Multiple sequence alignment - TraesCS5B01G189100

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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 TraesCS5B01G189100 chr5B 100.000 5272 0 0 1 5272 341053856 341059127 0.000000e+00 9736.0
1 TraesCS5B01G189100 chr5B 77.545 334 69 6 4795 5125 462635201 462635531 4.170000e-46 196.0
2 TraesCS5B01G189100 chr5D 91.961 4677 232 69 57 4667 299812968 299817566 0.000000e+00 6421.0
3 TraesCS5B01G189100 chr5D 93.367 603 39 1 4670 5271 299820240 299820842 0.000000e+00 891.0
4 TraesCS5B01G189100 chr5D 88.830 188 21 0 2119 2306 489308349 489308162 1.140000e-56 231.0
5 TraesCS5B01G189100 chr5A 93.040 2270 85 25 2421 4667 397148532 397150751 0.000000e+00 3249.0
6 TraesCS5B01G189100 chr5A 91.512 2321 102 29 57 2322 397146197 397148477 0.000000e+00 3107.0
7 TraesCS5B01G189100 chr5A 91.639 598 44 2 4676 5271 397220613 397221206 0.000000e+00 822.0
8 TraesCS5B01G189100 chr5A 85.854 205 26 2 2102 2306 610458708 610458507 1.150000e-51 215.0
9 TraesCS5B01G189100 chr5A 77.126 341 74 4 4795 5132 446420953 446421292 1.500000e-45 195.0
10 TraesCS5B01G189100 chr1A 84.641 306 18 14 1007 1303 543638599 543638884 1.450000e-70 278.0
11 TraesCS5B01G189100 chr1A 76.968 343 70 9 4795 5132 50956855 50957193 2.510000e-43 187.0
12 TraesCS5B01G189100 chr1A 76.901 342 72 7 4795 5132 537886063 537885725 2.510000e-43 187.0
13 TraesCS5B01G189100 chr7B 77.810 347 69 8 4791 5132 564363492 564363149 1.920000e-49 207.0
14 TraesCS5B01G189100 chr3B 77.946 331 67 6 4806 5132 130136495 130136823 8.950000e-48 202.0
15 TraesCS5B01G189100 chr6D 77.391 345 70 8 4795 5134 470377977 470378318 1.160000e-46 198.0
16 TraesCS5B01G189100 chr3D 98.182 55 1 0 4 58 478067271 478067217 4.350000e-16 97.1
17 TraesCS5B01G189100 chr1B 94.828 58 3 0 1 58 619180228 619180171 2.020000e-14 91.6
18 TraesCS5B01G189100 chr2B 94.545 55 3 0 1 55 759338997 759339051 9.410000e-13 86.1
19 TraesCS5B01G189100 chr1D 91.071 56 3 2 1 55 423799232 423799286 2.040000e-09 75.0


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 TraesCS5B01G189100 chr5B 341053856 341059127 5271 False 9736 9736 100.000 1 5272 1 chr5B.!!$F1 5271
1 TraesCS5B01G189100 chr5D 299812968 299820842 7874 False 3656 6421 92.664 57 5271 2 chr5D.!!$F1 5214
2 TraesCS5B01G189100 chr5A 397146197 397150751 4554 False 3178 3249 92.276 57 4667 2 chr5A.!!$F3 4610
3 TraesCS5B01G189100 chr5A 397220613 397221206 593 False 822 822 91.639 4676 5271 1 chr5A.!!$F1 595

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
71 72 0.243636 ATTTTGCACCGTTGGCTAGC 59.756 50.0 6.04 6.04 0.00 3.42 F
224 225 0.759346 ACGAGAACAGCCTCACCTTT 59.241 50.0 0.00 0.00 32.86 3.11 F
806 829 0.814410 TGGCCACGTTGAAAAGCGTA 60.814 50.0 0.00 0.00 39.48 4.42 F
1856 1914 0.801067 ACGGCGCATTCTACTTCGTC 60.801 55.0 10.83 0.00 0.00 4.20 F
2740 2805 0.035056 AGTTCTGCATACAGCCACCC 60.035 55.0 0.00 0.00 44.10 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1081 1105 0.107508 CACCTGCTCCCATCGTGATT 60.108 55.000 0.00 0.0 0.00 2.57 R
1303 1336 0.169009 GCAGTTCGCCATTGAAGACC 59.831 55.000 0.00 0.0 32.94 3.85 R
2696 2761 0.255890 GCATTCTGGCCCTCAACCTA 59.744 55.000 0.00 0.0 0.00 3.08 R
3607 3693 2.031245 TCAAACTGCAAATACCAGCACG 60.031 45.455 0.00 0.0 36.62 5.34 R
4722 7482 0.036388 ATGATCCACACACCCGTGAC 60.036 55.000 0.96 0.0 46.80 3.67 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 2.750301 GAACGTGTGTCTCCAAAACC 57.250 50.000 0.00 0.00 0.00 3.27
20 21 1.332686 GAACGTGTGTCTCCAAAACCC 59.667 52.381 0.00 0.00 0.00 4.11
21 22 0.253610 ACGTGTGTCTCCAAAACCCA 59.746 50.000 0.00 0.00 0.00 4.51
22 23 1.340211 ACGTGTGTCTCCAAAACCCAA 60.340 47.619 0.00 0.00 0.00 4.12
23 24 1.953686 CGTGTGTCTCCAAAACCCAAT 59.046 47.619 0.00 0.00 0.00 3.16
24 25 2.287547 CGTGTGTCTCCAAAACCCAATG 60.288 50.000 0.00 0.00 0.00 2.82
25 26 2.693074 GTGTGTCTCCAAAACCCAATGT 59.307 45.455 0.00 0.00 0.00 2.71
26 27 2.955660 TGTGTCTCCAAAACCCAATGTC 59.044 45.455 0.00 0.00 0.00 3.06
27 28 2.955660 GTGTCTCCAAAACCCAATGTCA 59.044 45.455 0.00 0.00 0.00 3.58
28 29 3.573967 GTGTCTCCAAAACCCAATGTCAT 59.426 43.478 0.00 0.00 0.00 3.06
29 30 4.764823 GTGTCTCCAAAACCCAATGTCATA 59.235 41.667 0.00 0.00 0.00 2.15
30 31 5.009631 TGTCTCCAAAACCCAATGTCATAG 58.990 41.667 0.00 0.00 0.00 2.23
31 32 4.399303 GTCTCCAAAACCCAATGTCATAGG 59.601 45.833 1.11 1.11 0.00 2.57
32 33 4.044065 TCTCCAAAACCCAATGTCATAGGT 59.956 41.667 2.26 2.26 0.00 3.08
33 34 4.746466 TCCAAAACCCAATGTCATAGGTT 58.254 39.130 12.41 12.41 44.43 3.50
34 35 4.770010 TCCAAAACCCAATGTCATAGGTTC 59.230 41.667 16.66 0.00 41.72 3.62
35 36 4.526262 CCAAAACCCAATGTCATAGGTTCA 59.474 41.667 16.66 0.00 41.72 3.18
36 37 5.011533 CCAAAACCCAATGTCATAGGTTCAA 59.988 40.000 16.66 0.00 41.72 2.69
37 38 6.463614 CCAAAACCCAATGTCATAGGTTCAAA 60.464 38.462 16.66 0.00 41.72 2.69
38 39 6.933514 AAACCCAATGTCATAGGTTCAAAT 57.066 33.333 16.66 3.37 41.72 2.32
39 40 6.530019 AACCCAATGTCATAGGTTCAAATC 57.470 37.500 12.41 0.00 38.17 2.17
40 41 4.956075 ACCCAATGTCATAGGTTCAAATCC 59.044 41.667 2.26 0.00 0.00 3.01
41 42 5.203528 CCCAATGTCATAGGTTCAAATCCT 58.796 41.667 0.00 0.00 38.91 3.24
42 43 6.069088 ACCCAATGTCATAGGTTCAAATCCTA 60.069 38.462 2.26 0.00 41.08 2.94
43 44 6.263168 CCCAATGTCATAGGTTCAAATCCTAC 59.737 42.308 0.00 0.00 39.88 3.18
44 45 6.828273 CCAATGTCATAGGTTCAAATCCTACA 59.172 38.462 0.00 0.00 39.88 2.74
45 46 7.012704 CCAATGTCATAGGTTCAAATCCTACAG 59.987 40.741 0.00 0.00 39.88 2.74
46 47 6.867519 TGTCATAGGTTCAAATCCTACAGA 57.132 37.500 0.00 0.00 39.88 3.41
47 48 6.878317 TGTCATAGGTTCAAATCCTACAGAG 58.122 40.000 0.00 0.00 39.88 3.35
48 49 5.755861 GTCATAGGTTCAAATCCTACAGAGC 59.244 44.000 0.00 0.00 39.88 4.09
49 50 3.252974 AGGTTCAAATCCTACAGAGCG 57.747 47.619 0.00 0.00 33.04 5.03
50 51 2.567615 AGGTTCAAATCCTACAGAGCGT 59.432 45.455 0.00 0.00 33.04 5.07
51 52 2.673368 GGTTCAAATCCTACAGAGCGTG 59.327 50.000 0.00 0.00 0.00 5.34
52 53 3.585862 GTTCAAATCCTACAGAGCGTGA 58.414 45.455 0.00 0.00 0.00 4.35
53 54 4.184629 GTTCAAATCCTACAGAGCGTGAT 58.815 43.478 0.00 0.00 0.00 3.06
54 55 4.471904 TCAAATCCTACAGAGCGTGATT 57.528 40.909 0.00 0.00 0.00 2.57
55 56 4.832248 TCAAATCCTACAGAGCGTGATTT 58.168 39.130 0.00 0.00 0.00 2.17
71 72 0.243636 ATTTTGCACCGTTGGCTAGC 59.756 50.000 6.04 6.04 0.00 3.42
224 225 0.759346 ACGAGAACAGCCTCACCTTT 59.241 50.000 0.00 0.00 32.86 3.11
327 328 1.148310 CGAGTTCATGCCAAAGTCGT 58.852 50.000 12.39 0.00 42.05 4.34
659 665 2.672874 TCCGAACTTGATTCAGCATTCG 59.327 45.455 16.12 16.12 37.12 3.34
668 674 1.996292 TTCAGCATTCGTCTCTTCCG 58.004 50.000 0.00 0.00 0.00 4.30
712 722 2.224548 GCTGTGGTGGTCTACTTTCCTT 60.225 50.000 0.00 0.00 0.00 3.36
730 753 2.093869 CCTTGGTTGATGCCTGAATTGG 60.094 50.000 0.00 0.00 0.00 3.16
745 768 1.281925 ATTGGGTCCTCGATTGGGCT 61.282 55.000 0.00 0.00 0.00 5.19
754 777 6.270231 GGGTCCTCGATTGGGCTATAATATAT 59.730 42.308 0.00 0.00 0.00 0.86
806 829 0.814410 TGGCCACGTTGAAAAGCGTA 60.814 50.000 0.00 0.00 39.48 4.42
822 845 1.080093 GTAGTGCTAGTGTGCGGCA 60.080 57.895 0.00 0.00 35.36 5.69
950 974 1.811860 GTCTACGTGCGTGGGGTAT 59.188 57.895 7.55 0.00 0.00 2.73
1032 1056 4.790962 TCGCTCTACTCCGGCCGT 62.791 66.667 26.12 8.42 0.00 5.68
1081 1105 1.357258 GCTCGTACGTCGTCTCCTCA 61.357 60.000 16.05 0.00 40.80 3.86
1082 1106 1.073964 CTCGTACGTCGTCTCCTCAA 58.926 55.000 16.05 0.00 40.80 3.02
1085 1109 1.395954 CGTACGTCGTCTCCTCAATCA 59.604 52.381 7.22 0.00 34.52 2.57
1303 1336 2.076100 TCGAGGTAGCAAAAGCACATG 58.924 47.619 0.00 0.00 0.00 3.21
1304 1337 1.131126 CGAGGTAGCAAAAGCACATGG 59.869 52.381 0.00 0.00 0.00 3.66
1305 1338 2.162681 GAGGTAGCAAAAGCACATGGT 58.837 47.619 0.00 0.00 0.00 3.55
1308 1341 2.558359 GGTAGCAAAAGCACATGGTCTT 59.442 45.455 0.00 0.00 0.00 3.01
1309 1342 3.366374 GGTAGCAAAAGCACATGGTCTTC 60.366 47.826 0.00 0.00 0.00 2.87
1310 1343 2.309613 AGCAAAAGCACATGGTCTTCA 58.690 42.857 0.00 0.00 0.00 3.02
1311 1344 2.694628 AGCAAAAGCACATGGTCTTCAA 59.305 40.909 0.00 0.00 0.00 2.69
1312 1345 3.322828 AGCAAAAGCACATGGTCTTCAAT 59.677 39.130 0.00 0.00 0.00 2.57
1313 1346 3.430895 GCAAAAGCACATGGTCTTCAATG 59.569 43.478 0.00 2.35 0.00 2.82
1314 1347 3.947910 AAAGCACATGGTCTTCAATGG 57.052 42.857 0.00 0.00 0.00 3.16
1315 1348 1.180029 AGCACATGGTCTTCAATGGC 58.820 50.000 0.00 0.00 0.00 4.40
1544 1600 3.390521 CAGTGGGAGCAGCCGGTA 61.391 66.667 1.90 0.00 37.63 4.02
1653 1709 5.288952 GCAAAAACTCACTACCTACTCGATC 59.711 44.000 0.00 0.00 0.00 3.69
1659 1715 4.378774 TCACTACCTACTCGATCAGCTAC 58.621 47.826 0.00 0.00 0.00 3.58
1662 1718 6.014413 TCACTACCTACTCGATCAGCTACTAT 60.014 42.308 0.00 0.00 0.00 2.12
1663 1719 6.091577 CACTACCTACTCGATCAGCTACTATG 59.908 46.154 0.00 0.00 0.00 2.23
1664 1720 4.975631 ACCTACTCGATCAGCTACTATGT 58.024 43.478 0.00 0.00 0.00 2.29
1713 1771 0.875059 GCTTGGCTTAGAGTGCGTTT 59.125 50.000 0.00 0.00 0.00 3.60
1718 1776 1.652619 GGCTTAGAGTGCGTTTACGAC 59.347 52.381 6.44 2.08 43.02 4.34
1763 1821 4.083271 CCGTGAAGATTTCTTTCAAGGGAC 60.083 45.833 10.73 0.00 36.11 4.46
1856 1914 0.801067 ACGGCGCATTCTACTTCGTC 60.801 55.000 10.83 0.00 0.00 4.20
1931 1990 1.621107 GCAATGTGCATGTGTACTGC 58.379 50.000 0.00 0.00 44.26 4.40
1935 1997 2.849294 TGTGCATGTGTACTGCCTTA 57.151 45.000 3.40 0.00 38.89 2.69
1950 2013 4.036734 ACTGCCTTATTTCAAGTGTGTGTG 59.963 41.667 0.00 0.00 0.00 3.82
2010 2073 2.776913 CGAGGAGGGCTCGGTTCTC 61.777 68.421 0.00 0.00 40.27 2.87
2037 2100 1.810030 GATTGCGTGGGACGACTCC 60.810 63.158 0.00 0.00 46.05 3.85
2067 2130 3.677284 ATGGCAGAGCGCTGTGGAG 62.677 63.158 32.57 11.22 44.17 3.86
2073 2136 3.308014 GAGCGCTGTGGAGGAGCTT 62.308 63.158 18.48 0.00 39.71 3.74
2079 2142 1.649664 CTGTGGAGGAGCTTCAATCG 58.350 55.000 0.00 0.00 0.00 3.34
2104 2167 1.079875 GCACGAGGCATGGCATTTTG 61.080 55.000 22.64 13.08 43.97 2.44
2108 2171 1.994779 CGAGGCATGGCATTTTGTTTC 59.005 47.619 22.64 6.43 0.00 2.78
2109 2172 2.349590 GAGGCATGGCATTTTGTTTCC 58.650 47.619 22.64 0.00 0.00 3.13
2113 2176 2.078392 CATGGCATTTTGTTTCCCTGC 58.922 47.619 0.00 0.00 0.00 4.85
2117 2180 2.743664 GGCATTTTGTTTCCCTGCATTC 59.256 45.455 0.00 0.00 34.56 2.67
2146 2209 5.519206 GTGGAAGATAGTAAGTTAGCAACCG 59.481 44.000 0.00 0.00 0.00 4.44
2299 2362 1.813092 CGGATGATCAAAGGGAGCCAG 60.813 57.143 0.00 0.00 0.00 4.85
2328 2391 8.406297 GGAATTAGTCAAGGTAAACCATTCATC 58.594 37.037 1.26 0.00 38.89 2.92
2329 2392 6.978343 TTAGTCAAGGTAAACCATTCATCG 57.022 37.500 1.26 0.00 38.89 3.84
2358 2421 5.417580 ACTGTCTGCCAAAACAAAAACTAGA 59.582 36.000 0.00 0.00 0.00 2.43
2363 2426 4.396790 TGCCAAAACAAAAACTAGACGAGT 59.603 37.500 0.00 0.00 41.56 4.18
2366 2429 7.136772 GCCAAAACAAAAACTAGACGAGTAAT 58.863 34.615 0.00 0.00 37.44 1.89
2393 2456 8.974060 TTCTTTACCTGTCTTTTTGTGAGTAT 57.026 30.769 0.00 0.00 0.00 2.12
2409 2472 8.645814 TTGTGAGTATAGAGAGGTTTAGTTCA 57.354 34.615 0.00 0.00 0.00 3.18
2425 2488 7.039714 GGTTTAGTTCAACCAATCTCTTCCAAT 60.040 37.037 0.00 0.00 45.12 3.16
2426 2489 7.687941 TTAGTTCAACCAATCTCTTCCAATC 57.312 36.000 0.00 0.00 0.00 2.67
2436 2499 7.504911 ACCAATCTCTTCCAATCCTGATATTTG 59.495 37.037 0.00 0.00 0.00 2.32
2438 2501 9.565090 CAATCTCTTCCAATCCTGATATTTGTA 57.435 33.333 0.00 0.00 0.00 2.41
2440 2503 9.736414 ATCTCTTCCAATCCTGATATTTGTATG 57.264 33.333 0.00 0.00 0.00 2.39
2499 2563 9.980780 AACACTTATTTTCCATTTTTGTTTTCG 57.019 25.926 0.00 0.00 0.00 3.46
2524 2588 7.376866 CGACATATATTGAACTTGCCAATGAAC 59.623 37.037 0.00 0.00 35.94 3.18
2617 2682 5.479306 TGTTAGCTTGTCTGAAGGTATGTC 58.521 41.667 0.00 0.00 31.31 3.06
2623 2688 6.096423 AGCTTGTCTGAAGGTATGTCGTATTA 59.904 38.462 0.00 0.00 0.00 0.98
2630 2695 7.287005 TCTGAAGGTATGTCGTATTATTGTCCT 59.713 37.037 0.00 0.00 0.00 3.85
2636 2701 4.543689 TGTCGTATTATTGTCCTCTCCCT 58.456 43.478 0.00 0.00 0.00 4.20
2640 2705 5.839063 TCGTATTATTGTCCTCTCCCTTCAT 59.161 40.000 0.00 0.00 0.00 2.57
2641 2706 5.928839 CGTATTATTGTCCTCTCCCTTCATG 59.071 44.000 0.00 0.00 0.00 3.07
2642 2707 6.239317 CGTATTATTGTCCTCTCCCTTCATGA 60.239 42.308 0.00 0.00 0.00 3.07
2643 2708 6.776887 ATTATTGTCCTCTCCCTTCATGAT 57.223 37.500 0.00 0.00 0.00 2.45
2644 2709 3.920231 TTGTCCTCTCCCTTCATGATG 57.080 47.619 0.00 0.00 0.00 3.07
2645 2710 2.837947 TGTCCTCTCCCTTCATGATGT 58.162 47.619 0.00 0.00 0.00 3.06
2646 2711 3.994317 TGTCCTCTCCCTTCATGATGTA 58.006 45.455 0.00 0.00 0.00 2.29
2647 2712 3.706594 TGTCCTCTCCCTTCATGATGTAC 59.293 47.826 0.00 0.00 0.00 2.90
2648 2713 3.964031 GTCCTCTCCCTTCATGATGTACT 59.036 47.826 0.00 0.00 0.00 2.73
2649 2714 4.038642 GTCCTCTCCCTTCATGATGTACTC 59.961 50.000 0.00 0.00 0.00 2.59
2650 2715 3.963374 CCTCTCCCTTCATGATGTACTCA 59.037 47.826 0.00 0.00 38.53 3.41
2651 2716 4.592351 CCTCTCCCTTCATGATGTACTCAT 59.408 45.833 0.00 0.00 45.78 2.90
2652 2717 5.777223 CCTCTCCCTTCATGATGTACTCATA 59.223 44.000 0.00 0.00 42.91 2.15
2653 2718 6.440010 CCTCTCCCTTCATGATGTACTCATAT 59.560 42.308 0.00 0.00 42.91 1.78
2654 2719 7.363705 CCTCTCCCTTCATGATGTACTCATATC 60.364 44.444 0.00 0.00 42.91 1.63
2655 2720 7.012607 TCTCCCTTCATGATGTACTCATATCA 58.987 38.462 0.00 2.58 42.91 2.15
2656 2721 7.677319 TCTCCCTTCATGATGTACTCATATCAT 59.323 37.037 0.00 4.56 42.91 2.45
2657 2722 7.845037 TCCCTTCATGATGTACTCATATCATC 58.155 38.462 0.00 0.00 42.91 2.92
2691 2756 4.991153 AGATCATTCTGCGACTCTTGTA 57.009 40.909 0.00 0.00 0.00 2.41
2693 2758 5.288015 AGATCATTCTGCGACTCTTGTATG 58.712 41.667 0.00 0.00 0.00 2.39
2696 2761 6.149129 TCATTCTGCGACTCTTGTATGTAT 57.851 37.500 0.00 0.00 0.00 2.29
2740 2805 0.035056 AGTTCTGCATACAGCCACCC 60.035 55.000 0.00 0.00 44.10 4.61
2792 2857 2.072298 GTCTTCTGCGATGCACTTTCT 58.928 47.619 0.00 0.00 33.79 2.52
2810 2875 7.554476 GCACTTTCTTTTCTTCCTGATATACCT 59.446 37.037 0.00 0.00 0.00 3.08
2833 2917 4.899457 TGACCTTCAGAGTCCTGTTTAGAA 59.101 41.667 0.00 0.00 41.16 2.10
2835 2919 5.612351 ACCTTCAGAGTCCTGTTTAGAAAC 58.388 41.667 0.00 0.00 41.16 2.78
2901 2985 7.458038 GCTCTAGCACTGTTAAATAACTCTC 57.542 40.000 5.05 0.00 41.59 3.20
3214 3298 8.297470 ACACTGAATTTACTATAGTACGGGAA 57.703 34.615 12.25 4.81 0.00 3.97
3251 3335 4.276926 AGCTTGAGGCAAGTTAAGTTTCAG 59.723 41.667 8.74 0.00 42.77 3.02
3287 3371 2.672961 TGATCCTGGACTAGTTTGCG 57.327 50.000 0.00 0.00 0.00 4.85
3412 3496 2.174639 TGAGGTTGTTGTCAATCCCAGT 59.825 45.455 0.00 0.00 35.46 4.00
3498 3582 2.014857 TGAGGACGACGAGGTAATCTG 58.985 52.381 0.00 0.00 0.00 2.90
3501 3585 1.202268 GGACGACGAGGTAATCTGTGG 60.202 57.143 0.00 0.00 0.00 4.17
3504 3588 2.298163 ACGACGAGGTAATCTGTGGTTT 59.702 45.455 0.00 0.00 0.00 3.27
3557 3641 7.607607 AGGTATCATTTGAATTTTCTTTTGCCC 59.392 33.333 0.00 0.00 0.00 5.36
3564 3648 5.307204 TGAATTTTCTTTTGCCCTGGATTG 58.693 37.500 0.00 0.00 0.00 2.67
3619 3705 5.488341 ACTTGATACTTCGTGCTGGTATTT 58.512 37.500 0.00 0.00 0.00 1.40
3717 3803 2.024176 ACGAGATTATGGTGTGTGCC 57.976 50.000 0.00 0.00 0.00 5.01
3742 3829 7.933577 CCTGTATTCTGGCTGAAATGTTATCTA 59.066 37.037 10.95 0.00 38.29 1.98
3744 3831 9.276590 TGTATTCTGGCTGAAATGTTATCTATG 57.723 33.333 10.95 0.00 38.29 2.23
3748 3835 6.479990 TCTGGCTGAAATGTTATCTATGAACG 59.520 38.462 0.00 0.00 0.00 3.95
3749 3836 5.007626 TGGCTGAAATGTTATCTATGAACGC 59.992 40.000 0.00 0.00 0.00 4.84
3751 3838 6.293626 GGCTGAAATGTTATCTATGAACGCAT 60.294 38.462 0.00 0.00 38.54 4.73
3753 3840 8.446273 GCTGAAATGTTATCTATGAACGCATAT 58.554 33.333 0.00 0.00 36.45 1.78
3754 3841 9.750882 CTGAAATGTTATCTATGAACGCATATG 57.249 33.333 0.00 0.00 36.45 1.78
3755 3842 8.229811 TGAAATGTTATCTATGAACGCATATGC 58.770 33.333 18.08 18.08 36.45 3.14
3756 3843 7.671495 AATGTTATCTATGAACGCATATGCA 57.329 32.000 26.52 8.21 42.21 3.96
3757 3844 6.466308 TGTTATCTATGAACGCATATGCAC 57.534 37.500 26.52 16.81 42.21 4.57
3758 3845 6.223120 TGTTATCTATGAACGCATATGCACT 58.777 36.000 26.52 13.04 42.21 4.40
3759 3846 7.375053 TGTTATCTATGAACGCATATGCACTA 58.625 34.615 26.52 10.48 42.21 2.74
3760 3847 8.034804 TGTTATCTATGAACGCATATGCACTAT 58.965 33.333 26.52 16.20 42.21 2.12
3761 3848 8.873830 GTTATCTATGAACGCATATGCACTATT 58.126 33.333 26.52 14.54 42.21 1.73
3762 3849 6.710692 TCTATGAACGCATATGCACTATTG 57.289 37.500 26.52 11.94 42.21 1.90
3763 3850 6.223120 TCTATGAACGCATATGCACTATTGT 58.777 36.000 26.52 12.58 42.21 2.71
3764 3851 4.534794 TGAACGCATATGCACTATTGTG 57.465 40.909 26.52 10.54 46.37 3.33
3765 3852 3.938334 TGAACGCATATGCACTATTGTGT 59.062 39.130 26.52 11.17 45.44 3.72
3766 3853 4.394610 TGAACGCATATGCACTATTGTGTT 59.605 37.500 26.52 18.34 45.44 3.32
3767 3854 4.536364 ACGCATATGCACTATTGTGTTC 57.464 40.909 26.52 0.00 45.44 3.18
3768 3855 4.191544 ACGCATATGCACTATTGTGTTCT 58.808 39.130 26.52 0.00 45.44 3.01
3769 3856 4.034394 ACGCATATGCACTATTGTGTTCTG 59.966 41.667 26.52 8.04 45.44 3.02
3770 3857 4.034394 CGCATATGCACTATTGTGTTCTGT 59.966 41.667 26.52 0.00 45.44 3.41
3771 3858 5.234116 CGCATATGCACTATTGTGTTCTGTA 59.766 40.000 26.52 0.00 45.44 2.74
3772 3859 6.073602 CGCATATGCACTATTGTGTTCTGTAT 60.074 38.462 26.52 0.00 45.44 2.29
3773 3860 7.518848 CGCATATGCACTATTGTGTTCTGTATT 60.519 37.037 26.52 0.00 45.44 1.89
3774 3861 8.131100 GCATATGCACTATTGTGTTCTGTATTT 58.869 33.333 22.84 0.00 45.44 1.40
3779 3866 9.146984 TGCACTATTGTGTTCTGTATTTAGTAC 57.853 33.333 9.05 0.00 45.44 2.73
3824 3911 6.558009 TCTGAATGCTATTTTCTGATGTTGC 58.442 36.000 0.00 0.00 0.00 4.17
3852 3939 4.673534 AATTTTCGACCGTGGAATGTAC 57.326 40.909 0.00 0.00 0.00 2.90
3903 3990 3.351740 TGAAAGTGAGTTTGCTGTTGGA 58.648 40.909 0.00 0.00 0.00 3.53
4130 4218 4.323569 TCTCAGGTAGTCTCTGTCCAAT 57.676 45.455 0.00 0.00 34.15 3.16
4180 4268 9.638300 CTATTTGAAATGCTAACACGTTAGATC 57.362 33.333 18.82 11.35 43.90 2.75
4184 4272 8.181487 TGAAATGCTAACACGTTAGATCTTAC 57.819 34.615 18.82 0.00 43.90 2.34
4317 4405 7.768120 CAGAGATTACAATGCTTAGAAAGAGGT 59.232 37.037 0.00 0.00 0.00 3.85
4378 4466 7.642669 ACAACTTCAGTTTGTATCTGACATTG 58.357 34.615 12.62 12.62 40.90 2.82
4379 4467 6.808008 ACTTCAGTTTGTATCTGACATTGG 57.192 37.500 0.00 0.00 40.90 3.16
4380 4468 6.533730 ACTTCAGTTTGTATCTGACATTGGA 58.466 36.000 0.00 0.00 40.90 3.53
4431 4519 6.294731 CCTTCTACAGGGAAGTTTTGATTTGG 60.295 42.308 0.00 0.00 40.56 3.28
4667 4755 9.713713 TCAGTTTAGTGCAAAGTGTATATTACA 57.286 29.630 4.74 0.00 44.63 2.41
4722 7482 1.601759 GATGGGCATCGGGATGGTG 60.602 63.158 10.44 0.00 39.16 4.17
4739 7501 0.949105 GTGTCACGGGTGTGTGGATC 60.949 60.000 0.00 0.00 46.49 3.36
4749 7511 4.870426 CGGGTGTGTGGATCATATTATAGC 59.130 45.833 0.00 0.00 0.00 2.97
4755 7517 9.224267 GTGTGTGGATCATATTATAGCAAATCT 57.776 33.333 0.00 0.00 0.00 2.40
4786 7548 3.593442 TTCCCCATTGTCACTTTGAGT 57.407 42.857 0.00 0.00 0.00 3.41
4804 7566 4.614475 TGAGTCTAGATGGACCACAATCT 58.386 43.478 0.00 0.00 36.95 2.40
4830 7592 7.660617 TGAGTACTACTATTATTGACTCCCTCG 59.339 40.741 0.00 0.00 32.64 4.63
4833 7595 4.323553 ACTATTATTGACTCCCTCGCAC 57.676 45.455 0.00 0.00 0.00 5.34
4857 7619 5.124457 CGGTCTTCTTGTTCATCAAATGGAT 59.876 40.000 0.00 0.00 35.48 3.41
4935 7697 5.470047 AGATGGATTTGTAGTATCGGGTC 57.530 43.478 0.00 0.00 0.00 4.46
4949 7711 1.831736 TCGGGTCAGGAAAGGAAGATC 59.168 52.381 0.00 0.00 0.00 2.75
4997 7759 4.398044 GGCCTAAAACTAGCACATAAGCAA 59.602 41.667 0.00 0.00 36.85 3.91
4999 7761 5.973565 GCCTAAAACTAGCACATAAGCAATG 59.026 40.000 0.00 0.00 41.74 2.82
5003 7765 5.551760 AACTAGCACATAAGCAATGACAC 57.448 39.130 6.11 0.00 39.07 3.67
5004 7766 3.941483 ACTAGCACATAAGCAATGACACC 59.059 43.478 6.11 0.00 39.07 4.16
5055 7817 7.714813 TCATAGACTTTGTTGTCAATGAAGACA 59.285 33.333 14.31 0.00 46.12 3.41
5111 7873 4.265073 AGGGAGTGATCATTTGCTTGTAC 58.735 43.478 0.00 0.00 0.00 2.90
5132 7894 9.589111 TTGTACGTTGATGCATACTAATCTTTA 57.411 29.630 0.00 0.00 0.00 1.85
5142 7904 3.933861 ACTAATCTTTAGCACCAGGGG 57.066 47.619 0.00 0.00 0.00 4.79
5158 7920 2.432510 CAGGGGATCTGTGAAGTAGGAC 59.567 54.545 0.00 0.00 38.64 3.85
5161 7923 2.696187 GGGATCTGTGAAGTAGGACCTC 59.304 54.545 0.00 0.00 0.00 3.85
5211 7973 9.525826 AGAGAACATTTCCTAAAATCACTCATT 57.474 29.630 0.00 0.00 32.69 2.57
5237 7999 6.716934 AACATGTAGTTCTCTCACGGATAT 57.283 37.500 0.00 0.00 34.74 1.63
5243 8005 8.604640 TGTAGTTCTCTCACGGATATAGTAAG 57.395 38.462 0.00 0.00 0.00 2.34
5251 8013 3.255149 CACGGATATAGTAAGGCGGACTT 59.745 47.826 0.00 0.00 43.28 3.01
5271 8033 9.692749 CGGACTTATTATTCTTAATGTGCTCTA 57.307 33.333 0.00 0.00 30.64 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.332686 GGGTTTTGGAGACACACGTTC 59.667 52.381 0.00 0.00 42.67 3.95
1 2 1.340211 TGGGTTTTGGAGACACACGTT 60.340 47.619 0.00 0.00 42.67 3.99
2 3 0.253610 TGGGTTTTGGAGACACACGT 59.746 50.000 0.00 0.00 42.67 4.49
3 4 1.384525 TTGGGTTTTGGAGACACACG 58.615 50.000 0.00 0.00 42.67 4.49
4 5 2.693074 ACATTGGGTTTTGGAGACACAC 59.307 45.455 0.00 0.00 42.67 3.82
5 6 2.955660 GACATTGGGTTTTGGAGACACA 59.044 45.455 0.00 0.00 42.67 3.72
6 7 2.955660 TGACATTGGGTTTTGGAGACAC 59.044 45.455 0.00 0.00 42.67 3.67
7 8 3.304911 TGACATTGGGTTTTGGAGACA 57.695 42.857 0.00 0.00 39.83 3.41
8 9 4.399303 CCTATGACATTGGGTTTTGGAGAC 59.601 45.833 7.94 0.00 0.00 3.36
9 10 4.044065 ACCTATGACATTGGGTTTTGGAGA 59.956 41.667 18.43 0.00 0.00 3.71
10 11 4.344104 ACCTATGACATTGGGTTTTGGAG 58.656 43.478 18.43 0.00 0.00 3.86
11 12 4.396357 ACCTATGACATTGGGTTTTGGA 57.604 40.909 18.43 0.00 0.00 3.53
12 13 4.526262 TGAACCTATGACATTGGGTTTTGG 59.474 41.667 18.43 0.00 41.44 3.28
13 14 5.720371 TGAACCTATGACATTGGGTTTTG 57.280 39.130 18.43 0.00 41.44 2.44
14 15 6.739331 TTTGAACCTATGACATTGGGTTTT 57.261 33.333 18.43 5.59 41.44 2.43
15 16 6.070824 GGATTTGAACCTATGACATTGGGTTT 60.071 38.462 18.43 6.24 41.44 3.27
16 17 5.422012 GGATTTGAACCTATGACATTGGGTT 59.578 40.000 18.43 18.79 43.66 4.11
17 18 4.956075 GGATTTGAACCTATGACATTGGGT 59.044 41.667 18.43 13.11 0.00 4.51
18 19 5.203528 AGGATTTGAACCTATGACATTGGG 58.796 41.667 18.43 11.91 35.84 4.12
19 20 6.828273 TGTAGGATTTGAACCTATGACATTGG 59.172 38.462 13.60 13.60 41.25 3.16
20 21 7.770433 TCTGTAGGATTTGAACCTATGACATTG 59.230 37.037 0.00 0.00 41.25 2.82
21 22 7.861629 TCTGTAGGATTTGAACCTATGACATT 58.138 34.615 0.00 0.00 41.25 2.71
22 23 7.437713 TCTGTAGGATTTGAACCTATGACAT 57.562 36.000 0.00 0.00 41.25 3.06
23 24 6.630413 GCTCTGTAGGATTTGAACCTATGACA 60.630 42.308 0.00 0.00 41.25 3.58
24 25 5.755861 GCTCTGTAGGATTTGAACCTATGAC 59.244 44.000 0.00 0.00 41.25 3.06
25 26 5.451937 CGCTCTGTAGGATTTGAACCTATGA 60.452 44.000 0.00 0.00 41.25 2.15
26 27 4.747108 CGCTCTGTAGGATTTGAACCTATG 59.253 45.833 0.00 0.00 41.25 2.23
27 28 4.406003 ACGCTCTGTAGGATTTGAACCTAT 59.594 41.667 0.00 0.00 41.25 2.57
28 29 3.767673 ACGCTCTGTAGGATTTGAACCTA 59.232 43.478 0.00 0.00 38.76 3.08
29 30 2.567615 ACGCTCTGTAGGATTTGAACCT 59.432 45.455 0.00 0.00 41.05 3.50
30 31 2.673368 CACGCTCTGTAGGATTTGAACC 59.327 50.000 0.00 0.00 0.00 3.62
31 32 3.585862 TCACGCTCTGTAGGATTTGAAC 58.414 45.455 0.00 0.00 0.00 3.18
32 33 3.953712 TCACGCTCTGTAGGATTTGAA 57.046 42.857 0.00 0.00 0.00 2.69
33 34 4.471904 AATCACGCTCTGTAGGATTTGA 57.528 40.909 0.00 0.00 0.00 2.69
34 35 5.327091 CAAAATCACGCTCTGTAGGATTTG 58.673 41.667 0.00 0.00 37.99 2.32
35 36 4.142600 GCAAAATCACGCTCTGTAGGATTT 60.143 41.667 0.00 0.00 39.21 2.17
36 37 3.375299 GCAAAATCACGCTCTGTAGGATT 59.625 43.478 0.00 0.00 0.00 3.01
37 38 2.939103 GCAAAATCACGCTCTGTAGGAT 59.061 45.455 0.00 0.00 0.00 3.24
38 39 2.289382 TGCAAAATCACGCTCTGTAGGA 60.289 45.455 0.00 0.00 0.00 2.94
39 40 2.076100 TGCAAAATCACGCTCTGTAGG 58.924 47.619 0.00 0.00 0.00 3.18
40 41 2.159653 GGTGCAAAATCACGCTCTGTAG 60.160 50.000 0.00 0.00 37.83 2.74
41 42 1.804151 GGTGCAAAATCACGCTCTGTA 59.196 47.619 0.00 0.00 37.83 2.74
42 43 0.593128 GGTGCAAAATCACGCTCTGT 59.407 50.000 0.00 0.00 37.83 3.41
43 44 0.453282 CGGTGCAAAATCACGCTCTG 60.453 55.000 0.00 0.00 37.83 3.35
44 45 0.884704 ACGGTGCAAAATCACGCTCT 60.885 50.000 0.00 0.00 37.83 4.09
45 46 0.040425 AACGGTGCAAAATCACGCTC 60.040 50.000 0.00 0.00 37.83 5.03
46 47 0.317770 CAACGGTGCAAAATCACGCT 60.318 50.000 0.00 0.00 37.83 5.07
47 48 1.274798 CCAACGGTGCAAAATCACGC 61.275 55.000 0.00 0.00 37.83 5.34
48 49 1.274798 GCCAACGGTGCAAAATCACG 61.275 55.000 0.00 0.00 37.83 4.35
49 50 0.031994 AGCCAACGGTGCAAAATCAC 59.968 50.000 0.00 0.00 36.28 3.06
50 51 1.539388 CTAGCCAACGGTGCAAAATCA 59.461 47.619 0.00 0.00 0.00 2.57
51 52 1.732405 GCTAGCCAACGGTGCAAAATC 60.732 52.381 2.29 0.00 0.00 2.17
52 53 0.243636 GCTAGCCAACGGTGCAAAAT 59.756 50.000 2.29 0.00 0.00 1.82
53 54 0.821711 AGCTAGCCAACGGTGCAAAA 60.822 50.000 12.13 0.00 0.00 2.44
54 55 1.228124 AGCTAGCCAACGGTGCAAA 60.228 52.632 12.13 0.00 0.00 3.68
55 56 1.671054 GAGCTAGCCAACGGTGCAA 60.671 57.895 12.13 0.00 0.00 4.08
71 72 6.494893 TTCAATTCAAATCGTTAGTGGGAG 57.505 37.500 0.00 0.00 0.00 4.30
103 104 1.843851 TGTCTCCCTTGTTGTTCCTGT 59.156 47.619 0.00 0.00 0.00 4.00
224 225 2.613696 AGGGTATGCTGGGTGCCA 60.614 61.111 0.00 0.00 42.00 4.92
327 328 2.741985 CGCCGAGATGGTGCACAA 60.742 61.111 20.43 8.12 42.37 3.33
430 431 4.405358 CCCTGACTGAGAGCTTTAGAGAAT 59.595 45.833 0.00 0.00 0.00 2.40
432 433 3.360867 CCCTGACTGAGAGCTTTAGAGA 58.639 50.000 0.00 0.00 0.00 3.10
433 434 2.430332 CCCCTGACTGAGAGCTTTAGAG 59.570 54.545 0.00 0.00 0.00 2.43
434 435 2.225394 ACCCCTGACTGAGAGCTTTAGA 60.225 50.000 0.00 0.00 0.00 2.10
435 436 2.093764 CACCCCTGACTGAGAGCTTTAG 60.094 54.545 0.00 0.00 0.00 1.85
436 437 1.902508 CACCCCTGACTGAGAGCTTTA 59.097 52.381 0.00 0.00 0.00 1.85
437 438 0.689623 CACCCCTGACTGAGAGCTTT 59.310 55.000 0.00 0.00 0.00 3.51
640 642 3.369147 AGACGAATGCTGAATCAAGTTCG 59.631 43.478 16.96 16.96 42.73 3.95
685 693 2.172717 AGTAGACCACCACAGCAAGTTT 59.827 45.455 0.00 0.00 0.00 2.66
712 722 1.203162 ACCCAATTCAGGCATCAACCA 60.203 47.619 0.00 0.00 0.00 3.67
730 753 3.983044 ATTATAGCCCAATCGAGGACC 57.017 47.619 0.00 0.00 0.00 4.46
754 777 3.684305 CGTTCATTGCAGTTCCAGATGTA 59.316 43.478 0.00 0.00 0.00 2.29
761 784 0.109597 CAGCCGTTCATTGCAGTTCC 60.110 55.000 0.00 0.00 0.00 3.62
769 792 1.238439 CAACCAGTCAGCCGTTCATT 58.762 50.000 0.00 0.00 0.00 2.57
806 829 1.892819 ATCTGCCGCACACTAGCACT 61.893 55.000 0.00 0.00 32.06 4.40
811 834 2.494445 CCGATCTGCCGCACACTA 59.506 61.111 0.00 0.00 0.00 2.74
822 845 4.457496 CACGTGGCCAGCCGATCT 62.457 66.667 21.34 0.00 39.42 2.75
842 866 3.432252 CACAAACGTAAATCTCCGCTTCT 59.568 43.478 0.00 0.00 0.00 2.85
847 871 1.801771 TGGCACAAACGTAAATCTCCG 59.198 47.619 0.00 0.00 31.92 4.63
950 974 4.056092 TCTCGAGCGAGACACTATCTAA 57.944 45.455 17.70 0.00 45.26 2.10
997 1021 0.662374 GACGACGACGGTGACATTGT 60.662 55.000 12.58 0.00 44.46 2.71
1032 1056 4.144727 GGGCGGGAGGAGAGGAGA 62.145 72.222 0.00 0.00 0.00 3.71
1081 1105 0.107508 CACCTGCTCCCATCGTGATT 60.108 55.000 0.00 0.00 0.00 2.57
1082 1106 1.524002 CACCTGCTCCCATCGTGAT 59.476 57.895 0.00 0.00 0.00 3.06
1085 1109 3.402681 CCCACCTGCTCCCATCGT 61.403 66.667 0.00 0.00 0.00 3.73
1303 1336 0.169009 GCAGTTCGCCATTGAAGACC 59.831 55.000 0.00 0.00 32.94 3.85
1304 1337 0.179215 CGCAGTTCGCCATTGAAGAC 60.179 55.000 0.00 0.00 37.30 3.01
1305 1338 0.602638 ACGCAGTTCGCCATTGAAGA 60.603 50.000 0.00 0.00 37.78 2.87
1495 1548 3.648982 CGTTGCCGTTGCTGCTGA 61.649 61.111 0.00 0.00 38.71 4.26
1670 1728 9.064706 AGCTTTATCATAGTTCATCCAATTCAG 57.935 33.333 0.00 0.00 0.00 3.02
1678 1736 6.874288 AGCCAAGCTTTATCATAGTTCATC 57.126 37.500 0.00 0.00 33.89 2.92
1713 1771 0.322277 AGAGGAGGAACAGCGTCGTA 60.322 55.000 0.00 0.00 32.24 3.43
1718 1776 2.072298 CAAAGAAGAGGAGGAACAGCG 58.928 52.381 0.00 0.00 0.00 5.18
1856 1914 2.921754 GGATCGACTTACTTGTGGAACG 59.078 50.000 0.00 0.00 42.39 3.95
1931 1990 6.317789 ACATCACACACACTTGAAATAAGG 57.682 37.500 0.00 0.00 0.00 2.69
1935 1997 9.033481 CATTTTTACATCACACACACTTGAAAT 57.967 29.630 0.00 0.00 0.00 2.17
2037 2100 2.089980 CTCTGCCATGTCCAAGAAAGG 58.910 52.381 0.00 0.00 0.00 3.11
2067 2130 1.739466 TGCAATGTCGATTGAAGCTCC 59.261 47.619 2.94 0.00 41.49 4.70
2073 2136 1.358877 CCTCGTGCAATGTCGATTGA 58.641 50.000 2.94 0.00 41.49 2.57
2097 2160 3.667360 AGAATGCAGGGAAACAAAATGC 58.333 40.909 0.00 0.00 37.40 3.56
2104 2167 2.165030 CCACATGAGAATGCAGGGAAAC 59.835 50.000 0.00 0.00 0.00 2.78
2108 2171 2.022195 CTTCCACATGAGAATGCAGGG 58.978 52.381 0.00 0.00 0.00 4.45
2109 2172 2.995283 TCTTCCACATGAGAATGCAGG 58.005 47.619 0.00 0.00 0.00 4.85
2113 2176 8.954950 AACTTACTATCTTCCACATGAGAATG 57.045 34.615 0.00 0.00 0.00 2.67
2117 2180 7.492524 TGCTAACTTACTATCTTCCACATGAG 58.507 38.462 0.00 0.00 0.00 2.90
2146 2209 9.604626 GATATCTGCATACAAGTTCAAATTAGC 57.395 33.333 0.00 0.00 0.00 3.09
2206 2269 1.400494 AGATTTACGATGGCGGTTTGC 59.600 47.619 0.00 0.00 43.17 3.68
2299 2362 5.240121 TGGTTTACCTTGACTAATTCCGTC 58.760 41.667 0.00 1.86 36.82 4.79
2328 2391 1.771073 TTTTGGCAGACAGTGACGCG 61.771 55.000 3.53 3.53 36.69 6.01
2329 2392 0.317020 GTTTTGGCAGACAGTGACGC 60.317 55.000 0.00 0.00 36.69 5.19
2358 2421 8.672823 AAAGACAGGTAAAGAAAATTACTCGT 57.327 30.769 0.00 0.00 36.30 4.18
2366 2429 8.117813 ACTCACAAAAAGACAGGTAAAGAAAA 57.882 30.769 0.00 0.00 0.00 2.29
2370 2433 9.706691 TCTATACTCACAAAAAGACAGGTAAAG 57.293 33.333 0.00 0.00 0.00 1.85
2387 2450 8.064336 GGTTGAACTAAACCTCTCTATACTCA 57.936 38.462 0.00 0.00 45.25 3.41
2409 2472 4.934797 TCAGGATTGGAAGAGATTGGTT 57.065 40.909 0.00 0.00 0.00 3.67
2416 2479 9.565090 TTCATACAAATATCAGGATTGGAAGAG 57.435 33.333 0.00 0.00 0.00 2.85
2421 2484 8.118976 AGCATTCATACAAATATCAGGATTGG 57.881 34.615 0.00 0.00 0.00 3.16
2475 2539 9.631639 GTCGAAAACAAAAATGGAAAATAAGTG 57.368 29.630 0.00 0.00 0.00 3.16
2496 2560 6.993786 TTGGCAAGTTCAATATATGTCGAA 57.006 33.333 0.00 0.00 0.00 3.71
2497 2561 6.765512 TCATTGGCAAGTTCAATATATGTCGA 59.234 34.615 5.96 0.00 33.94 4.20
2499 2563 8.408601 AGTTCATTGGCAAGTTCAATATATGTC 58.591 33.333 5.96 0.00 33.94 3.06
2506 2570 7.816031 CAGAAATAGTTCATTGGCAAGTTCAAT 59.184 33.333 5.96 0.00 36.09 2.57
2617 2682 5.531122 TGAAGGGAGAGGACAATAATACG 57.469 43.478 0.00 0.00 0.00 3.06
2623 2688 3.784763 ACATCATGAAGGGAGAGGACAAT 59.215 43.478 0.00 0.00 0.00 2.71
2640 2705 9.463443 CGTAAACAAGATGATATGAGTACATCA 57.537 33.333 0.00 0.00 41.64 3.07
2641 2706 9.678941 TCGTAAACAAGATGATATGAGTACATC 57.321 33.333 0.00 0.00 40.14 3.06
2642 2707 9.684448 CTCGTAAACAAGATGATATGAGTACAT 57.316 33.333 0.00 0.00 40.16 2.29
2643 2708 8.899771 TCTCGTAAACAAGATGATATGAGTACA 58.100 33.333 0.00 0.00 32.99 2.90
2644 2709 9.731819 TTCTCGTAAACAAGATGATATGAGTAC 57.268 33.333 12.40 0.00 32.99 2.73
2645 2710 9.952188 CTTCTCGTAAACAAGATGATATGAGTA 57.048 33.333 12.40 6.65 32.99 2.59
2646 2711 8.687242 TCTTCTCGTAAACAAGATGATATGAGT 58.313 33.333 12.40 0.00 32.99 3.41
2647 2712 9.689976 ATCTTCTCGTAAACAAGATGATATGAG 57.310 33.333 0.00 0.00 35.88 2.90
2648 2713 9.684448 GATCTTCTCGTAAACAAGATGATATGA 57.316 33.333 0.00 0.00 37.07 2.15
2649 2714 9.468532 TGATCTTCTCGTAAACAAGATGATATG 57.531 33.333 0.00 0.00 37.07 1.78
2652 2717 8.954950 AATGATCTTCTCGTAAACAAGATGAT 57.045 30.769 0.00 0.48 37.07 2.45
2653 2718 8.253810 AGAATGATCTTCTCGTAAACAAGATGA 58.746 33.333 0.00 0.00 37.07 2.92
2654 2719 8.326713 CAGAATGATCTTCTCGTAAACAAGATG 58.673 37.037 0.00 0.00 39.69 2.90
2655 2720 7.010923 GCAGAATGATCTTCTCGTAAACAAGAT 59.989 37.037 0.00 0.00 39.69 2.40
2656 2721 6.311445 GCAGAATGATCTTCTCGTAAACAAGA 59.689 38.462 0.00 0.00 39.69 3.02
2657 2722 6.473521 GCAGAATGATCTTCTCGTAAACAAG 58.526 40.000 0.00 0.00 39.69 3.16
2691 2756 3.060479 TCTGGCCCTCAACCTATACAT 57.940 47.619 0.00 0.00 0.00 2.29
2693 2758 3.744660 CATTCTGGCCCTCAACCTATAC 58.255 50.000 0.00 0.00 0.00 1.47
2696 2761 0.255890 GCATTCTGGCCCTCAACCTA 59.744 55.000 0.00 0.00 0.00 3.08
2792 2857 7.182026 TGAAGGTCAGGTATATCAGGAAGAAAA 59.818 37.037 0.00 0.00 0.00 2.29
2810 2875 4.480115 TCTAAACAGGACTCTGAAGGTCA 58.520 43.478 0.00 0.00 43.49 4.02
2833 2917 5.003804 CACAAGGCATAAGTAAGACCTGTT 58.996 41.667 0.00 0.00 0.00 3.16
2835 2919 3.375299 GCACAAGGCATAAGTAAGACCTG 59.625 47.826 0.00 0.00 43.97 4.00
3120 3204 2.304092 TCGTACAAGGTGCCGATATCT 58.696 47.619 0.34 0.00 0.00 1.98
3205 3289 5.416271 TCTTCTTTATGCTTTCCCGTACT 57.584 39.130 0.00 0.00 0.00 2.73
3214 3298 4.157472 GCCTCAAGCTTCTTCTTTATGCTT 59.843 41.667 0.00 0.00 43.61 3.91
3251 3335 6.654161 CCAGGATCATATCTGAAATTGGACTC 59.346 42.308 0.00 0.00 33.87 3.36
3287 3371 2.072298 CTGCTGAGTACCAAGAGCAAC 58.928 52.381 0.00 0.00 40.80 4.17
3498 3582 4.576463 AGTGACAGAGAATGTTCAAACCAC 59.424 41.667 0.00 0.00 44.17 4.16
3501 3585 5.296780 TCCAAGTGACAGAGAATGTTCAAAC 59.703 40.000 0.00 0.00 44.17 2.93
3504 3588 4.380531 GTCCAAGTGACAGAGAATGTTCA 58.619 43.478 0.00 0.00 44.17 3.18
3534 3618 7.607223 CCAGGGCAAAAGAAAATTCAAATGATA 59.393 33.333 0.00 0.00 0.00 2.15
3557 3641 2.932614 GTCGATGTCTCCAACAATCCAG 59.067 50.000 0.00 0.00 42.37 3.86
3564 3648 3.851976 ACACTAGTCGATGTCTCCAAC 57.148 47.619 0.00 0.00 0.00 3.77
3607 3693 2.031245 TCAAACTGCAAATACCAGCACG 60.031 45.455 0.00 0.00 36.62 5.34
3619 3705 4.081406 AGCATTTAGGATGTCAAACTGCA 58.919 39.130 10.20 0.00 0.00 4.41
3717 3803 7.798596 AGATAACATTTCAGCCAGAATACAG 57.201 36.000 0.00 0.00 35.83 2.74
3730 3816 8.229811 TGCATATGCGTTCATAGATAACATTTC 58.770 33.333 22.21 0.00 45.83 2.17
3742 3829 5.099484 CACAATAGTGCATATGCGTTCAT 57.901 39.130 22.21 10.10 45.83 2.57
3753 3840 9.146984 GTACTAAATACAGAACACAATAGTGCA 57.853 33.333 0.00 0.00 40.36 4.57
3754 3841 8.318876 CGTACTAAATACAGAACACAATAGTGC 58.681 37.037 0.00 0.00 40.52 4.40
3755 3842 8.318876 GCGTACTAAATACAGAACACAATAGTG 58.681 37.037 0.00 0.00 41.66 2.74
3756 3843 8.030692 TGCGTACTAAATACAGAACACAATAGT 58.969 33.333 0.00 0.00 32.79 2.12
3757 3844 8.402326 TGCGTACTAAATACAGAACACAATAG 57.598 34.615 0.00 0.00 32.79 1.73
3758 3845 8.649841 GTTGCGTACTAAATACAGAACACAATA 58.350 33.333 0.00 0.00 32.79 1.90
3759 3846 7.360607 GGTTGCGTACTAAATACAGAACACAAT 60.361 37.037 0.00 0.00 32.79 2.71
3760 3847 6.073657 GGTTGCGTACTAAATACAGAACACAA 60.074 38.462 0.00 0.00 32.79 3.33
3761 3848 5.406175 GGTTGCGTACTAAATACAGAACACA 59.594 40.000 0.00 0.00 32.79 3.72
3762 3849 5.636543 AGGTTGCGTACTAAATACAGAACAC 59.363 40.000 0.00 0.00 32.79 3.32
3763 3850 5.786311 AGGTTGCGTACTAAATACAGAACA 58.214 37.500 0.00 0.00 32.79 3.18
3764 3851 7.998753 ATAGGTTGCGTACTAAATACAGAAC 57.001 36.000 0.00 0.00 32.79 3.01
3765 3852 8.252417 TCAATAGGTTGCGTACTAAATACAGAA 58.748 33.333 0.00 0.00 35.26 3.02
3766 3853 7.774134 TCAATAGGTTGCGTACTAAATACAGA 58.226 34.615 0.00 0.00 35.26 3.41
3767 3854 7.997107 TCAATAGGTTGCGTACTAAATACAG 57.003 36.000 0.00 0.00 35.26 2.74
3768 3855 7.439955 CCATCAATAGGTTGCGTACTAAATACA 59.560 37.037 0.00 0.00 35.26 2.29
3769 3856 7.440255 ACCATCAATAGGTTGCGTACTAAATAC 59.560 37.037 0.00 0.00 35.33 1.89
3770 3857 7.439955 CACCATCAATAGGTTGCGTACTAAATA 59.560 37.037 0.00 0.00 37.23 1.40
3771 3858 6.260050 CACCATCAATAGGTTGCGTACTAAAT 59.740 38.462 0.00 0.00 37.23 1.40
3772 3859 5.583061 CACCATCAATAGGTTGCGTACTAAA 59.417 40.000 0.00 0.00 37.23 1.85
3773 3860 5.105269 TCACCATCAATAGGTTGCGTACTAA 60.105 40.000 0.00 0.00 37.23 2.24
3774 3861 4.403113 TCACCATCAATAGGTTGCGTACTA 59.597 41.667 0.00 0.00 37.23 1.82
3775 3862 3.196901 TCACCATCAATAGGTTGCGTACT 59.803 43.478 0.00 0.00 37.23 2.73
3776 3863 3.527533 TCACCATCAATAGGTTGCGTAC 58.472 45.455 0.00 0.00 37.23 3.67
3779 3866 3.470709 AGATCACCATCAATAGGTTGCG 58.529 45.455 0.00 0.00 37.23 4.85
3824 3911 2.574322 CACGGTCGAAAATTTCTGCAG 58.426 47.619 7.63 7.63 0.00 4.41
3852 3939 2.260869 CCAACCAACAGGTCCAGCG 61.261 63.158 0.00 0.00 33.53 5.18
3903 3990 7.885399 ACTTTTCCAAGTAGTGCTGATCTAATT 59.115 33.333 0.00 0.00 41.81 1.40
4130 4218 7.896811 AGAAGTCAGTAATAACAGTCATGACA 58.103 34.615 27.02 7.35 38.38 3.58
4161 4249 7.031372 TCGTAAGATCTAACGTGTTAGCATTT 58.969 34.615 13.64 9.89 45.01 2.32
4180 4268 7.855904 ACTTTGCAAACTGAAAATAGTCGTAAG 59.144 33.333 8.05 0.00 0.00 2.34
4184 4272 6.472163 ACAACTTTGCAAACTGAAAATAGTCG 59.528 34.615 18.83 4.57 0.00 4.18
4304 4392 5.064834 CGTAATTTCCCACCTCTTTCTAAGC 59.935 44.000 0.00 0.00 0.00 3.09
4378 4466 4.385358 AAATAAACACATCGGGCATTCC 57.615 40.909 0.00 0.00 0.00 3.01
4379 4467 5.406649 TCAAAATAAACACATCGGGCATTC 58.593 37.500 0.00 0.00 0.00 2.67
4380 4468 5.398603 TCAAAATAAACACATCGGGCATT 57.601 34.783 0.00 0.00 0.00 3.56
4431 4519 7.534940 ATGAACTCCATTTGGAATCTTCCCAC 61.535 42.308 6.51 0.00 44.91 4.61
4722 7482 0.036388 ATGATCCACACACCCGTGAC 60.036 55.000 0.96 0.00 46.80 3.67
4739 7501 8.627208 ACCCAGTTGAGATTTGCTATAATATG 57.373 34.615 0.00 0.00 0.00 1.78
4786 7548 4.614475 ACTCAGATTGTGGTCCATCTAGA 58.386 43.478 0.00 0.00 0.00 2.43
4804 7566 7.660617 CGAGGGAGTCAATAATAGTAGTACTCA 59.339 40.741 5.96 0.00 34.86 3.41
4825 7587 1.738099 CAAGAAGACCGTGCGAGGG 60.738 63.158 2.26 0.00 35.02 4.30
4830 7592 2.143122 TGATGAACAAGAAGACCGTGC 58.857 47.619 0.00 0.00 0.00 5.34
4833 7595 4.455533 TCCATTTGATGAACAAGAAGACCG 59.544 41.667 0.00 0.00 39.77 4.79
4910 7672 6.659824 ACCCGATACTACAAATCCATCTTTT 58.340 36.000 0.00 0.00 0.00 2.27
4935 7697 5.656213 AAATTGCAGATCTTCCTTTCCTG 57.344 39.130 0.00 0.00 0.00 3.86
4949 7711 7.412563 CCATGCAAAGATTTCAGTAAATTGCAG 60.413 37.037 14.45 7.78 43.89 4.41
5111 7873 7.065894 GTGCTAAAGATTAGTATGCATCAACG 58.934 38.462 0.19 0.00 0.00 4.10
5142 7904 2.359531 CCGAGGTCCTACTTCACAGATC 59.640 54.545 0.00 0.00 0.00 2.75
5158 7920 2.159170 TGCAAAGGTTTGTTTTCCGAGG 60.159 45.455 4.45 0.00 40.24 4.63
5161 7923 2.887337 ACTGCAAAGGTTTGTTTTCCG 58.113 42.857 4.45 0.00 40.24 4.30
5227 7989 3.079578 TCCGCCTTACTATATCCGTGAG 58.920 50.000 0.00 0.00 0.00 3.51
5243 8005 6.204882 AGCACATTAAGAATAATAAGTCCGCC 59.795 38.462 0.00 0.00 30.50 6.13


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

AutoCloner maintained by Alex Coulton.