Multiple sequence alignment - TraesCS7B01G170600

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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 TraesCS7B01G170600 chr7B 100.000 5765 0 0 1 5765 242721103 242715339 0.000000e+00 10647.0
1 TraesCS7B01G170600 chr7B 88.816 152 3 8 3249 3392 242717789 242717644 2.140000e-39 174.0
2 TraesCS7B01G170600 chr7B 88.816 152 3 8 3315 3460 242717855 242717712 2.140000e-39 174.0
3 TraesCS7B01G170600 chr7B 93.421 76 3 2 3249 3322 242717719 242717644 1.700000e-20 111.0
4 TraesCS7B01G170600 chr7B 93.421 76 3 2 3385 3460 242717855 242717782 1.700000e-20 111.0
5 TraesCS7B01G170600 chr7B 97.561 41 1 0 2654 2694 732651723 732651683 2.880000e-08 71.3
6 TraesCS7B01G170600 chr7D 92.034 2109 57 32 42 2070 261815814 261817891 0.000000e+00 2861.0
7 TraesCS7B01G170600 chr7D 92.152 1338 76 16 2066 3384 261817967 261819294 0.000000e+00 1862.0
8 TraesCS7B01G170600 chr7D 95.583 815 18 7 4306 5118 261820331 261821129 0.000000e+00 1290.0
9 TraesCS7B01G170600 chr7D 95.115 655 21 7 3315 3965 261819163 261819810 0.000000e+00 1022.0
10 TraesCS7B01G170600 chr7D 93.235 340 19 3 5426 5765 261862263 261862598 1.120000e-136 497.0
11 TraesCS7B01G170600 chr7D 94.779 249 11 2 4062 4309 261819890 261820137 2.520000e-103 387.0
12 TraesCS7B01G170600 chr7D 90.868 219 12 6 5165 5381 261821131 261821343 2.630000e-73 287.0
13 TraesCS7B01G170600 chr7D 98.485 66 1 0 3249 3314 261819229 261819294 3.650000e-22 117.0
14 TraesCS7B01G170600 chr7D 97.778 45 0 1 2734 2778 358722558 358722515 6.190000e-10 76.8
15 TraesCS7B01G170600 chr7D 93.023 43 2 1 2230 2271 261818080 261818122 1.730000e-05 62.1
16 TraesCS7B01G170600 chr7D 100.000 29 0 0 1 29 261815799 261815827 3.000000e-03 54.7
17 TraesCS7B01G170600 chr7D 100.000 28 0 0 2670 2697 594065134 594065107 1.000000e-02 52.8
18 TraesCS7B01G170600 chr7A 93.189 1850 64 24 837 2657 284726874 284728690 0.000000e+00 2662.0
19 TraesCS7B01G170600 chr7A 91.139 869 54 18 3459 4309 284729247 284730110 0.000000e+00 1157.0
20 TraesCS7B01G170600 chr7A 92.214 822 38 12 4306 5123 284730209 284731008 0.000000e+00 1140.0
21 TraesCS7B01G170600 chr7A 89.467 807 35 18 42 827 284725763 284726540 0.000000e+00 974.0
22 TraesCS7B01G170600 chr7A 92.998 557 28 3 2734 3279 284728693 284729249 0.000000e+00 802.0
23 TraesCS7B01G170600 chr7A 90.796 565 36 5 5214 5765 284740240 284740801 0.000000e+00 741.0
24 TraesCS7B01G170600 chr7A 89.286 112 12 0 5110 5221 284738375 284738486 2.170000e-29 141.0
25 TraesCS7B01G170600 chr7A 97.917 48 1 0 2735 2782 262465909 262465956 3.700000e-12 84.2
26 TraesCS7B01G170600 chr5D 91.525 236 15 5 1087 1319 421841212 421841445 2.590000e-83 320.0
27 TraesCS7B01G170600 chr5D 83.969 131 21 0 4354 4484 421844393 421844523 6.060000e-25 126.0
28 TraesCS7B01G170600 chr5B 91.525 236 15 5 1087 1319 508253915 508254148 2.590000e-83 320.0
29 TraesCS7B01G170600 chr5B 95.833 48 2 0 2734 2781 34252139 34252186 1.720000e-10 78.7
30 TraesCS7B01G170600 chr5A 90.987 233 16 5 1087 1316 535354908 535355138 5.610000e-80 309.0
31 TraesCS7B01G170600 chr5A 83.206 131 22 0 4354 4484 535357996 535358126 2.820000e-23 121.0
32 TraesCS7B01G170600 chr5A 93.182 44 3 0 2653 2696 11064172 11064129 1.340000e-06 65.8
33 TraesCS7B01G170600 chr4B 77.079 445 74 21 3431 3858 2707808 2708241 1.250000e-56 231.0
34 TraesCS7B01G170600 chr4B 82.550 149 20 3 2993 3135 2696079 2696227 6.060000e-25 126.0
35 TraesCS7B01G170600 chr4B 97.917 48 1 0 2734 2781 642195605 642195652 3.700000e-12 84.2
36 TraesCS7B01G170600 chr4A 83.893 149 18 3 2993 3135 602376652 602376800 2.800000e-28 137.0
37 TraesCS7B01G170600 chr4A 89.041 73 3 4 2575 2645 602376460 602376529 1.030000e-12 86.1
38 TraesCS7B01G170600 chr4A 78.358 134 22 4 2655 2781 66145758 66145625 4.790000e-11 80.5
39 TraesCS7B01G170600 chr4D 76.393 305 39 20 2353 2645 3225921 3225638 3.620000e-27 134.0
40 TraesCS7B01G170600 chrUn 82.550 149 20 3 2993 3135 51905114 51905262 6.060000e-25 126.0
41 TraesCS7B01G170600 chrUn 82.550 149 20 3 2993 3135 324645023 324645171 6.060000e-25 126.0
42 TraesCS7B01G170600 chr6B 92.308 52 4 0 2739 2790 95494815 95494866 2.230000e-09 75.0
43 TraesCS7B01G170600 chr3D 97.674 43 1 0 2736 2778 115025348 115025306 2.230000e-09 75.0
44 TraesCS7B01G170600 chr3D 95.238 42 2 0 2657 2698 448432877 448432918 3.730000e-07 67.6
45 TraesCS7B01G170600 chr6D 95.556 45 2 0 2734 2778 14291348 14291392 8.010000e-09 73.1
46 TraesCS7B01G170600 chr1A 90.698 43 4 0 2654 2696 504525173 504525215 2.240000e-04 58.4


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 TraesCS7B01G170600 chr7B 242715339 242721103 5764 True 2243.400000 10647 92.8948 1 5765 5 chr7B.!!$R2 5764
1 TraesCS7B01G170600 chr7D 261815799 261821343 5544 False 882.533333 2861 94.6710 1 5381 9 chr7D.!!$F2 5380
2 TraesCS7B01G170600 chr7A 284725763 284731008 5245 False 1347.000000 2662 91.8014 42 5123 5 chr7A.!!$F2 5081
3 TraesCS7B01G170600 chr7A 284738375 284740801 2426 False 441.000000 741 90.0410 5110 5765 2 chr7A.!!$F3 655
4 TraesCS7B01G170600 chr5D 421841212 421844523 3311 False 223.000000 320 87.7470 1087 4484 2 chr5D.!!$F1 3397
5 TraesCS7B01G170600 chr5A 535354908 535358126 3218 False 215.000000 309 87.0965 1087 4484 2 chr5A.!!$F1 3397

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
37 38 0.972134 CAGAGGCTGGTCTGTCTCAA 59.028 55.0 11.07 0.0 40.82 3.02 F
1523 2127 0.108615 CGGACCTAGGCACTTCTGTG 60.109 60.0 9.30 0.0 46.37 3.66 F
1701 2312 0.865111 TTGTGTGGTCATTTCGCTCG 59.135 50.0 0.00 0.0 0.00 5.03 F
2496 3730 0.958876 CTGCTCATGTTGCTGCCTGA 60.959 55.0 12.86 0.0 0.00 3.86 F
3367 5187 0.959553 TGTGTCACCTCCTCTTCGAC 59.040 55.0 0.00 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1915 2625 1.077993 AGTAGGGACTGGACTGAAGCT 59.922 52.381 0.00 0.0 41.52 3.74 R
2985 4226 0.037447 AGTCCTGCAAGAAAGAGGGC 59.963 55.000 0.00 0.0 34.07 5.19 R
3348 5168 0.959553 GTCGAAGAGGAGGTGACACA 59.040 55.000 8.08 0.0 36.95 3.72 R
3771 5592 1.003118 GCATCCAAGGGCCGATGTATA 59.997 52.381 17.60 2.9 38.50 1.47 R
5095 7139 1.595382 GAATCCCGCCGATGACCTG 60.595 63.158 0.00 0.0 0.00 4.00 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 5.470845 CGAAATTGGGCTACTAAACAGAG 57.529 43.478 0.00 0.00 0.00 3.35
23 24 4.332819 CGAAATTGGGCTACTAAACAGAGG 59.667 45.833 0.00 0.00 0.00 3.69
24 25 2.781681 TTGGGCTACTAAACAGAGGC 57.218 50.000 0.00 0.00 35.13 4.70
25 26 1.952621 TGGGCTACTAAACAGAGGCT 58.047 50.000 0.00 0.00 36.11 4.58
26 27 1.555075 TGGGCTACTAAACAGAGGCTG 59.445 52.381 0.00 0.00 36.11 4.85
27 28 1.134371 GGGCTACTAAACAGAGGCTGG 60.134 57.143 0.00 0.00 35.51 4.85
28 29 1.555533 GGCTACTAAACAGAGGCTGGT 59.444 52.381 0.00 0.00 35.51 4.00
29 30 2.418884 GGCTACTAAACAGAGGCTGGTC 60.419 54.545 0.00 0.00 35.51 4.02
30 31 2.498078 GCTACTAAACAGAGGCTGGTCT 59.502 50.000 0.00 0.00 35.51 3.85
36 37 2.663566 CAGAGGCTGGTCTGTCTCA 58.336 57.895 11.07 0.00 40.82 3.27
37 38 0.972134 CAGAGGCTGGTCTGTCTCAA 59.028 55.000 11.07 0.00 40.82 3.02
38 39 1.345741 CAGAGGCTGGTCTGTCTCAAA 59.654 52.381 11.07 0.00 40.82 2.69
39 40 2.050144 AGAGGCTGGTCTGTCTCAAAA 58.950 47.619 11.07 0.00 40.82 2.44
40 41 2.439507 AGAGGCTGGTCTGTCTCAAAAA 59.560 45.455 11.07 0.00 40.82 1.94
472 526 2.609459 CTCGAGGCGCATTAACAATTCT 59.391 45.455 10.83 0.00 0.00 2.40
479 533 4.399978 GCGCATTAACAATTCTAACACGT 58.600 39.130 0.30 0.00 0.00 4.49
659 716 4.839121 TCCTCAAATGCAAATACTACGGT 58.161 39.130 0.00 0.00 0.00 4.83
777 839 6.376299 ACTCATCAAAGCAAAGATAAGCATCA 59.624 34.615 0.00 0.00 33.21 3.07
816 878 5.331069 TCCATATACTAGTAACCTGCCTCC 58.669 45.833 6.70 0.00 0.00 4.30
1319 1711 2.660258 AAGACCTGCGCTGGTTCGTT 62.660 55.000 35.37 25.63 41.00 3.85
1321 1713 2.357517 CCTGCGCTGGTTCGTTCT 60.358 61.111 24.00 0.00 0.00 3.01
1337 1729 5.873179 TCGTTCTCTTCTCTTCTCTTCTC 57.127 43.478 0.00 0.00 0.00 2.87
1391 1785 1.338200 CCGTCCAGCTAGCTTGACTTT 60.338 52.381 33.71 6.02 36.80 2.66
1422 2025 7.436933 GGTCTGATCTGATTTTTCCAAAGTTT 58.563 34.615 5.52 0.00 0.00 2.66
1445 2048 0.961753 CCTTTCTGGGTCACCTTTGC 59.038 55.000 0.00 0.00 37.76 3.68
1514 2118 2.897969 TGATTTATCCTCGGACCTAGGC 59.102 50.000 9.30 1.17 33.84 3.93
1523 2127 0.108615 CGGACCTAGGCACTTCTGTG 60.109 60.000 9.30 0.00 46.37 3.66
1630 2241 3.107661 GCGTGGTGCATTGCAAGC 61.108 61.111 13.94 12.62 41.47 4.01
1663 2274 3.992260 ACTACTCCGTACATGCTGATC 57.008 47.619 0.00 0.00 0.00 2.92
1700 2311 2.143122 TCTTGTGTGGTCATTTCGCTC 58.857 47.619 0.00 0.00 0.00 5.03
1701 2312 0.865111 TTGTGTGGTCATTTCGCTCG 59.135 50.000 0.00 0.00 0.00 5.03
1718 2329 1.462283 CTCGATGTGTGCAAAGTGAGG 59.538 52.381 0.00 0.00 0.00 3.86
1783 2397 2.356069 CGTGTCTCTAGCTGCATCTGTA 59.644 50.000 1.02 0.00 0.00 2.74
1788 2405 5.240403 TGTCTCTAGCTGCATCTGTATACTG 59.760 44.000 1.02 3.79 0.00 2.74
1802 2419 5.368816 TCTGTATACTGTAGAGGTCCTGCTA 59.631 44.000 0.00 0.00 0.00 3.49
1804 2421 2.146920 ACTGTAGAGGTCCTGCTACC 57.853 55.000 18.34 0.00 36.91 3.18
1915 2625 4.656100 TTGGACCATTTCATCTCTTGGA 57.344 40.909 0.00 0.00 33.36 3.53
2065 3179 4.201812 CGTGGATGGTGCAAACTTATGTAG 60.202 45.833 0.00 0.00 0.00 2.74
2110 3304 5.125100 ACCAACAAACATGCTGTTCATAG 57.875 39.130 10.10 4.16 40.14 2.23
2125 3320 6.238676 GCTGTTCATAGACATCAGCATCATTT 60.239 38.462 9.99 0.00 46.95 2.32
2179 3410 2.024414 GGAACATATGTGTGCCCCTTC 58.976 52.381 9.63 0.10 46.97 3.46
2195 3428 3.467803 CCCTTCTGTTCTTCGTCTGTTT 58.532 45.455 0.00 0.00 0.00 2.83
2239 3472 3.133141 AGTGAGCTCCTTTGTTCTTCC 57.867 47.619 12.15 0.00 0.00 3.46
2264 3497 7.869429 CCTCTGTTTAAGATGCATGTTTTCTTT 59.131 33.333 14.96 0.00 33.29 2.52
2314 3547 2.202932 CGGAAGCCGTAGCAGCAT 60.203 61.111 0.00 0.00 42.73 3.79
2363 3596 8.966069 AGCTAGGAATTTTTAGTTGATCTACC 57.034 34.615 3.54 0.00 0.00 3.18
2496 3730 0.958876 CTGCTCATGTTGCTGCCTGA 60.959 55.000 12.86 0.00 0.00 3.86
2499 3733 1.085091 CTCATGTTGCTGCCTGACTC 58.915 55.000 0.00 0.00 0.00 3.36
2590 3824 7.533426 TCTATGCTCAAGCTCTGAAAAATTTC 58.467 34.615 3.32 0.00 42.66 2.17
2693 3928 8.147704 TGAATTAATTGACGCATCCTCTATACA 58.852 33.333 5.17 0.00 0.00 2.29
2700 3935 3.641436 ACGCATCCTCTATACAATGTCCA 59.359 43.478 0.00 0.00 0.00 4.02
2701 3936 4.284490 ACGCATCCTCTATACAATGTCCAT 59.716 41.667 0.00 0.00 0.00 3.41
2702 3937 5.221722 ACGCATCCTCTATACAATGTCCATT 60.222 40.000 0.00 0.00 0.00 3.16
2705 3940 8.197439 CGCATCCTCTATACAATGTCCATTATA 58.803 37.037 0.00 0.00 0.00 0.98
2706 3941 9.319143 GCATCCTCTATACAATGTCCATTATAC 57.681 37.037 0.00 0.00 0.00 1.47
2716 3951 8.908786 ACAATGTCCATTATACATAGAGGTTG 57.091 34.615 0.00 0.00 36.56 3.77
2718 3953 5.538118 TGTCCATTATACATAGAGGTTGCG 58.462 41.667 0.00 0.00 0.00 4.85
2721 3956 5.303333 TCCATTATACATAGAGGTTGCGTCA 59.697 40.000 0.00 0.00 0.00 4.35
2722 3957 6.014584 TCCATTATACATAGAGGTTGCGTCAT 60.015 38.462 0.00 0.00 0.00 3.06
2724 3959 7.173218 CCATTATACATAGAGGTTGCGTCATTT 59.827 37.037 0.00 0.00 0.00 2.32
2725 3960 9.203421 CATTATACATAGAGGTTGCGTCATTTA 57.797 33.333 0.00 0.00 0.00 1.40
2727 3962 9.772973 TTATACATAGAGGTTGCGTCATTTAAT 57.227 29.630 0.00 0.00 0.00 1.40
2729 3964 7.391148 ACATAGAGGTTGCGTCATTTAATTT 57.609 32.000 0.00 0.00 0.00 1.82
2730 3965 7.250569 ACATAGAGGTTGCGTCATTTAATTTG 58.749 34.615 0.00 0.00 0.00 2.32
2751 3991 2.104792 GGGACATTGTATAGAGGCTGCA 59.895 50.000 0.50 0.00 0.00 4.41
2831 4071 6.894339 ACCAGGTTTTCATTAACGAGAAAT 57.106 33.333 0.00 0.00 34.10 2.17
2893 4133 9.404348 CTGATCTGCTGTAATATAACACACTAG 57.596 37.037 0.00 0.00 0.00 2.57
2958 4199 6.687105 GGTGTATTTGTTCGTGATAATTGCTC 59.313 38.462 0.00 0.00 0.00 4.26
3044 4301 2.281070 ACAGCACTGTTCCTGGCG 60.281 61.111 0.00 0.00 41.83 5.69
3168 4425 7.324178 GTTCAGACTGAGGTCAACTTATATGT 58.676 38.462 5.10 0.00 44.36 2.29
3246 4937 9.449719 ACTATAAAACTGTGAGGATTTAGGTTG 57.550 33.333 0.00 0.00 0.00 3.77
3251 4942 5.805728 ACTGTGAGGATTTAGGTTGTTAGG 58.194 41.667 0.00 0.00 0.00 2.69
3299 5119 2.795175 TGTGTCACCTCTTCGACTTC 57.205 50.000 0.00 0.00 33.18 3.01
3312 5132 6.387041 TCTTCGACTTCAGTTTTCTCACTA 57.613 37.500 0.00 0.00 0.00 2.74
3313 5133 6.207213 TCTTCGACTTCAGTTTTCTCACTAC 58.793 40.000 0.00 0.00 0.00 2.73
3314 5134 5.769484 TCGACTTCAGTTTTCTCACTACT 57.231 39.130 0.00 0.00 0.00 2.57
3315 5135 6.872628 TCGACTTCAGTTTTCTCACTACTA 57.127 37.500 0.00 0.00 0.00 1.82
3316 5136 6.900189 TCGACTTCAGTTTTCTCACTACTAG 58.100 40.000 0.00 0.00 0.00 2.57
3317 5137 6.709397 TCGACTTCAGTTTTCTCACTACTAGA 59.291 38.462 0.00 0.00 0.00 2.43
3318 5138 6.797995 CGACTTCAGTTTTCTCACTACTAGAC 59.202 42.308 0.00 0.00 0.00 2.59
3319 5139 7.520131 CGACTTCAGTTTTCTCACTACTAGACA 60.520 40.741 0.00 0.00 0.00 3.41
3320 5140 8.184304 ACTTCAGTTTTCTCACTACTAGACAT 57.816 34.615 0.00 0.00 0.00 3.06
3321 5141 8.643324 ACTTCAGTTTTCTCACTACTAGACATT 58.357 33.333 0.00 0.00 0.00 2.71
3324 5144 9.298250 TCAGTTTTCTCACTACTAGACATTAGT 57.702 33.333 0.00 0.00 0.00 2.24
3325 5145 9.915629 CAGTTTTCTCACTACTAGACATTAGTT 57.084 33.333 0.00 0.00 0.00 2.24
3326 5146 9.915629 AGTTTTCTCACTACTAGACATTAGTTG 57.084 33.333 0.00 0.00 0.00 3.16
3327 5147 9.909644 GTTTTCTCACTACTAGACATTAGTTGA 57.090 33.333 0.00 0.00 0.00 3.18
3355 5175 8.723942 ATATGGAGTCTTATTTCTTGTGTCAC 57.276 34.615 0.00 0.00 0.00 3.67
3356 5176 5.305585 TGGAGTCTTATTTCTTGTGTCACC 58.694 41.667 0.00 0.00 0.00 4.02
3357 5177 5.071788 TGGAGTCTTATTTCTTGTGTCACCT 59.928 40.000 0.00 0.00 0.00 4.00
3358 5178 5.639931 GGAGTCTTATTTCTTGTGTCACCTC 59.360 44.000 0.00 0.00 0.00 3.85
3359 5179 5.552178 AGTCTTATTTCTTGTGTCACCTCC 58.448 41.667 0.00 0.00 0.00 4.30
3360 5180 5.308237 AGTCTTATTTCTTGTGTCACCTCCT 59.692 40.000 0.00 0.00 0.00 3.69
3361 5181 5.639931 GTCTTATTTCTTGTGTCACCTCCTC 59.360 44.000 0.00 0.00 0.00 3.71
3362 5182 5.544176 TCTTATTTCTTGTGTCACCTCCTCT 59.456 40.000 0.00 0.00 0.00 3.69
3363 5183 4.713792 ATTTCTTGTGTCACCTCCTCTT 57.286 40.909 0.00 0.00 0.00 2.85
3364 5184 3.753294 TTCTTGTGTCACCTCCTCTTC 57.247 47.619 0.00 0.00 0.00 2.87
3365 5185 1.613925 TCTTGTGTCACCTCCTCTTCG 59.386 52.381 0.00 0.00 0.00 3.79
3366 5186 1.613925 CTTGTGTCACCTCCTCTTCGA 59.386 52.381 0.00 0.00 0.00 3.71
3367 5187 0.959553 TGTGTCACCTCCTCTTCGAC 59.040 55.000 0.00 0.00 0.00 4.20
3368 5188 1.249407 GTGTCACCTCCTCTTCGACT 58.751 55.000 0.00 0.00 0.00 4.18
3369 5189 1.614413 GTGTCACCTCCTCTTCGACTT 59.386 52.381 0.00 0.00 0.00 3.01
3370 5190 1.887198 TGTCACCTCCTCTTCGACTTC 59.113 52.381 0.00 0.00 0.00 3.01
3371 5191 1.887198 GTCACCTCCTCTTCGACTTCA 59.113 52.381 0.00 0.00 0.00 3.02
3372 5192 2.094957 GTCACCTCCTCTTCGACTTCAG 60.095 54.545 0.00 0.00 0.00 3.02
3373 5193 1.889829 CACCTCCTCTTCGACTTCAGT 59.110 52.381 0.00 0.00 0.00 3.41
3374 5194 2.297597 CACCTCCTCTTCGACTTCAGTT 59.702 50.000 0.00 0.00 0.00 3.16
3375 5195 2.966516 ACCTCCTCTTCGACTTCAGTTT 59.033 45.455 0.00 0.00 0.00 2.66
3376 5196 3.388350 ACCTCCTCTTCGACTTCAGTTTT 59.612 43.478 0.00 0.00 0.00 2.43
3377 5197 4.141688 ACCTCCTCTTCGACTTCAGTTTTT 60.142 41.667 0.00 0.00 0.00 1.94
3378 5198 4.449405 CCTCCTCTTCGACTTCAGTTTTTC 59.551 45.833 0.00 0.00 0.00 2.29
3379 5199 5.018539 TCCTCTTCGACTTCAGTTTTTCA 57.981 39.130 0.00 0.00 0.00 2.69
3380 5200 4.809426 TCCTCTTCGACTTCAGTTTTTCAC 59.191 41.667 0.00 0.00 0.00 3.18
3381 5201 4.811557 CCTCTTCGACTTCAGTTTTTCACT 59.188 41.667 0.00 0.00 35.35 3.41
3477 5298 5.560966 CCATTCCTGGTTGTATGTTGTAC 57.439 43.478 0.00 0.00 37.79 2.90
3532 5353 3.153919 GTTGTATCTTTGCCCCTTGTGA 58.846 45.455 0.00 0.00 0.00 3.58
3538 5359 2.019984 CTTTGCCCCTTGTGATAGCTC 58.980 52.381 0.00 0.00 0.00 4.09
3561 5382 7.409343 GCTCGTTTTGCATGTTAATCTGTTTAC 60.409 37.037 0.00 0.00 0.00 2.01
3593 5414 2.438021 TCCTCTTATTGCCGCCAATACT 59.562 45.455 0.00 0.00 42.11 2.12
3600 5421 7.221450 TCTTATTGCCGCCAATACTAACTTAT 58.779 34.615 0.00 0.00 42.11 1.73
3668 5489 2.681848 GCTCATCCTTCAACCTCACATG 59.318 50.000 0.00 0.00 0.00 3.21
3802 5623 2.827322 CCCTTGGATGCAGAATTGAACA 59.173 45.455 0.00 0.00 0.00 3.18
3977 5816 9.567848 AAGATACAATTTTAAAGCACCAATACG 57.432 29.630 0.00 0.00 0.00 3.06
3982 5821 7.923878 ACAATTTTAAAGCACCAATACGAACTT 59.076 29.630 0.00 0.00 0.00 2.66
3984 5823 6.870971 TTTAAAGCACCAATACGAACTTCT 57.129 33.333 0.00 0.00 0.00 2.85
3986 5825 7.966246 TTAAAGCACCAATACGAACTTCTTA 57.034 32.000 0.00 0.00 0.00 2.10
3987 5826 6.870971 AAAGCACCAATACGAACTTCTTAA 57.129 33.333 0.00 0.00 0.00 1.85
3988 5827 6.870971 AAGCACCAATACGAACTTCTTAAA 57.129 33.333 0.00 0.00 0.00 1.52
3992 5831 4.698780 ACCAATACGAACTTCTTAAAGGCC 59.301 41.667 0.00 0.00 36.78 5.19
3994 5833 5.357032 CCAATACGAACTTCTTAAAGGCCAT 59.643 40.000 5.01 0.00 36.78 4.40
3995 5834 6.458342 CCAATACGAACTTCTTAAAGGCCATC 60.458 42.308 5.01 0.00 36.78 3.51
3996 5835 4.287766 ACGAACTTCTTAAAGGCCATCT 57.712 40.909 5.01 0.00 36.78 2.90
3997 5836 5.416271 ACGAACTTCTTAAAGGCCATCTA 57.584 39.130 5.01 0.00 36.78 1.98
3998 5837 5.990668 ACGAACTTCTTAAAGGCCATCTAT 58.009 37.500 5.01 0.00 36.78 1.98
4001 5840 7.657761 ACGAACTTCTTAAAGGCCATCTATATG 59.342 37.037 5.01 0.00 36.78 1.78
4029 5868 7.703058 AAATATTCGAAAAGAGTGGTCCAAT 57.297 32.000 0.00 0.00 0.00 3.16
4040 5879 3.452627 GAGTGGTCCAATGTCCAGATACT 59.547 47.826 0.00 0.00 34.16 2.12
4263 6104 5.659440 ATTTTACCTAGTTGCATGTTGGG 57.341 39.130 0.00 0.00 0.00 4.12
4283 6124 3.128938 GGGATGGTATCGGTATCTTCTCG 59.871 52.174 2.25 0.00 0.00 4.04
4543 6581 3.410631 AACATGTGATAACCGGTGACA 57.589 42.857 8.52 9.77 0.00 3.58
4614 6652 2.243810 GGGGTGGTGTAAAATCTGCAA 58.756 47.619 0.00 0.00 0.00 4.08
4615 6653 2.831526 GGGGTGGTGTAAAATCTGCAAT 59.168 45.455 0.00 0.00 0.00 3.56
4906 6944 0.776176 ATTGGGGAGGCCATGAGATC 59.224 55.000 5.01 0.00 0.00 2.75
4935 6973 6.633500 TTTTCGATGGTCATGTTCTCTTTT 57.367 33.333 0.00 0.00 0.00 2.27
4974 7013 1.399791 GTTGTAGCTCTGAGCATTGGC 59.600 52.381 29.49 14.98 45.56 4.52
4992 7031 2.437897 CTGGCCAGGTTTCCAGCT 59.562 61.111 26.14 0.00 42.79 4.24
5041 7083 2.498885 GGCCTTGGATTCTGCTGAATTT 59.501 45.455 18.52 0.00 42.43 1.82
5054 7096 0.310543 TGAATTTGCAGTGCCGTCAC 59.689 50.000 13.72 2.29 43.44 3.67
5062 7104 3.401095 GTGCCGTCACGTCAACAA 58.599 55.556 0.00 0.00 32.98 2.83
5064 7106 0.097325 GTGCCGTCACGTCAACAAAA 59.903 50.000 0.00 0.00 32.98 2.44
5065 7107 0.097325 TGCCGTCACGTCAACAAAAC 59.903 50.000 0.00 0.00 0.00 2.43
5066 7108 0.375803 GCCGTCACGTCAACAAAACT 59.624 50.000 0.00 0.00 0.00 2.66
5067 7109 1.854434 GCCGTCACGTCAACAAAACTG 60.854 52.381 0.00 0.00 0.00 3.16
5068 7110 1.661617 CCGTCACGTCAACAAAACTGA 59.338 47.619 0.00 0.00 0.00 3.41
5069 7111 2.094575 CCGTCACGTCAACAAAACTGAA 59.905 45.455 0.00 0.00 0.00 3.02
5070 7112 3.242608 CCGTCACGTCAACAAAACTGAAT 60.243 43.478 0.00 0.00 0.00 2.57
5071 7113 3.718864 CGTCACGTCAACAAAACTGAATG 59.281 43.478 0.00 0.00 0.00 2.67
5092 7134 4.318332 TGAGAGTTGTTGTTCAGGCTATG 58.682 43.478 0.00 0.00 0.00 2.23
5095 7139 1.202348 GTTGTTGTTCAGGCTATGGGC 59.798 52.381 0.00 0.00 40.90 5.36
5096 7140 0.403655 TGTTGTTCAGGCTATGGGCA 59.596 50.000 5.19 0.00 44.01 5.36
5127 7171 2.706890 GGGATTCGGCTTGTTTCACTA 58.293 47.619 0.00 0.00 0.00 2.74
5146 7190 6.184789 TCACTAAGAAAAGGTCTGGTTTTGT 58.815 36.000 0.00 0.00 36.40 2.83
5155 7199 8.911918 AAAAGGTCTGGTTTTGTTTAGTTTTT 57.088 26.923 0.00 0.00 0.00 1.94
5200 7244 8.624776 CCTAGTTCAATCTTTTGTCAAAACTCT 58.375 33.333 6.65 1.91 31.99 3.24
5217 7261 5.931441 AACTCTGCAGTTTCATCACTAAC 57.069 39.130 14.67 0.00 40.16 2.34
5312 9117 6.174760 GCCATACATTATAAATCCCGTGGTA 58.825 40.000 0.00 0.00 0.00 3.25
5319 9124 8.877195 ACATTATAAATCCCGTGGTATTAGAGT 58.123 33.333 0.00 0.00 0.00 3.24
5320 9125 9.367444 CATTATAAATCCCGTGGTATTAGAGTC 57.633 37.037 0.00 0.00 0.00 3.36
5327 9134 3.319405 CCGTGGTATTAGAGTCTCTGCAT 59.681 47.826 12.92 7.06 0.00 3.96
5373 9180 0.462759 GATTAGAACGCCCAGCTGCT 60.463 55.000 8.66 0.00 0.00 4.24
5380 9187 2.800541 CGCCCAGCTGCTCCTGATA 61.801 63.158 8.66 0.00 34.77 2.15
5383 9190 1.683011 GCCCAGCTGCTCCTGATAAAA 60.683 52.381 8.66 0.00 34.77 1.52
5385 9192 3.294214 CCCAGCTGCTCCTGATAAAAAT 58.706 45.455 8.66 0.00 34.77 1.82
5394 9201 5.927689 TGCTCCTGATAAAAATGCAAACTTG 59.072 36.000 0.00 0.00 0.00 3.16
5399 9206 6.587608 CCTGATAAAAATGCAAACTTGACCTC 59.412 38.462 0.00 0.00 0.00 3.85
5406 9213 1.597027 AAACTTGACCTCCCGTGCG 60.597 57.895 0.00 0.00 0.00 5.34
5430 9237 3.632189 TCAGATGATGCAGTACGATTCG 58.368 45.455 4.14 4.14 0.00 3.34
5439 9246 0.739561 AGTACGATTCGTCTCCCTGC 59.260 55.000 16.10 0.00 41.54 4.85
5442 9249 1.471119 ACGATTCGTCTCCCTGCTTA 58.529 50.000 5.75 0.00 33.69 3.09
5445 9252 2.541556 GATTCGTCTCCCTGCTTACAC 58.458 52.381 0.00 0.00 0.00 2.90
5451 9258 2.563179 GTCTCCCTGCTTACACTTGAGA 59.437 50.000 0.00 0.00 0.00 3.27
5452 9259 2.828520 TCTCCCTGCTTACACTTGAGAG 59.171 50.000 0.00 0.00 0.00 3.20
5453 9260 1.902508 TCCCTGCTTACACTTGAGAGG 59.097 52.381 0.00 0.00 0.00 3.69
5454 9261 1.902508 CCCTGCTTACACTTGAGAGGA 59.097 52.381 0.00 0.00 0.00 3.71
5469 9276 1.657751 GAGGATGGCGGAAAACCAGC 61.658 60.000 0.00 0.00 42.95 4.85
5506 9313 7.599245 ACCTCGTCGAGAATATTTAAATCCATC 59.401 37.037 23.74 2.22 0.00 3.51
5538 9345 0.320374 AAGAAACCGACGAGATGGCA 59.680 50.000 0.00 0.00 0.00 4.92
5628 9443 1.452145 GCCGGCAAGTTTGAAGTCCA 61.452 55.000 24.80 0.00 0.00 4.02
5641 9456 2.737376 GTCCACGAGACGGCAACC 60.737 66.667 0.00 0.00 35.30 3.77
5645 9460 2.915659 ACGAGACGGCAACCCTCA 60.916 61.111 0.00 0.00 33.72 3.86
5690 9505 4.524328 TCTCACCACGATATGCATAGTCAT 59.476 41.667 12.79 0.00 0.00 3.06
5691 9506 5.011023 TCTCACCACGATATGCATAGTCATT 59.989 40.000 12.79 0.00 0.00 2.57
5697 9512 4.237724 CGATATGCATAGTCATTGACGGT 58.762 43.478 12.79 1.53 37.67 4.83
5733 9551 6.765036 AGTTGTCATAGTCAATGATGATGGTC 59.235 38.462 7.27 3.57 46.21 4.02
5738 9556 6.703165 TCATAGTCAATGATGATGGTCGAAAG 59.297 38.462 7.27 0.00 39.77 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 0.972134 TTGAGACAGACCAGCCTCTG 59.028 55.000 2.79 2.79 43.06 3.35
19 20 1.722034 TTTGAGACAGACCAGCCTCT 58.278 50.000 0.00 0.00 0.00 3.69
20 21 2.550830 TTTTGAGACAGACCAGCCTC 57.449 50.000 0.00 0.00 0.00 4.70
44 45 2.113986 GTGTGCCACCAGCCTCTT 59.886 61.111 0.00 0.00 42.71 2.85
68 69 1.416813 CTTGCTGCGTCTCGTCCATC 61.417 60.000 0.00 0.00 0.00 3.51
375 422 2.574399 GACCTCGTGGAGTGGAGC 59.426 66.667 11.17 0.00 36.98 4.70
429 481 3.352748 TAGCGGAGTGGGGAGGGA 61.353 66.667 0.00 0.00 0.00 4.20
472 526 3.371591 GGTGTGTTGACTTGAACGTGTTA 59.628 43.478 0.00 0.00 0.00 2.41
479 533 2.489971 GATCCGGTGTGTTGACTTGAA 58.510 47.619 0.00 0.00 0.00 2.69
739 797 3.520290 TGATGAGTCACCGGTTCATAC 57.480 47.619 18.06 12.73 32.03 2.39
827 889 3.136750 CCTCGGGAGATCAGGCTG 58.863 66.667 8.58 8.58 38.80 4.85
828 890 2.841988 GCCTCGGGAGATCAGGCT 60.842 66.667 12.60 0.00 42.55 4.58
1319 1711 4.462483 GGCAAGAGAAGAGAAGAGAAGAGA 59.538 45.833 0.00 0.00 0.00 3.10
1321 1713 3.513515 GGGCAAGAGAAGAGAAGAGAAGA 59.486 47.826 0.00 0.00 0.00 2.87
1350 1744 2.454336 TCGAGAGGATAGCTTTGGGA 57.546 50.000 0.00 0.00 0.00 4.37
1391 1785 1.399714 AATCAGATCAGACCGCGGTA 58.600 50.000 34.36 17.68 0.00 4.02
1422 2025 2.118403 AGGTGACCCAGAAAGGAAGA 57.882 50.000 0.00 0.00 41.22 2.87
1476 2080 8.139989 GGATAAATCAGGTTCATGATTCCAAAG 58.860 37.037 16.38 8.38 46.64 2.77
1523 2127 1.544724 TATGCCTCACCCACAAAAGC 58.455 50.000 0.00 0.00 0.00 3.51
1630 2241 5.786264 ACGGAGTAGTAATATTCCACTGG 57.214 43.478 11.66 0.00 41.94 4.00
1663 2274 1.826385 AGAATTTCAGCGTTCCCCAG 58.174 50.000 0.00 0.00 0.00 4.45
1700 2311 1.511850 TCCTCACTTTGCACACATCG 58.488 50.000 0.00 0.00 0.00 3.84
1701 2312 3.988379 TTTCCTCACTTTGCACACATC 57.012 42.857 0.00 0.00 0.00 3.06
1718 2329 2.224018 TGGAACAGGCACATGCTTTTTC 60.224 45.455 3.48 5.15 41.70 2.29
1783 2397 3.204606 TGGTAGCAGGACCTCTACAGTAT 59.795 47.826 22.20 0.00 40.46 2.12
1788 2405 3.798202 CATTTGGTAGCAGGACCTCTAC 58.202 50.000 16.70 16.70 40.46 2.59
1802 2419 2.799126 TCATAGAACGGGCATTTGGT 57.201 45.000 0.00 0.00 0.00 3.67
1804 2421 4.353737 CACATTCATAGAACGGGCATTTG 58.646 43.478 0.00 0.00 0.00 2.32
1915 2625 1.077993 AGTAGGGACTGGACTGAAGCT 59.922 52.381 0.00 0.00 41.52 3.74
2065 3179 8.296713 TGGTTCTTTTTCTCATGCAAATAGTAC 58.703 33.333 0.00 0.00 0.00 2.73
2110 3304 6.561614 ACAAGAATGAAATGATGCTGATGTC 58.438 36.000 0.00 0.00 0.00 3.06
2125 3320 7.265647 TCCGAAACACAAATTACAAGAATGA 57.734 32.000 0.00 0.00 0.00 2.57
2179 3410 4.686091 TGCATCTAAACAGACGAAGAACAG 59.314 41.667 0.00 0.00 0.00 3.16
2195 3428 3.755905 TCCGCAAAGAAAACATGCATCTA 59.244 39.130 0.00 0.00 40.04 1.98
2239 3472 8.697067 CAAAGAAAACATGCATCTTAAACAGAG 58.303 33.333 0.00 0.00 33.87 3.35
2264 3497 0.038618 TAGAGCTGCTTCGTTTCGCA 60.039 50.000 2.53 0.00 34.54 5.10
2305 3538 2.159170 AGAAGGAAGACGATGCTGCTAC 60.159 50.000 0.00 0.00 0.00 3.58
2314 3547 4.456222 CACTGTCTAGAAGAAGGAAGACGA 59.544 45.833 0.00 0.00 40.99 4.20
2363 3596 0.819582 CCCCAGCAGCAAACATAAGG 59.180 55.000 0.00 0.00 0.00 2.69
2496 3730 8.798859 ATCATAACATTCAAACAGCTAAGAGT 57.201 30.769 0.00 0.00 0.00 3.24
2499 3733 8.127327 CCTGATCATAACATTCAAACAGCTAAG 58.873 37.037 0.00 0.00 0.00 2.18
2693 3928 6.650807 CGCAACCTCTATGTATAATGGACATT 59.349 38.462 2.80 2.80 38.47 2.71
2700 3935 9.772973 TTAAATGACGCAACCTCTATGTATAAT 57.227 29.630 0.00 0.00 0.00 1.28
2701 3936 9.772973 ATTAAATGACGCAACCTCTATGTATAA 57.227 29.630 0.00 0.00 0.00 0.98
2702 3937 9.772973 AATTAAATGACGCAACCTCTATGTATA 57.227 29.630 0.00 0.00 0.00 1.47
2705 3940 7.250569 CAAATTAAATGACGCAACCTCTATGT 58.749 34.615 0.00 0.00 0.00 2.29
2706 3941 6.692681 CCAAATTAAATGACGCAACCTCTATG 59.307 38.462 0.00 0.00 0.00 2.23
2708 3943 5.124776 CCCAAATTAAATGACGCAACCTCTA 59.875 40.000 0.00 0.00 0.00 2.43
2709 3944 4.082245 CCCAAATTAAATGACGCAACCTCT 60.082 41.667 0.00 0.00 0.00 3.69
2712 3947 3.924073 GTCCCAAATTAAATGACGCAACC 59.076 43.478 0.00 0.00 0.00 3.77
2714 3949 4.855715 TGTCCCAAATTAAATGACGCAA 57.144 36.364 0.00 0.00 0.00 4.85
2715 3950 5.167121 CAATGTCCCAAATTAAATGACGCA 58.833 37.500 0.00 0.00 0.00 5.24
2716 3951 5.167845 ACAATGTCCCAAATTAAATGACGC 58.832 37.500 0.00 0.00 0.00 5.19
2721 3956 8.860088 GCCTCTATACAATGTCCCAAATTAAAT 58.140 33.333 0.00 0.00 0.00 1.40
2722 3957 8.058847 AGCCTCTATACAATGTCCCAAATTAAA 58.941 33.333 0.00 0.00 0.00 1.52
2724 3959 6.998074 CAGCCTCTATACAATGTCCCAAATTA 59.002 38.462 0.00 0.00 0.00 1.40
2725 3960 5.829924 CAGCCTCTATACAATGTCCCAAATT 59.170 40.000 0.00 0.00 0.00 1.82
2727 3962 4.780815 CAGCCTCTATACAATGTCCCAAA 58.219 43.478 0.00 0.00 0.00 3.28
2729 3964 2.104792 GCAGCCTCTATACAATGTCCCA 59.895 50.000 0.00 0.00 0.00 4.37
2730 3965 2.104792 TGCAGCCTCTATACAATGTCCC 59.895 50.000 0.00 0.00 0.00 4.46
2751 3991 4.286032 TCCCTCCGATCCGAATTAATTGAT 59.714 41.667 5.17 3.10 0.00 2.57
2831 4071 5.419155 CACTTCACTATCAGTAGAGACCCAA 59.581 44.000 0.00 0.00 28.99 4.12
2883 4123 4.405680 ACTGATATGGCAGCTAGTGTGTTA 59.594 41.667 0.00 0.00 39.51 2.41
2893 4133 5.954296 ATTTATCACACTGATATGGCAGC 57.046 39.130 0.00 0.00 38.94 5.25
2982 4223 1.133513 TCCTGCAAGAAAGAGGGCAAA 60.134 47.619 0.00 0.00 35.59 3.68
2985 4226 0.037447 AGTCCTGCAAGAAAGAGGGC 59.963 55.000 0.00 0.00 34.07 5.19
3044 4301 2.474410 AGCTGCAGTACAACCTAACC 57.526 50.000 16.64 0.00 0.00 2.85
3125 4382 5.290885 TCTGAACCGAATCATGTAAATGACG 59.709 40.000 0.00 0.00 32.79 4.35
3168 4425 4.686191 ATGCAAAATTGTCCTTGTCCAA 57.314 36.364 0.00 0.00 0.00 3.53
3244 4935 8.052748 ACTCCATAATCAACTAATGCCTAACAA 58.947 33.333 0.00 0.00 0.00 2.83
3245 4936 7.573710 ACTCCATAATCAACTAATGCCTAACA 58.426 34.615 0.00 0.00 0.00 2.41
3246 4937 7.934120 AGACTCCATAATCAACTAATGCCTAAC 59.066 37.037 0.00 0.00 0.00 2.34
3299 5119 9.915629 AACTAATGTCTAGTAGTGAGAAAACTG 57.084 33.333 0.00 0.00 37.72 3.16
3329 5149 9.817809 GTGACACAAGAAATAAGACTCCATATA 57.182 33.333 0.00 0.00 0.00 0.86
3330 5150 7.770897 GGTGACACAAGAAATAAGACTCCATAT 59.229 37.037 8.08 0.00 0.00 1.78
3331 5151 7.038302 AGGTGACACAAGAAATAAGACTCCATA 60.038 37.037 8.08 0.00 0.00 2.74
3332 5152 5.940470 GGTGACACAAGAAATAAGACTCCAT 59.060 40.000 8.08 0.00 0.00 3.41
3333 5153 5.071788 AGGTGACACAAGAAATAAGACTCCA 59.928 40.000 8.08 0.00 0.00 3.86
3334 5154 5.552178 AGGTGACACAAGAAATAAGACTCC 58.448 41.667 8.08 0.00 0.00 3.85
3335 5155 5.639931 GGAGGTGACACAAGAAATAAGACTC 59.360 44.000 8.08 0.18 0.00 3.36
3336 5156 5.308237 AGGAGGTGACACAAGAAATAAGACT 59.692 40.000 8.08 0.00 0.00 3.24
3337 5157 5.552178 AGGAGGTGACACAAGAAATAAGAC 58.448 41.667 8.08 0.00 0.00 3.01
3338 5158 5.544176 AGAGGAGGTGACACAAGAAATAAGA 59.456 40.000 8.08 0.00 0.00 2.10
3339 5159 5.799213 AGAGGAGGTGACACAAGAAATAAG 58.201 41.667 8.08 0.00 0.00 1.73
3340 5160 5.825593 AGAGGAGGTGACACAAGAAATAA 57.174 39.130 8.08 0.00 0.00 1.40
3341 5161 5.566826 CGAAGAGGAGGTGACACAAGAAATA 60.567 44.000 8.08 0.00 0.00 1.40
3342 5162 4.646572 GAAGAGGAGGTGACACAAGAAAT 58.353 43.478 8.08 0.00 0.00 2.17
3343 5163 3.492656 CGAAGAGGAGGTGACACAAGAAA 60.493 47.826 8.08 0.00 0.00 2.52
3344 5164 2.035961 CGAAGAGGAGGTGACACAAGAA 59.964 50.000 8.08 0.00 0.00 2.52
3345 5165 1.613925 CGAAGAGGAGGTGACACAAGA 59.386 52.381 8.08 0.00 0.00 3.02
3346 5166 1.613925 TCGAAGAGGAGGTGACACAAG 59.386 52.381 8.08 0.00 0.00 3.16
3347 5167 1.340248 GTCGAAGAGGAGGTGACACAA 59.660 52.381 8.08 0.00 36.95 3.33
3348 5168 0.959553 GTCGAAGAGGAGGTGACACA 59.040 55.000 8.08 0.00 36.95 3.72
3349 5169 1.249407 AGTCGAAGAGGAGGTGACAC 58.751 55.000 0.00 0.00 36.95 3.67
3350 5170 1.887198 GAAGTCGAAGAGGAGGTGACA 59.113 52.381 0.00 0.00 36.95 3.58
3351 5171 1.887198 TGAAGTCGAAGAGGAGGTGAC 59.113 52.381 0.00 0.00 36.95 3.67
3352 5172 2.163509 CTGAAGTCGAAGAGGAGGTGA 58.836 52.381 0.00 0.00 36.95 4.02
3353 5173 1.889829 ACTGAAGTCGAAGAGGAGGTG 59.110 52.381 0.00 0.00 36.95 4.00
3354 5174 2.296073 ACTGAAGTCGAAGAGGAGGT 57.704 50.000 0.00 0.00 36.95 3.85
3355 5175 3.669251 AAACTGAAGTCGAAGAGGAGG 57.331 47.619 0.00 0.00 36.95 4.30
3356 5176 5.050490 TGAAAAACTGAAGTCGAAGAGGAG 58.950 41.667 0.00 0.00 36.95 3.69
3357 5177 4.809426 GTGAAAAACTGAAGTCGAAGAGGA 59.191 41.667 0.00 0.00 36.95 3.71
3358 5178 4.811557 AGTGAAAAACTGAAGTCGAAGAGG 59.188 41.667 0.00 0.00 37.88 3.69
3359 5179 5.975410 AGTGAAAAACTGAAGTCGAAGAG 57.025 39.130 0.00 0.00 37.88 2.85
3360 5180 6.570692 AGTAGTGAAAAACTGAAGTCGAAGA 58.429 36.000 0.00 0.00 40.26 2.87
3361 5181 6.830114 AGTAGTGAAAAACTGAAGTCGAAG 57.170 37.500 0.00 0.00 40.26 3.79
3362 5182 7.646922 GTCTAGTAGTGAAAAACTGAAGTCGAA 59.353 37.037 0.00 0.00 40.26 3.71
3363 5183 7.137426 GTCTAGTAGTGAAAAACTGAAGTCGA 58.863 38.462 0.00 0.00 40.26 4.20
3364 5184 6.916387 TGTCTAGTAGTGAAAAACTGAAGTCG 59.084 38.462 0.00 0.00 40.26 4.18
3365 5185 8.819643 ATGTCTAGTAGTGAAAAACTGAAGTC 57.180 34.615 0.00 0.00 40.26 3.01
3411 5231 3.053455 GTCGAAGAGGTGACACAAGAAG 58.947 50.000 8.08 0.00 36.95 2.85
3477 5298 3.859961 GTGATACTGACATCTTGTGGACG 59.140 47.826 0.00 0.00 0.00 4.79
3532 5353 6.094048 ACAGATTAACATGCAAAACGAGCTAT 59.906 34.615 0.00 0.00 0.00 2.97
3538 5359 6.861055 AGGTAAACAGATTAACATGCAAAACG 59.139 34.615 0.00 0.00 33.34 3.60
3561 5382 4.156739 GGCAATAAGAGGAAGTTCACAAGG 59.843 45.833 5.01 0.00 0.00 3.61
3593 5414 8.890410 ACCTGGACAGTAAGTCTAATAAGTTA 57.110 34.615 0.00 0.00 46.72 2.24
3600 5421 5.244626 GGTACAACCTGGACAGTAAGTCTAA 59.755 44.000 0.00 0.00 40.25 2.10
3770 5591 2.699954 CATCCAAGGGCCGATGTATAC 58.300 52.381 10.68 0.00 32.82 1.47
3771 5592 1.003118 GCATCCAAGGGCCGATGTATA 59.997 52.381 17.60 2.90 38.50 1.47
3778 5599 1.039233 AATTCTGCATCCAAGGGCCG 61.039 55.000 0.00 0.00 0.00 6.13
3820 5641 9.846248 ACAATCTGCTCAAAAACATATCTTAAC 57.154 29.630 0.00 0.00 0.00 2.01
3956 5777 7.430441 AGTTCGTATTGGTGCTTTAAAATTGT 58.570 30.769 0.00 0.00 0.00 2.71
3958 5779 8.357402 AGAAGTTCGTATTGGTGCTTTAAAATT 58.643 29.630 0.00 0.00 0.00 1.82
3960 5781 7.266922 AGAAGTTCGTATTGGTGCTTTAAAA 57.733 32.000 0.00 0.00 0.00 1.52
3969 5808 4.698780 GGCCTTTAAGAAGTTCGTATTGGT 59.301 41.667 0.00 0.00 0.00 3.67
3977 5816 9.732130 ATCATATAGATGGCCTTTAAGAAGTTC 57.268 33.333 3.32 0.00 35.06 3.01
4001 5840 8.889717 TGGACCACTCTTTTCGAATATTTAATC 58.110 33.333 0.00 0.00 0.00 1.75
4004 5843 8.673711 CATTGGACCACTCTTTTCGAATATTTA 58.326 33.333 0.00 0.00 0.00 1.40
4013 5852 3.486383 TGGACATTGGACCACTCTTTTC 58.514 45.455 0.00 0.00 33.85 2.29
4029 5868 5.042463 TGTTCACCAAAAGTATCTGGACA 57.958 39.130 0.00 0.00 36.49 4.02
4040 5879 4.021544 ACTGTTCTGCTTTGTTCACCAAAA 60.022 37.500 0.00 0.00 42.31 2.44
4263 6104 3.757493 ACCGAGAAGATACCGATACCATC 59.243 47.826 0.00 0.00 0.00 3.51
4345 6383 6.014840 ACGAGTATCCAAGACCTAAAAAGACA 60.015 38.462 0.00 0.00 0.00 3.41
4519 6557 5.941058 TGTCACCGGTTATCACATGTTAAAT 59.059 36.000 2.97 0.00 0.00 1.40
4543 6581 1.951510 CAAGACTGCACCGCAACAT 59.048 52.632 0.00 0.00 38.41 2.71
4906 6944 3.282021 ACATGACCATCGAAAATGGAGG 58.718 45.455 10.49 0.00 41.64 4.30
4935 6973 4.644234 ACAACACCAGATCAACACAAATGA 59.356 37.500 0.00 0.00 0.00 2.57
4984 7023 1.888512 GATGTTGGCTCAAGCTGGAAA 59.111 47.619 1.46 0.00 41.70 3.13
4992 7031 2.957402 AACTGGAGATGTTGGCTCAA 57.043 45.000 0.00 0.00 34.07 3.02
5041 7083 4.214327 TGACGTGACGGCACTGCA 62.214 61.111 21.24 14.37 41.22 4.41
5054 7096 5.409643 ACTCTCATTCAGTTTTGTTGACG 57.590 39.130 0.00 0.00 0.00 4.35
5055 7097 6.555315 ACAACTCTCATTCAGTTTTGTTGAC 58.445 36.000 0.00 0.00 37.53 3.18
5056 7098 6.757897 ACAACTCTCATTCAGTTTTGTTGA 57.242 33.333 0.00 0.00 37.53 3.18
5057 7099 7.213252 CAACAACTCTCATTCAGTTTTGTTG 57.787 36.000 9.22 9.22 42.70 3.33
5061 7103 7.156876 TGAACAACAACTCTCATTCAGTTTT 57.843 32.000 0.00 0.00 31.40 2.43
5062 7104 6.183360 CCTGAACAACAACTCTCATTCAGTTT 60.183 38.462 10.06 0.00 40.82 2.66
5064 7106 4.818546 CCTGAACAACAACTCTCATTCAGT 59.181 41.667 10.06 0.00 40.82 3.41
5065 7107 4.320057 GCCTGAACAACAACTCTCATTCAG 60.320 45.833 5.08 5.08 41.65 3.02
5066 7108 3.565482 GCCTGAACAACAACTCTCATTCA 59.435 43.478 0.00 0.00 0.00 2.57
5067 7109 3.817647 AGCCTGAACAACAACTCTCATTC 59.182 43.478 0.00 0.00 0.00 2.67
5068 7110 3.825328 AGCCTGAACAACAACTCTCATT 58.175 40.909 0.00 0.00 0.00 2.57
5069 7111 3.498774 AGCCTGAACAACAACTCTCAT 57.501 42.857 0.00 0.00 0.00 2.90
5070 7112 4.318332 CATAGCCTGAACAACAACTCTCA 58.682 43.478 0.00 0.00 0.00 3.27
5071 7113 3.686726 CCATAGCCTGAACAACAACTCTC 59.313 47.826 0.00 0.00 0.00 3.20
5095 7139 1.595382 GAATCCCGCCGATGACCTG 60.595 63.158 0.00 0.00 0.00 4.00
5096 7140 2.822399 GAATCCCGCCGATGACCT 59.178 61.111 0.00 0.00 0.00 3.85
5127 7171 7.476540 ACTAAACAAAACCAGACCTTTTCTT 57.523 32.000 0.00 0.00 28.96 2.52
5159 7203 9.860898 GATTGAACTAGGAAAAATTGCACTAAT 57.139 29.630 0.00 0.00 0.00 1.73
5161 7205 8.635765 AGATTGAACTAGGAAAAATTGCACTA 57.364 30.769 0.00 0.00 0.00 2.74
5200 7244 3.743521 AGCTGTTAGTGATGAAACTGCA 58.256 40.909 16.00 0.00 40.85 4.41
5217 7261 7.295201 CAAAAATGTTGGAATCATTGAAGCTG 58.705 34.615 0.00 0.00 35.95 4.24
5373 9180 6.267471 AGGTCAAGTTTGCATTTTTATCAGGA 59.733 34.615 0.00 0.00 0.00 3.86
5380 9187 3.492482 CGGGAGGTCAAGTTTGCATTTTT 60.492 43.478 0.00 0.00 0.00 1.94
5383 9190 1.247567 CGGGAGGTCAAGTTTGCATT 58.752 50.000 0.00 0.00 0.00 3.56
5385 9192 0.817634 CACGGGAGGTCAAGTTTGCA 60.818 55.000 0.00 0.00 0.00 4.08
5394 9201 4.451150 TGATGCGCACGGGAGGTC 62.451 66.667 14.90 4.82 0.00 3.85
5399 9206 1.596203 ATCATCTGATGCGCACGGG 60.596 57.895 14.90 5.50 32.68 5.28
5424 9231 1.134367 TGTAAGCAGGGAGACGAATCG 59.866 52.381 0.00 0.00 0.00 3.34
5430 9237 2.563179 TCTCAAGTGTAAGCAGGGAGAC 59.437 50.000 0.00 0.00 0.00 3.36
5439 9246 2.544685 CGCCATCCTCTCAAGTGTAAG 58.455 52.381 0.00 0.00 0.00 2.34
5442 9249 0.904865 TCCGCCATCCTCTCAAGTGT 60.905 55.000 0.00 0.00 0.00 3.55
5445 9252 1.740025 GTTTTCCGCCATCCTCTCAAG 59.260 52.381 0.00 0.00 0.00 3.02
5451 9258 1.678970 GCTGGTTTTCCGCCATCCT 60.679 57.895 0.00 0.00 44.36 3.24
5452 9259 2.885113 GCTGGTTTTCCGCCATCC 59.115 61.111 0.00 0.00 44.36 3.51
5469 9276 2.034066 ACGAGGTGTTGGCATGGG 59.966 61.111 0.00 0.00 0.00 4.00
5628 9443 2.227089 GATGAGGGTTGCCGTCTCGT 62.227 60.000 8.94 0.00 38.97 4.18
5666 9481 4.230657 GACTATGCATATCGTGGTGAGAC 58.769 47.826 6.92 0.00 0.00 3.36
5671 9486 4.991056 GTCAATGACTATGCATATCGTGGT 59.009 41.667 6.92 0.70 0.00 4.16
5690 9505 4.039973 ACAACTTAAGATCCTCACCGTCAA 59.960 41.667 10.09 0.00 0.00 3.18
5691 9506 3.576982 ACAACTTAAGATCCTCACCGTCA 59.423 43.478 10.09 0.00 0.00 4.35
5697 9512 7.718334 TGACTATGACAACTTAAGATCCTCA 57.282 36.000 10.09 4.62 0.00 3.86


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

AutoCloner maintained by Alex Coulton.