Multiple sequence alignment - TraesCS4A01G352000

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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 TraesCS4A01G352000 chr4A 100.000 7196 0 0 1 7196 627586833 627594028 0.000000e+00 13289
1 TraesCS4A01G352000 chr6B 98.305 4661 42 28 1876 6520 533999135 534003774 0.000000e+00 8135
2 TraesCS4A01G352000 chr6B 97.809 4655 57 28 1876 6520 401411704 401416323 0.000000e+00 7989
3 TraesCS4A01G352000 chr6B 93.928 2075 81 18 1876 3936 637177026 637174983 0.000000e+00 3092
4 TraesCS4A01G352000 chr6B 94.107 1137 47 16 5387 6520 502018348 502017229 0.000000e+00 1711
5 TraesCS4A01G352000 chr6B 97.801 682 6 8 6519 7196 534003820 534004496 0.000000e+00 1168
6 TraesCS4A01G352000 chr6B 93.239 710 10 14 724 1399 533998124 533998829 0.000000e+00 1011
7 TraesCS4A01G352000 chr6B 92.665 559 23 14 713 1265 401410221 401410767 0.000000e+00 789
8 TraesCS4A01G352000 chr6B 96.795 468 11 4 1403 1869 401410993 401411457 0.000000e+00 778
9 TraesCS4A01G352000 chr6B 91.513 542 25 13 6519 7046 401416367 401416901 0.000000e+00 726
10 TraesCS4A01G352000 chr6B 90.164 305 4 13 1119 1399 401410659 401410961 2.450000e-99 374
11 TraesCS4A01G352000 chr6B 83.673 196 31 1 518 713 81024220 81024414 4.430000e-42 183
12 TraesCS4A01G352000 chr6B 100.000 83 0 0 1403 1485 533998861 533998943 3.480000e-33 154
13 TraesCS4A01G352000 chr2B 98.110 4604 56 26 1876 6470 91070661 91075242 0.000000e+00 7991
14 TraesCS4A01G352000 chr2B 97.712 1530 22 13 4994 6520 91076083 91077602 0.000000e+00 2619
15 TraesCS4A01G352000 chr2B 98.088 680 7 6 6519 7196 91077646 91078321 0.000000e+00 1179
16 TraesCS4A01G352000 chr2B 93.484 706 13 15 723 1399 91069223 91069924 0.000000e+00 1018
17 TraesCS4A01G352000 chr2B 97.077 479 9 5 1403 1879 91069956 91070431 0.000000e+00 802
18 TraesCS4A01G352000 chr2A 98.219 3650 27 19 2879 6520 172554635 172551016 0.000000e+00 6346
19 TraesCS4A01G352000 chr2A 98.521 3178 30 13 1876 5049 646836947 646833783 0.000000e+00 5592
20 TraesCS4A01G352000 chr2A 98.088 680 7 5 6519 7196 172550972 172550297 0.000000e+00 1179
21 TraesCS4A01G352000 chr2A 94.151 701 13 11 726 1402 172557143 172556447 0.000000e+00 1042
22 TraesCS4A01G352000 chr2A 97.908 478 7 3 1403 1879 172556418 172555943 0.000000e+00 824
23 TraesCS4A01G352000 chr2A 97.275 477 10 3 1403 1879 646837672 646837199 0.000000e+00 806
24 TraesCS4A01G352000 chr2A 90.997 311 4 11 1113 1399 646838014 646837704 1.450000e-106 398
25 TraesCS4A01G352000 chr7A 99.060 3510 12 7 3013 6520 286988668 286985178 0.000000e+00 6279
26 TraesCS4A01G352000 chr7A 99.043 1150 5 4 730 1879 286991110 286989967 0.000000e+00 2058
27 TraesCS4A01G352000 chr7A 99.352 1080 6 1 1876 2955 286989742 286988664 0.000000e+00 1954
28 TraesCS4A01G352000 chr7A 99.265 680 3 2 6519 7196 286985134 286984455 0.000000e+00 1227
29 TraesCS4A01G352000 chr7A 80.674 564 79 21 6517 7065 86142898 86142350 1.870000e-110 411
30 TraesCS4A01G352000 chr7A 83.981 206 29 4 518 723 657880502 657880703 2.050000e-45 195
31 TraesCS4A01G352000 chr7A 88.430 121 11 3 1663 1783 657016062 657015945 7.530000e-30 143
32 TraesCS4A01G352000 chrUn 95.299 3531 129 25 1876 5391 12545142 12541634 0.000000e+00 5566
33 TraesCS4A01G352000 chr7B 93.021 3525 183 35 1876 5378 35216044 35219527 0.000000e+00 5088
34 TraesCS4A01G352000 chr7B 95.523 3194 99 24 2215 5391 654101175 654104341 0.000000e+00 5066
35 TraesCS4A01G352000 chr7B 94.195 1137 45 17 5387 6520 725140849 725139731 0.000000e+00 1714
36 TraesCS4A01G352000 chr7B 88.628 554 43 13 726 1268 710080296 710079752 0.000000e+00 656
37 TraesCS4A01G352000 chr7B 83.808 562 64 16 727 1268 654099514 654100068 6.440000e-140 508
38 TraesCS4A01G352000 chr7B 78.641 412 63 20 1425 1827 655573453 655573848 4.310000e-62 250
39 TraesCS4A01G352000 chr7B 83.732 209 28 5 517 723 27490966 27491170 7.370000e-45 193
40 TraesCS4A01G352000 chr7B 82.843 204 34 1 510 713 23209016 23208814 1.590000e-41 182
41 TraesCS4A01G352000 chr5B 93.013 2390 125 21 3012 5378 3900088 3897718 0.000000e+00 3450
42 TraesCS4A01G352000 chr5B 94.019 1137 47 16 5387 6520 571456555 571455437 0.000000e+00 1703
43 TraesCS4A01G352000 chr5B 93.662 1136 52 17 5387 6520 3897661 3896544 0.000000e+00 1681
44 TraesCS4A01G352000 chr5B 91.470 551 28 13 727 1268 571461002 571460462 0.000000e+00 739
45 TraesCS4A01G352000 chr5B 88.082 537 44 15 726 1251 3902120 3901593 2.850000e-173 619
46 TraesCS4A01G352000 chr5B 83.981 206 32 1 518 723 477556973 477556769 5.700000e-46 196
47 TraesCS4A01G352000 chr3B 89.720 535 28 12 3104 3618 199681158 199681685 0.000000e+00 658
48 TraesCS4A01G352000 chr3B 89.105 257 21 7 6920 7175 199684807 199685057 5.420000e-81 313
49 TraesCS4A01G352000 chr3B 88.327 257 23 7 6920 7175 772742264 772742014 1.170000e-77 302
50 TraesCS4A01G352000 chr3B 78.378 222 36 11 6940 7157 199684870 199685083 4.530000e-27 134
51 TraesCS4A01G352000 chr5D 86.018 565 22 11 4 520 541531856 541531301 2.930000e-153 553
52 TraesCS4A01G352000 chr2D 81.959 582 76 20 6519 7087 506288422 506288987 3.930000e-127 466
53 TraesCS4A01G352000 chr2D 85.714 189 22 2 536 724 599889320 599889503 2.050000e-45 195
54 TraesCS4A01G352000 chr7D 82.593 540 68 19 6517 7042 511208303 511208830 3.060000e-123 453
55 TraesCS4A01G352000 chr7D 80.996 542 79 18 6517 7045 568332196 568332726 6.720000e-110 409
56 TraesCS4A01G352000 chr3A 85.337 341 42 6 1488 1825 16254337 16254002 5.340000e-91 346
57 TraesCS4A01G352000 chr6D 84.058 207 32 1 517 723 324114530 324114735 1.580000e-46 198
58 TraesCS4A01G352000 chr6D 82.927 205 34 1 519 723 296674638 296674435 4.430000e-42 183
59 TraesCS4A01G352000 chr4D 82.609 207 35 1 517 723 411306310 411306515 1.590000e-41 182
60 TraesCS4A01G352000 chr5A 89.024 82 7 2 1700 1780 10041884 10041964 4.590000e-17 100


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 TraesCS4A01G352000 chr4A 627586833 627594028 7195 False 13289.000000 13289 100.000000 1 7196 1 chr4A.!!$F1 7195
1 TraesCS4A01G352000 chr6B 637174983 637177026 2043 True 3092.000000 3092 93.928000 1876 3936 1 chr6B.!!$R2 2060
2 TraesCS4A01G352000 chr6B 533998124 534004496 6372 False 2617.000000 8135 97.336250 724 7196 4 chr6B.!!$F3 6472
3 TraesCS4A01G352000 chr6B 401410221 401416901 6680 False 2131.200000 7989 93.789200 713 7046 5 chr6B.!!$F2 6333
4 TraesCS4A01G352000 chr6B 502017229 502018348 1119 True 1711.000000 1711 94.107000 5387 6520 1 chr6B.!!$R1 1133
5 TraesCS4A01G352000 chr2B 91069223 91078321 9098 False 2721.800000 7991 96.894200 723 7196 5 chr2B.!!$F1 6473
6 TraesCS4A01G352000 chr2A 172550297 172557143 6846 True 2347.750000 6346 97.091500 726 7196 4 chr2A.!!$R1 6470
7 TraesCS4A01G352000 chr2A 646833783 646838014 4231 True 2265.333333 5592 95.597667 1113 5049 3 chr2A.!!$R2 3936
8 TraesCS4A01G352000 chr7A 286984455 286991110 6655 True 2879.500000 6279 99.180000 730 7196 4 chr7A.!!$R3 6466
9 TraesCS4A01G352000 chr7A 86142350 86142898 548 True 411.000000 411 80.674000 6517 7065 1 chr7A.!!$R1 548
10 TraesCS4A01G352000 chrUn 12541634 12545142 3508 True 5566.000000 5566 95.299000 1876 5391 1 chrUn.!!$R1 3515
11 TraesCS4A01G352000 chr7B 35216044 35219527 3483 False 5088.000000 5088 93.021000 1876 5378 1 chr7B.!!$F2 3502
12 TraesCS4A01G352000 chr7B 654099514 654104341 4827 False 2787.000000 5066 89.665500 727 5391 2 chr7B.!!$F4 4664
13 TraesCS4A01G352000 chr7B 725139731 725140849 1118 True 1714.000000 1714 94.195000 5387 6520 1 chr7B.!!$R3 1133
14 TraesCS4A01G352000 chr7B 710079752 710080296 544 True 656.000000 656 88.628000 726 1268 1 chr7B.!!$R2 542
15 TraesCS4A01G352000 chr5B 3896544 3902120 5576 True 1916.666667 3450 91.585667 726 6520 3 chr5B.!!$R2 5794
16 TraesCS4A01G352000 chr5B 571455437 571461002 5565 True 1221.000000 1703 92.744500 727 6520 2 chr5B.!!$R3 5793
17 TraesCS4A01G352000 chr3B 199681158 199685083 3925 False 368.333333 658 85.734333 3104 7175 3 chr3B.!!$F1 4071
18 TraesCS4A01G352000 chr5D 541531301 541531856 555 True 553.000000 553 86.018000 4 520 1 chr5D.!!$R1 516
19 TraesCS4A01G352000 chr2D 506288422 506288987 565 False 466.000000 466 81.959000 6519 7087 1 chr2D.!!$F1 568
20 TraesCS4A01G352000 chr7D 511208303 511208830 527 False 453.000000 453 82.593000 6517 7042 1 chr7D.!!$F1 525
21 TraesCS4A01G352000 chr7D 568332196 568332726 530 False 409.000000 409 80.996000 6517 7045 1 chr7D.!!$F2 528

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
34 35 0.676736 TTTTGCGGGTAAAAGGGCAG 59.323 50.000 0.00 0.0 36.66 4.85 F
186 199 0.923358 TATCCACCCAACCCATCCAC 59.077 55.000 0.00 0.0 0.00 4.02 F
406 452 1.533625 TCGTCTTTGAGCCATTTGGG 58.466 50.000 0.00 0.0 40.85 4.12 F
499 548 1.538950 GGACGTCGAGAACCTAACTGT 59.461 52.381 9.92 0.0 0.00 3.55 F
545 594 1.944709 CCGTTCGGATTTATTGGTCCC 59.055 52.381 5.19 0.0 0.00 4.46 F
546 595 1.944709 CGTTCGGATTTATTGGTCCCC 59.055 52.381 0.00 0.0 0.00 4.81 F
637 686 2.159531 ACGTCGTTGGATTCGTATTCGA 60.160 45.455 0.00 0.0 44.66 3.71 F
1546 1772 3.069158 GCTAGTAATAAGAACCAGCGGGA 59.931 47.826 10.86 0.0 38.05 5.14 F
2961 4050 3.394606 ACATCCCGCCTATGTATTTTCCT 59.605 43.478 0.00 0.0 35.82 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1947 2917 1.148310 CACCAGAGTTACCTGCAACG 58.852 55.000 0.00 0.00 33.50 4.10 R
2731 3709 4.761975 CATGGGATGGAAAAAGGACATTG 58.238 43.478 0.00 0.00 0.00 2.82 R
2961 4050 6.209788 GGGGTGTTAATACTCCATTGACAAAA 59.790 38.462 15.93 0.00 42.73 2.44 R
4149 5302 1.825474 GAGACGTTCCCTTCCATCTCA 59.175 52.381 0.00 0.00 34.12 3.27 R
4515 5670 1.770658 ACCATATTAGGAGCTGCAGCA 59.229 47.619 38.24 19.65 45.16 4.41 R
5250 6414 9.417561 ACATCATTGGATCATATTTTCAGAGTT 57.582 29.630 0.00 0.00 0.00 3.01 R
5343 6507 6.472016 TCCAACATCAATTAGAGTTGCTACA 58.528 36.000 0.13 0.00 39.86 2.74 R
5865 7084 6.768483 TCTCCTTCATATTTCCGATGCATAA 58.232 36.000 0.00 0.00 0.00 1.90 R
6375 9920 3.193267 CGGGAGAAATGCTTCATCCAAAA 59.807 43.478 0.00 0.00 33.72 2.44 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
32 33 3.991242 TTTTTGCGGGTAAAAGGGC 57.009 47.368 0.00 0.00 31.80 5.19
34 35 0.676736 TTTTGCGGGTAAAAGGGCAG 59.323 50.000 0.00 0.00 36.66 4.85
41 42 1.338107 GGTAAAAGGGCAGCCACTTT 58.662 50.000 15.19 16.75 38.48 2.66
42 43 2.521126 GGTAAAAGGGCAGCCACTTTA 58.479 47.619 21.57 16.73 35.99 1.85
44 45 3.513912 GGTAAAAGGGCAGCCACTTTATT 59.486 43.478 21.57 13.28 35.99 1.40
47 48 5.816955 AAAAGGGCAGCCACTTTATTTTA 57.183 34.783 21.57 0.00 35.99 1.52
59 65 5.627780 CCACTTTATTTTACGTGGCAAAGAC 59.372 40.000 0.00 0.00 40.27 3.01
62 68 8.018520 CACTTTATTTTACGTGGCAAAGACATA 58.981 33.333 0.00 0.00 0.00 2.29
159 172 2.032178 GCCATGGAAATAACTGCTCGAC 59.968 50.000 18.40 0.00 0.00 4.20
164 177 2.872858 GGAAATAACTGCTCGACCCATC 59.127 50.000 0.00 0.00 0.00 3.51
177 190 1.780309 GACCCATCCATATCCACCCAA 59.220 52.381 0.00 0.00 0.00 4.12
180 193 1.203050 CCATCCATATCCACCCAACCC 60.203 57.143 0.00 0.00 0.00 4.11
181 194 1.498576 CATCCATATCCACCCAACCCA 59.501 52.381 0.00 0.00 0.00 4.51
183 196 1.780309 TCCATATCCACCCAACCCATC 59.220 52.381 0.00 0.00 0.00 3.51
184 197 1.203050 CCATATCCACCCAACCCATCC 60.203 57.143 0.00 0.00 0.00 3.51
185 198 1.498576 CATATCCACCCAACCCATCCA 59.501 52.381 0.00 0.00 0.00 3.41
186 199 0.923358 TATCCACCCAACCCATCCAC 59.077 55.000 0.00 0.00 0.00 4.02
187 200 1.874299 ATCCACCCAACCCATCCACC 61.874 60.000 0.00 0.00 0.00 4.61
262 277 2.294791 CCATGGACTCCTTCGTAGCTAG 59.705 54.545 5.56 0.00 0.00 3.42
264 279 3.920231 TGGACTCCTTCGTAGCTAGTA 57.080 47.619 0.00 0.00 0.00 1.82
312 327 4.202305 ACTTTTCCCGCAAAATCCAATTCA 60.202 37.500 0.00 0.00 33.34 2.57
321 336 6.457257 CCGCAAAATCCAATTCAAATCCAATC 60.457 38.462 0.00 0.00 0.00 2.67
326 341 5.920193 TCCAATTCAAATCCAATCCAGTC 57.080 39.130 0.00 0.00 0.00 3.51
406 452 1.533625 TCGTCTTTGAGCCATTTGGG 58.466 50.000 0.00 0.00 40.85 4.12
416 462 2.965805 CCATTTGGGCTCAGCTTGA 58.034 52.632 0.00 0.00 0.00 3.02
492 541 4.790861 GGCCGGACGTCGAGAACC 62.791 72.222 5.05 7.55 42.43 3.62
494 543 2.401766 GCCGGACGTCGAGAACCTA 61.402 63.158 5.05 0.00 42.43 3.08
499 548 1.538950 GGACGTCGAGAACCTAACTGT 59.461 52.381 9.92 0.00 0.00 3.55
508 557 4.483311 GAGAACCTAACTGTTCCACTACG 58.517 47.826 0.00 0.00 44.55 3.51
512 561 6.886459 AGAACCTAACTGTTCCACTACGTATA 59.114 38.462 0.00 0.00 44.55 1.47
520 569 5.994250 TGTTCCACTACGTATACTCCTACT 58.006 41.667 0.00 0.00 0.00 2.57
521 570 7.124573 TGTTCCACTACGTATACTCCTACTA 57.875 40.000 0.00 0.00 0.00 1.82
522 571 7.739825 TGTTCCACTACGTATACTCCTACTAT 58.260 38.462 0.00 0.00 0.00 2.12
523 572 7.875041 TGTTCCACTACGTATACTCCTACTATC 59.125 40.741 0.00 0.00 0.00 2.08
524 573 7.789202 TCCACTACGTATACTCCTACTATCT 57.211 40.000 0.00 0.00 0.00 1.98
525 574 7.835822 TCCACTACGTATACTCCTACTATCTC 58.164 42.308 0.00 0.00 0.00 2.75
526 575 7.041107 CCACTACGTATACTCCTACTATCTCC 58.959 46.154 0.00 0.00 0.00 3.71
527 576 6.751425 CACTACGTATACTCCTACTATCTCCG 59.249 46.154 0.00 0.00 0.00 4.63
528 577 5.736951 ACGTATACTCCTACTATCTCCGT 57.263 43.478 0.56 0.00 0.00 4.69
529 578 6.107901 ACGTATACTCCTACTATCTCCGTT 57.892 41.667 0.56 0.00 0.00 4.44
530 579 6.162777 ACGTATACTCCTACTATCTCCGTTC 58.837 44.000 0.56 0.00 0.00 3.95
531 580 5.288232 CGTATACTCCTACTATCTCCGTTCG 59.712 48.000 0.56 0.00 0.00 3.95
532 581 2.848691 ACTCCTACTATCTCCGTTCGG 58.151 52.381 4.74 4.74 0.00 4.30
533 582 2.437281 ACTCCTACTATCTCCGTTCGGA 59.563 50.000 13.34 13.34 0.00 4.55
534 583 3.072768 ACTCCTACTATCTCCGTTCGGAT 59.927 47.826 14.34 3.64 33.34 4.18
535 584 4.073549 CTCCTACTATCTCCGTTCGGATT 58.926 47.826 14.34 8.00 33.34 3.01
536 585 4.467769 TCCTACTATCTCCGTTCGGATTT 58.532 43.478 14.34 7.67 33.34 2.17
537 586 5.624159 TCCTACTATCTCCGTTCGGATTTA 58.376 41.667 14.34 8.35 33.34 1.40
538 587 6.243900 TCCTACTATCTCCGTTCGGATTTAT 58.756 40.000 14.34 10.67 33.34 1.40
539 588 6.718454 TCCTACTATCTCCGTTCGGATTTATT 59.282 38.462 14.34 6.56 33.34 1.40
540 589 6.807230 CCTACTATCTCCGTTCGGATTTATTG 59.193 42.308 14.34 11.18 33.34 1.90
541 590 5.539048 ACTATCTCCGTTCGGATTTATTGG 58.461 41.667 14.34 1.64 33.34 3.16
542 591 3.899052 TCTCCGTTCGGATTTATTGGT 57.101 42.857 14.34 0.00 33.34 3.67
543 592 3.788937 TCTCCGTTCGGATTTATTGGTC 58.211 45.455 14.34 0.00 33.34 4.02
544 593 2.870411 CTCCGTTCGGATTTATTGGTCC 59.130 50.000 14.34 0.00 33.34 4.46
545 594 1.944709 CCGTTCGGATTTATTGGTCCC 59.055 52.381 5.19 0.00 0.00 4.46
546 595 1.944709 CGTTCGGATTTATTGGTCCCC 59.055 52.381 0.00 0.00 0.00 4.81
547 596 2.420967 CGTTCGGATTTATTGGTCCCCT 60.421 50.000 0.00 0.00 0.00 4.79
548 597 3.628008 GTTCGGATTTATTGGTCCCCTT 58.372 45.455 0.00 0.00 0.00 3.95
549 598 4.021229 GTTCGGATTTATTGGTCCCCTTT 58.979 43.478 0.00 0.00 0.00 3.11
550 599 5.195185 GTTCGGATTTATTGGTCCCCTTTA 58.805 41.667 0.00 0.00 0.00 1.85
551 600 5.453866 TCGGATTTATTGGTCCCCTTTAA 57.546 39.130 0.00 0.00 0.00 1.52
552 601 5.828871 TCGGATTTATTGGTCCCCTTTAAA 58.171 37.500 0.00 0.00 0.00 1.52
553 602 6.254522 TCGGATTTATTGGTCCCCTTTAAAA 58.745 36.000 0.00 0.00 0.00 1.52
554 603 6.898521 TCGGATTTATTGGTCCCCTTTAAAAT 59.101 34.615 0.00 0.00 0.00 1.82
555 604 7.400627 TCGGATTTATTGGTCCCCTTTAAAATT 59.599 33.333 0.00 0.00 0.00 1.82
556 605 8.044309 CGGATTTATTGGTCCCCTTTAAAATTT 58.956 33.333 0.00 0.00 0.00 1.82
557 606 9.173021 GGATTTATTGGTCCCCTTTAAAATTTG 57.827 33.333 0.00 0.00 0.00 2.32
558 607 9.733556 GATTTATTGGTCCCCTTTAAAATTTGT 57.266 29.630 0.00 0.00 0.00 2.83
559 608 8.910351 TTTATTGGTCCCCTTTAAAATTTGTG 57.090 30.769 0.00 0.00 0.00 3.33
560 609 5.959583 TTGGTCCCCTTTAAAATTTGTGT 57.040 34.783 0.00 0.00 0.00 3.72
561 610 5.959583 TGGTCCCCTTTAAAATTTGTGTT 57.040 34.783 0.00 0.00 0.00 3.32
562 611 7.433537 TTGGTCCCCTTTAAAATTTGTGTTA 57.566 32.000 0.00 0.00 0.00 2.41
563 612 7.056844 TGGTCCCCTTTAAAATTTGTGTTAG 57.943 36.000 0.00 0.00 0.00 2.34
564 613 6.612049 TGGTCCCCTTTAAAATTTGTGTTAGT 59.388 34.615 0.00 0.00 0.00 2.24
565 614 7.125963 TGGTCCCCTTTAAAATTTGTGTTAGTT 59.874 33.333 0.00 0.00 0.00 2.24
566 615 7.988599 GGTCCCCTTTAAAATTTGTGTTAGTTT 59.011 33.333 0.00 0.00 0.00 2.66
567 616 9.386010 GTCCCCTTTAAAATTTGTGTTAGTTTT 57.614 29.630 0.00 0.00 0.00 2.43
568 617 9.961264 TCCCCTTTAAAATTTGTGTTAGTTTTT 57.039 25.926 0.00 0.00 0.00 1.94
569 618 9.995957 CCCCTTTAAAATTTGTGTTAGTTTTTG 57.004 29.630 0.00 0.00 0.00 2.44
622 671 9.562583 AATGCATGTTAATAAAAATTACGTCGT 57.437 25.926 0.00 2.21 0.00 4.34
623 672 8.951954 TGCATGTTAATAAAAATTACGTCGTT 57.048 26.923 1.78 0.00 0.00 3.85
624 673 8.841822 TGCATGTTAATAAAAATTACGTCGTTG 58.158 29.630 1.78 0.00 0.00 4.10
625 674 8.308320 GCATGTTAATAAAAATTACGTCGTTGG 58.692 33.333 1.78 0.00 0.00 3.77
626 675 9.544314 CATGTTAATAAAAATTACGTCGTTGGA 57.456 29.630 1.78 0.00 0.00 3.53
630 679 7.942145 AATAAAAATTACGTCGTTGGATTCG 57.058 32.000 1.78 0.00 0.00 3.34
631 680 4.996062 AAAATTACGTCGTTGGATTCGT 57.004 36.364 1.78 0.00 39.74 3.85
632 681 6.464895 AAAAATTACGTCGTTGGATTCGTA 57.535 33.333 1.78 0.00 37.66 3.43
633 682 6.651755 AAAATTACGTCGTTGGATTCGTAT 57.348 33.333 1.78 0.00 38.29 3.06
634 683 6.651755 AAATTACGTCGTTGGATTCGTATT 57.348 33.333 1.78 0.00 38.29 1.89
635 684 5.878261 ATTACGTCGTTGGATTCGTATTC 57.122 39.130 1.78 0.00 38.29 1.75
636 685 2.179589 ACGTCGTTGGATTCGTATTCG 58.820 47.619 0.00 0.00 34.78 3.34
637 686 2.159531 ACGTCGTTGGATTCGTATTCGA 60.160 45.455 0.00 0.00 44.66 3.71
653 702 8.468720 TCGTATTCGAACATAGTTTTCAATGA 57.531 30.769 0.00 0.00 43.34 2.57
654 703 9.093970 TCGTATTCGAACATAGTTTTCAATGAT 57.906 29.630 0.00 0.00 43.34 2.45
687 736 7.664082 TTTTTGTCATGTGTGAACATTTTGT 57.336 28.000 0.00 0.00 35.80 2.83
688 737 7.664082 TTTTGTCATGTGTGAACATTTTGTT 57.336 28.000 0.00 0.00 44.37 2.83
689 738 8.763049 TTTTGTCATGTGTGAACATTTTGTTA 57.237 26.923 0.00 0.00 41.28 2.41
690 739 7.984002 TTGTCATGTGTGAACATTTTGTTAG 57.016 32.000 0.00 0.00 41.28 2.34
691 740 7.094508 TGTCATGTGTGAACATTTTGTTAGT 57.905 32.000 0.00 0.00 41.28 2.24
692 741 7.542890 TGTCATGTGTGAACATTTTGTTAGTT 58.457 30.769 0.00 0.00 41.28 2.24
693 742 8.678199 TGTCATGTGTGAACATTTTGTTAGTTA 58.322 29.630 0.00 0.00 41.28 2.24
694 743 9.509855 GTCATGTGTGAACATTTTGTTAGTTAA 57.490 29.630 0.00 0.00 41.28 2.01
1546 1772 3.069158 GCTAGTAATAAGAACCAGCGGGA 59.931 47.826 10.86 0.00 38.05 5.14
1572 1798 5.122239 TGCATGATTAAGTTCTTTCTGTCCG 59.878 40.000 0.00 0.00 0.00 4.79
1734 1961 7.937700 AGATTGGGGAGAGAATATAGTTTGA 57.062 36.000 0.00 0.00 0.00 2.69
1808 2035 4.275443 GGTGTTTGGTTACGGAAATACACA 59.725 41.667 13.95 0.63 37.08 3.72
1929 2899 8.760569 GGTTTTATGGTTTTATTGACTTGTGTG 58.239 33.333 0.00 0.00 0.00 3.82
2679 3655 7.658525 TGCAACATTATGAAATACCTCCATT 57.341 32.000 0.00 0.00 0.00 3.16
2961 4050 3.394606 ACATCCCGCCTATGTATTTTCCT 59.605 43.478 0.00 0.00 35.82 3.36
3568 4716 4.405358 ACCTTCTGTTTTTGCTTCATCCAA 59.595 37.500 0.00 0.00 0.00 3.53
3773 4926 9.019656 TGTGACTAAAATGTACAATAATTGGCT 57.980 29.630 0.00 0.00 34.12 4.75
4149 5302 5.295787 TCGTGAGCAACAAATAGTGAGTTTT 59.704 36.000 0.00 0.00 0.00 2.43
5250 6414 4.058817 ACTTTTGTTTCGCACCACAAAAA 58.941 34.783 14.51 1.11 46.85 1.94
5343 6507 6.629128 TGACAACATCTGTTTGAAACACATT 58.371 32.000 6.66 0.00 38.84 2.71
5865 7084 5.964758 TCAACATTCTTGCTTGTTTCAACT 58.035 33.333 0.00 0.00 33.93 3.16
6311 9855 2.473984 GCGCGTTCATATGTACCCTAAC 59.526 50.000 8.43 0.59 0.00 2.34
6375 9920 7.782049 TGTAAACCGATGATAACTTGATCTCT 58.218 34.615 0.00 0.00 0.00 3.10
6739 10379 7.446931 TCAAGGCTTTTTCCTTTTTCAAACTTT 59.553 29.630 0.00 0.00 43.62 2.66
6790 10432 7.628769 AAAGCTTCAACCATTGTTTGAAAAT 57.371 28.000 10.13 0.56 30.42 1.82
6916 10676 4.751767 AGCTTCAACCATGTTTTCCAAA 57.248 36.364 0.00 0.00 0.00 3.28
6917 10677 5.096443 AGCTTCAACCATGTTTTCCAAAA 57.904 34.783 0.00 0.00 0.00 2.44
6918 10678 5.683681 AGCTTCAACCATGTTTTCCAAAAT 58.316 33.333 0.00 0.00 0.00 1.82
6919 10679 5.759763 AGCTTCAACCATGTTTTCCAAAATC 59.240 36.000 0.00 0.00 0.00 2.17
6920 10680 5.759763 GCTTCAACCATGTTTTCCAAAATCT 59.240 36.000 0.00 0.00 0.00 2.40
6921 10681 6.260714 GCTTCAACCATGTTTTCCAAAATCTT 59.739 34.615 0.00 0.00 0.00 2.40
6922 10682 7.201723 GCTTCAACCATGTTTTCCAAAATCTTT 60.202 33.333 0.00 0.00 0.00 2.52
6923 10683 8.572855 TTCAACCATGTTTTCCAAAATCTTTT 57.427 26.923 0.00 0.00 0.00 2.27
6924 10684 8.207521 TCAACCATGTTTTCCAAAATCTTTTC 57.792 30.769 0.00 0.00 0.00 2.29
6925 10685 7.826252 TCAACCATGTTTTCCAAAATCTTTTCA 59.174 29.630 0.00 0.00 0.00 2.69
6926 10686 8.457261 CAACCATGTTTTCCAAAATCTTTTCAA 58.543 29.630 0.00 0.00 0.00 2.69
6927 10687 7.984391 ACCATGTTTTCCAAAATCTTTTCAAC 58.016 30.769 0.00 0.00 0.00 3.18
6928 10688 7.066887 ACCATGTTTTCCAAAATCTTTTCAACC 59.933 33.333 0.00 0.00 0.00 3.77
6929 10689 7.066766 CCATGTTTTCCAAAATCTTTTCAACCA 59.933 33.333 0.00 0.00 0.00 3.67
6930 10690 8.623030 CATGTTTTCCAAAATCTTTTCAACCAT 58.377 29.630 0.00 0.00 0.00 3.55
6931 10691 8.572855 TGTTTTCCAAAATCTTTTCAACCATT 57.427 26.923 0.00 0.00 0.00 3.16
6932 10692 9.672673 TGTTTTCCAAAATCTTTTCAACCATTA 57.327 25.926 0.00 0.00 0.00 1.90
6961 10721 7.650834 TTGCTTCAACCATGTTTAATAAAGC 57.349 32.000 0.00 0.00 37.64 3.51
6962 10722 6.991938 TGCTTCAACCATGTTTAATAAAGCT 58.008 32.000 0.00 0.00 37.91 3.74
6963 10723 7.441017 TGCTTCAACCATGTTTAATAAAGCTT 58.559 30.769 0.00 0.00 37.91 3.74
6964 10724 7.598493 TGCTTCAACCATGTTTAATAAAGCTTC 59.402 33.333 0.00 0.00 37.91 3.86
6965 10725 7.598493 GCTTCAACCATGTTTAATAAAGCTTCA 59.402 33.333 0.00 0.00 35.06 3.02
6966 10726 9.474920 CTTCAACCATGTTTAATAAAGCTTCAA 57.525 29.630 0.00 0.00 0.00 2.69
6967 10727 9.995003 TTCAACCATGTTTAATAAAGCTTCAAT 57.005 25.926 0.00 0.00 0.00 2.57
6968 10728 9.638239 TCAACCATGTTTAATAAAGCTTCAATC 57.362 29.630 0.00 0.00 0.00 2.67
6969 10729 9.421806 CAACCATGTTTAATAAAGCTTCAATCA 57.578 29.630 0.00 0.00 0.00 2.57
6973 10733 9.910511 CATGTTTAATAAAGCTTCAATCATTGC 57.089 29.630 0.00 0.00 0.00 3.56
6974 10734 9.880157 ATGTTTAATAAAGCTTCAATCATTGCT 57.120 25.926 0.00 0.00 37.37 3.91
6975 10735 9.709495 TGTTTAATAAAGCTTCAATCATTGCTT 57.291 25.926 0.00 0.00 46.11 3.91
6976 10736 9.962759 GTTTAATAAAGCTTCAATCATTGCTTG 57.037 29.630 0.00 0.00 43.80 4.01
6977 10737 9.926158 TTTAATAAAGCTTCAATCATTGCTTGA 57.074 25.926 0.00 0.00 43.80 3.02
6978 10738 9.926158 TTAATAAAGCTTCAATCATTGCTTGAA 57.074 25.926 13.38 13.38 43.80 2.69
6979 10739 8.836268 AATAAAGCTTCAATCATTGCTTGAAA 57.164 26.923 14.56 2.98 43.80 2.69
6980 10740 8.836268 ATAAAGCTTCAATCATTGCTTGAAAA 57.164 26.923 14.56 0.00 43.80 2.29
6981 10741 7.556733 AAAGCTTCAATCATTGCTTGAAAAA 57.443 28.000 14.56 0.00 43.80 1.94
6982 10742 6.780706 AGCTTCAATCATTGCTTGAAAAAG 57.219 33.333 14.56 6.60 40.89 2.27
6983 10743 5.178809 AGCTTCAATCATTGCTTGAAAAAGC 59.821 36.000 14.56 14.07 40.89 3.51
6984 10744 5.178809 GCTTCAATCATTGCTTGAAAAAGCT 59.821 36.000 14.56 0.00 45.66 3.74
6985 10745 6.293244 GCTTCAATCATTGCTTGAAAAAGCTT 60.293 34.615 14.56 0.00 45.66 3.74
6986 10746 6.774354 TCAATCATTGCTTGAAAAAGCTTC 57.226 33.333 11.39 0.00 45.66 3.86
6987 10747 6.282167 TCAATCATTGCTTGAAAAAGCTTCA 58.718 32.000 11.39 0.00 45.66 3.02
6988 10748 6.762187 TCAATCATTGCTTGAAAAAGCTTCAA 59.238 30.769 11.39 0.00 45.66 2.69
6989 10749 5.971895 TCATTGCTTGAAAAAGCTTCAAC 57.028 34.783 11.39 0.00 45.66 3.18
6990 10750 4.810491 TCATTGCTTGAAAAAGCTTCAACC 59.190 37.500 11.39 0.00 45.66 3.77
6991 10751 3.883830 TGCTTGAAAAAGCTTCAACCA 57.116 38.095 11.39 0.00 45.66 3.67
6992 10752 4.405116 TGCTTGAAAAAGCTTCAACCAT 57.595 36.364 11.39 0.00 45.66 3.55
6993 10753 4.121317 TGCTTGAAAAAGCTTCAACCATG 58.879 39.130 11.39 0.12 45.66 3.66
6994 10754 4.122046 GCTTGAAAAAGCTTCAACCATGT 58.878 39.130 0.00 0.00 42.32 3.21
6995 10755 4.571984 GCTTGAAAAAGCTTCAACCATGTT 59.428 37.500 0.00 0.00 42.32 2.71
6996 10756 5.065090 GCTTGAAAAAGCTTCAACCATGTTT 59.935 36.000 0.00 0.00 42.32 2.83
6997 10757 6.403527 GCTTGAAAAAGCTTCAACCATGTTTT 60.404 34.615 0.00 0.00 42.32 2.43
6998 10758 6.660887 TGAAAAAGCTTCAACCATGTTTTC 57.339 33.333 0.00 3.51 35.22 2.29
6999 10759 5.584251 TGAAAAAGCTTCAACCATGTTTTCC 59.416 36.000 0.00 0.00 34.25 3.13
7000 10760 4.751767 AAAGCTTCAACCATGTTTTCCA 57.248 36.364 0.00 0.00 0.00 3.53
7001 10761 4.751767 AAGCTTCAACCATGTTTTCCAA 57.248 36.364 0.00 0.00 0.00 3.53
7087 10872 4.469657 TCCTACAAGCTTCAACCATGTTT 58.530 39.130 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 3.498082 CCACGTAAAATAAAGTGGCTGC 58.502 45.455 0.29 0.00 46.06 5.25
41 42 6.149640 TGCTTATGTCTTTGCCACGTAAAATA 59.850 34.615 0.00 0.00 0.00 1.40
42 43 5.048364 TGCTTATGTCTTTGCCACGTAAAAT 60.048 36.000 0.00 0.00 0.00 1.82
44 45 3.815962 TGCTTATGTCTTTGCCACGTAAA 59.184 39.130 0.00 0.00 0.00 2.01
47 48 1.890876 TGCTTATGTCTTTGCCACGT 58.109 45.000 0.00 0.00 0.00 4.49
59 65 6.864685 TGCACAAGAAAGAAGAAATGCTTATG 59.135 34.615 0.00 0.00 36.83 1.90
62 68 5.266733 TGCACAAGAAAGAAGAAATGCTT 57.733 34.783 0.00 0.00 40.25 3.91
159 172 1.203050 GGTTGGGTGGATATGGATGGG 60.203 57.143 0.00 0.00 0.00 4.00
164 177 1.203050 GGATGGGTTGGGTGGATATGG 60.203 57.143 0.00 0.00 0.00 2.74
177 190 1.059584 TGTGTGTCTGGTGGATGGGT 61.060 55.000 0.00 0.00 0.00 4.51
180 193 2.485426 GTGAATGTGTGTCTGGTGGATG 59.515 50.000 0.00 0.00 0.00 3.51
181 194 2.783135 GTGAATGTGTGTCTGGTGGAT 58.217 47.619 0.00 0.00 0.00 3.41
183 196 0.867746 CGTGAATGTGTGTCTGGTGG 59.132 55.000 0.00 0.00 0.00 4.61
184 197 1.526887 GACGTGAATGTGTGTCTGGTG 59.473 52.381 0.00 0.00 0.00 4.17
185 198 1.865865 GACGTGAATGTGTGTCTGGT 58.134 50.000 0.00 0.00 0.00 4.00
186 199 0.784178 CGACGTGAATGTGTGTCTGG 59.216 55.000 0.00 0.00 0.00 3.86
187 200 1.766069 TCGACGTGAATGTGTGTCTG 58.234 50.000 0.00 0.00 0.00 3.51
216 229 5.835113 AACATTAAGATGGTTTCCCGATG 57.165 39.130 0.00 0.00 37.60 3.84
262 277 4.435651 GCAATGACGAAAACCAGCTAGTAC 60.436 45.833 0.00 0.00 0.00 2.73
264 279 2.484264 GCAATGACGAAAACCAGCTAGT 59.516 45.455 0.00 0.00 0.00 2.57
312 327 1.340991 CCCCACGACTGGATTGGATTT 60.341 52.381 0.00 0.00 40.55 2.17
321 336 4.394712 GCTGGACCCCACGACTGG 62.395 72.222 0.00 0.00 37.29 4.00
345 363 1.261480 ACACAGACCTCTCGCATTCT 58.739 50.000 0.00 0.00 0.00 2.40
406 452 1.880340 CCGTCGGATCAAGCTGAGC 60.880 63.158 4.91 0.00 30.81 4.26
416 462 0.811616 GCATGCTTCTTCCGTCGGAT 60.812 55.000 16.23 0.00 0.00 4.18
491 540 6.238593 GGAGTATACGTAGTGGAACAGTTAGG 60.239 46.154 0.08 0.00 40.27 2.69
492 541 6.541641 AGGAGTATACGTAGTGGAACAGTTAG 59.458 42.308 0.08 0.00 40.27 2.34
494 543 5.259632 AGGAGTATACGTAGTGGAACAGTT 58.740 41.667 0.08 0.00 40.27 3.16
499 548 8.200024 AGATAGTAGGAGTATACGTAGTGGAA 57.800 38.462 0.08 0.00 45.73 3.53
508 557 5.580297 CCGAACGGAGATAGTAGGAGTATAC 59.420 48.000 7.53 0.00 37.50 1.47
512 561 2.437281 TCCGAACGGAGATAGTAGGAGT 59.563 50.000 12.04 0.00 39.76 3.85
525 574 1.944709 GGGACCAATAAATCCGAACGG 59.055 52.381 6.94 6.94 35.67 4.44
541 590 8.951787 AAACTAACACAAATTTTAAAGGGGAC 57.048 30.769 0.00 0.00 0.00 4.46
542 591 9.961264 AAAAACTAACACAAATTTTAAAGGGGA 57.039 25.926 0.00 0.00 0.00 4.81
543 592 9.995957 CAAAAACTAACACAAATTTTAAAGGGG 57.004 29.630 0.00 0.00 0.00 4.79
596 645 9.562583 ACGACGTAATTTTTATTAACATGCATT 57.437 25.926 0.00 0.00 0.00 3.56
597 646 9.562583 AACGACGTAATTTTTATTAACATGCAT 57.437 25.926 0.00 0.00 0.00 3.96
598 647 8.841822 CAACGACGTAATTTTTATTAACATGCA 58.158 29.630 0.00 0.00 0.00 3.96
599 648 8.308320 CCAACGACGTAATTTTTATTAACATGC 58.692 33.333 0.00 0.00 0.00 4.06
600 649 9.544314 TCCAACGACGTAATTTTTATTAACATG 57.456 29.630 0.00 0.00 0.00 3.21
604 653 9.475505 CGAATCCAACGACGTAATTTTTATTAA 57.524 29.630 0.00 0.00 0.00 1.40
605 654 8.655092 ACGAATCCAACGACGTAATTTTTATTA 58.345 29.630 0.00 0.00 37.22 0.98
606 655 7.520686 ACGAATCCAACGACGTAATTTTTATT 58.479 30.769 0.00 0.00 37.22 1.40
607 656 7.064060 ACGAATCCAACGACGTAATTTTTAT 57.936 32.000 0.00 0.00 37.22 1.40
608 657 6.464895 ACGAATCCAACGACGTAATTTTTA 57.535 33.333 0.00 0.00 37.22 1.52
609 658 5.347012 ACGAATCCAACGACGTAATTTTT 57.653 34.783 0.00 0.00 37.22 1.94
610 659 4.996062 ACGAATCCAACGACGTAATTTT 57.004 36.364 0.00 0.00 37.22 1.82
611 660 6.506827 CGAATACGAATCCAACGACGTAATTT 60.507 38.462 0.00 0.00 42.70 1.82
612 661 5.052172 CGAATACGAATCCAACGACGTAATT 60.052 40.000 0.00 1.77 42.70 1.40
613 662 4.438797 CGAATACGAATCCAACGACGTAAT 59.561 41.667 0.00 0.00 42.70 1.89
614 663 3.785521 CGAATACGAATCCAACGACGTAA 59.214 43.478 0.00 0.00 42.70 3.18
615 664 3.063316 TCGAATACGAATCCAACGACGTA 59.937 43.478 0.00 0.00 45.74 3.57
616 665 2.159531 TCGAATACGAATCCAACGACGT 60.160 45.455 0.00 0.00 45.74 4.34
617 666 2.443387 TCGAATACGAATCCAACGACG 58.557 47.619 0.00 0.00 45.74 5.12
663 712 7.664082 ACAAAATGTTCACACATGACAAAAA 57.336 28.000 0.00 0.00 43.34 1.94
664 713 7.664082 AACAAAATGTTCACACATGACAAAA 57.336 28.000 0.00 0.00 43.34 2.44
665 714 8.031864 ACTAACAAAATGTTCACACATGACAAA 58.968 29.630 0.00 0.00 43.34 2.83
666 715 7.542890 ACTAACAAAATGTTCACACATGACAA 58.457 30.769 0.00 0.00 43.34 3.18
667 716 7.094508 ACTAACAAAATGTTCACACATGACA 57.905 32.000 0.00 0.00 43.34 3.58
668 717 7.985634 AACTAACAAAATGTTCACACATGAC 57.014 32.000 0.00 0.00 43.34 3.06
715 764 8.474831 GCCACAAACACTTCCCTAATATTTTAT 58.525 33.333 0.00 0.00 0.00 1.40
716 765 7.093684 GGCCACAAACACTTCCCTAATATTTTA 60.094 37.037 0.00 0.00 0.00 1.52
717 766 6.295632 GGCCACAAACACTTCCCTAATATTTT 60.296 38.462 0.00 0.00 0.00 1.82
718 767 5.186992 GGCCACAAACACTTCCCTAATATTT 59.813 40.000 0.00 0.00 0.00 1.40
719 768 4.709886 GGCCACAAACACTTCCCTAATATT 59.290 41.667 0.00 0.00 0.00 1.28
720 769 4.278310 GGCCACAAACACTTCCCTAATAT 58.722 43.478 0.00 0.00 0.00 1.28
721 770 3.692690 GGCCACAAACACTTCCCTAATA 58.307 45.455 0.00 0.00 0.00 0.98
722 771 2.525368 GGCCACAAACACTTCCCTAAT 58.475 47.619 0.00 0.00 0.00 1.73
723 772 1.816183 CGGCCACAAACACTTCCCTAA 60.816 52.381 2.24 0.00 0.00 2.69
724 773 0.250553 CGGCCACAAACACTTCCCTA 60.251 55.000 2.24 0.00 0.00 3.53
798 847 1.816074 GCAACGGTGTCCTTGGATAA 58.184 50.000 0.66 0.00 0.00 1.75
849 911 8.581253 AAAATGACTTTGGAAGGGATAACTAG 57.419 34.615 0.00 0.00 0.00 2.57
1546 1772 7.542025 GGACAGAAAGAACTTAATCATGCAAT 58.458 34.615 0.00 0.00 0.00 3.56
1572 1798 6.938542 AGAATCAGCGACGAGAAATAATTTC 58.061 36.000 0.00 0.00 39.96 2.17
1734 1961 4.713321 ACCATTATCTGCCAAGCTTGATTT 59.287 37.500 28.05 9.83 0.00 2.17
1808 2035 5.187576 ACAAAAAGGTACATAATGCCAGCAT 59.812 36.000 0.00 0.00 34.94 3.79
1947 2917 1.148310 CACCAGAGTTACCTGCAACG 58.852 55.000 0.00 0.00 33.50 4.10
2731 3709 4.761975 CATGGGATGGAAAAAGGACATTG 58.238 43.478 0.00 0.00 0.00 2.82
2961 4050 6.209788 GGGGTGTTAATACTCCATTGACAAAA 59.790 38.462 15.93 0.00 42.73 2.44
4149 5302 1.825474 GAGACGTTCCCTTCCATCTCA 59.175 52.381 0.00 0.00 34.12 3.27
4515 5670 1.770658 ACCATATTAGGAGCTGCAGCA 59.229 47.619 38.24 19.65 45.16 4.41
5250 6414 9.417561 ACATCATTGGATCATATTTTCAGAGTT 57.582 29.630 0.00 0.00 0.00 3.01
5343 6507 6.472016 TCCAACATCAATTAGAGTTGCTACA 58.528 36.000 0.13 0.00 39.86 2.74
5865 7084 6.768483 TCTCCTTCATATTTCCGATGCATAA 58.232 36.000 0.00 0.00 0.00 1.90
6311 9855 6.347079 ACACAACATGTTTACCGAAGTTATCG 60.347 38.462 8.77 0.00 45.18 2.92
6375 9920 3.193267 CGGGAGAAATGCTTCATCCAAAA 59.807 43.478 0.00 0.00 33.72 2.44
6739 10379 8.948631 TTAAACATGGTTGAAGCAAAATAACA 57.051 26.923 6.16 0.00 0.00 2.41
6790 10432 4.440880 CTTTTGGAAACATGGTTGAAGCA 58.559 39.130 0.00 0.00 42.32 3.91
6935 10695 8.555361 GCTTTATTAAACATGGTTGAAGCAAAA 58.445 29.630 20.89 3.73 37.50 2.44
6936 10696 7.930865 AGCTTTATTAAACATGGTTGAAGCAAA 59.069 29.630 24.50 12.32 39.39 3.68
6937 10697 7.441017 AGCTTTATTAAACATGGTTGAAGCAA 58.559 30.769 24.50 7.89 39.39 3.91
6938 10698 6.991938 AGCTTTATTAAACATGGTTGAAGCA 58.008 32.000 24.50 0.00 39.39 3.91
6939 10699 7.598493 TGAAGCTTTATTAAACATGGTTGAAGC 59.402 33.333 19.40 19.40 37.75 3.86
6940 10700 9.474920 TTGAAGCTTTATTAAACATGGTTGAAG 57.525 29.630 6.16 6.34 0.00 3.02
6941 10701 9.995003 ATTGAAGCTTTATTAAACATGGTTGAA 57.005 25.926 6.16 0.00 0.00 2.69
6942 10702 9.638239 GATTGAAGCTTTATTAAACATGGTTGA 57.362 29.630 6.16 0.00 0.00 3.18
6943 10703 9.421806 TGATTGAAGCTTTATTAAACATGGTTG 57.578 29.630 6.16 0.00 0.00 3.77
6947 10707 9.910511 GCAATGATTGAAGCTTTATTAAACATG 57.089 29.630 9.76 0.00 0.00 3.21
6948 10708 9.880157 AGCAATGATTGAAGCTTTATTAAACAT 57.120 25.926 9.76 2.52 32.52 2.71
6949 10709 9.709495 AAGCAATGATTGAAGCTTTATTAAACA 57.291 25.926 9.76 0.18 44.22 2.83
6950 10710 9.962759 CAAGCAATGATTGAAGCTTTATTAAAC 57.037 29.630 9.76 0.00 44.22 2.01
6951 10711 9.926158 TCAAGCAATGATTGAAGCTTTATTAAA 57.074 25.926 11.81 0.00 44.22 1.52
6952 10712 9.926158 TTCAAGCAATGATTGAAGCTTTATTAA 57.074 25.926 20.88 0.00 41.88 1.40
6953 10713 9.926158 TTTCAAGCAATGATTGAAGCTTTATTA 57.074 25.926 22.95 6.68 46.09 0.98
6954 10714 8.836268 TTTCAAGCAATGATTGAAGCTTTATT 57.164 26.923 22.95 0.00 46.09 1.40
6955 10715 8.836268 TTTTCAAGCAATGATTGAAGCTTTAT 57.164 26.923 22.95 0.00 46.09 1.40
6956 10716 8.659925 TTTTTCAAGCAATGATTGAAGCTTTA 57.340 26.923 22.95 8.65 46.09 1.85
6957 10717 7.556733 TTTTTCAAGCAATGATTGAAGCTTT 57.443 28.000 22.95 0.00 46.09 3.51
6958 10718 7.186021 CTTTTTCAAGCAATGATTGAAGCTT 57.814 32.000 22.95 0.00 46.09 3.74
6959 10719 6.780706 CTTTTTCAAGCAATGATTGAAGCT 57.219 33.333 22.95 0.00 46.09 3.74
6973 10733 6.667007 AAACATGGTTGAAGCTTTTTCAAG 57.333 33.333 0.00 0.00 38.88 3.02
6974 10734 6.093357 GGAAAACATGGTTGAAGCTTTTTCAA 59.907 34.615 20.22 0.00 34.57 2.69
6975 10735 5.584251 GGAAAACATGGTTGAAGCTTTTTCA 59.416 36.000 20.22 0.00 34.57 2.69
6976 10736 5.584251 TGGAAAACATGGTTGAAGCTTTTTC 59.416 36.000 0.00 14.96 32.95 2.29
6977 10737 5.495640 TGGAAAACATGGTTGAAGCTTTTT 58.504 33.333 0.00 0.00 0.00 1.94
6978 10738 5.096443 TGGAAAACATGGTTGAAGCTTTT 57.904 34.783 0.00 0.00 0.00 2.27
6979 10739 4.751767 TGGAAAACATGGTTGAAGCTTT 57.248 36.364 0.00 0.00 0.00 3.51
6980 10740 4.751767 TTGGAAAACATGGTTGAAGCTT 57.248 36.364 0.00 0.00 0.00 3.74
6981 10741 4.751767 TTTGGAAAACATGGTTGAAGCT 57.248 36.364 0.00 0.00 0.00 3.74
6982 10742 4.260743 GCTTTTGGAAAACATGGTTGAAGC 60.261 41.667 0.00 5.04 0.00 3.86
6983 10743 5.118286 AGCTTTTGGAAAACATGGTTGAAG 58.882 37.500 0.00 0.00 0.00 3.02
6984 10744 5.096443 AGCTTTTGGAAAACATGGTTGAA 57.904 34.783 0.00 0.00 0.00 2.69
6985 10745 4.751767 AGCTTTTGGAAAACATGGTTGA 57.248 36.364 0.00 0.00 0.00 3.18
6986 10746 4.874966 TGAAGCTTTTGGAAAACATGGTTG 59.125 37.500 0.00 0.00 0.00 3.77
6987 10747 5.096443 TGAAGCTTTTGGAAAACATGGTT 57.904 34.783 0.00 0.00 0.00 3.67
6988 10748 4.751767 TGAAGCTTTTGGAAAACATGGT 57.248 36.364 0.00 0.00 0.00 3.55
6989 10749 4.273235 GGTTGAAGCTTTTGGAAAACATGG 59.727 41.667 0.00 0.00 0.00 3.66
6990 10750 4.874966 TGGTTGAAGCTTTTGGAAAACATG 59.125 37.500 0.00 0.00 0.00 3.21
6991 10751 5.096443 TGGTTGAAGCTTTTGGAAAACAT 57.904 34.783 0.00 0.00 0.00 2.71
6992 10752 4.543590 TGGTTGAAGCTTTTGGAAAACA 57.456 36.364 0.00 0.00 0.00 2.83
6993 10753 7.728847 ATAATGGTTGAAGCTTTTGGAAAAC 57.271 32.000 0.00 0.00 0.00 2.43
6994 10754 8.744568 AAATAATGGTTGAAGCTTTTGGAAAA 57.255 26.923 0.00 0.00 0.00 2.29
6995 10755 8.744568 AAAATAATGGTTGAAGCTTTTGGAAA 57.255 26.923 0.00 0.00 0.00 3.13
6996 10756 8.744568 AAAAATAATGGTTGAAGCTTTTGGAA 57.255 26.923 0.00 0.00 0.00 3.53
6997 10757 7.989741 TGAAAAATAATGGTTGAAGCTTTTGGA 59.010 29.630 0.00 0.00 0.00 3.53
6998 10758 8.152309 TGAAAAATAATGGTTGAAGCTTTTGG 57.848 30.769 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.