Multiple sequence alignment - TraesCS2B01G148300

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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 TraesCS2B01G148300 chr2B 100.000 4019 0 0 1 4019 114373465 114377483 0.000000e+00 7422.0
1 TraesCS2B01G148300 chr2B 89.810 893 69 18 3133 4014 439856986 439856105 0.000000e+00 1125.0
2 TraesCS2B01G148300 chr2B 77.204 465 86 13 399 846 453133871 453134332 1.850000e-63 254.0
3 TraesCS2B01G148300 chr2D 88.153 3140 267 59 54 3133 74978711 74981805 0.000000e+00 3640.0
4 TraesCS2B01G148300 chr2D 88.814 894 70 24 3134 4014 523521414 523520538 0.000000e+00 1070.0
5 TraesCS2B01G148300 chr2A 90.757 1677 93 24 1479 3133 74162970 74164606 0.000000e+00 2182.0
6 TraesCS2B01G148300 chr2A 92.721 577 28 6 887 1449 74162402 74162978 0.000000e+00 821.0
7 TraesCS2B01G148300 chr2A 88.163 245 25 4 50 292 74150536 74150778 5.080000e-74 289.0
8 TraesCS2B01G148300 chr2A 87.234 94 8 4 2172 2263 676365575 676365666 1.980000e-18 104.0
9 TraesCS2B01G148300 chr2A 89.024 82 8 1 2173 2253 163467153 163467234 2.560000e-17 100.0
10 TraesCS2B01G148300 chr6B 93.588 889 44 12 3134 4019 640603403 640602525 0.000000e+00 1314.0
11 TraesCS2B01G148300 chr6B 75.578 389 78 10 407 781 120834704 120834319 4.130000e-40 176.0
12 TraesCS2B01G148300 chr6B 85.366 82 11 1 2164 2244 125340316 125340397 2.570000e-12 84.2
13 TraesCS2B01G148300 chr3B 92.308 871 57 8 3153 4018 63711741 63710876 0.000000e+00 1229.0
14 TraesCS2B01G148300 chr3B 85.897 78 10 1 2168 2244 217984919 217984996 9.260000e-12 82.4
15 TraesCS2B01G148300 chr4B 91.339 889 61 15 3134 4014 631540553 631541433 0.000000e+00 1201.0
16 TraesCS2B01G148300 chr1B 90.258 893 63 16 3134 4014 564628784 564627904 0.000000e+00 1146.0
17 TraesCS2B01G148300 chr1B 79.384 422 69 14 434 845 685664693 685665106 8.500000e-72 281.0
18 TraesCS2B01G148300 chr5B 88.976 889 83 12 3134 4014 248306727 248307608 0.000000e+00 1085.0
19 TraesCS2B01G148300 chr3D 88.989 890 73 19 3134 4014 357204091 357204964 0.000000e+00 1077.0
20 TraesCS2B01G148300 chr7D 88.814 894 71 25 3134 4014 291597032 291596155 0.000000e+00 1070.0
21 TraesCS2B01G148300 chr7D 95.455 44 1 1 173 216 146183016 146182974 7.210000e-08 69.4
22 TraesCS2B01G148300 chr6D 77.083 432 82 11 402 820 466897362 466896935 2.420000e-57 233.0
23 TraesCS2B01G148300 chr6D 79.070 258 40 11 597 847 225945954 225945704 8.940000e-37 165.0
24 TraesCS2B01G148300 chr3A 78.613 346 60 11 414 747 533978953 533978610 2.430000e-52 217.0
25 TraesCS2B01G148300 chr3A 89.286 84 7 2 2171 2252 466063519 466063602 1.980000e-18 104.0
26 TraesCS2B01G148300 chr7B 75.569 483 93 21 381 846 484270488 484270962 8.750000e-52 215.0
27 TraesCS2B01G148300 chr7B 75.852 352 64 12 434 773 137543691 137543349 4.160000e-35 159.0
28 TraesCS2B01G148300 chr7B 89.535 86 5 4 2168 2250 12532076 12532160 5.490000e-19 106.0
29 TraesCS2B01G148300 chr7B 89.157 83 8 1 2168 2249 485523901 485523983 7.110000e-18 102.0
30 TraesCS2B01G148300 chr4A 76.376 436 75 22 423 841 662987310 662986886 4.070000e-50 209.0
31 TraesCS2B01G148300 chr7A 75.000 428 93 11 432 846 102329981 102329555 6.860000e-43 185.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G148300 chr2B 114373465 114377483 4018 False 7422.0 7422 100.000 1 4019 1 chr2B.!!$F1 4018
1 TraesCS2B01G148300 chr2B 439856105 439856986 881 True 1125.0 1125 89.810 3133 4014 1 chr2B.!!$R1 881
2 TraesCS2B01G148300 chr2D 74978711 74981805 3094 False 3640.0 3640 88.153 54 3133 1 chr2D.!!$F1 3079
3 TraesCS2B01G148300 chr2D 523520538 523521414 876 True 1070.0 1070 88.814 3134 4014 1 chr2D.!!$R1 880
4 TraesCS2B01G148300 chr2A 74162402 74164606 2204 False 1501.5 2182 91.739 887 3133 2 chr2A.!!$F4 2246
5 TraesCS2B01G148300 chr6B 640602525 640603403 878 True 1314.0 1314 93.588 3134 4019 1 chr6B.!!$R2 885
6 TraesCS2B01G148300 chr3B 63710876 63711741 865 True 1229.0 1229 92.308 3153 4018 1 chr3B.!!$R1 865
7 TraesCS2B01G148300 chr4B 631540553 631541433 880 False 1201.0 1201 91.339 3134 4014 1 chr4B.!!$F1 880
8 TraesCS2B01G148300 chr1B 564627904 564628784 880 True 1146.0 1146 90.258 3134 4014 1 chr1B.!!$R1 880
9 TraesCS2B01G148300 chr5B 248306727 248307608 881 False 1085.0 1085 88.976 3134 4014 1 chr5B.!!$F1 880
10 TraesCS2B01G148300 chr3D 357204091 357204964 873 False 1077.0 1077 88.989 3134 4014 1 chr3D.!!$F1 880
11 TraesCS2B01G148300 chr7D 291596155 291597032 877 True 1070.0 1070 88.814 3134 4014 1 chr7D.!!$R2 880

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
701 739 0.111639 TGTTGGTCCTTGGCCTTACC 59.888 55.0 3.32 6.87 39.84 2.85 F
1631 1693 0.037975 CCCAAGCAACTTGTCATGCC 60.038 55.0 6.58 0.00 43.57 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2625 2700 0.401356 TGGCAGATGAACTTGCCTCA 59.599 50.0 15.62 0.0 40.67 3.86 R
3030 3117 0.036671 AAGCTAACACGTACCAGGCC 60.037 55.0 0.00 0.0 0.00 5.19 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
243 248 4.599047 TCACAAATTTAGCAAGGTTGGG 57.401 40.909 0.00 0.00 0.00 4.12
265 270 4.318050 GGAAAAATGCAACGAAAGAAGCAC 60.318 41.667 0.00 0.00 44.09 4.40
292 297 2.519013 AGTTCCATCCAGAAGTTTGCC 58.481 47.619 0.00 0.00 0.00 4.52
301 306 0.886490 AGAAGTTTGCCTGCACCTCG 60.886 55.000 0.00 0.00 0.00 4.63
329 335 7.603180 AAAAAGTTTAGAATTCCTCTGCCTT 57.397 32.000 0.65 0.00 35.41 4.35
330 336 6.825944 AAAGTTTAGAATTCCTCTGCCTTC 57.174 37.500 0.65 0.00 35.41 3.46
334 340 1.012841 GAATTCCTCTGCCTTCTGCG 58.987 55.000 0.00 0.00 45.60 5.18
340 346 3.571119 CTGCCTTCTGCGGTTCTG 58.429 61.111 0.00 0.00 45.60 3.02
341 347 2.669569 TGCCTTCTGCGGTTCTGC 60.670 61.111 0.00 0.00 45.60 4.26
342 348 3.435186 GCCTTCTGCGGTTCTGCC 61.435 66.667 1.01 0.00 0.00 4.85
343 349 2.747855 CCTTCTGCGGTTCTGCCC 60.748 66.667 1.01 0.00 0.00 5.36
368 374 2.344203 CCAGTCCGCTTCGTCTCCT 61.344 63.158 0.00 0.00 0.00 3.69
369 375 1.030488 CCAGTCCGCTTCGTCTCCTA 61.030 60.000 0.00 0.00 0.00 2.94
379 385 3.800604 GCTTCGTCTCCTATGGCTTTAGG 60.801 52.174 7.52 7.52 40.21 2.69
381 387 1.344763 CGTCTCCTATGGCTTTAGGGG 59.655 57.143 12.29 9.96 40.68 4.79
382 388 2.690840 GTCTCCTATGGCTTTAGGGGA 58.309 52.381 11.27 11.27 44.91 4.81
383 389 3.655972 TCTCCTATGGCTTTAGGGGAT 57.344 47.619 11.27 0.00 42.74 3.85
384 390 3.521727 TCTCCTATGGCTTTAGGGGATC 58.478 50.000 11.27 0.00 42.74 3.36
385 391 3.116356 TCTCCTATGGCTTTAGGGGATCA 60.116 47.826 11.27 0.00 42.74 2.92
386 392 3.848975 CTCCTATGGCTTTAGGGGATCAT 59.151 47.826 7.89 0.00 41.71 2.45
388 394 3.588842 CCTATGGCTTTAGGGGATCATGA 59.411 47.826 0.00 0.00 35.96 3.07
390 396 1.494721 TGGCTTTAGGGGATCATGACC 59.505 52.381 0.00 1.30 0.00 4.02
397 403 3.031916 GGGATCATGACCCATGCTG 57.968 57.895 21.69 0.00 46.05 4.41
398 404 0.538977 GGGATCATGACCCATGCTGG 60.539 60.000 21.69 0.00 46.05 4.85
420 442 1.861575 CGGAGAGCTTCGATTTTAGCC 59.138 52.381 3.24 0.00 38.14 3.93
430 452 4.413495 TCGATTTTAGCCGTTTCTTTGG 57.587 40.909 0.00 0.00 0.00 3.28
442 464 4.364860 CGTTTCTTTGGGTTTTGTTAGGG 58.635 43.478 0.00 0.00 0.00 3.53
446 468 5.601583 TCTTTGGGTTTTGTTAGGGTTTC 57.398 39.130 0.00 0.00 0.00 2.78
448 470 6.433441 TCTTTGGGTTTTGTTAGGGTTTCTA 58.567 36.000 0.00 0.00 0.00 2.10
456 478 4.755266 TGTTAGGGTTTCTATCCTGCTC 57.245 45.455 0.00 0.00 34.75 4.26
470 492 2.811317 GCTCAGGAAGGCGTGACG 60.811 66.667 0.00 0.00 35.30 4.35
471 493 2.125912 CTCAGGAAGGCGTGACGG 60.126 66.667 7.25 0.00 35.30 4.79
490 512 1.424493 GCGGCGGTTCTCTGAAGATG 61.424 60.000 9.78 0.00 0.00 2.90
497 519 5.007136 GGCGGTTCTCTGAAGATGAAATAAG 59.993 44.000 0.00 0.00 0.00 1.73
517 547 4.008916 AGATTCTTTCTACCTAGCCCCA 57.991 45.455 0.00 0.00 30.96 4.96
521 551 3.046374 TCTTTCTACCTAGCCCCATTCC 58.954 50.000 0.00 0.00 0.00 3.01
522 552 2.579624 TTCTACCTAGCCCCATTCCA 57.420 50.000 0.00 0.00 0.00 3.53
524 554 0.398318 CTACCTAGCCCCATTCCAGC 59.602 60.000 0.00 0.00 0.00 4.85
526 556 2.443394 CCTAGCCCCATTCCAGCGA 61.443 63.158 0.00 0.00 0.00 4.93
536 566 1.933181 CATTCCAGCGATGCGTTTAGA 59.067 47.619 0.00 0.00 0.00 2.10
537 567 1.355971 TTCCAGCGATGCGTTTAGAC 58.644 50.000 0.00 0.00 0.00 2.59
548 578 2.128035 GCGTTTAGACTCATCGATGGG 58.872 52.381 23.80 23.80 0.00 4.00
549 579 2.128035 CGTTTAGACTCATCGATGGGC 58.872 52.381 25.25 17.25 0.00 5.36
551 581 1.399714 TTAGACTCATCGATGGGCGT 58.600 50.000 25.25 18.31 41.80 5.68
558 588 3.094062 ATCGATGGGCGTGTGGAGG 62.094 63.158 0.00 0.00 41.80 4.30
566 596 1.664965 GCGTGTGGAGGTGTGTCTC 60.665 63.158 0.00 0.00 0.00 3.36
567 597 2.041976 CGTGTGGAGGTGTGTCTCT 58.958 57.895 0.00 0.00 34.39 3.10
577 607 2.043115 AGGTGTGTCTCTGGTGGATCTA 59.957 50.000 0.00 0.00 0.00 1.98
579 609 3.452627 GGTGTGTCTCTGGTGGATCTATT 59.547 47.826 0.00 0.00 0.00 1.73
587 617 5.250543 TCTCTGGTGGATCTATTTTTGGTGA 59.749 40.000 0.00 0.00 0.00 4.02
592 622 7.638444 TGGTGGATCTATTTTTGGTGAATCTA 58.362 34.615 0.00 0.00 0.00 1.98
596 626 9.056005 TGGATCTATTTTTGGTGAATCTATTCG 57.944 33.333 0.00 0.00 39.62 3.34
600 630 9.273016 TCTATTTTTGGTGAATCTATTCGGATC 57.727 33.333 0.00 0.00 39.62 3.36
611 648 7.175119 TGAATCTATTCGGATCTGTTCGTCTAT 59.825 37.037 0.42 0.00 39.62 1.98
612 649 6.242508 TCTATTCGGATCTGTTCGTCTATG 57.757 41.667 0.42 0.00 0.00 2.23
623 660 4.242475 TGTTCGTCTATGTTCATGTGTCC 58.758 43.478 0.00 0.00 0.00 4.02
625 662 4.371855 TCGTCTATGTTCATGTGTCCTC 57.628 45.455 0.00 0.00 0.00 3.71
626 663 4.017126 TCGTCTATGTTCATGTGTCCTCT 58.983 43.478 0.00 0.00 0.00 3.69
627 664 4.108336 CGTCTATGTTCATGTGTCCTCTG 58.892 47.826 0.00 0.00 0.00 3.35
632 669 2.437651 TGTTCATGTGTCCTCTGGTTGA 59.562 45.455 0.00 0.00 0.00 3.18
635 672 4.371624 TCATGTGTCCTCTGGTTGAATT 57.628 40.909 0.00 0.00 0.00 2.17
636 673 4.326826 TCATGTGTCCTCTGGTTGAATTC 58.673 43.478 0.00 0.00 0.00 2.17
639 676 4.792068 TGTGTCCTCTGGTTGAATTCTTT 58.208 39.130 7.05 0.00 0.00 2.52
644 681 4.937620 TCCTCTGGTTGAATTCTTTCGATG 59.062 41.667 7.05 0.00 34.39 3.84
652 689 7.498900 TGGTTGAATTCTTTCGATGTATGCTAT 59.501 33.333 7.05 0.00 34.39 2.97
657 694 6.530913 TTCTTTCGATGTATGCTATGCTTC 57.469 37.500 0.00 0.00 0.00 3.86
662 699 4.692155 TCGATGTATGCTATGCTTCATTGG 59.308 41.667 0.00 0.00 0.00 3.16
666 703 0.394216 TGCTATGCTTCATTGGCGGT 60.394 50.000 0.00 0.00 0.00 5.68
668 705 1.667236 CTATGCTTCATTGGCGGTGA 58.333 50.000 0.00 0.00 0.00 4.02
671 708 2.121291 TGCTTCATTGGCGGTGATTA 57.879 45.000 0.00 0.00 0.00 1.75
682 720 2.752903 GGCGGTGATTATTTTCTGGTGT 59.247 45.455 0.00 0.00 0.00 4.16
684 722 3.190535 GCGGTGATTATTTTCTGGTGTGT 59.809 43.478 0.00 0.00 0.00 3.72
692 730 2.818751 TTTCTGGTGTGTTGGTCCTT 57.181 45.000 0.00 0.00 0.00 3.36
693 731 2.051334 TTCTGGTGTGTTGGTCCTTG 57.949 50.000 0.00 0.00 0.00 3.61
695 733 1.454847 TGGTGTGTTGGTCCTTGGC 60.455 57.895 0.00 0.00 0.00 4.52
696 734 2.200337 GGTGTGTTGGTCCTTGGCC 61.200 63.158 0.00 0.00 0.00 5.36
697 735 1.152756 GTGTGTTGGTCCTTGGCCT 60.153 57.895 3.32 0.00 0.00 5.19
698 736 0.755327 GTGTGTTGGTCCTTGGCCTT 60.755 55.000 3.32 0.00 0.00 4.35
699 737 0.847373 TGTGTTGGTCCTTGGCCTTA 59.153 50.000 3.32 0.00 0.00 2.69
700 738 1.244816 GTGTTGGTCCTTGGCCTTAC 58.755 55.000 3.32 0.00 0.00 2.34
701 739 0.111639 TGTTGGTCCTTGGCCTTACC 59.888 55.000 3.32 6.87 39.84 2.85
709 747 2.652530 TGGCCTTACCACGACGAC 59.347 61.111 3.32 0.00 46.36 4.34
733 771 5.534207 TCCCGACTTTCTACTACAACAAA 57.466 39.130 0.00 0.00 0.00 2.83
738 776 8.132995 CCCGACTTTCTACTACAACAAATTTTT 58.867 33.333 0.00 0.00 0.00 1.94
741 779 9.459640 GACTTTCTACTACAACAAATTTTTCCC 57.540 33.333 0.00 0.00 0.00 3.97
742 780 8.132995 ACTTTCTACTACAACAAATTTTTCCCG 58.867 33.333 0.00 0.00 0.00 5.14
747 785 2.698274 ACAACAAATTTTTCCCGGCTCT 59.302 40.909 0.00 0.00 0.00 4.09
749 787 2.593026 ACAAATTTTTCCCGGCTCTGA 58.407 42.857 0.00 0.00 0.00 3.27
750 788 3.165071 ACAAATTTTTCCCGGCTCTGAT 58.835 40.909 0.00 0.00 0.00 2.90
792 831 2.042831 GCGCCTTGGCTCACTTCAT 61.043 57.895 10.12 0.00 0.00 2.57
797 836 3.678806 CGCCTTGGCTCACTTCATTACTA 60.679 47.826 10.12 0.00 0.00 1.82
798 837 4.261801 GCCTTGGCTCACTTCATTACTAA 58.738 43.478 4.11 0.00 0.00 2.24
804 843 6.817184 TGGCTCACTTCATTACTAATAGTCC 58.183 40.000 0.00 0.00 0.00 3.85
807 846 7.201920 GGCTCACTTCATTACTAATAGTCCTCA 60.202 40.741 0.00 0.00 0.00 3.86
821 860 2.015587 GTCCTCACTAGGTGGTCTACG 58.984 57.143 0.00 0.00 44.09 3.51
822 861 0.739561 CCTCACTAGGTGGTCTACGC 59.260 60.000 0.00 0.00 38.19 4.42
825 864 3.211865 CTCACTAGGTGGTCTACGCATA 58.788 50.000 0.00 0.00 33.87 3.14
835 874 5.162075 GTGGTCTACGCATATGGAGTATTC 58.838 45.833 4.56 0.00 31.11 1.75
840 879 7.441458 GGTCTACGCATATGGAGTATTCTTTTT 59.559 37.037 4.56 0.00 31.11 1.94
955 1001 1.152567 TGGGCCACAAACCTGAAGG 60.153 57.895 0.00 0.00 42.17 3.46
1084 1130 1.745489 GCTTCCGATGCCGAGGTTT 60.745 57.895 0.00 0.00 38.22 3.27
1151 1197 2.641305 TCGAGAACTGTAGCCCTAGTC 58.359 52.381 0.00 0.00 0.00 2.59
1209 1255 9.003658 GTTCATGGATTATCGAATTAGGACATT 57.996 33.333 0.00 0.00 0.00 2.71
1228 1281 2.554272 CGGTGTAGGTTTGTGCGC 59.446 61.111 0.00 0.00 0.00 6.09
1349 1411 2.360350 CACCGGCTGCTGGAACAT 60.360 61.111 33.15 8.62 38.20 2.71
1361 1423 5.390991 GCTGCTGGAACATAACTTCAGTTAC 60.391 44.000 1.42 0.00 42.55 2.50
1392 1454 4.523943 CCAAACAGATGTTCCAGAATCCAA 59.476 41.667 0.00 0.00 37.25 3.53
1401 1463 3.154827 TCCAGAATCCAAACCTTGTCC 57.845 47.619 0.00 0.00 0.00 4.02
1439 1501 1.741770 AAGGCGTCGGCTCATCAAC 60.742 57.895 22.65 0.00 37.50 3.18
1443 1505 1.781555 CGTCGGCTCATCAACACAC 59.218 57.895 0.00 0.00 0.00 3.82
1452 1514 3.120991 GCTCATCAACACACTTGTCGTAC 60.121 47.826 0.00 0.00 33.55 3.67
1460 1522 6.926826 TCAACACACTTGTCGTACTGATTATT 59.073 34.615 0.00 0.00 33.55 1.40
1461 1523 6.706055 ACACACTTGTCGTACTGATTATTG 57.294 37.500 0.00 0.00 0.00 1.90
1472 1534 5.456186 CGTACTGATTATTGGGGAAGGGATT 60.456 44.000 0.00 0.00 0.00 3.01
1479 1541 7.947890 TGATTATTGGGGAAGGGATTGTATAAC 59.052 37.037 0.00 0.00 0.00 1.89
1510 1572 6.309737 CCACATTTGAAGCTCTGAATTTTAGC 59.690 38.462 0.00 0.00 36.48 3.09
1543 1605 5.012561 ACAGGACAGGGCAGATAATCTAATC 59.987 44.000 0.00 0.00 0.00 1.75
1631 1693 0.037975 CCCAAGCAACTTGTCATGCC 60.038 55.000 6.58 0.00 43.57 4.40
1639 1701 2.231215 ACTTGTCATGCCGCTCTATC 57.769 50.000 0.00 0.00 0.00 2.08
1665 1727 1.607148 CCACTGGCTATGATGCATGTG 59.393 52.381 2.46 2.99 37.40 3.21
1672 1734 5.299949 TGGCTATGATGCATGTGTAACTAG 58.700 41.667 2.46 0.00 33.79 2.57
1732 1794 4.222886 TGTTTTGTTGACACTTGACGTTG 58.777 39.130 0.00 0.00 0.00 4.10
1733 1795 3.479505 TTTGTTGACACTTGACGTTGG 57.520 42.857 0.00 0.00 0.00 3.77
1782 1844 5.163322 TGGAAAACTTACTGGAGTCGGTTTA 60.163 40.000 9.14 0.00 34.37 2.01
1899 1962 0.322008 GTTGCCTGTCTAGCTGCCTT 60.322 55.000 0.00 0.00 0.00 4.35
1905 1968 2.170187 CCTGTCTAGCTGCCTTCAGAAT 59.830 50.000 0.00 0.00 42.95 2.40
1906 1969 3.370315 CCTGTCTAGCTGCCTTCAGAATT 60.370 47.826 0.00 0.00 42.95 2.17
1907 1970 4.141846 CCTGTCTAGCTGCCTTCAGAATTA 60.142 45.833 0.00 0.00 42.95 1.40
1908 1971 4.759782 TGTCTAGCTGCCTTCAGAATTAC 58.240 43.478 0.00 0.00 42.95 1.89
1909 1972 3.799420 GTCTAGCTGCCTTCAGAATTACG 59.201 47.826 0.00 0.00 42.95 3.18
1910 1973 2.029838 AGCTGCCTTCAGAATTACGG 57.970 50.000 0.00 0.00 42.95 4.02
1911 1974 1.555075 AGCTGCCTTCAGAATTACGGA 59.445 47.619 0.00 0.00 42.95 4.69
1912 1975 1.936547 GCTGCCTTCAGAATTACGGAG 59.063 52.381 0.00 0.00 42.95 4.63
1925 1988 4.768130 ATTACGGAGTACGATCCATCAG 57.232 45.455 0.00 0.00 45.76 2.90
1957 2027 7.833682 TGGTGTCCTAACATATTGATTTGACAT 59.166 33.333 0.00 0.00 37.81 3.06
2141 2214 4.139786 TCTACTACCTATACCAACGGCTG 58.860 47.826 0.00 0.00 0.00 4.85
2166 2239 5.698089 TGCTCATGCTGTATGAATAAGTAGC 59.302 40.000 9.67 8.07 44.84 3.58
2169 2242 5.991606 TCATGCTGTATGAATAAGTAGCACC 59.008 40.000 5.94 0.00 42.69 5.01
2178 2251 0.252375 TAAGTAGCACCCCCTCCGTT 60.252 55.000 0.00 0.00 0.00 4.44
2277 2351 2.996444 CAATCCTGCAGCGATGCTA 58.004 52.632 27.55 12.66 36.40 3.49
2280 2354 1.406065 ATCCTGCAGCGATGCTACCT 61.406 55.000 27.55 6.37 36.40 3.08
2309 2383 9.829507 TTTGTTTCTTTATTGATGGTGAACAAT 57.170 25.926 0.00 0.00 39.53 2.71
2310 2384 9.474920 TTGTTTCTTTATTGATGGTGAACAATC 57.525 29.630 0.00 0.00 37.75 2.67
2322 2396 4.950475 TGGTGAACAATCCAAAGTGTGTTA 59.050 37.500 0.00 0.00 33.19 2.41
2358 2432 3.883779 CATGGAATGCGAAGACACG 57.116 52.632 0.00 0.00 37.62 4.49
2405 2479 9.020731 TCTATTGCACGGATGTCTTAATAGATA 57.979 33.333 0.00 0.00 33.30 1.98
2406 2480 9.295214 CTATTGCACGGATGTCTTAATAGATAG 57.705 37.037 0.00 0.00 31.59 2.08
2407 2481 6.025749 TGCACGGATGTCTTAATAGATAGG 57.974 41.667 0.00 0.00 31.86 2.57
2457 2531 4.522789 ACACATGTGTCCCCTAAATGTTTC 59.477 41.667 25.76 0.00 40.24 2.78
2465 2539 5.311121 TGTCCCCTAAATGTTTCCTGTCTTA 59.689 40.000 0.00 0.00 0.00 2.10
2576 2651 4.141482 TGGGTATTTAGGAGGAGCATGTTC 60.141 45.833 0.04 0.04 0.00 3.18
2622 2697 1.408822 CCTTGTTCACTAGATGGCCCC 60.409 57.143 0.00 0.00 0.00 5.80
2625 2700 1.273838 TGTTCACTAGATGGCCCCTCT 60.274 52.381 0.00 5.08 0.00 3.69
2876 2955 1.373570 GACAATCAAAGAGGCGGAGG 58.626 55.000 0.00 0.00 0.00 4.30
2906 2985 2.433970 AGAAGCCTCTGATAAGCTGGAC 59.566 50.000 0.00 0.00 36.84 4.02
2921 3000 3.577415 AGCTGGACCTCGTAAAACTAGTT 59.423 43.478 1.12 1.12 0.00 2.24
2928 3007 7.816031 TGGACCTCGTAAAACTAGTTCTATTTG 59.184 37.037 8.95 0.00 0.00 2.32
2942 3021 5.069781 AGTTCTATTTGGGATTCGAGAGAGG 59.930 44.000 0.00 0.00 43.69 3.69
2974 3053 2.930887 GCAAACCTGTCTATGTGCTCGA 60.931 50.000 0.00 0.00 0.00 4.04
2982 3061 3.056891 TGTCTATGTGCTCGATGTTGACA 60.057 43.478 0.00 0.00 0.00 3.58
2999 3078 6.295249 TGTTGACATCATTGTTGGAGTTAGA 58.705 36.000 0.16 0.00 35.79 2.10
3009 3096 9.349713 TCATTGTTGGAGTTAGATTAAACTGTT 57.650 29.630 0.00 0.00 39.78 3.16
3010 3097 9.398170 CATTGTTGGAGTTAGATTAAACTGTTG 57.602 33.333 0.00 0.00 39.78 3.33
3012 3099 8.149973 TGTTGGAGTTAGATTAAACTGTTGTC 57.850 34.615 0.00 0.00 39.78 3.18
3014 3101 7.074653 TGGAGTTAGATTAAACTGTTGTCCT 57.925 36.000 0.00 0.00 39.78 3.85
3018 3105 7.963532 AGTTAGATTAAACTGTTGTCCTGAGA 58.036 34.615 0.00 0.00 38.28 3.27
3030 3117 5.416639 TGTTGTCCTGAGATTGATGAAATGG 59.583 40.000 0.00 0.00 0.00 3.16
3032 3119 3.317430 GTCCTGAGATTGATGAAATGGGC 59.683 47.826 0.00 0.00 0.00 5.36
3044 3131 0.111639 AAATGGGCCTGGTACGTGTT 59.888 50.000 4.53 0.00 0.00 3.32
3051 3138 2.159000 GGCCTGGTACGTGTTAGCTTAT 60.159 50.000 0.00 0.00 0.00 1.73
3052 3139 3.068590 GGCCTGGTACGTGTTAGCTTATA 59.931 47.826 0.00 0.00 0.00 0.98
3053 3140 4.262335 GGCCTGGTACGTGTTAGCTTATAT 60.262 45.833 0.00 0.00 0.00 0.86
3074 3161 9.710900 TTATATAGCAGTAATGTGTTGATCAGG 57.289 33.333 0.00 0.00 0.00 3.86
3075 3162 3.012518 AGCAGTAATGTGTTGATCAGGC 58.987 45.455 0.00 0.00 0.00 4.85
3083 3170 3.466836 TGTGTTGATCAGGCCGATTATC 58.533 45.455 10.72 7.03 33.17 1.75
3104 3191 0.091344 GTGTCGACGAACATTGAGCG 59.909 55.000 11.62 0.00 0.00 5.03
3119 3210 3.186047 GCGGCGTGTTGCTATCGT 61.186 61.111 9.37 0.00 45.43 3.73
3140 3231 4.091365 CGTAGCAAAAGATGAATGTCGTGA 59.909 41.667 0.00 0.00 0.00 4.35
3147 3238 7.306749 GCAAAAGATGAATGTCGTGAAATTGTT 60.307 33.333 0.00 0.00 0.00 2.83
3149 3240 8.955061 AAAGATGAATGTCGTGAAATTGTTAG 57.045 30.769 0.00 0.00 0.00 2.34
3257 3352 4.336993 ACGCAACACAAGACAAGGATTTAA 59.663 37.500 0.00 0.00 0.00 1.52
3259 3354 5.399301 CGCAACACAAGACAAGGATTTAAAG 59.601 40.000 0.00 0.00 0.00 1.85
3272 3367 2.694616 TTTAAAGAGCTTTGGGCCCT 57.305 45.000 25.70 0.15 43.05 5.19
3317 3412 3.823873 CCCTACATGTTGTTTGTGGCTAA 59.176 43.478 2.30 0.00 0.00 3.09
3328 3423 7.880713 TGTTGTTTGTGGCTAAGTCTCATTATA 59.119 33.333 0.00 0.00 0.00 0.98
3353 3448 3.459063 GGGAGTCGCCGGTAAGCT 61.459 66.667 1.90 0.00 37.63 3.74
3354 3449 2.123428 GGGAGTCGCCGGTAAGCTA 61.123 63.158 1.90 0.00 37.63 3.32
3361 3456 1.448922 CGCCGGTAAGCTAGCTCTCT 61.449 60.000 19.65 5.00 0.00 3.10
3363 3458 1.137282 GCCGGTAAGCTAGCTCTCTTT 59.863 52.381 19.65 4.14 0.00 2.52
3364 3459 2.361438 GCCGGTAAGCTAGCTCTCTTTA 59.639 50.000 19.65 3.00 0.00 1.85
3365 3460 3.551250 GCCGGTAAGCTAGCTCTCTTTAG 60.551 52.174 19.65 5.30 0.00 1.85
3369 3466 6.432107 CGGTAAGCTAGCTCTCTTTAGTTAG 58.568 44.000 19.65 0.00 34.44 2.34
3403 3509 2.110721 AGATTGTTTCTTGCCTCCCCTT 59.889 45.455 0.00 0.00 0.00 3.95
3460 3566 0.538118 GGCGGGTTACATGTGGAGTA 59.462 55.000 9.11 0.00 0.00 2.59
3625 3731 1.112113 GTCTTCTATCTGACCCGCCA 58.888 55.000 0.00 0.00 0.00 5.69
3669 3776 1.087501 CTCGTGAGTCGTCTGATCCA 58.912 55.000 0.00 0.00 40.80 3.41
3747 3855 2.004733 GTCTGGCCGCGTTATACTTTT 58.995 47.619 4.92 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
225 230 6.934048 TTTTTCCCAACCTTGCTAAATTTG 57.066 33.333 0.00 0.00 0.00 2.32
231 236 2.968574 TGCATTTTTCCCAACCTTGCTA 59.031 40.909 0.00 0.00 0.00 3.49
232 237 1.767681 TGCATTTTTCCCAACCTTGCT 59.232 42.857 0.00 0.00 0.00 3.91
243 248 4.504097 AGTGCTTCTTTCGTTGCATTTTTC 59.496 37.500 0.00 0.00 37.76 2.29
265 270 4.583871 ACTTCTGGATGGAACTAGCAAAG 58.416 43.478 0.00 0.00 0.00 2.77
276 281 0.529378 GCAGGCAAACTTCTGGATGG 59.471 55.000 0.00 0.00 0.00 3.51
280 285 0.825010 AGGTGCAGGCAAACTTCTGG 60.825 55.000 0.00 0.00 0.00 3.86
311 317 4.265073 GCAGAAGGCAGAGGAATTCTAAA 58.735 43.478 5.23 0.00 43.97 1.85
313 319 2.159043 CGCAGAAGGCAGAGGAATTCTA 60.159 50.000 5.23 0.00 45.17 2.10
316 322 0.393537 CCGCAGAAGGCAGAGGAATT 60.394 55.000 0.00 0.00 45.17 2.17
317 323 1.222936 CCGCAGAAGGCAGAGGAAT 59.777 57.895 0.00 0.00 45.17 3.01
325 331 3.435186 GGCAGAACCGCAGAAGGC 61.435 66.667 0.00 0.00 39.90 4.35
350 356 1.030488 TAGGAGACGAAGCGGACTGG 61.030 60.000 0.00 0.00 0.00 4.00
352 358 1.025812 CATAGGAGACGAAGCGGACT 58.974 55.000 0.00 0.00 0.00 3.85
359 365 2.698797 CCCTAAAGCCATAGGAGACGAA 59.301 50.000 12.82 0.00 44.46 3.85
362 368 2.690840 TCCCCTAAAGCCATAGGAGAC 58.309 52.381 12.82 0.00 44.46 3.36
368 374 3.330701 GGTCATGATCCCCTAAAGCCATA 59.669 47.826 0.00 0.00 0.00 2.74
369 375 2.108952 GGTCATGATCCCCTAAAGCCAT 59.891 50.000 0.00 0.00 0.00 4.40
379 385 3.031916 CAGCATGGGTCATGATCCC 57.968 57.895 22.55 21.33 43.81 3.85
391 397 3.694058 AAGCTCTCCGCCCAGCATG 62.694 63.158 0.00 0.00 40.39 4.06
392 398 3.397613 GAAGCTCTCCGCCCAGCAT 62.398 63.158 0.00 0.00 40.39 3.79
393 399 4.087892 GAAGCTCTCCGCCCAGCA 62.088 66.667 0.00 0.00 40.39 4.41
395 401 2.303549 AATCGAAGCTCTCCGCCCAG 62.304 60.000 0.00 0.00 40.39 4.45
396 402 1.899437 AAATCGAAGCTCTCCGCCCA 61.899 55.000 0.00 0.00 40.39 5.36
397 403 0.744771 AAAATCGAAGCTCTCCGCCC 60.745 55.000 0.00 0.00 40.39 6.13
398 404 1.861575 CTAAAATCGAAGCTCTCCGCC 59.138 52.381 0.00 0.00 40.39 6.13
399 405 1.259244 GCTAAAATCGAAGCTCTCCGC 59.741 52.381 0.00 0.00 35.80 5.54
401 407 1.861575 CGGCTAAAATCGAAGCTCTCC 59.138 52.381 6.77 0.00 38.80 3.71
402 408 2.541556 ACGGCTAAAATCGAAGCTCTC 58.458 47.619 6.77 0.00 38.80 3.20
403 409 2.674796 ACGGCTAAAATCGAAGCTCT 57.325 45.000 6.77 0.00 38.80 4.09
404 410 3.371285 AGAAACGGCTAAAATCGAAGCTC 59.629 43.478 6.77 0.00 38.80 4.09
406 412 3.741805 AGAAACGGCTAAAATCGAAGC 57.258 42.857 0.00 0.00 38.03 3.86
407 413 4.851558 CCAAAGAAACGGCTAAAATCGAAG 59.148 41.667 0.00 0.00 0.00 3.79
409 415 3.189702 CCCAAAGAAACGGCTAAAATCGA 59.810 43.478 0.00 0.00 0.00 3.59
411 417 4.514781 ACCCAAAGAAACGGCTAAAATC 57.485 40.909 0.00 0.00 0.00 2.17
412 418 4.948341 AACCCAAAGAAACGGCTAAAAT 57.052 36.364 0.00 0.00 0.00 1.82
420 442 4.142116 ACCCTAACAAAACCCAAAGAAACG 60.142 41.667 0.00 0.00 0.00 3.60
430 452 5.105877 GCAGGATAGAAACCCTAACAAAACC 60.106 44.000 0.00 0.00 0.00 3.27
470 492 2.579684 ATCTTCAGAGAACCGCCGCC 62.580 60.000 0.00 0.00 35.07 6.13
471 493 1.153549 ATCTTCAGAGAACCGCCGC 60.154 57.895 0.00 0.00 35.07 6.53
490 512 7.662258 GGGGCTAGGTAGAAAGAATCTTATTTC 59.338 40.741 0.00 2.58 39.71 2.17
497 519 4.984146 ATGGGGCTAGGTAGAAAGAATC 57.016 45.455 0.00 0.00 0.00 2.52
504 526 2.040144 GCTGGAATGGGGCTAGGTAGA 61.040 57.143 0.00 0.00 0.00 2.59
506 528 1.407656 CGCTGGAATGGGGCTAGGTA 61.408 60.000 0.00 0.00 0.00 3.08
517 547 1.933853 GTCTAAACGCATCGCTGGAAT 59.066 47.619 0.00 0.00 0.00 3.01
521 551 1.629013 TGAGTCTAAACGCATCGCTG 58.371 50.000 0.00 0.00 29.56 5.18
522 552 2.586258 ATGAGTCTAAACGCATCGCT 57.414 45.000 0.00 0.00 41.40 4.93
526 556 3.384668 CCATCGATGAGTCTAAACGCAT 58.615 45.455 26.86 0.00 46.89 4.73
536 566 1.153568 CACACGCCCATCGATGAGT 60.154 57.895 26.86 18.84 41.67 3.41
537 567 1.884464 CCACACGCCCATCGATGAG 60.884 63.158 26.86 15.28 41.67 2.90
544 574 3.249189 ACACCTCCACACGCCCAT 61.249 61.111 0.00 0.00 0.00 4.00
548 578 1.664965 GAGACACACCTCCACACGC 60.665 63.158 0.00 0.00 0.00 5.34
549 579 0.319040 CAGAGACACACCTCCACACG 60.319 60.000 0.00 0.00 33.76 4.49
551 581 0.398522 ACCAGAGACACACCTCCACA 60.399 55.000 0.00 0.00 33.76 4.17
558 588 4.744795 AATAGATCCACCAGAGACACAC 57.255 45.455 0.00 0.00 0.00 3.82
566 596 6.604795 AGATTCACCAAAAATAGATCCACCAG 59.395 38.462 0.00 0.00 0.00 4.00
567 597 6.493166 AGATTCACCAAAAATAGATCCACCA 58.507 36.000 0.00 0.00 0.00 4.17
577 607 7.557719 ACAGATCCGAATAGATTCACCAAAAAT 59.442 33.333 3.31 0.00 36.61 1.82
579 609 6.414732 ACAGATCCGAATAGATTCACCAAAA 58.585 36.000 3.31 0.00 36.61 2.44
587 617 5.776173 AGACGAACAGATCCGAATAGATT 57.224 39.130 0.00 0.00 0.00 2.40
592 622 4.920640 ACATAGACGAACAGATCCGAAT 57.079 40.909 0.00 0.00 0.00 3.34
595 625 4.028852 TGAACATAGACGAACAGATCCG 57.971 45.455 0.00 0.00 0.00 4.18
596 626 5.233050 CACATGAACATAGACGAACAGATCC 59.767 44.000 0.00 0.00 0.00 3.36
600 630 4.327357 GGACACATGAACATAGACGAACAG 59.673 45.833 0.00 0.00 0.00 3.16
611 648 2.437651 TCAACCAGAGGACACATGAACA 59.562 45.455 0.00 0.00 0.00 3.18
612 649 3.126001 TCAACCAGAGGACACATGAAC 57.874 47.619 0.00 0.00 0.00 3.18
636 673 5.912360 TGAAGCATAGCATACATCGAAAG 57.088 39.130 0.00 0.00 0.00 2.62
639 676 4.692155 CCAATGAAGCATAGCATACATCGA 59.308 41.667 0.00 0.00 0.00 3.59
644 681 2.095567 CCGCCAATGAAGCATAGCATAC 60.096 50.000 0.00 0.00 0.00 2.39
652 689 2.121291 TAATCACCGCCAATGAAGCA 57.879 45.000 0.00 0.00 0.00 3.91
657 694 4.142182 ACCAGAAAATAATCACCGCCAATG 60.142 41.667 0.00 0.00 0.00 2.82
662 699 3.190535 ACACACCAGAAAATAATCACCGC 59.809 43.478 0.00 0.00 0.00 5.68
666 703 5.242838 GGACCAACACACCAGAAAATAATCA 59.757 40.000 0.00 0.00 0.00 2.57
668 705 5.393866 AGGACCAACACACCAGAAAATAAT 58.606 37.500 0.00 0.00 0.00 1.28
671 708 3.312736 AGGACCAACACACCAGAAAAT 57.687 42.857 0.00 0.00 0.00 1.82
682 720 0.111639 GGTAAGGCCAAGGACCAACA 59.888 55.000 5.01 0.00 37.17 3.33
684 722 2.558066 TGGTAAGGCCAAGGACCAA 58.442 52.632 5.01 0.00 45.94 3.67
692 730 1.466025 AAGTCGTCGTGGTAAGGCCA 61.466 55.000 5.01 0.00 46.95 5.36
693 731 0.735287 GAAGTCGTCGTGGTAAGGCC 60.735 60.000 0.00 0.00 37.90 5.19
695 733 0.108945 GGGAAGTCGTCGTGGTAAGG 60.109 60.000 0.00 0.00 0.00 2.69
696 734 0.455633 CGGGAAGTCGTCGTGGTAAG 60.456 60.000 0.00 0.00 0.00 2.34
697 735 0.888736 TCGGGAAGTCGTCGTGGTAA 60.889 55.000 0.00 0.00 0.00 2.85
698 736 1.302431 TCGGGAAGTCGTCGTGGTA 60.302 57.895 0.00 0.00 0.00 3.25
699 737 2.595463 TCGGGAAGTCGTCGTGGT 60.595 61.111 0.00 0.00 0.00 4.16
700 738 2.126580 GTCGGGAAGTCGTCGTGG 60.127 66.667 0.00 0.00 0.00 4.94
701 739 0.318445 AAAGTCGGGAAGTCGTCGTG 60.318 55.000 0.00 0.00 0.00 4.35
702 740 0.039708 GAAAGTCGGGAAGTCGTCGT 60.040 55.000 0.00 0.00 0.00 4.34
703 741 0.240411 AGAAAGTCGGGAAGTCGTCG 59.760 55.000 0.00 0.00 0.00 5.12
704 742 2.487372 AGTAGAAAGTCGGGAAGTCGTC 59.513 50.000 0.00 0.00 0.00 4.20
705 743 2.512705 AGTAGAAAGTCGGGAAGTCGT 58.487 47.619 0.00 0.00 0.00 4.34
709 747 5.130292 TGTTGTAGTAGAAAGTCGGGAAG 57.870 43.478 0.00 0.00 0.00 3.46
733 771 2.648059 CTCATCAGAGCCGGGAAAAAT 58.352 47.619 2.18 0.00 34.61 1.82
738 776 2.444706 CCCTCATCAGAGCCGGGA 60.445 66.667 2.18 0.00 40.68 5.14
741 779 2.506061 CCCTCCCTCATCAGAGCCG 61.506 68.421 0.00 0.00 40.68 5.52
742 780 2.146061 CCCCTCCCTCATCAGAGCC 61.146 68.421 0.00 0.00 40.68 4.70
747 785 2.142761 CATCGCCCCTCCCTCATCA 61.143 63.158 0.00 0.00 0.00 3.07
749 787 2.143419 GTCATCGCCCCTCCCTCAT 61.143 63.158 0.00 0.00 0.00 2.90
750 788 2.764128 GTCATCGCCCCTCCCTCA 60.764 66.667 0.00 0.00 0.00 3.86
781 819 7.056844 AGGACTATTAGTAATGAAGTGAGCC 57.943 40.000 5.61 0.96 0.00 4.70
804 843 1.460504 TGCGTAGACCACCTAGTGAG 58.539 55.000 0.00 0.00 35.23 3.51
807 846 2.891580 CCATATGCGTAGACCACCTAGT 59.108 50.000 0.00 0.00 0.00 2.57
876 919 2.390938 GTTGCAAGCTTAAACGAACCC 58.609 47.619 0.00 0.00 0.00 4.11
955 1001 0.473326 ATGAGCTGGATGGGAAGAGC 59.527 55.000 0.00 0.00 0.00 4.09
1084 1130 1.679305 GGAGGAGACAGACGGAGCA 60.679 63.158 0.00 0.00 0.00 4.26
1116 1162 1.941294 TCTCGAACGGAGCAGAGATAC 59.059 52.381 0.00 0.00 42.82 2.24
1117 1163 2.327200 TCTCGAACGGAGCAGAGATA 57.673 50.000 0.00 0.00 42.82 1.98
1151 1197 2.480416 CCTTAGCGCACCAGACTTCTAG 60.480 54.545 11.47 0.00 0.00 2.43
1209 1255 2.248135 CGCACAAACCTACACCGCA 61.248 57.895 0.00 0.00 0.00 5.69
1228 1281 2.527547 GAAATCAAGCCCACCACGCG 62.528 60.000 3.53 3.53 0.00 6.01
1349 1411 4.643463 TGGGAATTGCGTAACTGAAGTTA 58.357 39.130 0.00 0.00 39.31 2.24
1361 1423 3.244976 GAACATCTGTTTGGGAATTGCG 58.755 45.455 0.00 0.00 38.56 4.85
1392 1454 3.774766 AGAAAAGCAAAAGGGACAAGGTT 59.225 39.130 0.00 0.00 0.00 3.50
1401 1463 4.301628 CTTGGCTACAGAAAAGCAAAAGG 58.698 43.478 0.00 0.00 41.93 3.11
1427 1489 1.202639 ACAAGTGTGTTGATGAGCCGA 60.203 47.619 0.00 0.00 32.58 5.54
1439 1501 5.063438 CCCAATAATCAGTACGACAAGTGTG 59.937 44.000 0.00 0.00 0.00 3.82
1443 1505 5.018539 TCCCCAATAATCAGTACGACAAG 57.981 43.478 0.00 0.00 0.00 3.16
1452 1514 4.808042 ACAATCCCTTCCCCAATAATCAG 58.192 43.478 0.00 0.00 0.00 2.90
1460 1522 5.806955 AAAGTTATACAATCCCTTCCCCA 57.193 39.130 0.00 0.00 0.00 4.96
1461 1523 5.163447 GCAAAAGTTATACAATCCCTTCCCC 60.163 44.000 0.00 0.00 0.00 4.81
1472 1534 6.644592 GCTTCAAATGTGGCAAAAGTTATACA 59.355 34.615 0.00 0.00 0.00 2.29
1479 1541 3.739300 CAGAGCTTCAAATGTGGCAAAAG 59.261 43.478 0.00 0.00 0.00 2.27
1510 1572 3.941483 CTGCCCTGTCCTGTAATAACAAG 59.059 47.826 0.00 0.00 34.49 3.16
1543 1605 2.756760 CCTCCATCTGTGAATTTGTGGG 59.243 50.000 0.00 0.00 0.00 4.61
1631 1693 0.593518 CAGTGGCAGACGATAGAGCG 60.594 60.000 0.00 0.00 41.38 5.03
1665 1727 8.010540 GCTCAAAGAACAGCTAAAACTAGTTAC 58.989 37.037 8.92 0.00 32.48 2.50
1672 1734 6.208644 TCATTGCTCAAAGAACAGCTAAAAC 58.791 36.000 0.00 0.00 36.53 2.43
1732 1794 2.658285 TCCATGTGGCAGATCATTTCC 58.342 47.619 0.00 0.00 34.44 3.13
1733 1795 3.490419 GCTTCCATGTGGCAGATCATTTC 60.490 47.826 2.77 0.00 29.45 2.17
1782 1844 4.337836 TCAAGCACAACATAACACACACAT 59.662 37.500 0.00 0.00 0.00 3.21
1899 1962 4.201657 TGGATCGTACTCCGTAATTCTGA 58.798 43.478 0.00 0.00 38.21 3.27
1905 1968 3.562973 GTCTGATGGATCGTACTCCGTAA 59.437 47.826 0.00 0.00 38.21 3.18
1906 1969 3.136763 GTCTGATGGATCGTACTCCGTA 58.863 50.000 0.00 0.00 38.21 4.02
1907 1970 1.948145 GTCTGATGGATCGTACTCCGT 59.052 52.381 0.00 0.00 38.21 4.69
1908 1971 1.267261 GGTCTGATGGATCGTACTCCG 59.733 57.143 0.00 0.00 38.21 4.63
1909 1972 2.034812 GTGGTCTGATGGATCGTACTCC 59.965 54.545 0.00 0.00 35.74 3.85
1910 1973 2.952978 AGTGGTCTGATGGATCGTACTC 59.047 50.000 0.00 0.00 0.00 2.59
1911 1974 2.690497 CAGTGGTCTGATGGATCGTACT 59.310 50.000 0.00 0.00 43.76 2.73
1912 1975 2.223829 CCAGTGGTCTGATGGATCGTAC 60.224 54.545 0.00 0.00 43.76 3.67
1925 1988 4.755266 ATATGTTAGGACACCAGTGGTC 57.245 45.455 13.31 1.44 38.91 4.02
1957 2027 3.637911 AAATTGCGTCTATACCCACCA 57.362 42.857 0.00 0.00 0.00 4.17
2098 2171 4.018960 AGAGCAACATCCCAAGATTAGTGT 60.019 41.667 0.00 0.00 0.00 3.55
2099 2172 4.521146 AGAGCAACATCCCAAGATTAGTG 58.479 43.478 0.00 0.00 0.00 2.74
2141 2214 5.998454 ACTTATTCATACAGCATGAGCAC 57.002 39.130 0.00 0.00 44.47 4.40
2166 2239 0.843984 ATTATGGAACGGAGGGGGTG 59.156 55.000 0.00 0.00 0.00 4.61
2169 2242 6.171213 GTTCTTATATTATGGAACGGAGGGG 58.829 44.000 7.88 0.00 0.00 4.79
2237 2311 6.461110 TGCTAAAAATAGTACTACTCCGCT 57.539 37.500 4.31 0.00 0.00 5.52
2238 2312 7.095732 GGATTGCTAAAAATAGTACTACTCCGC 60.096 40.741 4.31 4.53 0.00 5.54
2277 2351 7.710475 CACCATCAATAAAGAAACAAAACAGGT 59.290 33.333 0.00 0.00 0.00 4.00
2280 2354 9.092876 GTTCACCATCAATAAAGAAACAAAACA 57.907 29.630 0.00 0.00 0.00 2.83
2309 2383 7.285629 TGGTCAAATACATTAACACACTTTGGA 59.714 33.333 0.00 0.00 0.00 3.53
2310 2384 7.429633 TGGTCAAATACATTAACACACTTTGG 58.570 34.615 0.00 0.00 0.00 3.28
2322 2396 5.857471 CCATGTGGATGGTCAAATACATT 57.143 39.130 0.00 0.00 43.98 2.71
2435 2509 4.082245 GGAAACATTTAGGGGACACATGTG 60.082 45.833 24.25 24.25 29.88 3.21
2457 2531 6.605119 AGGATTCCACCATAAATAAGACAGG 58.395 40.000 5.29 0.00 0.00 4.00
2576 2651 2.509052 TGTGAGGTGTCTCTTTCACG 57.491 50.000 0.00 0.00 42.09 4.35
2622 2697 2.008329 GCAGATGAACTTGCCTCAGAG 58.992 52.381 0.00 0.00 0.00 3.35
2625 2700 0.401356 TGGCAGATGAACTTGCCTCA 59.599 50.000 15.62 0.00 40.67 3.86
2674 2749 2.624838 CAGCAAGACATTCTTTGGTGGT 59.375 45.455 8.15 0.00 33.78 4.16
2876 2955 4.605640 ATCAGAGGCTTCTCTATCTTGC 57.394 45.455 0.00 0.00 45.45 4.01
2906 2985 7.325694 TCCCAAATAGAACTAGTTTTACGAGG 58.674 38.462 10.02 10.25 0.00 4.63
2921 3000 3.322254 GCCTCTCTCGAATCCCAAATAGA 59.678 47.826 0.00 0.00 0.00 1.98
2928 3007 0.249114 GAACGCCTCTCTCGAATCCC 60.249 60.000 0.00 0.00 0.00 3.85
2974 3053 6.942005 TCTAACTCCAACAATGATGTCAACAT 59.058 34.615 0.00 0.00 39.40 2.71
2982 3061 9.520515 ACAGTTTAATCTAACTCCAACAATGAT 57.479 29.630 0.00 0.00 36.24 2.45
2985 3064 9.131791 ACAACAGTTTAATCTAACTCCAACAAT 57.868 29.630 0.00 0.00 36.24 2.71
2986 3065 8.514330 ACAACAGTTTAATCTAACTCCAACAA 57.486 30.769 0.00 0.00 36.24 2.83
2997 3076 7.453393 TCAATCTCAGGACAACAGTTTAATCT 58.547 34.615 0.00 0.00 0.00 2.40
2999 3078 7.884877 TCATCAATCTCAGGACAACAGTTTAAT 59.115 33.333 0.00 0.00 0.00 1.40
3009 3096 4.529897 CCCATTTCATCAATCTCAGGACA 58.470 43.478 0.00 0.00 0.00 4.02
3010 3097 3.317430 GCCCATTTCATCAATCTCAGGAC 59.683 47.826 0.00 0.00 0.00 3.85
3012 3099 2.626743 GGCCCATTTCATCAATCTCAGG 59.373 50.000 0.00 0.00 0.00 3.86
3014 3101 3.293337 CAGGCCCATTTCATCAATCTCA 58.707 45.455 0.00 0.00 0.00 3.27
3018 3105 2.555732 ACCAGGCCCATTTCATCAAT 57.444 45.000 0.00 0.00 0.00 2.57
3030 3117 0.036671 AAGCTAACACGTACCAGGCC 60.037 55.000 0.00 0.00 0.00 5.19
3051 3138 5.991606 GCCTGATCAACACATTACTGCTATA 59.008 40.000 0.00 0.00 0.00 1.31
3052 3139 4.818546 GCCTGATCAACACATTACTGCTAT 59.181 41.667 0.00 0.00 0.00 2.97
3053 3140 4.191544 GCCTGATCAACACATTACTGCTA 58.808 43.478 0.00 0.00 0.00 3.49
3065 3152 2.069273 CGGATAATCGGCCTGATCAAC 58.931 52.381 0.00 0.00 35.84 3.18
3074 3161 1.266786 CGTCGACACGGATAATCGGC 61.267 60.000 17.16 0.00 42.73 5.54
3075 3162 0.305617 TCGTCGACACGGATAATCGG 59.694 55.000 17.16 0.00 46.70 4.18
3083 3170 0.708370 CTCAATGTTCGTCGACACGG 59.292 55.000 17.16 0.00 46.70 4.94
3119 3210 6.552859 TTTCACGACATTCATCTTTTGCTA 57.447 33.333 0.00 0.00 0.00 3.49
3140 3231 4.322057 AGGACATCTGCCCTAACAATTT 57.678 40.909 0.00 0.00 0.00 1.82
3147 3238 3.116096 ACACTAAGGACATCTGCCCTA 57.884 47.619 0.00 0.00 31.36 3.53
3149 3240 3.798202 CTTACACTAAGGACATCTGCCC 58.202 50.000 0.00 0.00 32.17 5.36
3259 3354 2.730129 TTTCCCAGGGCCCAAAGCTC 62.730 60.000 27.56 0.00 45.27 4.09
3272 3367 3.943671 ATTACCGGATGATGTTTCCCA 57.056 42.857 9.46 0.00 0.00 4.37
3328 3423 1.443407 CGGCGACTCCCTCATGATT 59.557 57.895 0.00 0.00 0.00 2.57
3353 3448 6.063404 GGCTAGACCTAACTAAAGAGAGCTA 58.937 44.000 0.00 0.00 34.51 3.32
3354 3449 4.891168 GGCTAGACCTAACTAAAGAGAGCT 59.109 45.833 0.00 0.00 34.51 4.09
3361 3456 6.587560 TCTCTAGGGCTAGACCTAACTAAA 57.412 41.667 24.97 3.92 42.32 1.85
3363 3458 6.102910 ACAATCTCTAGGGCTAGACCTAACTA 59.897 42.308 24.97 13.07 42.32 2.24
3364 3459 5.103430 ACAATCTCTAGGGCTAGACCTAACT 60.103 44.000 24.97 7.38 42.32 2.24
3365 3460 5.141910 ACAATCTCTAGGGCTAGACCTAAC 58.858 45.833 24.97 0.00 42.32 2.34
3369 3466 4.651962 AGAAACAATCTCTAGGGCTAGACC 59.348 45.833 6.47 6.47 37.28 3.85
3423 3529 5.021458 CCCGCCCCTCTAACTTATATAAGA 58.979 45.833 25.83 6.60 37.08 2.10
3497 3603 4.702131 GCAAGACCCAGACTTGTATTCAAT 59.298 41.667 0.00 0.00 44.25 2.57
3625 3731 1.414181 CGACTCACAGATGGCCCTAAT 59.586 52.381 0.00 0.00 0.00 1.73
3637 3743 3.295273 ACGAGCTGGCGACTCACA 61.295 61.111 1.33 0.00 33.58 3.58
3736 3844 1.667212 GACCCGGCCAAAAGTATAACG 59.333 52.381 2.24 0.00 0.00 3.18
3739 3847 3.181452 GGTATGACCCGGCCAAAAGTATA 60.181 47.826 2.24 0.00 30.04 1.47
3772 3880 1.306654 TGAGGGCTAATGTCGGGGT 60.307 57.895 0.00 0.00 0.00 4.95
3810 3919 7.593825 AGTTATTTGCAGGATCAGTTTAACAC 58.406 34.615 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.