Multiple sequence alignment - TraesCS3B01G269200

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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 TraesCS3B01G269200 chr3B 100.000 3675 0 0 468 4142 433757787 433761461 0.000000e+00 6787.0
1 TraesCS3B01G269200 chr3B 94.081 321 19 0 468 788 785308772 785308452 4.810000e-134 488.0
2 TraesCS3B01G269200 chr3B 92.835 321 20 2 470 790 52620908 52621225 2.920000e-126 462.0
3 TraesCS3B01G269200 chr3B 100.000 193 0 0 1 193 433757320 433757512 1.420000e-94 357.0
4 TraesCS3B01G269200 chr3B 97.315 149 4 0 1 149 221817799 221817651 1.910000e-63 254.0
5 TraesCS3B01G269200 chr3B 96.644 149 5 0 1 149 52620608 52620756 8.890000e-62 248.0
6 TraesCS3B01G269200 chr3B 96.644 149 5 0 1 149 53036731 53036583 8.890000e-62 248.0
7 TraesCS3B01G269200 chr3D 94.279 1276 51 10 2165 3435 335207554 335208812 0.000000e+00 1932.0
8 TraesCS3B01G269200 chr3D 86.335 1105 79 34 825 1899 335206256 335207318 0.000000e+00 1138.0
9 TraesCS3B01G269200 chr3D 83.774 265 19 12 1899 2161 335207275 335207517 3.220000e-56 230.0
10 TraesCS3B01G269200 chr3D 98.113 53 1 0 141 193 31843529 31843477 4.410000e-15 93.5
11 TraesCS3B01G269200 chr3A 93.907 1231 49 13 2199 3427 453307474 453308680 0.000000e+00 1834.0
12 TraesCS3B01G269200 chr3A 98.738 713 9 0 3430 4142 740898869 740898157 0.000000e+00 1267.0
13 TraesCS3B01G269200 chr3A 86.141 1104 69 34 825 1899 453306199 453307247 0.000000e+00 1114.0
14 TraesCS3B01G269200 chr3A 91.768 328 27 0 468 795 502521145 502520818 1.360000e-124 457.0
15 TraesCS3B01G269200 chr3A 82.014 278 25 17 1899 2165 453307204 453307467 3.240000e-51 213.0
16 TraesCS3B01G269200 chr2B 98.878 713 8 0 3430 4142 16022971 16022259 0.000000e+00 1273.0
17 TraesCS3B01G269200 chr2B 95.410 305 14 0 484 788 51101472 51101776 1.730000e-133 486.0
18 TraesCS3B01G269200 chr5A 98.455 712 10 1 3431 4142 659856259 659855549 0.000000e+00 1253.0
19 TraesCS3B01G269200 chr6B 98.317 713 12 0 3430 4142 644824836 644825548 0.000000e+00 1251.0
20 TraesCS3B01G269200 chr6B 94.081 321 16 1 468 788 422971353 422971670 6.230000e-133 484.0
21 TraesCS3B01G269200 chr6B 96.644 149 5 0 1 149 701896391 701896243 8.890000e-62 248.0
22 TraesCS3B01G269200 chr1A 96.643 715 23 1 3429 4142 501061888 501061174 0.000000e+00 1186.0
23 TraesCS3B01G269200 chr1A 86.792 212 9 5 1 193 312743253 312743464 6.970000e-53 219.0
24 TraesCS3B01G269200 chr1A 98.113 53 1 0 141 193 484339885 484339833 4.410000e-15 93.5
25 TraesCS3B01G269200 chr7A 90.331 724 58 6 3430 4142 714028651 714027929 0.000000e+00 939.0
26 TraesCS3B01G269200 chr7A 89.227 724 65 7 3430 4142 603505709 603506430 0.000000e+00 893.0
27 TraesCS3B01G269200 chr2A 90.291 721 58 7 3430 4142 17875223 17875939 0.000000e+00 933.0
28 TraesCS3B01G269200 chr4B 89.088 724 64 8 3430 4142 87429585 87428866 0.000000e+00 885.0
29 TraesCS3B01G269200 chr4B 94.393 321 18 0 468 788 516868921 516868601 1.030000e-135 494.0
30 TraesCS3B01G269200 chr4B 93.210 324 19 1 468 788 17020417 17020094 1.350000e-129 473.0
31 TraesCS3B01G269200 chr4B 90.576 191 18 0 1 191 602657129 602657319 1.910000e-63 254.0
32 TraesCS3B01G269200 chr4B 100.000 53 0 0 141 193 89004403 89004455 9.480000e-17 99.0
33 TraesCS3B01G269200 chr7B 95.298 319 15 0 473 791 735949085 735948767 1.330000e-139 507.0
34 TraesCS3B01G269200 chr7B 96.644 149 5 0 1 149 730822983 730823131 8.890000e-62 248.0
35 TraesCS3B01G269200 chr7B 96.622 148 5 0 2 149 612975478 612975331 3.200000e-61 246.0
36 TraesCS3B01G269200 chr1B 93.189 323 17 2 468 790 1744329 1744646 1.740000e-128 470.0
37 TraesCS3B01G269200 chr1B 96.622 148 5 0 2 149 1744030 1744177 3.200000e-61 246.0
38 TraesCS3B01G269200 chr5B 97.315 149 3 1 1 149 711855663 711855516 6.870000e-63 252.0
39 TraesCS3B01G269200 chr5B 79.245 212 38 6 2391 2599 670128964 670129172 4.320000e-30 143.0
40 TraesCS3B01G269200 chr4A 79.343 213 36 5 2391 2599 641382996 641382788 4.320000e-30 143.0
41 TraesCS3B01G269200 chr6A 100.000 53 0 0 141 193 591408496 591408444 9.480000e-17 99.0
42 TraesCS3B01G269200 chr6A 98.113 53 1 0 141 193 497992993 497993045 4.410000e-15 93.5
43 TraesCS3B01G269200 chr6A 98.113 53 1 0 141 193 584520804 584520752 4.410000e-15 93.5
44 TraesCS3B01G269200 chr6A 98.113 53 1 0 141 193 595585191 595585243 4.410000e-15 93.5


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 TraesCS3B01G269200 chr3B 433757320 433761461 4141 False 3572.000000 6787 100.000000 1 4142 2 chr3B.!!$F2 4141
1 TraesCS3B01G269200 chr3B 52620608 52621225 617 False 355.000000 462 94.739500 1 790 2 chr3B.!!$F1 789
2 TraesCS3B01G269200 chr3D 335206256 335208812 2556 False 1100.000000 1932 88.129333 825 3435 3 chr3D.!!$F1 2610
3 TraesCS3B01G269200 chr3A 740898157 740898869 712 True 1267.000000 1267 98.738000 3430 4142 1 chr3A.!!$R2 712
4 TraesCS3B01G269200 chr3A 453306199 453308680 2481 False 1053.666667 1834 87.354000 825 3427 3 chr3A.!!$F1 2602
5 TraesCS3B01G269200 chr2B 16022259 16022971 712 True 1273.000000 1273 98.878000 3430 4142 1 chr2B.!!$R1 712
6 TraesCS3B01G269200 chr5A 659855549 659856259 710 True 1253.000000 1253 98.455000 3431 4142 1 chr5A.!!$R1 711
7 TraesCS3B01G269200 chr6B 644824836 644825548 712 False 1251.000000 1251 98.317000 3430 4142 1 chr6B.!!$F2 712
8 TraesCS3B01G269200 chr1A 501061174 501061888 714 True 1186.000000 1186 96.643000 3429 4142 1 chr1A.!!$R2 713
9 TraesCS3B01G269200 chr7A 714027929 714028651 722 True 939.000000 939 90.331000 3430 4142 1 chr7A.!!$R1 712
10 TraesCS3B01G269200 chr7A 603505709 603506430 721 False 893.000000 893 89.227000 3430 4142 1 chr7A.!!$F1 712
11 TraesCS3B01G269200 chr2A 17875223 17875939 716 False 933.000000 933 90.291000 3430 4142 1 chr2A.!!$F1 712
12 TraesCS3B01G269200 chr4B 87428866 87429585 719 True 885.000000 885 89.088000 3430 4142 1 chr4B.!!$R2 712
13 TraesCS3B01G269200 chr1B 1744030 1744646 616 False 358.000000 470 94.905500 2 790 2 chr1B.!!$F1 788

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
676 729 0.248743 CGCGCCCAACTCGTTATAGA 60.249 55.0 0.00 0.0 0.0 1.98 F
809 862 0.323360 ACCCAACAATCCATCCCGTG 60.323 55.0 0.00 0.0 0.0 4.94 F
906 962 0.456653 AATGGCGCGACAATGAAAGC 60.457 50.0 23.46 0.0 0.0 3.51 F
2299 2439 0.038599 TGGGTCGTGCTCCTACTGTA 59.961 55.0 0.00 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2126 2233 0.103208 GTGCCTCGGTGGAGACATAG 59.897 60.0 0.00 0.0 46.14 2.23 R
2167 2307 0.467844 TGCACACTCCAATGCCACTT 60.468 50.0 0.00 0.0 41.33 3.16 R
2655 2800 0.523072 CCTGGTTGTTGGCGATGAAG 59.477 55.0 0.00 0.0 0.00 3.02 R
4084 4241 0.378962 TGTTACACACTTTGCGCACC 59.621 50.0 11.12 0.0 0.00 5.01 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
487 540 2.732094 GTCGCGGCTGTACAACGT 60.732 61.111 17.54 0.00 0.00 3.99
676 729 0.248743 CGCGCCCAACTCGTTATAGA 60.249 55.000 0.00 0.00 0.00 1.98
677 730 1.488527 GCGCCCAACTCGTTATAGAG 58.511 55.000 0.00 0.00 43.56 2.43
686 739 2.657296 GTTATAGAGCGCGCGCCA 60.657 61.111 46.98 33.61 43.17 5.69
692 745 1.084935 TAGAGCGCGCGCCATTTTTA 61.085 50.000 46.98 26.86 43.17 1.52
790 843 2.677902 CGGCTGTTGGAGATGCTCTAAA 60.678 50.000 0.00 0.00 33.06 1.85
791 844 2.680339 GGCTGTTGGAGATGCTCTAAAC 59.320 50.000 0.00 0.00 33.06 2.01
792 845 2.680339 GCTGTTGGAGATGCTCTAAACC 59.320 50.000 0.00 0.00 33.06 3.27
793 846 3.274288 CTGTTGGAGATGCTCTAAACCC 58.726 50.000 0.00 0.00 33.06 4.11
794 847 2.642311 TGTTGGAGATGCTCTAAACCCA 59.358 45.455 0.00 0.00 33.06 4.51
795 848 3.073798 TGTTGGAGATGCTCTAAACCCAA 59.926 43.478 0.00 0.00 33.06 4.12
796 849 3.350219 TGGAGATGCTCTAAACCCAAC 57.650 47.619 0.00 0.00 0.00 3.77
797 850 2.642311 TGGAGATGCTCTAAACCCAACA 59.358 45.455 0.00 0.00 0.00 3.33
798 851 3.073798 TGGAGATGCTCTAAACCCAACAA 59.926 43.478 0.00 0.00 0.00 2.83
799 852 4.263905 TGGAGATGCTCTAAACCCAACAAT 60.264 41.667 0.00 0.00 0.00 2.71
800 853 4.336713 GGAGATGCTCTAAACCCAACAATC 59.663 45.833 0.00 0.00 0.00 2.67
801 854 4.273318 AGATGCTCTAAACCCAACAATCC 58.727 43.478 0.00 0.00 0.00 3.01
802 855 3.517296 TGCTCTAAACCCAACAATCCA 57.483 42.857 0.00 0.00 0.00 3.41
803 856 4.046286 TGCTCTAAACCCAACAATCCAT 57.954 40.909 0.00 0.00 0.00 3.41
804 857 4.016444 TGCTCTAAACCCAACAATCCATC 58.984 43.478 0.00 0.00 0.00 3.51
805 858 3.381590 GCTCTAAACCCAACAATCCATCC 59.618 47.826 0.00 0.00 0.00 3.51
806 859 3.954258 CTCTAAACCCAACAATCCATCCC 59.046 47.826 0.00 0.00 0.00 3.85
807 860 1.555967 AAACCCAACAATCCATCCCG 58.444 50.000 0.00 0.00 0.00 5.14
808 861 0.407918 AACCCAACAATCCATCCCGT 59.592 50.000 0.00 0.00 0.00 5.28
809 862 0.323360 ACCCAACAATCCATCCCGTG 60.323 55.000 0.00 0.00 0.00 4.94
810 863 1.666209 CCCAACAATCCATCCCGTGC 61.666 60.000 0.00 0.00 0.00 5.34
811 864 0.964860 CCAACAATCCATCCCGTGCA 60.965 55.000 0.00 0.00 0.00 4.57
812 865 1.105457 CAACAATCCATCCCGTGCAT 58.895 50.000 0.00 0.00 0.00 3.96
813 866 1.066002 CAACAATCCATCCCGTGCATC 59.934 52.381 0.00 0.00 0.00 3.91
814 867 0.548031 ACAATCCATCCCGTGCATCT 59.452 50.000 0.00 0.00 0.00 2.90
815 868 1.768275 ACAATCCATCCCGTGCATCTA 59.232 47.619 0.00 0.00 0.00 1.98
816 869 2.373169 ACAATCCATCCCGTGCATCTAT 59.627 45.455 0.00 0.00 0.00 1.98
817 870 2.745821 CAATCCATCCCGTGCATCTATG 59.254 50.000 0.00 0.00 0.00 2.23
818 871 1.423584 TCCATCCCGTGCATCTATGT 58.576 50.000 0.00 0.00 0.00 2.29
819 872 1.070601 TCCATCCCGTGCATCTATGTG 59.929 52.381 0.00 0.00 0.00 3.21
820 873 0.870393 CATCCCGTGCATCTATGTGC 59.130 55.000 0.00 0.00 45.25 4.57
835 888 6.154203 TCTATGTGCACAACAAAATGGAAA 57.846 33.333 25.72 0.00 43.61 3.13
843 896 5.331098 CACAACAAAATGGAAAACCAAAGC 58.669 37.500 0.00 0.00 0.00 3.51
863 916 1.376466 CCCCTGACAAGTGGGTCTG 59.624 63.158 0.00 0.00 41.82 3.51
879 935 1.807742 GTCTGCGTCTACAGTCTGAGT 59.192 52.381 6.91 0.00 38.84 3.41
898 954 1.195900 GTTTTACTCAATGGCGCGACA 59.804 47.619 21.39 21.39 0.00 4.35
899 955 1.514003 TTTACTCAATGGCGCGACAA 58.486 45.000 23.46 0.00 0.00 3.18
905 961 1.135717 TCAATGGCGCGACAATGAAAG 60.136 47.619 29.69 10.96 27.95 2.62
906 962 0.456653 AATGGCGCGACAATGAAAGC 60.457 50.000 23.46 0.00 0.00 3.51
907 963 1.308069 ATGGCGCGACAATGAAAGCT 61.308 50.000 23.46 0.00 0.00 3.74
917 985 5.385617 CGACAATGAAAGCTTTTGGTCTAG 58.614 41.667 14.05 3.13 0.00 2.43
951 1019 2.106938 CTTCAGCTCGCCGCCATA 59.893 61.111 0.00 0.00 40.39 2.74
1036 1116 4.386413 CACCAGTTGCTCTGTCCC 57.614 61.111 8.23 0.00 42.19 4.46
1047 1127 2.125753 CTGTCCCTGCTCGTGCTC 60.126 66.667 11.19 0.00 40.48 4.26
1152 1232 2.053865 CCCCTACTACGCCAACGGA 61.054 63.158 0.00 0.00 46.04 4.69
1370 1450 8.534778 CATTTTGCTCAACTTTTCTCTTTGTAC 58.465 33.333 0.00 0.00 0.00 2.90
1371 1451 6.751514 TTGCTCAACTTTTCTCTTTGTACA 57.248 33.333 0.00 0.00 0.00 2.90
1372 1452 6.363577 TGCTCAACTTTTCTCTTTGTACAG 57.636 37.500 0.00 0.00 0.00 2.74
1374 1454 6.374333 TGCTCAACTTTTCTCTTTGTACAGTT 59.626 34.615 0.00 0.00 0.00 3.16
1375 1455 7.094377 TGCTCAACTTTTCTCTTTGTACAGTTT 60.094 33.333 0.00 0.00 0.00 2.66
1376 1456 7.755373 GCTCAACTTTTCTCTTTGTACAGTTTT 59.245 33.333 0.00 0.00 0.00 2.43
1377 1457 9.626045 CTCAACTTTTCTCTTTGTACAGTTTTT 57.374 29.630 0.00 0.00 0.00 1.94
1404 1484 6.613755 TTTTGCGCTAACTTTTCTCTTAGT 57.386 33.333 9.73 0.00 0.00 2.24
1405 1485 7.718272 TTTTGCGCTAACTTTTCTCTTAGTA 57.282 32.000 9.73 0.00 0.00 1.82
1406 1486 6.946229 TTGCGCTAACTTTTCTCTTAGTAG 57.054 37.500 9.73 0.00 0.00 2.57
1407 1487 6.022163 TGCGCTAACTTTTCTCTTAGTAGT 57.978 37.500 9.73 0.00 0.00 2.73
1408 1488 6.453092 TGCGCTAACTTTTCTCTTAGTAGTT 58.547 36.000 9.73 0.00 33.89 2.24
1409 1489 6.927381 TGCGCTAACTTTTCTCTTAGTAGTTT 59.073 34.615 9.73 0.00 31.94 2.66
1410 1490 7.440255 TGCGCTAACTTTTCTCTTAGTAGTTTT 59.560 33.333 9.73 0.00 31.94 2.43
1411 1491 8.281194 GCGCTAACTTTTCTCTTAGTAGTTTTT 58.719 33.333 0.00 0.00 31.94 1.94
1447 1527 6.159293 GGTTTCTTGGATCATTTGGTTCTTC 58.841 40.000 0.00 0.00 0.00 2.87
1448 1528 6.239289 GGTTTCTTGGATCATTTGGTTCTTCA 60.239 38.462 0.00 0.00 0.00 3.02
1449 1529 6.579666 TTCTTGGATCATTTGGTTCTTCAG 57.420 37.500 0.00 0.00 0.00 3.02
1451 1531 3.091545 TGGATCATTTGGTTCTTCAGCC 58.908 45.455 0.00 0.00 0.00 4.85
1452 1532 3.091545 GGATCATTTGGTTCTTCAGCCA 58.908 45.455 0.00 0.00 0.00 4.75
1454 1534 2.238521 TCATTTGGTTCTTCAGCCACC 58.761 47.619 0.00 0.00 34.02 4.61
1463 1549 6.194235 TGGTTCTTCAGCCACCATATAATTT 58.806 36.000 0.00 0.00 35.57 1.82
1465 1551 6.321181 GGTTCTTCAGCCACCATATAATTTGA 59.679 38.462 0.00 0.00 0.00 2.69
1467 1553 5.827797 TCTTCAGCCACCATATAATTTGACC 59.172 40.000 0.00 0.00 0.00 4.02
1471 1557 4.834496 AGCCACCATATAATTTGACCATGG 59.166 41.667 11.19 11.19 41.60 3.66
1489 1575 2.408565 TGGTTCTGTTTCCCTGAGAGT 58.591 47.619 0.00 0.00 0.00 3.24
1491 1577 3.971305 TGGTTCTGTTTCCCTGAGAGTAA 59.029 43.478 0.00 0.00 0.00 2.24
1499 1585 7.013274 TCTGTTTCCCTGAGAGTAATTTTGTTG 59.987 37.037 0.00 0.00 0.00 3.33
1500 1586 6.605594 TGTTTCCCTGAGAGTAATTTTGTTGT 59.394 34.615 0.00 0.00 0.00 3.32
1501 1587 6.633500 TTCCCTGAGAGTAATTTTGTTGTG 57.367 37.500 0.00 0.00 0.00 3.33
1502 1588 5.070001 TCCCTGAGAGTAATTTTGTTGTGG 58.930 41.667 0.00 0.00 0.00 4.17
1503 1589 4.827284 CCCTGAGAGTAATTTTGTTGTGGT 59.173 41.667 0.00 0.00 0.00 4.16
1540 1630 1.337118 GCAGGGGTTGGATTTTGTGA 58.663 50.000 0.00 0.00 0.00 3.58
1596 1686 4.357918 ACTGAGCCTTGTGAACAACTAT 57.642 40.909 0.00 0.00 0.00 2.12
1623 1713 3.418684 TTTGGAGGGAAGAAGCAGTAC 57.581 47.619 0.00 0.00 0.00 2.73
1727 1823 6.248433 ACAAGAACCATGTCAAGGTATGAAT 58.752 36.000 0.00 0.00 40.50 2.57
1780 1876 5.415701 TCTTGCAAGCCTTTACCATCTTTAG 59.584 40.000 21.99 0.00 0.00 1.85
1782 1878 5.811190 TGCAAGCCTTTACCATCTTTAGTA 58.189 37.500 0.00 0.00 0.00 1.82
1783 1879 6.423182 TGCAAGCCTTTACCATCTTTAGTAT 58.577 36.000 0.00 0.00 0.00 2.12
1784 1880 7.570132 TGCAAGCCTTTACCATCTTTAGTATA 58.430 34.615 0.00 0.00 0.00 1.47
1785 1881 7.715249 TGCAAGCCTTTACCATCTTTAGTATAG 59.285 37.037 0.00 0.00 0.00 1.31
1786 1882 7.715686 GCAAGCCTTTACCATCTTTAGTATAGT 59.284 37.037 0.00 0.00 0.00 2.12
1787 1883 9.614792 CAAGCCTTTACCATCTTTAGTATAGTT 57.385 33.333 0.00 0.00 0.00 2.24
1821 1917 5.049405 CCATTATTTGGTCTGTAATCTCCGC 60.049 44.000 0.00 0.00 40.99 5.54
1823 1919 2.961526 TTGGTCTGTAATCTCCGCTC 57.038 50.000 0.00 0.00 0.00 5.03
1827 1923 2.584236 GTCTGTAATCTCCGCTCCCTA 58.416 52.381 0.00 0.00 0.00 3.53
1828 1924 2.293955 GTCTGTAATCTCCGCTCCCTAC 59.706 54.545 0.00 0.00 0.00 3.18
1833 1929 1.997256 ATCTCCGCTCCCTACCTCGT 61.997 60.000 0.00 0.00 0.00 4.18
1839 1935 0.460459 GCTCCCTACCTCGTTGAAGC 60.460 60.000 0.00 0.00 0.00 3.86
1864 1960 8.862550 CAAAGATGCTTAGTTTTCTTCTTGTT 57.137 30.769 0.00 0.00 0.00 2.83
1865 1961 9.950680 CAAAGATGCTTAGTTTTCTTCTTGTTA 57.049 29.630 0.00 0.00 0.00 2.41
1871 1967 9.048446 TGCTTAGTTTTCTTCTTGTTATTACGT 57.952 29.630 0.00 0.00 0.00 3.57
1872 1968 9.314501 GCTTAGTTTTCTTCTTGTTATTACGTG 57.685 33.333 0.00 0.00 0.00 4.49
1873 1969 9.807386 CTTAGTTTTCTTCTTGTTATTACGTGG 57.193 33.333 0.00 0.00 0.00 4.94
1874 1970 7.198306 AGTTTTCTTCTTGTTATTACGTGGG 57.802 36.000 0.00 0.00 0.00 4.61
1875 1971 6.993902 AGTTTTCTTCTTGTTATTACGTGGGA 59.006 34.615 0.00 0.00 0.00 4.37
1876 1972 7.172703 AGTTTTCTTCTTGTTATTACGTGGGAG 59.827 37.037 0.00 0.00 0.00 4.30
1877 1973 5.988310 TCTTCTTGTTATTACGTGGGAGA 57.012 39.130 0.00 0.00 0.00 3.71
1878 1974 6.349243 TCTTCTTGTTATTACGTGGGAGAA 57.651 37.500 0.00 0.00 0.00 2.87
1879 1975 6.761312 TCTTCTTGTTATTACGTGGGAGAAA 58.239 36.000 0.00 0.00 0.00 2.52
1880 1976 7.391620 TCTTCTTGTTATTACGTGGGAGAAAT 58.608 34.615 0.00 0.00 0.00 2.17
1881 1977 7.881232 TCTTCTTGTTATTACGTGGGAGAAATT 59.119 33.333 0.00 0.00 0.00 1.82
1882 1978 9.158233 CTTCTTGTTATTACGTGGGAGAAATTA 57.842 33.333 0.00 0.00 0.00 1.40
1883 1979 9.675464 TTCTTGTTATTACGTGGGAGAAATTAT 57.325 29.630 0.00 0.00 0.00 1.28
1893 1989 8.575649 ACGTGGGAGAAATTATAAGATTTTGT 57.424 30.769 0.00 0.00 29.75 2.83
1894 1990 8.458843 ACGTGGGAGAAATTATAAGATTTTGTG 58.541 33.333 0.00 0.00 29.75 3.33
1895 1991 8.673711 CGTGGGAGAAATTATAAGATTTTGTGA 58.326 33.333 0.00 0.00 29.75 3.58
2043 2149 5.242795 CCTTCCGGGGATAAATATTCACT 57.757 43.478 0.00 0.00 0.00 3.41
2045 2151 6.775708 CCTTCCGGGGATAAATATTCACTAA 58.224 40.000 0.00 0.00 0.00 2.24
2046 2152 7.228590 CCTTCCGGGGATAAATATTCACTAAA 58.771 38.462 0.00 0.00 0.00 1.85
2048 2154 7.383156 TCCGGGGATAAATATTCACTAAAGT 57.617 36.000 0.00 0.00 0.00 2.66
2049 2155 8.495160 TCCGGGGATAAATATTCACTAAAGTA 57.505 34.615 0.00 0.00 0.00 2.24
2050 2156 9.108111 TCCGGGGATAAATATTCACTAAAGTAT 57.892 33.333 0.00 0.00 0.00 2.12
2060 2166 9.561069 AATATTCACTAAAGTATAGCAAGGTGG 57.439 33.333 0.00 0.00 0.00 4.61
2061 2167 4.766375 TCACTAAAGTATAGCAAGGTGGC 58.234 43.478 0.00 0.00 0.00 5.01
2062 2168 4.224147 TCACTAAAGTATAGCAAGGTGGCA 59.776 41.667 0.00 0.00 35.83 4.92
2063 2169 5.104527 TCACTAAAGTATAGCAAGGTGGCAT 60.105 40.000 0.00 0.00 35.83 4.40
2064 2170 5.008019 CACTAAAGTATAGCAAGGTGGCATG 59.992 44.000 0.00 0.00 35.83 4.06
2065 2171 1.972872 AGTATAGCAAGGTGGCATGC 58.027 50.000 9.90 9.90 42.87 4.06
2075 2181 2.103042 GTGGCATGCTCGAGGTCAC 61.103 63.158 18.92 11.69 0.00 3.67
2083 2189 1.278238 GCTCGAGGTCACAATAACGG 58.722 55.000 15.58 0.00 0.00 4.44
2084 2190 1.135199 GCTCGAGGTCACAATAACGGA 60.135 52.381 15.58 0.00 0.00 4.69
2085 2191 2.673043 GCTCGAGGTCACAATAACGGAA 60.673 50.000 15.58 0.00 0.00 4.30
2086 2192 2.921754 CTCGAGGTCACAATAACGGAAC 59.078 50.000 3.91 0.00 0.00 3.62
2089 2195 3.855950 CGAGGTCACAATAACGGAACTAC 59.144 47.826 0.00 0.00 0.00 2.73
2094 2200 5.574443 GGTCACAATAACGGAACTACAGTAC 59.426 44.000 0.00 0.00 0.00 2.73
2095 2201 5.284660 GTCACAATAACGGAACTACAGTACG 59.715 44.000 5.24 5.24 35.56 3.67
2117 2224 5.238650 ACGTAGTAACATTTTTGCTCTGCTT 59.761 36.000 0.00 0.00 41.94 3.91
2119 2226 6.736853 CGTAGTAACATTTTTGCTCTGCTTAC 59.263 38.462 0.00 0.00 0.00 2.34
2121 2228 7.277174 AGTAACATTTTTGCTCTGCTTACTT 57.723 32.000 0.00 0.00 0.00 2.24
2122 2229 8.391075 AGTAACATTTTTGCTCTGCTTACTTA 57.609 30.769 0.00 0.00 0.00 2.24
2126 2233 7.807680 ACATTTTTGCTCTGCTTACTTAGTAC 58.192 34.615 0.00 0.00 0.00 2.73
2134 2241 7.012515 TGCTCTGCTTACTTAGTACTATGTCTC 59.987 40.741 21.12 13.31 0.00 3.36
2163 2270 3.577649 CACCGACAGTGTCTCAGTATT 57.422 47.619 20.64 0.00 41.93 1.89
2167 2307 3.440522 CCGACAGTGTCTCAGTATTCAGA 59.559 47.826 20.64 0.00 0.00 3.27
2172 2312 5.167121 CAGTGTCTCAGTATTCAGAAGTGG 58.833 45.833 0.00 0.00 0.00 4.00
2239 2379 2.654863 GTGGGAATACTGTTGGATGGG 58.345 52.381 0.00 0.00 0.00 4.00
2279 2419 2.492484 GACTAGTCCAACATCACTCGGT 59.508 50.000 12.13 0.00 0.00 4.69
2284 2424 3.322514 CAACATCACTCGGTTGGGT 57.677 52.632 0.00 0.00 40.44 4.51
2299 2439 0.038599 TGGGTCGTGCTCCTACTGTA 59.961 55.000 0.00 0.00 0.00 2.74
2305 2445 3.128938 GTCGTGCTCCTACTGTAACTCAT 59.871 47.826 0.00 0.00 0.00 2.90
2321 2461 5.919272 AACTCATTGCGACATGATGATAG 57.081 39.130 0.00 0.00 0.00 2.08
2333 2473 6.040209 ACATGATGATAGCTCTCTGAATCC 57.960 41.667 0.00 0.00 0.00 3.01
2342 2482 5.965033 AGCTCTCTGAATCCCTTTATTGA 57.035 39.130 0.00 0.00 0.00 2.57
2375 2520 1.581934 CTCGTGACAACTTTGCCTCA 58.418 50.000 0.00 0.00 0.00 3.86
2727 2872 4.394712 CCGGACCAGTGGCTGTCC 62.395 72.222 9.78 8.23 32.43 4.02
2907 3052 1.668419 GCATGGTCTACGCCAAGATT 58.332 50.000 0.00 0.00 42.48 2.40
2913 3058 2.856557 GGTCTACGCCAAGATTTACGAC 59.143 50.000 0.00 0.00 0.00 4.34
3127 3272 3.486252 GACGGGAGCGGGAAGATCG 62.486 68.421 0.00 0.00 35.79 3.69
3152 3297 3.559171 GGTGGCAATTAGAGAAGACCACA 60.559 47.826 11.04 0.00 46.22 4.17
3171 3316 2.158957 ACAGACCACGACAACAACAGAT 60.159 45.455 0.00 0.00 0.00 2.90
3204 3349 8.841444 ACTTTATATAATGCGTGCTTTCTTTG 57.159 30.769 7.99 0.00 0.00 2.77
3205 3350 8.673711 ACTTTATATAATGCGTGCTTTCTTTGA 58.326 29.630 7.99 0.00 0.00 2.69
3246 3391 5.598005 AGTTCTCCTCGAGATGATTCAAGAT 59.402 40.000 15.71 0.00 38.56 2.40
3247 3392 6.098124 AGTTCTCCTCGAGATGATTCAAGATT 59.902 38.462 15.71 0.00 38.56 2.40
3248 3393 7.286546 AGTTCTCCTCGAGATGATTCAAGATTA 59.713 37.037 15.71 0.00 38.56 1.75
3341 3486 6.152661 TGTTTTCTTCAGTGTTCTTGTGGATT 59.847 34.615 0.00 0.00 0.00 3.01
3373 3518 3.129813 CCAAATGTGGTGGACTGATCATG 59.870 47.826 0.00 0.00 40.42 3.07
3374 3519 2.723322 ATGTGGTGGACTGATCATGG 57.277 50.000 0.00 0.00 0.00 3.66
3377 3522 1.003580 GTGGTGGACTGATCATGGTGT 59.996 52.381 0.00 0.00 0.00 4.16
3378 3523 2.236146 GTGGTGGACTGATCATGGTGTA 59.764 50.000 0.00 0.00 0.00 2.90
3379 3524 2.909662 TGGTGGACTGATCATGGTGTAA 59.090 45.455 0.00 0.00 0.00 2.41
3380 3525 3.055167 TGGTGGACTGATCATGGTGTAAG 60.055 47.826 0.00 0.00 0.00 2.34
3381 3526 3.535561 GTGGACTGATCATGGTGTAAGG 58.464 50.000 0.00 0.00 0.00 2.69
3382 3527 2.092968 TGGACTGATCATGGTGTAAGGC 60.093 50.000 0.00 0.00 0.00 4.35
3383 3528 2.171448 GGACTGATCATGGTGTAAGGCT 59.829 50.000 0.00 0.00 0.00 4.58
3384 3529 3.201290 GACTGATCATGGTGTAAGGCTG 58.799 50.000 0.00 0.00 0.00 4.85
3385 3530 2.092753 ACTGATCATGGTGTAAGGCTGG 60.093 50.000 0.00 0.00 0.00 4.85
3386 3531 1.312815 GATCATGGTGTAAGGCTGGC 58.687 55.000 0.00 0.00 0.00 4.85
3389 3534 1.202989 TCATGGTGTAAGGCTGGCAAA 60.203 47.619 3.38 0.00 0.00 3.68
3411 3556 1.065418 AGCCGGTGATTAGAACCTTGG 60.065 52.381 1.90 0.00 35.39 3.61
3427 3572 4.332828 ACCTTGGTCATACTGGCTTTTAC 58.667 43.478 0.00 0.00 0.00 2.01
4013 4170 9.321562 TCGTAAATATCCTCGCTTAATTTTCTT 57.678 29.630 0.00 0.00 0.00 2.52
4084 4241 1.301009 GCCCTCCTAGAAATCGCCG 60.301 63.158 0.00 0.00 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 0.041663 CGCGAAGAAAAACAAGGCGA 60.042 50.000 0.00 0.00 44.36 5.54
553 606 1.534697 CTCTCCTCCTCCTACGCCT 59.465 63.158 0.00 0.00 0.00 5.52
644 697 4.439472 GCGCGCGGTCGAAAACAT 62.439 61.111 33.06 0.00 38.10 2.71
677 730 3.593896 CGTAAAAATGGCGCGCGC 61.594 61.111 44.40 44.40 41.06 6.86
727 780 5.445845 CCGCAAATTAGTCTGTTTTAACGT 58.554 37.500 0.00 0.00 0.00 3.99
730 783 4.468643 CGCCGCAAATTAGTCTGTTTTAA 58.531 39.130 0.00 0.00 0.00 1.52
758 811 0.793861 CAACAGCCGCGCTAAACTAA 59.206 50.000 5.56 0.00 36.40 2.24
790 843 0.323360 CACGGGATGGATTGTTGGGT 60.323 55.000 0.00 0.00 0.00 4.51
791 844 1.666209 GCACGGGATGGATTGTTGGG 61.666 60.000 0.00 0.00 0.00 4.12
792 845 0.964860 TGCACGGGATGGATTGTTGG 60.965 55.000 0.00 0.00 0.00 3.77
793 846 1.066002 GATGCACGGGATGGATTGTTG 59.934 52.381 0.00 0.00 39.93 3.33
794 847 1.064463 AGATGCACGGGATGGATTGTT 60.064 47.619 0.00 0.00 39.93 2.83
795 848 0.548031 AGATGCACGGGATGGATTGT 59.452 50.000 0.00 0.00 39.93 2.71
796 849 2.549064 TAGATGCACGGGATGGATTG 57.451 50.000 0.00 0.00 39.93 2.67
797 850 2.373169 ACATAGATGCACGGGATGGATT 59.627 45.455 0.00 0.00 39.93 3.01
798 851 1.980765 ACATAGATGCACGGGATGGAT 59.019 47.619 0.00 0.00 43.10 3.41
799 852 1.070601 CACATAGATGCACGGGATGGA 59.929 52.381 0.00 0.00 0.00 3.41
800 853 1.516161 CACATAGATGCACGGGATGG 58.484 55.000 0.00 0.00 0.00 3.51
801 854 0.870393 GCACATAGATGCACGGGATG 59.130 55.000 0.00 0.00 45.39 3.51
802 855 3.312404 GCACATAGATGCACGGGAT 57.688 52.632 0.00 0.00 45.39 3.85
803 856 4.855105 GCACATAGATGCACGGGA 57.145 55.556 0.00 0.00 45.39 5.14
809 862 4.327898 CCATTTTGTTGTGCACATAGATGC 59.672 41.667 22.39 7.61 46.32 3.91
810 863 5.712004 TCCATTTTGTTGTGCACATAGATG 58.288 37.500 22.39 17.63 34.43 2.90
811 864 5.981088 TCCATTTTGTTGTGCACATAGAT 57.019 34.783 22.39 7.29 34.43 1.98
812 865 5.781210 TTCCATTTTGTTGTGCACATAGA 57.219 34.783 22.39 2.25 34.43 1.98
813 866 6.292811 GGTTTTCCATTTTGTTGTGCACATAG 60.293 38.462 22.39 5.61 40.31 2.23
814 867 5.525378 GGTTTTCCATTTTGTTGTGCACATA 59.475 36.000 22.39 10.42 40.31 2.29
815 868 4.335037 GGTTTTCCATTTTGTTGTGCACAT 59.665 37.500 22.39 0.45 40.31 3.21
816 869 3.686726 GGTTTTCCATTTTGTTGTGCACA 59.313 39.130 17.42 17.42 40.31 4.57
817 870 3.686726 TGGTTTTCCATTTTGTTGTGCAC 59.313 39.130 10.75 10.75 46.22 4.57
818 871 3.942829 TGGTTTTCCATTTTGTTGTGCA 58.057 36.364 0.00 0.00 46.22 4.57
863 916 4.796369 AGTAAAACTCAGACTGTAGACGC 58.204 43.478 1.59 0.00 0.00 5.19
879 935 1.514003 TGTCGCGCCATTGAGTAAAA 58.486 45.000 0.00 0.00 0.00 1.52
898 954 7.014230 TGCTTAACTAGACCAAAAGCTTTCATT 59.986 33.333 13.10 0.00 42.34 2.57
899 955 6.490040 TGCTTAACTAGACCAAAAGCTTTCAT 59.510 34.615 13.10 0.46 42.34 2.57
905 961 3.190744 GGGTGCTTAACTAGACCAAAAGC 59.809 47.826 0.00 4.72 42.22 3.51
906 962 4.215613 GTGGGTGCTTAACTAGACCAAAAG 59.784 45.833 0.00 0.00 0.00 2.27
907 963 4.139038 GTGGGTGCTTAACTAGACCAAAA 58.861 43.478 0.00 0.00 0.00 2.44
917 985 3.633361 AGCTCAGTGGGTGCTTAAC 57.367 52.632 0.00 0.00 43.47 2.01
943 1011 3.211963 CTGGTTGGCTATGGCGGC 61.212 66.667 0.00 0.00 39.81 6.53
951 1019 1.544314 GCTCTCTGAAACTGGTTGGCT 60.544 52.381 0.00 0.00 0.00 4.75
956 1024 0.106708 TTGCGCTCTCTGAAACTGGT 59.893 50.000 9.73 0.00 0.00 4.00
1036 1116 3.117171 GCACAGGAGCACGAGCAG 61.117 66.667 7.77 0.00 45.49 4.24
1047 1127 2.124983 CCTCCATGGACGCACAGG 60.125 66.667 11.44 5.62 38.35 4.00
1339 1419 4.162131 AGAAAAGTTGAGCAAAATGTGGGT 59.838 37.500 0.00 0.00 0.00 4.51
1342 1422 7.063780 ACAAAGAGAAAAGTTGAGCAAAATGTG 59.936 33.333 0.00 0.00 0.00 3.21
1380 1460 7.023197 ACTAAGAGAAAAGTTAGCGCAAAAA 57.977 32.000 11.47 0.00 30.57 1.94
1385 1465 6.947903 AACTACTAAGAGAAAAGTTAGCGC 57.052 37.500 0.00 0.00 30.57 5.92
1408 1488 5.451242 CCAAGAAACCGGATGTTCAGAAAAA 60.451 40.000 9.46 0.00 35.67 1.94
1409 1489 4.037446 CCAAGAAACCGGATGTTCAGAAAA 59.963 41.667 9.46 0.00 35.67 2.29
1410 1490 3.568007 CCAAGAAACCGGATGTTCAGAAA 59.432 43.478 9.46 0.00 35.67 2.52
1411 1491 3.146066 CCAAGAAACCGGATGTTCAGAA 58.854 45.455 9.46 0.00 35.67 3.02
1412 1492 2.370519 TCCAAGAAACCGGATGTTCAGA 59.629 45.455 9.46 4.76 35.67 3.27
1413 1493 2.778299 TCCAAGAAACCGGATGTTCAG 58.222 47.619 9.46 5.73 35.67 3.02
1414 1494 2.940994 TCCAAGAAACCGGATGTTCA 57.059 45.000 9.46 0.00 35.67 3.18
1415 1495 3.343617 TGATCCAAGAAACCGGATGTTC 58.656 45.455 9.46 8.89 42.21 3.18
1421 1501 2.825532 ACCAAATGATCCAAGAAACCGG 59.174 45.455 0.00 0.00 0.00 5.28
1447 1527 5.279106 CCATGGTCAAATTATATGGTGGCTG 60.279 44.000 2.57 0.00 34.88 4.85
1448 1528 4.834496 CCATGGTCAAATTATATGGTGGCT 59.166 41.667 2.57 0.00 34.88 4.75
1449 1529 5.138125 CCATGGTCAAATTATATGGTGGC 57.862 43.478 2.57 0.00 34.88 5.01
1454 1534 9.520204 GAAACAGAACCATGGTCAAATTATATG 57.480 33.333 20.07 10.66 0.00 1.78
1463 1549 1.780309 AGGGAAACAGAACCATGGTCA 59.220 47.619 20.07 0.00 0.00 4.02
1465 1551 1.780309 TCAGGGAAACAGAACCATGGT 59.220 47.619 13.00 13.00 38.31 3.55
1467 1553 3.244700 ACTCTCAGGGAAACAGAACCATG 60.245 47.826 0.00 0.00 38.99 3.66
1471 1557 7.013369 ACAAAATTACTCTCAGGGAAACAGAAC 59.987 37.037 0.00 0.00 0.00 3.01
1489 1575 7.730364 AACAACAACAACCACAACAAAATTA 57.270 28.000 0.00 0.00 0.00 1.40
1491 1577 6.038714 ACAAACAACAACAACCACAACAAAAT 59.961 30.769 0.00 0.00 0.00 1.82
1499 1585 1.388431 CGCACAAACAACAACAACCAC 59.612 47.619 0.00 0.00 0.00 4.16
1500 1586 1.000163 ACGCACAAACAACAACAACCA 60.000 42.857 0.00 0.00 0.00 3.67
1501 1587 1.388431 CACGCACAAACAACAACAACC 59.612 47.619 0.00 0.00 0.00 3.77
1502 1588 1.201758 GCACGCACAAACAACAACAAC 60.202 47.619 0.00 0.00 0.00 3.32
1503 1589 1.063806 GCACGCACAAACAACAACAA 58.936 45.000 0.00 0.00 0.00 2.83
1540 1630 3.390639 CCATTCTTCCTAGCCTCAGACAT 59.609 47.826 0.00 0.00 0.00 3.06
1596 1686 3.820557 CTTCTTCCCTCCAAAAGTGTCA 58.179 45.455 0.00 0.00 0.00 3.58
1623 1713 1.517832 CCCTCTTGCCCACTCTACG 59.482 63.158 0.00 0.00 0.00 3.51
1654 1744 3.390639 AAGAAGCCATCTTCAGATCCGAT 59.609 43.478 7.65 0.00 45.42 4.18
1670 1760 3.307379 ACGGAGTTGGTGAAGAAGC 57.693 52.632 0.00 0.00 37.78 3.86
1727 1823 7.129622 CGTTGCAAGTTACTCAAGATTTGTTA 58.870 34.615 0.00 0.00 0.00 2.41
1810 1906 1.217183 AGGTAGGGAGCGGAGATTACA 59.783 52.381 0.00 0.00 0.00 2.41
1818 1914 1.601419 TTCAACGAGGTAGGGAGCGG 61.601 60.000 0.00 0.00 0.00 5.52
1819 1915 0.179134 CTTCAACGAGGTAGGGAGCG 60.179 60.000 0.00 0.00 0.00 5.03
1821 1917 0.895530 TGCTTCAACGAGGTAGGGAG 59.104 55.000 0.00 0.00 0.00 4.30
1823 1919 2.076863 CTTTGCTTCAACGAGGTAGGG 58.923 52.381 0.00 0.00 0.00 3.53
1827 1923 1.537202 GCATCTTTGCTTCAACGAGGT 59.463 47.619 0.00 0.00 45.77 3.85
1828 1924 2.253392 GCATCTTTGCTTCAACGAGG 57.747 50.000 0.00 0.00 45.77 4.63
1839 1935 8.862550 AACAAGAAGAAAACTAAGCATCTTTG 57.137 30.769 0.00 0.00 32.54 2.77
1867 1963 9.675464 ACAAAATCTTATAATTTCTCCCACGTA 57.325 29.630 0.00 0.00 0.00 3.57
1868 1964 8.458843 CACAAAATCTTATAATTTCTCCCACGT 58.541 33.333 0.00 0.00 0.00 4.49
1869 1965 8.673711 TCACAAAATCTTATAATTTCTCCCACG 58.326 33.333 0.00 0.00 0.00 4.94
1890 1986 8.714179 CCACGTAACAATAATAAGACTTCACAA 58.286 33.333 0.00 0.00 0.00 3.33
1891 1987 7.332430 CCCACGTAACAATAATAAGACTTCACA 59.668 37.037 0.00 0.00 0.00 3.58
1892 1988 7.546667 TCCCACGTAACAATAATAAGACTTCAC 59.453 37.037 0.00 0.00 0.00 3.18
1893 1989 7.613585 TCCCACGTAACAATAATAAGACTTCA 58.386 34.615 0.00 0.00 0.00 3.02
1894 1990 7.977853 TCTCCCACGTAACAATAATAAGACTTC 59.022 37.037 0.00 0.00 0.00 3.01
1895 1991 7.844009 TCTCCCACGTAACAATAATAAGACTT 58.156 34.615 0.00 0.00 0.00 3.01
1896 1992 7.414222 TCTCCCACGTAACAATAATAAGACT 57.586 36.000 0.00 0.00 0.00 3.24
1897 1993 8.385858 GTTTCTCCCACGTAACAATAATAAGAC 58.614 37.037 0.00 0.00 0.00 3.01
1898 1994 8.316214 AGTTTCTCCCACGTAACAATAATAAGA 58.684 33.333 0.00 0.00 0.00 2.10
1899 1995 8.488651 AGTTTCTCCCACGTAACAATAATAAG 57.511 34.615 0.00 0.00 0.00 1.73
1900 1996 9.369904 GTAGTTTCTCCCACGTAACAATAATAA 57.630 33.333 0.00 0.00 0.00 1.40
1901 1997 8.530311 TGTAGTTTCTCCCACGTAACAATAATA 58.470 33.333 0.00 0.00 0.00 0.98
1908 2004 4.874970 TCTTGTAGTTTCTCCCACGTAAC 58.125 43.478 0.00 0.00 0.00 2.50
2043 2149 3.882888 GCATGCCACCTTGCTATACTTTA 59.117 43.478 6.36 0.00 38.64 1.85
2045 2151 2.092212 AGCATGCCACCTTGCTATACTT 60.092 45.455 15.66 0.00 46.80 2.24
2046 2152 1.492176 AGCATGCCACCTTGCTATACT 59.508 47.619 15.66 0.00 46.80 2.12
2053 2159 2.110967 CCTCGAGCATGCCACCTTG 61.111 63.158 15.66 0.00 0.00 3.61
2055 2161 3.005539 ACCTCGAGCATGCCACCT 61.006 61.111 15.66 0.00 0.00 4.00
2056 2162 2.512515 GACCTCGAGCATGCCACC 60.513 66.667 15.66 2.97 0.00 4.61
2057 2163 2.103042 GTGACCTCGAGCATGCCAC 61.103 63.158 15.66 9.65 0.00 5.01
2058 2164 2.110757 TTGTGACCTCGAGCATGCCA 62.111 55.000 15.66 0.00 0.00 4.92
2059 2165 0.745845 ATTGTGACCTCGAGCATGCC 60.746 55.000 15.66 4.99 0.00 4.40
2060 2166 1.939974 TATTGTGACCTCGAGCATGC 58.060 50.000 10.51 10.51 0.00 4.06
2061 2167 2.282555 CGTTATTGTGACCTCGAGCATG 59.717 50.000 6.99 0.00 0.00 4.06
2062 2168 2.540515 CGTTATTGTGACCTCGAGCAT 58.459 47.619 6.99 0.00 0.00 3.79
2063 2169 1.403647 CCGTTATTGTGACCTCGAGCA 60.404 52.381 6.99 0.00 0.00 4.26
2064 2170 1.135199 TCCGTTATTGTGACCTCGAGC 60.135 52.381 6.99 0.00 0.00 5.03
2065 2171 2.921754 GTTCCGTTATTGTGACCTCGAG 59.078 50.000 5.13 5.13 0.00 4.04
2066 2172 2.559668 AGTTCCGTTATTGTGACCTCGA 59.440 45.455 0.00 0.00 0.00 4.04
2067 2173 2.955614 AGTTCCGTTATTGTGACCTCG 58.044 47.619 0.00 0.00 0.00 4.63
2068 2174 4.813027 TGTAGTTCCGTTATTGTGACCTC 58.187 43.478 0.00 0.00 0.00 3.85
2089 2195 7.227461 CAGAGCAAAAATGTTACTACGTACTG 58.773 38.462 0.00 0.00 0.00 2.74
2094 2200 5.283060 AGCAGAGCAAAAATGTTACTACG 57.717 39.130 0.00 0.00 0.00 3.51
2095 2201 7.807680 AGTAAGCAGAGCAAAAATGTTACTAC 58.192 34.615 0.00 0.00 29.78 2.73
2098 2204 8.290325 ACTAAGTAAGCAGAGCAAAAATGTTAC 58.710 33.333 0.00 0.00 0.00 2.50
2103 2210 9.892130 ATAGTACTAAGTAAGCAGAGCAAAAAT 57.108 29.630 6.70 0.00 0.00 1.82
2104 2211 9.151471 CATAGTACTAAGTAAGCAGAGCAAAAA 57.849 33.333 6.70 0.00 0.00 1.94
2117 2224 6.239217 TCGGTGGAGACATAGTACTAAGTA 57.761 41.667 10.60 0.00 46.14 2.24
2119 2226 4.515944 CCTCGGTGGAGACATAGTACTAAG 59.484 50.000 6.70 5.02 46.14 2.18
2121 2228 3.746751 GCCTCGGTGGAGACATAGTACTA 60.747 52.174 4.77 4.77 46.14 1.82
2122 2229 2.933573 CCTCGGTGGAGACATAGTACT 58.066 52.381 0.00 0.00 46.14 2.73
2126 2233 0.103208 GTGCCTCGGTGGAGACATAG 59.897 60.000 0.00 0.00 46.14 2.23
2134 2241 4.742201 CTGTCGGTGCCTCGGTGG 62.742 72.222 0.00 0.00 39.35 4.61
2157 2264 4.264253 TCCAATGCCACTTCTGAATACTG 58.736 43.478 0.00 0.00 0.00 2.74
2161 2268 3.087031 CACTCCAATGCCACTTCTGAAT 58.913 45.455 0.00 0.00 0.00 2.57
2162 2269 2.158623 ACACTCCAATGCCACTTCTGAA 60.159 45.455 0.00 0.00 0.00 3.02
2163 2270 1.421268 ACACTCCAATGCCACTTCTGA 59.579 47.619 0.00 0.00 0.00 3.27
2167 2307 0.467844 TGCACACTCCAATGCCACTT 60.468 50.000 0.00 0.00 41.33 3.16
2172 2312 3.733077 GCTTCTTATGCACACTCCAATGC 60.733 47.826 0.00 0.00 42.40 3.56
2266 2406 1.156736 GACCCAACCGAGTGATGTTG 58.843 55.000 0.00 0.00 41.13 3.33
2271 2411 2.732016 CACGACCCAACCGAGTGA 59.268 61.111 0.00 0.00 35.03 3.41
2279 2419 0.830444 ACAGTAGGAGCACGACCCAA 60.830 55.000 0.00 0.00 0.00 4.12
2284 2424 2.786777 TGAGTTACAGTAGGAGCACGA 58.213 47.619 0.00 0.00 0.00 4.35
2299 2439 4.212847 GCTATCATCATGTCGCAATGAGTT 59.787 41.667 6.12 0.00 39.84 3.01
2305 2445 3.320256 AGAGAGCTATCATCATGTCGCAA 59.680 43.478 11.60 0.00 0.00 4.85
2321 2461 5.295540 GTGTCAATAAAGGGATTCAGAGAGC 59.704 44.000 0.00 0.00 0.00 4.09
2333 2473 1.339631 TGCCGGGAGTGTCAATAAAGG 60.340 52.381 2.18 0.00 0.00 3.11
2375 2520 2.086869 CGGTCTTCCATGATGCAAAGT 58.913 47.619 0.00 0.00 0.00 2.66
2655 2800 0.523072 CCTGGTTGTTGGCGATGAAG 59.477 55.000 0.00 0.00 0.00 3.02
2727 2872 4.803426 GCCTGGTCGTCGGAGCTG 62.803 72.222 0.00 0.00 41.26 4.24
2907 3052 4.170062 CTCCGCGCCGAGTCGTAA 62.170 66.667 16.38 0.00 0.00 3.18
3152 3297 2.102420 TCATCTGTTGTTGTCGTGGTCT 59.898 45.455 0.00 0.00 0.00 3.85
3171 3316 8.523658 AGCACGCATTATATAAAGTAGAGATCA 58.476 33.333 0.00 0.00 0.00 2.92
3204 3349 3.444703 ACTTGACTCACTCACACACTC 57.555 47.619 0.00 0.00 0.00 3.51
3205 3350 3.449018 AGAACTTGACTCACTCACACACT 59.551 43.478 0.00 0.00 0.00 3.55
3246 3391 6.082031 TCCTTCTCTCCCGGATGAATAATAA 58.918 40.000 0.73 0.00 0.00 1.40
3247 3392 5.651303 TCCTTCTCTCCCGGATGAATAATA 58.349 41.667 0.73 0.00 0.00 0.98
3248 3393 4.493618 TCCTTCTCTCCCGGATGAATAAT 58.506 43.478 0.73 0.00 0.00 1.28
3373 3518 0.598065 CTGTTTGCCAGCCTTACACC 59.402 55.000 0.00 0.00 33.59 4.16
3385 3530 1.448985 TCTAATCACCGGCTGTTTGC 58.551 50.000 0.00 0.00 41.94 3.68
3386 3531 2.161609 GGTTCTAATCACCGGCTGTTTG 59.838 50.000 0.00 0.00 0.00 2.93
3389 3534 1.276622 AGGTTCTAATCACCGGCTGT 58.723 50.000 0.00 0.00 39.56 4.40
4013 4170 3.133691 GCTCAGACGATAAATGATGGCA 58.866 45.455 0.00 0.00 0.00 4.92
4084 4241 0.378962 TGTTACACACTTTGCGCACC 59.621 50.000 11.12 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.