Multiple sequence alignment - TraesCS5B01G385400

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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 TraesCS5B01G385400 chr5B 100.000 2773 0 0 1 2773 565095564 565098336 0.000000e+00 5121.0
1 TraesCS5B01G385400 chr5B 87.805 328 17 6 2462 2771 565152764 565153086 2.030000e-96 363.0
2 TraesCS5B01G385400 chr5B 91.011 178 10 2 2290 2467 565152466 565152637 4.620000e-58 235.0
3 TraesCS5B01G385400 chr5A 86.224 980 75 29 976 1950 579410252 579409328 0.000000e+00 1007.0
4 TraesCS5B01G385400 chr5A 90.857 350 21 6 628 976 579410631 579410292 2.520000e-125 459.0
5 TraesCS5B01G385400 chr5A 83.857 446 21 19 209 631 579411091 579410674 7.250000e-101 377.0
6 TraesCS5B01G385400 chr5A 82.474 97 11 6 2153 2246 694880897 694880990 2.290000e-11 80.5
7 TraesCS5B01G385400 chr5A 94.737 38 2 0 2030 2067 579408853 579408816 2.980000e-05 60.2
8 TraesCS5B01G385400 chr5D 88.173 854 47 12 994 1818 459926608 459927436 0.000000e+00 968.0
9 TraesCS5B01G385400 chr5D 87.730 652 40 19 218 851 459925502 459926131 0.000000e+00 725.0
10 TraesCS5B01G385400 chr5D 88.517 209 15 4 2564 2771 459929843 459930043 7.670000e-61 244.0
11 TraesCS5B01G385400 chr5D 83.333 96 14 2 2153 2246 219299956 219300051 1.370000e-13 87.9
12 TraesCS5B01G385400 chr4A 85.605 653 48 23 76 699 563452149 563451514 0.000000e+00 643.0
13 TraesCS5B01G385400 chr7D 84.536 97 10 5 2153 2246 274468124 274468218 1.060000e-14 91.6
14 TraesCS5B01G385400 chr1D 84.783 92 10 4 2153 2242 47526652 47526563 3.800000e-14 89.8
15 TraesCS5B01G385400 chr6D 85.393 89 8 5 2161 2246 145278104 145278190 1.370000e-13 87.9
16 TraesCS5B01G385400 chr6D 83.505 97 11 5 2153 2246 377642891 377642985 4.920000e-13 86.1
17 TraesCS5B01G385400 chr6D 84.270 89 10 4 2153 2239 283850906 283850992 1.770000e-12 84.2
18 TraesCS5B01G385400 chr3D 83.871 93 10 5 2153 2242 41968665 41968575 1.770000e-12 84.2
19 TraesCS5B01G385400 chr2D 81.443 97 12 5 2153 2246 299052740 299052647 1.070000e-09 75.0


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 TraesCS5B01G385400 chr5B 565095564 565098336 2772 False 5121.000000 5121 100.00000 1 2773 1 chr5B.!!$F1 2772
1 TraesCS5B01G385400 chr5B 565152466 565153086 620 False 299.000000 363 89.40800 2290 2771 2 chr5B.!!$F2 481
2 TraesCS5B01G385400 chr5A 579408816 579411091 2275 True 475.800000 1007 88.91875 209 2067 4 chr5A.!!$R1 1858
3 TraesCS5B01G385400 chr5D 459925502 459930043 4541 False 645.666667 968 88.14000 218 2771 3 chr5D.!!$F2 2553
4 TraesCS5B01G385400 chr4A 563451514 563452149 635 True 643.000000 643 85.60500 76 699 1 chr4A.!!$R1 623

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
55 56 0.179192 ACGCGAACGATAAGCACGTA 60.179 50.0 15.93 0.0 43.16 3.57 F
56 57 0.223022 CGCGAACGATAAGCACGTAC 59.777 55.0 0.00 0.0 43.16 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1334 1828 0.455633 CGCGGGTGTATATACCTCGC 60.456 60.0 28.29 28.29 46.94 5.03 R
1804 2329 0.878961 GTTCGCGTCCTGAACCAAGT 60.879 55.0 5.77 0.00 39.80 3.16 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
21 22 1.819903 AGAAGAGGAGACCTTGTACGC 59.180 52.381 0.00 0.00 31.76 4.42
22 23 0.896226 AAGAGGAGACCTTGTACGCC 59.104 55.000 0.00 0.00 31.76 5.68
23 24 1.139095 GAGGAGACCTTGTACGCCG 59.861 63.158 0.00 0.00 31.76 6.46
24 25 1.303888 AGGAGACCTTGTACGCCGA 60.304 57.895 0.00 0.00 0.00 5.54
25 26 1.139095 GGAGACCTTGTACGCCGAG 59.861 63.158 0.00 0.00 0.00 4.63
26 27 1.593296 GGAGACCTTGTACGCCGAGT 61.593 60.000 0.00 0.00 0.00 4.18
27 28 1.089920 GAGACCTTGTACGCCGAGTA 58.910 55.000 0.00 0.00 0.00 2.59
38 39 1.329906 ACGCCGAGTACAAGATAGACG 59.670 52.381 0.00 0.00 0.00 4.18
39 40 1.756367 GCCGAGTACAAGATAGACGC 58.244 55.000 0.00 0.00 0.00 5.19
40 41 1.920705 GCCGAGTACAAGATAGACGCG 60.921 57.143 3.53 3.53 36.35 6.01
41 42 1.596260 CCGAGTACAAGATAGACGCGA 59.404 52.381 15.93 0.00 38.45 5.87
42 43 2.031314 CCGAGTACAAGATAGACGCGAA 59.969 50.000 15.93 0.00 38.45 4.70
43 44 3.027710 CGAGTACAAGATAGACGCGAAC 58.972 50.000 15.93 6.52 38.45 3.95
45 46 2.674852 AGTACAAGATAGACGCGAACGA 59.325 45.455 15.93 2.88 43.93 3.85
46 47 2.846039 ACAAGATAGACGCGAACGAT 57.154 45.000 15.93 8.29 43.93 3.73
47 48 3.957671 ACAAGATAGACGCGAACGATA 57.042 42.857 15.93 0.00 43.93 2.92
48 49 4.282950 ACAAGATAGACGCGAACGATAA 57.717 40.909 15.93 0.00 43.93 1.75
49 50 4.280461 ACAAGATAGACGCGAACGATAAG 58.720 43.478 15.93 0.00 43.93 1.73
50 51 2.918616 AGATAGACGCGAACGATAAGC 58.081 47.619 15.93 0.00 43.93 3.09
51 52 2.289820 AGATAGACGCGAACGATAAGCA 59.710 45.455 15.93 0.00 43.93 3.91
52 53 1.818850 TAGACGCGAACGATAAGCAC 58.181 50.000 15.93 0.00 43.93 4.40
53 54 1.132199 AGACGCGAACGATAAGCACG 61.132 55.000 15.93 0.00 43.93 5.34
54 55 1.400990 GACGCGAACGATAAGCACGT 61.401 55.000 15.93 0.00 45.89 4.49
55 56 0.179192 ACGCGAACGATAAGCACGTA 60.179 50.000 15.93 0.00 43.16 3.57
56 57 0.223022 CGCGAACGATAAGCACGTAC 59.777 55.000 0.00 0.00 43.16 3.67
57 58 1.261989 GCGAACGATAAGCACGTACA 58.738 50.000 0.00 0.00 43.16 2.90
58 59 1.007729 GCGAACGATAAGCACGTACAC 60.008 52.381 0.00 0.00 43.16 2.90
59 60 2.244251 CGAACGATAAGCACGTACACA 58.756 47.619 0.00 0.00 43.16 3.72
60 61 2.026038 CGAACGATAAGCACGTACACAC 59.974 50.000 0.00 0.00 43.16 3.82
96 97 3.758023 CACACACACCATCACCAACATAT 59.242 43.478 0.00 0.00 0.00 1.78
102 103 3.063861 CACCATCACCAACATATGTCACG 59.936 47.826 9.23 2.15 0.00 4.35
114 115 5.685841 ACATATGTCACGCACTTAAACAAC 58.314 37.500 1.41 0.00 0.00 3.32
115 116 5.237561 ACATATGTCACGCACTTAAACAACA 59.762 36.000 1.41 0.00 0.00 3.33
116 117 3.392769 TGTCACGCACTTAAACAACAC 57.607 42.857 0.00 0.00 0.00 3.32
117 118 3.004171 TGTCACGCACTTAAACAACACT 58.996 40.909 0.00 0.00 0.00 3.55
122 123 4.961551 CACGCACTTAAACAACACTTACAG 59.038 41.667 0.00 0.00 0.00 2.74
142 147 6.291648 ACAGAAGATTAAGATCACAGAGCA 57.708 37.500 0.00 0.00 34.60 4.26
143 148 6.339730 ACAGAAGATTAAGATCACAGAGCAG 58.660 40.000 0.00 0.00 34.60 4.24
144 149 5.234757 CAGAAGATTAAGATCACAGAGCAGC 59.765 44.000 0.00 0.00 34.60 5.25
145 150 5.129155 AGAAGATTAAGATCACAGAGCAGCT 59.871 40.000 0.00 0.00 34.60 4.24
147 152 5.743117 AGATTAAGATCACAGAGCAGCTTT 58.257 37.500 0.00 0.00 34.60 3.51
148 153 6.882656 AGATTAAGATCACAGAGCAGCTTTA 58.117 36.000 0.00 0.00 34.60 1.85
149 154 6.760770 AGATTAAGATCACAGAGCAGCTTTAC 59.239 38.462 0.00 0.00 34.60 2.01
150 155 3.969287 AGATCACAGAGCAGCTTTACA 57.031 42.857 0.00 0.00 0.00 2.41
151 156 4.484537 AGATCACAGAGCAGCTTTACAT 57.515 40.909 0.00 0.00 0.00 2.29
174 179 3.711086 GATGAAGTCATCGCAGAAGCTA 58.289 45.455 5.57 0.00 43.58 3.32
175 180 3.156511 TGAAGTCATCGCAGAAGCTAG 57.843 47.619 0.00 0.00 43.58 3.42
176 181 2.493675 TGAAGTCATCGCAGAAGCTAGT 59.506 45.455 0.00 0.00 43.58 2.57
177 182 3.056536 TGAAGTCATCGCAGAAGCTAGTT 60.057 43.478 0.00 0.00 43.58 2.24
187 192 5.124936 TCGCAGAAGCTAGTTCAATACAGTA 59.875 40.000 0.00 0.00 37.67 2.74
206 211 4.500117 CAGTACACACATGTTTGTTGCAAG 59.500 41.667 21.82 9.25 40.48 4.01
211 231 4.567558 CACACATGTTTGTTGCAAGTGAAT 59.432 37.500 16.75 0.00 37.64 2.57
232 254 2.030412 ACGTGCACTGCCGAATCA 59.970 55.556 16.19 0.00 0.00 2.57
290 312 2.424956 CCAAGCCACTTAAGATTGAGCC 59.575 50.000 10.09 0.00 0.00 4.70
330 358 2.336554 TTCAACGTACGCTACTGGAC 57.663 50.000 16.72 0.00 0.00 4.02
462 495 2.822561 TGCTCAAAGTGGTTTGTTCACA 59.177 40.909 0.00 0.00 43.22 3.58
465 498 4.202050 GCTCAAAGTGGTTTGTTCACAGAT 60.202 41.667 0.00 0.00 43.22 2.90
467 500 6.618287 TCAAAGTGGTTTGTTCACAGATAG 57.382 37.500 0.00 0.00 43.22 2.08
495 529 4.622456 GCAACCGTGGCAACCGTG 62.622 66.667 0.00 0.00 0.00 4.94
496 530 3.206246 CAACCGTGGCAACCGTGT 61.206 61.111 0.00 0.00 0.00 4.49
497 531 2.898343 AACCGTGGCAACCGTGTC 60.898 61.111 0.00 0.00 0.00 3.67
663 773 1.050204 TGTTACTGTTACTGGCCGGT 58.950 50.000 23.52 23.52 0.00 5.28
666 776 2.216750 TACTGTTACTGGCCGGTCGC 62.217 60.000 23.73 15.77 0.00 5.19
746 857 2.128035 GATCGTACAGATTCTTGCCGG 58.872 52.381 0.00 0.00 40.26 6.13
806 917 0.802494 CCCATGCAACTCCGTGTAAC 59.198 55.000 0.00 0.00 0.00 2.50
843 954 1.134995 TGCACCGTGATCTGTCATCTC 60.135 52.381 1.65 0.00 36.60 2.75
861 972 1.448189 CTGTGCTCTCAGCCTCAGC 60.448 63.158 5.35 0.00 41.51 4.26
879 990 3.537206 CTTCCCCCATCGATCCGGC 62.537 68.421 0.00 0.00 0.00 6.13
904 1015 4.530857 CATCGACCTCCCACGGCC 62.531 72.222 0.00 0.00 0.00 6.13
931 1042 7.709947 TCGGCATATATAAATTACTACTCCGG 58.290 38.462 0.00 0.00 0.00 5.14
932 1043 6.420008 CGGCATATATAAATTACTACTCCGGC 59.580 42.308 0.00 0.00 0.00 6.13
933 1044 7.270047 GGCATATATAAATTACTACTCCGGCA 58.730 38.462 0.00 0.00 0.00 5.69
951 1062 0.583438 CAGAGTGGTGTGTTTCTGCG 59.417 55.000 0.00 0.00 31.68 5.18
987 1114 2.096248 GTACACACAGAGAGGGAGAGG 58.904 57.143 0.00 0.00 0.00 3.69
1019 1511 1.548269 GATGGATCGGAGGAGGATCAC 59.452 57.143 0.00 0.00 41.62 3.06
1095 1587 8.812513 AATCTGTTCCTCAATTGATTCATGTA 57.187 30.769 8.96 0.00 0.00 2.29
1109 1601 6.842676 TGATTCATGTAGGAGAGTAGCTAGA 58.157 40.000 0.00 0.00 0.00 2.43
1127 1621 4.317980 GCTAGACGATCGAGTAGTGTGTAC 60.318 50.000 24.34 4.35 0.00 2.90
1128 1622 3.859443 AGACGATCGAGTAGTGTGTACT 58.141 45.455 24.34 0.00 40.99 2.73
1129 1623 5.003692 AGACGATCGAGTAGTGTGTACTA 57.996 43.478 24.34 0.00 38.36 1.82
1130 1624 5.042593 AGACGATCGAGTAGTGTGTACTAG 58.957 45.833 24.34 0.00 39.96 2.57
1131 1625 4.118410 ACGATCGAGTAGTGTGTACTAGG 58.882 47.826 24.34 0.00 39.96 3.02
1132 1626 4.118410 CGATCGAGTAGTGTGTACTAGGT 58.882 47.826 10.26 0.00 39.96 3.08
1233 1727 4.493747 GACGAGGCGGAGAACGGG 62.494 72.222 0.00 0.00 44.51 5.28
1329 1823 1.228063 GCAGATGCCGGTCATGGAT 60.228 57.895 14.84 0.46 35.05 3.41
1447 1941 1.302192 GTACGTGTGGGTGTGGCAT 60.302 57.895 0.00 0.00 0.00 4.40
1547 2053 2.915659 AGCGACAACCTCCCGTCA 60.916 61.111 0.00 0.00 32.24 4.35
1634 2144 2.414029 CCACCGGATCAATCGTGTTTTG 60.414 50.000 9.46 0.00 0.00 2.44
1644 2165 2.254546 TCGTGTTTTGCTCCTGATGT 57.745 45.000 0.00 0.00 0.00 3.06
1787 2311 1.779569 CGTAGCCGCCATTAACTAGG 58.220 55.000 0.00 0.00 0.00 3.02
1789 2313 2.607282 CGTAGCCGCCATTAACTAGGAG 60.607 54.545 0.00 0.00 0.00 3.69
1790 2314 1.497161 AGCCGCCATTAACTAGGAGT 58.503 50.000 0.00 0.00 0.00 3.85
1791 2315 2.674420 AGCCGCCATTAACTAGGAGTA 58.326 47.619 0.00 0.00 0.00 2.59
1792 2316 2.364647 AGCCGCCATTAACTAGGAGTAC 59.635 50.000 0.00 0.00 0.00 2.73
1795 2319 3.383825 CCGCCATTAACTAGGAGTACAGT 59.616 47.826 0.00 0.00 0.00 3.55
1800 2325 7.174599 CGCCATTAACTAGGAGTACAGTACTAT 59.825 40.741 13.51 8.02 39.59 2.12
1827 2352 0.669318 GGTTCAGGACGCGAACATGA 60.669 55.000 15.93 16.82 43.70 3.07
1831 2356 0.374758 CAGGACGCGAACATGATTGG 59.625 55.000 15.93 0.00 0.00 3.16
1836 2361 0.098728 CGCGAACATGATTGGTTCCC 59.901 55.000 0.00 0.00 41.16 3.97
1845 2370 1.303309 GATTGGTTCCCGCAGATGAG 58.697 55.000 0.00 0.00 0.00 2.90
1858 2383 0.546267 AGATGAGGAGGCACAGGTGT 60.546 55.000 0.91 0.00 0.00 4.16
1859 2384 0.326264 GATGAGGAGGCACAGGTGTT 59.674 55.000 0.91 0.00 0.00 3.32
1865 2390 1.202818 GGAGGCACAGGTGTTCTTTCT 60.203 52.381 0.91 0.00 0.00 2.52
1870 2395 3.128349 GCACAGGTGTTCTTTCTACGAA 58.872 45.455 0.91 0.00 0.00 3.85
1874 2399 5.175856 CACAGGTGTTCTTTCTACGAAAGAG 59.824 44.000 15.93 8.52 37.54 2.85
1893 2418 1.374252 CACGAGGTGCCACACTACC 60.374 63.158 0.00 0.00 37.23 3.18
1911 2436 3.003173 TCTCCCCTGCTTCCCGTG 61.003 66.667 0.00 0.00 0.00 4.94
1912 2437 4.101448 CTCCCCTGCTTCCCGTGG 62.101 72.222 0.00 0.00 0.00 4.94
1950 2606 9.555727 GTGCTAGTATTAATATTGTTTCCTCCA 57.444 33.333 0.00 0.00 0.00 3.86
1972 2628 7.105588 TCCATGCTTCGCTCATGTAAATATAT 58.894 34.615 0.00 0.00 39.60 0.86
1973 2629 8.257306 TCCATGCTTCGCTCATGTAAATATATA 58.743 33.333 0.00 0.00 39.60 0.86
1974 2630 9.049523 CCATGCTTCGCTCATGTAAATATATAT 57.950 33.333 0.00 0.00 39.60 0.86
1994 2650 8.747538 ATATATATGGATTAGTTTTTCGGGGC 57.252 34.615 0.00 0.00 0.00 5.80
1998 3057 4.798882 TGGATTAGTTTTTCGGGGCATAT 58.201 39.130 0.00 0.00 0.00 1.78
2001 3060 6.834451 TGGATTAGTTTTTCGGGGCATATTTA 59.166 34.615 0.00 0.00 0.00 1.40
2071 3154 7.945134 AGTGAATAATATCATTTGGACTTGCC 58.055 34.615 0.00 0.00 37.10 4.52
2081 3164 0.881118 TGGACTTGCCAAATCGAAGC 59.119 50.000 0.00 0.00 45.87 3.86
2083 3166 1.168714 GACTTGCCAAATCGAAGCCT 58.831 50.000 0.00 0.00 0.00 4.58
2085 3168 2.747446 GACTTGCCAAATCGAAGCCTTA 59.253 45.455 0.00 0.00 0.00 2.69
2086 3169 3.356290 ACTTGCCAAATCGAAGCCTTAT 58.644 40.909 0.00 0.00 0.00 1.73
2087 3170 4.523083 ACTTGCCAAATCGAAGCCTTATA 58.477 39.130 0.00 0.00 0.00 0.98
2088 3171 5.133221 ACTTGCCAAATCGAAGCCTTATAT 58.867 37.500 0.00 0.00 0.00 0.86
2089 3172 5.009010 ACTTGCCAAATCGAAGCCTTATATG 59.991 40.000 0.00 0.00 0.00 1.78
2090 3173 4.713553 TGCCAAATCGAAGCCTTATATGA 58.286 39.130 0.00 0.00 0.00 2.15
2092 3175 5.412594 TGCCAAATCGAAGCCTTATATGATC 59.587 40.000 0.00 0.00 0.00 2.92
2093 3176 5.412594 GCCAAATCGAAGCCTTATATGATCA 59.587 40.000 0.00 0.00 0.00 2.92
2094 3177 6.402983 GCCAAATCGAAGCCTTATATGATCAG 60.403 42.308 0.09 0.00 0.00 2.90
2095 3178 6.402983 CCAAATCGAAGCCTTATATGATCAGC 60.403 42.308 0.09 0.00 0.00 4.26
2096 3179 5.674052 ATCGAAGCCTTATATGATCAGCT 57.326 39.130 0.09 0.00 0.00 4.24
2097 3180 6.782082 ATCGAAGCCTTATATGATCAGCTA 57.218 37.500 0.09 0.00 0.00 3.32
2098 3181 6.201226 TCGAAGCCTTATATGATCAGCTAG 57.799 41.667 0.09 2.07 0.00 3.42
2099 3182 5.712446 TCGAAGCCTTATATGATCAGCTAGT 59.288 40.000 0.09 0.00 0.00 2.57
2100 3183 5.804473 CGAAGCCTTATATGATCAGCTAGTG 59.196 44.000 0.09 0.00 0.00 2.74
2101 3184 5.083533 AGCCTTATATGATCAGCTAGTGC 57.916 43.478 0.09 0.22 40.05 4.40
2102 3185 4.529769 AGCCTTATATGATCAGCTAGTGCA 59.470 41.667 0.09 0.00 42.74 4.57
2111 3222 3.266510 TCAGCTAGTGCACTTATTGGG 57.733 47.619 27.06 10.35 42.74 4.12
2115 3226 2.017049 CTAGTGCACTTATTGGGTGGC 58.983 52.381 27.06 0.00 35.47 5.01
2120 3231 2.230660 GCACTTATTGGGTGGCCTATC 58.769 52.381 3.32 0.00 35.47 2.08
2122 3233 3.688414 GCACTTATTGGGTGGCCTATCTT 60.688 47.826 3.32 0.00 35.47 2.40
2123 3234 4.137543 CACTTATTGGGTGGCCTATCTTC 58.862 47.826 3.32 0.00 0.00 2.87
2125 3236 4.141390 ACTTATTGGGTGGCCTATCTTCTG 60.141 45.833 3.32 0.00 0.00 3.02
2126 3237 1.668826 TTGGGTGGCCTATCTTCTGT 58.331 50.000 3.32 0.00 0.00 3.41
2128 3239 2.116238 TGGGTGGCCTATCTTCTGTAC 58.884 52.381 3.32 0.00 0.00 2.90
2157 3268 8.738645 CCTTGTGGCTTATATATAATTCCCTC 57.261 38.462 15.70 12.57 0.00 4.30
2158 3269 8.552296 CCTTGTGGCTTATATATAATTCCCTCT 58.448 37.037 15.70 0.00 0.00 3.69
2163 3274 9.393786 TGGCTTATATATAATTCCCTCTATCCC 57.606 37.037 15.70 0.00 0.00 3.85
2164 3275 9.393786 GGCTTATATATAATTCCCTCTATCCCA 57.606 37.037 5.64 0.00 0.00 4.37
2176 3287 8.554490 TTCCCTCTATCCCATAATATAAGAGC 57.446 38.462 0.00 0.00 0.00 4.09
2177 3288 7.662083 TCCCTCTATCCCATAATATAAGAGCA 58.338 38.462 0.00 0.00 0.00 4.26
2178 3289 8.299871 TCCCTCTATCCCATAATATAAGAGCAT 58.700 37.037 0.00 0.00 0.00 3.79
2179 3290 9.607333 CCCTCTATCCCATAATATAAGAGCATA 57.393 37.037 0.00 0.00 0.00 3.14
2195 3306 6.992063 AGAGCATATTTTACAGAACACTGG 57.008 37.500 0.00 0.00 36.12 4.00
2196 3307 6.476378 AGAGCATATTTTACAGAACACTGGT 58.524 36.000 0.00 0.00 36.12 4.00
2197 3308 6.372659 AGAGCATATTTTACAGAACACTGGTG 59.627 38.462 0.00 0.00 36.12 4.17
2199 3310 6.149474 AGCATATTTTACAGAACACTGGTGTC 59.851 38.462 6.84 1.84 44.13 3.67
2200 3311 6.534059 CATATTTTACAGAACACTGGTGTCG 58.466 40.000 6.84 2.30 44.13 4.35
2201 3312 3.804786 TTTACAGAACACTGGTGTCGA 57.195 42.857 6.84 0.00 44.13 4.20
2202 3313 3.804786 TTACAGAACACTGGTGTCGAA 57.195 42.857 6.84 0.00 44.13 3.71
2203 3314 2.684001 ACAGAACACTGGTGTCGAAA 57.316 45.000 6.84 0.00 44.13 3.46
2204 3315 2.980568 ACAGAACACTGGTGTCGAAAA 58.019 42.857 6.84 0.00 44.13 2.29
2205 3316 3.541632 ACAGAACACTGGTGTCGAAAAT 58.458 40.909 6.84 0.00 44.13 1.82
2206 3317 4.699637 ACAGAACACTGGTGTCGAAAATA 58.300 39.130 6.84 0.00 44.13 1.40
2207 3318 4.510340 ACAGAACACTGGTGTCGAAAATAC 59.490 41.667 6.84 0.00 44.13 1.89
2208 3319 4.509970 CAGAACACTGGTGTCGAAAATACA 59.490 41.667 6.84 0.00 44.13 2.29
2209 3320 5.179368 CAGAACACTGGTGTCGAAAATACAT 59.821 40.000 6.84 0.00 44.13 2.29
2210 3321 5.763204 AGAACACTGGTGTCGAAAATACATT 59.237 36.000 6.84 0.00 44.13 2.71
2211 3322 6.262273 AGAACACTGGTGTCGAAAATACATTT 59.738 34.615 6.84 0.00 44.13 2.32
2212 3323 7.442969 AGAACACTGGTGTCGAAAATACATTTA 59.557 33.333 6.84 0.00 44.13 1.40
2213 3324 7.681939 ACACTGGTGTCGAAAATACATTTAT 57.318 32.000 0.01 0.00 40.24 1.40
2214 3325 8.780846 ACACTGGTGTCGAAAATACATTTATA 57.219 30.769 0.01 0.00 40.24 0.98
2215 3326 9.391006 ACACTGGTGTCGAAAATACATTTATAT 57.609 29.630 0.01 0.00 40.24 0.86
2230 3341 7.845537 ACATTTATATTATGGGATGGAGGGA 57.154 36.000 0.00 0.00 0.00 4.20
2231 3342 7.876371 ACATTTATATTATGGGATGGAGGGAG 58.124 38.462 0.00 0.00 0.00 4.30
2234 3345 7.989947 TTATATTATGGGATGGAGGGAGTAC 57.010 40.000 0.00 0.00 0.00 2.73
2237 3348 3.943269 ATGGGATGGAGGGAGTACATA 57.057 47.619 0.00 0.00 0.00 2.29
2238 3349 3.717507 TGGGATGGAGGGAGTACATAA 57.282 47.619 0.00 0.00 0.00 1.90
2249 3360 5.805728 AGGGAGTACATAAGAACTTTGTGG 58.194 41.667 0.00 0.00 0.00 4.17
2250 3361 5.309806 AGGGAGTACATAAGAACTTTGTGGT 59.690 40.000 0.00 0.00 0.00 4.16
2251 3362 5.642491 GGGAGTACATAAGAACTTTGTGGTC 59.358 44.000 0.00 0.00 0.00 4.02
2252 3363 5.347907 GGAGTACATAAGAACTTTGTGGTCG 59.652 44.000 0.00 0.00 37.49 4.79
2253 3364 4.689345 AGTACATAAGAACTTTGTGGTCGC 59.311 41.667 0.00 0.00 37.49 5.19
2255 3366 2.228138 TAAGAACTTTGTGGTCGCGT 57.772 45.000 5.77 0.00 37.49 6.01
2256 3367 1.375551 AAGAACTTTGTGGTCGCGTT 58.624 45.000 5.77 0.00 37.49 4.84
2258 3369 1.862827 AGAACTTTGTGGTCGCGTTAC 59.137 47.619 5.77 4.55 37.49 2.50
2259 3370 1.862827 GAACTTTGTGGTCGCGTTACT 59.137 47.619 5.77 0.00 0.00 2.24
2260 3371 1.494824 ACTTTGTGGTCGCGTTACTC 58.505 50.000 5.77 0.00 0.00 2.59
2262 3373 0.600782 TTTGTGGTCGCGTTACTCCC 60.601 55.000 5.77 0.00 0.00 4.30
2263 3374 2.505557 GTGGTCGCGTTACTCCCG 60.506 66.667 5.77 0.00 0.00 5.14
2264 3375 2.985282 TGGTCGCGTTACTCCCGT 60.985 61.111 5.77 0.00 0.00 5.28
2265 3376 2.259511 GGTCGCGTTACTCCCGTT 59.740 61.111 5.77 0.00 0.00 4.44
2266 3377 1.803117 GGTCGCGTTACTCCCGTTC 60.803 63.158 5.77 0.00 0.00 3.95
2267 3378 1.081242 GTCGCGTTACTCCCGTTCA 60.081 57.895 5.77 0.00 0.00 3.18
2268 3379 0.664166 GTCGCGTTACTCCCGTTCAA 60.664 55.000 5.77 0.00 0.00 2.69
2269 3380 0.244450 TCGCGTTACTCCCGTTCAAT 59.756 50.000 5.77 0.00 0.00 2.57
2270 3381 1.073177 CGCGTTACTCCCGTTCAATT 58.927 50.000 0.00 0.00 0.00 2.32
2271 3382 1.060122 CGCGTTACTCCCGTTCAATTC 59.940 52.381 0.00 0.00 0.00 2.17
2272 3383 2.344025 GCGTTACTCCCGTTCAATTCT 58.656 47.619 0.00 0.00 0.00 2.40
2273 3384 3.514645 GCGTTACTCCCGTTCAATTCTA 58.485 45.455 0.00 0.00 0.00 2.10
2274 3385 3.550678 GCGTTACTCCCGTTCAATTCTAG 59.449 47.826 0.00 0.00 0.00 2.43
2275 3386 4.676196 GCGTTACTCCCGTTCAATTCTAGA 60.676 45.833 0.00 0.00 0.00 2.43
2276 3387 4.797349 CGTTACTCCCGTTCAATTCTAGAC 59.203 45.833 0.00 0.00 0.00 2.59
2277 3388 5.392811 CGTTACTCCCGTTCAATTCTAGACT 60.393 44.000 0.00 0.00 0.00 3.24
2278 3389 6.183360 CGTTACTCCCGTTCAATTCTAGACTA 60.183 42.308 0.00 0.00 0.00 2.59
2279 3390 7.542025 GTTACTCCCGTTCAATTCTAGACTAA 58.458 38.462 0.00 0.00 0.00 2.24
2280 3391 6.600882 ACTCCCGTTCAATTCTAGACTAAA 57.399 37.500 0.00 0.00 0.00 1.85
2281 3392 6.396450 ACTCCCGTTCAATTCTAGACTAAAC 58.604 40.000 0.00 0.00 0.00 2.01
2282 3393 6.014840 ACTCCCGTTCAATTCTAGACTAAACA 60.015 38.462 0.00 0.00 0.00 2.83
2283 3394 6.761312 TCCCGTTCAATTCTAGACTAAACAA 58.239 36.000 0.00 0.00 0.00 2.83
2284 3395 7.218614 TCCCGTTCAATTCTAGACTAAACAAA 58.781 34.615 0.00 0.00 0.00 2.83
2285 3396 7.716123 TCCCGTTCAATTCTAGACTAAACAAAA 59.284 33.333 0.00 0.00 0.00 2.44
2286 3397 8.015658 CCCGTTCAATTCTAGACTAAACAAAAG 58.984 37.037 0.00 0.00 0.00 2.27
2287 3398 8.770828 CCGTTCAATTCTAGACTAAACAAAAGA 58.229 33.333 0.00 0.00 0.00 2.52
2288 3399 9.582223 CGTTCAATTCTAGACTAAACAAAAGAC 57.418 33.333 0.00 0.00 0.00 3.01
2405 3681 6.969993 ACATTTGGGTAAAAACTTGAGCTA 57.030 33.333 0.00 0.00 0.00 3.32
2414 5081 9.774413 GGGTAAAAACTTGAGCTAAGCTATATA 57.226 33.333 0.00 0.00 39.88 0.86
2424 5091 7.099764 TGAGCTAAGCTATATATGAAGCCAAC 58.900 38.462 4.21 0.00 39.88 3.77
2502 5320 3.996480 ACCTGCTAAAGAGTGAACAGAC 58.004 45.455 0.00 0.00 0.00 3.51
2565 5401 5.090652 TGTACGAAGCAATGAAGACAAAC 57.909 39.130 0.00 0.00 0.00 2.93
2594 5498 7.232941 AGAGGTACTAGCTGAAAAGACTTGTAA 59.767 37.037 0.00 0.00 41.55 2.41
2595 5499 7.908453 AGGTACTAGCTGAAAAGACTTGTAAT 58.092 34.615 0.00 0.00 36.02 1.89
2596 5500 9.032624 AGGTACTAGCTGAAAAGACTTGTAATA 57.967 33.333 0.00 0.00 36.02 0.98
2600 5504 9.810545 ACTAGCTGAAAAGACTTGTAATATCTC 57.189 33.333 0.00 0.00 0.00 2.75
2662 5566 6.509418 TGGTTAATAGTTCCAGCAACATTC 57.491 37.500 0.00 0.00 37.48 2.67
2711 5615 3.826524 TCCATAAAAGACACAGTGCCAA 58.173 40.909 0.00 0.00 0.00 4.52
2712 5616 4.211125 TCCATAAAAGACACAGTGCCAAA 58.789 39.130 0.00 0.00 0.00 3.28
2713 5617 4.037446 TCCATAAAAGACACAGTGCCAAAC 59.963 41.667 0.00 0.00 0.00 2.93
2714 5618 4.202101 CCATAAAAGACACAGTGCCAAACA 60.202 41.667 0.00 0.00 0.00 2.83
2715 5619 3.951775 AAAAGACACAGTGCCAAACAA 57.048 38.095 0.00 0.00 0.00 2.83
2771 5681 9.179909 TCCTTGTGACAAAAAGACTACAAATAA 57.820 29.630 0.00 0.00 0.00 1.40
2772 5682 9.965824 CCTTGTGACAAAAAGACTACAAATAAT 57.034 29.630 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.015327 GCGTACAAGGTCTCCTCTTCTA 58.985 50.000 0.00 0.00 30.89 2.10
1 2 1.819903 GCGTACAAGGTCTCCTCTTCT 59.180 52.381 0.00 0.00 30.89 2.85
2 3 1.135053 GGCGTACAAGGTCTCCTCTTC 60.135 57.143 0.00 0.00 30.89 2.87
3 4 0.896226 GGCGTACAAGGTCTCCTCTT 59.104 55.000 0.00 0.00 30.89 2.85
4 5 1.313812 CGGCGTACAAGGTCTCCTCT 61.314 60.000 0.00 0.00 30.89 3.69
5 6 1.139095 CGGCGTACAAGGTCTCCTC 59.861 63.158 0.00 0.00 30.89 3.71
6 7 1.303888 TCGGCGTACAAGGTCTCCT 60.304 57.895 6.85 0.00 33.87 3.69
7 8 1.139095 CTCGGCGTACAAGGTCTCC 59.861 63.158 6.85 0.00 0.00 3.71
8 9 1.089920 TACTCGGCGTACAAGGTCTC 58.910 55.000 6.85 0.00 0.00 3.36
9 10 0.807496 GTACTCGGCGTACAAGGTCT 59.193 55.000 6.85 0.00 46.21 3.85
10 11 3.319245 GTACTCGGCGTACAAGGTC 57.681 57.895 6.85 0.00 46.21 3.85
16 17 3.603401 CGTCTATCTTGTACTCGGCGTAC 60.603 52.174 6.85 3.49 46.94 3.67
17 18 2.541346 CGTCTATCTTGTACTCGGCGTA 59.459 50.000 6.85 0.00 0.00 4.42
18 19 1.329906 CGTCTATCTTGTACTCGGCGT 59.670 52.381 6.85 0.00 0.00 5.68
19 20 1.920705 GCGTCTATCTTGTACTCGGCG 60.921 57.143 0.00 0.00 0.00 6.46
20 21 1.756367 GCGTCTATCTTGTACTCGGC 58.244 55.000 0.00 0.00 0.00 5.54
21 22 1.596260 TCGCGTCTATCTTGTACTCGG 59.404 52.381 5.77 0.00 0.00 4.63
22 23 3.027710 GTTCGCGTCTATCTTGTACTCG 58.972 50.000 5.77 0.00 0.00 4.18
23 24 3.027710 CGTTCGCGTCTATCTTGTACTC 58.972 50.000 5.77 0.00 35.57 2.59
24 25 2.674852 TCGTTCGCGTCTATCTTGTACT 59.325 45.455 5.77 0.00 42.11 2.73
25 26 3.043635 TCGTTCGCGTCTATCTTGTAC 57.956 47.619 5.77 0.00 42.11 2.90
26 27 3.957671 ATCGTTCGCGTCTATCTTGTA 57.042 42.857 5.77 0.00 42.11 2.41
27 28 2.846039 ATCGTTCGCGTCTATCTTGT 57.154 45.000 5.77 0.00 42.11 3.16
28 29 3.118157 GCTTATCGTTCGCGTCTATCTTG 59.882 47.826 5.77 0.00 42.11 3.02
29 30 3.242969 TGCTTATCGTTCGCGTCTATCTT 60.243 43.478 5.77 0.00 42.11 2.40
30 31 2.289820 TGCTTATCGTTCGCGTCTATCT 59.710 45.455 5.77 0.00 42.11 1.98
31 32 2.401063 GTGCTTATCGTTCGCGTCTATC 59.599 50.000 5.77 0.00 42.11 2.08
32 33 2.382519 GTGCTTATCGTTCGCGTCTAT 58.617 47.619 5.77 1.27 42.11 1.98
33 34 1.818850 GTGCTTATCGTTCGCGTCTA 58.181 50.000 5.77 0.00 42.11 2.59
34 35 1.132199 CGTGCTTATCGTTCGCGTCT 61.132 55.000 5.77 0.00 42.11 4.18
35 36 1.266089 CGTGCTTATCGTTCGCGTC 59.734 57.895 5.77 0.00 42.11 5.19
36 37 0.179192 TACGTGCTTATCGTTCGCGT 60.179 50.000 5.77 5.44 46.59 6.01
37 38 0.223022 GTACGTGCTTATCGTTCGCG 59.777 55.000 0.00 0.00 41.72 5.87
38 39 1.007729 GTGTACGTGCTTATCGTTCGC 60.008 52.381 4.97 0.00 41.72 4.70
39 40 2.026038 GTGTGTACGTGCTTATCGTTCG 59.974 50.000 4.97 0.00 41.72 3.95
40 41 2.026038 CGTGTGTACGTGCTTATCGTTC 59.974 50.000 4.97 0.00 44.99 3.95
41 42 1.980844 CGTGTGTACGTGCTTATCGTT 59.019 47.619 4.97 0.00 44.99 3.85
42 43 1.609932 CGTGTGTACGTGCTTATCGT 58.390 50.000 4.97 0.00 44.99 3.73
68 69 3.578089 GATGGTGTGTGTGTGCGCG 62.578 63.158 0.00 0.00 0.00 6.86
69 70 2.252260 GATGGTGTGTGTGTGCGC 59.748 61.111 0.00 0.00 0.00 6.09
70 71 1.279539 GTGATGGTGTGTGTGTGCG 59.720 57.895 0.00 0.00 0.00 5.34
71 72 1.100463 TGGTGATGGTGTGTGTGTGC 61.100 55.000 0.00 0.00 0.00 4.57
72 73 1.065401 GTTGGTGATGGTGTGTGTGTG 59.935 52.381 0.00 0.00 0.00 3.82
73 74 1.340502 TGTTGGTGATGGTGTGTGTGT 60.341 47.619 0.00 0.00 0.00 3.72
74 75 1.387539 TGTTGGTGATGGTGTGTGTG 58.612 50.000 0.00 0.00 0.00 3.82
82 83 2.032054 GCGTGACATATGTTGGTGATGG 59.968 50.000 10.30 0.00 0.00 3.51
96 97 3.004171 AGTGTTGTTTAAGTGCGTGACA 58.996 40.909 0.00 0.00 0.00 3.58
102 103 7.011828 TCTTCTGTAAGTGTTGTTTAAGTGC 57.988 36.000 0.00 0.00 34.13 4.40
114 115 9.299963 CTCTGTGATCTTAATCTTCTGTAAGTG 57.700 37.037 0.00 0.00 34.13 3.16
115 116 7.978975 GCTCTGTGATCTTAATCTTCTGTAAGT 59.021 37.037 0.00 0.00 34.13 2.24
116 117 7.978414 TGCTCTGTGATCTTAATCTTCTGTAAG 59.022 37.037 0.00 0.00 32.75 2.34
117 118 7.840931 TGCTCTGTGATCTTAATCTTCTGTAA 58.159 34.615 0.00 0.00 32.75 2.41
122 123 5.358922 AGCTGCTCTGTGATCTTAATCTTC 58.641 41.667 0.00 0.00 32.75 2.87
131 136 4.633126 TCAATGTAAAGCTGCTCTGTGATC 59.367 41.667 1.00 0.00 0.00 2.92
174 179 7.282224 ACAAACATGTGTGTACTGTATTGAACT 59.718 33.333 20.37 0.00 37.67 3.01
175 180 7.414436 ACAAACATGTGTGTACTGTATTGAAC 58.586 34.615 20.37 0.00 37.67 3.18
176 181 7.561021 ACAAACATGTGTGTACTGTATTGAA 57.439 32.000 20.37 0.00 37.67 2.69
177 182 7.413644 CAACAAACATGTGTGTACTGTATTGA 58.586 34.615 21.92 0.00 37.67 2.57
187 192 3.056962 TCACTTGCAACAAACATGTGTGT 60.057 39.130 16.25 16.25 41.46 3.72
206 211 0.384725 GCAGTGCACGTGTCATTCAC 60.385 55.000 18.38 15.48 43.03 3.18
211 231 2.987282 ATTCGGCAGTGCACGTGTCA 62.987 55.000 18.61 12.78 0.00 3.58
232 254 3.857665 CGTACTTGCATACTGATCGTGTT 59.142 43.478 0.00 0.00 0.00 3.32
290 312 5.920840 TGAATTATTTCGTCGAGCAGGATAG 59.079 40.000 0.00 0.00 34.39 2.08
429 457 1.728971 CTTTGAGCATCGAGTGGTGAC 59.271 52.381 4.63 0.00 39.00 3.67
462 495 1.667154 TTGCCACGCGAGCTCTATCT 61.667 55.000 15.93 0.00 0.00 1.98
465 498 2.126071 GTTGCCACGCGAGCTCTA 60.126 61.111 15.93 2.58 0.00 2.43
487 521 2.127270 CATGCACGACACGGTTGC 60.127 61.111 0.00 0.00 0.00 4.17
490 524 3.345808 GCACATGCACGACACGGT 61.346 61.111 0.00 0.00 41.59 4.83
491 525 4.428922 CGCACATGCACGACACGG 62.429 66.667 4.49 0.00 42.21 4.94
663 773 0.177373 TGCTACTACTCTCCTCGCGA 59.823 55.000 9.26 9.26 0.00 5.87
666 776 1.069568 CGCATGCTACTACTCTCCTCG 60.070 57.143 17.13 0.00 0.00 4.63
746 857 2.747855 CGGTGCCTGGCCTCTTTC 60.748 66.667 17.53 0.00 0.00 2.62
806 917 0.638746 GCATCTCACCGACGTTTACG 59.361 55.000 0.00 0.00 46.33 3.18
817 928 1.284657 CAGATCACGGTGCATCTCAC 58.715 55.000 15.52 0.00 44.90 3.51
818 929 0.897621 ACAGATCACGGTGCATCTCA 59.102 50.000 15.52 0.00 0.00 3.27
824 935 1.135915 AGAGATGACAGATCACGGTGC 59.864 52.381 2.51 0.00 37.79 5.01
843 954 1.448189 GCTGAGGCTGAGAGCACAG 60.448 63.158 4.75 13.81 44.75 3.66
861 972 2.743718 CCGGATCGATGGGGGAAG 59.256 66.667 0.54 0.00 0.00 3.46
862 973 3.556306 GCCGGATCGATGGGGGAA 61.556 66.667 5.05 0.00 0.00 3.97
879 990 2.511600 GAGGTCGATGGTTGGCGG 60.512 66.667 0.00 0.00 0.00 6.13
880 991 2.511600 GGAGGTCGATGGTTGGCG 60.512 66.667 0.00 0.00 0.00 5.69
881 992 2.124695 GGGAGGTCGATGGTTGGC 60.125 66.667 0.00 0.00 0.00 4.52
904 1015 7.861372 CGGAGTAGTAATTTATATATGCCGAGG 59.139 40.741 0.00 0.00 34.88 4.63
932 1043 0.583438 CGCAGAAACACACCACTCTG 59.417 55.000 0.00 0.00 38.66 3.35
933 1044 0.532862 CCGCAGAAACACACCACTCT 60.533 55.000 0.00 0.00 0.00 3.24
938 1049 1.515521 CTTCCCCGCAGAAACACACC 61.516 60.000 0.00 0.00 0.00 4.16
951 1062 3.322828 TGTGTACAGTAACTCACTTCCCC 59.677 47.826 0.00 0.00 34.26 4.81
981 1108 0.834612 TCGTCTCTCTCTCCCTCTCC 59.165 60.000 0.00 0.00 0.00 3.71
987 1114 1.804151 CGATCCATCGTCTCTCTCTCC 59.196 57.143 0.55 0.00 44.74 3.71
1067 1559 7.325660 TGAATCAATTGAGGAACAGATTAGC 57.674 36.000 14.54 0.00 0.00 3.09
1095 1587 2.629137 TCGATCGTCTAGCTACTCTCCT 59.371 50.000 15.94 0.00 0.00 3.69
1109 1601 4.118410 CCTAGTACACACTACTCGATCGT 58.882 47.826 15.94 0.00 36.14 3.73
1127 1621 3.123621 GCTGAACAAACATCACGACCTAG 59.876 47.826 0.00 0.00 0.00 3.02
1128 1622 3.064207 GCTGAACAAACATCACGACCTA 58.936 45.455 0.00 0.00 0.00 3.08
1129 1623 1.873591 GCTGAACAAACATCACGACCT 59.126 47.619 0.00 0.00 0.00 3.85
1130 1624 1.873591 AGCTGAACAAACATCACGACC 59.126 47.619 0.00 0.00 0.00 4.79
1131 1625 2.543848 TCAGCTGAACAAACATCACGAC 59.456 45.455 15.67 0.00 0.00 4.34
1132 1626 2.832563 TCAGCTGAACAAACATCACGA 58.167 42.857 15.67 0.00 0.00 4.35
1215 1709 4.831307 CCGTTCTCCGCCTCGTCG 62.831 72.222 0.00 0.00 34.38 5.12
1329 1823 0.599558 GTGTATATACCTCGCGGCCA 59.400 55.000 6.13 0.00 0.00 5.36
1334 1828 0.455633 CGCGGGTGTATATACCTCGC 60.456 60.000 28.29 28.29 46.94 5.03
1399 1893 1.639298 GACTGTGTTGATGGCGAGGC 61.639 60.000 0.00 0.00 0.00 4.70
1400 1894 1.021390 GGACTGTGTTGATGGCGAGG 61.021 60.000 0.00 0.00 0.00 4.63
1547 2053 1.901085 GATGAAGGCCTGGACGTCT 59.099 57.895 16.54 2.31 0.00 4.18
1634 2144 4.110493 GGTACGCACATCAGGAGC 57.890 61.111 0.00 0.00 0.00 4.70
1774 2298 4.650754 ACTGTACTCCTAGTTAATGGCG 57.349 45.455 0.00 0.00 0.00 5.69
1787 2311 9.918630 TGAACCAAGTTAAATAGTACTGTACTC 57.081 33.333 22.79 8.60 40.14 2.59
1789 2313 9.148104 CCTGAACCAAGTTAAATAGTACTGTAC 57.852 37.037 9.93 9.93 0.00 2.90
1790 2314 9.092338 TCCTGAACCAAGTTAAATAGTACTGTA 57.908 33.333 5.39 0.00 0.00 2.74
1791 2315 7.876582 GTCCTGAACCAAGTTAAATAGTACTGT 59.123 37.037 5.39 0.00 0.00 3.55
1792 2316 7.063074 CGTCCTGAACCAAGTTAAATAGTACTG 59.937 40.741 5.39 0.00 0.00 2.74
1795 2319 5.870978 GCGTCCTGAACCAAGTTAAATAGTA 59.129 40.000 0.00 0.00 0.00 1.82
1800 2325 1.868498 CGCGTCCTGAACCAAGTTAAA 59.132 47.619 0.00 0.00 0.00 1.52
1804 2329 0.878961 GTTCGCGTCCTGAACCAAGT 60.879 55.000 5.77 0.00 39.80 3.16
1831 2356 1.144936 CCTCCTCATCTGCGGGAAC 59.855 63.158 0.00 0.00 0.00 3.62
1836 2361 1.521010 CTGTGCCTCCTCATCTGCG 60.521 63.158 0.00 0.00 0.00 5.18
1845 2370 1.202818 AGAAAGAACACCTGTGCCTCC 60.203 52.381 0.00 0.00 0.00 4.30
1858 2383 4.227538 CTCGTGCTCTTTCGTAGAAAGAA 58.772 43.478 21.04 8.99 45.90 2.52
1859 2384 3.366070 CCTCGTGCTCTTTCGTAGAAAGA 60.366 47.826 19.95 19.95 45.90 2.52
1865 2390 3.786809 CACCTCGTGCTCTTTCGTA 57.213 52.632 0.00 0.00 0.00 3.43
1877 2402 3.377656 AGGTAGTGTGGCACCTCG 58.622 61.111 16.26 0.00 41.44 4.63
1893 2418 2.685380 ACGGGAAGCAGGGGAGAG 60.685 66.667 0.00 0.00 0.00 3.20
1894 2419 3.003173 CACGGGAAGCAGGGGAGA 61.003 66.667 0.00 0.00 0.00 3.71
1972 2628 5.942961 TGCCCCGAAAAACTAATCCATATA 58.057 37.500 0.00 0.00 0.00 0.86
1973 2629 4.798882 TGCCCCGAAAAACTAATCCATAT 58.201 39.130 0.00 0.00 0.00 1.78
1974 2630 4.237976 TGCCCCGAAAAACTAATCCATA 57.762 40.909 0.00 0.00 0.00 2.74
1975 2631 3.094484 TGCCCCGAAAAACTAATCCAT 57.906 42.857 0.00 0.00 0.00 3.41
1976 2632 2.588464 TGCCCCGAAAAACTAATCCA 57.412 45.000 0.00 0.00 0.00 3.41
1977 2633 5.784578 AATATGCCCCGAAAAACTAATCC 57.215 39.130 0.00 0.00 0.00 3.01
1979 2635 7.507616 TCCATAAATATGCCCCGAAAAACTAAT 59.492 33.333 0.00 0.00 32.40 1.73
1980 2636 6.834451 TCCATAAATATGCCCCGAAAAACTAA 59.166 34.615 0.00 0.00 32.40 2.24
1982 2638 5.205056 TCCATAAATATGCCCCGAAAAACT 58.795 37.500 0.00 0.00 32.40 2.66
1983 2639 5.523438 TCCATAAATATGCCCCGAAAAAC 57.477 39.130 0.00 0.00 32.40 2.43
1986 2642 8.429237 AATTAATCCATAAATATGCCCCGAAA 57.571 30.769 0.00 0.00 32.40 3.46
1987 2643 8.429237 AAATTAATCCATAAATATGCCCCGAA 57.571 30.769 0.00 0.00 32.40 4.30
1989 2645 9.150348 GAAAAATTAATCCATAAATATGCCCCG 57.850 33.333 0.00 0.00 32.40 5.73
2070 3153 6.402983 GCTGATCATATAAGGCTTCGATTTGG 60.403 42.308 1.30 0.00 0.00 3.28
2071 3154 6.370994 AGCTGATCATATAAGGCTTCGATTTG 59.629 38.462 1.30 0.00 0.00 2.32
2078 3161 5.012458 TGCACTAGCTGATCATATAAGGCTT 59.988 40.000 9.81 4.58 42.74 4.35
2080 3163 4.629200 GTGCACTAGCTGATCATATAAGGC 59.371 45.833 10.32 0.00 42.74 4.35
2081 3164 6.035368 AGTGCACTAGCTGATCATATAAGG 57.965 41.667 20.16 0.00 42.74 2.69
2083 3166 9.428097 CAATAAGTGCACTAGCTGATCATATAA 57.572 33.333 22.01 0.00 42.74 0.98
2085 3168 6.877855 CCAATAAGTGCACTAGCTGATCATAT 59.122 38.462 22.01 7.92 42.74 1.78
2086 3169 6.226052 CCAATAAGTGCACTAGCTGATCATA 58.774 40.000 22.01 5.64 42.74 2.15
2087 3170 5.061853 CCAATAAGTGCACTAGCTGATCAT 58.938 41.667 22.01 3.16 42.74 2.45
2088 3171 4.445453 CCAATAAGTGCACTAGCTGATCA 58.555 43.478 22.01 0.00 42.74 2.92
2089 3172 3.812053 CCCAATAAGTGCACTAGCTGATC 59.188 47.826 22.01 0.00 42.74 2.92
2090 3173 3.200825 ACCCAATAAGTGCACTAGCTGAT 59.799 43.478 22.01 5.66 42.74 2.90
2092 3175 2.679837 CACCCAATAAGTGCACTAGCTG 59.320 50.000 22.01 16.27 42.74 4.24
2093 3176 2.356125 CCACCCAATAAGTGCACTAGCT 60.356 50.000 22.01 7.35 42.74 3.32
2094 3177 2.017049 CCACCCAATAAGTGCACTAGC 58.983 52.381 22.01 0.00 42.57 3.42
2095 3178 2.017049 GCCACCCAATAAGTGCACTAG 58.983 52.381 22.01 10.46 33.75 2.57
2096 3179 1.340600 GGCCACCCAATAAGTGCACTA 60.341 52.381 22.01 9.11 33.75 2.74
2097 3180 0.611896 GGCCACCCAATAAGTGCACT 60.612 55.000 15.25 15.25 33.75 4.40
2098 3181 0.611896 AGGCCACCCAATAAGTGCAC 60.612 55.000 9.40 9.40 33.75 4.57
2099 3182 0.995803 TAGGCCACCCAATAAGTGCA 59.004 50.000 5.01 0.00 33.75 4.57
2100 3183 2.158608 AGATAGGCCACCCAATAAGTGC 60.159 50.000 5.01 0.00 33.75 4.40
2101 3184 3.864789 AGATAGGCCACCCAATAAGTG 57.135 47.619 5.01 0.00 34.91 3.16
2102 3185 4.047883 AGAAGATAGGCCACCCAATAAGT 58.952 43.478 5.01 0.00 0.00 2.24
2111 3222 1.068741 CCCGTACAGAAGATAGGCCAC 59.931 57.143 5.01 0.00 0.00 5.01
2115 3226 1.705873 AGGCCCGTACAGAAGATAGG 58.294 55.000 0.00 0.00 0.00 2.57
2120 3231 0.673644 CCACAAGGCCCGTACAGAAG 60.674 60.000 0.00 0.00 0.00 2.85
2122 3233 3.065306 CCACAAGGCCCGTACAGA 58.935 61.111 0.00 0.00 0.00 3.41
2150 3261 9.165057 GCTCTTATATTATGGGATAGAGGGAAT 57.835 37.037 0.00 0.00 0.00 3.01
2151 3262 8.129001 TGCTCTTATATTATGGGATAGAGGGAA 58.871 37.037 0.00 0.00 0.00 3.97
2152 3263 7.662083 TGCTCTTATATTATGGGATAGAGGGA 58.338 38.462 0.00 0.00 0.00 4.20
2153 3264 7.921041 TGCTCTTATATTATGGGATAGAGGG 57.079 40.000 0.00 0.00 0.00 4.30
2169 3280 9.113838 CCAGTGTTCTGTAAAATATGCTCTTAT 57.886 33.333 0.00 0.00 39.82 1.73
2170 3281 8.100791 ACCAGTGTTCTGTAAAATATGCTCTTA 58.899 33.333 0.00 0.00 39.82 2.10
2171 3282 6.942576 ACCAGTGTTCTGTAAAATATGCTCTT 59.057 34.615 0.00 0.00 39.82 2.85
2172 3283 6.372659 CACCAGTGTTCTGTAAAATATGCTCT 59.627 38.462 0.00 0.00 39.82 4.09
2173 3284 6.149474 ACACCAGTGTTCTGTAAAATATGCTC 59.851 38.462 0.00 0.00 41.83 4.26
2174 3285 6.003950 ACACCAGTGTTCTGTAAAATATGCT 58.996 36.000 0.00 0.00 41.83 3.79
2175 3286 6.254281 ACACCAGTGTTCTGTAAAATATGC 57.746 37.500 0.00 0.00 41.83 3.14
2176 3287 6.367695 TCGACACCAGTGTTCTGTAAAATATG 59.632 38.462 4.68 0.00 45.05 1.78
2177 3288 6.460781 TCGACACCAGTGTTCTGTAAAATAT 58.539 36.000 4.68 0.00 45.05 1.28
2178 3289 5.845103 TCGACACCAGTGTTCTGTAAAATA 58.155 37.500 4.68 0.00 45.05 1.40
2179 3290 4.699637 TCGACACCAGTGTTCTGTAAAAT 58.300 39.130 4.68 0.00 45.05 1.82
2180 3291 4.126208 TCGACACCAGTGTTCTGTAAAA 57.874 40.909 4.68 0.00 45.05 1.52
2181 3292 3.804786 TCGACACCAGTGTTCTGTAAA 57.195 42.857 4.68 0.00 45.05 2.01
2182 3293 3.804786 TTCGACACCAGTGTTCTGTAA 57.195 42.857 4.68 0.00 45.05 2.41
2183 3294 3.804786 TTTCGACACCAGTGTTCTGTA 57.195 42.857 4.68 0.00 45.05 2.74
2184 3295 2.684001 TTTCGACACCAGTGTTCTGT 57.316 45.000 4.68 0.00 45.05 3.41
2185 3296 4.509970 TGTATTTTCGACACCAGTGTTCTG 59.490 41.667 4.68 0.00 45.05 3.02
2186 3297 4.699637 TGTATTTTCGACACCAGTGTTCT 58.300 39.130 4.68 0.00 45.05 3.01
2187 3298 5.607119 ATGTATTTTCGACACCAGTGTTC 57.393 39.130 4.68 0.00 45.05 3.18
2188 3299 6.385649 AAATGTATTTTCGACACCAGTGTT 57.614 33.333 4.68 0.00 45.05 3.32
2204 3315 9.533068 TCCCTCCATCCCATAATATAAATGTAT 57.467 33.333 0.00 0.00 0.00 2.29
2205 3316 8.941639 TCCCTCCATCCCATAATATAAATGTA 57.058 34.615 0.00 0.00 0.00 2.29
2206 3317 7.465563 ACTCCCTCCATCCCATAATATAAATGT 59.534 37.037 0.00 0.00 0.00 2.71
2207 3318 7.876371 ACTCCCTCCATCCCATAATATAAATG 58.124 38.462 0.00 0.00 0.00 2.32
2208 3319 9.004231 GTACTCCCTCCATCCCATAATATAAAT 57.996 37.037 0.00 0.00 0.00 1.40
2209 3320 7.964867 TGTACTCCCTCCATCCCATAATATAAA 59.035 37.037 0.00 0.00 0.00 1.40
2210 3321 7.492552 TGTACTCCCTCCATCCCATAATATAA 58.507 38.462 0.00 0.00 0.00 0.98
2211 3322 7.063801 TGTACTCCCTCCATCCCATAATATA 57.936 40.000 0.00 0.00 0.00 0.86
2212 3323 5.927465 TGTACTCCCTCCATCCCATAATAT 58.073 41.667 0.00 0.00 0.00 1.28
2213 3324 5.363124 TGTACTCCCTCCATCCCATAATA 57.637 43.478 0.00 0.00 0.00 0.98
2214 3325 4.228237 TGTACTCCCTCCATCCCATAAT 57.772 45.455 0.00 0.00 0.00 1.28
2215 3326 3.717507 TGTACTCCCTCCATCCCATAA 57.282 47.619 0.00 0.00 0.00 1.90
2216 3327 3.943269 ATGTACTCCCTCCATCCCATA 57.057 47.619 0.00 0.00 0.00 2.74
2217 3328 2.823460 ATGTACTCCCTCCATCCCAT 57.177 50.000 0.00 0.00 0.00 4.00
2218 3329 3.208922 TCTTATGTACTCCCTCCATCCCA 59.791 47.826 0.00 0.00 0.00 4.37
2219 3330 3.858135 TCTTATGTACTCCCTCCATCCC 58.142 50.000 0.00 0.00 0.00 3.85
2220 3331 4.902448 AGTTCTTATGTACTCCCTCCATCC 59.098 45.833 0.00 0.00 0.00 3.51
2221 3332 6.487299 AAGTTCTTATGTACTCCCTCCATC 57.513 41.667 0.00 0.00 0.00 3.51
2222 3333 6.215636 ACAAAGTTCTTATGTACTCCCTCCAT 59.784 38.462 0.00 0.00 0.00 3.41
2223 3334 5.546499 ACAAAGTTCTTATGTACTCCCTCCA 59.454 40.000 0.00 0.00 0.00 3.86
2224 3335 5.875359 CACAAAGTTCTTATGTACTCCCTCC 59.125 44.000 0.00 0.00 0.00 4.30
2225 3336 5.875359 CCACAAAGTTCTTATGTACTCCCTC 59.125 44.000 0.00 0.00 0.00 4.30
2226 3337 5.309806 ACCACAAAGTTCTTATGTACTCCCT 59.690 40.000 0.00 0.00 0.00 4.20
2227 3338 5.557866 ACCACAAAGTTCTTATGTACTCCC 58.442 41.667 0.00 0.00 0.00 4.30
2228 3339 5.347907 CGACCACAAAGTTCTTATGTACTCC 59.652 44.000 0.00 0.00 0.00 3.85
2229 3340 5.163982 GCGACCACAAAGTTCTTATGTACTC 60.164 44.000 0.00 0.00 0.00 2.59
2230 3341 4.689345 GCGACCACAAAGTTCTTATGTACT 59.311 41.667 0.00 0.00 0.00 2.73
2231 3342 4.433805 CGCGACCACAAAGTTCTTATGTAC 60.434 45.833 0.00 0.00 0.00 2.90
2234 3345 2.478894 ACGCGACCACAAAGTTCTTATG 59.521 45.455 15.93 0.00 0.00 1.90
2237 3348 1.375551 AACGCGACCACAAAGTTCTT 58.624 45.000 15.93 0.00 0.00 2.52
2238 3349 1.862827 GTAACGCGACCACAAAGTTCT 59.137 47.619 15.93 0.00 0.00 3.01
2252 3363 2.344025 AGAATTGAACGGGAGTAACGC 58.656 47.619 0.00 0.00 46.69 4.84
2253 3364 4.797349 GTCTAGAATTGAACGGGAGTAACG 59.203 45.833 0.00 0.00 46.69 3.18
2255 3366 7.707624 TTAGTCTAGAATTGAACGGGAGTAA 57.292 36.000 0.00 0.00 46.69 2.24
2256 3367 7.177216 TGTTTAGTCTAGAATTGAACGGGAGTA 59.823 37.037 0.00 0.00 46.69 2.59
2258 3369 6.395629 TGTTTAGTCTAGAATTGAACGGGAG 58.604 40.000 0.00 0.00 0.00 4.30
2259 3370 6.349243 TGTTTAGTCTAGAATTGAACGGGA 57.651 37.500 0.00 0.00 0.00 5.14
2260 3371 7.429636 TTTGTTTAGTCTAGAATTGAACGGG 57.570 36.000 0.00 0.00 0.00 5.28
2262 3373 9.582223 GTCTTTTGTTTAGTCTAGAATTGAACG 57.418 33.333 0.00 0.00 0.00 3.95
2296 3407 8.517062 AATTAGGATCCAGAATTGAACTGAAG 57.483 34.615 15.82 0.00 37.54 3.02
2297 3408 8.742777 CAAATTAGGATCCAGAATTGAACTGAA 58.257 33.333 19.82 0.00 37.54 3.02
2359 3470 8.338072 TGTTAGTAAACAAGGTTTCTGTTTGA 57.662 30.769 10.40 0.00 42.60 2.69
2379 3655 7.433680 AGCTCAAGTTTTTACCCAAATGTTAG 58.566 34.615 0.00 0.00 0.00 2.34
2402 3678 7.173218 TGTTGTTGGCTTCATATATAGCTTAGC 59.827 37.037 7.30 0.00 37.54 3.09
2405 3681 7.056635 ACTGTTGTTGGCTTCATATATAGCTT 58.943 34.615 7.30 0.00 37.54 3.74
2414 5081 4.220602 GGGAATTACTGTTGTTGGCTTCAT 59.779 41.667 0.00 0.00 0.00 2.57
2415 5082 3.572255 GGGAATTACTGTTGTTGGCTTCA 59.428 43.478 0.00 0.00 0.00 3.02
2424 5091 5.269505 TGTGGTTTTGGGAATTACTGTTG 57.730 39.130 0.00 0.00 0.00 3.33
2502 5320 1.998315 CTGACTTCTGTTCAGGCATCG 59.002 52.381 0.00 0.00 0.00 3.84
2565 5401 5.417580 AGTCTTTTCAGCTAGTACCTCTCTG 59.582 44.000 0.00 0.00 0.00 3.35
2594 5498 7.079048 AGATGGAGGTTTAGTTCAGGAGATAT 58.921 38.462 0.00 0.00 0.00 1.63
2595 5499 6.444704 AGATGGAGGTTTAGTTCAGGAGATA 58.555 40.000 0.00 0.00 0.00 1.98
2596 5500 5.284582 AGATGGAGGTTTAGTTCAGGAGAT 58.715 41.667 0.00 0.00 0.00 2.75
2600 5504 7.442666 GCTAATTAGATGGAGGTTTAGTTCAGG 59.557 40.741 16.85 0.00 0.00 3.86
2662 5566 0.036952 AACGGCATGACTCTGTCCAG 60.037 55.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.