Multiple sequence alignment - TraesCS5D01G432400

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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 TraesCS5D01G432400 chr5D 100.000 2171 0 0 1 2171 488581133 488578963 0.000000e+00 4010
1 TraesCS5D01G432400 chr5D 97.025 874 26 0 1298 2171 348566080 348565207 0.000000e+00 1471
2 TraesCS5D01G432400 chr5D 96.911 874 27 0 1298 2171 252765889 252766762 0.000000e+00 1465
3 TraesCS5D01G432400 chr5D 97.819 321 7 0 976 1296 446178701 446178381 2.430000e-154 555
4 TraesCS5D01G432400 chr6D 97.546 978 24 0 1 978 44584757 44583780 0.000000e+00 1674
5 TraesCS5D01G432400 chr6D 97.538 975 23 1 1 975 452489001 452489974 0.000000e+00 1666
6 TraesCS5D01G432400 chr6D 98.131 321 6 0 976 1296 168262073 168261753 5.230000e-156 560
7 TraesCS5D01G432400 chr6D 97.819 321 7 0 976 1296 458919719 458919399 2.430000e-154 555
8 TraesCS5D01G432400 chr4D 97.546 978 24 0 1 978 26297329 26296352 0.000000e+00 1674
9 TraesCS5D01G432400 chr4D 97.641 975 22 1 1 975 117989926 117990899 0.000000e+00 1672
10 TraesCS5D01G432400 chr4D 97.444 978 25 0 1 978 5905789 5904812 0.000000e+00 1668
11 TraesCS5D01G432400 chr1D 97.641 975 23 0 1 975 402845851 402846825 0.000000e+00 1674
12 TraesCS5D01G432400 chr1D 97.538 975 24 0 1 975 316864486 316865460 0.000000e+00 1668
13 TraesCS5D01G432400 chr1D 97.444 978 25 0 1 978 376605522 376604545 0.000000e+00 1668
14 TraesCS5D01G432400 chr1D 97.819 321 7 0 976 1296 254393709 254394029 2.430000e-154 555
15 TraesCS5D01G432400 chr3D 97.444 978 25 0 1 978 312698667 312697690 0.000000e+00 1668
16 TraesCS5D01G432400 chr3D 96.682 874 29 0 1298 2171 412853638 412852765 0.000000e+00 1454
17 TraesCS5D01G432400 chr3D 96.571 875 29 1 1298 2171 372307085 372306211 0.000000e+00 1448
18 TraesCS5D01G432400 chr3D 96.568 874 27 2 1298 2171 435016659 435015789 0.000000e+00 1445
19 TraesCS5D01G432400 chr3D 96.355 878 31 1 1295 2171 480199632 480200509 0.000000e+00 1443
20 TraesCS5D01G432400 chr7D 97.025 874 26 0 1298 2171 114951578 114950705 0.000000e+00 1471
21 TraesCS5D01G432400 chr7D 96.568 874 30 0 1298 2171 222607595 222606722 0.000000e+00 1448
22 TraesCS5D01G432400 chr7D 98.131 321 6 0 976 1296 231578659 231578979 5.230000e-156 560
23 TraesCS5D01G432400 chr2D 97.018 872 26 0 1300 2171 538107257 538108128 0.000000e+00 1467
24 TraesCS5D01G432400 chrUn 98.131 321 6 0 976 1296 216514200 216514520 5.230000e-156 560
25 TraesCS5D01G432400 chrUn 98.131 321 6 0 976 1296 286269183 286268863 5.230000e-156 560
26 TraesCS5D01G432400 chr3B 98.131 321 6 0 976 1296 101915583 101915263 5.230000e-156 560
27 TraesCS5D01G432400 chr3A 98.131 321 6 0 976 1296 66013218 66013538 5.230000e-156 560


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 TraesCS5D01G432400 chr5D 488578963 488581133 2170 True 4010 4010 100.000 1 2171 1 chr5D.!!$R3 2170
1 TraesCS5D01G432400 chr5D 348565207 348566080 873 True 1471 1471 97.025 1298 2171 1 chr5D.!!$R1 873
2 TraesCS5D01G432400 chr5D 252765889 252766762 873 False 1465 1465 96.911 1298 2171 1 chr5D.!!$F1 873
3 TraesCS5D01G432400 chr6D 44583780 44584757 977 True 1674 1674 97.546 1 978 1 chr6D.!!$R1 977
4 TraesCS5D01G432400 chr6D 452489001 452489974 973 False 1666 1666 97.538 1 975 1 chr6D.!!$F1 974
5 TraesCS5D01G432400 chr4D 26296352 26297329 977 True 1674 1674 97.546 1 978 1 chr4D.!!$R2 977
6 TraesCS5D01G432400 chr4D 117989926 117990899 973 False 1672 1672 97.641 1 975 1 chr4D.!!$F1 974
7 TraesCS5D01G432400 chr4D 5904812 5905789 977 True 1668 1668 97.444 1 978 1 chr4D.!!$R1 977
8 TraesCS5D01G432400 chr1D 402845851 402846825 974 False 1674 1674 97.641 1 975 1 chr1D.!!$F3 974
9 TraesCS5D01G432400 chr1D 316864486 316865460 974 False 1668 1668 97.538 1 975 1 chr1D.!!$F2 974
10 TraesCS5D01G432400 chr1D 376604545 376605522 977 True 1668 1668 97.444 1 978 1 chr1D.!!$R1 977
11 TraesCS5D01G432400 chr3D 312697690 312698667 977 True 1668 1668 97.444 1 978 1 chr3D.!!$R1 977
12 TraesCS5D01G432400 chr3D 412852765 412853638 873 True 1454 1454 96.682 1298 2171 1 chr3D.!!$R3 873
13 TraesCS5D01G432400 chr3D 372306211 372307085 874 True 1448 1448 96.571 1298 2171 1 chr3D.!!$R2 873
14 TraesCS5D01G432400 chr3D 435015789 435016659 870 True 1445 1445 96.568 1298 2171 1 chr3D.!!$R4 873
15 TraesCS5D01G432400 chr3D 480199632 480200509 877 False 1443 1443 96.355 1295 2171 1 chr3D.!!$F1 876
16 TraesCS5D01G432400 chr7D 114950705 114951578 873 True 1471 1471 97.025 1298 2171 1 chr7D.!!$R1 873
17 TraesCS5D01G432400 chr7D 222606722 222607595 873 True 1448 1448 96.568 1298 2171 1 chr7D.!!$R2 873
18 TraesCS5D01G432400 chr2D 538107257 538108128 871 False 1467 1467 97.018 1300 2171 1 chr2D.!!$F1 871

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
780 781 1.282875 CCGCATACTCGATCGCTCA 59.717 57.895 11.09 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1839 1841 1.877576 CTGCAGTGTGCTCCTCCGTA 61.878 60.0 5.25 0.0 45.31 4.02 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
102 103 9.394767 CCCGTAAATATTGAATCATATGATGGA 57.605 33.333 18.85 8.41 34.49 3.41
346 347 6.324770 TGATGACTTGAGCCATATAACTCAGA 59.675 38.462 6.88 0.59 43.43 3.27
374 375 1.476833 GGAATCGGCCAGGCAATTCTA 60.477 52.381 26.33 4.48 34.73 2.10
780 781 1.282875 CCGCATACTCGATCGCTCA 59.717 57.895 11.09 0.00 0.00 4.26
975 976 5.163561 ACAAGTGAAAACGGTGAACATGATT 60.164 36.000 0.00 0.00 0.00 2.57
978 979 7.214467 AGTGAAAACGGTGAACATGATTTAT 57.786 32.000 0.00 0.00 0.00 1.40
979 980 7.305474 AGTGAAAACGGTGAACATGATTTATC 58.695 34.615 0.00 0.00 0.00 1.75
980 981 7.174946 AGTGAAAACGGTGAACATGATTTATCT 59.825 33.333 0.00 0.00 0.00 1.98
981 982 8.447833 GTGAAAACGGTGAACATGATTTATCTA 58.552 33.333 0.00 0.00 0.00 1.98
982 983 9.004717 TGAAAACGGTGAACATGATTTATCTAA 57.995 29.630 0.00 0.00 0.00 2.10
983 984 9.834628 GAAAACGGTGAACATGATTTATCTAAA 57.165 29.630 0.00 0.00 0.00 1.85
1012 1013 8.786826 AATCAAGTTATTAATGACTGGACGAA 57.213 30.769 17.29 0.00 30.28 3.85
1013 1014 8.786826 ATCAAGTTATTAATGACTGGACGAAA 57.213 30.769 17.29 0.00 30.28 3.46
1014 1015 8.025243 TCAAGTTATTAATGACTGGACGAAAC 57.975 34.615 13.14 0.00 0.00 2.78
1015 1016 6.980051 AGTTATTAATGACTGGACGAAACC 57.020 37.500 11.78 0.00 0.00 3.27
1016 1017 6.469410 AGTTATTAATGACTGGACGAAACCA 58.531 36.000 11.78 0.00 38.33 3.67
1017 1018 6.938030 AGTTATTAATGACTGGACGAAACCAA 59.062 34.615 11.78 0.00 39.59 3.67
1018 1019 5.880054 ATTAATGACTGGACGAAACCAAG 57.120 39.130 0.00 0.00 39.59 3.61
1019 1020 3.485463 AATGACTGGACGAAACCAAGA 57.515 42.857 0.00 0.00 39.59 3.02
1020 1021 2.992124 TGACTGGACGAAACCAAGAA 57.008 45.000 0.00 0.00 39.59 2.52
1021 1022 3.269538 TGACTGGACGAAACCAAGAAA 57.730 42.857 0.00 0.00 39.59 2.52
1022 1023 3.815809 TGACTGGACGAAACCAAGAAAT 58.184 40.909 0.00 0.00 39.59 2.17
1023 1024 4.963373 TGACTGGACGAAACCAAGAAATA 58.037 39.130 0.00 0.00 39.59 1.40
1024 1025 5.369833 TGACTGGACGAAACCAAGAAATAA 58.630 37.500 0.00 0.00 39.59 1.40
1025 1026 5.237779 TGACTGGACGAAACCAAGAAATAAC 59.762 40.000 0.00 0.00 39.59 1.89
1026 1027 4.517832 ACTGGACGAAACCAAGAAATAACC 59.482 41.667 0.00 0.00 39.59 2.85
1027 1028 3.822167 TGGACGAAACCAAGAAATAACCC 59.178 43.478 0.00 0.00 36.96 4.11
1028 1029 3.192001 GGACGAAACCAAGAAATAACCCC 59.808 47.826 0.00 0.00 0.00 4.95
1029 1030 4.077108 GACGAAACCAAGAAATAACCCCT 58.923 43.478 0.00 0.00 0.00 4.79
1030 1031 4.476297 ACGAAACCAAGAAATAACCCCTT 58.524 39.130 0.00 0.00 0.00 3.95
1031 1032 5.633117 ACGAAACCAAGAAATAACCCCTTA 58.367 37.500 0.00 0.00 0.00 2.69
1032 1033 6.250711 ACGAAACCAAGAAATAACCCCTTAT 58.749 36.000 0.00 0.00 0.00 1.73
1033 1034 6.152154 ACGAAACCAAGAAATAACCCCTTATG 59.848 38.462 0.00 0.00 0.00 1.90
1034 1035 6.152154 CGAAACCAAGAAATAACCCCTTATGT 59.848 38.462 0.00 0.00 0.00 2.29
1035 1036 6.850752 AACCAAGAAATAACCCCTTATGTG 57.149 37.500 0.00 0.00 0.00 3.21
1036 1037 4.709886 ACCAAGAAATAACCCCTTATGTGC 59.290 41.667 0.00 0.00 0.00 4.57
1037 1038 4.202010 CCAAGAAATAACCCCTTATGTGCG 60.202 45.833 0.00 0.00 0.00 5.34
1038 1039 4.497291 AGAAATAACCCCTTATGTGCGA 57.503 40.909 0.00 0.00 0.00 5.10
1039 1040 4.850680 AGAAATAACCCCTTATGTGCGAA 58.149 39.130 0.00 0.00 0.00 4.70
1040 1041 5.258051 AGAAATAACCCCTTATGTGCGAAA 58.742 37.500 0.00 0.00 0.00 3.46
1041 1042 5.891551 AGAAATAACCCCTTATGTGCGAAAT 59.108 36.000 0.00 0.00 0.00 2.17
1042 1043 6.379988 AGAAATAACCCCTTATGTGCGAAATT 59.620 34.615 0.00 0.00 0.00 1.82
1043 1044 7.558444 AGAAATAACCCCTTATGTGCGAAATTA 59.442 33.333 0.00 0.00 0.00 1.40
1044 1045 7.833285 AATAACCCCTTATGTGCGAAATTAT 57.167 32.000 0.00 0.00 0.00 1.28
1045 1046 8.927675 AATAACCCCTTATGTGCGAAATTATA 57.072 30.769 0.00 0.00 0.00 0.98
1046 1047 9.528489 AATAACCCCTTATGTGCGAAATTATAT 57.472 29.630 0.00 0.00 0.00 0.86
1048 1049 8.927675 AACCCCTTATGTGCGAAATTATATAA 57.072 30.769 0.00 0.00 0.00 0.98
1049 1050 8.561738 ACCCCTTATGTGCGAAATTATATAAG 57.438 34.615 1.02 0.00 31.63 1.73
1050 1051 8.380099 ACCCCTTATGTGCGAAATTATATAAGA 58.620 33.333 1.02 0.00 32.81 2.10
1051 1052 9.396022 CCCCTTATGTGCGAAATTATATAAGAT 57.604 33.333 1.02 0.00 32.81 2.40
1055 1056 7.865706 ATGTGCGAAATTATATAAGATCCCC 57.134 36.000 1.02 0.00 0.00 4.81
1056 1057 7.016153 TGTGCGAAATTATATAAGATCCCCT 57.984 36.000 1.02 0.00 0.00 4.79
1057 1058 7.458397 TGTGCGAAATTATATAAGATCCCCTT 58.542 34.615 1.02 0.00 38.87 3.95
1058 1059 7.942341 TGTGCGAAATTATATAAGATCCCCTTT 59.058 33.333 1.02 0.00 36.34 3.11
1059 1060 9.444600 GTGCGAAATTATATAAGATCCCCTTTA 57.555 33.333 1.02 0.00 36.34 1.85
1071 1072 9.942526 ATAAGATCCCCTTTAAGATCAAACAAT 57.057 29.630 0.00 0.00 41.16 2.71
1072 1073 8.670521 AAGATCCCCTTTAAGATCAAACAATT 57.329 30.769 0.00 0.00 41.16 2.32
1073 1074 8.298729 AGATCCCCTTTAAGATCAAACAATTC 57.701 34.615 0.00 0.00 41.16 2.17
1074 1075 6.850752 TCCCCTTTAAGATCAAACAATTCC 57.149 37.500 0.00 0.00 0.00 3.01
1075 1076 6.318913 TCCCCTTTAAGATCAAACAATTCCA 58.681 36.000 0.00 0.00 0.00 3.53
1076 1077 6.959366 TCCCCTTTAAGATCAAACAATTCCAT 59.041 34.615 0.00 0.00 0.00 3.41
1077 1078 7.124147 TCCCCTTTAAGATCAAACAATTCCATC 59.876 37.037 0.00 0.00 0.00 3.51
1078 1079 6.974622 CCCTTTAAGATCAAACAATTCCATCG 59.025 38.462 0.00 0.00 0.00 3.84
1079 1080 7.148086 CCCTTTAAGATCAAACAATTCCATCGA 60.148 37.037 0.00 0.00 0.00 3.59
1080 1081 8.243426 CCTTTAAGATCAAACAATTCCATCGAA 58.757 33.333 0.00 0.00 0.00 3.71
1081 1082 9.793252 CTTTAAGATCAAACAATTCCATCGAAT 57.207 29.630 0.00 0.00 40.58 3.34
1094 1095 8.455903 AATTCCATCGAATTGATTATGACTGT 57.544 30.769 0.00 0.00 45.12 3.55
1095 1096 9.559732 AATTCCATCGAATTGATTATGACTGTA 57.440 29.630 0.00 0.00 45.12 2.74
1096 1097 9.730705 ATTCCATCGAATTGATTATGACTGTAT 57.269 29.630 0.00 0.00 35.00 2.29
1097 1098 8.538409 TCCATCGAATTGATTATGACTGTATG 57.462 34.615 0.00 0.00 34.13 2.39
1098 1099 8.150296 TCCATCGAATTGATTATGACTGTATGT 58.850 33.333 0.00 0.00 34.13 2.29
1099 1100 8.225777 CCATCGAATTGATTATGACTGTATGTG 58.774 37.037 0.00 0.00 34.13 3.21
1100 1101 8.768019 CATCGAATTGATTATGACTGTATGTGT 58.232 33.333 0.00 0.00 34.13 3.72
1101 1102 8.130307 TCGAATTGATTATGACTGTATGTGTG 57.870 34.615 0.00 0.00 0.00 3.82
1102 1103 7.978975 TCGAATTGATTATGACTGTATGTGTGA 59.021 33.333 0.00 0.00 0.00 3.58
1103 1104 8.768019 CGAATTGATTATGACTGTATGTGTGAT 58.232 33.333 0.00 0.00 0.00 3.06
1106 1107 8.593492 TTGATTATGACTGTATGTGTGATAGC 57.407 34.615 0.00 0.00 0.00 2.97
1107 1108 7.725251 TGATTATGACTGTATGTGTGATAGCA 58.275 34.615 0.00 0.00 0.00 3.49
1108 1109 8.370182 TGATTATGACTGTATGTGTGATAGCAT 58.630 33.333 0.00 0.00 0.00 3.79
1109 1110 8.768957 ATTATGACTGTATGTGTGATAGCATC 57.231 34.615 0.00 0.00 0.00 3.91
1110 1111 5.859205 TGACTGTATGTGTGATAGCATCT 57.141 39.130 0.00 0.00 0.00 2.90
1111 1112 6.959639 TGACTGTATGTGTGATAGCATCTA 57.040 37.500 0.00 0.00 0.00 1.98
1112 1113 6.739112 TGACTGTATGTGTGATAGCATCTAC 58.261 40.000 0.00 0.00 0.00 2.59
1113 1114 6.547510 TGACTGTATGTGTGATAGCATCTACT 59.452 38.462 0.00 0.00 0.00 2.57
1114 1115 7.719633 TGACTGTATGTGTGATAGCATCTACTA 59.280 37.037 0.00 0.00 0.00 1.82
1115 1116 8.642935 ACTGTATGTGTGATAGCATCTACTAT 57.357 34.615 0.00 0.00 35.53 2.12
1116 1117 9.740710 ACTGTATGTGTGATAGCATCTACTATA 57.259 33.333 0.00 0.00 32.95 1.31
1117 1118 9.995957 CTGTATGTGTGATAGCATCTACTATAC 57.004 37.037 0.00 0.00 32.95 1.47
1118 1119 9.515226 TGTATGTGTGATAGCATCTACTATACA 57.485 33.333 0.00 0.00 32.95 2.29
1121 1122 7.886338 TGTGTGATAGCATCTACTATACAAGG 58.114 38.462 0.00 0.00 32.95 3.61
1122 1123 7.724061 TGTGTGATAGCATCTACTATACAAGGA 59.276 37.037 0.00 0.00 32.95 3.36
1123 1124 8.577296 GTGTGATAGCATCTACTATACAAGGAA 58.423 37.037 0.00 0.00 32.95 3.36
1124 1125 9.314133 TGTGATAGCATCTACTATACAAGGAAT 57.686 33.333 0.00 0.00 32.95 3.01
1141 1142 8.230472 ACAAGGAATATCAATGAACCTCATTC 57.770 34.615 0.00 0.00 43.03 2.67
1142 1143 8.057623 ACAAGGAATATCAATGAACCTCATTCT 58.942 33.333 0.00 0.00 43.03 2.40
1143 1144 8.910944 CAAGGAATATCAATGAACCTCATTCTT 58.089 33.333 0.00 0.00 43.03 2.52
1144 1145 8.461249 AGGAATATCAATGAACCTCATTCTTG 57.539 34.615 0.00 0.00 43.03 3.02
1145 1146 7.014038 AGGAATATCAATGAACCTCATTCTTGC 59.986 37.037 0.00 0.00 43.03 4.01
1146 1147 7.201848 GGAATATCAATGAACCTCATTCTTGCA 60.202 37.037 0.00 0.00 43.03 4.08
1147 1148 5.988310 ATCAATGAACCTCATTCTTGCAA 57.012 34.783 0.00 0.00 43.03 4.08
1148 1149 5.988310 TCAATGAACCTCATTCTTGCAAT 57.012 34.783 0.00 0.00 43.03 3.56
1149 1150 6.349243 TCAATGAACCTCATTCTTGCAATT 57.651 33.333 0.00 0.00 43.03 2.32
1150 1151 6.160684 TCAATGAACCTCATTCTTGCAATTG 58.839 36.000 0.00 0.00 43.03 2.32
1151 1152 3.916761 TGAACCTCATTCTTGCAATTGC 58.083 40.909 23.69 23.69 38.25 3.56
1152 1153 3.575256 TGAACCTCATTCTTGCAATTGCT 59.425 39.130 29.37 7.66 38.92 3.91
1153 1154 3.863142 ACCTCATTCTTGCAATTGCTC 57.137 42.857 29.37 4.02 42.66 4.26
1154 1155 2.163010 ACCTCATTCTTGCAATTGCTCG 59.837 45.455 29.37 19.85 42.66 5.03
1155 1156 2.479049 CCTCATTCTTGCAATTGCTCGG 60.479 50.000 29.37 18.71 42.66 4.63
1156 1157 1.473677 TCATTCTTGCAATTGCTCGGG 59.526 47.619 29.37 16.50 42.66 5.14
1157 1158 1.473677 CATTCTTGCAATTGCTCGGGA 59.526 47.619 29.37 18.26 42.66 5.14
1158 1159 1.838112 TTCTTGCAATTGCTCGGGAT 58.162 45.000 29.37 0.00 42.66 3.85
1159 1160 2.708216 TCTTGCAATTGCTCGGGATA 57.292 45.000 29.37 6.12 42.66 2.59
1160 1161 2.288666 TCTTGCAATTGCTCGGGATAC 58.711 47.619 29.37 0.00 42.66 2.24
1175 1176 3.847671 GGATACCCTCTTTTAGCTGCT 57.152 47.619 7.57 7.57 0.00 4.24
1176 1177 4.957684 GGATACCCTCTTTTAGCTGCTA 57.042 45.455 5.02 5.02 0.00 3.49
1177 1178 4.888917 GGATACCCTCTTTTAGCTGCTAG 58.111 47.826 9.62 0.25 0.00 3.42
1178 1179 4.262678 GGATACCCTCTTTTAGCTGCTAGG 60.263 50.000 9.62 8.84 0.00 3.02
1179 1180 2.552367 ACCCTCTTTTAGCTGCTAGGT 58.448 47.619 9.62 9.54 0.00 3.08
1180 1181 2.502130 ACCCTCTTTTAGCTGCTAGGTC 59.498 50.000 9.62 0.00 0.00 3.85
1181 1182 2.769095 CCCTCTTTTAGCTGCTAGGTCT 59.231 50.000 9.62 0.00 0.00 3.85
1182 1183 3.961408 CCCTCTTTTAGCTGCTAGGTCTA 59.039 47.826 9.62 0.00 0.00 2.59
1183 1184 4.591072 CCCTCTTTTAGCTGCTAGGTCTAT 59.409 45.833 9.62 0.00 0.00 1.98
1184 1185 5.071115 CCCTCTTTTAGCTGCTAGGTCTATT 59.929 44.000 9.62 0.00 0.00 1.73
1185 1186 6.408662 CCCTCTTTTAGCTGCTAGGTCTATTT 60.409 42.308 9.62 0.00 0.00 1.40
1186 1187 6.704050 CCTCTTTTAGCTGCTAGGTCTATTTC 59.296 42.308 9.62 0.00 0.00 2.17
1187 1188 7.418483 CCTCTTTTAGCTGCTAGGTCTATTTCT 60.418 40.741 9.62 0.00 0.00 2.52
1188 1189 7.852263 TCTTTTAGCTGCTAGGTCTATTTCTT 58.148 34.615 9.62 0.00 0.00 2.52
1189 1190 8.978472 TCTTTTAGCTGCTAGGTCTATTTCTTA 58.022 33.333 9.62 0.00 0.00 2.10
1190 1191 9.255304 CTTTTAGCTGCTAGGTCTATTTCTTAG 57.745 37.037 9.62 0.00 0.00 2.18
1191 1192 7.899648 TTAGCTGCTAGGTCTATTTCTTAGT 57.100 36.000 9.62 0.00 0.00 2.24
1192 1193 6.800072 AGCTGCTAGGTCTATTTCTTAGTT 57.200 37.500 0.00 0.00 0.00 2.24
1193 1194 6.811954 AGCTGCTAGGTCTATTTCTTAGTTC 58.188 40.000 0.00 0.00 0.00 3.01
1194 1195 6.381420 AGCTGCTAGGTCTATTTCTTAGTTCA 59.619 38.462 0.00 0.00 0.00 3.18
1195 1196 7.042335 GCTGCTAGGTCTATTTCTTAGTTCAA 58.958 38.462 0.00 0.00 0.00 2.69
1196 1197 7.223777 GCTGCTAGGTCTATTTCTTAGTTCAAG 59.776 40.741 0.00 0.00 35.38 3.02
1197 1198 8.362464 TGCTAGGTCTATTTCTTAGTTCAAGA 57.638 34.615 0.00 0.00 41.66 3.02
1198 1199 8.982723 TGCTAGGTCTATTTCTTAGTTCAAGAT 58.017 33.333 0.00 0.00 42.88 2.40
1199 1200 9.471084 GCTAGGTCTATTTCTTAGTTCAAGATC 57.529 37.037 0.00 0.00 42.88 2.75
1200 1201 9.974980 CTAGGTCTATTTCTTAGTTCAAGATCC 57.025 37.037 0.00 0.00 42.88 3.36
1201 1202 7.797062 AGGTCTATTTCTTAGTTCAAGATCCC 58.203 38.462 0.00 0.00 42.88 3.85
1202 1203 7.625682 AGGTCTATTTCTTAGTTCAAGATCCCT 59.374 37.037 0.00 0.00 42.88 4.20
1203 1204 7.929245 GGTCTATTTCTTAGTTCAAGATCCCTC 59.071 40.741 0.00 0.00 42.88 4.30
1204 1205 8.700973 GTCTATTTCTTAGTTCAAGATCCCTCT 58.299 37.037 0.00 0.00 42.88 3.69
1205 1206 9.273137 TCTATTTCTTAGTTCAAGATCCCTCTT 57.727 33.333 0.00 0.00 42.88 2.85
1208 1209 8.437274 TTTCTTAGTTCAAGATCCCTCTTACT 57.563 34.615 0.00 0.00 42.88 2.24
1209 1210 9.543231 TTTCTTAGTTCAAGATCCCTCTTACTA 57.457 33.333 0.00 0.00 42.88 1.82
1210 1211 9.543231 TTCTTAGTTCAAGATCCCTCTTACTAA 57.457 33.333 9.00 9.00 42.88 2.24
1211 1212 8.968969 TCTTAGTTCAAGATCCCTCTTACTAAC 58.031 37.037 6.63 4.26 39.78 2.34
1212 1213 8.896722 TTAGTTCAAGATCCCTCTTACTAACT 57.103 34.615 6.63 9.19 39.78 2.24
1213 1214 7.176589 AGTTCAAGATCCCTCTTACTAACTG 57.823 40.000 0.00 0.00 39.78 3.16
1214 1215 6.155393 AGTTCAAGATCCCTCTTACTAACTGG 59.845 42.308 0.00 0.00 39.78 4.00
1215 1216 5.838955 TCAAGATCCCTCTTACTAACTGGA 58.161 41.667 0.00 0.00 39.78 3.86
1216 1217 6.261435 TCAAGATCCCTCTTACTAACTGGAA 58.739 40.000 0.00 0.00 39.78 3.53
1217 1218 6.903534 TCAAGATCCCTCTTACTAACTGGAAT 59.096 38.462 0.00 0.00 39.78 3.01
1218 1219 8.065627 TCAAGATCCCTCTTACTAACTGGAATA 58.934 37.037 0.00 0.00 39.78 1.75
1219 1220 8.705594 CAAGATCCCTCTTACTAACTGGAATAA 58.294 37.037 0.00 0.00 39.78 1.40
1220 1221 8.855804 AGATCCCTCTTACTAACTGGAATAAA 57.144 34.615 0.00 0.00 0.00 1.40
1221 1222 9.280456 AGATCCCTCTTACTAACTGGAATAAAA 57.720 33.333 0.00 0.00 0.00 1.52
1222 1223 9.549078 GATCCCTCTTACTAACTGGAATAAAAG 57.451 37.037 0.00 0.00 0.00 2.27
1223 1224 8.674925 TCCCTCTTACTAACTGGAATAAAAGA 57.325 34.615 0.00 0.00 0.00 2.52
1224 1225 9.108111 TCCCTCTTACTAACTGGAATAAAAGAA 57.892 33.333 0.00 0.00 0.00 2.52
1225 1226 9.907229 CCCTCTTACTAACTGGAATAAAAGAAT 57.093 33.333 0.00 0.00 0.00 2.40
1242 1243 7.541122 AAAAGAATTAGTAGATCTGTTCCGC 57.459 36.000 5.18 0.00 0.00 5.54
1243 1244 5.203060 AGAATTAGTAGATCTGTTCCGCC 57.797 43.478 5.18 0.00 0.00 6.13
1244 1245 4.039366 AGAATTAGTAGATCTGTTCCGCCC 59.961 45.833 5.18 0.00 0.00 6.13
1245 1246 2.447408 TAGTAGATCTGTTCCGCCCA 57.553 50.000 5.18 0.00 0.00 5.36
1246 1247 1.568504 AGTAGATCTGTTCCGCCCAA 58.431 50.000 5.18 0.00 0.00 4.12
1247 1248 1.906574 AGTAGATCTGTTCCGCCCAAA 59.093 47.619 5.18 0.00 0.00 3.28
1248 1249 2.304761 AGTAGATCTGTTCCGCCCAAAA 59.695 45.455 5.18 0.00 0.00 2.44
1249 1250 2.514458 AGATCTGTTCCGCCCAAAAT 57.486 45.000 0.00 0.00 0.00 1.82
1250 1251 2.094675 AGATCTGTTCCGCCCAAAATG 58.905 47.619 0.00 0.00 0.00 2.32
1251 1252 1.134946 GATCTGTTCCGCCCAAAATGG 59.865 52.381 0.00 0.00 37.25 3.16
1261 1262 1.079197 CCAAAATGGGAAAGGGCGC 60.079 57.895 0.00 0.00 32.67 6.53
1262 1263 1.543944 CCAAAATGGGAAAGGGCGCT 61.544 55.000 7.64 0.00 32.67 5.92
1263 1264 1.181786 CAAAATGGGAAAGGGCGCTA 58.818 50.000 7.64 0.00 0.00 4.26
1264 1265 1.134946 CAAAATGGGAAAGGGCGCTAG 59.865 52.381 7.64 0.00 0.00 3.42
1265 1266 0.395724 AAATGGGAAAGGGCGCTAGG 60.396 55.000 7.64 0.00 0.00 3.02
1266 1267 2.284515 AATGGGAAAGGGCGCTAGGG 62.285 60.000 7.64 1.65 0.00 3.53
1267 1268 3.408853 GGGAAAGGGCGCTAGGGT 61.409 66.667 7.64 0.00 0.00 4.34
1268 1269 2.675371 GGAAAGGGCGCTAGGGTT 59.325 61.111 7.64 0.00 0.00 4.11
1269 1270 1.629181 GGGAAAGGGCGCTAGGGTTA 61.629 60.000 7.64 0.00 0.00 2.85
1270 1271 0.472898 GGAAAGGGCGCTAGGGTTAT 59.527 55.000 7.64 0.00 0.00 1.89
1271 1272 1.594331 GAAAGGGCGCTAGGGTTATG 58.406 55.000 7.64 0.00 0.00 1.90
1272 1273 1.140252 GAAAGGGCGCTAGGGTTATGA 59.860 52.381 7.64 0.00 0.00 2.15
1273 1274 1.209621 AAGGGCGCTAGGGTTATGAA 58.790 50.000 7.64 0.00 0.00 2.57
1274 1275 0.468648 AGGGCGCTAGGGTTATGAAC 59.531 55.000 7.64 0.00 0.00 3.18
1275 1276 0.468648 GGGCGCTAGGGTTATGAACT 59.531 55.000 7.64 0.00 0.00 3.01
1276 1277 1.134189 GGGCGCTAGGGTTATGAACTT 60.134 52.381 7.64 0.00 0.00 2.66
1277 1278 2.103601 GGGCGCTAGGGTTATGAACTTA 59.896 50.000 7.64 0.00 0.00 2.24
1278 1279 3.244457 GGGCGCTAGGGTTATGAACTTAT 60.244 47.826 7.64 0.00 0.00 1.73
1279 1280 4.020839 GGGCGCTAGGGTTATGAACTTATA 60.021 45.833 7.64 0.00 0.00 0.98
1280 1281 5.511888 GGGCGCTAGGGTTATGAACTTATAA 60.512 44.000 7.64 0.00 0.00 0.98
1281 1282 6.171213 GGCGCTAGGGTTATGAACTTATAAT 58.829 40.000 7.64 0.00 0.00 1.28
1282 1283 6.313164 GGCGCTAGGGTTATGAACTTATAATC 59.687 42.308 7.64 0.00 0.00 1.75
1283 1284 6.872020 GCGCTAGGGTTATGAACTTATAATCA 59.128 38.462 8.77 0.00 0.00 2.57
1284 1285 7.549488 GCGCTAGGGTTATGAACTTATAATCAT 59.451 37.037 8.77 6.76 39.50 2.45
1285 1286 8.873830 CGCTAGGGTTATGAACTTATAATCATG 58.126 37.037 10.54 0.00 36.93 3.07
1286 1287 9.167311 GCTAGGGTTATGAACTTATAATCATGG 57.833 37.037 10.54 0.00 36.93 3.66
1295 1296 8.818141 TGAACTTATAATCATGGAATCGACTC 57.182 34.615 0.00 0.00 0.00 3.36
1296 1297 8.421002 TGAACTTATAATCATGGAATCGACTCA 58.579 33.333 0.00 0.00 0.00 3.41
1693 1695 7.136289 GAGGAGTTAATCTTCGATATCGTCT 57.864 40.000 23.61 10.50 40.80 4.18
1839 1841 3.671411 ACAGAACGCTCGCTCCGT 61.671 61.111 0.00 0.00 41.24 4.69
1942 1944 2.166459 CCTGATACCTTCAAGCGAGTCA 59.834 50.000 0.00 0.00 32.78 3.41
2035 2037 1.792949 GTCAAGCGACGAAATCTGTGT 59.207 47.619 0.00 0.00 31.07 3.72
2113 2115 2.203153 ACGTCCCATAATGCGGCC 60.203 61.111 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 0.539986 ATACCGCGGGATCTGTTGTT 59.460 50.000 31.76 6.43 0.00 2.83
374 375 3.463048 TCTTAGTTAGGAACCGGGTCT 57.537 47.619 21.19 8.11 0.00 3.85
668 669 2.690778 GCATTGACTGCCGTGTCCC 61.691 63.158 0.00 0.00 45.66 4.46
780 781 0.887933 GGGTGCCGTGAATTTGACAT 59.112 50.000 0.00 0.00 0.00 3.06
986 987 9.878667 TTCGTCCAGTCATTAATAACTTGATTA 57.121 29.630 0.00 0.00 0.00 1.75
987 988 8.786826 TTCGTCCAGTCATTAATAACTTGATT 57.213 30.769 0.00 0.00 0.00 2.57
988 989 8.665685 GTTTCGTCCAGTCATTAATAACTTGAT 58.334 33.333 0.00 0.00 0.00 2.57
989 990 7.118680 GGTTTCGTCCAGTCATTAATAACTTGA 59.881 37.037 0.00 0.00 0.00 3.02
990 991 7.094975 TGGTTTCGTCCAGTCATTAATAACTTG 60.095 37.037 0.00 0.00 33.19 3.16
991 992 6.938030 TGGTTTCGTCCAGTCATTAATAACTT 59.062 34.615 0.00 0.00 33.19 2.66
992 993 6.469410 TGGTTTCGTCCAGTCATTAATAACT 58.531 36.000 0.00 0.00 33.19 2.24
993 994 6.730960 TGGTTTCGTCCAGTCATTAATAAC 57.269 37.500 0.00 0.00 33.19 1.89
994 995 7.162761 TCTTGGTTTCGTCCAGTCATTAATAA 58.837 34.615 0.00 0.00 38.80 1.40
995 996 6.703319 TCTTGGTTTCGTCCAGTCATTAATA 58.297 36.000 0.00 0.00 38.80 0.98
996 997 5.556915 TCTTGGTTTCGTCCAGTCATTAAT 58.443 37.500 0.00 0.00 38.80 1.40
997 998 4.963373 TCTTGGTTTCGTCCAGTCATTAA 58.037 39.130 0.00 0.00 38.80 1.40
998 999 4.610605 TCTTGGTTTCGTCCAGTCATTA 57.389 40.909 0.00 0.00 38.80 1.90
999 1000 3.485463 TCTTGGTTTCGTCCAGTCATT 57.515 42.857 0.00 0.00 38.80 2.57
1000 1001 3.485463 TTCTTGGTTTCGTCCAGTCAT 57.515 42.857 0.00 0.00 38.80 3.06
1001 1002 2.992124 TTCTTGGTTTCGTCCAGTCA 57.008 45.000 0.00 0.00 38.80 3.41
1002 1003 5.334646 GGTTATTTCTTGGTTTCGTCCAGTC 60.335 44.000 0.00 0.00 38.80 3.51
1003 1004 4.517832 GGTTATTTCTTGGTTTCGTCCAGT 59.482 41.667 0.00 0.00 38.80 4.00
1004 1005 4.082949 GGGTTATTTCTTGGTTTCGTCCAG 60.083 45.833 0.00 0.00 38.80 3.86
1005 1006 3.822167 GGGTTATTTCTTGGTTTCGTCCA 59.178 43.478 0.00 0.00 35.49 4.02
1006 1007 3.192001 GGGGTTATTTCTTGGTTTCGTCC 59.808 47.826 0.00 0.00 0.00 4.79
1007 1008 4.077108 AGGGGTTATTTCTTGGTTTCGTC 58.923 43.478 0.00 0.00 0.00 4.20
1008 1009 4.108501 AGGGGTTATTTCTTGGTTTCGT 57.891 40.909 0.00 0.00 0.00 3.85
1009 1010 6.152154 ACATAAGGGGTTATTTCTTGGTTTCG 59.848 38.462 0.00 0.00 0.00 3.46
1010 1011 7.320399 CACATAAGGGGTTATTTCTTGGTTTC 58.680 38.462 0.00 0.00 0.00 2.78
1011 1012 6.295632 GCACATAAGGGGTTATTTCTTGGTTT 60.296 38.462 0.00 0.00 0.00 3.27
1012 1013 5.186992 GCACATAAGGGGTTATTTCTTGGTT 59.813 40.000 0.00 0.00 0.00 3.67
1013 1014 4.709886 GCACATAAGGGGTTATTTCTTGGT 59.290 41.667 0.00 0.00 0.00 3.67
1014 1015 4.202010 CGCACATAAGGGGTTATTTCTTGG 60.202 45.833 0.00 0.00 0.00 3.61
1015 1016 4.638421 TCGCACATAAGGGGTTATTTCTTG 59.362 41.667 0.00 0.00 0.00 3.02
1016 1017 4.850680 TCGCACATAAGGGGTTATTTCTT 58.149 39.130 0.00 0.00 0.00 2.52
1017 1018 4.497291 TCGCACATAAGGGGTTATTTCT 57.503 40.909 0.00 0.00 0.00 2.52
1018 1019 5.570234 TTTCGCACATAAGGGGTTATTTC 57.430 39.130 0.00 0.00 0.00 2.17
1019 1020 6.538945 AATTTCGCACATAAGGGGTTATTT 57.461 33.333 0.00 0.00 0.00 1.40
1020 1021 7.833285 ATAATTTCGCACATAAGGGGTTATT 57.167 32.000 0.00 0.00 0.00 1.40
1023 1024 8.927675 TTATATAATTTCGCACATAAGGGGTT 57.072 30.769 0.00 0.00 0.00 4.11
1024 1025 8.380099 TCTTATATAATTTCGCACATAAGGGGT 58.620 33.333 0.00 0.00 30.48 4.95
1025 1026 8.786826 TCTTATATAATTTCGCACATAAGGGG 57.213 34.615 0.00 0.00 30.48 4.79
1029 1030 9.391006 GGGGATCTTATATAATTTCGCACATAA 57.609 33.333 16.74 0.00 0.00 1.90
1030 1031 8.768397 AGGGGATCTTATATAATTTCGCACATA 58.232 33.333 16.74 0.00 0.00 2.29
1031 1032 7.633789 AGGGGATCTTATATAATTTCGCACAT 58.366 34.615 16.74 6.21 0.00 3.21
1032 1033 7.016153 AGGGGATCTTATATAATTTCGCACA 57.984 36.000 16.74 0.00 0.00 4.57
1033 1034 7.923414 AAGGGGATCTTATATAATTTCGCAC 57.077 36.000 16.74 10.27 33.14 5.34
1045 1046 9.942526 ATTGTTTGATCTTAAAGGGGATCTTAT 57.057 29.630 0.00 0.00 39.09 1.73
1046 1047 9.768215 AATTGTTTGATCTTAAAGGGGATCTTA 57.232 29.630 0.00 0.00 39.09 2.10
1047 1048 8.670521 AATTGTTTGATCTTAAAGGGGATCTT 57.329 30.769 0.00 0.00 39.09 2.40
1048 1049 7.343057 GGAATTGTTTGATCTTAAAGGGGATCT 59.657 37.037 0.00 0.00 39.09 2.75
1049 1050 7.124147 TGGAATTGTTTGATCTTAAAGGGGATC 59.876 37.037 0.00 0.00 38.87 3.36
1050 1051 6.959366 TGGAATTGTTTGATCTTAAAGGGGAT 59.041 34.615 0.00 0.00 0.00 3.85
1051 1052 6.318913 TGGAATTGTTTGATCTTAAAGGGGA 58.681 36.000 0.00 0.00 0.00 4.81
1052 1053 6.603940 TGGAATTGTTTGATCTTAAAGGGG 57.396 37.500 0.00 0.00 0.00 4.79
1053 1054 6.974622 CGATGGAATTGTTTGATCTTAAAGGG 59.025 38.462 0.00 0.00 0.00 3.95
1054 1055 7.761409 TCGATGGAATTGTTTGATCTTAAAGG 58.239 34.615 0.00 0.00 0.00 3.11
1055 1056 9.793252 ATTCGATGGAATTGTTTGATCTTAAAG 57.207 29.630 0.00 0.00 39.90 1.85
1070 1071 9.730705 ATACAGTCATAATCAATTCGATGGAAT 57.269 29.630 0.00 0.00 44.69 3.01
1071 1072 8.992073 CATACAGTCATAATCAATTCGATGGAA 58.008 33.333 0.00 0.00 33.40 3.53
1072 1073 8.150296 ACATACAGTCATAATCAATTCGATGGA 58.850 33.333 0.00 0.00 33.40 3.41
1073 1074 8.225777 CACATACAGTCATAATCAATTCGATGG 58.774 37.037 0.00 0.00 33.40 3.51
1074 1075 8.768019 ACACATACAGTCATAATCAATTCGATG 58.232 33.333 0.00 0.00 33.40 3.84
1075 1076 8.768019 CACACATACAGTCATAATCAATTCGAT 58.232 33.333 0.00 0.00 35.12 3.59
1076 1077 7.978975 TCACACATACAGTCATAATCAATTCGA 59.021 33.333 0.00 0.00 0.00 3.71
1077 1078 8.130307 TCACACATACAGTCATAATCAATTCG 57.870 34.615 0.00 0.00 0.00 3.34
1080 1081 9.212641 GCTATCACACATACAGTCATAATCAAT 57.787 33.333 0.00 0.00 0.00 2.57
1081 1082 8.203485 TGCTATCACACATACAGTCATAATCAA 58.797 33.333 0.00 0.00 0.00 2.57
1082 1083 7.725251 TGCTATCACACATACAGTCATAATCA 58.275 34.615 0.00 0.00 0.00 2.57
1083 1084 8.768957 ATGCTATCACACATACAGTCATAATC 57.231 34.615 0.00 0.00 0.00 1.75
1084 1085 8.591940 AGATGCTATCACACATACAGTCATAAT 58.408 33.333 0.00 0.00 0.00 1.28
1085 1086 7.955918 AGATGCTATCACACATACAGTCATAA 58.044 34.615 0.00 0.00 0.00 1.90
1086 1087 7.530426 AGATGCTATCACACATACAGTCATA 57.470 36.000 0.00 0.00 0.00 2.15
1087 1088 6.416631 AGATGCTATCACACATACAGTCAT 57.583 37.500 0.00 0.00 0.00 3.06
1088 1089 5.859205 AGATGCTATCACACATACAGTCA 57.141 39.130 0.00 0.00 0.00 3.41
1089 1090 6.976088 AGTAGATGCTATCACACATACAGTC 58.024 40.000 0.00 0.00 0.00 3.51
1090 1091 6.968263 AGTAGATGCTATCACACATACAGT 57.032 37.500 0.00 0.00 0.00 3.55
1091 1092 9.995957 GTATAGTAGATGCTATCACACATACAG 57.004 37.037 0.00 0.00 34.00 2.74
1092 1093 9.515226 TGTATAGTAGATGCTATCACACATACA 57.485 33.333 0.00 0.00 34.00 2.29
1095 1096 8.526978 CCTTGTATAGTAGATGCTATCACACAT 58.473 37.037 0.00 0.00 34.00 3.21
1096 1097 7.724061 TCCTTGTATAGTAGATGCTATCACACA 59.276 37.037 0.00 0.00 34.00 3.72
1097 1098 8.112016 TCCTTGTATAGTAGATGCTATCACAC 57.888 38.462 0.00 0.00 34.00 3.82
1098 1099 8.706322 TTCCTTGTATAGTAGATGCTATCACA 57.294 34.615 0.00 0.00 34.00 3.58
1114 1115 9.872684 AATGAGGTTCATTGATATTCCTTGTAT 57.127 29.630 3.65 0.00 44.68 2.29
1115 1116 9.342308 GAATGAGGTTCATTGATATTCCTTGTA 57.658 33.333 8.88 0.00 46.20 2.41
1116 1117 8.057623 AGAATGAGGTTCATTGATATTCCTTGT 58.942 33.333 8.88 0.00 46.20 3.16
1117 1118 8.461249 AGAATGAGGTTCATTGATATTCCTTG 57.539 34.615 8.88 0.00 46.20 3.61
1118 1119 8.910944 CAAGAATGAGGTTCATTGATATTCCTT 58.089 33.333 8.88 2.48 46.20 3.36
1119 1120 7.014038 GCAAGAATGAGGTTCATTGATATTCCT 59.986 37.037 8.88 0.00 46.20 3.36
1120 1121 7.144000 GCAAGAATGAGGTTCATTGATATTCC 58.856 38.462 8.88 0.00 46.20 3.01
1121 1122 7.709947 TGCAAGAATGAGGTTCATTGATATTC 58.290 34.615 8.88 0.00 46.20 1.75
1122 1123 7.649533 TGCAAGAATGAGGTTCATTGATATT 57.350 32.000 8.88 0.00 46.20 1.28
1123 1124 7.649533 TTGCAAGAATGAGGTTCATTGATAT 57.350 32.000 8.88 0.00 46.20 1.63
1124 1125 7.649533 ATTGCAAGAATGAGGTTCATTGATA 57.350 32.000 4.94 0.00 46.20 2.15
1125 1126 5.988310 TTGCAAGAATGAGGTTCATTGAT 57.012 34.783 8.88 0.00 46.20 2.57
1126 1127 5.988310 ATTGCAAGAATGAGGTTCATTGA 57.012 34.783 4.94 0.00 46.20 2.57
1127 1128 5.163893 GCAATTGCAAGAATGAGGTTCATTG 60.164 40.000 25.36 0.71 42.86 2.82
1128 1129 4.933400 GCAATTGCAAGAATGAGGTTCATT 59.067 37.500 25.36 4.09 44.19 2.57
1129 1130 4.222145 AGCAATTGCAAGAATGAGGTTCAT 59.778 37.500 30.89 2.50 45.16 2.57
1130 1131 3.575256 AGCAATTGCAAGAATGAGGTTCA 59.425 39.130 30.89 0.00 45.16 3.18
1131 1132 4.171754 GAGCAATTGCAAGAATGAGGTTC 58.828 43.478 30.89 12.05 45.16 3.62
1132 1133 3.366679 CGAGCAATTGCAAGAATGAGGTT 60.367 43.478 30.89 6.65 45.16 3.50
1133 1134 2.163010 CGAGCAATTGCAAGAATGAGGT 59.837 45.455 30.89 7.20 45.16 3.85
1134 1135 2.479049 CCGAGCAATTGCAAGAATGAGG 60.479 50.000 30.89 16.84 45.16 3.86
1135 1136 2.479049 CCCGAGCAATTGCAAGAATGAG 60.479 50.000 30.89 12.44 45.16 2.90
1136 1137 1.473677 CCCGAGCAATTGCAAGAATGA 59.526 47.619 30.89 0.00 45.16 2.57
1137 1138 1.473677 TCCCGAGCAATTGCAAGAATG 59.526 47.619 30.89 14.34 45.16 2.67
1138 1139 1.838112 TCCCGAGCAATTGCAAGAAT 58.162 45.000 30.89 11.11 45.16 2.40
1139 1140 1.838112 ATCCCGAGCAATTGCAAGAA 58.162 45.000 30.89 15.40 45.16 2.52
1140 1141 2.288666 GTATCCCGAGCAATTGCAAGA 58.711 47.619 30.89 20.55 45.16 3.02
1141 1142 1.334869 GGTATCCCGAGCAATTGCAAG 59.665 52.381 30.89 22.52 45.16 4.01
1142 1143 1.388547 GGTATCCCGAGCAATTGCAA 58.611 50.000 30.89 0.00 45.16 4.08
1143 1144 0.465460 GGGTATCCCGAGCAATTGCA 60.465 55.000 30.89 11.51 37.46 4.08
1144 1145 2.331265 GGGTATCCCGAGCAATTGC 58.669 57.895 23.05 23.05 35.93 3.56
1154 1155 2.439880 AGCAGCTAAAAGAGGGTATCCC 59.560 50.000 0.00 0.00 45.90 3.85
1155 1156 3.847671 AGCAGCTAAAAGAGGGTATCC 57.152 47.619 0.00 0.00 0.00 2.59
1156 1157 4.345547 ACCTAGCAGCTAAAAGAGGGTATC 59.654 45.833 12.09 0.00 0.00 2.24
1157 1158 4.299485 ACCTAGCAGCTAAAAGAGGGTAT 58.701 43.478 12.09 0.00 0.00 2.73
1158 1159 3.705072 GACCTAGCAGCTAAAAGAGGGTA 59.295 47.826 12.09 0.00 0.00 3.69
1159 1160 2.502130 GACCTAGCAGCTAAAAGAGGGT 59.498 50.000 12.09 10.18 0.00 4.34
1160 1161 2.769095 AGACCTAGCAGCTAAAAGAGGG 59.231 50.000 12.09 7.25 0.00 4.30
1161 1162 5.799827 ATAGACCTAGCAGCTAAAAGAGG 57.200 43.478 3.09 5.07 0.00 3.69
1162 1163 7.496747 AGAAATAGACCTAGCAGCTAAAAGAG 58.503 38.462 3.09 0.00 0.00 2.85
1163 1164 7.425224 AGAAATAGACCTAGCAGCTAAAAGA 57.575 36.000 3.09 0.00 0.00 2.52
1164 1165 9.255304 CTAAGAAATAGACCTAGCAGCTAAAAG 57.745 37.037 3.09 0.00 33.04 2.27
1165 1166 8.759782 ACTAAGAAATAGACCTAGCAGCTAAAA 58.240 33.333 3.09 0.00 35.47 1.52
1166 1167 8.307582 ACTAAGAAATAGACCTAGCAGCTAAA 57.692 34.615 3.09 0.00 35.47 1.85
1167 1168 7.899648 ACTAAGAAATAGACCTAGCAGCTAA 57.100 36.000 3.09 0.00 35.47 3.09
1168 1169 7.560262 TGAACTAAGAAATAGACCTAGCAGCTA 59.440 37.037 1.13 1.13 35.47 3.32
1169 1170 6.381420 TGAACTAAGAAATAGACCTAGCAGCT 59.619 38.462 0.00 0.00 35.47 4.24
1170 1171 6.574350 TGAACTAAGAAATAGACCTAGCAGC 58.426 40.000 0.00 0.00 35.47 5.25
1171 1172 8.470805 TCTTGAACTAAGAAATAGACCTAGCAG 58.529 37.037 0.00 0.00 42.31 4.24
1172 1173 8.362464 TCTTGAACTAAGAAATAGACCTAGCA 57.638 34.615 0.00 0.00 42.31 3.49
1186 1187 8.973182 AGTTAGTAAGAGGGATCTTGAACTAAG 58.027 37.037 11.12 0.00 34.29 2.18
1187 1188 8.750298 CAGTTAGTAAGAGGGATCTTGAACTAA 58.250 37.037 8.35 8.35 32.65 2.24
1188 1189 7.342284 CCAGTTAGTAAGAGGGATCTTGAACTA 59.658 40.741 11.28 5.87 32.42 2.24
1189 1190 6.155393 CCAGTTAGTAAGAGGGATCTTGAACT 59.845 42.308 0.81 5.28 33.14 3.01
1190 1191 6.154706 TCCAGTTAGTAAGAGGGATCTTGAAC 59.845 42.308 0.81 3.41 0.00 3.18
1191 1192 6.261435 TCCAGTTAGTAAGAGGGATCTTGAA 58.739 40.000 0.81 0.00 0.00 2.69
1192 1193 5.838955 TCCAGTTAGTAAGAGGGATCTTGA 58.161 41.667 0.81 0.00 0.00 3.02
1193 1194 6.546428 TTCCAGTTAGTAAGAGGGATCTTG 57.454 41.667 0.81 0.00 0.00 3.02
1194 1195 8.855804 TTATTCCAGTTAGTAAGAGGGATCTT 57.144 34.615 0.00 0.00 0.00 2.40
1195 1196 8.855804 TTTATTCCAGTTAGTAAGAGGGATCT 57.144 34.615 0.00 0.00 0.00 2.75
1196 1197 9.549078 CTTTTATTCCAGTTAGTAAGAGGGATC 57.451 37.037 0.00 0.00 0.00 3.36
1197 1198 9.280456 TCTTTTATTCCAGTTAGTAAGAGGGAT 57.720 33.333 1.10 1.10 0.00 3.85
1198 1199 8.674925 TCTTTTATTCCAGTTAGTAAGAGGGA 57.325 34.615 1.75 0.00 0.00 4.20
1199 1200 9.907229 ATTCTTTTATTCCAGTTAGTAAGAGGG 57.093 33.333 1.75 0.00 0.00 4.30
1216 1217 9.262358 GCGGAACAGATCTACTAATTCTTTTAT 57.738 33.333 0.00 0.00 0.00 1.40
1217 1218 7.709613 GGCGGAACAGATCTACTAATTCTTTTA 59.290 37.037 0.00 0.00 0.00 1.52
1218 1219 6.539103 GGCGGAACAGATCTACTAATTCTTTT 59.461 38.462 0.00 0.00 0.00 2.27
1219 1220 6.049790 GGCGGAACAGATCTACTAATTCTTT 58.950 40.000 0.00 0.00 0.00 2.52
1220 1221 5.453480 GGGCGGAACAGATCTACTAATTCTT 60.453 44.000 0.00 0.00 0.00 2.52
1221 1222 4.039366 GGGCGGAACAGATCTACTAATTCT 59.961 45.833 0.00 0.00 0.00 2.40
1222 1223 4.202223 TGGGCGGAACAGATCTACTAATTC 60.202 45.833 0.00 0.00 0.00 2.17
1223 1224 3.709653 TGGGCGGAACAGATCTACTAATT 59.290 43.478 0.00 0.00 0.00 1.40
1224 1225 3.305720 TGGGCGGAACAGATCTACTAAT 58.694 45.455 0.00 0.00 0.00 1.73
1225 1226 2.742348 TGGGCGGAACAGATCTACTAA 58.258 47.619 0.00 0.00 0.00 2.24
1226 1227 2.447408 TGGGCGGAACAGATCTACTA 57.553 50.000 0.00 0.00 0.00 1.82
1227 1228 1.568504 TTGGGCGGAACAGATCTACT 58.431 50.000 0.00 0.00 0.00 2.57
1228 1229 2.396590 TTTGGGCGGAACAGATCTAC 57.603 50.000 0.00 0.00 0.00 2.59
1229 1230 3.278574 CATTTTGGGCGGAACAGATCTA 58.721 45.455 0.00 0.00 0.00 1.98
1230 1231 2.094675 CATTTTGGGCGGAACAGATCT 58.905 47.619 0.00 0.00 0.00 2.75
1231 1232 1.134946 CCATTTTGGGCGGAACAGATC 59.865 52.381 0.00 0.00 32.67 2.75
1232 1233 1.185315 CCATTTTGGGCGGAACAGAT 58.815 50.000 0.00 0.00 32.67 2.90
1233 1234 2.652313 CCATTTTGGGCGGAACAGA 58.348 52.632 0.00 0.00 32.67 3.41
1243 1244 1.079197 GCGCCCTTTCCCATTTTGG 60.079 57.895 0.00 0.00 37.25 3.28
1244 1245 1.134946 CTAGCGCCCTTTCCCATTTTG 59.865 52.381 2.29 0.00 0.00 2.44
1245 1246 1.474330 CTAGCGCCCTTTCCCATTTT 58.526 50.000 2.29 0.00 0.00 1.82
1246 1247 0.395724 CCTAGCGCCCTTTCCCATTT 60.396 55.000 2.29 0.00 0.00 2.32
1247 1248 1.227383 CCTAGCGCCCTTTCCCATT 59.773 57.895 2.29 0.00 0.00 3.16
1248 1249 2.757124 CCCTAGCGCCCTTTCCCAT 61.757 63.158 2.29 0.00 0.00 4.00
1249 1250 3.407967 CCCTAGCGCCCTTTCCCA 61.408 66.667 2.29 0.00 0.00 4.37
1250 1251 1.629181 TAACCCTAGCGCCCTTTCCC 61.629 60.000 2.29 0.00 0.00 3.97
1251 1252 0.472898 ATAACCCTAGCGCCCTTTCC 59.527 55.000 2.29 0.00 0.00 3.13
1252 1253 1.140252 TCATAACCCTAGCGCCCTTTC 59.860 52.381 2.29 0.00 0.00 2.62
1253 1254 1.209621 TCATAACCCTAGCGCCCTTT 58.790 50.000 2.29 0.00 0.00 3.11
1254 1255 1.134189 GTTCATAACCCTAGCGCCCTT 60.134 52.381 2.29 0.00 0.00 3.95
1255 1256 0.468648 GTTCATAACCCTAGCGCCCT 59.531 55.000 2.29 0.00 0.00 5.19
1256 1257 0.468648 AGTTCATAACCCTAGCGCCC 59.531 55.000 2.29 0.00 0.00 6.13
1257 1258 2.327200 AAGTTCATAACCCTAGCGCC 57.673 50.000 2.29 0.00 0.00 6.53
1258 1259 6.872020 TGATTATAAGTTCATAACCCTAGCGC 59.128 38.462 0.00 0.00 0.00 5.92
1259 1260 8.873830 CATGATTATAAGTTCATAACCCTAGCG 58.126 37.037 2.05 0.00 31.50 4.26
1260 1261 9.167311 CCATGATTATAAGTTCATAACCCTAGC 57.833 37.037 0.00 0.00 31.50 3.42
1269 1270 9.429359 GAGTCGATTCCATGATTATAAGTTCAT 57.571 33.333 0.00 0.00 32.87 2.57
1270 1271 8.421002 TGAGTCGATTCCATGATTATAAGTTCA 58.579 33.333 5.38 0.00 0.00 3.18
1271 1272 8.818141 TGAGTCGATTCCATGATTATAAGTTC 57.182 34.615 5.38 0.00 0.00 3.01
1272 1273 9.613428 TTTGAGTCGATTCCATGATTATAAGTT 57.387 29.630 5.38 0.00 0.00 2.66
1273 1274 9.265901 CTTTGAGTCGATTCCATGATTATAAGT 57.734 33.333 5.38 0.00 0.00 2.24
1274 1275 9.481340 TCTTTGAGTCGATTCCATGATTATAAG 57.519 33.333 5.38 0.00 0.00 1.73
1275 1276 9.481340 CTCTTTGAGTCGATTCCATGATTATAA 57.519 33.333 5.38 0.00 0.00 0.98
1276 1277 8.090831 CCTCTTTGAGTCGATTCCATGATTATA 58.909 37.037 5.38 0.00 0.00 0.98
1277 1278 6.933521 CCTCTTTGAGTCGATTCCATGATTAT 59.066 38.462 5.38 0.00 0.00 1.28
1278 1279 6.283694 CCTCTTTGAGTCGATTCCATGATTA 58.716 40.000 5.38 0.00 0.00 1.75
1279 1280 5.121811 CCTCTTTGAGTCGATTCCATGATT 58.878 41.667 5.38 0.00 0.00 2.57
1280 1281 4.444022 CCCTCTTTGAGTCGATTCCATGAT 60.444 45.833 5.38 0.00 0.00 2.45
1281 1282 3.118629 CCCTCTTTGAGTCGATTCCATGA 60.119 47.826 5.38 1.91 0.00 3.07
1282 1283 3.118629 TCCCTCTTTGAGTCGATTCCATG 60.119 47.826 5.38 0.00 0.00 3.66
1283 1284 3.107601 TCCCTCTTTGAGTCGATTCCAT 58.892 45.455 5.38 0.00 0.00 3.41
1284 1285 2.536066 TCCCTCTTTGAGTCGATTCCA 58.464 47.619 5.38 0.00 0.00 3.53
1285 1286 3.263261 GTTCCCTCTTTGAGTCGATTCC 58.737 50.000 5.38 0.00 0.00 3.01
1286 1287 2.924290 CGTTCCCTCTTTGAGTCGATTC 59.076 50.000 0.13 0.13 0.00 2.52
1287 1288 2.353803 CCGTTCCCTCTTTGAGTCGATT 60.354 50.000 0.00 0.00 0.00 3.34
1288 1289 1.204941 CCGTTCCCTCTTTGAGTCGAT 59.795 52.381 0.00 0.00 0.00 3.59
1289 1290 0.601558 CCGTTCCCTCTTTGAGTCGA 59.398 55.000 0.00 0.00 0.00 4.20
1290 1291 0.601558 TCCGTTCCCTCTTTGAGTCG 59.398 55.000 0.00 0.00 0.00 4.18
1291 1292 2.689646 CTTCCGTTCCCTCTTTGAGTC 58.310 52.381 0.00 0.00 0.00 3.36
1292 1293 1.270893 GCTTCCGTTCCCTCTTTGAGT 60.271 52.381 0.00 0.00 0.00 3.41
1293 1294 1.443802 GCTTCCGTTCCCTCTTTGAG 58.556 55.000 0.00 0.00 0.00 3.02
1294 1295 0.320421 CGCTTCCGTTCCCTCTTTGA 60.320 55.000 0.00 0.00 0.00 2.69
1295 1296 2.162716 CGCTTCCGTTCCCTCTTTG 58.837 57.895 0.00 0.00 0.00 2.77
1296 1297 4.695560 CGCTTCCGTTCCCTCTTT 57.304 55.556 0.00 0.00 0.00 2.52
1456 1458 1.347320 GTGAGGTGAAATCCGTCGAC 58.653 55.000 5.18 5.18 0.00 4.20
1839 1841 1.877576 CTGCAGTGTGCTCCTCCGTA 61.878 60.000 5.25 0.00 45.31 4.02
1923 1925 2.166459 CCTGACTCGCTTGAAGGTATCA 59.834 50.000 0.00 0.00 35.85 2.15


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

AutoCloner maintained by Alex Coulton.