Multiple sequence alignment - TraesCS1A01G197500

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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 TraesCS1A01G197500 chr1A 100.000 3474 0 0 1 3474 355349383 355345910 0.000000e+00 6416.0
1 TraesCS1A01G197500 chr1A 100.000 1177 0 0 3778 4954 355345606 355344430 0.000000e+00 2174.0
2 TraesCS1A01G197500 chr1A 95.082 122 6 0 1 122 412553901 412554022 5.060000e-45 193.0
3 TraesCS1A01G197500 chr1A 84.694 196 27 3 2421 2614 527245794 527245988 5.060000e-45 193.0
4 TraesCS1A01G197500 chr1A 94.355 124 7 0 1 124 117123754 117123877 1.820000e-44 191.0
5 TraesCS1A01G197500 chr1A 93.478 46 2 1 4893 4938 143815849 143815893 3.200000e-07 67.6
6 TraesCS1A01G197500 chr1A 93.478 46 2 1 4886 4931 481924418 481924462 3.200000e-07 67.6
7 TraesCS1A01G197500 chr1D 92.930 1754 83 24 696 2427 283622961 283621227 0.000000e+00 2514.0
8 TraesCS1A01G197500 chr1D 95.148 1113 37 6 3779 4882 283619724 283618620 0.000000e+00 1740.0
9 TraesCS1A01G197500 chr1D 91.587 1046 46 9 2421 3455 283621175 283620161 0.000000e+00 1406.0
10 TraesCS1A01G197500 chr1D 88.983 472 39 10 136 602 283623929 283623466 5.560000e-159 571.0
11 TraesCS1A01G197500 chr1D 79.762 168 23 9 514 680 374739786 374739943 1.460000e-20 111.0
12 TraesCS1A01G197500 chr1B 96.280 1156 30 6 1974 3126 385300401 385299256 0.000000e+00 1884.0
13 TraesCS1A01G197500 chr1B 93.984 1147 34 9 3778 4915 385298669 385297549 0.000000e+00 1703.0
14 TraesCS1A01G197500 chr1B 93.200 1103 37 13 855 1941 385301481 385300401 0.000000e+00 1587.0
15 TraesCS1A01G197500 chr1B 94.788 307 13 1 3116 3419 385299097 385298791 4.490000e-130 475.0
16 TraesCS1A01G197500 chr1B 81.429 140 24 2 1654 1791 47810074 47810213 4.050000e-21 113.0
17 TraesCS1A01G197500 chr1B 83.898 118 19 0 1674 1791 164196849 164196966 4.050000e-21 113.0
18 TraesCS1A01G197500 chr1B 89.091 55 4 2 4893 4946 6423562 6423509 3.200000e-07 67.6
19 TraesCS1A01G197500 chr2A 85.149 202 27 3 2421 2620 733160121 733160321 2.340000e-48 204.0
20 TraesCS1A01G197500 chr2A 84.343 198 28 3 2421 2616 777014525 777014721 1.820000e-44 191.0
21 TraesCS1A01G197500 chr4A 95.968 124 4 1 1 124 575963524 575963402 3.020000e-47 200.0
22 TraesCS1A01G197500 chr4A 84.848 198 27 3 2421 2616 617657237 617657433 3.910000e-46 196.0
23 TraesCS1A01G197500 chr7A 96.639 119 4 0 1 119 158826604 158826486 1.090000e-46 198.0
24 TraesCS1A01G197500 chr7A 97.436 39 1 0 4893 4931 562274922 562274960 3.200000e-07 67.6
25 TraesCS1A01G197500 chr6A 95.902 122 5 0 1 122 128388722 128388843 1.090000e-46 198.0
26 TraesCS1A01G197500 chr6A 96.610 118 4 0 1 118 405308673 405308790 3.910000e-46 196.0
27 TraesCS1A01G197500 chr6A 93.077 130 8 1 1 129 87598288 87598417 6.550000e-44 189.0
28 TraesCS1A01G197500 chr3A 96.610 118 4 0 1 118 683695395 683695278 3.910000e-46 196.0
29 TraesCS1A01G197500 chr3A 95.082 122 5 1 1 122 315977482 315977362 1.820000e-44 191.0
30 TraesCS1A01G197500 chr3B 84.772 197 27 3 2421 2615 155822942 155823137 1.410000e-45 195.0
31 TraesCS1A01G197500 chr3B 84.080 201 29 3 2421 2620 452109408 452109606 1.820000e-44 191.0
32 TraesCS1A01G197500 chr5D 84.343 198 30 1 2421 2617 136352044 136352241 5.060000e-45 193.0
33 TraesCS1A01G197500 chr7B 76.358 313 50 21 377 680 481832165 481832462 4.000000e-31 147.0
34 TraesCS1A01G197500 chr7B 82.941 170 16 10 518 680 485077258 485077095 1.860000e-29 141.0
35 TraesCS1A01G197500 chr7B 83.471 121 20 0 1674 1794 544327009 544326889 4.050000e-21 113.0
36 TraesCS1A01G197500 chr2B 85.833 120 16 1 1675 1794 220900059 220899941 5.210000e-25 126.0
37 TraesCS1A01G197500 chr2B 95.455 44 1 1 4888 4931 40453277 40453235 8.900000e-08 69.4
38 TraesCS1A01G197500 chrUn 83.898 118 19 0 1674 1791 235812430 235812547 4.050000e-21 113.0
39 TraesCS1A01G197500 chrUn 83.471 121 20 0 1674 1794 382475545 382475425 4.050000e-21 113.0
40 TraesCS1A01G197500 chr4B 81.295 139 25 1 1654 1791 64840745 64840883 1.460000e-20 111.0
41 TraesCS1A01G197500 chr6B 81.022 137 25 1 1659 1794 456050468 456050332 1.890000e-19 108.0
42 TraesCS1A01G197500 chr5B 84.404 109 13 4 574 680 92678252 92678146 2.440000e-18 104.0
43 TraesCS1A01G197500 chr7D 74.098 305 45 19 380 680 85918511 85918237 1.470000e-15 95.3
44 TraesCS1A01G197500 chr6D 89.655 58 3 3 4893 4947 264679145 264679088 2.470000e-08 71.3
45 TraesCS1A01G197500 chr3D 89.655 58 3 2 4893 4947 403700674 403700731 2.470000e-08 71.3
46 TraesCS1A01G197500 chr5A 97.222 36 1 0 4893 4928 401142951 401142986 1.490000e-05 62.1


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 TraesCS1A01G197500 chr1A 355344430 355349383 4953 True 4295.00 6416 100.000 1 4954 2 chr1A.!!$R1 4953
1 TraesCS1A01G197500 chr1D 283618620 283623929 5309 True 1557.75 2514 92.162 136 4882 4 chr1D.!!$R1 4746
2 TraesCS1A01G197500 chr1B 385297549 385301481 3932 True 1412.25 1884 94.563 855 4915 4 chr1B.!!$R2 4060

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
104 105 0.037232 CCTCAAGGGTCTGACGGAAC 60.037 60.000 1.07 0.0 0.00 3.62 F
822 1273 0.179084 CAAGGAGCGGCGAATAGGAA 60.179 55.000 12.98 0.0 0.00 3.36 F
918 1369 0.396060 GGCTGGGCTATCTTCTCAGG 59.604 60.000 0.00 0.0 0.00 3.86 F
927 1378 1.786937 ATCTTCTCAGGACGCTCCAT 58.213 50.000 6.78 0.0 39.61 3.41 F
1161 1628 2.435059 GGCTCGCTGTTCCACTCC 60.435 66.667 0.00 0.0 0.00 3.85 F
2946 3498 0.179001 TCACCAGTCCTCGAGTGTCA 60.179 55.000 12.31 0.0 31.64 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1736 2206 1.069906 CCAAAGTACACGCTTGAGCAC 60.070 52.381 0.0 0.0 42.21 4.40 R
1738 2208 1.194772 GACCAAAGTACACGCTTGAGC 59.805 52.381 0.0 0.0 37.78 4.26 R
1741 2211 1.937223 TGTGACCAAAGTACACGCTTG 59.063 47.619 0.0 0.0 37.35 4.01 R
1742 2212 2.319136 TGTGACCAAAGTACACGCTT 57.681 45.000 0.0 0.0 37.35 4.68 R
3152 3873 1.144969 CTAACTCGTCTTTTGCGGCA 58.855 50.000 0.0 0.0 0.00 5.69 R
4699 5548 0.112412 AAAACCTGAGGCCCGAATGT 59.888 50.000 0.0 0.0 0.00 2.71 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
22 23 5.759506 TTCGTTGTTTCCAGCTTAAATCA 57.240 34.783 0.00 0.00 0.00 2.57
23 24 5.103290 TCGTTGTTTCCAGCTTAAATCAC 57.897 39.130 0.00 0.00 0.00 3.06
24 25 3.906008 CGTTGTTTCCAGCTTAAATCACG 59.094 43.478 9.18 9.18 0.00 4.35
25 26 3.552604 TGTTTCCAGCTTAAATCACGC 57.447 42.857 0.00 0.00 0.00 5.34
26 27 2.095969 TGTTTCCAGCTTAAATCACGCG 60.096 45.455 3.53 3.53 0.00 6.01
27 28 2.087501 TTCCAGCTTAAATCACGCGA 57.912 45.000 15.93 0.00 0.00 5.87
28 29 1.640428 TCCAGCTTAAATCACGCGAG 58.360 50.000 15.93 4.59 0.00 5.03
29 30 0.652592 CCAGCTTAAATCACGCGAGG 59.347 55.000 15.93 4.29 0.00 4.63
30 31 1.640428 CAGCTTAAATCACGCGAGGA 58.360 50.000 15.93 10.85 0.00 3.71
31 32 1.590238 CAGCTTAAATCACGCGAGGAG 59.410 52.381 15.93 0.00 0.00 3.69
32 33 1.476891 AGCTTAAATCACGCGAGGAGA 59.523 47.619 15.93 5.34 0.00 3.71
33 34 2.101582 AGCTTAAATCACGCGAGGAGAT 59.898 45.455 15.93 7.73 0.00 2.75
34 35 2.866762 GCTTAAATCACGCGAGGAGATT 59.133 45.455 15.93 13.56 40.21 2.40
35 36 3.302740 GCTTAAATCACGCGAGGAGATTG 60.303 47.826 15.93 0.00 39.05 2.67
36 37 2.672961 AAATCACGCGAGGAGATTGA 57.327 45.000 15.93 4.01 39.05 2.57
37 38 2.672961 AATCACGCGAGGAGATTGAA 57.327 45.000 15.93 0.00 38.14 2.69
38 39 1.927895 ATCACGCGAGGAGATTGAAC 58.072 50.000 15.93 0.00 0.00 3.18
39 40 0.456142 TCACGCGAGGAGATTGAACG 60.456 55.000 15.93 0.00 0.00 3.95
40 41 0.732880 CACGCGAGGAGATTGAACGT 60.733 55.000 15.93 0.00 0.00 3.99
41 42 0.806868 ACGCGAGGAGATTGAACGTA 59.193 50.000 15.93 0.00 0.00 3.57
42 43 1.202154 ACGCGAGGAGATTGAACGTAG 60.202 52.381 15.93 0.00 0.00 3.51
43 44 1.063616 CGCGAGGAGATTGAACGTAGA 59.936 52.381 0.00 0.00 0.00 2.59
44 45 2.287069 CGCGAGGAGATTGAACGTAGAT 60.287 50.000 0.00 0.00 0.00 1.98
45 46 3.301706 GCGAGGAGATTGAACGTAGATC 58.698 50.000 0.00 0.00 0.00 2.75
46 47 3.546617 CGAGGAGATTGAACGTAGATCG 58.453 50.000 0.00 0.00 46.00 3.69
47 48 3.607310 CGAGGAGATTGAACGTAGATCGG 60.607 52.174 0.00 0.00 44.69 4.18
48 49 3.288964 AGGAGATTGAACGTAGATCGGT 58.711 45.455 0.00 0.00 44.57 4.69
49 50 4.458397 AGGAGATTGAACGTAGATCGGTA 58.542 43.478 0.00 0.00 40.67 4.02
50 51 4.515944 AGGAGATTGAACGTAGATCGGTAG 59.484 45.833 0.00 0.00 40.67 3.18
51 52 4.320348 GGAGATTGAACGTAGATCGGTAGG 60.320 50.000 0.00 0.00 40.67 3.18
52 53 3.568853 AGATTGAACGTAGATCGGTAGGG 59.431 47.826 0.00 0.00 40.67 3.53
53 54 1.683943 TGAACGTAGATCGGTAGGGG 58.316 55.000 0.00 0.00 40.67 4.79
54 55 1.212688 TGAACGTAGATCGGTAGGGGA 59.787 52.381 0.00 0.00 40.67 4.81
55 56 1.878734 GAACGTAGATCGGTAGGGGAG 59.121 57.143 0.00 0.00 40.67 4.30
56 57 1.135094 ACGTAGATCGGTAGGGGAGA 58.865 55.000 0.00 0.00 44.69 3.71
57 58 1.072015 ACGTAGATCGGTAGGGGAGAG 59.928 57.143 0.00 0.00 44.69 3.20
58 59 1.347050 CGTAGATCGGTAGGGGAGAGA 59.653 57.143 0.00 0.00 35.71 3.10
59 60 2.027007 CGTAGATCGGTAGGGGAGAGAT 60.027 54.545 0.00 0.00 35.71 2.75
60 61 2.891191 AGATCGGTAGGGGAGAGATC 57.109 55.000 0.00 0.00 38.29 2.75
61 62 2.354328 AGATCGGTAGGGGAGAGATCT 58.646 52.381 0.00 0.00 42.02 2.75
62 63 2.307686 AGATCGGTAGGGGAGAGATCTC 59.692 54.545 15.29 15.29 42.90 2.75
70 71 2.801421 GAGAGATCTCCGCGCACA 59.199 61.111 19.30 0.00 37.02 4.57
71 72 1.587613 GAGAGATCTCCGCGCACAC 60.588 63.158 19.30 0.00 37.02 3.82
72 73 2.583593 GAGATCTCCGCGCACACC 60.584 66.667 12.00 0.00 0.00 4.16
73 74 4.148825 AGATCTCCGCGCACACCC 62.149 66.667 8.75 0.00 0.00 4.61
74 75 4.148825 GATCTCCGCGCACACCCT 62.149 66.667 8.75 0.00 0.00 4.34
75 76 2.758327 ATCTCCGCGCACACCCTA 60.758 61.111 8.75 0.00 0.00 3.53
76 77 2.685387 GATCTCCGCGCACACCCTAG 62.685 65.000 8.75 0.00 0.00 3.02
77 78 3.760035 CTCCGCGCACACCCTAGT 61.760 66.667 8.75 0.00 0.00 2.57
88 89 2.365408 CACCCTAGTGTTCGAACCTC 57.635 55.000 24.78 17.20 39.30 3.85
89 90 1.616865 CACCCTAGTGTTCGAACCTCA 59.383 52.381 24.78 8.97 39.30 3.86
90 91 2.036733 CACCCTAGTGTTCGAACCTCAA 59.963 50.000 24.78 3.77 39.30 3.02
91 92 2.299297 ACCCTAGTGTTCGAACCTCAAG 59.701 50.000 24.78 15.73 0.00 3.02
92 93 2.353803 CCCTAGTGTTCGAACCTCAAGG 60.354 54.545 24.78 22.28 42.17 3.61
93 94 2.353803 CCTAGTGTTCGAACCTCAAGGG 60.354 54.545 24.78 14.77 40.27 3.95
102 103 4.113617 CCTCAAGGGTCTGACGGA 57.886 61.111 1.07 0.00 0.00 4.69
103 104 2.362242 CCTCAAGGGTCTGACGGAA 58.638 57.895 1.07 0.00 0.00 4.30
104 105 0.037232 CCTCAAGGGTCTGACGGAAC 60.037 60.000 1.07 0.00 0.00 3.62
118 119 2.763651 GGAACCCGAAATCCGACAG 58.236 57.895 0.00 0.00 41.76 3.51
119 120 0.248289 GGAACCCGAAATCCGACAGA 59.752 55.000 0.00 0.00 41.76 3.41
120 121 1.134491 GGAACCCGAAATCCGACAGAT 60.134 52.381 0.00 0.00 41.76 2.90
121 122 2.101917 GGAACCCGAAATCCGACAGATA 59.898 50.000 0.00 0.00 41.76 1.98
122 123 2.884894 ACCCGAAATCCGACAGATAC 57.115 50.000 0.00 0.00 41.76 2.24
123 124 2.104967 ACCCGAAATCCGACAGATACA 58.895 47.619 0.00 0.00 41.76 2.29
124 125 2.159142 ACCCGAAATCCGACAGATACAC 60.159 50.000 0.00 0.00 41.76 2.90
125 126 2.470821 CCGAAATCCGACAGATACACC 58.529 52.381 0.00 0.00 41.76 4.16
126 127 2.117137 CGAAATCCGACAGATACACCG 58.883 52.381 0.00 0.00 41.76 4.94
127 128 2.470821 GAAATCCGACAGATACACCGG 58.529 52.381 0.00 0.00 43.02 5.28
129 130 2.485677 TCCGACAGATACACCGGAC 58.514 57.895 9.46 0.00 45.04 4.79
130 131 0.322726 TCCGACAGATACACCGGACA 60.323 55.000 9.46 0.00 45.04 4.02
131 132 0.528924 CCGACAGATACACCGGACAA 59.471 55.000 9.46 0.00 44.29 3.18
132 133 1.067425 CCGACAGATACACCGGACAAA 60.067 52.381 9.46 0.00 44.29 2.83
133 134 2.418197 CCGACAGATACACCGGACAAAT 60.418 50.000 9.46 0.00 44.29 2.32
134 135 3.259064 CGACAGATACACCGGACAAATT 58.741 45.455 9.46 0.00 0.00 1.82
146 147 4.223659 CCGGACAAATTTTAGAAACACGG 58.776 43.478 0.00 0.00 0.00 4.94
290 293 8.870160 AAACATGAACAAATTTCGAAATCAGA 57.130 26.923 22.93 5.79 0.00 3.27
292 295 8.285776 ACATGAACAAATTTCGAAATCAGAAC 57.714 30.769 22.93 14.64 0.00 3.01
293 296 7.920151 ACATGAACAAATTTCGAAATCAGAACA 59.080 29.630 22.93 18.85 0.00 3.18
417 421 7.326789 ACAAAAATGCTGAAACTATGAACATCG 59.673 33.333 0.00 0.00 0.00 3.84
651 1097 9.634163 GTAGAAGAAAGAAAAACAGAAAAACCA 57.366 29.630 0.00 0.00 0.00 3.67
656 1102 7.602644 AGAAAGAAAAACAGAAAAACCAGGTTC 59.397 33.333 4.93 0.00 0.00 3.62
683 1129 5.600669 AACCATCTAGAAGGTTCCCTTTT 57.399 39.130 23.53 3.26 44.82 2.27
684 1130 5.600669 ACCATCTAGAAGGTTCCCTTTTT 57.399 39.130 13.93 0.00 44.82 1.94
717 1163 2.039348 TCTAGAAGGTTCCCAAAACCGG 59.961 50.000 0.00 0.00 44.82 5.28
779 1230 1.299648 GCTCCCTGTGTGTGGCATA 59.700 57.895 0.00 0.00 0.00 3.14
791 1242 1.743252 TGGCATATGCGTTGCGTCA 60.743 52.632 21.04 8.87 43.26 4.35
795 1246 1.727535 GCATATGCGTTGCGTCAACAA 60.728 47.619 12.82 9.36 43.70 2.83
820 1271 2.247437 GCAAGGAGCGGCGAATAGG 61.247 63.158 12.98 0.00 0.00 2.57
821 1272 1.441729 CAAGGAGCGGCGAATAGGA 59.558 57.895 12.98 0.00 0.00 2.94
822 1273 0.179084 CAAGGAGCGGCGAATAGGAA 60.179 55.000 12.98 0.00 0.00 3.36
918 1369 0.396060 GGCTGGGCTATCTTCTCAGG 59.604 60.000 0.00 0.00 0.00 3.86
927 1378 1.786937 ATCTTCTCAGGACGCTCCAT 58.213 50.000 6.78 0.00 39.61 3.41
1161 1628 2.435059 GGCTCGCTGTTCCACTCC 60.435 66.667 0.00 0.00 0.00 3.85
1207 1674 3.274586 CGGTGATGGCGATGCAGG 61.275 66.667 0.00 0.00 0.00 4.85
1356 1824 2.751259 TGCCTGCATTTCTGAATCTCAC 59.249 45.455 0.00 0.00 0.00 3.51
1374 1842 3.649986 GGTGGTGTGCGTGTCAGC 61.650 66.667 0.00 0.00 37.71 4.26
1532 2000 5.569059 CACGTTTTGCTTAAATTGCTCTAGG 59.431 40.000 0.00 0.00 0.00 3.02
1641 2109 5.867174 CCACACATTCGAATTAGTACTGTCA 59.133 40.000 8.21 0.00 0.00 3.58
1726 2196 4.680934 GCACATAATTGCGCTTAATGTG 57.319 40.909 26.67 26.67 40.37 3.21
1727 2197 4.104776 GCACATAATTGCGCTTAATGTGT 58.895 39.130 28.84 18.77 39.79 3.72
1728 2198 4.027458 GCACATAATTGCGCTTAATGTGTG 60.027 41.667 28.84 25.38 39.79 3.82
1729 2199 4.027458 CACATAATTGCGCTTAATGTGTGC 60.027 41.667 24.56 0.00 40.87 4.57
1735 2205 4.368874 TGCGCTTAATGTGTGCATAATT 57.631 36.364 9.73 0.00 44.53 1.40
1736 2206 4.104066 TGCGCTTAATGTGTGCATAATTG 58.896 39.130 9.73 0.00 44.53 2.32
1737 2207 4.104776 GCGCTTAATGTGTGCATAATTGT 58.895 39.130 0.00 0.00 40.28 2.71
1738 2208 4.027458 GCGCTTAATGTGTGCATAATTGTG 60.027 41.667 0.00 0.00 40.28 3.33
1739 2209 4.027458 CGCTTAATGTGTGCATAATTGTGC 60.027 41.667 19.24 19.24 45.25 4.57
1740 2210 5.104374 GCTTAATGTGTGCATAATTGTGCT 58.896 37.500 24.97 8.81 45.27 4.40
1741 2211 5.230726 GCTTAATGTGTGCATAATTGTGCTC 59.769 40.000 24.97 21.77 45.27 4.26
1742 2212 4.787260 AATGTGTGCATAATTGTGCTCA 57.213 36.364 24.97 23.84 45.27 4.26
1798 2268 6.043411 GGTGGCAAAACACACAACTATTTTA 58.957 36.000 0.00 0.00 43.08 1.52
1840 2322 7.052248 TCATGTCTCTCAAATCACAAGCATAT 58.948 34.615 0.00 0.00 0.00 1.78
1867 2349 4.218417 GGATAACAGCTGCTTTTCTTTCCA 59.782 41.667 15.27 0.00 0.00 3.53
1910 2392 3.799432 ACCAAAGTATAGTTGCCACCA 57.201 42.857 0.00 0.00 0.00 4.17
1960 2442 0.179145 GCAAATGCTAGCCTGCTGTG 60.179 55.000 20.41 9.09 38.21 3.66
1968 2450 3.880846 GCCTGCTGTGGCGCATAC 61.881 66.667 10.83 8.58 43.74 2.39
2203 2686 4.692625 ACTTAGCAACTACAGCATCTGTTG 59.307 41.667 4.70 5.89 42.59 3.33
2340 2823 6.042781 TGTGAGATAAGTCTGTTTAACACCCT 59.957 38.462 0.00 0.00 33.97 4.34
2370 2853 1.272704 GCTTTGGACCATTTCCCTCCT 60.273 52.381 0.00 0.00 45.17 3.69
2495 3038 6.148811 CCTGTGGAACGTAGTACAAATGATTT 59.851 38.462 0.38 0.00 45.00 2.17
2606 3149 8.951243 AGTCCTATGAATTTCTTTTCTAGCAAC 58.049 33.333 0.00 0.00 0.00 4.17
2656 3200 6.248569 TCTAGCCCCTTGACCTAATTAAAG 57.751 41.667 0.00 0.00 0.00 1.85
2657 3201 4.948062 AGCCCCTTGACCTAATTAAAGT 57.052 40.909 0.00 0.00 0.00 2.66
2658 3202 6.904654 TCTAGCCCCTTGACCTAATTAAAGTA 59.095 38.462 0.00 0.00 0.00 2.24
2659 3203 6.592207 AGCCCCTTGACCTAATTAAAGTAT 57.408 37.500 0.00 0.00 0.00 2.12
2660 3204 6.981737 AGCCCCTTGACCTAATTAAAGTATT 58.018 36.000 0.00 0.00 0.00 1.89
2661 3205 8.109560 AGCCCCTTGACCTAATTAAAGTATTA 57.890 34.615 0.00 0.00 0.00 0.98
2662 3206 8.562635 AGCCCCTTGACCTAATTAAAGTATTAA 58.437 33.333 0.00 0.00 35.57 1.40
2663 3207 9.192642 GCCCCTTGACCTAATTAAAGTATTAAA 57.807 33.333 0.00 0.00 34.80 1.52
2748 3300 5.053145 GGCAGATTAGACATCGTTTGATCT 58.947 41.667 0.00 0.00 30.49 2.75
2816 3368 0.463295 CATCTGACTTGGCCGATGCT 60.463 55.000 0.00 0.00 37.74 3.79
2946 3498 0.179001 TCACCAGTCCTCGAGTGTCA 60.179 55.000 12.31 0.00 31.64 3.58
3065 3617 2.111878 AGTCAGCCACTGTGTGCC 59.888 61.111 14.77 1.09 32.26 5.01
3071 3623 3.667282 CCACTGTGTGCCAGCTGC 61.667 66.667 8.66 4.57 45.68 5.25
3228 3955 1.227943 GCCACAGAGTGCCTTGTCA 60.228 57.895 0.00 0.00 31.34 3.58
3296 4023 1.381928 GGTCCATCGACGAGGCTGTA 61.382 60.000 3.51 0.00 40.17 2.74
3419 4146 5.661458 TGAGCTAAGCCAGTGTCTAATTAC 58.339 41.667 0.00 0.00 0.00 1.89
3444 4171 3.297134 ACTGGCCGATAAATCATGGTT 57.703 42.857 0.00 0.00 0.00 3.67
3473 4200 8.044060 GGTATAATTACCCGGTTTTATTAGGC 57.956 38.462 0.00 0.00 41.91 3.93
3887 4727 3.750652 CCAAGGAAGCAAAGAGAAGACTC 59.249 47.826 0.00 0.00 42.90 3.36
4026 4868 6.949352 ATACTGATTGCCAACTTATCTTGG 57.051 37.500 0.00 0.00 43.36 3.61
4038 4880 6.659242 CCAACTTATCTTGGTACATTTGTCCT 59.341 38.462 0.00 0.00 39.30 3.85
4235 5077 6.109359 CAGTAAGGAAACTCTATGTCCCTTG 58.891 44.000 0.00 0.00 42.68 3.61
4315 5157 7.672983 TTGTAGAAATTCAGAGGACATTGTC 57.327 36.000 8.34 8.34 0.00 3.18
4358 5200 2.535984 CTCGAATCACATAGTTCACCGC 59.464 50.000 0.00 0.00 0.00 5.68
4366 5208 3.974401 CACATAGTTCACCGCTTTGTTTG 59.026 43.478 0.00 0.00 0.00 2.93
4507 5356 5.505324 GCAGGTTGAATCTGAGTATGAATGC 60.505 44.000 10.11 0.00 34.36 3.56
4528 5377 3.458189 CGTACCCAAGGATAAAGAGCAG 58.542 50.000 0.00 0.00 0.00 4.24
4553 5402 7.717875 AGCGTTTATTGGCCATATAGAAAGTTA 59.282 33.333 6.09 0.00 0.00 2.24
4699 5548 3.254060 GTCGTCTGAGCTTTTATCTGCA 58.746 45.455 0.00 0.00 0.00 4.41
4915 5764 3.377172 CCATCCGTCCCAAAATAAGTGTC 59.623 47.826 0.00 0.00 0.00 3.67
4916 5765 2.690786 TCCGTCCCAAAATAAGTGTCG 58.309 47.619 0.00 0.00 0.00 4.35
4917 5766 1.129811 CCGTCCCAAAATAAGTGTCGC 59.870 52.381 0.00 0.00 0.00 5.19
4918 5767 2.073816 CGTCCCAAAATAAGTGTCGCT 58.926 47.619 0.00 0.00 0.00 4.93
4919 5768 2.159707 CGTCCCAAAATAAGTGTCGCTG 60.160 50.000 0.00 0.00 0.00 5.18
4920 5769 3.071479 GTCCCAAAATAAGTGTCGCTGA 58.929 45.455 0.00 0.00 0.00 4.26
4921 5770 3.689649 GTCCCAAAATAAGTGTCGCTGAT 59.310 43.478 0.00 0.00 0.00 2.90
4922 5771 4.156008 GTCCCAAAATAAGTGTCGCTGATT 59.844 41.667 0.00 0.00 29.37 2.57
4923 5772 4.764823 TCCCAAAATAAGTGTCGCTGATTT 59.235 37.500 3.21 3.21 39.41 2.17
4924 5773 5.941058 TCCCAAAATAAGTGTCGCTGATTTA 59.059 36.000 8.84 0.00 37.29 1.40
4925 5774 6.093495 TCCCAAAATAAGTGTCGCTGATTTAG 59.907 38.462 8.84 4.74 37.29 1.85
4926 5775 6.128007 CCCAAAATAAGTGTCGCTGATTTAGT 60.128 38.462 8.84 0.00 37.29 2.24
4927 5776 7.065324 CCCAAAATAAGTGTCGCTGATTTAGTA 59.935 37.037 8.84 0.00 37.29 1.82
4928 5777 7.903431 CCAAAATAAGTGTCGCTGATTTAGTAC 59.097 37.037 8.84 0.00 37.29 2.73
4929 5778 8.440059 CAAAATAAGTGTCGCTGATTTAGTACA 58.560 33.333 8.84 0.00 37.29 2.90
4930 5779 8.542497 AAATAAGTGTCGCTGATTTAGTACAA 57.458 30.769 6.91 0.00 36.68 2.41
4931 5780 7.757097 ATAAGTGTCGCTGATTTAGTACAAG 57.243 36.000 0.00 0.00 0.00 3.16
4932 5781 5.386958 AGTGTCGCTGATTTAGTACAAGA 57.613 39.130 0.00 0.00 0.00 3.02
4933 5782 5.967088 AGTGTCGCTGATTTAGTACAAGAT 58.033 37.500 0.00 0.00 0.00 2.40
4934 5783 5.807520 AGTGTCGCTGATTTAGTACAAGATG 59.192 40.000 0.00 0.00 0.00 2.90
4935 5784 5.805486 GTGTCGCTGATTTAGTACAAGATGA 59.195 40.000 0.00 0.00 0.00 2.92
4936 5785 5.805486 TGTCGCTGATTTAGTACAAGATGAC 59.195 40.000 0.00 0.00 0.00 3.06
4937 5786 5.805486 GTCGCTGATTTAGTACAAGATGACA 59.195 40.000 0.00 0.00 0.00 3.58
4938 5787 5.805486 TCGCTGATTTAGTACAAGATGACAC 59.195 40.000 0.00 0.00 0.00 3.67
4939 5788 5.807520 CGCTGATTTAGTACAAGATGACACT 59.192 40.000 0.00 0.00 0.00 3.55
4940 5789 6.311445 CGCTGATTTAGTACAAGATGACACTT 59.689 38.462 0.00 0.00 0.00 3.16
4941 5790 7.488150 CGCTGATTTAGTACAAGATGACACTTA 59.512 37.037 0.00 0.00 0.00 2.24
4942 5791 9.319143 GCTGATTTAGTACAAGATGACACTTAT 57.681 33.333 0.00 0.00 0.00 1.73
4948 5797 7.986085 AGTACAAGATGACACTTATTTTGCT 57.014 32.000 0.00 0.00 0.00 3.91
4949 5798 8.396272 AGTACAAGATGACACTTATTTTGCTT 57.604 30.769 0.00 0.00 0.00 3.91
4950 5799 8.507249 AGTACAAGATGACACTTATTTTGCTTC 58.493 33.333 0.00 0.00 0.00 3.86
4951 5800 7.275888 ACAAGATGACACTTATTTTGCTTCA 57.724 32.000 0.00 0.00 0.00 3.02
4952 5801 7.715657 ACAAGATGACACTTATTTTGCTTCAA 58.284 30.769 0.00 0.00 0.00 2.69
4953 5802 7.864379 ACAAGATGACACTTATTTTGCTTCAAG 59.136 33.333 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.516090 GTGATTTAAGCTGGAAACAACGAA 58.484 37.500 0.00 0.00 42.06 3.85
1 2 4.319190 CGTGATTTAAGCTGGAAACAACGA 60.319 41.667 17.35 0.00 42.06 3.85
2 3 3.906008 CGTGATTTAAGCTGGAAACAACG 59.094 43.478 12.42 12.42 42.06 4.10
3 4 3.668656 GCGTGATTTAAGCTGGAAACAAC 59.331 43.478 0.00 0.00 42.06 3.32
4 5 3.608241 CGCGTGATTTAAGCTGGAAACAA 60.608 43.478 0.00 0.00 42.06 2.83
5 6 2.095969 CGCGTGATTTAAGCTGGAAACA 60.096 45.455 0.00 0.00 39.59 2.83
6 7 2.158841 TCGCGTGATTTAAGCTGGAAAC 59.841 45.455 5.77 0.00 0.00 2.78
7 8 2.415168 CTCGCGTGATTTAAGCTGGAAA 59.585 45.455 5.77 0.00 0.00 3.13
8 9 1.999735 CTCGCGTGATTTAAGCTGGAA 59.000 47.619 5.77 0.00 0.00 3.53
9 10 1.640428 CTCGCGTGATTTAAGCTGGA 58.360 50.000 5.77 0.00 0.00 3.86
10 11 0.652592 CCTCGCGTGATTTAAGCTGG 59.347 55.000 10.21 0.00 0.00 4.85
11 12 1.590238 CTCCTCGCGTGATTTAAGCTG 59.410 52.381 10.21 0.00 0.00 4.24
12 13 1.476891 TCTCCTCGCGTGATTTAAGCT 59.523 47.619 10.21 0.00 0.00 3.74
13 14 1.922570 TCTCCTCGCGTGATTTAAGC 58.077 50.000 10.21 0.00 0.00 3.09
14 15 4.112634 TCAATCTCCTCGCGTGATTTAAG 58.887 43.478 10.21 0.00 33.43 1.85
15 16 4.118093 TCAATCTCCTCGCGTGATTTAA 57.882 40.909 10.21 3.12 33.43 1.52
16 17 3.793797 TCAATCTCCTCGCGTGATTTA 57.206 42.857 10.21 3.72 33.43 1.40
17 18 2.672961 TCAATCTCCTCGCGTGATTT 57.327 45.000 10.21 1.09 33.43 2.17
18 19 2.271800 GTTCAATCTCCTCGCGTGATT 58.728 47.619 10.21 10.89 35.54 2.57
19 20 1.799181 CGTTCAATCTCCTCGCGTGAT 60.799 52.381 10.21 5.40 0.00 3.06
20 21 0.456142 CGTTCAATCTCCTCGCGTGA 60.456 55.000 10.21 5.32 0.00 4.35
21 22 0.732880 ACGTTCAATCTCCTCGCGTG 60.733 55.000 5.77 2.75 0.00 5.34
22 23 0.806868 TACGTTCAATCTCCTCGCGT 59.193 50.000 5.77 0.00 35.29 6.01
23 24 1.063616 TCTACGTTCAATCTCCTCGCG 59.936 52.381 0.00 0.00 0.00 5.87
24 25 2.846039 TCTACGTTCAATCTCCTCGC 57.154 50.000 0.00 0.00 0.00 5.03
25 26 3.546617 CGATCTACGTTCAATCTCCTCG 58.453 50.000 0.00 0.00 37.22 4.63
26 27 3.315749 ACCGATCTACGTTCAATCTCCTC 59.684 47.826 0.00 0.00 40.78 3.71
27 28 3.288964 ACCGATCTACGTTCAATCTCCT 58.711 45.455 0.00 0.00 40.78 3.69
28 29 3.712091 ACCGATCTACGTTCAATCTCC 57.288 47.619 0.00 0.00 40.78 3.71
29 30 4.320348 CCCTACCGATCTACGTTCAATCTC 60.320 50.000 0.00 0.00 40.78 2.75
30 31 3.568853 CCCTACCGATCTACGTTCAATCT 59.431 47.826 0.00 0.00 40.78 2.40
31 32 3.305199 CCCCTACCGATCTACGTTCAATC 60.305 52.174 0.00 0.00 40.78 2.67
32 33 2.626743 CCCCTACCGATCTACGTTCAAT 59.373 50.000 0.00 0.00 40.78 2.57
33 34 2.026641 CCCCTACCGATCTACGTTCAA 58.973 52.381 0.00 0.00 40.78 2.69
34 35 1.212688 TCCCCTACCGATCTACGTTCA 59.787 52.381 0.00 0.00 40.78 3.18
35 36 1.878734 CTCCCCTACCGATCTACGTTC 59.121 57.143 0.00 0.00 40.78 3.95
36 37 1.492176 TCTCCCCTACCGATCTACGTT 59.508 52.381 0.00 0.00 40.78 3.99
37 38 1.072015 CTCTCCCCTACCGATCTACGT 59.928 57.143 0.00 0.00 40.78 3.57
38 39 1.347050 TCTCTCCCCTACCGATCTACG 59.653 57.143 0.00 0.00 42.18 3.51
39 40 3.264964 AGATCTCTCCCCTACCGATCTAC 59.735 52.174 0.00 0.00 39.08 2.59
40 41 3.520317 GAGATCTCTCCCCTACCGATCTA 59.480 52.174 15.80 0.00 40.46 1.98
41 42 2.307686 GAGATCTCTCCCCTACCGATCT 59.692 54.545 15.80 0.00 42.39 2.75
42 43 2.718563 GAGATCTCTCCCCTACCGATC 58.281 57.143 15.80 0.00 37.02 3.69
43 44 2.891191 GAGATCTCTCCCCTACCGAT 57.109 55.000 15.80 0.00 37.02 4.18
53 54 1.587613 GTGTGCGCGGAGATCTCTC 60.588 63.158 21.81 12.91 42.14 3.20
54 55 2.492090 GTGTGCGCGGAGATCTCT 59.508 61.111 21.81 0.00 0.00 3.10
55 56 2.583593 GGTGTGCGCGGAGATCTC 60.584 66.667 14.75 14.75 0.00 2.75
56 57 4.148825 GGGTGTGCGCGGAGATCT 62.149 66.667 8.15 0.00 0.00 2.75
57 58 2.685387 CTAGGGTGTGCGCGGAGATC 62.685 65.000 8.83 2.94 0.00 2.75
58 59 2.758327 TAGGGTGTGCGCGGAGAT 60.758 61.111 8.83 0.00 0.00 2.75
59 60 3.449227 CTAGGGTGTGCGCGGAGA 61.449 66.667 8.83 0.00 0.00 3.71
60 61 3.760035 ACTAGGGTGTGCGCGGAG 61.760 66.667 8.83 0.00 0.00 4.63
61 62 4.063967 CACTAGGGTGTGCGCGGA 62.064 66.667 8.83 0.00 38.54 5.54
70 71 2.005370 TGAGGTTCGAACACTAGGGT 57.995 50.000 28.24 0.00 0.00 4.34
71 72 2.353803 CCTTGAGGTTCGAACACTAGGG 60.354 54.545 28.54 21.37 31.84 3.53
72 73 2.353803 CCCTTGAGGTTCGAACACTAGG 60.354 54.545 28.89 28.89 33.52 3.02
73 74 2.960819 CCCTTGAGGTTCGAACACTAG 58.039 52.381 28.24 23.23 0.00 2.57
85 86 0.037232 GTTCCGTCAGACCCTTGAGG 60.037 60.000 0.00 0.00 43.78 3.86
86 87 0.037232 GGTTCCGTCAGACCCTTGAG 60.037 60.000 0.00 0.00 0.00 3.02
87 88 2.055299 GGTTCCGTCAGACCCTTGA 58.945 57.895 0.00 0.00 0.00 3.02
88 89 4.695560 GGTTCCGTCAGACCCTTG 57.304 61.111 0.00 0.00 0.00 3.61
100 101 0.248289 TCTGTCGGATTTCGGGTTCC 59.752 55.000 0.00 0.00 39.77 3.62
101 102 2.311124 ATCTGTCGGATTTCGGGTTC 57.689 50.000 0.00 0.00 39.77 3.62
102 103 2.498481 TGTATCTGTCGGATTTCGGGTT 59.502 45.455 0.00 0.00 39.77 4.11
103 104 2.104967 TGTATCTGTCGGATTTCGGGT 58.895 47.619 0.00 0.00 39.77 5.28
104 105 2.470821 GTGTATCTGTCGGATTTCGGG 58.529 52.381 0.00 0.00 39.77 5.14
105 106 2.470821 GGTGTATCTGTCGGATTTCGG 58.529 52.381 0.00 0.00 39.77 4.30
106 107 2.117137 CGGTGTATCTGTCGGATTTCG 58.883 52.381 0.00 0.00 40.90 3.46
107 108 2.100252 TCCGGTGTATCTGTCGGATTTC 59.900 50.000 0.00 0.00 45.37 2.17
108 109 2.104967 TCCGGTGTATCTGTCGGATTT 58.895 47.619 0.00 0.00 45.37 2.17
109 110 1.771565 TCCGGTGTATCTGTCGGATT 58.228 50.000 0.00 0.00 45.37 3.01
110 111 3.507675 TCCGGTGTATCTGTCGGAT 57.492 52.632 0.00 0.00 45.37 4.18
112 113 0.528924 TTGTCCGGTGTATCTGTCGG 59.471 55.000 0.00 0.00 43.42 4.79
113 114 2.357327 TTTGTCCGGTGTATCTGTCG 57.643 50.000 0.00 0.00 0.00 4.35
114 115 5.622770 AAAATTTGTCCGGTGTATCTGTC 57.377 39.130 0.00 0.00 0.00 3.51
115 116 6.469410 TCTAAAATTTGTCCGGTGTATCTGT 58.531 36.000 0.00 0.00 0.00 3.41
116 117 6.978343 TCTAAAATTTGTCCGGTGTATCTG 57.022 37.500 0.00 0.00 0.00 2.90
117 118 7.446013 TGTTTCTAAAATTTGTCCGGTGTATCT 59.554 33.333 0.00 0.00 0.00 1.98
118 119 7.536281 GTGTTTCTAAAATTTGTCCGGTGTATC 59.464 37.037 0.00 0.00 0.00 2.24
119 120 7.364970 GTGTTTCTAAAATTTGTCCGGTGTAT 58.635 34.615 0.00 0.00 0.00 2.29
120 121 6.511444 CGTGTTTCTAAAATTTGTCCGGTGTA 60.511 38.462 0.00 0.00 0.00 2.90
121 122 5.584442 GTGTTTCTAAAATTTGTCCGGTGT 58.416 37.500 0.00 0.00 0.00 4.16
122 123 4.673311 CGTGTTTCTAAAATTTGTCCGGTG 59.327 41.667 0.00 0.00 0.00 4.94
123 124 4.261280 CCGTGTTTCTAAAATTTGTCCGGT 60.261 41.667 0.00 0.00 0.00 5.28
124 125 4.023878 TCCGTGTTTCTAAAATTTGTCCGG 60.024 41.667 0.00 0.00 0.00 5.14
125 126 5.098218 TCCGTGTTTCTAAAATTTGTCCG 57.902 39.130 0.00 0.00 0.00 4.79
126 127 7.758613 TTTTCCGTGTTTCTAAAATTTGTCC 57.241 32.000 0.00 0.00 0.00 4.02
287 290 9.323985 TGTTCCCAATTTTCTAAAAATGTTCTG 57.676 29.630 0.00 0.00 29.05 3.02
288 291 9.898152 TTGTTCCCAATTTTCTAAAAATGTTCT 57.102 25.926 0.00 0.00 29.05 3.01
493 498 9.626045 CTTCAAAGTGTACTTTTCTTTTCAAGT 57.374 29.630 7.25 0.00 43.07 3.16
494 499 9.840427 TCTTCAAAGTGTACTTTTCTTTTCAAG 57.160 29.630 7.25 5.44 43.07 3.02
507 512 9.567848 TTTTCATGTTTTCTCTTCAAAGTGTAC 57.432 29.630 0.00 0.00 0.00 2.90
625 1071 9.634163 TGGTTTTTCTGTTTTTCTTTCTTCTAC 57.366 29.630 0.00 0.00 0.00 2.59
651 1097 3.491766 TCTAGATGGTTCCCAGAACCT 57.508 47.619 23.21 11.64 40.88 3.50
656 1102 3.118223 GGAACCTTCTAGATGGTTCCCAG 60.118 52.174 44.89 21.55 40.55 4.45
683 1129 8.166422 GGAACCTTCTAGATTCAACTCAAAAA 57.834 34.615 6.84 0.00 0.00 1.94
684 1130 7.745620 GGAACCTTCTAGATTCAACTCAAAA 57.254 36.000 6.84 0.00 0.00 2.44
779 1230 1.685302 GAATTGTTGACGCAACGCAT 58.315 45.000 14.86 8.80 46.13 4.73
791 1242 0.517316 GCTCCTTGCGTCGAATTGTT 59.483 50.000 0.00 0.00 0.00 2.83
806 1257 0.179081 AACTTCCTATTCGCCGCTCC 60.179 55.000 0.00 0.00 0.00 4.70
918 1369 1.537776 CCTCATCTGTCATGGAGCGTC 60.538 57.143 0.00 0.00 0.00 5.19
927 1378 2.106566 GCTTCTCTCCCTCATCTGTCA 58.893 52.381 0.00 0.00 0.00 3.58
1044 1511 1.229853 GGTGGGGGAGGAGAGGAAA 60.230 63.158 0.00 0.00 0.00 3.13
1087 1554 4.798682 GCGGAAGGGGAGGGAGGA 62.799 72.222 0.00 0.00 0.00 3.71
1356 1824 3.337889 CTGACACGCACACCACCG 61.338 66.667 0.00 0.00 0.00 4.94
1489 1957 2.546789 GTGAGTACGTTGTGGAAAAGGG 59.453 50.000 0.00 0.00 0.00 3.95
1532 2000 7.226720 ACCGTCATCAATTAGAAATACATGGAC 59.773 37.037 0.00 0.00 0.00 4.02
1728 2198 2.179589 CACGCTTGAGCACAATTATGC 58.820 47.619 0.00 0.00 46.50 3.14
1729 2199 3.476295 ACACGCTTGAGCACAATTATG 57.524 42.857 0.00 0.00 42.21 1.90
1730 2200 4.253685 AGTACACGCTTGAGCACAATTAT 58.746 39.130 0.00 0.00 42.21 1.28
1731 2201 3.659786 AGTACACGCTTGAGCACAATTA 58.340 40.909 0.00 0.00 42.21 1.40
1732 2202 2.494059 AGTACACGCTTGAGCACAATT 58.506 42.857 0.00 0.00 42.21 2.32
1733 2203 2.169832 AGTACACGCTTGAGCACAAT 57.830 45.000 0.00 0.00 42.21 2.71
1734 2204 1.948104 AAGTACACGCTTGAGCACAA 58.052 45.000 0.00 0.00 42.21 3.33
1735 2205 1.597195 CAAAGTACACGCTTGAGCACA 59.403 47.619 0.00 0.00 42.21 4.57
1736 2206 1.069906 CCAAAGTACACGCTTGAGCAC 60.070 52.381 0.00 0.00 42.21 4.40
1737 2207 1.225855 CCAAAGTACACGCTTGAGCA 58.774 50.000 0.00 0.00 42.21 4.26
1738 2208 1.194772 GACCAAAGTACACGCTTGAGC 59.805 52.381 0.00 0.00 37.78 4.26
1739 2209 2.221055 GTGACCAAAGTACACGCTTGAG 59.779 50.000 0.00 0.00 0.00 3.02
1740 2210 2.206750 GTGACCAAAGTACACGCTTGA 58.793 47.619 0.00 0.00 0.00 3.02
1741 2211 1.937223 TGTGACCAAAGTACACGCTTG 59.063 47.619 0.00 0.00 37.35 4.01
1742 2212 2.319136 TGTGACCAAAGTACACGCTT 57.681 45.000 0.00 0.00 37.35 4.68
1840 2322 2.472695 AAAGCAGCTGTTATCCGTCA 57.527 45.000 16.64 0.00 0.00 4.35
1867 2349 6.435904 GGTATAGATAGATCAGGAGCAACTGT 59.564 42.308 7.43 0.00 39.48 3.55
1910 2392 5.901276 TCCGTATTTACTAAGATGGTCCCTT 59.099 40.000 0.00 0.00 34.06 3.95
1968 2450 2.511600 GTGTGGGAAGGATCGCCG 60.512 66.667 0.00 0.00 39.96 6.46
2340 2823 6.377146 GGAAATGGTCCAAAGCTGATACTTTA 59.623 38.462 0.00 0.00 46.97 1.85
2370 2853 6.073447 TCATGTTAATCAAAGAGGCCCTTA 57.927 37.500 0.00 0.00 34.00 2.69
2520 3063 6.938030 AGTTGGTCGTTTGATTTGTAGGAATA 59.062 34.615 0.00 0.00 0.00 1.75
2748 3300 3.130633 CGTCAACTGACTTCATTGACCA 58.869 45.455 18.57 0.00 46.16 4.02
2816 3368 3.399181 CTAAGGCGGCCCTGGTCA 61.399 66.667 17.02 0.00 41.90 4.02
2946 3498 2.189342 CCGAAAACACACAAAACGCAT 58.811 42.857 0.00 0.00 0.00 4.73
3071 3623 3.036633 GCTGACGAGATGTGTACATACG 58.963 50.000 16.54 16.54 39.88 3.06
3152 3873 1.144969 CTAACTCGTCTTTTGCGGCA 58.855 50.000 0.00 0.00 0.00 5.69
3228 3955 0.693049 AAGACCTCCGCATTGACCTT 59.307 50.000 0.00 0.00 0.00 3.50
3296 4023 1.827344 TGATCTCATGCTTCACCGAGT 59.173 47.619 0.00 0.00 0.00 4.18
3357 4084 1.036707 TCGATGTGATACGGATGCCA 58.963 50.000 0.00 0.00 0.00 4.92
3419 4146 4.216257 CCATGATTTATCGGCCAGTTTAGG 59.784 45.833 2.24 0.00 0.00 2.69
3788 4628 7.168469 TGGAATCATACATACAACGACATAACG 59.832 37.037 0.00 0.00 39.31 3.18
3792 4632 8.344831 CAATTGGAATCATACATACAACGACAT 58.655 33.333 0.00 0.00 0.00 3.06
3887 4727 1.648467 GCACTAAAGCAGGCTTCCGG 61.648 60.000 7.03 0.00 34.84 5.14
4026 4868 6.401367 GCAATGCATCAAAAGGACAAATGTAC 60.401 38.462 0.00 0.00 0.00 2.90
4038 4880 4.746535 ATCTGATGGCAATGCATCAAAA 57.253 36.364 7.79 6.29 37.37 2.44
4235 5077 4.681744 CTCACTGAATCTGAAGCTAGGAC 58.318 47.826 0.00 0.00 0.00 3.85
4315 5157 4.516698 AGAAAACACAGCACATAAGACAGG 59.483 41.667 0.00 0.00 0.00 4.00
4317 5159 4.211164 CGAGAAAACACAGCACATAAGACA 59.789 41.667 0.00 0.00 0.00 3.41
4318 5160 4.447724 TCGAGAAAACACAGCACATAAGAC 59.552 41.667 0.00 0.00 0.00 3.01
4319 5161 4.627058 TCGAGAAAACACAGCACATAAGA 58.373 39.130 0.00 0.00 0.00 2.10
4320 5162 4.990543 TCGAGAAAACACAGCACATAAG 57.009 40.909 0.00 0.00 0.00 1.73
4321 5163 5.468409 TGATTCGAGAAAACACAGCACATAA 59.532 36.000 0.00 0.00 0.00 1.90
4322 5164 4.994217 TGATTCGAGAAAACACAGCACATA 59.006 37.500 0.00 0.00 0.00 2.29
4323 5165 3.814842 TGATTCGAGAAAACACAGCACAT 59.185 39.130 0.00 0.00 0.00 3.21
4358 5200 7.305935 CGAATCACAACCACAATACAAACAAAG 60.306 37.037 0.00 0.00 0.00 2.77
4366 5208 4.250464 TCTCCGAATCACAACCACAATAC 58.750 43.478 0.00 0.00 0.00 1.89
4487 5336 5.725110 ACGCATTCATACTCAGATTCAAC 57.275 39.130 0.00 0.00 0.00 3.18
4507 5356 3.458189 CTGCTCTTTATCCTTGGGTACG 58.542 50.000 0.00 0.00 0.00 3.67
4528 5377 6.313744 ACTTTCTATATGGCCAATAAACGC 57.686 37.500 10.96 0.00 0.00 4.84
4553 5402 2.372837 ACCAATTGCAGCCCAAAAAGAT 59.627 40.909 0.00 0.00 36.92 2.40
4699 5548 0.112412 AAAACCTGAGGCCCGAATGT 59.888 50.000 0.00 0.00 0.00 2.71
4915 5764 5.807520 AGTGTCATCTTGTACTAAATCAGCG 59.192 40.000 0.00 0.00 0.00 5.18
4916 5765 7.602517 AAGTGTCATCTTGTACTAAATCAGC 57.397 36.000 0.00 0.00 0.00 4.26
4922 5771 9.502091 AGCAAAATAAGTGTCATCTTGTACTAA 57.498 29.630 0.00 0.00 0.00 2.24
4923 5772 9.502091 AAGCAAAATAAGTGTCATCTTGTACTA 57.498 29.630 0.00 0.00 0.00 1.82
4924 5773 7.986085 AGCAAAATAAGTGTCATCTTGTACT 57.014 32.000 0.00 0.00 0.00 2.73
4925 5774 8.289618 TGAAGCAAAATAAGTGTCATCTTGTAC 58.710 33.333 0.00 0.00 0.00 2.90
4926 5775 8.389779 TGAAGCAAAATAAGTGTCATCTTGTA 57.610 30.769 0.00 0.00 0.00 2.41
4927 5776 7.275888 TGAAGCAAAATAAGTGTCATCTTGT 57.724 32.000 0.00 0.00 0.00 3.16
4928 5777 8.224169 CTTGAAGCAAAATAAGTGTCATCTTG 57.776 34.615 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.