Multiple sequence alignment - TraesCS3D01G161200

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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 TraesCS3D01G161200 chr3D 100.000 3146 0 0 1 3146 131596769 131599914 0.000000e+00 5810
1 TraesCS3D01G161200 chr3A 83.516 1729 222 29 130 1812 623996979 623998690 0.000000e+00 1555
2 TraesCS3D01G161200 chr3A 81.644 888 146 13 2265 3146 623999155 624000031 0.000000e+00 721
3 TraesCS3D01G161200 chr5B 78.831 2173 399 38 1018 3146 72810310 72808155 0.000000e+00 1408
4 TraesCS3D01G161200 chr1D 77.083 1056 212 19 658 1707 55037049 55036018 1.630000e-162 582
5 TraesCS3D01G161200 chr1D 75.037 673 158 9 2468 3134 55033193 55032525 1.420000e-78 303
6 TraesCS3D01G161200 chr2A 77.836 961 186 22 658 1608 665948997 665948054 1.270000e-158 569
7 TraesCS3D01G161200 chr6A 77.732 961 187 20 658 1608 555924114 555923171 5.890000e-157 564
8 TraesCS3D01G161200 chr1B 75.304 1069 210 39 658 1707 648715884 648714851 2.210000e-126 462
9 TraesCS3D01G161200 chr6B 74.091 660 144 24 2503 3146 171975679 171976327 2.420000e-61 246


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 TraesCS3D01G161200 chr3D 131596769 131599914 3145 False 5810.0 5810 100.000 1 3146 1 chr3D.!!$F1 3145
1 TraesCS3D01G161200 chr3A 623996979 624000031 3052 False 1138.0 1555 82.580 130 3146 2 chr3A.!!$F1 3016
2 TraesCS3D01G161200 chr5B 72808155 72810310 2155 True 1408.0 1408 78.831 1018 3146 1 chr5B.!!$R1 2128
3 TraesCS3D01G161200 chr1D 55032525 55037049 4524 True 442.5 582 76.060 658 3134 2 chr1D.!!$R1 2476
4 TraesCS3D01G161200 chr2A 665948054 665948997 943 True 569.0 569 77.836 658 1608 1 chr2A.!!$R1 950
5 TraesCS3D01G161200 chr6A 555923171 555924114 943 True 564.0 564 77.732 658 1608 1 chr6A.!!$R1 950
6 TraesCS3D01G161200 chr1B 648714851 648715884 1033 True 462.0 462 75.304 658 1707 1 chr1B.!!$R1 1049
7 TraesCS3D01G161200 chr6B 171975679 171976327 648 False 246.0 246 74.091 2503 3146 1 chr6B.!!$F1 643

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
88 89 0.105039 CCCTCTCTACCGGTGCAATC 59.895 60.0 19.93 0.0 0.00 2.67 F
238 239 0.178861 TGCTCCCCTCCCTTTTCTCT 60.179 55.0 0.00 0.0 0.00 3.10 F
1812 3523 0.538118 ACGGGCTTATCCTAACGCAA 59.462 50.0 0.00 0.0 34.39 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1065 1107 0.099436 GATGCTCAATGAACGGTGCC 59.901 55.0 0.00 0.00 0.00 5.01 R
1943 3666 0.106469 CGTCCTCTCCATCTCTGGGA 60.106 60.0 0.00 0.00 43.34 4.37 R
2655 4907 0.319813 TGCACACTGATCTCGTGGTG 60.320 55.0 16.46 13.22 36.71 4.17 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
20 21 3.371102 TGTGCAGAACAGACTACTCAC 57.629 47.619 0.00 0.00 33.78 3.51
21 22 2.287608 TGTGCAGAACAGACTACTCACG 60.288 50.000 0.00 0.00 33.78 4.35
22 23 2.031069 GTGCAGAACAGACTACTCACGA 60.031 50.000 0.00 0.00 0.00 4.35
23 24 2.031069 TGCAGAACAGACTACTCACGAC 60.031 50.000 0.00 0.00 0.00 4.34
24 25 2.031069 GCAGAACAGACTACTCACGACA 60.031 50.000 0.00 0.00 0.00 4.35
25 26 3.816091 CAGAACAGACTACTCACGACAG 58.184 50.000 0.00 0.00 0.00 3.51
26 27 3.498777 CAGAACAGACTACTCACGACAGA 59.501 47.826 0.00 0.00 0.00 3.41
27 28 3.499157 AGAACAGACTACTCACGACAGAC 59.501 47.826 0.00 0.00 0.00 3.51
28 29 2.847441 ACAGACTACTCACGACAGACA 58.153 47.619 0.00 0.00 0.00 3.41
29 30 2.809119 ACAGACTACTCACGACAGACAG 59.191 50.000 0.00 0.00 0.00 3.51
30 31 2.160615 CAGACTACTCACGACAGACAGG 59.839 54.545 0.00 0.00 0.00 4.00
31 32 0.882474 ACTACTCACGACAGACAGGC 59.118 55.000 0.00 0.00 0.00 4.85
32 33 1.169577 CTACTCACGACAGACAGGCT 58.830 55.000 0.00 0.00 0.00 4.58
41 42 2.764944 CAGACAGGCTGCTTGCTAG 58.235 57.895 15.89 0.00 42.39 3.42
42 43 0.743701 CAGACAGGCTGCTTGCTAGG 60.744 60.000 15.89 0.00 42.39 3.02
43 44 2.045536 ACAGGCTGCTTGCTAGGC 60.046 61.111 15.89 9.33 42.39 3.93
44 45 2.045634 CAGGCTGCTTGCTAGGCA 60.046 61.111 0.00 0.00 42.62 4.75
45 46 1.676635 CAGGCTGCTTGCTAGGCAA 60.677 57.895 0.00 4.87 46.80 4.52
59 60 2.877691 GCAATGGCCACCGAACTC 59.122 61.111 8.16 0.00 0.00 3.01
60 61 1.971167 GCAATGGCCACCGAACTCA 60.971 57.895 8.16 0.00 0.00 3.41
61 62 1.315257 GCAATGGCCACCGAACTCAT 61.315 55.000 8.16 0.00 0.00 2.90
62 63 2.016604 GCAATGGCCACCGAACTCATA 61.017 52.381 8.16 0.00 0.00 2.15
63 64 2.575532 CAATGGCCACCGAACTCATAT 58.424 47.619 8.16 0.00 0.00 1.78
64 65 2.951642 CAATGGCCACCGAACTCATATT 59.048 45.455 8.16 0.00 0.00 1.28
65 66 2.799126 TGGCCACCGAACTCATATTT 57.201 45.000 0.00 0.00 0.00 1.40
66 67 2.639065 TGGCCACCGAACTCATATTTC 58.361 47.619 0.00 0.00 0.00 2.17
67 68 2.238646 TGGCCACCGAACTCATATTTCT 59.761 45.455 0.00 0.00 0.00 2.52
68 69 2.614057 GGCCACCGAACTCATATTTCTG 59.386 50.000 0.00 0.00 0.00 3.02
69 70 2.032178 GCCACCGAACTCATATTTCTGC 59.968 50.000 0.00 0.00 0.00 4.26
70 71 2.614057 CCACCGAACTCATATTTCTGCC 59.386 50.000 0.00 0.00 0.00 4.85
71 72 2.614057 CACCGAACTCATATTTCTGCCC 59.386 50.000 0.00 0.00 0.00 5.36
72 73 2.505819 ACCGAACTCATATTTCTGCCCT 59.494 45.455 0.00 0.00 0.00 5.19
73 74 3.134458 CCGAACTCATATTTCTGCCCTC 58.866 50.000 0.00 0.00 0.00 4.30
74 75 3.181461 CCGAACTCATATTTCTGCCCTCT 60.181 47.826 0.00 0.00 0.00 3.69
75 76 4.054671 CGAACTCATATTTCTGCCCTCTC 58.945 47.826 0.00 0.00 0.00 3.20
76 77 4.202202 CGAACTCATATTTCTGCCCTCTCT 60.202 45.833 0.00 0.00 0.00 3.10
77 78 5.010112 CGAACTCATATTTCTGCCCTCTCTA 59.990 44.000 0.00 0.00 0.00 2.43
78 79 5.799827 ACTCATATTTCTGCCCTCTCTAC 57.200 43.478 0.00 0.00 0.00 2.59
79 80 4.591072 ACTCATATTTCTGCCCTCTCTACC 59.409 45.833 0.00 0.00 0.00 3.18
80 81 3.574396 TCATATTTCTGCCCTCTCTACCG 59.426 47.826 0.00 0.00 0.00 4.02
81 82 1.123928 ATTTCTGCCCTCTCTACCGG 58.876 55.000 0.00 0.00 0.00 5.28
82 83 0.252103 TTTCTGCCCTCTCTACCGGT 60.252 55.000 13.98 13.98 0.00 5.28
83 84 0.970937 TTCTGCCCTCTCTACCGGTG 60.971 60.000 19.93 7.59 0.00 4.94
84 85 3.075005 TGCCCTCTCTACCGGTGC 61.075 66.667 19.93 10.94 0.00 5.01
85 86 3.075005 GCCCTCTCTACCGGTGCA 61.075 66.667 19.93 1.55 0.00 4.57
86 87 2.656069 GCCCTCTCTACCGGTGCAA 61.656 63.158 19.93 0.68 0.00 4.08
87 88 1.972660 GCCCTCTCTACCGGTGCAAT 61.973 60.000 19.93 0.00 0.00 3.56
88 89 0.105039 CCCTCTCTACCGGTGCAATC 59.895 60.000 19.93 0.00 0.00 2.67
89 90 1.115467 CCTCTCTACCGGTGCAATCT 58.885 55.000 19.93 0.00 0.00 2.40
90 91 1.482593 CCTCTCTACCGGTGCAATCTT 59.517 52.381 19.93 0.00 0.00 2.40
91 92 2.544685 CTCTCTACCGGTGCAATCTTG 58.455 52.381 19.93 0.00 0.00 3.02
92 93 2.166459 CTCTCTACCGGTGCAATCTTGA 59.834 50.000 19.93 3.24 0.00 3.02
93 94 2.565391 TCTCTACCGGTGCAATCTTGAA 59.435 45.455 19.93 0.00 0.00 2.69
94 95 3.007506 TCTCTACCGGTGCAATCTTGAAA 59.992 43.478 19.93 0.00 0.00 2.69
95 96 3.941483 CTCTACCGGTGCAATCTTGAAAT 59.059 43.478 19.93 0.00 0.00 2.17
96 97 3.689161 TCTACCGGTGCAATCTTGAAATG 59.311 43.478 19.93 0.00 0.00 2.32
97 98 1.545582 ACCGGTGCAATCTTGAAATGG 59.454 47.619 6.12 0.00 0.00 3.16
98 99 1.632422 CGGTGCAATCTTGAAATGGC 58.368 50.000 0.00 0.00 0.00 4.40
99 100 1.203052 CGGTGCAATCTTGAAATGGCT 59.797 47.619 0.00 0.00 0.00 4.75
100 101 2.613691 GGTGCAATCTTGAAATGGCTG 58.386 47.619 0.00 0.00 0.00 4.85
101 102 2.231964 GGTGCAATCTTGAAATGGCTGA 59.768 45.455 0.00 0.00 0.00 4.26
102 103 3.508762 GTGCAATCTTGAAATGGCTGAG 58.491 45.455 0.00 0.00 0.00 3.35
103 104 3.192001 GTGCAATCTTGAAATGGCTGAGA 59.808 43.478 0.00 0.00 0.00 3.27
104 105 3.827876 TGCAATCTTGAAATGGCTGAGAA 59.172 39.130 0.00 0.00 0.00 2.87
105 106 4.281435 TGCAATCTTGAAATGGCTGAGAAA 59.719 37.500 0.00 0.00 0.00 2.52
106 107 4.863131 GCAATCTTGAAATGGCTGAGAAAG 59.137 41.667 0.00 0.00 0.00 2.62
115 116 3.523806 GCTGAGAAAGCGGAAGAGT 57.476 52.632 0.00 0.00 43.45 3.24
116 117 2.656560 GCTGAGAAAGCGGAAGAGTA 57.343 50.000 0.00 0.00 43.45 2.59
117 118 2.535331 GCTGAGAAAGCGGAAGAGTAG 58.465 52.381 0.00 0.00 43.45 2.57
118 119 2.164624 GCTGAGAAAGCGGAAGAGTAGA 59.835 50.000 0.00 0.00 43.45 2.59
119 120 3.733684 GCTGAGAAAGCGGAAGAGTAGAG 60.734 52.174 0.00 0.00 43.45 2.43
120 121 3.687125 TGAGAAAGCGGAAGAGTAGAGA 58.313 45.455 0.00 0.00 0.00 3.10
121 122 3.692101 TGAGAAAGCGGAAGAGTAGAGAG 59.308 47.826 0.00 0.00 0.00 3.20
122 123 2.425668 AGAAAGCGGAAGAGTAGAGAGC 59.574 50.000 0.00 0.00 0.00 4.09
123 124 0.736053 AAGCGGAAGAGTAGAGAGCG 59.264 55.000 0.00 0.00 0.00 5.03
124 125 1.298788 GCGGAAGAGTAGAGAGCGC 60.299 63.158 0.00 0.00 0.00 5.92
125 126 1.720694 GCGGAAGAGTAGAGAGCGCT 61.721 60.000 11.27 11.27 0.00 5.92
126 127 0.306533 CGGAAGAGTAGAGAGCGCTC 59.693 60.000 30.01 30.01 41.62 5.03
224 225 3.412408 GTCCCCCTTCCCTGCTCC 61.412 72.222 0.00 0.00 0.00 4.70
228 229 3.093172 CCCTTCCCTGCTCCCCTC 61.093 72.222 0.00 0.00 0.00 4.30
230 231 3.093172 CTTCCCTGCTCCCCTCCC 61.093 72.222 0.00 0.00 0.00 4.30
231 232 3.626596 TTCCCTGCTCCCCTCCCT 61.627 66.667 0.00 0.00 0.00 4.20
233 234 2.615288 CCCTGCTCCCCTCCCTTT 60.615 66.667 0.00 0.00 0.00 3.11
234 235 2.241659 CCCTGCTCCCCTCCCTTTT 61.242 63.158 0.00 0.00 0.00 2.27
235 236 1.304617 CCTGCTCCCCTCCCTTTTC 59.695 63.158 0.00 0.00 0.00 2.29
236 237 1.210885 CCTGCTCCCCTCCCTTTTCT 61.211 60.000 0.00 0.00 0.00 2.52
237 238 0.254462 CTGCTCCCCTCCCTTTTCTC 59.746 60.000 0.00 0.00 0.00 2.87
238 239 0.178861 TGCTCCCCTCCCTTTTCTCT 60.179 55.000 0.00 0.00 0.00 3.10
252 253 0.617535 TTCTCTCCATGGCTTCCGGA 60.618 55.000 6.96 0.00 0.00 5.14
256 257 1.692395 TCCATGGCTTCCGGATCCA 60.692 57.895 23.23 23.23 0.00 3.41
258 259 1.528824 CATGGCTTCCGGATCCAGT 59.471 57.895 24.52 13.80 32.78 4.00
264 265 1.759459 CTTCCGGATCCAGTAGCCCC 61.759 65.000 13.41 0.00 0.00 5.80
285 286 1.211449 CTCTGTCTCGTCAGCGCTT 59.789 57.895 7.50 0.00 38.14 4.68
288 289 1.069924 CTGTCTCGTCAGCGCTTCAG 61.070 60.000 7.50 0.94 38.14 3.02
321 322 2.943978 CGTATCGGGGCTGGGGATC 61.944 68.421 0.00 0.00 0.00 3.36
350 351 3.982372 CTGGCTCGGCGCTTTCGTA 62.982 63.158 7.64 0.00 39.13 3.43
360 361 2.884207 CTTTCGTACTCGGCGGGC 60.884 66.667 6.72 0.00 37.69 6.13
378 379 4.796495 GGTGGTCCGGTGGATGGC 62.796 72.222 0.00 0.00 32.73 4.40
542 543 2.016393 CTGATTCCGCCGGAGCTGTA 62.016 60.000 5.05 0.00 36.60 2.74
543 544 1.367840 GATTCCGCCGGAGCTGTAT 59.632 57.895 5.05 0.00 36.60 2.29
567 568 3.329386 CCTCTGTTTCAGATGCTTCGAA 58.671 45.455 0.00 0.00 39.92 3.71
573 574 1.945387 TCAGATGCTTCGAAGATGGC 58.055 50.000 28.95 14.50 35.04 4.40
599 600 1.227556 GTCAGGACTGCACCAACGT 60.228 57.895 0.00 0.00 0.00 3.99
632 640 2.750657 CCTCCCTGGCCATGTCTCC 61.751 68.421 5.51 0.00 0.00 3.71
635 643 2.750657 CCCTGGCCATGTCTCCTCC 61.751 68.421 5.51 0.00 0.00 4.30
642 650 1.556373 CCATGTCTCCTCCCAGTGCA 61.556 60.000 0.00 0.00 0.00 4.57
653 661 3.385384 CAGTGCAGGGAGCCTCGA 61.385 66.667 0.00 0.00 44.83 4.04
656 664 2.283894 TGCAGGGAGCCTCGAAGA 60.284 61.111 0.00 0.00 44.83 2.87
696 731 4.459089 GCAGGTCGGAGGCACCTC 62.459 72.222 8.26 8.26 42.85 3.85
717 752 3.570212 AGGCACCGGCTTTGAGGT 61.570 61.111 0.00 0.00 42.34 3.85
789 824 3.646715 CGCCCAACCTCCCTTCCA 61.647 66.667 0.00 0.00 0.00 3.53
819 860 3.964875 CGGTTATGCATGCGGGGC 61.965 66.667 14.09 3.40 0.00 5.80
839 880 1.067283 CCGTCTGAGATCTGTGTGCTT 60.067 52.381 0.00 0.00 0.00 3.91
862 904 2.511600 GTCGGAGGGCATGAACGG 60.512 66.667 0.00 0.00 0.00 4.44
863 905 3.000819 TCGGAGGGCATGAACGGT 61.001 61.111 0.00 0.00 0.00 4.83
866 908 1.299976 GGAGGGCATGAACGGTCTT 59.700 57.895 0.33 0.00 0.00 3.01
887 929 2.753043 CGGAGGCTGCATTTGGCT 60.753 61.111 6.86 0.00 45.15 4.75
892 934 2.263540 GCTGCATTTGGCTGTGGG 59.736 61.111 0.00 0.00 45.15 4.61
962 1004 2.870372 GCGATTTCGGCACAGCTT 59.130 55.556 1.75 0.00 40.23 3.74
966 1008 1.937546 GATTTCGGCACAGCTTGGGG 61.938 60.000 0.00 0.00 0.00 4.96
1002 1044 5.095490 GCTTTTCCGTTCATAAGTTCCATG 58.905 41.667 0.00 0.00 0.00 3.66
1031 1073 0.682532 TTCTGGTGGTGTTTGCTGCA 60.683 50.000 0.00 0.00 0.00 4.41
1048 1090 1.295792 GCACACGAGTTCAGGAACAA 58.704 50.000 14.06 0.00 43.47 2.83
1054 1096 2.213499 CGAGTTCAGGAACAAAGCACT 58.787 47.619 14.06 0.00 43.47 4.40
1055 1097 2.032549 CGAGTTCAGGAACAAAGCACTG 60.033 50.000 14.06 0.00 43.47 3.66
1056 1098 2.291741 GAGTTCAGGAACAAAGCACTGG 59.708 50.000 14.06 0.00 43.47 4.00
1057 1099 1.032014 TTCAGGAACAAAGCACTGGC 58.968 50.000 0.00 0.00 41.61 4.85
1058 1100 4.759195 GTTCAGGAACAAAGCACTGGCG 62.759 54.545 7.27 0.00 42.14 5.69
1089 1131 1.202222 CCGTTCATTGAGCATCTTGGC 60.202 52.381 1.35 0.00 34.92 4.52
1176 1218 1.051008 TGGACATCATGATCGAGGGG 58.949 55.000 4.86 0.00 0.00 4.79
1199 1241 2.110967 CGTCTCATGCTTGGGCCAG 61.111 63.158 6.23 2.11 37.74 4.85
1261 1303 3.959975 GTTTGGCGCCGCAGACAA 61.960 61.111 23.90 6.19 37.36 3.18
1341 1383 2.815647 CCGGCGTTCAGGAAGCTC 60.816 66.667 6.01 0.00 0.00 4.09
1351 1393 3.706373 GGAAGCTCTGGGTGCCGA 61.706 66.667 0.00 0.00 0.00 5.54
1495 1537 1.748403 GCATCTGGGTCGGATAGCA 59.252 57.895 0.00 0.00 0.00 3.49
1557 1599 1.229658 CCAGGGAGGAGAGTGGGTT 60.230 63.158 0.00 0.00 41.22 4.11
1582 1624 2.651361 CTTGGACTCGCGGAGTGT 59.349 61.111 14.47 5.47 43.53 3.55
1599 1641 1.221840 GTGTGATGATCGGGGTGCT 59.778 57.895 0.00 0.00 0.00 4.40
1625 1667 1.806568 GATCGCATTTTCCGGCCAA 59.193 52.632 2.24 0.00 0.00 4.52
1738 2037 4.683334 GCGCTTTGGCCGTCACAC 62.683 66.667 0.00 0.00 34.44 3.82
1742 2041 2.904866 TTTGGCCGTCACACCTGC 60.905 61.111 0.00 0.00 0.00 4.85
1743 2042 4.947147 TTGGCCGTCACACCTGCC 62.947 66.667 0.00 0.00 44.27 4.85
1772 3483 3.667282 CCACGACGACCGGACTGT 61.667 66.667 9.46 4.57 43.93 3.55
1784 3495 2.283529 GGACTGTTCGGGAGCAGGA 61.284 63.158 15.47 0.00 42.88 3.86
1812 3523 0.538118 ACGGGCTTATCCTAACGCAA 59.462 50.000 0.00 0.00 34.39 4.85
1813 3524 1.065998 ACGGGCTTATCCTAACGCAAA 60.066 47.619 0.00 0.00 34.39 3.68
1814 3525 1.597663 CGGGCTTATCCTAACGCAAAG 59.402 52.381 0.00 0.00 34.39 2.77
1817 3528 3.267483 GGCTTATCCTAACGCAAAGTGA 58.733 45.455 0.00 0.00 0.00 3.41
1819 3530 4.181578 GCTTATCCTAACGCAAAGTGAGA 58.818 43.478 0.00 0.00 32.77 3.27
1821 3532 5.277058 GCTTATCCTAACGCAAAGTGAGATG 60.277 44.000 0.00 0.00 32.77 2.90
1822 3533 2.346803 TCCTAACGCAAAGTGAGATGC 58.653 47.619 0.00 0.00 32.77 3.91
1827 3538 1.575922 GCAAAGTGAGATGCGCACA 59.424 52.632 14.90 2.83 36.66 4.57
1856 3567 3.706373 AGCTGGCAATCGGACCGT 61.706 61.111 14.79 0.00 0.00 4.83
1861 3572 4.778143 GCAATCGGACCGTGCCCT 62.778 66.667 16.50 0.00 31.94 5.19
1863 3574 3.782443 AATCGGACCGTGCCCTCC 61.782 66.667 14.79 0.00 0.00 4.30
1866 3577 4.760047 CGGACCGTGCCCTCCAAG 62.760 72.222 5.48 0.00 0.00 3.61
1876 3599 2.280079 CCTCCAAGGGGCCAATCC 59.720 66.667 4.39 0.00 0.00 3.01
1878 3601 1.076485 CTCCAAGGGGCCAATCCTG 60.076 63.158 4.39 0.00 34.34 3.86
1880 3603 2.625460 CCAAGGGGCCAATCCTGGA 61.625 63.158 4.39 0.00 46.92 3.86
1882 3605 1.230281 AAGGGGCCAATCCTGGAGA 60.230 57.895 4.39 0.00 46.92 3.71
1884 3607 1.076705 GGGGCCAATCCTGGAGAAC 60.077 63.158 4.39 0.00 46.92 3.01
1887 3610 1.034292 GGCCAATCCTGGAGAACAGC 61.034 60.000 1.52 0.60 46.92 4.40
1940 3663 2.106332 GGTACGGGCGGATCAGTG 59.894 66.667 0.00 0.00 0.00 3.66
1943 3666 2.431454 TACGGGCGGATCAGTGCAT 61.431 57.895 0.00 0.00 0.00 3.96
1963 3686 0.396417 CCCAGAGATGGAGAGGACGT 60.396 60.000 0.00 0.00 0.00 4.34
1968 3691 0.681564 AGATGGAGAGGACGTTCGCT 60.682 55.000 0.00 0.00 0.00 4.93
1970 3693 0.681564 ATGGAGAGGACGTTCGCTCT 60.682 55.000 24.42 6.43 30.32 4.09
1972 3695 1.306642 GGAGAGGACGTTCGCTCTGA 61.307 60.000 24.42 0.00 28.66 3.27
1973 3696 0.736053 GAGAGGACGTTCGCTCTGAT 59.264 55.000 19.28 0.00 28.66 2.90
1977 3700 0.807667 GGACGTTCGCTCTGATGCAT 60.808 55.000 0.00 0.00 0.00 3.96
1978 3701 1.536072 GGACGTTCGCTCTGATGCATA 60.536 52.381 0.00 0.00 0.00 3.14
1982 3705 2.487934 GTTCGCTCTGATGCATATGGT 58.512 47.619 0.00 0.00 0.00 3.55
1986 3709 2.149578 GCTCTGATGCATATGGTGGAC 58.850 52.381 0.00 0.00 0.00 4.02
2075 3798 3.458163 TCGATGGCGACCAGGGAC 61.458 66.667 4.90 0.00 42.51 4.46
2105 3828 0.252881 ATGAGGACAAGGAGGCTGGA 60.253 55.000 0.00 0.00 0.00 3.86
2119 3919 1.153667 CTGGAAGCGCTCAGAGGAC 60.154 63.158 18.67 2.22 33.11 3.85
2120 3920 1.881903 CTGGAAGCGCTCAGAGGACA 61.882 60.000 18.67 6.39 33.11 4.02
2128 3928 0.396417 GCTCAGAGGACAGCTAGGGA 60.396 60.000 0.00 0.00 32.48 4.20
2148 3948 3.702048 GGCCACCACCGCTAGACA 61.702 66.667 0.00 0.00 0.00 3.41
2152 3952 1.541310 CCACCACCGCTAGACAAGGA 61.541 60.000 0.00 0.00 0.00 3.36
2184 4021 2.125147 CGGCTTGCAGGATCGGAA 60.125 61.111 0.00 0.00 0.00 4.30
2186 4023 1.305219 CGGCTTGCAGGATCGGAAAA 61.305 55.000 0.00 0.00 0.00 2.29
2187 4024 0.887933 GGCTTGCAGGATCGGAAAAA 59.112 50.000 0.00 0.00 0.00 1.94
2190 4027 2.424956 GCTTGCAGGATCGGAAAAAGAT 59.575 45.455 0.00 0.00 0.00 2.40
2205 4042 1.584724 AAGATGGGGATTCGTCTGGT 58.415 50.000 0.00 0.00 33.67 4.00
2217 4054 2.848679 TCTGGTGTGAGGCTGGCA 60.849 61.111 3.38 0.00 0.00 4.92
2245 4082 1.118356 GGAGATCCTGACGGAGGCAT 61.118 60.000 0.00 0.00 44.06 4.40
2247 4084 0.397675 AGATCCTGACGGAGGCATCA 60.398 55.000 0.00 0.00 44.06 3.07
2252 4089 2.107953 GACGGAGGCATCAGAGGC 59.892 66.667 5.30 0.00 0.00 4.70
2254 4091 2.108566 CGGAGGCATCAGAGGCTG 59.891 66.667 7.07 0.00 45.32 4.85
2297 4134 4.982701 GCAGTTGCTGGGCTGGGT 62.983 66.667 0.00 0.00 38.21 4.51
2318 4156 1.457346 CCAGTCCTGAGTTGATTGGC 58.543 55.000 0.00 0.00 33.58 4.52
2321 4159 0.955428 GTCCTGAGTTGATTGGCGCA 60.955 55.000 10.83 0.00 0.00 6.09
2380 4227 4.858680 GCTAGCGCCTGGGGGTTC 62.859 72.222 20.77 9.56 34.45 3.62
2381 4228 3.399181 CTAGCGCCTGGGGGTTCA 61.399 66.667 20.77 3.00 34.45 3.18
2384 4231 4.660938 GCGCCTGGGGGTTCAGTT 62.661 66.667 13.07 0.00 33.14 3.16
2422 4670 0.179119 GGTTGATGGGACTACGTCGG 60.179 60.000 0.00 0.00 32.65 4.79
2426 4674 2.624437 GATGGGACTACGTCGGGTGC 62.624 65.000 0.00 0.28 32.65 5.01
2447 4695 0.105862 CATGCAGGTGGGGATCCAAT 60.106 55.000 15.23 0.00 46.04 3.16
2460 4708 1.968493 GATCCAATCCTGCATGGCAAT 59.032 47.619 0.00 0.00 38.41 3.56
2477 4725 1.259770 CAATGAGATCGTCGTGCATGG 59.740 52.381 5.98 0.00 0.00 3.66
2499 4747 2.184830 CACCCAGGATGAGCATGCG 61.185 63.158 13.01 0.00 39.69 4.73
2586 4838 1.600636 CCTGAAGAAACTGGCGCCA 60.601 57.895 30.59 30.59 0.00 5.69
2595 4847 1.764571 AACTGGCGCCACCACTTCTA 61.765 55.000 29.03 0.00 46.36 2.10
2614 4866 7.718753 CACTTCTAAAGGAGATTGAAGGCATAT 59.281 37.037 0.00 0.00 38.60 1.78
2616 4868 6.537355 TCTAAAGGAGATTGAAGGCATATGG 58.463 40.000 4.56 0.00 0.00 2.74
2638 4890 0.250597 GGTACAAACGGGCCAAGACT 60.251 55.000 4.39 0.00 0.00 3.24
2640 4892 0.759959 TACAAACGGGCCAAGACTCA 59.240 50.000 4.39 0.00 0.00 3.41
2655 4907 0.108138 ACTCATTCACACCTAGGCGC 60.108 55.000 9.30 0.00 0.00 6.53
2674 4926 0.319813 CACCACGAGATCAGTGTGCA 60.320 55.000 16.64 0.00 37.88 4.57
2684 4936 0.322648 TCAGTGTGCACATCAGGGAG 59.677 55.000 24.69 8.12 0.00 4.30
2721 4973 4.129737 GCCGCGGAGACAGTGCTA 62.130 66.667 33.48 0.00 0.00 3.49
2766 5018 0.829602 ATGATCTGGCGGTCTCGGAT 60.830 55.000 0.00 0.00 36.79 4.18
2802 5054 2.344741 GCTACGAACGATGTTTGACTCC 59.655 50.000 4.01 0.00 0.00 3.85
2803 5055 2.814280 ACGAACGATGTTTGACTCCT 57.186 45.000 4.01 0.00 0.00 3.69
2814 5066 1.118965 TTGACTCCTCGGTGCAGGAA 61.119 55.000 0.00 0.00 42.35 3.36
2817 5069 1.194781 ACTCCTCGGTGCAGGAACAT 61.195 55.000 0.00 0.00 42.35 2.71
2823 5075 0.957395 CGGTGCAGGAACATCAGCTT 60.957 55.000 0.00 0.00 0.00 3.74
2825 5077 1.740025 GGTGCAGGAACATCAGCTTAC 59.260 52.381 0.00 0.00 0.00 2.34
2829 5081 0.613260 AGGAACATCAGCTTACGGCA 59.387 50.000 0.00 0.00 44.79 5.69
2856 5108 3.118775 CGGCCATATTCGGGAAGATCATA 60.119 47.826 2.24 0.00 0.00 2.15
2865 5117 2.106511 CGGGAAGATCATACCCACCAAT 59.893 50.000 17.67 0.00 43.40 3.16
2918 5172 4.635699 TGTCAGTCTAGACAGTAGTGGA 57.364 45.455 24.44 7.40 43.18 4.02
2923 5177 3.007723 AGTCTAGACAGTAGTGGACGTGA 59.992 47.826 24.44 0.00 0.00 4.35
2930 5184 1.676635 TAGTGGACGTGACTCGGGG 60.677 63.158 0.00 0.00 44.69 5.73
2938 5192 1.215647 GTGACTCGGGGTGCACTAG 59.784 63.158 17.98 11.53 0.00 2.57
2939 5193 1.982395 TGACTCGGGGTGCACTAGG 60.982 63.158 17.98 6.02 0.00 3.02
2972 5227 1.370414 CGCCGCTTTGGAAGTTGTG 60.370 57.895 0.00 0.00 42.00 3.33
2977 5232 1.601903 CGCTTTGGAAGTTGTGTGCTA 59.398 47.619 0.00 0.00 0.00 3.49
2993 5248 0.179081 GCTAGAACGTTAGGGGGCTG 60.179 60.000 0.00 0.00 0.00 4.85
3074 5329 6.617782 ATCATATGTATCCTGGAGTCCAAG 57.382 41.667 14.17 7.48 30.80 3.61
3075 5330 5.715921 TCATATGTATCCTGGAGTCCAAGA 58.284 41.667 14.17 13.52 30.80 3.02
3080 5335 2.461300 TCCTGGAGTCCAAGATCGAT 57.539 50.000 14.17 0.00 30.80 3.59
3102 5357 0.250338 GGTGGACCAGTTCACTGTCC 60.250 60.000 9.05 15.96 42.27 4.02
3104 5359 1.968493 GTGGACCAGTTCACTGTCCTA 59.032 52.381 20.18 10.51 42.27 2.94
3116 5371 1.027357 CTGTCCTACAATGCATGGGC 58.973 55.000 5.94 1.93 41.68 5.36
3122 5377 0.469705 TACAATGCATGGGCCCATCC 60.470 55.000 35.42 27.82 40.13 3.51
3135 5390 1.494721 GCCCATCCTATGAGGGTTTCA 59.505 52.381 0.00 0.00 44.69 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.287608 CGTGAGTAGTCTGTTCTGCACA 60.288 50.000 0.00 0.00 0.00 4.57
1 2 2.031069 TCGTGAGTAGTCTGTTCTGCAC 60.031 50.000 0.00 0.00 0.00 4.57
2 3 2.031069 GTCGTGAGTAGTCTGTTCTGCA 60.031 50.000 0.00 0.00 0.00 4.41
3 4 2.031069 TGTCGTGAGTAGTCTGTTCTGC 60.031 50.000 0.00 0.00 0.00 4.26
5 6 3.499157 GTCTGTCGTGAGTAGTCTGTTCT 59.501 47.826 0.00 0.00 0.00 3.01
6 7 3.250280 TGTCTGTCGTGAGTAGTCTGTTC 59.750 47.826 0.00 0.00 0.00 3.18
7 8 3.211865 TGTCTGTCGTGAGTAGTCTGTT 58.788 45.455 0.00 0.00 0.00 3.16
8 9 2.809119 CTGTCTGTCGTGAGTAGTCTGT 59.191 50.000 0.00 0.00 0.00 3.41
10 11 2.428491 CCTGTCTGTCGTGAGTAGTCT 58.572 52.381 0.00 0.00 0.00 3.24
11 12 1.135632 GCCTGTCTGTCGTGAGTAGTC 60.136 57.143 0.00 0.00 0.00 2.59
12 13 0.882474 GCCTGTCTGTCGTGAGTAGT 59.118 55.000 0.00 0.00 0.00 2.73
13 14 1.135546 CAGCCTGTCTGTCGTGAGTAG 60.136 57.143 0.00 0.00 38.02 2.57
14 15 0.881796 CAGCCTGTCTGTCGTGAGTA 59.118 55.000 0.00 0.00 38.02 2.59
15 16 1.662608 CAGCCTGTCTGTCGTGAGT 59.337 57.895 0.00 0.00 38.02 3.41
16 17 1.735920 GCAGCCTGTCTGTCGTGAG 60.736 63.158 0.00 0.00 44.66 3.51
17 18 1.748329 AAGCAGCCTGTCTGTCGTGA 61.748 55.000 0.00 0.00 44.66 4.35
18 19 1.301244 AAGCAGCCTGTCTGTCGTG 60.301 57.895 0.00 0.00 44.66 4.35
19 20 1.301244 CAAGCAGCCTGTCTGTCGT 60.301 57.895 0.00 0.00 44.66 4.34
20 21 2.675056 GCAAGCAGCCTGTCTGTCG 61.675 63.158 0.00 0.00 44.66 4.35
21 22 3.261933 GCAAGCAGCCTGTCTGTC 58.738 61.111 0.00 0.00 44.66 3.51
26 27 2.416107 TTGCCTAGCAAGCAGCCTGT 62.416 55.000 0.00 0.00 43.99 4.00
27 28 1.676635 TTGCCTAGCAAGCAGCCTG 60.677 57.895 0.00 0.00 43.99 4.85
28 29 2.759114 TTGCCTAGCAAGCAGCCT 59.241 55.556 0.00 0.00 43.99 4.58
42 43 1.315257 ATGAGTTCGGTGGCCATTGC 61.315 55.000 9.72 0.00 0.00 3.56
43 44 2.036958 TATGAGTTCGGTGGCCATTG 57.963 50.000 9.72 4.44 0.00 2.82
44 45 3.297134 AATATGAGTTCGGTGGCCATT 57.703 42.857 9.72 0.00 0.00 3.16
45 46 3.117888 AGAAATATGAGTTCGGTGGCCAT 60.118 43.478 9.72 0.00 0.00 4.40
46 47 2.238646 AGAAATATGAGTTCGGTGGCCA 59.761 45.455 0.00 0.00 0.00 5.36
47 48 2.614057 CAGAAATATGAGTTCGGTGGCC 59.386 50.000 0.00 0.00 0.00 5.36
48 49 2.032178 GCAGAAATATGAGTTCGGTGGC 59.968 50.000 0.00 0.00 0.00 5.01
49 50 2.614057 GGCAGAAATATGAGTTCGGTGG 59.386 50.000 0.00 0.00 0.00 4.61
50 51 2.614057 GGGCAGAAATATGAGTTCGGTG 59.386 50.000 0.00 0.00 0.00 4.94
51 52 2.505819 AGGGCAGAAATATGAGTTCGGT 59.494 45.455 0.00 0.00 0.00 4.69
52 53 3.134458 GAGGGCAGAAATATGAGTTCGG 58.866 50.000 0.00 0.00 0.00 4.30
53 54 4.054671 GAGAGGGCAGAAATATGAGTTCG 58.945 47.826 0.00 0.00 0.00 3.95
54 55 5.289083 AGAGAGGGCAGAAATATGAGTTC 57.711 43.478 0.00 0.00 0.00 3.01
55 56 5.071115 GGTAGAGAGGGCAGAAATATGAGTT 59.929 44.000 0.00 0.00 0.00 3.01
56 57 4.591072 GGTAGAGAGGGCAGAAATATGAGT 59.409 45.833 0.00 0.00 0.00 3.41
57 58 4.321601 CGGTAGAGAGGGCAGAAATATGAG 60.322 50.000 0.00 0.00 0.00 2.90
58 59 3.574396 CGGTAGAGAGGGCAGAAATATGA 59.426 47.826 0.00 0.00 0.00 2.15
59 60 3.306364 CCGGTAGAGAGGGCAGAAATATG 60.306 52.174 0.00 0.00 0.00 1.78
60 61 2.900546 CCGGTAGAGAGGGCAGAAATAT 59.099 50.000 0.00 0.00 0.00 1.28
61 62 2.317040 CCGGTAGAGAGGGCAGAAATA 58.683 52.381 0.00 0.00 0.00 1.40
62 63 1.123928 CCGGTAGAGAGGGCAGAAAT 58.876 55.000 0.00 0.00 0.00 2.17
63 64 0.252103 ACCGGTAGAGAGGGCAGAAA 60.252 55.000 4.49 0.00 0.00 2.52
64 65 0.970937 CACCGGTAGAGAGGGCAGAA 60.971 60.000 6.87 0.00 0.00 3.02
65 66 1.379977 CACCGGTAGAGAGGGCAGA 60.380 63.158 6.87 0.00 0.00 4.26
66 67 3.082579 GCACCGGTAGAGAGGGCAG 62.083 68.421 6.87 0.00 0.00 4.85
67 68 3.075005 GCACCGGTAGAGAGGGCA 61.075 66.667 6.87 0.00 0.00 5.36
68 69 1.972660 ATTGCACCGGTAGAGAGGGC 61.973 60.000 6.87 5.10 0.00 5.19
69 70 0.105039 GATTGCACCGGTAGAGAGGG 59.895 60.000 6.87 0.00 0.00 4.30
70 71 1.115467 AGATTGCACCGGTAGAGAGG 58.885 55.000 6.87 0.00 0.00 3.69
71 72 2.166459 TCAAGATTGCACCGGTAGAGAG 59.834 50.000 6.87 0.00 0.00 3.20
72 73 2.176045 TCAAGATTGCACCGGTAGAGA 58.824 47.619 6.87 0.00 0.00 3.10
73 74 2.672961 TCAAGATTGCACCGGTAGAG 57.327 50.000 6.87 0.00 0.00 2.43
74 75 3.410631 TTTCAAGATTGCACCGGTAGA 57.589 42.857 6.87 0.00 0.00 2.59
75 76 3.181497 CCATTTCAAGATTGCACCGGTAG 60.181 47.826 6.87 2.73 0.00 3.18
76 77 2.752354 CCATTTCAAGATTGCACCGGTA 59.248 45.455 6.87 0.00 0.00 4.02
77 78 1.545582 CCATTTCAAGATTGCACCGGT 59.454 47.619 0.00 0.00 0.00 5.28
78 79 1.736696 GCCATTTCAAGATTGCACCGG 60.737 52.381 0.00 0.00 0.00 5.28
79 80 1.203052 AGCCATTTCAAGATTGCACCG 59.797 47.619 0.00 0.00 0.00 4.94
80 81 2.231964 TCAGCCATTTCAAGATTGCACC 59.768 45.455 0.00 0.00 0.00 5.01
81 82 3.192001 TCTCAGCCATTTCAAGATTGCAC 59.808 43.478 0.00 0.00 0.00 4.57
82 83 3.423749 TCTCAGCCATTTCAAGATTGCA 58.576 40.909 0.00 0.00 0.00 4.08
83 84 4.445452 TTCTCAGCCATTTCAAGATTGC 57.555 40.909 0.00 0.00 0.00 3.56
84 85 4.863131 GCTTTCTCAGCCATTTCAAGATTG 59.137 41.667 0.00 0.00 43.65 2.67
85 86 5.069501 GCTTTCTCAGCCATTTCAAGATT 57.930 39.130 0.00 0.00 43.65 2.40
86 87 4.715527 GCTTTCTCAGCCATTTCAAGAT 57.284 40.909 0.00 0.00 43.65 2.40
97 98 2.164624 TCTACTCTTCCGCTTTCTCAGC 59.835 50.000 0.00 0.00 46.31 4.26
98 99 3.692101 TCTCTACTCTTCCGCTTTCTCAG 59.308 47.826 0.00 0.00 0.00 3.35
99 100 3.687125 TCTCTACTCTTCCGCTTTCTCA 58.313 45.455 0.00 0.00 0.00 3.27
100 101 3.488553 GCTCTCTACTCTTCCGCTTTCTC 60.489 52.174 0.00 0.00 0.00 2.87
101 102 2.425668 GCTCTCTACTCTTCCGCTTTCT 59.574 50.000 0.00 0.00 0.00 2.52
102 103 2.793237 CGCTCTCTACTCTTCCGCTTTC 60.793 54.545 0.00 0.00 0.00 2.62
103 104 1.133407 CGCTCTCTACTCTTCCGCTTT 59.867 52.381 0.00 0.00 0.00 3.51
104 105 0.736053 CGCTCTCTACTCTTCCGCTT 59.264 55.000 0.00 0.00 0.00 4.68
105 106 1.720694 GCGCTCTCTACTCTTCCGCT 61.721 60.000 0.00 0.00 37.27 5.52
106 107 1.298788 GCGCTCTCTACTCTTCCGC 60.299 63.158 0.00 0.00 0.00 5.54
107 108 0.306533 GAGCGCTCTCTACTCTTCCG 59.693 60.000 29.88 0.00 36.42 4.30
208 209 4.760220 GGGAGCAGGGAAGGGGGA 62.760 72.222 0.00 0.00 0.00 4.81
211 212 3.093172 GAGGGGAGCAGGGAAGGG 61.093 72.222 0.00 0.00 0.00 3.95
213 214 3.093172 GGGAGGGGAGCAGGGAAG 61.093 72.222 0.00 0.00 0.00 3.46
214 215 2.730196 AAAGGGAGGGGAGCAGGGAA 62.730 60.000 0.00 0.00 0.00 3.97
219 220 0.178861 AGAGAAAAGGGAGGGGAGCA 60.179 55.000 0.00 0.00 0.00 4.26
222 223 0.496382 TGGAGAGAAAAGGGAGGGGA 59.504 55.000 0.00 0.00 0.00 4.81
224 225 1.213926 CCATGGAGAGAAAAGGGAGGG 59.786 57.143 5.56 0.00 0.00 4.30
228 229 2.373224 GAAGCCATGGAGAGAAAAGGG 58.627 52.381 18.40 0.00 0.00 3.95
230 231 2.012673 CGGAAGCCATGGAGAGAAAAG 58.987 52.381 18.40 0.00 0.00 2.27
231 232 1.340017 CCGGAAGCCATGGAGAGAAAA 60.340 52.381 18.40 0.00 0.00 2.29
233 234 0.617535 TCCGGAAGCCATGGAGAGAA 60.618 55.000 18.40 0.00 0.00 2.87
234 235 0.399091 ATCCGGAAGCCATGGAGAGA 60.399 55.000 18.40 2.74 34.75 3.10
235 236 0.034616 GATCCGGAAGCCATGGAGAG 59.965 60.000 18.40 0.79 34.75 3.20
236 237 1.410850 GGATCCGGAAGCCATGGAGA 61.411 60.000 18.40 1.57 34.75 3.71
237 238 1.072159 GGATCCGGAAGCCATGGAG 59.928 63.158 18.40 0.01 34.75 3.86
238 239 1.692395 TGGATCCGGAAGCCATGGA 60.692 57.895 21.71 3.36 35.96 3.41
264 265 2.888863 GCTGACGAGACAGAGGGG 59.111 66.667 6.75 0.00 39.94 4.79
270 271 1.081175 CTGAAGCGCTGACGAGACA 60.081 57.895 12.58 2.29 43.93 3.41
303 304 2.923035 ATCCCCAGCCCCGATACG 60.923 66.667 0.00 0.00 0.00 3.06
306 307 2.527875 GAGATCCCCAGCCCCGAT 60.528 66.667 0.00 0.00 0.00 4.18
313 314 3.237741 GGAGCCCGAGATCCCCAG 61.238 72.222 0.00 0.00 43.18 4.45
338 339 3.245315 CCGAGTACGAAAGCGCCG 61.245 66.667 2.29 2.67 42.48 6.46
343 344 2.884207 GCCCGCCGAGTACGAAAG 60.884 66.667 0.00 0.00 42.66 2.62
344 345 4.781959 CGCCCGCCGAGTACGAAA 62.782 66.667 0.00 0.00 42.66 3.46
447 448 3.381333 CTGATGCTGCAGAGCCCGA 62.381 63.158 20.43 0.00 45.57 5.14
449 450 3.210528 GCTGATGCTGCAGAGCCC 61.211 66.667 20.43 0.00 45.57 5.19
454 455 2.895865 CTCCCGCTGATGCTGCAG 60.896 66.667 10.11 10.11 38.91 4.41
458 459 3.790437 CCACCTCCCGCTGATGCT 61.790 66.667 0.00 0.00 36.97 3.79
510 511 2.691674 GAATCAGCCTCCGCTCCGAG 62.692 65.000 0.00 0.00 43.95 4.63
528 529 3.536917 CCATACAGCTCCGGCGGA 61.537 66.667 29.14 29.14 44.37 5.54
546 547 2.964740 TCGAAGCATCTGAAACAGAGG 58.035 47.619 8.70 8.70 44.08 3.69
573 574 2.202797 CAGTCCTGACGCCGATGG 60.203 66.667 0.00 0.00 36.20 3.51
582 583 1.227527 CACGTTGGTGCAGTCCTGA 60.228 57.895 0.00 0.00 37.35 3.86
623 631 1.222936 GCACTGGGAGGAGACATGG 59.777 63.158 0.00 0.00 0.00 3.66
635 643 4.463879 CGAGGCTCCCTGCACTGG 62.464 72.222 9.32 0.00 45.15 4.00
642 650 3.144193 CGCTCTTCGAGGCTCCCT 61.144 66.667 9.32 0.00 41.67 4.20
647 655 1.590259 GATCACCGCTCTTCGAGGC 60.590 63.158 0.00 0.00 41.67 4.70
668 703 3.426568 GACCTGCGAGCAACCTGC 61.427 66.667 0.00 0.00 45.46 4.85
717 752 0.970937 CTAGGCTCCGACAACCTCCA 60.971 60.000 0.00 0.00 34.92 3.86
805 846 4.497984 ACGGCCCCGCATGCATAA 62.498 61.111 19.57 0.00 44.19 1.90
819 860 0.529833 AGCACACAGATCTCAGACGG 59.470 55.000 0.00 0.00 0.00 4.79
862 904 2.817396 GCAGCCTCCGCTCAAGAC 60.817 66.667 0.00 0.00 43.95 3.01
863 905 2.189191 AATGCAGCCTCCGCTCAAGA 62.189 55.000 0.00 0.00 43.95 3.02
866 908 2.042259 CAAATGCAGCCTCCGCTCA 61.042 57.895 0.00 0.00 43.95 4.26
881 923 0.322098 CGTACATCCCCACAGCCAAA 60.322 55.000 0.00 0.00 0.00 3.28
887 929 0.611200 CTCCAACGTACATCCCCACA 59.389 55.000 0.00 0.00 0.00 4.17
892 934 0.824759 AGCTCCTCCAACGTACATCC 59.175 55.000 0.00 0.00 0.00 3.51
962 1004 1.976474 GCGAAATCTTGGCACCCCA 60.976 57.895 0.00 0.00 40.06 4.96
966 1008 2.328473 GGAAAAGCGAAATCTTGGCAC 58.672 47.619 0.00 0.00 36.79 5.01
974 1016 5.622770 ACTTATGAACGGAAAAGCGAAAT 57.377 34.783 0.00 0.00 0.00 2.17
1002 1044 1.376037 CCACCAGAAAGTCCTCCGC 60.376 63.158 0.00 0.00 0.00 5.54
1031 1073 1.940613 GCTTTGTTCCTGAACTCGTGT 59.059 47.619 11.03 0.00 41.67 4.49
1060 1102 3.361977 AATGAACGGTGCCGCCAC 61.362 61.111 10.87 3.26 44.19 5.01
1065 1107 0.099436 GATGCTCAATGAACGGTGCC 59.901 55.000 0.00 0.00 0.00 5.01
1068 1110 2.086869 CCAAGATGCTCAATGAACGGT 58.913 47.619 0.00 0.00 0.00 4.83
1126 1168 4.256180 CACCCTAGATGCCGCCCC 62.256 72.222 0.00 0.00 0.00 5.80
1127 1169 2.520536 ATCACCCTAGATGCCGCCC 61.521 63.158 0.00 0.00 0.00 6.13
1137 1179 1.622607 CCTGAACCCGCATCACCCTA 61.623 60.000 0.00 0.00 0.00 3.53
1141 1183 2.040544 CCACCTGAACCCGCATCAC 61.041 63.158 0.00 0.00 0.00 3.06
1176 1218 0.533755 CCCAAGCATGAGACGGGATC 60.534 60.000 0.00 0.00 39.44 3.36
1221 1263 2.434884 ATCAAGCACGCACTCCCG 60.435 61.111 0.00 0.00 0.00 5.14
1255 1297 1.002868 CCTCCCTGCTGGTTGTCTG 60.003 63.158 9.00 0.00 34.77 3.51
1261 1303 1.462238 ACAAGTCCTCCCTGCTGGT 60.462 57.895 9.00 0.00 34.77 4.00
1328 1370 0.671781 CACCCAGAGCTTCCTGAACG 60.672 60.000 4.03 0.00 36.29 3.95
1332 1374 2.045536 GGCACCCAGAGCTTCCTG 60.046 66.667 0.00 0.00 0.00 3.86
1441 1483 1.079750 GTGGCGAGAAGTCCCTCAC 60.080 63.158 0.00 0.00 32.86 3.51
1485 1527 0.386113 GACCACTCCTGCTATCCGAC 59.614 60.000 0.00 0.00 0.00 4.79
1495 1537 2.681778 CCCGCTCTGACCACTCCT 60.682 66.667 0.00 0.00 0.00 3.69
1557 1599 2.031012 CGAGTCCAAGGCTGCACA 59.969 61.111 0.50 0.00 0.00 4.57
1582 1624 1.221566 CAGCACCCCGATCATCACA 59.778 57.895 0.00 0.00 0.00 3.58
1584 1626 2.910360 CCAGCACCCCGATCATCA 59.090 61.111 0.00 0.00 0.00 3.07
1599 1641 1.701545 GAAAATGCGATCGTCGGCCA 61.702 55.000 17.81 5.87 40.84 5.36
1605 1647 2.469516 GGCCGGAAAATGCGATCGT 61.470 57.895 17.81 0.00 30.86 3.73
1608 1650 1.510844 GTTGGCCGGAAAATGCGAT 59.489 52.632 5.05 0.00 30.86 4.58
1611 1653 1.443702 GTCGTTGGCCGGAAAATGC 60.444 57.895 5.05 0.00 37.11 3.56
1689 1731 1.147824 CGGAAGCCTCCATGCAGAT 59.852 57.895 1.47 0.00 42.58 2.90
1723 2022 2.594592 AGGTGTGACGGCCAAAGC 60.595 61.111 2.24 0.00 38.76 3.51
1772 3483 3.296709 GAACGCTCCTGCTCCCGAA 62.297 63.158 0.00 0.00 36.97 4.30
1797 3508 4.181578 TCTCACTTTGCGTTAGGATAAGC 58.818 43.478 0.00 0.00 0.00 3.09
1812 3523 3.571119 GCTGTGCGCATCTCACTT 58.429 55.556 15.91 0.00 38.92 3.16
1846 3557 3.782443 GGAGGGCACGGTCCGATT 61.782 66.667 20.51 0.00 29.39 3.34
1859 3570 2.280079 GGATTGGCCCCTTGGAGG 59.720 66.667 0.00 0.00 34.30 4.30
1860 3571 1.076485 CAGGATTGGCCCCTTGGAG 60.076 63.158 0.00 0.00 37.37 3.86
1861 3572 2.625460 CCAGGATTGGCCCCTTGGA 61.625 63.158 11.14 0.00 37.73 3.53
1863 3574 1.076485 CTCCAGGATTGGCCCCTTG 60.076 63.158 0.00 0.00 44.63 3.61
1865 3576 1.230281 TTCTCCAGGATTGGCCCCT 60.230 57.895 0.00 0.00 44.63 4.79
1866 3577 1.076705 GTTCTCCAGGATTGGCCCC 60.077 63.158 0.00 0.00 44.63 5.80
1869 3592 1.372087 CGCTGTTCTCCAGGATTGGC 61.372 60.000 0.00 0.00 44.63 4.52
1876 3599 2.099431 GCAGCTCGCTGTTCTCCAG 61.099 63.158 19.00 0.00 45.24 3.86
1878 3601 2.817396 GGCAGCTCGCTGTTCTCC 60.817 66.667 19.00 8.80 45.24 3.71
1880 3603 3.630013 TGGGCAGCTCGCTGTTCT 61.630 61.111 19.00 0.00 45.24 3.01
1882 3605 4.254709 TGTGGGCAGCTCGCTGTT 62.255 61.111 19.00 0.00 45.24 3.16
1884 3607 4.383861 TCTGTGGGCAGCTCGCTG 62.384 66.667 14.30 14.30 46.15 5.18
1887 3610 3.699894 ACCTCTGTGGGCAGCTCG 61.700 66.667 0.33 0.00 42.29 5.03
1928 3651 2.592861 GGATGCACTGATCCGCCC 60.593 66.667 0.00 0.00 32.77 6.13
1943 3666 0.106469 CGTCCTCTCCATCTCTGGGA 60.106 60.000 0.00 0.00 43.34 4.37
1955 3678 0.453793 CATCAGAGCGAACGTCCTCT 59.546 55.000 7.34 7.34 38.91 3.69
1963 3686 2.486918 CACCATATGCATCAGAGCGAA 58.513 47.619 0.19 0.00 37.31 4.70
1968 3691 2.105306 CTGGTCCACCATATGCATCAGA 59.895 50.000 0.19 0.00 46.46 3.27
1970 3693 1.143481 CCTGGTCCACCATATGCATCA 59.857 52.381 0.19 0.00 46.46 3.07
1972 3695 1.422781 CTCCTGGTCCACCATATGCAT 59.577 52.381 3.79 3.79 46.46 3.96
1973 3696 0.839277 CTCCTGGTCCACCATATGCA 59.161 55.000 0.00 0.00 46.46 3.96
1977 3700 0.686441 CGGTCTCCTGGTCCACCATA 60.686 60.000 0.00 0.00 46.46 2.74
1978 3701 1.990060 CGGTCTCCTGGTCCACCAT 60.990 63.158 0.00 0.00 46.46 3.55
1990 3713 4.593864 GGGATCAGCGCCGGTCTC 62.594 72.222 2.29 0.00 0.00 3.36
2031 3754 4.767255 CACCGGCTCAGTCTGGGC 62.767 72.222 16.95 16.95 44.90 5.36
2032 3755 4.767255 GCACCGGCTCAGTCTGGG 62.767 72.222 0.00 0.00 36.80 4.45
2075 3798 1.222936 GTCCTCATCTGTGGCCCTG 59.777 63.158 0.00 0.00 0.00 4.45
2079 3802 0.615331 TCCTTGTCCTCATCTGTGGC 59.385 55.000 0.00 0.00 0.00 5.01
2081 3804 1.406614 GCCTCCTTGTCCTCATCTGTG 60.407 57.143 0.00 0.00 0.00 3.66
2082 3805 0.908198 GCCTCCTTGTCCTCATCTGT 59.092 55.000 0.00 0.00 0.00 3.41
2105 3828 0.967887 TAGCTGTCCTCTGAGCGCTT 60.968 55.000 13.26 0.00 40.34 4.68
2108 3831 1.732917 CCTAGCTGTCCTCTGAGCG 59.267 63.158 0.00 0.00 40.34 5.03
2110 3833 1.691196 CTCCCTAGCTGTCCTCTGAG 58.309 60.000 0.00 0.00 0.00 3.35
2111 3834 0.260230 CCTCCCTAGCTGTCCTCTGA 59.740 60.000 0.00 0.00 0.00 3.27
2114 3914 1.458588 CCCCTCCCTAGCTGTCCTC 60.459 68.421 0.00 0.00 0.00 3.71
2119 3919 3.483869 GTGGCCCCTCCCTAGCTG 61.484 72.222 0.00 0.00 0.00 4.24
2120 3920 4.825679 GGTGGCCCCTCCCTAGCT 62.826 72.222 0.00 0.00 0.00 3.32
2141 3941 1.069978 GATCCTGCCTCCTTGTCTAGC 59.930 57.143 0.00 0.00 0.00 3.42
2148 3948 2.041265 ACCGGATCCTGCCTCCTT 59.959 61.111 9.46 0.00 0.00 3.36
2175 4012 2.205342 TCCCCATCTTTTTCCGATCCT 58.795 47.619 0.00 0.00 0.00 3.24
2179 4016 2.026636 ACGAATCCCCATCTTTTTCCGA 60.027 45.455 0.00 0.00 0.00 4.55
2184 4021 2.308866 ACCAGACGAATCCCCATCTTTT 59.691 45.455 0.00 0.00 0.00 2.27
2186 4023 1.210478 CACCAGACGAATCCCCATCTT 59.790 52.381 0.00 0.00 0.00 2.40
2187 4024 0.833287 CACCAGACGAATCCCCATCT 59.167 55.000 0.00 0.00 0.00 2.90
2190 4027 0.834261 TCACACCAGACGAATCCCCA 60.834 55.000 0.00 0.00 0.00 4.96
2205 4042 4.783621 GCCGATGCCAGCCTCACA 62.784 66.667 0.00 0.00 0.00 3.58
2217 4054 2.522923 AGGATCTCCTGCGCCGAT 60.523 61.111 4.18 1.13 46.55 4.18
2245 4082 0.617820 GGGGTAGGAACAGCCTCTGA 60.618 60.000 0.29 0.00 46.97 3.27
2247 4084 0.119358 AAGGGGTAGGAACAGCCTCT 59.881 55.000 0.00 0.00 46.97 3.69
2252 4089 0.391263 GTCGCAAGGGGTAGGAACAG 60.391 60.000 0.00 0.00 38.47 3.16
2253 4090 1.675219 GTCGCAAGGGGTAGGAACA 59.325 57.895 0.00 0.00 38.47 3.18
2254 4091 1.078637 GGTCGCAAGGGGTAGGAAC 60.079 63.158 0.00 0.00 38.47 3.62
2259 4096 3.324108 GTGGGGTCGCAAGGGGTA 61.324 66.667 0.00 0.00 38.47 3.69
2297 4134 1.630369 CCAATCAACTCAGGACTGGGA 59.370 52.381 6.14 0.00 34.49 4.37
2380 4227 2.032550 CCGCAGCATCCAATAGAAACTG 59.967 50.000 0.00 0.00 35.56 3.16
2381 4228 2.292267 CCGCAGCATCCAATAGAAACT 58.708 47.619 0.00 0.00 0.00 2.66
2384 4231 1.667236 CACCGCAGCATCCAATAGAA 58.333 50.000 0.00 0.00 0.00 2.10
2441 4689 1.691976 CATTGCCATGCAGGATTGGAT 59.308 47.619 8.28 0.00 40.61 3.41
2447 4695 1.812708 CGATCTCATTGCCATGCAGGA 60.813 52.381 0.00 0.00 40.61 3.86
2460 4708 1.141665 CCCATGCACGACGATCTCA 59.858 57.895 0.00 0.00 0.00 3.27
2477 4725 2.439156 GCTCATCCTGGGTGTGCC 60.439 66.667 20.51 5.43 31.76 5.01
2482 4730 2.191375 CGCATGCTCATCCTGGGT 59.809 61.111 17.13 0.00 0.00 4.51
2499 4747 1.337118 CAGATAGGCTCTCCTCCACC 58.663 60.000 0.00 0.00 43.06 4.61
2586 4838 5.804771 GCCTTCAATCTCCTTTAGAAGTGGT 60.805 44.000 0.00 0.00 37.89 4.16
2595 4847 4.477249 CCCATATGCCTTCAATCTCCTTT 58.523 43.478 0.00 0.00 0.00 3.11
2616 4868 3.510559 TTGGCCCGTTTGTACCCCC 62.511 63.158 0.00 0.00 0.00 5.40
2624 4876 1.202879 TGAATGAGTCTTGGCCCGTTT 60.203 47.619 0.00 0.00 0.00 3.60
2625 4877 0.400213 TGAATGAGTCTTGGCCCGTT 59.600 50.000 0.00 0.00 0.00 4.44
2638 4890 0.391130 GTGCGCCTAGGTGTGAATGA 60.391 55.000 23.09 0.00 0.00 2.57
2640 4892 1.078426 GGTGCGCCTAGGTGTGAAT 60.078 57.895 23.09 0.00 0.00 2.57
2655 4907 0.319813 TGCACACTGATCTCGTGGTG 60.320 55.000 16.46 13.22 36.71 4.17
2661 4913 2.277969 CCTGATGTGCACACTGATCTC 58.722 52.381 24.37 15.22 0.00 2.75
2674 4926 0.908198 GTCTTCCTGCTCCCTGATGT 59.092 55.000 0.00 0.00 0.00 3.06
2684 4936 1.869690 GTCGCTTTGGTCTTCCTGC 59.130 57.895 0.00 0.00 34.23 4.85
2721 4973 2.982488 AGTGATCCCCAGAGTTTTGAGT 59.018 45.455 0.00 0.00 0.00 3.41
2787 5039 1.343465 ACCGAGGAGTCAAACATCGTT 59.657 47.619 0.00 0.00 39.36 3.85
2788 5040 0.966920 ACCGAGGAGTCAAACATCGT 59.033 50.000 0.00 0.00 39.36 3.73
2802 5054 1.364626 GCTGATGTTCCTGCACCGAG 61.365 60.000 0.00 0.00 0.00 4.63
2803 5055 1.375908 GCTGATGTTCCTGCACCGA 60.376 57.895 0.00 0.00 0.00 4.69
2814 5066 1.290203 CGATTGCCGTAAGCTGATGT 58.710 50.000 0.00 0.00 44.23 3.06
2817 5069 2.164663 CGCGATTGCCGTAAGCTGA 61.165 57.895 0.00 0.00 44.23 4.26
2829 5081 1.671054 CCCGAATATGGCCGCGATT 60.671 57.895 8.23 0.00 0.00 3.34
2856 5108 0.686224 CACATGCCAAATTGGTGGGT 59.314 50.000 14.17 6.35 40.46 4.51
2865 5117 1.246056 GCTCCAGCTCACATGCCAAA 61.246 55.000 0.00 0.00 38.21 3.28
2918 5172 4.295119 GTGCACCCCGAGTCACGT 62.295 66.667 5.22 0.00 40.78 4.49
2923 5177 1.535687 AACCTAGTGCACCCCGAGT 60.536 57.895 14.63 1.21 0.00 4.18
2930 5184 2.622436 GACATGGAGAACCTAGTGCAC 58.378 52.381 9.40 9.40 37.04 4.57
2938 5192 2.740714 GCGTGCGACATGGAGAACC 61.741 63.158 0.00 0.00 0.00 3.62
2939 5193 2.740714 GGCGTGCGACATGGAGAAC 61.741 63.158 0.00 0.00 0.00 3.01
2960 5215 3.311322 CGTTCTAGCACACAACTTCCAAA 59.689 43.478 0.00 0.00 0.00 3.28
2972 5227 0.461516 GCCCCCTAACGTTCTAGCAC 60.462 60.000 2.82 0.00 0.00 4.40
2977 5232 0.323957 GTTCAGCCCCCTAACGTTCT 59.676 55.000 2.82 0.00 0.00 3.01
2993 5248 3.057245 CCTTTTTCTTAGCAGGGCTGTTC 60.057 47.826 0.07 0.00 40.10 3.18
3074 5329 1.705873 ACTGGTCCACCCTATCGATC 58.294 55.000 0.00 0.00 34.29 3.69
3075 5330 2.040178 GAACTGGTCCACCCTATCGAT 58.960 52.381 2.16 2.16 34.29 3.59
3080 5335 1.348064 CAGTGAACTGGTCCACCCTA 58.652 55.000 2.35 0.00 40.20 3.53
3102 5357 0.963962 GATGGGCCCATGCATTGTAG 59.036 55.000 42.21 0.00 40.13 2.74
3104 5359 1.763256 GGATGGGCCCATGCATTGT 60.763 57.895 42.23 21.21 43.01 2.71
3116 5371 2.780010 AGTGAAACCCTCATAGGATGGG 59.220 50.000 9.51 9.51 46.07 4.00
3122 5377 5.859495 GGGAGATAAGTGAAACCCTCATAG 58.141 45.833 0.00 0.00 37.80 2.23


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

AutoCloner maintained by Alex Coulton.