Multiple sequence alignment - TraesCS5A01G541200

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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 TraesCS5A01G541200 chr5A 100.000 2242 0 0 1591 3832 698163299 698161058 0.000000e+00 4141.0
1 TraesCS5A01G541200 chr5A 100.000 1362 0 0 1 1362 698164889 698163528 0.000000e+00 2516.0
2 TraesCS5A01G541200 chr5A 84.042 1059 149 17 1782 2835 698179778 698178735 0.000000e+00 1002.0
3 TraesCS5A01G541200 chr5A 80.773 905 92 49 488 1362 698181116 698180264 1.940000e-177 632.0
4 TraesCS5A01G541200 chr4B 91.110 1991 156 13 1768 3748 657527390 657529369 0.000000e+00 2676.0
5 TraesCS5A01G541200 chr4B 86.945 1126 79 24 51 1135 657525532 657526630 0.000000e+00 1203.0
6 TraesCS5A01G541200 chr4B 84.615 1066 142 16 1782 2835 657516626 657517681 0.000000e+00 1040.0
7 TraesCS5A01G541200 chr4B 82.472 890 101 33 493 1362 657497910 657498764 0.000000e+00 728.0
8 TraesCS5A01G541200 chr4B 82.438 894 98 36 493 1362 657515095 657515953 0.000000e+00 726.0
9 TraesCS5A01G541200 chr4B 90.244 410 21 11 920 1311 657509718 657510126 5.670000e-143 518.0
10 TraesCS5A01G541200 chr4B 93.478 92 6 0 1651 1742 657527168 657527259 1.860000e-28 137.0
11 TraesCS5A01G541200 chr4B 88.000 75 8 1 3759 3832 320048345 320048419 1.900000e-13 87.9
12 TraesCS5A01G541200 chr4D 91.059 2002 141 20 1752 3748 509283486 509281518 0.000000e+00 2671.0
13 TraesCS5A01G541200 chr4D 87.528 1323 114 16 81 1362 509285151 509283839 0.000000e+00 1482.0
14 TraesCS5A01G541200 chr4D 84.868 1064 138 17 1782 2835 509339975 509338925 0.000000e+00 1051.0
15 TraesCS5A01G541200 chr4D 83.554 906 97 26 488 1362 509341476 509340592 0.000000e+00 800.0
16 TraesCS5A01G541200 chr4D 85.714 462 61 4 3018 3478 509338602 509338145 2.070000e-132 483.0
17 TraesCS5A01G541200 chr4D 85.424 295 24 5 471 762 509355856 509355578 4.840000e-74 289.0
18 TraesCS5A01G541200 chr4D 89.427 227 21 2 490 713 509326341 509326115 2.250000e-72 283.0
19 TraesCS5A01G541200 chr4D 89.908 109 9 2 1643 1750 509283751 509283644 5.160000e-29 139.0
20 TraesCS5A01G541200 chrUn 86.976 1121 79 22 60 1138 402488984 402487889 0.000000e+00 1199.0
21 TraesCS5A01G541200 chrUn 86.606 545 64 7 2297 2835 343816555 343817096 9.170000e-166 593.0
22 TraesCS5A01G541200 chrUn 90.244 410 21 10 920 1311 324637550 324637142 5.670000e-143 518.0
23 TraesCS5A01G541200 chrUn 91.781 73 3 2 3760 3832 102841657 102841726 8.760000e-17 99.0
24 TraesCS5A01G541200 chr6A 90.909 88 7 1 3746 3832 606228652 606228739 2.420000e-22 117.0
25 TraesCS5A01G541200 chr3A 90.123 81 7 1 3753 3832 617304391 617304311 1.880000e-18 104.0
26 TraesCS5A01G541200 chr3A 93.443 61 4 0 3759 3819 617304205 617304265 1.470000e-14 91.6
27 TraesCS5A01G541200 chr5B 91.781 73 6 0 3760 3832 596944394 596944322 6.770000e-18 102.0
28 TraesCS5A01G541200 chr3B 90.411 73 7 0 3760 3832 650072223 650072151 3.150000e-16 97.1
29 TraesCS5A01G541200 chr5D 93.333 60 4 0 3760 3819 559835524 559835465 5.270000e-14 89.8
30 TraesCS5A01G541200 chr1D 91.803 61 5 0 3759 3819 6330172 6330232 6.820000e-13 86.1


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 TraesCS5A01G541200 chr5A 698161058 698164889 3831 True 3328.500000 4141 100.000000 1 3832 2 chr5A.!!$R1 3831
1 TraesCS5A01G541200 chr5A 698178735 698181116 2381 True 817.000000 1002 82.407500 488 2835 2 chr5A.!!$R2 2347
2 TraesCS5A01G541200 chr4B 657525532 657529369 3837 False 1338.666667 2676 90.511000 51 3748 3 chr4B.!!$F5 3697
3 TraesCS5A01G541200 chr4B 657515095 657517681 2586 False 883.000000 1040 83.526500 493 2835 2 chr4B.!!$F4 2342
4 TraesCS5A01G541200 chr4B 657497910 657498764 854 False 728.000000 728 82.472000 493 1362 1 chr4B.!!$F2 869
5 TraesCS5A01G541200 chr4D 509281518 509285151 3633 True 1430.666667 2671 89.498333 81 3748 3 chr4D.!!$R3 3667
6 TraesCS5A01G541200 chr4D 509338145 509341476 3331 True 778.000000 1051 84.712000 488 3478 3 chr4D.!!$R4 2990
7 TraesCS5A01G541200 chrUn 402487889 402488984 1095 True 1199.000000 1199 86.976000 60 1138 1 chrUn.!!$R2 1078
8 TraesCS5A01G541200 chrUn 343816555 343817096 541 False 593.000000 593 86.606000 2297 2835 1 chrUn.!!$F2 538

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
22 23 0.035317 TGCTTTGCGGATCACAGTCT 59.965 50.0 0.0 0.0 0.00 3.24 F
192 196 0.323957 GACTTCGGCACCCCTAAAGT 59.676 55.0 0.0 0.0 37.43 2.66 F
1108 1183 0.388134 GCGCGAGTACCAGTTCTTCA 60.388 55.0 12.1 0.0 0.00 3.02 F
1209 1287 1.091771 GCAGATCATGGACCACACCG 61.092 60.0 0.0 0.0 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1189 1267 0.035152 GGTGTGGTCCATGATCTGCA 60.035 55.000 0.00 0.0 0.00 4.41 R
1636 1720 0.550914 ACAAACACTCTGCCTTGGGA 59.449 50.000 0.00 0.0 0.00 4.37 R
2508 3167 1.135199 GCAGAATGGCACCTGAACATG 60.135 52.381 19.19 0.0 35.86 3.21 R
2864 3589 1.358152 AACTCCTCCCATCGGTCAAA 58.642 50.000 0.00 0.0 0.00 2.69 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
18 19 3.863681 GTTTGCTTTGCGGATCACA 57.136 47.368 0.00 0.00 0.00 3.58
19 20 1.689959 GTTTGCTTTGCGGATCACAG 58.310 50.000 0.00 0.00 0.00 3.66
20 21 1.001378 GTTTGCTTTGCGGATCACAGT 60.001 47.619 0.00 0.00 0.00 3.55
21 22 0.874390 TTGCTTTGCGGATCACAGTC 59.126 50.000 0.00 0.00 0.00 3.51
22 23 0.035317 TGCTTTGCGGATCACAGTCT 59.965 50.000 0.00 0.00 0.00 3.24
23 24 0.723981 GCTTTGCGGATCACAGTCTC 59.276 55.000 0.00 0.00 0.00 3.36
24 25 0.994995 CTTTGCGGATCACAGTCTCG 59.005 55.000 0.00 0.00 0.00 4.04
25 26 1.014044 TTTGCGGATCACAGTCTCGC 61.014 55.000 3.70 3.70 45.60 5.03
26 27 2.583593 GCGGATCACAGTCTCGCC 60.584 66.667 0.00 0.00 40.44 5.54
27 28 2.278206 CGGATCACAGTCTCGCCG 60.278 66.667 0.00 0.00 0.00 6.46
28 29 2.761195 CGGATCACAGTCTCGCCGA 61.761 63.158 0.00 0.00 41.11 5.54
29 30 1.226717 GGATCACAGTCTCGCCGAC 60.227 63.158 0.00 0.00 43.17 4.79
36 37 2.868920 GTCTCGCCGACGTCTCTT 59.131 61.111 14.70 0.00 41.18 2.85
37 38 1.512310 GTCTCGCCGACGTCTCTTG 60.512 63.158 14.70 0.79 41.18 3.02
38 39 2.202492 CTCGCCGACGTCTCTTGG 60.202 66.667 14.70 8.44 41.18 3.61
39 40 2.979197 CTCGCCGACGTCTCTTGGT 61.979 63.158 14.70 0.00 41.18 3.67
40 41 2.504244 CGCCGACGTCTCTTGGTC 60.504 66.667 14.70 3.26 33.53 4.02
41 42 2.963371 GCCGACGTCTCTTGGTCT 59.037 61.111 14.70 0.00 0.00 3.85
42 43 1.444553 GCCGACGTCTCTTGGTCTG 60.445 63.158 14.70 0.00 0.00 3.51
43 44 1.444553 CCGACGTCTCTTGGTCTGC 60.445 63.158 14.70 0.00 0.00 4.26
44 45 1.797933 CGACGTCTCTTGGTCTGCG 60.798 63.158 14.70 0.00 0.00 5.18
45 46 1.286260 GACGTCTCTTGGTCTGCGT 59.714 57.895 8.70 0.00 35.20 5.24
46 47 0.729816 GACGTCTCTTGGTCTGCGTC 60.730 60.000 8.70 0.00 41.04 5.19
47 48 1.797933 CGTCTCTTGGTCTGCGTCG 60.798 63.158 0.00 0.00 0.00 5.12
48 49 1.579932 GTCTCTTGGTCTGCGTCGA 59.420 57.895 0.00 0.00 0.00 4.20
49 50 0.729816 GTCTCTTGGTCTGCGTCGAC 60.730 60.000 5.18 5.18 0.00 4.20
50 51 1.797933 CTCTTGGTCTGCGTCGACG 60.798 63.158 32.57 32.57 43.27 5.12
51 52 2.183858 CTCTTGGTCTGCGTCGACGA 62.184 60.000 39.74 23.16 43.02 4.20
52 53 1.797933 CTTGGTCTGCGTCGACGAG 60.798 63.158 39.74 29.94 43.02 4.18
53 54 2.459421 CTTGGTCTGCGTCGACGAGT 62.459 60.000 39.74 0.00 43.02 4.18
54 55 2.067091 TTGGTCTGCGTCGACGAGTT 62.067 55.000 39.74 0.00 43.02 3.01
55 56 1.796749 GGTCTGCGTCGACGAGTTC 60.797 63.158 39.74 22.62 43.02 3.01
56 57 1.796749 GTCTGCGTCGACGAGTTCC 60.797 63.158 39.74 22.25 43.02 3.62
57 58 1.964891 TCTGCGTCGACGAGTTCCT 60.965 57.895 39.74 0.00 43.02 3.36
58 59 0.671472 TCTGCGTCGACGAGTTCCTA 60.671 55.000 39.74 14.77 43.02 2.94
71 72 1.546476 AGTTCCTACTCGTTGCCTCTG 59.454 52.381 0.00 0.00 0.00 3.35
116 117 0.901827 TTGCTACATCAAGGCGGAGA 59.098 50.000 0.00 0.00 0.00 3.71
126 127 1.415672 AAGGCGGAGACCCAAAGACA 61.416 55.000 0.00 0.00 31.70 3.41
157 161 4.221422 ATAGTGCGCCGCCGATGT 62.221 61.111 6.63 0.00 36.29 3.06
163 167 3.043713 CGCCGCCGATGTATGCAT 61.044 61.111 3.79 3.79 38.18 3.96
166 170 1.862123 CCGCCGATGTATGCATGAC 59.138 57.895 10.16 4.48 35.07 3.06
192 196 0.323957 GACTTCGGCACCCCTAAAGT 59.676 55.000 0.00 0.00 37.43 2.66
239 244 7.941053 ATATGGGTGTATTTGTAAGGTCCTA 57.059 36.000 0.00 0.00 0.00 2.94
273 278 3.961480 ATGGTTTTAAGCCTCTTTGCC 57.039 42.857 0.00 0.00 0.00 4.52
304 309 5.705609 AAGTTCAACACCCATCACATTAC 57.294 39.130 0.00 0.00 0.00 1.89
313 318 9.567848 CAACACCCATCACATTACTATTTTTAC 57.432 33.333 0.00 0.00 0.00 2.01
317 322 8.836413 ACCCATCACATTACTATTTTTACGATG 58.164 33.333 0.00 0.00 0.00 3.84
354 359 9.953697 TTGTTAACTTAAAATGTAGCGTCAAAT 57.046 25.926 7.22 0.00 0.00 2.32
399 420 0.458370 GCGGCCTTTGCAATACCAAG 60.458 55.000 0.00 0.00 40.13 3.61
412 433 4.556699 GCAATACCAAGTGTCTGTCCAAAC 60.557 45.833 0.00 0.00 0.00 2.93
455 481 8.662781 TTGACAATGCTAAAGTCATATAGGAC 57.337 34.615 9.51 9.51 41.42 3.85
457 483 7.136822 ACAATGCTAAAGTCATATAGGACCA 57.863 36.000 13.67 5.07 38.59 4.02
464 494 7.652507 GCTAAAGTCATATAGGACCAACACTAC 59.347 40.741 13.67 0.00 38.59 2.73
467 497 5.363005 AGTCATATAGGACCAACACTACACC 59.637 44.000 13.67 0.00 38.59 4.16
469 499 3.975168 ATAGGACCAACACTACACCAC 57.025 47.619 0.00 0.00 0.00 4.16
473 503 3.712733 AGGACCAACACTACACCACTAAA 59.287 43.478 0.00 0.00 0.00 1.85
486 516 4.953579 ACACCACTAAATGTTCCACAACTT 59.046 37.500 0.00 0.00 33.17 2.66
799 847 6.850317 GCTAATTCTCAGATCGAATCTTTTGC 59.150 38.462 0.00 0.00 37.58 3.68
856 907 0.487325 TGGAGGAGGGAGAGACACAA 59.513 55.000 0.00 0.00 0.00 3.33
857 908 0.899019 GGAGGAGGGAGAGACACAAC 59.101 60.000 0.00 0.00 0.00 3.32
861 912 1.416401 GGAGGGAGAGACACAACACAA 59.584 52.381 0.00 0.00 0.00 3.33
899 955 4.880696 AGGTGCCTTAGTAGTTAGTACTCG 59.119 45.833 0.00 0.00 41.42 4.18
903 959 4.568760 GCCTTAGTAGTTAGTACTCGTCGT 59.431 45.833 0.00 0.00 41.42 4.34
933 989 2.060050 TCTTCCTCGACATCTCTCCC 57.940 55.000 0.00 0.00 0.00 4.30
984 1049 1.403679 ACAAGCAAGCAAGCAAACGTA 59.596 42.857 3.19 0.00 36.85 3.57
1074 1140 1.699656 CGCCCGTTCTTCAGCATCAG 61.700 60.000 0.00 0.00 0.00 2.90
1075 1141 1.372087 GCCCGTTCTTCAGCATCAGG 61.372 60.000 0.00 0.00 0.00 3.86
1077 1143 1.339055 CCCGTTCTTCAGCATCAGGAA 60.339 52.381 0.00 0.00 0.00 3.36
1108 1183 0.388134 GCGCGAGTACCAGTTCTTCA 60.388 55.000 12.10 0.00 0.00 3.02
1136 1214 3.867783 CCACCACCACCACCACGA 61.868 66.667 0.00 0.00 0.00 4.35
1189 1267 1.153524 TCAGCCAATTGCCACCACT 59.846 52.632 0.00 0.00 42.71 4.00
1209 1287 1.091771 GCAGATCATGGACCACACCG 61.092 60.000 0.00 0.00 0.00 4.94
1260 1341 2.037367 AGGCTCACGCTGGAGGTA 59.963 61.111 4.01 0.00 35.41 3.08
1353 1437 8.251721 AGTAGTACTACTGCTTAATTGTTCCAG 58.748 37.037 30.33 0.00 44.11 3.86
1623 1707 8.394877 TCACGTAATTCTGTTAATTTATGCTGG 58.605 33.333 0.00 0.00 0.00 4.85
1625 1709 8.736244 ACGTAATTCTGTTAATTTATGCTGGTT 58.264 29.630 0.00 0.00 0.00 3.67
1639 1723 8.635765 TTTATGCTGGTTGAATATAATCTCCC 57.364 34.615 0.00 0.00 0.00 4.30
1649 1782 5.608437 TGAATATAATCTCCCAAGGCAGAGT 59.392 40.000 0.00 0.00 0.00 3.24
1702 1946 1.352017 TGGGCACTCACATCATCAGTT 59.648 47.619 0.00 0.00 0.00 3.16
1710 1954 6.237942 GCACTCACATCATCAGTTACACATAC 60.238 42.308 0.00 0.00 0.00 2.39
1852 2491 7.978099 ATATATATACTGGATCAGTGCACCA 57.022 36.000 14.63 2.55 45.01 4.17
1858 2497 3.087031 CTGGATCAGTGCACCATCTTTT 58.913 45.455 14.63 0.00 33.08 2.27
1995 2636 2.717044 CGTAGTGGCCGGGTGATCA 61.717 63.158 2.18 0.00 0.00 2.92
2023 2664 5.475719 ACCGAGTTCATAAAACTGATCGAA 58.524 37.500 0.00 0.00 32.18 3.71
2058 2699 4.710324 ACAGACCAAAACCTCACGAAATA 58.290 39.130 0.00 0.00 0.00 1.40
2089 2735 8.915654 CAAGATCCTTGTTTAATTAGTTTGCAC 58.084 33.333 0.00 0.00 0.00 4.57
2115 2761 8.749354 CCAGGAAATTGCCTACTTAATTACTTT 58.251 33.333 4.05 0.00 36.22 2.66
2177 2823 5.885230 TGATCCAGATCACAATTGTTGAC 57.115 39.130 8.77 3.07 42.42 3.18
2179 2825 3.073678 TCCAGATCACAATTGTTGACGG 58.926 45.455 8.77 11.08 0.00 4.79
2215 2861 3.574614 AGCAATTCATAAAACCGTGCAC 58.425 40.909 6.82 6.82 32.98 4.57
2232 2882 1.802880 GCACAGATGTACAGGGCTACG 60.803 57.143 0.33 0.00 31.59 3.51
2242 2892 2.202824 GGGCTACGCGTATGCACA 60.203 61.111 28.84 9.45 42.97 4.57
2348 2998 7.357951 GAAGTTGTTCTCTTCCATTGTCTAG 57.642 40.000 0.00 0.00 36.33 2.43
2422 3080 8.454106 CAATTCTGGTTAATAAGAGACCAACTG 58.546 37.037 0.00 0.00 42.47 3.16
2446 3105 9.784531 CTGTACTTCATAAACAGGGAATATCAT 57.215 33.333 0.00 0.00 37.55 2.45
2459 3118 7.038088 ACAGGGAATATCATGTACATATCTGCA 60.038 37.037 8.32 0.00 0.00 4.41
2467 3126 3.872696 TGTACATATCTGCAACCCACAG 58.127 45.455 0.00 0.00 36.44 3.66
2478 3137 2.293399 GCAACCCACAGGAAAAGTACAG 59.707 50.000 0.00 0.00 36.73 2.74
2492 3151 6.073711 GGAAAAGTACAGAACTGCACTCTTAC 60.074 42.308 7.96 0.00 36.24 2.34
2508 3167 7.277981 TGCACTCTTACGATTATTTTCCTCTTC 59.722 37.037 0.00 0.00 0.00 2.87
2670 3331 0.973496 GGAGAAGAGGAAGAGGCGGT 60.973 60.000 0.00 0.00 0.00 5.68
2693 3354 3.499918 GCTATGACAAGCAAATCCGCTAT 59.500 43.478 5.18 0.00 42.89 2.97
2756 3417 0.887387 GCCGCTTTGTCAAGGTACCA 60.887 55.000 15.94 0.00 0.00 3.25
2772 3433 2.816958 CAGAAGCCGCTGCATCGT 60.817 61.111 9.34 0.00 40.09 3.73
2774 3435 3.918220 GAAGCCGCTGCATCGTCG 61.918 66.667 9.34 0.27 41.13 5.12
2874 3599 5.371115 AGTTGGTTATTGTTTGACCGATG 57.629 39.130 0.00 0.00 36.22 3.84
2938 3663 8.437742 GCAGACCAATCAAAGAAAATGTATTTG 58.562 33.333 0.00 0.00 35.68 2.32
3067 3873 6.017770 CACCAACTCAAAGTTAAATACGGACA 60.018 38.462 0.00 0.00 36.03 4.02
3124 3932 7.962964 TGACGACTTATCAAGAGTGAAAAAT 57.037 32.000 0.00 0.00 37.30 1.82
3163 3971 1.234615 AACCATCACGACCGCCAAAG 61.235 55.000 0.00 0.00 0.00 2.77
3261 4069 7.359262 TGTATATTACAAAGCTGTGTGTCAC 57.641 36.000 20.28 10.25 36.96 3.67
3326 4134 2.881513 TGCACGAATGAGGCACTTTAAA 59.118 40.909 0.00 0.00 41.55 1.52
3339 4147 7.446931 TGAGGCACTTTAAAAGAATATGTCACA 59.553 33.333 0.00 0.00 41.55 3.58
3354 4162 5.981088 ATGTCACATTGCATGGAAAACTA 57.019 34.783 2.94 0.00 33.60 2.24
3365 4173 7.225784 TGCATGGAAAACTATAAACATGTGT 57.774 32.000 0.00 0.00 38.29 3.72
3371 4179 9.214957 TGGAAAACTATAAACATGTGTAGACAG 57.785 33.333 15.93 9.28 34.87 3.51
3508 4316 3.559655 TCATTCATCCATTTAACCTCGCG 59.440 43.478 0.00 0.00 0.00 5.87
3530 4338 9.932699 TCGCGAATATAGATAGCTAGTTAATTC 57.067 33.333 6.20 4.44 0.00 2.17
3541 4349 4.096382 AGCTAGTTAATTCGTTTGGCCATG 59.904 41.667 6.09 0.00 0.00 3.66
3595 4403 2.000447 GTGTCACCGCCTTTATCACTC 59.000 52.381 0.00 0.00 0.00 3.51
3604 4412 3.580731 GCCTTTATCACTCGGAGATAGC 58.419 50.000 12.86 0.00 33.89 2.97
3610 4418 2.302260 TCACTCGGAGATAGCTGAAGG 58.698 52.381 12.86 0.00 33.89 3.46
3671 4480 2.012673 GGTGCAAACCAGATCAGCTAG 58.987 52.381 0.00 0.00 0.00 3.42
3687 4496 8.263640 AGATCAGCTAGACAAGATAACAATGTT 58.736 33.333 3.43 3.43 0.00 2.71
3690 4499 6.744537 CAGCTAGACAAGATAACAATGTTTGC 59.255 38.462 3.17 0.00 0.00 3.68
3748 4557 6.491745 TGATCCAACAAGTTGCCAAATACTAA 59.508 34.615 1.81 0.00 39.16 2.24
3749 4558 6.325919 TCCAACAAGTTGCCAAATACTAAG 57.674 37.500 1.81 0.00 39.16 2.18
3750 4559 5.242838 TCCAACAAGTTGCCAAATACTAAGG 59.757 40.000 1.81 0.00 39.16 2.69
3751 4560 5.242838 CCAACAAGTTGCCAAATACTAAGGA 59.757 40.000 1.81 0.00 39.16 3.36
3752 4561 5.959618 ACAAGTTGCCAAATACTAAGGAC 57.040 39.130 1.81 0.00 0.00 3.85
3753 4562 4.765339 ACAAGTTGCCAAATACTAAGGACC 59.235 41.667 1.81 0.00 0.00 4.46
3754 4563 4.650972 AGTTGCCAAATACTAAGGACCA 57.349 40.909 0.00 0.00 0.00 4.02
3755 4564 4.589908 AGTTGCCAAATACTAAGGACCAG 58.410 43.478 0.00 0.00 0.00 4.00
3756 4565 4.042934 AGTTGCCAAATACTAAGGACCAGT 59.957 41.667 0.00 0.00 0.00 4.00
3757 4566 4.650972 TGCCAAATACTAAGGACCAGTT 57.349 40.909 0.00 0.00 0.00 3.16
3758 4567 4.585879 TGCCAAATACTAAGGACCAGTTC 58.414 43.478 0.00 0.00 0.00 3.01
3759 4568 4.288626 TGCCAAATACTAAGGACCAGTTCT 59.711 41.667 0.00 0.00 0.00 3.01
3760 4569 5.222048 TGCCAAATACTAAGGACCAGTTCTT 60.222 40.000 0.00 0.00 0.00 2.52
3761 4570 5.710567 GCCAAATACTAAGGACCAGTTCTTT 59.289 40.000 0.00 0.00 0.00 2.52
3762 4571 6.208797 GCCAAATACTAAGGACCAGTTCTTTT 59.791 38.462 0.00 0.00 0.00 2.27
3763 4572 7.593825 CCAAATACTAAGGACCAGTTCTTTTG 58.406 38.462 0.00 0.00 0.00 2.44
3764 4573 7.230712 CCAAATACTAAGGACCAGTTCTTTTGT 59.769 37.037 0.00 0.39 34.47 2.83
3765 4574 8.630037 CAAATACTAAGGACCAGTTCTTTTGTT 58.370 33.333 0.00 0.00 32.76 2.83
3766 4575 7.745620 ATACTAAGGACCAGTTCTTTTGTTG 57.254 36.000 0.00 0.00 32.76 3.33
3767 4576 4.887655 ACTAAGGACCAGTTCTTTTGTTGG 59.112 41.667 0.00 0.00 36.76 3.77
3768 4577 2.031870 AGGACCAGTTCTTTTGTTGGC 58.968 47.619 0.00 0.00 33.98 4.52
3769 4578 2.031870 GGACCAGTTCTTTTGTTGGCT 58.968 47.619 0.00 0.00 33.98 4.75
3770 4579 2.430694 GGACCAGTTCTTTTGTTGGCTT 59.569 45.455 0.00 0.00 33.98 4.35
3771 4580 3.490933 GGACCAGTTCTTTTGTTGGCTTC 60.491 47.826 0.00 0.00 33.98 3.86
3772 4581 2.430694 ACCAGTTCTTTTGTTGGCTTCC 59.569 45.455 0.00 0.00 33.98 3.46
3773 4582 2.430332 CCAGTTCTTTTGTTGGCTTCCA 59.570 45.455 0.00 0.00 0.00 3.53
3774 4583 3.491447 CCAGTTCTTTTGTTGGCTTCCAG 60.491 47.826 0.00 0.00 33.81 3.86
3775 4584 3.381272 CAGTTCTTTTGTTGGCTTCCAGA 59.619 43.478 0.00 0.00 33.81 3.86
3776 4585 4.023291 AGTTCTTTTGTTGGCTTCCAGAA 58.977 39.130 0.00 0.00 33.81 3.02
3777 4586 4.651045 AGTTCTTTTGTTGGCTTCCAGAAT 59.349 37.500 0.00 0.00 33.81 2.40
3778 4587 5.833131 AGTTCTTTTGTTGGCTTCCAGAATA 59.167 36.000 0.00 0.00 33.81 1.75
3779 4588 6.323739 AGTTCTTTTGTTGGCTTCCAGAATAA 59.676 34.615 0.00 0.00 33.81 1.40
3780 4589 6.331369 TCTTTTGTTGGCTTCCAGAATAAG 57.669 37.500 0.00 0.00 33.81 1.73
3781 4590 4.519540 TTTGTTGGCTTCCAGAATAAGC 57.480 40.909 0.00 0.00 46.90 3.09
3782 4591 3.439857 TGTTGGCTTCCAGAATAAGCT 57.560 42.857 7.65 0.00 46.81 3.74
3783 4592 3.084039 TGTTGGCTTCCAGAATAAGCTG 58.916 45.455 7.65 0.00 46.81 4.24
3784 4593 1.755179 TGGCTTCCAGAATAAGCTGC 58.245 50.000 7.65 0.00 46.81 5.25
3785 4594 1.028130 GGCTTCCAGAATAAGCTGCC 58.972 55.000 7.65 0.00 46.81 4.85
3786 4595 1.028130 GCTTCCAGAATAAGCTGCCC 58.972 55.000 0.00 0.00 44.75 5.36
3787 4596 1.685148 CTTCCAGAATAAGCTGCCCC 58.315 55.000 0.00 0.00 34.56 5.80
3788 4597 0.258774 TTCCAGAATAAGCTGCCCCC 59.741 55.000 0.00 0.00 34.56 5.40
3789 4598 0.624500 TCCAGAATAAGCTGCCCCCT 60.625 55.000 0.00 0.00 34.56 4.79
3790 4599 1.140312 CCAGAATAAGCTGCCCCCTA 58.860 55.000 0.00 0.00 34.56 3.53
3791 4600 1.202818 CCAGAATAAGCTGCCCCCTAC 60.203 57.143 0.00 0.00 34.56 3.18
3792 4601 1.141185 AGAATAAGCTGCCCCCTACC 58.859 55.000 0.00 0.00 0.00 3.18
3793 4602 1.141185 GAATAAGCTGCCCCCTACCT 58.859 55.000 0.00 0.00 0.00 3.08
3794 4603 2.090153 AGAATAAGCTGCCCCCTACCTA 60.090 50.000 0.00 0.00 0.00 3.08
3795 4604 2.031495 ATAAGCTGCCCCCTACCTAG 57.969 55.000 0.00 0.00 0.00 3.02
3796 4605 0.763223 TAAGCTGCCCCCTACCTAGC 60.763 60.000 0.00 0.00 34.71 3.42
3797 4606 2.446802 GCTGCCCCCTACCTAGCT 60.447 66.667 0.00 0.00 0.00 3.32
3798 4607 2.073101 GCTGCCCCCTACCTAGCTT 61.073 63.158 0.00 0.00 0.00 3.74
3799 4608 1.636769 GCTGCCCCCTACCTAGCTTT 61.637 60.000 0.00 0.00 0.00 3.51
3800 4609 0.919710 CTGCCCCCTACCTAGCTTTT 59.080 55.000 0.00 0.00 0.00 2.27
3801 4610 1.285078 CTGCCCCCTACCTAGCTTTTT 59.715 52.381 0.00 0.00 0.00 1.94
3802 4611 1.283905 TGCCCCCTACCTAGCTTTTTC 59.716 52.381 0.00 0.00 0.00 2.29
3803 4612 1.564818 GCCCCCTACCTAGCTTTTTCT 59.435 52.381 0.00 0.00 0.00 2.52
3804 4613 2.775960 GCCCCCTACCTAGCTTTTTCTA 59.224 50.000 0.00 0.00 0.00 2.10
3805 4614 3.201487 GCCCCCTACCTAGCTTTTTCTAA 59.799 47.826 0.00 0.00 0.00 2.10
3806 4615 4.324797 GCCCCCTACCTAGCTTTTTCTAAA 60.325 45.833 0.00 0.00 0.00 1.85
3807 4616 5.808710 GCCCCCTACCTAGCTTTTTCTAAAA 60.809 44.000 0.00 0.00 0.00 1.52
3808 4617 5.886474 CCCCCTACCTAGCTTTTTCTAAAAG 59.114 44.000 0.00 7.38 0.00 2.27
3816 4625 4.066646 GCTTTTTCTAAAAGCCCAACCA 57.933 40.909 20.63 0.00 45.01 3.67
3817 4626 4.447290 GCTTTTTCTAAAAGCCCAACCAA 58.553 39.130 20.63 0.00 45.01 3.67
3818 4627 4.878971 GCTTTTTCTAAAAGCCCAACCAAA 59.121 37.500 20.63 0.00 45.01 3.28
3819 4628 5.530915 GCTTTTTCTAAAAGCCCAACCAAAT 59.469 36.000 20.63 0.00 45.01 2.32
3820 4629 6.039270 GCTTTTTCTAAAAGCCCAACCAAATT 59.961 34.615 20.63 0.00 45.01 1.82
3821 4630 7.227711 GCTTTTTCTAAAAGCCCAACCAAATTA 59.772 33.333 20.63 0.00 45.01 1.40
3822 4631 9.114952 CTTTTTCTAAAAGCCCAACCAAATTAA 57.885 29.630 0.00 0.00 0.00 1.40
3823 4632 9.634021 TTTTTCTAAAAGCCCAACCAAATTAAT 57.366 25.926 0.00 0.00 0.00 1.40
3824 4633 9.634021 TTTTCTAAAAGCCCAACCAAATTAATT 57.366 25.926 0.00 0.00 0.00 1.40
3825 4634 9.634021 TTTCTAAAAGCCCAACCAAATTAATTT 57.366 25.926 7.64 7.64 0.00 1.82
3826 4635 9.634021 TTCTAAAAGCCCAACCAAATTAATTTT 57.366 25.926 10.77 0.00 0.00 1.82
3827 4636 9.634021 TCTAAAAGCCCAACCAAATTAATTTTT 57.366 25.926 10.77 1.65 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.266718 GACTGTGATCCGCAAAGCAAA 59.733 47.619 0.00 0.00 35.04 3.68
2 3 0.874390 GACTGTGATCCGCAAAGCAA 59.126 50.000 0.00 0.00 35.04 3.91
4 5 0.723981 GAGACTGTGATCCGCAAAGC 59.276 55.000 0.00 0.00 35.04 3.51
6 7 1.014044 GCGAGACTGTGATCCGCAAA 61.014 55.000 0.00 0.00 44.55 3.68
8 9 2.181777 GCGAGACTGTGATCCGCA 59.818 61.111 0.00 0.00 44.55 5.69
9 10 2.583593 GGCGAGACTGTGATCCGC 60.584 66.667 0.00 0.00 44.45 5.54
10 11 2.278206 CGGCGAGACTGTGATCCG 60.278 66.667 0.00 0.00 0.00 4.18
11 12 1.226717 GTCGGCGAGACTGTGATCC 60.227 63.158 11.20 0.00 46.13 3.36
12 13 4.386245 GTCGGCGAGACTGTGATC 57.614 61.111 11.20 0.00 46.13 2.92
19 20 1.512310 CAAGAGACGTCGGCGAGAC 60.512 63.158 20.03 7.21 46.16 3.36
20 21 2.687805 CCAAGAGACGTCGGCGAGA 61.688 63.158 20.03 0.00 42.00 4.04
21 22 2.202492 CCAAGAGACGTCGGCGAG 60.202 66.667 20.03 7.37 42.00 5.03
22 23 2.974489 GACCAAGAGACGTCGGCGA 61.974 63.158 20.03 4.99 42.00 5.54
23 24 2.504244 GACCAAGAGACGTCGGCG 60.504 66.667 8.42 8.42 44.93 6.46
24 25 1.444553 CAGACCAAGAGACGTCGGC 60.445 63.158 10.46 6.64 34.10 5.54
25 26 1.444553 GCAGACCAAGAGACGTCGG 60.445 63.158 10.46 7.82 34.10 4.79
26 27 1.797933 CGCAGACCAAGAGACGTCG 60.798 63.158 10.46 0.00 34.10 5.12
27 28 0.729816 GACGCAGACCAAGAGACGTC 60.730 60.000 7.70 7.70 42.36 4.34
28 29 1.286260 GACGCAGACCAAGAGACGT 59.714 57.895 0.00 0.00 36.30 4.34
29 30 1.797933 CGACGCAGACCAAGAGACG 60.798 63.158 0.00 0.00 0.00 4.18
30 31 0.729816 GTCGACGCAGACCAAGAGAC 60.730 60.000 0.00 0.00 35.22 3.36
31 32 1.579932 GTCGACGCAGACCAAGAGA 59.420 57.895 0.00 0.00 35.22 3.10
32 33 1.797933 CGTCGACGCAGACCAAGAG 60.798 63.158 26.59 0.00 37.85 2.85
33 34 2.183858 CTCGTCGACGCAGACCAAGA 62.184 60.000 32.19 11.40 37.85 3.02
34 35 1.797933 CTCGTCGACGCAGACCAAG 60.798 63.158 32.19 18.51 37.85 3.61
35 36 2.067091 AACTCGTCGACGCAGACCAA 62.067 55.000 32.19 12.91 37.85 3.67
36 37 2.453773 GAACTCGTCGACGCAGACCA 62.454 60.000 32.19 13.67 37.85 4.02
37 38 1.796749 GAACTCGTCGACGCAGACC 60.797 63.158 32.19 19.89 37.85 3.85
38 39 1.796749 GGAACTCGTCGACGCAGAC 60.797 63.158 32.19 23.41 39.60 3.51
39 40 0.671472 TAGGAACTCGTCGACGCAGA 60.671 55.000 32.19 15.20 41.75 4.26
40 41 0.520827 GTAGGAACTCGTCGACGCAG 60.521 60.000 32.19 28.15 41.75 5.18
41 42 0.952497 AGTAGGAACTCGTCGACGCA 60.952 55.000 32.19 19.50 41.75 5.24
42 43 0.247616 GAGTAGGAACTCGTCGACGC 60.248 60.000 32.19 18.11 42.66 5.19
43 44 3.873828 GAGTAGGAACTCGTCGACG 57.126 57.895 31.30 31.30 42.66 5.12
51 52 1.546476 CAGAGGCAACGAGTAGGAACT 59.454 52.381 0.00 0.00 46.39 3.01
52 53 1.997669 CAGAGGCAACGAGTAGGAAC 58.002 55.000 0.00 0.00 46.39 3.62
53 54 0.246635 GCAGAGGCAACGAGTAGGAA 59.753 55.000 0.00 0.00 46.39 3.36
54 55 1.890894 GCAGAGGCAACGAGTAGGA 59.109 57.895 0.00 0.00 46.39 2.94
55 56 4.504132 GCAGAGGCAACGAGTAGG 57.496 61.111 0.00 0.00 46.39 3.18
67 68 0.251077 AAACCCAGGAGCTTGCAGAG 60.251 55.000 0.00 0.00 0.00 3.35
71 72 1.039856 TTTGAAACCCAGGAGCTTGC 58.960 50.000 0.00 0.00 0.00 4.01
94 95 0.451783 CCGCCTTGATGTAGCAAACC 59.548 55.000 0.00 0.00 0.00 3.27
116 117 1.071471 CTCGGTGCTGTCTTTGGGT 59.929 57.895 0.00 0.00 0.00 4.51
141 145 2.852180 ATACATCGGCGGCGCACTA 61.852 57.895 34.36 18.24 0.00 2.74
213 217 7.742767 AGGACCTTACAAATACACCCATATAC 58.257 38.462 0.00 0.00 0.00 1.47
284 289 7.391148 AATAGTAATGTGATGGGTGTTGAAC 57.609 36.000 0.00 0.00 0.00 3.18
288 293 8.455682 CGTAAAAATAGTAATGTGATGGGTGTT 58.544 33.333 0.00 0.00 0.00 3.32
313 318 9.710979 TTAAGTTAACAAAAACACTCTTCATCG 57.289 29.630 8.61 0.00 0.00 3.84
354 359 2.701951 TGCTCATCATGCTCTGTATCCA 59.298 45.455 0.00 0.00 0.00 3.41
362 367 0.247974 GCGTGTTGCTCATCATGCTC 60.248 55.000 14.53 0.00 41.56 4.26
422 444 7.977904 TGACTTTAGCATTGTCAATATGTCAG 58.022 34.615 0.00 0.00 37.71 3.51
423 445 7.920160 TGACTTTAGCATTGTCAATATGTCA 57.080 32.000 0.00 4.59 37.71 3.58
431 457 7.147567 TGGTCCTATATGACTTTAGCATTGTCA 60.148 37.037 7.91 0.00 43.53 3.58
455 481 5.048991 GGAACATTTAGTGGTGTAGTGTTGG 60.049 44.000 0.00 0.00 0.00 3.77
457 483 5.529800 GTGGAACATTTAGTGGTGTAGTGTT 59.470 40.000 0.00 0.00 44.52 3.32
486 516 8.511321 CATGGCAATACTAAACAGAAAAGTACA 58.489 33.333 0.00 0.00 0.00 2.90
705 748 4.948621 CGGAATAGATACTACCCCTCGATT 59.051 45.833 0.00 0.00 0.00 3.34
714 757 4.212847 TGAGTGCGTCGGAATAGATACTAC 59.787 45.833 0.00 0.00 0.00 2.73
716 759 3.211865 TGAGTGCGTCGGAATAGATACT 58.788 45.455 0.00 0.00 0.00 2.12
799 847 1.375652 CAGTGAGCTGCAGACCAGG 60.376 63.158 20.43 5.54 42.03 4.45
825 874 1.002990 TCCTCCACTGCACTGCATG 60.003 57.895 3.64 5.46 38.13 4.06
856 907 4.042934 ACCTTGAAATAGCTAGGGTTGTGT 59.957 41.667 0.00 0.00 35.47 3.72
857 908 4.396166 CACCTTGAAATAGCTAGGGTTGTG 59.604 45.833 0.00 0.00 35.47 3.33
861 912 2.092375 GGCACCTTGAAATAGCTAGGGT 60.092 50.000 0.00 0.00 35.47 4.34
899 955 4.231439 GAGGAAGAAGAAGAGACAACGAC 58.769 47.826 0.00 0.00 0.00 4.34
903 959 3.889538 TGTCGAGGAAGAAGAAGAGACAA 59.110 43.478 0.00 0.00 34.91 3.18
933 989 2.983592 GGTTTGGTGCGTGGAGGG 60.984 66.667 0.00 0.00 0.00 4.30
947 1011 3.616317 GCTTGTTTGTTTCTGGTGTGGTT 60.616 43.478 0.00 0.00 0.00 3.67
984 1049 0.392336 GCATACTGCAGCTAGCTCCT 59.608 55.000 16.15 0.00 44.26 3.69
1033 1099 3.434319 CATGTGGTGCGGGCAGTC 61.434 66.667 0.00 0.00 0.00 3.51
1074 1140 4.025401 CGCAGCCGGTGTTGTTCC 62.025 66.667 1.90 0.00 0.00 3.62
1108 1183 4.218686 GTGGTGGTGGCCTTGGGT 62.219 66.667 3.32 0.00 0.00 4.51
1165 1243 2.568090 GCAATTGGCTGACGGTGG 59.432 61.111 7.72 0.00 40.25 4.61
1166 1244 2.267351 TGGCAATTGGCTGACGGTG 61.267 57.895 29.53 0.00 44.01 4.94
1167 1245 2.115052 TGGCAATTGGCTGACGGT 59.885 55.556 29.53 0.00 44.01 4.83
1171 1249 1.153524 AGTGGTGGCAATTGGCTGA 59.846 52.632 29.53 10.60 44.01 4.26
1179 1257 0.038599 ATGATCTGCAGTGGTGGCAA 59.961 50.000 14.67 0.00 41.39 4.52
1189 1267 0.035152 GGTGTGGTCCATGATCTGCA 60.035 55.000 0.00 0.00 0.00 4.41
1209 1287 2.544277 TGCAGCTGCTGTTTCATGAAAC 60.544 45.455 34.41 34.41 43.49 2.78
1260 1341 4.947147 TTTTGGCCGCCTGCGTCT 62.947 61.111 11.61 0.00 42.61 4.18
1276 1357 1.975407 GCAGCAGGTGAGCCATGTT 60.975 57.895 3.02 0.00 37.19 2.71
1305 1386 1.303317 GATGGTGGTTCTTGGCCGT 60.303 57.895 0.00 0.00 0.00 5.68
1307 1388 1.303317 ACGATGGTGGTTCTTGGCC 60.303 57.895 0.00 0.00 0.00 5.36
1308 1389 0.605319 TCACGATGGTGGTTCTTGGC 60.605 55.000 8.09 0.00 44.50 4.52
1315 1396 3.083122 AGTACTACTCACGATGGTGGT 57.917 47.619 8.09 7.48 44.50 4.16
1623 1707 6.299141 TCTGCCTTGGGAGATTATATTCAAC 58.701 40.000 6.79 0.00 0.00 3.18
1625 1709 5.608437 ACTCTGCCTTGGGAGATTATATTCA 59.392 40.000 11.21 0.00 34.11 2.57
1628 1712 4.910304 ACACTCTGCCTTGGGAGATTATAT 59.090 41.667 11.21 0.00 34.11 0.86
1630 1714 3.118531 ACACTCTGCCTTGGGAGATTAT 58.881 45.455 11.21 0.00 34.11 1.28
1632 1716 1.366319 ACACTCTGCCTTGGGAGATT 58.634 50.000 11.21 3.37 34.11 2.40
1633 1717 1.366319 AACACTCTGCCTTGGGAGAT 58.634 50.000 11.21 0.24 34.11 2.75
1636 1720 0.550914 ACAAACACTCTGCCTTGGGA 59.449 50.000 0.00 0.00 0.00 4.37
1637 1721 0.670162 CACAAACACTCTGCCTTGGG 59.330 55.000 0.00 0.00 0.00 4.12
1638 1722 1.392589 ACACAAACACTCTGCCTTGG 58.607 50.000 0.00 0.00 0.00 3.61
1639 1723 3.508744 AAACACAAACACTCTGCCTTG 57.491 42.857 0.00 0.00 0.00 3.61
1649 1782 6.475076 GCATCAACTGATACAAAACACAAACA 59.525 34.615 0.00 0.00 32.63 2.83
1687 1925 6.935167 TGTATGTGTAACTGATGATGTGAGT 58.065 36.000 0.00 0.00 38.04 3.41
1753 2000 6.013379 TGTATTGCTTGTTCCCATAAAGGAA 58.987 36.000 0.00 0.00 43.77 3.36
1754 2001 5.575157 TGTATTGCTTGTTCCCATAAAGGA 58.425 37.500 0.00 0.00 41.22 3.36
1755 2002 5.913137 TGTATTGCTTGTTCCCATAAAGG 57.087 39.130 0.00 0.00 37.03 3.11
1766 2369 3.312421 GCGTGGACATATGTATTGCTTGT 59.688 43.478 8.71 0.00 0.00 3.16
1844 2483 7.385752 CACATAAAATGAAAAAGATGGTGCACT 59.614 33.333 17.98 0.00 0.00 4.40
1845 2484 7.360269 CCACATAAAATGAAAAAGATGGTGCAC 60.360 37.037 8.80 8.80 0.00 4.57
1952 2592 6.013293 GGAAGCAATTATGGGGAGTAGTATCT 60.013 42.308 0.00 0.00 0.00 1.98
1995 2636 7.435488 CGATCAGTTTTATGAACTCGGTAGATT 59.565 37.037 0.00 0.00 31.31 2.40
2023 2664 6.462909 GGTTTTGGTCTGTTTTGGATCTGATT 60.463 38.462 0.00 0.00 0.00 2.57
2029 2670 4.099419 GTGAGGTTTTGGTCTGTTTTGGAT 59.901 41.667 0.00 0.00 0.00 3.41
2089 2735 7.881775 AGTAATTAAGTAGGCAATTTCCTGG 57.118 36.000 6.93 0.00 37.01 4.45
2155 2801 4.392754 CGTCAACAATTGTGATCTGGATCA 59.607 41.667 12.82 8.96 44.83 2.92
2177 2823 8.514136 TGAATTGCTAAAAATGTTTAACTCCG 57.486 30.769 0.00 0.00 0.00 4.63
2232 2882 5.637810 AGGTGTATTATGTATGTGCATACGC 59.362 40.000 15.07 0.00 44.97 4.42
2281 2931 1.400242 GCGCACAGTCCAAACTCAATC 60.400 52.381 0.30 0.00 31.71 2.67
2422 3080 9.561069 ACATGATATTCCCTGTTTATGAAGTAC 57.439 33.333 0.00 0.00 0.00 2.73
2446 3105 3.370421 CCTGTGGGTTGCAGATATGTACA 60.370 47.826 0.00 0.00 36.12 2.90
2459 3118 4.079958 AGTTCTGTACTTTTCCTGTGGGTT 60.080 41.667 0.00 0.00 31.29 4.11
2467 3126 4.381411 AGAGTGCAGTTCTGTACTTTTCC 58.619 43.478 20.57 10.69 34.96 3.13
2492 3151 7.066284 ACCTGAACATGAAGAGGAAAATAATCG 59.934 37.037 13.37 0.00 0.00 3.34
2508 3167 1.135199 GCAGAATGGCACCTGAACATG 60.135 52.381 19.19 0.00 35.86 3.21
2533 3194 3.003068 GCTAATAGTGCTGGTGAATGCAG 59.997 47.826 0.00 0.00 40.06 4.41
2611 3272 1.387539 CTCTCTCTCCTGCATCGTCA 58.612 55.000 0.00 0.00 0.00 4.35
2756 3417 2.510238 GACGATGCAGCGGCTTCT 60.510 61.111 29.52 6.73 40.88 2.85
2772 3433 3.691342 CGAAGCTGGGGGTGACGA 61.691 66.667 0.00 0.00 0.00 4.20
2864 3589 1.358152 AACTCCTCCCATCGGTCAAA 58.642 50.000 0.00 0.00 0.00 2.69
2874 3599 5.501156 AGTCAAATCAACATAACTCCTCCC 58.499 41.667 0.00 0.00 0.00 4.30
2982 3707 3.897141 AAGTAGCTAGCCTCCTCAAAC 57.103 47.619 12.13 0.00 0.00 2.93
3103 3911 7.364522 TCCATTTTTCACTCTTGATAAGTCG 57.635 36.000 0.00 0.00 0.00 4.18
3109 3917 6.018469 TCCCAATCCATTTTTCACTCTTGAT 58.982 36.000 0.00 0.00 0.00 2.57
3112 3920 5.397360 ACTCCCAATCCATTTTTCACTCTT 58.603 37.500 0.00 0.00 0.00 2.85
3115 3923 6.953520 TCATAACTCCCAATCCATTTTTCACT 59.046 34.615 0.00 0.00 0.00 3.41
3119 3927 8.893563 TTACTCATAACTCCCAATCCATTTTT 57.106 30.769 0.00 0.00 0.00 1.94
3124 3932 5.251932 TGGTTTACTCATAACTCCCAATCCA 59.748 40.000 0.00 0.00 0.00 3.41
3163 3971 9.102757 TCTCTCTCAAAATAAGCATTGTACATC 57.897 33.333 0.00 0.00 0.00 3.06
3204 4012 6.207417 ACAAGGTTCAACTCATATTTGGTGAG 59.793 38.462 1.85 1.85 46.60 3.51
3261 4069 9.442047 CTATGATAAGGCCTCAAATTAGTTAGG 57.558 37.037 5.23 0.00 0.00 2.69
3304 4112 0.877071 AAAGTGCCTCATTCGTGCAG 59.123 50.000 0.00 0.00 35.33 4.41
3307 4115 5.356882 TCTTTTAAAGTGCCTCATTCGTG 57.643 39.130 4.53 0.00 0.00 4.35
3326 4134 6.778834 TTCCATGCAATGTGACATATTCTT 57.221 33.333 0.00 0.00 44.81 2.52
3339 4147 8.313292 ACACATGTTTATAGTTTTCCATGCAAT 58.687 29.630 0.00 0.00 34.49 3.56
3354 4162 8.993121 GCTATTATGCTGTCTACACATGTTTAT 58.007 33.333 0.00 0.00 0.00 1.40
3371 4179 5.381174 TGGATGATTTGCAGCTATTATGC 57.619 39.130 0.00 0.00 44.11 3.14
3463 4271 8.997621 TGAATGTACAAACTTACCTCATAGAC 57.002 34.615 0.00 0.00 0.00 2.59
3530 4338 1.732077 CGATCAAACCATGGCCAAACG 60.732 52.381 10.96 7.52 0.00 3.60
3541 4349 5.294306 ACACATACACATGATCGATCAAACC 59.706 40.000 30.41 2.96 40.69 3.27
3595 4403 1.202580 CCCAACCTTCAGCTATCTCCG 60.203 57.143 0.00 0.00 0.00 4.63
3604 4412 0.329261 TGCCATCTCCCAACCTTCAG 59.671 55.000 0.00 0.00 0.00 3.02
3610 4418 2.040544 CCGTGTGCCATCTCCCAAC 61.041 63.158 0.00 0.00 0.00 3.77
3671 4480 5.132897 TGGGCAAACATTGTTATCTTGTC 57.867 39.130 1.76 0.00 0.00 3.18
3687 4496 2.042979 AGCTTCCCTTTATCTTGGGCAA 59.957 45.455 0.00 0.00 43.04 4.52
3690 4499 5.449553 ACAATAGCTTCCCTTTATCTTGGG 58.550 41.667 0.00 0.00 44.66 4.12
3748 4557 2.031870 GCCAACAAAAGAACTGGTCCT 58.968 47.619 0.00 0.00 0.00 3.85
3749 4558 2.031870 AGCCAACAAAAGAACTGGTCC 58.968 47.619 0.00 0.00 0.00 4.46
3750 4559 3.490933 GGAAGCCAACAAAAGAACTGGTC 60.491 47.826 0.00 0.00 0.00 4.02
3751 4560 2.430694 GGAAGCCAACAAAAGAACTGGT 59.569 45.455 0.00 0.00 0.00 4.00
3752 4561 2.430332 TGGAAGCCAACAAAAGAACTGG 59.570 45.455 0.00 0.00 0.00 4.00
3753 4562 3.381272 TCTGGAAGCCAACAAAAGAACTG 59.619 43.478 0.00 0.00 30.80 3.16
3754 4563 3.631250 TCTGGAAGCCAACAAAAGAACT 58.369 40.909 0.00 0.00 30.80 3.01
3755 4564 4.385358 TTCTGGAAGCCAACAAAAGAAC 57.615 40.909 0.00 0.00 30.80 3.01
3756 4565 6.723298 TTATTCTGGAAGCCAACAAAAGAA 57.277 33.333 0.00 0.00 30.80 2.52
3757 4566 5.278957 GCTTATTCTGGAAGCCAACAAAAGA 60.279 40.000 0.00 0.00 42.90 2.52
3758 4567 4.925646 GCTTATTCTGGAAGCCAACAAAAG 59.074 41.667 0.00 0.00 42.90 2.27
3759 4568 4.881920 GCTTATTCTGGAAGCCAACAAAA 58.118 39.130 0.00 0.00 42.90 2.44
3760 4569 4.519540 GCTTATTCTGGAAGCCAACAAA 57.480 40.909 0.00 0.00 42.90 2.83
3768 4577 1.685148 GGGGCAGCTTATTCTGGAAG 58.315 55.000 0.00 0.00 34.74 3.46
3769 4578 0.258774 GGGGGCAGCTTATTCTGGAA 59.741 55.000 0.00 0.00 34.74 3.53
3770 4579 0.624500 AGGGGGCAGCTTATTCTGGA 60.625 55.000 0.00 0.00 34.74 3.86
3771 4580 1.140312 TAGGGGGCAGCTTATTCTGG 58.860 55.000 0.00 0.00 34.74 3.86
3772 4581 1.202818 GGTAGGGGGCAGCTTATTCTG 60.203 57.143 0.00 0.00 37.15 3.02
3773 4582 1.141185 GGTAGGGGGCAGCTTATTCT 58.859 55.000 0.00 0.00 0.00 2.40
3774 4583 1.141185 AGGTAGGGGGCAGCTTATTC 58.859 55.000 0.00 0.00 0.00 1.75
3775 4584 2.339769 CTAGGTAGGGGGCAGCTTATT 58.660 52.381 0.00 0.00 0.00 1.40
3776 4585 2.031495 CTAGGTAGGGGGCAGCTTAT 57.969 55.000 0.00 0.00 0.00 1.73
3777 4586 0.763223 GCTAGGTAGGGGGCAGCTTA 60.763 60.000 0.00 0.00 0.00 3.09
3778 4587 2.073101 GCTAGGTAGGGGGCAGCTT 61.073 63.158 0.00 0.00 0.00 3.74
3779 4588 2.446802 GCTAGGTAGGGGGCAGCT 60.447 66.667 0.00 0.00 0.00 4.24
3780 4589 1.636769 AAAGCTAGGTAGGGGGCAGC 61.637 60.000 0.00 0.00 0.00 5.25
3781 4590 0.919710 AAAAGCTAGGTAGGGGGCAG 59.080 55.000 0.00 0.00 0.00 4.85
3782 4591 1.283905 GAAAAAGCTAGGTAGGGGGCA 59.716 52.381 0.00 0.00 0.00 5.36
3783 4592 1.564818 AGAAAAAGCTAGGTAGGGGGC 59.435 52.381 0.00 0.00 0.00 5.80
3784 4593 5.446260 TTTAGAAAAAGCTAGGTAGGGGG 57.554 43.478 0.00 0.00 0.00 5.40
3785 4594 5.357314 GCTTTTAGAAAAAGCTAGGTAGGGG 59.643 44.000 23.25 0.00 46.64 4.79
3786 4595 6.438259 GCTTTTAGAAAAAGCTAGGTAGGG 57.562 41.667 23.25 0.00 46.64 3.53
3796 4605 7.566760 AATTTGGTTGGGCTTTTAGAAAAAG 57.433 32.000 7.59 7.59 0.00 2.27
3797 4606 9.634021 ATTAATTTGGTTGGGCTTTTAGAAAAA 57.366 25.926 0.00 0.00 0.00 1.94
3798 4607 9.634021 AATTAATTTGGTTGGGCTTTTAGAAAA 57.366 25.926 0.00 0.00 0.00 2.29
3799 4608 9.634021 AAATTAATTTGGTTGGGCTTTTAGAAA 57.366 25.926 12.62 0.00 0.00 2.52
3800 4609 9.634021 AAAATTAATTTGGTTGGGCTTTTAGAA 57.366 25.926 14.04 0.00 0.00 2.10
3801 4610 9.634021 AAAAATTAATTTGGTTGGGCTTTTAGA 57.366 25.926 14.04 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.