Multiple sequence alignment - TraesCS6A01G328700

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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 TraesCS6A01G328700 chr6A 100.000 2848 0 0 1 2848 562270855 562273702 0.000000e+00 5260.0
1 TraesCS6A01G328700 chr6A 92.298 805 36 10 16 820 562402736 562401958 0.000000e+00 1120.0
2 TraesCS6A01G328700 chr6A 81.281 1405 119 70 367 1709 562471253 562469931 0.000000e+00 1005.0
3 TraesCS6A01G328700 chr6A 85.782 844 54 35 762 1569 562488267 562487454 0.000000e+00 833.0
4 TraesCS6A01G328700 chr6A 82.803 1006 90 40 739 1709 562250473 562251430 0.000000e+00 822.0
5 TraesCS6A01G328700 chr6A 81.852 1080 95 62 820 1857 562400790 562399770 0.000000e+00 815.0
6 TraesCS6A01G328700 chr6A 80.337 178 15 9 1711 1888 291949389 291949232 1.790000e-22 117.0
7 TraesCS6A01G328700 chr6D 86.905 1596 89 55 291 1857 418770791 418769287 0.000000e+00 1679.0
8 TraesCS6A01G328700 chr6D 81.544 1425 106 69 367 1712 418883710 418882364 0.000000e+00 1029.0
9 TraesCS6A01G328700 chr6D 84.701 804 46 35 1074 1859 418732918 418733662 0.000000e+00 732.0
10 TraesCS6A01G328700 chr6D 82.024 929 69 50 721 1605 418893102 418892228 0.000000e+00 701.0
11 TraesCS6A01G328700 chr6D 82.290 559 48 23 367 888 418732252 418732796 1.210000e-118 436.0
12 TraesCS6A01G328700 chr6D 77.312 692 91 36 2087 2745 418733883 418734541 5.840000e-92 348.0
13 TraesCS6A01G328700 chr6D 88.406 69 2 5 2745 2808 105825983 105826050 8.460000e-11 78.7
14 TraesCS6A01G328700 chr6B 85.952 1203 97 35 363 1546 631192612 631193761 0.000000e+00 1219.0
15 TraesCS6A01G328700 chr6B 82.026 1402 116 70 376 1696 631535623 631534277 0.000000e+00 1068.0
16 TraesCS6A01G328700 chr6B 80.945 1375 129 72 367 1712 631741789 631740519 0.000000e+00 965.0
17 TraesCS6A01G328700 chr6B 92.916 607 29 7 943 1546 631246254 631245659 0.000000e+00 870.0
18 TraesCS6A01G328700 chr6B 90.365 602 37 10 2018 2609 630918582 630917992 0.000000e+00 771.0
19 TraesCS6A01G328700 chr6B 85.531 781 58 29 919 1694 631844110 631843380 0.000000e+00 765.0
20 TraesCS6A01G328700 chr6B 87.942 481 43 10 343 820 631247063 631246595 1.150000e-153 553.0
21 TraesCS6A01G328700 chr6B 92.063 252 19 1 1761 2012 630918953 630918703 1.260000e-93 353.0
22 TraesCS6A01G328700 chr6B 77.734 512 58 33 2087 2584 631194387 631194856 2.180000e-66 263.0
23 TraesCS6A01G328700 chr6B 88.356 146 8 6 144 283 631247437 631247295 1.760000e-37 167.0
24 TraesCS6A01G328700 chr6B 78.571 308 25 16 368 640 631846270 631845969 6.310000e-37 165.0
25 TraesCS6A01G328700 chr6B 77.580 281 34 17 2089 2360 631244984 631244724 2.960000e-30 143.0
26 TraesCS6A01G328700 chr6B 75.771 227 15 10 1633 1859 631193843 631194029 8.460000e-11 78.7
27 TraesCS6A01G328700 chr6B 82.759 87 4 6 2739 2823 613615639 613615716 1.830000e-07 67.6
28 TraesCS6A01G328700 chr2B 82.192 292 35 9 1908 2198 1241251 1240976 4.740000e-58 235.0
29 TraesCS6A01G328700 chr4D 86.829 205 21 3 1997 2198 125489715 125489916 1.030000e-54 224.0
30 TraesCS6A01G328700 chr4D 88.235 68 4 3 2741 2807 54132695 54132631 8.460000e-11 78.7
31 TraesCS6A01G328700 chr4D 87.500 64 2 3 2756 2813 37514006 37513943 5.090000e-08 69.4
32 TraesCS6A01G328700 chr4D 87.302 63 5 2 2745 2807 54132631 54132690 5.090000e-08 69.4
33 TraesCS6A01G328700 chr1D 87.324 71 5 3 2738 2807 493113492 493113559 8.460000e-11 78.7
34 TraesCS6A01G328700 chr1D 87.302 63 5 2 2745 2807 493113559 493113500 5.090000e-08 69.4
35 TraesCS6A01G328700 chr3B 89.062 64 1 4 2750 2807 172050824 172050887 1.090000e-09 75.0
36 TraesCS6A01G328700 chr1A 86.111 72 6 3 2742 2809 579105988 579106059 1.090000e-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 TraesCS6A01G328700 chr6A 562270855 562273702 2847 False 5260.000000 5260 100.000000 1 2848 1 chr6A.!!$F2 2847
1 TraesCS6A01G328700 chr6A 562469931 562471253 1322 True 1005.000000 1005 81.281000 367 1709 1 chr6A.!!$R2 1342
2 TraesCS6A01G328700 chr6A 562399770 562402736 2966 True 967.500000 1120 87.075000 16 1857 2 chr6A.!!$R4 1841
3 TraesCS6A01G328700 chr6A 562487454 562488267 813 True 833.000000 833 85.782000 762 1569 1 chr6A.!!$R3 807
4 TraesCS6A01G328700 chr6A 562250473 562251430 957 False 822.000000 822 82.803000 739 1709 1 chr6A.!!$F1 970
5 TraesCS6A01G328700 chr6D 418769287 418770791 1504 True 1679.000000 1679 86.905000 291 1857 1 chr6D.!!$R1 1566
6 TraesCS6A01G328700 chr6D 418882364 418883710 1346 True 1029.000000 1029 81.544000 367 1712 1 chr6D.!!$R2 1345
7 TraesCS6A01G328700 chr6D 418892228 418893102 874 True 701.000000 701 82.024000 721 1605 1 chr6D.!!$R3 884
8 TraesCS6A01G328700 chr6D 418732252 418734541 2289 False 505.333333 732 81.434333 367 2745 3 chr6D.!!$F2 2378
9 TraesCS6A01G328700 chr6B 631534277 631535623 1346 True 1068.000000 1068 82.026000 376 1696 1 chr6B.!!$R1 1320
10 TraesCS6A01G328700 chr6B 631740519 631741789 1270 True 965.000000 965 80.945000 367 1712 1 chr6B.!!$R2 1345
11 TraesCS6A01G328700 chr6B 630917992 630918953 961 True 562.000000 771 91.214000 1761 2609 2 chr6B.!!$R3 848
12 TraesCS6A01G328700 chr6B 631192612 631194856 2244 False 520.233333 1219 79.819000 363 2584 3 chr6B.!!$F2 2221
13 TraesCS6A01G328700 chr6B 631843380 631846270 2890 True 465.000000 765 82.051000 368 1694 2 chr6B.!!$R5 1326
14 TraesCS6A01G328700 chr6B 631244724 631247437 2713 True 433.250000 870 86.698500 144 2360 4 chr6B.!!$R4 2216

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
829 3497 0.100682 ACGATCCATCCGACACGAAG 59.899 55.0 0.0 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2790 6578 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.0 0.0 0.0 0.0 4.12 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
26 27 2.100879 GAGCAGTGAGGAACGGTGGT 62.101 60.000 0.00 0.00 0.00 4.16
57 58 4.143333 CTACCCCCGTGTCGGCAG 62.143 72.222 0.00 0.00 46.86 4.85
100 101 2.934553 GGGTAGTATGACGTTTTCCTGC 59.065 50.000 0.00 0.00 0.00 4.85
104 105 1.463444 GTATGACGTTTTCCTGCGCTT 59.537 47.619 9.73 0.00 0.00 4.68
119 120 2.159324 TGCGCTTGTTCAAATGACAACA 60.159 40.909 9.73 0.00 0.00 3.33
122 123 4.088496 GCGCTTGTTCAAATGACAACATAC 59.912 41.667 0.00 0.00 35.50 2.39
124 125 5.914635 CGCTTGTTCAAATGACAACATACTT 59.085 36.000 0.00 0.00 35.50 2.24
139 140 9.376075 GACAACATACTTAGGATATCATGATGG 57.624 37.037 18.72 2.64 0.00 3.51
155 159 2.886523 TGATGGGCTTGAGAAACAACAG 59.113 45.455 0.00 0.00 34.56 3.16
245 252 7.674471 GTCTGCTAGACAAAAAGGAAATAGT 57.326 36.000 10.30 0.00 44.45 2.12
246 253 8.773404 GTCTGCTAGACAAAAAGGAAATAGTA 57.227 34.615 10.30 0.00 44.45 1.82
276 283 2.158928 TCATCATGATGACACGATGCCA 60.159 45.455 30.27 8.14 43.54 4.92
481 672 1.747355 CATCAACATCTCTTGTGGCCC 59.253 52.381 0.00 0.00 38.99 5.80
519 738 1.301423 CGGGAACACACTCGGAAAAA 58.699 50.000 0.00 0.00 0.00 1.94
683 983 3.753434 ACTCTCACTGCTCCGCCG 61.753 66.667 0.00 0.00 0.00 6.46
687 987 3.701604 CTCACTGCTCCGCCGTACC 62.702 68.421 0.00 0.00 0.00 3.34
688 988 3.760035 CACTGCTCCGCCGTACCT 61.760 66.667 0.00 0.00 0.00 3.08
689 989 2.044650 ACTGCTCCGCCGTACCTA 60.045 61.111 0.00 0.00 0.00 3.08
690 990 1.455217 ACTGCTCCGCCGTACCTAT 60.455 57.895 0.00 0.00 0.00 2.57
691 991 1.286260 CTGCTCCGCCGTACCTATC 59.714 63.158 0.00 0.00 0.00 2.08
692 992 2.143594 CTGCTCCGCCGTACCTATCC 62.144 65.000 0.00 0.00 0.00 2.59
693 993 2.952245 CTCCGCCGTACCTATCCG 59.048 66.667 0.00 0.00 0.00 4.18
694 994 2.595463 TCCGCCGTACCTATCCGG 60.595 66.667 0.00 0.00 46.90 5.14
829 3497 0.100682 ACGATCCATCCGACACGAAG 59.899 55.000 0.00 0.00 0.00 3.79
834 3503 3.000819 ATCCGACACGAAGGCCCA 61.001 61.111 0.00 0.00 0.00 5.36
837 3506 2.742372 CGACACGAAGGCCCAAGG 60.742 66.667 0.00 0.00 0.00 3.61
857 3531 4.397832 GGCCGGGTTCCGTAGCAA 62.398 66.667 2.18 0.00 46.80 3.91
1006 4064 2.896801 GAAGCACACCGCACCACAG 61.897 63.158 0.00 0.00 46.13 3.66
1007 4065 3.399105 AAGCACACCGCACCACAGA 62.399 57.895 0.00 0.00 46.13 3.41
1107 4210 4.828925 GAGAGGGCGGCTGCAGTC 62.829 72.222 21.31 12.92 45.35 3.51
1526 4659 4.039245 GTCACCTCCTGATCGATTATCCAA 59.961 45.833 0.00 0.00 33.22 3.53
1596 4765 1.519455 GCGGGAGGAGTTCATCGTG 60.519 63.158 0.00 0.00 0.00 4.35
1597 4766 1.890894 CGGGAGGAGTTCATCGTGT 59.109 57.895 0.00 0.00 0.00 4.49
1598 4767 0.246635 CGGGAGGAGTTCATCGTGTT 59.753 55.000 0.00 0.00 0.00 3.32
1599 4768 1.337823 CGGGAGGAGTTCATCGTGTTT 60.338 52.381 0.00 0.00 0.00 2.83
1600 4769 2.347731 GGGAGGAGTTCATCGTGTTTC 58.652 52.381 0.00 0.00 0.00 2.78
1601 4770 2.028020 GGGAGGAGTTCATCGTGTTTCT 60.028 50.000 0.00 0.00 0.00 2.52
1602 4771 2.996621 GGAGGAGTTCATCGTGTTTCTG 59.003 50.000 0.00 0.00 0.00 3.02
1603 4772 2.413453 GAGGAGTTCATCGTGTTTCTGC 59.587 50.000 0.00 0.00 0.00 4.26
1604 4773 1.464997 GGAGTTCATCGTGTTTCTGCC 59.535 52.381 0.00 0.00 0.00 4.85
1605 4774 2.143122 GAGTTCATCGTGTTTCTGCCA 58.857 47.619 0.00 0.00 0.00 4.92
1679 4859 5.160607 AGAGAGATACCAGATACGGAGAG 57.839 47.826 0.00 0.00 0.00 3.20
1681 4861 3.653836 AGAGATACCAGATACGGAGAGGT 59.346 47.826 0.00 0.00 36.40 3.85
1696 4876 2.360801 GAGAGGTATGAGAGGCAGTCAC 59.639 54.545 0.00 0.00 0.00 3.67
1697 4877 2.103373 GAGGTATGAGAGGCAGTCACA 58.897 52.381 0.00 0.00 0.00 3.58
1698 4878 1.827969 AGGTATGAGAGGCAGTCACAC 59.172 52.381 0.00 0.00 0.00 3.82
1736 4931 7.951806 TCTGGGATCCATATTGCTTATGATTTT 59.048 33.333 15.23 0.00 40.22 1.82
1739 4934 7.038799 GGGATCCATATTGCTTATGATTTTGGT 60.039 37.037 15.23 0.00 40.22 3.67
1740 4935 8.370182 GGATCCATATTGCTTATGATTTTGGTT 58.630 33.333 6.95 0.00 40.22 3.67
1741 4936 9.768662 GATCCATATTGCTTATGATTTTGGTTT 57.231 29.630 8.32 0.00 40.22 3.27
1743 4938 9.956640 TCCATATTGCTTATGATTTTGGTTTTT 57.043 25.926 8.32 0.00 40.22 1.94
1744 4939 9.991388 CCATATTGCTTATGATTTTGGTTTTTG 57.009 29.630 8.32 0.00 40.22 2.44
1748 4943 7.630470 TGCTTATGATTTTGGTTTTTGTACG 57.370 32.000 0.00 0.00 0.00 3.67
1749 4944 6.642950 TGCTTATGATTTTGGTTTTTGTACGG 59.357 34.615 0.00 0.00 0.00 4.02
1750 4945 6.400621 GCTTATGATTTTGGTTTTTGTACGGC 60.401 38.462 0.00 0.00 0.00 5.68
1751 4946 4.657436 TGATTTTGGTTTTTGTACGGCT 57.343 36.364 0.00 0.00 0.00 5.52
1752 4947 5.012328 TGATTTTGGTTTTTGTACGGCTT 57.988 34.783 0.00 0.00 0.00 4.35
1753 4948 5.420409 TGATTTTGGTTTTTGTACGGCTTT 58.580 33.333 0.00 0.00 0.00 3.51
1758 4953 4.674475 TGGTTTTTGTACGGCTTTCTTTC 58.326 39.130 0.00 0.00 0.00 2.62
1779 5164 3.265221 TCTCTTCTGATTCTTGCCCATGT 59.735 43.478 0.00 0.00 0.00 3.21
1803 5191 8.793592 TGTGCATGTATACTACTACTAGATTGG 58.206 37.037 4.17 0.00 0.00 3.16
1861 5250 5.407502 TGAATTCGAACACAGTCGTCATAT 58.592 37.500 0.00 0.00 41.80 1.78
1876 5265 5.528690 GTCGTCATATATATACAGCCCCGTA 59.471 44.000 0.00 0.00 0.00 4.02
1992 5573 2.093310 CAGTTCAGCAGTGCTAATGTCG 59.907 50.000 19.26 4.23 36.40 4.35
1995 5576 3.038788 TCAGCAGTGCTAATGTCGAAA 57.961 42.857 19.26 0.00 36.40 3.46
2016 5597 0.942962 GGCGATGAAGCAAGATCAGG 59.057 55.000 0.00 0.00 39.27 3.86
2023 5719 8.199928 GCGATGAAGCAAGATCAGGATTACTG 62.200 46.154 0.00 0.00 41.87 2.74
2044 5740 2.817396 GGCAGACAGGCTTCGAGC 60.817 66.667 0.00 0.00 41.46 5.03
2046 5742 1.809209 GCAGACAGGCTTCGAGCTC 60.809 63.158 2.73 2.73 41.99 4.09
2056 5752 4.764896 TCGAGCTCGATAGGCGTA 57.235 55.556 33.84 10.40 44.22 4.42
2057 5753 2.232750 TCGAGCTCGATAGGCGTAC 58.767 57.895 33.84 0.00 44.22 3.67
2058 5754 0.531311 TCGAGCTCGATAGGCGTACA 60.531 55.000 33.84 8.80 44.22 2.90
2059 5755 0.517755 CGAGCTCGATAGGCGTACAT 59.482 55.000 32.06 0.00 43.02 2.29
2060 5756 1.730612 CGAGCTCGATAGGCGTACATA 59.269 52.381 32.06 0.00 43.02 2.29
2072 5771 5.023533 AGGCGTACATATGATCTTGTGTT 57.976 39.130 14.70 2.27 0.00 3.32
2183 5919 0.804989 CTTTCCGCTGGTGGATTCAC 59.195 55.000 3.60 0.00 42.91 3.18
2200 5936 2.430244 CGTCGTGTCGTTCAGGGG 60.430 66.667 0.00 0.00 33.36 4.79
2201 5937 2.732658 GTCGTGTCGTTCAGGGGT 59.267 61.111 4.11 0.00 33.36 4.95
2206 5942 4.029809 GTCGTTCAGGGGTGGGGG 62.030 72.222 0.00 0.00 0.00 5.40
2207 5943 4.585216 TCGTTCAGGGGTGGGGGT 62.585 66.667 0.00 0.00 0.00 4.95
2208 5944 3.576259 CGTTCAGGGGTGGGGGTT 61.576 66.667 0.00 0.00 0.00 4.11
2209 5945 2.439245 GTTCAGGGGTGGGGGTTC 59.561 66.667 0.00 0.00 0.00 3.62
2210 5946 3.253838 TTCAGGGGTGGGGGTTCG 61.254 66.667 0.00 0.00 0.00 3.95
2211 5947 3.795977 TTCAGGGGTGGGGGTTCGA 62.796 63.158 0.00 0.00 0.00 3.71
2212 5948 3.015145 CAGGGGTGGGGGTTCGAT 61.015 66.667 0.00 0.00 0.00 3.59
2213 5949 2.691252 AGGGGTGGGGGTTCGATC 60.691 66.667 0.00 0.00 0.00 3.69
2214 5950 3.012722 GGGGTGGGGGTTCGATCA 61.013 66.667 0.00 0.00 0.00 2.92
2215 5951 2.383601 GGGGTGGGGGTTCGATCAT 61.384 63.158 0.00 0.00 0.00 2.45
2216 5952 1.148498 GGGTGGGGGTTCGATCATC 59.852 63.158 0.00 0.00 0.00 2.92
2217 5953 1.632018 GGGTGGGGGTTCGATCATCA 61.632 60.000 0.00 0.00 0.00 3.07
2218 5954 0.463833 GGTGGGGGTTCGATCATCAC 60.464 60.000 0.00 0.00 0.00 3.06
2221 5957 1.065491 TGGGGGTTCGATCATCACTTG 60.065 52.381 0.00 0.00 0.00 3.16
2240 5990 2.648059 TGATCAGCATCGAGTCTGAGA 58.352 47.619 19.67 9.87 41.95 3.27
2308 6062 1.150081 CCTGATCCCCAGCACATCC 59.850 63.158 0.00 0.00 41.57 3.51
2324 6092 5.015710 AGCACATCCTCCATATCTACCTCTA 59.984 44.000 0.00 0.00 0.00 2.43
2325 6093 5.359576 GCACATCCTCCATATCTACCTCTAG 59.640 48.000 0.00 0.00 0.00 2.43
2328 6096 6.448714 ACATCCTCCATATCTACCTCTAGCTA 59.551 42.308 0.00 0.00 0.00 3.32
2331 6099 6.102027 TCCTCCATATCTACCTCTAGCTATCC 59.898 46.154 0.00 0.00 0.00 2.59
2361 6129 8.830580 TCTTGCTTTCTGGATTATTATTCGAAG 58.169 33.333 3.35 0.00 0.00 3.79
2362 6130 8.731275 TTGCTTTCTGGATTATTATTCGAAGA 57.269 30.769 3.35 0.00 0.00 2.87
2378 6146 2.712709 GAAGACCCTACTTGGCTTTCC 58.287 52.381 0.00 0.00 0.00 3.13
2397 6165 1.305465 TGATGCAAAGCCAGGCCAT 60.305 52.632 8.22 3.92 0.00 4.40
2489 6257 5.447548 CGGAGAGTAGTAGTACAGTTTCAGC 60.448 48.000 10.33 0.00 0.00 4.26
2498 6266 0.814457 ACAGTTTCAGCGGCACAAAA 59.186 45.000 1.45 0.00 0.00 2.44
2499 6267 1.199624 CAGTTTCAGCGGCACAAAAC 58.800 50.000 1.45 9.46 32.97 2.43
2520 6293 8.528917 AAAACACTTTTGAAAGTACAGGTTTC 57.471 30.769 16.42 0.00 46.89 2.78
2521 6294 6.827586 ACACTTTTGAAAGTACAGGTTTCA 57.172 33.333 8.66 5.02 46.89 2.69
2600 6374 9.765795 TTTAAACGACATTGAATTAACCCATTT 57.234 25.926 0.00 0.00 0.00 2.32
2601 6375 7.650834 AAACGACATTGAATTAACCCATTTG 57.349 32.000 0.00 0.00 0.00 2.32
2602 6376 5.167845 ACGACATTGAATTAACCCATTTGC 58.832 37.500 0.00 0.00 0.00 3.68
2615 6395 2.159393 CCCATTTGCAACGTAGTGGATG 60.159 50.000 0.00 0.00 45.00 3.51
2616 6396 2.159393 CCATTTGCAACGTAGTGGATGG 60.159 50.000 0.00 3.12 45.00 3.51
2634 6414 0.752743 GGATACAGGCCATGCAGCAA 60.753 55.000 5.01 0.00 0.00 3.91
2639 6419 1.751927 AGGCCATGCAGCAACTAGC 60.752 57.895 5.01 0.00 46.19 3.42
2661 6441 4.509970 GCCAGTACATATGACAATTACGCA 59.490 41.667 10.38 0.00 0.00 5.24
2663 6443 6.593072 CCAGTACATATGACAATTACGCATG 58.407 40.000 10.38 0.00 0.00 4.06
2688 6476 1.068610 CGGTCGTGCATCACCATTTTT 60.069 47.619 15.34 0.00 32.33 1.94
2689 6477 2.327568 GGTCGTGCATCACCATTTTTG 58.672 47.619 11.28 0.00 32.33 2.44
2690 6478 2.030363 GGTCGTGCATCACCATTTTTGA 60.030 45.455 11.28 0.00 32.33 2.69
2691 6479 3.367292 GGTCGTGCATCACCATTTTTGAT 60.367 43.478 11.28 0.00 33.81 2.57
2693 6481 4.324402 GTCGTGCATCACCATTTTTGATTC 59.676 41.667 0.00 0.00 30.98 2.52
2701 6489 7.704472 GCATCACCATTTTTGATTCGGTATAAA 59.296 33.333 0.00 0.00 30.98 1.40
2704 6492 8.798402 TCACCATTTTTGATTCGGTATAAACTT 58.202 29.630 0.00 0.00 0.00 2.66
2726 6514 8.340618 ACTTAACATAATGCTCTTTGACATGT 57.659 30.769 0.00 0.00 0.00 3.21
2729 6517 4.400251 ACATAATGCTCTTTGACATGTGGG 59.600 41.667 1.15 0.00 0.00 4.61
2731 6519 0.478072 TGCTCTTTGACATGTGGGGT 59.522 50.000 1.15 0.00 0.00 4.95
2735 6523 1.073763 TCTTTGACATGTGGGGTCCTG 59.926 52.381 1.15 0.00 34.36 3.86
2736 6524 0.850100 TTTGACATGTGGGGTCCTGT 59.150 50.000 1.15 0.00 34.36 4.00
2745 6533 5.489637 ACATGTGGGGTCCTGTAACTTATTA 59.510 40.000 0.00 0.00 0.00 0.98
2746 6534 5.425196 TGTGGGGTCCTGTAACTTATTAC 57.575 43.478 0.00 0.00 41.07 1.89
2747 6535 5.095809 TGTGGGGTCCTGTAACTTATTACT 58.904 41.667 0.00 0.00 41.24 2.24
2748 6536 5.548836 TGTGGGGTCCTGTAACTTATTACTT 59.451 40.000 0.00 0.00 41.24 2.24
2749 6537 6.111382 GTGGGGTCCTGTAACTTATTACTTC 58.889 44.000 0.00 0.00 41.24 3.01
2750 6538 5.190330 TGGGGTCCTGTAACTTATTACTTCC 59.810 44.000 0.00 0.00 41.24 3.46
2751 6539 5.427806 GGGGTCCTGTAACTTATTACTTCCT 59.572 44.000 0.00 0.00 41.24 3.36
2752 6540 6.069789 GGGGTCCTGTAACTTATTACTTCCTT 60.070 42.308 0.00 0.00 41.24 3.36
2753 6541 7.046652 GGGTCCTGTAACTTATTACTTCCTTC 58.953 42.308 0.00 0.00 41.24 3.46
2754 6542 7.310858 GGGTCCTGTAACTTATTACTTCCTTCA 60.311 40.741 0.00 0.00 41.24 3.02
2755 6543 8.265764 GGTCCTGTAACTTATTACTTCCTTCAT 58.734 37.037 0.00 0.00 41.24 2.57
2756 6544 9.315525 GTCCTGTAACTTATTACTTCCTTCATC 57.684 37.037 0.00 0.00 41.24 2.92
2757 6545 8.483758 TCCTGTAACTTATTACTTCCTTCATCC 58.516 37.037 0.00 0.00 41.24 3.51
2758 6546 7.715686 CCTGTAACTTATTACTTCCTTCATCCC 59.284 40.741 0.00 0.00 41.24 3.85
2759 6547 8.153221 TGTAACTTATTACTTCCTTCATCCCA 57.847 34.615 0.00 0.00 41.24 4.37
2760 6548 8.607713 TGTAACTTATTACTTCCTTCATCCCAA 58.392 33.333 0.00 0.00 41.24 4.12
2761 6549 9.457436 GTAACTTATTACTTCCTTCATCCCAAA 57.543 33.333 0.00 0.00 38.15 3.28
2762 6550 8.950007 AACTTATTACTTCCTTCATCCCAAAA 57.050 30.769 0.00 0.00 0.00 2.44
2763 6551 9.547279 AACTTATTACTTCCTTCATCCCAAAAT 57.453 29.630 0.00 0.00 0.00 1.82
2764 6552 9.547279 ACTTATTACTTCCTTCATCCCAAAATT 57.453 29.630 0.00 0.00 0.00 1.82
2766 6554 9.768215 TTATTACTTCCTTCATCCCAAAATTCT 57.232 29.630 0.00 0.00 0.00 2.40
2767 6555 8.670521 ATTACTTCCTTCATCCCAAAATTCTT 57.329 30.769 0.00 0.00 0.00 2.52
2768 6556 6.350629 ACTTCCTTCATCCCAAAATTCTTG 57.649 37.500 0.00 0.00 0.00 3.02
2769 6557 5.840693 ACTTCCTTCATCCCAAAATTCTTGT 59.159 36.000 0.00 0.00 0.00 3.16
2770 6558 5.982890 TCCTTCATCCCAAAATTCTTGTC 57.017 39.130 0.00 0.00 0.00 3.18
2771 6559 5.644188 TCCTTCATCCCAAAATTCTTGTCT 58.356 37.500 0.00 0.00 0.00 3.41
2772 6560 6.077322 TCCTTCATCCCAAAATTCTTGTCTT 58.923 36.000 0.00 0.00 0.00 3.01
2773 6561 7.237982 TCCTTCATCCCAAAATTCTTGTCTTA 58.762 34.615 0.00 0.00 0.00 2.10
2774 6562 7.728083 TCCTTCATCCCAAAATTCTTGTCTTAA 59.272 33.333 0.00 0.00 0.00 1.85
2775 6563 8.367156 CCTTCATCCCAAAATTCTTGTCTTAAA 58.633 33.333 0.00 0.00 0.00 1.52
2776 6564 9.933723 CTTCATCCCAAAATTCTTGTCTTAAAT 57.066 29.630 0.00 0.00 0.00 1.40
2797 6585 9.685828 TTAAATTAAGACAAGAATTTTGGGACG 57.314 29.630 0.00 0.00 36.77 4.79
2798 6586 5.699097 TTAAGACAAGAATTTTGGGACGG 57.301 39.130 0.00 0.00 0.00 4.79
2799 6587 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2800 6588 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2801 6589 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2802 6590 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2803 6591 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
2804 6592 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
2805 6593 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
2806 6594 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
2807 6595 1.961133 TTTTGGGACGGAGGGAGTAT 58.039 50.000 0.00 0.00 0.00 2.12
2808 6596 1.200519 TTTGGGACGGAGGGAGTATG 58.799 55.000 0.00 0.00 0.00 2.39
2809 6597 0.042131 TTGGGACGGAGGGAGTATGT 59.958 55.000 0.00 0.00 0.00 2.29
2810 6598 0.042131 TGGGACGGAGGGAGTATGTT 59.958 55.000 0.00 0.00 0.00 2.71
2811 6599 0.464452 GGGACGGAGGGAGTATGTTG 59.536 60.000 0.00 0.00 0.00 3.33
2812 6600 0.179081 GGACGGAGGGAGTATGTTGC 60.179 60.000 0.00 0.00 0.00 4.17
2813 6601 0.824759 GACGGAGGGAGTATGTTGCT 59.175 55.000 0.00 0.00 0.00 3.91
2814 6602 1.207329 GACGGAGGGAGTATGTTGCTT 59.793 52.381 0.00 0.00 0.00 3.91
2815 6603 1.066143 ACGGAGGGAGTATGTTGCTTG 60.066 52.381 0.00 0.00 0.00 4.01
2816 6604 1.207089 CGGAGGGAGTATGTTGCTTGA 59.793 52.381 0.00 0.00 0.00 3.02
2817 6605 2.633488 GGAGGGAGTATGTTGCTTGAC 58.367 52.381 0.00 0.00 0.00 3.18
2818 6606 2.271800 GAGGGAGTATGTTGCTTGACG 58.728 52.381 0.00 0.00 0.00 4.35
2819 6607 1.623811 AGGGAGTATGTTGCTTGACGT 59.376 47.619 0.00 0.00 0.00 4.34
2820 6608 1.732259 GGGAGTATGTTGCTTGACGTG 59.268 52.381 0.00 0.00 0.00 4.49
2821 6609 1.128692 GGAGTATGTTGCTTGACGTGC 59.871 52.381 0.00 0.00 0.00 5.34
2822 6610 2.069273 GAGTATGTTGCTTGACGTGCT 58.931 47.619 0.00 0.00 34.74 4.40
2823 6611 3.250744 GAGTATGTTGCTTGACGTGCTA 58.749 45.455 0.00 0.00 32.64 3.49
2824 6612 3.254060 AGTATGTTGCTTGACGTGCTAG 58.746 45.455 0.00 0.00 31.03 3.42
2825 6613 1.442769 ATGTTGCTTGACGTGCTAGG 58.557 50.000 0.00 0.00 0.00 3.02
2826 6614 1.227999 TGTTGCTTGACGTGCTAGGC 61.228 55.000 0.00 0.00 0.00 3.93
2827 6615 2.027073 TTGCTTGACGTGCTAGGCG 61.027 57.895 0.00 0.00 0.00 5.52
2828 6616 2.126071 GCTTGACGTGCTAGGCGA 60.126 61.111 0.00 0.00 0.00 5.54
2829 6617 1.519455 GCTTGACGTGCTAGGCGAT 60.519 57.895 0.00 0.00 0.00 4.58
2830 6618 1.084370 GCTTGACGTGCTAGGCGATT 61.084 55.000 0.00 0.00 0.00 3.34
2831 6619 0.924090 CTTGACGTGCTAGGCGATTC 59.076 55.000 0.00 0.00 0.00 2.52
2832 6620 0.530744 TTGACGTGCTAGGCGATTCT 59.469 50.000 0.00 0.00 0.00 2.40
2833 6621 1.385528 TGACGTGCTAGGCGATTCTA 58.614 50.000 0.00 0.00 0.00 2.10
2834 6622 1.065102 TGACGTGCTAGGCGATTCTAC 59.935 52.381 0.00 0.00 0.00 2.59
2835 6623 1.065102 GACGTGCTAGGCGATTCTACA 59.935 52.381 0.00 0.00 0.00 2.74
2836 6624 1.681793 ACGTGCTAGGCGATTCTACAT 59.318 47.619 0.00 0.00 0.00 2.29
2837 6625 2.882761 ACGTGCTAGGCGATTCTACATA 59.117 45.455 0.00 0.00 0.00 2.29
2838 6626 3.317149 ACGTGCTAGGCGATTCTACATAA 59.683 43.478 0.00 0.00 0.00 1.90
2839 6627 4.022242 ACGTGCTAGGCGATTCTACATAAT 60.022 41.667 0.00 0.00 0.00 1.28
2840 6628 4.923871 CGTGCTAGGCGATTCTACATAATT 59.076 41.667 0.00 0.00 0.00 1.40
2841 6629 6.090783 CGTGCTAGGCGATTCTACATAATTA 58.909 40.000 0.00 0.00 0.00 1.40
2842 6630 6.033619 CGTGCTAGGCGATTCTACATAATTAC 59.966 42.308 0.00 0.00 0.00 1.89
2843 6631 6.866770 GTGCTAGGCGATTCTACATAATTACA 59.133 38.462 0.00 0.00 0.00 2.41
2844 6632 7.545965 GTGCTAGGCGATTCTACATAATTACAT 59.454 37.037 0.00 0.00 0.00 2.29
2845 6633 8.745590 TGCTAGGCGATTCTACATAATTACATA 58.254 33.333 0.00 0.00 0.00 2.29
2846 6634 9.582431 GCTAGGCGATTCTACATAATTACATAA 57.418 33.333 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.548357 TTCCTCACTGCTCCCTGCTC 61.548 60.000 0.00 0.00 43.37 4.26
1 2 1.537397 TTCCTCACTGCTCCCTGCT 60.537 57.895 0.00 0.00 43.37 4.24
2 3 1.376553 GTTCCTCACTGCTCCCTGC 60.377 63.158 0.00 0.00 43.25 4.85
3 4 1.079543 CGTTCCTCACTGCTCCCTG 60.080 63.158 0.00 0.00 0.00 4.45
4 5 2.286523 CCGTTCCTCACTGCTCCCT 61.287 63.158 0.00 0.00 0.00 4.20
5 6 2.266055 CCGTTCCTCACTGCTCCC 59.734 66.667 0.00 0.00 0.00 4.30
6 7 1.374758 CACCGTTCCTCACTGCTCC 60.375 63.158 0.00 0.00 0.00 4.70
7 8 1.374758 CCACCGTTCCTCACTGCTC 60.375 63.158 0.00 0.00 0.00 4.26
8 9 2.140792 ACCACCGTTCCTCACTGCT 61.141 57.895 0.00 0.00 0.00 4.24
9 10 1.961277 CACCACCGTTCCTCACTGC 60.961 63.158 0.00 0.00 0.00 4.40
10 11 1.301716 CCACCACCGTTCCTCACTG 60.302 63.158 0.00 0.00 0.00 3.66
11 12 3.148084 CCACCACCGTTCCTCACT 58.852 61.111 0.00 0.00 0.00 3.41
12 13 2.668550 GCCACCACCGTTCCTCAC 60.669 66.667 0.00 0.00 0.00 3.51
13 14 4.308458 CGCCACCACCGTTCCTCA 62.308 66.667 0.00 0.00 0.00 3.86
26 27 1.902556 GGTAGAAACCCTAGCGCCA 59.097 57.895 2.29 0.00 40.21 5.69
70 71 1.075076 CATACTACCCCGACCCCCA 60.075 63.158 0.00 0.00 0.00 4.96
100 101 5.451908 AGTATGTTGTCATTTGAACAAGCG 58.548 37.500 0.00 0.00 35.76 4.68
104 105 8.862325 ATCCTAAGTATGTTGTCATTTGAACA 57.138 30.769 0.00 0.00 36.54 3.18
119 120 7.404104 TCAAGCCCATCATGATATCCTAAGTAT 59.596 37.037 8.15 0.00 0.00 2.12
122 123 6.058553 TCAAGCCCATCATGATATCCTAAG 57.941 41.667 8.15 0.00 0.00 2.18
124 125 5.344566 TCTCAAGCCCATCATGATATCCTA 58.655 41.667 8.15 0.00 0.00 2.94
134 135 2.886523 CTGTTGTTTCTCAAGCCCATCA 59.113 45.455 0.00 0.00 36.66 3.07
139 140 1.609072 GGGACTGTTGTTTCTCAAGCC 59.391 52.381 0.00 0.00 36.66 4.35
155 159 0.641048 AAGGAGGGTAGGGTAGGGAC 59.359 60.000 0.00 0.00 0.00 4.46
276 283 6.751514 TGCATACATGGTTTATTTCTCGTT 57.248 33.333 0.00 0.00 0.00 3.85
481 672 3.342370 TACGCGACTGCTGCTCCAG 62.342 63.158 15.93 3.15 39.65 3.86
683 983 1.101331 CGGGATAGCCGGATAGGTAC 58.899 60.000 5.05 0.00 43.70 3.34
687 987 0.965866 TGAGCGGGATAGCCGGATAG 60.966 60.000 5.05 0.00 36.66 2.08
688 988 1.076014 TGAGCGGGATAGCCGGATA 59.924 57.895 5.05 2.29 36.66 2.59
689 989 2.203640 TGAGCGGGATAGCCGGAT 60.204 61.111 5.05 0.00 36.66 4.18
690 990 3.224324 GTGAGCGGGATAGCCGGA 61.224 66.667 5.05 0.00 36.66 5.14
691 991 4.301027 GGTGAGCGGGATAGCCGG 62.301 72.222 0.00 0.00 38.01 6.13
692 992 4.647615 CGGTGAGCGGGATAGCCG 62.648 72.222 0.00 0.00 38.01 5.52
693 993 4.971125 GCGGTGAGCGGGATAGCC 62.971 72.222 6.08 0.00 38.01 3.93
765 2242 2.031120 TCGGAATAATCGGGTTACGGT 58.969 47.619 0.00 0.00 44.45 4.83
795 2273 3.756677 CGTGTGCGTCGCTGACAG 61.757 66.667 19.50 0.00 32.09 3.51
941 3996 1.633852 CTGCTTCTGCTTGGCTCGAC 61.634 60.000 0.00 0.00 40.48 4.20
1006 4064 2.203015 AGGTGTGCGTGTGTGGTC 60.203 61.111 0.00 0.00 0.00 4.02
1007 4065 2.203015 GAGGTGTGCGTGTGTGGT 60.203 61.111 0.00 0.00 0.00 4.16
1603 4772 4.436998 GTCGTCTCCGGCAGGTGG 62.437 72.222 1.81 0.00 38.92 4.61
1604 4773 3.680786 TGTCGTCTCCGGCAGGTG 61.681 66.667 1.81 0.00 45.14 4.00
1652 4832 4.006989 CGTATCTGGTATCTCTCTCCCTG 58.993 52.174 0.00 0.00 0.00 4.45
1679 4859 1.827969 AGTGTGACTGCCTCTCATACC 59.172 52.381 0.00 0.00 31.84 2.73
1681 4861 3.291584 CCTAGTGTGACTGCCTCTCATA 58.708 50.000 0.00 0.00 0.00 2.15
1696 4876 4.282195 GGATCCCAGACTAATCACCTAGTG 59.718 50.000 0.00 0.00 32.14 2.74
1697 4877 4.078571 TGGATCCCAGACTAATCACCTAGT 60.079 45.833 9.90 0.00 34.76 2.57
1698 4878 4.483950 TGGATCCCAGACTAATCACCTAG 58.516 47.826 9.90 0.00 0.00 3.02
1736 4931 4.399934 AGAAAGAAAGCCGTACAAAAACCA 59.600 37.500 0.00 0.00 0.00 3.67
1739 4934 6.317893 AGAAGAGAAAGAAAGCCGTACAAAAA 59.682 34.615 0.00 0.00 0.00 1.94
1740 4935 5.820947 AGAAGAGAAAGAAAGCCGTACAAAA 59.179 36.000 0.00 0.00 0.00 2.44
1741 4936 5.236478 CAGAAGAGAAAGAAAGCCGTACAAA 59.764 40.000 0.00 0.00 0.00 2.83
1742 4937 4.750098 CAGAAGAGAAAGAAAGCCGTACAA 59.250 41.667 0.00 0.00 0.00 2.41
1743 4938 4.038763 TCAGAAGAGAAAGAAAGCCGTACA 59.961 41.667 0.00 0.00 0.00 2.90
1744 4939 4.557205 TCAGAAGAGAAAGAAAGCCGTAC 58.443 43.478 0.00 0.00 0.00 3.67
1745 4940 4.866508 TCAGAAGAGAAAGAAAGCCGTA 57.133 40.909 0.00 0.00 0.00 4.02
1746 4941 3.753294 TCAGAAGAGAAAGAAAGCCGT 57.247 42.857 0.00 0.00 0.00 5.68
1747 4942 4.934602 AGAATCAGAAGAGAAAGAAAGCCG 59.065 41.667 0.00 0.00 0.00 5.52
1748 4943 6.610456 CAAGAATCAGAAGAGAAAGAAAGCC 58.390 40.000 0.00 0.00 0.00 4.35
1749 4944 6.085573 GCAAGAATCAGAAGAGAAAGAAAGC 58.914 40.000 0.00 0.00 0.00 3.51
1750 4945 6.349197 GGGCAAGAATCAGAAGAGAAAGAAAG 60.349 42.308 0.00 0.00 0.00 2.62
1751 4946 5.474876 GGGCAAGAATCAGAAGAGAAAGAAA 59.525 40.000 0.00 0.00 0.00 2.52
1752 4947 5.006386 GGGCAAGAATCAGAAGAGAAAGAA 58.994 41.667 0.00 0.00 0.00 2.52
1753 4948 4.042062 TGGGCAAGAATCAGAAGAGAAAGA 59.958 41.667 0.00 0.00 0.00 2.52
1758 4953 3.377485 CACATGGGCAAGAATCAGAAGAG 59.623 47.826 0.00 0.00 0.00 2.85
1779 5164 8.935614 ACCAATCTAGTAGTAGTATACATGCA 57.064 34.615 5.50 0.00 46.26 3.96
1803 5191 7.781548 ATACATCGGTGGTCTGTTAATTAAC 57.218 36.000 19.44 19.44 36.74 2.01
1816 5204 7.780008 TCAACTGTTAATTATACATCGGTGG 57.220 36.000 0.00 0.00 0.00 4.61
1847 5236 6.127703 GGGCTGTATATATATGACGACTGTGT 60.128 42.308 5.44 0.00 0.00 3.72
1892 5285 0.179032 TGGAAGCAAGTCAAGCGGAA 60.179 50.000 0.00 0.00 37.01 4.30
1971 5545 2.093310 CGACATTAGCACTGCTGAACTG 59.907 50.000 14.15 4.48 40.10 3.16
1992 5573 0.796312 TCTTGCTTCATCGCCGTTTC 59.204 50.000 0.00 0.00 0.00 2.78
1995 5576 0.108186 TGATCTTGCTTCATCGCCGT 60.108 50.000 0.00 0.00 0.00 5.68
2023 5719 0.175760 TCGAAGCCTGTCTGCCATAC 59.824 55.000 0.00 0.00 0.00 2.39
2030 5726 1.675972 TCGAGCTCGAAGCCTGTCT 60.676 57.895 35.16 0.00 46.30 3.41
2044 5740 5.743026 AGATCATATGTACGCCTATCGAG 57.257 43.478 1.90 0.00 41.67 4.04
2046 5742 5.513141 CACAAGATCATATGTACGCCTATCG 59.487 44.000 1.90 0.00 45.38 2.92
2055 5751 5.988287 TGAGGCAACACAAGATCATATGTA 58.012 37.500 1.90 0.00 41.41 2.29
2056 5752 4.847198 TGAGGCAACACAAGATCATATGT 58.153 39.130 1.90 0.00 41.41 2.29
2057 5753 5.823209 TTGAGGCAACACAAGATCATATG 57.177 39.130 0.00 0.00 42.46 1.78
2072 5771 3.194116 GCTTTCATGAAAGGATTGAGGCA 59.806 43.478 36.91 8.72 45.85 4.75
2183 5919 2.430244 CCCCTGAACGACACGACG 60.430 66.667 0.00 0.00 39.31 5.12
2200 5936 0.541863 AGTGATGATCGAACCCCCAC 59.458 55.000 0.00 0.00 0.00 4.61
2201 5937 1.065491 CAAGTGATGATCGAACCCCCA 60.065 52.381 0.00 0.00 0.00 4.96
2212 5948 3.131755 ACTCGATGCTGATCAAGTGATGA 59.868 43.478 0.00 0.00 43.67 2.92
2213 5949 3.455327 ACTCGATGCTGATCAAGTGATG 58.545 45.455 0.00 0.00 34.37 3.07
2214 5950 3.384146 AGACTCGATGCTGATCAAGTGAT 59.616 43.478 0.00 0.00 37.51 3.06
2215 5951 2.757314 AGACTCGATGCTGATCAAGTGA 59.243 45.455 0.00 0.00 25.06 3.41
2216 5952 2.858941 CAGACTCGATGCTGATCAAGTG 59.141 50.000 8.53 0.00 34.06 3.16
2217 5953 2.757314 TCAGACTCGATGCTGATCAAGT 59.243 45.455 11.91 0.00 36.31 3.16
2218 5954 3.066481 TCTCAGACTCGATGCTGATCAAG 59.934 47.826 15.16 6.58 40.11 3.02
2221 5957 2.030893 CCTCTCAGACTCGATGCTGATC 60.031 54.545 15.16 0.00 40.11 2.92
2230 5978 0.254747 ACCTCCTCCTCTCAGACTCG 59.745 60.000 0.00 0.00 0.00 4.18
2240 5990 1.273552 CCTCTTTCCTCACCTCCTCCT 60.274 57.143 0.00 0.00 0.00 3.69
2289 6040 1.527844 GATGTGCTGGGGATCAGGC 60.528 63.158 0.00 0.00 43.54 4.85
2290 6041 1.150081 GGATGTGCTGGGGATCAGG 59.850 63.158 0.00 0.00 43.54 3.86
2308 6062 6.102615 AGGGATAGCTAGAGGTAGATATGGAG 59.897 46.154 0.00 0.00 37.87 3.86
2324 6092 4.268359 CAGAAAGCAAGAAAGGGATAGCT 58.732 43.478 0.00 0.00 0.00 3.32
2325 6093 3.379688 CCAGAAAGCAAGAAAGGGATAGC 59.620 47.826 0.00 0.00 0.00 2.97
2328 6096 3.814504 TCCAGAAAGCAAGAAAGGGAT 57.185 42.857 0.00 0.00 0.00 3.85
2331 6099 9.741647 GAATAATAATCCAGAAAGCAAGAAAGG 57.258 33.333 0.00 0.00 0.00 3.11
2378 6146 1.327690 ATGGCCTGGCTTTGCATCAG 61.328 55.000 19.68 0.00 0.00 2.90
2397 6165 0.718904 GTGTGTATCATGCGTTGCGA 59.281 50.000 0.00 0.00 0.00 5.10
2489 6257 3.677596 ACTTTCAAAAGTGTTTTGTGCCG 59.322 39.130 7.32 3.33 46.80 5.69
2516 6289 7.120432 AGCAGAGAAGAATTAGGTGAATGAAAC 59.880 37.037 0.00 0.00 0.00 2.78
2518 6291 6.715280 AGCAGAGAAGAATTAGGTGAATGAA 58.285 36.000 0.00 0.00 0.00 2.57
2519 6292 6.305272 AGCAGAGAAGAATTAGGTGAATGA 57.695 37.500 0.00 0.00 0.00 2.57
2520 6293 6.998968 AAGCAGAGAAGAATTAGGTGAATG 57.001 37.500 0.00 0.00 0.00 2.67
2521 6294 8.414629 AAAAAGCAGAGAAGAATTAGGTGAAT 57.585 30.769 0.00 0.00 0.00 2.57
2595 6369 2.159393 CCATCCACTACGTTGCAAATGG 60.159 50.000 0.00 4.27 37.08 3.16
2600 6374 2.498078 TGTATCCATCCACTACGTTGCA 59.502 45.455 0.00 0.00 0.00 4.08
2601 6375 3.123804 CTGTATCCATCCACTACGTTGC 58.876 50.000 0.00 0.00 0.00 4.17
2602 6376 3.717707 CCTGTATCCATCCACTACGTTG 58.282 50.000 0.00 0.00 0.00 4.10
2615 6395 0.752743 TTGCTGCATGGCCTGTATCC 60.753 55.000 1.84 0.00 0.00 2.59
2616 6396 0.383231 GTTGCTGCATGGCCTGTATC 59.617 55.000 1.84 0.00 0.00 2.24
2622 6402 2.779033 GGCTAGTTGCTGCATGGCC 61.779 63.158 13.69 13.69 42.39 5.36
2624 6404 0.679002 ACTGGCTAGTTGCTGCATGG 60.679 55.000 1.84 0.00 42.39 3.66
2631 6411 4.693283 TGTCATATGTACTGGCTAGTTGC 58.307 43.478 8.46 2.69 38.36 4.17
2634 6414 7.145985 CGTAATTGTCATATGTACTGGCTAGT 58.854 38.462 8.18 8.18 40.99 2.57
2639 6419 6.593072 CATGCGTAATTGTCATATGTACTGG 58.407 40.000 1.90 0.00 0.00 4.00
2640 6420 6.073369 GCATGCGTAATTGTCATATGTACTG 58.927 40.000 0.00 0.00 0.00 2.74
2641 6421 5.107491 CGCATGCGTAATTGTCATATGTACT 60.107 40.000 31.33 0.00 34.35 2.73
2691 6479 9.826574 AGAGCATTATGTTAAGTTTATACCGAA 57.173 29.630 0.00 0.00 0.00 4.30
2701 6489 8.239314 CACATGTCAAAGAGCATTATGTTAAGT 58.761 33.333 0.00 0.00 0.00 2.24
2704 6492 6.095300 CCCACATGTCAAAGAGCATTATGTTA 59.905 38.462 0.00 0.00 0.00 2.41
2707 6495 4.202080 CCCCACATGTCAAAGAGCATTATG 60.202 45.833 0.00 0.00 0.00 1.90
2708 6496 3.956199 CCCCACATGTCAAAGAGCATTAT 59.044 43.478 0.00 0.00 0.00 1.28
2710 6498 2.173519 CCCCACATGTCAAAGAGCATT 58.826 47.619 0.00 0.00 0.00 3.56
2712 6500 0.478072 ACCCCACATGTCAAAGAGCA 59.522 50.000 0.00 0.00 0.00 4.26
2714 6502 1.352352 AGGACCCCACATGTCAAAGAG 59.648 52.381 0.00 0.00 34.36 2.85
2716 6504 1.202927 ACAGGACCCCACATGTCAAAG 60.203 52.381 0.00 0.00 34.36 2.77
2723 6511 5.729718 AGTAATAAGTTACAGGACCCCACAT 59.270 40.000 1.71 0.00 42.13 3.21
2726 6514 5.190330 GGAAGTAATAAGTTACAGGACCCCA 59.810 44.000 1.71 0.00 42.13 4.96
2729 6517 7.618137 TGAAGGAAGTAATAAGTTACAGGACC 58.382 38.462 1.71 0.00 42.13 4.46
2731 6519 8.483758 GGATGAAGGAAGTAATAAGTTACAGGA 58.516 37.037 1.71 0.00 42.13 3.86
2735 6523 9.457436 TTTGGGATGAAGGAAGTAATAAGTTAC 57.543 33.333 0.00 0.00 40.40 2.50
2745 6533 5.840693 ACAAGAATTTTGGGATGAAGGAAGT 59.159 36.000 5.68 0.00 0.00 3.01
2746 6534 6.210185 AGACAAGAATTTTGGGATGAAGGAAG 59.790 38.462 5.68 0.00 0.00 3.46
2747 6535 6.077322 AGACAAGAATTTTGGGATGAAGGAA 58.923 36.000 5.68 0.00 0.00 3.36
2748 6536 5.644188 AGACAAGAATTTTGGGATGAAGGA 58.356 37.500 5.68 0.00 0.00 3.36
2749 6537 5.990120 AGACAAGAATTTTGGGATGAAGG 57.010 39.130 5.68 0.00 0.00 3.46
2750 6538 9.933723 ATTTAAGACAAGAATTTTGGGATGAAG 57.066 29.630 5.68 0.00 0.00 3.02
2771 6559 9.685828 CGTCCCAAAATTCTTGTCTTAATTTAA 57.314 29.630 0.00 0.00 34.93 1.52
2772 6560 8.301002 CCGTCCCAAAATTCTTGTCTTAATTTA 58.699 33.333 0.00 0.00 34.93 1.40
2773 6561 7.014808 TCCGTCCCAAAATTCTTGTCTTAATTT 59.985 33.333 0.00 0.00 36.98 1.82
2774 6562 6.492087 TCCGTCCCAAAATTCTTGTCTTAATT 59.508 34.615 0.00 0.00 0.00 1.40
2775 6563 6.007703 TCCGTCCCAAAATTCTTGTCTTAAT 58.992 36.000 0.00 0.00 0.00 1.40
2776 6564 5.378332 TCCGTCCCAAAATTCTTGTCTTAA 58.622 37.500 0.00 0.00 0.00 1.85
2777 6565 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2778 6566 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2779 6567 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2780 6568 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2781 6569 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2782 6570 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2783 6571 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2784 6572 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2785 6573 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2786 6574 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2787 6575 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2788 6576 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
2789 6577 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
2790 6578 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
2791 6579 0.042131 AACATACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
2792 6580 0.464452 CAACATACTCCCTCCGTCCC 59.536 60.000 0.00 0.00 0.00 4.46
2793 6581 0.179081 GCAACATACTCCCTCCGTCC 60.179 60.000 0.00 0.00 0.00 4.79
2794 6582 0.824759 AGCAACATACTCCCTCCGTC 59.175 55.000 0.00 0.00 0.00 4.79
2795 6583 1.066143 CAAGCAACATACTCCCTCCGT 60.066 52.381 0.00 0.00 0.00 4.69
2796 6584 1.207089 TCAAGCAACATACTCCCTCCG 59.793 52.381 0.00 0.00 0.00 4.63
2797 6585 2.633488 GTCAAGCAACATACTCCCTCC 58.367 52.381 0.00 0.00 0.00 4.30
2798 6586 2.271800 CGTCAAGCAACATACTCCCTC 58.728 52.381 0.00 0.00 0.00 4.30
2799 6587 1.623811 ACGTCAAGCAACATACTCCCT 59.376 47.619 0.00 0.00 0.00 4.20
2800 6588 1.732259 CACGTCAAGCAACATACTCCC 59.268 52.381 0.00 0.00 0.00 4.30
2801 6589 1.128692 GCACGTCAAGCAACATACTCC 59.871 52.381 0.00 0.00 0.00 3.85
2802 6590 2.069273 AGCACGTCAAGCAACATACTC 58.931 47.619 0.00 0.00 0.00 2.59
2803 6591 2.169832 AGCACGTCAAGCAACATACT 57.830 45.000 0.00 0.00 0.00 2.12
2804 6592 2.348666 CCTAGCACGTCAAGCAACATAC 59.651 50.000 0.00 0.00 0.00 2.39
2805 6593 2.616960 CCTAGCACGTCAAGCAACATA 58.383 47.619 0.00 0.00 0.00 2.29
2806 6594 1.442769 CCTAGCACGTCAAGCAACAT 58.557 50.000 0.00 0.00 0.00 2.71
2807 6595 1.227999 GCCTAGCACGTCAAGCAACA 61.228 55.000 0.00 0.00 0.00 3.33
2808 6596 1.497722 GCCTAGCACGTCAAGCAAC 59.502 57.895 0.00 0.00 0.00 4.17
2809 6597 2.027073 CGCCTAGCACGTCAAGCAA 61.027 57.895 0.00 0.00 0.00 3.91
2810 6598 2.225791 ATCGCCTAGCACGTCAAGCA 62.226 55.000 0.00 0.00 0.00 3.91
2811 6599 1.084370 AATCGCCTAGCACGTCAAGC 61.084 55.000 3.71 0.00 0.00 4.01
2812 6600 0.924090 GAATCGCCTAGCACGTCAAG 59.076 55.000 3.71 0.00 0.00 3.02
2813 6601 0.530744 AGAATCGCCTAGCACGTCAA 59.469 50.000 3.71 0.00 0.00 3.18
2814 6602 1.065102 GTAGAATCGCCTAGCACGTCA 59.935 52.381 3.71 0.00 0.00 4.35
2815 6603 1.065102 TGTAGAATCGCCTAGCACGTC 59.935 52.381 3.71 0.00 0.00 4.34
2816 6604 1.100510 TGTAGAATCGCCTAGCACGT 58.899 50.000 3.71 0.00 0.00 4.49
2817 6605 2.423926 ATGTAGAATCGCCTAGCACG 57.576 50.000 0.00 0.00 0.00 5.34
2818 6606 6.866770 TGTAATTATGTAGAATCGCCTAGCAC 59.133 38.462 0.00 0.00 0.00 4.40
2819 6607 6.988522 TGTAATTATGTAGAATCGCCTAGCA 58.011 36.000 0.00 0.00 0.00 3.49
2820 6608 9.582431 TTATGTAATTATGTAGAATCGCCTAGC 57.418 33.333 0.00 0.00 0.00 3.42


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

AutoCloner maintained by Alex Coulton.