Multiple sequence alignment - TraesCS2D01G009600

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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 TraesCS2D01G009600 chr2D 100.000 7084 0 0 1 7084 5157690 5164773 0.000000e+00 13082.0
1 TraesCS2D01G009600 chr2D 94.800 750 32 4 1 750 47657272 47656530 0.000000e+00 1162.0
2 TraesCS2D01G009600 chr2D 81.022 274 44 8 6582 6854 610356612 610356878 2.000000e-50 211.0
3 TraesCS2D01G009600 chr2B 95.602 3479 108 20 1690 5133 6315550 6312082 0.000000e+00 5535.0
4 TraesCS2D01G009600 chr2B 90.579 1210 61 23 5313 6499 6311824 6310645 0.000000e+00 1554.0
5 TraesCS2D01G009600 chr2B 91.592 559 32 6 868 1415 6316390 6315836 0.000000e+00 758.0
6 TraesCS2D01G009600 chr2B 92.149 242 17 2 1413 1653 6315791 6315551 2.450000e-89 340.0
7 TraesCS2D01G009600 chr2B 92.593 189 14 0 5129 5317 6312044 6311856 9.050000e-69 272.0
8 TraesCS2D01G009600 chr2B 88.991 109 12 0 3569 3677 703596917 703596809 1.240000e-27 135.0
9 TraesCS2D01G009600 chr2A 93.414 3538 139 46 1834 5317 3443148 3446645 0.000000e+00 5156.0
10 TraesCS2D01G009600 chr2A 92.327 1199 70 14 5313 6499 3446677 3447865 0.000000e+00 1685.0
11 TraesCS2D01G009600 chr2A 85.213 940 85 34 822 1723 3442225 3443148 0.000000e+00 917.0
12 TraesCS2D01G009600 chr2A 87.909 397 45 1 4152 4545 726019870 726020266 1.390000e-126 464.0
13 TraesCS2D01G009600 chr2A 87.817 394 45 1 4155 4545 695304486 695304093 6.480000e-125 459.0
14 TraesCS2D01G009600 chr2A 85.788 387 47 5 4193 4576 214686199 214686580 3.080000e-108 403.0
15 TraesCS2D01G009600 chr2A 93.991 233 9 4 6854 7084 3448240 3448469 1.460000e-91 348.0
16 TraesCS2D01G009600 chr2A 90.377 239 14 4 6565 6795 3447978 3448215 8.930000e-79 305.0
17 TraesCS2D01G009600 chr2A 91.743 109 9 0 3569 3677 214686085 214686193 1.230000e-32 152.0
18 TraesCS2D01G009600 chr5A 95.067 750 30 6 1 750 612874907 612874165 0.000000e+00 1173.0
19 TraesCS2D01G009600 chr5A 94.667 750 29 7 1 750 470149086 470148348 0.000000e+00 1153.0
20 TraesCS2D01G009600 chr5A 83.594 128 15 5 6788 6909 245502281 245502154 1.610000e-21 115.0
21 TraesCS2D01G009600 chr6A 91.892 518 29 9 1 512 364214359 364213849 0.000000e+00 712.0
22 TraesCS2D01G009600 chr1A 87.597 387 42 3 4193 4576 523145217 523144834 1.810000e-120 444.0
23 TraesCS2D01G009600 chr1A 86.528 386 46 3 4194 4576 524983514 524983896 3.060000e-113 420.0
24 TraesCS2D01G009600 chr1A 88.983 118 13 0 3569 3686 523145332 523145215 5.730000e-31 147.0
25 TraesCS2D01G009600 chr1A 90.826 109 10 0 3569 3677 524983399 524983507 5.730000e-31 147.0
26 TraesCS2D01G009600 chr3A 85.316 395 45 4 4155 4546 655522964 655522580 5.150000e-106 396.0
27 TraesCS2D01G009600 chr3A 85.795 176 23 2 1 176 463820655 463820828 1.210000e-42 185.0
28 TraesCS2D01G009600 chr3A 91.743 109 9 0 3569 3677 588140314 588140206 1.230000e-32 152.0
29 TraesCS2D01G009600 chr1B 95.798 238 10 0 514 751 142832367 142832130 1.110000e-102 385.0
30 TraesCS2D01G009600 chr1B 83.051 177 27 3 1 176 595494120 595493946 2.650000e-34 158.0
31 TraesCS2D01G009600 chr1D 94.958 238 12 0 514 751 375796208 375796445 2.410000e-99 374.0
32 TraesCS2D01G009600 chr1D 83.979 387 45 3 4193 4576 480316695 480316323 8.740000e-94 355.0
33 TraesCS2D01G009600 chr1D 80.808 99 11 7 6991 7084 62146182 62146087 3.550000e-08 71.3
34 TraesCS2D01G009600 chr5D 94.239 243 14 0 514 756 2601513 2601271 8.680000e-99 372.0
35 TraesCS2D01G009600 chr7D 94.515 237 13 0 514 750 511622597 511622361 4.040000e-97 366.0
36 TraesCS2D01G009600 chr5B 94.515 237 13 0 514 750 702399173 702399409 4.040000e-97 366.0
37 TraesCS2D01G009600 chr5B 92.095 253 18 1 514 764 491300792 491300540 8.740000e-94 355.0
38 TraesCS2D01G009600 chr5B 83.862 347 35 18 167 512 290582781 290583107 1.920000e-80 311.0
39 TraesCS2D01G009600 chr5B 82.609 184 28 4 4 186 352314510 352314330 7.360000e-35 159.0
40 TraesCS2D01G009600 chr7B 85.014 347 30 19 167 512 40957365 40957690 4.100000e-87 333.0
41 TraesCS2D01G009600 chr7B 83.430 344 36 18 167 509 558923179 558923502 4.150000e-77 300.0
42 TraesCS2D01G009600 chr7B 82.486 177 28 3 1 176 699541087 699540913 1.230000e-32 152.0
43 TraesCS2D01G009600 chr7B 74.550 389 53 27 6564 6921 19536723 19537096 2.070000e-25 128.0
44 TraesCS2D01G009600 chr3B 84.104 346 33 19 167 511 644001728 644001404 1.480000e-81 315.0
45 TraesCS2D01G009600 chr3B 82.486 177 28 3 1 176 147678303 147678477 1.230000e-32 152.0
46 TraesCS2D01G009600 chr3B 74.486 243 37 13 6690 6910 658426740 658426979 1.640000e-11 82.4
47 TraesCS2D01G009600 chr4A 91.262 206 11 5 186 385 359183586 359183790 2.520000e-69 274.0
48 TraesCS2D01G009600 chr3D 78.049 328 51 17 6598 6908 134828881 134829204 3.370000e-43 187.0
49 TraesCS2D01G009600 chr3D 94.595 37 2 0 7048 7084 74330996 74330960 2.760000e-04 58.4
50 TraesCS2D01G009600 chr4D 91.743 109 9 0 3569 3677 158362573 158362465 1.230000e-32 152.0
51 TraesCS2D01G009600 chr6D 82.828 99 12 4 6788 6884 276128394 276128299 4.550000e-12 84.2
52 TraesCS2D01G009600 chrUn 86.765 68 8 1 6788 6854 354652576 354652643 2.740000e-09 75.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G009600 chr2D 5157690 5164773 7083 False 13082.0 13082 100.0000 1 7084 1 chr2D.!!$F1 7083
1 TraesCS2D01G009600 chr2D 47656530 47657272 742 True 1162.0 1162 94.8000 1 750 1 chr2D.!!$R1 749
2 TraesCS2D01G009600 chr2B 6310645 6316390 5745 True 1691.8 5535 92.5030 868 6499 5 chr2B.!!$R2 5631
3 TraesCS2D01G009600 chr2A 3442225 3448469 6244 False 1682.2 5156 91.0644 822 7084 5 chr2A.!!$F2 6262
4 TraesCS2D01G009600 chr5A 612874165 612874907 742 True 1173.0 1173 95.0670 1 750 1 chr5A.!!$R3 749
5 TraesCS2D01G009600 chr5A 470148348 470149086 738 True 1153.0 1153 94.6670 1 750 1 chr5A.!!$R2 749
6 TraesCS2D01G009600 chr6A 364213849 364214359 510 True 712.0 712 91.8920 1 512 1 chr6A.!!$R1 511

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
864 871 0.178938 TTTCCAGCATTGGCCCTTCA 60.179 50.0 0.0 0.0 44.63 3.02 F
1355 1372 0.179145 CCTGCGTGTAGTTACTCCGG 60.179 60.0 0.0 0.0 0.00 5.14 F
1390 1407 0.368907 CGGTCGTGCTTTATCGGTTG 59.631 55.0 0.0 0.0 0.00 3.77 F
1623 1692 0.600057 GAAAGAAGCAAGCCTGTGGG 59.400 55.0 0.0 0.0 0.00 4.61 F
2043 2124 0.827368 CAGCCTCTGAACTACCCCTC 59.173 60.0 0.0 0.0 32.44 4.30 F
3390 3509 0.684479 GGGGAGAACCTTTGGATGGC 60.684 60.0 0.0 0.0 40.03 4.40 F
4970 5107 1.241165 TTGCATGTCTTCTGCTGTGG 58.759 50.0 0.0 0.0 40.34 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 2127 0.178998 GATGGGAGATGCAGGCATGT 60.179 55.000 12.12 7.66 36.70 3.21 R
2703 2820 0.392706 TCGTGCACTCTGTGTCCATT 59.607 50.000 16.19 0.00 35.75 3.16 R
3086 3204 2.224606 CGCCCTATGTTGCATCAGAAT 58.775 47.619 3.50 0.00 0.00 2.40 R
3390 3509 1.597854 TGCCCTTGCAACAGAGTCG 60.598 57.895 0.00 0.00 46.66 4.18 R
3703 3825 1.073284 GGTCAAGGGAGCAAGGTACAA 59.927 52.381 0.00 0.00 41.19 2.41 R
5097 5240 1.131126 CCATTTGGCAGCTACGAACAG 59.869 52.381 0.00 0.00 0.00 3.16 R
6876 7181 0.244450 CATGGTTCCATGTGCACCAC 59.756 55.000 20.05 3.13 43.44 4.16 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
50 51 4.357918 AGAGCAACTACCAACAAGTGAT 57.642 40.909 0.00 0.00 0.00 3.06
55 56 7.448469 AGAGCAACTACCAACAAGTGATTTTAT 59.552 33.333 0.00 0.00 0.00 1.40
134 135 4.127171 TGCCACTCACTCTGACTAAAAAC 58.873 43.478 0.00 0.00 0.00 2.43
143 144 4.586001 ACTCTGACTAAAAACGGTCACCTA 59.414 41.667 0.00 0.00 0.00 3.08
147 148 4.341806 TGACTAAAAACGGTCACCTACTCA 59.658 41.667 0.00 0.00 0.00 3.41
178 179 6.540189 AGCAACTGACCAATGAAGTATATGTC 59.460 38.462 0.00 0.00 0.00 3.06
181 182 8.950210 CAACTGACCAATGAAGTATATGTCTTT 58.050 33.333 0.00 0.00 0.00 2.52
440 447 1.707239 AAGGCGACGTCGTTGCAAAA 61.707 50.000 35.48 0.00 44.12 2.44
446 453 0.655733 ACGTCGTTGCAAAAGGACAG 59.344 50.000 20.05 15.90 37.40 3.51
512 519 4.251543 ACCAGAACAAAATTAAAGGCCG 57.748 40.909 0.00 0.00 0.00 6.13
619 626 9.543018 GTTATCAGTTTACATTACAAGTGAAGC 57.457 33.333 0.00 0.00 36.24 3.86
648 655 6.117911 TCAGTTATTATGCAATTGTGTCCG 57.882 37.500 7.40 0.00 0.00 4.79
726 733 3.782889 AAATATTTCAGAAGCCCGTGC 57.217 42.857 0.00 0.00 37.95 5.34
750 757 1.066605 CGCACGGGCATACTACTAGTT 59.933 52.381 11.77 0.00 41.24 2.24
751 758 2.480759 CGCACGGGCATACTACTAGTTT 60.481 50.000 11.77 0.00 41.24 2.66
752 759 3.528532 GCACGGGCATACTACTAGTTTT 58.471 45.455 3.77 0.00 40.72 2.43
753 760 3.937079 GCACGGGCATACTACTAGTTTTT 59.063 43.478 3.77 0.00 40.72 1.94
754 761 5.111293 GCACGGGCATACTACTAGTTTTTA 58.889 41.667 3.77 0.00 40.72 1.52
755 762 5.756833 GCACGGGCATACTACTAGTTTTTAT 59.243 40.000 3.77 0.00 40.72 1.40
756 763 6.259387 GCACGGGCATACTACTAGTTTTTATT 59.741 38.462 3.77 0.00 40.72 1.40
757 764 7.439056 GCACGGGCATACTACTAGTTTTTATTA 59.561 37.037 3.77 0.00 40.72 0.98
758 765 9.485206 CACGGGCATACTACTAGTTTTTATTAT 57.515 33.333 0.00 0.00 0.00 1.28
759 766 9.485206 ACGGGCATACTACTAGTTTTTATTATG 57.515 33.333 0.00 0.00 0.00 1.90
760 767 9.485206 CGGGCATACTACTAGTTTTTATTATGT 57.515 33.333 0.00 0.00 0.00 2.29
778 785 9.788889 TTATTATGTCTGATTGATTGAGATGCT 57.211 29.630 0.00 0.00 0.00 3.79
779 786 8.693120 ATTATGTCTGATTGATTGAGATGCTT 57.307 30.769 0.00 0.00 0.00 3.91
780 787 8.515695 TTATGTCTGATTGATTGAGATGCTTT 57.484 30.769 0.00 0.00 0.00 3.51
781 788 6.190954 TGTCTGATTGATTGAGATGCTTTG 57.809 37.500 0.00 0.00 0.00 2.77
782 789 5.708697 TGTCTGATTGATTGAGATGCTTTGT 59.291 36.000 0.00 0.00 0.00 2.83
783 790 6.880529 TGTCTGATTGATTGAGATGCTTTGTA 59.119 34.615 0.00 0.00 0.00 2.41
784 791 7.555195 TGTCTGATTGATTGAGATGCTTTGTAT 59.445 33.333 0.00 0.00 0.00 2.29
785 792 8.404000 GTCTGATTGATTGAGATGCTTTGTATT 58.596 33.333 0.00 0.00 0.00 1.89
786 793 8.963725 TCTGATTGATTGAGATGCTTTGTATTT 58.036 29.630 0.00 0.00 0.00 1.40
787 794 9.582431 CTGATTGATTGAGATGCTTTGTATTTT 57.418 29.630 0.00 0.00 0.00 1.82
788 795 9.577110 TGATTGATTGAGATGCTTTGTATTTTC 57.423 29.630 0.00 0.00 0.00 2.29
789 796 8.624701 ATTGATTGAGATGCTTTGTATTTTCG 57.375 30.769 0.00 0.00 0.00 3.46
790 797 6.554419 TGATTGAGATGCTTTGTATTTTCGG 58.446 36.000 0.00 0.00 0.00 4.30
791 798 5.957842 TTGAGATGCTTTGTATTTTCGGT 57.042 34.783 0.00 0.00 0.00 4.69
792 799 5.295431 TGAGATGCTTTGTATTTTCGGTG 57.705 39.130 0.00 0.00 0.00 4.94
793 800 5.000591 TGAGATGCTTTGTATTTTCGGTGA 58.999 37.500 0.00 0.00 0.00 4.02
794 801 5.647658 TGAGATGCTTTGTATTTTCGGTGAT 59.352 36.000 0.00 0.00 0.00 3.06
795 802 6.150976 TGAGATGCTTTGTATTTTCGGTGATT 59.849 34.615 0.00 0.00 0.00 2.57
796 803 6.924111 AGATGCTTTGTATTTTCGGTGATTT 58.076 32.000 0.00 0.00 0.00 2.17
797 804 7.378181 AGATGCTTTGTATTTTCGGTGATTTT 58.622 30.769 0.00 0.00 0.00 1.82
798 805 7.872483 AGATGCTTTGTATTTTCGGTGATTTTT 59.128 29.630 0.00 0.00 0.00 1.94
823 830 8.742125 TTTATAATAGATCTGATCCCTGGTGT 57.258 34.615 13.83 0.00 0.00 4.16
824 831 9.837681 TTTATAATAGATCTGATCCCTGGTGTA 57.162 33.333 13.83 0.00 0.00 2.90
825 832 9.837681 TTATAATAGATCTGATCCCTGGTGTAA 57.162 33.333 13.83 3.53 0.00 2.41
826 833 8.742125 ATAATAGATCTGATCCCTGGTGTAAA 57.258 34.615 13.83 0.00 0.00 2.01
827 834 7.451731 AATAGATCTGATCCCTGGTGTAAAA 57.548 36.000 13.83 0.00 0.00 1.52
828 835 5.983333 AGATCTGATCCCTGGTGTAAAAT 57.017 39.130 13.83 0.00 0.00 1.82
829 836 6.332976 AGATCTGATCCCTGGTGTAAAATT 57.667 37.500 13.83 0.00 0.00 1.82
830 837 6.735556 AGATCTGATCCCTGGTGTAAAATTT 58.264 36.000 13.83 0.00 0.00 1.82
831 838 6.604795 AGATCTGATCCCTGGTGTAAAATTTG 59.395 38.462 13.83 0.00 0.00 2.32
832 839 4.462483 TCTGATCCCTGGTGTAAAATTTGC 59.538 41.667 0.00 0.00 0.00 3.68
833 840 4.155709 TGATCCCTGGTGTAAAATTTGCA 58.844 39.130 0.00 0.00 0.00 4.08
834 841 4.021544 TGATCCCTGGTGTAAAATTTGCAC 60.022 41.667 16.74 16.74 44.22 4.57
835 842 3.571590 TCCCTGGTGTAAAATTTGCACT 58.428 40.909 22.33 0.00 44.35 4.40
836 843 3.320541 TCCCTGGTGTAAAATTTGCACTG 59.679 43.478 22.33 16.08 44.35 3.66
864 871 0.178938 TTTCCAGCATTGGCCCTTCA 60.179 50.000 0.00 0.00 44.63 3.02
866 873 2.353610 CCAGCATTGGCCCTTCACC 61.354 63.158 0.00 0.00 42.56 4.02
938 945 1.451387 ATAAAACCCTCGGCGCAGG 60.451 57.895 10.83 8.52 0.00 4.85
1285 1298 2.748251 CGCGGTAATGCCCCACAA 60.748 61.111 0.00 0.00 0.00 3.33
1342 1359 1.586154 GCTTGTGGTAATGCCTGCGT 61.586 55.000 0.00 0.00 38.35 5.24
1349 1366 2.234168 TGGTAATGCCTGCGTGTAGTTA 59.766 45.455 0.00 0.00 38.35 2.24
1352 1369 2.295253 ATGCCTGCGTGTAGTTACTC 57.705 50.000 0.00 0.00 0.00 2.59
1353 1370 0.245539 TGCCTGCGTGTAGTTACTCC 59.754 55.000 0.00 0.00 0.00 3.85
1355 1372 0.179145 CCTGCGTGTAGTTACTCCGG 60.179 60.000 0.00 0.00 0.00 5.14
1356 1373 0.524862 CTGCGTGTAGTTACTCCGGT 59.475 55.000 0.00 0.00 0.00 5.28
1360 1377 2.863704 GCGTGTAGTTACTCCGGTGTTT 60.864 50.000 15.36 4.06 0.00 2.83
1363 1380 4.563061 GTGTAGTTACTCCGGTGTTTGAT 58.437 43.478 15.36 1.89 0.00 2.57
1367 1384 0.687920 TACTCCGGTGTTTGATGGCA 59.312 50.000 15.36 0.00 0.00 4.92
1368 1385 0.889186 ACTCCGGTGTTTGATGGCAC 60.889 55.000 2.61 0.00 35.07 5.01
1386 1403 1.320555 CACTTCGGTCGTGCTTTATCG 59.679 52.381 0.00 0.00 0.00 2.92
1390 1407 0.368907 CGGTCGTGCTTTATCGGTTG 59.631 55.000 0.00 0.00 0.00 3.77
1391 1408 1.435577 GGTCGTGCTTTATCGGTTGT 58.564 50.000 0.00 0.00 0.00 3.32
1393 1410 1.392510 GTCGTGCTTTATCGGTTGTCC 59.607 52.381 0.00 0.00 0.00 4.02
1446 1510 9.178758 AGGCTAAATAGTTTCTAGAAATTGGTG 57.821 33.333 20.41 9.38 32.36 4.17
1491 1555 2.812011 GTTTTGCCTCGACACTAATGGT 59.188 45.455 0.00 0.00 0.00 3.55
1503 1567 7.755591 TCGACACTAATGGTTAGTAAGTACAG 58.244 38.462 2.35 0.00 44.32 2.74
1538 1606 6.856426 GCAAGAACCACTTACTGAATACAAAC 59.144 38.462 0.00 0.00 37.03 2.93
1548 1616 2.333926 TGAATACAAACGCGAGGACTG 58.666 47.619 15.93 4.55 0.00 3.51
1592 1660 3.520290 ATGCATGCTCTGTTTCATTGG 57.480 42.857 20.33 0.00 0.00 3.16
1623 1692 0.600057 GAAAGAAGCAAGCCTGTGGG 59.400 55.000 0.00 0.00 0.00 4.61
1649 1718 7.228308 GCTATGGATTTCTCTCTAATGCAAGTT 59.772 37.037 0.00 0.00 36.99 2.66
1653 1722 4.908601 TTCTCTCTAATGCAAGTTCCCA 57.091 40.909 0.00 0.00 0.00 4.37
1657 1726 5.649395 TCTCTCTAATGCAAGTTCCCATTTG 59.351 40.000 0.00 3.40 33.93 2.32
1664 1733 3.763360 TGCAAGTTCCCATTTGTGGATAG 59.237 43.478 0.00 0.00 0.00 2.08
1747 1816 9.522804 CTCTTGTTACTATGATCTTTACCACTC 57.477 37.037 0.00 0.00 0.00 3.51
1772 1848 2.935201 GCATGTCCTTGTCAGACTGATC 59.065 50.000 8.73 3.45 35.21 2.92
1785 1861 6.073765 TGTCAGACTGATCGCTTTCTTTAAAC 60.074 38.462 8.73 0.00 0.00 2.01
1899 1975 4.620184 GCGACTTAACACTCGTTATGTTCT 59.380 41.667 5.25 0.00 42.74 3.01
1950 2031 3.930848 GGCCTGCTTTGATTTTCAATGAG 59.069 43.478 0.00 0.00 36.11 2.90
1976 2057 3.907221 TGGGGCTACCTTACTAGTAGTG 58.093 50.000 13.29 0.00 39.54 2.74
2043 2124 0.827368 CAGCCTCTGAACTACCCCTC 59.173 60.000 0.00 0.00 32.44 4.30
2046 2127 2.315155 AGCCTCTGAACTACCCCTCTTA 59.685 50.000 0.00 0.00 0.00 2.10
2079 2160 4.645535 TCTCCCATCACTTTTTGTCTCTG 58.354 43.478 0.00 0.00 0.00 3.35
2091 2191 1.039785 TGTCTCTGCTATGCGCTCCT 61.040 55.000 9.73 0.00 40.11 3.69
2201 2302 4.457603 TGTTGGTCGTCATCTTAATTTGGG 59.542 41.667 0.00 0.00 0.00 4.12
2204 2305 5.180271 TGGTCGTCATCTTAATTTGGGTAC 58.820 41.667 0.00 0.00 0.00 3.34
2205 2306 4.269363 GGTCGTCATCTTAATTTGGGTACG 59.731 45.833 0.00 0.00 0.00 3.67
2351 2452 5.807011 GCTTATTTGGCTCAGGTATTGTTTG 59.193 40.000 0.00 0.00 0.00 2.93
2352 2453 6.572314 GCTTATTTGGCTCAGGTATTGTTTGT 60.572 38.462 0.00 0.00 0.00 2.83
2405 2522 7.810282 CCTGAACCTATAACTCATAACTGATCG 59.190 40.741 0.00 0.00 0.00 3.69
2495 2612 2.973694 TCCGTATGGACTAACTTGCC 57.026 50.000 0.00 0.00 40.17 4.52
2703 2820 8.644216 TCAGGTCTGTCTTTTACACTTGTTATA 58.356 33.333 0.00 0.00 33.45 0.98
2918 3036 4.730966 TCATAGTGGTCCTCTCATACTCC 58.269 47.826 0.00 0.00 0.00 3.85
3390 3509 0.684479 GGGGAGAACCTTTGGATGGC 60.684 60.000 0.00 0.00 40.03 4.40
3574 3696 5.655532 GGGTTAGGTACTCATGACACTAAGA 59.344 44.000 0.00 0.00 41.75 2.10
3620 3742 2.629017 AATGGATTGGAAGTGCCCTT 57.371 45.000 0.00 0.00 34.97 3.95
3656 3778 1.905637 TGCAGAGTTGACCTAGTCGA 58.094 50.000 0.00 0.00 34.95 4.20
3703 3825 7.256368 GGAAGATAATAGATTTCCGGGAGAAGT 60.256 40.741 0.00 0.00 35.40 3.01
3786 3908 3.136443 TGGGAGCTGATATTACTTGTGGG 59.864 47.826 0.00 0.00 0.00 4.61
3862 3984 6.742363 GCTGGTCTGTTCCATCATCATATGTA 60.742 42.308 1.90 0.00 36.84 2.29
4268 4394 6.889301 AAAGGCCTTTAACTGTTAAGGTAC 57.111 37.500 29.47 11.47 0.00 3.34
4354 4484 7.819900 TGATTCTAGGTAAGAACAGCTTTCTTC 59.180 37.037 20.13 14.21 46.90 2.87
4634 4764 5.995565 TGTCAAGGTTAGTATGTACAGCT 57.004 39.130 0.33 4.86 0.00 4.24
4729 4866 4.982295 GTGAACCACATTTTAGCTTGGAAC 59.018 41.667 6.87 1.56 34.08 3.62
4776 4913 7.334421 TGAATTATGCTCCAGTGTTTAGTCTTC 59.666 37.037 0.00 0.00 0.00 2.87
4886 5023 4.696877 TGTTTAATGCTCTCCATGTGTCTG 59.303 41.667 0.00 0.00 33.49 3.51
4970 5107 1.241165 TTGCATGTCTTCTGCTGTGG 58.759 50.000 0.00 0.00 40.34 4.17
4994 5131 5.294306 GCTCAACTGCAGCATATAAACTGTA 59.706 40.000 15.27 2.66 36.82 2.74
5030 5167 5.419155 TGTTCCTCTTCTACGAATGTCTCAT 59.581 40.000 0.00 0.00 0.00 2.90
5233 5418 6.622896 GCAAACTCGGTATTACTTGAATGCTT 60.623 38.462 0.00 0.00 31.26 3.91
5464 5685 2.944129 TGGCAGCCTTGGATATTTACC 58.056 47.619 14.15 0.00 0.00 2.85
5473 5694 7.118390 CAGCCTTGGATATTTACCGAGATAAAG 59.882 40.741 0.00 0.00 40.36 1.85
5606 5829 8.072321 TCAGCTCTGAGAGTATGTAGAAATTT 57.928 34.615 11.64 0.00 34.14 1.82
5630 5853 6.171921 TGGACATTTTCCTTGCCATATTTTG 58.828 36.000 0.00 0.00 46.10 2.44
5661 5885 3.687125 TGTATGGCCCATCGTTTAAACA 58.313 40.909 18.07 6.11 0.00 2.83
5756 5993 4.392940 CCATTTCCTACTAGAATGGCTGG 58.607 47.826 7.09 5.30 42.18 4.85
6053 6296 4.043200 GCGCCCAAGCACAAGTCC 62.043 66.667 0.00 0.00 39.83 3.85
6083 6326 2.951745 CGCGCTGAGAACGGCTAG 60.952 66.667 5.56 0.00 45.30 3.42
6091 6334 3.677424 GCTGAGAACGGCTAGAAGAATGT 60.677 47.826 0.00 0.00 44.22 2.71
6108 6351 5.125356 AGAATGTCGCATGATGGTTATTCA 58.875 37.500 0.00 0.00 0.00 2.57
6124 6367 8.310406 TGGTTATTCAGCAGTTTATATGATCG 57.690 34.615 0.00 0.00 0.00 3.69
6125 6368 7.095229 TGGTTATTCAGCAGTTTATATGATCGC 60.095 37.037 0.00 0.00 0.00 4.58
6126 6369 7.118390 GGTTATTCAGCAGTTTATATGATCGCT 59.882 37.037 0.00 0.00 0.00 4.93
6127 6370 6.718454 ATTCAGCAGTTTATATGATCGCTC 57.282 37.500 0.00 0.00 0.00 5.03
6128 6371 4.560128 TCAGCAGTTTATATGATCGCTCC 58.440 43.478 0.00 0.00 0.00 4.70
6129 6372 3.681897 CAGCAGTTTATATGATCGCTCCC 59.318 47.826 0.00 0.00 0.00 4.30
6130 6373 3.324846 AGCAGTTTATATGATCGCTCCCA 59.675 43.478 0.00 0.00 0.00 4.37
6131 6374 4.065088 GCAGTTTATATGATCGCTCCCAA 58.935 43.478 0.00 0.00 0.00 4.12
6132 6375 4.153117 GCAGTTTATATGATCGCTCCCAAG 59.847 45.833 0.00 0.00 0.00 3.61
6133 6376 4.153117 CAGTTTATATGATCGCTCCCAAGC 59.847 45.833 0.00 0.00 45.56 4.01
6167 6410 6.146347 GCGTCTCTTCTCAGTTAGTTTGAAAT 59.854 38.462 0.00 0.00 0.00 2.17
6202 6445 2.804986 TGTTGCCTGCCTCATAATGA 57.195 45.000 0.00 0.00 0.00 2.57
6369 6618 7.986085 ATGTTATTGGTGCCTCAGTTATATC 57.014 36.000 0.00 0.00 0.00 1.63
6391 6640 7.615582 ATCGCTTAATTTTCTCATCAGTGAA 57.384 32.000 0.00 0.00 33.05 3.18
6646 6951 4.019792 ACATAGTCAACCAATGCTCACA 57.980 40.909 0.00 0.00 0.00 3.58
6678 6983 0.109781 CAAAGAAATGACCGCCGTGG 60.110 55.000 0.00 0.00 46.41 4.94
6781 7086 5.116180 TCTCCATTAAGAATACCACAAGCG 58.884 41.667 0.00 0.00 0.00 4.68
6795 7100 3.363970 CCACAAGCGTCAATACTTCACAC 60.364 47.826 0.00 0.00 0.00 3.82
6798 7103 4.083855 ACAAGCGTCAATACTTCACACATG 60.084 41.667 0.00 0.00 0.00 3.21
6799 7104 3.925379 AGCGTCAATACTTCACACATGA 58.075 40.909 0.00 0.00 0.00 3.07
6800 7105 3.928992 AGCGTCAATACTTCACACATGAG 59.071 43.478 0.00 0.00 35.83 2.90
6801 7106 3.679980 GCGTCAATACTTCACACATGAGT 59.320 43.478 0.00 0.00 35.83 3.41
6802 7107 4.862574 GCGTCAATACTTCACACATGAGTA 59.137 41.667 0.00 0.00 35.83 2.59
6803 7108 5.004821 GCGTCAATACTTCACACATGAGTAG 59.995 44.000 0.00 0.00 35.83 2.57
6804 7109 6.322491 CGTCAATACTTCACACATGAGTAGA 58.678 40.000 0.00 0.00 35.83 2.59
6805 7110 6.806739 CGTCAATACTTCACACATGAGTAGAA 59.193 38.462 0.00 4.07 35.83 2.10
6807 7112 8.598924 GTCAATACTTCACACATGAGTAGAATG 58.401 37.037 0.00 1.14 35.83 2.67
6808 7113 7.765819 TCAATACTTCACACATGAGTAGAATGG 59.234 37.037 0.00 0.00 35.83 3.16
6810 7115 5.482908 ACTTCACACATGAGTAGAATGGTC 58.517 41.667 0.00 0.00 35.83 4.02
6811 7116 4.110036 TCACACATGAGTAGAATGGTCG 57.890 45.455 0.00 0.00 0.00 4.79
6812 7117 3.761752 TCACACATGAGTAGAATGGTCGA 59.238 43.478 0.00 0.00 0.00 4.20
6814 7119 3.119101 ACACATGAGTAGAATGGTCGACC 60.119 47.826 28.17 28.17 30.15 4.79
6825 7130 2.754946 TGGTCGACCAGGTTTGATAC 57.245 50.000 33.23 3.01 42.01 2.24
6842 7147 9.733556 GGTTTGATACCCCAAAATTTTAGAATT 57.266 29.630 2.44 0.00 41.43 2.17
6985 7291 4.016962 ACCCTTGTACCTACCCATACAT 57.983 45.455 0.00 0.00 31.55 2.29
6986 7292 5.160511 ACCCTTGTACCTACCCATACATA 57.839 43.478 0.00 0.00 31.55 2.29
6987 7293 4.903649 ACCCTTGTACCTACCCATACATAC 59.096 45.833 0.00 0.00 31.55 2.39
7043 7349 7.640597 ACCCTTATTTGGTAAGCATTTACTC 57.359 36.000 0.00 0.00 38.78 2.59
7045 7351 6.540914 CCCTTATTTGGTAAGCATTTACTCGA 59.459 38.462 0.00 0.00 38.78 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 6.691388 GTGAGTCGCATCCCAATTTAATAAAC 59.309 38.462 0.00 0.00 0.00 2.01
134 135 3.187700 GCTAAATGTGAGTAGGTGACCG 58.812 50.000 0.00 0.00 0.00 4.79
143 144 4.085357 TGGTCAGTTGCTAAATGTGAGT 57.915 40.909 0.00 0.00 0.00 3.41
147 148 5.536161 ACTTCATTGGTCAGTTGCTAAATGT 59.464 36.000 0.00 0.00 0.00 2.71
260 261 7.507304 TCTCATTTTGTAAAATCGACGAGTTC 58.493 34.615 11.33 0.42 36.52 3.01
374 381 3.390311 TGTCCATCTCAATCCCTCTCATG 59.610 47.826 0.00 0.00 0.00 3.07
492 499 4.234574 GACGGCCTTTAATTTTGTTCTGG 58.765 43.478 0.00 0.00 0.00 3.86
573 580 8.300286 TGATAACAAAAAGGCAAATTGACGATA 58.700 29.630 0.00 0.00 0.00 2.92
619 626 8.239314 ACACAATTGCATAATAACTGAAGTCTG 58.761 33.333 5.05 0.00 0.00 3.51
628 635 4.499040 GCACGGACACAATTGCATAATAAC 59.501 41.667 5.05 0.00 34.97 1.89
648 655 5.907207 TCACAGGAAGAGACAATATAGCAC 58.093 41.667 0.00 0.00 0.00 4.40
703 710 4.618227 GCACGGGCTTCTGAAATATTTTGT 60.618 41.667 0.00 0.00 36.96 2.83
726 733 1.153529 TAGTATGCCCGTGCGTTGG 60.154 57.895 0.00 0.00 41.78 3.77
752 759 9.788889 AGCATCTCAATCAATCAGACATAATAA 57.211 29.630 0.00 0.00 0.00 1.40
753 760 9.788889 AAGCATCTCAATCAATCAGACATAATA 57.211 29.630 0.00 0.00 0.00 0.98
754 761 8.693120 AAGCATCTCAATCAATCAGACATAAT 57.307 30.769 0.00 0.00 0.00 1.28
755 762 8.403236 CAAAGCATCTCAATCAATCAGACATAA 58.597 33.333 0.00 0.00 0.00 1.90
756 763 7.555195 ACAAAGCATCTCAATCAATCAGACATA 59.445 33.333 0.00 0.00 0.00 2.29
757 764 6.377429 ACAAAGCATCTCAATCAATCAGACAT 59.623 34.615 0.00 0.00 0.00 3.06
758 765 5.708697 ACAAAGCATCTCAATCAATCAGACA 59.291 36.000 0.00 0.00 0.00 3.41
759 766 6.192234 ACAAAGCATCTCAATCAATCAGAC 57.808 37.500 0.00 0.00 0.00 3.51
760 767 8.515695 AATACAAAGCATCTCAATCAATCAGA 57.484 30.769 0.00 0.00 0.00 3.27
761 768 9.582431 AAAATACAAAGCATCTCAATCAATCAG 57.418 29.630 0.00 0.00 0.00 2.90
762 769 9.577110 GAAAATACAAAGCATCTCAATCAATCA 57.423 29.630 0.00 0.00 0.00 2.57
763 770 8.740369 CGAAAATACAAAGCATCTCAATCAATC 58.260 33.333 0.00 0.00 0.00 2.67
764 771 7.703621 CCGAAAATACAAAGCATCTCAATCAAT 59.296 33.333 0.00 0.00 0.00 2.57
765 772 7.028962 CCGAAAATACAAAGCATCTCAATCAA 58.971 34.615 0.00 0.00 0.00 2.57
766 773 6.150976 ACCGAAAATACAAAGCATCTCAATCA 59.849 34.615 0.00 0.00 0.00 2.57
767 774 6.470235 CACCGAAAATACAAAGCATCTCAATC 59.530 38.462 0.00 0.00 0.00 2.67
768 775 6.150976 TCACCGAAAATACAAAGCATCTCAAT 59.849 34.615 0.00 0.00 0.00 2.57
769 776 5.471797 TCACCGAAAATACAAAGCATCTCAA 59.528 36.000 0.00 0.00 0.00 3.02
770 777 5.000591 TCACCGAAAATACAAAGCATCTCA 58.999 37.500 0.00 0.00 0.00 3.27
771 778 5.545658 TCACCGAAAATACAAAGCATCTC 57.454 39.130 0.00 0.00 0.00 2.75
772 779 6.515272 AATCACCGAAAATACAAAGCATCT 57.485 33.333 0.00 0.00 0.00 2.90
773 780 7.581011 AAAATCACCGAAAATACAAAGCATC 57.419 32.000 0.00 0.00 0.00 3.91
774 781 7.961325 AAAAATCACCGAAAATACAAAGCAT 57.039 28.000 0.00 0.00 0.00 3.79
797 804 9.170890 ACACCAGGGATCAGATCTATTATAAAA 57.829 33.333 10.36 0.00 0.00 1.52
798 805 8.742125 ACACCAGGGATCAGATCTATTATAAA 57.258 34.615 10.36 0.00 0.00 1.40
799 806 9.837681 TTACACCAGGGATCAGATCTATTATAA 57.162 33.333 10.36 0.00 0.00 0.98
800 807 9.837681 TTTACACCAGGGATCAGATCTATTATA 57.162 33.333 10.36 0.00 0.00 0.98
801 808 8.742125 TTTACACCAGGGATCAGATCTATTAT 57.258 34.615 10.36 0.00 0.00 1.28
802 809 8.561536 TTTTACACCAGGGATCAGATCTATTA 57.438 34.615 10.36 0.00 0.00 0.98
803 810 7.451731 TTTTACACCAGGGATCAGATCTATT 57.548 36.000 10.36 0.00 0.00 1.73
804 811 7.639062 ATTTTACACCAGGGATCAGATCTAT 57.361 36.000 10.36 0.00 0.00 1.98
805 812 7.451731 AATTTTACACCAGGGATCAGATCTA 57.548 36.000 10.36 0.00 0.00 1.98
806 813 5.983333 ATTTTACACCAGGGATCAGATCT 57.017 39.130 10.36 0.00 0.00 2.75
807 814 6.681368 GCAAATTTTACACCAGGGATCAGATC 60.681 42.308 1.18 1.18 0.00 2.75
808 815 5.127682 GCAAATTTTACACCAGGGATCAGAT 59.872 40.000 0.00 0.00 0.00 2.90
809 816 4.462483 GCAAATTTTACACCAGGGATCAGA 59.538 41.667 0.00 0.00 0.00 3.27
810 817 4.220382 TGCAAATTTTACACCAGGGATCAG 59.780 41.667 0.00 0.00 0.00 2.90
811 818 4.021544 GTGCAAATTTTACACCAGGGATCA 60.022 41.667 9.13 0.00 0.00 2.92
812 819 4.220602 AGTGCAAATTTTACACCAGGGATC 59.779 41.667 14.57 0.00 34.83 3.36
813 820 4.021192 CAGTGCAAATTTTACACCAGGGAT 60.021 41.667 14.57 0.00 34.83 3.85
814 821 3.320541 CAGTGCAAATTTTACACCAGGGA 59.679 43.478 14.57 0.00 34.83 4.20
815 822 3.320541 TCAGTGCAAATTTTACACCAGGG 59.679 43.478 14.57 5.80 34.83 4.45
816 823 4.582701 TCAGTGCAAATTTTACACCAGG 57.417 40.909 14.57 7.62 34.83 4.45
817 824 6.900568 TTTTCAGTGCAAATTTTACACCAG 57.099 33.333 14.57 9.72 34.83 4.00
842 849 2.781403 AGGGCCAATGCTGGAAATAT 57.219 45.000 6.18 0.00 46.92 1.28
846 853 0.899717 GTGAAGGGCCAATGCTGGAA 60.900 55.000 6.18 0.00 46.92 3.53
864 871 3.906846 TGGGATGGCAATTTACAAAAGGT 59.093 39.130 0.00 0.00 0.00 3.50
866 873 4.892433 TGTGGGATGGCAATTTACAAAAG 58.108 39.130 0.00 0.00 0.00 2.27
946 953 3.181967 CTACAGCCTGCGCGTGAC 61.182 66.667 8.43 0.00 41.18 3.67
1342 1359 4.561938 CCATCAAACACCGGAGTAACTACA 60.562 45.833 9.46 0.00 0.00 2.74
1349 1366 0.889186 GTGCCATCAAACACCGGAGT 60.889 55.000 9.46 2.22 0.00 3.85
1352 1369 0.240945 GAAGTGCCATCAAACACCGG 59.759 55.000 0.00 0.00 37.51 5.28
1353 1370 0.110238 CGAAGTGCCATCAAACACCG 60.110 55.000 0.00 0.00 37.51 4.94
1355 1372 0.951558 ACCGAAGTGCCATCAAACAC 59.048 50.000 0.00 0.00 37.05 3.32
1356 1373 1.234821 GACCGAAGTGCCATCAAACA 58.765 50.000 0.00 0.00 0.00 2.83
1360 1377 1.374125 CACGACCGAAGTGCCATCA 60.374 57.895 0.00 0.00 32.52 3.07
1367 1384 1.625616 CGATAAAGCACGACCGAAGT 58.374 50.000 0.00 0.00 0.00 3.01
1368 1385 0.921347 CCGATAAAGCACGACCGAAG 59.079 55.000 0.00 0.00 0.00 3.79
1386 1403 5.788055 ACAAACAAATTTTTCGGACAACC 57.212 34.783 0.00 0.00 0.00 3.77
1390 1407 5.006261 CCTCCAACAAACAAATTTTTCGGAC 59.994 40.000 0.00 0.00 0.00 4.79
1391 1408 5.105310 TCCTCCAACAAACAAATTTTTCGGA 60.105 36.000 0.00 0.00 0.00 4.55
1393 1410 6.654793 TTCCTCCAACAAACAAATTTTTCG 57.345 33.333 0.00 0.00 0.00 3.46
1402 1419 2.627699 GCCTGAATTCCTCCAACAAACA 59.372 45.455 2.27 0.00 0.00 2.83
1403 1420 2.893489 AGCCTGAATTCCTCCAACAAAC 59.107 45.455 2.27 0.00 0.00 2.93
1405 1422 2.978156 AGCCTGAATTCCTCCAACAA 57.022 45.000 2.27 0.00 0.00 2.83
1446 1510 0.954452 CTTGTCAAGGCAGGTTCACC 59.046 55.000 4.52 0.00 0.00 4.02
1491 1555 7.046292 TGCTCACAACTTCTGTACTTACTAA 57.954 36.000 0.00 0.00 36.10 2.24
1503 1567 2.945668 AGTGGTTCTTGCTCACAACTTC 59.054 45.455 0.00 0.00 34.17 3.01
1538 1606 1.804151 TGAAAATTTCCAGTCCTCGCG 59.196 47.619 0.00 0.00 0.00 5.87
1548 1616 4.462483 TCATACAGGCCAGTGAAAATTTCC 59.538 41.667 11.70 0.00 0.00 3.13
1592 1660 8.678199 AGGCTTGCTTCTTTCATAAACTATAAC 58.322 33.333 0.00 0.00 0.00 1.89
1623 1692 6.709846 ACTTGCATTAGAGAGAAATCCATAGC 59.290 38.462 0.00 0.00 0.00 2.97
1624 1693 8.674263 AACTTGCATTAGAGAGAAATCCATAG 57.326 34.615 0.00 0.00 0.00 2.23
1626 1695 6.545298 GGAACTTGCATTAGAGAGAAATCCAT 59.455 38.462 0.00 0.00 0.00 3.41
1628 1697 5.298026 GGGAACTTGCATTAGAGAGAAATCC 59.702 44.000 0.00 0.00 0.00 3.01
1674 1743 7.879160 TCACAAAAGTAACAATTACTCGGGTAT 59.121 33.333 0.00 0.00 45.33 2.73
1678 1747 7.749126 GGAATCACAAAAGTAACAATTACTCGG 59.251 37.037 1.85 0.00 45.33 4.63
1679 1748 8.504005 AGGAATCACAAAAGTAACAATTACTCG 58.496 33.333 1.85 0.00 45.33 4.18
1747 1816 2.028294 AGTCTGACAAGGACATGCTCAG 60.028 50.000 10.88 0.00 36.29 3.35
1772 1848 3.840763 GCGATGAGTGTTTAAAGAAAGCG 59.159 43.478 0.00 0.00 0.00 4.68
1785 1861 4.447054 CCAGCTTATAAAGAGCGATGAGTG 59.553 45.833 0.00 0.00 44.71 3.51
1861 1937 7.009357 GTGTTAAGTCGCTTCCAACTTAGATAG 59.991 40.741 0.00 0.00 38.73 2.08
1950 2031 5.369409 ACTAGTAAGGTAGCCCCAAATTC 57.631 43.478 0.00 0.00 34.66 2.17
2043 2124 1.134007 TGGGAGATGCAGGCATGTAAG 60.134 52.381 12.12 0.00 36.70 2.34
2046 2127 0.178998 GATGGGAGATGCAGGCATGT 60.179 55.000 12.12 7.66 36.70 3.21
2091 2191 9.305925 CTACGAAGCATGCAGATATTTATGATA 57.694 33.333 21.98 0.00 0.00 2.15
2351 2452 3.996363 GACCAAATCAAGAATGGCCAAAC 59.004 43.478 10.96 7.02 37.77 2.93
2352 2453 3.903090 AGACCAAATCAAGAATGGCCAAA 59.097 39.130 10.96 0.00 37.77 3.28
2405 2522 3.729217 GGTTTCTGCGAAAGTAACAAAGC 59.271 43.478 9.24 0.00 37.78 3.51
2495 2612 5.666969 TCTTTGTGTGTACCAGAAAATCG 57.333 39.130 7.65 0.00 36.05 3.34
2703 2820 0.392706 TCGTGCACTCTGTGTCCATT 59.607 50.000 16.19 0.00 35.75 3.16
2861 2979 5.500234 AGATGCAGTAAAATCACTAGGCAA 58.500 37.500 0.00 0.00 32.97 4.52
3086 3204 2.224606 CGCCCTATGTTGCATCAGAAT 58.775 47.619 3.50 0.00 0.00 2.40
3390 3509 1.597854 TGCCCTTGCAACAGAGTCG 60.598 57.895 0.00 0.00 46.66 4.18
3447 3569 4.388577 AACAAAATTACCAGCTCCTCCT 57.611 40.909 0.00 0.00 0.00 3.69
3448 3570 4.767409 AGAAACAAAATTACCAGCTCCTCC 59.233 41.667 0.00 0.00 0.00 4.30
3449 3571 5.335976 CCAGAAACAAAATTACCAGCTCCTC 60.336 44.000 0.00 0.00 0.00 3.71
3574 3696 2.160721 TTAGGATCTTCAGGCTCCGT 57.839 50.000 0.00 0.00 34.13 4.69
3620 3742 5.372343 TCTGCAAGAGCTTGGGATATTTA 57.628 39.130 11.78 0.00 38.67 1.40
3656 3778 5.127491 TCCTTTCACGTAAATGAGGTGTTT 58.873 37.500 0.00 0.00 43.16 2.83
3693 3815 1.944430 GCAAGGTACAACTTCTCCCGG 60.944 57.143 0.00 0.00 0.00 5.73
3703 3825 1.073284 GGTCAAGGGAGCAAGGTACAA 59.927 52.381 0.00 0.00 41.19 2.41
3786 3908 3.591196 TTTGTGCACATAGCCATTTCC 57.409 42.857 22.39 0.00 44.83 3.13
3862 3984 5.806654 AAGACACAAAAAGGGCATATGTT 57.193 34.783 4.29 0.00 0.00 2.71
4290 4416 4.635765 GGTGAGCACAACAATTCTGCTATA 59.364 41.667 2.75 0.00 41.40 1.31
4291 4417 3.441572 GGTGAGCACAACAATTCTGCTAT 59.558 43.478 2.75 0.00 41.40 2.97
4354 4484 3.423154 GCACGGTTCCTGCCTTCG 61.423 66.667 0.00 0.00 0.00 3.79
4682 4818 6.211184 ACAATCATGCTTTCCCAAAATACTCA 59.789 34.615 0.00 0.00 0.00 3.41
4729 4866 6.018589 TCACTGATCTAGAACTGAACACAG 57.981 41.667 12.82 0.00 37.63 3.66
4776 4913 8.997960 CATTGAAATTTTGGTCGAAAGTTTTTG 58.002 29.630 3.06 0.18 34.56 2.44
4806 4943 8.159447 TGAATAGCACTTATTCTTATGGCAGAT 58.841 33.333 0.00 0.00 45.24 2.90
4886 5023 7.145323 AGTACCATTCACACAAAATACAAAGC 58.855 34.615 0.00 0.00 0.00 3.51
4949 5086 2.034939 CCACAGCAGAAGACATGCAAAA 59.965 45.455 0.00 0.00 46.31 2.44
4970 5107 4.095483 ACAGTTTATATGCTGCAGTTGAGC 59.905 41.667 16.64 1.04 36.26 4.26
4994 5131 8.076178 CGTAGAAGAGGAACAAATGTGAAAATT 58.924 33.333 0.00 0.00 0.00 1.82
5019 5156 6.520272 AGAAGAGGGATAAATGAGACATTCG 58.480 40.000 0.00 0.00 0.00 3.34
5082 5225 3.244770 ACGAACAGGGACCAAATGTACAT 60.245 43.478 1.41 1.41 0.00 2.29
5085 5228 3.618019 GCTACGAACAGGGACCAAATGTA 60.618 47.826 0.00 0.00 0.00 2.29
5086 5229 2.874457 GCTACGAACAGGGACCAAATGT 60.874 50.000 0.00 0.00 0.00 2.71
5097 5240 1.131126 CCATTTGGCAGCTACGAACAG 59.869 52.381 0.00 0.00 0.00 3.16
5284 5469 8.738106 CATCTCATCTAGTACAGATATGCAGAA 58.262 37.037 0.00 0.00 42.40 3.02
5464 5685 4.631813 CAGTCCCTTTGTTCCTTTATCTCG 59.368 45.833 0.00 0.00 0.00 4.04
5473 5694 3.202151 TGATATCCCAGTCCCTTTGTTCC 59.798 47.826 0.00 0.00 0.00 3.62
5527 5748 2.848691 TCCAAACCGAACCGTGTAAAT 58.151 42.857 0.00 0.00 0.00 1.40
5533 5754 0.107557 AGTGTTCCAAACCGAACCGT 60.108 50.000 0.00 0.00 41.24 4.83
5536 5757 0.666374 CCCAGTGTTCCAAACCGAAC 59.334 55.000 0.00 0.00 42.10 3.95
5580 5801 7.838079 ATTTCTACATACTCTCAGAGCTGAT 57.162 36.000 11.00 0.00 39.13 2.90
5606 5829 8.008187 GTCAAAATATGGCAAGGAAAATGTCCA 61.008 37.037 0.00 0.00 40.53 4.02
5630 5853 0.107165 GGGCCATACAACTCCCTGTC 60.107 60.000 4.39 0.00 35.87 3.51
6053 6296 3.530104 GCGCGGTCGTACGAGTTG 61.530 66.667 20.18 12.34 38.14 3.16
6083 6326 5.679734 ATAACCATCATGCGACATTCTTC 57.320 39.130 0.00 0.00 0.00 2.87
6091 6334 2.874086 CTGCTGAATAACCATCATGCGA 59.126 45.455 0.00 0.00 0.00 5.10
6108 6351 3.324846 TGGGAGCGATCATATAAACTGCT 59.675 43.478 1.84 0.00 0.00 4.24
6125 6368 1.220169 CGCGATCTGATGCTTGGGAG 61.220 60.000 0.00 0.00 0.00 4.30
6126 6369 1.227350 CGCGATCTGATGCTTGGGA 60.227 57.895 0.00 0.00 0.00 4.37
6127 6370 1.493950 GACGCGATCTGATGCTTGGG 61.494 60.000 15.93 0.00 0.00 4.12
6128 6371 0.529337 AGACGCGATCTGATGCTTGG 60.529 55.000 15.93 0.00 35.81 3.61
6129 6372 0.851495 GAGACGCGATCTGATGCTTG 59.149 55.000 15.93 0.00 38.00 4.01
6130 6373 0.743688 AGAGACGCGATCTGATGCTT 59.256 50.000 15.93 0.00 38.00 3.91
6131 6374 0.743688 AAGAGACGCGATCTGATGCT 59.256 50.000 15.93 2.58 38.00 3.79
6132 6375 1.127701 GAAGAGACGCGATCTGATGC 58.872 55.000 15.93 0.12 38.00 3.91
6133 6376 2.032675 TGAGAAGAGACGCGATCTGATG 59.967 50.000 15.93 0.00 38.00 3.07
6136 6379 1.400142 ACTGAGAAGAGACGCGATCTG 59.600 52.381 15.93 6.01 38.00 2.90
6202 6445 9.394767 TGATGTTGCACAATACTACTGAATAAT 57.605 29.630 0.00 0.00 0.00 1.28
6215 6460 3.194755 ACAGCATCATGATGTTGCACAAT 59.805 39.130 37.57 23.07 45.71 2.71
6217 6462 2.164338 ACAGCATCATGATGTTGCACA 58.836 42.857 37.57 0.00 45.71 4.57
6250 6499 4.326504 AAAGCAACCACCATTCAGAAAG 57.673 40.909 0.00 0.00 0.00 2.62
6346 6595 5.989168 CGATATAACTGAGGCACCAATAACA 59.011 40.000 0.00 0.00 0.00 2.41
6357 6606 9.261180 TGAGAAAATTAAGCGATATAACTGAGG 57.739 33.333 0.00 0.00 0.00 3.86
6369 6618 8.679288 ATTTTCACTGATGAGAAAATTAAGCG 57.321 30.769 7.17 0.00 44.80 4.68
6391 6640 5.679601 GTTTGAGAGAGAGAGGCCATATTT 58.320 41.667 5.01 0.00 0.00 1.40
6640 6943 6.902341 TCTTTGTGAAACTTCATATGTGAGC 58.098 36.000 1.90 0.00 39.73 4.26
6646 6951 8.023128 CGGTCATTTCTTTGTGAAACTTCATAT 58.977 33.333 0.00 0.00 46.08 1.78
6671 6976 2.519377 TTATCCAGAATACCACGGCG 57.481 50.000 4.80 4.80 0.00 6.46
6761 7066 4.634004 TGACGCTTGTGGTATTCTTAATGG 59.366 41.667 0.00 0.00 0.00 3.16
6764 7069 7.101054 AGTATTGACGCTTGTGGTATTCTTAA 58.899 34.615 0.00 0.00 0.00 1.85
6778 7083 3.925379 TCATGTGTGAAGTATTGACGCT 58.075 40.909 0.00 0.00 43.22 5.07
6781 7086 8.598924 CATTCTACTCATGTGTGAAGTATTGAC 58.401 37.037 10.62 0.00 33.05 3.18
6795 7100 3.491619 CCTGGTCGACCATTCTACTCATG 60.492 52.174 36.21 20.07 46.46 3.07
6798 7103 2.100989 ACCTGGTCGACCATTCTACTC 58.899 52.381 36.21 6.73 46.46 2.59
6799 7104 2.233305 ACCTGGTCGACCATTCTACT 57.767 50.000 36.21 12.98 46.46 2.57
6800 7105 3.000727 CAAACCTGGTCGACCATTCTAC 58.999 50.000 36.21 8.29 46.46 2.59
6801 7106 2.901192 TCAAACCTGGTCGACCATTCTA 59.099 45.455 36.21 17.15 46.46 2.10
6802 7107 1.697432 TCAAACCTGGTCGACCATTCT 59.303 47.619 36.21 20.37 46.46 2.40
6803 7108 2.178912 TCAAACCTGGTCGACCATTC 57.821 50.000 36.21 10.27 46.46 2.67
6804 7109 2.879103 ATCAAACCTGGTCGACCATT 57.121 45.000 36.21 25.66 46.46 3.16
6805 7110 2.093128 GGTATCAAACCTGGTCGACCAT 60.093 50.000 36.21 21.18 46.46 3.55
6807 7112 2.019948 GGTATCAAACCTGGTCGACC 57.980 55.000 28.17 28.17 45.75 4.79
6876 7181 0.244450 CATGGTTCCATGTGCACCAC 59.756 55.000 20.05 3.13 43.44 4.16
6877 7182 2.656049 CATGGTTCCATGTGCACCA 58.344 52.632 20.05 2.97 44.75 4.17
6956 7262 4.141846 GGGTAGGTACAAGGGTTTACTAGC 60.142 50.000 0.00 0.00 0.00 3.42
7030 7336 8.662141 TCTTTGGTAAATCGAGTAAATGCTTAC 58.338 33.333 0.00 0.00 38.16 2.34


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

AutoCloner maintained by Alex Coulton.