Multiple sequence alignment - TraesCS7B01G124600

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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 TraesCS7B01G124600 chr7B 100.000 5084 0 0 1 5084 145930727 145935810 0.000000e+00 9389.0
1 TraesCS7B01G124600 chr7B 88.889 1809 159 26 3019 4798 145825821 145827616 0.000000e+00 2189.0
2 TraesCS7B01G124600 chr7B 92.679 1284 70 12 3034 4304 145966796 145968068 0.000000e+00 1829.0
3 TraesCS7B01G124600 chr7B 93.296 1074 60 3 1869 2933 145965655 145966725 0.000000e+00 1574.0
4 TraesCS7B01G124600 chr7B 86.384 874 68 21 695 1564 145823681 145824507 0.000000e+00 907.0
5 TraesCS7B01G124600 chr7B 87.066 634 45 24 937 1564 145964826 145965428 0.000000e+00 682.0
6 TraesCS7B01G124600 chr7B 90.604 447 39 2 1853 2296 145824754 145825200 1.580000e-164 590.0
7 TraesCS7B01G124600 chr7B 91.811 403 33 0 2447 2849 145825369 145825771 3.440000e-156 562.0
8 TraesCS7B01G124600 chr7B 83.127 403 59 8 4192 4591 145968073 145968469 4.840000e-95 359.0
9 TraesCS7B01G124600 chr7B 85.271 129 18 1 4956 5084 145970363 145970490 1.150000e-26 132.0
10 TraesCS7B01G124600 chr7B 96.774 62 2 0 4 65 145964074 145964135 2.500000e-18 104.0
11 TraesCS7B01G124600 chr7D 95.532 2059 72 7 3034 5084 180072893 180074939 0.000000e+00 3275.0
12 TraesCS7B01G124600 chr7D 92.462 1247 65 6 1720 2954 180071596 180072825 0.000000e+00 1755.0
13 TraesCS7B01G124600 chr7D 90.490 1020 82 11 1839 2849 180014904 180015917 0.000000e+00 1332.0
14 TraesCS7B01G124600 chr7D 93.932 824 50 0 3526 4349 180016468 180017291 0.000000e+00 1245.0
15 TraesCS7B01G124600 chr7D 87.217 1017 94 20 627 1626 180013775 180014772 0.000000e+00 1125.0
16 TraesCS7B01G124600 chr7D 85.561 1115 81 39 691 1762 180070634 180071711 0.000000e+00 1094.0
17 TraesCS7B01G124600 chr7D 91.779 596 36 9 4484 5070 180017293 180017884 0.000000e+00 817.0
18 TraesCS7B01G124600 chr7D 91.943 422 34 0 3073 3494 180015985 180016406 4.380000e-165 592.0
19 TraesCS7B01G124600 chr7D 92.949 156 10 1 1644 1798 180071556 180071711 5.120000e-55 226.0
20 TraesCS7B01G124600 chr7D 96.774 62 2 0 4 65 180070201 180070262 2.500000e-18 104.0
21 TraesCS7B01G124600 chr7A 93.866 2054 110 6 3034 5084 184328413 184330453 0.000000e+00 3081.0
22 TraesCS7B01G124600 chr7A 89.291 1905 162 27 3019 4896 184171467 184173356 0.000000e+00 2350.0
23 TraesCS7B01G124600 chr7A 90.666 1307 92 15 3073 4349 184318093 184319399 0.000000e+00 1711.0
24 TraesCS7B01G124600 chr7A 93.762 1074 55 3 1869 2933 184327272 184328342 0.000000e+00 1602.0
25 TraesCS7B01G124600 chr7A 90.000 1020 87 11 1839 2849 184317012 184318025 0.000000e+00 1304.0
26 TraesCS7B01G124600 chr7A 88.586 990 58 24 627 1564 184326056 184327042 0.000000e+00 1151.0
27 TraesCS7B01G124600 chr7A 85.560 1018 120 18 1853 2849 184170406 184171417 0.000000e+00 1040.0
28 TraesCS7B01G124600 chr7A 88.588 885 40 24 1 843 184315280 184316145 0.000000e+00 1018.0
29 TraesCS7B01G124600 chr7A 86.030 859 67 29 711 1564 184169352 184170162 0.000000e+00 872.0
30 TraesCS7B01G124600 chr7A 90.180 611 35 16 4484 5084 184319401 184319996 0.000000e+00 773.0
31 TraesCS7B01G124600 chr7A 86.333 739 58 18 897 1626 184316176 184316880 0.000000e+00 765.0
32 TraesCS7B01G124600 chr7A 75.586 512 58 28 6 499 184168677 184169139 1.870000e-44 191.0
33 TraesCS7B01G124600 chr7A 96.667 60 1 1 4 63 184325832 184325890 1.160000e-16 99.0
34 TraesCS7B01G124600 chr7A 74.586 181 42 4 3635 3813 184171051 184171229 5.460000e-10 76.8
35 TraesCS7B01G124600 chr4A 88.605 509 46 2 2398 2894 726121113 726120605 4.350000e-170 608.0
36 TraesCS7B01G124600 chr4A 90.045 221 21 1 2970 3190 726120654 726120435 8.330000e-73 285.0
37 TraesCS7B01G124600 chr4A 90.476 189 9 4 3296 3484 726120143 726119964 1.830000e-59 241.0
38 TraesCS7B01G124600 chrUn 91.854 356 26 2 1853 2205 477165614 477165259 1.270000e-135 494.0
39 TraesCS7B01G124600 chr1D 92.405 79 5 1 1062 1139 475249067 475249145 1.500000e-20 111.0
40 TraesCS7B01G124600 chr1B 89.873 79 7 1 1062 1139 26337765 26337687 3.240000e-17 100.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G124600 chr7B 145930727 145935810 5083 False 9389.00 9389 100.000000 1 5084 1 chr7B.!!$F1 5083
1 TraesCS7B01G124600 chr7B 145823681 145827616 3935 False 1062.00 2189 89.422000 695 4798 4 chr7B.!!$F2 4103
2 TraesCS7B01G124600 chr7B 145964074 145970490 6416 False 780.00 1829 89.702167 4 5084 6 chr7B.!!$F3 5080
3 TraesCS7B01G124600 chr7D 180070201 180074939 4738 False 1290.80 3275 92.655600 4 5084 5 chr7D.!!$F2 5080
4 TraesCS7B01G124600 chr7D 180013775 180017884 4109 False 1022.20 1332 91.072200 627 5070 5 chr7D.!!$F1 4443
5 TraesCS7B01G124600 chr7A 184325832 184330453 4621 False 1483.25 3081 93.220250 4 5084 4 chr7A.!!$F3 5080
6 TraesCS7B01G124600 chr7A 184315280 184319996 4716 False 1114.20 1711 89.153400 1 5084 5 chr7A.!!$F2 5083
7 TraesCS7B01G124600 chr7A 184168677 184173356 4679 False 905.96 2350 82.210600 6 4896 5 chr7A.!!$F1 4890
8 TraesCS7B01G124600 chr4A 726119964 726121113 1149 True 378.00 608 89.708667 2398 3484 3 chr4A.!!$R1 1086

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
152 165 0.245266 TCACACACACGTCACACACT 59.755 50.0 0.00 0.0 0.00 3.55 F
1366 2095 0.826715 GGTGCTCATACTGCTCCTGA 59.173 55.0 0.00 0.0 39.95 3.86 F
2076 2910 0.169672 CCACTGCTTTTGCTGGATCG 59.830 55.0 0.00 0.0 46.73 3.69 F
2989 3856 0.251787 TACTGAGAGCACAGCAGGGA 60.252 55.0 8.42 0.0 41.06 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1642 2371 0.251354 TGCTCATCTGCTGTCTTCCC 59.749 55.000 0.00 0.0 0.00 3.97 R
3005 3893 0.183731 GGAAGCCCCAGTATTCCCTG 59.816 60.000 0.00 0.0 37.17 4.45 R
3866 5039 2.040278 AGCAAGTCCAAGACCATTGCTA 59.960 45.455 17.58 0.0 45.49 3.49 R
4891 6498 0.539986 GGTAGTCCCGCCAAAGATCA 59.460 55.000 0.00 0.0 0.00 2.92 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
86 98 0.754957 CCCCAACAAACCTCTGCACA 60.755 55.000 0.00 0.00 0.00 4.57
87 99 0.670162 CCCAACAAACCTCTGCACAG 59.330 55.000 0.00 0.00 0.00 3.66
125 137 3.773560 ACTAGAAGAGCCAAGTCTCAGT 58.226 45.455 0.00 0.00 35.59 3.41
126 138 3.761752 ACTAGAAGAGCCAAGTCTCAGTC 59.238 47.826 0.00 0.00 35.59 3.51
143 156 1.939934 AGTCCAATGTTCACACACACG 59.060 47.619 0.00 0.00 35.03 4.49
152 165 0.245266 TCACACACACGTCACACACT 59.755 50.000 0.00 0.00 0.00 3.55
332 366 4.396166 CCCCTTGAAAGCAACATACTAGTG 59.604 45.833 5.39 0.00 0.00 2.74
369 403 7.720442 TGGAAATACTACATGAGATGTCTGAG 58.280 38.462 0.00 0.00 43.67 3.35
411 449 4.869215 TGGATGTTTGTGCAAGTTGTATG 58.131 39.130 4.48 0.00 0.00 2.39
412 450 4.340666 TGGATGTTTGTGCAAGTTGTATGT 59.659 37.500 4.48 0.00 0.00 2.29
415 453 5.065704 TGTTTGTGCAAGTTGTATGTTGT 57.934 34.783 4.48 0.00 0.00 3.32
417 455 6.030849 TGTTTGTGCAAGTTGTATGTTGTAC 58.969 36.000 4.48 0.00 39.08 2.90
421 459 7.737972 TGTGCAAGTTGTATGTTGTACTATT 57.262 32.000 4.48 0.00 39.29 1.73
452 493 5.942236 TGACAGTACTGTACTACTACAAGGG 59.058 44.000 27.98 7.27 45.05 3.95
453 494 6.131972 ACAGTACTGTACTACTACAAGGGA 57.868 41.667 26.91 0.00 42.90 4.20
455 496 5.066246 CAGTACTGTACTACTACAAGGGAGC 59.934 48.000 19.32 0.00 37.23 4.70
489 532 3.316308 GCAACTAGGTAGGCATGGATTTG 59.684 47.826 0.00 0.00 0.00 2.32
499 542 6.493458 GGTAGGCATGGATTTGGTAAATATGT 59.507 38.462 0.00 0.00 0.00 2.29
500 543 6.655078 AGGCATGGATTTGGTAAATATGTC 57.345 37.500 0.00 0.00 0.00 3.06
501 544 5.241506 AGGCATGGATTTGGTAAATATGTCG 59.758 40.000 0.00 0.00 30.52 4.35
508 557 9.268268 TGGATTTGGTAAATATGTCGTAATCTC 57.732 33.333 0.00 0.00 0.00 2.75
555 604 1.885887 GCCCACATAAGTTTGTGCTGA 59.114 47.619 10.77 0.00 44.53 4.26
580 629 9.708092 GATCCAAATTAGGTAGGAATGTACTAC 57.292 37.037 0.00 0.00 39.99 2.73
596 645 6.594788 TGTACTACCTCCGTCTTAAAATGT 57.405 37.500 0.00 0.00 0.00 2.71
597 646 7.701539 TGTACTACCTCCGTCTTAAAATGTA 57.298 36.000 0.00 0.00 0.00 2.29
598 647 7.765307 TGTACTACCTCCGTCTTAAAATGTAG 58.235 38.462 0.00 0.00 0.00 2.74
599 648 7.611467 TGTACTACCTCCGTCTTAAAATGTAGA 59.389 37.037 0.00 0.00 0.00 2.59
600 649 7.098074 ACTACCTCCGTCTTAAAATGTAGAG 57.902 40.000 0.00 0.00 0.00 2.43
601 650 6.888632 ACTACCTCCGTCTTAAAATGTAGAGA 59.111 38.462 0.00 0.00 0.00 3.10
602 651 6.600882 ACCTCCGTCTTAAAATGTAGAGAA 57.399 37.500 0.00 0.00 0.00 2.87
603 652 7.001099 ACCTCCGTCTTAAAATGTAGAGAAA 57.999 36.000 0.00 0.00 0.00 2.52
604 653 7.621796 ACCTCCGTCTTAAAATGTAGAGAAAT 58.378 34.615 0.00 0.00 0.00 2.17
605 654 7.549488 ACCTCCGTCTTAAAATGTAGAGAAATG 59.451 37.037 0.00 0.00 0.00 2.32
689 747 5.851177 CGTAAGTTTGTGCTACTCCAAATTG 59.149 40.000 0.00 0.00 33.53 2.32
730 1035 1.850377 CTGCATGAAGCTAGGACTCG 58.150 55.000 0.00 0.00 45.94 4.18
839 1406 3.993692 TCCATGGGATATTATTGGTGGGT 59.006 43.478 13.02 0.00 0.00 4.51
843 1414 3.794399 TGGGATATTATTGGTGGGTTGGA 59.206 43.478 0.00 0.00 0.00 3.53
845 1416 5.102870 TGGGATATTATTGGTGGGTTGGAAT 60.103 40.000 0.00 0.00 0.00 3.01
846 1417 6.104840 TGGGATATTATTGGTGGGTTGGAATA 59.895 38.462 0.00 0.00 0.00 1.75
964 1607 4.211374 CCCACATACGCTACAATCTTTAGC 59.789 45.833 0.00 0.00 38.92 3.09
999 1644 6.483405 AGATTTTTCAAGGAATCTCAGAGCT 58.517 36.000 0.00 0.00 37.96 4.09
1080 1725 3.184683 GACGAGCCGCAGCAAGAG 61.185 66.667 0.00 0.00 43.56 2.85
1081 1726 4.749310 ACGAGCCGCAGCAAGAGG 62.749 66.667 0.00 0.00 43.56 3.69
1145 1871 2.262915 CGAGGCCGAGCTTCTGTT 59.737 61.111 0.00 0.00 38.22 3.16
1245 1971 1.584380 GCTTCTGGCAGGACAGCAAG 61.584 60.000 21.82 15.09 41.35 4.01
1366 2095 0.826715 GGTGCTCATACTGCTCCTGA 59.173 55.000 0.00 0.00 39.95 3.86
1586 2315 5.045872 TCAATGTCTGCGAGATATGTTCTG 58.954 41.667 0.00 0.00 33.74 3.02
1609 2338 4.385825 GGGTATTCGTGCATATTGGAAGA 58.614 43.478 0.00 0.00 0.00 2.87
1611 2340 5.473504 GGGTATTCGTGCATATTGGAAGAAT 59.526 40.000 12.82 12.82 45.21 2.40
1617 2346 6.582636 TCGTGCATATTGGAAGAATACTCTT 58.417 36.000 0.00 0.00 44.93 2.85
1626 2355 4.473196 TGGAAGAATACTCTTGGGCACATA 59.527 41.667 0.00 0.00 42.19 2.29
1627 2356 5.045213 TGGAAGAATACTCTTGGGCACATAA 60.045 40.000 0.00 0.00 42.19 1.90
1629 2358 6.016777 GGAAGAATACTCTTGGGCACATAATG 60.017 42.308 0.00 0.00 42.19 1.90
1632 2361 3.719268 ACTCTTGGGCACATAATGACA 57.281 42.857 0.00 0.00 38.59 3.58
1636 2365 2.127271 TGGGCACATAATGACACCAG 57.873 50.000 0.00 0.00 38.59 4.00
1637 2366 1.340893 TGGGCACATAATGACACCAGG 60.341 52.381 0.00 0.00 38.59 4.45
1639 2368 2.423373 GGGCACATAATGACACCAGGAT 60.423 50.000 0.00 0.00 38.59 3.24
1640 2369 2.880890 GGCACATAATGACACCAGGATC 59.119 50.000 0.00 0.00 35.73 3.36
1642 2371 3.562973 GCACATAATGACACCAGGATCAG 59.437 47.826 0.00 0.00 0.00 2.90
1643 2372 4.132336 CACATAATGACACCAGGATCAGG 58.868 47.826 0.00 0.00 0.00 3.86
1644 2373 3.137176 ACATAATGACACCAGGATCAGGG 59.863 47.826 8.16 4.56 0.00 4.45
1645 2374 1.971149 AATGACACCAGGATCAGGGA 58.029 50.000 8.73 0.00 0.00 4.20
1646 2375 1.971149 ATGACACCAGGATCAGGGAA 58.029 50.000 8.73 0.00 0.00 3.97
1666 2395 1.066286 AGACAGCAGATGAGCAAGGTC 60.066 52.381 0.00 0.00 36.85 3.85
1669 2398 0.252479 AGCAGATGAGCAAGGTCCAG 59.748 55.000 0.00 0.00 36.85 3.86
1674 2403 1.495579 ATGAGCAAGGTCCAGCAGGT 61.496 55.000 8.78 0.00 35.89 4.00
1702 2431 3.553922 GGAAGAGAGGATAACAGATGGCG 60.554 52.174 0.00 0.00 0.00 5.69
1722 2451 2.015587 GAAGAGGCCTCAAATGCAGAG 58.984 52.381 33.90 0.00 0.00 3.35
1792 2620 1.818642 CCAAGAGGCTTCAAGTCCAG 58.181 55.000 0.00 0.00 0.00 3.86
1793 2621 1.349026 CCAAGAGGCTTCAAGTCCAGA 59.651 52.381 0.00 0.00 0.00 3.86
1794 2622 2.614987 CCAAGAGGCTTCAAGTCCAGAG 60.615 54.545 0.00 0.00 0.00 3.35
1795 2623 2.301296 CAAGAGGCTTCAAGTCCAGAGA 59.699 50.000 0.00 0.00 0.00 3.10
1796 2624 2.178580 AGAGGCTTCAAGTCCAGAGAG 58.821 52.381 0.00 0.00 0.00 3.20
1797 2625 1.206849 GAGGCTTCAAGTCCAGAGAGG 59.793 57.143 0.00 0.00 39.47 3.69
1798 2626 1.203237 AGGCTTCAAGTCCAGAGAGGA 60.203 52.381 1.37 0.00 46.75 3.71
1809 2637 2.968574 TCCAGAGAGGATAACAGATGGC 59.031 50.000 0.00 0.00 43.07 4.40
1810 2638 2.038295 CCAGAGAGGATAACAGATGGCC 59.962 54.545 0.00 0.00 41.22 5.36
1811 2639 2.702478 CAGAGAGGATAACAGATGGCCA 59.298 50.000 8.56 8.56 0.00 5.36
1812 2640 3.135348 CAGAGAGGATAACAGATGGCCAA 59.865 47.826 10.96 0.00 0.00 4.52
1813 2641 3.390639 AGAGAGGATAACAGATGGCCAAG 59.609 47.826 10.96 5.45 0.00 3.61
1814 2642 3.118531 AGAGGATAACAGATGGCCAAGT 58.881 45.455 10.96 6.23 0.00 3.16
1815 2643 3.118112 AGAGGATAACAGATGGCCAAGTG 60.118 47.826 10.96 13.32 0.00 3.16
1816 2644 2.092212 AGGATAACAGATGGCCAAGTGG 60.092 50.000 10.96 1.96 38.53 4.00
1828 2656 2.074547 CCAAGTGGCTTCAAATGCAG 57.925 50.000 0.00 0.00 0.00 4.41
1829 2657 1.614903 CCAAGTGGCTTCAAATGCAGA 59.385 47.619 0.00 0.00 0.00 4.26
1830 2658 2.352421 CCAAGTGGCTTCAAATGCAGAG 60.352 50.000 0.00 0.00 0.00 3.35
1831 2659 2.555325 CAAGTGGCTTCAAATGCAGAGA 59.445 45.455 0.00 0.00 0.00 3.10
1832 2660 2.434428 AGTGGCTTCAAATGCAGAGAG 58.566 47.619 0.00 0.00 0.00 3.20
1833 2661 2.039480 AGTGGCTTCAAATGCAGAGAGA 59.961 45.455 0.00 0.00 0.00 3.10
1834 2662 2.816087 GTGGCTTCAAATGCAGAGAGAA 59.184 45.455 0.00 0.00 0.00 2.87
1835 2663 3.442977 GTGGCTTCAAATGCAGAGAGAAT 59.557 43.478 0.00 0.00 0.00 2.40
1836 2664 4.637534 GTGGCTTCAAATGCAGAGAGAATA 59.362 41.667 0.00 0.00 0.00 1.75
1837 2665 5.124457 GTGGCTTCAAATGCAGAGAGAATAA 59.876 40.000 0.00 0.00 0.00 1.40
1945 2779 1.065199 CAGTGACATATGTGGCAGGGT 60.065 52.381 14.43 0.00 46.12 4.34
2033 2867 0.956633 GACCACTATCCACGCCGATA 59.043 55.000 0.00 0.00 0.00 2.92
2076 2910 0.169672 CCACTGCTTTTGCTGGATCG 59.830 55.000 0.00 0.00 46.73 3.69
2298 3132 1.276421 GAACCTGCTCTGCCTAAGTCA 59.724 52.381 0.00 0.00 0.00 3.41
2303 3137 2.102084 CTGCTCTGCCTAAGTCAGCATA 59.898 50.000 0.00 0.00 35.74 3.14
2309 3143 4.162131 TCTGCCTAAGTCAGCATATGTTGA 59.838 41.667 17.28 17.28 38.56 3.18
2310 3144 4.445453 TGCCTAAGTCAGCATATGTTGAG 58.555 43.478 21.05 11.06 35.96 3.02
2311 3145 3.812053 GCCTAAGTCAGCATATGTTGAGG 59.188 47.826 21.05 18.48 35.96 3.86
2312 3146 4.384056 CCTAAGTCAGCATATGTTGAGGG 58.616 47.826 21.05 16.01 35.96 4.30
2391 3225 5.545063 TCATCACTGACTTGTTAGAACCA 57.455 39.130 0.00 0.00 0.00 3.67
2394 3228 3.709653 TCACTGACTTGTTAGAACCACCT 59.290 43.478 0.00 0.00 0.00 4.00
2395 3229 4.897076 TCACTGACTTGTTAGAACCACCTA 59.103 41.667 0.00 0.00 0.00 3.08
2396 3230 5.010719 TCACTGACTTGTTAGAACCACCTAG 59.989 44.000 0.00 0.00 0.00 3.02
2411 3251 3.451178 CCACCTAGCATACCAGTACAAGT 59.549 47.826 0.00 0.00 0.00 3.16
2421 3261 2.438021 ACCAGTACAAGTTCAGCCAGAA 59.562 45.455 0.00 0.00 0.00 3.02
2496 3363 1.973281 CATCCTTGCCGCCACAGTT 60.973 57.895 0.00 0.00 0.00 3.16
2543 3410 3.274288 CAGGAGGCTTTTGGACAGATAC 58.726 50.000 0.00 0.00 0.00 2.24
2592 3459 0.322456 TTTTGGAGGCCATCAGTCCG 60.322 55.000 5.01 0.00 31.53 4.79
2817 3684 2.944349 GTTCGTCCTAGTCCTCCTAGTG 59.056 54.545 0.00 0.00 41.48 2.74
2872 3739 2.590611 AGGACACTAGGGAATACTGGGA 59.409 50.000 0.00 0.00 0.00 4.37
2874 3741 2.365941 GACACTAGGGAATACTGGGAGC 59.634 54.545 0.00 0.00 0.00 4.70
2876 3743 2.103263 CACTAGGGAATACTGGGAGCAC 59.897 54.545 0.00 0.00 0.00 4.40
2877 3744 2.292918 ACTAGGGAATACTGGGAGCACA 60.293 50.000 0.00 0.00 0.00 4.57
2878 3745 1.207791 AGGGAATACTGGGAGCACAG 58.792 55.000 0.00 0.00 44.03 3.66
2879 3746 0.464554 GGGAATACTGGGAGCACAGC 60.465 60.000 0.00 0.00 42.21 4.40
2880 3747 0.253044 GGAATACTGGGAGCACAGCA 59.747 55.000 0.00 0.00 42.21 4.41
2881 3748 1.661341 GAATACTGGGAGCACAGCAG 58.339 55.000 0.00 0.00 42.21 4.24
2882 3749 0.254178 AATACTGGGAGCACAGCAGG 59.746 55.000 0.00 0.00 42.21 4.85
2883 3750 1.630126 ATACTGGGAGCACAGCAGGG 61.630 60.000 0.00 0.00 42.21 4.45
2884 3751 2.746947 TACTGGGAGCACAGCAGGGA 62.747 60.000 0.00 0.00 42.21 4.20
2885 3752 2.853542 TGGGAGCACAGCAGGGAA 60.854 61.111 0.00 0.00 0.00 3.97
2886 3753 2.207501 CTGGGAGCACAGCAGGGAAT 62.208 60.000 0.00 0.00 0.00 3.01
2887 3754 1.751927 GGGAGCACAGCAGGGAATG 60.752 63.158 0.00 0.00 0.00 2.67
2929 3796 0.694771 TGAGAGCACAGCAGGGAATT 59.305 50.000 0.00 0.00 0.00 2.17
2930 3797 1.339438 TGAGAGCACAGCAGGGAATTC 60.339 52.381 0.00 0.00 0.00 2.17
2931 3798 0.990374 AGAGCACAGCAGGGAATTCT 59.010 50.000 5.23 0.00 0.00 2.40
2932 3799 1.093159 GAGCACAGCAGGGAATTCTG 58.907 55.000 5.23 0.00 37.79 3.02
2933 3800 0.694771 AGCACAGCAGGGAATTCTGA 59.305 50.000 5.23 0.00 36.93 3.27
2934 3801 1.093159 GCACAGCAGGGAATTCTGAG 58.907 55.000 5.23 0.00 36.93 3.35
2935 3802 1.339438 GCACAGCAGGGAATTCTGAGA 60.339 52.381 5.23 0.00 36.93 3.27
2936 3803 2.630158 CACAGCAGGGAATTCTGAGAG 58.370 52.381 5.23 0.00 36.93 3.20
2937 3804 1.065564 ACAGCAGGGAATTCTGAGAGC 60.066 52.381 5.23 3.46 36.93 4.09
2938 3805 1.065636 CAGCAGGGAATTCTGAGAGCA 60.066 52.381 5.23 0.00 36.93 4.26
2939 3806 1.065564 AGCAGGGAATTCTGAGAGCAC 60.066 52.381 5.23 0.00 36.93 4.40
2940 3807 1.339438 GCAGGGAATTCTGAGAGCACA 60.339 52.381 5.23 0.00 36.93 4.57
2941 3808 2.630158 CAGGGAATTCTGAGAGCACAG 58.370 52.381 5.23 0.00 36.93 3.66
2942 3809 1.065564 AGGGAATTCTGAGAGCACAGC 60.066 52.381 5.23 0.00 37.75 4.40
2943 3810 1.339438 GGGAATTCTGAGAGCACAGCA 60.339 52.381 5.23 0.00 37.75 4.41
2944 3811 2.008329 GGAATTCTGAGAGCACAGCAG 58.992 52.381 5.23 0.00 37.75 4.24
2945 3812 2.008329 GAATTCTGAGAGCACAGCAGG 58.992 52.381 0.00 0.00 37.75 4.85
2946 3813 0.252479 ATTCTGAGAGCACAGCAGGG 59.748 55.000 0.00 0.00 37.75 4.45
2947 3814 0.833409 TTCTGAGAGCACAGCAGGGA 60.833 55.000 0.00 0.00 37.75 4.20
2948 3815 0.833409 TCTGAGAGCACAGCAGGGAA 60.833 55.000 0.00 0.00 37.75 3.97
2949 3816 0.252479 CTGAGAGCACAGCAGGGAAT 59.748 55.000 0.00 0.00 0.00 3.01
2950 3817 1.483827 CTGAGAGCACAGCAGGGAATA 59.516 52.381 0.00 0.00 0.00 1.75
2951 3818 1.208052 TGAGAGCACAGCAGGGAATAC 59.792 52.381 0.00 0.00 0.00 1.89
2952 3819 1.484240 GAGAGCACAGCAGGGAATACT 59.516 52.381 0.00 0.00 0.00 2.12
2953 3820 1.209019 AGAGCACAGCAGGGAATACTG 59.791 52.381 0.00 0.00 41.41 2.74
2954 3821 1.208052 GAGCACAGCAGGGAATACTGA 59.792 52.381 0.00 0.00 40.97 3.41
2955 3822 1.209019 AGCACAGCAGGGAATACTGAG 59.791 52.381 0.00 0.00 40.97 3.35
2956 3823 1.208052 GCACAGCAGGGAATACTGAGA 59.792 52.381 0.00 0.00 40.97 3.27
2957 3824 2.158842 GCACAGCAGGGAATACTGAGAT 60.159 50.000 0.00 0.00 40.97 2.75
2958 3825 3.726607 CACAGCAGGGAATACTGAGATC 58.273 50.000 0.00 0.00 40.97 2.75
2959 3826 3.133542 CACAGCAGGGAATACTGAGATCA 59.866 47.826 0.00 0.00 40.97 2.92
2960 3827 3.133721 ACAGCAGGGAATACTGAGATCAC 59.866 47.826 0.00 0.00 40.97 3.06
2961 3828 3.133542 CAGCAGGGAATACTGAGATCACA 59.866 47.826 0.00 0.00 40.97 3.58
2962 3829 3.387374 AGCAGGGAATACTGAGATCACAG 59.613 47.826 17.41 17.41 40.97 3.66
2963 3830 3.386078 GCAGGGAATACTGAGATCACAGA 59.614 47.826 24.57 10.20 40.97 3.41
2964 3831 4.141846 GCAGGGAATACTGAGATCACAGAA 60.142 45.833 24.57 0.00 40.97 3.02
2965 3832 5.599732 CAGGGAATACTGAGATCACAGAAG 58.400 45.833 24.57 1.98 40.97 2.85
2966 3833 4.653341 AGGGAATACTGAGATCACAGAAGG 59.347 45.833 24.57 1.63 40.63 3.46
2967 3834 4.202305 GGGAATACTGAGATCACAGAAGGG 60.202 50.000 24.57 1.27 40.63 3.95
2968 3835 4.651503 GGAATACTGAGATCACAGAAGGGA 59.348 45.833 24.57 6.56 40.63 4.20
2969 3836 5.129485 GGAATACTGAGATCACAGAAGGGAA 59.871 44.000 24.57 5.22 40.63 3.97
2970 3837 6.183361 GGAATACTGAGATCACAGAAGGGAAT 60.183 42.308 24.57 5.00 40.63 3.01
2971 3838 7.015682 GGAATACTGAGATCACAGAAGGGAATA 59.984 40.741 24.57 6.95 40.63 1.75
2972 3839 5.606348 ACTGAGATCACAGAAGGGAATAC 57.394 43.478 24.57 0.00 40.63 1.89
2973 3840 5.276440 ACTGAGATCACAGAAGGGAATACT 58.724 41.667 24.57 0.00 40.63 2.12
2974 3841 5.128499 ACTGAGATCACAGAAGGGAATACTG 59.872 44.000 24.57 0.00 40.63 2.74
2975 3842 5.272402 TGAGATCACAGAAGGGAATACTGA 58.728 41.667 0.00 0.00 35.85 3.41
2976 3843 5.362143 TGAGATCACAGAAGGGAATACTGAG 59.638 44.000 0.00 0.00 35.85 3.35
2977 3844 5.523588 AGATCACAGAAGGGAATACTGAGA 58.476 41.667 0.00 0.00 36.22 3.27
2978 3845 5.598005 AGATCACAGAAGGGAATACTGAGAG 59.402 44.000 0.00 0.00 35.55 3.20
2979 3846 3.449018 TCACAGAAGGGAATACTGAGAGC 59.551 47.826 0.00 0.00 35.85 4.09
2980 3847 3.196469 CACAGAAGGGAATACTGAGAGCA 59.804 47.826 0.00 0.00 35.85 4.26
2981 3848 3.196685 ACAGAAGGGAATACTGAGAGCAC 59.803 47.826 0.00 0.00 35.85 4.40
2982 3849 3.196469 CAGAAGGGAATACTGAGAGCACA 59.804 47.826 0.00 0.00 34.07 4.57
2983 3850 3.450457 AGAAGGGAATACTGAGAGCACAG 59.550 47.826 0.00 0.00 42.78 3.66
2984 3851 1.484240 AGGGAATACTGAGAGCACAGC 59.516 52.381 0.00 0.00 41.06 4.40
2985 3852 1.208052 GGGAATACTGAGAGCACAGCA 59.792 52.381 0.00 0.00 41.06 4.41
2986 3853 2.548875 GGAATACTGAGAGCACAGCAG 58.451 52.381 0.00 4.45 41.06 4.24
2987 3854 2.548875 GAATACTGAGAGCACAGCAGG 58.451 52.381 8.42 0.00 41.06 4.85
2988 3855 0.829333 ATACTGAGAGCACAGCAGGG 59.171 55.000 8.42 0.00 41.06 4.45
2989 3856 0.251787 TACTGAGAGCACAGCAGGGA 60.252 55.000 8.42 0.00 41.06 4.20
2990 3857 1.123861 ACTGAGAGCACAGCAGGGAA 61.124 55.000 8.42 0.00 41.06 3.97
2991 3858 0.673022 CTGAGAGCACAGCAGGGAAC 60.673 60.000 0.00 0.00 0.00 3.62
3004 3892 1.002888 CAGGGAACACTGAGAGCACAT 59.997 52.381 0.00 0.00 40.97 3.21
3005 3893 1.277557 AGGGAACACTGAGAGCACATC 59.722 52.381 0.00 0.00 0.00 3.06
3032 3920 4.064768 TGGGGCTTCCATGGCAGG 62.065 66.667 13.60 3.99 41.46 4.85
3099 4044 2.479566 AAGATTTGCAGAAGAGGCGA 57.520 45.000 0.00 0.00 0.00 5.54
3239 4187 0.595567 CGTGACGAGTTCCGAAACCA 60.596 55.000 0.00 0.00 41.76 3.67
3313 4447 5.082059 CAGTAATTCTGTTGCTTGTTAGCG 58.918 41.667 0.00 0.00 43.27 4.26
3337 4471 2.019984 GGCTATGCAAGAAAGGTCTGG 58.980 52.381 0.00 0.00 33.05 3.86
3541 4714 1.241315 GCGGCCTTCTAAGCACCAAA 61.241 55.000 0.00 0.00 0.00 3.28
3866 5039 6.696441 GAGATCTCTCTTTGCCATGAAAAT 57.304 37.500 15.80 0.00 39.81 1.82
3994 5167 5.215160 TCATCTACATCGTCATTCATGTCG 58.785 41.667 0.00 0.65 39.92 4.35
4060 5233 0.606401 AAAGTGGGTGCGATGTCTGG 60.606 55.000 0.00 0.00 0.00 3.86
4240 5544 2.025981 TGCTCAAGGCCATCATGTAGTT 60.026 45.455 5.01 0.00 40.92 2.24
4304 5608 5.467735 CAGATGACAACTGTGAGATGTGAAA 59.532 40.000 4.61 0.00 31.03 2.69
4313 5620 5.829924 ACTGTGAGATGTGAAATGGTTCTTT 59.170 36.000 0.00 0.00 34.60 2.52
4352 5659 9.613428 CAATATGTGGAATTACCTTCTGAAGTA 57.387 33.333 15.72 6.22 39.86 2.24
4685 6230 3.125829 CACTGACACCTTCATTGGATTCG 59.874 47.826 0.00 0.00 32.45 3.34
4890 6497 2.191128 TTTGCAAGAGAGGAAGGAGC 57.809 50.000 0.00 0.00 0.00 4.70
4891 6498 1.356124 TTGCAAGAGAGGAAGGAGCT 58.644 50.000 0.00 0.00 0.00 4.09
4952 6564 4.933134 TGATGAAATTCCATCAACAGGGA 58.067 39.130 4.69 0.00 46.88 4.20
4957 6569 2.806945 TTCCATCAACAGGGACCATC 57.193 50.000 0.00 0.00 30.00 3.51
5002 7965 6.586463 GTCTGATGAATTTCTCTGTAACACGA 59.414 38.462 0.00 0.00 0.00 4.35
5074 8038 3.127721 GTCTCAGCTTGCCAAACTAATCC 59.872 47.826 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 137 1.937223 GACGTGTGTGTGAACATTGGA 59.063 47.619 0.00 0.00 31.49 3.53
126 138 1.668237 TGACGTGTGTGTGAACATTGG 59.332 47.619 0.00 0.00 31.49 3.16
143 156 1.602377 GGGCTACAACAAGTGTGTGAC 59.398 52.381 0.00 0.00 41.89 3.67
152 165 5.860941 TTTCAATTTCAGGGCTACAACAA 57.139 34.783 0.00 0.00 0.00 2.83
311 344 4.697352 AGCACTAGTATGTTGCTTTCAAGG 59.303 41.667 0.00 0.00 31.93 3.61
353 387 3.908476 AGCCTCTCAGACATCTCATGTA 58.092 45.455 0.00 0.00 45.03 2.29
355 389 3.823281 AAGCCTCTCAGACATCTCATG 57.177 47.619 0.00 0.00 0.00 3.07
369 403 2.262423 AGACAGTGTTCCAAAGCCTC 57.738 50.000 0.00 0.00 0.00 4.70
411 449 7.980099 AGTACTGTCAAGCCATAATAGTACAAC 59.020 37.037 0.00 0.00 40.67 3.32
412 450 7.979537 CAGTACTGTCAAGCCATAATAGTACAA 59.020 37.037 15.06 0.00 40.67 2.41
415 453 7.655521 ACAGTACTGTCAAGCCATAATAGTA 57.344 36.000 22.95 0.00 40.24 1.82
417 455 7.717568 AGTACAGTACTGTCAAGCCATAATAG 58.282 38.462 31.11 0.00 43.74 1.73
421 459 6.185511 AGTAGTACAGTACTGTCAAGCCATA 58.814 40.000 31.11 9.26 43.74 2.74
455 496 6.595716 GCCTACCTAGTTGCAATAGGATATTG 59.404 42.308 27.58 17.11 42.15 1.90
471 514 3.864789 ACCAAATCCATGCCTACCTAG 57.135 47.619 0.00 0.00 0.00 3.02
473 516 4.601406 TTTACCAAATCCATGCCTACCT 57.399 40.909 0.00 0.00 0.00 3.08
489 532 8.870879 GCCTAATGAGATTACGACATATTTACC 58.129 37.037 0.00 0.00 0.00 2.85
499 542 4.202223 GGGTTCAGCCTAATGAGATTACGA 60.202 45.833 0.00 0.00 37.43 3.43
500 543 4.058817 GGGTTCAGCCTAATGAGATTACG 58.941 47.826 0.00 0.00 37.43 3.18
501 544 5.036117 TGGGTTCAGCCTAATGAGATTAC 57.964 43.478 0.00 0.00 37.43 1.89
580 629 7.549488 ACATTTCTCTACATTTTAAGACGGAGG 59.451 37.037 0.00 0.00 0.00 4.30
597 646 8.515414 GCCTACAAAAACATCTTACATTTCTCT 58.485 33.333 0.00 0.00 0.00 3.10
598 647 8.515414 AGCCTACAAAAACATCTTACATTTCTC 58.485 33.333 0.00 0.00 0.00 2.87
599 648 8.409358 AGCCTACAAAAACATCTTACATTTCT 57.591 30.769 0.00 0.00 0.00 2.52
602 651 9.243105 ACATAGCCTACAAAAACATCTTACATT 57.757 29.630 0.00 0.00 0.00 2.71
603 652 8.807948 ACATAGCCTACAAAAACATCTTACAT 57.192 30.769 0.00 0.00 0.00 2.29
604 653 9.727859 TTACATAGCCTACAAAAACATCTTACA 57.272 29.630 0.00 0.00 0.00 2.41
610 659 9.632638 ATCAGATTACATAGCCTACAAAAACAT 57.367 29.630 0.00 0.00 0.00 2.71
689 747 6.456501 CAGCATATTTACTACACTCCTACCC 58.543 44.000 0.00 0.00 0.00 3.69
730 1035 4.429108 CTTTTCTGCAGTCTACTCCTAGC 58.571 47.826 14.67 0.00 0.00 3.42
839 1406 7.060421 GGGAAGTGGACAAGATAATATTCCAA 58.940 38.462 0.00 0.00 38.09 3.53
843 1414 5.953571 GGGGGAAGTGGACAAGATAATATT 58.046 41.667 0.00 0.00 0.00 1.28
846 1417 3.953542 GGGGGAAGTGGACAAGATAAT 57.046 47.619 0.00 0.00 0.00 1.28
964 1607 4.808364 CCTTGAAAAATCTCTAGCTCCTCG 59.192 45.833 0.00 0.00 0.00 4.63
980 1623 5.426509 TCCATAGCTCTGAGATTCCTTGAAA 59.573 40.000 9.28 0.00 0.00 2.69
1012 1657 1.390565 GCATTGCCATTCTGCTCTCT 58.609 50.000 0.00 0.00 33.15 3.10
1102 1747 3.745803 GTCTTGCTGCAGCTGCCC 61.746 66.667 36.61 25.02 42.66 5.36
1103 1748 4.099170 CGTCTTGCTGCAGCTGCC 62.099 66.667 36.61 21.13 42.66 4.85
1140 1866 3.006967 GGTACTTCCTCAGCTTCAACAGA 59.993 47.826 0.00 0.00 0.00 3.41
1145 1871 1.902508 CCAGGTACTTCCTCAGCTTCA 59.097 52.381 0.00 0.00 46.24 3.02
1383 2112 3.458163 CGGAGCCAGACCGCCTTA 61.458 66.667 0.00 0.00 43.74 2.69
1402 2131 2.244117 ATCATGGCGAACTGGAGCGT 62.244 55.000 0.00 0.00 0.00 5.07
1564 2293 4.210746 CCAGAACATATCTCGCAGACATTG 59.789 45.833 0.00 0.00 35.73 2.82
1586 2315 3.134574 TCCAATATGCACGAATACCCC 57.865 47.619 0.00 0.00 0.00 4.95
1609 2338 5.590259 GTGTCATTATGTGCCCAAGAGTATT 59.410 40.000 0.00 0.00 0.00 1.89
1611 2340 4.513442 GTGTCATTATGTGCCCAAGAGTA 58.487 43.478 0.00 0.00 0.00 2.59
1617 2346 1.340893 CCTGGTGTCATTATGTGCCCA 60.341 52.381 0.00 0.00 0.00 5.36
1626 2355 1.971149 TCCCTGATCCTGGTGTCATT 58.029 50.000 5.31 0.00 0.00 2.57
1627 2356 1.842562 CTTCCCTGATCCTGGTGTCAT 59.157 52.381 5.31 0.00 0.00 3.06
1629 2358 1.208293 GTCTTCCCTGATCCTGGTGTC 59.792 57.143 0.00 0.00 0.00 3.67
1632 2361 1.577736 CTGTCTTCCCTGATCCTGGT 58.422 55.000 0.00 0.00 0.00 4.00
1636 2365 1.198713 TCTGCTGTCTTCCCTGATCC 58.801 55.000 0.00 0.00 0.00 3.36
1637 2366 2.433604 TCATCTGCTGTCTTCCCTGATC 59.566 50.000 0.00 0.00 0.00 2.92
1639 2368 1.829849 CTCATCTGCTGTCTTCCCTGA 59.170 52.381 0.00 0.00 0.00 3.86
1640 2369 1.743091 GCTCATCTGCTGTCTTCCCTG 60.743 57.143 0.00 0.00 0.00 4.45
1642 2371 0.251354 TGCTCATCTGCTGTCTTCCC 59.749 55.000 0.00 0.00 0.00 3.97
1643 2372 2.008329 CTTGCTCATCTGCTGTCTTCC 58.992 52.381 0.00 0.00 0.00 3.46
1644 2373 2.008329 CCTTGCTCATCTGCTGTCTTC 58.992 52.381 0.00 0.00 0.00 2.87
1645 2374 1.350351 ACCTTGCTCATCTGCTGTCTT 59.650 47.619 0.00 0.00 0.00 3.01
1646 2375 0.982704 ACCTTGCTCATCTGCTGTCT 59.017 50.000 0.00 0.00 0.00 3.41
1666 2395 0.397941 TCTTCCAACTGACCTGCTGG 59.602 55.000 8.29 8.29 39.83 4.85
1669 2398 1.338579 CCTCTCTTCCAACTGACCTGC 60.339 57.143 0.00 0.00 0.00 4.85
1674 2403 5.333581 TCTGTTATCCTCTCTTCCAACTGA 58.666 41.667 0.00 0.00 0.00 3.41
1702 2431 2.015587 CTCTGCATTTGAGGCCTCTTC 58.984 52.381 32.28 16.61 0.00 2.87
1710 2439 4.059511 CTGCTATCCTCTCTGCATTTGAG 58.940 47.826 0.00 0.00 34.79 3.02
1722 2451 1.696336 TCTTGGCCATCTGCTATCCTC 59.304 52.381 6.09 0.00 40.92 3.71
1746 2475 5.668471 TCTGTTATCCTCTCTGCATTTGAG 58.332 41.667 0.00 0.00 0.00 3.02
1790 2618 2.702478 TGGCCATCTGTTATCCTCTCTG 59.298 50.000 0.00 0.00 0.00 3.35
1791 2619 3.051940 TGGCCATCTGTTATCCTCTCT 57.948 47.619 0.00 0.00 0.00 3.10
1792 2620 3.135530 ACTTGGCCATCTGTTATCCTCTC 59.864 47.826 6.09 0.00 0.00 3.20
1793 2621 3.118112 CACTTGGCCATCTGTTATCCTCT 60.118 47.826 6.09 0.00 0.00 3.69
1794 2622 3.209410 CACTTGGCCATCTGTTATCCTC 58.791 50.000 6.09 0.00 0.00 3.71
1795 2623 2.092212 CCACTTGGCCATCTGTTATCCT 60.092 50.000 6.09 0.00 0.00 3.24
1796 2624 2.301346 CCACTTGGCCATCTGTTATCC 58.699 52.381 6.09 0.00 0.00 2.59
1809 2637 1.614903 TCTGCATTTGAAGCCACTTGG 59.385 47.619 0.00 0.00 38.53 3.61
1810 2638 2.555325 TCTCTGCATTTGAAGCCACTTG 59.445 45.455 0.00 0.00 0.00 3.16
1811 2639 2.818432 CTCTCTGCATTTGAAGCCACTT 59.182 45.455 0.00 0.00 0.00 3.16
1812 2640 2.039480 TCTCTCTGCATTTGAAGCCACT 59.961 45.455 0.00 0.00 0.00 4.00
1813 2641 2.430465 TCTCTCTGCATTTGAAGCCAC 58.570 47.619 0.00 0.00 0.00 5.01
1814 2642 2.865119 TCTCTCTGCATTTGAAGCCA 57.135 45.000 0.00 0.00 0.00 4.75
1815 2643 5.124457 TGTTATTCTCTCTGCATTTGAAGCC 59.876 40.000 0.00 0.00 0.00 4.35
1816 2644 6.093219 TCTGTTATTCTCTCTGCATTTGAAGC 59.907 38.462 0.00 0.00 0.00 3.86
1817 2645 7.606858 TCTGTTATTCTCTCTGCATTTGAAG 57.393 36.000 0.00 0.00 0.00 3.02
1818 2646 7.825761 TCATCTGTTATTCTCTCTGCATTTGAA 59.174 33.333 0.00 0.00 0.00 2.69
1819 2647 7.333323 TCATCTGTTATTCTCTCTGCATTTGA 58.667 34.615 0.00 0.00 0.00 2.69
1820 2648 7.254829 CCTCATCTGTTATTCTCTCTGCATTTG 60.255 40.741 0.00 0.00 0.00 2.32
1821 2649 6.766944 CCTCATCTGTTATTCTCTCTGCATTT 59.233 38.462 0.00 0.00 0.00 2.32
1822 2650 6.289834 CCTCATCTGTTATTCTCTCTGCATT 58.710 40.000 0.00 0.00 0.00 3.56
1823 2651 5.742546 GCCTCATCTGTTATTCTCTCTGCAT 60.743 44.000 0.00 0.00 0.00 3.96
1824 2652 4.442612 GCCTCATCTGTTATTCTCTCTGCA 60.443 45.833 0.00 0.00 0.00 4.41
1825 2653 4.057432 GCCTCATCTGTTATTCTCTCTGC 58.943 47.826 0.00 0.00 0.00 4.26
1826 2654 5.534207 AGCCTCATCTGTTATTCTCTCTG 57.466 43.478 0.00 0.00 0.00 3.35
1827 2655 5.660417 TGAAGCCTCATCTGTTATTCTCTCT 59.340 40.000 0.00 0.00 0.00 3.10
1828 2656 5.911752 TGAAGCCTCATCTGTTATTCTCTC 58.088 41.667 0.00 0.00 0.00 3.20
1829 2657 5.946942 TGAAGCCTCATCTGTTATTCTCT 57.053 39.130 0.00 0.00 0.00 3.10
1830 2658 6.820656 TCTTTGAAGCCTCATCTGTTATTCTC 59.179 38.462 0.00 0.00 0.00 2.87
1831 2659 6.715280 TCTTTGAAGCCTCATCTGTTATTCT 58.285 36.000 0.00 0.00 0.00 2.40
1832 2660 6.992063 TCTTTGAAGCCTCATCTGTTATTC 57.008 37.500 0.00 0.00 0.00 1.75
1833 2661 7.170965 TCTTCTTTGAAGCCTCATCTGTTATT 58.829 34.615 2.71 0.00 0.00 1.40
1834 2662 6.715280 TCTTCTTTGAAGCCTCATCTGTTAT 58.285 36.000 2.71 0.00 0.00 1.89
1835 2663 6.014242 TCTCTTCTTTGAAGCCTCATCTGTTA 60.014 38.462 2.71 0.00 0.00 2.41
1836 2664 4.978099 TCTTCTTTGAAGCCTCATCTGTT 58.022 39.130 2.71 0.00 0.00 3.16
1837 2665 4.285517 TCTCTTCTTTGAAGCCTCATCTGT 59.714 41.667 2.71 0.00 0.00 3.41
1945 2779 0.774491 AAGCCACCTGGAGGGGTTAA 60.774 55.000 19.63 0.00 42.67 2.01
2033 2867 3.439857 TGCAATAGAAGAAGGCCTTGT 57.560 42.857 26.25 18.00 34.68 3.16
2076 2910 3.252701 GGACCATGATGATGATGACAAGC 59.747 47.826 0.00 0.00 0.00 4.01
2183 3017 2.019249 TGCAACTTCCAGCAGCATATC 58.981 47.619 0.00 0.00 35.51 1.63
2250 3084 5.104610 ACACTGAATGATGAGGTAGAGCAAT 60.105 40.000 0.00 0.00 0.00 3.56
2298 3132 3.716353 TGATGGTACCCTCAACATATGCT 59.284 43.478 16.62 0.00 0.00 3.79
2303 3137 2.354704 CGTGTGATGGTACCCTCAACAT 60.355 50.000 20.02 0.42 0.00 2.71
2309 3143 2.754648 ACACGTGTGATGGTACCCT 58.245 52.632 22.71 0.00 0.00 4.34
2353 3187 3.932089 GTGATGAAAGTCCTCAGCTTCTC 59.068 47.826 0.00 0.00 32.85 2.87
2391 3225 4.775780 TGAACTTGTACTGGTATGCTAGGT 59.224 41.667 0.00 0.00 0.00 3.08
2394 3228 4.382685 GGCTGAACTTGTACTGGTATGCTA 60.383 45.833 0.00 0.00 0.00 3.49
2395 3229 3.600388 GCTGAACTTGTACTGGTATGCT 58.400 45.455 0.00 0.00 0.00 3.79
2396 3230 2.678336 GGCTGAACTTGTACTGGTATGC 59.322 50.000 0.00 0.00 0.00 3.14
2411 3251 1.949525 GAGTGCTGTTTTCTGGCTGAA 59.050 47.619 2.37 2.37 0.00 3.02
2421 3261 0.679505 TAGTGCCTCGAGTGCTGTTT 59.320 50.000 21.36 10.37 0.00 2.83
2496 3363 0.840288 TCAGCCCAGCTTGGAAGGTA 60.840 55.000 8.31 0.00 40.96 3.08
2543 3410 1.611977 CAGCAATATGCCCATCACTGG 59.388 52.381 0.00 0.00 46.52 4.00
2592 3459 1.373570 AGAATGCCTTGTAGCGCTTC 58.626 50.000 18.68 12.25 34.65 3.86
2817 3684 7.438459 AGAATATGAAGTACAACATAGGCGAAC 59.562 37.037 14.16 5.74 33.46 3.95
2888 3755 2.110901 ATTCCTTGCTGTGCTCTCAG 57.889 50.000 0.00 0.00 38.35 3.35
2889 3756 2.568956 AGTATTCCTTGCTGTGCTCTCA 59.431 45.455 0.00 0.00 0.00 3.27
2890 3757 2.935201 CAGTATTCCTTGCTGTGCTCTC 59.065 50.000 0.00 0.00 33.73 3.20
2891 3758 2.568956 TCAGTATTCCTTGCTGTGCTCT 59.431 45.455 0.00 0.00 38.98 4.09
2902 3769 2.168106 CTGCTGTGCTCTCAGTATTCCT 59.832 50.000 1.64 0.00 37.70 3.36
2929 3796 0.833409 TTCCCTGCTGTGCTCTCAGA 60.833 55.000 9.21 0.00 37.61 3.27
2930 3797 0.252479 ATTCCCTGCTGTGCTCTCAG 59.748 55.000 0.00 0.00 38.35 3.35
2931 3798 1.208052 GTATTCCCTGCTGTGCTCTCA 59.792 52.381 0.00 0.00 0.00 3.27
2932 3799 1.484240 AGTATTCCCTGCTGTGCTCTC 59.516 52.381 0.00 0.00 0.00 3.20
2933 3800 1.209019 CAGTATTCCCTGCTGTGCTCT 59.791 52.381 0.00 0.00 33.30 4.09
2934 3801 1.208052 TCAGTATTCCCTGCTGTGCTC 59.792 52.381 0.00 0.00 38.59 4.26
2935 3802 1.209019 CTCAGTATTCCCTGCTGTGCT 59.791 52.381 0.00 0.00 38.59 4.40
2936 3803 1.208052 TCTCAGTATTCCCTGCTGTGC 59.792 52.381 0.00 0.00 38.59 4.57
2937 3804 3.133542 TGATCTCAGTATTCCCTGCTGTG 59.866 47.826 0.00 0.00 38.59 3.66
2938 3805 3.133721 GTGATCTCAGTATTCCCTGCTGT 59.866 47.826 0.00 0.00 38.59 4.40
2939 3806 3.133542 TGTGATCTCAGTATTCCCTGCTG 59.866 47.826 0.00 0.00 38.81 4.41
2940 3807 3.378512 TGTGATCTCAGTATTCCCTGCT 58.621 45.455 0.00 0.00 32.32 4.24
2941 3808 3.386078 TCTGTGATCTCAGTATTCCCTGC 59.614 47.826 20.99 0.00 36.85 4.85
2942 3809 5.453057 CCTTCTGTGATCTCAGTATTCCCTG 60.453 48.000 20.99 2.91 36.85 4.45
2943 3810 4.653341 CCTTCTGTGATCTCAGTATTCCCT 59.347 45.833 20.99 0.00 36.85 4.20
2944 3811 4.202305 CCCTTCTGTGATCTCAGTATTCCC 60.202 50.000 20.99 0.00 36.85 3.97
2945 3812 4.651503 TCCCTTCTGTGATCTCAGTATTCC 59.348 45.833 20.99 0.00 36.85 3.01
2946 3813 5.860941 TCCCTTCTGTGATCTCAGTATTC 57.139 43.478 20.99 0.00 36.85 1.75
2947 3814 6.821616 ATTCCCTTCTGTGATCTCAGTATT 57.178 37.500 20.99 2.38 36.85 1.89
2948 3815 7.015098 CAGTATTCCCTTCTGTGATCTCAGTAT 59.985 40.741 20.99 10.56 36.85 2.12
2949 3816 6.322456 CAGTATTCCCTTCTGTGATCTCAGTA 59.678 42.308 20.99 12.89 36.85 2.74
2950 3817 5.128499 CAGTATTCCCTTCTGTGATCTCAGT 59.872 44.000 20.99 6.00 36.85 3.41
2951 3818 5.362143 TCAGTATTCCCTTCTGTGATCTCAG 59.638 44.000 16.95 16.95 36.85 3.35
2952 3819 5.272402 TCAGTATTCCCTTCTGTGATCTCA 58.728 41.667 0.00 0.00 0.00 3.27
2953 3820 5.596361 TCTCAGTATTCCCTTCTGTGATCTC 59.404 44.000 0.00 0.00 30.40 2.75
2954 3821 5.523588 TCTCAGTATTCCCTTCTGTGATCT 58.476 41.667 0.00 0.00 30.40 2.75
2955 3822 5.738783 GCTCTCAGTATTCCCTTCTGTGATC 60.739 48.000 0.00 0.00 33.43 2.92
2956 3823 4.100808 GCTCTCAGTATTCCCTTCTGTGAT 59.899 45.833 0.00 0.00 33.43 3.06
2957 3824 3.449018 GCTCTCAGTATTCCCTTCTGTGA 59.551 47.826 0.00 0.00 33.06 3.58
2958 3825 3.196469 TGCTCTCAGTATTCCCTTCTGTG 59.804 47.826 0.00 0.00 0.00 3.66
2959 3826 3.196685 GTGCTCTCAGTATTCCCTTCTGT 59.803 47.826 0.00 0.00 0.00 3.41
2960 3827 3.196469 TGTGCTCTCAGTATTCCCTTCTG 59.804 47.826 0.00 0.00 0.00 3.02
2961 3828 3.445008 TGTGCTCTCAGTATTCCCTTCT 58.555 45.455 0.00 0.00 0.00 2.85
2962 3829 3.791245 CTGTGCTCTCAGTATTCCCTTC 58.209 50.000 0.00 0.00 0.00 3.46
2963 3830 2.093235 GCTGTGCTCTCAGTATTCCCTT 60.093 50.000 1.64 0.00 37.70 3.95
2964 3831 1.484240 GCTGTGCTCTCAGTATTCCCT 59.516 52.381 1.64 0.00 37.70 4.20
2965 3832 1.208052 TGCTGTGCTCTCAGTATTCCC 59.792 52.381 1.64 0.00 37.70 3.97
2966 3833 2.548875 CTGCTGTGCTCTCAGTATTCC 58.451 52.381 1.64 0.00 37.70 3.01
2967 3834 2.548875 CCTGCTGTGCTCTCAGTATTC 58.451 52.381 7.47 0.00 37.70 1.75
2968 3835 1.209019 CCCTGCTGTGCTCTCAGTATT 59.791 52.381 7.47 0.00 37.70 1.89
2969 3836 0.829333 CCCTGCTGTGCTCTCAGTAT 59.171 55.000 7.47 0.00 37.70 2.12
2970 3837 0.251787 TCCCTGCTGTGCTCTCAGTA 60.252 55.000 7.47 2.73 37.70 2.74
2971 3838 1.123861 TTCCCTGCTGTGCTCTCAGT 61.124 55.000 7.47 0.00 37.70 3.41
2972 3839 0.673022 GTTCCCTGCTGTGCTCTCAG 60.673 60.000 0.00 0.00 38.35 3.35
2973 3840 1.372683 GTTCCCTGCTGTGCTCTCA 59.627 57.895 0.00 0.00 0.00 3.27
2974 3841 0.952984 GTGTTCCCTGCTGTGCTCTC 60.953 60.000 0.00 0.00 0.00 3.20
2975 3842 1.072159 GTGTTCCCTGCTGTGCTCT 59.928 57.895 0.00 0.00 0.00 4.09
2976 3843 1.072159 AGTGTTCCCTGCTGTGCTC 59.928 57.895 0.00 0.00 0.00 4.26
2977 3844 1.228063 CAGTGTTCCCTGCTGTGCT 60.228 57.895 0.00 0.00 0.00 4.40
2978 3845 1.227943 TCAGTGTTCCCTGCTGTGC 60.228 57.895 0.00 0.00 32.32 4.57
2979 3846 0.394192 TCTCAGTGTTCCCTGCTGTG 59.606 55.000 0.00 0.00 32.32 3.66
2980 3847 0.683973 CTCTCAGTGTTCCCTGCTGT 59.316 55.000 0.00 0.00 32.32 4.40
2981 3848 0.673022 GCTCTCAGTGTTCCCTGCTG 60.673 60.000 0.00 0.00 32.32 4.41
2982 3849 1.123861 TGCTCTCAGTGTTCCCTGCT 61.124 55.000 0.00 0.00 32.32 4.24
2983 3850 0.952984 GTGCTCTCAGTGTTCCCTGC 60.953 60.000 0.00 0.00 32.32 4.85
2984 3851 0.394192 TGTGCTCTCAGTGTTCCCTG 59.606 55.000 0.00 0.00 0.00 4.45
2985 3852 1.277557 GATGTGCTCTCAGTGTTCCCT 59.722 52.381 0.00 0.00 0.00 4.20
2986 3853 1.002430 TGATGTGCTCTCAGTGTTCCC 59.998 52.381 0.00 0.00 0.00 3.97
2987 3854 2.344950 CTGATGTGCTCTCAGTGTTCC 58.655 52.381 0.00 0.00 36.26 3.62
2988 3855 2.344950 CCTGATGTGCTCTCAGTGTTC 58.655 52.381 11.60 0.00 38.77 3.18
2989 3856 1.002888 CCCTGATGTGCTCTCAGTGTT 59.997 52.381 11.60 0.00 38.77 3.32
2990 3857 0.612229 CCCTGATGTGCTCTCAGTGT 59.388 55.000 11.60 0.00 38.77 3.55
2991 3858 0.900421 TCCCTGATGTGCTCTCAGTG 59.100 55.000 11.60 0.00 38.77 3.66
3004 3892 1.213296 GAAGCCCCAGTATTCCCTGA 58.787 55.000 0.00 0.00 34.23 3.86
3005 3893 0.183731 GGAAGCCCCAGTATTCCCTG 59.816 60.000 0.00 0.00 37.17 4.45
3032 3920 2.604912 ACCAGGATTTTGGGAGGTTC 57.395 50.000 0.00 0.00 42.76 3.62
3099 4044 2.618241 TGCGAGCAACATCAGAAACTTT 59.382 40.909 0.00 0.00 0.00 2.66
3190 4138 3.231736 ACCTGCTCGGTGTCCGTT 61.232 61.111 8.03 0.00 46.80 4.44
3239 4187 8.478877 CATTGAAGTAGAAGAACACCCTATAGT 58.521 37.037 0.00 0.00 0.00 2.12
3313 4447 3.118445 AGACCTTTCTTGCATAGCCTCTC 60.118 47.826 0.00 0.00 0.00 3.20
3327 4461 2.284190 GCATAGCACTCCAGACCTTTC 58.716 52.381 0.00 0.00 0.00 2.62
3407 4541 4.036027 CAGATGTTGACACTTTTCTGCAGT 59.964 41.667 14.67 0.00 0.00 4.40
3541 4714 5.430886 TCTCGTGTGATTCATTGATGGATT 58.569 37.500 0.00 0.00 0.00 3.01
3681 4854 2.046285 CCGGTCATCAGGCCAAACC 61.046 63.158 5.01 3.61 39.61 3.27
3866 5039 2.040278 AGCAAGTCCAAGACCATTGCTA 59.960 45.455 17.58 0.00 45.49 3.49
3994 5167 3.617669 CCACTTCGTCAAATGACAACAC 58.382 45.455 13.51 0.00 44.99 3.32
4060 5233 2.099756 AGTTGCAACAGAAGCACCTTTC 59.900 45.455 30.11 0.00 42.54 2.62
4098 5282 0.546747 TCCTGGTTCCCCGTCAGATT 60.547 55.000 0.00 0.00 0.00 2.40
4240 5544 7.930325 TCACATTCAAAGAATGCACCAAATAAA 59.070 29.630 17.12 0.00 0.00 1.40
4330 5637 8.934023 TTTTACTTCAGAAGGTAATTCCACAT 57.066 30.769 14.90 0.00 38.84 3.21
4352 5659 8.667463 GCATATTCATGTAGGCAAACAATTTTT 58.333 29.630 0.00 0.00 34.40 1.94
4424 5741 4.371855 TGTCAGTTAGCATTCTCTACCG 57.628 45.455 0.00 0.00 0.00 4.02
4685 6230 2.561478 TAACAGGGCAACTCAACTCC 57.439 50.000 0.00 0.00 0.00 3.85
4890 6497 1.473434 GGTAGTCCCGCCAAAGATCAG 60.473 57.143 0.00 0.00 0.00 2.90
4891 6498 0.539986 GGTAGTCCCGCCAAAGATCA 59.460 55.000 0.00 0.00 0.00 2.92
4952 6564 0.622665 CAAGGGCTCTTCCTGATGGT 59.377 55.000 0.00 0.00 37.20 3.55
4957 6569 0.689623 ACTGACAAGGGCTCTTCCTG 59.310 55.000 0.00 0.00 37.20 3.86


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

AutoCloner maintained by Alex Coulton.