Multiple sequence alignment - TraesCS1A01G306500

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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 TraesCS1A01G306500 chr1A 100.000 4475 0 0 1 4475 498591650 498596124 0.000000e+00 8264.0
1 TraesCS1A01G306500 chr1A 83.120 468 58 16 2289 2755 498540063 498539616 1.500000e-109 407.0
2 TraesCS1A01G306500 chr1D 92.595 1553 76 24 1070 2605 403331890 403333420 0.000000e+00 2194.0
3 TraesCS1A01G306500 chr1D 92.150 1465 89 12 2642 4085 403333420 403334879 0.000000e+00 2045.0
4 TraesCS1A01G306500 chr1D 86.777 363 41 5 2387 2748 403282457 403282101 9.020000e-107 398.0
5 TraesCS1A01G306500 chr1D 82.353 357 36 12 3126 3478 403281827 403281494 7.330000e-73 285.0
6 TraesCS1A01G306500 chr1B 91.320 1394 64 19 3027 4386 542429649 542431019 0.000000e+00 1851.0
7 TraesCS1A01G306500 chr1B 93.601 1047 49 12 2062 3105 542428617 542429648 0.000000e+00 1546.0
8 TraesCS1A01G306500 chr1B 90.331 755 44 12 1291 2035 542427567 542428302 0.000000e+00 963.0
9 TraesCS1A01G306500 chr1B 80.386 673 85 29 2157 2809 542576590 542577235 6.780000e-128 468.0
10 TraesCS1A01G306500 chr1B 83.547 468 56 15 2289 2755 542140637 542140190 6.920000e-113 418.0
11 TraesCS1A01G306500 chr1B 78.596 285 21 20 1287 1567 542575795 542576043 7.750000e-33 152.0
12 TraesCS1A01G306500 chr1B 88.189 127 2 2 1110 1236 542427431 542427544 6.040000e-29 139.0
13 TraesCS1A01G306500 chr1B 100.000 33 0 0 2041 2073 542428585 542428617 1.340000e-05 62.1
14 TraesCS1A01G306500 chr3D 96.042 1036 41 0 1 1036 323092849 323093884 0.000000e+00 1687.0


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 TraesCS1A01G306500 chr1A 498591650 498596124 4474 False 8264.00 8264 100.0000 1 4475 1 chr1A.!!$F1 4474
1 TraesCS1A01G306500 chr1D 403331890 403334879 2989 False 2119.50 2194 92.3725 1070 4085 2 chr1D.!!$F1 3015
2 TraesCS1A01G306500 chr1D 403281494 403282457 963 True 341.50 398 84.5650 2387 3478 2 chr1D.!!$R1 1091
3 TraesCS1A01G306500 chr1B 542427431 542431019 3588 False 912.22 1851 92.6882 1110 4386 5 chr1B.!!$F1 3276
4 TraesCS1A01G306500 chr1B 542575795 542577235 1440 False 310.00 468 79.4910 1287 2809 2 chr1B.!!$F2 1522
5 TraesCS1A01G306500 chr3D 323092849 323093884 1035 False 1687.00 1687 96.0420 1 1036 1 chr3D.!!$F1 1035

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
763 764 0.543410 TAGCCGTCTTTGACCTCCCA 60.543 55.000 0.00 0.0 0.00 4.37 F
1063 1064 0.032267 GCCCGGTCTGCTACTATGAC 59.968 60.000 0.00 0.0 0.00 3.06 F
1706 1727 0.811915 AGGAGATCACCGACGACTTG 59.188 55.000 3.31 0.0 34.73 3.16 F
1719 1740 1.585006 GACTTGACGAAGGGCGAGA 59.415 57.895 0.00 0.0 44.57 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1757 1781 0.323629 TTGACCATTGACCGACCTCC 59.676 55.000 0.00 0.00 0.00 4.30 R
2277 2669 1.687123 AGAGGCGACTTGTGTTAGTGT 59.313 47.619 0.00 0.00 44.43 3.55 R
3216 3761 0.963962 ATGTCCTTTTGCACTGCAGG 59.036 50.000 19.93 8.27 40.61 4.85 R
3664 4211 1.065418 GGTAGTGATGACTGTTGGGGG 60.065 57.143 0.00 0.00 33.21 5.40 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
37 38 1.699634 CAGAAGTGGGGGACTTTCTCA 59.300 52.381 0.00 0.00 45.48 3.27
115 116 1.679680 CCTCGGACTAGCGGTTCATAA 59.320 52.381 0.00 0.00 0.00 1.90
274 275 2.545113 CGTCACCCTAACCCACATATCG 60.545 54.545 0.00 0.00 0.00 2.92
280 281 3.005897 CCCTAACCCACATATCGACTCTG 59.994 52.174 0.00 0.00 0.00 3.35
299 300 1.967779 TGTCAAACACCATCTCCGAGA 59.032 47.619 0.00 0.00 0.00 4.04
302 303 2.231478 TCAAACACCATCTCCGAGAGTC 59.769 50.000 4.07 0.00 0.00 3.36
323 324 5.581085 AGTCTCGTTTTTCCTTCATATTCCG 59.419 40.000 0.00 0.00 0.00 4.30
333 334 5.787380 TCCTTCATATTCCGTCATGATCAG 58.213 41.667 0.00 0.00 31.50 2.90
334 335 5.539955 TCCTTCATATTCCGTCATGATCAGA 59.460 40.000 0.00 0.00 31.50 3.27
340 341 5.598416 ATTCCGTCATGATCAGAACACTA 57.402 39.130 0.00 0.00 0.00 2.74
349 350 9.334693 GTCATGATCAGAACACTAAAATCAAAC 57.665 33.333 0.00 0.00 0.00 2.93
386 387 8.598924 CATTGTTCATAACATGTCTGTAGTCTC 58.401 37.037 0.00 0.00 41.79 3.36
486 487 4.268884 CCGAGTCATAGCTTTTTCTAGTGC 59.731 45.833 0.00 0.00 0.00 4.40
526 527 1.001269 GGTACAAGCCTTCCCCACC 60.001 63.158 0.00 0.00 0.00 4.61
621 622 1.302907 AGAACCATGCCTCCCAATCT 58.697 50.000 0.00 0.00 0.00 2.40
648 649 4.609247 GCTCGACGTCGGATCCGG 62.609 72.222 35.05 20.49 40.29 5.14
665 666 1.966451 GGGGTCTTGCACTCCAACG 60.966 63.158 0.00 0.00 46.74 4.10
701 702 4.706842 TCTCTGTTATTTAGGCCATCCC 57.293 45.455 5.01 0.00 0.00 3.85
702 703 3.394606 TCTCTGTTATTTAGGCCATCCCC 59.605 47.826 5.01 0.00 0.00 4.81
707 708 1.318934 ATTTAGGCCATCCCCCTTGT 58.681 50.000 5.01 0.00 33.88 3.16
754 755 2.851263 TCATTGGTGTAGCCGTCTTT 57.149 45.000 0.00 0.00 41.21 2.52
755 756 2.422597 TCATTGGTGTAGCCGTCTTTG 58.577 47.619 0.00 0.00 41.21 2.77
757 758 1.873698 TTGGTGTAGCCGTCTTTGAC 58.126 50.000 0.00 0.00 41.21 3.18
763 764 0.543410 TAGCCGTCTTTGACCTCCCA 60.543 55.000 0.00 0.00 0.00 4.37
797 798 1.004918 GCCGCCGCCTTAGATGTAT 60.005 57.895 0.00 0.00 0.00 2.29
801 802 1.335597 CGCCGCCTTAGATGTATTCGA 60.336 52.381 0.00 0.00 0.00 3.71
817 818 6.579865 TGTATTCGAGTTATTCTTCTTCCCC 58.420 40.000 0.00 0.00 0.00 4.81
818 819 3.795623 TCGAGTTATTCTTCTTCCCCG 57.204 47.619 0.00 0.00 0.00 5.73
868 869 1.974875 CATGAGCAGCAGCCCACAA 60.975 57.895 0.00 0.00 43.56 3.33
1036 1037 1.149627 CCTTTTCGTGGTGGACCCA 59.850 57.895 0.00 0.00 42.51 4.51
1043 1044 2.618139 TGGTGGACCCACTCTCCA 59.382 61.111 17.67 5.67 45.52 3.86
1044 1045 1.536418 TGGTGGACCCACTCTCCAG 60.536 63.158 17.67 0.00 45.52 3.86
1045 1046 2.665603 GTGGACCCACTCTCCAGC 59.334 66.667 11.73 0.00 43.12 4.85
1046 1047 2.607750 TGGACCCACTCTCCAGCC 60.608 66.667 0.00 0.00 32.52 4.85
1047 1048 3.403558 GGACCCACTCTCCAGCCC 61.404 72.222 0.00 0.00 0.00 5.19
1048 1049 3.775654 GACCCACTCTCCAGCCCG 61.776 72.222 0.00 0.00 0.00 6.13
1051 1052 3.775654 CCACTCTCCAGCCCGGTC 61.776 72.222 0.00 0.00 35.57 4.79
1052 1053 2.681778 CACTCTCCAGCCCGGTCT 60.682 66.667 0.00 0.00 35.57 3.85
1053 1054 2.681778 ACTCTCCAGCCCGGTCTG 60.682 66.667 5.25 5.25 35.57 3.51
1054 1055 4.154347 CTCTCCAGCCCGGTCTGC 62.154 72.222 7.07 0.00 35.57 4.26
1055 1056 4.704103 TCTCCAGCCCGGTCTGCT 62.704 66.667 7.07 1.69 40.41 4.24
1056 1057 2.759973 CTCCAGCCCGGTCTGCTA 60.760 66.667 7.07 0.00 36.81 3.49
1057 1058 3.075005 TCCAGCCCGGTCTGCTAC 61.075 66.667 7.07 0.00 36.81 3.58
1058 1059 3.077556 CCAGCCCGGTCTGCTACT 61.078 66.667 7.07 0.00 36.81 2.57
1059 1060 1.756950 CCAGCCCGGTCTGCTACTA 60.757 63.158 7.07 0.00 36.81 1.82
1060 1061 1.115930 CCAGCCCGGTCTGCTACTAT 61.116 60.000 7.07 0.00 36.81 2.12
1061 1062 0.032678 CAGCCCGGTCTGCTACTATG 59.967 60.000 0.00 0.00 36.81 2.23
1062 1063 0.106167 AGCCCGGTCTGCTACTATGA 60.106 55.000 0.00 0.00 37.28 2.15
1063 1064 0.032267 GCCCGGTCTGCTACTATGAC 59.968 60.000 0.00 0.00 0.00 3.06
1064 1065 1.693627 CCCGGTCTGCTACTATGACT 58.306 55.000 0.00 0.00 0.00 3.41
1065 1066 2.860009 CCCGGTCTGCTACTATGACTA 58.140 52.381 0.00 0.00 0.00 2.59
1066 1067 2.814919 CCCGGTCTGCTACTATGACTAG 59.185 54.545 0.00 0.00 0.00 2.57
1067 1068 2.226912 CCGGTCTGCTACTATGACTAGC 59.773 54.545 0.00 0.00 37.68 3.42
1068 1069 2.226912 CGGTCTGCTACTATGACTAGCC 59.773 54.545 0.00 0.00 36.54 3.93
1069 1070 3.492337 GGTCTGCTACTATGACTAGCCT 58.508 50.000 0.00 0.00 36.54 4.58
1070 1071 3.892588 GGTCTGCTACTATGACTAGCCTT 59.107 47.826 0.00 0.00 36.54 4.35
1071 1072 5.071370 GGTCTGCTACTATGACTAGCCTTA 58.929 45.833 0.00 0.00 36.54 2.69
1072 1073 5.712917 GGTCTGCTACTATGACTAGCCTTAT 59.287 44.000 0.00 0.00 36.54 1.73
1073 1074 6.349777 GGTCTGCTACTATGACTAGCCTTATG 60.350 46.154 0.00 0.00 36.54 1.90
1074 1075 5.184096 TCTGCTACTATGACTAGCCTTATGC 59.816 44.000 0.00 0.00 36.54 3.14
1075 1076 4.220821 TGCTACTATGACTAGCCTTATGCC 59.779 45.833 0.00 0.00 42.71 4.40
1076 1077 4.220821 GCTACTATGACTAGCCTTATGCCA 59.779 45.833 0.00 0.00 42.71 4.92
1077 1078 5.105146 GCTACTATGACTAGCCTTATGCCAT 60.105 44.000 0.00 0.00 42.71 4.40
1078 1079 6.096987 GCTACTATGACTAGCCTTATGCCATA 59.903 42.308 0.00 0.00 42.71 2.74
1079 1080 6.287589 ACTATGACTAGCCTTATGCCATAC 57.712 41.667 0.00 0.00 42.71 2.39
1108 1109 3.270877 CACATTTTCCCCCTCTAGAACG 58.729 50.000 0.00 0.00 0.00 3.95
1114 1115 1.569548 TCCCCCTCTAGAACGACTCAT 59.430 52.381 0.00 0.00 0.00 2.90
1167 1169 4.475135 GCGAGTCCCCTTGGCCTC 62.475 72.222 3.32 0.00 0.00 4.70
1190 1192 1.726853 CCAGTTCAGTTTCCTAGGCG 58.273 55.000 2.96 0.00 0.00 5.52
1561 1575 2.515901 GCCTGGTGAGTGTGGGTT 59.484 61.111 0.00 0.00 0.00 4.11
1613 1627 0.819582 TCCCGTCCTCCGATTTGTAC 59.180 55.000 0.00 0.00 39.56 2.90
1615 1629 0.822164 CCGTCCTCCGATTTGTACCT 59.178 55.000 0.00 0.00 39.56 3.08
1629 1643 3.703286 TGTACCTGTATCACCGATTCG 57.297 47.619 0.00 0.00 0.00 3.34
1634 1648 3.637229 ACCTGTATCACCGATTCGAGATT 59.363 43.478 7.83 0.00 0.00 2.40
1636 1650 4.261614 CCTGTATCACCGATTCGAGATTCA 60.262 45.833 7.83 12.47 0.00 2.57
1638 1652 4.338400 TGTATCACCGATTCGAGATTCAGT 59.662 41.667 7.83 0.00 0.00 3.41
1639 1653 5.529800 TGTATCACCGATTCGAGATTCAGTA 59.470 40.000 7.83 0.00 0.00 2.74
1640 1654 5.713792 ATCACCGATTCGAGATTCAGTAT 57.286 39.130 7.83 0.00 0.00 2.12
1641 1655 4.860072 TCACCGATTCGAGATTCAGTATG 58.140 43.478 7.83 0.00 37.54 2.39
1642 1656 3.426859 CACCGATTCGAGATTCAGTATGC 59.573 47.826 7.83 0.00 34.76 3.14
1644 1658 2.658802 CGATTCGAGATTCAGTATGCGG 59.341 50.000 0.00 0.00 34.76 5.69
1645 1659 3.609409 CGATTCGAGATTCAGTATGCGGA 60.609 47.826 0.00 0.00 34.76 5.54
1646 1660 3.355626 TTCGAGATTCAGTATGCGGAG 57.644 47.619 0.00 0.00 34.76 4.63
1647 1661 2.572290 TCGAGATTCAGTATGCGGAGA 58.428 47.619 0.00 0.00 34.76 3.71
1648 1662 2.290916 TCGAGATTCAGTATGCGGAGAC 59.709 50.000 0.00 0.00 34.76 3.36
1649 1663 2.033424 CGAGATTCAGTATGCGGAGACA 59.967 50.000 4.07 0.00 34.76 3.41
1650 1664 3.637432 GAGATTCAGTATGCGGAGACAG 58.363 50.000 4.07 0.00 34.76 3.51
1651 1665 2.363680 AGATTCAGTATGCGGAGACAGG 59.636 50.000 4.07 0.00 34.76 4.00
1660 1681 2.574399 GGAGACAGGTGCTCGTCC 59.426 66.667 0.00 0.00 33.19 4.79
1671 1692 1.812922 GCTCGTCCTGTGCTGATGG 60.813 63.158 0.00 0.00 34.28 3.51
1698 1719 1.207089 TGCAGGTTAAGGAGATCACCG 59.793 52.381 3.31 0.00 34.19 4.94
1704 1725 2.414994 TAAGGAGATCACCGACGACT 57.585 50.000 3.31 0.00 34.73 4.18
1706 1727 0.811915 AGGAGATCACCGACGACTTG 59.188 55.000 3.31 0.00 34.73 3.16
1719 1740 1.585006 GACTTGACGAAGGGCGAGA 59.415 57.895 0.00 0.00 44.57 4.04
1757 1781 2.734673 GGCGCTCTTCTCGTTGCAG 61.735 63.158 7.64 0.00 0.00 4.41
1803 1827 3.814005 AACCTGCCGTGTACTATTAGG 57.186 47.619 0.00 0.00 0.00 2.69
1861 1885 6.593382 GCAATAGTTCTGAGAATTGTGAGACT 59.407 38.462 0.00 0.00 32.99 3.24
1911 1935 1.938577 CTGAATCTGAATGCTCCGGTG 59.061 52.381 0.00 0.00 0.00 4.94
1914 1938 2.029838 ATCTGAATGCTCCGGTGTTC 57.970 50.000 0.00 0.27 0.00 3.18
1940 1964 5.122239 TGCAGTTGATACATCTGTTTAGCAC 59.878 40.000 10.22 0.00 34.69 4.40
1951 1975 5.627499 TCTGTTTAGCACCATGATTGTTC 57.373 39.130 0.00 0.00 0.00 3.18
2035 2066 8.058667 TCTCGTTGTTTGGTCTAAGATATACA 57.941 34.615 0.00 0.00 0.00 2.29
2038 2069 7.758076 TCGTTGTTTGGTCTAAGATATACACTG 59.242 37.037 0.00 0.00 0.00 3.66
2147 2518 4.430441 AGTGAGGAAGAGGTAGTCCAAAT 58.570 43.478 0.00 0.00 36.28 2.32
2148 2519 4.846940 AGTGAGGAAGAGGTAGTCCAAATT 59.153 41.667 0.00 0.00 36.28 1.82
2149 2520 5.310857 AGTGAGGAAGAGGTAGTCCAAATTT 59.689 40.000 0.00 0.00 36.28 1.82
2150 2521 6.004574 GTGAGGAAGAGGTAGTCCAAATTTT 58.995 40.000 0.00 0.00 36.28 1.82
2151 2522 6.490381 GTGAGGAAGAGGTAGTCCAAATTTTT 59.510 38.462 0.00 0.00 36.28 1.94
2193 2565 3.188159 TGGTTATGTATCTGAACGCCC 57.812 47.619 0.00 0.00 0.00 6.13
2242 2632 4.871557 AGTACAACGACACAAGTGCTTTTA 59.128 37.500 0.00 0.00 0.00 1.52
2571 2965 4.821805 TCACTGAATGAACACTTCCTTTCC 59.178 41.667 0.00 0.00 33.02 3.13
2604 2998 1.761784 TGCAAAAGGAAACATGGCAGT 59.238 42.857 0.00 0.00 0.00 4.40
2605 2999 2.224018 TGCAAAAGGAAACATGGCAGTC 60.224 45.455 0.00 0.00 0.00 3.51
2606 3000 2.224018 GCAAAAGGAAACATGGCAGTCA 60.224 45.455 0.00 0.00 0.00 3.41
2607 3001 3.555586 GCAAAAGGAAACATGGCAGTCAT 60.556 43.478 0.00 0.00 36.31 3.06
2608 3002 4.321899 GCAAAAGGAAACATGGCAGTCATA 60.322 41.667 0.00 0.00 34.12 2.15
2609 3003 5.782047 CAAAAGGAAACATGGCAGTCATAA 58.218 37.500 0.00 0.00 34.12 1.90
2610 3004 6.222389 CAAAAGGAAACATGGCAGTCATAAA 58.778 36.000 0.00 0.00 34.12 1.40
2611 3005 6.418057 AAAGGAAACATGGCAGTCATAAAA 57.582 33.333 0.00 0.00 34.12 1.52
2612 3006 5.649782 AGGAAACATGGCAGTCATAAAAG 57.350 39.130 0.00 0.00 34.12 2.27
2613 3007 4.082026 AGGAAACATGGCAGTCATAAAAGC 60.082 41.667 0.00 0.00 34.12 3.51
2614 3008 4.321899 GGAAACATGGCAGTCATAAAAGCA 60.322 41.667 0.00 0.00 34.12 3.91
2615 3009 5.410355 AAACATGGCAGTCATAAAAGCAT 57.590 34.783 0.00 0.00 34.12 3.79
2616 3010 5.410355 AACATGGCAGTCATAAAAGCATT 57.590 34.783 0.00 0.00 34.12 3.56
2617 3011 5.410355 ACATGGCAGTCATAAAAGCATTT 57.590 34.783 0.00 0.00 34.67 2.32
2618 3012 5.413499 ACATGGCAGTCATAAAAGCATTTC 58.587 37.500 0.00 0.00 32.67 2.17
2619 3013 5.047164 ACATGGCAGTCATAAAAGCATTTCA 60.047 36.000 0.00 0.00 32.67 2.69
2620 3014 5.465532 TGGCAGTCATAAAAGCATTTCAA 57.534 34.783 0.00 0.00 37.28 2.69
2621 3015 6.040209 TGGCAGTCATAAAAGCATTTCAAT 57.960 33.333 0.00 0.00 37.28 2.57
2622 3016 6.465948 TGGCAGTCATAAAAGCATTTCAATT 58.534 32.000 0.00 0.00 37.28 2.32
2623 3017 6.935771 TGGCAGTCATAAAAGCATTTCAATTT 59.064 30.769 0.00 0.00 37.28 1.82
2624 3018 7.118101 TGGCAGTCATAAAAGCATTTCAATTTC 59.882 33.333 0.00 0.00 37.28 2.17
2625 3019 7.118101 GGCAGTCATAAAAGCATTTCAATTTCA 59.882 33.333 0.00 0.00 37.28 2.69
2626 3020 8.166706 GCAGTCATAAAAGCATTTCAATTTCAG 58.833 33.333 0.00 0.00 37.28 3.02
2627 3021 8.653338 CAGTCATAAAAGCATTTCAATTTCAGG 58.347 33.333 0.00 0.00 37.28 3.86
2628 3022 8.587608 AGTCATAAAAGCATTTCAATTTCAGGA 58.412 29.630 0.00 0.00 37.28 3.86
2629 3023 9.374838 GTCATAAAAGCATTTCAATTTCAGGAT 57.625 29.630 0.00 0.00 37.28 3.24
2630 3024 9.590451 TCATAAAAGCATTTCAATTTCAGGATC 57.410 29.630 0.00 0.00 37.28 3.36
2631 3025 9.373603 CATAAAAGCATTTCAATTTCAGGATCA 57.626 29.630 0.00 0.00 37.28 2.92
2633 3027 8.488651 AAAAGCATTTCAATTTCAGGATCATC 57.511 30.769 0.00 0.00 37.28 2.92
2634 3028 7.419711 AAGCATTTCAATTTCAGGATCATCT 57.580 32.000 0.00 0.00 0.00 2.90
2635 3029 7.419711 AGCATTTCAATTTCAGGATCATCTT 57.580 32.000 0.00 0.00 0.00 2.40
2636 3030 7.848128 AGCATTTCAATTTCAGGATCATCTTT 58.152 30.769 0.00 0.00 0.00 2.52
2637 3031 7.764443 AGCATTTCAATTTCAGGATCATCTTTG 59.236 33.333 0.00 0.00 0.00 2.77
2638 3032 7.465513 GCATTTCAATTTCAGGATCATCTTTGC 60.466 37.037 0.00 0.00 0.00 3.68
2639 3033 6.845758 TTCAATTTCAGGATCATCTTTGCT 57.154 33.333 0.00 0.00 0.00 3.91
2640 3034 6.845758 TCAATTTCAGGATCATCTTTGCTT 57.154 33.333 0.00 0.00 0.00 3.91
2685 3116 3.114809 CGATGTTGTTTCAAGCTGCAAA 58.885 40.909 1.02 0.00 0.00 3.68
2957 3420 7.828712 ACTTACCTCGAGGATATAAACATAGC 58.171 38.462 37.69 0.00 38.94 2.97
2960 3423 6.634805 ACCTCGAGGATATAAACATAGCATG 58.365 40.000 37.69 4.77 38.94 4.06
3025 3490 2.369532 AGCTTGGGTACTGTTTTACCGA 59.630 45.455 0.00 0.00 42.39 4.69
3030 3495 3.006110 TGGGTACTGTTTTACCGAGACAG 59.994 47.826 1.51 1.51 42.39 3.51
3034 3499 6.350445 GGGTACTGTTTTACCGAGACAGATAA 60.350 42.308 9.45 0.00 42.39 1.75
3502 4049 1.141858 GGTTGGGATCATCTGACCTCC 59.858 57.143 0.00 0.00 0.00 4.30
3557 4104 1.225745 GCGTTTCTGCGAACATCCG 60.226 57.895 0.00 0.00 0.00 4.18
3600 4147 5.245751 TGGCATGAAACTGTTGTGGATTTAT 59.754 36.000 0.00 0.00 0.00 1.40
3602 4149 6.158598 GCATGAAACTGTTGTGGATTTATGT 58.841 36.000 0.00 0.00 0.00 2.29
3608 4155 9.691362 GAAACTGTTGTGGATTTATGTACAAAT 57.309 29.630 0.00 0.00 35.12 2.32
3612 4159 9.474920 CTGTTGTGGATTTATGTACAAATGTTT 57.525 29.630 0.00 0.00 35.12 2.83
3638 4185 7.230510 TGAAACTGTTTGCTGTAACCTAATCAT 59.769 33.333 11.03 0.00 0.00 2.45
3645 4192 4.635765 TGCTGTAACCTAATCATTGCACTC 59.364 41.667 0.00 0.00 0.00 3.51
3664 4211 5.631096 GCACTCTAAAAACTGCCTTCAATTC 59.369 40.000 0.00 0.00 0.00 2.17
3687 4234 2.038426 CCCAACAGTCATCACTACCACA 59.962 50.000 0.00 0.00 0.00 4.17
3741 4292 0.180642 ACTGCCTGAGATCAGCATGG 59.819 55.000 4.23 0.00 42.47 3.66
3775 4326 1.677217 GGAAGTTCAGGCTGGTGCTAG 60.677 57.143 15.73 0.00 39.59 3.42
3778 4329 1.912043 AGTTCAGGCTGGTGCTAGAAT 59.088 47.619 15.73 0.00 39.59 2.40
3799 4350 1.830477 ACAGCCTCCAAGATCACTCTC 59.170 52.381 0.00 0.00 0.00 3.20
3815 4366 8.200792 AGATCACTCTCCAGATATTGTAAACAC 58.799 37.037 0.00 0.00 0.00 3.32
3816 4367 7.239763 TCACTCTCCAGATATTGTAAACACA 57.760 36.000 0.00 0.00 0.00 3.72
3874 4425 5.045578 GGGTATGCCTATGGTATCACAGAAT 60.046 44.000 0.00 0.00 34.45 2.40
3891 4448 8.347004 TCACAGAATGCTTTTGAATTATGGTA 57.653 30.769 0.00 0.00 40.17 3.25
3925 4490 1.072965 AGACAGGGCTTCACAGGAAAG 59.927 52.381 0.00 0.00 31.35 2.62
3989 4554 6.115446 TCACTACTCATGAAAAATAGGCAGG 58.885 40.000 0.00 0.00 0.00 4.85
4067 4633 9.862371 TTATCAAAACAATTATTGTAACGGCAT 57.138 25.926 11.23 2.56 44.59 4.40
4108 4674 4.299586 TGAGACTAATGAAATGGTGGCA 57.700 40.909 0.00 0.00 0.00 4.92
4109 4675 4.858850 TGAGACTAATGAAATGGTGGCAT 58.141 39.130 0.00 0.00 0.00 4.40
4162 4729 6.304356 TCTGCATTGACTTTGAAACTAGTG 57.696 37.500 0.00 0.00 0.00 2.74
4171 4738 0.679505 TGAAACTAGTGGCTGTCGCT 59.320 50.000 0.00 0.00 39.84 4.93
4184 4751 4.083324 TGGCTGTCGCTTAAATTTTCTGAG 60.083 41.667 0.00 0.00 36.09 3.35
4185 4752 4.154195 GGCTGTCGCTTAAATTTTCTGAGA 59.846 41.667 0.00 0.00 36.09 3.27
4235 4802 3.305131 GGAACCAAAAAGAAACGCCTAGG 60.305 47.826 3.67 3.67 0.00 3.02
4239 4806 0.872388 AAAAGAAACGCCTAGGCACG 59.128 50.000 32.47 19.84 42.06 5.34
4270 4837 3.878778 ACAATGTCTGAATAGCAGGGAC 58.121 45.455 0.00 0.00 44.98 4.46
4271 4838 3.264193 ACAATGTCTGAATAGCAGGGACA 59.736 43.478 0.00 0.00 44.98 4.02
4298 4884 7.374975 AGAAATTATTCCAGATAGAACGGGA 57.625 36.000 0.00 0.00 36.12 5.14
4314 4900 1.757118 CGGGAGGAAGAACATGCTAGA 59.243 52.381 0.00 0.00 0.00 2.43
4339 4935 2.273619 AGGAAGGAGAAGCACCTTGAT 58.726 47.619 0.00 0.00 46.14 2.57
4352 4949 7.651027 AAGCACCTTGATAGCTTGATTTATT 57.349 32.000 0.00 0.00 45.99 1.40
4353 4950 7.651027 AGCACCTTGATAGCTTGATTTATTT 57.349 32.000 0.00 0.00 34.37 1.40
4398 4995 5.725325 TTTTGAGGACATGATGCAATTGA 57.275 34.783 10.34 0.00 0.00 2.57
4399 4996 4.976224 TTGAGGACATGATGCAATTGAG 57.024 40.909 10.34 0.00 0.00 3.02
4400 4997 2.686405 TGAGGACATGATGCAATTGAGC 59.314 45.455 10.34 0.00 0.00 4.26
4413 5010 6.864360 TGCAATTGAGCAAAGCTTTTTATT 57.136 29.167 9.53 2.51 42.46 1.40
4414 5011 6.660722 TGCAATTGAGCAAAGCTTTTTATTG 58.339 32.000 9.53 14.28 42.46 1.90
4415 5012 6.260493 TGCAATTGAGCAAAGCTTTTTATTGT 59.740 30.769 9.53 0.00 42.46 2.71
4416 5013 7.134163 GCAATTGAGCAAAGCTTTTTATTGTT 58.866 30.769 9.53 0.00 39.88 2.83
4417 5014 7.321984 GCAATTGAGCAAAGCTTTTTATTGTTC 59.678 33.333 9.53 6.96 39.88 3.18
4418 5015 8.553696 CAATTGAGCAAAGCTTTTTATTGTTCT 58.446 29.630 9.53 0.00 39.88 3.01
4419 5016 7.698836 TTGAGCAAAGCTTTTTATTGTTCTC 57.301 32.000 9.53 2.79 39.88 2.87
4420 5017 6.804677 TGAGCAAAGCTTTTTATTGTTCTCA 58.195 32.000 9.53 5.30 39.88 3.27
4421 5018 6.919662 TGAGCAAAGCTTTTTATTGTTCTCAG 59.080 34.615 9.53 0.00 39.88 3.35
4422 5019 6.809869 AGCAAAGCTTTTTATTGTTCTCAGT 58.190 32.000 9.53 0.00 33.89 3.41
4423 5020 7.940850 AGCAAAGCTTTTTATTGTTCTCAGTA 58.059 30.769 9.53 0.00 33.89 2.74
4424 5021 7.862873 AGCAAAGCTTTTTATTGTTCTCAGTAC 59.137 33.333 9.53 0.00 33.89 2.73
4425 5022 7.862873 GCAAAGCTTTTTATTGTTCTCAGTACT 59.137 33.333 9.53 0.00 0.00 2.73
4426 5023 9.736023 CAAAGCTTTTTATTGTTCTCAGTACTT 57.264 29.630 9.53 0.00 0.00 2.24
4427 5024 9.952188 AAAGCTTTTTATTGTTCTCAGTACTTC 57.048 29.630 5.69 0.00 0.00 3.01
4428 5025 8.100508 AGCTTTTTATTGTTCTCAGTACTTCC 57.899 34.615 0.00 0.00 0.00 3.46
4429 5026 7.015877 GCTTTTTATTGTTCTCAGTACTTCCG 58.984 38.462 0.00 0.00 0.00 4.30
4430 5027 7.307811 GCTTTTTATTGTTCTCAGTACTTCCGT 60.308 37.037 0.00 0.00 0.00 4.69
4431 5028 7.647907 TTTTATTGTTCTCAGTACTTCCGTC 57.352 36.000 0.00 0.00 0.00 4.79
4432 5029 4.866508 ATTGTTCTCAGTACTTCCGTCA 57.133 40.909 0.00 0.00 0.00 4.35
4433 5030 3.917329 TGTTCTCAGTACTTCCGTCAG 57.083 47.619 0.00 0.00 0.00 3.51
4434 5031 3.483421 TGTTCTCAGTACTTCCGTCAGA 58.517 45.455 0.00 0.00 0.00 3.27
4435 5032 4.079970 TGTTCTCAGTACTTCCGTCAGAT 58.920 43.478 0.00 0.00 0.00 2.90
4436 5033 4.082733 TGTTCTCAGTACTTCCGTCAGATG 60.083 45.833 0.00 0.00 0.00 2.90
4437 5034 3.951663 TCTCAGTACTTCCGTCAGATGA 58.048 45.455 0.00 0.00 0.00 2.92
4438 5035 4.332828 TCTCAGTACTTCCGTCAGATGAA 58.667 43.478 0.00 0.00 0.00 2.57
4439 5036 4.396478 TCTCAGTACTTCCGTCAGATGAAG 59.604 45.833 9.89 9.89 42.86 3.02
4443 5040 3.753294 ACTTCCGTCAGATGAAGTGTT 57.247 42.857 14.41 0.00 46.97 3.32
4444 5041 4.073293 ACTTCCGTCAGATGAAGTGTTT 57.927 40.909 14.41 0.00 46.97 2.83
4445 5042 3.809832 ACTTCCGTCAGATGAAGTGTTTG 59.190 43.478 14.41 0.00 46.97 2.93
4446 5043 3.469008 TCCGTCAGATGAAGTGTTTGT 57.531 42.857 0.00 0.00 0.00 2.83
4447 5044 3.130633 TCCGTCAGATGAAGTGTTTGTG 58.869 45.455 0.00 0.00 0.00 3.33
4448 5045 2.349817 CCGTCAGATGAAGTGTTTGTGC 60.350 50.000 0.00 0.00 0.00 4.57
4449 5046 2.287644 CGTCAGATGAAGTGTTTGTGCA 59.712 45.455 0.00 0.00 0.00 4.57
4450 5047 3.605461 CGTCAGATGAAGTGTTTGTGCAG 60.605 47.826 0.00 0.00 0.00 4.41
4451 5048 2.880268 TCAGATGAAGTGTTTGTGCAGG 59.120 45.455 0.00 0.00 0.00 4.85
4452 5049 2.620115 CAGATGAAGTGTTTGTGCAGGT 59.380 45.455 0.00 0.00 0.00 4.00
4453 5050 2.880890 AGATGAAGTGTTTGTGCAGGTC 59.119 45.455 0.00 0.00 0.00 3.85
4454 5051 2.121291 TGAAGTGTTTGTGCAGGTCA 57.879 45.000 0.00 0.00 0.00 4.02
4455 5052 2.653726 TGAAGTGTTTGTGCAGGTCAT 58.346 42.857 0.00 0.00 0.00 3.06
4456 5053 3.023119 TGAAGTGTTTGTGCAGGTCATT 58.977 40.909 0.00 0.00 0.00 2.57
4457 5054 3.181488 TGAAGTGTTTGTGCAGGTCATTG 60.181 43.478 0.00 0.00 0.00 2.82
4458 5055 2.378038 AGTGTTTGTGCAGGTCATTGT 58.622 42.857 0.00 0.00 0.00 2.71
4459 5056 3.550820 AGTGTTTGTGCAGGTCATTGTA 58.449 40.909 0.00 0.00 0.00 2.41
4460 5057 4.144297 AGTGTTTGTGCAGGTCATTGTAT 58.856 39.130 0.00 0.00 0.00 2.29
4461 5058 4.584325 AGTGTTTGTGCAGGTCATTGTATT 59.416 37.500 0.00 0.00 0.00 1.89
4462 5059 5.068987 AGTGTTTGTGCAGGTCATTGTATTT 59.931 36.000 0.00 0.00 0.00 1.40
4463 5060 5.402270 GTGTTTGTGCAGGTCATTGTATTTC 59.598 40.000 0.00 0.00 0.00 2.17
4464 5061 5.068329 TGTTTGTGCAGGTCATTGTATTTCA 59.932 36.000 0.00 0.00 0.00 2.69
4465 5062 5.781210 TTGTGCAGGTCATTGTATTTCAA 57.219 34.783 0.00 0.00 40.53 2.69
4466 5063 5.781210 TGTGCAGGTCATTGTATTTCAAA 57.219 34.783 0.00 0.00 39.62 2.69
4467 5064 6.154203 TGTGCAGGTCATTGTATTTCAAAA 57.846 33.333 0.00 0.00 39.62 2.44
4468 5065 6.215121 TGTGCAGGTCATTGTATTTCAAAAG 58.785 36.000 0.00 0.00 39.62 2.27
4469 5066 6.183360 TGTGCAGGTCATTGTATTTCAAAAGT 60.183 34.615 0.00 0.00 39.62 2.66
4470 5067 7.013750 TGTGCAGGTCATTGTATTTCAAAAGTA 59.986 33.333 0.00 0.00 39.62 2.24
4471 5068 8.028938 GTGCAGGTCATTGTATTTCAAAAGTAT 58.971 33.333 0.00 0.00 39.62 2.12
4472 5069 8.584157 TGCAGGTCATTGTATTTCAAAAGTATT 58.416 29.630 0.00 0.00 39.62 1.89
4473 5070 8.863049 GCAGGTCATTGTATTTCAAAAGTATTG 58.137 33.333 0.00 0.00 39.62 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.909610 TCCCCCACTTCTGCTTCGAT 60.910 55.000 0.00 0.00 0.00 3.59
37 38 5.186198 GGCACATGGTTTGACTTCTACTAT 58.814 41.667 0.00 0.00 0.00 2.12
94 95 2.017559 ATGAACCGCTAGTCCGAGGC 62.018 60.000 0.00 0.00 0.00 4.70
128 129 3.304928 GGAAACCAGTTACGAGTTCGAGA 60.305 47.826 8.72 0.00 43.02 4.04
274 275 3.330267 GGAGATGGTGTTTGACAGAGTC 58.670 50.000 0.00 0.00 0.00 3.36
280 281 2.028930 ACTCTCGGAGATGGTGTTTGAC 60.029 50.000 8.39 0.00 33.89 3.18
299 300 5.581085 CGGAATATGAAGGAAAAACGAGACT 59.419 40.000 0.00 0.00 0.00 3.24
302 303 5.350365 TGACGGAATATGAAGGAAAAACGAG 59.650 40.000 0.00 0.00 0.00 4.18
323 324 9.334693 GTTTGATTTTAGTGTTCTGATCATGAC 57.665 33.333 0.00 0.00 0.00 3.06
333 334 5.691754 CCTTGGCAGTTTGATTTTAGTGTTC 59.308 40.000 0.00 0.00 0.00 3.18
334 335 5.600696 CCTTGGCAGTTTGATTTTAGTGTT 58.399 37.500 0.00 0.00 0.00 3.32
340 341 1.072173 GGGCCTTGGCAGTTTGATTTT 59.928 47.619 14.04 0.00 0.00 1.82
349 350 1.186917 TGAACAATGGGCCTTGGCAG 61.187 55.000 14.04 0.54 0.00 4.85
410 411 3.012844 AGGGACAGGGGCTCAAATATTTT 59.987 43.478 0.00 0.00 0.00 1.82
425 426 1.622811 AGAAGCTCAGTTCAGGGACAG 59.377 52.381 0.00 0.00 0.00 3.51
486 487 2.254459 CTCGTCCGATGAACAAGACAG 58.746 52.381 0.00 0.00 0.00 3.51
526 527 0.453793 AGAGTTCGAGATGGTCTGCG 59.546 55.000 0.00 0.00 0.00 5.18
621 622 0.939577 GACGTCGAGCTTGTCTGCAA 60.940 55.000 0.00 0.00 34.99 4.08
648 649 1.966451 CCGTTGGAGTGCAAGACCC 60.966 63.158 0.00 0.00 0.00 4.46
665 666 7.888250 ATAACAGAGAAGAATCAAAATCCCC 57.112 36.000 0.00 0.00 0.00 4.81
763 764 4.385405 GCAGCCACTCCAGCGACT 62.385 66.667 0.00 0.00 34.64 4.18
778 779 1.754380 ATACATCTAAGGCGGCGGCA 61.754 55.000 34.87 15.33 42.47 5.69
797 798 3.677976 GCGGGGAAGAAGAATAACTCGAA 60.678 47.826 0.00 0.00 0.00 3.71
801 802 1.134491 CGGCGGGGAAGAAGAATAACT 60.134 52.381 0.00 0.00 0.00 2.24
824 825 0.249489 ACTGCGGATGATAAGGCGAC 60.249 55.000 0.00 0.00 0.00 5.19
857 858 3.177884 TCCCTGTTGTGGGCTGCT 61.178 61.111 0.00 0.00 46.67 4.24
858 859 2.674380 CTCCCTGTTGTGGGCTGC 60.674 66.667 0.00 0.00 46.67 5.25
868 869 1.279271 CCAAGAACGGATTCTCCCTGT 59.721 52.381 0.00 0.00 44.82 4.00
1036 1037 2.681778 CAGACCGGGCTGGAGAGT 60.682 66.667 31.05 0.00 42.00 3.24
1037 1038 4.154347 GCAGACCGGGCTGGAGAG 62.154 72.222 37.82 13.88 42.00 3.20
1038 1039 3.296842 TAGCAGACCGGGCTGGAGA 62.297 63.158 37.82 8.05 42.62 3.71
1039 1040 2.759973 TAGCAGACCGGGCTGGAG 60.760 66.667 37.82 14.74 42.62 3.86
1040 1041 2.219449 TAGTAGCAGACCGGGCTGGA 62.219 60.000 37.82 4.41 42.62 3.86
1041 1042 1.115930 ATAGTAGCAGACCGGGCTGG 61.116 60.000 37.82 20.12 42.62 4.85
1042 1043 0.032678 CATAGTAGCAGACCGGGCTG 59.967 60.000 34.13 34.13 42.62 4.85
1043 1044 0.106167 TCATAGTAGCAGACCGGGCT 60.106 55.000 2.12 2.12 45.18 5.19
1044 1045 0.032267 GTCATAGTAGCAGACCGGGC 59.968 60.000 6.32 0.52 0.00 6.13
1045 1046 1.693627 AGTCATAGTAGCAGACCGGG 58.306 55.000 6.32 0.00 32.82 5.73
1046 1047 2.226912 GCTAGTCATAGTAGCAGACCGG 59.773 54.545 0.00 0.00 44.49 5.28
1047 1048 2.226912 GGCTAGTCATAGTAGCAGACCG 59.773 54.545 14.05 0.00 46.36 4.79
1048 1049 3.492337 AGGCTAGTCATAGTAGCAGACC 58.508 50.000 14.05 0.00 46.36 3.85
1049 1050 6.616947 CATAAGGCTAGTCATAGTAGCAGAC 58.383 44.000 14.05 0.00 46.36 3.51
1050 1051 5.184096 GCATAAGGCTAGTCATAGTAGCAGA 59.816 44.000 14.05 1.48 46.36 4.26
1051 1052 5.406649 GCATAAGGCTAGTCATAGTAGCAG 58.593 45.833 14.05 2.24 46.36 4.24
1052 1053 4.220821 GGCATAAGGCTAGTCATAGTAGCA 59.779 45.833 14.05 0.00 46.36 3.49
1053 1054 4.220821 TGGCATAAGGCTAGTCATAGTAGC 59.779 45.833 0.00 5.38 44.40 3.58
1054 1055 5.984695 TGGCATAAGGCTAGTCATAGTAG 57.015 43.478 0.00 0.00 44.01 2.57
1055 1056 7.182760 AGTATGGCATAAGGCTAGTCATAGTA 58.817 38.462 9.14 0.00 44.01 1.82
1056 1057 6.019748 AGTATGGCATAAGGCTAGTCATAGT 58.980 40.000 9.14 8.97 44.01 2.12
1057 1058 6.537453 AGTATGGCATAAGGCTAGTCATAG 57.463 41.667 9.14 0.00 44.01 2.23
1058 1059 6.380274 GGTAGTATGGCATAAGGCTAGTCATA 59.620 42.308 9.14 5.15 44.01 2.15
1059 1060 5.187967 GGTAGTATGGCATAAGGCTAGTCAT 59.812 44.000 9.14 6.80 44.01 3.06
1060 1061 4.527038 GGTAGTATGGCATAAGGCTAGTCA 59.473 45.833 9.14 0.00 44.01 3.41
1061 1062 4.527038 TGGTAGTATGGCATAAGGCTAGTC 59.473 45.833 9.14 3.62 44.01 2.59
1062 1063 4.489737 TGGTAGTATGGCATAAGGCTAGT 58.510 43.478 9.14 0.00 44.01 2.57
1063 1064 5.423015 CATGGTAGTATGGCATAAGGCTAG 58.577 45.833 9.14 0.00 44.01 3.42
1064 1065 4.323485 GCATGGTAGTATGGCATAAGGCTA 60.323 45.833 9.14 4.10 44.01 3.93
1065 1066 3.560025 GCATGGTAGTATGGCATAAGGCT 60.560 47.826 9.14 5.10 44.01 4.58
1066 1067 2.749621 GCATGGTAGTATGGCATAAGGC 59.250 50.000 9.14 2.84 43.74 4.35
1067 1068 3.753272 GTGCATGGTAGTATGGCATAAGG 59.247 47.826 9.14 0.00 0.00 2.69
1068 1069 4.388485 TGTGCATGGTAGTATGGCATAAG 58.612 43.478 9.14 0.00 0.00 1.73
1069 1070 4.429854 TGTGCATGGTAGTATGGCATAA 57.570 40.909 9.14 0.00 0.00 1.90
1070 1071 4.639078 ATGTGCATGGTAGTATGGCATA 57.361 40.909 2.32 2.32 0.00 3.14
1071 1072 3.513909 ATGTGCATGGTAGTATGGCAT 57.486 42.857 4.88 4.88 0.00 4.40
1072 1073 3.295585 AATGTGCATGGTAGTATGGCA 57.704 42.857 0.00 0.00 0.00 4.92
1073 1074 4.499696 GGAAAATGTGCATGGTAGTATGGC 60.500 45.833 0.00 0.00 0.00 4.40
1074 1075 4.037923 GGGAAAATGTGCATGGTAGTATGG 59.962 45.833 0.00 0.00 0.00 2.74
1075 1076 4.037923 GGGGAAAATGTGCATGGTAGTATG 59.962 45.833 0.00 0.00 0.00 2.39
1076 1077 4.215109 GGGGAAAATGTGCATGGTAGTAT 58.785 43.478 0.00 0.00 0.00 2.12
1077 1078 3.626222 GGGGGAAAATGTGCATGGTAGTA 60.626 47.826 0.00 0.00 0.00 1.82
1078 1079 2.456577 GGGGAAAATGTGCATGGTAGT 58.543 47.619 0.00 0.00 0.00 2.73
1079 1080 1.756538 GGGGGAAAATGTGCATGGTAG 59.243 52.381 0.00 0.00 0.00 3.18
1108 1109 5.455525 GCGTGGCATAAATGTAAAATGAGTC 59.544 40.000 0.00 0.00 0.00 3.36
1167 1169 2.611518 CTAGGAAACTGAACTGGCTCG 58.388 52.381 0.00 0.00 43.88 5.03
1613 1627 3.924918 ATCTCGAATCGGTGATACAGG 57.075 47.619 1.76 0.00 0.00 4.00
1615 1629 4.338400 ACTGAATCTCGAATCGGTGATACA 59.662 41.667 1.76 0.00 33.97 2.29
1629 1643 3.551863 CCTGTCTCCGCATACTGAATCTC 60.552 52.174 0.00 0.00 0.00 2.75
1634 1648 0.817654 CACCTGTCTCCGCATACTGA 59.182 55.000 0.00 0.00 0.00 3.41
1636 1650 0.972983 AGCACCTGTCTCCGCATACT 60.973 55.000 0.00 0.00 0.00 2.12
1638 1652 1.816537 GAGCACCTGTCTCCGCATA 59.183 57.895 0.00 0.00 0.00 3.14
1639 1653 2.581354 GAGCACCTGTCTCCGCAT 59.419 61.111 0.00 0.00 0.00 4.73
1640 1654 4.056125 CGAGCACCTGTCTCCGCA 62.056 66.667 0.00 0.00 0.00 5.69
1641 1655 3.973267 GACGAGCACCTGTCTCCGC 62.973 68.421 0.00 0.00 32.37 5.54
1642 1656 2.179517 GACGAGCACCTGTCTCCG 59.820 66.667 0.00 0.00 32.37 4.63
1644 1658 1.214062 CAGGACGAGCACCTGTCTC 59.786 63.158 0.00 0.00 46.71 3.36
1645 1659 3.371021 CAGGACGAGCACCTGTCT 58.629 61.111 0.00 0.00 46.71 3.41
1649 1663 2.919856 AGCACAGGACGAGCACCT 60.920 61.111 0.00 0.00 38.40 4.00
1650 1664 2.513026 ATCAGCACAGGACGAGCACC 62.513 60.000 0.00 0.00 32.95 5.01
1651 1665 1.079543 ATCAGCACAGGACGAGCAC 60.080 57.895 0.00 0.00 32.95 4.40
1660 1681 4.171005 CTGCAAATTTACCATCAGCACAG 58.829 43.478 0.00 0.00 0.00 3.66
1671 1692 7.251281 GTGATCTCCTTAACCTGCAAATTTAC 58.749 38.462 0.00 0.00 0.00 2.01
1698 1719 2.087009 CGCCCTTCGTCAAGTCGTC 61.087 63.158 0.00 0.00 0.00 4.20
1704 1725 0.606096 TTCATCTCGCCCTTCGTCAA 59.394 50.000 0.00 0.00 39.67 3.18
1706 1727 0.806492 GGTTCATCTCGCCCTTCGTC 60.806 60.000 0.00 0.00 39.67 4.20
1719 1740 1.905215 CTGAGGAGTCCAGTGGTTCAT 59.095 52.381 12.86 6.19 0.00 2.57
1757 1781 0.323629 TTGACCATTGACCGACCTCC 59.676 55.000 0.00 0.00 0.00 4.30
1882 1906 4.820716 AGCATTCAGATTCAGGAACTATGC 59.179 41.667 0.00 0.00 36.02 3.14
1911 1935 5.808042 ACAGATGTATCAACTGCATGAAC 57.192 39.130 0.00 0.00 37.71 3.18
1914 1938 6.183360 TGCTAAACAGATGTATCAACTGCATG 60.183 38.462 6.87 0.00 37.71 4.06
1940 1964 2.564062 AGCCACCAAAGAACAATCATGG 59.436 45.455 0.00 0.00 39.46 3.66
1951 1975 2.270352 TGAGTTACCAGCCACCAAAG 57.730 50.000 0.00 0.00 0.00 2.77
2035 2066 2.009774 GTTGCAAGACACAGTGACAGT 58.990 47.619 7.81 0.00 0.00 3.55
2038 2069 4.811555 TTATGTTGCAAGACACAGTGAC 57.188 40.909 7.81 0.10 31.30 3.67
2182 2553 2.514458 AAATCCTTGGGCGTTCAGAT 57.486 45.000 0.00 0.00 0.00 2.90
2185 2556 3.278574 CAGATAAATCCTTGGGCGTTCA 58.721 45.455 0.00 0.00 0.00 3.18
2276 2668 2.889045 AGAGGCGACTTGTGTTAGTGTA 59.111 45.455 0.00 0.00 44.43 2.90
2277 2669 1.687123 AGAGGCGACTTGTGTTAGTGT 59.313 47.619 0.00 0.00 44.43 3.55
2278 2670 2.440539 AGAGGCGACTTGTGTTAGTG 57.559 50.000 0.00 0.00 44.43 2.74
2604 2998 9.590451 GATCCTGAAATTGAAATGCTTTTATGA 57.410 29.630 0.00 0.00 0.00 2.15
2605 2999 9.373603 TGATCCTGAAATTGAAATGCTTTTATG 57.626 29.630 0.00 0.00 0.00 1.90
2607 3001 9.590451 GATGATCCTGAAATTGAAATGCTTTTA 57.410 29.630 0.00 0.00 0.00 1.52
2608 3002 8.319146 AGATGATCCTGAAATTGAAATGCTTTT 58.681 29.630 0.00 0.00 0.00 2.27
2609 3003 7.848128 AGATGATCCTGAAATTGAAATGCTTT 58.152 30.769 0.00 0.00 0.00 3.51
2610 3004 7.419711 AGATGATCCTGAAATTGAAATGCTT 57.580 32.000 0.00 0.00 0.00 3.91
2611 3005 7.419711 AAGATGATCCTGAAATTGAAATGCT 57.580 32.000 0.00 0.00 0.00 3.79
2612 3006 7.465513 GCAAAGATGATCCTGAAATTGAAATGC 60.466 37.037 0.00 0.00 0.00 3.56
2613 3007 7.764443 AGCAAAGATGATCCTGAAATTGAAATG 59.236 33.333 0.00 0.00 0.00 2.32
2614 3008 7.848128 AGCAAAGATGATCCTGAAATTGAAAT 58.152 30.769 0.00 0.00 0.00 2.17
2615 3009 7.235935 AGCAAAGATGATCCTGAAATTGAAA 57.764 32.000 0.00 0.00 0.00 2.69
2616 3010 6.845758 AGCAAAGATGATCCTGAAATTGAA 57.154 33.333 0.00 0.00 0.00 2.69
2617 3011 6.845758 AAGCAAAGATGATCCTGAAATTGA 57.154 33.333 0.00 0.00 0.00 2.57
2618 3012 7.900782 AAAAGCAAAGATGATCCTGAAATTG 57.099 32.000 0.00 0.00 0.00 2.32
2621 3015 9.426837 CAAATAAAAGCAAAGATGATCCTGAAA 57.573 29.630 0.00 0.00 0.00 2.69
2622 3016 8.805175 TCAAATAAAAGCAAAGATGATCCTGAA 58.195 29.630 0.00 0.00 0.00 3.02
2623 3017 8.352137 TCAAATAAAAGCAAAGATGATCCTGA 57.648 30.769 0.00 0.00 0.00 3.86
2624 3018 9.031360 CATCAAATAAAAGCAAAGATGATCCTG 57.969 33.333 0.00 0.00 34.79 3.86
2625 3019 8.755977 ACATCAAATAAAAGCAAAGATGATCCT 58.244 29.630 0.00 0.00 36.26 3.24
2626 3020 8.814235 CACATCAAATAAAAGCAAAGATGATCC 58.186 33.333 0.00 0.00 36.26 3.36
2627 3021 9.362539 ACACATCAAATAAAAGCAAAGATGATC 57.637 29.630 0.00 0.00 36.26 2.92
2628 3022 9.715121 AACACATCAAATAAAAGCAAAGATGAT 57.285 25.926 0.00 0.00 36.26 2.45
2813 3268 4.676723 GCAAGCTATAATTGTTTTCCCGCA 60.677 41.667 0.00 0.00 0.00 5.69
3216 3761 0.963962 ATGTCCTTTTGCACTGCAGG 59.036 50.000 19.93 8.27 40.61 4.85
3219 3764 2.669391 GCTGTATGTCCTTTTGCACTGC 60.669 50.000 0.00 0.00 0.00 4.40
3268 3813 8.511604 AAACATCTTCCATTAGTATCACCAAG 57.488 34.615 0.00 0.00 0.00 3.61
3502 4049 3.604875 ATTCAAATGGAGCAAAGCAGG 57.395 42.857 0.00 0.00 0.00 4.85
3557 4104 3.319122 GCCATTTGACAACCCATATCCTC 59.681 47.826 0.00 0.00 0.00 3.71
3600 4147 6.870965 AGCAAACAGTTTCAAACATTTGTACA 59.129 30.769 21.81 0.00 39.73 2.90
3602 4149 6.870965 ACAGCAAACAGTTTCAAACATTTGTA 59.129 30.769 21.81 0.00 39.73 2.41
3608 4155 5.047660 AGGTTACAGCAAACAGTTTCAAACA 60.048 36.000 2.41 0.00 0.00 2.83
3612 4159 6.544197 TGATTAGGTTACAGCAAACAGTTTCA 59.456 34.615 0.00 0.00 0.00 2.69
3638 4185 3.951037 TGAAGGCAGTTTTTAGAGTGCAA 59.049 39.130 6.97 0.00 45.62 4.08
3645 4192 4.322725 GGGGGAATTGAAGGCAGTTTTTAG 60.323 45.833 0.00 0.00 0.00 1.85
3664 4211 1.065418 GGTAGTGATGACTGTTGGGGG 60.065 57.143 0.00 0.00 33.21 5.40
3741 4292 2.191128 ACTTCCTGATGACACAAGCC 57.809 50.000 0.00 0.00 0.00 4.35
3775 4326 4.100808 AGAGTGATCTTGGAGGCTGTATTC 59.899 45.833 0.00 0.00 0.00 1.75
3778 4329 3.027412 GAGAGTGATCTTGGAGGCTGTA 58.973 50.000 0.00 0.00 0.00 2.74
3874 4425 7.978975 GGCAATTACTACCATAATTCAAAAGCA 59.021 33.333 0.00 0.00 33.40 3.91
3912 4477 6.072112 TCAATTGTTACTTTCCTGTGAAGC 57.928 37.500 5.13 0.00 0.00 3.86
3917 4482 7.939039 TCATCTCTTCAATTGTTACTTTCCTGT 59.061 33.333 5.13 0.00 0.00 4.00
3980 4545 1.215423 GGGAATGTGGACCTGCCTATT 59.785 52.381 0.00 0.00 37.63 1.73
3989 4554 4.216257 GCATGTACATATGGGAATGTGGAC 59.784 45.833 8.32 0.00 40.29 4.02
4046 4612 5.872070 CCCATGCCGTTACAATAATTGTTTT 59.128 36.000 0.00 0.00 42.22 2.43
4052 4618 3.826157 CCATCCCATGCCGTTACAATAAT 59.174 43.478 0.00 0.00 0.00 1.28
4063 4629 0.179067 CACATTTGCCATCCCATGCC 60.179 55.000 0.00 0.00 0.00 4.40
4067 4633 4.092279 TCATTTACACATTTGCCATCCCA 58.908 39.130 0.00 0.00 0.00 4.37
4103 4669 5.503662 TTCATTGATCACACATATGCCAC 57.496 39.130 1.58 0.00 0.00 5.01
4108 4674 6.548622 CCCTCCTTTTCATTGATCACACATAT 59.451 38.462 0.00 0.00 0.00 1.78
4109 4675 5.887598 CCCTCCTTTTCATTGATCACACATA 59.112 40.000 0.00 0.00 0.00 2.29
4162 4729 4.154195 TCTCAGAAAATTTAAGCGACAGCC 59.846 41.667 0.00 0.00 46.67 4.85
4202 4769 9.817809 GTTTCTTTTTGGTTCCTTCTTCTTATT 57.182 29.630 0.00 0.00 0.00 1.40
4203 4770 8.135529 CGTTTCTTTTTGGTTCCTTCTTCTTAT 58.864 33.333 0.00 0.00 0.00 1.73
4204 4771 7.477494 CGTTTCTTTTTGGTTCCTTCTTCTTA 58.523 34.615 0.00 0.00 0.00 2.10
4205 4772 6.330278 CGTTTCTTTTTGGTTCCTTCTTCTT 58.670 36.000 0.00 0.00 0.00 2.52
4206 4773 5.678871 GCGTTTCTTTTTGGTTCCTTCTTCT 60.679 40.000 0.00 0.00 0.00 2.85
4207 4774 4.503007 GCGTTTCTTTTTGGTTCCTTCTTC 59.497 41.667 0.00 0.00 0.00 2.87
4222 4789 2.033194 GCGTGCCTAGGCGTTTCTT 61.033 57.895 28.28 0.00 45.51 2.52
4235 4802 1.468520 ACATTGTATCACTTGGCGTGC 59.531 47.619 0.00 0.00 43.46 5.34
4239 4806 5.824904 ATTCAGACATTGTATCACTTGGC 57.175 39.130 0.00 0.00 0.00 4.52
4270 4837 9.197694 CCGTTCTATCTGGAATAATTTCTACTG 57.802 37.037 0.00 0.00 32.16 2.74
4271 4838 8.368668 CCCGTTCTATCTGGAATAATTTCTACT 58.631 37.037 0.00 0.00 32.16 2.57
4314 4900 1.615384 GGTGCTTCTCCTTCCTTGCAT 60.615 52.381 0.00 0.00 32.98 3.96
4375 4972 6.099159 TCAATTGCATCATGTCCTCAAAAA 57.901 33.333 0.00 0.00 0.00 1.94
4386 4983 3.887621 AGCTTTGCTCAATTGCATCAT 57.112 38.095 0.00 0.00 42.96 2.45
4387 4984 3.671008 AAGCTTTGCTCAATTGCATCA 57.329 38.095 0.00 0.00 42.96 3.07
4388 4985 5.352643 AAAAAGCTTTGCTCAATTGCATC 57.647 34.783 13.54 0.00 42.96 3.91
4389 4986 7.040961 ACAATAAAAAGCTTTGCTCAATTGCAT 60.041 29.630 13.54 2.11 42.96 3.96
4390 4987 6.260493 ACAATAAAAAGCTTTGCTCAATTGCA 59.740 30.769 13.54 0.00 38.25 4.08
4391 4988 6.661669 ACAATAAAAAGCTTTGCTCAATTGC 58.338 32.000 13.54 0.00 38.25 3.56
4392 4989 8.553696 AGAACAATAAAAAGCTTTGCTCAATTG 58.446 29.630 13.54 17.80 38.25 2.32
4393 4990 8.667076 AGAACAATAAAAAGCTTTGCTCAATT 57.333 26.923 13.54 4.61 38.25 2.32
4394 4991 7.927629 TGAGAACAATAAAAAGCTTTGCTCAAT 59.072 29.630 13.54 0.00 38.25 2.57
4395 4992 7.264221 TGAGAACAATAAAAAGCTTTGCTCAA 58.736 30.769 13.54 0.00 38.25 3.02
4396 4993 6.804677 TGAGAACAATAAAAAGCTTTGCTCA 58.195 32.000 13.54 5.53 38.25 4.26
4397 4994 6.920210 ACTGAGAACAATAAAAAGCTTTGCTC 59.080 34.615 13.54 2.67 38.25 4.26
4398 4995 6.809869 ACTGAGAACAATAAAAAGCTTTGCT 58.190 32.000 13.54 5.87 42.56 3.91
4399 4996 7.862873 AGTACTGAGAACAATAAAAAGCTTTGC 59.137 33.333 13.54 0.00 0.00 3.68
4400 4997 9.736023 AAGTACTGAGAACAATAAAAAGCTTTG 57.264 29.630 13.54 2.66 0.00 2.77
4401 4998 9.952188 GAAGTACTGAGAACAATAAAAAGCTTT 57.048 29.630 5.69 5.69 0.00 3.51
4402 4999 8.568794 GGAAGTACTGAGAACAATAAAAAGCTT 58.431 33.333 0.00 0.00 0.00 3.74
4403 5000 7.095187 CGGAAGTACTGAGAACAATAAAAAGCT 60.095 37.037 0.00 0.00 0.00 3.74
4404 5001 7.015877 CGGAAGTACTGAGAACAATAAAAAGC 58.984 38.462 0.00 0.00 0.00 3.51
4405 5002 8.084590 ACGGAAGTACTGAGAACAATAAAAAG 57.915 34.615 0.00 0.00 46.88 2.27
4424 5021 3.809832 ACAAACACTTCATCTGACGGAAG 59.190 43.478 15.48 15.48 44.68 3.46
4425 5022 3.559655 CACAAACACTTCATCTGACGGAA 59.440 43.478 0.00 0.00 0.00 4.30
4426 5023 3.130633 CACAAACACTTCATCTGACGGA 58.869 45.455 0.00 0.00 0.00 4.69
4427 5024 2.349817 GCACAAACACTTCATCTGACGG 60.350 50.000 0.00 0.00 0.00 4.79
4428 5025 2.287644 TGCACAAACACTTCATCTGACG 59.712 45.455 0.00 0.00 0.00 4.35
4429 5026 3.304257 CCTGCACAAACACTTCATCTGAC 60.304 47.826 0.00 0.00 0.00 3.51
4430 5027 2.880268 CCTGCACAAACACTTCATCTGA 59.120 45.455 0.00 0.00 0.00 3.27
4431 5028 2.620115 ACCTGCACAAACACTTCATCTG 59.380 45.455 0.00 0.00 0.00 2.90
4432 5029 2.880890 GACCTGCACAAACACTTCATCT 59.119 45.455 0.00 0.00 0.00 2.90
4433 5030 2.618241 TGACCTGCACAAACACTTCATC 59.382 45.455 0.00 0.00 0.00 2.92
4434 5031 2.653726 TGACCTGCACAAACACTTCAT 58.346 42.857 0.00 0.00 0.00 2.57
4435 5032 2.121291 TGACCTGCACAAACACTTCA 57.879 45.000 0.00 0.00 0.00 3.02
4436 5033 3.181487 ACAATGACCTGCACAAACACTTC 60.181 43.478 0.00 0.00 0.00 3.01
4437 5034 2.760092 ACAATGACCTGCACAAACACTT 59.240 40.909 0.00 0.00 0.00 3.16
4438 5035 2.378038 ACAATGACCTGCACAAACACT 58.622 42.857 0.00 0.00 0.00 3.55
4439 5036 2.869233 ACAATGACCTGCACAAACAC 57.131 45.000 0.00 0.00 0.00 3.32
4440 5037 5.068329 TGAAATACAATGACCTGCACAAACA 59.932 36.000 0.00 0.00 0.00 2.83
4441 5038 5.527951 TGAAATACAATGACCTGCACAAAC 58.472 37.500 0.00 0.00 0.00 2.93
4442 5039 5.781210 TGAAATACAATGACCTGCACAAA 57.219 34.783 0.00 0.00 0.00 2.83
4443 5040 5.781210 TTGAAATACAATGACCTGCACAA 57.219 34.783 0.00 0.00 33.18 3.33
4444 5041 5.781210 TTTGAAATACAATGACCTGCACA 57.219 34.783 0.00 0.00 38.36 4.57
4445 5042 6.215845 ACTTTTGAAATACAATGACCTGCAC 58.784 36.000 0.00 0.00 38.36 4.57
4446 5043 6.403866 ACTTTTGAAATACAATGACCTGCA 57.596 33.333 0.00 0.00 38.36 4.41
4447 5044 8.863049 CAATACTTTTGAAATACAATGACCTGC 58.137 33.333 0.00 0.00 38.36 4.85


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

AutoCloner maintained by Alex Coulton.