Multiple sequence alignment - TraesCS6B01G430400

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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 TraesCS6B01G430400 chr6B 100.000 2767 0 0 1 2767 698104022 698106788 0.000000e+00 5110
1 TraesCS6B01G430400 chr6B 87.108 2102 209 27 1 2055 698988751 698990837 0.000000e+00 2324
2 TraesCS6B01G430400 chr6B 88.962 1676 157 16 423 2087 698976254 698977912 0.000000e+00 2045
3 TraesCS6B01G430400 chr6B 85.944 498 63 5 2271 2764 698990862 698991356 2.440000e-145 525
4 TraesCS6B01G430400 chr6B 81.010 495 77 8 2271 2763 698977898 698978377 7.230000e-101 377
5 TraesCS6B01G430400 chr6D 89.199 1722 160 15 375 2087 459246316 459248020 0.000000e+00 2126
6 TraesCS6B01G430400 chr6D 89.087 1686 154 21 413 2087 458975502 458977168 0.000000e+00 2067
7 TraesCS6B01G430400 chr6D 85.871 2003 209 27 150 2087 459263220 459265213 0.000000e+00 2063
8 TraesCS6B01G430400 chr6D 88.026 1403 129 30 375 1763 459051629 459053006 0.000000e+00 1624
9 TraesCS6B01G430400 chr6D 87.903 496 58 2 2271 2764 458977154 458977649 1.430000e-162 582
10 TraesCS6B01G430400 chr6D 87.033 509 50 7 2271 2764 459058450 459058957 6.690000e-156 560
11 TraesCS6B01G430400 chr6D 84.318 491 66 6 2271 2753 459265199 459265686 1.160000e-128 470
12 TraesCS6B01G430400 chr6D 82.556 493 71 6 2271 2763 459248006 459248483 1.190000e-113 420
13 TraesCS6B01G430400 chr6D 88.450 329 28 3 1759 2087 459058146 459058464 3.340000e-104 388
14 TraesCS6B01G430400 chr6D 96.335 191 7 0 2082 2272 418875373 418875183 5.750000e-82 315
15 TraesCS6B01G430400 chr6A 88.863 1688 155 23 413 2087 605337487 605339154 0.000000e+00 2045
16 TraesCS6B01G430400 chr6A 89.518 1555 138 14 541 2087 605361582 605363119 0.000000e+00 1945
17 TraesCS6B01G430400 chr6A 88.323 1139 122 7 666 1797 605368720 605369854 0.000000e+00 1356
18 TraesCS6B01G430400 chr6A 86.290 496 59 6 2271 2764 605339140 605339628 5.250000e-147 531
19 TraesCS6B01G430400 chr6A 84.708 497 68 6 2271 2763 605370172 605370664 8.910000e-135 490
20 TraesCS6B01G430400 chr6A 82.794 494 68 5 2271 2763 605363105 605363582 2.550000e-115 425
21 TraesCS6B01G430400 chr6A 89.516 248 21 4 1844 2087 605369940 605370186 2.680000e-80 309
22 TraesCS6B01G430400 chr6A 95.288 191 9 0 2082 2272 4914416 4914226 1.250000e-78 303
23 TraesCS6B01G430400 chr5D 96.373 193 7 0 2081 2273 420900875 420901067 4.450000e-83 318
24 TraesCS6B01G430400 chr3D 93.780 209 9 3 2075 2283 337532045 337532249 7.440000e-81 311
25 TraesCS6B01G430400 chr3D 91.346 208 17 1 2071 2278 40793797 40794003 1.620000e-72 283
26 TraesCS6B01G430400 chr3D 86.458 96 12 1 2065 2160 435123393 435123299 1.360000e-18 104
27 TraesCS6B01G430400 chr7D 95.812 191 8 0 2082 2272 565658677 565658867 2.680000e-80 309
28 TraesCS6B01G430400 chr4B 93.269 208 12 2 2073 2279 222860630 222860836 3.460000e-79 305
29 TraesCS6B01G430400 chr4B 95.312 192 8 1 2082 2273 49469542 49469732 1.250000e-78 303
30 TraesCS6B01G430400 chr2D 96.703 182 6 0 2091 2272 526614155 526613974 1.250000e-78 303
31 TraesCS6B01G430400 chr2D 95.294 85 4 0 2076 2160 406704977 406705061 4.810000e-28 135
32 TraesCS6B01G430400 chr4A 94.388 196 11 0 2078 2273 136617829 136618024 4.480000e-78 302


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 TraesCS6B01G430400 chr6B 698104022 698106788 2766 False 5110.000000 5110 100.000000 1 2767 1 chr6B.!!$F1 2766
1 TraesCS6B01G430400 chr6B 698988751 698991356 2605 False 1424.500000 2324 86.526000 1 2764 2 chr6B.!!$F3 2763
2 TraesCS6B01G430400 chr6B 698976254 698978377 2123 False 1211.000000 2045 84.986000 423 2763 2 chr6B.!!$F2 2340
3 TraesCS6B01G430400 chr6D 459051629 459053006 1377 False 1624.000000 1624 88.026000 375 1763 1 chr6D.!!$F1 1388
4 TraesCS6B01G430400 chr6D 458975502 458977649 2147 False 1324.500000 2067 88.495000 413 2764 2 chr6D.!!$F2 2351
5 TraesCS6B01G430400 chr6D 459246316 459248483 2167 False 1273.000000 2126 85.877500 375 2763 2 chr6D.!!$F4 2388
6 TraesCS6B01G430400 chr6D 459263220 459265686 2466 False 1266.500000 2063 85.094500 150 2753 2 chr6D.!!$F5 2603
7 TraesCS6B01G430400 chr6D 459058146 459058957 811 False 474.000000 560 87.741500 1759 2764 2 chr6D.!!$F3 1005
8 TraesCS6B01G430400 chr6A 605337487 605339628 2141 False 1288.000000 2045 87.576500 413 2764 2 chr6A.!!$F1 2351
9 TraesCS6B01G430400 chr6A 605361582 605363582 2000 False 1185.000000 1945 86.156000 541 2763 2 chr6A.!!$F2 2222
10 TraesCS6B01G430400 chr6A 605368720 605370664 1944 False 718.333333 1356 87.515667 666 2763 3 chr6A.!!$F3 2097

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
765 798 0.031449 AGAGCGGAAGAGCGCTATTC 59.969 55.0 31.49 31.49 45.14 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2236 2353 0.044855 AGGACATTGGAGGGTAGGCT 59.955 55.0 0.0 0.0 0.0 4.58 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
43 45 1.383799 TCCAATTGGAGGGTGCAGG 59.616 57.895 23.63 0.00 39.78 4.85
54 56 4.326255 GTGCAGGTTAGCAGCCAT 57.674 55.556 0.00 0.00 46.69 4.40
61 63 1.565759 AGGTTAGCAGCCATTGGATGA 59.434 47.619 24.64 1.35 42.34 2.92
146 148 7.946043 AGTTAGTATGTAAAACACATTCGTCG 58.054 34.615 0.00 0.00 46.01 5.12
167 169 7.223971 TCGTCGGAATAATTTATCAAGGAACTG 59.776 37.037 0.00 0.00 40.86 3.16
219 221 0.037046 CTGGAAACATTTGGCCAGCC 60.037 55.000 5.11 0.38 41.17 4.85
231 233 2.906897 CCAGCCGCCAACACAGTT 60.907 61.111 0.00 0.00 0.00 3.16
244 246 4.082245 CCAACACAGTTGTTCCAAAGTCTT 60.082 41.667 8.83 0.00 44.57 3.01
313 315 0.179081 GGCGGGAGAGTGAATGTACC 60.179 60.000 0.00 0.00 0.00 3.34
315 317 0.527817 CGGGAGAGTGAATGTACCGC 60.528 60.000 0.00 0.00 33.01 5.68
316 318 0.535335 GGGAGAGTGAATGTACCGCA 59.465 55.000 0.00 0.00 0.00 5.69
322 324 0.604243 GTGAATGTACCGCACCACCA 60.604 55.000 0.00 0.00 31.76 4.17
327 329 3.632080 TACCGCACCACCACCCTG 61.632 66.667 0.00 0.00 0.00 4.45
343 345 4.010349 CACCCTGGTTTGAGTCCTATTTC 58.990 47.826 0.00 0.00 0.00 2.17
344 346 3.916989 ACCCTGGTTTGAGTCCTATTTCT 59.083 43.478 0.00 0.00 0.00 2.52
350 352 6.003950 TGGTTTGAGTCCTATTTCTTTGGAG 58.996 40.000 0.00 0.00 0.00 3.86
361 363 6.312180 CCTATTTCTTTGGAGCTTGAATTTGC 59.688 38.462 0.00 0.00 0.00 3.68
363 365 1.723003 CTTTGGAGCTTGAATTTGCGC 59.277 47.619 0.00 0.00 0.00 6.09
365 367 0.241749 TGGAGCTTGAATTTGCGCTG 59.758 50.000 9.73 0.00 31.96 5.18
373 375 4.521943 CTTGAATTTGCGCTGCTATCTAC 58.478 43.478 9.73 0.00 0.00 2.59
377 404 1.403814 TTGCGCTGCTATCTACCTCT 58.596 50.000 9.73 0.00 0.00 3.69
464 491 2.169561 TCCGGCATAAGTTGTCTATGCA 59.830 45.455 14.75 0.00 45.97 3.96
514 542 2.919772 TGACTACCACTCCATCCAGA 57.080 50.000 0.00 0.00 0.00 3.86
515 543 2.457598 TGACTACCACTCCATCCAGAC 58.542 52.381 0.00 0.00 0.00 3.51
550 579 8.863049 CATGTTGTGCAGGATTCTAATTTTAAC 58.137 33.333 0.00 0.00 0.00 2.01
600 629 5.815222 CCAAATGTTACCATACTCGTGATGA 59.185 40.000 0.00 0.00 0.00 2.92
602 631 7.401860 CAAATGTTACCATACTCGTGATGAAG 58.598 38.462 0.00 0.00 0.00 3.02
603 632 4.430007 TGTTACCATACTCGTGATGAAGC 58.570 43.478 0.00 0.00 0.00 3.86
610 639 2.408050 ACTCGTGATGAAGCTGTTCAC 58.592 47.619 11.86 11.86 45.58 3.18
633 664 6.257411 CACGTGAGAAATAGATTGCTTGAGAT 59.743 38.462 10.90 0.00 0.00 2.75
636 667 7.010830 CGTGAGAAATAGATTGCTTGAGATTCA 59.989 37.037 0.00 0.00 0.00 2.57
671 702 8.717821 TGCATGTAGTTCATACTTGTAAGAAAC 58.282 33.333 0.00 0.00 40.17 2.78
681 712 8.296713 TCATACTTGTAAGAAACATTTGGCTTC 58.703 33.333 0.00 0.00 38.10 3.86
695 728 8.045176 ACATTTGGCTTCTGAAACTAACTATC 57.955 34.615 0.00 0.00 0.00 2.08
716 749 8.612619 ACTATCTAGCAAATGTTTAAATCGTGG 58.387 33.333 0.00 0.00 0.00 4.94
728 761 6.038382 TGTTTAAATCGTGGTTGCTTACAGAA 59.962 34.615 0.00 0.00 0.00 3.02
729 762 6.621316 TTAAATCGTGGTTGCTTACAGAAA 57.379 33.333 0.00 0.00 0.00 2.52
742 775 4.925646 GCTTACAGAAAGAATTTTGGCAGG 59.074 41.667 0.00 0.00 39.27 4.85
747 780 6.515832 ACAGAAAGAATTTTGGCAGGTAAAG 58.484 36.000 0.00 0.00 39.27 1.85
762 795 1.100510 TAAAGAGCGGAAGAGCGCTA 58.899 50.000 11.50 0.00 46.21 4.26
765 798 0.031449 AGAGCGGAAGAGCGCTATTC 59.969 55.000 31.49 31.49 45.14 1.75
774 807 5.904080 CGGAAGAGCGCTATTCTAAAAATTG 59.096 40.000 35.55 16.42 31.92 2.32
782 815 4.500477 GCTATTCTAAAAATTGCACTGCCG 59.500 41.667 0.00 0.00 0.00 5.69
786 819 1.039856 AAAAATTGCACTGCCGGTCT 58.960 45.000 1.90 0.00 0.00 3.85
792 825 1.672356 GCACTGCCGGTCTTGTCAT 60.672 57.895 1.90 0.00 0.00 3.06
801 834 1.136252 CGGTCTTGTCATGTTTGCTCG 60.136 52.381 0.00 0.00 0.00 5.03
809 842 5.469373 TGTCATGTTTGCTCGTAATCATC 57.531 39.130 0.00 0.00 0.00 2.92
819 852 1.135112 TCGTAATCATCTGCGTGTGCT 60.135 47.619 0.00 0.00 43.34 4.40
830 863 1.950216 TGCGTGTGCTTTGTTTGGATA 59.050 42.857 0.00 0.00 43.34 2.59
870 903 6.591935 AGAACACAGTTCCATACTTTTCTCA 58.408 36.000 6.29 0.00 33.85 3.27
871 904 7.227156 AGAACACAGTTCCATACTTTTCTCAT 58.773 34.615 6.29 0.00 33.85 2.90
876 909 8.783093 CACAGTTCCATACTTTTCTCATTGTAA 58.217 33.333 0.00 0.00 33.85 2.41
1022 1063 2.158957 TGTCAGGAACTTCGAGCACTTT 60.159 45.455 0.00 0.00 34.60 2.66
1040 1081 0.950555 TTTGCTGAGCTTCGCGATGT 60.951 50.000 21.31 9.74 0.00 3.06
1054 1095 5.696260 TCGCGATGTAAACTTGAAGTATG 57.304 39.130 3.71 0.00 0.00 2.39
1095 1136 7.897575 AGAAATTGTACTTGCAACAAACAAA 57.102 28.000 16.19 5.20 40.05 2.83
1137 1178 1.000843 GGACATGGAGGTTTTGGCAAC 59.999 52.381 0.00 0.00 0.00 4.17
1140 1181 0.958822 ATGGAGGTTTTGGCAACGTC 59.041 50.000 0.00 1.00 42.51 4.34
1194 1235 8.523915 AGAGCAACATAATTGTATTTCCATCA 57.476 30.769 0.00 0.00 34.06 3.07
1217 1258 8.121305 TCATGTTTGACCTAAAAGTATGCAAT 57.879 30.769 0.00 0.00 0.00 3.56
1236 1278 3.756082 ATTGCCAGGGGACATTAGAAA 57.244 42.857 0.00 0.00 0.00 2.52
1287 1329 0.476808 TAAGGGTTCTGGCCAGGGAA 60.477 55.000 32.23 17.91 0.00 3.97
1288 1330 2.035783 GGGTTCTGGCCAGGGAAC 59.964 66.667 32.23 27.17 40.49 3.62
1349 1391 3.123050 GCAGCACAAAAACTTGGTTAGG 58.877 45.455 0.00 0.00 0.00 2.69
1434 1493 0.250684 TCTGGACGCCATGCTTTTCA 60.251 50.000 0.00 0.00 30.82 2.69
1441 1500 2.420022 ACGCCATGCTTTTCAGTATGTC 59.580 45.455 0.00 0.00 40.58 3.06
1451 1510 5.390991 GCTTTTCAGTATGTCCTGCTTACAC 60.391 44.000 0.00 0.00 37.40 2.90
1487 1546 8.918202 TTCAGTAAGTAATGAAATCAACCAGT 57.082 30.769 0.00 0.00 37.35 4.00
1488 1547 8.322906 TCAGTAAGTAATGAAATCAACCAGTG 57.677 34.615 0.00 0.00 0.00 3.66
1489 1548 8.154203 TCAGTAAGTAATGAAATCAACCAGTGA 58.846 33.333 0.00 0.00 41.67 3.41
1512 1573 7.224362 GTGAGACTGATGTTATCTCTCAATTGG 59.776 40.741 5.42 0.00 40.24 3.16
1581 1642 8.734386 GGCCAATAAGATTCGAGATAATCAAAT 58.266 33.333 0.00 0.00 38.16 2.32
1709 1770 6.808008 AAGATATCTGATTTTGGTATGGCG 57.192 37.500 5.86 0.00 0.00 5.69
1776 1837 6.370442 TGTTGTTGGCACATAGTAAGTGATAC 59.630 38.462 9.65 4.46 39.30 2.24
1800 1891 7.198390 ACACTGCATGAATTATCTTTATGCAC 58.802 34.615 11.81 0.00 46.31 4.57
1814 1905 7.759489 TCTTTATGCACTATTCTTGTGGTTT 57.241 32.000 0.00 0.00 36.08 3.27
1927 2036 9.330063 TCTGATGTATATAGCTTTGGAGTTTTG 57.670 33.333 0.00 0.00 0.00 2.44
1928 2037 9.330063 CTGATGTATATAGCTTTGGAGTTTTGA 57.670 33.333 0.00 0.00 0.00 2.69
2011 2120 7.674348 TCCAGCATTATAGCCTATGTAAGTACT 59.326 37.037 0.00 0.00 34.23 2.73
2022 2131 8.705594 AGCCTATGTAAGTACTATGACATGTTT 58.294 33.333 20.33 0.00 34.46 2.83
2078 2195 6.704289 CTGAAAGGAATAAGAATGGATGCA 57.296 37.500 0.00 0.00 0.00 3.96
2079 2196 6.704289 TGAAAGGAATAAGAATGGATGCAG 57.296 37.500 0.00 0.00 0.00 4.41
2080 2197 5.595542 TGAAAGGAATAAGAATGGATGCAGG 59.404 40.000 0.00 0.00 0.00 4.85
2081 2198 3.494332 AGGAATAAGAATGGATGCAGGC 58.506 45.455 0.00 0.00 0.00 4.85
2082 2199 3.117398 AGGAATAAGAATGGATGCAGGCA 60.117 43.478 0.00 0.00 0.00 4.75
2083 2200 3.255149 GGAATAAGAATGGATGCAGGCAG 59.745 47.826 0.00 0.00 0.00 4.85
2084 2201 3.589951 ATAAGAATGGATGCAGGCAGT 57.410 42.857 0.00 0.00 0.00 4.40
2085 2202 1.471119 AAGAATGGATGCAGGCAGTG 58.529 50.000 0.00 0.00 0.00 3.66
2086 2203 0.395311 AGAATGGATGCAGGCAGTGG 60.395 55.000 0.00 0.00 0.00 4.00
2087 2204 2.012902 GAATGGATGCAGGCAGTGGC 62.013 60.000 9.02 9.02 40.13 5.01
2091 2208 4.666253 ATGCAGGCAGTGGCGGTT 62.666 61.111 17.61 3.92 42.47 4.44
2094 2211 4.641645 CAGGCAGTGGCGGTTCCA 62.642 66.667 11.51 0.00 44.18 3.53
2108 2225 2.206900 TCCACCAGGGAGGCTTCA 59.793 61.111 0.00 0.00 42.15 3.02
2109 2226 1.463214 TCCACCAGGGAGGCTTCAA 60.463 57.895 0.00 0.00 42.15 2.69
2110 2227 0.846427 TCCACCAGGGAGGCTTCAAT 60.846 55.000 0.00 0.00 42.15 2.57
2111 2228 0.918983 CCACCAGGGAGGCTTCAATA 59.081 55.000 0.00 0.00 43.14 1.90
2112 2229 1.133976 CCACCAGGGAGGCTTCAATAG 60.134 57.143 0.00 0.00 43.14 1.73
2113 2230 1.133976 CACCAGGGAGGCTTCAATAGG 60.134 57.143 0.00 0.00 43.14 2.57
2132 2249 2.801077 GCTTAAGCCTACCCTCCAAA 57.199 50.000 17.00 0.00 34.31 3.28
2133 2250 3.081710 GCTTAAGCCTACCCTCCAAAA 57.918 47.619 17.00 0.00 34.31 2.44
2134 2251 3.632333 GCTTAAGCCTACCCTCCAAAAT 58.368 45.455 17.00 0.00 34.31 1.82
2135 2252 3.632604 GCTTAAGCCTACCCTCCAAAATC 59.367 47.826 17.00 0.00 34.31 2.17
2136 2253 2.828661 AAGCCTACCCTCCAAAATCC 57.171 50.000 0.00 0.00 0.00 3.01
2137 2254 1.987080 AGCCTACCCTCCAAAATCCT 58.013 50.000 0.00 0.00 0.00 3.24
2138 2255 3.145559 AGCCTACCCTCCAAAATCCTA 57.854 47.619 0.00 0.00 0.00 2.94
2139 2256 3.681311 AGCCTACCCTCCAAAATCCTAT 58.319 45.455 0.00 0.00 0.00 2.57
2140 2257 4.055094 AGCCTACCCTCCAAAATCCTATT 58.945 43.478 0.00 0.00 0.00 1.73
2141 2258 4.482398 AGCCTACCCTCCAAAATCCTATTT 59.518 41.667 0.00 0.00 0.00 1.40
2142 2259 5.674958 AGCCTACCCTCCAAAATCCTATTTA 59.325 40.000 0.00 0.00 0.00 1.40
2143 2260 6.161526 AGCCTACCCTCCAAAATCCTATTTAA 59.838 38.462 0.00 0.00 0.00 1.52
2144 2261 6.490381 GCCTACCCTCCAAAATCCTATTTAAG 59.510 42.308 0.00 0.00 0.00 1.85
2145 2262 6.490381 CCTACCCTCCAAAATCCTATTTAAGC 59.510 42.308 0.00 0.00 0.00 3.09
2146 2263 6.092346 ACCCTCCAAAATCCTATTTAAGCT 57.908 37.500 0.00 0.00 0.00 3.74
2147 2264 7.220890 ACCCTCCAAAATCCTATTTAAGCTA 57.779 36.000 0.00 0.00 0.00 3.32
2148 2265 7.648770 ACCCTCCAAAATCCTATTTAAGCTAA 58.351 34.615 0.00 0.00 0.00 3.09
2149 2266 8.119891 ACCCTCCAAAATCCTATTTAAGCTAAA 58.880 33.333 0.00 0.00 0.00 1.85
2150 2267 8.414003 CCCTCCAAAATCCTATTTAAGCTAAAC 58.586 37.037 0.00 0.00 0.00 2.01
2151 2268 8.966868 CCTCCAAAATCCTATTTAAGCTAAACA 58.033 33.333 0.00 0.00 0.00 2.83
2160 2277 9.391006 TCCTATTTAAGCTAAACATACCACTTG 57.609 33.333 0.00 0.00 0.00 3.16
2161 2278 9.391006 CCTATTTAAGCTAAACATACCACTTGA 57.609 33.333 0.00 0.00 0.00 3.02
2163 2280 8.630054 ATTTAAGCTAAACATACCACTTGACA 57.370 30.769 0.00 0.00 0.00 3.58
2164 2281 8.453238 TTTAAGCTAAACATACCACTTGACAA 57.547 30.769 0.00 0.00 0.00 3.18
2165 2282 6.560253 AAGCTAAACATACCACTTGACAAG 57.440 37.500 13.77 13.77 0.00 3.16
2166 2283 5.621193 AGCTAAACATACCACTTGACAAGT 58.379 37.500 15.23 15.23 44.06 3.16
2167 2284 6.765403 AGCTAAACATACCACTTGACAAGTA 58.235 36.000 20.17 6.14 40.46 2.24
2168 2285 7.394816 AGCTAAACATACCACTTGACAAGTAT 58.605 34.615 20.17 13.75 40.46 2.12
2169 2286 8.537016 AGCTAAACATACCACTTGACAAGTATA 58.463 33.333 20.17 15.34 40.46 1.47
2170 2287 9.326413 GCTAAACATACCACTTGACAAGTATAT 57.674 33.333 20.17 16.72 40.46 0.86
2173 2290 9.959721 AAACATACCACTTGACAAGTATATTCT 57.040 29.630 20.17 8.04 40.46 2.40
2174 2291 8.948631 ACATACCACTTGACAAGTATATTCTG 57.051 34.615 20.17 14.33 40.46 3.02
2175 2292 7.987458 ACATACCACTTGACAAGTATATTCTGG 59.013 37.037 20.17 16.70 40.46 3.86
2176 2293 6.374417 ACCACTTGACAAGTATATTCTGGT 57.626 37.500 20.17 17.29 40.46 4.00
2177 2294 6.173339 ACCACTTGACAAGTATATTCTGGTG 58.827 40.000 20.17 5.36 40.46 4.17
2178 2295 5.065218 CCACTTGACAAGTATATTCTGGTGC 59.935 44.000 20.17 0.00 40.46 5.01
2179 2296 5.877012 CACTTGACAAGTATATTCTGGTGCT 59.123 40.000 20.17 0.00 40.46 4.40
2180 2297 6.372659 CACTTGACAAGTATATTCTGGTGCTT 59.627 38.462 20.17 0.00 40.46 3.91
2181 2298 6.942576 ACTTGACAAGTATATTCTGGTGCTTT 59.057 34.615 19.28 0.00 40.69 3.51
2182 2299 8.100791 ACTTGACAAGTATATTCTGGTGCTTTA 58.899 33.333 19.28 0.00 40.69 1.85
2183 2300 7.843490 TGACAAGTATATTCTGGTGCTTTAC 57.157 36.000 0.00 0.00 0.00 2.01
2184 2301 7.390823 TGACAAGTATATTCTGGTGCTTTACA 58.609 34.615 0.00 0.00 0.00 2.41
2185 2302 8.046708 TGACAAGTATATTCTGGTGCTTTACAT 58.953 33.333 0.00 0.00 0.00 2.29
2186 2303 8.213518 ACAAGTATATTCTGGTGCTTTACATG 57.786 34.615 0.00 0.00 0.00 3.21
2187 2304 6.867662 AGTATATTCTGGTGCTTTACATGC 57.132 37.500 0.00 0.00 0.00 4.06
2188 2305 6.356556 AGTATATTCTGGTGCTTTACATGCA 58.643 36.000 0.00 0.00 38.19 3.96
2189 2306 6.828273 AGTATATTCTGGTGCTTTACATGCAA 59.172 34.615 0.00 0.00 42.41 4.08
2195 2312 4.650545 GGTGCTTTACATGCAACAATTG 57.349 40.909 3.24 3.24 46.39 2.32
2220 2337 7.909777 CAATGCATTTGCTAATTAGACTCAG 57.090 36.000 16.85 3.84 42.66 3.35
2221 2338 7.700505 CAATGCATTTGCTAATTAGACTCAGA 58.299 34.615 16.85 0.89 42.66 3.27
2222 2339 7.870509 ATGCATTTGCTAATTAGACTCAGAA 57.129 32.000 16.85 0.00 42.66 3.02
2223 2340 7.686438 TGCATTTGCTAATTAGACTCAGAAA 57.314 32.000 16.85 5.06 42.66 2.52
2224 2341 8.109705 TGCATTTGCTAATTAGACTCAGAAAA 57.890 30.769 16.85 0.00 42.66 2.29
2225 2342 8.742777 TGCATTTGCTAATTAGACTCAGAAAAT 58.257 29.630 16.85 0.44 42.66 1.82
2226 2343 9.017669 GCATTTGCTAATTAGACTCAGAAAATG 57.982 33.333 16.85 13.23 38.21 2.32
2229 2346 8.621532 TTGCTAATTAGACTCAGAAAATGTGT 57.378 30.769 16.85 0.00 38.31 3.72
2230 2347 8.032952 TGCTAATTAGACTCAGAAAATGTGTG 57.967 34.615 16.85 0.00 35.80 3.82
2231 2348 7.661437 TGCTAATTAGACTCAGAAAATGTGTGT 59.339 33.333 16.85 0.00 35.80 3.72
2232 2349 8.507249 GCTAATTAGACTCAGAAAATGTGTGTT 58.493 33.333 16.85 0.00 35.80 3.32
2238 2355 7.196331 AGACTCAGAAAATGTGTGTTTTAAGC 58.804 34.615 0.00 0.00 35.80 3.09
2239 2356 6.273071 ACTCAGAAAATGTGTGTTTTAAGCC 58.727 36.000 0.00 0.00 34.41 4.35
2240 2357 6.096846 ACTCAGAAAATGTGTGTTTTAAGCCT 59.903 34.615 0.00 0.00 34.41 4.58
2241 2358 7.284489 ACTCAGAAAATGTGTGTTTTAAGCCTA 59.716 33.333 0.00 0.00 34.41 3.93
2242 2359 7.422399 TCAGAAAATGTGTGTTTTAAGCCTAC 58.578 34.615 0.00 0.00 31.80 3.18
2243 2360 6.640907 CAGAAAATGTGTGTTTTAAGCCTACC 59.359 38.462 0.00 0.00 31.80 3.18
2244 2361 5.462530 AAATGTGTGTTTTAAGCCTACCC 57.537 39.130 0.00 0.00 0.00 3.69
2245 2362 3.868619 TGTGTGTTTTAAGCCTACCCT 57.131 42.857 0.00 0.00 0.00 4.34
2246 2363 3.746940 TGTGTGTTTTAAGCCTACCCTC 58.253 45.455 0.00 0.00 0.00 4.30
2247 2364 3.079578 GTGTGTTTTAAGCCTACCCTCC 58.920 50.000 0.00 0.00 0.00 4.30
2248 2365 2.712087 TGTGTTTTAAGCCTACCCTCCA 59.288 45.455 0.00 0.00 0.00 3.86
2249 2366 3.138653 TGTGTTTTAAGCCTACCCTCCAA 59.861 43.478 0.00 0.00 0.00 3.53
2250 2367 4.202631 TGTGTTTTAAGCCTACCCTCCAAT 60.203 41.667 0.00 0.00 0.00 3.16
2251 2368 4.157840 GTGTTTTAAGCCTACCCTCCAATG 59.842 45.833 0.00 0.00 0.00 2.82
2252 2369 4.202631 TGTTTTAAGCCTACCCTCCAATGT 60.203 41.667 0.00 0.00 0.00 2.71
2253 2370 3.926058 TTAAGCCTACCCTCCAATGTC 57.074 47.619 0.00 0.00 0.00 3.06
2254 2371 0.919710 AAGCCTACCCTCCAATGTCC 59.080 55.000 0.00 0.00 0.00 4.02
2255 2372 0.044855 AGCCTACCCTCCAATGTCCT 59.955 55.000 0.00 0.00 0.00 3.85
2256 2373 0.181350 GCCTACCCTCCAATGTCCTG 59.819 60.000 0.00 0.00 0.00 3.86
2257 2374 0.181350 CCTACCCTCCAATGTCCTGC 59.819 60.000 0.00 0.00 0.00 4.85
2258 2375 1.207791 CTACCCTCCAATGTCCTGCT 58.792 55.000 0.00 0.00 0.00 4.24
2259 2376 2.398588 CTACCCTCCAATGTCCTGCTA 58.601 52.381 0.00 0.00 0.00 3.49
2260 2377 1.668826 ACCCTCCAATGTCCTGCTAA 58.331 50.000 0.00 0.00 0.00 3.09
2261 2378 1.992557 ACCCTCCAATGTCCTGCTAAA 59.007 47.619 0.00 0.00 0.00 1.85
2262 2379 2.582636 ACCCTCCAATGTCCTGCTAAAT 59.417 45.455 0.00 0.00 0.00 1.40
2263 2380 3.011708 ACCCTCCAATGTCCTGCTAAATT 59.988 43.478 0.00 0.00 0.00 1.82
2264 2381 3.633986 CCCTCCAATGTCCTGCTAAATTC 59.366 47.826 0.00 0.00 0.00 2.17
2265 2382 3.313526 CCTCCAATGTCCTGCTAAATTCG 59.686 47.826 0.00 0.00 0.00 3.34
2266 2383 2.682856 TCCAATGTCCTGCTAAATTCGC 59.317 45.455 0.00 0.00 0.00 4.70
2267 2384 2.223572 CCAATGTCCTGCTAAATTCGCC 60.224 50.000 0.00 0.00 0.00 5.54
2268 2385 2.418368 ATGTCCTGCTAAATTCGCCA 57.582 45.000 0.00 0.00 0.00 5.69
2269 2386 1.448985 TGTCCTGCTAAATTCGCCAC 58.551 50.000 0.00 0.00 0.00 5.01
2293 2410 0.547553 TGCAGGCATGGAGCTTATGA 59.452 50.000 14.08 0.00 44.79 2.15
2303 2420 2.175499 TGGAGCTTATGAAAGGATGGGG 59.825 50.000 0.00 0.00 32.98 4.96
2330 2447 7.017645 CACAAAGGATTTTATTGACTCGTCAG 58.982 38.462 0.00 0.00 37.23 3.51
2335 2452 6.369065 AGGATTTTATTGACTCGTCAGTTGTC 59.631 38.462 0.37 0.00 41.13 3.18
2340 2457 0.386985 GACTCGTCAGTTGTCGGGAC 60.387 60.000 5.69 0.00 30.63 4.46
2347 2464 1.760613 TCAGTTGTCGGGACTTGTTCT 59.239 47.619 0.00 0.00 0.00 3.01
2420 2541 3.736100 CAAATGCGCGGCCACTCA 61.736 61.111 8.83 0.00 0.00 3.41
2429 2550 1.434622 GCGGCCACTCATGTCATCAG 61.435 60.000 2.24 0.00 0.00 2.90
2432 2553 1.661341 GCCACTCATGTCATCAGTCC 58.339 55.000 0.00 0.00 0.00 3.85
2466 2587 8.176105 TCTGGAGAATGGAGATATATCACTTCT 58.824 37.037 15.08 13.13 0.00 2.85
2502 2623 8.844244 AGAGCCTATGTATTTTGCAGAAAATAG 58.156 33.333 4.21 7.09 42.23 1.73
2519 2640 9.887629 CAGAAAATAGCTATGATACTGATGGAT 57.112 33.333 7.09 0.00 0.00 3.41
2525 2646 7.250032 AGCTATGATACTGATGGATTAGCAA 57.750 36.000 0.00 0.00 34.66 3.91
2572 2693 9.137459 AGTAACATGAGCATTACAGTACTAGAT 57.863 33.333 0.00 0.00 34.36 1.98
2587 2709 2.041891 ACTAGATGGACGCTAGCCCTAT 59.958 50.000 9.66 4.72 39.10 2.57
2590 2712 1.618837 GATGGACGCTAGCCCTATCAA 59.381 52.381 9.66 0.00 0.00 2.57
2593 2730 1.618837 GGACGCTAGCCCTATCAATCA 59.381 52.381 9.66 0.00 0.00 2.57
2599 2736 6.296026 ACGCTAGCCCTATCAATCAAATTTA 58.704 36.000 9.66 0.00 0.00 1.40
2633 2771 9.835389 TTGTAGGTACTTTTTACAACTGTATGT 57.165 29.630 0.00 2.24 41.75 2.29
2717 2872 2.254152 TCAACTCTGGTAGCTCCCAT 57.746 50.000 0.00 0.00 33.00 4.00
2719 2874 3.719871 TCAACTCTGGTAGCTCCCATAA 58.280 45.455 0.00 0.00 33.00 1.90
2755 2911 8.983307 AGGTCTAAATGTTCTTACTAAAGACG 57.017 34.615 0.00 0.00 41.48 4.18
2764 2920 5.961396 TCTTACTAAAGACGCTTCTCACT 57.039 39.130 0.00 0.00 36.80 3.41
2765 2921 7.040892 TGTTCTTACTAAAGACGCTTCTCACTA 60.041 37.037 0.00 0.00 41.48 2.74
2766 2922 7.444629 TCTTACTAAAGACGCTTCTCACTAA 57.555 36.000 0.00 0.00 36.80 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.851686 AATTGGATAAGCTATTGTGTTCTCATA 57.148 29.630 0.00 0.00 0.00 2.15
6 7 8.627403 CAATTGGATAAGCTATTGTGTTCTCAT 58.373 33.333 0.00 0.00 0.00 2.90
7 8 7.067372 CCAATTGGATAAGCTATTGTGTTCTCA 59.933 37.037 20.50 0.00 37.39 3.27
8 9 7.283127 TCCAATTGGATAAGCTATTGTGTTCTC 59.717 37.037 23.63 0.00 39.78 2.87
9 10 7.118723 TCCAATTGGATAAGCTATTGTGTTCT 58.881 34.615 23.63 0.00 39.78 3.01
10 11 7.333528 TCCAATTGGATAAGCTATTGTGTTC 57.666 36.000 23.63 0.00 39.78 3.18
15 17 5.242393 CACCCTCCAATTGGATAAGCTATTG 59.758 44.000 27.20 12.04 44.46 1.90
18 20 3.435026 GCACCCTCCAATTGGATAAGCTA 60.435 47.826 27.20 3.55 44.46 3.32
43 45 3.282021 TCTTCATCCAATGGCTGCTAAC 58.718 45.455 0.00 0.00 0.00 2.34
52 54 9.193133 GCTCATATTTTCATTCTTCATCCAATG 57.807 33.333 0.00 0.00 0.00 2.82
54 56 8.296211 TGCTCATATTTTCATTCTTCATCCAA 57.704 30.769 0.00 0.00 0.00 3.53
61 63 6.322969 TCCTGCATGCTCATATTTTCATTCTT 59.677 34.615 20.33 0.00 0.00 2.52
139 141 8.557029 GTTCCTTGATAAATTATTCCGACGAAT 58.443 33.333 0.00 0.00 41.67 3.34
141 143 7.223971 CAGTTCCTTGATAAATTATTCCGACGA 59.776 37.037 0.00 0.00 0.00 4.20
143 145 7.012421 AGCAGTTCCTTGATAAATTATTCCGAC 59.988 37.037 0.00 0.00 0.00 4.79
146 148 8.907885 AGAAGCAGTTCCTTGATAAATTATTCC 58.092 33.333 0.00 0.00 32.48 3.01
199 201 0.968405 GCTGGCCAAATGTTTCCAGA 59.032 50.000 7.01 0.00 46.80 3.86
290 292 0.745845 CATTCACTCTCCCGCCCTTG 60.746 60.000 0.00 0.00 0.00 3.61
292 294 0.325296 TACATTCACTCTCCCGCCCT 60.325 55.000 0.00 0.00 0.00 5.19
322 324 3.916989 AGAAATAGGACTCAAACCAGGGT 59.083 43.478 0.00 0.00 0.00 4.34
327 329 5.106118 GCTCCAAAGAAATAGGACTCAAACC 60.106 44.000 0.00 0.00 0.00 3.27
331 333 5.013079 TCAAGCTCCAAAGAAATAGGACTCA 59.987 40.000 0.00 0.00 0.00 3.41
343 345 1.723003 GCGCAAATTCAAGCTCCAAAG 59.277 47.619 0.30 0.00 0.00 2.77
344 346 1.340889 AGCGCAAATTCAAGCTCCAAA 59.659 42.857 11.47 0.00 34.48 3.28
350 352 2.114825 GATAGCAGCGCAAATTCAAGC 58.885 47.619 11.47 0.00 0.00 4.01
361 363 4.036971 ACTTGTAAGAGGTAGATAGCAGCG 59.963 45.833 0.00 0.00 0.00 5.18
363 365 7.101652 TGAACTTGTAAGAGGTAGATAGCAG 57.898 40.000 0.00 0.00 0.00 4.24
365 367 8.630917 TGTATGAACTTGTAAGAGGTAGATAGC 58.369 37.037 0.00 0.00 0.00 2.97
373 375 7.607991 ACTTGGATTGTATGAACTTGTAAGAGG 59.392 37.037 0.00 0.00 0.00 3.69
377 404 8.684386 TTGACTTGGATTGTATGAACTTGTAA 57.316 30.769 0.00 0.00 0.00 2.41
440 467 2.851263 AGACAACTTATGCCGGAACA 57.149 45.000 5.05 0.00 0.00 3.18
445 472 4.512944 AGATTGCATAGACAACTTATGCCG 59.487 41.667 12.98 0.00 44.18 5.69
492 519 3.099905 CTGGATGGAGTGGTAGTCAAGA 58.900 50.000 0.00 0.00 0.00 3.02
493 520 3.099905 TCTGGATGGAGTGGTAGTCAAG 58.900 50.000 0.00 0.00 0.00 3.02
494 521 2.832129 GTCTGGATGGAGTGGTAGTCAA 59.168 50.000 0.00 0.00 0.00 3.18
499 527 1.906574 GTTGGTCTGGATGGAGTGGTA 59.093 52.381 0.00 0.00 0.00 3.25
550 579 7.965107 GGACATACAAAAACTTCTGCTTGATAG 59.035 37.037 0.00 0.00 0.00 2.08
600 629 4.883083 TCTATTTCTCACGTGAACAGCTT 58.117 39.130 20.49 5.28 0.00 3.74
602 631 5.554636 CAATCTATTTCTCACGTGAACAGC 58.445 41.667 20.49 0.00 0.00 4.40
603 632 5.349817 AGCAATCTATTTCTCACGTGAACAG 59.650 40.000 20.49 8.37 0.00 3.16
610 639 6.841443 ATCTCAAGCAATCTATTTCTCACG 57.159 37.500 0.00 0.00 0.00 4.35
633 664 5.588246 TGAACTACATGCACTTTGTCTTGAA 59.412 36.000 0.00 0.00 0.00 2.69
636 667 6.936900 AGTATGAACTACATGCACTTTGTCTT 59.063 34.615 0.00 0.00 42.58 3.01
643 674 7.611770 TCTTACAAGTATGAACTACATGCACT 58.388 34.615 0.00 0.00 42.58 4.40
671 702 8.273780 AGATAGTTAGTTTCAGAAGCCAAATG 57.726 34.615 0.00 0.00 0.00 2.32
695 728 6.183359 GCAACCACGATTTAAACATTTGCTAG 60.183 38.462 0.00 0.00 35.15 3.42
716 749 5.752955 TGCCAAAATTCTTTCTGTAAGCAAC 59.247 36.000 0.00 0.00 33.66 4.17
728 761 4.321230 CGCTCTTTACCTGCCAAAATTCTT 60.321 41.667 0.00 0.00 0.00 2.52
729 762 3.191371 CGCTCTTTACCTGCCAAAATTCT 59.809 43.478 0.00 0.00 0.00 2.40
762 795 3.258123 ACCGGCAGTGCAATTTTTAGAAT 59.742 39.130 18.61 0.00 0.00 2.40
765 798 2.228822 AGACCGGCAGTGCAATTTTTAG 59.771 45.455 18.61 0.00 0.00 1.85
774 807 1.672356 ATGACAAGACCGGCAGTGC 60.672 57.895 6.55 6.55 0.00 4.40
782 815 1.873591 ACGAGCAAACATGACAAGACC 59.126 47.619 0.00 0.00 0.00 3.85
786 819 5.643348 AGATGATTACGAGCAAACATGACAA 59.357 36.000 0.00 0.00 0.00 3.18
792 825 2.348362 CGCAGATGATTACGAGCAAACA 59.652 45.455 0.00 0.00 0.00 2.83
801 834 3.120199 ACAAAGCACACGCAGATGATTAC 60.120 43.478 0.00 0.00 42.27 1.89
809 842 0.100325 TCCAAACAAAGCACACGCAG 59.900 50.000 0.00 0.00 42.27 5.18
819 852 6.166984 TCCAAAGTTGCATATCCAAACAAA 57.833 33.333 0.00 0.00 0.00 2.83
830 863 3.821033 GTGTTCTACCTCCAAAGTTGCAT 59.179 43.478 0.00 0.00 0.00 3.96
876 909 7.363268 GCACCTAGAAACATGATTGAGGAAAAT 60.363 37.037 16.14 0.00 0.00 1.82
879 912 4.943705 GCACCTAGAAACATGATTGAGGAA 59.056 41.667 16.14 0.00 0.00 3.36
880 913 4.225942 AGCACCTAGAAACATGATTGAGGA 59.774 41.667 16.14 0.00 0.00 3.71
887 920 5.692115 TGGAATAGCACCTAGAAACATGA 57.308 39.130 0.00 0.00 0.00 3.07
895 928 9.376075 CACATAGAAATATGGAATAGCACCTAG 57.624 37.037 0.78 0.00 28.50 3.02
897 930 6.656693 GCACATAGAAATATGGAATAGCACCT 59.343 38.462 0.78 0.00 28.50 4.00
898 931 6.656693 AGCACATAGAAATATGGAATAGCACC 59.343 38.462 0.78 0.00 28.50 5.01
899 932 7.678947 AGCACATAGAAATATGGAATAGCAC 57.321 36.000 0.78 0.00 28.50 4.40
942 981 4.641541 CCTATCAGGAACATTGATGCACAA 59.358 41.667 0.00 0.00 37.67 3.33
944 983 3.004106 GCCTATCAGGAACATTGATGCAC 59.996 47.826 0.00 0.00 37.67 4.57
996 1037 2.353208 GCTCGAAGTTCCTGACATCAGT 60.353 50.000 8.06 0.00 42.27 3.41
1095 1136 4.946157 CCAAGCATGTTGGAGTTAGAGAAT 59.054 41.667 17.28 0.00 42.06 2.40
1137 1178 4.293415 ACTTTCACGTTACCTTGTAGACG 58.707 43.478 0.00 0.00 41.00 4.18
1140 1181 6.700520 AGAGAAACTTTCACGTTACCTTGTAG 59.299 38.462 4.34 0.00 0.00 2.74
1181 1222 8.642935 TTAGGTCAAACATGATGGAAATACAA 57.357 30.769 0.00 0.00 0.00 2.41
1194 1235 7.331687 GCAATTGCATACTTTTAGGTCAAACAT 59.668 33.333 25.36 0.00 41.59 2.71
1217 1258 3.534357 TTTTCTAATGTCCCCTGGCAA 57.466 42.857 0.00 0.00 0.00 4.52
1236 1278 3.417101 TCACGGCAATTTCTGTACCATT 58.583 40.909 0.00 0.00 0.00 3.16
1253 1295 3.671716 ACCCTTACTTAGCCTTTTCACG 58.328 45.455 0.00 0.00 0.00 4.35
1265 1307 0.698818 CCTGGCCAGAACCCTTACTT 59.301 55.000 34.91 0.00 0.00 2.24
1287 1329 8.641498 ATTACTTCATTTCTGAATTCCAGTGT 57.359 30.769 2.27 0.00 43.38 3.55
1288 1330 9.994432 GTATTACTTCATTTCTGAATTCCAGTG 57.006 33.333 2.27 0.00 43.38 3.66
1349 1391 0.729690 GGATGCAGAAACCGAGAAGC 59.270 55.000 0.00 0.00 0.00 3.86
1409 1451 0.598065 GCATGGCGTCCAGACTTTTT 59.402 50.000 4.90 0.00 36.75 1.94
1434 1493 3.619979 GCAAGGTGTAAGCAGGACATACT 60.620 47.826 0.00 0.00 36.26 2.12
1441 1500 1.327303 TTTGGCAAGGTGTAAGCAGG 58.673 50.000 0.00 0.00 36.26 4.85
1451 1510 7.601856 TCATTACTTACTGAAATTTGGCAAGG 58.398 34.615 0.00 0.00 0.00 3.61
1487 1546 7.093156 ACCAATTGAGAGATAACATCAGTCTCA 60.093 37.037 7.12 0.00 40.58 3.27
1488 1547 7.224362 CACCAATTGAGAGATAACATCAGTCTC 59.776 40.741 7.12 0.00 38.88 3.36
1489 1548 7.046652 CACCAATTGAGAGATAACATCAGTCT 58.953 38.462 7.12 0.00 0.00 3.24
1581 1642 3.759815 AAGAAGTCCTCTAGCTACCCA 57.240 47.619 0.00 0.00 32.46 4.51
1709 1770 2.227388 CTGATTGCCGCCAAATATCCTC 59.773 50.000 0.00 0.00 34.05 3.71
1828 1919 9.405587 CCGTTGTTTGAATACAGAACATAATTT 57.594 29.630 0.00 0.00 33.73 1.82
1829 1920 8.573035 ACCGTTGTTTGAATACAGAACATAATT 58.427 29.630 0.00 0.00 33.73 1.40
1830 1921 8.106247 ACCGTTGTTTGAATACAGAACATAAT 57.894 30.769 0.00 0.00 33.73 1.28
1831 1922 7.499321 ACCGTTGTTTGAATACAGAACATAA 57.501 32.000 0.00 0.00 33.73 1.90
1832 1923 7.499321 AACCGTTGTTTGAATACAGAACATA 57.501 32.000 0.00 0.00 33.73 2.29
1833 1924 6.385649 AACCGTTGTTTGAATACAGAACAT 57.614 33.333 0.00 0.00 33.73 2.71
1842 1933 4.778904 CGACATGTAACCGTTGTTTGAAT 58.221 39.130 0.00 0.00 35.87 2.57
1851 1960 0.319083 TTCAGGCGACATGTAACCGT 59.681 50.000 0.00 0.00 0.00 4.83
1927 2036 5.300539 TGAGCCACTCACAATCTCTAGTATC 59.699 44.000 0.00 0.00 35.39 2.24
1928 2037 5.204292 TGAGCCACTCACAATCTCTAGTAT 58.796 41.667 0.00 0.00 35.39 2.12
2055 2164 6.238953 CCTGCATCCATTCTTATTCCTTTCAG 60.239 42.308 0.00 0.00 0.00 3.02
2063 2172 3.635373 CACTGCCTGCATCCATTCTTATT 59.365 43.478 0.00 0.00 0.00 1.40
2074 2191 4.666253 AACCGCCACTGCCTGCAT 62.666 61.111 0.00 0.00 0.00 3.96
2077 2194 4.641645 TGGAACCGCCACTGCCTG 62.642 66.667 0.00 0.00 43.33 4.85
2089 2206 1.002011 GAAGCCTCCCTGGTGGAAC 60.002 63.158 8.46 0.00 44.57 3.62
2090 2207 1.065410 TTGAAGCCTCCCTGGTGGAA 61.065 55.000 8.46 0.00 44.57 3.53
2091 2208 0.846427 ATTGAAGCCTCCCTGGTGGA 60.846 55.000 8.46 0.00 42.41 4.02
2092 2209 0.918983 TATTGAAGCCTCCCTGGTGG 59.081 55.000 0.00 0.00 38.35 4.61
2093 2210 1.133976 CCTATTGAAGCCTCCCTGGTG 60.134 57.143 0.00 0.00 38.35 4.17
2094 2211 1.216990 CCTATTGAAGCCTCCCTGGT 58.783 55.000 0.00 0.00 38.35 4.00
2095 2212 0.179006 GCCTATTGAAGCCTCCCTGG 60.179 60.000 0.00 0.00 39.35 4.45
2096 2213 0.842635 AGCCTATTGAAGCCTCCCTG 59.157 55.000 0.00 0.00 0.00 4.45
2097 2214 1.601248 AAGCCTATTGAAGCCTCCCT 58.399 50.000 0.00 0.00 0.00 4.20
2098 2215 3.481453 CTTAAGCCTATTGAAGCCTCCC 58.519 50.000 0.00 0.00 0.00 4.30
2099 2216 2.881513 GCTTAAGCCTATTGAAGCCTCC 59.118 50.000 17.00 0.00 38.68 4.30
2113 2230 2.801077 TTTGGAGGGTAGGCTTAAGC 57.199 50.000 19.53 19.53 41.14 3.09
2114 2231 4.079730 AGGATTTTGGAGGGTAGGCTTAAG 60.080 45.833 0.00 0.00 0.00 1.85
2115 2232 3.856206 AGGATTTTGGAGGGTAGGCTTAA 59.144 43.478 0.00 0.00 0.00 1.85
2116 2233 3.470868 AGGATTTTGGAGGGTAGGCTTA 58.529 45.455 0.00 0.00 0.00 3.09
2117 2234 2.288525 AGGATTTTGGAGGGTAGGCTT 58.711 47.619 0.00 0.00 0.00 4.35
2118 2235 1.987080 AGGATTTTGGAGGGTAGGCT 58.013 50.000 0.00 0.00 0.00 4.58
2119 2236 4.455070 AATAGGATTTTGGAGGGTAGGC 57.545 45.455 0.00 0.00 0.00 3.93
2120 2237 6.490381 GCTTAAATAGGATTTTGGAGGGTAGG 59.510 42.308 0.00 0.00 0.00 3.18
2121 2238 7.290813 AGCTTAAATAGGATTTTGGAGGGTAG 58.709 38.462 0.00 0.00 0.00 3.18
2122 2239 7.220890 AGCTTAAATAGGATTTTGGAGGGTA 57.779 36.000 0.00 0.00 0.00 3.69
2123 2240 6.092346 AGCTTAAATAGGATTTTGGAGGGT 57.908 37.500 0.00 0.00 0.00 4.34
2124 2241 8.414003 GTTTAGCTTAAATAGGATTTTGGAGGG 58.586 37.037 0.00 0.00 0.00 4.30
2125 2242 8.966868 TGTTTAGCTTAAATAGGATTTTGGAGG 58.033 33.333 0.00 0.00 0.00 4.30
2134 2251 9.391006 CAAGTGGTATGTTTAGCTTAAATAGGA 57.609 33.333 0.00 0.00 0.00 2.94
2135 2252 9.391006 TCAAGTGGTATGTTTAGCTTAAATAGG 57.609 33.333 0.00 0.00 0.00 2.57
2137 2254 9.727859 TGTCAAGTGGTATGTTTAGCTTAAATA 57.272 29.630 0.00 0.00 0.00 1.40
2138 2255 8.630054 TGTCAAGTGGTATGTTTAGCTTAAAT 57.370 30.769 0.00 0.00 0.00 1.40
2139 2256 8.453238 TTGTCAAGTGGTATGTTTAGCTTAAA 57.547 30.769 0.00 0.00 0.00 1.52
2140 2257 7.717875 ACTTGTCAAGTGGTATGTTTAGCTTAA 59.282 33.333 17.49 0.00 41.01 1.85
2141 2258 7.221450 ACTTGTCAAGTGGTATGTTTAGCTTA 58.779 34.615 17.49 0.00 41.01 3.09
2142 2259 6.062095 ACTTGTCAAGTGGTATGTTTAGCTT 58.938 36.000 17.49 0.00 41.01 3.74
2143 2260 5.621193 ACTTGTCAAGTGGTATGTTTAGCT 58.379 37.500 17.49 0.00 41.01 3.32
2144 2261 5.941948 ACTTGTCAAGTGGTATGTTTAGC 57.058 39.130 17.49 0.00 41.01 3.09
2147 2264 9.959721 AGAATATACTTGTCAAGTGGTATGTTT 57.040 29.630 25.41 10.98 42.84 2.83
2148 2265 9.383519 CAGAATATACTTGTCAAGTGGTATGTT 57.616 33.333 25.41 15.89 42.84 2.71
2149 2266 7.987458 CCAGAATATACTTGTCAAGTGGTATGT 59.013 37.037 25.41 9.00 42.84 2.29
2150 2267 7.987458 ACCAGAATATACTTGTCAAGTGGTATG 59.013 37.037 25.41 15.86 42.84 2.39
2151 2268 7.987458 CACCAGAATATACTTGTCAAGTGGTAT 59.013 37.037 25.41 19.25 42.84 2.73
2152 2269 7.327975 CACCAGAATATACTTGTCAAGTGGTA 58.672 38.462 25.41 18.09 42.84 3.25
2153 2270 6.173339 CACCAGAATATACTTGTCAAGTGGT 58.827 40.000 25.41 18.86 42.84 4.16
2154 2271 5.065218 GCACCAGAATATACTTGTCAAGTGG 59.935 44.000 25.41 18.29 42.84 4.00
2155 2272 5.877012 AGCACCAGAATATACTTGTCAAGTG 59.123 40.000 25.41 10.44 42.84 3.16
2156 2273 6.054860 AGCACCAGAATATACTTGTCAAGT 57.945 37.500 21.48 21.48 45.40 3.16
2157 2274 6.992063 AAGCACCAGAATATACTTGTCAAG 57.008 37.500 11.17 11.17 0.00 3.02
2158 2275 7.880713 TGTAAAGCACCAGAATATACTTGTCAA 59.119 33.333 0.00 0.00 0.00 3.18
2159 2276 7.390823 TGTAAAGCACCAGAATATACTTGTCA 58.609 34.615 0.00 0.00 0.00 3.58
2160 2277 7.843490 TGTAAAGCACCAGAATATACTTGTC 57.157 36.000 0.00 0.00 0.00 3.18
2161 2278 7.201732 GCATGTAAAGCACCAGAATATACTTGT 60.202 37.037 0.00 0.00 0.00 3.16
2162 2279 7.134815 GCATGTAAAGCACCAGAATATACTTG 58.865 38.462 0.00 0.00 0.00 3.16
2163 2280 6.828273 TGCATGTAAAGCACCAGAATATACTT 59.172 34.615 0.00 0.00 37.02 2.24
2164 2281 6.356556 TGCATGTAAAGCACCAGAATATACT 58.643 36.000 0.00 0.00 37.02 2.12
2165 2282 6.618287 TGCATGTAAAGCACCAGAATATAC 57.382 37.500 0.00 0.00 37.02 1.47
2166 2283 6.601217 TGTTGCATGTAAAGCACCAGAATATA 59.399 34.615 0.00 0.00 42.54 0.86
2167 2284 5.418524 TGTTGCATGTAAAGCACCAGAATAT 59.581 36.000 0.00 0.00 42.54 1.28
2168 2285 4.764308 TGTTGCATGTAAAGCACCAGAATA 59.236 37.500 0.00 0.00 42.54 1.75
2169 2286 3.573538 TGTTGCATGTAAAGCACCAGAAT 59.426 39.130 0.00 0.00 42.54 2.40
2170 2287 2.954989 TGTTGCATGTAAAGCACCAGAA 59.045 40.909 0.00 0.00 42.54 3.02
2171 2288 2.580962 TGTTGCATGTAAAGCACCAGA 58.419 42.857 0.00 0.00 42.54 3.86
2172 2289 3.367992 TTGTTGCATGTAAAGCACCAG 57.632 42.857 0.00 0.00 42.54 4.00
2173 2290 4.056740 CAATTGTTGCATGTAAAGCACCA 58.943 39.130 0.00 0.00 42.54 4.17
2174 2291 4.650545 CAATTGTTGCATGTAAAGCACC 57.349 40.909 0.00 0.00 42.54 5.01
2196 2313 7.700505 TCTGAGTCTAATTAGCAAATGCATTG 58.299 34.615 13.82 8.49 45.16 2.82
2197 2314 7.870509 TCTGAGTCTAATTAGCAAATGCATT 57.129 32.000 5.99 5.99 45.16 3.56
2198 2315 7.870509 TTCTGAGTCTAATTAGCAAATGCAT 57.129 32.000 7.67 0.00 45.16 3.96
2199 2316 7.686438 TTTCTGAGTCTAATTAGCAAATGCA 57.314 32.000 7.67 0.00 45.16 3.96
2200 2317 9.017669 CATTTTCTGAGTCTAATTAGCAAATGC 57.982 33.333 7.67 0.00 42.49 3.56
2203 2320 9.066892 ACACATTTTCTGAGTCTAATTAGCAAA 57.933 29.630 7.67 1.15 0.00 3.68
2204 2321 8.506437 CACACATTTTCTGAGTCTAATTAGCAA 58.494 33.333 7.67 0.00 0.00 3.91
2205 2322 7.661437 ACACACATTTTCTGAGTCTAATTAGCA 59.339 33.333 7.67 0.00 0.00 3.49
2206 2323 8.034058 ACACACATTTTCTGAGTCTAATTAGC 57.966 34.615 7.67 3.49 0.00 3.09
2212 2329 8.342634 GCTTAAAACACACATTTTCTGAGTCTA 58.657 33.333 0.00 0.00 33.80 2.59
2213 2330 7.196331 GCTTAAAACACACATTTTCTGAGTCT 58.804 34.615 0.00 0.00 33.80 3.24
2214 2331 6.417930 GGCTTAAAACACACATTTTCTGAGTC 59.582 38.462 0.00 0.00 33.80 3.36
2215 2332 6.096846 AGGCTTAAAACACACATTTTCTGAGT 59.903 34.615 0.00 0.00 33.80 3.41
2216 2333 6.507023 AGGCTTAAAACACACATTTTCTGAG 58.493 36.000 0.00 0.00 33.80 3.35
2217 2334 6.463995 AGGCTTAAAACACACATTTTCTGA 57.536 33.333 0.00 0.00 33.80 3.27
2218 2335 6.640907 GGTAGGCTTAAAACACACATTTTCTG 59.359 38.462 0.00 0.00 33.80 3.02
2219 2336 6.239204 GGGTAGGCTTAAAACACACATTTTCT 60.239 38.462 0.00 0.00 33.80 2.52
2220 2337 5.924254 GGGTAGGCTTAAAACACACATTTTC 59.076 40.000 0.00 0.00 33.80 2.29
2221 2338 5.600898 AGGGTAGGCTTAAAACACACATTTT 59.399 36.000 0.00 0.00 35.89 1.82
2222 2339 5.144832 AGGGTAGGCTTAAAACACACATTT 58.855 37.500 0.00 0.00 0.00 2.32
2223 2340 4.736473 AGGGTAGGCTTAAAACACACATT 58.264 39.130 0.00 0.00 0.00 2.71
2224 2341 4.332828 GAGGGTAGGCTTAAAACACACAT 58.667 43.478 0.00 0.00 0.00 3.21
2225 2342 3.497227 GGAGGGTAGGCTTAAAACACACA 60.497 47.826 0.00 0.00 0.00 3.72
2226 2343 3.079578 GGAGGGTAGGCTTAAAACACAC 58.920 50.000 0.00 0.00 0.00 3.82
2227 2344 2.712087 TGGAGGGTAGGCTTAAAACACA 59.288 45.455 0.00 0.00 0.00 3.72
2228 2345 3.428413 TGGAGGGTAGGCTTAAAACAC 57.572 47.619 0.00 0.00 0.00 3.32
2229 2346 4.202631 ACATTGGAGGGTAGGCTTAAAACA 60.203 41.667 0.00 0.00 0.00 2.83
2230 2347 4.341487 ACATTGGAGGGTAGGCTTAAAAC 58.659 43.478 0.00 0.00 0.00 2.43
2231 2348 4.569015 GGACATTGGAGGGTAGGCTTAAAA 60.569 45.833 0.00 0.00 0.00 1.52
2232 2349 3.053917 GGACATTGGAGGGTAGGCTTAAA 60.054 47.826 0.00 0.00 0.00 1.52
2233 2350 2.508300 GGACATTGGAGGGTAGGCTTAA 59.492 50.000 0.00 0.00 0.00 1.85
2234 2351 2.124411 GGACATTGGAGGGTAGGCTTA 58.876 52.381 0.00 0.00 0.00 3.09
2235 2352 0.919710 GGACATTGGAGGGTAGGCTT 59.080 55.000 0.00 0.00 0.00 4.35
2236 2353 0.044855 AGGACATTGGAGGGTAGGCT 59.955 55.000 0.00 0.00 0.00 4.58
2237 2354 0.181350 CAGGACATTGGAGGGTAGGC 59.819 60.000 0.00 0.00 0.00 3.93
2238 2355 0.181350 GCAGGACATTGGAGGGTAGG 59.819 60.000 0.00 0.00 0.00 3.18
2239 2356 1.207791 AGCAGGACATTGGAGGGTAG 58.792 55.000 0.00 0.00 0.00 3.18
2240 2357 2.561209 TAGCAGGACATTGGAGGGTA 57.439 50.000 0.00 0.00 0.00 3.69
2241 2358 1.668826 TTAGCAGGACATTGGAGGGT 58.331 50.000 0.00 0.00 0.00 4.34
2242 2359 2.806945 TTTAGCAGGACATTGGAGGG 57.193 50.000 0.00 0.00 0.00 4.30
2243 2360 3.313526 CGAATTTAGCAGGACATTGGAGG 59.686 47.826 0.00 0.00 0.00 4.30
2244 2361 3.242870 GCGAATTTAGCAGGACATTGGAG 60.243 47.826 0.00 0.00 34.19 3.86
2245 2362 2.682856 GCGAATTTAGCAGGACATTGGA 59.317 45.455 0.00 0.00 34.19 3.53
2246 2363 2.223572 GGCGAATTTAGCAGGACATTGG 60.224 50.000 3.89 0.00 36.08 3.16
2247 2364 2.423185 TGGCGAATTTAGCAGGACATTG 59.577 45.455 3.89 0.00 36.08 2.82
2248 2365 2.423538 GTGGCGAATTTAGCAGGACATT 59.576 45.455 3.89 0.00 36.08 2.71
2249 2366 2.017049 GTGGCGAATTTAGCAGGACAT 58.983 47.619 3.89 0.00 36.08 3.06
2250 2367 1.003118 AGTGGCGAATTTAGCAGGACA 59.997 47.619 3.89 0.00 36.08 4.02
2251 2368 1.398390 CAGTGGCGAATTTAGCAGGAC 59.602 52.381 3.89 0.00 36.08 3.85
2252 2369 1.678728 CCAGTGGCGAATTTAGCAGGA 60.679 52.381 0.00 0.00 36.08 3.86
2253 2370 0.734889 CCAGTGGCGAATTTAGCAGG 59.265 55.000 0.00 0.00 36.08 4.85
2254 2371 1.737838 TCCAGTGGCGAATTTAGCAG 58.262 50.000 3.51 0.00 36.08 4.24
2255 2372 2.016318 CATCCAGTGGCGAATTTAGCA 58.984 47.619 3.51 0.00 36.08 3.49
2256 2373 1.268743 GCATCCAGTGGCGAATTTAGC 60.269 52.381 3.51 0.00 0.00 3.09
2257 2374 2.016318 TGCATCCAGTGGCGAATTTAG 58.984 47.619 3.51 0.00 0.00 1.85
2258 2375 2.016318 CTGCATCCAGTGGCGAATTTA 58.984 47.619 3.51 0.00 34.31 1.40
2259 2376 0.813184 CTGCATCCAGTGGCGAATTT 59.187 50.000 3.51 0.00 34.31 1.82
2260 2377 1.033746 CCTGCATCCAGTGGCGAATT 61.034 55.000 3.51 0.00 37.38 2.17
2261 2378 1.452651 CCTGCATCCAGTGGCGAAT 60.453 57.895 3.51 0.00 37.38 3.34
2262 2379 2.046023 CCTGCATCCAGTGGCGAA 60.046 61.111 3.51 0.00 37.38 4.70
2263 2380 4.783621 GCCTGCATCCAGTGGCGA 62.784 66.667 3.51 0.00 37.38 5.54
2265 2382 2.441532 ATGCCTGCATCCAGTGGC 60.442 61.111 3.51 5.48 45.10 5.01
2266 2383 2.125326 CCATGCCTGCATCCAGTGG 61.125 63.158 1.40 1.40 37.38 4.00
2267 2384 1.077285 TCCATGCCTGCATCCAGTG 60.077 57.895 0.70 0.00 37.38 3.66
2268 2385 1.226542 CTCCATGCCTGCATCCAGT 59.773 57.895 0.70 0.00 37.38 4.00
2269 2386 2.194212 GCTCCATGCCTGCATCCAG 61.194 63.158 0.70 2.38 38.85 3.86
2293 2410 1.786441 TCCTTTGTGTCCCCATCCTTT 59.214 47.619 0.00 0.00 0.00 3.11
2303 2420 6.899114 ACGAGTCAATAAAATCCTTTGTGTC 58.101 36.000 0.00 0.00 0.00 3.67
2318 2435 1.336887 CCCGACAACTGACGAGTCAAT 60.337 52.381 7.38 0.00 39.39 2.57
2330 2447 2.528041 AGAGAACAAGTCCCGACAAC 57.472 50.000 0.00 0.00 0.00 3.32
2335 2452 5.701290 AGTTTCATTAAGAGAACAAGTCCCG 59.299 40.000 0.00 0.00 0.00 5.14
2340 2457 9.367444 ACCGTATAGTTTCATTAAGAGAACAAG 57.633 33.333 0.00 0.00 0.00 3.16
2347 2464 6.704493 GGATGCACCGTATAGTTTCATTAAGA 59.296 38.462 0.00 0.00 0.00 2.10
2384 2505 1.098050 GGGCTGCCTTGAACACATAG 58.902 55.000 19.68 0.00 0.00 2.23
2420 2541 3.843027 AGAAAGGACAGGACTGATGACAT 59.157 43.478 6.29 0.00 0.00 3.06
2429 2550 3.604582 CATTCTCCAGAAAGGACAGGAC 58.395 50.000 0.00 0.00 43.07 3.85
2432 2553 3.517100 TCTCCATTCTCCAGAAAGGACAG 59.483 47.826 8.86 2.35 44.20 3.51
2466 2587 6.824958 AATACATAGGCTCTTTTGGAGGTA 57.175 37.500 0.00 0.00 42.08 3.08
2502 2623 7.912056 TTTGCTAATCCATCAGTATCATAGC 57.088 36.000 0.00 0.00 36.08 2.97
2525 2646 9.030301 GTTACTTGCACAATTCACAGTATTTTT 57.970 29.630 0.00 0.00 0.00 1.94
2541 2662 5.106555 ACTGTAATGCTCATGTTACTTGCAC 60.107 40.000 0.00 0.00 36.44 4.57
2547 2668 9.186323 CATCTAGTACTGTAATGCTCATGTTAC 57.814 37.037 5.39 0.00 0.00 2.50
2572 2693 1.618837 GATTGATAGGGCTAGCGTCCA 59.381 52.381 9.00 0.00 37.38 4.02
2609 2746 8.642020 CGACATACAGTTGTAAAAAGTACCTAC 58.358 37.037 0.00 0.00 33.76 3.18
2633 2771 9.104965 CAATACAAATACCAGTTTCTTATCCGA 57.895 33.333 0.00 0.00 0.00 4.55
2690 2844 5.755861 GGAGCTACCAGAGTTGAAATACATC 59.244 44.000 0.00 0.00 38.79 3.06
2705 2859 3.897239 CCATTTGTTATGGGAGCTACCA 58.103 45.455 23.14 23.14 46.24 3.25
2717 2872 7.027874 ACATTTAGACCTCTCCCATTTGTTA 57.972 36.000 0.00 0.00 0.00 2.41
2719 2874 5.520748 ACATTTAGACCTCTCCCATTTGT 57.479 39.130 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.