Multiple sequence alignment - TraesCS6B01G181800

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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 TraesCS6B01G181800 chr6B 100.000 5390 0 0 1 5390 203918913 203924302 0.000000e+00 9954.0
1 TraesCS6B01G181800 chr6B 96.698 424 13 1 201 624 203913626 203914048 0.000000e+00 704.0
2 TraesCS6B01G181800 chr6D 95.052 2607 79 12 2832 5390 114231307 114233911 0.000000e+00 4054.0
3 TraesCS6B01G181800 chr6D 94.485 1233 47 10 1603 2825 114230042 114231263 0.000000e+00 1881.0
4 TraesCS6B01G181800 chr6D 95.455 242 9 2 687 928 114228652 114228891 8.470000e-103 385.0
5 TraesCS6B01G181800 chr6D 83.374 409 27 22 949 1349 114228875 114229250 1.860000e-89 340.0
6 TraesCS6B01G181800 chr6D 94.611 167 6 1 1392 1558 114229880 114230043 6.930000e-64 255.0
7 TraesCS6B01G181800 chr6D 100.000 33 0 0 1415 1447 114229849 114229881 1.620000e-05 62.1
8 TraesCS6B01G181800 chr6A 90.370 3053 181 43 1603 4565 142781192 142784221 0.000000e+00 3904.0
9 TraesCS6B01G181800 chr6A 93.505 816 33 13 4595 5390 142784410 142785225 0.000000e+00 1195.0
10 TraesCS6B01G181800 chr6A 83.914 746 62 36 624 1349 142779847 142780554 0.000000e+00 660.0
11 TraesCS6B01G181800 chr6A 95.139 144 7 0 1415 1558 142781050 142781193 1.510000e-55 228.0
12 TraesCS6B01G181800 chr5B 88.474 642 55 8 1 625 366019835 366020474 0.000000e+00 758.0
13 TraesCS6B01G181800 chr5B 89.227 427 40 6 202 624 366014554 366014978 3.700000e-146 529.0
14 TraesCS6B01G181800 chr1B 88.125 640 58 7 1 625 295100772 295101408 0.000000e+00 745.0
15 TraesCS6B01G181800 chr3D 83.699 638 88 12 1 624 239572875 239572240 6.010000e-164 588.0
16 TraesCS6B01G181800 chr5D 83.412 639 85 11 2 624 407786614 407785981 1.680000e-159 573.0
17 TraesCS6B01G181800 chr5A 81.931 642 75 19 1 624 559589428 559588810 6.230000e-139 505.0
18 TraesCS6B01G181800 chrUn 83.803 426 59 9 208 628 832312 832732 3.910000e-106 396.0
19 TraesCS6B01G181800 chrUn 83.803 426 59 9 208 628 306059426 306059006 3.910000e-106 396.0
20 TraesCS6B01G181800 chrUn 83.803 426 59 9 208 628 397319221 397319641 3.910000e-106 396.0
21 TraesCS6B01G181800 chrUn 86.784 227 18 1 1 215 831384 831610 5.390000e-60 243.0
22 TraesCS6B01G181800 chr7B 90.909 77 7 0 1010 1086 660362506 660362430 2.660000e-18 104.0
23 TraesCS6B01G181800 chr7B 89.610 77 8 0 1010 1086 699156223 699156147 1.240000e-16 99.0
24 TraesCS6B01G181800 chr7A 90.909 77 7 0 1010 1086 679927431 679927355 2.660000e-18 104.0
25 TraesCS6B01G181800 chr7D 89.610 77 8 0 1010 1086 588068112 588068036 1.240000e-16 99.0
26 TraesCS6B01G181800 chr2B 89.610 77 8 0 1010 1086 369808732 369808656 1.240000e-16 99.0
27 TraesCS6B01G181800 chr2D 98.113 53 1 0 3399 3451 647737805 647737753 5.750000e-15 93.5


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 TraesCS6B01G181800 chr6B 203918913 203924302 5389 False 9954.00 9954 100.0000 1 5390 1 chr6B.!!$F2 5389
1 TraesCS6B01G181800 chr6D 114228652 114233911 5259 False 1162.85 4054 93.8295 687 5390 6 chr6D.!!$F1 4703
2 TraesCS6B01G181800 chr6A 142779847 142785225 5378 False 1496.75 3904 90.7320 624 5390 4 chr6A.!!$F1 4766
3 TraesCS6B01G181800 chr5B 366019835 366020474 639 False 758.00 758 88.4740 1 625 1 chr5B.!!$F2 624
4 TraesCS6B01G181800 chr1B 295100772 295101408 636 False 745.00 745 88.1250 1 625 1 chr1B.!!$F1 624
5 TraesCS6B01G181800 chr3D 239572240 239572875 635 True 588.00 588 83.6990 1 624 1 chr3D.!!$R1 623
6 TraesCS6B01G181800 chr5D 407785981 407786614 633 True 573.00 573 83.4120 2 624 1 chr5D.!!$R1 622
7 TraesCS6B01G181800 chr5A 559588810 559589428 618 True 505.00 505 81.9310 1 624 1 chr5A.!!$R1 623
8 TraesCS6B01G181800 chrUn 831384 832732 1348 False 319.50 396 85.2935 1 628 2 chrUn.!!$F2 627

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
577 1308 0.530744 AGCGATGAACGGCTGTAGAA 59.469 50.0 0.00 0.00 42.83 2.10 F
1561 2910 0.032017 TCCTCCTTGCCTCCTACTCC 60.032 60.0 0.00 0.00 0.00 3.85 F
1567 2916 0.253160 TTGCCTCCTACTCCATGGGT 60.253 55.0 13.02 11.37 0.00 4.51 F
1569 2918 0.470341 GCCTCCTACTCCATGGGTTC 59.530 60.0 13.02 0.00 0.00 3.62 F
2346 3708 0.973632 TGATCACTGCCCTGTTACGT 59.026 50.0 0.00 0.00 0.00 3.57 F
3808 5230 0.401356 TTTCTGGCAGCACATCTGGA 59.599 50.0 10.34 0.00 43.06 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1740 3099 0.315568 GTAGGATCGCCTTCTCGCAT 59.684 55.000 0.00 0.0 43.90 4.73 R
3363 4779 0.961019 TTCCATTGCCAGCAGTTGTC 59.039 50.000 0.00 0.0 0.00 3.18 R
3425 4841 2.686915 GAGATGAACAGAAATGGGCTGG 59.313 50.000 0.00 0.0 37.69 4.85 R
3591 5008 4.653341 AGAGTTTGACAGGAGAGGGATATG 59.347 45.833 0.00 0.0 0.00 1.78 R
3843 5265 0.251297 CTCCATTGGTTGGCTGGTGA 60.251 55.000 1.86 0.0 46.01 4.02 R
4688 6350 1.399089 ACAGGGTTTTTGTCACGTTCG 59.601 47.619 0.00 0.0 0.00 3.95 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
74 75 1.534959 TGCCTCTCTGACTGCACCT 60.535 57.895 0.00 0.00 0.00 4.00
128 141 3.947868 TCAGAGCTTGAAGAGGGATTTG 58.052 45.455 0.00 0.00 31.34 2.32
275 1000 6.100404 TCAGACAAGAATTTGGGGAATTTG 57.900 37.500 0.00 0.00 38.06 2.32
282 1007 5.831103 AGAATTTGGGGAATTTGAGCTAGA 58.169 37.500 0.00 0.00 38.06 2.43
283 1008 6.256053 AGAATTTGGGGAATTTGAGCTAGAA 58.744 36.000 0.00 0.00 38.06 2.10
299 1025 7.198390 TGAGCTAGAATTTTCATTGCATTAGC 58.802 34.615 0.00 0.00 42.57 3.09
378 1106 2.237143 ACATGCCTCGAATGGAAGAGAA 59.763 45.455 0.00 0.00 36.65 2.87
513 1244 1.655959 GATCGACGAAGGAGAGCGC 60.656 63.158 0.00 0.00 0.00 5.92
536 1267 1.597663 CATTCCAGCGAACCGTTATCC 59.402 52.381 0.00 0.00 0.00 2.59
539 1270 2.101783 TCCAGCGAACCGTTATCCTTA 58.898 47.619 0.00 0.00 0.00 2.69
547 1278 3.622166 ACCGTTATCCTTACTTGGTGG 57.378 47.619 0.00 0.00 0.00 4.61
577 1308 0.530744 AGCGATGAACGGCTGTAGAA 59.469 50.000 0.00 0.00 42.83 2.10
581 1312 3.364062 CGATGAACGGCTGTAGAAGTAG 58.636 50.000 0.00 0.00 38.46 2.57
583 1314 1.890489 TGAACGGCTGTAGAAGTAGCA 59.110 47.619 0.00 0.00 41.63 3.49
618 1349 2.044908 AGGGGATTTTCAGAATTGGGCT 59.955 45.455 0.00 0.00 0.00 5.19
629 1360 0.673437 AATTGGGCTTGACACGGTTG 59.327 50.000 0.00 0.00 0.00 3.77
643 1374 2.668550 GTTGCGGGCGGTTCTTCT 60.669 61.111 0.00 0.00 0.00 2.85
657 1391 4.720046 GGTTCTTCTTCTTCTTGGTCCTT 58.280 43.478 0.00 0.00 0.00 3.36
660 1394 3.973973 TCTTCTTCTTCTTGGTCCTTCCA 59.026 43.478 0.00 0.00 45.60 3.53
670 1404 0.804989 GGTCCTTCCATGCGTTTCTG 59.195 55.000 0.00 0.00 35.97 3.02
729 1467 2.224769 ACGTCACCACCCATGATTCTTT 60.225 45.455 0.00 0.00 0.00 2.52
730 1468 2.420022 CGTCACCACCCATGATTCTTTC 59.580 50.000 0.00 0.00 0.00 2.62
731 1469 3.690460 GTCACCACCCATGATTCTTTCT 58.310 45.455 0.00 0.00 0.00 2.52
732 1470 3.691609 GTCACCACCCATGATTCTTTCTC 59.308 47.826 0.00 0.00 0.00 2.87
733 1471 3.588842 TCACCACCCATGATTCTTTCTCT 59.411 43.478 0.00 0.00 0.00 3.10
734 1472 3.944015 CACCACCCATGATTCTTTCTCTC 59.056 47.826 0.00 0.00 0.00 3.20
831 1569 1.464376 GGCACCGATGGAGCTAGCTA 61.464 60.000 19.38 2.78 39.22 3.32
874 1615 2.604686 TCAACGAGAGCCAGCCCT 60.605 61.111 0.00 0.00 0.00 5.19
1086 1846 0.753262 ACAGCGACTTCAAGGTCAGT 59.247 50.000 0.00 0.00 36.12 3.41
1090 1850 1.269831 GCGACTTCAAGGTCAGTCACT 60.270 52.381 0.00 0.00 39.64 3.41
1091 1851 2.398498 CGACTTCAAGGTCAGTCACTG 58.602 52.381 0.00 0.00 39.64 3.66
1092 1852 2.139118 GACTTCAAGGTCAGTCACTGC 58.861 52.381 0.00 0.00 39.49 4.40
1093 1853 1.202698 ACTTCAAGGTCAGTCACTGCC 60.203 52.381 0.00 4.99 0.00 4.85
1094 1854 0.836606 TTCAAGGTCAGTCACTGCCA 59.163 50.000 17.39 0.00 32.75 4.92
1095 1855 0.106708 TCAAGGTCAGTCACTGCCAC 59.893 55.000 17.39 4.81 32.75 5.01
1096 1856 0.886490 CAAGGTCAGTCACTGCCACC 60.886 60.000 17.39 12.92 32.75 4.61
1097 1857 1.344953 AAGGTCAGTCACTGCCACCA 61.345 55.000 16.16 0.00 32.76 4.17
1098 1858 1.148273 GGTCAGTCACTGCCACCAA 59.852 57.895 10.24 0.00 31.30 3.67
1099 1859 0.250901 GGTCAGTCACTGCCACCAAT 60.251 55.000 10.24 0.00 31.30 3.16
1100 1860 0.877071 GTCAGTCACTGCCACCAATG 59.123 55.000 0.00 0.00 0.00 2.82
1101 1861 0.890542 TCAGTCACTGCCACCAATGC 60.891 55.000 0.00 0.00 0.00 3.56
1102 1862 1.151221 AGTCACTGCCACCAATGCA 59.849 52.632 0.00 0.00 37.17 3.96
1103 1863 0.251474 AGTCACTGCCACCAATGCAT 60.251 50.000 0.00 0.00 38.22 3.96
1104 1864 0.604578 GTCACTGCCACCAATGCATT 59.395 50.000 5.99 5.99 38.22 3.56
1107 1867 0.810648 ACTGCCACCAATGCATTACG 59.189 50.000 12.53 7.86 38.22 3.18
1108 1868 0.526096 CTGCCACCAATGCATTACGC 60.526 55.000 12.53 11.32 38.22 4.42
1128 1888 1.110518 ATGCATGCATGGGCGATTCA 61.111 50.000 31.74 15.08 45.35 2.57
1136 1898 1.727511 ATGGGCGATTCATTGTGCGG 61.728 55.000 0.00 0.00 0.00 5.69
1138 1900 1.062525 GGCGATTCATTGTGCGGTC 59.937 57.895 0.00 0.00 0.00 4.79
1147 1909 2.487762 TCATTGTGCGGTCAATTTCTCC 59.512 45.455 0.04 0.00 36.10 3.71
1148 1910 1.974265 TTGTGCGGTCAATTTCTCCA 58.026 45.000 0.00 0.00 0.00 3.86
1152 1914 2.749621 GTGCGGTCAATTTCTCCATTCT 59.250 45.455 0.00 0.00 0.00 2.40
1153 1915 3.009723 TGCGGTCAATTTCTCCATTCTC 58.990 45.455 0.00 0.00 0.00 2.87
1154 1916 3.009723 GCGGTCAATTTCTCCATTCTCA 58.990 45.455 0.00 0.00 0.00 3.27
1155 1917 3.440173 GCGGTCAATTTCTCCATTCTCAA 59.560 43.478 0.00 0.00 0.00 3.02
1157 1919 5.731686 GCGGTCAATTTCTCCATTCTCAATC 60.732 44.000 0.00 0.00 0.00 2.67
1158 1920 5.355071 CGGTCAATTTCTCCATTCTCAATCA 59.645 40.000 0.00 0.00 0.00 2.57
1161 1923 7.919621 GGTCAATTTCTCCATTCTCAATCAATC 59.080 37.037 0.00 0.00 0.00 2.67
1162 1924 7.642978 GTCAATTTCTCCATTCTCAATCAATCG 59.357 37.037 0.00 0.00 0.00 3.34
1165 1927 3.118298 TCTCCATTCTCAATCAATCGCCA 60.118 43.478 0.00 0.00 0.00 5.69
1166 1928 3.208594 TCCATTCTCAATCAATCGCCAG 58.791 45.455 0.00 0.00 0.00 4.85
1168 1930 1.009078 TTCTCAATCAATCGCCAGCG 58.991 50.000 5.50 5.50 41.35 5.18
1188 1950 2.464380 CGAACGCAACGCAAAATTACAA 59.536 40.909 0.00 0.00 0.00 2.41
1189 1951 3.118809 CGAACGCAACGCAAAATTACAAT 59.881 39.130 0.00 0.00 0.00 2.71
1190 1952 4.614417 GAACGCAACGCAAAATTACAATC 58.386 39.130 0.00 0.00 0.00 2.67
1191 1953 3.896122 ACGCAACGCAAAATTACAATCT 58.104 36.364 0.00 0.00 0.00 2.40
1192 1954 5.037015 ACGCAACGCAAAATTACAATCTA 57.963 34.783 0.00 0.00 0.00 1.98
1193 1955 5.086058 ACGCAACGCAAAATTACAATCTAG 58.914 37.500 0.00 0.00 0.00 2.43
1194 1956 4.028509 CGCAACGCAAAATTACAATCTAGC 60.029 41.667 0.00 0.00 0.00 3.42
1195 1957 5.095490 GCAACGCAAAATTACAATCTAGCT 58.905 37.500 0.00 0.00 0.00 3.32
1196 1958 5.572896 GCAACGCAAAATTACAATCTAGCTT 59.427 36.000 0.00 0.00 0.00 3.74
1197 1959 6.089417 GCAACGCAAAATTACAATCTAGCTTT 59.911 34.615 0.00 0.00 0.00 3.51
1198 1960 7.439490 CAACGCAAAATTACAATCTAGCTTTG 58.561 34.615 0.00 0.00 0.00 2.77
1199 1961 5.572896 ACGCAAAATTACAATCTAGCTTTGC 59.427 36.000 0.00 6.56 42.19 3.68
1201 1963 6.308766 CGCAAAATTACAATCTAGCTTTGCTT 59.691 34.615 12.97 0.00 42.99 3.91
1202 1964 7.450627 GCAAAATTACAATCTAGCTTTGCTTG 58.549 34.615 8.86 0.00 42.28 4.01
1203 1965 7.412237 GCAAAATTACAATCTAGCTTTGCTTGG 60.412 37.037 8.86 0.00 42.28 3.61
1204 1966 5.841957 ATTACAATCTAGCTTTGCTTGGG 57.158 39.130 0.00 0.00 40.44 4.12
1205 1967 2.450476 ACAATCTAGCTTTGCTTGGGG 58.550 47.619 0.00 0.00 40.44 4.96
1206 1968 1.753073 CAATCTAGCTTTGCTTGGGGG 59.247 52.381 0.00 0.00 40.44 5.40
1207 1969 1.002857 ATCTAGCTTTGCTTGGGGGT 58.997 50.000 0.00 0.00 40.44 4.95
1208 1970 0.777446 TCTAGCTTTGCTTGGGGGTT 59.223 50.000 0.00 0.00 40.44 4.11
1209 1971 0.890683 CTAGCTTTGCTTGGGGGTTG 59.109 55.000 0.00 0.00 40.44 3.77
1210 1972 0.541764 TAGCTTTGCTTGGGGGTTGG 60.542 55.000 0.00 0.00 40.44 3.77
1211 1973 2.882677 GCTTTGCTTGGGGGTTGGG 61.883 63.158 0.00 0.00 0.00 4.12
1302 2064 0.861837 CCACGTCAGAAGTGAGCAAC 59.138 55.000 17.21 0.00 41.83 4.17
1304 2066 0.753262 ACGTCAGAAGTGAGCAACCT 59.247 50.000 0.00 0.00 31.53 3.50
1319 2081 2.289002 GCAACCTATCCGCTCTTTCATG 59.711 50.000 0.00 0.00 0.00 3.07
1326 2088 1.162800 CCGCTCTTTCATGGCCTAGC 61.163 60.000 3.32 0.71 0.00 3.42
1332 2094 4.339247 GCTCTTTCATGGCCTAGCAAATTA 59.661 41.667 3.32 0.00 0.00 1.40
1333 2095 5.010415 GCTCTTTCATGGCCTAGCAAATTAT 59.990 40.000 3.32 0.00 0.00 1.28
1334 2096 6.207417 GCTCTTTCATGGCCTAGCAAATTATA 59.793 38.462 3.32 0.00 0.00 0.98
1335 2097 7.574592 GCTCTTTCATGGCCTAGCAAATTATAG 60.575 40.741 3.32 0.00 0.00 1.31
1341 2103 3.007614 GGCCTAGCAAATTATAGGGACGA 59.992 47.826 0.00 0.00 39.23 4.20
1349 2111 7.283329 AGCAAATTATAGGGACGATTTCTCTT 58.717 34.615 0.00 0.00 36.07 2.85
1350 2112 7.442666 AGCAAATTATAGGGACGATTTCTCTTC 59.557 37.037 0.00 0.00 36.07 2.87
1351 2113 7.442666 GCAAATTATAGGGACGATTTCTCTTCT 59.557 37.037 0.00 0.00 36.07 2.85
1352 2114 8.983724 CAAATTATAGGGACGATTTCTCTTCTC 58.016 37.037 0.00 0.00 36.07 2.87
1353 2115 8.485578 AATTATAGGGACGATTTCTCTTCTCT 57.514 34.615 0.00 0.00 36.07 3.10
1354 2116 7.899648 TTATAGGGACGATTTCTCTTCTCTT 57.100 36.000 0.00 0.00 36.07 2.85
1357 2119 5.870706 AGGGACGATTTCTCTTCTCTTTTT 58.129 37.500 0.00 0.00 25.50 1.94
1383 2550 2.982470 GTTTCTTCTTTTGCATGGCTCG 59.018 45.455 0.00 0.00 0.00 5.03
1388 2555 1.159285 CTTTTGCATGGCTCGTCAGA 58.841 50.000 0.00 0.00 0.00 3.27
1396 2563 2.879002 TGGCTCGTCAGATTCATCTC 57.121 50.000 0.00 0.00 34.22 2.75
1407 2574 5.005203 GTCAGATTCATCTCGTAAGCTTGTG 59.995 44.000 9.86 0.81 34.22 3.33
1453 2802 3.947834 AGAAATATTCTTGGCAACCTCGG 59.052 43.478 0.00 0.00 36.36 4.63
1500 2849 1.852942 ACTGCATATACGCCTTGTCG 58.147 50.000 0.00 0.00 0.00 4.35
1558 2907 0.833949 CCTTCCTCCTTGCCTCCTAC 59.166 60.000 0.00 0.00 0.00 3.18
1559 2908 1.623834 CCTTCCTCCTTGCCTCCTACT 60.624 57.143 0.00 0.00 0.00 2.57
1560 2909 1.760029 CTTCCTCCTTGCCTCCTACTC 59.240 57.143 0.00 0.00 0.00 2.59
1561 2910 0.032017 TCCTCCTTGCCTCCTACTCC 60.032 60.000 0.00 0.00 0.00 3.85
1562 2911 0.325671 CCTCCTTGCCTCCTACTCCA 60.326 60.000 0.00 0.00 0.00 3.86
1563 2912 1.694048 CCTCCTTGCCTCCTACTCCAT 60.694 57.143 0.00 0.00 0.00 3.41
1564 2913 1.415659 CTCCTTGCCTCCTACTCCATG 59.584 57.143 0.00 0.00 0.00 3.66
1565 2914 0.471617 CCTTGCCTCCTACTCCATGG 59.528 60.000 4.97 4.97 0.00 3.66
1566 2915 0.471617 CTTGCCTCCTACTCCATGGG 59.528 60.000 13.02 5.22 0.00 4.00
1567 2916 0.253160 TTGCCTCCTACTCCATGGGT 60.253 55.000 13.02 11.37 0.00 4.51
1568 2917 0.253160 TGCCTCCTACTCCATGGGTT 60.253 55.000 13.02 1.11 0.00 4.11
1569 2918 0.470341 GCCTCCTACTCCATGGGTTC 59.530 60.000 13.02 0.00 0.00 3.62
1570 2919 1.132500 CCTCCTACTCCATGGGTTCC 58.868 60.000 13.02 0.00 0.00 3.62
1571 2920 1.625228 CCTCCTACTCCATGGGTTCCA 60.625 57.143 13.02 0.00 38.19 3.53
1572 2921 2.412591 CTCCTACTCCATGGGTTCCAT 58.587 52.381 13.02 0.00 46.37 3.41
1573 2922 3.587498 CTCCTACTCCATGGGTTCCATA 58.413 50.000 13.02 0.00 43.15 2.74
1574 2923 3.973973 CTCCTACTCCATGGGTTCCATAA 59.026 47.826 13.02 0.00 43.15 1.90
1575 2924 4.376223 TCCTACTCCATGGGTTCCATAAA 58.624 43.478 13.02 0.00 43.15 1.40
1576 2925 4.165372 TCCTACTCCATGGGTTCCATAAAC 59.835 45.833 13.02 0.00 43.15 2.01
1577 2926 4.080015 CCTACTCCATGGGTTCCATAAACA 60.080 45.833 13.02 0.00 43.15 2.83
1578 2927 3.697166 ACTCCATGGGTTCCATAAACAC 58.303 45.455 13.02 0.00 43.15 3.32
1579 2928 3.333680 ACTCCATGGGTTCCATAAACACT 59.666 43.478 13.02 0.00 43.15 3.55
1580 2929 3.947834 CTCCATGGGTTCCATAAACACTC 59.052 47.826 13.02 0.00 43.15 3.51
1581 2930 3.591527 TCCATGGGTTCCATAAACACTCT 59.408 43.478 13.02 0.00 43.15 3.24
1582 2931 4.044065 TCCATGGGTTCCATAAACACTCTT 59.956 41.667 13.02 0.00 43.15 2.85
1583 2932 5.251932 TCCATGGGTTCCATAAACACTCTTA 59.748 40.000 13.02 0.00 43.15 2.10
1584 2933 6.069088 TCCATGGGTTCCATAAACACTCTTAT 60.069 38.462 13.02 0.00 43.15 1.73
1585 2934 7.128109 TCCATGGGTTCCATAAACACTCTTATA 59.872 37.037 13.02 0.00 43.15 0.98
1586 2935 7.944554 CCATGGGTTCCATAAACACTCTTATAT 59.055 37.037 2.85 0.00 43.15 0.86
1587 2936 9.354673 CATGGGTTCCATAAACACTCTTATATT 57.645 33.333 0.00 0.00 43.15 1.28
1611 2960 5.255397 TGGGACACAGGAGTATCAATTTT 57.745 39.130 0.00 0.00 36.25 1.82
1618 2967 6.825721 ACACAGGAGTATCAATTTTCTCATCC 59.174 38.462 0.00 0.00 36.25 3.51
1629 2981 4.916041 TTTTCTCATCCTCCACTCATGT 57.084 40.909 0.00 0.00 0.00 3.21
1712 3071 5.130350 GCCATCTTATTGTAGGTTGCCTTA 58.870 41.667 0.00 0.00 34.61 2.69
1740 3099 5.126545 ACGTTGATAGTGATACACAGGCTTA 59.873 40.000 4.75 0.00 36.74 3.09
1787 3146 2.671682 GAGTTCCTGGCCCACTCC 59.328 66.667 0.00 0.00 32.26 3.85
1923 3285 3.254629 TGCATCAAGGAGGCAAGAC 57.745 52.632 2.80 0.00 46.20 3.01
1944 3306 3.053662 CCGAAGGCAATGGCATTTG 57.946 52.632 10.65 7.57 45.27 2.32
1945 3307 1.085501 CCGAAGGCAATGGCATTTGC 61.086 55.000 10.65 16.41 45.27 3.68
2067 3429 1.002544 CTCTTTCTGGAGGAACGGCTT 59.997 52.381 0.00 0.00 33.13 4.35
2111 3473 1.411493 GACATCGAAACCGAGCGTCC 61.411 60.000 0.00 0.00 39.64 4.79
2138 3500 1.229359 CTCCCCAGCATTCTGCCAT 59.771 57.895 0.00 0.00 46.52 4.40
2158 3520 5.163237 GCCATGGTAGGGACTATGTCTTTTA 60.163 44.000 14.67 0.00 45.60 1.52
2159 3521 6.289064 CCATGGTAGGGACTATGTCTTTTAC 58.711 44.000 2.57 0.00 45.60 2.01
2166 3528 4.873827 GGGACTATGTCTTTTACGCAATCA 59.126 41.667 0.00 0.00 32.47 2.57
2257 3619 2.656069 TAGAACCAGGACGCTGCCC 61.656 63.158 0.00 0.00 0.00 5.36
2346 3708 0.973632 TGATCACTGCCCTGTTACGT 59.026 50.000 0.00 0.00 0.00 3.57
2423 3785 5.063180 TGAAGGTTTAGCATGCTCAAATG 57.937 39.130 26.57 0.00 0.00 2.32
2462 3824 7.013007 GCATTAGCCTTGGTAAACCACAAGT 62.013 44.000 0.07 0.00 41.84 3.16
2503 3865 6.399639 AGGTTGTCGTTTCCATTTTACAAT 57.600 33.333 0.00 0.00 0.00 2.71
2714 4090 6.962182 TCTCATTGGTATGATCCAGTTCTTT 58.038 36.000 0.00 0.00 39.94 2.52
2804 4180 7.814107 TGTCATCTTCTTTATGCCAAATTTGTC 59.186 33.333 16.73 4.74 0.00 3.18
2805 4181 8.031277 GTCATCTTCTTTATGCCAAATTTGTCT 58.969 33.333 16.73 3.90 0.00 3.41
2982 4395 3.944015 CACATCCCTTCACCTTGATCTTC 59.056 47.826 0.00 0.00 0.00 2.87
3053 4466 3.000041 TCTAATGTGCTTTTCATCGCGT 59.000 40.909 5.77 0.00 0.00 6.01
3114 4527 2.028130 AGGAGTACATCAGAGAAGCGG 58.972 52.381 0.00 0.00 0.00 5.52
3174 4587 4.083537 TGTTCTACAAATAAGCGCAAGTGG 60.084 41.667 11.47 0.00 41.68 4.00
3253 4669 4.408276 ACAGTGAGAGGAAGCTACTAACA 58.592 43.478 0.00 0.00 0.00 2.41
3363 4779 1.517257 CTACGCCTGAGCCTGAACG 60.517 63.158 0.00 0.00 34.57 3.95
3591 5008 2.166664 AGGTACAGAAGAAGATCGCCAC 59.833 50.000 0.00 0.00 0.00 5.01
3716 5138 3.126000 GCTCCCAAATGTTCTTCGAGAAG 59.874 47.826 6.51 6.51 34.42 2.85
3718 5140 2.162408 CCCAAATGTTCTTCGAGAAGGC 59.838 50.000 12.32 7.07 34.42 4.35
3729 5151 4.829492 TCTTCGAGAAGGCATCATCAGATA 59.171 41.667 12.32 0.00 38.88 1.98
3747 5169 6.475504 TCAGATATTCTTTTTGGTCTCTGCA 58.524 36.000 0.00 0.00 31.26 4.41
3782 5204 4.389890 AGCAAAGCATCAACTTGTCAAA 57.610 36.364 0.00 0.00 0.00 2.69
3808 5230 0.401356 TTTCTGGCAGCACATCTGGA 59.599 50.000 10.34 0.00 43.06 3.86
3859 5281 0.037975 GCTTCACCAGCCAACCAATG 60.038 55.000 0.00 0.00 43.65 2.82
4005 5466 3.889538 ACATAATGCTACTCGACAGCCTA 59.110 43.478 10.87 4.44 38.29 3.93
4015 5476 2.612672 CTCGACAGCCTATACGAAGACA 59.387 50.000 0.00 0.00 34.50 3.41
4017 5478 2.355132 CGACAGCCTATACGAAGACAGT 59.645 50.000 0.00 0.00 0.00 3.55
4036 5497 3.086391 GCGAGGAGGCAGCAGATCA 62.086 63.158 0.00 0.00 0.00 2.92
4039 5500 2.191641 GGAGGCAGCAGATCACCC 59.808 66.667 0.00 0.00 0.00 4.61
4053 5514 1.079405 CACCCGCGTGACCTACAAT 60.079 57.895 4.92 0.00 43.14 2.71
4097 5558 0.319297 CCCTTCGAAACGAACGACCT 60.319 55.000 0.00 0.00 41.05 3.85
4199 5660 3.242518 CTCAACAACATCAGCAGCAATG 58.757 45.455 0.00 0.24 0.00 2.82
4212 5673 0.181350 AGCAATGCTACTACCAGCCC 59.819 55.000 5.69 0.00 41.04 5.19
4243 5731 1.004044 AGCAGCAGCAGTATTTCCAGT 59.996 47.619 3.17 0.00 45.49 4.00
4281 5775 0.622665 AGTATTTCCAGCAGCAGCCT 59.377 50.000 0.00 0.00 43.56 4.58
4352 5846 3.035363 TCACTGACCTTGTAACACTGGA 58.965 45.455 0.00 0.00 0.00 3.86
4360 5854 3.265791 CTTGTAACACTGGATGCTCCTC 58.734 50.000 4.21 0.00 37.46 3.71
4379 5873 5.606505 TCCTCCAAAACAAGGCAATTTAAC 58.393 37.500 0.00 0.00 32.37 2.01
4407 5901 0.968393 GAATTGCCCGGCCCTGTTTA 60.968 55.000 7.03 0.00 0.00 2.01
4525 6026 5.964758 TGACCTTTGCAATATCCACATTTC 58.035 37.500 0.00 0.00 0.00 2.17
4526 6027 5.479724 TGACCTTTGCAATATCCACATTTCA 59.520 36.000 0.00 0.00 0.00 2.69
4528 6029 6.767456 ACCTTTGCAATATCCACATTTCAAA 58.233 32.000 0.00 0.00 32.57 2.69
4556 6059 8.633075 AACATGACAAGTACAACTTCATTTTG 57.367 30.769 0.00 0.00 36.03 2.44
4688 6350 1.691434 TGTGTCCAAAAAGAATGGGCC 59.309 47.619 0.00 0.00 42.00 5.80
4777 6451 9.449719 GAAATACAAGAATGAGAGGAAAAGGTA 57.550 33.333 0.00 0.00 0.00 3.08
4949 6626 5.221422 CCCTGGATCTCTGTTAAGAAGCTAG 60.221 48.000 0.00 0.00 30.03 3.42
5343 7020 5.373854 AGGATTAGTGAGGCATAAGGGAAAT 59.626 40.000 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 0.972134 TTCAGGTGCAGTCAGAGAGG 59.028 55.000 0.00 0.00 0.00 3.69
74 75 1.227999 GCAGTTAGTGGCAGCGTTCA 61.228 55.000 0.00 0.00 0.00 3.18
128 141 2.032681 AGGTTGGCTTCGGCTGTC 59.967 61.111 0.00 0.00 41.44 3.51
180 193 2.254152 TTGGTATCAGAGGCCAGTCT 57.746 50.000 5.01 0.00 33.41 3.24
275 1000 7.620397 GCTAATGCAATGAAAATTCTAGCTC 57.380 36.000 0.00 0.00 39.41 4.09
299 1025 2.866762 GCGTGCTATCTACTTTCCCTTG 59.133 50.000 0.00 0.00 0.00 3.61
352 1078 2.905075 TCCATTCGAGGCATGTACAAG 58.095 47.619 0.00 0.00 0.00 3.16
421 1150 1.603678 CCATGTGCGCTTTGCTTTCTT 60.604 47.619 9.73 0.00 46.63 2.52
513 1244 0.673644 AACGGTTCGCTGGAATGGAG 60.674 55.000 0.00 0.00 34.05 3.86
536 1267 0.899720 TCGTAGGGCCACCAAGTAAG 59.100 55.000 6.18 0.00 40.13 2.34
539 1270 0.907704 TCATCGTAGGGCCACCAAGT 60.908 55.000 6.18 0.00 40.13 3.16
547 1278 0.032130 TTCATCGCTCATCGTAGGGC 59.968 55.000 0.00 0.00 39.67 5.19
577 1308 0.951040 GTTTCAGCGTGCCTGCTACT 60.951 55.000 0.00 0.00 45.23 2.57
581 1312 2.253452 CTGTTTCAGCGTGCCTGC 59.747 61.111 0.00 0.00 41.50 4.85
583 1314 2.281761 CCCTGTTTCAGCGTGCCT 60.282 61.111 0.00 0.00 0.00 4.75
629 1360 1.636570 GAAGAAGAAGAACCGCCCGC 61.637 60.000 0.00 0.00 0.00 6.13
636 1367 4.757657 GGAAGGACCAAGAAGAAGAAGAAC 59.242 45.833 0.00 0.00 38.79 3.01
657 1391 0.684535 TCTGTCCAGAAACGCATGGA 59.315 50.000 0.00 0.00 43.34 3.41
660 1394 0.322975 AGCTCTGTCCAGAAACGCAT 59.677 50.000 8.98 0.00 36.94 4.73
729 1467 2.170397 AGCACGATGAGAGAGAGAGAGA 59.830 50.000 0.00 0.00 0.00 3.10
730 1468 2.545526 GAGCACGATGAGAGAGAGAGAG 59.454 54.545 0.00 0.00 0.00 3.20
731 1469 2.093235 TGAGCACGATGAGAGAGAGAGA 60.093 50.000 0.00 0.00 0.00 3.10
732 1470 2.287769 TGAGCACGATGAGAGAGAGAG 58.712 52.381 0.00 0.00 0.00 3.20
733 1471 2.409948 TGAGCACGATGAGAGAGAGA 57.590 50.000 0.00 0.00 0.00 3.10
734 1472 3.500558 TTTGAGCACGATGAGAGAGAG 57.499 47.619 0.00 0.00 0.00 3.20
831 1569 1.713597 GCGCTAATTTTGGCAAAGCT 58.286 45.000 16.92 9.76 33.91 3.74
1086 1846 1.818060 GTAATGCATTGGTGGCAGTGA 59.182 47.619 22.27 0.00 45.68 3.41
1090 1850 1.510383 GCGTAATGCATTGGTGGCA 59.490 52.632 22.27 0.00 46.66 4.92
1091 1851 4.400410 GCGTAATGCATTGGTGGC 57.600 55.556 22.27 14.64 45.45 5.01
1110 1870 1.110518 ATGAATCGCCCATGCATGCA 61.111 50.000 25.04 25.04 37.32 3.96
1116 1876 0.593008 CGCACAATGAATCGCCCATG 60.593 55.000 0.00 0.00 0.00 3.66
1122 1882 2.830772 ATTGACCGCACAATGAATCG 57.169 45.000 4.88 0.00 38.76 3.34
1123 1883 4.737054 AGAAATTGACCGCACAATGAATC 58.263 39.130 6.17 6.02 39.88 2.52
1128 1888 2.513753 TGGAGAAATTGACCGCACAAT 58.486 42.857 0.00 0.00 41.43 2.71
1136 1898 7.642978 CGATTGATTGAGAATGGAGAAATTGAC 59.357 37.037 0.00 0.00 0.00 3.18
1138 1900 6.417044 GCGATTGATTGAGAATGGAGAAATTG 59.583 38.462 0.00 0.00 0.00 2.32
1147 1909 2.601504 CGCTGGCGATTGATTGAGAATG 60.602 50.000 9.51 0.00 42.83 2.67
1148 1910 1.600957 CGCTGGCGATTGATTGAGAAT 59.399 47.619 9.51 0.00 42.83 2.40
1152 1914 4.930592 TCGCTGGCGATTGATTGA 57.069 50.000 13.78 0.00 44.01 2.57
1168 1930 4.381566 AGATTGTAATTTTGCGTTGCGTTC 59.618 37.500 0.00 0.00 0.00 3.95
1170 1932 3.896122 AGATTGTAATTTTGCGTTGCGT 58.104 36.364 0.00 0.00 0.00 5.24
1171 1933 4.028509 GCTAGATTGTAATTTTGCGTTGCG 60.029 41.667 0.00 0.00 0.00 4.85
1172 1934 5.095490 AGCTAGATTGTAATTTTGCGTTGC 58.905 37.500 0.00 0.00 0.00 4.17
1173 1935 7.439490 CAAAGCTAGATTGTAATTTTGCGTTG 58.561 34.615 12.28 12.28 35.83 4.10
1174 1936 6.089417 GCAAAGCTAGATTGTAATTTTGCGTT 59.911 34.615 0.00 3.66 39.34 4.84
1175 1937 5.572896 GCAAAGCTAGATTGTAATTTTGCGT 59.427 36.000 0.00 0.00 39.34 5.24
1176 1938 6.012962 GCAAAGCTAGATTGTAATTTTGCG 57.987 37.500 0.00 0.00 39.34 4.85
1177 1939 7.412237 CCAAGCAAAGCTAGATTGTAATTTTGC 60.412 37.037 13.78 10.14 45.43 3.68
1178 1940 7.063780 CCCAAGCAAAGCTAGATTGTAATTTTG 59.936 37.037 13.78 0.25 38.25 2.44
1179 1941 7.099120 CCCAAGCAAAGCTAGATTGTAATTTT 58.901 34.615 13.78 0.00 38.25 1.82
1180 1942 6.351286 CCCCAAGCAAAGCTAGATTGTAATTT 60.351 38.462 13.78 0.00 38.25 1.82
1181 1943 5.127682 CCCCAAGCAAAGCTAGATTGTAATT 59.872 40.000 13.78 0.00 38.25 1.40
1182 1944 4.646492 CCCCAAGCAAAGCTAGATTGTAAT 59.354 41.667 13.78 0.00 38.25 1.89
1183 1945 4.016444 CCCCAAGCAAAGCTAGATTGTAA 58.984 43.478 13.78 0.00 38.25 2.41
1185 1947 2.450476 CCCCAAGCAAAGCTAGATTGT 58.550 47.619 13.78 0.00 38.25 2.71
1188 1950 1.002857 ACCCCCAAGCAAAGCTAGAT 58.997 50.000 0.00 0.00 38.25 1.98
1189 1951 0.777446 AACCCCCAAGCAAAGCTAGA 59.223 50.000 0.00 0.00 38.25 2.43
1190 1952 0.890683 CAACCCCCAAGCAAAGCTAG 59.109 55.000 0.00 0.00 38.25 3.42
1191 1953 0.541764 CCAACCCCCAAGCAAAGCTA 60.542 55.000 0.00 0.00 38.25 3.32
1192 1954 1.838396 CCAACCCCCAAGCAAAGCT 60.838 57.895 0.00 0.00 42.56 3.74
1193 1955 2.743060 CCAACCCCCAAGCAAAGC 59.257 61.111 0.00 0.00 0.00 3.51
1194 1956 1.459348 ACCCAACCCCCAAGCAAAG 60.459 57.895 0.00 0.00 0.00 2.77
1195 1957 1.764054 CACCCAACCCCCAAGCAAA 60.764 57.895 0.00 0.00 0.00 3.68
1196 1958 2.123077 CACCCAACCCCCAAGCAA 60.123 61.111 0.00 0.00 0.00 3.91
1197 1959 4.232061 CCACCCAACCCCCAAGCA 62.232 66.667 0.00 0.00 0.00 3.91
1199 1961 2.613576 AAACCCACCCAACCCCCAAG 62.614 60.000 0.00 0.00 0.00 3.61
1201 1963 3.036959 AAACCCACCCAACCCCCA 61.037 61.111 0.00 0.00 0.00 4.96
1202 1964 2.525629 CAAACCCACCCAACCCCC 60.526 66.667 0.00 0.00 0.00 5.40
1203 1965 1.835267 GTCAAACCCACCCAACCCC 60.835 63.158 0.00 0.00 0.00 4.95
1204 1966 1.075896 TGTCAAACCCACCCAACCC 60.076 57.895 0.00 0.00 0.00 4.11
1205 1967 1.112916 CCTGTCAAACCCACCCAACC 61.113 60.000 0.00 0.00 0.00 3.77
1206 1968 0.106419 TCCTGTCAAACCCACCCAAC 60.106 55.000 0.00 0.00 0.00 3.77
1207 1969 0.856982 ATCCTGTCAAACCCACCCAA 59.143 50.000 0.00 0.00 0.00 4.12
1208 1970 0.856982 AATCCTGTCAAACCCACCCA 59.143 50.000 0.00 0.00 0.00 4.51
1209 1971 1.618343 CAAATCCTGTCAAACCCACCC 59.382 52.381 0.00 0.00 0.00 4.61
1210 1972 1.618343 CCAAATCCTGTCAAACCCACC 59.382 52.381 0.00 0.00 0.00 4.61
1211 1973 2.593026 TCCAAATCCTGTCAAACCCAC 58.407 47.619 0.00 0.00 0.00 4.61
1302 2064 1.517242 GCCATGAAAGAGCGGATAGG 58.483 55.000 0.00 0.00 0.00 2.57
1304 2066 1.131638 AGGCCATGAAAGAGCGGATA 58.868 50.000 5.01 0.00 0.00 2.59
1319 2081 3.007614 TCGTCCCTATAATTTGCTAGGCC 59.992 47.826 0.00 0.00 34.36 5.19
1326 2088 8.894768 AGAAGAGAAATCGTCCCTATAATTTG 57.105 34.615 0.00 0.00 0.00 2.32
1332 2094 6.800072 AAAGAGAAGAGAAATCGTCCCTAT 57.200 37.500 0.00 0.00 0.00 2.57
1333 2095 6.607004 AAAAGAGAAGAGAAATCGTCCCTA 57.393 37.500 0.00 0.00 0.00 3.53
1334 2096 5.491323 AAAAGAGAAGAGAAATCGTCCCT 57.509 39.130 0.00 0.00 0.00 4.20
1357 2119 4.269844 GCCATGCAAAAGAAGAAACGAAAA 59.730 37.500 0.00 0.00 0.00 2.29
1358 2120 3.801594 GCCATGCAAAAGAAGAAACGAAA 59.198 39.130 0.00 0.00 0.00 3.46
1359 2121 3.068024 AGCCATGCAAAAGAAGAAACGAA 59.932 39.130 0.00 0.00 0.00 3.85
1360 2122 2.622942 AGCCATGCAAAAGAAGAAACGA 59.377 40.909 0.00 0.00 0.00 3.85
1362 2124 2.982470 CGAGCCATGCAAAAGAAGAAAC 59.018 45.455 0.00 0.00 0.00 2.78
1363 2125 2.622942 ACGAGCCATGCAAAAGAAGAAA 59.377 40.909 0.00 0.00 0.00 2.52
1364 2126 2.226437 GACGAGCCATGCAAAAGAAGAA 59.774 45.455 0.00 0.00 0.00 2.52
1365 2127 1.806542 GACGAGCCATGCAAAAGAAGA 59.193 47.619 0.00 0.00 0.00 2.87
1366 2128 1.536766 TGACGAGCCATGCAAAAGAAG 59.463 47.619 0.00 0.00 0.00 2.85
1367 2129 1.536766 CTGACGAGCCATGCAAAAGAA 59.463 47.619 0.00 0.00 0.00 2.52
1368 2130 1.159285 CTGACGAGCCATGCAAAAGA 58.841 50.000 0.00 0.00 0.00 2.52
1376 2543 2.288091 CGAGATGAATCTGACGAGCCAT 60.288 50.000 0.00 0.00 37.25 4.40
1377 2544 1.066152 CGAGATGAATCTGACGAGCCA 59.934 52.381 0.00 0.00 37.25 4.75
1383 2550 5.005203 CACAAGCTTACGAGATGAATCTGAC 59.995 44.000 0.00 0.00 37.25 3.51
1388 2555 6.237942 CGAAATCACAAGCTTACGAGATGAAT 60.238 38.462 0.00 0.00 0.00 2.57
1396 2563 2.407361 ACGACGAAATCACAAGCTTACG 59.593 45.455 0.00 0.00 0.00 3.18
1407 2574 1.654105 ACAATGCGAGACGACGAAATC 59.346 47.619 0.00 0.00 35.09 2.17
1500 2849 2.550830 TTGTCTTGGACAGCCTTCTC 57.449 50.000 0.72 0.00 43.69 2.87
1558 2907 3.947834 GAGTGTTTATGGAACCCATGGAG 59.052 47.826 15.22 5.95 44.84 3.86
1559 2908 3.591527 AGAGTGTTTATGGAACCCATGGA 59.408 43.478 15.22 0.00 44.84 3.41
1560 2909 3.968265 AGAGTGTTTATGGAACCCATGG 58.032 45.455 4.14 4.14 44.84 3.66
1561 2910 8.924511 ATATAAGAGTGTTTATGGAACCCATG 57.075 34.615 8.64 0.00 44.84 3.66
1573 2922 7.993183 CCTGTGTCCCATAATATAAGAGTGTTT 59.007 37.037 0.00 0.00 0.00 2.83
1574 2923 7.347222 TCCTGTGTCCCATAATATAAGAGTGTT 59.653 37.037 0.00 0.00 0.00 3.32
1575 2924 6.844388 TCCTGTGTCCCATAATATAAGAGTGT 59.156 38.462 0.00 0.00 0.00 3.55
1576 2925 7.015682 ACTCCTGTGTCCCATAATATAAGAGTG 59.984 40.741 0.00 0.00 0.00 3.51
1577 2926 7.076446 ACTCCTGTGTCCCATAATATAAGAGT 58.924 38.462 0.00 0.00 0.00 3.24
1578 2927 7.546250 ACTCCTGTGTCCCATAATATAAGAG 57.454 40.000 0.00 0.00 0.00 2.85
1579 2928 9.256228 GATACTCCTGTGTCCCATAATATAAGA 57.744 37.037 0.00 0.00 0.00 2.10
1580 2929 9.035890 TGATACTCCTGTGTCCCATAATATAAG 57.964 37.037 0.00 0.00 34.04 1.73
1581 2930 8.966155 TGATACTCCTGTGTCCCATAATATAA 57.034 34.615 0.00 0.00 34.04 0.98
1582 2931 8.966155 TTGATACTCCTGTGTCCCATAATATA 57.034 34.615 0.00 0.00 34.04 0.86
1583 2932 7.872061 TTGATACTCCTGTGTCCCATAATAT 57.128 36.000 0.00 0.00 34.04 1.28
1584 2933 7.872061 ATTGATACTCCTGTGTCCCATAATA 57.128 36.000 0.00 0.00 34.04 0.98
1585 2934 6.770286 ATTGATACTCCTGTGTCCCATAAT 57.230 37.500 0.00 0.00 34.04 1.28
1586 2935 6.575244 AATTGATACTCCTGTGTCCCATAA 57.425 37.500 0.00 0.00 34.04 1.90
1587 2936 6.575244 AAATTGATACTCCTGTGTCCCATA 57.425 37.500 0.00 0.00 34.04 2.74
1588 2937 5.456921 AAATTGATACTCCTGTGTCCCAT 57.543 39.130 0.00 0.00 34.04 4.00
1589 2938 4.927267 AAATTGATACTCCTGTGTCCCA 57.073 40.909 0.00 0.00 34.04 4.37
1590 2939 5.501156 AGAAAATTGATACTCCTGTGTCCC 58.499 41.667 0.00 0.00 34.04 4.46
1591 2940 6.173339 TGAGAAAATTGATACTCCTGTGTCC 58.827 40.000 0.00 0.00 34.04 4.02
1592 2941 7.011857 GGATGAGAAAATTGATACTCCTGTGTC 59.988 40.741 0.00 0.00 35.29 3.67
1593 2942 6.825721 GGATGAGAAAATTGATACTCCTGTGT 59.174 38.462 0.00 0.00 0.00 3.72
1594 2943 7.052873 AGGATGAGAAAATTGATACTCCTGTG 58.947 38.462 0.00 0.00 0.00 3.66
1595 2944 7.205515 AGGATGAGAAAATTGATACTCCTGT 57.794 36.000 0.00 0.00 0.00 4.00
1596 2945 6.709846 GGAGGATGAGAAAATTGATACTCCTG 59.290 42.308 0.00 0.00 38.15 3.86
1597 2946 6.388100 TGGAGGATGAGAAAATTGATACTCCT 59.612 38.462 9.90 0.00 40.94 3.69
1598 2947 6.484977 GTGGAGGATGAGAAAATTGATACTCC 59.515 42.308 0.00 0.00 40.78 3.85
1599 2948 7.278875 AGTGGAGGATGAGAAAATTGATACTC 58.721 38.462 0.00 0.00 0.00 2.59
1600 2949 7.092712 TGAGTGGAGGATGAGAAAATTGATACT 60.093 37.037 0.00 0.00 0.00 2.12
1601 2950 7.050377 TGAGTGGAGGATGAGAAAATTGATAC 58.950 38.462 0.00 0.00 0.00 2.24
1602 2951 7.199167 TGAGTGGAGGATGAGAAAATTGATA 57.801 36.000 0.00 0.00 0.00 2.15
1603 2952 6.070951 TGAGTGGAGGATGAGAAAATTGAT 57.929 37.500 0.00 0.00 0.00 2.57
1611 2960 3.717576 AGAACATGAGTGGAGGATGAGA 58.282 45.455 0.00 0.00 0.00 3.27
1618 2967 6.531503 TTCTAACCTAGAACATGAGTGGAG 57.468 41.667 0.00 0.00 39.73 3.86
1655 3011 5.619981 GCAGTAGTTAATGTGCTGAAAAGGG 60.620 44.000 9.23 0.00 32.97 3.95
1712 3071 6.100004 CCTGTGTATCACTATCAACGTCTTT 58.900 40.000 0.00 0.00 35.11 2.52
1740 3099 0.315568 GTAGGATCGCCTTCTCGCAT 59.684 55.000 0.00 0.00 43.90 4.73
1923 3285 1.606885 AATGCCATTGCCTTCGGGTG 61.607 55.000 0.00 0.00 37.45 4.61
1940 3302 5.594926 GATCAAGAATCGGGAAATGCAAAT 58.405 37.500 0.00 0.00 0.00 2.32
1941 3303 4.997565 GATCAAGAATCGGGAAATGCAAA 58.002 39.130 0.00 0.00 0.00 3.68
1942 3304 4.637483 GATCAAGAATCGGGAAATGCAA 57.363 40.909 0.00 0.00 0.00 4.08
1965 3327 2.092968 TCAGTTGAGGCGCCATTTCTAT 60.093 45.455 31.54 5.22 0.00 1.98
2052 3414 0.832135 ACTCAAGCCGTTCCTCCAGA 60.832 55.000 0.00 0.00 0.00 3.86
2067 3429 8.255206 TCGTATTTTAGATTCCTAAAGCACTCA 58.745 33.333 0.00 0.00 43.43 3.41
2111 3473 0.975135 ATGCTGGGGAGATCTCATCG 59.025 55.000 23.85 10.04 0.00 3.84
2138 3500 4.142093 GCGTAAAAGACATAGTCCCTACCA 60.142 45.833 0.00 0.00 32.18 3.25
2166 3528 2.162319 AAACAAAATTTCGCCGCCAT 57.838 40.000 0.00 0.00 0.00 4.40
2257 3619 3.204306 TGCTCCATAAGATCAAGGCAG 57.796 47.619 0.00 0.00 0.00 4.85
2346 3708 4.689612 AAACAGTTCTCAGAGCCAGTAA 57.310 40.909 0.00 0.00 0.00 2.24
2423 3785 7.693969 AGGCTAATGCATATTGAATAAGGTC 57.306 36.000 0.00 0.00 41.91 3.85
2519 3881 4.380531 CAACACACCGCCATAAGATATCT 58.619 43.478 0.00 0.00 0.00 1.98
2664 4040 8.202461 TCCGGAAATCTATGGTTATACTTCAT 57.798 34.615 0.00 0.00 0.00 2.57
2665 4041 7.606135 TCCGGAAATCTATGGTTATACTTCA 57.394 36.000 0.00 0.00 0.00 3.02
2666 4042 8.532819 AGATCCGGAAATCTATGGTTATACTTC 58.467 37.037 9.01 0.00 34.21 3.01
2714 4090 1.541015 GCATCATACCTCGGCATGTCA 60.541 52.381 0.00 0.00 0.00 3.58
2804 4180 8.457261 AGCTAGAATTCAAAGCAATAACAGAAG 58.543 33.333 25.67 0.00 38.75 2.85
2805 4181 8.340618 AGCTAGAATTCAAAGCAATAACAGAA 57.659 30.769 25.67 0.00 38.75 3.02
2982 4395 3.941483 AGTCATTTAGCCTTCCATCGTTG 59.059 43.478 0.00 0.00 0.00 4.10
3053 4466 1.562475 GGGGGTGGCTGTAGAACATTA 59.438 52.381 0.00 0.00 0.00 1.90
3114 4527 1.003839 TCCTGATTGTGGGACGTGC 60.004 57.895 0.00 0.00 0.00 5.34
3253 4669 1.065126 GTTGGAGCTTCCTGGCTGTAT 60.065 52.381 0.00 0.00 43.20 2.29
3363 4779 0.961019 TTCCATTGCCAGCAGTTGTC 59.039 50.000 0.00 0.00 0.00 3.18
3425 4841 2.686915 GAGATGAACAGAAATGGGCTGG 59.313 50.000 0.00 0.00 37.69 4.85
3591 5008 4.653341 AGAGTTTGACAGGAGAGGGATATG 59.347 45.833 0.00 0.00 0.00 1.78
3716 5138 7.014038 AGACCAAAAAGAATATCTGATGATGCC 59.986 37.037 0.00 0.00 34.32 4.40
3718 5140 9.339850 AGAGACCAAAAAGAATATCTGATGATG 57.660 33.333 0.00 0.00 34.32 3.07
3729 5151 5.416952 CCTACATGCAGAGACCAAAAAGAAT 59.583 40.000 0.00 0.00 0.00 2.40
3747 5169 3.054139 TGCTTTGCTTCCATCTCCTACAT 60.054 43.478 0.00 0.00 0.00 2.29
3782 5204 1.824230 TGTGCTGCCAGAAAACAAGTT 59.176 42.857 0.00 0.00 0.00 2.66
3843 5265 0.251297 CTCCATTGGTTGGCTGGTGA 60.251 55.000 1.86 0.00 46.01 4.02
4005 5466 1.402259 CTCCTCGCACTGTCTTCGTAT 59.598 52.381 0.00 0.00 0.00 3.06
4015 5476 4.079850 CTGCTGCCTCCTCGCACT 62.080 66.667 0.00 0.00 34.35 4.40
4017 5478 3.079478 ATCTGCTGCCTCCTCGCA 61.079 61.111 0.00 0.00 37.19 5.10
4036 5497 1.079405 CATTGTAGGTCACGCGGGT 60.079 57.895 8.89 0.00 0.00 5.28
4039 5500 1.695893 CTGCCATTGTAGGTCACGCG 61.696 60.000 3.53 3.53 0.00 6.01
4053 5514 2.598394 GCTTGTCCAAGGCTGCCA 60.598 61.111 22.65 0.00 38.80 4.92
4097 5558 2.722094 AGCTGTTGGATATGGCGAAAA 58.278 42.857 0.00 0.00 0.00 2.29
4107 5568 2.981560 CGGCGCAAAGCTGTTGGAT 61.982 57.895 10.83 0.00 46.91 3.41
4199 5660 2.506472 GCTGGGGCTGGTAGTAGC 59.494 66.667 0.00 0.00 42.94 3.58
4224 5712 1.399791 GACTGGAAATACTGCTGCTGC 59.600 52.381 8.89 8.89 40.20 5.25
4243 5731 1.078637 GGTGCTGATGCTGCTGAGA 60.079 57.895 0.00 0.00 40.48 3.27
4281 5775 2.011548 GCCGGATGCACACAATACTGA 61.012 52.381 5.05 0.00 40.77 3.41
4352 5846 1.260544 GCCTTGTTTTGGAGGAGCAT 58.739 50.000 0.00 0.00 34.91 3.79
4360 5854 5.970612 GCAAAGTTAAATTGCCTTGTTTTGG 59.029 36.000 13.62 0.00 45.73 3.28
4379 5873 0.171903 CCGGGCAATTCAGAGCAAAG 59.828 55.000 0.00 0.00 0.00 2.77
4407 5901 8.976353 GTACCCATCTATATTGACTGAGATCAT 58.024 37.037 0.00 0.00 0.00 2.45
4525 6026 7.540400 TGAAGTTGTACTTGTCATGTTTGTTTG 59.460 33.333 0.00 0.00 38.80 2.93
4526 6027 7.598278 TGAAGTTGTACTTGTCATGTTTGTTT 58.402 30.769 0.00 0.00 38.80 2.83
4528 6029 6.751514 TGAAGTTGTACTTGTCATGTTTGT 57.248 33.333 0.00 0.00 38.80 2.83
4571 6074 8.887264 TTTTTACTCTGCTGGGGAAATATTTA 57.113 30.769 1.14 0.00 0.00 1.40
4572 6075 7.790782 TTTTTACTCTGCTGGGGAAATATTT 57.209 32.000 1.14 0.00 0.00 1.40
4688 6350 1.399089 ACAGGGTTTTTGTCACGTTCG 59.601 47.619 0.00 0.00 0.00 3.95
4777 6451 6.449698 CATGTTTCTGTTAGCTGTCCATTTT 58.550 36.000 0.00 0.00 0.00 1.82
5242 6919 6.127814 GCAGTCATTCTGAAGAATTCCATTCA 60.128 38.462 0.65 5.93 46.93 2.57


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

AutoCloner maintained by Alex Coulton.