Multiple sequence alignment - TraesCS5B01G549800

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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 TraesCS5B01G549800 chr5B 100.000 4730 0 0 1 4730 701464367 701459638 0.000000e+00 8735.0
1 TraesCS5B01G549800 chr4A 91.509 1272 72 14 2253 3501 617943165 617944423 0.000000e+00 1718.0
2 TraesCS5B01G549800 chr4A 92.096 1126 51 18 3355 4456 617944589 617945700 0.000000e+00 1552.0
3 TraesCS5B01G549800 chr4A 82.933 1125 80 55 1242 2294 617942066 617943150 0.000000e+00 911.0
4 TraesCS5B01G549800 chr4A 92.593 54 4 0 4663 4716 617945734 617945787 1.410000e-10 78.7
5 TraesCS5B01G549800 chr5D 90.622 1237 75 19 2290 3501 549857471 549856251 0.000000e+00 1604.0
6 TraesCS5B01G549800 chr5D 91.278 1158 51 21 3469 4601 549855962 549854830 0.000000e+00 1533.0
7 TraesCS5B01G549800 chr5D 80.778 1259 85 71 996 2182 549858689 549857516 0.000000e+00 839.0
8 TraesCS5B01G549800 chr5D 90.071 141 3 1 4590 4730 549854808 549854679 6.290000e-39 172.0
9 TraesCS5B01G549800 chr5D 100.000 44 0 0 2210 2253 549857516 549857473 1.090000e-11 82.4
10 TraesCS5B01G549800 chr3B 96.405 918 19 4 1 909 581345119 581346031 0.000000e+00 1500.0
11 TraesCS5B01G549800 chr3B 95.311 917 28 5 1 907 607523535 607524446 0.000000e+00 1441.0
12 TraesCS5B01G549800 chr7A 96.296 918 20 4 1 909 206573000 206572088 0.000000e+00 1495.0
13 TraesCS5B01G549800 chr7A 92.568 915 51 8 1 905 491890688 491889781 0.000000e+00 1297.0
14 TraesCS5B01G549800 chr7A 92.393 723 42 9 191 905 549320716 549321433 0.000000e+00 1018.0
15 TraesCS5B01G549800 chr2B 96.061 914 22 5 1 905 142886730 142885822 0.000000e+00 1476.0
16 TraesCS5B01G549800 chr1B 95.098 918 29 11 1 909 23815384 23814474 0.000000e+00 1432.0
17 TraesCS5B01G549800 chr1B 94.872 819 29 6 1 810 48529200 48528386 0.000000e+00 1267.0
18 TraesCS5B01G549800 chr1B 94.679 639 22 6 277 907 388024930 388024296 0.000000e+00 981.0
19 TraesCS5B01G549800 chr2D 94.910 884 31 5 31 905 197524330 197525208 0.000000e+00 1371.0
20 TraesCS5B01G549800 chr3A 92.912 917 47 6 1 905 1717262 1718172 0.000000e+00 1317.0


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 TraesCS5B01G549800 chr5B 701459638 701464367 4729 True 8735.000 8735 100.00000 1 4730 1 chr5B.!!$R1 4729
1 TraesCS5B01G549800 chr4A 617942066 617945787 3721 False 1064.925 1718 89.78275 1242 4716 4 chr4A.!!$F1 3474
2 TraesCS5B01G549800 chr5D 549854679 549858689 4010 True 846.080 1604 90.54980 996 4730 5 chr5D.!!$R1 3734
3 TraesCS5B01G549800 chr3B 581345119 581346031 912 False 1500.000 1500 96.40500 1 909 1 chr3B.!!$F1 908
4 TraesCS5B01G549800 chr3B 607523535 607524446 911 False 1441.000 1441 95.31100 1 907 1 chr3B.!!$F2 906
5 TraesCS5B01G549800 chr7A 206572088 206573000 912 True 1495.000 1495 96.29600 1 909 1 chr7A.!!$R1 908
6 TraesCS5B01G549800 chr7A 491889781 491890688 907 True 1297.000 1297 92.56800 1 905 1 chr7A.!!$R2 904
7 TraesCS5B01G549800 chr7A 549320716 549321433 717 False 1018.000 1018 92.39300 191 905 1 chr7A.!!$F1 714
8 TraesCS5B01G549800 chr2B 142885822 142886730 908 True 1476.000 1476 96.06100 1 905 1 chr2B.!!$R1 904
9 TraesCS5B01G549800 chr1B 23814474 23815384 910 True 1432.000 1432 95.09800 1 909 1 chr1B.!!$R1 908
10 TraesCS5B01G549800 chr1B 48528386 48529200 814 True 1267.000 1267 94.87200 1 810 1 chr1B.!!$R2 809
11 TraesCS5B01G549800 chr1B 388024296 388024930 634 True 981.000 981 94.67900 277 907 1 chr1B.!!$R3 630
12 TraesCS5B01G549800 chr2D 197524330 197525208 878 False 1371.000 1371 94.91000 31 905 1 chr2D.!!$F1 874
13 TraesCS5B01G549800 chr3A 1717262 1718172 910 False 1317.000 1317 92.91200 1 905 1 chr3A.!!$F1 904

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
925 942 0.180642 TTGTTGACAGGTTACCGGCA 59.819 50.0 0.0 0.0 0.0 5.69 F
1313 1337 0.037232 CAACCACGACTCTTCTCCCC 60.037 60.0 0.0 0.0 0.0 4.81 F
2473 2672 0.037447 GCTGCTTCCTCCTTCAACCT 59.963 55.0 0.0 0.0 0.0 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2175 2314 0.179227 CACACACACACACACACACG 60.179 55.0 0.00 0.00 0.00 4.49 R
2482 2681 0.255890 TAGGAACCCCTTGATGCTGC 59.744 55.0 0.00 0.00 40.78 5.25 R
4407 5293 0.539986 TTCGCACCCTGGGAATAGAC 59.460 55.0 22.23 0.61 43.09 2.59 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
219 221 8.802267 AGTAGTTTTGCATAATTTAAGCTTCCA 58.198 29.630 0.00 0.00 0.00 3.53
280 282 2.872245 TCTTGCTCCGAGTGAAAACTTG 59.128 45.455 0.00 0.00 0.00 3.16
363 366 5.337571 CCAACTTCTAATGTCAGAGCACCTA 60.338 44.000 0.00 0.00 0.00 3.08
442 445 7.125792 AGACCCACAAATCAATACCTACTAG 57.874 40.000 0.00 0.00 0.00 2.57
523 528 7.043454 TGAAATGAACGAACAAACAAAACTG 57.957 32.000 0.00 0.00 0.00 3.16
566 571 6.047231 ACTCAGTAGTAACACCTCAAACAAC 58.953 40.000 0.00 0.00 32.84 3.32
889 906 3.802685 ACACGCTCAACTCAACTAGTTTC 59.197 43.478 5.07 0.00 46.61 2.78
923 940 4.577834 AAAATTGTTGACAGGTTACCGG 57.422 40.909 0.00 0.00 0.00 5.28
924 941 1.530323 ATTGTTGACAGGTTACCGGC 58.470 50.000 0.00 0.00 0.00 6.13
925 942 0.180642 TTGTTGACAGGTTACCGGCA 59.819 50.000 0.00 0.00 0.00 5.69
926 943 0.533308 TGTTGACAGGTTACCGGCAC 60.533 55.000 0.00 0.00 0.00 5.01
927 944 0.533308 GTTGACAGGTTACCGGCACA 60.533 55.000 0.00 0.00 0.00 4.57
928 945 0.250124 TTGACAGGTTACCGGCACAG 60.250 55.000 0.00 0.00 0.00 3.66
929 946 2.032071 ACAGGTTACCGGCACAGC 59.968 61.111 0.00 0.00 0.00 4.40
930 947 3.118454 CAGGTTACCGGCACAGCG 61.118 66.667 0.00 0.00 0.00 5.18
953 970 2.670251 CGGGGTGGCGTGCTTTTA 60.670 61.111 0.00 0.00 0.00 1.52
954 971 2.686816 CGGGGTGGCGTGCTTTTAG 61.687 63.158 0.00 0.00 0.00 1.85
955 972 2.566529 GGGTGGCGTGCTTTTAGC 59.433 61.111 0.00 0.00 42.82 3.09
956 973 1.971695 GGGTGGCGTGCTTTTAGCT 60.972 57.895 0.00 0.00 42.97 3.32
957 974 0.675522 GGGTGGCGTGCTTTTAGCTA 60.676 55.000 0.00 0.00 42.97 3.32
958 975 0.446616 GGTGGCGTGCTTTTAGCTAC 59.553 55.000 0.00 0.00 42.97 3.58
959 976 1.439679 GTGGCGTGCTTTTAGCTACT 58.560 50.000 0.00 0.00 42.97 2.57
960 977 1.128692 GTGGCGTGCTTTTAGCTACTG 59.871 52.381 0.00 0.00 42.97 2.74
961 978 1.270625 TGGCGTGCTTTTAGCTACTGT 60.271 47.619 0.00 0.00 42.97 3.55
962 979 2.028839 TGGCGTGCTTTTAGCTACTGTA 60.029 45.455 0.00 0.00 42.97 2.74
963 980 2.603560 GGCGTGCTTTTAGCTACTGTAG 59.396 50.000 10.48 10.48 42.97 2.74
964 981 3.508762 GCGTGCTTTTAGCTACTGTAGA 58.491 45.455 18.64 0.00 42.97 2.59
965 982 4.113354 GCGTGCTTTTAGCTACTGTAGAT 58.887 43.478 18.64 14.70 42.97 1.98
966 983 5.279384 GCGTGCTTTTAGCTACTGTAGATA 58.721 41.667 18.64 13.61 42.97 1.98
967 984 5.399892 GCGTGCTTTTAGCTACTGTAGATAG 59.600 44.000 18.64 7.86 42.97 2.08
968 985 6.726230 CGTGCTTTTAGCTACTGTAGATAGA 58.274 40.000 18.64 8.99 42.97 1.98
969 986 7.364200 CGTGCTTTTAGCTACTGTAGATAGAT 58.636 38.462 18.64 0.00 42.97 1.98
970 987 8.504815 CGTGCTTTTAGCTACTGTAGATAGATA 58.495 37.037 18.64 0.00 42.97 1.98
971 988 9.834628 GTGCTTTTAGCTACTGTAGATAGATAG 57.165 37.037 18.64 13.87 42.97 2.08
972 989 9.015367 TGCTTTTAGCTACTGTAGATAGATAGG 57.985 37.037 18.64 7.58 42.97 2.57
973 990 9.016438 GCTTTTAGCTACTGTAGATAGATAGGT 57.984 37.037 18.64 0.00 38.45 3.08
976 993 9.669887 TTTAGCTACTGTAGATAGATAGGTAGC 57.330 37.037 18.64 12.42 46.01 3.58
977 994 6.655930 AGCTACTGTAGATAGATAGGTAGCC 58.344 44.000 18.64 0.00 46.49 3.93
978 995 6.215841 AGCTACTGTAGATAGATAGGTAGCCA 59.784 42.308 18.64 0.00 46.49 4.75
979 996 6.885376 GCTACTGTAGATAGATAGGTAGCCAA 59.115 42.308 18.64 0.00 42.41 4.52
980 997 7.066525 GCTACTGTAGATAGATAGGTAGCCAAG 59.933 44.444 18.64 0.00 42.41 3.61
981 998 6.854578 ACTGTAGATAGATAGGTAGCCAAGT 58.145 40.000 0.00 0.00 0.00 3.16
982 999 7.299134 ACTGTAGATAGATAGGTAGCCAAGTT 58.701 38.462 0.00 0.00 0.00 2.66
983 1000 8.446394 ACTGTAGATAGATAGGTAGCCAAGTTA 58.554 37.037 0.00 0.00 0.00 2.24
984 1001 9.298250 CTGTAGATAGATAGGTAGCCAAGTTAA 57.702 37.037 0.00 0.00 0.00 2.01
985 1002 9.298250 TGTAGATAGATAGGTAGCCAAGTTAAG 57.702 37.037 0.00 0.00 0.00 1.85
986 1003 7.784470 AGATAGATAGGTAGCCAAGTTAAGG 57.216 40.000 0.00 0.00 0.00 2.69
992 1009 4.390048 GCCAAGTTAAGGCGGACA 57.610 55.556 0.00 0.00 43.15 4.02
993 1010 1.873863 GCCAAGTTAAGGCGGACAC 59.126 57.895 0.00 0.00 43.15 3.67
994 1011 1.583495 GCCAAGTTAAGGCGGACACC 61.583 60.000 0.00 0.00 43.15 4.16
1005 1022 0.960364 GCGGACACCACACCATGATT 60.960 55.000 0.00 0.00 0.00 2.57
1006 1023 0.804364 CGGACACCACACCATGATTG 59.196 55.000 0.00 0.00 0.00 2.67
1007 1024 1.610363 CGGACACCACACCATGATTGA 60.610 52.381 0.00 0.00 0.00 2.57
1019 1036 4.755629 CACCATGATTGATGATGGAGACTC 59.244 45.833 15.08 0.00 43.21 3.36
1020 1037 4.659368 ACCATGATTGATGATGGAGACTCT 59.341 41.667 15.08 0.00 43.21 3.24
1021 1038 5.842874 ACCATGATTGATGATGGAGACTCTA 59.157 40.000 15.08 0.00 43.21 2.43
1023 1040 6.014413 CCATGATTGATGATGGAGACTCTACT 60.014 42.308 3.68 0.00 43.21 2.57
1025 1042 7.791587 CATGATTGATGATGGAGACTCTACTCC 60.792 44.444 1.74 7.68 43.97 3.85
1038 1055 0.187361 CTACTCCCTCTCCCTCCAGG 59.813 65.000 0.00 0.00 0.00 4.45
1044 1061 2.039624 TCTCCCTCCAGGCTCCAC 59.960 66.667 0.00 0.00 34.51 4.02
1045 1062 3.086600 CTCCCTCCAGGCTCCACC 61.087 72.222 0.00 0.00 39.61 4.61
1046 1063 3.931631 CTCCCTCCAGGCTCCACCA 62.932 68.421 0.00 0.00 43.14 4.17
1047 1064 3.721706 CCCTCCAGGCTCCACCAC 61.722 72.222 0.00 0.00 43.14 4.16
1048 1065 2.930019 CCTCCAGGCTCCACCACA 60.930 66.667 0.00 0.00 43.14 4.17
1049 1066 2.348998 CTCCAGGCTCCACCACAC 59.651 66.667 0.00 0.00 43.14 3.82
1074 1091 1.001517 ACAGCAGGCGAGAGAGAGA 60.002 57.895 0.00 0.00 0.00 3.10
1075 1092 1.031571 ACAGCAGGCGAGAGAGAGAG 61.032 60.000 0.00 0.00 0.00 3.20
1076 1093 0.747644 CAGCAGGCGAGAGAGAGAGA 60.748 60.000 0.00 0.00 0.00 3.10
1077 1094 0.464373 AGCAGGCGAGAGAGAGAGAG 60.464 60.000 0.00 0.00 0.00 3.20
1078 1095 0.463654 GCAGGCGAGAGAGAGAGAGA 60.464 60.000 0.00 0.00 0.00 3.10
1079 1096 1.586422 CAGGCGAGAGAGAGAGAGAG 58.414 60.000 0.00 0.00 0.00 3.20
1080 1097 1.134401 CAGGCGAGAGAGAGAGAGAGT 60.134 57.143 0.00 0.00 0.00 3.24
1081 1098 2.102420 CAGGCGAGAGAGAGAGAGAGTA 59.898 54.545 0.00 0.00 0.00 2.59
1082 1099 2.972713 AGGCGAGAGAGAGAGAGAGTAT 59.027 50.000 0.00 0.00 0.00 2.12
1110 1127 2.016905 AGGCCATAGGTAGTAGCAGG 57.983 55.000 5.01 1.99 0.00 4.85
1111 1128 1.503784 AGGCCATAGGTAGTAGCAGGA 59.496 52.381 5.01 0.00 0.00 3.86
1112 1129 2.090719 AGGCCATAGGTAGTAGCAGGAA 60.091 50.000 5.01 0.00 0.00 3.36
1114 1131 2.698797 GCCATAGGTAGTAGCAGGAACA 59.301 50.000 1.58 0.00 0.00 3.18
1115 1132 3.243907 GCCATAGGTAGTAGCAGGAACAG 60.244 52.174 1.58 0.00 0.00 3.16
1116 1133 4.215908 CCATAGGTAGTAGCAGGAACAGA 58.784 47.826 1.58 0.00 0.00 3.41
1117 1134 4.279671 CCATAGGTAGTAGCAGGAACAGAG 59.720 50.000 1.58 0.00 0.00 3.35
1118 1135 3.741245 AGGTAGTAGCAGGAACAGAGA 57.259 47.619 1.58 0.00 0.00 3.10
1119 1136 4.258457 AGGTAGTAGCAGGAACAGAGAT 57.742 45.455 1.58 0.00 0.00 2.75
1120 1137 4.211920 AGGTAGTAGCAGGAACAGAGATC 58.788 47.826 1.58 0.00 0.00 2.75
1122 1139 4.586841 GGTAGTAGCAGGAACAGAGATCAT 59.413 45.833 0.00 0.00 0.00 2.45
1123 1140 4.935352 AGTAGCAGGAACAGAGATCATC 57.065 45.455 0.00 0.00 0.00 2.92
1125 1142 4.713814 AGTAGCAGGAACAGAGATCATCAA 59.286 41.667 0.00 0.00 0.00 2.57
1126 1143 4.774660 AGCAGGAACAGAGATCATCAAT 57.225 40.909 0.00 0.00 0.00 2.57
1128 1145 4.163649 AGCAGGAACAGAGATCATCAATCA 59.836 41.667 0.00 0.00 36.79 2.57
1129 1146 4.272991 GCAGGAACAGAGATCATCAATCAC 59.727 45.833 0.00 0.00 36.79 3.06
1130 1147 5.425630 CAGGAACAGAGATCATCAATCACA 58.574 41.667 0.00 0.00 36.79 3.58
1131 1148 5.878669 CAGGAACAGAGATCATCAATCACAA 59.121 40.000 0.00 0.00 36.79 3.33
1132 1149 5.879223 AGGAACAGAGATCATCAATCACAAC 59.121 40.000 0.00 0.00 36.79 3.32
1133 1150 5.220548 GGAACAGAGATCATCAATCACAACG 60.221 44.000 0.00 0.00 36.79 4.10
1134 1151 4.186926 ACAGAGATCATCAATCACAACGG 58.813 43.478 0.00 0.00 36.79 4.44
1136 1153 4.507021 CAGAGATCATCAATCACAACGGAG 59.493 45.833 0.00 0.00 36.79 4.63
1137 1154 3.201290 AGATCATCAATCACAACGGAGC 58.799 45.455 0.00 0.00 36.79 4.70
1138 1155 1.737838 TCATCAATCACAACGGAGCC 58.262 50.000 0.00 0.00 0.00 4.70
1235 1253 4.742201 GGCGAGCGACAGGAAGCA 62.742 66.667 0.00 0.00 35.48 3.91
1262 1286 0.801251 CGGCAGCAAGAAGAAGAAGG 59.199 55.000 0.00 0.00 0.00 3.46
1293 1317 0.655733 CGGACGCCATAATGGTCAAC 59.344 55.000 0.00 0.00 40.46 3.18
1313 1337 0.037232 CAACCACGACTCTTCTCCCC 60.037 60.000 0.00 0.00 0.00 4.81
1314 1338 1.192803 AACCACGACTCTTCTCCCCC 61.193 60.000 0.00 0.00 0.00 5.40
1315 1339 1.305381 CCACGACTCTTCTCCCCCT 60.305 63.158 0.00 0.00 0.00 4.79
1316 1340 1.324005 CCACGACTCTTCTCCCCCTC 61.324 65.000 0.00 0.00 0.00 4.30
1317 1341 1.000612 ACGACTCTTCTCCCCCTCC 59.999 63.158 0.00 0.00 0.00 4.30
1318 1342 1.308326 CGACTCTTCTCCCCCTCCT 59.692 63.158 0.00 0.00 0.00 3.69
1399 1426 2.198980 CCTCCTCCTACCCCCTCG 59.801 72.222 0.00 0.00 0.00 4.63
1487 1516 2.437281 GCTCCTTCTCTGAATCCCATCA 59.563 50.000 0.00 0.00 0.00 3.07
1488 1517 3.072768 GCTCCTTCTCTGAATCCCATCAT 59.927 47.826 0.00 0.00 0.00 2.45
1489 1518 4.803588 GCTCCTTCTCTGAATCCCATCATC 60.804 50.000 0.00 0.00 0.00 2.92
1490 1519 3.649981 TCCTTCTCTGAATCCCATCATCC 59.350 47.826 0.00 0.00 0.00 3.51
1491 1520 3.393609 CCTTCTCTGAATCCCATCATCCA 59.606 47.826 0.00 0.00 0.00 3.41
1492 1521 4.505215 CCTTCTCTGAATCCCATCATCCAG 60.505 50.000 0.00 0.00 0.00 3.86
1559 1617 1.093496 CGGAAATGGCCGTAAGTCCC 61.093 60.000 13.93 4.46 46.07 4.46
1560 1618 0.750546 GGAAATGGCCGTAAGTCCCC 60.751 60.000 0.00 0.00 0.00 4.81
1561 1619 1.078001 AAATGGCCGTAAGTCCCCG 60.078 57.895 0.00 0.00 0.00 5.73
1562 1620 3.692370 AATGGCCGTAAGTCCCCGC 62.692 63.158 0.00 0.00 0.00 6.13
1625 1692 2.258591 CGTCTCCGAGGTGTGGTG 59.741 66.667 0.00 0.00 35.63 4.17
1626 1693 2.657237 GTCTCCGAGGTGTGGTGG 59.343 66.667 0.00 0.00 0.00 4.61
1627 1694 2.603473 TCTCCGAGGTGTGGTGGG 60.603 66.667 0.00 0.00 0.00 4.61
1628 1695 3.706373 CTCCGAGGTGTGGTGGGG 61.706 72.222 0.00 0.00 0.00 4.96
1631 1698 4.329545 CGAGGTGTGGTGGGGGTG 62.330 72.222 0.00 0.00 0.00 4.61
1667 1734 0.676782 CTTGGATCCGTGGGTTGACC 60.677 60.000 7.39 0.00 40.81 4.02
1702 1769 2.284190 CGAGCAAGGGAAGATTCTTCC 58.716 52.381 29.86 29.86 37.86 3.46
1706 1773 3.591079 AGCAAGGGAAGATTCTTCCTCTT 59.409 43.478 33.74 29.90 38.61 2.85
1758 1849 0.107456 ATCGCCTTCGGATTGCAGAT 59.893 50.000 0.00 2.17 36.13 2.90
1780 1871 1.148867 TGCCATTCCTTTTCTTCCCCA 59.851 47.619 0.00 0.00 0.00 4.96
1788 1883 2.305927 CCTTTTCTTCCCCAGTGCTAGA 59.694 50.000 0.00 0.00 0.00 2.43
1800 1895 4.323485 CCCAGTGCTAGATTTGACCAACTA 60.323 45.833 0.00 0.00 0.00 2.24
1805 1900 5.578727 GTGCTAGATTTGACCAACTAGTCAG 59.421 44.000 0.00 0.00 46.90 3.51
1806 1901 5.246203 TGCTAGATTTGACCAACTAGTCAGT 59.754 40.000 0.00 0.00 46.90 3.41
1807 1902 5.808030 GCTAGATTTGACCAACTAGTCAGTC 59.192 44.000 15.14 15.14 46.90 3.51
1808 1903 4.810790 AGATTTGACCAACTAGTCAGTCG 58.189 43.478 16.31 0.00 46.90 4.18
1828 1923 2.540361 CGTATTCTGCTTGCTGGATTGC 60.540 50.000 0.00 0.00 0.00 3.56
1854 1949 2.763215 TGGGGACACAGATTGCCC 59.237 61.111 0.00 0.00 39.58 5.36
1855 1950 1.852157 TGGGGACACAGATTGCCCT 60.852 57.895 0.00 0.00 39.98 5.19
1856 1951 1.379044 GGGGACACAGATTGCCCTG 60.379 63.158 0.00 0.00 39.98 4.45
1857 1952 2.048603 GGGACACAGATTGCCCTGC 61.049 63.158 0.00 0.00 38.12 4.85
1858 1953 2.401766 GGACACAGATTGCCCTGCG 61.402 63.158 0.00 0.00 37.68 5.18
1859 1954 3.044059 GACACAGATTGCCCTGCGC 62.044 63.158 0.00 0.00 37.68 6.09
1873 1972 1.153107 TGCGCCTCCATGGAATCAG 60.153 57.895 17.00 8.70 38.35 2.90
1904 2003 4.278170 TCCATGGAATAAATGTGCCGATTC 59.722 41.667 13.46 0.00 0.00 2.52
1917 2017 2.161410 TGCCGATTCTTCATTTTCACCG 59.839 45.455 0.00 0.00 0.00 4.94
1938 2038 4.191544 CGAAATGGCAACCAAGATCTAGA 58.808 43.478 0.00 0.00 36.95 2.43
1944 2044 4.761739 TGGCAACCAAGATCTAGACTTTTG 59.238 41.667 0.00 5.17 0.00 2.44
1945 2045 4.762251 GGCAACCAAGATCTAGACTTTTGT 59.238 41.667 0.00 0.00 0.00 2.83
1949 2049 8.349983 GCAACCAAGATCTAGACTTTTGTTTTA 58.650 33.333 0.00 0.00 0.00 1.52
1993 2093 0.457035 GCGTATCCGGTGGTACAAGA 59.543 55.000 0.00 0.00 35.09 3.02
1994 2094 1.535437 GCGTATCCGGTGGTACAAGAG 60.535 57.143 0.00 0.00 35.09 2.85
2004 2105 3.556423 GGTGGTACAAGAGTAGTTGGTGG 60.556 52.174 0.00 0.00 44.16 4.61
2008 2109 2.572290 ACAAGAGTAGTTGGTGGCAAC 58.428 47.619 0.00 0.00 35.43 4.17
2025 2126 3.330267 GCAACCCTTGTTTTTGTTGTCA 58.670 40.909 0.00 0.00 40.08 3.58
2026 2127 3.370672 GCAACCCTTGTTTTTGTTGTCAG 59.629 43.478 0.00 0.00 40.08 3.51
2076 2203 2.195922 GTTGAGCAAAACTGCAGTTGG 58.804 47.619 31.73 25.71 38.44 3.77
2099 2238 9.875691 TTGGCACTATAACAGATAATATGCTAG 57.124 33.333 0.00 0.00 0.00 3.42
2116 2255 2.741878 GCTAGCAGGCGAGGTCAAATAA 60.742 50.000 10.63 0.00 0.00 1.40
2153 2292 9.513906 TTTAGTGATGATTAGTCAAATGGAACA 57.486 29.630 0.00 0.00 39.97 3.18
2175 2314 4.999950 CACCCCTCTACATCTTATTCATGC 59.000 45.833 0.00 0.00 0.00 4.06
2193 2332 1.906994 GCGTGTGTGTGTGTGTGTGT 61.907 55.000 0.00 0.00 0.00 3.72
2195 2334 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2354 2553 7.556275 TCTTATCTCTTTGTCCAGTTGTGTTTT 59.444 33.333 0.00 0.00 0.00 2.43
2363 2562 4.879545 GTCCAGTTGTGTTTTTGGTCTCTA 59.120 41.667 0.00 0.00 32.51 2.43
2445 2644 9.836864 TCTGCTCATCACATGTTAATTTATAGT 57.163 29.630 0.00 0.00 0.00 2.12
2464 2663 4.195225 AGTACTAACAAGCTGCTTCCTC 57.805 45.455 12.82 0.00 0.00 3.71
2465 2664 2.481289 ACTAACAAGCTGCTTCCTCC 57.519 50.000 12.82 0.00 0.00 4.30
2473 2672 0.037447 GCTGCTTCCTCCTTCAACCT 59.963 55.000 0.00 0.00 0.00 3.50
2482 2681 2.616510 CCTCCTTCAACCTTACCAGCAG 60.617 54.545 0.00 0.00 0.00 4.24
2483 2682 1.168714 CCTTCAACCTTACCAGCAGC 58.831 55.000 0.00 0.00 0.00 5.25
2484 2683 1.545428 CCTTCAACCTTACCAGCAGCA 60.545 52.381 0.00 0.00 0.00 4.41
2485 2684 1.808945 CTTCAACCTTACCAGCAGCAG 59.191 52.381 0.00 0.00 0.00 4.24
2524 2723 1.192146 TTGGGAACTGGGAGGACGAG 61.192 60.000 0.00 0.00 0.00 4.18
2569 2774 1.175983 AAAACGCCCGCAAATCTCCA 61.176 50.000 0.00 0.00 0.00 3.86
2578 2783 1.039785 GCAAATCTCCAGGAAGGCCC 61.040 60.000 0.00 0.00 37.29 5.80
2599 2804 1.136336 GTCAACCAGAACGATCGCAAC 60.136 52.381 16.60 6.85 0.00 4.17
2600 2805 0.165944 CAACCAGAACGATCGCAACC 59.834 55.000 16.60 1.63 0.00 3.77
2770 2975 4.760047 ACACATGCCGAGTCGCCC 62.760 66.667 7.12 0.39 0.00 6.13
2776 2981 4.778143 GCCGAGTCGCCCAACCAT 62.778 66.667 7.12 0.00 0.00 3.55
2803 3008 1.000506 GGTGACCAGAGCAACTACGAA 59.999 52.381 0.00 0.00 0.00 3.85
2894 3099 0.995024 AGGTGGGGTTTCATCTCCTG 59.005 55.000 0.00 0.00 0.00 3.86
2926 3131 2.358737 GGTTCTGCTCCCACCACG 60.359 66.667 0.00 0.00 0.00 4.94
2982 3187 2.268298 CGATGAAACGGTAAGGTCCTG 58.732 52.381 0.00 0.00 0.00 3.86
2984 3189 1.719529 TGAAACGGTAAGGTCCTGGA 58.280 50.000 0.00 0.00 0.00 3.86
2997 3202 0.251354 TCCTGGATGCTTCTGTGAGC 59.749 55.000 0.00 0.00 43.00 4.26
3045 3255 8.585018 TCTTCTTTGTGTACTGACTATGAATGA 58.415 33.333 0.00 0.00 0.00 2.57
3046 3256 9.208022 CTTCTTTGTGTACTGACTATGAATGAA 57.792 33.333 0.00 0.00 0.00 2.57
3117 3331 1.461127 GCGTACTTTCTGAAGTGCTGG 59.539 52.381 2.25 0.00 45.46 4.85
3163 3377 1.227205 GAGAGGATCAGCTGTGCCG 60.227 63.158 14.67 0.00 37.82 5.69
3190 3404 2.834549 TGGAGACTGGGATGAGAAAGAC 59.165 50.000 0.00 0.00 0.00 3.01
3330 3544 5.221342 ACAGATATGAATCTTCGGTGAGTCC 60.221 44.000 0.00 0.00 40.65 3.85
3351 3566 3.435327 CCGCTTTAATCTTGTGTACTGCA 59.565 43.478 0.00 0.00 0.00 4.41
3371 3911 1.069049 AGCTGGTTTCACCACAAATGC 59.931 47.619 0.00 0.00 44.79 3.56
3502 4363 6.550108 AGATAATTGCTTGCTTCATCTCCAAT 59.450 34.615 0.00 0.00 0.00 3.16
3504 4365 4.970662 TTGCTTGCTTCATCTCCAATAC 57.029 40.909 0.00 0.00 0.00 1.89
3506 4367 5.357742 TGCTTGCTTCATCTCCAATACTA 57.642 39.130 0.00 0.00 0.00 1.82
3575 4436 2.879756 GCCCAGCAATGTTACTTCTGGA 60.880 50.000 8.05 0.00 45.31 3.86
3576 4437 2.749621 CCCAGCAATGTTACTTCTGGAC 59.250 50.000 8.05 0.00 45.31 4.02
3577 4438 3.560025 CCCAGCAATGTTACTTCTGGACT 60.560 47.826 8.05 0.00 45.31 3.85
3579 4440 4.154918 CCAGCAATGTTACTTCTGGACTTC 59.845 45.833 0.53 0.00 45.31 3.01
3580 4441 4.999950 CAGCAATGTTACTTCTGGACTTCT 59.000 41.667 0.00 0.00 0.00 2.85
3581 4442 5.471456 CAGCAATGTTACTTCTGGACTTCTT 59.529 40.000 0.00 0.00 0.00 2.52
3615 4492 5.793026 GCTTATGGTAGCAATATCTCAGC 57.207 43.478 0.00 0.00 40.89 4.26
3741 4618 1.600916 GAAGTGACACCCACCCTGC 60.601 63.158 0.84 0.00 46.87 4.85
3799 4676 7.446931 TGAAATGAGTAGCCAAATCTGTTGTTA 59.553 33.333 0.00 0.00 0.00 2.41
3800 4677 7.944729 AATGAGTAGCCAAATCTGTTGTTAT 57.055 32.000 0.00 0.00 0.00 1.89
3801 4678 7.944729 ATGAGTAGCCAAATCTGTTGTTATT 57.055 32.000 0.00 0.00 0.00 1.40
3968 4845 2.532250 AGCAGGTTGGGAAATAAGGG 57.468 50.000 0.00 0.00 0.00 3.95
3997 4874 2.959507 AAACTTGTCACAAGCCAACC 57.040 45.000 17.93 0.00 0.00 3.77
3998 4875 1.111277 AACTTGTCACAAGCCAACCC 58.889 50.000 17.93 0.00 0.00 4.11
4067 4944 8.532186 ACAGACAGTAGTTGATATTCTGATCT 57.468 34.615 2.83 0.00 34.41 2.75
4105 4982 6.204688 GCAGATTGTCCGGTGAAATTCATATA 59.795 38.462 0.00 0.00 0.00 0.86
4204 5081 8.495949 ACAGACTAGTAAATTCAAACAATGACG 58.504 33.333 0.00 0.00 37.92 4.35
4211 5088 1.802069 TCAAACAATGACGGCGATCA 58.198 45.000 16.62 14.34 31.50 2.92
4317 5203 5.063944 GGCAACATGTTCTATGTACTGACAG 59.936 44.000 8.48 0.00 39.50 3.51
4319 5205 6.811665 GCAACATGTTCTATGTACTGACAGTA 59.188 38.462 8.48 11.37 39.50 2.74
4395 5281 3.057596 GCCAGAGAGATCTGTAGGATTCG 60.058 52.174 13.30 0.00 36.06 3.34
4407 5293 2.126914 AGGATTCGATTTCTCTCGCG 57.873 50.000 0.00 0.00 38.52 5.87
4466 5352 2.160117 GCGAAACAATGCATGTGAAACG 60.160 45.455 0.00 4.09 42.99 3.60
4539 5425 5.894807 ACATGTTTAATCACATAAGCTGCC 58.105 37.500 0.00 0.00 35.51 4.85
4559 5445 2.926200 CCTCGACACTTTGTCTGCTATG 59.074 50.000 4.87 0.00 44.85 2.23
4566 5452 4.993584 ACACTTTGTCTGCTATGTTCTCTG 59.006 41.667 0.00 0.00 0.00 3.35
4571 5457 6.590234 TTGTCTGCTATGTTCTCTGTTCTA 57.410 37.500 0.00 0.00 0.00 2.10
4576 5462 8.244802 GTCTGCTATGTTCTCTGTTCTACTAAA 58.755 37.037 0.00 0.00 0.00 1.85
4672 5590 4.167307 AGGTTTGAAGAAACTGGTAAGGGA 59.833 41.667 0.00 0.00 41.21 4.20
4675 5593 6.461092 GGTTTGAAGAAACTGGTAAGGGAAAG 60.461 42.308 0.00 0.00 41.21 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
219 221 0.540365 CCCTTTGACATGGCCACTGT 60.540 55.000 8.16 14.36 0.00 3.55
244 246 1.201921 GCAAGAAAGGTATGTGACGCG 60.202 52.381 3.53 3.53 0.00 6.01
280 282 5.258622 CCTTTTGATTCGTCGATCATTGAC 58.741 41.667 0.00 0.00 36.05 3.18
412 415 5.817816 GGTATTGATTTGTGGGTCTACTCTG 59.182 44.000 0.00 0.00 0.00 3.35
442 445 4.397417 CCTCCTGACTGATCATTGTTTTCC 59.603 45.833 0.00 0.00 33.22 3.13
523 528 3.403038 AGTCCAGTCACATACTTGTTGC 58.597 45.455 0.00 0.00 35.76 4.17
609 617 5.239744 TCTCTTTGACTGACTGACTGACTAC 59.760 44.000 0.00 0.00 0.00 2.73
610 618 5.377478 TCTCTTTGACTGACTGACTGACTA 58.623 41.667 0.00 0.00 0.00 2.59
611 619 4.211125 TCTCTTTGACTGACTGACTGACT 58.789 43.478 0.00 0.00 0.00 3.41
612 620 4.576216 TCTCTTTGACTGACTGACTGAC 57.424 45.455 0.00 0.00 0.00 3.51
613 621 4.586421 ACATCTCTTTGACTGACTGACTGA 59.414 41.667 0.00 0.00 0.00 3.41
614 622 4.685165 CACATCTCTTTGACTGACTGACTG 59.315 45.833 0.00 0.00 0.00 3.51
909 926 0.250124 CTGTGCCGGTAACCTGTCAA 60.250 55.000 1.90 0.00 0.00 3.18
910 927 1.369692 CTGTGCCGGTAACCTGTCA 59.630 57.895 1.90 0.00 0.00 3.58
911 928 2.033194 GCTGTGCCGGTAACCTGTC 61.033 63.158 1.90 0.00 0.00 3.51
912 929 2.032071 GCTGTGCCGGTAACCTGT 59.968 61.111 1.90 0.00 0.00 4.00
913 930 3.118454 CGCTGTGCCGGTAACCTG 61.118 66.667 1.90 0.00 0.00 4.00
936 953 2.670251 TAAAAGCACGCCACCCCG 60.670 61.111 0.00 0.00 0.00 5.73
937 954 2.989881 GCTAAAAGCACGCCACCCC 61.990 63.158 0.00 0.00 41.89 4.95
938 955 0.675522 TAGCTAAAAGCACGCCACCC 60.676 55.000 1.22 0.00 45.56 4.61
939 956 0.446616 GTAGCTAAAAGCACGCCACC 59.553 55.000 0.00 0.00 45.56 4.61
940 957 1.128692 CAGTAGCTAAAAGCACGCCAC 59.871 52.381 0.00 0.00 45.56 5.01
941 958 1.270625 ACAGTAGCTAAAAGCACGCCA 60.271 47.619 0.00 0.00 45.56 5.69
942 959 1.439679 ACAGTAGCTAAAAGCACGCC 58.560 50.000 0.00 0.00 45.56 5.68
943 960 3.508762 TCTACAGTAGCTAAAAGCACGC 58.491 45.455 2.26 0.00 45.56 5.34
944 961 6.726230 TCTATCTACAGTAGCTAAAAGCACG 58.274 40.000 2.26 0.00 45.56 5.34
945 962 9.834628 CTATCTATCTACAGTAGCTAAAAGCAC 57.165 37.037 2.26 0.00 45.56 4.40
946 963 9.015367 CCTATCTATCTACAGTAGCTAAAAGCA 57.985 37.037 2.26 0.00 45.56 3.91
947 964 9.016438 ACCTATCTATCTACAGTAGCTAAAAGC 57.984 37.037 2.26 0.00 42.84 3.51
950 967 9.669887 GCTACCTATCTATCTACAGTAGCTAAA 57.330 37.037 11.03 0.00 44.81 1.85
951 968 8.266473 GGCTACCTATCTATCTACAGTAGCTAA 58.734 40.741 16.20 0.00 46.49 3.09
952 969 7.402361 TGGCTACCTATCTATCTACAGTAGCTA 59.598 40.741 16.20 9.57 46.49 3.32
953 970 6.215841 TGGCTACCTATCTATCTACAGTAGCT 59.784 42.308 16.20 0.00 46.49 3.32
954 971 6.416415 TGGCTACCTATCTATCTACAGTAGC 58.584 44.000 10.06 10.06 46.54 3.58
955 972 8.104566 ACTTGGCTACCTATCTATCTACAGTAG 58.895 40.741 0.47 0.47 0.00 2.57
956 973 7.986704 ACTTGGCTACCTATCTATCTACAGTA 58.013 38.462 0.00 0.00 0.00 2.74
957 974 6.854578 ACTTGGCTACCTATCTATCTACAGT 58.145 40.000 0.00 0.00 0.00 3.55
958 975 7.768807 AACTTGGCTACCTATCTATCTACAG 57.231 40.000 0.00 0.00 0.00 2.74
959 976 9.298250 CTTAACTTGGCTACCTATCTATCTACA 57.702 37.037 0.00 0.00 0.00 2.74
960 977 8.741841 CCTTAACTTGGCTACCTATCTATCTAC 58.258 40.741 0.00 0.00 0.00 2.59
961 978 7.396623 GCCTTAACTTGGCTACCTATCTATCTA 59.603 40.741 0.00 0.00 46.38 1.98
962 979 6.211785 GCCTTAACTTGGCTACCTATCTATCT 59.788 42.308 0.00 0.00 46.38 1.98
963 980 6.399743 GCCTTAACTTGGCTACCTATCTATC 58.600 44.000 0.00 0.00 46.38 2.08
964 981 6.361768 GCCTTAACTTGGCTACCTATCTAT 57.638 41.667 0.00 0.00 46.38 1.98
965 982 5.803237 GCCTTAACTTGGCTACCTATCTA 57.197 43.478 0.00 0.00 46.38 1.98
966 983 4.691326 GCCTTAACTTGGCTACCTATCT 57.309 45.455 0.00 0.00 46.38 1.98
975 992 1.583495 GGTGTCCGCCTTAACTTGGC 61.583 60.000 0.00 0.00 46.42 4.52
976 993 0.250553 TGGTGTCCGCCTTAACTTGG 60.251 55.000 0.00 0.00 0.00 3.61
977 994 0.872388 GTGGTGTCCGCCTTAACTTG 59.128 55.000 0.00 0.00 0.00 3.16
978 995 0.470766 TGTGGTGTCCGCCTTAACTT 59.529 50.000 0.00 0.00 32.22 2.66
979 996 0.250166 GTGTGGTGTCCGCCTTAACT 60.250 55.000 0.00 0.00 32.22 2.24
980 997 1.232621 GGTGTGGTGTCCGCCTTAAC 61.233 60.000 0.00 0.00 32.22 2.01
981 998 1.071814 GGTGTGGTGTCCGCCTTAA 59.928 57.895 0.00 0.00 32.22 1.85
982 999 1.485294 ATGGTGTGGTGTCCGCCTTA 61.485 55.000 0.00 0.00 32.22 2.69
983 1000 2.829384 ATGGTGTGGTGTCCGCCTT 61.829 57.895 0.00 0.00 32.22 4.35
984 1001 3.249189 ATGGTGTGGTGTCCGCCT 61.249 61.111 0.00 0.00 32.22 5.52
985 1002 2.819984 ATCATGGTGTGGTGTCCGCC 62.820 60.000 0.00 0.00 32.22 6.13
986 1003 0.960364 AATCATGGTGTGGTGTCCGC 60.960 55.000 0.00 0.00 34.12 5.54
987 1004 0.804364 CAATCATGGTGTGGTGTCCG 59.196 55.000 0.00 0.00 0.00 4.79
988 1005 2.198827 TCAATCATGGTGTGGTGTCC 57.801 50.000 0.00 0.00 0.00 4.02
989 1006 3.346315 TCATCAATCATGGTGTGGTGTC 58.654 45.455 0.00 0.00 38.85 3.67
990 1007 3.438216 TCATCAATCATGGTGTGGTGT 57.562 42.857 0.00 0.00 38.85 4.16
991 1008 3.067601 CCATCATCAATCATGGTGTGGTG 59.932 47.826 0.00 0.00 41.59 4.17
992 1009 3.053470 TCCATCATCAATCATGGTGTGGT 60.053 43.478 0.00 0.00 41.59 4.16
993 1010 3.558033 TCCATCATCAATCATGGTGTGG 58.442 45.455 0.00 5.07 41.59 4.17
994 1011 4.275196 GTCTCCATCATCAATCATGGTGTG 59.725 45.833 0.00 0.00 41.59 3.82
1019 1036 0.187361 CCTGGAGGGAGAGGGAGTAG 59.813 65.000 0.00 0.00 37.23 2.57
1020 1037 1.950748 GCCTGGAGGGAGAGGGAGTA 61.951 65.000 0.00 0.00 37.23 2.59
1021 1038 3.114390 CCTGGAGGGAGAGGGAGT 58.886 66.667 0.00 0.00 37.23 3.85
1023 1040 2.955246 AGCCTGGAGGGAGAGGGA 60.955 66.667 0.00 0.00 37.23 4.20
1025 1042 2.445654 GGAGCCTGGAGGGAGAGG 60.446 72.222 0.00 0.00 37.23 3.69
1027 1044 2.039624 GTGGAGCCTGGAGGGAGA 59.960 66.667 0.00 0.00 37.23 3.71
1038 1055 2.594592 GGTGTGGTGTGGTGGAGC 60.595 66.667 0.00 0.00 0.00 4.70
1044 1061 2.124362 TGCTGTGGTGTGGTGTGG 60.124 61.111 0.00 0.00 0.00 4.17
1045 1062 2.188829 CCTGCTGTGGTGTGGTGTG 61.189 63.158 0.00 0.00 0.00 3.82
1046 1063 2.192979 CCTGCTGTGGTGTGGTGT 59.807 61.111 0.00 0.00 0.00 4.16
1047 1064 3.289834 GCCTGCTGTGGTGTGGTG 61.290 66.667 0.00 0.00 0.00 4.17
1048 1065 4.935495 CGCCTGCTGTGGTGTGGT 62.935 66.667 0.00 0.00 33.25 4.16
1049 1066 4.624364 TCGCCTGCTGTGGTGTGG 62.624 66.667 0.00 0.00 38.63 4.17
1082 1099 9.328975 TGCTACTACCTATGGCCTTAATAATAA 57.671 33.333 3.32 0.00 0.00 1.40
1095 1112 5.133941 TCTCTGTTCCTGCTACTACCTATG 58.866 45.833 0.00 0.00 0.00 2.23
1104 1121 5.364735 TGATTGATGATCTCTGTTCCTGCTA 59.635 40.000 0.00 0.00 35.69 3.49
1106 1123 4.272991 GTGATTGATGATCTCTGTTCCTGC 59.727 45.833 0.00 0.00 35.69 4.85
1110 1127 5.220548 CCGTTGTGATTGATGATCTCTGTTC 60.221 44.000 0.00 0.00 35.69 3.18
1111 1128 4.633126 CCGTTGTGATTGATGATCTCTGTT 59.367 41.667 0.00 0.00 35.69 3.16
1112 1129 4.081476 TCCGTTGTGATTGATGATCTCTGT 60.081 41.667 0.00 0.00 35.69 3.41
1114 1131 4.691175 CTCCGTTGTGATTGATGATCTCT 58.309 43.478 0.00 0.00 35.69 3.10
1115 1132 3.247173 GCTCCGTTGTGATTGATGATCTC 59.753 47.826 0.00 0.00 35.69 2.75
1116 1133 3.201290 GCTCCGTTGTGATTGATGATCT 58.799 45.455 0.00 0.00 35.69 2.75
1117 1134 2.289002 GGCTCCGTTGTGATTGATGATC 59.711 50.000 0.00 0.00 35.21 2.92
1118 1135 2.292267 GGCTCCGTTGTGATTGATGAT 58.708 47.619 0.00 0.00 0.00 2.45
1119 1136 1.737838 GGCTCCGTTGTGATTGATGA 58.262 50.000 0.00 0.00 0.00 2.92
1120 1137 0.374758 CGGCTCCGTTGTGATTGATG 59.625 55.000 0.00 0.00 34.35 3.07
1122 1139 2.032634 GCGGCTCCGTTGTGATTGA 61.033 57.895 10.24 0.00 42.09 2.57
1123 1140 2.480555 GCGGCTCCGTTGTGATTG 59.519 61.111 10.24 0.00 42.09 2.67
1125 1142 4.015406 TGGCGGCTCCGTTGTGAT 62.015 61.111 11.43 0.00 42.09 3.06
1126 1143 4.980805 GTGGCGGCTCCGTTGTGA 62.981 66.667 11.43 0.00 42.09 3.58
1154 1172 2.267324 GTGGAGAGTGGAGGCTGC 59.733 66.667 0.00 0.00 0.00 5.25
1157 1175 4.459089 GCGGTGGAGAGTGGAGGC 62.459 72.222 0.00 0.00 0.00 4.70
1213 1231 4.749310 CCTGTCGCTCGCCTGCTT 62.749 66.667 0.00 0.00 0.00 3.91
1215 1233 4.742201 TTCCTGTCGCTCGCCTGC 62.742 66.667 0.00 0.00 0.00 4.85
1216 1234 2.507992 CTTCCTGTCGCTCGCCTG 60.508 66.667 0.00 0.00 0.00 4.85
1221 1239 2.047844 TGCTGCTTCCTGTCGCTC 60.048 61.111 0.00 0.00 0.00 5.03
1262 1286 1.135083 TGGCGTCCGATTCTTCTTCTC 60.135 52.381 0.00 0.00 0.00 2.87
1293 1317 0.037232 GGGAGAAGAGTCGTGGTTGG 60.037 60.000 0.00 0.00 0.00 3.77
1313 1337 0.478507 GGAGAGGAGAGGAGAGGAGG 59.521 65.000 0.00 0.00 0.00 4.30
1314 1338 0.478507 GGGAGAGGAGAGGAGAGGAG 59.521 65.000 0.00 0.00 0.00 3.69
1315 1339 0.253868 TGGGAGAGGAGAGGAGAGGA 60.254 60.000 0.00 0.00 0.00 3.71
1316 1340 0.185901 CTGGGAGAGGAGAGGAGAGG 59.814 65.000 0.00 0.00 0.00 3.69
1317 1341 0.468029 GCTGGGAGAGGAGAGGAGAG 60.468 65.000 0.00 0.00 0.00 3.20
1318 1342 0.923729 AGCTGGGAGAGGAGAGGAGA 60.924 60.000 0.00 0.00 0.00 3.71
1469 1498 3.393609 TGGATGATGGGATTCAGAGAAGG 59.606 47.826 0.00 0.00 0.00 3.46
1487 1516 2.459086 GCCTCCTGGATGGCTGGAT 61.459 63.158 22.27 0.00 45.26 3.41
1488 1517 3.092511 GCCTCCTGGATGGCTGGA 61.093 66.667 22.27 0.00 45.26 3.86
1560 1618 3.976701 AACCAATGGAGCGAGGGCG 62.977 63.158 6.16 0.00 46.35 6.13
1561 1619 2.044946 AACCAATGGAGCGAGGGC 60.045 61.111 6.16 0.00 40.37 5.19
1562 1620 3.909662 CAACCAATGGAGCGAGGG 58.090 61.111 6.16 0.00 0.00 4.30
1677 1744 1.977293 ATCTTCCCTTGCTCGCCTCC 61.977 60.000 0.00 0.00 0.00 4.30
1702 1769 0.682209 CCCACATGGCCCAAGAAGAG 60.682 60.000 0.00 0.00 0.00 2.85
1706 1773 0.413037 AAATCCCACATGGCCCAAGA 59.587 50.000 0.00 0.00 0.00 3.02
1758 1849 3.012274 TGGGGAAGAAAAGGAATGGCATA 59.988 43.478 0.00 0.00 0.00 3.14
1780 1871 5.246203 TGACTAGTTGGTCAAATCTAGCACT 59.754 40.000 0.00 0.00 42.35 4.40
1788 1883 4.602340 ACGACTGACTAGTTGGTCAAAT 57.398 40.909 20.99 9.31 44.24 2.32
1800 1895 2.232452 AGCAAGCAGAATACGACTGACT 59.768 45.455 0.00 0.00 37.54 3.41
1805 1900 2.010145 TCCAGCAAGCAGAATACGAC 57.990 50.000 0.00 0.00 0.00 4.34
1806 1901 2.938451 CAATCCAGCAAGCAGAATACGA 59.062 45.455 0.00 0.00 0.00 3.43
1807 1902 2.540361 GCAATCCAGCAAGCAGAATACG 60.540 50.000 0.00 0.00 0.00 3.06
1808 1903 2.223665 GGCAATCCAGCAAGCAGAATAC 60.224 50.000 0.00 0.00 35.83 1.89
1828 1923 4.351054 GTGTCCCCACCAGCCAGG 62.351 72.222 0.00 0.00 45.67 4.45
1843 1938 3.818787 GGCGCAGGGCAATCTGTG 61.819 66.667 10.83 9.27 46.16 3.66
1853 1948 1.895707 GATTCCATGGAGGCGCAGG 60.896 63.158 15.53 0.38 37.29 4.85
1854 1949 1.153107 TGATTCCATGGAGGCGCAG 60.153 57.895 15.53 0.00 37.29 5.18
1855 1950 1.153107 CTGATTCCATGGAGGCGCA 60.153 57.895 15.53 10.58 37.29 6.09
1856 1951 0.749454 AACTGATTCCATGGAGGCGC 60.749 55.000 15.53 0.00 37.29 6.53
1857 1952 1.402968 CAAACTGATTCCATGGAGGCG 59.597 52.381 15.53 7.62 37.29 5.52
1858 1953 2.450476 ACAAACTGATTCCATGGAGGC 58.550 47.619 15.53 11.49 37.29 4.70
1859 1954 4.338879 AGAACAAACTGATTCCATGGAGG 58.661 43.478 15.53 9.23 39.47 4.30
1873 1972 6.311200 GCACATTTATTCCATGGAGAACAAAC 59.689 38.462 15.53 0.00 25.73 2.93
1904 2003 3.911868 TGCCATTTCGGTGAAAATGAAG 58.088 40.909 10.16 0.00 45.40 3.02
1917 2017 5.189180 AGTCTAGATCTTGGTTGCCATTTC 58.811 41.667 0.00 0.00 31.53 2.17
1938 2038 7.933033 ACATTTCTGGATGCATAAAACAAAAGT 59.067 29.630 0.00 0.00 0.00 2.66
1944 2044 8.483307 AAATCACATTTCTGGATGCATAAAAC 57.517 30.769 0.00 0.00 0.00 2.43
1945 2045 8.937884 CAAAATCACATTTCTGGATGCATAAAA 58.062 29.630 0.00 0.00 0.00 1.52
1949 2049 6.045072 ACAAAATCACATTTCTGGATGCAT 57.955 33.333 0.00 0.00 0.00 3.96
2004 2105 3.330267 TGACAACAAAAACAAGGGTTGC 58.670 40.909 0.00 0.00 43.23 4.17
2008 2109 5.576447 AGTACTGACAACAAAAACAAGGG 57.424 39.130 0.00 0.00 0.00 3.95
2009 2110 7.316544 AGTAGTACTGACAACAAAAACAAGG 57.683 36.000 5.39 0.00 0.00 3.61
2017 2118 8.773645 CATCAAATCAAGTAGTACTGACAACAA 58.226 33.333 5.39 0.00 0.00 2.83
2018 2119 8.147704 TCATCAAATCAAGTAGTACTGACAACA 58.852 33.333 5.39 0.00 0.00 3.33
2076 2203 8.932945 TGCTAGCATATTATCTGTTATAGTGC 57.067 34.615 14.93 0.00 0.00 4.40
2080 2207 7.068226 TCGCCTGCTAGCATATTATCTGTTATA 59.932 37.037 19.72 0.00 0.00 0.98
2087 2226 3.118956 ACCTCGCCTGCTAGCATATTATC 60.119 47.826 19.72 3.18 0.00 1.75
2089 2228 2.231478 GACCTCGCCTGCTAGCATATTA 59.769 50.000 19.72 3.86 0.00 0.98
2099 2238 1.448985 TGTTATTTGACCTCGCCTGC 58.551 50.000 0.00 0.00 0.00 4.85
2153 2292 4.262635 CGCATGAATAAGATGTAGAGGGGT 60.263 45.833 0.00 0.00 0.00 4.95
2175 2314 0.179227 CACACACACACACACACACG 60.179 55.000 0.00 0.00 0.00 4.49
2354 2553 8.198109 GCATACTAAATGAACTCTAGAGACCAA 58.802 37.037 26.57 8.94 0.00 3.67
2363 2562 5.355350 GCACTTGGCATACTAAATGAACTCT 59.645 40.000 0.00 0.00 43.97 3.24
2440 2639 6.040616 GGAGGAAGCAGCTTGTTAGTACTATA 59.959 42.308 13.91 0.00 0.00 1.31
2442 2641 4.159879 GGAGGAAGCAGCTTGTTAGTACTA 59.840 45.833 13.91 0.00 0.00 1.82
2443 2642 3.055747 GGAGGAAGCAGCTTGTTAGTACT 60.056 47.826 13.91 0.00 0.00 2.73
2444 2643 3.055747 AGGAGGAAGCAGCTTGTTAGTAC 60.056 47.826 13.91 0.00 0.00 2.73
2445 2644 3.173965 AGGAGGAAGCAGCTTGTTAGTA 58.826 45.455 13.91 0.00 0.00 1.82
2464 2663 1.168714 GCTGCTGGTAAGGTTGAAGG 58.831 55.000 0.00 0.00 0.00 3.46
2465 2664 1.808945 CTGCTGCTGGTAAGGTTGAAG 59.191 52.381 0.00 0.00 0.00 3.02
2473 2672 1.456296 CTTGATGCTGCTGCTGGTAA 58.544 50.000 17.00 6.14 40.48 2.85
2482 2681 0.255890 TAGGAACCCCTTGATGCTGC 59.744 55.000 0.00 0.00 40.78 5.25
2483 2682 2.806945 TTAGGAACCCCTTGATGCTG 57.193 50.000 0.00 0.00 40.78 4.41
2484 2683 4.337264 AATTTAGGAACCCCTTGATGCT 57.663 40.909 0.00 0.00 40.78 3.79
2485 2684 4.383010 CCAAATTTAGGAACCCCTTGATGC 60.383 45.833 0.00 0.00 40.78 3.91
2569 2774 2.852075 TGGTTGACGGGCCTTCCT 60.852 61.111 7.65 0.00 0.00 3.36
2578 2783 1.006825 TGCGATCGTTCTGGTTGACG 61.007 55.000 17.81 0.00 0.00 4.35
2683 2888 0.875059 GCCTTTCGTCCCTGTTCTTG 59.125 55.000 0.00 0.00 0.00 3.02
2776 2981 4.290093 AGTTGCTCTGGTCACCATATCTA 58.710 43.478 0.00 0.00 30.82 1.98
2793 2998 2.778679 CAGCGCCTTCGTAGTTGC 59.221 61.111 2.29 0.00 38.14 4.17
2905 3110 2.352805 GTGGGAGCAGAACCCCTG 59.647 66.667 0.00 0.00 46.21 4.45
2982 3187 3.077617 GAGGCTCACAGAAGCATCC 57.922 57.895 10.25 0.00 45.00 3.51
2984 3189 0.982704 ACTGAGGCTCACAGAAGCAT 59.017 50.000 14.43 0.00 44.35 3.79
3077 3291 5.287226 ACGCATACCAGCAGTAATACTTAC 58.713 41.667 0.00 0.00 33.70 2.34
3096 3310 2.135139 CAGCACTTCAGAAAGTACGCA 58.865 47.619 4.21 0.00 43.99 5.24
3098 3312 2.476619 CACCAGCACTTCAGAAAGTACG 59.523 50.000 0.00 0.00 43.99 3.67
3117 3331 1.255084 GCACGTGCAAAAATCACACAC 59.745 47.619 34.52 0.00 41.59 3.82
3163 3377 3.261897 TCTCATCCCAGTCTCCAAACTTC 59.738 47.826 0.00 0.00 0.00 3.01
3330 3544 4.641954 CTGCAGTACACAAGATTAAAGCG 58.358 43.478 5.25 0.00 0.00 4.68
3339 3554 1.597742 AACCAGCTGCAGTACACAAG 58.402 50.000 16.64 0.23 0.00 3.16
3371 3911 7.984050 AGAATCTTTACTCCACATGTATGACAG 59.016 37.037 0.00 0.00 0.00 3.51
3446 3986 2.568956 AGGTGCACTATCTTGCTTCTGA 59.431 45.455 17.98 0.00 43.41 3.27
3447 3987 2.983229 AGGTGCACTATCTTGCTTCTG 58.017 47.619 17.98 0.00 43.41 3.02
3451 3991 4.282195 GGTATCTAGGTGCACTATCTTGCT 59.718 45.833 17.98 5.77 43.41 3.91
3554 4415 1.474077 CCAGAAGTAACATTGCTGGGC 59.526 52.381 0.00 0.00 41.81 5.36
3575 4436 7.038941 ACCATAAGCAACTACTCTACAAGAAGT 60.039 37.037 0.00 0.00 0.00 3.01
3576 4437 7.324178 ACCATAAGCAACTACTCTACAAGAAG 58.676 38.462 0.00 0.00 0.00 2.85
3577 4438 7.241042 ACCATAAGCAACTACTCTACAAGAA 57.759 36.000 0.00 0.00 0.00 2.52
3579 4440 6.697892 GCTACCATAAGCAACTACTCTACAAG 59.302 42.308 0.00 0.00 42.30 3.16
3580 4441 6.570692 GCTACCATAAGCAACTACTCTACAA 58.429 40.000 0.00 0.00 42.30 2.41
3581 4442 6.145338 GCTACCATAAGCAACTACTCTACA 57.855 41.667 0.00 0.00 42.30 2.74
3668 4545 0.596600 AAGCAGACACACACGTACCG 60.597 55.000 0.00 0.00 0.00 4.02
3741 4618 1.206132 TCGCCACAGGTATGTTACAGG 59.794 52.381 0.00 0.00 37.65 4.00
3799 4676 9.935682 CGCTATAACATAACATCTCAACAAAAT 57.064 29.630 0.00 0.00 0.00 1.82
3800 4677 9.157104 TCGCTATAACATAACATCTCAACAAAA 57.843 29.630 0.00 0.00 0.00 2.44
3801 4678 8.710835 TCGCTATAACATAACATCTCAACAAA 57.289 30.769 0.00 0.00 0.00 2.83
3968 4845 5.331532 GCTTGTGACAAGTTTTACAAATCGC 60.332 40.000 24.51 4.56 33.19 4.58
3997 4874 6.540914 TCTTTTTCACGGCCTTTACTATATGG 59.459 38.462 0.00 0.00 0.00 2.74
3998 4875 7.548196 TCTTTTTCACGGCCTTTACTATATG 57.452 36.000 0.00 0.00 0.00 1.78
4067 4944 3.743521 ACAATCTGCTCAGCTGTTGTAA 58.256 40.909 14.67 0.00 33.83 2.41
4152 5029 5.946377 ACCTCCAGAATCCAGATTTTACAAC 59.054 40.000 0.00 0.00 0.00 3.32
4204 5081 2.464459 CGCTGGACCTTTGATCGCC 61.464 63.158 0.00 0.00 0.00 5.54
4211 5088 1.477295 GTAGTAGAGCGCTGGACCTTT 59.523 52.381 18.48 0.00 0.00 3.11
4395 5281 3.243434 TGGGAATAGACGCGAGAGAAATC 60.243 47.826 15.93 0.00 0.00 2.17
4407 5293 0.539986 TTCGCACCCTGGGAATAGAC 59.460 55.000 22.23 0.61 43.09 2.59
4447 5333 4.681025 ACATCGTTTCACATGCATTGTTTC 59.319 37.500 0.00 0.00 36.00 2.78
4466 5352 2.783275 CGCTGCTGCTGACACATC 59.217 61.111 14.03 0.00 36.97 3.06
4491 5377 8.584600 GTTTAGAAAGTACATGTGTATCAGACG 58.415 37.037 9.11 0.00 32.54 4.18
4492 5378 9.419297 TGTTTAGAAAGTACATGTGTATCAGAC 57.581 33.333 9.11 0.00 32.54 3.51
4559 5445 9.810545 ATGCTTCTATTTAGTAGAACAGAGAAC 57.189 33.333 0.00 0.00 42.94 3.01
4571 5457 7.986085 ACACACAGAAATGCTTCTATTTAGT 57.014 32.000 0.00 0.00 40.05 2.24
4576 5462 6.467677 ACACTACACACAGAAATGCTTCTAT 58.532 36.000 0.00 0.00 40.05 1.98
4579 5465 5.389935 GCTACACTACACACAGAAATGCTTC 60.390 44.000 0.00 0.00 0.00 3.86
4582 5468 3.745975 TGCTACACTACACACAGAAATGC 59.254 43.478 0.00 0.00 0.00 3.56
4584 5470 5.243954 TCTCTGCTACACTACACACAGAAAT 59.756 40.000 0.00 0.00 34.05 2.17
4588 5474 4.710423 ATCTCTGCTACACTACACACAG 57.290 45.455 0.00 0.00 0.00 3.66
4613 5531 1.717113 CATGCGACACTTGCAACATTG 59.283 47.619 0.00 0.00 46.87 2.82
4620 5538 0.040157 TTTCTGCATGCGACACTTGC 60.040 50.000 14.09 0.00 46.82 4.01


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

AutoCloner maintained by Alex Coulton.