Multiple sequence alignment - TraesCS4B01G328500

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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 TraesCS4B01G328500 chr4B 100.000 4012 0 0 4169 8180 619446885 619450896 0.000000e+00 7409.0
1 TraesCS4B01G328500 chr4B 100.000 3802 0 0 1 3802 619442717 619446518 0.000000e+00 7022.0
2 TraesCS4B01G328500 chr4B 82.169 1789 219 48 4169 5920 171625391 171623666 0.000000e+00 1445.0
3 TraesCS4B01G328500 chr4B 83.094 1183 138 30 6122 7285 171623667 171622528 0.000000e+00 1020.0
4 TraesCS4B01G328500 chr4B 83.227 787 112 18 3007 3786 171626187 171625414 0.000000e+00 704.0
5 TraesCS4B01G328500 chr4B 85.240 542 50 19 2352 2878 171626714 171626188 1.560000e-146 531.0
6 TraesCS4B01G328500 chr4B 80.921 456 37 24 783 1190 171628633 171628180 1.710000e-81 315.0
7 TraesCS4B01G328500 chr4B 94.000 50 2 1 5919 5968 217854218 217854170 3.170000e-09 75.0
8 TraesCS4B01G328500 chr4B 87.273 55 6 1 7485 7538 549548395 549548341 2.470000e-05 62.1
9 TraesCS4B01G328500 chr4D 94.017 3493 160 38 4169 7638 485619334 485622800 0.000000e+00 5247.0
10 TraesCS4B01G328500 chr4D 94.151 2103 84 21 1713 3796 485617247 485619329 0.000000e+00 3166.0
11 TraesCS4B01G328500 chr4D 82.451 1795 217 44 4169 5920 110078512 110080251 0.000000e+00 1480.0
12 TraesCS4B01G328500 chr4D 94.164 634 25 7 700 1327 485612554 485613181 0.000000e+00 955.0
13 TraesCS4B01G328500 chr4D 94.346 619 31 4 1 618 485611941 485612556 0.000000e+00 946.0
14 TraesCS4B01G328500 chr4D 85.277 686 84 10 6127 6799 110080255 110080936 0.000000e+00 691.0
15 TraesCS4B01G328500 chr4D 93.023 473 29 3 7711 8180 485623211 485623682 0.000000e+00 688.0
16 TraesCS4B01G328500 chr4D 82.824 786 106 21 3007 3786 110077727 110078489 0.000000e+00 676.0
17 TraesCS4B01G328500 chr4D 89.101 367 24 12 2352 2703 110077234 110077599 7.530000e-120 442.0
18 TraesCS4B01G328500 chr4D 93.923 181 4 4 1546 1721 485613184 485613362 4.870000e-67 267.0
19 TraesCS4B01G328500 chr4D 79.851 402 30 32 821 1186 110075430 110075816 6.340000e-61 246.0
20 TraesCS4B01G328500 chr4D 90.132 152 15 0 5973 6124 120352255 120352406 1.800000e-46 198.0
21 TraesCS4B01G328500 chr4D 90.667 150 12 2 5973 6120 339064953 339065102 1.800000e-46 198.0
22 TraesCS4B01G328500 chr4D 96.364 110 4 0 2754 2863 110077601 110077710 1.810000e-41 182.0
23 TraesCS4B01G328500 chr5A 90.613 1598 103 21 1317 2876 666347121 666348709 0.000000e+00 2076.0
24 TraesCS4B01G328500 chr5A 87.330 1768 165 34 4169 5920 666349520 666351244 0.000000e+00 1969.0
25 TraesCS4B01G328500 chr5A 88.564 822 62 16 2966 3783 666348705 666349498 0.000000e+00 968.0
26 TraesCS4B01G328500 chr5A 83.664 906 91 36 6628 7496 666351972 666352857 0.000000e+00 800.0
27 TraesCS4B01G328500 chr5A 87.151 537 35 15 709 1241 666346608 666347114 5.500000e-161 579.0
28 TraesCS4B01G328500 chr5A 94.925 335 16 1 1 334 666345417 666345751 2.620000e-144 523.0
29 TraesCS4B01G328500 chr5A 89.320 206 19 3 5918 6120 569717171 569717376 1.050000e-63 255.0
30 TraesCS4B01G328500 chr5A 89.091 55 5 1 5914 5968 657479467 657479414 5.300000e-07 67.6
31 TraesCS4B01G328500 chr4A 83.744 1581 189 33 4382 5920 466640971 466639417 0.000000e+00 1434.0
32 TraesCS4B01G328500 chr4A 85.242 1179 139 21 6127 7285 466639413 466638250 0.000000e+00 1181.0
33 TraesCS4B01G328500 chr4A 83.629 788 108 19 3007 3786 466641945 466641171 0.000000e+00 721.0
34 TraesCS4B01G328500 chr4A 84.725 563 49 25 2352 2878 466642507 466641946 5.620000e-146 529.0
35 TraesCS4B01G328500 chr4A 80.000 460 34 27 783 1186 466644290 466643833 3.740000e-73 287.0
36 TraesCS4B01G328500 chr4A 89.474 152 15 1 5973 6123 132995432 132995281 3.010000e-44 191.0
37 TraesCS4B01G328500 chr4A 84.181 177 24 4 5971 6144 622124103 622123928 1.410000e-37 169.0
38 TraesCS4B01G328500 chrUn 82.390 318 47 7 2362 2672 206992618 206992933 1.350000e-67 268.0
39 TraesCS4B01G328500 chrUn 81.818 319 48 8 2362 2672 237129943 237129627 8.140000e-65 259.0
40 TraesCS4B01G328500 chrUn 80.505 277 43 10 6268 6536 207002296 207002569 1.390000e-47 202.0
41 TraesCS4B01G328500 chrUn 88.235 102 10 2 600 701 15864358 15864259 4.010000e-23 121.0
42 TraesCS4B01G328500 chrUn 91.765 85 7 0 2756 2840 237129582 237129498 1.440000e-22 119.0
43 TraesCS4B01G328500 chrUn 92.683 41 3 0 7498 7538 71541065 71541025 8.870000e-05 60.2
44 TraesCS4B01G328500 chrUn 92.683 41 3 0 7495 7535 71565846 71565886 8.870000e-05 60.2
45 TraesCS4B01G328500 chrUn 92.683 41 3 0 7498 7538 162812863 162812823 8.870000e-05 60.2
46 TraesCS4B01G328500 chrUn 94.737 38 2 0 7498 7535 165511057 165511094 8.870000e-05 60.2
47 TraesCS4B01G328500 chrUn 94.737 38 2 0 7498 7535 165543351 165543388 8.870000e-05 60.2
48 TraesCS4B01G328500 chr5D 86.408 206 16 4 5918 6120 450540009 450540205 1.790000e-51 215.0
49 TraesCS4B01G328500 chr5D 100.000 28 0 0 2893 2920 358219747 358219720 1.500000e-02 52.8
50 TraesCS4B01G328500 chr3B 89.375 160 16 1 5973 6131 394097911 394097752 5.010000e-47 200.0
51 TraesCS4B01G328500 chr3D 88.820 161 16 2 5973 6131 298595020 298594860 6.480000e-46 196.0
52 TraesCS4B01G328500 chr3D 92.593 54 2 2 2912 2964 545225969 545226021 8.800000e-10 76.8
53 TraesCS4B01G328500 chr3D 88.889 63 2 2 2285 2347 3045058 3045115 1.140000e-08 73.1
54 TraesCS4B01G328500 chr5B 89.542 153 13 2 5973 6124 491101600 491101750 3.010000e-44 191.0
55 TraesCS4B01G328500 chr5B 88.136 59 2 4 2281 2339 493128978 493128925 1.910000e-06 65.8
56 TraesCS4B01G328500 chr5B 100.000 29 0 0 2904 2932 19440836 19440864 4.000000e-03 54.7
57 TraesCS4B01G328500 chr5B 100.000 28 0 0 2286 2313 430683573 430683600 1.500000e-02 52.8
58 TraesCS4B01G328500 chr2D 89.796 147 15 0 5974 6120 170509556 170509702 1.080000e-43 189.0
59 TraesCS4B01G328500 chr2D 93.878 49 2 1 5920 5968 394789679 394789726 1.140000e-08 73.1
60 TraesCS4B01G328500 chr2D 90.698 43 2 2 1450 1492 317943574 317943534 1.000000e-03 56.5
61 TraesCS4B01G328500 chr2B 83.537 164 23 4 5980 6142 376496880 376497040 5.110000e-32 150.0
62 TraesCS4B01G328500 chr2B 93.182 88 6 0 616 703 558427622 558427535 6.660000e-26 130.0
63 TraesCS4B01G328500 chr2B 87.838 74 9 0 2876 2949 46945942 46946015 4.070000e-13 87.9
64 TraesCS4B01G328500 chr1B 96.512 86 3 0 616 701 656007381 656007296 8.560000e-30 143.0
65 TraesCS4B01G328500 chr1B 93.182 88 6 0 616 703 10962787 10962874 6.660000e-26 130.0
66 TraesCS4B01G328500 chr1B 84.507 71 9 1 350 418 577610440 577610370 1.470000e-07 69.4
67 TraesCS4B01G328500 chr1B 89.583 48 3 1 7490 7535 289603649 289603696 8.870000e-05 60.2
68 TraesCS4B01G328500 chr7B 94.318 88 5 0 616 703 430307413 430307326 1.430000e-27 135.0
69 TraesCS4B01G328500 chr7B 92.982 57 3 1 2894 2949 533846748 533846804 1.890000e-11 82.4
70 TraesCS4B01G328500 chr7B 91.071 56 4 1 5913 5968 158072616 158072670 3.170000e-09 75.0
71 TraesCS4B01G328500 chr1D 82.036 167 19 8 5973 6136 465779767 465779925 1.850000e-26 132.0
72 TraesCS4B01G328500 chr6B 93.182 88 6 0 616 703 31796178 31796265 6.660000e-26 130.0
73 TraesCS4B01G328500 chr7A 89.899 99 7 3 604 701 581849906 581850002 3.100000e-24 124.0
74 TraesCS4B01G328500 chr7A 91.304 46 2 2 1437 1482 214782179 214782222 2.470000e-05 62.1
75 TraesCS4B01G328500 chr6A 88.000 100 10 2 602 701 579814399 579814302 5.190000e-22 117.0
76 TraesCS4B01G328500 chr6A 92.000 50 4 0 356 405 101982954 101983003 4.100000e-08 71.3
77 TraesCS4B01G328500 chr1A 87.255 102 11 2 606 706 4364917 4365017 1.870000e-21 115.0
78 TraesCS4B01G328500 chr1A 85.417 96 11 3 2879 2971 347924346 347924251 6.760000e-16 97.1
79 TraesCS4B01G328500 chr2A 88.889 90 10 0 2875 2964 60193321 60193410 2.410000e-20 111.0
80 TraesCS4B01G328500 chr2A 93.878 49 2 1 5920 5968 532857159 532857206 1.140000e-08 73.1
81 TraesCS4B01G328500 chr2A 84.507 71 8 2 350 418 649477849 649477780 5.300000e-07 67.6
82 TraesCS4B01G328500 chr2A 88.000 50 5 1 350 399 670308736 670308688 3.190000e-04 58.4
83 TraesCS4B01G328500 chr7D 91.176 68 6 0 2868 2935 266396263 266396196 8.740000e-15 93.5
84 TraesCS4B01G328500 chr3A 96.000 50 1 1 5919 5968 69662536 69662584 6.810000e-11 80.5
85 TraesCS4B01G328500 chr6D 97.561 41 1 0 7498 7538 26119912 26119952 4.100000e-08 71.3
86 TraesCS4B01G328500 chr6D 100.000 28 0 0 349 376 267238807 267238780 1.500000e-02 52.8


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 TraesCS4B01G328500 chr4B 619442717 619450896 8179 False 7215.500000 7409 100.000000 1 8180 2 chr4B.!!$F1 8179
1 TraesCS4B01G328500 chr4B 171622528 171628633 6105 True 803.000000 1445 82.930200 783 7285 5 chr4B.!!$R3 6502
2 TraesCS4B01G328500 chr4D 485611941 485623682 11741 False 1878.166667 5247 93.937333 1 8180 6 chr4D.!!$F4 8179
3 TraesCS4B01G328500 chr4D 110075430 110080936 5506 False 619.500000 1480 85.978000 821 6799 6 chr4D.!!$F3 5978
4 TraesCS4B01G328500 chr5A 666345417 666352857 7440 False 1152.500000 2076 88.707833 1 7496 6 chr5A.!!$F2 7495
5 TraesCS4B01G328500 chr4A 466638250 466644290 6040 True 830.400000 1434 83.468000 783 7285 5 chr4A.!!$R3 6502

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
907 1498 1.383523 GGCTTGGCTTAGCTTACCTG 58.616 55.000 3.59 0.0 40.99 4.00 F
1315 1974 0.678950 TCTCACGATGCAGACACCAA 59.321 50.000 0.00 0.0 0.00 3.67 F
1948 6938 0.647410 CTCATTAGCACCAACTCGCG 59.353 55.000 0.00 0.0 0.00 5.87 F
2316 7506 2.014335 TCACAATGATGCAGAGACCG 57.986 50.000 0.00 0.0 0.00 4.79 F
2326 7516 2.362120 AGAGACCGGGGGTACGTG 60.362 66.667 6.32 0.0 35.25 4.49 F
3801 9042 2.680339 CCATAACACACACACACACACA 59.320 45.455 0.00 0.0 0.00 3.72 F
4245 9486 2.699846 TGAAGACAAGCAAAAGGGCAAT 59.300 40.909 0.00 0.0 35.83 3.56 F
5287 10609 3.196300 AGGGCCCATATGCATAAGATCT 58.804 45.455 27.56 0.0 0.00 2.75 F
5667 11010 1.168407 TTGCAGCTGTGAGCAGTTCC 61.168 55.000 16.64 0.0 45.56 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1862 6683 1.137282 TGCCGCGGTGACTAATAATGA 59.863 47.619 28.70 0.00 0.00 2.57 R
3186 8418 0.394762 TGCTTTGCAGGCTGATAGGG 60.395 55.000 20.86 4.68 33.32 3.53 R
3395 8631 0.817013 GGGACGTGACATACCGGTAA 59.183 55.000 20.22 0.00 0.00 2.85 R
3731 8972 3.199946 GTCAGACCCCAATTAGACCATCA 59.800 47.826 0.00 0.00 0.00 3.07 R
4272 9515 4.346730 TCAGAGACCAATTGCAAATGGAT 58.653 39.130 34.83 23.67 39.12 3.41 R
5299 10621 1.766496 TCTGGTTTCCGAGTGGTTCTT 59.234 47.619 0.00 0.00 36.30 2.52 R
5462 10789 2.147958 TGGTCCAAAATGTGTAGCGTC 58.852 47.619 0.00 0.00 0.00 5.19 R
6877 12486 0.623723 GGGCCCATGAGAACCTACAA 59.376 55.000 19.95 0.00 0.00 2.41 R
7541 13186 0.240145 TACAAGGTGCGACGAGTCAG 59.760 55.000 0.00 0.00 0.00 3.51 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
136 138 3.499048 CACTGACGTATGTAGTCACACC 58.501 50.000 0.00 0.00 42.91 4.16
186 188 3.010027 TCTGGTCCATGTGATTAGCCAAA 59.990 43.478 0.00 0.00 0.00 3.28
229 231 6.719829 TGAGTCCATATATCAACTCCACGTAT 59.280 38.462 16.20 0.00 37.85 3.06
247 249 1.892209 ATGTGTCACCCTTTTCGTCC 58.108 50.000 0.00 0.00 0.00 4.79
313 316 3.141767 AGACTAACCTGGTTGAAAGCC 57.858 47.619 22.04 4.25 0.00 4.35
372 375 7.169476 GTCTTAACCAAGTCTCAGTCAAGTAAC 59.831 40.741 0.00 0.00 33.20 2.50
429 443 7.678837 AGGAAAATTTTGCACATATCTCCAAA 58.321 30.769 22.35 0.00 0.00 3.28
455 469 5.405571 ACAATGTTATGAACAGTCGACTGAC 59.594 40.000 43.55 34.08 46.59 3.51
467 481 4.522297 GTCGACTGACATTTAGCAATCC 57.478 45.455 8.70 0.00 44.82 3.01
468 482 4.184629 GTCGACTGACATTTAGCAATCCT 58.815 43.478 8.70 0.00 44.82 3.24
471 485 5.105513 TCGACTGACATTTAGCAATCCTGTA 60.106 40.000 0.00 0.00 0.00 2.74
576 1138 6.146184 CGCTCAACTGAAAATTTACTCTCTCA 59.854 38.462 0.00 0.00 0.00 3.27
610 1180 3.738282 GCACTACTGACTGCATGCTATAC 59.262 47.826 20.33 8.36 33.31 1.47
617 1187 9.295214 CTACTGACTGCATGCTATACATATTAC 57.705 37.037 20.33 0.00 36.64 1.89
618 1188 7.901029 ACTGACTGCATGCTATACATATTACT 58.099 34.615 20.33 0.00 36.64 2.24
619 1189 8.031864 ACTGACTGCATGCTATACATATTACTC 58.968 37.037 20.33 0.00 36.64 2.59
620 1190 7.323420 TGACTGCATGCTATACATATTACTCC 58.677 38.462 20.33 0.00 36.64 3.85
621 1191 6.644347 ACTGCATGCTATACATATTACTCCC 58.356 40.000 20.33 0.00 36.64 4.30
622 1192 6.441924 ACTGCATGCTATACATATTACTCCCT 59.558 38.462 20.33 0.00 36.64 4.20
623 1193 6.878317 TGCATGCTATACATATTACTCCCTC 58.122 40.000 20.33 0.00 36.64 4.30
624 1194 6.127054 TGCATGCTATACATATTACTCCCTCC 60.127 42.308 20.33 0.00 36.64 4.30
625 1195 6.507900 CATGCTATACATATTACTCCCTCCG 58.492 44.000 0.00 0.00 36.64 4.63
626 1196 5.577100 TGCTATACATATTACTCCCTCCGT 58.423 41.667 0.00 0.00 0.00 4.69
627 1197 6.014647 TGCTATACATATTACTCCCTCCGTT 58.985 40.000 0.00 0.00 0.00 4.44
628 1198 6.495872 TGCTATACATATTACTCCCTCCGTTT 59.504 38.462 0.00 0.00 0.00 3.60
629 1199 7.015877 TGCTATACATATTACTCCCTCCGTTTT 59.984 37.037 0.00 0.00 0.00 2.43
630 1200 8.526147 GCTATACATATTACTCCCTCCGTTTTA 58.474 37.037 0.00 0.00 0.00 1.52
639 1209 8.726870 TTACTCCCTCCGTTTTAAAATAGATG 57.273 34.615 3.52 2.01 0.00 2.90
640 1210 6.954232 ACTCCCTCCGTTTTAAAATAGATGA 58.046 36.000 3.52 3.96 0.00 2.92
641 1211 6.822170 ACTCCCTCCGTTTTAAAATAGATGAC 59.178 38.462 3.52 0.00 0.00 3.06
642 1212 6.117488 TCCCTCCGTTTTAAAATAGATGACC 58.883 40.000 3.52 0.00 0.00 4.02
643 1213 5.298527 CCCTCCGTTTTAAAATAGATGACCC 59.701 44.000 3.52 0.00 0.00 4.46
644 1214 5.883673 CCTCCGTTTTAAAATAGATGACCCA 59.116 40.000 3.52 0.00 0.00 4.51
645 1215 6.376018 CCTCCGTTTTAAAATAGATGACCCAA 59.624 38.462 3.52 0.00 0.00 4.12
646 1216 7.148355 TCCGTTTTAAAATAGATGACCCAAC 57.852 36.000 3.52 0.00 0.00 3.77
647 1217 6.943718 TCCGTTTTAAAATAGATGACCCAACT 59.056 34.615 3.52 0.00 0.00 3.16
648 1218 7.449086 TCCGTTTTAAAATAGATGACCCAACTT 59.551 33.333 3.52 0.00 0.00 2.66
649 1219 8.085909 CCGTTTTAAAATAGATGACCCAACTTT 58.914 33.333 3.52 0.00 0.00 2.66
650 1220 9.124807 CGTTTTAAAATAGATGACCCAACTTTC 57.875 33.333 3.52 0.00 0.00 2.62
691 1261 5.835113 ATTGGGTCATCTATTTTGGAACG 57.165 39.130 0.00 0.00 0.00 3.95
692 1262 4.561500 TGGGTCATCTATTTTGGAACGA 57.438 40.909 0.00 0.00 0.00 3.85
693 1263 4.912586 TGGGTCATCTATTTTGGAACGAA 58.087 39.130 0.00 0.00 0.00 3.85
694 1264 4.941263 TGGGTCATCTATTTTGGAACGAAG 59.059 41.667 0.00 0.00 0.00 3.79
695 1265 4.335594 GGGTCATCTATTTTGGAACGAAGG 59.664 45.833 0.00 0.00 0.00 3.46
696 1266 5.183228 GGTCATCTATTTTGGAACGAAGGA 58.817 41.667 0.00 0.00 0.00 3.36
697 1267 5.646360 GGTCATCTATTTTGGAACGAAGGAA 59.354 40.000 0.00 0.00 0.00 3.36
698 1268 6.183360 GGTCATCTATTTTGGAACGAAGGAAG 60.183 42.308 0.00 0.00 0.00 3.46
699 1269 6.371825 GTCATCTATTTTGGAACGAAGGAAGT 59.628 38.462 0.00 0.00 0.00 3.01
700 1270 7.548075 GTCATCTATTTTGGAACGAAGGAAGTA 59.452 37.037 0.00 0.00 0.00 2.24
719 1289 6.801862 GGAAGTACAAGAATTCCATTTTCGTG 59.198 38.462 0.65 0.00 41.78 4.35
769 1339 4.873746 GATCTATCGATGGTTTCCCTCA 57.126 45.455 8.54 0.00 0.00 3.86
771 1341 5.799213 GATCTATCGATGGTTTCCCTCATT 58.201 41.667 8.54 0.00 0.00 2.57
907 1498 1.383523 GGCTTGGCTTAGCTTACCTG 58.616 55.000 3.59 0.00 40.99 4.00
975 1580 7.744087 TGTCTGTCAGTGCAGTTATTTAATT 57.256 32.000 12.36 0.00 37.70 1.40
1208 1849 4.142665 TGCGTCACAACTCTACATCTAGAC 60.143 45.833 0.00 0.00 0.00 2.59
1209 1850 4.095185 GCGTCACAACTCTACATCTAGACT 59.905 45.833 0.00 0.00 0.00 3.24
1210 1851 5.293814 GCGTCACAACTCTACATCTAGACTA 59.706 44.000 0.00 0.00 0.00 2.59
1211 1852 6.510478 GCGTCACAACTCTACATCTAGACTAG 60.510 46.154 2.81 2.81 0.00 2.57
1250 1897 5.220892 CGCTCTACCCAAGTACTCTTAGAAG 60.221 48.000 0.00 0.00 32.07 2.85
1253 1900 6.982899 TCTACCCAAGTACTCTTAGAAGGAT 58.017 40.000 0.00 0.00 32.07 3.24
1315 1974 0.678950 TCTCACGATGCAGACACCAA 59.321 50.000 0.00 0.00 0.00 3.67
1443 2214 9.429359 GAGGGATAGAATTTGGCGATATATATG 57.571 37.037 0.00 0.00 0.00 1.78
1445 2216 7.661437 GGGATAGAATTTGGCGATATATATGCA 59.339 37.037 0.00 0.00 0.00 3.96
1489 2260 6.798427 AGATAGCTAACCACTCTCATTTCA 57.202 37.500 0.00 0.00 0.00 2.69
1491 2262 7.271511 AGATAGCTAACCACTCTCATTTCAAG 58.728 38.462 0.00 0.00 0.00 3.02
1492 2263 5.489792 AGCTAACCACTCTCATTTCAAGA 57.510 39.130 0.00 0.00 0.00 3.02
1493 2264 5.486526 AGCTAACCACTCTCATTTCAAGAG 58.513 41.667 0.00 0.00 44.77 2.85
1494 2265 5.247110 AGCTAACCACTCTCATTTCAAGAGA 59.753 40.000 7.12 0.00 42.39 3.10
1495 2266 5.350091 GCTAACCACTCTCATTTCAAGAGAC 59.650 44.000 7.12 0.00 42.39 3.36
1499 2271 5.419155 ACCACTCTCATTTCAAGAGACGATA 59.581 40.000 7.12 0.00 42.39 2.92
1503 2275 9.127006 CACTCTCATTTCAAGAGACGATATATG 57.873 37.037 7.12 0.00 42.39 1.78
1504 2276 9.072375 ACTCTCATTTCAAGAGACGATATATGA 57.928 33.333 7.12 0.00 42.39 2.15
1505 2277 9.905171 CTCTCATTTCAAGAGACGATATATGAA 57.095 33.333 0.00 0.00 42.39 2.57
1512 2284 8.076714 TCAAGAGACGATATATGAACATTTGC 57.923 34.615 0.00 0.00 0.00 3.68
1513 2285 7.171508 TCAAGAGACGATATATGAACATTTGCC 59.828 37.037 0.00 0.00 0.00 4.52
1535 2401 3.908978 CGATGATAGCTAGCTAACACGTG 59.091 47.826 30.21 20.51 34.86 4.49
1536 2402 3.079960 TGATAGCTAGCTAACACGTGC 57.920 47.619 27.47 11.57 31.73 5.34
1538 2404 3.130516 TGATAGCTAGCTAACACGTGCTT 59.869 43.478 27.47 8.44 40.35 3.91
1623 2494 2.505405 CAGCTCTGCCAATATCAGCAT 58.495 47.619 0.49 0.00 38.56 3.79
1682 2566 9.288576 ACATCTCACTTTGATCAGTTTAATTGA 57.711 29.630 0.00 0.00 0.00 2.57
1710 2594 3.679980 CCATATCTTCTTCGCATAACCCG 59.320 47.826 0.00 0.00 0.00 5.28
1722 6501 5.284079 TCGCATAACCCGACTAACTAAATC 58.716 41.667 0.00 0.00 0.00 2.17
1831 6644 8.947115 CATATATGCAGATATATCTTGGCATGG 58.053 37.037 31.64 21.21 42.73 3.66
1836 6649 5.066117 GCAGATATATCTTGGCATGGACATG 59.934 44.000 12.75 7.91 37.15 3.21
1862 6683 5.179452 ACTCTTGCCACCATAGTTGTAAT 57.821 39.130 0.00 0.00 0.00 1.89
1912 6902 6.351711 CCAATTCACTCTCATAGGTCTCACTT 60.352 42.308 0.00 0.00 0.00 3.16
1940 6930 3.906720 TGGAACCTACTCATTAGCACC 57.093 47.619 0.00 0.00 0.00 5.01
1943 6933 3.939592 GGAACCTACTCATTAGCACCAAC 59.060 47.826 0.00 0.00 0.00 3.77
1946 6936 3.119101 ACCTACTCATTAGCACCAACTCG 60.119 47.826 0.00 0.00 0.00 4.18
1948 6938 0.647410 CTCATTAGCACCAACTCGCG 59.353 55.000 0.00 0.00 0.00 5.87
1983 7134 4.314961 TGCATGGCTTATCGGTAATACTG 58.685 43.478 0.00 0.00 0.00 2.74
2052 7224 5.022282 ACACAAAGGATGGGTTTTCTTTG 57.978 39.130 11.57 11.57 45.84 2.77
2219 7392 4.386711 CCGGTCTTCTTGGTAAGAAAGTT 58.613 43.478 0.00 0.00 46.13 2.66
2316 7506 2.014335 TCACAATGATGCAGAGACCG 57.986 50.000 0.00 0.00 0.00 4.79
2326 7516 2.362120 AGAGACCGGGGGTACGTG 60.362 66.667 6.32 0.00 35.25 4.49
2511 7709 9.626045 AGCAAACTTTTCTGCTGTAATAAATAC 57.374 29.630 0.00 0.00 46.97 1.89
2518 7716 4.745125 TCTGCTGTAATAAATACGCTCAGC 59.255 41.667 0.00 0.00 44.39 4.26
2679 7885 5.422012 CCCAATAAAGGTATCCAAGTTTGCT 59.578 40.000 0.00 0.00 0.00 3.91
2719 7926 6.480524 TGTCATAGAAGAACCAAAATCACG 57.519 37.500 0.00 0.00 0.00 4.35
2752 7980 5.738619 ATTTATGTGGCATGCATGATGAT 57.261 34.783 30.64 16.48 33.31 2.45
2917 8148 9.378551 TCATAATAAGTATCGCAGTTTTGAACT 57.621 29.630 0.00 0.00 44.06 3.01
2925 8156 3.807622 TCGCAGTTTTGAACTAACCTCAG 59.192 43.478 0.00 0.00 40.46 3.35
2926 8157 3.560068 CGCAGTTTTGAACTAACCTCAGT 59.440 43.478 0.00 0.00 40.46 3.41
3230 8462 4.540359 TCCGAACCTATTTTCCGAGAAA 57.460 40.909 0.00 0.00 0.00 2.52
3265 8497 9.386010 TGGAAGGTATACATGTTGTGTAAATAC 57.614 33.333 2.30 3.88 45.87 1.89
3395 8631 5.039920 TGTTCTAATCAGCTGCATATGGT 57.960 39.130 9.47 0.00 0.00 3.55
3625 8864 2.775911 TCCAGATCTGAGCCAACAAG 57.224 50.000 24.62 3.94 0.00 3.16
3677 8916 3.505680 TGCAGTCGCCTGTAATTGAAAAT 59.494 39.130 0.00 0.00 41.02 1.82
3690 8929 8.774890 TGTAATTGAAAATGCAGCATTTGTAT 57.225 26.923 29.88 20.36 42.32 2.29
3691 8930 9.866798 TGTAATTGAAAATGCAGCATTTGTATA 57.133 25.926 29.88 17.42 42.32 1.47
3731 8972 6.575162 AAACTGAGAACTGTTGAAGTGTTT 57.425 33.333 0.00 0.78 39.81 2.83
3754 8995 2.915869 TGGTCTAATTGGGGTCTGACT 58.084 47.619 7.85 0.00 0.00 3.41
3757 8998 3.519913 GGTCTAATTGGGGTCTGACTTCT 59.480 47.826 7.85 0.00 0.00 2.85
3798 9039 5.933187 TTATCCATAACACACACACACAC 57.067 39.130 0.00 0.00 0.00 3.82
3799 9040 3.268023 TCCATAACACACACACACACA 57.732 42.857 0.00 0.00 0.00 3.72
3800 9041 2.939756 TCCATAACACACACACACACAC 59.060 45.455 0.00 0.00 0.00 3.82
3801 9042 2.680339 CCATAACACACACACACACACA 59.320 45.455 0.00 0.00 0.00 3.72
4245 9486 2.699846 TGAAGACAAGCAAAAGGGCAAT 59.300 40.909 0.00 0.00 35.83 3.56
4272 9515 9.166173 CTATGTGTCAATGTTGAATTCCTCTAA 57.834 33.333 2.27 0.00 39.21 2.10
4455 9715 8.641498 AGAAATGTATTGTGATTCAGGAGTTT 57.359 30.769 0.00 0.00 0.00 2.66
4607 9867 9.942850 ATTCACATTCCCCTTAAAACATAAAAG 57.057 29.630 0.00 0.00 0.00 2.27
4614 9874 8.073467 TCCCCTTAAAACATAAAAGCTAATGG 57.927 34.615 8.11 0.00 0.00 3.16
4758 10027 8.858094 AGGTATAAGTTATAACTCTACCAGTGC 58.142 37.037 33.10 19.77 43.13 4.40
4764 10033 6.874134 AGTTATAACTCTACCAGTGCACTTTG 59.126 38.462 18.94 14.12 34.56 2.77
4843 10113 6.990349 ACTACAACTACTGTTAAATGTGCACT 59.010 34.615 19.41 0.00 39.64 4.40
4877 10147 5.636965 CGATTGCCTCTAGGATGTTCATAAG 59.363 44.000 0.00 0.00 37.39 1.73
5034 10319 6.042781 TCACTTTTGGACCTACACTACTTCAT 59.957 38.462 0.00 0.00 0.00 2.57
5068 10354 3.475774 GCGGTGTCCACGTAAGCG 61.476 66.667 0.00 0.00 45.62 4.68
5078 10364 3.315191 GTCCACGTAAGCGGGTTATACTA 59.685 47.826 2.65 0.00 40.86 1.82
5149 10447 4.324254 GGTGAGGGTGAAAGGATGACATAA 60.324 45.833 0.00 0.00 0.00 1.90
5197 10512 6.833041 TGTTGGTAGGAAATAGAGACACAAA 58.167 36.000 0.00 0.00 0.00 2.83
5211 10526 6.573434 AGAGACACAAACCCATTTTCTTTTC 58.427 36.000 0.00 0.00 0.00 2.29
5246 10565 9.825972 TTTCTTATTTTAGAACTTGAATGCGAG 57.174 29.630 0.00 0.00 34.04 5.03
5287 10609 3.196300 AGGGCCCATATGCATAAGATCT 58.804 45.455 27.56 0.00 0.00 2.75
5513 10841 9.836076 GTCTTATTGTTGTACTGGTTAAATTCC 57.164 33.333 0.00 0.00 0.00 3.01
5661 11004 1.709147 CCCGTATTGCAGCTGTGAGC 61.709 60.000 16.64 0.34 42.84 4.26
5667 11010 1.168407 TTGCAGCTGTGAGCAGTTCC 61.168 55.000 16.64 0.00 45.56 3.62
5668 11011 1.598962 GCAGCTGTGAGCAGTTCCA 60.599 57.895 16.64 0.00 45.56 3.53
5979 11328 8.593945 TTTTTGAAAAGTCAGGCCTATATCAT 57.406 30.769 3.98 0.00 34.49 2.45
5981 11330 9.693739 TTTTGAAAAGTCAGGCCTATATCATTA 57.306 29.630 3.98 0.00 34.49 1.90
5982 11331 9.693739 TTTGAAAAGTCAGGCCTATATCATTAA 57.306 29.630 3.98 0.00 34.49 1.40
5983 11332 9.693739 TTGAAAAGTCAGGCCTATATCATTAAA 57.306 29.630 3.98 0.00 34.49 1.52
5984 11333 9.866655 TGAAAAGTCAGGCCTATATCATTAAAT 57.133 29.630 3.98 0.00 0.00 1.40
5989 11338 9.678260 AGTCAGGCCTATATCATTAAATTCATC 57.322 33.333 3.98 0.00 0.00 2.92
6075 11432 5.462034 TTGGTCAAAGTTTGCAAATTTCG 57.538 34.783 18.78 9.48 0.00 3.46
6186 11543 6.970484 CATAAGGTTTACATTATGGTCCAGC 58.030 40.000 15.76 0.00 43.13 4.85
6226 11584 8.429641 TGGCCCTAATAAAACAAATACAAACAA 58.570 29.630 0.00 0.00 0.00 2.83
6227 11585 8.714179 GGCCCTAATAAAACAAATACAAACAAC 58.286 33.333 0.00 0.00 0.00 3.32
6623 11991 6.376581 CCCACTTAATCAGAAGCTTCTCAAAT 59.623 38.462 26.18 16.22 34.74 2.32
6799 12400 5.377478 GCCTACCAGCACCTTCTTTTATAT 58.623 41.667 0.00 0.00 0.00 0.86
6904 12513 1.978617 CTCATGGGCCCAAAAGCGT 60.979 57.895 32.58 8.38 0.00 5.07
6931 12540 4.568072 TGCTGCTTTCTTTCCAGGTATA 57.432 40.909 0.00 0.00 0.00 1.47
7026 12639 8.615211 CAGTACATGTGCAATTAATCAGTATGT 58.385 33.333 16.62 0.00 37.40 2.29
7198 12813 1.406860 GCTGCTGGAACCCCCAAAAA 61.407 55.000 0.00 0.00 46.07 1.94
7285 12900 7.092444 ACAAGTCCTATACAATCCTCAATCCAA 60.092 37.037 0.00 0.00 0.00 3.53
7374 13000 9.226606 AGATAGTGTGTAAATTTTTCCGATGAA 57.773 29.630 0.00 0.00 0.00 2.57
7410 13055 4.122046 GCCCTCATGCAACCATTATTTTC 58.878 43.478 0.00 0.00 0.00 2.29
7438 13083 8.712285 TTCTCCCACTAAACATAAATTACTCG 57.288 34.615 0.00 0.00 0.00 4.18
7441 13086 7.051623 TCCCACTAAACATAAATTACTCGCAT 58.948 34.615 0.00 0.00 0.00 4.73
7469 13114 5.289434 CCGTCCTAAGTAAATACGTGAAACC 59.711 44.000 0.00 0.00 31.87 3.27
7491 13136 5.129815 ACCGAAATGCCACCTACTTATCTTA 59.870 40.000 0.00 0.00 0.00 2.10
7496 13141 9.736023 GAAATGCCACCTACTTATCTTATTTTG 57.264 33.333 0.00 0.00 0.00 2.44
7541 13186 3.003378 GTGCGGGCTAGAATTTCATTACC 59.997 47.826 0.00 0.00 0.00 2.85
7548 13193 5.463724 GGCTAGAATTTCATTACCTGACTCG 59.536 44.000 0.00 0.00 32.17 4.18
7551 13196 5.103000 AGAATTTCATTACCTGACTCGTCG 58.897 41.667 0.00 0.00 32.17 5.12
7605 13250 5.466728 GCATTACTTGACTCTTCTTGTGTCA 59.533 40.000 0.00 0.00 44.37 3.58
7621 13266 7.167535 TCTTGTGTCATCCTATTGTGAATTGA 58.832 34.615 0.00 0.00 0.00 2.57
7823 13806 5.007136 GGTTGTGTTCTTCTGTCTTCAAGAG 59.993 44.000 0.00 0.00 30.32 2.85
7916 13899 9.683870 AAATACATTTTCCATATGTTTGCCATT 57.316 25.926 1.24 0.00 37.42 3.16
7923 13906 4.954826 TCCATATGTTTGCCATTGTCATCA 59.045 37.500 1.24 0.00 34.86 3.07
7933 13916 4.750598 TGCCATTGTCATCAATTTTGTGTG 59.249 37.500 0.00 0.00 41.66 3.82
7956 13939 4.214119 GCCATATGCATCTGTAACGATGTT 59.786 41.667 0.19 0.00 42.14 2.71
7992 13975 5.965918 GTGTCTTGTTCTCACTTGCTAAAAC 59.034 40.000 0.00 0.00 0.00 2.43
8042 14025 5.991606 ACGTATGATACCCATATGCATATGC 59.008 40.000 32.60 21.09 44.72 3.14
8049 14032 4.161876 ACCCATATGCATATGCCATTTGT 58.838 39.130 32.60 20.64 38.99 2.83
8052 14035 5.511716 CCCATATGCATATGCCATTTGTTGT 60.512 40.000 32.60 1.80 38.99 3.32
8157 14142 8.265055 TCTTGAATAATTATCGAAACCACCTCT 58.735 33.333 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 127 2.057830 CAGGGCTGGTGTGACTACA 58.942 57.895 0.00 0.00 0.00 2.74
186 188 5.336451 GGACTCATTTAGGTTGCCGATTTTT 60.336 40.000 0.00 0.00 0.00 1.94
229 231 0.531090 CGGACGAAAAGGGTGACACA 60.531 55.000 8.08 0.00 0.00 3.72
247 249 5.507637 ACTCCCTATATACCATGTAGGACG 58.492 45.833 9.77 4.20 44.32 4.79
410 424 9.537192 CATTGTATTTGGAGATATGTGCAAAAT 57.463 29.630 20.62 12.80 40.59 1.82
422 436 8.862325 ACTGTTCATAACATTGTATTTGGAGA 57.138 30.769 0.00 0.00 41.26 3.71
425 439 7.692291 GTCGACTGTTCATAACATTGTATTTGG 59.308 37.037 8.70 0.00 41.26 3.28
429 443 7.275779 GTCAGTCGACTGTTCATAACATTGTAT 59.724 37.037 37.21 0.39 44.12 2.29
501 515 9.191376 GTTGTCACATATACGTATTTTCGTTTC 57.809 33.333 14.33 0.00 43.80 2.78
617 1187 6.260271 GGTCATCTATTTTAAAACGGAGGGAG 59.740 42.308 1.97 0.00 0.00 4.30
618 1188 6.117488 GGTCATCTATTTTAAAACGGAGGGA 58.883 40.000 1.97 4.48 0.00 4.20
619 1189 5.298527 GGGTCATCTATTTTAAAACGGAGGG 59.701 44.000 1.97 2.46 0.00 4.30
620 1190 5.883673 TGGGTCATCTATTTTAAAACGGAGG 59.116 40.000 1.97 6.55 0.00 4.30
621 1191 6.995511 TGGGTCATCTATTTTAAAACGGAG 57.004 37.500 1.97 1.74 0.00 4.63
622 1192 6.943718 AGTTGGGTCATCTATTTTAAAACGGA 59.056 34.615 1.97 5.09 0.00 4.69
623 1193 7.153217 AGTTGGGTCATCTATTTTAAAACGG 57.847 36.000 1.97 0.00 0.00 4.44
624 1194 9.124807 GAAAGTTGGGTCATCTATTTTAAAACG 57.875 33.333 1.97 0.00 0.00 3.60
665 1235 8.247562 CGTTCCAAAATAGATGACCCAATTTTA 58.752 33.333 0.00 0.00 31.97 1.52
666 1236 7.039363 TCGTTCCAAAATAGATGACCCAATTTT 60.039 33.333 0.00 0.00 33.07 1.82
667 1237 6.435904 TCGTTCCAAAATAGATGACCCAATTT 59.564 34.615 0.00 0.00 0.00 1.82
668 1238 5.949354 TCGTTCCAAAATAGATGACCCAATT 59.051 36.000 0.00 0.00 0.00 2.32
669 1239 5.505780 TCGTTCCAAAATAGATGACCCAAT 58.494 37.500 0.00 0.00 0.00 3.16
670 1240 4.912586 TCGTTCCAAAATAGATGACCCAA 58.087 39.130 0.00 0.00 0.00 4.12
671 1241 4.561500 TCGTTCCAAAATAGATGACCCA 57.438 40.909 0.00 0.00 0.00 4.51
672 1242 4.335594 CCTTCGTTCCAAAATAGATGACCC 59.664 45.833 0.00 0.00 0.00 4.46
673 1243 5.183228 TCCTTCGTTCCAAAATAGATGACC 58.817 41.667 0.00 0.00 0.00 4.02
674 1244 6.371825 ACTTCCTTCGTTCCAAAATAGATGAC 59.628 38.462 0.00 0.00 0.00 3.06
675 1245 6.472887 ACTTCCTTCGTTCCAAAATAGATGA 58.527 36.000 0.00 0.00 0.00 2.92
676 1246 6.743575 ACTTCCTTCGTTCCAAAATAGATG 57.256 37.500 0.00 0.00 0.00 2.90
677 1247 7.391620 TGTACTTCCTTCGTTCCAAAATAGAT 58.608 34.615 0.00 0.00 0.00 1.98
678 1248 6.761312 TGTACTTCCTTCGTTCCAAAATAGA 58.239 36.000 0.00 0.00 0.00 1.98
679 1249 7.386848 TCTTGTACTTCCTTCGTTCCAAAATAG 59.613 37.037 0.00 0.00 0.00 1.73
680 1250 7.218614 TCTTGTACTTCCTTCGTTCCAAAATA 58.781 34.615 0.00 0.00 0.00 1.40
681 1251 6.059484 TCTTGTACTTCCTTCGTTCCAAAAT 58.941 36.000 0.00 0.00 0.00 1.82
682 1252 5.430007 TCTTGTACTTCCTTCGTTCCAAAA 58.570 37.500 0.00 0.00 0.00 2.44
683 1253 5.026038 TCTTGTACTTCCTTCGTTCCAAA 57.974 39.130 0.00 0.00 0.00 3.28
684 1254 4.675976 TCTTGTACTTCCTTCGTTCCAA 57.324 40.909 0.00 0.00 0.00 3.53
685 1255 4.675976 TTCTTGTACTTCCTTCGTTCCA 57.324 40.909 0.00 0.00 0.00 3.53
686 1256 5.121925 GGAATTCTTGTACTTCCTTCGTTCC 59.878 44.000 5.23 0.00 36.36 3.62
687 1257 5.699458 TGGAATTCTTGTACTTCCTTCGTTC 59.301 40.000 5.23 0.00 39.36 3.95
688 1258 5.617252 TGGAATTCTTGTACTTCCTTCGTT 58.383 37.500 5.23 0.00 39.36 3.85
689 1259 5.223449 TGGAATTCTTGTACTTCCTTCGT 57.777 39.130 5.23 0.00 39.36 3.85
690 1260 6.743575 AATGGAATTCTTGTACTTCCTTCG 57.256 37.500 5.23 0.00 39.36 3.79
691 1261 7.750903 CGAAAATGGAATTCTTGTACTTCCTTC 59.249 37.037 5.23 6.75 39.36 3.46
692 1262 7.230712 ACGAAAATGGAATTCTTGTACTTCCTT 59.769 33.333 5.23 3.69 39.36 3.36
693 1263 6.715264 ACGAAAATGGAATTCTTGTACTTCCT 59.285 34.615 5.23 0.00 39.36 3.36
694 1264 6.801862 CACGAAAATGGAATTCTTGTACTTCC 59.198 38.462 5.23 4.30 33.67 3.46
695 1265 7.581476 TCACGAAAATGGAATTCTTGTACTTC 58.419 34.615 5.23 1.39 33.67 3.01
696 1266 7.504924 TCACGAAAATGGAATTCTTGTACTT 57.495 32.000 5.23 0.00 33.67 2.24
697 1267 7.174946 ACATCACGAAAATGGAATTCTTGTACT 59.825 33.333 5.23 0.00 33.67 2.73
698 1268 7.305474 ACATCACGAAAATGGAATTCTTGTAC 58.695 34.615 5.23 0.00 33.67 2.90
699 1269 7.174080 TGACATCACGAAAATGGAATTCTTGTA 59.826 33.333 5.23 0.00 33.67 2.41
700 1270 6.016360 TGACATCACGAAAATGGAATTCTTGT 60.016 34.615 5.23 0.00 33.67 3.16
769 1339 0.976641 TCGGTCTCAGGCTGACAAAT 59.023 50.000 14.43 0.00 36.26 2.32
771 1341 1.112916 TGTCGGTCTCAGGCTGACAA 61.113 55.000 18.99 2.40 45.79 3.18
907 1498 7.421530 CACTATGTTGTGGTGTTATATAGGC 57.578 40.000 0.00 0.00 34.84 3.93
1208 1849 3.581755 AGCGACGACTCTATCTAGCTAG 58.418 50.000 15.01 15.01 30.49 3.42
1209 1850 3.256383 AGAGCGACGACTCTATCTAGCTA 59.744 47.826 16.69 0.00 45.25 3.32
1210 1851 2.036733 AGAGCGACGACTCTATCTAGCT 59.963 50.000 16.69 0.00 45.25 3.32
1211 1852 2.409975 AGAGCGACGACTCTATCTAGC 58.590 52.381 16.69 0.00 45.25 3.42
1220 1861 0.608582 ACTTGGGTAGAGCGACGACT 60.609 55.000 0.00 0.00 0.00 4.18
1341 2087 7.473366 TGTGAAACAGTTATTTTCTAACGCAA 58.527 30.769 0.00 0.00 45.67 4.85
1396 2150 6.044404 CCCTCCTATCATACCCTGTTTAATGT 59.956 42.308 0.00 0.00 0.00 2.71
1407 2161 7.569240 CCAAATTCTATCCCTCCTATCATACC 58.431 42.308 0.00 0.00 0.00 2.73
1417 2184 9.429359 CATATATATCGCCAAATTCTATCCCTC 57.571 37.037 0.00 0.00 0.00 4.30
1465 2236 7.898014 TGAAATGAGAGTGGTTAGCTATCTA 57.102 36.000 0.00 0.00 0.00 1.98
1470 2241 5.247110 TCTCTTGAAATGAGAGTGGTTAGCT 59.753 40.000 0.00 0.00 41.58 3.32
1471 2242 5.350091 GTCTCTTGAAATGAGAGTGGTTAGC 59.650 44.000 0.00 0.00 46.24 3.09
1472 2243 5.574830 CGTCTCTTGAAATGAGAGTGGTTAG 59.425 44.000 0.00 0.00 46.24 2.34
1473 2244 5.243060 TCGTCTCTTGAAATGAGAGTGGTTA 59.757 40.000 0.00 0.00 46.24 2.85
1474 2245 4.039245 TCGTCTCTTGAAATGAGAGTGGTT 59.961 41.667 0.00 0.00 46.24 3.67
1475 2246 3.574396 TCGTCTCTTGAAATGAGAGTGGT 59.426 43.478 0.00 0.00 46.24 4.16
1476 2247 4.179926 TCGTCTCTTGAAATGAGAGTGG 57.820 45.455 0.00 0.00 46.24 4.00
1477 2248 9.127006 CATATATCGTCTCTTGAAATGAGAGTG 57.873 37.037 0.00 0.00 46.24 3.51
1481 2252 9.468532 TGTTCATATATCGTCTCTTGAAATGAG 57.531 33.333 0.00 0.00 39.31 2.90
1482 2253 9.987272 ATGTTCATATATCGTCTCTTGAAATGA 57.013 29.630 0.00 0.00 0.00 2.57
1489 2260 6.146184 CGGCAAATGTTCATATATCGTCTCTT 59.854 38.462 0.00 0.00 0.00 2.85
1491 2262 5.633601 TCGGCAAATGTTCATATATCGTCTC 59.366 40.000 0.00 0.00 0.00 3.36
1492 2263 5.538118 TCGGCAAATGTTCATATATCGTCT 58.462 37.500 0.00 0.00 0.00 4.18
1493 2264 5.839262 TCGGCAAATGTTCATATATCGTC 57.161 39.130 0.00 0.00 0.00 4.20
1494 2265 5.931724 TCATCGGCAAATGTTCATATATCGT 59.068 36.000 0.00 0.00 0.00 3.73
1495 2266 6.407475 TCATCGGCAAATGTTCATATATCG 57.593 37.500 0.00 0.00 0.00 2.92
1499 2271 5.942236 AGCTATCATCGGCAAATGTTCATAT 59.058 36.000 0.00 0.00 0.00 1.78
1503 2275 4.377841 GCTAGCTATCATCGGCAAATGTTC 60.378 45.833 7.70 0.00 0.00 3.18
1504 2276 3.499918 GCTAGCTATCATCGGCAAATGTT 59.500 43.478 7.70 0.00 0.00 2.71
1505 2277 3.070018 GCTAGCTATCATCGGCAAATGT 58.930 45.455 7.70 0.00 0.00 2.71
1512 2284 3.058155 ACGTGTTAGCTAGCTATCATCGG 60.058 47.826 32.33 26.43 32.83 4.18
1513 2285 3.908978 CACGTGTTAGCTAGCTATCATCG 59.091 47.826 30.39 30.39 32.83 3.84
1623 2494 4.781775 TGAAGTACAAGAAGGGGAACAA 57.218 40.909 0.00 0.00 0.00 2.83
1682 2566 2.299013 TGCGAAGAAGATATGGCGGTAT 59.701 45.455 0.00 0.00 0.00 2.73
1710 2594 5.952033 ACTGAGGTCACGATTTAGTTAGTC 58.048 41.667 0.00 0.00 0.00 2.59
1837 6650 2.489329 CAACTATGGTGGCAAGAGTTGG 59.511 50.000 15.54 1.99 42.03 3.77
1839 6652 3.508845 ACAACTATGGTGGCAAGAGTT 57.491 42.857 0.00 0.00 0.00 3.01
1862 6683 1.137282 TGCCGCGGTGACTAATAATGA 59.863 47.619 28.70 0.00 0.00 2.57
1912 6902 6.374333 GCTAATGAGTAGGTTCCATGTTTCAA 59.626 38.462 0.00 0.00 0.00 2.69
1943 6933 4.972286 TGCATCAAATAGATAACGCGAG 57.028 40.909 15.93 0.00 34.43 5.03
1946 6936 4.083110 AGCCATGCATCAAATAGATAACGC 60.083 41.667 0.00 0.00 34.43 4.84
1948 6938 7.907045 CGATAAGCCATGCATCAAATAGATAAC 59.093 37.037 0.00 0.00 34.43 1.89
1983 7134 5.856455 CCATGGAGTTTTTATGTTCGACAAC 59.144 40.000 5.56 0.00 0.00 3.32
2316 7506 1.519246 GAGGTTAGCACGTACCCCC 59.481 63.158 1.53 0.00 34.90 5.40
2350 7543 4.139786 GACATGGACATCAGCATACCATT 58.860 43.478 0.00 0.00 38.99 3.16
2679 7885 9.563748 TTCTATGACATAATTGATGCTGATTGA 57.436 29.630 0.00 0.00 39.39 2.57
2719 7926 7.599621 TGCATGCCACATAAATATTTTCTATGC 59.400 33.333 16.68 12.48 36.25 3.14
2752 7980 5.275067 AGCCTGCAAAAGTCAACAATTAA 57.725 34.783 0.00 0.00 0.00 1.40
2903 8134 3.799366 TGAGGTTAGTTCAAAACTGCGA 58.201 40.909 2.65 0.00 42.84 5.10
2953 8184 6.109359 CCTGTCAAAAATACTACTCCCTCAG 58.891 44.000 0.00 0.00 0.00 3.35
3186 8418 0.394762 TGCTTTGCAGGCTGATAGGG 60.395 55.000 20.86 4.68 33.32 3.53
3190 8422 2.626743 GGATATTGCTTTGCAGGCTGAT 59.373 45.455 20.86 3.05 40.61 2.90
3230 8462 8.522830 CAACATGTATACCTTCCAAAAACAGAT 58.477 33.333 0.00 0.00 0.00 2.90
3395 8631 0.817013 GGGACGTGACATACCGGTAA 59.183 55.000 20.22 0.00 0.00 2.85
3483 8719 7.510549 TGTCTCCAAGTTGAAAAATAAGAGG 57.489 36.000 3.87 0.00 0.00 3.69
3625 8864 8.854614 ATTAAGAAATACATGTGGCCTATCTC 57.145 34.615 9.11 0.00 0.00 2.75
3677 8916 6.114767 TGATCAGAAGTATACAAATGCTGCA 58.885 36.000 4.13 4.13 0.00 4.41
3731 8972 3.199946 GTCAGACCCCAATTAGACCATCA 59.800 47.826 0.00 0.00 0.00 3.07
3754 8995 5.930837 ATTGTTTTTGTGTCCCTCAAGAA 57.069 34.783 0.00 0.00 0.00 2.52
3757 8998 6.325028 TGGATAATTGTTTTTGTGTCCCTCAA 59.675 34.615 0.00 0.00 0.00 3.02
4235 9476 5.481473 ACATTGACACATAGATTGCCCTTTT 59.519 36.000 0.00 0.00 0.00 2.27
4245 9486 7.397221 AGAGGAATTCAACATTGACACATAGA 58.603 34.615 7.93 0.00 36.83 1.98
4272 9515 4.346730 TCAGAGACCAATTGCAAATGGAT 58.653 39.130 34.83 23.67 39.12 3.41
4376 9636 4.286032 AGTGTCTCCTGGTAGCAAACATTA 59.714 41.667 0.00 0.00 0.00 1.90
4380 9640 2.841442 AGTGTCTCCTGGTAGCAAAC 57.159 50.000 0.00 0.00 0.00 2.93
4455 9715 2.667470 CGGAACTTCTCTATGGGGAGA 58.333 52.381 0.00 0.00 40.16 3.71
4812 10081 8.833493 ACATTTAACAGTAGTTGTAGTTGAACC 58.167 33.333 0.00 0.00 39.73 3.62
4843 10113 9.653287 CATCCTAGAGGCAATCGTAATATTTTA 57.347 33.333 0.00 0.00 34.44 1.52
4877 10147 7.928307 ATATACATGGCAGAATGTTCCATAC 57.072 36.000 0.00 0.00 36.92 2.39
4965 10248 7.231925 GGTTTCCCTTTGGACTATTTGAAAGTA 59.768 37.037 0.00 0.00 41.57 2.24
4975 10258 5.370289 TGAACTTAGGTTTCCCTTTGGACTA 59.630 40.000 0.00 0.00 41.57 2.59
5034 10319 3.863681 GCATCAGCGAAAACCACAA 57.136 47.368 0.00 0.00 0.00 3.33
5068 10354 4.591929 TGGCAACCACTTTAGTATAACCC 58.408 43.478 0.00 0.00 0.00 4.11
5098 10384 6.649141 ACACTATTATCGAACTTGCTTGTCAA 59.351 34.615 0.00 0.00 0.00 3.18
5149 10447 9.045745 ACAATTTATCTTCTCTCTTCTCCTCTT 57.954 33.333 0.00 0.00 0.00 2.85
5188 10503 6.337356 TGAAAAGAAAATGGGTTTGTGTCTC 58.663 36.000 0.00 0.00 0.00 3.36
5191 10506 7.936496 AATTGAAAAGAAAATGGGTTTGTGT 57.064 28.000 0.00 0.00 0.00 3.72
5287 10609 4.095185 CGAGTGGTTCTTGTTACCAAAACA 59.905 41.667 0.00 0.00 46.62 2.83
5299 10621 1.766496 TCTGGTTTCCGAGTGGTTCTT 59.234 47.619 0.00 0.00 36.30 2.52
5351 10677 2.806244 ACAGTCGAAAACAAATCCGGAG 59.194 45.455 11.34 0.00 0.00 4.63
5452 10779 7.705325 CCAAAATGTGTAGCGTCTTAGTAGTAT 59.295 37.037 0.00 0.00 0.00 2.12
5462 10789 2.147958 TGGTCCAAAATGTGTAGCGTC 58.852 47.619 0.00 0.00 0.00 5.19
5661 11004 7.072263 AGATCCATAGGAAATAGTGGAACTG 57.928 40.000 2.76 0.00 41.56 3.16
5667 11010 8.915057 AAATGTGAGATCCATAGGAAATAGTG 57.085 34.615 0.00 0.00 34.34 2.74
5862 11208 4.778579 AGTCATGTTTGAGATGAGATGGG 58.221 43.478 0.00 0.00 30.39 4.00
6092 11449 8.772250 CCCTCCATTCCATAATGTAGTACATAT 58.228 37.037 16.08 9.14 37.97 1.78
6095 11452 6.147473 TCCCTCCATTCCATAATGTAGTACA 58.853 40.000 5.24 5.24 40.84 2.90
6097 11454 7.888514 ATTCCCTCCATTCCATAATGTAGTA 57.111 36.000 0.00 0.00 40.84 1.82
6120 11477 8.716674 ATAATCCCACTGCTCAAAATCAATAT 57.283 30.769 0.00 0.00 0.00 1.28
6281 11639 8.190784 AGTCGTCTGATCAAAATTTTCAAAGTT 58.809 29.630 0.00 0.00 0.00 2.66
6322 11686 4.805192 ACAGCACTGTTTTGCAAAATACAG 59.195 37.500 29.61 29.61 45.62 2.74
6369 11733 3.798337 GCCAATTGAGAATACAAATGCCG 59.202 43.478 7.12 0.00 31.67 5.69
6371 11735 5.290158 CAGTGCCAATTGAGAATACAAATGC 59.710 40.000 7.12 0.00 31.67 3.56
6623 11991 6.096001 GTCCGGTCTTATCAAGGAACTAGTTA 59.904 42.308 8.42 0.00 38.49 2.24
6799 12400 9.502091 GCATATGAACCTAATACCAAGTAATGA 57.498 33.333 6.97 0.00 0.00 2.57
6874 12483 3.117663 GGGCCCATGAGAACCTACAATTA 60.118 47.826 19.95 0.00 0.00 1.40
6877 12486 0.623723 GGGCCCATGAGAACCTACAA 59.376 55.000 19.95 0.00 0.00 2.41
6904 12513 2.957680 TGGAAAGAAAGCAGCATGTTGA 59.042 40.909 14.38 0.00 39.31 3.18
7007 12620 7.307337 CGCATAGACATACTGATTAATTGCACA 60.307 37.037 0.00 0.00 0.00 4.57
7026 12639 3.574284 AGTTTTGCAATTGCGCATAGA 57.426 38.095 24.58 3.77 45.83 1.98
7198 12813 5.183530 TCACATCATCCATTCTTCCACTT 57.816 39.130 0.00 0.00 0.00 3.16
7319 12934 9.613428 CAGTTCAAGGTATTACATTAAGGATCA 57.387 33.333 0.00 0.00 0.00 2.92
7374 13000 5.893255 TGCATGAGGGCAAATAAAATAGTCT 59.107 36.000 0.00 0.00 41.65 3.24
7410 13055 9.462606 AGTAATTTATGTTTAGTGGGAGAAAGG 57.537 33.333 0.00 0.00 0.00 3.11
7438 13083 5.051240 CGTATTTACTTAGGACGGACAATGC 60.051 44.000 0.00 0.00 0.00 3.56
7441 13086 5.182950 TCACGTATTTACTTAGGACGGACAA 59.817 40.000 0.00 0.00 37.83 3.18
7469 13114 7.730364 AATAAGATAAGTAGGTGGCATTTCG 57.270 36.000 0.00 0.00 0.00 3.46
7491 13136 1.618343 GGGCCACTGTGTTAGCAAAAT 59.382 47.619 4.39 0.00 0.00 1.82
7496 13141 3.431725 GCGGGCCACTGTGTTAGC 61.432 66.667 4.39 3.06 0.00 3.09
7541 13186 0.240145 TACAAGGTGCGACGAGTCAG 59.760 55.000 0.00 0.00 0.00 3.51
7693 13338 9.630098 CTTTTCATGTTATACAGACAAAGCAAT 57.370 29.630 0.00 0.00 0.00 3.56
7694 13339 8.081633 CCTTTTCATGTTATACAGACAAAGCAA 58.918 33.333 0.00 0.00 0.00 3.91
7695 13340 7.446931 TCCTTTTCATGTTATACAGACAAAGCA 59.553 33.333 0.00 0.00 0.00 3.91
7696 13341 7.816640 TCCTTTTCATGTTATACAGACAAAGC 58.183 34.615 0.00 0.00 0.00 3.51
7697 13342 9.219603 TCTCCTTTTCATGTTATACAGACAAAG 57.780 33.333 0.00 0.00 0.00 2.77
7698 13343 9.739276 ATCTCCTTTTCATGTTATACAGACAAA 57.261 29.630 0.00 0.00 0.00 2.83
7699 13344 9.383519 GATCTCCTTTTCATGTTATACAGACAA 57.616 33.333 0.00 0.00 0.00 3.18
7700 13345 7.987458 GGATCTCCTTTTCATGTTATACAGACA 59.013 37.037 0.00 0.00 0.00 3.41
7701 13346 7.987458 TGGATCTCCTTTTCATGTTATACAGAC 59.013 37.037 0.00 0.00 36.82 3.51
7702 13347 7.987458 GTGGATCTCCTTTTCATGTTATACAGA 59.013 37.037 0.00 0.00 36.82 3.41
7703 13348 7.770433 TGTGGATCTCCTTTTCATGTTATACAG 59.230 37.037 0.00 0.00 36.82 2.74
7704 13349 7.629157 TGTGGATCTCCTTTTCATGTTATACA 58.371 34.615 0.00 0.00 36.82 2.29
7705 13350 8.682936 ATGTGGATCTCCTTTTCATGTTATAC 57.317 34.615 0.00 0.00 36.82 1.47
7706 13351 9.699410 AAATGTGGATCTCCTTTTCATGTTATA 57.301 29.630 0.00 0.00 36.82 0.98
7707 13352 8.599624 AAATGTGGATCTCCTTTTCATGTTAT 57.400 30.769 0.00 0.00 36.82 1.89
7708 13353 8.421249 AAAATGTGGATCTCCTTTTCATGTTA 57.579 30.769 0.00 0.00 36.82 2.41
7709 13354 6.923199 AAATGTGGATCTCCTTTTCATGTT 57.077 33.333 0.00 0.00 36.82 2.71
7714 13697 8.531146 TCCAATAAAAATGTGGATCTCCTTTTC 58.469 33.333 0.00 0.00 36.51 2.29
7788 13771 6.747280 CAGAAGAACACAACCACTAAAAACAG 59.253 38.462 0.00 0.00 0.00 3.16
7799 13782 4.876107 TCTTGAAGACAGAAGAACACAACC 59.124 41.667 0.00 0.00 0.00 3.77
7803 13786 8.594881 TTTATCTCTTGAAGACAGAAGAACAC 57.405 34.615 0.00 0.00 36.65 3.32
7896 13879 6.709281 TGACAATGGCAAACATATGGAAAAT 58.291 32.000 7.80 0.00 39.40 1.82
7902 13885 7.780008 AATTGATGACAATGGCAAACATATG 57.220 32.000 0.00 0.00 44.67 1.78
7910 13893 4.750598 CACACAAAATTGATGACAATGGCA 59.249 37.500 0.00 0.00 44.67 4.92
7915 13898 4.397481 TGGCACACAAAATTGATGACAA 57.603 36.364 7.82 0.00 40.42 3.18
7933 13916 4.332186 CATCGTTACAGATGCATATGGC 57.668 45.455 24.21 13.06 41.09 4.40
7944 13927 9.365311 CACAAAAAGTAACTAACATCGTTACAG 57.635 33.333 13.50 3.40 45.60 2.74
7949 13932 7.781548 AGACACAAAAAGTAACTAACATCGT 57.218 32.000 0.00 0.00 0.00 3.73
7956 13939 8.662141 GTGAGAACAAGACACAAAAAGTAACTA 58.338 33.333 0.00 0.00 35.06 2.24
8023 14006 4.858965 TGGCATATGCATATGGGTATCA 57.141 40.909 36.01 16.01 44.36 2.15
8069 14052 9.845740 ATGCCACATATTTAGACATGTAAACTA 57.154 29.630 0.00 0.00 33.66 2.24
8070 14053 8.623903 CATGCCACATATTTAGACATGTAAACT 58.376 33.333 0.00 0.00 33.66 2.66
8071 14054 7.379529 GCATGCCACATATTTAGACATGTAAAC 59.620 37.037 6.36 0.00 36.63 2.01
8087 14070 5.183969 CAGCTAGATATTAGCATGCCACAT 58.816 41.667 15.66 6.58 42.68 3.21
8134 14119 8.265055 AGAAGAGGTGGTTTCGATAATTATTCA 58.735 33.333 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.