Multiple sequence alignment - TraesCS2A01G554800

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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 TraesCS2A01G554800 chr2A 100.000 2735 0 0 1 2735 759590825 759588091 0.000000e+00 5051.0
1 TraesCS2A01G554800 chr2B 93.646 1086 50 6 755 1837 775770760 775769691 0.000000e+00 1605.0
2 TraesCS2A01G554800 chr2B 89.919 1111 73 10 1254 2362 775740775 775739702 0.000000e+00 1395.0
3 TraesCS2A01G554800 chr2B 86.589 686 71 9 1 682 637681230 637681898 0.000000e+00 737.0
4 TraesCS2A01G554800 chr2B 95.441 329 13 2 755 1081 775741549 775741221 8.680000e-145 523.0
5 TraesCS2A01G554800 chr2B 92.033 364 24 2 2367 2730 775739387 775739029 8.740000e-140 507.0
6 TraesCS2A01G554800 chr2B 88.169 355 23 4 2376 2730 775769173 775768838 3.280000e-109 405.0
7 TraesCS2A01G554800 chr2B 94.048 168 10 0 2025 2192 775769597 775769430 3.490000e-64 255.0
8 TraesCS2A01G554800 chr2B 98.701 77 1 0 1187 1263 775741222 775741146 1.320000e-28 137.0
9 TraesCS2A01G554800 chr2B 91.753 97 8 0 1870 1966 775769687 775769591 4.750000e-28 135.0
10 TraesCS2A01G554800 chr2B 100.000 45 0 0 2288 2332 775749503 775749459 1.750000e-12 84.2
11 TraesCS2A01G554800 chr7A 90.351 684 64 1 1 682 311218798 311219481 0.000000e+00 896.0
12 TraesCS2A01G554800 chr1A 87.791 688 81 2 1 685 553737028 553736341 0.000000e+00 802.0
13 TraesCS2A01G554800 chr2D 85.426 693 87 9 1 689 78513356 78514038 0.000000e+00 708.0
14 TraesCS2A01G554800 chr5D 85.933 654 78 11 40 689 325458531 325457888 0.000000e+00 686.0
15 TraesCS2A01G554800 chr3B 84.880 668 91 7 24 689 715290912 715290253 0.000000e+00 665.0
16 TraesCS2A01G554800 chr4A 85.469 640 83 7 1 638 738091713 738091082 0.000000e+00 658.0
17 TraesCS2A01G554800 chr1D 83.454 689 109 4 1 685 298504224 298504911 1.070000e-178 636.0
18 TraesCS2A01G554800 chr3D 85.921 554 75 3 134 685 253535710 253536262 3.030000e-164 588.0
19 TraesCS2A01G554800 chr3D 77.138 1111 178 52 755 1810 57175403 57176492 2.360000e-160 575.0
20 TraesCS2A01G554800 chr3D 77.134 621 104 26 1208 1810 57388761 57388161 2.630000e-85 326.0
21 TraesCS2A01G554800 chr6D 100.000 28 0 0 1746 1773 432671314 432671287 5.000000e-03 52.8


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 TraesCS2A01G554800 chr2A 759588091 759590825 2734 True 5051.0 5051 100.0000 1 2735 1 chr2A.!!$R1 2734
1 TraesCS2A01G554800 chr2B 637681230 637681898 668 False 737.0 737 86.5890 1 682 1 chr2B.!!$F1 681
2 TraesCS2A01G554800 chr2B 775739029 775741549 2520 True 640.5 1395 94.0235 755 2730 4 chr2B.!!$R2 1975
3 TraesCS2A01G554800 chr2B 775768838 775770760 1922 True 600.0 1605 91.9040 755 2730 4 chr2B.!!$R3 1975
4 TraesCS2A01G554800 chr7A 311218798 311219481 683 False 896.0 896 90.3510 1 682 1 chr7A.!!$F1 681
5 TraesCS2A01G554800 chr1A 553736341 553737028 687 True 802.0 802 87.7910 1 685 1 chr1A.!!$R1 684
6 TraesCS2A01G554800 chr2D 78513356 78514038 682 False 708.0 708 85.4260 1 689 1 chr2D.!!$F1 688
7 TraesCS2A01G554800 chr5D 325457888 325458531 643 True 686.0 686 85.9330 40 689 1 chr5D.!!$R1 649
8 TraesCS2A01G554800 chr3B 715290253 715290912 659 True 665.0 665 84.8800 24 689 1 chr3B.!!$R1 665
9 TraesCS2A01G554800 chr4A 738091082 738091713 631 True 658.0 658 85.4690 1 638 1 chr4A.!!$R1 637
10 TraesCS2A01G554800 chr1D 298504224 298504911 687 False 636.0 636 83.4540 1 685 1 chr1D.!!$F1 684
11 TraesCS2A01G554800 chr3D 253535710 253536262 552 False 588.0 588 85.9210 134 685 1 chr3D.!!$F2 551
12 TraesCS2A01G554800 chr3D 57175403 57176492 1089 False 575.0 575 77.1380 755 1810 1 chr3D.!!$F1 1055
13 TraesCS2A01G554800 chr3D 57388161 57388761 600 True 326.0 326 77.1340 1208 1810 1 chr3D.!!$R1 602

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
333 340 0.028242 CTCGATCTGGAGAACGACGG 59.972 60.0 5.04 0.0 42.87 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1877 2432 0.03759 TAGTGGGGCGCATTCTTTGT 59.962 50.0 10.83 0.0 0.0 2.83 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
46 47 4.078516 GCGGCCGAACTACCACCT 62.079 66.667 33.48 0.00 0.00 4.00
93 98 1.304282 GTGCAGGGGGTCACATCAT 59.696 57.895 0.00 0.00 33.63 2.45
210 217 0.250989 GAGATCGGACGGGAGGAGAT 60.251 60.000 0.00 0.00 0.00 2.75
333 340 0.028242 CTCGATCTGGAGAACGACGG 59.972 60.000 5.04 0.00 42.87 4.79
401 408 8.871686 AGGTTTTCAATTCAAACTTGATGTAC 57.128 30.769 8.86 0.00 37.00 2.90
424 431 0.515564 ACGTAGTTGTTGGCGAATGC 59.484 50.000 0.00 0.00 37.78 3.56
464 471 2.091852 GAAGGCATCGGAGATGATCC 57.908 55.000 13.56 6.43 45.12 3.36
491 498 3.595691 GAGCCGATGGTCCATACAG 57.404 57.895 3.72 0.00 32.76 2.74
660 667 2.604614 GGCGTCGCTCAAAAACTCAAAT 60.605 45.455 18.11 0.00 0.00 2.32
669 676 5.525012 GCTCAAAAACTCAAATTTCCAAGCT 59.475 36.000 0.00 0.00 0.00 3.74
691 698 4.247781 ATGAAGCCATGAAGCCGG 57.752 55.556 0.00 0.00 0.00 6.13
696 703 3.908081 GCCATGAAGCCGGCCATG 61.908 66.667 28.77 28.77 42.82 3.66
697 704 2.124193 CCATGAAGCCGGCCATGA 60.124 61.111 34.04 17.54 41.88 3.07
698 705 1.753848 CCATGAAGCCGGCCATGAA 60.754 57.895 34.04 15.44 41.88 2.57
699 706 1.731433 CCATGAAGCCGGCCATGAAG 61.731 60.000 34.04 20.91 41.88 3.02
700 707 1.454479 ATGAAGCCGGCCATGAAGG 60.454 57.895 26.15 0.00 41.84 3.46
709 716 4.528674 CCATGAAGGCGTGAGGAG 57.471 61.111 0.00 0.00 32.63 3.69
710 717 1.599047 CCATGAAGGCGTGAGGAGT 59.401 57.895 0.00 0.00 32.63 3.85
711 718 0.036010 CCATGAAGGCGTGAGGAGTT 60.036 55.000 0.00 0.00 32.63 3.01
712 719 1.611673 CCATGAAGGCGTGAGGAGTTT 60.612 52.381 0.00 0.00 32.63 2.66
713 720 1.466167 CATGAAGGCGTGAGGAGTTTG 59.534 52.381 0.00 0.00 32.63 2.93
714 721 0.756294 TGAAGGCGTGAGGAGTTTGA 59.244 50.000 0.00 0.00 0.00 2.69
715 722 1.149148 GAAGGCGTGAGGAGTTTGAC 58.851 55.000 0.00 0.00 0.00 3.18
716 723 0.600255 AAGGCGTGAGGAGTTTGACG 60.600 55.000 0.00 0.00 34.93 4.35
718 725 3.550656 CGTGAGGAGTTTGACGCC 58.449 61.111 0.00 0.00 38.44 5.68
724 731 2.922740 AGGAGTTTGACGCCTTACAA 57.077 45.000 0.00 0.00 46.59 2.41
725 732 2.490991 AGGAGTTTGACGCCTTACAAC 58.509 47.619 0.00 0.00 46.59 3.32
726 733 1.193874 GGAGTTTGACGCCTTACAACG 59.806 52.381 0.00 0.00 35.03 4.10
727 734 0.584876 AGTTTGACGCCTTACAACGC 59.415 50.000 0.00 0.00 0.00 4.84
728 735 0.305313 GTTTGACGCCTTACAACGCA 59.695 50.000 0.00 0.00 0.00 5.24
729 736 1.015109 TTTGACGCCTTACAACGCAA 58.985 45.000 0.00 0.00 0.00 4.85
730 737 0.305313 TTGACGCCTTACAACGCAAC 59.695 50.000 0.00 0.00 0.00 4.17
731 738 1.205820 GACGCCTTACAACGCAACC 59.794 57.895 0.00 0.00 0.00 3.77
732 739 2.172419 CGCCTTACAACGCAACCG 59.828 61.111 0.00 0.00 41.14 4.44
743 750 1.708027 CGCAACCGTACTTAGCAGC 59.292 57.895 0.00 0.00 0.00 5.25
744 751 0.736325 CGCAACCGTACTTAGCAGCT 60.736 55.000 0.00 0.00 0.00 4.24
745 752 1.439679 GCAACCGTACTTAGCAGCTT 58.560 50.000 0.00 0.00 0.00 3.74
746 753 1.128692 GCAACCGTACTTAGCAGCTTG 59.871 52.381 0.00 0.00 0.00 4.01
747 754 2.413837 CAACCGTACTTAGCAGCTTGT 58.586 47.619 0.00 2.87 0.00 3.16
748 755 2.365408 ACCGTACTTAGCAGCTTGTC 57.635 50.000 0.00 0.00 0.00 3.18
749 756 1.067071 ACCGTACTTAGCAGCTTGTCC 60.067 52.381 0.00 0.00 0.00 4.02
750 757 1.641577 CGTACTTAGCAGCTTGTCCC 58.358 55.000 0.00 0.00 0.00 4.46
751 758 1.641577 GTACTTAGCAGCTTGTCCCG 58.358 55.000 0.00 0.00 0.00 5.14
752 759 1.203994 GTACTTAGCAGCTTGTCCCGA 59.796 52.381 0.00 0.00 0.00 5.14
753 760 0.247736 ACTTAGCAGCTTGTCCCGAG 59.752 55.000 0.00 0.00 0.00 4.63
882 890 2.956964 GATCGTCGGCTTCAGCGG 60.957 66.667 0.00 0.00 43.26 5.52
991 1000 1.154454 ACCGTGTACCACCAGGAGA 59.846 57.895 0.00 0.00 38.69 3.71
1032 1041 1.672030 TGACATGAAGGCCGCAGTG 60.672 57.895 0.00 0.00 0.00 3.66
1081 1227 1.074775 GTGGTCTGGTTCCCATGCA 59.925 57.895 0.00 0.00 32.32 3.96
1082 1228 0.962356 GTGGTCTGGTTCCCATGCAG 60.962 60.000 0.00 0.00 32.32 4.41
1083 1229 1.133181 TGGTCTGGTTCCCATGCAGA 61.133 55.000 0.00 0.00 30.82 4.26
1084 1230 0.393537 GGTCTGGTTCCCATGCAGAG 60.394 60.000 0.00 0.00 30.82 3.35
1085 1231 0.393537 GTCTGGTTCCCATGCAGAGG 60.394 60.000 0.00 0.00 30.82 3.69
1086 1232 0.842030 TCTGGTTCCCATGCAGAGGT 60.842 55.000 7.16 0.00 30.82 3.85
1087 1233 0.679002 CTGGTTCCCATGCAGAGGTG 60.679 60.000 7.16 0.00 30.82 4.00
1088 1234 1.380302 GGTTCCCATGCAGAGGTGT 59.620 57.895 7.16 0.00 0.00 4.16
1089 1235 0.962356 GGTTCCCATGCAGAGGTGTG 60.962 60.000 7.16 0.00 0.00 3.82
1090 1236 0.962356 GTTCCCATGCAGAGGTGTGG 60.962 60.000 7.16 1.17 0.00 4.17
1091 1237 1.426251 TTCCCATGCAGAGGTGTGGT 61.426 55.000 7.16 0.00 0.00 4.16
1092 1238 1.075482 CCCATGCAGAGGTGTGGTT 59.925 57.895 7.16 0.00 0.00 3.67
1093 1239 0.962356 CCCATGCAGAGGTGTGGTTC 60.962 60.000 7.16 0.00 0.00 3.62
1094 1240 0.037303 CCATGCAGAGGTGTGGTTCT 59.963 55.000 0.00 0.00 0.00 3.01
1095 1241 1.446907 CATGCAGAGGTGTGGTTCTC 58.553 55.000 0.00 0.00 0.00 2.87
1096 1242 0.036952 ATGCAGAGGTGTGGTTCTCG 60.037 55.000 0.00 0.00 35.34 4.04
1097 1243 2.029844 GCAGAGGTGTGGTTCTCGC 61.030 63.158 0.00 0.00 35.34 5.03
1098 1244 1.374758 CAGAGGTGTGGTTCTCGCC 60.375 63.158 0.00 0.00 35.34 5.54
1099 1245 2.432628 GAGGTGTGGTTCTCGCCG 60.433 66.667 0.00 0.00 40.03 6.46
1100 1246 4.681978 AGGTGTGGTTCTCGCCGC 62.682 66.667 0.00 0.00 40.03 6.53
1126 1272 4.883354 GCTCGGGCCAATGGGAGG 62.883 72.222 4.39 0.00 35.59 4.30
1127 1273 3.411517 CTCGGGCCAATGGGAGGT 61.412 66.667 4.39 0.00 35.59 3.85
1128 1274 3.406595 CTCGGGCCAATGGGAGGTC 62.407 68.421 4.39 0.00 35.59 3.85
1131 1277 2.597903 GGCCAATGGGAGGTCCTC 59.402 66.667 10.78 10.78 35.59 3.71
1142 1288 4.408821 GGTCCTCCACCGCATGCA 62.409 66.667 19.57 0.00 34.56 3.96
1143 1289 2.821366 GTCCTCCACCGCATGCAG 60.821 66.667 19.57 9.32 0.00 4.41
1144 1290 4.783621 TCCTCCACCGCATGCAGC 62.784 66.667 19.57 0.00 40.87 5.25
1145 1291 4.790962 CCTCCACCGCATGCAGCT 62.791 66.667 19.57 0.00 42.61 4.24
1146 1292 2.749044 CTCCACCGCATGCAGCTT 60.749 61.111 19.57 0.00 42.61 3.74
1147 1293 2.747460 TCCACCGCATGCAGCTTC 60.747 61.111 19.57 0.00 42.61 3.86
1148 1294 3.818787 CCACCGCATGCAGCTTCC 61.819 66.667 19.57 0.00 42.61 3.46
1149 1295 2.749044 CACCGCATGCAGCTTCCT 60.749 61.111 19.57 0.00 42.61 3.36
1150 1296 2.749044 ACCGCATGCAGCTTCCTG 60.749 61.111 19.57 0.00 42.61 3.86
1151 1297 2.749044 CCGCATGCAGCTTCCTGT 60.749 61.111 19.57 0.00 41.26 4.00
1152 1298 2.758089 CCGCATGCAGCTTCCTGTC 61.758 63.158 19.57 0.00 41.26 3.51
1153 1299 2.758089 CGCATGCAGCTTCCTGTCC 61.758 63.158 19.57 0.00 41.26 4.02
1154 1300 2.758089 GCATGCAGCTTCCTGTCCG 61.758 63.158 14.21 0.00 41.26 4.79
1155 1301 2.110967 CATGCAGCTTCCTGTCCGG 61.111 63.158 0.00 0.00 41.26 5.14
1156 1302 2.293318 ATGCAGCTTCCTGTCCGGA 61.293 57.895 0.00 0.00 41.26 5.14
1158 1304 2.035442 GCAGCTTCCTGTCCGGAAC 61.035 63.158 5.23 0.59 46.80 3.62
1159 1305 1.738099 CAGCTTCCTGTCCGGAACG 60.738 63.158 5.23 0.00 46.80 3.95
1171 1317 2.585153 GGAACGCCCTCCTCTTCC 59.415 66.667 0.00 0.00 32.21 3.46
1172 1318 2.291043 GGAACGCCCTCCTCTTCCA 61.291 63.158 0.00 0.00 33.60 3.53
1173 1319 1.677552 GAACGCCCTCCTCTTCCAA 59.322 57.895 0.00 0.00 0.00 3.53
1174 1320 0.391793 GAACGCCCTCCTCTTCCAAG 60.392 60.000 0.00 0.00 0.00 3.61
1175 1321 1.842381 AACGCCCTCCTCTTCCAAGG 61.842 60.000 0.00 0.00 37.81 3.61
1176 1322 1.990060 CGCCCTCCTCTTCCAAGGA 60.990 63.158 0.00 0.00 43.30 3.36
1177 1323 1.553690 CGCCCTCCTCTTCCAAGGAA 61.554 60.000 0.99 0.99 44.81 3.36
1187 1333 2.484889 CTTCCAAGGAAGGCTATACGC 58.515 52.381 18.98 0.00 45.60 4.42
1369 1901 3.521605 TCGTCGCCCGAGAATCAT 58.478 55.556 0.00 0.00 41.60 2.45
1452 1996 4.056125 CACCCAGAGCTGACGCGA 62.056 66.667 15.93 0.00 42.32 5.87
1483 2027 4.072088 GCGACCGTGCCTTGTTCG 62.072 66.667 0.00 0.00 0.00 3.95
1485 2029 2.241880 CGACCGTGCCTTGTTCGTT 61.242 57.895 0.00 0.00 0.00 3.85
1486 2030 1.568025 GACCGTGCCTTGTTCGTTC 59.432 57.895 0.00 0.00 0.00 3.95
1491 2035 0.868406 GTGCCTTGTTCGTTCCTCAG 59.132 55.000 0.00 0.00 0.00 3.35
1503 2047 1.135489 GTTCCTCAGCATGTACGACGA 60.135 52.381 0.00 0.00 37.40 4.20
1513 2057 0.887836 TGTACGACGACTGCCTGTCT 60.888 55.000 0.00 0.00 43.25 3.41
1580 2124 3.843240 CCACGCGCTTCTTCTCGC 61.843 66.667 5.73 0.00 46.98 5.03
1593 2137 3.691342 CTCGCGGTTCAGGTGGGA 61.691 66.667 6.13 0.00 0.00 4.37
1656 2209 0.528466 CGCAGTGCCAGATACACGAT 60.528 55.000 10.11 0.00 42.94 3.73
1724 2277 1.280133 CCATCTCCTCACTTTCTGCCA 59.720 52.381 0.00 0.00 0.00 4.92
1725 2278 2.092538 CCATCTCCTCACTTTCTGCCAT 60.093 50.000 0.00 0.00 0.00 4.40
1726 2279 2.775911 TCTCCTCACTTTCTGCCATG 57.224 50.000 0.00 0.00 0.00 3.66
1727 2280 1.093159 CTCCTCACTTTCTGCCATGC 58.907 55.000 0.00 0.00 0.00 4.06
1818 2373 4.342092 ACTGGAAAAAGATCAACAAGGTGG 59.658 41.667 0.00 0.00 0.00 4.61
1844 2399 2.310966 GCCGATTCCTCGCGATTCC 61.311 63.158 10.36 0.00 43.66 3.01
1848 2403 1.221414 GATTCCTCGCGATTCCAAGG 58.779 55.000 10.36 6.34 0.00 3.61
1858 2413 2.664916 CGATTCCAAGGTGCAAAACAG 58.335 47.619 0.00 0.00 0.00 3.16
1866 2421 4.107622 CAAGGTGCAAAACAGAAGTCTTG 58.892 43.478 0.00 0.00 0.00 3.02
1867 2422 3.356290 AGGTGCAAAACAGAAGTCTTGT 58.644 40.909 0.00 0.00 0.00 3.16
1868 2423 3.129287 AGGTGCAAAACAGAAGTCTTGTG 59.871 43.478 8.14 8.14 0.00 3.33
1877 2432 1.070134 AGAAGTCTTGTGTAAGGCGCA 59.930 47.619 10.83 0.00 43.29 6.09
1909 2464 0.108138 CCCACTAGGCCTCGAGTTTG 60.108 60.000 9.68 1.51 0.00 2.93
1910 2465 0.608640 CCACTAGGCCTCGAGTTTGT 59.391 55.000 9.68 1.19 0.00 2.83
1968 2523 4.099266 GTGGCAAATATACTTTGGGCATCA 59.901 41.667 0.00 0.00 33.34 3.07
1972 2527 6.154445 GCAAATATACTTTGGGCATCATCTG 58.846 40.000 8.66 0.00 0.00 2.90
1986 2541 6.406624 GGGCATCATCTGATCTTTTTGTTCAT 60.407 38.462 0.00 0.00 31.21 2.57
2022 2577 1.012086 CTCACCACTCATGCCGAATG 58.988 55.000 0.00 0.00 37.66 2.67
2035 2590 4.114997 GAATGGTTGGGCGCCGTG 62.115 66.667 22.54 0.00 0.00 4.94
2062 2617 5.816919 TCGAAAGTTCAAAACCATCAACTC 58.183 37.500 0.00 0.00 0.00 3.01
2085 2640 3.990469 GCTCGATTTGTCTTGTCTCAGAA 59.010 43.478 0.00 0.00 0.00 3.02
2134 2689 6.262601 TCAAATCCGTCAAGAAAGTTCAAAC 58.737 36.000 0.00 0.00 0.00 2.93
2142 2697 2.919228 AGAAAGTTCAAACGACTGCCT 58.081 42.857 0.00 0.00 0.00 4.75
2180 2735 1.996292 TTCGAGCTCACCTGAAATCG 58.004 50.000 15.40 0.00 35.00 3.34
2201 2756 2.294449 TATCTGGACCGCATAGAGCT 57.706 50.000 0.00 0.00 42.61 4.09
2215 2770 2.947127 AGAGCTTTGGGGATCTATGC 57.053 50.000 0.00 0.00 29.61 3.14
2218 2773 1.133668 AGCTTTGGGGATCTATGCCAC 60.134 52.381 2.75 0.00 40.49 5.01
2242 2797 7.708752 CACGTTTTAATTTTGTGGGCCATATAT 59.291 33.333 10.70 0.54 0.00 0.86
2275 2830 8.608185 ATTATCAAAATACAGGTTGATGGGTT 57.392 30.769 8.73 0.00 42.86 4.11
2276 2831 5.975693 TCAAAATACAGGTTGATGGGTTC 57.024 39.130 0.00 0.00 0.00 3.62
2277 2832 4.457603 TCAAAATACAGGTTGATGGGTTCG 59.542 41.667 0.00 0.00 0.00 3.95
2278 2833 3.992943 AATACAGGTTGATGGGTTCGA 57.007 42.857 0.00 0.00 0.00 3.71
2279 2834 3.543680 ATACAGGTTGATGGGTTCGAG 57.456 47.619 0.00 0.00 0.00 4.04
2280 2835 1.348064 ACAGGTTGATGGGTTCGAGA 58.652 50.000 0.00 0.00 0.00 4.04
2281 2836 1.909302 ACAGGTTGATGGGTTCGAGAT 59.091 47.619 0.00 0.00 0.00 2.75
2282 2837 3.104512 ACAGGTTGATGGGTTCGAGATA 58.895 45.455 0.00 0.00 0.00 1.98
2283 2838 3.133003 ACAGGTTGATGGGTTCGAGATAG 59.867 47.826 0.00 0.00 0.00 2.08
2284 2839 3.133003 CAGGTTGATGGGTTCGAGATAGT 59.867 47.826 0.00 0.00 0.00 2.12
2285 2840 4.341235 CAGGTTGATGGGTTCGAGATAGTA 59.659 45.833 0.00 0.00 0.00 1.82
2286 2841 4.960469 AGGTTGATGGGTTCGAGATAGTAA 59.040 41.667 0.00 0.00 0.00 2.24
2287 2842 5.048507 GGTTGATGGGTTCGAGATAGTAAC 58.951 45.833 0.00 0.00 0.00 2.50
2288 2843 5.163437 GGTTGATGGGTTCGAGATAGTAACT 60.163 44.000 0.00 0.00 0.00 2.24
2289 2844 5.769484 TGATGGGTTCGAGATAGTAACTC 57.231 43.478 0.00 0.00 0.00 3.01
2321 2876 1.668101 CTACCCACGAGTCCCTCTGC 61.668 65.000 0.00 0.00 0.00 4.26
2325 2880 2.997897 ACGAGTCCCTCTGCCCAC 60.998 66.667 0.00 0.00 0.00 4.61
2336 2891 0.107897 TCTGCCCACGATTTATGCGT 60.108 50.000 0.00 0.00 43.67 5.24
2356 2911 3.697166 GTCCCAAACTCTCTCTCTCTCT 58.303 50.000 0.00 0.00 0.00 3.10
2358 2913 3.591527 TCCCAAACTCTCTCTCTCTCTCT 59.408 47.826 0.00 0.00 0.00 3.10
2362 2917 5.338708 CCAAACTCTCTCTCTCTCTCTCTCT 60.339 48.000 0.00 0.00 0.00 3.10
2363 2918 5.606348 AACTCTCTCTCTCTCTCTCTCTC 57.394 47.826 0.00 0.00 0.00 3.20
2364 2919 4.877773 ACTCTCTCTCTCTCTCTCTCTCT 58.122 47.826 0.00 0.00 0.00 3.10
2365 2920 5.276440 ACTCTCTCTCTCTCTCTCTCTCTT 58.724 45.833 0.00 0.00 0.00 2.85
2370 3235 2.609459 CTCTCTCTCTCTCTCTTCGTGC 59.391 54.545 0.00 0.00 0.00 5.34
2395 3260 1.255667 ATGGCTGGCAGCTTTGGAAG 61.256 55.000 35.73 0.00 41.99 3.46
2437 3302 0.038892 CGCCAACATGCTCTGCTTTT 60.039 50.000 0.00 0.00 0.00 2.27
2448 3313 2.157863 GCTCTGCTTTTGTTCGTAGTCC 59.842 50.000 0.00 0.00 0.00 3.85
2450 3315 2.367567 TCTGCTTTTGTTCGTAGTCCCT 59.632 45.455 0.00 0.00 0.00 4.20
2481 3346 1.478510 AGAGCACGAATCCGACATCTT 59.521 47.619 0.00 0.00 39.50 2.40
2493 3358 3.118992 TCCGACATCTTCATTGACTCTGG 60.119 47.826 0.00 0.00 0.00 3.86
2494 3359 3.368843 CCGACATCTTCATTGACTCTGGT 60.369 47.826 0.00 0.00 0.00 4.00
2495 3360 3.615937 CGACATCTTCATTGACTCTGGTG 59.384 47.826 0.00 0.00 0.00 4.17
2496 3361 4.573900 GACATCTTCATTGACTCTGGTGT 58.426 43.478 0.00 0.00 0.00 4.16
2581 3446 1.067416 TCGATGATAGTGTGCGGGC 59.933 57.895 0.00 0.00 0.00 6.13
2642 3507 0.034574 TGTTGACTGCCAGGTTGTGT 60.035 50.000 0.00 0.00 0.00 3.72
2711 3576 4.551603 GCAGTCAAACAAGCAGATATAGCG 60.552 45.833 0.00 0.00 37.01 4.26
2721 3586 8.671384 ACAAGCAGATATAGCGGTAAAAATTA 57.329 30.769 0.00 0.00 37.01 1.40
2724 3589 9.726438 AAGCAGATATAGCGGTAAAAATTATCT 57.274 29.630 0.00 3.77 37.01 1.98
2730 3595 9.975218 ATATAGCGGTAAAAATTATCTCCCAAT 57.025 29.630 0.00 0.00 0.00 3.16
2731 3596 6.391227 AGCGGTAAAAATTATCTCCCAATG 57.609 37.500 0.00 0.00 0.00 2.82
2732 3597 5.891551 AGCGGTAAAAATTATCTCCCAATGT 59.108 36.000 0.00 0.00 0.00 2.71
2733 3598 6.039382 AGCGGTAAAAATTATCTCCCAATGTC 59.961 38.462 0.00 0.00 0.00 3.06
2734 3599 6.183360 GCGGTAAAAATTATCTCCCAATGTCA 60.183 38.462 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.408700 AGGAGACGGAGGTGGTAGTT 59.591 55.000 0.00 0.00 0.00 2.24
46 47 4.881057 GAGGATCGAGGAGACGGA 57.119 61.111 0.00 0.00 0.00 4.69
93 98 0.259065 ACTGGGAGAGCGGACAGATA 59.741 55.000 0.00 0.00 35.08 1.98
136 143 4.111053 GTCGGCCCCTCCTTTCCC 62.111 72.222 0.00 0.00 0.00 3.97
210 217 1.817520 CGCCATTGTGCCCATCGTA 60.818 57.895 0.00 0.00 0.00 3.43
401 408 1.424403 TCGCCAACAACTACGTCATG 58.576 50.000 0.00 0.00 0.00 3.07
424 431 0.370273 GTCGTAAATCCAGCTGCACG 59.630 55.000 8.66 11.78 0.00 5.34
452 459 1.882623 CGTCAGATGGATCATCTCCGA 59.117 52.381 15.52 7.06 46.83 4.55
464 471 1.300465 CCATCGGCTCCGTCAGATG 60.300 63.158 8.28 4.69 40.74 2.90
491 498 1.071987 AAAAACGTCCTCCCGGTCC 59.928 57.895 0.00 0.00 0.00 4.46
660 667 1.259609 CTTCATGGCCAGCTTGGAAA 58.740 50.000 13.05 0.00 40.96 3.13
692 699 0.036010 AACTCCTCACGCCTTCATGG 60.036 55.000 0.00 0.00 39.35 3.66
693 700 1.466167 CAAACTCCTCACGCCTTCATG 59.534 52.381 0.00 0.00 0.00 3.07
694 701 1.347707 TCAAACTCCTCACGCCTTCAT 59.652 47.619 0.00 0.00 0.00 2.57
695 702 0.756294 TCAAACTCCTCACGCCTTCA 59.244 50.000 0.00 0.00 0.00 3.02
696 703 1.149148 GTCAAACTCCTCACGCCTTC 58.851 55.000 0.00 0.00 0.00 3.46
697 704 0.600255 CGTCAAACTCCTCACGCCTT 60.600 55.000 0.00 0.00 0.00 4.35
698 705 1.006102 CGTCAAACTCCTCACGCCT 60.006 57.895 0.00 0.00 0.00 5.52
699 706 3.550656 CGTCAAACTCCTCACGCC 58.449 61.111 0.00 0.00 0.00 5.68
701 708 0.600255 AAGGCGTCAAACTCCTCACG 60.600 55.000 0.00 0.00 30.85 4.35
702 709 2.067013 GTAAGGCGTCAAACTCCTCAC 58.933 52.381 0.00 0.00 30.85 3.51
703 710 1.689813 TGTAAGGCGTCAAACTCCTCA 59.310 47.619 0.00 0.00 30.85 3.86
704 711 2.450609 TGTAAGGCGTCAAACTCCTC 57.549 50.000 0.00 0.00 30.85 3.71
705 712 2.490991 GTTGTAAGGCGTCAAACTCCT 58.509 47.619 0.00 0.00 34.16 3.69
706 713 1.193874 CGTTGTAAGGCGTCAAACTCC 59.806 52.381 0.00 0.00 0.00 3.85
707 714 1.398071 GCGTTGTAAGGCGTCAAACTC 60.398 52.381 0.00 0.00 0.00 3.01
708 715 0.584876 GCGTTGTAAGGCGTCAAACT 59.415 50.000 0.00 0.00 0.00 2.66
709 716 0.305313 TGCGTTGTAAGGCGTCAAAC 59.695 50.000 5.04 0.00 42.35 2.93
710 717 1.015109 TTGCGTTGTAAGGCGTCAAA 58.985 45.000 5.04 0.00 42.35 2.69
711 718 0.305313 GTTGCGTTGTAAGGCGTCAA 59.695 50.000 5.04 0.00 42.35 3.18
712 719 1.500512 GGTTGCGTTGTAAGGCGTCA 61.501 55.000 5.04 0.00 42.35 4.35
713 720 1.205820 GGTTGCGTTGTAAGGCGTC 59.794 57.895 5.04 0.00 42.35 5.19
714 721 2.600475 CGGTTGCGTTGTAAGGCGT 61.600 57.895 5.04 0.00 42.35 5.68
715 722 1.283613 TACGGTTGCGTTGTAAGGCG 61.284 55.000 5.04 0.00 42.35 5.52
716 723 0.164432 GTACGGTTGCGTTGTAAGGC 59.836 55.000 2.58 2.58 40.04 4.35
717 724 1.787012 AGTACGGTTGCGTTGTAAGG 58.213 50.000 0.00 0.00 0.00 2.69
718 725 3.181537 GCTAAGTACGGTTGCGTTGTAAG 60.182 47.826 0.00 0.00 0.00 2.34
719 726 2.730928 GCTAAGTACGGTTGCGTTGTAA 59.269 45.455 0.00 0.00 0.00 2.41
720 727 2.288091 TGCTAAGTACGGTTGCGTTGTA 60.288 45.455 0.00 0.00 0.00 2.41
721 728 1.142474 GCTAAGTACGGTTGCGTTGT 58.858 50.000 0.00 0.00 0.00 3.32
722 729 1.126113 CTGCTAAGTACGGTTGCGTTG 59.874 52.381 0.00 0.00 0.00 4.10
723 730 1.425412 CTGCTAAGTACGGTTGCGTT 58.575 50.000 0.00 0.00 0.00 4.84
724 731 1.012486 GCTGCTAAGTACGGTTGCGT 61.012 55.000 0.00 0.00 0.00 5.24
725 732 0.736325 AGCTGCTAAGTACGGTTGCG 60.736 55.000 0.00 0.00 0.00 4.85
726 733 1.128692 CAAGCTGCTAAGTACGGTTGC 59.871 52.381 0.90 0.00 0.00 4.17
727 734 2.412089 GACAAGCTGCTAAGTACGGTTG 59.588 50.000 0.90 0.00 39.84 3.77
728 735 2.612221 GGACAAGCTGCTAAGTACGGTT 60.612 50.000 0.90 0.00 0.00 4.44
729 736 1.067071 GGACAAGCTGCTAAGTACGGT 60.067 52.381 0.90 0.00 0.00 4.83
730 737 1.641577 GGACAAGCTGCTAAGTACGG 58.358 55.000 0.90 0.00 0.00 4.02
731 738 1.641577 GGGACAAGCTGCTAAGTACG 58.358 55.000 0.90 0.00 0.00 3.67
732 739 1.203994 TCGGGACAAGCTGCTAAGTAC 59.796 52.381 0.90 5.68 0.00 2.73
733 740 1.476891 CTCGGGACAAGCTGCTAAGTA 59.523 52.381 0.90 0.00 0.00 2.24
734 741 0.247736 CTCGGGACAAGCTGCTAAGT 59.752 55.000 0.90 4.81 0.00 2.24
735 742 0.460987 CCTCGGGACAAGCTGCTAAG 60.461 60.000 0.90 0.99 0.00 2.18
736 743 1.596934 CCTCGGGACAAGCTGCTAA 59.403 57.895 0.90 0.00 0.00 3.09
737 744 3.019003 GCCTCGGGACAAGCTGCTA 62.019 63.158 0.90 0.00 0.00 3.49
738 745 4.400961 GCCTCGGGACAAGCTGCT 62.401 66.667 0.00 0.00 0.00 4.24
739 746 4.400961 AGCCTCGGGACAAGCTGC 62.401 66.667 0.00 0.00 33.41 5.25
740 747 2.125350 GAGCCTCGGGACAAGCTG 60.125 66.667 0.00 0.00 35.23 4.24
741 748 2.284258 AGAGCCTCGGGACAAGCT 60.284 61.111 0.00 0.00 38.56 3.74
742 749 2.125350 CAGAGCCTCGGGACAAGC 60.125 66.667 0.00 0.00 0.00 4.01
743 750 2.125350 GCAGAGCCTCGGGACAAG 60.125 66.667 0.00 0.00 0.00 3.16
744 751 4.069232 CGCAGAGCCTCGGGACAA 62.069 66.667 0.00 0.00 0.00 3.18
746 753 4.500116 GTCGCAGAGCCTCGGGAC 62.500 72.222 14.28 14.28 36.95 4.46
1032 1041 3.117171 CTCGTCCTGCTGCTGCAC 61.117 66.667 14.93 4.40 45.31 4.57
1081 1227 2.932234 CGGCGAGAACCACACCTCT 61.932 63.158 0.00 0.00 0.00 3.69
1082 1228 2.432628 CGGCGAGAACCACACCTC 60.433 66.667 0.00 0.00 0.00 3.85
1083 1229 4.681978 GCGGCGAGAACCACACCT 62.682 66.667 12.98 0.00 0.00 4.00
1109 1255 4.883354 CCTCCCATTGGCCCGAGC 62.883 72.222 0.00 0.00 38.76 5.03
1110 1256 3.406595 GACCTCCCATTGGCCCGAG 62.407 68.421 0.00 0.00 0.00 4.63
1111 1257 3.407967 GACCTCCCATTGGCCCGA 61.408 66.667 0.00 0.00 0.00 5.14
1112 1258 4.506255 GGACCTCCCATTGGCCCG 62.506 72.222 0.00 0.00 34.14 6.13
1113 1259 3.023735 AGGACCTCCCATTGGCCC 61.024 66.667 0.00 0.00 37.41 5.80
1114 1260 2.597903 GAGGACCTCCCATTGGCC 59.402 66.667 10.74 0.00 37.41 5.36
1115 1261 2.597903 GGAGGACCTCCCATTGGC 59.402 66.667 28.16 2.54 44.36 4.52
1123 1269 2.187946 CATGCGGTGGAGGACCTC 59.812 66.667 13.60 13.60 43.55 3.85
1124 1270 4.101448 GCATGCGGTGGAGGACCT 62.101 66.667 0.00 0.00 43.55 3.85
1125 1271 4.408821 TGCATGCGGTGGAGGACC 62.409 66.667 14.09 0.00 42.07 4.46
1126 1272 2.821366 CTGCATGCGGTGGAGGAC 60.821 66.667 18.84 0.00 42.10 3.85
1127 1273 4.783621 GCTGCATGCGGTGGAGGA 62.784 66.667 26.79 0.00 45.55 3.71
1128 1274 4.790962 AGCTGCATGCGGTGGAGG 62.791 66.667 26.79 5.56 45.55 4.30
1136 1282 2.758089 CGGACAGGAAGCTGCATGC 61.758 63.158 11.82 11.82 43.29 4.06
1137 1283 2.110967 CCGGACAGGAAGCTGCATG 61.111 63.158 4.38 4.38 45.00 4.06
1138 1284 2.270205 CCGGACAGGAAGCTGCAT 59.730 61.111 0.00 0.00 45.00 3.96
1147 1293 4.452733 GAGGGCGTTCCGGACAGG 62.453 72.222 1.83 2.65 41.52 4.00
1148 1294 4.452733 GGAGGGCGTTCCGGACAG 62.453 72.222 1.83 1.41 41.52 3.51
1150 1296 4.144703 GAGGAGGGCGTTCCGGAC 62.145 72.222 1.83 0.00 42.29 4.79
1151 1297 3.899545 AAGAGGAGGGCGTTCCGGA 62.900 63.158 0.00 0.00 42.29 5.14
1152 1298 3.372554 GAAGAGGAGGGCGTTCCGG 62.373 68.421 0.00 0.00 42.29 5.14
1153 1299 2.184579 GAAGAGGAGGGCGTTCCG 59.815 66.667 1.58 0.00 42.29 4.30
1154 1300 1.838073 TTGGAAGAGGAGGGCGTTCC 61.838 60.000 0.00 0.00 39.22 3.62
1155 1301 0.391793 CTTGGAAGAGGAGGGCGTTC 60.392 60.000 0.00 0.00 0.00 3.95
1156 1302 1.679898 CTTGGAAGAGGAGGGCGTT 59.320 57.895 0.00 0.00 0.00 4.84
1157 1303 2.294078 CCTTGGAAGAGGAGGGCGT 61.294 63.158 0.00 0.00 39.25 5.68
1158 1304 1.553690 TTCCTTGGAAGAGGAGGGCG 61.554 60.000 0.00 0.00 46.09 6.13
1159 1305 0.254462 CTTCCTTGGAAGAGGAGGGC 59.746 60.000 21.34 0.00 46.09 5.19
1161 1307 0.254462 GCCTTCCTTGGAAGAGGAGG 59.746 60.000 25.99 13.84 46.09 4.30
1162 1308 1.284313 AGCCTTCCTTGGAAGAGGAG 58.716 55.000 25.99 13.10 46.09 3.69
1163 1309 2.642171 TAGCCTTCCTTGGAAGAGGA 57.358 50.000 25.99 10.75 43.99 3.71
1164 1310 3.243907 CGTATAGCCTTCCTTGGAAGAGG 60.244 52.174 25.99 15.12 38.20 3.69
1165 1311 3.800604 GCGTATAGCCTTCCTTGGAAGAG 60.801 52.174 25.99 17.87 40.81 2.85
1166 1312 2.102588 GCGTATAGCCTTCCTTGGAAGA 59.897 50.000 25.99 10.55 40.81 2.87
1167 1313 2.484889 GCGTATAGCCTTCCTTGGAAG 58.515 52.381 19.53 19.53 40.81 3.46
1168 1314 2.614829 GCGTATAGCCTTCCTTGGAA 57.385 50.000 1.86 1.86 40.81 3.53
1180 1326 1.806623 GCAGAACCTGGTGGCGTATAG 60.807 57.143 0.00 0.00 36.63 1.31
1181 1327 0.177141 GCAGAACCTGGTGGCGTATA 59.823 55.000 0.00 0.00 36.63 1.47
1182 1328 1.078426 GCAGAACCTGGTGGCGTAT 60.078 57.895 0.00 0.00 36.63 3.06
1183 1329 2.167398 GAGCAGAACCTGGTGGCGTA 62.167 60.000 0.00 0.00 42.53 4.42
1184 1330 3.537206 GAGCAGAACCTGGTGGCGT 62.537 63.158 0.00 0.00 42.53 5.68
1185 1331 2.743928 GAGCAGAACCTGGTGGCG 60.744 66.667 0.00 0.00 42.53 5.69
1186 1332 1.673665 CTGAGCAGAACCTGGTGGC 60.674 63.158 0.00 5.13 42.53 5.01
1187 1333 0.321122 GTCTGAGCAGAACCTGGTGG 60.321 60.000 0.00 0.00 42.53 4.61
1369 1901 2.554142 CAATAGTTGCGGCTCAGATGA 58.446 47.619 0.00 0.00 0.00 2.92
1409 1941 1.289109 ATTGTTGTCGCCGAAGTCCG 61.289 55.000 0.00 0.00 38.18 4.79
1483 2027 1.135489 TCGTCGTACATGCTGAGGAAC 60.135 52.381 0.00 0.00 0.00 3.62
1485 2029 0.450583 GTCGTCGTACATGCTGAGGA 59.549 55.000 0.00 0.00 0.00 3.71
1486 2030 0.452184 AGTCGTCGTACATGCTGAGG 59.548 55.000 0.00 0.00 0.00 3.86
1491 2035 1.153823 AGGCAGTCGTCGTACATGC 60.154 57.895 0.00 0.00 36.16 4.06
1503 2047 3.371021 CCGAGACAGACAGGCAGT 58.629 61.111 0.00 0.00 0.00 4.40
1513 2057 4.316823 AGGTCCCTGGCCGAGACA 62.317 66.667 18.15 0.00 31.99 3.41
1538 2082 0.253044 TAGATGGAGTTGCTGCCCAC 59.747 55.000 0.00 0.00 32.07 4.61
1580 2124 1.137086 CTAGTGATCCCACCTGAACCG 59.863 57.143 0.00 0.00 44.22 4.44
1581 2125 1.134371 GCTAGTGATCCCACCTGAACC 60.134 57.143 0.00 0.00 44.22 3.62
1683 2236 2.361104 GCAATGGTGAAGGGCCGA 60.361 61.111 0.00 0.00 0.00 5.54
1724 2277 1.133976 GGTCCACTTGCTAGGATGCAT 60.134 52.381 0.00 0.00 42.96 3.96
1725 2278 0.253044 GGTCCACTTGCTAGGATGCA 59.747 55.000 0.00 0.00 41.65 3.96
1726 2279 0.253044 TGGTCCACTTGCTAGGATGC 59.747 55.000 0.00 0.00 36.11 3.91
1727 2280 2.787473 TTGGTCCACTTGCTAGGATG 57.213 50.000 0.00 0.00 36.11 3.51
1818 2373 2.044946 AGGAATCGGCAACTGGGC 60.045 61.111 0.00 0.00 39.06 5.36
1844 2399 4.107622 CAAGACTTCTGTTTTGCACCTTG 58.892 43.478 0.00 0.00 32.77 3.61
1848 2403 4.096732 ACACAAGACTTCTGTTTTGCAC 57.903 40.909 0.00 0.00 40.60 4.57
1858 2413 1.194772 GTGCGCCTTACACAAGACTTC 59.805 52.381 4.18 0.00 37.96 3.01
1866 2421 2.584791 CATTCTTTGTGCGCCTTACAC 58.415 47.619 4.18 0.00 38.55 2.90
1867 2422 1.068610 GCATTCTTTGTGCGCCTTACA 60.069 47.619 4.18 0.00 32.29 2.41
1868 2423 1.617740 GCATTCTTTGTGCGCCTTAC 58.382 50.000 4.18 0.00 32.29 2.34
1877 2432 0.037590 TAGTGGGGCGCATTCTTTGT 59.962 50.000 10.83 0.00 0.00 2.83
1899 2454 4.532314 ACCCTAAACTACAAACTCGAGG 57.468 45.455 18.41 1.00 0.00 4.63
1900 2455 6.088616 CGTAAACCCTAAACTACAAACTCGAG 59.911 42.308 11.84 11.84 0.00 4.04
1902 2457 5.388786 GCGTAAACCCTAAACTACAAACTCG 60.389 44.000 0.00 0.00 0.00 4.18
1904 2459 4.756642 GGCGTAAACCCTAAACTACAAACT 59.243 41.667 0.00 0.00 0.00 2.66
1909 2464 4.192429 TGAGGCGTAAACCCTAAACTAC 57.808 45.455 0.00 0.00 31.41 2.73
1910 2465 4.467082 TGATGAGGCGTAAACCCTAAACTA 59.533 41.667 0.00 0.00 31.41 2.24
2000 2555 0.970427 TCGGCATGAGTGGTGAGCTA 60.970 55.000 0.00 0.00 0.00 3.32
2001 2556 1.830587 TTCGGCATGAGTGGTGAGCT 61.831 55.000 0.00 0.00 0.00 4.09
2022 2577 2.748647 ATAACACGGCGCCCAACC 60.749 61.111 23.46 0.00 0.00 3.77
2030 2585 3.799137 TTGAACTTTCGATAACACGGC 57.201 42.857 0.00 0.00 0.00 5.68
2035 2590 7.860872 AGTTGATGGTTTTGAACTTTCGATAAC 59.139 33.333 0.00 0.00 0.00 1.89
2062 2617 2.328473 TGAGACAAGACAAATCGAGCG 58.672 47.619 0.00 0.00 0.00 5.03
2085 2640 0.265553 ATATGCCATGGGTGCCCTTT 59.734 50.000 15.13 0.00 36.94 3.11
2094 2649 3.737032 TTTGATGTGCATATGCCATGG 57.263 42.857 26.40 7.63 41.18 3.66
2142 2697 0.690762 AAGCCAAAACGCCTCTCCTA 59.309 50.000 0.00 0.00 0.00 2.94
2180 2735 2.678324 GCTCTATGCGGTCCAGATAAC 58.322 52.381 0.00 0.00 0.00 1.89
2201 2756 0.916086 ACGTGGCATAGATCCCCAAA 59.084 50.000 0.00 0.00 0.00 3.28
2215 2770 2.803386 GGCCCACAAAATTAAAACGTGG 59.197 45.455 0.00 0.00 45.46 4.94
2218 2773 9.751542 TTATATATGGCCCACAAAATTAAAACG 57.248 29.630 0.00 0.00 0.00 3.60
2247 2802 9.316730 CCCATCAACCTGTATTTTGATAATTTG 57.683 33.333 0.00 0.00 39.86 2.32
2248 2803 9.045745 ACCCATCAACCTGTATTTTGATAATTT 57.954 29.630 0.00 0.00 39.86 1.82
2249 2804 8.608185 ACCCATCAACCTGTATTTTGATAATT 57.392 30.769 0.00 0.00 39.86 1.40
2250 2805 8.608185 AACCCATCAACCTGTATTTTGATAAT 57.392 30.769 0.00 0.00 39.86 1.28
2251 2806 7.148154 CGAACCCATCAACCTGTATTTTGATAA 60.148 37.037 0.00 0.00 39.86 1.75
2252 2807 6.317642 CGAACCCATCAACCTGTATTTTGATA 59.682 38.462 0.00 0.00 39.86 2.15
2255 2810 4.457603 TCGAACCCATCAACCTGTATTTTG 59.542 41.667 0.00 0.00 0.00 2.44
2262 2817 2.698855 ATCTCGAACCCATCAACCTG 57.301 50.000 0.00 0.00 0.00 4.00
2275 2830 8.262227 AGAGAGAAGAAAGAGTTACTATCTCGA 58.738 37.037 0.00 0.00 37.07 4.04
2276 2831 8.433421 AGAGAGAAGAAAGAGTTACTATCTCG 57.567 38.462 0.00 0.00 37.07 4.04
2277 2832 9.614792 AGAGAGAGAAGAAAGAGTTACTATCTC 57.385 37.037 0.00 0.00 40.60 2.75
2280 2835 9.623000 GGTAGAGAGAGAAGAAAGAGTTACTAT 57.377 37.037 0.00 0.00 0.00 2.12
2281 2836 8.048514 GGGTAGAGAGAGAAGAAAGAGTTACTA 58.951 40.741 0.00 0.00 0.00 1.82
2282 2837 6.888088 GGGTAGAGAGAGAAGAAAGAGTTACT 59.112 42.308 0.00 0.00 0.00 2.24
2283 2838 6.660094 TGGGTAGAGAGAGAAGAAAGAGTTAC 59.340 42.308 0.00 0.00 0.00 2.50
2284 2839 6.660094 GTGGGTAGAGAGAGAAGAAAGAGTTA 59.340 42.308 0.00 0.00 0.00 2.24
2285 2840 5.479027 GTGGGTAGAGAGAGAAGAAAGAGTT 59.521 44.000 0.00 0.00 0.00 3.01
2286 2841 5.014202 GTGGGTAGAGAGAGAAGAAAGAGT 58.986 45.833 0.00 0.00 0.00 3.24
2287 2842 4.095782 CGTGGGTAGAGAGAGAAGAAAGAG 59.904 50.000 0.00 0.00 0.00 2.85
2288 2843 4.011023 CGTGGGTAGAGAGAGAAGAAAGA 58.989 47.826 0.00 0.00 0.00 2.52
2289 2844 4.011023 TCGTGGGTAGAGAGAGAAGAAAG 58.989 47.826 0.00 0.00 0.00 2.62
2321 2876 0.462937 TGGGACGCATAAATCGTGGG 60.463 55.000 0.00 0.00 40.59 4.61
2325 2880 2.936498 AGAGTTTGGGACGCATAAATCG 59.064 45.455 0.00 0.00 0.00 3.34
2336 2891 3.591527 AGAGAGAGAGAGAGAGTTTGGGA 59.408 47.826 0.00 0.00 0.00 4.37
2395 3260 1.009829 CCACTAGATCCAAGTTGCGC 58.990 55.000 0.00 0.00 0.00 6.09
2437 3302 0.178955 TCACCCAGGGACTACGAACA 60.179 55.000 14.54 0.00 36.02 3.18
2448 3313 1.915266 TGCTCTCCAGTCACCCAGG 60.915 63.158 0.00 0.00 0.00 4.45
2450 3315 2.574018 CGTGCTCTCCAGTCACCCA 61.574 63.158 0.00 0.00 0.00 4.51
2481 3346 1.543208 GCCACACACCAGAGTCAATGA 60.543 52.381 0.00 0.00 0.00 2.57
2541 3406 1.305297 ATCCAGCCGTCTCACTCCA 60.305 57.895 0.00 0.00 0.00 3.86
2581 3446 3.803082 CATGTCCAAGCACCCGCG 61.803 66.667 0.00 0.00 45.49 6.46
2642 3507 1.339342 GCTTTGGGCTTACGGTTCCTA 60.339 52.381 0.00 0.00 38.06 2.94


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

AutoCloner maintained by Alex Coulton.