Multiple sequence alignment - TraesCS2D01G450900

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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 TraesCS2D01G450900 chr2D 100.000 3857 0 0 1 3857 560866989 560863133 0.000000e+00 7123.0
1 TraesCS2D01G450900 chr2D 93.878 49 2 1 408 455 562354664 562354616 5.350000e-09 73.1
2 TraesCS2D01G450900 chr2A 88.706 3214 222 80 694 3823 700673671 700670515 0.000000e+00 3794.0
3 TraesCS2D01G450900 chr2A 83.544 316 44 7 105 418 700674504 700674195 4.880000e-74 289.0
4 TraesCS2D01G450900 chr2B 92.750 2593 131 25 592 3161 669190650 669193208 0.000000e+00 3694.0
5 TraesCS2D01G450900 chr2B 91.932 409 27 6 1 408 669190160 669190563 5.590000e-158 568.0
6 TraesCS2D01G450900 chr2B 97.727 44 1 0 421 464 453811133 453811090 4.130000e-10 76.8
7 TraesCS2D01G450900 chr2B 93.750 48 2 1 411 458 670438140 670438186 1.920000e-08 71.3
8 TraesCS2D01G450900 chr7D 78.514 1871 321 47 1094 2919 621158603 621160437 0.000000e+00 1153.0
9 TraesCS2D01G450900 chr7D 78.835 1356 218 40 1589 2919 621203452 621204763 0.000000e+00 850.0
10 TraesCS2D01G450900 chr7D 82.199 382 64 3 1075 1453 621202777 621203157 3.720000e-85 326.0
11 TraesCS2D01G450900 chr7A 80.521 1304 194 33 1112 2392 715785589 715784323 0.000000e+00 946.0
12 TraesCS2D01G450900 chr7A 80.054 1103 184 26 1647 2731 715925501 715924417 0.000000e+00 785.0
13 TraesCS2D01G450900 chr7A 81.016 374 60 9 1089 1453 715925917 715925546 1.750000e-73 287.0
14 TraesCS2D01G450900 chr7B 78.378 1184 195 35 1550 2700 717226130 717224975 0.000000e+00 712.0
15 TraesCS2D01G450900 chr7B 78.125 1184 198 35 1550 2700 717150658 717149503 0.000000e+00 695.0
16 TraesCS2D01G450900 chr7B 95.745 47 1 1 407 452 648760005 648760051 1.490000e-09 75.0
17 TraesCS2D01G450900 chr7B 92.157 51 3 1 408 458 720496932 720496883 1.920000e-08 71.3
18 TraesCS2D01G450900 chr5D 96.000 50 2 0 408 457 547276054 547276005 8.880000e-12 82.4
19 TraesCS2D01G450900 chr5D 87.500 64 5 2 402 462 563411293 563411356 1.920000e-08 71.3
20 TraesCS2D01G450900 chrUn 95.918 49 1 1 408 455 108991137 108991089 1.150000e-10 78.7
21 TraesCS2D01G450900 chr3B 95.833 48 1 1 408 455 829248495 829248449 4.130000e-10 76.8


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 TraesCS2D01G450900 chr2D 560863133 560866989 3856 True 7123.0 7123 100.000 1 3857 1 chr2D.!!$R1 3856
1 TraesCS2D01G450900 chr2A 700670515 700674504 3989 True 2041.5 3794 86.125 105 3823 2 chr2A.!!$R1 3718
2 TraesCS2D01G450900 chr2B 669190160 669193208 3048 False 2131.0 3694 92.341 1 3161 2 chr2B.!!$F2 3160
3 TraesCS2D01G450900 chr7D 621158603 621160437 1834 False 1153.0 1153 78.514 1094 2919 1 chr7D.!!$F1 1825
4 TraesCS2D01G450900 chr7D 621202777 621204763 1986 False 588.0 850 80.517 1075 2919 2 chr7D.!!$F2 1844
5 TraesCS2D01G450900 chr7A 715784323 715785589 1266 True 946.0 946 80.521 1112 2392 1 chr7A.!!$R1 1280
6 TraesCS2D01G450900 chr7A 715924417 715925917 1500 True 536.0 785 80.535 1089 2731 2 chr7A.!!$R2 1642
7 TraesCS2D01G450900 chr7B 717224975 717226130 1155 True 712.0 712 78.378 1550 2700 1 chr7B.!!$R2 1150
8 TraesCS2D01G450900 chr7B 717149503 717150658 1155 True 695.0 695 78.125 1550 2700 1 chr7B.!!$R1 1150

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
420 422 0.257039 TACCAGTACTCCCTCCGTCC 59.743 60.0 0.00 0.0 0.00 4.79 F
1011 1295 0.460987 GGAGGACAATGTCGCTGGAG 60.461 60.0 7.35 0.0 32.65 3.86 F
1071 1355 0.460987 CAGAAGATCCGTCCAGCCAC 60.461 60.0 0.00 0.0 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2251 2801 0.534203 TGAAAGAAGTGACCGCCCAC 60.534 55.000 0.00 0.00 37.32 4.61 R
2766 3334 1.298157 TTCCATTCGCCACAGCTTCG 61.298 55.000 0.00 0.00 36.60 3.79 R
2871 3439 2.242043 CAAGCTATAGGGCCAATTGGG 58.758 52.381 25.73 8.36 40.85 4.12 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
59 60 4.710528 ATCTTTCGTTGTTTCGTCTCAC 57.289 40.909 0.00 0.00 0.00 3.51
60 61 3.513662 TCTTTCGTTGTTTCGTCTCACA 58.486 40.909 0.00 0.00 0.00 3.58
65 66 3.001838 TCGTTGTTTCGTCTCACATTTGG 59.998 43.478 0.00 0.00 0.00 3.28
67 68 4.319477 CGTTGTTTCGTCTCACATTTGGAT 60.319 41.667 0.00 0.00 0.00 3.41
79 80 8.299570 GTCTCACATTTGGATTTATCACACTTT 58.700 33.333 0.00 0.00 0.00 2.66
80 81 8.298854 TCTCACATTTGGATTTATCACACTTTG 58.701 33.333 0.00 0.00 0.00 2.77
83 84 6.496565 ACATTTGGATTTATCACACTTTGGGA 59.503 34.615 0.00 0.00 32.34 4.37
99 100 6.153340 CACTTTGGGATTAAGGTCAATGATGT 59.847 38.462 0.00 0.00 0.00 3.06
123 124 3.358118 TCGGTCATTATTTCCAAACCCC 58.642 45.455 0.00 0.00 0.00 4.95
158 159 3.176297 GGGACCCCACATCACCAA 58.824 61.111 0.00 0.00 35.81 3.67
169 170 7.132128 ACCCCACATCACCAATCTTATTTAAT 58.868 34.615 0.00 0.00 0.00 1.40
204 205 7.877097 AGATATGTTTGCATTTTTGCTGGTAAA 59.123 29.630 0.00 0.00 36.58 2.01
207 208 8.168472 ATGTTTGCATTTTTGCTGGTAAAGCC 62.168 38.462 0.00 0.00 41.06 4.35
258 259 5.029807 TGGCGTGTGAATTCATTCCTATA 57.970 39.130 12.12 0.00 35.97 1.31
297 298 3.849911 CGAGAGGAGCTAATGTTGTTGA 58.150 45.455 0.00 0.00 0.00 3.18
318 319 9.624697 TGTTGAACATGAATTAGTCAAAATAGC 57.375 29.630 0.00 0.00 40.50 2.97
358 360 2.106338 TGAGTGGACCAAAGATGCTTCA 59.894 45.455 0.00 0.00 0.00 3.02
394 396 8.690203 TTCCTCTGTTGATCAAAGATGTAAAA 57.310 30.769 10.35 2.02 0.00 1.52
396 398 7.174946 TCCTCTGTTGATCAAAGATGTAAAACC 59.825 37.037 10.35 0.00 0.00 3.27
397 399 7.175641 CCTCTGTTGATCAAAGATGTAAAACCT 59.824 37.037 10.35 0.00 0.00 3.50
399 401 6.980593 TGTTGATCAAAGATGTAAAACCTGG 58.019 36.000 10.35 0.00 0.00 4.45
401 403 7.069331 TGTTGATCAAAGATGTAAAACCTGGTT 59.931 33.333 10.35 6.18 0.00 3.67
402 404 8.573035 GTTGATCAAAGATGTAAAACCTGGTTA 58.427 33.333 13.37 0.00 0.00 2.85
403 405 8.106247 TGATCAAAGATGTAAAACCTGGTTAC 57.894 34.615 13.37 8.98 33.00 2.50
404 406 6.887626 TCAAAGATGTAAAACCTGGTTACC 57.112 37.500 13.37 4.42 31.63 2.85
405 407 6.366340 TCAAAGATGTAAAACCTGGTTACCA 58.634 36.000 13.37 3.29 31.63 3.25
417 419 1.109609 GGTTACCAGTACTCCCTCCG 58.890 60.000 0.00 0.00 0.00 4.63
418 420 1.618074 GGTTACCAGTACTCCCTCCGT 60.618 57.143 0.00 0.00 0.00 4.69
419 421 1.747924 GTTACCAGTACTCCCTCCGTC 59.252 57.143 0.00 0.00 0.00 4.79
420 422 0.257039 TACCAGTACTCCCTCCGTCC 59.743 60.000 0.00 0.00 0.00 4.79
422 424 0.613853 CCAGTACTCCCTCCGTCCAA 60.614 60.000 0.00 0.00 0.00 3.53
424 426 1.621814 CAGTACTCCCTCCGTCCAAAA 59.378 52.381 0.00 0.00 0.00 2.44
426 428 2.038164 AGTACTCCCTCCGTCCAAAAAC 59.962 50.000 0.00 0.00 0.00 2.43
428 430 1.574702 CTCCCTCCGTCCAAAAACGC 61.575 60.000 0.00 0.00 41.26 4.84
429 431 1.599797 CCCTCCGTCCAAAAACGCT 60.600 57.895 0.00 0.00 41.26 5.07
430 432 1.574702 CCCTCCGTCCAAAAACGCTC 61.575 60.000 0.00 0.00 41.26 5.03
435 437 4.178540 CTCCGTCCAAAAACGCTCTTATA 58.821 43.478 0.00 0.00 41.26 0.98
436 438 4.761975 TCCGTCCAAAAACGCTCTTATAT 58.238 39.130 0.00 0.00 41.26 0.86
437 439 5.180271 TCCGTCCAAAAACGCTCTTATATT 58.820 37.500 0.00 0.00 41.26 1.28
440 442 7.042321 TCCGTCCAAAAACGCTCTTATATTATG 60.042 37.037 0.00 0.00 41.26 1.90
441 443 7.069569 CGTCCAAAAACGCTCTTATATTATGG 58.930 38.462 0.00 0.00 35.64 2.74
444 446 7.227910 TCCAAAAACGCTCTTATATTATGGGAC 59.772 37.037 0.00 0.00 0.00 4.46
445 447 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
446 448 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
447 449 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
448 450 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
449 451 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
450 452 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
451 453 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
452 454 5.850278 TCTTATATTATGGGACGGAGGGAT 58.150 41.667 0.00 0.00 0.00 3.85
458 484 1.200519 TGGGACGGAGGGATTAGTTG 58.799 55.000 0.00 0.00 0.00 3.16
471 497 7.147461 GGAGGGATTAGTTGATAAAGAGGAAGT 60.147 40.741 0.00 0.00 0.00 3.01
472 498 8.164057 AGGGATTAGTTGATAAAGAGGAAGTT 57.836 34.615 0.00 0.00 0.00 2.66
473 499 9.280456 AGGGATTAGTTGATAAAGAGGAAGTTA 57.720 33.333 0.00 0.00 0.00 2.24
592 625 9.730420 TTTAGACAAGAGAAGTTAACAAATTGC 57.270 29.630 8.61 3.01 0.00 3.56
593 626 7.573968 AGACAAGAGAAGTTAACAAATTGCT 57.426 32.000 8.61 4.86 0.00 3.91
594 627 8.000780 AGACAAGAGAAGTTAACAAATTGCTT 57.999 30.769 8.61 1.07 0.00 3.91
595 628 8.470002 AGACAAGAGAAGTTAACAAATTGCTTT 58.530 29.630 8.61 0.00 0.00 3.51
596 629 9.087424 GACAAGAGAAGTTAACAAATTGCTTTT 57.913 29.630 8.61 0.00 0.00 2.27
599 632 8.803201 AGAGAAGTTAACAAATTGCTTTTAGC 57.197 30.769 8.61 0.00 42.82 3.09
632 665 3.876309 TTTTTAGGGGAGAGCAACAGT 57.124 42.857 0.00 0.00 0.00 3.55
633 666 3.876309 TTTTAGGGGAGAGCAACAGTT 57.124 42.857 0.00 0.00 0.00 3.16
634 667 4.986054 TTTTAGGGGAGAGCAACAGTTA 57.014 40.909 0.00 0.00 0.00 2.24
635 668 4.986054 TTTAGGGGAGAGCAACAGTTAA 57.014 40.909 0.00 0.00 0.00 2.01
636 669 2.861147 AGGGGAGAGCAACAGTTAAC 57.139 50.000 0.00 0.00 0.00 2.01
637 670 2.054799 AGGGGAGAGCAACAGTTAACA 58.945 47.619 8.61 0.00 0.00 2.41
638 671 2.441750 AGGGGAGAGCAACAGTTAACAA 59.558 45.455 8.61 0.00 0.00 2.83
639 672 3.117663 AGGGGAGAGCAACAGTTAACAAA 60.118 43.478 8.61 0.00 0.00 2.83
640 673 3.826729 GGGGAGAGCAACAGTTAACAAAT 59.173 43.478 8.61 0.00 0.00 2.32
641 674 4.280929 GGGGAGAGCAACAGTTAACAAATT 59.719 41.667 8.61 0.00 0.00 1.82
642 675 5.222631 GGGAGAGCAACAGTTAACAAATTG 58.777 41.667 8.61 9.78 0.00 2.32
749 1007 2.731721 CGCACGAACGCACCACTA 60.732 61.111 0.00 0.00 0.00 2.74
750 1008 2.716828 CGCACGAACGCACCACTAG 61.717 63.158 0.00 0.00 0.00 2.57
751 1009 3.011760 GCACGAACGCACCACTAGC 62.012 63.158 0.00 0.00 0.00 3.42
1011 1295 0.460987 GGAGGACAATGTCGCTGGAG 60.461 60.000 7.35 0.00 32.65 3.86
1062 1346 2.278857 CCGTCGGCAGAAGATCCG 60.279 66.667 0.00 0.00 46.52 4.18
1071 1355 0.460987 CAGAAGATCCGTCCAGCCAC 60.461 60.000 0.00 0.00 0.00 5.01
2019 2561 7.658982 TGATTATCTTGCTCATATCACTGAACC 59.341 37.037 0.00 0.00 0.00 3.62
2125 2671 4.673580 GCAGCAATGTCCTCTTTGTATGTG 60.674 45.833 0.00 0.00 33.21 3.21
2144 2690 1.417517 TGCTTCTCTGCTGGACTTTGA 59.582 47.619 0.00 0.00 0.00 2.69
2156 2702 6.222389 TGCTGGACTTTGATTTAATTTGTGG 58.778 36.000 0.00 0.00 0.00 4.17
2175 2721 4.227073 TGTGGTATCTGAAATCATGGACCA 59.773 41.667 0.00 0.00 31.95 4.02
2292 2843 4.993584 CAGAGCATGACAGAACTACAACTT 59.006 41.667 0.00 0.00 0.00 2.66
2407 2961 3.243401 GGTCTTACACCTTTGCACCTTTG 60.243 47.826 0.00 0.00 42.84 2.77
2438 2994 8.451908 AACTTAAGTTGATTTGCTCAGTAGTT 57.548 30.769 19.94 0.00 36.80 2.24
2445 3001 6.668541 TGATTTGCTCAGTAGTTATTCTGC 57.331 37.500 0.00 0.00 0.00 4.26
2455 3011 9.202273 CTCAGTAGTTATTCTGCCATCTTATTC 57.798 37.037 0.00 0.00 0.00 1.75
2458 3014 8.153550 AGTAGTTATTCTGCCATCTTATTCCAG 58.846 37.037 0.00 0.00 0.00 3.86
2469 3025 6.044682 CCATCTTATTCCAGTGGCATTTTTC 58.955 40.000 3.51 0.00 0.00 2.29
2479 3035 5.814705 CCAGTGGCATTTTTCTTGTGTTTTA 59.185 36.000 0.00 0.00 0.00 1.52
2547 3110 2.938798 CCCAGTGGGCCCTTGGTA 60.939 66.667 31.63 9.67 35.35 3.25
2557 3120 2.979678 GGGCCCTTGGTAGATTCATCTA 59.020 50.000 17.04 0.00 38.32 1.98
2644 3207 2.107950 TAACTGGAACCGCATTGAGG 57.892 50.000 4.73 4.73 0.00 3.86
2652 3215 2.338015 CCGCATTGAGGTGCAGCTT 61.338 57.895 21.18 0.42 45.30 3.74
2657 3220 1.068748 CATTGAGGTGCAGCTTGTGTC 60.069 52.381 21.18 7.53 0.00 3.67
2732 3300 4.221262 CAGTTTGGTTCCATTGGATGTGAT 59.779 41.667 6.15 0.00 0.00 3.06
2747 3315 4.039245 GGATGTGATCGGTATTCAGAAGGA 59.961 45.833 0.00 0.00 0.00 3.36
2760 3328 7.279758 GGTATTCAGAAGGAAGATCTCTTGTTG 59.720 40.741 0.00 0.00 39.30 3.33
2766 3334 2.489722 GGAAGATCTCTTGTTGGTTGGC 59.510 50.000 0.00 0.00 36.11 4.52
2821 3389 1.228094 TTGGACGATGCTGCAACCA 60.228 52.632 6.36 11.36 0.00 3.67
2864 3432 0.109735 GCCGAAGTTTAGTTGCCAGC 60.110 55.000 0.00 0.00 0.00 4.85
2871 3439 0.673437 TTTAGTTGCCAGCCACAAGC 59.327 50.000 0.00 0.00 44.25 4.01
2931 3501 1.266175 CTGCCTTTTGACTGCTGTGAG 59.734 52.381 0.00 0.00 0.00 3.51
2972 3542 9.387257 CATATGATTATTGATGCAGTAGGCTAA 57.613 33.333 0.00 0.00 45.15 3.09
3145 3724 4.084066 CGCACAGTTCTACAATTGCAAGTA 60.084 41.667 4.94 1.65 0.00 2.24
3169 3748 9.976511 GTATTGATTTTCCATCATCAATGTCAT 57.023 29.630 14.77 0.00 45.59 3.06
3171 3750 6.731164 TGATTTTCCATCATCAATGTCATCG 58.269 36.000 0.00 0.00 33.13 3.84
3172 3751 4.556942 TTTCCATCATCAATGTCATCGC 57.443 40.909 0.00 0.00 33.13 4.58
3173 3752 2.497138 TCCATCATCAATGTCATCGCC 58.503 47.619 0.00 0.00 33.13 5.54
3174 3753 2.158784 TCCATCATCAATGTCATCGCCA 60.159 45.455 0.00 0.00 33.13 5.69
3176 3755 3.365969 CCATCATCAATGTCATCGCCATG 60.366 47.826 0.00 0.00 33.13 3.66
3177 3756 2.921821 TCATCAATGTCATCGCCATGT 58.078 42.857 0.00 0.00 0.00 3.21
3178 3757 4.070630 TCATCAATGTCATCGCCATGTA 57.929 40.909 0.00 0.00 0.00 2.29
3179 3758 4.644498 TCATCAATGTCATCGCCATGTAT 58.356 39.130 0.00 0.00 0.00 2.29
3180 3759 5.065235 TCATCAATGTCATCGCCATGTATT 58.935 37.500 0.00 0.00 0.00 1.89
3182 3761 5.833406 TCAATGTCATCGCCATGTATTTT 57.167 34.783 0.00 0.00 0.00 1.82
3183 3762 6.934048 TCAATGTCATCGCCATGTATTTTA 57.066 33.333 0.00 0.00 0.00 1.52
3185 3764 6.542005 TCAATGTCATCGCCATGTATTTTACT 59.458 34.615 0.00 0.00 0.00 2.24
3187 3766 8.341903 CAATGTCATCGCCATGTATTTTACTTA 58.658 33.333 0.00 0.00 0.00 2.24
3188 3767 7.241663 TGTCATCGCCATGTATTTTACTTAC 57.758 36.000 0.00 0.00 0.00 2.34
3189 3768 6.019398 TGTCATCGCCATGTATTTTACTTACG 60.019 38.462 0.00 0.00 0.00 3.18
3191 3770 6.926826 TCATCGCCATGTATTTTACTTACGAT 59.073 34.615 0.00 0.00 36.08 3.73
3192 3771 6.758593 TCGCCATGTATTTTACTTACGATC 57.241 37.500 0.00 0.00 0.00 3.69
3194 3773 6.982141 TCGCCATGTATTTTACTTACGATCTT 59.018 34.615 0.00 0.00 0.00 2.40
3195 3774 7.042992 TCGCCATGTATTTTACTTACGATCTTG 60.043 37.037 0.00 0.00 0.00 3.02
3196 3775 7.254319 CGCCATGTATTTTACTTACGATCTTGT 60.254 37.037 0.00 0.00 0.00 3.16
3197 3776 8.062448 GCCATGTATTTTACTTACGATCTTGTC 58.938 37.037 0.00 0.00 0.00 3.18
3198 3777 8.548721 CCATGTATTTTACTTACGATCTTGTCC 58.451 37.037 0.00 0.00 0.00 4.02
3199 3778 9.093970 CATGTATTTTACTTACGATCTTGTCCA 57.906 33.333 0.00 0.00 0.00 4.02
3200 3779 9.661563 ATGTATTTTACTTACGATCTTGTCCAA 57.338 29.630 0.00 0.00 0.00 3.53
3201 3780 9.146984 TGTATTTTACTTACGATCTTGTCCAAG 57.853 33.333 0.47 0.47 39.71 3.61
3202 3781 6.476243 TTTTACTTACGATCTTGTCCAAGC 57.524 37.500 2.09 0.00 38.28 4.01
3203 3782 2.607187 ACTTACGATCTTGTCCAAGCG 58.393 47.619 2.09 4.22 38.28 4.68
3204 3783 2.230508 ACTTACGATCTTGTCCAAGCGA 59.769 45.455 12.05 0.00 38.28 4.93
3205 3784 3.119101 ACTTACGATCTTGTCCAAGCGAT 60.119 43.478 12.05 0.00 38.28 4.58
3206 3785 2.386661 ACGATCTTGTCCAAGCGATT 57.613 45.000 12.05 0.00 38.28 3.34
3207 3786 2.002586 ACGATCTTGTCCAAGCGATTG 58.997 47.619 6.39 6.39 38.28 2.67
3208 3787 2.270923 CGATCTTGTCCAAGCGATTGA 58.729 47.619 16.33 0.00 38.28 2.57
3209 3788 2.283617 CGATCTTGTCCAAGCGATTGAG 59.716 50.000 16.33 4.10 38.28 3.02
3210 3789 2.099141 TCTTGTCCAAGCGATTGAGG 57.901 50.000 16.33 0.00 38.28 3.86
3219 3798 0.108585 AGCGATTGAGGTTGTGTGGT 59.891 50.000 0.00 0.00 0.00 4.16
3231 3810 1.031235 TGTGTGGTGTCCTGCAATTG 58.969 50.000 0.00 0.00 0.00 2.32
3232 3811 1.317613 GTGTGGTGTCCTGCAATTGA 58.682 50.000 10.34 0.00 0.00 2.57
3234 3813 0.883833 GTGGTGTCCTGCAATTGAGG 59.116 55.000 10.34 12.92 0.00 3.86
3235 3814 0.770499 TGGTGTCCTGCAATTGAGGA 59.230 50.000 17.56 17.56 37.27 3.71
3236 3815 1.355381 TGGTGTCCTGCAATTGAGGAT 59.645 47.619 21.80 0.00 41.75 3.24
3237 3816 1.747355 GGTGTCCTGCAATTGAGGATG 59.253 52.381 21.80 3.24 41.75 3.51
3238 3817 1.747355 GTGTCCTGCAATTGAGGATGG 59.253 52.381 21.80 11.16 41.75 3.51
3239 3818 0.743097 GTCCTGCAATTGAGGATGGC 59.257 55.000 21.80 11.15 41.75 4.40
3240 3819 0.396139 TCCTGCAATTGAGGATGGCC 60.396 55.000 17.56 0.00 34.49 5.36
3282 3861 3.143807 TGAAGTCAAAAGCCGTGTTTG 57.856 42.857 0.00 0.00 37.32 2.93
3300 3907 6.738200 CGTGTTTGCAGTATGTTTATCTTCTG 59.262 38.462 0.00 0.00 39.31 3.02
3344 3951 7.410120 AACATATGAGATTTTCAGGTTTCCC 57.590 36.000 10.38 0.00 39.68 3.97
3348 3955 4.320870 TGAGATTTTCAGGTTTCCCGTAC 58.679 43.478 0.00 0.00 35.12 3.67
3376 3983 5.009010 CAGGATGTACTGAGTTTGTTTTGCT 59.991 40.000 0.00 0.00 40.97 3.91
3402 4009 5.191323 ACAGACTTCCCTGATCATTCTGATT 59.809 40.000 15.68 0.23 37.20 2.57
3409 4016 7.966339 TCCCTGATCATTCTGATTTTCATTT 57.034 32.000 0.00 0.00 37.20 2.32
3430 4037 1.414158 CCGTGGAGGGATCAGTATGT 58.586 55.000 0.00 0.00 34.71 2.29
3431 4038 2.594131 CCGTGGAGGGATCAGTATGTA 58.406 52.381 0.00 0.00 34.71 2.29
3432 4039 2.296471 CCGTGGAGGGATCAGTATGTAC 59.704 54.545 0.00 0.00 34.71 2.90
3433 4040 2.956333 CGTGGAGGGATCAGTATGTACA 59.044 50.000 0.00 0.00 37.40 2.90
3434 4041 3.383505 CGTGGAGGGATCAGTATGTACAA 59.616 47.826 0.00 0.00 37.40 2.41
3435 4042 4.694339 GTGGAGGGATCAGTATGTACAAC 58.306 47.826 0.00 0.00 37.40 3.32
3436 4043 4.406003 GTGGAGGGATCAGTATGTACAACT 59.594 45.833 0.00 2.19 37.40 3.16
3444 4051 7.363530 GGGATCAGTATGTACAACTAACTGTCA 60.364 40.741 20.88 10.50 38.88 3.58
3446 4053 7.520451 TCAGTATGTACAACTAACTGTCAGT 57.480 36.000 20.88 0.00 38.88 3.41
3460 4067 3.129287 ACTGTCAGTTTTGTTTCAGCTGG 59.871 43.478 15.13 0.00 0.00 4.85
3472 4079 1.951209 TCAGCTGGAGGGACAATGTA 58.049 50.000 15.13 0.00 0.00 2.29
3511 4118 3.056952 CAAGAATTGCATAGCACGTCC 57.943 47.619 0.00 0.00 40.39 4.79
3512 4119 2.679837 CAAGAATTGCATAGCACGTCCT 59.320 45.455 0.00 0.00 40.39 3.85
3513 4120 2.283298 AGAATTGCATAGCACGTCCTG 58.717 47.619 0.00 0.00 38.71 3.86
3514 4121 2.009774 GAATTGCATAGCACGTCCTGT 58.990 47.619 0.00 0.00 38.71 4.00
3534 4141 5.334879 CCTGTTCGTGTAAAATGGGAGAAAG 60.335 44.000 0.00 0.00 0.00 2.62
3543 4150 7.393515 GTGTAAAATGGGAGAAAGTCAAGGTAT 59.606 37.037 0.00 0.00 0.00 2.73
3556 4163 5.850614 AGTCAAGGTATCGTGTAAACAACT 58.149 37.500 0.00 0.00 0.00 3.16
3557 4164 6.985117 AGTCAAGGTATCGTGTAAACAACTA 58.015 36.000 0.00 0.00 0.00 2.24
3572 4179 9.658475 TGTAAACAACTAAACATGATTTTCTCG 57.342 29.630 0.00 0.00 0.00 4.04
3579 4186 1.131126 ACATGATTTTCTCGCTTGCCG 59.869 47.619 0.00 0.00 38.61 5.69
3593 4200 3.120338 CGCTTGCCGAGAAACTATCAAAA 60.120 43.478 0.00 0.00 40.02 2.44
3600 4207 5.316770 CCGAGAAACTATCAAAAGCTTTCG 58.683 41.667 13.10 0.22 0.00 3.46
3615 4222 6.560253 AAGCTTTCGATGTCTTGTAATGTT 57.440 33.333 0.00 0.00 0.00 2.71
3652 4268 5.450412 CCCTGATGTGGTTCCAAATTTATCG 60.450 44.000 0.00 0.00 0.00 2.92
3659 4275 4.180817 GGTTCCAAATTTATCGGCTTTGG 58.819 43.478 7.21 7.21 46.66 3.28
3660 4276 3.518634 TCCAAATTTATCGGCTTTGGC 57.481 42.857 8.39 0.00 45.49 4.52
3675 4291 2.243602 TTGGCTCGAGTTACCGTTTT 57.756 45.000 15.13 0.00 0.00 2.43
3676 4292 1.504359 TGGCTCGAGTTACCGTTTTG 58.496 50.000 15.13 0.00 0.00 2.44
3678 4294 1.869132 GGCTCGAGTTACCGTTTTGTT 59.131 47.619 15.13 0.00 0.00 2.83
3682 4298 4.143452 GCTCGAGTTACCGTTTTGTTACTC 60.143 45.833 15.13 0.00 40.01 2.59
3697 4337 5.105567 TGTTACTCAACTTGTTTCCCTGA 57.894 39.130 0.00 0.00 35.56 3.86
3700 4340 2.173569 ACTCAACTTGTTTCCCTGAGCT 59.826 45.455 0.00 0.00 37.60 4.09
3712 4352 7.577303 TGTTTCCCTGAGCTATTTTATGAGAT 58.423 34.615 0.00 0.00 0.00 2.75
3732 4372 7.885297 TGAGATAGTTTGTCCTTTTCAATTGG 58.115 34.615 5.42 0.00 0.00 3.16
3733 4373 7.039784 TGAGATAGTTTGTCCTTTTCAATTGGG 60.040 37.037 5.42 0.00 0.00 4.12
3734 4374 7.010160 AGATAGTTTGTCCTTTTCAATTGGGA 58.990 34.615 5.42 1.08 0.00 4.37
3735 4375 5.948742 AGTTTGTCCTTTTCAATTGGGAA 57.051 34.783 5.42 0.00 0.00 3.97
3736 4376 6.499106 AGTTTGTCCTTTTCAATTGGGAAT 57.501 33.333 5.42 0.00 0.00 3.01
3737 4377 6.290605 AGTTTGTCCTTTTCAATTGGGAATG 58.709 36.000 5.42 3.96 0.00 2.67
3738 4378 6.099557 AGTTTGTCCTTTTCAATTGGGAATGA 59.900 34.615 5.42 1.27 0.00 2.57
3739 4379 5.467035 TGTCCTTTTCAATTGGGAATGAC 57.533 39.130 5.42 12.55 0.00 3.06
3740 4380 5.147032 TGTCCTTTTCAATTGGGAATGACT 58.853 37.500 19.78 0.00 0.00 3.41
3741 4381 5.010922 TGTCCTTTTCAATTGGGAATGACTG 59.989 40.000 19.78 3.32 0.00 3.51
3742 4382 4.527816 TCCTTTTCAATTGGGAATGACTGG 59.472 41.667 5.42 0.00 0.00 4.00
3743 4383 3.959535 TTTCAATTGGGAATGACTGGC 57.040 42.857 5.42 0.00 0.00 4.85
3744 4384 2.905415 TCAATTGGGAATGACTGGCT 57.095 45.000 5.42 0.00 0.00 4.75
3745 4385 4.314522 TTCAATTGGGAATGACTGGCTA 57.685 40.909 5.42 0.00 0.00 3.93
3746 4386 3.889815 TCAATTGGGAATGACTGGCTAG 58.110 45.455 5.42 0.00 0.00 3.42
3747 4387 2.954318 CAATTGGGAATGACTGGCTAGG 59.046 50.000 0.85 0.00 0.00 3.02
3748 4388 1.668826 TTGGGAATGACTGGCTAGGT 58.331 50.000 0.85 0.00 0.00 3.08
3749 4389 1.668826 TGGGAATGACTGGCTAGGTT 58.331 50.000 0.85 0.00 0.00 3.50
3750 4390 2.840511 TGGGAATGACTGGCTAGGTTA 58.159 47.619 0.85 0.00 0.00 2.85
3751 4391 3.393687 TGGGAATGACTGGCTAGGTTAT 58.606 45.455 0.85 0.00 0.00 1.89
3752 4392 3.391296 TGGGAATGACTGGCTAGGTTATC 59.609 47.826 0.85 0.00 0.00 1.75
3753 4393 3.244596 GGGAATGACTGGCTAGGTTATCC 60.245 52.174 0.85 4.01 0.00 2.59
3755 4395 4.103311 GGAATGACTGGCTAGGTTATCCTT 59.897 45.833 0.85 0.00 42.12 3.36
3756 4396 5.398012 GGAATGACTGGCTAGGTTATCCTTT 60.398 44.000 0.85 0.00 42.12 3.11
3757 4397 5.717119 ATGACTGGCTAGGTTATCCTTTT 57.283 39.130 0.85 0.00 42.12 2.27
3760 4400 5.250774 TGACTGGCTAGGTTATCCTTTTTCT 59.749 40.000 0.85 0.00 42.12 2.52
3764 4404 7.610692 ACTGGCTAGGTTATCCTTTTTCTAAAC 59.389 37.037 0.85 0.00 42.12 2.01
3776 4416 3.426787 TTTCTAAACGGGAATGGCTGA 57.573 42.857 0.00 0.00 0.00 4.26
3778 4418 1.065709 TCTAAACGGGAATGGCTGACC 60.066 52.381 0.00 0.00 0.00 4.02
3796 4437 8.764558 TGGCTGACCTACTTTAACTTGAATATA 58.235 33.333 0.00 0.00 36.63 0.86
3831 4472 9.754382 ATCAAATTCAAATCATACCTAATGCAC 57.246 29.630 0.00 0.00 35.38 4.57
3832 4473 8.970020 TCAAATTCAAATCATACCTAATGCACT 58.030 29.630 0.00 0.00 35.38 4.40
3833 4474 9.241317 CAAATTCAAATCATACCTAATGCACTC 57.759 33.333 0.00 0.00 35.38 3.51
3834 4475 8.523915 AATTCAAATCATACCTAATGCACTCA 57.476 30.769 0.00 0.00 35.38 3.41
3835 4476 8.701908 ATTCAAATCATACCTAATGCACTCAT 57.298 30.769 0.00 0.00 35.38 2.90
3836 4477 7.500720 TCAAATCATACCTAATGCACTCATG 57.499 36.000 0.00 0.00 35.38 3.07
3849 4490 2.130272 ACTCATGCTAGGAGTGTCGA 57.870 50.000 4.98 0.00 43.65 4.20
3850 4491 1.746220 ACTCATGCTAGGAGTGTCGAC 59.254 52.381 9.11 9.11 43.65 4.20
3851 4492 1.066303 CTCATGCTAGGAGTGTCGACC 59.934 57.143 14.12 4.42 0.00 4.79
3852 4493 0.103208 CATGCTAGGAGTGTCGACCC 59.897 60.000 14.12 7.19 0.00 4.46
3853 4494 0.033011 ATGCTAGGAGTGTCGACCCT 60.033 55.000 14.12 14.66 0.00 4.34
3854 4495 0.251653 TGCTAGGAGTGTCGACCCTT 60.252 55.000 15.74 3.81 0.00 3.95
3855 4496 0.896226 GCTAGGAGTGTCGACCCTTT 59.104 55.000 15.74 4.53 0.00 3.11
3856 4497 1.135053 GCTAGGAGTGTCGACCCTTTC 60.135 57.143 15.74 5.83 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 6.934056 TCCCAAAGTGTGATAAATCCAAATG 58.066 36.000 0.00 0.00 0.00 2.32
60 61 7.738437 ATCCCAAAGTGTGATAAATCCAAAT 57.262 32.000 0.00 0.00 0.00 2.32
65 66 8.293699 ACCTTAATCCCAAAGTGTGATAAATC 57.706 34.615 0.00 0.00 0.00 2.17
67 68 7.235079 TGACCTTAATCCCAAAGTGTGATAAA 58.765 34.615 0.00 0.00 0.00 1.40
79 80 5.449297 TGACATCATTGACCTTAATCCCA 57.551 39.130 0.00 0.00 0.00 4.37
80 81 5.180117 CGATGACATCATTGACCTTAATCCC 59.820 44.000 15.58 0.00 39.56 3.85
83 84 5.684704 ACCGATGACATCATTGACCTTAAT 58.315 37.500 15.58 0.00 39.56 1.40
99 100 4.642885 GGGTTTGGAAATAATGACCGATGA 59.357 41.667 0.00 0.00 0.00 2.92
123 124 1.098050 CCCTTGCTTCAATCCCTTCG 58.902 55.000 0.00 0.00 0.00 3.79
135 136 2.535317 ATGTGGGGTCCCCTTGCT 60.535 61.111 28.11 7.26 45.70 3.91
204 205 4.098960 CAGTTATCAATGATGGCAAAGGCT 59.901 41.667 5.91 0.00 40.87 4.58
207 208 8.407832 TGATAACAGTTATCAATGATGGCAAAG 58.592 33.333 27.13 0.00 46.54 2.77
208 209 8.291191 TGATAACAGTTATCAATGATGGCAAA 57.709 30.769 27.13 5.71 46.54 3.68
209 210 7.878547 TGATAACAGTTATCAATGATGGCAA 57.121 32.000 27.13 6.15 46.54 4.52
258 259 3.952323 TCTCGGACGATACTCAAAGGATT 59.048 43.478 0.00 0.00 0.00 3.01
272 273 1.025812 ACATTAGCTCCTCTCGGACG 58.974 55.000 0.00 0.00 34.92 4.79
318 319 9.219603 TCCACTCATTACAAAACAAAGATCTAG 57.780 33.333 0.00 0.00 0.00 2.43
358 360 3.898123 TCAACAGAGGAAGTAGCTCAGTT 59.102 43.478 0.00 0.00 0.00 3.16
397 399 1.617804 CGGAGGGAGTACTGGTAACCA 60.618 57.143 0.00 0.00 0.00 3.67
399 401 1.747924 GACGGAGGGAGTACTGGTAAC 59.252 57.143 0.00 0.00 0.00 2.50
401 403 0.257039 GGACGGAGGGAGTACTGGTA 59.743 60.000 0.00 0.00 0.00 3.25
402 404 1.000107 GGACGGAGGGAGTACTGGT 60.000 63.158 0.00 0.00 0.00 4.00
403 405 0.613853 TTGGACGGAGGGAGTACTGG 60.614 60.000 0.00 0.00 0.00 4.00
404 406 1.263356 TTTGGACGGAGGGAGTACTG 58.737 55.000 0.00 0.00 0.00 2.74
405 407 2.019807 TTTTGGACGGAGGGAGTACT 57.980 50.000 0.00 0.00 0.00 2.73
406 408 2.420642 GTTTTTGGACGGAGGGAGTAC 58.579 52.381 0.00 0.00 0.00 2.73
413 415 1.226746 AAGAGCGTTTTTGGACGGAG 58.773 50.000 0.00 0.00 42.98 4.63
414 416 2.529780 TAAGAGCGTTTTTGGACGGA 57.470 45.000 0.00 0.00 42.98 4.69
415 417 5.479716 AATATAAGAGCGTTTTTGGACGG 57.520 39.130 0.00 0.00 42.98 4.79
417 419 7.227910 TCCCATAATATAAGAGCGTTTTTGGAC 59.772 37.037 0.00 0.00 0.00 4.02
418 420 7.227910 GTCCCATAATATAAGAGCGTTTTTGGA 59.772 37.037 0.00 0.00 0.00 3.53
419 421 7.360361 GTCCCATAATATAAGAGCGTTTTTGG 58.640 38.462 0.00 0.00 0.00 3.28
420 422 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
422 424 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
424 426 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
426 428 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
428 430 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
429 431 5.279562 TCCCTCCGTCCCATAATATAAGA 57.720 43.478 0.00 0.00 0.00 2.10
430 432 6.561519 AATCCCTCCGTCCCATAATATAAG 57.438 41.667 0.00 0.00 0.00 1.73
435 437 3.870559 ACTAATCCCTCCGTCCCATAAT 58.129 45.455 0.00 0.00 0.00 1.28
436 438 3.339713 ACTAATCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
437 439 2.969950 CAACTAATCCCTCCGTCCCATA 59.030 50.000 0.00 0.00 0.00 2.74
440 442 1.492764 TCAACTAATCCCTCCGTCCC 58.507 55.000 0.00 0.00 0.00 4.46
441 443 4.950205 TTATCAACTAATCCCTCCGTCC 57.050 45.455 0.00 0.00 0.00 4.79
444 446 5.304614 TCCTCTTTATCAACTAATCCCTCCG 59.695 44.000 0.00 0.00 0.00 4.63
445 447 6.749036 TCCTCTTTATCAACTAATCCCTCC 57.251 41.667 0.00 0.00 0.00 4.30
446 448 7.797062 ACTTCCTCTTTATCAACTAATCCCTC 58.203 38.462 0.00 0.00 0.00 4.30
447 449 7.757242 ACTTCCTCTTTATCAACTAATCCCT 57.243 36.000 0.00 0.00 0.00 4.20
573 606 9.249457 GCTAAAAGCAATTTGTTAACTTCTCTT 57.751 29.630 7.22 0.74 41.89 2.85
612 645 3.876309 ACTGTTGCTCTCCCCTAAAAA 57.124 42.857 0.00 0.00 0.00 1.94
613 646 3.876309 AACTGTTGCTCTCCCCTAAAA 57.124 42.857 0.00 0.00 0.00 1.52
614 647 4.103469 TGTTAACTGTTGCTCTCCCCTAAA 59.897 41.667 7.22 0.00 0.00 1.85
615 648 3.649023 TGTTAACTGTTGCTCTCCCCTAA 59.351 43.478 7.22 0.00 0.00 2.69
616 649 3.244582 TGTTAACTGTTGCTCTCCCCTA 58.755 45.455 7.22 0.00 0.00 3.53
617 650 2.054799 TGTTAACTGTTGCTCTCCCCT 58.945 47.619 7.22 0.00 0.00 4.79
618 651 2.561478 TGTTAACTGTTGCTCTCCCC 57.439 50.000 7.22 0.00 0.00 4.81
619 652 5.221244 ACAATTTGTTAACTGTTGCTCTCCC 60.221 40.000 7.22 0.00 0.00 4.30
620 653 5.831997 ACAATTTGTTAACTGTTGCTCTCC 58.168 37.500 7.22 0.00 0.00 3.71
621 654 7.153478 CAACAATTTGTTAACTGTTGCTCTC 57.847 36.000 19.38 0.00 41.39 3.20
652 685 6.146510 CCGCAAGCCGTATAAAAATATCTGTA 59.853 38.462 0.00 0.00 34.38 2.74
685 718 3.275338 GCTACTGGATGGCTGCGC 61.275 66.667 0.00 0.00 0.00 6.09
686 719 2.590007 GGCTACTGGATGGCTGCG 60.590 66.667 0.00 0.00 34.56 5.18
687 720 2.203266 GGGCTACTGGATGGCTGC 60.203 66.667 0.00 0.00 34.56 5.25
688 721 0.250640 GATGGGCTACTGGATGGCTG 60.251 60.000 0.00 0.00 34.56 4.85
689 722 0.695462 TGATGGGCTACTGGATGGCT 60.695 55.000 0.00 0.00 34.56 4.75
690 723 0.183492 TTGATGGGCTACTGGATGGC 59.817 55.000 0.00 0.00 0.00 4.40
691 724 1.202855 CCTTGATGGGCTACTGGATGG 60.203 57.143 0.00 0.00 0.00 3.51
692 725 2.267174 CCTTGATGGGCTACTGGATG 57.733 55.000 0.00 0.00 0.00 3.51
989 1273 2.511600 GCGACATTGTCCTCCCCG 60.512 66.667 11.12 0.35 0.00 5.73
1260 1549 4.779733 GACGGGGAGGAGCAGGGA 62.780 72.222 0.00 0.00 0.00 4.20
1469 1810 1.760480 GTGGCCTTTGTTGGGGTGT 60.760 57.895 3.32 0.00 0.00 4.16
1974 2492 6.690194 AATCATCATGGTAACTTCTGAAGC 57.310 37.500 17.00 1.86 37.61 3.86
2019 2561 6.325919 TGATAAAGTGCAAAGGTTAACAGG 57.674 37.500 8.10 0.00 0.00 4.00
2125 2671 2.175878 TCAAAGTCCAGCAGAGAAGC 57.824 50.000 0.00 0.00 0.00 3.86
2156 2702 7.775120 ACAAAATGGTCCATGATTTCAGATAC 58.225 34.615 4.74 0.00 0.00 2.24
2175 2721 7.008021 AGATGGCATTCAAGGTTAACAAAAT 57.992 32.000 8.10 0.00 0.00 1.82
2251 2801 0.534203 TGAAAGAAGTGACCGCCCAC 60.534 55.000 0.00 0.00 37.32 4.61
2260 2811 4.313282 TCTGTCATGCTCTGAAAGAAGTG 58.687 43.478 7.13 0.00 46.34 3.16
2292 2843 6.013379 CAGGGGCCTTCATATCTAACATAAGA 60.013 42.308 0.84 0.00 0.00 2.10
2355 2906 5.707066 AAAGCCTCTCCAGATTAGAACAT 57.293 39.130 0.00 0.00 0.00 2.71
2399 2953 3.883489 ACTTAAGTTGGAGTCAAAGGTGC 59.117 43.478 1.12 0.00 34.28 5.01
2438 2994 5.624159 CCACTGGAATAAGATGGCAGAATA 58.376 41.667 0.00 0.00 0.00 1.75
2445 3001 5.603170 AAAATGCCACTGGAATAAGATGG 57.397 39.130 0.00 0.00 0.00 3.51
2455 3011 3.457610 ACACAAGAAAAATGCCACTGG 57.542 42.857 0.00 0.00 0.00 4.00
2458 3014 9.220635 GAAATTAAAACACAAGAAAAATGCCAC 57.779 29.630 0.00 0.00 0.00 5.01
2469 3025 8.388319 TCAGAACAACGAAATTAAAACACAAG 57.612 30.769 0.00 0.00 0.00 3.16
2479 3035 5.748152 CACAACCATTCAGAACAACGAAATT 59.252 36.000 0.00 0.00 0.00 1.82
2547 3110 5.227593 ACCCCCACATAGTTAGATGAATCT 58.772 41.667 0.00 0.00 40.86 2.40
2557 3120 1.508256 GGCTCTACCCCCACATAGTT 58.492 55.000 0.00 0.00 0.00 2.24
2625 3188 1.349688 ACCTCAATGCGGTTCCAGTTA 59.650 47.619 0.00 0.00 0.00 2.24
2732 3300 5.450453 AGAGATCTTCCTTCTGAATACCGA 58.550 41.667 0.00 0.00 31.06 4.69
2747 3315 2.154462 CGCCAACCAACAAGAGATCTT 58.846 47.619 0.00 0.00 36.45 2.40
2760 3328 4.043200 GCCACAGCTTCGCCAACC 62.043 66.667 0.00 0.00 35.50 3.77
2766 3334 1.298157 TTCCATTCGCCACAGCTTCG 61.298 55.000 0.00 0.00 36.60 3.79
2871 3439 2.242043 CAAGCTATAGGGCCAATTGGG 58.758 52.381 25.73 8.36 40.85 4.12
2954 3524 6.591001 TCATTGTTAGCCTACTGCATCAATA 58.409 36.000 0.00 0.00 44.83 1.90
3018 3589 4.042187 GCAGGACATTATATCCCCTTCAGT 59.958 45.833 0.00 0.00 36.86 3.41
3161 3740 6.728200 AGTAAAATACATGGCGATGACATTG 58.272 36.000 16.26 0.00 33.36 2.82
3162 3741 6.942532 AGTAAAATACATGGCGATGACATT 57.057 33.333 16.26 10.83 33.36 2.71
3163 3742 6.942532 AAGTAAAATACATGGCGATGACAT 57.057 33.333 16.26 5.33 33.36 3.06
3164 3743 6.019398 CGTAAGTAAAATACATGGCGATGACA 60.019 38.462 16.26 3.06 33.36 3.58
3165 3744 6.199531 TCGTAAGTAAAATACATGGCGATGAC 59.800 38.462 16.26 1.85 39.48 3.06
3167 3746 6.519353 TCGTAAGTAAAATACATGGCGATG 57.481 37.500 7.21 7.21 39.48 3.84
3169 3748 6.509656 AGATCGTAAGTAAAATACATGGCGA 58.490 36.000 0.00 0.00 39.48 5.54
3170 3749 6.764877 AGATCGTAAGTAAAATACATGGCG 57.235 37.500 0.00 0.00 39.48 5.69
3171 3750 7.916552 ACAAGATCGTAAGTAAAATACATGGC 58.083 34.615 0.00 0.00 39.48 4.40
3172 3751 8.548721 GGACAAGATCGTAAGTAAAATACATGG 58.451 37.037 0.00 0.00 39.48 3.66
3173 3752 9.093970 TGGACAAGATCGTAAGTAAAATACATG 57.906 33.333 0.00 0.00 39.48 3.21
3174 3753 9.661563 TTGGACAAGATCGTAAGTAAAATACAT 57.338 29.630 0.00 0.00 39.48 2.29
3176 3755 8.114905 GCTTGGACAAGATCGTAAGTAAAATAC 58.885 37.037 15.76 0.00 40.79 1.89
3177 3756 7.009815 CGCTTGGACAAGATCGTAAGTAAAATA 59.990 37.037 15.76 0.00 40.79 1.40
3178 3757 6.183360 CGCTTGGACAAGATCGTAAGTAAAAT 60.183 38.462 15.76 0.00 40.79 1.82
3179 3758 5.119588 CGCTTGGACAAGATCGTAAGTAAAA 59.880 40.000 15.76 0.00 40.79 1.52
3180 3759 4.624024 CGCTTGGACAAGATCGTAAGTAAA 59.376 41.667 15.76 0.00 40.79 2.01
3182 3761 3.441222 TCGCTTGGACAAGATCGTAAGTA 59.559 43.478 15.76 0.00 40.79 2.24
3183 3762 2.230508 TCGCTTGGACAAGATCGTAAGT 59.769 45.455 15.76 0.00 40.79 2.24
3185 3764 3.520290 ATCGCTTGGACAAGATCGTAA 57.480 42.857 15.76 0.00 40.79 3.18
3187 3766 2.002586 CAATCGCTTGGACAAGATCGT 58.997 47.619 15.76 0.41 40.79 3.73
3188 3767 2.270923 TCAATCGCTTGGACAAGATCG 58.729 47.619 15.76 10.31 40.79 3.69
3189 3768 2.611292 CCTCAATCGCTTGGACAAGATC 59.389 50.000 15.76 0.00 40.79 2.75
3191 3770 1.347707 ACCTCAATCGCTTGGACAAGA 59.652 47.619 15.76 0.00 40.79 3.02
3192 3771 1.813513 ACCTCAATCGCTTGGACAAG 58.186 50.000 7.67 7.67 41.24 3.16
3194 3773 1.202758 ACAACCTCAATCGCTTGGACA 60.203 47.619 0.00 0.00 32.95 4.02
3195 3774 1.197721 CACAACCTCAATCGCTTGGAC 59.802 52.381 0.00 0.00 32.95 4.02
3196 3775 1.202758 ACACAACCTCAATCGCTTGGA 60.203 47.619 0.00 0.00 32.95 3.53
3197 3776 1.069022 CACACAACCTCAATCGCTTGG 60.069 52.381 0.00 0.00 32.95 3.61
3198 3777 1.069022 CCACACAACCTCAATCGCTTG 60.069 52.381 0.00 0.00 0.00 4.01
3199 3778 1.238439 CCACACAACCTCAATCGCTT 58.762 50.000 0.00 0.00 0.00 4.68
3200 3779 0.108585 ACCACACAACCTCAATCGCT 59.891 50.000 0.00 0.00 0.00 4.93
3201 3780 0.238289 CACCACACAACCTCAATCGC 59.762 55.000 0.00 0.00 0.00 4.58
3202 3781 1.531149 GACACCACACAACCTCAATCG 59.469 52.381 0.00 0.00 0.00 3.34
3203 3782 1.880027 GGACACCACACAACCTCAATC 59.120 52.381 0.00 0.00 0.00 2.67
3204 3783 1.494721 AGGACACCACACAACCTCAAT 59.505 47.619 0.00 0.00 0.00 2.57
3205 3784 0.916086 AGGACACCACACAACCTCAA 59.084 50.000 0.00 0.00 0.00 3.02
3206 3785 0.180171 CAGGACACCACACAACCTCA 59.820 55.000 0.00 0.00 0.00 3.86
3207 3786 1.166531 GCAGGACACCACACAACCTC 61.167 60.000 0.00 0.00 0.00 3.85
3208 3787 1.152963 GCAGGACACCACACAACCT 60.153 57.895 0.00 0.00 0.00 3.50
3209 3788 1.034838 TTGCAGGACACCACACAACC 61.035 55.000 0.00 0.00 0.00 3.77
3210 3789 1.032014 ATTGCAGGACACCACACAAC 58.968 50.000 0.00 0.00 0.00 3.32
3219 3798 1.956636 GCCATCCTCAATTGCAGGACA 60.957 52.381 21.52 7.79 43.10 4.02
3239 3818 2.755103 GTCTTGAACCAAGGCCAATAGG 59.245 50.000 5.01 2.98 39.83 2.57
3240 3819 3.690460 AGTCTTGAACCAAGGCCAATAG 58.310 45.455 5.01 0.00 45.97 1.73
3241 3820 3.806949 AGTCTTGAACCAAGGCCAATA 57.193 42.857 5.01 0.00 45.97 1.90
3242 3821 2.629617 CAAGTCTTGAACCAAGGCCAAT 59.370 45.455 5.01 0.00 45.97 3.16
3247 3826 4.199310 TGACTTCAAGTCTTGAACCAAGG 58.801 43.478 21.59 14.71 45.27 3.61
3248 3827 5.818136 TTGACTTCAAGTCTTGAACCAAG 57.182 39.130 21.59 15.14 45.27 3.61
3249 3828 6.582677 TTTTGACTTCAAGTCTTGAACCAA 57.417 33.333 21.59 21.99 45.27 3.67
3250 3829 5.393027 GCTTTTGACTTCAAGTCTTGAACCA 60.393 40.000 21.59 18.42 45.27 3.67
3251 3830 5.037385 GCTTTTGACTTCAAGTCTTGAACC 58.963 41.667 21.59 16.47 45.27 3.62
3252 3831 5.037385 GGCTTTTGACTTCAAGTCTTGAAC 58.963 41.667 21.59 14.44 45.27 3.18
3253 3832 4.201910 CGGCTTTTGACTTCAAGTCTTGAA 60.202 41.667 23.38 23.38 45.27 2.69
3254 3833 3.312421 CGGCTTTTGACTTCAAGTCTTGA 59.688 43.478 18.49 11.36 45.27 3.02
3255 3834 3.065371 ACGGCTTTTGACTTCAAGTCTTG 59.935 43.478 18.49 6.21 45.27 3.02
3256 3835 3.065371 CACGGCTTTTGACTTCAAGTCTT 59.935 43.478 18.49 0.00 45.27 3.01
3273 3852 2.415697 AAACATACTGCAAACACGGC 57.584 45.000 0.00 0.00 0.00 5.68
3276 3855 7.584987 ACAGAAGATAAACATACTGCAAACAC 58.415 34.615 0.00 0.00 0.00 3.32
3282 3861 6.708054 AGGCATACAGAAGATAAACATACTGC 59.292 38.462 0.00 0.00 0.00 4.40
3344 3951 2.097036 TCAGTACATCCTGTGGGTACG 58.903 52.381 0.00 0.00 41.62 3.67
3348 3955 3.244561 ACAAACTCAGTACATCCTGTGGG 60.245 47.826 0.00 0.00 34.02 4.61
3359 3966 6.821665 AGTCTGTAAGCAAAACAAACTCAGTA 59.178 34.615 0.00 0.00 0.00 2.74
3362 3969 6.404293 GGAAGTCTGTAAGCAAAACAAACTCA 60.404 38.462 0.00 0.00 26.84 3.41
3371 3978 4.041567 TGATCAGGGAAGTCTGTAAGCAAA 59.958 41.667 0.00 0.00 36.25 3.68
3376 3983 5.721480 TCAGAATGATCAGGGAAGTCTGTAA 59.279 40.000 0.09 0.00 42.56 2.41
3420 4027 8.244802 ACTGACAGTTAGTTGTACATACTGATC 58.755 37.037 23.39 18.48 36.17 2.92
3421 4028 8.123639 ACTGACAGTTAGTTGTACATACTGAT 57.876 34.615 23.39 13.68 36.17 2.90
3422 4029 7.520451 ACTGACAGTTAGTTGTACATACTGA 57.480 36.000 23.39 13.28 36.17 3.41
3423 4030 8.589335 AAACTGACAGTTAGTTGTACATACTG 57.411 34.615 20.85 18.56 37.47 2.74
3425 4032 8.823818 ACAAAACTGACAGTTAGTTGTACATAC 58.176 33.333 26.12 0.00 37.38 2.39
3426 4033 8.951787 ACAAAACTGACAGTTAGTTGTACATA 57.048 30.769 26.12 0.00 37.38 2.29
3427 4034 7.859325 ACAAAACTGACAGTTAGTTGTACAT 57.141 32.000 26.12 10.45 37.38 2.29
3428 4035 7.675962 AACAAAACTGACAGTTAGTTGTACA 57.324 32.000 26.95 0.00 37.87 2.90
3429 4036 8.231837 TGAAACAAAACTGACAGTTAGTTGTAC 58.768 33.333 26.95 23.57 37.87 2.90
3430 4037 8.325421 TGAAACAAAACTGACAGTTAGTTGTA 57.675 30.769 26.95 19.57 37.87 2.41
3431 4038 7.209471 TGAAACAAAACTGACAGTTAGTTGT 57.791 32.000 26.64 25.17 39.49 3.32
3432 4039 6.251376 GCTGAAACAAAACTGACAGTTAGTTG 59.749 38.462 26.64 24.70 37.47 3.16
3433 4040 6.151144 AGCTGAAACAAAACTGACAGTTAGTT 59.849 34.615 20.85 22.26 37.47 2.24
3434 4041 5.648092 AGCTGAAACAAAACTGACAGTTAGT 59.352 36.000 20.85 18.30 37.47 2.24
3435 4042 5.967674 CAGCTGAAACAAAACTGACAGTTAG 59.032 40.000 20.85 17.70 37.47 2.34
3436 4043 5.163663 CCAGCTGAAACAAAACTGACAGTTA 60.164 40.000 20.85 3.09 37.47 2.24
3444 4051 2.091885 TCCCTCCAGCTGAAACAAAACT 60.092 45.455 17.39 0.00 0.00 2.66
3446 4053 2.306847 GTCCCTCCAGCTGAAACAAAA 58.693 47.619 17.39 0.00 0.00 2.44
3460 4067 5.810080 ACTAGGCTTATACATTGTCCCTC 57.190 43.478 0.00 0.00 0.00 4.30
3507 4114 2.158841 CCCATTTTACACGAACAGGACG 59.841 50.000 0.00 0.00 0.00 4.79
3509 4116 3.325425 TCTCCCATTTTACACGAACAGGA 59.675 43.478 0.00 0.00 0.00 3.86
3510 4117 3.670625 TCTCCCATTTTACACGAACAGG 58.329 45.455 0.00 0.00 0.00 4.00
3511 4118 5.238650 ACTTTCTCCCATTTTACACGAACAG 59.761 40.000 0.00 0.00 0.00 3.16
3512 4119 5.127491 ACTTTCTCCCATTTTACACGAACA 58.873 37.500 0.00 0.00 0.00 3.18
3513 4120 5.237779 TGACTTTCTCCCATTTTACACGAAC 59.762 40.000 0.00 0.00 0.00 3.95
3514 4121 5.369833 TGACTTTCTCCCATTTTACACGAA 58.630 37.500 0.00 0.00 0.00 3.85
3519 4126 7.201617 CGATACCTTGACTTTCTCCCATTTTAC 60.202 40.741 0.00 0.00 0.00 2.01
3523 4130 4.225267 ACGATACCTTGACTTTCTCCCATT 59.775 41.667 0.00 0.00 0.00 3.16
3534 4141 7.642071 TTAGTTGTTTACACGATACCTTGAC 57.358 36.000 0.00 0.00 0.00 3.18
3543 4150 9.440784 GAAAATCATGTTTAGTTGTTTACACGA 57.559 29.630 0.00 0.00 0.00 4.35
3556 4163 4.671508 CGGCAAGCGAGAAAATCATGTTTA 60.672 41.667 0.00 0.00 0.00 2.01
3557 4164 3.578688 GGCAAGCGAGAAAATCATGTTT 58.421 40.909 0.00 0.00 0.00 2.83
3572 4179 4.406943 CTTTTGATAGTTTCTCGGCAAGC 58.593 43.478 0.00 0.00 0.00 4.01
3579 4186 7.522374 ACATCGAAAGCTTTTGATAGTTTCTC 58.478 34.615 32.19 8.62 38.84 2.87
3585 4192 6.835914 ACAAGACATCGAAAGCTTTTGATAG 58.164 36.000 32.19 27.16 38.84 2.08
3593 4200 5.700832 TCAACATTACAAGACATCGAAAGCT 59.299 36.000 0.00 0.00 0.00 3.74
3615 4222 7.392766 ACCACATCAGGGATAATCTAAATCA 57.607 36.000 0.00 0.00 0.00 2.57
3626 4233 3.763557 ATTTGGAACCACATCAGGGAT 57.236 42.857 0.00 0.00 0.00 3.85
3630 4237 5.581605 CCGATAAATTTGGAACCACATCAG 58.418 41.667 0.00 0.00 0.00 2.90
3652 4268 1.359459 CGGTAACTCGAGCCAAAGCC 61.359 60.000 13.61 5.72 41.25 4.35
3659 4275 3.737774 AGTAACAAAACGGTAACTCGAGC 59.262 43.478 13.61 0.00 0.00 5.03
3660 4276 4.977963 TGAGTAACAAAACGGTAACTCGAG 59.022 41.667 11.84 11.84 36.90 4.04
3675 4291 5.105567 TCAGGGAAACAAGTTGAGTAACA 57.894 39.130 10.54 0.00 39.30 2.41
3676 4292 4.023963 GCTCAGGGAAACAAGTTGAGTAAC 60.024 45.833 10.54 0.00 38.00 2.50
3678 4294 3.391296 AGCTCAGGGAAACAAGTTGAGTA 59.609 43.478 10.54 0.00 38.00 2.59
3682 4298 5.712152 AAATAGCTCAGGGAAACAAGTTG 57.288 39.130 0.00 0.00 0.00 3.16
3712 4352 7.288852 TCATTCCCAATTGAAAAGGACAAACTA 59.711 33.333 7.12 0.00 0.00 2.24
3724 4364 3.173953 AGCCAGTCATTCCCAATTGAA 57.826 42.857 7.12 0.00 0.00 2.69
3725 4365 2.905415 AGCCAGTCATTCCCAATTGA 57.095 45.000 7.12 0.00 0.00 2.57
3726 4366 2.954318 CCTAGCCAGTCATTCCCAATTG 59.046 50.000 0.00 0.00 0.00 2.32
3727 4367 2.582636 ACCTAGCCAGTCATTCCCAATT 59.417 45.455 0.00 0.00 0.00 2.32
3728 4368 2.208872 ACCTAGCCAGTCATTCCCAAT 58.791 47.619 0.00 0.00 0.00 3.16
3729 4369 1.668826 ACCTAGCCAGTCATTCCCAA 58.331 50.000 0.00 0.00 0.00 4.12
3730 4370 1.668826 AACCTAGCCAGTCATTCCCA 58.331 50.000 0.00 0.00 0.00 4.37
3731 4371 3.244596 GGATAACCTAGCCAGTCATTCCC 60.245 52.174 0.00 0.00 33.51 3.97
3732 4372 3.648545 AGGATAACCTAGCCAGTCATTCC 59.351 47.826 0.00 0.00 45.83 3.01
3733 4373 4.965200 AGGATAACCTAGCCAGTCATTC 57.035 45.455 0.00 0.00 45.83 2.67
3746 4386 6.822667 TTCCCGTTTAGAAAAAGGATAACC 57.177 37.500 6.01 0.00 33.29 2.85
3747 4387 7.255569 CCATTCCCGTTTAGAAAAAGGATAAC 58.744 38.462 6.01 0.00 33.29 1.89
3748 4388 6.127563 GCCATTCCCGTTTAGAAAAAGGATAA 60.128 38.462 6.01 1.71 33.29 1.75
3749 4389 5.358725 GCCATTCCCGTTTAGAAAAAGGATA 59.641 40.000 6.01 0.00 33.29 2.59
3750 4390 4.159693 GCCATTCCCGTTTAGAAAAAGGAT 59.840 41.667 6.01 0.00 33.29 3.24
3751 4391 3.508402 GCCATTCCCGTTTAGAAAAAGGA 59.492 43.478 6.01 0.00 33.29 3.36
3752 4392 3.509967 AGCCATTCCCGTTTAGAAAAAGG 59.490 43.478 0.00 0.00 0.00 3.11
3753 4393 4.217550 TCAGCCATTCCCGTTTAGAAAAAG 59.782 41.667 0.00 0.00 0.00 2.27
3754 4394 4.022676 GTCAGCCATTCCCGTTTAGAAAAA 60.023 41.667 0.00 0.00 0.00 1.94
3755 4395 3.504520 GTCAGCCATTCCCGTTTAGAAAA 59.495 43.478 0.00 0.00 0.00 2.29
3756 4396 3.078837 GTCAGCCATTCCCGTTTAGAAA 58.921 45.455 0.00 0.00 0.00 2.52
3757 4397 2.617021 GGTCAGCCATTCCCGTTTAGAA 60.617 50.000 0.00 0.00 34.09 2.10
3760 4400 0.988832 AGGTCAGCCATTCCCGTTTA 59.011 50.000 0.00 0.00 37.19 2.01
3764 4404 0.541863 AAGTAGGTCAGCCATTCCCG 59.458 55.000 0.00 0.00 37.19 5.14
3806 4447 8.970020 AGTGCATTAGGTATGATTTGAATTTGA 58.030 29.630 0.00 0.00 36.26 2.69
3808 4449 8.970020 TGAGTGCATTAGGTATGATTTGAATTT 58.030 29.630 0.00 0.00 36.26 1.82
3812 4453 7.500720 CATGAGTGCATTAGGTATGATTTGA 57.499 36.000 0.00 0.00 36.26 2.69
3830 4471 1.746220 GTCGACACTCCTAGCATGAGT 59.254 52.381 11.55 0.00 43.70 3.41
3831 4472 1.066303 GGTCGACACTCCTAGCATGAG 59.934 57.143 18.91 0.00 35.92 2.90
3832 4473 1.103803 GGTCGACACTCCTAGCATGA 58.896 55.000 18.91 0.00 0.00 3.07
3833 4474 0.103208 GGGTCGACACTCCTAGCATG 59.897 60.000 18.91 0.00 0.00 4.06
3834 4475 0.033011 AGGGTCGACACTCCTAGCAT 60.033 55.000 16.38 0.00 0.00 3.79
3835 4476 0.251653 AAGGGTCGACACTCCTAGCA 60.252 55.000 22.96 0.00 0.00 3.49
3836 4477 0.896226 AAAGGGTCGACACTCCTAGC 59.104 55.000 22.96 0.00 0.00 3.42
3837 4478 2.943449 GAAAGGGTCGACACTCCTAG 57.057 55.000 22.96 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.