Multiple sequence alignment - TraesCS4A01G190800

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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 TraesCS4A01G190800 chr4A 100.000 5091 0 0 1 5091 469511189 469516279 0.000000e+00 9402.0
1 TraesCS4A01G190800 chr4D 93.746 4525 117 46 628 5091 106417357 106412938 0.000000e+00 6636.0
2 TraesCS4A01G190800 chr4D 91.451 503 37 4 1 503 106417846 106417350 0.000000e+00 686.0
3 TraesCS4A01G190800 chr4B 94.608 2689 83 27 628 3292 149939456 149936806 0.000000e+00 4106.0
4 TraesCS4A01G190800 chr4B 88.269 1756 79 57 3360 5045 149936769 149935071 0.000000e+00 1984.0
5 TraesCS4A01G190800 chr4B 93.360 497 30 3 7 503 149940779 149940286 0.000000e+00 732.0
6 TraesCS4A01G190800 chr4B 91.650 503 27 4 1 503 149939936 149939449 0.000000e+00 682.0
7 TraesCS4A01G190800 chr4B 89.389 311 19 3 630 940 149940291 149939995 3.720000e-101 379.0
8 TraesCS4A01G190800 chr3B 89.787 235 12 5 3808 4036 422870651 422870879 1.790000e-74 291.0
9 TraesCS4A01G190800 chr5D 92.973 185 13 0 1933 2117 236663316 236663132 2.340000e-68 270.0
10 TraesCS4A01G190800 chr5D 92.262 168 10 3 1001 1168 236664330 236664166 8.520000e-58 235.0
11 TraesCS4A01G190800 chr5D 78.370 319 44 9 1280 1588 236664030 236663727 3.130000e-42 183.0
12 TraesCS4A01G190800 chr5A 92.973 185 13 0 1933 2117 318756379 318756563 2.340000e-68 270.0
13 TraesCS4A01G190800 chr5A 92.262 168 10 3 1001 1168 318755355 318755519 8.520000e-58 235.0
14 TraesCS4A01G190800 chr5A 75.203 617 79 41 1280 1849 318755658 318756247 1.840000e-54 224.0
15 TraesCS4A01G190800 chr5A 90.476 63 6 0 2186 2248 318756751 318756813 3.270000e-12 84.2
16 TraesCS4A01G190800 chr5B 92.432 185 14 0 1933 2117 268431926 268432110 1.090000e-66 265.0
17 TraesCS4A01G190800 chr5B 75.329 608 91 30 1280 1849 268431222 268431808 2.370000e-58 237.0
18 TraesCS4A01G190800 chr5B 91.667 168 11 3 1001 1168 268430922 268431086 3.960000e-56 230.0
19 TraesCS4A01G190800 chr6B 87.946 224 15 5 3819 4036 627263269 627263052 2.350000e-63 254.0
20 TraesCS4A01G190800 chr2D 89.691 194 20 0 1924 2117 55058427 55058620 1.090000e-61 248.0
21 TraesCS4A01G190800 chr2D 96.610 118 3 1 510 627 419101401 419101517 1.450000e-45 195.0
22 TraesCS4A01G190800 chr2B 89.691 194 20 0 1924 2117 86212086 86212279 1.090000e-61 248.0
23 TraesCS4A01G190800 chr2B 90.909 143 11 2 510 652 799177813 799177673 1.870000e-44 191.0
24 TraesCS4A01G190800 chr2B 90.210 143 12 2 510 652 799224159 799224019 8.700000e-43 185.0
25 TraesCS4A01G190800 chr7D 95.122 123 6 0 506 628 163740251 163740129 1.450000e-45 195.0
26 TraesCS4A01G190800 chr6D 95.122 123 6 0 506 628 466035088 466035210 1.450000e-45 195.0
27 TraesCS4A01G190800 chr6D 94.309 123 7 0 506 628 343217711 343217833 6.730000e-44 189.0
28 TraesCS4A01G190800 chr6D 94.309 123 7 0 506 628 343227766 343227644 6.730000e-44 189.0
29 TraesCS4A01G190800 chrUn 90.909 143 11 2 510 652 363273444 363273304 1.870000e-44 191.0
30 TraesCS4A01G190800 chrUn 90.210 143 12 2 510 652 330322504 330322364 8.700000e-43 185.0


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 TraesCS4A01G190800 chr4A 469511189 469516279 5090 False 9402.000000 9402 100.000000 1 5091 1 chr4A.!!$F1 5090
1 TraesCS4A01G190800 chr4D 106412938 106417846 4908 True 3661.000000 6636 92.598500 1 5091 2 chr4D.!!$R1 5090
2 TraesCS4A01G190800 chr4B 149935071 149940779 5708 True 1576.600000 4106 91.455200 1 5045 5 chr4B.!!$R1 5044
3 TraesCS4A01G190800 chr5D 236663132 236664330 1198 True 229.333333 270 87.868333 1001 2117 3 chr5D.!!$R1 1116
4 TraesCS4A01G190800 chr5A 318755355 318756813 1458 False 203.300000 270 87.728500 1001 2248 4 chr5A.!!$F1 1247
5 TraesCS4A01G190800 chr5B 268430922 268432110 1188 False 244.000000 265 86.476000 1001 2117 3 chr5B.!!$F1 1116

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
581 1420 0.034767 CAGATGACTGGCCCACATGT 60.035 55.000 0.00 0.00 40.14 3.21 F
584 1423 0.034767 ATGACTGGCCCACATGTCAG 60.035 55.000 9.77 9.98 39.14 3.51 F
592 1431 0.110295 CCCACATGTCAGTGACCCAA 59.890 55.000 20.43 2.34 42.05 4.12 F
598 1437 0.179020 TGTCAGTGACCCAAAGGCAG 60.179 55.000 20.43 0.00 36.11 4.85 F
624 1463 0.250295 TTAAGGCACTGAAGCTGCGT 60.250 50.000 0.00 0.00 40.86 5.24 F
625 1464 0.670546 TAAGGCACTGAAGCTGCGTC 60.671 55.000 8.69 8.69 40.86 5.19 F
1835 2774 0.820482 TCACCGAAGAGGACGTGTCA 60.820 55.000 0.00 0.00 45.00 3.58 F
1921 2876 2.028476 TCGACCGATCATTTGGTTGAGT 60.028 45.455 3.91 0.00 42.71 3.41 F
2979 4098 1.077068 CGTATGGGGCCAACATGGT 60.077 57.895 19.21 0.00 40.46 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1835 2774 0.951040 GTGCGCACCTGAAGTAGCTT 60.951 55.000 30.12 0.00 33.77 3.74 R
1871 2826 2.158943 GCAGAAGGCGGAGGTTTAGTAT 60.159 50.000 0.00 0.00 0.00 2.12 R
1884 2839 2.197577 GTCGACATTAGAGCAGAAGGC 58.802 52.381 11.55 0.00 45.30 4.35 R
2269 3384 3.304257 GCGCAAATAACTGATGATGAGGG 60.304 47.826 0.30 0.00 0.00 4.30 R
2270 3385 3.313249 TGCGCAAATAACTGATGATGAGG 59.687 43.478 8.16 0.00 0.00 3.86 R
2273 3388 4.039703 CCTTGCGCAAATAACTGATGATG 58.960 43.478 25.01 7.23 0.00 3.07 R
2783 3902 0.618968 ATCACCACCCTCCTCCTGAC 60.619 60.000 0.00 0.00 0.00 3.51 R
3559 4724 1.348036 GCTGGGGTCACTAGTTTGAGT 59.652 52.381 0.00 0.00 0.00 3.41 R
4631 5837 0.175989 GGATCGACCTGACCTTGACC 59.824 60.000 0.00 0.00 35.41 4.02 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
20 21 2.760385 GCCGTAGAGTGGGAGCCT 60.760 66.667 0.00 0.00 0.00 4.58
44 45 2.362369 CCCGTGCCTGAGGAGTGAT 61.362 63.158 0.65 0.00 0.00 3.06
47 48 0.738762 CGTGCCTGAGGAGTGATGTG 60.739 60.000 0.65 0.00 0.00 3.21
101 102 3.053619 ACTCCACCACCAAATATTCTCCC 60.054 47.826 0.00 0.00 0.00 4.30
103 104 2.092646 CCACCACCAAATATTCTCCCGA 60.093 50.000 0.00 0.00 0.00 5.14
114 115 7.013655 CCAAATATTCTCCCGAATCTTCACAAT 59.986 37.037 0.00 0.00 40.28 2.71
125 126 5.061311 CGAATCTTCACAATTTGGCAATGTC 59.939 40.000 0.00 0.00 0.00 3.06
152 153 0.681733 ACTGTCAGCGACACAAGGAT 59.318 50.000 0.00 0.00 37.67 3.24
243 244 3.340034 TGGCCTTAGTACATTTTCACGG 58.660 45.455 3.32 0.00 0.00 4.94
324 325 4.344865 CAACCGGTGGAGGGGGTG 62.345 72.222 8.52 0.00 34.12 4.61
424 427 0.038599 ACATGGAGTGGCAGATGCAA 59.961 50.000 7.19 0.00 44.36 4.08
428 431 0.322816 GGAGTGGCAGATGCAAAGGA 60.323 55.000 7.19 0.00 44.36 3.36
442 445 4.440880 TGCAAAGGAACAATTTTGACAGG 58.559 39.130 0.00 0.00 36.61 4.00
498 1337 2.613026 ACGCATTTGACCATATCGGA 57.387 45.000 0.00 0.00 38.63 4.55
499 1338 2.912771 ACGCATTTGACCATATCGGAA 58.087 42.857 0.00 0.00 38.63 4.30
500 1339 3.275143 ACGCATTTGACCATATCGGAAA 58.725 40.909 0.00 0.00 38.63 3.13
501 1340 3.692101 ACGCATTTGACCATATCGGAAAA 59.308 39.130 0.00 0.00 38.63 2.29
502 1341 4.156922 ACGCATTTGACCATATCGGAAAAA 59.843 37.500 0.00 0.00 38.63 1.94
519 1358 2.900122 AAAACGATGATGCTTCGGTG 57.100 45.000 7.47 0.00 40.83 4.94
520 1359 0.447801 AAACGATGATGCTTCGGTGC 59.552 50.000 7.47 0.00 40.83 5.01
521 1360 1.369091 AACGATGATGCTTCGGTGCC 61.369 55.000 7.47 0.00 40.83 5.01
522 1361 1.522355 CGATGATGCTTCGGTGCCT 60.522 57.895 0.00 0.00 33.05 4.75
523 1362 1.091771 CGATGATGCTTCGGTGCCTT 61.092 55.000 0.00 0.00 33.05 4.35
524 1363 1.806247 CGATGATGCTTCGGTGCCTTA 60.806 52.381 0.00 0.00 33.05 2.69
525 1364 2.288666 GATGATGCTTCGGTGCCTTAA 58.711 47.619 0.00 0.00 0.00 1.85
526 1365 1.737838 TGATGCTTCGGTGCCTTAAG 58.262 50.000 0.00 0.00 0.00 1.85
527 1366 1.017387 GATGCTTCGGTGCCTTAAGG 58.983 55.000 17.81 17.81 38.53 2.69
544 1383 4.164258 GCACCTGCCTTTGTGTCT 57.836 55.556 0.00 0.00 34.94 3.41
545 1384 3.322514 GCACCTGCCTTTGTGTCTA 57.677 52.632 0.00 0.00 34.94 2.59
546 1385 1.826385 GCACCTGCCTTTGTGTCTAT 58.174 50.000 0.00 0.00 34.94 1.98
547 1386 2.985896 GCACCTGCCTTTGTGTCTATA 58.014 47.619 0.00 0.00 34.94 1.31
548 1387 3.343617 GCACCTGCCTTTGTGTCTATAA 58.656 45.455 0.00 0.00 34.94 0.98
549 1388 3.127030 GCACCTGCCTTTGTGTCTATAAC 59.873 47.826 0.00 0.00 34.94 1.89
550 1389 4.323417 CACCTGCCTTTGTGTCTATAACA 58.677 43.478 0.00 0.00 34.78 2.41
551 1390 4.943705 CACCTGCCTTTGTGTCTATAACAT 59.056 41.667 0.00 0.00 40.80 2.71
552 1391 4.943705 ACCTGCCTTTGTGTCTATAACATG 59.056 41.667 0.00 0.00 40.80 3.21
553 1392 4.943705 CCTGCCTTTGTGTCTATAACATGT 59.056 41.667 0.00 0.00 40.80 3.21
554 1393 6.112734 CCTGCCTTTGTGTCTATAACATGTA 58.887 40.000 0.00 0.00 40.80 2.29
555 1394 6.258727 CCTGCCTTTGTGTCTATAACATGTAG 59.741 42.308 0.00 0.00 40.80 2.74
556 1395 6.112734 TGCCTTTGTGTCTATAACATGTAGG 58.887 40.000 0.00 0.00 40.80 3.18
557 1396 5.007724 GCCTTTGTGTCTATAACATGTAGGC 59.992 44.000 11.05 11.05 43.61 3.93
558 1397 5.527582 CCTTTGTGTCTATAACATGTAGGCC 59.472 44.000 0.00 0.00 40.80 5.19
559 1398 4.682778 TGTGTCTATAACATGTAGGCCC 57.317 45.455 0.00 0.00 40.80 5.80
560 1399 4.034410 TGTGTCTATAACATGTAGGCCCA 58.966 43.478 0.00 0.00 40.80 5.36
561 1400 4.471747 TGTGTCTATAACATGTAGGCCCAA 59.528 41.667 0.00 0.00 40.80 4.12
562 1401 4.814771 GTGTCTATAACATGTAGGCCCAAC 59.185 45.833 0.00 0.00 40.80 3.77
563 1402 4.471747 TGTCTATAACATGTAGGCCCAACA 59.528 41.667 10.73 10.73 31.20 3.33
564 1403 5.057149 GTCTATAACATGTAGGCCCAACAG 58.943 45.833 13.48 8.56 0.00 3.16
565 1404 4.966168 TCTATAACATGTAGGCCCAACAGA 59.034 41.667 13.48 2.07 0.00 3.41
566 1405 4.796110 ATAACATGTAGGCCCAACAGAT 57.204 40.909 13.48 5.64 0.00 2.90
567 1406 2.425143 ACATGTAGGCCCAACAGATG 57.575 50.000 13.48 10.29 0.00 2.90
568 1407 1.915489 ACATGTAGGCCCAACAGATGA 59.085 47.619 13.48 0.00 0.00 2.92
569 1408 2.292267 CATGTAGGCCCAACAGATGAC 58.708 52.381 13.48 0.00 0.00 3.06
570 1409 1.656587 TGTAGGCCCAACAGATGACT 58.343 50.000 0.00 0.00 0.00 3.41
580 1419 2.789842 CAGATGACTGGCCCACATG 58.210 57.895 0.00 0.00 40.14 3.21
581 1420 0.034767 CAGATGACTGGCCCACATGT 60.035 55.000 0.00 0.00 40.14 3.21
582 1421 0.254178 AGATGACTGGCCCACATGTC 59.746 55.000 0.00 1.56 0.00 3.06
583 1422 0.035152 GATGACTGGCCCACATGTCA 60.035 55.000 6.75 6.75 39.66 3.58
584 1423 0.034767 ATGACTGGCCCACATGTCAG 60.035 55.000 9.77 9.98 39.14 3.51
585 1424 1.376466 GACTGGCCCACATGTCAGT 59.624 57.895 15.59 15.59 42.37 3.41
586 1425 0.957395 GACTGGCCCACATGTCAGTG 60.957 60.000 19.37 0.00 40.13 3.66
587 1426 1.376086 CTGGCCCACATGTCAGTGA 59.624 57.895 0.00 0.00 42.05 3.41
588 1427 0.957395 CTGGCCCACATGTCAGTGAC 60.957 60.000 16.68 16.68 42.05 3.67
589 1428 1.675641 GGCCCACATGTCAGTGACC 60.676 63.158 20.43 2.99 42.05 4.02
590 1429 1.675641 GCCCACATGTCAGTGACCC 60.676 63.158 20.43 0.00 42.05 4.46
591 1430 1.760527 CCCACATGTCAGTGACCCA 59.239 57.895 20.43 3.20 42.05 4.51
592 1431 0.110295 CCCACATGTCAGTGACCCAA 59.890 55.000 20.43 2.34 42.05 4.12
593 1432 1.478471 CCCACATGTCAGTGACCCAAA 60.478 52.381 20.43 1.95 42.05 3.28
594 1433 1.881973 CCACATGTCAGTGACCCAAAG 59.118 52.381 20.43 8.14 42.05 2.77
595 1434 1.881973 CACATGTCAGTGACCCAAAGG 59.118 52.381 20.43 6.15 42.05 3.11
596 1435 0.883833 CATGTCAGTGACCCAAAGGC 59.116 55.000 20.43 0.00 36.11 4.35
597 1436 0.478072 ATGTCAGTGACCCAAAGGCA 59.522 50.000 20.43 0.00 36.11 4.75
598 1437 0.179020 TGTCAGTGACCCAAAGGCAG 60.179 55.000 20.43 0.00 36.11 4.85
599 1438 0.890996 GTCAGTGACCCAAAGGCAGG 60.891 60.000 12.54 0.00 36.11 4.85
600 1439 1.151450 CAGTGACCCAAAGGCAGGT 59.849 57.895 0.00 0.00 39.75 4.00
601 1440 1.151450 AGTGACCCAAAGGCAGGTG 59.849 57.895 0.00 0.00 36.17 4.00
602 1441 2.203480 TGACCCAAAGGCAGGTGC 60.203 61.111 0.00 0.00 36.17 5.01
622 1461 1.200948 CCTTTAAGGCACTGAAGCTGC 59.799 52.381 0.00 0.00 40.86 5.25
623 1462 0.874390 TTTAAGGCACTGAAGCTGCG 59.126 50.000 0.00 0.00 40.86 5.18
624 1463 0.250295 TTAAGGCACTGAAGCTGCGT 60.250 50.000 0.00 0.00 40.86 5.24
625 1464 0.670546 TAAGGCACTGAAGCTGCGTC 60.671 55.000 8.69 8.69 40.86 5.19
626 1465 3.426568 GGCACTGAAGCTGCGTCC 61.427 66.667 12.89 0.00 35.31 4.79
627 1466 3.426568 GCACTGAAGCTGCGTCCC 61.427 66.667 12.89 0.00 0.00 4.46
628 1467 3.114616 CACTGAAGCTGCGTCCCG 61.115 66.667 12.89 6.75 0.00 5.14
629 1468 4.379243 ACTGAAGCTGCGTCCCGG 62.379 66.667 12.89 0.00 0.00 5.73
642 1481 3.002102 GCGTCCCGGAAAAAGTTATACA 58.998 45.455 0.73 0.00 0.00 2.29
671 1510 5.843019 AAATTGAAAGAGAGGGAGTACCA 57.157 39.130 0.00 0.00 43.89 3.25
727 1566 6.707161 CCAAAATTTGAATGTGACAACCATCT 59.293 34.615 7.37 0.00 0.00 2.90
740 1579 5.187186 TGACAACCATCTCTCTAGGTAAACC 59.813 44.000 0.00 0.00 34.63 3.27
766 1605 1.071857 GAGAGGAAAACCTCAACCGGT 59.928 52.381 16.87 0.00 39.13 5.28
791 1630 4.387026 TGATGGAGGGAAACTGATTTGT 57.613 40.909 0.00 0.00 0.00 2.83
829 1668 3.801068 TTCCCAGCCCAACCCAACG 62.801 63.158 0.00 0.00 0.00 4.10
1308 2201 3.217743 CCCGAGGAGGAGTACGGC 61.218 72.222 0.00 0.00 45.00 5.68
1796 2735 1.068250 GCGCCAGATCTACCTCACC 59.932 63.158 0.00 0.00 0.00 4.02
1835 2774 0.820482 TCACCGAAGAGGACGTGTCA 60.820 55.000 0.00 0.00 45.00 3.58
1871 2826 4.340019 CACGCCGCCATTGTTGCA 62.340 61.111 0.00 0.00 0.00 4.08
1883 2838 4.440112 GCCATTGTTGCATACTAAACCTCC 60.440 45.833 0.00 0.00 0.00 4.30
1884 2839 4.201910 CCATTGTTGCATACTAAACCTCCG 60.202 45.833 0.00 0.00 0.00 4.63
1921 2876 2.028476 TCGACCGATCATTTGGTTGAGT 60.028 45.455 3.91 0.00 42.71 3.41
2267 3382 6.256757 GTGAGCATTTGAACACTCCTATCTAC 59.743 42.308 0.00 0.00 0.00 2.59
2268 3383 6.155221 TGAGCATTTGAACACTCCTATCTACT 59.845 38.462 0.00 0.00 0.00 2.57
2269 3384 6.578023 AGCATTTGAACACTCCTATCTACTC 58.422 40.000 0.00 0.00 0.00 2.59
2270 3385 5.755861 GCATTTGAACACTCCTATCTACTCC 59.244 44.000 0.00 0.00 0.00 3.85
2271 3386 5.934402 TTTGAACACTCCTATCTACTCCC 57.066 43.478 0.00 0.00 0.00 4.30
2272 3387 4.883021 TGAACACTCCTATCTACTCCCT 57.117 45.455 0.00 0.00 0.00 4.20
2273 3388 4.794334 TGAACACTCCTATCTACTCCCTC 58.206 47.826 0.00 0.00 0.00 4.30
2307 3422 2.307309 CGCAAGGCGTTTGACGAGA 61.307 57.895 4.46 0.00 46.05 4.04
2688 3803 4.161754 TGTTCAGAGCTCATCATGACATCT 59.838 41.667 17.77 0.00 0.00 2.90
2783 3902 2.575805 AAAGAAGGGAAGCAGGAGTG 57.424 50.000 0.00 0.00 0.00 3.51
2818 3937 1.593209 GATGGCAATGGCAATGGCG 60.593 57.895 22.07 0.00 45.56 5.69
2963 4082 5.399991 TCCTTGGGTGGATATTAGTATCGT 58.600 41.667 0.00 0.00 38.06 3.73
2979 4098 1.077068 CGTATGGGGCCAACATGGT 60.077 57.895 19.21 0.00 40.46 3.55
3056 4176 8.690203 TTCCATTAGAAAACTTGAACATCTCA 57.310 30.769 0.00 0.00 0.00 3.27
3297 4427 6.595794 CAAAGTGATGAAATGCATTTTGGAC 58.404 36.000 24.81 17.71 37.78 4.02
3325 4455 3.383825 GTGGACATTCACCGGAGTACTAT 59.616 47.826 9.46 0.00 0.00 2.12
3480 4624 2.948979 AGACATTGCAAAAAGGTGACGA 59.051 40.909 1.71 0.00 0.00 4.20
3554 4719 1.813786 ACGGGACTCGAAGAAGAGAAG 59.186 52.381 0.00 0.00 40.57 2.85
3555 4720 2.085320 CGGGACTCGAAGAAGAGAAGA 58.915 52.381 0.00 0.00 40.57 2.87
3556 4721 2.096819 CGGGACTCGAAGAAGAGAAGAG 59.903 54.545 0.00 0.00 40.57 2.85
3557 4722 3.349022 GGGACTCGAAGAAGAGAAGAGA 58.651 50.000 0.62 0.00 40.57 3.10
3558 4723 3.759618 GGGACTCGAAGAAGAGAAGAGAA 59.240 47.826 0.62 0.00 40.57 2.87
3559 4724 4.218852 GGGACTCGAAGAAGAGAAGAGAAA 59.781 45.833 0.62 0.00 40.57 2.52
3560 4725 5.158494 GGACTCGAAGAAGAGAAGAGAAAC 58.842 45.833 0.62 0.00 40.57 2.78
3561 4726 5.048294 GGACTCGAAGAAGAGAAGAGAAACT 60.048 44.000 0.62 0.00 40.57 2.66
3562 4727 6.009115 ACTCGAAGAAGAGAAGAGAAACTC 57.991 41.667 0.62 0.00 40.57 3.01
3563 4728 5.533154 ACTCGAAGAAGAGAAGAGAAACTCA 59.467 40.000 0.62 0.00 40.57 3.41
3564 4729 6.039941 ACTCGAAGAAGAGAAGAGAAACTCAA 59.960 38.462 0.62 0.00 40.57 3.02
3589 4754 2.084546 GTGACCCCAGCTAATGACAAC 58.915 52.381 0.00 0.00 0.00 3.32
3686 4856 0.376502 TTGATGTGTGTGCGTGTGTG 59.623 50.000 0.00 0.00 0.00 3.82
3966 5151 7.999679 TCCCTTCATGCTAATATCTGTTTTTG 58.000 34.615 0.00 0.00 0.00 2.44
3993 5178 7.649370 CTGCATCAGGAATTAGTACTACATG 57.351 40.000 0.91 0.00 0.00 3.21
4015 5200 9.429359 ACATGTTTGTGAGAAAATTGTTAACAA 57.571 25.926 22.58 22.58 35.97 2.83
4017 5202 8.818141 TGTTTGTGAGAAAATTGTTAACAACA 57.182 26.923 22.78 12.33 38.86 3.33
4018 5203 8.920665 TGTTTGTGAGAAAATTGTTAACAACAG 58.079 29.630 22.78 0.00 43.27 3.16
4019 5204 8.921670 GTTTGTGAGAAAATTGTTAACAACAGT 58.078 29.630 22.78 10.72 43.27 3.55
4020 5205 9.482627 TTTGTGAGAAAATTGTTAACAACAGTT 57.517 25.926 22.78 15.98 42.22 3.16
4110 5296 3.210227 GAATAGAGCAAAGAAGAGGGGC 58.790 50.000 0.00 0.00 0.00 5.80
4126 5312 0.753479 GGGCGTCATCTCCTCTCTGA 60.753 60.000 0.00 0.00 0.00 3.27
4163 5349 2.358582 TGTCAACAGCAACAATCACTGG 59.641 45.455 0.00 0.00 35.70 4.00
4185 5371 3.501445 GCTCAATCATGGTAGAAGGATGC 59.499 47.826 0.00 0.00 0.00 3.91
4188 5374 5.067954 TCAATCATGGTAGAAGGATGCATG 58.932 41.667 2.46 0.00 0.00 4.06
4189 5375 4.719026 ATCATGGTAGAAGGATGCATGT 57.281 40.909 2.46 0.00 0.00 3.21
4190 5376 5.830799 ATCATGGTAGAAGGATGCATGTA 57.169 39.130 2.46 0.00 0.00 2.29
4191 5377 5.219343 TCATGGTAGAAGGATGCATGTAG 57.781 43.478 2.46 0.00 0.00 2.74
4192 5378 4.040829 TCATGGTAGAAGGATGCATGTAGG 59.959 45.833 2.46 0.00 0.00 3.18
4193 5379 3.653164 TGGTAGAAGGATGCATGTAGGA 58.347 45.455 2.46 0.00 0.00 2.94
4274 5462 1.740380 CGTGTGATGACTGACCCCATC 60.740 57.143 0.00 0.00 39.55 3.51
4275 5463 1.278985 GTGTGATGACTGACCCCATCA 59.721 52.381 0.00 0.00 44.66 3.07
4516 5706 1.546476 ACCTAGTTCCTGCAAGAGTCG 59.454 52.381 0.00 0.00 34.07 4.18
4517 5707 1.819288 CCTAGTTCCTGCAAGAGTCGA 59.181 52.381 0.00 0.00 34.07 4.20
4518 5708 2.159310 CCTAGTTCCTGCAAGAGTCGAG 60.159 54.545 0.00 0.00 34.07 4.04
4519 5709 1.333177 AGTTCCTGCAAGAGTCGAGT 58.667 50.000 0.00 0.00 34.07 4.18
4520 5710 1.000283 AGTTCCTGCAAGAGTCGAGTG 60.000 52.381 0.00 0.00 34.07 3.51
4551 5746 2.293170 GAGCATAGCAAGGGGAAAGTC 58.707 52.381 0.00 0.00 0.00 3.01
4552 5747 1.635487 AGCATAGCAAGGGGAAAGTCA 59.365 47.619 0.00 0.00 0.00 3.41
4553 5748 2.041620 AGCATAGCAAGGGGAAAGTCAA 59.958 45.455 0.00 0.00 0.00 3.18
4630 5836 0.679505 CTCGGTCAGGTCAAGGTCAA 59.320 55.000 0.00 0.00 0.00 3.18
4631 5837 0.679505 TCGGTCAGGTCAAGGTCAAG 59.320 55.000 0.00 0.00 0.00 3.02
4632 5838 0.320771 CGGTCAGGTCAAGGTCAAGG 60.321 60.000 0.00 0.00 0.00 3.61
4633 5839 0.765510 GGTCAGGTCAAGGTCAAGGT 59.234 55.000 0.00 0.00 0.00 3.50
4634 5840 1.270893 GGTCAGGTCAAGGTCAAGGTC 60.271 57.143 0.00 0.00 0.00 3.85
4635 5841 1.416401 GTCAGGTCAAGGTCAAGGTCA 59.584 52.381 0.00 0.00 0.00 4.02
4636 5842 2.123589 TCAGGTCAAGGTCAAGGTCAA 58.876 47.619 0.00 0.00 0.00 3.18
4637 5843 2.104792 TCAGGTCAAGGTCAAGGTCAAG 59.895 50.000 0.00 0.00 0.00 3.02
4638 5844 1.421646 AGGTCAAGGTCAAGGTCAAGG 59.578 52.381 0.00 0.00 0.00 3.61
4639 5845 1.143073 GGTCAAGGTCAAGGTCAAGGT 59.857 52.381 0.00 0.00 0.00 3.50
4640 5846 2.495084 GTCAAGGTCAAGGTCAAGGTC 58.505 52.381 0.00 0.00 0.00 3.85
4641 5847 2.123589 TCAAGGTCAAGGTCAAGGTCA 58.876 47.619 0.00 0.00 0.00 4.02
4642 5848 2.104792 TCAAGGTCAAGGTCAAGGTCAG 59.895 50.000 0.00 0.00 0.00 3.51
4643 5849 1.059913 AGGTCAAGGTCAAGGTCAGG 58.940 55.000 0.00 0.00 0.00 3.86
4644 5850 0.765510 GGTCAAGGTCAAGGTCAGGT 59.234 55.000 0.00 0.00 0.00 4.00
4645 5851 1.270893 GGTCAAGGTCAAGGTCAGGTC 60.271 57.143 0.00 0.00 0.00 3.85
4646 5852 0.679505 TCAAGGTCAAGGTCAGGTCG 59.320 55.000 0.00 0.00 0.00 4.79
4682 5888 4.583907 TGTGGATCTCATCTCAGTCTGATC 59.416 45.833 2.22 0.00 0.00 2.92
4683 5889 4.828939 GTGGATCTCATCTCAGTCTGATCT 59.171 45.833 2.22 0.00 33.14 2.75
4684 5890 4.828387 TGGATCTCATCTCAGTCTGATCTG 59.172 45.833 2.22 4.39 36.85 2.90
4685 5891 5.072055 GGATCTCATCTCAGTCTGATCTGA 58.928 45.833 2.22 8.39 41.40 3.27
4686 5892 5.713389 GGATCTCATCTCAGTCTGATCTGAT 59.287 44.000 2.22 0.11 42.47 2.90
4770 5976 6.036517 GCCACTTTGTGACTAATGACTATCAG 59.963 42.308 0.00 0.00 35.23 2.90
4771 5977 7.099764 CCACTTTGTGACTAATGACTATCAGT 58.900 38.462 0.00 0.00 35.23 3.41
4777 5983 6.127366 TGTGACTAATGACTATCAGTGATGCA 60.127 38.462 16.15 11.06 0.00 3.96
4792 5998 4.177165 TGATGCATTGTGGACATCAAAC 57.823 40.909 0.00 0.00 45.27 2.93
4798 6004 2.270352 TGTGGACATCAAACTGGGTC 57.730 50.000 0.00 0.00 0.00 4.46
4829 6035 6.927294 AAATAACCTCTCCTTTGCTTATCG 57.073 37.500 0.00 0.00 0.00 2.92
4895 6125 7.088272 ACCGCATCTGGTTTAAAATAAAGAAC 58.912 34.615 0.00 0.00 39.99 3.01
4896 6126 7.039993 ACCGCATCTGGTTTAAAATAAAGAACT 60.040 33.333 0.00 0.00 39.99 3.01
4897 6127 7.484959 CCGCATCTGGTTTAAAATAAAGAACTC 59.515 37.037 0.00 0.00 0.00 3.01
4898 6128 8.020819 CGCATCTGGTTTAAAATAAAGAACTCA 58.979 33.333 0.00 0.00 0.00 3.41
4901 6131 9.914131 ATCTGGTTTAAAATAAAGAACTCAAGC 57.086 29.630 0.00 0.00 0.00 4.01
4902 6132 8.908903 TCTGGTTTAAAATAAAGAACTCAAGCA 58.091 29.630 0.00 0.00 0.00 3.91
4918 6148 3.260128 TCAAGCAATCTTCAGCAGAGAGA 59.740 43.478 0.00 0.00 33.87 3.10
4953 6185 2.429767 CCAGAGATGCAGGCGGAGA 61.430 63.158 0.00 0.00 0.00 3.71
5050 6285 4.662961 CAGTCACGGGCGCAGACA 62.663 66.667 20.47 0.00 37.00 3.41
5051 6286 4.363990 AGTCACGGGCGCAGACAG 62.364 66.667 20.47 0.00 37.00 3.51
5052 6287 4.357947 GTCACGGGCGCAGACAGA 62.358 66.667 10.83 0.00 37.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.970937 TCCAAGGCTCCCACTCTACG 60.971 60.000 0.00 0.00 0.00 3.51
16 17 4.115199 GGCACGGGATCCAAGGCT 62.115 66.667 15.23 0.00 0.00 4.58
20 21 2.669133 CCTCAGGCACGGGATCCAA 61.669 63.158 15.23 0.00 0.00 3.53
44 45 0.034756 CAAGGTGGGTCATCGACACA 59.965 55.000 5.60 0.00 44.26 3.72
47 48 2.100631 CGCAAGGTGGGTCATCGAC 61.101 63.158 0.00 0.00 0.00 4.20
101 102 4.925054 ACATTGCCAAATTGTGAAGATTCG 59.075 37.500 0.00 0.00 0.00 3.34
103 104 4.925054 CGACATTGCCAAATTGTGAAGATT 59.075 37.500 0.00 0.00 0.00 2.40
114 115 0.326595 TAGCCCTCGACATTGCCAAA 59.673 50.000 0.00 0.00 0.00 3.28
125 126 2.103143 CGCTGACAGTAGCCCTCG 59.897 66.667 3.99 0.00 40.59 4.63
152 153 2.375174 AGCCCTCAATCAAGGTTGTACA 59.625 45.455 0.00 0.00 34.34 2.90
243 244 0.878416 TAAGGCACGGAAACACATGC 59.122 50.000 0.00 0.00 37.35 4.06
327 328 0.106469 GCCTTTGAATCCTCTCCCCC 60.106 60.000 0.00 0.00 0.00 5.40
332 333 0.460987 CGCTCGCCTTTGAATCCTCT 60.461 55.000 0.00 0.00 0.00 3.69
387 390 1.215244 GTCCTTAAATACGCTCCCGC 58.785 55.000 0.00 0.00 38.22 6.13
390 393 4.058817 CTCCATGTCCTTAAATACGCTCC 58.941 47.826 0.00 0.00 0.00 4.70
424 427 5.278463 CGATGACCTGTCAAAATTGTTCCTT 60.278 40.000 3.79 0.00 43.58 3.36
428 431 5.530915 TCTTCGATGACCTGTCAAAATTGTT 59.469 36.000 3.79 0.00 43.58 2.83
442 445 7.068341 GTGATCAATGCTATTTCTTCGATGAC 58.932 38.462 0.00 0.00 0.00 3.06
499 1338 2.668279 GCACCGAAGCATCATCGTTTTT 60.668 45.455 0.00 0.00 38.60 1.94
500 1339 1.135689 GCACCGAAGCATCATCGTTTT 60.136 47.619 0.00 0.00 38.60 2.43
501 1340 0.447801 GCACCGAAGCATCATCGTTT 59.552 50.000 0.00 0.00 38.60 3.60
502 1341 1.369091 GGCACCGAAGCATCATCGTT 61.369 55.000 1.64 0.00 38.60 3.85
503 1342 1.815421 GGCACCGAAGCATCATCGT 60.815 57.895 1.64 0.00 38.60 3.73
504 1343 1.091771 AAGGCACCGAAGCATCATCG 61.092 55.000 1.64 0.00 39.92 3.84
505 1344 1.953559 TAAGGCACCGAAGCATCATC 58.046 50.000 1.64 0.00 35.83 2.92
506 1345 2.292267 CTTAAGGCACCGAAGCATCAT 58.708 47.619 0.00 0.00 35.83 2.45
507 1346 1.678728 CCTTAAGGCACCGAAGCATCA 60.679 52.381 9.00 0.00 35.83 3.07
508 1347 1.017387 CCTTAAGGCACCGAAGCATC 58.983 55.000 9.00 0.00 35.83 3.91
509 1348 3.175133 CCTTAAGGCACCGAAGCAT 57.825 52.632 9.00 0.00 35.83 3.79
510 1349 4.713946 CCTTAAGGCACCGAAGCA 57.286 55.556 9.00 0.00 35.83 3.91
527 1366 1.826385 ATAGACACAAAGGCAGGTGC 58.174 50.000 0.00 0.00 38.57 5.01
528 1367 4.323417 TGTTATAGACACAAAGGCAGGTG 58.677 43.478 2.29 2.29 40.78 4.00
529 1368 4.634012 TGTTATAGACACAAAGGCAGGT 57.366 40.909 0.00 0.00 32.00 4.00
530 1369 4.943705 ACATGTTATAGACACAAAGGCAGG 59.056 41.667 0.00 0.00 42.04 4.85
531 1370 6.258727 CCTACATGTTATAGACACAAAGGCAG 59.741 42.308 2.30 0.00 42.04 4.85
532 1371 6.112734 CCTACATGTTATAGACACAAAGGCA 58.887 40.000 2.30 0.00 42.04 4.75
533 1372 5.007724 GCCTACATGTTATAGACACAAAGGC 59.992 44.000 2.30 7.94 44.93 4.35
534 1373 5.527582 GGCCTACATGTTATAGACACAAAGG 59.472 44.000 2.30 0.58 42.04 3.11
535 1374 5.527582 GGGCCTACATGTTATAGACACAAAG 59.472 44.000 2.30 0.00 42.04 2.77
536 1375 5.045505 TGGGCCTACATGTTATAGACACAAA 60.046 40.000 2.30 0.00 42.04 2.83
537 1376 4.471747 TGGGCCTACATGTTATAGACACAA 59.528 41.667 2.30 0.00 42.04 3.33
538 1377 4.034410 TGGGCCTACATGTTATAGACACA 58.966 43.478 2.30 0.00 42.04 3.72
539 1378 4.682778 TGGGCCTACATGTTATAGACAC 57.317 45.455 2.30 0.00 42.04 3.67
540 1379 4.471747 TGTTGGGCCTACATGTTATAGACA 59.528 41.667 16.97 0.00 43.71 3.41
541 1380 5.031066 TGTTGGGCCTACATGTTATAGAC 57.969 43.478 16.97 0.00 0.00 2.59
542 1381 4.966168 TCTGTTGGGCCTACATGTTATAGA 59.034 41.667 20.85 10.13 0.00 1.98
543 1382 5.290493 TCTGTTGGGCCTACATGTTATAG 57.710 43.478 20.85 7.96 0.00 1.31
544 1383 5.368230 TCATCTGTTGGGCCTACATGTTATA 59.632 40.000 20.85 3.07 0.00 0.98
545 1384 4.165950 TCATCTGTTGGGCCTACATGTTAT 59.834 41.667 20.85 9.75 0.00 1.89
546 1385 3.521531 TCATCTGTTGGGCCTACATGTTA 59.478 43.478 20.85 7.95 0.00 2.41
547 1386 2.308570 TCATCTGTTGGGCCTACATGTT 59.691 45.455 20.85 6.53 0.00 2.71
548 1387 1.915489 TCATCTGTTGGGCCTACATGT 59.085 47.619 20.85 10.01 0.00 3.21
549 1388 2.092753 AGTCATCTGTTGGGCCTACATG 60.093 50.000 20.85 16.70 0.00 3.21
550 1389 2.092753 CAGTCATCTGTTGGGCCTACAT 60.093 50.000 20.85 4.81 36.97 2.29
551 1390 1.278985 CAGTCATCTGTTGGGCCTACA 59.721 52.381 19.53 19.53 36.97 2.74
552 1391 1.407437 CCAGTCATCTGTTGGGCCTAC 60.407 57.143 11.39 11.39 39.82 3.18
553 1392 0.911769 CCAGTCATCTGTTGGGCCTA 59.088 55.000 4.53 0.00 39.82 3.93
554 1393 1.687612 CCAGTCATCTGTTGGGCCT 59.312 57.895 4.53 0.00 39.82 5.19
555 1394 2.048603 GCCAGTCATCTGTTGGGCC 61.049 63.158 0.00 0.00 39.82 5.80
556 1395 3.595819 GCCAGTCATCTGTTGGGC 58.404 61.111 0.00 0.00 39.82 5.36
557 1396 1.379044 GGGCCAGTCATCTGTTGGG 60.379 63.158 4.39 0.00 39.82 4.12
558 1397 0.962356 GTGGGCCAGTCATCTGTTGG 60.962 60.000 6.40 0.00 39.82 3.77
559 1398 0.250858 TGTGGGCCAGTCATCTGTTG 60.251 55.000 6.40 0.00 39.82 3.33
560 1399 0.700564 ATGTGGGCCAGTCATCTGTT 59.299 50.000 6.40 0.00 39.82 3.16
561 1400 0.034767 CATGTGGGCCAGTCATCTGT 60.035 55.000 6.40 0.00 39.82 3.41
562 1401 0.034767 ACATGTGGGCCAGTCATCTG 60.035 55.000 6.40 0.96 41.01 2.90
563 1402 0.254178 GACATGTGGGCCAGTCATCT 59.746 55.000 16.97 2.47 0.00 2.90
564 1403 0.035152 TGACATGTGGGCCAGTCATC 60.035 55.000 19.75 10.98 36.20 2.92
565 1404 0.034767 CTGACATGTGGGCCAGTCAT 60.035 55.000 22.72 14.39 39.92 3.06
566 1405 1.376086 CTGACATGTGGGCCAGTCA 59.624 57.895 21.58 21.58 38.56 3.41
567 1406 0.957395 CACTGACATGTGGGCCAGTC 60.957 60.000 6.40 12.33 37.74 3.51
568 1407 1.073722 CACTGACATGTGGGCCAGT 59.926 57.895 6.40 7.66 40.15 4.00
569 1408 0.957395 GTCACTGACATGTGGGCCAG 60.957 60.000 6.40 6.93 38.40 4.85
570 1409 1.073025 GTCACTGACATGTGGGCCA 59.927 57.895 1.15 0.00 38.40 5.36
571 1410 1.675641 GGTCACTGACATGTGGGCC 60.676 63.158 1.15 0.00 38.40 5.80
572 1411 1.675641 GGGTCACTGACATGTGGGC 60.676 63.158 1.15 0.00 38.40 5.36
573 1412 0.110295 TTGGGTCACTGACATGTGGG 59.890 55.000 1.15 0.00 38.40 4.61
574 1413 1.881973 CTTTGGGTCACTGACATGTGG 59.118 52.381 1.15 0.00 38.40 4.17
575 1414 1.881973 CCTTTGGGTCACTGACATGTG 59.118 52.381 1.15 0.00 39.15 3.21
576 1415 1.819305 GCCTTTGGGTCACTGACATGT 60.819 52.381 11.34 0.00 33.68 3.21
577 1416 0.883833 GCCTTTGGGTCACTGACATG 59.116 55.000 11.34 0.00 33.68 3.21
578 1417 0.478072 TGCCTTTGGGTCACTGACAT 59.522 50.000 11.34 0.00 33.68 3.06
579 1418 0.179020 CTGCCTTTGGGTCACTGACA 60.179 55.000 11.34 0.00 33.68 3.58
580 1419 0.890996 CCTGCCTTTGGGTCACTGAC 60.891 60.000 0.00 0.00 34.45 3.51
581 1420 1.352622 ACCTGCCTTTGGGTCACTGA 61.353 55.000 0.00 0.00 34.45 3.41
582 1421 1.151450 ACCTGCCTTTGGGTCACTG 59.849 57.895 0.00 0.00 34.45 3.66
583 1422 1.151450 CACCTGCCTTTGGGTCACT 59.849 57.895 0.00 0.00 32.95 3.41
584 1423 2.564721 GCACCTGCCTTTGGGTCAC 61.565 63.158 0.00 0.00 32.95 3.67
585 1424 2.203480 GCACCTGCCTTTGGGTCA 60.203 61.111 0.00 0.00 32.95 4.02
602 1441 1.200948 GCAGCTTCAGTGCCTTAAAGG 59.799 52.381 0.00 0.00 38.80 3.11
603 1442 1.135859 CGCAGCTTCAGTGCCTTAAAG 60.136 52.381 0.00 0.00 37.67 1.85
604 1443 0.874390 CGCAGCTTCAGTGCCTTAAA 59.126 50.000 0.00 0.00 37.67 1.52
605 1444 0.250295 ACGCAGCTTCAGTGCCTTAA 60.250 50.000 0.00 0.00 37.67 1.85
606 1445 0.670546 GACGCAGCTTCAGTGCCTTA 60.671 55.000 0.00 0.00 37.67 2.69
607 1446 1.963338 GACGCAGCTTCAGTGCCTT 60.963 57.895 0.00 0.00 37.67 4.35
608 1447 2.358003 GACGCAGCTTCAGTGCCT 60.358 61.111 0.00 0.00 37.67 4.75
609 1448 3.426568 GGACGCAGCTTCAGTGCC 61.427 66.667 0.69 0.00 37.67 5.01
610 1449 3.426568 GGGACGCAGCTTCAGTGC 61.427 66.667 0.69 0.00 37.58 4.40
623 1462 5.335113 GGTTGTGTATAACTTTTTCCGGGAC 60.335 44.000 0.00 0.00 0.00 4.46
624 1463 4.761227 GGTTGTGTATAACTTTTTCCGGGA 59.239 41.667 0.00 0.00 0.00 5.14
625 1464 4.763279 AGGTTGTGTATAACTTTTTCCGGG 59.237 41.667 0.00 0.00 0.00 5.73
626 1465 5.952526 AGGTTGTGTATAACTTTTTCCGG 57.047 39.130 0.00 0.00 0.00 5.14
627 1466 9.902196 AATTTAGGTTGTGTATAACTTTTTCCG 57.098 29.630 0.00 0.00 0.00 4.30
642 1481 6.183361 ACTCCCTCTCTTTCAATTTAGGTTGT 60.183 38.462 0.00 0.00 0.00 3.32
671 1510 5.930837 TGGTTGTCCTGAGTTTCATTTTT 57.069 34.783 0.00 0.00 34.23 1.94
727 1566 6.556495 TCCTCTCTATACGGTTTACCTAGAGA 59.444 42.308 18.15 18.15 41.36 3.10
766 1605 4.868172 ATCAGTTTCCCTCCATCAATGA 57.132 40.909 0.00 0.00 0.00 2.57
791 1630 1.131638 AGTGCAGTGTCTTCTTCCCA 58.868 50.000 0.00 0.00 0.00 4.37
829 1668 1.002900 TGAAATAAATAGCGCGGCTGC 60.003 47.619 8.83 7.70 40.10 5.25
946 1794 1.327690 TGATTTCTCGGAGGGGACGG 61.328 60.000 4.96 0.00 0.00 4.79
987 1835 1.227147 GTCCATTGCGCCGCTAGTA 60.227 57.895 11.67 0.00 0.00 1.82
1308 2201 4.504916 CTCGCCGGAGACCAGCAG 62.505 72.222 5.05 0.00 43.27 4.24
1796 2735 4.452733 GTGGAGTCGGCGGGGAAG 62.453 72.222 7.21 0.00 0.00 3.46
1835 2774 0.951040 GTGCGCACCTGAAGTAGCTT 60.951 55.000 30.12 0.00 33.77 3.74
1871 2826 2.158943 GCAGAAGGCGGAGGTTTAGTAT 60.159 50.000 0.00 0.00 0.00 2.12
1884 2839 2.197577 GTCGACATTAGAGCAGAAGGC 58.802 52.381 11.55 0.00 45.30 4.35
2267 3382 4.212847 CGCAAATAACTGATGATGAGGGAG 59.787 45.833 0.00 0.00 0.00 4.30
2268 3383 4.129380 CGCAAATAACTGATGATGAGGGA 58.871 43.478 0.00 0.00 0.00 4.20
2269 3384 3.304257 GCGCAAATAACTGATGATGAGGG 60.304 47.826 0.30 0.00 0.00 4.30
2270 3385 3.313249 TGCGCAAATAACTGATGATGAGG 59.687 43.478 8.16 0.00 0.00 3.86
2271 3386 4.541085 TGCGCAAATAACTGATGATGAG 57.459 40.909 8.16 0.00 0.00 2.90
2272 3387 4.201940 CCTTGCGCAAATAACTGATGATGA 60.202 41.667 25.01 0.00 0.00 2.92
2273 3388 4.039703 CCTTGCGCAAATAACTGATGATG 58.960 43.478 25.01 7.23 0.00 3.07
2783 3902 0.618968 ATCACCACCCTCCTCCTGAC 60.619 60.000 0.00 0.00 0.00 3.51
2818 3937 1.751927 CCTGCTTGGGACTGCCATC 60.752 63.158 0.00 0.00 35.15 3.51
2963 4082 2.334006 AAAACCATGTTGGCCCCATA 57.666 45.000 0.00 0.00 42.67 2.74
3065 4185 7.985184 TGATACTACATGTTACAGGATGGTTTC 59.015 37.037 2.30 5.05 43.62 2.78
3121 4241 9.935682 CATAAAGTTATTATCGTTGAAGCACAT 57.064 29.630 0.00 0.00 0.00 3.21
3128 4248 9.589111 TGTACTGCATAAAGTTATTATCGTTGA 57.411 29.630 0.00 0.00 0.00 3.18
3201 4321 8.754991 TCTGGTGATACCTTTTGAAAGTTTTA 57.245 30.769 3.09 0.00 39.58 1.52
3202 4322 7.654022 TCTGGTGATACCTTTTGAAAGTTTT 57.346 32.000 3.09 0.00 39.58 2.43
3257 4387 5.551760 CACTTTGGTGAATGTCCACTATC 57.448 43.478 0.00 0.00 45.61 2.08
3297 4427 3.605634 TCCGGTGAATGTCCACTATTTG 58.394 45.455 0.00 0.00 37.24 2.32
3325 4455 7.360643 TCCCCTTTTAGTTACCCAAAAAGTAA 58.639 34.615 11.51 0.00 38.13 2.24
3455 4592 5.063312 CGTCACCTTTTTGCAATGTCTTTTT 59.937 36.000 0.00 0.00 0.00 1.94
3480 4624 2.308866 AGCACCACAAAAGCCTATACCT 59.691 45.455 0.00 0.00 0.00 3.08
3524 4669 4.100035 TCTTCGAGTCCCGTCTAGTATGTA 59.900 45.833 0.00 0.00 39.75 2.29
3526 4671 3.464907 TCTTCGAGTCCCGTCTAGTATG 58.535 50.000 0.00 0.00 39.75 2.39
3554 4719 4.202326 TGGGGTCACTAGTTTGAGTTTCTC 60.202 45.833 0.00 0.00 0.00 2.87
3555 4720 3.714798 TGGGGTCACTAGTTTGAGTTTCT 59.285 43.478 0.00 0.00 0.00 2.52
3556 4721 4.065789 CTGGGGTCACTAGTTTGAGTTTC 58.934 47.826 0.00 0.00 0.00 2.78
3557 4722 3.747708 GCTGGGGTCACTAGTTTGAGTTT 60.748 47.826 0.00 0.00 0.00 2.66
3558 4723 2.224548 GCTGGGGTCACTAGTTTGAGTT 60.225 50.000 0.00 0.00 0.00 3.01
3559 4724 1.348036 GCTGGGGTCACTAGTTTGAGT 59.652 52.381 0.00 0.00 0.00 3.41
3560 4725 1.625818 AGCTGGGGTCACTAGTTTGAG 59.374 52.381 0.00 0.00 0.00 3.02
3561 4726 1.729586 AGCTGGGGTCACTAGTTTGA 58.270 50.000 0.00 0.00 0.00 2.69
3562 4727 3.695830 TTAGCTGGGGTCACTAGTTTG 57.304 47.619 0.00 0.00 0.00 2.93
3563 4728 3.844211 TCATTAGCTGGGGTCACTAGTTT 59.156 43.478 0.00 0.00 0.00 2.66
3564 4729 3.197983 GTCATTAGCTGGGGTCACTAGTT 59.802 47.826 0.00 0.00 0.00 2.24
3989 5174 8.994429 TGTTAACAATTTTCTCACAAACATGT 57.006 26.923 5.64 0.00 0.00 3.21
3990 5175 9.687717 GTTGTTAACAATTTTCTCACAAACATG 57.312 29.630 23.11 0.00 38.24 3.21
3993 5178 8.921670 ACTGTTGTTAACAATTTTCTCACAAAC 58.078 29.630 23.11 7.66 41.61 2.93
4015 5200 9.896645 AATTTATCATCTCACTCACATAACTGT 57.103 29.630 0.00 0.00 35.44 3.55
4017 5202 9.896645 ACAATTTATCATCTCACTCACATAACT 57.103 29.630 0.00 0.00 0.00 2.24
4022 5207 9.897744 GAAAAACAATTTATCATCTCACTCACA 57.102 29.630 0.00 0.00 0.00 3.58
4023 5208 9.346725 GGAAAAACAATTTATCATCTCACTCAC 57.653 33.333 0.00 0.00 0.00 3.51
4026 5211 9.525826 AGAGGAAAAACAATTTATCATCTCACT 57.474 29.630 0.00 0.00 29.30 3.41
4110 5296 2.479389 GCACTTCAGAGAGGAGATGACG 60.479 54.545 0.00 0.00 0.00 4.35
4126 5312 2.047061 TGACACTTACTCCCAGCACTT 58.953 47.619 0.00 0.00 0.00 3.16
4163 5349 3.501445 GCATCCTTCTACCATGATTGAGC 59.499 47.826 0.00 0.00 0.00 4.26
4274 5462 1.384525 TTTCCGACCACCACTTGTTG 58.615 50.000 0.00 0.00 0.00 3.33
4275 5463 2.131776 TTTTCCGACCACCACTTGTT 57.868 45.000 0.00 0.00 0.00 2.83
4276 5464 2.021457 CTTTTTCCGACCACCACTTGT 58.979 47.619 0.00 0.00 0.00 3.16
4288 5476 3.702330 ACGCTTTCCTTTTCTTTTTCCG 58.298 40.909 0.00 0.00 0.00 4.30
4437 5627 8.563123 TGCTGCTACCATATACTACTAACTAG 57.437 38.462 0.00 0.00 0.00 2.57
4516 5706 2.795297 CTCGGCTCGACTCCACTC 59.205 66.667 0.53 0.00 0.00 3.51
4517 5707 3.444805 GCTCGGCTCGACTCCACT 61.445 66.667 0.53 0.00 0.00 4.00
4518 5708 1.725557 TATGCTCGGCTCGACTCCAC 61.726 60.000 0.53 0.00 0.00 4.02
4519 5709 1.448119 CTATGCTCGGCTCGACTCCA 61.448 60.000 0.53 0.00 0.00 3.86
4520 5710 1.284408 CTATGCTCGGCTCGACTCC 59.716 63.158 0.00 0.00 0.00 3.85
4551 5746 8.762426 GTTTCTAGTAAGTACTTTCCACACTTG 58.238 37.037 14.49 11.28 37.73 3.16
4552 5747 7.930325 GGTTTCTAGTAAGTACTTTCCACACTT 59.070 37.037 14.49 0.00 37.73 3.16
4553 5748 7.070322 TGGTTTCTAGTAAGTACTTTCCACACT 59.930 37.037 14.49 12.78 37.73 3.55
4630 5836 1.187087 GATCGACCTGACCTTGACCT 58.813 55.000 0.00 0.00 0.00 3.85
4631 5837 0.175989 GGATCGACCTGACCTTGACC 59.824 60.000 0.00 0.00 35.41 4.02
4632 5838 3.742983 GGATCGACCTGACCTTGAC 57.257 57.895 0.00 0.00 35.41 3.18
4642 5848 2.069273 CACACAAACAGAGGATCGACC 58.931 52.381 0.00 0.00 42.67 4.79
4643 5849 2.069273 CCACACAAACAGAGGATCGAC 58.931 52.381 0.00 0.00 42.67 4.20
4644 5850 1.967779 TCCACACAAACAGAGGATCGA 59.032 47.619 0.00 0.00 42.67 3.59
4645 5851 2.455674 TCCACACAAACAGAGGATCG 57.544 50.000 0.00 0.00 42.67 3.69
4682 5888 6.473778 CGGTATACTTGTTCTTCTGTCATCAG 59.526 42.308 2.25 0.00 42.54 2.90
4683 5889 6.071560 ACGGTATACTTGTTCTTCTGTCATCA 60.072 38.462 2.25 0.00 0.00 3.07
4684 5890 6.331061 ACGGTATACTTGTTCTTCTGTCATC 58.669 40.000 2.25 0.00 0.00 2.92
4685 5891 6.071560 TGACGGTATACTTGTTCTTCTGTCAT 60.072 38.462 2.25 0.00 35.66 3.06
4686 5892 5.242171 TGACGGTATACTTGTTCTTCTGTCA 59.758 40.000 2.25 0.00 37.38 3.58
4723 5929 0.959372 CTGCTGCCAGGAGTCAAAGG 60.959 60.000 4.87 0.00 35.38 3.11
4770 5976 3.853831 TTGATGTCCACAATGCATCAC 57.146 42.857 0.00 0.00 45.64 3.06
4771 5977 3.827876 AGTTTGATGTCCACAATGCATCA 59.172 39.130 0.00 0.00 44.72 3.07
4777 5983 3.157087 GACCCAGTTTGATGTCCACAAT 58.843 45.455 0.00 0.00 0.00 2.71
4792 5998 5.770162 AGAGGTTATTTTCACAAAGACCCAG 59.230 40.000 0.00 0.00 34.63 4.45
4798 6004 6.642540 GCAAAGGAGAGGTTATTTTCACAAAG 59.357 38.462 0.00 0.00 0.00 2.77
4829 6035 5.065731 TCGGTCCTATCTTCTTCTAACGAAC 59.934 44.000 0.00 0.00 0.00 3.95
4870 6080 6.827586 TCTTTATTTTAAACCAGATGCGGT 57.172 33.333 0.00 0.00 42.71 5.68
4871 6081 7.312899 AGTTCTTTATTTTAAACCAGATGCGG 58.687 34.615 0.00 0.00 0.00 5.69
4892 6122 3.750130 TCTGCTGAAGATTGCTTGAGTTC 59.250 43.478 0.00 0.00 37.62 3.01
4895 6125 3.597255 TCTCTGCTGAAGATTGCTTGAG 58.403 45.455 0.00 0.00 38.25 3.02
4896 6126 3.260128 TCTCTCTGCTGAAGATTGCTTGA 59.740 43.478 0.00 0.00 33.61 3.02
4897 6127 3.597255 TCTCTCTGCTGAAGATTGCTTG 58.403 45.455 0.00 0.00 33.61 4.01
4898 6128 3.514706 TCTCTCTCTGCTGAAGATTGCTT 59.485 43.478 0.00 0.00 36.96 3.91
4900 6130 3.450578 CTCTCTCTCTGCTGAAGATTGC 58.549 50.000 0.00 0.00 33.29 3.56
4901 6131 3.181473 CCCTCTCTCTCTGCTGAAGATTG 60.181 52.174 0.00 0.00 33.29 2.67
4902 6132 3.033184 CCCTCTCTCTCTGCTGAAGATT 58.967 50.000 0.00 0.00 33.29 2.40
4904 6134 1.341877 CCCCTCTCTCTCTGCTGAAGA 60.342 57.143 0.00 0.88 0.00 2.87
4906 6136 0.325110 CCCCCTCTCTCTCTGCTGAA 60.325 60.000 0.00 0.00 0.00 3.02
4918 6148 1.077445 GGCTTTTGCTTCCCCCTCT 59.923 57.895 0.00 0.00 46.54 3.69
4953 6185 2.776536 CCATCTCATCACTTTCCCCTCT 59.223 50.000 0.00 0.00 0.00 3.69
5048 6283 2.561419 ACACACACGGTAAGCTATCTGT 59.439 45.455 0.00 0.00 0.00 3.41
5049 6284 3.179830 GACACACACGGTAAGCTATCTG 58.820 50.000 0.00 0.00 0.00 2.90
5050 6285 2.165845 GGACACACACGGTAAGCTATCT 59.834 50.000 0.00 0.00 0.00 1.98
5051 6286 2.165845 AGGACACACACGGTAAGCTATC 59.834 50.000 0.00 0.00 0.00 2.08
5052 6287 2.176889 AGGACACACACGGTAAGCTAT 58.823 47.619 0.00 0.00 0.00 2.97


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

AutoCloner maintained by Alex Coulton.