Multiple sequence alignment - TraesCS1B01G082000

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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 TraesCS1B01G082000 chr1B 100.000 2219 0 0 1 2219 65449265 65451483 0.000000e+00 4098
1 TraesCS1B01G082000 chr1B 92.449 874 57 4 1355 2219 446775837 446774964 0.000000e+00 1240
2 TraesCS1B01G082000 chr4B 95.248 1010 44 3 1 1007 513154646 513153638 0.000000e+00 1596
3 TraesCS1B01G082000 chr2D 95.252 1011 43 4 1 1007 47472278 47471269 0.000000e+00 1596
4 TraesCS1B01G082000 chr2D 95.248 1010 45 3 1 1007 178661831 178660822 0.000000e+00 1596
5 TraesCS1B01G082000 chr2D 95.134 1007 46 2 1 1004 101399117 101398111 0.000000e+00 1585
6 TraesCS1B01G082000 chr7D 95.134 1007 46 2 1 1004 194545310 194546316 0.000000e+00 1585
7 TraesCS1B01G082000 chr7D 92.273 880 52 7 1349 2219 446112647 446113519 0.000000e+00 1234
8 TraesCS1B01G082000 chr6D 94.950 1010 48 2 1 1007 270489964 270488955 0.000000e+00 1580
9 TraesCS1B01G082000 chr6D 95.035 1007 44 3 1 1004 363171145 363172148 0.000000e+00 1578
10 TraesCS1B01G082000 chr6B 94.950 1010 45 3 1 1007 178701874 178700868 0.000000e+00 1578
11 TraesCS1B01G082000 chr6B 92.343 875 57 5 1355 2219 40468363 40467489 0.000000e+00 1236
12 TraesCS1B01G082000 chr6B 92.343 875 56 7 1355 2219 284565671 284564798 0.000000e+00 1234
13 TraesCS1B01G082000 chr6B 92.229 875 57 7 1355 2219 569957176 569956303 0.000000e+00 1229
14 TraesCS1B01G082000 chr1D 94.851 1010 49 2 1 1007 349140835 349141844 0.000000e+00 1574
15 TraesCS1B01G082000 chr1D 97.436 351 9 0 1004 1354 254499299 254499649 1.130000e-167 599
16 TraesCS1B01G082000 chr7B 92.168 881 59 6 1349 2219 199443017 199443897 0.000000e+00 1236
17 TraesCS1B01G082000 chr5B 92.334 874 57 5 1356 2219 216540872 216541745 0.000000e+00 1234
18 TraesCS1B01G082000 chr2B 92.343 875 54 7 1355 2219 621122885 621122014 0.000000e+00 1232
19 TraesCS1B01G082000 chr5D 92.114 875 59 5 1355 2219 42395855 42394981 0.000000e+00 1225
20 TraesCS1B01G082000 chr5D 98.291 351 6 0 1004 1354 560873769 560874119 1.130000e-172 616
21 TraesCS1B01G082000 chr5D 97.708 349 8 0 1004 1352 6199981 6199633 3.150000e-168 601
22 TraesCS1B01G082000 chr5D 97.443 352 7 2 1004 1354 329163478 329163828 1.130000e-167 599
23 TraesCS1B01G082000 chr3B 97.721 351 8 0 1004 1354 201515981 201516331 2.440000e-169 604
24 TraesCS1B01G082000 chr1A 96.581 351 11 1 1004 1354 168449269 168448920 4.110000e-162 580
25 TraesCS1B01G082000 chr4D 96.011 351 14 0 1004 1354 19917794 19918144 2.470000e-159 571
26 TraesCS1B01G082000 chr7A 95.157 351 16 1 1004 1354 352192724 352192375 8.950000e-154 553
27 TraesCS1B01G082000 chrUn 98.403 313 5 0 1004 1316 30306050 30305738 3.220000e-153 551


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 TraesCS1B01G082000 chr1B 65449265 65451483 2218 False 4098 4098 100.000 1 2219 1 chr1B.!!$F1 2218
1 TraesCS1B01G082000 chr1B 446774964 446775837 873 True 1240 1240 92.449 1355 2219 1 chr1B.!!$R1 864
2 TraesCS1B01G082000 chr4B 513153638 513154646 1008 True 1596 1596 95.248 1 1007 1 chr4B.!!$R1 1006
3 TraesCS1B01G082000 chr2D 47471269 47472278 1009 True 1596 1596 95.252 1 1007 1 chr2D.!!$R1 1006
4 TraesCS1B01G082000 chr2D 178660822 178661831 1009 True 1596 1596 95.248 1 1007 1 chr2D.!!$R3 1006
5 TraesCS1B01G082000 chr2D 101398111 101399117 1006 True 1585 1585 95.134 1 1004 1 chr2D.!!$R2 1003
6 TraesCS1B01G082000 chr7D 194545310 194546316 1006 False 1585 1585 95.134 1 1004 1 chr7D.!!$F1 1003
7 TraesCS1B01G082000 chr7D 446112647 446113519 872 False 1234 1234 92.273 1349 2219 1 chr7D.!!$F2 870
8 TraesCS1B01G082000 chr6D 270488955 270489964 1009 True 1580 1580 94.950 1 1007 1 chr6D.!!$R1 1006
9 TraesCS1B01G082000 chr6D 363171145 363172148 1003 False 1578 1578 95.035 1 1004 1 chr6D.!!$F1 1003
10 TraesCS1B01G082000 chr6B 178700868 178701874 1006 True 1578 1578 94.950 1 1007 1 chr6B.!!$R2 1006
11 TraesCS1B01G082000 chr6B 40467489 40468363 874 True 1236 1236 92.343 1355 2219 1 chr6B.!!$R1 864
12 TraesCS1B01G082000 chr6B 284564798 284565671 873 True 1234 1234 92.343 1355 2219 1 chr6B.!!$R3 864
13 TraesCS1B01G082000 chr6B 569956303 569957176 873 True 1229 1229 92.229 1355 2219 1 chr6B.!!$R4 864
14 TraesCS1B01G082000 chr1D 349140835 349141844 1009 False 1574 1574 94.851 1 1007 1 chr1D.!!$F2 1006
15 TraesCS1B01G082000 chr7B 199443017 199443897 880 False 1236 1236 92.168 1349 2219 1 chr7B.!!$F1 870
16 TraesCS1B01G082000 chr5B 216540872 216541745 873 False 1234 1234 92.334 1356 2219 1 chr5B.!!$F1 863
17 TraesCS1B01G082000 chr2B 621122014 621122885 871 True 1232 1232 92.343 1355 2219 1 chr2B.!!$R1 864
18 TraesCS1B01G082000 chr5D 42394981 42395855 874 True 1225 1225 92.114 1355 2219 1 chr5D.!!$R2 864

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
452 456 4.804597 AGCTCAAAAAGAGGGTTAAACCT 58.195 39.13 13.26 13.26 44.86 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1300 1307 0.10104 CCGCGGTCGAACTACCATAA 59.899 55.0 19.5 0.0 39.71 1.9 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
452 456 4.804597 AGCTCAAAAAGAGGGTTAAACCT 58.195 39.130 13.26 13.26 44.86 3.50
467 471 6.377146 GGGTTAAACCTACACATGATGTGAAT 59.623 38.462 30.26 12.77 43.79 2.57
482 489 9.784680 CATGATGTGAATAAGAGAAAGAAAAGG 57.215 33.333 0.00 0.00 0.00 3.11
512 519 5.286221 AGCAAAGGTAGAAAGGTATCCCTA 58.714 41.667 0.00 0.00 41.56 3.53
549 556 7.512130 TGCTCCTATTACTCATTGTGATGATT 58.488 34.615 0.00 0.00 41.28 2.57
725 732 5.827797 TGGGGATGCTATGTTTAATGAAGAC 59.172 40.000 0.00 0.00 0.00 3.01
777 784 9.999009 ATGAGCAAATTTATTATGATGATAGCG 57.001 29.630 0.00 0.00 0.00 4.26
805 812 9.125026 GCCTCCTATTTATGATGGTTATATTGG 57.875 37.037 0.00 0.00 0.00 3.16
817 824 5.258051 TGGTTATATTGGTGAAAGTGGGTC 58.742 41.667 0.00 0.00 0.00 4.46
848 855 8.091449 AGAGTGTCAACTTTAGGAAGTAATGAG 58.909 37.037 0.00 0.00 45.18 2.90
930 937 8.116753 CGGTCATGACTTTATTTAGTGATGAAC 58.883 37.037 24.50 10.08 45.80 3.18
937 944 8.788325 ACTTTATTTAGTGATGAACCCACTAC 57.212 34.615 0.00 0.00 44.13 2.73
961 968 7.212274 ACTTTGGAAGAGGTTTCAATTGATTG 58.788 34.615 9.40 0.00 39.10 2.67
1017 1024 3.684103 GTGATGACACAAACCGTTGAA 57.316 42.857 0.00 0.00 45.32 2.69
1018 1025 3.617669 GTGATGACACAAACCGTTGAAG 58.382 45.455 0.00 0.00 45.32 3.02
1019 1026 3.311322 GTGATGACACAAACCGTTGAAGA 59.689 43.478 0.00 0.00 45.32 2.87
1020 1027 4.024048 GTGATGACACAAACCGTTGAAGAT 60.024 41.667 0.00 0.00 45.32 2.40
1021 1028 5.178623 GTGATGACACAAACCGTTGAAGATA 59.821 40.000 0.00 0.00 45.32 1.98
1022 1029 5.408299 TGATGACACAAACCGTTGAAGATAG 59.592 40.000 0.00 0.00 38.20 2.08
1023 1030 4.699637 TGACACAAACCGTTGAAGATAGT 58.300 39.130 0.00 0.00 38.20 2.12
1024 1031 5.120399 TGACACAAACCGTTGAAGATAGTT 58.880 37.500 0.00 0.00 38.20 2.24
1025 1032 5.235616 TGACACAAACCGTTGAAGATAGTTC 59.764 40.000 0.00 0.00 38.20 3.01
1026 1033 5.365619 ACACAAACCGTTGAAGATAGTTCT 58.634 37.500 0.00 0.00 38.20 3.01
1027 1034 6.518493 ACACAAACCGTTGAAGATAGTTCTA 58.482 36.000 0.00 0.00 38.20 2.10
1028 1035 6.987992 ACACAAACCGTTGAAGATAGTTCTAA 59.012 34.615 0.00 0.00 38.20 2.10
1029 1036 7.496591 ACACAAACCGTTGAAGATAGTTCTAAA 59.503 33.333 0.00 0.00 38.20 1.85
1030 1037 7.797123 CACAAACCGTTGAAGATAGTTCTAAAC 59.203 37.037 0.00 0.00 38.20 2.01
1031 1038 7.041576 ACAAACCGTTGAAGATAGTTCTAAACC 60.042 37.037 0.00 0.00 38.20 3.27
1032 1039 6.356186 ACCGTTGAAGATAGTTCTAAACCT 57.644 37.500 0.00 0.00 30.38 3.50
1033 1040 7.472334 ACCGTTGAAGATAGTTCTAAACCTA 57.528 36.000 0.00 0.00 30.38 3.08
1034 1041 7.545489 ACCGTTGAAGATAGTTCTAAACCTAG 58.455 38.462 0.00 0.00 30.38 3.02
1035 1042 6.979238 CCGTTGAAGATAGTTCTAAACCTAGG 59.021 42.308 7.41 7.41 30.38 3.02
1036 1043 6.476053 CGTTGAAGATAGTTCTAAACCTAGGC 59.524 42.308 9.30 0.00 30.38 3.93
1037 1044 6.481434 TGAAGATAGTTCTAAACCTAGGCC 57.519 41.667 9.30 0.00 0.00 5.19
1038 1045 5.962031 TGAAGATAGTTCTAAACCTAGGCCA 59.038 40.000 9.30 0.00 0.00 5.36
1039 1046 6.442564 TGAAGATAGTTCTAAACCTAGGCCAA 59.557 38.462 9.30 0.00 0.00 4.52
1040 1047 6.886178 AGATAGTTCTAAACCTAGGCCAAA 57.114 37.500 9.30 0.00 0.00 3.28
1041 1048 7.266905 AGATAGTTCTAAACCTAGGCCAAAA 57.733 36.000 9.30 0.00 0.00 2.44
1042 1049 7.110810 AGATAGTTCTAAACCTAGGCCAAAAC 58.889 38.462 9.30 7.54 0.00 2.43
1043 1050 5.056553 AGTTCTAAACCTAGGCCAAAACA 57.943 39.130 9.30 0.00 0.00 2.83
1044 1051 5.451354 AGTTCTAAACCTAGGCCAAAACAA 58.549 37.500 9.30 0.00 0.00 2.83
1045 1052 5.894964 AGTTCTAAACCTAGGCCAAAACAAA 59.105 36.000 9.30 0.00 0.00 2.83
1046 1053 5.777850 TCTAAACCTAGGCCAAAACAAAC 57.222 39.130 9.30 0.00 0.00 2.93
1047 1054 5.451354 TCTAAACCTAGGCCAAAACAAACT 58.549 37.500 9.30 0.00 0.00 2.66
1048 1055 4.400529 AAACCTAGGCCAAAACAAACTG 57.599 40.909 9.30 0.00 0.00 3.16
1049 1056 2.316108 ACCTAGGCCAAAACAAACTGG 58.684 47.619 9.30 0.00 35.67 4.00
1050 1057 2.316108 CCTAGGCCAAAACAAACTGGT 58.684 47.619 5.01 0.00 34.97 4.00
1051 1058 2.035832 CCTAGGCCAAAACAAACTGGTG 59.964 50.000 5.01 0.00 34.97 4.17
1052 1059 1.567357 AGGCCAAAACAAACTGGTGT 58.433 45.000 5.01 0.00 34.97 4.16
1053 1060 2.741145 AGGCCAAAACAAACTGGTGTA 58.259 42.857 5.01 0.00 34.97 2.90
1054 1061 2.693074 AGGCCAAAACAAACTGGTGTAG 59.307 45.455 5.01 0.00 34.97 2.74
1055 1062 2.223947 GGCCAAAACAAACTGGTGTAGG 60.224 50.000 0.00 0.00 34.97 3.18
1056 1063 2.429250 GCCAAAACAAACTGGTGTAGGT 59.571 45.455 0.00 0.00 34.97 3.08
1057 1064 3.633065 GCCAAAACAAACTGGTGTAGGTA 59.367 43.478 0.00 0.00 34.97 3.08
1058 1065 4.261447 GCCAAAACAAACTGGTGTAGGTAG 60.261 45.833 0.00 0.00 34.97 3.18
1059 1066 4.885325 CCAAAACAAACTGGTGTAGGTAGT 59.115 41.667 0.00 0.00 0.00 2.73
1060 1067 5.358725 CCAAAACAAACTGGTGTAGGTAGTT 59.641 40.000 0.00 0.00 36.29 2.24
1061 1068 6.127563 CCAAAACAAACTGGTGTAGGTAGTTT 60.128 38.462 0.00 0.00 43.30 2.66
1062 1069 7.067251 CCAAAACAAACTGGTGTAGGTAGTTTA 59.933 37.037 0.00 0.00 41.30 2.01
1063 1070 7.558161 AAACAAACTGGTGTAGGTAGTTTAC 57.442 36.000 0.00 0.00 41.30 2.01
1064 1071 6.490241 ACAAACTGGTGTAGGTAGTTTACT 57.510 37.500 0.00 0.00 41.30 2.24
1065 1072 6.285990 ACAAACTGGTGTAGGTAGTTTACTG 58.714 40.000 0.00 0.00 41.30 2.74
1066 1073 6.098695 ACAAACTGGTGTAGGTAGTTTACTGA 59.901 38.462 0.00 0.00 41.30 3.41
1067 1074 6.736110 AACTGGTGTAGGTAGTTTACTGAA 57.264 37.500 0.00 0.00 30.98 3.02
1068 1075 6.736110 ACTGGTGTAGGTAGTTTACTGAAA 57.264 37.500 0.00 0.00 0.00 2.69
1069 1076 6.519382 ACTGGTGTAGGTAGTTTACTGAAAC 58.481 40.000 0.00 0.00 44.56 2.78
1070 1077 5.857268 TGGTGTAGGTAGTTTACTGAAACC 58.143 41.667 0.00 0.00 45.21 3.27
1071 1078 5.221702 TGGTGTAGGTAGTTTACTGAAACCC 60.222 44.000 0.00 0.00 45.21 4.11
1072 1079 5.012458 GGTGTAGGTAGTTTACTGAAACCCT 59.988 44.000 0.00 1.40 45.21 4.34
1073 1080 6.464892 GGTGTAGGTAGTTTACTGAAACCCTT 60.465 42.308 4.41 0.00 45.21 3.95
1074 1081 6.426025 GTGTAGGTAGTTTACTGAAACCCTTG 59.574 42.308 4.41 0.00 45.21 3.61
1075 1082 5.899631 AGGTAGTTTACTGAAACCCTTGA 57.100 39.130 0.00 0.00 45.21 3.02
1076 1083 6.256643 AGGTAGTTTACTGAAACCCTTGAA 57.743 37.500 0.00 0.00 45.21 2.69
1077 1084 6.849151 AGGTAGTTTACTGAAACCCTTGAAT 58.151 36.000 0.00 0.00 45.21 2.57
1078 1085 7.295340 AGGTAGTTTACTGAAACCCTTGAATT 58.705 34.615 0.00 0.00 45.21 2.17
1079 1086 7.447545 AGGTAGTTTACTGAAACCCTTGAATTC 59.552 37.037 0.00 0.00 45.21 2.17
1080 1087 6.313744 AGTTTACTGAAACCCTTGAATTCG 57.686 37.500 0.04 0.00 45.21 3.34
1081 1088 5.240844 AGTTTACTGAAACCCTTGAATTCGG 59.759 40.000 0.04 0.00 45.21 4.30
1082 1089 3.502123 ACTGAAACCCTTGAATTCGGA 57.498 42.857 5.02 0.00 34.34 4.55
1083 1090 3.827722 ACTGAAACCCTTGAATTCGGAA 58.172 40.909 5.02 0.00 34.34 4.30
1084 1091 4.407365 ACTGAAACCCTTGAATTCGGAAT 58.593 39.130 5.02 0.00 34.34 3.01
1085 1092 5.566469 ACTGAAACCCTTGAATTCGGAATA 58.434 37.500 3.22 0.00 34.34 1.75
1086 1093 6.187682 ACTGAAACCCTTGAATTCGGAATAT 58.812 36.000 3.22 0.00 34.34 1.28
1087 1094 6.095440 ACTGAAACCCTTGAATTCGGAATATG 59.905 38.462 3.22 0.00 34.34 1.78
1088 1095 5.359576 TGAAACCCTTGAATTCGGAATATGG 59.640 40.000 3.22 1.62 0.00 2.74
1089 1096 3.832527 ACCCTTGAATTCGGAATATGGG 58.167 45.455 17.00 17.00 38.13 4.00
1090 1097 3.461831 ACCCTTGAATTCGGAATATGGGA 59.538 43.478 22.13 3.15 36.20 4.37
1091 1098 4.079443 ACCCTTGAATTCGGAATATGGGAA 60.079 41.667 22.13 5.89 36.20 3.97
1092 1099 4.892934 CCCTTGAATTCGGAATATGGGAAA 59.107 41.667 14.85 1.30 34.34 3.13
1093 1100 5.010012 CCCTTGAATTCGGAATATGGGAAAG 59.990 44.000 14.85 8.35 34.34 2.62
1094 1101 5.594317 CCTTGAATTCGGAATATGGGAAAGT 59.406 40.000 3.22 0.00 0.00 2.66
1095 1102 6.238759 CCTTGAATTCGGAATATGGGAAAGTC 60.239 42.308 3.22 0.00 0.00 3.01
1096 1103 4.814234 TGAATTCGGAATATGGGAAAGTCG 59.186 41.667 3.22 0.00 0.00 4.18
1097 1104 2.234300 TCGGAATATGGGAAAGTCGC 57.766 50.000 0.00 0.00 0.00 5.19
1098 1105 1.202604 TCGGAATATGGGAAAGTCGCC 60.203 52.381 0.00 0.00 0.00 5.54
1099 1106 1.605753 GGAATATGGGAAAGTCGCCC 58.394 55.000 0.00 0.00 46.22 6.13
1100 1107 1.605753 GAATATGGGAAAGTCGCCCC 58.394 55.000 0.00 0.00 45.40 5.80
1101 1108 0.179029 AATATGGGAAAGTCGCCCCG 60.179 55.000 0.00 0.00 45.40 5.73
1102 1109 2.052047 ATATGGGAAAGTCGCCCCGG 62.052 60.000 0.00 0.00 45.40 5.73
1105 1112 4.340246 GGAAAGTCGCCCCGGGTT 62.340 66.667 21.85 5.43 0.00 4.11
1106 1113 3.053896 GAAAGTCGCCCCGGGTTG 61.054 66.667 21.85 11.70 0.00 3.77
1107 1114 4.653888 AAAGTCGCCCCGGGTTGG 62.654 66.667 21.85 8.14 37.55 3.77
1116 1123 2.285144 CCGGGTTGGGGGACTACT 60.285 66.667 0.00 0.00 0.00 2.57
1117 1124 2.364780 CCGGGTTGGGGGACTACTC 61.365 68.421 0.00 0.00 0.00 2.59
1118 1125 2.364780 CGGGTTGGGGGACTACTCC 61.365 68.421 0.00 0.00 35.54 3.85
1119 1126 1.082392 GGGTTGGGGGACTACTCCT 59.918 63.158 0.00 0.00 36.76 3.69
1120 1127 0.549413 GGGTTGGGGGACTACTCCTT 60.549 60.000 0.00 0.00 36.76 3.36
1121 1128 1.369403 GGTTGGGGGACTACTCCTTT 58.631 55.000 0.00 0.00 36.76 3.11
1122 1129 1.709115 GGTTGGGGGACTACTCCTTTT 59.291 52.381 0.00 0.00 36.76 2.27
1123 1130 2.914941 GGTTGGGGGACTACTCCTTTTA 59.085 50.000 0.00 0.00 36.76 1.52
1124 1131 3.526430 GGTTGGGGGACTACTCCTTTTAT 59.474 47.826 0.00 0.00 36.76 1.40
1125 1132 4.524053 GTTGGGGGACTACTCCTTTTATG 58.476 47.826 0.00 0.00 36.76 1.90
1126 1133 3.120108 TGGGGGACTACTCCTTTTATGG 58.880 50.000 0.00 0.00 36.76 2.74
1127 1134 2.442126 GGGGGACTACTCCTTTTATGGG 59.558 54.545 0.00 0.00 36.76 4.00
1128 1135 2.442126 GGGGACTACTCCTTTTATGGGG 59.558 54.545 0.00 0.00 36.68 4.96
1129 1136 3.120898 GGGACTACTCCTTTTATGGGGT 58.879 50.000 0.00 0.00 44.25 4.95
1130 1137 3.526430 GGGACTACTCCTTTTATGGGGTT 59.474 47.826 0.00 0.00 37.59 4.11
1131 1138 4.384978 GGGACTACTCCTTTTATGGGGTTC 60.385 50.000 0.00 0.00 37.59 3.62
1132 1139 4.439968 GACTACTCCTTTTATGGGGTTCG 58.560 47.826 0.00 0.00 37.59 3.95
1133 1140 2.124277 ACTCCTTTTATGGGGTTCGC 57.876 50.000 0.00 0.00 37.59 4.70
1134 1141 1.353022 ACTCCTTTTATGGGGTTCGCA 59.647 47.619 0.00 0.00 37.59 5.10
1135 1142 2.224917 ACTCCTTTTATGGGGTTCGCAA 60.225 45.455 0.00 0.00 37.59 4.85
1136 1143 3.023832 CTCCTTTTATGGGGTTCGCAAT 58.976 45.455 0.00 0.00 0.00 3.56
1137 1144 2.757868 TCCTTTTATGGGGTTCGCAATG 59.242 45.455 0.00 0.00 0.00 2.82
1138 1145 2.159114 CCTTTTATGGGGTTCGCAATGG 60.159 50.000 0.00 0.00 0.00 3.16
1139 1146 0.820871 TTTATGGGGTTCGCAATGGC 59.179 50.000 0.00 0.00 0.00 4.40
1140 1147 0.033601 TTATGGGGTTCGCAATGGCT 60.034 50.000 0.00 0.00 38.10 4.75
1141 1148 0.033601 TATGGGGTTCGCAATGGCTT 60.034 50.000 0.00 0.00 38.10 4.35
1142 1149 0.904394 ATGGGGTTCGCAATGGCTTT 60.904 50.000 0.00 0.00 38.10 3.51
1143 1150 0.251386 TGGGGTTCGCAATGGCTTTA 60.251 50.000 0.00 0.00 38.10 1.85
1144 1151 1.111277 GGGGTTCGCAATGGCTTTAT 58.889 50.000 0.00 0.00 38.10 1.40
1145 1152 1.480545 GGGGTTCGCAATGGCTTTATT 59.519 47.619 0.00 0.00 38.10 1.40
1146 1153 2.481276 GGGGTTCGCAATGGCTTTATTC 60.481 50.000 0.00 0.00 38.10 1.75
1147 1154 2.450160 GGTTCGCAATGGCTTTATTCG 58.550 47.619 0.00 0.00 38.10 3.34
1148 1155 1.846175 GTTCGCAATGGCTTTATTCGC 59.154 47.619 0.00 0.00 38.10 4.70
1149 1156 1.378531 TCGCAATGGCTTTATTCGCT 58.621 45.000 0.00 0.00 38.10 4.93
1150 1157 2.556257 TCGCAATGGCTTTATTCGCTA 58.444 42.857 0.00 0.00 38.10 4.26
1151 1158 3.138304 TCGCAATGGCTTTATTCGCTAT 58.862 40.909 0.00 0.00 38.10 2.97
1152 1159 4.311606 TCGCAATGGCTTTATTCGCTATA 58.688 39.130 0.00 0.00 38.10 1.31
1153 1160 4.935205 TCGCAATGGCTTTATTCGCTATAT 59.065 37.500 0.00 0.00 38.10 0.86
1154 1161 5.411361 TCGCAATGGCTTTATTCGCTATATT 59.589 36.000 0.00 0.00 38.10 1.28
1155 1162 5.734498 CGCAATGGCTTTATTCGCTATATTC 59.266 40.000 0.00 0.00 38.10 1.75
1156 1163 6.030228 GCAATGGCTTTATTCGCTATATTCC 58.970 40.000 0.00 0.00 36.96 3.01
1157 1164 6.127897 GCAATGGCTTTATTCGCTATATTCCT 60.128 38.462 0.00 0.00 36.96 3.36
1158 1165 7.065803 GCAATGGCTTTATTCGCTATATTCCTA 59.934 37.037 0.00 0.00 36.96 2.94
1159 1166 9.113838 CAATGGCTTTATTCGCTATATTCCTAT 57.886 33.333 0.00 0.00 0.00 2.57
1160 1167 8.894768 ATGGCTTTATTCGCTATATTCCTATC 57.105 34.615 0.00 0.00 0.00 2.08
1161 1168 8.079211 TGGCTTTATTCGCTATATTCCTATCT 57.921 34.615 0.00 0.00 0.00 1.98
1162 1169 9.197306 TGGCTTTATTCGCTATATTCCTATCTA 57.803 33.333 0.00 0.00 0.00 1.98
1201 1208 6.657836 ATAATTCTTCCGTTTTACTGGACG 57.342 37.500 0.00 0.00 38.90 4.79
1202 1209 3.731652 TTCTTCCGTTTTACTGGACGA 57.268 42.857 0.00 0.00 41.53 4.20
1203 1210 3.731652 TCTTCCGTTTTACTGGACGAA 57.268 42.857 0.00 0.00 41.53 3.85
1204 1211 4.057406 TCTTCCGTTTTACTGGACGAAA 57.943 40.909 0.00 0.00 41.53 3.46
1205 1212 4.634199 TCTTCCGTTTTACTGGACGAAAT 58.366 39.130 0.00 0.00 41.53 2.17
1206 1213 5.058490 TCTTCCGTTTTACTGGACGAAATT 58.942 37.500 0.00 0.00 41.53 1.82
1207 1214 5.528320 TCTTCCGTTTTACTGGACGAAATTT 59.472 36.000 0.00 0.00 41.53 1.82
1208 1215 5.754543 TCCGTTTTACTGGACGAAATTTT 57.245 34.783 0.00 0.00 41.53 1.82
1209 1216 6.857777 TCCGTTTTACTGGACGAAATTTTA 57.142 33.333 0.00 0.00 41.53 1.52
1210 1217 7.256756 TCCGTTTTACTGGACGAAATTTTAA 57.743 32.000 0.00 0.00 41.53 1.52
1211 1218 7.131565 TCCGTTTTACTGGACGAAATTTTAAC 58.868 34.615 0.00 0.00 41.53 2.01
1212 1219 6.360414 CCGTTTTACTGGACGAAATTTTAACC 59.640 38.462 0.00 0.00 41.53 2.85
1213 1220 6.911511 CGTTTTACTGGACGAAATTTTAACCA 59.088 34.615 0.00 1.93 41.53 3.67
1214 1221 7.431668 CGTTTTACTGGACGAAATTTTAACCAA 59.568 33.333 10.66 0.00 41.53 3.67
1215 1222 9.251792 GTTTTACTGGACGAAATTTTAACCAAT 57.748 29.630 10.66 5.59 0.00 3.16
1216 1223 9.819267 TTTTACTGGACGAAATTTTAACCAATT 57.181 25.926 10.66 5.63 0.00 2.32
1219 1226 7.599171 ACTGGACGAAATTTTAACCAATTAGG 58.401 34.615 10.66 0.00 45.67 2.69
1250 1257 8.709272 ACTAACTAAAACTAGGAAGTCAGAGT 57.291 34.615 0.00 0.00 33.75 3.24
1251 1258 9.145442 ACTAACTAAAACTAGGAAGTCAGAGTT 57.855 33.333 0.00 0.00 35.93 3.01
1252 1259 9.984190 CTAACTAAAACTAGGAAGTCAGAGTTT 57.016 33.333 0.00 4.73 42.45 2.66
1254 1261 9.682465 AACTAAAACTAGGAAGTCAGAGTTTTT 57.318 29.630 19.35 7.56 45.30 1.94
1255 1262 9.327628 ACTAAAACTAGGAAGTCAGAGTTTTTC 57.672 33.333 19.35 0.00 45.30 2.29
1256 1263 7.569639 AAAACTAGGAAGTCAGAGTTTTTCC 57.430 36.000 12.99 0.00 45.30 3.13
1257 1264 5.888982 ACTAGGAAGTCAGAGTTTTTCCA 57.111 39.130 5.07 0.00 41.19 3.53
1258 1265 6.441088 ACTAGGAAGTCAGAGTTTTTCCAT 57.559 37.500 5.07 0.00 41.19 3.41
1259 1266 6.468543 ACTAGGAAGTCAGAGTTTTTCCATC 58.531 40.000 5.07 0.00 41.19 3.51
1260 1267 4.657013 AGGAAGTCAGAGTTTTTCCATCC 58.343 43.478 5.07 0.00 41.19 3.51
1261 1268 4.104738 AGGAAGTCAGAGTTTTTCCATCCA 59.895 41.667 5.07 0.00 41.19 3.41
1262 1269 4.827284 GGAAGTCAGAGTTTTTCCATCCAA 59.173 41.667 0.00 0.00 39.09 3.53
1263 1270 5.301805 GGAAGTCAGAGTTTTTCCATCCAAA 59.698 40.000 0.00 0.00 39.09 3.28
1264 1271 6.183360 GGAAGTCAGAGTTTTTCCATCCAAAA 60.183 38.462 0.00 0.00 39.09 2.44
1265 1272 6.790232 AGTCAGAGTTTTTCCATCCAAAAA 57.210 33.333 0.00 0.00 33.72 1.94
1316 1323 7.606858 TCTAGATATTATGGTAGTTCGACCG 57.393 40.000 0.00 0.00 42.99 4.79
1317 1324 5.056894 AGATATTATGGTAGTTCGACCGC 57.943 43.478 0.00 0.00 42.99 5.68
1318 1325 2.129823 ATTATGGTAGTTCGACCGCG 57.870 50.000 0.00 0.00 42.99 6.46
1319 1326 0.101040 TTATGGTAGTTCGACCGCGG 59.899 55.000 26.86 26.86 42.99 6.46
1320 1327 0.747644 TATGGTAGTTCGACCGCGGA 60.748 55.000 35.90 6.51 42.99 5.54
1321 1328 1.597797 ATGGTAGTTCGACCGCGGAA 61.598 55.000 35.90 13.88 42.99 4.30
1322 1329 1.140375 GGTAGTTCGACCGCGGAAT 59.860 57.895 35.90 11.07 38.28 3.01
1323 1330 0.459063 GGTAGTTCGACCGCGGAATT 60.459 55.000 35.90 15.36 38.28 2.17
1324 1331 1.353076 GTAGTTCGACCGCGGAATTT 58.647 50.000 35.90 9.58 38.28 1.82
1325 1332 1.728425 GTAGTTCGACCGCGGAATTTT 59.272 47.619 35.90 9.07 38.28 1.82
1326 1333 1.232119 AGTTCGACCGCGGAATTTTT 58.768 45.000 35.90 8.10 38.28 1.94
1349 1356 8.801882 TTTTTGTTTCGGTATCTCTGGAATAT 57.198 30.769 0.00 0.00 0.00 1.28
1350 1357 7.786178 TTTGTTTCGGTATCTCTGGAATATG 57.214 36.000 0.00 0.00 0.00 1.78
1351 1358 6.724893 TGTTTCGGTATCTCTGGAATATGA 57.275 37.500 0.00 0.00 0.00 2.15
1352 1359 6.749139 TGTTTCGGTATCTCTGGAATATGAG 58.251 40.000 0.00 0.00 0.00 2.90
1353 1360 6.323996 TGTTTCGGTATCTCTGGAATATGAGT 59.676 38.462 0.00 0.00 0.00 3.41
1576 1587 6.884280 AATGCTTTAGGTGCTGGTTATATC 57.116 37.500 0.00 0.00 0.00 1.63
1684 1695 8.017946 CCTCTCTATGTGCTTAAAGTTTTGAAC 58.982 37.037 0.00 0.00 0.00 3.18
1756 1767 6.719370 AGTTGTTTGCTCACAAAATCCCTATA 59.281 34.615 3.21 0.00 46.94 1.31
1889 1913 0.031178 AAGGCAGAAAAGCGCTTGTG 59.969 50.000 25.80 21.29 34.64 3.33
2005 2029 2.683362 GTGCCATGTAAGACCTTTAGGC 59.317 50.000 0.00 0.00 41.15 3.93
2138 2162 6.127479 TGCTATGGATTGGTACACAAATTTCC 60.127 38.462 0.00 2.36 43.46 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
320 323 8.919145 TCTCTTCCCTTTCATTAGTATTCTCTC 58.081 37.037 0.00 0.00 0.00 3.20
467 471 4.884668 TCTCCGCCTTTTCTTTCTCTTA 57.115 40.909 0.00 0.00 0.00 2.10
472 476 1.880027 TGCTTCTCCGCCTTTTCTTTC 59.120 47.619 0.00 0.00 0.00 2.62
482 489 2.094762 TTCTACCTTTGCTTCTCCGC 57.905 50.000 0.00 0.00 0.00 5.54
512 519 6.426587 AGTAATAGGAGCAACATCATTTGGT 58.573 36.000 0.00 0.00 39.89 3.67
725 732 6.451064 AAACTTGGGAGGCTAAAAATATCG 57.549 37.500 0.00 0.00 0.00 2.92
777 784 9.686683 AATATAACCATCATAAATAGGAGGCAC 57.313 33.333 0.00 0.00 0.00 5.01
805 812 2.104963 ACTCTTCCAGACCCACTTTCAC 59.895 50.000 0.00 0.00 0.00 3.18
817 824 5.215252 TCCTAAAGTTGACACTCTTCCAG 57.785 43.478 0.00 0.00 30.45 3.86
848 855 1.272480 ACACCCTCCAAAATAGTGGGC 60.272 52.381 0.00 0.00 40.98 5.36
904 911 7.770801 TCATCACTAAATAAAGTCATGACCG 57.229 36.000 22.21 3.81 32.76 4.79
930 937 3.790089 AACCTCTTCCAAAGTAGTGGG 57.210 47.619 0.00 0.00 39.34 4.61
937 944 7.170320 CACAATCAATTGAAACCTCTTCCAAAG 59.830 37.037 13.09 0.00 40.14 2.77
961 968 5.931441 AGTAGCAACTTTGTTCTCATCAC 57.069 39.130 0.00 0.00 29.00 3.06
1007 1014 7.222161 AGGTTTAGAACTATCTTCAACGGTTT 58.778 34.615 0.00 0.00 37.10 3.27
1008 1015 6.766429 AGGTTTAGAACTATCTTCAACGGTT 58.234 36.000 0.00 0.00 37.10 4.44
1009 1016 6.356186 AGGTTTAGAACTATCTTCAACGGT 57.644 37.500 0.00 0.00 37.10 4.83
1010 1017 6.979238 CCTAGGTTTAGAACTATCTTCAACGG 59.021 42.308 0.00 0.00 37.10 4.44
1011 1018 6.476053 GCCTAGGTTTAGAACTATCTTCAACG 59.524 42.308 11.31 0.00 37.10 4.10
1012 1019 6.762187 GGCCTAGGTTTAGAACTATCTTCAAC 59.238 42.308 11.31 0.00 37.10 3.18
1013 1020 6.442564 TGGCCTAGGTTTAGAACTATCTTCAA 59.557 38.462 11.31 0.00 37.10 2.69
1014 1021 5.962031 TGGCCTAGGTTTAGAACTATCTTCA 59.038 40.000 11.31 0.00 37.10 3.02
1015 1022 6.481434 TGGCCTAGGTTTAGAACTATCTTC 57.519 41.667 11.31 0.00 37.10 2.87
1016 1023 6.886178 TTGGCCTAGGTTTAGAACTATCTT 57.114 37.500 11.31 0.00 37.10 2.40
1017 1024 6.886178 TTTGGCCTAGGTTTAGAACTATCT 57.114 37.500 11.31 0.00 39.82 1.98
1018 1025 6.882678 TGTTTTGGCCTAGGTTTAGAACTATC 59.117 38.462 11.31 0.00 0.00 2.08
1019 1026 6.786122 TGTTTTGGCCTAGGTTTAGAACTAT 58.214 36.000 11.31 0.00 0.00 2.12
1020 1027 6.190346 TGTTTTGGCCTAGGTTTAGAACTA 57.810 37.500 11.31 0.00 0.00 2.24
1021 1028 5.056553 TGTTTTGGCCTAGGTTTAGAACT 57.943 39.130 11.31 0.00 0.00 3.01
1022 1029 5.777850 TTGTTTTGGCCTAGGTTTAGAAC 57.222 39.130 11.31 9.85 0.00 3.01
1023 1030 5.894964 AGTTTGTTTTGGCCTAGGTTTAGAA 59.105 36.000 11.31 0.00 0.00 2.10
1024 1031 5.300792 CAGTTTGTTTTGGCCTAGGTTTAGA 59.699 40.000 11.31 0.00 0.00 2.10
1025 1032 5.508994 CCAGTTTGTTTTGGCCTAGGTTTAG 60.509 44.000 11.31 0.00 0.00 1.85
1026 1033 4.342665 CCAGTTTGTTTTGGCCTAGGTTTA 59.657 41.667 11.31 0.00 0.00 2.01
1027 1034 3.133901 CCAGTTTGTTTTGGCCTAGGTTT 59.866 43.478 11.31 0.00 0.00 3.27
1028 1035 2.698274 CCAGTTTGTTTTGGCCTAGGTT 59.302 45.455 11.31 0.00 0.00 3.50
1029 1036 2.316108 CCAGTTTGTTTTGGCCTAGGT 58.684 47.619 11.31 0.00 0.00 3.08
1030 1037 2.035832 CACCAGTTTGTTTTGGCCTAGG 59.964 50.000 3.67 3.67 38.03 3.02
1031 1038 2.693074 ACACCAGTTTGTTTTGGCCTAG 59.307 45.455 3.32 0.00 38.03 3.02
1032 1039 2.741145 ACACCAGTTTGTTTTGGCCTA 58.259 42.857 3.32 0.00 38.03 3.93
1033 1040 1.567357 ACACCAGTTTGTTTTGGCCT 58.433 45.000 3.32 0.00 38.03 5.19
1034 1041 2.223947 CCTACACCAGTTTGTTTTGGCC 60.224 50.000 0.00 0.00 38.03 5.36
1035 1042 2.429250 ACCTACACCAGTTTGTTTTGGC 59.571 45.455 0.00 0.00 38.03 4.52
1036 1043 4.885325 ACTACCTACACCAGTTTGTTTTGG 59.115 41.667 0.00 0.00 40.38 3.28
1037 1044 6.445357 AACTACCTACACCAGTTTGTTTTG 57.555 37.500 0.00 0.00 0.00 2.44
1038 1045 7.830697 AGTAAACTACCTACACCAGTTTGTTTT 59.169 33.333 8.73 0.00 41.36 2.43
1039 1046 7.281549 CAGTAAACTACCTACACCAGTTTGTTT 59.718 37.037 8.73 0.00 41.36 2.83
1040 1047 6.764560 CAGTAAACTACCTACACCAGTTTGTT 59.235 38.462 8.73 0.00 41.36 2.83
1041 1048 6.098695 TCAGTAAACTACCTACACCAGTTTGT 59.901 38.462 8.73 0.00 41.36 2.83
1042 1049 6.518493 TCAGTAAACTACCTACACCAGTTTG 58.482 40.000 8.73 0.00 41.36 2.93
1043 1050 6.736110 TCAGTAAACTACCTACACCAGTTT 57.264 37.500 4.56 4.56 43.16 2.66
1044 1051 6.736110 TTCAGTAAACTACCTACACCAGTT 57.264 37.500 0.00 0.00 34.03 3.16
1045 1052 6.463472 GGTTTCAGTAAACTACCTACACCAGT 60.463 42.308 0.00 0.00 43.76 4.00
1046 1053 5.930569 GGTTTCAGTAAACTACCTACACCAG 59.069 44.000 0.00 0.00 43.76 4.00
1047 1054 5.221702 GGGTTTCAGTAAACTACCTACACCA 60.222 44.000 0.00 0.00 43.76 4.17
1048 1055 5.012458 AGGGTTTCAGTAAACTACCTACACC 59.988 44.000 0.00 0.00 43.76 4.16
1049 1056 6.106648 AGGGTTTCAGTAAACTACCTACAC 57.893 41.667 0.00 0.00 43.76 2.90
1050 1057 6.327104 TCAAGGGTTTCAGTAAACTACCTACA 59.673 38.462 0.00 0.00 43.76 2.74
1051 1058 6.762333 TCAAGGGTTTCAGTAAACTACCTAC 58.238 40.000 0.00 0.00 43.76 3.18
1052 1059 6.999705 TCAAGGGTTTCAGTAAACTACCTA 57.000 37.500 0.00 0.00 43.76 3.08
1053 1060 5.899631 TCAAGGGTTTCAGTAAACTACCT 57.100 39.130 0.00 0.00 43.76 3.08
1054 1061 7.520451 AATTCAAGGGTTTCAGTAAACTACC 57.480 36.000 0.00 0.00 43.76 3.18
1055 1062 7.295930 CGAATTCAAGGGTTTCAGTAAACTAC 58.704 38.462 6.22 0.00 43.76 2.73
1056 1063 6.428771 CCGAATTCAAGGGTTTCAGTAAACTA 59.571 38.462 6.22 0.00 43.76 2.24
1057 1064 5.240844 CCGAATTCAAGGGTTTCAGTAAACT 59.759 40.000 6.22 0.00 43.76 2.66
1058 1065 5.239963 TCCGAATTCAAGGGTTTCAGTAAAC 59.760 40.000 6.22 0.00 43.58 2.01
1059 1066 5.378332 TCCGAATTCAAGGGTTTCAGTAAA 58.622 37.500 6.22 0.00 0.00 2.01
1060 1067 4.975631 TCCGAATTCAAGGGTTTCAGTAA 58.024 39.130 6.22 0.00 0.00 2.24
1061 1068 4.627284 TCCGAATTCAAGGGTTTCAGTA 57.373 40.909 6.22 0.00 0.00 2.74
1062 1069 3.502123 TCCGAATTCAAGGGTTTCAGT 57.498 42.857 6.22 0.00 0.00 3.41
1063 1070 6.460123 CCATATTCCGAATTCAAGGGTTTCAG 60.460 42.308 6.22 0.00 0.00 3.02
1064 1071 5.359576 CCATATTCCGAATTCAAGGGTTTCA 59.640 40.000 6.22 0.00 0.00 2.69
1065 1072 5.221244 CCCATATTCCGAATTCAAGGGTTTC 60.221 44.000 6.22 0.00 0.00 2.78
1066 1073 4.649218 CCCATATTCCGAATTCAAGGGTTT 59.351 41.667 6.22 0.00 0.00 3.27
1067 1074 4.079443 TCCCATATTCCGAATTCAAGGGTT 60.079 41.667 6.22 0.00 35.31 4.11
1068 1075 3.461831 TCCCATATTCCGAATTCAAGGGT 59.538 43.478 6.22 0.00 35.31 4.34
1069 1076 4.098914 TCCCATATTCCGAATTCAAGGG 57.901 45.455 6.22 6.29 35.09 3.95
1070 1077 5.594317 ACTTTCCCATATTCCGAATTCAAGG 59.406 40.000 6.22 0.00 0.00 3.61
1071 1078 6.511767 CGACTTTCCCATATTCCGAATTCAAG 60.512 42.308 6.22 0.00 0.00 3.02
1072 1079 5.295787 CGACTTTCCCATATTCCGAATTCAA 59.704 40.000 6.22 0.00 0.00 2.69
1073 1080 4.814234 CGACTTTCCCATATTCCGAATTCA 59.186 41.667 6.22 0.00 0.00 2.57
1074 1081 4.319549 GCGACTTTCCCATATTCCGAATTC 60.320 45.833 0.00 0.00 0.00 2.17
1075 1082 3.564225 GCGACTTTCCCATATTCCGAATT 59.436 43.478 0.00 0.00 0.00 2.17
1076 1083 3.139077 GCGACTTTCCCATATTCCGAAT 58.861 45.455 0.00 0.00 0.00 3.34
1077 1084 2.557317 GCGACTTTCCCATATTCCGAA 58.443 47.619 0.00 0.00 0.00 4.30
1078 1085 1.202604 GGCGACTTTCCCATATTCCGA 60.203 52.381 0.00 0.00 0.00 4.55
1079 1086 1.226746 GGCGACTTTCCCATATTCCG 58.773 55.000 0.00 0.00 0.00 4.30
1080 1087 1.605753 GGGCGACTTTCCCATATTCC 58.394 55.000 0.00 0.00 43.37 3.01
1081 1088 1.605753 GGGGCGACTTTCCCATATTC 58.394 55.000 0.06 0.00 45.73 1.75
1082 1089 0.179029 CGGGGCGACTTTCCCATATT 60.179 55.000 0.06 0.00 45.73 1.28
1083 1090 1.450211 CGGGGCGACTTTCCCATAT 59.550 57.895 0.06 0.00 45.73 1.78
1084 1091 2.737881 CCGGGGCGACTTTCCCATA 61.738 63.158 0.00 0.00 45.73 2.74
1085 1092 4.109675 CCGGGGCGACTTTCCCAT 62.110 66.667 0.00 0.00 45.73 4.00
1088 1095 4.340246 AACCCGGGGCGACTTTCC 62.340 66.667 27.92 0.00 0.00 3.13
1089 1096 3.053896 CAACCCGGGGCGACTTTC 61.054 66.667 27.92 0.00 0.00 2.62
1090 1097 4.653888 CCAACCCGGGGCGACTTT 62.654 66.667 27.92 5.54 0.00 2.66
1099 1106 2.285144 AGTAGTCCCCCAACCCGG 60.285 66.667 0.00 0.00 0.00 5.73
1100 1107 2.364780 GGAGTAGTCCCCCAACCCG 61.365 68.421 5.14 0.00 36.76 5.28
1101 1108 0.549413 AAGGAGTAGTCCCCCAACCC 60.549 60.000 13.30 0.00 45.26 4.11
1102 1109 1.369403 AAAGGAGTAGTCCCCCAACC 58.631 55.000 13.30 0.00 45.26 3.77
1103 1110 4.524053 CATAAAAGGAGTAGTCCCCCAAC 58.476 47.826 13.30 0.00 45.26 3.77
1104 1111 3.526019 CCATAAAAGGAGTAGTCCCCCAA 59.474 47.826 13.30 0.00 45.26 4.12
1105 1112 3.120108 CCATAAAAGGAGTAGTCCCCCA 58.880 50.000 13.30 0.00 45.26 4.96
1106 1113 2.442126 CCCATAAAAGGAGTAGTCCCCC 59.558 54.545 13.30 0.00 45.26 5.40
1107 1114 2.442126 CCCCATAAAAGGAGTAGTCCCC 59.558 54.545 13.30 0.00 45.26 4.81
1108 1115 3.120898 ACCCCATAAAAGGAGTAGTCCC 58.879 50.000 13.30 0.00 45.26 4.46
1109 1116 4.682589 CGAACCCCATAAAAGGAGTAGTCC 60.683 50.000 8.73 8.73 44.33 3.85
1110 1117 4.439968 CGAACCCCATAAAAGGAGTAGTC 58.560 47.826 0.00 0.00 0.00 2.59
1111 1118 3.370209 GCGAACCCCATAAAAGGAGTAGT 60.370 47.826 0.00 0.00 0.00 2.73
1112 1119 3.203716 GCGAACCCCATAAAAGGAGTAG 58.796 50.000 0.00 0.00 0.00 2.57
1113 1120 2.572556 TGCGAACCCCATAAAAGGAGTA 59.427 45.455 0.00 0.00 0.00 2.59
1114 1121 1.353022 TGCGAACCCCATAAAAGGAGT 59.647 47.619 0.00 0.00 0.00 3.85
1115 1122 2.122783 TGCGAACCCCATAAAAGGAG 57.877 50.000 0.00 0.00 0.00 3.69
1116 1123 2.588464 TTGCGAACCCCATAAAAGGA 57.412 45.000 0.00 0.00 0.00 3.36
1117 1124 2.159114 CCATTGCGAACCCCATAAAAGG 60.159 50.000 0.00 0.00 0.00 3.11
1118 1125 2.738321 GCCATTGCGAACCCCATAAAAG 60.738 50.000 0.00 0.00 0.00 2.27
1119 1126 1.205893 GCCATTGCGAACCCCATAAAA 59.794 47.619 0.00 0.00 0.00 1.52
1120 1127 0.820871 GCCATTGCGAACCCCATAAA 59.179 50.000 0.00 0.00 0.00 1.40
1121 1128 0.033601 AGCCATTGCGAACCCCATAA 60.034 50.000 0.00 0.00 44.33 1.90
1122 1129 0.033601 AAGCCATTGCGAACCCCATA 60.034 50.000 0.00 0.00 44.33 2.74
1123 1130 0.904394 AAAGCCATTGCGAACCCCAT 60.904 50.000 0.00 0.00 44.33 4.00
1124 1131 0.251386 TAAAGCCATTGCGAACCCCA 60.251 50.000 0.00 0.00 44.33 4.96
1125 1132 1.111277 ATAAAGCCATTGCGAACCCC 58.889 50.000 0.00 0.00 44.33 4.95
1126 1133 2.794631 CGAATAAAGCCATTGCGAACCC 60.795 50.000 0.00 0.00 44.33 4.11
1127 1134 2.450160 CGAATAAAGCCATTGCGAACC 58.550 47.619 0.00 0.00 44.33 3.62
1128 1135 1.846175 GCGAATAAAGCCATTGCGAAC 59.154 47.619 0.00 0.00 44.33 3.95
1129 1136 1.742831 AGCGAATAAAGCCATTGCGAA 59.257 42.857 0.00 0.00 44.33 4.70
1130 1137 1.378531 AGCGAATAAAGCCATTGCGA 58.621 45.000 0.00 0.00 44.33 5.10
1131 1138 3.542712 ATAGCGAATAAAGCCATTGCG 57.457 42.857 0.00 0.00 44.33 4.85
1132 1139 6.030228 GGAATATAGCGAATAAAGCCATTGC 58.970 40.000 0.00 0.00 34.64 3.56
1133 1140 7.383102 AGGAATATAGCGAATAAAGCCATTG 57.617 36.000 0.00 0.00 34.64 2.82
1134 1141 9.331282 GATAGGAATATAGCGAATAAAGCCATT 57.669 33.333 0.00 0.00 34.64 3.16
1135 1142 8.709308 AGATAGGAATATAGCGAATAAAGCCAT 58.291 33.333 0.00 0.00 34.64 4.40
1136 1143 8.079211 AGATAGGAATATAGCGAATAAAGCCA 57.921 34.615 0.00 0.00 34.64 4.75
1175 1182 8.658609 CGTCCAGTAAAACGGAAGAATTATAAA 58.341 33.333 0.00 0.00 33.13 1.40
1176 1183 8.034215 TCGTCCAGTAAAACGGAAGAATTATAA 58.966 33.333 0.00 0.00 36.94 0.98
1177 1184 7.546358 TCGTCCAGTAAAACGGAAGAATTATA 58.454 34.615 0.00 0.00 36.94 0.98
1178 1185 6.400568 TCGTCCAGTAAAACGGAAGAATTAT 58.599 36.000 0.00 0.00 36.94 1.28
1179 1186 5.782047 TCGTCCAGTAAAACGGAAGAATTA 58.218 37.500 0.00 0.00 36.94 1.40
1180 1187 4.634199 TCGTCCAGTAAAACGGAAGAATT 58.366 39.130 0.00 0.00 36.94 2.17
1181 1188 4.261578 TCGTCCAGTAAAACGGAAGAAT 57.738 40.909 0.00 0.00 36.94 2.40
1182 1189 3.731652 TCGTCCAGTAAAACGGAAGAA 57.268 42.857 0.00 0.00 36.94 2.52
1183 1190 3.731652 TTCGTCCAGTAAAACGGAAGA 57.268 42.857 0.00 0.00 37.91 2.87
1184 1191 5.352643 AATTTCGTCCAGTAAAACGGAAG 57.647 39.130 0.00 0.00 39.55 3.46
1185 1192 5.754543 AAATTTCGTCCAGTAAAACGGAA 57.245 34.783 0.00 0.00 40.40 4.30
1186 1193 5.754543 AAAATTTCGTCCAGTAAAACGGA 57.245 34.783 0.00 0.00 39.31 4.69
1187 1194 6.360414 GGTTAAAATTTCGTCCAGTAAAACGG 59.640 38.462 0.00 0.00 39.31 4.44
1188 1195 6.911511 TGGTTAAAATTTCGTCCAGTAAAACG 59.088 34.615 0.00 0.00 40.17 3.60
1189 1196 8.631676 TTGGTTAAAATTTCGTCCAGTAAAAC 57.368 30.769 0.00 0.00 0.00 2.43
1190 1197 9.819267 AATTGGTTAAAATTTCGTCCAGTAAAA 57.181 25.926 0.00 0.00 0.00 1.52
1193 1200 8.732531 CCTAATTGGTTAAAATTTCGTCCAGTA 58.267 33.333 0.00 0.00 32.16 2.74
1194 1201 7.599171 CCTAATTGGTTAAAATTTCGTCCAGT 58.401 34.615 0.00 0.00 32.16 4.00
1224 1231 9.804977 ACTCTGACTTCCTAGTTTTAGTTAGTA 57.195 33.333 0.00 0.00 33.84 1.82
1225 1232 8.709272 ACTCTGACTTCCTAGTTTTAGTTAGT 57.291 34.615 0.00 0.00 33.84 2.24
1226 1233 9.984190 AAACTCTGACTTCCTAGTTTTAGTTAG 57.016 33.333 0.00 0.00 38.65 2.34
1228 1235 9.682465 AAAAACTCTGACTTCCTAGTTTTAGTT 57.318 29.630 11.23 3.63 46.19 2.24
1229 1236 9.327628 GAAAAACTCTGACTTCCTAGTTTTAGT 57.672 33.333 11.23 0.00 46.19 2.24
1230 1237 8.775527 GGAAAAACTCTGACTTCCTAGTTTTAG 58.224 37.037 11.23 0.00 46.19 1.85
1231 1238 8.269317 TGGAAAAACTCTGACTTCCTAGTTTTA 58.731 33.333 11.23 0.00 46.19 1.52
1233 1240 6.659824 TGGAAAAACTCTGACTTCCTAGTTT 58.340 36.000 0.00 0.00 42.40 2.66
1234 1241 6.248569 TGGAAAAACTCTGACTTCCTAGTT 57.751 37.500 0.00 0.00 38.53 2.24
1235 1242 5.888982 TGGAAAAACTCTGACTTCCTAGT 57.111 39.130 0.00 0.00 38.53 2.57
1236 1243 5.877564 GGATGGAAAAACTCTGACTTCCTAG 59.122 44.000 0.00 0.00 38.53 3.02
1237 1244 5.309543 TGGATGGAAAAACTCTGACTTCCTA 59.690 40.000 0.00 0.00 38.53 2.94
1238 1245 4.104738 TGGATGGAAAAACTCTGACTTCCT 59.895 41.667 0.00 0.00 38.53 3.36
1239 1246 4.398319 TGGATGGAAAAACTCTGACTTCC 58.602 43.478 0.00 0.00 38.26 3.46
1240 1247 6.391227 TTTGGATGGAAAAACTCTGACTTC 57.609 37.500 0.00 0.00 0.00 3.01
1241 1248 6.790232 TTTTGGATGGAAAAACTCTGACTT 57.210 33.333 0.00 0.00 0.00 3.01
1242 1249 6.790232 TTTTTGGATGGAAAAACTCTGACT 57.210 33.333 0.00 0.00 31.39 3.41
1290 1297 8.509690 CGGTCGAACTACCATAATATCTAGAAA 58.490 37.037 0.00 0.00 39.71 2.52
1291 1298 7.361542 GCGGTCGAACTACCATAATATCTAGAA 60.362 40.741 0.00 0.00 39.71 2.10
1292 1299 6.093219 GCGGTCGAACTACCATAATATCTAGA 59.907 42.308 0.00 0.00 39.71 2.43
1293 1300 6.256686 GCGGTCGAACTACCATAATATCTAG 58.743 44.000 0.00 0.00 39.71 2.43
1294 1301 5.163824 CGCGGTCGAACTACCATAATATCTA 60.164 44.000 0.00 0.00 39.71 1.98
1295 1302 4.379186 CGCGGTCGAACTACCATAATATCT 60.379 45.833 0.00 0.00 39.71 1.98
1296 1303 3.850273 CGCGGTCGAACTACCATAATATC 59.150 47.826 0.00 0.00 39.71 1.63
1297 1304 3.366679 CCGCGGTCGAACTACCATAATAT 60.367 47.826 19.50 0.00 39.71 1.28
1298 1305 2.030893 CCGCGGTCGAACTACCATAATA 60.031 50.000 19.50 0.00 39.71 0.98
1299 1306 1.269413 CCGCGGTCGAACTACCATAAT 60.269 52.381 19.50 0.00 39.71 1.28
1300 1307 0.101040 CCGCGGTCGAACTACCATAA 59.899 55.000 19.50 0.00 39.71 1.90
1301 1308 0.747644 TCCGCGGTCGAACTACCATA 60.748 55.000 27.15 0.00 39.71 2.74
1302 1309 1.597797 TTCCGCGGTCGAACTACCAT 61.598 55.000 27.15 0.00 39.71 3.55
1303 1310 1.597797 ATTCCGCGGTCGAACTACCA 61.598 55.000 27.15 0.00 39.71 3.25
1304 1311 0.459063 AATTCCGCGGTCGAACTACC 60.459 55.000 27.15 0.00 38.10 3.18
1305 1312 1.353076 AAATTCCGCGGTCGAACTAC 58.647 50.000 27.15 0.00 38.10 2.73
1306 1313 2.083167 AAAATTCCGCGGTCGAACTA 57.917 45.000 27.15 0.00 38.10 2.24
1307 1314 1.232119 AAAAATTCCGCGGTCGAACT 58.768 45.000 27.15 0.00 38.10 3.01
1308 1315 3.759550 AAAAATTCCGCGGTCGAAC 57.240 47.368 27.15 0.00 38.10 3.95
1324 1331 8.673711 CATATTCCAGAGATACCGAAACAAAAA 58.326 33.333 0.00 0.00 0.00 1.94
1325 1332 8.044309 TCATATTCCAGAGATACCGAAACAAAA 58.956 33.333 0.00 0.00 0.00 2.44
1326 1333 7.561251 TCATATTCCAGAGATACCGAAACAAA 58.439 34.615 0.00 0.00 0.00 2.83
1327 1334 7.119709 TCATATTCCAGAGATACCGAAACAA 57.880 36.000 0.00 0.00 0.00 2.83
1328 1335 6.323996 ACTCATATTCCAGAGATACCGAAACA 59.676 38.462 0.00 0.00 35.83 2.83
1329 1336 6.750148 ACTCATATTCCAGAGATACCGAAAC 58.250 40.000 0.00 0.00 35.83 2.78
1330 1337 6.778069 AGACTCATATTCCAGAGATACCGAAA 59.222 38.462 0.00 0.00 35.83 3.46
1331 1338 6.307776 AGACTCATATTCCAGAGATACCGAA 58.692 40.000 0.00 0.00 35.83 4.30
1332 1339 5.882040 AGACTCATATTCCAGAGATACCGA 58.118 41.667 0.00 0.00 35.83 4.69
1333 1340 6.582677 AAGACTCATATTCCAGAGATACCG 57.417 41.667 0.00 0.00 35.83 4.02
1334 1341 7.978975 GCATAAGACTCATATTCCAGAGATACC 59.021 40.741 0.00 0.00 35.83 2.73
1335 1342 8.748412 AGCATAAGACTCATATTCCAGAGATAC 58.252 37.037 0.00 0.00 35.83 2.24
1336 1343 8.891985 AGCATAAGACTCATATTCCAGAGATA 57.108 34.615 0.00 0.00 35.83 1.98
1337 1344 7.795534 AGCATAAGACTCATATTCCAGAGAT 57.204 36.000 0.00 0.00 35.83 2.75
1338 1345 8.891985 ATAGCATAAGACTCATATTCCAGAGA 57.108 34.615 0.00 0.00 35.83 3.10
1684 1695 4.525912 AGGAAGGCAAAACAAGCATAAG 57.474 40.909 0.00 0.00 0.00 1.73
1756 1767 7.563724 TTTAAGTCTAACCCACTTCCTATGT 57.436 36.000 0.00 0.00 35.63 2.29
1839 1851 5.839063 AGGCATGATGATTTCAATGATCCTT 59.161 36.000 0.00 0.00 38.03 3.36
1842 1854 6.151312 AGCTAGGCATGATGATTTCAATGATC 59.849 38.462 0.00 0.00 38.03 2.92
1889 1913 4.079385 AGGTAAATATTGGGTTGTCTCCCC 60.079 45.833 0.00 0.00 46.48 4.81
1990 2014 5.163581 CGTAAGCTAGCCTAAAGGTCTTACA 60.164 44.000 12.13 0.00 36.67 2.41
2005 2029 4.995124 ACACAACTATCACCGTAAGCTAG 58.005 43.478 0.00 0.00 0.00 3.42
2089 2113 3.754188 AGAATCAGATCAAAAGCACGC 57.246 42.857 0.00 0.00 0.00 5.34
2181 2209 7.883833 ACAGTCTGTAGTAATCTGTAACTCTCA 59.116 37.037 2.87 0.00 37.55 3.27


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

AutoCloner maintained by Alex Coulton.