Multiple sequence alignment - TraesCS5B01G486600

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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 TraesCS5B01G486600 chr5B 100.000 4791 0 0 946 5736 657887813 657883023 0.000000e+00 8848
1 TraesCS5B01G486600 chr5B 100.000 667 0 0 1 667 657888758 657888092 0.000000e+00 1232
2 TraesCS5B01G486600 chr5B 93.069 101 6 1 81 180 440363199 440363299 4.630000e-31 147
3 TraesCS5B01G486600 chr5D 91.972 2815 119 44 2946 5706 521523611 521520850 0.000000e+00 3847
4 TraesCS5B01G486600 chr5D 93.151 1898 67 27 947 2806 521525668 521523796 0.000000e+00 2726
5 TraesCS5B01G486600 chr5D 93.621 486 31 0 182 667 521526172 521525687 0.000000e+00 726
6 TraesCS5B01G486600 chr5D 96.842 95 3 0 1 95 521526262 521526168 5.950000e-35 159
7 TraesCS5B01G486600 chr5D 97.647 85 2 0 2804 2888 521523693 521523609 4.630000e-31 147
8 TraesCS5B01G486600 chr5A 90.744 2312 117 47 2896 5150 649854596 649852325 0.000000e+00 2994
9 TraesCS5B01G486600 chr5A 90.844 1529 64 28 1400 2897 649856037 649854554 0.000000e+00 1978
10 TraesCS5B01G486600 chr5A 93.827 486 27 3 184 667 649856940 649856456 0.000000e+00 728
11 TraesCS5B01G486600 chr5A 90.526 95 9 0 4642 4736 649861439 649861533 6.030000e-25 126
12 TraesCS5B01G486600 chr7B 92.547 644 18 13 969 1612 591221904 591221291 0.000000e+00 896
13 TraesCS5B01G486600 chr7B 87.562 201 21 4 2206 2404 397211151 397211349 4.470000e-56 230
14 TraesCS5B01G486600 chr7B 87.562 201 21 4 2206 2404 397278797 397278995 4.470000e-56 230
15 TraesCS5B01G486600 chr7D 93.390 469 15 9 946 1411 82900288 82900743 0.000000e+00 680
16 TraesCS5B01G486600 chr7D 76.955 486 73 22 2188 2660 636660916 636661375 2.070000e-59 241
17 TraesCS5B01G486600 chr7D 76.605 483 79 13 2425 2897 636660612 636661070 9.610000e-58 235
18 TraesCS5B01G486600 chr4D 84.596 396 45 8 2332 2726 452847281 452846901 4.190000e-101 379
19 TraesCS5B01G486600 chr2B 84.596 396 45 8 2332 2726 105842044 105842424 4.190000e-101 379
20 TraesCS5B01G486600 chr2B 94.059 101 5 1 81 180 646146030 646145930 9.950000e-33 152
21 TraesCS5B01G486600 chr2B 93.069 101 6 1 81 180 1095263 1095163 4.630000e-31 147
22 TraesCS5B01G486600 chr1B 84.422 398 46 8 2332 2728 682391579 682391961 1.510000e-100 377
23 TraesCS5B01G486600 chr6B 84.091 396 47 8 2332 2726 19972614 19972994 9.080000e-98 368
24 TraesCS5B01G486600 chr6B 86.878 221 24 4 2332 2551 19949734 19949950 5.740000e-60 243
25 TraesCS5B01G486600 chr6B 86.425 221 25 4 2332 2551 19930315 19930531 2.670000e-58 237
26 TraesCS5B01G486600 chr6B 93.069 101 6 1 81 180 655975823 655975923 4.630000e-31 147
27 TraesCS5B01G486600 chr2D 83.556 225 35 2 1413 1636 261957192 261957415 5.820000e-50 209
28 TraesCS5B01G486600 chr3B 98.851 87 1 0 91 177 59039000 59038914 7.700000e-34 156
29 TraesCS5B01G486600 chr4B 93.069 101 6 1 81 180 116796937 116797037 4.630000e-31 147
30 TraesCS5B01G486600 chr4B 93.069 101 6 1 81 180 421804426 421804326 4.630000e-31 147
31 TraesCS5B01G486600 chr4A 92.157 102 7 1 92 193 207366891 207366991 5.990000e-30 143
32 TraesCS5B01G486600 chr1A 92.929 99 5 2 90 187 344497751 344497654 5.990000e-30 143


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 TraesCS5B01G486600 chr5B 657883023 657888758 5735 True 5040 8848 100.0000 1 5736 2 chr5B.!!$R1 5735
1 TraesCS5B01G486600 chr5D 521520850 521526262 5412 True 1521 3847 94.6466 1 5706 5 chr5D.!!$R1 5705
2 TraesCS5B01G486600 chr5A 649852325 649856940 4615 True 1900 2994 91.8050 184 5150 3 chr5A.!!$R1 4966
3 TraesCS5B01G486600 chr7B 591221291 591221904 613 True 896 896 92.5470 969 1612 1 chr7B.!!$R1 643
4 TraesCS5B01G486600 chr7D 636660612 636661375 763 False 238 241 76.7800 2188 2897 2 chr7D.!!$F2 709

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
97 98 0.320697 AACAGTTCGCTGGTACTCCC 59.679 55.000 0.0 0.0 44.66 4.30 F
106 107 0.613853 CTGGTACTCCCTCCGTTCCA 60.614 60.000 0.0 0.0 32.07 3.53 F
1661 1675 0.598065 ATTTTGGACTGCTGCCGTTC 59.402 50.000 0.0 0.0 0.00 3.95 F
2005 2040 0.671796 GGGCTTGCGGTTACTTGTTT 59.328 50.000 0.0 0.0 0.00 2.83 F
2706 2786 1.270839 TGCTTCTGTGTAGTTCCCAGC 60.271 52.381 0.0 0.0 0.00 4.85 F
4543 4798 0.256464 AGGAAGACGAGGACGAGGAT 59.744 55.000 0.0 0.0 42.66 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1660 1674 1.005228 TCGGTAAAGGAGGAGGAGGA 58.995 55.000 0.00 0.00 0.00 3.71 R
1664 1678 1.134560 CGAACTCGGTAAAGGAGGAGG 59.865 57.143 0.00 0.00 35.82 4.30 R
3101 3305 0.170339 GTTTTCATCTTTCCCGCGGG 59.830 55.000 39.13 39.13 0.00 6.13 R
3103 3307 0.878416 TGGTTTTCATCTTTCCCGCG 59.122 50.000 0.00 0.00 0.00 6.46 R
4645 4900 0.028902 GGGTTATCCGCACGCATTTC 59.971 55.000 0.00 0.00 33.83 2.17 R
5405 5690 0.385390 GTGGGGATTGCTTTATGGCG 59.615 55.000 0.00 0.00 34.52 5.69 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
60 61 5.074746 TCCCTATCTACTGTAGCATGGAA 57.925 43.478 9.98 0.00 0.00 3.53
94 95 2.132762 CGAAAACAGTTCGCTGGTACT 58.867 47.619 0.00 0.00 46.01 2.73
95 96 2.155155 CGAAAACAGTTCGCTGGTACTC 59.845 50.000 0.00 0.00 46.01 2.59
97 98 0.320697 AACAGTTCGCTGGTACTCCC 59.679 55.000 0.00 0.00 44.66 4.30
100 101 0.971447 AGTTCGCTGGTACTCCCTCC 60.971 60.000 0.00 0.00 0.00 4.30
101 102 2.050350 TTCGCTGGTACTCCCTCCG 61.050 63.158 0.00 0.00 0.00 4.63
102 103 2.754658 CGCTGGTACTCCCTCCGT 60.755 66.667 0.00 0.00 0.00 4.69
104 105 1.516423 GCTGGTACTCCCTCCGTTC 59.484 63.158 0.00 0.00 0.00 3.95
106 107 0.613853 CTGGTACTCCCTCCGTTCCA 60.614 60.000 0.00 0.00 32.07 3.53
108 109 0.978907 GGTACTCCCTCCGTTCCAAA 59.021 55.000 0.00 0.00 0.00 3.28
110 111 2.026542 GGTACTCCCTCCGTTCCAAAAT 60.027 50.000 0.00 0.00 0.00 1.82
112 113 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
113 114 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
114 115 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
115 116 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
117 118 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
118 119 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
119 120 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
120 121 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
121 122 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
122 123 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
123 124 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
124 125 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
125 126 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
126 127 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
128 129 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
135 136 9.975218 ATAGATGACCCAACTTTGTATTAAACT 57.025 29.630 0.00 0.00 0.00 2.66
136 137 8.706322 AGATGACCCAACTTTGTATTAAACTT 57.294 30.769 0.00 0.00 0.00 2.66
139 140 8.983702 TGACCCAACTTTGTATTAAACTTAGT 57.016 30.769 0.00 0.00 0.00 2.24
142 143 9.850198 ACCCAACTTTGTATTAAACTTAGTACA 57.150 29.630 0.00 1.84 35.09 2.90
169 170 9.753674 AAGTTGAGTTATCTATTTTGGAATGGA 57.246 29.630 0.00 0.00 37.20 3.41
170 171 9.401058 AGTTGAGTTATCTATTTTGGAATGGAG 57.599 33.333 0.00 0.00 36.39 3.86
171 172 8.624776 GTTGAGTTATCTATTTTGGAATGGAGG 58.375 37.037 0.00 0.00 36.39 4.30
172 173 7.290061 TGAGTTATCTATTTTGGAATGGAGGG 58.710 38.462 0.00 0.00 36.39 4.30
173 174 7.128728 TGAGTTATCTATTTTGGAATGGAGGGA 59.871 37.037 0.00 0.00 36.39 4.20
175 176 7.129504 AGTTATCTATTTTGGAATGGAGGGAGT 59.870 37.037 0.00 0.00 36.39 3.85
176 177 8.437575 GTTATCTATTTTGGAATGGAGGGAGTA 58.562 37.037 0.00 0.00 36.39 2.59
177 178 6.500589 TCTATTTTGGAATGGAGGGAGTAG 57.499 41.667 0.00 0.00 30.37 2.57
178 179 5.970640 TCTATTTTGGAATGGAGGGAGTAGT 59.029 40.000 0.00 0.00 30.37 2.73
180 181 5.431179 TTTTGGAATGGAGGGAGTAGTAC 57.569 43.478 0.00 0.00 0.00 2.73
243 244 2.123018 ATGGTCCATAGCCCTCATCA 57.877 50.000 1.24 0.00 0.00 3.07
463 464 2.599281 TCTTCGCCACACTCCCGA 60.599 61.111 0.00 0.00 0.00 5.14
540 542 2.044555 CCGCGTCAGAGACCTACCA 61.045 63.158 4.92 0.00 0.00 3.25
1647 1661 2.402378 CCGCAAACGAACGGTAATTTTG 59.598 45.455 0.00 1.73 44.46 2.44
1648 1662 2.402378 CGCAAACGAACGGTAATTTTGG 59.598 45.455 0.00 0.00 43.93 3.28
1649 1663 3.630101 GCAAACGAACGGTAATTTTGGA 58.370 40.909 0.00 0.00 0.00 3.53
1650 1664 3.422876 GCAAACGAACGGTAATTTTGGAC 59.577 43.478 0.00 0.00 0.00 4.02
1651 1665 4.790444 GCAAACGAACGGTAATTTTGGACT 60.790 41.667 0.00 0.00 0.00 3.85
1652 1666 4.477302 AACGAACGGTAATTTTGGACTG 57.523 40.909 0.00 0.00 0.00 3.51
1653 1667 2.224784 ACGAACGGTAATTTTGGACTGC 59.775 45.455 0.00 0.00 0.00 4.40
1654 1668 2.482721 CGAACGGTAATTTTGGACTGCT 59.517 45.455 0.00 0.00 0.00 4.24
1655 1669 3.666902 CGAACGGTAATTTTGGACTGCTG 60.667 47.826 0.00 0.00 0.00 4.41
1656 1670 1.539827 ACGGTAATTTTGGACTGCTGC 59.460 47.619 0.00 0.00 0.00 5.25
1657 1671 1.135402 CGGTAATTTTGGACTGCTGCC 60.135 52.381 0.00 0.00 0.00 4.85
1658 1672 1.135402 GGTAATTTTGGACTGCTGCCG 60.135 52.381 0.00 0.00 0.00 5.69
1659 1673 1.539827 GTAATTTTGGACTGCTGCCGT 59.460 47.619 0.00 0.00 0.00 5.68
1660 1674 1.039856 AATTTTGGACTGCTGCCGTT 58.960 45.000 0.00 0.00 0.00 4.44
1661 1675 0.598065 ATTTTGGACTGCTGCCGTTC 59.402 50.000 0.00 0.00 0.00 3.95
1662 1676 1.452145 TTTTGGACTGCTGCCGTTCC 61.452 55.000 0.00 2.54 0.00 3.62
1663 1677 2.337879 TTTGGACTGCTGCCGTTCCT 62.338 55.000 11.24 0.00 0.00 3.36
1664 1678 2.435059 GGACTGCTGCCGTTCCTC 60.435 66.667 0.00 0.00 0.00 3.71
1665 1679 2.435059 GACTGCTGCCGTTCCTCC 60.435 66.667 0.00 0.00 0.00 4.30
1666 1680 2.925170 ACTGCTGCCGTTCCTCCT 60.925 61.111 0.00 0.00 0.00 3.69
1667 1681 2.125350 CTGCTGCCGTTCCTCCTC 60.125 66.667 0.00 0.00 0.00 3.71
1668 1682 3.672295 CTGCTGCCGTTCCTCCTCC 62.672 68.421 0.00 0.00 0.00 4.30
1669 1683 3.394836 GCTGCCGTTCCTCCTCCT 61.395 66.667 0.00 0.00 0.00 3.69
1670 1684 2.896443 CTGCCGTTCCTCCTCCTC 59.104 66.667 0.00 0.00 0.00 3.71
1671 1685 2.683933 TGCCGTTCCTCCTCCTCC 60.684 66.667 0.00 0.00 0.00 4.30
1672 1686 2.364448 GCCGTTCCTCCTCCTCCT 60.364 66.667 0.00 0.00 0.00 3.69
1673 1687 1.990614 GCCGTTCCTCCTCCTCCTT 60.991 63.158 0.00 0.00 0.00 3.36
1674 1688 1.554583 GCCGTTCCTCCTCCTCCTTT 61.555 60.000 0.00 0.00 0.00 3.11
1675 1689 1.861982 CCGTTCCTCCTCCTCCTTTA 58.138 55.000 0.00 0.00 0.00 1.85
1676 1690 1.481363 CCGTTCCTCCTCCTCCTTTAC 59.519 57.143 0.00 0.00 0.00 2.01
1677 1691 1.481363 CGTTCCTCCTCCTCCTTTACC 59.519 57.143 0.00 0.00 0.00 2.85
1678 1692 1.481363 GTTCCTCCTCCTCCTTTACCG 59.519 57.143 0.00 0.00 0.00 4.02
1692 1706 3.864003 CCTTTACCGAGTTCGATTTCTCC 59.136 47.826 2.59 0.00 43.02 3.71
1693 1707 4.381718 CCTTTACCGAGTTCGATTTCTCCT 60.382 45.833 2.59 0.00 43.02 3.69
1694 1708 2.656560 ACCGAGTTCGATTTCTCCTG 57.343 50.000 2.59 0.00 43.02 3.86
1700 1714 2.303022 AGTTCGATTTCTCCTGGCTTGA 59.697 45.455 0.00 0.00 0.00 3.02
1701 1715 2.675348 GTTCGATTTCTCCTGGCTTGAG 59.325 50.000 0.00 0.00 0.00 3.02
1712 1743 5.126061 TCTCCTGGCTTGAGAAAATATTTGC 59.874 40.000 0.39 0.00 35.98 3.68
1934 1969 5.066505 GTGCTCCTCTCTTTGTTTCTTTTCA 59.933 40.000 0.00 0.00 0.00 2.69
1989 2024 4.376146 TGTTTCAGTTTGCTTTATTGGGC 58.624 39.130 0.00 0.00 0.00 5.36
1994 2029 1.726248 GTTTGCTTTATTGGGCTTGCG 59.274 47.619 0.00 0.00 0.00 4.85
2005 2040 0.671796 GGGCTTGCGGTTACTTGTTT 59.328 50.000 0.00 0.00 0.00 2.83
2007 2042 1.607148 GGCTTGCGGTTACTTGTTTCT 59.393 47.619 0.00 0.00 0.00 2.52
2170 2209 2.519013 AGTTCCATCCTTGCAGTTTCC 58.481 47.619 0.00 0.00 0.00 3.13
2206 2262 3.186119 CATTTTTGTGTTTGCGGTGACT 58.814 40.909 0.00 0.00 0.00 3.41
2447 2509 6.729187 AGTTGAAGAAGTTGTGCATTTACTC 58.271 36.000 0.00 0.00 0.00 2.59
2552 2627 6.492087 TGCAGTTTTAGGGCTTTTACAGTATT 59.508 34.615 0.00 0.00 0.00 1.89
2574 2649 1.469703 TCATGCTGAATGACCAAAGCG 59.530 47.619 0.00 0.00 40.50 4.68
2706 2786 1.270839 TGCTTCTGTGTAGTTCCCAGC 60.271 52.381 0.00 0.00 0.00 4.85
2769 2849 3.351740 TGTTTGTGGTGATGAACTGTGT 58.648 40.909 0.00 0.00 0.00 3.72
2832 3019 4.818546 CCGAAGATCAAAGTGCCATCTATT 59.181 41.667 0.00 0.00 0.00 1.73
2887 3074 7.440523 TCTTCTCACAAAGAATAAAGAAGGC 57.559 36.000 9.36 0.00 43.06 4.35
2888 3075 7.227156 TCTTCTCACAAAGAATAAAGAAGGCT 58.773 34.615 9.36 0.00 43.06 4.58
2889 3076 7.389053 TCTTCTCACAAAGAATAAAGAAGGCTC 59.611 37.037 9.36 0.00 43.06 4.70
2890 3077 6.773638 TCTCACAAAGAATAAAGAAGGCTCT 58.226 36.000 0.00 0.00 0.00 4.09
2891 3078 7.227156 TCTCACAAAGAATAAAGAAGGCTCTT 58.773 34.615 0.00 0.00 44.11 2.85
2892 3079 8.375506 TCTCACAAAGAATAAAGAAGGCTCTTA 58.624 33.333 0.00 0.00 41.23 2.10
2893 3080 9.171877 CTCACAAAGAATAAAGAAGGCTCTTAT 57.828 33.333 0.00 0.00 41.23 1.73
2905 3092 8.916628 AAGAAGGCTCTTATATTCCAAGATTC 57.083 34.615 0.00 0.00 40.26 2.52
2906 3093 8.273923 AGAAGGCTCTTATATTCCAAGATTCT 57.726 34.615 0.00 0.00 31.82 2.40
2907 3094 8.722422 AGAAGGCTCTTATATTCCAAGATTCTT 58.278 33.333 0.00 0.00 30.31 2.52
2908 3095 8.916628 AAGGCTCTTATATTCCAAGATTCTTC 57.083 34.615 0.00 0.00 31.82 2.87
2909 3096 8.273923 AGGCTCTTATATTCCAAGATTCTTCT 57.726 34.615 0.00 0.00 31.82 2.85
2910 3097 8.722422 AGGCTCTTATATTCCAAGATTCTTCTT 58.278 33.333 0.00 0.00 43.09 2.52
2911 3098 8.998377 GGCTCTTATATTCCAAGATTCTTCTTC 58.002 37.037 0.00 0.00 40.28 2.87
2912 3099 9.777297 GCTCTTATATTCCAAGATTCTTCTTCT 57.223 33.333 0.00 0.00 40.28 2.85
2918 3105 9.745018 ATATTCCAAGATTCTTCTTCTCACAAA 57.255 29.630 0.00 0.00 40.28 2.83
2919 3106 7.880160 TTCCAAGATTCTTCTTCTCACAAAA 57.120 32.000 0.00 0.00 40.28 2.44
2920 3107 8.469309 TTCCAAGATTCTTCTTCTCACAAAAT 57.531 30.769 0.00 0.00 40.28 1.82
2921 3108 9.573166 TTCCAAGATTCTTCTTCTCACAAAATA 57.427 29.630 0.00 0.00 40.28 1.40
2922 3109 9.573166 TCCAAGATTCTTCTTCTCACAAAATAA 57.427 29.630 0.00 0.00 40.28 1.40
2923 3110 9.837525 CCAAGATTCTTCTTCTCACAAAATAAG 57.162 33.333 0.00 0.00 40.28 1.73
2931 3118 9.890352 CTTCTTCTCACAAAATAAGAAAGAAGG 57.110 33.333 11.73 0.00 39.00 3.46
2932 3119 7.875971 TCTTCTCACAAAATAAGAAAGAAGGC 58.124 34.615 8.79 0.00 39.00 4.35
2933 3120 7.721399 TCTTCTCACAAAATAAGAAAGAAGGCT 59.279 33.333 8.79 0.00 39.00 4.58
2934 3121 7.440523 TCTCACAAAATAAGAAAGAAGGCTC 57.559 36.000 0.00 0.00 0.00 4.70
2935 3122 7.227156 TCTCACAAAATAAGAAAGAAGGCTCT 58.773 34.615 0.00 0.00 0.00 4.09
2936 3123 7.721399 TCTCACAAAATAAGAAAGAAGGCTCTT 59.279 33.333 0.00 0.00 44.11 2.85
2937 3124 8.918202 TCACAAAATAAGAAAGAAGGCTCTTA 57.082 30.769 0.00 0.00 41.23 2.10
2938 3125 9.520515 TCACAAAATAAGAAAGAAGGCTCTTAT 57.479 29.630 0.00 0.00 43.51 1.73
2945 3132 7.872113 AAGAAAGAAGGCTCTTATATTGGTG 57.128 36.000 0.00 0.00 41.23 4.17
3248 3456 8.496751 GGAATCTTTCTTACACTAACTTGTGTC 58.503 37.037 3.46 0.00 46.90 3.67
3329 3537 7.985184 CCTTAGTACTTCATATACCTTGTGCAA 59.015 37.037 0.00 0.00 0.00 4.08
3337 3545 3.508845 ATACCTTGTGCAACTTCAGGT 57.491 42.857 8.21 8.21 42.54 4.00
3473 3687 3.917988 TGTCAGTGTGTCACTCATCATC 58.082 45.455 4.27 0.00 43.43 2.92
3512 3726 2.017049 CAATTGGACCACGAGAATCCC 58.983 52.381 0.00 0.00 0.00 3.85
3664 3889 2.949177 TTGCTCACTTGAGGGCTTTA 57.051 45.000 8.32 0.00 42.29 1.85
3698 3923 6.521151 AATTATTTCAGAAGGCTTCACAGG 57.479 37.500 27.70 14.40 0.00 4.00
3747 3973 1.895131 CAGTAATTTTGGTGGCCTGCT 59.105 47.619 3.32 0.00 0.00 4.24
3767 3993 7.492994 GCCTGCTATGCTAGTAATCTATTTACC 59.507 40.741 0.00 0.00 41.01 2.85
3768 3994 8.531982 CCTGCTATGCTAGTAATCTATTTACCA 58.468 37.037 0.00 0.00 41.01 3.25
3779 4005 6.732896 AATCTATTTACCATCCGTGACTCT 57.267 37.500 0.00 0.00 0.00 3.24
3815 4041 2.354821 GCACTAAAGATAAAGGCCCACG 59.645 50.000 0.00 0.00 0.00 4.94
3860 4086 2.174639 TGTGAAGCCTATATTGTGGGGG 59.825 50.000 0.00 0.00 0.00 5.40
3881 4108 6.535540 GGGGGAAATCTAACTAAGAAGATCC 58.464 44.000 0.00 0.00 37.89 3.36
3918 4168 6.128172 GCACTTGCTATACTGTTCTTGATGTT 60.128 38.462 0.00 0.00 38.21 2.71
3974 4224 4.378459 GCCACATGTAGCTGTCAAGTTTAC 60.378 45.833 9.16 0.00 0.00 2.01
3983 4233 1.601903 TGTCAAGTTTACGCCAAGCTG 59.398 47.619 0.00 0.00 0.00 4.24
4064 4318 5.469479 CCATTTTGAGTACTTCCGCAAATT 58.531 37.500 7.94 3.39 31.20 1.82
4073 4327 2.029918 ACTTCCGCAAATTCCTTCTTGC 60.030 45.455 0.00 0.00 43.61 4.01
4127 4381 4.588528 TGGCTGCTTTTTGTCCTAAGAAAT 59.411 37.500 0.00 0.00 0.00 2.17
4129 4383 5.991606 GGCTGCTTTTTGTCCTAAGAAATTT 59.008 36.000 0.00 0.00 0.00 1.82
4184 4438 2.248280 TGTGTATCAAGTTGGTGCGT 57.752 45.000 2.34 0.00 0.00 5.24
4297 4551 7.035004 CCAAATGTGTATGAAAGTATGGTTGG 58.965 38.462 0.00 0.00 0.00 3.77
4543 4798 0.256464 AGGAAGACGAGGACGAGGAT 59.744 55.000 0.00 0.00 42.66 3.24
4615 4870 0.807667 CAAGCGAGTTCTGGATCGGG 60.808 60.000 0.00 0.00 39.31 5.14
4624 4879 1.153369 CTGGATCGGGTGCGACATT 60.153 57.895 0.00 0.00 0.00 2.71
4796 5051 3.941483 CCCATCTGATCAAACTACACCAC 59.059 47.826 0.00 0.00 0.00 4.16
4797 5052 3.941483 CCATCTGATCAAACTACACCACC 59.059 47.826 0.00 0.00 0.00 4.61
4798 5053 4.565444 CCATCTGATCAAACTACACCACCA 60.565 45.833 0.00 0.00 0.00 4.17
4863 5118 3.096092 CTCTAGAAACTGTGCTCCCTCT 58.904 50.000 0.00 0.00 0.00 3.69
4864 5119 3.093057 TCTAGAAACTGTGCTCCCTCTC 58.907 50.000 0.00 0.00 0.00 3.20
4911 5166 4.019860 AGGTGCTGTGAAAGACTGATACAT 60.020 41.667 0.00 0.00 0.00 2.29
4912 5167 5.187772 AGGTGCTGTGAAAGACTGATACATA 59.812 40.000 0.00 0.00 0.00 2.29
4913 5168 5.292101 GGTGCTGTGAAAGACTGATACATAC 59.708 44.000 0.00 0.00 0.00 2.39
4927 5182 8.560355 ACTGATACATACTAGCTCATACTCTG 57.440 38.462 0.00 0.00 0.00 3.35
5071 5326 5.029654 GGCTTGTGTTTTTGCAAAATGAAG 58.970 37.500 24.39 20.91 0.00 3.02
5087 5342 6.661304 AAATGAAGTGCCTTTCTTTGATCT 57.339 33.333 0.00 0.00 0.00 2.75
5127 5398 2.808906 AGTACAGGGGCCAAAGAATC 57.191 50.000 4.39 0.00 0.00 2.52
5187 5459 4.514441 ACTGTTCATCTGTTTGAGCTTCAG 59.486 41.667 0.00 0.00 0.00 3.02
5221 5493 6.434340 ACCAAAGTGAAGGATTTCTACAATCC 59.566 38.462 5.58 5.58 45.08 3.01
5222 5494 6.434028 CCAAAGTGAAGGATTTCTACAATCCA 59.566 38.462 14.60 0.00 46.70 3.41
5223 5495 7.123247 CCAAAGTGAAGGATTTCTACAATCCAT 59.877 37.037 14.60 3.98 46.70 3.41
5225 5497 6.125029 AGTGAAGGATTTCTACAATCCATGG 58.875 40.000 4.97 4.97 46.70 3.66
5226 5498 6.069440 AGTGAAGGATTTCTACAATCCATGGA 60.069 38.462 18.88 18.88 46.70 3.41
5227 5499 6.261826 GTGAAGGATTTCTACAATCCATGGAG 59.738 42.308 21.33 10.10 46.70 3.86
5228 5500 4.723309 AGGATTTCTACAATCCATGGAGC 58.277 43.478 21.33 0.00 46.70 4.70
5235 5519 3.446442 ACAATCCATGGAGCTCTTTGT 57.554 42.857 21.33 20.68 0.00 2.83
5238 5522 3.567478 ATCCATGGAGCTCTTTGTACC 57.433 47.619 21.33 0.00 0.00 3.34
5241 5525 3.012518 CCATGGAGCTCTTTGTACCAAG 58.987 50.000 14.64 0.19 34.28 3.61
5267 5551 4.022329 CCAAGGTCTATTTGGTGGTTTGTC 60.022 45.833 0.00 0.00 40.15 3.18
5271 5555 5.301805 AGGTCTATTTGGTGGTTTGTCTTTG 59.698 40.000 0.00 0.00 0.00 2.77
5331 5615 4.730949 TCCTACGAATTGAACACCTAGG 57.269 45.455 7.41 7.41 0.00 3.02
5341 5626 4.974645 TGAACACCTAGGTCTGACAAAT 57.025 40.909 12.84 0.00 34.06 2.32
5349 5634 5.731678 ACCTAGGTCTGACAAATATCCCTTT 59.268 40.000 9.21 0.00 0.00 3.11
5364 5649 1.548582 CCCTTTGCACAACTCTCCCAT 60.549 52.381 0.00 0.00 0.00 4.00
5382 5667 1.244019 ATGGAAGAAGCCACGGTTGC 61.244 55.000 0.00 0.00 41.56 4.17
5391 5676 1.218316 CCACGGTTGCTCCCTACTC 59.782 63.158 0.00 0.00 0.00 2.59
5405 5690 1.208293 CCTACTCCCAAGTTCTGCTCC 59.792 57.143 0.00 0.00 36.92 4.70
5442 5727 1.291877 ACCGAAATGTCGCTGCACTC 61.292 55.000 0.00 0.00 46.28 3.51
5465 5750 3.366374 GCTAATGTTTGAGGAACCTGCAC 60.366 47.826 0.00 0.00 37.45 4.57
5495 5780 4.391830 ACACATCAATAGTTAACCGCACTG 59.608 41.667 0.88 0.00 0.00 3.66
5539 5824 7.731054 ACATTTTAACATCCTAAACTTTGGCA 58.269 30.769 0.00 0.00 0.00 4.92
5540 5825 8.374743 ACATTTTAACATCCTAAACTTTGGCAT 58.625 29.630 0.00 0.00 0.00 4.40
5541 5826 8.658609 CATTTTAACATCCTAAACTTTGGCATG 58.341 33.333 0.00 0.00 0.00 4.06
5542 5827 6.909550 TTAACATCCTAAACTTTGGCATGT 57.090 33.333 0.00 0.00 31.26 3.21
5543 5828 8.410673 TTTAACATCCTAAACTTTGGCATGTA 57.589 30.769 0.00 0.00 30.53 2.29
5544 5829 6.909550 AACATCCTAAACTTTGGCATGTAA 57.090 33.333 0.00 0.00 30.53 2.41
5545 5830 6.267496 ACATCCTAAACTTTGGCATGTAAC 57.733 37.500 0.00 0.00 29.72 2.50
5546 5831 5.185056 ACATCCTAAACTTTGGCATGTAACC 59.815 40.000 0.00 0.00 29.72 2.85
5547 5832 4.083565 TCCTAAACTTTGGCATGTAACCC 58.916 43.478 0.00 0.00 0.00 4.11
5548 5833 3.119637 CCTAAACTTTGGCATGTAACCCG 60.120 47.826 0.00 0.00 0.00 5.28
5549 5834 0.601057 AACTTTGGCATGTAACCCGC 59.399 50.000 0.00 0.00 0.00 6.13
5550 5835 1.248101 ACTTTGGCATGTAACCCGCC 61.248 55.000 0.00 0.00 46.43 6.13
5551 5836 1.944234 CTTTGGCATGTAACCCGCCC 61.944 60.000 0.00 0.00 45.63 6.13
5552 5837 2.433646 TTTGGCATGTAACCCGCCCT 62.434 55.000 0.00 0.00 45.63 5.19
5553 5838 2.828549 GGCATGTAACCCGCCCTG 60.829 66.667 0.00 0.00 40.07 4.45
5554 5839 3.518068 GCATGTAACCCGCCCTGC 61.518 66.667 0.00 0.00 0.00 4.85
5555 5840 2.828549 CATGTAACCCGCCCTGCC 60.829 66.667 0.00 0.00 0.00 4.85
5573 5858 1.886655 GCCCTCACCCGTGAAAAGAAT 60.887 52.381 0.00 0.00 39.39 2.40
5618 5903 0.827368 CTCCAACAGCTCCCTACTCC 59.173 60.000 0.00 0.00 0.00 3.85
5621 5906 0.909610 CAACAGCTCCCTACTCCCCA 60.910 60.000 0.00 0.00 0.00 4.96
5688 5974 5.830457 AGCAGCTTCCCTATTCCTATTTTTC 59.170 40.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 3.006940 TGTTTTCGAACAGAGTGTGCTT 58.993 40.909 0.00 0.00 0.00 3.91
94 95 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
95 96 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
97 98 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
100 101 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
101 102 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
102 103 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
104 105 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
110 111 9.802039 AAGTTTAATACAAAGTTGGGTCATCTA 57.198 29.630 0.00 0.00 0.00 1.98
113 114 9.582648 ACTAAGTTTAATACAAAGTTGGGTCAT 57.417 29.630 5.88 0.00 0.00 3.06
114 115 8.983702 ACTAAGTTTAATACAAAGTTGGGTCA 57.016 30.769 5.88 0.00 0.00 4.02
143 144 9.753674 TCCATTCCAAAATAGATAACTCAACTT 57.246 29.630 0.00 0.00 0.00 2.66
144 145 9.401058 CTCCATTCCAAAATAGATAACTCAACT 57.599 33.333 0.00 0.00 0.00 3.16
145 146 8.624776 CCTCCATTCCAAAATAGATAACTCAAC 58.375 37.037 0.00 0.00 0.00 3.18
146 147 7.779798 CCCTCCATTCCAAAATAGATAACTCAA 59.220 37.037 0.00 0.00 0.00 3.02
150 151 7.290813 ACTCCCTCCATTCCAAAATAGATAAC 58.709 38.462 0.00 0.00 0.00 1.89
151 152 7.465900 ACTCCCTCCATTCCAAAATAGATAA 57.534 36.000 0.00 0.00 0.00 1.75
152 153 7.794683 ACTACTCCCTCCATTCCAAAATAGATA 59.205 37.037 0.00 0.00 0.00 1.98
154 155 5.970640 ACTACTCCCTCCATTCCAAAATAGA 59.029 40.000 0.00 0.00 0.00 1.98
155 156 6.253946 ACTACTCCCTCCATTCCAAAATAG 57.746 41.667 0.00 0.00 0.00 1.73
158 159 4.081309 CGTACTACTCCCTCCATTCCAAAA 60.081 45.833 0.00 0.00 0.00 2.44
159 160 3.449737 CGTACTACTCCCTCCATTCCAAA 59.550 47.826 0.00 0.00 0.00 3.28
163 164 4.459330 ACTACGTACTACTCCCTCCATTC 58.541 47.826 0.00 0.00 0.00 2.67
164 165 4.516652 ACTACGTACTACTCCCTCCATT 57.483 45.455 0.00 0.00 0.00 3.16
166 167 4.033709 ACTACTACGTACTACTCCCTCCA 58.966 47.826 0.00 0.00 0.00 3.86
167 168 4.141824 ACACTACTACGTACTACTCCCTCC 60.142 50.000 0.00 0.00 0.00 4.30
169 170 5.428184 AACACTACTACGTACTACTCCCT 57.572 43.478 0.00 0.00 0.00 4.20
170 171 6.502136 AAAACACTACTACGTACTACTCCC 57.498 41.667 0.00 0.00 0.00 4.30
171 172 7.183433 GCTAAAACACTACTACGTACTACTCC 58.817 42.308 0.00 0.00 0.00 3.85
172 173 7.065204 AGGCTAAAACACTACTACGTACTACTC 59.935 40.741 0.00 0.00 0.00 2.59
173 174 6.881602 AGGCTAAAACACTACTACGTACTACT 59.118 38.462 0.00 0.00 0.00 2.57
175 176 6.036083 CGAGGCTAAAACACTACTACGTACTA 59.964 42.308 0.00 0.00 0.00 1.82
176 177 5.163814 CGAGGCTAAAACACTACTACGTACT 60.164 44.000 0.00 0.00 0.00 2.73
177 178 5.024555 CGAGGCTAAAACACTACTACGTAC 58.975 45.833 0.00 0.00 0.00 3.67
178 179 4.695455 ACGAGGCTAAAACACTACTACGTA 59.305 41.667 0.00 0.00 0.00 3.57
180 181 4.088823 ACGAGGCTAAAACACTACTACG 57.911 45.455 0.00 0.00 0.00 3.51
260 261 2.185867 GTCGCCTGCCGTTGGATA 59.814 61.111 0.00 0.00 38.35 2.59
523 525 1.136984 GTGGTAGGTCTCTGACGCG 59.863 63.158 3.53 3.53 32.65 6.01
531 533 1.075450 GGGGATCCGTGGTAGGTCT 60.075 63.158 5.45 0.00 0.00 3.85
1171 1185 1.614241 GCTACGAGAGGGGCAAAGGA 61.614 60.000 0.00 0.00 33.96 3.36
1630 1644 4.790444 GCAGTCCAAAATTACCGTTCGTTT 60.790 41.667 0.00 0.00 0.00 3.60
1647 1661 2.435059 GAGGAACGGCAGCAGTCC 60.435 66.667 0.00 2.52 0.00 3.85
1648 1662 2.435059 GGAGGAACGGCAGCAGTC 60.435 66.667 0.00 0.00 0.00 3.51
1649 1663 2.925170 AGGAGGAACGGCAGCAGT 60.925 61.111 0.00 0.00 0.00 4.40
1650 1664 2.125350 GAGGAGGAACGGCAGCAG 60.125 66.667 0.00 0.00 0.00 4.24
1651 1665 3.706373 GGAGGAGGAACGGCAGCA 61.706 66.667 0.00 0.00 0.00 4.41
1652 1666 3.378399 GAGGAGGAGGAACGGCAGC 62.378 68.421 0.00 0.00 0.00 5.25
1653 1667 2.726351 GGAGGAGGAGGAACGGCAG 61.726 68.421 0.00 0.00 0.00 4.85
1654 1668 2.683933 GGAGGAGGAGGAACGGCA 60.684 66.667 0.00 0.00 0.00 5.69
1655 1669 1.554583 AAAGGAGGAGGAGGAACGGC 61.555 60.000 0.00 0.00 0.00 5.68
1656 1670 1.481363 GTAAAGGAGGAGGAGGAACGG 59.519 57.143 0.00 0.00 0.00 4.44
1657 1671 1.481363 GGTAAAGGAGGAGGAGGAACG 59.519 57.143 0.00 0.00 0.00 3.95
1658 1672 1.481363 CGGTAAAGGAGGAGGAGGAAC 59.519 57.143 0.00 0.00 0.00 3.62
1659 1673 1.360162 TCGGTAAAGGAGGAGGAGGAA 59.640 52.381 0.00 0.00 0.00 3.36
1660 1674 1.005228 TCGGTAAAGGAGGAGGAGGA 58.995 55.000 0.00 0.00 0.00 3.71
1661 1675 1.342175 ACTCGGTAAAGGAGGAGGAGG 60.342 57.143 0.00 0.00 35.82 4.30
1662 1676 2.146920 ACTCGGTAAAGGAGGAGGAG 57.853 55.000 0.00 0.00 35.82 3.69
1663 1677 2.454538 GAACTCGGTAAAGGAGGAGGA 58.545 52.381 0.00 0.00 35.82 3.71
1664 1678 1.134560 CGAACTCGGTAAAGGAGGAGG 59.865 57.143 0.00 0.00 35.82 4.30
1665 1679 2.089980 TCGAACTCGGTAAAGGAGGAG 58.910 52.381 0.00 0.00 40.29 3.69
1666 1680 2.205022 TCGAACTCGGTAAAGGAGGA 57.795 50.000 0.00 0.00 40.29 3.71
1667 1681 3.521947 AATCGAACTCGGTAAAGGAGG 57.478 47.619 0.00 0.00 40.29 4.30
1668 1682 4.745649 AGAAATCGAACTCGGTAAAGGAG 58.254 43.478 0.00 0.00 40.29 3.69
1669 1683 4.381292 GGAGAAATCGAACTCGGTAAAGGA 60.381 45.833 0.00 0.00 40.29 3.36
1670 1684 3.864003 GGAGAAATCGAACTCGGTAAAGG 59.136 47.826 0.00 0.00 40.29 3.11
1671 1685 4.563184 CAGGAGAAATCGAACTCGGTAAAG 59.437 45.833 0.00 0.00 40.29 1.85
1672 1686 4.491676 CAGGAGAAATCGAACTCGGTAAA 58.508 43.478 0.00 0.00 40.29 2.01
1673 1687 3.119245 CCAGGAGAAATCGAACTCGGTAA 60.119 47.826 0.00 0.00 40.29 2.85
1674 1688 2.426024 CCAGGAGAAATCGAACTCGGTA 59.574 50.000 0.00 0.00 40.29 4.02
1675 1689 1.204941 CCAGGAGAAATCGAACTCGGT 59.795 52.381 0.00 0.00 40.29 4.69
1676 1690 1.927895 CCAGGAGAAATCGAACTCGG 58.072 55.000 0.00 0.00 40.29 4.63
1677 1691 1.134965 AGCCAGGAGAAATCGAACTCG 60.135 52.381 0.00 0.00 41.45 4.18
1678 1692 2.675348 CAAGCCAGGAGAAATCGAACTC 59.325 50.000 0.00 0.00 0.00 3.01
1692 1706 7.009907 GCTAAAGCAAATATTTTCTCAAGCCAG 59.990 37.037 16.62 8.24 41.59 4.85
1693 1707 6.813152 GCTAAAGCAAATATTTTCTCAAGCCA 59.187 34.615 16.62 0.71 41.59 4.75
1694 1708 7.038048 AGCTAAAGCAAATATTTTCTCAAGCC 58.962 34.615 20.54 10.38 45.16 4.35
1934 1969 3.535561 CCTCCGATACACTCAAAGCAAT 58.464 45.455 0.00 0.00 0.00 3.56
1989 2024 5.169836 AGAAAGAAACAAGTAACCGCAAG 57.830 39.130 0.00 0.00 0.00 4.01
1994 2029 7.696872 GTCACAGAAAGAAAGAAACAAGTAACC 59.303 37.037 0.00 0.00 0.00 2.85
2005 2040 3.071602 CCAGAGGGTCACAGAAAGAAAGA 59.928 47.826 0.00 0.00 0.00 2.52
2007 2042 2.106511 CCCAGAGGGTCACAGAAAGAAA 59.893 50.000 0.00 0.00 38.25 2.52
2115 2153 6.806249 CACGCAATCCTTTATTTGTGTATGTT 59.194 34.615 1.99 0.00 31.31 2.71
2170 2209 6.582295 ACACAAAAATGTTCTTTATAGCAGCG 59.418 34.615 0.00 0.00 0.00 5.18
2206 2262 5.312895 AGTTGTGACAATGTGGCATAGTTA 58.687 37.500 0.00 0.00 37.93 2.24
2311 2367 2.909662 ACCCTTCTCCTTCTTTCTGAGG 59.090 50.000 0.00 0.00 0.00 3.86
2418 2480 7.426929 AATGCACAACTTCTTCAACTACTAG 57.573 36.000 0.00 0.00 0.00 2.57
2447 2509 5.107989 GCTTCGTATACACATTACATCACCG 60.108 44.000 3.32 0.00 0.00 4.94
2552 2627 6.930371 GACGCTTTGGTCATTCAGCATGATA 61.930 44.000 0.00 0.00 44.11 2.15
2706 2786 4.954092 AAATTCTTTAGAGCAGCCGAAG 57.046 40.909 0.00 0.00 0.00 3.79
2769 2849 3.554934 AGAGCAAGTTGTGGAAATGTGA 58.445 40.909 4.48 0.00 0.00 3.58
2886 3073 9.777297 AGAAGAAGAATCTTGGAATATAAGAGC 57.223 33.333 0.00 0.00 45.91 4.09
2892 3079 9.745018 TTTGTGAGAAGAAGAATCTTGGAATAT 57.255 29.630 0.00 0.00 45.91 1.28
2893 3080 9.573166 TTTTGTGAGAAGAAGAATCTTGGAATA 57.427 29.630 0.00 0.00 45.91 1.75
2894 3081 8.469309 TTTTGTGAGAAGAAGAATCTTGGAAT 57.531 30.769 0.00 0.00 45.91 3.01
2895 3082 7.880160 TTTTGTGAGAAGAAGAATCTTGGAA 57.120 32.000 0.00 0.00 45.91 3.53
2896 3083 9.573166 TTATTTTGTGAGAAGAAGAATCTTGGA 57.427 29.630 0.00 0.00 45.91 3.53
2897 3084 9.837525 CTTATTTTGTGAGAAGAAGAATCTTGG 57.162 33.333 0.00 0.00 45.91 3.61
2905 3092 9.890352 CCTTCTTTCTTATTTTGTGAGAAGAAG 57.110 33.333 12.96 12.96 40.44 2.85
2906 3093 8.352942 GCCTTCTTTCTTATTTTGTGAGAAGAA 58.647 33.333 10.76 0.00 40.44 2.52
2907 3094 7.721399 AGCCTTCTTTCTTATTTTGTGAGAAGA 59.279 33.333 10.76 0.00 40.44 2.87
2908 3095 7.880105 AGCCTTCTTTCTTATTTTGTGAGAAG 58.120 34.615 0.00 0.00 38.72 2.85
2909 3096 7.721399 AGAGCCTTCTTTCTTATTTTGTGAGAA 59.279 33.333 0.00 0.00 31.27 2.87
2910 3097 7.227156 AGAGCCTTCTTTCTTATTTTGTGAGA 58.773 34.615 0.00 0.00 0.00 3.27
2911 3098 7.446001 AGAGCCTTCTTTCTTATTTTGTGAG 57.554 36.000 0.00 0.00 0.00 3.51
2912 3099 7.823745 AAGAGCCTTCTTTCTTATTTTGTGA 57.176 32.000 0.00 0.00 40.79 3.58
2919 3106 9.566432 CACCAATATAAGAGCCTTCTTTCTTAT 57.434 33.333 10.51 10.51 44.54 1.73
2920 3107 7.993183 CCACCAATATAAGAGCCTTCTTTCTTA 59.007 37.037 0.00 0.00 40.79 2.10
2921 3108 6.830838 CCACCAATATAAGAGCCTTCTTTCTT 59.169 38.462 0.00 0.00 40.79 2.52
2922 3109 6.360618 CCACCAATATAAGAGCCTTCTTTCT 58.639 40.000 0.00 0.00 40.79 2.52
2923 3110 5.009110 GCCACCAATATAAGAGCCTTCTTTC 59.991 44.000 0.00 0.00 40.79 2.62
2924 3111 4.889995 GCCACCAATATAAGAGCCTTCTTT 59.110 41.667 0.00 0.00 40.79 2.52
2925 3112 4.464947 GCCACCAATATAAGAGCCTTCTT 58.535 43.478 0.00 0.00 45.45 2.52
2926 3113 3.495100 CGCCACCAATATAAGAGCCTTCT 60.495 47.826 0.00 0.00 34.29 2.85
2927 3114 2.808543 CGCCACCAATATAAGAGCCTTC 59.191 50.000 0.00 0.00 0.00 3.46
2928 3115 2.487265 CCGCCACCAATATAAGAGCCTT 60.487 50.000 0.00 0.00 0.00 4.35
2929 3116 1.072331 CCGCCACCAATATAAGAGCCT 59.928 52.381 0.00 0.00 0.00 4.58
2930 3117 1.523758 CCGCCACCAATATAAGAGCC 58.476 55.000 0.00 0.00 0.00 4.70
2931 3118 1.071699 TCCCGCCACCAATATAAGAGC 59.928 52.381 0.00 0.00 0.00 4.09
2932 3119 2.550208 GGTCCCGCCACCAATATAAGAG 60.550 54.545 0.00 0.00 36.32 2.85
2933 3120 1.418637 GGTCCCGCCACCAATATAAGA 59.581 52.381 0.00 0.00 36.32 2.10
2934 3121 1.142060 TGGTCCCGCCACCAATATAAG 59.858 52.381 1.33 0.00 43.88 1.73
2935 3122 1.214217 TGGTCCCGCCACCAATATAA 58.786 50.000 1.33 0.00 43.88 0.98
2936 3123 2.932404 TGGTCCCGCCACCAATATA 58.068 52.632 1.33 0.00 43.88 0.86
2937 3124 3.748370 TGGTCCCGCCACCAATAT 58.252 55.556 1.33 0.00 43.88 1.28
2945 3132 2.124278 GGAAGGAATGGTCCCGCC 60.124 66.667 0.00 0.00 46.30 6.13
3000 3202 3.005050 CACAAAAGAGAGCAAGATGGCAA 59.995 43.478 0.00 0.00 35.83 4.52
3101 3305 0.170339 GTTTTCATCTTTCCCGCGGG 59.830 55.000 39.13 39.13 0.00 6.13
3102 3306 0.170339 GGTTTTCATCTTTCCCGCGG 59.830 55.000 21.04 21.04 0.00 6.46
3103 3307 0.878416 TGGTTTTCATCTTTCCCGCG 59.122 50.000 0.00 0.00 0.00 6.46
3248 3456 4.578928 AGGTGTAAGGTGCACAAACTAAAG 59.421 41.667 20.43 0.00 38.51 1.85
3287 3495 3.578716 ACTAAGGCAGCAAACTCTCACTA 59.421 43.478 0.00 0.00 0.00 2.74
3329 3537 4.400884 TGCACATTACAAACAACCTGAAGT 59.599 37.500 0.00 0.00 0.00 3.01
3337 3545 8.768955 GGTCAAAATTATGCACATTACAAACAA 58.231 29.630 0.00 0.00 0.00 2.83
3406 3619 9.047947 AGGAGTATGGTACTAAAGTGAAGATTT 57.952 33.333 0.00 0.00 39.59 2.17
3407 3620 8.611051 AGGAGTATGGTACTAAAGTGAAGATT 57.389 34.615 0.00 0.00 39.59 2.40
3408 3621 8.611051 AAGGAGTATGGTACTAAAGTGAAGAT 57.389 34.615 0.00 0.00 39.59 2.40
3418 3631 4.508551 TCCACGAAGGAGTATGGTACTA 57.491 45.455 0.00 0.00 43.07 1.82
3473 3687 7.012327 TCCAATTGTTAATTTCTAGAGATGGCG 59.988 37.037 4.43 0.00 0.00 5.69
3664 3889 9.002600 GCCTTCTGAAATAATTTGTTCCAAAAT 57.997 29.630 0.00 0.00 0.00 1.82
3747 3973 9.251440 ACGGATGGTAAATAGATTACTAGCATA 57.749 33.333 3.14 0.00 41.54 3.14
3767 3993 3.249091 CAAGAGAACAGAGTCACGGATG 58.751 50.000 0.00 0.00 0.00 3.51
3768 3994 2.894126 ACAAGAGAACAGAGTCACGGAT 59.106 45.455 0.00 0.00 0.00 4.18
3815 4041 5.762218 ACCACTTTCAATATAGATGAGCAGC 59.238 40.000 0.00 0.00 0.00 5.25
3860 4086 6.702282 CGGTGGATCTTCTTAGTTAGATTTCC 59.298 42.308 0.00 0.00 31.46 3.13
3861 4087 6.702282 CCGGTGGATCTTCTTAGTTAGATTTC 59.298 42.308 0.00 0.00 31.46 2.17
3876 4103 1.224592 GCATGGAACCGGTGGATCT 59.775 57.895 8.52 0.00 0.00 2.75
3877 4104 1.077787 TGCATGGAACCGGTGGATC 60.078 57.895 8.52 0.83 0.00 3.36
3878 4105 1.378514 GTGCATGGAACCGGTGGAT 60.379 57.895 8.52 0.00 0.00 3.41
3879 4106 2.033448 GTGCATGGAACCGGTGGA 59.967 61.111 8.52 0.00 0.00 4.02
3881 4108 1.580942 CAAGTGCATGGAACCGGTG 59.419 57.895 8.52 0.00 0.00 4.94
3927 4177 7.591426 GGCAAGAACTAAATAACAGAACACTTG 59.409 37.037 0.00 0.00 34.83 3.16
3983 4233 7.539712 TCTTGTGCAATCAGTAAATAGCTAC 57.460 36.000 0.00 0.00 0.00 3.58
4053 4307 2.599659 GCAAGAAGGAATTTGCGGAAG 58.400 47.619 0.00 0.00 40.09 3.46
4064 4318 6.650807 CACTAATAACAGAACAGCAAGAAGGA 59.349 38.462 0.00 0.00 0.00 3.36
4297 4551 1.673665 CTGTCCCTGTGCTTCCTGC 60.674 63.158 0.00 0.00 43.25 4.85
4525 4780 0.382515 CATCCTCGTCCTCGTCTTCC 59.617 60.000 0.00 0.00 38.33 3.46
4543 4798 2.612212 GGTTTCGCTGTGTTCTTCTTCA 59.388 45.455 0.00 0.00 0.00 3.02
4582 4837 0.655208 CGCTTGCGTTGTATATGCCA 59.345 50.000 6.86 0.00 38.02 4.92
4594 4849 1.746727 CGATCCAGAACTCGCTTGCG 61.747 60.000 8.87 8.87 0.00 4.85
4615 4870 2.571611 CGCTCGCAAATGTCGCAC 60.572 61.111 0.00 0.00 0.00 5.34
4624 4879 4.243008 TGGAACCACCGCTCGCAA 62.243 61.111 0.00 0.00 42.61 4.85
4645 4900 0.028902 GGGTTATCCGCACGCATTTC 59.971 55.000 0.00 0.00 33.83 2.17
4758 5013 4.500116 GGTCAGAGACGGCGGCTC 62.500 72.222 34.67 34.67 32.65 4.70
4761 5016 3.432051 GATGGGTCAGAGACGGCGG 62.432 68.421 13.24 0.00 32.65 6.13
4762 5017 2.105128 GATGGGTCAGAGACGGCG 59.895 66.667 4.80 4.80 32.65 6.46
4796 5051 3.555586 CCTTGGGCAGAAAAGAAACATGG 60.556 47.826 0.00 0.00 0.00 3.66
4797 5052 3.070015 ACCTTGGGCAGAAAAGAAACATG 59.930 43.478 0.00 0.00 0.00 3.21
4798 5053 3.308401 ACCTTGGGCAGAAAAGAAACAT 58.692 40.909 0.00 0.00 0.00 2.71
4863 5118 2.690026 GCTAGGAGACTACCACATGGGA 60.690 54.545 0.00 0.00 43.67 4.37
4864 5119 1.689273 GCTAGGAGACTACCACATGGG 59.311 57.143 2.32 0.00 43.67 4.00
4911 5166 5.306114 TGCTACCAGAGTATGAGCTAGTA 57.694 43.478 0.00 0.00 31.58 1.82
4912 5167 4.171878 TGCTACCAGAGTATGAGCTAGT 57.828 45.455 0.00 0.00 31.58 2.57
4913 5168 5.720371 AATGCTACCAGAGTATGAGCTAG 57.280 43.478 0.00 0.00 31.58 3.42
4927 5182 8.904099 ACCAAGTAAACATCTATAATGCTACC 57.096 34.615 0.00 0.00 0.00 3.18
4946 5201 5.126869 TGAACACATCAAATGACAACCAAGT 59.873 36.000 0.00 0.00 34.30 3.16
5071 5326 4.067896 TCAGACAGATCAAAGAAAGGCAC 58.932 43.478 0.00 0.00 0.00 5.01
5087 5342 2.365635 GCTAGGGGCCCTCAGACA 60.366 66.667 32.78 10.68 34.61 3.41
5127 5398 8.012957 AGTCCTGTGTTTAATCTACCTGATAG 57.987 38.462 0.00 0.00 34.45 2.08
5187 5459 6.581171 ATCCTTCACTTTGGTTCATTTCTC 57.419 37.500 0.00 0.00 0.00 2.87
5235 5519 6.057321 CCAAATAGACCTTGGTACTTGGTA 57.943 41.667 10.83 0.00 38.85 3.25
5292 5576 6.645415 TCGTAGGAATTGAAGAAACAAGAGAC 59.355 38.462 0.00 0.00 33.22 3.36
5322 5606 5.104485 GGGATATTTGTCAGACCTAGGTGTT 60.104 44.000 22.10 4.14 0.00 3.32
5330 5614 4.016444 TGCAAAGGGATATTTGTCAGACC 58.984 43.478 0.00 0.00 41.31 3.85
5331 5615 4.458989 TGTGCAAAGGGATATTTGTCAGAC 59.541 41.667 0.00 0.00 41.31 3.51
5341 5626 2.026262 GGGAGAGTTGTGCAAAGGGATA 60.026 50.000 0.00 0.00 0.00 2.59
5349 5634 0.770499 TTCCATGGGAGAGTTGTGCA 59.230 50.000 13.02 0.00 31.21 4.57
5364 5649 1.896660 GCAACCGTGGCTTCTTCCA 60.897 57.895 0.00 0.00 0.00 3.53
5382 5667 1.208293 GCAGAACTTGGGAGTAGGGAG 59.792 57.143 0.00 0.00 34.21 4.30
5405 5690 0.385390 GTGGGGATTGCTTTATGGCG 59.615 55.000 0.00 0.00 34.52 5.69
5434 5719 1.464608 TCAAACATTAGCGAGTGCAGC 59.535 47.619 0.00 0.00 46.23 5.25
5442 5727 2.159517 GCAGGTTCCTCAAACATTAGCG 60.160 50.000 0.00 0.00 39.81 4.26
5465 5750 6.546395 GGTTAACTATTGATGTGTGCTTGAG 58.454 40.000 5.42 0.00 0.00 3.02
5514 5799 7.731054 TGCCAAAGTTTAGGATGTTAAAATGT 58.269 30.769 7.90 0.00 0.00 2.71
5539 5824 4.123545 GGGCAGGGCGGGTTACAT 62.124 66.667 0.00 0.00 0.00 2.29
5541 5826 4.484872 GAGGGCAGGGCGGGTTAC 62.485 72.222 0.00 0.00 0.00 2.50
5550 5835 2.690653 TTTTCACGGGTGAGGGCAGG 62.691 60.000 1.37 0.00 41.13 4.85
5551 5836 1.228124 TTTTCACGGGTGAGGGCAG 60.228 57.895 1.37 0.00 41.13 4.85
5552 5837 1.228124 CTTTTCACGGGTGAGGGCA 60.228 57.895 1.37 0.00 41.13 5.36
5553 5838 0.536460 TTCTTTTCACGGGTGAGGGC 60.536 55.000 1.37 0.00 41.13 5.19
5554 5839 2.200373 ATTCTTTTCACGGGTGAGGG 57.800 50.000 1.37 0.00 41.13 4.30
5555 5840 4.700213 ACATTATTCTTTTCACGGGTGAGG 59.300 41.667 1.37 0.00 41.13 3.86
5573 5858 9.847224 GGAGAAATTAGATCTTAACCCACATTA 57.153 33.333 0.00 0.00 0.00 1.90
5628 5913 4.720046 TGTGCCAACTTCACTATACCAAA 58.280 39.130 0.00 0.00 35.58 3.28
5663 5949 6.515512 AAAATAGGAATAGGGAAGCTGCTA 57.484 37.500 0.90 0.00 0.00 3.49
5668 5954 9.746457 ATCATAGAAAAATAGGAATAGGGAAGC 57.254 33.333 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.