778 TAGCTGGTTCGCTCGGTGC 62.643 63.158 0.00 0.00 41.30 5.01
2732 3077 0.669318 TTTAGCTGGTTCGCTCGGTG 60.669 55.000 0.00 0.00 41.30 4.94
2733 3078 0.034337 TTTTAGCTGGTTCGCTCGGT 59.966 50.000 0.00 0.00 41.30 4.69
2735 3080 1.656095 CTCTTTTAGCTGGTTCGCTCG 59.344 52.381 0.00 0.00 41.30 5.03
2736 3081 2.689646 ACTCTTTTAGCTGGTTCGCTC 58.310 47.619 0.00 0.00 41.30 5.03
2737 3082 2.841442 ACTCTTTTAGCTGGTTCGCT 57.159 45.000 0.00 0.00 43.83 4.93
2738 3083 3.586892 ACTACTCTTTTAGCTGGTTCGC 58.413 45.455 0.00 0.00 0.00 4.70
2739 3084 5.952033 AGTACTACTCTTTTAGCTGGTTCG 58.048 41.667 0.00 0.00 0.00 3.95
2740 3085 8.054152 AGTAGTACTACTCTTTTAGCTGGTTC 57.946 38.462 26.61 0.00 42.30 3.62
2806 3198 3.427670 TCACGAGCGTGTGTGAGA 58.572 55.556 20.71 0.00 45.55 3.27
2814 3206 2.530177 CATGTAAGTGATCACGAGCGT 58.470 47.619 19.85 11.82 36.20 5.07
2817 3209 3.867493 ACATGCATGTAAGTGATCACGAG 59.133 43.478 30.50 8.64 39.68 4.18
2818 3210 3.618150 CACATGCATGTAAGTGATCACGA 59.382 43.478 30.92 9.66 39.39 4.35
2819 3211 3.242511 CCACATGCATGTAAGTGATCACG 60.243 47.826 30.92 14.67 39.39 4.35
2820 3212 3.940852 TCCACATGCATGTAAGTGATCAC 59.059 43.478 30.92 18.47 39.39 3.06
2822 3214 6.429078 ACATATCCACATGCATGTAAGTGATC 59.571 38.462 30.92 0.00 39.39 2.92
2824 3216 5.683681 ACATATCCACATGCATGTAAGTGA 58.316 37.500 30.92 22.96 39.39 3.41
2825 3217 7.495135 TTACATATCCACATGCATGTAAGTG 57.505 36.000 30.92 23.91 38.36 3.16
2826 3218 7.255242 GCTTTACATATCCACATGCATGTAAGT 60.255 37.037 30.92 19.99 42.00 2.24
2828 3220 6.016360 GGCTTTACATATCCACATGCATGTAA 60.016 38.462 30.92 21.88 40.36 2.41
2829 3221 5.473162 GGCTTTACATATCCACATGCATGTA 59.527 40.000 30.92 17.97 39.39 2.29
2830 3222 4.279169 GGCTTTACATATCCACATGCATGT 59.721 41.667 26.61 26.61 42.84 3.21
2898 3315 5.598416 ACTTAATGCCCTTTTTCCTATGC 57.402 39.130 0.00 0.00 0.00 3.14
2899 3316 7.013369 GGAGTACTTAATGCCCTTTTTCCTATG 59.987 40.741 0.00 0.00 0.00 2.23
2913 3335 4.553678 TCCACCCCTAGGAGTACTTAATG 58.446 47.826 11.48 0.00 36.73 1.90
2916 3338 3.629282 GCTTCCACCCCTAGGAGTACTTA 60.629 52.174 11.48 0.00 36.33 2.24
2924 3346 0.031616 AGAGAGCTTCCACCCCTAGG 60.032 60.000 0.06 0.06 40.04 3.02
2925 3347 1.342474 TGAGAGAGCTTCCACCCCTAG 60.342 57.143 0.00 0.00 0.00 3.02
2929 3841 2.026822 TCAATTGAGAGAGCTTCCACCC 60.027 50.000 3.38 0.00 0.00 4.61
2993 3909 1.476488 ACTCCACAAAACACAAGGCAC 59.524 47.619 0.00 0.00 0.00 5.01
2994 3910 1.748493 GACTCCACAAAACACAAGGCA 59.252 47.619 0.00 0.00 0.00 4.75
2997 3913 3.242870 GCTCTGACTCCACAAAACACAAG 60.243 47.826 0.00 0.00 0.00 3.16
3012 3929 0.951040 CCCGTTGGAGTTGCTCTGAC 60.951 60.000 0.00 0.00 0.00 3.51
3014 3931 2.328099 GCCCGTTGGAGTTGCTCTG 61.328 63.158 0.00 0.00 0.00 3.35
3070 4056 2.112297 GTCTGGCCGACCCAAACA 59.888 61.111 14.46 0.00 44.81 2.83
3214 4206 1.658994 CTTCGTGGCCGGCTTTAATA 58.341 50.000 28.56 6.95 33.95 0.98
3238 4230 3.735029 GGACGCGTGGACTCTCGT 61.735 66.667 20.70 0.00 37.92 4.18
3301 4302 1.369091 GACGACGACGCCTAGGGTAA 61.369 60.000 11.72 0.00 43.96 2.85
3303 4304 3.130160 GACGACGACGCCTAGGGT 61.130 66.667 11.72 6.76 43.96 4.34


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

AutoCloner maintained by Alex Coulton.