Multiple sequence alignment - TraesCS2A01G168200

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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 TraesCS2A01G168200 chr2A 100.000 6520 0 0 1 6520 121146857 121140338 0.000000e+00 12041.0
1 TraesCS2A01G168200 chr2A 88.448 1411 112 21 1479 2853 33321348 33319953 0.000000e+00 1655.0
2 TraesCS2A01G168200 chr2B 93.472 5545 232 57 836 6295 171035136 171029637 0.000000e+00 8115.0
3 TraesCS2A01G168200 chr2B 84.233 1408 104 39 1479 2853 51137590 51138912 0.000000e+00 1262.0
4 TraesCS2A01G168200 chr2B 76.020 809 92 48 195 955 171035882 171035128 6.300000e-85 326.0
5 TraesCS2A01G168200 chr2B 83.886 211 27 3 6130 6334 326569807 326569598 1.850000e-45 195.0
6 TraesCS2A01G168200 chr2B 85.052 194 10 7 1 187 171036109 171035928 5.190000e-41 180.0
7 TraesCS2A01G168200 chr2D 95.452 4859 151 38 1619 6431 119070803 119065969 0.000000e+00 7685.0
8 TraesCS2A01G168200 chr2D 88.046 1213 84 24 1479 2656 31032466 31033652 0.000000e+00 1380.0
9 TraesCS2A01G168200 chr2D 90.333 600 35 10 780 1376 119071380 119070801 0.000000e+00 765.0
10 TraesCS2A01G168200 chr2D 85.602 507 35 7 2728 3208 31038187 31038681 1.260000e-136 497.0
11 TraesCS2A01G168200 chr2D 80.431 603 58 30 1 561 119072972 119072388 7.870000e-109 405.0
12 TraesCS2A01G168200 chr2D 97.000 100 2 1 6422 6520 119065864 119065765 4.040000e-37 167.0
13 TraesCS2A01G168200 chr6B 84.235 425 29 17 2437 2853 591930115 591929721 4.770000e-101 379.0
14 TraesCS2A01G168200 chr6B 100.000 31 0 0 6085 6115 579486967 579486937 2.540000e-04 58.4
15 TraesCS2A01G168200 chr7A 91.351 185 16 0 2157 2341 19004467 19004651 3.020000e-63 254.0
16 TraesCS2A01G168200 chr7A 79.498 239 32 8 6085 6315 352599538 352599309 3.150000e-33 154.0
17 TraesCS2A01G168200 chr7D 77.635 389 63 18 1691 2057 18680318 18680704 1.420000e-51 215.0


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 TraesCS2A01G168200 chr2A 121140338 121146857 6519 True 12041.000000 12041 100.000 1 6520 1 chr2A.!!$R2 6519
1 TraesCS2A01G168200 chr2A 33319953 33321348 1395 True 1655.000000 1655 88.448 1479 2853 1 chr2A.!!$R1 1374
2 TraesCS2A01G168200 chr2B 171029637 171036109 6472 True 2873.666667 8115 84.848 1 6295 3 chr2B.!!$R2 6294
3 TraesCS2A01G168200 chr2B 51137590 51138912 1322 False 1262.000000 1262 84.233 1479 2853 1 chr2B.!!$F1 1374
4 TraesCS2A01G168200 chr2D 119065765 119072972 7207 True 2255.500000 7685 90.804 1 6520 4 chr2D.!!$R1 6519
5 TraesCS2A01G168200 chr2D 31032466 31033652 1186 False 1380.000000 1380 88.046 1479 2656 1 chr2D.!!$F1 1177

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
356 428 0.035317 TCGGTCTCTGCATGCACTTT 59.965 50.000 18.46 0.00 0.00 2.66 F
449 524 0.036388 TTCGCAAGCTGGAACTAGGG 60.036 55.000 0.00 0.00 37.18 3.53 F
1023 2047 0.178992 TCTGGTTCCCAAAGCACAGG 60.179 55.000 0.00 0.00 37.94 4.00 F
1138 2165 1.003233 GTTGTGTGGGAGGAGGCTC 60.003 63.158 5.78 5.78 0.00 4.70 F
3073 4221 0.250513 CCTTGGAGAAGTTCCTCGGG 59.749 60.000 0.00 0.00 46.92 5.14 F
4135 5288 1.468520 CCGTGGTCATTTGCAACTAGG 59.531 52.381 0.00 0.00 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2006 3108 0.299003 GCAAATACTCAGCGACGCTC 59.701 55.000 21.67 0.95 36.40 5.03 R
2244 3352 1.808945 GATGACAAGTGCCTGTTCAGG 59.191 52.381 13.88 13.88 0.00 3.86 R
2769 3892 0.248949 GGGTACCGAGACTGCGAATC 60.249 60.000 5.65 0.00 40.86 2.52 R
3097 4245 3.226777 ACCATGAGGAGAGAGGATAACG 58.773 50.000 0.00 0.00 38.69 3.18 R
4701 5857 0.463204 CAGAGATCCAGCGGATGTGT 59.537 55.000 13.68 6.67 43.27 3.72 R
5601 6758 2.352715 GGACAAGCAAAGGCATAACACC 60.353 50.000 0.00 0.00 44.61 4.16 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
33 34 1.065358 CGTGTATAAATAGGGGCGCG 58.935 55.000 0.00 0.00 0.00 6.86
38 39 3.649216 TATAAATAGGGGCGCGGGCAC 62.649 57.143 26.61 23.52 43.79 5.01
89 90 4.596585 CACCAAACCCGGGCCAGT 62.597 66.667 24.08 10.68 0.00 4.00
91 92 2.989253 CCAAACCCGGGCCAGTTC 60.989 66.667 24.08 0.00 0.00 3.01
92 93 3.361977 CAAACCCGGGCCAGTTCG 61.362 66.667 24.08 0.00 0.00 3.95
166 175 3.572255 GCAAGGTAAAGAAACCATGTCCA 59.428 43.478 0.00 0.00 42.40 4.02
181 190 4.398319 CATGTCCAGTTTCCCTGTACTTT 58.602 43.478 0.00 0.00 39.74 2.66
187 234 5.605488 TCCAGTTTCCCTGTACTTTAAGAGT 59.395 40.000 0.00 0.00 39.74 3.24
190 237 3.975168 TCCCTGTACTTTAAGAGTGGC 57.025 47.619 0.00 0.00 39.48 5.01
193 240 5.278061 TCCCTGTACTTTAAGAGTGGCTAT 58.722 41.667 0.00 0.00 39.48 2.97
203 250 0.618458 GAGTGGCTATGGTTGGGACA 59.382 55.000 0.00 0.00 0.00 4.02
204 251 0.328258 AGTGGCTATGGTTGGGACAC 59.672 55.000 0.00 0.00 39.29 3.67
212 259 0.178955 TGGTTGGGACACTACGGAGA 60.179 55.000 0.00 0.00 39.29 3.71
214 261 2.291735 TGGTTGGGACACTACGGAGATA 60.292 50.000 0.00 0.00 39.29 1.98
215 262 2.762327 GGTTGGGACACTACGGAGATAA 59.238 50.000 0.00 0.00 39.29 1.75
216 263 3.429960 GGTTGGGACACTACGGAGATAAC 60.430 52.174 0.00 0.00 39.29 1.89
248 295 4.633565 GCCTAGTTTCAGTGATTCAAGAGG 59.366 45.833 0.00 0.00 0.00 3.69
296 347 2.164624 TCTTCAGCTTAGGTTCGAGAGC 59.835 50.000 0.00 0.00 35.42 4.09
311 362 9.244292 AGGTTCGAGAGCATATATACTGATAAA 57.756 33.333 0.00 0.00 0.00 1.40
343 407 4.342665 GGATTAATCTGGTCTTCTCGGTCT 59.657 45.833 14.95 0.00 0.00 3.85
356 428 0.035317 TCGGTCTCTGCATGCACTTT 59.965 50.000 18.46 0.00 0.00 2.66
364 436 0.758310 TGCATGCACTTTGGGTCCAA 60.758 50.000 18.46 0.00 0.00 3.53
374 446 3.580319 GGGTCCAAGCCCTGGTGT 61.580 66.667 2.51 0.00 46.51 4.16
376 448 2.829384 GGTCCAAGCCCTGGTGTCA 61.829 63.158 2.51 0.00 46.51 3.58
378 450 0.962356 GTCCAAGCCCTGGTGTCATG 60.962 60.000 2.51 0.00 46.51 3.07
381 455 1.001641 AAGCCCTGGTGTCATGCTC 60.002 57.895 0.00 0.00 32.13 4.26
400 474 1.066143 TCTTGGTTGCTGTAGCTAGCC 60.066 52.381 12.13 0.00 43.02 3.93
401 475 0.690192 TTGGTTGCTGTAGCTAGCCA 59.310 50.000 12.13 1.86 43.02 4.75
402 476 0.250234 TGGTTGCTGTAGCTAGCCAG 59.750 55.000 12.13 13.63 43.02 4.85
411 485 2.677228 GCTAGCCAGCCCAAAGGA 59.323 61.111 2.29 0.00 42.37 3.36
412 486 1.452833 GCTAGCCAGCCCAAAGGAG 60.453 63.158 2.29 0.00 42.37 3.69
413 487 1.915078 GCTAGCCAGCCCAAAGGAGA 61.915 60.000 2.29 0.00 42.37 3.71
434 508 5.949233 GAAGATCTTCTCTCTTCTTTCGC 57.051 43.478 25.26 0.00 43.39 4.70
436 510 5.398603 AGATCTTCTCTCTTCTTTCGCAA 57.601 39.130 0.00 0.00 0.00 4.85
437 511 5.410067 AGATCTTCTCTCTTCTTTCGCAAG 58.590 41.667 0.00 0.00 0.00 4.01
438 512 3.321497 TCTTCTCTCTTCTTTCGCAAGC 58.679 45.455 0.00 0.00 37.18 4.01
449 524 0.036388 TTCGCAAGCTGGAACTAGGG 60.036 55.000 0.00 0.00 37.18 3.53
453 528 0.678048 CAAGCTGGAACTAGGGTGGC 60.678 60.000 0.00 0.00 0.00 5.01
471 546 3.713902 CAGAGTGGGTGAACTGCTT 57.286 52.632 0.00 0.00 0.00 3.91
508 583 3.591196 ATTACGCCGGTTTGTACACTA 57.409 42.857 1.90 0.00 0.00 2.74
509 584 3.377346 TTACGCCGGTTTGTACACTAA 57.623 42.857 1.90 0.00 0.00 2.24
513 588 2.737783 CGCCGGTTTGTACACTAAATCA 59.262 45.455 1.90 0.00 0.00 2.57
561 639 3.023119 ACTGTAGAGATCCAGTGCAGAG 58.977 50.000 10.39 0.00 40.30 3.35
583 1433 1.951510 CATACCATGCATGTCCGCC 59.048 57.895 24.58 0.00 0.00 6.13
584 1434 0.535780 CATACCATGCATGTCCGCCT 60.536 55.000 24.58 1.21 0.00 5.52
585 1435 0.535780 ATACCATGCATGTCCGCCTG 60.536 55.000 24.58 10.29 0.00 4.85
586 1436 1.909459 TACCATGCATGTCCGCCTGT 61.909 55.000 24.58 15.33 0.00 4.00
587 1437 2.767445 CCATGCATGTCCGCCTGTG 61.767 63.158 24.58 2.77 0.00 3.66
588 1438 2.042259 CATGCATGTCCGCCTGTGT 61.042 57.895 18.91 0.00 0.00 3.72
589 1439 2.042259 ATGCATGTCCGCCTGTGTG 61.042 57.895 0.00 0.00 0.00 3.82
590 1440 3.434319 GCATGTCCGCCTGTGTGG 61.434 66.667 0.00 0.00 43.93 4.17
591 1441 2.747460 CATGTCCGCCTGTGTGGG 60.747 66.667 0.00 0.00 42.73 4.61
592 1442 2.927856 ATGTCCGCCTGTGTGGGA 60.928 61.111 0.00 0.00 42.73 4.37
597 1447 2.671070 CGCCTGTGTGGGATCCTT 59.329 61.111 12.58 0.00 36.00 3.36
614 1464 3.935456 TTCGGGGAGGCCAGGCTTA 62.935 63.158 12.43 0.00 0.00 3.09
617 1467 2.835049 GGGGAGGCCAGGCTTATCC 61.835 68.421 12.43 15.88 0.00 2.59
636 1508 3.797039 TCCTCAGTTTGAGCATATTCGG 58.203 45.455 0.54 0.00 42.98 4.30
643 1515 5.352569 CAGTTTGAGCATATTCGGAGTTTCT 59.647 40.000 0.00 0.00 0.00 2.52
655 1527 3.253188 TCGGAGTTTCTGGAATGCAAAAG 59.747 43.478 0.00 0.00 0.00 2.27
668 1540 6.434028 TGGAATGCAAAAGTAAATCTAGCAGT 59.566 34.615 0.00 0.00 34.11 4.40
669 1541 7.039784 TGGAATGCAAAAGTAAATCTAGCAGTT 60.040 33.333 0.00 0.00 34.11 3.16
670 1542 7.814587 GGAATGCAAAAGTAAATCTAGCAGTTT 59.185 33.333 0.00 0.00 34.11 2.66
671 1543 9.196552 GAATGCAAAAGTAAATCTAGCAGTTTT 57.803 29.630 0.00 0.00 34.11 2.43
672 1544 9.546428 AATGCAAAAGTAAATCTAGCAGTTTTT 57.454 25.926 0.00 0.00 34.11 1.94
708 1580 7.079475 TCCTATTTTACGCAACTTGTTAAAGC 58.921 34.615 0.00 0.00 36.84 3.51
709 1581 7.040961 TCCTATTTTACGCAACTTGTTAAAGCT 60.041 33.333 0.00 0.00 36.84 3.74
710 1582 8.231837 CCTATTTTACGCAACTTGTTAAAGCTA 58.768 33.333 0.00 0.00 36.84 3.32
711 1583 9.769093 CTATTTTACGCAACTTGTTAAAGCTAT 57.231 29.630 0.00 0.00 36.84 2.97
714 1586 9.947669 TTTTACGCAACTTGTTAAAGCTATTAA 57.052 25.926 0.00 0.00 36.84 1.40
715 1587 8.938047 TTACGCAACTTGTTAAAGCTATTAAC 57.062 30.769 17.46 17.46 36.84 2.01
716 1588 7.198306 ACGCAACTTGTTAAAGCTATTAACT 57.802 32.000 21.46 8.38 36.84 2.24
717 1589 7.645402 ACGCAACTTGTTAAAGCTATTAACTT 58.355 30.769 21.46 11.93 36.84 2.66
718 1590 8.132995 ACGCAACTTGTTAAAGCTATTAACTTT 58.867 29.630 21.46 14.01 40.37 2.66
719 1591 8.964150 CGCAACTTGTTAAAGCTATTAACTTTT 58.036 29.630 21.46 13.80 38.31 2.27
724 1596 9.129209 CTTGTTAAAGCTATTAACTTTTCCTGC 57.871 33.333 21.46 0.00 38.31 4.85
725 1597 8.172352 TGTTAAAGCTATTAACTTTTCCTGCA 57.828 30.769 21.46 0.00 38.31 4.41
726 1598 8.296713 TGTTAAAGCTATTAACTTTTCCTGCAG 58.703 33.333 21.46 6.78 38.31 4.41
727 1599 8.512138 GTTAAAGCTATTAACTTTTCCTGCAGA 58.488 33.333 17.39 0.00 38.31 4.26
728 1600 6.502136 AAGCTATTAACTTTTCCTGCAGAC 57.498 37.500 17.39 0.00 0.00 3.51
729 1601 4.944317 AGCTATTAACTTTTCCTGCAGACC 59.056 41.667 17.39 0.00 0.00 3.85
730 1602 4.700213 GCTATTAACTTTTCCTGCAGACCA 59.300 41.667 17.39 0.00 0.00 4.02
731 1603 5.183140 GCTATTAACTTTTCCTGCAGACCAA 59.817 40.000 17.39 1.58 0.00 3.67
732 1604 6.294508 GCTATTAACTTTTCCTGCAGACCAAA 60.295 38.462 17.39 8.28 0.00 3.28
733 1605 5.514274 TTAACTTTTCCTGCAGACCAAAG 57.486 39.130 17.39 20.06 0.00 2.77
734 1606 1.683385 ACTTTTCCTGCAGACCAAAGC 59.317 47.619 17.39 0.00 0.00 3.51
735 1607 1.959282 CTTTTCCTGCAGACCAAAGCT 59.041 47.619 17.39 0.00 0.00 3.74
736 1608 2.949177 TTTCCTGCAGACCAAAGCTA 57.051 45.000 17.39 0.00 0.00 3.32
737 1609 3.439857 TTTCCTGCAGACCAAAGCTAT 57.560 42.857 17.39 0.00 0.00 2.97
738 1610 3.439857 TTCCTGCAGACCAAAGCTATT 57.560 42.857 17.39 0.00 0.00 1.73
739 1611 4.568072 TTCCTGCAGACCAAAGCTATTA 57.432 40.909 17.39 0.00 0.00 0.98
740 1612 4.568072 TCCTGCAGACCAAAGCTATTAA 57.432 40.909 17.39 0.00 0.00 1.40
741 1613 4.261801 TCCTGCAGACCAAAGCTATTAAC 58.738 43.478 17.39 0.00 0.00 2.01
742 1614 4.019321 TCCTGCAGACCAAAGCTATTAACT 60.019 41.667 17.39 0.00 0.00 2.24
743 1615 4.333926 CCTGCAGACCAAAGCTATTAACTC 59.666 45.833 17.39 0.00 0.00 3.01
744 1616 5.165961 TGCAGACCAAAGCTATTAACTCT 57.834 39.130 0.00 0.00 0.00 3.24
745 1617 4.937620 TGCAGACCAAAGCTATTAACTCTG 59.062 41.667 0.00 0.00 0.00 3.35
746 1618 4.938226 GCAGACCAAAGCTATTAACTCTGT 59.062 41.667 0.00 0.00 0.00 3.41
747 1619 6.106673 GCAGACCAAAGCTATTAACTCTGTA 58.893 40.000 0.00 0.00 0.00 2.74
748 1620 6.036191 GCAGACCAAAGCTATTAACTCTGTAC 59.964 42.308 0.00 0.00 0.00 2.90
749 1621 7.324178 CAGACCAAAGCTATTAACTCTGTACT 58.676 38.462 0.00 0.00 0.00 2.73
750 1622 7.489757 CAGACCAAAGCTATTAACTCTGTACTC 59.510 40.741 0.00 0.00 0.00 2.59
751 1623 6.641474 ACCAAAGCTATTAACTCTGTACTCC 58.359 40.000 0.00 0.00 0.00 3.85
778 1661 7.553504 AGTTTTTCCAAGGCCAGTAATTAAT 57.446 32.000 5.01 0.00 0.00 1.40
812 1723 2.493414 TGTGGATCATGTGCATGTCA 57.507 45.000 11.38 6.75 39.72 3.58
819 1730 6.205270 GTGGATCATGTGCATGTCATTGTATA 59.795 38.462 11.38 0.00 39.72 1.47
821 1732 7.449086 TGGATCATGTGCATGTCATTGTATAAT 59.551 33.333 11.38 0.00 39.72 1.28
824 1735 8.907222 TCATGTGCATGTCATTGTATAATACT 57.093 30.769 11.38 0.00 39.72 2.12
825 1736 9.995003 TCATGTGCATGTCATTGTATAATACTA 57.005 29.630 11.38 0.00 39.72 1.82
827 1738 8.831715 TGTGCATGTCATTGTATAATACTAGG 57.168 34.615 0.00 0.00 0.00 3.02
829 1740 9.144747 GTGCATGTCATTGTATAATACTAGGAG 57.855 37.037 0.00 0.00 0.00 3.69
866 1883 6.524734 TGATCCGTTTCTATTATCTGCATGT 58.475 36.000 0.00 0.00 0.00 3.21
870 1887 5.406780 CCGTTTCTATTATCTGCATGTCCTC 59.593 44.000 0.00 0.00 0.00 3.71
871 1888 5.406780 CGTTTCTATTATCTGCATGTCCTCC 59.593 44.000 0.00 0.00 0.00 4.30
873 1890 6.692849 TTCTATTATCTGCATGTCCTCCAT 57.307 37.500 0.00 0.00 0.00 3.41
921 1945 1.598130 GTTCCGTGCTCCTGTGCTT 60.598 57.895 0.00 0.00 0.00 3.91
1023 2047 0.178992 TCTGGTTCCCAAAGCACAGG 60.179 55.000 0.00 0.00 37.94 4.00
1067 2091 1.807142 CGCCAACCTTTCTTCTTCCTC 59.193 52.381 0.00 0.00 0.00 3.71
1068 2092 2.163509 GCCAACCTTTCTTCTTCCTCC 58.836 52.381 0.00 0.00 0.00 4.30
1077 2101 3.878237 TCTTCTTCCTCCGGCTCTATA 57.122 47.619 0.00 0.00 0.00 1.31
1125 2152 2.281070 ACAGAGCGCCCTGTTGTG 60.281 61.111 19.85 3.77 44.32 3.33
1127 2154 2.281070 AGAGCGCCCTGTTGTGTG 60.281 61.111 2.29 0.00 0.00 3.82
1138 2165 1.003233 GTTGTGTGGGAGGAGGCTC 60.003 63.158 5.78 5.78 0.00 4.70
1213 2240 1.927527 AGCAATGGGGGAGACTGCT 60.928 57.895 0.00 0.00 38.50 4.24
1218 2245 3.086600 GGGGGAGACTGCTGGAGG 61.087 72.222 0.14 0.00 0.00 4.30
1261 2288 4.148825 GTGAGGGAGCGCATCGGT 62.149 66.667 11.47 0.00 41.33 4.69
1317 2344 1.067495 CGTCTTCTCAAGGTCTGTCCC 60.067 57.143 0.00 0.00 36.75 4.46
1347 2374 1.920325 AGGCTAGACTGGCTGCCAA 60.920 57.895 23.51 6.73 40.84 4.52
1354 2381 2.162681 AGACTGGCTGCCAATTTGTAC 58.837 47.619 23.51 10.54 30.80 2.90
1367 2394 5.290158 GCCAATTTGTACAAATCTCTGCATG 59.710 40.000 29.10 21.50 39.88 4.06
1369 2396 6.309494 CCAATTTGTACAAATCTCTGCATGTG 59.691 38.462 29.10 20.33 39.88 3.21
1373 2400 4.931601 TGTACAAATCTCTGCATGTGAGAC 59.068 41.667 18.19 9.19 42.46 3.36
1374 2401 4.011966 ACAAATCTCTGCATGTGAGACA 57.988 40.909 18.19 3.29 42.46 3.41
1375 2402 3.750130 ACAAATCTCTGCATGTGAGACAC 59.250 43.478 18.19 0.00 42.46 3.67
1396 2427 4.272504 CACGGTTAAGCGATGAATTATGGT 59.727 41.667 31.61 3.37 0.00 3.55
1404 2435 3.374745 CGATGAATTATGGTTGCCTTGC 58.625 45.455 0.00 0.00 0.00 4.01
1417 2448 4.495844 GGTTGCCTTGCGTATTTCTATGTC 60.496 45.833 0.00 0.00 0.00 3.06
1444 2475 6.438425 TGCTATAGTATGAGCTGGATCAATGA 59.562 38.462 0.00 0.00 39.54 2.57
1445 2476 7.125356 TGCTATAGTATGAGCTGGATCAATGAT 59.875 37.037 0.00 0.00 39.54 2.45
1474 2507 8.950208 TTTCTTTACAAAATTTGTACCAAGGG 57.050 30.769 20.94 9.65 45.16 3.95
1542 2576 7.224949 GCATTTCTATATAATACCGCTCCTTCC 59.775 40.741 0.00 0.00 0.00 3.46
1845 2907 2.671854 GGTTTGCACCACCAAAACG 58.328 52.632 9.09 0.00 43.61 3.60
1899 2969 6.541641 GCTCTTGATCTGTTGGTTTCTCATAT 59.458 38.462 0.00 0.00 0.00 1.78
2006 3108 1.876156 GAGCTTGGTGTTGAGGAGTTG 59.124 52.381 0.00 0.00 0.00 3.16
2063 3165 2.213499 GCGAATGGAAGGTATCTGTGG 58.787 52.381 0.00 0.00 0.00 4.17
2244 3352 1.999071 TTGGCAACGGTGTGCAGTTC 61.999 55.000 0.66 0.00 46.81 3.01
2379 3487 4.631377 TGTCTTGCTTTGTAGATTGGATCG 59.369 41.667 0.00 0.00 0.00 3.69
2400 3509 4.155826 TCGTTTGGCTTTGTAGATTGGATG 59.844 41.667 0.00 0.00 0.00 3.51
2429 3542 7.284716 TCGACTATATCTTTGCTGAAGGTTCTA 59.715 37.037 1.47 0.00 35.98 2.10
2489 3604 6.201425 GCTTACATCATTTGTTAATGGCATGG 59.799 38.462 0.00 0.00 41.23 3.66
2491 3606 3.162202 TCATTTGTTAATGGCATGGCG 57.838 42.857 15.27 0.00 41.23 5.69
2538 3655 2.827800 TATGAGCATAGTCAGCCTGC 57.172 50.000 0.00 0.00 36.15 4.85
2606 3723 6.294899 GCCCTGATGATATGTGCATTTTGTAT 60.295 38.462 0.00 0.00 0.00 2.29
2707 3830 1.209504 TGGAACTACCATACCTGCTGC 59.790 52.381 0.00 0.00 44.64 5.25
2715 3838 4.443978 ACCATACCTGCTGCTTAATCAT 57.556 40.909 0.00 0.00 0.00 2.45
2718 3841 4.214971 CCATACCTGCTGCTTAATCATGAC 59.785 45.833 0.00 0.00 0.00 3.06
2769 3892 2.416547 GACCATGATGTTGAACGACAGG 59.583 50.000 0.00 0.00 32.19 4.00
2782 3905 0.863538 CGACAGGATTCGCAGTCTCG 60.864 60.000 0.00 0.00 31.03 4.04
2905 4034 8.919777 ATCATCATACACATGATCACTGAAAT 57.080 30.769 0.00 0.00 46.88 2.17
2914 4043 7.613022 ACACATGATCACTGAAATCCTTATTGT 59.387 33.333 0.00 0.00 0.00 2.71
3073 4221 0.250513 CCTTGGAGAAGTTCCTCGGG 59.749 60.000 0.00 0.00 46.92 5.14
3097 4245 4.021192 ACAATCCCAATGGTGTTCAATGTC 60.021 41.667 0.00 0.00 0.00 3.06
3176 4324 1.486726 CTGGTGGACAGGTAGAATCCC 59.513 57.143 0.00 0.00 43.70 3.85
3181 4329 2.316677 TGGACAGGTAGAATCCCCTACA 59.683 50.000 0.00 0.00 40.48 2.74
3182 4330 3.051341 TGGACAGGTAGAATCCCCTACAT 60.051 47.826 0.00 0.00 40.48 2.29
3185 4333 4.832492 ACAGGTAGAATCCCCTACATCAT 58.168 43.478 0.00 0.00 40.48 2.45
3195 4343 5.255397 TCCCCTACATCATTTTTGACAGT 57.745 39.130 0.00 0.00 0.00 3.55
3371 4519 8.786826 TCGACATTACACCAAAGATTCTAATT 57.213 30.769 0.00 0.00 0.00 1.40
3411 4561 5.712004 ACATGATCGAATATGAGCTCTCTG 58.288 41.667 16.19 0.81 0.00 3.35
3414 4564 6.884280 TGATCGAATATGAGCTCTCTGTTA 57.116 37.500 16.19 0.00 0.00 2.41
3415 4565 7.459795 TGATCGAATATGAGCTCTCTGTTAT 57.540 36.000 16.19 0.96 0.00 1.89
3416 4566 8.567285 TGATCGAATATGAGCTCTCTGTTATA 57.433 34.615 16.19 3.43 0.00 0.98
3417 4567 9.014297 TGATCGAATATGAGCTCTCTGTTATAA 57.986 33.333 16.19 0.00 0.00 0.98
3418 4568 9.847706 GATCGAATATGAGCTCTCTGTTATAAA 57.152 33.333 16.19 0.00 0.00 1.40
3419 4569 9.632807 ATCGAATATGAGCTCTCTGTTATAAAC 57.367 33.333 16.19 1.79 0.00 2.01
3420 4570 8.851145 TCGAATATGAGCTCTCTGTTATAAACT 58.149 33.333 16.19 0.00 0.00 2.66
3421 4571 9.469807 CGAATATGAGCTCTCTGTTATAAACTT 57.530 33.333 16.19 0.00 0.00 2.66
3808 4960 3.187637 GCAACCTAGTCGCATGTTTGTTA 59.812 43.478 0.00 0.00 0.00 2.41
3851 5004 2.973694 TGTACGCATTCTACCCCTTC 57.026 50.000 0.00 0.00 0.00 3.46
3984 5137 5.243207 TCCGACCTTTACTGGAAGAAATTC 58.757 41.667 0.00 0.00 37.43 2.17
4044 5197 2.546778 CTGATTGCAATGAACCATGCC 58.453 47.619 18.59 0.00 0.00 4.40
4131 5284 1.729131 CGCCGTGGTCATTTGCAAC 60.729 57.895 0.00 0.00 0.00 4.17
4135 5288 1.468520 CCGTGGTCATTTGCAACTAGG 59.531 52.381 0.00 0.00 0.00 3.02
4152 5305 8.486210 TGCAACTAGGATAAACTGATCTAATGT 58.514 33.333 0.00 0.00 0.00 2.71
4376 5529 5.117406 TGAGGAGCTACTCTTCAGTGATA 57.883 43.478 26.31 0.00 40.72 2.15
4441 5597 8.827177 TGACTTATAAAATAGATTGCCTACCG 57.173 34.615 0.00 0.00 0.00 4.02
4701 5857 4.698201 TGAACAGTACAACCTGATTGGA 57.302 40.909 0.00 0.00 43.20 3.53
4855 6011 5.388111 TCACGACATTTACTAGTTCTGACG 58.612 41.667 0.00 10.83 0.00 4.35
4917 6074 4.279145 TCTATGAGGCTTTCGGTCTTACT 58.721 43.478 0.00 0.00 0.00 2.24
4992 6149 4.197750 GTCCAGCTGAGATCATTGTGAAT 58.802 43.478 17.39 0.00 0.00 2.57
5432 6589 5.739752 TGATAATTTCAGCTCGGTTCATG 57.260 39.130 0.00 0.00 0.00 3.07
5601 6758 0.033228 GATGGAGCACAGATCGGAGG 59.967 60.000 0.00 0.00 0.00 4.30
6014 7177 6.870971 TGGTAACAGTGAAACCAAATCTAC 57.129 37.500 15.87 0.00 46.17 2.59
6015 7178 6.358178 TGGTAACAGTGAAACCAAATCTACA 58.642 36.000 15.87 0.00 46.17 2.74
6016 7179 7.001674 TGGTAACAGTGAAACCAAATCTACAT 58.998 34.615 15.87 0.00 46.17 2.29
6017 7180 7.040755 TGGTAACAGTGAAACCAAATCTACATG 60.041 37.037 15.87 0.00 46.17 3.21
6018 7181 7.174253 GGTAACAGTGAAACCAAATCTACATGA 59.826 37.037 0.00 0.00 37.80 3.07
6019 7182 6.808008 ACAGTGAAACCAAATCTACATGAG 57.192 37.500 0.00 0.00 37.80 2.90
6020 7183 5.707298 ACAGTGAAACCAAATCTACATGAGG 59.293 40.000 0.00 0.00 37.80 3.86
6303 7496 6.894339 AAGGTAATTTCGTTCTTGTGGAAT 57.106 33.333 0.00 0.00 36.24 3.01
6424 7617 8.959676 AACTCCCTAAACTATATAGGAAGAGG 57.040 38.462 14.25 13.01 42.16 3.69
6450 7758 3.515104 ACTTGACAAATAGGGGGCAATTG 59.485 43.478 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 4.899239 GAGATGGCTGGGCGACGG 62.899 72.222 0.00 0.00 0.00 4.79
97 98 4.974989 ACGTCACCGGGGAAACGC 62.975 66.667 17.10 0.00 38.64 4.84
98 99 1.834458 GAAACGTCACCGGGGAAACG 61.834 60.000 8.74 13.13 40.77 3.60
99 100 1.509644 GGAAACGTCACCGGGGAAAC 61.510 60.000 8.74 0.00 38.78 2.78
100 101 1.227913 GGAAACGTCACCGGGGAAA 60.228 57.895 8.74 0.00 38.78 3.13
101 102 1.698067 AAGGAAACGTCACCGGGGAA 61.698 55.000 8.74 0.00 38.78 3.97
107 108 1.871676 GAGGAACAAGGAAACGTCACC 59.128 52.381 0.00 0.00 0.00 4.02
124 125 2.837291 CAGAGGAGGAGGGCGAGG 60.837 72.222 0.00 0.00 0.00 4.63
153 162 2.447047 AGGGAAACTGGACATGGTTTCT 59.553 45.455 18.61 4.26 45.90 2.52
166 175 5.745181 GCCACTCTTAAAGTACAGGGAAACT 60.745 44.000 0.00 0.00 36.07 2.66
181 190 2.504175 GTCCCAACCATAGCCACTCTTA 59.496 50.000 0.00 0.00 0.00 2.10
187 234 1.557832 GTAGTGTCCCAACCATAGCCA 59.442 52.381 0.00 0.00 0.00 4.75
190 237 2.100916 CTCCGTAGTGTCCCAACCATAG 59.899 54.545 0.00 0.00 0.00 2.23
193 240 0.178955 TCTCCGTAGTGTCCCAACCA 60.179 55.000 0.00 0.00 0.00 3.67
203 250 1.063114 AGCCCCAGTTATCTCCGTAGT 60.063 52.381 0.00 0.00 0.00 2.73
204 251 1.705873 AGCCCCAGTTATCTCCGTAG 58.294 55.000 0.00 0.00 0.00 3.51
212 259 2.797285 ACTAGGCTAGCCCCAGTTAT 57.203 50.000 30.42 12.43 36.58 1.89
214 261 1.560146 GAAACTAGGCTAGCCCCAGTT 59.440 52.381 31.61 31.61 41.05 3.16
215 262 1.205055 GAAACTAGGCTAGCCCCAGT 58.795 55.000 30.42 27.76 36.58 4.00
216 263 1.139853 CTGAAACTAGGCTAGCCCCAG 59.860 57.143 30.42 27.10 36.58 4.45
248 295 1.168714 AAGAGAATTTCGCAGCACCC 58.831 50.000 2.95 0.00 0.00 4.61
311 362 8.112183 AGAAGACCAGATTAATCCACAATCTTT 58.888 33.333 11.92 0.00 40.05 2.52
314 365 6.201806 CGAGAAGACCAGATTAATCCACAATC 59.798 42.308 11.92 4.61 33.43 2.67
320 384 4.342665 AGACCGAGAAGACCAGATTAATCC 59.657 45.833 11.92 0.00 0.00 3.01
328 392 0.172352 GCAGAGACCGAGAAGACCAG 59.828 60.000 0.00 0.00 0.00 4.00
343 407 0.895100 GGACCCAAAGTGCATGCAGA 60.895 55.000 23.41 0.00 36.67 4.26
364 436 1.495579 AAGAGCATGACACCAGGGCT 61.496 55.000 0.00 0.00 38.88 5.19
372 444 1.241165 CAGCAACCAAGAGCATGACA 58.759 50.000 0.00 0.00 0.00 3.58
374 446 2.703416 CTACAGCAACCAAGAGCATGA 58.297 47.619 0.00 0.00 0.00 3.07
376 448 1.004044 AGCTACAGCAACCAAGAGCAT 59.996 47.619 3.70 0.00 45.16 3.79
378 450 2.275318 CTAGCTACAGCAACCAAGAGC 58.725 52.381 3.70 0.00 45.16 4.09
381 455 1.339055 TGGCTAGCTACAGCAACCAAG 60.339 52.381 15.72 0.00 43.67 3.61
400 474 3.054508 AGAAGATCTTCTCCTTTGGGCTG 60.055 47.826 28.70 0.00 46.13 4.85
401 475 3.188773 AGAAGATCTTCTCCTTTGGGCT 58.811 45.455 28.70 6.45 46.13 5.19
402 476 3.643199 AGAAGATCTTCTCCTTTGGGC 57.357 47.619 28.70 3.95 46.13 5.36
413 487 5.398603 TGCGAAAGAAGAGAGAAGATCTT 57.601 39.130 7.95 7.95 38.84 2.40
425 499 1.876156 AGTTCCAGCTTGCGAAAGAAG 59.124 47.619 7.54 0.00 0.00 2.85
428 502 1.734465 CCTAGTTCCAGCTTGCGAAAG 59.266 52.381 0.00 0.00 0.00 2.62
430 504 0.036388 CCCTAGTTCCAGCTTGCGAA 60.036 55.000 0.00 0.00 0.00 4.70
432 506 1.021390 CACCCTAGTTCCAGCTTGCG 61.021 60.000 0.00 0.00 0.00 4.85
433 507 0.678048 CCACCCTAGTTCCAGCTTGC 60.678 60.000 0.00 0.00 0.00 4.01
434 508 0.678048 GCCACCCTAGTTCCAGCTTG 60.678 60.000 0.00 0.00 0.00 4.01
436 510 1.538876 TGCCACCCTAGTTCCAGCT 60.539 57.895 0.00 0.00 0.00 4.24
437 511 1.078143 CTGCCACCCTAGTTCCAGC 60.078 63.158 0.00 0.00 0.00 4.85
438 512 0.539051 CTCTGCCACCCTAGTTCCAG 59.461 60.000 0.00 0.00 0.00 3.86
449 524 0.886490 CAGTTCACCCACTCTGCCAC 60.886 60.000 0.00 0.00 0.00 5.01
453 528 1.233019 CAAGCAGTTCACCCACTCTG 58.767 55.000 0.00 0.00 0.00 3.35
508 583 1.382522 CCATGCGCCTACACTGATTT 58.617 50.000 4.18 0.00 0.00 2.17
509 584 0.464373 CCCATGCGCCTACACTGATT 60.464 55.000 4.18 0.00 0.00 2.57
523 598 2.159099 ACAGTACTGACATACGCCCATG 60.159 50.000 29.30 0.00 0.00 3.66
535 613 3.948473 GCACTGGATCTCTACAGTACTGA 59.052 47.826 29.30 11.77 45.52 3.41
571 1421 2.042259 CACACAGGCGGACATGCAT 61.042 57.895 0.00 0.00 36.28 3.96
578 1428 3.399181 GGATCCCACACAGGCGGA 61.399 66.667 0.00 0.00 35.39 5.54
580 1430 1.450312 GAAGGATCCCACACAGGCG 60.450 63.158 8.55 0.00 35.39 5.52
582 1432 4.941609 CGAAGGATCCCACACAGG 57.058 61.111 8.55 0.00 37.03 4.00
597 1447 3.714078 ATAAGCCTGGCCTCCCCGA 62.714 63.158 16.57 0.00 35.87 5.14
617 1467 4.437239 ACTCCGAATATGCTCAAACTGAG 58.563 43.478 0.00 0.00 46.90 3.35
636 1508 8.084684 AGATTTACTTTTGCATTCCAGAAACTC 58.915 33.333 0.00 0.00 0.00 3.01
643 1515 6.434028 ACTGCTAGATTTACTTTTGCATTCCA 59.566 34.615 0.00 0.00 31.82 3.53
693 1565 8.502161 AAAGTTAATAGCTTTAACAAGTTGCG 57.498 30.769 22.31 0.00 37.35 4.85
708 1580 6.817765 TTGGTCTGCAGGAAAAGTTAATAG 57.182 37.500 15.13 0.00 0.00 1.73
709 1581 6.294508 GCTTTGGTCTGCAGGAAAAGTTAATA 60.295 38.462 24.63 0.30 31.86 0.98
710 1582 5.509670 GCTTTGGTCTGCAGGAAAAGTTAAT 60.510 40.000 24.63 0.00 31.86 1.40
711 1583 4.202111 GCTTTGGTCTGCAGGAAAAGTTAA 60.202 41.667 24.63 8.29 31.86 2.01
714 1586 1.683385 GCTTTGGTCTGCAGGAAAAGT 59.317 47.619 24.63 0.00 31.86 2.66
715 1587 1.959282 AGCTTTGGTCTGCAGGAAAAG 59.041 47.619 22.08 22.08 0.00 2.27
716 1588 2.071778 AGCTTTGGTCTGCAGGAAAA 57.928 45.000 15.13 10.97 0.00 2.29
717 1589 2.949177 TAGCTTTGGTCTGCAGGAAA 57.051 45.000 15.13 9.72 0.00 3.13
718 1590 3.439857 AATAGCTTTGGTCTGCAGGAA 57.560 42.857 15.13 1.58 0.00 3.36
719 1591 4.019321 AGTTAATAGCTTTGGTCTGCAGGA 60.019 41.667 15.13 0.00 0.00 3.86
720 1592 4.265073 AGTTAATAGCTTTGGTCTGCAGG 58.735 43.478 15.13 0.00 0.00 4.85
721 1593 5.064452 CAGAGTTAATAGCTTTGGTCTGCAG 59.936 44.000 7.63 7.63 0.00 4.41
722 1594 4.937620 CAGAGTTAATAGCTTTGGTCTGCA 59.062 41.667 0.00 0.00 0.00 4.41
723 1595 4.938226 ACAGAGTTAATAGCTTTGGTCTGC 59.062 41.667 0.00 0.00 34.75 4.26
724 1596 7.324178 AGTACAGAGTTAATAGCTTTGGTCTG 58.676 38.462 0.00 0.00 36.95 3.51
725 1597 7.363968 GGAGTACAGAGTTAATAGCTTTGGTCT 60.364 40.741 0.00 0.00 0.00 3.85
726 1598 6.757478 GGAGTACAGAGTTAATAGCTTTGGTC 59.243 42.308 0.00 0.00 0.00 4.02
727 1599 6.212791 TGGAGTACAGAGTTAATAGCTTTGGT 59.787 38.462 0.00 0.00 0.00 3.67
728 1600 6.640518 TGGAGTACAGAGTTAATAGCTTTGG 58.359 40.000 0.00 0.00 0.00 3.28
729 1601 8.547967 TTTGGAGTACAGAGTTAATAGCTTTG 57.452 34.615 0.00 0.00 0.00 2.77
730 1602 8.376270 ACTTTGGAGTACAGAGTTAATAGCTTT 58.624 33.333 0.00 0.00 41.35 3.51
731 1603 7.908453 ACTTTGGAGTACAGAGTTAATAGCTT 58.092 34.615 0.00 0.00 41.35 3.74
732 1604 7.483580 ACTTTGGAGTACAGAGTTAATAGCT 57.516 36.000 0.00 0.00 41.35 3.32
740 1612 5.751586 TGGAAAAACTTTGGAGTACAGAGT 58.248 37.500 0.00 0.00 45.59 3.24
741 1613 6.238759 CCTTGGAAAAACTTTGGAGTACAGAG 60.239 42.308 0.00 0.00 37.33 3.35
742 1614 5.592688 CCTTGGAAAAACTTTGGAGTACAGA 59.407 40.000 0.00 0.00 34.21 3.41
743 1615 5.736207 GCCTTGGAAAAACTTTGGAGTACAG 60.736 44.000 0.00 0.00 34.21 2.74
744 1616 4.098807 GCCTTGGAAAAACTTTGGAGTACA 59.901 41.667 0.00 0.00 34.21 2.90
745 1617 4.500887 GGCCTTGGAAAAACTTTGGAGTAC 60.501 45.833 0.00 0.00 34.21 2.73
746 1618 3.639561 GGCCTTGGAAAAACTTTGGAGTA 59.360 43.478 0.00 0.00 34.21 2.59
747 1619 2.434336 GGCCTTGGAAAAACTTTGGAGT 59.566 45.455 0.00 0.00 37.87 3.85
748 1620 2.433970 TGGCCTTGGAAAAACTTTGGAG 59.566 45.455 3.32 0.00 0.00 3.86
749 1621 2.433970 CTGGCCTTGGAAAAACTTTGGA 59.566 45.455 3.32 0.00 0.00 3.53
750 1622 2.170397 ACTGGCCTTGGAAAAACTTTGG 59.830 45.455 3.32 0.00 0.00 3.28
751 1623 3.541996 ACTGGCCTTGGAAAAACTTTG 57.458 42.857 3.32 0.00 0.00 2.77
778 1661 3.222173 TCCACAAGGCAAGAAGCTTAA 57.778 42.857 0.00 0.00 44.79 1.85
824 1735 8.757982 ACGGATCAAGTAATTTAGTACTCCTA 57.242 34.615 0.00 0.00 33.05 2.94
825 1736 7.657023 ACGGATCAAGTAATTTAGTACTCCT 57.343 36.000 0.00 0.00 33.05 3.69
827 1738 9.583765 AGAAACGGATCAAGTAATTTAGTACTC 57.416 33.333 0.00 0.00 33.05 2.59
870 1887 1.821136 GGCTCTCCAGTTTTCCAATGG 59.179 52.381 0.00 0.00 35.30 3.16
871 1888 2.490903 CAGGCTCTCCAGTTTTCCAATG 59.509 50.000 0.00 0.00 33.74 2.82
873 1890 1.819305 GCAGGCTCTCCAGTTTTCCAA 60.819 52.381 0.00 0.00 33.74 3.53
1044 2068 1.266989 GAAGAAGAAAGGTTGGCGTGG 59.733 52.381 0.00 0.00 0.00 4.94
1077 2101 4.462132 ACGATGCATGAGCTCTACTGATAT 59.538 41.667 16.19 8.00 42.74 1.63
1234 2261 1.153489 CTCCCTCACGCTGTGGATG 60.153 63.158 8.46 1.46 33.04 3.51
1261 2288 1.219124 GTGCGCAGAGAGGGAATCA 59.781 57.895 12.22 0.00 0.00 2.57
1317 2344 3.622163 CAGTCTAGCCTGCAAAAGATCAG 59.378 47.826 0.00 0.00 0.00 2.90
1347 2374 6.656270 TCTCACATGCAGAGATTTGTACAAAT 59.344 34.615 29.33 29.33 43.14 2.32
1354 2381 3.181523 CGTGTCTCACATGCAGAGATTTG 60.182 47.826 18.17 9.47 43.41 2.32
1367 2394 1.654105 CATCGCTTAACCGTGTCTCAC 59.346 52.381 0.00 0.00 0.00 3.51
1369 2396 2.273370 TCATCGCTTAACCGTGTCTC 57.727 50.000 0.00 0.00 0.00 3.36
1373 2400 4.272504 ACCATAATTCATCGCTTAACCGTG 59.727 41.667 0.00 0.00 0.00 4.94
1374 2401 4.448210 ACCATAATTCATCGCTTAACCGT 58.552 39.130 0.00 0.00 0.00 4.83
1375 2402 5.204833 CAACCATAATTCATCGCTTAACCG 58.795 41.667 0.00 0.00 0.00 4.44
1396 2427 4.257731 TGACATAGAAATACGCAAGGCAA 58.742 39.130 0.00 0.00 46.39 4.52
1417 2448 6.218108 TGATCCAGCTCATACTATAGCATG 57.782 41.667 6.62 6.62 41.32 4.06
1465 2496 4.770531 AGTTCTTTTAATGGCCCTTGGTAC 59.229 41.667 0.00 0.00 0.00 3.34
1469 2502 5.185635 TCATCAGTTCTTTTAATGGCCCTTG 59.814 40.000 0.00 0.00 0.00 3.61
1474 2507 7.542025 ACTTCATCATCAGTTCTTTTAATGGC 58.458 34.615 0.00 0.00 0.00 4.40
1529 2563 2.505819 AGACAAATGGAAGGAGCGGTAT 59.494 45.455 0.00 0.00 0.00 2.73
1533 2567 3.923017 AAAAGACAAATGGAAGGAGCG 57.077 42.857 0.00 0.00 0.00 5.03
1845 2907 0.520404 CTGGAATGACAGTGCAGTGC 59.480 55.000 21.57 8.58 33.81 4.40
1899 2969 2.439507 GAGGGATGACAATTGCCTCCTA 59.560 50.000 14.78 0.00 43.73 2.94
2006 3108 0.299003 GCAAATACTCAGCGACGCTC 59.701 55.000 21.67 0.95 36.40 5.03
2123 3231 4.098349 TGCTGCAATTTGAACAGAAGAAGT 59.902 37.500 0.00 0.00 33.10 3.01
2244 3352 1.808945 GATGACAAGTGCCTGTTCAGG 59.191 52.381 13.88 13.88 0.00 3.86
2361 3469 4.155826 CCAAACGATCCAATCTACAAAGCA 59.844 41.667 0.00 0.00 0.00 3.91
2379 3487 5.643379 TCATCCAATCTACAAAGCCAAAC 57.357 39.130 0.00 0.00 0.00 2.93
2400 3509 6.926272 ACCTTCAGCAAAGATATAGTCGAATC 59.074 38.462 0.00 0.00 37.12 2.52
2439 3554 6.254157 CCTGTCAGTTTTCAACAACAAAGATG 59.746 38.462 0.00 0.00 31.72 2.90
2489 3604 8.625651 TGCCTTTAGATATATCTAAGAGATCGC 58.374 37.037 26.46 22.53 46.56 4.58
2491 3606 9.965824 GCTGCCTTTAGATATATCTAAGAGATC 57.034 37.037 26.46 20.41 46.56 2.75
2512 3629 3.001414 CTGACTATGCTCATATGCTGCC 58.999 50.000 14.81 3.65 0.00 4.85
2695 3818 4.214971 GTCATGATTAAGCAGCAGGTATGG 59.785 45.833 0.00 0.00 0.00 2.74
2696 3819 4.084171 CGTCATGATTAAGCAGCAGGTATG 60.084 45.833 0.00 0.00 0.00 2.39
2698 3821 3.132111 TCGTCATGATTAAGCAGCAGGTA 59.868 43.478 0.00 0.00 0.00 3.08
2715 3838 8.492673 AGAAAGAAAATATTACATGCTCGTCA 57.507 30.769 0.00 0.00 0.00 4.35
2718 3841 9.994432 AGAAAGAAAGAAAATATTACATGCTCG 57.006 29.630 0.00 0.00 0.00 5.03
2769 3892 0.248949 GGGTACCGAGACTGCGAATC 60.249 60.000 5.65 0.00 40.86 2.52
2914 4043 7.431084 GCAACGATTTTAGTTCTTTGTTGAGAA 59.569 33.333 5.99 0.00 36.14 2.87
3073 4221 4.021192 ACATTGAACACCATTGGGATTGTC 60.021 41.667 7.78 0.00 38.05 3.18
3097 4245 3.226777 ACCATGAGGAGAGAGGATAACG 58.773 50.000 0.00 0.00 38.69 3.18
3176 4324 7.424803 TGTCAAACTGTCAAAAATGATGTAGG 58.575 34.615 0.00 0.00 0.00 3.18
3182 4330 9.474920 GGAAATATGTCAAACTGTCAAAAATGA 57.525 29.630 0.00 0.00 0.00 2.57
3185 4333 8.912988 AGAGGAAATATGTCAAACTGTCAAAAA 58.087 29.630 0.00 0.00 0.00 1.94
3252 4400 3.668141 TGGGTTGCCATGACATAAGAT 57.332 42.857 0.00 0.00 0.00 2.40
3254 4402 3.822735 CCTATGGGTTGCCATGACATAAG 59.177 47.826 0.00 0.00 0.00 1.73
3273 4421 6.608002 ACTTGGTCCAAAATGTAAACAACCTA 59.392 34.615 5.64 0.00 0.00 3.08
3276 4424 6.822073 GACTTGGTCCAAAATGTAAACAAC 57.178 37.500 5.64 0.00 0.00 3.32
3371 4519 6.814644 CGATCATGTTGGGTACTAAACTTACA 59.185 38.462 10.97 0.00 0.00 2.41
3389 4539 5.712004 ACAGAGAGCTCATATTCGATCATG 58.288 41.667 17.77 1.33 0.00 3.07
3511 4661 1.376037 GGTGCCAAGGACCTTCTCG 60.376 63.158 2.91 0.00 0.00 4.04
3808 4960 2.224548 GGTAACTCCCAACTTGTGAGCT 60.225 50.000 1.49 0.00 0.00 4.09
3829 4981 1.416401 AGGGGTAGAATGCGTACATGG 59.584 52.381 0.00 0.00 36.36 3.66
3851 5004 6.567959 TGAGAATACATCTTGTACTGAGCAG 58.432 40.000 0.00 0.00 38.96 4.24
3939 5092 5.313712 GAGTTGGGATACTTGGTTTTCTCA 58.686 41.667 0.00 0.00 0.00 3.27
3984 5137 2.359531 GGAGAAGTGGTAGTGATCCTCG 59.640 54.545 0.00 0.00 0.00 4.63
4044 5197 4.377839 AGTACTGGTGATGATGAAGTCG 57.622 45.455 0.00 0.00 0.00 4.18
4152 5305 6.861055 GTCCTTGCTGAAAATTGAACGATAAA 59.139 34.615 0.00 0.00 0.00 1.40
4160 5313 2.293122 CGGTGTCCTTGCTGAAAATTGA 59.707 45.455 0.00 0.00 0.00 2.57
4219 5372 0.535335 GGACAACACGATAGAGGCCA 59.465 55.000 5.01 0.00 41.38 5.36
4376 5529 3.418995 ACTTGTGCTCAGCATTCTCAAT 58.581 40.909 0.54 0.00 41.91 2.57
4441 5597 5.811100 GGTAGTCAAGTTAGATAACCAGCAC 59.189 44.000 0.00 0.00 36.88 4.40
4522 5678 4.020573 AGTCATATTCTTGACACGGTCCAA 60.021 41.667 7.28 0.00 46.81 3.53
4608 5764 1.202927 ACCTTTCCATGGTCACCACAG 60.203 52.381 12.58 0.00 35.80 3.66
4701 5857 0.463204 CAGAGATCCAGCGGATGTGT 59.537 55.000 13.68 6.67 43.27 3.72
4917 6074 2.773661 ACATGTCATGGCCTCTATCACA 59.226 45.455 17.08 0.00 33.60 3.58
4992 6149 2.524640 TGGTAGCCGGACACACCA 60.525 61.111 5.05 9.37 38.72 4.17
5432 6589 6.128418 GGCACAGAGAAATTAAGTCTCAAGAC 60.128 42.308 17.05 1.79 43.39 3.01
5601 6758 2.352715 GGACAAGCAAAGGCATAACACC 60.353 50.000 0.00 0.00 44.61 4.16
5848 7011 6.611613 AGGATTTTGAATCTTCCTTTTCCC 57.388 37.500 1.21 0.00 34.98 3.97
6014 7177 7.044181 AGTTCAATGTGTATGTAGACCTCATG 58.956 38.462 0.00 0.00 0.00 3.07
6015 7178 7.187824 AGTTCAATGTGTATGTAGACCTCAT 57.812 36.000 0.00 0.00 0.00 2.90
6016 7179 6.605471 AGTTCAATGTGTATGTAGACCTCA 57.395 37.500 0.00 0.00 0.00 3.86
6017 7180 6.535508 GGAAGTTCAATGTGTATGTAGACCTC 59.464 42.308 5.01 0.00 0.00 3.85
6018 7181 6.213600 AGGAAGTTCAATGTGTATGTAGACCT 59.786 38.462 5.01 0.00 0.00 3.85
6019 7182 6.407202 AGGAAGTTCAATGTGTATGTAGACC 58.593 40.000 5.01 0.00 0.00 3.85
6020 7183 9.250624 GATAGGAAGTTCAATGTGTATGTAGAC 57.749 37.037 5.01 0.00 0.00 2.59
6303 7496 0.041535 TAGGGTGCGAGGGGTTCTTA 59.958 55.000 0.00 0.00 0.00 2.10
6372 7565 7.062749 TGTAGCCCTATCCAGTATTTTAGTG 57.937 40.000 0.00 0.00 0.00 2.74
6383 7576 3.908103 GGGAGTTAATGTAGCCCTATCCA 59.092 47.826 0.00 0.00 35.86 3.41
6384 7577 4.168883 AGGGAGTTAATGTAGCCCTATCC 58.831 47.826 0.00 0.00 47.00 2.59
6424 7617 2.685819 GCCCCCTATTTGTCAAGTACCC 60.686 54.545 0.00 0.00 0.00 3.69
6450 7758 1.621107 CTCACCGTCATTTGCAATGC 58.379 50.000 0.00 0.00 0.00 3.56
6466 7774 3.491766 AAGGTATCAAGAGGTCCCTCA 57.508 47.619 15.48 0.00 44.99 3.86


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

AutoCloner maintained by Alex Coulton.