Multiple sequence alignment - TraesCS7D01G067900

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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 TraesCS7D01G067900 chr7D 100.000 2623 0 0 1 2623 38549947 38547325 0.000000e+00 4844.0
1 TraesCS7D01G067900 chr7D 83.890 689 98 9 741 1420 38584945 38584261 0.000000e+00 645.0
2 TraesCS7D01G067900 chr7D 83.056 661 86 15 1964 2623 38508650 38508015 6.290000e-161 577.0
3 TraesCS7D01G067900 chr7D 86.653 487 56 7 957 1442 38509531 38509053 4.970000e-147 531.0
4 TraesCS7D01G067900 chr7D 88.636 132 14 1 746 876 38509685 38509554 2.700000e-35 159.0
5 TraesCS7D01G067900 chr5D 97.761 536 12 0 109 644 184875436 184875971 0.000000e+00 924.0
6 TraesCS7D01G067900 chr5D 93.750 112 7 0 1 112 184875297 184875408 4.490000e-38 169.0
7 TraesCS7D01G067900 chr5D 85.714 77 11 0 1641 1717 41816814 41816890 6.020000e-12 82.4
8 TraesCS7D01G067900 chr6D 97.020 537 15 1 109 644 362177891 362177355 0.000000e+00 902.0
9 TraesCS7D01G067900 chr6A 96.828 536 17 0 109 644 83465897 83466432 0.000000e+00 896.0
10 TraesCS7D01G067900 chr6A 95.370 108 5 0 5 112 83465762 83465869 3.470000e-39 172.0
11 TraesCS7D01G067900 chr3A 96.828 536 17 0 109 644 719692070 719691535 0.000000e+00 896.0
12 TraesCS7D01G067900 chr3A 95.327 107 5 0 1 107 720176685 720176791 1.250000e-38 171.0
13 TraesCS7D01G067900 chr3A 94.393 107 6 0 1 107 720147710 720147816 5.810000e-37 165.0
14 TraesCS7D01G067900 chr3A 92.105 114 8 1 1 114 719692209 719692097 2.700000e-35 159.0
15 TraesCS7D01G067900 chr3A 82.353 85 15 0 1631 1715 45243108 45243024 1.010000e-09 75.0
16 TraesCS7D01G067900 chr7B 96.811 533 17 0 109 641 103898132 103898664 0.000000e+00 891.0
17 TraesCS7D01G067900 chr7B 93.750 112 7 0 1 112 103897993 103898104 4.490000e-38 169.0
18 TraesCS7D01G067900 chr7B 89.333 75 6 2 1631 1703 703990842 703990768 2.780000e-15 93.5
19 TraesCS7D01G067900 chr7A 96.082 536 15 4 109 644 29817625 29817096 0.000000e+00 869.0
20 TraesCS7D01G067900 chr7A 96.429 112 4 0 1 112 29817764 29817653 4.460000e-43 185.0
21 TraesCS7D01G067900 chr7A 82.967 182 19 4 1742 1918 38357520 38357346 1.260000e-33 154.0
22 TraesCS7D01G067900 chr7A 85.039 127 19 0 747 873 38365551 38365425 2.120000e-26 130.0
23 TraesCS7D01G067900 chr4B 96.060 533 21 0 109 641 429371050 429371582 0.000000e+00 869.0
24 TraesCS7D01G067900 chr2A 95.167 538 24 2 109 644 752762537 752762000 0.000000e+00 848.0
25 TraesCS7D01G067900 chr5B 95.122 533 26 0 109 641 422053633 422054165 0.000000e+00 841.0
26 TraesCS7D01G067900 chr5B 95.536 112 5 0 1 112 422053494 422053605 2.070000e-41 180.0
27 TraesCS7D01G067900 chr3B 86.692 526 62 7 2098 2623 497701034 497701551 6.290000e-161 577.0
28 TraesCS7D01G067900 chr3D 86.180 521 64 7 2104 2623 42393143 42392630 8.200000e-155 556.0
29 TraesCS7D01G067900 chr3D 85.606 528 65 9 2101 2623 2356698 2356177 6.380000e-151 544.0
30 TraesCS7D01G067900 chr4D 94.393 107 5 1 1 107 426872840 426872945 2.090000e-36 163.0
31 TraesCS7D01G067900 chr4D 87.013 77 10 0 1641 1717 307492617 307492693 1.290000e-13 87.9
32 TraesCS7D01G067900 chr2D 89.610 77 8 0 1641 1717 534121346 534121422 5.970000e-17 99.0
33 TraesCS7D01G067900 chr2D 83.721 86 14 0 1630 1715 633559827 633559912 6.020000e-12 82.4
34 TraesCS7D01G067900 chr2D 82.609 92 15 1 1631 1721 36277534 36277625 2.160000e-11 80.5
35 TraesCS7D01G067900 chr6B 86.047 86 10 2 1630 1714 561686539 561686623 1.000000e-14 91.6
36 TraesCS7D01G067900 chrUn 85.526 76 11 0 1640 1715 31863621 31863546 2.160000e-11 80.5


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 TraesCS7D01G067900 chr7D 38547325 38549947 2622 True 4844.000000 4844 100.0000 1 2623 1 chr7D.!!$R1 2622
1 TraesCS7D01G067900 chr7D 38584261 38584945 684 True 645.000000 645 83.8900 741 1420 1 chr7D.!!$R2 679
2 TraesCS7D01G067900 chr7D 38508015 38509685 1670 True 422.333333 577 86.1150 746 2623 3 chr7D.!!$R3 1877
3 TraesCS7D01G067900 chr5D 184875297 184875971 674 False 546.500000 924 95.7555 1 644 2 chr5D.!!$F2 643
4 TraesCS7D01G067900 chr6D 362177355 362177891 536 True 902.000000 902 97.0200 109 644 1 chr6D.!!$R1 535
5 TraesCS7D01G067900 chr6A 83465762 83466432 670 False 534.000000 896 96.0990 5 644 2 chr6A.!!$F1 639
6 TraesCS7D01G067900 chr3A 719691535 719692209 674 True 527.500000 896 94.4665 1 644 2 chr3A.!!$R2 643
7 TraesCS7D01G067900 chr7B 103897993 103898664 671 False 530.000000 891 95.2805 1 641 2 chr7B.!!$F1 640
8 TraesCS7D01G067900 chr7A 29817096 29817764 668 True 527.000000 869 96.2555 1 644 2 chr7A.!!$R3 643
9 TraesCS7D01G067900 chr4B 429371050 429371582 532 False 869.000000 869 96.0600 109 641 1 chr4B.!!$F1 532
10 TraesCS7D01G067900 chr2A 752762000 752762537 537 True 848.000000 848 95.1670 109 644 1 chr2A.!!$R1 535
11 TraesCS7D01G067900 chr5B 422053494 422054165 671 False 510.500000 841 95.3290 1 641 2 chr5B.!!$F1 640
12 TraesCS7D01G067900 chr3B 497701034 497701551 517 False 577.000000 577 86.6920 2098 2623 1 chr3B.!!$F1 525
13 TraesCS7D01G067900 chr3D 42392630 42393143 513 True 556.000000 556 86.1800 2104 2623 1 chr3D.!!$R2 519
14 TraesCS7D01G067900 chr3D 2356177 2356698 521 True 544.000000 544 85.6060 2101 2623 1 chr3D.!!$R1 522

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
697 732 0.034896 TTCTTGGGACGAGCTTGACC 59.965 55.0 13.54 13.54 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1961 2039 0.037232 CGAGGAAACCACAGACCTCC 60.037 60.0 0.0 0.0 43.98 4.3 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
21 22 2.284699 CCTCTTCACCCCCGTCCT 60.285 66.667 0.00 0.00 0.00 3.85
223 256 3.655211 CCTGGTGCTCCCCTGCTT 61.655 66.667 1.59 0.00 0.00 3.91
526 560 1.494721 TCACACCTTTCTCTGGCCTTT 59.505 47.619 3.32 0.00 0.00 3.11
551 585 2.100418 TGATCATCGAGGCTTCTCTGTG 59.900 50.000 0.00 0.00 35.43 3.66
644 679 3.996363 CTGCTCTAGTGTGTGTTGCATTA 59.004 43.478 0.00 0.00 0.00 1.90
645 680 4.384940 TGCTCTAGTGTGTGTTGCATTAA 58.615 39.130 0.00 0.00 0.00 1.40
646 681 4.819088 TGCTCTAGTGTGTGTTGCATTAAA 59.181 37.500 0.00 0.00 0.00 1.52
647 682 5.473162 TGCTCTAGTGTGTGTTGCATTAAAT 59.527 36.000 0.00 0.00 0.00 1.40
648 683 6.652900 TGCTCTAGTGTGTGTTGCATTAAATA 59.347 34.615 0.00 0.00 0.00 1.40
649 684 7.148423 TGCTCTAGTGTGTGTTGCATTAAATAG 60.148 37.037 0.00 0.00 0.00 1.73
650 685 7.148407 GCTCTAGTGTGTGTTGCATTAAATAGT 60.148 37.037 0.00 0.00 0.00 2.12
651 686 8.028540 TCTAGTGTGTGTTGCATTAAATAGTG 57.971 34.615 0.00 0.00 0.00 2.74
652 687 6.012658 AGTGTGTGTTGCATTAAATAGTGG 57.987 37.500 0.00 0.00 0.00 4.00
653 688 4.621034 GTGTGTGTTGCATTAAATAGTGGC 59.379 41.667 0.00 0.00 0.00 5.01
654 689 4.173256 GTGTGTTGCATTAAATAGTGGCC 58.827 43.478 0.00 0.00 0.00 5.36
655 690 3.829026 TGTGTTGCATTAAATAGTGGCCA 59.171 39.130 0.00 0.00 0.00 5.36
656 691 4.173256 GTGTTGCATTAAATAGTGGCCAC 58.827 43.478 29.22 29.22 0.00 5.01
657 692 3.829026 TGTTGCATTAAATAGTGGCCACA 59.171 39.130 36.39 22.64 0.00 4.17
658 693 4.082300 TGTTGCATTAAATAGTGGCCACAG 60.082 41.667 36.39 15.96 0.00 3.66
659 694 3.696045 TGCATTAAATAGTGGCCACAGT 58.304 40.909 36.39 21.84 0.00 3.55
660 695 3.694072 TGCATTAAATAGTGGCCACAGTC 59.306 43.478 36.39 11.15 0.00 3.51
661 696 3.066760 GCATTAAATAGTGGCCACAGTCC 59.933 47.826 36.39 10.72 0.00 3.85
662 697 4.269183 CATTAAATAGTGGCCACAGTCCA 58.731 43.478 36.39 16.31 0.00 4.02
663 698 4.584638 TTAAATAGTGGCCACAGTCCAT 57.415 40.909 36.39 18.01 35.81 3.41
664 699 2.717639 AATAGTGGCCACAGTCCATC 57.282 50.000 36.39 8.24 35.81 3.51
665 700 1.885049 ATAGTGGCCACAGTCCATCT 58.115 50.000 36.39 16.49 35.81 2.90
674 709 3.602104 CAGTCCATCTGGCCCATTT 57.398 52.632 0.00 0.00 40.23 2.32
675 710 1.396653 CAGTCCATCTGGCCCATTTC 58.603 55.000 0.00 0.00 40.23 2.17
676 711 1.064166 CAGTCCATCTGGCCCATTTCT 60.064 52.381 0.00 0.00 40.23 2.52
677 712 1.642762 AGTCCATCTGGCCCATTTCTT 59.357 47.619 0.00 0.00 34.44 2.52
678 713 2.043526 AGTCCATCTGGCCCATTTCTTT 59.956 45.455 0.00 0.00 34.44 2.52
679 714 2.833943 GTCCATCTGGCCCATTTCTTTT 59.166 45.455 0.00 0.00 34.44 2.27
680 715 3.099141 TCCATCTGGCCCATTTCTTTTC 58.901 45.455 0.00 0.00 34.44 2.29
681 716 3.102204 CCATCTGGCCCATTTCTTTTCT 58.898 45.455 0.00 0.00 0.00 2.52
682 717 3.516700 CCATCTGGCCCATTTCTTTTCTT 59.483 43.478 0.00 0.00 0.00 2.52
683 718 4.501071 CATCTGGCCCATTTCTTTTCTTG 58.499 43.478 0.00 0.00 0.00 3.02
684 719 2.899256 TCTGGCCCATTTCTTTTCTTGG 59.101 45.455 0.00 0.00 0.00 3.61
690 725 4.425577 CCATTTCTTTTCTTGGGACGAG 57.574 45.455 0.00 0.00 0.00 4.18
691 726 3.366374 CCATTTCTTTTCTTGGGACGAGC 60.366 47.826 0.00 0.00 0.00 5.03
692 727 2.930826 TTCTTTTCTTGGGACGAGCT 57.069 45.000 0.00 0.00 0.00 4.09
693 728 2.930826 TCTTTTCTTGGGACGAGCTT 57.069 45.000 0.00 0.00 0.00 3.74
694 729 2.494059 TCTTTTCTTGGGACGAGCTTG 58.506 47.619 0.00 0.00 0.00 4.01
695 730 2.104111 TCTTTTCTTGGGACGAGCTTGA 59.896 45.455 8.31 0.00 0.00 3.02
696 731 1.878953 TTTCTTGGGACGAGCTTGAC 58.121 50.000 8.31 0.42 0.00 3.18
697 732 0.034896 TTCTTGGGACGAGCTTGACC 59.965 55.000 13.54 13.54 0.00 4.02
698 733 1.738099 CTTGGGACGAGCTTGACCG 60.738 63.158 15.16 3.72 0.00 4.79
699 734 2.154798 CTTGGGACGAGCTTGACCGA 62.155 60.000 15.16 9.51 0.00 4.69
700 735 2.126031 GGGACGAGCTTGACCGAC 60.126 66.667 15.16 1.77 0.00 4.79
701 736 2.126031 GGACGAGCTTGACCGACC 60.126 66.667 8.31 2.90 34.09 4.79
702 737 2.126031 GACGAGCTTGACCGACCC 60.126 66.667 8.31 0.00 0.00 4.46
703 738 3.966026 GACGAGCTTGACCGACCCG 62.966 68.421 8.31 0.00 0.00 5.28
718 753 4.880537 CCGGCGGCAGCTAGTGAG 62.881 72.222 15.42 0.00 44.37 3.51
727 762 2.838225 GCTAGTGAGCCCCGCCTA 60.838 66.667 0.00 0.00 43.49 3.93
728 763 2.862223 GCTAGTGAGCCCCGCCTAG 61.862 68.421 0.00 0.00 43.49 3.02
729 764 1.455959 CTAGTGAGCCCCGCCTAGT 60.456 63.158 0.00 0.00 0.00 2.57
730 765 1.001248 TAGTGAGCCCCGCCTAGTT 59.999 57.895 0.00 0.00 0.00 2.24
731 766 1.041447 TAGTGAGCCCCGCCTAGTTC 61.041 60.000 0.00 0.00 0.00 3.01
732 767 3.458163 TGAGCCCCGCCTAGTTCG 61.458 66.667 0.00 0.00 0.00 3.95
733 768 3.459063 GAGCCCCGCCTAGTTCGT 61.459 66.667 0.00 0.00 0.00 3.85
734 769 3.001406 AGCCCCGCCTAGTTCGTT 61.001 61.111 0.00 0.00 0.00 3.85
735 770 2.510918 GCCCCGCCTAGTTCGTTC 60.511 66.667 0.00 0.00 0.00 3.95
736 771 2.975536 CCCCGCCTAGTTCGTTCA 59.024 61.111 0.00 0.00 0.00 3.18
737 772 1.294138 CCCCGCCTAGTTCGTTCAA 59.706 57.895 0.00 0.00 0.00 2.69
738 773 0.107848 CCCCGCCTAGTTCGTTCAAT 60.108 55.000 0.00 0.00 0.00 2.57
739 774 1.677820 CCCCGCCTAGTTCGTTCAATT 60.678 52.381 0.00 0.00 0.00 2.32
743 778 2.348666 CGCCTAGTTCGTTCAATTCAGG 59.651 50.000 0.00 0.00 0.00 3.86
748 783 1.582610 TTCGTTCAATTCAGGGCGGC 61.583 55.000 0.00 0.00 0.00 6.53
749 784 2.885113 GTTCAATTCAGGGCGGCC 59.115 61.111 22.67 22.67 0.00 6.13
766 801 2.738521 CCTTGCAGGACGGTGTCG 60.739 66.667 0.00 0.00 37.67 4.35
767 802 2.738521 CTTGCAGGACGGTGTCGG 60.739 66.667 0.00 0.00 41.39 4.79
807 842 1.067071 CCTCTCCCACTCCGTAAACAC 60.067 57.143 0.00 0.00 0.00 3.32
820 855 2.418197 CGTAAACACTGGATCCCGTCAT 60.418 50.000 9.90 0.00 0.00 3.06
876 911 1.606889 GTCAGAGTCGGTGTCCCCT 60.607 63.158 0.00 0.00 0.00 4.79
877 912 1.606601 TCAGAGTCGGTGTCCCCTG 60.607 63.158 0.00 0.00 0.00 4.45
878 913 1.908793 CAGAGTCGGTGTCCCCTGT 60.909 63.158 0.00 0.00 0.00 4.00
880 915 2.603776 AGTCGGTGTCCCCTGTCC 60.604 66.667 0.00 0.00 0.00 4.02
881 916 4.065281 GTCGGTGTCCCCTGTCCG 62.065 72.222 0.00 0.00 43.65 4.79
900 935 2.106683 CGGCGTCCATGGACTTTCC 61.107 63.158 35.84 30.09 42.54 3.13
909 944 1.299648 TGGACTTTCCATCCTGCCG 59.700 57.895 0.00 0.00 42.67 5.69
928 963 1.300620 CGTCACCGCTCCTTCAACA 60.301 57.895 0.00 0.00 0.00 3.33
934 970 2.325082 CGCTCCTTCAACAACCCGG 61.325 63.158 0.00 0.00 0.00 5.73
986 1027 6.317893 ACGTGTATATATATCATCAGTCGGCA 59.682 38.462 0.00 0.00 0.00 5.69
1019 1060 2.622942 GCACATCCAAACCAGAGTTCAA 59.377 45.455 0.00 0.00 34.19 2.69
1026 1067 4.398044 TCCAAACCAGAGTTCAAAGACAAC 59.602 41.667 0.00 0.00 34.19 3.32
1034 1075 4.058817 GAGTTCAAAGACAACGTCAGGAT 58.941 43.478 0.00 0.00 34.60 3.24
1075 1116 4.629092 GGAAAGAAGAGTCGTTTGGTACT 58.371 43.478 0.00 0.00 0.00 2.73
1077 1118 3.555917 AGAAGAGTCGTTTGGTACTCG 57.444 47.619 0.00 0.00 45.47 4.18
1078 1119 3.144506 AGAAGAGTCGTTTGGTACTCGA 58.855 45.455 0.00 0.00 45.47 4.04
1105 1146 3.139077 ACCAAGTTTGCTAGGAAACTCG 58.861 45.455 33.84 28.21 43.83 4.18
1177 1218 0.107654 TCTCGATCCTCAGCTCGTCA 60.108 55.000 0.00 0.00 36.33 4.35
1249 1293 2.436824 GGAGGAAAGCAGGCGACC 60.437 66.667 0.00 0.00 0.00 4.79
1273 1317 0.767375 AGAAGCAGCAGGAGGACAAA 59.233 50.000 0.00 0.00 0.00 2.83
1305 1349 2.604686 ACGGGCAGAGAGGAAGCA 60.605 61.111 0.00 0.00 0.00 3.91
1363 1407 2.525055 GAGCTCAACTGCTTCGAGTAG 58.475 52.381 9.40 0.00 44.17 2.57
1388 1432 0.616111 ATCCTCTTGAGTGGGTCGCT 60.616 55.000 0.00 0.00 0.00 4.93
1399 1443 4.803426 GGTCGCTGGCTGTCTCCG 62.803 72.222 0.00 0.00 0.00 4.63
1400 1444 3.749064 GTCGCTGGCTGTCTCCGA 61.749 66.667 0.00 0.00 0.00 4.55
1402 1446 3.753434 CGCTGGCTGTCTCCGAGT 61.753 66.667 0.00 0.00 0.00 4.18
1424 1468 7.851472 CGAGTAGTTTTTCTCCTTTTTCACTTC 59.149 37.037 0.00 0.00 0.00 3.01
1426 1470 6.222038 AGTTTTTCTCCTTTTTCACTTCCC 57.778 37.500 0.00 0.00 0.00 3.97
1429 1473 4.469469 TTCTCCTTTTTCACTTCCCCAT 57.531 40.909 0.00 0.00 0.00 4.00
1435 1479 4.335416 CTTTTTCACTTCCCCATCTGCTA 58.665 43.478 0.00 0.00 0.00 3.49
1436 1480 3.350219 TTTCACTTCCCCATCTGCTAC 57.650 47.619 0.00 0.00 0.00 3.58
1437 1481 2.254152 TCACTTCCCCATCTGCTACT 57.746 50.000 0.00 0.00 0.00 2.57
1441 1485 4.082125 CACTTCCCCATCTGCTACTTTTT 58.918 43.478 0.00 0.00 0.00 1.94
1464 1539 8.576936 TTTTTACGTTTGGTTGATTATTGACC 57.423 30.769 0.00 0.00 0.00 4.02
1474 1549 7.685481 TGGTTGATTATTGACCAAGAGACTTA 58.315 34.615 0.00 0.00 40.31 2.24
1475 1550 7.606456 TGGTTGATTATTGACCAAGAGACTTAC 59.394 37.037 0.00 0.00 40.31 2.34
1481 1556 4.537135 TGACCAAGAGACTTACCATGTC 57.463 45.455 0.00 0.00 34.88 3.06
1502 1577 2.606725 CCACAGCGAGAGAATGAATGAC 59.393 50.000 0.00 0.00 0.00 3.06
1505 1580 3.122297 CAGCGAGAGAATGAATGACCTC 58.878 50.000 0.00 0.00 0.00 3.85
1507 1582 2.863137 GCGAGAGAATGAATGACCTCAC 59.137 50.000 0.00 0.00 0.00 3.51
1509 1584 4.498241 CGAGAGAATGAATGACCTCACAA 58.502 43.478 0.00 0.00 0.00 3.33
1511 1586 5.233902 CGAGAGAATGAATGACCTCACAATC 59.766 44.000 0.00 0.00 0.00 2.67
1514 1589 5.563592 AGAATGAATGACCTCACAATCACA 58.436 37.500 0.00 0.00 0.00 3.58
1517 1592 4.067192 TGAATGACCTCACAATCACACAG 58.933 43.478 0.00 0.00 0.00 3.66
1519 1594 3.558931 TGACCTCACAATCACACAGTT 57.441 42.857 0.00 0.00 0.00 3.16
1525 1600 4.096231 CCTCACAATCACACAGTTGTTTGA 59.904 41.667 3.83 3.83 38.84 2.69
1534 1609 6.781138 TCACACAGTTGTTTGATTTACTGAC 58.219 36.000 7.97 0.00 40.24 3.51
1537 1612 4.219033 CAGTTGTTTGATTTACTGACGCC 58.781 43.478 0.00 0.00 40.24 5.68
1539 1614 4.578928 AGTTGTTTGATTTACTGACGCCTT 59.421 37.500 0.00 0.00 0.00 4.35
1540 1615 4.481930 TGTTTGATTTACTGACGCCTTG 57.518 40.909 0.00 0.00 0.00 3.61
1541 1616 3.880490 TGTTTGATTTACTGACGCCTTGT 59.120 39.130 0.00 0.00 0.00 3.16
1543 1618 5.703592 TGTTTGATTTACTGACGCCTTGTAT 59.296 36.000 0.00 0.00 0.00 2.29
1547 1622 6.811954 TGATTTACTGACGCCTTGTATATGA 58.188 36.000 0.00 0.00 0.00 2.15
1550 1625 3.995199 ACTGACGCCTTGTATATGATGG 58.005 45.455 0.00 0.00 0.00 3.51
1562 1637 7.065324 CCTTGTATATGATGGTGTTTACGTTGT 59.935 37.037 0.00 0.00 0.00 3.32
1565 1640 7.766738 TGTATATGATGGTGTTTACGTTGTGAT 59.233 33.333 0.00 0.00 0.00 3.06
1572 1647 4.901881 GGTGTTTACGTTGTGATTCGAAAG 59.098 41.667 0.00 0.00 0.00 2.62
1573 1648 4.901881 GTGTTTACGTTGTGATTCGAAAGG 59.098 41.667 0.00 0.00 0.00 3.11
1576 1651 6.645827 TGTTTACGTTGTGATTCGAAAGGATA 59.354 34.615 0.00 0.00 0.00 2.59
1578 1653 5.526010 ACGTTGTGATTCGAAAGGATAAC 57.474 39.130 0.00 3.25 30.27 1.89
1580 1655 5.699458 ACGTTGTGATTCGAAAGGATAACTT 59.301 36.000 0.00 0.00 42.52 2.66
1595 1670 7.555965 AAGGATAACTTTTCACCAATAATGGC 58.444 34.615 0.00 0.00 43.39 4.40
1596 1671 7.180051 AAGGATAACTTTTCACCAATAATGGCA 59.820 33.333 0.00 0.00 43.39 4.92
1605 1680 2.310538 CCAATAATGGCAGGTTCCTCC 58.689 52.381 0.00 0.00 40.58 4.30
1611 1686 2.840753 GGCAGGTTCCTCCCACCAA 61.841 63.158 0.00 0.00 36.67 3.67
1613 1688 1.303643 CAGGTTCCTCCCACCAAGC 60.304 63.158 0.00 0.00 36.67 4.01
1618 1693 3.589542 CCTCCCACCAAGCCCCAA 61.590 66.667 0.00 0.00 0.00 4.12
1681 1756 9.384764 AGCTTTTAGATCACTACTTTAATGACC 57.615 33.333 0.00 0.00 0.00 4.02
1682 1757 9.384764 GCTTTTAGATCACTACTTTAATGACCT 57.615 33.333 0.00 0.00 0.00 3.85
1706 1781 9.869757 CCTAAATACTTTTACATTTCTTTGGGG 57.130 33.333 0.00 0.00 0.00 4.96
1709 1784 7.718334 ATACTTTTACATTTCTTTGGGGAGG 57.282 36.000 0.00 0.00 0.00 4.30
1710 1785 4.838423 ACTTTTACATTTCTTTGGGGAGGG 59.162 41.667 0.00 0.00 0.00 4.30
1711 1786 4.750833 TTTACATTTCTTTGGGGAGGGA 57.249 40.909 0.00 0.00 0.00 4.20
1712 1787 2.907458 ACATTTCTTTGGGGAGGGAG 57.093 50.000 0.00 0.00 0.00 4.30
1719 1794 2.642807 TCTTTGGGGAGGGAGTACTTTG 59.357 50.000 0.00 0.00 0.00 2.77
1760 1836 8.902806 CAGTATATGCAAAGAAAAGGGATAACA 58.097 33.333 0.00 0.00 0.00 2.41
1761 1837 9.125026 AGTATATGCAAAGAAAAGGGATAACAG 57.875 33.333 0.00 0.00 0.00 3.16
1770 1846 6.543735 AGAAAAGGGATAACAGCACTAGTTT 58.456 36.000 0.00 0.00 0.00 2.66
1784 1861 3.307242 CACTAGTTTATTGGCTCGAGTGC 59.693 47.826 15.13 0.33 30.11 4.40
1797 1874 1.668751 TCGAGTGCCAAACAAAGTGTC 59.331 47.619 0.00 0.00 0.00 3.67
1799 1876 2.033299 CGAGTGCCAAACAAAGTGTCAT 59.967 45.455 0.00 0.00 0.00 3.06
1800 1877 3.374745 GAGTGCCAAACAAAGTGTCATG 58.625 45.455 0.00 0.00 0.00 3.07
1801 1878 2.101249 AGTGCCAAACAAAGTGTCATGG 59.899 45.455 8.19 8.19 39.12 3.66
1802 1879 2.100584 GTGCCAAACAAAGTGTCATGGA 59.899 45.455 14.17 1.62 38.69 3.41
1803 1880 2.964464 TGCCAAACAAAGTGTCATGGAT 59.036 40.909 14.17 0.00 38.69 3.41
1804 1881 4.022416 GTGCCAAACAAAGTGTCATGGATA 60.022 41.667 14.17 3.38 38.69 2.59
1814 1891 1.552792 TGTCATGGATAGACACGCCAA 59.447 47.619 0.00 0.00 40.80 4.52
1837 1914 3.725819 TTGTCGACCAACGCCAAG 58.274 55.556 14.12 0.00 35.00 3.61
1857 1935 0.178990 GTTGTTGCCCTGGAGAGGTT 60.179 55.000 0.00 0.00 37.73 3.50
1861 1939 1.282157 GTTGCCCTGGAGAGGTTGTAT 59.718 52.381 0.00 0.00 37.73 2.29
1868 1946 3.068873 CCTGGAGAGGTTGTATACAGAGC 59.931 52.174 5.56 7.28 34.16 4.09
1901 1979 2.162408 GCAACACCAATAGGAGCTCAAC 59.838 50.000 17.19 0.00 38.69 3.18
1903 1981 1.985159 ACACCAATAGGAGCTCAACCA 59.015 47.619 17.19 0.00 38.69 3.67
1910 1988 3.426568 GAGCTCAACCACAGGCGC 61.427 66.667 9.40 0.00 0.00 6.53
1923 2001 3.273048 GGCGCTATGGCAAACACA 58.727 55.556 7.64 0.00 44.08 3.72
1924 2002 1.809207 GGCGCTATGGCAAACACAT 59.191 52.632 7.64 0.00 44.08 3.21
1925 2003 0.173255 GGCGCTATGGCAAACACATT 59.827 50.000 7.64 0.00 44.08 2.71
1926 2004 1.548986 GCGCTATGGCAAACACATTC 58.451 50.000 0.00 0.00 38.60 2.67
1927 2005 1.133025 GCGCTATGGCAAACACATTCT 59.867 47.619 0.00 0.00 38.60 2.40
1928 2006 2.354510 GCGCTATGGCAAACACATTCTA 59.645 45.455 0.00 0.00 38.60 2.10
1929 2007 3.788797 GCGCTATGGCAAACACATTCTAC 60.789 47.826 0.00 0.00 38.60 2.59
1930 2008 3.623060 CGCTATGGCAAACACATTCTACT 59.377 43.478 0.74 0.00 38.60 2.57
1931 2009 4.260375 CGCTATGGCAAACACATTCTACTC 60.260 45.833 0.74 0.00 38.60 2.59
1932 2010 4.260375 GCTATGGCAAACACATTCTACTCG 60.260 45.833 0.00 0.00 38.54 4.18
1933 2011 3.394674 TGGCAAACACATTCTACTCGA 57.605 42.857 0.00 0.00 0.00 4.04
1934 2012 3.937814 TGGCAAACACATTCTACTCGAT 58.062 40.909 0.00 0.00 0.00 3.59
1935 2013 4.323417 TGGCAAACACATTCTACTCGATT 58.677 39.130 0.00 0.00 0.00 3.34
1936 2014 4.154015 TGGCAAACACATTCTACTCGATTG 59.846 41.667 0.00 0.00 0.00 2.67
1937 2015 4.391830 GGCAAACACATTCTACTCGATTGA 59.608 41.667 0.00 0.00 0.00 2.57
1938 2016 5.316770 GCAAACACATTCTACTCGATTGAC 58.683 41.667 0.00 0.00 0.00 3.18
1939 2017 5.120830 GCAAACACATTCTACTCGATTGACT 59.879 40.000 0.00 0.00 0.00 3.41
1940 2018 6.528826 CAAACACATTCTACTCGATTGACTG 58.471 40.000 0.00 0.00 0.00 3.51
1941 2019 4.177026 ACACATTCTACTCGATTGACTGC 58.823 43.478 0.00 0.00 0.00 4.40
1942 2020 3.241553 CACATTCTACTCGATTGACTGCG 59.758 47.826 0.00 0.00 0.00 5.18
1943 2021 3.128764 ACATTCTACTCGATTGACTGCGA 59.871 43.478 0.00 0.00 35.01 5.10
1944 2022 2.826979 TCTACTCGATTGACTGCGAC 57.173 50.000 0.00 0.00 32.51 5.19
1945 2023 2.081462 TCTACTCGATTGACTGCGACA 58.919 47.619 0.00 0.00 32.51 4.35
1946 2024 2.096013 TCTACTCGATTGACTGCGACAG 59.904 50.000 5.47 5.47 37.52 3.51
1947 2025 0.734253 ACTCGATTGACTGCGACAGC 60.734 55.000 6.74 1.91 45.41 4.40
1959 2037 4.640113 GACAGCATGCGCGCGATC 62.640 66.667 37.18 18.14 45.49 3.69
1961 2039 4.645024 CAGCATGCGCGCGATCAG 62.645 66.667 37.18 20.23 45.49 2.90
1979 2057 1.002544 CAGGAGGTCTGTGGTTTCCTC 59.997 57.143 0.00 0.00 43.84 3.71
1990 2068 1.281899 GGTTTCCTCGAGAGATTGCG 58.718 55.000 15.71 0.00 40.84 4.85
2018 2096 3.055240 GGATAGAGGCCATCTTCTCCATG 60.055 52.174 5.01 0.00 39.64 3.66
2026 2104 3.452474 CCATCTTCTCCATGTCGAAGTC 58.548 50.000 16.29 0.00 38.20 3.01
2030 2108 3.574396 TCTTCTCCATGTCGAAGTCTGTT 59.426 43.478 16.29 0.00 38.20 3.16
2033 2111 1.967779 TCCATGTCGAAGTCTGTTGGA 59.032 47.619 0.00 0.00 0.00 3.53
2050 2128 1.098050 GGAATGCTCAACGCCTCAAT 58.902 50.000 0.00 0.00 38.05 2.57
2062 2140 2.297895 CCTCAATGGTGTCCCCGGA 61.298 63.158 0.73 0.00 35.15 5.14
2063 2141 1.078426 CTCAATGGTGTCCCCGGAC 60.078 63.158 0.73 6.95 44.77 4.79
2072 2150 2.682136 TCCCCGGACGCTGAATCA 60.682 61.111 0.73 0.00 0.00 2.57
2078 2156 0.716108 CGGACGCTGAATCAACTGTC 59.284 55.000 1.91 1.91 0.00 3.51
2080 2158 0.716108 GACGCTGAATCAACTGTCGG 59.284 55.000 0.00 0.00 0.00 4.79
2087 2165 1.550976 GAATCAACTGTCGGAGAGGGT 59.449 52.381 7.12 0.00 36.95 4.34
2142 2220 3.772853 TTGTGTGCTCCGGCTGCTT 62.773 57.895 17.67 0.00 39.59 3.91
2146 2224 2.683572 TGCTCCGGCTGCTTCCTA 60.684 61.111 17.67 0.00 39.59 2.94
2148 2226 1.147153 GCTCCGGCTGCTTCCTATT 59.853 57.895 11.24 0.00 35.22 1.73
2156 2234 3.555966 GGCTGCTTCCTATTAACCACAT 58.444 45.455 0.00 0.00 0.00 3.21
2159 2237 4.137543 CTGCTTCCTATTAACCACATCCC 58.862 47.826 0.00 0.00 0.00 3.85
2178 2256 9.672673 CACATCCCTTAGATACATAATTTAGGG 57.327 37.037 0.00 0.00 32.37 3.53
2215 2293 2.389713 CGCTCCGCCATTAGAAATTG 57.610 50.000 0.00 0.00 0.00 2.32
2278 2363 2.771943 CCAATCACCTACCTCTAAGCCA 59.228 50.000 0.00 0.00 0.00 4.75
2281 2367 1.007238 TCACCTACCTCTAAGCCAGCT 59.993 52.381 0.00 0.00 0.00 4.24
2312 2398 2.438868 ATTGGAAAAGAAGCAACGCC 57.561 45.000 0.00 0.00 0.00 5.68
2319 2405 2.663826 AAGAAGCAACGCCAACAAAA 57.336 40.000 0.00 0.00 0.00 2.44
2368 2454 4.690719 TGATGCCGGGCGAACGTT 62.691 61.111 15.40 0.00 0.00 3.99
2449 2535 1.277580 CCCTGCCATTCTCCACCTCT 61.278 60.000 0.00 0.00 0.00 3.69
2451 2537 1.202330 CTGCCATTCTCCACCTCTCT 58.798 55.000 0.00 0.00 0.00 3.10
2460 2547 1.156322 TCCACCTCTCTCCCTTCCCT 61.156 60.000 0.00 0.00 0.00 4.20
2462 2549 1.221781 CCACCTCTCTCCCTTCCCTAT 59.778 57.143 0.00 0.00 0.00 2.57
2465 2552 1.505538 CCTCTCTCCCTTCCCTATCCA 59.494 57.143 0.00 0.00 0.00 3.41
2469 2556 3.209843 TCTCTCCCTTCCCTATCCAATCA 59.790 47.826 0.00 0.00 0.00 2.57
2473 2560 1.776667 CCTTCCCTATCCAATCAGGCA 59.223 52.381 0.00 0.00 37.29 4.75
2490 2577 1.897423 CACCTACCTGTGCGATCCA 59.103 57.895 0.00 0.00 0.00 3.41
2522 2609 4.159879 GGAGAATAGAACTCCGGTCTTCAA 59.840 45.833 0.00 0.00 43.25 2.69
2553 2640 7.189693 TGTTAGATGTTAGAAGCTTGTGTTG 57.810 36.000 2.10 0.00 0.00 3.33
2558 2645 8.220755 AGATGTTAGAAGCTTGTGTTGTTTTA 57.779 30.769 2.10 0.00 0.00 1.52
2592 2679 9.082313 GATTGTAATCCATCATTCCCTTTATGT 57.918 33.333 0.00 0.00 0.00 2.29
2599 2686 8.010733 TCCATCATTCCCTTTATGTTGATTTC 57.989 34.615 0.00 0.00 0.00 2.17
2600 2687 7.069826 TCCATCATTCCCTTTATGTTGATTTCC 59.930 37.037 0.00 0.00 0.00 3.13
2607 2694 8.045720 TCCCTTTATGTTGATTTCCTAGCTAT 57.954 34.615 0.00 0.00 0.00 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.068915 GGTTTTCACCCGGGGTCTA 58.931 57.895 27.92 4.46 37.03 2.59
78 79 0.670546 CTCCAACAAGGACGCGACAT 60.671 55.000 15.93 0.00 43.07 3.06
79 80 1.300620 CTCCAACAAGGACGCGACA 60.301 57.895 15.93 0.00 43.07 4.35
526 560 0.105593 GAAGCCTCGATGATCAGCCA 59.894 55.000 5.18 0.00 0.00 4.75
551 585 1.555967 AGTCAACAGAGAGAGGAGCC 58.444 55.000 0.00 0.00 0.00 4.70
644 679 2.578021 AGATGGACTGTGGCCACTATTT 59.422 45.455 34.75 17.07 38.44 1.40
645 680 2.092753 CAGATGGACTGTGGCCACTATT 60.093 50.000 34.75 19.61 41.30 1.73
646 681 1.487976 CAGATGGACTGTGGCCACTAT 59.512 52.381 34.75 23.29 41.30 2.12
647 682 0.904649 CAGATGGACTGTGGCCACTA 59.095 55.000 34.75 20.52 41.30 2.74
648 683 1.681666 CAGATGGACTGTGGCCACT 59.318 57.895 34.75 17.79 41.30 4.00
649 684 1.377725 CCAGATGGACTGTGGCCAC 60.378 63.158 29.67 29.67 44.40 5.01
650 685 3.080641 CCAGATGGACTGTGGCCA 58.919 61.111 0.00 0.00 44.40 5.36
653 688 1.929860 ATGGGCCAGATGGACTGTGG 61.930 60.000 13.78 0.00 44.77 4.17
654 689 0.033796 AATGGGCCAGATGGACTGTG 60.034 55.000 13.78 0.00 44.77 3.66
655 690 0.706433 AAATGGGCCAGATGGACTGT 59.294 50.000 13.78 0.00 44.77 3.55
656 691 1.064166 AGAAATGGGCCAGATGGACTG 60.064 52.381 13.78 0.00 44.77 3.51
657 692 1.302907 AGAAATGGGCCAGATGGACT 58.697 50.000 13.78 2.54 44.77 3.85
658 693 2.149973 AAGAAATGGGCCAGATGGAC 57.850 50.000 13.78 0.00 44.61 4.02
659 694 2.925966 AAAGAAATGGGCCAGATGGA 57.074 45.000 13.78 0.00 37.39 3.41
660 695 3.102204 AGAAAAGAAATGGGCCAGATGG 58.898 45.455 13.78 0.00 38.53 3.51
661 696 4.501071 CAAGAAAAGAAATGGGCCAGATG 58.499 43.478 13.78 0.00 0.00 2.90
662 697 3.516700 CCAAGAAAAGAAATGGGCCAGAT 59.483 43.478 13.78 2.23 0.00 2.90
663 698 2.899256 CCAAGAAAAGAAATGGGCCAGA 59.101 45.455 13.78 0.00 0.00 3.86
664 699 2.027837 CCCAAGAAAAGAAATGGGCCAG 60.028 50.000 13.78 0.00 45.56 4.85
665 700 1.977129 CCCAAGAAAAGAAATGGGCCA 59.023 47.619 9.61 9.61 45.56 5.36
666 701 2.768253 CCCAAGAAAAGAAATGGGCC 57.232 50.000 0.00 0.00 45.56 5.80
669 704 3.366374 GCTCGTCCCAAGAAAAGAAATGG 60.366 47.826 0.00 0.00 0.00 3.16
670 705 3.503748 AGCTCGTCCCAAGAAAAGAAATG 59.496 43.478 0.00 0.00 0.00 2.32
671 706 3.756117 AGCTCGTCCCAAGAAAAGAAAT 58.244 40.909 0.00 0.00 0.00 2.17
672 707 3.208747 AGCTCGTCCCAAGAAAAGAAA 57.791 42.857 0.00 0.00 0.00 2.52
673 708 2.878406 CAAGCTCGTCCCAAGAAAAGAA 59.122 45.455 0.00 0.00 0.00 2.52
674 709 2.104111 TCAAGCTCGTCCCAAGAAAAGA 59.896 45.455 0.00 0.00 0.00 2.52
675 710 2.224314 GTCAAGCTCGTCCCAAGAAAAG 59.776 50.000 0.00 0.00 0.00 2.27
676 711 2.218603 GTCAAGCTCGTCCCAAGAAAA 58.781 47.619 0.00 0.00 0.00 2.29
677 712 1.542547 GGTCAAGCTCGTCCCAAGAAA 60.543 52.381 0.00 0.00 0.00 2.52
678 713 0.034896 GGTCAAGCTCGTCCCAAGAA 59.965 55.000 0.00 0.00 0.00 2.52
679 714 1.671742 GGTCAAGCTCGTCCCAAGA 59.328 57.895 0.00 0.00 0.00 3.02
680 715 1.738099 CGGTCAAGCTCGTCCCAAG 60.738 63.158 0.00 0.00 0.00 3.61
681 716 2.204461 TCGGTCAAGCTCGTCCCAA 61.204 57.895 0.00 0.00 0.00 4.12
682 717 2.599281 TCGGTCAAGCTCGTCCCA 60.599 61.111 0.00 0.00 0.00 4.37
683 718 2.126031 GTCGGTCAAGCTCGTCCC 60.126 66.667 0.00 0.00 0.00 4.46
684 719 2.126031 GGTCGGTCAAGCTCGTCC 60.126 66.667 0.00 0.00 0.00 4.79
685 720 2.126031 GGGTCGGTCAAGCTCGTC 60.126 66.667 0.00 0.00 0.00 4.20
686 721 4.052229 CGGGTCGGTCAAGCTCGT 62.052 66.667 0.00 0.00 0.00 4.18
687 722 4.796231 CCGGGTCGGTCAAGCTCG 62.796 72.222 0.00 0.00 42.73 5.03
701 736 4.880537 CTCACTAGCTGCCGCCGG 62.881 72.222 0.00 0.00 36.60 6.13
711 746 1.043673 AACTAGGCGGGGCTCACTAG 61.044 60.000 10.58 10.58 39.00 2.57
712 747 1.001248 AACTAGGCGGGGCTCACTA 59.999 57.895 0.00 0.00 0.00 2.74
713 748 2.284699 AACTAGGCGGGGCTCACT 60.285 61.111 0.00 0.00 0.00 3.41
714 749 2.187163 GAACTAGGCGGGGCTCAC 59.813 66.667 0.00 0.00 0.00 3.51
715 750 3.458163 CGAACTAGGCGGGGCTCA 61.458 66.667 0.00 0.00 0.00 4.26
716 751 2.902759 GAACGAACTAGGCGGGGCTC 62.903 65.000 11.20 0.00 0.00 4.70
717 752 3.001406 AACGAACTAGGCGGGGCT 61.001 61.111 11.20 0.00 0.00 5.19
718 753 2.510918 GAACGAACTAGGCGGGGC 60.511 66.667 11.20 0.00 0.00 5.80
719 754 0.107848 ATTGAACGAACTAGGCGGGG 60.108 55.000 11.20 0.00 0.00 5.73
720 755 1.664151 GAATTGAACGAACTAGGCGGG 59.336 52.381 11.20 0.00 0.00 6.13
721 756 2.343101 TGAATTGAACGAACTAGGCGG 58.657 47.619 11.20 0.00 0.00 6.13
722 757 2.348666 CCTGAATTGAACGAACTAGGCG 59.651 50.000 5.82 5.82 0.00 5.52
723 758 2.678336 CCCTGAATTGAACGAACTAGGC 59.322 50.000 0.00 0.00 0.00 3.93
724 759 2.678336 GCCCTGAATTGAACGAACTAGG 59.322 50.000 0.00 0.00 0.00 3.02
725 760 2.348666 CGCCCTGAATTGAACGAACTAG 59.651 50.000 0.00 0.00 0.00 2.57
726 761 2.343101 CGCCCTGAATTGAACGAACTA 58.657 47.619 0.00 0.00 0.00 2.24
727 762 1.156736 CGCCCTGAATTGAACGAACT 58.843 50.000 0.00 0.00 0.00 3.01
728 763 0.168128 CCGCCCTGAATTGAACGAAC 59.832 55.000 0.00 0.00 0.00 3.95
729 764 1.582610 GCCGCCCTGAATTGAACGAA 61.583 55.000 0.00 0.00 0.00 3.85
730 765 2.038269 GCCGCCCTGAATTGAACGA 61.038 57.895 0.00 0.00 0.00 3.85
731 766 2.485122 GCCGCCCTGAATTGAACG 59.515 61.111 0.00 0.00 0.00 3.95
732 767 2.710902 GGGCCGCCCTGAATTGAAC 61.711 63.158 22.31 0.00 41.34 3.18
733 768 2.362375 GGGCCGCCCTGAATTGAA 60.362 61.111 22.31 0.00 41.34 2.69
780 815 1.920835 GAGTGGGAGAGGTGGCCTT 60.921 63.158 3.32 0.00 31.76 4.35
782 817 3.403558 GGAGTGGGAGAGGTGGCC 61.404 72.222 0.00 0.00 0.00 5.36
807 842 2.817258 GAGAGAGTATGACGGGATCCAG 59.183 54.545 15.23 12.90 0.00 3.86
820 855 3.759086 AGCAAGAACGACATGAGAGAGTA 59.241 43.478 0.00 0.00 0.00 2.59
894 929 2.436646 CGCGGCAGGATGGAAAGT 60.437 61.111 0.00 0.00 35.86 2.66
897 932 3.700970 TGACGCGGCAGGATGGAA 61.701 61.111 12.71 0.00 35.86 3.53
916 951 2.325082 CCGGGTTGTTGAAGGAGCG 61.325 63.158 0.00 0.00 0.00 5.03
928 963 4.295199 GGGGAGGCAAACCGGGTT 62.295 66.667 6.59 6.59 42.76 4.11
959 1000 8.010540 GCCGACTGATGATATATATACACGTAG 58.989 40.741 0.00 0.00 0.00 3.51
978 1019 0.888736 TTTCCCACACATGCCGACTG 60.889 55.000 0.00 0.00 0.00 3.51
1019 1060 4.523173 TGTTCTCTATCCTGACGTTGTCTT 59.477 41.667 0.00 0.00 33.15 3.01
1026 1067 2.685388 TGCTCTGTTCTCTATCCTGACG 59.315 50.000 0.00 0.00 0.00 4.35
1034 1075 1.067565 CCGCTGTTGCTCTGTTCTCTA 60.068 52.381 0.00 0.00 36.97 2.43
1075 1116 1.495584 GCAAACTTGGTCTGCGTCGA 61.496 55.000 0.00 0.00 0.00 4.20
1077 1118 1.461127 CTAGCAAACTTGGTCTGCGTC 59.539 52.381 0.00 0.00 41.05 5.19
1078 1119 1.512926 CTAGCAAACTTGGTCTGCGT 58.487 50.000 0.00 0.00 41.05 5.24
1126 1167 1.264045 TGTCCATGGTCGATCAGCCA 61.264 55.000 12.58 7.57 39.33 4.75
1230 1271 4.082523 TCGCCTGCTTTCCTCCGG 62.083 66.667 0.00 0.00 0.00 5.14
1237 1278 1.374758 CTTCTCGGTCGCCTGCTTT 60.375 57.895 0.00 0.00 0.00 3.51
1249 1293 0.459934 CCTCCTGCTGCTTCTTCTCG 60.460 60.000 0.00 0.00 0.00 4.04
1292 1336 1.521616 CCTCCTGCTTCCTCTCTGC 59.478 63.158 0.00 0.00 0.00 4.26
1322 1366 3.733960 GAACTCCGGCGCAAACCC 61.734 66.667 10.83 0.00 0.00 4.11
1388 1432 1.629043 AAACTACTCGGAGACAGCCA 58.371 50.000 12.86 0.00 0.00 4.75
1399 1443 8.129840 GGAAGTGAAAAAGGAGAAAAACTACTC 58.870 37.037 0.00 0.00 39.17 2.59
1400 1444 7.068348 GGGAAGTGAAAAAGGAGAAAAACTACT 59.932 37.037 0.00 0.00 42.45 2.57
1402 1446 6.322969 GGGGAAGTGAAAAAGGAGAAAAACTA 59.677 38.462 0.00 0.00 0.00 2.24
1441 1485 7.273320 TGGTCAATAATCAACCAAACGTAAA 57.727 32.000 0.00 0.00 40.04 2.01
1442 1486 6.879276 TGGTCAATAATCAACCAAACGTAA 57.121 33.333 0.00 0.00 40.04 3.18
1450 1525 7.065923 GGTAAGTCTCTTGGTCAATAATCAACC 59.934 40.741 0.00 0.00 0.00 3.77
1455 1530 7.633789 ACATGGTAAGTCTCTTGGTCAATAAT 58.366 34.615 0.00 0.00 0.00 1.28
1456 1531 7.016153 ACATGGTAAGTCTCTTGGTCAATAA 57.984 36.000 0.00 0.00 0.00 1.40
1459 1534 4.262894 GGACATGGTAAGTCTCTTGGTCAA 60.263 45.833 0.00 0.00 36.29 3.18
1464 1539 4.248859 CTGTGGACATGGTAAGTCTCTTG 58.751 47.826 0.00 0.00 36.29 3.02
1474 1549 0.900182 TCTCTCGCTGTGGACATGGT 60.900 55.000 0.00 0.00 0.00 3.55
1475 1550 0.247460 TTCTCTCGCTGTGGACATGG 59.753 55.000 0.00 0.00 0.00 3.66
1481 1556 2.606725 GTCATTCATTCTCTCGCTGTGG 59.393 50.000 0.00 0.00 0.00 4.17
1502 1577 4.096231 TCAAACAACTGTGTGATTGTGAGG 59.904 41.667 0.00 0.00 37.36 3.86
1511 1586 5.676744 CGTCAGTAAATCAAACAACTGTGTG 59.323 40.000 0.00 0.00 40.18 3.82
1514 1589 4.261031 GGCGTCAGTAAATCAAACAACTGT 60.261 41.667 0.00 0.00 40.18 3.55
1517 1592 4.483476 AGGCGTCAGTAAATCAAACAAC 57.517 40.909 0.00 0.00 0.00 3.32
1519 1594 3.880490 ACAAGGCGTCAGTAAATCAAACA 59.120 39.130 0.00 0.00 0.00 2.83
1525 1600 6.650807 CCATCATATACAAGGCGTCAGTAAAT 59.349 38.462 0.00 0.00 0.00 1.40
1534 1609 5.333035 CGTAAACACCATCATATACAAGGCG 60.333 44.000 0.00 0.00 0.00 5.52
1537 1612 7.902917 CACAACGTAAACACCATCATATACAAG 59.097 37.037 0.00 0.00 0.00 3.16
1539 1614 7.097834 TCACAACGTAAACACCATCATATACA 58.902 34.615 0.00 0.00 0.00 2.29
1540 1615 7.528481 TCACAACGTAAACACCATCATATAC 57.472 36.000 0.00 0.00 0.00 1.47
1541 1616 8.725405 AATCACAACGTAAACACCATCATATA 57.275 30.769 0.00 0.00 0.00 0.86
1543 1618 6.183360 CGAATCACAACGTAAACACCATCATA 60.183 38.462 0.00 0.00 0.00 2.15
1547 1622 4.059511 TCGAATCACAACGTAAACACCAT 58.940 39.130 0.00 0.00 0.00 3.55
1550 1625 4.901881 CCTTTCGAATCACAACGTAAACAC 59.098 41.667 0.00 0.00 0.00 3.32
1562 1637 6.712998 TGGTGAAAAGTTATCCTTTCGAATCA 59.287 34.615 0.00 0.00 42.62 2.57
1565 1640 6.945938 TTGGTGAAAAGTTATCCTTTCGAA 57.054 33.333 0.00 0.00 42.62 3.71
1572 1647 6.872920 TGCCATTATTGGTGAAAAGTTATCC 58.127 36.000 5.58 0.00 45.57 2.59
1573 1648 6.980397 CCTGCCATTATTGGTGAAAAGTTATC 59.020 38.462 5.58 0.00 45.57 1.75
1576 1651 4.592778 ACCTGCCATTATTGGTGAAAAGTT 59.407 37.500 5.58 0.00 45.57 2.66
1578 1653 4.806640 ACCTGCCATTATTGGTGAAAAG 57.193 40.909 5.58 0.00 45.57 2.27
1580 1655 3.513515 GGAACCTGCCATTATTGGTGAAA 59.486 43.478 5.58 0.00 45.57 2.69
1581 1656 3.096092 GGAACCTGCCATTATTGGTGAA 58.904 45.455 5.58 0.00 45.57 3.18
1582 1657 2.311542 AGGAACCTGCCATTATTGGTGA 59.688 45.455 5.58 0.00 45.57 4.02
1583 1658 2.689983 GAGGAACCTGCCATTATTGGTG 59.310 50.000 5.58 0.00 45.57 4.17
1584 1659 2.358195 GGAGGAACCTGCCATTATTGGT 60.358 50.000 5.58 0.00 39.39 3.67
1585 1660 2.310538 GGAGGAACCTGCCATTATTGG 58.689 52.381 0.00 0.00 39.83 3.16
1594 1669 1.303643 CTTGGTGGGAGGAACCTGC 60.304 63.158 3.76 3.76 38.60 4.85
1595 1670 1.303643 GCTTGGTGGGAGGAACCTG 60.304 63.158 0.00 0.00 38.60 4.00
1596 1671 2.539081 GGCTTGGTGGGAGGAACCT 61.539 63.158 0.00 0.00 38.60 3.50
1597 1672 2.035783 GGCTTGGTGGGAGGAACC 59.964 66.667 0.00 0.00 38.26 3.62
1598 1673 2.035783 GGGCTTGGTGGGAGGAAC 59.964 66.667 0.00 0.00 0.00 3.62
1599 1674 3.264845 GGGGCTTGGTGGGAGGAA 61.265 66.667 0.00 0.00 0.00 3.36
1600 1675 4.608514 TGGGGCTTGGTGGGAGGA 62.609 66.667 0.00 0.00 0.00 3.71
1601 1676 2.671384 TTTTGGGGCTTGGTGGGAGG 62.671 60.000 0.00 0.00 0.00 4.30
1602 1677 0.762461 TTTTTGGGGCTTGGTGGGAG 60.762 55.000 0.00 0.00 0.00 4.30
1603 1678 1.314867 TTTTTGGGGCTTGGTGGGA 59.685 52.632 0.00 0.00 0.00 4.37
1604 1679 3.978164 TTTTTGGGGCTTGGTGGG 58.022 55.556 0.00 0.00 0.00 4.61
1655 1730 9.384764 GGTCATTAAAGTAGTGATCTAAAAGCT 57.615 33.333 0.00 0.00 0.00 3.74
1656 1731 9.384764 AGGTCATTAAAGTAGTGATCTAAAAGC 57.615 33.333 0.00 0.00 34.56 3.51
1680 1755 9.869757 CCCCAAAGAAATGTAAAAGTATTTAGG 57.130 33.333 0.00 0.00 37.28 2.69
1683 1758 8.593679 CCTCCCCAAAGAAATGTAAAAGTATTT 58.406 33.333 0.00 0.00 42.41 1.40
1684 1759 7.180229 CCCTCCCCAAAGAAATGTAAAAGTATT 59.820 37.037 0.00 0.00 0.00 1.89
1685 1760 6.667848 CCCTCCCCAAAGAAATGTAAAAGTAT 59.332 38.462 0.00 0.00 0.00 2.12
1686 1761 6.014012 CCCTCCCCAAAGAAATGTAAAAGTA 58.986 40.000 0.00 0.00 0.00 2.24
1687 1762 4.838423 CCCTCCCCAAAGAAATGTAAAAGT 59.162 41.667 0.00 0.00 0.00 2.66
1688 1763 5.083821 TCCCTCCCCAAAGAAATGTAAAAG 58.916 41.667 0.00 0.00 0.00 2.27
1689 1764 5.081315 TCCCTCCCCAAAGAAATGTAAAA 57.919 39.130 0.00 0.00 0.00 1.52
1690 1765 4.107311 ACTCCCTCCCCAAAGAAATGTAAA 59.893 41.667 0.00 0.00 0.00 2.01
1691 1766 3.660669 ACTCCCTCCCCAAAGAAATGTAA 59.339 43.478 0.00 0.00 0.00 2.41
1692 1767 3.265489 ACTCCCTCCCCAAAGAAATGTA 58.735 45.455 0.00 0.00 0.00 2.29
1693 1768 2.073776 ACTCCCTCCCCAAAGAAATGT 58.926 47.619 0.00 0.00 0.00 2.71
1694 1769 2.907458 ACTCCCTCCCCAAAGAAATG 57.093 50.000 0.00 0.00 0.00 2.32
1695 1770 3.542604 AGTACTCCCTCCCCAAAGAAAT 58.457 45.455 0.00 0.00 0.00 2.17
1696 1771 2.999928 AGTACTCCCTCCCCAAAGAAA 58.000 47.619 0.00 0.00 0.00 2.52
1697 1772 2.735259 AGTACTCCCTCCCCAAAGAA 57.265 50.000 0.00 0.00 0.00 2.52
1698 1773 2.642807 CAAAGTACTCCCTCCCCAAAGA 59.357 50.000 0.00 0.00 0.00 2.52
1699 1774 2.375509 ACAAAGTACTCCCTCCCCAAAG 59.624 50.000 0.00 0.00 0.00 2.77
1700 1775 2.424793 ACAAAGTACTCCCTCCCCAAA 58.575 47.619 0.00 0.00 0.00 3.28
1701 1776 2.127651 ACAAAGTACTCCCTCCCCAA 57.872 50.000 0.00 0.00 0.00 4.12
1702 1777 2.127651 AACAAAGTACTCCCTCCCCA 57.872 50.000 0.00 0.00 0.00 4.96
1703 1778 3.179685 ACTAACAAAGTACTCCCTCCCC 58.820 50.000 0.00 0.00 36.36 4.81
1760 1836 3.195825 ACTCGAGCCAATAAACTAGTGCT 59.804 43.478 13.61 0.00 0.00 4.40
1761 1837 3.307242 CACTCGAGCCAATAAACTAGTGC 59.693 47.826 13.61 0.00 0.00 4.40
1784 1861 5.473162 TGTCTATCCATGACACTTTGTTTGG 59.527 40.000 0.00 3.86 39.23 3.28
1797 1874 0.930310 CGTTGGCGTGTCTATCCATG 59.070 55.000 0.00 0.00 0.00 3.66
1799 1876 4.902308 CGTTGGCGTGTCTATCCA 57.098 55.556 0.00 0.00 0.00 3.41
1811 1888 0.531090 TTGGTCGACAAGGACGTTGG 60.531 55.000 18.91 0.00 40.90 3.77
1812 1889 0.580104 GTTGGTCGACAAGGACGTTG 59.420 55.000 18.91 6.34 40.38 4.10
1814 1891 1.299620 CGTTGGTCGACAAGGACGT 60.300 57.895 18.91 0.00 45.38 4.34
1825 1902 0.248866 CAACAACCTTGGCGTTGGTC 60.249 55.000 12.20 0.00 41.74 4.02
1837 1914 1.303643 CCTCTCCAGGGCAACAACC 60.304 63.158 0.00 0.00 35.89 3.77
1857 1935 1.739035 GCGCCACAAGCTCTGTATACA 60.739 52.381 5.25 5.25 40.39 2.29
1861 1939 2.047274 GGCGCCACAAGCTCTGTA 60.047 61.111 24.80 0.00 40.39 2.74
1868 1946 3.594775 TGTTGCTGGCGCCACAAG 61.595 61.111 31.41 22.69 38.66 3.16
1876 1954 1.098050 CTCCTATTGGTGTTGCTGGC 58.902 55.000 0.00 0.00 34.23 4.85
1884 1962 2.290260 TGTGGTTGAGCTCCTATTGGTG 60.290 50.000 12.15 0.00 34.23 4.17
1890 1968 1.888436 CGCCTGTGGTTGAGCTCCTA 61.888 60.000 12.15 0.00 0.00 2.94
1901 1979 2.045708 TTTGCCATAGCGCCTGTGG 61.046 57.895 16.46 16.46 44.07 4.17
1903 1981 1.303236 TGTTTGCCATAGCGCCTGT 60.303 52.632 2.29 0.00 44.31 4.00
1910 1988 5.109210 TCGAGTAGAATGTGTTTGCCATAG 58.891 41.667 0.00 0.00 0.00 2.23
1917 1995 5.120830 GCAGTCAATCGAGTAGAATGTGTTT 59.879 40.000 11.71 0.00 31.79 2.83
1918 1996 4.627467 GCAGTCAATCGAGTAGAATGTGTT 59.373 41.667 11.71 0.00 31.79 3.32
1919 1997 4.177026 GCAGTCAATCGAGTAGAATGTGT 58.823 43.478 11.71 0.00 31.79 3.72
1920 1998 3.241553 CGCAGTCAATCGAGTAGAATGTG 59.758 47.826 11.71 10.79 32.72 3.21
1921 1999 3.128764 TCGCAGTCAATCGAGTAGAATGT 59.871 43.478 11.71 0.00 31.79 2.71
1922 2000 3.483922 GTCGCAGTCAATCGAGTAGAATG 59.516 47.826 7.38 7.38 35.21 2.67
1923 2001 3.128764 TGTCGCAGTCAATCGAGTAGAAT 59.871 43.478 0.00 0.00 35.21 2.40
1924 2002 2.486592 TGTCGCAGTCAATCGAGTAGAA 59.513 45.455 0.00 0.00 35.21 2.10
1925 2003 2.081462 TGTCGCAGTCAATCGAGTAGA 58.919 47.619 0.00 0.00 35.21 2.59
1926 2004 2.445316 CTGTCGCAGTCAATCGAGTAG 58.555 52.381 0.00 0.00 35.21 2.57
1927 2005 1.467543 GCTGTCGCAGTCAATCGAGTA 60.468 52.381 8.32 0.00 35.21 2.59
1928 2006 0.734253 GCTGTCGCAGTCAATCGAGT 60.734 55.000 8.32 0.00 35.21 4.18
1929 2007 0.733909 TGCTGTCGCAGTCAATCGAG 60.734 55.000 8.32 0.00 42.25 4.04
1930 2008 1.288752 TGCTGTCGCAGTCAATCGA 59.711 52.632 8.32 0.00 42.25 3.59
1931 2009 3.860717 TGCTGTCGCAGTCAATCG 58.139 55.556 8.32 0.00 42.25 3.34
1942 2020 4.640113 GATCGCGCGCATGCTGTC 62.640 66.667 32.61 14.48 39.65 3.51
1944 2022 4.645024 CTGATCGCGCGCATGCTG 62.645 66.667 32.61 17.84 39.65 4.41
1947 2025 3.699484 CTCCTGATCGCGCGCATG 61.699 66.667 32.61 16.35 0.00 4.06
1948 2026 4.957684 CCTCCTGATCGCGCGCAT 62.958 66.667 32.61 22.65 0.00 4.73
1951 2029 3.893763 AGACCTCCTGATCGCGCG 61.894 66.667 26.76 26.76 0.00 6.86
1952 2030 2.279120 CAGACCTCCTGATCGCGC 60.279 66.667 0.00 0.00 45.78 6.86
1953 2031 1.226802 CACAGACCTCCTGATCGCG 60.227 63.158 0.00 0.00 45.78 5.87
1954 2032 1.142748 CCACAGACCTCCTGATCGC 59.857 63.158 0.00 0.00 45.78 4.58
1955 2033 0.898320 AACCACAGACCTCCTGATCG 59.102 55.000 0.00 0.00 45.78 3.69
1956 2034 2.355209 GGAAACCACAGACCTCCTGATC 60.355 54.545 0.00 0.00 45.78 2.92
1957 2035 1.630878 GGAAACCACAGACCTCCTGAT 59.369 52.381 0.00 0.00 45.78 2.90
1958 2036 1.056660 GGAAACCACAGACCTCCTGA 58.943 55.000 0.00 0.00 45.78 3.86
1960 2038 1.353091 GAGGAAACCACAGACCTCCT 58.647 55.000 0.00 0.00 41.89 3.69
1961 2039 0.037232 CGAGGAAACCACAGACCTCC 60.037 60.000 0.00 0.00 43.98 4.30
1962 2040 0.966920 TCGAGGAAACCACAGACCTC 59.033 55.000 0.00 0.00 43.58 3.85
1979 2057 2.169789 CCAGCCACGCAATCTCTCG 61.170 63.158 0.00 0.00 0.00 4.04
2018 2096 2.413453 GAGCATTCCAACAGACTTCGAC 59.587 50.000 0.00 0.00 0.00 4.20
2062 2140 0.317160 TCCGACAGTTGATTCAGCGT 59.683 50.000 0.00 0.00 0.00 5.07
2063 2141 0.994995 CTCCGACAGTTGATTCAGCG 59.005 55.000 0.00 0.00 0.00 5.18
2068 2146 1.645710 ACCCTCTCCGACAGTTGATT 58.354 50.000 0.00 0.00 0.00 2.57
2072 2150 1.371558 GCAACCCTCTCCGACAGTT 59.628 57.895 0.00 0.00 0.00 3.16
2093 2171 2.310538 CACAGGATATTTTCCCCAGGC 58.689 52.381 0.00 0.00 46.81 4.85
2097 2175 2.091885 TGGAGCACAGGATATTTTCCCC 60.092 50.000 0.00 0.00 46.81 4.81
2142 2220 8.014263 TGTATCTAAGGGATGTGGTTAATAGGA 58.986 37.037 0.00 0.00 35.98 2.94
2178 2256 0.510359 CGCTCGGCTTGCATCTTATC 59.490 55.000 0.00 0.00 0.00 1.75
2180 2258 2.173669 GCGCTCGGCTTGCATCTTA 61.174 57.895 0.00 0.00 39.11 2.10
2205 2283 5.543790 AGGGTGTTCTTTGCCAATTTCTAAT 59.456 36.000 0.00 0.00 0.00 1.73
2215 2293 1.337167 GCATTCAGGGTGTTCTTTGCC 60.337 52.381 0.00 0.00 0.00 4.52
2221 2299 4.782019 TTTGTATGCATTCAGGGTGTTC 57.218 40.909 3.54 0.00 0.00 3.18
2256 2334 3.039011 GGCTTAGAGGTAGGTGATTGGA 58.961 50.000 0.00 0.00 0.00 3.53
2259 2337 2.436173 GCTGGCTTAGAGGTAGGTGATT 59.564 50.000 0.00 0.00 0.00 2.57
2260 2338 2.043227 GCTGGCTTAGAGGTAGGTGAT 58.957 52.381 0.00 0.00 0.00 3.06
2278 2363 0.971386 CCAATTTGGGAACAGCAGCT 59.029 50.000 7.60 0.00 44.54 4.24
2281 2367 3.708631 TCTTTTCCAATTTGGGAACAGCA 59.291 39.130 15.37 0.00 46.28 4.41
2312 2398 2.547855 GCCCAAAGCCCTACTTTTGTTG 60.548 50.000 0.00 0.00 46.73 3.33
2337 2423 4.015406 ATCACAGGTTCGCCGCCA 62.015 61.111 0.00 0.00 43.66 5.69
2368 2454 4.961511 GTCAGCACCGTGGCGACA 62.962 66.667 0.00 0.00 37.31 4.35
2375 2461 2.649034 CCAGTACGTCAGCACCGT 59.351 61.111 0.00 1.14 42.06 4.83
2433 2519 1.198713 GAGAGAGGTGGAGAATGGCA 58.801 55.000 0.00 0.00 0.00 4.92
2449 2535 3.591789 CTGATTGGATAGGGAAGGGAGA 58.408 50.000 0.00 0.00 0.00 3.71
2451 2537 2.706350 CCTGATTGGATAGGGAAGGGA 58.294 52.381 0.00 0.00 38.35 4.20
2460 2547 3.060479 AGGTAGGTGCCTGATTGGATA 57.940 47.619 0.12 0.00 37.50 2.59
2462 2549 3.417330 AGGTAGGTGCCTGATTGGA 57.583 52.632 0.12 0.00 37.50 3.53
2473 2560 0.753262 GATGGATCGCACAGGTAGGT 59.247 55.000 0.00 0.00 0.00 3.08
2490 2577 2.952978 AGTTCTATTCTCCAGCGTCGAT 59.047 45.455 0.00 0.00 0.00 3.59
2522 2609 9.155975 CAAGCTTCTAACATCTAACAACATACT 57.844 33.333 0.00 0.00 0.00 2.12
2544 2631 4.266502 TCAAACGCATAAAACAACACAAGC 59.733 37.500 0.00 0.00 0.00 4.01
2553 2640 7.804614 TGGATTACAATCAAACGCATAAAAC 57.195 32.000 4.45 0.00 37.15 2.43
2558 2645 5.833406 TGATGGATTACAATCAAACGCAT 57.167 34.783 4.45 0.00 37.15 4.73
2592 2679 9.784531 CCAAGATAGAAATAGCTAGGAAATCAA 57.215 33.333 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.