Multiple sequence alignment - TraesCS1D01G416100

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 TraesCS1D01G416100 chr1D 100.000 3728 0 0 1 3728 475170598 475174325 0.000000e+00 6885.0
1 TraesCS1D01G416100 chr1D 73.420 1392 290 57 1208 2569 473623544 473622203 8.000000e-122 448.0
2 TraesCS1D01G416100 chr1D 72.212 1076 221 45 1208 2247 486334224 486333191 4.020000e-65 259.0
3 TraesCS1D01G416100 chr1D 100.000 112 0 0 3947 4058 475174544 475174655 1.480000e-49 207.0
4 TraesCS1D01G416100 chr1B 91.937 3609 173 44 186 3728 660452802 660456358 0.000000e+00 4944.0
5 TraesCS1D01G416100 chr1B 81.893 243 36 6 1208 1449 658511567 658511332 8.900000e-47 198.0
6 TraesCS1D01G416100 chr1B 97.321 112 3 0 3947 4058 660456405 660456516 1.490000e-44 191.0
7 TraesCS1D01G416100 chr1B 97.321 112 3 0 3947 4058 660565355 660565466 1.490000e-44 191.0
8 TraesCS1D01G416100 chr1B 90.299 134 13 0 1212 1345 658319862 658319729 4.170000e-40 176.0
9 TraesCS1D01G416100 chr1B 87.943 141 17 0 1205 1345 658403855 658403995 2.510000e-37 167.0
10 TraesCS1D01G416100 chr1B 80.864 162 28 2 2408 2569 113212637 113212479 1.530000e-24 124.0
11 TraesCS1D01G416100 chr1B 80.864 162 28 2 2408 2569 113314998 113314840 1.530000e-24 124.0
12 TraesCS1D01G416100 chr1B 80.864 162 28 2 2408 2569 113497786 113497628 1.530000e-24 124.0
13 TraesCS1D01G416100 chr1A 96.141 2669 87 6 949 3607 570855583 570858245 0.000000e+00 4344.0
14 TraesCS1D01G416100 chr1A 73.199 1388 301 50 1208 2569 567988666 567987324 1.730000e-118 436.0
15 TraesCS1D01G416100 chr1A 71.523 1510 318 67 1208 2662 583991137 583989685 1.830000e-78 303.0
16 TraesCS1D01G416100 chr1A 97.980 99 2 0 3960 4058 570858334 570858432 5.390000e-39 172.0
17 TraesCS1D01G416100 chr1A 96.825 63 2 0 3607 3669 570858268 570858330 5.550000e-19 106.0
18 TraesCS1D01G416100 chr1A 100.000 38 0 0 1074 1111 583991262 583991225 2.020000e-08 71.3
19 TraesCS1D01G416100 chrUn 80.117 171 31 2 2399 2569 372933778 372933945 1.530000e-24 124.0
20 TraesCS1D01G416100 chrUn 77.114 201 39 6 2349 2547 83253928 83254123 4.290000e-20 110.0
21 TraesCS1D01G416100 chr7A 77.612 201 38 6 2349 2547 700980660 700980465 9.220000e-22 115.0
22 TraesCS1D01G416100 chr7A 81.600 125 19 4 2349 2471 700944296 700944174 2.580000e-17 100.0
23 TraesCS1D01G416100 chr7A 72.727 297 70 9 2364 2656 701005281 701004992 5.590000e-14 89.8
24 TraesCS1D01G416100 chr7A 81.034 116 17 4 2368 2480 700963368 700963255 2.010000e-13 87.9
25 TraesCS1D01G416100 chr7A 80.734 109 13 7 2382 2486 611487266 611487162 1.210000e-10 78.7
26 TraesCS1D01G416100 chr7A 75.839 149 29 6 2418 2564 644457536 644457679 7.280000e-08 69.4
27 TraesCS1D01G416100 chr7D 77.451 204 34 9 2364 2563 611013808 611013613 1.190000e-20 111.0
28 TraesCS1D01G416100 chr5A 85.714 91 12 1 691 780 546765225 546765315 1.200000e-15 95.3
29 TraesCS1D01G416100 chr2D 94.444 54 2 1 678 730 25013347 25013294 9.350000e-12 82.4
30 TraesCS1D01G416100 chr7B 85.135 74 9 2 686 757 591068716 591068789 1.560000e-09 75.0
31 TraesCS1D01G416100 chr6B 95.238 42 2 0 675 716 497019084 497019125 2.620000e-07 67.6


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 TraesCS1D01G416100 chr1D 475170598 475174655 4057 False 3546.000000 6885 100.000 1 4058 2 chr1D.!!$F1 4057
1 TraesCS1D01G416100 chr1D 473622203 473623544 1341 True 448.000000 448 73.420 1208 2569 1 chr1D.!!$R1 1361
2 TraesCS1D01G416100 chr1D 486333191 486334224 1033 True 259.000000 259 72.212 1208 2247 1 chr1D.!!$R2 1039
3 TraesCS1D01G416100 chr1B 660452802 660456516 3714 False 2567.500000 4944 94.629 186 4058 2 chr1B.!!$F3 3872
4 TraesCS1D01G416100 chr1A 570855583 570858432 2849 False 1540.666667 4344 96.982 949 4058 3 chr1A.!!$F1 3109
5 TraesCS1D01G416100 chr1A 567987324 567988666 1342 True 436.000000 436 73.199 1208 2569 1 chr1A.!!$R1 1361

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
170 171 0.037326 CAGTGCTTTACCTCTGGCGA 60.037 55.0 0.00 0.0 0.00 5.54 F
173 174 0.107703 TGCTTTACCTCTGGCGATGG 60.108 55.0 0.00 0.0 0.00 3.51 F
777 798 0.108396 TCATATGGATGGGGTGTGCG 59.892 55.0 2.13 0.0 33.49 5.34 F
779 800 0.179020 ATATGGATGGGGTGTGCGTG 60.179 55.0 0.00 0.0 0.00 5.34 F
832 859 0.294887 GCGACTTCGATAACACTGCG 59.705 55.0 2.02 0.0 43.02 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1963 2029 1.613437 CCATGAGACAACAACCCCAAC 59.387 52.381 0.00 0.00 0.00 3.77 R
2272 2348 9.788960 GATTAAGTCTAACCCAATGTTGATTTC 57.211 33.333 0.00 0.00 37.83 2.17 R
2623 2700 4.229096 GCATCTCGAGAAGCTCTATTCTG 58.771 47.826 29.96 16.17 39.63 3.02 R
2907 2984 1.022982 TGGAATCTTGAGCTGCTGCG 61.023 55.000 7.01 0.00 45.42 5.18 R
3164 3241 0.974010 CCCTCGTGCTGGGTTAGGTA 60.974 60.000 0.00 0.00 39.82 3.08 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
51 52 5.731599 TTTTGAATTCGCAAGCATTTTGT 57.268 30.435 0.04 0.00 31.97 2.83
52 53 6.834959 TTTTGAATTCGCAAGCATTTTGTA 57.165 29.167 0.04 0.00 31.97 2.41
53 54 6.834959 TTTGAATTCGCAAGCATTTTGTAA 57.165 29.167 0.04 0.00 31.97 2.41
54 55 6.834959 TTGAATTCGCAAGCATTTTGTAAA 57.165 29.167 0.04 0.00 31.97 2.01
55 56 7.418840 TTGAATTCGCAAGCATTTTGTAAAT 57.581 28.000 0.04 0.00 31.97 1.40
56 57 7.418840 TGAATTCGCAAGCATTTTGTAAATT 57.581 28.000 0.04 0.00 31.97 1.82
57 58 7.859598 TGAATTCGCAAGCATTTTGTAAATTT 58.140 26.923 0.04 0.00 31.97 1.82
58 59 8.008844 TGAATTCGCAAGCATTTTGTAAATTTC 58.991 29.630 0.04 0.00 31.97 2.17
59 60 7.656707 ATTCGCAAGCATTTTGTAAATTTCT 57.343 28.000 0.00 0.00 37.18 2.52
60 61 8.755696 ATTCGCAAGCATTTTGTAAATTTCTA 57.244 26.923 0.00 0.00 37.18 2.10
61 62 8.581057 TTCGCAAGCATTTTGTAAATTTCTAA 57.419 26.923 0.00 0.00 37.18 2.10
62 63 8.581057 TCGCAAGCATTTTGTAAATTTCTAAA 57.419 26.923 0.00 0.00 37.18 1.85
63 64 9.202273 TCGCAAGCATTTTGTAAATTTCTAAAT 57.798 25.926 0.00 0.00 37.18 1.40
121 122 9.040939 ACACAATTCAAAATAAAAGTAACTGCC 57.959 29.630 0.00 0.00 0.00 4.85
122 123 9.039870 CACAATTCAAAATAAAAGTAACTGCCA 57.960 29.630 0.00 0.00 0.00 4.92
123 124 9.606631 ACAATTCAAAATAAAAGTAACTGCCAA 57.393 25.926 0.00 0.00 0.00 4.52
151 152 7.637709 AACCAACGAAAGAAAATATTTCAGC 57.362 32.000 0.10 0.00 36.63 4.26
152 153 6.744112 ACCAACGAAAGAAAATATTTCAGCA 58.256 32.000 0.10 0.00 36.63 4.41
153 154 6.863126 ACCAACGAAAGAAAATATTTCAGCAG 59.137 34.615 0.10 0.00 36.63 4.24
154 155 6.863126 CCAACGAAAGAAAATATTTCAGCAGT 59.137 34.615 0.10 0.00 36.63 4.40
155 156 7.148918 CCAACGAAAGAAAATATTTCAGCAGTG 60.149 37.037 0.10 0.00 36.63 3.66
156 157 5.858581 ACGAAAGAAAATATTTCAGCAGTGC 59.141 36.000 7.13 7.13 36.63 4.40
157 158 6.088824 CGAAAGAAAATATTTCAGCAGTGCT 58.911 36.000 13.14 13.14 40.77 4.40
158 159 6.583806 CGAAAGAAAATATTTCAGCAGTGCTT 59.416 34.615 16.89 3.15 36.40 3.91
159 160 7.115378 CGAAAGAAAATATTTCAGCAGTGCTTT 59.885 33.333 16.89 4.28 36.40 3.51
160 161 9.410556 GAAAGAAAATATTTCAGCAGTGCTTTA 57.589 29.630 16.89 3.50 36.40 1.85
161 162 8.748380 AAGAAAATATTTCAGCAGTGCTTTAC 57.252 30.769 16.89 4.69 36.40 2.01
162 163 7.315890 AGAAAATATTTCAGCAGTGCTTTACC 58.684 34.615 16.89 2.10 36.40 2.85
163 164 6.840780 AAATATTTCAGCAGTGCTTTACCT 57.159 33.333 16.89 2.01 36.40 3.08
164 165 6.442513 AATATTTCAGCAGTGCTTTACCTC 57.557 37.500 16.89 0.00 36.40 3.85
165 166 3.492102 TTTCAGCAGTGCTTTACCTCT 57.508 42.857 16.89 0.00 36.40 3.69
166 167 2.462456 TCAGCAGTGCTTTACCTCTG 57.538 50.000 16.89 2.25 36.40 3.35
167 168 1.002430 TCAGCAGTGCTTTACCTCTGG 59.998 52.381 16.89 0.35 36.40 3.86
168 169 0.322008 AGCAGTGCTTTACCTCTGGC 60.322 55.000 13.14 0.00 33.89 4.85
169 170 1.639298 GCAGTGCTTTACCTCTGGCG 61.639 60.000 8.18 0.00 0.00 5.69
170 171 0.037326 CAGTGCTTTACCTCTGGCGA 60.037 55.000 0.00 0.00 0.00 5.54
171 172 0.905357 AGTGCTTTACCTCTGGCGAT 59.095 50.000 0.00 0.00 0.00 4.58
172 173 1.009829 GTGCTTTACCTCTGGCGATG 58.990 55.000 0.00 0.00 0.00 3.84
173 174 0.107703 TGCTTTACCTCTGGCGATGG 60.108 55.000 0.00 0.00 0.00 3.51
174 175 0.815615 GCTTTACCTCTGGCGATGGG 60.816 60.000 0.00 0.00 0.00 4.00
175 176 0.815615 CTTTACCTCTGGCGATGGGC 60.816 60.000 0.00 0.00 42.51 5.36
184 185 3.846180 GCGATGGGCCAATGATGT 58.154 55.556 11.89 0.00 34.80 3.06
185 186 3.019964 GCGATGGGCCAATGATGTA 57.980 52.632 11.89 0.00 34.80 2.29
186 187 0.877071 GCGATGGGCCAATGATGTAG 59.123 55.000 11.89 0.00 34.80 2.74
187 188 0.877071 CGATGGGCCAATGATGTAGC 59.123 55.000 11.89 0.00 0.00 3.58
188 189 1.544093 CGATGGGCCAATGATGTAGCT 60.544 52.381 11.89 0.00 0.00 3.32
189 190 2.157738 GATGGGCCAATGATGTAGCTC 58.842 52.381 11.89 0.00 0.00 4.09
190 191 0.183492 TGGGCCAATGATGTAGCTCC 59.817 55.000 2.13 0.00 0.00 4.70
202 203 4.657504 TGATGTAGCTCCTTCCTCATGATT 59.342 41.667 0.00 0.00 0.00 2.57
237 238 8.438676 TTTTGTTTCTTTGTTCTGTTTGGAAA 57.561 26.923 0.00 0.00 0.00 3.13
555 575 7.559533 TGCCATGTACATTGTTTTGGATAGTAT 59.440 33.333 13.86 0.00 0.00 2.12
557 577 7.862372 CCATGTACATTGTTTTGGATAGTATGC 59.138 37.037 5.37 0.00 0.00 3.14
560 580 8.240682 TGTACATTGTTTTGGATAGTATGCAAC 58.759 33.333 15.83 7.87 40.40 4.17
567 587 5.554822 TTGGATAGTATGCAACGTTTTCC 57.445 39.130 12.58 0.00 35.60 3.13
573 593 7.642586 GGATAGTATGCAACGTTTTCCATAAAC 59.357 37.037 0.00 0.00 0.00 2.01
593 613 1.002900 CGTGAACATTGTTGCGAACCT 60.003 47.619 6.80 0.00 0.00 3.50
594 614 2.650608 GTGAACATTGTTGCGAACCTC 58.349 47.619 6.80 0.00 0.00 3.85
603 624 2.432628 GCGAACCTCCTGTGGTCG 60.433 66.667 0.00 0.00 39.83 4.79
605 626 2.663196 GAACCTCCTGTGGTCGGG 59.337 66.667 0.00 0.00 39.83 5.14
612 633 0.763604 TCCTGTGGTCGGGTGGTTAA 60.764 55.000 0.00 0.00 40.77 2.01
613 634 0.321298 CCTGTGGTCGGGTGGTTAAG 60.321 60.000 0.00 0.00 35.48 1.85
615 636 1.278127 CTGTGGTCGGGTGGTTAAGAT 59.722 52.381 0.00 0.00 0.00 2.40
618 639 1.276989 TGGTCGGGTGGTTAAGATGAC 59.723 52.381 0.00 0.00 0.00 3.06
620 641 2.289819 GGTCGGGTGGTTAAGATGACAA 60.290 50.000 0.00 0.00 0.00 3.18
622 643 3.374058 GTCGGGTGGTTAAGATGACAATG 59.626 47.826 0.00 0.00 0.00 2.82
623 644 2.682856 CGGGTGGTTAAGATGACAATGG 59.317 50.000 0.00 0.00 0.00 3.16
628 649 5.236478 GGTGGTTAAGATGACAATGGTATCG 59.764 44.000 0.00 0.00 0.00 2.92
631 652 5.295787 GGTTAAGATGACAATGGTATCGCAA 59.704 40.000 0.00 0.00 0.00 4.85
633 654 3.206150 AGATGACAATGGTATCGCAACC 58.794 45.455 0.00 0.00 40.19 3.77
636 657 2.297701 GACAATGGTATCGCAACCCAT 58.702 47.619 3.87 0.00 40.68 4.00
639 660 2.260844 ATGGTATCGCAACCCATCAG 57.739 50.000 3.87 0.00 38.90 2.90
671 692 8.589335 AGTTGTATACTTAATATTGGTGCTCG 57.411 34.615 4.17 0.00 31.29 5.03
675 696 4.818534 ACTTAATATTGGTGCTCGCATG 57.181 40.909 0.00 0.00 0.00 4.06
676 697 4.199310 ACTTAATATTGGTGCTCGCATGT 58.801 39.130 0.00 0.00 0.00 3.21
677 698 5.364778 ACTTAATATTGGTGCTCGCATGTA 58.635 37.500 0.00 0.00 0.00 2.29
678 699 5.466728 ACTTAATATTGGTGCTCGCATGTAG 59.533 40.000 0.00 0.00 0.00 2.74
679 700 3.751479 ATATTGGTGCTCGCATGTAGA 57.249 42.857 0.00 0.00 0.00 2.59
680 701 1.656652 ATTGGTGCTCGCATGTAGAC 58.343 50.000 0.00 0.00 0.00 2.59
681 702 0.735978 TTGGTGCTCGCATGTAGACG 60.736 55.000 0.00 0.00 0.00 4.18
682 703 1.153823 GGTGCTCGCATGTAGACGT 60.154 57.895 0.00 0.00 0.00 4.34
684 705 0.640768 GTGCTCGCATGTAGACGTTC 59.359 55.000 0.00 0.00 0.00 3.95
685 706 0.457853 TGCTCGCATGTAGACGTTCC 60.458 55.000 0.00 0.00 0.00 3.62
686 707 1.146358 GCTCGCATGTAGACGTTCCC 61.146 60.000 0.00 0.00 0.00 3.97
687 708 0.172578 CTCGCATGTAGACGTTCCCA 59.827 55.000 0.00 0.00 0.00 4.37
689 710 1.202371 TCGCATGTAGACGTTCCCATC 60.202 52.381 0.00 0.00 0.00 3.51
690 711 1.209128 GCATGTAGACGTTCCCATCG 58.791 55.000 0.00 0.00 0.00 3.84
692 713 2.460918 CATGTAGACGTTCCCATCGAC 58.539 52.381 0.00 0.00 0.00 4.20
693 714 1.830279 TGTAGACGTTCCCATCGACT 58.170 50.000 0.00 0.00 37.18 4.18
722 743 3.483574 CGCATGTGGTGACTTCGTAAATC 60.484 47.826 0.00 0.00 0.00 2.17
724 745 4.201724 GCATGTGGTGACTTCGTAAATCTC 60.202 45.833 0.00 0.00 0.00 2.75
725 746 4.594123 TGTGGTGACTTCGTAAATCTCA 57.406 40.909 0.00 0.00 0.00 3.27
726 747 4.951254 TGTGGTGACTTCGTAAATCTCAA 58.049 39.130 0.00 0.00 0.00 3.02
727 748 4.988540 TGTGGTGACTTCGTAAATCTCAAG 59.011 41.667 0.00 0.00 0.00 3.02
728 749 5.221362 TGTGGTGACTTCGTAAATCTCAAGA 60.221 40.000 0.00 0.00 0.00 3.02
729 750 5.869888 GTGGTGACTTCGTAAATCTCAAGAT 59.130 40.000 0.00 0.00 36.07 2.40
731 752 5.230306 GGTGACTTCGTAAATCTCAAGATCG 59.770 44.000 0.00 0.00 32.75 3.69
732 753 5.800941 GTGACTTCGTAAATCTCAAGATCGT 59.199 40.000 0.00 0.00 32.75 3.73
733 754 6.965500 GTGACTTCGTAAATCTCAAGATCGTA 59.035 38.462 0.00 0.00 32.75 3.43
734 755 7.644551 GTGACTTCGTAAATCTCAAGATCGTAT 59.355 37.037 0.00 0.00 32.75 3.06
735 756 7.644157 TGACTTCGTAAATCTCAAGATCGTATG 59.356 37.037 0.00 0.00 32.75 2.39
736 757 6.418226 ACTTCGTAAATCTCAAGATCGTATGC 59.582 38.462 0.00 0.00 32.75 3.14
742 763 2.432146 TCTCAAGATCGTATGCTGGCTT 59.568 45.455 0.00 0.00 0.00 4.35
746 767 4.122776 CAAGATCGTATGCTGGCTTAGTT 58.877 43.478 0.00 0.00 0.00 2.24
757 778 1.968493 TGGCTTAGTTTCTCGAGGTGT 59.032 47.619 13.56 0.00 0.00 4.16
763 784 6.043411 GCTTAGTTTCTCGAGGTGTTCATAT 58.957 40.000 13.56 0.00 0.00 1.78
768 789 4.590850 TCTCGAGGTGTTCATATGGATG 57.409 45.455 13.56 0.00 0.00 3.51
769 790 3.321968 TCTCGAGGTGTTCATATGGATGG 59.678 47.826 13.56 0.00 33.49 3.51
776 797 1.956477 GTTCATATGGATGGGGTGTGC 59.044 52.381 2.13 0.00 33.49 4.57
777 798 0.108396 TCATATGGATGGGGTGTGCG 59.892 55.000 2.13 0.00 33.49 5.34
779 800 0.179020 ATATGGATGGGGTGTGCGTG 60.179 55.000 0.00 0.00 0.00 5.34
782 803 3.737172 GATGGGGTGTGCGTGTGC 61.737 66.667 0.00 0.00 43.20 4.57
783 804 4.269523 ATGGGGTGTGCGTGTGCT 62.270 61.111 0.00 0.00 43.34 4.40
790 811 0.455972 GTGTGCGTGTGCTTGTGTTT 60.456 50.000 0.00 0.00 43.34 2.83
795 816 3.059188 GTGCGTGTGCTTGTGTTTATAGT 60.059 43.478 0.00 0.00 43.34 2.12
796 817 4.150980 GTGCGTGTGCTTGTGTTTATAGTA 59.849 41.667 0.00 0.00 43.34 1.82
798 819 4.201685 GCGTGTGCTTGTGTTTATAGTAGG 60.202 45.833 0.00 0.00 38.39 3.18
800 821 5.243207 GTGTGCTTGTGTTTATAGTAGGGT 58.757 41.667 0.00 0.00 0.00 4.34
804 825 6.018180 GTGCTTGTGTTTATAGTAGGGTATGC 60.018 42.308 0.00 0.00 0.00 3.14
805 826 6.126883 TGCTTGTGTTTATAGTAGGGTATGCT 60.127 38.462 0.00 0.00 0.00 3.79
824 851 2.863739 CTTGTGTGAGCGACTTCGATA 58.136 47.619 2.02 0.00 43.02 2.92
825 852 3.242518 CTTGTGTGAGCGACTTCGATAA 58.757 45.455 2.02 0.00 43.02 1.75
826 853 2.592194 TGTGTGAGCGACTTCGATAAC 58.408 47.619 2.02 0.00 39.43 1.89
827 854 2.030628 TGTGTGAGCGACTTCGATAACA 60.031 45.455 2.90 2.90 45.68 2.41
828 855 2.592194 TGTGAGCGACTTCGATAACAC 58.408 47.619 2.90 2.80 43.36 3.32
829 856 2.228103 TGTGAGCGACTTCGATAACACT 59.772 45.455 2.90 0.00 43.36 3.55
830 857 2.594654 GTGAGCGACTTCGATAACACTG 59.405 50.000 2.02 0.00 38.86 3.66
831 858 1.584308 GAGCGACTTCGATAACACTGC 59.416 52.381 2.02 0.00 43.02 4.40
832 859 0.294887 GCGACTTCGATAACACTGCG 59.705 55.000 2.02 0.00 43.02 5.18
833 860 1.614385 CGACTTCGATAACACTGCGT 58.386 50.000 0.00 0.00 43.02 5.24
836 863 3.237660 CGACTTCGATAACACTGCGTTAG 59.762 47.826 0.00 0.00 43.26 2.34
839 866 5.224888 ACTTCGATAACACTGCGTTAGAAA 58.775 37.500 0.00 0.00 43.26 2.52
840 867 5.693104 ACTTCGATAACACTGCGTTAGAAAA 59.307 36.000 0.00 0.00 43.26 2.29
844 871 7.669098 TCGATAACACTGCGTTAGAAAAATAC 58.331 34.615 0.00 0.00 43.26 1.89
849 876 6.772078 ACACTGCGTTAGAAAAATACTATGC 58.228 36.000 0.00 0.00 0.00 3.14
852 879 7.748683 CACTGCGTTAGAAAAATACTATGCAAA 59.251 33.333 0.00 0.00 34.10 3.68
855 882 9.123709 TGCGTTAGAAAAATACTATGCAAAAAG 57.876 29.630 0.00 0.00 32.70 2.27
874 904 8.603181 GCAAAAAGACATTTGTTTCTACATTGT 58.397 29.630 0.00 0.00 41.34 2.71
908 938 2.335316 TTTTACAACGCTGACAGGGT 57.665 45.000 18.72 18.72 43.70 4.34
909 939 1.873698 TTTACAACGCTGACAGGGTC 58.126 50.000 23.74 0.00 40.76 4.46
910 940 0.753867 TTACAACGCTGACAGGGTCA 59.246 50.000 23.74 10.74 40.76 4.02
921 951 2.606519 AGGGTCAACGCTGGGCTA 60.607 61.111 0.00 0.00 37.77 3.93
929 959 0.324460 AACGCTGGGCTAGGTCTACT 60.324 55.000 0.00 0.00 0.00 2.57
935 965 2.432119 GGCTAGGTCTACTGCCCTC 58.568 63.158 0.00 0.00 37.39 4.30
965 995 2.692557 CGTCACATCCTCTCTCCAGAAT 59.307 50.000 0.00 0.00 0.00 2.40
996 1027 2.027100 ACGTTCCCCAATTCTCCTTCTC 60.027 50.000 0.00 0.00 0.00 2.87
1795 1861 2.186125 CGCCTCTGCATCAGCTCA 59.814 61.111 0.00 0.00 42.74 4.26
1963 2029 2.859992 GGCACCTAAACTGGAGCTG 58.140 57.895 0.00 0.00 42.15 4.24
2055 2122 0.944311 ATCGCGCATTCGACATACCC 60.944 55.000 8.75 0.00 41.62 3.69
2316 2392 2.022129 CACGACCCGCTGAACTGTC 61.022 63.158 0.00 0.00 0.00 3.51
2499 2576 2.497107 ATTACGATGGTAACCGGACG 57.503 50.000 9.46 4.58 41.19 4.79
2623 2700 1.266124 GCGTAAACGGTTGCAAGTGC 61.266 55.000 0.00 0.00 40.23 4.40
2777 2854 0.741221 GCCTTTCCAGAGATCGCGTT 60.741 55.000 5.77 0.00 0.00 4.84
2907 2984 2.808906 ACCAGGATTTAGGAGGTTGC 57.191 50.000 0.00 0.00 0.00 4.17
3255 3332 3.653078 ATTTTCGGCGGGGTCCCA 61.653 61.111 10.98 0.00 35.37 4.37
3272 3349 1.338960 CCCATTTGTGTTTCCATGCCC 60.339 52.381 0.00 0.00 0.00 5.36
3331 3408 0.742635 TGTCTGCGCCGCATTTCATA 60.743 50.000 14.15 0.00 38.13 2.15
3337 3414 4.033990 TGCGCCGCATTTCATATTTTTA 57.966 36.364 8.16 0.00 31.71 1.52
3530 3608 2.108700 CAGTTCTGTTTTTCCGTTGCG 58.891 47.619 0.00 0.00 0.00 4.85
3661 3762 7.252612 TCTTAGTCCAATGAGTCAACCAATA 57.747 36.000 0.00 0.00 0.00 1.90
3671 3772 3.334691 AGTCAACCAATATCCACACACG 58.665 45.455 0.00 0.00 0.00 4.49
3683 3784 0.584396 CACACACGCAATGTAACGGT 59.416 50.000 0.00 0.00 40.64 4.83
3694 3795 5.379827 GCAATGTAACGGTACTCTGTTTTC 58.620 41.667 12.67 0.00 42.38 2.29
3984 4085 1.455822 TTCATGGACAAAGGGGGACT 58.544 50.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 6.116680 ACAAAATGCTTGCGAATTCAAAAA 57.883 29.167 6.22 0.00 0.00 1.94
29 30 5.731599 ACAAAATGCTTGCGAATTCAAAA 57.268 30.435 6.22 0.00 0.00 2.44
30 31 6.834959 TTACAAAATGCTTGCGAATTCAAA 57.165 29.167 6.22 0.00 0.00 2.69
31 32 6.834959 TTTACAAAATGCTTGCGAATTCAA 57.165 29.167 6.22 0.00 0.00 2.69
32 33 7.418840 AATTTACAAAATGCTTGCGAATTCA 57.581 28.000 6.22 0.00 0.00 2.57
33 34 8.223100 AGAAATTTACAAAATGCTTGCGAATTC 58.777 29.630 0.00 0.00 0.00 2.17
34 35 8.086851 AGAAATTTACAAAATGCTTGCGAATT 57.913 26.923 0.00 0.00 0.00 2.17
35 36 7.656707 AGAAATTTACAAAATGCTTGCGAAT 57.343 28.000 0.00 0.00 0.00 3.34
36 37 8.581057 TTAGAAATTTACAAAATGCTTGCGAA 57.419 26.923 0.00 0.00 0.00 4.70
37 38 8.581057 TTTAGAAATTTACAAAATGCTTGCGA 57.419 26.923 0.00 0.00 0.00 5.10
95 96 9.040939 GGCAGTTACTTTTATTTTGAATTGTGT 57.959 29.630 0.00 0.00 0.00 3.72
96 97 9.039870 TGGCAGTTACTTTTATTTTGAATTGTG 57.960 29.630 0.00 0.00 0.00 3.33
97 98 9.606631 TTGGCAGTTACTTTTATTTTGAATTGT 57.393 25.926 0.00 0.00 0.00 2.71
125 126 8.547894 GCTGAAATATTTTCTTTCGTTGGTTTT 58.452 29.630 1.43 0.00 35.77 2.43
126 127 7.708752 TGCTGAAATATTTTCTTTCGTTGGTTT 59.291 29.630 1.43 0.00 35.77 3.27
127 128 7.206687 TGCTGAAATATTTTCTTTCGTTGGTT 58.793 30.769 1.43 0.00 35.77 3.67
128 129 6.744112 TGCTGAAATATTTTCTTTCGTTGGT 58.256 32.000 1.43 0.00 35.77 3.67
129 130 6.863126 ACTGCTGAAATATTTTCTTTCGTTGG 59.137 34.615 1.43 0.00 35.77 3.77
130 131 7.617935 GCACTGCTGAAATATTTTCTTTCGTTG 60.618 37.037 1.43 0.00 35.77 4.10
131 132 6.363357 GCACTGCTGAAATATTTTCTTTCGTT 59.637 34.615 1.43 0.00 35.77 3.85
132 133 5.858581 GCACTGCTGAAATATTTTCTTTCGT 59.141 36.000 1.43 0.00 35.77 3.85
133 134 6.088824 AGCACTGCTGAAATATTTTCTTTCG 58.911 36.000 1.67 0.00 37.57 3.46
134 135 7.880059 AAGCACTGCTGAAATATTTTCTTTC 57.120 32.000 3.73 0.00 39.62 2.62
135 136 9.196552 GTAAAGCACTGCTGAAATATTTTCTTT 57.803 29.630 3.73 5.45 39.62 2.52
136 137 7.814587 GGTAAAGCACTGCTGAAATATTTTCTT 59.185 33.333 3.73 0.00 39.62 2.52
137 138 7.177392 AGGTAAAGCACTGCTGAAATATTTTCT 59.823 33.333 3.73 0.00 39.62 2.52
138 139 7.315890 AGGTAAAGCACTGCTGAAATATTTTC 58.684 34.615 3.73 0.00 39.62 2.29
139 140 7.177392 AGAGGTAAAGCACTGCTGAAATATTTT 59.823 33.333 3.73 0.00 39.62 1.82
140 141 6.660949 AGAGGTAAAGCACTGCTGAAATATTT 59.339 34.615 3.73 0.00 39.62 1.40
141 142 6.094603 CAGAGGTAAAGCACTGCTGAAATATT 59.905 38.462 3.73 0.00 39.62 1.28
142 143 5.587844 CAGAGGTAAAGCACTGCTGAAATAT 59.412 40.000 3.73 0.00 39.62 1.28
143 144 4.937620 CAGAGGTAAAGCACTGCTGAAATA 59.062 41.667 3.73 0.00 39.62 1.40
144 145 3.755378 CAGAGGTAAAGCACTGCTGAAAT 59.245 43.478 3.73 0.00 39.62 2.17
145 146 3.141398 CAGAGGTAAAGCACTGCTGAAA 58.859 45.455 3.73 0.00 39.62 2.69
146 147 2.550855 CCAGAGGTAAAGCACTGCTGAA 60.551 50.000 3.73 0.00 39.62 3.02
147 148 1.002430 CCAGAGGTAAAGCACTGCTGA 59.998 52.381 3.73 0.00 39.62 4.26
148 149 1.446907 CCAGAGGTAAAGCACTGCTG 58.553 55.000 3.73 0.00 39.62 4.41
149 150 0.322008 GCCAGAGGTAAAGCACTGCT 60.322 55.000 0.00 0.00 42.56 4.24
150 151 1.639298 CGCCAGAGGTAAAGCACTGC 61.639 60.000 0.00 0.00 0.00 4.40
151 152 0.037326 TCGCCAGAGGTAAAGCACTG 60.037 55.000 0.35 0.35 0.00 3.66
152 153 0.905357 ATCGCCAGAGGTAAAGCACT 59.095 50.000 0.00 0.00 0.00 4.40
153 154 1.009829 CATCGCCAGAGGTAAAGCAC 58.990 55.000 0.00 0.00 0.00 4.40
154 155 0.107703 CCATCGCCAGAGGTAAAGCA 60.108 55.000 0.00 0.00 0.00 3.91
155 156 0.815615 CCCATCGCCAGAGGTAAAGC 60.816 60.000 0.00 0.00 0.00 3.51
156 157 0.815615 GCCCATCGCCAGAGGTAAAG 60.816 60.000 0.00 0.00 0.00 1.85
157 158 1.223487 GCCCATCGCCAGAGGTAAA 59.777 57.895 0.00 0.00 0.00 2.01
158 159 2.908015 GCCCATCGCCAGAGGTAA 59.092 61.111 0.00 0.00 0.00 2.85
167 168 0.877071 CTACATCATTGGCCCATCGC 59.123 55.000 0.00 0.00 0.00 4.58
168 169 0.877071 GCTACATCATTGGCCCATCG 59.123 55.000 0.00 0.00 0.00 3.84
169 170 2.157738 GAGCTACATCATTGGCCCATC 58.842 52.381 0.00 0.00 0.00 3.51
170 171 1.202976 GGAGCTACATCATTGGCCCAT 60.203 52.381 0.00 0.00 0.00 4.00
171 172 0.183492 GGAGCTACATCATTGGCCCA 59.817 55.000 0.00 0.00 0.00 5.36
172 173 0.475906 AGGAGCTACATCATTGGCCC 59.524 55.000 0.00 0.00 0.00 5.80
173 174 2.225467 GAAGGAGCTACATCATTGGCC 58.775 52.381 0.00 0.00 0.00 5.36
174 175 2.158696 AGGAAGGAGCTACATCATTGGC 60.159 50.000 3.13 0.00 0.00 4.52
175 176 3.135348 TGAGGAAGGAGCTACATCATTGG 59.865 47.826 3.13 0.00 0.00 3.16
176 177 4.412796 TGAGGAAGGAGCTACATCATTG 57.587 45.455 3.13 0.00 0.00 2.82
177 178 4.657504 TCATGAGGAAGGAGCTACATCATT 59.342 41.667 3.13 0.00 33.81 2.57
178 179 4.229639 TCATGAGGAAGGAGCTACATCAT 58.770 43.478 3.13 0.00 35.88 2.45
179 180 3.646534 TCATGAGGAAGGAGCTACATCA 58.353 45.455 3.13 0.00 0.00 3.07
180 181 4.888326 ATCATGAGGAAGGAGCTACATC 57.112 45.455 0.00 0.00 0.00 3.06
181 182 5.643421 AAATCATGAGGAAGGAGCTACAT 57.357 39.130 0.00 0.00 0.00 2.29
182 183 5.190528 AGAAAATCATGAGGAAGGAGCTACA 59.809 40.000 0.00 0.00 0.00 2.74
183 184 5.679601 AGAAAATCATGAGGAAGGAGCTAC 58.320 41.667 0.09 0.00 0.00 3.58
184 185 5.664908 AGAGAAAATCATGAGGAAGGAGCTA 59.335 40.000 0.09 0.00 0.00 3.32
185 186 4.474287 AGAGAAAATCATGAGGAAGGAGCT 59.526 41.667 0.09 0.00 0.00 4.09
186 187 4.779696 AGAGAAAATCATGAGGAAGGAGC 58.220 43.478 0.09 0.00 0.00 4.70
187 188 6.098695 AGAGAGAGAAAATCATGAGGAAGGAG 59.901 42.308 0.09 0.00 0.00 3.69
188 189 5.963253 AGAGAGAGAAAATCATGAGGAAGGA 59.037 40.000 0.09 0.00 0.00 3.36
189 190 6.237887 AGAGAGAGAAAATCATGAGGAAGG 57.762 41.667 0.09 0.00 0.00 3.46
190 191 8.452534 CAAAAGAGAGAGAAAATCATGAGGAAG 58.547 37.037 0.09 0.00 0.00 3.46
202 203 9.014297 AGAACAAAGAAACAAAAGAGAGAGAAA 57.986 29.630 0.00 0.00 0.00 2.52
530 550 6.207691 ACTATCCAAAACAATGTACATGGC 57.792 37.500 9.63 0.00 0.00 4.40
531 551 7.862372 GCATACTATCCAAAACAATGTACATGG 59.138 37.037 9.63 9.19 0.00 3.66
534 554 7.929941 TGCATACTATCCAAAACAATGTACA 57.070 32.000 0.00 0.00 0.00 2.90
537 557 6.072175 ACGTTGCATACTATCCAAAACAATGT 60.072 34.615 0.00 0.00 32.69 2.71
542 562 6.307077 GGAAAACGTTGCATACTATCCAAAAC 59.693 38.462 0.00 0.00 0.00 2.43
567 587 4.215201 TCGCAACAATGTTCACGTTTATG 58.785 39.130 14.92 0.00 0.00 1.90
573 593 1.002900 AGGTTCGCAACAATGTTCACG 60.003 47.619 10.69 10.69 0.00 4.35
574 594 2.604614 GGAGGTTCGCAACAATGTTCAC 60.605 50.000 0.00 0.00 0.00 3.18
577 597 1.608590 CAGGAGGTTCGCAACAATGTT 59.391 47.619 0.00 0.00 0.00 2.71
593 613 0.763604 TTAACCACCCGACCACAGGA 60.764 55.000 0.00 0.00 0.00 3.86
594 614 0.321298 CTTAACCACCCGACCACAGG 60.321 60.000 0.00 0.00 0.00 4.00
603 624 3.697166 ACCATTGTCATCTTAACCACCC 58.303 45.455 0.00 0.00 0.00 4.61
605 626 5.277345 GCGATACCATTGTCATCTTAACCAC 60.277 44.000 0.00 0.00 0.00 4.16
612 633 3.206150 GGTTGCGATACCATTGTCATCT 58.794 45.455 1.88 0.00 38.12 2.90
613 634 2.290641 GGGTTGCGATACCATTGTCATC 59.709 50.000 8.41 0.00 40.09 2.92
615 636 1.003696 TGGGTTGCGATACCATTGTCA 59.996 47.619 8.41 0.00 40.09 3.58
618 639 2.291465 CTGATGGGTTGCGATACCATTG 59.709 50.000 12.81 7.15 44.62 2.82
622 643 3.006672 CCTGATGGGTTGCGATACC 57.993 57.895 0.00 0.00 37.47 2.73
647 668 7.042321 TGCGAGCACCAATATTAAGTATACAAC 60.042 37.037 5.50 0.00 0.00 3.32
649 670 6.517605 TGCGAGCACCAATATTAAGTATACA 58.482 36.000 5.50 0.00 0.00 2.29
650 671 7.117812 ACATGCGAGCACCAATATTAAGTATAC 59.882 37.037 0.00 0.00 0.00 1.47
653 674 5.364778 ACATGCGAGCACCAATATTAAGTA 58.635 37.500 0.00 0.00 0.00 2.24
658 679 3.809832 GTCTACATGCGAGCACCAATATT 59.190 43.478 0.00 0.00 0.00 1.28
665 686 0.640768 GAACGTCTACATGCGAGCAC 59.359 55.000 0.00 0.00 0.00 4.40
671 692 1.202371 TCGATGGGAACGTCTACATGC 60.202 52.381 3.91 0.00 44.51 4.06
675 696 1.798079 GCAGTCGATGGGAACGTCTAC 60.798 57.143 0.00 0.00 44.51 2.59
676 697 0.454600 GCAGTCGATGGGAACGTCTA 59.545 55.000 0.00 0.00 44.51 2.59
677 698 1.215647 GCAGTCGATGGGAACGTCT 59.784 57.895 0.00 0.00 44.51 4.18
678 699 2.158959 CGCAGTCGATGGGAACGTC 61.159 63.158 0.00 0.00 44.43 4.34
679 700 2.126071 CGCAGTCGATGGGAACGT 60.126 61.111 0.00 0.00 44.43 3.99
680 701 2.180769 TCGCAGTCGATGGGAACG 59.819 61.111 10.59 0.00 46.90 3.95
699 720 1.011968 TACGAAGTCACCACATGCGC 61.012 55.000 0.00 0.00 43.93 6.09
702 723 4.929211 TGAGATTTACGAAGTCACCACATG 59.071 41.667 0.00 0.00 43.93 3.21
703 724 5.147330 TGAGATTTACGAAGTCACCACAT 57.853 39.130 0.00 0.00 43.93 3.21
705 726 5.227908 TCTTGAGATTTACGAAGTCACCAC 58.772 41.667 0.00 0.00 43.93 4.16
708 729 5.800941 ACGATCTTGAGATTTACGAAGTCAC 59.199 40.000 7.35 0.00 37.04 3.67
722 743 2.522836 AGCCAGCATACGATCTTGAG 57.477 50.000 0.00 0.00 0.00 3.02
724 745 3.722147 ACTAAGCCAGCATACGATCTTG 58.278 45.455 0.00 0.00 0.00 3.02
725 746 4.408182 AACTAAGCCAGCATACGATCTT 57.592 40.909 0.00 0.00 0.00 2.40
726 747 4.100189 AGAAACTAAGCCAGCATACGATCT 59.900 41.667 0.00 0.00 0.00 2.75
727 748 4.372656 AGAAACTAAGCCAGCATACGATC 58.627 43.478 0.00 0.00 0.00 3.69
728 749 4.372656 GAGAAACTAAGCCAGCATACGAT 58.627 43.478 0.00 0.00 0.00 3.73
729 750 3.733988 CGAGAAACTAAGCCAGCATACGA 60.734 47.826 0.00 0.00 0.00 3.43
731 752 3.782046 TCGAGAAACTAAGCCAGCATAC 58.218 45.455 0.00 0.00 0.00 2.39
732 753 3.181475 CCTCGAGAAACTAAGCCAGCATA 60.181 47.826 15.71 0.00 0.00 3.14
733 754 2.419297 CCTCGAGAAACTAAGCCAGCAT 60.419 50.000 15.71 0.00 0.00 3.79
734 755 1.066858 CCTCGAGAAACTAAGCCAGCA 60.067 52.381 15.71 0.00 0.00 4.41
735 756 1.066787 ACCTCGAGAAACTAAGCCAGC 60.067 52.381 15.71 0.00 0.00 4.85
736 757 2.028930 ACACCTCGAGAAACTAAGCCAG 60.029 50.000 15.71 0.00 0.00 4.85
742 763 5.655090 TCCATATGAACACCTCGAGAAACTA 59.345 40.000 15.71 0.00 0.00 2.24
746 767 4.202253 CCATCCATATGAACACCTCGAGAA 60.202 45.833 15.71 0.00 34.84 2.87
757 778 1.476652 CGCACACCCCATCCATATGAA 60.477 52.381 3.65 0.00 34.84 2.57
763 784 3.565214 ACACGCACACCCCATCCA 61.565 61.111 0.00 0.00 0.00 3.41
768 789 3.964875 CAAGCACACGCACACCCC 61.965 66.667 0.00 0.00 42.27 4.95
769 790 3.209097 ACAAGCACACGCACACCC 61.209 61.111 0.00 0.00 42.27 4.61
776 797 4.328983 CCCTACTATAAACACAAGCACACG 59.671 45.833 0.00 0.00 0.00 4.49
777 798 5.243207 ACCCTACTATAAACACAAGCACAC 58.757 41.667 0.00 0.00 0.00 3.82
779 800 6.018180 GCATACCCTACTATAAACACAAGCAC 60.018 42.308 0.00 0.00 0.00 4.40
782 803 7.769044 ACAAGCATACCCTACTATAAACACAAG 59.231 37.037 0.00 0.00 0.00 3.16
783 804 7.551262 CACAAGCATACCCTACTATAAACACAA 59.449 37.037 0.00 0.00 0.00 3.33
790 811 5.010719 GCTCACACAAGCATACCCTACTATA 59.989 44.000 0.00 0.00 42.05 1.31
795 816 1.134818 CGCTCACACAAGCATACCCTA 60.135 52.381 0.00 0.00 42.62 3.53
796 817 0.391661 CGCTCACACAAGCATACCCT 60.392 55.000 0.00 0.00 42.62 4.34
798 819 0.721718 GTCGCTCACACAAGCATACC 59.278 55.000 0.00 0.00 42.62 2.73
800 821 2.337583 GAAGTCGCTCACACAAGCATA 58.662 47.619 0.00 0.00 42.62 3.14
804 825 1.702886 ATCGAAGTCGCTCACACAAG 58.297 50.000 0.00 0.00 39.60 3.16
805 826 2.984471 GTTATCGAAGTCGCTCACACAA 59.016 45.455 0.00 0.00 39.60 3.33
824 851 7.094975 TGCATAGTATTTTTCTAACGCAGTGTT 60.095 33.333 4.42 4.42 45.00 3.32
825 852 6.370442 TGCATAGTATTTTTCTAACGCAGTGT 59.630 34.615 0.00 0.00 45.00 3.55
826 853 6.771076 TGCATAGTATTTTTCTAACGCAGTG 58.229 36.000 0.00 0.00 45.00 3.66
828 855 8.667987 TTTTGCATAGTATTTTTCTAACGCAG 57.332 30.769 0.00 0.00 34.15 5.18
829 856 9.123709 CTTTTTGCATAGTATTTTTCTAACGCA 57.876 29.630 0.00 0.00 32.26 5.24
830 857 9.337091 TCTTTTTGCATAGTATTTTTCTAACGC 57.663 29.630 0.00 0.00 0.00 4.84
844 871 9.462174 TGTAGAAACAAATGTCTTTTTGCATAG 57.538 29.630 0.00 0.00 39.65 2.23
848 875 8.603181 ACAATGTAGAAACAAATGTCTTTTTGC 58.397 29.630 0.00 0.00 39.65 3.68
892 922 0.753867 TTGACCCTGTCAGCGTTGTA 59.246 50.000 0.00 0.00 43.69 2.41
893 923 0.814010 GTTGACCCTGTCAGCGTTGT 60.814 55.000 0.00 0.00 43.69 3.32
894 924 1.941812 GTTGACCCTGTCAGCGTTG 59.058 57.895 0.00 0.00 43.69 4.10
895 925 4.456806 GTTGACCCTGTCAGCGTT 57.543 55.556 0.00 0.00 43.69 4.84
898 928 2.031163 AGCGTTGACCCTGTCAGC 59.969 61.111 0.00 1.51 43.69 4.26
899 929 1.669115 CCAGCGTTGACCCTGTCAG 60.669 63.158 0.00 0.00 43.69 3.51
900 930 2.425592 CCAGCGTTGACCCTGTCA 59.574 61.111 0.00 0.00 41.09 3.58
901 931 2.358737 CCCAGCGTTGACCCTGTC 60.359 66.667 0.00 0.00 0.00 3.51
902 932 4.643387 GCCCAGCGTTGACCCTGT 62.643 66.667 0.00 0.00 0.00 4.00
903 933 2.859273 CTAGCCCAGCGTTGACCCTG 62.859 65.000 0.00 0.00 0.00 4.45
904 934 2.606519 TAGCCCAGCGTTGACCCT 60.607 61.111 0.00 0.00 0.00 4.34
905 935 2.125106 CTAGCCCAGCGTTGACCC 60.125 66.667 0.00 0.00 0.00 4.46
906 936 2.125106 CCTAGCCCAGCGTTGACC 60.125 66.667 0.00 0.00 0.00 4.02
907 937 1.448013 GACCTAGCCCAGCGTTGAC 60.448 63.158 0.00 0.00 0.00 3.18
908 938 0.323999 TAGACCTAGCCCAGCGTTGA 60.324 55.000 0.00 0.00 0.00 3.18
909 939 0.179108 GTAGACCTAGCCCAGCGTTG 60.179 60.000 0.00 0.00 0.00 4.10
910 940 0.324460 AGTAGACCTAGCCCAGCGTT 60.324 55.000 0.00 0.00 0.00 4.84
935 965 0.463204 AGGATGTGACGGAGATGCAG 59.537 55.000 0.00 0.00 0.00 4.41
939 969 2.582052 GAGAGAGGATGTGACGGAGAT 58.418 52.381 0.00 0.00 0.00 2.75
1182 1224 3.382803 CTTCTCTGCTGCTCCCGGG 62.383 68.421 16.85 16.85 0.00 5.73
1654 1720 2.359850 TGCTTGAGGCGCGGAAAT 60.360 55.556 8.83 0.00 45.43 2.17
1795 1861 3.637926 GAAGCGCCTAACCGTCGGT 62.638 63.158 12.23 12.23 37.65 4.69
1963 2029 1.613437 CCATGAGACAACAACCCCAAC 59.387 52.381 0.00 0.00 0.00 3.77
2272 2348 9.788960 GATTAAGTCTAACCCAATGTTGATTTC 57.211 33.333 0.00 0.00 37.83 2.17
2316 2392 8.462143 AGAACTGAATTAGTAACACATACACG 57.538 34.615 0.00 0.00 39.18 4.49
2344 2420 8.500753 AACGAAATAATATAAAGGCAGTCACA 57.499 30.769 0.00 0.00 0.00 3.58
2623 2700 4.229096 GCATCTCGAGAAGCTCTATTCTG 58.771 47.826 29.96 16.17 39.63 3.02
2907 2984 1.022982 TGGAATCTTGAGCTGCTGCG 61.023 55.000 7.01 0.00 45.42 5.18
3164 3241 0.974010 CCCTCGTGCTGGGTTAGGTA 60.974 60.000 0.00 0.00 39.82 3.08
3255 3332 5.180837 CTTCCGGGCATGGAAACACAAAT 62.181 47.826 0.00 0.00 46.95 2.32
3305 3382 3.022287 CGGCGCAGACACACTTTT 58.978 55.556 10.83 0.00 27.25 2.27
3306 3383 3.649986 GCGGCGCAGACACACTTT 61.650 61.111 29.21 0.00 27.25 2.66
3331 3408 6.428159 AGCGAGACACTCTGAAACATAAAAAT 59.572 34.615 0.00 0.00 0.00 1.82
3337 3414 3.393089 AAGCGAGACACTCTGAAACAT 57.607 42.857 0.00 0.00 0.00 2.71
3454 3532 6.234177 CAAAGAGTGAAGATTTACCCTGTCT 58.766 40.000 0.00 0.00 0.00 3.41
3503 3581 5.183228 ACGGAAAAACAGAACTGAAGAAGA 58.817 37.500 8.87 0.00 0.00 2.87
3530 3608 1.929836 CACAGAGATGAAACGCTAGCC 59.070 52.381 9.66 0.00 0.00 3.93
3661 3762 1.463056 CGTTACATTGCGTGTGTGGAT 59.537 47.619 4.94 0.00 42.24 3.41
3671 3772 5.049954 TGAAAACAGAGTACCGTTACATTGC 60.050 40.000 0.00 0.00 0.00 3.56
3683 3784 5.779241 AGGGGATGATTGAAAACAGAGTA 57.221 39.130 0.00 0.00 0.00 2.59
3694 3795 5.404466 TTGTAGCAAAAAGGGGATGATTG 57.596 39.130 0.00 0.00 0.00 2.67
3984 4085 8.741841 CAATGATATATTACCAATGCATGTCCA 58.258 33.333 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.