Multiple sequence alignment - TraesCS1D01G420100

Loading Multiple Alignment...

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 TraesCS1D01G420100 chr1D 100.000 3337 0 0 1 3337 476762574 476765910 0.000000e+00 6163.0
1 TraesCS1D01G420100 chr1D 95.806 453 8 4 1 443 11751047 11751498 0.000000e+00 721.0
2 TraesCS1D01G420100 chr1D 86.343 659 66 14 1695 2352 476592278 476591643 0.000000e+00 697.0
3 TraesCS1D01G420100 chr1D 90.335 269 26 0 1357 1625 476592636 476592368 1.470000e-93 353.0
4 TraesCS1D01G420100 chr1D 91.803 122 4 4 391 509 61780006 61780124 7.410000e-37 165.0
5 TraesCS1D01G420100 chr1D 92.105 114 8 1 397 509 433015749 433015636 3.450000e-35 159.0
6 TraesCS1D01G420100 chr1D 85.714 119 17 0 1706 1824 476759008 476758890 3.500000e-25 126.0
7 TraesCS1D01G420100 chr1A 93.022 1734 72 18 686 2395 572675940 572677648 0.000000e+00 2486.0
8 TraesCS1D01G420100 chr1A 89.501 1362 123 9 1007 2352 572361110 572359753 0.000000e+00 1705.0
9 TraesCS1D01G420100 chr1A 95.326 599 26 2 2741 3337 572678325 572678923 0.000000e+00 950.0
10 TraesCS1D01G420100 chr1A 94.508 437 8 4 1 426 27502891 27502460 0.000000e+00 660.0
11 TraesCS1D01G420100 chr1A 85.764 288 12 6 2458 2745 572677869 572678127 9.120000e-71 278.0
12 TraesCS1D01G420100 chr1A 91.429 70 5 1 2388 2456 572677715 572677784 9.860000e-16 95.3
13 TraesCS1D01G420100 chr1B 92.483 1756 99 15 674 2401 664016300 664018050 0.000000e+00 2481.0
14 TraesCS1D01G420100 chr1B 88.171 1378 132 20 996 2352 662942316 662940949 0.000000e+00 1613.0
15 TraesCS1D01G420100 chr1B 87.315 607 42 12 2052 2646 664082921 664083504 0.000000e+00 662.0
16 TraesCS1D01G420100 chr1B 82.616 604 55 26 2394 2973 664018299 664018876 3.870000e-134 488.0
17 TraesCS1D01G420100 chr1B 83.444 302 41 6 3027 3321 664018888 664019187 4.240000e-69 272.0
18 TraesCS1D01G420100 chr1B 84.874 119 18 0 1706 1824 659956226 659956108 1.630000e-23 121.0
19 TraesCS1D01G420100 chr1B 95.745 47 2 0 2601 2647 120657836 120657882 3.570000e-10 76.8
20 TraesCS1D01G420100 chr5A 89.602 654 61 3 996 1642 674545267 674544614 0.000000e+00 824.0
21 TraesCS1D01G420100 chr5A 88.855 664 68 2 1692 2352 674544523 674543863 0.000000e+00 811.0
22 TraesCS1D01G420100 chr2D 95.340 515 9 1 1 515 39319079 39319578 0.000000e+00 804.0
23 TraesCS1D01G420100 chr2D 97.511 442 9 2 1 441 171865484 171865924 0.000000e+00 754.0
24 TraesCS1D01G420100 chr2D 84.874 119 18 0 1706 1824 39315511 39315393 1.630000e-23 121.0
25 TraesCS1D01G420100 chr5D 97.738 442 9 1 1 441 483822045 483822486 0.000000e+00 760.0
26 TraesCS1D01G420100 chr5D 91.870 123 4 6 387 509 505948801 505948917 2.060000e-37 167.0
27 TraesCS1D01G420100 chr7D 90.135 223 10 7 226 440 29574097 29574315 2.540000e-71 279.0
28 TraesCS1D01G420100 chr3D 89.823 226 12 6 226 443 107202666 107202444 2.540000e-71 279.0
29 TraesCS1D01G420100 chr3D 88.987 227 14 6 226 443 107203295 107203071 1.530000e-68 270.0
30 TraesCS1D01G420100 chr3D 91.339 127 3 6 390 514 535654458 535654338 2.060000e-37 167.0
31 TraesCS1D01G420100 chr4D 88.938 226 11 8 226 443 403006602 403006383 1.970000e-67 267.0
32 TraesCS1D01G420100 chr4D 91.200 125 5 5 390 509 12938502 12938379 7.410000e-37 165.0
33 TraesCS1D01G420100 chrUn 93.443 122 4 4 387 508 90107337 90107454 9.510000e-41 178.0
34 TraesCS1D01G420100 chr7A 84.848 165 20 3 1 161 283942640 283942803 9.580000e-36 161.0
35 TraesCS1D01G420100 chr7A 93.333 45 3 0 2609 2653 726510302 726510258 2.150000e-07 67.6
36 TraesCS1D01G420100 chr4A 80.374 214 39 2 1443 1656 633360744 633360954 3.450000e-35 159.0
37 TraesCS1D01G420100 chr4B 84.800 125 19 0 1700 1824 238161266 238161390 3.500000e-25 126.0
38 TraesCS1D01G420100 chr3B 97.500 40 1 0 2608 2647 241680509 241680470 5.970000e-08 69.4
39 TraesCS1D01G420100 chr3B 95.122 41 2 0 2607 2647 76488406 76488446 7.730000e-07 65.8
40 TraesCS1D01G420100 chr3B 95.122 41 2 0 2607 2647 621148534 621148574 7.730000e-07 65.8
41 TraesCS1D01G420100 chr5B 85.714 56 7 1 2594 2648 145921928 145921983 1.290000e-04 58.4
42 TraesCS1D01G420100 chr3A 100.000 30 0 0 2648 2677 711049877 711049848 4.650000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G420100 chr1D 476762574 476765910 3336 False 6163.000000 6163 100.00000 1 3337 1 chr1D.!!$F3 3336
1 TraesCS1D01G420100 chr1D 476591643 476592636 993 True 525.000000 697 88.33900 1357 2352 2 chr1D.!!$R3 995
2 TraesCS1D01G420100 chr1A 572359753 572361110 1357 True 1705.000000 1705 89.50100 1007 2352 1 chr1A.!!$R2 1345
3 TraesCS1D01G420100 chr1A 572675940 572678923 2983 False 952.325000 2486 91.38525 686 3337 4 chr1A.!!$F1 2651
4 TraesCS1D01G420100 chr1B 662940949 662942316 1367 True 1613.000000 1613 88.17100 996 2352 1 chr1B.!!$R2 1356
5 TraesCS1D01G420100 chr1B 664016300 664019187 2887 False 1080.333333 2481 86.18100 674 3321 3 chr1B.!!$F3 2647
6 TraesCS1D01G420100 chr1B 664082921 664083504 583 False 662.000000 662 87.31500 2052 2646 1 chr1B.!!$F2 594
7 TraesCS1D01G420100 chr5A 674543863 674545267 1404 True 817.500000 824 89.22850 996 2352 2 chr5A.!!$R1 1356
8 TraesCS1D01G420100 chr3D 107202444 107203295 851 True 274.500000 279 89.40500 226 443 2 chr3D.!!$R2 217

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
646 656 0.040058 TACCTACGGCTGAACCTGGA 59.960 55.0 0.0 0.0 35.61 3.86 F
648 658 0.108138 CCTACGGCTGAACCTGGAAG 60.108 60.0 0.0 0.0 35.61 3.46 F
652 662 0.250295 CGGCTGAACCTGGAAGACAA 60.250 55.0 0.0 0.0 34.07 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1607 1747 0.179108 GATTACCTGGCTTCTCGCGT 60.179 55.0 5.77 0.0 40.44 6.01 R
2321 2623 1.663695 CACTTCACTTGTTCACCGGT 58.336 50.0 0.00 0.0 0.00 5.28 R
2536 3184 7.591006 AACACATTACCACATTAAGTACTCG 57.409 36.0 0.00 0.0 0.00 4.18 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 4.203076 CGACCCCGTGTCCCGATC 62.203 72.222 0.00 0.00 41.18 3.69
33 34 3.072468 GACCCCGTGTCCCGATCA 61.072 66.667 0.00 0.00 38.09 2.92
34 35 3.075005 ACCCCGTGTCCCGATCAG 61.075 66.667 0.00 0.00 39.56 2.90
35 36 3.849951 CCCCGTGTCCCGATCAGG 61.850 72.222 0.00 0.00 39.56 3.86
36 37 4.530857 CCCGTGTCCCGATCAGGC 62.531 72.222 0.00 0.00 39.56 4.85
37 38 4.873129 CCGTGTCCCGATCAGGCG 62.873 72.222 0.00 0.00 39.56 5.52
64 65 3.471806 GAGGCCGAGGGTCCCTTC 61.472 72.222 13.13 0.63 31.76 3.46
65 66 3.986116 GAGGCCGAGGGTCCCTTCT 62.986 68.421 13.13 7.76 31.76 2.85
66 67 3.009714 GGCCGAGGGTCCCTTCTT 61.010 66.667 13.13 0.00 31.76 2.52
67 68 2.269241 GCCGAGGGTCCCTTCTTG 59.731 66.667 13.13 2.65 31.76 3.02
68 69 2.593956 GCCGAGGGTCCCTTCTTGT 61.594 63.158 13.13 0.00 31.76 3.16
69 70 1.597461 CCGAGGGTCCCTTCTTGTC 59.403 63.158 13.13 0.00 31.76 3.18
70 71 1.215647 CGAGGGTCCCTTCTTGTCG 59.784 63.158 13.13 6.21 31.76 4.35
71 72 1.597461 GAGGGTCCCTTCTTGTCGG 59.403 63.158 13.13 0.00 31.76 4.79
72 73 2.046217 GGGTCCCTTCTTGTCGGC 60.046 66.667 0.00 0.00 0.00 5.54
73 74 2.046217 GGTCCCTTCTTGTCGGCC 60.046 66.667 0.00 0.00 0.00 6.13
74 75 2.747686 GTCCCTTCTTGTCGGCCA 59.252 61.111 2.24 0.00 0.00 5.36
75 76 1.299976 GTCCCTTCTTGTCGGCCAT 59.700 57.895 2.24 0.00 0.00 4.40
76 77 1.026718 GTCCCTTCTTGTCGGCCATG 61.027 60.000 2.24 0.00 0.00 3.66
77 78 1.750399 CCCTTCTTGTCGGCCATGG 60.750 63.158 7.63 7.63 0.00 3.66
78 79 1.299648 CCTTCTTGTCGGCCATGGA 59.700 57.895 18.40 0.00 0.00 3.41
79 80 0.107017 CCTTCTTGTCGGCCATGGAT 60.107 55.000 18.40 0.00 0.00 3.41
80 81 1.019673 CTTCTTGTCGGCCATGGATG 58.980 55.000 18.40 6.62 0.00 3.51
81 82 1.031571 TTCTTGTCGGCCATGGATGC 61.032 55.000 18.40 0.00 0.00 3.91
82 83 2.440065 TTGTCGGCCATGGATGCC 60.440 61.111 18.40 8.85 45.70 4.40
91 92 3.846180 ATGGATGCCATGGCGTTC 58.154 55.556 31.62 29.77 43.39 3.95
92 93 2.354343 TGGATGCCATGGCGTTCA 59.646 55.556 32.50 32.50 42.78 3.18
93 94 1.076850 TGGATGCCATGGCGTTCAT 60.077 52.632 32.50 20.39 40.40 2.57
102 103 3.530260 GGCGTTCATGGCCCATGG 61.530 66.667 23.20 4.14 44.97 3.66
117 118 2.046988 TGGCACACGAGCTCCATG 60.047 61.111 8.47 9.61 34.17 3.66
118 119 3.503363 GGCACACGAGCTCCATGC 61.503 66.667 18.61 18.61 43.29 4.06
119 120 3.503363 GCACACGAGCTCCATGCC 61.503 66.667 16.84 4.76 44.23 4.40
120 121 2.821366 CACACGAGCTCCATGCCC 60.821 66.667 8.47 0.00 44.23 5.36
122 123 4.147449 CACGAGCTCCATGCCCGA 62.147 66.667 8.47 0.00 46.01 5.14
123 124 3.842923 ACGAGCTCCATGCCCGAG 61.843 66.667 8.47 0.00 46.01 4.63
142 143 2.682952 GCAATTGCGATGAGAGATGG 57.317 50.000 15.87 0.00 0.00 3.51
143 144 1.334779 GCAATTGCGATGAGAGATGGC 60.335 52.381 15.87 0.00 0.00 4.40
144 145 1.070108 CAATTGCGATGAGAGATGGCG 60.070 52.381 0.00 0.00 0.00 5.69
145 146 0.602106 ATTGCGATGAGAGATGGCGG 60.602 55.000 0.00 0.00 0.00 6.13
146 147 3.040763 GCGATGAGAGATGGCGGC 61.041 66.667 0.00 0.00 0.00 6.53
147 148 2.732468 CGATGAGAGATGGCGGCG 60.732 66.667 0.51 0.51 0.00 6.46
148 149 2.356793 GATGAGAGATGGCGGCGG 60.357 66.667 9.78 0.00 0.00 6.13
149 150 4.615815 ATGAGAGATGGCGGCGGC 62.616 66.667 27.76 27.76 38.90 6.53
189 190 4.179579 GAGCGGAATGGCGGCAAC 62.180 66.667 18.31 13.37 44.52 4.17
207 208 2.960129 GGCGTACGAGCGGAATGG 60.960 66.667 21.65 0.00 38.18 3.16
208 209 3.627218 GCGTACGAGCGGAATGGC 61.627 66.667 21.65 0.00 0.00 4.40
209 210 3.320078 CGTACGAGCGGAATGGCG 61.320 66.667 10.44 0.00 38.18 5.69
210 211 2.960129 GTACGAGCGGAATGGCGG 60.960 66.667 0.00 0.00 38.18 6.13
211 212 4.884257 TACGAGCGGAATGGCGGC 62.884 66.667 0.00 0.00 42.62 6.53
260 261 2.029666 CGATCGATGGGAGTGGGC 59.970 66.667 10.26 0.00 0.00 5.36
267 272 0.466922 GATGGGAGTGGGCAAGGATG 60.467 60.000 0.00 0.00 0.00 3.51
285 290 2.710096 TGGGGATCGATGGAGTTTTC 57.290 50.000 0.54 0.00 0.00 2.29
346 354 1.749258 GGCAACGAAGGATGGGGTC 60.749 63.158 0.00 0.00 0.00 4.46
347 355 2.106683 GCAACGAAGGATGGGGTCG 61.107 63.158 0.00 0.00 40.56 4.79
406 415 4.060667 GTGGGATGGGGTGGGGTG 62.061 72.222 0.00 0.00 0.00 4.61
489 499 3.000684 GGGGGACTATTCAACCAACTC 57.999 52.381 0.00 0.00 0.00 3.01
490 500 2.629051 GGGGACTATTCAACCAACTCG 58.371 52.381 0.00 0.00 0.00 4.18
510 520 5.050126 TCGTCCATTAGGAGTAGAGATGT 57.950 43.478 0.00 0.00 46.92 3.06
511 521 6.183810 TCGTCCATTAGGAGTAGAGATGTA 57.816 41.667 0.00 0.00 46.92 2.29
513 523 5.998981 CGTCCATTAGGAGTAGAGATGTAGT 59.001 44.000 0.00 0.00 46.92 2.73
514 524 6.072948 CGTCCATTAGGAGTAGAGATGTAGTG 60.073 46.154 0.00 0.00 46.92 2.74
515 525 5.770663 TCCATTAGGAGTAGAGATGTAGTGC 59.229 44.000 0.00 0.00 39.61 4.40
517 527 3.284793 AGGAGTAGAGATGTAGTGCGT 57.715 47.619 0.00 0.00 0.00 5.24
518 528 3.622630 AGGAGTAGAGATGTAGTGCGTT 58.377 45.455 0.00 0.00 0.00 4.84
519 529 4.017808 AGGAGTAGAGATGTAGTGCGTTT 58.982 43.478 0.00 0.00 0.00 3.60
520 530 5.191426 AGGAGTAGAGATGTAGTGCGTTTA 58.809 41.667 0.00 0.00 0.00 2.01
521 531 5.297278 AGGAGTAGAGATGTAGTGCGTTTAG 59.703 44.000 0.00 0.00 0.00 1.85
522 532 5.296283 GGAGTAGAGATGTAGTGCGTTTAGA 59.704 44.000 0.00 0.00 0.00 2.10
523 533 6.183360 GGAGTAGAGATGTAGTGCGTTTAGAA 60.183 42.308 0.00 0.00 0.00 2.10
524 534 7.154435 AGTAGAGATGTAGTGCGTTTAGAAA 57.846 36.000 0.00 0.00 0.00 2.52
525 535 7.251994 AGTAGAGATGTAGTGCGTTTAGAAAG 58.748 38.462 0.00 0.00 0.00 2.62
526 536 6.268825 AGAGATGTAGTGCGTTTAGAAAGA 57.731 37.500 0.00 0.00 0.00 2.52
527 537 6.688578 AGAGATGTAGTGCGTTTAGAAAGAA 58.311 36.000 0.00 0.00 0.00 2.52
528 538 7.152645 AGAGATGTAGTGCGTTTAGAAAGAAA 58.847 34.615 0.00 0.00 0.00 2.52
531 541 7.656137 AGATGTAGTGCGTTTAGAAAGAAAAGA 59.344 33.333 0.00 0.00 0.00 2.52
532 542 7.542534 TGTAGTGCGTTTAGAAAGAAAAGAA 57.457 32.000 0.00 0.00 0.00 2.52
533 543 7.976826 TGTAGTGCGTTTAGAAAGAAAAGAAA 58.023 30.769 0.00 0.00 0.00 2.52
534 544 8.617809 TGTAGTGCGTTTAGAAAGAAAAGAAAT 58.382 29.630 0.00 0.00 0.00 2.17
536 546 6.851330 AGTGCGTTTAGAAAGAAAAGAAATCG 59.149 34.615 0.00 0.00 0.00 3.34
537 547 5.623673 TGCGTTTAGAAAGAAAAGAAATCGC 59.376 36.000 0.00 0.00 38.29 4.58
538 548 5.219605 GCGTTTAGAAAGAAAAGAAATCGCG 60.220 40.000 0.00 0.00 0.00 5.87
539 549 5.280678 CGTTTAGAAAGAAAAGAAATCGCGG 59.719 40.000 6.13 0.00 0.00 6.46
540 550 6.368213 GTTTAGAAAGAAAAGAAATCGCGGA 58.632 36.000 6.13 0.00 0.00 5.54
541 551 6.548441 TTAGAAAGAAAAGAAATCGCGGAA 57.452 33.333 6.13 0.00 0.00 4.30
543 553 6.013842 AGAAAGAAAAGAAATCGCGGAATT 57.986 33.333 6.13 0.00 0.00 2.17
544 554 5.858581 AGAAAGAAAAGAAATCGCGGAATTG 59.141 36.000 6.13 0.00 0.00 2.32
545 555 3.501950 AGAAAAGAAATCGCGGAATTGC 58.498 40.909 6.13 0.00 0.00 3.56
546 556 3.057596 AGAAAAGAAATCGCGGAATTGCA 60.058 39.130 6.13 0.00 34.15 4.08
547 557 2.549633 AAGAAATCGCGGAATTGCAG 57.450 45.000 6.13 0.00 34.15 4.41
548 558 1.737838 AGAAATCGCGGAATTGCAGA 58.262 45.000 6.13 0.00 34.15 4.26
549 559 2.292267 AGAAATCGCGGAATTGCAGAT 58.708 42.857 6.13 0.00 32.33 2.90
550 560 2.684881 AGAAATCGCGGAATTGCAGATT 59.315 40.909 6.13 10.45 38.65 2.40
551 561 3.129287 AGAAATCGCGGAATTGCAGATTT 59.871 39.130 21.60 21.60 43.64 2.17
552 562 3.508744 AATCGCGGAATTGCAGATTTT 57.491 38.095 6.13 0.00 35.87 1.82
553 563 2.261037 TCGCGGAATTGCAGATTTTG 57.739 45.000 6.13 0.00 34.15 2.44
554 564 1.539388 TCGCGGAATTGCAGATTTTGT 59.461 42.857 6.13 0.00 34.15 2.83
555 565 2.030363 TCGCGGAATTGCAGATTTTGTT 60.030 40.909 6.13 0.00 34.15 2.83
556 566 2.730928 CGCGGAATTGCAGATTTTGTTT 59.269 40.909 0.00 0.00 34.15 2.83
557 567 3.181541 CGCGGAATTGCAGATTTTGTTTC 60.182 43.478 0.00 0.00 34.15 2.78
558 568 3.989817 GCGGAATTGCAGATTTTGTTTCT 59.010 39.130 0.00 0.00 34.15 2.52
559 569 4.448732 GCGGAATTGCAGATTTTGTTTCTT 59.551 37.500 0.00 0.00 34.15 2.52
560 570 5.050159 GCGGAATTGCAGATTTTGTTTCTTT 60.050 36.000 0.00 0.00 34.15 2.52
561 571 6.357198 CGGAATTGCAGATTTTGTTTCTTTG 58.643 36.000 0.00 0.00 0.00 2.77
562 572 6.018832 CGGAATTGCAGATTTTGTTTCTTTGT 60.019 34.615 0.00 0.00 0.00 2.83
563 573 7.465781 CGGAATTGCAGATTTTGTTTCTTTGTT 60.466 33.333 0.00 0.00 0.00 2.83
564 574 8.183536 GGAATTGCAGATTTTGTTTCTTTGTTT 58.816 29.630 0.00 0.00 0.00 2.83
565 575 9.213819 GAATTGCAGATTTTGTTTCTTTGTTTC 57.786 29.630 0.00 0.00 0.00 2.78
566 576 6.329838 TGCAGATTTTGTTTCTTTGTTTCG 57.670 33.333 0.00 0.00 0.00 3.46
567 577 5.866633 TGCAGATTTTGTTTCTTTGTTTCGT 59.133 32.000 0.00 0.00 0.00 3.85
568 578 6.177822 GCAGATTTTGTTTCTTTGTTTCGTG 58.822 36.000 0.00 0.00 0.00 4.35
569 579 6.034470 GCAGATTTTGTTTCTTTGTTTCGTGA 59.966 34.615 0.00 0.00 0.00 4.35
570 580 7.603515 CAGATTTTGTTTCTTTGTTTCGTGAG 58.396 34.615 0.00 0.00 0.00 3.51
571 581 7.273381 CAGATTTTGTTTCTTTGTTTCGTGAGT 59.727 33.333 0.00 0.00 0.00 3.41
572 582 7.812669 AGATTTTGTTTCTTTGTTTCGTGAGTT 59.187 29.630 0.00 0.00 0.00 3.01
573 583 6.683090 TTTGTTTCTTTGTTTCGTGAGTTG 57.317 33.333 0.00 0.00 0.00 3.16
574 584 5.365403 TGTTTCTTTGTTTCGTGAGTTGT 57.635 34.783 0.00 0.00 0.00 3.32
575 585 6.483385 TGTTTCTTTGTTTCGTGAGTTGTA 57.517 33.333 0.00 0.00 0.00 2.41
576 586 6.539324 TGTTTCTTTGTTTCGTGAGTTGTAG 58.461 36.000 0.00 0.00 0.00 2.74
577 587 6.369340 TGTTTCTTTGTTTCGTGAGTTGTAGA 59.631 34.615 0.00 0.00 0.00 2.59
578 588 5.961395 TCTTTGTTTCGTGAGTTGTAGAC 57.039 39.130 0.00 0.00 0.00 2.59
579 589 5.412640 TCTTTGTTTCGTGAGTTGTAGACA 58.587 37.500 0.00 0.00 0.00 3.41
580 590 5.870433 TCTTTGTTTCGTGAGTTGTAGACAA 59.130 36.000 0.00 0.00 0.00 3.18
581 591 5.712217 TTGTTTCGTGAGTTGTAGACAAG 57.288 39.130 0.00 0.00 36.39 3.16
582 592 5.001237 TGTTTCGTGAGTTGTAGACAAGA 57.999 39.130 0.00 0.00 36.39 3.02
583 593 5.597806 TGTTTCGTGAGTTGTAGACAAGAT 58.402 37.500 0.00 0.00 36.39 2.40
584 594 6.046593 TGTTTCGTGAGTTGTAGACAAGATT 58.953 36.000 0.00 0.00 36.39 2.40
585 595 7.204604 TGTTTCGTGAGTTGTAGACAAGATTA 58.795 34.615 0.00 0.00 36.39 1.75
586 596 7.870954 TGTTTCGTGAGTTGTAGACAAGATTAT 59.129 33.333 0.00 0.00 36.39 1.28
587 597 7.812309 TTCGTGAGTTGTAGACAAGATTATG 57.188 36.000 0.00 0.00 36.39 1.90
588 598 6.920817 TCGTGAGTTGTAGACAAGATTATGT 58.079 36.000 0.00 0.00 36.39 2.29
589 599 7.375834 TCGTGAGTTGTAGACAAGATTATGTT 58.624 34.615 0.00 0.00 36.39 2.71
590 600 8.517056 TCGTGAGTTGTAGACAAGATTATGTTA 58.483 33.333 0.00 0.00 36.39 2.41
591 601 9.135843 CGTGAGTTGTAGACAAGATTATGTTAA 57.864 33.333 0.00 0.00 36.39 2.01
603 613 9.143631 ACAAGATTATGTTAAAAATTGCAGAGC 57.856 29.630 0.00 0.00 0.00 4.09
604 614 9.142515 CAAGATTATGTTAAAAATTGCAGAGCA 57.857 29.630 0.00 0.00 36.47 4.26
605 615 9.880157 AAGATTATGTTAAAAATTGCAGAGCAT 57.120 25.926 0.00 0.00 38.76 3.79
606 616 9.309516 AGATTATGTTAAAAATTGCAGAGCATG 57.690 29.630 0.00 0.00 38.76 4.06
627 637 4.096732 GCGTTTGCAATTTACATCTCCT 57.903 40.909 0.00 0.00 42.15 3.69
628 638 5.229921 GCGTTTGCAATTTACATCTCCTA 57.770 39.130 0.00 0.00 42.15 2.94
629 639 5.028375 GCGTTTGCAATTTACATCTCCTAC 58.972 41.667 0.00 0.00 42.15 3.18
630 640 5.569413 CGTTTGCAATTTACATCTCCTACC 58.431 41.667 0.00 0.00 0.00 3.18
631 641 5.354234 CGTTTGCAATTTACATCTCCTACCT 59.646 40.000 0.00 0.00 0.00 3.08
632 642 6.537301 CGTTTGCAATTTACATCTCCTACCTA 59.463 38.462 0.00 0.00 0.00 3.08
633 643 7.465513 CGTTTGCAATTTACATCTCCTACCTAC 60.466 40.741 0.00 0.00 0.00 3.18
634 644 5.597806 TGCAATTTACATCTCCTACCTACG 58.402 41.667 0.00 0.00 0.00 3.51
635 645 4.989168 GCAATTTACATCTCCTACCTACGG 59.011 45.833 0.00 0.00 0.00 4.02
636 646 4.868314 ATTTACATCTCCTACCTACGGC 57.132 45.455 0.00 0.00 0.00 5.68
637 647 3.589951 TTACATCTCCTACCTACGGCT 57.410 47.619 0.00 0.00 0.00 5.52
638 648 1.693627 ACATCTCCTACCTACGGCTG 58.306 55.000 0.00 0.00 0.00 4.85
639 649 1.214673 ACATCTCCTACCTACGGCTGA 59.785 52.381 0.00 0.00 0.00 4.26
640 650 2.307768 CATCTCCTACCTACGGCTGAA 58.692 52.381 0.00 0.00 0.00 3.02
641 651 1.760192 TCTCCTACCTACGGCTGAAC 58.240 55.000 0.00 0.00 0.00 3.18
642 652 0.745468 CTCCTACCTACGGCTGAACC 59.255 60.000 0.00 0.00 0.00 3.62
643 653 0.333993 TCCTACCTACGGCTGAACCT 59.666 55.000 0.00 0.00 35.61 3.50
644 654 0.460311 CCTACCTACGGCTGAACCTG 59.540 60.000 0.00 0.00 35.61 4.00
645 655 0.460311 CTACCTACGGCTGAACCTGG 59.540 60.000 0.00 0.00 35.61 4.45
646 656 0.040058 TACCTACGGCTGAACCTGGA 59.960 55.000 0.00 0.00 35.61 3.86
647 657 0.834687 ACCTACGGCTGAACCTGGAA 60.835 55.000 0.00 0.00 35.61 3.53
648 658 0.108138 CCTACGGCTGAACCTGGAAG 60.108 60.000 0.00 0.00 35.61 3.46
649 659 0.895530 CTACGGCTGAACCTGGAAGA 59.104 55.000 0.00 0.00 34.07 2.87
650 660 0.606604 TACGGCTGAACCTGGAAGAC 59.393 55.000 0.00 0.00 34.07 3.01
651 661 1.371183 CGGCTGAACCTGGAAGACA 59.629 57.895 0.00 0.00 34.07 3.41
652 662 0.250295 CGGCTGAACCTGGAAGACAA 60.250 55.000 0.00 0.00 34.07 3.18
653 663 1.528129 GGCTGAACCTGGAAGACAAG 58.472 55.000 0.00 0.00 34.07 3.16
654 664 1.072331 GGCTGAACCTGGAAGACAAGA 59.928 52.381 0.00 0.00 34.07 3.02
655 665 2.290577 GGCTGAACCTGGAAGACAAGAT 60.291 50.000 0.00 0.00 34.07 2.40
656 666 3.416156 GCTGAACCTGGAAGACAAGATT 58.584 45.455 0.00 0.00 34.07 2.40
657 667 4.565652 GGCTGAACCTGGAAGACAAGATTA 60.566 45.833 0.00 0.00 34.07 1.75
658 668 5.189180 GCTGAACCTGGAAGACAAGATTAT 58.811 41.667 0.00 0.00 34.07 1.28
659 669 5.065731 GCTGAACCTGGAAGACAAGATTATG 59.934 44.000 0.00 0.00 34.07 1.90
660 670 6.126863 TGAACCTGGAAGACAAGATTATGT 57.873 37.500 0.00 0.00 34.07 2.29
661 671 6.542821 TGAACCTGGAAGACAAGATTATGTT 58.457 36.000 0.00 0.00 34.07 2.71
662 672 7.004086 TGAACCTGGAAGACAAGATTATGTTT 58.996 34.615 0.00 0.00 34.07 2.83
663 673 7.174946 TGAACCTGGAAGACAAGATTATGTTTC 59.825 37.037 0.00 0.00 34.07 2.78
664 674 5.946377 ACCTGGAAGACAAGATTATGTTTCC 59.054 40.000 0.00 11.24 38.96 3.13
665 675 6.183347 CCTGGAAGACAAGATTATGTTTCCT 58.817 40.000 15.59 0.00 39.09 3.36
666 676 6.317391 CCTGGAAGACAAGATTATGTTTCCTC 59.683 42.308 15.59 0.00 39.09 3.71
667 677 7.020827 TGGAAGACAAGATTATGTTTCCTCT 57.979 36.000 15.59 0.00 39.09 3.69
668 678 7.461749 TGGAAGACAAGATTATGTTTCCTCTT 58.538 34.615 15.59 0.00 39.09 2.85
669 679 7.944554 TGGAAGACAAGATTATGTTTCCTCTTT 59.055 33.333 15.59 0.00 39.09 2.52
670 680 8.797438 GGAAGACAAGATTATGTTTCCTCTTTT 58.203 33.333 11.03 0.00 37.43 2.27
718 728 9.850628 AGATTGTGTTAGAAATCATGAAATGTG 57.149 29.630 0.00 0.00 46.80 3.21
794 808 1.618074 GCCTTCCAATGCTCCTTTCCT 60.618 52.381 0.00 0.00 0.00 3.36
928 942 4.752879 GCCGTTGCCGCCTCAGTA 62.753 66.667 0.00 0.00 0.00 2.74
1036 1056 1.816679 ATCGTCGGACCGATCACGA 60.817 57.895 25.43 25.43 43.74 4.35
1244 1384 3.181290 CTTCGAGCGCGTGATGCA 61.181 61.111 10.30 0.00 46.97 3.96
1383 1523 1.105457 CCAACTGGATCGGGTACGTA 58.895 55.000 0.00 0.00 38.30 3.57
1417 1557 4.020617 CAGGGAAGGCGGTGCTCA 62.021 66.667 0.00 0.00 0.00 4.26
1607 1747 0.626382 TCCACCCACAACAAGGACAA 59.374 50.000 0.00 0.00 0.00 3.18
1644 1795 2.684001 TCTTGTGACCAAACGACAGT 57.316 45.000 0.00 0.00 0.00 3.55
1802 2001 4.335647 CTGGCCACCCTGAACGCT 62.336 66.667 0.00 0.00 32.15 5.07
1834 2033 1.196808 CGAAAACGGCTACAACTGCAT 59.803 47.619 0.00 0.00 0.00 3.96
1981 2183 4.402528 CCGGGACATCGTGCCCAA 62.403 66.667 0.00 0.00 44.94 4.12
2397 2956 4.992688 TGCACGAAAGACAGTTGATTTTT 58.007 34.783 0.00 0.00 0.00 1.94
2456 3102 4.939509 TGGAAGCTTCGTAGTAAATTGC 57.060 40.909 19.91 2.46 0.00 3.56
2536 3184 9.290483 CTCTCAGTGTTTTAAAAGAAAAAGTCC 57.710 33.333 0.00 0.00 0.00 3.85
2685 3337 7.768807 AGTTGCAGAGGGACTACTATTATAG 57.231 40.000 0.00 0.00 41.55 1.31
2935 3801 8.670135 CAATGCATGTCAATACAATTCCATTTT 58.330 29.630 0.00 0.00 39.58 1.82
3103 3970 3.573538 AGCAATAAAGGATGCACACACAA 59.426 39.130 0.00 0.00 44.95 3.33
3106 3973 6.071447 AGCAATAAAGGATGCACACACAAATA 60.071 34.615 0.00 0.00 44.95 1.40
3107 3974 6.589523 GCAATAAAGGATGCACACACAAATAA 59.410 34.615 0.00 0.00 42.12 1.40
3108 3975 7.117523 GCAATAAAGGATGCACACACAAATAAA 59.882 33.333 0.00 0.00 42.12 1.40
3109 3976 9.153721 CAATAAAGGATGCACACACAAATAAAT 57.846 29.630 0.00 0.00 0.00 1.40
3110 3977 9.723601 AATAAAGGATGCACACACAAATAAATT 57.276 25.926 0.00 0.00 0.00 1.82
3307 4181 4.020573 TCCTTCTTTCTCACGGAATGCTTA 60.021 41.667 0.00 0.00 33.53 3.09
3325 4199 9.132521 GAATGCTTATATTGTACATGCATTTCC 57.867 33.333 19.94 11.52 45.62 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.072468 TGATCGGGACACGGGGTC 61.072 66.667 0.57 0.57 46.20 4.46
17 18 3.075005 CTGATCGGGACACGGGGT 61.075 66.667 0.00 0.00 44.45 4.95
18 19 3.849951 CCTGATCGGGACACGGGG 61.850 72.222 16.28 0.00 44.45 5.73
19 20 4.530857 GCCTGATCGGGACACGGG 62.531 72.222 25.54 0.00 44.45 5.28
20 21 4.873129 CGCCTGATCGGGACACGG 62.873 72.222 25.54 3.35 44.45 4.94
47 48 3.471806 GAAGGGACCCTCGGCCTC 61.472 72.222 15.27 3.04 30.89 4.70
48 49 3.564347 AAGAAGGGACCCTCGGCCT 62.564 63.158 15.27 6.20 30.89 5.19
49 50 3.009714 AAGAAGGGACCCTCGGCC 61.010 66.667 15.27 3.78 30.89 6.13
50 51 2.269241 CAAGAAGGGACCCTCGGC 59.731 66.667 15.27 6.70 30.89 5.54
51 52 1.597461 GACAAGAAGGGACCCTCGG 59.403 63.158 15.27 6.33 30.89 4.63
52 53 1.215647 CGACAAGAAGGGACCCTCG 59.784 63.158 15.27 8.47 30.89 4.63
53 54 1.597461 CCGACAAGAAGGGACCCTC 59.403 63.158 15.27 7.70 30.89 4.30
54 55 2.593956 GCCGACAAGAAGGGACCCT 61.594 63.158 7.44 7.44 33.87 4.34
55 56 2.046217 GCCGACAAGAAGGGACCC 60.046 66.667 0.59 0.59 0.00 4.46
56 57 2.046217 GGCCGACAAGAAGGGACC 60.046 66.667 0.00 0.00 0.00 4.46
57 58 1.026718 CATGGCCGACAAGAAGGGAC 61.027 60.000 0.00 0.00 0.00 4.46
58 59 1.299648 CATGGCCGACAAGAAGGGA 59.700 57.895 0.00 0.00 0.00 4.20
59 60 1.750399 CCATGGCCGACAAGAAGGG 60.750 63.158 0.00 0.00 0.00 3.95
60 61 0.107017 ATCCATGGCCGACAAGAAGG 60.107 55.000 6.96 0.00 0.00 3.46
61 62 1.019673 CATCCATGGCCGACAAGAAG 58.980 55.000 6.96 0.00 0.00 2.85
62 63 1.031571 GCATCCATGGCCGACAAGAA 61.032 55.000 6.96 0.00 0.00 2.52
63 64 1.451927 GCATCCATGGCCGACAAGA 60.452 57.895 6.96 0.00 0.00 3.02
64 65 2.484062 GGCATCCATGGCCGACAAG 61.484 63.158 6.96 0.00 46.49 3.16
65 66 2.440065 GGCATCCATGGCCGACAA 60.440 61.111 6.96 0.00 46.49 3.18
74 75 0.468585 ATGAACGCCATGGCATCCAT 60.469 50.000 34.93 27.45 46.37 3.41
75 76 1.076850 ATGAACGCCATGGCATCCA 60.077 52.632 34.93 26.57 42.06 3.41
76 77 1.361271 CATGAACGCCATGGCATCC 59.639 57.895 34.93 22.17 46.85 3.51
85 86 3.530260 CCATGGGCCATGAACGCC 61.530 66.667 41.10 3.04 43.81 5.68
86 87 4.211502 GCCATGGGCCATGAACGC 62.212 66.667 41.10 32.06 43.81 4.84
96 97 2.821366 GAGCTCGTGTGCCATGGG 60.821 66.667 15.13 0.00 0.00 4.00
97 98 2.821366 GGAGCTCGTGTGCCATGG 60.821 66.667 7.63 7.63 0.00 3.66
98 99 1.450848 ATGGAGCTCGTGTGCCATG 60.451 57.895 7.83 0.00 39.54 3.66
99 100 1.450848 CATGGAGCTCGTGTGCCAT 60.451 57.895 7.83 1.71 41.61 4.40
100 101 2.046988 CATGGAGCTCGTGTGCCA 60.047 61.111 7.83 0.00 34.45 4.92
101 102 3.503363 GCATGGAGCTCGTGTGCC 61.503 66.667 19.83 3.03 41.15 5.01
102 103 3.503363 GGCATGGAGCTCGTGTGC 61.503 66.667 21.43 21.43 44.79 4.57
103 104 2.821366 GGGCATGGAGCTCGTGTG 60.821 66.667 16.23 11.83 44.79 3.82
117 118 2.025156 CATCGCAATTGCTCGGGC 59.975 61.111 26.86 0.00 39.32 6.13
118 119 0.811219 TCTCATCGCAATTGCTCGGG 60.811 55.000 26.86 15.17 39.32 5.14
119 120 0.580578 CTCTCATCGCAATTGCTCGG 59.419 55.000 26.86 15.68 39.32 4.63
120 121 1.564207 TCTCTCATCGCAATTGCTCG 58.436 50.000 26.86 13.42 39.32 5.03
121 122 2.223611 CCATCTCTCATCGCAATTGCTC 59.776 50.000 26.86 0.76 39.32 4.26
122 123 2.219458 CCATCTCTCATCGCAATTGCT 58.781 47.619 26.86 7.64 39.32 3.91
123 124 1.334779 GCCATCTCTCATCGCAATTGC 60.335 52.381 20.76 20.76 37.78 3.56
124 125 1.070108 CGCCATCTCTCATCGCAATTG 60.070 52.381 0.00 0.00 0.00 2.32
125 126 1.224075 CGCCATCTCTCATCGCAATT 58.776 50.000 0.00 0.00 0.00 2.32
126 127 0.602106 CCGCCATCTCTCATCGCAAT 60.602 55.000 0.00 0.00 0.00 3.56
127 128 1.227350 CCGCCATCTCTCATCGCAA 60.227 57.895 0.00 0.00 0.00 4.85
128 129 2.418777 CCGCCATCTCTCATCGCA 59.581 61.111 0.00 0.00 0.00 5.10
129 130 3.040763 GCCGCCATCTCTCATCGC 61.041 66.667 0.00 0.00 0.00 4.58
130 131 2.732468 CGCCGCCATCTCTCATCG 60.732 66.667 0.00 0.00 0.00 3.84
131 132 2.356793 CCGCCGCCATCTCTCATC 60.357 66.667 0.00 0.00 0.00 2.92
132 133 4.615815 GCCGCCGCCATCTCTCAT 62.616 66.667 0.00 0.00 0.00 2.90
134 135 4.615815 ATGCCGCCGCCATCTCTC 62.616 66.667 0.00 0.00 0.00 3.20
135 136 4.923942 CATGCCGCCGCCATCTCT 62.924 66.667 0.00 0.00 0.00 3.10
172 173 4.179579 GTTGCCGCCATTCCGCTC 62.180 66.667 0.00 0.00 0.00 5.03
186 187 4.764336 TCCGCTCGTACGCCGTTG 62.764 66.667 20.84 10.86 37.94 4.10
187 188 3.346631 ATTCCGCTCGTACGCCGTT 62.347 57.895 20.84 7.95 37.94 4.44
188 189 3.818787 ATTCCGCTCGTACGCCGT 61.819 61.111 20.84 0.00 37.94 5.68
189 190 3.320078 CATTCCGCTCGTACGCCG 61.320 66.667 11.24 15.08 38.13 6.46
190 191 2.960129 CCATTCCGCTCGTACGCC 60.960 66.667 11.24 2.90 0.00 5.68
191 192 3.627218 GCCATTCCGCTCGTACGC 61.627 66.667 11.24 0.00 0.00 4.42
192 193 3.320078 CGCCATTCCGCTCGTACG 61.320 66.667 9.53 9.53 0.00 3.67
193 194 2.960129 CCGCCATTCCGCTCGTAC 60.960 66.667 0.00 0.00 0.00 3.67
194 195 4.884257 GCCGCCATTCCGCTCGTA 62.884 66.667 0.00 0.00 0.00 3.43
234 235 1.449423 CCATCGATCGTTGCCACCA 60.449 57.895 18.61 0.00 0.00 4.17
260 261 1.002888 CTCCATCGATCCCCATCCTTG 59.997 57.143 0.00 0.00 0.00 3.61
267 272 2.803492 CGAGAAAACTCCATCGATCCCC 60.803 54.545 0.00 0.00 37.35 4.81
379 388 4.720902 CATCCCACGCAGCCACCA 62.721 66.667 0.00 0.00 0.00 4.17
389 398 4.060667 CACCCCACCCCATCCCAC 62.061 72.222 0.00 0.00 0.00 4.61
404 413 0.179012 TTTTTCGTCACCTCCCCCAC 60.179 55.000 0.00 0.00 0.00 4.61
405 414 2.232622 TTTTTCGTCACCTCCCCCA 58.767 52.632 0.00 0.00 0.00 4.96
451 461 2.028876 CCCCACTTTCGTCTGGTTTTT 58.971 47.619 0.00 0.00 0.00 1.94
452 462 1.687563 CCCCACTTTCGTCTGGTTTT 58.312 50.000 0.00 0.00 0.00 2.43
453 463 0.179001 CCCCCACTTTCGTCTGGTTT 60.179 55.000 0.00 0.00 0.00 3.27
454 464 1.454539 CCCCCACTTTCGTCTGGTT 59.545 57.895 0.00 0.00 0.00 3.67
455 465 3.157680 CCCCCACTTTCGTCTGGT 58.842 61.111 0.00 0.00 0.00 4.00
469 479 2.679930 CGAGTTGGTTGAATAGTCCCCC 60.680 54.545 0.00 0.00 0.00 5.40
472 482 3.259902 GGACGAGTTGGTTGAATAGTCC 58.740 50.000 0.00 0.00 39.83 3.85
481 491 2.904434 ACTCCTAATGGACGAGTTGGTT 59.096 45.455 0.00 0.00 37.46 3.67
489 499 5.998981 ACTACATCTCTACTCCTAATGGACG 59.001 44.000 0.00 0.00 37.46 4.79
490 500 6.294286 GCACTACATCTCTACTCCTAATGGAC 60.294 46.154 0.00 0.00 37.46 4.02
510 520 8.007716 CGATTTCTTTTCTTTCTAAACGCACTA 58.992 33.333 0.00 0.00 0.00 2.74
511 521 6.851330 CGATTTCTTTTCTTTCTAAACGCACT 59.149 34.615 0.00 0.00 0.00 4.40
513 523 5.623673 GCGATTTCTTTTCTTTCTAAACGCA 59.376 36.000 0.00 0.00 39.63 5.24
514 524 5.219605 CGCGATTTCTTTTCTTTCTAAACGC 60.220 40.000 0.00 0.00 37.21 4.84
515 525 5.280678 CCGCGATTTCTTTTCTTTCTAAACG 59.719 40.000 8.23 0.00 0.00 3.60
517 527 6.548441 TCCGCGATTTCTTTTCTTTCTAAA 57.452 33.333 8.23 0.00 0.00 1.85
518 528 6.548441 TTCCGCGATTTCTTTTCTTTCTAA 57.452 33.333 8.23 0.00 0.00 2.10
519 529 6.737254 ATTCCGCGATTTCTTTTCTTTCTA 57.263 33.333 8.23 0.00 0.00 2.10
520 530 5.629079 ATTCCGCGATTTCTTTTCTTTCT 57.371 34.783 8.23 0.00 0.00 2.52
521 531 5.443301 GCAATTCCGCGATTTCTTTTCTTTC 60.443 40.000 8.23 0.00 0.00 2.62
522 532 4.385748 GCAATTCCGCGATTTCTTTTCTTT 59.614 37.500 8.23 0.00 0.00 2.52
523 533 3.920412 GCAATTCCGCGATTTCTTTTCTT 59.080 39.130 8.23 0.00 0.00 2.52
524 534 3.057596 TGCAATTCCGCGATTTCTTTTCT 60.058 39.130 8.23 0.00 33.35 2.52
525 535 3.241701 TGCAATTCCGCGATTTCTTTTC 58.758 40.909 8.23 0.00 33.35 2.29
526 536 3.057596 TCTGCAATTCCGCGATTTCTTTT 60.058 39.130 8.23 0.00 33.35 2.27
527 537 2.487762 TCTGCAATTCCGCGATTTCTTT 59.512 40.909 8.23 0.00 33.35 2.52
528 538 2.083774 TCTGCAATTCCGCGATTTCTT 58.916 42.857 8.23 0.00 33.35 2.52
531 541 3.508744 AAATCTGCAATTCCGCGATTT 57.491 38.095 8.23 0.00 38.77 2.17
532 542 3.181397 CAAAATCTGCAATTCCGCGATT 58.819 40.909 8.23 0.00 37.00 3.34
533 543 2.164219 ACAAAATCTGCAATTCCGCGAT 59.836 40.909 8.23 0.00 33.35 4.58
534 544 1.539388 ACAAAATCTGCAATTCCGCGA 59.461 42.857 8.23 0.00 33.35 5.87
536 546 3.989817 AGAAACAAAATCTGCAATTCCGC 59.010 39.130 0.00 0.00 0.00 5.54
537 547 6.018832 ACAAAGAAACAAAATCTGCAATTCCG 60.019 34.615 0.00 0.00 0.00 4.30
538 548 7.250445 ACAAAGAAACAAAATCTGCAATTCC 57.750 32.000 0.00 0.00 0.00 3.01
539 549 9.213819 GAAACAAAGAAACAAAATCTGCAATTC 57.786 29.630 0.00 0.00 0.00 2.17
540 550 7.904461 CGAAACAAAGAAACAAAATCTGCAATT 59.096 29.630 0.00 0.00 0.00 2.32
541 551 7.064490 ACGAAACAAAGAAACAAAATCTGCAAT 59.936 29.630 0.00 0.00 0.00 3.56
543 553 5.866633 ACGAAACAAAGAAACAAAATCTGCA 59.133 32.000 0.00 0.00 0.00 4.41
544 554 6.034470 TCACGAAACAAAGAAACAAAATCTGC 59.966 34.615 0.00 0.00 0.00 4.26
545 555 7.273381 ACTCACGAAACAAAGAAACAAAATCTG 59.727 33.333 0.00 0.00 0.00 2.90
546 556 7.312899 ACTCACGAAACAAAGAAACAAAATCT 58.687 30.769 0.00 0.00 0.00 2.40
547 557 7.506296 ACTCACGAAACAAAGAAACAAAATC 57.494 32.000 0.00 0.00 0.00 2.17
548 558 7.383843 ACAACTCACGAAACAAAGAAACAAAAT 59.616 29.630 0.00 0.00 0.00 1.82
549 559 6.697892 ACAACTCACGAAACAAAGAAACAAAA 59.302 30.769 0.00 0.00 0.00 2.44
550 560 6.210078 ACAACTCACGAAACAAAGAAACAAA 58.790 32.000 0.00 0.00 0.00 2.83
551 561 5.764131 ACAACTCACGAAACAAAGAAACAA 58.236 33.333 0.00 0.00 0.00 2.83
552 562 5.365403 ACAACTCACGAAACAAAGAAACA 57.635 34.783 0.00 0.00 0.00 2.83
553 563 6.681599 GTCTACAACTCACGAAACAAAGAAAC 59.318 38.462 0.00 0.00 0.00 2.78
554 564 6.369340 TGTCTACAACTCACGAAACAAAGAAA 59.631 34.615 0.00 0.00 0.00 2.52
555 565 5.870433 TGTCTACAACTCACGAAACAAAGAA 59.130 36.000 0.00 0.00 0.00 2.52
556 566 5.412640 TGTCTACAACTCACGAAACAAAGA 58.587 37.500 0.00 0.00 0.00 2.52
557 567 5.712217 TGTCTACAACTCACGAAACAAAG 57.288 39.130 0.00 0.00 0.00 2.77
558 568 5.870433 TCTTGTCTACAACTCACGAAACAAA 59.130 36.000 0.00 0.00 0.00 2.83
559 569 5.412640 TCTTGTCTACAACTCACGAAACAA 58.587 37.500 0.00 0.00 0.00 2.83
560 570 5.001237 TCTTGTCTACAACTCACGAAACA 57.999 39.130 0.00 0.00 0.00 2.83
561 571 6.526566 AATCTTGTCTACAACTCACGAAAC 57.473 37.500 0.00 0.00 0.00 2.78
562 572 7.870954 ACATAATCTTGTCTACAACTCACGAAA 59.129 33.333 0.00 0.00 0.00 3.46
563 573 7.375834 ACATAATCTTGTCTACAACTCACGAA 58.624 34.615 0.00 0.00 0.00 3.85
564 574 6.920817 ACATAATCTTGTCTACAACTCACGA 58.079 36.000 0.00 0.00 0.00 4.35
565 575 7.582435 AACATAATCTTGTCTACAACTCACG 57.418 36.000 0.00 0.00 0.00 4.35
577 587 9.143631 GCTCTGCAATTTTTAACATAATCTTGT 57.856 29.630 0.00 0.00 0.00 3.16
578 588 9.142515 TGCTCTGCAATTTTTAACATAATCTTG 57.857 29.630 0.00 0.00 34.76 3.02
579 589 9.880157 ATGCTCTGCAATTTTTAACATAATCTT 57.120 25.926 0.00 0.00 43.62 2.40
580 590 9.309516 CATGCTCTGCAATTTTTAACATAATCT 57.690 29.630 0.00 0.00 43.62 2.40
597 607 0.734942 ATTGCAAACGCATGCTCTGC 60.735 50.000 21.74 21.74 46.54 4.26
598 608 1.705256 AATTGCAAACGCATGCTCTG 58.295 45.000 17.13 10.84 46.54 3.35
599 609 2.443887 AAATTGCAAACGCATGCTCT 57.556 40.000 17.13 0.00 46.54 4.09
600 610 2.985809 TGTAAATTGCAAACGCATGCTC 59.014 40.909 17.13 0.17 46.54 4.26
601 611 3.023946 TGTAAATTGCAAACGCATGCT 57.976 38.095 17.13 0.00 46.54 3.79
602 612 3.613737 AGATGTAAATTGCAAACGCATGC 59.386 39.130 7.91 7.91 46.58 4.06
603 613 4.266029 GGAGATGTAAATTGCAAACGCATG 59.734 41.667 1.71 0.00 39.68 4.06
604 614 4.158394 AGGAGATGTAAATTGCAAACGCAT 59.842 37.500 1.71 6.05 39.68 4.73
605 615 3.505680 AGGAGATGTAAATTGCAAACGCA 59.494 39.130 1.71 0.76 37.72 5.24
606 616 4.096732 AGGAGATGTAAATTGCAAACGC 57.903 40.909 1.71 0.00 0.00 4.84
607 617 5.354234 AGGTAGGAGATGTAAATTGCAAACG 59.646 40.000 1.71 0.00 0.00 3.60
608 618 6.759497 AGGTAGGAGATGTAAATTGCAAAC 57.241 37.500 1.71 0.00 0.00 2.93
609 619 6.537301 CGTAGGTAGGAGATGTAAATTGCAAA 59.463 38.462 1.71 0.00 0.00 3.68
610 620 6.046593 CGTAGGTAGGAGATGTAAATTGCAA 58.953 40.000 0.00 0.00 0.00 4.08
611 621 5.597806 CGTAGGTAGGAGATGTAAATTGCA 58.402 41.667 0.00 0.00 0.00 4.08
630 640 0.895530 TCTTCCAGGTTCAGCCGTAG 59.104 55.000 0.00 0.00 43.70 3.51
631 641 0.606604 GTCTTCCAGGTTCAGCCGTA 59.393 55.000 0.00 0.00 43.70 4.02
632 642 1.371558 GTCTTCCAGGTTCAGCCGT 59.628 57.895 0.00 0.00 43.70 5.68
633 643 0.250295 TTGTCTTCCAGGTTCAGCCG 60.250 55.000 0.00 0.00 43.70 5.52
634 644 1.072331 TCTTGTCTTCCAGGTTCAGCC 59.928 52.381 0.00 0.00 37.58 4.85
635 645 2.550830 TCTTGTCTTCCAGGTTCAGC 57.449 50.000 0.00 0.00 0.00 4.26
636 646 6.176183 ACATAATCTTGTCTTCCAGGTTCAG 58.824 40.000 0.00 0.00 0.00 3.02
637 647 6.126863 ACATAATCTTGTCTTCCAGGTTCA 57.873 37.500 0.00 0.00 0.00 3.18
638 648 7.362142 GGAAACATAATCTTGTCTTCCAGGTTC 60.362 40.741 10.75 0.00 37.09 3.62
639 649 6.434340 GGAAACATAATCTTGTCTTCCAGGTT 59.566 38.462 10.75 0.00 37.09 3.50
640 650 5.946377 GGAAACATAATCTTGTCTTCCAGGT 59.054 40.000 10.75 0.00 37.09 4.00
641 651 6.183347 AGGAAACATAATCTTGTCTTCCAGG 58.817 40.000 14.83 0.00 38.21 4.45
642 652 7.108847 AGAGGAAACATAATCTTGTCTTCCAG 58.891 38.462 14.83 0.00 38.21 3.86
643 653 7.020827 AGAGGAAACATAATCTTGTCTTCCA 57.979 36.000 14.83 0.00 38.21 3.53
644 654 7.929941 AAGAGGAAACATAATCTTGTCTTCC 57.070 36.000 0.00 0.00 37.22 3.46
685 695 4.742438 TTTCTAACACAATCTTGTCGCC 57.258 40.909 0.00 0.00 39.91 5.54
686 696 5.927030 TGATTTCTAACACAATCTTGTCGC 58.073 37.500 0.00 0.00 39.91 5.19
687 697 7.742151 TCATGATTTCTAACACAATCTTGTCG 58.258 34.615 0.00 0.00 39.91 4.35
694 704 7.546667 GCCACATTTCATGATTTCTAACACAAT 59.453 33.333 0.00 0.00 0.00 2.71
718 728 4.261197 GGTTCATCATGAATTCGGTTAGCC 60.261 45.833 2.67 0.00 38.79 3.93
782 796 1.283347 TCAGAGCAGGAAAGGAGCAT 58.717 50.000 0.00 0.00 0.00 3.79
783 797 1.209019 GATCAGAGCAGGAAAGGAGCA 59.791 52.381 0.00 0.00 0.00 4.26
787 801 2.093764 ACGAAGATCAGAGCAGGAAAGG 60.094 50.000 0.00 0.00 0.00 3.11
925 939 6.534475 TCTGTTGGTCGGTGTTTATATACT 57.466 37.500 0.00 0.00 0.00 2.12
928 942 4.189231 GCTCTGTTGGTCGGTGTTTATAT 58.811 43.478 0.00 0.00 0.00 0.86
970 984 4.073549 TCTTTCTCTAGCTCGGTATAGCC 58.926 47.826 0.00 0.00 43.86 3.93
1362 1502 2.167094 ACGTACCCGATCCAGTTGGAA 61.167 52.381 4.73 0.00 42.05 3.53
1401 1541 3.710722 CTGAGCACCGCCTTCCCT 61.711 66.667 0.00 0.00 0.00 4.20
1607 1747 0.179108 GATTACCTGGCTTCTCGCGT 60.179 55.000 5.77 0.00 40.44 6.01
2145 2444 3.771160 GTCCCGCTCCACCACGAT 61.771 66.667 0.00 0.00 0.00 3.73
2321 2623 1.663695 CACTTCACTTGTTCACCGGT 58.336 50.000 0.00 0.00 0.00 5.28
2401 2960 8.609617 TCCAGATAATAGACATCCCGAATATT 57.390 34.615 0.00 0.00 0.00 1.28
2536 3184 7.591006 AACACATTACCACATTAAGTACTCG 57.409 36.000 0.00 0.00 0.00 4.18
2578 3228 8.120465 TCTTAAGTAACAGCTTGAAAGAAAACG 58.880 33.333 1.63 0.00 0.00 3.60
2758 3612 3.636300 GCCCAATGCACATTTGTCCTATA 59.364 43.478 0.00 0.00 40.77 1.31
2785 3639 1.680735 GTTGTGTTGAACATGGGCTCA 59.319 47.619 0.00 0.00 38.99 4.26
3052 3919 4.149396 CCGAGACAAAACGGTACACTAAAG 59.851 45.833 0.00 0.00 43.53 1.85
3103 3970 9.733556 TCTACACTGTCCATTGTGTAATTTATT 57.266 29.630 7.27 0.00 45.31 1.40
3106 3973 8.458573 TTTCTACACTGTCCATTGTGTAATTT 57.541 30.769 7.27 0.00 45.31 1.82
3107 3974 8.458573 TTTTCTACACTGTCCATTGTGTAATT 57.541 30.769 7.27 0.00 45.31 1.40
3108 3975 8.349983 GTTTTTCTACACTGTCCATTGTGTAAT 58.650 33.333 7.27 0.00 45.31 1.89
3109 3976 7.337184 TGTTTTTCTACACTGTCCATTGTGTAA 59.663 33.333 7.27 0.00 45.31 2.41
3110 3977 6.824196 TGTTTTTCTACACTGTCCATTGTGTA 59.176 34.615 0.00 0.00 44.40 2.90
3146 4013 1.947456 GTTTCAAAGGGTGTCGCTTCT 59.053 47.619 0.00 0.00 35.61 2.85
3214 4082 3.626217 GGGCAAAGTTCCTTAATCCGTAG 59.374 47.826 0.00 0.00 0.00 3.51
3307 4181 8.172741 AGGAATAGGGAAATGCATGTACAATAT 58.827 33.333 0.00 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.