Multiple sequence alignment - TraesCS5B01G058400

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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 TraesCS5B01G058400 chr5B 100.000 4326 0 0 2300 6625 64259487 64263812 0.000000e+00 7989.0
1 TraesCS5B01G058400 chr5B 100.000 1980 0 0 1 1980 64257188 64259167 0.000000e+00 3657.0
2 TraesCS5B01G058400 chr5A 91.198 2988 201 31 2481 5431 57368690 57371652 0.000000e+00 4004.0
3 TraesCS5B01G058400 chr5A 91.025 1337 63 17 1 1310 57366658 57367964 0.000000e+00 1751.0
4 TraesCS5B01G058400 chr5A 92.991 1170 64 5 5457 6625 57373211 57374363 0.000000e+00 1690.0
5 TraesCS5B01G058400 chr5A 90.889 450 29 6 1306 1755 57368146 57368583 1.590000e-165 593.0
6 TraesCS5B01G058400 chr5A 93.258 356 24 0 5438 5793 57371694 57372049 5.890000e-145 525.0
7 TraesCS5B01G058400 chr5A 89.011 182 17 2 5839 6020 57372056 57372234 8.650000e-54 222.0
8 TraesCS5B01G058400 chr5A 85.321 109 15 1 2354 2462 57368596 57368703 1.950000e-20 111.0
9 TraesCS5B01G058400 chr5D 91.828 2900 167 32 2483 5337 66763248 66760374 0.000000e+00 3978.0
10 TraesCS5B01G058400 chr5D 91.489 846 50 13 5362 6188 66759132 66758290 0.000000e+00 1144.0
11 TraesCS5B01G058400 chr5D 97.521 605 10 4 1 603 66765808 66765207 0.000000e+00 1029.0
12 TraesCS5B01G058400 chr5D 88.904 730 37 11 595 1310 66765024 66764325 0.000000e+00 859.0
13 TraesCS5B01G058400 chr5D 94.495 436 19 1 6190 6625 66758204 66757774 0.000000e+00 667.0
14 TraesCS5B01G058400 chr5D 93.665 442 21 5 1306 1745 66764193 66763757 0.000000e+00 654.0
15 TraesCS5B01G058400 chr5D 87.702 496 31 13 5326 5793 66759842 66759349 9.710000e-153 551.0
16 TraesCS5B01G058400 chr5D 89.560 182 16 3 5839 6020 66759342 66759164 1.860000e-55 228.0
17 TraesCS5B01G058400 chr5D 91.489 141 10 2 1802 1941 66763749 66763610 6.780000e-45 193.0
18 TraesCS5B01G058400 chr5D 97.561 41 0 1 1941 1980 389057444 389057404 1.190000e-07 69.4
19 TraesCS5B01G058400 chr5D 100.000 35 0 0 1940 1974 445064085 445064119 1.540000e-06 65.8
20 TraesCS5B01G058400 chr3B 80.836 287 46 6 2481 2766 725582029 725582307 4.020000e-52 217.0
21 TraesCS5B01G058400 chr7A 94.828 58 1 2 1750 1806 29654006 29653950 9.150000e-14 89.8
22 TraesCS5B01G058400 chr4D 83.505 97 15 1 2736 2832 353920649 353920554 9.150000e-14 89.8
23 TraesCS5B01G058400 chr3D 97.561 41 0 1 1941 1980 26308334 26308294 1.190000e-07 69.4
24 TraesCS5B01G058400 chr3A 97.561 41 0 1 1941 1980 86383157 86383117 1.190000e-07 69.4
25 TraesCS5B01G058400 chr3A 100.000 36 0 0 1941 1976 264950320 264950285 4.290000e-07 67.6
26 TraesCS5B01G058400 chr1D 97.561 41 0 1 1941 1980 431455069 431455109 1.190000e-07 69.4
27 TraesCS5B01G058400 chr1D 94.444 36 1 1 1747 1781 142993227 142993262 3.000000e-03 54.7
28 TraesCS5B01G058400 chr1B 97.561 41 0 1 1941 1980 629093719 629093759 1.190000e-07 69.4
29 TraesCS5B01G058400 chr7D 100.000 36 0 0 1941 1976 595761678 595761643 4.290000e-07 67.6
30 TraesCS5B01G058400 chr4A 100.000 36 0 0 1941 1976 618167262 618167297 4.290000e-07 67.6
31 TraesCS5B01G058400 chr2D 100.000 28 0 0 1750 1777 75502831 75502804 1.200000e-02 52.8


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 TraesCS5B01G058400 chr5B 64257188 64263812 6624 False 5823.000000 7989 100.000000 1 6625 2 chr5B.!!$F1 6624
1 TraesCS5B01G058400 chr5A 57366658 57374363 7705 False 1270.857143 4004 90.527571 1 6625 7 chr5A.!!$F1 6624
2 TraesCS5B01G058400 chr5D 66757774 66765808 8034 True 1033.666667 3978 91.850333 1 6625 9 chr5D.!!$R2 6624

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
34 35 1.081840 GAACGAGTTTGCAGCAGCC 60.082 57.895 0.00 0.00 41.13 4.85 F
1156 1374 1.278127 GCTAGCAAGTAGGGTGGTTCA 59.722 52.381 10.63 0.00 0.00 3.18 F
1766 2185 0.033306 AGAACTACTCCCTCCGTCCC 60.033 60.000 0.00 0.00 0.00 4.46 F
1768 2187 0.115745 AACTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12 F
2616 3120 0.110823 CAAGAAGGAAAACGACGCCG 60.111 55.000 0.00 0.00 42.50 6.46 F
2815 3326 0.107508 GAGCAATCCTGTAGCTGCCA 60.108 55.000 0.00 0.00 39.02 4.92 F
3871 4419 0.643310 GTTCGACGCGTCAATATGCA 59.357 50.000 35.71 9.62 37.49 3.96 F
5389 6493 0.250727 TGGTGCCTGCTTTGTAGGAC 60.251 55.000 5.90 1.92 37.63 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1244 1475 1.194495 CGCCTACGAATCAACCGTAC 58.806 55.000 0.00 0.0 43.93 3.67 R
2377 2881 0.449388 CCACTTTGCCGATCTTCTGC 59.551 55.000 0.00 0.0 0.00 4.26 R
2570 3074 1.082756 GTCTTGTTTGCTCGTGGCG 60.083 57.895 0.00 0.0 45.43 5.69 R
2691 3195 1.302033 CTGCCGTGGCCTCCATATC 60.302 63.158 8.69 0.0 41.09 1.63 R
4437 4996 0.595095 CTGTGAAGAACTTGGGCAGC 59.405 55.000 0.00 0.0 0.00 5.25 R
4624 5183 1.193874 GTGGAAACAGCGAGGTTAACG 59.806 52.381 0.00 0.0 44.46 3.18 R
5537 6680 0.655733 CATTCGGCCGGTCATTGTAC 59.344 55.000 27.83 0.0 0.00 2.90 R
6249 8975 0.305313 TGTTCGCAAACTACAACCGC 59.695 50.000 0.00 0.0 36.30 5.68 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
34 35 1.081840 GAACGAGTTTGCAGCAGCC 60.082 57.895 0.00 0.00 41.13 4.85
432 444 3.236047 TCTGAGCCTACTGGTGTTGTAA 58.764 45.455 0.00 0.00 35.27 2.41
433 445 3.258372 TCTGAGCCTACTGGTGTTGTAAG 59.742 47.826 0.00 0.00 35.27 2.34
434 446 2.289444 TGAGCCTACTGGTGTTGTAAGC 60.289 50.000 0.00 0.00 35.27 3.09
435 447 1.978580 AGCCTACTGGTGTTGTAAGCT 59.021 47.619 0.00 0.00 34.12 3.74
436 448 2.028020 AGCCTACTGGTGTTGTAAGCTC 60.028 50.000 0.00 0.00 33.85 4.09
437 449 2.028020 GCCTACTGGTGTTGTAAGCTCT 60.028 50.000 0.00 0.00 35.27 4.09
438 450 3.194968 GCCTACTGGTGTTGTAAGCTCTA 59.805 47.826 0.00 0.00 35.27 2.43
524 539 1.651737 AGGGCATGGTGTAGTGTGTA 58.348 50.000 0.00 0.00 0.00 2.90
543 558 1.745489 GCCTAGCACCCTTGGTTCG 60.745 63.158 0.00 0.00 36.49 3.95
623 829 3.342377 TGTCATGTTCCTGCCGATTTA 57.658 42.857 0.00 0.00 0.00 1.40
628 834 6.038161 TGTCATGTTCCTGCCGATTTATTTAG 59.962 38.462 0.00 0.00 0.00 1.85
666 872 3.260632 TGGATGCTGCTGTAACTGTAAGA 59.739 43.478 0.00 0.00 37.43 2.10
674 880 3.120511 GCTGTAACTGTAAGACTGCAAGC 60.121 47.826 11.66 0.00 36.23 4.01
678 884 2.673833 ACTGTAAGACTGCAAGCGTAC 58.326 47.619 0.00 0.00 34.81 3.67
778 991 3.016613 TACGAGGGGCCCAGATGGA 62.017 63.158 27.72 4.53 37.39 3.41
839 1057 3.074412 TGAAAGAAATTCAGTCCCTCGC 58.926 45.455 0.00 0.00 43.08 5.03
840 1058 3.244561 TGAAAGAAATTCAGTCCCTCGCT 60.245 43.478 0.00 0.00 43.08 4.93
960 1178 5.440685 CGTTTTTGTCGCTTAATCTCACTT 58.559 37.500 0.00 0.00 0.00 3.16
1006 1224 1.446791 CAGAGAGGAGCCATGGAGC 59.553 63.158 18.40 5.75 0.00 4.70
1104 1322 3.365465 CCTCGCCTCGTAAGTGATCTATG 60.365 52.174 0.00 0.00 39.48 2.23
1105 1323 3.473625 TCGCCTCGTAAGTGATCTATGA 58.526 45.455 0.00 0.00 39.48 2.15
1106 1324 3.250280 TCGCCTCGTAAGTGATCTATGAC 59.750 47.826 0.00 0.00 39.48 3.06
1107 1325 3.609644 CGCCTCGTAAGTGATCTATGACC 60.610 52.174 0.00 0.00 39.48 4.02
1108 1326 3.318275 GCCTCGTAAGTGATCTATGACCA 59.682 47.826 0.00 0.00 39.48 4.02
1109 1327 4.021894 GCCTCGTAAGTGATCTATGACCAT 60.022 45.833 0.00 0.00 39.48 3.55
1110 1328 5.704888 CCTCGTAAGTGATCTATGACCATC 58.295 45.833 0.00 0.00 39.48 3.51
1156 1374 1.278127 GCTAGCAAGTAGGGTGGTTCA 59.722 52.381 10.63 0.00 0.00 3.18
1175 1393 2.534903 GCCCCGCGATTTACTGCTC 61.535 63.158 8.23 0.00 0.00 4.26
1200 1418 2.202837 GGCGCCGGTTTCGACTAT 60.203 61.111 12.58 0.00 39.00 2.12
1244 1475 4.157958 GCGAGGCTTTGCTCTGCG 62.158 66.667 0.00 0.00 0.00 5.18
1256 1487 0.645868 GCTCTGCGTACGGTTGATTC 59.354 55.000 18.39 0.00 0.00 2.52
1477 1894 2.168521 TCGGGCTACATGGAAGAAGAAG 59.831 50.000 0.00 0.00 0.00 2.85
1519 1936 5.330455 TCTTCTCACGCAGTTCTATCATT 57.670 39.130 0.00 0.00 41.61 2.57
1549 1966 3.624326 TTTTGCGATGTTTGACTCCAG 57.376 42.857 0.00 0.00 0.00 3.86
1553 1970 1.470098 GCGATGTTTGACTCCAGCATT 59.530 47.619 0.00 0.00 0.00 3.56
1649 2066 4.647424 TGAAGGAAAACAATCACCACAC 57.353 40.909 0.00 0.00 0.00 3.82
1650 2067 4.277476 TGAAGGAAAACAATCACCACACT 58.723 39.130 0.00 0.00 0.00 3.55
1664 2081 0.883833 CACACTGTCAGAATTGGCCC 59.116 55.000 6.91 0.00 0.00 5.80
1669 2086 3.007182 CACTGTCAGAATTGGCCCATTTT 59.993 43.478 6.91 0.00 0.00 1.82
1671 2088 4.837860 ACTGTCAGAATTGGCCCATTTTAA 59.162 37.500 6.91 0.00 0.00 1.52
1674 2091 6.777782 TGTCAGAATTGGCCCATTTTAATTT 58.222 32.000 3.13 0.00 0.00 1.82
1745 2164 4.579869 TGAGGGAAAATCTAGCAGAACAC 58.420 43.478 0.00 0.00 0.00 3.32
1755 2174 6.597832 ATCTAGCAGAACACAAGAACTACT 57.402 37.500 0.00 0.00 0.00 2.57
1756 2175 6.015027 TCTAGCAGAACACAAGAACTACTC 57.985 41.667 0.00 0.00 0.00 2.59
1757 2176 3.996480 AGCAGAACACAAGAACTACTCC 58.004 45.455 0.00 0.00 0.00 3.85
1758 2177 3.067833 GCAGAACACAAGAACTACTCCC 58.932 50.000 0.00 0.00 0.00 4.30
1759 2178 3.244249 GCAGAACACAAGAACTACTCCCT 60.244 47.826 0.00 0.00 0.00 4.20
1760 2179 4.561105 CAGAACACAAGAACTACTCCCTC 58.439 47.826 0.00 0.00 0.00 4.30
1761 2180 3.579151 AGAACACAAGAACTACTCCCTCC 59.421 47.826 0.00 0.00 0.00 4.30
1762 2181 1.893801 ACACAAGAACTACTCCCTCCG 59.106 52.381 0.00 0.00 0.00 4.63
1763 2182 1.893801 CACAAGAACTACTCCCTCCGT 59.106 52.381 0.00 0.00 0.00 4.69
1764 2183 2.094649 CACAAGAACTACTCCCTCCGTC 60.095 54.545 0.00 0.00 0.00 4.79
1765 2184 1.477295 CAAGAACTACTCCCTCCGTCC 59.523 57.143 0.00 0.00 0.00 4.79
1766 2185 0.033306 AGAACTACTCCCTCCGTCCC 60.033 60.000 0.00 0.00 0.00 4.46
1767 2186 0.324091 GAACTACTCCCTCCGTCCCA 60.324 60.000 0.00 0.00 0.00 4.37
1768 2187 0.115745 AACTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
1769 2188 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
1770 2189 1.273666 ACTACTCCCTCCGTCCCAAAT 60.274 52.381 0.00 0.00 0.00 2.32
1771 2190 2.023695 ACTACTCCCTCCGTCCCAAATA 60.024 50.000 0.00 0.00 0.00 1.40
1772 2191 2.191981 ACTCCCTCCGTCCCAAATAT 57.808 50.000 0.00 0.00 0.00 1.28
1773 2192 3.339713 ACTCCCTCCGTCCCAAATATA 57.660 47.619 0.00 0.00 0.00 0.86
1774 2193 3.660959 ACTCCCTCCGTCCCAAATATAA 58.339 45.455 0.00 0.00 0.00 0.98
1775 2194 3.646637 ACTCCCTCCGTCCCAAATATAAG 59.353 47.826 0.00 0.00 0.00 1.73
1776 2195 3.901844 CTCCCTCCGTCCCAAATATAAGA 59.098 47.826 0.00 0.00 0.00 2.10
1777 2196 3.644738 TCCCTCCGTCCCAAATATAAGAC 59.355 47.826 0.00 0.00 0.00 3.01
1785 2204 7.614674 CGTCCCAAATATAAGACGTTACTAC 57.385 40.000 3.39 0.00 45.25 2.73
1786 2205 7.195646 CGTCCCAAATATAAGACGTTACTACA 58.804 38.462 3.39 0.00 45.25 2.74
1787 2206 7.864379 CGTCCCAAATATAAGACGTTACTACAT 59.136 37.037 3.39 0.00 45.25 2.29
1788 2207 9.189723 GTCCCAAATATAAGACGTTACTACATC 57.810 37.037 0.00 0.00 0.00 3.06
1789 2208 8.362639 TCCCAAATATAAGACGTTACTACATCC 58.637 37.037 0.00 0.00 0.00 3.51
1790 2209 8.145767 CCCAAATATAAGACGTTACTACATCCA 58.854 37.037 0.00 0.00 0.00 3.41
1791 2210 9.537192 CCAAATATAAGACGTTACTACATCCAA 57.463 33.333 0.00 0.00 0.00 3.53
1799 2218 8.687292 AGACGTTACTACATCCAATATACTCA 57.313 34.615 0.00 0.00 0.00 3.41
1800 2219 9.128404 AGACGTTACTACATCCAATATACTCAA 57.872 33.333 0.00 0.00 0.00 3.02
1836 2256 8.020819 TGTTTATGTTTTCAAGAATAGCTTCCG 58.979 33.333 0.00 0.00 33.60 4.30
1916 2336 2.469274 AGCTCATGTCACCAGTGAAG 57.531 50.000 1.23 0.00 41.85 3.02
1956 2460 2.275380 AAAACATGGTGCCCGGAGC 61.275 57.895 0.73 5.29 44.14 4.70
1976 2480 1.761198 CAGAGAGACATGGGATGCTCA 59.239 52.381 0.00 0.00 36.53 4.26
1977 2481 1.761784 AGAGAGACATGGGATGCTCAC 59.238 52.381 0.00 0.00 36.53 3.51
2351 2855 1.006102 ACGGCTCCAAACTCGACTG 60.006 57.895 0.00 0.00 0.00 3.51
2361 2865 3.571571 CAAACTCGACTGGATCAACGTA 58.428 45.455 0.00 0.00 0.00 3.57
2375 2879 1.486145 AACGTACCCCCACCAAGAGG 61.486 60.000 0.00 0.00 42.21 3.69
2381 2885 2.935481 CCCACCAAGAGGGGCAGA 60.935 66.667 0.00 0.00 42.90 4.26
2390 2894 2.688666 AGGGGCAGAAGATCGGCA 60.689 61.111 4.95 0.00 39.36 5.69
2421 2925 3.081409 GACCCAGCCTAGCCGGAA 61.081 66.667 5.05 0.00 33.16 4.30
2462 2966 3.488721 GCACCATCGAAGTCGTACATAGT 60.489 47.826 0.00 0.00 40.80 2.12
2463 2967 4.035684 CACCATCGAAGTCGTACATAGTG 58.964 47.826 0.00 0.00 40.80 2.74
2464 2968 3.693085 ACCATCGAAGTCGTACATAGTGT 59.307 43.478 0.00 0.00 40.80 3.55
2465 2969 4.157289 ACCATCGAAGTCGTACATAGTGTT 59.843 41.667 0.00 0.00 40.80 3.32
2466 2970 4.733887 CCATCGAAGTCGTACATAGTGTTC 59.266 45.833 0.00 0.00 40.80 3.18
2467 2971 4.346734 TCGAAGTCGTACATAGTGTTCC 57.653 45.455 0.00 0.00 40.80 3.62
2468 2972 3.127548 TCGAAGTCGTACATAGTGTTCCC 59.872 47.826 0.00 0.00 40.80 3.97
2469 2973 3.432782 GAAGTCGTACATAGTGTTCCCG 58.567 50.000 0.00 0.00 0.00 5.14
2470 2974 1.133790 AGTCGTACATAGTGTTCCCGC 59.866 52.381 0.00 0.00 0.00 6.13
2471 2975 1.135315 GTCGTACATAGTGTTCCCGCA 60.135 52.381 0.00 0.00 0.00 5.69
2472 2976 1.545136 TCGTACATAGTGTTCCCGCAA 59.455 47.619 0.00 0.00 0.00 4.85
2473 2977 2.029200 TCGTACATAGTGTTCCCGCAAA 60.029 45.455 0.00 0.00 0.00 3.68
2474 2978 2.737783 CGTACATAGTGTTCCCGCAAAA 59.262 45.455 0.00 0.00 0.00 2.44
2475 2979 3.186817 CGTACATAGTGTTCCCGCAAAAA 59.813 43.478 0.00 0.00 0.00 1.94
2498 3002 4.530710 AAAGAAGTCGTACATAGTGCCA 57.469 40.909 0.00 0.00 0.00 4.92
2505 3009 1.801395 CGTACATAGTGCCACGGAAGG 60.801 57.143 0.00 0.00 0.00 3.46
2564 3068 2.433970 CAACATCCCCAAAACCAACACT 59.566 45.455 0.00 0.00 0.00 3.55
2570 3074 2.235891 CCCAAAACCAACACTAGGGAC 58.764 52.381 0.00 0.00 36.96 4.46
2574 3078 1.412453 AACCAACACTAGGGACGCCA 61.412 55.000 0.00 0.00 0.00 5.69
2615 3119 1.223187 TCAAGAAGGAAAACGACGCC 58.777 50.000 0.00 0.00 0.00 5.68
2616 3120 0.110823 CAAGAAGGAAAACGACGCCG 60.111 55.000 0.00 0.00 42.50 6.46
2649 3153 1.818363 CGTCCGATCCGAGGAGTCA 60.818 63.158 0.00 0.00 38.65 3.41
2656 3160 2.223745 GATCCGAGGAGTCAGACCTAC 58.776 57.143 0.00 0.00 37.93 3.18
2657 3161 1.287217 TCCGAGGAGTCAGACCTACT 58.713 55.000 0.00 0.00 37.93 2.57
2664 3168 3.166679 GGAGTCAGACCTACTGTTTCCT 58.833 50.000 0.00 0.00 45.86 3.36
2665 3169 3.056465 GGAGTCAGACCTACTGTTTCCTG 60.056 52.174 0.00 0.00 45.86 3.86
2670 3174 0.763035 ACCTACTGTTTCCTGCGGTT 59.237 50.000 0.00 0.00 0.00 4.44
2691 3195 2.620251 TCGAAGAGGGGCACATATTG 57.380 50.000 0.00 0.00 0.00 1.90
2692 3196 2.115427 TCGAAGAGGGGCACATATTGA 58.885 47.619 0.00 0.00 0.00 2.57
2693 3197 2.705658 TCGAAGAGGGGCACATATTGAT 59.294 45.455 0.00 0.00 0.00 2.57
2694 3198 3.901222 TCGAAGAGGGGCACATATTGATA 59.099 43.478 0.00 0.00 0.00 2.15
2695 3199 4.532126 TCGAAGAGGGGCACATATTGATAT 59.468 41.667 0.00 0.00 0.00 1.63
2696 3200 4.633126 CGAAGAGGGGCACATATTGATATG 59.367 45.833 8.98 8.98 44.37 1.78
2704 3208 3.441572 GCACATATTGATATGGAGGCCAC 59.558 47.826 5.01 0.00 43.38 5.01
2734 3238 0.396811 CCAAGGAGGGAACGACACTT 59.603 55.000 0.00 0.00 29.26 3.16
2758 3269 4.060038 GTTGCCGCTGCCAGCATT 62.060 61.111 18.21 0.00 42.58 3.56
2789 3300 2.039462 GGGATTTTGCCCTGGCCT 59.961 61.111 3.32 0.00 45.12 5.19
2793 3304 1.953231 GATTTTGCCCTGGCCTGAGC 61.953 60.000 11.88 10.54 41.09 4.26
2805 3316 1.913722 CCTGAGCCTGAGCAATCCT 59.086 57.895 0.00 0.00 43.56 3.24
2811 3322 0.179936 GCCTGAGCAATCCTGTAGCT 59.820 55.000 0.00 0.00 42.17 3.32
2815 3326 0.107508 GAGCAATCCTGTAGCTGCCA 60.108 55.000 0.00 0.00 39.02 4.92
2892 3408 6.716284 AGGAGCTAGTTTTGCTATTTTCTCT 58.284 36.000 0.00 0.00 41.30 3.10
2940 3456 6.896307 TGTTTAAAGAAGGGGAAAACTACCAA 59.104 34.615 0.00 0.00 32.57 3.67
2963 3479 8.839343 CCAAGATGTGTTAATATGCTGTGATTA 58.161 33.333 0.00 0.00 0.00 1.75
2976 3494 5.423015 TGCTGTGATTATCTCTCACCTTTC 58.577 41.667 1.37 0.00 41.87 2.62
3022 3540 8.573035 GGATTATATCTAGAGTAGCTACATGGC 58.427 40.741 25.28 11.50 0.00 4.40
3087 3612 6.856135 TTGCATGACTTGAGATGCTAATAG 57.144 37.500 0.00 0.00 44.46 1.73
3164 3690 2.288457 TGAGCACCTTCTTTCTGTCTCG 60.288 50.000 0.00 0.00 0.00 4.04
3249 3775 4.142988 TGAATTATTTCCGTCGCAACAGTC 60.143 41.667 0.00 0.00 0.00 3.51
3301 3827 3.487574 GCCGTAGAACATCGATTCTTGAG 59.512 47.826 6.59 0.34 39.65 3.02
3336 3862 9.772973 TCAACAAGTATACACTGTTATCTGTTT 57.227 29.630 17.92 0.00 34.36 2.83
3369 3896 9.394477 AGAAGCAAACAGAAACGTAATATTTTC 57.606 29.630 0.00 0.00 32.76 2.29
3371 3898 6.799925 AGCAAACAGAAACGTAATATTTTCGG 59.200 34.615 14.12 6.85 36.91 4.30
3372 3899 6.451960 GCAAACAGAAACGTAATATTTTCGGC 60.452 38.462 14.12 6.24 36.91 5.54
3439 3966 9.467258 CACAATATTTTTGGTCCAATGCTATAG 57.533 33.333 4.80 0.00 0.00 1.31
3453 3980 6.820656 CCAATGCTATAGAAGAACTGTCTGTT 59.179 38.462 3.21 0.00 42.38 3.16
3454 3981 7.981789 CCAATGCTATAGAAGAACTGTCTGTTA 59.018 37.037 3.21 0.00 39.30 2.41
3455 3982 9.371136 CAATGCTATAGAAGAACTGTCTGTTAA 57.629 33.333 3.21 0.00 39.30 2.01
3456 3983 9.944376 AATGCTATAGAAGAACTGTCTGTTAAA 57.056 29.630 3.21 0.00 39.30 1.52
3464 4009 9.930693 AGAAGAACTGTCTGTTAAATACCTTAG 57.069 33.333 0.00 0.00 39.30 2.18
3522 4067 7.559590 AATACAGTGGATCTTTAAGATGTGC 57.440 36.000 12.63 2.19 34.53 4.57
3549 4094 9.976511 ATATCATTGAAAAACAAGGCATCTATG 57.023 29.630 0.00 0.00 42.02 2.23
3608 4153 5.272402 TCAATGTAGATTGTCCTCCTCTCA 58.728 41.667 11.96 0.00 40.09 3.27
3636 4182 8.581253 TTATTTCTCCTCTCATTTCCCTTTTC 57.419 34.615 0.00 0.00 0.00 2.29
3871 4419 0.643310 GTTCGACGCGTCAATATGCA 59.357 50.000 35.71 9.62 37.49 3.96
3897 4445 4.413087 GTCTCAGAAGCATGCAAAAGATG 58.587 43.478 21.98 9.49 0.00 2.90
3898 4446 4.155462 GTCTCAGAAGCATGCAAAAGATGA 59.845 41.667 21.98 13.11 0.00 2.92
4101 4652 1.552792 GAGGAGGTGAGAAGGGTTCTG 59.447 57.143 0.00 0.00 40.87 3.02
4102 4653 1.132689 AGGAGGTGAGAAGGGTTCTGT 60.133 52.381 0.00 0.00 40.87 3.41
4107 4658 2.147150 GTGAGAAGGGTTCTGTGCTTC 58.853 52.381 0.00 0.00 40.87 3.86
4108 4659 2.050144 TGAGAAGGGTTCTGTGCTTCT 58.950 47.619 0.00 0.00 40.87 2.85
4112 4663 5.483937 TGAGAAGGGTTCTGTGCTTCTTATA 59.516 40.000 0.00 0.00 40.87 0.98
4182 4739 5.587388 AATTTAGCACCATGGACATTCAG 57.413 39.130 21.47 0.00 0.00 3.02
4326 4885 4.276926 GGGTCAGTTTATGCTCCATCATTC 59.723 45.833 0.00 0.00 0.00 2.67
4335 4894 1.467734 GCTCCATCATTCGATCATGGC 59.532 52.381 11.30 0.00 37.57 4.40
4350 4909 2.203294 GGCGTTGGTGACCCAGTT 60.203 61.111 0.00 0.00 43.15 3.16
4399 4958 7.015877 GCAGTAAGTTATTTTGCAGAGTACAC 58.984 38.462 0.00 0.00 34.99 2.90
4433 4992 7.137490 TCTTAGCTGACTTGATTGAAATGTG 57.863 36.000 0.00 0.00 0.00 3.21
4437 4996 6.444633 AGCTGACTTGATTGAAATGTGAAAG 58.555 36.000 0.00 0.00 0.00 2.62
4449 5008 1.032014 TGTGAAAGCTGCCCAAGTTC 58.968 50.000 0.00 0.00 0.00 3.01
4457 5016 1.815408 GCTGCCCAAGTTCTTCACAGA 60.815 52.381 0.00 0.00 0.00 3.41
4467 5026 8.359642 CCCAAGTTCTTCACAGAAAATTAATGA 58.640 33.333 0.00 0.00 40.90 2.57
4494 5053 5.754782 TGAACTACCGACCATAGTACCTTA 58.245 41.667 0.00 0.00 32.47 2.69
4496 5055 6.263842 TGAACTACCGACCATAGTACCTTATG 59.736 42.308 0.00 0.00 32.47 1.90
4508 5067 5.700402 AGTACCTTATGGAGCAACTTGAT 57.300 39.130 0.81 0.00 37.04 2.57
4509 5068 6.067217 AGTACCTTATGGAGCAACTTGATT 57.933 37.500 0.81 0.00 37.04 2.57
4535 5094 6.844696 TTGCGTATCCTTTCTGCTAAATAG 57.155 37.500 0.00 0.00 0.00 1.73
4554 5113 6.884280 AATAGCATTACAATGTCCTAAGCC 57.116 37.500 4.02 0.00 38.65 4.35
4561 5120 7.862873 GCATTACAATGTCCTAAGCCTATTTTC 59.137 37.037 4.02 0.00 38.65 2.29
4581 5140 3.740115 TCTTTGAAGCAGTGTCCTAACC 58.260 45.455 0.00 0.00 0.00 2.85
4588 5147 3.658725 AGCAGTGTCCTAACCCTATGAT 58.341 45.455 0.00 0.00 0.00 2.45
4624 5183 6.369890 TGTTCTGCTGTTAATCTTCATCAGAC 59.630 38.462 0.00 0.00 36.83 3.51
4659 5218 5.607477 TGTTTCCACTTCTGTAGTTTCGAT 58.393 37.500 0.00 0.00 33.85 3.59
4691 5250 6.154021 GGACCCTACAACTGTCATAACTTCTA 59.846 42.308 0.00 0.00 0.00 2.10
4700 5259 9.950680 CAACTGTCATAACTTCTACACAATTTT 57.049 29.630 0.00 0.00 0.00 1.82
5006 5565 2.554893 TCGTGTTTCTAATGGCCAAACC 59.445 45.455 10.96 2.75 39.84 3.27
5095 5655 0.827089 CACAGGTTTGCCCATCCACA 60.827 55.000 0.00 0.00 34.66 4.17
5154 5715 8.262601 TGTATCTAATTCCATTTCCTGCTCTA 57.737 34.615 0.00 0.00 0.00 2.43
5207 5768 1.464608 CAGCATGGCGGGTAATTATCG 59.535 52.381 0.00 6.77 0.00 2.92
5270 5831 6.435430 TGCTTACATACAGCCACATAAAAG 57.565 37.500 0.00 0.00 36.33 2.27
5292 5853 5.564550 AGGCTCATTCAGTGTCTTATGTTT 58.435 37.500 0.00 0.00 0.00 2.83
5322 5883 4.625607 ACCCTATGCATTAGCTTAGACC 57.374 45.455 3.54 0.00 46.11 3.85
5365 6469 6.479095 ACAATTTATGCCAAAAATGGTTCG 57.521 33.333 0.00 0.00 28.09 3.95
5368 6472 6.720012 ATTTATGCCAAAAATGGTTCGTTC 57.280 33.333 0.00 0.00 0.00 3.95
5369 6473 3.742433 ATGCCAAAAATGGTTCGTTCA 57.258 38.095 0.00 0.00 0.00 3.18
5372 6476 2.736192 GCCAAAAATGGTTCGTTCATGG 59.264 45.455 0.00 0.00 0.00 3.66
5379 6483 1.210155 GTTCGTTCATGGTGCCTGC 59.790 57.895 0.00 0.00 0.00 4.85
5389 6493 0.250727 TGGTGCCTGCTTTGTAGGAC 60.251 55.000 5.90 1.92 37.63 3.85
5434 6540 8.159229 ACCATAGGAAAACCTACATAAGAAGT 57.841 34.615 0.00 0.00 0.00 3.01
5436 6542 9.462606 CCATAGGAAAACCTACATAAGAAGTTT 57.537 33.333 0.00 0.00 32.26 2.66
5443 6584 7.430992 AACCTACATAAGAAGTTTTCGGTTC 57.569 36.000 0.00 0.00 34.02 3.62
5446 6587 7.664318 ACCTACATAAGAAGTTTTCGGTTCAAT 59.336 33.333 0.00 0.00 34.02 2.57
5450 6591 8.576442 ACATAAGAAGTTTTCGGTTCAATGAAT 58.424 29.630 0.00 0.00 34.02 2.57
5499 6642 9.424319 TCATAGAATTTCTGAACACTACAACTC 57.576 33.333 9.22 0.00 0.00 3.01
5503 6646 6.867662 ATTTCTGAACACTACAACTCCTTG 57.132 37.500 0.00 0.00 0.00 3.61
5537 6680 8.511465 AAATTTGTCTTGTGAATCAGATTTCG 57.489 30.769 0.00 0.00 0.00 3.46
5581 6724 6.677431 GCTGAGCTTATCATGGAGTCAAAAAG 60.677 42.308 0.00 0.00 37.28 2.27
5617 6760 4.579340 TGTAATCAGATCGGTGGACTACTC 59.421 45.833 0.00 0.00 0.00 2.59
5678 6821 8.738199 TTTCGGTAATAATAGTTGCTCTATCG 57.262 34.615 3.31 0.00 38.29 2.92
5733 6876 2.325583 TCCATCCGTGGTGATTTAGC 57.674 50.000 0.00 0.00 46.16 3.09
5734 6877 1.557371 TCCATCCGTGGTGATTTAGCA 59.443 47.619 0.00 0.00 46.16 3.49
5775 6918 3.624861 CCCATCAATTTGTTCTCGAGGAG 59.375 47.826 13.56 0.00 0.00 3.69
5794 8435 6.255887 CGAGGAGTAACTCAATAAATGACACC 59.744 42.308 0.00 0.00 37.34 4.16
5856 8497 8.336801 ACATTCCTATTTGTAACTTTCCTGTC 57.663 34.615 0.00 0.00 0.00 3.51
5882 8523 9.823647 CTGTATACAGTTCTGAATCCATAAAGT 57.176 33.333 22.48 0.00 39.09 2.66
5943 8584 3.254166 ACTTCAGTTCATGTGTTGATGGC 59.746 43.478 0.00 0.00 33.34 4.40
5961 8602 6.171213 TGATGGCAAATTGTTGATGCAATAA 58.829 32.000 0.00 0.00 41.80 1.40
6120 8762 4.275689 CCAGTTTGTTCTTGATGCACAGTA 59.724 41.667 0.00 0.00 0.00 2.74
6121 8763 5.221028 CCAGTTTGTTCTTGATGCACAGTAA 60.221 40.000 0.00 0.00 0.00 2.24
6124 8766 6.318648 AGTTTGTTCTTGATGCACAGTAAAGA 59.681 34.615 0.00 0.00 0.00 2.52
6127 8769 6.494842 TGTTCTTGATGCACAGTAAAGAAAC 58.505 36.000 10.76 7.65 38.28 2.78
6131 8773 7.715657 TCTTGATGCACAGTAAAGAAACAATT 58.284 30.769 0.00 0.00 0.00 2.32
6135 8777 7.434897 TGATGCACAGTAAAGAAACAATTGAAC 59.565 33.333 13.59 2.96 0.00 3.18
6146 8788 7.704789 AGAAACAATTGAACAATTTCTCTGC 57.295 32.000 13.59 0.35 38.84 4.26
6255 8981 3.568093 CTTTGGTCCAAAGCGGTTG 57.432 52.632 27.36 7.87 43.07 3.77
6256 8982 0.744281 CTTTGGTCCAAAGCGGTTGT 59.256 50.000 27.36 0.00 43.07 3.32
6257 8983 1.950909 CTTTGGTCCAAAGCGGTTGTA 59.049 47.619 27.36 0.00 43.07 2.41
6258 8984 1.600023 TTGGTCCAAAGCGGTTGTAG 58.400 50.000 0.40 0.00 35.23 2.74
6259 8985 0.470766 TGGTCCAAAGCGGTTGTAGT 59.529 50.000 0.00 0.00 35.23 2.73
6260 8986 1.134037 TGGTCCAAAGCGGTTGTAGTT 60.134 47.619 0.00 0.00 35.23 2.24
6264 8990 1.394697 CAAAGCGGTTGTAGTTTGCG 58.605 50.000 0.00 0.00 32.08 4.85
6306 9043 8.833493 CATGCTCTGATAGTAAATTGTTGATGA 58.167 33.333 0.00 0.00 0.00 2.92
6323 9060 8.334263 TGTTGATGAATGCTAAACATCTTGTA 57.666 30.769 0.00 0.00 38.34 2.41
6324 9061 8.236586 TGTTGATGAATGCTAAACATCTTGTAC 58.763 33.333 0.00 0.00 38.34 2.90
6325 9062 8.454106 GTTGATGAATGCTAAACATCTTGTACT 58.546 33.333 0.00 0.00 38.34 2.73
6326 9063 9.665719 TTGATGAATGCTAAACATCTTGTACTA 57.334 29.630 0.00 0.00 38.34 1.82
6327 9064 9.098355 TGATGAATGCTAAACATCTTGTACTAC 57.902 33.333 0.00 0.00 38.34 2.73
6412 9149 9.574516 AAGAAACAATAATATCCATAGTGACCC 57.425 33.333 0.00 0.00 0.00 4.46
6418 9155 9.367160 CAATAATATCCATAGTGACCCCTTTTT 57.633 33.333 0.00 0.00 0.00 1.94
6508 9245 2.025981 ACTCAAGGCTGGCATCATTACA 60.026 45.455 3.38 0.00 0.00 2.41
6509 9246 2.617308 CTCAAGGCTGGCATCATTACAG 59.383 50.000 3.38 0.00 35.40 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 3.570638 CAAGGCATGCGAGGCTCG 61.571 66.667 31.40 31.40 44.47 5.03
432 444 5.537188 CAGAGAAACAAGAACAGTAGAGCT 58.463 41.667 0.00 0.00 0.00 4.09
433 445 4.151512 GCAGAGAAACAAGAACAGTAGAGC 59.848 45.833 0.00 0.00 0.00 4.09
434 446 5.292765 TGCAGAGAAACAAGAACAGTAGAG 58.707 41.667 0.00 0.00 0.00 2.43
435 447 5.276461 TGCAGAGAAACAAGAACAGTAGA 57.724 39.130 0.00 0.00 0.00 2.59
436 448 5.991328 TTGCAGAGAAACAAGAACAGTAG 57.009 39.130 0.00 0.00 0.00 2.57
437 449 6.751514 TTTTGCAGAGAAACAAGAACAGTA 57.248 33.333 0.00 0.00 0.00 2.74
438 450 5.643379 TTTTGCAGAGAAACAAGAACAGT 57.357 34.783 0.00 0.00 0.00 3.55
524 539 1.685820 GAACCAAGGGTGCTAGGCT 59.314 57.895 0.00 0.00 35.34 4.58
615 821 7.148306 TGGAAACAAGAGACTAAATAAATCGGC 60.148 37.037 0.00 0.00 37.44 5.54
666 872 0.389391 AGACAGTGTACGCTTGCAGT 59.611 50.000 6.11 1.12 0.00 4.40
678 884 2.154462 GGAAATCCACACCAGACAGTG 58.846 52.381 0.00 0.00 43.65 3.66
691 897 1.457346 CAGCTCACACTGGGAAATCC 58.543 55.000 0.00 0.00 33.85 3.01
751 964 1.700955 GGCCCCTCGTACTAATCTCA 58.299 55.000 0.00 0.00 0.00 3.27
762 975 2.615227 CTTTCCATCTGGGCCCCTCG 62.615 65.000 22.27 8.04 36.21 4.63
778 991 5.738619 AACAAAAGAACAGGTGGAACTTT 57.261 34.783 0.00 0.00 36.74 2.66
837 1055 0.370273 CGGTTCCGATTCAGAAAGCG 59.630 55.000 5.19 2.63 43.65 4.68
838 1056 1.661112 CTCGGTTCCGATTCAGAAAGC 59.339 52.381 14.34 0.00 37.83 3.51
839 1057 2.668457 CACTCGGTTCCGATTCAGAAAG 59.332 50.000 14.34 3.23 37.83 2.62
840 1058 2.611971 CCACTCGGTTCCGATTCAGAAA 60.612 50.000 14.34 0.00 37.83 2.52
860 1078 5.215252 TCATTCCTATCCGATTCAACTCC 57.785 43.478 0.00 0.00 0.00 3.85
960 1178 2.892334 GCGCGTGCTGTTCTTCCAA 61.892 57.895 15.02 0.00 38.39 3.53
1156 1374 2.513897 GCAGTAAATCGCGGGGCT 60.514 61.111 6.13 0.00 0.00 5.19
1197 1415 1.726322 GCCGCAGCTCGTCGTATAG 60.726 63.158 0.00 0.00 36.19 1.31
1244 1475 1.194495 CGCCTACGAATCAACCGTAC 58.806 55.000 0.00 0.00 43.93 3.67
1256 1487 4.891727 AATCAGCCGCCGCCTACG 62.892 66.667 0.00 0.00 39.67 3.51
1362 1779 1.927174 CGGCGAAACTCCTACAAGATG 59.073 52.381 0.00 0.00 0.00 2.90
1477 1894 2.146073 AAAGGCCGCTCACATTGTGC 62.146 55.000 12.04 0.43 32.98 4.57
1549 1966 3.181514 GCATGCAATCTGGAAAACAATGC 60.182 43.478 14.21 0.00 35.19 3.56
1553 1970 4.705991 TGATAGCATGCAATCTGGAAAACA 59.294 37.500 21.98 1.14 0.00 2.83
1649 2066 3.967332 AAAATGGGCCAATTCTGACAG 57.033 42.857 11.89 0.00 0.00 3.51
1650 2067 6.371595 AATTAAAATGGGCCAATTCTGACA 57.628 33.333 11.89 0.00 0.00 3.58
1745 2164 1.477295 GGACGGAGGGAGTAGTTCTTG 59.523 57.143 0.00 0.00 0.00 3.02
1755 2174 3.644738 GTCTTATATTTGGGACGGAGGGA 59.355 47.826 0.00 0.00 0.00 4.20
1756 2175 3.554337 CGTCTTATATTTGGGACGGAGGG 60.554 52.174 0.00 0.00 44.92 4.30
1757 2176 3.650139 CGTCTTATATTTGGGACGGAGG 58.350 50.000 0.00 0.00 44.92 4.30
1762 2181 9.189723 GATGTAGTAACGTCTTATATTTGGGAC 57.810 37.037 0.00 0.00 38.41 4.46
1763 2182 8.362639 GGATGTAGTAACGTCTTATATTTGGGA 58.637 37.037 0.00 0.00 40.82 4.37
1764 2183 8.145767 TGGATGTAGTAACGTCTTATATTTGGG 58.854 37.037 0.00 0.00 40.82 4.12
1765 2184 9.537192 TTGGATGTAGTAACGTCTTATATTTGG 57.463 33.333 0.00 0.00 40.82 3.28
1773 2192 9.128404 TGAGTATATTGGATGTAGTAACGTCTT 57.872 33.333 0.00 0.00 40.82 3.01
1774 2193 8.687292 TGAGTATATTGGATGTAGTAACGTCT 57.313 34.615 0.00 0.00 40.82 4.18
1775 2194 9.178427 GTTGAGTATATTGGATGTAGTAACGTC 57.822 37.037 0.00 0.00 40.37 4.34
1776 2195 8.689061 TGTTGAGTATATTGGATGTAGTAACGT 58.311 33.333 0.00 0.00 0.00 3.99
1777 2196 9.692749 ATGTTGAGTATATTGGATGTAGTAACG 57.307 33.333 0.00 0.00 0.00 3.18
1814 2233 7.606456 AGTTCGGAAGCTATTCTTGAAAACATA 59.394 33.333 0.00 0.00 34.15 2.29
1826 2245 2.500098 TGGTGCTAGTTCGGAAGCTATT 59.500 45.455 2.23 0.00 39.53 1.73
1827 2246 2.101582 CTGGTGCTAGTTCGGAAGCTAT 59.898 50.000 2.23 0.00 39.53 2.97
1859 2279 8.812972 GTTTTAGAATATTCCTTTCCCCTTTGT 58.187 33.333 11.92 0.00 0.00 2.83
1956 2460 1.761198 TGAGCATCCCATGTCTCTCTG 59.239 52.381 0.00 0.00 35.71 3.35
2303 2807 1.003718 GGGGGTTCTTGTGAGGTCG 60.004 63.158 0.00 0.00 0.00 4.79
2340 2844 2.404215 ACGTTGATCCAGTCGAGTTTG 58.596 47.619 0.00 0.00 0.00 2.93
2351 2855 1.222661 GGTGGGGGTACGTTGATCC 59.777 63.158 0.00 0.00 0.00 3.36
2375 2879 0.678048 ACTTTGCCGATCTTCTGCCC 60.678 55.000 0.00 0.00 0.00 5.36
2377 2881 0.449388 CCACTTTGCCGATCTTCTGC 59.551 55.000 0.00 0.00 0.00 4.26
2381 2885 0.962356 CAGCCCACTTTGCCGATCTT 60.962 55.000 0.00 0.00 0.00 2.40
2390 2894 2.116125 GGTCCTGCAGCCCACTTT 59.884 61.111 8.66 0.00 0.00 2.66
2421 2925 1.423161 GCTTCCCCCATATCTTCTGCT 59.577 52.381 0.00 0.00 0.00 4.24
2424 2928 1.777272 GGTGCTTCCCCCATATCTTCT 59.223 52.381 0.00 0.00 0.00 2.85
2430 2934 0.692756 TCGATGGTGCTTCCCCCATA 60.693 55.000 0.00 0.00 41.51 2.74
2475 2979 5.178809 GTGGCACTATGTACGACTTCTTTTT 59.821 40.000 11.13 0.00 0.00 1.94
2476 2980 4.689345 GTGGCACTATGTACGACTTCTTTT 59.311 41.667 11.13 0.00 0.00 2.27
2477 2981 4.243270 GTGGCACTATGTACGACTTCTTT 58.757 43.478 11.13 0.00 0.00 2.52
2478 2982 3.672511 CGTGGCACTATGTACGACTTCTT 60.673 47.826 16.72 0.00 38.72 2.52
2479 2983 2.159421 CGTGGCACTATGTACGACTTCT 60.159 50.000 16.72 0.00 38.72 2.85
2480 2984 2.182825 CGTGGCACTATGTACGACTTC 58.817 52.381 16.72 0.00 38.72 3.01
2481 2985 1.135199 CCGTGGCACTATGTACGACTT 60.135 52.381 16.72 0.00 38.72 3.01
2482 2986 0.454600 CCGTGGCACTATGTACGACT 59.545 55.000 16.72 0.00 38.72 4.18
2483 2987 0.452987 TCCGTGGCACTATGTACGAC 59.547 55.000 16.72 0.00 38.72 4.34
2484 2988 1.133598 CTTCCGTGGCACTATGTACGA 59.866 52.381 16.72 0.00 38.72 3.43
2485 2989 1.556564 CTTCCGTGGCACTATGTACG 58.443 55.000 16.72 0.00 36.39 3.67
2486 2990 1.935933 CCTTCCGTGGCACTATGTAC 58.064 55.000 16.72 0.00 0.00 2.90
2527 3031 2.370349 TGTTGGATGTCACGTTGGTTT 58.630 42.857 0.00 0.00 0.00 3.27
2564 3068 2.575893 TTTGCTCGTGGCGTCCCTA 61.576 57.895 0.00 0.00 45.43 3.53
2570 3074 1.082756 GTCTTGTTTGCTCGTGGCG 60.083 57.895 0.00 0.00 45.43 5.69
2574 3078 1.772063 GCACCGTCTTGTTTGCTCGT 61.772 55.000 0.00 0.00 32.00 4.18
2643 3147 3.056465 CAGGAAACAGTAGGTCTGACTCC 60.056 52.174 7.85 4.21 46.27 3.85
2664 3168 2.646175 CCCCTCTTCGAGAACCGCA 61.646 63.158 0.00 0.00 38.37 5.69
2665 3169 2.184579 CCCCTCTTCGAGAACCGC 59.815 66.667 0.00 0.00 38.37 5.68
2670 3174 2.088104 ATATGTGCCCCTCTTCGAGA 57.912 50.000 0.00 0.00 0.00 4.04
2690 3194 2.043604 CTGCCGTGGCCTCCATATCA 62.044 60.000 8.69 0.00 41.09 2.15
2691 3195 1.302033 CTGCCGTGGCCTCCATATC 60.302 63.158 8.69 0.00 41.09 1.63
2692 3196 2.831770 CTGCCGTGGCCTCCATAT 59.168 61.111 8.69 0.00 41.09 1.78
2693 3197 4.175337 GCTGCCGTGGCCTCCATA 62.175 66.667 8.69 0.00 41.09 2.74
2758 3269 2.146146 AATCCCTGCTCAGCTTGCCA 62.146 55.000 0.00 0.00 0.00 4.92
2766 3277 4.440145 GGGCAAAATCCCTGCTCA 57.560 55.556 0.00 0.00 43.13 4.26
2789 3300 1.483827 CTACAGGATTGCTCAGGCTCA 59.516 52.381 0.00 0.00 39.59 4.26
2793 3304 1.950828 CAGCTACAGGATTGCTCAGG 58.049 55.000 0.00 0.00 37.28 3.86
2805 3316 1.690893 GATCCTGATCTGGCAGCTACA 59.309 52.381 10.34 8.60 35.04 2.74
2833 3344 2.288458 TCGACCAACGTTTGATTTCCAC 59.712 45.455 6.35 0.00 43.13 4.02
2892 3408 6.207221 ACATGAAAAATGTGCACTGACTGATA 59.793 34.615 19.41 0.00 0.00 2.15
2963 3479 3.582208 ACTGCTGAAGAAAGGTGAGAGAT 59.418 43.478 0.00 0.00 0.00 2.75
2964 3480 2.968574 ACTGCTGAAGAAAGGTGAGAGA 59.031 45.455 0.00 0.00 0.00 3.10
2965 3481 3.399440 ACTGCTGAAGAAAGGTGAGAG 57.601 47.619 0.00 0.00 0.00 3.20
3022 3540 6.148948 TGCTCAAAATTGAAAAGATGTACCG 58.851 36.000 0.00 0.00 36.64 4.02
3278 3804 3.130516 TCAAGAATCGATGTTCTACGGCT 59.869 43.478 0.00 0.00 37.46 5.52
3301 3827 9.840427 ACAGTGTATACTTGTTGATAAAAATGC 57.160 29.630 4.17 0.00 34.07 3.56
3369 3896 4.204012 TGAATCTAAAATAGGTTGGGCCG 58.796 43.478 0.00 0.00 43.70 6.13
3371 3898 6.930731 TGTTTGAATCTAAAATAGGTTGGGC 58.069 36.000 0.00 0.00 0.00 5.36
3372 3899 7.396055 TCCTGTTTGAATCTAAAATAGGTTGGG 59.604 37.037 10.31 0.00 43.01 4.12
3439 3966 9.924650 TCTAAGGTATTTAACAGACAGTTCTTC 57.075 33.333 0.00 0.00 41.64 2.87
3453 3980 7.837689 TCTGACTAGGTGCTTCTAAGGTATTTA 59.162 37.037 0.00 0.00 0.00 1.40
3454 3981 6.668283 TCTGACTAGGTGCTTCTAAGGTATTT 59.332 38.462 0.00 0.00 0.00 1.40
3455 3982 6.097129 GTCTGACTAGGTGCTTCTAAGGTATT 59.903 42.308 0.00 0.00 0.00 1.89
3456 3983 5.595133 GTCTGACTAGGTGCTTCTAAGGTAT 59.405 44.000 0.00 0.00 0.00 2.73
3464 4009 3.728845 TGTTTGTCTGACTAGGTGCTTC 58.271 45.455 9.51 0.00 0.00 3.86
3522 4067 9.976511 ATAGATGCCTTGTTTTTCAATGATATG 57.023 29.630 0.00 0.00 35.35 1.78
3536 4081 9.632638 AATAACAATTAGACATAGATGCCTTGT 57.367 29.630 0.00 0.00 0.00 3.16
3563 4108 8.815565 TTGATAAGGTTCATTGTTATGCCTTA 57.184 30.769 0.00 0.00 39.11 2.69
3608 4153 9.552695 AAAGGGAAATGAGAGGAGAAATAAAAT 57.447 29.630 0.00 0.00 0.00 1.82
3636 4182 6.449635 TTGTTAAATATAGCAGTTGCCCAG 57.550 37.500 0.00 0.00 43.38 4.45
3677 4224 7.528996 TGTTCCAGTGATTTCATCAGATTTT 57.471 32.000 0.00 0.00 40.53 1.82
3692 4240 8.268850 AGCTAACATAAACTATTGTTCCAGTG 57.731 34.615 0.00 0.00 34.96 3.66
3749 4297 6.992715 AGTGGTATTATTAAGTGGATCAGCAC 59.007 38.462 0.00 0.00 33.36 4.40
3871 4419 2.502142 TGCATGCTTCTGAGACCAAT 57.498 45.000 20.33 0.00 0.00 3.16
3897 4445 9.956720 AATATCTTCATTTGAATTCGGTGAATC 57.043 29.630 15.74 0.00 30.29 2.52
3898 4446 9.740239 CAATATCTTCATTTGAATTCGGTGAAT 57.260 29.630 15.74 8.48 33.25 2.57
3959 4507 0.749091 TTGCATCAAGCTGGGATCGG 60.749 55.000 0.00 0.00 45.94 4.18
4022 4570 8.783093 CACCATTGTGTCAATAACTTTAGAAGA 58.217 33.333 0.00 0.00 37.72 2.87
4023 4571 8.955061 CACCATTGTGTCAATAACTTTAGAAG 57.045 34.615 0.00 0.00 37.72 2.85
4049 4600 5.630121 TGTGCTTCTTTTGGATCCTAAAGA 58.370 37.500 33.85 33.85 42.62 2.52
4050 4601 5.964958 TGTGCTTCTTTTGGATCCTAAAG 57.035 39.130 31.25 31.25 39.11 1.85
4182 4739 4.925646 GGCATTTCAGAAAAAGTGATGGAC 59.074 41.667 0.00 0.00 0.00 4.02
4326 4885 1.705337 GGTCACCAACGCCATGATCG 61.705 60.000 0.00 0.00 0.00 3.69
4350 4909 6.458206 GCGGCTTTACAAATATGTCATTCTCA 60.458 38.462 0.00 0.00 41.05 3.27
4399 4958 3.589988 AGTCAGCTAAGAAACATGTCCG 58.410 45.455 0.00 0.00 0.00 4.79
4433 4992 1.956477 TGAAGAACTTGGGCAGCTTTC 59.044 47.619 0.00 0.00 0.00 2.62
4437 4996 0.595095 CTGTGAAGAACTTGGGCAGC 59.405 55.000 0.00 0.00 0.00 5.25
4449 5008 8.857216 GTTCAGCATCATTAATTTTCTGTGAAG 58.143 33.333 0.00 0.00 0.00 3.02
4457 5016 7.415206 GGTCGGTAGTTCAGCATCATTAATTTT 60.415 37.037 0.00 0.00 0.00 1.82
4467 5026 3.031736 ACTATGGTCGGTAGTTCAGCAT 58.968 45.455 0.00 0.00 33.04 3.79
4509 5068 5.950758 TTAGCAGAAAGGATACGCAAAAA 57.049 34.783 0.00 0.00 46.39 1.94
4535 5094 6.884280 AATAGGCTTAGGACATTGTAATGC 57.116 37.500 4.58 0.00 40.04 3.56
4554 5113 6.566197 AGGACACTGCTTCAAAGAAAATAG 57.434 37.500 0.00 0.00 0.00 1.73
4561 5120 2.814336 GGGTTAGGACACTGCTTCAAAG 59.186 50.000 0.00 0.00 0.00 2.77
4581 5140 6.072838 GCAGAACAATCACATACCATCATAGG 60.073 42.308 0.00 0.00 0.00 2.57
4588 5147 4.019792 ACAGCAGAACAATCACATACCA 57.980 40.909 0.00 0.00 0.00 3.25
4624 5183 1.193874 GTGGAAACAGCGAGGTTAACG 59.806 52.381 0.00 0.00 44.46 3.18
4659 5218 3.248024 ACAGTTGTAGGGTCCATTCTCA 58.752 45.455 0.00 0.00 0.00 3.27
4691 5250 5.297278 TCACGGTAAAGTAGCAAAATTGTGT 59.703 36.000 0.00 0.00 0.00 3.72
4700 5259 5.451381 CCATCTGTATCACGGTAAAGTAGCA 60.451 44.000 0.00 0.00 0.00 3.49
5006 5565 5.410924 TGTCAATGAACCTGAGACGATAAG 58.589 41.667 0.00 0.00 32.08 1.73
5095 5655 3.368116 GCATCTCAAAGGAGCAAAGCATT 60.368 43.478 0.00 0.00 41.13 3.56
5146 5707 3.609853 TGGCAAACAGTAATAGAGCAGG 58.390 45.455 0.00 0.00 0.00 4.85
5154 5715 4.082125 CTCTTTCCCTGGCAAACAGTAAT 58.918 43.478 0.00 0.00 46.06 1.89
5207 5768 1.556911 TGAGAGGCAAGAATGGAGGAC 59.443 52.381 0.00 0.00 0.00 3.85
5270 5831 5.886960 AAACATAAGACACTGAATGAGCC 57.113 39.130 0.00 0.00 0.00 4.70
5304 5865 4.635223 TGCAGGTCTAAGCTAATGCATAG 58.365 43.478 0.00 0.00 40.61 2.23
5305 5866 4.687901 TGCAGGTCTAAGCTAATGCATA 57.312 40.909 0.00 0.00 42.74 3.14
5306 5867 3.565764 TGCAGGTCTAAGCTAATGCAT 57.434 42.857 0.00 0.00 42.74 3.96
5348 6452 4.855715 TGAACGAACCATTTTTGGCATA 57.144 36.364 0.00 0.00 0.00 3.14
5354 6458 3.389221 GCACCATGAACGAACCATTTTT 58.611 40.909 0.00 0.00 0.00 1.94
5365 6469 0.675633 ACAAAGCAGGCACCATGAAC 59.324 50.000 0.00 0.00 0.00 3.18
5368 6472 0.813184 CCTACAAAGCAGGCACCATG 59.187 55.000 0.00 0.00 0.00 3.66
5369 6473 0.698238 TCCTACAAAGCAGGCACCAT 59.302 50.000 0.00 0.00 32.82 3.55
5372 6476 2.762535 TAGTCCTACAAAGCAGGCAC 57.237 50.000 0.00 0.00 32.82 5.01
5475 6618 8.598041 AGGAGTTGTAGTGTTCAGAAATTCTAT 58.402 33.333 0.00 0.00 0.00 1.98
5476 6619 7.963532 AGGAGTTGTAGTGTTCAGAAATTCTA 58.036 34.615 0.00 0.00 0.00 2.10
5480 6623 5.239525 GCAAGGAGTTGTAGTGTTCAGAAAT 59.760 40.000 0.00 0.00 35.92 2.17
5499 6642 3.004734 AGACAAATTTTGAGACGGCAAGG 59.995 43.478 15.81 0.00 0.00 3.61
5503 6646 3.730715 CACAAGACAAATTTTGAGACGGC 59.269 43.478 15.81 0.00 0.00 5.68
5537 6680 0.655733 CATTCGGCCGGTCATTGTAC 59.344 55.000 27.83 0.00 0.00 2.90
5581 6724 2.877168 CTGATTACAAGATCTGCAGCCC 59.123 50.000 9.47 2.69 0.00 5.19
5617 6760 3.012518 CAGAAACATGGGGTCTAGCTTG 58.987 50.000 0.00 0.00 0.00 4.01
5666 6809 2.586258 AACATCGCGATAGAGCAACT 57.414 45.000 23.22 0.00 36.85 3.16
5672 6815 6.308371 TCTATGTACAAACATCGCGATAGA 57.692 37.500 23.22 13.68 42.92 1.98
5677 6820 7.043656 TGACTTATTCTATGTACAAACATCGCG 60.044 37.037 0.00 0.00 42.92 5.87
5678 6821 8.126871 TGACTTATTCTATGTACAAACATCGC 57.873 34.615 0.00 0.00 42.92 4.58
5752 6895 3.263170 TCCTCGAGAACAAATTGATGGGA 59.737 43.478 15.71 0.00 0.00 4.37
5775 6918 7.681939 TGAAGGGTGTCATTTATTGAGTTAC 57.318 36.000 0.00 0.00 34.17 2.50
5882 8523 9.899661 AACTACAGCCATTTATTATCACTGTAA 57.100 29.630 0.00 0.00 38.33 2.41
5943 8584 7.853524 ACACAACTTATTGCATCAACAATTTG 58.146 30.769 0.00 0.00 40.64 2.32
5961 8602 7.717875 TCTTAAGGTTGCAACTTATACACAACT 59.282 33.333 27.64 10.30 40.29 3.16
6023 8664 7.162082 CAGTTATCTTACTGTTTCCTCCAAGT 58.838 38.462 0.00 0.00 40.48 3.16
6120 8762 8.606602 GCAGAGAAATTGTTCAATTGTTTCTTT 58.393 29.630 17.27 11.70 38.74 2.52
6121 8763 7.765360 TGCAGAGAAATTGTTCAATTGTTTCTT 59.235 29.630 17.27 8.67 38.74 2.52
6124 8766 8.441312 AATGCAGAGAAATTGTTCAATTGTTT 57.559 26.923 10.84 0.00 36.09 2.83
6127 8769 7.884816 AGAATGCAGAGAAATTGTTCAATTG 57.115 32.000 10.84 0.00 36.09 2.32
6131 8773 8.846943 TTACTAGAATGCAGAGAAATTGTTCA 57.153 30.769 0.00 0.00 36.09 3.18
6203 8929 3.498397 CGGAACTGTGCAAACAGAACTAT 59.502 43.478 12.57 0.00 39.99 2.12
6204 8930 2.869801 CGGAACTGTGCAAACAGAACTA 59.130 45.455 12.57 0.00 39.99 2.24
6209 8935 1.261619 GACTCGGAACTGTGCAAACAG 59.738 52.381 4.36 4.36 43.03 3.16
6227 8953 1.886886 TGGACCAAAGCTTTACGGAC 58.113 50.000 19.55 13.99 0.00 4.79
6249 8975 0.305313 TGTTCGCAAACTACAACCGC 59.695 50.000 0.00 0.00 36.30 5.68
6250 8976 2.570169 CATGTTCGCAAACTACAACCG 58.430 47.619 0.00 0.00 36.30 4.44
6251 8977 2.550606 TCCATGTTCGCAAACTACAACC 59.449 45.455 0.00 0.00 36.30 3.77
6252 8978 3.889196 TCCATGTTCGCAAACTACAAC 57.111 42.857 0.00 0.00 36.30 3.32
6253 8979 3.304391 GCTTCCATGTTCGCAAACTACAA 60.304 43.478 0.00 0.00 36.30 2.41
6254 8980 2.225491 GCTTCCATGTTCGCAAACTACA 59.775 45.455 0.00 0.00 36.30 2.74
6255 8981 2.225491 TGCTTCCATGTTCGCAAACTAC 59.775 45.455 0.00 0.00 36.30 2.73
6256 8982 2.483877 CTGCTTCCATGTTCGCAAACTA 59.516 45.455 0.00 0.00 36.30 2.24
6257 8983 1.267806 CTGCTTCCATGTTCGCAAACT 59.732 47.619 0.00 0.00 36.30 2.66
6258 8984 1.001378 ACTGCTTCCATGTTCGCAAAC 60.001 47.619 0.00 0.00 35.85 2.93
6259 8985 1.317613 ACTGCTTCCATGTTCGCAAA 58.682 45.000 0.00 0.00 31.24 3.68
6260 8986 1.266718 GAACTGCTTCCATGTTCGCAA 59.733 47.619 0.00 0.00 32.25 4.85
6306 9043 8.792830 ACATGTAGTACAAGATGTTTAGCATT 57.207 30.769 12.27 0.00 38.06 3.56
6323 9060 5.701290 GTCTCTTAAGGTTGCAACATGTAGT 59.299 40.000 29.55 11.40 0.00 2.73
6324 9061 5.700832 TGTCTCTTAAGGTTGCAACATGTAG 59.299 40.000 29.55 21.76 0.00 2.74
6325 9062 5.616270 TGTCTCTTAAGGTTGCAACATGTA 58.384 37.500 29.55 15.45 0.00 2.29
6326 9063 4.460263 TGTCTCTTAAGGTTGCAACATGT 58.540 39.130 29.55 16.42 0.00 3.21
6327 9064 5.437289 TTGTCTCTTAAGGTTGCAACATG 57.563 39.130 29.55 12.40 0.00 3.21
6361 9098 2.450476 GCCATGGGTCATCTTTTGAGT 58.550 47.619 15.13 0.00 34.17 3.41
6412 9149 6.421801 CACCAAGAAATTGCTCAGTAAAAAGG 59.578 38.462 0.00 0.00 0.00 3.11
6418 9155 4.365514 TCCACCAAGAAATTGCTCAGTA 57.634 40.909 0.00 0.00 0.00 2.74
6508 9245 1.849039 CTTTGGAGATCATGTCCCCCT 59.151 52.381 0.00 0.00 32.49 4.79
6509 9246 1.133668 CCTTTGGAGATCATGTCCCCC 60.134 57.143 0.00 0.00 32.49 5.40


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

AutoCloner maintained by Alex Coulton.