Multiple sequence alignment - TraesCS3A01G139800

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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 TraesCS3A01G139800 chr3A 100.000 2348 0 0 1 2348 118545567 118547914 0.000000e+00 4337.0
1 TraesCS3A01G139800 chr3B 89.278 970 68 14 446 1407 162639999 162639058 0.000000e+00 1182.0
2 TraesCS3A01G139800 chr3B 98.829 427 4 1 1 427 8511244 8511669 0.000000e+00 760.0
3 TraesCS3A01G139800 chr3B 84.337 332 48 3 874 1201 162688895 162688564 2.910000e-84 322.0
4 TraesCS3A01G139800 chr3B 91.855 221 15 2 1641 1860 162638582 162638364 2.930000e-79 305.0
5 TraesCS3A01G139800 chr3B 88.306 248 22 6 1862 2105 162638204 162637960 8.210000e-75 291.0
6 TraesCS3A01G139800 chr3D 88.911 983 60 16 445 1407 111956894 111955941 0.000000e+00 1166.0
7 TraesCS3A01G139800 chr3D 84.135 416 58 6 793 1201 111964238 111963824 1.690000e-106 396.0
8 TraesCS3A01G139800 chr3D 88.983 236 19 3 1641 1876 111955454 111955226 3.820000e-73 285.0
9 TraesCS3A01G139800 chr3D 90.789 76 6 1 1898 1972 111955227 111955152 1.480000e-17 100.0
10 TraesCS3A01G139800 chr7B 98.477 394 5 1 34 427 39928906 39929298 0.000000e+00 693.0
11 TraesCS3A01G139800 chr7B 100.000 47 0 0 1 47 39927234 39927280 1.160000e-13 87.9
12 TraesCS3A01G139800 chr1A 85.388 438 41 8 1 427 12172224 12171799 1.290000e-117 433.0
13 TraesCS3A01G139800 chr6A 80.856 444 38 23 1 430 50251627 50251217 2.930000e-79 305.0
14 TraesCS3A01G139800 chr6A 79.279 444 44 23 1 429 50867502 50867092 1.380000e-67 267.0
15 TraesCS3A01G139800 chr5B 80.320 437 39 22 1 426 325690800 325690400 1.060000e-73 287.0


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 TraesCS3A01G139800 chr3A 118545567 118547914 2347 False 4337.000000 4337 100.0000 1 2348 1 chr3A.!!$F1 2347
1 TraesCS3A01G139800 chr3B 162637960 162639999 2039 True 592.666667 1182 89.8130 446 2105 3 chr3B.!!$R2 1659
2 TraesCS3A01G139800 chr3D 111955152 111956894 1742 True 517.000000 1166 89.5610 445 1972 3 chr3D.!!$R2 1527
3 TraesCS3A01G139800 chr7B 39927234 39929298 2064 False 390.450000 693 99.2385 1 427 2 chr7B.!!$F1 426

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
233 1873 0.236711 CAACAGCTCAGGCAAAGTCG 59.763 55.0 0.0 0.0 41.7 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2121 4246 0.036671 AAATCTTGACCCGACCGACC 60.037 55.0 0.0 0.0 0.0 4.79 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
119 1759 1.421646 CCTCCGCCTCCCAATATCTTT 59.578 52.381 0.00 0.00 0.00 2.52
233 1873 0.236711 CAACAGCTCAGGCAAAGTCG 59.763 55.000 0.00 0.00 41.70 4.18
245 1885 0.613260 CAAAGTCGGGAGGTGGATGA 59.387 55.000 0.00 0.00 0.00 2.92
361 2001 3.000819 TCACGGCCTCACGGGAAT 61.001 61.111 0.00 0.00 44.30 3.01
431 2071 4.587189 GGCCGAGCGTTCGCCTAT 62.587 66.667 16.81 0.00 45.38 2.57
432 2072 3.330853 GCCGAGCGTTCGCCTATG 61.331 66.667 16.81 3.29 45.38 2.23
433 2073 2.411701 CCGAGCGTTCGCCTATGA 59.588 61.111 16.81 0.00 45.38 2.15
434 2074 1.226859 CCGAGCGTTCGCCTATGAA 60.227 57.895 16.81 0.00 45.38 2.57
435 2075 0.597637 CCGAGCGTTCGCCTATGAAT 60.598 55.000 16.81 0.00 45.38 2.57
436 2076 1.335597 CCGAGCGTTCGCCTATGAATA 60.336 52.381 16.81 0.00 45.38 1.75
437 2077 2.390938 CGAGCGTTCGCCTATGAATAA 58.609 47.619 9.17 0.00 40.36 1.40
438 2078 2.405357 CGAGCGTTCGCCTATGAATAAG 59.595 50.000 9.17 0.00 40.36 1.73
439 2079 2.135933 AGCGTTCGCCTATGAATAAGC 58.864 47.619 13.54 0.00 0.00 3.09
443 2083 2.162716 CGCCTATGAATAAGCGCCC 58.837 57.895 2.29 0.00 42.31 6.13
464 2104 2.772077 TGCAAGTTAGGGTCGCAATA 57.228 45.000 0.00 0.00 0.00 1.90
477 2117 3.861113 GGTCGCAATACTGATCGTTTACA 59.139 43.478 0.00 0.00 0.00 2.41
478 2118 4.327898 GGTCGCAATACTGATCGTTTACAA 59.672 41.667 0.00 0.00 0.00 2.41
480 2120 4.924462 TCGCAATACTGATCGTTTACAACA 59.076 37.500 0.00 0.00 0.00 3.33
494 2134 7.416022 TCGTTTACAACAACCGAATAAAATGT 58.584 30.769 0.00 0.00 0.00 2.71
560 2214 3.762288 TGCTACCTACTTCAACAGATCGT 59.238 43.478 0.00 0.00 0.00 3.73
563 2217 1.920574 CCTACTTCAACAGATCGTGCG 59.079 52.381 0.00 0.00 0.00 5.34
579 2233 3.188667 TCGTGCGATCATATACAGGAGTC 59.811 47.826 0.00 0.00 0.00 3.36
581 2235 2.826128 TGCGATCATATACAGGAGTCCC 59.174 50.000 5.25 0.00 0.00 4.46
593 2247 3.273654 AGTCCCGGACTCCCTGGA 61.274 66.667 14.84 0.00 38.71 3.86
594 2248 2.284405 GTCCCGGACTCCCTGGAA 60.284 66.667 10.59 0.00 45.73 3.53
698 2352 4.170062 CGCGGACGGCTCTAACGA 62.170 66.667 0.00 0.00 40.44 3.85
699 2353 2.578981 GCGGACGGCTCTAACGAC 60.579 66.667 0.00 0.00 39.11 4.34
700 2354 2.277120 CGGACGGCTCTAACGACG 60.277 66.667 0.00 0.00 34.93 5.12
741 2395 2.469147 CGTTTCATCGTCCATCATCTCG 59.531 50.000 0.00 0.00 0.00 4.04
849 2509 3.050275 GCGTTGGACAGGAGCCAC 61.050 66.667 0.00 0.00 34.56 5.01
867 2527 2.976350 ACGTCGACGCACTCCTGA 60.976 61.111 35.92 0.00 44.43 3.86
921 2581 3.507009 GTCTCCCCCTCGTCGACG 61.507 72.222 31.30 31.30 41.45 5.12
1314 2975 5.835280 AGACAGGTTGGTGATCTCAAAATTT 59.165 36.000 0.00 0.00 0.00 1.82
1315 2976 6.324770 AGACAGGTTGGTGATCTCAAAATTTT 59.675 34.615 0.00 0.00 0.00 1.82
1317 2978 5.697633 CAGGTTGGTGATCTCAAAATTTTGG 59.302 40.000 26.45 18.26 38.66 3.28
1318 2979 5.602145 AGGTTGGTGATCTCAAAATTTTGGA 59.398 36.000 26.45 21.97 38.66 3.53
1331 2992 5.813513 AAATTTTGGATGGTTCTCTTGCT 57.186 34.783 0.00 0.00 0.00 3.91
1355 3016 6.423182 TGGGACAGATCATTTAGGTTTTAGG 58.577 40.000 0.00 0.00 0.00 2.69
1356 3017 6.011981 TGGGACAGATCATTTAGGTTTTAGGT 60.012 38.462 0.00 0.00 0.00 3.08
1357 3018 7.183112 TGGGACAGATCATTTAGGTTTTAGGTA 59.817 37.037 0.00 0.00 0.00 3.08
1432 3393 1.528586 GCATCATGCACGTATGTCTCC 59.471 52.381 4.20 0.00 44.26 3.71
1442 3403 8.559536 CATGCACGTATGTCTCCTTTAAATAAT 58.440 33.333 0.00 0.00 0.00 1.28
1484 3445 3.819368 TGCTTATTTATGCTGCTGGCTA 58.181 40.909 0.00 0.00 42.39 3.93
1498 3459 6.373495 TGCTGCTGGCTAATCAATAGATTATG 59.627 38.462 0.00 0.00 43.71 1.90
1547 3508 1.857837 CAACATGTCAACGTTTTGCCC 59.142 47.619 0.00 0.00 32.17 5.36
1555 3516 4.762765 TGTCAACGTTTTGCCCAGTATATT 59.237 37.500 0.00 0.00 32.17 1.28
1559 3522 5.560966 ACGTTTTGCCCAGTATATTTCAG 57.439 39.130 0.00 0.00 0.00 3.02
1568 3531 9.725019 TTGCCCAGTATATTTCAGTAGATTATG 57.275 33.333 0.00 0.00 0.00 1.90
1570 3533 9.944376 GCCCAGTATATTTCAGTAGATTATGAA 57.056 33.333 0.00 0.00 33.73 2.57
1712 3675 7.554835 CAGAGTTGACCTACTAGACAGAGTAAT 59.445 40.741 0.00 0.00 31.57 1.89
1776 3740 2.671888 GAGCCACGAACTTAGCTTTACC 59.328 50.000 0.00 0.00 35.23 2.85
1840 3804 3.051940 TCCATTGGAGGTAGAGATGCT 57.948 47.619 0.00 0.00 0.00 3.79
1860 3824 9.360901 AGATGCTTCTTGACTTGAGATATACTA 57.639 33.333 0.00 0.00 0.00 1.82
1891 4013 9.464714 TCACTTGATATAAACTAATCTCTTCGC 57.535 33.333 0.00 0.00 0.00 4.70
1893 4015 8.421784 ACTTGATATAAACTAATCTCTTCGCCA 58.578 33.333 0.00 0.00 0.00 5.69
1894 4016 8.589335 TTGATATAAACTAATCTCTTCGCCAC 57.411 34.615 0.00 0.00 0.00 5.01
1930 4052 0.950836 CCTGCACGAATGGTCAAACA 59.049 50.000 0.00 0.00 0.00 2.83
1951 4074 6.804534 ACATGTTTTTATGTCGTTGTTGTG 57.195 33.333 0.00 0.00 36.60 3.33
1963 4086 5.099575 GTCGTTGTTGTGGACTTTTTGATT 58.900 37.500 0.00 0.00 0.00 2.57
1966 4089 5.685511 CGTTGTTGTGGACTTTTTGATTAGG 59.314 40.000 0.00 0.00 0.00 2.69
1972 4095 5.467399 TGTGGACTTTTTGATTAGGTGTACG 59.533 40.000 0.00 0.00 0.00 3.67
1977 4100 8.811378 GGACTTTTTGATTAGGTGTACGTATAC 58.189 37.037 13.54 13.54 0.00 1.47
1978 4101 9.578439 GACTTTTTGATTAGGTGTACGTATACT 57.422 33.333 19.98 11.12 32.00 2.12
1981 4104 8.931385 TTTTGATTAGGTGTACGTATACTTCC 57.069 34.615 19.98 5.96 32.00 3.46
2003 4128 9.185192 CTTCCATGTTCTGAAAAGTATGTTTTC 57.815 33.333 7.75 7.75 0.00 2.29
2004 4129 8.231692 TCCATGTTCTGAAAAGTATGTTTTCA 57.768 30.769 13.96 13.96 0.00 2.69
2054 4179 6.264832 TCAAAAACGGTCATATCATCAATGC 58.735 36.000 0.00 0.00 0.00 3.56
2056 4181 5.833406 AAACGGTCATATCATCAATGCAA 57.167 34.783 0.00 0.00 0.00 4.08
2057 4182 5.833406 AACGGTCATATCATCAATGCAAA 57.167 34.783 0.00 0.00 0.00 3.68
2061 4186 7.267128 ACGGTCATATCATCAATGCAAATTTT 58.733 30.769 0.00 0.00 0.00 1.82
2062 4187 7.436080 ACGGTCATATCATCAATGCAAATTTTC 59.564 33.333 0.00 0.00 0.00 2.29
2063 4188 7.650504 CGGTCATATCATCAATGCAAATTTTCT 59.349 33.333 0.00 0.00 0.00 2.52
2064 4189 9.970395 GGTCATATCATCAATGCAAATTTTCTA 57.030 29.630 0.00 0.00 0.00 2.10
2127 4252 6.834168 ACTATTTTTCATGAAATGGTCGGT 57.166 33.333 21.10 12.28 46.73 4.69
2128 4253 6.852664 ACTATTTTTCATGAAATGGTCGGTC 58.147 36.000 21.10 0.00 46.73 4.79
2129 4254 3.822594 TTTTCATGAAATGGTCGGTCG 57.177 42.857 21.10 0.00 46.73 4.79
2130 4255 1.732941 TTCATGAAATGGTCGGTCGG 58.267 50.000 5.45 0.00 46.73 4.79
2131 4256 0.107897 TCATGAAATGGTCGGTCGGG 60.108 55.000 0.00 0.00 46.73 5.14
2132 4257 0.392461 CATGAAATGGTCGGTCGGGT 60.392 55.000 0.00 0.00 41.79 5.28
2133 4258 0.107848 ATGAAATGGTCGGTCGGGTC 60.108 55.000 0.00 0.00 0.00 4.46
2134 4259 1.294138 GAAATGGTCGGTCGGGTCA 59.706 57.895 0.00 0.00 0.00 4.02
2135 4260 0.320946 GAAATGGTCGGTCGGGTCAA 60.321 55.000 0.00 0.00 0.00 3.18
2136 4261 0.321298 AAATGGTCGGTCGGGTCAAG 60.321 55.000 0.00 0.00 0.00 3.02
2137 4262 1.189524 AATGGTCGGTCGGGTCAAGA 61.190 55.000 0.00 0.00 0.00 3.02
2138 4263 0.976073 ATGGTCGGTCGGGTCAAGAT 60.976 55.000 0.00 0.00 0.00 2.40
2139 4264 1.189524 TGGTCGGTCGGGTCAAGATT 61.190 55.000 0.00 0.00 0.00 2.40
2140 4265 0.036671 GGTCGGTCGGGTCAAGATTT 60.037 55.000 0.00 0.00 0.00 2.17
2141 4266 1.609841 GGTCGGTCGGGTCAAGATTTT 60.610 52.381 0.00 0.00 0.00 1.82
2142 4267 2.148768 GTCGGTCGGGTCAAGATTTTT 58.851 47.619 0.00 0.00 0.00 1.94
2143 4268 2.159037 GTCGGTCGGGTCAAGATTTTTC 59.841 50.000 0.00 0.00 0.00 2.29
2144 4269 2.038033 TCGGTCGGGTCAAGATTTTTCT 59.962 45.455 0.00 0.00 0.00 2.52
2145 4270 2.812011 CGGTCGGGTCAAGATTTTTCTT 59.188 45.455 0.00 0.00 0.00 2.52
2146 4271 3.364964 CGGTCGGGTCAAGATTTTTCTTG 60.365 47.826 9.00 9.00 46.11 3.02
2147 4272 3.565516 GTCGGGTCAAGATTTTTCTTGC 58.434 45.455 10.19 6.32 44.82 4.01
2148 4273 3.004315 GTCGGGTCAAGATTTTTCTTGCA 59.996 43.478 10.19 0.00 44.82 4.08
2149 4274 3.634448 TCGGGTCAAGATTTTTCTTGCAA 59.366 39.130 10.19 0.00 44.82 4.08
2150 4275 4.280677 TCGGGTCAAGATTTTTCTTGCAAT 59.719 37.500 0.00 0.00 44.82 3.56
2151 4276 4.622740 CGGGTCAAGATTTTTCTTGCAATC 59.377 41.667 0.00 0.00 44.82 2.67
2152 4277 5.565439 CGGGTCAAGATTTTTCTTGCAATCT 60.565 40.000 0.00 0.00 44.82 2.40
2153 4278 6.349280 CGGGTCAAGATTTTTCTTGCAATCTA 60.349 38.462 0.00 0.00 44.82 1.98
2154 4279 7.031975 GGGTCAAGATTTTTCTTGCAATCTAG 58.968 38.462 0.00 0.00 44.82 2.43
2155 4280 7.031975 GGTCAAGATTTTTCTTGCAATCTAGG 58.968 38.462 0.00 0.00 44.82 3.02
2156 4281 7.309438 GGTCAAGATTTTTCTTGCAATCTAGGT 60.309 37.037 0.00 0.00 44.82 3.08
2157 4282 8.730680 GTCAAGATTTTTCTTGCAATCTAGGTA 58.269 33.333 0.00 0.00 44.82 3.08
2158 4283 9.466497 TCAAGATTTTTCTTGCAATCTAGGTAT 57.534 29.630 0.00 0.00 44.82 2.73
2159 4284 9.727627 CAAGATTTTTCTTGCAATCTAGGTATC 57.272 33.333 0.00 0.00 38.55 2.24
2160 4285 9.692325 AAGATTTTTCTTGCAATCTAGGTATCT 57.308 29.630 0.00 0.61 38.55 1.98
2161 4286 9.118300 AGATTTTTCTTGCAATCTAGGTATCTG 57.882 33.333 0.00 0.00 37.87 2.90
2162 4287 9.113838 GATTTTTCTTGCAATCTAGGTATCTGA 57.886 33.333 0.00 0.00 0.00 3.27
2163 4288 8.862325 TTTTTCTTGCAATCTAGGTATCTGAA 57.138 30.769 0.00 0.00 0.00 3.02
2164 4289 7.849804 TTTCTTGCAATCTAGGTATCTGAAC 57.150 36.000 0.00 0.00 0.00 3.18
2165 4290 5.918608 TCTTGCAATCTAGGTATCTGAACC 58.081 41.667 0.00 2.10 40.06 3.62
2178 4303 6.678878 GGTATCTGAACCTTTCTTTGAAACC 58.321 40.000 2.91 0.00 36.53 3.27
2179 4304 6.264518 GGTATCTGAACCTTTCTTTGAAACCA 59.735 38.462 0.00 0.00 36.53 3.67
2180 4305 6.983906 ATCTGAACCTTTCTTTGAAACCAT 57.016 33.333 0.00 0.00 0.00 3.55
2181 4306 9.010029 GTATCTGAACCTTTCTTTGAAACCATA 57.990 33.333 0.00 0.00 0.00 2.74
2182 4307 7.889873 TCTGAACCTTTCTTTGAAACCATAA 57.110 32.000 0.00 0.00 0.00 1.90
2183 4308 8.299990 TCTGAACCTTTCTTTGAAACCATAAA 57.700 30.769 0.00 0.00 0.00 1.40
2184 4309 8.194769 TCTGAACCTTTCTTTGAAACCATAAAC 58.805 33.333 0.00 0.00 0.00 2.01
2185 4310 8.073467 TGAACCTTTCTTTGAAACCATAAACT 57.927 30.769 0.00 0.00 0.00 2.66
2186 4311 8.536175 TGAACCTTTCTTTGAAACCATAAACTT 58.464 29.630 0.00 0.00 0.00 2.66
2187 4312 9.378551 GAACCTTTCTTTGAAACCATAAACTTT 57.621 29.630 0.00 0.00 0.00 2.66
2188 4313 9.733556 AACCTTTCTTTGAAACCATAAACTTTT 57.266 25.926 0.00 0.00 0.00 2.27
2189 4314 9.733556 ACCTTTCTTTGAAACCATAAACTTTTT 57.266 25.926 0.00 0.00 0.00 1.94
2234 4359 9.874205 TTCATATCCATCAACTTTTTCCAAATC 57.126 29.630 0.00 0.00 0.00 2.17
2235 4360 8.190122 TCATATCCATCAACTTTTTCCAAATCG 58.810 33.333 0.00 0.00 0.00 3.34
2236 4361 6.588719 ATCCATCAACTTTTTCCAAATCGA 57.411 33.333 0.00 0.00 0.00 3.59
2237 4362 6.398234 TCCATCAACTTTTTCCAAATCGAA 57.602 33.333 0.00 0.00 0.00 3.71
2238 4363 6.810911 TCCATCAACTTTTTCCAAATCGAAA 58.189 32.000 0.00 0.00 0.00 3.46
2239 4364 7.268586 TCCATCAACTTTTTCCAAATCGAAAA 58.731 30.769 0.00 0.00 39.39 2.29
2240 4365 7.437862 TCCATCAACTTTTTCCAAATCGAAAAG 59.562 33.333 0.00 6.33 41.45 2.27
2241 4366 7.437862 CCATCAACTTTTTCCAAATCGAAAAGA 59.562 33.333 12.99 0.91 41.45 2.52
2242 4367 8.816144 CATCAACTTTTTCCAAATCGAAAAGAA 58.184 29.630 12.99 0.00 41.45 2.52
2243 4368 8.764524 TCAACTTTTTCCAAATCGAAAAGAAA 57.235 26.923 12.99 5.19 41.45 2.52
2244 4369 9.209175 TCAACTTTTTCCAAATCGAAAAGAAAA 57.791 25.926 12.99 10.03 41.45 2.29
2245 4370 9.986833 CAACTTTTTCCAAATCGAAAAGAAAAT 57.013 25.926 12.99 0.00 41.45 1.82
2251 4376 9.980780 TTTCCAAATCGAAAAGAAAATTCAAAC 57.019 25.926 0.00 0.00 0.00 2.93
2252 4377 8.940768 TCCAAATCGAAAAGAAAATTCAAACT 57.059 26.923 0.00 0.00 0.00 2.66
2253 4378 9.030301 TCCAAATCGAAAAGAAAATTCAAACTC 57.970 29.630 0.00 0.00 0.00 3.01
2254 4379 8.275632 CCAAATCGAAAAGAAAATTCAAACTCC 58.724 33.333 0.00 0.00 0.00 3.85
2255 4380 9.034544 CAAATCGAAAAGAAAATTCAAACTCCT 57.965 29.630 0.00 0.00 0.00 3.69
2258 4383 9.899226 ATCGAAAAGAAAATTCAAACTCCTAAG 57.101 29.630 0.00 0.00 0.00 2.18
2259 4384 7.860872 TCGAAAAGAAAATTCAAACTCCTAAGC 59.139 33.333 0.00 0.00 0.00 3.09
2260 4385 7.862873 CGAAAAGAAAATTCAAACTCCTAAGCT 59.137 33.333 0.00 0.00 0.00 3.74
2261 4386 9.534565 GAAAAGAAAATTCAAACTCCTAAGCTT 57.465 29.630 3.48 3.48 0.00 3.74
2262 4387 9.890629 AAAAGAAAATTCAAACTCCTAAGCTTT 57.109 25.926 3.20 0.00 0.00 3.51
2263 4388 9.890629 AAAGAAAATTCAAACTCCTAAGCTTTT 57.109 25.926 3.20 0.00 0.00 2.27
2264 4389 9.890629 AAGAAAATTCAAACTCCTAAGCTTTTT 57.109 25.926 3.20 0.00 0.00 1.94
2265 4390 9.534565 AGAAAATTCAAACTCCTAAGCTTTTTC 57.465 29.630 3.20 3.82 0.00 2.29
2266 4391 8.662781 AAAATTCAAACTCCTAAGCTTTTTCC 57.337 30.769 3.20 0.00 0.00 3.13
2267 4392 6.976934 ATTCAAACTCCTAAGCTTTTTCCA 57.023 33.333 3.20 0.00 0.00 3.53
2268 4393 6.783708 TTCAAACTCCTAAGCTTTTTCCAA 57.216 33.333 3.20 0.00 0.00 3.53
2269 4394 6.976934 TCAAACTCCTAAGCTTTTTCCAAT 57.023 33.333 3.20 0.00 0.00 3.16
2270 4395 7.360113 TCAAACTCCTAAGCTTTTTCCAATT 57.640 32.000 3.20 0.00 0.00 2.32
2271 4396 7.791029 TCAAACTCCTAAGCTTTTTCCAATTT 58.209 30.769 3.20 0.00 0.00 1.82
2272 4397 7.926018 TCAAACTCCTAAGCTTTTTCCAATTTC 59.074 33.333 3.20 0.00 0.00 2.17
2273 4398 6.346477 ACTCCTAAGCTTTTTCCAATTTCC 57.654 37.500 3.20 0.00 0.00 3.13
2274 4399 5.048013 ACTCCTAAGCTTTTTCCAATTTCCG 60.048 40.000 3.20 0.00 0.00 4.30
2275 4400 4.219725 TCCTAAGCTTTTTCCAATTTCCGG 59.780 41.667 3.20 0.00 0.00 5.14
2276 4401 3.401033 AAGCTTTTTCCAATTTCCGGG 57.599 42.857 0.00 0.00 0.00 5.73
2277 4402 2.325484 AGCTTTTTCCAATTTCCGGGT 58.675 42.857 0.00 0.00 0.00 5.28
2278 4403 2.703536 AGCTTTTTCCAATTTCCGGGTT 59.296 40.909 0.00 0.00 0.00 4.11
2279 4404 3.135712 AGCTTTTTCCAATTTCCGGGTTT 59.864 39.130 0.00 0.00 0.00 3.27
2280 4405 3.880490 GCTTTTTCCAATTTCCGGGTTTT 59.120 39.130 0.00 0.00 0.00 2.43
2281 4406 4.336993 GCTTTTTCCAATTTCCGGGTTTTT 59.663 37.500 0.00 0.00 0.00 1.94
2307 4432 9.883142 TTTAATTCATGAACTTTTCACAAACCT 57.117 25.926 11.07 0.00 43.48 3.50
2308 4433 7.775397 AATTCATGAACTTTTCACAAACCTG 57.225 32.000 11.07 0.00 43.48 4.00
2309 4434 4.681744 TCATGAACTTTTCACAAACCTGC 58.318 39.130 0.00 0.00 43.48 4.85
2310 4435 3.143807 TGAACTTTTCACAAACCTGCG 57.856 42.857 0.00 0.00 34.08 5.18
2311 4436 2.750166 TGAACTTTTCACAAACCTGCGA 59.250 40.909 0.00 0.00 34.08 5.10
2312 4437 3.191581 TGAACTTTTCACAAACCTGCGAA 59.808 39.130 0.00 0.00 34.08 4.70
2313 4438 3.145212 ACTTTTCACAAACCTGCGAAC 57.855 42.857 0.00 0.00 0.00 3.95
2314 4439 2.490115 ACTTTTCACAAACCTGCGAACA 59.510 40.909 0.00 0.00 0.00 3.18
2315 4440 3.130340 ACTTTTCACAAACCTGCGAACAT 59.870 39.130 0.00 0.00 0.00 2.71
2316 4441 3.791973 TTTCACAAACCTGCGAACATT 57.208 38.095 0.00 0.00 0.00 2.71
2317 4442 3.791973 TTCACAAACCTGCGAACATTT 57.208 38.095 0.00 0.00 0.00 2.32
2318 4443 3.791973 TCACAAACCTGCGAACATTTT 57.208 38.095 0.00 0.00 0.00 1.82
2319 4444 3.443037 TCACAAACCTGCGAACATTTTG 58.557 40.909 0.00 0.00 35.91 2.44
2320 4445 3.119316 TCACAAACCTGCGAACATTTTGT 60.119 39.130 0.00 0.00 40.17 2.83
2321 4446 3.242712 CACAAACCTGCGAACATTTTGTC 59.757 43.478 0.00 0.00 38.72 3.18
2322 4447 3.119316 ACAAACCTGCGAACATTTTGTCA 60.119 39.130 0.00 0.00 37.34 3.58
2323 4448 3.791973 AACCTGCGAACATTTTGTCAA 57.208 38.095 0.00 0.00 0.00 3.18
2324 4449 3.791973 ACCTGCGAACATTTTGTCAAA 57.208 38.095 0.00 0.00 0.00 2.69
2325 4450 4.320608 ACCTGCGAACATTTTGTCAAAT 57.679 36.364 0.00 0.00 32.36 2.32
2326 4451 4.298332 ACCTGCGAACATTTTGTCAAATC 58.702 39.130 0.00 0.00 29.41 2.17
2327 4452 3.674753 CCTGCGAACATTTTGTCAAATCC 59.325 43.478 0.00 0.00 29.41 3.01
2328 4453 3.304257 TGCGAACATTTTGTCAAATCCG 58.696 40.909 0.00 0.90 29.41 4.18
2329 4454 3.243234 TGCGAACATTTTGTCAAATCCGT 60.243 39.130 0.00 0.00 29.41 4.69
2330 4455 3.119463 GCGAACATTTTGTCAAATCCGTG 59.881 43.478 0.00 0.00 29.41 4.94
2331 4456 4.532276 CGAACATTTTGTCAAATCCGTGA 58.468 39.130 0.00 0.00 29.41 4.35
2332 4457 4.973051 CGAACATTTTGTCAAATCCGTGAA 59.027 37.500 0.00 0.00 29.41 3.18
2333 4458 5.108405 CGAACATTTTGTCAAATCCGTGAAC 60.108 40.000 0.00 0.00 29.41 3.18
2334 4459 4.616953 ACATTTTGTCAAATCCGTGAACC 58.383 39.130 0.00 0.00 29.41 3.62
2335 4460 4.340950 ACATTTTGTCAAATCCGTGAACCT 59.659 37.500 0.00 0.00 29.41 3.50
2336 4461 4.993029 TTTTGTCAAATCCGTGAACCTT 57.007 36.364 0.00 0.00 0.00 3.50
2337 4462 4.993029 TTTGTCAAATCCGTGAACCTTT 57.007 36.364 0.00 0.00 0.00 3.11
2338 4463 4.993029 TTGTCAAATCCGTGAACCTTTT 57.007 36.364 0.00 0.00 0.00 2.27
2339 4464 4.561735 TGTCAAATCCGTGAACCTTTTC 57.438 40.909 0.00 0.00 0.00 2.29
2340 4465 3.002862 TGTCAAATCCGTGAACCTTTTCG 59.997 43.478 0.00 0.00 34.04 3.46
2341 4466 2.550606 TCAAATCCGTGAACCTTTTCGG 59.449 45.455 0.00 0.00 43.65 4.30
2342 4467 0.879090 AATCCGTGAACCTTTTCGGC 59.121 50.000 0.00 0.00 42.28 5.54
2343 4468 0.958876 ATCCGTGAACCTTTTCGGCC 60.959 55.000 0.00 0.00 42.28 6.13
2344 4469 2.554272 CGTGAACCTTTTCGGCCG 59.446 61.111 22.12 22.12 34.04 6.13
2345 4470 2.248835 CGTGAACCTTTTCGGCCGT 61.249 57.895 27.15 2.66 34.04 5.68
2346 4471 1.281656 GTGAACCTTTTCGGCCGTG 59.718 57.895 27.15 13.58 34.04 4.94
2347 4472 2.254350 GAACCTTTTCGGCCGTGC 59.746 61.111 27.15 0.00 35.61 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 1759 0.339859 AGGGGAGCTGGTCTACATCA 59.660 55.000 6.83 0.00 0.00 3.07
233 1873 2.224305 CGGATAAGTTCATCCACCTCCC 60.224 54.545 3.24 0.00 44.16 4.30
245 1885 6.410942 TCATCACATCTCATCGGATAAGTT 57.589 37.500 0.00 0.00 0.00 2.66
326 1966 3.866582 CCCATCCCGCACTCCCTC 61.867 72.222 0.00 0.00 0.00 4.30
427 2067 1.470098 GCATGGGCGCTTATTCATAGG 59.530 52.381 7.64 0.00 0.00 2.57
428 2068 2.153645 TGCATGGGCGCTTATTCATAG 58.846 47.619 7.64 1.56 45.35 2.23
429 2069 2.268762 TGCATGGGCGCTTATTCATA 57.731 45.000 7.64 0.00 45.35 2.15
430 2070 1.338973 CTTGCATGGGCGCTTATTCAT 59.661 47.619 7.64 1.15 45.35 2.57
431 2071 0.740149 CTTGCATGGGCGCTTATTCA 59.260 50.000 7.64 0.00 45.35 2.57
432 2072 0.740737 ACTTGCATGGGCGCTTATTC 59.259 50.000 7.64 0.00 45.35 1.75
433 2073 1.185315 AACTTGCATGGGCGCTTATT 58.815 45.000 7.64 0.00 45.35 1.40
434 2074 1.949525 CTAACTTGCATGGGCGCTTAT 59.050 47.619 7.64 0.00 45.35 1.73
435 2075 1.378531 CTAACTTGCATGGGCGCTTA 58.621 50.000 7.64 0.00 45.35 3.09
436 2076 1.315257 CCTAACTTGCATGGGCGCTT 61.315 55.000 7.64 0.00 45.35 4.68
437 2077 1.750399 CCTAACTTGCATGGGCGCT 60.750 57.895 7.64 0.00 45.35 5.92
438 2078 2.774799 CCCTAACTTGCATGGGCGC 61.775 63.158 0.00 0.00 45.35 6.53
439 2079 1.376609 GACCCTAACTTGCATGGGCG 61.377 60.000 4.44 0.00 45.35 6.13
440 2080 1.376609 CGACCCTAACTTGCATGGGC 61.377 60.000 4.44 0.00 43.25 5.36
441 2081 1.376609 GCGACCCTAACTTGCATGGG 61.377 60.000 4.44 6.18 44.89 4.00
442 2082 0.676466 TGCGACCCTAACTTGCATGG 60.676 55.000 4.44 0.00 0.00 3.66
443 2083 1.164411 TTGCGACCCTAACTTGCATG 58.836 50.000 0.00 0.00 35.20 4.06
477 2117 4.981674 CAGCACACATTTTATTCGGTTGTT 59.018 37.500 0.00 0.00 0.00 2.83
478 2118 4.545610 CAGCACACATTTTATTCGGTTGT 58.454 39.130 0.00 0.00 0.00 3.32
480 2120 3.574614 GCAGCACACATTTTATTCGGTT 58.425 40.909 0.00 0.00 0.00 4.44
494 2134 1.152902 AGAGCTTGTTGGCAGCACA 60.153 52.632 2.60 0.00 34.17 4.57
560 2214 2.826128 GGGACTCCTGTATATGATCGCA 59.174 50.000 0.00 0.00 0.00 5.10
563 2217 3.444388 GTCCGGGACTCCTGTATATGATC 59.556 52.174 19.92 0.00 0.00 2.92
581 2235 1.279271 AGTCATTTTCCAGGGAGTCCG 59.721 52.381 2.26 0.00 38.33 4.79
590 2244 2.423185 CGGCAATAGCAGTCATTTTCCA 59.577 45.455 0.00 0.00 44.61 3.53
593 2247 2.094675 AGCGGCAATAGCAGTCATTTT 58.905 42.857 1.45 0.00 44.61 1.82
594 2248 1.672881 GAGCGGCAATAGCAGTCATTT 59.327 47.619 1.45 0.00 44.61 2.32
682 2336 2.578981 GTCGTTAGAGCCGTCCGC 60.579 66.667 0.00 0.00 37.98 5.54
711 2365 0.317160 ACGATGAAACGCTGTCTCCA 59.683 50.000 0.00 0.00 36.70 3.86
849 2509 2.529005 ATCAGGAGTGCGTCGACGTG 62.529 60.000 35.48 25.02 42.22 4.49
867 2527 2.649831 CTGCAAGCACCTGTTCCAT 58.350 52.632 0.00 0.00 0.00 3.41
981 2641 2.445438 CGCGCTCTTCCCGTCTTTC 61.445 63.158 5.56 0.00 0.00 2.62
984 2644 3.141488 ATCGCGCTCTTCCCGTCT 61.141 61.111 5.56 0.00 0.00 4.18
1214 2874 1.866171 CTCATACATCGCGCCGTTCG 61.866 60.000 0.00 0.00 42.12 3.95
1215 2875 1.548973 CCTCATACATCGCGCCGTTC 61.549 60.000 0.00 0.00 0.00 3.95
1223 2883 2.365293 TCCACCATGTCCTCATACATCG 59.635 50.000 0.00 0.00 38.01 3.84
1276 2937 8.972127 CACCAACCTGTCTACATATATATAGCT 58.028 37.037 0.00 0.00 0.00 3.32
1277 2938 8.967918 TCACCAACCTGTCTACATATATATAGC 58.032 37.037 0.00 0.00 0.00 2.97
1280 2941 9.775539 AGATCACCAACCTGTCTACATATATAT 57.224 33.333 0.00 0.00 0.00 0.86
1289 2950 5.560722 TTTTGAGATCACCAACCTGTCTA 57.439 39.130 0.00 0.00 0.00 2.59
1314 2975 1.272092 CCCAGCAAGAGAACCATCCAA 60.272 52.381 0.00 0.00 0.00 3.53
1315 2976 0.329261 CCCAGCAAGAGAACCATCCA 59.671 55.000 0.00 0.00 0.00 3.41
1317 2978 1.003580 TGTCCCAGCAAGAGAACCATC 59.996 52.381 0.00 0.00 0.00 3.51
1318 2979 1.004044 CTGTCCCAGCAAGAGAACCAT 59.996 52.381 0.00 0.00 0.00 3.55
1331 2992 6.011981 ACCTAAAACCTAAATGATCTGTCCCA 60.012 38.462 0.00 0.00 0.00 4.37
1350 3011 6.864685 CGAAATAGTCGGCATACATACCTAAA 59.135 38.462 0.00 0.00 46.45 1.85
1352 3013 5.946298 CGAAATAGTCGGCATACATACCTA 58.054 41.667 0.00 0.00 46.45 3.08
1353 3014 4.806330 CGAAATAGTCGGCATACATACCT 58.194 43.478 0.00 0.00 46.45 3.08
1382 3044 8.806429 TTCATCTCAAAAATTGCTGGAGTATA 57.194 30.769 0.00 0.00 0.00 1.47
1383 3045 7.707624 TTCATCTCAAAAATTGCTGGAGTAT 57.292 32.000 0.00 0.00 0.00 2.12
1384 3046 7.523293 TTTCATCTCAAAAATTGCTGGAGTA 57.477 32.000 0.00 0.00 0.00 2.59
1385 3047 6.409524 TTTCATCTCAAAAATTGCTGGAGT 57.590 33.333 0.00 0.00 0.00 3.85
1386 3048 7.900782 ATTTTCATCTCAAAAATTGCTGGAG 57.099 32.000 0.00 0.00 33.62 3.86
1394 3056 8.181573 GCATGATGCAATTTTCATCTCAAAAAT 58.818 29.630 13.36 0.00 44.26 1.82
1397 3358 6.656314 GCATGATGCAATTTTCATCTCAAA 57.344 33.333 13.36 0.69 44.26 2.69
1412 3373 1.528586 GGAGACATACGTGCATGATGC 59.471 52.381 14.17 11.12 45.29 3.91
1424 3385 9.679661 TTCAGTGCATTATTTAAAGGAGACATA 57.320 29.630 0.00 0.00 0.00 2.29
1460 3421 5.125100 GCCAGCAGCATAAATAAGCAATA 57.875 39.130 0.00 0.00 42.97 1.90
1498 3459 5.180680 CCACATGACCACATCATCACATATC 59.819 44.000 0.00 0.00 45.52 1.63
1516 3477 2.880822 GACATGTTGTCGACCACATG 57.119 50.000 39.96 39.96 43.80 3.21
1568 3531 9.468532 AAAATCAGTTCAGCTAAAGAACATTTC 57.531 29.630 15.47 0.00 45.93 2.17
1667 3630 9.912634 CAACTCTGTTACCAATTGAATTATTGT 57.087 29.630 7.12 0.00 34.42 2.71
1672 3635 6.777580 AGGTCAACTCTGTTACCAATTGAATT 59.222 34.615 7.12 0.00 34.29 2.17
1673 3636 6.306987 AGGTCAACTCTGTTACCAATTGAAT 58.693 36.000 7.12 0.00 34.29 2.57
1682 3645 6.654161 TCTGTCTAGTAGGTCAACTCTGTTAC 59.346 42.308 0.00 0.00 0.00 2.50
1686 3649 5.250200 ACTCTGTCTAGTAGGTCAACTCTG 58.750 45.833 0.00 0.00 0.00 3.35
1700 3663 9.547753 GCAATTGGAAATCTATTACTCTGTCTA 57.452 33.333 7.72 0.00 0.00 2.59
1750 3714 1.795768 CTAAGTTCGTGGCTCTTGCA 58.204 50.000 0.00 0.00 41.91 4.08
1751 3715 0.444260 GCTAAGTTCGTGGCTCTTGC 59.556 55.000 0.00 0.00 38.76 4.01
1776 3740 7.254863 CCCTTCAACCTTCATTTTGAAAATGTG 60.255 37.037 24.86 17.23 40.36 3.21
1893 4015 3.382546 GCAGGCAATTCCACATCATTAGT 59.617 43.478 0.00 0.00 37.29 2.24
1894 4016 3.382227 TGCAGGCAATTCCACATCATTAG 59.618 43.478 0.00 0.00 37.29 1.73
1930 4052 5.974751 GTCCACAACAACGACATAAAAACAT 59.025 36.000 0.00 0.00 0.00 2.71
1951 4074 7.838771 ATACGTACACCTAATCAAAAAGTCC 57.161 36.000 0.00 0.00 0.00 3.85
1963 4086 6.830324 AGAACATGGAAGTATACGTACACCTA 59.170 38.462 5.81 0.00 33.62 3.08
1966 4089 6.558009 TCAGAACATGGAAGTATACGTACAC 58.442 40.000 5.81 0.00 33.09 2.90
1977 4100 9.185192 GAAAACATACTTTTCAGAACATGGAAG 57.815 33.333 0.00 0.00 38.08 3.46
1978 4101 8.690884 TGAAAACATACTTTTCAGAACATGGAA 58.309 29.630 0.00 0.00 41.74 3.53
1980 4103 8.870160 TTGAAAACATACTTTTCAGAACATGG 57.130 30.769 7.96 0.00 45.55 3.66
2020 4145 6.597832 ATGACCGTTTTTGATTATTTCCCA 57.402 33.333 0.00 0.00 0.00 4.37
2031 4156 6.035217 TGCATTGATGATATGACCGTTTTTG 58.965 36.000 0.00 0.00 0.00 2.44
2070 4195 9.183368 TGCATGTATTTCCTATGTAAATGTCAA 57.817 29.630 0.00 0.00 0.00 3.18
2105 4230 5.965334 CGACCGACCATTTCATGAAAAATAG 59.035 40.000 23.91 14.70 33.56 1.73
2106 4231 5.163703 CCGACCGACCATTTCATGAAAAATA 60.164 40.000 23.91 2.26 33.56 1.40
2107 4232 4.380444 CCGACCGACCATTTCATGAAAAAT 60.380 41.667 23.91 12.59 33.56 1.82
2108 4233 3.057876 CCGACCGACCATTTCATGAAAAA 60.058 43.478 23.91 3.45 33.56 1.94
2109 4234 2.486203 CCGACCGACCATTTCATGAAAA 59.514 45.455 23.91 8.65 33.56 2.29
2110 4235 2.080693 CCGACCGACCATTTCATGAAA 58.919 47.619 22.52 22.52 34.46 2.69
2111 4236 1.677518 CCCGACCGACCATTTCATGAA 60.678 52.381 3.38 3.38 0.00 2.57
2112 4237 0.107897 CCCGACCGACCATTTCATGA 60.108 55.000 0.00 0.00 0.00 3.07
2113 4238 0.392461 ACCCGACCGACCATTTCATG 60.392 55.000 0.00 0.00 0.00 3.07
2114 4239 0.107848 GACCCGACCGACCATTTCAT 60.108 55.000 0.00 0.00 0.00 2.57
2115 4240 1.294138 GACCCGACCGACCATTTCA 59.706 57.895 0.00 0.00 0.00 2.69
2116 4241 0.320946 TTGACCCGACCGACCATTTC 60.321 55.000 0.00 0.00 0.00 2.17
2117 4242 0.321298 CTTGACCCGACCGACCATTT 60.321 55.000 0.00 0.00 0.00 2.32
2118 4243 1.189524 TCTTGACCCGACCGACCATT 61.190 55.000 0.00 0.00 0.00 3.16
2119 4244 0.976073 ATCTTGACCCGACCGACCAT 60.976 55.000 0.00 0.00 0.00 3.55
2120 4245 1.189524 AATCTTGACCCGACCGACCA 61.190 55.000 0.00 0.00 0.00 4.02
2121 4246 0.036671 AAATCTTGACCCGACCGACC 60.037 55.000 0.00 0.00 0.00 4.79
2122 4247 1.804601 AAAATCTTGACCCGACCGAC 58.195 50.000 0.00 0.00 0.00 4.79
2123 4248 2.038033 AGAAAAATCTTGACCCGACCGA 59.962 45.455 0.00 0.00 0.00 4.69
2124 4249 2.423577 AGAAAAATCTTGACCCGACCG 58.576 47.619 0.00 0.00 0.00 4.79
2134 4259 9.692325 AGATACCTAGATTGCAAGAAAAATCTT 57.308 29.630 4.94 0.00 41.97 2.40
2135 4260 9.118300 CAGATACCTAGATTGCAAGAAAAATCT 57.882 33.333 4.94 4.18 43.71 2.40
2136 4261 9.113838 TCAGATACCTAGATTGCAAGAAAAATC 57.886 33.333 4.94 0.00 33.77 2.17
2137 4262 9.466497 TTCAGATACCTAGATTGCAAGAAAAAT 57.534 29.630 4.94 0.00 0.00 1.82
2138 4263 8.730680 GTTCAGATACCTAGATTGCAAGAAAAA 58.269 33.333 4.94 0.00 0.00 1.94
2139 4264 7.336931 GGTTCAGATACCTAGATTGCAAGAAAA 59.663 37.037 4.94 0.00 35.23 2.29
2140 4265 6.823689 GGTTCAGATACCTAGATTGCAAGAAA 59.176 38.462 4.94 0.00 35.23 2.52
2141 4266 6.156949 AGGTTCAGATACCTAGATTGCAAGAA 59.843 38.462 4.94 0.00 46.65 2.52
2142 4267 5.663106 AGGTTCAGATACCTAGATTGCAAGA 59.337 40.000 4.94 0.00 46.65 3.02
2143 4268 5.923204 AGGTTCAGATACCTAGATTGCAAG 58.077 41.667 4.94 0.00 46.65 4.01
2144 4269 5.957771 AGGTTCAGATACCTAGATTGCAA 57.042 39.130 0.00 0.00 46.65 4.08
2154 4279 6.264518 TGGTTTCAAAGAAAGGTTCAGATACC 59.735 38.462 0.00 0.00 38.53 2.73
2155 4280 7.272037 TGGTTTCAAAGAAAGGTTCAGATAC 57.728 36.000 0.00 0.00 0.00 2.24
2156 4281 9.581289 TTATGGTTTCAAAGAAAGGTTCAGATA 57.419 29.630 0.00 0.00 0.00 1.98
2157 4282 6.983906 ATGGTTTCAAAGAAAGGTTCAGAT 57.016 33.333 0.00 0.00 0.00 2.90
2158 4283 7.889873 TTATGGTTTCAAAGAAAGGTTCAGA 57.110 32.000 0.00 0.00 0.00 3.27
2159 4284 8.197439 AGTTTATGGTTTCAAAGAAAGGTTCAG 58.803 33.333 0.00 0.00 0.00 3.02
2160 4285 8.073467 AGTTTATGGTTTCAAAGAAAGGTTCA 57.927 30.769 0.00 0.00 0.00 3.18
2161 4286 8.942338 AAGTTTATGGTTTCAAAGAAAGGTTC 57.058 30.769 0.00 0.00 0.00 3.62
2162 4287 9.733556 AAAAGTTTATGGTTTCAAAGAAAGGTT 57.266 25.926 0.00 0.00 0.00 3.50
2163 4288 9.733556 AAAAAGTTTATGGTTTCAAAGAAAGGT 57.266 25.926 0.00 0.00 0.00 3.50
2208 4333 9.874205 GATTTGGAAAAAGTTGATGGATATGAA 57.126 29.630 0.00 0.00 0.00 2.57
2209 4334 8.190122 CGATTTGGAAAAAGTTGATGGATATGA 58.810 33.333 0.00 0.00 0.00 2.15
2210 4335 8.190122 TCGATTTGGAAAAAGTTGATGGATATG 58.810 33.333 0.00 0.00 0.00 1.78
2211 4336 8.292444 TCGATTTGGAAAAAGTTGATGGATAT 57.708 30.769 0.00 0.00 0.00 1.63
2212 4337 7.695480 TCGATTTGGAAAAAGTTGATGGATA 57.305 32.000 0.00 0.00 0.00 2.59
2213 4338 6.588719 TCGATTTGGAAAAAGTTGATGGAT 57.411 33.333 0.00 0.00 0.00 3.41
2214 4339 6.398234 TTCGATTTGGAAAAAGTTGATGGA 57.602 33.333 0.00 0.00 0.00 3.41
2215 4340 7.437862 TCTTTTCGATTTGGAAAAAGTTGATGG 59.562 33.333 6.68 0.00 43.20 3.51
2216 4341 8.351495 TCTTTTCGATTTGGAAAAAGTTGATG 57.649 30.769 6.68 0.00 43.20 3.07
2217 4342 8.940768 TTCTTTTCGATTTGGAAAAAGTTGAT 57.059 26.923 6.68 0.00 43.20 2.57
2218 4343 8.764524 TTTCTTTTCGATTTGGAAAAAGTTGA 57.235 26.923 6.68 0.00 43.20 3.18
2219 4344 9.986833 ATTTTCTTTTCGATTTGGAAAAAGTTG 57.013 25.926 14.93 0.00 43.20 3.16
2225 4350 9.980780 GTTTGAATTTTCTTTTCGATTTGGAAA 57.019 25.926 0.00 0.00 34.28 3.13
2226 4351 9.377312 AGTTTGAATTTTCTTTTCGATTTGGAA 57.623 25.926 0.00 0.00 0.00 3.53
2227 4352 8.940768 AGTTTGAATTTTCTTTTCGATTTGGA 57.059 26.923 0.00 0.00 0.00 3.53
2228 4353 8.275632 GGAGTTTGAATTTTCTTTTCGATTTGG 58.724 33.333 0.00 0.00 0.00 3.28
2229 4354 9.034544 AGGAGTTTGAATTTTCTTTTCGATTTG 57.965 29.630 0.00 0.00 0.00 2.32
2232 4357 9.899226 CTTAGGAGTTTGAATTTTCTTTTCGAT 57.101 29.630 0.00 0.00 0.00 3.59
2233 4358 7.860872 GCTTAGGAGTTTGAATTTTCTTTTCGA 59.139 33.333 0.00 0.00 0.00 3.71
2234 4359 7.862873 AGCTTAGGAGTTTGAATTTTCTTTTCG 59.137 33.333 0.00 0.00 0.00 3.46
2235 4360 9.534565 AAGCTTAGGAGTTTGAATTTTCTTTTC 57.465 29.630 0.00 0.00 0.00 2.29
2236 4361 9.890629 AAAGCTTAGGAGTTTGAATTTTCTTTT 57.109 25.926 0.00 0.00 0.00 2.27
2237 4362 9.890629 AAAAGCTTAGGAGTTTGAATTTTCTTT 57.109 25.926 0.00 0.00 0.00 2.52
2238 4363 9.890629 AAAAAGCTTAGGAGTTTGAATTTTCTT 57.109 25.926 0.00 0.00 0.00 2.52
2239 4364 9.534565 GAAAAAGCTTAGGAGTTTGAATTTTCT 57.465 29.630 0.00 0.00 0.00 2.52
2240 4365 8.765219 GGAAAAAGCTTAGGAGTTTGAATTTTC 58.235 33.333 0.00 1.13 0.00 2.29
2241 4366 8.264347 TGGAAAAAGCTTAGGAGTTTGAATTTT 58.736 29.630 0.00 0.00 0.00 1.82
2242 4367 7.791029 TGGAAAAAGCTTAGGAGTTTGAATTT 58.209 30.769 0.00 0.00 0.00 1.82
2243 4368 7.360113 TGGAAAAAGCTTAGGAGTTTGAATT 57.640 32.000 0.00 0.00 0.00 2.17
2244 4369 6.976934 TGGAAAAAGCTTAGGAGTTTGAAT 57.023 33.333 0.00 0.00 0.00 2.57
2245 4370 6.783708 TTGGAAAAAGCTTAGGAGTTTGAA 57.216 33.333 0.00 0.00 0.00 2.69
2246 4371 6.976934 ATTGGAAAAAGCTTAGGAGTTTGA 57.023 33.333 0.00 0.00 0.00 2.69
2247 4372 7.171508 GGAAATTGGAAAAAGCTTAGGAGTTTG 59.828 37.037 0.00 0.00 0.00 2.93
2248 4373 7.217200 GGAAATTGGAAAAAGCTTAGGAGTTT 58.783 34.615 0.00 0.00 0.00 2.66
2249 4374 6.516693 CGGAAATTGGAAAAAGCTTAGGAGTT 60.517 38.462 0.00 0.00 0.00 3.01
2250 4375 5.048013 CGGAAATTGGAAAAAGCTTAGGAGT 60.048 40.000 0.00 0.00 0.00 3.85
2251 4376 5.402398 CGGAAATTGGAAAAAGCTTAGGAG 58.598 41.667 0.00 0.00 0.00 3.69
2252 4377 4.219725 CCGGAAATTGGAAAAAGCTTAGGA 59.780 41.667 0.00 0.00 0.00 2.94
2253 4378 4.494484 CCGGAAATTGGAAAAAGCTTAGG 58.506 43.478 0.00 0.00 0.00 2.69
2254 4379 4.021456 ACCCGGAAATTGGAAAAAGCTTAG 60.021 41.667 0.73 0.00 0.00 2.18
2255 4380 3.898741 ACCCGGAAATTGGAAAAAGCTTA 59.101 39.130 0.73 0.00 0.00 3.09
2256 4381 2.703536 ACCCGGAAATTGGAAAAAGCTT 59.296 40.909 0.73 0.00 0.00 3.74
2257 4382 2.325484 ACCCGGAAATTGGAAAAAGCT 58.675 42.857 0.73 0.00 0.00 3.74
2258 4383 2.831685 ACCCGGAAATTGGAAAAAGC 57.168 45.000 0.73 0.00 0.00 3.51
2281 4406 9.883142 AGGTTTGTGAAAAGTTCATGAATTAAA 57.117 25.926 12.12 1.12 42.47 1.52
2282 4407 9.311916 CAGGTTTGTGAAAAGTTCATGAATTAA 57.688 29.630 12.12 0.00 42.47 1.40
2283 4408 7.437862 GCAGGTTTGTGAAAAGTTCATGAATTA 59.562 33.333 12.12 0.00 42.47 1.40
2284 4409 6.258507 GCAGGTTTGTGAAAAGTTCATGAATT 59.741 34.615 12.12 4.21 42.47 2.17
2285 4410 5.754890 GCAGGTTTGTGAAAAGTTCATGAAT 59.245 36.000 12.12 0.00 42.47 2.57
2286 4411 5.108517 GCAGGTTTGTGAAAAGTTCATGAA 58.891 37.500 3.38 3.38 42.47 2.57
2287 4412 4.681744 GCAGGTTTGTGAAAAGTTCATGA 58.318 39.130 0.00 0.00 42.47 3.07
2288 4413 3.486841 CGCAGGTTTGTGAAAAGTTCATG 59.513 43.478 0.00 0.00 42.47 3.07
2289 4414 3.380004 TCGCAGGTTTGTGAAAAGTTCAT 59.620 39.130 0.00 0.00 42.47 2.57
2290 4415 2.750166 TCGCAGGTTTGTGAAAAGTTCA 59.250 40.909 0.00 0.00 40.68 3.18
2291 4416 3.414549 TCGCAGGTTTGTGAAAAGTTC 57.585 42.857 0.00 0.00 40.68 3.01
2298 4423 3.119316 ACAAAATGTTCGCAGGTTTGTGA 60.119 39.130 9.75 0.00 42.57 3.58
2299 4424 3.186119 ACAAAATGTTCGCAGGTTTGTG 58.814 40.909 9.75 0.00 42.57 3.33
2300 4425 3.119316 TGACAAAATGTTCGCAGGTTTGT 60.119 39.130 10.12 10.12 44.72 2.83
2301 4426 3.443037 TGACAAAATGTTCGCAGGTTTG 58.557 40.909 0.00 0.00 39.74 2.93
2302 4427 3.791973 TGACAAAATGTTCGCAGGTTT 57.208 38.095 0.00 0.00 0.00 3.27
2303 4428 3.791973 TTGACAAAATGTTCGCAGGTT 57.208 38.095 0.00 0.00 0.00 3.50
2304 4429 3.791973 TTTGACAAAATGTTCGCAGGT 57.208 38.095 0.00 0.00 0.00 4.00
2305 4430 3.674753 GGATTTGACAAAATGTTCGCAGG 59.325 43.478 4.41 0.00 36.10 4.85
2306 4431 3.361644 CGGATTTGACAAAATGTTCGCAG 59.638 43.478 4.41 0.00 36.10 5.18
2307 4432 3.243234 ACGGATTTGACAAAATGTTCGCA 60.243 39.130 4.41 0.00 36.10 5.10
2308 4433 3.119463 CACGGATTTGACAAAATGTTCGC 59.881 43.478 4.41 0.00 36.10 4.70
2309 4434 4.532276 TCACGGATTTGACAAAATGTTCG 58.468 39.130 4.41 2.00 36.10 3.95
2310 4435 5.174943 GGTTCACGGATTTGACAAAATGTTC 59.825 40.000 4.41 0.00 36.10 3.18
2311 4436 5.047188 GGTTCACGGATTTGACAAAATGTT 58.953 37.500 4.41 0.00 36.10 2.71
2312 4437 4.340950 AGGTTCACGGATTTGACAAAATGT 59.659 37.500 4.41 1.28 36.10 2.71
2313 4438 4.870363 AGGTTCACGGATTTGACAAAATG 58.130 39.130 4.41 2.14 36.10 2.32
2314 4439 5.529581 AAGGTTCACGGATTTGACAAAAT 57.470 34.783 4.41 0.00 38.74 1.82
2315 4440 4.993029 AAGGTTCACGGATTTGACAAAA 57.007 36.364 4.41 0.00 0.00 2.44
2316 4441 4.993029 AAAGGTTCACGGATTTGACAAA 57.007 36.364 2.48 2.48 0.00 2.83
2317 4442 4.496673 CGAAAAGGTTCACGGATTTGACAA 60.497 41.667 0.00 0.00 32.89 3.18
2318 4443 3.002862 CGAAAAGGTTCACGGATTTGACA 59.997 43.478 0.00 0.00 32.89 3.58
2319 4444 3.551551 CGAAAAGGTTCACGGATTTGAC 58.448 45.455 0.00 0.00 32.89 3.18
2320 4445 2.550606 CCGAAAAGGTTCACGGATTTGA 59.449 45.455 0.00 0.00 46.94 2.69
2321 4446 2.920647 GCCGAAAAGGTTCACGGATTTG 60.921 50.000 0.00 0.00 46.94 2.32
2322 4447 1.268625 GCCGAAAAGGTTCACGGATTT 59.731 47.619 0.00 0.00 46.94 2.17
2323 4448 0.879090 GCCGAAAAGGTTCACGGATT 59.121 50.000 0.00 0.00 46.94 3.01
2324 4449 0.958876 GGCCGAAAAGGTTCACGGAT 60.959 55.000 0.00 0.00 46.94 4.18
2325 4450 1.598685 GGCCGAAAAGGTTCACGGA 60.599 57.895 0.00 0.00 46.94 4.69
2326 4451 2.951458 GGCCGAAAAGGTTCACGG 59.049 61.111 0.00 0.00 46.74 4.94
2327 4452 2.248835 ACGGCCGAAAAGGTTCACG 61.249 57.895 35.90 0.00 43.70 4.35
2328 4453 1.281656 CACGGCCGAAAAGGTTCAC 59.718 57.895 35.90 0.00 43.70 3.18
2329 4454 2.548295 GCACGGCCGAAAAGGTTCA 61.548 57.895 35.90 0.00 43.70 3.18
2330 4455 2.254350 GCACGGCCGAAAAGGTTC 59.746 61.111 35.90 7.04 43.70 3.62


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

AutoCloner maintained by Alex Coulton.