Multiple sequence alignment - TraesCS4B01G167700

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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 TraesCS4B01G167700 chr4B 100.000 3153 0 0 1 3153 366924857 366928009 0.000000e+00 5823.0
1 TraesCS4B01G167700 chr4B 95.082 122 6 0 598 719 97557137 97557016 3.210000e-45 193.0
2 TraesCS4B01G167700 chr4A 87.337 1453 52 56 1564 2935 192628694 192627293 0.000000e+00 1543.0
3 TraesCS4B01G167700 chr4A 87.066 518 29 10 716 1217 192629507 192629012 4.600000e-153 551.0
4 TraesCS4B01G167700 chr4A 95.455 220 6 1 1240 1455 192629020 192628801 6.470000e-92 348.0
5 TraesCS4B01G167700 chr4A 83.728 338 50 4 1 335 176620660 176620325 6.560000e-82 315.0
6 TraesCS4B01G167700 chr4A 80.418 383 60 11 7 380 468212776 468212400 8.610000e-71 278.0
7 TraesCS4B01G167700 chr4A 96.154 78 3 0 3075 3152 192626983 192626906 9.180000e-26 128.0
8 TraesCS4B01G167700 chr4A 97.297 37 1 0 772 808 636101381 636101417 2.630000e-06 63.9
9 TraesCS4B01G167700 chr4D 89.417 926 33 31 2251 3152 296726932 296727816 0.000000e+00 1107.0
10 TraesCS4B01G167700 chr4D 93.683 744 19 8 1510 2240 296726154 296726882 0.000000e+00 1088.0
11 TraesCS4B01G167700 chr4D 92.068 769 24 9 772 1509 296725353 296726115 0.000000e+00 1048.0
12 TraesCS4B01G167700 chr4D 83.663 606 73 9 2 599 296721100 296721687 5.950000e-152 547.0
13 TraesCS4B01G167700 chr5D 84.635 384 54 4 2 380 386050478 386050095 8.260000e-101 377.0
14 TraesCS4B01G167700 chr5D 91.667 48 3 1 1462 1509 381152016 381151970 7.300000e-07 65.8
15 TraesCS4B01G167700 chr7D 83.333 384 52 10 4 380 104589651 104589273 8.370000e-91 344.0
16 TraesCS4B01G167700 chr7D 97.222 36 0 1 1940 1975 554334112 554334078 3.400000e-05 60.2
17 TraesCS4B01G167700 chr6A 83.065 372 52 7 28 388 61681155 61681526 8.430000e-86 327.0
18 TraesCS4B01G167700 chr3A 81.156 398 56 15 5 391 181108345 181107956 5.110000e-78 302.0
19 TraesCS4B01G167700 chr3D 82.540 315 50 4 48 358 95617887 95617574 4.010000e-69 272.0
20 TraesCS4B01G167700 chr3D 97.059 34 1 0 1937 1970 580364117 580364084 1.220000e-04 58.4
21 TraesCS4B01G167700 chr3D 97.059 34 0 1 1938 1970 64194820 64194787 4.390000e-04 56.5
22 TraesCS4B01G167700 chr2D 78.117 393 68 11 2 384 164538126 164538510 1.890000e-57 233.0
23 TraesCS4B01G167700 chr6B 95.968 124 5 0 596 719 642731137 642731014 5.330000e-48 202.0
24 TraesCS4B01G167700 chr6B 97.368 38 1 0 1472 1509 284242255 284242218 7.300000e-07 65.8
25 TraesCS4B01G167700 chr3B 95.833 120 5 0 595 714 655032743 655032862 8.920000e-46 195.0
26 TraesCS4B01G167700 chr3B 94.400 125 6 1 590 714 31105785 31105662 1.150000e-44 191.0
27 TraesCS4B01G167700 chr3B 95.918 49 1 1 1476 1523 68873000 68872952 9.380000e-11 78.7
28 TraesCS4B01G167700 chr2B 95.122 123 5 1 597 719 620927841 620927720 3.210000e-45 193.0
29 TraesCS4B01G167700 chr2B 95.082 122 6 0 596 717 788660477 788660356 3.210000e-45 193.0
30 TraesCS4B01G167700 chr2B 93.701 127 6 2 595 719 4566761 4566635 4.150000e-44 189.0
31 TraesCS4B01G167700 chr2B 88.679 53 5 1 1477 1529 408191267 408191318 2.630000e-06 63.9
32 TraesCS4B01G167700 chr2B 100.000 32 0 0 1939 1970 52655439 52655408 3.400000e-05 60.2
33 TraesCS4B01G167700 chr5B 92.537 134 7 3 586 717 575820823 575820691 4.150000e-44 189.0
34 TraesCS4B01G167700 chr1B 90.071 141 11 3 594 733 60059021 60059159 2.500000e-41 180.0
35 TraesCS4B01G167700 chr6D 85.567 97 14 0 716 812 3332445 3332349 5.560000e-18 102.0
36 TraesCS4B01G167700 chr6D 85.567 97 14 0 716 812 3338325 3338229 5.560000e-18 102.0
37 TraesCS4B01G167700 chr1D 93.478 46 1 2 1474 1518 394892016 394891972 2.030000e-07 67.6
38 TraesCS4B01G167700 chr1D 100.000 35 0 0 1475 1509 160902312 160902346 7.300000e-07 65.8
39 TraesCS4B01G167700 chr1D 100.000 30 0 0 1941 1970 101285191 101285162 4.390000e-04 56.5
40 TraesCS4B01G167700 chr1A 100.000 35 0 0 1475 1509 157827341 157827307 7.300000e-07 65.8
41 TraesCS4B01G167700 chr7B 92.857 42 2 1 1468 1509 63936143 63936183 3.400000e-05 60.2
42 TraesCS4B01G167700 chr7B 100.000 32 0 0 1940 1971 600566670 600566701 3.400000e-05 60.2
43 TraesCS4B01G167700 chrUn 100.000 30 0 0 1941 1970 134242334 134242305 4.390000e-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 TraesCS4B01G167700 chr4B 366924857 366928009 3152 False 5823.0 5823 100.00000 1 3153 1 chr4B.!!$F1 3152
1 TraesCS4B01G167700 chr4A 192626906 192629507 2601 True 642.5 1543 91.50300 716 3152 4 chr4A.!!$R3 2436
2 TraesCS4B01G167700 chr4D 296721100 296727816 6716 False 947.5 1107 89.70775 2 3152 4 chr4D.!!$F1 3150

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
710 718 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.20 F
1824 5520 0.253044 TTTCCATCCTCGAGGCCTTG 59.747 55.0 27.39 21.29 34.44 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 5756 1.603802 CATCAGGTTCTGCACGTTTGT 59.396 47.619 0.0 0.0 0.00 2.83 R
2989 6803 0.105964 TTAGCCAACGCACAGACAGT 59.894 50.000 0.0 0.0 37.52 3.55 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
19 20 0.391130 TGATGGTGGCGTTGTCTAGC 60.391 55.000 0.00 0.00 0.00 3.42
20 21 0.391130 GATGGTGGCGTTGTCTAGCA 60.391 55.000 0.00 0.00 34.54 3.49
23 24 0.391130 GGTGGCGTTGTCTAGCATCA 60.391 55.000 0.00 0.00 34.54 3.07
29 30 2.892374 CGTTGTCTAGCATCATGGTGA 58.108 47.619 11.02 0.00 0.00 4.02
36 37 0.458543 AGCATCATGGTGACGTCGAC 60.459 55.000 11.02 5.18 0.00 4.20
41 42 0.662077 CATGGTGACGTCGACGACAA 60.662 55.000 41.52 27.35 44.35 3.18
46 47 0.110509 TGACGTCGACGACAACTAGC 60.111 55.000 41.52 19.46 40.57 3.42
50 51 0.456312 GTCGACGACAACTAGCCCTG 60.456 60.000 22.66 0.00 32.09 4.45
76 77 1.516386 CGATGCGTCGGTACAGCTT 60.516 57.895 20.66 0.00 44.00 3.74
84 85 3.302480 GCGTCGGTACAGCTTTGAATATG 60.302 47.826 0.00 0.00 0.00 1.78
94 95 2.554032 GCTTTGAATATGGATCGGTGGG 59.446 50.000 0.00 0.00 0.00 4.61
147 151 1.541310 GGTGTGTGTCCCAGATCCGA 61.541 60.000 0.00 0.00 0.00 4.55
148 152 0.537188 GTGTGTGTCCCAGATCCGAT 59.463 55.000 0.00 0.00 0.00 4.18
170 174 3.843800 TGGCTTGGTTGGGGCCTT 61.844 61.111 0.84 0.00 45.45 4.35
178 182 1.365999 GTTGGGGCCTTCGGTTTTG 59.634 57.895 0.84 0.00 0.00 2.44
179 183 1.075896 TTGGGGCCTTCGGTTTTGT 60.076 52.632 0.84 0.00 0.00 2.83
183 187 1.541379 GGGCCTTCGGTTTTGTATGT 58.459 50.000 0.84 0.00 0.00 2.29
193 197 5.120399 TCGGTTTTGTATGTTAGGCTATGG 58.880 41.667 0.00 0.00 0.00 2.74
197 201 3.106242 TGTATGTTAGGCTATGGTGCG 57.894 47.619 0.00 0.00 0.00 5.34
202 206 1.134491 GTTAGGCTATGGTGCGAGGTT 60.134 52.381 0.00 0.00 0.00 3.50
204 208 0.392998 AGGCTATGGTGCGAGGTTTG 60.393 55.000 0.00 0.00 0.00 2.93
214 218 3.243602 GGTGCGAGGTTTGTTTGGTATTT 60.244 43.478 0.00 0.00 0.00 1.40
217 221 3.243602 GCGAGGTTTGTTTGGTATTTGGT 60.244 43.478 0.00 0.00 0.00 3.67
228 232 5.423704 TTGGTATTTGGTTCGGACTATCA 57.576 39.130 0.00 0.00 0.00 2.15
230 234 5.180271 TGGTATTTGGTTCGGACTATCAAC 58.820 41.667 0.00 0.00 0.00 3.18
238 242 2.262637 TCGGACTATCAACACCCCTTT 58.737 47.619 0.00 0.00 0.00 3.11
242 246 4.141801 CGGACTATCAACACCCCTTTATCA 60.142 45.833 0.00 0.00 0.00 2.15
252 256 5.755849 ACACCCCTTTATCAAGTGGATAAG 58.244 41.667 0.27 0.00 46.34 1.73
261 265 7.526142 TTATCAAGTGGATAAGAGTAGCGAT 57.474 36.000 0.00 0.00 42.22 4.58
262 266 8.631480 TTATCAAGTGGATAAGAGTAGCGATA 57.369 34.615 0.00 0.00 42.22 2.92
263 267 6.561737 TCAAGTGGATAAGAGTAGCGATAG 57.438 41.667 0.00 0.00 0.00 2.08
279 283 3.470709 CGATAGATGTTGCCAAGATGGT 58.529 45.455 0.00 0.00 38.05 3.55
282 286 3.377253 AGATGTTGCCAAGATGGTGAT 57.623 42.857 0.00 0.00 40.46 3.06
289 293 3.084039 TGCCAAGATGGTGATTTCAGAC 58.916 45.455 0.00 0.00 40.46 3.51
290 294 2.096496 GCCAAGATGGTGATTTCAGACG 59.904 50.000 0.00 0.00 40.46 4.18
347 351 7.880160 ATAACTAATAAAGTGGCTGAATGCA 57.120 32.000 0.00 0.00 39.83 3.96
349 353 6.140303 ACTAATAAAGTGGCTGAATGCATG 57.860 37.500 0.00 0.00 45.15 4.06
350 354 4.395959 AATAAAGTGGCTGAATGCATGG 57.604 40.909 0.00 0.00 45.15 3.66
369 377 3.242291 CCAGATAGGCCGGGGTCC 61.242 72.222 2.18 0.00 0.00 4.46
371 379 2.201771 AGATAGGCCGGGGTCCTC 59.798 66.667 2.18 0.00 35.21 3.71
380 388 1.202769 CCGGGGTCCTCCACCTTTTA 61.203 60.000 0.00 0.00 45.95 1.52
384 392 3.162666 GGGGTCCTCCACCTTTTAAAAG 58.837 50.000 19.19 19.19 45.95 2.27
430 438 5.106157 GGAACCGAACATGAAAACATGAGAT 60.106 40.000 15.53 3.30 36.48 2.75
436 444 3.127548 ACATGAAAACATGAGATCACGGC 59.872 43.478 15.53 0.00 36.48 5.68
437 445 3.057969 TGAAAACATGAGATCACGGCT 57.942 42.857 0.00 0.00 0.00 5.52
438 446 4.200838 TGAAAACATGAGATCACGGCTA 57.799 40.909 0.00 0.00 0.00 3.93
472 480 9.250624 GATGGCTACATATTTCGATATTACTCC 57.749 37.037 0.00 0.00 37.47 3.85
475 483 7.921745 GGCTACATATTTCGATATTACTCCCTC 59.078 40.741 0.00 0.00 0.00 4.30
478 486 7.324178 ACATATTTCGATATTACTCCCTCTGC 58.676 38.462 0.00 0.00 0.00 4.26
480 488 2.526432 TCGATATTACTCCCTCTGCCC 58.474 52.381 0.00 0.00 0.00 5.36
481 489 2.110188 TCGATATTACTCCCTCTGCCCT 59.890 50.000 0.00 0.00 0.00 5.19
482 490 3.332783 TCGATATTACTCCCTCTGCCCTA 59.667 47.826 0.00 0.00 0.00 3.53
607 615 7.039882 ACATTACTTGTGTTATACTCCTTCCG 58.960 38.462 0.00 0.00 37.11 4.30
608 616 3.858247 ACTTGTGTTATACTCCTTCCGC 58.142 45.455 0.00 0.00 0.00 5.54
609 617 2.973694 TGTGTTATACTCCTTCCGCC 57.026 50.000 0.00 0.00 0.00 6.13
610 618 1.483415 TGTGTTATACTCCTTCCGCCC 59.517 52.381 0.00 0.00 0.00 6.13
611 619 1.483415 GTGTTATACTCCTTCCGCCCA 59.517 52.381 0.00 0.00 0.00 5.36
612 620 1.760613 TGTTATACTCCTTCCGCCCAG 59.239 52.381 0.00 0.00 0.00 4.45
613 621 2.037144 GTTATACTCCTTCCGCCCAGA 58.963 52.381 0.00 0.00 0.00 3.86
614 622 2.433239 GTTATACTCCTTCCGCCCAGAA 59.567 50.000 0.00 0.00 0.00 3.02
615 623 1.807814 ATACTCCTTCCGCCCAGAAT 58.192 50.000 0.00 0.00 0.00 2.40
616 624 1.580059 TACTCCTTCCGCCCAGAATT 58.420 50.000 0.00 0.00 0.00 2.17
617 625 1.580059 ACTCCTTCCGCCCAGAATTA 58.420 50.000 0.00 0.00 0.00 1.40
618 626 1.209747 ACTCCTTCCGCCCAGAATTAC 59.790 52.381 0.00 0.00 0.00 1.89
619 627 1.486726 CTCCTTCCGCCCAGAATTACT 59.513 52.381 0.00 0.00 0.00 2.24
620 628 1.913419 TCCTTCCGCCCAGAATTACTT 59.087 47.619 0.00 0.00 0.00 2.24
621 629 2.017049 CCTTCCGCCCAGAATTACTTG 58.983 52.381 0.00 0.00 0.00 3.16
622 630 2.618045 CCTTCCGCCCAGAATTACTTGT 60.618 50.000 0.00 0.00 0.00 3.16
623 631 2.396590 TCCGCCCAGAATTACTTGTC 57.603 50.000 0.00 0.00 0.00 3.18
624 632 1.626321 TCCGCCCAGAATTACTTGTCA 59.374 47.619 0.00 0.00 0.00 3.58
625 633 2.238646 TCCGCCCAGAATTACTTGTCAT 59.761 45.455 0.00 0.00 0.00 3.06
626 634 3.016736 CCGCCCAGAATTACTTGTCATT 58.983 45.455 0.00 0.00 0.00 2.57
627 635 4.080807 TCCGCCCAGAATTACTTGTCATTA 60.081 41.667 0.00 0.00 0.00 1.90
628 636 4.638421 CCGCCCAGAATTACTTGTCATTAA 59.362 41.667 0.00 0.00 0.00 1.40
629 637 5.124776 CCGCCCAGAATTACTTGTCATTAAA 59.875 40.000 0.00 0.00 0.00 1.52
630 638 6.349777 CCGCCCAGAATTACTTGTCATTAAAA 60.350 38.462 0.00 0.00 0.00 1.52
631 639 7.257722 CGCCCAGAATTACTTGTCATTAAAAT 58.742 34.615 0.00 0.00 0.00 1.82
632 640 8.402472 CGCCCAGAATTACTTGTCATTAAAATA 58.598 33.333 0.00 0.00 0.00 1.40
633 641 9.736023 GCCCAGAATTACTTGTCATTAAAATAG 57.264 33.333 0.00 0.00 0.00 1.73
689 697 9.499479 ACATCTAGATACATCCATTTCAATGAC 57.501 33.333 4.54 0.00 38.70 3.06
690 698 9.498176 CATCTAGATACATCCATTTCAATGACA 57.502 33.333 4.54 0.00 38.70 3.58
692 700 9.551734 TCTAGATACATCCATTTCAATGACAAG 57.448 33.333 0.81 0.00 38.70 3.16
693 701 9.334947 CTAGATACATCCATTTCAATGACAAGT 57.665 33.333 0.81 0.00 38.70 3.16
695 703 9.857656 AGATACATCCATTTCAATGACAAGTAT 57.142 29.630 0.81 4.50 38.70 2.12
699 707 8.253113 ACATCCATTTCAATGACAAGTATTTCC 58.747 33.333 0.81 0.00 38.70 3.13
700 708 6.851609 TCCATTTCAATGACAAGTATTTCCG 58.148 36.000 0.81 0.00 38.70 4.30
701 709 6.035843 CCATTTCAATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 38.70 5.14
702 710 6.127758 CCATTTCAATGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 38.70 5.14
703 711 5.873179 TTCAATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 0.00 4.79
704 712 3.930229 TCAATGACAAGTATTTCCGGACG 59.070 43.478 1.83 0.00 0.00 4.79
705 713 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
706 714 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
707 715 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
708 716 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
709 717 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
710 718 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
711 719 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
712 720 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
713 721 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
714 722 0.032813 TTTCCGGACGGAGGGAGTAT 60.033 55.000 13.64 0.00 46.06 2.12
725 733 6.170846 ACGGAGGGAGTATATTTGTTTAGG 57.829 41.667 0.00 0.00 0.00 2.69
758 766 8.212312 TGTGTTTAGACATGTTTTAGGGTTAGA 58.788 33.333 0.00 0.00 38.23 2.10
945 4577 2.166254 CCACAAGCTCTCTCTTCCTCTC 59.834 54.545 0.00 0.00 0.00 3.20
946 4578 3.091545 CACAAGCTCTCTCTTCCTCTCT 58.908 50.000 0.00 0.00 0.00 3.10
963 4595 1.139308 CTGCTGTCTCTCTCGCCTG 59.861 63.158 0.00 0.00 0.00 4.85
969 4601 2.055042 TCTCTCTCGCCTGGCTTCC 61.055 63.158 17.92 0.00 0.00 3.46
973 4605 0.813210 CTCTCGCCTGGCTTCCATTC 60.813 60.000 17.92 0.00 30.82 2.67
974 4606 1.078214 CTCGCCTGGCTTCCATTCA 60.078 57.895 17.92 0.00 30.82 2.57
987 4619 3.708403 TCCATTCAGAGATTGTGCTGT 57.292 42.857 0.00 0.00 33.90 4.40
1092 4734 2.810274 CTCCCATGCTGTAATTGATCCG 59.190 50.000 0.00 0.00 0.00 4.18
1093 4735 1.881973 CCCATGCTGTAATTGATCCGG 59.118 52.381 0.00 0.00 0.00 5.14
1147 4789 3.379372 AGTTGTGCAATCTCCACATATGC 59.621 43.478 1.58 0.00 42.23 3.14
1186 4828 1.005037 ATCGAGCTGGTTGTGCGAA 60.005 52.632 0.00 0.00 34.46 4.70
1204 4846 1.740025 GAACTTCACCATGCCTGCTAC 59.260 52.381 0.00 0.00 0.00 3.58
1218 4860 3.687212 GCCTGCTACCTCTTTCTTTCTTC 59.313 47.826 0.00 0.00 0.00 2.87
1221 4863 5.641636 CCTGCTACCTCTTTCTTTCTTCTTC 59.358 44.000 0.00 0.00 0.00 2.87
1238 4884 9.860898 TTTCTTCTTCCTTTCTTTCTTTCTTTG 57.139 29.630 0.00 0.00 0.00 2.77
1610 5300 6.317391 GGAGATTTGGATTGAAACAGTAGGAG 59.683 42.308 0.00 0.00 0.00 3.69
1616 5308 5.542635 TGGATTGAAACAGTAGGAGTACACT 59.457 40.000 0.00 0.00 0.00 3.55
1617 5309 5.869888 GGATTGAAACAGTAGGAGTACACTG 59.130 44.000 8.99 8.99 46.15 3.66
1618 5310 4.252971 TGAAACAGTAGGAGTACACTGC 57.747 45.455 10.18 4.64 44.89 4.40
1619 5311 3.639561 TGAAACAGTAGGAGTACACTGCA 59.360 43.478 10.18 0.00 44.89 4.41
1620 5312 3.662247 AACAGTAGGAGTACACTGCAC 57.338 47.619 10.18 0.55 44.89 4.57
1661 5353 1.079197 CCGCTCCTACACACATGCA 60.079 57.895 0.00 0.00 0.00 3.96
1662 5354 0.462581 CCGCTCCTACACACATGCAT 60.463 55.000 0.00 0.00 0.00 3.96
1663 5355 0.654160 CGCTCCTACACACATGCATG 59.346 55.000 25.09 25.09 0.00 4.06
1664 5356 0.379669 GCTCCTACACACATGCATGC 59.620 55.000 26.53 11.82 0.00 4.06
1773 5469 1.203052 GGGTCGTTCCTCGTCAATGTA 59.797 52.381 0.30 0.00 40.80 2.29
1824 5520 0.253044 TTTCCATCCTCGAGGCCTTG 59.747 55.000 27.39 21.29 34.44 3.61
1915 5611 1.351350 GAGGGGAGGTAACAACAAGCT 59.649 52.381 0.00 0.00 41.41 3.74
1916 5612 2.570302 GAGGGGAGGTAACAACAAGCTA 59.430 50.000 0.00 0.00 41.41 3.32
2011 5711 9.586435 CTGACCAAAAGAAGAAAACAAATTAGT 57.414 29.630 0.00 0.00 0.00 2.24
2170 5881 4.040068 CGCAAGCTAGCAGATCCC 57.960 61.111 18.83 0.00 0.00 3.85
2214 5928 9.552114 GTCAAGCATCTCAATAACATATATTGC 57.448 33.333 3.83 0.00 35.50 3.56
2240 5954 8.830915 TTAATCTGGTCTATTGACTCTCTCTT 57.169 34.615 7.24 0.00 42.54 2.85
2276 6039 1.239296 TGTTCGTCTCCGGTGATCGT 61.239 55.000 20.07 0.00 37.11 3.73
2446 6212 0.953960 GTTGGGGCCTTGTGTCGTAG 60.954 60.000 0.84 0.00 0.00 3.51
2447 6213 1.412453 TTGGGGCCTTGTGTCGTAGT 61.412 55.000 0.84 0.00 0.00 2.73
2448 6214 0.542467 TGGGGCCTTGTGTCGTAGTA 60.542 55.000 0.84 0.00 0.00 1.82
2480 6246 9.599866 CATATATGTACTCTTTCTCCAACAACA 57.400 33.333 4.43 0.00 0.00 3.33
2483 6249 5.492895 TGTACTCTTTCTCCAACAACAACA 58.507 37.500 0.00 0.00 0.00 3.33
2484 6250 5.941058 TGTACTCTTTCTCCAACAACAACAA 59.059 36.000 0.00 0.00 0.00 2.83
2485 6251 5.310720 ACTCTTTCTCCAACAACAACAAC 57.689 39.130 0.00 0.00 0.00 3.32
2486 6252 4.764823 ACTCTTTCTCCAACAACAACAACA 59.235 37.500 0.00 0.00 0.00 3.33
2487 6253 5.242838 ACTCTTTCTCCAACAACAACAACAA 59.757 36.000 0.00 0.00 0.00 2.83
2515 6281 1.747206 GCAGGATGTACATGTCCACCC 60.747 57.143 14.43 7.00 39.31 4.61
2610 6377 6.247229 TGTTGCCTGGATAATAAAGCTCTA 57.753 37.500 0.00 0.00 0.00 2.43
2611 6378 6.291377 TGTTGCCTGGATAATAAAGCTCTAG 58.709 40.000 0.00 0.00 0.00 2.43
2693 6487 2.795329 CCCAATGGCTTCACAAGTAGT 58.205 47.619 0.00 0.00 0.00 2.73
2698 6492 6.349300 CCAATGGCTTCACAAGTAGTAGTAT 58.651 40.000 0.00 0.00 0.00 2.12
2699 6493 6.258727 CCAATGGCTTCACAAGTAGTAGTATG 59.741 42.308 0.00 0.00 0.00 2.39
2701 6495 6.208988 TGGCTTCACAAGTAGTAGTATGAG 57.791 41.667 0.00 0.00 0.00 2.90
2702 6496 5.715279 TGGCTTCACAAGTAGTAGTATGAGT 59.285 40.000 0.00 0.00 0.00 3.41
2703 6497 6.888088 TGGCTTCACAAGTAGTAGTATGAGTA 59.112 38.462 0.00 0.00 0.00 2.59
2704 6498 7.067129 TGGCTTCACAAGTAGTAGTATGAGTAG 59.933 40.741 0.00 0.00 0.00 2.57
2705 6499 7.282675 GGCTTCACAAGTAGTAGTATGAGTAGA 59.717 40.741 0.00 0.00 0.00 2.59
2706 6500 8.675504 GCTTCACAAGTAGTAGTATGAGTAGAA 58.324 37.037 0.00 0.00 0.00 2.10
2815 6609 1.277557 AGGAAAGCAGCGAATGAGAGT 59.722 47.619 0.00 0.00 0.00 3.24
2816 6610 1.396301 GGAAAGCAGCGAATGAGAGTG 59.604 52.381 0.00 0.00 0.00 3.51
2817 6611 0.801251 AAAGCAGCGAATGAGAGTGC 59.199 50.000 0.00 0.00 0.00 4.40
2818 6612 0.321034 AAGCAGCGAATGAGAGTGCA 60.321 50.000 0.00 0.00 36.57 4.57
2819 6613 0.107800 AGCAGCGAATGAGAGTGCAT 60.108 50.000 0.00 0.00 36.57 3.96
2820 6614 1.137675 AGCAGCGAATGAGAGTGCATA 59.862 47.619 0.00 0.00 36.57 3.14
2885 6689 3.111038 GCCAAGGCAACGATAGGC 58.889 61.111 6.14 0.00 46.39 3.93
2891 6697 1.227674 GGCAACGATAGGCAGAGGG 60.228 63.158 0.00 0.00 43.77 4.30
2892 6698 1.522569 GCAACGATAGGCAGAGGGT 59.477 57.895 0.00 0.00 43.77 4.34
2893 6699 0.530870 GCAACGATAGGCAGAGGGTC 60.531 60.000 0.00 0.00 43.77 4.46
2894 6700 1.115467 CAACGATAGGCAGAGGGTCT 58.885 55.000 0.00 0.00 43.77 3.85
2935 6749 2.125147 CATTGGCGCGAGGAGGAA 60.125 61.111 12.10 0.00 0.00 3.36
2936 6750 1.745115 CATTGGCGCGAGGAGGAAA 60.745 57.895 12.10 0.00 0.00 3.13
2937 6751 1.002624 ATTGGCGCGAGGAGGAAAA 60.003 52.632 12.10 0.00 0.00 2.29
2938 6752 1.026718 ATTGGCGCGAGGAGGAAAAG 61.027 55.000 12.10 0.00 0.00 2.27
2939 6753 2.047179 GGCGCGAGGAGGAAAAGT 60.047 61.111 12.10 0.00 0.00 2.66
2941 6755 0.390735 GGCGCGAGGAGGAAAAGTAA 60.391 55.000 12.10 0.00 0.00 2.24
2942 6756 1.000145 GCGCGAGGAGGAAAAGTAAG 59.000 55.000 12.10 0.00 0.00 2.34
2943 6757 1.672145 GCGCGAGGAGGAAAAGTAAGT 60.672 52.381 12.10 0.00 0.00 2.24
2945 6759 3.841643 CGCGAGGAGGAAAAGTAAGTAA 58.158 45.455 0.00 0.00 0.00 2.24
2946 6760 3.611549 CGCGAGGAGGAAAAGTAAGTAAC 59.388 47.826 0.00 0.00 0.00 2.50
2947 6761 3.611549 GCGAGGAGGAAAAGTAAGTAACG 59.388 47.826 0.00 0.00 0.00 3.18
2949 6763 4.082571 CGAGGAGGAAAAGTAAGTAACGGA 60.083 45.833 0.00 0.00 0.00 4.69
2950 6764 5.402997 AGGAGGAAAAGTAAGTAACGGAG 57.597 43.478 0.00 0.00 0.00 4.63
2989 6803 1.431195 TTTAGGGAGCACAAGGGCCA 61.431 55.000 6.18 0.00 0.00 5.36
3038 7108 1.677942 ACGTACTCCTACTAGGCTGC 58.322 55.000 0.00 0.00 34.61 5.25
3039 7109 0.953003 CGTACTCCTACTAGGCTGCC 59.047 60.000 11.65 11.65 34.61 4.85
3040 7110 1.477195 CGTACTCCTACTAGGCTGCCT 60.477 57.143 26.52 26.52 34.61 4.75
3041 7111 1.957877 GTACTCCTACTAGGCTGCCTG 59.042 57.143 30.83 21.35 34.61 4.85
3057 7127 3.665675 CTGGCTGGCTACCCGTGAC 62.666 68.421 2.00 0.00 0.00 3.67
3087 7157 4.942481 TGTGCTTCACGCGACGCT 62.942 61.111 15.93 1.85 43.27 5.07
3120 7190 2.438021 CAGTATTTACCAGGCCCAGCTA 59.562 50.000 0.00 0.00 0.00 3.32
3152 7222 3.311110 AGTTTCCAGCTCCGGCGA 61.311 61.111 9.30 0.00 44.37 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.391130 GCTAGACAACGCCACCATCA 60.391 55.000 0.00 0.00 0.00 3.07
17 18 0.458543 GTCGACGTCACCATGATGCT 60.459 55.000 17.16 0.00 36.89 3.79
19 20 0.179174 TCGTCGACGTCACCATGATG 60.179 55.000 34.40 9.57 39.24 3.07
20 21 0.179171 GTCGTCGACGTCACCATGAT 60.179 55.000 34.40 0.00 40.80 2.45
23 24 0.662374 GTTGTCGTCGACGTCACCAT 60.662 55.000 31.79 0.00 37.16 3.55
29 30 1.208614 GGCTAGTTGTCGTCGACGT 59.791 57.895 34.40 19.32 40.80 4.34
36 37 1.003839 TTGCCAGGGCTAGTTGTCG 60.004 57.895 12.19 0.00 42.51 4.35
41 42 3.404773 GACCTTGCCAGGGCTAGT 58.595 61.111 18.13 9.90 46.61 2.57
46 47 2.825836 GCATCGACCTTGCCAGGG 60.826 66.667 8.98 0.00 46.01 4.45
67 68 4.452455 CCGATCCATATTCAAAGCTGTACC 59.548 45.833 0.00 0.00 0.00 3.34
73 74 2.554032 CCCACCGATCCATATTCAAAGC 59.446 50.000 0.00 0.00 0.00 3.51
76 77 3.313791 TCTCCCACCGATCCATATTCAA 58.686 45.455 0.00 0.00 0.00 2.69
84 85 2.427753 GCCATCTCCCACCGATCC 59.572 66.667 0.00 0.00 0.00 3.36
125 129 3.254024 ATCTGGGACACACACCGGC 62.254 63.158 0.00 0.00 33.03 6.13
126 130 1.079127 GATCTGGGACACACACCGG 60.079 63.158 0.00 0.00 34.34 5.28
127 131 1.079127 GGATCTGGGACACACACCG 60.079 63.158 0.00 0.00 0.00 4.94
147 151 1.864669 CCCCAACCAAGCCACATTAT 58.135 50.000 0.00 0.00 0.00 1.28
148 152 0.902516 GCCCCAACCAAGCCACATTA 60.903 55.000 0.00 0.00 0.00 1.90
170 174 5.120399 CCATAGCCTAACATACAAAACCGA 58.880 41.667 0.00 0.00 0.00 4.69
178 182 3.318017 CTCGCACCATAGCCTAACATAC 58.682 50.000 0.00 0.00 0.00 2.39
179 183 2.299013 CCTCGCACCATAGCCTAACATA 59.701 50.000 0.00 0.00 0.00 2.29
183 187 1.200519 AACCTCGCACCATAGCCTAA 58.799 50.000 0.00 0.00 0.00 2.69
193 197 3.636282 AATACCAAACAAACCTCGCAC 57.364 42.857 0.00 0.00 0.00 5.34
197 201 4.979815 CGAACCAAATACCAAACAAACCTC 59.020 41.667 0.00 0.00 0.00 3.85
202 206 4.208746 AGTCCGAACCAAATACCAAACAA 58.791 39.130 0.00 0.00 0.00 2.83
204 208 5.644636 TGATAGTCCGAACCAAATACCAAAC 59.355 40.000 0.00 0.00 0.00 2.93
214 218 1.276989 GGGTGTTGATAGTCCGAACCA 59.723 52.381 0.00 0.00 0.00 3.67
217 221 1.946984 AGGGGTGTTGATAGTCCGAA 58.053 50.000 0.00 0.00 0.00 4.30
228 232 4.675063 ATCCACTTGATAAAGGGGTGTT 57.325 40.909 11.19 0.00 43.86 3.32
230 234 6.001449 TCTTATCCACTTGATAAAGGGGTG 57.999 41.667 11.19 1.13 43.59 4.61
238 242 8.101419 TCTATCGCTACTCTTATCCACTTGATA 58.899 37.037 0.00 0.00 34.76 2.15
242 246 6.717540 ACATCTATCGCTACTCTTATCCACTT 59.282 38.462 0.00 0.00 0.00 3.16
252 256 3.371102 TGGCAACATCTATCGCTACTC 57.629 47.619 0.00 0.00 46.17 2.59
289 293 8.922058 ACCTTACAAAGTAATACATCAGTACG 57.078 34.615 0.00 0.00 32.91 3.67
327 331 5.526115 CCATGCATTCAGCCACTTTATTAG 58.474 41.667 0.00 0.00 44.83 1.73
335 339 2.497770 GGCCATGCATTCAGCCAC 59.502 61.111 21.72 1.69 45.07 5.01
337 341 2.760799 TGGGCCATGCATTCAGCC 60.761 61.111 19.48 19.48 44.83 4.85
342 346 0.541296 GCCTATCTGGGCCATGCATT 60.541 55.000 6.72 0.00 45.92 3.56
389 397 8.432359 GTTCGGTTCCATTAAAATGCTAAAAAG 58.568 33.333 0.00 0.00 35.08 2.27
390 398 7.926555 TGTTCGGTTCCATTAAAATGCTAAAAA 59.073 29.630 0.00 0.00 35.08 1.94
391 399 7.434492 TGTTCGGTTCCATTAAAATGCTAAAA 58.566 30.769 0.00 0.00 35.08 1.52
392 400 6.982852 TGTTCGGTTCCATTAAAATGCTAAA 58.017 32.000 0.00 0.00 35.08 1.85
394 402 6.375736 TCATGTTCGGTTCCATTAAAATGCTA 59.624 34.615 0.00 0.00 35.08 3.49
395 403 5.184864 TCATGTTCGGTTCCATTAAAATGCT 59.815 36.000 0.00 0.00 35.08 3.79
396 404 5.406649 TCATGTTCGGTTCCATTAAAATGC 58.593 37.500 0.00 0.00 35.08 3.56
397 405 7.881643 TTTCATGTTCGGTTCCATTAAAATG 57.118 32.000 0.00 0.00 36.17 2.32
398 406 7.928706 TGTTTTCATGTTCGGTTCCATTAAAAT 59.071 29.630 0.00 0.00 30.98 1.82
430 438 1.541588 CCATCTGATCGATAGCCGTGA 59.458 52.381 0.00 0.00 39.75 4.35
436 444 7.378194 CGAAATATGTAGCCATCTGATCGATAG 59.622 40.741 0.00 0.00 30.81 2.08
437 445 7.067008 TCGAAATATGTAGCCATCTGATCGATA 59.933 37.037 0.00 0.00 32.25 2.92
438 446 6.038985 CGAAATATGTAGCCATCTGATCGAT 58.961 40.000 0.00 0.00 30.81 3.59
457 465 4.020128 GGGCAGAGGGAGTAATATCGAAAT 60.020 45.833 0.00 0.00 0.00 2.17
471 479 4.225942 TGCAAGATATTATAGGGCAGAGGG 59.774 45.833 0.00 0.00 0.00 4.30
472 480 5.426689 TGCAAGATATTATAGGGCAGAGG 57.573 43.478 0.00 0.00 0.00 3.69
475 483 8.114331 TCATTTTGCAAGATATTATAGGGCAG 57.886 34.615 1.59 0.00 0.00 4.85
510 518 9.702253 TCTTACTTAATACTTCCTCAGTCTCAT 57.298 33.333 0.00 0.00 36.88 2.90
567 575 7.458397 ACAAGTAATGTGGAATGAAGGAAGTA 58.542 34.615 0.00 0.00 41.93 2.24
568 576 6.306987 ACAAGTAATGTGGAATGAAGGAAGT 58.693 36.000 0.00 0.00 41.93 3.01
582 590 7.039882 CGGAAGGAGTATAACACAAGTAATGT 58.960 38.462 0.00 0.00 45.34 2.71
583 591 6.018994 GCGGAAGGAGTATAACACAAGTAATG 60.019 42.308 0.00 0.00 0.00 1.90
599 607 1.486726 AGTAATTCTGGGCGGAAGGAG 59.513 52.381 0.00 0.00 0.00 3.69
600 608 1.580059 AGTAATTCTGGGCGGAAGGA 58.420 50.000 0.00 0.00 0.00 3.36
601 609 2.017049 CAAGTAATTCTGGGCGGAAGG 58.983 52.381 0.00 0.00 0.00 3.46
602 610 2.678336 GACAAGTAATTCTGGGCGGAAG 59.322 50.000 0.00 0.00 0.00 3.46
603 611 2.039216 TGACAAGTAATTCTGGGCGGAA 59.961 45.455 0.00 0.00 0.00 4.30
604 612 1.626321 TGACAAGTAATTCTGGGCGGA 59.374 47.619 0.00 0.00 0.00 5.54
605 613 2.107950 TGACAAGTAATTCTGGGCGG 57.892 50.000 0.00 0.00 0.00 6.13
606 614 5.811399 TTAATGACAAGTAATTCTGGGCG 57.189 39.130 0.00 0.00 0.00 6.13
607 615 9.736023 CTATTTTAATGACAAGTAATTCTGGGC 57.264 33.333 0.00 0.00 0.00 5.36
663 671 9.499479 GTCATTGAAATGGATGTATCTAGATGT 57.501 33.333 15.79 1.25 37.03 3.06
664 672 9.498176 TGTCATTGAAATGGATGTATCTAGATG 57.502 33.333 15.79 0.00 37.03 2.90
666 674 9.551734 CTTGTCATTGAAATGGATGTATCTAGA 57.448 33.333 0.00 0.00 37.03 2.43
667 675 9.334947 ACTTGTCATTGAAATGGATGTATCTAG 57.665 33.333 3.31 0.00 37.03 2.43
669 677 9.857656 ATACTTGTCATTGAAATGGATGTATCT 57.142 29.630 3.31 0.00 37.03 1.98
673 681 8.253113 GGAAATACTTGTCATTGAAATGGATGT 58.747 33.333 3.31 2.77 37.03 3.06
674 682 7.433131 CGGAAATACTTGTCATTGAAATGGATG 59.567 37.037 3.31 0.00 37.03 3.51
675 683 7.416664 CCGGAAATACTTGTCATTGAAATGGAT 60.417 37.037 0.00 0.00 37.03 3.41
676 684 6.127758 CCGGAAATACTTGTCATTGAAATGGA 60.128 38.462 0.00 0.00 37.03 3.41
677 685 6.035843 CCGGAAATACTTGTCATTGAAATGG 58.964 40.000 0.00 0.00 37.03 3.16
678 686 6.747280 GTCCGGAAATACTTGTCATTGAAATG 59.253 38.462 5.23 0.00 37.75 2.32
679 687 6.403200 CGTCCGGAAATACTTGTCATTGAAAT 60.403 38.462 5.23 0.00 0.00 2.17
680 688 5.106869 CGTCCGGAAATACTTGTCATTGAAA 60.107 40.000 5.23 0.00 0.00 2.69
681 689 4.390603 CGTCCGGAAATACTTGTCATTGAA 59.609 41.667 5.23 0.00 0.00 2.69
682 690 3.930229 CGTCCGGAAATACTTGTCATTGA 59.070 43.478 5.23 0.00 0.00 2.57
683 691 3.063452 CCGTCCGGAAATACTTGTCATTG 59.937 47.826 5.23 0.00 37.50 2.82
684 692 3.055675 TCCGTCCGGAAATACTTGTCATT 60.056 43.478 5.23 0.00 42.05 2.57
685 693 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
686 694 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
687 695 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
688 696 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
689 697 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
690 698 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
691 699 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
692 700 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
693 701 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
694 702 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
695 703 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
696 704 0.846015 TATACTCCCTCCGTCCGGAA 59.154 55.000 5.23 0.00 44.66 4.30
697 705 1.070604 ATATACTCCCTCCGTCCGGA 58.929 55.000 0.00 0.00 42.90 5.14
698 706 1.920610 AATATACTCCCTCCGTCCGG 58.079 55.000 0.00 0.00 0.00 5.14
699 707 2.626743 ACAAATATACTCCCTCCGTCCG 59.373 50.000 0.00 0.00 0.00 4.79
700 708 4.684484 AACAAATATACTCCCTCCGTCC 57.316 45.455 0.00 0.00 0.00 4.79
701 709 6.183360 ACCTAAACAAATATACTCCCTCCGTC 60.183 42.308 0.00 0.00 0.00 4.79
702 710 5.664457 ACCTAAACAAATATACTCCCTCCGT 59.336 40.000 0.00 0.00 0.00 4.69
703 711 6.170846 ACCTAAACAAATATACTCCCTCCG 57.829 41.667 0.00 0.00 0.00 4.63
704 712 8.026396 TGTACCTAAACAAATATACTCCCTCC 57.974 38.462 0.00 0.00 0.00 4.30
705 713 8.921205 TCTGTACCTAAACAAATATACTCCCTC 58.079 37.037 0.00 0.00 0.00 4.30
706 714 8.849543 TCTGTACCTAAACAAATATACTCCCT 57.150 34.615 0.00 0.00 0.00 4.20
707 715 9.490379 CATCTGTACCTAAACAAATATACTCCC 57.510 37.037 0.00 0.00 0.00 4.30
945 4577 1.139308 CAGGCGAGAGAGACAGCAG 59.861 63.158 0.00 0.00 0.00 4.24
946 4578 2.346541 CCAGGCGAGAGAGACAGCA 61.347 63.158 0.00 0.00 0.00 4.41
963 4595 2.098770 GCACAATCTCTGAATGGAAGCC 59.901 50.000 0.00 0.00 0.00 4.35
969 4601 3.079578 ACCACAGCACAATCTCTGAATG 58.920 45.455 0.00 0.00 34.57 2.67
973 4605 0.520404 GCACCACAGCACAATCTCTG 59.480 55.000 0.00 0.00 36.45 3.35
974 4606 0.952497 CGCACCACAGCACAATCTCT 60.952 55.000 0.00 0.00 0.00 3.10
987 4619 1.406898 GACATCATCTCTCTCGCACCA 59.593 52.381 0.00 0.00 0.00 4.17
1092 4734 0.919780 AGAAACTAAGGGGAGGGGCC 60.920 60.000 0.00 0.00 0.00 5.80
1093 4735 0.547075 GAGAAACTAAGGGGAGGGGC 59.453 60.000 0.00 0.00 0.00 5.80
1147 4789 4.466567 TCGTAGGCGAAAAATGCATATG 57.533 40.909 0.00 0.00 44.92 1.78
1186 4828 0.035056 GGTAGCAGGCATGGTGAAGT 60.035 55.000 14.17 0.00 37.78 3.01
1204 4846 7.815840 AAGAAAGGAAGAAGAAAGAAAGAGG 57.184 36.000 0.00 0.00 0.00 3.69
1218 4860 9.645059 AAGAAACAAAGAAAGAAAGAAAGGAAG 57.355 29.630 0.00 0.00 0.00 3.46
1221 4863 9.645059 AGAAAGAAACAAAGAAAGAAAGAAAGG 57.355 29.630 0.00 0.00 0.00 3.11
1238 4884 5.372547 AATTAAGTCGCCCAGAAAGAAAC 57.627 39.130 0.00 0.00 0.00 2.78
1466 5116 3.390639 ACGGAGGAAGTACTAGCTAGCTA 59.609 47.826 22.85 22.85 0.00 3.32
1467 5117 2.173143 ACGGAGGAAGTACTAGCTAGCT 59.827 50.000 23.12 23.12 0.00 3.32
1535 5225 4.275196 GGAAAAGAAGAAACGCCACTACTT 59.725 41.667 0.00 0.00 0.00 2.24
1610 5300 7.200455 TCTACATATGTATGTGTGCAGTGTAC 58.800 38.462 15.81 4.15 45.77 2.90
1616 5308 7.232534 TCCTACATCTACATATGTATGTGTGCA 59.767 37.037 27.12 16.21 45.77 4.57
1617 5309 7.542477 GTCCTACATCTACATATGTATGTGTGC 59.458 40.741 27.12 17.34 45.77 4.57
1618 5310 8.029522 GGTCCTACATCTACATATGTATGTGTG 58.970 40.741 27.12 20.39 45.77 3.82
1619 5311 7.094334 CGGTCCTACATCTACATATGTATGTGT 60.094 40.741 24.92 24.77 45.77 3.72
1620 5312 7.251281 CGGTCCTACATCTACATATGTATGTG 58.749 42.308 24.92 21.74 45.77 3.21
1661 5353 3.840078 AGGGTTTTGGAAGCTTTATGCAT 59.160 39.130 3.79 3.79 45.94 3.96
1662 5354 3.238597 AGGGTTTTGGAAGCTTTATGCA 58.761 40.909 0.00 0.00 45.94 3.96
1663 5355 3.368427 GGAGGGTTTTGGAAGCTTTATGC 60.368 47.826 0.00 0.00 43.29 3.14
1664 5356 3.195610 GGGAGGGTTTTGGAAGCTTTATG 59.804 47.826 0.00 0.00 33.81 1.90
1773 5469 1.612726 GGGCAGCTCTTGTCTGACAAT 60.613 52.381 22.28 6.14 41.31 2.71
1824 5520 2.266055 CTGAGGCCCAACTCGTCC 59.734 66.667 0.00 0.00 40.39 4.79
1982 5682 6.834168 TTGTTTTCTTCTTTTGGTCAGTCT 57.166 33.333 0.00 0.00 0.00 3.24
2011 5711 8.217111 TGGAAATCATCATATGGCTTACAGTAA 58.783 33.333 2.13 0.00 0.00 2.24
2048 5756 1.603802 CATCAGGTTCTGCACGTTTGT 59.396 47.619 0.00 0.00 0.00 2.83
2185 5896 4.200838 TGTTATTGAGATGCTTGACGGA 57.799 40.909 0.00 0.00 0.00 4.69
2214 5928 8.463930 AGAGAGAGTCAATAGACCAGATTAAG 57.536 38.462 0.00 0.00 46.15 1.85
2232 5946 7.713507 CACGGTAGGGAGATATATAAGAGAGAG 59.286 44.444 0.00 0.00 0.00 3.20
2240 5954 5.809001 ACGAACACGGTAGGGAGATATATA 58.191 41.667 0.00 0.00 0.00 0.86
2276 6039 5.930569 CGAGAATAGGCATCTCATCATTCAA 59.069 40.000 13.15 0.00 42.79 2.69
2448 6214 9.516546 TGGAGAAAGAGTACATATATGATACGT 57.483 33.333 19.63 0.00 0.00 3.57
2493 6259 2.555199 GTGGACATGTACATCCTGCTC 58.445 52.381 15.33 0.00 35.86 4.26
2515 6281 2.440627 TCTCATCAGGTTCATGGATGGG 59.559 50.000 8.46 5.92 40.17 4.00
2698 6492 8.607459 GTTGCTTAGTACGTACTATTCTACTCA 58.393 37.037 30.56 18.40 38.48 3.41
2699 6493 8.607459 TGTTGCTTAGTACGTACTATTCTACTC 58.393 37.037 30.56 18.95 38.48 2.59
2701 6495 8.394121 ACTGTTGCTTAGTACGTACTATTCTAC 58.606 37.037 30.56 26.94 38.48 2.59
2702 6496 8.393366 CACTGTTGCTTAGTACGTACTATTCTA 58.607 37.037 30.56 19.90 38.48 2.10
2703 6497 7.249147 CACTGTTGCTTAGTACGTACTATTCT 58.751 38.462 30.56 12.23 38.48 2.40
2704 6498 6.471519 CCACTGTTGCTTAGTACGTACTATTC 59.528 42.308 30.56 24.33 38.48 1.75
2705 6499 6.327934 CCACTGTTGCTTAGTACGTACTATT 58.672 40.000 30.56 12.93 38.48 1.73
2706 6500 5.163581 CCCACTGTTGCTTAGTACGTACTAT 60.164 44.000 30.56 14.25 38.48 2.12
2707 6501 4.156556 CCCACTGTTGCTTAGTACGTACTA 59.843 45.833 27.51 27.51 37.73 1.82
2708 6502 3.057033 CCCACTGTTGCTTAGTACGTACT 60.057 47.826 29.62 29.62 40.24 2.73
2709 6503 3.248266 CCCACTGTTGCTTAGTACGTAC 58.752 50.000 18.10 18.10 0.00 3.67
2710 6504 2.892852 ACCCACTGTTGCTTAGTACGTA 59.107 45.455 0.00 0.00 0.00 3.57
2711 6505 1.690352 ACCCACTGTTGCTTAGTACGT 59.310 47.619 0.00 0.00 0.00 3.57
2712 6506 2.066262 CACCCACTGTTGCTTAGTACG 58.934 52.381 0.00 0.00 0.00 3.67
2713 6507 2.806244 CACACCCACTGTTGCTTAGTAC 59.194 50.000 0.00 0.00 0.00 2.73
2716 6510 1.603802 CACACACCCACTGTTGCTTAG 59.396 52.381 0.00 0.00 0.00 2.18
2817 6611 6.588756 GGGTTAAATCAATCAGCATGCATATG 59.411 38.462 21.98 9.94 37.36 1.78
2818 6612 6.570957 CGGGTTAAATCAATCAGCATGCATAT 60.571 38.462 21.98 9.80 34.76 1.78
2819 6613 5.278414 CGGGTTAAATCAATCAGCATGCATA 60.278 40.000 21.98 7.54 34.76 3.14
2820 6614 4.500205 CGGGTTAAATCAATCAGCATGCAT 60.500 41.667 21.98 1.94 34.76 3.96
2856 6660 2.642254 CCTTGGCATGCAGGTGGTG 61.642 63.158 21.36 1.77 0.00 4.17
2857 6661 2.283388 CCTTGGCATGCAGGTGGT 60.283 61.111 21.36 0.00 0.00 4.16
2858 6662 3.766691 GCCTTGGCATGCAGGTGG 61.767 66.667 21.36 15.84 32.06 4.61
2891 6697 2.711922 ATCGGCCGACCTCACAGAC 61.712 63.158 33.75 0.00 0.00 3.51
2892 6698 2.362503 ATCGGCCGACCTCACAGA 60.363 61.111 33.75 4.52 0.00 3.41
2893 6699 2.202797 CATCGGCCGACCTCACAG 60.203 66.667 33.75 10.55 0.00 3.66
2894 6700 3.770040 CCATCGGCCGACCTCACA 61.770 66.667 33.75 6.41 0.00 3.58
2935 6749 3.192212 CCTCCGTCTCCGTTACTTACTTT 59.808 47.826 0.00 0.00 0.00 2.66
2936 6750 2.751806 CCTCCGTCTCCGTTACTTACTT 59.248 50.000 0.00 0.00 0.00 2.24
2937 6751 2.290577 ACCTCCGTCTCCGTTACTTACT 60.291 50.000 0.00 0.00 0.00 2.24
2938 6752 2.087646 ACCTCCGTCTCCGTTACTTAC 58.912 52.381 0.00 0.00 0.00 2.34
2939 6753 2.086869 CACCTCCGTCTCCGTTACTTA 58.913 52.381 0.00 0.00 0.00 2.24
2941 6755 0.964358 CCACCTCCGTCTCCGTTACT 60.964 60.000 0.00 0.00 0.00 2.24
2942 6756 1.246737 ACCACCTCCGTCTCCGTTAC 61.247 60.000 0.00 0.00 0.00 2.50
2943 6757 1.075482 ACCACCTCCGTCTCCGTTA 59.925 57.895 0.00 0.00 0.00 3.18
2945 6759 2.989824 CACCACCTCCGTCTCCGT 60.990 66.667 0.00 0.00 0.00 4.69
2946 6760 4.436998 GCACCACCTCCGTCTCCG 62.437 72.222 0.00 0.00 0.00 4.63
2947 6761 4.083862 GGCACCACCTCCGTCTCC 62.084 72.222 0.00 0.00 34.51 3.71
2949 6763 0.691078 ATATGGCACCACCTCCGTCT 60.691 55.000 0.00 0.00 40.22 4.18
2950 6764 0.249911 GATATGGCACCACCTCCGTC 60.250 60.000 0.00 0.00 40.22 4.79
2989 6803 0.105964 TTAGCCAACGCACAGACAGT 59.894 50.000 0.00 0.00 37.52 3.55
3038 7108 4.473520 CACGGGTAGCCAGCCAGG 62.474 72.222 12.31 0.00 42.89 4.45
3039 7109 3.390521 TCACGGGTAGCCAGCCAG 61.391 66.667 12.31 0.00 42.89 4.85
3040 7110 3.702048 GTCACGGGTAGCCAGCCA 61.702 66.667 12.31 0.00 42.89 4.75
3041 7111 3.665675 CTGTCACGGGTAGCCAGCC 62.666 68.421 12.31 0.00 39.08 4.85
3057 7127 0.603707 AAGCACACCCGTGTCATCTG 60.604 55.000 0.00 0.00 45.50 2.90
3087 7157 4.469586 TGGTAAATACTGATGCAGGTCAGA 59.530 41.667 21.34 7.80 46.77 3.27
3120 7190 4.397420 TGGAAACTGTTACACTCATGCAT 58.603 39.130 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.