Multiple sequence alignment - TraesCS3B01G572200

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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 TraesCS3B01G572200 chr3B 100.000 3806 0 0 1 3806 803198462 803202267 0.000000e+00 7029.0
1 TraesCS3B01G572200 chr3B 96.328 1770 55 4 647 2415 802720949 802719189 0.000000e+00 2900.0
2 TraesCS3B01G572200 chr3B 83.194 2035 286 23 866 2886 802705057 802703065 0.000000e+00 1812.0
3 TraesCS3B01G572200 chr3B 95.341 837 33 4 2459 3294 802719194 802718363 0.000000e+00 1325.0
4 TraesCS3B01G572200 chr3B 93.277 476 30 2 3333 3806 802718367 802717892 0.000000e+00 701.0
5 TraesCS3B01G572200 chr3B 88.000 275 33 0 84 358 802721474 802721200 3.670000e-85 326.0
6 TraesCS3B01G572200 chr3B 95.652 69 3 0 582 650 802721128 802721060 1.120000e-20 111.0
7 TraesCS3B01G572200 chr3B 95.000 60 1 1 1 58 802721531 802721472 4.050000e-15 93.5
8 TraesCS3B01G572200 chr3B 85.333 75 11 0 582 656 680070206 680070280 1.130000e-10 78.7
9 TraesCS3B01G572200 chr2B 81.857 937 131 16 2887 3795 222218182 222217257 0.000000e+00 752.0
10 TraesCS3B01G572200 chr2B 91.192 193 15 2 394 586 598572048 598572238 1.050000e-65 261.0
11 TraesCS3B01G572200 chr7D 81.095 968 116 35 2887 3801 263658800 263657847 0.000000e+00 712.0
12 TraesCS3B01G572200 chr7D 78.975 956 139 34 2889 3795 95042240 95041298 2.530000e-166 595.0
13 TraesCS3B01G572200 chr7D 86.765 68 9 0 585 652 438162539 438162472 4.080000e-10 76.8
14 TraesCS3B01G572200 chr7A 80.853 961 119 35 2887 3795 286763254 286762307 0.000000e+00 695.0
15 TraesCS3B01G572200 chr5B 79.299 942 131 35 2889 3780 145038238 145039165 5.440000e-168 601.0
16 TraesCS3B01G572200 chr5B 81.037 675 101 18 2887 3551 238579443 238580100 2.620000e-141 512.0
17 TraesCS3B01G572200 chr5B 95.337 193 8 1 393 585 554817866 554817675 4.780000e-79 305.0
18 TraesCS3B01G572200 chr5B 96.622 148 5 0 438 585 706037141 706037288 2.940000e-61 246.0
19 TraesCS3B01G572200 chr5B 90.173 173 14 3 3622 3792 629278634 629278805 4.950000e-54 222.0
20 TraesCS3B01G572200 chr5B 90.173 173 14 3 3622 3792 629361205 629361376 4.950000e-54 222.0
21 TraesCS3B01G572200 chr4D 81.018 727 103 23 2889 3597 328836495 328835786 2.590000e-151 545.0
22 TraesCS3B01G572200 chr4D 87.586 145 18 0 214 358 83140419 83140563 6.540000e-38 169.0
23 TraesCS3B01G572200 chr1B 81.536 677 96 22 2887 3551 350152392 350153051 7.240000e-147 531.0
24 TraesCS3B01G572200 chr1B 80.826 678 102 20 2887 3551 609220178 609219516 1.220000e-139 507.0
25 TraesCS3B01G572200 chr1B 90.541 370 22 7 582 951 545274977 545274621 9.570000e-131 477.0
26 TraesCS3B01G572200 chr1B 89.143 175 18 1 3622 3795 362189902 362190076 2.300000e-52 217.0
27 TraesCS3B01G572200 chr1B 87.435 191 18 4 171 358 545275236 545275049 8.280000e-52 215.0
28 TraesCS3B01G572200 chr3D 79.681 753 119 19 2887 3619 347721702 347722440 2.620000e-141 512.0
29 TraesCS3B01G572200 chr3D 88.439 173 19 1 3622 3793 372416537 372416365 1.390000e-49 207.0
30 TraesCS3B01G572200 chr3D 84.615 78 12 0 582 659 318640520 318640597 1.130000e-10 78.7
31 TraesCS3B01G572200 chr3A 80.889 675 103 21 2889 3551 31229624 31230284 3.390000e-140 508.0
32 TraesCS3B01G572200 chr3A 83.929 168 22 4 193 358 726769150 726768986 5.090000e-34 156.0
33 TraesCS3B01G572200 chr3A 82.796 93 12 4 582 670 145383080 145382988 3.150000e-11 80.5
34 TraesCS3B01G572200 chr4B 77.602 884 131 40 2972 3806 85538800 85537935 1.240000e-129 473.0
35 TraesCS3B01G572200 chr4B 93.000 200 10 4 386 585 638526441 638526636 4.810000e-74 289.0
36 TraesCS3B01G572200 chr4B 85.135 74 11 0 582 655 230239354 230239427 4.080000e-10 76.8
37 TraesCS3B01G572200 chr1A 80.120 669 104 23 2891 3549 131049275 131048626 4.450000e-129 472.0
38 TraesCS3B01G572200 chr1A 86.082 194 24 1 393 586 535488901 535488711 4.980000e-49 206.0
39 TraesCS3B01G572200 chr1A 87.500 72 9 0 585 656 431670256 431670185 2.440000e-12 84.2
40 TraesCS3B01G572200 chr2A 75.355 775 138 38 2852 3600 38835971 38836718 1.320000e-84 324.0
41 TraesCS3B01G572200 chr2A 88.542 192 18 2 395 586 195581417 195581604 2.960000e-56 230.0
42 TraesCS3B01G572200 chr2A 86.806 144 19 0 215 358 249754459 249754602 1.090000e-35 161.0
43 TraesCS3B01G572200 chr2A 85.333 75 11 0 582 656 606559437 606559511 1.130000e-10 78.7
44 TraesCS3B01G572200 chr7B 92.784 194 10 3 392 585 741677516 741677327 1.040000e-70 278.0
45 TraesCS3B01G572200 chr7B 92.268 194 11 2 392 585 661452162 661452351 4.840000e-69 272.0
46 TraesCS3B01G572200 chr7B 88.889 144 12 4 217 358 402809755 402809614 1.410000e-39 174.0
47 TraesCS3B01G572200 chr6B 94.667 150 8 0 436 585 15295583 15295434 2.290000e-57 233.0
48 TraesCS3B01G572200 chr6B 86.897 145 18 1 214 358 683376073 683376216 1.090000e-35 161.0
49 TraesCS3B01G572200 chr6D 86.806 144 19 0 215 358 90134890 90135033 1.090000e-35 161.0
50 TraesCS3B01G572200 chr4A 86.806 144 19 0 215 358 213025418 213025561 1.090000e-35 161.0


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 TraesCS3B01G572200 chr3B 803198462 803202267 3805 False 7029.000000 7029 100.000 1 3806 1 chr3B.!!$F2 3805
1 TraesCS3B01G572200 chr3B 802703065 802705057 1992 True 1812.000000 1812 83.194 866 2886 1 chr3B.!!$R1 2020
2 TraesCS3B01G572200 chr3B 802717892 802721531 3639 True 909.416667 2900 93.933 1 3806 6 chr3B.!!$R2 3805
3 TraesCS3B01G572200 chr2B 222217257 222218182 925 True 752.000000 752 81.857 2887 3795 1 chr2B.!!$R1 908
4 TraesCS3B01G572200 chr7D 263657847 263658800 953 True 712.000000 712 81.095 2887 3801 1 chr7D.!!$R2 914
5 TraesCS3B01G572200 chr7D 95041298 95042240 942 True 595.000000 595 78.975 2889 3795 1 chr7D.!!$R1 906
6 TraesCS3B01G572200 chr7A 286762307 286763254 947 True 695.000000 695 80.853 2887 3795 1 chr7A.!!$R1 908
7 TraesCS3B01G572200 chr5B 145038238 145039165 927 False 601.000000 601 79.299 2889 3780 1 chr5B.!!$F1 891
8 TraesCS3B01G572200 chr5B 238579443 238580100 657 False 512.000000 512 81.037 2887 3551 1 chr5B.!!$F2 664
9 TraesCS3B01G572200 chr4D 328835786 328836495 709 True 545.000000 545 81.018 2889 3597 1 chr4D.!!$R1 708
10 TraesCS3B01G572200 chr1B 350152392 350153051 659 False 531.000000 531 81.536 2887 3551 1 chr1B.!!$F1 664
11 TraesCS3B01G572200 chr1B 609219516 609220178 662 True 507.000000 507 80.826 2887 3551 1 chr1B.!!$R1 664
12 TraesCS3B01G572200 chr1B 545274621 545275236 615 True 346.000000 477 88.988 171 951 2 chr1B.!!$R2 780
13 TraesCS3B01G572200 chr3D 347721702 347722440 738 False 512.000000 512 79.681 2887 3619 1 chr3D.!!$F2 732
14 TraesCS3B01G572200 chr3A 31229624 31230284 660 False 508.000000 508 80.889 2889 3551 1 chr3A.!!$F1 662
15 TraesCS3B01G572200 chr4B 85537935 85538800 865 True 473.000000 473 77.602 2972 3806 1 chr4B.!!$R1 834
16 TraesCS3B01G572200 chr1A 131048626 131049275 649 True 472.000000 472 80.120 2891 3549 1 chr1A.!!$R1 658
17 TraesCS3B01G572200 chr2A 38835971 38836718 747 False 324.000000 324 75.355 2852 3600 1 chr2A.!!$F1 748

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
547 570 0.107165 GGAAGAGGCGCCCTGTTTAT 60.107 55.0 26.15 0.94 37.25 1.40 F
549 572 0.328258 AAGAGGCGCCCTGTTTATGT 59.672 50.0 26.15 0.00 33.05 2.29 F
576 599 0.608130 TCTTCATCCGGTGTGTCCAG 59.392 55.0 0.00 1.36 35.57 3.86 F
577 600 0.608130 CTTCATCCGGTGTGTCCAGA 59.392 55.0 0.00 0.00 35.57 3.86 F
2351 2489 0.962855 GCTTCTGGTTCTGGAAGGCC 60.963 60.0 0.00 0.00 39.25 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2128 2266 1.204312 GTTGCTTCGCGAAGTCACC 59.796 57.895 40.02 28.8 40.45 4.02 R
2433 2571 2.099098 GCACCGATTATTTTCACCCTGG 59.901 50.000 0.00 0.0 0.00 4.45 R
2436 2574 3.632145 AGATGCACCGATTATTTTCACCC 59.368 43.478 0.00 0.0 0.00 4.61 R
2658 2799 3.135348 TGCATCCCTGAGTAAAGATCCAG 59.865 47.826 0.00 0.0 0.00 3.86 R
3606 3796 2.312424 TGCCCCCTTTATCGGTTTTT 57.688 45.000 0.00 0.0 0.00 1.94 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
26 27 3.266772 TGTCCATGGATTGGCCCTATATC 59.733 47.826 19.62 0.05 46.01 1.63
64 67 3.570212 GGCACCCCGGATGGCTAT 61.570 66.667 20.54 0.00 39.45 2.97
65 68 2.515901 GCACCCCGGATGGCTATT 59.484 61.111 0.73 0.00 0.00 1.73
66 69 1.898574 GCACCCCGGATGGCTATTG 60.899 63.158 0.73 0.00 0.00 1.90
67 70 1.531748 CACCCCGGATGGCTATTGT 59.468 57.895 0.73 0.00 0.00 2.71
68 71 0.819259 CACCCCGGATGGCTATTGTG 60.819 60.000 0.73 0.00 0.00 3.33
69 72 1.228245 CCCCGGATGGCTATTGTGG 60.228 63.158 0.73 0.00 0.00 4.17
70 73 1.898574 CCCGGATGGCTATTGTGGC 60.899 63.158 0.73 0.00 0.00 5.01
71 74 1.149174 CCGGATGGCTATTGTGGCT 59.851 57.895 0.00 0.00 0.00 4.75
72 75 0.886490 CCGGATGGCTATTGTGGCTC 60.886 60.000 0.00 0.00 0.00 4.70
73 76 0.107456 CGGATGGCTATTGTGGCTCT 59.893 55.000 0.00 0.00 0.00 4.09
74 77 1.344438 CGGATGGCTATTGTGGCTCTA 59.656 52.381 0.00 0.00 0.00 2.43
75 78 2.027745 CGGATGGCTATTGTGGCTCTAT 60.028 50.000 0.00 0.00 0.00 1.98
76 79 3.195610 CGGATGGCTATTGTGGCTCTATA 59.804 47.826 0.00 0.00 0.00 1.31
77 80 4.322725 CGGATGGCTATTGTGGCTCTATAA 60.323 45.833 0.00 0.00 0.00 0.98
78 81 5.560724 GGATGGCTATTGTGGCTCTATAAA 58.439 41.667 0.00 0.00 0.00 1.40
79 82 6.003950 GGATGGCTATTGTGGCTCTATAAAA 58.996 40.000 0.00 0.00 0.00 1.52
80 83 6.072452 GGATGGCTATTGTGGCTCTATAAAAC 60.072 42.308 0.00 0.00 0.00 2.43
81 84 5.750524 TGGCTATTGTGGCTCTATAAAACA 58.249 37.500 0.00 0.00 0.00 2.83
82 85 6.184068 TGGCTATTGTGGCTCTATAAAACAA 58.816 36.000 0.00 0.00 35.41 2.83
83 86 6.318648 TGGCTATTGTGGCTCTATAAAACAAG 59.681 38.462 0.00 0.00 34.50 3.16
84 87 6.238759 GGCTATTGTGGCTCTATAAAACAAGG 60.239 42.308 0.00 0.00 34.50 3.61
85 88 6.542370 GCTATTGTGGCTCTATAAAACAAGGA 59.458 38.462 0.00 0.00 34.50 3.36
95 98 2.844122 AAAACAAGGACGTGTGCTTC 57.156 45.000 3.61 0.00 39.28 3.86
103 106 1.604396 GACGTGTGCTTCGTAGTCTC 58.396 55.000 0.00 0.00 41.64 3.36
154 157 4.082463 CCCTTGTGTCTAGTCTCTCACTTC 60.082 50.000 0.00 0.00 36.43 3.01
155 158 4.378978 CCTTGTGTCTAGTCTCTCACTTCG 60.379 50.000 0.00 0.00 36.43 3.79
157 160 2.085320 TGTCTAGTCTCTCACTTCGGC 58.915 52.381 0.00 0.00 36.43 5.54
225 228 1.688772 TACTCCAGTACTCCATCCGC 58.311 55.000 0.00 0.00 0.00 5.54
238 241 8.867097 AGTACTCCATCCGCTTCTAAATATAAA 58.133 33.333 0.00 0.00 0.00 1.40
239 242 7.964604 ACTCCATCCGCTTCTAAATATAAAC 57.035 36.000 0.00 0.00 0.00 2.01
284 290 8.630917 ACTGACTACATACAGATGTATACAACC 58.369 37.037 10.14 5.14 45.42 3.77
337 343 5.924254 TGCTTCGTATGTAGTACATATTGGC 59.076 40.000 22.65 21.47 42.39 4.52
342 348 6.638063 TCGTATGTAGTACATATTGGCGTTTC 59.362 38.462 22.65 8.44 42.39 2.78
355 361 9.950680 CATATTGGCGTTTCTAAAATGTCTTAT 57.049 29.630 0.00 0.00 0.00 1.73
388 411 9.352784 CTTTTTAATGATTTCAATGCGGACTAA 57.647 29.630 0.00 0.00 0.00 2.24
396 419 9.868277 TGATTTCAATGCGGACTAAATATTTTT 57.132 25.926 5.91 0.00 0.00 1.94
442 465 4.948062 GGGCTCCCCACCTAAATATATT 57.052 45.455 0.00 0.00 44.65 1.28
443 466 5.270979 GGGCTCCCCACCTAAATATATTT 57.729 43.478 14.86 14.86 44.65 1.40
444 467 5.262009 GGGCTCCCCACCTAAATATATTTC 58.738 45.833 13.95 0.00 44.65 2.17
445 468 5.015284 GGGCTCCCCACCTAAATATATTTCT 59.985 44.000 13.95 0.00 44.65 2.52
446 469 6.181190 GGCTCCCCACCTAAATATATTTCTC 58.819 44.000 13.95 0.00 0.00 2.87
447 470 6.240176 GGCTCCCCACCTAAATATATTTCTCA 60.240 42.308 13.95 0.00 0.00 3.27
448 471 7.231467 GCTCCCCACCTAAATATATTTCTCAA 58.769 38.462 13.95 0.00 0.00 3.02
449 472 7.391833 GCTCCCCACCTAAATATATTTCTCAAG 59.608 40.741 13.95 6.38 0.00 3.02
450 473 8.344939 TCCCCACCTAAATATATTTCTCAAGT 57.655 34.615 13.95 3.89 0.00 3.16
451 474 8.787818 TCCCCACCTAAATATATTTCTCAAGTT 58.212 33.333 13.95 0.00 0.00 2.66
452 475 9.421399 CCCCACCTAAATATATTTCTCAAGTTT 57.579 33.333 13.95 0.00 0.00 2.66
463 486 5.682943 TTTCTCAAGTTTGTAACCCATCG 57.317 39.130 0.00 0.00 0.00 3.84
464 487 4.345859 TCTCAAGTTTGTAACCCATCGT 57.654 40.909 0.00 0.00 0.00 3.73
465 488 4.710324 TCTCAAGTTTGTAACCCATCGTT 58.290 39.130 0.00 0.00 38.57 3.85
466 489 5.856156 TCTCAAGTTTGTAACCCATCGTTA 58.144 37.500 0.00 0.00 35.79 3.18
467 490 5.929992 TCTCAAGTTTGTAACCCATCGTTAG 59.070 40.000 0.00 0.00 37.62 2.34
468 491 5.856156 TCAAGTTTGTAACCCATCGTTAGA 58.144 37.500 0.00 0.00 37.62 2.10
469 492 5.697633 TCAAGTTTGTAACCCATCGTTAGAC 59.302 40.000 0.00 0.00 37.62 2.59
470 493 5.479124 AGTTTGTAACCCATCGTTAGACT 57.521 39.130 0.00 0.00 37.62 3.24
471 494 6.594788 AGTTTGTAACCCATCGTTAGACTA 57.405 37.500 0.00 0.00 37.62 2.59
472 495 6.996509 AGTTTGTAACCCATCGTTAGACTAA 58.003 36.000 0.00 0.00 37.62 2.24
473 496 7.618137 AGTTTGTAACCCATCGTTAGACTAAT 58.382 34.615 0.00 0.00 37.62 1.73
474 497 8.098912 AGTTTGTAACCCATCGTTAGACTAATT 58.901 33.333 0.00 0.00 37.62 1.40
475 498 9.369904 GTTTGTAACCCATCGTTAGACTAATTA 57.630 33.333 0.00 0.00 37.62 1.40
476 499 8.931385 TTGTAACCCATCGTTAGACTAATTAC 57.069 34.615 0.00 2.65 37.62 1.89
477 500 8.065473 TGTAACCCATCGTTAGACTAATTACA 57.935 34.615 9.62 9.62 37.62 2.41
478 501 8.530311 TGTAACCCATCGTTAGACTAATTACAA 58.470 33.333 10.66 0.42 37.62 2.41
479 502 9.369904 GTAACCCATCGTTAGACTAATTACAAA 57.630 33.333 0.00 0.00 37.62 2.83
480 503 8.488651 AACCCATCGTTAGACTAATTACAAAG 57.511 34.615 0.00 0.00 30.96 2.77
481 504 7.844009 ACCCATCGTTAGACTAATTACAAAGA 58.156 34.615 0.00 0.00 0.00 2.52
482 505 7.980099 ACCCATCGTTAGACTAATTACAAAGAG 59.020 37.037 0.00 0.00 0.00 2.85
483 506 7.438459 CCCATCGTTAGACTAATTACAAAGAGG 59.562 40.741 0.00 0.00 0.00 3.69
484 507 8.195436 CCATCGTTAGACTAATTACAAAGAGGA 58.805 37.037 0.00 0.00 0.00 3.71
485 508 9.582431 CATCGTTAGACTAATTACAAAGAGGAA 57.418 33.333 0.00 0.00 0.00 3.36
496 519 8.579850 AATTACAAAGAGGAATTACATGAGCA 57.420 30.769 0.00 0.00 0.00 4.26
497 520 5.886960 ACAAAGAGGAATTACATGAGCAC 57.113 39.130 0.00 0.00 0.00 4.40
498 521 4.393062 ACAAAGAGGAATTACATGAGCACG 59.607 41.667 0.00 0.00 0.00 5.34
499 522 3.895232 AGAGGAATTACATGAGCACGT 57.105 42.857 0.00 0.00 0.00 4.49
500 523 3.525537 AGAGGAATTACATGAGCACGTG 58.474 45.455 12.28 12.28 38.80 4.49
501 524 3.055819 AGAGGAATTACATGAGCACGTGT 60.056 43.478 18.38 13.62 46.32 4.49
502 525 4.159693 AGAGGAATTACATGAGCACGTGTA 59.840 41.667 18.38 11.59 43.38 2.90
503 526 4.433615 AGGAATTACATGAGCACGTGTAG 58.566 43.478 18.38 5.43 45.36 2.74
504 527 4.081642 AGGAATTACATGAGCACGTGTAGT 60.082 41.667 18.38 10.29 45.36 2.73
505 528 4.267928 GGAATTACATGAGCACGTGTAGTC 59.732 45.833 18.38 14.88 45.36 2.59
506 529 2.537639 TACATGAGCACGTGTAGTCG 57.462 50.000 18.38 6.16 43.38 4.18
507 530 0.596577 ACATGAGCACGTGTAGTCGT 59.403 50.000 18.38 10.17 43.38 4.34
517 540 3.341823 ACGTGTAGTCGTGATAAGAGGT 58.658 45.455 0.00 0.00 42.56 3.85
518 541 4.507710 ACGTGTAGTCGTGATAAGAGGTA 58.492 43.478 0.00 0.00 42.56 3.08
519 542 4.569966 ACGTGTAGTCGTGATAAGAGGTAG 59.430 45.833 0.00 0.00 42.56 3.18
520 543 4.025061 CGTGTAGTCGTGATAAGAGGTAGG 60.025 50.000 0.00 0.00 0.00 3.18
521 544 5.121811 GTGTAGTCGTGATAAGAGGTAGGA 58.878 45.833 0.00 0.00 0.00 2.94
522 545 5.587844 GTGTAGTCGTGATAAGAGGTAGGAA 59.412 44.000 0.00 0.00 0.00 3.36
523 546 5.587844 TGTAGTCGTGATAAGAGGTAGGAAC 59.412 44.000 0.00 0.00 0.00 3.62
524 547 4.597004 AGTCGTGATAAGAGGTAGGAACA 58.403 43.478 0.00 0.00 0.00 3.18
525 548 4.398673 AGTCGTGATAAGAGGTAGGAACAC 59.601 45.833 0.00 0.00 0.00 3.32
526 549 3.698040 TCGTGATAAGAGGTAGGAACACC 59.302 47.826 0.00 0.00 39.02 4.16
527 550 3.446161 CGTGATAAGAGGTAGGAACACCA 59.554 47.826 0.00 0.00 41.40 4.17
528 551 4.440250 CGTGATAAGAGGTAGGAACACCAG 60.440 50.000 0.00 0.00 41.40 4.00
529 552 4.030913 TGATAAGAGGTAGGAACACCAGG 58.969 47.826 0.00 0.00 41.40 4.45
530 553 2.715763 AAGAGGTAGGAACACCAGGA 57.284 50.000 0.00 0.00 41.40 3.86
531 554 2.715763 AGAGGTAGGAACACCAGGAA 57.284 50.000 0.00 0.00 41.40 3.36
532 555 2.541466 AGAGGTAGGAACACCAGGAAG 58.459 52.381 0.00 0.00 41.40 3.46
533 556 2.111972 AGAGGTAGGAACACCAGGAAGA 59.888 50.000 0.00 0.00 41.40 2.87
534 557 2.498078 GAGGTAGGAACACCAGGAAGAG 59.502 54.545 0.00 0.00 41.40 2.85
535 558 1.555533 GGTAGGAACACCAGGAAGAGG 59.444 57.143 0.00 0.00 38.55 3.69
536 559 1.066071 GTAGGAACACCAGGAAGAGGC 60.066 57.143 0.00 0.00 0.00 4.70
537 560 1.376037 GGAACACCAGGAAGAGGCG 60.376 63.158 0.00 0.00 0.00 5.52
538 561 2.032681 AACACCAGGAAGAGGCGC 59.967 61.111 0.00 0.00 0.00 6.53
539 562 3.553095 AACACCAGGAAGAGGCGCC 62.553 63.158 21.89 21.89 0.00 6.53
540 563 4.785453 CACCAGGAAGAGGCGCCC 62.785 72.222 26.15 15.34 0.00 6.13
542 565 4.479993 CCAGGAAGAGGCGCCCTG 62.480 72.222 26.15 22.01 45.28 4.45
543 566 3.710722 CAGGAAGAGGCGCCCTGT 61.711 66.667 26.15 8.19 41.81 4.00
544 567 2.930562 AGGAAGAGGCGCCCTGTT 60.931 61.111 26.15 14.62 39.93 3.16
545 568 2.034221 GGAAGAGGCGCCCTGTTT 59.966 61.111 26.15 12.64 37.25 2.83
546 569 1.198759 AGGAAGAGGCGCCCTGTTTA 61.199 55.000 26.15 0.00 37.25 2.01
547 570 0.107165 GGAAGAGGCGCCCTGTTTAT 60.107 55.000 26.15 0.94 37.25 1.40
548 571 1.017387 GAAGAGGCGCCCTGTTTATG 58.983 55.000 26.15 0.00 37.25 1.90
549 572 0.328258 AAGAGGCGCCCTGTTTATGT 59.672 50.000 26.15 0.00 33.05 2.29
550 573 1.200519 AGAGGCGCCCTGTTTATGTA 58.799 50.000 26.15 0.00 31.76 2.29
551 574 1.134491 AGAGGCGCCCTGTTTATGTAC 60.134 52.381 26.15 0.00 31.76 2.90
552 575 0.909623 AGGCGCCCTGTTTATGTACT 59.090 50.000 26.15 0.00 29.57 2.73
553 576 1.014352 GGCGCCCTGTTTATGTACTG 58.986 55.000 18.11 0.00 0.00 2.74
554 577 1.014352 GCGCCCTGTTTATGTACTGG 58.986 55.000 0.00 0.00 37.01 4.00
555 578 1.677820 GCGCCCTGTTTATGTACTGGT 60.678 52.381 0.00 0.00 35.89 4.00
556 579 2.706890 CGCCCTGTTTATGTACTGGTT 58.293 47.619 0.00 0.00 35.89 3.67
557 580 3.078837 CGCCCTGTTTATGTACTGGTTT 58.921 45.455 0.00 0.00 35.89 3.27
558 581 3.126343 CGCCCTGTTTATGTACTGGTTTC 59.874 47.826 0.00 0.00 35.89 2.78
559 582 4.332828 GCCCTGTTTATGTACTGGTTTCT 58.667 43.478 0.00 0.00 35.89 2.52
560 583 4.765339 GCCCTGTTTATGTACTGGTTTCTT 59.235 41.667 0.00 0.00 35.89 2.52
561 584 5.106277 GCCCTGTTTATGTACTGGTTTCTTC 60.106 44.000 0.00 0.00 35.89 2.87
562 585 6.001460 CCCTGTTTATGTACTGGTTTCTTCA 58.999 40.000 0.00 0.00 35.89 3.02
563 586 6.659242 CCCTGTTTATGTACTGGTTTCTTCAT 59.341 38.462 0.00 0.00 35.89 2.57
564 587 7.148239 CCCTGTTTATGTACTGGTTTCTTCATC 60.148 40.741 0.00 0.00 35.89 2.92
565 588 7.148239 CCTGTTTATGTACTGGTTTCTTCATCC 60.148 40.741 0.00 0.00 33.75 3.51
566 589 6.370442 TGTTTATGTACTGGTTTCTTCATCCG 59.630 38.462 0.00 0.00 0.00 4.18
567 590 3.328382 TGTACTGGTTTCTTCATCCGG 57.672 47.619 0.00 0.00 0.00 5.14
568 591 2.635915 TGTACTGGTTTCTTCATCCGGT 59.364 45.455 0.00 0.00 42.55 5.28
569 592 2.185004 ACTGGTTTCTTCATCCGGTG 57.815 50.000 0.00 0.00 39.10 4.94
570 593 1.420138 ACTGGTTTCTTCATCCGGTGT 59.580 47.619 0.00 0.00 39.10 4.16
571 594 1.806542 CTGGTTTCTTCATCCGGTGTG 59.193 52.381 0.00 1.81 0.00 3.82
572 595 1.142060 TGGTTTCTTCATCCGGTGTGT 59.858 47.619 0.00 0.00 0.00 3.72
573 596 1.804748 GGTTTCTTCATCCGGTGTGTC 59.195 52.381 0.00 0.00 0.00 3.67
574 597 1.804748 GTTTCTTCATCCGGTGTGTCC 59.195 52.381 0.00 0.00 0.00 4.02
575 598 1.052617 TTCTTCATCCGGTGTGTCCA 58.947 50.000 0.00 0.00 35.57 4.02
576 599 0.608130 TCTTCATCCGGTGTGTCCAG 59.392 55.000 0.00 1.36 35.57 3.86
577 600 0.608130 CTTCATCCGGTGTGTCCAGA 59.392 55.000 0.00 0.00 35.57 3.86
580 603 1.913262 ATCCGGTGTGTCCAGAGCA 60.913 57.895 0.00 0.00 35.57 4.26
591 614 4.526650 TGTGTCCAGAGCATTAGAGTGTAA 59.473 41.667 0.00 0.00 0.00 2.41
634 657 2.094906 TGTAGTTCGTGGTGGAATCTCG 60.095 50.000 0.00 0.00 0.00 4.04
685 822 6.539103 GGGAATAGTAGCTGGTAAAGAAAGTG 59.461 42.308 0.00 0.00 0.00 3.16
686 823 7.104290 GGAATAGTAGCTGGTAAAGAAAGTGT 58.896 38.462 0.00 0.00 0.00 3.55
687 824 7.064728 GGAATAGTAGCTGGTAAAGAAAGTGTG 59.935 40.741 0.00 0.00 0.00 3.82
693 830 3.271729 TGGTAAAGAAAGTGTGCACGAA 58.728 40.909 13.13 0.00 36.20 3.85
737 874 9.522804 CCTATAGAAATATGCGACTAATCCTTC 57.477 37.037 0.00 0.00 0.00 3.46
748 885 5.639931 GCGACTAATCCTTCTTTTCTGTTCT 59.360 40.000 0.00 0.00 0.00 3.01
810 947 2.949451 ATCGATTCGAGTTCTGTGCT 57.051 45.000 14.81 0.00 39.91 4.40
888 1025 7.672983 TCACTGGATAGACTTCATTTTCAAC 57.327 36.000 0.00 0.00 0.00 3.18
923 1060 6.636666 TGCTACGTAGTACAATTTGCTAAC 57.363 37.500 22.98 2.68 45.11 2.34
943 1080 6.295745 GCTAACCTTTAAGTTGACCTAGACCT 60.296 42.308 0.00 0.00 0.00 3.85
1026 1164 6.098695 TGAAGCGGGGTAATAGTAATACAGTT 59.901 38.462 0.00 0.00 0.00 3.16
1061 1199 1.267121 ATACTGGTGCTGGTCGTCTT 58.733 50.000 0.00 0.00 0.00 3.01
1072 1210 2.680841 CTGGTCGTCTTGGTTTTGTTGA 59.319 45.455 0.00 0.00 0.00 3.18
1098 1236 4.681942 GGTAGTGTTCGATCTGATACATGC 59.318 45.833 0.00 0.00 0.00 4.06
1172 1310 7.954248 CGGTGTAATATATACAGTCGACACTAC 59.046 40.741 19.50 0.00 36.90 2.73
1236 1374 4.697756 CTGACAAGGCGCGGGGAA 62.698 66.667 8.83 0.00 0.00 3.97
1313 1451 4.201950 GCGGTACATCTTGCTTGAAATCAT 60.202 41.667 0.00 0.00 0.00 2.45
1330 1468 4.858680 TTGTCGCGGGCACACCAA 62.859 61.111 6.13 0.00 40.22 3.67
1395 1533 3.259876 TCGGTTATCTTGTTGGTAGCACT 59.740 43.478 0.00 0.00 0.00 4.40
1608 1746 1.457346 CAGAAGATGCAAGGTCCCAC 58.543 55.000 0.00 0.00 0.00 4.61
1711 1849 4.884668 AATCCTTCGTTTCTACCAGACA 57.115 40.909 0.00 0.00 0.00 3.41
2351 2489 0.962855 GCTTCTGGTTCTGGAAGGCC 60.963 60.000 0.00 0.00 39.25 5.19
2414 2552 7.040409 AGCCTGGCAAAGCACTAATATTATTAC 60.040 37.037 22.65 0.00 0.00 1.89
2415 2553 7.593825 CCTGGCAAAGCACTAATATTATTACC 58.406 38.462 0.00 0.00 0.00 2.85
2416 2554 7.309194 CCTGGCAAAGCACTAATATTATTACCC 60.309 40.741 0.00 0.00 0.00 3.69
2418 2556 6.492087 GGCAAAGCACTAATATTATTACCCCA 59.508 38.462 0.00 0.00 0.00 4.96
2424 2562 7.937394 AGCACTAATATTATTACCCCAGTTGAC 59.063 37.037 0.00 0.00 0.00 3.18
2430 2568 6.742559 ATTATTACCCCAGTTGACGTCTAT 57.257 37.500 17.92 0.00 0.00 1.98
2433 2571 5.779529 TTACCCCAGTTGACGTCTATATC 57.220 43.478 17.92 0.00 0.00 1.63
2436 2574 3.005897 CCCCAGTTGACGTCTATATCCAG 59.994 52.174 17.92 0.00 0.00 3.86
2658 2799 0.753262 ACCATCCTGAGTACCATCGC 59.247 55.000 0.00 0.00 0.00 4.58
2678 2822 3.737850 GCTGGATCTTTACTCAGGGATG 58.262 50.000 0.00 0.00 0.00 3.51
2691 2835 5.698104 ACTCAGGGATGCATCATGAATTTA 58.302 37.500 27.25 8.69 0.00 1.40
2712 2856 2.094762 ATAGCTCGTTGGTGGTTGAC 57.905 50.000 0.00 0.00 0.00 3.18
2739 2883 0.761802 GGGACTATCCAGCAGAAGGG 59.238 60.000 0.00 0.00 38.64 3.95
2813 2957 9.586150 GCTTGTATTTGTATCATAAGTTCATCG 57.414 33.333 0.00 0.00 0.00 3.84
2908 3057 4.941713 TGTTGGAAATATGCCCTAAAGGT 58.058 39.130 0.00 0.00 38.26 3.50
3226 3396 6.426646 ACCCTCATATCAAGTATCTGTTCC 57.573 41.667 0.00 0.00 0.00 3.62
3298 3469 9.507280 GTTGGTTATATCAAACATCACTTCATG 57.493 33.333 0.00 0.00 0.00 3.07
3321 3492 3.117512 ACTGGGTGATCACAAAGGTTCTT 60.118 43.478 26.47 4.99 0.00 2.52
3335 3506 7.607991 CACAAAGGTTCTTTACAGGTATCTCAT 59.392 37.037 0.00 0.00 0.00 2.90
3340 3511 7.988028 AGGTTCTTTACAGGTATCTCATAAAGC 59.012 37.037 9.91 1.09 33.22 3.51
3376 3552 4.248859 CACTCGAGACTGGAATTTGTCAT 58.751 43.478 21.68 0.00 35.81 3.06
3565 3754 2.031465 GGGTTCGCCGGACAAAGA 59.969 61.111 5.05 0.00 38.45 2.52
3601 3791 5.420409 GGATTAACTGAGTCCTCGACATTT 58.580 41.667 0.00 0.00 34.60 2.32
3606 3796 3.576982 ACTGAGTCCTCGACATTTTGGTA 59.423 43.478 0.00 0.00 34.60 3.25
3635 3853 0.253630 AAAGGGGGCATCTAGGTCCA 60.254 55.000 0.00 0.00 32.89 4.02
3636 3854 0.028642 AAGGGGGCATCTAGGTCCAT 60.029 55.000 0.00 0.00 32.89 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 61 5.750524 TGTTTTATAGAGCCACAATAGCCA 58.249 37.500 0.00 0.00 0.00 4.75
59 62 6.238759 CCTTGTTTTATAGAGCCACAATAGCC 60.239 42.308 0.00 0.00 0.00 3.93
60 63 6.542370 TCCTTGTTTTATAGAGCCACAATAGC 59.458 38.462 0.00 0.00 0.00 2.97
61 64 7.254455 CGTCCTTGTTTTATAGAGCCACAATAG 60.254 40.741 0.00 0.00 0.00 1.73
62 65 6.537301 CGTCCTTGTTTTATAGAGCCACAATA 59.463 38.462 0.00 0.00 0.00 1.90
63 66 5.354234 CGTCCTTGTTTTATAGAGCCACAAT 59.646 40.000 0.00 0.00 0.00 2.71
64 67 4.693566 CGTCCTTGTTTTATAGAGCCACAA 59.306 41.667 0.00 0.00 0.00 3.33
65 68 4.250464 CGTCCTTGTTTTATAGAGCCACA 58.750 43.478 0.00 0.00 0.00 4.17
66 69 4.092968 CACGTCCTTGTTTTATAGAGCCAC 59.907 45.833 0.00 0.00 0.00 5.01
67 70 4.250464 CACGTCCTTGTTTTATAGAGCCA 58.750 43.478 0.00 0.00 0.00 4.75
68 71 4.092968 CACACGTCCTTGTTTTATAGAGCC 59.907 45.833 0.00 0.00 0.00 4.70
69 72 4.435651 GCACACGTCCTTGTTTTATAGAGC 60.436 45.833 0.00 0.00 0.00 4.09
70 73 4.929808 AGCACACGTCCTTGTTTTATAGAG 59.070 41.667 0.00 0.00 0.00 2.43
71 74 4.890088 AGCACACGTCCTTGTTTTATAGA 58.110 39.130 0.00 0.00 0.00 1.98
72 75 5.607119 AAGCACACGTCCTTGTTTTATAG 57.393 39.130 0.00 0.00 0.00 1.31
73 76 4.150980 CGAAGCACACGTCCTTGTTTTATA 59.849 41.667 0.00 0.00 0.00 0.98
74 77 3.059188 CGAAGCACACGTCCTTGTTTTAT 60.059 43.478 0.00 0.00 0.00 1.40
75 78 2.285756 CGAAGCACACGTCCTTGTTTTA 59.714 45.455 0.00 0.00 0.00 1.52
76 79 1.063469 CGAAGCACACGTCCTTGTTTT 59.937 47.619 0.00 0.00 0.00 2.43
77 80 0.655733 CGAAGCACACGTCCTTGTTT 59.344 50.000 0.00 0.00 0.00 2.83
78 81 0.461339 ACGAAGCACACGTCCTTGTT 60.461 50.000 0.00 0.00 39.87 2.83
79 82 0.386476 TACGAAGCACACGTCCTTGT 59.614 50.000 6.17 0.00 43.62 3.16
80 83 1.060713 CTACGAAGCACACGTCCTTG 58.939 55.000 6.17 0.00 43.62 3.61
81 84 0.672342 ACTACGAAGCACACGTCCTT 59.328 50.000 6.17 0.00 43.62 3.36
82 85 0.240411 GACTACGAAGCACACGTCCT 59.760 55.000 6.17 0.00 43.62 3.85
83 86 0.240411 AGACTACGAAGCACACGTCC 59.760 55.000 6.17 0.00 43.62 4.79
84 87 1.197264 AGAGACTACGAAGCACACGTC 59.803 52.381 6.17 0.00 43.62 4.34
85 88 1.197264 GAGAGACTACGAAGCACACGT 59.803 52.381 7.81 7.81 45.75 4.49
95 98 6.981379 TGTTTTCTTTTACGAGAGACTACG 57.019 37.500 0.00 0.00 0.00 3.51
103 106 5.154222 GGCCAAGATGTTTTCTTTTACGAG 58.846 41.667 0.00 0.00 42.15 4.18
122 125 1.150536 GACACAAGGGAAGTGGCCA 59.849 57.895 0.00 0.00 39.12 5.36
123 126 0.690762 TAGACACAAGGGAAGTGGCC 59.309 55.000 0.00 0.00 46.27 5.36
154 157 2.981859 AACTGTACCTCCTTATGCCG 57.018 50.000 0.00 0.00 0.00 5.69
155 158 5.924825 CGTAATAACTGTACCTCCTTATGCC 59.075 44.000 0.00 0.00 0.00 4.40
157 160 8.411683 AGAACGTAATAACTGTACCTCCTTATG 58.588 37.037 0.00 0.00 0.00 1.90
295 301 6.017933 CGAAGCAAAATGAGTGAATCTACAC 58.982 40.000 0.00 0.00 40.60 2.90
317 323 5.694231 ACGCCAATATGTACTACATACGA 57.306 39.130 17.38 0.11 43.13 3.43
370 393 9.868277 AAAAATATTTAGTCCGCATTGAAATCA 57.132 25.926 0.01 0.00 0.00 2.57
421 444 4.948062 AATATATTTAGGTGGGGAGCCC 57.052 45.455 0.00 0.00 45.71 5.19
422 445 6.140968 AGAAATATATTTAGGTGGGGAGCC 57.859 41.667 10.68 0.00 0.00 4.70
423 446 6.779860 TGAGAAATATATTTAGGTGGGGAGC 58.220 40.000 10.68 0.00 0.00 4.70
424 447 8.440771 ACTTGAGAAATATATTTAGGTGGGGAG 58.559 37.037 10.68 4.65 0.00 4.30
425 448 8.344939 ACTTGAGAAATATATTTAGGTGGGGA 57.655 34.615 10.68 0.00 0.00 4.81
426 449 8.996651 AACTTGAGAAATATATTTAGGTGGGG 57.003 34.615 10.68 2.25 0.00 4.96
437 460 9.104965 CGATGGGTTACAAACTTGAGAAATATA 57.895 33.333 0.00 0.00 0.00 0.86
438 461 7.610305 ACGATGGGTTACAAACTTGAGAAATAT 59.390 33.333 0.00 0.00 0.00 1.28
439 462 6.938030 ACGATGGGTTACAAACTTGAGAAATA 59.062 34.615 0.00 0.00 0.00 1.40
440 463 5.768164 ACGATGGGTTACAAACTTGAGAAAT 59.232 36.000 0.00 0.00 0.00 2.17
441 464 5.127491 ACGATGGGTTACAAACTTGAGAAA 58.873 37.500 0.00 0.00 0.00 2.52
442 465 4.710324 ACGATGGGTTACAAACTTGAGAA 58.290 39.130 0.00 0.00 0.00 2.87
443 466 4.345859 ACGATGGGTTACAAACTTGAGA 57.654 40.909 0.00 0.00 0.00 3.27
444 467 5.929992 TCTAACGATGGGTTACAAACTTGAG 59.070 40.000 0.00 0.00 40.09 3.02
445 468 5.697633 GTCTAACGATGGGTTACAAACTTGA 59.302 40.000 0.00 0.00 40.09 3.02
446 469 5.699458 AGTCTAACGATGGGTTACAAACTTG 59.301 40.000 0.00 0.00 40.09 3.16
447 470 5.861727 AGTCTAACGATGGGTTACAAACTT 58.138 37.500 0.00 0.00 40.09 2.66
448 471 5.479124 AGTCTAACGATGGGTTACAAACT 57.521 39.130 0.00 0.00 40.09 2.66
449 472 7.838771 ATTAGTCTAACGATGGGTTACAAAC 57.161 36.000 0.00 0.00 40.09 2.93
450 473 9.369904 GTAATTAGTCTAACGATGGGTTACAAA 57.630 33.333 0.00 0.00 40.09 2.83
451 474 8.530311 TGTAATTAGTCTAACGATGGGTTACAA 58.470 33.333 8.99 0.00 40.09 2.41
452 475 8.065473 TGTAATTAGTCTAACGATGGGTTACA 57.935 34.615 7.93 7.93 40.09 2.41
453 476 8.931385 TTGTAATTAGTCTAACGATGGGTTAC 57.069 34.615 0.00 0.00 40.09 2.50
454 477 9.590451 CTTTGTAATTAGTCTAACGATGGGTTA 57.410 33.333 0.00 0.00 40.09 2.85
455 478 8.316214 TCTTTGTAATTAGTCTAACGATGGGTT 58.684 33.333 0.00 0.00 42.75 4.11
456 479 7.844009 TCTTTGTAATTAGTCTAACGATGGGT 58.156 34.615 0.00 0.00 0.00 4.51
457 480 7.438459 CCTCTTTGTAATTAGTCTAACGATGGG 59.562 40.741 0.00 0.00 0.00 4.00
458 481 8.195436 TCCTCTTTGTAATTAGTCTAACGATGG 58.805 37.037 0.00 0.00 0.00 3.51
459 482 9.582431 TTCCTCTTTGTAATTAGTCTAACGATG 57.418 33.333 0.00 0.00 0.00 3.84
470 493 9.679661 TGCTCATGTAATTCCTCTTTGTAATTA 57.320 29.630 0.00 0.00 0.00 1.40
471 494 8.462016 GTGCTCATGTAATTCCTCTTTGTAATT 58.538 33.333 0.00 0.00 0.00 1.40
472 495 7.201644 CGTGCTCATGTAATTCCTCTTTGTAAT 60.202 37.037 0.00 0.00 0.00 1.89
473 496 6.092122 CGTGCTCATGTAATTCCTCTTTGTAA 59.908 38.462 0.00 0.00 0.00 2.41
474 497 5.580691 CGTGCTCATGTAATTCCTCTTTGTA 59.419 40.000 0.00 0.00 0.00 2.41
475 498 4.393062 CGTGCTCATGTAATTCCTCTTTGT 59.607 41.667 0.00 0.00 0.00 2.83
476 499 4.393062 ACGTGCTCATGTAATTCCTCTTTG 59.607 41.667 0.00 0.00 0.00 2.77
477 500 4.393062 CACGTGCTCATGTAATTCCTCTTT 59.607 41.667 0.82 0.00 0.00 2.52
478 501 3.935203 CACGTGCTCATGTAATTCCTCTT 59.065 43.478 0.82 0.00 0.00 2.85
479 502 3.055819 ACACGTGCTCATGTAATTCCTCT 60.056 43.478 17.22 0.00 0.00 3.69
480 503 3.262420 ACACGTGCTCATGTAATTCCTC 58.738 45.455 17.22 0.00 0.00 3.71
481 504 3.334583 ACACGTGCTCATGTAATTCCT 57.665 42.857 17.22 0.00 0.00 3.36
482 505 4.181578 ACTACACGTGCTCATGTAATTCC 58.818 43.478 17.22 0.00 31.09 3.01
483 506 4.027621 CGACTACACGTGCTCATGTAATTC 60.028 45.833 17.22 0.00 31.09 2.17
484 507 3.857665 CGACTACACGTGCTCATGTAATT 59.142 43.478 17.22 0.00 31.09 1.40
485 508 3.119602 ACGACTACACGTGCTCATGTAAT 60.120 43.478 17.22 0.00 44.84 1.89
486 509 2.227149 ACGACTACACGTGCTCATGTAA 59.773 45.455 17.22 0.00 44.84 2.41
487 510 1.808343 ACGACTACACGTGCTCATGTA 59.192 47.619 17.22 0.00 44.84 2.29
488 511 0.596577 ACGACTACACGTGCTCATGT 59.403 50.000 17.22 6.49 44.84 3.21
489 512 3.401577 ACGACTACACGTGCTCATG 57.598 52.632 17.22 5.78 44.84 3.07
497 520 4.025061 CCTACCTCTTATCACGACTACACG 60.025 50.000 0.00 0.00 39.31 4.49
498 521 5.121811 TCCTACCTCTTATCACGACTACAC 58.878 45.833 0.00 0.00 0.00 2.90
499 522 5.363562 TCCTACCTCTTATCACGACTACA 57.636 43.478 0.00 0.00 0.00 2.74
500 523 5.587844 TGTTCCTACCTCTTATCACGACTAC 59.412 44.000 0.00 0.00 0.00 2.73
501 524 5.587844 GTGTTCCTACCTCTTATCACGACTA 59.412 44.000 0.00 0.00 0.00 2.59
502 525 4.398673 GTGTTCCTACCTCTTATCACGACT 59.601 45.833 0.00 0.00 0.00 4.18
503 526 4.439837 GGTGTTCCTACCTCTTATCACGAC 60.440 50.000 0.00 0.00 37.74 4.34
504 527 3.698040 GGTGTTCCTACCTCTTATCACGA 59.302 47.826 0.00 0.00 37.74 4.35
505 528 3.446161 TGGTGTTCCTACCTCTTATCACG 59.554 47.826 0.00 0.00 41.43 4.35
506 529 4.141914 CCTGGTGTTCCTACCTCTTATCAC 60.142 50.000 0.00 0.00 41.43 3.06
507 530 4.030913 CCTGGTGTTCCTACCTCTTATCA 58.969 47.826 0.00 0.00 41.43 2.15
508 531 4.287552 TCCTGGTGTTCCTACCTCTTATC 58.712 47.826 0.00 0.00 41.43 1.75
509 532 4.348020 TCCTGGTGTTCCTACCTCTTAT 57.652 45.455 0.00 0.00 41.43 1.73
510 533 3.839323 TCCTGGTGTTCCTACCTCTTA 57.161 47.619 0.00 0.00 41.43 2.10
511 534 2.715763 TCCTGGTGTTCCTACCTCTT 57.284 50.000 0.00 0.00 41.43 2.85
512 535 2.111972 TCTTCCTGGTGTTCCTACCTCT 59.888 50.000 0.00 0.00 41.43 3.69
513 536 2.498078 CTCTTCCTGGTGTTCCTACCTC 59.502 54.545 0.00 0.00 41.43 3.85
514 537 2.541466 CTCTTCCTGGTGTTCCTACCT 58.459 52.381 0.00 0.00 41.43 3.08
515 538 1.555533 CCTCTTCCTGGTGTTCCTACC 59.444 57.143 0.00 0.00 41.24 3.18
516 539 1.066071 GCCTCTTCCTGGTGTTCCTAC 60.066 57.143 0.00 0.00 34.23 3.18
517 540 1.276622 GCCTCTTCCTGGTGTTCCTA 58.723 55.000 0.00 0.00 34.23 2.94
518 541 1.831652 CGCCTCTTCCTGGTGTTCCT 61.832 60.000 0.00 0.00 34.23 3.36
519 542 1.376037 CGCCTCTTCCTGGTGTTCC 60.376 63.158 0.00 0.00 0.00 3.62
520 543 2.035442 GCGCCTCTTCCTGGTGTTC 61.035 63.158 0.00 0.00 37.40 3.18
521 544 2.032681 GCGCCTCTTCCTGGTGTT 59.967 61.111 0.00 0.00 37.40 3.32
522 545 4.021925 GGCGCCTCTTCCTGGTGT 62.022 66.667 22.15 0.00 37.40 4.16
523 546 4.785453 GGGCGCCTCTTCCTGGTG 62.785 72.222 28.56 0.00 38.07 4.17
525 548 4.479993 CAGGGCGCCTCTTCCTGG 62.480 72.222 28.56 5.65 43.09 4.45
527 550 1.198759 TAAACAGGGCGCCTCTTCCT 61.199 55.000 28.56 11.88 0.00 3.36
528 551 0.107165 ATAAACAGGGCGCCTCTTCC 60.107 55.000 28.56 9.28 0.00 3.46
529 552 1.017387 CATAAACAGGGCGCCTCTTC 58.983 55.000 28.56 9.72 0.00 2.87
530 553 0.328258 ACATAAACAGGGCGCCTCTT 59.672 50.000 28.56 16.17 0.00 2.85
531 554 1.134491 GTACATAAACAGGGCGCCTCT 60.134 52.381 28.56 19.05 0.00 3.69
532 555 1.134491 AGTACATAAACAGGGCGCCTC 60.134 52.381 28.56 16.85 0.00 4.70
533 556 0.909623 AGTACATAAACAGGGCGCCT 59.090 50.000 28.56 8.66 0.00 5.52
534 557 1.014352 CAGTACATAAACAGGGCGCC 58.986 55.000 21.18 21.18 0.00 6.53
535 558 1.014352 CCAGTACATAAACAGGGCGC 58.986 55.000 0.00 0.00 0.00 6.53
536 559 2.396590 ACCAGTACATAAACAGGGCG 57.603 50.000 0.00 0.00 30.62 6.13
537 560 4.332828 AGAAACCAGTACATAAACAGGGC 58.667 43.478 0.00 0.00 30.62 5.19
538 561 6.001460 TGAAGAAACCAGTACATAAACAGGG 58.999 40.000 0.00 0.00 30.62 4.45
539 562 7.148239 GGATGAAGAAACCAGTACATAAACAGG 60.148 40.741 0.00 0.00 32.55 4.00
540 563 7.413000 CGGATGAAGAAACCAGTACATAAACAG 60.413 40.741 0.00 0.00 0.00 3.16
541 564 6.370442 CGGATGAAGAAACCAGTACATAAACA 59.630 38.462 0.00 0.00 0.00 2.83
542 565 6.183360 CCGGATGAAGAAACCAGTACATAAAC 60.183 42.308 0.00 0.00 0.00 2.01
543 566 5.878116 CCGGATGAAGAAACCAGTACATAAA 59.122 40.000 0.00 0.00 0.00 1.40
544 567 5.046159 ACCGGATGAAGAAACCAGTACATAA 60.046 40.000 9.46 0.00 0.00 1.90
545 568 4.468510 ACCGGATGAAGAAACCAGTACATA 59.531 41.667 9.46 0.00 0.00 2.29
546 569 3.263425 ACCGGATGAAGAAACCAGTACAT 59.737 43.478 9.46 0.00 0.00 2.29
547 570 2.635915 ACCGGATGAAGAAACCAGTACA 59.364 45.455 9.46 0.00 0.00 2.90
548 571 3.000727 CACCGGATGAAGAAACCAGTAC 58.999 50.000 9.46 0.00 0.00 2.73
549 572 2.635915 ACACCGGATGAAGAAACCAGTA 59.364 45.455 9.46 0.00 0.00 2.74
550 573 1.420138 ACACCGGATGAAGAAACCAGT 59.580 47.619 9.46 0.00 0.00 4.00
551 574 1.806542 CACACCGGATGAAGAAACCAG 59.193 52.381 9.46 0.00 0.00 4.00
552 575 1.142060 ACACACCGGATGAAGAAACCA 59.858 47.619 9.46 0.00 0.00 3.67
553 576 1.804748 GACACACCGGATGAAGAAACC 59.195 52.381 9.46 0.00 0.00 3.27
554 577 1.804748 GGACACACCGGATGAAGAAAC 59.195 52.381 9.46 0.00 0.00 2.78
555 578 1.418264 TGGACACACCGGATGAAGAAA 59.582 47.619 9.46 0.00 42.61 2.52
556 579 1.052617 TGGACACACCGGATGAAGAA 58.947 50.000 9.46 0.00 42.61 2.52
557 580 2.753319 TGGACACACCGGATGAAGA 58.247 52.632 9.46 0.00 42.61 2.87
564 587 0.249120 TAATGCTCTGGACACACCGG 59.751 55.000 0.00 0.00 45.93 5.28
565 588 1.204704 TCTAATGCTCTGGACACACCG 59.795 52.381 0.00 0.00 42.61 4.94
566 589 2.234908 ACTCTAATGCTCTGGACACACC 59.765 50.000 0.00 0.00 39.54 4.16
567 590 3.257393 CACTCTAATGCTCTGGACACAC 58.743 50.000 0.00 0.00 0.00 3.82
568 591 2.899900 ACACTCTAATGCTCTGGACACA 59.100 45.455 0.00 0.00 0.00 3.72
569 592 3.601443 ACACTCTAATGCTCTGGACAC 57.399 47.619 0.00 0.00 0.00 3.67
570 593 5.738619 TTTACACTCTAATGCTCTGGACA 57.261 39.130 0.00 0.00 0.00 4.02
571 594 7.617041 AAATTTACACTCTAATGCTCTGGAC 57.383 36.000 0.00 0.00 0.00 4.02
572 595 8.540388 AGTAAATTTACACTCTAATGCTCTGGA 58.460 33.333 26.06 0.00 36.12 3.86
573 596 8.723942 AGTAAATTTACACTCTAATGCTCTGG 57.276 34.615 26.06 0.00 36.12 3.86
574 597 9.371136 TGAGTAAATTTACACTCTAATGCTCTG 57.629 33.333 26.06 0.00 41.46 3.35
605 628 4.825634 TCCACCACGAACTACATATAGAGG 59.174 45.833 0.00 0.00 32.23 3.69
685 822 3.372206 AGCAAATCATACTCTTCGTGCAC 59.628 43.478 6.82 6.82 33.21 4.57
686 823 3.599343 AGCAAATCATACTCTTCGTGCA 58.401 40.909 0.00 0.00 33.21 4.57
687 824 4.337763 CAAGCAAATCATACTCTTCGTGC 58.662 43.478 0.00 0.00 0.00 5.34
693 830 3.659183 AGGCCAAGCAAATCATACTCT 57.341 42.857 5.01 0.00 0.00 3.24
755 892 7.436118 CAAGGAACATGGATCTTTTTGAGAAA 58.564 34.615 0.00 0.00 38.06 2.52
756 893 6.517194 GCAAGGAACATGGATCTTTTTGAGAA 60.517 38.462 0.00 0.00 38.06 2.87
757 894 5.047802 GCAAGGAACATGGATCTTTTTGAGA 60.048 40.000 0.00 0.00 39.13 3.27
758 895 5.166398 GCAAGGAACATGGATCTTTTTGAG 58.834 41.667 0.00 0.00 0.00 3.02
923 1060 6.531021 TCAAAGGTCTAGGTCAACTTAAAGG 58.469 40.000 0.00 0.00 0.00 3.11
1037 1175 2.686915 ACGACCAGCACCAGTATACTAC 59.313 50.000 4.74 0.00 0.00 2.73
1061 1199 3.958018 ACACTACCAGTCAACAAAACCA 58.042 40.909 0.00 0.00 0.00 3.67
1072 1210 4.948004 TGTATCAGATCGAACACTACCAGT 59.052 41.667 0.00 0.00 0.00 4.00
1098 1236 8.833231 TGGAGTCTTCTTTAACAGTATTCAAG 57.167 34.615 0.00 0.00 0.00 3.02
1144 1282 5.997129 TGTCGACTGTATATATTACACCGGA 59.003 40.000 17.92 0.00 0.00 5.14
1172 1310 5.575157 TCTTCCTATAGGCATCAGGACTAG 58.425 45.833 14.50 0.00 41.51 2.57
1313 1451 4.858680 TTGGTGTGCCCGCGACAA 62.859 61.111 8.23 0.00 35.15 3.18
1330 1468 5.339008 TCGATAGCAAATGTTACACCTCT 57.661 39.130 0.00 0.00 0.00 3.69
1395 1533 7.914427 TGGAGCTTCCATAAAGAAGTATCTA 57.086 36.000 3.47 0.00 42.67 1.98
1608 1746 7.287927 TCTGAAACCATCTGGATAACTACTAGG 59.712 40.741 2.55 0.00 38.94 3.02
1612 1750 6.284459 CCTCTGAAACCATCTGGATAACTAC 58.716 44.000 2.55 0.00 38.94 2.73
1711 1849 5.104941 TGTTCTCAAGATCAATCATACGGGT 60.105 40.000 0.00 0.00 0.00 5.28
2128 2266 1.204312 GTTGCTTCGCGAAGTCACC 59.796 57.895 40.02 28.80 40.45 4.02
2414 2552 2.963101 TGGATATAGACGTCAACTGGGG 59.037 50.000 19.50 0.00 0.00 4.96
2415 2553 3.005897 CCTGGATATAGACGTCAACTGGG 59.994 52.174 19.50 5.47 0.00 4.45
2416 2554 3.005897 CCCTGGATATAGACGTCAACTGG 59.994 52.174 19.50 12.68 0.00 4.00
2418 2556 3.637229 CACCCTGGATATAGACGTCAACT 59.363 47.826 19.50 4.01 0.00 3.16
2424 2562 7.275779 CGATTATTTTCACCCTGGATATAGACG 59.724 40.741 0.00 0.00 0.00 4.18
2430 2568 5.373222 CACCGATTATTTTCACCCTGGATA 58.627 41.667 0.00 0.00 0.00 2.59
2433 2571 2.099098 GCACCGATTATTTTCACCCTGG 59.901 50.000 0.00 0.00 0.00 4.45
2436 2574 3.632145 AGATGCACCGATTATTTTCACCC 59.368 43.478 0.00 0.00 0.00 4.61
2658 2799 3.135348 TGCATCCCTGAGTAAAGATCCAG 59.865 47.826 0.00 0.00 0.00 3.86
2678 2822 7.907045 CCAACGAGCTATATAAATTCATGATGC 59.093 37.037 0.00 0.00 0.00 3.91
2691 2835 3.737047 CGTCAACCACCAACGAGCTATAT 60.737 47.826 0.00 0.00 38.65 0.86
2712 2856 1.323412 CTGGATAGTCCCTGTCCTCG 58.677 60.000 8.27 0.00 41.45 4.63
2732 2876 1.676967 GCCTTGAGCCACCCTTCTG 60.677 63.158 0.00 0.00 34.35 3.02
2813 2957 3.798337 GCAACATAAAGTACATGCATGGC 59.202 43.478 29.41 20.86 32.90 4.40
3061 3213 7.122650 GGAAACCTTAACCATCTTTGATCATCA 59.877 37.037 0.00 0.00 0.00 3.07
3062 3214 7.340487 AGGAAACCTTAACCATCTTTGATCATC 59.660 37.037 0.00 0.00 0.00 2.92
3063 3215 7.184862 AGGAAACCTTAACCATCTTTGATCAT 58.815 34.615 0.00 0.00 0.00 2.45
3270 3440 9.072375 TGAAGTGATGTTTGATATAACCAACAA 57.928 29.630 4.15 0.00 0.00 2.83
3271 3441 8.628630 TGAAGTGATGTTTGATATAACCAACA 57.371 30.769 2.72 2.72 0.00 3.33
3272 3442 9.507280 CATGAAGTGATGTTTGATATAACCAAC 57.493 33.333 0.00 0.00 0.00 3.77
3279 3449 6.544931 CCCAGTCATGAAGTGATGTTTGATAT 59.455 38.462 0.00 0.00 39.48 1.63
3298 3469 2.568623 ACCTTTGTGATCACCCAGTC 57.431 50.000 22.85 0.00 0.00 3.51
3321 3492 7.101054 ACAAACGCTTTATGAGATACCTGTAA 58.899 34.615 0.00 0.00 0.00 2.41
3335 3506 5.118050 CGAGTGTGATCTAACAAACGCTTTA 59.882 40.000 0.00 0.00 33.72 1.85
3340 3511 4.321217 GTCTCGAGTGTGATCTAACAAACG 59.679 45.833 13.13 1.25 33.67 3.60
3601 3791 4.087907 CCCCCTTTATCGGTTTTTACCAA 58.912 43.478 0.00 0.00 0.00 3.67
3606 3796 2.312424 TGCCCCCTTTATCGGTTTTT 57.688 45.000 0.00 0.00 0.00 1.94
3635 3853 7.845037 TGCTCTCCGATCAATAATCAATAGAT 58.155 34.615 0.00 0.00 33.65 1.98
3636 3854 7.039434 ACTGCTCTCCGATCAATAATCAATAGA 60.039 37.037 0.00 0.00 33.65 1.98


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

AutoCloner maintained by Alex Coulton.