Multiple sequence alignment - TraesCS7B01G023900

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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 TraesCS7B01G023900 chr7B 100.000 3429 0 0 1 3429 22832028 22835456 0.000000e+00 6333
1 TraesCS7B01G023900 chr7B 98.922 2040 21 1 1391 3429 22709732 22711771 0.000000e+00 3644
2 TraesCS7B01G023900 chr7B 98.087 2039 33 2 1391 3429 22668002 22670034 0.000000e+00 3544
3 TraesCS7B01G023900 chr7B 98.401 1501 20 3 1391 2888 22963727 22965226 0.000000e+00 2636
4 TraesCS7B01G023900 chr7B 98.169 1420 24 2 2010 3429 22893360 22894777 0.000000e+00 2477
5 TraesCS7B01G023900 chr7B 98.031 1422 25 2 2010 3429 22772235 22773655 0.000000e+00 2468
6 TraesCS7B01G023900 chr7B 98.886 987 9 1 1 987 22962753 22963737 0.000000e+00 1760
7 TraesCS7B01G023900 chr7B 98.886 987 8 2 1 987 22891812 22892795 0.000000e+00 1759
8 TraesCS7B01G023900 chr7B 98.278 987 15 1 1 987 22708758 22709742 0.000000e+00 1727
9 TraesCS7B01G023900 chr7B 98.176 987 16 1 1 987 22770687 22771671 0.000000e+00 1722
10 TraesCS7B01G023900 chr7B 98.075 987 16 2 1 987 22667029 22668012 0.000000e+00 1714
11 TraesCS7B01G023900 chr7B 96.732 918 25 4 1 918 23007977 23008889 0.000000e+00 1524
12 TraesCS7B01G023900 chr7B 82.430 1070 158 20 1392 2454 23410939 23411985 0.000000e+00 907
13 TraesCS7B01G023900 chr7B 95.928 442 18 0 2988 3429 22968268 22968709 0.000000e+00 717
14 TraesCS7B01G023900 chr7B 95.475 442 20 0 2988 3429 22714383 22714824 0.000000e+00 706
15 TraesCS7B01G023900 chr7D 94.752 2039 73 4 1391 3429 76503216 76505220 0.000000e+00 3142
16 TraesCS7B01G023900 chr7D 95.452 1979 60 2 1451 3429 76521420 76523368 0.000000e+00 3129
17 TraesCS7B01G023900 chr7D 96.657 987 30 2 1 987 76502243 76503226 0.000000e+00 1637
18 TraesCS7B01G023900 chr7D 97.935 775 13 2 213 987 76520388 76521159 0.000000e+00 1339
19 TraesCS7B01G023900 chr7D 94.250 713 34 4 2430 3141 76482578 76483284 0.000000e+00 1083
20 TraesCS7B01G023900 chr7D 82.540 1071 157 25 1392 2454 76725918 76726966 0.000000e+00 915
21 TraesCS7B01G023900 chr7D 84.831 890 112 13 1392 2266 76628876 76629757 0.000000e+00 874
22 TraesCS7B01G023900 chr7A 94.600 2000 89 9 1391 3385 80539254 80541239 0.000000e+00 3077
23 TraesCS7B01G023900 chr7A 95.776 947 34 4 43 987 80538322 80539264 0.000000e+00 1522
24 TraesCS7B01G023900 chr3B 94.417 412 15 3 987 1390 5168017 5168428 8.080000e-176 627
25 TraesCS7B01G023900 chr6B 94.377 409 18 5 987 1390 528908628 528908220 1.040000e-174 623
26 TraesCS7B01G023900 chr6B 94.417 412 12 8 987 1390 670020069 670019661 1.040000e-174 623
27 TraesCS7B01G023900 chr6B 93.627 408 19 4 987 1390 701069121 701069525 1.360000e-168 603
28 TraesCS7B01G023900 chr4B 94.404 411 14 6 987 1390 633150437 633150029 1.040000e-174 623
29 TraesCS7B01G023900 chr4B 93.269 416 17 6 987 1391 183514118 183514533 1.360000e-168 603
30 TraesCS7B01G023900 chr4A 93.056 432 20 7 987 1409 713367493 713367063 1.040000e-174 623
31 TraesCS7B01G023900 chr5B 93.674 411 18 4 987 1390 36079064 36079473 2.930000e-170 608
32 TraesCS7B01G023900 chr2B 93.447 412 18 5 987 1390 643205051 643205461 1.360000e-168 603


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 TraesCS7B01G023900 chr7B 22832028 22835456 3428 False 6333.000000 6333 100.000000 1 3429 1 chr7B.!!$F1 3428
1 TraesCS7B01G023900 chr7B 22667029 22670034 3005 False 2629.000000 3544 98.081000 1 3429 2 chr7B.!!$F4 3428
2 TraesCS7B01G023900 chr7B 22891812 22894777 2965 False 2118.000000 2477 98.527500 1 3429 2 chr7B.!!$F7 3428
3 TraesCS7B01G023900 chr7B 22770687 22773655 2968 False 2095.000000 2468 98.103500 1 3429 2 chr7B.!!$F6 3428
4 TraesCS7B01G023900 chr7B 22708758 22714824 6066 False 2025.666667 3644 97.558333 1 3429 3 chr7B.!!$F5 3428
5 TraesCS7B01G023900 chr7B 22962753 22968709 5956 False 1704.333333 2636 97.738333 1 3429 3 chr7B.!!$F8 3428
6 TraesCS7B01G023900 chr7B 23007977 23008889 912 False 1524.000000 1524 96.732000 1 918 1 chr7B.!!$F2 917
7 TraesCS7B01G023900 chr7B 23410939 23411985 1046 False 907.000000 907 82.430000 1392 2454 1 chr7B.!!$F3 1062
8 TraesCS7B01G023900 chr7D 76502243 76505220 2977 False 2389.500000 3142 95.704500 1 3429 2 chr7D.!!$F4 3428
9 TraesCS7B01G023900 chr7D 76520388 76523368 2980 False 2234.000000 3129 96.693500 213 3429 2 chr7D.!!$F5 3216
10 TraesCS7B01G023900 chr7D 76482578 76483284 706 False 1083.000000 1083 94.250000 2430 3141 1 chr7D.!!$F1 711
11 TraesCS7B01G023900 chr7D 76725918 76726966 1048 False 915.000000 915 82.540000 1392 2454 1 chr7D.!!$F3 1062
12 TraesCS7B01G023900 chr7D 76628876 76629757 881 False 874.000000 874 84.831000 1392 2266 1 chr7D.!!$F2 874
13 TraesCS7B01G023900 chr7A 80538322 80541239 2917 False 2299.500000 3077 95.188000 43 3385 2 chr7A.!!$F1 3342

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
885 888 3.118038 ACAGGTCTAAGTTTTGCACAGGA 60.118 43.478 0.00 0.0 0.00 3.86 F
1375 1378 0.390492 CTCATATGAGCTCGGGTGCA 59.610 55.000 19.47 0.0 35.13 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 2034 4.764823 CCATCTGTTAGGCTTGGTTAAACA 59.235 41.667 0.0 0.0 0.0 2.83 R
3208 6437 2.001872 GCATCAATTTTTCCCCTTGCG 58.998 47.619 0.0 0.0 0.0 4.85 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
876 879 8.101419 CCTTAGTTGGATTACAGGTCTAAGTTT 58.899 37.037 0.00 0.00 36.34 2.66
877 880 9.503399 CTTAGTTGGATTACAGGTCTAAGTTTT 57.497 33.333 0.00 0.00 35.08 2.43
881 884 5.472137 TGGATTACAGGTCTAAGTTTTGCAC 59.528 40.000 0.00 0.00 0.00 4.57
885 888 3.118038 ACAGGTCTAAGTTTTGCACAGGA 60.118 43.478 0.00 0.00 0.00 3.86
976 979 8.428063 GCACTCCAAGCATTCTATATATAGGAT 58.572 37.037 17.81 12.95 0.00 3.24
994 997 7.700022 ATAGGATACATCTACCCGAAAGTAC 57.300 40.000 0.00 0.00 41.41 2.73
995 998 4.831710 AGGATACATCTACCCGAAAGTACC 59.168 45.833 0.00 0.00 41.41 3.34
996 999 4.831710 GGATACATCTACCCGAAAGTACCT 59.168 45.833 0.00 0.00 0.00 3.08
997 1000 5.303845 GGATACATCTACCCGAAAGTACCTT 59.696 44.000 0.00 0.00 0.00 3.50
998 1001 6.183360 GGATACATCTACCCGAAAGTACCTTT 60.183 42.308 0.00 0.00 36.29 3.11
999 1002 5.082251 ACATCTACCCGAAAGTACCTTTC 57.918 43.478 6.64 6.64 44.29 2.62
1000 1003 4.776308 ACATCTACCCGAAAGTACCTTTCT 59.224 41.667 13.19 0.29 45.19 2.52
1001 1004 4.796038 TCTACCCGAAAGTACCTTTCTG 57.204 45.455 13.19 7.81 45.19 3.02
1002 1005 2.180432 ACCCGAAAGTACCTTTCTGC 57.820 50.000 13.19 0.00 45.19 4.26
1003 1006 1.697982 ACCCGAAAGTACCTTTCTGCT 59.302 47.619 13.19 0.00 45.19 4.24
1004 1007 2.289506 ACCCGAAAGTACCTTTCTGCTC 60.290 50.000 13.19 0.00 45.19 4.26
1005 1008 2.347731 CCGAAAGTACCTTTCTGCTCC 58.652 52.381 13.19 0.00 45.19 4.70
1006 1009 2.347731 CGAAAGTACCTTTCTGCTCCC 58.652 52.381 13.19 0.00 45.19 4.30
1007 1010 2.347731 GAAAGTACCTTTCTGCTCCCG 58.652 52.381 9.00 0.00 44.33 5.14
1008 1011 1.640917 AAGTACCTTTCTGCTCCCGA 58.359 50.000 0.00 0.00 0.00 5.14
1009 1012 1.187087 AGTACCTTTCTGCTCCCGAG 58.813 55.000 0.00 0.00 0.00 4.63
1030 1033 2.416747 CTCATTTGAGCTCGGTGAACA 58.583 47.619 9.64 0.00 35.13 3.18
1031 1034 2.414481 CTCATTTGAGCTCGGTGAACAG 59.586 50.000 9.64 0.00 35.13 3.16
1032 1035 2.146342 CATTTGAGCTCGGTGAACAGT 58.854 47.619 9.64 0.00 0.00 3.55
1033 1036 3.006430 TCATTTGAGCTCGGTGAACAGTA 59.994 43.478 9.64 0.00 0.00 2.74
1034 1037 3.462483 TTTGAGCTCGGTGAACAGTAA 57.538 42.857 9.64 0.00 0.00 2.24
1035 1038 3.462483 TTGAGCTCGGTGAACAGTAAA 57.538 42.857 9.64 0.00 0.00 2.01
1036 1039 3.462483 TGAGCTCGGTGAACAGTAAAA 57.538 42.857 9.64 0.00 0.00 1.52
1037 1040 4.002906 TGAGCTCGGTGAACAGTAAAAT 57.997 40.909 9.64 0.00 0.00 1.82
1038 1041 3.994392 TGAGCTCGGTGAACAGTAAAATC 59.006 43.478 9.64 0.00 0.00 2.17
1039 1042 3.994392 GAGCTCGGTGAACAGTAAAATCA 59.006 43.478 0.00 0.00 0.00 2.57
1040 1043 4.385825 AGCTCGGTGAACAGTAAAATCAA 58.614 39.130 0.00 0.00 0.00 2.57
1041 1044 4.819630 AGCTCGGTGAACAGTAAAATCAAA 59.180 37.500 0.00 0.00 0.00 2.69
1042 1045 5.298276 AGCTCGGTGAACAGTAAAATCAAAA 59.702 36.000 0.00 0.00 0.00 2.44
1043 1046 5.974751 GCTCGGTGAACAGTAAAATCAAAAA 59.025 36.000 0.00 0.00 0.00 1.94
1087 1090 9.889128 AAAAATTCCAAAAACAATCTCAGAGAA 57.111 25.926 3.63 0.00 0.00 2.87
1088 1091 9.889128 AAAATTCCAAAAACAATCTCAGAGAAA 57.111 25.926 3.63 0.00 0.00 2.52
1089 1092 8.877808 AATTCCAAAAACAATCTCAGAGAAAC 57.122 30.769 3.63 0.00 0.00 2.78
1090 1093 7.403312 TTCCAAAAACAATCTCAGAGAAACA 57.597 32.000 3.63 0.00 0.00 2.83
1091 1094 7.587037 TCCAAAAACAATCTCAGAGAAACAT 57.413 32.000 3.63 0.00 0.00 2.71
1092 1095 8.010733 TCCAAAAACAATCTCAGAGAAACATT 57.989 30.769 3.63 0.00 0.00 2.71
1093 1096 7.922278 TCCAAAAACAATCTCAGAGAAACATTG 59.078 33.333 3.63 7.06 0.00 2.82
1094 1097 7.922278 CCAAAAACAATCTCAGAGAAACATTGA 59.078 33.333 15.53 0.00 0.00 2.57
1095 1098 8.749499 CAAAAACAATCTCAGAGAAACATTGAC 58.251 33.333 15.53 0.00 0.00 3.18
1096 1099 7.572523 AAACAATCTCAGAGAAACATTGACA 57.427 32.000 15.53 0.00 0.00 3.58
1097 1100 7.572523 AACAATCTCAGAGAAACATTGACAA 57.427 32.000 15.53 0.00 0.00 3.18
1098 1101 7.572523 ACAATCTCAGAGAAACATTGACAAA 57.427 32.000 15.53 0.00 0.00 2.83
1099 1102 7.999679 ACAATCTCAGAGAAACATTGACAAAA 58.000 30.769 15.53 0.00 0.00 2.44
1100 1103 8.133627 ACAATCTCAGAGAAACATTGACAAAAG 58.866 33.333 15.53 0.00 0.00 2.27
1101 1104 7.814264 ATCTCAGAGAAACATTGACAAAAGT 57.186 32.000 3.63 0.00 0.00 2.66
1102 1105 7.630242 TCTCAGAGAAACATTGACAAAAGTT 57.370 32.000 0.00 0.00 0.00 2.66
1103 1106 7.697691 TCTCAGAGAAACATTGACAAAAGTTC 58.302 34.615 0.00 5.33 0.00 3.01
1104 1107 7.554118 TCTCAGAGAAACATTGACAAAAGTTCT 59.446 33.333 0.00 9.17 0.00 3.01
1105 1108 8.731275 TCAGAGAAACATTGACAAAAGTTCTA 57.269 30.769 9.09 0.00 0.00 2.10
1106 1109 9.173021 TCAGAGAAACATTGACAAAAGTTCTAA 57.827 29.630 9.09 0.00 0.00 2.10
1107 1110 9.443283 CAGAGAAACATTGACAAAAGTTCTAAG 57.557 33.333 9.09 3.77 0.00 2.18
1108 1111 9.178758 AGAGAAACATTGACAAAAGTTCTAAGT 57.821 29.630 9.09 0.00 0.00 2.24
1109 1112 9.226345 GAGAAACATTGACAAAAGTTCTAAGTG 57.774 33.333 9.09 0.00 0.00 3.16
1110 1113 8.190784 AGAAACATTGACAAAAGTTCTAAGTGG 58.809 33.333 9.09 0.00 0.00 4.00
1111 1114 7.404671 AACATTGACAAAAGTTCTAAGTGGT 57.595 32.000 0.00 0.00 0.00 4.16
1112 1115 7.404671 ACATTGACAAAAGTTCTAAGTGGTT 57.595 32.000 0.00 0.00 0.00 3.67
1113 1116 7.257722 ACATTGACAAAAGTTCTAAGTGGTTG 58.742 34.615 0.00 0.00 0.00 3.77
1114 1117 5.243426 TGACAAAAGTTCTAAGTGGTTGC 57.757 39.130 0.00 0.00 0.00 4.17
1115 1118 4.702612 TGACAAAAGTTCTAAGTGGTTGCA 59.297 37.500 0.00 0.00 0.00 4.08
1116 1119 5.184096 TGACAAAAGTTCTAAGTGGTTGCAA 59.816 36.000 0.00 0.00 0.00 4.08
1117 1120 6.031751 ACAAAAGTTCTAAGTGGTTGCAAA 57.968 33.333 0.00 0.00 0.00 3.68
1118 1121 6.459923 ACAAAAGTTCTAAGTGGTTGCAAAA 58.540 32.000 0.00 0.00 0.00 2.44
1119 1122 6.931840 ACAAAAGTTCTAAGTGGTTGCAAAAA 59.068 30.769 0.00 0.00 0.00 1.94
1120 1123 7.606073 ACAAAAGTTCTAAGTGGTTGCAAAAAT 59.394 29.630 0.00 0.00 0.00 1.82
1121 1124 8.450180 CAAAAGTTCTAAGTGGTTGCAAAAATT 58.550 29.630 0.00 0.61 0.00 1.82
1122 1125 7.770801 AAGTTCTAAGTGGTTGCAAAAATTC 57.229 32.000 0.00 0.00 0.00 2.17
1123 1126 6.872920 AGTTCTAAGTGGTTGCAAAAATTCA 58.127 32.000 0.00 0.00 0.00 2.57
1124 1127 7.500141 AGTTCTAAGTGGTTGCAAAAATTCAT 58.500 30.769 0.00 0.00 0.00 2.57
1125 1128 7.653311 AGTTCTAAGTGGTTGCAAAAATTCATC 59.347 33.333 0.00 0.00 0.00 2.92
1126 1129 7.048629 TCTAAGTGGTTGCAAAAATTCATCA 57.951 32.000 0.00 0.00 0.00 3.07
1127 1130 7.669427 TCTAAGTGGTTGCAAAAATTCATCAT 58.331 30.769 0.00 0.00 0.00 2.45
1128 1131 6.548441 AAGTGGTTGCAAAAATTCATCATG 57.452 33.333 0.00 0.00 0.00 3.07
1129 1132 5.856156 AGTGGTTGCAAAAATTCATCATGA 58.144 33.333 0.00 0.00 0.00 3.07
1130 1133 6.289834 AGTGGTTGCAAAAATTCATCATGAA 58.710 32.000 1.59 1.59 41.09 2.57
1131 1134 6.766944 AGTGGTTGCAAAAATTCATCATGAAA 59.233 30.769 3.63 0.00 40.12 2.69
1132 1135 7.446013 AGTGGTTGCAAAAATTCATCATGAAAT 59.554 29.630 3.63 0.00 40.12 2.17
1133 1136 7.747357 GTGGTTGCAAAAATTCATCATGAAATC 59.253 33.333 3.63 0.00 40.12 2.17
1134 1137 7.444487 TGGTTGCAAAAATTCATCATGAAATCA 59.556 29.630 3.63 0.00 40.12 2.57
1135 1138 7.747357 GGTTGCAAAAATTCATCATGAAATCAC 59.253 33.333 3.63 0.00 40.12 3.06
1136 1139 7.964604 TGCAAAAATTCATCATGAAATCACA 57.035 28.000 3.63 0.00 40.12 3.58
1137 1140 8.554835 TGCAAAAATTCATCATGAAATCACAT 57.445 26.923 3.63 0.00 40.12 3.21
1138 1141 9.004717 TGCAAAAATTCATCATGAAATCACATT 57.995 25.926 3.63 0.00 40.12 2.71
1139 1142 9.485591 GCAAAAATTCATCATGAAATCACATTC 57.514 29.630 3.63 0.00 40.12 2.67
1140 1143 9.982291 CAAAAATTCATCATGAAATCACATTCC 57.018 29.630 3.63 0.00 40.12 3.01
1141 1144 9.953565 AAAAATTCATCATGAAATCACATTCCT 57.046 25.926 3.63 0.00 40.12 3.36
1142 1145 8.942338 AAATTCATCATGAAATCACATTCCTG 57.058 30.769 3.63 0.00 40.12 3.86
1143 1146 7.655521 ATTCATCATGAAATCACATTCCTGT 57.344 32.000 3.63 0.00 40.12 4.00
1144 1147 8.756486 ATTCATCATGAAATCACATTCCTGTA 57.244 30.769 3.63 0.00 40.12 2.74
1145 1148 8.578448 TTCATCATGAAATCACATTCCTGTAA 57.422 30.769 0.00 0.00 32.71 2.41
1146 1149 8.217131 TCATCATGAAATCACATTCCTGTAAG 57.783 34.615 0.00 0.00 33.14 2.34
1181 1184 6.622833 AAAACAAATTCAGCCTCCAAAATG 57.377 33.333 0.00 0.00 0.00 2.32
1182 1185 3.667360 ACAAATTCAGCCTCCAAAATGC 58.333 40.909 0.00 0.00 0.00 3.56
1183 1186 3.325716 ACAAATTCAGCCTCCAAAATGCT 59.674 39.130 0.00 0.00 35.25 3.79
1184 1187 4.202388 ACAAATTCAGCCTCCAAAATGCTT 60.202 37.500 0.00 0.00 31.77 3.91
1185 1188 4.628963 AATTCAGCCTCCAAAATGCTTT 57.371 36.364 0.00 0.00 31.77 3.51
1186 1189 4.628963 ATTCAGCCTCCAAAATGCTTTT 57.371 36.364 0.00 0.00 31.77 2.27
1204 1207 6.804677 TGCTTTTGAAAGTAGCATTTTCAGA 58.195 32.000 0.45 4.38 43.22 3.27
1205 1208 6.919662 TGCTTTTGAAAGTAGCATTTTCAGAG 59.080 34.615 0.45 11.39 43.22 3.35
1206 1209 6.920210 GCTTTTGAAAGTAGCATTTTCAGAGT 59.080 34.615 5.47 0.00 43.22 3.24
1207 1210 8.076178 GCTTTTGAAAGTAGCATTTTCAGAGTA 58.924 33.333 5.47 0.00 43.22 2.59
1208 1211 9.387123 CTTTTGAAAGTAGCATTTTCAGAGTAC 57.613 33.333 9.30 0.00 43.22 2.73
1209 1212 7.435068 TTGAAAGTAGCATTTTCAGAGTACC 57.565 36.000 9.30 0.00 43.22 3.34
1210 1213 5.637810 TGAAAGTAGCATTTTCAGAGTACCG 59.362 40.000 6.29 0.00 39.05 4.02
1211 1214 5.401531 AAGTAGCATTTTCAGAGTACCGA 57.598 39.130 0.00 0.00 0.00 4.69
1212 1215 5.599999 AGTAGCATTTTCAGAGTACCGAT 57.400 39.130 0.00 0.00 0.00 4.18
1213 1216 5.978814 AGTAGCATTTTCAGAGTACCGATT 58.021 37.500 0.00 0.00 0.00 3.34
1214 1217 7.108841 AGTAGCATTTTCAGAGTACCGATTA 57.891 36.000 0.00 0.00 0.00 1.75
1215 1218 7.727181 AGTAGCATTTTCAGAGTACCGATTAT 58.273 34.615 0.00 0.00 0.00 1.28
1216 1219 8.204836 AGTAGCATTTTCAGAGTACCGATTATT 58.795 33.333 0.00 0.00 0.00 1.40
1217 1220 7.865706 AGCATTTTCAGAGTACCGATTATTT 57.134 32.000 0.00 0.00 0.00 1.40
1218 1221 8.281212 AGCATTTTCAGAGTACCGATTATTTT 57.719 30.769 0.00 0.00 0.00 1.82
1219 1222 8.739972 AGCATTTTCAGAGTACCGATTATTTTT 58.260 29.630 0.00 0.00 0.00 1.94
1235 1238 2.264005 TTTTTGCCACGCCTTCTAGA 57.736 45.000 0.00 0.00 0.00 2.43
1236 1239 2.264005 TTTTGCCACGCCTTCTAGAA 57.736 45.000 4.81 4.81 0.00 2.10
1237 1240 2.264005 TTTGCCACGCCTTCTAGAAA 57.736 45.000 6.63 0.00 0.00 2.52
1238 1241 2.489938 TTGCCACGCCTTCTAGAAAT 57.510 45.000 6.63 0.00 0.00 2.17
1239 1242 1.737838 TGCCACGCCTTCTAGAAATG 58.262 50.000 6.63 2.12 0.00 2.32
1240 1243 1.003118 TGCCACGCCTTCTAGAAATGT 59.997 47.619 6.63 2.59 0.00 2.71
1241 1244 1.398390 GCCACGCCTTCTAGAAATGTG 59.602 52.381 17.92 17.92 0.00 3.21
1242 1245 2.935238 GCCACGCCTTCTAGAAATGTGA 60.935 50.000 23.01 0.00 0.00 3.58
1243 1246 3.535561 CCACGCCTTCTAGAAATGTGAT 58.464 45.455 23.01 7.98 0.00 3.06
1244 1247 3.941483 CCACGCCTTCTAGAAATGTGATT 59.059 43.478 23.01 3.88 0.00 2.57
1245 1248 4.396166 CCACGCCTTCTAGAAATGTGATTT 59.604 41.667 23.01 3.35 34.64 2.17
1246 1249 5.447818 CCACGCCTTCTAGAAATGTGATTTC 60.448 44.000 23.01 0.00 46.90 2.17
1260 1263 9.519905 GAAATGTGATTTCATGACGAATTTTTG 57.480 29.630 0.00 0.00 46.05 2.44
1261 1264 6.450845 TGTGATTTCATGACGAATTTTTGC 57.549 33.333 0.00 0.00 32.32 3.68
1262 1265 5.981915 TGTGATTTCATGACGAATTTTTGCA 59.018 32.000 0.00 0.00 32.32 4.08
1263 1266 6.478016 TGTGATTTCATGACGAATTTTTGCAA 59.522 30.769 0.00 0.00 32.32 4.08
1264 1267 7.005380 GTGATTTCATGACGAATTTTTGCAAG 58.995 34.615 0.00 0.00 32.32 4.01
1265 1268 4.970472 TTCATGACGAATTTTTGCAAGC 57.030 36.364 0.00 0.00 0.00 4.01
1266 1269 3.974912 TCATGACGAATTTTTGCAAGCA 58.025 36.364 0.00 0.00 0.00 3.91
1267 1270 3.735240 TCATGACGAATTTTTGCAAGCAC 59.265 39.130 0.00 0.00 0.00 4.40
1268 1271 3.435105 TGACGAATTTTTGCAAGCACT 57.565 38.095 0.00 0.00 0.00 4.40
1269 1272 3.779759 TGACGAATTTTTGCAAGCACTT 58.220 36.364 0.00 0.00 0.00 3.16
1270 1273 4.926244 TGACGAATTTTTGCAAGCACTTA 58.074 34.783 0.00 0.00 0.00 2.24
1271 1274 5.344066 TGACGAATTTTTGCAAGCACTTAA 58.656 33.333 0.00 0.00 0.00 1.85
1272 1275 5.807520 TGACGAATTTTTGCAAGCACTTAAA 59.192 32.000 0.00 0.00 0.00 1.52
1273 1276 6.311445 TGACGAATTTTTGCAAGCACTTAAAA 59.689 30.769 0.00 0.00 0.00 1.52
1274 1277 6.474364 ACGAATTTTTGCAAGCACTTAAAAC 58.526 32.000 0.00 0.00 0.00 2.43
1275 1278 6.312672 ACGAATTTTTGCAAGCACTTAAAACT 59.687 30.769 0.00 0.00 0.00 2.66
1276 1279 7.148490 ACGAATTTTTGCAAGCACTTAAAACTT 60.148 29.630 0.00 0.47 0.00 2.66
1277 1280 7.691877 CGAATTTTTGCAAGCACTTAAAACTTT 59.308 29.630 0.00 0.00 0.00 2.66
1278 1281 9.340695 GAATTTTTGCAAGCACTTAAAACTTTT 57.659 25.926 0.00 0.00 0.00 2.27
1279 1282 8.672214 ATTTTTGCAAGCACTTAAAACTTTTG 57.328 26.923 0.00 0.00 0.00 2.44
1280 1283 4.856115 TGCAAGCACTTAAAACTTTTGC 57.144 36.364 0.00 0.00 39.72 3.68
1281 1284 3.620821 TGCAAGCACTTAAAACTTTTGCC 59.379 39.130 4.14 0.00 38.82 4.52
1282 1285 3.620821 GCAAGCACTTAAAACTTTTGCCA 59.379 39.130 0.00 0.00 34.85 4.92
1283 1286 4.094146 GCAAGCACTTAAAACTTTTGCCAA 59.906 37.500 0.00 0.00 34.85 4.52
1284 1287 5.220835 GCAAGCACTTAAAACTTTTGCCAAT 60.221 36.000 0.00 0.00 34.85 3.16
1285 1288 5.989551 AGCACTTAAAACTTTTGCCAATG 57.010 34.783 0.00 0.00 33.48 2.82
1286 1289 5.427378 AGCACTTAAAACTTTTGCCAATGT 58.573 33.333 0.00 0.00 33.48 2.71
1287 1290 5.879777 AGCACTTAAAACTTTTGCCAATGTT 59.120 32.000 0.00 0.00 33.48 2.71
1288 1291 6.374053 AGCACTTAAAACTTTTGCCAATGTTT 59.626 30.769 8.26 8.26 40.32 2.83
1289 1292 6.686679 GCACTTAAAACTTTTGCCAATGTTTC 59.313 34.615 12.91 0.01 38.61 2.78
1290 1293 7.413988 GCACTTAAAACTTTTGCCAATGTTTCT 60.414 33.333 12.91 7.82 38.61 2.52
1291 1294 9.092876 CACTTAAAACTTTTGCCAATGTTTCTA 57.907 29.630 12.91 7.13 38.61 2.10
1292 1295 9.093970 ACTTAAAACTTTTGCCAATGTTTCTAC 57.906 29.630 12.91 0.00 38.61 2.59
1293 1296 6.918892 AAAACTTTTGCCAATGTTTCTACC 57.081 33.333 12.91 0.00 38.61 3.18
1294 1297 5.606348 AACTTTTGCCAATGTTTCTACCA 57.394 34.783 0.00 0.00 28.24 3.25
1295 1298 5.606348 ACTTTTGCCAATGTTTCTACCAA 57.394 34.783 0.00 0.00 0.00 3.67
1296 1299 5.983540 ACTTTTGCCAATGTTTCTACCAAA 58.016 33.333 0.00 0.00 0.00 3.28
1297 1300 6.410540 ACTTTTGCCAATGTTTCTACCAAAA 58.589 32.000 0.00 0.00 32.08 2.44
1298 1301 6.881602 ACTTTTGCCAATGTTTCTACCAAAAA 59.118 30.769 0.00 0.00 32.46 1.94
1354 1357 6.452494 TTTTTGATTTTACTGTTCACCCGA 57.548 33.333 0.00 0.00 0.00 5.14
1355 1358 5.682943 TTTGATTTTACTGTTCACCCGAG 57.317 39.130 0.00 0.00 0.00 4.63
1356 1359 3.071479 TGATTTTACTGTTCACCCGAGC 58.929 45.455 0.00 0.00 0.00 5.03
1357 1360 2.922740 TTTTACTGTTCACCCGAGCT 57.077 45.000 0.00 0.00 0.00 4.09
1358 1361 2.450609 TTTACTGTTCACCCGAGCTC 57.549 50.000 2.73 2.73 0.00 4.09
1359 1362 1.334160 TTACTGTTCACCCGAGCTCA 58.666 50.000 15.40 0.00 0.00 4.26
1360 1363 1.557099 TACTGTTCACCCGAGCTCAT 58.443 50.000 15.40 0.00 0.00 2.90
1361 1364 1.557099 ACTGTTCACCCGAGCTCATA 58.443 50.000 15.40 0.00 0.00 2.15
1362 1365 2.111384 ACTGTTCACCCGAGCTCATAT 58.889 47.619 15.40 0.00 0.00 1.78
1363 1366 2.159043 ACTGTTCACCCGAGCTCATATG 60.159 50.000 15.40 8.10 0.00 1.78
1364 1367 2.101415 CTGTTCACCCGAGCTCATATGA 59.899 50.000 15.40 10.42 0.00 2.15
1365 1368 2.101415 TGTTCACCCGAGCTCATATGAG 59.899 50.000 25.64 25.64 44.75 2.90
1374 1377 3.207677 CTCATATGAGCTCGGGTGC 57.792 57.895 19.47 0.00 35.13 5.01
1375 1378 0.390492 CTCATATGAGCTCGGGTGCA 59.610 55.000 19.47 0.00 35.13 4.57
1376 1379 0.390492 TCATATGAGCTCGGGTGCAG 59.610 55.000 9.64 0.00 34.99 4.41
1377 1380 0.390492 CATATGAGCTCGGGTGCAGA 59.610 55.000 9.64 0.00 34.99 4.26
1378 1381 1.123077 ATATGAGCTCGGGTGCAGAA 58.877 50.000 9.64 0.00 34.99 3.02
1379 1382 0.901827 TATGAGCTCGGGTGCAGAAA 59.098 50.000 9.64 0.00 34.99 2.52
1380 1383 0.674895 ATGAGCTCGGGTGCAGAAAC 60.675 55.000 9.64 0.00 34.99 2.78
1381 1384 1.004440 GAGCTCGGGTGCAGAAACT 60.004 57.895 0.00 0.00 34.99 2.66
1382 1385 1.004440 AGCTCGGGTGCAGAAACTC 60.004 57.895 0.00 0.00 34.99 3.01
1383 1386 2.035442 GCTCGGGTGCAGAAACTCC 61.035 63.158 0.00 0.00 0.00 3.85
1384 1387 1.371183 CTCGGGTGCAGAAACTCCA 59.629 57.895 0.00 0.00 0.00 3.86
1385 1388 0.951040 CTCGGGTGCAGAAACTCCAC 60.951 60.000 0.00 0.00 0.00 4.02
1386 1389 2.317609 CGGGTGCAGAAACTCCACG 61.318 63.158 0.00 0.00 0.00 4.94
1387 1390 1.227853 GGGTGCAGAAACTCCACGT 60.228 57.895 0.00 0.00 0.00 4.49
1388 1391 1.228657 GGGTGCAGAAACTCCACGTC 61.229 60.000 0.00 0.00 0.00 4.34
1389 1392 1.228657 GGTGCAGAAACTCCACGTCC 61.229 60.000 0.00 0.00 0.00 4.79
1621 1837 5.190528 AGACATGTCAGTTCCCTTGTATGAT 59.809 40.000 27.02 0.00 0.00 2.45
1817 2033 2.282391 GGTGTGCATGTCCAGGCA 60.282 61.111 2.02 2.02 46.53 4.75
2091 2322 7.653311 ACTTTCTATTTTGAACATGAAACAGGC 59.347 33.333 0.00 0.00 0.00 4.85
3088 6317 1.559682 ACAAAGATATCACCCAGGCGT 59.440 47.619 5.32 0.00 0.00 5.68
3208 6437 8.377681 CACAAAAGATTTGTGCATTGATGTATC 58.622 33.333 19.37 0.00 42.52 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
191 194 3.987868 CGCACATGTACGCCTTTAGATAT 59.012 43.478 5.37 0.00 0.00 1.63
817 820 5.939883 TGACTAGTTTTCCATGTCAGGATTG 59.060 40.000 0.00 0.00 37.56 2.67
876 879 7.575414 TTAGACTTTTTAACATCCTGTGCAA 57.425 32.000 0.00 0.00 0.00 4.08
877 880 7.575414 TTTAGACTTTTTAACATCCTGTGCA 57.425 32.000 0.00 0.00 0.00 4.57
881 884 9.796120 TGTTGTTTTAGACTTTTTAACATCCTG 57.204 29.630 0.00 0.00 0.00 3.86
991 994 3.742983 CTCGGGAGCAGAAAGGTAC 57.257 57.895 0.00 0.00 0.00 3.34
1010 1013 2.414481 CTGTTCACCGAGCTCAAATGAG 59.586 50.000 15.40 6.05 44.75 2.90
1011 1014 2.224281 ACTGTTCACCGAGCTCAAATGA 60.224 45.455 15.40 10.78 0.00 2.57
1012 1015 2.146342 ACTGTTCACCGAGCTCAAATG 58.854 47.619 15.40 8.47 0.00 2.32
1013 1016 2.550830 ACTGTTCACCGAGCTCAAAT 57.449 45.000 15.40 0.00 0.00 2.32
1014 1017 3.462483 TTACTGTTCACCGAGCTCAAA 57.538 42.857 15.40 0.00 0.00 2.69
1015 1018 3.462483 TTTACTGTTCACCGAGCTCAA 57.538 42.857 15.40 0.00 0.00 3.02
1016 1019 3.462483 TTTTACTGTTCACCGAGCTCA 57.538 42.857 15.40 0.00 0.00 4.26
1017 1020 3.994392 TGATTTTACTGTTCACCGAGCTC 59.006 43.478 2.73 2.73 0.00 4.09
1018 1021 4.002906 TGATTTTACTGTTCACCGAGCT 57.997 40.909 0.00 0.00 0.00 4.09
1019 1022 4.742438 TTGATTTTACTGTTCACCGAGC 57.258 40.909 0.00 0.00 0.00 5.03
1061 1064 9.889128 TTCTCTGAGATTGTTTTTGGAATTTTT 57.111 25.926 8.42 0.00 0.00 1.94
1062 1065 9.889128 TTTCTCTGAGATTGTTTTTGGAATTTT 57.111 25.926 8.42 0.00 0.00 1.82
1063 1066 9.317936 GTTTCTCTGAGATTGTTTTTGGAATTT 57.682 29.630 8.42 0.00 0.00 1.82
1064 1067 8.477256 TGTTTCTCTGAGATTGTTTTTGGAATT 58.523 29.630 8.42 0.00 0.00 2.17
1065 1068 8.010733 TGTTTCTCTGAGATTGTTTTTGGAAT 57.989 30.769 8.42 0.00 0.00 3.01
1066 1069 7.403312 TGTTTCTCTGAGATTGTTTTTGGAA 57.597 32.000 8.42 0.00 0.00 3.53
1067 1070 7.587037 ATGTTTCTCTGAGATTGTTTTTGGA 57.413 32.000 8.42 0.00 0.00 3.53
1068 1071 7.922278 TCAATGTTTCTCTGAGATTGTTTTTGG 59.078 33.333 8.42 0.00 0.00 3.28
1069 1072 8.749499 GTCAATGTTTCTCTGAGATTGTTTTTG 58.251 33.333 8.42 8.29 0.00 2.44
1070 1073 8.469200 TGTCAATGTTTCTCTGAGATTGTTTTT 58.531 29.630 8.42 0.00 0.00 1.94
1071 1074 7.999679 TGTCAATGTTTCTCTGAGATTGTTTT 58.000 30.769 8.42 0.00 0.00 2.43
1072 1075 7.572523 TGTCAATGTTTCTCTGAGATTGTTT 57.427 32.000 8.42 0.00 0.00 2.83
1073 1076 7.572523 TTGTCAATGTTTCTCTGAGATTGTT 57.427 32.000 8.42 0.00 0.00 2.83
1074 1077 7.572523 TTTGTCAATGTTTCTCTGAGATTGT 57.427 32.000 8.42 0.00 0.00 2.71
1075 1078 8.133627 ACTTTTGTCAATGTTTCTCTGAGATTG 58.866 33.333 8.42 9.92 0.00 2.67
1076 1079 8.230472 ACTTTTGTCAATGTTTCTCTGAGATT 57.770 30.769 8.42 0.00 0.00 2.40
1077 1080 7.814264 ACTTTTGTCAATGTTTCTCTGAGAT 57.186 32.000 8.42 0.00 0.00 2.75
1078 1081 7.554118 AGAACTTTTGTCAATGTTTCTCTGAGA 59.446 33.333 2.58 2.58 31.96 3.27
1079 1082 7.701445 AGAACTTTTGTCAATGTTTCTCTGAG 58.299 34.615 0.00 0.00 31.96 3.35
1080 1083 7.630242 AGAACTTTTGTCAATGTTTCTCTGA 57.370 32.000 6.10 0.00 31.96 3.27
1081 1084 9.443283 CTTAGAACTTTTGTCAATGTTTCTCTG 57.557 33.333 6.42 0.64 31.96 3.35
1082 1085 9.178758 ACTTAGAACTTTTGTCAATGTTTCTCT 57.821 29.630 6.42 3.36 31.96 3.10
1083 1086 9.226345 CACTTAGAACTTTTGTCAATGTTTCTC 57.774 33.333 6.42 0.00 31.96 2.87
1084 1087 8.190784 CCACTTAGAACTTTTGTCAATGTTTCT 58.809 33.333 6.10 6.96 31.96 2.52
1085 1088 7.973944 ACCACTTAGAACTTTTGTCAATGTTTC 59.026 33.333 6.10 1.04 31.96 2.78
1086 1089 7.836842 ACCACTTAGAACTTTTGTCAATGTTT 58.163 30.769 6.10 0.00 31.96 2.83
1087 1090 7.404671 ACCACTTAGAACTTTTGTCAATGTT 57.595 32.000 4.72 4.72 33.94 2.71
1088 1091 7.257722 CAACCACTTAGAACTTTTGTCAATGT 58.742 34.615 0.00 0.00 0.00 2.71
1089 1092 6.198966 GCAACCACTTAGAACTTTTGTCAATG 59.801 38.462 0.00 0.00 0.00 2.82
1090 1093 6.127479 TGCAACCACTTAGAACTTTTGTCAAT 60.127 34.615 0.00 0.00 0.00 2.57
1091 1094 5.184096 TGCAACCACTTAGAACTTTTGTCAA 59.816 36.000 0.00 0.00 0.00 3.18
1092 1095 4.702612 TGCAACCACTTAGAACTTTTGTCA 59.297 37.500 0.00 0.00 0.00 3.58
1093 1096 5.243426 TGCAACCACTTAGAACTTTTGTC 57.757 39.130 0.00 0.00 0.00 3.18
1094 1097 5.652994 TTGCAACCACTTAGAACTTTTGT 57.347 34.783 0.00 0.00 0.00 2.83
1095 1098 6.959671 TTTTGCAACCACTTAGAACTTTTG 57.040 33.333 0.00 0.00 0.00 2.44
1096 1099 8.560355 AATTTTTGCAACCACTTAGAACTTTT 57.440 26.923 0.00 0.00 0.00 2.27
1097 1100 7.821846 TGAATTTTTGCAACCACTTAGAACTTT 59.178 29.630 0.00 0.00 0.00 2.66
1098 1101 7.327214 TGAATTTTTGCAACCACTTAGAACTT 58.673 30.769 0.00 0.00 0.00 2.66
1099 1102 6.872920 TGAATTTTTGCAACCACTTAGAACT 58.127 32.000 0.00 0.00 0.00 3.01
1100 1103 7.437862 TGATGAATTTTTGCAACCACTTAGAAC 59.562 33.333 0.00 0.00 0.00 3.01
1101 1104 7.495901 TGATGAATTTTTGCAACCACTTAGAA 58.504 30.769 0.00 0.00 0.00 2.10
1102 1105 7.048629 TGATGAATTTTTGCAACCACTTAGA 57.951 32.000 0.00 0.00 0.00 2.10
1103 1106 7.599621 TCATGATGAATTTTTGCAACCACTTAG 59.400 33.333 0.00 0.00 0.00 2.18
1104 1107 7.440198 TCATGATGAATTTTTGCAACCACTTA 58.560 30.769 0.00 0.00 0.00 2.24
1105 1108 6.289834 TCATGATGAATTTTTGCAACCACTT 58.710 32.000 0.00 0.00 0.00 3.16
1106 1109 5.856156 TCATGATGAATTTTTGCAACCACT 58.144 33.333 0.00 0.00 0.00 4.00
1107 1110 6.542574 TTCATGATGAATTTTTGCAACCAC 57.457 33.333 3.29 0.00 30.26 4.16
1108 1111 7.444487 TGATTTCATGATGAATTTTTGCAACCA 59.556 29.630 8.90 0.00 36.11 3.67
1109 1112 7.747357 GTGATTTCATGATGAATTTTTGCAACC 59.253 33.333 8.90 0.00 36.11 3.77
1110 1113 8.283992 TGTGATTTCATGATGAATTTTTGCAAC 58.716 29.630 8.90 1.15 36.11 4.17
1111 1114 8.379457 TGTGATTTCATGATGAATTTTTGCAA 57.621 26.923 8.90 0.00 36.11 4.08
1112 1115 7.964604 TGTGATTTCATGATGAATTTTTGCA 57.035 28.000 8.90 1.87 36.11 4.08
1113 1116 9.485591 GAATGTGATTTCATGATGAATTTTTGC 57.514 29.630 8.90 0.00 36.11 3.68
1114 1117 9.982291 GGAATGTGATTTCATGATGAATTTTTG 57.018 29.630 8.90 0.00 36.11 2.44
1115 1118 9.953565 AGGAATGTGATTTCATGATGAATTTTT 57.046 25.926 8.90 0.00 36.11 1.94
1116 1119 9.378551 CAGGAATGTGATTTCATGATGAATTTT 57.621 29.630 8.90 0.00 39.18 1.82
1117 1120 8.537016 ACAGGAATGTGATTTCATGATGAATTT 58.463 29.630 8.90 0.00 39.18 1.82
1118 1121 8.074613 ACAGGAATGTGATTTCATGATGAATT 57.925 30.769 8.90 5.47 39.18 2.17
1119 1122 7.655521 ACAGGAATGTGATTTCATGATGAAT 57.344 32.000 8.90 0.00 39.18 2.57
1120 1123 8.578448 TTACAGGAATGTGATTTCATGATGAA 57.422 30.769 3.29 3.29 39.18 2.57
1121 1124 7.283807 CCTTACAGGAATGTGATTTCATGATGA 59.716 37.037 0.00 0.00 39.18 2.92
1122 1125 7.423199 CCTTACAGGAATGTGATTTCATGATG 58.577 38.462 0.00 0.00 39.18 3.07
1123 1126 6.040166 GCCTTACAGGAATGTGATTTCATGAT 59.960 38.462 0.00 0.00 39.18 2.45
1124 1127 5.357878 GCCTTACAGGAATGTGATTTCATGA 59.642 40.000 5.92 0.00 39.18 3.07
1125 1128 5.585390 GCCTTACAGGAATGTGATTTCATG 58.415 41.667 0.00 0.00 41.77 3.07
1126 1129 4.336433 CGCCTTACAGGAATGTGATTTCAT 59.664 41.667 0.00 0.00 37.67 2.57
1127 1130 3.689161 CGCCTTACAGGAATGTGATTTCA 59.311 43.478 0.00 0.00 37.67 2.69
1128 1131 3.689649 ACGCCTTACAGGAATGTGATTTC 59.310 43.478 0.00 0.00 37.67 2.17
1129 1132 3.440173 CACGCCTTACAGGAATGTGATTT 59.560 43.478 0.00 0.00 37.67 2.17
1130 1133 3.009723 CACGCCTTACAGGAATGTGATT 58.990 45.455 0.00 0.00 37.67 2.57
1131 1134 2.632377 CACGCCTTACAGGAATGTGAT 58.368 47.619 0.00 0.00 37.67 3.06
1132 1135 1.338674 CCACGCCTTACAGGAATGTGA 60.339 52.381 10.25 0.00 37.67 3.58
1133 1136 1.086696 CCACGCCTTACAGGAATGTG 58.913 55.000 0.00 0.00 37.67 3.21
1134 1137 0.676782 GCCACGCCTTACAGGAATGT 60.677 55.000 0.00 0.00 37.67 2.71
1135 1138 0.676466 TGCCACGCCTTACAGGAATG 60.676 55.000 0.00 0.00 37.67 2.67
1136 1139 0.037590 TTGCCACGCCTTACAGGAAT 59.962 50.000 0.00 0.00 37.67 3.01
1137 1140 0.179015 TTTGCCACGCCTTACAGGAA 60.179 50.000 0.00 0.00 37.67 3.36
1138 1141 0.179015 TTTTGCCACGCCTTACAGGA 60.179 50.000 0.00 0.00 37.67 3.86
1139 1142 0.671251 TTTTTGCCACGCCTTACAGG 59.329 50.000 0.00 0.00 38.80 4.00
1157 1160 6.459985 GCATTTTGGAGGCTGAATTTGTTTTT 60.460 34.615 0.00 0.00 0.00 1.94
1158 1161 5.008911 GCATTTTGGAGGCTGAATTTGTTTT 59.991 36.000 0.00 0.00 0.00 2.43
1159 1162 4.516321 GCATTTTGGAGGCTGAATTTGTTT 59.484 37.500 0.00 0.00 0.00 2.83
1160 1163 4.067192 GCATTTTGGAGGCTGAATTTGTT 58.933 39.130 0.00 0.00 0.00 2.83
1161 1164 3.325716 AGCATTTTGGAGGCTGAATTTGT 59.674 39.130 0.00 0.00 36.34 2.83
1162 1165 3.934068 AGCATTTTGGAGGCTGAATTTG 58.066 40.909 0.00 0.00 36.34 2.32
1163 1166 4.628963 AAGCATTTTGGAGGCTGAATTT 57.371 36.364 0.00 0.00 38.04 1.82
1164 1167 4.628963 AAAGCATTTTGGAGGCTGAATT 57.371 36.364 0.00 0.00 31.62 2.17
1181 1184 6.920210 ACTCTGAAAATGCTACTTTCAAAAGC 59.080 34.615 2.43 0.00 41.10 3.51
1182 1185 9.387123 GTACTCTGAAAATGCTACTTTCAAAAG 57.613 33.333 0.97 0.97 41.10 2.27
1183 1186 8.349983 GGTACTCTGAAAATGCTACTTTCAAAA 58.650 33.333 8.91 2.31 41.10 2.44
1184 1187 7.307751 CGGTACTCTGAAAATGCTACTTTCAAA 60.308 37.037 8.91 0.00 41.10 2.69
1185 1188 6.147164 CGGTACTCTGAAAATGCTACTTTCAA 59.853 38.462 8.91 2.50 41.10 2.69
1186 1189 5.637810 CGGTACTCTGAAAATGCTACTTTCA 59.362 40.000 7.77 7.77 39.79 2.69
1187 1190 5.867716 TCGGTACTCTGAAAATGCTACTTTC 59.132 40.000 0.00 0.00 34.09 2.62
1188 1191 5.790593 TCGGTACTCTGAAAATGCTACTTT 58.209 37.500 0.00 0.00 0.00 2.66
1189 1192 5.401531 TCGGTACTCTGAAAATGCTACTT 57.598 39.130 0.00 0.00 0.00 2.24
1190 1193 5.599999 ATCGGTACTCTGAAAATGCTACT 57.400 39.130 0.00 0.00 32.29 2.57
1191 1194 7.948278 ATAATCGGTACTCTGAAAATGCTAC 57.052 36.000 0.00 0.00 32.29 3.58
1192 1195 8.958119 AAATAATCGGTACTCTGAAAATGCTA 57.042 30.769 0.00 0.00 32.29 3.49
1193 1196 7.865706 AAATAATCGGTACTCTGAAAATGCT 57.134 32.000 0.00 0.00 32.29 3.79
1194 1197 8.911247 AAAAATAATCGGTACTCTGAAAATGC 57.089 30.769 0.00 0.00 32.29 3.56
1216 1219 2.264005 TCTAGAAGGCGTGGCAAAAA 57.736 45.000 0.00 0.00 0.00 1.94
1217 1220 2.264005 TTCTAGAAGGCGTGGCAAAA 57.736 45.000 0.00 0.00 0.00 2.44
1218 1221 2.264005 TTTCTAGAAGGCGTGGCAAA 57.736 45.000 5.12 0.00 0.00 3.68
1219 1222 2.083774 CATTTCTAGAAGGCGTGGCAA 58.916 47.619 5.12 0.00 0.00 4.52
1220 1223 1.003118 ACATTTCTAGAAGGCGTGGCA 59.997 47.619 5.12 0.00 0.00 4.92
1221 1224 1.398390 CACATTTCTAGAAGGCGTGGC 59.602 52.381 17.07 0.00 0.00 5.01
1222 1225 2.972625 TCACATTTCTAGAAGGCGTGG 58.027 47.619 21.32 7.48 0.00 4.94
1223 1226 5.122239 TGAAATCACATTTCTAGAAGGCGTG 59.878 40.000 18.08 18.08 46.71 5.34
1224 1227 5.245531 TGAAATCACATTTCTAGAAGGCGT 58.754 37.500 5.12 1.78 46.71 5.68
1225 1228 5.801350 TGAAATCACATTTCTAGAAGGCG 57.199 39.130 5.12 1.16 46.71 5.52
1226 1229 7.192232 GTCATGAAATCACATTTCTAGAAGGC 58.808 38.462 5.12 0.00 46.71 4.35
1227 1230 7.278646 TCGTCATGAAATCACATTTCTAGAAGG 59.721 37.037 5.12 5.08 46.71 3.46
1228 1231 8.189709 TCGTCATGAAATCACATTTCTAGAAG 57.810 34.615 5.12 0.00 46.71 2.85
1229 1232 8.546597 TTCGTCATGAAATCACATTTCTAGAA 57.453 30.769 0.00 0.00 46.71 2.10
1230 1233 8.722480 ATTCGTCATGAAATCACATTTCTAGA 57.278 30.769 0.00 0.00 46.71 2.43
1231 1234 9.778993 AAATTCGTCATGAAATCACATTTCTAG 57.221 29.630 0.00 3.72 46.71 2.43
1233 1236 9.480053 AAAAATTCGTCATGAAATCACATTTCT 57.520 25.926 0.00 0.00 46.71 2.52
1234 1237 9.519905 CAAAAATTCGTCATGAAATCACATTTC 57.480 29.630 0.00 2.55 46.75 2.17
1235 1238 8.011106 GCAAAAATTCGTCATGAAATCACATTT 58.989 29.630 0.00 0.00 40.71 2.32
1236 1239 7.171167 TGCAAAAATTCGTCATGAAATCACATT 59.829 29.630 0.00 0.00 40.71 2.71
1237 1240 6.645827 TGCAAAAATTCGTCATGAAATCACAT 59.354 30.769 0.00 0.00 40.71 3.21
1238 1241 5.981915 TGCAAAAATTCGTCATGAAATCACA 59.018 32.000 0.00 0.00 40.71 3.58
1239 1242 6.450845 TGCAAAAATTCGTCATGAAATCAC 57.549 33.333 0.00 0.00 40.71 3.06
1240 1243 6.346758 GCTTGCAAAAATTCGTCATGAAATCA 60.347 34.615 0.00 0.00 40.71 2.57
1241 1244 6.011277 GCTTGCAAAAATTCGTCATGAAATC 58.989 36.000 0.00 0.00 40.71 2.17
1242 1245 5.466058 TGCTTGCAAAAATTCGTCATGAAAT 59.534 32.000 0.00 0.00 40.71 2.17
1243 1246 4.807834 TGCTTGCAAAAATTCGTCATGAAA 59.192 33.333 0.00 0.00 40.71 2.69
1244 1247 4.208873 GTGCTTGCAAAAATTCGTCATGAA 59.791 37.500 0.00 0.00 41.81 2.57
1245 1248 3.735240 GTGCTTGCAAAAATTCGTCATGA 59.265 39.130 0.00 0.00 0.00 3.07
1246 1249 3.737266 AGTGCTTGCAAAAATTCGTCATG 59.263 39.130 0.00 0.00 0.00 3.07
1247 1250 3.981211 AGTGCTTGCAAAAATTCGTCAT 58.019 36.364 0.00 0.00 0.00 3.06
1248 1251 3.435105 AGTGCTTGCAAAAATTCGTCA 57.565 38.095 0.00 0.00 0.00 4.35
1249 1252 5.881637 TTAAGTGCTTGCAAAAATTCGTC 57.118 34.783 0.00 0.00 0.00 4.20
1250 1253 6.312672 AGTTTTAAGTGCTTGCAAAAATTCGT 59.687 30.769 0.00 0.00 0.00 3.85
1251 1254 6.704819 AGTTTTAAGTGCTTGCAAAAATTCG 58.295 32.000 0.00 0.00 0.00 3.34
1252 1255 8.894409 AAAGTTTTAAGTGCTTGCAAAAATTC 57.106 26.923 0.00 0.00 29.83 2.17
1253 1256 9.127006 CAAAAGTTTTAAGTGCTTGCAAAAATT 57.873 25.926 0.00 0.00 31.70 1.82
1254 1257 7.273164 GCAAAAGTTTTAAGTGCTTGCAAAAAT 59.727 29.630 0.00 0.00 38.03 1.82
1255 1258 6.580416 GCAAAAGTTTTAAGTGCTTGCAAAAA 59.420 30.769 0.00 0.00 38.03 1.94
1256 1259 6.082984 GCAAAAGTTTTAAGTGCTTGCAAAA 58.917 32.000 0.00 0.00 38.03 2.44
1257 1260 5.391416 GGCAAAAGTTTTAAGTGCTTGCAAA 60.391 36.000 0.00 0.00 39.48 3.68
1258 1261 4.094146 GGCAAAAGTTTTAAGTGCTTGCAA 59.906 37.500 9.28 0.00 39.48 4.08
1259 1262 3.620821 GGCAAAAGTTTTAAGTGCTTGCA 59.379 39.130 9.28 0.00 39.48 4.08
1260 1263 3.620821 TGGCAAAAGTTTTAAGTGCTTGC 59.379 39.130 9.28 3.62 37.54 4.01
1261 1264 5.793026 TTGGCAAAAGTTTTAAGTGCTTG 57.207 34.783 0.00 0.00 35.53 4.01
1262 1265 5.879777 ACATTGGCAAAAGTTTTAAGTGCTT 59.120 32.000 3.01 0.00 35.53 3.91
1263 1266 5.427378 ACATTGGCAAAAGTTTTAAGTGCT 58.573 33.333 3.01 0.00 35.53 4.40
1264 1267 5.733226 ACATTGGCAAAAGTTTTAAGTGC 57.267 34.783 3.01 0.88 34.42 4.40
1265 1268 7.973601 AGAAACATTGGCAAAAGTTTTAAGTG 58.026 30.769 25.07 10.79 37.33 3.16
1266 1269 9.093970 GTAGAAACATTGGCAAAAGTTTTAAGT 57.906 29.630 25.07 16.52 37.33 2.24
1267 1270 8.547894 GGTAGAAACATTGGCAAAAGTTTTAAG 58.452 33.333 25.07 4.76 37.33 1.85
1268 1271 8.041323 TGGTAGAAACATTGGCAAAAGTTTTAA 58.959 29.630 25.07 17.27 37.33 1.52
1269 1272 7.556844 TGGTAGAAACATTGGCAAAAGTTTTA 58.443 30.769 25.07 18.40 37.33 1.52
1270 1273 6.410540 TGGTAGAAACATTGGCAAAAGTTTT 58.589 32.000 25.07 19.06 37.33 2.43
1271 1274 5.983540 TGGTAGAAACATTGGCAAAAGTTT 58.016 33.333 24.76 24.76 39.28 2.66
1272 1275 5.606348 TGGTAGAAACATTGGCAAAAGTT 57.394 34.783 3.01 9.78 0.00 2.66
1273 1276 5.606348 TTGGTAGAAACATTGGCAAAAGT 57.394 34.783 3.01 3.13 0.00 2.66
1274 1277 6.917217 TTTTGGTAGAAACATTGGCAAAAG 57.083 33.333 3.01 2.40 0.00 2.27
1331 1334 6.452494 TCGGGTGAACAGTAAAATCAAAAA 57.548 33.333 0.00 0.00 0.00 1.94
1332 1335 5.506649 GCTCGGGTGAACAGTAAAATCAAAA 60.507 40.000 0.00 0.00 0.00 2.44
1333 1336 4.023536 GCTCGGGTGAACAGTAAAATCAAA 60.024 41.667 0.00 0.00 0.00 2.69
1334 1337 3.500680 GCTCGGGTGAACAGTAAAATCAA 59.499 43.478 0.00 0.00 0.00 2.57
1335 1338 3.071479 GCTCGGGTGAACAGTAAAATCA 58.929 45.455 0.00 0.00 0.00 2.57
1336 1339 3.335579 AGCTCGGGTGAACAGTAAAATC 58.664 45.455 0.00 0.00 0.00 2.17
1337 1340 3.244422 TGAGCTCGGGTGAACAGTAAAAT 60.244 43.478 9.64 0.00 0.00 1.82
1338 1341 2.103432 TGAGCTCGGGTGAACAGTAAAA 59.897 45.455 9.64 0.00 0.00 1.52
1339 1342 1.689813 TGAGCTCGGGTGAACAGTAAA 59.310 47.619 9.64 0.00 0.00 2.01
1340 1343 1.334160 TGAGCTCGGGTGAACAGTAA 58.666 50.000 9.64 0.00 0.00 2.24
1341 1344 1.557099 ATGAGCTCGGGTGAACAGTA 58.443 50.000 9.64 0.00 0.00 2.74
1342 1345 1.557099 TATGAGCTCGGGTGAACAGT 58.443 50.000 9.64 0.00 0.00 3.55
1343 1346 2.101415 TCATATGAGCTCGGGTGAACAG 59.899 50.000 9.64 0.00 0.00 3.16
1344 1347 2.101415 CTCATATGAGCTCGGGTGAACA 59.899 50.000 19.47 0.00 35.13 3.18
1345 1348 2.748605 CTCATATGAGCTCGGGTGAAC 58.251 52.381 19.47 0.00 35.13 3.18
1356 1359 0.390492 TGCACCCGAGCTCATATGAG 59.610 55.000 25.64 25.64 44.75 2.90
1357 1360 0.390492 CTGCACCCGAGCTCATATGA 59.610 55.000 15.40 5.07 34.99 2.15
1358 1361 0.390492 TCTGCACCCGAGCTCATATG 59.610 55.000 15.40 9.02 34.99 1.78
1359 1362 1.123077 TTCTGCACCCGAGCTCATAT 58.877 50.000 15.40 0.00 34.99 1.78
1360 1363 0.901827 TTTCTGCACCCGAGCTCATA 59.098 50.000 15.40 0.00 34.99 2.15
1361 1364 0.674895 GTTTCTGCACCCGAGCTCAT 60.675 55.000 15.40 0.00 34.99 2.90
1362 1365 1.301716 GTTTCTGCACCCGAGCTCA 60.302 57.895 15.40 0.00 34.99 4.26
1363 1366 1.004440 AGTTTCTGCACCCGAGCTC 60.004 57.895 2.73 2.73 34.99 4.09
1364 1367 1.004440 GAGTTTCTGCACCCGAGCT 60.004 57.895 0.00 0.00 34.99 4.09
1365 1368 2.035442 GGAGTTTCTGCACCCGAGC 61.035 63.158 0.00 0.00 0.00 5.03
1366 1369 0.951040 GTGGAGTTTCTGCACCCGAG 60.951 60.000 9.63 0.00 44.99 4.63
1367 1370 1.070786 GTGGAGTTTCTGCACCCGA 59.929 57.895 9.63 0.00 44.99 5.14
1368 1371 3.655481 GTGGAGTTTCTGCACCCG 58.345 61.111 9.63 0.00 44.99 5.28
1371 1374 0.249911 AGGACGTGGAGTTTCTGCAC 60.250 55.000 10.52 10.52 46.73 4.57
1372 1375 1.000506 GTAGGACGTGGAGTTTCTGCA 59.999 52.381 0.00 0.00 0.00 4.41
1373 1376 1.000506 TGTAGGACGTGGAGTTTCTGC 59.999 52.381 0.00 0.00 0.00 4.26
1374 1377 3.193691 AGATGTAGGACGTGGAGTTTCTG 59.806 47.826 0.00 0.00 0.00 3.02
1375 1378 3.432378 AGATGTAGGACGTGGAGTTTCT 58.568 45.455 0.00 0.00 0.00 2.52
1376 1379 3.870633 AGATGTAGGACGTGGAGTTTC 57.129 47.619 0.00 0.00 0.00 2.78
1377 1380 3.446516 GGTAGATGTAGGACGTGGAGTTT 59.553 47.826 0.00 0.00 0.00 2.66
1378 1381 3.022406 GGTAGATGTAGGACGTGGAGTT 58.978 50.000 0.00 0.00 0.00 3.01
1379 1382 2.652590 GGTAGATGTAGGACGTGGAGT 58.347 52.381 0.00 0.00 0.00 3.85
1380 1383 1.955080 GGGTAGATGTAGGACGTGGAG 59.045 57.143 0.00 0.00 0.00 3.86
1381 1384 1.567649 AGGGTAGATGTAGGACGTGGA 59.432 52.381 0.00 0.00 0.00 4.02
1382 1385 1.955080 GAGGGTAGATGTAGGACGTGG 59.045 57.143 0.00 0.00 0.00 4.94
1383 1386 2.933573 AGAGGGTAGATGTAGGACGTG 58.066 52.381 0.00 0.00 0.00 4.49
1384 1387 3.666345 AAGAGGGTAGATGTAGGACGT 57.334 47.619 0.00 0.00 0.00 4.34
1385 1388 6.005198 AGAATAAGAGGGTAGATGTAGGACG 58.995 44.000 0.00 0.00 0.00 4.79
1386 1389 7.235804 AGAGAATAAGAGGGTAGATGTAGGAC 58.764 42.308 0.00 0.00 0.00 3.85
1387 1390 7.073853 TGAGAGAATAAGAGGGTAGATGTAGGA 59.926 40.741 0.00 0.00 0.00 2.94
1388 1391 7.175990 GTGAGAGAATAAGAGGGTAGATGTAGG 59.824 44.444 0.00 0.00 0.00 3.18
1389 1392 7.721842 TGTGAGAGAATAAGAGGGTAGATGTAG 59.278 40.741 0.00 0.00 0.00 2.74
1621 1837 3.188159 ACAAGTGCAAGTTAACCTCGA 57.812 42.857 0.88 0.00 0.00 4.04
1817 2033 5.418840 CCATCTGTTAGGCTTGGTTAAACAT 59.581 40.000 0.00 0.00 30.33 2.71
1818 2034 4.764823 CCATCTGTTAGGCTTGGTTAAACA 59.235 41.667 0.00 0.00 0.00 2.83
2216 2447 4.917906 ACCATCTTCAAAAGTAGAGGCT 57.082 40.909 0.00 0.00 0.00 4.58
3208 6437 2.001872 GCATCAATTTTTCCCCTTGCG 58.998 47.619 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.