Multiple sequence alignment - TraesCS5A01G422700

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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 TraesCS5A01G422700 chr5A 100.000 8012 0 0 1 8012 608708434 608700423 0.000000e+00 14796.0
1 TraesCS5A01G422700 chr5A 81.786 560 83 13 6328 6881 608806834 608806288 1.230000e-122 451.0
2 TraesCS5A01G422700 chr5A 81.250 544 94 6 6326 6865 608813876 608813337 4.440000e-117 433.0
3 TraesCS5A01G422700 chr5A 94.737 171 9 0 2063 2233 585001810 585001640 4.770000e-67 267.0
4 TraesCS5A01G422700 chr5A 89.100 211 9 4 1005 1207 444593095 444593299 4.800000e-62 250.0
5 TraesCS5A01G422700 chr5A 82.609 230 25 8 3080 3294 608703174 608702945 1.060000e-43 189.0
6 TraesCS5A01G422700 chr5A 82.609 230 25 8 5261 5490 608705355 608705141 1.060000e-43 189.0
7 TraesCS5A01G422700 chr5D 96.743 7461 167 27 1 7420 487988161 487980736 0.000000e+00 12362.0
8 TraesCS5A01G422700 chr5D 85.915 497 40 15 7524 8012 487980626 487980152 3.340000e-138 503.0
9 TraesCS5A01G422700 chr5D 81.713 607 98 9 6326 6924 487994322 487993721 2.010000e-135 494.0
10 TraesCS5A01G422700 chr5D 84.348 230 21 8 3080 3294 487982925 487982696 2.270000e-50 211.0
11 TraesCS5A01G422700 chr5D 93.939 132 6 1 7432 7561 487980757 487980626 1.760000e-46 198.0
12 TraesCS5A01G422700 chr5D 82.609 230 25 7 5261 5490 487985091 487984877 1.060000e-43 189.0
13 TraesCS5A01G422700 chr5D 94.872 39 2 0 6497 6535 488161803 488161765 2.410000e-05 62.1
14 TraesCS5A01G422700 chr5D 96.774 31 1 0 5681 5711 398554957 398554927 1.500000e-02 52.8
15 TraesCS5A01G422700 chr5B 95.893 2508 71 7 4608 7086 600643985 600641481 0.000000e+00 4032.0
16 TraesCS5A01G422700 chr5B 97.306 1485 31 4 1 1484 600650218 600648742 0.000000e+00 2512.0
17 TraesCS5A01G422700 chr5B 96.357 1400 45 4 2713 4112 600647500 600646107 0.000000e+00 2298.0
18 TraesCS5A01G422700 chr5B 97.172 1167 24 6 1561 2718 600648744 600647578 0.000000e+00 1964.0
19 TraesCS5A01G422700 chr5B 95.797 571 22 2 4099 4667 600644552 600643982 0.000000e+00 920.0
20 TraesCS5A01G422700 chr5B 88.591 596 29 16 7432 8012 600641209 600640638 0.000000e+00 688.0
21 TraesCS5A01G422700 chr5B 91.857 307 12 4 7119 7420 600641486 600641188 4.470000e-112 416.0
22 TraesCS5A01G422700 chr5B 83.478 230 23 8 3080 3294 600643333 600643104 4.900000e-47 200.0
23 TraesCS5A01G422700 chr5B 79.832 238 33 8 5261 5498 600647137 600646915 8.320000e-35 159.0
24 TraesCS5A01G422700 chr6D 83.896 888 117 23 3813 4689 194228677 194227805 0.000000e+00 824.0
25 TraesCS5A01G422700 chr6D 82.400 875 129 23 3828 4689 200400292 200399430 0.000000e+00 739.0
26 TraesCS5A01G422700 chr6D 96.429 168 5 1 2062 2228 392278576 392278743 7.920000e-70 276.0
27 TraesCS5A01G422700 chr6D 85.057 87 12 1 5643 5729 65646256 65646171 3.980000e-13 87.9
28 TraesCS5A01G422700 chr6A 83.540 887 124 21 3813 4689 268963635 268962761 0.000000e+00 809.0
29 TraesCS5A01G422700 chr6A 82.883 888 120 28 3818 4689 270605643 270606514 0.000000e+00 769.0
30 TraesCS5A01G422700 chr3D 81.603 886 141 21 3813 4689 190252300 190253172 0.000000e+00 713.0
31 TraesCS5A01G422700 chr3D 84.882 721 92 15 3976 4689 287285149 287285859 0.000000e+00 712.0
32 TraesCS5A01G422700 chr3D 93.500 200 6 2 1005 1203 277606398 277606205 2.830000e-74 291.0
33 TraesCS5A01G422700 chr3D 96.610 59 2 0 946 1004 277606481 277606423 1.840000e-16 99.0
34 TraesCS5A01G422700 chr3D 86.154 65 4 4 3149 3208 532679144 532679080 1.870000e-06 65.8
35 TraesCS5A01G422700 chr7D 82.843 781 118 13 3901 4670 310183771 310184546 0.000000e+00 686.0
36 TraesCS5A01G422700 chr7D 86.380 279 6 11 950 1204 166199289 166199019 7.920000e-70 276.0
37 TraesCS5A01G422700 chr7D 95.238 168 8 0 2063 2230 598525680 598525847 4.770000e-67 267.0
38 TraesCS5A01G422700 chr7D 78.740 381 65 10 1265 1635 316380867 316380493 2.890000e-59 241.0
39 TraesCS5A01G422700 chr7D 92.982 114 5 2 830 942 166200016 166199905 6.430000e-36 163.0
40 TraesCS5A01G422700 chr7D 81.481 135 14 5 5352 5477 231395841 231395709 5.120000e-17 100.0
41 TraesCS5A01G422700 chr7B 80.587 886 152 18 3813 4689 118224153 118223279 0.000000e+00 665.0
42 TraesCS5A01G422700 chr1B 93.103 203 12 1 1003 1205 238981592 238981792 6.080000e-76 296.0
43 TraesCS5A01G422700 chr1B 95.614 114 4 1 829 942 655842404 655842292 1.780000e-41 182.0
44 TraesCS5A01G422700 chr1B 92.035 113 5 1 831 939 238980785 238980897 1.080000e-33 156.0
45 TraesCS5A01G422700 chr1B 94.915 59 2 1 946 1004 238981512 238981569 3.080000e-14 91.6
46 TraesCS5A01G422700 chr1B 91.525 59 5 0 5422 5480 678117297 678117239 1.850000e-11 82.4
47 TraesCS5A01G422700 chr4A 92.965 199 6 3 1006 1203 714558805 714558996 4.730000e-72 283.0
48 TraesCS5A01G422700 chr4A 97.436 39 1 0 946 984 714558724 714558762 5.190000e-07 67.6
49 TraesCS5A01G422700 chr2B 95.429 175 6 2 2063 2236 659694467 659694640 2.200000e-70 278.0
50 TraesCS5A01G422700 chr2B 100.000 31 0 0 1173 1203 97191051 97191021 3.120000e-04 58.4
51 TraesCS5A01G422700 chr3A 91.960 199 9 2 1006 1203 45156314 45156506 1.020000e-68 272.0
52 TraesCS5A01G422700 chr3A 90.256 195 17 2 2036 2228 66171237 66171043 3.710000e-63 254.0
53 TraesCS5A01G422700 chr1D 95.266 169 7 1 2061 2228 365727163 365727331 4.770000e-67 267.0
54 TraesCS5A01G422700 chr1D 94.253 174 4 1 1003 1176 335285984 335286151 2.220000e-65 261.0
55 TraesCS5A01G422700 chr1D 83.962 106 9 4 5393 5490 486927455 486927350 2.380000e-15 95.3
56 TraesCS5A01G422700 chr2A 94.706 170 9 0 2061 2230 755078064 755078233 1.710000e-66 265.0
57 TraesCS5A01G422700 chr2A 92.035 113 6 3 824 936 93850780 93850671 1.080000e-33 156.0
58 TraesCS5A01G422700 chr4D 90.547 201 13 1 1005 1205 432585168 432584974 2.220000e-65 261.0
59 TraesCS5A01G422700 chr4D 92.857 112 5 1 831 942 432585946 432585838 8.320000e-35 159.0
60 TraesCS5A01G422700 chr7A 77.892 389 70 9 1256 1635 348318137 348318518 2.250000e-55 228.0
61 TraesCS5A01G422700 chr7A 97.248 109 3 0 831 939 263351599 263351707 1.370000e-42 185.0
62 TraesCS5A01G422700 chr7A 88.785 107 6 1 1012 1118 263352408 263352508 8.440000e-25 126.0
63 TraesCS5A01G422700 chr3B 91.150 113 9 1 830 942 263984687 263984576 1.390000e-32 152.0
64 TraesCS5A01G422700 chr3B 81.746 126 15 4 5373 5490 790639903 790639778 1.840000e-16 99.0
65 TraesCS5A01G422700 chr2D 83.529 85 13 1 5643 5727 2040140 2040057 2.400000e-10 78.7


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 TraesCS5A01G422700 chr5A 608700423 608708434 8011 True 14796.000000 14796 100.000000 1 8012 1 chr5A.!!$R2 8011
1 TraesCS5A01G422700 chr5A 608806288 608806834 546 True 451.000000 451 81.786000 6328 6881 1 chr5A.!!$R3 553
2 TraesCS5A01G422700 chr5A 608813337 608813876 539 True 433.000000 433 81.250000 6326 6865 1 chr5A.!!$R4 539
3 TraesCS5A01G422700 chr5D 487980152 487988161 8009 True 4354.333333 12362 92.199000 1 8012 3 chr5D.!!$R4 8011
4 TraesCS5A01G422700 chr5D 487993721 487994322 601 True 494.000000 494 81.713000 6326 6924 1 chr5D.!!$R2 598
5 TraesCS5A01G422700 chr5B 600640638 600650218 9580 True 1465.444444 4032 91.809222 1 8012 9 chr5B.!!$R1 8011
6 TraesCS5A01G422700 chr6D 194227805 194228677 872 True 824.000000 824 83.896000 3813 4689 1 chr6D.!!$R2 876
7 TraesCS5A01G422700 chr6D 200399430 200400292 862 True 739.000000 739 82.400000 3828 4689 1 chr6D.!!$R3 861
8 TraesCS5A01G422700 chr6A 268962761 268963635 874 True 809.000000 809 83.540000 3813 4689 1 chr6A.!!$R1 876
9 TraesCS5A01G422700 chr6A 270605643 270606514 871 False 769.000000 769 82.883000 3818 4689 1 chr6A.!!$F1 871
10 TraesCS5A01G422700 chr3D 190252300 190253172 872 False 713.000000 713 81.603000 3813 4689 1 chr3D.!!$F1 876
11 TraesCS5A01G422700 chr3D 287285149 287285859 710 False 712.000000 712 84.882000 3976 4689 1 chr3D.!!$F2 713
12 TraesCS5A01G422700 chr7D 310183771 310184546 775 False 686.000000 686 82.843000 3901 4670 1 chr7D.!!$F1 769
13 TraesCS5A01G422700 chr7D 166199019 166200016 997 True 219.500000 276 89.681000 830 1204 2 chr7D.!!$R3 374
14 TraesCS5A01G422700 chr7B 118223279 118224153 874 True 665.000000 665 80.587000 3813 4689 1 chr7B.!!$R1 876
15 TraesCS5A01G422700 chr4D 432584974 432585946 972 True 210.000000 261 91.702000 831 1205 2 chr4D.!!$R1 374

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
539 541 3.865446 TGAGTGACACATTCCTGCATAG 58.135 45.455 8.59 0.0 0.0 2.23 F
1061 1701 1.132640 GTTCGACATCAACGCCAGC 59.867 57.895 0.00 0.0 0.0 4.85 F
2075 2801 0.320697 GCTGTGTACTCCCTCCGTTT 59.679 55.000 0.00 0.0 0.0 3.60 F
3110 3919 0.036388 GCACGATGGTTCCTTCCTCA 60.036 55.000 0.00 0.0 0.0 3.86 F
3933 4744 0.325296 TCTATCCAGGTTCAGGCCGT 60.325 55.000 0.00 0.0 0.0 5.68 F
5580 8036 0.032130 GTCTCCTGTGTTCACGCTCA 59.968 55.000 0.00 0.0 0.0 4.26 F
6247 8712 0.320421 GCGCTTCTTGTACCAGACCA 60.320 55.000 0.00 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1506 2148 2.004733 CCCGTTTCTTTACTAAGGCCG 58.995 52.381 0.00 0.0 32.02 6.13 R
2818 3627 1.969240 GCCCTCTGATCCCAAGACTCT 60.969 57.143 0.00 0.0 0.00 3.24 R
3305 4114 0.887247 CCGCCACCATTGAATTGACA 59.113 50.000 0.00 0.0 0.00 3.58 R
4747 7203 0.035439 ATTCACCGTCATGTCCCACC 60.035 55.000 0.00 0.0 0.00 4.61 R
5587 8043 0.033601 TGGAACAAGTGCCACCAACT 60.034 50.000 0.00 0.0 31.92 3.16 R
6756 9221 0.396435 ATGTCGGGAACTGCTTCACA 59.604 50.000 0.00 0.0 29.11 3.58 R
7830 10364 0.235926 GAGTCTGCGCACCAAGTTTC 59.764 55.000 5.66 0.0 0.00 2.78 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
335 337 5.885912 GGGGCTTGAGTATGAGAAAATGTTA 59.114 40.000 0.00 0.00 0.00 2.41
539 541 3.865446 TGAGTGACACATTCCTGCATAG 58.135 45.455 8.59 0.00 0.00 2.23
735 738 7.570607 ACTGAATTAGAGGGAAACTAGGATGAT 59.429 37.037 0.00 0.00 0.00 2.45
774 777 7.283580 CCGGTATTAAAATGGTCCTAACATCAA 59.716 37.037 0.00 0.00 0.00 2.57
1057 1697 4.812293 GAAGATAAGTTCGACATCAACGC 58.188 43.478 0.00 0.00 0.00 4.84
1058 1698 3.187700 AGATAAGTTCGACATCAACGCC 58.812 45.455 0.00 0.00 0.00 5.68
1059 1699 2.442212 TAAGTTCGACATCAACGCCA 57.558 45.000 0.00 0.00 0.00 5.69
1060 1700 1.148310 AAGTTCGACATCAACGCCAG 58.852 50.000 0.00 0.00 0.00 4.85
1061 1701 1.132640 GTTCGACATCAACGCCAGC 59.867 57.895 0.00 0.00 0.00 4.85
1495 2137 9.590451 TGTTCTCAAATTACTAATAAGGTACGG 57.410 33.333 0.00 0.00 0.00 4.02
1496 2138 9.807649 GTTCTCAAATTACTAATAAGGTACGGA 57.192 33.333 0.00 0.00 0.00 4.69
1507 2149 8.302438 ACTAATAAGGTACGGATTATTTCCTCG 58.698 37.037 12.01 0.00 42.99 4.63
1508 2150 4.332428 AAGGTACGGATTATTTCCTCGG 57.668 45.455 0.00 0.00 42.99 4.63
1509 2151 2.036862 AGGTACGGATTATTTCCTCGGC 59.963 50.000 0.00 0.00 42.99 5.54
1510 2152 2.410939 GTACGGATTATTTCCTCGGCC 58.589 52.381 0.00 0.00 42.99 6.13
1511 2153 1.129058 ACGGATTATTTCCTCGGCCT 58.871 50.000 0.00 0.00 42.99 5.19
1512 2154 1.489230 ACGGATTATTTCCTCGGCCTT 59.511 47.619 0.00 0.00 42.99 4.35
1513 2155 2.701951 ACGGATTATTTCCTCGGCCTTA 59.298 45.455 0.00 0.00 42.99 2.69
1514 2156 3.244112 ACGGATTATTTCCTCGGCCTTAG 60.244 47.826 0.00 0.00 42.99 2.18
1515 2157 3.244112 CGGATTATTTCCTCGGCCTTAGT 60.244 47.826 0.00 0.00 42.99 2.24
1516 2158 4.021719 CGGATTATTTCCTCGGCCTTAGTA 60.022 45.833 0.00 0.00 42.99 1.82
1517 2159 5.510179 CGGATTATTTCCTCGGCCTTAGTAA 60.510 44.000 0.00 0.00 42.99 2.24
1518 2160 6.293698 GGATTATTTCCTCGGCCTTAGTAAA 58.706 40.000 0.00 0.00 41.78 2.01
1519 2161 6.427242 GGATTATTTCCTCGGCCTTAGTAAAG 59.573 42.308 0.00 0.00 41.78 1.85
1520 2162 6.549433 TTATTTCCTCGGCCTTAGTAAAGA 57.451 37.500 0.00 0.00 34.37 2.52
1521 2163 4.895668 TTTCCTCGGCCTTAGTAAAGAA 57.104 40.909 0.00 0.00 34.37 2.52
1522 2164 4.895668 TTCCTCGGCCTTAGTAAAGAAA 57.104 40.909 0.00 0.00 34.37 2.52
1523 2165 4.198028 TCCTCGGCCTTAGTAAAGAAAC 57.802 45.455 0.00 0.00 34.37 2.78
1524 2166 2.928116 CCTCGGCCTTAGTAAAGAAACG 59.072 50.000 0.00 0.00 34.37 3.60
1525 2167 2.928116 CTCGGCCTTAGTAAAGAAACGG 59.072 50.000 0.00 0.00 34.37 4.44
1526 2168 2.004733 CGGCCTTAGTAAAGAAACGGG 58.995 52.381 0.00 0.00 34.37 5.28
1527 2169 2.354003 CGGCCTTAGTAAAGAAACGGGA 60.354 50.000 0.00 0.00 34.37 5.14
1528 2170 3.680754 CGGCCTTAGTAAAGAAACGGGAT 60.681 47.826 0.00 0.00 34.37 3.85
1529 2171 4.267536 GGCCTTAGTAAAGAAACGGGATT 58.732 43.478 0.00 0.00 34.37 3.01
1530 2172 5.430886 GGCCTTAGTAAAGAAACGGGATTA 58.569 41.667 0.00 0.00 34.37 1.75
1531 2173 5.526479 GGCCTTAGTAAAGAAACGGGATTAG 59.474 44.000 0.00 0.00 34.37 1.73
1532 2174 6.343703 GCCTTAGTAAAGAAACGGGATTAGA 58.656 40.000 0.00 0.00 34.37 2.10
1533 2175 6.990939 GCCTTAGTAAAGAAACGGGATTAGAT 59.009 38.462 0.00 0.00 34.37 1.98
1534 2176 7.498239 GCCTTAGTAAAGAAACGGGATTAGATT 59.502 37.037 0.00 0.00 34.37 2.40
1535 2177 9.392259 CCTTAGTAAAGAAACGGGATTAGATTT 57.608 33.333 0.00 0.00 34.37 2.17
1538 2180 8.959705 AGTAAAGAAACGGGATTAGATTTAGG 57.040 34.615 0.00 0.00 0.00 2.69
1539 2181 7.991460 AGTAAAGAAACGGGATTAGATTTAGGG 59.009 37.037 0.00 0.00 0.00 3.53
1540 2182 6.570654 AAGAAACGGGATTAGATTTAGGGA 57.429 37.500 0.00 0.00 0.00 4.20
1541 2183 6.570654 AGAAACGGGATTAGATTTAGGGAA 57.429 37.500 0.00 0.00 0.00 3.97
1542 2184 6.965607 AGAAACGGGATTAGATTTAGGGAAA 58.034 36.000 0.00 0.00 0.00 3.13
1543 2185 7.407729 AGAAACGGGATTAGATTTAGGGAAAA 58.592 34.615 0.00 0.00 0.00 2.29
1544 2186 7.338703 AGAAACGGGATTAGATTTAGGGAAAAC 59.661 37.037 0.00 0.00 0.00 2.43
1545 2187 6.069705 ACGGGATTAGATTTAGGGAAAACA 57.930 37.500 0.00 0.00 0.00 2.83
1546 2188 6.486941 ACGGGATTAGATTTAGGGAAAACAA 58.513 36.000 0.00 0.00 0.00 2.83
1547 2189 6.376299 ACGGGATTAGATTTAGGGAAAACAAC 59.624 38.462 0.00 0.00 0.00 3.32
1548 2190 6.602009 CGGGATTAGATTTAGGGAAAACAACT 59.398 38.462 0.00 0.00 0.00 3.16
1549 2191 7.415206 CGGGATTAGATTTAGGGAAAACAACTG 60.415 40.741 0.00 0.00 0.00 3.16
1550 2192 7.614192 GGGATTAGATTTAGGGAAAACAACTGA 59.386 37.037 0.00 0.00 0.00 3.41
1551 2193 9.020731 GGATTAGATTTAGGGAAAACAACTGAA 57.979 33.333 0.00 0.00 0.00 3.02
1555 2197 8.306313 AGATTTAGGGAAAACAACTGAAAAGT 57.694 30.769 0.00 0.00 0.00 2.66
1556 2198 8.414003 AGATTTAGGGAAAACAACTGAAAAGTC 58.586 33.333 0.00 0.00 0.00 3.01
1557 2199 7.469537 TTTAGGGAAAACAACTGAAAAGTCA 57.530 32.000 0.00 0.00 0.00 3.41
1558 2200 7.654022 TTAGGGAAAACAACTGAAAAGTCAT 57.346 32.000 0.00 0.00 31.85 3.06
1559 2201 5.906073 AGGGAAAACAACTGAAAAGTCATG 58.094 37.500 0.00 0.00 31.85 3.07
1560 2202 5.656416 AGGGAAAACAACTGAAAAGTCATGA 59.344 36.000 0.00 0.00 31.85 3.07
1561 2203 5.748630 GGGAAAACAACTGAAAAGTCATGAC 59.251 40.000 18.47 18.47 31.85 3.06
1860 2579 8.871686 AAAAATTAGACTGAACATTCACCAAC 57.128 30.769 0.00 0.00 32.90 3.77
2028 2754 1.136891 ACACCAAGAAAGCAGCCAAAC 59.863 47.619 0.00 0.00 0.00 2.93
2075 2801 0.320697 GCTGTGTACTCCCTCCGTTT 59.679 55.000 0.00 0.00 0.00 3.60
2218 2944 5.773176 AGAAAGACAAATATTTGGGAACGGT 59.227 36.000 27.43 8.70 42.34 4.83
2408 3134 3.239449 TCAGTCCAGACACACCTACATT 58.761 45.455 0.00 0.00 0.00 2.71
2707 3433 1.954382 ACATGCAGCATTATGGCTCAG 59.046 47.619 4.69 0.00 43.68 3.35
2845 3654 2.107953 GATCAGAGGGCGTGCCTC 59.892 66.667 11.25 6.54 36.10 4.70
2944 3753 5.536538 GGATAGCTTGGGGGAAAAGAATTAG 59.463 44.000 0.00 0.00 0.00 1.73
3000 3809 2.844348 ACCTCCCCTTATATTATGGCGG 59.156 50.000 0.00 0.00 0.00 6.13
3016 3825 1.743394 GGCGGGTCCAAGTTCTATTTG 59.257 52.381 0.00 0.00 34.01 2.32
3110 3919 0.036388 GCACGATGGTTCCTTCCTCA 60.036 55.000 0.00 0.00 0.00 3.86
3305 4114 1.691976 TCCTGGTGTCATCGTGAGTTT 59.308 47.619 0.00 0.00 0.00 2.66
3371 4180 1.873165 GGCAGCGATTTCGTGGAAA 59.127 52.632 1.55 0.00 42.22 3.13
3485 4294 1.969923 CCACACATTCACAATTGGGGT 59.030 47.619 8.08 0.00 0.00 4.95
3530 4339 1.227556 ACCACAACGCTCGCTTTCT 60.228 52.632 0.00 0.00 0.00 2.52
3533 4342 1.419374 CACAACGCTCGCTTTCTAGT 58.581 50.000 0.00 0.00 0.00 2.57
3590 4399 7.148641 CACTTCAGTAGTTGTAGACATCAAGT 58.851 38.462 0.00 0.00 33.85 3.16
3792 4601 1.887242 GGCATAAGCATGGCGACGA 60.887 57.895 0.00 0.00 46.42 4.20
3933 4744 0.325296 TCTATCCAGGTTCAGGCCGT 60.325 55.000 0.00 0.00 0.00 5.68
3959 4772 2.110578 GGGCGTAAAACCCTACTCCTA 58.889 52.381 0.00 0.00 44.68 2.94
4289 6680 1.893801 CCCTACCTTCTTGACACGTCT 59.106 52.381 0.00 0.00 0.00 4.18
4472 6868 1.376037 GGAGCTTGTCGGTCTTGGG 60.376 63.158 0.00 0.00 40.01 4.12
4476 6872 0.818040 GCTTGTCGGTCTTGGGTTGT 60.818 55.000 0.00 0.00 0.00 3.32
4745 7201 2.438434 GCAGGGGCGTTGTGCTAT 60.438 61.111 0.00 0.00 45.43 2.97
4747 7203 2.114670 CAGGGGCGTTGTGCTATGG 61.115 63.158 0.00 0.00 45.43 2.74
4828 7284 1.477377 GCATGATGGGTGGTGCATCTA 60.477 52.381 0.00 0.00 37.52 1.98
4881 7337 2.338015 GGTGGTCTCGAGTGGCGTA 61.338 63.158 13.13 0.00 41.80 4.42
5010 7466 4.397832 GGGTTTGGGCGGTAGCGA 62.398 66.667 20.16 0.00 46.35 4.93
5045 7501 0.309612 CCTTGGTCGGTTTTGAACGG 59.690 55.000 0.00 0.00 0.00 4.44
5048 7504 3.423179 GTCGGTTTTGAACGGCCA 58.577 55.556 2.24 0.00 0.00 5.36
5149 7605 2.113807 TGACATGATGCTGGCTAGAGT 58.886 47.619 0.00 0.00 0.00 3.24
5300 7756 1.065410 TTCCTCCCTTGCCTTGTCCA 61.065 55.000 0.00 0.00 0.00 4.02
5414 7870 2.646175 GGCTGCACGGGTGACTCTA 61.646 63.158 0.50 0.00 0.00 2.43
5508 7964 3.128589 GTGTTGTCATGACTGGTGTGTTT 59.871 43.478 25.55 0.00 0.00 2.83
5580 8036 0.032130 GTCTCCTGTGTTCACGCTCA 59.968 55.000 0.00 0.00 0.00 4.26
5679 8135 5.925506 TCCTCATCACTTTGTATCGGTTA 57.074 39.130 0.00 0.00 0.00 2.85
5753 8209 6.153680 AGGACTATACTTGAAGTCTTCTGTGG 59.846 42.308 13.67 9.34 41.53 4.17
5761 8217 7.509546 ACTTGAAGTCTTCTGTGGATAAAAGA 58.490 34.615 13.67 0.00 0.00 2.52
5820 8276 3.284617 CATGAATCTTCCATCCACAGCA 58.715 45.455 0.00 0.00 0.00 4.41
5887 8343 4.572389 CACCCAAGTAGCAGATACATCAAC 59.428 45.833 0.00 0.00 36.79 3.18
5893 8349 5.773575 AGTAGCAGATACATCAACGTATGG 58.226 41.667 0.00 0.00 36.79 2.74
5945 8401 1.134877 GTACGCCCTCTGTCCCTAAAC 60.135 57.143 0.00 0.00 0.00 2.01
6211 8676 6.360370 AGTCCGTACATTCCTGCATATATT 57.640 37.500 0.00 0.00 0.00 1.28
6225 8690 7.771826 TCCTGCATATATTCACATACATCATGG 59.228 37.037 0.00 0.00 39.13 3.66
6247 8712 0.320421 GCGCTTCTTGTACCAGACCA 60.320 55.000 0.00 0.00 0.00 4.02
6756 9221 7.383687 TCGATAACTCTACCTTGTGTTTCATT 58.616 34.615 0.00 0.00 0.00 2.57
6798 9266 2.125512 GAGAAGGTCGCCACGCAT 60.126 61.111 0.00 0.00 0.00 4.73
7017 9505 6.017400 AGCTTGTTAGATGGTTGAAACATG 57.983 37.500 0.00 0.00 32.31 3.21
7022 9510 3.947910 AGATGGTTGAAACATGGCTTG 57.052 42.857 0.00 0.00 0.00 4.01
7069 9557 1.419381 TGCCACAACTAGTCAGTCCA 58.581 50.000 0.00 0.00 32.29 4.02
7109 9597 2.572104 CAGAACTAGTTGTTAGCCCCCT 59.428 50.000 14.14 0.00 39.30 4.79
7110 9598 2.572104 AGAACTAGTTGTTAGCCCCCTG 59.428 50.000 14.14 0.00 39.30 4.45
7111 9599 2.337359 ACTAGTTGTTAGCCCCCTGA 57.663 50.000 0.00 0.00 32.25 3.86
7345 9838 6.753107 TTCTTTTAATGGAAATCGAGGGAC 57.247 37.500 0.00 0.00 0.00 4.46
7392 9885 4.886496 AAAACCTGAGTACTGAGGTACC 57.114 45.455 30.99 2.73 46.81 3.34
7393 9886 3.829728 AACCTGAGTACTGAGGTACCT 57.170 47.619 30.99 16.26 46.81 3.08
7394 9887 4.942363 AACCTGAGTACTGAGGTACCTA 57.058 45.455 30.99 0.00 46.81 3.08
7395 9888 5.469210 AACCTGAGTACTGAGGTACCTAT 57.531 43.478 30.99 14.79 46.81 2.57
7397 9890 5.840081 ACCTGAGTACTGAGGTACCTATTT 58.160 41.667 30.00 5.17 46.81 1.40
7399 9892 6.154706 ACCTGAGTACTGAGGTACCTATTTTG 59.845 42.308 30.00 6.01 46.81 2.44
7400 9893 5.974108 TGAGTACTGAGGTACCTATTTTGC 58.026 41.667 16.29 1.17 46.81 3.68
7401 9894 5.105064 TGAGTACTGAGGTACCTATTTTGCC 60.105 44.000 16.29 0.34 46.81 4.52
7402 9895 4.781087 AGTACTGAGGTACCTATTTTGCCA 59.219 41.667 16.29 5.69 46.81 4.92
7403 9896 4.222124 ACTGAGGTACCTATTTTGCCAG 57.778 45.455 16.29 17.58 0.00 4.85
7404 9897 3.844211 ACTGAGGTACCTATTTTGCCAGA 59.156 43.478 24.02 0.00 0.00 3.86
7405 9898 4.475016 ACTGAGGTACCTATTTTGCCAGAT 59.525 41.667 24.02 10.74 0.00 2.90
7406 9899 5.665812 ACTGAGGTACCTATTTTGCCAGATA 59.334 40.000 24.02 0.00 0.00 1.98
7407 9900 6.157994 ACTGAGGTACCTATTTTGCCAGATAA 59.842 38.462 24.02 0.00 0.00 1.75
7408 9901 7.147302 ACTGAGGTACCTATTTTGCCAGATAAT 60.147 37.037 24.02 5.80 0.00 1.28
7409 9902 7.582719 TGAGGTACCTATTTTGCCAGATAATT 58.417 34.615 16.29 0.00 0.00 1.40
7410 9903 8.058847 TGAGGTACCTATTTTGCCAGATAATTT 58.941 33.333 16.29 0.00 0.00 1.82
7411 9904 8.838649 AGGTACCTATTTTGCCAGATAATTTT 57.161 30.769 14.41 0.00 0.00 1.82
7412 9905 9.930158 AGGTACCTATTTTGCCAGATAATTTTA 57.070 29.630 14.41 0.00 0.00 1.52
7443 9936 3.756082 TTGAGGGGTGCCAGATAATTT 57.244 42.857 0.00 0.00 0.00 1.82
7496 9991 7.557724 TGTGTAATGTAATCGGTCCAATAGAA 58.442 34.615 0.00 0.00 0.00 2.10
7554 10086 6.036577 TGGTGCTGTTTTTCTTTTCTTCTT 57.963 33.333 0.00 0.00 0.00 2.52
7583 10115 1.962807 CATTCAGCCCACTGGAAAACA 59.037 47.619 0.00 0.00 44.59 2.83
7595 10127 2.217750 TGGAAAACACACCATCGTCAG 58.782 47.619 0.00 0.00 0.00 3.51
7596 10128 2.218603 GGAAAACACACCATCGTCAGT 58.781 47.619 0.00 0.00 0.00 3.41
7597 10129 2.616842 GGAAAACACACCATCGTCAGTT 59.383 45.455 0.00 0.00 0.00 3.16
7598 10130 3.303791 GGAAAACACACCATCGTCAGTTC 60.304 47.826 0.00 0.00 0.00 3.01
7599 10131 2.613026 AACACACCATCGTCAGTTCA 57.387 45.000 0.00 0.00 0.00 3.18
7600 10132 2.154854 ACACACCATCGTCAGTTCAG 57.845 50.000 0.00 0.00 0.00 3.02
7601 10133 1.270305 ACACACCATCGTCAGTTCAGG 60.270 52.381 0.00 0.00 0.00 3.86
7602 10134 1.048601 ACACCATCGTCAGTTCAGGT 58.951 50.000 0.00 0.00 0.00 4.00
7603 10135 1.432514 CACCATCGTCAGTTCAGGTG 58.567 55.000 0.00 0.00 40.32 4.00
7604 10136 1.048601 ACCATCGTCAGTTCAGGTGT 58.951 50.000 0.00 0.00 0.00 4.16
7605 10137 1.270305 ACCATCGTCAGTTCAGGTGTG 60.270 52.381 0.00 0.00 0.00 3.82
7606 10138 1.432514 CATCGTCAGTTCAGGTGTGG 58.567 55.000 0.00 0.00 0.00 4.17
7607 10139 1.048601 ATCGTCAGTTCAGGTGTGGT 58.951 50.000 0.00 0.00 0.00 4.16
7608 10140 1.694844 TCGTCAGTTCAGGTGTGGTA 58.305 50.000 0.00 0.00 0.00 3.25
7609 10141 1.611977 TCGTCAGTTCAGGTGTGGTAG 59.388 52.381 0.00 0.00 0.00 3.18
7610 10142 1.611977 CGTCAGTTCAGGTGTGGTAGA 59.388 52.381 0.00 0.00 0.00 2.59
7611 10143 2.231478 CGTCAGTTCAGGTGTGGTAGAT 59.769 50.000 0.00 0.00 0.00 1.98
7612 10144 3.673594 CGTCAGTTCAGGTGTGGTAGATC 60.674 52.174 0.00 0.00 0.00 2.75
7613 10145 3.258372 GTCAGTTCAGGTGTGGTAGATCA 59.742 47.826 0.00 0.00 0.00 2.92
7620 10152 3.624861 CAGGTGTGGTAGATCAGATTTGC 59.375 47.826 0.00 0.00 0.00 3.68
7637 10169 5.827797 AGATTTGCTTTTCCAAGTACTCACA 59.172 36.000 0.00 0.00 31.86 3.58
7638 10170 6.491403 AGATTTGCTTTTCCAAGTACTCACAT 59.509 34.615 0.00 0.00 31.86 3.21
7651 10183 8.141268 CCAAGTACTCACATTGTTAATTTGGTT 58.859 33.333 0.00 0.00 0.00 3.67
7661 10193 7.281999 ACATTGTTAATTTGGTTGGTTTCAAGG 59.718 33.333 0.00 0.00 32.92 3.61
7711 10245 3.689649 AGGAATTTCGGACGATTCAAAGG 59.310 43.478 12.61 0.00 34.67 3.11
7751 10285 7.462571 TTCCCTAAAGCTTCCTTTGTTATTC 57.537 36.000 0.00 0.00 41.24 1.75
7754 10288 8.387813 TCCCTAAAGCTTCCTTTGTTATTCTAA 58.612 33.333 0.00 0.00 41.24 2.10
7830 10364 4.866486 GCTTTTGCCATGAGGTAATCAAAG 59.134 41.667 0.00 0.00 39.36 2.77
7833 10368 6.662865 TTTGCCATGAGGTAATCAAAGAAA 57.337 33.333 0.00 0.00 42.53 2.52
7834 10369 5.643379 TGCCATGAGGTAATCAAAGAAAC 57.357 39.130 0.00 0.00 42.53 2.78
7842 10377 4.023193 AGGTAATCAAAGAAACTTGGTGCG 60.023 41.667 0.00 0.00 0.00 5.34
7845 10380 1.065401 TCAAAGAAACTTGGTGCGCAG 59.935 47.619 12.22 0.12 0.00 5.18
7971 10517 2.427410 CAGCGCGGCAACAGAAAC 60.427 61.111 8.83 0.00 0.00 2.78
7980 10526 3.705604 CGGCAACAGAAACACAGAAAAT 58.294 40.909 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
366 368 7.658167 TCTTTTATACGAACAACACTTCCATGA 59.342 33.333 0.00 0.00 0.00 3.07
735 738 6.896021 TTTAATACCGGTTCCAAATTCACA 57.104 33.333 15.04 0.00 0.00 3.58
948 1562 3.201930 ACATAGTGATGGTGGCAATGGTA 59.798 43.478 0.00 0.00 37.39 3.25
1057 1697 7.036423 CGATAGATAGCAATGTTGGTGCTGG 62.036 48.000 9.11 0.00 46.41 4.85
1058 1698 4.084171 CGATAGATAGCAATGTTGGTGCTG 60.084 45.833 9.11 0.00 46.41 4.41
1060 1700 4.058124 TCGATAGATAGCAATGTTGGTGC 58.942 43.478 7.64 0.00 42.67 5.01
1130 1771 3.880490 TGCTTCACAACAACGTAGGAAAT 59.120 39.130 0.00 0.00 0.00 2.17
1238 1880 4.892433 TGGCCTGAAATGGTTTATTTGTG 58.108 39.130 3.32 0.00 39.06 3.33
1494 2136 7.688574 TCTTTACTAAGGCCGAGGAAATAATCC 60.689 40.741 16.03 0.00 39.02 3.01
1495 2137 7.215085 TCTTTACTAAGGCCGAGGAAATAATC 58.785 38.462 16.03 0.00 32.02 1.75
1496 2138 7.133133 TCTTTACTAAGGCCGAGGAAATAAT 57.867 36.000 16.03 0.00 32.02 1.28
1497 2139 6.549433 TCTTTACTAAGGCCGAGGAAATAA 57.451 37.500 16.03 7.30 32.02 1.40
1498 2140 6.549433 TTCTTTACTAAGGCCGAGGAAATA 57.451 37.500 16.03 8.47 32.02 1.40
1499 2141 5.431179 TTCTTTACTAAGGCCGAGGAAAT 57.569 39.130 16.03 0.00 32.02 2.17
1500 2142 4.895668 TTCTTTACTAAGGCCGAGGAAA 57.104 40.909 15.15 15.15 32.02 3.13
1501 2143 4.572909 GTTTCTTTACTAAGGCCGAGGAA 58.427 43.478 11.85 6.94 32.02 3.36
1502 2144 3.367703 CGTTTCTTTACTAAGGCCGAGGA 60.368 47.826 11.85 0.54 32.02 3.71
1503 2145 2.928116 CGTTTCTTTACTAAGGCCGAGG 59.072 50.000 11.85 1.90 32.02 4.63
1504 2146 2.928116 CCGTTTCTTTACTAAGGCCGAG 59.072 50.000 0.00 0.72 32.02 4.63
1505 2147 2.354003 CCCGTTTCTTTACTAAGGCCGA 60.354 50.000 0.00 0.00 32.02 5.54
1506 2148 2.004733 CCCGTTTCTTTACTAAGGCCG 58.995 52.381 0.00 0.00 32.02 6.13
1507 2149 3.339253 TCCCGTTTCTTTACTAAGGCC 57.661 47.619 0.00 0.00 32.02 5.19
1508 2150 6.343703 TCTAATCCCGTTTCTTTACTAAGGC 58.656 40.000 0.00 0.00 32.02 4.35
1509 2151 8.959705 AATCTAATCCCGTTTCTTTACTAAGG 57.040 34.615 0.00 0.00 32.02 2.69
1513 2155 7.991460 CCCTAAATCTAATCCCGTTTCTTTACT 59.009 37.037 0.00 0.00 0.00 2.24
1514 2156 7.989170 TCCCTAAATCTAATCCCGTTTCTTTAC 59.011 37.037 0.00 0.00 0.00 2.01
1515 2157 8.093118 TCCCTAAATCTAATCCCGTTTCTTTA 57.907 34.615 0.00 0.00 0.00 1.85
1516 2158 6.965607 TCCCTAAATCTAATCCCGTTTCTTT 58.034 36.000 0.00 0.00 0.00 2.52
1517 2159 6.570654 TCCCTAAATCTAATCCCGTTTCTT 57.429 37.500 0.00 0.00 0.00 2.52
1518 2160 6.570654 TTCCCTAAATCTAATCCCGTTTCT 57.429 37.500 0.00 0.00 0.00 2.52
1519 2161 7.121611 TGTTTTCCCTAAATCTAATCCCGTTTC 59.878 37.037 0.00 0.00 0.00 2.78
1520 2162 6.949463 TGTTTTCCCTAAATCTAATCCCGTTT 59.051 34.615 0.00 0.00 0.00 3.60
1521 2163 6.486941 TGTTTTCCCTAAATCTAATCCCGTT 58.513 36.000 0.00 0.00 0.00 4.44
1522 2164 6.069705 TGTTTTCCCTAAATCTAATCCCGT 57.930 37.500 0.00 0.00 0.00 5.28
1523 2165 6.602009 AGTTGTTTTCCCTAAATCTAATCCCG 59.398 38.462 0.00 0.00 0.00 5.14
1524 2166 7.614192 TCAGTTGTTTTCCCTAAATCTAATCCC 59.386 37.037 0.00 0.00 0.00 3.85
1525 2167 8.575649 TCAGTTGTTTTCCCTAAATCTAATCC 57.424 34.615 0.00 0.00 0.00 3.01
1529 2171 9.416284 ACTTTTCAGTTGTTTTCCCTAAATCTA 57.584 29.630 0.00 0.00 0.00 1.98
1530 2172 8.306313 ACTTTTCAGTTGTTTTCCCTAAATCT 57.694 30.769 0.00 0.00 0.00 2.40
1531 2173 8.194769 TGACTTTTCAGTTGTTTTCCCTAAATC 58.805 33.333 0.00 0.00 31.22 2.17
1532 2174 8.073467 TGACTTTTCAGTTGTTTTCCCTAAAT 57.927 30.769 0.00 0.00 31.22 1.40
1533 2175 7.469537 TGACTTTTCAGTTGTTTTCCCTAAA 57.530 32.000 0.00 0.00 31.22 1.85
1534 2176 7.340743 TCATGACTTTTCAGTTGTTTTCCCTAA 59.659 33.333 0.00 0.00 34.35 2.69
1535 2177 6.831353 TCATGACTTTTCAGTTGTTTTCCCTA 59.169 34.615 0.00 0.00 34.35 3.53
1536 2178 5.656416 TCATGACTTTTCAGTTGTTTTCCCT 59.344 36.000 0.00 0.00 34.35 4.20
1537 2179 5.748630 GTCATGACTTTTCAGTTGTTTTCCC 59.251 40.000 18.83 0.00 34.35 3.97
1538 2180 6.564328 AGTCATGACTTTTCAGTTGTTTTCC 58.436 36.000 22.89 0.00 38.83 3.13
1553 2195 8.052748 ACAGATACTAGAAGAGAAGTCATGACT 58.947 37.037 22.89 22.89 44.94 3.41
1554 2196 8.128582 CACAGATACTAGAAGAGAAGTCATGAC 58.871 40.741 18.47 18.47 0.00 3.06
1555 2197 8.049721 TCACAGATACTAGAAGAGAAGTCATGA 58.950 37.037 0.00 0.00 0.00 3.07
1556 2198 8.219546 TCACAGATACTAGAAGAGAAGTCATG 57.780 38.462 0.00 0.00 0.00 3.07
1557 2199 8.849168 CATCACAGATACTAGAAGAGAAGTCAT 58.151 37.037 0.00 0.00 0.00 3.06
1558 2200 8.049721 TCATCACAGATACTAGAAGAGAAGTCA 58.950 37.037 0.00 0.00 0.00 3.41
1559 2201 8.445275 TCATCACAGATACTAGAAGAGAAGTC 57.555 38.462 0.00 0.00 0.00 3.01
1560 2202 8.995027 ATCATCACAGATACTAGAAGAGAAGT 57.005 34.615 0.00 0.00 0.00 3.01
1731 2449 5.973899 TTGCAATACTGAACCATGCTTTA 57.026 34.783 0.00 0.00 37.86 1.85
1860 2579 4.286910 CAATTGTTGTTTACCTGGTGTCG 58.713 43.478 10.23 0.00 0.00 4.35
1934 2653 9.905713 ATAAAGCTTGATTGAATTCTAGGTACA 57.094 29.630 0.00 0.00 30.81 2.90
2028 2754 8.385111 GCAACATTTCTCCATATTGACAAATTG 58.615 33.333 0.00 0.00 0.00 2.32
2464 3190 3.643320 ACAGGCAGATAATGAAGGATCGA 59.357 43.478 0.00 0.00 0.00 3.59
2581 3307 7.376072 GCATTTTATCTGCCGTAATTGTTCTAC 59.624 37.037 0.00 0.00 33.44 2.59
2818 3627 1.969240 GCCCTCTGATCCCAAGACTCT 60.969 57.143 0.00 0.00 0.00 3.24
2869 3678 2.039879 GCCTACCCGGTGGATATTCATT 59.960 50.000 1.71 0.00 34.81 2.57
2944 3753 7.698130 CCGGAATTCTCAAGTCATCAATAAAAC 59.302 37.037 5.23 0.00 0.00 2.43
3000 3809 5.561679 AGGAAGACAAATAGAACTTGGACC 58.438 41.667 0.00 0.00 0.00 4.46
3305 4114 0.887247 CCGCCACCATTGAATTGACA 59.113 50.000 0.00 0.00 0.00 3.58
3366 4175 2.176798 TCTTTCAAGCCCCTCTTTTCCA 59.823 45.455 0.00 0.00 31.27 3.53
3371 4180 2.625639 TCTCTCTTTCAAGCCCCTCTT 58.374 47.619 0.00 0.00 34.78 2.85
3530 4339 5.586877 TCCCTAAAAGCTCTAAGGTCACTA 58.413 41.667 7.26 0.00 0.00 2.74
3533 4342 4.783227 ACATCCCTAAAAGCTCTAAGGTCA 59.217 41.667 7.26 0.00 0.00 4.02
3590 4399 5.239306 CACACTTTCAGTTCAAAGCCATAGA 59.761 40.000 0.00 0.00 36.93 1.98
3792 4601 3.453679 GAGGGAGAAGAGCCGCGT 61.454 66.667 4.92 0.00 0.00 6.01
3933 4744 1.531128 GGGTTTTACGCCCCCACAA 60.531 57.895 0.00 0.00 40.26 3.33
3959 4772 5.705400 CCCCAAGTAAATCCACCATAGAAT 58.295 41.667 0.00 0.00 0.00 2.40
4289 6680 9.967451 TTAAACTTTATTGACACCCATCTCATA 57.033 29.630 0.00 0.00 0.00 2.15
4341 6733 2.039613 GGCTTAGGGAAGATCATCAGGG 59.960 54.545 0.00 0.00 34.25 4.45
4745 7201 2.528127 ACCGTCATGTCCCACCCA 60.528 61.111 0.00 0.00 0.00 4.51
4747 7203 0.035439 ATTCACCGTCATGTCCCACC 60.035 55.000 0.00 0.00 0.00 4.61
5010 7466 2.629617 CCAAGGAACAATTCACAAGGCT 59.370 45.455 0.00 0.00 0.00 4.58
5048 7504 3.717294 GGACTCCACGGGCCATGT 61.717 66.667 4.39 0.00 0.00 3.21
5149 7605 3.612251 GGGAACGAGGATCACCGA 58.388 61.111 12.03 0.00 41.83 4.69
5221 7677 4.415150 AGATGGCGGCCCACACAG 62.415 66.667 17.97 0.00 45.77 3.66
5300 7756 0.178924 AAAAGCAGGCACCTTGGGAT 60.179 50.000 0.00 0.00 0.00 3.85
5476 7932 1.733912 CATGACAACACCAGGATCACG 59.266 52.381 0.00 0.00 0.00 4.35
5508 7964 0.320374 CAAGAGGCACCGAAGTACCA 59.680 55.000 0.00 0.00 30.92 3.25
5580 8036 0.255890 AGTGCCACCAACTCAACACT 59.744 50.000 0.00 0.00 33.71 3.55
5587 8043 0.033601 TGGAACAAGTGCCACCAACT 60.034 50.000 0.00 0.00 31.92 3.16
5820 8276 5.805728 AGGACGGTGTTTAGAAATCAGATT 58.194 37.500 0.00 0.00 0.00 2.40
5887 8343 2.603110 CCGTCAGTTTGATCACCATACG 59.397 50.000 0.00 2.42 32.88 3.06
5893 8349 0.321653 AGGGCCGTCAGTTTGATCAC 60.322 55.000 0.00 0.00 0.00 3.06
5945 8401 5.856126 TTAAACTGCCAAGACGTCTTATG 57.144 39.130 29.28 22.88 34.28 1.90
6035 8497 1.868930 GCATCGAGTCTGAGCTCCATG 60.869 57.143 12.15 1.51 37.23 3.66
6116 8581 3.077484 AGGAATGACACAATGGACAGG 57.923 47.619 0.00 0.00 0.00 4.00
6211 8676 1.670295 GCGCAACCATGATGTATGTGA 59.330 47.619 0.30 0.00 34.87 3.58
6225 8690 1.194772 GTCTGGTACAAGAAGCGCAAC 59.805 52.381 11.47 2.34 38.70 4.17
6247 8712 6.818142 TGTTATGTTTCGTGTCATGATCTCAT 59.182 34.615 0.00 4.48 36.96 2.90
6756 9221 0.396435 ATGTCGGGAACTGCTTCACA 59.604 50.000 0.00 0.00 29.11 3.58
6939 9425 1.455773 TCCGCCATCGTCTCTGGAT 60.456 57.895 0.00 0.00 35.70 3.41
7017 9505 3.512516 GAGCACGATGGGCAAGCC 61.513 66.667 1.52 1.52 0.00 4.35
7069 9557 2.020720 TGGTTCGCACAAGACAAACAT 58.979 42.857 0.00 0.00 0.00 2.71
7109 9597 5.350091 TCAAATAAAATCGCACGACTCATCA 59.650 36.000 0.00 0.00 0.00 3.07
7110 9598 5.795766 TCAAATAAAATCGCACGACTCATC 58.204 37.500 0.00 0.00 0.00 2.92
7111 9599 5.794687 TCAAATAAAATCGCACGACTCAT 57.205 34.783 0.00 0.00 0.00 2.90
7420 9913 3.534357 TTATCTGGCACCCCTCAAAAA 57.466 42.857 0.00 0.00 0.00 1.94
7421 9914 3.756082 ATTATCTGGCACCCCTCAAAA 57.244 42.857 0.00 0.00 0.00 2.44
7422 9915 3.756082 AATTATCTGGCACCCCTCAAA 57.244 42.857 0.00 0.00 0.00 2.69
7423 9916 3.756082 AAATTATCTGGCACCCCTCAA 57.244 42.857 0.00 0.00 0.00 3.02
7424 9917 3.756082 AAAATTATCTGGCACCCCTCA 57.244 42.857 0.00 0.00 0.00 3.86
7425 9918 5.635120 AGATAAAATTATCTGGCACCCCTC 58.365 41.667 13.49 0.00 45.99 4.30
7426 9919 5.669798 AGATAAAATTATCTGGCACCCCT 57.330 39.130 13.49 0.00 45.99 4.79
7443 9936 7.017498 TCACAAAGCAAACGTAAACAGATAA 57.983 32.000 0.00 0.00 0.00 1.75
7496 9991 2.034066 CCTGGCAATGTGTCCGGT 59.966 61.111 0.00 0.00 0.00 5.28
7583 10115 1.048601 ACCTGAACTGACGATGGTGT 58.951 50.000 0.00 0.00 0.00 4.16
7595 10127 4.744795 ATCTGATCTACCACACCTGAAC 57.255 45.455 0.00 0.00 0.00 3.18
7596 10128 5.491070 CAAATCTGATCTACCACACCTGAA 58.509 41.667 0.00 0.00 0.00 3.02
7597 10129 4.623886 GCAAATCTGATCTACCACACCTGA 60.624 45.833 0.00 0.00 0.00 3.86
7598 10130 3.624861 GCAAATCTGATCTACCACACCTG 59.375 47.826 0.00 0.00 0.00 4.00
7599 10131 3.521126 AGCAAATCTGATCTACCACACCT 59.479 43.478 0.00 0.00 0.00 4.00
7600 10132 3.878778 AGCAAATCTGATCTACCACACC 58.121 45.455 0.00 0.00 0.00 4.16
7601 10133 5.886960 AAAGCAAATCTGATCTACCACAC 57.113 39.130 0.00 0.00 0.00 3.82
7602 10134 5.415701 GGAAAAGCAAATCTGATCTACCACA 59.584 40.000 0.00 0.00 0.00 4.17
7603 10135 5.415701 TGGAAAAGCAAATCTGATCTACCAC 59.584 40.000 0.00 0.00 0.00 4.16
7604 10136 5.569355 TGGAAAAGCAAATCTGATCTACCA 58.431 37.500 0.00 0.00 0.00 3.25
7605 10137 6.151817 ACTTGGAAAAGCAAATCTGATCTACC 59.848 38.462 0.00 0.00 0.00 3.18
7606 10138 7.150783 ACTTGGAAAAGCAAATCTGATCTAC 57.849 36.000 0.00 0.00 0.00 2.59
7607 10139 8.103305 AGTACTTGGAAAAGCAAATCTGATCTA 58.897 33.333 0.00 0.00 0.00 1.98
7608 10140 6.944862 AGTACTTGGAAAAGCAAATCTGATCT 59.055 34.615 0.00 0.00 0.00 2.75
7609 10141 7.094634 TGAGTACTTGGAAAAGCAAATCTGATC 60.095 37.037 0.00 0.00 0.00 2.92
7610 10142 6.716628 TGAGTACTTGGAAAAGCAAATCTGAT 59.283 34.615 0.00 0.00 0.00 2.90
7611 10143 6.017109 GTGAGTACTTGGAAAAGCAAATCTGA 60.017 38.462 0.00 0.00 0.00 3.27
7612 10144 6.145535 GTGAGTACTTGGAAAAGCAAATCTG 58.854 40.000 0.00 0.00 0.00 2.90
7613 10145 5.827797 TGTGAGTACTTGGAAAAGCAAATCT 59.172 36.000 0.00 0.00 0.00 2.40
7620 10152 9.965824 AATTAACAATGTGAGTACTTGGAAAAG 57.034 29.630 0.00 0.00 0.00 2.27
7637 10169 6.262049 GCCTTGAAACCAACCAAATTAACAAT 59.738 34.615 0.00 0.00 0.00 2.71
7638 10170 5.586643 GCCTTGAAACCAACCAAATTAACAA 59.413 36.000 0.00 0.00 0.00 2.83
7651 10183 2.746279 TCAAAGGAGCCTTGAAACCA 57.254 45.000 1.91 0.00 36.26 3.67
7688 10222 4.437390 CCTTTGAATCGTCCGAAATTCCTG 60.437 45.833 0.00 0.00 32.11 3.86
7751 10285 8.893219 TGAGTGGCTTGAGTTTCATATATTAG 57.107 34.615 0.00 0.00 0.00 1.73
7754 10288 8.757982 ATTTGAGTGGCTTGAGTTTCATATAT 57.242 30.769 0.00 0.00 0.00 0.86
7830 10364 0.235926 GAGTCTGCGCACCAAGTTTC 59.764 55.000 5.66 0.00 0.00 2.78
7833 10368 0.250467 AATGAGTCTGCGCACCAAGT 60.250 50.000 5.66 0.00 0.00 3.16
7834 10369 0.877071 AAATGAGTCTGCGCACCAAG 59.123 50.000 5.66 0.00 0.00 3.61
7842 10377 4.631813 ACTGGAATCGTAAAATGAGTCTGC 59.368 41.667 0.00 0.00 29.78 4.26
7845 10380 6.147164 TGAACACTGGAATCGTAAAATGAGTC 59.853 38.462 0.00 0.00 0.00 3.36
7957 10503 1.369209 CTGTGTTTCTGTTGCCGCG 60.369 57.895 0.00 0.00 0.00 6.46
7966 10512 2.884639 CCGGTCCATTTTCTGTGTTTCT 59.115 45.455 0.00 0.00 0.00 2.52
7971 10517 2.423538 GGAATCCGGTCCATTTTCTGTG 59.576 50.000 6.23 0.00 37.65 3.66
7980 10526 0.323629 GAACACTGGAATCCGGTCCA 59.676 55.000 11.50 12.91 41.86 4.02


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

AutoCloner maintained by Alex Coulton.