Multiple sequence alignment - TraesCS5D01G264700

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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 TraesCS5D01G264700 chr5D 100.000 5857 0 0 1 5857 369385178 369391034 0.000000e+00 10816.0
1 TraesCS5D01G264700 chr5D 84.848 462 54 9 5068 5525 369416871 369417320 8.950000e-123 451.0
2 TraesCS5D01G264700 chr5D 83.849 291 27 12 4549 4836 369415981 369416254 5.820000e-65 259.0
3 TraesCS5D01G264700 chr5D 88.021 192 23 0 5560 5751 369390665 369390856 1.640000e-55 228.0
4 TraesCS5D01G264700 chr5D 88.021 192 23 0 5488 5679 369390737 369390928 1.640000e-55 228.0
5 TraesCS5D01G264700 chr5D 84.167 120 19 0 5632 5751 369390665 369390784 3.710000e-22 117.0
6 TraesCS5D01G264700 chr5D 84.167 120 19 0 5488 5607 369390809 369390928 3.710000e-22 117.0
7 TraesCS5D01G264700 chr5A 90.081 2339 158 32 3468 5749 471916681 471919002 0.000000e+00 2966.0
8 TraesCS5D01G264700 chr5A 88.370 1883 128 38 309 2143 471913380 471915219 0.000000e+00 2180.0
9 TraesCS5D01G264700 chr5A 92.976 840 45 3 2639 3468 471915777 471916612 0.000000e+00 1212.0
10 TraesCS5D01G264700 chr5A 86.308 409 41 11 2230 2638 471915350 471915743 1.170000e-116 431.0
11 TraesCS5D01G264700 chr5A 81.416 452 55 16 1500 1937 288910649 288911085 5.620000e-90 342.0
12 TraesCS5D01G264700 chr5A 80.430 465 47 16 5068 5525 471922393 471922820 1.230000e-81 315.0
13 TraesCS5D01G264700 chr5A 88.210 229 25 2 5524 5751 471918740 471918967 7.480000e-69 272.0
14 TraesCS5D01G264700 chr5A 84.337 249 35 4 5488 5734 471918920 471919166 2.110000e-59 241.0
15 TraesCS5D01G264700 chr5A 85.714 161 23 0 5596 5756 471918740 471918900 2.810000e-38 171.0
16 TraesCS5D01G264700 chr5A 78.694 291 26 22 4549 4836 471921911 471922168 1.690000e-35 161.0
17 TraesCS5D01G264700 chr5B 93.859 1612 74 13 3469 5063 438219982 438221585 0.000000e+00 2405.0
18 TraesCS5D01G264700 chr5B 89.844 1920 111 36 263 2143 438216585 438218459 0.000000e+00 2388.0
19 TraesCS5D01G264700 chr5B 93.683 839 40 2 2639 3468 438219020 438219854 0.000000e+00 1243.0
20 TraesCS5D01G264700 chr5B 86.466 665 63 7 5087 5751 438221788 438222425 0.000000e+00 704.0
21 TraesCS5D01G264700 chr5B 83.991 456 52 5 5068 5523 438482852 438483286 9.080000e-113 418.0
22 TraesCS5D01G264700 chr5B 84.151 265 36 2 5488 5746 438222342 438222606 9.740000e-63 252.0
23 TraesCS5D01G264700 chr5B 83.271 269 43 2 5488 5755 438222270 438222537 4.530000e-61 246.0
24 TraesCS5D01G264700 chr5B 83.058 242 27 10 1989 2228 24644466 24644237 2.140000e-49 207.0
25 TraesCS5D01G264700 chr5B 82.061 262 19 9 1 236 438216257 438216516 1.290000e-46 198.0
26 TraesCS5D01G264700 chr5B 91.045 134 8 2 4549 4682 438482225 438482354 1.680000e-40 178.0
27 TraesCS5D01G264700 chr4B 88.917 1200 86 22 985 2159 169927360 169926183 0.000000e+00 1435.0
28 TraesCS5D01G264700 chr4B 92.713 741 37 5 2220 2954 169926184 169925455 0.000000e+00 1053.0
29 TraesCS5D01G264700 chr4B 92.424 66 3 1 21 86 416117127 416117190 6.250000e-15 93.5
30 TraesCS5D01G264700 chr6D 81.517 725 96 20 1326 2029 472445900 472445193 3.960000e-156 562.0
31 TraesCS5D01G264700 chr7B 80.862 580 108 3 3535 4112 164976492 164977070 2.490000e-123 453.0
32 TraesCS5D01G264700 chr7A 80.000 580 113 3 3535 4112 211810467 211811045 5.420000e-115 425.0
33 TraesCS5D01G264700 chr7A 89.899 99 4 3 5759 5857 668572919 668573011 7.970000e-24 122.0
34 TraesCS5D01G264700 chr6A 81.658 398 55 11 1646 2029 617542291 617542684 1.230000e-81 315.0
35 TraesCS5D01G264700 chr6A 89.796 98 4 2 5760 5857 17012255 17012164 2.870000e-23 121.0
36 TraesCS5D01G264700 chr3A 85.477 241 24 5 1989 2228 181710903 181711133 2.110000e-59 241.0
37 TraesCS5D01G264700 chr3A 89.796 98 5 1 5760 5857 711738266 711738174 2.870000e-23 121.0
38 TraesCS5D01G264700 chr3A 89.796 98 4 2 5760 5857 732629936 732630027 2.870000e-23 121.0
39 TraesCS5D01G264700 chr6B 82.500 240 32 6 1989 2228 717164816 717164587 9.950000e-48 202.0
40 TraesCS5D01G264700 chr2A 90.816 98 3 2 5760 5857 412504932 412505023 6.160000e-25 126.0
41 TraesCS5D01G264700 chr4A 89.796 98 4 2 5760 5857 601186977 601187068 2.870000e-23 121.0
42 TraesCS5D01G264700 chr2D 89.796 98 4 2 5760 5857 587658430 587658521 2.870000e-23 121.0
43 TraesCS5D01G264700 chr2D 89.796 98 4 2 5760 5857 594375705 594375796 2.870000e-23 121.0
44 TraesCS5D01G264700 chr1A 89.796 98 4 2 5760 5857 556656327 556656418 2.870000e-23 121.0


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 TraesCS5D01G264700 chr5D 369385178 369391034 5856 False 2301.200000 10816 88.875200 1 5857 5 chr5D.!!$F1 5856
1 TraesCS5D01G264700 chr5D 369415981 369417320 1339 False 355.000000 451 84.348500 4549 5525 2 chr5D.!!$F2 976
2 TraesCS5D01G264700 chr5A 471913380 471922820 9440 False 883.222222 2966 86.124444 309 5756 9 chr5A.!!$F2 5447
3 TraesCS5D01G264700 chr5B 438216257 438222606 6349 False 1062.285714 2405 87.619286 1 5755 7 chr5B.!!$F1 5754
4 TraesCS5D01G264700 chr5B 438482225 438483286 1061 False 298.000000 418 87.518000 4549 5523 2 chr5B.!!$F2 974
5 TraesCS5D01G264700 chr4B 169925455 169927360 1905 True 1244.000000 1435 90.815000 985 2954 2 chr4B.!!$R1 1969
6 TraesCS5D01G264700 chr6D 472445193 472445900 707 True 562.000000 562 81.517000 1326 2029 1 chr6D.!!$R1 703
7 TraesCS5D01G264700 chr7B 164976492 164977070 578 False 453.000000 453 80.862000 3535 4112 1 chr7B.!!$F1 577
8 TraesCS5D01G264700 chr7A 211810467 211811045 578 False 425.000000 425 80.000000 3535 4112 1 chr7A.!!$F1 577

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
651 739 0.112412 ACCGCTCCCAAATCCAAACT 59.888 50.0 0.00 0.00 0.00 2.66 F
652 740 0.527565 CCGCTCCCAAATCCAAACTG 59.472 55.0 0.00 0.00 0.00 3.16 F
1955 2113 0.103208 ACGGACGAGCAGATGGATTC 59.897 55.0 0.00 0.00 0.00 2.52 F
2171 2330 0.250684 TTGCTTGGCAAGGACGATCA 60.251 50.0 27.25 13.34 43.99 2.92 F
2172 2331 0.250684 TGCTTGGCAAGGACGATCAA 60.251 50.0 27.25 0.00 34.76 2.57 F
2194 2353 0.394899 CCTTGCCTGCCCCTTCTAAG 60.395 60.0 0.00 0.00 0.00 2.18 F
2195 2354 0.394899 CTTGCCTGCCCCTTCTAAGG 60.395 60.0 1.47 1.47 46.06 2.69 F
3448 3715 0.672342 GCCAGGCTGCTGATTAATGG 59.328 55.0 9.56 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 2113 0.322648 TGCTATCGCCAGGATGATGG 59.677 55.000 5.14 3.62 43.72 3.51 R
2175 2334 0.394899 CTTAGAAGGGGCAGGCAAGG 60.395 60.000 0.00 0.00 0.00 3.61 R
3421 3688 0.972134 CAGCAGCCTGGCTAGCTATA 59.028 55.000 31.12 0.60 43.68 1.31 R
4159 4564 2.495669 GGGATATACTCTGCTCAGCTCC 59.504 54.545 0.00 0.00 0.00 4.70 R
4225 4630 5.140747 AGTGTTGGTGAAGTACAGAGATC 57.859 43.478 0.00 0.00 0.00 2.75 R
4229 4634 6.437477 AGATCATAGTGTTGGTGAAGTACAGA 59.563 38.462 0.00 0.00 0.00 3.41 R
4371 4783 2.517450 CGAGCGATCAAGCGGGAAC 61.517 63.158 0.00 0.00 43.00 3.62 R
4919 5630 0.035439 ATCGAAATTCGTGTGGGGCT 60.035 50.000 15.34 0.00 41.35 5.19 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
23 24 3.385433 CCCCATCATCATTTGCTGCTTTA 59.615 43.478 0.00 0.00 0.00 1.85
24 25 4.141892 CCCCATCATCATTTGCTGCTTTAA 60.142 41.667 0.00 0.00 0.00 1.52
25 26 4.807304 CCCATCATCATTTGCTGCTTTAAC 59.193 41.667 0.00 0.00 0.00 2.01
71 75 3.750130 CGGTACTACTACTACGATGCCAT 59.250 47.826 0.00 0.00 0.00 4.40
78 82 0.664761 ACTACGATGCCATGCAATGC 59.335 50.000 0.00 0.00 44.97 3.56
90 94 1.868469 TGCAATGCAAGCAACCTTTC 58.132 45.000 5.01 0.00 39.39 2.62
94 98 0.319405 ATGCAAGCAACCTTTCTGCC 59.681 50.000 0.00 0.00 40.86 4.85
97 101 1.202568 GCAAGCAACCTTTCTGCCTTT 60.203 47.619 0.00 0.00 40.86 3.11
100 104 1.413812 AGCAACCTTTCTGCCTTTTGG 59.586 47.619 0.00 0.00 40.86 3.28
115 119 2.920076 TTTGGTGGCCTGCGTCCTTT 62.920 55.000 3.32 0.00 0.00 3.11
130 134 1.416401 TCCTTTGTTTCTCCTCACGCT 59.584 47.619 0.00 0.00 0.00 5.07
157 178 0.170561 AGCTGCCACGAACGTACTAG 59.829 55.000 0.00 0.00 0.00 2.57
163 184 2.160417 GCCACGAACGTACTAGTGTACT 59.840 50.000 5.39 0.00 44.97 2.73
204 225 0.731514 TGCAACTGCTCGTACGTAGC 60.732 55.000 23.84 23.84 42.66 3.58
205 226 1.730593 GCAACTGCTCGTACGTAGCG 61.731 60.000 24.42 21.48 43.11 4.26
207 228 2.024305 CTGCTCGTACGTAGCGGG 59.976 66.667 27.01 19.98 43.11 6.13
209 230 3.204827 GCTCGTACGTAGCGGGGA 61.205 66.667 16.05 0.00 0.00 4.81
210 231 2.550101 GCTCGTACGTAGCGGGGAT 61.550 63.158 16.05 0.00 0.00 3.85
212 233 1.849976 CTCGTACGTAGCGGGGATCC 61.850 65.000 16.05 1.92 0.00 3.36
256 305 3.958860 GGCGGGGCCTGCTGATAT 61.959 66.667 34.70 0.00 46.69 1.63
258 307 3.150949 CGGGGCCTGCTGATATGA 58.849 61.111 0.84 0.00 0.00 2.15
259 308 1.681666 CGGGGCCTGCTGATATGAT 59.318 57.895 0.84 0.00 0.00 2.45
260 309 0.904649 CGGGGCCTGCTGATATGATA 59.095 55.000 0.84 0.00 0.00 2.15
261 310 1.487976 CGGGGCCTGCTGATATGATAT 59.512 52.381 0.84 0.00 0.00 1.63
268 335 5.128499 GGCCTGCTGATATGATATAGTCTGT 59.872 44.000 0.00 0.00 0.00 3.41
289 356 1.546923 TGAAGGTTCTGGCGATTCGTA 59.453 47.619 8.03 0.00 0.00 3.43
362 438 0.392998 AAAGAATGGCGCCGTCTGAT 60.393 50.000 27.65 18.73 0.00 2.90
374 450 2.611292 GCCGTCTGATTCTTCTGAATGG 59.389 50.000 0.00 0.00 42.43 3.16
380 456 5.413833 GTCTGATTCTTCTGAATGGAAAGCA 59.586 40.000 0.00 0.00 42.43 3.91
651 739 0.112412 ACCGCTCCCAAATCCAAACT 59.888 50.000 0.00 0.00 0.00 2.66
652 740 0.527565 CCGCTCCCAAATCCAAACTG 59.472 55.000 0.00 0.00 0.00 3.16
653 741 1.533625 CGCTCCCAAATCCAAACTGA 58.466 50.000 0.00 0.00 0.00 3.41
654 742 1.200020 CGCTCCCAAATCCAAACTGAC 59.800 52.381 0.00 0.00 0.00 3.51
655 743 2.238521 GCTCCCAAATCCAAACTGACA 58.761 47.619 0.00 0.00 0.00 3.58
723 811 2.643551 TGCTTAGCAAATGTAGGAGCC 58.356 47.619 3.67 0.00 34.76 4.70
760 848 9.416284 TCTTACATCTCTGTACCACACATTATA 57.584 33.333 0.00 0.00 37.58 0.98
829 917 7.809238 AGAAACATCTCCATGAAATCCATCTA 58.191 34.615 0.00 0.00 31.94 1.98
992 1094 2.503061 CATCCTGAGCCCGGACTG 59.497 66.667 0.73 0.00 32.41 3.51
1090 1203 3.125573 GGAAAAGCGACGCCCCTC 61.126 66.667 17.79 10.04 0.00 4.30
1091 1204 3.125573 GAAAAGCGACGCCCCTCC 61.126 66.667 17.79 0.00 0.00 4.30
1092 1205 4.717313 AAAAGCGACGCCCCTCCC 62.717 66.667 17.79 0.00 0.00 4.30
1364 1496 3.242446 GGCGAAGATCCGTTCTTGATTTC 60.242 47.826 2.87 0.00 44.88 2.17
1375 1507 3.848272 TCTTGATTTCATTTGGGCGTC 57.152 42.857 0.00 0.00 0.00 5.19
1479 1612 1.157585 GGTTTCTCTCGCCAAAGGTC 58.842 55.000 0.00 0.00 0.00 3.85
1524 1658 2.159627 CGTTTTGCTTGCCTAATCTCGT 59.840 45.455 0.00 0.00 0.00 4.18
1525 1659 3.725010 CGTTTTGCTTGCCTAATCTCGTC 60.725 47.826 0.00 0.00 0.00 4.20
1526 1660 2.024176 TTGCTTGCCTAATCTCGTCC 57.976 50.000 0.00 0.00 0.00 4.79
1528 1662 1.137086 TGCTTGCCTAATCTCGTCCTC 59.863 52.381 0.00 0.00 0.00 3.71
1568 1710 6.920817 TGACTGTAGTAGATCGTGAAAATGT 58.079 36.000 0.00 0.00 0.00 2.71
1580 1722 8.908903 AGATCGTGAAAATGTTAGAGAGATAGT 58.091 33.333 0.00 0.00 0.00 2.12
1629 1771 5.083533 ACAAATGAACCAACTTCTTGCAA 57.916 34.783 0.00 0.00 0.00 4.08
1662 1805 1.560860 GCAGTCGCCAGTTGAGTCAC 61.561 60.000 0.00 0.00 0.00 3.67
1688 1831 4.621034 GTGGGTAAACGCATCTGATTTTTG 59.379 41.667 3.02 0.00 40.93 2.44
1689 1832 4.279671 TGGGTAAACGCATCTGATTTTTGT 59.720 37.500 0.00 0.00 33.68 2.83
1691 1834 5.118510 GGGTAAACGCATCTGATTTTTGTTG 59.881 40.000 0.00 0.00 0.00 3.33
1693 1836 4.582701 AACGCATCTGATTTTTGTTGGA 57.417 36.364 0.00 0.00 0.00 3.53
1695 1838 5.138125 ACGCATCTGATTTTTGTTGGAAT 57.862 34.783 0.00 0.00 0.00 3.01
1696 1839 5.540911 ACGCATCTGATTTTTGTTGGAATT 58.459 33.333 0.00 0.00 0.00 2.17
1736 1880 6.638096 TTTGCAGATTTGACAATTGAGAGA 57.362 33.333 13.59 0.00 0.00 3.10
1877 2027 2.559785 CCATCAGGTGGTTGCTGTC 58.440 57.895 0.00 0.00 43.44 3.51
1955 2113 0.103208 ACGGACGAGCAGATGGATTC 59.897 55.000 0.00 0.00 0.00 2.52
1957 2115 0.465705 GGACGAGCAGATGGATTCCA 59.534 55.000 8.08 8.08 38.19 3.53
2003 2161 1.556911 GAAGAGCAGGATGGACAAGGA 59.443 52.381 0.00 0.00 35.86 3.36
2059 2217 4.141846 GGTAGAGCACAAAGATGGATCTGA 60.142 45.833 0.00 0.00 37.19 3.27
2081 2239 4.541085 TGCATCAGAGAATAACATTGCG 57.459 40.909 0.00 0.00 0.00 4.85
2091 2249 4.096382 AGAATAACATTGCGGGAACACATC 59.904 41.667 0.00 0.00 0.00 3.06
2108 2266 2.129555 ATCCTGCGGCAAACCTGACT 62.130 55.000 3.44 0.00 0.00 3.41
2129 2288 6.037830 TGACTTCGTCTTTGGAAAAGGTAAAG 59.962 38.462 0.20 0.00 33.15 1.85
2158 2317 8.674263 ATTAGAGAAGACCAATCTATTGCTTG 57.326 34.615 0.00 0.00 36.48 4.01
2160 2319 3.950395 AGAAGACCAATCTATTGCTTGGC 59.050 43.478 9.30 3.68 44.74 4.52
2161 2320 3.370840 AGACCAATCTATTGCTTGGCA 57.629 42.857 9.30 0.00 44.74 4.92
2165 2324 8.951722 AAGACCAATCTATTGCTTGGCAAGGA 62.952 42.308 27.25 23.01 42.71 3.36
2170 2329 2.555123 TTGCTTGGCAAGGACGATC 58.445 52.632 27.25 10.90 43.99 3.69
2171 2330 0.250684 TTGCTTGGCAAGGACGATCA 60.251 50.000 27.25 13.34 43.99 2.92
2172 2331 0.250684 TGCTTGGCAAGGACGATCAA 60.251 50.000 27.25 0.00 34.76 2.57
2173 2332 0.449388 GCTTGGCAAGGACGATCAAG 59.551 55.000 27.25 0.00 38.18 3.02
2175 2334 0.960364 TTGGCAAGGACGATCAAGCC 60.960 55.000 0.00 0.00 42.32 4.35
2176 2335 2.115291 GGCAAGGACGATCAAGCCC 61.115 63.158 0.00 0.00 36.17 5.19
2177 2336 1.078143 GCAAGGACGATCAAGCCCT 60.078 57.895 0.00 0.00 0.00 5.19
2178 2337 0.678048 GCAAGGACGATCAAGCCCTT 60.678 55.000 0.00 0.00 39.42 3.95
2179 2338 1.089920 CAAGGACGATCAAGCCCTTG 58.910 55.000 14.12 14.12 46.36 3.61
2180 2339 0.678048 AAGGACGATCAAGCCCTTGC 60.678 55.000 3.18 0.00 40.24 4.01
2181 2340 2.115291 GGACGATCAAGCCCTTGCC 61.115 63.158 3.18 0.00 40.24 4.52
2182 2341 1.078143 GACGATCAAGCCCTTGCCT 60.078 57.895 3.18 0.00 40.24 4.75
2183 2342 1.372087 GACGATCAAGCCCTTGCCTG 61.372 60.000 3.18 0.00 40.24 4.85
2184 2343 2.768492 CGATCAAGCCCTTGCCTGC 61.768 63.158 3.18 0.00 40.24 4.85
2185 2344 2.363406 ATCAAGCCCTTGCCTGCC 60.363 61.111 3.18 0.00 40.24 4.85
2186 2345 3.970746 ATCAAGCCCTTGCCTGCCC 62.971 63.158 3.18 0.00 40.24 5.36
2191 2350 3.665971 CCCTTGCCTGCCCCTTCT 61.666 66.667 0.00 0.00 0.00 2.85
2192 2351 2.308722 CCCTTGCCTGCCCCTTCTA 61.309 63.158 0.00 0.00 0.00 2.10
2193 2352 1.691219 CCTTGCCTGCCCCTTCTAA 59.309 57.895 0.00 0.00 0.00 2.10
2194 2353 0.394899 CCTTGCCTGCCCCTTCTAAG 60.395 60.000 0.00 0.00 0.00 2.18
2195 2354 0.394899 CTTGCCTGCCCCTTCTAAGG 60.395 60.000 1.47 1.47 46.06 2.69
2210 2369 5.163120 CCTTCTAAGGGAGGGGGTAAATTAC 60.163 48.000 0.42 0.00 42.66 1.89
2280 2483 8.109634 ACCTTGTTCCATCACATCTTTATTACT 58.890 33.333 0.00 0.00 0.00 2.24
2281 2484 9.613428 CCTTGTTCCATCACATCTTTATTACTA 57.387 33.333 0.00 0.00 0.00 1.82
2284 2487 9.817809 TGTTCCATCACATCTTTATTACTACTC 57.182 33.333 0.00 0.00 0.00 2.59
2285 2488 9.817809 GTTCCATCACATCTTTATTACTACTCA 57.182 33.333 0.00 0.00 0.00 3.41
2286 2489 9.817809 TTCCATCACATCTTTATTACTACTCAC 57.182 33.333 0.00 0.00 0.00 3.51
2287 2490 9.201989 TCCATCACATCTTTATTACTACTCACT 57.798 33.333 0.00 0.00 0.00 3.41
2304 2507 4.705991 ACTCACTTACTCAGTACCTAAGCC 59.294 45.833 0.00 0.00 32.76 4.35
2314 2517 5.216622 TCAGTACCTAAGCCCATACTCATT 58.783 41.667 0.00 0.00 0.00 2.57
2352 2558 1.608055 TGTGCACTGAATGAACTGGG 58.392 50.000 19.41 0.00 37.80 4.45
2434 2640 7.431249 CAAAGACATTGCAGCCATCTTAATAT 58.569 34.615 5.38 0.00 31.00 1.28
2493 2701 1.004918 AGCGGTACTGTTCTGTGGC 60.005 57.895 3.10 0.00 0.00 5.01
2524 2732 8.934023 TCTTACCTTTTTGTGAACATTAGGAT 57.066 30.769 10.99 2.22 0.00 3.24
2560 2768 4.582701 AAGAGCGATTAGATGTCCTGAG 57.417 45.455 0.00 0.00 0.00 3.35
2578 2786 8.206867 TGTCCTGAGAATCCACTCTTATATTTG 58.793 37.037 0.00 0.00 37.73 2.32
2894 3160 2.294449 AGGATATCCAGCGAGCACTA 57.706 50.000 23.81 0.00 38.89 2.74
2992 3258 7.803189 GTCATTATTGGTGTCTTGTACTTTGTG 59.197 37.037 0.00 0.00 0.00 3.33
2998 3264 3.942748 GTGTCTTGTACTTTGTGTTGGGA 59.057 43.478 0.00 0.00 0.00 4.37
3072 3338 2.760634 TAAAAGCGATGGAGCAGACA 57.239 45.000 0.00 0.00 40.15 3.41
3090 3356 2.432510 GACACTGGGTAGGATCAAGAGG 59.567 54.545 0.00 0.00 0.00 3.69
3133 3399 0.973632 TGTGAACAGGCTCCGTACAT 59.026 50.000 0.00 0.00 0.00 2.29
3134 3400 1.067142 TGTGAACAGGCTCCGTACATC 60.067 52.381 0.00 0.00 0.00 3.06
3141 3407 0.759346 GGCTCCGTACATCCCTTCAT 59.241 55.000 0.00 0.00 0.00 2.57
3174 3440 3.993081 AGCGTCTTCAATCTCACAGAAAG 59.007 43.478 0.00 0.00 0.00 2.62
3255 3521 2.480073 CCCATTGCGGCTTACAAATGAG 60.480 50.000 10.50 0.00 0.00 2.90
3276 3542 6.662755 TGAGTATTATTCCAGCAACTCCAAT 58.337 36.000 0.00 0.00 33.94 3.16
3315 3581 5.755409 ATATGGAAAAGTTGGAAAACCCC 57.245 39.130 0.00 0.00 0.00 4.95
3316 3582 2.834113 TGGAAAAGTTGGAAAACCCCA 58.166 42.857 0.00 0.00 0.00 4.96
3436 3703 4.141287 CGAGATATATAGCTAGCCAGGCT 58.859 47.826 20.63 20.63 43.41 4.58
3448 3715 0.672342 GCCAGGCTGCTGATTAATGG 59.328 55.000 9.56 0.00 0.00 3.16
3449 3716 0.672342 CCAGGCTGCTGATTAATGGC 59.328 55.000 9.56 0.00 0.00 4.40
3456 3723 3.067742 GCTGCTGATTAATGGCTGTGAAT 59.932 43.478 14.01 0.00 0.00 2.57
3463 3730 5.647658 TGATTAATGGCTGTGAATCGACTTT 59.352 36.000 0.00 0.00 32.12 2.66
3472 3866 5.412526 TGTGAATCGACTTTTGTTGTACC 57.587 39.130 0.00 0.00 35.36 3.34
3580 3974 1.662629 CACATTGTGACAGATCGGCTC 59.337 52.381 11.45 0.00 35.23 4.70
3744 4138 2.431954 TACTACTTCGGGAGTGGGAG 57.568 55.000 4.71 0.00 40.87 4.30
4191 4596 7.653503 AGCAGAGTATATCCCCTAATAAGCTA 58.346 38.462 0.00 0.00 0.00 3.32
4225 4630 5.116180 TGCCGTATTTTGATCTACAAGGAG 58.884 41.667 0.00 0.00 39.77 3.69
4371 4783 1.368374 GACGTTTTGGAACCGCACG 60.368 57.895 0.00 7.42 36.91 5.34
4467 4879 2.351726 GGCATCCGTCATTCACTACAAC 59.648 50.000 0.00 0.00 0.00 3.32
4498 4910 1.905843 CCCTGGCTCGAGATCGGAT 60.906 63.158 18.75 0.00 40.29 4.18
4682 5094 9.760926 TGTAAGATATCTGGAGCATCTACTATT 57.239 33.333 5.86 0.00 33.73 1.73
4836 5531 8.853345 CATTTTTGTACTTACTGATGTGAATGC 58.147 33.333 0.00 0.00 0.00 3.56
4839 5534 7.686438 TTGTACTTACTGATGTGAATGCAAT 57.314 32.000 0.00 0.00 0.00 3.56
4868 5563 6.833041 TGGTAGAAAAACTATGTCCAGTTCA 58.167 36.000 0.00 0.00 37.78 3.18
4870 5565 7.942341 TGGTAGAAAAACTATGTCCAGTTCATT 59.058 33.333 0.00 0.00 37.78 2.57
4872 5567 7.133891 AGAAAAACTATGTCCAGTTCATTCG 57.866 36.000 0.00 0.00 37.78 3.34
4881 5576 3.123621 GTCCAGTTCATTCGTACTGCAAG 59.876 47.826 0.00 0.00 38.76 4.01
4919 5630 2.100749 TCAGTTCGTTCTCTGTTCTGCA 59.899 45.455 0.00 0.00 33.89 4.41
4938 5650 0.035439 AGCCCCACACGAATTTCGAT 60.035 50.000 24.50 9.79 43.74 3.59
4956 5668 4.323417 TCGATGTGGTTTCTGTGCTTATT 58.677 39.130 0.00 0.00 0.00 1.40
4959 5671 4.846779 TGTGGTTTCTGTGCTTATTTCC 57.153 40.909 0.00 0.00 0.00 3.13
4971 5683 6.121590 TGTGCTTATTTCCATCAGCTGAATA 58.878 36.000 22.50 10.69 31.69 1.75
4985 5697 7.812309 TCAGCTGAATAATCGTAATAATCCG 57.188 36.000 15.67 0.00 0.00 4.18
4996 5708 4.031991 TCGTAATAATCCGCACGAAGTTTG 59.968 41.667 0.00 0.00 41.61 2.93
5037 6160 0.608035 GGCTCCCAATGACCGTTCAA 60.608 55.000 0.00 0.00 34.61 2.69
5051 6174 5.919707 TGACCGTTCAAAATGTGATCAAATG 59.080 36.000 0.00 0.00 35.70 2.32
5063 6186 5.841810 TGTGATCAAATGGAACTGAAAACC 58.158 37.500 0.00 0.00 0.00 3.27
5064 6187 5.598005 TGTGATCAAATGGAACTGAAAACCT 59.402 36.000 0.00 0.00 0.00 3.50
5065 6188 6.775142 TGTGATCAAATGGAACTGAAAACCTA 59.225 34.615 0.00 0.00 0.00 3.08
5176 6478 3.380479 TGTTGAGATTCGTTTCTCCGT 57.620 42.857 12.61 0.00 41.24 4.69
5177 6479 4.508461 TGTTGAGATTCGTTTCTCCGTA 57.492 40.909 12.61 0.26 41.24 4.02
5225 6532 7.324135 GCCTATATATATACGCTCTTTTCGCTC 59.676 40.741 13.45 0.00 0.00 5.03
5226 6536 8.343366 CCTATATATATACGCTCTTTTCGCTCA 58.657 37.037 0.00 0.00 0.00 4.26
5228 6538 8.789881 ATATATATACGCTCTTTTCGCTCATC 57.210 34.615 0.00 0.00 0.00 2.92
5230 6540 0.247736 ACGCTCTTTTCGCTCATCCT 59.752 50.000 0.00 0.00 0.00 3.24
5233 6543 2.626840 GCTCTTTTCGCTCATCCTTCT 58.373 47.619 0.00 0.00 0.00 2.85
5246 6569 2.910688 TCCTTCTGAAGTTTCGCTGT 57.089 45.000 15.72 0.00 0.00 4.40
5255 6578 2.735478 TTTCGCTGTGTACGCCCG 60.735 61.111 3.51 7.08 0.00 6.13
5258 6581 4.415332 CGCTGTGTACGCCCGTCT 62.415 66.667 3.51 0.00 0.00 4.18
5261 6584 1.897398 GCTGTGTACGCCCGTCTTTG 61.897 60.000 3.51 0.00 0.00 2.77
5269 6592 2.464459 GCCCGTCTTTGCGATCAGG 61.464 63.158 0.00 0.00 0.00 3.86
5320 6655 3.597728 GCTCCTAGAGTCCGCGGG 61.598 72.222 27.83 7.70 31.39 6.13
5321 6656 3.597728 CTCCTAGAGTCCGCGGGC 61.598 72.222 25.39 25.39 0.00 6.13
5322 6657 4.435970 TCCTAGAGTCCGCGGGCA 62.436 66.667 34.17 10.86 0.00 5.36
5323 6658 3.905678 CCTAGAGTCCGCGGGCAG 61.906 72.222 34.17 20.71 0.00 4.85
5324 6659 4.577246 CTAGAGTCCGCGGGCAGC 62.577 72.222 34.17 23.30 43.95 5.25
5542 6949 4.830765 CGCGGCCCCGAAGATGAA 62.831 66.667 11.48 0.00 42.83 2.57
5765 10927 2.429930 CCGGAGGCCAGTGTTTGA 59.570 61.111 5.01 0.00 46.14 2.69
5766 10928 1.228124 CCGGAGGCCAGTGTTTGAA 60.228 57.895 5.01 0.00 46.14 2.69
5767 10929 0.609131 CCGGAGGCCAGTGTTTGAAT 60.609 55.000 5.01 0.00 46.14 2.57
5768 10930 1.247567 CGGAGGCCAGTGTTTGAATT 58.752 50.000 5.01 0.00 0.00 2.17
5769 10931 1.613437 CGGAGGCCAGTGTTTGAATTT 59.387 47.619 5.01 0.00 0.00 1.82
5770 10932 2.035832 CGGAGGCCAGTGTTTGAATTTT 59.964 45.455 5.01 0.00 0.00 1.82
5771 10933 3.392882 GGAGGCCAGTGTTTGAATTTTG 58.607 45.455 5.01 0.00 0.00 2.44
5772 10934 2.802247 GAGGCCAGTGTTTGAATTTTGC 59.198 45.455 5.01 0.00 0.00 3.68
5773 10935 2.435437 AGGCCAGTGTTTGAATTTTGCT 59.565 40.909 5.01 0.00 0.00 3.91
5774 10936 3.640967 AGGCCAGTGTTTGAATTTTGCTA 59.359 39.130 5.01 0.00 0.00 3.49
5775 10937 3.989817 GGCCAGTGTTTGAATTTTGCTAG 59.010 43.478 0.00 0.00 0.00 3.42
5776 10938 4.501400 GGCCAGTGTTTGAATTTTGCTAGT 60.501 41.667 0.00 0.00 0.00 2.57
5777 10939 5.278758 GGCCAGTGTTTGAATTTTGCTAGTA 60.279 40.000 0.00 0.00 0.00 1.82
5778 10940 5.858581 GCCAGTGTTTGAATTTTGCTAGTAG 59.141 40.000 0.00 0.00 0.00 2.57
5779 10941 6.381801 CCAGTGTTTGAATTTTGCTAGTAGG 58.618 40.000 0.00 0.00 0.00 3.18
5780 10942 5.858581 CAGTGTTTGAATTTTGCTAGTAGGC 59.141 40.000 0.00 0.00 0.00 3.93
5781 10943 5.048013 AGTGTTTGAATTTTGCTAGTAGGCC 60.048 40.000 0.00 0.00 0.00 5.19
5782 10944 5.048013 GTGTTTGAATTTTGCTAGTAGGCCT 60.048 40.000 11.78 11.78 0.00 5.19
5783 10945 5.538433 TGTTTGAATTTTGCTAGTAGGCCTT 59.462 36.000 12.58 0.00 0.00 4.35
5784 10946 6.041523 TGTTTGAATTTTGCTAGTAGGCCTTT 59.958 34.615 12.58 1.84 0.00 3.11
5785 10947 5.643379 TGAATTTTGCTAGTAGGCCTTTG 57.357 39.130 12.58 0.00 0.00 2.77
5786 10948 4.462483 TGAATTTTGCTAGTAGGCCTTTGG 59.538 41.667 12.58 2.81 0.00 3.28
5812 10974 3.417069 GCCCAAAGCCCAACTAAAATT 57.583 42.857 0.00 0.00 34.35 1.82
5813 10975 3.334691 GCCCAAAGCCCAACTAAAATTC 58.665 45.455 0.00 0.00 34.35 2.17
5814 10976 3.007940 GCCCAAAGCCCAACTAAAATTCT 59.992 43.478 0.00 0.00 34.35 2.40
5815 10977 4.568956 CCCAAAGCCCAACTAAAATTCTG 58.431 43.478 0.00 0.00 0.00 3.02
5816 10978 4.283212 CCCAAAGCCCAACTAAAATTCTGA 59.717 41.667 0.00 0.00 0.00 3.27
5817 10979 5.221621 CCCAAAGCCCAACTAAAATTCTGAA 60.222 40.000 0.00 0.00 0.00 3.02
5818 10980 6.287525 CCAAAGCCCAACTAAAATTCTGAAA 58.712 36.000 0.00 0.00 0.00 2.69
5819 10981 6.936335 CCAAAGCCCAACTAAAATTCTGAAAT 59.064 34.615 0.00 0.00 0.00 2.17
5820 10982 7.445096 CCAAAGCCCAACTAAAATTCTGAAATT 59.555 33.333 0.00 0.00 36.64 1.82
5821 10983 8.498358 CAAAGCCCAACTAAAATTCTGAAATTC 58.502 33.333 0.00 0.00 33.93 2.17
5822 10984 7.544804 AGCCCAACTAAAATTCTGAAATTCT 57.455 32.000 0.00 0.00 33.93 2.40
5823 10985 7.606349 AGCCCAACTAAAATTCTGAAATTCTC 58.394 34.615 0.00 0.00 33.93 2.87
5824 10986 7.452813 AGCCCAACTAAAATTCTGAAATTCTCT 59.547 33.333 0.00 0.00 33.93 3.10
5825 10987 8.090831 GCCCAACTAAAATTCTGAAATTCTCTT 58.909 33.333 0.00 0.00 33.93 2.85
5826 10988 9.415544 CCCAACTAAAATTCTGAAATTCTCTTG 57.584 33.333 0.00 0.00 33.93 3.02
5830 10992 8.797438 ACTAAAATTCTGAAATTCTCTTGACCC 58.203 33.333 0.00 0.00 33.93 4.46
5831 10993 7.601705 AAAATTCTGAAATTCTCTTGACCCA 57.398 32.000 0.00 0.00 33.93 4.51
5832 10994 7.787623 AAATTCTGAAATTCTCTTGACCCAT 57.212 32.000 0.00 0.00 33.93 4.00
5833 10995 7.787623 AATTCTGAAATTCTCTTGACCCATT 57.212 32.000 0.00 0.00 28.70 3.16
5834 10996 6.824305 TTCTGAAATTCTCTTGACCCATTC 57.176 37.500 0.00 0.00 0.00 2.67
5835 10997 5.879763 TCTGAAATTCTCTTGACCCATTCA 58.120 37.500 0.00 0.00 0.00 2.57
5836 10998 6.487828 TCTGAAATTCTCTTGACCCATTCAT 58.512 36.000 0.00 0.00 32.84 2.57
5837 10999 7.632861 TCTGAAATTCTCTTGACCCATTCATA 58.367 34.615 0.00 0.00 32.84 2.15
5838 11000 7.554118 TCTGAAATTCTCTTGACCCATTCATAC 59.446 37.037 0.00 0.00 32.84 2.39
5839 11001 7.174413 TGAAATTCTCTTGACCCATTCATACA 58.826 34.615 0.00 0.00 32.84 2.29
5840 11002 7.121168 TGAAATTCTCTTGACCCATTCATACAC 59.879 37.037 0.00 0.00 32.84 2.90
5841 11003 5.497464 TTCTCTTGACCCATTCATACACA 57.503 39.130 0.00 0.00 32.84 3.72
5842 11004 5.698741 TCTCTTGACCCATTCATACACAT 57.301 39.130 0.00 0.00 32.84 3.21
5843 11005 6.806668 TCTCTTGACCCATTCATACACATA 57.193 37.500 0.00 0.00 32.84 2.29
5844 11006 7.379059 TCTCTTGACCCATTCATACACATAT 57.621 36.000 0.00 0.00 32.84 1.78
5845 11007 7.219322 TCTCTTGACCCATTCATACACATATG 58.781 38.462 0.00 0.00 39.79 1.78
5846 11008 6.899089 TCTTGACCCATTCATACACATATGT 58.101 36.000 1.41 1.41 43.30 2.29
5847 11009 6.767423 TCTTGACCCATTCATACACATATGTG 59.233 38.462 29.97 29.97 42.11 3.21
5848 11010 6.657875 TTGACCCATTCATACACATATGTGA 58.342 36.000 36.36 22.22 40.29 3.58
5849 11011 6.767423 TTGACCCATTCATACACATATGTGAG 59.233 38.462 36.36 25.14 40.29 3.51
5850 11012 7.583220 TTGACCCATTCATACACATATGTGAGT 60.583 37.037 36.36 22.75 40.29 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.153353 CCGTGTGTATCGGCTTTGTT 58.847 50.000 0.00 0.00 41.48 2.83
24 25 2.835605 CCGTGTGTATCGGCTTTGT 58.164 52.632 0.00 0.00 41.48 2.83
51 54 4.023450 TGCATGGCATCGTAGTAGTAGTAC 60.023 45.833 0.00 5.22 31.71 2.73
52 55 4.139038 TGCATGGCATCGTAGTAGTAGTA 58.861 43.478 0.00 0.00 31.71 1.82
53 56 2.956333 TGCATGGCATCGTAGTAGTAGT 59.044 45.455 0.00 0.00 31.71 2.73
54 57 3.643159 TGCATGGCATCGTAGTAGTAG 57.357 47.619 0.00 0.00 31.71 2.57
71 75 1.413445 AGAAAGGTTGCTTGCATTGCA 59.587 42.857 7.38 7.38 38.80 4.08
78 82 2.867975 CAAAAGGCAGAAAGGTTGCTTG 59.132 45.455 0.00 0.00 41.27 4.01
94 98 2.644992 GACGCAGGCCACCAAAAG 59.355 61.111 5.01 0.00 0.00 2.27
97 101 3.429372 AAAGGACGCAGGCCACCAA 62.429 57.895 5.01 0.00 0.00 3.67
100 104 1.734388 AAACAAAGGACGCAGGCCAC 61.734 55.000 5.01 0.00 0.00 5.01
115 119 0.750249 TGACAGCGTGAGGAGAAACA 59.250 50.000 0.00 0.00 0.00 2.83
130 134 2.939133 TTCGTGGCAGCTTGCTGACA 62.939 55.000 25.32 25.32 44.28 3.58
157 178 5.401674 GCCAAGATATGCTTACGTAGTACAC 59.598 44.000 0.38 0.00 45.76 2.90
163 184 2.363038 ACCGCCAAGATATGCTTACGTA 59.637 45.455 0.00 0.00 35.02 3.57
256 305 6.630413 GCCAGAACCTTCAACAGACTATATCA 60.630 42.308 0.00 0.00 0.00 2.15
258 307 5.675538 GCCAGAACCTTCAACAGACTATAT 58.324 41.667 0.00 0.00 0.00 0.86
259 308 4.381612 CGCCAGAACCTTCAACAGACTATA 60.382 45.833 0.00 0.00 0.00 1.31
260 309 3.617531 CGCCAGAACCTTCAACAGACTAT 60.618 47.826 0.00 0.00 0.00 2.12
261 310 2.288825 CGCCAGAACCTTCAACAGACTA 60.289 50.000 0.00 0.00 0.00 2.59
268 335 1.270625 ACGAATCGCCAGAACCTTCAA 60.271 47.619 1.15 0.00 0.00 2.69
304 380 2.583593 GGTGATCGACCTGCTCGC 60.584 66.667 6.98 0.00 42.62 5.03
362 438 2.226437 GCGTGCTTTCCATTCAGAAGAA 59.774 45.455 0.00 0.00 38.31 2.52
374 450 1.160137 ATCCTTGAGTGCGTGCTTTC 58.840 50.000 0.00 0.00 0.00 2.62
380 456 3.567397 AGGTATCTATCCTTGAGTGCGT 58.433 45.455 0.00 0.00 30.18 5.24
477 558 3.625853 TGGGTGAATGTTGTCAGAAACA 58.374 40.909 0.00 0.00 43.82 2.83
478 559 4.853924 ATGGGTGAATGTTGTCAGAAAC 57.146 40.909 0.00 0.00 0.00 2.78
482 563 6.527722 CGAATTAAATGGGTGAATGTTGTCAG 59.472 38.462 0.00 0.00 0.00 3.51
483 564 6.385843 CGAATTAAATGGGTGAATGTTGTCA 58.614 36.000 0.00 0.00 0.00 3.58
484 565 5.804979 CCGAATTAAATGGGTGAATGTTGTC 59.195 40.000 0.00 0.00 0.00 3.18
485 566 5.719173 CCGAATTAAATGGGTGAATGTTGT 58.281 37.500 0.00 0.00 0.00 3.32
486 567 4.566360 GCCGAATTAAATGGGTGAATGTTG 59.434 41.667 0.00 0.00 0.00 3.33
681 769 3.773418 TTGGTCAGATTTGGTTCGGTA 57.227 42.857 0.00 0.00 0.00 4.02
739 827 8.893219 ACAATATAATGTGTGGTACAGAGATG 57.107 34.615 0.00 0.00 43.80 2.90
1036 1138 0.468585 GTTTCGGGAAGGGTTTGGGT 60.469 55.000 0.00 0.00 0.00 4.51
1040 1153 1.699730 CTTGGTTTCGGGAAGGGTTT 58.300 50.000 0.00 0.00 0.00 3.27
1364 1496 1.666888 GCAAGACAAGACGCCCAAATG 60.667 52.381 0.00 0.00 0.00 2.32
1375 1507 1.572085 CCTCGCCACTGCAAGACAAG 61.572 60.000 0.00 0.00 37.43 3.16
1425 1558 4.704833 CGGCCACACCAGACTGGG 62.705 72.222 25.34 16.00 43.37 4.45
1429 1562 1.153168 ATATGCGGCCACACCAGAC 60.153 57.895 2.24 0.00 39.03 3.51
1479 1612 2.343426 GGGAAGGAAAAGCGGCCTG 61.343 63.158 0.00 0.00 34.00 4.85
1524 1658 0.693049 GTGAAGCCTTCCCTTGAGGA 59.307 55.000 1.21 0.00 45.68 3.71
1525 1659 0.695347 AGTGAAGCCTTCCCTTGAGG 59.305 55.000 1.21 0.00 37.35 3.86
1526 1660 1.349026 TCAGTGAAGCCTTCCCTTGAG 59.651 52.381 1.21 0.00 0.00 3.02
1528 1662 1.072965 AGTCAGTGAAGCCTTCCCTTG 59.927 52.381 1.21 0.00 0.00 3.61
1568 1710 9.915629 GAAAACAGACTCAAACTATCTCTCTAA 57.084 33.333 0.00 0.00 0.00 2.10
1580 1722 4.331968 ACTGTGGTGAAAACAGACTCAAA 58.668 39.130 10.35 0.00 46.55 2.69
1662 1805 1.078708 AGATGCGTTTACCCACGGG 60.079 57.895 0.00 0.00 40.69 5.28
1688 1831 4.619160 GCAATTCACCCAGAGAATTCCAAC 60.619 45.833 0.65 0.00 42.17 3.77
1689 1832 3.511146 GCAATTCACCCAGAGAATTCCAA 59.489 43.478 0.65 0.00 42.17 3.53
1691 1834 3.359950 AGCAATTCACCCAGAGAATTCC 58.640 45.455 0.65 0.00 42.17 3.01
1693 1836 5.544650 CAAAAGCAATTCACCCAGAGAATT 58.455 37.500 0.00 0.00 44.21 2.17
1695 1838 3.243839 GCAAAAGCAATTCACCCAGAGAA 60.244 43.478 0.00 0.00 0.00 2.87
1696 1839 2.297033 GCAAAAGCAATTCACCCAGAGA 59.703 45.455 0.00 0.00 0.00 3.10
1736 1880 0.984995 GGTTCTTGTGCTCCCCTAGT 59.015 55.000 0.00 0.00 0.00 2.57
1816 1960 7.416777 GGTCCTCCCATGTATCAATTTTCTTTC 60.417 40.741 0.00 0.00 0.00 2.62
1877 2027 1.728971 GACTGAGCACTGTCATTTCCG 59.271 52.381 14.61 0.00 42.08 4.30
1955 2113 0.322648 TGCTATCGCCAGGATGATGG 59.677 55.000 5.14 3.62 43.72 3.51
1957 2115 2.469274 CTTGCTATCGCCAGGATGAT 57.531 50.000 0.00 0.00 39.69 2.45
2003 2161 3.512724 CCTGCAACTCCTTTTCATCCATT 59.487 43.478 0.00 0.00 0.00 3.16
2032 2190 3.055819 TCCATCTTTGTGCTCTACCTCAC 60.056 47.826 0.00 0.00 0.00 3.51
2037 2195 5.016051 TCAGATCCATCTTTGTGCTCTAC 57.984 43.478 0.00 0.00 34.22 2.59
2059 2217 4.023450 CCGCAATGTTATTCTCTGATGCAT 60.023 41.667 0.00 0.00 33.00 3.96
2108 2266 6.762702 AACTTTACCTTTTCCAAAGACGAA 57.237 33.333 0.00 0.00 34.20 3.85
2157 2316 1.377202 GGCTTGATCGTCCTTGCCA 60.377 57.895 0.00 0.00 40.04 4.92
2158 2317 2.115291 GGGCTTGATCGTCCTTGCC 61.115 63.158 0.00 0.00 39.61 4.52
2160 2319 3.558674 AAGGGCTTGATCGTCCTTG 57.441 52.632 5.78 0.00 46.70 3.61
2165 2324 3.081554 AGGCAAGGGCTTGATCGT 58.918 55.556 0.00 0.00 42.93 3.73
2175 2334 0.394899 CTTAGAAGGGGCAGGCAAGG 60.395 60.000 0.00 0.00 0.00 3.61
2176 2335 0.394899 CCTTAGAAGGGGCAGGCAAG 60.395 60.000 0.00 0.00 42.66 4.01
2177 2336 1.691219 CCTTAGAAGGGGCAGGCAA 59.309 57.895 0.00 0.00 42.66 4.52
2178 2337 3.415186 CCTTAGAAGGGGCAGGCA 58.585 61.111 0.00 0.00 42.66 4.75
2186 2345 2.581479 TTACCCCCTCCCTTAGAAGG 57.419 55.000 0.92 0.92 46.06 3.46
2187 2346 5.670818 AGTAATTTACCCCCTCCCTTAGAAG 59.329 44.000 2.92 0.00 0.00 2.85
2188 2347 5.430745 CAGTAATTTACCCCCTCCCTTAGAA 59.569 44.000 2.92 0.00 0.00 2.10
2189 2348 4.973211 CAGTAATTTACCCCCTCCCTTAGA 59.027 45.833 2.92 0.00 0.00 2.10
2191 2350 4.049318 CCAGTAATTTACCCCCTCCCTTA 58.951 47.826 2.92 0.00 0.00 2.69
2192 2351 2.856864 CCAGTAATTTACCCCCTCCCTT 59.143 50.000 2.92 0.00 0.00 3.95
2193 2352 2.048150 TCCAGTAATTTACCCCCTCCCT 59.952 50.000 2.92 0.00 0.00 4.20
2194 2353 2.495227 TCCAGTAATTTACCCCCTCCC 58.505 52.381 2.92 0.00 0.00 4.30
2195 2354 3.784202 TCTTCCAGTAATTTACCCCCTCC 59.216 47.826 2.92 0.00 0.00 4.30
2196 2355 4.473922 AGTCTTCCAGTAATTTACCCCCTC 59.526 45.833 2.92 0.00 0.00 4.30
2210 2369 2.568956 TCCAGGATTCACAGTCTTCCAG 59.431 50.000 0.00 0.00 0.00 3.86
2280 2483 5.884792 GGCTTAGGTACTGAGTAAGTGAGTA 59.115 44.000 0.00 0.00 44.55 2.59
2281 2484 4.705991 GGCTTAGGTACTGAGTAAGTGAGT 59.294 45.833 0.00 0.00 44.55 3.41
2282 2485 4.098196 GGGCTTAGGTACTGAGTAAGTGAG 59.902 50.000 0.00 0.00 44.55 3.51
2283 2486 4.021916 GGGCTTAGGTACTGAGTAAGTGA 58.978 47.826 0.00 0.00 44.55 3.41
2284 2487 3.767673 TGGGCTTAGGTACTGAGTAAGTG 59.232 47.826 0.00 0.00 44.55 3.16
2285 2488 4.057063 TGGGCTTAGGTACTGAGTAAGT 57.943 45.455 0.00 0.00 44.55 2.24
2286 2489 5.834204 AGTATGGGCTTAGGTACTGAGTAAG 59.166 44.000 0.00 0.00 44.55 2.34
2287 2490 5.774179 AGTATGGGCTTAGGTACTGAGTAA 58.226 41.667 0.00 0.00 44.55 2.24
2314 2517 6.765989 GTGCACAAATATCTTACCTCCATACA 59.234 38.462 13.17 0.00 0.00 2.29
2320 2523 6.985188 TTCAGTGCACAAATATCTTACCTC 57.015 37.500 21.04 0.00 0.00 3.85
2327 2530 6.032094 CCAGTTCATTCAGTGCACAAATATC 58.968 40.000 21.04 10.97 0.00 1.63
2389 2595 8.529476 GTCTTTGGGAGTAGTCATAGAGTAAAA 58.471 37.037 0.00 0.00 0.00 1.52
2394 2600 6.723298 ATGTCTTTGGGAGTAGTCATAGAG 57.277 41.667 0.00 0.00 0.00 2.43
2493 2701 6.626302 TGTTCACAAAAAGGTAAGAAACAGG 58.374 36.000 0.00 0.00 0.00 4.00
2524 2732 5.700722 TCGCTCTTAACTCAGTGTTCTAA 57.299 39.130 0.00 0.00 39.89 2.10
2607 2821 1.871039 GCGACTGACCAAACAAGCTAA 59.129 47.619 0.00 0.00 0.00 3.09
2618 2832 2.593346 ATGATCTCTTGCGACTGACC 57.407 50.000 0.00 0.00 0.00 4.02
2659 2906 0.883833 AGCGCTTTCCTGGACAATTG 59.116 50.000 2.64 3.24 0.00 2.32
2894 3160 1.671979 CATCATCGGTTGCATCACCT 58.328 50.000 6.03 0.00 34.22 4.00
2992 3258 9.832445 TGTAAGTTCAGAGATAATTATCCCAAC 57.168 33.333 19.67 16.02 33.17 3.77
3072 3338 3.312890 CATCCTCTTGATCCTACCCAGT 58.687 50.000 0.00 0.00 0.00 4.00
3090 3356 1.337071 CCTGAGCAACCATCATGCATC 59.663 52.381 0.00 0.00 46.22 3.91
3133 3399 2.026822 GCTCCTCTGTTGAATGAAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
3134 3400 2.363683 GCTCCTCTGTTGAATGAAGGG 58.636 52.381 0.00 0.00 0.00 3.95
3141 3407 1.686587 TGAAGACGCTCCTCTGTTGAA 59.313 47.619 0.00 0.00 0.00 2.69
3174 3440 4.061596 GTTGAGCTAGATAGTTGGCATCC 58.938 47.826 0.00 0.00 0.00 3.51
3222 3488 1.202222 CGCAATGGGAGACAATGAAGC 60.202 52.381 0.00 0.00 31.41 3.86
3225 3491 1.031571 GCCGCAATGGGAGACAATGA 61.032 55.000 0.00 0.00 38.63 2.57
3296 3562 2.834113 TGGGGTTTTCCAACTTTTCCA 58.166 42.857 0.00 0.00 42.91 3.53
3310 3576 3.877735 GCATAGTGATGGAGTTTGGGGTT 60.878 47.826 0.00 0.00 33.26 4.11
3413 3680 3.254657 GCCTGGCTAGCTATATATCTCGG 59.745 52.174 15.72 4.51 0.00 4.63
3414 3681 4.023279 CAGCCTGGCTAGCTATATATCTCG 60.023 50.000 22.90 0.00 38.95 4.04
3418 3685 3.387374 CAGCAGCCTGGCTAGCTATATAT 59.613 47.826 31.12 15.56 43.68 0.86
3419 3686 2.762887 CAGCAGCCTGGCTAGCTATATA 59.237 50.000 31.12 0.00 43.68 0.86
3420 3687 1.554160 CAGCAGCCTGGCTAGCTATAT 59.446 52.381 31.12 16.36 43.68 0.86
3421 3688 0.972134 CAGCAGCCTGGCTAGCTATA 59.028 55.000 31.12 0.60 43.68 1.31
3436 3703 3.313249 CGATTCACAGCCATTAATCAGCA 59.687 43.478 9.15 0.00 0.00 4.41
3448 3715 3.952535 ACAACAAAAGTCGATTCACAGC 58.047 40.909 0.00 0.00 0.00 4.40
3449 3716 5.007234 TGGTACAACAAAAGTCGATTCACAG 59.993 40.000 0.00 0.00 31.92 3.66
3580 3974 5.034797 CACATCTTCATTGCAGCATAGTTG 58.965 41.667 0.00 0.54 0.00 3.16
4159 4564 2.495669 GGGATATACTCTGCTCAGCTCC 59.504 54.545 0.00 0.00 0.00 4.70
4225 4630 5.140747 AGTGTTGGTGAAGTACAGAGATC 57.859 43.478 0.00 0.00 0.00 2.75
4229 4634 6.437477 AGATCATAGTGTTGGTGAAGTACAGA 59.563 38.462 0.00 0.00 0.00 3.41
4371 4783 2.517450 CGAGCGATCAAGCGGGAAC 61.517 63.158 0.00 0.00 43.00 3.62
4467 4879 1.524008 GCCAGGGTTTCAGGTTTCCG 61.524 60.000 0.00 0.00 0.00 4.30
4470 4882 0.537371 CGAGCCAGGGTTTCAGGTTT 60.537 55.000 0.00 0.00 0.00 3.27
4498 4910 5.933463 ACCAGTATTTTCGGTATTTCGACAA 59.067 36.000 0.00 0.00 39.01 3.18
4682 5094 3.131400 GGCACCTTTACCACTGAAAAACA 59.869 43.478 0.00 0.00 0.00 2.83
4683 5095 3.713288 GGCACCTTTACCACTGAAAAAC 58.287 45.455 0.00 0.00 0.00 2.43
4811 5506 8.575589 TGCATTCACATCAGTAAGTACAAAAAT 58.424 29.630 0.00 0.00 0.00 1.82
4839 5534 9.802039 ACTGGACATAGTTTTTCTACCATTTTA 57.198 29.630 0.00 0.00 0.00 1.52
4881 5576 0.804364 TGACCATTCGCATTGCAGAC 59.196 50.000 9.69 0.00 0.00 3.51
4882 5577 1.089112 CTGACCATTCGCATTGCAGA 58.911 50.000 9.69 4.37 0.00 4.26
4884 5579 1.199789 GAACTGACCATTCGCATTGCA 59.800 47.619 9.69 0.00 0.00 4.08
4885 5580 1.791555 CGAACTGACCATTCGCATTGC 60.792 52.381 0.00 0.00 42.11 3.56
4886 5581 2.163826 CGAACTGACCATTCGCATTG 57.836 50.000 0.00 0.00 42.11 2.82
4892 5587 3.654414 ACAGAGAACGAACTGACCATTC 58.346 45.455 0.00 0.00 37.54 2.67
4893 5588 3.753294 ACAGAGAACGAACTGACCATT 57.247 42.857 0.00 0.00 37.54 3.16
4895 5590 2.693591 AGAACAGAGAACGAACTGACCA 59.306 45.455 0.00 0.00 37.54 4.02
4896 5591 3.053455 CAGAACAGAGAACGAACTGACC 58.947 50.000 0.00 0.00 37.54 4.02
4919 5630 0.035439 ATCGAAATTCGTGTGGGGCT 60.035 50.000 15.34 0.00 41.35 5.19
4938 5650 4.211125 TGGAAATAAGCACAGAAACCACA 58.789 39.130 0.00 0.00 0.00 4.17
4956 5668 9.725019 ATTATTACGATTATTCAGCTGATGGAA 57.275 29.630 19.04 12.21 0.00 3.53
4959 5671 8.323854 CGGATTATTACGATTATTCAGCTGATG 58.676 37.037 19.04 6.18 0.00 3.07
4971 5683 4.365723 ACTTCGTGCGGATTATTACGATT 58.634 39.130 0.00 0.00 43.89 3.34
4985 5697 0.179124 TGGGTTTGCAAACTTCGTGC 60.179 50.000 34.39 20.18 42.55 5.34
4996 5708 1.151172 CGTTTGCAACCTGGGTTTGC 61.151 55.000 13.46 13.46 36.00 3.68
5037 6160 7.442062 GGTTTTCAGTTCCATTTGATCACATTT 59.558 33.333 0.00 0.00 0.00 2.32
5051 6174 9.498176 TTGTTAAGATACTAGGTTTTCAGTTCC 57.502 33.333 0.00 0.00 0.00 3.62
5064 6187 8.781196 CGCCTACACTATCTTGTTAAGATACTA 58.219 37.037 7.08 0.00 46.09 1.82
5065 6188 7.284944 ACGCCTACACTATCTTGTTAAGATACT 59.715 37.037 7.08 0.00 46.09 2.12
5090 6392 6.261158 GGATTAGGGCTCATCTTCTTGTTAAC 59.739 42.308 0.00 0.00 0.00 2.01
5210 6517 1.476891 AGGATGAGCGAAAAGAGCGTA 59.523 47.619 0.00 0.00 40.04 4.42
5211 6518 0.247736 AGGATGAGCGAAAAGAGCGT 59.752 50.000 0.00 0.00 40.04 5.07
5220 6527 3.589988 GAAACTTCAGAAGGATGAGCGA 58.410 45.455 14.90 0.00 0.00 4.93
5225 6532 3.070018 ACAGCGAAACTTCAGAAGGATG 58.930 45.455 14.90 7.81 0.00 3.51
5226 6536 3.070018 CACAGCGAAACTTCAGAAGGAT 58.930 45.455 14.90 2.47 0.00 3.24
5228 6538 2.213499 ACACAGCGAAACTTCAGAAGG 58.787 47.619 14.90 0.00 0.00 3.46
5230 6540 2.792674 CGTACACAGCGAAACTTCAGAA 59.207 45.455 0.00 0.00 0.00 3.02
5233 6543 0.856641 GCGTACACAGCGAAACTTCA 59.143 50.000 0.00 0.00 0.00 3.02
5255 6578 4.092091 CAGAGTTAACCTGATCGCAAAGAC 59.908 45.833 15.18 0.00 33.65 3.01
5258 6581 2.742053 GCAGAGTTAACCTGATCGCAAA 59.258 45.455 21.28 0.00 33.65 3.68
5261 6584 2.197577 GAGCAGAGTTAACCTGATCGC 58.802 52.381 21.28 12.05 37.33 4.58
5269 6592 2.475487 GTGAACGGTGAGCAGAGTTAAC 59.525 50.000 0.00 0.00 0.00 2.01
5602 7081 3.838271 GTCTGCTCGCCATCGGGA 61.838 66.667 0.00 0.00 38.83 5.14
5603 7082 4.899239 GGTCTGCTCGCCATCGGG 62.899 72.222 0.00 0.00 39.71 5.14
5746 10908 2.852075 AAACACTGGCCTCCGGGA 60.852 61.111 3.32 0.00 33.40 5.14
5747 10909 2.672996 CAAACACTGGCCTCCGGG 60.673 66.667 3.32 0.00 33.40 5.73
5748 10910 0.609131 ATTCAAACACTGGCCTCCGG 60.609 55.000 3.32 0.00 35.68 5.14
5749 10911 1.247567 AATTCAAACACTGGCCTCCG 58.752 50.000 3.32 0.00 0.00 4.63
5750 10912 3.392882 CAAAATTCAAACACTGGCCTCC 58.607 45.455 3.32 0.00 0.00 4.30
5751 10913 2.802247 GCAAAATTCAAACACTGGCCTC 59.198 45.455 3.32 0.00 0.00 4.70
5752 10914 2.435437 AGCAAAATTCAAACACTGGCCT 59.565 40.909 3.32 0.00 0.00 5.19
5753 10915 2.837498 AGCAAAATTCAAACACTGGCC 58.163 42.857 0.00 0.00 0.00 5.36
5754 10916 4.620982 ACTAGCAAAATTCAAACACTGGC 58.379 39.130 0.00 0.00 0.00 4.85
5755 10917 6.381801 CCTACTAGCAAAATTCAAACACTGG 58.618 40.000 0.00 0.00 0.00 4.00
5756 10918 5.858581 GCCTACTAGCAAAATTCAAACACTG 59.141 40.000 0.00 0.00 0.00 3.66
5757 10919 5.048013 GGCCTACTAGCAAAATTCAAACACT 60.048 40.000 0.00 0.00 0.00 3.55
5758 10920 5.048013 AGGCCTACTAGCAAAATTCAAACAC 60.048 40.000 1.29 0.00 0.00 3.32
5759 10921 5.076873 AGGCCTACTAGCAAAATTCAAACA 58.923 37.500 1.29 0.00 0.00 2.83
5760 10922 5.644977 AGGCCTACTAGCAAAATTCAAAC 57.355 39.130 1.29 0.00 0.00 2.93
5761 10923 6.454795 CAAAGGCCTACTAGCAAAATTCAAA 58.545 36.000 5.16 0.00 0.00 2.69
5762 10924 5.047377 CCAAAGGCCTACTAGCAAAATTCAA 60.047 40.000 5.16 0.00 0.00 2.69
5763 10925 4.462483 CCAAAGGCCTACTAGCAAAATTCA 59.538 41.667 5.16 0.00 0.00 2.57
5764 10926 4.678044 GCCAAAGGCCTACTAGCAAAATTC 60.678 45.833 5.16 0.00 44.06 2.17
5765 10927 3.195610 GCCAAAGGCCTACTAGCAAAATT 59.804 43.478 5.16 0.00 44.06 1.82
5766 10928 2.760650 GCCAAAGGCCTACTAGCAAAAT 59.239 45.455 5.16 0.00 44.06 1.82
5767 10929 2.167662 GCCAAAGGCCTACTAGCAAAA 58.832 47.619 5.16 0.00 44.06 2.44
5768 10930 1.834188 GCCAAAGGCCTACTAGCAAA 58.166 50.000 5.16 0.00 44.06 3.68
5769 10931 3.569873 GCCAAAGGCCTACTAGCAA 57.430 52.632 5.16 0.00 44.06 3.91
5792 10954 3.007940 AGAATTTTAGTTGGGCTTTGGGC 59.992 43.478 0.00 0.00 40.90 5.36
5793 10955 4.283212 TCAGAATTTTAGTTGGGCTTTGGG 59.717 41.667 0.00 0.00 0.00 4.12
5794 10956 5.467035 TCAGAATTTTAGTTGGGCTTTGG 57.533 39.130 0.00 0.00 0.00 3.28
5795 10957 7.967890 ATTTCAGAATTTTAGTTGGGCTTTG 57.032 32.000 0.00 0.00 0.00 2.77
5796 10958 8.432013 AGAATTTCAGAATTTTAGTTGGGCTTT 58.568 29.630 0.00 0.00 35.65 3.51
5797 10959 7.966812 AGAATTTCAGAATTTTAGTTGGGCTT 58.033 30.769 0.00 0.00 35.65 4.35
5798 10960 7.452813 AGAGAATTTCAGAATTTTAGTTGGGCT 59.547 33.333 0.00 0.00 35.65 5.19
5799 10961 7.606349 AGAGAATTTCAGAATTTTAGTTGGGC 58.394 34.615 0.00 0.00 35.65 5.36
5800 10962 9.415544 CAAGAGAATTTCAGAATTTTAGTTGGG 57.584 33.333 0.00 0.00 35.65 4.12
5804 10966 8.797438 GGGTCAAGAGAATTTCAGAATTTTAGT 58.203 33.333 0.00 0.00 35.65 2.24
5805 10967 8.796475 TGGGTCAAGAGAATTTCAGAATTTTAG 58.204 33.333 0.00 0.00 35.65 1.85
5806 10968 8.704849 TGGGTCAAGAGAATTTCAGAATTTTA 57.295 30.769 0.00 0.00 35.65 1.52
5807 10969 7.601705 TGGGTCAAGAGAATTTCAGAATTTT 57.398 32.000 0.00 0.00 35.65 1.82
5808 10970 7.787623 ATGGGTCAAGAGAATTTCAGAATTT 57.212 32.000 0.00 0.00 35.65 1.82
5809 10971 7.452501 TGAATGGGTCAAGAGAATTTCAGAATT 59.547 33.333 0.00 0.00 33.99 2.17
5810 10972 6.950041 TGAATGGGTCAAGAGAATTTCAGAAT 59.050 34.615 0.00 0.00 31.51 2.40
5811 10973 6.306199 TGAATGGGTCAAGAGAATTTCAGAA 58.694 36.000 0.00 0.00 31.51 3.02
5812 10974 5.879763 TGAATGGGTCAAGAGAATTTCAGA 58.120 37.500 0.00 0.00 31.51 3.27
5813 10975 6.770746 ATGAATGGGTCAAGAGAATTTCAG 57.229 37.500 0.00 0.00 40.50 3.02
5814 10976 7.121168 GTGTATGAATGGGTCAAGAGAATTTCA 59.879 37.037 0.00 0.00 40.50 2.69
5815 10977 7.121168 TGTGTATGAATGGGTCAAGAGAATTTC 59.879 37.037 0.00 0.00 40.50 2.17
5816 10978 6.947733 TGTGTATGAATGGGTCAAGAGAATTT 59.052 34.615 0.00 0.00 40.50 1.82
5817 10979 6.484288 TGTGTATGAATGGGTCAAGAGAATT 58.516 36.000 0.00 0.00 40.50 2.17
5818 10980 6.065976 TGTGTATGAATGGGTCAAGAGAAT 57.934 37.500 0.00 0.00 40.50 2.40
5819 10981 5.497464 TGTGTATGAATGGGTCAAGAGAA 57.503 39.130 0.00 0.00 40.50 2.87
5820 10982 5.698741 ATGTGTATGAATGGGTCAAGAGA 57.301 39.130 0.00 0.00 40.50 3.10
5821 10983 6.994496 ACATATGTGTATGAATGGGTCAAGAG 59.006 38.462 7.78 0.00 40.50 2.85
5822 10984 6.767423 CACATATGTGTATGAATGGGTCAAGA 59.233 38.462 24.91 0.00 40.12 3.02
5823 10985 6.767423 TCACATATGTGTATGAATGGGTCAAG 59.233 38.462 30.03 3.98 45.76 3.02
5824 10986 6.657875 TCACATATGTGTATGAATGGGTCAA 58.342 36.000 30.03 7.71 45.76 3.18
5825 10987 6.126796 ACTCACATATGTGTATGAATGGGTCA 60.127 38.462 30.03 9.68 45.76 4.02
5826 10988 6.203530 CACTCACATATGTGTATGAATGGGTC 59.796 42.308 30.03 0.00 45.76 4.46
5827 10989 6.057533 CACTCACATATGTGTATGAATGGGT 58.942 40.000 30.03 10.10 45.76 4.51
5828 10990 5.471116 CCACTCACATATGTGTATGAATGGG 59.529 44.000 30.03 18.37 45.76 4.00
5829 10991 6.290605 TCCACTCACATATGTGTATGAATGG 58.709 40.000 30.03 25.45 45.76 3.16
5830 10992 6.988580 ACTCCACTCACATATGTGTATGAATG 59.011 38.462 30.03 21.62 45.76 2.67
5831 10993 6.988580 CACTCCACTCACATATGTGTATGAAT 59.011 38.462 30.03 16.38 45.76 2.57
5832 10994 6.340522 CACTCCACTCACATATGTGTATGAA 58.659 40.000 30.03 15.73 45.76 2.57
5833 10995 5.906073 CACTCCACTCACATATGTGTATGA 58.094 41.667 30.03 21.17 45.76 2.15


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

AutoCloner maintained by Alex Coulton.