Multiple sequence alignment - TraesCS4D01G306300

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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 TraesCS4D01G306300 chr4D 100.000 2447 0 0 1 2447 474604111 474601665 0.000000e+00 4519.0
1 TraesCS4D01G306300 chr4D 100.000 1978 0 0 4059 6036 474600053 474598076 0.000000e+00 3653.0
2 TraesCS4D01G306300 chr4D 100.000 992 0 0 2724 3715 474601388 474600397 0.000000e+00 1832.0
3 TraesCS4D01G306300 chr4D 86.477 1198 102 29 900 2046 474701376 474700188 0.000000e+00 1260.0
4 TraesCS4D01G306300 chr4D 77.901 991 153 36 4582 5542 474699044 474698090 1.900000e-154 556.0
5 TraesCS4D01G306300 chr4D 87.273 220 21 6 498 716 474701737 474701524 1.680000e-60 244.0
6 TraesCS4D01G306300 chr4D 90.291 103 10 0 1426 1528 8150937 8150835 1.060000e-27 135.0
7 TraesCS4D01G306300 chr4A 89.988 1698 108 25 4211 5885 681658030 681659688 0.000000e+00 2137.0
8 TraesCS4D01G306300 chr4A 85.947 1352 88 32 4188 5516 681610177 681611449 0.000000e+00 1351.0
9 TraesCS4D01G306300 chr4A 92.401 908 44 10 1550 2447 681653819 681654711 0.000000e+00 1271.0
10 TraesCS4D01G306300 chr4A 90.100 697 46 8 1557 2245 681593693 681594374 0.000000e+00 883.0
11 TraesCS4D01G306300 chr4A 88.759 685 47 10 897 1551 681592976 681593660 0.000000e+00 811.0
12 TraesCS4D01G306300 chr4A 86.695 699 58 15 880 1551 681653103 681653793 0.000000e+00 743.0
13 TraesCS4D01G306300 chr4A 91.279 516 31 4 2741 3247 681608601 681609111 0.000000e+00 691.0
14 TraesCS4D01G306300 chr4A 94.177 395 14 4 2741 3130 681654767 681655157 1.450000e-165 593.0
15 TraesCS4D01G306300 chr4A 91.011 356 24 8 5541 5891 681611445 681611797 1.970000e-129 473.0
16 TraesCS4D01G306300 chr4A 87.088 364 26 9 3355 3715 681656231 681656576 5.670000e-105 392.0
17 TraesCS4D01G306300 chr4A 90.036 281 21 3 3431 3709 681609789 681610064 2.070000e-94 357.0
18 TraesCS4D01G306300 chr4A 94.574 129 6 1 3310 3438 681609244 681609371 1.330000e-46 198.0
19 TraesCS4D01G306300 chr4A 95.192 104 4 1 2314 2416 681608365 681608468 4.840000e-36 163.0
20 TraesCS4D01G306300 chr4A 81.579 114 15 2 551 664 681652846 681652953 8.330000e-14 89.8
21 TraesCS4D01G306300 chr4A 86.885 61 6 2 3222 3280 490601900 490601960 3.900000e-07 67.6
22 TraesCS4D01G306300 chr4B 87.616 1728 114 33 4190 5890 598456191 598454537 0.000000e+00 1914.0
23 TraesCS4D01G306300 chr4B 85.940 1202 107 25 897 2046 599170607 599169416 0.000000e+00 1227.0
24 TraesCS4D01G306300 chr4B 93.095 840 28 8 714 1547 598459440 598458625 0.000000e+00 1203.0
25 TraesCS4D01G306300 chr4B 93.848 699 27 7 1550 2245 598458584 598457899 0.000000e+00 1038.0
26 TraesCS4D01G306300 chr4B 96.711 608 19 1 1 607 598460237 598459630 0.000000e+00 1011.0
27 TraesCS4D01G306300 chr4B 87.297 677 56 13 897 1548 598914012 598913341 0.000000e+00 747.0
28 TraesCS4D01G306300 chr4B 92.994 471 24 5 2744 3213 598457560 598457098 0.000000e+00 678.0
29 TraesCS4D01G306300 chr4B 87.959 490 50 6 1559 2046 598913303 598912821 2.440000e-158 569.0
30 TraesCS4D01G306300 chr4B 91.282 390 25 5 3310 3697 598456917 598456535 1.930000e-144 523.0
31 TraesCS4D01G306300 chr4B 88.918 388 31 3 998 1373 598603088 598602701 9.160000e-128 468.0
32 TraesCS4D01G306300 chr4B 76.721 915 151 35 4665 5546 598911558 598910673 2.560000e-123 453.0
33 TraesCS4D01G306300 chr4B 92.032 251 16 4 1796 2046 598602366 598602120 3.460000e-92 350.0
34 TraesCS4D01G306300 chr4B 94.022 184 9 2 2234 2415 598457880 598457697 1.660000e-70 278.0
35 TraesCS4D01G306300 chr4B 87.727 220 20 6 498 716 598914324 598914111 3.610000e-62 250.0
36 TraesCS4D01G306300 chr4B 87.727 220 20 6 498 716 599170961 599170748 3.610000e-62 250.0
37 TraesCS4D01G306300 chr4B 86.364 220 23 6 498 716 598603666 598603453 3.640000e-57 233.0
38 TraesCS4D01G306300 chr4B 96.800 125 4 0 592 716 598459604 598459480 6.130000e-50 209.0
39 TraesCS4D01G306300 chr4B 80.588 170 25 7 2908 3075 396453625 396453788 2.280000e-24 124.0
40 TraesCS4D01G306300 chr4B 83.088 136 22 1 1 135 598915199 598915064 8.220000e-24 122.0
41 TraesCS4D01G306300 chr4B 98.361 61 1 0 3247 3307 598456928 598456988 2.300000e-19 108.0
42 TraesCS4D01G306300 chr4B 89.655 58 2 3 3243 3297 587850326 587850382 3.020000e-08 71.3
43 TraesCS4D01G306300 chr3B 75.450 611 112 26 932 1528 13731862 13732448 4.640000e-66 263.0
44 TraesCS4D01G306300 chr3B 83.908 87 12 2 2919 3005 587988040 587988124 1.390000e-11 82.4
45 TraesCS4D01G306300 chr2D 96.104 154 6 0 5883 6036 81439075 81438922 1.000000e-62 252.0
46 TraesCS4D01G306300 chr2D 96.129 155 5 1 5882 6036 399036107 399035954 1.000000e-62 252.0
47 TraesCS4D01G306300 chr7A 94.805 154 8 0 5883 6036 694794394 694794241 2.170000e-59 241.0
48 TraesCS4D01G306300 chr7A 93.506 154 10 0 5883 6036 694931986 694931833 4.710000e-56 230.0
49 TraesCS4D01G306300 chr7A 93.506 154 10 0 5883 6036 694972537 694972384 4.710000e-56 230.0
50 TraesCS4D01G306300 chr7A 93.506 154 10 0 5883 6036 695058232 695058079 4.710000e-56 230.0
51 TraesCS4D01G306300 chr2B 94.805 154 8 0 5883 6036 731016743 731016590 2.170000e-59 241.0
52 TraesCS4D01G306300 chr2B 83.784 74 12 0 2917 2990 729137891 729137818 3.020000e-08 71.3
53 TraesCS4D01G306300 chr2B 83.333 66 9 1 3090 3153 539286169 539286104 6.530000e-05 60.2
54 TraesCS4D01G306300 chr3D 94.805 154 7 1 5883 6036 548987848 548988000 7.820000e-59 239.0
55 TraesCS4D01G306300 chr1D 94.194 155 8 1 5882 6036 450211747 450211594 1.010000e-57 235.0
56 TraesCS4D01G306300 chr1D 93.023 43 2 1 3238 3280 342132515 342132474 1.820000e-05 62.1
57 TraesCS4D01G306300 chr3A 74.778 563 97 31 979 1528 11704930 11704400 1.700000e-50 211.0
58 TraesCS4D01G306300 chr3A 87.097 124 16 0 1596 1719 11676816 11676693 2.270000e-29 141.0
59 TraesCS4D01G306300 chr3A 87.097 124 16 0 1596 1719 11704263 11704140 2.270000e-29 141.0
60 TraesCS4D01G306300 chr7D 82.653 98 17 0 2918 3015 230463721 230463818 3.000000e-13 87.9
61 TraesCS4D01G306300 chr6D 100.000 36 0 0 3245 3280 9669795 9669760 3.900000e-07 67.6
62 TraesCS4D01G306300 chr6D 100.000 36 0 0 3245 3280 24554565 24554530 3.900000e-07 67.6
63 TraesCS4D01G306300 chr6D 100.000 36 0 0 3245 3280 24554591 24554626 3.900000e-07 67.6
64 TraesCS4D01G306300 chr5A 88.679 53 2 4 3249 3300 219252539 219252588 1.820000e-05 62.1
65 TraesCS4D01G306300 chr5B 86.792 53 3 2 3251 3303 105763744 105763696 8.450000e-04 56.5


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 TraesCS4D01G306300 chr4D 474598076 474604111 6035 True 3334.666667 4519 100.000000 1 6036 3 chr4D.!!$R2 6035
1 TraesCS4D01G306300 chr4D 474698090 474701737 3647 True 686.666667 1260 83.883667 498 5542 3 chr4D.!!$R3 5044
2 TraesCS4D01G306300 chr4A 681652846 681659688 6842 False 870.966667 2137 88.654667 551 5885 6 chr4A.!!$F4 5334
3 TraesCS4D01G306300 chr4A 681592976 681594374 1398 False 847.000000 883 89.429500 897 2245 2 chr4A.!!$F2 1348
4 TraesCS4D01G306300 chr4A 681608365 681611797 3432 False 538.833333 1351 91.339833 2314 5891 6 chr4A.!!$F3 3577
5 TraesCS4D01G306300 chr4B 598454537 598460237 5700 True 856.750000 1914 93.296000 1 5890 8 chr4B.!!$R1 5889
6 TraesCS4D01G306300 chr4B 599169416 599170961 1545 True 738.500000 1227 86.833500 498 2046 2 chr4B.!!$R4 1548
7 TraesCS4D01G306300 chr4B 598910673 598915199 4526 True 428.200000 747 84.558400 1 5546 5 chr4B.!!$R3 5545
8 TraesCS4D01G306300 chr4B 598602120 598603666 1546 True 350.333333 468 89.104667 498 2046 3 chr4B.!!$R2 1548
9 TraesCS4D01G306300 chr3B 13731862 13732448 586 False 263.000000 263 75.450000 932 1528 1 chr3B.!!$F1 596

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
616 1242 1.439679 CACCTTTTCCGTGGTCTAGC 58.560 55.000 0.00 0.0 33.75 3.42 F
2298 3347 0.320421 GCCTACAACGGCTGACTCAA 60.320 55.000 0.00 0.0 46.63 3.02 F
2359 3409 1.229400 ACGCTTAAGGGGAGTGGGA 60.229 57.895 22.06 0.0 0.00 4.37 F
4094 6642 0.394938 TGCTGCCGGAGTGTCTTTTA 59.605 50.000 5.05 0.0 0.00 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2347 3396 0.042881 GTCCTACTCCCACTCCCCTT 59.957 60.000 0.00 0.00 0.00 3.95 R
4074 6563 1.166531 AAAAGACACTCCGGCAGCAC 61.167 55.000 0.00 0.00 0.00 4.40 R
4134 6682 8.523915 AAGGTTGATAACATTTGATGCTATCA 57.476 30.769 8.99 8.99 43.04 2.15 R
5905 10336 0.250858 CACATTGGAGGTGAGCCACA 60.251 55.000 7.49 0.00 38.54 4.17 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
527 1112 2.578586 AATCCAGCTGACATGGCCCC 62.579 60.000 17.39 0.00 37.76 5.80
616 1242 1.439679 CACCTTTTCCGTGGTCTAGC 58.560 55.000 0.00 0.00 33.75 3.42
664 1290 3.390639 AGAGATAGCCAGGATCCAACAAG 59.609 47.826 15.82 0.00 0.00 3.16
686 1312 9.010029 ACAAGTATGATTGTTAACTGTTTAGGG 57.990 33.333 7.22 0.00 40.47 3.53
736 1404 4.284490 GGGAGCTTTTTCTTTTGGAGGAAT 59.716 41.667 0.00 0.00 0.00 3.01
947 1623 9.810545 GCTTAACTACTCTATCATTTCTGTCTT 57.189 33.333 0.00 0.00 0.00 3.01
1073 1908 2.203181 GCAGCAGGATCCAGGAGC 60.203 66.667 15.82 12.15 0.00 4.70
1210 2048 1.535685 GGAATCATCAGCCCAGCCT 59.464 57.895 0.00 0.00 0.00 4.58
1310 2163 2.202623 CAGCGACGCCCTGTCTAC 60.203 66.667 17.79 0.00 45.87 2.59
1311 2164 2.675423 AGCGACGCCCTGTCTACA 60.675 61.111 17.79 0.00 45.87 2.74
1402 2264 1.594293 CTTTCCGGCGTGTCACAGT 60.594 57.895 6.01 0.00 0.00 3.55
1403 2265 1.153329 TTTCCGGCGTGTCACAGTT 60.153 52.632 6.01 0.00 0.00 3.16
1406 2268 1.667830 CCGGCGTGTCACAGTTGAT 60.668 57.895 6.01 0.00 33.11 2.57
1417 2279 1.225704 CAGTTGATGAGGAGGGCCC 59.774 63.158 16.46 16.46 33.31 5.80
1543 2501 4.034510 GCCTCAAGGTCTTTGAATATGTCG 59.965 45.833 0.00 0.00 44.84 4.35
1551 2519 5.368989 GTCTTTGAATATGTCGAATCCCCT 58.631 41.667 0.00 0.00 0.00 4.79
1552 2520 5.237344 GTCTTTGAATATGTCGAATCCCCTG 59.763 44.000 0.00 0.00 0.00 4.45
1555 2553 3.243737 TGAATATGTCGAATCCCCTGTCG 60.244 47.826 0.00 0.00 38.62 4.35
1581 2579 7.010091 GGGAAATGCTTAATTGATTTGGTTACG 59.990 37.037 0.00 0.00 0.00 3.18
1590 2588 9.557338 TTAATTGATTTGGTTACGTTATTTCCG 57.443 29.630 0.00 0.00 0.00 4.30
1653 2654 2.028130 AGATACGTGAAGGAGCTCCAG 58.972 52.381 33.90 20.23 38.89 3.86
1719 2720 2.430921 GAGACCGTGGTGCTCGTG 60.431 66.667 0.00 0.00 0.00 4.35
1977 2985 2.601562 GGCGTCCACCGTGATTATC 58.398 57.895 0.00 0.00 39.32 1.75
2020 3028 9.416794 CAAGTTATCATCAGTAATACTAGCTGG 57.583 37.037 0.00 0.00 0.00 4.85
2021 3029 8.713708 AGTTATCATCAGTAATACTAGCTGGT 57.286 34.615 8.18 8.18 0.00 4.00
2022 3030 8.580720 AGTTATCATCAGTAATACTAGCTGGTG 58.419 37.037 13.76 2.16 41.33 4.17
2023 3031 5.201713 TCATCAGTAATACTAGCTGGTGC 57.798 43.478 13.76 0.67 40.19 5.01
2073 3084 4.094887 TGCTCAATTGGAATCGTTAGCTTC 59.905 41.667 5.42 0.00 0.00 3.86
2074 3085 4.094887 GCTCAATTGGAATCGTTAGCTTCA 59.905 41.667 5.42 0.00 0.00 3.02
2075 3086 5.220931 GCTCAATTGGAATCGTTAGCTTCAT 60.221 40.000 5.42 0.00 0.00 2.57
2076 3087 6.678900 GCTCAATTGGAATCGTTAGCTTCATT 60.679 38.462 5.42 0.00 0.00 2.57
2077 3088 7.467267 GCTCAATTGGAATCGTTAGCTTCATTA 60.467 37.037 5.42 0.00 0.00 1.90
2179 3195 7.390027 AGAACATGTCTACAGCTCAAACTAAT 58.610 34.615 0.00 0.00 33.56 1.73
2180 3196 8.531982 AGAACATGTCTACAGCTCAAACTAATA 58.468 33.333 0.00 0.00 33.56 0.98
2181 3197 8.709386 AACATGTCTACAGCTCAAACTAATAG 57.291 34.615 0.00 0.00 0.00 1.73
2182 3198 7.841956 ACATGTCTACAGCTCAAACTAATAGT 58.158 34.615 0.00 0.00 0.00 2.12
2183 3199 8.967918 ACATGTCTACAGCTCAAACTAATAGTA 58.032 33.333 0.00 0.00 0.00 1.82
2184 3200 9.457110 CATGTCTACAGCTCAAACTAATAGTAG 57.543 37.037 0.00 0.00 0.00 2.57
2287 3336 1.673923 GGTAAGGGTGTCGCCTACAAC 60.674 57.143 1.66 0.00 45.78 3.32
2298 3347 0.320421 GCCTACAACGGCTGACTCAA 60.320 55.000 0.00 0.00 46.63 3.02
2359 3409 1.229400 ACGCTTAAGGGGAGTGGGA 60.229 57.895 22.06 0.00 0.00 4.37
2829 3933 9.618890 CTCTTTGGATTGAAGGATAAACATAGA 57.381 33.333 0.00 0.00 0.00 1.98
2998 4103 1.734465 CTTCGAGAAGTCCAATGCACC 59.266 52.381 4.76 0.00 33.87 5.01
3022 4127 3.380320 GCACTCTTTCTCTCTCTACCCTC 59.620 52.174 0.00 0.00 0.00 4.30
3023 4128 4.855340 CACTCTTTCTCTCTCTACCCTCT 58.145 47.826 0.00 0.00 0.00 3.69
3024 4129 4.881850 CACTCTTTCTCTCTCTACCCTCTC 59.118 50.000 0.00 0.00 0.00 3.20
3025 4130 4.079958 ACTCTTTCTCTCTCTACCCTCTCC 60.080 50.000 0.00 0.00 0.00 3.71
3072 4177 4.263462 TGTGTTTTCTCCTATGCACCATCT 60.263 41.667 0.00 0.00 0.00 2.90
3149 5106 3.700154 CATGTCATCTCAGTCCTACGTG 58.300 50.000 0.00 0.00 0.00 4.49
3163 5120 3.074412 CCTACGTGTTCAATTTCCTGCT 58.926 45.455 0.00 0.00 0.00 4.24
3176 5133 6.092122 TCAATTTCCTGCTATACAAACAGTCG 59.908 38.462 0.00 0.00 0.00 4.18
3247 5236 5.280011 GGTGATGTGAAGGGAAAGAAGAGTA 60.280 44.000 0.00 0.00 0.00 2.59
3250 5296 5.215252 TGTGAAGGGAAAGAAGAGTAGTG 57.785 43.478 0.00 0.00 0.00 2.74
3252 5298 5.544176 TGTGAAGGGAAAGAAGAGTAGTGAT 59.456 40.000 0.00 0.00 0.00 3.06
3257 5303 8.437274 AAGGGAAAGAAGAGTAGTGATCTAAA 57.563 34.615 0.00 0.00 0.00 1.85
3259 5305 8.536175 AGGGAAAGAAGAGTAGTGATCTAAAAG 58.464 37.037 0.00 0.00 0.00 2.27
3351 5412 9.816787 TTTTGGATACCTTAAGTGGTTATTTCT 57.183 29.630 0.97 0.00 41.22 2.52
3475 5963 7.122353 TGTGGGAGTAGTCAACTAGTTAGATTC 59.878 40.741 8.04 2.18 39.07 2.52
3603 6092 5.241506 AGAAGTGTTACACCATGTTGATTGG 59.758 40.000 12.28 0.00 40.26 3.16
3609 6098 6.945435 TGTTACACCATGTTGATTGGAACTAT 59.055 34.615 0.00 0.00 37.69 2.12
3689 6178 4.040936 AGAGAGAGTGCAAGAGTCCTAA 57.959 45.455 0.00 0.00 0.00 2.69
3701 6190 9.632807 GTGCAAGAGTCCTAATAGAATATGTAG 57.367 37.037 0.00 0.00 0.00 2.74
4094 6642 0.394938 TGCTGCCGGAGTGTCTTTTA 59.605 50.000 5.05 0.00 0.00 1.52
4099 6647 1.272807 CCGGAGTGTCTTTTAGGGGA 58.727 55.000 0.00 0.00 0.00 4.81
4113 6661 9.984190 GTCTTTTAGGGGACTATATCAACTTAG 57.016 37.037 0.00 0.00 43.94 2.18
4133 6681 9.436957 AACTTAGAAATAGTCAATCGACATTGT 57.563 29.630 0.00 0.00 45.23 2.71
4134 6682 9.436957 ACTTAGAAATAGTCAATCGACATTGTT 57.563 29.630 0.00 0.00 45.23 2.83
4135 6683 9.694520 CTTAGAAATAGTCAATCGACATTGTTG 57.305 33.333 0.00 0.00 45.23 3.33
4145 6693 6.315891 TCAATCGACATTGTTGATAGCATCAA 59.684 34.615 17.91 6.91 41.16 2.57
4239 7693 1.917955 AGCAATATGTTGACGACGACG 59.082 47.619 6.35 5.58 37.53 5.12
4301 7756 9.712305 ATACATCTTTATTTTCACTATCCTCCG 57.288 33.333 0.00 0.00 0.00 4.63
4315 7770 1.075050 TCCTCCGTGTCCACTCTAGTT 59.925 52.381 0.00 0.00 0.00 2.24
4434 7894 4.278975 ACTCAAAATCTCCCTGACACTC 57.721 45.455 0.00 0.00 0.00 3.51
4439 7900 5.532406 TCAAAATCTCCCTGACACTCAAAAG 59.468 40.000 0.00 0.00 0.00 2.27
4445 7906 4.199310 TCCCTGACACTCAAAAGACTTTG 58.801 43.478 0.06 0.00 42.88 2.77
4456 7917 7.009540 CACTCAAAAGACTTTGGATTGTTTCAC 59.990 37.037 12.43 0.00 41.98 3.18
4534 7999 8.080417 TCTCCGATACAAAATCTAATTAGGACG 58.920 37.037 12.54 5.72 0.00 4.79
4560 8025 6.127647 TGGCACATTCTTCAAGATGGTAATTC 60.128 38.462 0.00 0.00 0.00 2.17
4579 8044 1.735018 TCGACCACCAATTTATGCACG 59.265 47.619 0.00 0.00 0.00 5.34
4718 9068 3.848272 ATAAATGTTTGGCGGACACAG 57.152 42.857 0.00 0.00 0.00 3.66
4758 9119 0.037303 CAGTCTGGAGGCATGTGGTT 59.963 55.000 0.00 0.00 0.00 3.67
4778 9140 6.094603 GTGGTTGTAAGCATCAATCTCTTCAT 59.905 38.462 0.00 0.00 38.81 2.57
4801 9166 7.860373 TCATAGCAACAACAGAAAACATTGTAC 59.140 33.333 0.00 0.00 35.54 2.90
4802 9167 6.207691 AGCAACAACAGAAAACATTGTACT 57.792 33.333 0.00 0.00 35.54 2.73
4803 9168 6.035843 AGCAACAACAGAAAACATTGTACTG 58.964 36.000 13.30 13.30 35.54 2.74
4971 9337 4.082733 CGTCAACACAGAGGAGATTGTAGA 60.083 45.833 0.00 0.00 0.00 2.59
5013 9379 2.294233 ACCAACATAGCAGCAACAACAG 59.706 45.455 0.00 0.00 0.00 3.16
5038 9407 6.567050 CAGTGGCAGCAACAATTATTAAGAT 58.433 36.000 1.78 0.00 0.00 2.40
5043 9412 8.093307 TGGCAGCAACAATTATTAAGATTTGAA 58.907 29.630 10.73 0.00 0.00 2.69
5063 9448 8.891671 TTTGAAAATCAAGAAGAAGGATTTGG 57.108 30.769 0.00 0.00 40.17 3.28
5202 9594 5.704053 TGATATGCTATGGCTGATTTGTCTG 59.296 40.000 1.68 0.00 39.59 3.51
5236 9628 3.118261 GGTTGGATGCATGAGAACTAGGA 60.118 47.826 2.46 0.00 0.00 2.94
5243 9643 6.767902 GGATGCATGAGAACTAGGATACAAAA 59.232 38.462 2.46 0.00 41.41 2.44
5291 9691 2.294791 CGATCTAGAGGATGGTGGTCAC 59.705 54.545 0.00 0.00 34.33 3.67
5299 9699 2.376518 AGGATGGTGGTCACTCATTTGT 59.623 45.455 0.93 0.00 0.00 2.83
5358 9759 7.175119 AGTTGGTAGGAGTCAAGCTTTTTATTC 59.825 37.037 0.00 0.00 0.00 1.75
5367 9768 6.708949 AGTCAAGCTTTTTATTCGTCCACTTA 59.291 34.615 0.00 0.00 0.00 2.24
5382 9788 4.808364 GTCCACTTAGCTGTTCTGATCATC 59.192 45.833 0.00 0.00 0.00 2.92
5476 9890 8.588290 ATCTCACAAAATAGTAGTCTCTCACT 57.412 34.615 0.00 0.00 39.41 3.41
5493 9908 1.873591 CACTATAATGGGCGACAAGGC 59.126 52.381 0.00 0.00 45.91 4.35
5554 9975 0.252197 GTCCATAGCCACCCGAAACT 59.748 55.000 0.00 0.00 0.00 2.66
5622 10043 0.379669 GGATCAGGCAAATGCACGAG 59.620 55.000 7.80 0.00 44.36 4.18
5640 10062 5.790495 GCACGAGAAATTGTCTTTGTGATAC 59.210 40.000 12.08 0.00 41.83 2.24
5686 10110 8.530311 TGACCATTATTTTCTATGCAAACATGT 58.470 29.630 0.00 0.00 37.04 3.21
5808 10239 8.099364 TGATTCACAAAATCTTAAGAGGTCAC 57.901 34.615 11.53 0.00 0.00 3.67
5894 10325 2.702592 TTGCGGGTATTAGACAAGGG 57.297 50.000 0.00 0.00 0.00 3.95
5895 10326 1.575419 TGCGGGTATTAGACAAGGGT 58.425 50.000 0.00 0.00 0.00 4.34
5896 10327 1.910671 TGCGGGTATTAGACAAGGGTT 59.089 47.619 0.00 0.00 0.00 4.11
5897 10328 2.306512 TGCGGGTATTAGACAAGGGTTT 59.693 45.455 0.00 0.00 0.00 3.27
5898 10329 3.244981 TGCGGGTATTAGACAAGGGTTTT 60.245 43.478 0.00 0.00 0.00 2.43
5899 10330 4.019501 TGCGGGTATTAGACAAGGGTTTTA 60.020 41.667 0.00 0.00 0.00 1.52
5900 10331 4.573607 GCGGGTATTAGACAAGGGTTTTAG 59.426 45.833 0.00 0.00 0.00 1.85
5901 10332 5.121105 CGGGTATTAGACAAGGGTTTTAGG 58.879 45.833 0.00 0.00 0.00 2.69
5902 10333 5.443283 GGGTATTAGACAAGGGTTTTAGGG 58.557 45.833 0.00 0.00 0.00 3.53
5903 10334 5.044624 GGGTATTAGACAAGGGTTTTAGGGT 60.045 44.000 0.00 0.00 0.00 4.34
5904 10335 6.487828 GGTATTAGACAAGGGTTTTAGGGTT 58.512 40.000 0.00 0.00 0.00 4.11
5905 10336 6.950041 GGTATTAGACAAGGGTTTTAGGGTTT 59.050 38.462 0.00 0.00 0.00 3.27
5906 10337 6.911250 ATTAGACAAGGGTTTTAGGGTTTG 57.089 37.500 0.00 0.00 0.00 2.93
5907 10338 4.259933 AGACAAGGGTTTTAGGGTTTGT 57.740 40.909 0.00 0.00 0.00 2.83
5908 10339 3.958147 AGACAAGGGTTTTAGGGTTTGTG 59.042 43.478 0.00 0.00 0.00 3.33
5909 10340 3.035363 ACAAGGGTTTTAGGGTTTGTGG 58.965 45.455 0.00 0.00 0.00 4.17
5910 10341 1.712056 AGGGTTTTAGGGTTTGTGGC 58.288 50.000 0.00 0.00 0.00 5.01
5911 10342 1.219469 AGGGTTTTAGGGTTTGTGGCT 59.781 47.619 0.00 0.00 0.00 4.75
5912 10343 1.616865 GGGTTTTAGGGTTTGTGGCTC 59.383 52.381 0.00 0.00 0.00 4.70
5913 10344 2.312390 GGTTTTAGGGTTTGTGGCTCA 58.688 47.619 0.00 0.00 0.00 4.26
5914 10345 2.035449 GGTTTTAGGGTTTGTGGCTCAC 59.965 50.000 0.00 0.00 34.56 3.51
5915 10346 1.989706 TTTAGGGTTTGTGGCTCACC 58.010 50.000 3.33 0.00 32.73 4.02
5916 10347 1.145571 TTAGGGTTTGTGGCTCACCT 58.854 50.000 3.20 3.20 36.63 4.00
5917 10348 0.690762 TAGGGTTTGTGGCTCACCTC 59.309 55.000 1.02 0.00 36.63 3.85
5918 10349 1.603739 GGGTTTGTGGCTCACCTCC 60.604 63.158 3.33 3.55 36.63 4.30
5919 10350 1.150536 GGTTTGTGGCTCACCTCCA 59.849 57.895 3.33 0.00 36.63 3.86
5920 10351 0.467290 GGTTTGTGGCTCACCTCCAA 60.467 55.000 3.33 0.00 35.01 3.53
5921 10352 1.620822 GTTTGTGGCTCACCTCCAAT 58.379 50.000 3.33 0.00 35.01 3.16
5922 10353 1.270550 GTTTGTGGCTCACCTCCAATG 59.729 52.381 3.33 0.00 35.01 2.82
5923 10354 0.478072 TTGTGGCTCACCTCCAATGT 59.522 50.000 3.33 0.00 35.01 2.71
5924 10355 0.250858 TGTGGCTCACCTCCAATGTG 60.251 55.000 3.33 0.00 35.01 3.21
5925 10356 0.962356 GTGGCTCACCTCCAATGTGG 60.962 60.000 0.00 0.00 39.43 4.17
5926 10357 1.379044 GGCTCACCTCCAATGTGGG 60.379 63.158 0.00 0.00 38.32 4.61
5927 10358 1.379044 GCTCACCTCCAATGTGGGG 60.379 63.158 0.00 0.00 37.90 4.96
5928 10359 2.078452 CTCACCTCCAATGTGGGGT 58.922 57.895 0.00 0.00 40.30 4.95
5929 10360 4.421365 CACCTCCAATGTGGGGTG 57.579 61.111 15.89 15.89 45.56 4.61
5930 10361 4.348684 ACCTCCAATGTGGGGTGA 57.651 55.556 6.64 0.00 38.89 4.02
5931 10362 1.767692 ACCTCCAATGTGGGGTGAC 59.232 57.895 6.64 0.00 38.89 3.67
5952 10383 9.628500 GGTGACCTTTTCATTATATAAAGAGGT 57.372 33.333 8.90 8.90 36.32 3.85
5982 10413 8.942669 AACAATGTACAATACAATTACACGTG 57.057 30.769 15.48 15.48 42.76 4.49
5983 10414 7.523219 ACAATGTACAATACAATTACACGTGG 58.477 34.615 21.57 3.64 42.76 4.94
5984 10415 6.671614 ATGTACAATACAATTACACGTGGG 57.328 37.500 21.57 6.21 42.76 4.61
5985 10416 4.936411 TGTACAATACAATTACACGTGGGG 59.064 41.667 21.57 6.57 35.38 4.96
5986 10417 2.750712 ACAATACAATTACACGTGGGGC 59.249 45.455 21.57 0.00 0.00 5.80
5987 10418 2.047002 ATACAATTACACGTGGGGCC 57.953 50.000 21.57 0.00 0.00 5.80
5988 10419 0.985760 TACAATTACACGTGGGGCCT 59.014 50.000 21.57 0.00 0.00 5.19
5989 10420 0.985760 ACAATTACACGTGGGGCCTA 59.014 50.000 21.57 0.00 0.00 3.93
5990 10421 1.065709 ACAATTACACGTGGGGCCTAG 60.066 52.381 21.57 5.86 0.00 3.02
5991 10422 1.065709 CAATTACACGTGGGGCCTAGT 60.066 52.381 21.57 0.00 0.00 2.57
5992 10423 2.163810 ATTACACGTGGGGCCTAGTA 57.836 50.000 21.57 0.00 0.00 1.82
5993 10424 2.163810 TTACACGTGGGGCCTAGTAT 57.836 50.000 21.57 0.00 0.00 2.12
5994 10425 3.311167 TTACACGTGGGGCCTAGTATA 57.689 47.619 21.57 0.00 0.00 1.47
5995 10426 2.393630 ACACGTGGGGCCTAGTATAT 57.606 50.000 21.57 0.00 0.00 0.86
5996 10427 3.530928 ACACGTGGGGCCTAGTATATA 57.469 47.619 21.57 0.00 0.00 0.86
5997 10428 3.160269 ACACGTGGGGCCTAGTATATAC 58.840 50.000 21.57 4.60 0.00 1.47
5998 10429 3.159472 CACGTGGGGCCTAGTATATACA 58.841 50.000 15.18 0.94 0.00 2.29
5999 10430 3.192844 CACGTGGGGCCTAGTATATACAG 59.807 52.174 15.18 9.74 0.00 2.74
6000 10431 3.074985 ACGTGGGGCCTAGTATATACAGA 59.925 47.826 15.18 1.89 0.00 3.41
6001 10432 3.695060 CGTGGGGCCTAGTATATACAGAG 59.305 52.174 15.18 10.87 0.00 3.35
6002 10433 4.675038 GTGGGGCCTAGTATATACAGAGT 58.325 47.826 15.18 0.00 0.00 3.24
6003 10434 4.705991 GTGGGGCCTAGTATATACAGAGTC 59.294 50.000 15.18 4.20 0.00 3.36
6004 10435 4.606697 TGGGGCCTAGTATATACAGAGTCT 59.393 45.833 15.18 0.00 0.00 3.24
6005 10436 5.794289 TGGGGCCTAGTATATACAGAGTCTA 59.206 44.000 15.18 0.00 0.00 2.59
6006 10437 6.276330 TGGGGCCTAGTATATACAGAGTCTAA 59.724 42.308 15.18 0.00 0.00 2.10
6007 10438 6.602803 GGGGCCTAGTATATACAGAGTCTAAC 59.397 46.154 15.18 0.00 0.00 2.34
6008 10439 7.173722 GGGCCTAGTATATACAGAGTCTAACA 58.826 42.308 15.18 0.00 0.00 2.41
6009 10440 7.121020 GGGCCTAGTATATACAGAGTCTAACAC 59.879 44.444 15.18 0.00 0.00 3.32
6010 10441 7.121020 GGCCTAGTATATACAGAGTCTAACACC 59.879 44.444 15.18 0.00 0.00 4.16
6011 10442 7.121020 GCCTAGTATATACAGAGTCTAACACCC 59.879 44.444 15.18 0.00 0.00 4.61
6012 10443 8.384718 CCTAGTATATACAGAGTCTAACACCCT 58.615 40.741 15.18 0.00 0.00 4.34
6013 10444 9.439500 CTAGTATATACAGAGTCTAACACCCTC 57.561 40.741 15.18 0.00 0.00 4.30
6014 10445 7.232910 AGTATATACAGAGTCTAACACCCTCC 58.767 42.308 15.18 0.00 0.00 4.30
6015 10446 1.939980 ACAGAGTCTAACACCCTCCC 58.060 55.000 0.00 0.00 0.00 4.30
6016 10447 1.433592 ACAGAGTCTAACACCCTCCCT 59.566 52.381 0.00 0.00 0.00 4.20
6017 10448 2.104170 CAGAGTCTAACACCCTCCCTC 58.896 57.143 0.00 0.00 0.00 4.30
6018 10449 1.717077 AGAGTCTAACACCCTCCCTCA 59.283 52.381 0.00 0.00 0.00 3.86
6019 10450 2.111972 AGAGTCTAACACCCTCCCTCAA 59.888 50.000 0.00 0.00 0.00 3.02
6020 10451 3.108376 GAGTCTAACACCCTCCCTCAAT 58.892 50.000 0.00 0.00 0.00 2.57
6021 10452 3.108376 AGTCTAACACCCTCCCTCAATC 58.892 50.000 0.00 0.00 0.00 2.67
6022 10453 3.108376 GTCTAACACCCTCCCTCAATCT 58.892 50.000 0.00 0.00 0.00 2.40
6023 10454 3.519913 GTCTAACACCCTCCCTCAATCTT 59.480 47.826 0.00 0.00 0.00 2.40
6024 10455 4.715297 GTCTAACACCCTCCCTCAATCTTA 59.285 45.833 0.00 0.00 0.00 2.10
6025 10456 5.189145 GTCTAACACCCTCCCTCAATCTTAA 59.811 44.000 0.00 0.00 0.00 1.85
6026 10457 4.302559 AACACCCTCCCTCAATCTTAAC 57.697 45.455 0.00 0.00 0.00 2.01
6027 10458 2.576648 ACACCCTCCCTCAATCTTAACC 59.423 50.000 0.00 0.00 0.00 2.85
6028 10459 1.838077 ACCCTCCCTCAATCTTAACCG 59.162 52.381 0.00 0.00 0.00 4.44
6029 10460 1.838077 CCCTCCCTCAATCTTAACCGT 59.162 52.381 0.00 0.00 0.00 4.83
6030 10461 2.420129 CCCTCCCTCAATCTTAACCGTG 60.420 54.545 0.00 0.00 0.00 4.94
6031 10462 2.280628 CTCCCTCAATCTTAACCGTGC 58.719 52.381 0.00 0.00 0.00 5.34
6032 10463 1.906574 TCCCTCAATCTTAACCGTGCT 59.093 47.619 0.00 0.00 0.00 4.40
6033 10464 2.093658 TCCCTCAATCTTAACCGTGCTC 60.094 50.000 0.00 0.00 0.00 4.26
6034 10465 2.354704 CCCTCAATCTTAACCGTGCTCA 60.355 50.000 0.00 0.00 0.00 4.26
6035 10466 2.932614 CCTCAATCTTAACCGTGCTCAG 59.067 50.000 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.442047 CCTTTATATATGATGTCCTTCCTGAAC 57.558 37.037 0.00 0.00 0.00 3.18
239 241 8.210946 TGTCTAATTGAAGTATAAGTGATGGGG 58.789 37.037 0.00 0.00 0.00 4.96
465 1042 9.868277 CTCTGTCTCAAAATGTAAGTATCTTCT 57.132 33.333 0.00 0.00 0.00 2.85
527 1112 7.040478 TGTTTGACTCTCCTATTGTCCAAATTG 60.040 37.037 0.00 0.00 0.00 2.32
616 1242 5.048224 GCCTGGATCCAGTGAAAATGATATG 60.048 44.000 34.49 18.31 42.15 1.78
645 1271 3.567478 ACTTGTTGGATCCTGGCTATC 57.433 47.619 14.23 0.00 0.00 2.08
664 1290 8.241367 CCAACCCTAAACAGTTAACAATCATAC 58.759 37.037 8.61 0.00 0.00 2.39
686 1312 2.038426 AGCCTAAAACAAATGGGCCAAC 59.962 45.455 11.89 0.00 43.36 3.77
947 1623 0.608130 ACCTAGCTCGTGCAACATCA 59.392 50.000 12.58 0.00 42.74 3.07
1106 1944 3.695606 GGAGCGCCTGGAGACACA 61.696 66.667 2.29 0.00 35.60 3.72
1186 2024 1.614711 GGCTGATGATTCCCCCACA 59.385 57.895 0.00 0.00 0.00 4.17
1191 2029 1.530183 GGCTGGGCTGATGATTCCC 60.530 63.158 0.00 0.00 40.47 3.97
1210 2048 2.743538 GTGCACAGCCGCATCAGA 60.744 61.111 13.17 0.00 45.26 3.27
1297 2150 0.737715 CAGCTTGTAGACAGGGCGTC 60.738 60.000 0.00 0.00 45.77 5.19
1308 2161 1.234821 CGCCAAAGTTCCAGCTTGTA 58.765 50.000 0.00 0.00 0.00 2.41
1310 2163 1.372128 GCGCCAAAGTTCCAGCTTG 60.372 57.895 0.00 0.00 0.00 4.01
1311 2164 1.529244 AGCGCCAAAGTTCCAGCTT 60.529 52.632 2.29 0.00 0.00 3.74
1402 2264 2.696125 GGGGGCCCTCCTCATCAA 60.696 66.667 24.38 0.00 35.56 2.57
1403 2265 4.037413 TGGGGGCCCTCCTCATCA 62.037 66.667 22.40 6.97 42.20 3.07
1406 2268 4.608514 TTGTGGGGGCCCTCCTCA 62.609 66.667 22.40 22.67 45.63 3.86
1551 2519 5.913137 AATCAATTAAGCATTTCCCGACA 57.087 34.783 0.00 0.00 0.00 4.35
1552 2520 5.519927 CCAAATCAATTAAGCATTTCCCGAC 59.480 40.000 0.00 0.00 0.00 4.79
1555 2553 7.010091 CGTAACCAAATCAATTAAGCATTTCCC 59.990 37.037 0.00 0.00 0.00 3.97
1581 2579 5.047847 TCCATCTGATCGAACGGAAATAAC 58.952 41.667 8.40 0.00 0.00 1.89
1590 2588 2.555199 CCCTTGTCCATCTGATCGAAC 58.445 52.381 0.00 0.00 0.00 3.95
1977 2985 1.756408 TTGCCTTTGCCATGGTGGTG 61.756 55.000 14.67 1.86 40.46 4.17
2020 3028 1.627424 GTGGATAACGTACGCGCAC 59.373 57.895 16.72 1.24 42.83 5.34
2021 3029 4.075997 GTGGATAACGTACGCGCA 57.924 55.556 16.72 0.16 42.83 6.09
2047 3057 2.857592 ACGATTCCAATTGAGCATGC 57.142 45.000 10.51 10.51 0.00 4.06
2077 3088 9.758651 GTTTGAATTTTCTACAGGGTACAAATT 57.241 29.630 0.00 0.00 0.00 1.82
2124 3140 4.494484 GCACACCCCTTCAATTATTTCAC 58.506 43.478 0.00 0.00 0.00 3.18
2179 3195 9.142515 CATACGTCCACAACATTTTTACTACTA 57.857 33.333 0.00 0.00 0.00 1.82
2180 3196 7.360607 GCATACGTCCACAACATTTTTACTACT 60.361 37.037 0.00 0.00 0.00 2.57
2181 3197 6.739550 GCATACGTCCACAACATTTTTACTAC 59.260 38.462 0.00 0.00 0.00 2.73
2182 3198 6.427242 TGCATACGTCCACAACATTTTTACTA 59.573 34.615 0.00 0.00 0.00 1.82
2183 3199 5.239744 TGCATACGTCCACAACATTTTTACT 59.760 36.000 0.00 0.00 0.00 2.24
2184 3200 5.453648 TGCATACGTCCACAACATTTTTAC 58.546 37.500 0.00 0.00 0.00 2.01
2287 3336 0.247460 TGGTGAGATTGAGTCAGCCG 59.753 55.000 0.00 0.00 40.93 5.52
2298 3347 4.279145 ACAACTATCCTACGTGGTGAGAT 58.721 43.478 0.00 0.00 37.07 2.75
2347 3396 0.042881 GTCCTACTCCCACTCCCCTT 59.957 60.000 0.00 0.00 0.00 3.95
2359 3409 5.036916 TCATATTTTGAGTGGGGTCCTACT 58.963 41.667 5.69 5.69 0.00 2.57
2798 3902 3.679389 TCCTTCAATCCAAAGAGAGTGC 58.321 45.455 0.00 0.00 32.02 4.40
2998 4103 3.130340 GGGTAGAGAGAGAAAGAGTGCAG 59.870 52.174 0.00 0.00 0.00 4.41
3022 4127 2.468301 TGGAGGATTGAGAGAGGGAG 57.532 55.000 0.00 0.00 0.00 4.30
3023 4128 2.948889 TTGGAGGATTGAGAGAGGGA 57.051 50.000 0.00 0.00 0.00 4.20
3024 4129 4.516652 ATTTTGGAGGATTGAGAGAGGG 57.483 45.455 0.00 0.00 0.00 4.30
3025 4130 5.994250 TGTATTTTGGAGGATTGAGAGAGG 58.006 41.667 0.00 0.00 0.00 3.69
3072 4177 9.412460 ACATGAATTTCATTAGAGATGCCTTTA 57.588 29.630 9.19 0.00 34.28 1.85
3149 5106 7.593825 ACTGTTTGTATAGCAGGAAATTGAAC 58.406 34.615 0.00 0.00 34.79 3.18
3163 5120 7.972277 GTCTTAGTTGGATCGACTGTTTGTATA 59.028 37.037 9.84 0.00 29.93 1.47
3224 5184 4.646572 ACTCTTCTTTCCCTTCACATCAC 58.353 43.478 0.00 0.00 0.00 3.06
3297 5343 9.452287 GGTACTCCCTCTGTACTCTAATATAAG 57.548 40.741 0.00 0.00 39.89 1.73
3298 5344 9.180282 AGGTACTCCCTCTGTACTCTAATATAA 57.820 37.037 0.00 0.00 40.71 0.98
3300 5346 7.651229 AGGTACTCCCTCTGTACTCTAATAT 57.349 40.000 0.00 0.00 40.71 1.28
3308 5354 4.285260 TCCAAAAAGGTACTCCCTCTGTAC 59.715 45.833 0.00 0.00 45.47 2.90
3395 5456 9.406828 CAATATGATTGGCATTAACAGAGAATG 57.593 33.333 0.00 0.00 38.44 2.67
3438 5924 4.595986 ACTACTCCCACACACAAAAACTT 58.404 39.130 0.00 0.00 0.00 2.66
3475 5963 6.655003 AGAAATCAATGGGTAGTGTACAACAG 59.345 38.462 0.00 0.00 0.00 3.16
3585 6074 5.705609 AGTTCCAATCAACATGGTGTAAC 57.294 39.130 11.27 8.70 39.09 2.50
3668 6157 2.603075 AGGACTCTTGCACTCTCTCT 57.397 50.000 0.00 0.00 0.00 3.10
3669 6158 5.825679 TCTATTAGGACTCTTGCACTCTCTC 59.174 44.000 0.00 0.00 0.00 3.20
4073 6562 3.537206 AAGACACTCCGGCAGCACC 62.537 63.158 0.00 0.00 0.00 5.01
4074 6563 1.166531 AAAAGACACTCCGGCAGCAC 61.167 55.000 0.00 0.00 0.00 4.40
4087 6635 9.984190 CTAAGTTGATATAGTCCCCTAAAAGAC 57.016 37.037 0.00 0.00 0.00 3.01
4094 6642 9.900112 ACTATTTCTAAGTTGATATAGTCCCCT 57.100 33.333 10.03 0.00 36.92 4.79
4113 6661 9.855361 CTATCAACAATGTCGATTGACTATTTC 57.145 33.333 14.27 0.00 45.70 2.17
4134 6682 8.523915 AAGGTTGATAACATTTGATGCTATCA 57.476 30.769 8.99 8.99 43.04 2.15
4135 6683 9.807649 AAAAGGTTGATAACATTTGATGCTATC 57.192 29.630 5.28 4.99 43.69 2.08
4434 7894 7.832503 AAGTGAAACAATCCAAAGTCTTTTG 57.167 32.000 0.00 0.00 41.43 2.44
4516 7978 5.123344 GTGCCACGTCCTAATTAGATTTTGT 59.877 40.000 14.28 2.59 0.00 2.83
4534 7999 2.821969 ACCATCTTGAAGAATGTGCCAC 59.178 45.455 0.00 0.00 0.00 5.01
4560 8025 1.735018 TCGTGCATAAATTGGTGGTCG 59.265 47.619 0.00 0.00 0.00 4.79
4693 9043 5.241949 TGTGTCCGCCAAACATTTATAAAGT 59.758 36.000 3.94 0.02 0.00 2.66
4694 9044 5.704888 TGTGTCCGCCAAACATTTATAAAG 58.295 37.500 3.94 0.00 0.00 1.85
4695 9045 5.241949 ACTGTGTCCGCCAAACATTTATAAA 59.758 36.000 0.00 0.00 0.00 1.40
4696 9046 4.762765 ACTGTGTCCGCCAAACATTTATAA 59.237 37.500 0.00 0.00 0.00 0.98
4699 9049 2.577700 ACTGTGTCCGCCAAACATTTA 58.422 42.857 0.00 0.00 0.00 1.40
4718 9068 8.464404 AGACTGAAGTTTAACCCTTTTTACAAC 58.536 33.333 0.00 0.00 0.00 3.32
4758 9119 6.585416 TGCTATGAAGAGATTGATGCTTACA 58.415 36.000 0.00 0.00 0.00 2.41
4778 9140 7.192913 CAGTACAATGTTTTCTGTTGTTGCTA 58.807 34.615 0.00 0.00 37.30 3.49
4971 9337 3.550437 ACAGTGCAGAGTTGAGTCTTT 57.450 42.857 0.00 0.00 0.00 2.52
5013 9379 2.660189 ATAATTGTTGCTGCCACTGC 57.340 45.000 5.42 0.00 38.26 4.40
5038 9407 8.703743 TCCAAATCCTTCTTCTTGATTTTCAAA 58.296 29.630 0.00 0.00 36.77 2.69
5043 9412 8.884124 TGTATCCAAATCCTTCTTCTTGATTT 57.116 30.769 0.00 0.00 38.80 2.17
5116 9504 3.304257 CGACCTCTGCATTAATTGATGGC 60.304 47.826 11.75 5.31 0.00 4.40
5126 9515 1.995376 AAAAACCCGACCTCTGCATT 58.005 45.000 0.00 0.00 0.00 3.56
5163 9554 6.102897 AGCATATCAGGTCATTACACCTAC 57.897 41.667 0.00 0.00 45.81 3.18
5165 9556 9.635155 GCCATAGCATATCAGGTCATTACACCT 62.635 44.444 0.00 0.00 42.93 4.00
5236 9628 8.995027 TGGCTTATACATCTTCCATTTTGTAT 57.005 30.769 0.00 0.00 38.47 2.29
5243 9643 6.319658 CACAACTTGGCTTATACATCTTCCAT 59.680 38.462 0.00 0.00 0.00 3.41
5291 9691 3.614870 GCACTAAAAGGCCCACAAATGAG 60.615 47.826 0.00 0.00 0.00 2.90
5299 9699 1.892474 GATTGTGCACTAAAAGGCCCA 59.108 47.619 19.41 0.00 0.00 5.36
5343 9743 5.358298 AGTGGACGAATAAAAAGCTTGAC 57.642 39.130 0.00 0.00 0.00 3.18
5358 9759 2.724977 TCAGAACAGCTAAGTGGACG 57.275 50.000 0.00 0.00 0.00 4.79
5367 9768 3.383620 GATCCGATGATCAGAACAGCT 57.616 47.619 0.09 0.00 45.63 4.24
5382 9788 1.961277 GTAAGGGCGCCATGATCCG 60.961 63.158 30.85 0.00 0.00 4.18
5476 9890 1.202758 CCTGCCTTGTCGCCCATTATA 60.203 52.381 0.00 0.00 0.00 0.98
5543 9964 1.066454 GTGACCAAAAGTTTCGGGTGG 59.934 52.381 14.66 9.09 32.77 4.61
5640 10062 7.936584 TGGTCAAAGTACCATCTTAAAAACTG 58.063 34.615 0.00 0.00 44.68 3.16
5808 10239 9.790389 GAGGTGTACCGATCTAATCAATTATAG 57.210 37.037 0.00 0.00 42.08 1.31
5876 10307 1.575419 ACCCTTGTCTAATACCCGCA 58.425 50.000 0.00 0.00 0.00 5.69
5877 10308 2.704464 AACCCTTGTCTAATACCCGC 57.296 50.000 0.00 0.00 0.00 6.13
5878 10309 5.121105 CCTAAAACCCTTGTCTAATACCCG 58.879 45.833 0.00 0.00 0.00 5.28
5879 10310 5.044624 ACCCTAAAACCCTTGTCTAATACCC 60.045 44.000 0.00 0.00 0.00 3.69
5881 10312 7.449395 ACAAACCCTAAAACCCTTGTCTAATAC 59.551 37.037 0.00 0.00 0.00 1.89
5882 10313 7.449086 CACAAACCCTAAAACCCTTGTCTAATA 59.551 37.037 0.00 0.00 0.00 0.98
5883 10314 6.266786 CACAAACCCTAAAACCCTTGTCTAAT 59.733 38.462 0.00 0.00 0.00 1.73
5884 10315 5.595133 CACAAACCCTAAAACCCTTGTCTAA 59.405 40.000 0.00 0.00 0.00 2.10
5887 10318 3.069016 CCACAAACCCTAAAACCCTTGTC 59.931 47.826 0.00 0.00 0.00 3.18
5889 10320 2.224185 GCCACAAACCCTAAAACCCTTG 60.224 50.000 0.00 0.00 0.00 3.61
5891 10322 1.219469 AGCCACAAACCCTAAAACCCT 59.781 47.619 0.00 0.00 0.00 4.34
5893 10324 2.035449 GTGAGCCACAAACCCTAAAACC 59.965 50.000 1.01 0.00 34.08 3.27
5894 10325 2.035449 GGTGAGCCACAAACCCTAAAAC 59.965 50.000 7.49 0.00 35.86 2.43
5895 10326 2.091555 AGGTGAGCCACAAACCCTAAAA 60.092 45.455 7.49 0.00 35.86 1.52
5896 10327 1.497286 AGGTGAGCCACAAACCCTAAA 59.503 47.619 7.49 0.00 35.86 1.85
5897 10328 1.073284 GAGGTGAGCCACAAACCCTAA 59.927 52.381 7.49 0.00 35.86 2.69
5898 10329 0.690762 GAGGTGAGCCACAAACCCTA 59.309 55.000 7.49 0.00 35.86 3.53
5899 10330 1.456287 GAGGTGAGCCACAAACCCT 59.544 57.895 7.49 0.00 35.86 4.34
5900 10331 1.603739 GGAGGTGAGCCACAAACCC 60.604 63.158 7.49 0.32 35.86 4.11
5901 10332 0.467290 TTGGAGGTGAGCCACAAACC 60.467 55.000 7.49 7.37 35.86 3.27
5902 10333 1.270550 CATTGGAGGTGAGCCACAAAC 59.729 52.381 7.49 0.00 37.41 2.93
5903 10334 1.133513 ACATTGGAGGTGAGCCACAAA 60.134 47.619 7.49 0.00 37.41 2.83
5904 10335 0.478072 ACATTGGAGGTGAGCCACAA 59.522 50.000 7.49 0.00 37.95 3.33
5905 10336 0.250858 CACATTGGAGGTGAGCCACA 60.251 55.000 7.49 0.00 38.54 4.17
5906 10337 0.962356 CCACATTGGAGGTGAGCCAC 60.962 60.000 0.00 0.00 40.96 5.01
5907 10338 1.379916 CCACATTGGAGGTGAGCCA 59.620 57.895 0.00 0.00 40.96 4.75
5908 10339 1.379044 CCCACATTGGAGGTGAGCC 60.379 63.158 0.00 0.00 40.96 4.70
5909 10340 1.379044 CCCCACATTGGAGGTGAGC 60.379 63.158 0.00 0.00 40.96 4.26
5910 10341 2.078452 ACCCCACATTGGAGGTGAG 58.922 57.895 4.98 0.00 40.96 3.51
5911 10342 4.348684 ACCCCACATTGGAGGTGA 57.651 55.556 4.98 0.00 40.96 4.02
5912 10343 4.421365 CACCCCACATTGGAGGTG 57.579 61.111 14.63 14.63 45.56 4.00
5913 10344 1.767692 GTCACCCCACATTGGAGGT 59.232 57.895 0.00 0.00 40.96 3.85
5914 10345 1.000896 GGTCACCCCACATTGGAGG 60.001 63.158 0.00 0.00 40.96 4.30
5915 10346 0.405585 AAGGTCACCCCACATTGGAG 59.594 55.000 0.00 0.00 40.96 3.86
5916 10347 0.856982 AAAGGTCACCCCACATTGGA 59.143 50.000 0.00 0.00 40.96 3.53
5917 10348 1.618343 GAAAAGGTCACCCCACATTGG 59.382 52.381 0.00 0.00 37.25 3.16
5918 10349 2.315176 TGAAAAGGTCACCCCACATTG 58.685 47.619 0.00 0.00 34.66 2.82
5919 10350 2.765689 TGAAAAGGTCACCCCACATT 57.234 45.000 0.00 0.00 34.66 2.71
5920 10351 2.999185 ATGAAAAGGTCACCCCACAT 57.001 45.000 0.00 0.00 39.72 3.21
5921 10352 2.765689 AATGAAAAGGTCACCCCACA 57.234 45.000 0.00 0.00 39.72 4.17
5922 10353 8.528044 TTTATATAATGAAAAGGTCACCCCAC 57.472 34.615 0.00 0.00 39.72 4.61
5923 10354 8.561769 TCTTTATATAATGAAAAGGTCACCCCA 58.438 33.333 8.26 0.00 39.72 4.96
5924 10355 8.990163 TCTTTATATAATGAAAAGGTCACCCC 57.010 34.615 8.26 0.00 39.72 4.95
5925 10356 9.067986 CCTCTTTATATAATGAAAAGGTCACCC 57.932 37.037 11.11 0.00 39.72 4.61
5926 10357 9.628500 ACCTCTTTATATAATGAAAAGGTCACC 57.372 33.333 11.11 0.00 39.72 4.02
5957 10388 8.018520 CCACGTGTAATTGTATTGTACATTGTT 58.981 33.333 15.65 0.00 38.68 2.83
5958 10389 7.361371 CCCACGTGTAATTGTATTGTACATTGT 60.361 37.037 15.65 0.00 38.68 2.71
5959 10390 6.964370 CCCACGTGTAATTGTATTGTACATTG 59.036 38.462 15.65 0.00 38.68 2.82
5960 10391 6.094325 CCCCACGTGTAATTGTATTGTACATT 59.906 38.462 15.65 0.00 38.68 2.71
5961 10392 5.587043 CCCCACGTGTAATTGTATTGTACAT 59.413 40.000 15.65 0.00 38.68 2.29
5962 10393 4.936411 CCCCACGTGTAATTGTATTGTACA 59.064 41.667 15.65 0.00 36.79 2.90
5963 10394 4.201841 GCCCCACGTGTAATTGTATTGTAC 60.202 45.833 15.65 0.00 0.00 2.90
5964 10395 3.940221 GCCCCACGTGTAATTGTATTGTA 59.060 43.478 15.65 0.00 0.00 2.41
5965 10396 2.750712 GCCCCACGTGTAATTGTATTGT 59.249 45.455 15.65 0.00 0.00 2.71
5966 10397 2.098443 GGCCCCACGTGTAATTGTATTG 59.902 50.000 15.65 0.00 0.00 1.90
5967 10398 2.025699 AGGCCCCACGTGTAATTGTATT 60.026 45.455 15.65 0.00 0.00 1.89
5968 10399 1.562475 AGGCCCCACGTGTAATTGTAT 59.438 47.619 15.65 0.00 0.00 2.29
5969 10400 0.985760 AGGCCCCACGTGTAATTGTA 59.014 50.000 15.65 0.00 0.00 2.41
5970 10401 0.985760 TAGGCCCCACGTGTAATTGT 59.014 50.000 15.65 0.00 0.00 2.71
5971 10402 1.065709 ACTAGGCCCCACGTGTAATTG 60.066 52.381 15.65 0.00 0.00 2.32
5972 10403 1.282382 ACTAGGCCCCACGTGTAATT 58.718 50.000 15.65 0.00 0.00 1.40
5973 10404 2.163810 TACTAGGCCCCACGTGTAAT 57.836 50.000 15.65 0.00 0.00 1.89
5974 10405 2.163810 ATACTAGGCCCCACGTGTAA 57.836 50.000 15.65 0.00 0.00 2.41
5975 10406 3.530928 ATATACTAGGCCCCACGTGTA 57.469 47.619 15.65 0.00 0.00 2.90
5976 10407 2.393630 ATATACTAGGCCCCACGTGT 57.606 50.000 15.65 0.00 0.00 4.49
5977 10408 3.159472 TGTATATACTAGGCCCCACGTG 58.841 50.000 9.08 9.08 0.00 4.49
5978 10409 3.074985 TCTGTATATACTAGGCCCCACGT 59.925 47.826 13.89 0.00 0.00 4.49
5979 10410 3.693807 TCTGTATATACTAGGCCCCACG 58.306 50.000 13.89 0.00 0.00 4.94
5980 10411 4.675038 ACTCTGTATATACTAGGCCCCAC 58.325 47.826 13.89 0.00 0.00 4.61
5981 10412 4.606697 AGACTCTGTATATACTAGGCCCCA 59.393 45.833 13.89 0.00 0.00 4.96
5982 10413 5.195848 AGACTCTGTATATACTAGGCCCC 57.804 47.826 13.89 4.09 0.00 5.80
5983 10414 7.121020 GTGTTAGACTCTGTATATACTAGGCCC 59.879 44.444 13.89 5.82 0.00 5.80
5984 10415 7.121020 GGTGTTAGACTCTGTATATACTAGGCC 59.879 44.444 13.89 0.00 0.00 5.19
5985 10416 7.121020 GGGTGTTAGACTCTGTATATACTAGGC 59.879 44.444 13.89 12.62 0.00 3.93
5986 10417 8.384718 AGGGTGTTAGACTCTGTATATACTAGG 58.615 40.741 13.89 6.29 32.30 3.02
5987 10418 9.439500 GAGGGTGTTAGACTCTGTATATACTAG 57.561 40.741 13.89 12.73 34.47 2.57
5988 10419 8.381636 GGAGGGTGTTAGACTCTGTATATACTA 58.618 40.741 13.89 1.97 34.47 1.82
5989 10420 7.232910 GGAGGGTGTTAGACTCTGTATATACT 58.767 42.308 13.89 0.00 34.47 2.12
5990 10421 6.433716 GGGAGGGTGTTAGACTCTGTATATAC 59.566 46.154 5.89 5.89 34.47 1.47
5991 10422 6.334774 AGGGAGGGTGTTAGACTCTGTATATA 59.665 42.308 0.00 0.00 34.47 0.86
5992 10423 5.136392 AGGGAGGGTGTTAGACTCTGTATAT 59.864 44.000 0.00 0.00 34.47 0.86
5993 10424 4.481280 AGGGAGGGTGTTAGACTCTGTATA 59.519 45.833 0.00 0.00 34.47 1.47
5994 10425 3.272551 AGGGAGGGTGTTAGACTCTGTAT 59.727 47.826 0.00 0.00 34.47 2.29
5995 10426 2.653366 AGGGAGGGTGTTAGACTCTGTA 59.347 50.000 0.00 0.00 34.47 2.74
5996 10427 1.433592 AGGGAGGGTGTTAGACTCTGT 59.566 52.381 0.00 0.00 34.47 3.41
5997 10428 2.104170 GAGGGAGGGTGTTAGACTCTG 58.896 57.143 0.00 0.00 34.47 3.35
5998 10429 1.717077 TGAGGGAGGGTGTTAGACTCT 59.283 52.381 0.00 0.00 38.54 3.24
5999 10430 2.233305 TGAGGGAGGGTGTTAGACTC 57.767 55.000 0.00 0.00 0.00 3.36
6000 10431 2.715763 TTGAGGGAGGGTGTTAGACT 57.284 50.000 0.00 0.00 0.00 3.24
6001 10432 3.108376 AGATTGAGGGAGGGTGTTAGAC 58.892 50.000 0.00 0.00 0.00 2.59
6002 10433 3.491766 AGATTGAGGGAGGGTGTTAGA 57.508 47.619 0.00 0.00 0.00 2.10
6003 10434 5.429130 GTTAAGATTGAGGGAGGGTGTTAG 58.571 45.833 0.00 0.00 0.00 2.34
6004 10435 4.226620 GGTTAAGATTGAGGGAGGGTGTTA 59.773 45.833 0.00 0.00 0.00 2.41
6005 10436 3.010250 GGTTAAGATTGAGGGAGGGTGTT 59.990 47.826 0.00 0.00 0.00 3.32
6006 10437 2.576648 GGTTAAGATTGAGGGAGGGTGT 59.423 50.000 0.00 0.00 0.00 4.16
6007 10438 2.420129 CGGTTAAGATTGAGGGAGGGTG 60.420 54.545 0.00 0.00 0.00 4.61
6008 10439 1.838077 CGGTTAAGATTGAGGGAGGGT 59.162 52.381 0.00 0.00 0.00 4.34
6009 10440 1.838077 ACGGTTAAGATTGAGGGAGGG 59.162 52.381 0.00 0.00 0.00 4.30
6010 10441 2.906354 CACGGTTAAGATTGAGGGAGG 58.094 52.381 0.00 0.00 0.00 4.30
6011 10442 2.093447 AGCACGGTTAAGATTGAGGGAG 60.093 50.000 0.00 0.00 0.00 4.30
6012 10443 1.906574 AGCACGGTTAAGATTGAGGGA 59.093 47.619 0.00 0.00 0.00 4.20
6013 10444 2.280628 GAGCACGGTTAAGATTGAGGG 58.719 52.381 0.00 0.00 0.00 4.30
6014 10445 2.932614 CTGAGCACGGTTAAGATTGAGG 59.067 50.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.