Multiple sequence alignment - TraesCS5A01G225500

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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 TraesCS5A01G225500 chr5A 100.000 3131 0 0 1 3131 441111019 441114149 0.000000e+00 5782.0
1 TraesCS5A01G225500 chr5A 94.444 72 4 0 1 72 441098467 441098538 9.180000e-21 111.0
2 TraesCS5A01G225500 chr5D 91.401 2256 139 24 72 2316 339967256 339969467 0.000000e+00 3040.0
3 TraesCS5A01G225500 chr5D 95.349 645 18 7 2496 3131 339969799 339970440 0.000000e+00 1014.0
4 TraesCS5A01G225500 chr5D 94.643 56 2 1 2445 2499 339969461 339969516 5.560000e-13 86.1
5 TraesCS5A01G225500 chr5B 90.262 1602 101 20 72 1661 399021813 399023371 0.000000e+00 2043.0
6 TraesCS5A01G225500 chr5B 94.211 380 22 0 1749 2128 399023443 399023822 5.820000e-162 580.0
7 TraesCS5A01G225500 chr5B 92.899 338 18 3 2497 2833 399024690 399025022 1.310000e-133 486.0
8 TraesCS5A01G225500 chr5B 93.939 198 10 2 2936 3131 399025674 399025871 6.560000e-77 298.0
9 TraesCS5A01G225500 chr5B 94.410 161 7 2 2804 2963 399025028 399025187 2.410000e-61 246.0
10 TraesCS5A01G225500 chr6A 94.521 73 4 0 1 73 359642740 359642668 2.550000e-21 113.0
11 TraesCS5A01G225500 chr7A 93.151 73 5 0 1 73 540317151 540317223 1.190000e-19 108.0
12 TraesCS5A01G225500 chr7A 91.667 72 3 3 2 72 508499624 508499693 2.570000e-16 97.1
13 TraesCS5A01G225500 chr3A 93.056 72 5 0 1 72 621566916 621566845 4.270000e-19 106.0
14 TraesCS5A01G225500 chr7D 94.118 68 2 2 7 73 161061647 161061581 5.520000e-18 102.0
15 TraesCS5A01G225500 chr4A 91.781 73 6 0 1 73 131304454 131304526 5.520000e-18 102.0
16 TraesCS5A01G225500 chr2A 91.781 73 4 2 1 72 457276966 457276895 1.990000e-17 100.0
17 TraesCS5A01G225500 chr2A 89.474 76 5 3 1 75 412243462 412243389 3.320000e-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 TraesCS5A01G225500 chr5A 441111019 441114149 3130 False 5782.000000 5782 100.000000 1 3131 1 chr5A.!!$F2 3130
1 TraesCS5A01G225500 chr5D 339967256 339970440 3184 False 1380.033333 3040 93.797667 72 3131 3 chr5D.!!$F1 3059
2 TraesCS5A01G225500 chr5B 399021813 399025871 4058 False 730.600000 2043 93.144200 72 3131 5 chr5B.!!$F1 3059

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
805 816 0.10412 TGACACACTGGTTCGTGAGG 59.896 55.0 0.0 0.0 38.27 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2382 2425 0.035317 ACATTGTTGGCTCGAGCTCA 59.965 50.0 34.46 26.77 41.7 4.26 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
19 20 2.029838 AAGCTTCCTAGTTGCGATGG 57.970 50.000 0.00 0.00 0.00 3.51
20 21 0.905357 AGCTTCCTAGTTGCGATGGT 59.095 50.000 0.00 0.00 0.00 3.55
21 22 1.134670 AGCTTCCTAGTTGCGATGGTC 60.135 52.381 0.00 0.00 0.00 4.02
22 23 1.405526 GCTTCCTAGTTGCGATGGTCA 60.406 52.381 0.00 0.00 0.00 4.02
23 24 2.743183 GCTTCCTAGTTGCGATGGTCAT 60.743 50.000 0.00 0.00 0.00 3.06
24 25 3.492656 GCTTCCTAGTTGCGATGGTCATA 60.493 47.826 0.00 0.00 0.00 2.15
25 26 3.728076 TCCTAGTTGCGATGGTCATAC 57.272 47.619 0.00 0.00 0.00 2.39
26 27 2.034179 TCCTAGTTGCGATGGTCATACG 59.966 50.000 0.00 0.00 0.00 3.06
27 28 2.034179 CCTAGTTGCGATGGTCATACGA 59.966 50.000 0.00 0.00 0.00 3.43
28 29 1.922570 AGTTGCGATGGTCATACGAC 58.077 50.000 0.00 0.00 41.80 4.34
29 30 1.476891 AGTTGCGATGGTCATACGACT 59.523 47.619 0.00 4.60 42.21 4.18
30 31 2.686405 AGTTGCGATGGTCATACGACTA 59.314 45.455 0.00 0.00 42.21 2.59
31 32 3.129813 AGTTGCGATGGTCATACGACTAA 59.870 43.478 0.00 0.00 42.21 2.24
32 33 3.349488 TGCGATGGTCATACGACTAAG 57.651 47.619 0.00 0.00 42.21 2.18
33 34 2.686405 TGCGATGGTCATACGACTAAGT 59.314 45.455 0.00 0.00 42.21 2.24
34 35 3.242969 TGCGATGGTCATACGACTAAGTC 60.243 47.826 0.00 0.00 42.21 3.01
35 36 3.852572 GCGATGGTCATACGACTAAGTCC 60.853 52.174 0.00 0.00 42.21 3.85
36 37 3.564644 CGATGGTCATACGACTAAGTCCT 59.435 47.826 0.00 0.00 42.21 3.85
37 38 4.036498 CGATGGTCATACGACTAAGTCCTT 59.964 45.833 0.00 0.00 42.21 3.36
38 39 4.978083 TGGTCATACGACTAAGTCCTTC 57.022 45.455 0.00 0.00 42.21 3.46
39 40 4.597004 TGGTCATACGACTAAGTCCTTCT 58.403 43.478 0.00 0.00 42.21 2.85
40 41 4.398358 TGGTCATACGACTAAGTCCTTCTG 59.602 45.833 0.00 0.00 42.21 3.02
41 42 4.398673 GGTCATACGACTAAGTCCTTCTGT 59.601 45.833 0.00 0.00 42.21 3.41
42 43 5.105837 GGTCATACGACTAAGTCCTTCTGTT 60.106 44.000 0.00 0.00 42.21 3.16
43 44 6.094603 GGTCATACGACTAAGTCCTTCTGTTA 59.905 42.308 0.00 0.00 42.21 2.41
44 45 7.188157 GTCATACGACTAAGTCCTTCTGTTAG 58.812 42.308 0.00 0.00 39.22 2.34
45 46 6.318144 TCATACGACTAAGTCCTTCTGTTAGG 59.682 42.308 0.00 0.00 36.59 2.69
46 47 4.660168 ACGACTAAGTCCTTCTGTTAGGA 58.340 43.478 0.00 0.00 42.02 2.94
53 54 3.895232 TCCTTCTGTTAGGACATCTGC 57.105 47.619 0.00 0.00 39.40 4.26
54 55 2.501723 TCCTTCTGTTAGGACATCTGCC 59.498 50.000 0.00 0.00 39.40 4.85
55 56 2.544685 CTTCTGTTAGGACATCTGCCG 58.455 52.381 0.00 0.00 34.72 5.69
56 57 1.557099 TCTGTTAGGACATCTGCCGT 58.443 50.000 0.00 0.00 34.72 5.68
57 58 1.204704 TCTGTTAGGACATCTGCCGTG 59.795 52.381 0.00 0.00 34.72 4.94
58 59 1.204704 CTGTTAGGACATCTGCCGTGA 59.795 52.381 0.00 0.00 34.72 4.35
59 60 1.067142 TGTTAGGACATCTGCCGTGAC 60.067 52.381 0.00 0.00 0.00 3.67
60 61 1.067142 GTTAGGACATCTGCCGTGACA 60.067 52.381 0.00 0.00 0.00 3.58
61 62 1.262417 TAGGACATCTGCCGTGACAA 58.738 50.000 0.00 0.00 0.00 3.18
62 63 0.615331 AGGACATCTGCCGTGACAAT 59.385 50.000 0.00 0.00 0.00 2.71
63 64 1.003580 AGGACATCTGCCGTGACAATT 59.996 47.619 0.00 0.00 0.00 2.32
64 65 1.398390 GGACATCTGCCGTGACAATTC 59.602 52.381 0.00 0.00 0.00 2.17
65 66 1.061131 GACATCTGCCGTGACAATTCG 59.939 52.381 0.00 0.00 0.00 3.34
66 67 1.337728 ACATCTGCCGTGACAATTCGA 60.338 47.619 0.00 0.00 0.00 3.71
67 68 1.061131 CATCTGCCGTGACAATTCGAC 59.939 52.381 0.00 0.00 0.00 4.20
68 69 1.006825 TCTGCCGTGACAATTCGACG 61.007 55.000 0.00 0.00 0.00 5.12
69 70 1.006825 CTGCCGTGACAATTCGACGA 61.007 55.000 0.00 0.00 35.05 4.20
70 71 1.279527 TGCCGTGACAATTCGACGAC 61.280 55.000 0.00 0.00 35.05 4.34
198 200 4.050852 AGCAACAGAAAGAAAAGGCAAG 57.949 40.909 0.00 0.00 0.00 4.01
210 212 2.829914 GGCAAGCCCATCGATGCA 60.830 61.111 20.25 0.00 40.51 3.96
217 219 1.954528 CCCATCGATGCATGCTTCC 59.045 57.895 23.52 10.42 0.00 3.46
220 222 0.881600 CATCGATGCATGCTTCCGGA 60.882 55.000 23.52 17.33 0.00 5.14
226 228 2.708216 TGCATGCTTCCGGAGAAATA 57.292 45.000 20.33 0.00 0.00 1.40
227 229 2.997980 TGCATGCTTCCGGAGAAATAA 58.002 42.857 20.33 0.00 0.00 1.40
228 230 3.351740 TGCATGCTTCCGGAGAAATAAA 58.648 40.909 20.33 0.00 0.00 1.40
229 231 3.953612 TGCATGCTTCCGGAGAAATAAAT 59.046 39.130 20.33 0.00 0.00 1.40
230 232 4.202040 TGCATGCTTCCGGAGAAATAAATG 60.202 41.667 20.33 4.77 0.00 2.32
231 233 4.036734 GCATGCTTCCGGAGAAATAAATGA 59.963 41.667 11.37 0.00 0.00 2.57
275 277 3.007940 TGGGAGGATTTACCATAGCATCG 59.992 47.826 0.00 0.00 42.04 3.84
277 279 4.499183 GGAGGATTTACCATAGCATCGAG 58.501 47.826 0.00 0.00 42.04 4.04
287 289 4.576463 ACCATAGCATCGAGTTTCCATTTC 59.424 41.667 0.00 0.00 0.00 2.17
320 322 4.529897 TCTACCGTAGCATCTAAGGTTCA 58.470 43.478 14.72 2.41 36.49 3.18
332 334 0.540365 AAGGTTCACTGCACATGGGG 60.540 55.000 0.00 0.00 0.00 4.96
362 364 3.971245 AGTTCTCAAATCTTCTCCGCT 57.029 42.857 0.00 0.00 0.00 5.52
363 365 4.278975 AGTTCTCAAATCTTCTCCGCTT 57.721 40.909 0.00 0.00 0.00 4.68
364 366 3.999663 AGTTCTCAAATCTTCTCCGCTTG 59.000 43.478 0.00 0.00 0.00 4.01
365 367 3.961480 TCTCAAATCTTCTCCGCTTGA 57.039 42.857 0.00 0.00 0.00 3.02
366 368 4.478206 TCTCAAATCTTCTCCGCTTGAT 57.522 40.909 0.00 0.00 0.00 2.57
367 369 4.437239 TCTCAAATCTTCTCCGCTTGATC 58.563 43.478 0.00 0.00 0.00 2.92
368 370 4.161189 TCTCAAATCTTCTCCGCTTGATCT 59.839 41.667 0.00 0.00 0.00 2.75
369 371 4.836825 TCAAATCTTCTCCGCTTGATCTT 58.163 39.130 0.00 0.00 0.00 2.40
370 372 4.872691 TCAAATCTTCTCCGCTTGATCTTC 59.127 41.667 0.00 0.00 0.00 2.87
371 373 2.568696 TCTTCTCCGCTTGATCTTCG 57.431 50.000 0.00 0.00 0.00 3.79
372 374 0.926846 CTTCTCCGCTTGATCTTCGC 59.073 55.000 0.00 0.00 0.00 4.70
373 375 0.532573 TTCTCCGCTTGATCTTCGCT 59.467 50.000 0.00 0.00 0.00 4.93
374 376 0.179127 TCTCCGCTTGATCTTCGCTG 60.179 55.000 0.00 0.00 0.00 5.18
375 377 1.760268 CTCCGCTTGATCTTCGCTGC 61.760 60.000 0.00 0.00 0.00 5.25
376 378 2.102438 CCGCTTGATCTTCGCTGCA 61.102 57.895 0.00 0.00 0.00 4.41
377 379 1.059994 CGCTTGATCTTCGCTGCAC 59.940 57.895 0.00 0.00 0.00 4.57
378 380 1.629345 CGCTTGATCTTCGCTGCACA 61.629 55.000 0.00 0.00 0.00 4.57
418 420 4.674885 GCTCTAACGGTACCAGTCTTCTTC 60.675 50.000 13.54 0.00 0.00 2.87
466 468 1.946768 TCCACTTGCACGAAAAGGAAG 59.053 47.619 0.00 0.00 39.89 3.46
468 470 2.357637 CCACTTGCACGAAAAGGAAGAA 59.642 45.455 0.00 0.00 37.78 2.52
480 482 0.249911 AGGAAGAACACCTCGTGTGC 60.250 55.000 0.00 0.00 46.79 4.57
506 508 5.408604 GGCTACGGACATAATTATGTTGAGG 59.591 44.000 27.48 19.29 46.20 3.86
572 574 6.808008 TGAATTTGTCTGAATGTTCTCTCC 57.192 37.500 0.00 0.00 0.00 3.71
597 599 2.292267 CTGCACAACAGGAGTTCAGTT 58.708 47.619 0.00 0.00 43.19 3.16
598 600 2.288666 TGCACAACAGGAGTTCAGTTC 58.711 47.619 0.00 0.00 35.28 3.01
599 601 2.288666 GCACAACAGGAGTTCAGTTCA 58.711 47.619 0.00 0.00 35.28 3.18
600 602 2.289002 GCACAACAGGAGTTCAGTTCAG 59.711 50.000 0.00 0.00 35.28 3.02
601 603 3.535561 CACAACAGGAGTTCAGTTCAGT 58.464 45.455 0.00 0.00 35.28 3.41
602 604 4.693283 CACAACAGGAGTTCAGTTCAGTA 58.307 43.478 0.00 0.00 35.28 2.74
603 605 5.116180 CACAACAGGAGTTCAGTTCAGTAA 58.884 41.667 0.00 0.00 35.28 2.24
604 606 5.584649 CACAACAGGAGTTCAGTTCAGTAAA 59.415 40.000 0.00 0.00 35.28 2.01
627 629 6.449830 ACAACCTACTCCATAAGAAACCTT 57.550 37.500 0.00 0.00 0.00 3.50
645 647 1.461091 TTGAGGTCAAGGACGCGACT 61.461 55.000 15.93 7.85 32.65 4.18
648 650 0.526662 AGGTCAAGGACGCGACTAAG 59.473 55.000 15.93 7.32 32.65 2.18
649 651 0.524862 GGTCAAGGACGCGACTAAGA 59.475 55.000 15.93 9.58 32.65 2.10
661 665 4.624452 ACGCGACTAAGAAATAACCACTTC 59.376 41.667 15.93 0.00 0.00 3.01
668 672 8.514330 ACTAAGAAATAACCACTTCACACAAA 57.486 30.769 0.00 0.00 0.00 2.83
703 710 2.029369 GTGGTCACCCGCAACGTA 59.971 61.111 0.00 0.00 41.16 3.57
704 711 1.594836 GTGGTCACCCGCAACGTAA 60.595 57.895 0.00 0.00 41.16 3.18
726 737 8.004344 CGTAAGTGTGCAGTTCTAATATATTGC 58.996 37.037 8.28 3.23 0.00 3.56
727 738 9.046296 GTAAGTGTGCAGTTCTAATATATTGCT 57.954 33.333 8.28 0.00 33.00 3.91
729 740 8.824159 AGTGTGCAGTTCTAATATATTGCTAG 57.176 34.615 8.28 0.00 33.00 3.42
730 741 7.386299 AGTGTGCAGTTCTAATATATTGCTAGC 59.614 37.037 8.10 8.10 33.00 3.42
746 757 1.405821 CTAGCATCGGTCGTCCTCTTT 59.594 52.381 0.00 0.00 0.00 2.52
758 769 3.120792 CGTCCTCTTTCTGACGTGAAAA 58.879 45.455 0.00 0.00 46.83 2.29
762 773 6.591261 GTCCTCTTTCTGACGTGAAAAATAC 58.409 40.000 0.00 0.00 35.79 1.89
798 809 0.401738 CAGGGGATGACACACTGGTT 59.598 55.000 0.00 0.00 0.00 3.67
799 810 0.693049 AGGGGATGACACACTGGTTC 59.307 55.000 0.00 0.00 0.00 3.62
800 811 0.673644 GGGGATGACACACTGGTTCG 60.674 60.000 0.00 0.00 0.00 3.95
805 816 0.104120 TGACACACTGGTTCGTGAGG 59.896 55.000 0.00 0.00 38.27 3.86
827 838 2.220615 ATTGGTCGATGCGTCCGTCA 62.221 55.000 0.00 0.00 37.84 4.35
847 858 1.912043 AGTCAAGTCAATGGGAGAGGG 59.088 52.381 0.00 0.00 0.00 4.30
850 861 1.635487 CAAGTCAATGGGAGAGGGGAA 59.365 52.381 0.00 0.00 0.00 3.97
851 862 1.290134 AGTCAATGGGAGAGGGGAAC 58.710 55.000 0.00 0.00 0.00 3.62
852 863 0.991920 GTCAATGGGAGAGGGGAACA 59.008 55.000 0.00 0.00 0.00 3.18
853 864 0.991920 TCAATGGGAGAGGGGAACAC 59.008 55.000 0.00 0.00 0.00 3.32
854 865 0.392998 CAATGGGAGAGGGGAACACG 60.393 60.000 0.00 0.00 0.00 4.49
898 909 3.814283 GACCTGCATCAATCAATCTCCTC 59.186 47.826 0.00 0.00 0.00 3.71
903 914 1.945387 TCAATCAATCTCCTCGCAGC 58.055 50.000 0.00 0.00 0.00 5.25
907 918 1.880340 CAATCTCCTCGCAGCGTCC 60.880 63.158 15.93 0.00 0.00 4.79
942 953 2.107552 ACAAAATTCTCGGTTCCTCCCA 59.892 45.455 0.00 0.00 0.00 4.37
943 954 2.488153 CAAAATTCTCGGTTCCTCCCAC 59.512 50.000 0.00 0.00 0.00 4.61
944 955 0.249398 AATTCTCGGTTCCTCCCACG 59.751 55.000 0.00 0.00 0.00 4.94
949 960 2.112297 GGTTCCTCCCACGTTGCA 59.888 61.111 0.00 0.00 0.00 4.08
966 977 1.064758 TGCAAGGTGCCTATACAAGGG 60.065 52.381 0.00 0.00 46.65 3.95
967 978 1.211949 GCAAGGTGCCTATACAAGGGA 59.788 52.381 0.00 0.00 46.65 4.20
1056 1067 2.279784 CTTCTCCCGCTCATCGCC 60.280 66.667 0.00 0.00 36.73 5.54
1085 1096 2.735237 GGTCCGGTCGATGATCCC 59.265 66.667 0.00 0.00 0.00 3.85
1124 1135 8.347004 TCTCCATGAATATTTTTGTAACTGCA 57.653 30.769 0.00 0.00 0.00 4.41
1288 1299 4.056125 CTCCAGCGTCAGCCGTCA 62.056 66.667 0.00 0.00 46.67 4.35
1458 1469 2.640684 CGACAACGCATTGGCATTC 58.359 52.632 0.00 0.00 45.07 2.67
1470 1481 1.750399 GGCATTCCCATCACGCACT 60.750 57.895 0.00 0.00 0.00 4.40
1473 1484 0.107508 CATTCCCATCACGCACTCCT 60.108 55.000 0.00 0.00 0.00 3.69
1485 1496 3.684305 CACGCACTCCTTGTTGATTATCA 59.316 43.478 0.00 0.00 0.00 2.15
1518 1529 2.548057 TGACATGAACGGTGCTTTCTTC 59.452 45.455 0.00 0.00 0.00 2.87
1661 1672 2.158943 CCCCGTGAAGAAGAAGGTATCC 60.159 54.545 0.00 0.00 0.00 2.59
1663 1674 3.134804 CCCGTGAAGAAGAAGGTATCCAT 59.865 47.826 0.00 0.00 0.00 3.41
1664 1675 4.372656 CCGTGAAGAAGAAGGTATCCATC 58.627 47.826 0.00 0.00 0.00 3.51
1665 1676 4.372656 CGTGAAGAAGAAGGTATCCATCC 58.627 47.826 0.00 0.00 0.00 3.51
1689 1700 7.345653 TCCATGTGTTCTAAATAGTCATCTCCT 59.654 37.037 0.00 0.00 0.00 3.69
1710 1721 3.036091 TGTTCTACCCCATGCTACCTAC 58.964 50.000 0.00 0.00 0.00 3.18
1728 1739 0.740868 ACGTTCGCACCCATGATCAG 60.741 55.000 0.09 0.00 0.00 2.90
1839 1882 0.323087 ACAACCACGCTAAATCCCCC 60.323 55.000 0.00 0.00 0.00 5.40
1872 1915 2.358737 GGCAACGAGTCCACAGGG 60.359 66.667 0.00 0.00 0.00 4.45
1873 1916 2.426023 GCAACGAGTCCACAGGGT 59.574 61.111 0.00 0.00 34.93 4.34
1879 1922 2.282674 AGTCCACAGGGTACGCGA 60.283 61.111 15.93 0.00 34.93 5.87
1884 1927 2.282674 ACAGGGTACGCGAGGTCA 60.283 61.111 15.93 0.00 0.00 4.02
1886 1929 2.282674 AGGGTACGCGAGGTCACA 60.283 61.111 15.93 0.00 0.00 3.58
1938 1981 1.002251 CGGACGATCAGGCTAGAAGAC 60.002 57.143 0.00 0.00 0.00 3.01
2043 2086 4.728772 TGTTGGACAAGATGGTGAATTCT 58.271 39.130 7.05 0.00 0.00 2.40
2110 2153 5.649831 GTGGCTGAGAGAATACTGGAAAATT 59.350 40.000 0.00 0.00 0.00 1.82
2155 2198 3.014623 GCCCAAGTATTTAGGTGTGGAC 58.985 50.000 0.00 0.00 0.00 4.02
2198 2241 6.915843 GGTGGTTTCTTATGGTATAATTTGCG 59.084 38.462 0.00 0.00 0.00 4.85
2213 2256 2.697431 TTGCGCGTTTGCTATTTCTT 57.303 40.000 8.43 0.00 39.65 2.52
2267 2310 0.178950 AGCACAGTGGAGTCAGGAGA 60.179 55.000 1.84 0.00 0.00 3.71
2268 2311 0.246086 GCACAGTGGAGTCAGGAGAG 59.754 60.000 1.84 0.00 0.00 3.20
2269 2312 0.246086 CACAGTGGAGTCAGGAGAGC 59.754 60.000 0.00 0.00 0.00 4.09
2270 2313 0.902516 ACAGTGGAGTCAGGAGAGCC 60.903 60.000 0.00 0.00 0.00 4.70
2278 2321 1.133513 AGTCAGGAGAGCCGATCTGAT 60.134 52.381 0.00 0.00 38.84 2.90
2285 2328 1.800283 GAGCCGATCTGATGCCGAGA 61.800 60.000 0.00 0.00 0.00 4.04
2301 2344 0.941463 GAGATGGCCATAGTGTCGCG 60.941 60.000 20.84 0.00 0.00 5.87
2302 2345 1.956170 GATGGCCATAGTGTCGCGG 60.956 63.158 20.84 0.00 0.00 6.46
2303 2346 3.460672 ATGGCCATAGTGTCGCGGG 62.461 63.158 19.18 0.00 0.00 6.13
2304 2347 4.157120 GGCCATAGTGTCGCGGGT 62.157 66.667 6.13 0.00 0.00 5.28
2305 2348 2.890474 GCCATAGTGTCGCGGGTG 60.890 66.667 6.13 0.00 0.00 4.61
2306 2349 2.890474 CCATAGTGTCGCGGGTGC 60.890 66.667 6.13 0.00 37.91 5.01
2307 2350 2.125713 CATAGTGTCGCGGGTGCA 60.126 61.111 6.13 0.00 42.97 4.57
2308 2351 2.167219 CATAGTGTCGCGGGTGCAG 61.167 63.158 6.13 0.00 42.97 4.41
2309 2352 3.371097 ATAGTGTCGCGGGTGCAGG 62.371 63.158 6.13 0.00 42.97 4.85
2317 2360 3.136123 CGGGTGCAGGCAAGGATG 61.136 66.667 0.00 0.00 0.00 3.51
2318 2361 2.356278 GGGTGCAGGCAAGGATGA 59.644 61.111 0.00 0.00 0.00 2.92
2319 2362 1.751927 GGGTGCAGGCAAGGATGAG 60.752 63.158 0.00 0.00 0.00 2.90
2320 2363 1.751927 GGTGCAGGCAAGGATGAGG 60.752 63.158 0.00 0.00 0.00 3.86
2321 2364 1.751927 GTGCAGGCAAGGATGAGGG 60.752 63.158 0.00 0.00 0.00 4.30
2322 2365 2.233566 TGCAGGCAAGGATGAGGGT 61.234 57.895 0.00 0.00 0.00 4.34
2323 2366 1.000396 GCAGGCAAGGATGAGGGTT 60.000 57.895 0.00 0.00 0.00 4.11
2324 2367 1.318158 GCAGGCAAGGATGAGGGTTG 61.318 60.000 0.00 0.00 0.00 3.77
2325 2368 0.682209 CAGGCAAGGATGAGGGTTGG 60.682 60.000 0.00 0.00 0.00 3.77
2326 2369 2.054453 GGCAAGGATGAGGGTTGGC 61.054 63.158 0.00 0.00 39.25 4.52
2327 2370 2.054453 GCAAGGATGAGGGTTGGCC 61.054 63.158 0.00 0.00 0.00 5.36
2328 2371 1.750399 CAAGGATGAGGGTTGGCCG 60.750 63.158 0.00 0.00 34.97 6.13
2329 2372 2.983879 AAGGATGAGGGTTGGCCGG 61.984 63.158 0.00 0.00 34.97 6.13
2330 2373 3.728373 GGATGAGGGTTGGCCGGT 61.728 66.667 1.90 0.00 34.97 5.28
2331 2374 2.438434 GATGAGGGTTGGCCGGTG 60.438 66.667 1.90 0.00 34.97 4.94
2332 2375 4.740822 ATGAGGGTTGGCCGGTGC 62.741 66.667 1.90 0.00 34.97 5.01
2348 2391 4.894896 GCGGGTGGGGGCCTATTG 62.895 72.222 0.84 0.00 0.00 1.90
2349 2392 4.894896 CGGGTGGGGGCCTATTGC 62.895 72.222 0.84 0.00 40.16 3.56
2350 2393 3.749870 GGGTGGGGGCCTATTGCA 61.750 66.667 0.84 0.00 43.89 4.08
2351 2394 2.608759 GGTGGGGGCCTATTGCAT 59.391 61.111 0.84 0.00 43.89 3.96
2352 2395 1.075301 GGTGGGGGCCTATTGCATT 60.075 57.895 0.84 0.00 43.89 3.56
2353 2396 0.690744 GGTGGGGGCCTATTGCATTT 60.691 55.000 0.84 0.00 43.89 2.32
2354 2397 1.203237 GTGGGGGCCTATTGCATTTT 58.797 50.000 0.84 0.00 43.89 1.82
2355 2398 1.138859 GTGGGGGCCTATTGCATTTTC 59.861 52.381 0.84 0.00 43.89 2.29
2356 2399 0.389025 GGGGGCCTATTGCATTTTCG 59.611 55.000 0.84 0.00 43.89 3.46
2357 2400 1.111277 GGGGCCTATTGCATTTTCGT 58.889 50.000 0.84 0.00 43.89 3.85
2358 2401 1.067060 GGGGCCTATTGCATTTTCGTC 59.933 52.381 0.84 0.00 43.89 4.20
2359 2402 1.268539 GGGCCTATTGCATTTTCGTCG 60.269 52.381 0.84 0.00 43.89 5.12
2360 2403 1.466855 GCCTATTGCATTTTCGTCGC 58.533 50.000 0.00 0.00 40.77 5.19
2361 2404 1.859998 GCCTATTGCATTTTCGTCGCC 60.860 52.381 0.00 0.00 40.77 5.54
2362 2405 1.594518 CCTATTGCATTTTCGTCGCCG 60.595 52.381 0.00 0.00 0.00 6.46
2363 2406 0.247894 TATTGCATTTTCGTCGCCGC 60.248 50.000 0.00 0.00 0.00 6.53
2364 2407 1.922135 ATTGCATTTTCGTCGCCGCT 61.922 50.000 0.00 0.00 0.00 5.52
2365 2408 2.276680 GCATTTTCGTCGCCGCTC 60.277 61.111 0.00 0.00 0.00 5.03
2366 2409 2.020016 CATTTTCGTCGCCGCTCG 59.980 61.111 0.00 0.00 40.15 5.03
2367 2410 3.186047 ATTTTCGTCGCCGCTCGG 61.186 61.111 3.56 3.56 39.05 4.63
2368 2411 3.636313 ATTTTCGTCGCCGCTCGGA 62.636 57.895 13.11 0.00 39.05 4.55
2369 2412 2.901051 ATTTTCGTCGCCGCTCGGAT 62.901 55.000 13.11 0.00 39.05 4.18
2370 2413 3.636313 TTTCGTCGCCGCTCGGATT 62.636 57.895 13.11 0.00 39.05 3.01
2371 2414 4.847516 TCGTCGCCGCTCGGATTG 62.848 66.667 13.11 1.02 39.05 2.67
2373 2416 4.508128 GTCGCCGCTCGGATTGGA 62.508 66.667 13.11 0.44 39.05 3.53
2374 2417 3.536917 TCGCCGCTCGGATTGGAT 61.537 61.111 13.11 0.00 39.05 3.41
2375 2418 2.197605 TCGCCGCTCGGATTGGATA 61.198 57.895 13.11 0.00 39.05 2.59
2376 2419 1.734477 CGCCGCTCGGATTGGATAG 60.734 63.158 13.11 0.00 37.50 2.08
2377 2420 1.367840 GCCGCTCGGATTGGATAGT 59.632 57.895 13.11 0.00 37.50 2.12
2378 2421 0.667792 GCCGCTCGGATTGGATAGTC 60.668 60.000 13.11 0.00 37.50 2.59
2379 2422 0.038159 CCGCTCGGATTGGATAGTCC 60.038 60.000 1.35 0.00 37.50 3.85
2386 2429 2.966050 GGATTGGATAGTCCGATGAGC 58.034 52.381 3.46 0.00 40.72 4.26
2387 2430 2.564947 GGATTGGATAGTCCGATGAGCT 59.435 50.000 3.46 0.00 40.72 4.09
2402 2445 0.723981 GAGCTCGAGCCAACAATGTC 59.276 55.000 32.94 17.63 43.38 3.06
2423 2466 4.301505 ACAGCTATGTTGGTGGCG 57.698 55.556 0.00 0.00 35.63 5.69
2424 2467 1.676968 ACAGCTATGTTGGTGGCGA 59.323 52.632 0.00 0.00 35.63 5.54
2425 2468 0.391661 ACAGCTATGTTGGTGGCGAG 60.392 55.000 0.00 0.00 35.63 5.03
2426 2469 1.450312 AGCTATGTTGGTGGCGAGC 60.450 57.895 0.00 0.00 0.00 5.03
2427 2470 2.813179 GCTATGTTGGTGGCGAGCG 61.813 63.158 0.00 0.00 0.00 5.03
2428 2471 2.813179 CTATGTTGGTGGCGAGCGC 61.813 63.158 6.27 6.27 41.06 5.92
2429 2472 3.309436 TATGTTGGTGGCGAGCGCT 62.309 57.895 11.27 11.27 41.60 5.92
2491 2534 0.980525 GTAGAGACGACGCGGTTTTC 59.019 55.000 12.47 0.53 0.00 2.29
2523 3342 5.181811 TGCTAGGTGATTGAATTTGTGAGTG 59.818 40.000 0.00 0.00 0.00 3.51
2584 3403 7.557719 CCTTGAACCAACATATCCTACAATCTT 59.442 37.037 0.00 0.00 0.00 2.40
2674 3501 0.597568 TCATGGAAAACCGCTTGCAG 59.402 50.000 0.00 0.00 29.57 4.41
2726 3553 9.606631 TTATAAACTGACTGCAAAAACCATTTT 57.393 25.926 0.00 0.00 39.30 1.82
2765 3592 3.496884 GCATGTTTCGTCCAGTTTACTCA 59.503 43.478 0.00 0.00 0.00 3.41
2825 3653 9.632638 CATATTTGGAGACCCCCTATTATTATG 57.367 37.037 0.00 0.00 0.00 1.90
2941 3805 5.424252 TGATTAGGTGGTAGTCCAAACTAGG 59.576 44.000 0.00 0.00 46.15 3.02
2963 3827 5.598417 AGGCCTCATTGTTCTTTGTTTTAGT 59.402 36.000 0.00 0.00 0.00 2.24
3023 4403 8.819845 TGTAAGATGATATCTGCTACCATGAAT 58.180 33.333 3.98 0.00 40.13 2.57
3085 4465 7.684937 ACGGTAGATCTATGAGTGGTATTAC 57.315 40.000 5.57 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.279271 ACCATCGCAACTAGGAAGCTT 59.721 47.619 0.00 0.00 0.00 3.74
1 2 0.905357 ACCATCGCAACTAGGAAGCT 59.095 50.000 0.00 0.00 0.00 3.74
2 3 1.291132 GACCATCGCAACTAGGAAGC 58.709 55.000 0.00 0.00 0.00 3.86
3 4 2.672961 TGACCATCGCAACTAGGAAG 57.327 50.000 0.00 0.00 0.00 3.46
4 5 3.490249 CGTATGACCATCGCAACTAGGAA 60.490 47.826 0.00 0.00 0.00 3.36
5 6 2.034179 CGTATGACCATCGCAACTAGGA 59.966 50.000 0.00 0.00 0.00 2.94
6 7 2.034179 TCGTATGACCATCGCAACTAGG 59.966 50.000 0.00 0.00 0.00 3.02
7 8 3.043586 GTCGTATGACCATCGCAACTAG 58.956 50.000 3.50 0.00 39.30 2.57
8 9 2.686405 AGTCGTATGACCATCGCAACTA 59.314 45.455 11.55 0.00 46.74 2.24
9 10 1.476891 AGTCGTATGACCATCGCAACT 59.523 47.619 11.55 0.00 46.74 3.16
10 11 1.922570 AGTCGTATGACCATCGCAAC 58.077 50.000 11.55 0.00 46.74 4.17
11 12 3.129813 ACTTAGTCGTATGACCATCGCAA 59.870 43.478 11.55 0.00 46.74 4.85
12 13 2.686405 ACTTAGTCGTATGACCATCGCA 59.314 45.455 11.55 0.00 46.74 5.10
13 14 3.298317 GACTTAGTCGTATGACCATCGC 58.702 50.000 11.55 0.00 46.74 4.58
14 15 3.564644 AGGACTTAGTCGTATGACCATCG 59.435 47.826 11.55 1.24 46.74 3.84
15 16 5.299782 AGAAGGACTTAGTCGTATGACCATC 59.700 44.000 11.55 4.54 46.74 3.51
16 17 5.067936 CAGAAGGACTTAGTCGTATGACCAT 59.932 44.000 11.55 0.00 46.74 3.55
17 18 4.398358 CAGAAGGACTTAGTCGTATGACCA 59.602 45.833 11.55 0.00 46.74 4.02
18 19 4.398673 ACAGAAGGACTTAGTCGTATGACC 59.601 45.833 19.79 2.47 46.74 4.02
19 20 5.564048 ACAGAAGGACTTAGTCGTATGAC 57.436 43.478 19.79 7.01 45.86 3.06
20 21 6.318144 CCTAACAGAAGGACTTAGTCGTATGA 59.682 42.308 19.79 5.09 39.15 2.15
21 22 6.318144 TCCTAACAGAAGGACTTAGTCGTATG 59.682 42.308 8.04 11.97 40.86 2.39
22 23 6.421485 TCCTAACAGAAGGACTTAGTCGTAT 58.579 40.000 8.04 0.00 40.86 3.06
23 24 5.809001 TCCTAACAGAAGGACTTAGTCGTA 58.191 41.667 8.04 0.00 40.86 3.43
24 25 4.660168 TCCTAACAGAAGGACTTAGTCGT 58.340 43.478 6.27 3.84 40.86 4.34
33 34 2.501723 GGCAGATGTCCTAACAGAAGGA 59.498 50.000 0.00 0.00 43.58 3.36
34 35 2.739932 CGGCAGATGTCCTAACAGAAGG 60.740 54.545 0.00 0.00 39.20 3.46
35 36 2.093973 ACGGCAGATGTCCTAACAGAAG 60.094 50.000 0.00 0.00 39.20 2.85
36 37 1.899814 ACGGCAGATGTCCTAACAGAA 59.100 47.619 0.00 0.00 39.20 3.02
37 38 1.204704 CACGGCAGATGTCCTAACAGA 59.795 52.381 0.00 0.00 39.20 3.41
38 39 1.204704 TCACGGCAGATGTCCTAACAG 59.795 52.381 0.00 0.00 39.20 3.16
39 40 1.067142 GTCACGGCAGATGTCCTAACA 60.067 52.381 0.00 0.00 40.38 2.41
40 41 1.067142 TGTCACGGCAGATGTCCTAAC 60.067 52.381 0.00 0.00 0.00 2.34
41 42 1.262417 TGTCACGGCAGATGTCCTAA 58.738 50.000 0.00 0.00 0.00 2.69
42 43 1.262417 TTGTCACGGCAGATGTCCTA 58.738 50.000 0.00 0.00 0.00 2.94
43 44 0.615331 ATTGTCACGGCAGATGTCCT 59.385 50.000 0.00 0.00 0.00 3.85
44 45 1.398390 GAATTGTCACGGCAGATGTCC 59.602 52.381 0.00 0.00 0.00 4.02
45 46 1.061131 CGAATTGTCACGGCAGATGTC 59.939 52.381 0.00 0.00 0.00 3.06
46 47 1.078709 CGAATTGTCACGGCAGATGT 58.921 50.000 0.00 0.00 0.00 3.06
47 48 1.061131 GTCGAATTGTCACGGCAGATG 59.939 52.381 0.00 0.00 34.20 2.90
48 49 1.359848 GTCGAATTGTCACGGCAGAT 58.640 50.000 0.00 0.00 34.20 2.90
49 50 1.006825 CGTCGAATTGTCACGGCAGA 61.007 55.000 0.00 0.00 33.63 4.26
50 51 1.006825 TCGTCGAATTGTCACGGCAG 61.007 55.000 0.00 0.00 33.63 4.85
51 52 1.007154 TCGTCGAATTGTCACGGCA 60.007 52.632 0.00 0.00 33.63 5.69
52 53 1.279527 TGTCGTCGAATTGTCACGGC 61.280 55.000 0.00 0.00 35.12 5.68
53 54 0.433492 GTGTCGTCGAATTGTCACGG 59.567 55.000 0.00 0.00 32.57 4.94
54 55 1.125270 TGTGTCGTCGAATTGTCACG 58.875 50.000 0.00 0.00 32.81 4.35
55 56 2.538449 ACTTGTGTCGTCGAATTGTCAC 59.462 45.455 0.00 0.93 0.00 3.67
56 57 2.816689 ACTTGTGTCGTCGAATTGTCA 58.183 42.857 0.00 0.00 0.00 3.58
57 58 4.207635 TGTTACTTGTGTCGTCGAATTGTC 59.792 41.667 0.00 0.00 0.00 3.18
58 59 4.114073 TGTTACTTGTGTCGTCGAATTGT 58.886 39.130 0.00 0.00 0.00 2.71
59 60 4.702247 TGTTACTTGTGTCGTCGAATTG 57.298 40.909 0.00 0.00 0.00 2.32
60 61 7.170320 AGTTTATGTTACTTGTGTCGTCGAATT 59.830 33.333 0.00 0.00 0.00 2.17
61 62 6.643770 AGTTTATGTTACTTGTGTCGTCGAAT 59.356 34.615 0.00 0.00 0.00 3.34
62 63 5.978919 AGTTTATGTTACTTGTGTCGTCGAA 59.021 36.000 0.00 0.00 0.00 3.71
63 64 5.522456 AGTTTATGTTACTTGTGTCGTCGA 58.478 37.500 0.00 0.00 0.00 4.20
64 65 5.817616 AGTTTATGTTACTTGTGTCGTCG 57.182 39.130 0.00 0.00 0.00 5.12
65 66 6.347160 GGGAAGTTTATGTTACTTGTGTCGTC 60.347 42.308 0.00 0.00 36.04 4.20
66 67 5.467735 GGGAAGTTTATGTTACTTGTGTCGT 59.532 40.000 0.00 0.00 36.04 4.34
67 68 5.106830 GGGGAAGTTTATGTTACTTGTGTCG 60.107 44.000 0.00 0.00 36.04 4.35
68 69 6.002082 AGGGGAAGTTTATGTTACTTGTGTC 58.998 40.000 0.00 0.00 36.04 3.67
69 70 5.948842 AGGGGAAGTTTATGTTACTTGTGT 58.051 37.500 0.00 0.00 36.04 3.72
70 71 6.001460 TGAGGGGAAGTTTATGTTACTTGTG 58.999 40.000 0.00 0.00 36.04 3.33
157 159 7.818930 TGTTGCTTTTTCTTTCTCACATTTTCT 59.181 29.630 0.00 0.00 0.00 2.52
198 200 1.285023 GAAGCATGCATCGATGGGC 59.715 57.895 26.00 13.79 0.00 5.36
210 212 4.823989 CCTCATTTATTTCTCCGGAAGCAT 59.176 41.667 5.23 0.00 32.61 3.79
217 219 8.144478 TGAGAATAGACCTCATTTATTTCTCCG 58.856 37.037 0.00 0.00 35.89 4.63
220 222 9.319143 CGTTGAGAATAGACCTCATTTATTTCT 57.681 33.333 0.00 0.00 40.02 2.52
226 228 5.422214 ACCGTTGAGAATAGACCTCATTT 57.578 39.130 0.00 0.00 40.02 2.32
227 229 5.892119 TCTACCGTTGAGAATAGACCTCATT 59.108 40.000 0.00 0.00 40.02 2.57
228 230 5.446860 TCTACCGTTGAGAATAGACCTCAT 58.553 41.667 0.00 0.00 40.02 2.90
229 231 4.851843 TCTACCGTTGAGAATAGACCTCA 58.148 43.478 0.00 0.00 38.74 3.86
230 232 5.831702 TTCTACCGTTGAGAATAGACCTC 57.168 43.478 0.00 0.00 0.00 3.85
231 233 5.069251 CCATTCTACCGTTGAGAATAGACCT 59.931 44.000 4.05 0.00 40.83 3.85
275 277 8.893219 AGATTTCAAAAAGGAAATGGAAACTC 57.107 30.769 5.92 0.00 45.05 3.01
277 279 8.988934 GGTAGATTTCAAAAAGGAAATGGAAAC 58.011 33.333 5.92 0.39 45.05 2.78
287 289 5.873179 TGCTACGGTAGATTTCAAAAAGG 57.127 39.130 19.02 0.00 0.00 3.11
320 322 1.362224 AACTAGACCCCATGTGCAGT 58.638 50.000 0.00 0.00 0.00 4.40
362 364 1.001624 CGATGTGCAGCGAAGATCAA 58.998 50.000 3.59 0.00 43.75 2.57
363 365 0.108662 ACGATGTGCAGCGAAGATCA 60.109 50.000 16.73 0.00 43.75 2.92
364 366 0.574454 GACGATGTGCAGCGAAGATC 59.426 55.000 16.73 0.00 43.75 2.75
365 367 0.108662 TGACGATGTGCAGCGAAGAT 60.109 50.000 16.73 0.00 43.75 2.40
366 368 0.319469 TTGACGATGTGCAGCGAAGA 60.319 50.000 16.73 0.00 43.75 2.87
367 369 0.094216 CTTGACGATGTGCAGCGAAG 59.906 55.000 16.73 6.84 43.75 3.79
368 370 0.599991 ACTTGACGATGTGCAGCGAA 60.600 50.000 16.73 1.68 43.75 4.70
369 371 1.006220 ACTTGACGATGTGCAGCGA 60.006 52.632 16.73 0.00 43.75 4.93
370 372 1.010935 AGACTTGACGATGTGCAGCG 61.011 55.000 8.33 8.33 46.76 5.18
371 373 1.127582 GAAGACTTGACGATGTGCAGC 59.872 52.381 0.00 0.00 0.00 5.25
372 374 1.388093 CGAAGACTTGACGATGTGCAG 59.612 52.381 0.00 0.00 0.00 4.41
373 375 1.418373 CGAAGACTTGACGATGTGCA 58.582 50.000 0.00 0.00 0.00 4.57
374 376 0.093705 GCGAAGACTTGACGATGTGC 59.906 55.000 0.00 0.00 0.00 4.57
375 377 1.388093 CAGCGAAGACTTGACGATGTG 59.612 52.381 6.43 0.00 38.35 3.21
376 378 1.702886 CAGCGAAGACTTGACGATGT 58.297 50.000 6.43 0.00 38.35 3.06
377 379 0.368227 GCAGCGAAGACTTGACGATG 59.632 55.000 9.46 9.46 44.29 3.84
378 380 0.244994 AGCAGCGAAGACTTGACGAT 59.755 50.000 0.00 0.00 0.00 3.73
456 458 2.221055 CACGAGGTGTTCTTCCTTTTCG 59.779 50.000 0.00 0.00 35.20 3.46
466 468 2.607892 GCCAGCACACGAGGTGTTC 61.608 63.158 12.21 0.00 45.08 3.18
480 482 5.989168 TCAACATAATTATGTCCGTAGCCAG 59.011 40.000 27.07 11.45 45.55 4.85
506 508 1.357258 CTGATGCAGTCGCTGTCCAC 61.357 60.000 8.32 0.92 39.64 4.02
572 574 2.591429 TCCTGTTGTGCAGCACGG 60.591 61.111 20.67 15.07 43.71 4.94
588 590 6.985059 AGTAGGTTGTTTACTGAACTGAACTC 59.015 38.462 0.00 0.00 39.08 3.01
597 599 7.786046 TCTTATGGAGTAGGTTGTTTACTGA 57.214 36.000 0.00 0.00 31.74 3.41
598 600 8.718734 GTTTCTTATGGAGTAGGTTGTTTACTG 58.281 37.037 0.00 0.00 31.74 2.74
599 601 7.881751 GGTTTCTTATGGAGTAGGTTGTTTACT 59.118 37.037 0.00 0.00 34.19 2.24
600 602 7.881751 AGGTTTCTTATGGAGTAGGTTGTTTAC 59.118 37.037 0.00 0.00 0.00 2.01
601 603 7.981142 AGGTTTCTTATGGAGTAGGTTGTTTA 58.019 34.615 0.00 0.00 0.00 2.01
602 604 6.849151 AGGTTTCTTATGGAGTAGGTTGTTT 58.151 36.000 0.00 0.00 0.00 2.83
603 605 6.449830 AGGTTTCTTATGGAGTAGGTTGTT 57.550 37.500 0.00 0.00 0.00 2.83
604 606 6.043938 TCAAGGTTTCTTATGGAGTAGGTTGT 59.956 38.462 0.00 0.00 0.00 3.32
627 629 0.607217 TAGTCGCGTCCTTGACCTCA 60.607 55.000 5.77 0.00 35.71 3.86
645 647 7.284489 AGCTTTGTGTGAAGTGGTTATTTCTTA 59.716 33.333 0.00 0.00 0.00 2.10
648 650 5.831997 AGCTTTGTGTGAAGTGGTTATTTC 58.168 37.500 0.00 0.00 0.00 2.17
649 651 5.852282 AGCTTTGTGTGAAGTGGTTATTT 57.148 34.783 0.00 0.00 0.00 1.40
661 665 6.246332 CGTCGTATTCAATTTAGCTTTGTGTG 59.754 38.462 0.00 0.00 0.00 3.82
668 672 4.501071 ACCACGTCGTATTCAATTTAGCT 58.499 39.130 0.00 0.00 0.00 3.32
701 708 9.046296 AGCAATATATTAGAACTGCACACTTAC 57.954 33.333 7.39 0.00 32.21 2.34
703 710 9.265901 CTAGCAATATATTAGAACTGCACACTT 57.734 33.333 7.39 0.00 32.21 3.16
704 711 7.386299 GCTAGCAATATATTAGAACTGCACACT 59.614 37.037 10.63 0.00 32.21 3.55
722 733 0.249489 GGACGACCGATGCTAGCAAT 60.249 55.000 23.54 10.46 0.00 3.56
724 735 1.725557 GAGGACGACCGATGCTAGCA 61.726 60.000 21.85 21.85 41.83 3.49
725 736 1.008309 GAGGACGACCGATGCTAGC 60.008 63.158 8.10 8.10 41.83 3.42
726 737 1.025812 AAGAGGACGACCGATGCTAG 58.974 55.000 0.00 0.00 41.83 3.42
727 738 1.404391 GAAAGAGGACGACCGATGCTA 59.596 52.381 0.00 0.00 41.83 3.49
728 739 0.173708 GAAAGAGGACGACCGATGCT 59.826 55.000 0.00 0.00 41.83 3.79
729 740 0.173708 AGAAAGAGGACGACCGATGC 59.826 55.000 0.00 0.00 41.83 3.91
730 741 1.472878 TCAGAAAGAGGACGACCGATG 59.527 52.381 0.00 0.00 41.83 3.84
746 757 2.396601 ACGCGTATTTTTCACGTCAGA 58.603 42.857 11.67 0.00 41.41 3.27
754 765 1.060122 CCTCCGTGACGCGTATTTTTC 59.940 52.381 13.97 0.00 39.32 2.29
755 766 1.073177 CCTCCGTGACGCGTATTTTT 58.927 50.000 13.97 0.00 39.32 1.94
758 769 1.138247 GTCCTCCGTGACGCGTATT 59.862 57.895 13.97 0.00 39.32 1.89
770 781 1.381327 TCATCCCCTGACGTCCTCC 60.381 63.158 14.12 0.00 0.00 4.30
798 809 2.616960 CATCGACCAATTTCCTCACGA 58.383 47.619 0.00 0.00 0.00 4.35
799 810 1.062587 GCATCGACCAATTTCCTCACG 59.937 52.381 0.00 0.00 0.00 4.35
800 811 1.062587 CGCATCGACCAATTTCCTCAC 59.937 52.381 0.00 0.00 0.00 3.51
805 816 0.026285 CGGACGCATCGACCAATTTC 59.974 55.000 8.24 0.00 41.25 2.17
827 838 1.912043 CCCTCTCCCATTGACTTGACT 59.088 52.381 0.00 0.00 0.00 3.41
847 858 2.737376 GCCCTCGTGTCGTGTTCC 60.737 66.667 0.00 0.00 0.00 3.62
850 861 3.598715 TTCGCCCTCGTGTCGTGT 61.599 61.111 0.00 0.00 36.96 4.49
851 862 3.103911 GTTCGCCCTCGTGTCGTG 61.104 66.667 0.00 0.00 36.96 4.35
852 863 4.695231 CGTTCGCCCTCGTGTCGT 62.695 66.667 0.00 0.00 36.96 4.34
853 864 3.678717 ATCGTTCGCCCTCGTGTCG 62.679 63.158 0.00 0.00 36.96 4.35
854 865 1.872679 GATCGTTCGCCCTCGTGTC 60.873 63.158 0.00 0.00 36.96 3.67
903 914 4.477975 GTGAGGACGCCGAGGACG 62.478 72.222 0.00 0.00 39.43 4.79
907 918 0.878523 TTTTGTGTGAGGACGCCGAG 60.879 55.000 0.00 0.00 0.00 4.63
913 924 3.139077 ACCGAGAATTTTGTGTGAGGAC 58.861 45.455 0.00 0.00 0.00 3.85
917 928 3.813166 GAGGAACCGAGAATTTTGTGTGA 59.187 43.478 0.00 0.00 0.00 3.58
949 960 2.846950 ACTCCCTTGTATAGGCACCTT 58.153 47.619 0.00 0.00 43.27 3.50
966 977 1.946650 GCATCAGGCGTCGCTACTC 60.947 63.158 18.11 0.00 0.00 2.59
967 978 2.105128 GCATCAGGCGTCGCTACT 59.895 61.111 18.11 3.40 0.00 2.57
1085 1096 3.329814 TCATGGAGATCATCAATGAGGGG 59.670 47.826 7.69 0.00 42.47 4.79
1124 1135 1.151668 GAACGCAGTGATCAGCAAGT 58.848 50.000 0.00 0.00 45.00 3.16
1458 1469 0.606401 AACAAGGAGTGCGTGATGGG 60.606 55.000 4.31 0.00 0.00 4.00
1470 1481 3.055458 TGGCTCGTGATAATCAACAAGGA 60.055 43.478 0.00 0.00 0.00 3.36
1473 1484 3.065233 GCATGGCTCGTGATAATCAACAA 59.935 43.478 0.00 0.00 0.00 2.83
1485 1496 4.970621 ATGTCATGCATGGCTCGT 57.029 50.000 29.96 16.86 36.26 4.18
1571 1582 4.680237 CGCGTCACCTTCTGCCCA 62.680 66.667 0.00 0.00 0.00 5.36
1661 1672 8.899427 AGATGACTATTTAGAACACATGGATG 57.101 34.615 0.00 0.00 0.00 3.51
1663 1674 7.345653 AGGAGATGACTATTTAGAACACATGGA 59.654 37.037 0.00 0.00 0.00 3.41
1664 1675 7.440556 CAGGAGATGACTATTTAGAACACATGG 59.559 40.741 0.00 0.00 0.00 3.66
1665 1676 7.984050 ACAGGAGATGACTATTTAGAACACATG 59.016 37.037 0.00 0.00 0.00 3.21
1689 1700 2.263895 AGGTAGCATGGGGTAGAACA 57.736 50.000 0.00 0.00 0.00 3.18
1710 1721 1.431488 CCTGATCATGGGTGCGAACG 61.431 60.000 0.00 0.00 0.00 3.95
1728 1739 6.749923 AATTCAGCAAAATCTCAGAGTACC 57.250 37.500 0.00 0.00 0.00 3.34
1872 1915 2.506438 GGCTGTGACCTCGCGTAC 60.506 66.667 5.77 0.00 0.00 3.67
1873 1916 4.111016 CGGCTGTGACCTCGCGTA 62.111 66.667 5.77 0.00 0.00 4.42
1938 1981 1.372582 CTGACCCATGGTTCGTCATG 58.627 55.000 18.94 11.49 42.92 3.07
1985 2028 0.544595 AGGCGTAACAACCTCCCTCT 60.545 55.000 0.00 0.00 0.00 3.69
2016 2059 3.390967 TCACCATCTTGTCCAACAGAAGA 59.609 43.478 0.00 0.00 0.00 2.87
2023 2066 5.221904 TGAGAGAATTCACCATCTTGTCCAA 60.222 40.000 8.44 0.00 0.00 3.53
2043 2086 6.459710 GCATGAAATCTGCATCATTCTTGAGA 60.460 38.462 17.79 0.00 39.46 3.27
2110 2153 0.985760 TAACTTAGCCGGGCTGGAAA 59.014 50.000 31.26 16.57 40.10 3.13
2155 2198 3.365264 CCACCATTGTGTCGACATTTCTG 60.365 47.826 23.12 15.79 41.09 3.02
2198 2241 2.911102 GCTGACAAGAAATAGCAAACGC 59.089 45.455 0.00 0.00 36.24 4.84
2213 2256 3.944650 TGCTTACAAAGTTTCAGCTGACA 59.055 39.130 18.03 7.33 0.00 3.58
2267 2310 1.184322 ATCTCGGCATCAGATCGGCT 61.184 55.000 0.00 0.00 0.00 5.52
2268 2311 1.013005 CATCTCGGCATCAGATCGGC 61.013 60.000 0.00 0.00 0.00 5.54
2269 2312 0.389556 CCATCTCGGCATCAGATCGG 60.390 60.000 0.00 0.00 0.00 4.18
2270 2313 3.119107 CCATCTCGGCATCAGATCG 57.881 57.895 0.00 0.00 0.00 3.69
2285 2328 2.108976 CCGCGACACTATGGCCAT 59.891 61.111 24.45 24.45 0.00 4.40
2292 2335 4.063967 CCTGCACCCGCGACACTA 62.064 66.667 8.23 0.00 42.97 2.74
2301 2344 1.751927 CTCATCCTTGCCTGCACCC 60.752 63.158 0.00 0.00 0.00 4.61
2302 2345 1.751927 CCTCATCCTTGCCTGCACC 60.752 63.158 0.00 0.00 0.00 5.01
2303 2346 1.751927 CCCTCATCCTTGCCTGCAC 60.752 63.158 0.00 0.00 0.00 4.57
2304 2347 1.792757 AACCCTCATCCTTGCCTGCA 61.793 55.000 0.00 0.00 0.00 4.41
2305 2348 1.000396 AACCCTCATCCTTGCCTGC 60.000 57.895 0.00 0.00 0.00 4.85
2306 2349 0.682209 CCAACCCTCATCCTTGCCTG 60.682 60.000 0.00 0.00 0.00 4.85
2307 2350 1.693640 CCAACCCTCATCCTTGCCT 59.306 57.895 0.00 0.00 0.00 4.75
2308 2351 2.054453 GCCAACCCTCATCCTTGCC 61.054 63.158 0.00 0.00 0.00 4.52
2309 2352 2.054453 GGCCAACCCTCATCCTTGC 61.054 63.158 0.00 0.00 0.00 4.01
2310 2353 1.750399 CGGCCAACCCTCATCCTTG 60.750 63.158 2.24 0.00 0.00 3.61
2311 2354 2.677228 CGGCCAACCCTCATCCTT 59.323 61.111 2.24 0.00 0.00 3.36
2312 2355 3.411517 CCGGCCAACCCTCATCCT 61.412 66.667 2.24 0.00 0.00 3.24
2313 2356 3.728373 ACCGGCCAACCCTCATCC 61.728 66.667 0.00 0.00 0.00 3.51
2314 2357 2.438434 CACCGGCCAACCCTCATC 60.438 66.667 0.00 0.00 0.00 2.92
2315 2358 4.740822 GCACCGGCCAACCCTCAT 62.741 66.667 0.00 0.00 0.00 2.90
2331 2374 4.894896 CAATAGGCCCCCACCCGC 62.895 72.222 0.00 0.00 0.00 6.13
2332 2375 4.894896 GCAATAGGCCCCCACCCG 62.895 72.222 0.00 0.00 36.11 5.28
2333 2376 2.603933 AATGCAATAGGCCCCCACCC 62.604 60.000 0.00 0.00 43.89 4.61
2334 2377 0.690744 AAATGCAATAGGCCCCCACC 60.691 55.000 0.00 0.00 43.89 4.61
2335 2378 1.138859 GAAAATGCAATAGGCCCCCAC 59.861 52.381 0.00 0.00 43.89 4.61
2336 2379 1.494960 GAAAATGCAATAGGCCCCCA 58.505 50.000 0.00 0.00 43.89 4.96
2337 2380 0.389025 CGAAAATGCAATAGGCCCCC 59.611 55.000 0.00 0.00 43.89 5.40
2338 2381 1.067060 GACGAAAATGCAATAGGCCCC 59.933 52.381 0.00 0.00 43.89 5.80
2339 2382 1.268539 CGACGAAAATGCAATAGGCCC 60.269 52.381 0.00 0.00 43.89 5.80
2340 2383 1.859998 GCGACGAAAATGCAATAGGCC 60.860 52.381 0.00 0.00 43.89 5.19
2341 2384 1.466855 GCGACGAAAATGCAATAGGC 58.533 50.000 0.00 0.00 45.13 3.93
2342 2385 2.105323 GGCGACGAAAATGCAATAGG 57.895 50.000 0.00 0.00 0.00 2.57
2356 2399 2.416244 TATCCAATCCGAGCGGCGAC 62.416 60.000 12.98 1.23 44.57 5.19
2357 2400 2.142357 CTATCCAATCCGAGCGGCGA 62.142 60.000 12.98 0.00 44.57 5.54
2358 2401 1.734477 CTATCCAATCCGAGCGGCG 60.734 63.158 0.51 0.51 40.47 6.46
2359 2402 0.667792 GACTATCCAATCCGAGCGGC 60.668 60.000 3.59 0.00 34.68 6.53
2360 2403 0.038159 GGACTATCCAATCCGAGCGG 60.038 60.000 1.74 1.74 36.28 5.52
2361 2404 3.498676 GGACTATCCAATCCGAGCG 57.501 57.895 0.00 0.00 36.28 5.03
2366 2409 2.564947 AGCTCATCGGACTATCCAATCC 59.435 50.000 0.00 0.00 35.91 3.01
2367 2410 3.843999 GAGCTCATCGGACTATCCAATC 58.156 50.000 9.40 0.00 35.91 2.67
2368 2411 3.951775 GAGCTCATCGGACTATCCAAT 57.048 47.619 9.40 0.00 35.91 3.16
2380 2423 1.329906 CATTGTTGGCTCGAGCTCATC 59.670 52.381 34.46 26.26 41.70 2.92
2381 2424 1.339438 ACATTGTTGGCTCGAGCTCAT 60.339 47.619 34.46 17.15 41.70 2.90
2382 2425 0.035317 ACATTGTTGGCTCGAGCTCA 59.965 50.000 34.46 26.77 41.70 4.26
2383 2426 0.723981 GACATTGTTGGCTCGAGCTC 59.276 55.000 34.46 24.64 41.70 4.09
2384 2427 1.016130 CGACATTGTTGGCTCGAGCT 61.016 55.000 34.46 14.31 41.70 4.09
2385 2428 1.421485 CGACATTGTTGGCTCGAGC 59.579 57.895 29.38 29.38 41.14 5.03
2386 2429 1.291184 TGCGACATTGTTGGCTCGAG 61.291 55.000 8.45 8.45 0.00 4.04
2387 2430 0.882484 TTGCGACATTGTTGGCTCGA 60.882 50.000 12.91 0.00 0.00 4.04
2393 2436 2.967459 TAGCTGTTGCGACATTGTTG 57.033 45.000 7.38 0.00 45.42 3.33
2435 2478 3.612371 AAGTCCTCGCTCGTGACGC 62.612 63.158 0.00 0.00 34.24 5.19
2436 2479 1.797933 CAAGTCCTCGCTCGTGACG 60.798 63.158 0.00 0.00 34.24 4.35
2437 2480 2.089349 GCAAGTCCTCGCTCGTGAC 61.089 63.158 6.60 6.60 0.00 3.67
2438 2481 2.258591 GCAAGTCCTCGCTCGTGA 59.741 61.111 0.00 0.00 0.00 4.35
2439 2482 2.811317 GGCAAGTCCTCGCTCGTG 60.811 66.667 0.00 0.00 0.00 4.35
2440 2483 3.288308 CTGGCAAGTCCTCGCTCGT 62.288 63.158 0.00 0.00 35.26 4.18
2491 2534 2.034179 TCAATCACCTAGCATACGTCGG 59.966 50.000 0.00 0.00 0.00 4.79
2493 2536 6.037172 ACAAATTCAATCACCTAGCATACGTC 59.963 38.462 0.00 0.00 0.00 4.34
2494 2537 5.880332 ACAAATTCAATCACCTAGCATACGT 59.120 36.000 0.00 0.00 0.00 3.57
2523 3342 1.803555 GCTTCTGAGACCTCAAACAGC 59.196 52.381 1.08 5.38 39.39 4.40
2584 3403 0.704076 ATGCTTAAGGCCTTGACCCA 59.296 50.000 28.77 18.37 40.92 4.51
2726 3553 5.585820 ACATGCAATAGATGAAACATGCA 57.414 34.783 0.37 0.37 46.43 3.96
2732 3559 5.414144 TGGACGAAACATGCAATAGATGAAA 59.586 36.000 0.00 0.00 0.00 2.69
2765 3592 5.217978 TGCTCTCTTCCAAATTTTTGCAT 57.782 34.783 0.00 0.00 36.86 3.96
2941 3805 6.503524 TGACTAAAACAAAGAACAATGAGGC 58.496 36.000 0.00 0.00 0.00 4.70
2963 3827 6.524734 AGACACACTCTACATTTTCACATGA 58.475 36.000 0.00 0.00 0.00 3.07
3023 4403 6.625740 GCTTTGAGGCTTGCACTTTCATTATA 60.626 38.462 0.00 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.