Multiple sequence alignment - TraesCS2D01G346400

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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 TraesCS2D01G346400 chr2D 100.000 6266 0 0 1 6266 443247837 443241572 0.000000e+00 11572
1 TraesCS2D01G346400 chr2D 81.443 679 72 30 1 645 206643688 206643030 2.020000e-139 507
2 TraesCS2D01G346400 chr2D 91.964 224 13 4 646 864 174333825 174334048 6.100000e-80 309
3 TraesCS2D01G346400 chr2D 92.086 139 11 0 2202 2340 443244376 443244514 4.960000e-46 196
4 TraesCS2D01G346400 chr2D 89.610 154 16 0 3309 3462 443245483 443245636 4.960000e-46 196
5 TraesCS2D01G346400 chr2D 95.798 119 5 0 1789 1907 215846386 215846504 6.410000e-45 193
6 TraesCS2D01G346400 chr2D 94.355 124 6 1 1785 1908 109700470 109700348 8.290000e-44 189
7 TraesCS2D01G346400 chr2D 90.588 85 3 2 863 943 443263823 443263740 2.390000e-19 108
8 TraesCS2D01G346400 chr2B 95.921 4388 103 24 1906 6266 522204103 522199765 0.000000e+00 7042
9 TraesCS2D01G346400 chr2B 93.084 1041 47 13 764 1791 522205126 522204098 0.000000e+00 1500
10 TraesCS2D01G346400 chr2B 90.667 225 16 4 646 866 328863304 328863081 1.710000e-75 294
11 TraesCS2D01G346400 chr2B 90.260 154 15 0 3309 3462 522203649 522203802 1.070000e-47 202
12 TraesCS2D01G346400 chr2B 91.176 136 12 0 2202 2337 522202530 522202665 1.070000e-42 185
13 TraesCS2D01G346400 chr2A 94.936 3199 110 29 2250 5426 586898849 586895681 0.000000e+00 4963
14 TraesCS2D01G346400 chr2A 96.352 932 15 5 863 1791 586899915 586899000 0.000000e+00 1515
15 TraesCS2D01G346400 chr2A 93.696 809 22 10 5467 6266 586895478 586894690 0.000000e+00 1184
16 TraesCS2D01G346400 chr2A 91.304 161 13 1 3846 4005 141506470 141506310 1.060000e-52 219
17 TraesCS2D01G346400 chr2A 90.728 151 14 0 2202 2352 586897632 586897782 1.070000e-47 202
18 TraesCS2D01G346400 chr2A 86.164 159 6 3 1906 2056 586899001 586898851 2.340000e-34 158
19 TraesCS2D01G346400 chr1D 92.150 1070 50 15 2397 3457 62921466 62920422 0.000000e+00 1480
20 TraesCS2D01G346400 chr1D 98.613 649 5 3 1 645 123146943 123146295 0.000000e+00 1146
21 TraesCS2D01G346400 chr1D 98.613 649 4 3 1 645 123138850 123138203 0.000000e+00 1144
22 TraesCS2D01G346400 chr1D 95.062 648 25 6 2 645 23017867 23018511 0.000000e+00 1013
23 TraesCS2D01G346400 chr1D 94.892 646 26 5 1 642 23025951 23026593 0.000000e+00 1003
24 TraesCS2D01G346400 chr1D 91.556 225 15 3 646 866 346873177 346873401 2.190000e-79 307
25 TraesCS2D01G346400 chr1D 91.139 158 12 2 3846 4001 156133492 156133335 4.920000e-51 213
26 TraesCS2D01G346400 chr6D 91.405 1082 57 11 2397 3467 13483286 13482230 0.000000e+00 1450
27 TraesCS2D01G346400 chr6D 90.043 231 17 4 646 870 407822698 407822928 1.710000e-75 294
28 TraesCS2D01G346400 chr6D 91.304 161 13 1 3846 4005 392273074 392273234 1.060000e-52 219
29 TraesCS2D01G346400 chr6D 90.798 163 14 1 3846 4007 256728450 256728612 3.800000e-52 217
30 TraesCS2D01G346400 chr6D 90.798 163 14 1 3846 4007 256729247 256729409 3.800000e-52 217
31 TraesCS2D01G346400 chr6D 88.202 178 20 1 2786 2963 411400279 411400103 1.770000e-50 211
32 TraesCS2D01G346400 chr6D 95.902 122 3 1 1786 1905 178852322 178852201 4.960000e-46 196
33 TraesCS2D01G346400 chr6D 88.816 152 15 2 2202 2352 13482235 13482385 1.070000e-42 185
34 TraesCS2D01G346400 chr6D 88.742 151 17 0 2202 2352 365457342 365457492 1.070000e-42 185
35 TraesCS2D01G346400 chr6D 89.437 142 13 2 1777 1916 4235800 4235941 1.790000e-40 178
36 TraesCS2D01G346400 chr5D 91.144 1084 53 19 2397 3467 14039586 14038533 0.000000e+00 1430
37 TraesCS2D01G346400 chr5D 95.511 646 23 4 4 645 251253141 251252498 0.000000e+00 1027
38 TraesCS2D01G346400 chr5D 94.145 649 28 6 1 645 251261334 251260692 0.000000e+00 979
39 TraesCS2D01G346400 chr5D 92.721 577 30 12 76 645 2416087 2416658 0.000000e+00 822
40 TraesCS2D01G346400 chr5D 90.749 227 14 5 646 866 321715631 321715406 4.750000e-76 296
41 TraesCS2D01G346400 chr5D 92.366 131 7 3 1788 1916 461071763 461071634 3.860000e-42 183
42 TraesCS2D01G346400 chr5A 91.070 1075 53 18 2397 3464 689187422 689188460 0.000000e+00 1413
43 TraesCS2D01G346400 chr5A 95.000 400 17 3 2397 2795 707262803 707262406 5.330000e-175 625
44 TraesCS2D01G346400 chrUn 90.167 1078 55 12 2412 3464 46171904 46172955 0.000000e+00 1356
45 TraesCS2D01G346400 chr3D 97.218 647 13 4 1 645 74566908 74567551 0.000000e+00 1090
46 TraesCS2D01G346400 chr3D 96.754 647 15 5 1 645 74574953 74575595 0.000000e+00 1074
47 TraesCS2D01G346400 chr3D 90.135 223 18 2 646 864 400451965 400452187 2.860000e-73 287
48 TraesCS2D01G346400 chr3D 94.531 128 7 0 1787 1914 14846791 14846664 1.380000e-46 198
49 TraesCS2D01G346400 chr6A 88.480 842 43 13 2397 3231 163151640 163152434 0.000000e+00 968
50 TraesCS2D01G346400 chr6A 95.000 400 17 3 2397 2795 540799364 540799761 5.330000e-175 625
51 TraesCS2D01G346400 chr6A 90.798 163 13 2 3840 4001 411770247 411770408 3.800000e-52 217
52 TraesCS2D01G346400 chr7D 88.553 463 44 4 2202 2657 123364089 123363629 2.550000e-153 553
53 TraesCS2D01G346400 chr7D 92.810 153 10 1 3846 3997 34757018 34756866 2.940000e-53 220
54 TraesCS2D01G346400 chr7D 87.821 156 19 0 2202 2357 22992539 22992694 3.860000e-42 183
55 TraesCS2D01G346400 chr6B 92.140 229 13 5 646 869 608336493 608336265 1.010000e-82 318
56 TraesCS2D01G346400 chr6B 96.774 124 2 1 1786 1907 293966166 293966289 8.230000e-49 206
57 TraesCS2D01G346400 chr4D 90.222 225 19 2 646 867 245111450 245111674 2.210000e-74 291
58 TraesCS2D01G346400 chr5B 89.224 232 18 5 646 871 472274055 472273825 3.700000e-72 283
59 TraesCS2D01G346400 chr1B 93.182 132 8 1 1786 1917 611680419 611680549 6.410000e-45 193
60 TraesCS2D01G346400 chr7B 92.424 132 9 1 1786 1916 340642030 340642161 2.980000e-43 187


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G346400 chr2D 443241572 443247837 6265 True 11572 11572 100.0000 1 6266 1 chr2D.!!$R3 6265
1 TraesCS2D01G346400 chr2D 206643030 206643688 658 True 507 507 81.4430 1 645 1 chr2D.!!$R2 644
2 TraesCS2D01G346400 chr2B 522199765 522205126 5361 True 4271 7042 94.5025 764 6266 2 chr2B.!!$R2 5502
3 TraesCS2D01G346400 chr2A 586894690 586899915 5225 True 1955 4963 92.7870 863 6266 4 chr2A.!!$R2 5403
4 TraesCS2D01G346400 chr1D 62920422 62921466 1044 True 1480 1480 92.1500 2397 3457 1 chr1D.!!$R1 1060
5 TraesCS2D01G346400 chr1D 123146295 123146943 648 True 1146 1146 98.6130 1 645 1 chr1D.!!$R3 644
6 TraesCS2D01G346400 chr1D 123138203 123138850 647 True 1144 1144 98.6130 1 645 1 chr1D.!!$R2 644
7 TraesCS2D01G346400 chr1D 23017867 23018511 644 False 1013 1013 95.0620 2 645 1 chr1D.!!$F1 643
8 TraesCS2D01G346400 chr1D 23025951 23026593 642 False 1003 1003 94.8920 1 642 1 chr1D.!!$F2 641
9 TraesCS2D01G346400 chr6D 13482230 13483286 1056 True 1450 1450 91.4050 2397 3467 1 chr6D.!!$R1 1070
10 TraesCS2D01G346400 chr6D 256728450 256729409 959 False 217 217 90.7980 3846 4007 2 chr6D.!!$F6 161
11 TraesCS2D01G346400 chr5D 14038533 14039586 1053 True 1430 1430 91.1440 2397 3467 1 chr5D.!!$R1 1070
12 TraesCS2D01G346400 chr5D 251252498 251253141 643 True 1027 1027 95.5110 4 645 1 chr5D.!!$R2 641
13 TraesCS2D01G346400 chr5D 251260692 251261334 642 True 979 979 94.1450 1 645 1 chr5D.!!$R3 644
14 TraesCS2D01G346400 chr5D 2416087 2416658 571 False 822 822 92.7210 76 645 1 chr5D.!!$F1 569
15 TraesCS2D01G346400 chr5A 689187422 689188460 1038 False 1413 1413 91.0700 2397 3464 1 chr5A.!!$F1 1067
16 TraesCS2D01G346400 chrUn 46171904 46172955 1051 False 1356 1356 90.1670 2412 3464 1 chrUn.!!$F1 1052
17 TraesCS2D01G346400 chr3D 74566908 74567551 643 False 1090 1090 97.2180 1 645 1 chr3D.!!$F1 644
18 TraesCS2D01G346400 chr3D 74574953 74575595 642 False 1074 1074 96.7540 1 645 1 chr3D.!!$F2 644
19 TraesCS2D01G346400 chr6A 163151640 163152434 794 False 968 968 88.4800 2397 3231 1 chr6A.!!$F1 834

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
676 715 0.174617 GAGAGGAAAGAGGAGTGCGG 59.825 60.000 0.0 0.0 0.00 5.69 F
1099 1155 0.906756 CTCCTCAGCTTCCACCTCCA 60.907 60.000 0.0 0.0 0.00 3.86 F
1816 1873 0.237498 CCGTCCGAAAAAGCTTGTCC 59.763 55.000 0.0 0.0 0.00 4.02 F
3041 3112 0.106769 TGCTTGAACTGGCTCCACAA 60.107 50.000 0.0 0.0 0.00 3.33 F
3046 3117 0.169009 GAACTGGCTCCACAATTCGC 59.831 55.000 0.0 0.0 0.00 4.70 F
3050 3121 0.254462 TGGCTCCACAATTCGCCATA 59.746 50.000 0.0 0.0 46.75 2.74 F
3057 3128 0.623723 ACAATTCGCCATACACCCCT 59.376 50.000 0.0 0.0 0.00 4.79 F
3059 3130 0.751643 AATTCGCCATACACCCCTGC 60.752 55.000 0.0 0.0 0.00 4.85 F
3105 3204 1.699083 TCTCATGGGTCAAGAGCACAA 59.301 47.619 0.0 0.0 30.47 3.33 F
4034 4187 3.250040 ACTGTCCACAAACTTGCGATAAC 59.750 43.478 0.0 0.0 0.00 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1797 1854 0.237498 GGACAAGCTTTTTCGGACGG 59.763 55.000 0.0 0.0 0.00 4.79 R
3019 3090 0.250467 TGGAGCCAGTTCAAGCAGAC 60.250 55.000 0.0 0.0 0.00 3.51 R
3047 3118 0.394352 GACTTGGGCAGGGGTGTATG 60.394 60.000 0.0 0.0 0.00 2.39 R
4739 4974 2.232941 ACGAAAGGGCGTAAGAGAATCA 59.767 45.455 0.0 0.0 43.61 2.57 R
4777 5012 5.111293 GGAAACACAAGGGAAATGCATATG 58.889 41.667 0.0 0.0 0.00 1.78 R
5056 5291 3.183775 CGAAGTTGTGGAAGGTAAACGAG 59.816 47.826 0.0 0.0 0.00 4.18 R
5068 5303 3.313012 TCACTGGTATCGAAGTTGTGG 57.687 47.619 0.0 0.0 0.00 4.17 R
5193 5440 4.024556 GCATAATCGAAGTTCCATCACCAG 60.025 45.833 0.0 0.0 0.00 4.00 R
5208 5455 4.024302 TCGTGACTACCTACAGCATAATCG 60.024 45.833 0.0 0.0 0.00 3.34 R
5745 6300 1.687494 GCGAGTTGATGCGTGGAGTC 61.687 60.000 0.0 0.0 0.00 3.36 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
145 157 2.285977 GGACACGCGGATAATTTTCCT 58.714 47.619 12.47 0.00 33.30 3.36
361 376 8.593945 AGAATTAAGATAACAAAGGCATTGGA 57.406 30.769 7.43 0.00 43.66 3.53
475 500 1.355381 TCACCATGTGCATTTCCCTCT 59.645 47.619 0.00 0.00 32.98 3.69
669 708 2.580867 CGCGCGAGAGGAAAGAGG 60.581 66.667 28.94 0.00 0.00 3.69
670 709 2.885861 GCGCGAGAGGAAAGAGGA 59.114 61.111 12.10 0.00 0.00 3.71
671 710 1.226831 GCGCGAGAGGAAAGAGGAG 60.227 63.158 12.10 0.00 0.00 3.69
672 711 1.939769 GCGCGAGAGGAAAGAGGAGT 61.940 60.000 12.10 0.00 0.00 3.85
673 712 0.179150 CGCGAGAGGAAAGAGGAGTG 60.179 60.000 0.00 0.00 0.00 3.51
674 713 0.459411 GCGAGAGGAAAGAGGAGTGC 60.459 60.000 0.00 0.00 0.00 4.40
675 714 0.179150 CGAGAGGAAAGAGGAGTGCG 60.179 60.000 0.00 0.00 0.00 5.34
676 715 0.174617 GAGAGGAAAGAGGAGTGCGG 59.825 60.000 0.00 0.00 0.00 5.69
677 716 1.219393 GAGGAAAGAGGAGTGCGGG 59.781 63.158 0.00 0.00 0.00 6.13
678 717 1.536662 AGGAAAGAGGAGTGCGGGT 60.537 57.895 0.00 0.00 0.00 5.28
679 718 1.128188 AGGAAAGAGGAGTGCGGGTT 61.128 55.000 0.00 0.00 0.00 4.11
680 719 0.955919 GGAAAGAGGAGTGCGGGTTG 60.956 60.000 0.00 0.00 0.00 3.77
681 720 0.955919 GAAAGAGGAGTGCGGGTTGG 60.956 60.000 0.00 0.00 0.00 3.77
682 721 2.411765 AAAGAGGAGTGCGGGTTGGG 62.412 60.000 0.00 0.00 0.00 4.12
683 722 4.410400 GAGGAGTGCGGGTTGGGG 62.410 72.222 0.00 0.00 0.00 4.96
703 742 2.145397 GGAGATTTTCCTCCCAACCC 57.855 55.000 0.00 0.00 45.44 4.11
704 743 1.641192 GGAGATTTTCCTCCCAACCCT 59.359 52.381 0.00 0.00 45.44 4.34
705 744 2.043115 GGAGATTTTCCTCCCAACCCTT 59.957 50.000 0.00 0.00 45.44 3.95
706 745 3.268595 GGAGATTTTCCTCCCAACCCTTA 59.731 47.826 0.00 0.00 45.44 2.69
707 746 4.079154 GGAGATTTTCCTCCCAACCCTTAT 60.079 45.833 0.00 0.00 45.44 1.73
708 747 5.519808 GAGATTTTCCTCCCAACCCTTATT 58.480 41.667 0.00 0.00 0.00 1.40
709 748 5.915628 AGATTTTCCTCCCAACCCTTATTT 58.084 37.500 0.00 0.00 0.00 1.40
710 749 5.958380 AGATTTTCCTCCCAACCCTTATTTC 59.042 40.000 0.00 0.00 0.00 2.17
711 750 5.348259 TTTTCCTCCCAACCCTTATTTCT 57.652 39.130 0.00 0.00 0.00 2.52
712 751 6.471942 TTTTCCTCCCAACCCTTATTTCTA 57.528 37.500 0.00 0.00 0.00 2.10
713 752 5.446260 TTCCTCCCAACCCTTATTTCTAC 57.554 43.478 0.00 0.00 0.00 2.59
714 753 4.440808 TCCTCCCAACCCTTATTTCTACA 58.559 43.478 0.00 0.00 0.00 2.74
715 754 4.473559 TCCTCCCAACCCTTATTTCTACAG 59.526 45.833 0.00 0.00 0.00 2.74
716 755 4.385310 CCTCCCAACCCTTATTTCTACAGG 60.385 50.000 0.00 0.00 0.00 4.00
717 756 4.180723 TCCCAACCCTTATTTCTACAGGT 58.819 43.478 0.00 0.00 0.00 4.00
718 757 4.604490 TCCCAACCCTTATTTCTACAGGTT 59.396 41.667 0.00 0.00 38.10 3.50
720 759 5.897377 CAACCCTTATTTCTACAGGTTGG 57.103 43.478 11.06 0.00 46.70 3.77
721 760 4.586306 ACCCTTATTTCTACAGGTTGGG 57.414 45.455 0.00 0.00 38.13 4.12
722 761 4.180723 ACCCTTATTTCTACAGGTTGGGA 58.819 43.478 0.00 0.00 36.20 4.37
723 762 4.604490 ACCCTTATTTCTACAGGTTGGGAA 59.396 41.667 0.00 0.00 36.20 3.97
724 763 5.075344 ACCCTTATTTCTACAGGTTGGGAAA 59.925 40.000 0.00 0.00 36.20 3.13
725 764 6.194967 CCCTTATTTCTACAGGTTGGGAAAT 58.805 40.000 12.88 12.88 37.52 2.17
726 765 7.036425 ACCCTTATTTCTACAGGTTGGGAAATA 60.036 37.037 0.00 0.00 36.32 1.40
727 766 7.502561 CCCTTATTTCTACAGGTTGGGAAATAG 59.497 40.741 13.55 10.44 37.41 1.73
728 767 8.053355 CCTTATTTCTACAGGTTGGGAAATAGT 58.947 37.037 13.55 0.00 37.41 2.12
729 768 9.462606 CTTATTTCTACAGGTTGGGAAATAGTT 57.537 33.333 13.55 0.00 37.41 2.24
730 769 9.816787 TTATTTCTACAGGTTGGGAAATAGTTT 57.183 29.630 13.55 0.00 37.41 2.66
731 770 7.519032 TTTCTACAGGTTGGGAAATAGTTTG 57.481 36.000 0.00 0.00 0.00 2.93
732 771 6.442541 TCTACAGGTTGGGAAATAGTTTGA 57.557 37.500 0.00 0.00 0.00 2.69
733 772 6.843752 TCTACAGGTTGGGAAATAGTTTGAA 58.156 36.000 0.00 0.00 0.00 2.69
734 773 6.940298 TCTACAGGTTGGGAAATAGTTTGAAG 59.060 38.462 0.00 0.00 0.00 3.02
735 774 4.832823 ACAGGTTGGGAAATAGTTTGAAGG 59.167 41.667 0.00 0.00 0.00 3.46
736 775 4.832823 CAGGTTGGGAAATAGTTTGAAGGT 59.167 41.667 0.00 0.00 0.00 3.50
737 776 5.304357 CAGGTTGGGAAATAGTTTGAAGGTT 59.696 40.000 0.00 0.00 0.00 3.50
738 777 5.304357 AGGTTGGGAAATAGTTTGAAGGTTG 59.696 40.000 0.00 0.00 0.00 3.77
739 778 5.510690 GGTTGGGAAATAGTTTGAAGGTTGG 60.511 44.000 0.00 0.00 0.00 3.77
740 779 5.068215 TGGGAAATAGTTTGAAGGTTGGA 57.932 39.130 0.00 0.00 0.00 3.53
741 780 4.830600 TGGGAAATAGTTTGAAGGTTGGAC 59.169 41.667 0.00 0.00 0.00 4.02
742 781 4.219944 GGGAAATAGTTTGAAGGTTGGACC 59.780 45.833 0.00 0.00 38.99 4.46
772 811 4.703379 TTTACGGGTTTGAGGGTTTAGA 57.297 40.909 0.00 0.00 0.00 2.10
780 819 5.489249 GGTTTGAGGGTTTAGAGGTTCTAG 58.511 45.833 0.00 0.00 29.56 2.43
784 823 6.398655 TGAGGGTTTAGAGGTTCTAGTCTA 57.601 41.667 0.00 0.00 29.56 2.59
787 826 6.137559 AGGGTTTAGAGGTTCTAGTCTATGG 58.862 44.000 0.00 0.00 29.56 2.74
788 827 5.221481 GGGTTTAGAGGTTCTAGTCTATGGC 60.221 48.000 0.00 0.00 29.56 4.40
789 828 5.599242 GGTTTAGAGGTTCTAGTCTATGGCT 59.401 44.000 0.00 0.00 29.56 4.75
837 877 7.992295 AGTAGTTAATTTTAGGGGTTTGAGGA 58.008 34.615 0.00 0.00 0.00 3.71
841 881 8.593679 AGTTAATTTTAGGGGTTTGAGGATTTG 58.406 33.333 0.00 0.00 0.00 2.32
842 882 8.590204 GTTAATTTTAGGGGTTTGAGGATTTGA 58.410 33.333 0.00 0.00 0.00 2.69
845 885 2.073776 AGGGGTTTGAGGATTTGAGGT 58.926 47.619 0.00 0.00 0.00 3.85
846 886 2.041755 AGGGGTTTGAGGATTTGAGGTC 59.958 50.000 0.00 0.00 0.00 3.85
847 887 2.041755 GGGGTTTGAGGATTTGAGGTCT 59.958 50.000 0.00 0.00 0.00 3.85
849 889 3.003480 GGTTTGAGGATTTGAGGTCTCG 58.997 50.000 0.00 0.00 0.00 4.04
854 894 3.948473 TGAGGATTTGAGGTCTCGACTAG 59.052 47.826 0.00 0.00 0.00 2.57
855 895 4.200874 GAGGATTTGAGGTCTCGACTAGA 58.799 47.826 0.00 0.00 0.00 2.43
888 928 2.320587 GCAGTGGTCGAAGCCTGTG 61.321 63.158 7.91 0.84 0.00 3.66
915 958 1.094785 CCAGCAGTAAAACCCATCGG 58.905 55.000 0.00 0.00 0.00 4.18
926 969 5.855740 AAAACCCATCGGAAGTACAAAAA 57.144 34.783 0.00 0.00 0.00 1.94
986 1035 2.757099 GCCCGTAGAACCCCGAGA 60.757 66.667 0.00 0.00 0.00 4.04
987 1036 2.132352 GCCCGTAGAACCCCGAGAT 61.132 63.158 0.00 0.00 0.00 2.75
1099 1155 0.906756 CTCCTCAGCTTCCACCTCCA 60.907 60.000 0.00 0.00 0.00 3.86
1108 1164 3.402681 CCACCTCCATCCACCGCT 61.403 66.667 0.00 0.00 0.00 5.52
1277 1333 4.383770 GCTGTTTGGTAGAAGGCCACTATA 60.384 45.833 5.01 0.00 35.46 1.31
1447 1503 2.230508 TCGAAGTGATACCGTTGAAGCT 59.769 45.455 0.00 0.00 0.00 3.74
1795 1852 7.912719 AGAGCCTTTCTTCATTATATACTCCC 58.087 38.462 0.00 0.00 29.61 4.30
1796 1853 7.737149 AGAGCCTTTCTTCATTATATACTCCCT 59.263 37.037 0.00 0.00 29.61 4.20
1797 1854 7.912719 AGCCTTTCTTCATTATATACTCCCTC 58.087 38.462 0.00 0.00 0.00 4.30
1798 1855 7.037945 AGCCTTTCTTCATTATATACTCCCTCC 60.038 40.741 0.00 0.00 0.00 4.30
1799 1856 7.324178 CCTTTCTTCATTATATACTCCCTCCG 58.676 42.308 0.00 0.00 0.00 4.63
1800 1857 7.038941 CCTTTCTTCATTATATACTCCCTCCGT 60.039 40.741 0.00 0.00 0.00 4.69
1801 1858 7.463961 TTCTTCATTATATACTCCCTCCGTC 57.536 40.000 0.00 0.00 0.00 4.79
1802 1859 5.950549 TCTTCATTATATACTCCCTCCGTCC 59.049 44.000 0.00 0.00 0.00 4.79
1803 1860 4.267536 TCATTATATACTCCCTCCGTCCG 58.732 47.826 0.00 0.00 0.00 4.79
1804 1861 4.019051 TCATTATATACTCCCTCCGTCCGA 60.019 45.833 0.00 0.00 0.00 4.55
1805 1862 2.965671 ATATACTCCCTCCGTCCGAA 57.034 50.000 0.00 0.00 0.00 4.30
1806 1863 2.734755 TATACTCCCTCCGTCCGAAA 57.265 50.000 0.00 0.00 0.00 3.46
1807 1864 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
1808 1865 1.631405 TACTCCCTCCGTCCGAAAAA 58.369 50.000 0.00 0.00 0.00 1.94
1809 1866 0.320697 ACTCCCTCCGTCCGAAAAAG 59.679 55.000 0.00 0.00 0.00 2.27
1810 1867 1.004200 TCCCTCCGTCCGAAAAAGC 60.004 57.895 0.00 0.00 0.00 3.51
1811 1868 1.003718 CCCTCCGTCCGAAAAAGCT 60.004 57.895 0.00 0.00 0.00 3.74
1812 1869 0.605589 CCCTCCGTCCGAAAAAGCTT 60.606 55.000 0.00 0.00 0.00 3.74
1813 1870 0.517316 CCTCCGTCCGAAAAAGCTTG 59.483 55.000 0.00 0.00 0.00 4.01
1814 1871 1.226746 CTCCGTCCGAAAAAGCTTGT 58.773 50.000 0.00 0.00 0.00 3.16
1815 1872 1.194772 CTCCGTCCGAAAAAGCTTGTC 59.805 52.381 0.00 0.00 0.00 3.18
1816 1873 0.237498 CCGTCCGAAAAAGCTTGTCC 59.763 55.000 0.00 0.00 0.00 4.02
1817 1874 0.237498 CGTCCGAAAAAGCTTGTCCC 59.763 55.000 0.00 0.00 0.00 4.46
1818 1875 1.314730 GTCCGAAAAAGCTTGTCCCA 58.685 50.000 0.00 0.00 0.00 4.37
1819 1876 1.679153 GTCCGAAAAAGCTTGTCCCAA 59.321 47.619 0.00 0.00 0.00 4.12
1820 1877 1.953686 TCCGAAAAAGCTTGTCCCAAG 59.046 47.619 0.00 0.00 0.00 3.61
1821 1878 1.602920 CCGAAAAAGCTTGTCCCAAGC 60.603 52.381 18.69 18.69 43.31 4.01
1828 1885 1.393603 GCTTGTCCCAAGCTTATCCC 58.606 55.000 18.97 0.00 40.01 3.85
1829 1886 1.064389 GCTTGTCCCAAGCTTATCCCT 60.064 52.381 18.97 0.00 40.01 4.20
1830 1887 2.924421 CTTGTCCCAAGCTTATCCCTC 58.076 52.381 0.00 0.00 0.00 4.30
1831 1888 1.965414 TGTCCCAAGCTTATCCCTCA 58.035 50.000 0.00 0.00 0.00 3.86
1832 1889 2.274542 TGTCCCAAGCTTATCCCTCAA 58.725 47.619 0.00 0.00 0.00 3.02
1833 1890 2.647299 TGTCCCAAGCTTATCCCTCAAA 59.353 45.455 0.00 0.00 0.00 2.69
1834 1891 3.269381 TGTCCCAAGCTTATCCCTCAAAT 59.731 43.478 0.00 0.00 0.00 2.32
1835 1892 4.476846 TGTCCCAAGCTTATCCCTCAAATA 59.523 41.667 0.00 0.00 0.00 1.40
1836 1893 5.044476 TGTCCCAAGCTTATCCCTCAAATAA 60.044 40.000 0.00 0.00 0.00 1.40
1837 1894 5.891551 GTCCCAAGCTTATCCCTCAAATAAA 59.108 40.000 0.00 0.00 0.00 1.40
1838 1895 6.551227 GTCCCAAGCTTATCCCTCAAATAAAT 59.449 38.462 0.00 0.00 0.00 1.40
1839 1896 6.550854 TCCCAAGCTTATCCCTCAAATAAATG 59.449 38.462 0.00 0.00 0.00 2.32
1840 1897 6.324770 CCCAAGCTTATCCCTCAAATAAATGT 59.675 38.462 0.00 0.00 0.00 2.71
1841 1898 7.505585 CCCAAGCTTATCCCTCAAATAAATGTA 59.494 37.037 0.00 0.00 0.00 2.29
1842 1899 9.082313 CCAAGCTTATCCCTCAAATAAATGTAT 57.918 33.333 0.00 0.00 0.00 2.29
1849 1906 8.854614 ATCCCTCAAATAAATGTATCTAGCAC 57.145 34.615 0.00 0.00 0.00 4.40
1850 1907 8.034313 TCCCTCAAATAAATGTATCTAGCACT 57.966 34.615 0.00 0.00 0.00 4.40
1851 1908 9.154632 TCCCTCAAATAAATGTATCTAGCACTA 57.845 33.333 0.00 0.00 0.00 2.74
1852 1909 9.778741 CCCTCAAATAAATGTATCTAGCACTAA 57.221 33.333 0.00 0.00 0.00 2.24
1859 1916 7.849804 AAATGTATCTAGCACTAACTTGGTG 57.150 36.000 0.97 0.97 37.70 4.17
1871 1928 5.986135 CACTAACTTGGTGCTAGATACATCC 59.014 44.000 0.00 0.00 0.00 3.51
1872 1929 5.661312 ACTAACTTGGTGCTAGATACATCCA 59.339 40.000 0.00 0.00 0.00 3.41
1873 1930 5.636903 AACTTGGTGCTAGATACATCCAT 57.363 39.130 0.00 0.00 0.00 3.41
1874 1931 5.636903 ACTTGGTGCTAGATACATCCATT 57.363 39.130 0.00 0.00 0.00 3.16
1875 1932 6.006275 ACTTGGTGCTAGATACATCCATTT 57.994 37.500 0.00 0.00 0.00 2.32
1876 1933 5.824624 ACTTGGTGCTAGATACATCCATTTG 59.175 40.000 0.00 0.00 0.00 2.32
1877 1934 5.628797 TGGTGCTAGATACATCCATTTGA 57.371 39.130 0.00 0.00 0.00 2.69
1878 1935 5.614308 TGGTGCTAGATACATCCATTTGAG 58.386 41.667 0.00 0.00 0.00 3.02
1879 1936 4.999950 GGTGCTAGATACATCCATTTGAGG 59.000 45.833 0.00 0.00 0.00 3.86
1880 1937 4.999950 GTGCTAGATACATCCATTTGAGGG 59.000 45.833 0.00 0.00 0.00 4.30
1881 1938 4.907269 TGCTAGATACATCCATTTGAGGGA 59.093 41.667 0.00 0.00 39.14 4.20
1882 1939 5.221722 TGCTAGATACATCCATTTGAGGGAC 60.222 44.000 0.00 0.00 37.23 4.46
1883 1940 5.221722 GCTAGATACATCCATTTGAGGGACA 60.222 44.000 0.00 0.00 37.23 4.02
1884 1941 5.715439 AGATACATCCATTTGAGGGACAA 57.285 39.130 0.00 0.00 37.23 3.18
1885 1942 5.688807 AGATACATCCATTTGAGGGACAAG 58.311 41.667 0.00 0.00 39.77 3.16
1886 1943 3.814504 ACATCCATTTGAGGGACAAGT 57.185 42.857 0.00 0.00 39.77 3.16
1887 1944 4.118168 ACATCCATTTGAGGGACAAGTT 57.882 40.909 0.00 0.00 39.77 2.66
1888 1945 4.482990 ACATCCATTTGAGGGACAAGTTT 58.517 39.130 0.00 0.00 39.77 2.66
1889 1946 4.901250 ACATCCATTTGAGGGACAAGTTTT 59.099 37.500 0.00 0.00 39.77 2.43
1890 1947 5.366477 ACATCCATTTGAGGGACAAGTTTTT 59.634 36.000 0.00 0.00 39.77 1.94
1910 1967 2.294449 TCGGATGGAGGGAGTAGATG 57.706 55.000 0.00 0.00 0.00 2.90
1919 1976 5.148502 TGGAGGGAGTAGATGGTAAATCTC 58.851 45.833 0.00 0.00 0.00 2.75
1970 2032 1.897423 CATCACGTGTAGGAGCCCA 59.103 57.895 16.51 0.00 0.00 5.36
1995 2057 8.552865 CACAATGCCATAATTTCATGTAAATGG 58.447 33.333 10.08 10.08 37.85 3.16
2224 2294 9.557338 CTAGGATAAGTATATTTTTCGTCCTCG 57.443 37.037 0.00 0.00 35.38 4.63
2235 2305 1.081376 CGTCCTCGAACTCTTGCGT 60.081 57.895 0.00 0.00 39.71 5.24
2381 2451 7.374272 TCAGCTATATTCAGTTCAGACTATGC 58.626 38.462 0.00 0.00 33.90 3.14
3019 3090 2.436646 AACTTGCCGAGGATGCCG 60.437 61.111 0.00 0.00 0.00 5.69
3040 3111 0.535780 CTGCTTGAACTGGCTCCACA 60.536 55.000 0.00 0.00 0.00 4.17
3041 3112 0.106769 TGCTTGAACTGGCTCCACAA 60.107 50.000 0.00 0.00 0.00 3.33
3042 3113 1.251251 GCTTGAACTGGCTCCACAAT 58.749 50.000 0.00 0.00 0.00 2.71
3043 3114 1.615392 GCTTGAACTGGCTCCACAATT 59.385 47.619 0.00 0.00 0.00 2.32
3044 3115 2.352127 GCTTGAACTGGCTCCACAATTC 60.352 50.000 0.00 0.00 0.00 2.17
3045 3116 1.522668 TGAACTGGCTCCACAATTCG 58.477 50.000 0.00 0.00 0.00 3.34
3046 3117 0.169009 GAACTGGCTCCACAATTCGC 59.831 55.000 0.00 0.00 0.00 4.70
3047 3118 1.244019 AACTGGCTCCACAATTCGCC 61.244 55.000 0.00 0.00 42.78 5.54
3049 3120 1.001020 TGGCTCCACAATTCGCCAT 60.001 52.632 0.00 0.00 46.75 4.40
3050 3121 0.254462 TGGCTCCACAATTCGCCATA 59.746 50.000 0.00 0.00 46.75 2.74
3051 3122 0.663153 GGCTCCACAATTCGCCATAC 59.337 55.000 0.00 0.00 42.06 2.39
3052 3123 1.378531 GCTCCACAATTCGCCATACA 58.621 50.000 0.00 0.00 0.00 2.29
3053 3124 1.064060 GCTCCACAATTCGCCATACAC 59.936 52.381 0.00 0.00 0.00 2.90
3054 3125 1.670811 CTCCACAATTCGCCATACACC 59.329 52.381 0.00 0.00 0.00 4.16
3055 3126 0.738389 CCACAATTCGCCATACACCC 59.262 55.000 0.00 0.00 0.00 4.61
3056 3127 0.738389 CACAATTCGCCATACACCCC 59.262 55.000 0.00 0.00 0.00 4.95
3057 3128 0.623723 ACAATTCGCCATACACCCCT 59.376 50.000 0.00 0.00 0.00 4.79
3058 3129 1.024271 CAATTCGCCATACACCCCTG 58.976 55.000 0.00 0.00 0.00 4.45
3059 3130 0.751643 AATTCGCCATACACCCCTGC 60.752 55.000 0.00 0.00 0.00 4.85
3060 3131 2.624674 ATTCGCCATACACCCCTGCC 62.625 60.000 0.00 0.00 0.00 4.85
3061 3132 4.875713 CGCCATACACCCCTGCCC 62.876 72.222 0.00 0.00 0.00 5.36
3105 3204 1.699083 TCTCATGGGTCAAGAGCACAA 59.301 47.619 0.00 0.00 30.47 3.33
3169 3283 4.954118 TCACCACCGGGCCAGACT 62.954 66.667 6.32 0.00 37.90 3.24
3627 3779 6.265577 GCCCTACAAATGTTATTTAGCACAG 58.734 40.000 0.00 0.00 0.00 3.66
4034 4187 3.250040 ACTGTCCACAAACTTGCGATAAC 59.750 43.478 0.00 0.00 0.00 1.89
4424 4577 5.860941 TGTTTTCTTTTGGGACTTGCATA 57.139 34.783 0.00 0.00 0.00 3.14
4443 4596 7.345422 TGCATATAGGAGAGAGCTATGAATC 57.655 40.000 0.00 0.00 0.00 2.52
5068 5303 4.383173 TGTTCTTTCCCTCGTTTACCTTC 58.617 43.478 0.00 0.00 0.00 3.46
5193 5440 3.368571 GGACAAGCTGGCAGGTGC 61.369 66.667 21.35 12.43 41.14 5.01
5208 5455 1.168714 GGTGCTGGTGATGGAACTTC 58.831 55.000 0.00 0.00 0.00 3.01
5262 5509 6.739112 ACTTTGAGAATGAAAGCTGGTTTAC 58.261 36.000 4.63 0.56 43.40 2.01
5324 5573 8.367911 TGTTCTACTATGTCCATTATGGCTAAG 58.632 37.037 6.33 4.07 37.47 2.18
5363 5612 1.751351 TCGGAGTCTATCTGTTGGCTG 59.249 52.381 0.00 0.00 35.60 4.85
5364 5613 1.478510 CGGAGTCTATCTGTTGGCTGT 59.521 52.381 0.00 0.00 0.00 4.40
5365 5614 2.736719 CGGAGTCTATCTGTTGGCTGTG 60.737 54.545 0.00 0.00 0.00 3.66
5366 5615 2.497675 GGAGTCTATCTGTTGGCTGTGA 59.502 50.000 0.00 0.00 0.00 3.58
5367 5616 3.133721 GGAGTCTATCTGTTGGCTGTGAT 59.866 47.826 0.00 0.00 0.00 3.06
5451 5841 2.176798 TGGTTGGGAAGAGGTCAATGTT 59.823 45.455 0.00 0.00 0.00 2.71
5465 6015 4.955811 TCAATGTTGACTGTGACTACCT 57.044 40.909 0.00 0.00 31.01 3.08
5475 6025 5.163509 TGACTGTGACTACCTGCATAATCTC 60.164 44.000 0.00 0.00 0.00 2.75
5488 6038 6.700960 CCTGCATAATCTCGATCAATAGATCC 59.299 42.308 0.00 0.00 46.42 3.36
5605 6160 6.431198 GAACTTCTCGAAGATAGTGAGAGT 57.569 41.667 13.22 0.00 39.70 3.24
5606 6161 6.827586 AACTTCTCGAAGATAGTGAGAGTT 57.172 37.500 13.22 0.06 39.70 3.01
5607 6162 6.827586 ACTTCTCGAAGATAGTGAGAGTTT 57.172 37.500 13.22 0.00 39.70 2.66
5608 6163 6.848451 ACTTCTCGAAGATAGTGAGAGTTTC 58.152 40.000 13.22 0.00 39.70 2.78
5609 6164 6.431543 ACTTCTCGAAGATAGTGAGAGTTTCA 59.568 38.462 13.22 0.00 39.70 2.69
5610 6165 6.429791 TCTCGAAGATAGTGAGAGTTTCAG 57.570 41.667 0.00 0.00 33.22 3.02
5611 6166 6.174049 TCTCGAAGATAGTGAGAGTTTCAGA 58.826 40.000 0.00 0.00 33.22 3.27
5612 6167 6.315144 TCTCGAAGATAGTGAGAGTTTCAGAG 59.685 42.308 0.00 0.00 33.22 3.35
5745 6300 1.669115 CAGAAGACCAGCACACCCG 60.669 63.158 0.00 0.00 0.00 5.28
5802 6360 0.602638 CTTTACAGGCACGTCAGGCA 60.603 55.000 2.28 0.00 36.37 4.75
5803 6361 0.882927 TTTACAGGCACGTCAGGCAC 60.883 55.000 2.28 0.00 36.37 5.01
5851 6410 2.509336 CCAAGCCTACACGGAGCG 60.509 66.667 0.00 0.00 33.16 5.03
5852 6411 2.571757 CAAGCCTACACGGAGCGA 59.428 61.111 0.00 0.00 33.16 4.93
5853 6412 1.080093 CAAGCCTACACGGAGCGAA 60.080 57.895 0.00 0.00 33.16 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 157 2.223456 CGTGCACATTTTGGTGAGTTCA 60.223 45.455 18.64 0.00 41.32 3.18
361 376 7.122650 AGCTTACCATAACACACTTGCAATATT 59.877 33.333 0.00 0.00 0.00 1.28
648 687 4.129737 TTTCCTCTCGCGCGGGAG 62.130 66.667 44.60 44.60 42.17 4.30
649 688 4.129737 CTTTCCTCTCGCGCGGGA 62.130 66.667 32.87 32.87 0.00 5.14
650 689 4.129737 TCTTTCCTCTCGCGCGGG 62.130 66.667 31.69 29.48 0.00 6.13
651 690 2.580867 CTCTTTCCTCTCGCGCGG 60.581 66.667 31.69 20.60 0.00 6.46
652 691 2.580867 CCTCTTTCCTCTCGCGCG 60.581 66.667 26.76 26.76 0.00 6.86
653 692 1.226831 CTCCTCTTTCCTCTCGCGC 60.227 63.158 0.00 0.00 0.00 6.86
654 693 0.179150 CACTCCTCTTTCCTCTCGCG 60.179 60.000 0.00 0.00 0.00 5.87
655 694 0.459411 GCACTCCTCTTTCCTCTCGC 60.459 60.000 0.00 0.00 0.00 5.03
656 695 0.179150 CGCACTCCTCTTTCCTCTCG 60.179 60.000 0.00 0.00 0.00 4.04
657 696 0.174617 CCGCACTCCTCTTTCCTCTC 59.825 60.000 0.00 0.00 0.00 3.20
658 697 1.261238 CCCGCACTCCTCTTTCCTCT 61.261 60.000 0.00 0.00 0.00 3.69
659 698 1.219393 CCCGCACTCCTCTTTCCTC 59.781 63.158 0.00 0.00 0.00 3.71
660 699 1.128188 AACCCGCACTCCTCTTTCCT 61.128 55.000 0.00 0.00 0.00 3.36
661 700 0.955919 CAACCCGCACTCCTCTTTCC 60.956 60.000 0.00 0.00 0.00 3.13
662 701 0.955919 CCAACCCGCACTCCTCTTTC 60.956 60.000 0.00 0.00 0.00 2.62
663 702 1.073199 CCAACCCGCACTCCTCTTT 59.927 57.895 0.00 0.00 0.00 2.52
664 703 2.750350 CCAACCCGCACTCCTCTT 59.250 61.111 0.00 0.00 0.00 2.85
665 704 3.322466 CCCAACCCGCACTCCTCT 61.322 66.667 0.00 0.00 0.00 3.69
666 705 4.410400 CCCCAACCCGCACTCCTC 62.410 72.222 0.00 0.00 0.00 3.71
685 724 3.458044 AAGGGTTGGGAGGAAAATCTC 57.542 47.619 0.00 0.00 0.00 2.75
686 725 5.552430 AATAAGGGTTGGGAGGAAAATCT 57.448 39.130 0.00 0.00 0.00 2.40
687 726 5.958380 AGAAATAAGGGTTGGGAGGAAAATC 59.042 40.000 0.00 0.00 0.00 2.17
688 727 5.915628 AGAAATAAGGGTTGGGAGGAAAAT 58.084 37.500 0.00 0.00 0.00 1.82
689 728 5.348259 AGAAATAAGGGTTGGGAGGAAAA 57.652 39.130 0.00 0.00 0.00 2.29
690 729 5.313772 TGTAGAAATAAGGGTTGGGAGGAAA 59.686 40.000 0.00 0.00 0.00 3.13
691 730 4.853276 TGTAGAAATAAGGGTTGGGAGGAA 59.147 41.667 0.00 0.00 0.00 3.36
692 731 4.440808 TGTAGAAATAAGGGTTGGGAGGA 58.559 43.478 0.00 0.00 0.00 3.71
693 732 4.385310 CCTGTAGAAATAAGGGTTGGGAGG 60.385 50.000 0.00 0.00 0.00 4.30
694 733 4.227527 ACCTGTAGAAATAAGGGTTGGGAG 59.772 45.833 0.00 0.00 35.24 4.30
695 734 4.180723 ACCTGTAGAAATAAGGGTTGGGA 58.819 43.478 0.00 0.00 35.24 4.37
696 735 4.586306 ACCTGTAGAAATAAGGGTTGGG 57.414 45.455 0.00 0.00 35.24 4.12
697 736 5.897377 CAACCTGTAGAAATAAGGGTTGG 57.103 43.478 12.99 0.00 45.51 3.77
699 738 4.604490 TCCCAACCTGTAGAAATAAGGGTT 59.396 41.667 0.00 0.00 37.51 4.11
700 739 4.180723 TCCCAACCTGTAGAAATAAGGGT 58.819 43.478 0.00 0.00 35.24 4.34
701 740 4.855298 TCCCAACCTGTAGAAATAAGGG 57.145 45.455 0.00 0.00 35.24 3.95
702 741 8.053355 ACTATTTCCCAACCTGTAGAAATAAGG 58.947 37.037 0.00 0.00 39.45 2.69
703 742 9.462606 AACTATTTCCCAACCTGTAGAAATAAG 57.537 33.333 0.00 0.00 39.45 1.73
704 743 9.816787 AAACTATTTCCCAACCTGTAGAAATAA 57.183 29.630 0.00 0.00 39.45 1.40
705 744 9.238368 CAAACTATTTCCCAACCTGTAGAAATA 57.762 33.333 0.00 0.00 39.17 1.40
706 745 7.947890 TCAAACTATTTCCCAACCTGTAGAAAT 59.052 33.333 0.00 0.00 40.86 2.17
707 746 7.291566 TCAAACTATTTCCCAACCTGTAGAAA 58.708 34.615 0.00 0.00 33.13 2.52
708 747 6.843752 TCAAACTATTTCCCAACCTGTAGAA 58.156 36.000 0.00 0.00 0.00 2.10
709 748 6.442541 TCAAACTATTTCCCAACCTGTAGA 57.557 37.500 0.00 0.00 0.00 2.59
710 749 6.151144 CCTTCAAACTATTTCCCAACCTGTAG 59.849 42.308 0.00 0.00 0.00 2.74
711 750 6.007703 CCTTCAAACTATTTCCCAACCTGTA 58.992 40.000 0.00 0.00 0.00 2.74
712 751 4.832823 CCTTCAAACTATTTCCCAACCTGT 59.167 41.667 0.00 0.00 0.00 4.00
713 752 4.832823 ACCTTCAAACTATTTCCCAACCTG 59.167 41.667 0.00 0.00 0.00 4.00
714 753 5.074746 ACCTTCAAACTATTTCCCAACCT 57.925 39.130 0.00 0.00 0.00 3.50
715 754 5.510690 CCAACCTTCAAACTATTTCCCAACC 60.511 44.000 0.00 0.00 0.00 3.77
716 755 5.303333 TCCAACCTTCAAACTATTTCCCAAC 59.697 40.000 0.00 0.00 0.00 3.77
717 756 5.303333 GTCCAACCTTCAAACTATTTCCCAA 59.697 40.000 0.00 0.00 0.00 4.12
718 757 4.830600 GTCCAACCTTCAAACTATTTCCCA 59.169 41.667 0.00 0.00 0.00 4.37
719 758 4.219944 GGTCCAACCTTCAAACTATTTCCC 59.780 45.833 0.00 0.00 34.73 3.97
720 759 5.386958 GGTCCAACCTTCAAACTATTTCC 57.613 43.478 0.00 0.00 34.73 3.13
749 788 5.444176 TCTAAACCCTCAAACCCGTAAAAA 58.556 37.500 0.00 0.00 0.00 1.94
750 789 5.046288 TCTAAACCCTCAAACCCGTAAAA 57.954 39.130 0.00 0.00 0.00 1.52
751 790 4.505390 CCTCTAAACCCTCAAACCCGTAAA 60.505 45.833 0.00 0.00 0.00 2.01
752 791 3.008266 CCTCTAAACCCTCAAACCCGTAA 59.992 47.826 0.00 0.00 0.00 3.18
753 792 2.568509 CCTCTAAACCCTCAAACCCGTA 59.431 50.000 0.00 0.00 0.00 4.02
754 793 1.350019 CCTCTAAACCCTCAAACCCGT 59.650 52.381 0.00 0.00 0.00 5.28
755 794 1.350019 ACCTCTAAACCCTCAAACCCG 59.650 52.381 0.00 0.00 0.00 5.28
756 795 3.074094 AGAACCTCTAAACCCTCAAACCC 59.926 47.826 0.00 0.00 0.00 4.11
757 796 4.368565 AGAACCTCTAAACCCTCAAACC 57.631 45.455 0.00 0.00 0.00 3.27
758 797 6.014413 AGACTAGAACCTCTAAACCCTCAAAC 60.014 42.308 0.00 0.00 0.00 2.93
759 798 6.082707 AGACTAGAACCTCTAAACCCTCAAA 58.917 40.000 0.00 0.00 0.00 2.69
760 799 5.652324 AGACTAGAACCTCTAAACCCTCAA 58.348 41.667 0.00 0.00 0.00 3.02
761 800 5.272405 AGACTAGAACCTCTAAACCCTCA 57.728 43.478 0.00 0.00 0.00 3.86
762 801 6.265876 CCATAGACTAGAACCTCTAAACCCTC 59.734 46.154 0.00 0.00 0.00 4.30
769 808 7.735326 AAAAAGCCATAGACTAGAACCTCTA 57.265 36.000 0.00 0.00 0.00 2.43
814 854 9.831682 AAATCCTCAAACCCCTAAAATTAACTA 57.168 29.630 0.00 0.00 0.00 2.24
815 855 8.593679 CAAATCCTCAAACCCCTAAAATTAACT 58.406 33.333 0.00 0.00 0.00 2.24
820 860 5.721480 CCTCAAATCCTCAAACCCCTAAAAT 59.279 40.000 0.00 0.00 0.00 1.82
825 865 2.041755 GACCTCAAATCCTCAAACCCCT 59.958 50.000 0.00 0.00 0.00 4.79
826 866 2.041755 AGACCTCAAATCCTCAAACCCC 59.958 50.000 0.00 0.00 0.00 4.95
831 871 3.165875 AGTCGAGACCTCAAATCCTCAA 58.834 45.455 0.00 0.00 0.00 3.02
845 885 5.087391 TCTTAGAGCAAGTCTAGTCGAGA 57.913 43.478 0.00 0.00 39.05 4.04
846 886 4.272504 CCTCTTAGAGCAAGTCTAGTCGAG 59.727 50.000 3.26 0.00 39.05 4.04
847 887 4.193090 CCTCTTAGAGCAAGTCTAGTCGA 58.807 47.826 3.26 0.00 39.05 4.20
849 889 3.067601 GCCCTCTTAGAGCAAGTCTAGTC 59.932 52.174 3.26 0.00 39.05 2.59
854 894 1.552792 ACTGCCCTCTTAGAGCAAGTC 59.447 52.381 3.26 0.00 35.79 3.01
855 895 1.277557 CACTGCCCTCTTAGAGCAAGT 59.722 52.381 3.26 4.05 35.79 3.16
856 896 1.406614 CCACTGCCCTCTTAGAGCAAG 60.407 57.143 3.26 3.44 35.79 4.01
857 897 0.615331 CCACTGCCCTCTTAGAGCAA 59.385 55.000 3.26 0.00 35.79 3.91
888 928 2.557056 GGTTTTACTGCTGGGGAGAAAC 59.443 50.000 0.00 0.00 0.00 2.78
915 958 3.058432 GGCGAGAAGGGTTTTTGTACTTC 60.058 47.826 0.00 0.00 39.59 3.01
986 1035 6.031964 TGACAAGAAGGGGTCTATAGAGAT 57.968 41.667 1.64 0.00 34.56 2.75
987 1036 5.193930 TCTGACAAGAAGGGGTCTATAGAGA 59.806 44.000 1.64 0.00 34.56 3.10
1099 1155 2.897972 GGTCGGTAAGCGGTGGAT 59.102 61.111 0.00 0.00 0.00 3.41
1131 1187 4.056125 GGCAGGTTTCTTGCGGCC 62.056 66.667 0.00 0.00 0.00 6.13
1238 1294 1.105759 CAGCATCTAAGGGGCAAGGC 61.106 60.000 0.00 0.00 0.00 4.35
1277 1333 7.418337 AGACCTAACAAGGAACAAACAAAAT 57.582 32.000 0.00 0.00 0.00 1.82
1447 1503 2.574018 CGGCCCGATATCAGGAGCA 61.574 63.158 9.30 0.00 0.00 4.26
1789 1846 1.547372 CTTTTTCGGACGGAGGGAGTA 59.453 52.381 0.00 0.00 0.00 2.59
1790 1847 0.320697 CTTTTTCGGACGGAGGGAGT 59.679 55.000 0.00 0.00 0.00 3.85
1791 1848 1.019805 GCTTTTTCGGACGGAGGGAG 61.020 60.000 0.00 0.00 0.00 4.30
1792 1849 1.004200 GCTTTTTCGGACGGAGGGA 60.004 57.895 0.00 0.00 0.00 4.20
1793 1850 0.605589 AAGCTTTTTCGGACGGAGGG 60.606 55.000 0.00 0.00 0.00 4.30
1794 1851 0.517316 CAAGCTTTTTCGGACGGAGG 59.483 55.000 0.00 0.00 0.00 4.30
1795 1852 1.194772 GACAAGCTTTTTCGGACGGAG 59.805 52.381 0.00 0.00 0.00 4.63
1796 1853 1.223187 GACAAGCTTTTTCGGACGGA 58.777 50.000 0.00 0.00 0.00 4.69
1797 1854 0.237498 GGACAAGCTTTTTCGGACGG 59.763 55.000 0.00 0.00 0.00 4.79
1798 1855 0.237498 GGGACAAGCTTTTTCGGACG 59.763 55.000 0.00 0.00 0.00 4.79
1799 1856 1.314730 TGGGACAAGCTTTTTCGGAC 58.685 50.000 0.00 0.00 31.92 4.79
1800 1857 3.811031 TGGGACAAGCTTTTTCGGA 57.189 47.368 0.00 0.00 31.92 4.55
1812 1869 1.965414 TGAGGGATAAGCTTGGGACA 58.035 50.000 9.86 0.00 0.00 4.02
1813 1870 3.366052 TTTGAGGGATAAGCTTGGGAC 57.634 47.619 9.86 0.00 0.00 4.46
1814 1871 5.725551 TTATTTGAGGGATAAGCTTGGGA 57.274 39.130 9.86 0.00 0.00 4.37
1815 1872 6.324770 ACATTTATTTGAGGGATAAGCTTGGG 59.675 38.462 9.86 0.00 0.00 4.12
1816 1873 7.352079 ACATTTATTTGAGGGATAAGCTTGG 57.648 36.000 9.86 0.00 0.00 3.61
1823 1880 9.944376 GTGCTAGATACATTTATTTGAGGGATA 57.056 33.333 0.00 0.00 0.00 2.59
1824 1881 8.664079 AGTGCTAGATACATTTATTTGAGGGAT 58.336 33.333 0.00 0.00 0.00 3.85
1825 1882 8.034313 AGTGCTAGATACATTTATTTGAGGGA 57.966 34.615 0.00 0.00 0.00 4.20
1826 1883 9.778741 TTAGTGCTAGATACATTTATTTGAGGG 57.221 33.333 0.00 0.00 0.00 4.30
1833 1890 9.547753 CACCAAGTTAGTGCTAGATACATTTAT 57.452 33.333 0.00 0.00 0.00 1.40
1834 1891 8.942338 CACCAAGTTAGTGCTAGATACATTTA 57.058 34.615 0.00 0.00 0.00 1.40
1835 1892 7.849804 CACCAAGTTAGTGCTAGATACATTT 57.150 36.000 0.00 0.00 0.00 2.32
1847 1904 5.986135 GGATGTATCTAGCACCAAGTTAGTG 59.014 44.000 0.00 0.00 38.30 2.74
1848 1905 5.661312 TGGATGTATCTAGCACCAAGTTAGT 59.339 40.000 0.00 0.00 33.25 2.24
1849 1906 6.161855 TGGATGTATCTAGCACCAAGTTAG 57.838 41.667 0.00 0.00 32.79 2.34
1850 1907 6.747414 ATGGATGTATCTAGCACCAAGTTA 57.253 37.500 0.00 0.00 0.00 2.24
1851 1908 5.636903 ATGGATGTATCTAGCACCAAGTT 57.363 39.130 0.00 0.00 0.00 2.66
1852 1909 5.636903 AATGGATGTATCTAGCACCAAGT 57.363 39.130 0.00 0.00 0.00 3.16
1853 1910 6.057533 TCAAATGGATGTATCTAGCACCAAG 58.942 40.000 0.00 0.00 0.00 3.61
1854 1911 6.000246 TCAAATGGATGTATCTAGCACCAA 58.000 37.500 0.00 0.00 0.00 3.67
1855 1912 5.455183 CCTCAAATGGATGTATCTAGCACCA 60.455 44.000 0.00 0.00 0.00 4.17
1856 1913 4.999950 CCTCAAATGGATGTATCTAGCACC 59.000 45.833 0.00 0.00 0.00 5.01
1857 1914 4.999950 CCCTCAAATGGATGTATCTAGCAC 59.000 45.833 0.00 0.00 0.00 4.40
1858 1915 4.907269 TCCCTCAAATGGATGTATCTAGCA 59.093 41.667 0.00 0.00 0.00 3.49
1859 1916 5.221722 TGTCCCTCAAATGGATGTATCTAGC 60.222 44.000 0.00 0.00 33.65 3.42
1860 1917 6.425210 TGTCCCTCAAATGGATGTATCTAG 57.575 41.667 0.00 0.00 33.65 2.43
1861 1918 6.386927 ACTTGTCCCTCAAATGGATGTATCTA 59.613 38.462 0.00 0.00 35.48 1.98
1862 1919 5.192522 ACTTGTCCCTCAAATGGATGTATCT 59.807 40.000 0.00 0.00 35.48 1.98
1863 1920 5.440610 ACTTGTCCCTCAAATGGATGTATC 58.559 41.667 0.00 0.00 35.48 2.24
1864 1921 5.456921 ACTTGTCCCTCAAATGGATGTAT 57.543 39.130 0.00 0.00 35.48 2.29
1865 1922 4.927267 ACTTGTCCCTCAAATGGATGTA 57.073 40.909 0.00 0.00 35.48 2.29
1866 1923 3.814504 ACTTGTCCCTCAAATGGATGT 57.185 42.857 0.00 0.00 35.48 3.06
1867 1924 5.473066 AAAACTTGTCCCTCAAATGGATG 57.527 39.130 0.00 0.00 35.48 3.51
1887 1944 3.446968 TCTACTCCCTCCATCCGAAAAA 58.553 45.455 0.00 0.00 0.00 1.94
1888 1945 3.110293 TCTACTCCCTCCATCCGAAAA 57.890 47.619 0.00 0.00 0.00 2.29
1889 1946 2.840640 TCTACTCCCTCCATCCGAAA 57.159 50.000 0.00 0.00 0.00 3.46
1890 1947 2.598565 CATCTACTCCCTCCATCCGAA 58.401 52.381 0.00 0.00 0.00 4.30
1891 1948 1.203063 CCATCTACTCCCTCCATCCGA 60.203 57.143 0.00 0.00 0.00 4.55
1892 1949 1.261480 CCATCTACTCCCTCCATCCG 58.739 60.000 0.00 0.00 0.00 4.18
1893 1950 2.407340 ACCATCTACTCCCTCCATCC 57.593 55.000 0.00 0.00 0.00 3.51
1894 1951 5.782845 AGATTTACCATCTACTCCCTCCATC 59.217 44.000 0.00 0.00 0.00 3.51
1895 1952 5.731924 AGATTTACCATCTACTCCCTCCAT 58.268 41.667 0.00 0.00 0.00 3.41
1896 1953 5.148502 GAGATTTACCATCTACTCCCTCCA 58.851 45.833 0.00 0.00 0.00 3.86
1897 1954 5.011227 GTGAGATTTACCATCTACTCCCTCC 59.989 48.000 0.00 0.00 0.00 4.30
1898 1955 5.598830 TGTGAGATTTACCATCTACTCCCTC 59.401 44.000 0.00 0.00 0.00 4.30
1899 1956 5.529289 TGTGAGATTTACCATCTACTCCCT 58.471 41.667 0.00 0.00 0.00 4.20
1900 1957 5.871396 TGTGAGATTTACCATCTACTCCC 57.129 43.478 0.00 0.00 0.00 4.30
1901 1958 8.738645 AATTTGTGAGATTTACCATCTACTCC 57.261 34.615 0.00 0.00 0.00 3.85
1970 2032 7.716123 CCCATTTACATGAAATTATGGCATTGT 59.284 33.333 4.78 4.52 35.45 2.71
1995 2057 1.379527 CCCGAACAGGAAAGCATACC 58.620 55.000 0.00 0.00 45.00 2.73
2056 2126 3.939066 AGTACCTTGGTTGACAGTATGC 58.061 45.455 0.00 0.00 42.53 3.14
2224 2294 6.948777 CGATTTCTAAACTTACGCAAGAGTTC 59.051 38.462 1.47 0.00 43.62 3.01
2235 2305 7.001099 AGTTGAGGGACGATTTCTAAACTTA 57.999 36.000 0.00 0.00 0.00 2.24
2309 2379 1.276989 CCTTAAGCGTTACCAGGGACA 59.723 52.381 0.00 0.00 0.00 4.02
2381 2451 3.823873 AGTCTGGACCGAATATAGCTGAG 59.176 47.826 0.00 0.00 0.00 3.35
2514 2585 5.106157 ACAAGGTCTGAACAAAGAAAGTGTG 60.106 40.000 0.00 0.00 0.00 3.82
3019 3090 0.250467 TGGAGCCAGTTCAAGCAGAC 60.250 55.000 0.00 0.00 0.00 3.51
3040 3111 0.751643 GCAGGGGTGTATGGCGAATT 60.752 55.000 0.00 0.00 0.00 2.17
3041 3112 1.152963 GCAGGGGTGTATGGCGAAT 60.153 57.895 0.00 0.00 0.00 3.34
3042 3113 2.270850 GCAGGGGTGTATGGCGAA 59.729 61.111 0.00 0.00 0.00 4.70
3043 3114 3.792736 GGCAGGGGTGTATGGCGA 61.793 66.667 0.00 0.00 31.92 5.54
3044 3115 4.875713 GGGCAGGGGTGTATGGCG 62.876 72.222 0.00 0.00 42.55 5.69
3045 3116 3.295386 TTGGGCAGGGGTGTATGGC 62.295 63.158 0.00 0.00 41.01 4.40
3046 3117 1.076777 CTTGGGCAGGGGTGTATGG 60.077 63.158 0.00 0.00 0.00 2.74
3047 3118 0.394352 GACTTGGGCAGGGGTGTATG 60.394 60.000 0.00 0.00 0.00 2.39
3048 3119 1.910580 CGACTTGGGCAGGGGTGTAT 61.911 60.000 0.00 0.00 0.00 2.29
3049 3120 2.589157 CGACTTGGGCAGGGGTGTA 61.589 63.158 0.00 0.00 0.00 2.90
3050 3121 3.953775 CGACTTGGGCAGGGGTGT 61.954 66.667 0.00 0.00 0.00 4.16
3056 3127 3.726517 CAACGGCGACTTGGGCAG 61.727 66.667 16.62 0.00 0.00 4.85
3169 3283 3.202001 GCGATTTAGGCAGCGGCA 61.202 61.111 11.88 0.00 43.71 5.69
3496 3648 5.182169 TGTCTATTTTTATCCCACGGGTT 57.818 39.130 1.07 0.00 36.47 4.11
3810 3962 5.024118 ACTTACAGGTAAGCACAGACCTAT 58.976 41.667 16.89 0.00 44.54 2.57
3928 4080 7.423844 TGGACTACATACTGACTGAAATGAT 57.576 36.000 0.00 0.00 0.00 2.45
3967 4119 6.202954 CCCTCCGTTCACAAATATAAGATGTC 59.797 42.308 0.00 0.00 0.00 3.06
4424 4577 9.940974 ATCATAAGATTCATAGCTCTCTCCTAT 57.059 33.333 0.00 0.00 0.00 2.57
4739 4974 2.232941 ACGAAAGGGCGTAAGAGAATCA 59.767 45.455 0.00 0.00 43.61 2.57
4776 5011 5.337491 GGAAACACAAGGGAAATGCATATGT 60.337 40.000 0.00 0.00 0.00 2.29
4777 5012 5.111293 GGAAACACAAGGGAAATGCATATG 58.889 41.667 0.00 0.00 0.00 1.78
5056 5291 3.183775 CGAAGTTGTGGAAGGTAAACGAG 59.816 47.826 0.00 0.00 0.00 4.18
5068 5303 3.313012 TCACTGGTATCGAAGTTGTGG 57.687 47.619 0.00 0.00 0.00 4.17
5193 5440 4.024556 GCATAATCGAAGTTCCATCACCAG 60.025 45.833 0.00 0.00 0.00 4.00
5208 5455 4.024302 TCGTGACTACCTACAGCATAATCG 60.024 45.833 0.00 0.00 0.00 3.34
5262 5509 2.417924 GCCATACTGGTCAGACTCACAG 60.418 54.545 4.84 2.24 40.46 3.66
5324 5573 3.190874 CGACAGATGGCTAGGAAAGAAC 58.809 50.000 0.00 0.00 0.00 3.01
5393 5648 4.885325 AGTCCACGAAAACATACCAAAAGT 59.115 37.500 0.00 0.00 0.00 2.66
5451 5841 4.711846 AGATTATGCAGGTAGTCACAGTCA 59.288 41.667 0.00 0.00 0.00 3.41
5454 5844 4.036852 TCGAGATTATGCAGGTAGTCACAG 59.963 45.833 0.00 0.00 0.00 3.66
5455 5845 3.951680 TCGAGATTATGCAGGTAGTCACA 59.048 43.478 0.00 0.00 0.00 3.58
5456 5846 4.569761 TCGAGATTATGCAGGTAGTCAC 57.430 45.455 0.00 0.00 0.00 3.67
5458 5848 5.378292 TGATCGAGATTATGCAGGTAGTC 57.622 43.478 0.00 0.00 0.00 2.59
5459 5849 5.791336 TTGATCGAGATTATGCAGGTAGT 57.209 39.130 0.00 0.00 0.00 2.73
5460 5850 7.766283 TCTATTGATCGAGATTATGCAGGTAG 58.234 38.462 0.00 0.00 0.00 3.18
5488 6038 3.501950 GAATGCCGTTTCTTAGCAAAGG 58.498 45.455 0.00 0.00 40.46 3.11
5605 6160 4.776349 TGTAGTTGGCTTTCACTCTGAAA 58.224 39.130 0.00 0.00 43.37 2.69
5606 6161 4.415881 TGTAGTTGGCTTTCACTCTGAA 57.584 40.909 0.00 0.00 34.03 3.02
5607 6162 4.380531 CTTGTAGTTGGCTTTCACTCTGA 58.619 43.478 0.00 0.00 0.00 3.27
5608 6163 3.058639 GCTTGTAGTTGGCTTTCACTCTG 60.059 47.826 0.00 0.00 0.00 3.35
5609 6164 3.142174 GCTTGTAGTTGGCTTTCACTCT 58.858 45.455 0.00 0.00 0.00 3.24
5610 6165 2.878406 TGCTTGTAGTTGGCTTTCACTC 59.122 45.455 0.00 0.00 0.00 3.51
5611 6166 2.930950 TGCTTGTAGTTGGCTTTCACT 58.069 42.857 0.00 0.00 0.00 3.41
5612 6167 3.923017 ATGCTTGTAGTTGGCTTTCAC 57.077 42.857 0.00 0.00 0.00 3.18
5745 6300 1.687494 GCGAGTTGATGCGTGGAGTC 61.687 60.000 0.00 0.00 0.00 3.36
5866 6425 2.040178 CAAGCGGGGGAACTAGATAGT 58.960 52.381 0.00 0.00 38.39 2.12


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

AutoCloner maintained by Alex Coulton.