Multiple sequence alignment - TraesCS5D01G289500

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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 TraesCS5D01G289500 chr5D 100.000 4854 0 0 1 4854 388103292 388108145 0.000000e+00 8964.0
1 TraesCS5D01G289500 chr5D 84.937 239 32 2 1170 1408 388426218 388426452 6.280000e-59 239.0
2 TraesCS5D01G289500 chr5D 82.301 226 22 6 1103 1328 388414070 388414277 3.860000e-41 180.0
3 TraesCS5D01G289500 chr5D 84.375 160 21 3 988 1146 388424087 388424243 2.340000e-33 154.0
4 TraesCS5D01G289500 chr5A 94.351 1841 77 8 2180 4006 491297775 491299602 0.000000e+00 2798.0
5 TraesCS5D01G289500 chr5A 88.669 2224 123 53 1 2187 491295247 491297378 0.000000e+00 2591.0
6 TraesCS5D01G289500 chr5A 96.747 707 17 6 4004 4706 491299647 491300351 0.000000e+00 1173.0
7 TraesCS5D01G289500 chr5A 83.135 421 49 9 988 1408 491313328 491313726 9.930000e-97 364.0
8 TraesCS5D01G289500 chr5A 97.315 149 4 0 4706 4854 491300392 491300540 2.240000e-63 254.0
9 TraesCS5D01G289500 chr5B 92.422 1544 70 31 1 1526 466780662 466782176 0.000000e+00 2159.0
10 TraesCS5D01G289500 chr5B 92.457 928 47 11 2387 3294 466782166 466783090 0.000000e+00 1304.0
11 TraesCS5D01G289500 chr5B 93.963 762 32 9 3309 4057 466784797 466785557 0.000000e+00 1140.0
12 TraesCS5D01G289500 chr5B 92.600 527 30 9 4188 4706 466785559 466786084 0.000000e+00 749.0
13 TraesCS5D01G289500 chr5B 83.777 413 44 12 996 1408 466968300 466968689 2.130000e-98 370.0
14 TraesCS5D01G289500 chr5B 82.809 413 47 13 996 1408 466949653 466950041 1.000000e-91 348.0
15 TraesCS5D01G289500 chr5B 96.000 150 5 1 4706 4854 466786124 466786273 4.850000e-60 243.0
16 TraesCS5D01G289500 chr1B 88.022 718 53 14 83 781 507473074 507473777 0.000000e+00 819.0
17 TraesCS5D01G289500 chr1B 85.273 421 40 9 988 1408 507472755 507472357 9.720000e-112 414.0
18 TraesCS5D01G289500 chr1B 94.737 57 2 1 804 860 507544089 507544144 2.410000e-13 87.9
19 TraesCS5D01G289500 chr1D 87.225 728 51 20 83 783 378869405 378870117 0.000000e+00 791.0
20 TraesCS5D01G289500 chr1D 84.323 421 44 8 988 1408 378869086 378868688 4.550000e-105 392.0
21 TraesCS5D01G289500 chr1D 90.588 85 3 2 776 860 378871060 378871139 1.850000e-19 108.0
22 TraesCS5D01G289500 chr1A 84.787 447 27 11 83 511 479711308 479711731 1.260000e-110 411.0
23 TraesCS5D01G289500 chr1A 80.814 344 41 12 988 1328 479710994 479710673 3.750000e-61 246.0
24 TraesCS5D01G289500 chr6D 78.740 508 51 30 1002 1505 106953093 106953547 2.210000e-73 287.0
25 TraesCS5D01G289500 chr6B 80.247 162 23 5 3736 3895 79881620 79881466 3.970000e-21 113.0


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 TraesCS5D01G289500 chr5D 388103292 388108145 4853 False 8964.0 8964 100.0000 1 4854 1 chr5D.!!$F1 4853
1 TraesCS5D01G289500 chr5A 491295247 491300540 5293 False 1704.0 2798 94.2705 1 4854 4 chr5A.!!$F2 4853
2 TraesCS5D01G289500 chr5B 466780662 466786273 5611 False 1119.0 2159 93.4884 1 4854 5 chr5B.!!$F3 4853
3 TraesCS5D01G289500 chr1B 507473074 507473777 703 False 819.0 819 88.0220 83 781 1 chr1B.!!$F1 698
4 TraesCS5D01G289500 chr1D 378869405 378871139 1734 False 449.5 791 88.9065 83 860 2 chr1D.!!$F1 777

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
533 574 0.103208 CCTCAGAATCGTCGGGGAAG 59.897 60.0 0.00 0.00 0.00 3.46 F
829 1829 0.114364 AAAAGGATGCGAAAGGGGGT 59.886 50.0 0.00 0.00 0.00 4.95 F
830 1830 0.114364 AAAGGATGCGAAAGGGGGTT 59.886 50.0 0.00 0.00 0.00 4.11 F
972 1983 0.176219 AGTGTGACGGGTCGTTGAAA 59.824 50.0 0.00 0.00 41.37 2.69 F
1496 2518 0.179275 CGTGTGCATGACGTCTTTCG 60.179 55.0 17.92 8.04 46.00 3.46 F
2784 4229 0.329596 AACCACTGATTCCCTGGAGC 59.670 55.0 0.00 0.00 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1904 2930 0.178953 AACATCAGTGGCCCTTGCTT 60.179 50.000 0.0 0.0 37.74 3.91 R
2784 4229 0.246360 TGGTCAGTGTCAGGCATACG 59.754 55.000 0.0 0.0 0.00 3.06 R
2830 4275 3.071479 AGTAATTTCGTGATGCCGTTGT 58.929 40.909 0.0 0.0 0.00 3.32 R
2915 4360 1.407989 GCTCCAGGGGATGACTTTCTG 60.408 57.143 0.0 0.0 0.00 3.02 R
3380 6529 1.722751 GCACAGTTCGATTGCAAGACG 60.723 52.381 18.4 18.4 36.22 4.18 R
4075 7279 0.108424 CCGAGAAGAGGGCAGACAAG 60.108 60.000 0.0 0.0 0.00 3.16 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
228 241 0.390603 TACCGAGGACCAACAATGCG 60.391 55.000 0.00 0.00 0.00 4.73
295 309 1.152777 CCAACTGGGGCAGTGAACA 60.153 57.895 0.00 0.00 44.62 3.18
323 338 1.132453 GAGCAGTAACAAAATCGGGGC 59.868 52.381 0.00 0.00 0.00 5.80
350 365 1.927174 CTAACGACTTGCTGAATCCCG 59.073 52.381 0.00 0.00 0.00 5.14
428 468 1.664649 CGAAACGAGCAGGACAGCA 60.665 57.895 0.00 0.00 36.85 4.41
429 469 1.221466 CGAAACGAGCAGGACAGCAA 61.221 55.000 0.00 0.00 36.85 3.91
533 574 0.103208 CCTCAGAATCGTCGGGGAAG 59.897 60.000 0.00 0.00 0.00 3.46
633 674 2.813474 CGGAAATCGCCACGAGCA 60.813 61.111 0.00 0.00 44.04 4.26
654 695 1.063649 GAAGATACGCGCCGAGACA 59.936 57.895 5.73 0.00 0.00 3.41
829 1829 0.114364 AAAAGGATGCGAAAGGGGGT 59.886 50.000 0.00 0.00 0.00 4.95
830 1830 0.114364 AAAGGATGCGAAAGGGGGTT 59.886 50.000 0.00 0.00 0.00 4.11
937 1948 3.294493 TGTGCGGCCTGCCTTTTC 61.294 61.111 15.40 3.96 45.60 2.29
964 1975 1.227438 CGTTTCCAGTGTGACGGGT 60.227 57.895 0.00 0.00 34.90 5.28
972 1983 0.176219 AGTGTGACGGGTCGTTGAAA 59.824 50.000 0.00 0.00 41.37 2.69
976 1987 2.683867 TGTGACGGGTCGTTGAAATTTT 59.316 40.909 0.00 0.00 41.37 1.82
977 1988 3.128938 TGTGACGGGTCGTTGAAATTTTT 59.871 39.130 0.00 0.00 41.37 1.94
978 1989 3.484285 GTGACGGGTCGTTGAAATTTTTG 59.516 43.478 0.00 0.00 41.37 2.44
981 1992 3.631227 ACGGGTCGTTGAAATTTTTGGTA 59.369 39.130 0.00 0.00 36.35 3.25
982 1993 4.223659 CGGGTCGTTGAAATTTTTGGTAG 58.776 43.478 0.00 0.00 0.00 3.18
983 1994 4.552355 GGGTCGTTGAAATTTTTGGTAGG 58.448 43.478 0.00 0.00 0.00 3.18
984 1995 4.038282 GGGTCGTTGAAATTTTTGGTAGGT 59.962 41.667 0.00 0.00 0.00 3.08
985 1996 5.452216 GGGTCGTTGAAATTTTTGGTAGGTT 60.452 40.000 0.00 0.00 0.00 3.50
986 1997 6.238981 GGGTCGTTGAAATTTTTGGTAGGTTA 60.239 38.462 0.00 0.00 0.00 2.85
987 1998 6.638063 GGTCGTTGAAATTTTTGGTAGGTTAC 59.362 38.462 0.00 0.00 0.00 2.50
988 1999 7.194962 GTCGTTGAAATTTTTGGTAGGTTACA 58.805 34.615 0.00 0.00 0.00 2.41
989 2000 7.377662 GTCGTTGAAATTTTTGGTAGGTTACAG 59.622 37.037 0.00 0.00 0.00 2.74
995 2010 0.899720 TTGGTAGGTTACAGGGAGCG 59.100 55.000 0.00 0.00 0.00 5.03
1187 2205 2.154462 CCTCTTGCGGTTGATCTGTTT 58.846 47.619 0.00 0.00 0.00 2.83
1188 2206 2.095567 CCTCTTGCGGTTGATCTGTTTG 60.096 50.000 0.00 0.00 0.00 2.93
1189 2207 2.549754 CTCTTGCGGTTGATCTGTTTGT 59.450 45.455 0.00 0.00 0.00 2.83
1190 2208 2.948979 TCTTGCGGTTGATCTGTTTGTT 59.051 40.909 0.00 0.00 0.00 2.83
1191 2209 2.772568 TGCGGTTGATCTGTTTGTTG 57.227 45.000 0.00 0.00 0.00 3.33
1192 2210 1.268999 TGCGGTTGATCTGTTTGTTGC 60.269 47.619 0.00 0.00 0.00 4.17
1193 2211 1.001378 GCGGTTGATCTGTTTGTTGCT 60.001 47.619 0.00 0.00 0.00 3.91
1194 2212 2.543653 GCGGTTGATCTGTTTGTTGCTT 60.544 45.455 0.00 0.00 0.00 3.91
1195 2213 3.300009 CGGTTGATCTGTTTGTTGCTTC 58.700 45.455 0.00 0.00 0.00 3.86
1196 2214 3.003689 CGGTTGATCTGTTTGTTGCTTCT 59.996 43.478 0.00 0.00 0.00 2.85
1197 2215 4.293415 GGTTGATCTGTTTGTTGCTTCTG 58.707 43.478 0.00 0.00 0.00 3.02
1198 2216 3.631145 TGATCTGTTTGTTGCTTCTGC 57.369 42.857 0.00 0.00 40.20 4.26
1199 2217 2.294233 TGATCTGTTTGTTGCTTCTGCC 59.706 45.455 0.00 0.00 38.71 4.85
1228 2250 1.338674 TGTGGATAGTTCAGCGGGTTG 60.339 52.381 0.00 0.00 0.00 3.77
1229 2251 0.392461 TGGATAGTTCAGCGGGTTGC 60.392 55.000 0.00 0.00 46.98 4.17
1413 2435 1.472082 TGTTTGATGAAATGCCGCGAT 59.528 42.857 8.23 0.00 0.00 4.58
1415 2437 3.035942 GTTTGATGAAATGCCGCGATAC 58.964 45.455 8.23 0.00 0.00 2.24
1420 2442 2.469826 TGAAATGCCGCGATACTACAG 58.530 47.619 8.23 0.00 0.00 2.74
1439 2461 3.192001 ACAGCATGGTTATTTGCTCTGTG 59.808 43.478 0.00 0.00 45.83 3.66
1496 2518 0.179275 CGTGTGCATGACGTCTTTCG 60.179 55.000 17.92 8.04 46.00 3.46
1561 2583 1.379527 GCAAACAGTAGGGGAATCCG 58.620 55.000 0.00 0.00 41.52 4.18
1563 2585 1.280998 CAAACAGTAGGGGAATCCGGT 59.719 52.381 0.00 0.00 41.52 5.28
1564 2586 2.502538 CAAACAGTAGGGGAATCCGGTA 59.497 50.000 0.00 0.00 41.52 4.02
1565 2587 2.789323 ACAGTAGGGGAATCCGGTAT 57.211 50.000 0.00 0.00 41.52 2.73
1566 2588 3.909427 ACAGTAGGGGAATCCGGTATA 57.091 47.619 0.00 0.00 41.52 1.47
1569 2591 5.160386 ACAGTAGGGGAATCCGGTATAAAT 58.840 41.667 0.00 0.00 41.52 1.40
1646 2668 1.434513 ATGGCCCCCAACAGAACAGA 61.435 55.000 0.00 0.00 36.95 3.41
1647 2669 1.152830 GGCCCCCAACAGAACAGAA 59.847 57.895 0.00 0.00 0.00 3.02
1648 2670 0.469144 GGCCCCCAACAGAACAGAAA 60.469 55.000 0.00 0.00 0.00 2.52
1649 2671 1.408969 GCCCCCAACAGAACAGAAAA 58.591 50.000 0.00 0.00 0.00 2.29
1672 2694 2.990740 AGGGAGAGGAGCCTATACTG 57.009 55.000 0.00 0.00 0.00 2.74
1683 2705 8.425703 AGAGGAGCCTATACTGATAAAAAGAAC 58.574 37.037 0.00 0.00 0.00 3.01
1707 2729 6.544564 ACAAAATGGAAACTAGAGAAAACCGA 59.455 34.615 0.00 0.00 0.00 4.69
1827 2853 1.536709 GCCAACCAACAAGTGAAGCAG 60.537 52.381 0.00 0.00 0.00 4.24
1828 2854 1.067516 CCAACCAACAAGTGAAGCAGG 59.932 52.381 0.00 0.00 0.00 4.85
1868 2894 2.288666 TCCAATCATTACGCTGCTTCC 58.711 47.619 0.00 0.00 0.00 3.46
1900 2926 6.772716 TCCATAAGGCAGATGAAACTATTTCC 59.227 38.462 0.60 0.00 35.21 3.13
1904 2930 5.759059 AGGCAGATGAAACTATTTCCATGA 58.241 37.500 0.00 0.00 38.90 3.07
1916 2942 0.899717 TTCCATGAAGCAAGGGCCAC 60.900 55.000 6.18 0.00 42.56 5.01
1927 2953 2.298729 GCAAGGGCCACTGATGTTAAAA 59.701 45.455 6.18 0.00 0.00 1.52
1985 3011 2.787473 TAGAGCACAATTCACCCCAG 57.213 50.000 0.00 0.00 0.00 4.45
2016 3042 5.527951 TCGTCCAGTGTCTTCTATCTATCAC 59.472 44.000 0.00 0.00 0.00 3.06
2040 3066 3.118884 TCTCTTGTATTAAGCCGGTCCAC 60.119 47.826 1.90 0.00 0.00 4.02
2063 3089 6.010219 ACAGTTAATAGCCACATGAAAACCT 58.990 36.000 0.00 0.00 0.00 3.50
2157 3184 7.152645 TCAACTTATAATATCCCGCAGAAGAC 58.847 38.462 0.00 0.00 0.00 3.01
2187 3214 4.324267 CAGACTGGGAGGATTTAAACGTT 58.676 43.478 0.00 0.00 0.00 3.99
2189 3216 4.286291 AGACTGGGAGGATTTAAACGTTCT 59.714 41.667 0.00 0.00 0.00 3.01
2190 3217 4.981812 ACTGGGAGGATTTAAACGTTCTT 58.018 39.130 0.00 0.00 0.00 2.52
2192 3219 4.975631 TGGGAGGATTTAAACGTTCTTGA 58.024 39.130 0.00 0.00 0.00 3.02
2193 3220 5.001232 TGGGAGGATTTAAACGTTCTTGAG 58.999 41.667 0.00 0.00 0.00 3.02
2194 3221 4.142665 GGGAGGATTTAAACGTTCTTGAGC 60.143 45.833 0.00 0.00 0.00 4.26
2195 3222 4.454504 GGAGGATTTAAACGTTCTTGAGCA 59.545 41.667 0.00 0.00 0.00 4.26
2196 3223 5.390991 GGAGGATTTAAACGTTCTTGAGCAG 60.391 44.000 0.00 0.00 0.00 4.24
2211 3644 3.759581 TGAGCAGGAGAGCTTCATTTTT 58.240 40.909 0.00 0.00 46.75 1.94
2222 3655 5.240403 AGAGCTTCATTTTTGACTTCCAGAC 59.760 40.000 0.00 0.00 0.00 3.51
2315 3749 6.040278 TGTTCAGTAATGTCATCTTTTTGCCA 59.960 34.615 0.00 0.00 0.00 4.92
2319 3753 7.014134 TCAGTAATGTCATCTTTTTGCCAAAGA 59.986 33.333 9.88 9.88 40.17 2.52
2341 3777 3.513912 ACACGATCCTAATCTTGTCCACA 59.486 43.478 0.00 0.00 39.46 4.17
2367 3803 7.518161 TGTGTAATAGCAGTCTTTTGAATTCG 58.482 34.615 0.04 0.00 0.00 3.34
2485 3929 3.236816 CACTCAAACGTTCATTGGATGC 58.763 45.455 0.00 0.00 0.00 3.91
2536 3980 7.881775 AATACTTTGACTTTCAAGTTGAGGT 57.118 32.000 5.56 9.17 39.88 3.85
2657 4102 5.418840 TGGAAAGATTGCAGGAGGAAAATAC 59.581 40.000 0.00 0.00 0.00 1.89
2723 4168 2.287009 GCTTGGCTACATTATTGGACGC 60.287 50.000 0.00 0.00 0.00 5.19
2728 4173 3.125316 GGCTACATTATTGGACGCTATGC 59.875 47.826 0.00 0.00 0.00 3.14
2784 4229 0.329596 AACCACTGATTCCCTGGAGC 59.670 55.000 0.00 0.00 0.00 4.70
2830 4275 0.968901 AATAGAGCCGACGGTGTCCA 60.969 55.000 16.73 2.31 0.00 4.02
2915 4360 9.937175 GAAGTGTATCTACCAAATAGCAAATTC 57.063 33.333 0.00 0.00 0.00 2.17
2971 4416 8.598041 CCTCCTATCTATGCTAAGGTAATGTTT 58.402 37.037 0.00 0.00 0.00 2.83
2982 4427 7.500892 TGCTAAGGTAATGTTTCTTTTCTCACA 59.499 33.333 0.00 0.00 0.00 3.58
3060 4510 8.301002 GTTTGTTTAAAATGGCAGTGTAGGATA 58.699 33.333 0.00 0.00 0.00 2.59
3101 4551 8.109705 AGAGTGCATAAATTGTTCATTGTGTA 57.890 30.769 0.00 0.00 0.00 2.90
3195 4645 7.387948 ACGATTTATCTATCAGGTGTTATTGGC 59.612 37.037 0.00 0.00 0.00 4.52
3294 4750 8.673711 GCTTTGTTATCACAGTGGTTATAATGA 58.326 33.333 0.00 0.00 33.22 2.57
3340 6488 5.730296 GCTTAGTATCCAAGCTGATAGGA 57.270 43.478 0.00 0.00 44.04 2.94
3341 6489 6.293004 GCTTAGTATCCAAGCTGATAGGAT 57.707 41.667 12.94 12.94 44.04 3.24
3359 6507 4.199310 AGGATATTTGTGGTGTCCAATCG 58.801 43.478 0.00 0.00 34.18 3.34
3372 6520 6.149807 TGGTGTCCAATCGGATTTTTACTTAC 59.850 38.462 0.00 0.00 45.33 2.34
3374 6522 7.550196 GGTGTCCAATCGGATTTTTACTTACTA 59.450 37.037 0.00 0.00 45.33 1.82
3377 6526 9.159364 GTCCAATCGGATTTTTACTTACTAAGT 57.841 33.333 6.68 6.68 45.33 2.24
3395 6544 4.385244 AAGTTACGTCTTGCAATCGAAC 57.615 40.909 23.87 20.93 0.00 3.95
3462 6615 2.168521 ACCATCAGTCCCACTTATCACG 59.831 50.000 0.00 0.00 0.00 4.35
3503 6656 7.762159 TGACAAACTTTTTCCCAACAGAATAAC 59.238 33.333 0.00 0.00 0.00 1.89
3563 6717 1.782044 CCACAAATTTGCAGAACCGG 58.218 50.000 18.12 0.00 0.00 5.28
3748 6906 4.664688 ATCAAGGGATGAACTGGAAACT 57.335 40.909 0.00 0.00 42.54 2.66
3805 6963 4.678509 TTGTCAAGTTGATAATGGACGC 57.321 40.909 9.18 0.00 0.00 5.19
3834 6992 3.284323 TCTCTCCTTCGACAAAGTTCG 57.716 47.619 0.00 0.00 40.53 3.95
3865 7023 1.593750 GCCCTGACAGATAGCAGCG 60.594 63.158 3.32 0.00 0.00 5.18
3918 7076 9.442047 CTGAACTTCTGATCTTGTAAAGGTATT 57.558 33.333 0.00 0.00 46.24 1.89
3958 7116 5.309020 AGGATGTATACTCAGTGCCATGAAT 59.691 40.000 4.17 0.00 0.00 2.57
4059 7263 1.668751 TGGACAACAAGCGTTTCTGTC 59.331 47.619 12.68 12.68 31.13 3.51
4074 7278 2.333926 TCTGTCGTGCTAAAACATCGG 58.666 47.619 0.00 0.00 0.00 4.18
4075 7279 0.793861 TGTCGTGCTAAAACATCGGC 59.206 50.000 0.00 0.00 0.00 5.54
4079 7283 1.196808 CGTGCTAAAACATCGGCTTGT 59.803 47.619 0.00 0.00 0.00 3.16
4124 7328 7.116090 CGATAAAGTTGCCAGATAGATCTTCAG 59.884 40.741 0.00 0.00 34.22 3.02
4176 7381 4.283337 TGGAATCGTATCCACTTCCACTA 58.717 43.478 7.68 0.00 44.52 2.74
4269 7474 5.441718 TCTGACTTCAGGGATAATGCTTT 57.558 39.130 6.40 0.00 43.91 3.51
4314 7520 7.891498 AGGTACTTTTTGGTGTGTTTCTAAT 57.109 32.000 0.00 0.00 27.25 1.73
4469 7676 0.322997 TAATCACCGTTTGGCCCCTG 60.323 55.000 0.00 0.00 39.70 4.45
4523 7732 0.379669 GGCAATGAAGGTGATGCTCG 59.620 55.000 0.00 0.00 38.79 5.03
4832 8088 8.391106 CAAGTTTTCTTATGAAATACTCCCTCG 58.609 37.037 4.77 0.00 41.24 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
228 241 2.096417 CACGAACGAGTGGTTGGATTTC 60.096 50.000 7.02 0.00 39.50 2.17
280 294 0.179018 GTTCTGTTCACTGCCCCAGT 60.179 55.000 0.00 0.00 46.51 4.00
295 309 2.902705 TTGTTACTGCTCGTGGTTCT 57.097 45.000 0.00 0.00 0.00 3.01
323 338 5.856126 TTCAGCAAGTCGTTAGGTTTATG 57.144 39.130 0.00 0.00 0.00 1.90
370 393 1.218047 CTCCGGCTTGATCGTTCCA 59.782 57.895 0.00 0.00 0.00 3.53
373 396 1.218316 GGTCTCCGGCTTGATCGTT 59.782 57.895 0.00 0.00 0.00 3.85
374 397 2.722201 GGGTCTCCGGCTTGATCGT 61.722 63.158 0.00 0.00 0.00 3.73
445 485 4.515567 GCTACCTTAGGAATTGGGAAATCG 59.484 45.833 4.77 0.00 0.00 3.34
448 488 3.371166 CGGCTACCTTAGGAATTGGGAAA 60.371 47.826 4.77 0.00 0.00 3.13
633 674 0.814410 TCTCGGCGCGTATCTTCTCT 60.814 55.000 8.43 0.00 0.00 3.10
683 724 3.938253 TCGTCCGATCGAGCTCGC 61.938 66.667 30.97 16.97 39.60 5.03
924 1935 3.064324 CCCAGAAAAGGCAGGCCG 61.064 66.667 4.37 0.00 41.95 6.13
934 1945 2.116556 GAAACGGGCCCCCAGAAA 59.883 61.111 18.66 0.00 35.37 2.52
937 1948 4.740822 CTGGAAACGGGCCCCCAG 62.741 72.222 25.19 25.19 40.01 4.45
964 1975 7.330900 TGTAACCTACCAAAAATTTCAACGA 57.669 32.000 0.00 0.00 0.00 3.85
972 1983 4.341487 GCTCCCTGTAACCTACCAAAAAT 58.659 43.478 0.00 0.00 0.00 1.82
976 1987 0.899720 CGCTCCCTGTAACCTACCAA 59.100 55.000 0.00 0.00 0.00 3.67
977 1988 0.974010 CCGCTCCCTGTAACCTACCA 60.974 60.000 0.00 0.00 0.00 3.25
978 1989 0.974525 ACCGCTCCCTGTAACCTACC 60.975 60.000 0.00 0.00 0.00 3.18
981 1992 1.988406 GGACCGCTCCCTGTAACCT 60.988 63.158 0.00 0.00 0.00 3.50
982 1993 1.623542 ATGGACCGCTCCCTGTAACC 61.624 60.000 0.00 0.00 35.34 2.85
983 1994 0.462047 CATGGACCGCTCCCTGTAAC 60.462 60.000 0.00 0.00 35.34 2.50
984 1995 1.622607 CCATGGACCGCTCCCTGTAA 61.623 60.000 5.56 0.00 35.34 2.41
985 1996 2.063979 CCATGGACCGCTCCCTGTA 61.064 63.158 5.56 0.00 35.34 2.74
986 1997 3.402681 CCATGGACCGCTCCCTGT 61.403 66.667 5.56 0.00 35.34 4.00
987 1998 4.864334 GCCATGGACCGCTCCCTG 62.864 72.222 18.40 0.00 35.34 4.45
1166 2181 0.036010 ACAGATCAACCGCAAGAGGG 60.036 55.000 0.00 0.00 43.02 4.30
1187 2205 3.286751 GCACCGGCAGAAGCAACA 61.287 61.111 0.00 0.00 44.61 3.33
1188 2206 4.389576 CGCACCGGCAGAAGCAAC 62.390 66.667 0.00 0.00 44.61 4.17
1192 2210 4.093952 CAAGCGCACCGGCAGAAG 62.094 66.667 11.47 0.00 41.24 2.85
1193 2211 4.927782 ACAAGCGCACCGGCAGAA 62.928 61.111 11.47 0.00 41.24 3.02
1198 2216 2.125310 TATCCACAAGCGCACCGG 60.125 61.111 11.47 0.00 0.00 5.28
1199 2217 1.019278 AACTATCCACAAGCGCACCG 61.019 55.000 11.47 0.00 0.00 4.94
1228 2250 2.159212 TGCTCCACAACATATGCAATGC 60.159 45.455 1.58 0.00 0.00 3.56
1229 2251 3.490249 CCTGCTCCACAACATATGCAATG 60.490 47.826 1.58 2.47 0.00 2.82
1230 2252 2.691526 CCTGCTCCACAACATATGCAAT 59.308 45.455 1.58 0.00 0.00 3.56
1231 2253 2.093890 CCTGCTCCACAACATATGCAA 58.906 47.619 1.58 0.00 0.00 4.08
1232 2254 1.281577 TCCTGCTCCACAACATATGCA 59.718 47.619 1.58 0.00 0.00 3.96
1233 2255 2.042686 TCCTGCTCCACAACATATGC 57.957 50.000 1.58 0.00 0.00 3.14
1234 2256 2.352651 CGTTCCTGCTCCACAACATATG 59.647 50.000 0.00 0.00 0.00 1.78
1235 2257 2.027192 ACGTTCCTGCTCCACAACATAT 60.027 45.455 0.00 0.00 0.00 1.78
1347 2369 1.218316 GTAGTACAGCTTGCCGCCT 59.782 57.895 0.00 0.00 40.39 5.52
1420 2442 4.439305 TTCACAGAGCAAATAACCATGC 57.561 40.909 0.00 0.00 42.87 4.06
1439 2461 0.249741 ACGGCCACGGTAGCATATTC 60.250 55.000 2.24 0.00 46.48 1.75
1605 2627 6.459573 CCATCTCAACCCCAATGTAAAATACG 60.460 42.308 0.00 0.00 0.00 3.06
1606 2628 6.682861 GCCATCTCAACCCCAATGTAAAATAC 60.683 42.308 0.00 0.00 0.00 1.89
1607 2629 5.362430 GCCATCTCAACCCCAATGTAAAATA 59.638 40.000 0.00 0.00 0.00 1.40
1608 2630 4.162131 GCCATCTCAACCCCAATGTAAAAT 59.838 41.667 0.00 0.00 0.00 1.82
1649 2671 4.410555 CAGTATAGGCTCCTCTCCCTTTTT 59.589 45.833 0.00 0.00 32.65 1.94
1655 2677 6.919775 TTTTATCAGTATAGGCTCCTCTCC 57.080 41.667 0.00 0.00 0.00 3.71
1683 2705 6.966021 TCGGTTTTCTCTAGTTTCCATTTTG 58.034 36.000 0.00 0.00 0.00 2.44
1707 2729 7.182060 TGGATTGCTTCTATTTCTTAAACCCT 58.818 34.615 0.00 0.00 0.00 4.34
1724 2746 1.891150 CCACTGAAAGCTTGGATTGCT 59.109 47.619 0.00 0.00 43.32 3.91
1836 2862 9.868277 AGCGTAATGATTGGATTTTTGATTAAA 57.132 25.926 0.00 0.00 0.00 1.52
1839 2865 6.256321 GCAGCGTAATGATTGGATTTTTGATT 59.744 34.615 0.00 0.00 0.00 2.57
1840 2866 5.750067 GCAGCGTAATGATTGGATTTTTGAT 59.250 36.000 0.00 0.00 0.00 2.57
1846 2872 3.316308 GGAAGCAGCGTAATGATTGGATT 59.684 43.478 0.00 0.00 0.00 3.01
1852 2878 3.696051 ACATTTGGAAGCAGCGTAATGAT 59.304 39.130 8.71 0.00 0.00 2.45
1900 2926 0.609957 TCAGTGGCCCTTGCTTCATG 60.610 55.000 0.00 0.00 37.74 3.07
1904 2930 0.178953 AACATCAGTGGCCCTTGCTT 60.179 50.000 0.00 0.00 37.74 3.91
1927 2953 6.945435 TCAGAGAGTCTAGAGAACATCTGTTT 59.055 38.462 14.90 0.00 39.20 2.83
1985 3011 3.057174 AGAAGACACTGGACGATTGAGTC 60.057 47.826 0.00 0.00 40.25 3.36
2016 3042 3.114065 GACCGGCTTAATACAAGAGACG 58.886 50.000 0.00 0.00 41.46 4.18
2040 3066 6.515272 AGGTTTTCATGTGGCTATTAACTG 57.485 37.500 0.00 0.00 0.00 3.16
2106 3132 4.329545 TGTCTCCAGGTTGCCCGC 62.330 66.667 0.00 0.00 35.12 6.13
2157 3184 1.007238 TCCTCCCAGTCTGGAACCTAG 59.993 57.143 21.23 8.89 40.96 3.02
2187 3214 1.637338 TGAAGCTCTCCTGCTCAAGA 58.363 50.000 0.00 0.00 43.24 3.02
2189 3216 3.430042 AAATGAAGCTCTCCTGCTCAA 57.570 42.857 0.00 0.00 43.24 3.02
2190 3217 3.430042 AAAATGAAGCTCTCCTGCTCA 57.570 42.857 0.00 0.00 43.24 4.26
2192 3219 3.505293 GTCAAAAATGAAGCTCTCCTGCT 59.495 43.478 0.00 0.00 46.40 4.24
2193 3220 3.505293 AGTCAAAAATGAAGCTCTCCTGC 59.495 43.478 0.00 0.00 0.00 4.85
2194 3221 5.335504 GGAAGTCAAAAATGAAGCTCTCCTG 60.336 44.000 0.00 0.00 0.00 3.86
2195 3222 4.764308 GGAAGTCAAAAATGAAGCTCTCCT 59.236 41.667 0.00 0.00 0.00 3.69
2196 3223 4.520492 TGGAAGTCAAAAATGAAGCTCTCC 59.480 41.667 0.00 0.00 0.00 3.71
2211 3644 4.431378 TGGGGTTATTAGTCTGGAAGTCA 58.569 43.478 0.00 0.00 33.76 3.41
2222 3655 1.231963 AGGGGGCTTGGGGTTATTAG 58.768 55.000 0.00 0.00 0.00 1.73
2287 3721 7.274250 GCAAAAAGATGACATTACTGAACATCC 59.726 37.037 15.18 5.04 38.79 3.51
2341 3777 8.177663 CGAATTCAAAAGACTGCTATTACACAT 58.822 33.333 6.22 0.00 0.00 3.21
2525 3969 1.064758 AGCCAACACACCTCAACTTGA 60.065 47.619 0.00 0.00 0.00 3.02
2657 4102 4.864334 GCATCCCAGGAGCACCCG 62.864 72.222 0.00 0.00 40.87 5.28
2748 4193 5.768164 CAGTGGTTTCACAAGTAGGGTTATT 59.232 40.000 0.00 0.00 45.91 1.40
2784 4229 0.246360 TGGTCAGTGTCAGGCATACG 59.754 55.000 0.00 0.00 0.00 3.06
2830 4275 3.071479 AGTAATTTCGTGATGCCGTTGT 58.929 40.909 0.00 0.00 0.00 3.32
2888 4333 7.534085 TTTGCTATTTGGTAGATACACTTCG 57.466 36.000 0.00 0.00 31.71 3.79
2915 4360 1.407989 GCTCCAGGGGATGACTTTCTG 60.408 57.143 0.00 0.00 0.00 3.02
3060 4510 4.947388 TGCACTCTTGTAGAAAACCTTGTT 59.053 37.500 0.00 0.00 0.00 2.83
3195 4645 2.497138 TCCATGTGCACAGAAAGACAG 58.503 47.619 25.84 7.20 0.00 3.51
3340 6488 4.229304 TCCGATTGGACACCACAAATAT 57.771 40.909 0.00 0.00 40.17 1.28
3341 6489 3.704800 TCCGATTGGACACCACAAATA 57.295 42.857 0.00 0.00 40.17 1.40
3372 6520 5.345202 AGTTCGATTGCAAGACGTAACTTAG 59.655 40.000 23.14 4.00 30.33 2.18
3374 6522 4.056050 AGTTCGATTGCAAGACGTAACTT 58.944 39.130 23.14 15.52 30.33 2.66
3377 6526 3.183574 CACAGTTCGATTGCAAGACGTAA 59.816 43.478 21.78 14.58 0.00 3.18
3380 6529 1.722751 GCACAGTTCGATTGCAAGACG 60.723 52.381 18.40 18.40 36.22 4.18
3440 6592 3.383505 CGTGATAAGTGGGACTGATGGTA 59.616 47.826 0.00 0.00 0.00 3.25
3441 6593 2.168521 CGTGATAAGTGGGACTGATGGT 59.831 50.000 0.00 0.00 0.00 3.55
3451 6603 3.543680 ATGAGAACCCGTGATAAGTGG 57.456 47.619 0.00 0.00 0.00 4.00
3462 6615 4.036380 AGTTTGTCACGAAAATGAGAACCC 59.964 41.667 0.00 0.00 32.06 4.11
3503 6656 6.810911 ACCACTACATGCTTAGAATCACTAG 58.189 40.000 0.00 0.00 32.30 2.57
3615 6769 9.586732 AAACTGCTAAGCCCAAATTCATATATA 57.413 29.630 0.00 0.00 0.00 0.86
3748 6906 2.333926 CCGTCACACTTGCTTTCGATA 58.666 47.619 0.00 0.00 0.00 2.92
3805 6963 1.200252 TCGAAGGAGAGAAAGCTGACG 59.800 52.381 0.00 0.00 0.00 4.35
3834 6992 2.038557 TGTCAGGGCAAACTAGGAAGTC 59.961 50.000 0.00 0.00 33.75 3.01
3918 7076 5.894298 ACATCCTAATGCAGATTGAGGTA 57.106 39.130 0.00 0.00 36.26 3.08
3958 7116 1.215673 TGGGGTTGTTTTAGGCTGTCA 59.784 47.619 0.00 0.00 0.00 3.58
4059 7263 1.196808 ACAAGCCGATGTTTTAGCACG 59.803 47.619 0.00 0.00 0.00 5.34
4074 7278 0.739112 CGAGAAGAGGGCAGACAAGC 60.739 60.000 0.00 0.00 0.00 4.01
4075 7279 0.108424 CCGAGAAGAGGGCAGACAAG 60.108 60.000 0.00 0.00 0.00 3.16
4176 7381 6.715347 AAACAGTAAACAAGGAGAGCAAAT 57.285 33.333 0.00 0.00 0.00 2.32
4278 7483 6.502863 ACCAAAAAGTACCTAGTCCCTATGAA 59.497 38.462 0.00 0.00 0.00 2.57
4279 7484 6.027482 ACCAAAAAGTACCTAGTCCCTATGA 58.973 40.000 0.00 0.00 0.00 2.15
4314 7520 8.792830 AGAGACATTAGCAAGCAACTTAATAA 57.207 30.769 0.00 0.00 0.00 1.40
4469 7676 2.857448 TCGCAACAACGATTCGGC 59.143 55.556 11.29 2.70 37.09 5.54
4523 7732 6.951788 ACTGAGTAGTTGTCGAACTGAAGTTC 60.952 42.308 12.30 12.30 42.66 3.01
4706 7921 7.691050 GGACTTTTATACGTATGCAAACAAGAC 59.309 37.037 18.37 7.01 0.00 3.01
4832 8088 2.981859 ACGTCTTACATCATGGGACC 57.018 50.000 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.