Multiple sequence alignment - TraesCS5B01G562500

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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 TraesCS5B01G562500 chr5B 100.000 3566 0 0 1 3566 708339110 708335545 0.000000e+00 6586.0
1 TraesCS5B01G562500 chr5B 97.260 73 1 1 432 504 321218063 321218134 4.830000e-24 122.0
2 TraesCS5B01G562500 chr5B 95.082 61 3 0 3495 3555 703175920 703175980 2.930000e-16 97.1
3 TraesCS5B01G562500 chr5D 92.540 2386 132 24 551 2915 564975749 564978109 0.000000e+00 3378.0
4 TraesCS5B01G562500 chr5D 89.744 429 32 5 1 428 564975019 564975436 4.050000e-149 538.0
5 TraesCS5B01G562500 chr5D 95.082 61 3 0 3495 3555 157060649 157060589 2.930000e-16 97.1
6 TraesCS5B01G562500 chr4A 91.306 2059 121 23 859 2907 606411121 606413131 0.000000e+00 2758.0
7 TraesCS5B01G562500 chr4A 85.950 242 30 4 2925 3163 684960145 684959905 4.570000e-64 255.0
8 TraesCS5B01G562500 chr4A 87.023 131 13 3 734 861 606410889 606411018 1.030000e-30 145.0
9 TraesCS5B01G562500 chr4A 91.111 90 4 4 433 521 440964837 440964923 6.250000e-23 119.0
10 TraesCS5B01G562500 chr4A 95.652 46 2 0 1 46 606410870 606410915 1.370000e-09 75.0
11 TraesCS5B01G562500 chr7D 80.374 642 95 19 2922 3556 180068655 180069272 3.240000e-125 459.0
12 TraesCS5B01G562500 chr7D 84.615 247 33 5 2921 3163 439631869 439631624 1.280000e-59 241.0
13 TraesCS5B01G562500 chr7D 84.711 242 33 4 2925 3163 603341026 603340786 4.600000e-59 239.0
14 TraesCS5B01G562500 chr7D 83.884 242 35 4 2925 3163 25022565 25022325 9.960000e-56 228.0
15 TraesCS5B01G562500 chr7D 93.750 80 3 2 433 511 5068156 5068078 6.250000e-23 119.0
16 TraesCS5B01G562500 chr7D 95.000 60 3 0 3495 3554 550887680 550887739 1.050000e-15 95.3
17 TraesCS5B01G562500 chr7A 84.898 245 33 4 2922 3163 158344036 158344279 9.890000e-61 244.0
18 TraesCS5B01G562500 chrUn 87.619 210 24 2 2925 3132 97654488 97654279 3.560000e-60 243.0
19 TraesCS5B01G562500 chrUn 79.375 160 29 4 3398 3556 469688654 469688810 3.760000e-20 110.0
20 TraesCS5B01G562500 chr3B 85.000 240 35 1 2931 3169 689181276 689181037 3.560000e-60 243.0
21 TraesCS5B01G562500 chr1D 87.143 210 25 2 2925 3132 406846189 406845980 1.650000e-58 237.0
22 TraesCS5B01G562500 chr1D 90.805 87 6 2 433 519 232558472 232558556 8.090000e-22 115.0
23 TraesCS5B01G562500 chr3D 83.402 241 36 4 2925 3163 610529825 610529587 1.670000e-53 220.0
24 TraesCS5B01G562500 chr3D 93.671 79 3 2 433 511 550993773 550993849 2.250000e-22 117.0
25 TraesCS5B01G562500 chr2D 80.932 236 21 7 1309 1544 263488329 263488540 7.920000e-37 165.0
26 TraesCS5B01G562500 chr2D 92.771 83 5 1 432 514 592288587 592288506 6.250000e-23 119.0
27 TraesCS5B01G562500 chr7B 86.301 146 19 1 3415 3559 553021986 553021841 1.330000e-34 158.0
28 TraesCS5B01G562500 chr2B 80.625 160 27 4 3398 3556 77848498 77848654 1.740000e-23 121.0
29 TraesCS5B01G562500 chr2B 79.375 160 29 4 3398 3556 77801576 77801732 3.760000e-20 110.0
30 TraesCS5B01G562500 chr6A 93.750 80 4 1 432 511 557970119 557970041 6.250000e-23 119.0
31 TraesCS5B01G562500 chr4B 93.750 80 4 1 433 512 351875031 351875109 6.250000e-23 119.0
32 TraesCS5B01G562500 chr6D 91.765 85 5 2 433 516 95294975 95294892 2.250000e-22 117.0
33 TraesCS5B01G562500 chr2A 93.443 61 4 0 3495 3555 30022873 30022813 1.360000e-14 91.6


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 TraesCS5B01G562500 chr5B 708335545 708339110 3565 True 6586.000000 6586 100.000 1 3566 1 chr5B.!!$R1 3565
1 TraesCS5B01G562500 chr5D 564975019 564978109 3090 False 1958.000000 3378 91.142 1 2915 2 chr5D.!!$F1 2914
2 TraesCS5B01G562500 chr4A 606410870 606413131 2261 False 992.666667 2758 91.327 1 2907 3 chr4A.!!$F2 2906
3 TraesCS5B01G562500 chr7D 180068655 180069272 617 False 459.000000 459 80.374 2922 3556 1 chr7D.!!$F1 634

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
393 395 0.033796 TCCCTCCGTCCTCGTAATGT 60.034 55.0 0.0 0.0 35.01 2.71 F
892 1244 0.753262 ACTGCCGTCACCATATCTCC 59.247 55.0 0.0 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1806 2178 2.182030 GCCGTCTTGGTCTCCTCG 59.818 66.667 0.0 0.0 41.21 4.63 R
2701 3076 0.383231 GCATTCCAAGGCTCCATTCG 59.617 55.000 0.0 0.0 32.08 3.34 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
54 55 0.345146 TCATCCACCTATCCCACCCA 59.655 55.000 0.00 0.00 0.00 4.51
58 59 3.377154 TCCACCTATCCCACCCATATT 57.623 47.619 0.00 0.00 0.00 1.28
64 65 7.037153 TCCACCTATCCCACCCATATTTATTAC 60.037 40.741 0.00 0.00 0.00 1.89
82 83 1.296392 CGGTCAGTCCATGCCTCAA 59.704 57.895 0.00 0.00 35.57 3.02
84 85 1.679944 CGGTCAGTCCATGCCTCAATT 60.680 52.381 0.00 0.00 35.57 2.32
85 86 2.450476 GGTCAGTCCATGCCTCAATTT 58.550 47.619 0.00 0.00 35.97 1.82
86 87 2.827921 GGTCAGTCCATGCCTCAATTTT 59.172 45.455 0.00 0.00 35.97 1.82
87 88 3.119352 GGTCAGTCCATGCCTCAATTTTC 60.119 47.826 0.00 0.00 35.97 2.29
100 101 8.558973 TGCCTCAATTTTCTTTTTCTTCAAAA 57.441 26.923 0.00 0.00 33.12 2.44
117 118 2.171870 CAAAAAGTAGGATAGCCCCGGA 59.828 50.000 0.73 0.00 34.66 5.14
150 151 8.786898 CATTAGTTGCACAAAGCCATATAGTAT 58.213 33.333 0.00 0.00 44.83 2.12
221 222 9.959749 AATGTAATCATCACGTTGTAAAAAGTT 57.040 25.926 0.00 0.00 32.56 2.66
260 262 5.641783 ATGGCATTTTAAATTTGTTGGCC 57.358 34.783 0.00 0.00 39.29 5.36
261 263 4.464008 TGGCATTTTAAATTTGTTGGCCA 58.536 34.783 0.00 0.00 45.75 5.36
283 285 5.213675 CACGGATAATTTCTCGGTCTACTC 58.786 45.833 0.00 0.00 0.00 2.59
288 290 9.111613 CGGATAATTTCTCGGTCTACTCTATAT 57.888 37.037 0.00 0.00 0.00 0.86
330 332 9.639601 TGAGTATTGAGTAGTAAACATGTTCAG 57.360 33.333 12.39 0.00 0.00 3.02
351 353 9.846248 GTTCAGCATGTTATTAAGAATTTGTCT 57.154 29.630 0.00 0.00 35.96 3.41
387 389 0.465824 ATGTACTCCCTCCGTCCTCG 60.466 60.000 0.00 0.00 0.00 4.63
388 390 1.077858 GTACTCCCTCCGTCCTCGT 60.078 63.158 0.00 0.00 35.01 4.18
389 391 0.179000 GTACTCCCTCCGTCCTCGTA 59.821 60.000 0.00 0.00 35.01 3.43
390 392 0.911769 TACTCCCTCCGTCCTCGTAA 59.088 55.000 0.00 0.00 35.01 3.18
391 393 0.258194 ACTCCCTCCGTCCTCGTAAT 59.742 55.000 0.00 0.00 35.01 1.89
392 394 0.669077 CTCCCTCCGTCCTCGTAATG 59.331 60.000 0.00 0.00 35.01 1.90
393 395 0.033796 TCCCTCCGTCCTCGTAATGT 60.034 55.000 0.00 0.00 35.01 2.71
394 396 1.212688 TCCCTCCGTCCTCGTAATGTA 59.787 52.381 0.00 0.00 35.01 2.29
395 397 2.026641 CCCTCCGTCCTCGTAATGTAA 58.973 52.381 0.00 0.00 35.01 2.41
396 398 2.034305 CCCTCCGTCCTCGTAATGTAAG 59.966 54.545 0.00 0.00 35.01 2.34
397 399 2.947652 CCTCCGTCCTCGTAATGTAAGA 59.052 50.000 0.00 0.00 35.01 2.10
398 400 3.003482 CCTCCGTCCTCGTAATGTAAGAG 59.997 52.174 0.00 0.00 34.63 2.85
399 401 3.614092 TCCGTCCTCGTAATGTAAGAGT 58.386 45.455 0.00 0.00 33.27 3.24
400 402 3.376234 TCCGTCCTCGTAATGTAAGAGTG 59.624 47.826 0.00 0.00 33.27 3.51
401 403 3.488721 CCGTCCTCGTAATGTAAGAGTGG 60.489 52.174 0.00 0.00 33.27 4.00
402 404 3.128242 CGTCCTCGTAATGTAAGAGTGGT 59.872 47.826 0.00 0.00 33.27 4.16
403 405 4.380233 CGTCCTCGTAATGTAAGAGTGGTT 60.380 45.833 0.00 0.00 33.27 3.67
404 406 5.476614 GTCCTCGTAATGTAAGAGTGGTTT 58.523 41.667 0.00 0.00 33.27 3.27
405 407 5.930569 GTCCTCGTAATGTAAGAGTGGTTTT 59.069 40.000 0.00 0.00 33.27 2.43
406 408 7.092716 GTCCTCGTAATGTAAGAGTGGTTTTA 58.907 38.462 0.00 0.00 33.27 1.52
407 409 7.599998 GTCCTCGTAATGTAAGAGTGGTTTTAA 59.400 37.037 0.00 0.00 33.27 1.52
408 410 7.599998 TCCTCGTAATGTAAGAGTGGTTTTAAC 59.400 37.037 0.00 0.00 33.27 2.01
409 411 7.385752 CCTCGTAATGTAAGAGTGGTTTTAACA 59.614 37.037 0.00 0.00 33.27 2.41
410 412 8.075593 TCGTAATGTAAGAGTGGTTTTAACAC 57.924 34.615 0.00 0.00 39.10 3.32
511 513 6.563163 AGAGGACGGAGGGAGTAATATTTAT 58.437 40.000 0.00 0.00 0.00 1.40
518 520 8.491958 ACGGAGGGAGTAATATTTATTCTTGTT 58.508 33.333 0.00 0.00 0.00 2.83
537 539 7.780313 TCTTGTTTTAGAACGACGAAATAGTG 58.220 34.615 0.00 0.00 38.65 2.74
538 540 7.436080 TCTTGTTTTAGAACGACGAAATAGTGT 59.564 33.333 0.00 0.00 38.65 3.55
539 541 6.869473 TGTTTTAGAACGACGAAATAGTGTG 58.131 36.000 0.00 0.00 38.65 3.82
540 542 6.074195 TGTTTTAGAACGACGAAATAGTGTGG 60.074 38.462 0.00 0.00 38.65 4.17
542 544 2.063266 GAACGACGAAATAGTGTGGCA 58.937 47.619 0.00 0.00 0.00 4.92
560 799 5.772521 GTGGCAAACACTGTGAAATCTTAT 58.227 37.500 15.86 0.00 46.72 1.73
561 800 5.630680 GTGGCAAACACTGTGAAATCTTATG 59.369 40.000 15.86 2.83 46.72 1.90
564 803 5.691305 GCAAACACTGTGAAATCTTATGCAA 59.309 36.000 15.86 0.00 0.00 4.08
567 806 8.767085 CAAACACTGTGAAATCTTATGCAAATT 58.233 29.630 15.86 0.00 0.00 1.82
568 807 8.891671 AACACTGTGAAATCTTATGCAAATTT 57.108 26.923 15.86 0.00 0.00 1.82
569 808 8.301730 ACACTGTGAAATCTTATGCAAATTTG 57.698 30.769 15.86 14.03 0.00 2.32
571 810 8.644619 CACTGTGAAATCTTATGCAAATTTGAG 58.355 33.333 22.31 10.04 0.00 3.02
573 812 9.414295 CTGTGAAATCTTATGCAAATTTGAGAA 57.586 29.630 22.31 10.35 0.00 2.87
584 823 8.693542 ATGCAAATTTGAGAATTAACTAGTGC 57.306 30.769 22.31 1.54 34.44 4.40
647 886 9.869844 GGTCTTGATATTTATTTCTCAATCACG 57.130 33.333 0.00 0.00 0.00 4.35
665 904 9.435688 TCAATCACGGAGTATAAATATGGATTG 57.564 33.333 0.00 0.00 41.61 2.67
666 905 7.849804 ATCACGGAGTATAAATATGGATTGC 57.150 36.000 0.00 0.00 41.61 3.56
682 921 6.469782 TGGATTGCCAAATTTCTATCCTTC 57.530 37.500 16.03 0.00 42.49 3.46
683 922 6.197168 TGGATTGCCAAATTTCTATCCTTCT 58.803 36.000 16.03 0.00 42.49 2.85
685 924 7.147846 TGGATTGCCAAATTTCTATCCTTCTTC 60.148 37.037 16.03 0.00 42.49 2.87
701 945 4.420206 CTTCTTCCCTTTTCTCCCCAAAT 58.580 43.478 0.00 0.00 0.00 2.32
705 949 3.506398 TCCCTTTTCTCCCCAAATCAAC 58.494 45.455 0.00 0.00 0.00 3.18
715 959 1.669502 CCCAAATCAACCACATGCACG 60.670 52.381 0.00 0.00 0.00 5.34
725 969 1.535028 CCACATGCACGAAGTTGCTAA 59.465 47.619 0.00 0.00 41.61 3.09
727 971 3.549827 CCACATGCACGAAGTTGCTAAAA 60.550 43.478 0.00 0.00 41.61 1.52
772 1016 1.985159 TCCACCTACTTGCTCCACATT 59.015 47.619 0.00 0.00 0.00 2.71
773 1017 2.027192 TCCACCTACTTGCTCCACATTC 60.027 50.000 0.00 0.00 0.00 2.67
775 1019 3.614092 CACCTACTTGCTCCACATTCAT 58.386 45.455 0.00 0.00 0.00 2.57
780 1024 5.183713 CCTACTTGCTCCACATTCATTTTGA 59.816 40.000 0.00 0.00 0.00 2.69
844 1091 5.665916 AATTTGGGATCAGTTTGGATCAC 57.334 39.130 5.63 2.29 45.87 3.06
847 1094 2.290896 TGGGATCAGTTTGGATCACCAC 60.291 50.000 3.21 0.00 45.23 4.16
853 1100 3.012518 CAGTTTGGATCACCACATCTCC 58.987 50.000 0.00 0.00 46.80 3.71
892 1244 0.753262 ACTGCCGTCACCATATCTCC 59.247 55.000 0.00 0.00 0.00 3.71
895 1247 2.562738 CTGCCGTCACCATATCTCCATA 59.437 50.000 0.00 0.00 0.00 2.74
915 1267 5.462068 CCATATCTTTGCATTGCATCACTTG 59.538 40.000 12.95 6.59 38.76 3.16
944 1297 3.397482 GTTTTGCTCTGCTCTCTTCTCA 58.603 45.455 0.00 0.00 0.00 3.27
945 1298 3.977134 TTTGCTCTGCTCTCTTCTCAT 57.023 42.857 0.00 0.00 0.00 2.90
1557 1929 1.153823 CCCGCTCAAGTCGTACCTG 60.154 63.158 0.00 0.00 0.00 4.00
1737 2109 4.450122 GTGCTCGCGTCCGACGTA 62.450 66.667 21.37 9.87 44.73 3.57
1989 2361 3.618351 CCTCAACTTCGACTACCTCCTA 58.382 50.000 0.00 0.00 0.00 2.94
2334 2706 2.589157 CGGGTTCTACCTGGTGGCA 61.589 63.158 10.23 0.00 41.01 4.92
2436 2808 2.032223 AGCCTGACTGTGCTGCTG 59.968 61.111 0.00 0.00 36.23 4.41
2555 2927 1.375013 CACCCCAAAATGCTGCTGC 60.375 57.895 8.89 8.89 40.20 5.25
2556 2928 1.534717 ACCCCAAAATGCTGCTGCT 60.535 52.632 17.00 0.00 40.48 4.24
2557 2929 1.079405 CCCCAAAATGCTGCTGCTG 60.079 57.895 17.00 6.37 40.48 4.41
2562 2934 0.239347 AAAATGCTGCTGCTGACGTC 59.761 50.000 17.00 9.11 40.48 4.34
2578 2950 1.204941 ACGTCTGACCATAACTCCAGC 59.795 52.381 1.55 0.00 0.00 4.85
2586 2958 4.473196 TGACCATAACTCCAGCCATTAAGA 59.527 41.667 0.00 0.00 0.00 2.10
2590 2962 6.157994 ACCATAACTCCAGCCATTAAGAAGTA 59.842 38.462 0.00 0.00 0.00 2.24
2591 2963 6.708054 CCATAACTCCAGCCATTAAGAAGTAG 59.292 42.308 0.00 0.00 0.00 2.57
2592 2964 5.763876 AACTCCAGCCATTAAGAAGTAGT 57.236 39.130 0.00 0.00 0.00 2.73
2593 2965 5.091261 ACTCCAGCCATTAAGAAGTAGTG 57.909 43.478 0.00 0.00 0.00 2.74
2594 2966 4.532521 ACTCCAGCCATTAAGAAGTAGTGT 59.467 41.667 0.00 0.00 0.00 3.55
2595 2967 4.832248 TCCAGCCATTAAGAAGTAGTGTG 58.168 43.478 0.00 0.00 0.00 3.82
2596 2968 4.530553 TCCAGCCATTAAGAAGTAGTGTGA 59.469 41.667 0.00 0.00 0.00 3.58
2598 2970 5.882557 CCAGCCATTAAGAAGTAGTGTGAAT 59.117 40.000 0.00 0.00 0.00 2.57
2599 2971 6.375455 CCAGCCATTAAGAAGTAGTGTGAATT 59.625 38.462 0.00 0.00 0.00 2.17
2621 2993 9.869844 GAATTAATCTGAGTGCAATGTACATAC 57.130 33.333 9.21 3.87 0.00 2.39
2622 2994 9.618890 AATTAATCTGAGTGCAATGTACATACT 57.381 29.630 9.21 9.14 0.00 2.12
2623 2995 6.915544 AATCTGAGTGCAATGTACATACTG 57.084 37.500 13.29 8.53 0.00 2.74
2624 2996 4.183865 TCTGAGTGCAATGTACATACTGC 58.816 43.478 20.79 20.79 35.32 4.40
2625 2997 4.081476 TCTGAGTGCAATGTACATACTGCT 60.081 41.667 25.36 15.08 35.78 4.24
2626 2998 4.183865 TGAGTGCAATGTACATACTGCTC 58.816 43.478 25.36 22.49 35.78 4.26
2675 3050 9.981114 AGATTTTGTTTTGAAATCGGTAGAATT 57.019 25.926 4.50 0.00 44.35 2.17
2701 3076 2.060980 ATGAGGGAGGTGAGGCGAC 61.061 63.158 0.00 0.00 0.00 5.19
2714 3089 2.464459 GGCGACGAATGGAGCCTTG 61.464 63.158 0.00 0.00 45.67 3.61
2732 3107 2.559698 TGGAATGCTTTCTCCGACAA 57.440 45.000 11.68 0.00 34.14 3.18
2739 3114 2.223144 TGCTTTCTCCGACAATGTTTCG 59.777 45.455 0.00 0.00 36.20 3.46
2744 3119 2.002586 CTCCGACAATGTTTCGCTCAT 58.997 47.619 0.00 0.00 35.06 2.90
2760 3135 3.603532 GCTCATTCACTCACTCATTCCA 58.396 45.455 0.00 0.00 0.00 3.53
2761 3136 4.197750 GCTCATTCACTCACTCATTCCAT 58.802 43.478 0.00 0.00 0.00 3.41
2784 3159 5.351233 AGTGCTCTAATCTAATCGAGTCG 57.649 43.478 6.09 6.09 0.00 4.18
2797 3172 7.907194 TCTAATCGAGTCGACTATACATATGC 58.093 38.462 20.09 1.22 39.18 3.14
2800 3175 5.928153 TCGAGTCGACTATACATATGCAAG 58.072 41.667 20.09 0.33 0.00 4.01
2811 3186 9.277783 ACTATACATATGCAAGGATGAAACTTC 57.722 33.333 12.16 0.00 0.00 3.01
2822 3197 5.783111 AGGATGAAACTTCGGAAATTTTGG 58.217 37.500 0.00 0.00 0.00 3.28
2852 3227 9.498307 GGAAACAATAACCTTATAATTGTGTCG 57.502 33.333 10.72 0.00 43.90 4.35
2861 3236 8.425577 ACCTTATAATTGTGTCGAAGAAGATG 57.574 34.615 0.00 0.00 39.69 2.90
2868 3243 2.093467 GTGTCGAAGAAGATGAGCAAGC 59.907 50.000 0.00 0.00 39.69 4.01
2872 3247 2.348059 CGAAGAAGATGAGCAAGCTGAC 59.652 50.000 0.00 0.00 0.00 3.51
2881 3256 2.029844 GCAAGCTGACGAGTGGACC 61.030 63.158 0.00 0.00 0.00 4.46
2885 3260 3.680786 CTGACGAGTGGACCCGCA 61.681 66.667 2.17 0.00 0.00 5.69
2897 3272 0.526211 GACCCGCAGAACATTTTCCC 59.474 55.000 0.00 0.00 31.28 3.97
2901 3276 0.447801 CGCAGAACATTTTCCCCTCG 59.552 55.000 0.00 0.00 31.28 4.63
2907 3282 1.064825 ACATTTTCCCCTCGGAGTGT 58.935 50.000 4.02 0.00 40.10 3.55
2908 3283 2.262637 ACATTTTCCCCTCGGAGTGTA 58.737 47.619 4.02 0.00 40.10 2.90
2909 3284 2.236395 ACATTTTCCCCTCGGAGTGTAG 59.764 50.000 4.02 0.00 40.10 2.74
2910 3285 2.019807 TTTTCCCCTCGGAGTGTAGT 57.980 50.000 4.02 0.00 40.10 2.73
2911 3286 1.263356 TTTCCCCTCGGAGTGTAGTG 58.737 55.000 4.02 0.00 40.10 2.74
2912 3287 1.255667 TTCCCCTCGGAGTGTAGTGC 61.256 60.000 4.02 0.00 40.10 4.40
2914 3289 1.258445 CCCCTCGGAGTGTAGTGCTT 61.258 60.000 4.02 0.00 0.00 3.91
2915 3290 1.471119 CCCTCGGAGTGTAGTGCTTA 58.529 55.000 4.02 0.00 0.00 3.09
2916 3291 1.134560 CCCTCGGAGTGTAGTGCTTAC 59.865 57.143 4.02 0.00 0.00 2.34
2917 3292 2.093106 CCTCGGAGTGTAGTGCTTACT 58.907 52.381 4.02 0.00 33.23 2.24
2918 3293 2.097791 CCTCGGAGTGTAGTGCTTACTC 59.902 54.545 4.02 0.00 39.98 2.59
2919 3294 2.747989 CTCGGAGTGTAGTGCTTACTCA 59.252 50.000 14.03 0.00 41.93 3.41
2920 3295 3.151554 TCGGAGTGTAGTGCTTACTCAA 58.848 45.455 14.03 4.08 41.93 3.02
2921 3296 3.190744 TCGGAGTGTAGTGCTTACTCAAG 59.809 47.826 14.03 9.56 41.93 3.02
2922 3297 3.673594 CGGAGTGTAGTGCTTACTCAAGG 60.674 52.174 14.03 4.26 41.93 3.61
2923 3298 3.258622 GGAGTGTAGTGCTTACTCAAGGT 59.741 47.826 14.03 0.00 41.93 3.50
2924 3299 4.262506 GGAGTGTAGTGCTTACTCAAGGTT 60.263 45.833 14.03 0.00 41.93 3.50
2925 3300 4.632153 AGTGTAGTGCTTACTCAAGGTTG 58.368 43.478 0.00 0.00 33.23 3.77
2926 3301 3.186613 GTGTAGTGCTTACTCAAGGTTGC 59.813 47.826 0.00 0.00 33.23 4.17
2927 3302 2.638480 AGTGCTTACTCAAGGTTGCA 57.362 45.000 0.00 0.00 35.21 4.08
2928 3303 3.146104 AGTGCTTACTCAAGGTTGCAT 57.854 42.857 0.00 0.00 38.02 3.96
2929 3304 2.816087 AGTGCTTACTCAAGGTTGCATG 59.184 45.455 0.00 0.00 38.02 4.06
2937 3312 2.818432 CTCAAGGTTGCATGAAAGCTCT 59.182 45.455 18.43 6.55 36.90 4.09
2961 3336 2.352915 GTGAGCCGCTCGAGATCG 60.353 66.667 18.75 11.22 41.45 3.69
2966 3341 2.824901 GCCGCTCGAGATCGACTCA 61.825 63.158 18.75 3.07 45.14 3.41
2972 3347 3.843541 CGCTCGAGATCGACTCATATTTC 59.156 47.826 18.75 0.00 45.14 2.17
2973 3348 4.611581 CGCTCGAGATCGACTCATATTTCA 60.612 45.833 18.75 0.00 45.14 2.69
2977 3352 5.009110 TCGAGATCGACTCATATTTCAGCTT 59.991 40.000 0.00 0.00 45.14 3.74
2980 3355 5.982516 AGATCGACTCATATTTCAGCTTGAC 59.017 40.000 0.00 0.00 0.00 3.18
2982 3357 5.344066 TCGACTCATATTTCAGCTTGACTC 58.656 41.667 0.00 0.00 0.00 3.36
2987 3362 5.586339 TCATATTTCAGCTTGACTCGAGAG 58.414 41.667 21.68 7.40 0.00 3.20
2988 3363 2.071688 TTTCAGCTTGACTCGAGAGC 57.928 50.000 21.68 17.76 36.68 4.09
3008 3383 3.063180 AGCGAATCAAGAAGAAATGAGCG 59.937 43.478 0.00 0.00 33.30 5.03
3009 3384 3.062639 GCGAATCAAGAAGAAATGAGCGA 59.937 43.478 0.00 0.00 32.45 4.93
3016 3392 6.398095 TCAAGAAGAAATGAGCGAGTATGAA 58.602 36.000 0.00 0.00 0.00 2.57
3025 3401 8.942338 AAATGAGCGAGTATGAACACTTTATA 57.058 30.769 0.00 0.00 0.00 0.98
3032 3408 7.007546 GCGAGTATGAACACTTTATATAGCTCG 59.992 40.741 0.00 0.00 41.33 5.03
3042 3418 7.804129 ACACTTTATATAGCTCGATCGAGAAAC 59.196 37.037 41.45 26.50 44.53 2.78
3058 3434 4.495422 GAGAAACGAGGTAATCTTGAGCA 58.505 43.478 0.00 0.00 0.00 4.26
3067 3443 4.757149 AGGTAATCTTGAGCAAACACTGAC 59.243 41.667 0.00 0.00 0.00 3.51
3077 3453 2.061773 CAAACACTGACTCGCTCGATT 58.938 47.619 0.00 0.00 0.00 3.34
3078 3454 2.440539 AACACTGACTCGCTCGATTT 57.559 45.000 0.00 0.00 0.00 2.17
3079 3455 2.440539 ACACTGACTCGCTCGATTTT 57.559 45.000 0.00 0.00 0.00 1.82
3080 3456 3.570926 ACACTGACTCGCTCGATTTTA 57.429 42.857 0.00 0.00 0.00 1.52
3081 3457 3.243336 ACACTGACTCGCTCGATTTTAC 58.757 45.455 0.00 0.00 0.00 2.01
3082 3458 2.599082 CACTGACTCGCTCGATTTTACC 59.401 50.000 0.00 0.00 0.00 2.85
3083 3459 2.492484 ACTGACTCGCTCGATTTTACCT 59.508 45.455 0.00 0.00 0.00 3.08
3084 3460 3.109619 CTGACTCGCTCGATTTTACCTC 58.890 50.000 0.00 0.00 0.00 3.85
3085 3461 2.110226 GACTCGCTCGATTTTACCTCG 58.890 52.381 0.00 0.00 37.47 4.63
3086 3462 1.741706 ACTCGCTCGATTTTACCTCGA 59.258 47.619 0.00 0.00 42.44 4.04
3087 3463 2.358267 ACTCGCTCGATTTTACCTCGAT 59.642 45.455 0.00 0.00 43.53 3.59
3091 3467 3.609644 CGCTCGATTTTACCTCGATAGCT 60.610 47.826 0.00 0.00 43.53 3.32
3197 3573 9.595823 AAAAATACTGTCTAGTATATGCACGTT 57.404 29.630 0.00 0.00 46.75 3.99
3200 3576 9.841880 AATACTGTCTAGTATATGCACGTTATG 57.158 33.333 0.00 0.00 46.75 1.90
3201 3577 7.273320 ACTGTCTAGTATATGCACGTTATGT 57.727 36.000 0.00 0.00 34.74 2.29
3202 3578 8.387190 ACTGTCTAGTATATGCACGTTATGTA 57.613 34.615 0.00 0.00 34.74 2.29
3203 3579 8.288208 ACTGTCTAGTATATGCACGTTATGTAC 58.712 37.037 0.00 7.84 34.74 2.90
3245 3621 9.781633 TTTCTACTACCAAACATGTAAGCTTAA 57.218 29.630 7.99 0.00 0.00 1.85
3253 3629 8.802267 ACCAAACATGTAAGCTTAATTATGTGT 58.198 29.630 22.57 17.91 0.00 3.72
3256 3632 6.795399 ACATGTAAGCTTAATTATGTGTGGC 58.205 36.000 21.79 4.22 0.00 5.01
3277 3653 4.359706 GCGAAAATTTAGCCCTGTTATGG 58.640 43.478 0.00 0.00 0.00 2.74
3284 3660 4.431416 TTAGCCCTGTTATGGTATGTGG 57.569 45.455 0.00 0.00 0.00 4.17
3286 3662 2.172717 AGCCCTGTTATGGTATGTGGTC 59.827 50.000 0.00 0.00 0.00 4.02
3288 3664 3.808728 CCCTGTTATGGTATGTGGTCAG 58.191 50.000 0.00 0.00 0.00 3.51
3289 3665 3.454447 CCCTGTTATGGTATGTGGTCAGA 59.546 47.826 0.00 0.00 0.00 3.27
3290 3666 4.442706 CCTGTTATGGTATGTGGTCAGAC 58.557 47.826 0.00 0.00 35.35 3.51
3291 3667 4.081142 CCTGTTATGGTATGTGGTCAGACA 60.081 45.833 2.17 0.00 37.50 3.41
3292 3668 5.396772 CCTGTTATGGTATGTGGTCAGACAT 60.397 44.000 2.17 0.00 37.50 3.06
3293 3669 5.427378 TGTTATGGTATGTGGTCAGACATG 58.573 41.667 2.17 0.00 37.50 3.21
3294 3670 5.045942 TGTTATGGTATGTGGTCAGACATGT 60.046 40.000 0.00 0.00 37.50 3.21
3295 3671 3.333029 TGGTATGTGGTCAGACATGTG 57.667 47.619 1.15 0.00 37.50 3.21
3297 3673 3.262420 GGTATGTGGTCAGACATGTGTC 58.738 50.000 1.15 5.01 45.08 3.67
3317 3693 8.402798 TGTGTCAAGTATCATGTTATTTTGGT 57.597 30.769 0.00 0.00 0.00 3.67
3336 3713 4.973168 TGGTAAAAGTTGAGAGCAGACAT 58.027 39.130 0.00 0.00 0.00 3.06
3337 3714 4.756642 TGGTAAAAGTTGAGAGCAGACATG 59.243 41.667 0.00 0.00 0.00 3.21
3354 3731 7.330900 CAGACATGCCTTCATTTTATTCTCT 57.669 36.000 0.00 0.00 0.00 3.10
3356 3733 7.701078 CAGACATGCCTTCATTTTATTCTCTTG 59.299 37.037 0.00 0.00 0.00 3.02
3360 3737 7.701539 TGCCTTCATTTTATTCTCTTGCTAA 57.298 32.000 0.00 0.00 0.00 3.09
3449 3826 9.128107 CATAATGGTTTCTTATGTTGTGTTGTC 57.872 33.333 0.00 0.00 33.72 3.18
3455 3832 3.991773 TCTTATGTTGTGTTGTCGCCTAC 59.008 43.478 0.00 0.00 0.00 3.18
3463 3840 3.998341 TGTGTTGTCGCCTACCTTATTTC 59.002 43.478 0.00 0.00 0.00 2.17
3471 3848 7.087639 TGTCGCCTACCTTATTTCAAAATTTG 58.912 34.615 0.00 0.00 0.00 2.32
3472 3849 7.088272 GTCGCCTACCTTATTTCAAAATTTGT 58.912 34.615 5.56 0.00 0.00 2.83
3473 3850 7.061789 GTCGCCTACCTTATTTCAAAATTTGTG 59.938 37.037 5.56 0.00 0.00 3.33
3474 3851 6.183360 CGCCTACCTTATTTCAAAATTTGTGC 60.183 38.462 5.56 0.00 0.00 4.57
3477 3854 9.353999 CCTACCTTATTTCAAAATTTGTGCTAC 57.646 33.333 5.56 0.00 0.00 3.58
3478 3855 9.906660 CTACCTTATTTCAAAATTTGTGCTACA 57.093 29.630 5.56 0.00 0.00 2.74
3480 3857 9.777297 ACCTTATTTCAAAATTTGTGCTACATT 57.223 25.926 5.56 0.00 0.00 2.71
3546 3923 4.814771 TCGACTCGAGATCATTACAAGCTA 59.185 41.667 21.68 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 0.958822 ACGAGGGCATGTGAAAAACC 59.041 50.000 0.00 0.00 0.00 3.27
54 55 5.938125 GGCATGGACTGACCGTAATAAATAT 59.062 40.000 0.00 0.00 42.61 1.28
58 59 2.769663 AGGCATGGACTGACCGTAATAA 59.230 45.455 0.00 0.00 42.61 1.40
64 65 0.107508 ATTGAGGCATGGACTGACCG 60.108 55.000 0.00 0.00 42.61 4.79
100 101 1.433592 AGATCCGGGGCTATCCTACTT 59.566 52.381 0.00 0.00 35.33 2.24
106 107 1.188219 TGCAGAGATCCGGGGCTATC 61.188 60.000 0.00 0.00 0.00 2.08
201 202 7.476667 TGAACAACTTTTTACAACGTGATGAT 58.523 30.769 0.00 0.00 0.00 2.45
242 243 4.752101 TCCGTGGCCAACAAATTTAAAATG 59.248 37.500 7.24 0.00 0.00 2.32
260 262 5.008811 AGAGTAGACCGAGAAATTATCCGTG 59.991 44.000 0.00 0.00 0.00 4.94
261 263 5.131784 AGAGTAGACCGAGAAATTATCCGT 58.868 41.667 0.00 0.00 0.00 4.69
306 308 8.094548 TGCTGAACATGTTTACTACTCAATACT 58.905 33.333 13.36 0.00 0.00 2.12
307 309 8.251750 TGCTGAACATGTTTACTACTCAATAC 57.748 34.615 13.36 0.00 0.00 1.89
309 311 7.928307 ATGCTGAACATGTTTACTACTCAAT 57.072 32.000 13.36 0.00 37.70 2.57
338 340 9.502091 TTCTTTGCTAGCTAGACAAATTCTTAA 57.498 29.630 28.00 19.23 35.55 1.85
341 343 7.986085 TTTCTTTGCTAGCTAGACAAATTCT 57.014 32.000 28.00 0.00 38.51 2.40
351 353 7.042335 GGAGTACATCTTTTCTTTGCTAGCTA 58.958 38.462 17.23 5.31 0.00 3.32
356 358 5.248380 AGGGAGTACATCTTTTCTTTGCT 57.752 39.130 0.00 0.00 0.00 3.91
389 391 8.833493 GTGTAGTGTTAAAACCACTCTTACATT 58.167 33.333 0.82 0.00 0.00 2.71
390 392 8.208903 AGTGTAGTGTTAAAACCACTCTTACAT 58.791 33.333 0.82 0.00 0.00 2.29
391 393 7.558604 AGTGTAGTGTTAAAACCACTCTTACA 58.441 34.615 0.82 0.00 0.00 2.41
392 394 9.189723 CTAGTGTAGTGTTAAAACCACTCTTAC 57.810 37.037 10.04 5.06 35.08 2.34
393 395 8.917088 ACTAGTGTAGTGTTAAAACCACTCTTA 58.083 33.333 10.04 0.00 37.69 2.10
394 396 7.789026 ACTAGTGTAGTGTTAAAACCACTCTT 58.211 34.615 10.04 0.00 37.69 2.85
395 397 7.357429 ACTAGTGTAGTGTTAAAACCACTCT 57.643 36.000 10.04 7.36 37.69 3.24
430 432 9.982291 GTGTCAAAAACGCTCTTATATTATGAA 57.018 29.630 0.00 0.00 35.42 2.57
431 433 9.378551 AGTGTCAAAAACGCTCTTATATTATGA 57.621 29.630 0.00 0.00 45.69 2.15
474 476 6.267014 CCCTCCGTCCTCTTAATATAAGAACA 59.733 42.308 1.87 0.00 0.00 3.18
476 478 6.617538 TCCCTCCGTCCTCTTAATATAAGAA 58.382 40.000 1.87 0.00 0.00 2.52
478 480 6.011481 ACTCCCTCCGTCCTCTTAATATAAG 58.989 44.000 0.00 0.00 0.00 1.73
482 484 3.967467 ACTCCCTCCGTCCTCTTAATA 57.033 47.619 0.00 0.00 0.00 0.98
487 489 4.472690 AATATTACTCCCTCCGTCCTCT 57.527 45.455 0.00 0.00 0.00 3.69
489 491 7.017531 AGAATAAATATTACTCCCTCCGTCCT 58.982 38.462 0.00 0.00 0.00 3.85
491 493 8.148999 ACAAGAATAAATATTACTCCCTCCGTC 58.851 37.037 0.00 0.00 0.00 4.79
493 495 8.904099 AACAAGAATAAATATTACTCCCTCCG 57.096 34.615 0.00 0.00 0.00 4.63
511 513 8.270799 CACTATTTCGTCGTTCTAAAACAAGAA 58.729 33.333 0.00 0.00 34.93 2.52
518 520 4.386652 GCCACACTATTTCGTCGTTCTAAA 59.613 41.667 0.00 0.00 0.00 1.85
537 539 3.715628 AGATTTCACAGTGTTTGCCAC 57.284 42.857 0.00 0.00 44.89 5.01
538 540 5.771469 CATAAGATTTCACAGTGTTTGCCA 58.229 37.500 0.00 0.00 0.00 4.92
539 541 4.622740 GCATAAGATTTCACAGTGTTTGCC 59.377 41.667 0.00 0.00 0.00 4.52
540 542 5.221880 TGCATAAGATTTCACAGTGTTTGC 58.778 37.500 0.00 0.00 0.00 3.68
542 544 8.891671 AATTTGCATAAGATTTCACAGTGTTT 57.108 26.923 0.00 0.00 0.00 2.83
560 799 6.801377 CGCACTAGTTAATTCTCAAATTTGCA 59.199 34.615 13.54 0.00 36.49 4.08
561 800 7.021196 TCGCACTAGTTAATTCTCAAATTTGC 58.979 34.615 13.54 0.00 36.49 3.68
568 807 9.594478 TCATAAATTCGCACTAGTTAATTCTCA 57.406 29.630 0.00 0.00 0.00 3.27
571 810 9.434559 GGTTCATAAATTCGCACTAGTTAATTC 57.565 33.333 0.00 0.00 0.00 2.17
573 812 8.500753 TGGTTCATAAATTCGCACTAGTTAAT 57.499 30.769 0.00 0.00 0.00 1.40
640 879 8.177663 GCAATCCATATTTATACTCCGTGATTG 58.822 37.037 0.00 0.00 0.00 2.67
665 904 5.204292 AGGGAAGAAGGATAGAAATTTGGC 58.796 41.667 0.00 0.00 0.00 4.52
666 905 7.724490 AAAGGGAAGAAGGATAGAAATTTGG 57.276 36.000 0.00 0.00 0.00 3.28
675 914 3.786450 GGGGAGAAAAGGGAAGAAGGATA 59.214 47.826 0.00 0.00 0.00 2.59
676 915 2.583101 GGGGAGAAAAGGGAAGAAGGAT 59.417 50.000 0.00 0.00 0.00 3.24
679 918 3.525800 TTGGGGAGAAAAGGGAAGAAG 57.474 47.619 0.00 0.00 0.00 2.85
681 920 3.401002 TGATTTGGGGAGAAAAGGGAAGA 59.599 43.478 0.00 0.00 0.00 2.87
682 921 3.778265 TGATTTGGGGAGAAAAGGGAAG 58.222 45.455 0.00 0.00 0.00 3.46
683 922 3.901222 GTTGATTTGGGGAGAAAAGGGAA 59.099 43.478 0.00 0.00 0.00 3.97
685 924 2.567169 GGTTGATTTGGGGAGAAAAGGG 59.433 50.000 0.00 0.00 0.00 3.95
701 945 1.333308 CAACTTCGTGCATGTGGTTGA 59.667 47.619 26.57 0.82 36.99 3.18
705 949 4.539152 GCAACTTCGTGCATGTGG 57.461 55.556 5.68 2.77 44.29 4.17
729 973 2.228822 GACACGGAGGCATGTGAATTTT 59.771 45.455 10.16 0.00 39.38 1.82
730 974 1.812571 GACACGGAGGCATGTGAATTT 59.187 47.619 10.16 0.00 39.38 1.82
731 975 1.271325 TGACACGGAGGCATGTGAATT 60.271 47.619 10.16 0.00 39.38 2.17
732 976 0.324614 TGACACGGAGGCATGTGAAT 59.675 50.000 10.16 0.00 39.38 2.57
772 1016 8.313292 ACCAGCAATTTATTTAGCTCAAAATGA 58.687 29.630 4.95 0.00 34.61 2.57
773 1017 8.483307 ACCAGCAATTTATTTAGCTCAAAATG 57.517 30.769 4.95 0.77 34.61 2.32
775 1019 9.585099 CATACCAGCAATTTATTTAGCTCAAAA 57.415 29.630 0.00 0.00 34.61 2.44
780 1024 5.598005 TGCCATACCAGCAATTTATTTAGCT 59.402 36.000 0.00 0.00 37.28 3.32
830 1077 4.521146 GAGATGTGGTGATCCAAACTGAT 58.479 43.478 0.00 0.00 46.15 2.90
833 1080 2.915604 AGGAGATGTGGTGATCCAAACT 59.084 45.455 0.00 0.00 46.15 2.66
844 1091 3.379372 CAGGCATACAAAAGGAGATGTGG 59.621 47.826 0.00 0.00 0.00 4.17
847 1094 5.128205 TGATCAGGCATACAAAAGGAGATG 58.872 41.667 0.00 0.00 0.00 2.90
853 1100 5.346822 GCAGTTTTGATCAGGCATACAAAAG 59.653 40.000 0.00 0.00 40.92 2.27
892 1244 6.510746 CAAGTGATGCAATGCAAAGATATG 57.489 37.500 13.45 4.01 43.62 1.78
915 1267 3.050275 AGAGCAAAACGGCCGAGC 61.050 61.111 35.90 27.39 0.00 5.03
916 1268 2.863153 CAGAGCAAAACGGCCGAG 59.137 61.111 35.90 19.06 0.00 4.63
1557 1929 2.716017 CGTCACCTCCTGGGAGCTC 61.716 68.421 4.71 4.71 40.69 4.09
1806 2178 2.182030 GCCGTCTTGGTCTCCTCG 59.818 66.667 0.00 0.00 41.21 4.63
1863 2235 2.620112 GCACGTGTTGAGGCAGCAT 61.620 57.895 18.38 0.00 0.00 3.79
1989 2361 2.590007 GAGAGCATGCCGGCGAAT 60.590 61.111 23.90 7.88 39.27 3.34
2427 2799 1.302752 GATCACCACCAGCAGCACA 60.303 57.895 0.00 0.00 0.00 4.57
2525 2897 2.282462 GGGGTGCCTCCTTGTGTG 60.282 66.667 0.00 0.00 36.25 3.82
2526 2898 1.943730 TTTGGGGTGCCTCCTTGTGT 61.944 55.000 0.00 0.00 36.25 3.72
2555 2927 2.492088 TGGAGTTATGGTCAGACGTCAG 59.508 50.000 19.50 10.43 0.00 3.51
2556 2928 2.492088 CTGGAGTTATGGTCAGACGTCA 59.508 50.000 19.50 0.00 0.00 4.35
2557 2929 2.735762 GCTGGAGTTATGGTCAGACGTC 60.736 54.545 7.70 7.70 0.00 4.34
2562 2934 3.287867 AATGGCTGGAGTTATGGTCAG 57.712 47.619 0.00 0.00 0.00 3.51
2586 2958 7.161404 TGCACTCAGATTAATTCACACTACTT 58.839 34.615 0.00 0.00 0.00 2.24
2590 2962 6.432162 ACATTGCACTCAGATTAATTCACACT 59.568 34.615 0.00 0.00 0.00 3.55
2591 2963 6.615088 ACATTGCACTCAGATTAATTCACAC 58.385 36.000 0.00 0.00 0.00 3.82
2592 2964 6.822667 ACATTGCACTCAGATTAATTCACA 57.177 33.333 0.00 0.00 0.00 3.58
2593 2965 7.751732 TGTACATTGCACTCAGATTAATTCAC 58.248 34.615 0.00 0.00 0.00 3.18
2594 2966 7.920160 TGTACATTGCACTCAGATTAATTCA 57.080 32.000 0.00 0.00 0.00 2.57
2595 2967 9.869844 GTATGTACATTGCACTCAGATTAATTC 57.130 33.333 14.77 0.00 0.00 2.17
2596 2968 9.618890 AGTATGTACATTGCACTCAGATTAATT 57.381 29.630 14.77 0.00 0.00 1.40
2598 2970 7.011389 GCAGTATGTACATTGCACTCAGATTAA 59.989 37.037 22.07 0.00 39.31 1.40
2599 2971 6.479990 GCAGTATGTACATTGCACTCAGATTA 59.520 38.462 22.07 0.00 39.31 1.75
2621 2993 5.426504 AGTTTCATCTTCATGTAGGAGCAG 58.573 41.667 0.00 0.00 0.00 4.24
2622 2994 5.426689 AGTTTCATCTTCATGTAGGAGCA 57.573 39.130 0.00 0.00 0.00 4.26
2623 2995 6.404074 CCAAAGTTTCATCTTCATGTAGGAGC 60.404 42.308 0.00 0.00 0.00 4.70
2624 2996 6.881065 TCCAAAGTTTCATCTTCATGTAGGAG 59.119 38.462 0.00 0.00 0.00 3.69
2625 2997 6.778821 TCCAAAGTTTCATCTTCATGTAGGA 58.221 36.000 0.00 0.00 0.00 2.94
2626 2998 6.881065 TCTCCAAAGTTTCATCTTCATGTAGG 59.119 38.462 0.00 0.00 0.00 3.18
2675 3050 3.455910 CCTCACCTCCCTCATGACAATTA 59.544 47.826 0.00 0.00 0.00 1.40
2681 3056 2.060383 CGCCTCACCTCCCTCATGA 61.060 63.158 0.00 0.00 0.00 3.07
2684 3059 2.680352 GTCGCCTCACCTCCCTCA 60.680 66.667 0.00 0.00 0.00 3.86
2685 3060 3.827898 CGTCGCCTCACCTCCCTC 61.828 72.222 0.00 0.00 0.00 4.30
2701 3076 0.383231 GCATTCCAAGGCTCCATTCG 59.617 55.000 0.00 0.00 32.08 3.34
2714 3089 2.749621 ACATTGTCGGAGAAAGCATTCC 59.250 45.455 0.00 0.00 39.69 3.01
2732 3107 3.668447 AGTGAGTGAATGAGCGAAACAT 58.332 40.909 0.00 0.00 0.00 2.71
2739 3114 3.603532 TGGAATGAGTGAGTGAATGAGC 58.396 45.455 0.00 0.00 0.00 4.26
2744 3119 4.223700 AGCACTATGGAATGAGTGAGTGAA 59.776 41.667 6.22 0.00 44.88 3.18
2760 3135 6.874664 TCGACTCGATTAGATTAGAGCACTAT 59.125 38.462 0.00 0.00 34.31 2.12
2761 3136 6.145858 GTCGACTCGATTAGATTAGAGCACTA 59.854 42.308 8.70 0.00 38.42 2.74
2784 3159 8.839310 AGTTTCATCCTTGCATATGTATAGTC 57.161 34.615 4.29 0.00 0.00 2.59
2797 3172 6.146021 CCAAAATTTCCGAAGTTTCATCCTTG 59.854 38.462 2.43 0.00 31.30 3.61
2800 3175 5.538118 ACCAAAATTTCCGAAGTTTCATCC 58.462 37.500 2.43 0.00 31.30 3.51
2811 3186 5.803020 TTGTTTCCAAACCAAAATTTCCG 57.197 34.783 0.00 0.00 38.11 4.30
2837 3212 8.648557 TCATCTTCTTCGACACAATTATAAGG 57.351 34.615 0.00 0.00 0.00 2.69
2852 3227 2.348059 CGTCAGCTTGCTCATCTTCTTC 59.652 50.000 0.00 0.00 0.00 2.87
2861 3236 1.011451 GTCCACTCGTCAGCTTGCTC 61.011 60.000 0.00 0.00 0.00 4.26
2868 3243 3.633094 CTGCGGGTCCACTCGTCAG 62.633 68.421 0.11 5.12 0.00 3.51
2872 3247 2.432628 GTTCTGCGGGTCCACTCG 60.433 66.667 0.00 0.00 0.00 4.18
2881 3256 0.811281 GAGGGGAAAATGTTCTGCGG 59.189 55.000 0.00 0.00 33.92 5.69
2884 3259 2.290323 ACTCCGAGGGGAAAATGTTCTG 60.290 50.000 0.00 0.00 43.27 3.02
2885 3260 1.985895 ACTCCGAGGGGAAAATGTTCT 59.014 47.619 0.00 0.00 43.27 3.01
2897 3272 2.093106 AGTAAGCACTACACTCCGAGG 58.907 52.381 0.00 0.00 31.45 4.63
2901 3276 3.258622 ACCTTGAGTAAGCACTACACTCC 59.741 47.826 8.89 0.00 38.32 3.85
2907 3282 3.762407 TGCAACCTTGAGTAAGCACTA 57.238 42.857 0.00 0.00 35.44 2.74
2908 3283 2.638480 TGCAACCTTGAGTAAGCACT 57.362 45.000 0.00 0.00 35.44 4.40
2909 3284 2.813754 TCATGCAACCTTGAGTAAGCAC 59.186 45.455 0.00 0.00 40.94 4.40
2910 3285 3.138884 TCATGCAACCTTGAGTAAGCA 57.861 42.857 0.00 0.00 41.93 3.91
2911 3286 4.479619 CTTTCATGCAACCTTGAGTAAGC 58.520 43.478 0.00 0.00 32.40 3.09
2912 3287 4.217118 AGCTTTCATGCAACCTTGAGTAAG 59.783 41.667 0.00 0.00 34.99 2.34
2914 3289 3.753272 GAGCTTTCATGCAACCTTGAGTA 59.247 43.478 0.00 0.00 34.99 2.59
2915 3290 2.555757 GAGCTTTCATGCAACCTTGAGT 59.444 45.455 0.00 0.00 34.99 3.41
2916 3291 2.818432 AGAGCTTTCATGCAACCTTGAG 59.182 45.455 0.00 0.00 34.99 3.02
2917 3292 2.867624 AGAGCTTTCATGCAACCTTGA 58.132 42.857 0.00 0.00 34.99 3.02
2918 3293 3.128242 CCTAGAGCTTTCATGCAACCTTG 59.872 47.826 0.00 0.00 34.99 3.61
2919 3294 3.350833 CCTAGAGCTTTCATGCAACCTT 58.649 45.455 0.00 0.00 34.99 3.50
2920 3295 2.943199 GCCTAGAGCTTTCATGCAACCT 60.943 50.000 0.00 0.00 38.99 3.50
2921 3296 1.403323 GCCTAGAGCTTTCATGCAACC 59.597 52.381 0.00 0.00 38.99 3.77
2922 3297 2.840296 GCCTAGAGCTTTCATGCAAC 57.160 50.000 0.00 0.00 38.99 4.17
2961 3336 5.344066 TCGAGTCAAGCTGAAATATGAGTC 58.656 41.667 8.13 8.13 38.36 3.36
2966 3341 4.367450 GCTCTCGAGTCAAGCTGAAATAT 58.633 43.478 13.13 0.00 33.23 1.28
2972 3347 0.109551 TTCGCTCTCGAGTCAAGCTG 60.110 55.000 18.98 13.56 46.34 4.24
2973 3348 0.814457 ATTCGCTCTCGAGTCAAGCT 59.186 50.000 18.98 1.96 46.34 3.74
2980 3355 3.412981 TCTTCTTGATTCGCTCTCGAG 57.587 47.619 5.93 5.93 46.34 4.04
2982 3357 4.564372 TCATTTCTTCTTGATTCGCTCTCG 59.436 41.667 0.00 0.00 0.00 4.04
2987 3362 3.062639 TCGCTCATTTCTTCTTGATTCGC 59.937 43.478 0.00 0.00 0.00 4.70
2988 3363 4.328440 ACTCGCTCATTTCTTCTTGATTCG 59.672 41.667 0.00 0.00 0.00 3.34
2991 3366 6.577103 TCATACTCGCTCATTTCTTCTTGAT 58.423 36.000 0.00 0.00 0.00 2.57
2994 3369 6.091441 GTGTTCATACTCGCTCATTTCTTCTT 59.909 38.462 0.00 0.00 0.00 2.52
2996 3371 5.578727 AGTGTTCATACTCGCTCATTTCTTC 59.421 40.000 0.00 0.00 0.00 2.87
2999 3374 5.786401 AAGTGTTCATACTCGCTCATTTC 57.214 39.130 0.00 0.00 0.00 2.17
3016 3392 7.436430 TTCTCGATCGAGCTATATAAAGTGT 57.564 36.000 34.92 0.00 41.71 3.55
3042 3418 3.997021 AGTGTTTGCTCAAGATTACCTCG 59.003 43.478 0.00 0.00 0.00 4.63
3046 3422 5.388890 CGAGTCAGTGTTTGCTCAAGATTAC 60.389 44.000 0.00 0.00 32.74 1.89
3048 3424 3.496130 CGAGTCAGTGTTTGCTCAAGATT 59.504 43.478 0.00 0.00 32.74 2.40
3058 3434 2.440539 AATCGAGCGAGTCAGTGTTT 57.559 45.000 0.00 0.00 0.00 2.83
3067 3443 2.470196 TCGAGGTAAAATCGAGCGAG 57.530 50.000 0.00 0.00 43.79 5.03
3178 3554 7.477733 CGTACATAACGTGCATATACTAGACAG 59.522 40.741 0.00 0.00 46.72 3.51
3180 3556 7.702069 CGTACATAACGTGCATATACTAGAC 57.298 40.000 0.00 0.00 46.72 2.59
3220 3596 9.953565 ATTAAGCTTACATGTTTGGTAGTAGAA 57.046 29.630 5.45 0.00 0.00 2.10
3221 3597 9.953565 AATTAAGCTTACATGTTTGGTAGTAGA 57.046 29.630 5.45 0.00 0.00 2.59
3237 3613 6.745159 TTTCGCCACACATAATTAAGCTTA 57.255 33.333 0.86 0.86 0.00 3.09
3240 3616 6.885735 AATTTTCGCCACACATAATTAAGC 57.114 33.333 0.00 0.00 0.00 3.09
3241 3617 8.531530 GCTAAATTTTCGCCACACATAATTAAG 58.468 33.333 0.00 0.00 0.00 1.85
3245 3621 5.348164 GGCTAAATTTTCGCCACACATAAT 58.652 37.500 20.23 0.00 43.25 1.28
3249 3625 1.271102 GGGCTAAATTTTCGCCACACA 59.729 47.619 24.09 0.00 45.53 3.72
3250 3626 1.544246 AGGGCTAAATTTTCGCCACAC 59.456 47.619 24.09 12.61 45.53 3.82
3252 3628 1.544246 ACAGGGCTAAATTTTCGCCAC 59.456 47.619 24.09 16.52 45.53 5.01
3253 3629 1.917872 ACAGGGCTAAATTTTCGCCA 58.082 45.000 24.09 0.00 45.53 5.69
3256 3632 5.576447 ACCATAACAGGGCTAAATTTTCG 57.424 39.130 0.00 0.00 0.00 3.46
3270 3646 5.045942 ACATGTCTGACCACATACCATAACA 60.046 40.000 5.17 0.00 35.10 2.41
3271 3647 5.294306 CACATGTCTGACCACATACCATAAC 59.706 44.000 5.17 0.00 35.10 1.89
3272 3648 5.045942 ACACATGTCTGACCACATACCATAA 60.046 40.000 5.17 0.00 35.10 1.90
3277 3653 3.925379 TGACACATGTCTGACCACATAC 58.075 45.455 12.98 0.00 44.99 2.39
3284 3660 5.871524 ACATGATACTTGACACATGTCTGAC 59.128 40.000 12.98 0.00 46.42 3.51
3290 3666 9.292846 CCAAAATAACATGATACTTGACACATG 57.707 33.333 0.00 0.00 43.56 3.21
3291 3667 9.023962 ACCAAAATAACATGATACTTGACACAT 57.976 29.630 0.00 0.00 0.00 3.21
3292 3668 8.402798 ACCAAAATAACATGATACTTGACACA 57.597 30.769 0.00 0.00 0.00 3.72
3336 3713 7.701539 TTAGCAAGAGAATAAAATGAAGGCA 57.298 32.000 0.00 0.00 0.00 4.75
3337 3714 9.242477 GAATTAGCAAGAGAATAAAATGAAGGC 57.758 33.333 0.00 0.00 0.00 4.35
3423 3800 9.128107 GACAACACAACATAAGAAACCATTATG 57.872 33.333 4.57 4.57 43.30 1.90
3430 3807 3.972502 GGCGACAACACAACATAAGAAAC 59.027 43.478 0.00 0.00 0.00 2.78
3434 3811 3.124636 GGTAGGCGACAACACAACATAAG 59.875 47.826 0.00 0.00 0.00 1.73
3436 3813 2.300723 AGGTAGGCGACAACACAACATA 59.699 45.455 0.00 0.00 0.00 2.29
3445 3822 6.827586 ATTTTGAAATAAGGTAGGCGACAA 57.172 33.333 0.00 0.00 0.00 3.18
3449 3826 6.183360 GCACAAATTTTGAAATAAGGTAGGCG 60.183 38.462 15.81 0.00 0.00 5.52
3493 3870 7.648510 CGACCTAGTTTCGAGCTAAATAAGATT 59.351 37.037 5.28 0.00 38.85 2.40


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

AutoCloner maintained by Alex Coulton.