Multiple sequence alignment - TraesCS6D01G353900

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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 TraesCS6D01G353900 chr6D 100.000 3529 0 0 1 3529 449375736 449379264 0.000000e+00 6517.0
1 TraesCS6D01G353900 chr6D 83.269 2343 300 65 425 2726 449145761 449143470 0.000000e+00 2071.0
2 TraesCS6D01G353900 chr6D 91.279 344 28 2 2725 3067 449141254 449140912 5.330000e-128 468.0
3 TraesCS6D01G353900 chr6D 82.438 484 70 7 2103 2574 449133071 449132591 3.280000e-110 409.0
4 TraesCS6D01G353900 chr6D 85.714 392 40 12 40 422 449146179 449145795 1.970000e-107 399.0
5 TraesCS6D01G353900 chr6D 83.163 196 26 4 3095 3283 449107696 449107501 4.680000e-39 172.0
6 TraesCS6D01G353900 chr6D 87.255 102 10 2 307 407 449365929 449366028 2.880000e-21 113.0
7 TraesCS6D01G353900 chr6D 93.333 60 4 0 3041 3100 449107831 449107772 4.850000e-14 89.8
8 TraesCS6D01G353900 chr6B 87.098 2054 205 23 542 2579 680988419 680990428 0.000000e+00 2270.0
9 TraesCS6D01G353900 chr6B 86.085 1732 217 20 901 2620 680737343 680735624 0.000000e+00 1842.0
10 TraesCS6D01G353900 chr6B 83.586 1779 247 20 810 2569 680931161 680932913 0.000000e+00 1626.0
11 TraesCS6D01G353900 chr6B 82.959 534 41 30 317 815 680929187 680929705 1.500000e-118 436.0
12 TraesCS6D01G353900 chr6B 86.877 381 36 6 2721 3100 680992767 680993134 7.050000e-112 414.0
13 TraesCS6D01G353900 chr6B 86.198 384 43 8 2721 3100 680936182 680936559 1.180000e-109 407.0
14 TraesCS6D01G353900 chr6B 88.492 252 20 7 2721 2968 680732246 680732000 2.660000e-76 296.0
15 TraesCS6D01G353900 chr6B 90.909 220 13 1 3094 3306 680993201 680993420 4.460000e-74 289.0
16 TraesCS6D01G353900 chr6B 87.500 232 23 3 195 422 680739300 680739071 2.700000e-66 263.0
17 TraesCS6D01G353900 chr6B 90.055 181 17 1 3095 3275 681370364 681370543 2.120000e-57 233.0
18 TraesCS6D01G353900 chr6B 83.920 199 20 6 3095 3283 680936627 680936823 2.800000e-41 180.0
19 TraesCS6D01G353900 chr6B 77.143 280 42 13 541 803 680898269 680897995 3.670000e-30 143.0
20 TraesCS6D01G353900 chr6B 81.065 169 17 8 40 194 680765346 680765179 1.720000e-23 121.0
21 TraesCS6D01G353900 chr6B 93.243 74 3 1 349 422 680737865 680737794 1.340000e-19 108.0
22 TraesCS6D01G353900 chr6B 85.870 92 11 2 872 963 680897997 680897908 2.900000e-16 97.1
23 TraesCS6D01G353900 chr6B 85.542 83 10 2 872 954 680764519 680764599 6.280000e-13 86.1
24 TraesCS6D01G353900 chr6B 85.938 64 4 2 3471 3529 680993431 680993494 2.940000e-06 63.9
25 TraesCS6D01G353900 chr6B 94.286 35 2 0 2919 2953 681259292 681259326 2.000000e-03 54.7
26 TraesCS6D01G353900 chr6A 94.084 1234 66 3 1499 2726 595162903 595164135 0.000000e+00 1868.0
27 TraesCS6D01G353900 chr6A 83.463 2062 280 40 542 2569 594990624 594988590 0.000000e+00 1862.0
28 TraesCS6D01G353900 chr6A 90.274 329 23 7 2725 3045 595165011 595165338 4.210000e-114 422.0
29 TraesCS6D01G353900 chr6A 86.645 307 31 6 2721 3019 602749365 602749061 7.300000e-87 331.0
30 TraesCS6D01G353900 chr6A 92.891 211 15 0 3095 3305 595165421 595165631 1.230000e-79 307.0
31 TraesCS6D01G353900 chr6A 79.607 407 37 18 2721 3100 594985413 594985026 2.100000e-62 250.0
32 TraesCS6D01G353900 chr6A 75.895 419 62 23 541 948 594995327 594995717 1.010000e-40 178.0
33 TraesCS6D01G353900 chrUn 85.910 1682 212 11 901 2569 214051006 214049337 0.000000e+00 1770.0
34 TraesCS6D01G353900 chrUn 85.875 1685 213 11 898 2569 240294076 240295748 0.000000e+00 1770.0
35 TraesCS6D01G353900 chrUn 83.466 1633 234 17 947 2569 263804628 263806234 0.000000e+00 1487.0
36 TraesCS6D01G353900 chrUn 83.435 1636 235 17 950 2575 289985332 289983723 0.000000e+00 1487.0
37 TraesCS6D01G353900 chrUn 85.152 660 94 3 898 1555 79443673 79444330 0.000000e+00 673.0
38 TraesCS6D01G353900 chrUn 88.329 377 37 5 2725 3100 214046082 214045712 2.500000e-121 446.0
39 TraesCS6D01G353900 chrUn 88.329 377 37 5 2725 3100 240299003 240299373 2.500000e-121 446.0
40 TraesCS6D01G353900 chrUn 77.178 482 62 32 333 784 263804050 263804513 1.640000e-58 237.0
41 TraesCS6D01G353900 chrUn 83.333 192 22 6 3101 3283 214045638 214045448 6.060000e-38 169.0
42 TraesCS6D01G353900 chrUn 82.828 198 24 6 3095 3283 240299441 240299637 6.060000e-38 169.0
43 TraesCS6D01G353900 chrUn 94.366 71 2 1 349 419 79443154 79443222 1.340000e-19 108.0
44 TraesCS6D01G353900 chrUn 93.243 74 3 1 349 422 214051528 214051457 1.340000e-19 108.0
45 TraesCS6D01G353900 chrUn 94.366 71 2 1 349 419 240293557 240293625 1.340000e-19 108.0
46 TraesCS6D01G353900 chrUn 77.157 197 29 9 541 726 240152073 240151882 2.240000e-17 100.0
47 TraesCS6D01G353900 chrUn 77.320 194 28 9 541 723 263942572 263942760 2.240000e-17 100.0
48 TraesCS6D01G353900 chrUn 81.148 122 11 9 333 446 320557057 320557174 1.750000e-13 87.9
49 TraesCS6D01G353900 chr5D 95.930 172 4 3 3297 3466 8845811 8845981 3.470000e-70 276.0
50 TraesCS6D01G353900 chr5D 95.930 172 4 3 3297 3466 365042916 365042746 3.470000e-70 276.0
51 TraesCS6D01G353900 chr5D 95.930 172 4 3 3297 3466 440541821 440541991 3.470000e-70 276.0
52 TraesCS6D01G353900 chr5D 95.930 172 4 3 3297 3466 470364273 470364443 3.470000e-70 276.0
53 TraesCS6D01G353900 chr5D 95.833 168 6 1 3304 3470 198477551 198477384 1.610000e-68 270.0
54 TraesCS6D01G353900 chr2B 96.429 168 5 1 3303 3469 687635781 687635614 3.470000e-70 276.0
55 TraesCS6D01G353900 chr1D 95.930 172 4 3 3297 3466 383864869 383864699 3.470000e-70 276.0
56 TraesCS6D01G353900 chr3D 94.857 175 6 3 3297 3469 407717086 407716913 1.610000e-68 270.0
57 TraesCS6D01G353900 chr3B 93.956 182 6 5 3287 3466 523154195 523154373 1.610000e-68 270.0


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 TraesCS6D01G353900 chr6D 449375736 449379264 3528 False 6517.000000 6517 100.000000 1 3529 1 chr6D.!!$F2 3528
1 TraesCS6D01G353900 chr6D 449140912 449146179 5267 True 979.333333 2071 86.754000 40 3067 3 chr6D.!!$R3 3027
2 TraesCS6D01G353900 chr6B 680988419 680993494 5075 False 759.225000 2270 87.705500 542 3529 4 chr6B.!!$F5 2987
3 TraesCS6D01G353900 chr6B 680929187 680936823 7636 False 662.250000 1626 84.165750 317 3283 4 chr6B.!!$F4 2966
4 TraesCS6D01G353900 chr6B 680732000 680739300 7300 True 627.250000 1842 88.830000 195 2968 4 chr6B.!!$R2 2773
5 TraesCS6D01G353900 chr6A 594985026 594990624 5598 True 1056.000000 1862 81.535000 542 3100 2 chr6A.!!$R2 2558
6 TraesCS6D01G353900 chr6A 595162903 595165631 2728 False 865.666667 1868 92.416333 1499 3305 3 chr6A.!!$F2 1806
7 TraesCS6D01G353900 chrUn 289983723 289985332 1609 True 1487.000000 1487 83.435000 950 2575 1 chrUn.!!$R2 1625
8 TraesCS6D01G353900 chrUn 263804050 263806234 2184 False 862.000000 1487 80.322000 333 2569 2 chrUn.!!$F5 2236
9 TraesCS6D01G353900 chrUn 214045448 214051528 6080 True 623.250000 1770 87.703750 349 3283 4 chrUn.!!$R3 2934
10 TraesCS6D01G353900 chrUn 240293557 240299637 6080 False 623.250000 1770 87.849500 349 3283 4 chrUn.!!$F4 2934
11 TraesCS6D01G353900 chrUn 79443154 79444330 1176 False 390.500000 673 89.759000 349 1555 2 chrUn.!!$F3 1206

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
53 54 0.035881 ATGATGCCCTGATGTAGCCG 59.964 55.0 0.0 0.0 0.00 5.52 F
993 3849 0.108520 GCCACCTGTTCGACGGAATA 60.109 55.0 0.0 0.0 34.05 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1051 3907 0.036164 AAGGACAGCACACGCCATAA 59.964 50.0 0.0 0.0 39.83 1.90 R
2879 12680 0.177141 TCGTTTAGATTCCCGGCAGG 59.823 55.0 0.0 0.0 37.24 4.85 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
20 21 1.732259 CTCTTATGGCGTGTGTTGTCC 59.268 52.381 0.00 0.00 0.00 4.02
21 22 1.346395 TCTTATGGCGTGTGTTGTCCT 59.654 47.619 0.00 0.00 0.00 3.85
22 23 2.151202 CTTATGGCGTGTGTTGTCCTT 58.849 47.619 0.00 0.00 0.00 3.36
23 24 1.803334 TATGGCGTGTGTTGTCCTTC 58.197 50.000 0.00 0.00 0.00 3.46
24 25 0.889186 ATGGCGTGTGTTGTCCTTCC 60.889 55.000 0.00 0.00 0.00 3.46
25 26 1.525077 GGCGTGTGTTGTCCTTCCA 60.525 57.895 0.00 0.00 0.00 3.53
26 27 1.507141 GGCGTGTGTTGTCCTTCCAG 61.507 60.000 0.00 0.00 0.00 3.86
27 28 1.941812 CGTGTGTTGTCCTTCCAGC 59.058 57.895 0.00 0.00 0.00 4.85
28 29 1.507141 CGTGTGTTGTCCTTCCAGCC 61.507 60.000 0.00 0.00 0.00 4.85
29 30 1.227823 TGTGTTGTCCTTCCAGCCG 60.228 57.895 0.00 0.00 0.00 5.52
30 31 1.966451 GTGTTGTCCTTCCAGCCGG 60.966 63.158 0.00 0.00 0.00 6.13
31 32 3.056328 GTTGTCCTTCCAGCCGGC 61.056 66.667 21.89 21.89 0.00 6.13
32 33 4.697756 TTGTCCTTCCAGCCGGCG 62.698 66.667 23.20 16.10 0.00 6.46
37 38 4.161295 CTTCCAGCCGGCGGATGA 62.161 66.667 42.33 26.10 42.34 2.92
38 39 3.466791 CTTCCAGCCGGCGGATGAT 62.467 63.158 42.33 16.44 42.34 2.45
39 40 3.755526 TTCCAGCCGGCGGATGATG 62.756 63.158 42.33 27.53 42.34 3.07
53 54 0.035881 ATGATGCCCTGATGTAGCCG 59.964 55.000 0.00 0.00 0.00 5.52
57 58 2.417516 CCCTGATGTAGCCGTCGG 59.582 66.667 6.99 6.99 33.45 4.79
60 61 3.151710 TGATGTAGCCGTCGGGGG 61.152 66.667 14.38 0.00 35.78 5.40
83 84 4.065281 CGGGGACAGGGACGACAC 62.065 72.222 0.00 0.00 0.00 3.67
84 85 4.065281 GGGGACAGGGACGACACG 62.065 72.222 0.00 0.00 0.00 4.49
85 86 4.065281 GGGACAGGGACGACACGG 62.065 72.222 0.00 0.00 0.00 4.94
100 101 3.736100 CGGCGGCTGCAACATCAA 61.736 61.111 21.31 0.00 45.35 2.57
112 113 3.433274 TGCAACATCAATGACGAAGAGAC 59.567 43.478 0.00 0.00 0.00 3.36
120 121 3.576004 ACGAAGAGACGTCCGAGG 58.424 61.111 13.01 0.63 43.02 4.63
125 126 1.743958 GAAGAGACGTCCGAGGATTGA 59.256 52.381 13.01 0.00 0.00 2.57
156 162 0.261991 AGAGGGTCCTCGGCATCTAA 59.738 55.000 10.98 0.00 46.90 2.10
161 167 2.093128 GGGTCCTCGGCATCTAAAAAGA 60.093 50.000 0.00 0.00 0.00 2.52
165 171 4.095036 GTCCTCGGCATCTAAAAAGAAAGG 59.905 45.833 0.00 0.00 0.00 3.11
174 181 3.991621 TCTAAAAAGAAAGGGGGAAGGGA 59.008 43.478 0.00 0.00 0.00 4.20
190 197 3.551635 AGGGATTAGAGGATGGTCGAT 57.448 47.619 0.00 0.00 0.00 3.59
209 216 1.446272 GGGGCGACGAAAGAGACAG 60.446 63.158 0.00 0.00 0.00 3.51
222 229 2.283173 GACAGGTTGGGCAAGGGG 60.283 66.667 0.00 0.00 0.00 4.79
284 292 5.572211 CGTGTCATCCGAAAATCATTTGAT 58.428 37.500 0.00 0.00 36.07 2.57
436 480 2.674220 CCTGTGGGGCCTCCTCTTC 61.674 68.421 0.00 0.00 36.20 2.87
442 486 1.631071 GGGGCCTCCTCTTCTTCCTG 61.631 65.000 0.84 0.00 0.00 3.86
463 507 1.000486 TTCGTCTCTCCCCTCCCTG 60.000 63.158 0.00 0.00 0.00 4.45
465 509 2.039624 GTCTCTCCCCTCCCTGCA 59.960 66.667 0.00 0.00 0.00 4.41
466 510 2.063378 GTCTCTCCCCTCCCTGCAG 61.063 68.421 6.78 6.78 0.00 4.41
467 515 3.478274 CTCTCCCCTCCCTGCAGC 61.478 72.222 8.66 0.00 0.00 5.25
468 516 4.337304 TCTCCCCTCCCTGCAGCA 62.337 66.667 8.66 0.00 0.00 4.41
469 517 3.795041 CTCCCCTCCCTGCAGCAG 61.795 72.222 16.23 16.23 0.00 4.24
500 564 2.125832 CCGCGCGAGGAAGGTAAA 60.126 61.111 34.63 0.00 0.00 2.01
502 566 1.445582 CGCGCGAGGAAGGTAAAGT 60.446 57.895 28.94 0.00 0.00 2.66
504 568 0.108756 GCGCGAGGAAGGTAAAGTCT 60.109 55.000 12.10 0.00 0.00 3.24
505 569 1.672145 GCGCGAGGAAGGTAAAGTCTT 60.672 52.381 12.10 0.00 0.00 3.01
506 570 1.993370 CGCGAGGAAGGTAAAGTCTTG 59.007 52.381 0.00 0.00 0.00 3.02
507 571 1.732809 GCGAGGAAGGTAAAGTCTTGC 59.267 52.381 0.00 0.00 33.59 4.01
508 572 2.347731 CGAGGAAGGTAAAGTCTTGCC 58.652 52.381 0.00 0.00 37.57 4.52
509 573 2.347731 GAGGAAGGTAAAGTCTTGCCG 58.652 52.381 0.00 0.00 41.89 5.69
510 574 1.697982 AGGAAGGTAAAGTCTTGCCGT 59.302 47.619 0.00 0.00 41.89 5.68
511 575 2.074576 GGAAGGTAAAGTCTTGCCGTC 58.925 52.381 11.39 11.39 42.40 4.79
512 576 2.074576 GAAGGTAAAGTCTTGCCGTCC 58.925 52.381 9.65 0.00 41.89 4.79
513 577 1.053424 AGGTAAAGTCTTGCCGTCCA 58.947 50.000 0.00 0.00 41.89 4.02
514 578 1.002087 AGGTAAAGTCTTGCCGTCCAG 59.998 52.381 0.00 0.00 41.89 3.86
515 579 1.270678 GGTAAAGTCTTGCCGTCCAGT 60.271 52.381 0.00 0.00 0.00 4.00
516 580 2.067013 GTAAAGTCTTGCCGTCCAGTC 58.933 52.381 0.00 0.00 0.00 3.51
517 581 0.250338 AAAGTCTTGCCGTCCAGTCC 60.250 55.000 0.00 0.00 0.00 3.85
518 582 2.047179 GTCTTGCCGTCCAGTCCC 60.047 66.667 0.00 0.00 0.00 4.46
519 583 2.203788 TCTTGCCGTCCAGTCCCT 60.204 61.111 0.00 0.00 0.00 4.20
520 584 2.046892 CTTGCCGTCCAGTCCCTG 60.047 66.667 0.00 0.00 0.00 4.45
521 585 2.847234 TTGCCGTCCAGTCCCTGT 60.847 61.111 0.00 0.00 0.00 4.00
522 586 2.397413 CTTGCCGTCCAGTCCCTGTT 62.397 60.000 0.00 0.00 0.00 3.16
526 591 2.358737 GTCCAGTCCCTGTTGCCG 60.359 66.667 0.00 0.00 0.00 5.69
527 592 2.847234 TCCAGTCCCTGTTGCCGT 60.847 61.111 0.00 0.00 0.00 5.68
765 2148 1.836802 GAAGAGGACTTGGATCTGCCT 59.163 52.381 0.00 0.00 36.39 4.75
766 2149 1.494960 AGAGGACTTGGATCTGCCTC 58.505 55.000 0.00 0.00 44.24 4.70
815 2201 1.743252 CTTGCTCTCCCAGTTCGGC 60.743 63.158 0.00 0.00 0.00 5.54
817 2203 2.125350 GCTCTCCCAGTTCGGCTG 60.125 66.667 0.00 0.00 44.63 4.85
826 3673 1.613630 AGTTCGGCTGATCCCCACT 60.614 57.895 0.00 0.00 0.00 4.00
858 3705 4.683432 GCTTCTTCAGCTGTCCGT 57.317 55.556 14.67 0.00 46.27 4.69
875 3726 0.315251 CGTGAGTTGAGGTGAGCTGA 59.685 55.000 0.00 0.00 0.00 4.26
910 3764 8.893560 TCCAATATTGATCTAGATGATTTCCCA 58.106 33.333 17.23 0.00 35.14 4.37
940 3796 1.369091 ATGCCACATTCGACCGCTTC 61.369 55.000 0.00 0.00 0.00 3.86
957 3813 4.084507 CGCTTCGTTTGCTAATTTCTCTG 58.915 43.478 0.00 0.00 0.00 3.35
993 3849 0.108520 GCCACCTGTTCGACGGAATA 60.109 55.000 0.00 0.00 34.05 1.75
1023 3879 2.276863 CTGCGGCGAGTGACAGAGAT 62.277 60.000 12.98 0.00 31.67 2.75
1024 3880 1.153745 GCGGCGAGTGACAGAGATT 60.154 57.895 12.98 0.00 0.00 2.40
1051 3907 3.999297 GACCTCCCCGACGAGCTCT 62.999 68.421 12.85 0.00 0.00 4.09
1173 4029 0.106918 TTGTCTTTGACGGGCCAACT 60.107 50.000 4.39 0.00 34.95 3.16
1185 4041 0.818040 GGCCAACTTTCCCGCGATAT 60.818 55.000 8.23 0.00 0.00 1.63
1187 4043 1.798813 GCCAACTTTCCCGCGATATAG 59.201 52.381 8.23 1.81 0.00 1.31
1211 4067 1.305201 TTCGAACAGTTGGTGAAGCC 58.695 50.000 0.00 0.00 37.90 4.35
1230 4086 2.498941 GGTCATCCATCTCCGCGGA 61.499 63.158 29.03 29.03 35.27 5.54
1236 4092 1.218047 CCATCTCCGCGGAAACTCA 59.782 57.895 30.53 10.98 0.00 3.41
1238 4094 0.108615 CATCTCCGCGGAAACTCACT 60.109 55.000 30.53 0.00 0.00 3.41
1261 4117 2.872858 CTCGTCAGGTGTGAGATCGATA 59.127 50.000 0.00 0.00 31.53 2.92
1263 4119 2.600084 CGTCAGGTGTGAGATCGATACG 60.600 54.545 0.00 0.00 31.53 3.06
1309 4165 0.249031 GTTCACAAACACCAGGCTGC 60.249 55.000 9.56 0.00 35.36 5.25
1365 4221 1.135915 CTCGTGGTAAGAGCTGCTGAT 59.864 52.381 7.01 0.00 0.00 2.90
1366 4222 1.134995 TCGTGGTAAGAGCTGCTGATG 60.135 52.381 7.01 0.00 0.00 3.07
1369 4225 3.676049 CGTGGTAAGAGCTGCTGATGTTA 60.676 47.826 7.01 0.00 0.00 2.41
1374 4230 6.127054 TGGTAAGAGCTGCTGATGTTAAGTAT 60.127 38.462 7.01 0.00 0.00 2.12
1379 4235 4.080919 AGCTGCTGATGTTAAGTATGACCA 60.081 41.667 0.00 0.00 0.00 4.02
1404 4260 0.390340 TGTTCGATGTGCCTCTCAGC 60.390 55.000 0.00 0.00 0.00 4.26
1492 4349 0.107945 CTCAGGCTGCCCAGTCTTAC 60.108 60.000 16.57 0.00 41.26 2.34
1643 4500 1.755959 CATCTCACTGCAGCTAGAGGT 59.244 52.381 23.25 17.44 0.00 3.85
1712 4570 2.428171 CTGCCCATGTTAACCTTGATGG 59.572 50.000 13.34 13.34 42.93 3.51
1779 4637 6.707440 AATTTTGTCTGTGGTTGTCATACA 57.293 33.333 0.00 0.00 0.00 2.29
1809 4667 1.002011 GGAGGGGGTGCTTCTCAAC 60.002 63.158 0.00 0.00 0.00 3.18
1909 4782 5.301805 ACTCTTGTTATTTGTCACCCAAAGG 59.698 40.000 0.00 0.00 45.79 3.11
2022 4901 3.396560 TGCATCTCAAATCGATGGCTAG 58.603 45.455 0.00 0.00 38.88 3.42
2164 5044 1.203288 TGGGATTTGAAATGGTGCCCT 60.203 47.619 12.08 0.00 35.15 5.19
2192 5072 8.908903 TCTTTGGCAAATTAAAGACTCTGTTAA 58.091 29.630 13.89 0.00 37.83 2.01
2219 5099 8.952278 TCAATAAATGTTTTACGGCTATTGACT 58.048 29.630 0.00 0.00 32.27 3.41
2233 5113 6.403636 CGGCTATTGACTTAGTTTGCATTCTT 60.404 38.462 0.00 0.00 0.00 2.52
2323 5205 8.761575 AGATAACAATGGTGCTGTTTTATTTG 57.238 30.769 0.00 0.00 38.05 2.32
2331 5213 4.744631 GGTGCTGTTTTATTTGAGGTGTTG 59.255 41.667 0.00 0.00 0.00 3.33
2412 5296 2.025887 ACAGGAGCCCAGGAAACAATAG 60.026 50.000 0.00 0.00 0.00 1.73
2448 5332 3.735746 GTGTGCATGCCTTAAGTTTGTTC 59.264 43.478 16.68 0.00 0.00 3.18
2501 5385 7.148656 GGGGTTCGTGAAATTTTGAATATGTTG 60.149 37.037 0.00 0.00 0.00 3.33
2536 5425 5.689068 GCATACTTCCAAATTAGCATCAAGC 59.311 40.000 0.00 0.00 46.19 4.01
2561 5450 1.100510 CCACGTCCGGACTCAGATTA 58.899 55.000 30.92 0.00 0.00 1.75
2644 9930 4.340381 CACCTCCAAATCCATCCAGATTTC 59.660 45.833 0.00 0.00 43.06 2.17
2830 12631 3.077359 CTCTGCCGGAAATCTGTCTTTT 58.923 45.455 5.05 0.00 0.00 2.27
2831 12632 4.020573 TCTCTGCCGGAAATCTGTCTTTTA 60.021 41.667 5.05 0.00 0.00 1.52
2832 12633 4.843728 TCTGCCGGAAATCTGTCTTTTAT 58.156 39.130 5.05 0.00 0.00 1.40
2834 12635 3.694072 TGCCGGAAATCTGTCTTTTATGG 59.306 43.478 5.05 0.00 0.00 2.74
2837 12638 5.336451 GCCGGAAATCTGTCTTTTATGGTTT 60.336 40.000 5.05 0.00 0.00 3.27
2866 12667 5.879237 TGCAACTTAGCAAGATATTTTCCG 58.121 37.500 3.37 0.00 42.46 4.30
2871 12672 6.786207 ACTTAGCAAGATATTTTCCGCTTTC 58.214 36.000 0.00 0.00 35.71 2.62
2879 12680 5.586643 AGATATTTTCCGCTTTCTCAGGAAC 59.413 40.000 0.00 0.00 43.00 3.62
2896 12697 2.014857 GAACCTGCCGGGAATCTAAAC 58.985 52.381 2.18 0.00 38.76 2.01
3010 12842 7.113965 CCGAAATTGTAAATGCATCTCTTATGC 59.886 37.037 0.00 3.05 44.76 3.14
3035 12867 2.494073 TGTGCGTCATCAGTATACACCA 59.506 45.455 5.50 0.00 0.00 4.17
3071 12903 2.649312 TCAGAAATCCTGGGTGTCCATT 59.351 45.455 0.00 0.00 43.11 3.16
3096 12928 3.555168 CGCTAATAATCCTGGGTGAGGTC 60.555 52.174 0.00 0.00 43.37 3.85
3181 13090 5.684704 TGTTTCATCTTGGTCTTGAAGACT 58.315 37.500 23.06 1.82 44.46 3.24
3186 13095 4.342862 TCTTGGTCTTGAAGACTGGAAG 57.657 45.455 23.06 20.08 44.46 3.46
3223 13135 7.451877 ACCTCTTGTATCTGTCTAGTCTGAAAA 59.548 37.037 1.12 0.00 0.00 2.29
3275 13188 4.019792 TGTGCTGAGTATGATGGTTTGT 57.980 40.909 0.00 0.00 0.00 2.83
3313 13233 4.304048 ACCTACAGATATACTCCCTCCG 57.696 50.000 0.00 0.00 0.00 4.63
3315 13235 4.106019 ACCTACAGATATACTCCCTCCGTT 59.894 45.833 0.00 0.00 0.00 4.44
3316 13236 5.078256 CCTACAGATATACTCCCTCCGTTT 58.922 45.833 0.00 0.00 0.00 3.60
3317 13237 5.183522 CCTACAGATATACTCCCTCCGTTTC 59.816 48.000 0.00 0.00 0.00 2.78
3318 13238 4.805744 ACAGATATACTCCCTCCGTTTCT 58.194 43.478 0.00 0.00 0.00 2.52
3319 13239 5.950023 ACAGATATACTCCCTCCGTTTCTA 58.050 41.667 0.00 0.00 0.00 2.10
3320 13240 6.371278 ACAGATATACTCCCTCCGTTTCTAA 58.629 40.000 0.00 0.00 0.00 2.10
3321 13241 6.837568 ACAGATATACTCCCTCCGTTTCTAAA 59.162 38.462 0.00 0.00 0.00 1.85
3322 13242 7.509659 ACAGATATACTCCCTCCGTTTCTAAAT 59.490 37.037 0.00 0.00 0.00 1.40
3323 13243 9.021807 CAGATATACTCCCTCCGTTTCTAAATA 57.978 37.037 0.00 0.00 0.00 1.40
3324 13244 9.771140 AGATATACTCCCTCCGTTTCTAAATAT 57.229 33.333 0.00 0.00 0.00 1.28
3327 13247 8.904099 ATACTCCCTCCGTTTCTAAATATTTG 57.096 34.615 11.05 1.65 0.00 2.32
3328 13248 6.718294 ACTCCCTCCGTTTCTAAATATTTGT 58.282 36.000 11.05 0.00 0.00 2.83
3329 13249 6.822170 ACTCCCTCCGTTTCTAAATATTTGTC 59.178 38.462 11.05 0.00 0.00 3.18
3330 13250 6.954232 TCCCTCCGTTTCTAAATATTTGTCT 58.046 36.000 11.05 0.00 0.00 3.41
3331 13251 7.399634 TCCCTCCGTTTCTAAATATTTGTCTT 58.600 34.615 11.05 0.00 0.00 3.01
3332 13252 7.886446 TCCCTCCGTTTCTAAATATTTGTCTTT 59.114 33.333 11.05 0.00 0.00 2.52
3333 13253 8.182227 CCCTCCGTTTCTAAATATTTGTCTTTC 58.818 37.037 11.05 0.00 0.00 2.62
3334 13254 8.947115 CCTCCGTTTCTAAATATTTGTCTTTCT 58.053 33.333 11.05 0.00 0.00 2.52
3365 13285 7.843490 TTTAACAAGTGACTACATATGGAGC 57.157 36.000 15.30 8.47 0.00 4.70
3366 13286 5.420725 AACAAGTGACTACATATGGAGCA 57.579 39.130 15.30 10.95 0.00 4.26
3367 13287 5.420725 ACAAGTGACTACATATGGAGCAA 57.579 39.130 15.30 0.16 0.00 3.91
3368 13288 5.804639 ACAAGTGACTACATATGGAGCAAA 58.195 37.500 15.30 0.00 0.00 3.68
3369 13289 6.237901 ACAAGTGACTACATATGGAGCAAAA 58.762 36.000 15.30 0.00 0.00 2.44
3370 13290 6.886459 ACAAGTGACTACATATGGAGCAAAAT 59.114 34.615 15.30 0.00 0.00 1.82
3371 13291 6.932356 AGTGACTACATATGGAGCAAAATG 57.068 37.500 15.30 0.00 0.00 2.32
3372 13292 6.653020 AGTGACTACATATGGAGCAAAATGA 58.347 36.000 15.30 0.00 0.00 2.57
3373 13293 6.765036 AGTGACTACATATGGAGCAAAATGAG 59.235 38.462 15.30 0.00 0.00 2.90
3374 13294 6.540189 GTGACTACATATGGAGCAAAATGAGT 59.460 38.462 15.30 0.00 0.00 3.41
3375 13295 6.539826 TGACTACATATGGAGCAAAATGAGTG 59.460 38.462 15.30 0.00 0.00 3.51
3376 13296 6.653020 ACTACATATGGAGCAAAATGAGTGA 58.347 36.000 15.30 0.00 0.00 3.41
3377 13297 7.112122 ACTACATATGGAGCAAAATGAGTGAA 58.888 34.615 15.30 0.00 0.00 3.18
3378 13298 7.776969 ACTACATATGGAGCAAAATGAGTGAAT 59.223 33.333 15.30 0.00 0.00 2.57
3379 13299 7.035840 ACATATGGAGCAAAATGAGTGAATC 57.964 36.000 7.80 0.00 0.00 2.52
3380 13300 6.832384 ACATATGGAGCAAAATGAGTGAATCT 59.168 34.615 7.80 0.00 0.00 2.40
3381 13301 7.994911 ACATATGGAGCAAAATGAGTGAATCTA 59.005 33.333 7.80 0.00 0.00 1.98
3382 13302 6.690194 ATGGAGCAAAATGAGTGAATCTAC 57.310 37.500 0.00 0.00 0.00 2.59
3383 13303 5.559770 TGGAGCAAAATGAGTGAATCTACA 58.440 37.500 0.00 0.00 0.00 2.74
3384 13304 5.412594 TGGAGCAAAATGAGTGAATCTACAC 59.587 40.000 0.00 0.00 40.60 2.90
3422 13342 4.438148 CATACATCCGTATGTTGTGTCCA 58.562 43.478 0.00 0.00 46.70 4.02
3423 13343 3.627395 ACATCCGTATGTTGTGTCCAT 57.373 42.857 0.00 0.00 44.07 3.41
3424 13344 3.950397 ACATCCGTATGTTGTGTCCATT 58.050 40.909 0.00 0.00 44.07 3.16
3425 13345 4.331968 ACATCCGTATGTTGTGTCCATTT 58.668 39.130 0.00 0.00 44.07 2.32
3426 13346 4.155826 ACATCCGTATGTTGTGTCCATTTG 59.844 41.667 0.00 0.00 44.07 2.32
3427 13347 4.009370 TCCGTATGTTGTGTCCATTTGA 57.991 40.909 0.00 0.00 0.00 2.69
3428 13348 4.390264 TCCGTATGTTGTGTCCATTTGAA 58.610 39.130 0.00 0.00 0.00 2.69
3429 13349 4.822350 TCCGTATGTTGTGTCCATTTGAAA 59.178 37.500 0.00 0.00 0.00 2.69
3430 13350 5.475220 TCCGTATGTTGTGTCCATTTGAAAT 59.525 36.000 0.00 0.00 0.00 2.17
3431 13351 5.572511 CCGTATGTTGTGTCCATTTGAAATG 59.427 40.000 10.84 10.84 0.00 2.32
3432 13352 5.060816 CGTATGTTGTGTCCATTTGAAATGC 59.939 40.000 12.26 0.87 0.00 3.56
3433 13353 3.726607 TGTTGTGTCCATTTGAAATGCC 58.273 40.909 12.26 5.75 0.00 4.40
3434 13354 3.387374 TGTTGTGTCCATTTGAAATGCCT 59.613 39.130 12.26 0.00 0.00 4.75
3435 13355 4.586421 TGTTGTGTCCATTTGAAATGCCTA 59.414 37.500 12.26 0.00 0.00 3.93
3436 13356 5.163513 GTTGTGTCCATTTGAAATGCCTAG 58.836 41.667 12.26 0.00 0.00 3.02
3437 13357 4.661222 TGTGTCCATTTGAAATGCCTAGA 58.339 39.130 12.26 1.83 0.00 2.43
3438 13358 5.076182 TGTGTCCATTTGAAATGCCTAGAA 58.924 37.500 12.26 0.00 0.00 2.10
3439 13359 5.538053 TGTGTCCATTTGAAATGCCTAGAAA 59.462 36.000 12.26 0.00 0.00 2.52
3440 13360 6.095377 GTGTCCATTTGAAATGCCTAGAAAG 58.905 40.000 12.26 0.00 0.00 2.62
3441 13361 6.009589 TGTCCATTTGAAATGCCTAGAAAGA 58.990 36.000 12.26 0.00 0.00 2.52
3442 13362 6.071952 TGTCCATTTGAAATGCCTAGAAAGAC 60.072 38.462 12.26 11.27 0.00 3.01
3443 13363 6.009589 TCCATTTGAAATGCCTAGAAAGACA 58.990 36.000 12.26 0.00 0.00 3.41
3444 13364 6.493115 TCCATTTGAAATGCCTAGAAAGACAA 59.507 34.615 12.26 0.00 0.00 3.18
3445 13365 7.015098 TCCATTTGAAATGCCTAGAAAGACAAA 59.985 33.333 12.26 0.00 0.00 2.83
3446 13366 7.820872 CCATTTGAAATGCCTAGAAAGACAAAT 59.179 33.333 12.26 0.00 36.38 2.32
3447 13367 9.859427 CATTTGAAATGCCTAGAAAGACAAATA 57.141 29.630 4.82 0.00 34.96 1.40
3450 13370 9.859427 TTGAAATGCCTAGAAAGACAAATATTG 57.141 29.630 0.00 0.00 0.00 1.90
3451 13371 8.469200 TGAAATGCCTAGAAAGACAAATATTGG 58.531 33.333 0.00 0.00 34.12 3.16
3452 13372 6.966534 ATGCCTAGAAAGACAAATATTGGG 57.033 37.500 0.00 0.00 34.12 4.12
3453 13373 6.073447 TGCCTAGAAAGACAAATATTGGGA 57.927 37.500 0.00 0.00 34.12 4.37
3454 13374 6.489603 TGCCTAGAAAGACAAATATTGGGAA 58.510 36.000 0.00 0.00 34.12 3.97
3455 13375 6.377146 TGCCTAGAAAGACAAATATTGGGAAC 59.623 38.462 0.00 0.00 34.12 3.62
3456 13376 6.458342 GCCTAGAAAGACAAATATTGGGAACG 60.458 42.308 0.00 0.00 34.12 3.95
3457 13377 5.897377 AGAAAGACAAATATTGGGAACGG 57.103 39.130 0.00 0.00 34.12 4.44
3458 13378 5.566469 AGAAAGACAAATATTGGGAACGGA 58.434 37.500 0.00 0.00 34.12 4.69
3459 13379 5.648092 AGAAAGACAAATATTGGGAACGGAG 59.352 40.000 0.00 0.00 34.12 4.63
3460 13380 3.886123 AGACAAATATTGGGAACGGAGG 58.114 45.455 0.00 0.00 34.12 4.30
3461 13381 2.949644 GACAAATATTGGGAACGGAGGG 59.050 50.000 0.00 0.00 34.12 4.30
3462 13382 2.578940 ACAAATATTGGGAACGGAGGGA 59.421 45.455 0.00 0.00 34.12 4.20
3463 13383 3.214328 CAAATATTGGGAACGGAGGGAG 58.786 50.000 0.00 0.00 0.00 4.30
3464 13384 2.191981 ATATTGGGAACGGAGGGAGT 57.808 50.000 0.00 0.00 0.00 3.85
3465 13385 2.852714 TATTGGGAACGGAGGGAGTA 57.147 50.000 0.00 0.00 0.00 2.59
3466 13386 2.191981 ATTGGGAACGGAGGGAGTAT 57.808 50.000 0.00 0.00 0.00 2.12
3467 13387 2.852714 TTGGGAACGGAGGGAGTATA 57.147 50.000 0.00 0.00 0.00 1.47
3468 13388 2.852714 TGGGAACGGAGGGAGTATAA 57.147 50.000 0.00 0.00 0.00 0.98
3469 13389 2.674420 TGGGAACGGAGGGAGTATAAG 58.326 52.381 0.00 0.00 0.00 1.73
3499 13419 0.679640 GGGTCATTGGATGCCACGAA 60.680 55.000 0.00 0.00 30.78 3.85
3503 13423 2.016318 TCATTGGATGCCACGAATGAC 58.984 47.619 11.39 0.00 39.02 3.06
3512 13437 0.797249 CCACGAATGACGAGTCGACC 60.797 60.000 21.50 10.96 42.24 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.732259 GGACAACACACGCCATAAGAG 59.268 52.381 0.00 0.00 0.00 2.85
1 2 1.346395 AGGACAACACACGCCATAAGA 59.654 47.619 0.00 0.00 0.00 2.10
3 4 2.147958 GAAGGACAACACACGCCATAA 58.852 47.619 0.00 0.00 0.00 1.90
4 5 1.609580 GGAAGGACAACACACGCCATA 60.610 52.381 0.00 0.00 0.00 2.74
5 6 0.889186 GGAAGGACAACACACGCCAT 60.889 55.000 0.00 0.00 0.00 4.40
6 7 1.525077 GGAAGGACAACACACGCCA 60.525 57.895 0.00 0.00 0.00 5.69
7 8 1.507141 CTGGAAGGACAACACACGCC 61.507 60.000 0.00 0.00 0.00 5.68
8 9 1.941812 CTGGAAGGACAACACACGC 59.058 57.895 0.00 0.00 0.00 5.34
9 10 1.507141 GGCTGGAAGGACAACACACG 61.507 60.000 0.00 0.00 0.00 4.49
10 11 1.507141 CGGCTGGAAGGACAACACAC 61.507 60.000 0.00 0.00 0.00 3.82
11 12 1.227823 CGGCTGGAAGGACAACACA 60.228 57.895 0.00 0.00 0.00 3.72
12 13 1.966451 CCGGCTGGAAGGACAACAC 60.966 63.158 5.28 0.00 37.49 3.32
13 14 2.429930 CCGGCTGGAAGGACAACA 59.570 61.111 5.28 0.00 37.49 3.33
14 15 3.056328 GCCGGCTGGAAGGACAAC 61.056 66.667 22.15 0.00 37.49 3.32
15 16 4.697756 CGCCGGCTGGAAGGACAA 62.698 66.667 26.68 0.00 37.49 3.18
20 21 3.466791 ATCATCCGCCGGCTGGAAG 62.467 63.158 33.19 29.55 39.39 3.46
21 22 3.479203 ATCATCCGCCGGCTGGAA 61.479 61.111 33.19 22.81 39.39 3.53
22 23 4.240103 CATCATCCGCCGGCTGGA 62.240 66.667 32.20 32.20 40.46 3.86
30 31 0.035317 TACATCAGGGCATCATCCGC 59.965 55.000 0.00 0.00 0.00 5.54
31 32 1.943046 GCTACATCAGGGCATCATCCG 60.943 57.143 0.00 0.00 0.00 4.18
32 33 1.612726 GGCTACATCAGGGCATCATCC 60.613 57.143 0.00 0.00 0.00 3.51
33 34 1.818642 GGCTACATCAGGGCATCATC 58.181 55.000 0.00 0.00 0.00 2.92
34 35 0.035881 CGGCTACATCAGGGCATCAT 59.964 55.000 0.00 0.00 0.00 2.45
35 36 1.337384 ACGGCTACATCAGGGCATCA 61.337 55.000 0.00 0.00 0.00 3.07
36 37 0.601311 GACGGCTACATCAGGGCATC 60.601 60.000 0.00 0.00 0.00 3.91
37 38 1.447643 GACGGCTACATCAGGGCAT 59.552 57.895 0.00 0.00 0.00 4.40
38 39 2.900273 GACGGCTACATCAGGGCA 59.100 61.111 0.00 0.00 0.00 5.36
39 40 2.279517 CGACGGCTACATCAGGGC 60.280 66.667 0.00 0.00 0.00 5.19
40 41 2.417516 CCGACGGCTACATCAGGG 59.582 66.667 0.00 0.00 0.00 4.45
41 42 2.417516 CCCGACGGCTACATCAGG 59.582 66.667 8.86 0.00 0.00 3.86
42 43 2.417516 CCCCGACGGCTACATCAG 59.582 66.667 8.86 0.00 0.00 2.90
81 82 4.465512 GATGTTGCAGCCGCCGTG 62.466 66.667 0.00 0.00 37.32 4.94
83 84 3.055080 ATTGATGTTGCAGCCGCCG 62.055 57.895 0.00 0.00 37.32 6.46
84 85 1.517694 CATTGATGTTGCAGCCGCC 60.518 57.895 0.00 0.00 37.32 6.13
85 86 0.799534 GTCATTGATGTTGCAGCCGC 60.800 55.000 0.00 0.00 39.24 6.53
120 121 1.035932 TCTCTCCCGTCCCGTCAATC 61.036 60.000 0.00 0.00 0.00 2.67
125 126 4.444081 CCCTCTCTCCCGTCCCGT 62.444 72.222 0.00 0.00 0.00 5.28
127 128 2.442458 GACCCTCTCTCCCGTCCC 60.442 72.222 0.00 0.00 0.00 4.46
128 129 2.442458 GGACCCTCTCTCCCGTCC 60.442 72.222 0.00 0.00 38.18 4.79
131 137 2.517402 CGAGGACCCTCTCTCCCG 60.517 72.222 13.62 0.00 40.69 5.14
134 140 1.456705 ATGCCGAGGACCCTCTCTC 60.457 63.158 13.62 3.94 40.69 3.20
135 141 1.456705 GATGCCGAGGACCCTCTCT 60.457 63.158 13.62 0.00 40.69 3.10
138 144 1.120530 TTTAGATGCCGAGGACCCTC 58.879 55.000 5.99 5.99 39.55 4.30
139 145 1.580059 TTTTAGATGCCGAGGACCCT 58.420 50.000 0.00 0.00 0.00 4.34
142 148 4.095036 CCTTTCTTTTTAGATGCCGAGGAC 59.905 45.833 0.00 0.00 0.00 3.85
156 162 3.943269 AATCCCTTCCCCCTTTCTTTT 57.057 42.857 0.00 0.00 0.00 2.27
161 167 2.048723 TCCTCTAATCCCTTCCCCCTTT 59.951 50.000 0.00 0.00 0.00 3.11
165 171 1.988846 CCATCCTCTAATCCCTTCCCC 59.011 57.143 0.00 0.00 0.00 4.81
174 181 2.260822 CCCCATCGACCATCCTCTAAT 58.739 52.381 0.00 0.00 0.00 1.73
190 197 2.154798 CTGTCTCTTTCGTCGCCCCA 62.155 60.000 0.00 0.00 0.00 4.96
198 205 0.250295 TGCCCAACCTGTCTCTTTCG 60.250 55.000 0.00 0.00 0.00 3.46
310 319 1.007387 CAAAAGGGGCGTCTGTTGC 60.007 57.895 0.00 0.00 0.00 4.17
356 368 2.375173 CCGGCCGGTTTAGATATACC 57.625 55.000 36.64 0.00 0.00 2.73
396 408 3.801997 CCCCCACCTAGCAGCTGG 61.802 72.222 17.12 0.68 0.00 4.85
419 431 1.204113 AAGAAGAGGAGGCCCCACAG 61.204 60.000 12.24 0.00 37.41 3.66
422 434 1.616628 GGAAGAAGAGGAGGCCCCA 60.617 63.158 12.24 0.00 37.41 4.96
423 435 1.307430 AGGAAGAAGAGGAGGCCCC 60.307 63.158 0.00 0.00 0.00 5.80
436 480 1.067495 GGGAGAGACGAACACAGGAAG 60.067 57.143 0.00 0.00 0.00 3.46
442 486 1.605971 GGGAGGGGAGAGACGAACAC 61.606 65.000 0.00 0.00 0.00 3.32
498 562 0.250338 GGACTGGACGGCAAGACTTT 60.250 55.000 0.00 0.00 0.00 2.66
500 564 2.584391 GGGACTGGACGGCAAGACT 61.584 63.158 0.00 0.00 0.00 3.24
502 566 2.203788 AGGGACTGGACGGCAAGA 60.204 61.111 0.00 0.00 37.18 3.02
513 577 2.915659 TCGACGGCAACAGGGACT 60.916 61.111 0.00 0.00 43.88 3.85
514 578 2.737376 GTCGACGGCAACAGGGAC 60.737 66.667 0.00 0.00 0.00 4.46
515 579 4.351938 CGTCGACGGCAACAGGGA 62.352 66.667 29.70 0.00 35.37 4.20
604 1967 3.535962 GAGGCCGGAGCAGAGGAG 61.536 72.222 5.05 0.00 42.56 3.69
693 2064 4.201679 TCCACGCGCGATGGGTAG 62.202 66.667 39.36 16.64 42.70 3.18
743 2125 1.556911 GCAGATCCAAGTCCTCTTCCA 59.443 52.381 0.00 0.00 0.00 3.53
747 2129 1.494960 GAGGCAGATCCAAGTCCTCT 58.505 55.000 0.00 0.00 40.02 3.69
765 2148 1.612146 TCCTCCGTTGCTGGATGGA 60.612 57.895 7.05 7.05 37.41 3.41
766 2149 1.450312 GTCCTCCGTTGCTGGATGG 60.450 63.158 0.00 0.00 37.41 3.51
791 2177 1.202330 ACTGGGAGAGCAAGAGGATG 58.798 55.000 0.00 0.00 0.00 3.51
815 2201 1.746615 CGGCAACAGTGGGGATCAG 60.747 63.158 0.00 0.00 0.00 2.90
817 2203 2.438434 CCGGCAACAGTGGGGATC 60.438 66.667 0.00 0.00 0.00 3.36
843 3690 1.040646 ACTCACGGACAGCTGAAGAA 58.959 50.000 23.35 0.00 0.00 2.52
844 3691 1.040646 AACTCACGGACAGCTGAAGA 58.959 50.000 23.35 9.19 0.00 2.87
858 3705 2.001076 TCTCAGCTCACCTCAACTCA 57.999 50.000 0.00 0.00 0.00 3.41
910 3764 0.107703 ATGTGGCATCACCGAATCGT 60.108 50.000 0.82 0.00 43.94 3.73
940 3796 4.083855 TGAGCACAGAGAAATTAGCAAACG 60.084 41.667 0.00 0.00 0.00 3.60
993 3849 4.521062 GCCGCAGCCATCTCGAGT 62.521 66.667 13.13 0.00 0.00 4.18
1051 3907 0.036164 AAGGACAGCACACGCCATAA 59.964 50.000 0.00 0.00 39.83 1.90
1083 3939 2.672908 CAGGTCTGCAGGGCATCA 59.327 61.111 15.13 0.00 38.13 3.07
1140 3996 2.887151 AGACAAATAGCAGGCTGGTT 57.113 45.000 25.69 5.96 0.00 3.67
1173 4029 0.390124 AACGGCTATATCGCGGGAAA 59.610 50.000 6.13 0.00 34.89 3.13
1185 4041 1.202557 ACCAACTGTTCGAAACGGCTA 60.203 47.619 0.00 0.00 41.56 3.93
1187 4043 0.316689 CACCAACTGTTCGAAACGGC 60.317 55.000 0.00 0.00 41.56 5.68
1211 4067 2.355126 CGCGGAGATGGATGACCG 60.355 66.667 0.00 0.00 46.74 4.79
1230 4086 2.431057 ACACCTGACGAGAAGTGAGTTT 59.569 45.455 0.00 0.00 31.83 2.66
1236 4092 1.982660 TCTCACACCTGACGAGAAGT 58.017 50.000 0.00 0.00 32.96 3.01
1238 4094 1.468914 CGATCTCACACCTGACGAGAA 59.531 52.381 0.00 0.00 39.15 2.87
1261 4117 1.653115 GCTCATCGTCGGGATACGT 59.347 57.895 0.00 0.00 43.31 3.57
1263 4119 1.081376 CGGCTCATCGTCGGGATAC 60.081 63.158 0.00 0.00 37.01 2.24
1309 4165 1.134995 TGCCAGAGCGTAGTCAATCAG 60.135 52.381 0.00 0.00 44.31 2.90
1365 4221 5.298989 ACACTGGTTGGTCATACTTAACA 57.701 39.130 0.00 0.00 0.00 2.41
1366 4222 5.107220 CGAACACTGGTTGGTCATACTTAAC 60.107 44.000 0.00 0.00 42.87 2.01
1369 4225 3.070446 TCGAACACTGGTTGGTCATACTT 59.930 43.478 0.00 0.00 42.87 2.24
1374 4230 1.140052 ACATCGAACACTGGTTGGTCA 59.860 47.619 0.00 0.00 42.87 4.02
1379 4235 0.108585 AGGCACATCGAACACTGGTT 59.891 50.000 0.00 0.00 40.76 3.67
1404 4260 1.279496 TGAGGTGTTGGGAGATGAGG 58.721 55.000 0.00 0.00 0.00 3.86
1492 4349 7.092137 TGCAGAATTGAATTGTTAGATCCTG 57.908 36.000 0.00 0.00 0.00 3.86
1643 4500 4.817318 AAAGGTGTCAAGCCTTCAAAAA 57.183 36.364 0.00 0.00 44.84 1.94
1712 4570 2.031420 CGACAATGATCATGGCATCCAC 60.031 50.000 9.46 0.00 35.80 4.02
1809 4667 1.080569 GGCAGCATTGGACAAACCG 60.081 57.895 0.00 0.00 42.61 4.44
1846 4704 4.638865 GGGCAAGTGTACCATTTTAGGTAG 59.361 45.833 0.00 0.00 44.43 3.18
1971 4849 5.353123 TGAAGATAAAGTACCAAATGCGACC 59.647 40.000 0.00 0.00 0.00 4.79
2119 4999 6.591935 TCTGTAGAGAAACTGGACAAATTGT 58.408 36.000 0.00 0.00 0.00 2.71
2192 5072 9.730420 GTCAATAGCCGTAAAACATTTATTGAT 57.270 29.630 7.14 0.00 37.95 2.57
2203 5083 6.205076 TGCAAACTAAGTCAATAGCCGTAAAA 59.795 34.615 0.00 0.00 0.00 1.52
2219 5099 6.017109 GGAGAGTGTTGAAGAATGCAAACTAA 60.017 38.462 0.00 0.00 33.62 2.24
2233 5113 3.960755 TCTCAAGAACTGGAGAGTGTTGA 59.039 43.478 4.95 0.00 35.34 3.18
2309 5191 5.348164 ACAACACCTCAAATAAAACAGCAC 58.652 37.500 0.00 0.00 0.00 4.40
2323 5205 1.741706 CAGCATCCATGACAACACCTC 59.258 52.381 0.00 0.00 0.00 3.85
2331 5213 4.978083 AGACAAATTCAGCATCCATGAC 57.022 40.909 0.00 0.00 0.00 3.06
2501 5385 2.367567 TGGAAGTATGCCGAATCTACCC 59.632 50.000 0.00 0.00 35.24 3.69
2536 5425 2.005960 GAGTCCGGACGTGGATCCTG 62.006 65.000 28.26 8.18 40.91 3.86
2606 9892 2.505819 GGAGGTGGTGTCATACATCCTT 59.494 50.000 13.50 0.00 42.72 3.36
2723 12521 7.147949 CCACCATTGCAGATTCTTTAGAGAAAT 60.148 37.037 0.00 0.00 44.61 2.17
2763 12561 1.623811 ACTTCACGGTCACAGGCTAAT 59.376 47.619 0.00 0.00 0.00 1.73
2837 12638 4.935352 ATCTTGCTAAGTTGCACCAAAA 57.065 36.364 0.00 0.00 43.20 2.44
2858 12659 4.007659 GGTTCCTGAGAAAGCGGAAAATA 58.992 43.478 0.00 0.00 38.45 1.40
2866 12667 1.301677 CGGCAGGTTCCTGAGAAAGC 61.302 60.000 21.32 5.65 36.24 3.51
2871 12672 1.915078 ATTCCCGGCAGGTTCCTGAG 61.915 60.000 21.32 13.61 36.24 3.35
2879 12680 0.177141 TCGTTTAGATTCCCGGCAGG 59.823 55.000 0.00 0.00 37.24 4.85
2896 12697 4.965062 ACATAGCAACGTTTTAACCATCG 58.035 39.130 0.00 0.00 0.00 3.84
2987 12819 7.212274 GGGCATAAGAGATGCATTTACAATTT 58.788 34.615 11.35 0.00 46.21 1.82
3010 12842 0.465705 ATACTGATGACGCACAGGGG 59.534 55.000 0.00 0.00 38.30 4.79
3035 12867 5.587844 GGATTTCTGATGCATGTACAGTTCT 59.412 40.000 2.46 0.00 33.93 3.01
3071 12903 2.171659 TCACCCAGGATTATTAGCGCAA 59.828 45.455 11.47 1.85 0.00 4.85
3096 12928 2.127496 CACTCAAGCAGCAACGCG 60.127 61.111 3.53 3.53 36.85 6.01
3223 13135 7.112779 ACCGGAATCAGAACAAAGATAGAAAT 58.887 34.615 9.46 0.00 0.00 2.17
3226 13138 5.186992 TGACCGGAATCAGAACAAAGATAGA 59.813 40.000 9.46 0.00 0.00 1.98
3229 13141 4.286297 TGACCGGAATCAGAACAAAGAT 57.714 40.909 9.46 0.00 0.00 2.40
3245 13158 2.654749 TACTCAGCACAAGATGACCG 57.345 50.000 0.00 0.00 34.77 4.79
3275 13188 9.647918 ATCTGTAGGTATCAAATCTGAGACTTA 57.352 33.333 0.00 0.00 42.36 2.24
3306 13226 6.954232 AGACAAATATTTAGAAACGGAGGGA 58.046 36.000 0.00 0.00 0.00 4.20
3307 13227 7.625828 AAGACAAATATTTAGAAACGGAGGG 57.374 36.000 0.00 0.00 0.00 4.30
3308 13228 8.947115 AGAAAGACAAATATTTAGAAACGGAGG 58.053 33.333 0.00 0.00 0.00 4.30
3339 13259 8.893727 GCTCCATATGTAGTCACTTGTTAAAAT 58.106 33.333 1.24 0.00 0.00 1.82
3340 13260 7.880713 TGCTCCATATGTAGTCACTTGTTAAAA 59.119 33.333 1.24 0.00 0.00 1.52
3341 13261 7.390823 TGCTCCATATGTAGTCACTTGTTAAA 58.609 34.615 1.24 0.00 0.00 1.52
3342 13262 6.941857 TGCTCCATATGTAGTCACTTGTTAA 58.058 36.000 1.24 0.00 0.00 2.01
3343 13263 6.538945 TGCTCCATATGTAGTCACTTGTTA 57.461 37.500 1.24 0.00 0.00 2.41
3344 13264 5.420725 TGCTCCATATGTAGTCACTTGTT 57.579 39.130 1.24 0.00 0.00 2.83
3345 13265 5.420725 TTGCTCCATATGTAGTCACTTGT 57.579 39.130 1.24 0.00 0.00 3.16
3346 13266 6.741992 TTTTGCTCCATATGTAGTCACTTG 57.258 37.500 1.24 0.00 0.00 3.16
3347 13267 7.112122 TCATTTTGCTCCATATGTAGTCACTT 58.888 34.615 1.24 0.00 0.00 3.16
3348 13268 6.653020 TCATTTTGCTCCATATGTAGTCACT 58.347 36.000 1.24 0.00 0.00 3.41
3349 13269 6.540189 ACTCATTTTGCTCCATATGTAGTCAC 59.460 38.462 1.24 0.00 0.00 3.67
3350 13270 6.539826 CACTCATTTTGCTCCATATGTAGTCA 59.460 38.462 1.24 0.00 0.00 3.41
3351 13271 6.763135 TCACTCATTTTGCTCCATATGTAGTC 59.237 38.462 1.24 0.00 0.00 2.59
3352 13272 6.653020 TCACTCATTTTGCTCCATATGTAGT 58.347 36.000 1.24 0.00 0.00 2.73
3353 13273 7.558161 TTCACTCATTTTGCTCCATATGTAG 57.442 36.000 1.24 0.00 0.00 2.74
3354 13274 7.994911 AGATTCACTCATTTTGCTCCATATGTA 59.005 33.333 1.24 0.00 0.00 2.29
3355 13275 6.832384 AGATTCACTCATTTTGCTCCATATGT 59.168 34.615 1.24 0.00 0.00 2.29
3356 13276 7.273320 AGATTCACTCATTTTGCTCCATATG 57.727 36.000 0.00 0.00 0.00 1.78
3357 13277 7.994911 TGTAGATTCACTCATTTTGCTCCATAT 59.005 33.333 0.00 0.00 0.00 1.78
3358 13278 7.280876 GTGTAGATTCACTCATTTTGCTCCATA 59.719 37.037 0.00 0.00 35.68 2.74
3359 13279 6.094603 GTGTAGATTCACTCATTTTGCTCCAT 59.905 38.462 0.00 0.00 35.68 3.41
3360 13280 5.412594 GTGTAGATTCACTCATTTTGCTCCA 59.587 40.000 0.00 0.00 35.68 3.86
3361 13281 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
3362 13282 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
3363 13283 7.516198 AAAGTGTAGATTCACTCATTTTGCT 57.484 32.000 0.00 0.00 46.25 3.91
3364 13284 9.677567 TTTAAAGTGTAGATTCACTCATTTTGC 57.322 29.630 0.00 0.00 46.25 3.68
3401 13321 4.746535 TGGACACAACATACGGATGTAT 57.253 40.909 15.10 2.23 45.93 2.29
3402 13322 4.746535 ATGGACACAACATACGGATGTA 57.253 40.909 15.10 0.00 45.93 2.29
3404 13324 4.394610 TCAAATGGACACAACATACGGATG 59.605 41.667 5.94 5.94 39.16 3.51
3405 13325 4.584874 TCAAATGGACACAACATACGGAT 58.415 39.130 0.00 0.00 0.00 4.18
3406 13326 4.009370 TCAAATGGACACAACATACGGA 57.991 40.909 0.00 0.00 0.00 4.69
3407 13327 4.757799 TTCAAATGGACACAACATACGG 57.242 40.909 0.00 0.00 0.00 4.02
3408 13328 5.060816 GCATTTCAAATGGACACAACATACG 59.939 40.000 12.14 0.00 0.00 3.06
3409 13329 5.348451 GGCATTTCAAATGGACACAACATAC 59.652 40.000 12.14 0.00 0.00 2.39
3410 13330 5.245751 AGGCATTTCAAATGGACACAACATA 59.754 36.000 12.14 0.00 0.00 2.29
3411 13331 4.040706 AGGCATTTCAAATGGACACAACAT 59.959 37.500 12.14 0.00 0.00 2.71
3412 13332 3.387374 AGGCATTTCAAATGGACACAACA 59.613 39.130 12.14 0.00 0.00 3.33
3413 13333 3.993920 AGGCATTTCAAATGGACACAAC 58.006 40.909 12.14 0.00 0.00 3.32
3414 13334 5.076182 TCTAGGCATTTCAAATGGACACAA 58.924 37.500 12.14 0.00 0.00 3.33
3415 13335 4.661222 TCTAGGCATTTCAAATGGACACA 58.339 39.130 12.14 0.00 0.00 3.72
3416 13336 5.643379 TTCTAGGCATTTCAAATGGACAC 57.357 39.130 12.14 0.00 0.00 3.67
3417 13337 6.009589 TCTTTCTAGGCATTTCAAATGGACA 58.990 36.000 12.14 0.00 0.00 4.02
3418 13338 6.071952 TGTCTTTCTAGGCATTTCAAATGGAC 60.072 38.462 12.14 8.23 29.10 4.02
3419 13339 6.009589 TGTCTTTCTAGGCATTTCAAATGGA 58.990 36.000 12.14 0.00 29.10 3.41
3420 13340 6.271488 TGTCTTTCTAGGCATTTCAAATGG 57.729 37.500 12.14 0.00 29.10 3.16
3421 13341 8.767478 ATTTGTCTTTCTAGGCATTTCAAATG 57.233 30.769 5.68 5.68 35.56 2.32
3424 13344 9.859427 CAATATTTGTCTTTCTAGGCATTTCAA 57.141 29.630 0.00 0.00 35.56 2.69
3425 13345 8.469200 CCAATATTTGTCTTTCTAGGCATTTCA 58.531 33.333 0.00 0.00 35.56 2.69
3426 13346 7.922811 CCCAATATTTGTCTTTCTAGGCATTTC 59.077 37.037 0.00 0.00 35.56 2.17
3427 13347 7.619302 TCCCAATATTTGTCTTTCTAGGCATTT 59.381 33.333 0.00 0.00 35.56 2.32
3428 13348 7.125391 TCCCAATATTTGTCTTTCTAGGCATT 58.875 34.615 0.00 0.00 35.56 3.56
3429 13349 6.672593 TCCCAATATTTGTCTTTCTAGGCAT 58.327 36.000 0.00 0.00 35.56 4.40
3430 13350 6.073447 TCCCAATATTTGTCTTTCTAGGCA 57.927 37.500 0.00 0.00 33.22 4.75
3431 13351 6.458342 CGTTCCCAATATTTGTCTTTCTAGGC 60.458 42.308 0.00 0.00 0.00 3.93
3432 13352 6.038271 CCGTTCCCAATATTTGTCTTTCTAGG 59.962 42.308 0.00 0.00 0.00 3.02
3433 13353 6.821665 TCCGTTCCCAATATTTGTCTTTCTAG 59.178 38.462 0.00 0.00 0.00 2.43
3434 13354 6.713276 TCCGTTCCCAATATTTGTCTTTCTA 58.287 36.000 0.00 0.00 0.00 2.10
3435 13355 5.566469 TCCGTTCCCAATATTTGTCTTTCT 58.434 37.500 0.00 0.00 0.00 2.52
3436 13356 5.163652 CCTCCGTTCCCAATATTTGTCTTTC 60.164 44.000 0.00 0.00 0.00 2.62
3437 13357 4.705023 CCTCCGTTCCCAATATTTGTCTTT 59.295 41.667 0.00 0.00 0.00 2.52
3438 13358 4.270008 CCTCCGTTCCCAATATTTGTCTT 58.730 43.478 0.00 0.00 0.00 3.01
3439 13359 3.371595 CCCTCCGTTCCCAATATTTGTCT 60.372 47.826 0.00 0.00 0.00 3.41
3440 13360 2.949644 CCCTCCGTTCCCAATATTTGTC 59.050 50.000 0.00 0.00 0.00 3.18
3441 13361 2.578940 TCCCTCCGTTCCCAATATTTGT 59.421 45.455 0.00 0.00 0.00 2.83
3442 13362 3.214328 CTCCCTCCGTTCCCAATATTTG 58.786 50.000 0.00 0.00 0.00 2.32
3443 13363 2.850568 ACTCCCTCCGTTCCCAATATTT 59.149 45.455 0.00 0.00 0.00 1.40
3444 13364 2.488836 ACTCCCTCCGTTCCCAATATT 58.511 47.619 0.00 0.00 0.00 1.28
3445 13365 2.191981 ACTCCCTCCGTTCCCAATAT 57.808 50.000 0.00 0.00 0.00 1.28
3446 13366 2.852714 TACTCCCTCCGTTCCCAATA 57.147 50.000 0.00 0.00 0.00 1.90
3447 13367 2.191981 ATACTCCCTCCGTTCCCAAT 57.808 50.000 0.00 0.00 0.00 3.16
3448 13368 2.852714 TATACTCCCTCCGTTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
3449 13369 2.245546 TCTTATACTCCCTCCGTTCCCA 59.754 50.000 0.00 0.00 0.00 4.37
3450 13370 2.892215 CTCTTATACTCCCTCCGTTCCC 59.108 54.545 0.00 0.00 0.00 3.97
3451 13371 3.822167 CTCTCTTATACTCCCTCCGTTCC 59.178 52.174 0.00 0.00 0.00 3.62
3452 13372 4.276431 CACTCTCTTATACTCCCTCCGTTC 59.724 50.000 0.00 0.00 0.00 3.95
3453 13373 4.079901 TCACTCTCTTATACTCCCTCCGTT 60.080 45.833 0.00 0.00 0.00 4.44
3454 13374 3.458857 TCACTCTCTTATACTCCCTCCGT 59.541 47.826 0.00 0.00 0.00 4.69
3455 13375 4.088056 TCACTCTCTTATACTCCCTCCG 57.912 50.000 0.00 0.00 0.00 4.63
3456 13376 5.245075 CCATTCACTCTCTTATACTCCCTCC 59.755 48.000 0.00 0.00 0.00 4.30
3457 13377 5.245075 CCCATTCACTCTCTTATACTCCCTC 59.755 48.000 0.00 0.00 0.00 4.30
3458 13378 5.151454 CCCATTCACTCTCTTATACTCCCT 58.849 45.833 0.00 0.00 0.00 4.20
3459 13379 4.284746 CCCCATTCACTCTCTTATACTCCC 59.715 50.000 0.00 0.00 0.00 4.30
3460 13380 4.902448 ACCCCATTCACTCTCTTATACTCC 59.098 45.833 0.00 0.00 0.00 3.85
3461 13381 5.598830 TGACCCCATTCACTCTCTTATACTC 59.401 44.000 0.00 0.00 0.00 2.59
3462 13382 5.529289 TGACCCCATTCACTCTCTTATACT 58.471 41.667 0.00 0.00 0.00 2.12
3463 13383 5.871396 TGACCCCATTCACTCTCTTATAC 57.129 43.478 0.00 0.00 0.00 1.47
3464 13384 6.183361 CCAATGACCCCATTCACTCTCTTATA 60.183 42.308 0.00 0.00 40.81 0.98
3465 13385 5.398353 CCAATGACCCCATTCACTCTCTTAT 60.398 44.000 0.00 0.00 40.81 1.73
3466 13386 4.080356 CCAATGACCCCATTCACTCTCTTA 60.080 45.833 0.00 0.00 40.81 2.10
3467 13387 3.308688 CCAATGACCCCATTCACTCTCTT 60.309 47.826 0.00 0.00 40.81 2.85
3468 13388 2.240667 CCAATGACCCCATTCACTCTCT 59.759 50.000 0.00 0.00 40.81 3.10
3469 13389 2.239654 TCCAATGACCCCATTCACTCTC 59.760 50.000 0.00 0.00 40.81 3.20
3499 13419 1.443872 GCAACGGTCGACTCGTCAT 60.444 57.895 25.13 12.98 40.18 3.06


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

AutoCloner maintained by Alex Coulton.