Multiple sequence alignment - TraesCS2B01G316200

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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 TraesCS2B01G316200 chr2B 100.000 2324 0 0 1 2324 451460993 451458670 0.000000e+00 4292
1 TraesCS2B01G316200 chr2B 98.167 982 18 0 3 984 451482712 451481731 0.000000e+00 1714
2 TraesCS2B01G316200 chr2B 97.866 984 19 2 1 983 122688522 122689504 0.000000e+00 1700
3 TraesCS2B01G316200 chr2B 97.764 984 22 0 1 984 77561848 77562831 0.000000e+00 1696
4 TraesCS2B01G316200 chr2B 93.083 1012 54 10 1315 2324 477219321 477220318 0.000000e+00 1467
5 TraesCS2B01G316200 chr2B 94.000 150 8 1 1314 1463 477389395 477389543 2.320000e-55 226
6 TraesCS2B01G316200 chr2B 91.391 151 13 0 1314 1464 182872665 182872515 8.420000e-50 207
7 TraesCS2B01G316200 chr5B 98.169 983 18 0 1 983 451493462 451492480 0.000000e+00 1716
8 TraesCS2B01G316200 chr5B 97.866 984 21 0 1 984 205729474 205728491 0.000000e+00 1701
9 TraesCS2B01G316200 chr5B 97.866 984 21 0 1 984 205737668 205736685 0.000000e+00 1701
10 TraesCS2B01G316200 chr3B 98.069 984 19 0 1 984 561061875 561062858 0.000000e+00 1712
11 TraesCS2B01G316200 chr3B 98.069 984 19 0 1 984 561070193 561071176 0.000000e+00 1712
12 TraesCS2B01G316200 chr3B 99.094 331 3 0 983 1313 201510256 201509926 1.540000e-166 595
13 TraesCS2B01G316200 chr3B 90.000 130 12 1 1315 1443 362509857 362509728 1.430000e-37 167
14 TraesCS2B01G316200 chr7B 98.069 984 18 1 1 983 405986018 405985035 0.000000e+00 1711
15 TraesCS2B01G316200 chr7B 93.379 1012 54 7 1315 2324 661485953 661486953 0.000000e+00 1485
16 TraesCS2B01G316200 chr7B 92.962 1023 56 11 1314 2324 383593268 383594286 0.000000e+00 1476
17 TraesCS2B01G316200 chr4B 95.747 1011 42 1 1314 2324 288969116 288968107 0.000000e+00 1628
18 TraesCS2B01G316200 chr4B 95.257 1012 46 2 1314 2324 63913730 63914740 0.000000e+00 1602
19 TraesCS2B01G316200 chr4B 95.274 931 42 2 1314 2244 288960941 288960013 0.000000e+00 1474
20 TraesCS2B01G316200 chr6B 93.701 1016 56 6 1315 2324 476829785 476830798 0.000000e+00 1515
21 TraesCS2B01G316200 chr6B 91.096 1022 76 11 1315 2324 509110605 509109587 0.000000e+00 1369
22 TraesCS2B01G316200 chr1B 93.676 1012 50 10 1315 2324 663036424 663035425 0.000000e+00 1502
23 TraesCS2B01G316200 chr5D 100.000 331 0 0 983 1313 240134833 240134503 1.530000e-171 612
24 TraesCS2B01G316200 chr5D 99.698 331 1 0 983 1313 449152025 449152355 7.100000e-170 606
25 TraesCS2B01G316200 chr5D 99.094 331 2 1 983 1313 6204147 6204476 5.530000e-166 593
26 TraesCS2B01G316200 chr1D 100.000 331 0 0 983 1313 483917475 483917805 1.530000e-171 612
27 TraesCS2B01G316200 chr1D 99.396 331 2 0 983 1313 254495140 254494810 3.300000e-168 601
28 TraesCS2B01G316200 chrUn 99.698 331 1 0 983 1313 441827380 441827710 7.100000e-170 606
29 TraesCS2B01G316200 chr3D 99.396 331 2 0 983 1313 21901218 21900888 3.300000e-168 601
30 TraesCS2B01G316200 chr2D 98.792 331 4 0 983 1313 334229623 334229293 7.150000e-165 590


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 TraesCS2B01G316200 chr2B 451458670 451460993 2323 True 4292 4292 100.000 1 2324 1 chr2B.!!$R2 2323
1 TraesCS2B01G316200 chr2B 451481731 451482712 981 True 1714 1714 98.167 3 984 1 chr2B.!!$R3 981
2 TraesCS2B01G316200 chr2B 122688522 122689504 982 False 1700 1700 97.866 1 983 1 chr2B.!!$F2 982
3 TraesCS2B01G316200 chr2B 77561848 77562831 983 False 1696 1696 97.764 1 984 1 chr2B.!!$F1 983
4 TraesCS2B01G316200 chr2B 477219321 477220318 997 False 1467 1467 93.083 1315 2324 1 chr2B.!!$F3 1009
5 TraesCS2B01G316200 chr5B 451492480 451493462 982 True 1716 1716 98.169 1 983 1 chr5B.!!$R3 982
6 TraesCS2B01G316200 chr5B 205728491 205729474 983 True 1701 1701 97.866 1 984 1 chr5B.!!$R1 983
7 TraesCS2B01G316200 chr5B 205736685 205737668 983 True 1701 1701 97.866 1 984 1 chr5B.!!$R2 983
8 TraesCS2B01G316200 chr3B 561061875 561062858 983 False 1712 1712 98.069 1 984 1 chr3B.!!$F1 983
9 TraesCS2B01G316200 chr3B 561070193 561071176 983 False 1712 1712 98.069 1 984 1 chr3B.!!$F2 983
10 TraesCS2B01G316200 chr7B 405985035 405986018 983 True 1711 1711 98.069 1 983 1 chr7B.!!$R1 982
11 TraesCS2B01G316200 chr7B 661485953 661486953 1000 False 1485 1485 93.379 1315 2324 1 chr7B.!!$F2 1009
12 TraesCS2B01G316200 chr7B 383593268 383594286 1018 False 1476 1476 92.962 1314 2324 1 chr7B.!!$F1 1010
13 TraesCS2B01G316200 chr4B 288968107 288969116 1009 True 1628 1628 95.747 1314 2324 1 chr4B.!!$R2 1010
14 TraesCS2B01G316200 chr4B 63913730 63914740 1010 False 1602 1602 95.257 1314 2324 1 chr4B.!!$F1 1010
15 TraesCS2B01G316200 chr4B 288960013 288960941 928 True 1474 1474 95.274 1314 2244 1 chr4B.!!$R1 930
16 TraesCS2B01G316200 chr6B 476829785 476830798 1013 False 1515 1515 93.701 1315 2324 1 chr6B.!!$F1 1009
17 TraesCS2B01G316200 chr6B 509109587 509110605 1018 True 1369 1369 91.096 1315 2324 1 chr6B.!!$R1 1009
18 TraesCS2B01G316200 chr1B 663035425 663036424 999 True 1502 1502 93.676 1315 2324 1 chr1B.!!$R1 1009

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
965 968 2.470057 TTGGGCCTTTTCTCCTTTGT 57.53 45.0 4.53 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1839 1854 3.718815 AGAACACGAAGAACTCCAAGAC 58.281 45.455 0.0 0.0 0.0 3.01 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
142 143 6.927381 CCAAATGAAGAGAGTTGCAAAGATTT 59.073 34.615 0.00 0.00 0.00 2.17
291 292 3.198635 ACCCATGGTCTATGTGAGAGTTG 59.801 47.826 11.73 0.00 33.72 3.16
542 544 5.771469 CAATCATCTAGTCTTCATCGAGCT 58.229 41.667 0.00 0.00 0.00 4.09
568 570 3.259123 GCAATCAAGAAAGGTGGTCCAAT 59.741 43.478 0.00 0.00 35.89 3.16
653 655 9.487442 TTGCCCTTGATAGGTTTTCTATTTTAT 57.513 29.630 0.00 0.00 40.19 1.40
758 760 3.184783 CGTATCGTTCGTAGAGAGCTCAT 59.815 47.826 17.77 6.59 38.43 2.90
960 963 4.415881 TTTTCTTTTGGGCCTTTTCTCC 57.584 40.909 4.53 0.00 0.00 3.71
965 968 2.470057 TTGGGCCTTTTCTCCTTTGT 57.530 45.000 4.53 0.00 0.00 2.83
1006 1009 9.527157 TCTAAGGTTAATTTGATTCAATGACCA 57.473 29.630 13.42 0.00 0.00 4.02
1007 1010 9.793252 CTAAGGTTAATTTGATTCAATGACCAG 57.207 33.333 13.42 3.36 0.00 4.00
1008 1011 8.421249 AAGGTTAATTTGATTCAATGACCAGA 57.579 30.769 13.42 0.00 0.00 3.86
1009 1012 8.059798 AGGTTAATTTGATTCAATGACCAGAG 57.940 34.615 13.42 0.00 0.00 3.35
1010 1013 7.671398 AGGTTAATTTGATTCAATGACCAGAGT 59.329 33.333 13.42 0.00 0.00 3.24
1011 1014 8.306761 GGTTAATTTGATTCAATGACCAGAGTT 58.693 33.333 0.00 0.00 0.00 3.01
1012 1015 9.346725 GTTAATTTGATTCAATGACCAGAGTTC 57.653 33.333 0.00 0.00 0.00 3.01
1013 1016 5.964958 TTTGATTCAATGACCAGAGTTCC 57.035 39.130 0.00 0.00 0.00 3.62
1014 1017 3.599343 TGATTCAATGACCAGAGTTCCG 58.401 45.455 0.00 0.00 0.00 4.30
1015 1018 1.808411 TTCAATGACCAGAGTTCCGC 58.192 50.000 0.00 0.00 0.00 5.54
1016 1019 0.389817 TCAATGACCAGAGTTCCGCG 60.390 55.000 0.00 0.00 0.00 6.46
1017 1020 0.389817 CAATGACCAGAGTTCCGCGA 60.390 55.000 8.23 0.00 0.00 5.87
1018 1021 0.108615 AATGACCAGAGTTCCGCGAG 60.109 55.000 8.23 0.00 0.00 5.03
1031 1034 3.847621 CGCGAGGATATATAGCCCG 57.152 57.895 13.48 16.21 30.36 6.13
1032 1035 0.311165 CGCGAGGATATATAGCCCGG 59.689 60.000 21.48 12.88 30.36 5.73
1033 1036 1.688772 GCGAGGATATATAGCCCGGA 58.311 55.000 21.48 0.00 30.36 5.14
1034 1037 1.609555 GCGAGGATATATAGCCCGGAG 59.390 57.143 21.48 10.49 30.36 4.63
1035 1038 2.748798 GCGAGGATATATAGCCCGGAGA 60.749 54.545 21.48 0.00 30.36 3.71
1036 1039 2.879646 CGAGGATATATAGCCCGGAGAC 59.120 54.545 13.48 0.00 30.36 3.36
1051 1054 2.571206 GGAGACGACGAACAAAAATGC 58.429 47.619 0.00 0.00 0.00 3.56
1052 1055 2.222624 GAGACGACGAACAAAAATGCG 58.777 47.619 0.00 0.00 0.00 4.73
1053 1056 1.595794 AGACGACGAACAAAAATGCGT 59.404 42.857 0.00 0.00 39.99 5.24
1054 1057 2.031191 AGACGACGAACAAAAATGCGTT 59.969 40.909 0.00 0.00 37.07 4.84
1055 1058 2.368685 ACGACGAACAAAAATGCGTTC 58.631 42.857 0.00 0.00 37.07 3.95
1056 1059 2.223066 ACGACGAACAAAAATGCGTTCA 60.223 40.909 0.00 0.00 41.28 3.18
1057 1060 2.970609 CGACGAACAAAAATGCGTTCAT 59.029 40.909 0.00 0.00 41.28 2.57
1058 1061 3.420576 CGACGAACAAAAATGCGTTCATT 59.579 39.130 0.00 0.00 44.32 2.57
1067 1070 3.383620 AATGCGTTCATTTGCCTCAAA 57.616 38.095 0.00 0.00 39.78 2.69
1068 1071 2.132740 TGCGTTCATTTGCCTCAAAC 57.867 45.000 0.00 0.00 36.13 2.93
1069 1072 1.680735 TGCGTTCATTTGCCTCAAACT 59.319 42.857 0.00 0.00 36.13 2.66
1070 1073 2.100584 TGCGTTCATTTGCCTCAAACTT 59.899 40.909 0.00 0.00 36.13 2.66
1071 1074 3.123050 GCGTTCATTTGCCTCAAACTTT 58.877 40.909 0.00 0.00 36.13 2.66
1072 1075 4.202060 TGCGTTCATTTGCCTCAAACTTTA 60.202 37.500 0.00 0.00 36.13 1.85
1073 1076 4.382754 GCGTTCATTTGCCTCAAACTTTAG 59.617 41.667 0.00 0.00 36.13 1.85
1074 1077 5.757886 CGTTCATTTGCCTCAAACTTTAGA 58.242 37.500 0.00 0.00 36.13 2.10
1075 1078 5.853282 CGTTCATTTGCCTCAAACTTTAGAG 59.147 40.000 0.00 0.00 36.13 2.43
1081 1084 2.992593 CCTCAAACTTTAGAGGGGCTC 58.007 52.381 0.00 0.00 46.11 4.70
1082 1085 2.305927 CCTCAAACTTTAGAGGGGCTCA 59.694 50.000 0.00 0.00 46.11 4.26
1083 1086 3.054065 CCTCAAACTTTAGAGGGGCTCAT 60.054 47.826 0.00 0.00 46.11 2.90
1084 1087 4.568592 CCTCAAACTTTAGAGGGGCTCATT 60.569 45.833 0.00 0.00 46.11 2.57
1085 1088 4.998051 TCAAACTTTAGAGGGGCTCATTT 58.002 39.130 0.00 0.00 32.06 2.32
1086 1089 6.134535 TCAAACTTTAGAGGGGCTCATTTA 57.865 37.500 0.00 0.00 32.06 1.40
1087 1090 6.548321 TCAAACTTTAGAGGGGCTCATTTAA 58.452 36.000 0.00 0.00 32.06 1.52
1088 1091 6.659242 TCAAACTTTAGAGGGGCTCATTTAAG 59.341 38.462 0.00 0.00 32.06 1.85
1089 1092 6.388619 AACTTTAGAGGGGCTCATTTAAGA 57.611 37.500 0.00 0.00 32.06 2.10
1090 1093 5.746284 ACTTTAGAGGGGCTCATTTAAGAC 58.254 41.667 0.00 0.00 32.06 3.01
1091 1094 5.489278 ACTTTAGAGGGGCTCATTTAAGACT 59.511 40.000 0.00 0.00 32.06 3.24
1092 1095 6.012421 ACTTTAGAGGGGCTCATTTAAGACTT 60.012 38.462 0.00 0.00 32.06 3.01
1093 1096 7.182206 ACTTTAGAGGGGCTCATTTAAGACTTA 59.818 37.037 0.00 0.00 32.06 2.24
1094 1097 7.504926 TTAGAGGGGCTCATTTAAGACTTAA 57.495 36.000 3.44 3.44 32.06 1.85
1095 1098 6.582929 AGAGGGGCTCATTTAAGACTTAAT 57.417 37.500 8.45 0.00 32.06 1.40
1096 1099 6.596621 AGAGGGGCTCATTTAAGACTTAATC 58.403 40.000 8.45 0.81 32.06 1.75
1097 1100 5.368989 AGGGGCTCATTTAAGACTTAATCG 58.631 41.667 8.45 3.64 0.00 3.34
1098 1101 5.130477 AGGGGCTCATTTAAGACTTAATCGA 59.870 40.000 8.45 7.38 0.00 3.59
1099 1102 5.820947 GGGGCTCATTTAAGACTTAATCGAA 59.179 40.000 8.45 0.00 0.00 3.71
1100 1103 6.486993 GGGGCTCATTTAAGACTTAATCGAAT 59.513 38.462 8.45 0.00 0.00 3.34
1101 1104 7.355778 GGGCTCATTTAAGACTTAATCGAATG 58.644 38.462 8.45 9.14 32.67 2.67
1102 1105 7.226720 GGGCTCATTTAAGACTTAATCGAATGA 59.773 37.037 14.81 14.81 36.01 2.57
1103 1106 8.778358 GGCTCATTTAAGACTTAATCGAATGAT 58.222 33.333 15.51 1.97 36.40 2.45
1109 1112 9.893634 TTTAAGACTTAATCGAATGATTACCCA 57.106 29.630 8.45 0.00 44.64 4.51
1110 1113 9.893634 TTAAGACTTAATCGAATGATTACCCAA 57.106 29.630 3.44 0.00 44.64 4.12
1111 1114 7.787725 AGACTTAATCGAATGATTACCCAAC 57.212 36.000 0.00 0.00 44.64 3.77
1112 1115 7.335627 AGACTTAATCGAATGATTACCCAACA 58.664 34.615 0.00 0.00 44.64 3.33
1113 1116 7.495934 AGACTTAATCGAATGATTACCCAACAG 59.504 37.037 0.00 0.00 44.64 3.16
1114 1117 6.542370 ACTTAATCGAATGATTACCCAACAGG 59.458 38.462 0.00 0.00 44.64 4.00
1115 1118 4.855340 AATCGAATGATTACCCAACAGGT 58.145 39.130 0.00 0.00 42.99 4.00
1127 1130 4.937201 CCCAACAGGTAAAAAGAGCTTT 57.063 40.909 0.00 0.00 0.00 3.51
1128 1131 5.276461 CCCAACAGGTAAAAAGAGCTTTT 57.724 39.130 2.51 2.51 43.88 2.27
1129 1132 5.049828 CCCAACAGGTAAAAAGAGCTTTTG 58.950 41.667 8.80 0.42 41.45 2.44
1130 1133 5.395214 CCCAACAGGTAAAAAGAGCTTTTGT 60.395 40.000 8.80 1.00 41.45 2.83
1131 1134 6.106003 CCAACAGGTAAAAAGAGCTTTTGTT 58.894 36.000 8.80 6.57 41.45 2.83
1132 1135 6.593770 CCAACAGGTAAAAAGAGCTTTTGTTT 59.406 34.615 8.80 1.12 41.45 2.83
1133 1136 7.201522 CCAACAGGTAAAAAGAGCTTTTGTTTC 60.202 37.037 8.80 0.00 41.45 2.78
1134 1137 6.338146 ACAGGTAAAAAGAGCTTTTGTTTCC 58.662 36.000 8.80 7.31 41.45 3.13
1135 1138 6.154534 ACAGGTAAAAAGAGCTTTTGTTTCCT 59.845 34.615 11.13 11.13 41.45 3.36
1136 1139 6.697455 CAGGTAAAAAGAGCTTTTGTTTCCTC 59.303 38.462 13.35 0.00 41.45 3.71
1137 1140 6.607600 AGGTAAAAAGAGCTTTTGTTTCCTCT 59.392 34.615 11.13 0.00 41.45 3.69
1138 1141 6.918569 GGTAAAAAGAGCTTTTGTTTCCTCTC 59.081 38.462 8.80 0.00 41.45 3.20
1139 1142 6.530019 AAAAAGAGCTTTTGTTTCCTCTCA 57.470 33.333 8.80 0.00 41.45 3.27
1140 1143 6.721704 AAAAGAGCTTTTGTTTCCTCTCAT 57.278 33.333 7.37 0.00 40.84 2.90
1141 1144 5.956068 AAGAGCTTTTGTTTCCTCTCATC 57.044 39.130 0.00 0.00 33.79 2.92
1142 1145 3.999663 AGAGCTTTTGTTTCCTCTCATCG 59.000 43.478 0.00 0.00 29.03 3.84
1143 1146 3.997021 GAGCTTTTGTTTCCTCTCATCGA 59.003 43.478 0.00 0.00 0.00 3.59
1144 1147 3.999663 AGCTTTTGTTTCCTCTCATCGAG 59.000 43.478 0.00 0.00 39.57 4.04
1145 1148 3.997021 GCTTTTGTTTCCTCTCATCGAGA 59.003 43.478 0.00 0.00 42.62 4.04
1146 1149 4.633565 GCTTTTGTTTCCTCTCATCGAGAT 59.366 41.667 0.00 0.00 42.62 2.75
1147 1150 5.812642 GCTTTTGTTTCCTCTCATCGAGATA 59.187 40.000 0.00 0.00 42.62 1.98
1148 1151 6.019156 GCTTTTGTTTCCTCTCATCGAGATAG 60.019 42.308 0.00 0.00 42.62 2.08
1149 1152 6.775594 TTTGTTTCCTCTCATCGAGATAGA 57.224 37.500 0.00 0.00 42.62 1.98
1150 1153 6.384258 TTGTTTCCTCTCATCGAGATAGAG 57.616 41.667 12.30 12.30 42.62 2.43
1156 1159 3.938963 CTCTCATCGAGATAGAGGTAGGC 59.061 52.174 11.68 0.00 42.62 3.93
1157 1160 3.328050 TCTCATCGAGATAGAGGTAGGCA 59.672 47.826 0.00 0.00 33.35 4.75
1158 1161 4.075682 CTCATCGAGATAGAGGTAGGCAA 58.924 47.826 0.00 0.00 0.00 4.52
1159 1162 4.470602 TCATCGAGATAGAGGTAGGCAAA 58.529 43.478 0.00 0.00 0.00 3.68
1160 1163 4.893524 TCATCGAGATAGAGGTAGGCAAAA 59.106 41.667 0.00 0.00 0.00 2.44
1161 1164 4.920640 TCGAGATAGAGGTAGGCAAAAG 57.079 45.455 0.00 0.00 0.00 2.27
1162 1165 4.533815 TCGAGATAGAGGTAGGCAAAAGA 58.466 43.478 0.00 0.00 0.00 2.52
1163 1166 4.580995 TCGAGATAGAGGTAGGCAAAAGAG 59.419 45.833 0.00 0.00 0.00 2.85
1164 1167 4.261825 CGAGATAGAGGTAGGCAAAAGAGG 60.262 50.000 0.00 0.00 0.00 3.69
1165 1168 3.970640 AGATAGAGGTAGGCAAAAGAGGG 59.029 47.826 0.00 0.00 0.00 4.30
1166 1169 2.344093 AGAGGTAGGCAAAAGAGGGA 57.656 50.000 0.00 0.00 0.00 4.20
1167 1170 2.852130 AGAGGTAGGCAAAAGAGGGAT 58.148 47.619 0.00 0.00 0.00 3.85
1168 1171 3.193782 AGAGGTAGGCAAAAGAGGGATT 58.806 45.455 0.00 0.00 0.00 3.01
1169 1172 3.593780 AGAGGTAGGCAAAAGAGGGATTT 59.406 43.478 0.00 0.00 0.00 2.17
1170 1173 4.044698 AGAGGTAGGCAAAAGAGGGATTTT 59.955 41.667 0.00 0.00 32.65 1.82
1171 1174 4.344978 AGGTAGGCAAAAGAGGGATTTTC 58.655 43.478 0.00 0.00 30.01 2.29
1172 1175 3.128764 GGTAGGCAAAAGAGGGATTTTCG 59.871 47.826 0.00 0.00 30.01 3.46
1173 1176 2.876581 AGGCAAAAGAGGGATTTTCGT 58.123 42.857 0.00 0.00 30.01 3.85
1174 1177 2.820197 AGGCAAAAGAGGGATTTTCGTC 59.180 45.455 0.00 0.00 30.01 4.20
1175 1178 2.414161 GGCAAAAGAGGGATTTTCGTCG 60.414 50.000 0.00 0.00 30.01 5.12
1176 1179 2.225727 GCAAAAGAGGGATTTTCGTCGT 59.774 45.455 0.00 0.00 30.01 4.34
1177 1180 3.304458 GCAAAAGAGGGATTTTCGTCGTT 60.304 43.478 0.00 0.00 30.01 3.85
1178 1181 4.791734 GCAAAAGAGGGATTTTCGTCGTTT 60.792 41.667 0.00 0.00 35.08 3.60
1179 1182 4.483476 AAAGAGGGATTTTCGTCGTTTG 57.517 40.909 0.00 0.00 0.00 2.93
1180 1183 3.121738 AGAGGGATTTTCGTCGTTTGT 57.878 42.857 0.00 0.00 0.00 2.83
1181 1184 2.806244 AGAGGGATTTTCGTCGTTTGTG 59.194 45.455 0.00 0.00 0.00 3.33
1182 1185 1.877443 AGGGATTTTCGTCGTTTGTGG 59.123 47.619 0.00 0.00 0.00 4.17
1183 1186 1.874872 GGGATTTTCGTCGTTTGTGGA 59.125 47.619 0.00 0.00 0.00 4.02
1184 1187 2.486592 GGGATTTTCGTCGTTTGTGGAT 59.513 45.455 0.00 0.00 0.00 3.41
1185 1188 3.425758 GGGATTTTCGTCGTTTGTGGATC 60.426 47.826 0.00 0.00 0.00 3.36
1186 1189 3.187637 GGATTTTCGTCGTTTGTGGATCA 59.812 43.478 0.00 0.00 0.00 2.92
1187 1190 3.595709 TTTTCGTCGTTTGTGGATCAC 57.404 42.857 0.00 0.00 34.56 3.06
1188 1191 2.519377 TTCGTCGTTTGTGGATCACT 57.481 45.000 0.00 0.00 35.11 3.41
1189 1192 2.060326 TCGTCGTTTGTGGATCACTC 57.940 50.000 0.00 0.00 35.11 3.51
1190 1193 0.708370 CGTCGTTTGTGGATCACTCG 59.292 55.000 0.00 3.05 35.11 4.18
1191 1194 1.068474 GTCGTTTGTGGATCACTCGG 58.932 55.000 0.00 0.00 35.11 4.63
1192 1195 0.963225 TCGTTTGTGGATCACTCGGA 59.037 50.000 0.00 0.00 35.11 4.55
1193 1196 1.548719 TCGTTTGTGGATCACTCGGAT 59.451 47.619 0.00 0.00 39.53 4.18
1194 1197 2.756207 TCGTTTGTGGATCACTCGGATA 59.244 45.455 0.00 0.00 36.00 2.59
1195 1198 3.193903 TCGTTTGTGGATCACTCGGATAA 59.806 43.478 0.00 0.00 36.00 1.75
1196 1199 3.930229 CGTTTGTGGATCACTCGGATAAA 59.070 43.478 0.00 0.00 36.00 1.40
1197 1200 4.201685 CGTTTGTGGATCACTCGGATAAAC 60.202 45.833 0.00 0.00 36.00 2.01
1198 1201 3.159353 TGTGGATCACTCGGATAAACG 57.841 47.619 0.00 0.00 36.00 3.60
1199 1202 1.859080 GTGGATCACTCGGATAAACGC 59.141 52.381 0.00 0.00 36.00 4.84
1200 1203 1.478916 TGGATCACTCGGATAAACGCA 59.521 47.619 0.00 0.00 36.00 5.24
1201 1204 2.128035 GGATCACTCGGATAAACGCAG 58.872 52.381 0.00 0.00 36.00 5.18
1202 1205 1.523095 GATCACTCGGATAAACGCAGC 59.477 52.381 0.00 0.00 36.00 5.25
1203 1206 0.245266 TCACTCGGATAAACGCAGCA 59.755 50.000 0.00 0.00 0.00 4.41
1204 1207 1.075542 CACTCGGATAAACGCAGCAA 58.924 50.000 0.00 0.00 0.00 3.91
1205 1208 1.076332 ACTCGGATAAACGCAGCAAC 58.924 50.000 0.00 0.00 0.00 4.17
1206 1209 0.025001 CTCGGATAAACGCAGCAACG 59.975 55.000 0.00 0.00 39.50 4.10
1207 1210 1.580132 CGGATAAACGCAGCAACGC 60.580 57.895 0.00 0.00 36.19 4.84
1215 1218 4.043168 GCAGCAACGCGGGTATAT 57.957 55.556 12.47 0.00 0.00 0.86
1216 1219 3.204505 GCAGCAACGCGGGTATATA 57.795 52.632 12.47 0.00 0.00 0.86
1217 1220 1.504359 GCAGCAACGCGGGTATATAA 58.496 50.000 12.47 0.00 0.00 0.98
1218 1221 1.868498 GCAGCAACGCGGGTATATAAA 59.132 47.619 12.47 0.00 0.00 1.40
1219 1222 2.096417 GCAGCAACGCGGGTATATAAAG 60.096 50.000 12.47 0.00 0.00 1.85
1220 1223 3.128349 CAGCAACGCGGGTATATAAAGT 58.872 45.455 12.47 0.00 0.00 2.66
1221 1224 4.300803 CAGCAACGCGGGTATATAAAGTA 58.699 43.478 12.47 0.00 0.00 2.24
1222 1225 4.927425 CAGCAACGCGGGTATATAAAGTAT 59.073 41.667 12.47 0.00 0.00 2.12
1223 1226 5.407387 CAGCAACGCGGGTATATAAAGTATT 59.593 40.000 12.47 0.00 0.00 1.89
1224 1227 5.636543 AGCAACGCGGGTATATAAAGTATTC 59.363 40.000 12.47 0.00 0.00 1.75
1225 1228 5.443693 GCAACGCGGGTATATAAAGTATTCG 60.444 44.000 12.47 0.00 0.00 3.34
1226 1229 5.627499 ACGCGGGTATATAAAGTATTCGA 57.373 39.130 12.47 0.00 0.00 3.71
1227 1230 6.199937 ACGCGGGTATATAAAGTATTCGAT 57.800 37.500 12.47 0.00 0.00 3.59
1228 1231 7.320443 ACGCGGGTATATAAAGTATTCGATA 57.680 36.000 12.47 0.00 0.00 2.92
1229 1232 7.412853 ACGCGGGTATATAAAGTATTCGATAG 58.587 38.462 12.47 0.00 0.00 2.08
1230 1233 7.066284 ACGCGGGTATATAAAGTATTCGATAGT 59.934 37.037 12.47 0.00 37.40 2.12
1231 1234 7.912250 CGCGGGTATATAAAGTATTCGATAGTT 59.088 37.037 0.00 0.00 37.40 2.24
1264 1267 9.787435 AATTAATACACAACCTGTACAAGAAGA 57.213 29.630 0.00 0.00 38.22 2.87
1265 1268 9.787435 ATTAATACACAACCTGTACAAGAAGAA 57.213 29.630 0.00 0.00 38.22 2.52
1266 1269 9.616156 TTAATACACAACCTGTACAAGAAGAAA 57.384 29.630 0.00 0.00 38.22 2.52
1267 1270 8.691661 AATACACAACCTGTACAAGAAGAAAT 57.308 30.769 0.00 0.00 38.22 2.17
1268 1271 8.691661 ATACACAACCTGTACAAGAAGAAATT 57.308 30.769 0.00 0.00 38.22 1.82
1269 1272 6.795399 ACACAACCTGTACAAGAAGAAATTG 58.205 36.000 0.00 0.00 0.00 2.32
1270 1273 6.601613 ACACAACCTGTACAAGAAGAAATTGA 59.398 34.615 0.00 0.00 0.00 2.57
1271 1274 7.285401 ACACAACCTGTACAAGAAGAAATTGAT 59.715 33.333 0.00 0.00 0.00 2.57
1272 1275 8.137437 CACAACCTGTACAAGAAGAAATTGATT 58.863 33.333 0.00 0.00 0.00 2.57
1273 1276 8.352942 ACAACCTGTACAAGAAGAAATTGATTC 58.647 33.333 0.00 0.00 38.39 2.52
1292 1295 7.969387 TGATTCTTAATCGTAAAATGCTTGC 57.031 32.000 0.00 0.00 40.84 4.01
1293 1296 7.534282 TGATTCTTAATCGTAAAATGCTTGCA 58.466 30.769 0.00 0.00 40.84 4.08
1294 1297 7.484641 TGATTCTTAATCGTAAAATGCTTGCAC 59.515 33.333 0.00 0.00 40.84 4.57
1295 1298 6.247727 TCTTAATCGTAAAATGCTTGCACA 57.752 33.333 0.00 0.00 0.00 4.57
1296 1299 6.673106 TCTTAATCGTAAAATGCTTGCACAA 58.327 32.000 0.00 0.00 0.00 3.33
1297 1300 6.801377 TCTTAATCGTAAAATGCTTGCACAAG 59.199 34.615 6.01 6.01 41.24 3.16
1298 1301 3.980646 TCGTAAAATGCTTGCACAAGT 57.019 38.095 11.77 0.00 40.45 3.16
1299 1302 5.621197 ATCGTAAAATGCTTGCACAAGTA 57.379 34.783 11.77 7.89 40.45 2.24
1300 1303 5.029650 TCGTAAAATGCTTGCACAAGTAG 57.970 39.130 11.77 0.00 40.45 2.57
1301 1304 3.603770 CGTAAAATGCTTGCACAAGTAGC 59.396 43.478 11.77 0.21 40.45 3.58
1302 1305 4.613622 CGTAAAATGCTTGCACAAGTAGCT 60.614 41.667 11.77 0.00 40.45 3.32
1303 1306 3.293311 AAATGCTTGCACAAGTAGCTG 57.707 42.857 11.77 0.00 40.45 4.24
1304 1307 1.901591 ATGCTTGCACAAGTAGCTGT 58.098 45.000 11.77 0.00 40.45 4.40
1305 1308 2.542020 TGCTTGCACAAGTAGCTGTA 57.458 45.000 11.77 0.00 40.45 2.74
1306 1309 3.057969 TGCTTGCACAAGTAGCTGTAT 57.942 42.857 11.77 0.00 40.45 2.29
1307 1310 3.002791 TGCTTGCACAAGTAGCTGTATC 58.997 45.455 11.77 0.00 40.45 2.24
1308 1311 3.002791 GCTTGCACAAGTAGCTGTATCA 58.997 45.455 11.77 0.00 40.45 2.15
1309 1312 3.436704 GCTTGCACAAGTAGCTGTATCAA 59.563 43.478 11.77 0.00 40.45 2.57
1310 1313 4.083324 GCTTGCACAAGTAGCTGTATCAAA 60.083 41.667 11.77 0.00 40.45 2.69
1311 1314 5.392380 GCTTGCACAAGTAGCTGTATCAAAT 60.392 40.000 11.77 0.00 40.45 2.32
1312 1315 5.801350 TGCACAAGTAGCTGTATCAAATC 57.199 39.130 0.00 0.00 0.00 2.17
1360 1363 3.768468 TCCAACAAACTTGGTTTCGTC 57.232 42.857 0.00 0.00 40.40 4.20
1413 1416 4.770010 TCAGTTTTGGTGTTCTGAAAAGGT 59.230 37.500 0.00 0.00 34.61 3.50
1510 1522 4.222847 GGCTACTTCCGCTCGGGG 62.223 72.222 8.59 4.78 36.01 5.73
1581 1594 1.472188 GTAGTACCGCTCCTCCAAGT 58.528 55.000 0.00 0.00 0.00 3.16
1583 1596 0.251653 AGTACCGCTCCTCCAAGTGA 60.252 55.000 0.00 0.00 0.00 3.41
1584 1597 0.108756 GTACCGCTCCTCCAAGTGAC 60.109 60.000 0.00 0.00 0.00 3.67
1624 1637 1.732259 CTGAGCACATAACGGTTGGAC 59.268 52.381 3.07 0.00 0.00 4.02
1696 1709 1.004918 AGCTCGTGTTCTTTCCCCG 60.005 57.895 0.00 0.00 0.00 5.73
1884 1900 7.499232 TCTTCTTTCGTTCTTCCTCTCATTTTT 59.501 33.333 0.00 0.00 0.00 1.94
2096 2114 1.227321 GACGGTTGGTGGTGTTCGA 60.227 57.895 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
291 292 4.021981 GGATACGTACCTAACCCCACATAC 60.022 50.000 0.00 0.00 0.00 2.39
542 544 3.482436 ACCACCTTTCTTGATTGCGTTA 58.518 40.909 0.00 0.00 0.00 3.18
568 570 2.897326 TGACGATCTTCACTCCCTCAAA 59.103 45.455 0.00 0.00 0.00 2.69
653 655 1.548719 CCACAACTACCATGAGACCGA 59.451 52.381 0.00 0.00 0.00 4.69
984 987 7.671398 ACTCTGGTCATTGAATCAAATTAACCT 59.329 33.333 15.42 0.23 0.00 3.50
985 988 7.830739 ACTCTGGTCATTGAATCAAATTAACC 58.169 34.615 0.00 6.19 0.00 2.85
986 989 9.346725 GAACTCTGGTCATTGAATCAAATTAAC 57.653 33.333 0.00 0.00 0.00 2.01
987 990 8.522830 GGAACTCTGGTCATTGAATCAAATTAA 58.477 33.333 0.00 0.00 0.00 1.40
988 991 7.148255 CGGAACTCTGGTCATTGAATCAAATTA 60.148 37.037 0.00 0.00 0.00 1.40
989 992 6.349611 CGGAACTCTGGTCATTGAATCAAATT 60.350 38.462 0.00 0.00 0.00 1.82
990 993 5.124457 CGGAACTCTGGTCATTGAATCAAAT 59.876 40.000 0.00 0.00 0.00 2.32
991 994 4.455533 CGGAACTCTGGTCATTGAATCAAA 59.544 41.667 0.00 0.00 0.00 2.69
992 995 4.002982 CGGAACTCTGGTCATTGAATCAA 58.997 43.478 0.00 0.00 0.00 2.57
993 996 3.599343 CGGAACTCTGGTCATTGAATCA 58.401 45.455 0.00 0.00 0.00 2.57
994 997 2.352960 GCGGAACTCTGGTCATTGAATC 59.647 50.000 0.00 0.00 0.00 2.52
995 998 2.359900 GCGGAACTCTGGTCATTGAAT 58.640 47.619 0.00 0.00 0.00 2.57
996 999 1.808411 GCGGAACTCTGGTCATTGAA 58.192 50.000 0.00 0.00 0.00 2.69
997 1000 0.389817 CGCGGAACTCTGGTCATTGA 60.390 55.000 0.00 0.00 0.00 2.57
998 1001 0.389817 TCGCGGAACTCTGGTCATTG 60.390 55.000 6.13 0.00 0.00 2.82
999 1002 0.108615 CTCGCGGAACTCTGGTCATT 60.109 55.000 6.13 0.00 0.00 2.57
1000 1003 1.513158 CTCGCGGAACTCTGGTCAT 59.487 57.895 6.13 0.00 0.00 3.06
1001 1004 2.636412 CCTCGCGGAACTCTGGTCA 61.636 63.158 6.13 0.00 0.00 4.02
1002 1005 1.668101 ATCCTCGCGGAACTCTGGTC 61.668 60.000 6.13 0.00 44.02 4.02
1003 1006 0.395311 TATCCTCGCGGAACTCTGGT 60.395 55.000 6.13 0.00 44.02 4.00
1004 1007 0.962489 ATATCCTCGCGGAACTCTGG 59.038 55.000 6.13 0.00 44.02 3.86
1005 1008 4.496673 GCTATATATCCTCGCGGAACTCTG 60.497 50.000 6.13 0.00 44.02 3.35
1006 1009 3.628487 GCTATATATCCTCGCGGAACTCT 59.372 47.826 6.13 0.00 44.02 3.24
1007 1010 3.243134 GGCTATATATCCTCGCGGAACTC 60.243 52.174 6.13 0.00 44.02 3.01
1008 1011 2.688958 GGCTATATATCCTCGCGGAACT 59.311 50.000 6.13 0.00 44.02 3.01
1009 1012 2.223758 GGGCTATATATCCTCGCGGAAC 60.224 54.545 6.13 0.00 44.02 3.62
1010 1013 2.029623 GGGCTATATATCCTCGCGGAA 58.970 52.381 6.13 0.00 44.02 4.30
1011 1014 1.688772 GGGCTATATATCCTCGCGGA 58.311 55.000 6.13 0.00 45.16 5.54
1012 1015 0.311165 CGGGCTATATATCCTCGCGG 59.689 60.000 6.13 0.00 0.00 6.46
1013 1016 0.311165 CCGGGCTATATATCCTCGCG 59.689 60.000 0.00 0.00 0.00 5.87
1014 1017 1.609555 CTCCGGGCTATATATCCTCGC 59.390 57.143 0.00 0.00 0.00 5.03
1015 1018 2.879646 GTCTCCGGGCTATATATCCTCG 59.120 54.545 0.00 4.95 0.00 4.63
1016 1019 2.879646 CGTCTCCGGGCTATATATCCTC 59.120 54.545 0.00 0.00 0.00 3.71
1017 1020 2.508716 TCGTCTCCGGGCTATATATCCT 59.491 50.000 0.00 0.00 33.95 3.24
1018 1021 2.617774 GTCGTCTCCGGGCTATATATCC 59.382 54.545 0.00 0.00 33.95 2.59
1019 1022 2.287373 CGTCGTCTCCGGGCTATATATC 59.713 54.545 0.00 0.00 33.95 1.63
1020 1023 2.093288 TCGTCGTCTCCGGGCTATATAT 60.093 50.000 0.00 0.00 33.95 0.86
1021 1024 1.276138 TCGTCGTCTCCGGGCTATATA 59.724 52.381 0.00 0.00 33.95 0.86
1022 1025 0.035881 TCGTCGTCTCCGGGCTATAT 59.964 55.000 0.00 0.00 33.95 0.86
1023 1026 0.179048 TTCGTCGTCTCCGGGCTATA 60.179 55.000 0.00 0.00 33.95 1.31
1024 1027 1.452651 TTCGTCGTCTCCGGGCTAT 60.453 57.895 0.00 0.00 33.95 2.97
1025 1028 2.046023 TTCGTCGTCTCCGGGCTA 60.046 61.111 0.00 0.00 33.95 3.93
1026 1029 3.745803 GTTCGTCGTCTCCGGGCT 61.746 66.667 0.00 0.00 33.95 5.19
1027 1030 3.562779 TTGTTCGTCGTCTCCGGGC 62.563 63.158 0.00 0.00 33.95 6.13
1028 1031 0.598158 TTTTGTTCGTCGTCTCCGGG 60.598 55.000 0.00 0.00 33.95 5.73
1029 1032 1.210870 TTTTTGTTCGTCGTCTCCGG 58.789 50.000 0.00 0.00 33.95 5.14
1030 1033 2.822827 CATTTTTGTTCGTCGTCTCCG 58.177 47.619 0.00 0.00 0.00 4.63
1031 1034 2.571206 GCATTTTTGTTCGTCGTCTCC 58.429 47.619 0.00 0.00 0.00 3.71
1032 1035 2.222624 CGCATTTTTGTTCGTCGTCTC 58.777 47.619 0.00 0.00 0.00 3.36
1033 1036 1.595794 ACGCATTTTTGTTCGTCGTCT 59.404 42.857 0.00 0.00 0.00 4.18
1034 1037 2.013286 ACGCATTTTTGTTCGTCGTC 57.987 45.000 0.00 0.00 0.00 4.20
1035 1038 2.223066 TGAACGCATTTTTGTTCGTCGT 60.223 40.909 0.00 0.00 45.75 4.34
1036 1039 2.367772 TGAACGCATTTTTGTTCGTCG 58.632 42.857 1.26 0.00 45.75 5.12
1037 1040 4.947077 AATGAACGCATTTTTGTTCGTC 57.053 36.364 0.81 0.00 45.75 4.20
1047 1050 3.059166 GTTTGAGGCAAATGAACGCATT 58.941 40.909 0.00 0.00 46.35 3.56
1048 1051 2.297033 AGTTTGAGGCAAATGAACGCAT 59.703 40.909 0.00 0.00 35.74 4.73
1049 1052 1.680735 AGTTTGAGGCAAATGAACGCA 59.319 42.857 0.00 0.00 35.74 5.24
1050 1053 2.422276 AGTTTGAGGCAAATGAACGC 57.578 45.000 0.00 0.00 35.74 4.84
1051 1054 5.757886 TCTAAAGTTTGAGGCAAATGAACG 58.242 37.500 0.00 0.00 35.74 3.95
1052 1055 6.152379 CCTCTAAAGTTTGAGGCAAATGAAC 58.848 40.000 16.26 0.00 41.83 3.18
1053 1056 5.243730 CCCTCTAAAGTTTGAGGCAAATGAA 59.756 40.000 20.21 0.00 45.15 2.57
1054 1057 4.766891 CCCTCTAAAGTTTGAGGCAAATGA 59.233 41.667 20.21 0.00 45.15 2.57
1055 1058 4.082026 CCCCTCTAAAGTTTGAGGCAAATG 60.082 45.833 20.21 11.33 45.15 2.32
1056 1059 4.089361 CCCCTCTAAAGTTTGAGGCAAAT 58.911 43.478 20.21 0.00 45.15 2.32
1057 1060 3.496331 CCCCTCTAAAGTTTGAGGCAAA 58.504 45.455 20.21 0.00 45.15 3.68
1058 1061 2.817839 GCCCCTCTAAAGTTTGAGGCAA 60.818 50.000 20.21 0.00 45.15 4.52
1059 1062 1.271926 GCCCCTCTAAAGTTTGAGGCA 60.272 52.381 20.21 0.00 45.15 4.75
1060 1063 1.004862 AGCCCCTCTAAAGTTTGAGGC 59.995 52.381 20.21 14.34 45.15 4.70
1061 1064 2.305927 TGAGCCCCTCTAAAGTTTGAGG 59.694 50.000 19.32 19.32 45.78 3.86
1062 1065 3.703001 TGAGCCCCTCTAAAGTTTGAG 57.297 47.619 0.00 3.57 0.00 3.02
1063 1066 4.657814 AATGAGCCCCTCTAAAGTTTGA 57.342 40.909 0.00 0.00 0.00 2.69
1064 1067 6.659242 TCTTAAATGAGCCCCTCTAAAGTTTG 59.341 38.462 0.00 0.00 0.00 2.93
1065 1068 6.659668 GTCTTAAATGAGCCCCTCTAAAGTTT 59.340 38.462 0.00 0.00 0.00 2.66
1066 1069 6.012421 AGTCTTAAATGAGCCCCTCTAAAGTT 60.012 38.462 0.00 0.00 0.00 2.66
1067 1070 5.489278 AGTCTTAAATGAGCCCCTCTAAAGT 59.511 40.000 0.00 0.00 0.00 2.66
1068 1071 5.995446 AGTCTTAAATGAGCCCCTCTAAAG 58.005 41.667 0.00 0.00 0.00 1.85
1069 1072 6.388619 AAGTCTTAAATGAGCCCCTCTAAA 57.611 37.500 0.00 0.00 0.00 1.85
1070 1073 7.504926 TTAAGTCTTAAATGAGCCCCTCTAA 57.495 36.000 2.40 0.00 0.00 2.10
1071 1074 7.471539 CGATTAAGTCTTAAATGAGCCCCTCTA 60.472 40.741 9.07 0.00 0.00 2.43
1072 1075 6.582929 ATTAAGTCTTAAATGAGCCCCTCT 57.417 37.500 9.07 0.00 0.00 3.69
1073 1076 5.467063 CGATTAAGTCTTAAATGAGCCCCTC 59.533 44.000 9.07 0.00 0.00 4.30
1074 1077 5.130477 TCGATTAAGTCTTAAATGAGCCCCT 59.870 40.000 9.07 0.00 0.00 4.79
1075 1078 5.365619 TCGATTAAGTCTTAAATGAGCCCC 58.634 41.667 9.07 0.00 0.00 5.80
1076 1079 6.920569 TTCGATTAAGTCTTAAATGAGCCC 57.079 37.500 9.07 0.00 0.00 5.19
1077 1080 8.142994 TCATTCGATTAAGTCTTAAATGAGCC 57.857 34.615 9.07 0.00 30.82 4.70
1083 1086 9.893634 TGGGTAATCATTCGATTAAGTCTTAAA 57.106 29.630 9.07 0.00 43.93 1.52
1084 1087 9.893634 TTGGGTAATCATTCGATTAAGTCTTAA 57.106 29.630 7.49 7.49 43.93 1.85
1085 1088 9.321562 GTTGGGTAATCATTCGATTAAGTCTTA 57.678 33.333 0.00 0.00 43.93 2.10
1086 1089 7.827236 TGTTGGGTAATCATTCGATTAAGTCTT 59.173 33.333 0.00 0.00 43.93 3.01
1087 1090 7.335627 TGTTGGGTAATCATTCGATTAAGTCT 58.664 34.615 0.00 0.00 43.93 3.24
1088 1091 7.254795 CCTGTTGGGTAATCATTCGATTAAGTC 60.255 40.741 0.00 0.00 43.93 3.01
1089 1092 6.542370 CCTGTTGGGTAATCATTCGATTAAGT 59.458 38.462 0.00 0.00 43.93 2.24
1090 1093 6.959361 CCTGTTGGGTAATCATTCGATTAAG 58.041 40.000 0.00 0.00 43.93 1.85
1091 1094 6.935741 CCTGTTGGGTAATCATTCGATTAA 57.064 37.500 0.00 0.00 43.93 1.40
1105 1108 4.714802 AAAAGCTCTTTTTACCTGTTGGGT 59.285 37.500 2.01 0.00 42.01 4.51
1106 1109 4.937201 AAAGCTCTTTTTACCTGTTGGG 57.063 40.909 0.00 0.00 41.89 4.12
1107 1110 5.660460 ACAAAAGCTCTTTTTACCTGTTGG 58.340 37.500 4.97 0.00 40.45 3.77
1108 1111 7.201522 GGAAACAAAAGCTCTTTTTACCTGTTG 60.202 37.037 4.97 0.00 40.45 3.33
1109 1112 6.816640 GGAAACAAAAGCTCTTTTTACCTGTT 59.183 34.615 4.97 4.68 40.45 3.16
1110 1113 6.154534 AGGAAACAAAAGCTCTTTTTACCTGT 59.845 34.615 4.97 0.00 40.45 4.00
1111 1114 6.573434 AGGAAACAAAAGCTCTTTTTACCTG 58.427 36.000 4.97 0.00 40.45 4.00
1112 1115 6.607600 AGAGGAAACAAAAGCTCTTTTTACCT 59.392 34.615 4.97 10.32 40.45 3.08
1113 1116 6.806751 AGAGGAAACAAAAGCTCTTTTTACC 58.193 36.000 4.97 6.67 40.45 2.85
1114 1117 7.480810 TGAGAGGAAACAAAAGCTCTTTTTAC 58.519 34.615 4.97 0.00 40.45 2.01
1115 1118 7.639113 TGAGAGGAAACAAAAGCTCTTTTTA 57.361 32.000 4.97 0.00 40.45 1.52
1116 1119 6.530019 TGAGAGGAAACAAAAGCTCTTTTT 57.470 33.333 4.97 0.00 40.45 1.94
1117 1120 6.514048 CGATGAGAGGAAACAAAAGCTCTTTT 60.514 38.462 2.01 2.01 42.91 2.27
1118 1121 5.049129 CGATGAGAGGAAACAAAAGCTCTTT 60.049 40.000 0.00 0.00 0.00 2.52
1119 1122 4.453819 CGATGAGAGGAAACAAAAGCTCTT 59.546 41.667 0.00 0.00 0.00 2.85
1120 1123 3.999663 CGATGAGAGGAAACAAAAGCTCT 59.000 43.478 0.00 0.00 0.00 4.09
1121 1124 3.997021 TCGATGAGAGGAAACAAAAGCTC 59.003 43.478 0.00 0.00 0.00 4.09
1122 1125 3.999663 CTCGATGAGAGGAAACAAAAGCT 59.000 43.478 0.00 0.00 43.20 3.74
1123 1126 3.997021 TCTCGATGAGAGGAAACAAAAGC 59.003 43.478 0.00 0.00 46.82 3.51
1124 1127 7.261325 TCTATCTCGATGAGAGGAAACAAAAG 58.739 38.462 2.68 0.00 46.82 2.27
1125 1128 7.170393 TCTATCTCGATGAGAGGAAACAAAA 57.830 36.000 2.68 0.00 46.82 2.44
1126 1129 6.775594 TCTATCTCGATGAGAGGAAACAAA 57.224 37.500 2.68 0.00 46.82 2.83
1127 1130 6.384258 CTCTATCTCGATGAGAGGAAACAA 57.616 41.667 9.45 0.00 46.82 2.83
1135 1138 3.328050 TGCCTACCTCTATCTCGATGAGA 59.672 47.826 0.00 0.00 43.20 3.27
1136 1139 3.680490 TGCCTACCTCTATCTCGATGAG 58.320 50.000 0.00 0.00 0.00 2.90
1137 1140 3.790089 TGCCTACCTCTATCTCGATGA 57.210 47.619 0.00 0.00 0.00 2.92
1138 1141 4.855715 TTTGCCTACCTCTATCTCGATG 57.144 45.455 0.00 0.00 0.00 3.84
1139 1142 5.141182 TCTTTTGCCTACCTCTATCTCGAT 58.859 41.667 0.00 0.00 0.00 3.59
1140 1143 4.533815 TCTTTTGCCTACCTCTATCTCGA 58.466 43.478 0.00 0.00 0.00 4.04
1141 1144 4.261825 CCTCTTTTGCCTACCTCTATCTCG 60.262 50.000 0.00 0.00 0.00 4.04
1142 1145 4.039852 CCCTCTTTTGCCTACCTCTATCTC 59.960 50.000 0.00 0.00 0.00 2.75
1143 1146 3.970640 CCCTCTTTTGCCTACCTCTATCT 59.029 47.826 0.00 0.00 0.00 1.98
1144 1147 3.967987 TCCCTCTTTTGCCTACCTCTATC 59.032 47.826 0.00 0.00 0.00 2.08
1145 1148 4.008916 TCCCTCTTTTGCCTACCTCTAT 57.991 45.455 0.00 0.00 0.00 1.98
1146 1149 3.484953 TCCCTCTTTTGCCTACCTCTA 57.515 47.619 0.00 0.00 0.00 2.43
1147 1150 2.344093 TCCCTCTTTTGCCTACCTCT 57.656 50.000 0.00 0.00 0.00 3.69
1148 1151 3.653835 AATCCCTCTTTTGCCTACCTC 57.346 47.619 0.00 0.00 0.00 3.85
1149 1152 4.344978 GAAAATCCCTCTTTTGCCTACCT 58.655 43.478 0.00 0.00 0.00 3.08
1150 1153 3.128764 CGAAAATCCCTCTTTTGCCTACC 59.871 47.826 0.00 0.00 0.00 3.18
1151 1154 3.756963 ACGAAAATCCCTCTTTTGCCTAC 59.243 43.478 0.00 0.00 0.00 3.18
1152 1155 4.007659 GACGAAAATCCCTCTTTTGCCTA 58.992 43.478 0.00 0.00 0.00 3.93
1153 1156 2.820197 GACGAAAATCCCTCTTTTGCCT 59.180 45.455 0.00 0.00 0.00 4.75
1154 1157 2.414161 CGACGAAAATCCCTCTTTTGCC 60.414 50.000 0.00 0.00 0.00 4.52
1155 1158 2.225727 ACGACGAAAATCCCTCTTTTGC 59.774 45.455 0.00 0.00 0.00 3.68
1156 1159 4.483476 AACGACGAAAATCCCTCTTTTG 57.517 40.909 0.00 0.00 0.00 2.44
1157 1160 4.337274 ACAAACGACGAAAATCCCTCTTTT 59.663 37.500 0.00 0.00 0.00 2.27
1158 1161 3.881089 ACAAACGACGAAAATCCCTCTTT 59.119 39.130 0.00 0.00 0.00 2.52
1159 1162 3.250040 CACAAACGACGAAAATCCCTCTT 59.750 43.478 0.00 0.00 0.00 2.85
1160 1163 2.806244 CACAAACGACGAAAATCCCTCT 59.194 45.455 0.00 0.00 0.00 3.69
1161 1164 2.095919 CCACAAACGACGAAAATCCCTC 60.096 50.000 0.00 0.00 0.00 4.30
1162 1165 1.877443 CCACAAACGACGAAAATCCCT 59.123 47.619 0.00 0.00 0.00 4.20
1163 1166 1.874872 TCCACAAACGACGAAAATCCC 59.125 47.619 0.00 0.00 0.00 3.85
1164 1167 3.187637 TGATCCACAAACGACGAAAATCC 59.812 43.478 0.00 0.00 0.00 3.01
1165 1168 4.084013 AGTGATCCACAAACGACGAAAATC 60.084 41.667 0.00 0.00 36.74 2.17
1166 1169 3.813166 AGTGATCCACAAACGACGAAAAT 59.187 39.130 0.00 0.00 36.74 1.82
1167 1170 3.199677 AGTGATCCACAAACGACGAAAA 58.800 40.909 0.00 0.00 36.74 2.29
1168 1171 2.798283 GAGTGATCCACAAACGACGAAA 59.202 45.455 0.00 0.00 36.74 3.46
1169 1172 2.400399 GAGTGATCCACAAACGACGAA 58.600 47.619 0.00 0.00 36.74 3.85
1170 1173 1.664874 CGAGTGATCCACAAACGACGA 60.665 52.381 0.00 0.00 36.74 4.20
1171 1174 0.708370 CGAGTGATCCACAAACGACG 59.292 55.000 0.00 0.00 36.74 5.12
1172 1175 1.068474 CCGAGTGATCCACAAACGAC 58.932 55.000 0.00 0.00 36.74 4.34
1173 1176 0.963225 TCCGAGTGATCCACAAACGA 59.037 50.000 0.00 0.00 36.74 3.85
1174 1177 2.010145 ATCCGAGTGATCCACAAACG 57.990 50.000 0.00 0.00 36.74 3.60
1175 1178 4.201685 CGTTTATCCGAGTGATCCACAAAC 60.202 45.833 0.00 0.00 36.74 2.93
1176 1179 3.930229 CGTTTATCCGAGTGATCCACAAA 59.070 43.478 0.00 0.00 36.74 2.83
1177 1180 3.517602 CGTTTATCCGAGTGATCCACAA 58.482 45.455 0.00 0.00 36.74 3.33
1178 1181 2.737359 GCGTTTATCCGAGTGATCCACA 60.737 50.000 0.00 0.00 36.74 4.17
1179 1182 1.859080 GCGTTTATCCGAGTGATCCAC 59.141 52.381 0.00 0.00 34.76 4.02
1180 1183 1.478916 TGCGTTTATCCGAGTGATCCA 59.521 47.619 0.00 0.00 34.76 3.41
1181 1184 2.128035 CTGCGTTTATCCGAGTGATCC 58.872 52.381 0.00 0.00 34.76 3.36
1182 1185 1.523095 GCTGCGTTTATCCGAGTGATC 59.477 52.381 0.00 0.00 34.76 2.92
1183 1186 1.134818 TGCTGCGTTTATCCGAGTGAT 60.135 47.619 0.00 0.00 37.49 3.06
1184 1187 0.245266 TGCTGCGTTTATCCGAGTGA 59.755 50.000 0.00 0.00 0.00 3.41
1185 1188 1.075542 TTGCTGCGTTTATCCGAGTG 58.924 50.000 0.00 0.00 0.00 3.51
1186 1189 1.076332 GTTGCTGCGTTTATCCGAGT 58.924 50.000 0.00 0.00 0.00 4.18
1187 1190 0.025001 CGTTGCTGCGTTTATCCGAG 59.975 55.000 0.00 0.00 0.00 4.63
1188 1191 1.962092 GCGTTGCTGCGTTTATCCGA 61.962 55.000 0.00 0.00 0.00 4.55
1189 1192 1.580132 GCGTTGCTGCGTTTATCCG 60.580 57.895 0.00 0.00 0.00 4.18
1190 1193 4.360101 GCGTTGCTGCGTTTATCC 57.640 55.556 0.00 0.00 0.00 2.59
1198 1201 1.504359 TTATATACCCGCGTTGCTGC 58.496 50.000 4.92 0.00 0.00 5.25
1199 1202 3.128349 ACTTTATATACCCGCGTTGCTG 58.872 45.455 4.92 0.00 0.00 4.41
1200 1203 3.464111 ACTTTATATACCCGCGTTGCT 57.536 42.857 4.92 0.00 0.00 3.91
1201 1204 5.443693 CGAATACTTTATATACCCGCGTTGC 60.444 44.000 4.92 0.00 0.00 4.17
1202 1205 5.858049 TCGAATACTTTATATACCCGCGTTG 59.142 40.000 4.92 0.00 0.00 4.10
1203 1206 6.012658 TCGAATACTTTATATACCCGCGTT 57.987 37.500 4.92 0.00 0.00 4.84
1204 1207 5.627499 TCGAATACTTTATATACCCGCGT 57.373 39.130 4.92 0.00 0.00 6.01
1205 1208 7.412853 ACTATCGAATACTTTATATACCCGCG 58.587 38.462 0.00 0.00 0.00 6.46
1238 1241 9.787435 TCTTCTTGTACAGGTTGTGTATTAATT 57.213 29.630 4.75 0.00 43.70 1.40
1239 1242 9.787435 TTCTTCTTGTACAGGTTGTGTATTAAT 57.213 29.630 4.75 0.00 43.70 1.40
1240 1243 9.616156 TTTCTTCTTGTACAGGTTGTGTATTAA 57.384 29.630 4.75 0.00 43.70 1.40
1241 1244 9.787435 ATTTCTTCTTGTACAGGTTGTGTATTA 57.213 29.630 4.75 0.00 43.70 0.98
1242 1245 8.691661 ATTTCTTCTTGTACAGGTTGTGTATT 57.308 30.769 4.75 0.00 43.70 1.89
1243 1246 8.567948 CAATTTCTTCTTGTACAGGTTGTGTAT 58.432 33.333 4.75 0.00 43.70 2.29
1244 1247 7.771361 TCAATTTCTTCTTGTACAGGTTGTGTA 59.229 33.333 4.75 0.00 40.94 2.90
1245 1248 6.601613 TCAATTTCTTCTTGTACAGGTTGTGT 59.398 34.615 4.75 0.00 43.86 3.72
1246 1249 7.026631 TCAATTTCTTCTTGTACAGGTTGTG 57.973 36.000 4.75 0.00 0.00 3.33
1247 1250 7.823745 ATCAATTTCTTCTTGTACAGGTTGT 57.176 32.000 4.75 0.00 0.00 3.32
1248 1251 8.571336 AGAATCAATTTCTTCTTGTACAGGTTG 58.429 33.333 4.75 1.62 42.15 3.77
1249 1252 8.697507 AGAATCAATTTCTTCTTGTACAGGTT 57.302 30.769 4.75 0.00 42.15 3.50
1266 1269 9.023967 GCAAGCATTTTACGATTAAGAATCAAT 57.976 29.630 0.00 0.00 37.78 2.57
1267 1270 8.026026 TGCAAGCATTTTACGATTAAGAATCAA 58.974 29.630 0.00 0.00 37.78 2.57
1268 1271 7.484641 GTGCAAGCATTTTACGATTAAGAATCA 59.515 33.333 0.00 0.00 37.78 2.57
1269 1272 7.484641 TGTGCAAGCATTTTACGATTAAGAATC 59.515 33.333 0.00 0.00 34.52 2.52
1270 1273 7.312154 TGTGCAAGCATTTTACGATTAAGAAT 58.688 30.769 0.00 0.00 0.00 2.40
1271 1274 6.673106 TGTGCAAGCATTTTACGATTAAGAA 58.327 32.000 0.00 0.00 0.00 2.52
1272 1275 6.247727 TGTGCAAGCATTTTACGATTAAGA 57.752 33.333 0.00 0.00 0.00 2.10
1273 1276 6.582295 ACTTGTGCAAGCATTTTACGATTAAG 59.418 34.615 11.43 0.00 41.99 1.85
1274 1277 6.442952 ACTTGTGCAAGCATTTTACGATTAA 58.557 32.000 11.43 0.00 41.99 1.40
1275 1278 6.007936 ACTTGTGCAAGCATTTTACGATTA 57.992 33.333 11.43 0.00 41.99 1.75
1276 1279 4.870363 ACTTGTGCAAGCATTTTACGATT 58.130 34.783 11.43 0.00 41.99 3.34
1277 1280 4.503741 ACTTGTGCAAGCATTTTACGAT 57.496 36.364 11.43 0.00 41.99 3.73
1278 1281 3.980646 ACTTGTGCAAGCATTTTACGA 57.019 38.095 11.43 0.00 41.99 3.43
1279 1282 3.603770 GCTACTTGTGCAAGCATTTTACG 59.396 43.478 11.43 0.00 41.99 3.18
1280 1283 4.618489 CAGCTACTTGTGCAAGCATTTTAC 59.382 41.667 9.84 0.00 41.99 2.01
1281 1284 4.278170 ACAGCTACTTGTGCAAGCATTTTA 59.722 37.500 9.84 0.00 41.99 1.52
1282 1285 3.068590 ACAGCTACTTGTGCAAGCATTTT 59.931 39.130 9.84 0.00 41.99 1.82
1283 1286 2.624838 ACAGCTACTTGTGCAAGCATTT 59.375 40.909 9.84 0.00 41.99 2.32
1284 1287 2.233271 ACAGCTACTTGTGCAAGCATT 58.767 42.857 9.84 0.00 41.99 3.56
1285 1288 1.901591 ACAGCTACTTGTGCAAGCAT 58.098 45.000 9.84 0.00 41.99 3.79
1286 1289 2.542020 TACAGCTACTTGTGCAAGCA 57.458 45.000 9.84 0.00 41.99 3.91
1287 1290 3.002791 TGATACAGCTACTTGTGCAAGC 58.997 45.455 11.43 0.00 41.99 4.01
1288 1291 5.611796 TTTGATACAGCTACTTGTGCAAG 57.388 39.130 10.09 10.09 43.79 4.01
1289 1292 5.163864 CGATTTGATACAGCTACTTGTGCAA 60.164 40.000 0.00 0.00 32.56 4.08
1290 1293 4.329801 CGATTTGATACAGCTACTTGTGCA 59.670 41.667 0.00 0.00 32.56 4.57
1291 1294 4.566759 TCGATTTGATACAGCTACTTGTGC 59.433 41.667 0.00 0.00 32.56 4.57
1292 1295 6.834959 ATCGATTTGATACAGCTACTTGTG 57.165 37.500 0.00 0.00 34.83 3.33
1293 1296 6.818644 ACAATCGATTTGATACAGCTACTTGT 59.181 34.615 8.21 0.00 38.76 3.16
1294 1297 7.121911 CACAATCGATTTGATACAGCTACTTG 58.878 38.462 8.21 0.00 38.76 3.16
1295 1298 6.818644 ACACAATCGATTTGATACAGCTACTT 59.181 34.615 20.06 0.00 38.76 2.24
1296 1299 6.341316 ACACAATCGATTTGATACAGCTACT 58.659 36.000 20.06 0.00 38.76 2.57
1297 1300 6.589830 ACACAATCGATTTGATACAGCTAC 57.410 37.500 20.06 0.00 38.76 3.58
1298 1301 7.042725 GCTAACACAATCGATTTGATACAGCTA 60.043 37.037 20.06 1.48 38.76 3.32
1299 1302 6.238211 GCTAACACAATCGATTTGATACAGCT 60.238 38.462 20.06 0.00 38.76 4.24
1300 1303 5.904080 GCTAACACAATCGATTTGATACAGC 59.096 40.000 20.06 15.16 38.76 4.40
1301 1304 6.422223 GGCTAACACAATCGATTTGATACAG 58.578 40.000 20.06 10.78 38.76 2.74
1302 1305 5.295787 GGGCTAACACAATCGATTTGATACA 59.704 40.000 20.06 2.49 38.76 2.29
1303 1306 5.527582 AGGGCTAACACAATCGATTTGATAC 59.472 40.000 20.06 11.03 38.76 2.24
1304 1307 5.680619 AGGGCTAACACAATCGATTTGATA 58.319 37.500 20.06 14.15 38.76 2.15
1305 1308 4.526970 AGGGCTAACACAATCGATTTGAT 58.473 39.130 20.06 13.87 38.76 2.57
1306 1309 3.950397 AGGGCTAACACAATCGATTTGA 58.050 40.909 20.06 0.00 38.76 2.69
1307 1310 4.082787 ACAAGGGCTAACACAATCGATTTG 60.083 41.667 8.21 12.42 41.36 2.32
1308 1311 4.079253 ACAAGGGCTAACACAATCGATTT 58.921 39.130 8.21 0.00 0.00 2.17
1309 1312 3.686016 ACAAGGGCTAACACAATCGATT 58.314 40.909 4.39 4.39 0.00 3.34
1310 1313 3.055094 AGACAAGGGCTAACACAATCGAT 60.055 43.478 0.00 0.00 0.00 3.59
1311 1314 2.301870 AGACAAGGGCTAACACAATCGA 59.698 45.455 0.00 0.00 0.00 3.59
1312 1315 2.673368 GAGACAAGGGCTAACACAATCG 59.327 50.000 0.00 0.00 0.00 3.34
1376 1379 4.100529 CAAAACTGACACAACTTCTGCAG 58.899 43.478 7.63 7.63 0.00 4.41
1530 1542 2.417515 GGTCAAAACAGCCCAACGAAAA 60.418 45.455 0.00 0.00 0.00 2.29
1532 1544 0.741915 GGTCAAAACAGCCCAACGAA 59.258 50.000 0.00 0.00 0.00 3.85
1581 1594 0.034756 ATGCACAAGCGGTACTGTCA 59.965 50.000 3.10 0.00 46.23 3.58
1583 1596 0.034756 TCATGCACAAGCGGTACTGT 59.965 50.000 3.10 0.00 46.23 3.55
1584 1597 0.443869 GTCATGCACAAGCGGTACTG 59.556 55.000 0.00 0.00 46.23 2.74
1648 1661 6.095580 GGATTAGGTTCATTGGGAAAGAAGAC 59.904 42.308 0.00 0.00 37.23 3.01
1696 1709 2.484889 AGCTCGAAGAAGGTCAACAAC 58.515 47.619 0.00 0.00 34.09 3.32
1748 1761 6.998673 CCTCTCTCTTTTCCCTCAAAAACTAA 59.001 38.462 0.00 0.00 33.40 2.24
1839 1854 3.718815 AGAACACGAAGAACTCCAAGAC 58.281 45.455 0.00 0.00 0.00 3.01
2096 2114 5.565439 GCTTTACACCACAATGATTGAGCTT 60.565 40.000 12.80 0.00 0.00 3.74


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

AutoCloner maintained by Alex Coulton.