Multiple sequence alignment - TraesCS7D01G001400

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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 TraesCS7D01G001400 chr7D 100.000 3505 0 0 1 3505 1259902 1256398 0.000000e+00 6473.0
1 TraesCS7D01G001400 chr7D 84.593 2025 268 22 1489 3500 1017984 1015991 0.000000e+00 1971.0
2 TraesCS7D01G001400 chr7D 84.340 2037 279 27 1493 3505 1198096 1196076 0.000000e+00 1958.0
3 TraesCS7D01G001400 chr7D 86.538 312 38 2 999 1310 1018406 1018099 1.200000e-89 340.0
4 TraesCS7D01G001400 chr7D 85.350 314 41 5 1003 1316 550072499 550072807 1.570000e-83 320.0
5 TraesCS7D01G001400 chr7A 84.570 2521 328 34 1001 3505 1417032 1419507 0.000000e+00 2444.0
6 TraesCS7D01G001400 chr7A 84.289 2024 287 21 1497 3505 763551 761544 0.000000e+00 1947.0
7 TraesCS7D01G001400 chr7A 88.580 324 32 3 1001 1324 680422 680104 4.240000e-104 388.0
8 TraesCS7D01G001400 chr7A 88.814 295 22 6 592 885 1416577 1416861 5.570000e-93 351.0
9 TraesCS7D01G001400 chr7A 85.375 253 24 8 208 448 1415835 1416086 2.090000e-62 250.0
10 TraesCS7D01G001400 chr7A 84.426 122 11 6 1 121 1410003 1410117 2.860000e-21 113.0
11 TraesCS7D01G001400 chr4A 84.990 2012 276 12 1509 3505 743758615 743756615 0.000000e+00 2019.0
12 TraesCS7D01G001400 chr4A 84.352 2045 282 24 1493 3505 743128164 743126126 0.000000e+00 1969.0
13 TraesCS7D01G001400 chr4A 83.621 2027 284 26 1493 3505 744039646 744041638 0.000000e+00 1860.0
14 TraesCS7D01G001400 chr4A 82.575 2043 301 24 1493 3505 743648484 743646467 0.000000e+00 1749.0
15 TraesCS7D01G001400 chr4A 81.209 1059 150 25 2458 3505 743771264 743770244 0.000000e+00 808.0
16 TraesCS7D01G001400 chr4A 86.293 321 41 1 999 1319 743159116 743158799 2.590000e-91 346.0
17 TraesCS7D01G001400 chr3B 83.978 2041 285 19 1493 3505 747710653 747712679 0.000000e+00 1919.0
18 TraesCS7D01G001400 chr3B 89.420 293 28 1 998 1290 747709963 747710252 1.990000e-97 366.0
19 TraesCS7D01G001400 chrUn 83.944 2018 301 19 1498 3505 89024233 89022229 0.000000e+00 1910.0
20 TraesCS7D01G001400 chrUn 88.715 576 45 12 1 563 89026693 89026125 0.000000e+00 686.0
21 TraesCS7D01G001400 chrUn 85.515 573 77 4 2926 3495 51459511 51460080 8.380000e-166 593.0
22 TraesCS7D01G001400 chrUn 89.753 283 17 9 592 869 89025867 89025592 5.570000e-93 351.0
23 TraesCS7D01G001400 chrUn 87.097 186 13 5 592 777 89033064 89032890 2.130000e-47 200.0
24 TraesCS7D01G001400 chr7B 83.972 2034 262 36 1493 3499 59641145 59639149 0.000000e+00 1892.0
25 TraesCS7D01G001400 chr7B 85.143 350 46 4 981 1329 111325717 111325373 1.550000e-93 353.0
26 TraesCS7D01G001400 chr7B 89.209 278 30 0 1045 1322 59641482 59641205 7.200000e-92 348.0
27 TraesCS7D01G001400 chr6D 84.050 1047 132 17 2487 3505 433469984 433468945 0.000000e+00 976.0
28 TraesCS7D01G001400 chr6B 85.363 854 100 15 2655 3505 654643395 654642564 0.000000e+00 861.0
29 TraesCS7D01G001400 chr5D 89.342 319 32 2 1001 1318 464451182 464451499 1.960000e-107 399.0
30 TraesCS7D01G001400 chr5D 100.000 28 0 0 419 446 113380944 113380917 6.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G001400 chr7D 1256398 1259902 3504 True 6473.000000 6473 100.000000 1 3505 1 chr7D.!!$R2 3504
1 TraesCS7D01G001400 chr7D 1196076 1198096 2020 True 1958.000000 1958 84.340000 1493 3505 1 chr7D.!!$R1 2012
2 TraesCS7D01G001400 chr7D 1015991 1018406 2415 True 1155.500000 1971 85.565500 999 3500 2 chr7D.!!$R3 2501
3 TraesCS7D01G001400 chr7A 761544 763551 2007 True 1947.000000 1947 84.289000 1497 3505 1 chr7A.!!$R2 2008
4 TraesCS7D01G001400 chr7A 1415835 1419507 3672 False 1015.000000 2444 86.253000 208 3505 3 chr7A.!!$F2 3297
5 TraesCS7D01G001400 chr4A 743756615 743758615 2000 True 2019.000000 2019 84.990000 1509 3505 1 chr4A.!!$R4 1996
6 TraesCS7D01G001400 chr4A 743126126 743128164 2038 True 1969.000000 1969 84.352000 1493 3505 1 chr4A.!!$R1 2012
7 TraesCS7D01G001400 chr4A 744039646 744041638 1992 False 1860.000000 1860 83.621000 1493 3505 1 chr4A.!!$F1 2012
8 TraesCS7D01G001400 chr4A 743646467 743648484 2017 True 1749.000000 1749 82.575000 1493 3505 1 chr4A.!!$R3 2012
9 TraesCS7D01G001400 chr4A 743770244 743771264 1020 True 808.000000 808 81.209000 2458 3505 1 chr4A.!!$R5 1047
10 TraesCS7D01G001400 chr3B 747709963 747712679 2716 False 1142.500000 1919 86.699000 998 3505 2 chr3B.!!$F1 2507
11 TraesCS7D01G001400 chrUn 89022229 89026693 4464 True 982.333333 1910 87.470667 1 3505 3 chrUn.!!$R2 3504
12 TraesCS7D01G001400 chrUn 51459511 51460080 569 False 593.000000 593 85.515000 2926 3495 1 chrUn.!!$F1 569
13 TraesCS7D01G001400 chr7B 59639149 59641482 2333 True 1120.000000 1892 86.590500 1045 3499 2 chr7B.!!$R2 2454
14 TraesCS7D01G001400 chr6D 433468945 433469984 1039 True 976.000000 976 84.050000 2487 3505 1 chr6D.!!$R1 1018
15 TraesCS7D01G001400 chr6B 654642564 654643395 831 True 861.000000 861 85.363000 2655 3505 1 chr6B.!!$R1 850

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
969 1396 0.103026 CGCATCGGGAGAGTTCATCA 59.897 55.0 0.0 0.0 45.48 3.07 F
974 1401 0.179134 CGGGAGAGTTCATCACCGTC 60.179 60.0 0.0 0.0 42.45 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2409 3954 0.035056 AGTGCAGGTACAATCCCAGC 60.035 55.0 0.0 0.0 0.0 4.85 R
2868 4468 0.105039 GGAGTCGGGGAGCTACAATG 59.895 60.0 0.0 0.0 0.0 2.82 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
37 39 7.865706 ATGATGAACGAATACTTTTTAGGCT 57.134 32.000 0.00 0.00 0.00 4.58
44 46 5.064325 ACGAATACTTTTTAGGCTAAAGGCG 59.936 40.000 18.30 15.90 46.23 5.52
58 60 4.319549 GCTAAAGGCGTAGGTATGCAATTC 60.320 45.833 0.00 0.00 39.92 2.17
65 67 2.348411 AGGTATGCAATTCTTCCCCG 57.652 50.000 0.00 0.00 0.00 5.73
123 125 4.041723 GCCAATGGTACGCAATTATTCAC 58.958 43.478 0.00 0.00 0.00 3.18
128 130 7.415765 CCAATGGTACGCAATTATTCACCTTAA 60.416 37.037 0.00 0.00 0.00 1.85
129 131 7.817418 ATGGTACGCAATTATTCACCTTAAT 57.183 32.000 0.00 0.00 0.00 1.40
130 132 7.633193 TGGTACGCAATTATTCACCTTAATT 57.367 32.000 0.00 0.00 31.13 1.40
131 133 8.734218 TGGTACGCAATTATTCACCTTAATTA 57.266 30.769 0.00 0.00 30.18 1.40
229 231 9.099454 GTCTCTAGGTTTACAATTGTTATGAGG 57.901 37.037 17.78 2.94 0.00 3.86
232 234 9.226606 TCTAGGTTTACAATTGTTATGAGGTTG 57.773 33.333 17.78 0.96 0.00 3.77
352 360 2.853705 AGACTCGTAGGGCTGTAGATC 58.146 52.381 0.00 0.00 0.00 2.75
359 367 0.820074 AGGGCTGTAGATCGAGACCG 60.820 60.000 8.26 0.00 42.97 4.79
367 375 0.179134 AGATCGAGACCGCCTTTTCG 60.179 55.000 0.00 0.00 35.37 3.46
368 376 1.753468 GATCGAGACCGCCTTTTCGC 61.753 60.000 0.00 0.00 35.37 4.70
378 386 0.955905 GCCTTTTCGCAAACTACCCA 59.044 50.000 0.00 0.00 0.00 4.51
453 466 8.783660 TCTCTCCAATCCATATTACTACTTGT 57.216 34.615 0.00 0.00 0.00 3.16
454 467 9.213777 TCTCTCCAATCCATATTACTACTTGTT 57.786 33.333 0.00 0.00 0.00 2.83
456 469 8.768397 TCTCCAATCCATATTACTACTTGTTGT 58.232 33.333 0.00 0.00 0.00 3.32
469 599 6.351327 CTACTTGTTGTAGCTTTATGGAGC 57.649 41.667 0.00 0.00 41.68 4.70
493 623 6.541278 GCGTAGGGAGTAATTTTATTTGGTCT 59.459 38.462 0.00 0.00 0.00 3.85
496 626 7.939784 AGGGAGTAATTTTATTTGGTCTGTC 57.060 36.000 0.00 0.00 0.00 3.51
527 657 1.604278 CGCGTCCTCTGTCTATCATCA 59.396 52.381 0.00 0.00 0.00 3.07
528 658 2.227626 CGCGTCCTCTGTCTATCATCAT 59.772 50.000 0.00 0.00 0.00 2.45
529 659 3.573598 GCGTCCTCTGTCTATCATCATG 58.426 50.000 0.00 0.00 0.00 3.07
539 669 3.993081 GTCTATCATCATGCCCGAGAAAG 59.007 47.826 0.00 0.00 0.00 2.62
542 672 0.749091 CATCATGCCCGAGAAAGCCA 60.749 55.000 0.00 0.00 0.00 4.75
548 678 1.460273 GCCCGAGAAAGCCAAAACCA 61.460 55.000 0.00 0.00 0.00 3.67
550 680 1.269569 CCCGAGAAAGCCAAAACCAAC 60.270 52.381 0.00 0.00 0.00 3.77
551 681 1.407258 CCGAGAAAGCCAAAACCAACA 59.593 47.619 0.00 0.00 0.00 3.33
552 682 2.459934 CGAGAAAGCCAAAACCAACAC 58.540 47.619 0.00 0.00 0.00 3.32
553 683 2.099098 CGAGAAAGCCAAAACCAACACT 59.901 45.455 0.00 0.00 0.00 3.55
554 684 3.706698 GAGAAAGCCAAAACCAACACTC 58.293 45.455 0.00 0.00 0.00 3.51
555 685 3.096092 AGAAAGCCAAAACCAACACTCA 58.904 40.909 0.00 0.00 0.00 3.41
556 686 2.959507 AAGCCAAAACCAACACTCAC 57.040 45.000 0.00 0.00 0.00 3.51
557 687 1.111277 AGCCAAAACCAACACTCACC 58.889 50.000 0.00 0.00 0.00 4.02
558 688 1.111277 GCCAAAACCAACACTCACCT 58.889 50.000 0.00 0.00 0.00 4.00
559 689 2.092103 AGCCAAAACCAACACTCACCTA 60.092 45.455 0.00 0.00 0.00 3.08
560 690 2.034179 GCCAAAACCAACACTCACCTAC 59.966 50.000 0.00 0.00 0.00 3.18
561 691 2.621526 CCAAAACCAACACTCACCTACC 59.378 50.000 0.00 0.00 0.00 3.18
562 692 3.551846 CAAAACCAACACTCACCTACCT 58.448 45.455 0.00 0.00 0.00 3.08
563 693 4.445162 CCAAAACCAACACTCACCTACCTA 60.445 45.833 0.00 0.00 0.00 3.08
564 694 5.127491 CAAAACCAACACTCACCTACCTAA 58.873 41.667 0.00 0.00 0.00 2.69
565 695 5.578157 AAACCAACACTCACCTACCTAAT 57.422 39.130 0.00 0.00 0.00 1.73
566 696 6.691255 AAACCAACACTCACCTACCTAATA 57.309 37.500 0.00 0.00 0.00 0.98
567 697 5.934402 ACCAACACTCACCTACCTAATAG 57.066 43.478 0.00 0.00 0.00 1.73
570 700 3.990369 ACACTCACCTACCTAATAGCCA 58.010 45.455 0.00 0.00 0.00 4.75
584 714 2.024176 TAGCCAACCTGGTGAGAGAA 57.976 50.000 0.00 0.00 40.46 2.87
586 716 0.957888 GCCAACCTGGTGAGAGAAGC 60.958 60.000 0.00 0.00 40.46 3.86
587 717 0.671781 CCAACCTGGTGAGAGAAGCG 60.672 60.000 0.00 0.00 31.35 4.68
619 991 9.918630 ATGTTCAGAGGTTGATTTTGAAATTAG 57.081 29.630 0.00 0.00 35.27 1.73
714 1086 9.554395 TCAAAATCAAATTTAAAGGGAGGAAAC 57.446 29.630 0.00 0.00 0.00 2.78
715 1087 9.336171 CAAAATCAAATTTAAAGGGAGGAAACA 57.664 29.630 0.00 0.00 0.00 2.83
716 1088 9.913310 AAAATCAAATTTAAAGGGAGGAAACAA 57.087 25.926 0.00 0.00 0.00 2.83
717 1089 8.902540 AATCAAATTTAAAGGGAGGAAACAAC 57.097 30.769 0.00 0.00 0.00 3.32
718 1090 7.425224 TCAAATTTAAAGGGAGGAAACAACA 57.575 32.000 0.00 0.00 0.00 3.33
743 1115 7.175467 CAGCAATCCATTTAATACTAGATGCCA 59.825 37.037 0.00 0.00 0.00 4.92
807 1179 4.735369 TCTTAAAATCTGTGGGAAGCCAA 58.265 39.130 0.00 0.00 0.00 4.52
860 1232 7.345691 TGGTGCAAAATCCTGAAATAGATAGA 58.654 34.615 0.00 0.00 0.00 1.98
890 1262 9.710900 TTGAATATGCCATACAAGATAGTACTG 57.289 33.333 5.39 0.00 0.00 2.74
925 1326 2.012902 GCCTCTGCAATCATGTGGCC 62.013 60.000 0.00 0.00 37.47 5.36
926 1327 1.721664 CCTCTGCAATCATGTGGCCG 61.722 60.000 0.00 0.00 0.00 6.13
927 1328 1.002257 TCTGCAATCATGTGGCCGT 60.002 52.632 0.00 0.00 0.00 5.68
930 1331 0.680601 TGCAATCATGTGGCCGTCAT 60.681 50.000 7.32 7.32 0.00 3.06
931 1332 1.308047 GCAATCATGTGGCCGTCATA 58.692 50.000 11.94 3.64 0.00 2.15
932 1333 1.002468 GCAATCATGTGGCCGTCATAC 60.002 52.381 11.94 0.00 0.00 2.39
936 1337 2.384828 TCATGTGGCCGTCATACTACT 58.615 47.619 11.94 0.00 0.00 2.57
937 1338 3.558033 TCATGTGGCCGTCATACTACTA 58.442 45.455 11.94 0.00 0.00 1.82
940 1341 2.686405 TGTGGCCGTCATACTACTAGTG 59.314 50.000 5.39 0.00 0.00 2.74
941 1342 2.686915 GTGGCCGTCATACTACTAGTGT 59.313 50.000 5.39 4.48 0.00 3.55
942 1343 3.879295 GTGGCCGTCATACTACTAGTGTA 59.121 47.826 5.39 6.64 0.00 2.90
946 1347 5.936956 GGCCGTCATACTACTAGTGTACTAT 59.063 44.000 5.39 0.00 0.00 2.12
948 1349 7.360776 GGCCGTCATACTACTAGTGTACTATTC 60.361 44.444 5.39 0.00 0.00 1.75
950 1351 8.924691 CCGTCATACTACTAGTGTACTATTCTC 58.075 40.741 5.39 0.00 0.00 2.87
969 1396 0.103026 CGCATCGGGAGAGTTCATCA 59.897 55.000 0.00 0.00 45.48 3.07
970 1397 1.576356 GCATCGGGAGAGTTCATCAC 58.424 55.000 0.00 0.00 45.48 3.06
971 1398 1.808133 GCATCGGGAGAGTTCATCACC 60.808 57.143 0.00 0.00 45.48 4.02
974 1401 0.179134 CGGGAGAGTTCATCACCGTC 60.179 60.000 0.00 0.00 42.45 4.79
975 1402 0.895530 GGGAGAGTTCATCACCGTCA 59.104 55.000 0.00 0.00 39.44 4.35
976 1403 1.404315 GGGAGAGTTCATCACCGTCAC 60.404 57.143 0.00 0.00 39.44 3.67
977 1404 1.404315 GGAGAGTTCATCACCGTCACC 60.404 57.143 0.00 0.00 0.00 4.02
978 1405 1.546476 GAGAGTTCATCACCGTCACCT 59.454 52.381 0.00 0.00 0.00 4.00
979 1406 1.273606 AGAGTTCATCACCGTCACCTG 59.726 52.381 0.00 0.00 0.00 4.00
980 1407 0.320771 AGTTCATCACCGTCACCTGC 60.321 55.000 0.00 0.00 0.00 4.85
981 1408 1.003839 TTCATCACCGTCACCTGCC 60.004 57.895 0.00 0.00 0.00 4.85
982 1409 2.779951 TTCATCACCGTCACCTGCCG 62.780 60.000 0.00 0.00 0.00 5.69
1343 2869 6.267471 TGTCCTGCCTTTCAATTTCAGTTTAT 59.733 34.615 0.00 0.00 0.00 1.40
1344 2870 7.154656 GTCCTGCCTTTCAATTTCAGTTTATT 58.845 34.615 0.00 0.00 0.00 1.40
1345 2871 7.657354 GTCCTGCCTTTCAATTTCAGTTTATTT 59.343 33.333 0.00 0.00 0.00 1.40
1350 2876 9.650371 GCCTTTCAATTTCAGTTTATTTGTTTC 57.350 29.630 0.00 0.00 0.00 2.78
1373 2899 6.355747 TCCAATTGGAAATGCAAGTCTTTTT 58.644 32.000 25.13 0.00 42.18 1.94
1375 2901 7.656948 TCCAATTGGAAATGCAAGTCTTTTTAG 59.343 33.333 25.13 0.00 42.18 1.85
1379 2905 8.419076 TTGGAAATGCAAGTCTTTTTAGTTTC 57.581 30.769 0.00 0.00 0.00 2.78
1380 2906 7.551585 TGGAAATGCAAGTCTTTTTAGTTTCA 58.448 30.769 0.00 0.00 0.00 2.69
1381 2907 7.706179 TGGAAATGCAAGTCTTTTTAGTTTCAG 59.294 33.333 0.00 0.00 0.00 3.02
1382 2908 7.706607 GGAAATGCAAGTCTTTTTAGTTTCAGT 59.293 33.333 0.00 0.00 0.00 3.41
1383 2909 9.087424 GAAATGCAAGTCTTTTTAGTTTCAGTT 57.913 29.630 0.00 0.00 0.00 3.16
1384 2910 9.435688 AAATGCAAGTCTTTTTAGTTTCAGTTT 57.564 25.926 0.00 0.00 0.00 2.66
1387 2913 9.567848 TGCAAGTCTTTTTAGTTTCAGTTTAAG 57.432 29.630 0.00 0.00 0.00 1.85
1404 2938 9.267084 TCAGTTTAAGGTTTTAATTGGAAATGC 57.733 29.630 0.00 0.00 0.00 3.56
1413 2947 6.799926 TTTAATTGGAAATGCAAGCCTTTC 57.200 33.333 12.49 12.49 32.37 2.62
1423 2957 5.726980 ATGCAAGCCTTTCAATTTCTGTA 57.273 34.783 0.00 0.00 0.00 2.74
1424 2958 5.125100 TGCAAGCCTTTCAATTTCTGTAG 57.875 39.130 0.00 0.00 0.00 2.74
1425 2959 4.826733 TGCAAGCCTTTCAATTTCTGTAGA 59.173 37.500 0.00 0.00 0.00 2.59
1426 2960 5.048504 TGCAAGCCTTTCAATTTCTGTAGAG 60.049 40.000 0.00 0.00 0.00 2.43
1427 2961 5.620879 GCAAGCCTTTCAATTTCTGTAGAGG 60.621 44.000 0.00 0.00 0.00 3.69
1428 2962 4.593956 AGCCTTTCAATTTCTGTAGAGGG 58.406 43.478 0.00 0.00 0.00 4.30
1429 2963 3.129462 GCCTTTCAATTTCTGTAGAGGGC 59.871 47.826 0.00 0.00 0.00 5.19
1430 2964 4.593956 CCTTTCAATTTCTGTAGAGGGCT 58.406 43.478 0.00 0.00 0.00 5.19
1431 2965 5.012893 CCTTTCAATTTCTGTAGAGGGCTT 58.987 41.667 0.00 0.00 0.00 4.35
1434 2968 5.241403 TCAATTTCTGTAGAGGGCTTTCA 57.759 39.130 0.00 0.00 0.00 2.69
1447 2981 4.106324 AGGGCTTTCATTTGGAAATGGAT 58.894 39.130 11.30 0.00 44.18 3.41
1448 2982 4.162888 AGGGCTTTCATTTGGAAATGGATC 59.837 41.667 11.30 0.00 44.18 3.36
1449 2983 4.114794 GGCTTTCATTTGGAAATGGATCG 58.885 43.478 11.30 0.67 44.18 3.69
1450 2984 4.114794 GCTTTCATTTGGAAATGGATCGG 58.885 43.478 11.30 0.23 44.18 4.18
1451 2985 4.142182 GCTTTCATTTGGAAATGGATCGGA 60.142 41.667 11.30 0.00 44.18 4.55
1453 2987 5.581126 TTCATTTGGAAATGGATCGGAAG 57.419 39.130 11.30 0.00 44.51 3.46
1455 2989 1.762708 TTGGAAATGGATCGGAAGCC 58.237 50.000 0.00 0.00 0.00 4.35
1460 2994 2.806945 AATGGATCGGAAGCCTTTCA 57.193 45.000 2.56 0.00 34.90 2.69
1467 3001 4.082245 GGATCGGAAGCCTTTCAATTTCAA 60.082 41.667 0.00 0.00 34.90 2.69
1468 3002 5.394553 GGATCGGAAGCCTTTCAATTTCAAT 60.395 40.000 0.00 0.00 34.90 2.57
1471 3005 5.695816 TCGGAAGCCTTTCAATTTCAATTTG 59.304 36.000 0.00 0.00 34.90 2.32
1472 3006 5.466393 CGGAAGCCTTTCAATTTCAATTTGT 59.534 36.000 0.00 0.00 34.90 2.83
1473 3007 6.018016 CGGAAGCCTTTCAATTTCAATTTGTT 60.018 34.615 0.00 0.00 34.90 2.83
1474 3008 7.467131 CGGAAGCCTTTCAATTTCAATTTGTTT 60.467 33.333 0.00 0.00 34.90 2.83
1475 3009 7.644945 GGAAGCCTTTCAATTTCAATTTGTTTG 59.355 33.333 0.00 0.79 34.90 2.93
1476 3010 7.628769 AGCCTTTCAATTTCAATTTGTTTGT 57.371 28.000 0.00 0.00 36.65 2.83
1477 3011 8.054152 AGCCTTTCAATTTCAATTTGTTTGTT 57.946 26.923 0.00 0.00 36.65 2.83
1479 3013 8.585436 GCCTTTCAATTTCAATTTGTTTGTTTG 58.415 29.630 0.00 0.00 36.65 2.93
1480 3014 9.623350 CCTTTCAATTTCAATTTGTTTGTTTGT 57.377 25.926 0.00 0.00 36.65 2.83
1484 3018 9.956720 TCAATTTCAATTTGTTTGTTTGTTTGT 57.043 22.222 0.00 0.00 36.65 2.83
1488 3022 9.573133 TTTCAATTTGTTTGTTTGTTTGTTTGT 57.427 22.222 0.00 0.00 36.65 2.83
1490 3024 9.573133 TCAATTTGTTTGTTTGTTTGTTTGTTT 57.427 22.222 0.00 0.00 36.65 2.83
1523 3057 1.565759 TCATTTCAGGTGCTGGGCTAT 59.434 47.619 0.00 0.00 31.51 2.97
1639 3173 5.008217 TGAACAATTTCCACTTCCTACAACG 59.992 40.000 0.00 0.00 0.00 4.10
1701 3235 4.989279 TGTGTCGATGAATCAGAGATCA 57.011 40.909 0.00 0.00 0.00 2.92
1772 3312 5.003160 CACTCCAACAACAGTAATGATGGA 58.997 41.667 5.42 8.08 44.50 3.41
1773 3313 5.003804 ACTCCAACAACAGTAATGATGGAC 58.996 41.667 5.42 0.00 42.63 4.02
1880 3422 4.624024 GTGATGCATCATTTTGAGTTGGTG 59.376 41.667 30.89 0.00 39.30 4.17
1909 3451 3.198068 TCTGTGTCTCTGACAAGTTTGC 58.802 45.455 1.73 0.00 44.49 3.68
1918 3460 4.245660 TCTGACAAGTTTGCTATCGAAGG 58.754 43.478 0.00 0.00 0.00 3.46
1976 3518 2.622064 AGTGTGGTTTGACTCAGACC 57.378 50.000 11.17 11.17 38.84 3.85
1994 3536 2.031516 CGAGGCACTGCACAAGGAG 61.032 63.158 2.82 0.00 41.55 3.69
2085 3627 4.862902 AAGTGGGACGATATGAGATCAG 57.137 45.455 0.00 0.00 0.00 2.90
2106 3648 2.270257 TTGTGCTCACATGCTGGCC 61.270 57.895 3.31 0.00 41.52 5.36
2107 3649 2.360852 GTGCTCACATGCTGGCCT 60.361 61.111 3.32 0.00 0.00 5.19
2116 3658 0.833287 CATGCTGGCCTAGGTAGTGT 59.167 55.000 11.31 0.43 0.00 3.55
2141 3683 3.782244 GTGACAAGCCGCAGCGAG 61.782 66.667 18.75 7.72 46.67 5.03
2225 3767 4.796038 ATCATGGGAGCTTTTTCACAAG 57.204 40.909 0.00 0.00 33.48 3.16
2264 3806 5.183904 GGAAGCAGAAAAGCAAGAGGAATTA 59.816 40.000 0.00 0.00 36.85 1.40
2279 3821 8.522830 CAAGAGGAATTAGTTTCAATGGCTAAA 58.477 33.333 0.00 0.00 35.94 1.85
2312 3854 3.274288 CAAGTGTAAGGGATTGCCTCTC 58.726 50.000 0.00 0.00 0.00 3.20
2354 3896 4.377022 GCTTTACTTCGTTCGAAGCATCAA 60.377 41.667 27.36 16.55 43.76 2.57
2409 3954 2.208431 GGAAGAATGACATCCTCGCAG 58.792 52.381 0.00 0.00 34.02 5.18
2466 4011 5.428496 TCACTTGTCATCAGAAGCAAAAG 57.572 39.130 0.00 0.00 0.00 2.27
2557 4102 8.416329 AGTTATGGATGGCAAATGACTTTATTC 58.584 33.333 0.00 0.00 0.00 1.75
2766 4359 7.228108 TCCATTCTACAAGAATCTTCATCATGC 59.772 37.037 0.00 0.00 42.67 4.06
2787 4380 3.194116 GCCAAGAAATTCTGCAAGGATCA 59.806 43.478 0.00 0.00 22.58 2.92
2808 4408 6.968131 TCAACAGATAGTTCATTACAGCAC 57.032 37.500 0.00 0.00 38.74 4.40
2830 4430 4.331717 ACGAAGTTCGACATTTGTCACTTT 59.668 37.500 30.77 0.74 43.74 2.66
2868 4468 3.550437 ACTATTGCAGTCATGGAGGAC 57.450 47.619 0.00 0.00 38.08 3.85
2872 4472 2.118313 TGCAGTCATGGAGGACATTG 57.882 50.000 0.00 0.00 40.29 2.82
2885 4485 0.824759 GACATTGTAGCTCCCCGACT 59.175 55.000 0.00 0.00 0.00 4.18
2893 4493 3.461773 CTCCCCGACTCCGCACAT 61.462 66.667 0.00 0.00 0.00 3.21
2923 4541 4.431661 CAAAAGGAGTTGGAGCAGATTC 57.568 45.455 0.00 0.00 0.00 2.52
2934 4570 3.949132 GGAGCAGATTCAGACTCCTTTT 58.051 45.455 10.69 0.00 44.41 2.27
2955 4591 7.877612 CCTTTTAGTATGGCCAAGTCAAAATTT 59.122 33.333 10.96 0.00 0.00 1.82
3009 4645 9.500785 TCAATCAAGACACATATGACAAACTTA 57.499 29.630 10.38 0.00 0.00 2.24
3132 4768 9.811995 GGTTGTGAAAAACTTAAGAAATTACCT 57.188 29.630 10.09 0.00 0.00 3.08
3270 4906 3.812262 TGTCATTGATAGTGATGCAGGG 58.188 45.455 0.00 0.00 0.00 4.45
3309 4945 7.573968 ACTCAAATATTTGAATCTAGGTGGC 57.426 36.000 26.57 0.00 45.61 5.01
3369 5005 3.676646 CAGAAAATGCTAAACAAGGCAGC 59.323 43.478 0.00 0.00 41.88 5.25
3421 5060 3.127030 GTCACTCGATTGGGAAAATGGAC 59.873 47.826 2.65 0.00 0.00 4.02
3422 5061 2.423538 CACTCGATTGGGAAAATGGACC 59.576 50.000 0.00 0.00 0.00 4.46
3455 5097 4.209911 CACACATGCTGGATATGAAGTACG 59.790 45.833 0.00 0.00 0.00 3.67
3460 5102 6.646653 ACATGCTGGATATGAAGTACGTAATG 59.353 38.462 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 19 7.361457 GCCTTTAGCCTAAAAAGTATTCGTTCA 60.361 37.037 0.00 0.00 33.05 3.18
37 39 5.031066 AGAATTGCATACCTACGCCTTTA 57.969 39.130 0.00 0.00 0.00 1.85
44 46 3.139077 CGGGGAAGAATTGCATACCTAC 58.861 50.000 0.00 0.00 38.65 3.18
58 60 8.424918 AGCTATAAATATCATGATACGGGGAAG 58.575 37.037 17.60 11.61 0.00 3.46
173 175 3.637229 TGATCTTGGCAGGTAGTACTAGC 59.363 47.826 21.85 21.85 0.00 3.42
177 179 4.572389 CACATTGATCTTGGCAGGTAGTAC 59.428 45.833 0.00 0.00 0.00 2.73
247 254 7.029563 GCCACATCGATTTGAGTTAATTTCTT 58.970 34.615 13.10 0.00 0.00 2.52
327 335 1.686110 AGCCCTACGAGTCTTGGGG 60.686 63.158 13.26 13.26 39.99 4.96
330 338 2.366533 TCTACAGCCCTACGAGTCTTG 58.633 52.381 0.00 0.00 0.00 3.02
352 360 1.837538 TTTGCGAAAAGGCGGTCTCG 61.838 55.000 0.00 0.00 39.81 4.04
359 367 0.955905 TGGGTAGTTTGCGAAAAGGC 59.044 50.000 0.00 0.00 0.00 4.35
429 442 9.265901 CAACAAGTAGTAATATGGATTGGAGAG 57.734 37.037 0.00 0.00 0.00 3.20
448 461 3.684788 CGCTCCATAAAGCTACAACAAGT 59.315 43.478 0.00 0.00 40.23 3.16
449 462 3.684788 ACGCTCCATAAAGCTACAACAAG 59.315 43.478 0.00 0.00 40.23 3.16
451 464 3.328382 ACGCTCCATAAAGCTACAACA 57.672 42.857 0.00 0.00 40.23 3.33
453 466 3.181469 CCCTACGCTCCATAAAGCTACAA 60.181 47.826 0.00 0.00 40.23 2.41
454 467 2.364324 CCCTACGCTCCATAAAGCTACA 59.636 50.000 0.00 0.00 40.23 2.74
456 469 2.891580 CTCCCTACGCTCCATAAAGCTA 59.108 50.000 0.00 0.00 40.23 3.32
457 470 1.689273 CTCCCTACGCTCCATAAAGCT 59.311 52.381 0.00 0.00 40.23 3.74
458 471 1.413077 ACTCCCTACGCTCCATAAAGC 59.587 52.381 0.00 0.00 38.97 3.51
459 472 4.931661 TTACTCCCTACGCTCCATAAAG 57.068 45.455 0.00 0.00 0.00 1.85
460 473 5.881923 AATTACTCCCTACGCTCCATAAA 57.118 39.130 0.00 0.00 0.00 1.40
461 474 5.881923 AAATTACTCCCTACGCTCCATAA 57.118 39.130 0.00 0.00 0.00 1.90
463 476 4.772886 AAAATTACTCCCTACGCTCCAT 57.227 40.909 0.00 0.00 0.00 3.41
464 477 5.881923 ATAAAATTACTCCCTACGCTCCA 57.118 39.130 0.00 0.00 0.00 3.86
465 478 6.017357 CCAAATAAAATTACTCCCTACGCTCC 60.017 42.308 0.00 0.00 0.00 4.70
469 599 7.551617 ACAGACCAAATAAAATTACTCCCTACG 59.448 37.037 0.00 0.00 0.00 3.51
527 657 0.603065 GTTTTGGCTTTCTCGGGCAT 59.397 50.000 0.00 0.00 38.95 4.40
528 658 1.460273 GGTTTTGGCTTTCTCGGGCA 61.460 55.000 0.00 0.00 37.47 5.36
529 659 1.289066 GGTTTTGGCTTTCTCGGGC 59.711 57.895 0.00 0.00 0.00 6.13
539 669 1.111277 AGGTGAGTGTTGGTTTTGGC 58.889 50.000 0.00 0.00 0.00 4.52
542 672 3.945640 AGGTAGGTGAGTGTTGGTTTT 57.054 42.857 0.00 0.00 0.00 2.43
548 678 4.359105 TGGCTATTAGGTAGGTGAGTGTT 58.641 43.478 0.00 0.00 0.00 3.32
550 680 4.443034 GGTTGGCTATTAGGTAGGTGAGTG 60.443 50.000 0.00 0.00 0.00 3.51
551 681 3.710165 GGTTGGCTATTAGGTAGGTGAGT 59.290 47.826 0.00 0.00 0.00 3.41
552 682 3.967987 AGGTTGGCTATTAGGTAGGTGAG 59.032 47.826 0.00 0.00 0.00 3.51
553 683 3.709653 CAGGTTGGCTATTAGGTAGGTGA 59.290 47.826 0.00 0.00 0.00 4.02
554 684 3.181454 CCAGGTTGGCTATTAGGTAGGTG 60.181 52.174 0.00 0.00 0.00 4.00
555 685 3.046374 CCAGGTTGGCTATTAGGTAGGT 58.954 50.000 0.00 0.00 0.00 3.08
556 686 3.046374 ACCAGGTTGGCTATTAGGTAGG 58.954 50.000 0.00 0.00 42.67 3.18
557 687 3.709653 TCACCAGGTTGGCTATTAGGTAG 59.290 47.826 0.00 0.00 42.67 3.18
558 688 3.709653 CTCACCAGGTTGGCTATTAGGTA 59.290 47.826 0.00 0.00 42.67 3.08
559 689 2.505819 CTCACCAGGTTGGCTATTAGGT 59.494 50.000 0.00 0.00 42.67 3.08
560 690 2.771943 TCTCACCAGGTTGGCTATTAGG 59.228 50.000 0.00 0.00 42.67 2.69
561 691 3.706594 TCTCTCACCAGGTTGGCTATTAG 59.293 47.826 0.00 0.00 42.67 1.73
562 692 3.719871 TCTCTCACCAGGTTGGCTATTA 58.280 45.455 0.00 0.00 42.67 0.98
563 693 2.551270 TCTCTCACCAGGTTGGCTATT 58.449 47.619 0.00 0.00 42.67 1.73
564 694 2.254152 TCTCTCACCAGGTTGGCTAT 57.746 50.000 0.00 0.00 42.67 2.97
565 695 1.902508 CTTCTCTCACCAGGTTGGCTA 59.097 52.381 0.00 0.00 42.67 3.93
566 696 0.689623 CTTCTCTCACCAGGTTGGCT 59.310 55.000 0.00 0.00 42.67 4.75
567 697 0.957888 GCTTCTCTCACCAGGTTGGC 60.958 60.000 0.00 0.00 42.67 4.52
570 700 0.034059 CACGCTTCTCTCACCAGGTT 59.966 55.000 0.00 0.00 0.00 3.50
584 714 1.276421 ACCTCTGAACATTAGCACGCT 59.724 47.619 0.00 0.00 0.00 5.07
586 716 3.325870 TCAACCTCTGAACATTAGCACG 58.674 45.455 0.00 0.00 0.00 5.34
587 717 5.886960 AATCAACCTCTGAACATTAGCAC 57.113 39.130 0.00 0.00 37.67 4.40
704 1076 2.519013 GATTGCTGTTGTTTCCTCCCT 58.481 47.619 0.00 0.00 0.00 4.20
707 1079 4.525912 AATGGATTGCTGTTGTTTCCTC 57.474 40.909 0.00 0.00 0.00 3.71
708 1080 4.961438 AAATGGATTGCTGTTGTTTCCT 57.039 36.364 0.00 0.00 0.00 3.36
710 1082 8.986477 AGTATTAAATGGATTGCTGTTGTTTC 57.014 30.769 0.00 0.00 0.00 2.78
713 1085 9.632638 ATCTAGTATTAAATGGATTGCTGTTGT 57.367 29.630 0.00 0.00 0.00 3.32
714 1086 9.888878 CATCTAGTATTAAATGGATTGCTGTTG 57.111 33.333 0.00 0.00 0.00 3.33
715 1087 8.571336 GCATCTAGTATTAAATGGATTGCTGTT 58.429 33.333 0.00 0.00 0.00 3.16
716 1088 7.175641 GGCATCTAGTATTAAATGGATTGCTGT 59.824 37.037 0.00 0.00 0.00 4.40
717 1089 7.175467 TGGCATCTAGTATTAAATGGATTGCTG 59.825 37.037 0.00 0.00 0.00 4.41
718 1090 7.233632 TGGCATCTAGTATTAAATGGATTGCT 58.766 34.615 0.00 0.00 0.00 3.91
743 1115 7.206981 AGAGATTTCACGTGTTTCATTTCAT 57.793 32.000 16.51 0.00 0.00 2.57
783 1155 3.696548 GGCTTCCCACAGATTTTAAGAGG 59.303 47.826 0.00 0.00 0.00 3.69
872 1244 6.816640 TGTTGAACAGTACTATCTTGTATGGC 59.183 38.462 0.00 0.00 0.00 4.40
873 1245 8.771920 TTGTTGAACAGTACTATCTTGTATGG 57.228 34.615 0.00 0.00 0.00 2.74
874 1246 9.639601 TCTTGTTGAACAGTACTATCTTGTATG 57.360 33.333 0.00 0.00 0.00 2.39
882 1254 9.765795 GGCTATTATCTTGTTGAACAGTACTAT 57.234 33.333 0.00 0.00 0.00 2.12
883 1255 8.978472 AGGCTATTATCTTGTTGAACAGTACTA 58.022 33.333 0.00 0.00 0.00 1.82
884 1256 7.852263 AGGCTATTATCTTGTTGAACAGTACT 58.148 34.615 0.00 0.00 0.00 2.73
885 1257 7.982354 AGAGGCTATTATCTTGTTGAACAGTAC 59.018 37.037 0.00 0.00 0.00 2.73
886 1258 7.981789 CAGAGGCTATTATCTTGTTGAACAGTA 59.018 37.037 0.00 0.00 0.00 2.74
887 1259 6.820656 CAGAGGCTATTATCTTGTTGAACAGT 59.179 38.462 0.00 0.00 0.00 3.55
888 1260 6.238320 GCAGAGGCTATTATCTTGTTGAACAG 60.238 42.308 0.00 0.00 36.96 3.16
889 1261 5.586243 GCAGAGGCTATTATCTTGTTGAACA 59.414 40.000 0.00 0.00 36.96 3.18
890 1262 5.586243 TGCAGAGGCTATTATCTTGTTGAAC 59.414 40.000 0.00 0.00 41.91 3.18
925 1326 8.637704 CGAGAATAGTACACTAGTAGTATGACG 58.362 40.741 1.57 0.00 43.01 4.35
926 1327 8.434661 GCGAGAATAGTACACTAGTAGTATGAC 58.565 40.741 1.57 1.73 43.01 3.06
927 1328 8.146412 TGCGAGAATAGTACACTAGTAGTATGA 58.854 37.037 1.57 0.00 43.01 2.15
930 1331 7.328005 CGATGCGAGAATAGTACACTAGTAGTA 59.672 40.741 1.57 0.00 39.70 1.82
931 1332 6.145858 CGATGCGAGAATAGTACACTAGTAGT 59.854 42.308 0.00 0.00 37.61 2.73
932 1333 6.401260 CCGATGCGAGAATAGTACACTAGTAG 60.401 46.154 0.00 0.00 0.00 2.57
936 1337 3.501062 CCCGATGCGAGAATAGTACACTA 59.499 47.826 0.00 0.00 0.00 2.74
937 1338 2.293677 CCCGATGCGAGAATAGTACACT 59.706 50.000 0.00 0.00 0.00 3.55
940 1341 2.812591 TCTCCCGATGCGAGAATAGTAC 59.187 50.000 0.00 0.00 33.44 2.73
941 1342 3.075148 CTCTCCCGATGCGAGAATAGTA 58.925 50.000 0.00 0.00 35.98 1.82
942 1343 1.883275 CTCTCCCGATGCGAGAATAGT 59.117 52.381 0.00 0.00 35.98 2.12
946 1347 0.456221 GAACTCTCCCGATGCGAGAA 59.544 55.000 0.00 0.00 35.98 2.87
948 1349 0.387202 ATGAACTCTCCCGATGCGAG 59.613 55.000 0.00 0.00 0.00 5.03
950 1351 0.103026 TGATGAACTCTCCCGATGCG 59.897 55.000 0.00 0.00 0.00 4.73
986 1413 2.202987 CCATCTGGGAGCAGTCGC 60.203 66.667 0.00 0.00 40.01 5.19
988 1415 0.463474 GAAGCCATCTGGGAGCAGTC 60.463 60.000 0.00 0.00 40.01 3.51
993 1420 1.530771 CAGGGAAGCCATCTGGGAG 59.469 63.158 0.00 0.00 40.01 4.30
995 1422 2.123982 GCAGGGAAGCCATCTGGG 60.124 66.667 0.00 0.00 40.85 4.45
996 1423 1.153005 GAGCAGGGAAGCCATCTGG 60.153 63.158 0.00 0.00 38.53 3.86
1183 2148 3.637273 GTCCTTGACCCACCGGCT 61.637 66.667 0.00 0.00 0.00 5.52
1277 2245 4.335647 AGCAGCGGTGGAACTGGG 62.336 66.667 17.54 0.00 45.56 4.45
1278 2246 2.743928 GAGCAGCGGTGGAACTGG 60.744 66.667 17.54 0.00 45.56 4.00
1282 2250 4.680237 CGTGGAGCAGCGGTGGAA 62.680 66.667 17.54 0.00 0.00 3.53
1350 2876 6.622833 AAAAAGACTTGCATTTCCAATTGG 57.377 33.333 19.08 19.08 0.00 3.16
1353 2879 8.962884 AAACTAAAAAGACTTGCATTTCCAAT 57.037 26.923 0.00 0.00 0.00 3.16
1379 2905 9.050601 TGCATTTCCAATTAAAACCTTAAACTG 57.949 29.630 0.00 0.00 30.87 3.16
1380 2906 9.620259 TTGCATTTCCAATTAAAACCTTAAACT 57.380 25.926 0.00 0.00 30.87 2.66
1381 2907 9.877137 CTTGCATTTCCAATTAAAACCTTAAAC 57.123 29.630 0.00 0.00 30.87 2.01
1382 2908 8.563732 GCTTGCATTTCCAATTAAAACCTTAAA 58.436 29.630 0.00 0.00 30.87 1.52
1383 2909 7.174080 GGCTTGCATTTCCAATTAAAACCTTAA 59.826 33.333 0.00 0.00 0.00 1.85
1384 2910 6.652900 GGCTTGCATTTCCAATTAAAACCTTA 59.347 34.615 0.00 0.00 0.00 2.69
1385 2911 5.473162 GGCTTGCATTTCCAATTAAAACCTT 59.527 36.000 0.00 0.00 0.00 3.50
1386 2912 5.003160 GGCTTGCATTTCCAATTAAAACCT 58.997 37.500 0.00 0.00 0.00 3.50
1387 2913 5.003160 AGGCTTGCATTTCCAATTAAAACC 58.997 37.500 0.00 0.00 0.00 3.27
1392 2918 5.480642 TGAAAGGCTTGCATTTCCAATTA 57.519 34.783 23.63 7.65 35.08 1.40
1394 2920 4.354893 TTGAAAGGCTTGCATTTCCAAT 57.645 36.364 23.63 0.00 35.08 3.16
1404 2938 5.105997 CCCTCTACAGAAATTGAAAGGCTTG 60.106 44.000 0.00 0.00 0.00 4.01
1413 2947 6.521151 AATGAAAGCCCTCTACAGAAATTG 57.479 37.500 0.00 0.00 0.00 2.32
1423 2957 3.516700 CCATTTCCAAATGAAAGCCCTCT 59.483 43.478 12.72 0.00 46.72 3.69
1424 2958 3.515104 TCCATTTCCAAATGAAAGCCCTC 59.485 43.478 12.72 0.00 46.72 4.30
1425 2959 3.519667 TCCATTTCCAAATGAAAGCCCT 58.480 40.909 12.72 0.00 46.72 5.19
1426 2960 3.979101 TCCATTTCCAAATGAAAGCCC 57.021 42.857 12.72 0.00 46.72 5.19
1427 2961 4.114794 CGATCCATTTCCAAATGAAAGCC 58.885 43.478 12.72 0.00 46.72 4.35
1428 2962 4.114794 CCGATCCATTTCCAAATGAAAGC 58.885 43.478 12.72 3.85 46.72 3.51
1429 2963 5.581126 TCCGATCCATTTCCAAATGAAAG 57.419 39.130 12.72 0.00 46.72 2.62
1430 2964 5.624281 GCTTCCGATCCATTTCCAAATGAAA 60.624 40.000 12.72 2.46 46.72 2.69
1431 2965 4.142182 GCTTCCGATCCATTTCCAAATGAA 60.142 41.667 12.72 0.00 46.72 2.57
1434 2968 2.695147 GGCTTCCGATCCATTTCCAAAT 59.305 45.455 0.00 0.00 0.00 2.32
1447 2981 5.467035 AATTGAAATTGAAAGGCTTCCGA 57.533 34.783 0.00 0.00 0.00 4.55
1448 2982 5.466393 ACAAATTGAAATTGAAAGGCTTCCG 59.534 36.000 0.00 0.00 0.00 4.30
1449 2983 6.866010 ACAAATTGAAATTGAAAGGCTTCC 57.134 33.333 0.00 0.00 0.00 3.46
1450 2984 8.183536 ACAAACAAATTGAAATTGAAAGGCTTC 58.816 29.630 0.00 0.00 41.85 3.86
1451 2985 8.054152 ACAAACAAATTGAAATTGAAAGGCTT 57.946 26.923 0.00 0.00 41.85 4.35
1453 2987 8.585436 CAAACAAACAAATTGAAATTGAAAGGC 58.415 29.630 0.00 0.00 41.85 4.35
1467 3001 8.917415 ACAAACAAACAAACAAACAAACAAAT 57.083 23.077 0.00 0.00 0.00 2.32
1468 3002 8.742554 AACAAACAAACAAACAAACAAACAAA 57.257 23.077 0.00 0.00 0.00 2.83
1471 3005 8.162906 ACAAACAAACAAACAAACAAACAAAC 57.837 26.923 0.00 0.00 0.00 2.93
1472 3006 8.742554 AACAAACAAACAAACAAACAAACAAA 57.257 23.077 0.00 0.00 0.00 2.83
1473 3007 8.638565 CAAACAAACAAACAAACAAACAAACAA 58.361 25.926 0.00 0.00 0.00 2.83
1474 3008 7.807907 ACAAACAAACAAACAAACAAACAAACA 59.192 25.926 0.00 0.00 0.00 2.83
1475 3009 8.162906 ACAAACAAACAAACAAACAAACAAAC 57.837 26.923 0.00 0.00 0.00 2.93
1476 3010 8.742554 AACAAACAAACAAACAAACAAACAAA 57.257 23.077 0.00 0.00 0.00 2.83
1477 3011 8.742554 AAACAAACAAACAAACAAACAAACAA 57.257 23.077 0.00 0.00 0.00 2.83
1479 3013 8.850452 TGAAAACAAACAAACAAACAAACAAAC 58.150 25.926 0.00 0.00 0.00 2.93
1480 3014 8.964420 TGAAAACAAACAAACAAACAAACAAA 57.036 23.077 0.00 0.00 0.00 2.83
1484 3018 9.787532 TGAAATGAAAACAAACAAACAAACAAA 57.212 22.222 0.00 0.00 0.00 2.83
1485 3019 9.443283 CTGAAATGAAAACAAACAAACAAACAA 57.557 25.926 0.00 0.00 0.00 2.83
1486 3020 8.072567 CCTGAAATGAAAACAAACAAACAAACA 58.927 29.630 0.00 0.00 0.00 2.83
1487 3021 8.073167 ACCTGAAATGAAAACAAACAAACAAAC 58.927 29.630 0.00 0.00 0.00 2.93
1488 3022 8.072567 CACCTGAAATGAAAACAAACAAACAAA 58.927 29.630 0.00 0.00 0.00 2.83
1490 3024 6.348050 GCACCTGAAATGAAAACAAACAAACA 60.348 34.615 0.00 0.00 0.00 2.83
1523 3057 2.281484 GGGCTGTCGGCTGTGAAA 60.281 61.111 3.10 0.00 41.46 2.69
1533 3067 1.876664 GGAAAAGAAGCGGGCTGTC 59.123 57.895 0.00 0.00 0.00 3.51
1545 3079 4.631813 CCTACTCATGGAAAGACGGAAAAG 59.368 45.833 0.00 0.00 0.00 2.27
1639 3173 0.322187 AATGGTTGGTGCCTCGGTAC 60.322 55.000 0.00 0.00 0.00 3.34
1701 3235 0.317160 TTGTCGTCTTGTCTGCCGAT 59.683 50.000 0.00 0.00 0.00 4.18
1772 3312 1.406887 GGGAGCACCGTGACATTATGT 60.407 52.381 1.65 0.00 36.97 2.29
1773 3313 1.299541 GGGAGCACCGTGACATTATG 58.700 55.000 1.65 0.00 36.97 1.90
1783 3323 1.153168 CCAACTATGGGGAGCACCG 60.153 63.158 0.00 0.00 43.51 4.94
1880 3422 5.781210 TGTCAGAGACACAGATCCATATC 57.219 43.478 0.00 0.00 37.67 1.63
1976 3518 2.031012 TCCTTGTGCAGTGCCTCG 59.969 61.111 13.72 0.00 0.00 4.63
1994 3536 2.038837 GCCCAACACCCGACTAAGC 61.039 63.158 0.00 0.00 0.00 3.09
2030 3572 1.838112 TCCAAACATCATCCAGCACC 58.162 50.000 0.00 0.00 0.00 5.01
2085 3627 0.039798 CCAGCATGTGAGCACAACAC 60.040 55.000 7.46 0.63 45.41 3.32
2106 3648 8.818057 GCTTGTCACAATTATAACACTACCTAG 58.182 37.037 0.00 0.00 0.00 3.02
2107 3649 7.767198 GGCTTGTCACAATTATAACACTACCTA 59.233 37.037 0.00 0.00 0.00 3.08
2116 3658 3.181501 GCTGCGGCTTGTCACAATTATAA 60.182 43.478 11.21 0.00 35.22 0.98
2141 3683 2.223665 GCCCATGATAGAAGCAACTTGC 60.224 50.000 5.55 5.55 45.46 4.01
2225 3767 2.627699 TGCTTCCCTTCCAAATGTGTTC 59.372 45.455 0.00 0.00 0.00 3.18
2264 3806 7.669722 TGGAGAATACTTTTAGCCATTGAAACT 59.330 33.333 0.00 0.00 0.00 2.66
2279 3821 5.546499 TCCCTTACACTTGTGGAGAATACTT 59.454 40.000 5.72 0.00 0.00 2.24
2354 3896 4.770010 TCCAAAACAGAAAACCACTGACTT 59.230 37.500 0.00 0.00 38.55 3.01
2409 3954 0.035056 AGTGCAGGTACAATCCCAGC 60.035 55.000 0.00 0.00 0.00 4.85
2476 4021 2.647299 TGGGGAAAATAGCACAGAAGGA 59.353 45.455 0.00 0.00 0.00 3.36
2557 4102 2.205022 TGGCCTCTTGTTTCTGATGG 57.795 50.000 3.32 0.00 0.00 3.51
2766 4359 5.166398 GTTGATCCTTGCAGAATTTCTTGG 58.834 41.667 0.00 0.00 0.00 3.61
2787 4380 5.720202 TCGTGCTGTAATGAACTATCTGTT 58.280 37.500 0.00 0.00 42.38 3.16
2868 4468 0.105039 GGAGTCGGGGAGCTACAATG 59.895 60.000 0.00 0.00 0.00 2.82
2872 4472 3.902086 GCGGAGTCGGGGAGCTAC 61.902 72.222 0.00 0.00 36.79 3.58
2885 4485 5.888724 TCCTTTTGGATTAATAATGTGCGGA 59.111 36.000 0.00 0.00 45.19 5.54
2923 4541 4.487714 TGGCCATACTAAAAGGAGTCTG 57.512 45.455 0.00 0.00 0.00 3.51
2934 4570 6.266558 ACACAAATTTTGACTTGGCCATACTA 59.733 34.615 6.09 0.00 0.00 1.82
2955 4591 3.006430 TCTTCAATGCTCGTAAGGACACA 59.994 43.478 0.00 0.00 38.47 3.72
3009 4645 6.109359 ACAGTCTAAATAGCGAAGATGCTTT 58.891 36.000 0.00 0.00 44.46 3.51
3057 4693 1.362224 ACATGGTAGTGGCTTCAGGT 58.638 50.000 0.00 0.00 0.00 4.00
3132 4768 7.892771 AGACTACTCATATATCTCATGCCTTCA 59.107 37.037 0.00 0.00 0.00 3.02
3270 4906 3.829886 TTGAGTTGATCAATTCCACGC 57.170 42.857 23.53 9.37 43.09 5.34
3309 4945 0.519077 GCTCAGTCAAAGAAAGGGCG 59.481 55.000 0.00 0.00 0.00 6.13
3369 5005 7.641411 CGTTTCAAATTATGCTTGGTAGAGATG 59.359 37.037 0.00 0.00 0.00 2.90
3372 5008 7.072177 TCGTTTCAAATTATGCTTGGTAGAG 57.928 36.000 0.00 0.00 0.00 2.43
3440 5082 6.868339 TGCATCATTACGTACTTCATATCCAG 59.132 38.462 0.00 0.00 0.00 3.86
3455 5097 9.160496 CCTCTAATATTCCTTCTGCATCATTAC 57.840 37.037 0.00 0.00 0.00 1.89
3460 5102 4.940654 GGCCTCTAATATTCCTTCTGCATC 59.059 45.833 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.