Multiple sequence alignment - TraesCS6B01G009700

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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 TraesCS6B01G009700 chr6B 100.000 4727 0 0 1 4727 6022940 6027666 0.000000e+00 8730.0
1 TraesCS6B01G009700 chr6B 74.250 1934 417 58 2139 4048 6271050 6269174 0.000000e+00 737.0
2 TraesCS6B01G009700 chr6B 89.796 245 23 1 1087 1331 6240806 6240564 3.550000e-81 313.0
3 TraesCS6B01G009700 chr6A 93.386 3432 181 19 669 4083 1894623 1898025 0.000000e+00 5038.0
4 TraesCS6B01G009700 chr6A 77.488 2150 406 52 1578 3679 1921932 1924051 0.000000e+00 1218.0
5 TraesCS6B01G009700 chr6A 91.290 597 22 11 4136 4727 1898022 1898593 0.000000e+00 787.0
6 TraesCS6B01G009700 chr6A 91.335 427 33 3 1 426 1893952 1894375 8.820000e-162 580.0
7 TraesCS6B01G009700 chr6A 85.484 186 27 0 1146 1331 1921749 1921934 1.340000e-45 195.0
8 TraesCS6B01G009700 chr6D 93.472 3079 158 25 669 3743 2911007 2914046 0.000000e+00 4532.0
9 TraesCS6B01G009700 chr6D 79.232 2109 382 38 1604 3690 3076590 3074516 0.000000e+00 1417.0
10 TraesCS6B01G009700 chr6D 78.416 1705 326 32 2133 3820 2897103 2898782 0.000000e+00 1072.0
11 TraesCS6B01G009700 chr6D 91.335 427 30 5 1 426 2910341 2910761 1.140000e-160 577.0
12 TraesCS6B01G009700 chr6D 83.039 566 52 19 794 1329 2895992 2896543 1.540000e-129 473.0
13 TraesCS6B01G009700 chr6D 85.000 440 43 13 1 424 2895108 2895540 4.370000e-115 425.0
14 TraesCS6B01G009700 chr6D 81.330 466 75 7 1604 2068 2896557 2897011 7.470000e-98 368.0
15 TraesCS6B01G009700 chr6D 90.083 242 24 0 1090 1331 3076843 3076602 9.870000e-82 315.0
16 TraesCS6B01G009700 chr6D 83.206 262 23 6 3826 4083 2914054 2914298 2.210000e-53 220.0
17 TraesCS6B01G009700 chr6D 86.842 152 19 1 2921 3071 2923222 2923373 8.140000e-38 169.0
18 TraesCS6B01G009700 chr6D 92.063 63 4 1 4280 4342 2914609 2914670 2.340000e-13 87.9


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 TraesCS6B01G009700 chr6B 6022940 6027666 4726 False 8730.000 8730 100.000000 1 4727 1 chr6B.!!$F1 4726
1 TraesCS6B01G009700 chr6B 6269174 6271050 1876 True 737.000 737 74.250000 2139 4048 1 chr6B.!!$R2 1909
2 TraesCS6B01G009700 chr6A 1893952 1898593 4641 False 2135.000 5038 92.003667 1 4727 3 chr6A.!!$F1 4726
3 TraesCS6B01G009700 chr6A 1921749 1924051 2302 False 706.500 1218 81.486000 1146 3679 2 chr6A.!!$F2 2533
4 TraesCS6B01G009700 chr6D 2910341 2914670 4329 False 1354.225 4532 90.019000 1 4342 4 chr6D.!!$F3 4341
5 TraesCS6B01G009700 chr6D 3074516 3076843 2327 True 866.000 1417 84.657500 1090 3690 2 chr6D.!!$R1 2600
6 TraesCS6B01G009700 chr6D 2895108 2898782 3674 False 584.500 1072 81.946250 1 3820 4 chr6D.!!$F2 3819

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
599 747 0.097499 CATCGCGCATTTTCAGAGCA 59.903 50.0 8.75 0.0 0.00 4.26 F
601 749 0.110238 TCGCGCATTTTCAGAGCAAC 60.110 50.0 8.75 0.0 0.00 4.17 F
1983 2264 0.246360 TGCTCCACGATGACGAACAT 59.754 50.0 0.00 0.0 42.66 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1995 2285 0.918258 TGCAAGCCCTCATGATACCA 59.082 50.0 0.00 0.0 0.0 3.25 R
2427 2756 1.028330 TGGCCTGGTAGTACTCGTCG 61.028 60.0 3.32 0.0 0.0 5.12 R
3728 4099 0.034670 GCCTTGATCCTGAGCCTGTT 60.035 55.0 0.00 0.0 0.0 3.16 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
70 71 6.467677 TGAGAATATATAAAGACCTGCTGCC 58.532 40.000 0.00 0.00 0.00 4.85
79 80 0.538287 GACCTGCTGCCTTCTTGGTT 60.538 55.000 0.00 0.00 38.35 3.67
90 91 1.334869 CTTCTTGGTTGTGGCAGTGAC 59.665 52.381 0.00 0.00 0.00 3.67
91 92 0.813610 TCTTGGTTGTGGCAGTGACG 60.814 55.000 0.00 0.00 0.00 4.35
193 195 1.301716 GGGCGGACGATGTATGCAT 60.302 57.895 3.79 3.79 38.18 3.96
194 196 1.568612 GGGCGGACGATGTATGCATG 61.569 60.000 10.16 0.00 35.07 4.06
196 198 1.224069 GCGGACGATGTATGCATGCT 61.224 55.000 20.33 7.07 35.07 3.79
256 258 6.825721 AGGTGATTCTAATGATCTTTGTGGTC 59.174 38.462 4.17 0.00 0.00 4.02
264 266 3.411446 TGATCTTTGTGGTCATGTGGTC 58.589 45.455 0.00 0.00 0.00 4.02
268 270 0.179234 TTGTGGTCATGTGGTCGTGT 59.821 50.000 0.00 0.00 32.85 4.49
387 404 5.068329 TCAAGTATGTGGTTTTGCATGTTGA 59.932 36.000 0.00 0.00 32.21 3.18
398 415 3.853831 TGCATGTTGACATCATTGGAC 57.146 42.857 0.00 0.00 33.61 4.02
435 542 3.000727 CGAAACCTTAGATCTTTGCCGT 58.999 45.455 0.00 0.00 0.00 5.68
440 547 2.607187 CTTAGATCTTTGCCGTCGTGT 58.393 47.619 0.00 0.00 0.00 4.49
443 550 2.279937 GATCTTTGCCGTCGTGTCGC 62.280 60.000 0.00 0.00 0.00 5.19
444 551 4.409588 CTTTGCCGTCGTGTCGCG 62.410 66.667 0.00 0.00 43.01 5.87
454 600 2.719354 GTGTCGCGCCAAAAACCT 59.281 55.556 0.00 0.00 0.00 3.50
460 606 2.411290 CGCCAAAAACCTGCACGT 59.589 55.556 0.00 0.00 0.00 4.49
464 610 1.591327 CAAAAACCTGCACGTGCCC 60.591 57.895 35.72 12.23 41.18 5.36
468 614 1.805428 AAACCTGCACGTGCCCATTC 61.805 55.000 35.72 9.88 41.18 2.67
489 636 0.254747 TATGGACCAAAAGAGGGGCG 59.745 55.000 0.00 0.00 32.63 6.13
498 645 2.800544 CAAAAGAGGGGCGATATGTACG 59.199 50.000 0.00 0.00 0.00 3.67
507 654 3.057456 GGGCGATATGTACGAGAAGTCAT 60.057 47.826 0.00 0.00 0.00 3.06
514 662 7.841277 CGATATGTACGAGAAGTCATGTTTTTG 59.159 37.037 0.00 0.00 0.00 2.44
517 665 5.465390 TGTACGAGAAGTCATGTTTTTGGAG 59.535 40.000 0.00 0.00 0.00 3.86
520 668 4.398319 GAGAAGTCATGTTTTTGGAGGGA 58.602 43.478 0.00 0.00 0.00 4.20
522 670 4.584743 AGAAGTCATGTTTTTGGAGGGAAC 59.415 41.667 0.00 0.00 0.00 3.62
523 671 2.884639 AGTCATGTTTTTGGAGGGAACG 59.115 45.455 0.00 0.00 0.00 3.95
525 673 2.621055 TCATGTTTTTGGAGGGAACGTG 59.379 45.455 0.00 0.00 40.11 4.49
528 676 1.448922 TTTTTGGAGGGAACGTGGCG 61.449 55.000 0.00 0.00 0.00 5.69
545 693 1.004918 CGAAGCCCTATTAGCCCCG 60.005 63.158 0.00 0.00 0.00 5.73
548 696 1.128188 AAGCCCTATTAGCCCCGAGG 61.128 60.000 0.00 0.00 0.00 4.63
561 709 1.227973 CCGAGGGGAAATGCCTAGC 60.228 63.158 0.00 0.00 36.66 3.42
562 710 1.526887 CGAGGGGAAATGCCTAGCA 59.473 57.895 0.00 0.00 44.86 3.49
563 711 0.815615 CGAGGGGAAATGCCTAGCAC 60.816 60.000 0.00 0.00 43.04 4.40
564 712 0.466372 GAGGGGAAATGCCTAGCACC 60.466 60.000 0.00 0.00 43.04 5.01
565 713 1.214305 AGGGGAAATGCCTAGCACCA 61.214 55.000 0.00 0.00 43.04 4.17
566 714 0.324275 GGGGAAATGCCTAGCACCAA 60.324 55.000 0.00 0.00 43.04 3.67
567 715 1.555967 GGGAAATGCCTAGCACCAAA 58.444 50.000 0.00 0.00 43.04 3.28
568 716 1.204704 GGGAAATGCCTAGCACCAAAC 59.795 52.381 0.00 0.00 43.04 2.93
569 717 1.892474 GGAAATGCCTAGCACCAAACA 59.108 47.619 0.00 0.00 43.04 2.83
570 718 2.352715 GGAAATGCCTAGCACCAAACAC 60.353 50.000 0.00 0.00 43.04 3.32
571 719 2.292828 AATGCCTAGCACCAAACACT 57.707 45.000 0.00 0.00 43.04 3.55
572 720 2.292828 ATGCCTAGCACCAAACACTT 57.707 45.000 0.00 0.00 43.04 3.16
573 721 1.317613 TGCCTAGCACCAAACACTTG 58.682 50.000 0.00 0.00 31.71 3.16
574 722 1.318576 GCCTAGCACCAAACACTTGT 58.681 50.000 0.00 0.00 0.00 3.16
575 723 1.681264 GCCTAGCACCAAACACTTGTT 59.319 47.619 0.00 0.00 40.50 2.83
576 724 4.440263 TGCCTAGCACCAAACACTTGTTT 61.440 43.478 1.35 1.35 40.28 2.83
577 725 3.430236 GCCTAGCACCAAACACTTGTTTT 60.430 43.478 4.56 0.00 45.07 2.43
578 726 4.111916 CCTAGCACCAAACACTTGTTTTG 58.888 43.478 4.56 4.67 45.07 2.44
579 727 3.951775 AGCACCAAACACTTGTTTTGA 57.048 38.095 11.70 0.00 45.07 2.69
580 728 3.584834 AGCACCAAACACTTGTTTTGAC 58.415 40.909 11.70 4.90 45.07 3.18
581 729 3.006323 AGCACCAAACACTTGTTTTGACA 59.994 39.130 11.70 0.00 45.07 3.58
582 730 3.932089 GCACCAAACACTTGTTTTGACAT 59.068 39.130 11.70 0.00 45.07 3.06
583 731 4.032786 GCACCAAACACTTGTTTTGACATC 59.967 41.667 11.70 0.00 45.07 3.06
584 732 4.265085 CACCAAACACTTGTTTTGACATCG 59.735 41.667 11.70 0.00 45.07 3.84
585 733 3.242712 CCAAACACTTGTTTTGACATCGC 59.757 43.478 4.56 0.00 45.07 4.58
586 734 2.383298 ACACTTGTTTTGACATCGCG 57.617 45.000 0.00 0.00 0.00 5.87
587 735 1.044725 CACTTGTTTTGACATCGCGC 58.955 50.000 0.00 0.00 0.00 6.86
588 736 0.660488 ACTTGTTTTGACATCGCGCA 59.340 45.000 8.75 0.00 0.00 6.09
589 737 1.266718 ACTTGTTTTGACATCGCGCAT 59.733 42.857 8.75 0.00 0.00 4.73
590 738 2.287547 ACTTGTTTTGACATCGCGCATT 60.288 40.909 8.75 0.00 0.00 3.56
591 739 2.414058 TGTTTTGACATCGCGCATTT 57.586 40.000 8.75 0.00 0.00 2.32
592 740 2.736978 TGTTTTGACATCGCGCATTTT 58.263 38.095 8.75 0.00 0.00 1.82
593 741 2.723658 TGTTTTGACATCGCGCATTTTC 59.276 40.909 8.75 0.00 0.00 2.29
594 742 2.695613 TTTGACATCGCGCATTTTCA 57.304 40.000 8.75 0.83 0.00 2.69
595 743 2.245795 TTGACATCGCGCATTTTCAG 57.754 45.000 8.75 0.00 0.00 3.02
596 744 1.437625 TGACATCGCGCATTTTCAGA 58.562 45.000 8.75 0.00 0.00 3.27
597 745 1.394572 TGACATCGCGCATTTTCAGAG 59.605 47.619 8.75 0.00 0.00 3.35
598 746 0.097674 ACATCGCGCATTTTCAGAGC 59.902 50.000 8.75 0.00 0.00 4.09
599 747 0.097499 CATCGCGCATTTTCAGAGCA 59.903 50.000 8.75 0.00 0.00 4.26
600 748 0.804364 ATCGCGCATTTTCAGAGCAA 59.196 45.000 8.75 0.00 0.00 3.91
601 749 0.110238 TCGCGCATTTTCAGAGCAAC 60.110 50.000 8.75 0.00 0.00 4.17
602 750 0.385849 CGCGCATTTTCAGAGCAACA 60.386 50.000 8.75 0.00 0.00 3.33
603 751 1.730121 CGCGCATTTTCAGAGCAACAT 60.730 47.619 8.75 0.00 0.00 2.71
604 752 2.331194 GCGCATTTTCAGAGCAACATT 58.669 42.857 0.30 0.00 0.00 2.71
605 753 2.733026 GCGCATTTTCAGAGCAACATTT 59.267 40.909 0.30 0.00 0.00 2.32
606 754 3.184986 GCGCATTTTCAGAGCAACATTTT 59.815 39.130 0.30 0.00 0.00 1.82
607 755 4.664891 GCGCATTTTCAGAGCAACATTTTC 60.665 41.667 0.30 0.00 0.00 2.29
608 756 4.682860 CGCATTTTCAGAGCAACATTTTCT 59.317 37.500 0.00 0.00 0.00 2.52
609 757 5.858049 CGCATTTTCAGAGCAACATTTTCTA 59.142 36.000 0.00 0.00 0.00 2.10
610 758 6.363088 CGCATTTTCAGAGCAACATTTTCTAA 59.637 34.615 0.00 0.00 0.00 2.10
611 759 7.096106 CGCATTTTCAGAGCAACATTTTCTAAA 60.096 33.333 0.00 0.00 0.00 1.85
612 760 8.715088 GCATTTTCAGAGCAACATTTTCTAAAT 58.285 29.630 0.00 0.00 0.00 1.40
615 763 9.598517 TTTTCAGAGCAACATTTTCTAAATTGT 57.401 25.926 0.00 0.00 34.90 2.71
616 764 9.598517 TTTCAGAGCAACATTTTCTAAATTGTT 57.401 25.926 8.97 8.97 40.85 2.83
617 765 9.598517 TTCAGAGCAACATTTTCTAAATTGTTT 57.401 25.926 11.17 1.86 39.23 2.83
618 766 9.248291 TCAGAGCAACATTTTCTAAATTGTTTC 57.752 29.630 11.17 8.17 39.23 2.78
619 767 8.490355 CAGAGCAACATTTTCTAAATTGTTTCC 58.510 33.333 11.17 7.34 39.23 3.13
620 768 8.203485 AGAGCAACATTTTCTAAATTGTTTCCA 58.797 29.630 11.17 0.00 39.23 3.53
621 769 8.907222 AGCAACATTTTCTAAATTGTTTCCAT 57.093 26.923 11.17 0.00 39.23 3.41
622 770 8.992073 AGCAACATTTTCTAAATTGTTTCCATC 58.008 29.630 11.17 2.82 39.23 3.51
623 771 8.772705 GCAACATTTTCTAAATTGTTTCCATCA 58.227 29.630 11.17 0.00 39.23 3.07
642 790 9.527157 TTCCATCATACTAACTTTGAAATTGGA 57.473 29.630 0.00 0.00 28.91 3.53
762 955 5.365619 TCTGAGAATAATTAAAGACCCGGC 58.634 41.667 0.00 0.00 0.00 6.13
763 956 5.130477 TCTGAGAATAATTAAAGACCCGGCT 59.870 40.000 0.00 0.00 0.00 5.52
764 957 5.751586 TGAGAATAATTAAAGACCCGGCTT 58.248 37.500 0.00 0.00 0.00 4.35
765 958 6.184789 TGAGAATAATTAAAGACCCGGCTTT 58.815 36.000 11.21 11.21 40.85 3.51
766 959 6.094881 TGAGAATAATTAAAGACCCGGCTTTG 59.905 38.462 15.06 0.00 38.47 2.77
767 960 5.949952 AGAATAATTAAAGACCCGGCTTTGT 59.050 36.000 15.06 0.00 38.47 2.83
783 976 3.411446 CTTTGTACATGGAGAAGTGCCA 58.589 45.455 0.00 0.00 40.24 4.92
920 1150 8.612619 CCAAAACTAGCAGTATAAATACCACAG 58.387 37.037 0.00 0.00 33.79 3.66
948 1186 1.623081 GCACAATGCAGCACACATGC 61.623 55.000 0.00 1.73 44.26 4.06
969 1207 2.418976 CACAAGTCAGCATCACCATCAG 59.581 50.000 0.00 0.00 0.00 2.90
971 1209 0.910338 AGTCAGCATCACCATCAGCT 59.090 50.000 0.00 0.00 37.95 4.24
972 1210 1.281287 AGTCAGCATCACCATCAGCTT 59.719 47.619 0.00 0.00 34.61 3.74
976 1214 2.097629 CAGCATCACCATCAGCTTCTTG 59.902 50.000 0.00 0.00 34.61 3.02
977 1215 1.202268 GCATCACCATCAGCTTCTTGC 60.202 52.381 0.00 0.00 43.29 4.01
1334 1597 4.030913 TCCTACATGTTCTCCCAGGTAAG 58.969 47.826 2.30 0.00 31.93 2.34
1335 1598 3.134804 CCTACATGTTCTCCCAGGTAAGG 59.865 52.174 2.30 0.00 31.93 2.69
1336 1599 2.632537 ACATGTTCTCCCAGGTAAGGT 58.367 47.619 0.00 0.00 0.00 3.50
1337 1600 2.986728 ACATGTTCTCCCAGGTAAGGTT 59.013 45.455 0.00 0.00 0.00 3.50
1338 1601 3.397955 ACATGTTCTCCCAGGTAAGGTTT 59.602 43.478 0.00 0.00 0.00 3.27
1339 1602 4.600111 ACATGTTCTCCCAGGTAAGGTTTA 59.400 41.667 0.00 0.00 0.00 2.01
1340 1603 5.073965 ACATGTTCTCCCAGGTAAGGTTTAA 59.926 40.000 0.00 0.00 0.00 1.52
1388 1651 9.762381 ATTACCAAACCTTAGTGAAATATCCAA 57.238 29.630 0.00 0.00 0.00 3.53
1389 1652 9.589461 TTACCAAACCTTAGTGAAATATCCAAA 57.411 29.630 0.00 0.00 0.00 3.28
1439 1702 6.389622 TCTATCGACGTTCACTTGATTTTG 57.610 37.500 0.00 0.00 0.00 2.44
1452 1715 7.954835 TCACTTGATTTTGATGGATTTTGACT 58.045 30.769 0.00 0.00 0.00 3.41
1516 1779 9.301153 ACGAAATTTTGAGGTTGCATATATTTC 57.699 29.630 12.54 0.00 0.00 2.17
1518 1781 9.515020 GAAATTTTGAGGTTGCATATATTTCGA 57.485 29.630 0.00 0.00 0.00 3.71
1522 1785 7.667043 TTGAGGTTGCATATATTTCGATACC 57.333 36.000 0.00 0.00 0.00 2.73
1650 1928 2.711547 TCTCCTCTGGATGATCCTCGTA 59.288 50.000 13.44 0.00 37.46 3.43
1671 1949 1.743252 GCTCCTCCGCAAGAAGGTG 60.743 63.158 0.00 0.00 43.02 4.00
1740 2018 2.005451 CGCTACAGCTTCTTTGATGCT 58.995 47.619 0.00 2.70 42.44 3.79
1815 2093 0.537143 ATGGCTTTGGCGTCAAGTCA 60.537 50.000 1.31 5.75 39.81 3.41
1914 2192 1.517257 CGACCTCGCGAAGAATGCT 60.517 57.895 12.53 0.00 0.00 3.79
1948 2226 1.142185 CTACATGGTGCAGCTCGTCG 61.142 60.000 18.08 6.45 0.00 5.12
1954 2232 2.049156 TGCAGCTCGTCGACAAGG 60.049 61.111 17.16 5.73 0.00 3.61
1983 2264 0.246360 TGCTCCACGATGACGAACAT 59.754 50.000 0.00 0.00 42.66 2.71
2251 2568 0.968405 GGAGAACATTTGCCTTGCCA 59.032 50.000 0.00 0.00 0.00 4.92
2331 2648 1.153647 CCCACAAGCACGCGATCTA 60.154 57.895 15.93 0.00 0.00 1.98
2346 2663 1.962570 ATCTAGTCCTCCGGGGCCTT 61.963 60.000 0.84 0.00 38.13 4.35
2427 2756 3.511934 TGGAACTAGAGCTGAGGTTTCTC 59.488 47.826 0.00 0.00 40.36 2.87
2520 2849 6.314648 TCATCTCCATCGTCTTCATCTTTTTG 59.685 38.462 0.00 0.00 0.00 2.44
2572 2901 0.770499 TGGCCACATCTTCAAGGTGA 59.230 50.000 4.13 0.00 34.52 4.02
2576 2905 3.370953 GGCCACATCTTCAAGGTGATAGT 60.371 47.826 4.13 0.00 34.52 2.12
2721 3050 2.286523 CCTCACGCTCACCCTCCTT 61.287 63.158 0.00 0.00 0.00 3.36
2751 3080 7.383572 GTCGAGACATATGAATTCTTGCAGTAT 59.616 37.037 10.38 0.00 0.00 2.12
2781 3110 4.000325 CTGATTGGTTCATTGTGTCCGTA 59.000 43.478 0.00 0.00 32.72 4.02
2905 3246 0.911769 GGTCCACCAGATCACCATGA 59.088 55.000 0.00 0.00 35.64 3.07
2919 3260 3.118629 TCACCATGATCAAGCTCCACTAC 60.119 47.826 0.00 0.00 0.00 2.73
3559 3930 1.294659 CTGGGCAGAACTTCTCGTGC 61.295 60.000 0.00 0.00 35.07 5.34
3691 4062 0.409484 CCCCAAGAACCACCAGGATT 59.591 55.000 0.00 0.00 38.69 3.01
3714 4085 0.108585 AGGTTCCATCGTGCAACTGT 59.891 50.000 0.00 0.00 31.75 3.55
3811 4182 7.754069 TGTTGTTTTGAAAAGAGTTGCATAG 57.246 32.000 0.00 0.00 0.00 2.23
3890 4261 1.137404 GCATTAGCTGGTTGGCGTG 59.863 57.895 0.00 0.00 37.91 5.34
3899 4270 3.386726 AGCTGGTTGGCGTGATAATACTA 59.613 43.478 0.00 0.00 37.29 1.82
3985 4358 0.242825 CTCATGCCAGTTGTGCTTGG 59.757 55.000 0.00 0.00 35.33 3.61
3996 4369 5.159209 CAGTTGTGCTTGGAGATGATTTTC 58.841 41.667 0.00 0.00 0.00 2.29
3997 4370 4.828939 AGTTGTGCTTGGAGATGATTTTCA 59.171 37.500 0.00 0.00 0.00 2.69
3998 4371 5.479375 AGTTGTGCTTGGAGATGATTTTCAT 59.521 36.000 0.00 0.00 40.34 2.57
4052 4430 7.912250 GCAGACATAGTGATTTTTATTGGTGAG 59.088 37.037 0.00 0.00 0.00 3.51
4080 4458 7.033530 ACAGAGCTACTCTATGTGTAATCAC 57.966 40.000 0.00 0.00 44.82 3.06
4081 4459 6.603599 ACAGAGCTACTCTATGTGTAATCACA 59.396 38.462 3.58 3.58 46.96 3.58
4082 4460 7.122799 ACAGAGCTACTCTATGTGTAATCACAA 59.877 37.037 5.18 0.00 46.51 3.33
4083 4461 7.647318 CAGAGCTACTCTATGTGTAATCACAAG 59.353 40.741 5.18 1.89 46.51 3.16
4084 4462 7.558081 AGAGCTACTCTATGTGTAATCACAAGA 59.442 37.037 5.18 8.40 43.73 3.02
4101 4479 7.672983 TCACAAGATGATGATGATGATGATG 57.327 36.000 0.00 0.00 29.99 3.07
4102 4480 7.450074 TCACAAGATGATGATGATGATGATGA 58.550 34.615 0.00 0.00 29.99 2.92
4103 4481 8.103305 TCACAAGATGATGATGATGATGATGAT 58.897 33.333 0.00 0.00 29.99 2.45
4104 4482 8.180267 CACAAGATGATGATGATGATGATGATG 58.820 37.037 0.00 0.00 0.00 3.07
4105 4483 8.103305 ACAAGATGATGATGATGATGATGATGA 58.897 33.333 0.00 0.00 0.00 2.92
4106 4484 9.118300 CAAGATGATGATGATGATGATGATGAT 57.882 33.333 0.00 0.00 0.00 2.45
4107 4485 8.674263 AGATGATGATGATGATGATGATGATG 57.326 34.615 0.00 0.00 0.00 3.07
4108 4486 8.489489 AGATGATGATGATGATGATGATGATGA 58.511 33.333 0.00 0.00 0.00 2.92
4109 4487 9.282569 GATGATGATGATGATGATGATGATGAT 57.717 33.333 0.00 0.00 0.00 2.45
4113 4491 8.420374 TGATGATGATGATGATGATGATAACG 57.580 34.615 0.00 0.00 0.00 3.18
4114 4492 8.255206 TGATGATGATGATGATGATGATAACGA 58.745 33.333 0.00 0.00 0.00 3.85
4115 4493 9.262358 GATGATGATGATGATGATGATAACGAT 57.738 33.333 0.00 0.00 0.00 3.73
4116 4494 8.420374 TGATGATGATGATGATGATAACGATG 57.580 34.615 0.00 0.00 0.00 3.84
4117 4495 7.494625 TGATGATGATGATGATGATAACGATGG 59.505 37.037 0.00 0.00 0.00 3.51
4118 4496 6.938507 TGATGATGATGATGATAACGATGGA 58.061 36.000 0.00 0.00 0.00 3.41
4119 4497 7.562135 TGATGATGATGATGATAACGATGGAT 58.438 34.615 0.00 0.00 0.00 3.41
4120 4498 7.494625 TGATGATGATGATGATAACGATGGATG 59.505 37.037 0.00 0.00 0.00 3.51
4121 4499 6.110707 TGATGATGATGATAACGATGGATGG 58.889 40.000 0.00 0.00 0.00 3.51
4122 4500 4.835678 TGATGATGATAACGATGGATGGG 58.164 43.478 0.00 0.00 0.00 4.00
4123 4501 3.701205 TGATGATAACGATGGATGGGG 57.299 47.619 0.00 0.00 0.00 4.96
4124 4502 2.305635 TGATGATAACGATGGATGGGGG 59.694 50.000 0.00 0.00 0.00 5.40
4125 4503 2.110753 TGATAACGATGGATGGGGGA 57.889 50.000 0.00 0.00 0.00 4.81
4126 4504 1.977854 TGATAACGATGGATGGGGGAG 59.022 52.381 0.00 0.00 0.00 4.30
4127 4505 1.978580 GATAACGATGGATGGGGGAGT 59.021 52.381 0.00 0.00 0.00 3.85
4128 4506 1.128200 TAACGATGGATGGGGGAGTG 58.872 55.000 0.00 0.00 0.00 3.51
4129 4507 2.111878 CGATGGATGGGGGAGTGC 59.888 66.667 0.00 0.00 0.00 4.40
4130 4508 2.745308 CGATGGATGGGGGAGTGCA 61.745 63.158 0.00 0.00 0.00 4.57
4131 4509 1.614711 GATGGATGGGGGAGTGCAA 59.385 57.895 0.00 0.00 0.00 4.08
4132 4510 0.753111 GATGGATGGGGGAGTGCAAC 60.753 60.000 0.00 0.00 0.00 4.17
4133 4511 2.438434 GGATGGGGGAGTGCAACG 60.438 66.667 0.00 0.00 45.86 4.10
4134 4512 2.438434 GATGGGGGAGTGCAACGG 60.438 66.667 0.00 0.00 45.86 4.44
4187 4565 1.419387 GATCTGGGCAAGGTATCAGCT 59.581 52.381 0.00 0.00 0.00 4.24
4224 4638 2.233271 GGGTTACCATGCATCCATCTG 58.767 52.381 2.98 0.00 36.50 2.90
4247 4661 1.135199 CACCCAGCAAGCAAAGCTATG 60.135 52.381 0.00 0.00 41.14 2.23
4273 4839 1.626686 ATCTCGATGTAGCAGGAGGG 58.373 55.000 0.00 0.00 0.00 4.30
4354 4924 3.670377 GCTTTGCTCCCGCGGTTT 61.670 61.111 26.12 0.00 39.65 3.27
4381 4951 6.808008 AATCTTTGGCTAATATGGTGATCG 57.192 37.500 0.00 0.00 0.00 3.69
4382 4952 5.545063 TCTTTGGCTAATATGGTGATCGA 57.455 39.130 0.00 0.00 0.00 3.59
4384 4954 6.166279 TCTTTGGCTAATATGGTGATCGATC 58.834 40.000 18.72 18.72 0.00 3.69
4385 4955 5.482163 TTGGCTAATATGGTGATCGATCA 57.518 39.130 23.99 23.99 0.00 2.92
4386 4956 5.077134 TGGCTAATATGGTGATCGATCAG 57.923 43.478 27.95 14.51 37.51 2.90
4387 4957 4.528206 TGGCTAATATGGTGATCGATCAGT 59.472 41.667 27.95 18.34 37.51 3.41
4388 4958 4.867047 GGCTAATATGGTGATCGATCAGTG 59.133 45.833 27.95 12.36 37.51 3.66
4389 4959 4.328440 GCTAATATGGTGATCGATCAGTGC 59.672 45.833 27.95 16.18 37.51 4.40
4390 4960 2.422276 TATGGTGATCGATCAGTGCG 57.578 50.000 27.95 0.00 37.51 5.34
4391 4961 0.877649 ATGGTGATCGATCAGTGCGC 60.878 55.000 27.95 15.46 37.51 6.09
4392 4962 1.227089 GGTGATCGATCAGTGCGCT 60.227 57.895 27.95 0.00 37.51 5.92
4393 4963 0.807667 GGTGATCGATCAGTGCGCTT 60.808 55.000 27.95 0.00 37.51 4.68
4394 4964 0.299895 GTGATCGATCAGTGCGCTTG 59.700 55.000 27.95 7.62 37.51 4.01
4395 4965 0.108662 TGATCGATCAGTGCGCTTGT 60.109 50.000 23.99 0.00 32.11 3.16
4396 4966 0.574454 GATCGATCAGTGCGCTTGTC 59.426 55.000 20.52 6.92 0.00 3.18
4397 4967 0.108662 ATCGATCAGTGCGCTTGTCA 60.109 50.000 9.73 0.00 0.00 3.58
4471 5041 2.069273 GAAACGAGTGGTGATGGAGTG 58.931 52.381 0.00 0.00 0.00 3.51
4473 5043 0.541998 ACGAGTGGTGATGGAGTGGA 60.542 55.000 0.00 0.00 0.00 4.02
4476 5046 1.902508 GAGTGGTGATGGAGTGGAGAA 59.097 52.381 0.00 0.00 0.00 2.87
4507 5077 1.826720 TCCACAAGACCCGGTACATAC 59.173 52.381 0.00 0.00 0.00 2.39
4508 5078 1.551430 CCACAAGACCCGGTACATACA 59.449 52.381 0.00 0.00 0.00 2.29
4509 5079 2.169769 CCACAAGACCCGGTACATACAT 59.830 50.000 0.00 0.00 0.00 2.29
4510 5080 3.385433 CCACAAGACCCGGTACATACATA 59.615 47.826 0.00 0.00 0.00 2.29
4520 5090 2.549349 GGTACATACATAGGTTGCCGGG 60.549 54.545 2.18 0.00 0.00 5.73
4546 5116 1.909700 ATTGTCGTCAAGGGTTGCAT 58.090 45.000 0.97 0.00 36.97 3.96
4581 5151 4.323257 GCCTACTAGACTTTAGGGCAACAA 60.323 45.833 0.00 0.00 36.16 2.83
4582 5152 5.176592 CCTACTAGACTTTAGGGCAACAAC 58.823 45.833 0.00 0.00 39.74 3.32
4583 5153 3.660865 ACTAGACTTTAGGGCAACAACG 58.339 45.455 0.00 0.00 39.74 4.10
4584 5154 2.632987 AGACTTTAGGGCAACAACGT 57.367 45.000 0.00 0.00 39.74 3.99
4641 5211 1.246649 TCACGCCATGATTGCAACTT 58.753 45.000 0.00 0.00 29.99 2.66
4651 5221 0.962356 ATTGCAACTTGAGGGAGGCG 60.962 55.000 0.00 0.00 0.00 5.52
4661 5231 2.110213 GGGAGGCGTTGACACACA 59.890 61.111 0.00 0.00 0.00 3.72
4678 5248 3.437049 CACACAAGTAGCTAAAGCCTTCC 59.563 47.826 0.00 0.00 43.38 3.46
4682 5252 1.486726 AGTAGCTAAAGCCTTCCGCAT 59.513 47.619 0.00 0.00 43.38 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 1.334869 GTCACTGCCACAACCAAGAAG 59.665 52.381 0.00 0.00 0.00 2.85
116 117 2.412870 CTGGGAAATATATGCGCACGA 58.587 47.619 14.90 3.61 0.00 4.35
182 184 3.303593 GGTTTGAGAGCATGCATACATCG 60.304 47.826 21.98 0.00 32.87 3.84
193 195 3.316308 GCTTTTTCTCTGGTTTGAGAGCA 59.684 43.478 0.00 0.00 43.05 4.26
194 196 3.304996 GGCTTTTTCTCTGGTTTGAGAGC 60.305 47.826 0.00 0.00 43.05 4.09
196 198 3.222603 GGGCTTTTTCTCTGGTTTGAGA 58.777 45.455 0.00 0.00 40.87 3.27
256 258 3.064682 TGAGAACAAAACACGACCACATG 59.935 43.478 0.00 0.00 0.00 3.21
264 266 4.794248 TCATGACTGAGAACAAAACACG 57.206 40.909 0.00 0.00 0.00 4.49
398 415 3.120649 GGTTTCGGTTGAGAAGAACATCG 60.121 47.826 0.00 0.00 0.00 3.84
440 547 3.212682 TGCAGGTTTTTGGCGCGA 61.213 55.556 12.10 0.00 0.00 5.87
443 550 1.943693 CACGTGCAGGTTTTTGGCG 60.944 57.895 9.81 0.00 0.00 5.69
444 551 2.237066 GCACGTGCAGGTTTTTGGC 61.237 57.895 34.52 6.18 41.59 4.52
446 592 1.591327 GGGCACGTGCAGGTTTTTG 60.591 57.895 38.60 0.00 44.36 2.44
448 594 1.398958 AATGGGCACGTGCAGGTTTT 61.399 50.000 38.60 21.76 44.36 2.43
454 600 1.023502 CATATGAATGGGCACGTGCA 58.976 50.000 38.60 22.42 44.36 4.57
464 610 4.586001 CCCCTCTTTTGGTCCATATGAATG 59.414 45.833 3.65 0.00 0.00 2.67
468 614 2.310538 GCCCCTCTTTTGGTCCATATG 58.689 52.381 0.00 0.00 0.00 1.78
477 624 2.800544 CGTACATATCGCCCCTCTTTTG 59.199 50.000 0.00 0.00 0.00 2.44
489 636 8.116753 CCAAAAACATGACTTCTCGTACATATC 58.883 37.037 0.00 0.00 0.00 1.63
498 645 4.398319 TCCCTCCAAAAACATGACTTCTC 58.602 43.478 0.00 0.00 0.00 2.87
507 654 1.394618 CCACGTTCCCTCCAAAAACA 58.605 50.000 0.00 0.00 0.00 2.83
514 662 2.434359 CTTCGCCACGTTCCCTCC 60.434 66.667 0.00 0.00 0.00 4.30
528 676 0.321996 CTCGGGGCTAATAGGGCTTC 59.678 60.000 0.00 0.00 0.00 3.86
545 693 0.466372 GGTGCTAGGCATTTCCCCTC 60.466 60.000 0.00 0.00 41.91 4.30
548 696 1.204704 GTTTGGTGCTAGGCATTTCCC 59.795 52.381 0.00 0.00 41.91 3.97
549 697 1.892474 TGTTTGGTGCTAGGCATTTCC 59.108 47.619 0.00 0.00 41.91 3.13
550 698 2.558359 AGTGTTTGGTGCTAGGCATTTC 59.442 45.455 0.00 0.00 41.91 2.17
551 699 2.597455 AGTGTTTGGTGCTAGGCATTT 58.403 42.857 0.00 0.00 41.91 2.32
552 700 2.292828 AGTGTTTGGTGCTAGGCATT 57.707 45.000 0.00 0.00 41.91 3.56
553 701 1.888512 CAAGTGTTTGGTGCTAGGCAT 59.111 47.619 0.00 0.00 41.91 4.40
556 704 4.111916 CAAAACAAGTGTTTGGTGCTAGG 58.888 43.478 10.05 0.00 46.47 3.02
557 705 4.798387 GTCAAAACAAGTGTTTGGTGCTAG 59.202 41.667 10.05 0.00 46.47 3.42
558 706 4.218635 TGTCAAAACAAGTGTTTGGTGCTA 59.781 37.500 10.05 0.00 46.47 3.49
559 707 3.006323 TGTCAAAACAAGTGTTTGGTGCT 59.994 39.130 10.05 0.00 46.47 4.40
560 708 3.321497 TGTCAAAACAAGTGTTTGGTGC 58.679 40.909 10.05 6.08 46.47 5.01
561 709 4.265085 CGATGTCAAAACAAGTGTTTGGTG 59.735 41.667 10.05 6.28 46.47 4.17
562 710 4.420168 CGATGTCAAAACAAGTGTTTGGT 58.580 39.130 10.05 0.00 46.47 3.67
563 711 3.242712 GCGATGTCAAAACAAGTGTTTGG 59.757 43.478 10.05 7.51 46.47 3.28
564 712 3.061928 CGCGATGTCAAAACAAGTGTTTG 60.062 43.478 10.05 5.40 46.47 2.93
566 714 2.715268 CGCGATGTCAAAACAAGTGTT 58.285 42.857 0.00 0.00 39.30 3.32
567 715 1.596954 GCGCGATGTCAAAACAAGTGT 60.597 47.619 12.10 0.00 39.30 3.55
568 716 1.044725 GCGCGATGTCAAAACAAGTG 58.955 50.000 12.10 0.00 39.30 3.16
569 717 0.660488 TGCGCGATGTCAAAACAAGT 59.340 45.000 12.10 0.00 39.30 3.16
570 718 1.967762 ATGCGCGATGTCAAAACAAG 58.032 45.000 12.10 0.00 39.30 3.16
571 719 2.414058 AATGCGCGATGTCAAAACAA 57.586 40.000 12.10 0.00 39.30 2.83
572 720 2.414058 AAATGCGCGATGTCAAAACA 57.586 40.000 12.10 0.00 40.38 2.83
573 721 2.723658 TGAAAATGCGCGATGTCAAAAC 59.276 40.909 12.10 0.00 0.00 2.43
574 722 2.979151 CTGAAAATGCGCGATGTCAAAA 59.021 40.909 12.10 0.00 0.00 2.44
575 723 2.225255 TCTGAAAATGCGCGATGTCAAA 59.775 40.909 12.10 0.00 0.00 2.69
576 724 1.803555 TCTGAAAATGCGCGATGTCAA 59.196 42.857 12.10 0.00 0.00 3.18
577 725 1.394572 CTCTGAAAATGCGCGATGTCA 59.605 47.619 12.10 4.88 0.00 3.58
578 726 1.853646 GCTCTGAAAATGCGCGATGTC 60.854 52.381 12.10 0.00 0.00 3.06
579 727 0.097674 GCTCTGAAAATGCGCGATGT 59.902 50.000 12.10 0.00 0.00 3.06
580 728 0.097499 TGCTCTGAAAATGCGCGATG 59.903 50.000 12.10 0.00 0.00 3.84
581 729 0.804364 TTGCTCTGAAAATGCGCGAT 59.196 45.000 12.10 0.00 0.00 4.58
582 730 0.110238 GTTGCTCTGAAAATGCGCGA 60.110 50.000 12.10 0.00 0.00 5.87
583 731 0.385849 TGTTGCTCTGAAAATGCGCG 60.386 50.000 0.00 0.00 0.00 6.86
584 732 1.986698 ATGTTGCTCTGAAAATGCGC 58.013 45.000 0.00 0.00 0.00 6.09
585 733 4.682860 AGAAAATGTTGCTCTGAAAATGCG 59.317 37.500 0.00 0.00 0.00 4.73
586 734 7.642071 TTAGAAAATGTTGCTCTGAAAATGC 57.358 32.000 0.00 0.00 0.00 3.56
589 737 9.598517 ACAATTTAGAAAATGTTGCTCTGAAAA 57.401 25.926 0.00 0.00 28.03 2.29
590 738 9.598517 AACAATTTAGAAAATGTTGCTCTGAAA 57.401 25.926 7.47 0.00 39.72 2.69
591 739 9.598517 AAACAATTTAGAAAATGTTGCTCTGAA 57.401 25.926 8.75 0.00 40.16 3.02
592 740 9.248291 GAAACAATTTAGAAAATGTTGCTCTGA 57.752 29.630 8.75 0.00 40.16 3.27
593 741 8.490355 GGAAACAATTTAGAAAATGTTGCTCTG 58.510 33.333 11.83 0.00 40.16 3.35
594 742 8.203485 TGGAAACAATTTAGAAAATGTTGCTCT 58.797 29.630 11.83 0.00 40.16 4.09
595 743 8.364129 TGGAAACAATTTAGAAAATGTTGCTC 57.636 30.769 11.83 6.51 40.16 4.26
616 764 9.527157 TCCAATTTCAAAGTTAGTATGATGGAA 57.473 29.630 0.00 0.00 30.69 3.53
617 765 8.956426 GTCCAATTTCAAAGTTAGTATGATGGA 58.044 33.333 0.00 0.00 30.98 3.41
618 766 8.739039 TGTCCAATTTCAAAGTTAGTATGATGG 58.261 33.333 0.00 0.00 0.00 3.51
625 773 9.883142 TTGAAAATGTCCAATTTCAAAGTTAGT 57.117 25.926 16.78 0.00 46.70 2.24
639 787 5.549742 AAATCCTGCTTTGAAAATGTCCA 57.450 34.783 0.00 0.00 0.00 4.02
698 891 1.369321 GGGCTAGGAAGAGCATCCG 59.631 63.158 0.00 0.00 44.76 4.18
762 955 3.411446 TGGCACTTCTCCATGTACAAAG 58.589 45.455 0.00 0.71 0.00 2.77
763 956 3.500448 TGGCACTTCTCCATGTACAAA 57.500 42.857 0.00 0.00 0.00 2.83
764 957 3.411446 CTTGGCACTTCTCCATGTACAA 58.589 45.455 0.00 0.00 32.92 2.41
765 958 2.290260 CCTTGGCACTTCTCCATGTACA 60.290 50.000 0.00 0.00 32.92 2.90
766 959 2.027192 TCCTTGGCACTTCTCCATGTAC 60.027 50.000 0.00 0.00 32.92 2.90
767 960 2.265367 TCCTTGGCACTTCTCCATGTA 58.735 47.619 0.00 0.00 32.92 2.29
783 976 0.034186 TTGGGCAGCATCGATTCCTT 60.034 50.000 0.00 0.00 0.00 3.36
920 1150 2.356695 TGCTGCATTGTGCTGATATGTC 59.643 45.455 12.14 0.00 45.31 3.06
940 1178 0.664224 TGCTGACTTGTGCATGTGTG 59.336 50.000 0.00 0.00 33.94 3.82
948 1186 2.418976 CTGATGGTGATGCTGACTTGTG 59.581 50.000 0.00 0.00 0.00 3.33
951 1189 1.281287 AGCTGATGGTGATGCTGACTT 59.719 47.619 0.00 0.00 34.19 3.01
954 1192 1.558294 AGAAGCTGATGGTGATGCTGA 59.442 47.619 0.00 0.00 35.79 4.26
957 1195 1.202268 GCAAGAAGCTGATGGTGATGC 60.202 52.381 0.00 0.00 41.15 3.91
976 1214 2.275748 GTCCCCCTTGCCCTTAGC 59.724 66.667 0.00 0.00 44.14 3.09
977 1215 0.914417 TCTGTCCCCCTTGCCCTTAG 60.914 60.000 0.00 0.00 0.00 2.18
979 1217 2.121506 TCTGTCCCCCTTGCCCTT 60.122 61.111 0.00 0.00 0.00 3.95
980 1218 2.612115 CTCTGTCCCCCTTGCCCT 60.612 66.667 0.00 0.00 0.00 5.19
981 1219 3.732849 CCTCTGTCCCCCTTGCCC 61.733 72.222 0.00 0.00 0.00 5.36
982 1220 4.432741 GCCTCTGTCCCCCTTGCC 62.433 72.222 0.00 0.00 0.00 4.52
983 1221 2.988839 ATGCCTCTGTCCCCCTTGC 61.989 63.158 0.00 0.00 0.00 4.01
984 1222 1.077212 CATGCCTCTGTCCCCCTTG 60.077 63.158 0.00 0.00 0.00 3.61
985 1223 2.311854 CCATGCCTCTGTCCCCCTT 61.312 63.158 0.00 0.00 0.00 3.95
992 1231 2.360852 GCAGCACCATGCCTCTGT 60.361 61.111 0.00 0.00 46.52 3.41
1061 1316 3.325870 ACGTTGTTGATGATGATGTCGT 58.674 40.909 0.00 0.00 0.00 4.34
1424 1687 7.381948 TCAAAATCCATCAAAATCAAGTGAACG 59.618 33.333 0.00 0.00 0.00 3.95
1432 1695 9.781633 AAATTCAGTCAAAATCCATCAAAATCA 57.218 25.926 0.00 0.00 0.00 2.57
1470 1733 8.665643 TTTCGTCCTAGATTCAAACAAGTTTA 57.334 30.769 0.00 0.00 0.00 2.01
1571 1834 2.305009 GCTTGCTCTTGGCCTATGAAT 58.695 47.619 3.32 0.00 40.92 2.57
1650 1928 1.612395 CCTTCTTGCGGAGGAGCTCT 61.612 60.000 14.64 0.00 38.13 4.09
1740 2018 4.056125 CGTGCAGCCTCCTCGACA 62.056 66.667 0.00 0.00 0.00 4.35
1791 2069 2.911509 ACGCCAAAGCCATGCACA 60.912 55.556 0.00 0.00 34.57 4.57
1815 2093 6.329460 TGAAGATCCAGAGGATGATGAAGAAT 59.671 38.462 2.74 0.00 43.27 2.40
1948 2226 1.212751 GCAATTGTCGGCCCTTGTC 59.787 57.895 7.40 0.00 0.00 3.18
1954 2232 2.877691 GTGGAGCAATTGTCGGCC 59.122 61.111 7.40 0.00 0.00 6.13
1983 2264 1.745115 GATACCAGCGCCAACTGCA 60.745 57.895 2.29 0.00 41.33 4.41
1995 2285 0.918258 TGCAAGCCCTCATGATACCA 59.082 50.000 0.00 0.00 0.00 3.25
2251 2568 2.072298 GAGCAACTTGAAGAGTGCGAT 58.928 47.619 15.90 4.32 39.00 4.58
2427 2756 1.028330 TGGCCTGGTAGTACTCGTCG 61.028 60.000 3.32 0.00 0.00 5.12
2721 3050 3.068165 AGAATTCATATGTCTCGACGGCA 59.932 43.478 8.44 0.00 0.00 5.69
2751 3080 3.708403 ATGAACCAATCAGAGAGCACA 57.292 42.857 0.00 0.00 42.53 4.57
2781 3110 3.199071 TCTTTCGGGCATAGGTGTACATT 59.801 43.478 0.00 0.00 0.00 2.71
2871 3212 1.080093 GACCTTGATGACGGCGTGA 60.080 57.895 21.19 10.60 0.00 4.35
2905 3246 1.751924 GTCGAGGTAGTGGAGCTTGAT 59.248 52.381 0.00 0.00 45.71 2.57
3691 4062 2.627945 GTTGCACGATGGAACCTGATA 58.372 47.619 9.92 0.00 41.94 2.15
3728 4099 0.034670 GCCTTGATCCTGAGCCTGTT 60.035 55.000 0.00 0.00 0.00 3.16
4019 4393 6.506500 AAAATCACTATGTCTGCTTCAAGG 57.493 37.500 0.00 0.00 0.00 3.61
4025 4399 7.611467 TCACCAATAAAAATCACTATGTCTGCT 59.389 33.333 0.00 0.00 0.00 4.24
4079 4457 8.103305 TCATCATCATCATCATCATCATCTTGT 58.897 33.333 0.00 0.00 0.00 3.16
4080 4458 8.498054 TCATCATCATCATCATCATCATCTTG 57.502 34.615 0.00 0.00 0.00 3.02
4081 4459 9.118300 CATCATCATCATCATCATCATCATCTT 57.882 33.333 0.00 0.00 0.00 2.40
4082 4460 8.489489 TCATCATCATCATCATCATCATCATCT 58.511 33.333 0.00 0.00 0.00 2.90
4083 4461 8.668510 TCATCATCATCATCATCATCATCATC 57.331 34.615 0.00 0.00 0.00 2.92
4087 4465 9.046296 CGTTATCATCATCATCATCATCATCAT 57.954 33.333 0.00 0.00 0.00 2.45
4088 4466 8.255206 TCGTTATCATCATCATCATCATCATCA 58.745 33.333 0.00 0.00 0.00 3.07
4089 4467 8.644318 TCGTTATCATCATCATCATCATCATC 57.356 34.615 0.00 0.00 0.00 2.92
4090 4468 9.046296 CATCGTTATCATCATCATCATCATCAT 57.954 33.333 0.00 0.00 0.00 2.45
4091 4469 7.494625 CCATCGTTATCATCATCATCATCATCA 59.505 37.037 0.00 0.00 0.00 3.07
4092 4470 7.709613 TCCATCGTTATCATCATCATCATCATC 59.290 37.037 0.00 0.00 0.00 2.92
4093 4471 7.562135 TCCATCGTTATCATCATCATCATCAT 58.438 34.615 0.00 0.00 0.00 2.45
4094 4472 6.938507 TCCATCGTTATCATCATCATCATCA 58.061 36.000 0.00 0.00 0.00 3.07
4095 4473 7.041984 CCATCCATCGTTATCATCATCATCATC 60.042 40.741 0.00 0.00 0.00 2.92
4096 4474 6.766467 CCATCCATCGTTATCATCATCATCAT 59.234 38.462 0.00 0.00 0.00 2.45
4097 4475 6.110707 CCATCCATCGTTATCATCATCATCA 58.889 40.000 0.00 0.00 0.00 3.07
4098 4476 5.526479 CCCATCCATCGTTATCATCATCATC 59.474 44.000 0.00 0.00 0.00 2.92
4099 4477 5.434408 CCCATCCATCGTTATCATCATCAT 58.566 41.667 0.00 0.00 0.00 2.45
4100 4478 4.323715 CCCCATCCATCGTTATCATCATCA 60.324 45.833 0.00 0.00 0.00 3.07
4101 4479 4.194640 CCCCATCCATCGTTATCATCATC 58.805 47.826 0.00 0.00 0.00 2.92
4102 4480 3.054139 CCCCCATCCATCGTTATCATCAT 60.054 47.826 0.00 0.00 0.00 2.45
4103 4481 2.305635 CCCCCATCCATCGTTATCATCA 59.694 50.000 0.00 0.00 0.00 3.07
4104 4482 2.571653 TCCCCCATCCATCGTTATCATC 59.428 50.000 0.00 0.00 0.00 2.92
4105 4483 2.573462 CTCCCCCATCCATCGTTATCAT 59.427 50.000 0.00 0.00 0.00 2.45
4106 4484 1.977854 CTCCCCCATCCATCGTTATCA 59.022 52.381 0.00 0.00 0.00 2.15
4107 4485 1.978580 ACTCCCCCATCCATCGTTATC 59.021 52.381 0.00 0.00 0.00 1.75
4108 4486 1.699634 CACTCCCCCATCCATCGTTAT 59.300 52.381 0.00 0.00 0.00 1.89
4109 4487 1.128200 CACTCCCCCATCCATCGTTA 58.872 55.000 0.00 0.00 0.00 3.18
4110 4488 1.915228 CACTCCCCCATCCATCGTT 59.085 57.895 0.00 0.00 0.00 3.85
4111 4489 2.746375 GCACTCCCCCATCCATCGT 61.746 63.158 0.00 0.00 0.00 3.73
4112 4490 2.111878 GCACTCCCCCATCCATCG 59.888 66.667 0.00 0.00 0.00 3.84
4113 4491 0.753111 GTTGCACTCCCCCATCCATC 60.753 60.000 0.00 0.00 0.00 3.51
4114 4492 1.307647 GTTGCACTCCCCCATCCAT 59.692 57.895 0.00 0.00 0.00 3.41
4115 4493 2.763215 GTTGCACTCCCCCATCCA 59.237 61.111 0.00 0.00 0.00 3.41
4116 4494 2.438434 CGTTGCACTCCCCCATCC 60.438 66.667 0.00 0.00 0.00 3.51
4117 4495 2.438434 CCGTTGCACTCCCCCATC 60.438 66.667 0.00 0.00 0.00 3.51
4118 4496 2.933287 TCCGTTGCACTCCCCCAT 60.933 61.111 0.00 0.00 0.00 4.00
4119 4497 3.948719 GTCCGTTGCACTCCCCCA 61.949 66.667 0.00 0.00 0.00 4.96
4120 4498 2.764637 ATTGTCCGTTGCACTCCCCC 62.765 60.000 0.00 0.00 0.00 5.40
4121 4499 1.303317 ATTGTCCGTTGCACTCCCC 60.303 57.895 0.00 0.00 0.00 4.81
4122 4500 1.875963 CATTGTCCGTTGCACTCCC 59.124 57.895 0.00 0.00 0.00 4.30
4123 4501 1.210155 GCATTGTCCGTTGCACTCC 59.790 57.895 0.00 0.00 38.72 3.85
4124 4502 1.948508 TGCATTGTCCGTTGCACTC 59.051 52.632 0.00 0.00 43.54 3.51
4125 4503 4.155950 TGCATTGTCCGTTGCACT 57.844 50.000 0.00 0.00 43.54 4.40
4128 4506 1.621107 CAAGATGCATTGTCCGTTGC 58.379 50.000 0.00 0.00 39.33 4.17
4129 4507 1.811965 TCCAAGATGCATTGTCCGTTG 59.188 47.619 0.00 0.00 0.00 4.10
4130 4508 2.198827 TCCAAGATGCATTGTCCGTT 57.801 45.000 0.00 0.00 0.00 4.44
4131 4509 1.812571 GTTCCAAGATGCATTGTCCGT 59.187 47.619 0.00 0.00 0.00 4.69
4132 4510 1.811965 TGTTCCAAGATGCATTGTCCG 59.188 47.619 0.00 0.00 0.00 4.79
4133 4511 5.278660 GGATATGTTCCAAGATGCATTGTCC 60.279 44.000 0.00 0.00 44.74 4.02
4134 4512 5.766222 GGATATGTTCCAAGATGCATTGTC 58.234 41.667 0.00 0.00 44.74 3.18
4187 4565 2.051692 ACCCAGCCTAGTGTTTGTACA 58.948 47.619 0.00 0.00 0.00 2.90
4214 4628 0.818445 CTGGGTGAGCAGATGGATGC 60.818 60.000 0.00 0.00 46.88 3.91
4215 4629 3.398694 CTGGGTGAGCAGATGGATG 57.601 57.895 0.00 0.00 0.00 3.51
4247 4661 4.991056 TCCTGCTACATCGAGATTAAATGC 59.009 41.667 0.00 0.00 0.00 3.56
4258 4824 0.674534 GGTACCCTCCTGCTACATCG 59.325 60.000 0.00 0.00 0.00 3.84
4273 4839 5.046878 TCCATCCATTACATATGACGGGTAC 60.047 44.000 10.38 0.00 0.00 3.34
4354 4924 9.453572 GATCACCATATTAGCCAAAGATTATCA 57.546 33.333 0.00 0.00 0.00 2.15
4381 4951 1.423056 GCTGACAAGCGCACTGATC 59.577 57.895 11.47 7.53 40.27 2.92
4382 4952 3.571119 GCTGACAAGCGCACTGAT 58.429 55.556 11.47 0.00 40.27 2.90
4391 4961 1.402968 ACTGCAACACAAGCTGACAAG 59.597 47.619 0.00 0.00 35.29 3.16
4392 4962 1.401552 GACTGCAACACAAGCTGACAA 59.598 47.619 0.00 0.00 35.29 3.18
4393 4963 1.016627 GACTGCAACACAAGCTGACA 58.983 50.000 0.00 0.00 35.29 3.58
4394 4964 1.016627 TGACTGCAACACAAGCTGAC 58.983 50.000 0.00 0.00 35.29 3.51
4395 4965 1.605232 CATGACTGCAACACAAGCTGA 59.395 47.619 0.00 0.00 35.29 4.26
4396 4966 2.046283 CATGACTGCAACACAAGCTG 57.954 50.000 0.00 0.00 37.04 4.24
4471 5041 6.094186 GTCTTGTGGAGGTATTCATTTTCTCC 59.906 42.308 0.00 0.00 43.06 3.71
4473 5043 5.946377 GGTCTTGTGGAGGTATTCATTTTCT 59.054 40.000 0.00 0.00 0.00 2.52
4476 5046 4.600062 GGGTCTTGTGGAGGTATTCATTT 58.400 43.478 0.00 0.00 0.00 2.32
4507 5077 2.588877 CGAGCCCGGCAACCTATG 60.589 66.667 13.15 0.00 0.00 2.23
4520 5090 0.721718 CCTTGACGACAATTCCGAGC 59.278 55.000 0.00 0.00 35.37 5.03
4560 5130 4.863131 CGTTGTTGCCCTAAAGTCTAGTAG 59.137 45.833 0.00 0.00 0.00 2.57
4562 5132 3.070590 ACGTTGTTGCCCTAAAGTCTAGT 59.929 43.478 0.00 0.00 0.00 2.57
4581 5151 3.490933 CCTCCATGATGATTGTCGTACGT 60.491 47.826 16.05 0.00 0.00 3.57
4582 5152 3.052745 CCTCCATGATGATTGTCGTACG 58.947 50.000 9.53 9.53 0.00 3.67
4583 5153 2.802816 GCCTCCATGATGATTGTCGTAC 59.197 50.000 0.00 0.00 0.00 3.67
4584 5154 2.433970 TGCCTCCATGATGATTGTCGTA 59.566 45.455 0.00 0.00 0.00 3.43
4641 5211 2.137528 TGTGTCAACGCCTCCCTCA 61.138 57.895 0.00 0.00 0.00 3.86
4651 5221 4.319549 GGCTTTAGCTACTTGTGTGTCAAC 60.320 45.833 0.00 0.00 41.70 3.18
4661 5231 1.278127 TGCGGAAGGCTTTAGCTACTT 59.722 47.619 22.18 0.00 44.05 2.24
4682 5252 2.481854 GAACCAAATGTGTGCATGCAA 58.518 42.857 24.58 7.64 35.15 4.08


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

AutoCloner maintained by Alex Coulton.