Multiple sequence alignment - TraesCS5A01G026100

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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 TraesCS5A01G026100 chr5A 100.000 3371 0 0 1 3371 21415941 21412571 0.000000e+00 6226.0
1 TraesCS5A01G026100 chr5A 87.296 1535 152 23 866 2371 21418641 21420161 0.000000e+00 1714.0
2 TraesCS5A01G026100 chr5A 96.386 83 3 0 783 865 18658660 18658578 1.630000e-28 137.0
3 TraesCS5A01G026100 chr5A 100.000 37 0 0 3310 3346 21412689 21412653 6.040000e-08 69.4
4 TraesCS5A01G026100 chr5D 86.879 1570 149 31 866 2390 32810128 32811685 0.000000e+00 1705.0
5 TraesCS5A01G026100 chr5D 91.246 971 61 14 1530 2483 32699374 32698411 0.000000e+00 1301.0
6 TraesCS5A01G026100 chr5D 92.185 627 29 9 56 667 32711764 32711143 0.000000e+00 869.0
7 TraesCS5A01G026100 chr5D 94.675 507 19 4 33 537 32710397 32709897 0.000000e+00 780.0
8 TraesCS5A01G026100 chr5D 90.171 468 29 5 875 1332 32709635 32709175 8.050000e-166 593.0
9 TraesCS5A01G026100 chr5D 86.374 433 50 6 999 1430 239492852 239493276 6.590000e-127 464.0
10 TraesCS5A01G026100 chr5D 84.244 311 20 8 3028 3315 32697126 32696822 3.310000e-70 276.0
11 TraesCS5A01G026100 chr5D 92.308 156 10 2 3160 3315 6162403 6162250 1.570000e-53 220.0
12 TraesCS5A01G026100 chr5D 92.308 156 10 2 3160 3315 503306379 503306532 1.570000e-53 220.0
13 TraesCS5A01G026100 chr5D 92.308 156 10 2 3160 3315 512405420 512405573 1.570000e-53 220.0
14 TraesCS5A01G026100 chr5D 94.186 86 5 0 2538 2623 32698306 32698221 7.590000e-27 132.0
15 TraesCS5A01G026100 chr5D 98.387 62 1 0 1 62 32712221 32712160 3.560000e-20 110.0
16 TraesCS5A01G026100 chr5D 97.826 46 1 0 1 46 32710460 32710415 2.790000e-11 80.5
17 TraesCS5A01G026100 chr5D 95.000 40 2 0 3310 3349 6162312 6162273 2.810000e-06 63.9
18 TraesCS5A01G026100 chr5D 95.000 40 2 0 3310 3349 6260305 6260266 2.810000e-06 63.9
19 TraesCS5A01G026100 chr5D 94.595 37 1 1 289 325 369381134 369381099 4.700000e-04 56.5
20 TraesCS5A01G026100 chr6B 84.514 1595 159 44 859 2403 683371490 683373046 0.000000e+00 1496.0
21 TraesCS5A01G026100 chr6B 85.910 511 59 7 1906 2403 683317379 683317889 1.780000e-147 532.0
22 TraesCS5A01G026100 chr6B 86.605 433 46 8 999 1430 705881144 705880723 5.090000e-128 468.0
23 TraesCS5A01G026100 chr6B 83.789 475 37 19 859 1300 683316878 683317345 6.730000e-112 414.0
24 TraesCS5A01G026100 chr6B 92.308 156 10 2 3160 3315 18745552 18745399 1.570000e-53 220.0
25 TraesCS5A01G026100 chr6B 100.000 33 0 0 511 543 507654699 507654667 1.010000e-05 62.1
26 TraesCS5A01G026100 chr2A 83.935 1606 159 38 859 2415 38614672 38613117 0.000000e+00 1445.0
27 TraesCS5A01G026100 chr2A 96.970 33 1 0 293 325 450477695 450477663 4.700000e-04 56.5
28 TraesCS5A01G026100 chr2D 84.447 913 106 16 1520 2415 605386712 605385819 0.000000e+00 867.0
29 TraesCS5A01G026100 chr2D 84.792 697 64 23 859 1525 605387631 605386947 0.000000e+00 662.0
30 TraesCS5A01G026100 chr2D 95.775 71 3 0 2810 2880 327614897 327614827 7.640000e-22 115.0
31 TraesCS5A01G026100 chr2D 95.714 70 2 1 2809 2877 376701189 376701258 9.890000e-21 111.0
32 TraesCS5A01G026100 chr2D 92.308 78 5 1 2804 2880 476694091 476694014 3.560000e-20 110.0
33 TraesCS5A01G026100 chr2D 100.000 29 0 0 297 325 15594364 15594392 2.000000e-03 54.7
34 TraesCS5A01G026100 chr3D 78.399 1287 217 44 1078 2337 50425054 50426306 0.000000e+00 780.0
35 TraesCS5A01G026100 chr3D 75.977 1407 253 61 999 2363 80569004 80567641 0.000000e+00 647.0
36 TraesCS5A01G026100 chr3D 74.701 1336 261 57 1085 2371 80417886 80416579 1.070000e-144 523.0
37 TraesCS5A01G026100 chr3D 75.703 498 97 16 1557 2042 80226749 80227234 9.410000e-56 228.0
38 TraesCS5A01G026100 chr3D 92.308 156 10 2 3160 3315 596659329 596659482 1.570000e-53 220.0
39 TraesCS5A01G026100 chr3D 97.561 82 1 1 783 863 528183554 528183635 4.540000e-29 139.0
40 TraesCS5A01G026100 chr3D 78.571 154 24 9 511 658 36593426 36593276 3.580000e-15 93.5
41 TraesCS5A01G026100 chr3D 95.000 40 2 0 3310 3349 222422554 222422515 2.810000e-06 63.9
42 TraesCS5A01G026100 chr3D 97.297 37 1 0 3310 3346 596659420 596659456 2.810000e-06 63.9
43 TraesCS5A01G026100 chr3A 78.116 1316 217 44 1078 2362 63485406 63486681 0.000000e+00 769.0
44 TraesCS5A01G026100 chr3A 96.429 84 3 0 783 866 9970260 9970343 4.540000e-29 139.0
45 TraesCS5A01G026100 chr3A 97.500 80 2 0 783 862 562100760 562100839 1.630000e-28 137.0
46 TraesCS5A01G026100 chr3B 78.036 1293 217 44 1079 2337 79979182 79980441 0.000000e+00 752.0
47 TraesCS5A01G026100 chr3B 74.554 1344 260 58 1078 2371 126299450 126298139 2.320000e-141 512.0
48 TraesCS5A01G026100 chr3B 90.511 137 12 1 3048 3184 744526150 744526015 2.670000e-41 180.0
49 TraesCS5A01G026100 chr3B 96.429 84 2 1 783 866 696703770 696703688 1.630000e-28 137.0
50 TraesCS5A01G026100 chr3B 94.595 74 3 1 3115 3188 786273246 786273174 2.750000e-21 113.0
51 TraesCS5A01G026100 chr3B 76.552 145 29 4 508 647 742633163 742633019 1.300000e-09 75.0
52 TraesCS5A01G026100 chr5B 89.343 563 34 12 1 548 24107322 24106771 0.000000e+00 684.0
53 TraesCS5A01G026100 chr5B 93.503 431 26 2 1556 1986 24104702 24104274 1.020000e-179 640.0
54 TraesCS5A01G026100 chr5B 89.548 354 29 3 1157 1509 24105045 24104699 3.090000e-120 442.0
55 TraesCS5A01G026100 chr5B 89.691 291 17 5 881 1159 24106646 24106357 3.200000e-95 359.0
56 TraesCS5A01G026100 chr5B 88.000 300 32 3 3032 3330 24101893 24101597 5.350000e-93 351.0
57 TraesCS5A01G026100 chr5B 87.451 255 25 4 2191 2438 24104276 24104022 1.530000e-73 287.0
58 TraesCS5A01G026100 chr5B 88.406 138 13 2 2678 2812 24102604 24102467 2.690000e-36 163.0
59 TraesCS5A01G026100 chr5B 96.341 82 3 0 784 865 465867863 465867782 5.870000e-28 135.0
60 TraesCS5A01G026100 chr5B 85.294 68 8 2 483 549 636282418 636282484 6.040000e-08 69.4
61 TraesCS5A01G026100 chr5B 94.595 37 2 0 289 325 438170237 438170201 1.310000e-04 58.4
62 TraesCS5A01G026100 chr7D 88.966 435 38 7 999 1430 500956174 500956601 2.300000e-146 529.0
63 TraesCS5A01G026100 chr7D 95.349 86 4 0 783 868 509201727 509201642 1.630000e-28 137.0
64 TraesCS5A01G026100 chr7D 92.308 78 2 3 2800 2874 447760517 447760441 1.280000e-19 108.0
65 TraesCS5A01G026100 chr7D 92.208 77 4 1 2809 2883 615904342 615904266 1.280000e-19 108.0
66 TraesCS5A01G026100 chr4A 92.308 156 10 2 3160 3315 309453693 309453540 1.570000e-53 220.0
67 TraesCS5A01G026100 chr1A 92.308 156 10 2 3160 3315 241517557 241517710 1.570000e-53 220.0
68 TraesCS5A01G026100 chr1A 97.778 90 0 2 783 872 44363340 44363427 1.620000e-33 154.0
69 TraesCS5A01G026100 chr1A 93.258 89 5 1 783 871 258741870 258741957 2.730000e-26 130.0
70 TraesCS5A01G026100 chr1A 94.595 74 1 3 2805 2877 349999471 349999542 9.890000e-21 111.0
71 TraesCS5A01G026100 chr1A 93.333 75 3 1 2809 2881 454330206 454330132 3.560000e-20 110.0
72 TraesCS5A01G026100 chr1A 97.297 37 1 0 3310 3346 241517648 241517684 2.810000e-06 63.9
73 TraesCS5A01G026100 chr7B 82.166 157 11 4 3048 3188 13162081 13162236 5.910000e-23 119.0
74 TraesCS5A01G026100 chr4D 94.737 76 3 1 2809 2884 427262322 427262396 2.130000e-22 117.0
75 TraesCS5A01G026100 chr7A 81.410 156 14 3 3048 3188 178608954 178609109 2.750000e-21 113.0
76 TraesCS5A01G026100 chr7A 94.444 36 0 2 290 325 30505006 30505039 2.000000e-03 54.7
77 TraesCS5A01G026100 chr1D 94.595 74 3 1 3115 3188 390214730 390214658 2.750000e-21 113.0
78 TraesCS5A01G026100 chr1D 97.297 37 1 0 3310 3346 254449615 254449651 2.810000e-06 63.9
79 TraesCS5A01G026100 chr1B 93.243 74 4 1 2807 2880 491239726 491239654 1.280000e-19 108.0
80 TraesCS5A01G026100 chr1B 95.122 41 2 0 3309 3349 331218752 331218712 7.810000e-07 65.8
81 TraesCS5A01G026100 chr6D 100.000 33 0 0 511 543 316800450 316800482 1.010000e-05 62.1


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 TraesCS5A01G026100 chr5A 21412571 21415941 3370 True 3147.700000 6226 100.000000 1 3371 2 chr5A.!!$R2 3370
1 TraesCS5A01G026100 chr5A 21418641 21420161 1520 False 1714.000000 1714 87.296000 866 2371 1 chr5A.!!$F1 1505
2 TraesCS5A01G026100 chr5D 32810128 32811685 1557 False 1705.000000 1705 86.879000 866 2390 1 chr5D.!!$F1 1524
3 TraesCS5A01G026100 chr5D 32696822 32699374 2552 True 569.666667 1301 89.892000 1530 3315 3 chr5D.!!$R4 1785
4 TraesCS5A01G026100 chr5D 32709175 32712221 3046 True 486.500000 869 94.648800 1 1332 5 chr5D.!!$R5 1331
5 TraesCS5A01G026100 chr6B 683371490 683373046 1556 False 1496.000000 1496 84.514000 859 2403 1 chr6B.!!$F1 1544
6 TraesCS5A01G026100 chr6B 683316878 683317889 1011 False 473.000000 532 84.849500 859 2403 2 chr6B.!!$F2 1544
7 TraesCS5A01G026100 chr2A 38613117 38614672 1555 True 1445.000000 1445 83.935000 859 2415 1 chr2A.!!$R1 1556
8 TraesCS5A01G026100 chr2D 605385819 605387631 1812 True 764.500000 867 84.619500 859 2415 2 chr2D.!!$R3 1556
9 TraesCS5A01G026100 chr3D 50425054 50426306 1252 False 780.000000 780 78.399000 1078 2337 1 chr3D.!!$F1 1259
10 TraesCS5A01G026100 chr3D 80567641 80569004 1363 True 647.000000 647 75.977000 999 2363 1 chr3D.!!$R3 1364
11 TraesCS5A01G026100 chr3D 80416579 80417886 1307 True 523.000000 523 74.701000 1085 2371 1 chr3D.!!$R2 1286
12 TraesCS5A01G026100 chr3A 63485406 63486681 1275 False 769.000000 769 78.116000 1078 2362 1 chr3A.!!$F2 1284
13 TraesCS5A01G026100 chr3B 79979182 79980441 1259 False 752.000000 752 78.036000 1079 2337 1 chr3B.!!$F1 1258
14 TraesCS5A01G026100 chr3B 126298139 126299450 1311 True 512.000000 512 74.554000 1078 2371 1 chr3B.!!$R1 1293
15 TraesCS5A01G026100 chr5B 24101597 24107322 5725 True 418.000000 684 89.420286 1 3330 7 chr5B.!!$R3 3329

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
151 554 0.387202 ACGATGAGAGATGGGCTTCG 59.613 55.000 0.0 0.0 35.94 3.79 F
209 612 0.803740 AGTCCGACTCACTTAGCGTC 59.196 55.000 0.0 0.0 0.00 5.19 F
1369 4544 1.078143 GGTTCTGCTTCTCCGGCAT 60.078 57.895 0.0 0.0 39.07 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1203 4353 0.322997 CGTCAGGGTCAGGAGAGTCT 60.323 60.0 0.0 0.0 0.00 3.24 R
1883 5325 0.725686 CACGATCTCGACGGTGTAGT 59.274 55.0 6.6 0.0 43.02 2.73 R
2428 5970 0.033504 AGCTGTCGTTCAACATCGGT 59.966 50.0 0.0 0.0 0.00 4.69 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 7.095607 GGTCAACGGCAACTATATTAAGAGATG 60.096 40.741 0.00 0.00 0.00 2.90
132 535 5.100259 GTGTAGCTATTACTGAAGCAACGA 58.900 41.667 0.00 0.00 41.32 3.85
151 554 0.387202 ACGATGAGAGATGGGCTTCG 59.613 55.000 0.00 0.00 35.94 3.79
182 585 8.197439 GCTAATGCTATGGGTTTTCATAAAGTT 58.803 33.333 0.00 0.00 36.03 2.66
209 612 0.803740 AGTCCGACTCACTTAGCGTC 59.196 55.000 0.00 0.00 0.00 5.19
219 622 4.857588 ACTCACTTAGCGTCATAAACTTCG 59.142 41.667 0.00 0.00 0.00 3.79
305 708 4.315803 CTTCTTCTTCTTCTTTGCGGGTA 58.684 43.478 0.00 0.00 0.00 3.69
443 861 7.169308 GCAAAATTAGCTAAGCTATCACTACGA 59.831 37.037 12.54 0.00 41.01 3.43
451 869 8.577296 AGCTAAGCTATCACTACGATTTATCAA 58.423 33.333 0.00 0.00 36.99 2.57
477 895 8.246430 AGTAATACATTATTCGACTGGGAAGA 57.754 34.615 0.00 0.00 0.00 2.87
503 921 5.116074 CACTTCTTTTCGTGATGCAAATCAC 59.884 40.000 9.92 9.92 45.48 3.06
615 1033 4.671880 TGGACGATGTAATTTTGTTCCG 57.328 40.909 0.00 0.00 0.00 4.30
639 1057 7.038048 CGAGATTAATGAAGCTAGCCATGATA 58.962 38.462 12.13 0.00 29.33 2.15
641 1059 7.915930 AGATTAATGAAGCTAGCCATGATAGT 58.084 34.615 12.13 0.00 26.63 2.12
680 2434 5.988310 TCAGTTCAATTGCCATTTCTGAT 57.012 34.783 0.00 0.00 0.00 2.90
749 2523 3.129813 GCAATTGATCACCTGCTTCATCA 59.870 43.478 17.25 0.00 0.00 3.07
781 2559 9.982651 TCCTAATTACTAATCATCTTGTAGCAC 57.017 33.333 0.00 0.00 0.00 4.40
786 2564 4.870426 ACTAATCATCTTGTAGCACCAACG 59.130 41.667 0.00 0.00 0.00 4.10
791 2569 4.021807 TCATCTTGTAGCACCAACGTAAGA 60.022 41.667 0.00 0.00 43.62 2.10
792 2570 4.530710 TCTTGTAGCACCAACGTAAGAT 57.469 40.909 0.00 0.00 43.62 2.40
794 2572 3.945981 TGTAGCACCAACGTAAGATCA 57.054 42.857 0.00 0.00 43.62 2.92
795 2573 4.260139 TGTAGCACCAACGTAAGATCAA 57.740 40.909 0.00 0.00 43.62 2.57
797 2575 4.629634 TGTAGCACCAACGTAAGATCAATG 59.370 41.667 0.00 0.00 43.62 2.82
798 2576 3.937814 AGCACCAACGTAAGATCAATGA 58.062 40.909 0.00 0.00 43.62 2.57
800 2578 5.670485 AGCACCAACGTAAGATCAATGATA 58.330 37.500 0.00 0.00 43.62 2.15
801 2579 6.291377 AGCACCAACGTAAGATCAATGATAT 58.709 36.000 0.00 0.00 43.62 1.63
803 2581 7.600375 AGCACCAACGTAAGATCAATGATATAG 59.400 37.037 0.00 0.00 43.62 1.31
805 2583 8.088365 CACCAACGTAAGATCAATGATATAGGA 58.912 37.037 12.27 0.00 43.62 2.94
806 2584 8.816894 ACCAACGTAAGATCAATGATATAGGAT 58.183 33.333 12.27 2.17 43.62 3.24
807 2585 9.658799 CCAACGTAAGATCAATGATATAGGATT 57.341 33.333 12.27 4.26 43.62 3.01
827 2605 8.627208 AGGATTTAGATGTGCAATACTTATGG 57.373 34.615 0.00 0.00 0.00 2.74
828 2606 7.175641 AGGATTTAGATGTGCAATACTTATGGC 59.824 37.037 0.00 0.00 33.16 4.40
829 2607 7.040478 GGATTTAGATGTGCAATACTTATGGCA 60.040 37.037 0.00 0.00 40.19 4.92
903 2681 4.082081 TCTCGCCAATCAAATCTGCAATTT 60.082 37.500 0.00 0.00 0.00 1.82
939 2723 3.486383 ACTTACCACATTTGTCACCCAG 58.514 45.455 0.00 0.00 0.00 4.45
982 2788 6.093617 AGAAGATGGAGGTAGGAACTTAGA 57.906 41.667 0.00 0.00 41.75 2.10
1201 4351 4.430765 CGTACGCCGGCTCAGGTT 62.431 66.667 26.68 3.79 0.00 3.50
1202 4352 2.508663 GTACGCCGGCTCAGGTTC 60.509 66.667 26.68 9.00 0.00 3.62
1203 4353 2.992689 TACGCCGGCTCAGGTTCA 60.993 61.111 26.68 0.00 0.00 3.18
1204 4354 3.001902 TACGCCGGCTCAGGTTCAG 62.002 63.158 26.68 7.84 0.00 3.02
1205 4355 4.069232 CGCCGGCTCAGGTTCAGA 62.069 66.667 26.68 0.00 0.00 3.27
1282 4444 1.375908 ATGCACGTCAACATCGGCT 60.376 52.632 0.00 0.00 0.00 5.52
1369 4544 1.078143 GGTTCTGCTTCTCCGGCAT 60.078 57.895 0.00 0.00 39.07 4.40
1525 4949 1.403323 GCCAGTACACCTACTCGTACC 59.597 57.143 0.00 0.00 39.03 3.34
1896 5338 1.722636 GGGCCTACTACACCGTCGAG 61.723 65.000 0.84 0.00 0.00 4.04
2126 5645 2.033602 GGACAAGGTGTTCCCGGG 59.966 66.667 16.85 16.85 38.74 5.73
2371 5900 1.078426 CCTCCCGCCTTTGTGTAGG 60.078 63.158 0.00 0.00 38.40 3.18
2393 5929 2.715624 CAAAGCTAATCGCCGGGC 59.284 61.111 9.54 9.54 40.39 6.13
2403 5939 1.808411 ATCGCCGGGCAGTAATAATG 58.192 50.000 20.71 0.00 0.00 1.90
2406 5948 0.865769 GCCGGGCAGTAATAATGACG 59.134 55.000 15.62 0.00 0.00 4.35
2420 5962 1.542492 ATGACGACGTTAGGGTCACT 58.458 50.000 0.13 0.00 42.83 3.41
2422 5964 2.503331 TGACGACGTTAGGGTCACTAA 58.497 47.619 0.13 0.00 39.31 2.24
2428 5970 5.357878 ACGACGTTAGGGTCACTAATAATCA 59.642 40.000 0.00 0.00 43.20 2.57
2430 5972 5.910614 ACGTTAGGGTCACTAATAATCACC 58.089 41.667 0.00 0.00 43.20 4.02
2446 5988 0.163788 CACCGATGTTGAACGACAGC 59.836 55.000 0.00 0.93 32.19 4.40
2447 5989 0.033504 ACCGATGTTGAACGACAGCT 59.966 50.000 8.46 0.00 33.95 4.24
2448 5990 1.271379 ACCGATGTTGAACGACAGCTA 59.729 47.619 8.46 0.00 33.95 3.32
2449 5991 1.654105 CCGATGTTGAACGACAGCTAC 59.346 52.381 8.46 0.00 33.95 3.58
2507 6049 4.759516 TTTTTGAAGGCGTCTATTGGAC 57.240 40.909 1.41 0.00 41.28 4.02
2510 6052 3.627395 TGAAGGCGTCTATTGGACATT 57.373 42.857 1.41 0.00 44.70 2.71
2511 6053 3.950397 TGAAGGCGTCTATTGGACATTT 58.050 40.909 1.41 0.00 44.70 2.32
2512 6054 4.331968 TGAAGGCGTCTATTGGACATTTT 58.668 39.130 1.41 0.00 44.70 1.82
2513 6055 4.394920 TGAAGGCGTCTATTGGACATTTTC 59.605 41.667 1.41 1.93 44.70 2.29
2515 6057 4.192317 AGGCGTCTATTGGACATTTTCTC 58.808 43.478 0.00 0.00 44.70 2.87
2516 6058 4.080863 AGGCGTCTATTGGACATTTTCTCT 60.081 41.667 0.00 0.00 44.70 3.10
2517 6059 4.636206 GGCGTCTATTGGACATTTTCTCTT 59.364 41.667 0.91 0.00 44.70 2.85
2518 6060 5.123979 GGCGTCTATTGGACATTTTCTCTTT 59.876 40.000 0.91 0.00 44.70 2.52
2519 6061 6.349363 GGCGTCTATTGGACATTTTCTCTTTT 60.349 38.462 0.91 0.00 44.70 2.27
2520 6062 6.524586 GCGTCTATTGGACATTTTCTCTTTTG 59.475 38.462 0.91 0.00 44.70 2.44
2522 6064 7.746475 CGTCTATTGGACATTTTCTCTTTTGAC 59.254 37.037 0.91 0.00 44.70 3.18
2523 6065 8.787852 GTCTATTGGACATTTTCTCTTTTGACT 58.212 33.333 0.00 0.00 43.94 3.41
2524 6066 8.786898 TCTATTGGACATTTTCTCTTTTGACTG 58.213 33.333 0.00 0.00 0.00 3.51
2525 6067 7.587037 ATTGGACATTTTCTCTTTTGACTGA 57.413 32.000 0.00 0.00 0.00 3.41
2526 6068 7.403312 TTGGACATTTTCTCTTTTGACTGAA 57.597 32.000 0.00 0.00 0.00 3.02
2527 6069 7.403312 TGGACATTTTCTCTTTTGACTGAAA 57.597 32.000 0.00 0.00 0.00 2.69
2528 6070 7.835822 TGGACATTTTCTCTTTTGACTGAAAA 58.164 30.769 0.00 0.00 40.90 2.29
2529 6071 8.477256 TGGACATTTTCTCTTTTGACTGAAAAT 58.523 29.630 0.00 0.00 44.71 1.82
2530 6072 9.965824 GGACATTTTCTCTTTTGACTGAAAATA 57.034 29.630 10.77 0.00 43.13 1.40
2535 6125 9.801873 TTTTCTCTTTTGACTGAAAATACAAGG 57.198 29.630 0.00 0.00 34.69 3.61
2536 6126 8.519799 TTCTCTTTTGACTGAAAATACAAGGT 57.480 30.769 0.00 0.00 32.98 3.50
2554 6144 6.597562 ACAAGGTGGAGTAATAACAAACAGA 58.402 36.000 0.00 0.00 0.00 3.41
2603 6196 9.924650 AGATCAAGAAATCAAATCCAAAAGAAG 57.075 29.630 0.00 0.00 0.00 2.85
2623 6216 1.073923 GGGAAGCAAAGAGACCAGGAA 59.926 52.381 0.00 0.00 0.00 3.36
2624 6217 2.489073 GGGAAGCAAAGAGACCAGGAAA 60.489 50.000 0.00 0.00 0.00 3.13
2625 6218 2.554462 GGAAGCAAAGAGACCAGGAAAC 59.446 50.000 0.00 0.00 0.00 2.78
2627 6220 3.297134 AGCAAAGAGACCAGGAAACAA 57.703 42.857 0.00 0.00 0.00 2.83
2628 6221 3.837355 AGCAAAGAGACCAGGAAACAAT 58.163 40.909 0.00 0.00 0.00 2.71
2629 6222 3.823304 AGCAAAGAGACCAGGAAACAATC 59.177 43.478 0.00 0.00 0.00 2.67
2630 6223 3.823304 GCAAAGAGACCAGGAAACAATCT 59.177 43.478 0.00 0.00 0.00 2.40
2632 6225 5.473504 GCAAAGAGACCAGGAAACAATCTAA 59.526 40.000 0.00 0.00 0.00 2.10
2633 6226 6.348868 GCAAAGAGACCAGGAAACAATCTAAG 60.349 42.308 0.00 0.00 0.00 2.18
2635 6228 5.799213 AGAGACCAGGAAACAATCTAAGTG 58.201 41.667 0.00 0.00 0.00 3.16
2639 7516 5.316987 ACCAGGAAACAATCTAAGTGAAGG 58.683 41.667 0.00 0.00 0.00 3.46
2643 7520 3.806949 AACAATCTAAGTGAAGGGCCA 57.193 42.857 6.18 0.00 0.00 5.36
2671 7549 9.273016 CTGAAACTTGAAGTTATTTCCAGTAGA 57.727 33.333 11.43 0.00 39.98 2.59
2673 7551 9.274206 GAAACTTGAAGTTATTTCCAGTAGACT 57.726 33.333 11.43 0.00 39.98 3.24
2687 7565 5.989777 TCCAGTAGACTTTCAAACTTACAGC 59.010 40.000 0.00 0.00 0.00 4.40
2720 7598 6.718454 TGAAATTCCAACAAACAAACACTG 57.282 33.333 0.00 0.00 0.00 3.66
2750 7628 9.851686 TGAAATTCATATACACTAAGGCTGAAT 57.148 29.630 0.00 0.00 34.33 2.57
2761 7642 6.040842 ACACTAAGGCTGAATTTGTTGTTCAT 59.959 34.615 0.00 0.00 35.26 2.57
2778 7659 3.819564 TCATCCCAAGGTGATTCTACG 57.180 47.619 0.00 0.00 0.00 3.51
2789 7670 5.242434 AGGTGATTCTACGCACATTAAACA 58.758 37.500 0.00 0.00 36.76 2.83
2815 7702 9.574516 ACCATAATTCATTAGAAATGTACTCCC 57.425 33.333 0.00 0.00 37.29 4.30
2816 7703 9.799106 CCATAATTCATTAGAAATGTACTCCCT 57.201 33.333 0.00 0.00 37.29 4.20
2819 7706 8.888579 AATTCATTAGAAATGTACTCCCTACG 57.111 34.615 0.00 0.00 37.29 3.51
2820 7707 7.414222 TTCATTAGAAATGTACTCCCTACGT 57.586 36.000 0.00 0.00 0.00 3.57
2821 7708 8.523915 TTCATTAGAAATGTACTCCCTACGTA 57.476 34.615 0.00 0.00 0.00 3.57
2822 7709 8.523915 TCATTAGAAATGTACTCCCTACGTAA 57.476 34.615 0.00 0.00 0.00 3.18
2823 7710 8.970020 TCATTAGAAATGTACTCCCTACGTAAA 58.030 33.333 0.00 0.00 0.00 2.01
2824 7711 9.245962 CATTAGAAATGTACTCCCTACGTAAAG 57.754 37.037 0.00 0.00 0.00 1.85
2825 7712 8.579850 TTAGAAATGTACTCCCTACGTAAAGA 57.420 34.615 0.00 0.00 0.00 2.52
2826 7713 7.472334 AGAAATGTACTCCCTACGTAAAGAA 57.528 36.000 0.00 0.00 0.00 2.52
2827 7714 7.899973 AGAAATGTACTCCCTACGTAAAGAAA 58.100 34.615 0.00 0.00 0.00 2.52
2828 7715 8.537858 AGAAATGTACTCCCTACGTAAAGAAAT 58.462 33.333 0.00 0.00 0.00 2.17
2829 7716 9.807649 GAAATGTACTCCCTACGTAAAGAAATA 57.192 33.333 0.00 0.00 0.00 1.40
2836 7723 8.358895 ACTCCCTACGTAAAGAAATATAAGAGC 58.641 37.037 0.00 0.00 0.00 4.09
2837 7724 7.365741 TCCCTACGTAAAGAAATATAAGAGCG 58.634 38.462 0.00 0.00 0.00 5.03
2838 7725 7.013655 TCCCTACGTAAAGAAATATAAGAGCGT 59.986 37.037 0.00 0.00 0.00 5.07
2839 7726 7.650903 CCCTACGTAAAGAAATATAAGAGCGTT 59.349 37.037 0.00 0.00 0.00 4.84
2840 7727 9.669353 CCTACGTAAAGAAATATAAGAGCGTTA 57.331 33.333 0.00 0.00 0.00 3.18
2843 7730 9.017669 ACGTAAAGAAATATAAGAGCGTTAGTG 57.982 33.333 0.00 0.00 0.00 2.74
2844 7731 9.229784 CGTAAAGAAATATAAGAGCGTTAGTGA 57.770 33.333 0.00 0.00 0.00 3.41
2852 7739 8.951954 ATATAAGAGCGTTAGTGATCTAAACG 57.048 34.615 17.65 17.65 37.81 3.60
2853 7740 3.436496 AGAGCGTTAGTGATCTAAACGC 58.564 45.455 28.97 28.97 45.31 4.84
2855 7742 3.820160 GCGTTAGTGATCTAAACGCTC 57.180 47.619 28.92 13.40 43.81 5.03
2856 7743 3.436496 GCGTTAGTGATCTAAACGCTCT 58.564 45.455 28.92 7.20 43.81 4.09
2857 7744 3.858238 GCGTTAGTGATCTAAACGCTCTT 59.142 43.478 28.92 0.00 43.81 2.85
2858 7745 5.032863 GCGTTAGTGATCTAAACGCTCTTA 58.967 41.667 28.92 0.00 43.81 2.10
2859 7746 5.686397 GCGTTAGTGATCTAAACGCTCTTAT 59.314 40.000 28.92 0.00 43.81 1.73
2860 7747 6.854892 GCGTTAGTGATCTAAACGCTCTTATA 59.145 38.462 28.92 0.00 43.81 0.98
2861 7748 7.537991 GCGTTAGTGATCTAAACGCTCTTATAT 59.462 37.037 28.92 0.00 43.81 0.86
2862 7749 9.395707 CGTTAGTGATCTAAACGCTCTTATATT 57.604 33.333 12.48 0.00 37.81 1.28
2871 7758 9.241317 TCTAAACGCTCTTATATTTCTTTACGG 57.759 33.333 0.00 0.00 0.00 4.02
2872 7759 9.241317 CTAAACGCTCTTATATTTCTTTACGGA 57.759 33.333 0.00 0.00 0.00 4.69
2873 7760 7.695869 AACGCTCTTATATTTCTTTACGGAG 57.304 36.000 0.00 0.00 0.00 4.63
2874 7761 6.214399 ACGCTCTTATATTTCTTTACGGAGG 58.786 40.000 0.00 0.00 0.00 4.30
2875 7762 5.634020 CGCTCTTATATTTCTTTACGGAGGG 59.366 44.000 0.00 0.00 0.00 4.30
2876 7763 6.516194 CGCTCTTATATTTCTTTACGGAGGGA 60.516 42.308 0.00 0.00 34.63 4.20
2877 7764 7.215085 GCTCTTATATTTCTTTACGGAGGGAA 58.785 38.462 0.00 0.00 0.00 3.97
2878 7765 7.878644 GCTCTTATATTTCTTTACGGAGGGAAT 59.121 37.037 0.00 0.00 0.00 3.01
2893 7780 5.986135 CGGAGGGAATAACTCTAGTTCAATG 59.014 44.000 0.00 0.00 39.31 2.82
2896 7783 7.365652 GGAGGGAATAACTCTAGTTCAATGGAA 60.366 40.741 0.00 0.00 39.31 3.53
2908 7795 6.773976 AGTTCAATGGAAAGAACACAAAGA 57.226 33.333 7.88 0.00 44.94 2.52
2909 7796 7.169158 AGTTCAATGGAAAGAACACAAAGAA 57.831 32.000 7.88 0.00 44.94 2.52
2910 7797 7.785033 AGTTCAATGGAAAGAACACAAAGAAT 58.215 30.769 7.88 0.00 44.94 2.40
2911 7798 8.260114 AGTTCAATGGAAAGAACACAAAGAATT 58.740 29.630 7.88 0.00 44.94 2.17
2912 7799 9.528018 GTTCAATGGAAAGAACACAAAGAATTA 57.472 29.630 0.00 0.00 42.72 1.40
2913 7800 9.748708 TTCAATGGAAAGAACACAAAGAATTAG 57.251 29.630 0.00 0.00 0.00 1.73
2914 7801 7.867403 TCAATGGAAAGAACACAAAGAATTAGC 59.133 33.333 0.00 0.00 0.00 3.09
2915 7802 6.959639 TGGAAAGAACACAAAGAATTAGCT 57.040 33.333 0.00 0.00 0.00 3.32
2916 7803 6.970484 TGGAAAGAACACAAAGAATTAGCTC 58.030 36.000 0.00 0.00 0.00 4.09
2917 7804 6.772716 TGGAAAGAACACAAAGAATTAGCTCT 59.227 34.615 0.00 0.00 0.00 4.09
2958 7846 9.667107 AGCAAGCTATAAATTTACTACACAAGA 57.333 29.630 0.00 0.00 0.00 3.02
2973 7861 8.050778 ACTACACAAGAAAAACAGAAATGACA 57.949 30.769 0.00 0.00 0.00 3.58
2983 8500 8.496707 AAAAACAGAAATGACAAGCAGAAAAT 57.503 26.923 0.00 0.00 0.00 1.82
2986 8503 7.047460 ACAGAAATGACAAGCAGAAAATTCT 57.953 32.000 0.00 0.00 38.25 2.40
2999 8522 8.189119 AGCAGAAAATTCTTATTACCCAACAA 57.811 30.769 0.00 0.00 34.74 2.83
3019 8542 5.350633 ACAAACATTTCACAACATGACCTG 58.649 37.500 0.00 0.00 36.92 4.00
3020 8543 5.105392 ACAAACATTTCACAACATGACCTGT 60.105 36.000 0.00 0.00 40.84 4.00
3021 8544 6.096141 ACAAACATTTCACAACATGACCTGTA 59.904 34.615 0.00 0.00 36.98 2.74
3022 8545 5.947228 ACATTTCACAACATGACCTGTAG 57.053 39.130 0.00 0.00 36.98 2.74
3023 8546 5.376625 ACATTTCACAACATGACCTGTAGT 58.623 37.500 0.00 0.00 36.98 2.73
3024 8547 6.530120 ACATTTCACAACATGACCTGTAGTA 58.470 36.000 0.00 0.00 36.98 1.82
3025 8548 7.168219 ACATTTCACAACATGACCTGTAGTAT 58.832 34.615 0.00 0.00 36.98 2.12
3026 8549 7.334421 ACATTTCACAACATGACCTGTAGTATC 59.666 37.037 0.00 0.00 36.98 2.24
3027 8550 6.605471 TTCACAACATGACCTGTAGTATCT 57.395 37.500 0.00 0.00 36.98 1.98
3028 8551 6.208988 TCACAACATGACCTGTAGTATCTC 57.791 41.667 0.00 0.00 36.98 2.75
3029 8552 5.127194 TCACAACATGACCTGTAGTATCTCC 59.873 44.000 0.00 0.00 36.98 3.71
3030 8553 5.023452 ACAACATGACCTGTAGTATCTCCA 58.977 41.667 0.00 0.00 36.98 3.86
3092 8648 9.298774 AGTAATACAAGTATAGAACTTTGCGTC 57.701 33.333 0.00 0.00 46.61 5.19
3099 8655 0.602905 AGAACTTTGCGTCTTCCCGG 60.603 55.000 0.00 0.00 0.00 5.73
3110 8666 0.988832 TCTTCCCGGTGGCTTGTTAT 59.011 50.000 0.00 0.00 0.00 1.89
3112 8668 1.472480 CTTCCCGGTGGCTTGTTATTG 59.528 52.381 0.00 0.00 0.00 1.90
3137 8712 8.941977 TGATGTGTTGTTAGTTTCATATGTACC 58.058 33.333 1.90 0.00 0.00 3.34
3216 8794 1.280421 GACTCTGGGCTTCCATCAAGT 59.720 52.381 0.00 0.00 40.27 3.16
3228 8806 5.182001 GCTTCCATCAAGTCACTACAACATT 59.818 40.000 0.00 0.00 34.13 2.71
3232 8810 7.619965 TCCATCAAGTCACTACAACATTGATA 58.380 34.615 0.00 0.00 35.73 2.15
3291 8869 4.721776 TCTAAGGGATGGTTAGTGCAAGAT 59.278 41.667 0.00 0.00 0.00 2.40
3296 8874 2.018542 TGGTTAGTGCAAGATACGGC 57.981 50.000 0.00 0.00 0.00 5.68
3297 8875 1.553248 TGGTTAGTGCAAGATACGGCT 59.447 47.619 0.00 0.00 0.00 5.52
3301 8879 1.726853 AGTGCAAGATACGGCTCAAC 58.273 50.000 0.00 0.00 0.00 3.18
3315 8893 4.879545 ACGGCTCAACAGAGTTTTCTTTTA 59.120 37.500 0.00 0.00 0.00 1.52
3317 8895 5.681543 CGGCTCAACAGAGTTTTCTTTTAAC 59.318 40.000 0.00 0.00 0.00 2.01
3318 8896 6.560711 GGCTCAACAGAGTTTTCTTTTAACA 58.439 36.000 0.00 0.00 0.00 2.41
3320 8898 7.706607 GGCTCAACAGAGTTTTCTTTTAACAAT 59.293 33.333 0.00 0.00 0.00 2.71
3326 8904 8.847196 ACAGAGTTTTCTTTTAACAATACCCTC 58.153 33.333 0.00 0.00 0.00 4.30
3343 8921 3.477210 CCTCTAAGGGATGGTTAGTGC 57.523 52.381 0.00 0.00 0.00 4.40
3344 8922 2.771943 CCTCTAAGGGATGGTTAGTGCA 59.228 50.000 0.00 0.00 0.00 4.57
3345 8923 3.199946 CCTCTAAGGGATGGTTAGTGCAA 59.800 47.826 0.00 0.00 0.00 4.08
3346 8924 4.141390 CCTCTAAGGGATGGTTAGTGCAAT 60.141 45.833 0.00 0.00 0.00 3.56
3347 8925 5.071788 CCTCTAAGGGATGGTTAGTGCAATA 59.928 44.000 0.00 0.00 0.00 1.90
3348 8926 5.925509 TCTAAGGGATGGTTAGTGCAATAC 58.074 41.667 0.00 0.00 0.00 1.89
3349 8927 4.584638 AAGGGATGGTTAGTGCAATACA 57.415 40.909 0.00 0.00 0.00 2.29
3350 8928 4.584638 AGGGATGGTTAGTGCAATACAA 57.415 40.909 0.00 0.00 0.00 2.41
3351 8929 4.929479 AGGGATGGTTAGTGCAATACAAA 58.071 39.130 0.00 0.00 0.00 2.83
3352 8930 5.329399 AGGGATGGTTAGTGCAATACAAAA 58.671 37.500 0.00 0.00 0.00 2.44
3353 8931 5.957774 AGGGATGGTTAGTGCAATACAAAAT 59.042 36.000 0.00 0.00 0.00 1.82
3354 8932 7.122715 AGGGATGGTTAGTGCAATACAAAATA 58.877 34.615 0.00 0.00 0.00 1.40
3355 8933 7.617723 AGGGATGGTTAGTGCAATACAAAATAA 59.382 33.333 0.00 0.00 0.00 1.40
3356 8934 8.254508 GGGATGGTTAGTGCAATACAAAATAAA 58.745 33.333 0.00 0.00 0.00 1.40
3357 8935 9.816354 GGATGGTTAGTGCAATACAAAATAAAT 57.184 29.630 0.00 0.00 0.00 1.40
3360 8938 9.796120 TGGTTAGTGCAATACAAAATAAATAGC 57.204 29.630 0.00 0.00 0.00 2.97
3361 8939 9.796120 GGTTAGTGCAATACAAAATAAATAGCA 57.204 29.630 0.00 0.00 0.00 3.49
3365 8943 9.357652 AGTGCAATACAAAATAAATAGCAACAG 57.642 29.630 0.00 0.00 0.00 3.16
3366 8944 9.139174 GTGCAATACAAAATAAATAGCAACAGT 57.861 29.630 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 3.686016 TGCCAAGAATGTACCTCTTTCC 58.314 45.455 4.91 1.48 30.58 3.13
132 535 0.387202 CGAAGCCCATCTCTCATCGT 59.613 55.000 0.00 0.00 0.00 3.73
151 554 4.391405 AAACCCATAGCATTAGCAAAGC 57.609 40.909 0.00 0.00 45.49 3.51
205 608 2.030457 CCATCACCGAAGTTTATGACGC 59.970 50.000 0.00 0.00 0.00 5.19
209 612 5.586243 AGATTGTCCATCACCGAAGTTTATG 59.414 40.000 0.00 0.00 33.75 1.90
219 622 2.026822 ACCACTGAGATTGTCCATCACC 60.027 50.000 0.00 0.00 33.75 4.02
367 770 6.074648 TGATTAGGTTGTGGTCCAGATTTTT 58.925 36.000 0.00 0.00 0.00 1.94
386 789 5.250543 TGAGGGAAGAACCATGACTTGATTA 59.749 40.000 0.00 0.00 41.20 1.75
451 869 8.701895 TCTTCCCAGTCGAATAATGTATTACTT 58.298 33.333 0.00 0.00 0.00 2.24
462 880 5.263968 GAAGTGATCTTCCCAGTCGAATA 57.736 43.478 0.00 0.00 42.85 1.75
463 881 4.130286 GAAGTGATCTTCCCAGTCGAAT 57.870 45.455 0.00 0.00 42.85 3.34
615 1033 8.040132 ACTATCATGGCTAGCTTCATTAATCTC 58.960 37.037 15.72 0.00 0.00 2.75
781 2559 9.658799 AATCCTATATCATTGATCTTACGTTGG 57.341 33.333 1.55 0.00 0.00 3.77
801 2579 9.725019 CCATAAGTATTGCACATCTAAATCCTA 57.275 33.333 0.00 0.00 0.00 2.94
803 2581 7.040478 TGCCATAAGTATTGCACATCTAAATCC 60.040 37.037 0.00 0.00 30.49 3.01
805 2583 7.822161 TGCCATAAGTATTGCACATCTAAAT 57.178 32.000 0.00 0.00 30.49 1.40
814 2592 6.173427 TCTAGATGTGCCATAAGTATTGCA 57.827 37.500 0.00 0.00 32.69 4.08
815 2593 7.069852 CATCTAGATGTGCCATAAGTATTGC 57.930 40.000 22.42 0.00 34.23 3.56
861 2639 6.238293 GGCGAGAAATTAGCGGTATACTTTTT 60.238 38.462 2.25 0.00 0.00 1.94
862 2640 5.235831 GGCGAGAAATTAGCGGTATACTTTT 59.764 40.000 2.25 0.00 0.00 2.27
863 2641 4.748600 GGCGAGAAATTAGCGGTATACTTT 59.251 41.667 2.25 0.00 0.00 2.66
864 2642 4.202182 TGGCGAGAAATTAGCGGTATACTT 60.202 41.667 2.25 0.00 0.00 2.24
865 2643 3.319972 TGGCGAGAAATTAGCGGTATACT 59.680 43.478 2.25 0.00 0.00 2.12
866 2644 3.645884 TGGCGAGAAATTAGCGGTATAC 58.354 45.455 0.00 0.00 0.00 1.47
867 2645 4.325028 TTGGCGAGAAATTAGCGGTATA 57.675 40.909 0.00 0.00 0.00 1.47
868 2646 2.902705 TGGCGAGAAATTAGCGGTAT 57.097 45.000 0.00 0.00 0.00 2.73
869 2647 2.676632 TTGGCGAGAAATTAGCGGTA 57.323 45.000 0.00 0.00 0.00 4.02
879 2657 2.435422 TGCAGATTTGATTGGCGAGAA 58.565 42.857 0.00 0.00 0.00 2.87
903 2681 5.308497 TGTGGTAAGTAAGGATTTGACAGGA 59.692 40.000 0.00 0.00 0.00 3.86
939 2723 6.879458 TCTTCTTCTCAGGGCAGTTTTAATAC 59.121 38.462 0.00 0.00 0.00 1.89
982 2788 7.148656 GCACGCCATTGACTGTTAATAATTTTT 60.149 33.333 0.00 0.00 0.00 1.94
1200 4350 1.429299 TCAGGGTCAGGAGAGTCTGAA 59.571 52.381 0.00 0.00 44.30 3.02
1201 4351 1.076438 TCAGGGTCAGGAGAGTCTGA 58.924 55.000 0.00 0.00 41.03 3.27
1202 4352 1.181786 GTCAGGGTCAGGAGAGTCTG 58.818 60.000 0.00 0.00 36.17 3.51
1203 4353 0.322997 CGTCAGGGTCAGGAGAGTCT 60.323 60.000 0.00 0.00 0.00 3.24
1204 4354 1.316706 CCGTCAGGGTCAGGAGAGTC 61.317 65.000 0.00 0.00 0.00 3.36
1205 4355 1.304547 CCGTCAGGGTCAGGAGAGT 60.305 63.158 0.00 0.00 0.00 3.24
1395 4579 3.973516 TCGAACACGCTGCTCCGT 61.974 61.111 0.00 0.00 43.11 4.69
1397 4581 3.112709 GGTCGAACACGCTGCTCC 61.113 66.667 0.00 0.00 0.00 4.70
1881 5323 2.033917 CACGATCTCGACGGTGTAGTAG 60.034 54.545 6.60 0.00 43.02 2.57
1883 5325 0.725686 CACGATCTCGACGGTGTAGT 59.274 55.000 6.60 0.00 43.02 2.73
1950 5451 2.408022 CCGGAGTCGACGATGACC 59.592 66.667 10.46 8.96 39.77 4.02
2043 5544 4.656117 TTCGGCGACTGCTTGCGA 62.656 61.111 10.16 0.00 42.25 5.10
2126 5645 2.388232 CCCAGCTCCAACGTAACGC 61.388 63.158 0.00 0.00 0.00 4.84
2337 5865 2.215093 GGAGGGGAGGGGTAAGATTTT 58.785 52.381 0.00 0.00 0.00 1.82
2390 5926 2.817901 ACGTCGTCATTATTACTGCCC 58.182 47.619 0.00 0.00 0.00 5.36
2393 5929 5.585390 ACCCTAACGTCGTCATTATTACTG 58.415 41.667 0.00 0.00 0.00 2.74
2403 5939 3.772060 ATTAGTGACCCTAACGTCGTC 57.228 47.619 0.00 0.00 38.45 4.20
2406 5948 5.981915 GGTGATTATTAGTGACCCTAACGTC 59.018 44.000 0.00 0.00 38.45 4.34
2420 5962 6.100668 TGTCGTTCAACATCGGTGATTATTA 58.899 36.000 0.65 0.00 0.00 0.98
2422 5964 4.500127 TGTCGTTCAACATCGGTGATTAT 58.500 39.130 0.65 0.00 0.00 1.28
2428 5970 0.033504 AGCTGTCGTTCAACATCGGT 59.966 50.000 0.00 0.00 0.00 4.69
2430 5972 1.654105 GGTAGCTGTCGTTCAACATCG 59.346 52.381 0.00 0.00 0.00 3.84
2446 5988 4.036498 CCAATAGACACTCGTGGTAGGTAG 59.964 50.000 1.77 0.00 34.19 3.18
2447 5989 3.949754 CCAATAGACACTCGTGGTAGGTA 59.050 47.826 1.77 0.00 34.19 3.08
2448 5990 2.758979 CCAATAGACACTCGTGGTAGGT 59.241 50.000 1.77 0.00 34.19 3.08
2449 5991 3.021695 TCCAATAGACACTCGTGGTAGG 58.978 50.000 1.77 0.00 34.19 3.18
2486 6028 4.759516 GTCCAATAGACGCCTTCAAAAA 57.240 40.909 0.00 0.00 35.30 1.94
2497 6039 8.787852 AGTCAAAAGAGAAAATGTCCAATAGAC 58.212 33.333 0.00 0.00 46.51 2.59
2498 6040 8.786898 CAGTCAAAAGAGAAAATGTCCAATAGA 58.213 33.333 0.00 0.00 0.00 1.98
2499 6041 8.786898 TCAGTCAAAAGAGAAAATGTCCAATAG 58.213 33.333 0.00 0.00 0.00 1.73
2500 6042 8.690203 TCAGTCAAAAGAGAAAATGTCCAATA 57.310 30.769 0.00 0.00 0.00 1.90
2501 6043 7.587037 TCAGTCAAAAGAGAAAATGTCCAAT 57.413 32.000 0.00 0.00 0.00 3.16
2502 6044 7.403312 TTCAGTCAAAAGAGAAAATGTCCAA 57.597 32.000 0.00 0.00 0.00 3.53
2503 6045 7.403312 TTTCAGTCAAAAGAGAAAATGTCCA 57.597 32.000 0.00 0.00 0.00 4.02
2504 6046 8.877808 ATTTTCAGTCAAAAGAGAAAATGTCC 57.122 30.769 10.19 0.00 44.46 4.02
2510 6052 8.966868 ACCTTGTATTTTCAGTCAAAAGAGAAA 58.033 29.630 0.00 0.00 37.40 2.52
2511 6053 8.405531 CACCTTGTATTTTCAGTCAAAAGAGAA 58.594 33.333 0.00 0.00 37.40 2.87
2512 6054 7.013274 CCACCTTGTATTTTCAGTCAAAAGAGA 59.987 37.037 0.00 0.00 37.40 3.10
2513 6055 7.013274 TCCACCTTGTATTTTCAGTCAAAAGAG 59.987 37.037 0.00 0.00 37.40 2.85
2515 6057 7.038154 TCCACCTTGTATTTTCAGTCAAAAG 57.962 36.000 0.00 0.00 37.40 2.27
2516 6058 6.605594 ACTCCACCTTGTATTTTCAGTCAAAA 59.394 34.615 0.00 0.00 38.38 2.44
2517 6059 6.126409 ACTCCACCTTGTATTTTCAGTCAAA 58.874 36.000 0.00 0.00 0.00 2.69
2518 6060 5.690865 ACTCCACCTTGTATTTTCAGTCAA 58.309 37.500 0.00 0.00 0.00 3.18
2519 6061 5.304686 ACTCCACCTTGTATTTTCAGTCA 57.695 39.130 0.00 0.00 0.00 3.41
2520 6062 7.923414 ATTACTCCACCTTGTATTTTCAGTC 57.077 36.000 0.00 0.00 0.00 3.51
2522 6064 9.226606 TGTTATTACTCCACCTTGTATTTTCAG 57.773 33.333 0.00 0.00 0.00 3.02
2523 6065 9.575868 TTGTTATTACTCCACCTTGTATTTTCA 57.424 29.630 0.00 0.00 0.00 2.69
2526 6068 9.357161 TGTTTGTTATTACTCCACCTTGTATTT 57.643 29.630 0.00 0.00 0.00 1.40
2527 6069 8.927675 TGTTTGTTATTACTCCACCTTGTATT 57.072 30.769 0.00 0.00 0.00 1.89
2528 6070 8.380099 TCTGTTTGTTATTACTCCACCTTGTAT 58.620 33.333 0.00 0.00 0.00 2.29
2529 6071 7.737869 TCTGTTTGTTATTACTCCACCTTGTA 58.262 34.615 0.00 0.00 0.00 2.41
2530 6072 6.597562 TCTGTTTGTTATTACTCCACCTTGT 58.402 36.000 0.00 0.00 0.00 3.16
2531 6073 7.504924 TTCTGTTTGTTATTACTCCACCTTG 57.495 36.000 0.00 0.00 0.00 3.61
2535 6125 6.348540 CCTGCTTCTGTTTGTTATTACTCCAC 60.349 42.308 0.00 0.00 0.00 4.02
2536 6126 5.705441 CCTGCTTCTGTTTGTTATTACTCCA 59.295 40.000 0.00 0.00 0.00 3.86
2554 6144 5.570320 TGCTACCTTTTTCTTATCCTGCTT 58.430 37.500 0.00 0.00 0.00 3.91
2603 6196 0.693049 TCCTGGTCTCTTTGCTTCCC 59.307 55.000 0.00 0.00 0.00 3.97
2623 6216 3.690460 CTGGCCCTTCACTTAGATTGTT 58.310 45.455 0.00 0.00 0.00 2.83
2624 6217 2.619074 GCTGGCCCTTCACTTAGATTGT 60.619 50.000 0.00 0.00 0.00 2.71
2625 6218 2.019984 GCTGGCCCTTCACTTAGATTG 58.980 52.381 0.00 0.00 0.00 2.67
2627 6220 1.211457 CAGCTGGCCCTTCACTTAGAT 59.789 52.381 5.57 0.00 0.00 1.98
2628 6221 0.615331 CAGCTGGCCCTTCACTTAGA 59.385 55.000 5.57 0.00 0.00 2.10
2629 6222 0.615331 TCAGCTGGCCCTTCACTTAG 59.385 55.000 15.13 0.00 0.00 2.18
2630 6223 1.064003 TTCAGCTGGCCCTTCACTTA 58.936 50.000 15.13 0.00 0.00 2.24
2632 6225 0.538287 GTTTCAGCTGGCCCTTCACT 60.538 55.000 15.13 0.00 0.00 3.41
2633 6226 0.538287 AGTTTCAGCTGGCCCTTCAC 60.538 55.000 15.13 0.65 0.00 3.18
2635 6228 0.600057 CAAGTTTCAGCTGGCCCTTC 59.400 55.000 15.13 0.00 0.00 3.46
2639 7516 1.322442 ACTTCAAGTTTCAGCTGGCC 58.678 50.000 15.13 0.00 0.00 5.36
2643 7520 6.547510 ACTGGAAATAACTTCAAGTTTCAGCT 59.452 34.615 8.41 0.00 44.72 4.24
2671 7549 4.573201 TGTTAGCGCTGTAAGTTTGAAAGT 59.427 37.500 22.90 0.00 35.30 2.66
2673 7551 5.487153 TTGTTAGCGCTGTAAGTTTGAAA 57.513 34.783 22.90 0.00 35.30 2.69
2687 7565 6.761731 TTGTTGGAATTTCATTTGTTAGCG 57.238 33.333 0.00 0.00 0.00 4.26
2720 7598 9.717942 AGCCTTAGTGTATATGAATTTCATCTC 57.282 33.333 14.99 7.94 38.26 2.75
2750 7628 3.636679 TCACCTTGGGATGAACAACAAA 58.363 40.909 0.00 0.00 0.00 2.83
2753 7631 4.082125 AGAATCACCTTGGGATGAACAAC 58.918 43.478 0.00 0.00 0.00 3.32
2761 7642 1.066430 GTGCGTAGAATCACCTTGGGA 60.066 52.381 0.00 0.00 0.00 4.37
2789 7670 9.574516 GGGAGTACATTTCTAATGAATTATGGT 57.425 33.333 6.42 0.00 29.33 3.55
2811 7698 7.537991 CGCTCTTATATTTCTTTACGTAGGGAG 59.462 40.741 0.00 0.00 0.00 4.30
2812 7699 7.013655 ACGCTCTTATATTTCTTTACGTAGGGA 59.986 37.037 0.00 0.00 0.00 4.20
2813 7700 7.144000 ACGCTCTTATATTTCTTTACGTAGGG 58.856 38.462 0.00 0.00 0.00 3.53
2817 7704 9.017669 CACTAACGCTCTTATATTTCTTTACGT 57.982 33.333 0.00 0.00 0.00 3.57
2818 7705 9.229784 TCACTAACGCTCTTATATTTCTTTACG 57.770 33.333 0.00 0.00 0.00 3.18
2826 7713 9.395707 CGTTTAGATCACTAACGCTCTTATATT 57.604 33.333 12.04 0.00 38.18 1.28
2827 7714 7.537991 GCGTTTAGATCACTAACGCTCTTATAT 59.462 37.037 28.85 0.00 44.73 0.86
2828 7715 6.854892 GCGTTTAGATCACTAACGCTCTTATA 59.145 38.462 28.85 0.00 44.73 0.98
2829 7716 5.686397 GCGTTTAGATCACTAACGCTCTTAT 59.314 40.000 28.85 0.00 44.73 1.73
2830 7717 5.032863 GCGTTTAGATCACTAACGCTCTTA 58.967 41.667 28.85 0.00 44.73 2.10
2831 7718 3.858238 GCGTTTAGATCACTAACGCTCTT 59.142 43.478 28.85 0.00 44.73 2.85
2832 7719 3.436496 GCGTTTAGATCACTAACGCTCT 58.564 45.455 28.85 0.00 44.73 4.09
2833 7720 3.820160 GCGTTTAGATCACTAACGCTC 57.180 47.619 28.85 13.04 44.73 5.03
2835 7722 3.436496 AGAGCGTTTAGATCACTAACGC 58.564 45.455 28.90 28.90 46.25 4.84
2836 7723 8.951954 ATATAAGAGCGTTTAGATCACTAACG 57.048 34.615 17.35 17.35 38.18 3.18
2845 7732 9.241317 CCGTAAAGAAATATAAGAGCGTTTAGA 57.759 33.333 0.00 0.00 0.00 2.10
2846 7733 9.241317 TCCGTAAAGAAATATAAGAGCGTTTAG 57.759 33.333 0.00 0.00 0.00 1.85
2847 7734 9.241317 CTCCGTAAAGAAATATAAGAGCGTTTA 57.759 33.333 0.00 0.00 0.00 2.01
2848 7735 7.224167 CCTCCGTAAAGAAATATAAGAGCGTTT 59.776 37.037 0.00 0.00 0.00 3.60
2849 7736 6.700520 CCTCCGTAAAGAAATATAAGAGCGTT 59.299 38.462 0.00 0.00 0.00 4.84
2850 7737 6.214399 CCTCCGTAAAGAAATATAAGAGCGT 58.786 40.000 0.00 0.00 0.00 5.07
2851 7738 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
2852 7739 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
2858 7745 8.935741 AGAGTTATTCCCTCCGTAAAGAAATAT 58.064 33.333 0.00 0.00 0.00 1.28
2859 7746 8.315220 AGAGTTATTCCCTCCGTAAAGAAATA 57.685 34.615 0.00 0.00 0.00 1.40
2860 7747 7.196637 AGAGTTATTCCCTCCGTAAAGAAAT 57.803 36.000 0.00 0.00 0.00 2.17
2861 7748 6.616237 AGAGTTATTCCCTCCGTAAAGAAA 57.384 37.500 0.00 0.00 0.00 2.52
2862 7749 6.894103 ACTAGAGTTATTCCCTCCGTAAAGAA 59.106 38.462 0.00 0.00 0.00 2.52
2863 7750 6.430007 ACTAGAGTTATTCCCTCCGTAAAGA 58.570 40.000 0.00 0.00 0.00 2.52
2864 7751 6.712179 ACTAGAGTTATTCCCTCCGTAAAG 57.288 41.667 0.00 0.00 0.00 1.85
2865 7752 6.664816 TGAACTAGAGTTATTCCCTCCGTAAA 59.335 38.462 0.00 0.00 38.56 2.01
2866 7753 6.189859 TGAACTAGAGTTATTCCCTCCGTAA 58.810 40.000 0.00 0.00 38.56 3.18
2867 7754 5.759059 TGAACTAGAGTTATTCCCTCCGTA 58.241 41.667 0.00 0.00 38.56 4.02
2868 7755 4.607239 TGAACTAGAGTTATTCCCTCCGT 58.393 43.478 0.00 0.00 38.56 4.69
2869 7756 5.593679 TTGAACTAGAGTTATTCCCTCCG 57.406 43.478 0.00 0.00 38.56 4.63
2870 7757 6.099845 TCCATTGAACTAGAGTTATTCCCTCC 59.900 42.308 0.00 0.00 38.56 4.30
2871 7758 7.125792 TCCATTGAACTAGAGTTATTCCCTC 57.874 40.000 0.00 0.00 38.56 4.30
2872 7759 7.510675 TTCCATTGAACTAGAGTTATTCCCT 57.489 36.000 0.00 0.00 38.56 4.20
2873 7760 8.047310 TCTTTCCATTGAACTAGAGTTATTCCC 58.953 37.037 0.00 0.00 38.56 3.97
2874 7761 9.449719 TTCTTTCCATTGAACTAGAGTTATTCC 57.550 33.333 0.00 0.00 38.56 3.01
2876 7763 9.793259 TGTTCTTTCCATTGAACTAGAGTTATT 57.207 29.630 0.00 0.00 41.99 1.40
2877 7764 9.220767 GTGTTCTTTCCATTGAACTAGAGTTAT 57.779 33.333 0.00 0.00 41.99 1.89
2878 7765 8.208224 TGTGTTCTTTCCATTGAACTAGAGTTA 58.792 33.333 0.00 0.00 41.99 2.24
2879 7766 7.054124 TGTGTTCTTTCCATTGAACTAGAGTT 58.946 34.615 0.00 0.00 41.99 3.01
2880 7767 6.591935 TGTGTTCTTTCCATTGAACTAGAGT 58.408 36.000 0.00 0.00 41.99 3.24
2881 7768 7.496529 TTGTGTTCTTTCCATTGAACTAGAG 57.503 36.000 0.00 0.00 41.99 2.43
2882 7769 7.773224 TCTTTGTGTTCTTTCCATTGAACTAGA 59.227 33.333 0.00 0.00 41.99 2.43
2893 7780 7.208225 AGAGCTAATTCTTTGTGTTCTTTCC 57.792 36.000 0.00 0.00 0.00 3.13
2896 7783 9.213799 CTTCTAGAGCTAATTCTTTGTGTTCTT 57.786 33.333 0.00 0.00 0.00 2.52
2908 7795 8.303876 GCTGCTAGTAATCTTCTAGAGCTAATT 58.696 37.037 4.45 0.00 37.62 1.40
2909 7796 7.450014 TGCTGCTAGTAATCTTCTAGAGCTAAT 59.550 37.037 0.00 0.00 38.25 1.73
2910 7797 6.773200 TGCTGCTAGTAATCTTCTAGAGCTAA 59.227 38.462 0.00 0.00 38.25 3.09
2911 7798 6.299922 TGCTGCTAGTAATCTTCTAGAGCTA 58.700 40.000 0.00 0.00 38.25 3.32
2912 7799 5.136828 TGCTGCTAGTAATCTTCTAGAGCT 58.863 41.667 0.00 0.00 38.25 4.09
2913 7800 5.446143 TGCTGCTAGTAATCTTCTAGAGC 57.554 43.478 0.00 9.46 37.62 4.09
2914 7801 5.920273 GCTTGCTGCTAGTAATCTTCTAGAG 59.080 44.000 12.43 0.00 37.62 2.43
2915 7802 5.837437 GCTTGCTGCTAGTAATCTTCTAGA 58.163 41.667 12.43 0.00 37.62 2.43
2931 7818 9.708222 CTTGTGTAGTAAATTTATAGCTTGCTG 57.292 33.333 5.26 0.00 0.00 4.41
2953 7841 6.397272 TGCTTGTCATTTCTGTTTTTCTTGT 58.603 32.000 0.00 0.00 0.00 3.16
2958 7846 7.903995 TTTTCTGCTTGTCATTTCTGTTTTT 57.096 28.000 0.00 0.00 0.00 1.94
2973 7861 8.189119 TGTTGGGTAATAAGAATTTTCTGCTT 57.811 30.769 0.00 0.00 37.65 3.91
2983 8500 8.696374 TGTGAAATGTTTGTTGGGTAATAAGAA 58.304 29.630 0.00 0.00 0.00 2.52
2986 8503 8.258007 TGTTGTGAAATGTTTGTTGGGTAATAA 58.742 29.630 0.00 0.00 0.00 1.40
2999 8522 5.827797 ACTACAGGTCATGTTGTGAAATGTT 59.172 36.000 3.95 0.00 44.62 2.71
3019 8542 9.874205 CAGTAGTATAGTACCTGGAGATACTAC 57.126 40.741 24.72 24.72 46.99 2.73
3020 8543 9.612879 ACAGTAGTATAGTACCTGGAGATACTA 57.387 37.037 13.14 8.76 38.07 1.82
3021 8544 8.508969 ACAGTAGTATAGTACCTGGAGATACT 57.491 38.462 13.14 9.67 37.20 2.12
3064 8620 9.297586 CGCAAAGTTCTATACTTGTATTACTGA 57.702 33.333 0.00 0.00 46.34 3.41
3079 8635 1.337447 CCGGGAAGACGCAAAGTTCTA 60.337 52.381 0.00 0.00 0.00 2.10
3089 8645 2.742372 CAAGCCACCGGGAAGACG 60.742 66.667 6.32 0.00 35.59 4.18
3092 8648 1.472480 CAATAACAAGCCACCGGGAAG 59.528 52.381 6.32 0.00 35.59 3.46
3099 8655 4.870363 ACAACACATCAATAACAAGCCAC 58.130 39.130 0.00 0.00 0.00 5.01
3112 8668 8.114290 CGGTACATATGAAACTAACAACACATC 58.886 37.037 10.38 0.00 0.00 3.06
3137 8712 5.111989 TCTGGAATTTCATGTTAGCTCTCG 58.888 41.667 0.00 0.00 0.00 4.04
3228 8806 9.480861 AGATCCTCGATTCCTATAACAATATCA 57.519 33.333 0.00 0.00 0.00 2.15
3239 8817 9.760077 GTATTGTTAAAAGATCCTCGATTCCTA 57.240 33.333 0.00 0.00 0.00 2.94
3285 8863 1.929836 CTCTGTTGAGCCGTATCTTGC 59.070 52.381 0.00 0.00 33.12 4.01
3291 8869 3.746045 AGAAAACTCTGTTGAGCCGTA 57.254 42.857 0.00 0.00 43.85 4.02
3301 8879 9.067986 AGAGGGTATTGTTAAAAGAAAACTCTG 57.932 33.333 0.00 0.00 0.00 3.35
3323 8901 2.771943 TGCACTAACCATCCCTTAGAGG 59.228 50.000 0.00 0.00 34.30 3.69
3326 8904 5.680619 TGTATTGCACTAACCATCCCTTAG 58.319 41.667 0.00 0.00 0.00 2.18
3330 8908 5.652994 TTTTGTATTGCACTAACCATCCC 57.347 39.130 0.00 0.00 0.00 3.85
3331 8909 9.816354 ATTTATTTTGTATTGCACTAACCATCC 57.184 29.630 0.00 0.00 0.00 3.51
3334 8912 9.796120 GCTATTTATTTTGTATTGCACTAACCA 57.204 29.630 0.00 0.00 0.00 3.67
3335 8913 9.796120 TGCTATTTATTTTGTATTGCACTAACC 57.204 29.630 0.00 0.00 0.00 2.85
3339 8917 9.357652 CTGTTGCTATTTATTTTGTATTGCACT 57.642 29.630 0.00 0.00 31.59 4.40
3340 8918 9.139174 ACTGTTGCTATTTATTTTGTATTGCAC 57.861 29.630 0.00 0.00 31.59 4.57


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

AutoCloner maintained by Alex Coulton.