Multiple sequence alignment - TraesCS3B01G374000

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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 TraesCS3B01G374000 chr3B 100.000 2201 0 0 1 2201 586726982 586729182 0.000000e+00 4065.0
1 TraesCS3B01G374000 chr3B 95.813 812 28 3 1 806 725179403 725180214 0.000000e+00 1306.0
2 TraesCS3B01G374000 chr5B 96.663 809 21 4 1 805 618139194 618140000 0.000000e+00 1339.0
3 TraesCS3B01G374000 chr5B 87.597 129 14 2 874 1000 506323553 506323425 4.900000e-32 148.0
4 TraesCS3B01G374000 chr5B 79.426 209 24 9 1875 2066 375173428 375173634 1.770000e-26 130.0
5 TraesCS3B01G374000 chr5B 89.189 74 7 1 804 876 506323649 506323576 8.370000e-15 91.6
6 TraesCS3B01G374000 chr5B 94.643 56 3 0 2047 2102 43836259 43836204 1.080000e-13 87.9
7 TraesCS3B01G374000 chr2B 96.415 809 24 3 1 805 29532042 29531235 0.000000e+00 1328.0
8 TraesCS3B01G374000 chr1B 96.168 809 28 1 1 806 297297503 297298311 0.000000e+00 1319.0
9 TraesCS3B01G374000 chr1B 95.191 811 34 3 1 806 59836712 59837522 0.000000e+00 1277.0
10 TraesCS3B01G374000 chr1B 95.307 277 12 1 999 1274 668810575 668810299 2.590000e-119 438.0
11 TraesCS3B01G374000 chr4A 95.797 809 31 2 1 806 733779109 733779917 0.000000e+00 1303.0
12 TraesCS3B01G374000 chr4B 95.426 809 33 2 1 805 526722506 526723314 0.000000e+00 1286.0
13 TraesCS3B01G374000 chr4B 79.048 105 19 3 2003 2104 96191385 96191489 3.920000e-08 69.4
14 TraesCS3B01G374000 chr5D 95.074 812 34 4 1 807 50995261 50996071 0.000000e+00 1273.0
15 TraesCS3B01G374000 chr5D 78.571 238 33 10 1877 2104 447951046 447951275 8.190000e-30 141.0
16 TraesCS3B01G374000 chr5D 91.525 59 5 0 928 986 463353224 463353282 5.040000e-12 82.4
17 TraesCS3B01G374000 chr6B 93.588 811 46 4 1 806 707905534 707906343 0.000000e+00 1205.0
18 TraesCS3B01G374000 chr3A 91.082 841 46 11 1275 2103 589199611 589200434 0.000000e+00 1110.0
19 TraesCS3B01G374000 chr3A 85.780 218 8 7 805 999 589199386 589199603 2.210000e-50 209.0
20 TraesCS3B01G374000 chr3A 95.294 85 2 1 2101 2185 589200528 589200610 1.370000e-27 134.0
21 TraesCS3B01G374000 chr3D 85.202 669 72 13 1533 2187 447574470 447575125 0.000000e+00 662.0
22 TraesCS3B01G374000 chr3D 95.455 154 7 0 1275 1428 447573948 447574101 1.690000e-61 246.0
23 TraesCS3B01G374000 chr3D 83.857 223 10 8 805 1001 447573720 447573942 2.880000e-44 189.0
24 TraesCS3B01G374000 chrUn 95.652 276 12 0 999 1274 251410883 251410608 5.580000e-121 444.0
25 TraesCS3B01G374000 chrUn 95.652 276 12 0 999 1274 405354420 405354695 5.580000e-121 444.0
26 TraesCS3B01G374000 chrUn 95.290 276 13 0 999 1274 189405671 189405946 2.590000e-119 438.0
27 TraesCS3B01G374000 chrUn 95.290 276 13 0 999 1274 413812493 413812768 2.590000e-119 438.0
28 TraesCS3B01G374000 chrUn 94.928 276 14 0 999 1274 452187850 452187575 1.210000e-117 433.0
29 TraesCS3B01G374000 chr7D 95.290 276 12 1 999 1274 381960573 381960299 9.330000e-119 436.0
30 TraesCS3B01G374000 chr7D 95.290 276 12 1 999 1274 382063266 382063540 9.330000e-119 436.0
31 TraesCS3B01G374000 chr7D 79.253 241 36 9 1876 2103 489905291 489905052 2.930000e-34 156.0
32 TraesCS3B01G374000 chr7D 82.581 155 21 5 805 958 112948668 112948519 4.930000e-27 132.0
33 TraesCS3B01G374000 chr7D 82.759 116 16 2 1283 1395 112947521 112947635 1.390000e-17 100.0
34 TraesCS3B01G374000 chr7D 89.041 73 8 0 805 877 112867787 112867715 8.370000e-15 91.6
35 TraesCS3B01G374000 chr7D 95.918 49 2 0 805 853 112947484 112947436 1.810000e-11 80.5
36 TraesCS3B01G374000 chr6D 95.290 276 12 1 999 1274 124530710 124530984 9.330000e-119 436.0
37 TraesCS3B01G374000 chr7A 79.365 252 35 13 1877 2113 556555349 556555100 6.290000e-36 161.0
38 TraesCS3B01G374000 chr7B 81.935 155 26 2 1961 2113 518400333 518400179 1.770000e-26 130.0
39 TraesCS3B01G374000 chr7B 81.935 155 26 2 1961 2113 518408705 518408551 1.770000e-26 130.0
40 TraesCS3B01G374000 chr7B 90.411 73 7 0 805 877 72436901 72436829 1.800000e-16 97.1
41 TraesCS3B01G374000 chr7B 92.308 39 3 0 963 1001 136617513 136617551 3.050000e-04 56.5
42 TraesCS3B01G374000 chr7B 100.000 28 0 0 974 1001 701010550 701010523 4.000000e-03 52.8
43 TraesCS3B01G374000 chr5A 78.539 219 24 8 805 1001 583606112 583606329 2.970000e-24 122.0
44 TraesCS3B01G374000 chr5A 84.906 106 13 2 2002 2105 445134055 445134159 1.070000e-18 104.0


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 TraesCS3B01G374000 chr3B 586726982 586729182 2200 False 4065.000000 4065 100.000000 1 2201 1 chr3B.!!$F1 2200
1 TraesCS3B01G374000 chr3B 725179403 725180214 811 False 1306.000000 1306 95.813000 1 806 1 chr3B.!!$F2 805
2 TraesCS3B01G374000 chr5B 618139194 618140000 806 False 1339.000000 1339 96.663000 1 805 1 chr5B.!!$F2 804
3 TraesCS3B01G374000 chr2B 29531235 29532042 807 True 1328.000000 1328 96.415000 1 805 1 chr2B.!!$R1 804
4 TraesCS3B01G374000 chr1B 297297503 297298311 808 False 1319.000000 1319 96.168000 1 806 1 chr1B.!!$F2 805
5 TraesCS3B01G374000 chr1B 59836712 59837522 810 False 1277.000000 1277 95.191000 1 806 1 chr1B.!!$F1 805
6 TraesCS3B01G374000 chr4A 733779109 733779917 808 False 1303.000000 1303 95.797000 1 806 1 chr4A.!!$F1 805
7 TraesCS3B01G374000 chr4B 526722506 526723314 808 False 1286.000000 1286 95.426000 1 805 1 chr4B.!!$F2 804
8 TraesCS3B01G374000 chr5D 50995261 50996071 810 False 1273.000000 1273 95.074000 1 807 1 chr5D.!!$F1 806
9 TraesCS3B01G374000 chr6B 707905534 707906343 809 False 1205.000000 1205 93.588000 1 806 1 chr6B.!!$F1 805
10 TraesCS3B01G374000 chr3A 589199386 589200610 1224 False 484.333333 1110 90.718667 805 2185 3 chr3A.!!$F1 1380
11 TraesCS3B01G374000 chr3D 447573720 447575125 1405 False 365.666667 662 88.171333 805 2187 3 chr3D.!!$F1 1382

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
638 644 2.092103 TGGGCTGTAGTGGTTTGTTTCT 60.092 45.455 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1574 1875 0.811616 GCGGTAGACAAGGGATGCAG 60.812 60.0 0.0 0.0 0.0 4.41 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
104 105 4.631247 AGCTTGCTGCAGCGTGGA 62.631 61.111 32.11 13.51 45.24 4.02
389 392 2.597510 GGTTTGGCTGGTCGGCTT 60.598 61.111 1.58 0.00 39.32 4.35
638 644 2.092103 TGGGCTGTAGTGGTTTGTTTCT 60.092 45.455 0.00 0.00 0.00 2.52
870 880 8.788813 CATTTAAGATGTTTCGAATTGCTGTAC 58.211 33.333 0.00 0.00 0.00 2.90
871 881 7.667043 TTAAGATGTTTCGAATTGCTGTACT 57.333 32.000 0.00 0.00 0.00 2.73
872 882 6.560253 AAGATGTTTCGAATTGCTGTACTT 57.440 33.333 0.00 0.00 0.00 2.24
873 883 6.560253 AGATGTTTCGAATTGCTGTACTTT 57.440 33.333 0.00 0.00 0.00 2.66
874 884 6.970484 AGATGTTTCGAATTGCTGTACTTTT 58.030 32.000 0.00 0.00 0.00 2.27
908 945 6.899393 TGATCCATTCTTACAAAAGCTGTT 57.101 33.333 0.00 0.00 39.64 3.16
909 946 7.288810 TGATCCATTCTTACAAAAGCTGTTT 57.711 32.000 0.00 0.00 39.64 2.83
1001 1038 9.334947 CACATGTCATAATTCTCCTTAACTGAT 57.665 33.333 0.00 0.00 0.00 2.90
1002 1039 9.334947 ACATGTCATAATTCTCCTTAACTGATG 57.665 33.333 0.00 0.00 0.00 3.07
1003 1040 8.781196 CATGTCATAATTCTCCTTAACTGATGG 58.219 37.037 0.00 0.00 0.00 3.51
1004 1041 7.282585 TGTCATAATTCTCCTTAACTGATGGG 58.717 38.462 0.00 0.00 0.00 4.00
1005 1042 7.127186 TGTCATAATTCTCCTTAACTGATGGGA 59.873 37.037 0.00 0.00 0.00 4.37
1006 1043 7.993183 GTCATAATTCTCCTTAACTGATGGGAA 59.007 37.037 0.00 0.00 0.00 3.97
1007 1044 8.727149 TCATAATTCTCCTTAACTGATGGGAAT 58.273 33.333 0.00 0.00 30.32 3.01
1010 1047 8.753497 AATTCTCCTTAACTGATGGGAATAAC 57.247 34.615 0.00 0.00 29.63 1.89
1011 1048 7.510675 TTCTCCTTAACTGATGGGAATAACT 57.489 36.000 0.00 0.00 0.00 2.24
1012 1049 8.618240 TTCTCCTTAACTGATGGGAATAACTA 57.382 34.615 0.00 0.00 0.00 2.24
1013 1050 8.618240 TCTCCTTAACTGATGGGAATAACTAA 57.382 34.615 0.00 0.00 0.00 2.24
1014 1051 8.705594 TCTCCTTAACTGATGGGAATAACTAAG 58.294 37.037 0.00 0.00 0.00 2.18
1015 1052 7.280356 TCCTTAACTGATGGGAATAACTAAGC 58.720 38.462 0.00 0.00 0.00 3.09
1016 1053 7.054124 CCTTAACTGATGGGAATAACTAAGCA 58.946 38.462 0.00 0.00 0.00 3.91
1017 1054 7.227512 CCTTAACTGATGGGAATAACTAAGCAG 59.772 40.741 0.00 0.00 0.00 4.24
1018 1055 5.957771 ACTGATGGGAATAACTAAGCAGA 57.042 39.130 0.00 0.00 0.00 4.26
1019 1056 6.313519 ACTGATGGGAATAACTAAGCAGAA 57.686 37.500 0.00 0.00 0.00 3.02
1020 1057 6.904626 ACTGATGGGAATAACTAAGCAGAAT 58.095 36.000 0.00 0.00 0.00 2.40
1021 1058 7.349598 ACTGATGGGAATAACTAAGCAGAATT 58.650 34.615 0.00 0.00 0.00 2.17
1022 1059 7.836183 ACTGATGGGAATAACTAAGCAGAATTT 59.164 33.333 0.00 0.00 0.00 1.82
1023 1060 8.593945 TGATGGGAATAACTAAGCAGAATTTT 57.406 30.769 0.00 0.00 0.00 1.82
1024 1061 8.469200 TGATGGGAATAACTAAGCAGAATTTTG 58.531 33.333 0.00 0.00 0.00 2.44
1025 1062 7.169158 TGGGAATAACTAAGCAGAATTTTGG 57.831 36.000 0.00 0.00 0.00 3.28
1026 1063 6.951198 TGGGAATAACTAAGCAGAATTTTGGA 59.049 34.615 0.00 0.00 0.00 3.53
1027 1064 7.453126 TGGGAATAACTAAGCAGAATTTTGGAA 59.547 33.333 0.00 0.00 0.00 3.53
1028 1065 8.311109 GGGAATAACTAAGCAGAATTTTGGAAA 58.689 33.333 0.00 0.00 0.00 3.13
1029 1066 9.875691 GGAATAACTAAGCAGAATTTTGGAAAT 57.124 29.630 0.00 0.00 0.00 2.17
1033 1070 6.393171 ACTAAGCAGAATTTTGGAAATGAGC 58.607 36.000 0.00 0.00 0.00 4.26
1034 1071 4.877378 AGCAGAATTTTGGAAATGAGCA 57.123 36.364 0.00 0.00 0.00 4.26
1035 1072 5.416271 AGCAGAATTTTGGAAATGAGCAT 57.584 34.783 0.00 0.00 0.00 3.79
1036 1073 5.175859 AGCAGAATTTTGGAAATGAGCATG 58.824 37.500 0.00 0.00 0.00 4.06
1037 1074 5.046878 AGCAGAATTTTGGAAATGAGCATGA 60.047 36.000 0.00 0.00 0.00 3.07
1038 1075 5.640357 GCAGAATTTTGGAAATGAGCATGAA 59.360 36.000 0.00 0.00 0.00 2.57
1039 1076 6.148150 GCAGAATTTTGGAAATGAGCATGAAA 59.852 34.615 0.00 0.00 0.00 2.69
1040 1077 7.148306 GCAGAATTTTGGAAATGAGCATGAAAT 60.148 33.333 0.00 0.00 0.00 2.17
1077 1114 9.382244 GAATTTTCTCATTATCCGTTATTTCCG 57.618 33.333 0.00 0.00 0.00 4.30
1078 1115 6.854496 TTTCTCATTATCCGTTATTTCCGG 57.146 37.500 0.00 0.00 46.83 5.14
1079 1116 4.890088 TCTCATTATCCGTTATTTCCGGG 58.110 43.478 0.00 0.00 45.51 5.73
1080 1117 4.345837 TCTCATTATCCGTTATTTCCGGGT 59.654 41.667 0.00 0.00 45.51 5.28
1081 1118 4.634199 TCATTATCCGTTATTTCCGGGTC 58.366 43.478 0.00 0.00 45.51 4.46
1082 1119 4.345837 TCATTATCCGTTATTTCCGGGTCT 59.654 41.667 0.00 0.00 45.51 3.85
1083 1120 4.758773 TTATCCGTTATTTCCGGGTCTT 57.241 40.909 0.00 0.00 45.51 3.01
1084 1121 3.639672 ATCCGTTATTTCCGGGTCTTT 57.360 42.857 0.00 0.00 45.51 2.52
1085 1122 3.421919 TCCGTTATTTCCGGGTCTTTT 57.578 42.857 0.00 0.00 45.51 2.27
1086 1123 3.337358 TCCGTTATTTCCGGGTCTTTTC 58.663 45.455 0.00 0.00 45.51 2.29
1087 1124 2.094734 CCGTTATTTCCGGGTCTTTTCG 59.905 50.000 0.00 0.00 41.78 3.46
1088 1125 2.738314 CGTTATTTCCGGGTCTTTTCGT 59.262 45.455 0.00 0.00 0.00 3.85
1089 1126 3.187022 CGTTATTTCCGGGTCTTTTCGTT 59.813 43.478 0.00 0.00 0.00 3.85
1090 1127 4.469552 GTTATTTCCGGGTCTTTTCGTTG 58.530 43.478 0.00 0.00 0.00 4.10
1091 1128 0.664224 TTTCCGGGTCTTTTCGTTGC 59.336 50.000 0.00 0.00 0.00 4.17
1092 1129 0.464013 TTCCGGGTCTTTTCGTTGCA 60.464 50.000 0.00 0.00 0.00 4.08
1093 1130 0.250553 TCCGGGTCTTTTCGTTGCAT 60.251 50.000 0.00 0.00 0.00 3.96
1094 1131 0.596082 CCGGGTCTTTTCGTTGCATT 59.404 50.000 0.00 0.00 0.00 3.56
1095 1132 1.401018 CCGGGTCTTTTCGTTGCATTC 60.401 52.381 0.00 0.00 0.00 2.67
1096 1133 1.265635 CGGGTCTTTTCGTTGCATTCA 59.734 47.619 0.00 0.00 0.00 2.57
1097 1134 2.661594 GGGTCTTTTCGTTGCATTCAC 58.338 47.619 0.00 0.00 0.00 3.18
1098 1135 2.293399 GGGTCTTTTCGTTGCATTCACT 59.707 45.455 0.00 0.00 0.00 3.41
1099 1136 3.243401 GGGTCTTTTCGTTGCATTCACTT 60.243 43.478 0.00 0.00 0.00 3.16
1100 1137 4.023536 GGGTCTTTTCGTTGCATTCACTTA 60.024 41.667 0.00 0.00 0.00 2.24
1101 1138 4.909880 GGTCTTTTCGTTGCATTCACTTAC 59.090 41.667 0.00 0.00 0.00 2.34
1102 1139 5.504994 GGTCTTTTCGTTGCATTCACTTACA 60.505 40.000 0.00 0.00 0.00 2.41
1103 1140 5.968848 GTCTTTTCGTTGCATTCACTTACAA 59.031 36.000 0.00 0.00 0.00 2.41
1104 1141 6.140737 GTCTTTTCGTTGCATTCACTTACAAG 59.859 38.462 0.00 0.00 0.00 3.16
1105 1142 5.743026 TTTCGTTGCATTCACTTACAAGA 57.257 34.783 0.00 0.00 0.00 3.02
1106 1143 5.743026 TTCGTTGCATTCACTTACAAGAA 57.257 34.783 0.00 0.00 0.00 2.52
1107 1144 5.342806 TCGTTGCATTCACTTACAAGAAG 57.657 39.130 0.00 0.00 0.00 2.85
1108 1145 5.053811 TCGTTGCATTCACTTACAAGAAGA 58.946 37.500 0.00 0.00 0.00 2.87
1109 1146 5.525745 TCGTTGCATTCACTTACAAGAAGAA 59.474 36.000 0.00 0.80 0.00 2.52
1110 1147 6.037720 TCGTTGCATTCACTTACAAGAAGAAA 59.962 34.615 0.00 0.00 31.44 2.52
1111 1148 6.140737 CGTTGCATTCACTTACAAGAAGAAAC 59.859 38.462 0.00 0.00 31.44 2.78
1112 1149 6.691754 TGCATTCACTTACAAGAAGAAACA 57.308 33.333 0.00 1.54 31.44 2.83
1113 1150 7.094508 TGCATTCACTTACAAGAAGAAACAA 57.905 32.000 0.00 0.00 31.44 2.83
1114 1151 6.972328 TGCATTCACTTACAAGAAGAAACAAC 59.028 34.615 0.00 0.00 31.44 3.32
1115 1152 6.417930 GCATTCACTTACAAGAAGAAACAACC 59.582 38.462 0.00 0.00 31.44 3.77
1116 1153 7.479980 CATTCACTTACAAGAAGAAACAACCA 58.520 34.615 0.00 0.00 31.44 3.67
1117 1154 6.431198 TCACTTACAAGAAGAAACAACCAC 57.569 37.500 0.00 0.00 0.00 4.16
1118 1155 5.355910 TCACTTACAAGAAGAAACAACCACC 59.644 40.000 0.00 0.00 0.00 4.61
1119 1156 5.124776 CACTTACAAGAAGAAACAACCACCA 59.875 40.000 0.00 0.00 0.00 4.17
1120 1157 5.357032 ACTTACAAGAAGAAACAACCACCAG 59.643 40.000 0.00 0.00 0.00 4.00
1121 1158 2.427095 ACAAGAAGAAACAACCACCAGC 59.573 45.455 0.00 0.00 0.00 4.85
1122 1159 1.308998 AGAAGAAACAACCACCAGCG 58.691 50.000 0.00 0.00 0.00 5.18
1123 1160 1.021968 GAAGAAACAACCACCAGCGT 58.978 50.000 0.00 0.00 0.00 5.07
1124 1161 1.404035 GAAGAAACAACCACCAGCGTT 59.596 47.619 0.00 0.00 0.00 4.84
1125 1162 1.470051 AGAAACAACCACCAGCGTTT 58.530 45.000 0.00 0.00 34.41 3.60
1126 1163 1.134175 AGAAACAACCACCAGCGTTTG 59.866 47.619 0.00 0.00 31.98 2.93
1134 1171 3.594775 CCAGCGTTTGGTGCAGCA 61.595 61.111 15.99 15.99 42.41 4.41
1135 1172 2.353839 CAGCGTTTGGTGCAGCAC 60.354 61.111 20.03 17.97 36.70 4.40
1136 1173 2.516930 AGCGTTTGGTGCAGCACT 60.517 55.556 24.75 9.64 34.40 4.40
1137 1174 2.120909 AGCGTTTGGTGCAGCACTT 61.121 52.632 24.75 0.00 34.40 3.16
1138 1175 1.945662 GCGTTTGGTGCAGCACTTG 60.946 57.895 24.75 11.85 34.40 3.16
1150 1187 1.788308 CAGCACTTGCATTTTGGTTCG 59.212 47.619 3.62 0.00 45.16 3.95
1151 1188 1.408702 AGCACTTGCATTTTGGTTCGT 59.591 42.857 3.62 0.00 45.16 3.85
1152 1189 2.159114 AGCACTTGCATTTTGGTTCGTT 60.159 40.909 3.62 0.00 45.16 3.85
1153 1190 2.218530 GCACTTGCATTTTGGTTCGTTC 59.781 45.455 0.00 0.00 41.59 3.95
1154 1191 3.705604 CACTTGCATTTTGGTTCGTTCT 58.294 40.909 0.00 0.00 0.00 3.01
1155 1192 4.111916 CACTTGCATTTTGGTTCGTTCTT 58.888 39.130 0.00 0.00 0.00 2.52
1156 1193 4.207019 CACTTGCATTTTGGTTCGTTCTTC 59.793 41.667 0.00 0.00 0.00 2.87
1157 1194 4.097892 ACTTGCATTTTGGTTCGTTCTTCT 59.902 37.500 0.00 0.00 0.00 2.85
1158 1195 4.647424 TGCATTTTGGTTCGTTCTTCTT 57.353 36.364 0.00 0.00 0.00 2.52
1159 1196 4.606961 TGCATTTTGGTTCGTTCTTCTTC 58.393 39.130 0.00 0.00 0.00 2.87
1160 1197 3.981416 GCATTTTGGTTCGTTCTTCTTCC 59.019 43.478 0.00 0.00 0.00 3.46
1161 1198 4.261614 GCATTTTGGTTCGTTCTTCTTCCT 60.262 41.667 0.00 0.00 0.00 3.36
1162 1199 5.736207 GCATTTTGGTTCGTTCTTCTTCCTT 60.736 40.000 0.00 0.00 0.00 3.36
1163 1200 5.907866 TTTTGGTTCGTTCTTCTTCCTTT 57.092 34.783 0.00 0.00 0.00 3.11
1164 1201 5.494632 TTTGGTTCGTTCTTCTTCCTTTC 57.505 39.130 0.00 0.00 0.00 2.62
1165 1202 3.473625 TGGTTCGTTCTTCTTCCTTTCC 58.526 45.455 0.00 0.00 0.00 3.13
1166 1203 3.135895 TGGTTCGTTCTTCTTCCTTTCCT 59.864 43.478 0.00 0.00 0.00 3.36
1167 1204 4.135306 GGTTCGTTCTTCTTCCTTTCCTT 58.865 43.478 0.00 0.00 0.00 3.36
1168 1205 4.023963 GGTTCGTTCTTCTTCCTTTCCTTG 60.024 45.833 0.00 0.00 0.00 3.61
1169 1206 3.740115 TCGTTCTTCTTCCTTTCCTTGG 58.260 45.455 0.00 0.00 0.00 3.61
1170 1207 3.135895 TCGTTCTTCTTCCTTTCCTTGGT 59.864 43.478 0.00 0.00 0.00 3.67
1171 1208 3.498777 CGTTCTTCTTCCTTTCCTTGGTC 59.501 47.826 0.00 0.00 0.00 4.02
1172 1209 4.720046 GTTCTTCTTCCTTTCCTTGGTCT 58.280 43.478 0.00 0.00 0.00 3.85
1173 1210 5.133941 GTTCTTCTTCCTTTCCTTGGTCTT 58.866 41.667 0.00 0.00 0.00 3.01
1174 1211 5.388599 TCTTCTTCCTTTCCTTGGTCTTT 57.611 39.130 0.00 0.00 0.00 2.52
1175 1212 5.377478 TCTTCTTCCTTTCCTTGGTCTTTC 58.623 41.667 0.00 0.00 0.00 2.62
1176 1213 3.740115 TCTTCCTTTCCTTGGTCTTTCG 58.260 45.455 0.00 0.00 0.00 3.46
1177 1214 3.135895 TCTTCCTTTCCTTGGTCTTTCGT 59.864 43.478 0.00 0.00 0.00 3.85
1178 1215 3.570912 TCCTTTCCTTGGTCTTTCGTT 57.429 42.857 0.00 0.00 0.00 3.85
1179 1216 3.473625 TCCTTTCCTTGGTCTTTCGTTC 58.526 45.455 0.00 0.00 0.00 3.95
1180 1217 2.552743 CCTTTCCTTGGTCTTTCGTTCC 59.447 50.000 0.00 0.00 0.00 3.62
1181 1218 1.873698 TTCCTTGGTCTTTCGTTCCG 58.126 50.000 0.00 0.00 0.00 4.30
1182 1219 0.754472 TCCTTGGTCTTTCGTTCCGT 59.246 50.000 0.00 0.00 0.00 4.69
1183 1220 1.145803 CCTTGGTCTTTCGTTCCGTC 58.854 55.000 0.00 0.00 0.00 4.79
1184 1221 1.539496 CCTTGGTCTTTCGTTCCGTCA 60.539 52.381 0.00 0.00 0.00 4.35
1185 1222 2.413837 CTTGGTCTTTCGTTCCGTCAT 58.586 47.619 0.00 0.00 0.00 3.06
1186 1223 3.581755 CTTGGTCTTTCGTTCCGTCATA 58.418 45.455 0.00 0.00 0.00 2.15
1187 1224 3.880047 TGGTCTTTCGTTCCGTCATAT 57.120 42.857 0.00 0.00 0.00 1.78
1188 1225 4.196626 TGGTCTTTCGTTCCGTCATATT 57.803 40.909 0.00 0.00 0.00 1.28
1189 1226 4.178540 TGGTCTTTCGTTCCGTCATATTC 58.821 43.478 0.00 0.00 0.00 1.75
1190 1227 3.554731 GGTCTTTCGTTCCGTCATATTCC 59.445 47.826 0.00 0.00 0.00 3.01
1191 1228 4.178540 GTCTTTCGTTCCGTCATATTCCA 58.821 43.478 0.00 0.00 0.00 3.53
1192 1229 4.628333 GTCTTTCGTTCCGTCATATTCCAA 59.372 41.667 0.00 0.00 0.00 3.53
1193 1230 5.121142 GTCTTTCGTTCCGTCATATTCCAAA 59.879 40.000 0.00 0.00 0.00 3.28
1194 1231 4.932268 TTCGTTCCGTCATATTCCAAAC 57.068 40.909 0.00 0.00 0.00 2.93
1195 1232 3.927854 TCGTTCCGTCATATTCCAAACA 58.072 40.909 0.00 0.00 0.00 2.83
1196 1233 4.316645 TCGTTCCGTCATATTCCAAACAA 58.683 39.130 0.00 0.00 0.00 2.83
1197 1234 4.152759 TCGTTCCGTCATATTCCAAACAAC 59.847 41.667 0.00 0.00 0.00 3.32
1198 1235 4.153475 CGTTCCGTCATATTCCAAACAACT 59.847 41.667 0.00 0.00 0.00 3.16
1199 1236 5.390613 GTTCCGTCATATTCCAAACAACTG 58.609 41.667 0.00 0.00 0.00 3.16
1200 1237 4.900684 TCCGTCATATTCCAAACAACTGA 58.099 39.130 0.00 0.00 0.00 3.41
1201 1238 5.496556 TCCGTCATATTCCAAACAACTGAT 58.503 37.500 0.00 0.00 0.00 2.90
1202 1239 5.584649 TCCGTCATATTCCAAACAACTGATC 59.415 40.000 0.00 0.00 0.00 2.92
1203 1240 5.586243 CCGTCATATTCCAAACAACTGATCT 59.414 40.000 0.00 0.00 0.00 2.75
1204 1241 6.761242 CCGTCATATTCCAAACAACTGATCTA 59.239 38.462 0.00 0.00 0.00 1.98
1205 1242 7.279981 CCGTCATATTCCAAACAACTGATCTAA 59.720 37.037 0.00 0.00 0.00 2.10
1206 1243 8.830580 CGTCATATTCCAAACAACTGATCTAAT 58.169 33.333 0.00 0.00 0.00 1.73
1214 1251 9.295825 TCCAAACAACTGATCTAATTACAATGT 57.704 29.630 0.00 0.00 0.00 2.71
1232 1269 7.095695 ACAATGTATTAACCACTAATGCACC 57.904 36.000 0.00 0.00 42.95 5.01
1233 1270 6.889722 ACAATGTATTAACCACTAATGCACCT 59.110 34.615 0.00 0.00 42.95 4.00
1234 1271 7.396055 ACAATGTATTAACCACTAATGCACCTT 59.604 33.333 0.00 0.00 42.95 3.50
1235 1272 7.954666 ATGTATTAACCACTAATGCACCTTT 57.045 32.000 0.00 0.00 42.95 3.11
1236 1273 7.768807 TGTATTAACCACTAATGCACCTTTT 57.231 32.000 0.00 0.00 37.59 2.27
1237 1274 8.184304 TGTATTAACCACTAATGCACCTTTTT 57.816 30.769 0.00 0.00 37.59 1.94
1260 1297 7.408756 TTTTTATCAAATCTCAGGGACATGG 57.591 36.000 0.00 0.00 0.00 3.66
1261 1298 5.715439 TTATCAAATCTCAGGGACATGGT 57.285 39.130 0.00 0.00 0.00 3.55
1262 1299 3.634397 TCAAATCTCAGGGACATGGTC 57.366 47.619 0.00 0.00 0.00 4.02
1263 1300 2.093500 TCAAATCTCAGGGACATGGTCG 60.093 50.000 0.00 0.00 32.65 4.79
1264 1301 1.866015 AATCTCAGGGACATGGTCGA 58.134 50.000 0.00 0.00 32.65 4.20
1265 1302 1.866015 ATCTCAGGGACATGGTCGAA 58.134 50.000 0.00 0.00 32.65 3.71
1266 1303 1.866015 TCTCAGGGACATGGTCGAAT 58.134 50.000 0.00 0.00 32.65 3.34
1267 1304 1.757118 TCTCAGGGACATGGTCGAATC 59.243 52.381 0.00 0.00 32.65 2.52
1268 1305 1.482182 CTCAGGGACATGGTCGAATCA 59.518 52.381 0.00 0.00 32.65 2.57
1269 1306 2.103771 CTCAGGGACATGGTCGAATCAT 59.896 50.000 0.00 0.00 32.65 2.45
1270 1307 2.158914 TCAGGGACATGGTCGAATCATG 60.159 50.000 21.36 21.36 45.31 3.07
1271 1308 2.118679 AGGGACATGGTCGAATCATGA 58.881 47.619 26.68 0.00 43.25 3.07
1272 1309 2.103771 AGGGACATGGTCGAATCATGAG 59.896 50.000 26.68 10.00 43.25 2.90
1273 1310 2.487934 GGACATGGTCGAATCATGAGG 58.512 52.381 26.68 9.46 43.25 3.86
1325 1362 1.338020 CCTGGAGTTGTGGTTTTCTGC 59.662 52.381 0.00 0.00 0.00 4.26
1374 1411 0.178947 TACCCCAGCCCCAAAAGTTG 60.179 55.000 0.00 0.00 0.00 3.16
1501 1596 0.793250 GCTTTGGAGAAGACAGACGC 59.207 55.000 0.00 0.00 0.00 5.19
1511 1790 2.049063 ACAGACGCGGTCAAGAGC 60.049 61.111 12.47 0.00 34.60 4.09
1521 1800 3.760035 TCAAGAGCCGGTCGCCTC 61.760 66.667 1.90 0.11 38.78 4.70
1538 1839 3.499737 CGAACCGGTGCCAGATGC 61.500 66.667 8.52 0.00 41.77 3.91
1562 1863 0.429736 CGCGTTCAGAACACTACACG 59.570 55.000 13.82 0.00 0.00 4.49
1574 1875 0.388134 ACTACACGACCACACATCGC 60.388 55.000 0.00 0.00 43.46 4.58
1595 1896 0.811616 GCATCCCTTGTCTACCGCAG 60.812 60.000 0.00 0.00 0.00 5.18
1632 1943 3.933332 CCTCGAAACTCATAAACTGACCC 59.067 47.826 0.00 0.00 0.00 4.46
1654 1968 2.695666 AGTCACACTATGGGATCCTTCG 59.304 50.000 12.58 0.58 29.44 3.79
1739 2053 6.327934 TCTACCGAATAGAGCAAAAGTGTAC 58.672 40.000 0.00 0.00 34.80 2.90
1740 2054 4.890088 ACCGAATAGAGCAAAAGTGTACA 58.110 39.130 0.00 0.00 0.00 2.90
1769 2083 2.104967 TCATACACCAACCTAGGGTCG 58.895 52.381 14.81 0.48 36.19 4.79
1818 2132 0.610232 AACCGGACTACCACGCTAGT 60.610 55.000 9.46 0.00 35.59 2.57
1870 2184 2.885894 CGGACTACCATCTACTTCCTCC 59.114 54.545 0.00 0.00 35.59 4.30
1894 2208 8.091449 TCCGCACCAAAATAATTGAAGTTTTAT 58.909 29.630 0.00 0.00 0.00 1.40
2086 2402 8.307483 TGACTTAAGACAATCCTAGAACTTCAG 58.693 37.037 10.09 0.00 0.00 3.02
2188 2600 6.439675 TTTTAAAGGTAAAACTGACAGCGT 57.560 33.333 1.25 0.00 34.87 5.07
2189 2601 3.963383 AAAGGTAAAACTGACAGCGTG 57.037 42.857 1.25 0.00 0.00 5.34
2190 2602 1.226746 AGGTAAAACTGACAGCGTGC 58.773 50.000 1.25 0.00 0.00 5.34
2191 2603 0.941542 GGTAAAACTGACAGCGTGCA 59.058 50.000 1.25 0.00 0.00 4.57
2192 2604 1.069906 GGTAAAACTGACAGCGTGCAG 60.070 52.381 1.25 0.00 38.10 4.41
2193 2605 1.597663 GTAAAACTGACAGCGTGCAGT 59.402 47.619 1.25 3.10 46.59 4.40
2195 2607 4.540153 ACTGACAGCGTGCAGTTT 57.460 50.000 1.25 0.00 42.33 2.66
2196 2608 2.016961 ACTGACAGCGTGCAGTTTG 58.983 52.632 1.25 0.00 42.33 2.93
2197 2609 1.280746 CTGACAGCGTGCAGTTTGG 59.719 57.895 0.00 0.00 0.00 3.28
2198 2610 1.439353 CTGACAGCGTGCAGTTTGGT 61.439 55.000 0.00 0.00 0.00 3.67
2199 2611 1.029408 TGACAGCGTGCAGTTTGGTT 61.029 50.000 0.00 0.00 0.00 3.67
2200 2612 0.941542 GACAGCGTGCAGTTTGGTTA 59.058 50.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 3.928779 GCCCCTGCCGATCATCGA 61.929 66.667 9.16 0.00 43.74 3.59
356 359 2.045438 CCACCGCCCAACTATGCA 60.045 61.111 0.00 0.00 0.00 3.96
389 392 2.075355 AAACCCCACCAGCCAATCGA 62.075 55.000 0.00 0.00 0.00 3.59
668 674 1.227556 AACGGCAGCTCGACAAAGT 60.228 52.632 9.87 0.00 0.00 2.66
877 887 9.748708 CTTTTGTAAGAATGGATCAAGTTTTCA 57.251 29.630 0.00 0.00 32.92 2.69
883 920 6.917533 ACAGCTTTTGTAAGAATGGATCAAG 58.082 36.000 0.00 0.00 38.56 3.02
888 925 8.635765 ATCTAAACAGCTTTTGTAAGAATGGA 57.364 30.769 0.00 0.00 39.73 3.41
1001 1038 6.951198 TCCAAAATTCTGCTTAGTTATTCCCA 59.049 34.615 0.00 0.00 0.00 4.37
1002 1039 7.404671 TCCAAAATTCTGCTTAGTTATTCCC 57.595 36.000 0.00 0.00 0.00 3.97
1003 1040 9.875691 ATTTCCAAAATTCTGCTTAGTTATTCC 57.124 29.630 0.00 0.00 0.00 3.01
1007 1044 8.028938 GCTCATTTCCAAAATTCTGCTTAGTTA 58.971 33.333 0.00 0.00 0.00 2.24
1008 1045 6.870439 GCTCATTTCCAAAATTCTGCTTAGTT 59.130 34.615 0.00 0.00 0.00 2.24
1009 1046 6.015180 TGCTCATTTCCAAAATTCTGCTTAGT 60.015 34.615 0.00 0.00 0.00 2.24
1010 1047 6.392354 TGCTCATTTCCAAAATTCTGCTTAG 58.608 36.000 0.00 0.00 0.00 2.18
1011 1048 6.343716 TGCTCATTTCCAAAATTCTGCTTA 57.656 33.333 0.00 0.00 0.00 3.09
1012 1049 5.217978 TGCTCATTTCCAAAATTCTGCTT 57.782 34.783 0.00 0.00 0.00 3.91
1013 1050 4.877378 TGCTCATTTCCAAAATTCTGCT 57.123 36.364 0.00 0.00 0.00 4.24
1014 1051 5.172934 TCATGCTCATTTCCAAAATTCTGC 58.827 37.500 0.00 0.00 0.00 4.26
1015 1052 7.661127 TTTCATGCTCATTTCCAAAATTCTG 57.339 32.000 0.00 0.00 0.00 3.02
1016 1053 7.881232 ACATTTCATGCTCATTTCCAAAATTCT 59.119 29.630 0.00 0.00 0.00 2.40
1017 1054 8.036273 ACATTTCATGCTCATTTCCAAAATTC 57.964 30.769 0.00 0.00 0.00 2.17
1018 1055 7.881232 AGACATTTCATGCTCATTTCCAAAATT 59.119 29.630 0.00 0.00 0.00 1.82
1019 1056 7.391620 AGACATTTCATGCTCATTTCCAAAAT 58.608 30.769 0.00 0.00 0.00 1.82
1020 1057 6.761312 AGACATTTCATGCTCATTTCCAAAA 58.239 32.000 0.00 0.00 0.00 2.44
1021 1058 6.349243 AGACATTTCATGCTCATTTCCAAA 57.651 33.333 0.00 0.00 0.00 3.28
1022 1059 5.988310 AGACATTTCATGCTCATTTCCAA 57.012 34.783 0.00 0.00 0.00 3.53
1023 1060 8.750515 TTATAGACATTTCATGCTCATTTCCA 57.249 30.769 0.00 0.00 0.00 3.53
1051 1088 9.382244 CGGAAATAACGGATAATGAGAAAATTC 57.618 33.333 0.00 0.00 0.00 2.17
1067 1104 2.738314 ACGAAAAGACCCGGAAATAACG 59.262 45.455 0.73 3.01 0.00 3.18
1068 1105 4.469552 CAACGAAAAGACCCGGAAATAAC 58.530 43.478 0.73 0.00 0.00 1.89
1069 1106 3.058085 GCAACGAAAAGACCCGGAAATAA 60.058 43.478 0.73 0.00 0.00 1.40
1070 1107 2.485038 GCAACGAAAAGACCCGGAAATA 59.515 45.455 0.73 0.00 0.00 1.40
1071 1108 1.268625 GCAACGAAAAGACCCGGAAAT 59.731 47.619 0.73 0.00 0.00 2.17
1072 1109 0.664224 GCAACGAAAAGACCCGGAAA 59.336 50.000 0.73 0.00 0.00 3.13
1073 1110 0.464013 TGCAACGAAAAGACCCGGAA 60.464 50.000 0.73 0.00 0.00 4.30
1074 1111 0.250553 ATGCAACGAAAAGACCCGGA 60.251 50.000 0.73 0.00 0.00 5.14
1075 1112 0.596082 AATGCAACGAAAAGACCCGG 59.404 50.000 0.00 0.00 0.00 5.73
1076 1113 1.265635 TGAATGCAACGAAAAGACCCG 59.734 47.619 0.00 0.00 0.00 5.28
1077 1114 2.293399 AGTGAATGCAACGAAAAGACCC 59.707 45.455 0.00 0.00 0.00 4.46
1078 1115 3.626028 AGTGAATGCAACGAAAAGACC 57.374 42.857 0.00 0.00 0.00 3.85
1079 1116 5.507077 TGTAAGTGAATGCAACGAAAAGAC 58.493 37.500 0.00 0.00 0.00 3.01
1080 1117 5.743026 TGTAAGTGAATGCAACGAAAAGA 57.257 34.783 0.00 0.00 0.00 2.52
1081 1118 6.198687 TCTTGTAAGTGAATGCAACGAAAAG 58.801 36.000 0.00 0.00 0.00 2.27
1082 1119 6.125327 TCTTGTAAGTGAATGCAACGAAAA 57.875 33.333 0.00 0.00 0.00 2.29
1083 1120 5.743026 TCTTGTAAGTGAATGCAACGAAA 57.257 34.783 0.00 0.00 0.00 3.46
1084 1121 5.525745 TCTTCTTGTAAGTGAATGCAACGAA 59.474 36.000 0.00 0.00 0.00 3.85
1085 1122 5.053811 TCTTCTTGTAAGTGAATGCAACGA 58.946 37.500 0.00 0.00 0.00 3.85
1086 1123 5.342806 TCTTCTTGTAAGTGAATGCAACG 57.657 39.130 0.00 0.00 0.00 4.10
1087 1124 6.972328 TGTTTCTTCTTGTAAGTGAATGCAAC 59.028 34.615 0.00 0.00 0.00 4.17
1088 1125 7.094508 TGTTTCTTCTTGTAAGTGAATGCAA 57.905 32.000 0.00 0.00 0.00 4.08
1089 1126 6.691754 TGTTTCTTCTTGTAAGTGAATGCA 57.308 33.333 0.00 0.00 0.00 3.96
1090 1127 6.417930 GGTTGTTTCTTCTTGTAAGTGAATGC 59.582 38.462 0.00 0.00 0.00 3.56
1091 1128 7.432252 GTGGTTGTTTCTTCTTGTAAGTGAATG 59.568 37.037 0.00 0.00 0.00 2.67
1092 1129 7.416326 GGTGGTTGTTTCTTCTTGTAAGTGAAT 60.416 37.037 0.00 0.00 0.00 2.57
1093 1130 6.127842 GGTGGTTGTTTCTTCTTGTAAGTGAA 60.128 38.462 0.00 0.00 0.00 3.18
1094 1131 5.355910 GGTGGTTGTTTCTTCTTGTAAGTGA 59.644 40.000 0.00 0.00 0.00 3.41
1095 1132 5.124776 TGGTGGTTGTTTCTTCTTGTAAGTG 59.875 40.000 0.00 0.00 0.00 3.16
1096 1133 5.258051 TGGTGGTTGTTTCTTCTTGTAAGT 58.742 37.500 0.00 0.00 0.00 2.24
1097 1134 5.733373 GCTGGTGGTTGTTTCTTCTTGTAAG 60.733 44.000 0.00 0.00 0.00 2.34
1098 1135 4.097286 GCTGGTGGTTGTTTCTTCTTGTAA 59.903 41.667 0.00 0.00 0.00 2.41
1099 1136 3.630312 GCTGGTGGTTGTTTCTTCTTGTA 59.370 43.478 0.00 0.00 0.00 2.41
1100 1137 2.427095 GCTGGTGGTTGTTTCTTCTTGT 59.573 45.455 0.00 0.00 0.00 3.16
1101 1138 2.541588 CGCTGGTGGTTGTTTCTTCTTG 60.542 50.000 0.00 0.00 0.00 3.02
1102 1139 1.676006 CGCTGGTGGTTGTTTCTTCTT 59.324 47.619 0.00 0.00 0.00 2.52
1103 1140 1.308998 CGCTGGTGGTTGTTTCTTCT 58.691 50.000 0.00 0.00 0.00 2.85
1104 1141 1.021968 ACGCTGGTGGTTGTTTCTTC 58.978 50.000 0.00 0.00 0.00 2.87
1105 1142 1.470051 AACGCTGGTGGTTGTTTCTT 58.530 45.000 0.00 0.00 0.00 2.52
1106 1143 1.134175 CAAACGCTGGTGGTTGTTTCT 59.866 47.619 4.01 0.00 32.58 2.52
1107 1144 1.555477 CAAACGCTGGTGGTTGTTTC 58.445 50.000 4.01 0.00 32.58 2.78
1108 1145 0.174617 CCAAACGCTGGTGGTTGTTT 59.825 50.000 10.40 0.00 40.78 2.83
1109 1146 1.813192 CCAAACGCTGGTGGTTGTT 59.187 52.632 10.40 0.00 40.78 2.83
1110 1147 3.520402 CCAAACGCTGGTGGTTGT 58.480 55.556 10.40 0.00 40.78 3.32
1118 1155 2.340453 AAGTGCTGCACCAAACGCTG 62.340 55.000 27.74 0.00 34.49 5.18
1119 1156 2.120909 AAGTGCTGCACCAAACGCT 61.121 52.632 27.74 5.88 34.49 5.07
1120 1157 1.945662 CAAGTGCTGCACCAAACGC 60.946 57.895 27.74 2.45 34.49 4.84
1121 1158 4.307258 CAAGTGCTGCACCAAACG 57.693 55.556 27.74 9.31 34.49 3.60
1130 1167 1.788308 CGAACCAAAATGCAAGTGCTG 59.212 47.619 4.69 0.00 42.66 4.41
1131 1168 1.408702 ACGAACCAAAATGCAAGTGCT 59.591 42.857 4.69 0.00 42.66 4.40
1132 1169 1.851658 ACGAACCAAAATGCAAGTGC 58.148 45.000 0.00 0.00 42.50 4.40
1133 1170 3.705604 AGAACGAACCAAAATGCAAGTG 58.294 40.909 0.00 0.00 0.00 3.16
1134 1171 4.097892 AGAAGAACGAACCAAAATGCAAGT 59.902 37.500 0.00 0.00 0.00 3.16
1135 1172 4.610945 AGAAGAACGAACCAAAATGCAAG 58.389 39.130 0.00 0.00 0.00 4.01
1136 1173 4.647424 AGAAGAACGAACCAAAATGCAA 57.353 36.364 0.00 0.00 0.00 4.08
1137 1174 4.499019 GGAAGAAGAACGAACCAAAATGCA 60.499 41.667 0.00 0.00 0.00 3.96
1138 1175 3.981416 GGAAGAAGAACGAACCAAAATGC 59.019 43.478 0.00 0.00 0.00 3.56
1139 1176 5.438761 AGGAAGAAGAACGAACCAAAATG 57.561 39.130 0.00 0.00 0.00 2.32
1140 1177 6.461092 GGAAAGGAAGAAGAACGAACCAAAAT 60.461 38.462 0.00 0.00 0.00 1.82
1141 1178 5.163591 GGAAAGGAAGAAGAACGAACCAAAA 60.164 40.000 0.00 0.00 0.00 2.44
1142 1179 4.337274 GGAAAGGAAGAAGAACGAACCAAA 59.663 41.667 0.00 0.00 0.00 3.28
1143 1180 3.881089 GGAAAGGAAGAAGAACGAACCAA 59.119 43.478 0.00 0.00 0.00 3.67
1144 1181 3.135895 AGGAAAGGAAGAAGAACGAACCA 59.864 43.478 0.00 0.00 0.00 3.67
1145 1182 3.741249 AGGAAAGGAAGAAGAACGAACC 58.259 45.455 0.00 0.00 0.00 3.62
1146 1183 4.023963 CCAAGGAAAGGAAGAAGAACGAAC 60.024 45.833 0.00 0.00 0.00 3.95
1147 1184 4.134563 CCAAGGAAAGGAAGAAGAACGAA 58.865 43.478 0.00 0.00 0.00 3.85
1148 1185 3.135895 ACCAAGGAAAGGAAGAAGAACGA 59.864 43.478 0.00 0.00 0.00 3.85
1149 1186 3.477530 ACCAAGGAAAGGAAGAAGAACG 58.522 45.455 0.00 0.00 0.00 3.95
1150 1187 4.720046 AGACCAAGGAAAGGAAGAAGAAC 58.280 43.478 0.00 0.00 0.00 3.01
1151 1188 5.388599 AAGACCAAGGAAAGGAAGAAGAA 57.611 39.130 0.00 0.00 0.00 2.52
1152 1189 5.377478 GAAAGACCAAGGAAAGGAAGAAGA 58.623 41.667 0.00 0.00 0.00 2.87
1153 1190 4.214332 CGAAAGACCAAGGAAAGGAAGAAG 59.786 45.833 0.00 0.00 0.00 2.85
1154 1191 4.134563 CGAAAGACCAAGGAAAGGAAGAA 58.865 43.478 0.00 0.00 0.00 2.52
1155 1192 3.135895 ACGAAAGACCAAGGAAAGGAAGA 59.864 43.478 0.00 0.00 0.00 2.87
1156 1193 3.477530 ACGAAAGACCAAGGAAAGGAAG 58.522 45.455 0.00 0.00 0.00 3.46
1157 1194 3.570912 ACGAAAGACCAAGGAAAGGAA 57.429 42.857 0.00 0.00 0.00 3.36
1158 1195 3.473625 GAACGAAAGACCAAGGAAAGGA 58.526 45.455 0.00 0.00 0.00 3.36
1159 1196 2.552743 GGAACGAAAGACCAAGGAAAGG 59.447 50.000 0.00 0.00 0.00 3.11
1160 1197 3.898517 GGAACGAAAGACCAAGGAAAG 57.101 47.619 0.00 0.00 0.00 2.62
1176 1213 5.180492 TCAGTTGTTTGGAATATGACGGAAC 59.820 40.000 0.00 0.00 0.00 3.62
1177 1214 5.309638 TCAGTTGTTTGGAATATGACGGAA 58.690 37.500 0.00 0.00 0.00 4.30
1178 1215 4.900684 TCAGTTGTTTGGAATATGACGGA 58.099 39.130 0.00 0.00 0.00 4.69
1179 1216 5.586243 AGATCAGTTGTTTGGAATATGACGG 59.414 40.000 0.00 0.00 0.00 4.79
1180 1217 6.668541 AGATCAGTTGTTTGGAATATGACG 57.331 37.500 0.00 0.00 0.00 4.35
1188 1225 9.295825 ACATTGTAATTAGATCAGTTGTTTGGA 57.704 29.630 0.00 0.00 0.00 3.53
1206 1243 8.679100 GGTGCATTAGTGGTTAATACATTGTAA 58.321 33.333 0.00 0.00 29.91 2.41
1207 1244 8.050325 AGGTGCATTAGTGGTTAATACATTGTA 58.950 33.333 0.00 0.00 29.91 2.41
1208 1245 6.889722 AGGTGCATTAGTGGTTAATACATTGT 59.110 34.615 0.00 0.00 29.91 2.71
1209 1246 7.333528 AGGTGCATTAGTGGTTAATACATTG 57.666 36.000 0.00 0.00 29.91 2.82
1210 1247 7.954666 AAGGTGCATTAGTGGTTAATACATT 57.045 32.000 0.00 0.00 29.91 2.71
1211 1248 7.954666 AAAGGTGCATTAGTGGTTAATACAT 57.045 32.000 0.00 0.00 29.91 2.29
1212 1249 7.768807 AAAAGGTGCATTAGTGGTTAATACA 57.231 32.000 0.00 0.00 30.75 2.29
1236 1273 6.953520 ACCATGTCCCTGAGATTTGATAAAAA 59.046 34.615 0.00 0.00 0.00 1.94
1237 1274 6.493166 ACCATGTCCCTGAGATTTGATAAAA 58.507 36.000 0.00 0.00 0.00 1.52
1238 1275 6.078456 ACCATGTCCCTGAGATTTGATAAA 57.922 37.500 0.00 0.00 0.00 1.40
1239 1276 5.684704 GACCATGTCCCTGAGATTTGATAA 58.315 41.667 0.00 0.00 0.00 1.75
1240 1277 4.202253 CGACCATGTCCCTGAGATTTGATA 60.202 45.833 0.00 0.00 0.00 2.15
1241 1278 3.432749 CGACCATGTCCCTGAGATTTGAT 60.433 47.826 0.00 0.00 0.00 2.57
1242 1279 2.093500 CGACCATGTCCCTGAGATTTGA 60.093 50.000 0.00 0.00 0.00 2.69
1243 1280 2.093500 TCGACCATGTCCCTGAGATTTG 60.093 50.000 0.00 0.00 0.00 2.32
1244 1281 2.187958 TCGACCATGTCCCTGAGATTT 58.812 47.619 0.00 0.00 0.00 2.17
1245 1282 1.866015 TCGACCATGTCCCTGAGATT 58.134 50.000 0.00 0.00 0.00 2.40
1246 1283 1.866015 TTCGACCATGTCCCTGAGAT 58.134 50.000 0.00 0.00 0.00 2.75
1247 1284 1.757118 GATTCGACCATGTCCCTGAGA 59.243 52.381 0.00 0.00 0.00 3.27
1248 1285 1.482182 TGATTCGACCATGTCCCTGAG 59.518 52.381 0.00 0.00 0.00 3.35
1249 1286 1.567357 TGATTCGACCATGTCCCTGA 58.433 50.000 0.00 0.00 0.00 3.86
1250 1287 2.158914 TCATGATTCGACCATGTCCCTG 60.159 50.000 20.12 3.02 41.45 4.45
1251 1288 2.103771 CTCATGATTCGACCATGTCCCT 59.896 50.000 20.12 0.00 41.45 4.20
1252 1289 2.487934 CTCATGATTCGACCATGTCCC 58.512 52.381 20.12 0.00 41.45 4.46
1253 1290 2.487934 CCTCATGATTCGACCATGTCC 58.512 52.381 20.12 0.00 41.45 4.02
1254 1291 1.869767 GCCTCATGATTCGACCATGTC 59.130 52.381 20.12 11.14 41.45 3.06
1255 1292 1.210234 TGCCTCATGATTCGACCATGT 59.790 47.619 20.12 0.00 41.45 3.21
1256 1293 1.871676 CTGCCTCATGATTCGACCATG 59.128 52.381 16.71 16.71 41.93 3.66
1257 1294 1.764723 TCTGCCTCATGATTCGACCAT 59.235 47.619 0.00 0.00 0.00 3.55
1258 1295 1.194218 TCTGCCTCATGATTCGACCA 58.806 50.000 0.00 0.00 0.00 4.02
1259 1296 1.936547 GTTCTGCCTCATGATTCGACC 59.063 52.381 0.00 0.00 0.00 4.79
1260 1297 2.621338 TGTTCTGCCTCATGATTCGAC 58.379 47.619 0.00 0.00 0.00 4.20
1261 1298 3.333029 TTGTTCTGCCTCATGATTCGA 57.667 42.857 0.00 0.00 0.00 3.71
1262 1299 4.627611 ATTTGTTCTGCCTCATGATTCG 57.372 40.909 0.00 0.00 0.00 3.34
1263 1300 6.090358 CACAAATTTGTTCTGCCTCATGATTC 59.910 38.462 21.10 0.00 39.91 2.52
1264 1301 5.929992 CACAAATTTGTTCTGCCTCATGATT 59.070 36.000 21.10 0.00 39.91 2.57
1265 1302 5.011329 ACACAAATTTGTTCTGCCTCATGAT 59.989 36.000 21.10 0.00 39.91 2.45
1266 1303 4.341806 ACACAAATTTGTTCTGCCTCATGA 59.658 37.500 21.10 0.00 39.91 3.07
1267 1304 4.624015 ACACAAATTTGTTCTGCCTCATG 58.376 39.130 21.10 8.57 39.91 3.07
1268 1305 4.942761 ACACAAATTTGTTCTGCCTCAT 57.057 36.364 21.10 0.00 39.91 2.90
1269 1306 4.734398 AACACAAATTTGTTCTGCCTCA 57.266 36.364 21.10 0.00 39.91 3.86
1270 1307 5.351458 AGAAACACAAATTTGTTCTGCCTC 58.649 37.500 21.10 11.49 38.82 4.70
1271 1308 5.343307 AGAAACACAAATTTGTTCTGCCT 57.657 34.783 21.10 11.53 38.82 4.75
1272 1309 5.351189 ACAAGAAACACAAATTTGTTCTGCC 59.649 36.000 21.10 9.62 38.82 4.85
1273 1310 6.407475 ACAAGAAACACAAATTTGTTCTGC 57.593 33.333 21.10 9.81 38.82 4.26
1325 1362 4.911390 ACCACAACTCCAGAGGATTTTAG 58.089 43.478 0.00 0.00 0.00 1.85
1374 1411 8.028938 ACAGTTGAGGAAATTGCACAAATATAC 58.971 33.333 0.00 0.00 0.00 1.47
1455 1550 1.304464 CCCAACCTTGCCTTCTCCC 60.304 63.158 0.00 0.00 0.00 4.30
1521 1800 3.499737 GCATCTGGCACCGGTTCG 61.500 66.667 2.97 0.00 43.97 3.95
1562 1863 1.709147 GGATGCAGCGATGTGTGGTC 61.709 60.000 1.22 0.00 0.00 4.02
1574 1875 0.811616 GCGGTAGACAAGGGATGCAG 60.812 60.000 0.00 0.00 0.00 4.41
1595 1896 3.660501 TCGAGGGATATATGTGTGTGC 57.339 47.619 0.00 0.00 0.00 4.57
1632 1943 3.491619 CGAAGGATCCCATAGTGTGACTG 60.492 52.174 8.55 0.00 0.00 3.51
1739 2053 5.253330 AGGTTGGTGTATGAATAGGTGTTG 58.747 41.667 0.00 0.00 0.00 3.33
1740 2054 5.514500 AGGTTGGTGTATGAATAGGTGTT 57.486 39.130 0.00 0.00 0.00 3.32
1746 2060 4.342951 CGACCCTAGGTTGGTGTATGAATA 59.657 45.833 8.29 0.00 35.25 1.75
1769 2083 4.225267 TGGAGAAGTTATTCTTGGAGGTCC 59.775 45.833 0.00 0.00 45.98 4.46
1818 2132 1.378531 GTTGTGTTGACTGACTGCCA 58.621 50.000 0.00 0.00 0.00 4.92
1821 2135 1.670811 GGTGGTTGTGTTGACTGACTG 59.329 52.381 0.00 0.00 0.00 3.51
1823 2137 1.745232 TGGTGGTTGTGTTGACTGAC 58.255 50.000 0.00 0.00 0.00 3.51
1824 2138 2.092699 TGATGGTGGTTGTGTTGACTGA 60.093 45.455 0.00 0.00 0.00 3.41
1825 2139 2.296792 TGATGGTGGTTGTGTTGACTG 58.703 47.619 0.00 0.00 0.00 3.51
1826 2140 2.727123 TGATGGTGGTTGTGTTGACT 57.273 45.000 0.00 0.00 0.00 3.41
1870 2184 8.920665 TCATAAAACTTCAATTATTTTGGTGCG 58.079 29.630 0.00 0.00 0.00 5.34
1927 2241 5.142061 TGCGGACTTTTCTATACACTTGA 57.858 39.130 0.00 0.00 0.00 3.02
1933 2247 7.148950 CGTAGATCATTGCGGACTTTTCTATAC 60.149 40.741 0.00 0.00 0.00 1.47
1943 2257 7.488150 TCATTAATATCGTAGATCATTGCGGAC 59.512 37.037 0.00 0.00 45.12 4.79
2037 2352 9.129209 GTCAAGCTTCATTAAATTAACCAAGTC 57.871 33.333 0.00 2.18 0.00 3.01
2086 2402 3.159472 ACCCCCTCCGTTTCAAAATAAC 58.841 45.455 0.00 0.00 0.00 1.89
2168 2580 3.249080 GCACGCTGTCAGTTTTACCTTTA 59.751 43.478 0.93 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.