Multiple sequence alignment - TraesCS7A01G423900

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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 TraesCS7A01G423900 chr7A 100.000 4458 0 0 1 4458 616751237 616746780 0.000000e+00 8233.0
1 TraesCS7A01G423900 chr7A 78.906 384 36 16 3497 3873 616734596 616734251 7.510000e-53 219.0
2 TraesCS7A01G423900 chr7A 84.685 222 28 6 3113 3330 616735289 616735070 2.700000e-52 217.0
3 TraesCS7A01G423900 chr7A 87.324 71 5 1 4007 4073 54191300 54191230 1.330000e-10 78.7
4 TraesCS7A01G423900 chr7B 87.844 2106 141 49 985 3033 579666731 579668778 0.000000e+00 2364.0
5 TraesCS7A01G423900 chr7B 94.450 973 50 3 5 975 475723905 475722935 0.000000e+00 1495.0
6 TraesCS7A01G423900 chr7B 94.433 970 51 2 5 972 665649515 665648547 0.000000e+00 1489.0
7 TraesCS7A01G423900 chr7B 89.759 830 49 18 3051 3870 579668823 579669626 0.000000e+00 1029.0
8 TraesCS7A01G423900 chr7B 95.984 498 17 2 5 502 568162514 568163008 0.000000e+00 806.0
9 TraesCS7A01G423900 chr7B 82.065 775 93 24 3106 3870 579778918 579779656 1.760000e-173 619.0
10 TraesCS7A01G423900 chr7B 93.317 419 26 1 558 974 568163009 568163427 6.340000e-173 617.0
11 TraesCS7A01G423900 chr7B 93.041 388 15 4 4074 4458 579670151 579670529 1.400000e-154 556.0
12 TraesCS7A01G423900 chr7B 87.129 101 11 2 4216 4315 579780242 579780341 3.640000e-21 113.0
13 TraesCS7A01G423900 chr7B 92.188 64 4 1 3879 3941 579669806 579669869 6.140000e-14 89.8
14 TraesCS7A01G423900 chr7B 86.076 79 7 4 204 279 665649395 665649318 1.030000e-11 82.4
15 TraesCS7A01G423900 chrUn 96.189 971 33 3 5 973 134400398 134399430 0.000000e+00 1585.0
16 TraesCS7A01G423900 chrUn 87.500 72 7 2 4009 4080 34213231 34213300 1.030000e-11 82.4
17 TraesCS7A01G423900 chrUn 86.076 79 7 4 204 279 134400279 134400202 1.030000e-11 82.4
18 TraesCS7A01G423900 chrUn 84.932 73 7 2 4009 4077 99106844 99106772 2.220000e-08 71.3
19 TraesCS7A01G423900 chr1B 95.756 966 38 2 5 968 426491766 426492730 0.000000e+00 1554.0
20 TraesCS7A01G423900 chr1B 86.076 79 7 4 204 279 426491886 426491963 1.030000e-11 82.4
21 TraesCS7A01G423900 chr2D 95.567 970 38 4 5 971 181589532 181588565 0.000000e+00 1548.0
22 TraesCS7A01G423900 chr2D 88.571 70 7 1 4008 4076 530385640 530385571 2.860000e-12 84.2
23 TraesCS7A01G423900 chr7D 91.629 884 45 17 1801 2666 536471110 536471982 0.000000e+00 1195.0
24 TraesCS7A01G423900 chr7D 92.159 778 43 8 3105 3873 536472531 536473299 0.000000e+00 1083.0
25 TraesCS7A01G423900 chr7D 87.994 708 50 21 1067 1746 536470018 536470718 0.000000e+00 804.0
26 TraesCS7A01G423900 chr7D 82.138 795 82 28 3106 3870 536491595 536492359 1.050000e-175 627.0
27 TraesCS7A01G423900 chr7D 96.835 316 7 2 2717 3030 536472133 536472447 3.950000e-145 525.0
28 TraesCS7A01G423900 chr7D 89.037 374 25 8 4074 4441 536473818 536474181 2.450000e-122 449.0
29 TraesCS7A01G423900 chr7D 94.828 58 3 0 3879 3936 536473479 536473536 1.710000e-14 91.6
30 TraesCS7A01G423900 chr5B 91.304 69 5 1 4009 4077 572349916 572349983 4.750000e-15 93.5
31 TraesCS7A01G423900 chr5B 86.301 73 5 3 4009 4077 100221044 100220973 1.720000e-09 75.0
32 TraesCS7A01G423900 chr4B 90.141 71 4 3 4009 4077 656826403 656826334 6.140000e-14 89.8
33 TraesCS7A01G423900 chr6B 87.342 79 6 2 3998 4076 49827688 49827762 2.210000e-13 87.9
34 TraesCS7A01G423900 chr6B 86.957 69 5 3 4008 4076 49827842 49827906 1.720000e-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 TraesCS7A01G423900 chr7A 616746780 616751237 4457 True 8233.000000 8233 100.000000 1 4458 1 chr7A.!!$R2 4457
1 TraesCS7A01G423900 chr7A 616734251 616735289 1038 True 218.000000 219 81.795500 3113 3873 2 chr7A.!!$R3 760
2 TraesCS7A01G423900 chr7B 475722935 475723905 970 True 1495.000000 1495 94.450000 5 975 1 chr7B.!!$R1 970
3 TraesCS7A01G423900 chr7B 579666731 579670529 3798 False 1009.700000 2364 90.708000 985 4458 4 chr7B.!!$F2 3473
4 TraesCS7A01G423900 chr7B 665648547 665649515 968 True 785.700000 1489 90.254500 5 972 2 chr7B.!!$R2 967
5 TraesCS7A01G423900 chr7B 568162514 568163427 913 False 711.500000 806 94.650500 5 974 2 chr7B.!!$F1 969
6 TraesCS7A01G423900 chr7B 579778918 579780341 1423 False 366.000000 619 84.597000 3106 4315 2 chr7B.!!$F3 1209
7 TraesCS7A01G423900 chrUn 134399430 134400398 968 True 833.700000 1585 91.132500 5 973 2 chrUn.!!$R2 968
8 TraesCS7A01G423900 chr1B 426491766 426492730 964 False 818.200000 1554 90.916000 5 968 2 chr1B.!!$F1 963
9 TraesCS7A01G423900 chr2D 181588565 181589532 967 True 1548.000000 1548 95.567000 5 971 1 chr2D.!!$R1 966
10 TraesCS7A01G423900 chr7D 536470018 536474181 4163 False 691.266667 1195 92.080333 1067 4441 6 chr7D.!!$F2 3374
11 TraesCS7A01G423900 chr7D 536491595 536492359 764 False 627.000000 627 82.138000 3106 3870 1 chr7D.!!$F1 764

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
417 421 0.244450 TCCTAAACGCGTCAACGGAT 59.756 50.0 14.44 0.0 40.23 4.18 F
2173 2607 0.250124 TAATATGCGGCCCGGTTCAG 60.250 55.0 4.77 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2256 2690 0.036952 CCTGCGGTGACAGATCAGTT 60.037 55.0 0.0 0.0 40.25 3.16 R
3873 4830 0.037160 TTCCAAGCATGAGCAGAGCA 59.963 50.0 0.0 0.0 45.49 4.26 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 4.454504 AGATTCGGCAACTCAATTAACGTT 59.545 37.500 5.88 5.88 0.00 3.99
191 192 4.380843 TCCCAAAATCTCCAAGCAACTA 57.619 40.909 0.00 0.00 0.00 2.24
258 260 4.824479 TCTCAGGCAAATCACATACTCA 57.176 40.909 0.00 0.00 0.00 3.41
383 387 1.516110 CATGATCACCTCTCCCCCTT 58.484 55.000 0.00 0.00 0.00 3.95
408 412 0.307760 GCCCATGAATCCTAAACGCG 59.692 55.000 3.53 3.53 0.00 6.01
415 419 1.060122 GAATCCTAAACGCGTCAACGG 59.940 52.381 14.44 11.38 40.23 4.44
417 421 0.244450 TCCTAAACGCGTCAACGGAT 59.756 50.000 14.44 0.00 40.23 4.18
428 432 1.202099 TCAACGGATTAGGGCCACCA 61.202 55.000 6.18 0.00 40.13 4.17
522 526 2.298661 AAGTCCCCTCGCCGGAAAT 61.299 57.895 5.05 0.00 33.16 2.17
524 528 3.006728 TCCCCTCGCCGGAAATGT 61.007 61.111 5.05 0.00 33.16 2.71
601 605 2.879233 GCGACCTTCACCCACTCCA 61.879 63.158 0.00 0.00 0.00 3.86
846 852 1.511768 GTAAGAAGGACGCCGAGCT 59.488 57.895 0.00 0.00 0.00 4.09
888 894 3.833559 AAAATCCTGGGTCACAATCCT 57.166 42.857 0.00 0.00 0.00 3.24
912 918 2.369629 CGTGTTGCGATCGAACGGT 61.370 57.895 21.57 0.00 44.77 4.83
923 929 2.027625 CGAACGGTTCTCAGGGTGC 61.028 63.158 17.94 0.00 0.00 5.01
968 974 5.640732 CATCCGACCACTTTTTAGGATTTG 58.359 41.667 0.00 0.00 36.45 2.32
975 981 5.248248 ACCACTTTTTAGGATTTGGGAATGG 59.752 40.000 0.00 0.00 0.00 3.16
976 982 5.248248 CCACTTTTTAGGATTTGGGAATGGT 59.752 40.000 0.00 0.00 0.00 3.55
977 983 6.439058 CCACTTTTTAGGATTTGGGAATGGTA 59.561 38.462 0.00 0.00 0.00 3.25
978 984 7.038658 CCACTTTTTAGGATTTGGGAATGGTAA 60.039 37.037 0.00 0.00 0.00 2.85
979 985 8.371699 CACTTTTTAGGATTTGGGAATGGTAAA 58.628 33.333 0.00 0.00 0.00 2.01
980 986 8.939932 ACTTTTTAGGATTTGGGAATGGTAAAA 58.060 29.630 0.00 0.00 0.00 1.52
981 987 9.435688 CTTTTTAGGATTTGGGAATGGTAAAAG 57.564 33.333 0.00 0.00 29.53 2.27
982 988 7.489239 TTTAGGATTTGGGAATGGTAAAAGG 57.511 36.000 0.00 0.00 0.00 3.11
983 989 3.774766 AGGATTTGGGAATGGTAAAAGGC 59.225 43.478 0.00 0.00 0.00 4.35
999 1005 0.613260 AGGCTAGCCACGAATCAACA 59.387 50.000 34.70 0.00 38.92 3.33
1000 1006 1.003118 AGGCTAGCCACGAATCAACAA 59.997 47.619 34.70 0.00 38.92 2.83
1115 1121 1.132199 CGCTCTAACGTGTACCGCAG 61.132 60.000 0.00 2.79 41.42 5.18
1146 1163 2.710902 CGTGTCGCCCATCCAGAGA 61.711 63.158 0.00 0.00 0.00 3.10
1208 1226 3.340727 GTGTCCACGACCTAATCCG 57.659 57.895 0.00 0.00 0.00 4.18
1242 1261 2.636227 CGATTCGATTCGCCGACGG 61.636 63.158 15.78 10.29 38.39 4.79
1293 1344 3.777925 CAACACGAAGAGGCGCGG 61.778 66.667 8.83 0.00 33.86 6.46
1414 1471 2.750237 CGCCCCCTTTCCCTTTCG 60.750 66.667 0.00 0.00 0.00 3.46
1495 1552 3.449227 GCCCGCCACCCTTTTAGC 61.449 66.667 0.00 0.00 0.00 3.09
1506 1563 1.696832 CCTTTTAGCCGCACGAGCTC 61.697 60.000 2.73 2.73 41.83 4.09
1509 1566 2.167398 TTTAGCCGCACGAGCTCCTT 62.167 55.000 8.47 0.00 41.83 3.36
1558 1627 2.273557 GTTCCTTATTTACGAGCGCCA 58.726 47.619 2.29 0.00 0.00 5.69
1559 1628 2.218953 TCCTTATTTACGAGCGCCAG 57.781 50.000 2.29 0.00 0.00 4.85
1669 1741 1.355916 CCGTCGTCCTCCTCGATTC 59.644 63.158 0.00 0.00 39.45 2.52
1670 1742 1.096386 CCGTCGTCCTCCTCGATTCT 61.096 60.000 0.00 0.00 39.45 2.40
1698 1770 3.712907 GCGGGGACACCAAGCCTA 61.713 66.667 0.00 0.00 40.22 3.93
1761 1850 2.092861 TCTTTTCTTGGTGAACCGTGGA 60.093 45.455 0.00 0.00 39.43 4.02
1762 1851 2.649531 TTTCTTGGTGAACCGTGGAT 57.350 45.000 0.00 0.00 39.43 3.41
1763 1852 1.890876 TTCTTGGTGAACCGTGGATG 58.109 50.000 0.00 0.00 39.43 3.51
1764 1853 0.762418 TCTTGGTGAACCGTGGATGT 59.238 50.000 0.00 0.00 39.43 3.06
1765 1854 0.874390 CTTGGTGAACCGTGGATGTG 59.126 55.000 0.00 0.00 39.43 3.21
1780 2195 0.534203 ATGTGGTTGACGTGGTGGAC 60.534 55.000 0.00 0.00 0.00 4.02
1826 2244 2.795389 GCGCGCCGTTCAGTTTTC 60.795 61.111 23.24 0.00 0.00 2.29
1865 2292 1.167851 TGCTGGAAATGGCGAAGAAG 58.832 50.000 0.00 0.00 0.00 2.85
1881 2308 6.125327 CGAAGAAGTCTTAGCATGTCTAGA 57.875 41.667 0.00 0.00 36.11 2.43
1884 2311 7.704472 CGAAGAAGTCTTAGCATGTCTAGAAAT 59.296 37.037 0.00 0.00 36.11 2.17
1895 2322 6.865205 AGCATGTCTAGAAATTTTGTTCTTGC 59.135 34.615 0.00 0.00 38.75 4.01
1906 2336 7.894376 AATTTTGTTCTTGCTGATGTTATGG 57.106 32.000 0.00 0.00 0.00 2.74
1933 2363 8.703336 CATGTTATAACATTCTAGTGACGATGG 58.297 37.037 25.20 8.05 46.95 3.51
1934 2364 7.778083 TGTTATAACATTCTAGTGACGATGGT 58.222 34.615 14.35 0.00 33.17 3.55
1937 2367 5.344743 AACATTCTAGTGACGATGGTGAT 57.655 39.130 0.00 0.00 0.00 3.06
1943 2376 7.770801 TTCTAGTGACGATGGTGATTAATTG 57.229 36.000 0.00 0.00 0.00 2.32
1990 2424 4.186926 CTCGGATCATTGTTCTGTGTGAT 58.813 43.478 0.00 0.00 34.23 3.06
1992 2426 4.392754 TCGGATCATTGTTCTGTGTGATTG 59.607 41.667 0.00 0.00 31.86 2.67
1995 2429 4.834357 TCATTGTTCTGTGTGATTGGTG 57.166 40.909 0.00 0.00 0.00 4.17
2154 2588 2.030007 TCGGTGTTTTCGACGGTAAGAT 60.030 45.455 0.00 0.00 0.00 2.40
2155 2589 3.190327 TCGGTGTTTTCGACGGTAAGATA 59.810 43.478 0.00 0.00 0.00 1.98
2158 2592 5.743398 CGGTGTTTTCGACGGTAAGATAATA 59.257 40.000 0.00 0.00 0.00 0.98
2161 2595 7.061634 GTGTTTTCGACGGTAAGATAATATGC 58.938 38.462 0.00 0.00 0.00 3.14
2162 2596 6.074729 TGTTTTCGACGGTAAGATAATATGCG 60.075 38.462 0.00 0.00 0.00 4.73
2163 2597 4.087510 TCGACGGTAAGATAATATGCGG 57.912 45.455 0.00 0.00 0.00 5.69
2164 2598 2.597305 CGACGGTAAGATAATATGCGGC 59.403 50.000 0.00 0.00 0.00 6.53
2165 2599 2.928116 GACGGTAAGATAATATGCGGCC 59.072 50.000 0.00 0.00 0.00 6.13
2166 2600 2.277084 CGGTAAGATAATATGCGGCCC 58.723 52.381 0.00 0.00 0.00 5.80
2167 2601 2.277084 GGTAAGATAATATGCGGCCCG 58.723 52.381 0.00 0.00 0.00 6.13
2168 2602 2.277084 GTAAGATAATATGCGGCCCGG 58.723 52.381 4.77 0.00 0.00 5.73
2169 2603 0.690762 AAGATAATATGCGGCCCGGT 59.309 50.000 4.77 0.00 0.00 5.28
2170 2604 0.690762 AGATAATATGCGGCCCGGTT 59.309 50.000 4.77 0.00 0.00 4.44
2171 2605 1.084289 GATAATATGCGGCCCGGTTC 58.916 55.000 4.77 0.00 0.00 3.62
2172 2606 0.398696 ATAATATGCGGCCCGGTTCA 59.601 50.000 4.77 0.00 0.00 3.18
2173 2607 0.250124 TAATATGCGGCCCGGTTCAG 60.250 55.000 4.77 0.00 0.00 3.02
2174 2608 1.978455 AATATGCGGCCCGGTTCAGA 61.978 55.000 4.77 0.00 0.00 3.27
2176 2610 2.587322 TATGCGGCCCGGTTCAGAAG 62.587 60.000 4.77 0.00 0.00 2.85
2177 2611 4.388499 GCGGCCCGGTTCAGAAGA 62.388 66.667 4.77 0.00 0.00 2.87
2178 2612 2.345991 CGGCCCGGTTCAGAAGAA 59.654 61.111 0.00 0.00 0.00 2.52
2180 2614 1.574702 CGGCCCGGTTCAGAAGAAAC 61.575 60.000 0.00 0.00 38.11 2.78
2181 2615 0.250770 GGCCCGGTTCAGAAGAAACT 60.251 55.000 0.00 0.00 39.36 2.66
2182 2616 1.002773 GGCCCGGTTCAGAAGAAACTA 59.997 52.381 0.00 0.00 39.36 2.24
2183 2617 2.551504 GGCCCGGTTCAGAAGAAACTAA 60.552 50.000 0.00 0.00 39.36 2.24
2186 2620 3.617263 CCCGGTTCAGAAGAAACTAATCG 59.383 47.826 0.00 0.00 39.36 3.34
2187 2621 4.243270 CCGGTTCAGAAGAAACTAATCGT 58.757 43.478 0.00 0.00 39.36 3.73
2188 2622 5.404946 CCGGTTCAGAAGAAACTAATCGTA 58.595 41.667 0.00 0.00 39.36 3.43
2189 2623 6.040878 CCGGTTCAGAAGAAACTAATCGTAT 58.959 40.000 0.00 0.00 39.36 3.06
2190 2624 6.534079 CCGGTTCAGAAGAAACTAATCGTATT 59.466 38.462 0.00 0.00 39.36 1.89
2191 2625 7.391786 CGGTTCAGAAGAAACTAATCGTATTG 58.608 38.462 0.00 0.00 39.36 1.90
2221 2655 7.961326 ATAAGCATTTTGGGTTCAGAGTTAT 57.039 32.000 0.00 0.00 0.00 1.89
2224 2658 5.416952 AGCATTTTGGGTTCAGAGTTATCAG 59.583 40.000 0.00 0.00 0.00 2.90
2256 2690 2.837532 TGCAGCATCGATGGCTAATA 57.162 45.000 26.00 10.41 40.23 0.98
2366 2800 3.056035 AGTTCTTCACCGATACCAAGTCC 60.056 47.826 0.00 0.00 0.00 3.85
2442 2884 7.769970 TGATCAGAACACATTGCAGAACATATA 59.230 33.333 0.00 0.00 0.00 0.86
2665 3107 1.523938 GCGGTGATGGTAAGCTCCC 60.524 63.158 0.00 0.00 0.00 4.30
2687 3189 2.684881 AGCGACATCATTTTGGGATCAC 59.315 45.455 0.00 0.00 0.00 3.06
2688 3190 2.423185 GCGACATCATTTTGGGATCACA 59.577 45.455 0.00 0.00 0.00 3.58
2763 3304 4.651778 TCATGACCCTCGTTCTTTTCAAT 58.348 39.130 0.00 0.00 0.00 2.57
2904 3447 1.745115 TTCGGCGCTGAATCTTGGG 60.745 57.895 27.37 0.00 0.00 4.12
3036 3579 4.537751 TCCAGAGATCAAGGTTCGTATCT 58.462 43.478 0.00 0.00 0.00 1.98
3038 3581 6.307776 TCCAGAGATCAAGGTTCGTATCTAT 58.692 40.000 0.00 0.00 0.00 1.98
3039 3582 6.778069 TCCAGAGATCAAGGTTCGTATCTATT 59.222 38.462 0.00 0.00 0.00 1.73
3040 3583 7.287927 TCCAGAGATCAAGGTTCGTATCTATTT 59.712 37.037 0.00 0.00 0.00 1.40
3042 3585 8.973378 CAGAGATCAAGGTTCGTATCTATTTTC 58.027 37.037 0.00 0.00 0.00 2.29
3043 3586 8.696374 AGAGATCAAGGTTCGTATCTATTTTCA 58.304 33.333 0.00 0.00 0.00 2.69
3044 3587 8.879342 AGATCAAGGTTCGTATCTATTTTCAG 57.121 34.615 0.00 0.00 0.00 3.02
3046 3589 8.879342 ATCAAGGTTCGTATCTATTTTCAGAG 57.121 34.615 0.00 0.00 0.00 3.35
3047 3590 7.837863 TCAAGGTTCGTATCTATTTTCAGAGT 58.162 34.615 0.00 0.00 0.00 3.24
3048 3591 8.311836 TCAAGGTTCGTATCTATTTTCAGAGTT 58.688 33.333 0.00 0.00 0.00 3.01
3049 3592 8.596380 CAAGGTTCGTATCTATTTTCAGAGTTC 58.404 37.037 0.00 0.00 0.00 3.01
3057 3637 6.433847 TCTATTTTCAGAGTTCTCCAACCA 57.566 37.500 0.00 0.00 32.22 3.67
3063 3643 3.070018 CAGAGTTCTCCAACCATGTCAC 58.930 50.000 0.00 0.00 32.22 3.67
3098 3678 5.776716 ACATTGTTCCCTGACATGAGATTTT 59.223 36.000 0.00 0.00 0.00 1.82
3200 3782 3.247442 CAACGAGGTAAACGCATCACTA 58.753 45.455 0.00 0.00 0.00 2.74
3205 3787 3.805207 AGGTAAACGCATCACTAATCCC 58.195 45.455 0.00 0.00 0.00 3.85
3207 3789 4.080526 AGGTAAACGCATCACTAATCCCTT 60.081 41.667 0.00 0.00 0.00 3.95
3211 3793 4.481368 ACGCATCACTAATCCCTTTACA 57.519 40.909 0.00 0.00 0.00 2.41
3212 3794 4.442706 ACGCATCACTAATCCCTTTACAG 58.557 43.478 0.00 0.00 0.00 2.74
3310 3893 1.248101 TGAAGCCGATCGTGGACTCA 61.248 55.000 15.09 6.46 0.00 3.41
3487 4432 2.774951 CGAAGCGCGTAGGTGTTCG 61.775 63.158 8.43 10.59 33.98 3.95
3569 4514 0.888619 TGCTTCACTCCAGTCTACCG 59.111 55.000 0.00 0.00 0.00 4.02
3621 4566 7.650504 TCAGCTGTTCTCATTTCAAATTTCAAG 59.349 33.333 14.67 0.00 0.00 3.02
3626 4571 9.874205 TGTTCTCATTTCAAATTTCAAGTTCTT 57.126 25.926 0.00 0.00 0.00 2.52
3637 4582 7.406799 AATTTCAAGTTCTTTAAATGTGCGG 57.593 32.000 5.76 0.00 0.00 5.69
3726 4671 6.647334 TGAAAATGTGGACAAGATGCTAAA 57.353 33.333 0.00 0.00 0.00 1.85
3730 4675 2.224744 TGTGGACAAGATGCTAAAGCCA 60.225 45.455 0.00 0.00 41.18 4.75
3838 4795 5.365619 GTTTCTGTTAGAAGGTTCACAGGA 58.634 41.667 9.24 0.46 35.37 3.86
3853 4810 0.319900 CAGGACACTTGACCAGACCG 60.320 60.000 0.58 0.00 32.26 4.79
3873 4830 3.430929 CCGCTTGCTCTGTATTCTACCTT 60.431 47.826 0.00 0.00 0.00 3.50
3874 4831 3.553511 CGCTTGCTCTGTATTCTACCTTG 59.446 47.826 0.00 0.00 0.00 3.61
3877 4834 4.392921 TGCTCTGTATTCTACCTTGCTC 57.607 45.455 0.00 0.00 0.00 4.26
3890 5154 0.452184 CTTGCTCTGCTCATGCTTGG 59.548 55.000 0.00 0.00 40.48 3.61
3941 5207 0.465278 GATTCCTCTCTGCCTTGCCC 60.465 60.000 0.00 0.00 0.00 5.36
3943 5209 1.426251 TTCCTCTCTGCCTTGCCCAA 61.426 55.000 0.00 0.00 0.00 4.12
3944 5210 1.075482 CCTCTCTGCCTTGCCCAAA 59.925 57.895 0.00 0.00 0.00 3.28
3945 5211 0.964358 CCTCTCTGCCTTGCCCAAAG 60.964 60.000 0.00 0.00 35.47 2.77
3946 5212 0.251077 CTCTCTGCCTTGCCCAAAGT 60.251 55.000 0.00 0.00 33.66 2.66
3947 5213 0.185901 TCTCTGCCTTGCCCAAAGTT 59.814 50.000 0.00 0.00 33.66 2.66
3948 5214 1.043022 CTCTGCCTTGCCCAAAGTTT 58.957 50.000 0.00 0.00 33.66 2.66
3973 5322 2.270352 AACGGGACTGCTCATTTTCA 57.730 45.000 0.00 0.00 0.00 2.69
3997 5482 4.202461 TGGAACTACTGGAAGACTGCAATT 60.202 41.667 0.00 0.00 37.43 2.32
4012 5497 7.584987 AGACTGCAATTTGTTATGTTGTACTC 58.415 34.615 0.00 0.00 0.00 2.59
4013 5498 6.677913 ACTGCAATTTGTTATGTTGTACTCC 58.322 36.000 0.00 0.00 0.00 3.85
4016 5501 6.072175 TGCAATTTGTTATGTTGTACTCCCTC 60.072 38.462 0.00 0.00 0.00 4.30
4019 5504 5.772393 TTGTTATGTTGTACTCCCTCCAT 57.228 39.130 0.00 0.00 0.00 3.41
4020 5505 5.353394 TGTTATGTTGTACTCCCTCCATC 57.647 43.478 0.00 0.00 0.00 3.51
4021 5506 4.163458 TGTTATGTTGTACTCCCTCCATCC 59.837 45.833 0.00 0.00 0.00 3.51
4022 5507 1.580059 TGTTGTACTCCCTCCATCCC 58.420 55.000 0.00 0.00 0.00 3.85
4023 5508 1.203376 TGTTGTACTCCCTCCATCCCA 60.203 52.381 0.00 0.00 0.00 4.37
4024 5509 1.913419 GTTGTACTCCCTCCATCCCAA 59.087 52.381 0.00 0.00 0.00 4.12
4025 5510 2.307686 GTTGTACTCCCTCCATCCCAAA 59.692 50.000 0.00 0.00 0.00 3.28
4026 5511 2.638325 TGTACTCCCTCCATCCCAAAA 58.362 47.619 0.00 0.00 0.00 2.44
4027 5512 3.197983 TGTACTCCCTCCATCCCAAAAT 58.802 45.455 0.00 0.00 0.00 1.82
4028 5513 4.376223 TGTACTCCCTCCATCCCAAAATA 58.624 43.478 0.00 0.00 0.00 1.40
4029 5514 4.791334 TGTACTCCCTCCATCCCAAAATAA 59.209 41.667 0.00 0.00 0.00 1.40
4030 5515 4.526438 ACTCCCTCCATCCCAAAATAAG 57.474 45.455 0.00 0.00 0.00 1.73
4031 5516 3.858638 ACTCCCTCCATCCCAAAATAAGT 59.141 43.478 0.00 0.00 0.00 2.24
4032 5517 4.210331 CTCCCTCCATCCCAAAATAAGTG 58.790 47.826 0.00 0.00 0.00 3.16
4033 5518 3.596046 TCCCTCCATCCCAAAATAAGTGT 59.404 43.478 0.00 0.00 0.00 3.55
4034 5519 3.954258 CCCTCCATCCCAAAATAAGTGTC 59.046 47.826 0.00 0.00 0.00 3.67
4035 5520 4.325344 CCCTCCATCCCAAAATAAGTGTCT 60.325 45.833 0.00 0.00 0.00 3.41
4036 5521 4.884164 CCTCCATCCCAAAATAAGTGTCTC 59.116 45.833 0.00 0.00 0.00 3.36
4037 5522 4.513442 TCCATCCCAAAATAAGTGTCTCG 58.487 43.478 0.00 0.00 0.00 4.04
4038 5523 4.224147 TCCATCCCAAAATAAGTGTCTCGA 59.776 41.667 0.00 0.00 0.00 4.04
4039 5524 4.941263 CCATCCCAAAATAAGTGTCTCGAA 59.059 41.667 0.00 0.00 0.00 3.71
4040 5525 5.163754 CCATCCCAAAATAAGTGTCTCGAAC 60.164 44.000 0.00 0.00 0.00 3.95
4041 5526 4.963373 TCCCAAAATAAGTGTCTCGAACA 58.037 39.130 0.00 0.00 34.78 3.18
4042 5527 5.369833 TCCCAAAATAAGTGTCTCGAACAA 58.630 37.500 2.65 0.00 40.31 2.83
4043 5528 5.468746 TCCCAAAATAAGTGTCTCGAACAAG 59.531 40.000 2.65 0.00 40.31 3.16
4044 5529 5.468746 CCCAAAATAAGTGTCTCGAACAAGA 59.531 40.000 2.65 0.00 40.31 3.02
4045 5530 6.149474 CCCAAAATAAGTGTCTCGAACAAGAT 59.851 38.462 2.65 0.00 40.31 2.40
4046 5531 7.017645 CCAAAATAAGTGTCTCGAACAAGATG 58.982 38.462 2.65 0.00 40.31 2.90
4047 5532 6.727824 AAATAAGTGTCTCGAACAAGATGG 57.272 37.500 2.65 0.00 40.31 3.51
4048 5533 5.661056 ATAAGTGTCTCGAACAAGATGGA 57.339 39.130 2.65 0.00 40.31 3.41
4049 5534 3.584406 AGTGTCTCGAACAAGATGGAG 57.416 47.619 2.65 0.00 40.31 3.86
4050 5535 3.157881 AGTGTCTCGAACAAGATGGAGA 58.842 45.455 2.65 0.00 40.31 3.71
4066 5551 3.670625 TGGAGACACTTATTTTGGGACG 58.329 45.455 0.00 0.00 33.40 4.79
4067 5552 3.007635 GGAGACACTTATTTTGGGACGG 58.992 50.000 0.00 0.00 0.00 4.79
4068 5553 3.307199 GGAGACACTTATTTTGGGACGGA 60.307 47.826 0.00 0.00 0.00 4.69
4069 5554 4.514401 GAGACACTTATTTTGGGACGGAT 58.486 43.478 0.00 0.00 0.00 4.18
4070 5555 4.261801 AGACACTTATTTTGGGACGGATG 58.738 43.478 0.00 0.00 0.00 3.51
4071 5556 3.352648 ACACTTATTTTGGGACGGATGG 58.647 45.455 0.00 0.00 0.00 3.51
4072 5557 3.009695 ACACTTATTTTGGGACGGATGGA 59.990 43.478 0.00 0.00 0.00 3.41
4073 5558 3.627577 CACTTATTTTGGGACGGATGGAG 59.372 47.826 0.00 0.00 0.00 3.86
4074 5559 3.265995 ACTTATTTTGGGACGGATGGAGT 59.734 43.478 0.00 0.00 0.00 3.85
4075 5560 4.472108 ACTTATTTTGGGACGGATGGAGTA 59.528 41.667 0.00 0.00 0.00 2.59
4076 5561 5.132144 ACTTATTTTGGGACGGATGGAGTAT 59.868 40.000 0.00 0.00 0.00 2.12
4077 5562 4.519906 ATTTTGGGACGGATGGAGTATT 57.480 40.909 0.00 0.00 0.00 1.89
4078 5563 5.640158 ATTTTGGGACGGATGGAGTATTA 57.360 39.130 0.00 0.00 0.00 0.98
4079 5564 5.640158 TTTTGGGACGGATGGAGTATTAT 57.360 39.130 0.00 0.00 0.00 1.28
4080 5565 4.884668 TTGGGACGGATGGAGTATTATC 57.115 45.455 0.00 0.00 0.00 1.75
4081 5566 4.127918 TGGGACGGATGGAGTATTATCT 57.872 45.455 0.00 0.00 0.00 1.98
4082 5567 4.489737 TGGGACGGATGGAGTATTATCTT 58.510 43.478 0.00 0.00 0.00 2.40
4083 5568 4.527038 TGGGACGGATGGAGTATTATCTTC 59.473 45.833 0.00 0.00 0.00 2.87
4084 5569 4.773149 GGGACGGATGGAGTATTATCTTCT 59.227 45.833 0.00 0.00 0.00 2.85
4126 5613 5.535753 AGTCCCATCAAACTTCAAAAAGG 57.464 39.130 0.00 0.00 36.78 3.11
4165 5652 7.665559 TGACAAATATAGAAGGCACTGTCTTTT 59.334 33.333 0.00 0.00 40.86 2.27
4206 5694 3.371898 GCAAATGCACTAAATCCCTTTGC 59.628 43.478 11.49 11.49 39.84 3.68
4218 5706 2.747855 CTTTGCGGCTGGGACCTC 60.748 66.667 0.00 0.00 0.00 3.85
4264 5752 4.750941 AGGTTTGGGGATCTTGAATTTGA 58.249 39.130 0.00 0.00 0.00 2.69
4358 5848 4.709886 CCCTGGGTTAATTTAGTTTGGGAG 59.290 45.833 3.97 0.00 33.14 4.30
4361 5851 5.326900 TGGGTTAATTTAGTTTGGGAGGTC 58.673 41.667 0.00 0.00 0.00 3.85
4376 5866 3.259625 GGGAGGTCTACTATCAGAATGGC 59.740 52.174 0.00 0.00 36.16 4.40
4400 5891 2.687935 TCCCTCTGCTCAAAACAACAAC 59.312 45.455 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.325203 AGAGAGGCTGGGGAGTCTTC 60.325 60.000 0.00 0.00 0.00 2.87
1 2 1.011595 TAGAGAGGCTGGGGAGTCTT 58.988 55.000 0.00 0.00 0.00 3.01
2 3 0.555769 CTAGAGAGGCTGGGGAGTCT 59.444 60.000 0.00 0.00 0.00 3.24
3 4 0.553819 TCTAGAGAGGCTGGGGAGTC 59.446 60.000 0.00 0.00 0.00 3.36
43 44 4.351704 AGTTTGTTAGGGGTTGCCTAACTA 59.648 41.667 9.39 0.00 45.58 2.24
276 278 1.675714 GGATCCGTTGTGTGCATCTCA 60.676 52.381 0.00 0.00 0.00 3.27
383 387 1.891933 TAGGATTCATGGGCACAGGA 58.108 50.000 0.00 0.00 35.29 3.86
408 412 0.746923 GGTGGCCCTAATCCGTTGAC 60.747 60.000 0.00 0.00 0.00 3.18
415 419 1.351350 GGGATAGTGGTGGCCCTAATC 59.649 57.143 0.00 0.00 37.59 1.75
417 421 0.696485 GGGGATAGTGGTGGCCCTAA 60.696 60.000 0.00 0.00 40.51 2.69
428 432 1.417890 CCATTTCTGCTCGGGGATAGT 59.582 52.381 0.00 0.00 0.00 2.12
596 600 1.265236 CTGCAGAAGAGAGGTGGAGT 58.735 55.000 8.42 0.00 0.00 3.85
601 605 0.907230 GGGGACTGCAGAAGAGAGGT 60.907 60.000 23.35 0.00 0.00 3.85
745 751 1.604378 CTTCTCCCCCGCACATCTT 59.396 57.895 0.00 0.00 0.00 2.40
814 820 4.039973 TCCTTCTTACGACAACCATCAACT 59.960 41.667 0.00 0.00 0.00 3.16
871 877 0.257039 GCAGGATTGTGACCCAGGAT 59.743 55.000 0.00 0.00 0.00 3.24
872 878 1.685224 GCAGGATTGTGACCCAGGA 59.315 57.895 0.00 0.00 0.00 3.86
883 889 2.945984 CAACACGCACGCAGGATT 59.054 55.556 0.00 0.00 0.00 3.01
888 894 4.070818 GATCGCAACACGCACGCA 62.071 61.111 0.00 0.00 42.60 5.24
907 913 2.030562 CGCACCCTGAGAACCGTT 59.969 61.111 0.00 0.00 0.00 4.44
912 918 2.343758 GAGCACGCACCCTGAGAA 59.656 61.111 0.00 0.00 0.00 2.87
968 974 2.307768 GGCTAGCCTTTTACCATTCCC 58.692 52.381 27.17 0.00 0.00 3.97
975 981 3.267483 TGATTCGTGGCTAGCCTTTTAC 58.733 45.455 33.07 21.67 36.94 2.01
976 982 3.620427 TGATTCGTGGCTAGCCTTTTA 57.380 42.857 33.07 17.00 36.94 1.52
977 983 2.488153 GTTGATTCGTGGCTAGCCTTTT 59.512 45.455 33.07 14.25 36.94 2.27
978 984 2.084546 GTTGATTCGTGGCTAGCCTTT 58.915 47.619 33.07 13.90 36.94 3.11
979 985 1.003118 TGTTGATTCGTGGCTAGCCTT 59.997 47.619 33.07 13.55 36.94 4.35
980 986 0.613260 TGTTGATTCGTGGCTAGCCT 59.387 50.000 33.07 14.04 36.94 4.58
981 987 1.448985 TTGTTGATTCGTGGCTAGCC 58.551 50.000 27.71 27.71 0.00 3.93
982 988 2.792542 GCATTGTTGATTCGTGGCTAGC 60.793 50.000 6.04 6.04 0.00 3.42
983 989 2.223340 GGCATTGTTGATTCGTGGCTAG 60.223 50.000 0.00 0.00 33.18 3.42
999 1005 3.474806 CGAACTTCTCGCGGCATT 58.525 55.556 6.13 0.00 41.49 3.56
1092 1098 1.870901 GTACACGTTAGAGCGCCCG 60.871 63.158 2.29 1.14 34.88 6.13
1146 1163 2.430921 CGAGAGGAAAGCGTGCGT 60.431 61.111 0.00 0.00 0.00 5.24
1250 1269 1.081641 TTTCGTGACTCGGCTCGAC 60.082 57.895 0.00 0.00 40.32 4.20
1293 1344 2.698763 GGACACCGTCGTCTCTCCC 61.699 68.421 1.99 0.00 36.12 4.30
1495 1552 2.507992 CTCAAGGAGCTCGTGCGG 60.508 66.667 10.16 3.32 45.42 5.69
1506 1563 0.321671 TCGGAGGCAGAAACTCAAGG 59.678 55.000 0.00 0.00 36.70 3.61
1509 1566 2.303022 AGAAATCGGAGGCAGAAACTCA 59.697 45.455 0.00 0.00 36.70 3.41
1558 1627 3.603330 AATGGTCCCAGGAGGCCCT 62.603 63.158 0.00 0.00 45.74 5.19
1559 1628 3.023735 AATGGTCCCAGGAGGCCC 61.024 66.667 0.00 0.00 34.51 5.80
1665 1737 1.961277 CGCGGTGCCCCATAGAATC 60.961 63.158 0.00 0.00 0.00 2.52
1698 1770 4.778143 GAACCCGCCGCCACTGAT 62.778 66.667 0.00 0.00 0.00 2.90
1729 1801 2.159462 CCAAGAAAAGAATCGCAGGAGC 60.159 50.000 0.00 0.00 37.42 4.70
1738 1810 3.317993 CCACGGTTCACCAAGAAAAGAAT 59.682 43.478 0.00 0.00 38.13 2.40
1746 1818 0.874390 CACATCCACGGTTCACCAAG 59.126 55.000 0.00 0.00 35.14 3.61
1761 1850 0.534203 GTCCACCACGTCAACCACAT 60.534 55.000 0.00 0.00 0.00 3.21
1762 1851 1.153329 GTCCACCACGTCAACCACA 60.153 57.895 0.00 0.00 0.00 4.17
1763 1852 2.241880 CGTCCACCACGTCAACCAC 61.242 63.158 0.00 0.00 44.07 4.16
1764 1853 2.107343 CGTCCACCACGTCAACCA 59.893 61.111 0.00 0.00 44.07 3.67
1811 2229 2.491308 GTTGAAAACTGAACGGCGC 58.509 52.632 6.90 0.00 45.32 6.53
1826 2244 4.036852 AGCATGCATGATCATCAGAAGTTG 59.963 41.667 30.64 0.00 0.00 3.16
1865 2292 9.548208 GAACAAAATTTCTAGACATGCTAAGAC 57.452 33.333 0.00 0.00 0.00 3.01
1881 2308 7.095102 GCCATAACATCAGCAAGAACAAAATTT 60.095 33.333 0.00 0.00 0.00 1.82
1884 2311 5.221402 TGCCATAACATCAGCAAGAACAAAA 60.221 36.000 0.00 0.00 30.97 2.44
1924 2354 5.794687 TCACAATTAATCACCATCGTCAC 57.205 39.130 0.00 0.00 0.00 3.67
1990 2424 6.477033 CACGATGGAAAACAAATTAACACCAA 59.523 34.615 0.00 0.00 0.00 3.67
1992 2426 5.404066 CCACGATGGAAAACAAATTAACACC 59.596 40.000 0.00 0.00 40.96 4.16
1995 2429 4.985409 TGCCACGATGGAAAACAAATTAAC 59.015 37.500 8.04 0.00 40.96 2.01
2154 2588 0.250124 CTGAACCGGGCCGCATATTA 60.250 55.000 23.20 2.93 0.00 0.98
2155 2589 1.525995 CTGAACCGGGCCGCATATT 60.526 57.895 23.20 11.62 0.00 1.28
2158 2592 3.976701 CTTCTGAACCGGGCCGCAT 62.977 63.158 23.20 11.46 0.00 4.73
2161 2595 1.302192 TTTCTTCTGAACCGGGCCG 60.302 57.895 21.46 21.46 31.02 6.13
2162 2596 0.250770 AGTTTCTTCTGAACCGGGCC 60.251 55.000 6.32 0.00 31.02 5.80
2163 2597 2.467566 TAGTTTCTTCTGAACCGGGC 57.532 50.000 6.32 0.00 31.02 6.13
2164 2598 3.617263 CGATTAGTTTCTTCTGAACCGGG 59.383 47.826 6.32 0.00 31.02 5.73
2165 2599 4.243270 ACGATTAGTTTCTTCTGAACCGG 58.757 43.478 0.00 0.00 31.02 5.28
2166 2600 7.063074 ACAATACGATTAGTTTCTTCTGAACCG 59.937 37.037 0.00 0.00 31.02 4.44
2167 2601 8.169268 CACAATACGATTAGTTTCTTCTGAACC 58.831 37.037 0.00 0.00 31.02 3.62
2168 2602 7.688578 GCACAATACGATTAGTTTCTTCTGAAC 59.311 37.037 0.00 0.00 31.02 3.18
2169 2603 7.386573 TGCACAATACGATTAGTTTCTTCTGAA 59.613 33.333 0.00 0.00 0.00 3.02
2170 2604 6.871492 TGCACAATACGATTAGTTTCTTCTGA 59.129 34.615 0.00 0.00 0.00 3.27
2171 2605 7.060600 TGCACAATACGATTAGTTTCTTCTG 57.939 36.000 0.00 0.00 0.00 3.02
2172 2606 7.667043 TTGCACAATACGATTAGTTTCTTCT 57.333 32.000 0.00 0.00 0.00 2.85
2173 2607 8.895932 ATTTGCACAATACGATTAGTTTCTTC 57.104 30.769 0.00 0.00 0.00 2.87
2176 2610 8.734030 GCTTATTTGCACAATACGATTAGTTTC 58.266 33.333 0.00 0.00 0.00 2.78
2177 2611 8.240682 TGCTTATTTGCACAATACGATTAGTTT 58.759 29.630 0.00 0.00 38.12 2.66
2178 2612 7.757526 TGCTTATTTGCACAATACGATTAGTT 58.242 30.769 0.00 0.00 38.12 2.24
2180 2614 8.786937 AATGCTTATTTGCACAATACGATTAG 57.213 30.769 0.00 0.00 46.33 1.73
2181 2615 9.579768 AAAATGCTTATTTGCACAATACGATTA 57.420 25.926 0.00 0.00 46.33 1.75
2182 2616 8.382130 CAAAATGCTTATTTGCACAATACGATT 58.618 29.630 0.00 0.00 46.33 3.34
2183 2617 7.010367 CCAAAATGCTTATTTGCACAATACGAT 59.990 33.333 0.00 0.00 46.33 3.73
2186 2620 6.371271 ACCCAAAATGCTTATTTGCACAATAC 59.629 34.615 0.00 0.00 46.33 1.89
2187 2621 6.471146 ACCCAAAATGCTTATTTGCACAATA 58.529 32.000 0.00 0.00 46.33 1.90
2188 2622 5.315348 ACCCAAAATGCTTATTTGCACAAT 58.685 33.333 0.00 0.00 46.33 2.71
2189 2623 4.712476 ACCCAAAATGCTTATTTGCACAA 58.288 34.783 0.00 0.00 46.33 3.33
2190 2624 4.348863 ACCCAAAATGCTTATTTGCACA 57.651 36.364 0.00 0.00 46.33 4.57
2191 2625 4.754114 TGAACCCAAAATGCTTATTTGCAC 59.246 37.500 0.00 0.00 46.33 4.57
2208 2642 4.154918 CAGTTTGCTGATAACTCTGAACCC 59.845 45.833 0.00 0.00 45.28 4.11
2242 2676 6.162079 ACAGATCAGTTATTAGCCATCGATG 58.838 40.000 18.76 18.76 0.00 3.84
2244 2678 5.301805 TGACAGATCAGTTATTAGCCATCGA 59.698 40.000 0.00 0.00 0.00 3.59
2256 2690 0.036952 CCTGCGGTGACAGATCAGTT 60.037 55.000 0.00 0.00 40.25 3.16
2366 2800 7.438459 GGGAAATATATAGCAGTACCAATAGCG 59.562 40.741 0.00 0.00 0.00 4.26
2405 2839 6.041423 TGTGTTCTGATCAAGAGAATGCTA 57.959 37.500 0.00 0.00 35.91 3.49
2442 2884 7.480760 AACATCAGTGCCCAATTAACTAATT 57.519 32.000 0.00 0.00 36.39 1.40
2446 2888 4.832266 TGAAACATCAGTGCCCAATTAACT 59.168 37.500 0.00 0.00 0.00 2.24
2447 2889 5.132897 TGAAACATCAGTGCCCAATTAAC 57.867 39.130 0.00 0.00 0.00 2.01
2665 3107 2.684374 TGATCCCAAAATGATGTCGCTG 59.316 45.455 0.00 0.00 0.00 5.18
2687 3189 1.153086 CGGAGGGAGCTGGGAAATG 60.153 63.158 0.00 0.00 0.00 2.32
2688 3190 3.324713 CGGAGGGAGCTGGGAAAT 58.675 61.111 0.00 0.00 0.00 2.17
2891 3434 1.065102 CAATGAGCCCAAGATTCAGCG 59.935 52.381 0.00 0.00 0.00 5.18
2892 3435 2.097825 ACAATGAGCCCAAGATTCAGC 58.902 47.619 0.00 0.00 0.00 4.26
3033 3576 7.020827 TGGTTGGAGAACTCTGAAAATAGAT 57.979 36.000 1.86 0.00 32.15 1.98
3034 3577 6.433847 TGGTTGGAGAACTCTGAAAATAGA 57.566 37.500 1.86 0.00 32.15 1.98
3036 3579 6.542821 ACATGGTTGGAGAACTCTGAAAATA 58.457 36.000 0.00 0.00 32.15 1.40
3038 3581 4.792068 ACATGGTTGGAGAACTCTGAAAA 58.208 39.130 0.00 0.00 32.15 2.29
3039 3582 4.141505 TGACATGGTTGGAGAACTCTGAAA 60.142 41.667 0.00 0.00 32.15 2.69
3040 3583 3.390967 TGACATGGTTGGAGAACTCTGAA 59.609 43.478 0.00 0.00 32.15 3.02
3042 3585 3.070018 GTGACATGGTTGGAGAACTCTG 58.930 50.000 0.00 0.00 32.15 3.35
3043 3586 2.039084 GGTGACATGGTTGGAGAACTCT 59.961 50.000 0.00 0.00 32.15 3.24
3044 3587 2.224523 TGGTGACATGGTTGGAGAACTC 60.225 50.000 0.00 0.00 33.40 3.01
3046 3589 2.270352 TGGTGACATGGTTGGAGAAC 57.730 50.000 0.00 0.00 33.40 3.01
3047 3590 2.441375 TCTTGGTGACATGGTTGGAGAA 59.559 45.455 0.00 0.00 42.32 2.87
3048 3591 2.054021 TCTTGGTGACATGGTTGGAGA 58.946 47.619 0.00 0.00 42.32 3.71
3049 3592 2.154462 GTCTTGGTGACATGGTTGGAG 58.846 52.381 0.00 0.00 44.73 3.86
3063 3643 3.891366 AGGGAACAATGTTTCTGTCTTGG 59.109 43.478 4.21 0.00 0.00 3.61
3098 3678 1.843851 ACCTCCTCCTGTTGTGTTTCA 59.156 47.619 0.00 0.00 0.00 2.69
3192 3772 3.565902 GCCTGTAAAGGGATTAGTGATGC 59.434 47.826 0.00 0.00 0.00 3.91
3195 3775 4.101114 TCAGCCTGTAAAGGGATTAGTGA 58.899 43.478 0.00 0.00 0.00 3.41
3200 3782 3.330701 TCAGTTCAGCCTGTAAAGGGATT 59.669 43.478 0.00 0.00 34.02 3.01
3205 3787 4.153117 GTGATGTCAGTTCAGCCTGTAAAG 59.847 45.833 0.00 0.00 34.02 1.85
3207 3789 3.070878 TGTGATGTCAGTTCAGCCTGTAA 59.929 43.478 0.00 0.00 34.02 2.41
3211 3793 1.610102 GCTGTGATGTCAGTTCAGCCT 60.610 52.381 11.09 0.00 43.55 4.58
3212 3794 0.801251 GCTGTGATGTCAGTTCAGCC 59.199 55.000 11.09 0.00 43.55 4.85
3310 3893 3.249189 TTCTTGGCCGCCTCCTGT 61.249 61.111 11.61 0.00 0.00 4.00
3425 4355 2.367512 GACAGGGGCTGGGGATCT 60.368 66.667 0.00 0.00 35.51 2.75
3487 4432 1.665599 GCACAACACATTGCCCTGC 60.666 57.895 0.00 0.00 39.66 4.85
3569 4514 5.545588 ACATACATGATCAGTACAGGCATC 58.454 41.667 0.00 0.00 0.00 3.91
3621 4566 2.727916 CGGAGCCGCACATTTAAAGAAC 60.728 50.000 0.00 0.00 0.00 3.01
3626 4571 1.022451 GGTCGGAGCCGCACATTTAA 61.022 55.000 3.59 0.00 39.59 1.52
3710 4655 2.436417 TGGCTTTAGCATCTTGTCCAC 58.564 47.619 3.88 0.00 44.36 4.02
3786 4731 3.331889 AGTTCTTTCATCCCCACTGTGAT 59.668 43.478 9.86 0.00 0.00 3.06
3787 4732 2.711009 AGTTCTTTCATCCCCACTGTGA 59.289 45.455 9.86 0.00 0.00 3.58
3838 4795 0.532862 CAAGCGGTCTGGTCAAGTGT 60.533 55.000 0.00 0.00 0.00 3.55
3853 4810 3.311048 GCAAGGTAGAATACAGAGCAAGC 59.689 47.826 0.00 0.00 45.43 4.01
3873 4830 0.037160 TTCCAAGCATGAGCAGAGCA 59.963 50.000 0.00 0.00 45.49 4.26
3874 4831 1.171308 TTTCCAAGCATGAGCAGAGC 58.829 50.000 0.00 0.00 45.49 4.09
3877 4834 1.203994 CCCTTTTCCAAGCATGAGCAG 59.796 52.381 0.00 0.00 45.49 4.24
3890 5154 4.381932 CCTGAATGGCATTGTACCCTTTTC 60.382 45.833 19.07 0.00 0.00 2.29
3941 5207 4.679654 GCAGTCCCGTTTAATCAAACTTTG 59.320 41.667 0.00 0.00 41.62 2.77
3943 5209 4.142038 AGCAGTCCCGTTTAATCAAACTT 58.858 39.130 0.00 0.00 41.62 2.66
3944 5210 3.751518 AGCAGTCCCGTTTAATCAAACT 58.248 40.909 0.00 0.00 41.62 2.66
3945 5211 3.500680 TGAGCAGTCCCGTTTAATCAAAC 59.499 43.478 0.00 0.00 40.60 2.93
3946 5212 3.745799 TGAGCAGTCCCGTTTAATCAAA 58.254 40.909 0.00 0.00 0.00 2.69
3947 5213 3.410631 TGAGCAGTCCCGTTTAATCAA 57.589 42.857 0.00 0.00 0.00 2.57
3948 5214 3.627395 ATGAGCAGTCCCGTTTAATCA 57.373 42.857 0.00 0.00 0.00 2.57
3973 5322 2.906389 TGCAGTCTTCCAGTAGTTCCAT 59.094 45.455 0.00 0.00 0.00 3.41
3997 5482 5.338871 GGATGGAGGGAGTACAACATAACAA 60.339 44.000 0.00 0.00 0.00 2.83
4012 5497 3.954258 GACACTTATTTTGGGATGGAGGG 59.046 47.826 0.00 0.00 0.00 4.30
4013 5498 4.860022 AGACACTTATTTTGGGATGGAGG 58.140 43.478 0.00 0.00 0.00 4.30
4016 5501 4.513442 TCGAGACACTTATTTTGGGATGG 58.487 43.478 0.00 0.00 0.00 3.51
4019 5504 4.963373 TGTTCGAGACACTTATTTTGGGA 58.037 39.130 0.00 0.00 32.00 4.37
4020 5505 5.468746 TCTTGTTCGAGACACTTATTTTGGG 59.531 40.000 0.76 0.00 38.18 4.12
4021 5506 6.539649 TCTTGTTCGAGACACTTATTTTGG 57.460 37.500 0.76 0.00 38.18 3.28
4022 5507 7.017645 CCATCTTGTTCGAGACACTTATTTTG 58.982 38.462 0.76 0.00 38.18 2.44
4023 5508 6.934645 TCCATCTTGTTCGAGACACTTATTTT 59.065 34.615 0.76 0.00 38.18 1.82
4024 5509 6.464222 TCCATCTTGTTCGAGACACTTATTT 58.536 36.000 0.76 0.00 38.18 1.40
4025 5510 6.037786 TCCATCTTGTTCGAGACACTTATT 57.962 37.500 0.76 0.00 38.18 1.40
4026 5511 5.419155 TCTCCATCTTGTTCGAGACACTTAT 59.581 40.000 0.76 0.00 38.18 1.73
4027 5512 4.765339 TCTCCATCTTGTTCGAGACACTTA 59.235 41.667 0.76 0.00 38.18 2.24
4028 5513 3.574396 TCTCCATCTTGTTCGAGACACTT 59.426 43.478 0.76 0.00 38.18 3.16
4029 5514 3.057174 GTCTCCATCTTGTTCGAGACACT 60.057 47.826 10.39 0.00 46.81 3.55
4030 5515 3.246619 GTCTCCATCTTGTTCGAGACAC 58.753 50.000 10.39 0.00 46.81 3.67
4031 5516 3.577649 GTCTCCATCTTGTTCGAGACA 57.422 47.619 10.39 0.00 46.81 3.41
4033 5518 3.157881 AGTGTCTCCATCTTGTTCGAGA 58.842 45.455 0.00 0.00 0.00 4.04
4034 5519 3.584406 AGTGTCTCCATCTTGTTCGAG 57.416 47.619 0.00 0.00 0.00 4.04
4035 5520 5.661056 ATAAGTGTCTCCATCTTGTTCGA 57.339 39.130 0.00 0.00 0.00 3.71
4036 5521 6.727824 AAATAAGTGTCTCCATCTTGTTCG 57.272 37.500 0.00 0.00 0.00 3.95
4037 5522 7.308435 CCAAAATAAGTGTCTCCATCTTGTTC 58.692 38.462 0.00 0.00 0.00 3.18
4038 5523 6.209391 CCCAAAATAAGTGTCTCCATCTTGTT 59.791 38.462 0.00 0.00 0.00 2.83
4039 5524 5.711976 CCCAAAATAAGTGTCTCCATCTTGT 59.288 40.000 0.00 0.00 0.00 3.16
4040 5525 5.945784 TCCCAAAATAAGTGTCTCCATCTTG 59.054 40.000 0.00 0.00 0.00 3.02
4041 5526 5.946377 GTCCCAAAATAAGTGTCTCCATCTT 59.054 40.000 0.00 0.00 0.00 2.40
4042 5527 5.501156 GTCCCAAAATAAGTGTCTCCATCT 58.499 41.667 0.00 0.00 0.00 2.90
4043 5528 4.332819 CGTCCCAAAATAAGTGTCTCCATC 59.667 45.833 0.00 0.00 0.00 3.51
4044 5529 4.261801 CGTCCCAAAATAAGTGTCTCCAT 58.738 43.478 0.00 0.00 0.00 3.41
4045 5530 3.558321 CCGTCCCAAAATAAGTGTCTCCA 60.558 47.826 0.00 0.00 0.00 3.86
4046 5531 3.007635 CCGTCCCAAAATAAGTGTCTCC 58.992 50.000 0.00 0.00 0.00 3.71
4047 5532 3.934068 TCCGTCCCAAAATAAGTGTCTC 58.066 45.455 0.00 0.00 0.00 3.36
4048 5533 4.261801 CATCCGTCCCAAAATAAGTGTCT 58.738 43.478 0.00 0.00 0.00 3.41
4049 5534 3.377172 CCATCCGTCCCAAAATAAGTGTC 59.623 47.826 0.00 0.00 0.00 3.67
4050 5535 3.009695 TCCATCCGTCCCAAAATAAGTGT 59.990 43.478 0.00 0.00 0.00 3.55
4051 5536 3.616219 TCCATCCGTCCCAAAATAAGTG 58.384 45.455 0.00 0.00 0.00 3.16
4052 5537 3.265995 ACTCCATCCGTCCCAAAATAAGT 59.734 43.478 0.00 0.00 0.00 2.24
4053 5538 3.886123 ACTCCATCCGTCCCAAAATAAG 58.114 45.455 0.00 0.00 0.00 1.73
4054 5539 5.640158 ATACTCCATCCGTCCCAAAATAA 57.360 39.130 0.00 0.00 0.00 1.40
4055 5540 5.640158 AATACTCCATCCGTCCCAAAATA 57.360 39.130 0.00 0.00 0.00 1.40
4056 5541 4.519906 AATACTCCATCCGTCCCAAAAT 57.480 40.909 0.00 0.00 0.00 1.82
4057 5542 5.368523 AGATAATACTCCATCCGTCCCAAAA 59.631 40.000 0.00 0.00 0.00 2.44
4058 5543 4.905456 AGATAATACTCCATCCGTCCCAAA 59.095 41.667 0.00 0.00 0.00 3.28
4059 5544 4.489737 AGATAATACTCCATCCGTCCCAA 58.510 43.478 0.00 0.00 0.00 4.12
4060 5545 4.127918 AGATAATACTCCATCCGTCCCA 57.872 45.455 0.00 0.00 0.00 4.37
4061 5546 4.773149 AGAAGATAATACTCCATCCGTCCC 59.227 45.833 0.00 0.00 0.00 4.46
4062 5547 5.712917 AGAGAAGATAATACTCCATCCGTCC 59.287 44.000 0.00 0.00 0.00 4.79
4063 5548 6.616947 CAGAGAAGATAATACTCCATCCGTC 58.383 44.000 0.00 0.00 0.00 4.79
4064 5549 5.047660 GCAGAGAAGATAATACTCCATCCGT 60.048 44.000 0.00 0.00 0.00 4.69
4065 5550 5.406649 GCAGAGAAGATAATACTCCATCCG 58.593 45.833 0.00 0.00 0.00 4.18
4066 5551 5.337975 GGGCAGAGAAGATAATACTCCATCC 60.338 48.000 0.00 0.00 0.00 3.51
4067 5552 5.247110 TGGGCAGAGAAGATAATACTCCATC 59.753 44.000 0.00 0.00 0.00 3.51
4068 5553 5.012561 GTGGGCAGAGAAGATAATACTCCAT 59.987 44.000 0.00 0.00 0.00 3.41
4069 5554 4.345257 GTGGGCAGAGAAGATAATACTCCA 59.655 45.833 0.00 0.00 0.00 3.86
4070 5555 4.262678 GGTGGGCAGAGAAGATAATACTCC 60.263 50.000 0.00 0.00 0.00 3.85
4071 5556 4.591072 AGGTGGGCAGAGAAGATAATACTC 59.409 45.833 0.00 0.00 0.00 2.59
4072 5557 4.561752 AGGTGGGCAGAGAAGATAATACT 58.438 43.478 0.00 0.00 0.00 2.12
4073 5558 4.965200 AGGTGGGCAGAGAAGATAATAC 57.035 45.455 0.00 0.00 0.00 1.89
4074 5559 5.667626 AGAAAGGTGGGCAGAGAAGATAATA 59.332 40.000 0.00 0.00 0.00 0.98
4075 5560 4.476479 AGAAAGGTGGGCAGAGAAGATAAT 59.524 41.667 0.00 0.00 0.00 1.28
4076 5561 3.846588 AGAAAGGTGGGCAGAGAAGATAA 59.153 43.478 0.00 0.00 0.00 1.75
4077 5562 3.454858 AGAAAGGTGGGCAGAGAAGATA 58.545 45.455 0.00 0.00 0.00 1.98
4078 5563 2.273619 AGAAAGGTGGGCAGAGAAGAT 58.726 47.619 0.00 0.00 0.00 2.40
4079 5564 1.734655 AGAAAGGTGGGCAGAGAAGA 58.265 50.000 0.00 0.00 0.00 2.87
4080 5565 2.575805 AAGAAAGGTGGGCAGAGAAG 57.424 50.000 0.00 0.00 0.00 2.85
4081 5566 4.657814 ATAAAGAAAGGTGGGCAGAGAA 57.342 40.909 0.00 0.00 0.00 2.87
4082 5567 5.250774 ACTTATAAAGAAAGGTGGGCAGAGA 59.749 40.000 0.00 0.00 0.00 3.10
4083 5568 5.501156 ACTTATAAAGAAAGGTGGGCAGAG 58.499 41.667 0.00 0.00 0.00 3.35
4084 5569 5.497474 GACTTATAAAGAAAGGTGGGCAGA 58.503 41.667 0.00 0.00 0.00 4.26
4165 5652 0.329261 CTCATGCCCTTCTCAACCCA 59.671 55.000 0.00 0.00 0.00 4.51
4206 5694 2.162338 TACAAACGAGGTCCCAGCCG 62.162 60.000 0.00 0.00 0.00 5.52
4218 5706 4.154195 CCTTCATCTTTGGGTCTACAAACG 59.846 45.833 0.00 0.00 35.57 3.60
4286 5774 8.224389 TGTGAATGTTCTTCAGAAAATCAGAA 57.776 30.769 0.00 0.00 35.58 3.02
4287 5775 7.806409 TGTGAATGTTCTTCAGAAAATCAGA 57.194 32.000 0.00 0.00 35.58 3.27
4288 5776 8.861033 TTTGTGAATGTTCTTCAGAAAATCAG 57.139 30.769 7.55 0.00 38.28 2.90
4289 5777 9.820725 AATTTGTGAATGTTCTTCAGAAAATCA 57.179 25.926 12.38 0.00 42.34 2.57
4291 5779 9.820725 TGAATTTGTGAATGTTCTTCAGAAAAT 57.179 25.926 12.38 6.23 42.34 1.82
4292 5780 9.820725 ATGAATTTGTGAATGTTCTTCAGAAAA 57.179 25.926 12.38 6.38 42.34 2.29
4293 5781 9.820725 AATGAATTTGTGAATGTTCTTCAGAAA 57.179 25.926 11.20 11.20 42.93 2.52
4358 5848 3.243724 AGGGCCATTCTGATAGTAGACC 58.756 50.000 6.18 0.00 0.00 3.85
4361 5851 2.569404 GGGAGGGCCATTCTGATAGTAG 59.431 54.545 6.18 0.00 35.15 2.57
4376 5866 0.401738 TGTTTTGAGCAGAGGGAGGG 59.598 55.000 0.00 0.00 0.00 4.30
4400 5891 4.697352 CAGTACCTCCATCAAAAGGAACAG 59.303 45.833 0.00 0.00 36.46 3.16


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

AutoCloner maintained by Alex Coulton.