Multiple sequence alignment - TraesCS2D01G065700

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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 TraesCS2D01G065700 chr2D 100.000 3368 0 0 1 3368 27905208 27908575 0.000000e+00 6220
1 TraesCS2D01G065700 chr2A 86.320 2807 177 104 686 3368 30130670 30133393 0.000000e+00 2865
2 TraesCS2D01G065700 chr2A 94.231 156 8 1 1 156 30129249 30129403 1.560000e-58 237
3 TraesCS2D01G065700 chr2B 86.949 1632 115 46 817 2366 44402806 44404421 0.000000e+00 1744
4 TraesCS2D01G065700 chr2B 85.294 544 54 15 2803 3339 44404879 44405403 3.820000e-149 538
5 TraesCS2D01G065700 chr2B 92.568 148 9 2 2543 2688 44404582 44404729 9.470000e-51 211
6 TraesCS2D01G065700 chr2B 87.719 171 7 4 1 157 44401092 44401262 1.600000e-43 187


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 TraesCS2D01G065700 chr2D 27905208 27908575 3367 False 6220 6220 100.0000 1 3368 1 chr2D.!!$F1 3367
1 TraesCS2D01G065700 chr2A 30129249 30133393 4144 False 1551 2865 90.2755 1 3368 2 chr2A.!!$F1 3367
2 TraesCS2D01G065700 chr2B 44401092 44405403 4311 False 670 1744 88.1325 1 3339 4 chr2B.!!$F1 3338

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
570 1562 0.036765 GCCCGCATCCCGACATAATA 60.037 55.0 0.00 0.0 40.02 0.98 F
795 1790 0.247655 GCACGATGCGTATGTGTTGG 60.248 55.0 14.02 0.0 38.32 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1446 2509 0.030235 GTTCACGCCCTGGAAACAAC 59.970 55.0 0.0 0.0 42.06 3.32 R
2535 3757 0.179140 CGCTGAAGCCTCTCTCTGTC 60.179 60.0 0.0 0.0 37.91 3.51 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
66 67 3.178865 ACATATATTGTCCTACCCCCGG 58.821 50.000 0.00 0.00 30.89 5.73
181 1023 2.873472 CGAGTCCGAGTCTAGCTGTTAT 59.127 50.000 0.00 0.00 38.22 1.89
185 1027 4.277174 AGTCCGAGTCTAGCTGTTATGATG 59.723 45.833 0.00 0.00 0.00 3.07
193 1035 7.061054 AGTCTAGCTGTTATGATGTGGTACTA 58.939 38.462 0.00 0.00 0.00 1.82
197 1039 7.655521 AGCTGTTATGATGTGGTACTACTAA 57.344 36.000 10.95 0.00 0.00 2.24
198 1040 8.251383 AGCTGTTATGATGTGGTACTACTAAT 57.749 34.615 10.95 4.46 0.00 1.73
199 1041 8.144478 AGCTGTTATGATGTGGTACTACTAATG 58.856 37.037 10.95 1.00 0.00 1.90
200 1042 7.926555 GCTGTTATGATGTGGTACTACTAATGT 59.073 37.037 10.95 0.00 0.00 2.71
237 1079 8.721133 ATATAATCCCTTTTTAGCCGGATTTT 57.279 30.769 5.05 1.52 41.32 1.82
246 1088 6.937436 TTTTAGCCGGATTTTCCTATCTTC 57.063 37.500 5.05 0.00 33.30 2.87
247 1089 3.113260 AGCCGGATTTTCCTATCTTCG 57.887 47.619 5.05 0.00 33.30 3.79
253 1095 5.444122 CGGATTTTCCTATCTTCGAAATGC 58.556 41.667 0.00 0.00 33.30 3.56
256 1098 3.536956 TTCCTATCTTCGAAATGCGGT 57.463 42.857 0.00 0.00 41.33 5.68
275 1117 9.612066 AATGCGGTTATCCAATTTATTTCAATT 57.388 25.926 0.00 0.00 0.00 2.32
297 1142 2.164827 TGTGGATGCTTAGCTTGCAATG 59.835 45.455 14.99 0.00 44.01 2.82
306 1151 0.333993 AGCTTGCAATGGGAGGATGT 59.666 50.000 0.00 0.00 0.00 3.06
310 1155 3.243636 GCTTGCAATGGGAGGATGTTATG 60.244 47.826 0.00 0.00 0.00 1.90
314 1159 5.514169 TGCAATGGGAGGATGTTATGTTTA 58.486 37.500 0.00 0.00 0.00 2.01
322 1167 6.867293 GGGAGGATGTTATGTTTATCTACGAC 59.133 42.308 0.00 0.00 0.00 4.34
323 1168 7.255871 GGGAGGATGTTATGTTTATCTACGACT 60.256 40.741 0.00 0.00 0.00 4.18
324 1169 8.790718 GGAGGATGTTATGTTTATCTACGACTA 58.209 37.037 0.00 0.00 0.00 2.59
325 1170 9.609950 GAGGATGTTATGTTTATCTACGACTAC 57.390 37.037 0.00 0.00 0.00 2.73
339 1184 3.604582 ACGACTACGAGTTAGCTTACCT 58.395 45.455 0.00 0.00 42.66 3.08
340 1185 3.373439 ACGACTACGAGTTAGCTTACCTG 59.627 47.826 0.00 0.00 42.66 4.00
364 1210 6.481976 TGGATACCTGTTGCTATTTCATTACG 59.518 38.462 0.00 0.00 0.00 3.18
385 1231 5.789774 CGTTGTTTTACTACGTACGTTCT 57.210 39.130 27.92 14.07 41.17 3.01
386 1232 6.888747 CGTTGTTTTACTACGTACGTTCTA 57.111 37.500 27.92 13.02 41.17 2.10
387 1233 7.302811 CGTTGTTTTACTACGTACGTTCTAA 57.697 36.000 27.92 17.96 41.17 2.10
391 1237 9.885934 TTGTTTTACTACGTACGTTCTAATGTA 57.114 29.630 27.92 15.69 0.00 2.29
392 1238 9.325150 TGTTTTACTACGTACGTTCTAATGTAC 57.675 33.333 27.92 17.22 44.22 2.90
397 1243 3.188460 ACGTACGTTCTAATGTACCGTGT 59.812 43.478 16.72 8.31 44.61 4.49
404 1250 4.787260 TCTAATGTACCGTGTGTGCTTA 57.213 40.909 0.00 0.00 0.00 3.09
411 1257 1.668751 ACCGTGTGTGCTTAAAGTGTG 59.331 47.619 0.00 0.00 0.00 3.82
412 1258 1.002900 CCGTGTGTGCTTAAAGTGTGG 60.003 52.381 0.00 0.00 0.00 4.17
416 1262 4.497340 CGTGTGTGCTTAAAGTGTGGAAAT 60.497 41.667 0.00 0.00 0.00 2.17
420 1266 8.293867 GTGTGTGCTTAAAGTGTGGAAATATTA 58.706 33.333 0.00 0.00 0.00 0.98
431 1277 8.142994 AGTGTGGAAATATTAATACTTGCTCG 57.857 34.615 9.17 0.00 0.00 5.03
435 1281 7.012044 GTGGAAATATTAATACTTGCTCGGTGT 59.988 37.037 9.17 0.00 0.00 4.16
439 1285 7.941795 ATATTAATACTTGCTCGGTGTGTAC 57.058 36.000 0.00 0.00 0.00 2.90
443 1289 2.955614 ACTTGCTCGGTGTGTACATAC 58.044 47.619 13.90 13.90 0.00 2.39
444 1290 1.917955 CTTGCTCGGTGTGTACATACG 59.082 52.381 15.51 12.35 0.00 3.06
445 1291 0.457166 TGCTCGGTGTGTACATACGC 60.457 55.000 15.51 13.65 37.23 4.42
446 1292 0.457166 GCTCGGTGTGTACATACGCA 60.457 55.000 15.51 1.15 43.66 5.24
447 1293 1.801395 GCTCGGTGTGTACATACGCAT 60.801 52.381 15.51 0.00 46.80 4.73
448 1294 2.542205 GCTCGGTGTGTACATACGCATA 60.542 50.000 15.51 1.72 46.80 3.14
450 1296 1.776897 CGGTGTGTACATACGCATACG 59.223 52.381 15.51 9.68 46.80 3.06
482 1328 2.278336 CGACTAAATCCGCGCCGA 60.278 61.111 0.00 0.00 0.00 5.54
483 1329 1.660575 CGACTAAATCCGCGCCGAT 60.661 57.895 5.36 5.36 0.00 4.18
485 1331 0.507358 GACTAAATCCGCGCCGATTC 59.493 55.000 21.44 8.13 31.14 2.52
486 1332 0.878961 ACTAAATCCGCGCCGATTCC 60.879 55.000 21.44 0.00 31.14 3.01
487 1333 1.886861 CTAAATCCGCGCCGATTCCG 61.887 60.000 21.44 12.93 31.14 4.30
494 1340 4.230002 CGCCGATTCCGCCCCTAA 62.230 66.667 0.00 0.00 0.00 2.69
495 1341 2.590859 GCCGATTCCGCCCCTAAC 60.591 66.667 0.00 0.00 0.00 2.34
497 1343 2.110420 CGATTCCGCCCCTAACCC 59.890 66.667 0.00 0.00 0.00 4.11
499 1345 2.043941 ATTCCGCCCCTAACCCCT 59.956 61.111 0.00 0.00 0.00 4.79
500 1346 0.765519 GATTCCGCCCCTAACCCCTA 60.766 60.000 0.00 0.00 0.00 3.53
505 1351 1.350310 CGCCCCTAACCCCTAACCAT 61.350 60.000 0.00 0.00 0.00 3.55
506 1352 0.185175 GCCCCTAACCCCTAACCATG 59.815 60.000 0.00 0.00 0.00 3.66
513 1505 0.846693 ACCCCTAACCATGAGCATCC 59.153 55.000 0.00 0.00 0.00 3.51
515 1507 1.215173 CCCCTAACCATGAGCATCCAA 59.785 52.381 0.00 0.00 0.00 3.53
518 1510 2.646930 CTAACCATGAGCATCCAAGCA 58.353 47.619 0.00 0.00 36.85 3.91
533 1525 1.865788 AAGCATGCGCCGTTTGTGAT 61.866 50.000 13.01 0.00 39.83 3.06
534 1526 1.869132 GCATGCGCCGTTTGTGATC 60.869 57.895 4.18 0.00 0.00 2.92
535 1527 1.226379 CATGCGCCGTTTGTGATCC 60.226 57.895 4.18 0.00 0.00 3.36
536 1528 2.749865 ATGCGCCGTTTGTGATCCG 61.750 57.895 4.18 0.00 0.00 4.18
537 1529 3.419759 GCGCCGTTTGTGATCCGT 61.420 61.111 0.00 0.00 0.00 4.69
538 1530 2.961669 GCGCCGTTTGTGATCCGTT 61.962 57.895 0.00 0.00 0.00 4.44
539 1531 1.572447 CGCCGTTTGTGATCCGTTT 59.428 52.632 0.00 0.00 0.00 3.60
540 1532 0.040781 CGCCGTTTGTGATCCGTTTT 60.041 50.000 0.00 0.00 0.00 2.43
541 1533 1.194997 CGCCGTTTGTGATCCGTTTTA 59.805 47.619 0.00 0.00 0.00 1.52
542 1534 2.159626 CGCCGTTTGTGATCCGTTTTAT 60.160 45.455 0.00 0.00 0.00 1.40
543 1535 3.422655 GCCGTTTGTGATCCGTTTTATC 58.577 45.455 0.00 0.00 0.00 1.75
544 1536 3.666001 CCGTTTGTGATCCGTTTTATCG 58.334 45.455 0.00 0.00 0.00 2.92
550 1542 5.013568 TGTGATCCGTTTTATCGTACCAT 57.986 39.130 0.00 0.00 0.00 3.55
569 1561 1.302511 GCCCGCATCCCGACATAAT 60.303 57.895 0.00 0.00 40.02 1.28
570 1562 0.036765 GCCCGCATCCCGACATAATA 60.037 55.000 0.00 0.00 40.02 0.98
571 1563 1.609580 GCCCGCATCCCGACATAATAA 60.610 52.381 0.00 0.00 40.02 1.40
578 1570 3.564235 TCCCGACATAATAATCCGACG 57.436 47.619 0.00 0.00 0.00 5.12
601 1593 0.442310 AACGCGACGACCATCAAATG 59.558 50.000 15.93 0.00 0.00 2.32
619 1612 2.617274 GCTGCCCGTTTCGCTTTCT 61.617 57.895 0.00 0.00 0.00 2.52
641 1634 3.507233 TGAATCCAGAGAAATGTTGGCAC 59.493 43.478 0.00 0.00 31.94 5.01
644 1637 2.086869 CCAGAGAAATGTTGGCACGAT 58.913 47.619 0.00 0.00 0.00 3.73
645 1638 2.159476 CCAGAGAAATGTTGGCACGATG 60.159 50.000 0.00 0.00 0.00 3.84
647 1640 1.470098 GAGAAATGTTGGCACGATGCT 59.530 47.619 9.31 0.00 44.28 3.79
648 1641 1.470098 AGAAATGTTGGCACGATGCTC 59.530 47.619 9.31 2.15 44.28 4.26
649 1642 0.168788 AAATGTTGGCACGATGCTCG 59.831 50.000 9.31 4.36 44.28 5.03
650 1643 1.647545 AATGTTGGCACGATGCTCGG 61.648 55.000 9.75 1.70 45.59 4.63
656 1649 3.554692 CACGATGCTCGGCCGAAC 61.555 66.667 30.53 25.91 45.59 3.95
669 1662 3.809400 CGAACCGACGAACGCGAC 61.809 66.667 15.93 5.44 41.64 5.19
675 1668 4.348081 GACGAACGCGACGACATA 57.652 55.556 28.40 0.00 41.64 2.29
676 1669 2.628972 GACGAACGCGACGACATAA 58.371 52.632 28.40 0.00 41.64 1.90
677 1670 1.186030 GACGAACGCGACGACATAAT 58.814 50.000 28.40 11.49 41.64 1.28
678 1671 2.365948 GACGAACGCGACGACATAATA 58.634 47.619 28.40 0.00 41.64 0.98
679 1672 2.777845 GACGAACGCGACGACATAATAA 59.222 45.455 28.40 0.00 41.64 1.40
680 1673 3.365832 ACGAACGCGACGACATAATAAT 58.634 40.909 28.40 7.68 41.64 1.28
681 1674 3.792956 ACGAACGCGACGACATAATAATT 59.207 39.130 28.40 3.69 41.64 1.40
682 1675 4.085924 ACGAACGCGACGACATAATAATTC 60.086 41.667 28.40 11.19 41.64 2.17
683 1676 4.350425 AACGCGACGACATAATAATTCG 57.650 40.909 15.93 0.00 38.73 3.34
684 1677 3.620761 ACGCGACGACATAATAATTCGA 58.379 40.909 15.93 0.00 36.58 3.71
693 1686 6.075728 ACGACATAATAATTCGACGAAACTCG 60.076 38.462 15.22 12.78 39.82 4.18
695 1688 3.920112 AATAATTCGACGAAACTCGGC 57.080 42.857 15.22 0.00 46.24 5.54
772 1767 4.431809 TGAAGCAAGTGTTTGAACCAATG 58.568 39.130 0.00 0.00 36.36 2.82
786 1781 1.209898 CAATGTTGGCACGATGCGT 59.790 52.632 0.00 0.00 46.21 5.24
787 1782 0.445829 CAATGTTGGCACGATGCGTA 59.554 50.000 0.00 0.00 46.21 4.42
788 1783 1.063912 CAATGTTGGCACGATGCGTAT 59.936 47.619 0.00 0.00 46.21 3.06
790 1785 0.672091 TGTTGGCACGATGCGTATGT 60.672 50.000 0.00 0.00 46.21 2.29
791 1786 0.247655 GTTGGCACGATGCGTATGTG 60.248 55.000 10.20 10.20 46.21 3.21
793 1788 0.672091 TGGCACGATGCGTATGTGTT 60.672 50.000 14.02 0.00 46.21 3.32
795 1790 0.247655 GCACGATGCGTATGTGTTGG 60.248 55.000 14.02 0.00 38.32 3.77
796 1791 0.373370 CACGATGCGTATGTGTTGGG 59.627 55.000 0.00 0.00 38.32 4.12
797 1792 0.036765 ACGATGCGTATGTGTTGGGT 60.037 50.000 0.00 0.00 38.73 4.51
798 1793 0.650512 CGATGCGTATGTGTTGGGTC 59.349 55.000 0.00 0.00 0.00 4.46
799 1794 1.739035 CGATGCGTATGTGTTGGGTCT 60.739 52.381 0.00 0.00 0.00 3.85
800 1795 1.933853 GATGCGTATGTGTTGGGTCTC 59.066 52.381 0.00 0.00 0.00 3.36
801 1796 0.036765 TGCGTATGTGTTGGGTCTCC 60.037 55.000 0.00 0.00 0.00 3.71
802 1797 0.036765 GCGTATGTGTTGGGTCTCCA 60.037 55.000 0.00 0.00 42.25 3.86
813 1808 3.732048 TGGGTCTCCAACTTTTATCCC 57.268 47.619 0.00 0.00 40.73 3.85
815 1810 2.310647 GGGTCTCCAACTTTTATCCCCA 59.689 50.000 0.00 0.00 0.00 4.96
863 1893 1.725665 GCTCCCGATTTAAACCGGC 59.274 57.895 16.07 0.38 44.07 6.13
895 1927 4.939368 CCACCGACCCAACCGCAA 62.939 66.667 0.00 0.00 0.00 4.85
927 1959 1.152735 TAGCCGTTGCCCAACCAAA 60.153 52.632 5.64 0.00 38.03 3.28
941 1977 2.262423 ACCAAACACTCTGCTTCCTC 57.738 50.000 0.00 0.00 0.00 3.71
942 1978 1.771255 ACCAAACACTCTGCTTCCTCT 59.229 47.619 0.00 0.00 0.00 3.69
943 1979 2.173569 ACCAAACACTCTGCTTCCTCTT 59.826 45.455 0.00 0.00 0.00 2.85
944 1980 2.810852 CCAAACACTCTGCTTCCTCTTC 59.189 50.000 0.00 0.00 0.00 2.87
945 1981 2.810852 CAAACACTCTGCTTCCTCTTCC 59.189 50.000 0.00 0.00 0.00 3.46
946 1982 0.605589 ACACTCTGCTTCCTCTTCCG 59.394 55.000 0.00 0.00 0.00 4.30
948 1984 0.892063 ACTCTGCTTCCTCTTCCGTC 59.108 55.000 0.00 0.00 0.00 4.79
991 2035 1.886730 TTCCCCGTCCTCTGATCCCT 61.887 60.000 0.00 0.00 0.00 4.20
992 2036 1.834822 CCCCGTCCTCTGATCCCTC 60.835 68.421 0.00 0.00 0.00 4.30
993 2037 1.834822 CCCGTCCTCTGATCCCTCC 60.835 68.421 0.00 0.00 0.00 4.30
1008 2052 1.231641 CTCCCCTCCGATGGACTCT 59.768 63.158 0.00 0.00 0.00 3.24
1165 2223 3.735237 TCGATAGATCCTGGCTGAAAC 57.265 47.619 0.00 0.00 42.67 2.78
1169 2227 1.076705 GATCCTGGCTGAAACCCCC 60.077 63.158 0.00 0.00 0.00 5.40
1170 2228 1.544917 ATCCTGGCTGAAACCCCCT 60.545 57.895 0.00 0.00 0.00 4.79
1171 2229 1.575447 ATCCTGGCTGAAACCCCCTC 61.575 60.000 0.00 0.00 0.00 4.30
1176 2234 1.062505 TGGCTGAAACCCCCTCTTTTT 60.063 47.619 0.00 0.00 0.00 1.94
1177 2235 1.618837 GGCTGAAACCCCCTCTTTTTC 59.381 52.381 0.00 0.00 0.00 2.29
1178 2236 1.618837 GCTGAAACCCCCTCTTTTTCC 59.381 52.381 0.00 0.00 0.00 3.13
1383 2446 2.718747 TAACCACGGTTCCAGCCACG 62.719 60.000 4.34 0.00 39.31 4.94
1387 2450 2.047655 CGGTTCCAGCCACGCTTA 60.048 61.111 0.00 0.00 36.40 3.09
1396 2459 1.324736 CAGCCACGCTTACGATTTCTC 59.675 52.381 0.00 0.00 43.93 2.87
1406 2469 1.068250 CGATTTCTCCTCTCCCCGC 59.932 63.158 0.00 0.00 0.00 6.13
1424 2487 3.187699 CTCCGATCCGACGCTCTGG 62.188 68.421 0.00 0.00 0.00 3.86
1427 2490 2.761195 CGATCCGACGCTCTGGTGA 61.761 63.158 0.00 0.00 0.00 4.02
1428 2491 1.736586 GATCCGACGCTCTGGTGAT 59.263 57.895 0.00 0.00 0.00 3.06
1432 2495 1.869574 CGACGCTCTGGTGATGACG 60.870 63.158 0.00 0.00 0.00 4.35
1443 2506 1.471964 GTGATGACGATCTGACGCTC 58.528 55.000 0.00 0.00 36.70 5.03
1444 2507 0.382158 TGATGACGATCTGACGCTCC 59.618 55.000 0.00 0.00 36.70 4.70
1445 2508 0.658829 GATGACGATCTGACGCTCCG 60.659 60.000 0.00 0.00 36.70 4.63
1446 2509 2.024871 GACGATCTGACGCTCCGG 59.975 66.667 0.00 0.00 36.70 5.14
1447 2510 2.750637 ACGATCTGACGCTCCGGT 60.751 61.111 0.00 0.00 36.70 5.28
1728 2820 0.521735 GGCCGCGAACAGAAAGAATT 59.478 50.000 8.23 0.00 0.00 2.17
1759 2857 2.570468 TTCACGCGATTTTCGTTGAG 57.430 45.000 15.93 0.00 42.81 3.02
1762 2860 0.788391 ACGCGATTTTCGTTGAGGAC 59.212 50.000 15.93 0.00 42.81 3.85
1766 2864 2.931320 GCGATTTTCGTTGAGGACTCCT 60.931 50.000 0.00 0.00 42.81 3.69
1781 2879 2.165437 GACTCCTCTGATTTGAGCGAGT 59.835 50.000 12.14 12.14 42.06 4.18
1783 2881 1.133216 TCCTCTGATTTGAGCGAGTCG 59.867 52.381 8.54 8.54 33.02 4.18
1784 2882 1.133216 CCTCTGATTTGAGCGAGTCGA 59.867 52.381 18.61 0.00 33.02 4.20
1785 2883 2.181205 CTCTGATTTGAGCGAGTCGAC 58.819 52.381 18.61 7.70 0.00 4.20
1793 2906 3.764049 GCGAGTCGACGGTTGTGC 61.764 66.667 18.61 5.51 0.00 4.57
1885 2998 3.067985 TGCGGTTCATGCAGGAGA 58.932 55.556 0.00 0.00 37.44 3.71
1974 3093 2.223525 CGAGGAAGACGACCTGGTAATC 60.224 54.545 0.00 0.00 37.93 1.75
1976 3095 2.496470 AGGAAGACGACCTGGTAATCAC 59.504 50.000 0.00 0.00 36.30 3.06
2005 3138 7.912056 TCTTCAGAATCAAAATCGACAGAAT 57.088 32.000 0.00 0.00 0.00 2.40
2012 3154 9.388506 AGAATCAAAATCGACAGAATCTGTTAT 57.611 29.630 17.79 11.26 45.44 1.89
2042 3188 3.243434 GCCTGGCTGATGATCAATCTTTG 60.243 47.826 12.43 0.00 36.15 2.77
2044 3190 4.202020 CCTGGCTGATGATCAATCTTTGTG 60.202 45.833 0.00 0.00 36.15 3.33
2045 3191 3.697542 TGGCTGATGATCAATCTTTGTGG 59.302 43.478 0.00 0.00 36.15 4.17
2046 3192 3.490419 GGCTGATGATCAATCTTTGTGGC 60.490 47.826 0.00 0.00 36.15 5.01
2136 3282 3.119096 GAGAACGCGAACCTGGCC 61.119 66.667 15.93 0.00 0.00 5.36
2202 3348 1.519719 CGCCCAGGAGGAAGAAGAG 59.480 63.158 0.00 0.00 38.24 2.85
2205 3351 1.494960 CCCAGGAGGAAGAAGAGGAG 58.505 60.000 0.00 0.00 38.24 3.69
2232 3378 4.436998 GACCACCTCCTCACCGCG 62.437 72.222 0.00 0.00 0.00 6.46
2298 3450 2.956964 CCGCTCGGCAAGATCGAC 60.957 66.667 6.30 0.00 40.58 4.20
2386 3587 3.507233 GTGAAATGTTGAGGATTCCTGCA 59.493 43.478 10.74 6.80 31.76 4.41
2390 3591 0.807496 GTTGAGGATTCCTGCAGCAC 59.193 55.000 10.74 1.36 31.76 4.40
2438 3654 1.439365 GCGTGCTTCAGTTTGAGCG 60.439 57.895 0.00 0.00 0.00 5.03
2440 3656 1.648720 GTGCTTCAGTTTGAGCGCA 59.351 52.632 11.47 0.00 33.99 6.09
2451 3670 4.057428 GAGCGCACTCTCCGGTGT 62.057 66.667 11.47 0.00 40.03 4.16
2454 3673 3.680786 CGCACTCTCCGGTGTCCA 61.681 66.667 0.00 0.00 39.21 4.02
2464 3683 0.250727 CCGGTGTCCAGATTTGGTGT 60.251 55.000 1.59 0.00 45.26 4.16
2470 3689 4.825085 GGTGTCCAGATTTGGTGTTTCTTA 59.175 41.667 1.59 0.00 45.26 2.10
2519 3741 6.744112 TGAATGTTAACCATGTTCCTTGTTC 58.256 36.000 2.48 0.00 32.82 3.18
2524 3746 6.549364 TGTTAACCATGTTCCTTGTTCATTCT 59.451 34.615 2.48 0.00 0.00 2.40
2525 3747 7.069331 TGTTAACCATGTTCCTTGTTCATTCTT 59.931 33.333 2.48 0.00 0.00 2.52
2526 3748 5.458041 ACCATGTTCCTTGTTCATTCTTG 57.542 39.130 0.00 0.00 0.00 3.02
2527 3749 4.895297 ACCATGTTCCTTGTTCATTCTTGT 59.105 37.500 0.00 0.00 0.00 3.16
2528 3750 5.363580 ACCATGTTCCTTGTTCATTCTTGTT 59.636 36.000 0.00 0.00 0.00 2.83
2529 3751 6.127083 ACCATGTTCCTTGTTCATTCTTGTTT 60.127 34.615 0.00 0.00 0.00 2.83
2530 3752 7.069331 ACCATGTTCCTTGTTCATTCTTGTTTA 59.931 33.333 0.00 0.00 0.00 2.01
2531 3753 8.090214 CCATGTTCCTTGTTCATTCTTGTTTAT 58.910 33.333 0.00 0.00 0.00 1.40
2532 3754 9.480053 CATGTTCCTTGTTCATTCTTGTTTATT 57.520 29.630 0.00 0.00 0.00 1.40
2533 3755 9.696917 ATGTTCCTTGTTCATTCTTGTTTATTC 57.303 29.630 0.00 0.00 0.00 1.75
2534 3756 8.690884 TGTTCCTTGTTCATTCTTGTTTATTCA 58.309 29.630 0.00 0.00 0.00 2.57
2535 3757 9.185192 GTTCCTTGTTCATTCTTGTTTATTCAG 57.815 33.333 0.00 0.00 0.00 3.02
2536 3758 8.690203 TCCTTGTTCATTCTTGTTTATTCAGA 57.310 30.769 0.00 0.00 0.00 3.27
2537 3759 8.567948 TCCTTGTTCATTCTTGTTTATTCAGAC 58.432 33.333 0.00 0.00 0.00 3.51
2538 3760 8.352201 CCTTGTTCATTCTTGTTTATTCAGACA 58.648 33.333 0.00 0.00 0.00 3.41
2539 3761 9.390795 CTTGTTCATTCTTGTTTATTCAGACAG 57.609 33.333 0.00 0.00 0.00 3.51
2540 3762 8.675705 TGTTCATTCTTGTTTATTCAGACAGA 57.324 30.769 0.00 0.00 0.00 3.41
2541 3763 8.777413 TGTTCATTCTTGTTTATTCAGACAGAG 58.223 33.333 0.00 0.00 0.00 3.35
2565 3787 0.933796 GCTTCAGCGCCTCAGATAAC 59.066 55.000 2.29 0.00 0.00 1.89
2608 3830 6.016860 TGCACAGATTATTAGCATGTTCCATC 60.017 38.462 0.00 0.00 0.00 3.51
2683 3907 1.409427 ACGAAATCATCTCCGGGAGTC 59.591 52.381 22.88 11.35 0.00 3.36
2694 3918 0.035056 CCGGGAGTCAATTCTGCCTT 60.035 55.000 0.00 0.00 42.52 4.35
2695 3919 1.089920 CGGGAGTCAATTCTGCCTTG 58.910 55.000 3.67 0.00 42.52 3.61
2696 3920 1.467920 GGGAGTCAATTCTGCCTTGG 58.532 55.000 0.00 0.00 41.67 3.61
2698 3922 2.026262 GGGAGTCAATTCTGCCTTGGTA 60.026 50.000 0.00 0.00 41.67 3.25
2699 3923 3.372025 GGGAGTCAATTCTGCCTTGGTAT 60.372 47.826 0.00 0.00 41.67 2.73
2700 3924 3.629398 GGAGTCAATTCTGCCTTGGTATG 59.371 47.826 0.00 0.00 0.00 2.39
2709 3933 5.366482 TCTGCCTTGGTATGCTTGTTATA 57.634 39.130 0.00 0.00 0.00 0.98
2720 3944 9.845740 TGGTATGCTTGTTATACAGATGTAAAT 57.154 29.630 0.00 0.00 33.66 1.40
2763 3988 1.630369 TGAAGTCTGAACCTGGGATGG 59.370 52.381 0.00 0.00 0.00 3.51
2799 4025 4.044426 GCAAAAGAAAATGAACGCAGACT 58.956 39.130 0.00 0.00 0.00 3.24
2800 4026 5.212194 GCAAAAGAAAATGAACGCAGACTA 58.788 37.500 0.00 0.00 0.00 2.59
2801 4027 5.340667 GCAAAAGAAAATGAACGCAGACTAG 59.659 40.000 0.00 0.00 0.00 2.57
2820 4102 1.832998 AGGCCATGAAAAATCGGCATT 59.167 42.857 5.01 0.00 46.75 3.56
2823 4105 3.430098 GGCCATGAAAAATCGGCATTACA 60.430 43.478 0.00 0.00 46.75 2.41
2865 4147 9.338622 TGATCTAGACAGAATAGACGATTTACA 57.661 33.333 0.00 0.00 33.50 2.41
2866 4148 9.820229 GATCTAGACAGAATAGACGATTTACAG 57.180 37.037 0.00 0.00 33.50 2.74
2867 4149 8.155821 TCTAGACAGAATAGACGATTTACAGG 57.844 38.462 0.00 0.00 0.00 4.00
2969 4264 4.034510 CGCTCCAACACCAATTAGAAGATC 59.965 45.833 0.00 0.00 0.00 2.75
3110 4405 0.099082 GAGAGTAGTTCTCGGGCGTG 59.901 60.000 0.00 0.00 46.86 5.34
3113 4408 1.153881 GTAGTTCTCGGGCGTGGAC 60.154 63.158 0.00 0.00 0.00 4.02
3176 4471 3.897141 TCGGTGTCATAACCTGCATAA 57.103 42.857 0.00 0.00 38.14 1.90
3194 4489 7.201848 CCTGCATAATCCACAGAACAAACATAT 60.202 37.037 0.00 0.00 33.10 1.78
3267 4562 4.483476 ACGGTTTGCTTACAGTTGAATC 57.517 40.909 0.00 0.00 0.00 2.52
3290 4585 3.452627 TCTTCCAGCCAAGTATCTTCCTC 59.547 47.826 0.00 0.00 0.00 3.71
3308 4603 2.422479 CCTCTCTCGGTCGAATACAACA 59.578 50.000 0.00 0.00 0.00 3.33
3341 4636 4.919754 GTCATGAAGTTTTCTGCACCATTC 59.080 41.667 0.00 0.00 38.45 2.67
3362 4657 8.237267 CCATTCCTTGACTGTTAACAACTATTC 58.763 37.037 10.03 2.43 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 136 9.622004 CTAAATGCATTATTCTAATTGCCTCAG 57.378 33.333 13.39 0.00 0.00 3.35
157 173 0.470766 AGCTAGACTCGGACTCGGAT 59.529 55.000 0.00 0.00 36.95 4.18
159 175 0.745128 ACAGCTAGACTCGGACTCGG 60.745 60.000 0.00 0.00 36.95 4.63
171 1013 7.278461 AGTAGTACCACATCATAACAGCTAG 57.722 40.000 0.00 0.00 0.00 3.42
173 1015 7.655521 TTAGTAGTACCACATCATAACAGCT 57.344 36.000 0.00 0.00 0.00 4.24
181 1023 9.856162 TCAGTATACATTAGTAGTACCACATCA 57.144 33.333 5.50 0.00 32.86 3.07
205 1047 9.613428 CGGCTAAAAAGGGATTATATCATATCA 57.387 33.333 0.00 0.00 0.00 2.15
206 1048 9.057089 CCGGCTAAAAAGGGATTATATCATATC 57.943 37.037 0.00 0.00 0.00 1.63
211 1053 7.939784 AATCCGGCTAAAAAGGGATTATATC 57.060 36.000 0.00 0.00 45.05 1.63
237 1079 3.536956 AACCGCATTTCGAAGATAGGA 57.463 42.857 15.47 0.00 41.67 2.94
246 1088 7.433719 TGAAATAAATTGGATAACCGCATTTCG 59.566 33.333 3.16 0.00 39.42 3.46
247 1089 8.641499 TGAAATAAATTGGATAACCGCATTTC 57.359 30.769 3.16 0.00 39.42 2.17
275 1117 1.908344 TGCAAGCTAAGCATCCACAA 58.092 45.000 9.48 0.00 37.02 3.33
288 1133 1.188863 AACATCCTCCCATTGCAAGC 58.811 50.000 4.94 0.00 0.00 4.01
297 1142 6.867293 GTCGTAGATAAACATAACATCCTCCC 59.133 42.308 0.00 0.00 40.67 4.30
310 1155 6.942891 AGCTAACTCGTAGTCGTAGATAAAC 58.057 40.000 0.00 0.00 40.67 2.01
314 1159 5.465056 GGTAAGCTAACTCGTAGTCGTAGAT 59.535 44.000 0.00 0.00 40.67 1.98
322 1167 5.048852 GGTATCCAGGTAAGCTAACTCGTAG 60.049 48.000 0.00 0.00 0.00 3.51
323 1168 4.823989 GGTATCCAGGTAAGCTAACTCGTA 59.176 45.833 0.00 0.00 0.00 3.43
324 1169 3.635836 GGTATCCAGGTAAGCTAACTCGT 59.364 47.826 0.00 0.00 0.00 4.18
325 1170 3.890147 AGGTATCCAGGTAAGCTAACTCG 59.110 47.826 0.00 0.00 0.00 4.18
332 1177 2.092914 AGCAACAGGTATCCAGGTAAGC 60.093 50.000 0.00 0.00 0.00 3.09
339 1184 6.481976 CGTAATGAAATAGCAACAGGTATCCA 59.518 38.462 0.00 0.00 0.00 3.41
340 1185 6.482308 ACGTAATGAAATAGCAACAGGTATCC 59.518 38.462 0.00 0.00 0.00 2.59
378 1224 4.475028 CACACACGGTACATTAGAACGTA 58.525 43.478 0.00 0.00 35.85 3.57
379 1225 3.311106 CACACACGGTACATTAGAACGT 58.689 45.455 0.00 0.00 38.43 3.99
380 1226 2.091588 GCACACACGGTACATTAGAACG 59.908 50.000 0.00 0.00 0.00 3.95
381 1227 3.323243 AGCACACACGGTACATTAGAAC 58.677 45.455 0.00 0.00 0.00 3.01
383 1229 3.671008 AAGCACACACGGTACATTAGA 57.329 42.857 0.00 0.00 0.00 2.10
384 1230 5.407387 ACTTTAAGCACACACGGTACATTAG 59.593 40.000 0.00 0.00 0.00 1.73
385 1231 5.177881 CACTTTAAGCACACACGGTACATTA 59.822 40.000 0.00 0.00 0.00 1.90
386 1232 4.024387 CACTTTAAGCACACACGGTACATT 60.024 41.667 0.00 0.00 0.00 2.71
387 1233 3.496884 CACTTTAAGCACACACGGTACAT 59.503 43.478 0.00 0.00 0.00 2.29
391 1237 1.668751 CACACTTTAAGCACACACGGT 59.331 47.619 0.00 0.00 0.00 4.83
392 1238 1.002900 CCACACTTTAAGCACACACGG 60.003 52.381 0.00 0.00 0.00 4.94
411 1257 7.012044 ACACACCGAGCAAGTATTAATATTTCC 59.988 37.037 0.00 0.00 0.00 3.13
412 1258 7.916552 ACACACCGAGCAAGTATTAATATTTC 58.083 34.615 0.00 0.00 0.00 2.17
416 1262 6.865411 TGTACACACCGAGCAAGTATTAATA 58.135 36.000 0.00 0.00 0.00 0.98
420 1266 3.671008 TGTACACACCGAGCAAGTATT 57.329 42.857 0.00 0.00 0.00 1.89
465 1311 1.213094 AATCGGCGCGGATTTAGTCG 61.213 55.000 30.64 13.20 32.89 4.18
466 1312 0.507358 GAATCGGCGCGGATTTAGTC 59.493 55.000 34.51 22.68 36.79 2.59
467 1313 0.878961 GGAATCGGCGCGGATTTAGT 60.879 55.000 34.51 19.32 36.79 2.24
468 1314 1.860078 GGAATCGGCGCGGATTTAG 59.140 57.895 34.51 7.84 36.79 1.85
479 1325 2.110420 GGTTAGGGGCGGAATCGG 59.890 66.667 0.00 0.00 36.79 4.18
482 1328 0.327770 TTAGGGGTTAGGGGCGGAAT 60.328 55.000 0.00 0.00 0.00 3.01
483 1329 1.082579 TTAGGGGTTAGGGGCGGAA 59.917 57.895 0.00 0.00 0.00 4.30
485 1331 2.749584 GGTTAGGGGTTAGGGGCGG 61.750 68.421 0.00 0.00 0.00 6.13
486 1332 1.350310 ATGGTTAGGGGTTAGGGGCG 61.350 60.000 0.00 0.00 0.00 6.13
487 1333 0.185175 CATGGTTAGGGGTTAGGGGC 59.815 60.000 0.00 0.00 0.00 5.80
488 1334 1.774856 CTCATGGTTAGGGGTTAGGGG 59.225 57.143 0.00 0.00 0.00 4.79
490 1336 1.843851 TGCTCATGGTTAGGGGTTAGG 59.156 52.381 0.00 0.00 0.00 2.69
491 1337 3.496870 GGATGCTCATGGTTAGGGGTTAG 60.497 52.174 0.00 0.00 0.00 2.34
493 1339 1.215423 GGATGCTCATGGTTAGGGGTT 59.785 52.381 0.00 0.00 0.00 4.11
494 1340 0.846693 GGATGCTCATGGTTAGGGGT 59.153 55.000 0.00 0.00 0.00 4.95
495 1341 0.846015 TGGATGCTCATGGTTAGGGG 59.154 55.000 0.00 0.00 0.00 4.79
497 1343 1.952296 GCTTGGATGCTCATGGTTAGG 59.048 52.381 0.00 0.00 0.00 2.69
499 1345 2.804986 TGCTTGGATGCTCATGGTTA 57.195 45.000 0.00 0.00 0.00 2.85
500 1346 1.754803 CATGCTTGGATGCTCATGGTT 59.245 47.619 0.00 0.00 34.32 3.67
505 1351 2.767445 GCGCATGCTTGGATGCTCA 61.767 57.895 21.19 0.00 45.60 4.26
506 1352 2.025727 GCGCATGCTTGGATGCTC 59.974 61.111 21.19 12.34 45.60 4.26
513 1505 2.050168 ACAAACGGCGCATGCTTG 60.050 55.556 17.13 14.95 42.25 4.01
515 1507 2.257286 GATCACAAACGGCGCATGCT 62.257 55.000 17.13 0.00 42.25 3.79
518 1510 2.749865 CGGATCACAAACGGCGCAT 61.750 57.895 10.83 0.00 0.00 4.73
533 1525 2.553086 GGCATGGTACGATAAAACGGA 58.447 47.619 0.00 0.00 37.61 4.69
534 1526 1.600485 GGGCATGGTACGATAAAACGG 59.400 52.381 0.00 0.00 37.61 4.44
535 1527 1.259507 CGGGCATGGTACGATAAAACG 59.740 52.381 0.00 0.00 39.31 3.60
536 1528 1.003223 GCGGGCATGGTACGATAAAAC 60.003 52.381 0.00 0.00 0.00 2.43
537 1529 1.301423 GCGGGCATGGTACGATAAAA 58.699 50.000 0.00 0.00 0.00 1.52
538 1530 0.178301 TGCGGGCATGGTACGATAAA 59.822 50.000 0.00 0.00 0.00 1.40
539 1531 0.394938 ATGCGGGCATGGTACGATAA 59.605 50.000 5.17 0.00 35.03 1.75
540 1532 0.037697 GATGCGGGCATGGTACGATA 60.038 55.000 11.44 0.00 36.70 2.92
541 1533 1.301716 GATGCGGGCATGGTACGAT 60.302 57.895 11.44 0.00 36.70 3.73
542 1534 2.108157 GATGCGGGCATGGTACGA 59.892 61.111 11.44 0.00 36.70 3.43
543 1535 2.972505 GGATGCGGGCATGGTACG 60.973 66.667 11.44 0.00 36.70 3.67
544 1536 2.594592 GGGATGCGGGCATGGTAC 60.595 66.667 11.44 0.00 36.70 3.34
550 1542 2.050836 ATTATGTCGGGATGCGGGCA 62.051 55.000 0.75 0.75 0.00 5.36
569 1561 1.386412 GTCGCGTTTTTCGTCGGATTA 59.614 47.619 5.77 0.00 42.13 1.75
570 1562 0.162294 GTCGCGTTTTTCGTCGGATT 59.838 50.000 5.77 0.00 42.13 3.01
571 1563 1.777199 GTCGCGTTTTTCGTCGGAT 59.223 52.632 5.77 0.00 42.13 4.18
578 1570 0.509499 TGATGGTCGTCGCGTTTTTC 59.491 50.000 5.77 0.00 0.00 2.29
601 1593 2.126850 GAAAGCGAAACGGGCAGC 60.127 61.111 0.00 0.00 0.00 5.25
619 1612 3.507233 GTGCCAACATTTCTCTGGATTCA 59.493 43.478 0.00 0.00 31.38 2.57
652 1645 3.809400 GTCGCGTTCGTCGGTTCG 61.809 66.667 5.77 0.00 40.26 3.95
653 1646 3.809400 CGTCGCGTTCGTCGGTTC 61.809 66.667 5.77 0.00 41.93 3.62
656 1649 2.884866 TATGTCGTCGCGTTCGTCGG 62.885 60.000 20.51 0.36 44.74 4.79
658 1651 1.186030 ATTATGTCGTCGCGTTCGTC 58.814 50.000 20.51 16.91 36.96 4.20
659 1652 2.456942 TATTATGTCGTCGCGTTCGT 57.543 45.000 20.51 8.92 36.96 3.85
660 1653 4.350425 AATTATTATGTCGTCGCGTTCG 57.650 40.909 5.77 12.96 0.00 3.95
661 1654 4.145243 TCGAATTATTATGTCGTCGCGTTC 59.855 41.667 5.77 0.00 36.21 3.95
662 1655 4.037021 TCGAATTATTATGTCGTCGCGTT 58.963 39.130 5.77 0.00 36.21 4.84
663 1656 3.419922 GTCGAATTATTATGTCGTCGCGT 59.580 43.478 5.77 0.00 36.21 6.01
664 1657 3.476094 CGTCGAATTATTATGTCGTCGCG 60.476 47.826 0.00 0.00 38.85 5.87
665 1658 3.660813 TCGTCGAATTATTATGTCGTCGC 59.339 43.478 6.98 0.00 42.90 5.19
666 1659 5.778459 TTCGTCGAATTATTATGTCGTCG 57.222 39.130 2.90 5.77 43.95 5.12
667 1660 7.146368 AGTTTCGTCGAATTATTATGTCGTC 57.854 36.000 8.78 0.00 36.21 4.20
668 1661 6.075728 CGAGTTTCGTCGAATTATTATGTCGT 60.076 38.462 8.78 0.00 42.85 4.34
669 1662 6.272317 CGAGTTTCGTCGAATTATTATGTCG 58.728 40.000 8.78 5.25 42.85 4.35
670 1663 6.569821 CCGAGTTTCGTCGAATTATTATGTC 58.430 40.000 8.78 0.00 42.85 3.06
671 1664 5.051240 GCCGAGTTTCGTCGAATTATTATGT 60.051 40.000 8.78 0.00 42.85 2.29
672 1665 5.363517 GCCGAGTTTCGTCGAATTATTATG 58.636 41.667 8.78 0.00 42.85 1.90
673 1666 4.446719 GGCCGAGTTTCGTCGAATTATTAT 59.553 41.667 8.78 0.00 42.85 1.28
674 1667 3.798337 GGCCGAGTTTCGTCGAATTATTA 59.202 43.478 8.78 0.00 42.85 0.98
675 1668 2.606272 GGCCGAGTTTCGTCGAATTATT 59.394 45.455 8.78 0.00 42.85 1.40
676 1669 2.199236 GGCCGAGTTTCGTCGAATTAT 58.801 47.619 8.78 0.00 42.85 1.28
677 1670 1.632422 GGCCGAGTTTCGTCGAATTA 58.368 50.000 8.78 0.00 42.85 1.40
678 1671 1.349259 CGGCCGAGTTTCGTCGAATT 61.349 55.000 24.07 0.14 42.85 2.17
679 1672 1.804326 CGGCCGAGTTTCGTCGAAT 60.804 57.895 24.07 0.00 42.85 3.34
680 1673 2.405061 TTCGGCCGAGTTTCGTCGAA 62.405 55.000 29.20 6.31 44.48 3.71
681 1674 2.906939 TTCGGCCGAGTTTCGTCGA 61.907 57.895 29.20 7.18 42.85 4.20
682 1675 2.429571 TTCGGCCGAGTTTCGTCG 60.430 61.111 29.20 0.00 38.40 5.12
683 1676 2.378084 GGTTCGGCCGAGTTTCGTC 61.378 63.158 29.20 12.91 38.40 4.20
684 1677 2.356673 GGTTCGGCCGAGTTTCGT 60.357 61.111 29.20 0.00 38.40 3.85
713 1706 0.623723 TGCTCATGGTTTAGGGGTCC 59.376 55.000 0.00 0.00 0.00 4.46
714 1707 2.019156 GCTGCTCATGGTTTAGGGGTC 61.019 57.143 0.00 0.00 0.00 4.46
721 1716 1.708341 AGTTTGGCTGCTCATGGTTT 58.292 45.000 0.00 0.00 0.00 3.27
772 1767 0.247655 CACATACGCATCGTGCCAAC 60.248 55.000 1.77 0.00 41.12 3.77
793 1788 2.310647 GGGGATAAAAGTTGGAGACCCA 59.689 50.000 0.00 0.00 41.64 4.51
795 1790 3.010250 AGTGGGGATAAAAGTTGGAGACC 59.990 47.826 0.00 0.00 0.00 3.85
796 1791 4.262617 GAGTGGGGATAAAAGTTGGAGAC 58.737 47.826 0.00 0.00 0.00 3.36
797 1792 3.265995 GGAGTGGGGATAAAAGTTGGAGA 59.734 47.826 0.00 0.00 0.00 3.71
798 1793 3.010138 TGGAGTGGGGATAAAAGTTGGAG 59.990 47.826 0.00 0.00 0.00 3.86
799 1794 2.990284 TGGAGTGGGGATAAAAGTTGGA 59.010 45.455 0.00 0.00 0.00 3.53
800 1795 3.089284 GTGGAGTGGGGATAAAAGTTGG 58.911 50.000 0.00 0.00 0.00 3.77
801 1796 4.034285 AGTGGAGTGGGGATAAAAGTTG 57.966 45.455 0.00 0.00 0.00 3.16
802 1797 4.741928 AAGTGGAGTGGGGATAAAAGTT 57.258 40.909 0.00 0.00 0.00 2.66
804 1799 7.415206 CGAATTAAAGTGGAGTGGGGATAAAAG 60.415 40.741 0.00 0.00 0.00 2.27
805 1800 6.376018 CGAATTAAAGTGGAGTGGGGATAAAA 59.624 38.462 0.00 0.00 0.00 1.52
808 1803 4.717778 TCGAATTAAAGTGGAGTGGGGATA 59.282 41.667 0.00 0.00 0.00 2.59
810 1805 2.907696 TCGAATTAAAGTGGAGTGGGGA 59.092 45.455 0.00 0.00 0.00 4.81
812 1807 3.007635 GGTCGAATTAAAGTGGAGTGGG 58.992 50.000 0.00 0.00 0.00 4.61
813 1808 2.671396 CGGTCGAATTAAAGTGGAGTGG 59.329 50.000 0.00 0.00 0.00 4.00
815 1810 3.672767 ACGGTCGAATTAAAGTGGAGT 57.327 42.857 0.00 0.00 0.00 3.85
874 1904 2.754375 GGTTGGGTCGGTGGATGT 59.246 61.111 0.00 0.00 0.00 3.06
880 1910 2.593436 CTTTGCGGTTGGGTCGGT 60.593 61.111 0.00 0.00 0.00 4.69
882 1912 3.254014 CTGCTTTGCGGTTGGGTCG 62.254 63.158 0.00 0.00 0.00 4.79
883 1913 1.856265 CTCTGCTTTGCGGTTGGGTC 61.856 60.000 0.00 0.00 36.18 4.46
895 1927 0.108424 CGGCTAGTTCTGCTCTGCTT 60.108 55.000 0.00 0.00 0.00 3.91
927 1959 0.605589 CGGAAGAGGAAGCAGAGTGT 59.394 55.000 0.00 0.00 0.00 3.55
941 1977 0.983378 ATGGGGGAGAAGGACGGAAG 60.983 60.000 0.00 0.00 0.00 3.46
942 1978 0.981277 GATGGGGGAGAAGGACGGAA 60.981 60.000 0.00 0.00 0.00 4.30
943 1979 1.382695 GATGGGGGAGAAGGACGGA 60.383 63.158 0.00 0.00 0.00 4.69
944 1980 2.797278 CGATGGGGGAGAAGGACGG 61.797 68.421 0.00 0.00 0.00 4.79
945 1981 2.815308 CGATGGGGGAGAAGGACG 59.185 66.667 0.00 0.00 0.00 4.79
946 1982 2.506472 GCGATGGGGGAGAAGGAC 59.494 66.667 0.00 0.00 0.00 3.85
948 1984 4.241555 CGGCGATGGGGGAGAAGG 62.242 72.222 0.00 0.00 0.00 3.46
973 2009 2.282446 GGGATCAGAGGACGGGGA 59.718 66.667 0.00 0.00 0.00 4.81
991 2035 1.075970 CAGAGTCCATCGGAGGGGA 60.076 63.158 9.08 2.89 29.39 4.81
992 2036 2.801631 GCAGAGTCCATCGGAGGGG 61.802 68.421 9.08 0.22 29.39 4.79
993 2037 2.801631 GGCAGAGTCCATCGGAGGG 61.802 68.421 1.39 1.39 29.39 4.30
1143 2187 3.949842 TTCAGCCAGGATCTATCGATG 57.050 47.619 8.54 0.00 0.00 3.84
1144 2188 3.007398 GGTTTCAGCCAGGATCTATCGAT 59.993 47.826 2.16 2.16 0.00 3.59
1165 2223 1.886655 CGGACAAGGAAAAAGAGGGGG 60.887 57.143 0.00 0.00 0.00 5.40
1169 2227 1.807142 GCTCCGGACAAGGAAAAAGAG 59.193 52.381 0.00 0.00 40.25 2.85
1170 2228 1.420138 AGCTCCGGACAAGGAAAAAGA 59.580 47.619 0.00 0.00 40.25 2.52
1171 2229 1.537202 CAGCTCCGGACAAGGAAAAAG 59.463 52.381 0.00 0.00 40.25 2.27
1176 2234 2.119611 TCCAGCTCCGGACAAGGA 59.880 61.111 0.00 4.80 38.80 3.36
1383 2446 2.224090 GGGGAGAGGAGAAATCGTAAGC 60.224 54.545 0.00 0.00 37.18 3.09
1384 2447 2.034812 CGGGGAGAGGAGAAATCGTAAG 59.965 54.545 0.00 0.00 0.00 2.34
1387 2450 1.677637 GCGGGGAGAGGAGAAATCGT 61.678 60.000 0.00 0.00 0.00 3.73
1396 2459 3.299190 GATCGGAGCGGGGAGAGG 61.299 72.222 0.00 0.00 0.00 3.69
1406 2469 2.329690 CAGAGCGTCGGATCGGAG 59.670 66.667 2.75 0.00 32.66 4.63
1424 2487 1.471964 GAGCGTCAGATCGTCATCAC 58.528 55.000 0.00 0.00 0.00 3.06
1427 2490 1.356979 CGGAGCGTCAGATCGTCAT 59.643 57.895 0.00 0.00 32.66 3.06
1428 2491 2.761195 CCGGAGCGTCAGATCGTCA 61.761 63.158 0.00 0.00 32.66 4.35
1432 2495 0.389948 AACAACCGGAGCGTCAGATC 60.390 55.000 9.46 0.00 0.00 2.75
1443 2506 3.361977 CGCCCTGGAAACAACCGG 61.362 66.667 0.00 0.00 42.06 5.28
1444 2507 2.593436 ACGCCCTGGAAACAACCG 60.593 61.111 0.00 0.00 42.06 4.44
1445 2508 1.104577 TTCACGCCCTGGAAACAACC 61.105 55.000 0.00 0.00 42.06 3.77
1446 2509 0.030235 GTTCACGCCCTGGAAACAAC 59.970 55.000 0.00 0.00 42.06 3.32
1447 2510 1.440938 CGTTCACGCCCTGGAAACAA 61.441 55.000 0.00 0.00 42.06 2.83
1474 2553 2.512515 GCCTGGGACGAGCACATC 60.513 66.667 0.00 0.00 0.00 3.06
1728 2820 3.489180 TCGCGTGAAAAACAAAAGGAA 57.511 38.095 5.77 0.00 0.00 3.36
1731 2823 4.884577 CGAAAATCGCGTGAAAAACAAAAG 59.115 37.500 5.77 0.00 31.14 2.27
1739 2831 2.349060 CCTCAACGAAAATCGCGTGAAA 60.349 45.455 5.77 0.00 45.12 2.69
1740 2832 1.193650 CCTCAACGAAAATCGCGTGAA 59.806 47.619 5.77 0.00 45.12 3.18
1741 2833 0.787787 CCTCAACGAAAATCGCGTGA 59.212 50.000 5.77 0.00 45.12 4.35
1759 2857 1.478510 TCGCTCAAATCAGAGGAGTCC 59.521 52.381 0.00 0.00 36.15 3.85
1762 2860 2.794282 CGACTCGCTCAAATCAGAGGAG 60.794 54.545 0.00 0.00 38.15 3.69
1766 2864 1.465856 CGTCGACTCGCTCAAATCAGA 60.466 52.381 14.70 0.00 0.00 3.27
1774 2872 2.081212 CACAACCGTCGACTCGCTC 61.081 63.158 14.70 0.00 0.00 5.03
1775 2873 2.050351 CACAACCGTCGACTCGCT 60.050 61.111 14.70 0.00 0.00 4.93
1776 2874 3.764049 GCACAACCGTCGACTCGC 61.764 66.667 14.70 3.18 0.00 5.03
1783 2881 4.012895 CTGCACCGCACAACCGTC 62.013 66.667 0.00 0.00 33.79 4.79
1974 3093 7.272084 GTCGATTTTGATTCTGAAGAAATGGTG 59.728 37.037 11.45 4.96 37.61 4.17
1976 3095 7.307694 TGTCGATTTTGATTCTGAAGAAATGG 58.692 34.615 11.45 10.65 37.61 3.16
1990 3123 8.322906 ACAATAACAGATTCTGTCGATTTTGA 57.677 30.769 19.23 0.00 44.62 2.69
2005 3138 2.819608 GCCAGGCAAGAACAATAACAGA 59.180 45.455 6.55 0.00 0.00 3.41
2012 3154 1.202915 TCATCAGCCAGGCAAGAACAA 60.203 47.619 15.80 0.00 0.00 2.83
2136 3282 2.685380 AGGCTCTGGTTCTCCCGG 60.685 66.667 0.00 0.00 41.48 5.73
2202 3348 2.039624 TGGTCCTCCAGCTCCTCC 59.960 66.667 0.00 0.00 39.03 4.30
2232 3378 2.439883 ACGGCCTCCTCGTAGGAC 60.440 66.667 0.00 1.81 40.06 3.85
2293 3439 2.099831 GTCGAACTCGCCGTCGAT 59.900 61.111 1.66 0.00 44.56 3.59
2386 3587 2.186826 GCAGAAACCACACCGTGCT 61.187 57.895 0.00 0.00 31.34 4.40
2390 3591 0.738389 AAACAGCAGAAACCACACCG 59.262 50.000 0.00 0.00 0.00 4.94
2438 3654 1.608717 ATCTGGACACCGGAGAGTGC 61.609 60.000 9.46 9.83 42.74 4.40
2440 3656 1.276421 CAAATCTGGACACCGGAGAGT 59.724 52.381 9.46 2.96 42.74 3.24
2451 3670 5.369833 TCGTTAAGAAACACCAAATCTGGA 58.630 37.500 0.00 0.00 46.59 3.86
2454 3673 7.362056 CCATCATCGTTAAGAAACACCAAATCT 60.362 37.037 0.00 0.00 35.16 2.40
2464 3683 5.957842 AACAAGCCATCATCGTTAAGAAA 57.042 34.783 0.00 0.00 0.00 2.52
2470 3689 4.769688 TGAGATAACAAGCCATCATCGTT 58.230 39.130 0.00 0.00 0.00 3.85
2519 3741 8.768957 TCTCTCTGTCTGAATAAACAAGAATG 57.231 34.615 0.00 0.00 0.00 2.67
2524 3746 5.247110 AGCCTCTCTCTGTCTGAATAAACAA 59.753 40.000 0.00 0.00 0.00 2.83
2525 3747 4.774726 AGCCTCTCTCTGTCTGAATAAACA 59.225 41.667 0.00 0.00 0.00 2.83
2526 3748 5.337578 AGCCTCTCTCTGTCTGAATAAAC 57.662 43.478 0.00 0.00 0.00 2.01
2527 3749 5.481824 TGAAGCCTCTCTCTGTCTGAATAAA 59.518 40.000 0.00 0.00 0.00 1.40
2528 3750 5.019470 TGAAGCCTCTCTCTGTCTGAATAA 58.981 41.667 0.00 0.00 0.00 1.40
2529 3751 4.604156 TGAAGCCTCTCTCTGTCTGAATA 58.396 43.478 0.00 0.00 0.00 1.75
2530 3752 3.439154 TGAAGCCTCTCTCTGTCTGAAT 58.561 45.455 0.00 0.00 0.00 2.57
2531 3753 2.824936 CTGAAGCCTCTCTCTGTCTGAA 59.175 50.000 0.00 0.00 0.00 3.02
2532 3754 2.445427 CTGAAGCCTCTCTCTGTCTGA 58.555 52.381 0.00 0.00 0.00 3.27
2533 3755 1.135024 GCTGAAGCCTCTCTCTGTCTG 60.135 57.143 0.00 0.00 34.31 3.51
2534 3756 1.185315 GCTGAAGCCTCTCTCTGTCT 58.815 55.000 0.00 0.00 34.31 3.41
2535 3757 0.179140 CGCTGAAGCCTCTCTCTGTC 60.179 60.000 0.00 0.00 37.91 3.51
2536 3758 1.889454 CGCTGAAGCCTCTCTCTGT 59.111 57.895 0.00 0.00 37.91 3.41
2537 3759 1.519013 GCGCTGAAGCCTCTCTCTG 60.519 63.158 0.00 0.00 37.91 3.35
2538 3760 2.891882 GCGCTGAAGCCTCTCTCT 59.108 61.111 0.00 0.00 37.91 3.10
2565 3787 4.142708 TGTGCAGTTACAACACAGTTTCTG 60.143 41.667 6.40 0.00 39.29 3.02
2608 3830 7.862512 AAAAGATTCAGAGCTTATGGAGAAG 57.137 36.000 0.00 0.00 29.85 2.85
2683 3907 3.194116 ACAAGCATACCAAGGCAGAATTG 59.806 43.478 0.00 0.00 33.96 2.32
2694 3918 9.845740 ATTTACATCTGTATAACAAGCATACCA 57.154 29.630 0.00 0.00 0.00 3.25
2699 3923 9.394767 ACATGATTTACATCTGTATAACAAGCA 57.605 29.630 0.00 0.00 37.07 3.91
2700 3924 9.869844 GACATGATTTACATCTGTATAACAAGC 57.130 33.333 0.00 0.00 37.07 4.01
2709 3933 7.765695 AAACAAGGACATGATTTACATCTGT 57.234 32.000 0.00 0.00 37.07 3.41
2720 3944 5.939883 CAGAGTGGAATAAACAAGGACATGA 59.060 40.000 0.00 0.00 0.00 3.07
2763 3988 4.287238 TCTTTTGCCTTTTCGTCAGAAC 57.713 40.909 0.00 0.00 35.86 3.01
2863 4145 1.699634 AGCACCACTTACATGTCCTGT 59.300 47.619 0.00 0.00 42.13 4.00
2864 4146 2.350522 GAGCACCACTTACATGTCCTG 58.649 52.381 0.00 0.00 0.00 3.86
2865 4147 1.066858 CGAGCACCACTTACATGTCCT 60.067 52.381 0.00 0.00 0.00 3.85
2866 4148 1.337823 ACGAGCACCACTTACATGTCC 60.338 52.381 0.00 0.00 0.00 4.02
2867 4149 2.080286 ACGAGCACCACTTACATGTC 57.920 50.000 0.00 0.00 0.00 3.06
2945 4240 2.107950 TCTAATTGGTGTTGGAGCGG 57.892 50.000 0.00 0.00 0.00 5.52
2947 4242 4.943705 TGATCTTCTAATTGGTGTTGGAGC 59.056 41.667 0.00 0.00 0.00 4.70
2969 4264 1.250328 TTGTGCTCCTCCATTTGCTG 58.750 50.000 0.00 0.00 0.00 4.41
3176 4471 6.039047 GCTCATGATATGTTTGTTCTGTGGAT 59.961 38.462 0.00 0.00 0.00 3.41
3194 4489 7.812690 AGTCATTTGCTTATTATGCTCATGA 57.187 32.000 0.00 0.00 31.79 3.07
3228 4523 5.616488 ACCGTTACGAATGCTTTGTTTAT 57.384 34.783 6.24 0.00 0.00 1.40
3229 4524 5.421212 AACCGTTACGAATGCTTTGTTTA 57.579 34.783 6.24 0.00 0.00 2.01
3267 4562 3.454082 AGGAAGATACTTGGCTGGAAGAG 59.546 47.826 0.00 0.00 34.07 2.85
3290 4585 2.174764 CGTGTTGTATTCGACCGAGAG 58.825 52.381 0.00 0.00 0.00 3.20
3308 4603 1.292223 CTTCATGACCGGTGTCCGT 59.708 57.895 14.63 0.00 46.80 4.69
3341 4636 8.567948 ACATTGAATAGTTGTTAACAGTCAAGG 58.432 33.333 19.52 19.52 36.00 3.61


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

AutoCloner maintained by Alex Coulton.