Multiple sequence alignment - TraesCS5A01G075600

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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 TraesCS5A01G075600 chr5A 100.000 3020 0 0 1 3020 90929757 90926738 0.000000e+00 5578
1 TraesCS5A01G075600 chr5B 93.219 1917 70 28 214 2123 102608072 102606209 0.000000e+00 2765
2 TraesCS5A01G075600 chr5B 91.304 437 19 9 2598 3016 102605782 102605347 2.020000e-161 579
3 TraesCS5A01G075600 chr5B 82.195 483 29 22 2141 2580 102606224 102605756 2.210000e-96 363
4 TraesCS5A01G075600 chr5D 93.131 1849 54 29 310 2123 95882869 95881059 0.000000e+00 2643
5 TraesCS5A01G075600 chr5D 92.723 481 23 8 2541 3018 95880584 95880113 0.000000e+00 684
6 TraesCS5A01G075600 chr5D 84.553 492 29 18 2141 2596 95881074 95880594 7.680000e-121 444
7 TraesCS5A01G075600 chr5D 82.903 310 45 6 2589 2893 554920886 554920580 3.840000e-69 272
8 TraesCS5A01G075600 chr7A 78.744 414 56 14 1196 1608 697984381 697983999 6.470000e-62 248
9 TraesCS5A01G075600 chr1B 85.311 177 24 2 1222 1398 73042670 73042844 6.650000e-42 182


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 TraesCS5A01G075600 chr5A 90926738 90929757 3019 True 5578.000000 5578 100.000000 1 3020 1 chr5A.!!$R1 3019
1 TraesCS5A01G075600 chr5B 102605347 102608072 2725 True 1235.666667 2765 88.906000 214 3016 3 chr5B.!!$R1 2802
2 TraesCS5A01G075600 chr5D 95880113 95882869 2756 True 1257.000000 2643 90.135667 310 3018 3 chr5D.!!$R2 2708

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
871 897 0.041982 ACACTCCTCCTCCTTCCTCC 59.958 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 2074 0.248907 GCTACGCGGCTATTGTCTGA 60.249 55.0 12.47 0.0 0.0 3.27 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
45 46 1.796253 CGGAGCTACGTGCAATTACGA 60.796 52.381 11.15 0.00 46.46 3.43
46 47 2.470821 GGAGCTACGTGCAATTACGAT 58.529 47.619 7.72 0.00 46.46 3.73
47 48 2.864343 GGAGCTACGTGCAATTACGATT 59.136 45.455 7.72 0.00 46.46 3.34
48 49 3.302480 GGAGCTACGTGCAATTACGATTG 60.302 47.826 7.72 0.00 46.46 2.67
49 50 3.517602 AGCTACGTGCAATTACGATTGA 58.482 40.909 7.72 0.00 46.46 2.57
50 51 3.930229 AGCTACGTGCAATTACGATTGAA 59.070 39.130 7.72 0.00 46.46 2.69
51 52 4.032900 AGCTACGTGCAATTACGATTGAAG 59.967 41.667 7.72 0.00 46.46 3.02
52 53 3.740044 ACGTGCAATTACGATTGAAGG 57.260 42.857 7.72 1.46 46.46 3.46
53 54 3.331150 ACGTGCAATTACGATTGAAGGA 58.669 40.909 7.72 0.00 46.46 3.36
54 55 3.370978 ACGTGCAATTACGATTGAAGGAG 59.629 43.478 7.72 0.00 46.46 3.69
55 56 3.242413 CGTGCAATTACGATTGAAGGAGG 60.242 47.826 3.47 0.00 46.46 4.30
56 57 3.065371 GTGCAATTACGATTGAAGGAGGG 59.935 47.826 3.47 0.00 44.37 4.30
57 58 2.618709 GCAATTACGATTGAAGGAGGGG 59.381 50.000 3.47 0.00 44.37 4.79
58 59 3.886123 CAATTACGATTGAAGGAGGGGT 58.114 45.455 0.00 0.00 44.37 4.95
59 60 4.270008 CAATTACGATTGAAGGAGGGGTT 58.730 43.478 0.00 0.00 44.37 4.11
60 61 5.433526 CAATTACGATTGAAGGAGGGGTTA 58.566 41.667 0.00 0.00 44.37 2.85
61 62 4.748277 TTACGATTGAAGGAGGGGTTAG 57.252 45.455 0.00 0.00 0.00 2.34
62 63 2.829023 ACGATTGAAGGAGGGGTTAGA 58.171 47.619 0.00 0.00 0.00 2.10
63 64 3.178865 ACGATTGAAGGAGGGGTTAGAA 58.821 45.455 0.00 0.00 0.00 2.10
64 65 3.055312 ACGATTGAAGGAGGGGTTAGAAC 60.055 47.826 0.00 0.00 0.00 3.01
74 75 3.471399 GTTAGAACCACGCTCCGC 58.529 61.111 0.00 0.00 0.00 5.54
89 90 4.803426 CGCGCGCTCTCCCTTTCT 62.803 66.667 30.48 0.00 0.00 2.52
90 91 2.435059 GCGCGCTCTCCCTTTCTT 60.435 61.111 26.67 0.00 0.00 2.52
91 92 2.744768 GCGCGCTCTCCCTTTCTTG 61.745 63.158 26.67 0.00 0.00 3.02
92 93 2.103042 CGCGCTCTCCCTTTCTTGG 61.103 63.158 5.56 0.00 0.00 3.61
93 94 1.296715 GCGCTCTCCCTTTCTTGGA 59.703 57.895 0.00 0.00 0.00 3.53
94 95 0.321653 GCGCTCTCCCTTTCTTGGAA 60.322 55.000 0.00 0.00 0.00 3.53
95 96 1.731720 CGCTCTCCCTTTCTTGGAAG 58.268 55.000 0.00 0.00 0.00 3.46
96 97 1.677217 CGCTCTCCCTTTCTTGGAAGG 60.677 57.143 0.68 0.68 44.74 3.46
97 98 1.352687 GCTCTCCCTTTCTTGGAAGGT 59.647 52.381 6.92 0.00 43.84 3.50
98 99 2.224892 GCTCTCCCTTTCTTGGAAGGTT 60.225 50.000 6.92 0.00 43.84 3.50
99 100 3.416156 CTCTCCCTTTCTTGGAAGGTTG 58.584 50.000 6.92 0.17 43.84 3.77
100 101 1.889170 CTCCCTTTCTTGGAAGGTTGC 59.111 52.381 6.92 0.00 43.84 4.17
101 102 0.969149 CCCTTTCTTGGAAGGTTGCC 59.031 55.000 6.92 0.00 43.84 4.52
102 103 0.598065 CCTTTCTTGGAAGGTTGCCG 59.402 55.000 0.00 0.00 41.06 5.69
103 104 1.604604 CTTTCTTGGAAGGTTGCCGA 58.395 50.000 0.00 0.00 0.00 5.54
104 105 1.953686 CTTTCTTGGAAGGTTGCCGAA 59.046 47.619 0.00 0.00 0.00 4.30
105 106 1.314730 TTCTTGGAAGGTTGCCGAAC 58.685 50.000 0.00 0.00 0.00 3.95
106 107 0.181587 TCTTGGAAGGTTGCCGAACA 59.818 50.000 0.00 0.00 33.27 3.18
107 108 0.593128 CTTGGAAGGTTGCCGAACAG 59.407 55.000 0.00 0.00 33.27 3.16
108 109 0.821711 TTGGAAGGTTGCCGAACAGG 60.822 55.000 0.00 0.00 44.97 4.00
109 110 1.971695 GGAAGGTTGCCGAACAGGG 60.972 63.158 0.00 0.00 41.48 4.45
122 123 5.441709 CCGAACAGGGCTTTAGTTAAAAA 57.558 39.130 0.00 0.00 35.97 1.94
144 145 2.983791 GCCAGGGCGGTGTTACTA 59.016 61.111 0.00 0.00 36.97 1.82
145 146 1.525442 GCCAGGGCGGTGTTACTAT 59.475 57.895 0.00 0.00 36.97 2.12
146 147 0.814010 GCCAGGGCGGTGTTACTATG 60.814 60.000 0.00 0.00 36.97 2.23
147 148 0.539986 CCAGGGCGGTGTTACTATGT 59.460 55.000 0.00 0.00 0.00 2.29
148 149 1.651987 CAGGGCGGTGTTACTATGTG 58.348 55.000 0.00 0.00 0.00 3.21
149 150 0.107848 AGGGCGGTGTTACTATGTGC 60.108 55.000 0.00 0.00 0.00 4.57
150 151 1.093496 GGGCGGTGTTACTATGTGCC 61.093 60.000 0.00 0.00 40.25 5.01
151 152 0.391927 GGCGGTGTTACTATGTGCCA 60.392 55.000 0.00 0.00 40.66 4.92
152 153 1.663695 GCGGTGTTACTATGTGCCAT 58.336 50.000 0.00 0.00 0.00 4.40
153 154 2.484065 GGCGGTGTTACTATGTGCCATA 60.484 50.000 0.00 0.00 40.66 2.74
154 155 2.542595 GCGGTGTTACTATGTGCCATAC 59.457 50.000 0.00 0.00 0.00 2.39
155 156 3.740141 GCGGTGTTACTATGTGCCATACT 60.740 47.826 0.00 0.00 0.00 2.12
156 157 4.439057 CGGTGTTACTATGTGCCATACTT 58.561 43.478 0.00 0.00 0.00 2.24
157 158 5.593968 CGGTGTTACTATGTGCCATACTTA 58.406 41.667 0.00 0.00 0.00 2.24
158 159 6.220930 CGGTGTTACTATGTGCCATACTTAT 58.779 40.000 0.00 0.00 0.00 1.73
159 160 6.145534 CGGTGTTACTATGTGCCATACTTATG 59.854 42.308 0.00 0.00 0.00 1.90
160 161 7.214381 GGTGTTACTATGTGCCATACTTATGA 58.786 38.462 0.00 0.00 35.75 2.15
161 162 7.170998 GGTGTTACTATGTGCCATACTTATGAC 59.829 40.741 0.00 0.00 35.75 3.06
162 163 7.709182 GTGTTACTATGTGCCATACTTATGACA 59.291 37.037 0.00 0.00 35.75 3.58
163 164 7.709182 TGTTACTATGTGCCATACTTATGACAC 59.291 37.037 8.33 8.33 44.20 3.67
164 165 6.485830 ACTATGTGCCATACTTATGACACT 57.514 37.500 14.42 5.53 44.24 3.55
165 166 6.889198 ACTATGTGCCATACTTATGACACTT 58.111 36.000 14.42 11.34 44.24 3.16
166 167 8.018537 ACTATGTGCCATACTTATGACACTTA 57.981 34.615 14.42 11.75 44.24 2.24
167 168 8.651389 ACTATGTGCCATACTTATGACACTTAT 58.349 33.333 14.42 5.81 44.24 1.73
168 169 7.969536 ATGTGCCATACTTATGACACTTATC 57.030 36.000 14.42 0.00 44.24 1.75
169 170 6.883744 TGTGCCATACTTATGACACTTATCA 58.116 36.000 14.42 0.00 44.24 2.15
170 171 7.508687 TGTGCCATACTTATGACACTTATCAT 58.491 34.615 14.42 0.00 44.24 2.45
171 172 7.992608 TGTGCCATACTTATGACACTTATCATT 59.007 33.333 14.42 0.00 44.24 2.57
172 173 8.840321 GTGCCATACTTATGACACTTATCATTT 58.160 33.333 8.07 0.00 41.80 2.32
202 203 8.848474 ATAAAGTAAACATATGGAATCGAGGG 57.152 34.615 7.80 0.00 0.00 4.30
203 204 5.228945 AGTAAACATATGGAATCGAGGGG 57.771 43.478 7.80 0.00 0.00 4.79
204 205 2.568623 AACATATGGAATCGAGGGGC 57.431 50.000 7.80 0.00 0.00 5.80
205 206 1.734655 ACATATGGAATCGAGGGGCT 58.265 50.000 7.80 0.00 0.00 5.19
206 207 2.902608 ACATATGGAATCGAGGGGCTA 58.097 47.619 7.80 0.00 0.00 3.93
207 208 3.248024 ACATATGGAATCGAGGGGCTAA 58.752 45.455 7.80 0.00 0.00 3.09
208 209 3.650942 ACATATGGAATCGAGGGGCTAAA 59.349 43.478 7.80 0.00 0.00 1.85
209 210 4.104102 ACATATGGAATCGAGGGGCTAAAA 59.896 41.667 7.80 0.00 0.00 1.52
210 211 3.884037 ATGGAATCGAGGGGCTAAAAT 57.116 42.857 0.00 0.00 0.00 1.82
211 212 4.993705 ATGGAATCGAGGGGCTAAAATA 57.006 40.909 0.00 0.00 0.00 1.40
212 213 4.781775 TGGAATCGAGGGGCTAAAATAA 57.218 40.909 0.00 0.00 0.00 1.40
414 415 3.144506 CACATATCCCTCCATTGAGTGC 58.855 50.000 0.00 0.00 36.86 4.40
482 483 2.124236 TGCATGCATCCATCGCCA 60.124 55.556 18.46 0.00 0.00 5.69
561 567 4.584743 GCCCCTCTTCTTTTCTTTTTCTCA 59.415 41.667 0.00 0.00 0.00 3.27
599 605 2.607635 CGCCTCTTTTGTACGCACATAT 59.392 45.455 0.00 0.00 33.76 1.78
600 606 3.799963 CGCCTCTTTTGTACGCACATATA 59.200 43.478 0.00 0.00 33.76 0.86
639 651 2.032924 AGAAAAGGAAAGAAACACGCGG 59.967 45.455 12.47 1.27 0.00 6.46
640 652 1.385528 AAAGGAAAGAAACACGCGGT 58.614 45.000 12.47 2.05 0.00 5.68
641 653 0.661020 AAGGAAAGAAACACGCGGTG 59.339 50.000 12.47 9.20 39.75 4.94
642 654 1.164041 AGGAAAGAAACACGCGGTGG 61.164 55.000 12.47 1.38 37.94 4.61
643 655 1.161563 GGAAAGAAACACGCGGTGGA 61.162 55.000 12.47 0.00 37.94 4.02
644 656 0.872388 GAAAGAAACACGCGGTGGAT 59.128 50.000 12.47 0.00 37.94 3.41
645 657 2.070783 GAAAGAAACACGCGGTGGATA 58.929 47.619 12.47 0.00 37.94 2.59
646 658 2.396590 AAGAAACACGCGGTGGATAT 57.603 45.000 12.47 0.00 37.94 1.63
647 659 3.530265 AAGAAACACGCGGTGGATATA 57.470 42.857 12.47 0.00 37.94 0.86
648 660 2.817901 AGAAACACGCGGTGGATATAC 58.182 47.619 12.47 0.00 37.94 1.47
649 661 2.166870 AGAAACACGCGGTGGATATACA 59.833 45.455 12.47 0.00 37.94 2.29
650 662 2.218953 AACACGCGGTGGATATACAG 57.781 50.000 12.47 0.00 37.94 2.74
651 663 0.249322 ACACGCGGTGGATATACAGC 60.249 55.000 12.47 7.09 37.94 4.40
652 664 0.944311 CACGCGGTGGATATACAGCC 60.944 60.000 12.47 4.26 38.32 4.85
653 665 1.365999 CGCGGTGGATATACAGCCA 59.634 57.895 11.53 0.00 38.09 4.75
654 666 0.667487 CGCGGTGGATATACAGCCAG 60.667 60.000 11.53 2.10 42.06 4.85
658 670 2.464157 GTGGATATACAGCCAGCCTC 57.536 55.000 0.00 0.00 42.06 4.70
659 671 1.694150 GTGGATATACAGCCAGCCTCA 59.306 52.381 0.00 0.00 42.06 3.86
676 688 5.295292 CAGCCTCATCGTCTGATAAAAATGT 59.705 40.000 0.00 0.00 32.18 2.71
871 897 0.041982 ACACTCCTCCTCCTTCCTCC 59.958 60.000 0.00 0.00 0.00 4.30
872 898 0.338120 CACTCCTCCTCCTTCCTCCT 59.662 60.000 0.00 0.00 0.00 3.69
902 936 3.361158 CGCCAACCATCGCAACCA 61.361 61.111 0.00 0.00 0.00 3.67
949 986 0.590682 CACAACACAGCACCGCATTA 59.409 50.000 0.00 0.00 0.00 1.90
957 994 0.734889 AGCACCGCATTACTCATTGC 59.265 50.000 0.00 0.00 35.50 3.56
958 995 0.734889 GCACCGCATTACTCATTGCT 59.265 50.000 0.00 0.00 36.71 3.91
959 996 1.532505 GCACCGCATTACTCATTGCTG 60.533 52.381 0.00 0.00 36.71 4.41
960 997 0.734889 ACCGCATTACTCATTGCTGC 59.265 50.000 0.00 0.00 36.71 5.25
988 1036 1.517210 GACCTCTCTATCGCCCCGTC 61.517 65.000 0.00 0.00 0.00 4.79
1011 1062 1.139734 CGTCGTCATGGTGAGGAGG 59.860 63.158 2.89 5.51 41.27 4.30
1059 1113 4.719369 GCGTCGTCGTGGAAGGCT 62.719 66.667 3.66 0.00 39.49 4.58
1317 1371 2.028484 TCGCAGACCGTGTTCACC 59.972 61.111 0.00 0.00 38.35 4.02
1668 1722 3.470567 GTCGTCTGCAACCTCGCG 61.471 66.667 0.00 0.00 33.35 5.87
1927 1981 0.873312 CGTGGTGCTGGAGATCATCG 60.873 60.000 0.00 0.00 0.00 3.84
2020 2074 2.435693 GGCGACCTCCAGGCATAGT 61.436 63.158 0.00 0.00 39.32 2.12
2095 2149 2.029020 TCAGACGGTCCAGAGAAACATG 60.029 50.000 4.14 0.00 0.00 3.21
2097 2151 0.396435 ACGGTCCAGAGAAACATGCA 59.604 50.000 0.00 0.00 0.00 3.96
2098 2152 0.798776 CGGTCCAGAGAAACATGCAC 59.201 55.000 0.00 0.00 0.00 4.57
2099 2153 1.609061 CGGTCCAGAGAAACATGCACT 60.609 52.381 0.00 0.00 0.00 4.40
2101 2155 3.679917 CGGTCCAGAGAAACATGCACTAT 60.680 47.826 0.00 0.00 0.00 2.12
2102 2156 4.441495 CGGTCCAGAGAAACATGCACTATA 60.441 45.833 0.00 0.00 0.00 1.31
2103 2157 4.811557 GGTCCAGAGAAACATGCACTATAC 59.188 45.833 0.00 0.00 0.00 1.47
2104 2158 5.419542 GTCCAGAGAAACATGCACTATACA 58.580 41.667 0.00 0.00 0.00 2.29
2105 2159 5.521735 GTCCAGAGAAACATGCACTATACAG 59.478 44.000 0.00 0.00 0.00 2.74
2106 2160 5.187772 TCCAGAGAAACATGCACTATACAGT 59.812 40.000 0.00 0.00 34.42 3.55
2107 2161 6.379988 TCCAGAGAAACATGCACTATACAGTA 59.620 38.462 0.00 0.00 32.21 2.74
2108 2162 6.699204 CCAGAGAAACATGCACTATACAGTAG 59.301 42.308 0.00 0.00 32.21 2.57
2109 2163 7.261325 CAGAGAAACATGCACTATACAGTAGT 58.739 38.462 0.00 0.00 32.21 2.73
2110 2164 8.406297 CAGAGAAACATGCACTATACAGTAGTA 58.594 37.037 0.00 0.00 32.21 1.82
2111 2165 8.967918 AGAGAAACATGCACTATACAGTAGTAA 58.032 33.333 0.00 0.00 33.13 2.24
2112 2166 9.582431 GAGAAACATGCACTATACAGTAGTAAA 57.418 33.333 0.00 0.00 33.13 2.01
2113 2167 9.367444 AGAAACATGCACTATACAGTAGTAAAC 57.633 33.333 0.00 0.00 33.13 2.01
2114 2168 9.367444 GAAACATGCACTATACAGTAGTAAACT 57.633 33.333 0.00 0.00 39.81 2.66
2351 2408 7.148069 GGAAAGAAACGAAGAATGATATGGGTT 60.148 37.037 0.00 0.00 0.00 4.11
2358 2415 5.356751 CGAAGAATGATATGGGTTGGTTCAA 59.643 40.000 0.00 0.00 0.00 2.69
2413 2494 3.064820 ACATGAACCGTTGTTGAAGACAC 59.935 43.478 0.00 0.00 38.18 3.67
2469 2552 4.285775 TGGTGATCACATCTGTCAGGTTTA 59.714 41.667 26.47 0.00 0.00 2.01
2477 2560 9.739276 ATCACATCTGTCAGGTTTAAATTTCTA 57.261 29.630 0.00 0.00 0.00 2.10
2503 2603 2.938451 TCAGCATACGGAGCATTGAAAG 59.062 45.455 0.00 0.00 0.00 2.62
2505 2605 2.679837 AGCATACGGAGCATTGAAAGTG 59.320 45.455 0.00 0.00 0.00 3.16
2564 2730 3.542712 AGCAATGCTGTAACTTCAACG 57.457 42.857 7.07 0.00 37.57 4.10
2577 2743 5.508200 AACTTCAACGGAAAATGCAGTTA 57.492 34.783 0.00 0.00 32.52 2.24
2580 2746 4.902443 TCAACGGAAAATGCAGTTACAA 57.098 36.364 0.00 0.00 0.00 2.41
2591 2757 3.357203 TGCAGTTACAAGGACCACAAAA 58.643 40.909 0.00 0.00 0.00 2.44
2642 2811 4.525996 TCCATACACCACAGATGAAATGG 58.474 43.478 0.00 0.00 39.57 3.16
2658 2827 2.587060 ATGGGTGATTAGGGGACAGA 57.413 50.000 0.00 0.00 0.00 3.41
2713 2882 5.415701 TGAATTAGCAACAGAGGACCATTTC 59.584 40.000 0.00 0.00 0.00 2.17
2776 2945 5.528690 CACTTCAGTTGATCAGGAGAACAAA 59.471 40.000 0.00 0.00 38.12 2.83
2778 2947 4.389374 TCAGTTGATCAGGAGAACAAACC 58.611 43.478 0.00 0.00 38.12 3.27
2779 2948 3.187227 CAGTTGATCAGGAGAACAAACCG 59.813 47.826 0.00 0.00 38.12 4.44
2785 2960 3.950397 TCAGGAGAACAAACCGCATATT 58.050 40.909 0.00 0.00 0.00 1.28
2874 3055 0.661020 ACTGTGCAAAGCGGTTACAC 59.339 50.000 20.46 20.46 0.00 2.90
2888 3069 6.040878 AGCGGTTACACAAAGATCAGTATAC 58.959 40.000 0.00 0.00 0.00 1.47
2921 3104 3.708451 TCACCTGGTTGAGCTATAGTGA 58.292 45.455 0.00 0.00 0.00 3.41
2935 3118 4.568359 GCTATAGTGATGTGTGTCAACCTG 59.432 45.833 0.84 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.515286 TAGCTCCGCTCCGAACCG 61.515 66.667 0.00 0.00 40.44 4.44
16 17 2.104530 GTAGCTCCGCTCCGAACC 59.895 66.667 0.00 0.00 40.44 3.62
17 18 2.278013 CGTAGCTCCGCTCCGAAC 60.278 66.667 0.00 0.00 40.32 3.95
18 19 2.749044 ACGTAGCTCCGCTCCGAA 60.749 61.111 7.80 0.00 40.32 4.30
19 20 3.506096 CACGTAGCTCCGCTCCGA 61.506 66.667 7.80 0.00 40.32 4.55
21 22 2.907897 ATTGCACGTAGCTCCGCTCC 62.908 60.000 0.00 0.00 45.94 4.70
22 23 1.084370 AATTGCACGTAGCTCCGCTC 61.084 55.000 0.00 0.00 45.94 5.03
23 24 0.174845 TAATTGCACGTAGCTCCGCT 59.825 50.000 0.00 0.00 45.94 5.52
24 25 0.300789 GTAATTGCACGTAGCTCCGC 59.699 55.000 0.00 0.00 45.94 5.54
25 26 0.570734 CGTAATTGCACGTAGCTCCG 59.429 55.000 0.00 0.00 45.94 4.63
26 27 1.917273 TCGTAATTGCACGTAGCTCC 58.083 50.000 10.54 0.00 45.94 4.70
27 28 3.550275 TCAATCGTAATTGCACGTAGCTC 59.450 43.478 10.54 0.00 45.94 4.09
28 29 3.517602 TCAATCGTAATTGCACGTAGCT 58.482 40.909 10.54 0.00 45.94 3.32
29 30 3.918258 TCAATCGTAATTGCACGTAGC 57.082 42.857 1.00 0.00 41.76 3.58
30 31 4.565166 TCCTTCAATCGTAATTGCACGTAG 59.435 41.667 1.00 0.00 41.76 3.51
31 32 4.496360 TCCTTCAATCGTAATTGCACGTA 58.504 39.130 1.00 0.00 41.76 3.57
32 33 3.331150 TCCTTCAATCGTAATTGCACGT 58.669 40.909 1.00 0.00 41.76 4.49
33 34 3.242413 CCTCCTTCAATCGTAATTGCACG 60.242 47.826 0.00 0.00 41.76 5.34
34 35 3.065371 CCCTCCTTCAATCGTAATTGCAC 59.935 47.826 0.00 0.00 41.76 4.57
35 36 3.278574 CCCTCCTTCAATCGTAATTGCA 58.721 45.455 0.00 0.00 41.76 4.08
36 37 2.618709 CCCCTCCTTCAATCGTAATTGC 59.381 50.000 0.00 0.00 41.76 3.56
37 38 3.886123 ACCCCTCCTTCAATCGTAATTG 58.114 45.455 0.00 0.00 43.10 2.32
38 39 4.586306 AACCCCTCCTTCAATCGTAATT 57.414 40.909 0.00 0.00 0.00 1.40
39 40 4.966805 TCTAACCCCTCCTTCAATCGTAAT 59.033 41.667 0.00 0.00 0.00 1.89
40 41 4.355549 TCTAACCCCTCCTTCAATCGTAA 58.644 43.478 0.00 0.00 0.00 3.18
41 42 3.985127 TCTAACCCCTCCTTCAATCGTA 58.015 45.455 0.00 0.00 0.00 3.43
42 43 2.829023 TCTAACCCCTCCTTCAATCGT 58.171 47.619 0.00 0.00 0.00 3.73
43 44 3.532542 GTTCTAACCCCTCCTTCAATCG 58.467 50.000 0.00 0.00 0.00 3.34
44 45 3.887352 GGTTCTAACCCCTCCTTCAATC 58.113 50.000 0.02 0.00 43.43 2.67
72 73 4.803426 AGAAAGGGAGAGCGCGCG 62.803 66.667 28.44 28.44 0.00 6.86
73 74 2.435059 AAGAAAGGGAGAGCGCGC 60.435 61.111 26.66 26.66 0.00 6.86
74 75 2.103042 CCAAGAAAGGGAGAGCGCG 61.103 63.158 0.00 0.00 0.00 6.86
75 76 0.321653 TTCCAAGAAAGGGAGAGCGC 60.322 55.000 0.00 0.00 35.46 5.92
76 77 1.677217 CCTTCCAAGAAAGGGAGAGCG 60.677 57.143 0.00 0.00 41.86 5.03
77 78 2.121291 CCTTCCAAGAAAGGGAGAGC 57.879 55.000 0.00 0.00 41.86 4.09
84 85 1.604604 TCGGCAACCTTCCAAGAAAG 58.395 50.000 0.00 0.00 0.00 2.62
85 86 1.679153 GTTCGGCAACCTTCCAAGAAA 59.321 47.619 0.00 0.00 0.00 2.52
86 87 1.314730 GTTCGGCAACCTTCCAAGAA 58.685 50.000 0.00 0.00 0.00 2.52
87 88 0.181587 TGTTCGGCAACCTTCCAAGA 59.818 50.000 0.00 0.00 0.00 3.02
88 89 0.593128 CTGTTCGGCAACCTTCCAAG 59.407 55.000 0.00 0.00 0.00 3.61
89 90 0.821711 CCTGTTCGGCAACCTTCCAA 60.822 55.000 0.00 0.00 0.00 3.53
90 91 1.228124 CCTGTTCGGCAACCTTCCA 60.228 57.895 0.00 0.00 0.00 3.53
91 92 1.971695 CCCTGTTCGGCAACCTTCC 60.972 63.158 0.00 0.00 0.00 3.46
92 93 3.668386 CCCTGTTCGGCAACCTTC 58.332 61.111 0.00 0.00 0.00 3.46
100 101 5.441709 TTTTTAACTAAAGCCCTGTTCGG 57.558 39.130 0.00 0.00 0.00 4.30
127 128 0.814010 CATAGTAACACCGCCCTGGC 60.814 60.000 0.00 0.00 43.94 4.85
128 129 0.539986 ACATAGTAACACCGCCCTGG 59.460 55.000 0.00 0.00 46.41 4.45
129 130 1.651987 CACATAGTAACACCGCCCTG 58.348 55.000 0.00 0.00 0.00 4.45
130 131 0.107848 GCACATAGTAACACCGCCCT 60.108 55.000 0.00 0.00 0.00 5.19
131 132 1.093496 GGCACATAGTAACACCGCCC 61.093 60.000 0.00 0.00 31.76 6.13
132 133 0.391927 TGGCACATAGTAACACCGCC 60.392 55.000 0.00 0.00 38.56 6.13
133 134 3.146783 TGGCACATAGTAACACCGC 57.853 52.632 0.00 0.00 0.00 5.68
147 148 8.978874 AAATGATAAGTGTCATAAGTATGGCA 57.021 30.769 1.46 1.46 45.17 4.92
176 177 9.938280 CCCTCGATTCCATATGTTTACTTTATA 57.062 33.333 1.24 0.00 0.00 0.98
177 178 7.883311 CCCCTCGATTCCATATGTTTACTTTAT 59.117 37.037 1.24 0.00 0.00 1.40
178 179 7.221450 CCCCTCGATTCCATATGTTTACTTTA 58.779 38.462 1.24 0.00 0.00 1.85
179 180 6.062095 CCCCTCGATTCCATATGTTTACTTT 58.938 40.000 1.24 0.00 0.00 2.66
180 181 5.621193 CCCCTCGATTCCATATGTTTACTT 58.379 41.667 1.24 0.00 0.00 2.24
181 182 4.505039 GCCCCTCGATTCCATATGTTTACT 60.505 45.833 1.24 0.00 0.00 2.24
182 183 3.751698 GCCCCTCGATTCCATATGTTTAC 59.248 47.826 1.24 0.00 0.00 2.01
183 184 3.650942 AGCCCCTCGATTCCATATGTTTA 59.349 43.478 1.24 0.00 0.00 2.01
184 185 2.443255 AGCCCCTCGATTCCATATGTTT 59.557 45.455 1.24 0.00 0.00 2.83
185 186 2.057922 AGCCCCTCGATTCCATATGTT 58.942 47.619 1.24 0.00 0.00 2.71
186 187 1.734655 AGCCCCTCGATTCCATATGT 58.265 50.000 1.24 0.00 0.00 2.29
187 188 3.981071 TTAGCCCCTCGATTCCATATG 57.019 47.619 0.00 0.00 0.00 1.78
188 189 4.993705 TTTTAGCCCCTCGATTCCATAT 57.006 40.909 0.00 0.00 0.00 1.78
189 190 4.993705 ATTTTAGCCCCTCGATTCCATA 57.006 40.909 0.00 0.00 0.00 2.74
190 191 3.884037 ATTTTAGCCCCTCGATTCCAT 57.116 42.857 0.00 0.00 0.00 3.41
191 192 4.165372 AGTTATTTTAGCCCCTCGATTCCA 59.835 41.667 0.00 0.00 0.00 3.53
192 193 4.715713 AGTTATTTTAGCCCCTCGATTCC 58.284 43.478 0.00 0.00 0.00 3.01
193 194 5.820947 TCAAGTTATTTTAGCCCCTCGATTC 59.179 40.000 0.00 0.00 0.00 2.52
194 195 5.589050 GTCAAGTTATTTTAGCCCCTCGATT 59.411 40.000 0.00 0.00 0.00 3.34
195 196 5.123936 GTCAAGTTATTTTAGCCCCTCGAT 58.876 41.667 0.00 0.00 0.00 3.59
196 197 4.510571 GTCAAGTTATTTTAGCCCCTCGA 58.489 43.478 0.00 0.00 0.00 4.04
197 198 3.626217 GGTCAAGTTATTTTAGCCCCTCG 59.374 47.826 0.00 0.00 0.00 4.63
198 199 3.626217 CGGTCAAGTTATTTTAGCCCCTC 59.374 47.826 0.00 0.00 0.00 4.30
199 200 3.264964 TCGGTCAAGTTATTTTAGCCCCT 59.735 43.478 0.00 0.00 0.00 4.79
200 201 3.613030 TCGGTCAAGTTATTTTAGCCCC 58.387 45.455 0.00 0.00 0.00 5.80
201 202 4.331992 GTCTCGGTCAAGTTATTTTAGCCC 59.668 45.833 0.00 0.00 0.00 5.19
202 203 4.933400 TGTCTCGGTCAAGTTATTTTAGCC 59.067 41.667 0.00 0.00 0.00 3.93
203 204 5.638234 ACTGTCTCGGTCAAGTTATTTTAGC 59.362 40.000 0.00 0.00 0.00 3.09
204 205 8.752766 TTACTGTCTCGGTCAAGTTATTTTAG 57.247 34.615 0.00 0.00 0.00 1.85
206 207 9.715121 TTATTACTGTCTCGGTCAAGTTATTTT 57.285 29.630 0.00 0.00 0.00 1.82
207 208 9.886132 ATTATTACTGTCTCGGTCAAGTTATTT 57.114 29.630 0.00 0.00 0.00 1.40
256 257 3.473923 TCATGTGTGATGTGTCTGTGT 57.526 42.857 0.00 0.00 0.00 3.72
266 267 1.296727 CGCTCAGCATCATGTGTGAT 58.703 50.000 0.00 0.00 45.87 3.06
267 268 2.758497 CGCTCAGCATCATGTGTGA 58.242 52.632 0.00 0.00 39.04 3.58
414 415 1.133025 GGGGTTTCTTGCATCACATCG 59.867 52.381 0.00 0.00 0.00 3.84
455 456 1.337541 GGATGCATGCAGATCGAGCTA 60.338 52.381 26.69 0.00 0.00 3.32
456 457 0.603172 GGATGCATGCAGATCGAGCT 60.603 55.000 26.69 6.16 0.00 4.09
457 458 0.883370 TGGATGCATGCAGATCGAGC 60.883 55.000 26.69 7.68 0.00 5.03
458 459 1.732809 GATGGATGCATGCAGATCGAG 59.267 52.381 26.69 0.00 0.00 4.04
527 528 2.893682 AAGAGGGGCGCATTGTAGGC 62.894 60.000 10.83 0.00 0.00 3.93
541 542 7.170489 GCCAAATGAGAAAAAGAAAAGAAGAGG 59.830 37.037 0.00 0.00 0.00 3.69
561 567 0.867086 GCGCATTGTGTTTGCCAAAT 59.133 45.000 0.30 0.00 36.75 2.32
599 605 2.105134 TCTTTCCGTTCCTTGCCTGTTA 59.895 45.455 0.00 0.00 0.00 2.41
600 606 1.133915 TCTTTCCGTTCCTTGCCTGTT 60.134 47.619 0.00 0.00 0.00 3.16
639 651 1.694150 TGAGGCTGGCTGTATATCCAC 59.306 52.381 9.06 0.00 0.00 4.02
640 652 2.101640 TGAGGCTGGCTGTATATCCA 57.898 50.000 9.06 0.00 0.00 3.41
641 653 2.417924 CGATGAGGCTGGCTGTATATCC 60.418 54.545 9.06 0.00 0.00 2.59
642 654 2.232452 ACGATGAGGCTGGCTGTATATC 59.768 50.000 9.06 6.41 0.00 1.63
643 655 2.232452 GACGATGAGGCTGGCTGTATAT 59.768 50.000 9.06 0.00 0.00 0.86
644 656 1.613925 GACGATGAGGCTGGCTGTATA 59.386 52.381 9.06 0.00 0.00 1.47
645 657 0.390860 GACGATGAGGCTGGCTGTAT 59.609 55.000 9.06 2.62 0.00 2.29
646 658 0.684479 AGACGATGAGGCTGGCTGTA 60.684 55.000 9.06 0.00 36.36 2.74
647 659 1.986757 AGACGATGAGGCTGGCTGT 60.987 57.895 9.06 0.00 36.36 4.40
648 660 2.898738 AGACGATGAGGCTGGCTG 59.101 61.111 9.06 0.00 36.36 4.85
653 665 5.431765 ACATTTTTATCAGACGATGAGGCT 58.568 37.500 0.00 0.00 42.53 4.58
654 666 5.557136 CGACATTTTTATCAGACGATGAGGC 60.557 44.000 0.00 0.00 42.53 4.70
655 667 5.748630 TCGACATTTTTATCAGACGATGAGG 59.251 40.000 0.00 0.00 42.53 3.86
656 668 6.812481 TCGACATTTTTATCAGACGATGAG 57.188 37.500 0.00 0.00 42.53 2.90
659 671 7.953158 ATCATCGACATTTTTATCAGACGAT 57.047 32.000 0.00 0.00 38.86 3.73
676 688 9.219603 CCAATTAGGCTAGAAATTAATCATCGA 57.780 33.333 0.00 0.00 0.00 3.59
734 754 0.475906 AGCAATCCACTCCTATGCCC 59.524 55.000 0.00 0.00 37.73 5.36
871 897 1.544825 TTGGCGGGAGGTCAAGAGAG 61.545 60.000 0.00 0.00 34.73 3.20
872 898 1.535444 TTGGCGGGAGGTCAAGAGA 60.535 57.895 0.00 0.00 34.73 3.10
902 936 2.817844 GAGTGGCGGAGTTTTTATGGTT 59.182 45.455 0.00 0.00 0.00 3.67
949 986 1.975407 GGCACAGGCAGCAATGAGT 60.975 57.895 3.95 0.00 43.71 3.41
957 994 4.767255 GAGGTCGGGCACAGGCAG 62.767 72.222 0.00 0.00 43.71 4.85
959 996 4.459089 GAGAGGTCGGGCACAGGC 62.459 72.222 0.00 0.00 40.13 4.85
960 997 0.757188 ATAGAGAGGTCGGGCACAGG 60.757 60.000 0.00 0.00 0.00 4.00
988 1036 3.478394 CACCATGACGACGTGCGG 61.478 66.667 4.58 5.23 46.49 5.69
1011 1062 4.106925 CCAGTCAGCAGCCCTCCC 62.107 72.222 0.00 0.00 0.00 4.30
1059 1113 2.692368 GCCCTCATCACCCTCCCA 60.692 66.667 0.00 0.00 0.00 4.37
1182 1236 1.225691 CGACGAGGAAGACGACGAC 60.226 63.158 0.00 0.00 46.85 4.34
1185 1239 2.484203 CCCGACGAGGAAGACGAC 59.516 66.667 0.00 0.00 45.00 4.34
1188 1242 4.144703 GCCCCCGACGAGGAAGAC 62.145 72.222 0.00 0.00 45.00 3.01
1927 1981 1.002366 CGGTAGAACATGCAGCTGAC 58.998 55.000 20.43 9.67 0.00 3.51
2020 2074 0.248907 GCTACGCGGCTATTGTCTGA 60.249 55.000 12.47 0.00 0.00 3.27
2104 2158 4.939052 ATGGCTATCGCAGTTTACTACT 57.061 40.909 0.00 0.00 38.10 2.57
2105 2159 5.522460 TGAAATGGCTATCGCAGTTTACTAC 59.478 40.000 0.00 0.00 38.10 2.73
2106 2160 5.666462 TGAAATGGCTATCGCAGTTTACTA 58.334 37.500 0.00 0.00 38.10 1.82
2107 2161 4.513442 TGAAATGGCTATCGCAGTTTACT 58.487 39.130 0.00 0.00 38.10 2.24
2108 2162 4.875544 TGAAATGGCTATCGCAGTTTAC 57.124 40.909 0.00 0.00 38.10 2.01
2109 2163 5.888691 TTTGAAATGGCTATCGCAGTTTA 57.111 34.783 0.00 0.00 38.10 2.01
2110 2164 4.782019 TTTGAAATGGCTATCGCAGTTT 57.218 36.364 0.00 0.00 38.10 2.66
2111 2165 4.782019 TTTTGAAATGGCTATCGCAGTT 57.218 36.364 0.00 0.00 38.10 3.16
2112 2166 4.782019 TTTTTGAAATGGCTATCGCAGT 57.218 36.364 0.00 0.00 38.10 4.40
2136 2190 7.686434 TGTAGAGCTATCCCAGTTTACTTTTT 58.314 34.615 0.00 0.00 0.00 1.94
2137 2191 7.253905 TGTAGAGCTATCCCAGTTTACTTTT 57.746 36.000 0.00 0.00 0.00 2.27
2138 2192 6.869206 TGTAGAGCTATCCCAGTTTACTTT 57.131 37.500 0.00 0.00 0.00 2.66
2139 2193 7.439108 AATGTAGAGCTATCCCAGTTTACTT 57.561 36.000 0.00 0.00 0.00 2.24
2178 2232 7.700656 AGGAAACAAACGAACAAAACTATTCAG 59.299 33.333 0.00 0.00 0.00 3.02
2209 2266 7.664731 ACATTTCATTTCCATGCCAACATAAAA 59.335 29.630 0.00 0.00 33.67 1.52
2210 2267 7.166851 ACATTTCATTTCCATGCCAACATAAA 58.833 30.769 0.00 0.00 33.67 1.40
2211 2268 6.709281 ACATTTCATTTCCATGCCAACATAA 58.291 32.000 0.00 0.00 33.67 1.90
2212 2269 6.297080 ACATTTCATTTCCATGCCAACATA 57.703 33.333 0.00 0.00 33.67 2.29
2213 2270 5.168647 ACATTTCATTTCCATGCCAACAT 57.831 34.783 0.00 0.00 36.79 2.71
2323 2380 7.254932 CCCATATCATTCTTCGTTTCTTTCCTC 60.255 40.741 0.00 0.00 0.00 3.71
2327 2384 7.362920 CCAACCCATATCATTCTTCGTTTCTTT 60.363 37.037 0.00 0.00 0.00 2.52
2328 2385 6.095440 CCAACCCATATCATTCTTCGTTTCTT 59.905 38.462 0.00 0.00 0.00 2.52
2329 2386 5.590259 CCAACCCATATCATTCTTCGTTTCT 59.410 40.000 0.00 0.00 0.00 2.52
2330 2387 5.357032 ACCAACCCATATCATTCTTCGTTTC 59.643 40.000 0.00 0.00 0.00 2.78
2331 2388 5.261216 ACCAACCCATATCATTCTTCGTTT 58.739 37.500 0.00 0.00 0.00 3.60
2332 2389 4.855340 ACCAACCCATATCATTCTTCGTT 58.145 39.130 0.00 0.00 0.00 3.85
2333 2390 4.503714 ACCAACCCATATCATTCTTCGT 57.496 40.909 0.00 0.00 0.00 3.85
2334 2391 4.881273 TGAACCAACCCATATCATTCTTCG 59.119 41.667 0.00 0.00 0.00 3.79
2335 2392 6.152661 TGTTGAACCAACCCATATCATTCTTC 59.847 38.462 7.29 0.00 42.96 2.87
2336 2393 6.015918 TGTTGAACCAACCCATATCATTCTT 58.984 36.000 7.29 0.00 42.96 2.52
2396 2470 5.850614 ACTATAGTGTCTTCAACAACGGTT 58.149 37.500 4.10 0.00 40.31 4.44
2400 2481 9.130312 CTTCTGTACTATAGTGTCTTCAACAAC 57.870 37.037 15.90 2.17 40.31 3.32
2469 2552 7.624360 TCCGTATGCTGAAACATAGAAATTT 57.376 32.000 0.00 0.00 33.27 1.82
2477 2560 2.401583 TGCTCCGTATGCTGAAACAT 57.598 45.000 0.00 0.00 0.00 2.71
2482 2565 2.689553 TTCAATGCTCCGTATGCTGA 57.310 45.000 0.00 0.00 0.00 4.26
2483 2566 2.679837 ACTTTCAATGCTCCGTATGCTG 59.320 45.455 0.00 0.00 0.00 4.41
2485 2568 2.792542 GCACTTTCAATGCTCCGTATGC 60.793 50.000 0.00 0.00 40.08 3.14
2546 2646 4.481930 TTCCGTTGAAGTTACAGCATTG 57.518 40.909 0.00 0.00 0.00 2.82
2564 2730 3.572255 TGGTCCTTGTAACTGCATTTTCC 59.428 43.478 0.00 0.00 0.00 3.13
2642 2811 2.043227 CTCCTCTGTCCCCTAATCACC 58.957 57.143 0.00 0.00 0.00 4.02
2658 2827 1.360852 TCTTCTCTTCTGCTCCCTCCT 59.639 52.381 0.00 0.00 0.00 3.69
2713 2882 1.811965 TCTGATGATGTGCAAAACGGG 59.188 47.619 0.00 0.00 0.00 5.28
2785 2960 3.297134 ACCCTGTCTTGAAAGAGCAAA 57.703 42.857 0.00 0.00 35.32 3.68
2863 3044 3.740115 ACTGATCTTTGTGTAACCGCTT 58.260 40.909 0.00 0.00 34.36 4.68
2888 3069 6.017605 GCTCAACCAGGTGATTCTACAATATG 60.018 42.308 0.00 0.00 0.00 1.78
2921 3104 3.258372 ACGATAGACAGGTTGACACACAT 59.742 43.478 0.00 0.00 41.38 3.21
2935 3118 2.740447 AGGCGGTTTTGAAACGATAGAC 59.260 45.455 1.84 0.00 39.77 2.59


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

AutoCloner maintained by Alex Coulton.