Multiple sequence alignment - TraesCS3D01G341900

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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 TraesCS3D01G341900 chr3D 100.000 3810 0 0 1 3810 454897530 454893721 0.000000e+00 7036.0
1 TraesCS3D01G341900 chr3D 83.140 172 21 5 2213 2381 454895142 454895308 2.370000e-32 150.0
2 TraesCS3D01G341900 chr3D 90.411 73 7 0 2249 2321 454895210 454895282 3.130000e-16 97.1
3 TraesCS3D01G341900 chr3D 100.000 28 0 0 2294 2321 454895203 454895176 7.000000e-03 52.8
4 TraesCS3D01G341900 chr3D 100.000 28 0 0 2328 2355 454895237 454895210 7.000000e-03 52.8
5 TraesCS3D01G341900 chr3B 92.094 2669 140 29 489 3122 597785660 597783028 0.000000e+00 3694.0
6 TraesCS3D01G341900 chr3B 88.534 532 19 16 2932 3439 597783119 597782606 1.170000e-169 606.0
7 TraesCS3D01G341900 chr3B 93.399 303 11 6 3504 3804 597782584 597782289 1.260000e-119 440.0
8 TraesCS3D01G341900 chr3B 89.272 261 23 5 89 346 597786184 597785926 4.750000e-84 322.0
9 TraesCS3D01G341900 chr3B 93.805 113 6 1 386 498 597785792 597785681 6.550000e-38 169.0
10 TraesCS3D01G341900 chr3B 84.153 183 18 8 2213 2390 597783756 597783932 2.350000e-37 167.0
11 TraesCS3D01G341900 chr3B 87.838 74 8 1 2249 2321 597783824 597783897 6.780000e-13 86.1
12 TraesCS3D01G341900 chr3B 100.000 28 0 0 2294 2321 597783817 597783790 7.000000e-03 52.8
13 TraesCS3D01G341900 chr3A 93.971 1443 63 11 928 2351 597168225 597166788 0.000000e+00 2161.0
14 TraesCS3D01G341900 chr3A 91.256 892 29 15 2929 3810 597166074 597165222 0.000000e+00 1170.0
15 TraesCS3D01G341900 chr3A 92.129 775 35 10 2359 3122 597166739 597165980 0.000000e+00 1070.0
16 TraesCS3D01G341900 chr3A 85.143 350 26 13 23 358 597169352 597169015 6.100000e-88 335.0
17 TraesCS3D01G341900 chr3A 87.814 279 21 6 489 756 597168822 597168546 7.940000e-82 315.0
18 TraesCS3D01G341900 chr3A 95.152 165 6 2 339 502 597169003 597168840 3.780000e-65 259.0
19 TraesCS3D01G341900 chr3A 88.136 177 17 1 751 927 597168425 597168253 1.390000e-49 207.0
20 TraesCS3D01G341900 chr3A 83.099 142 16 7 2253 2390 597166788 597166925 5.170000e-24 122.0
21 TraesCS3D01G341900 chr3A 91.781 73 6 0 2249 2321 597166818 597166890 6.730000e-18 102.0
22 TraesCS3D01G341900 chr3A 77.037 135 28 3 2249 2381 597166779 597166646 1.470000e-09 75.0
23 TraesCS3D01G341900 chr3A 95.652 46 2 0 2288 2333 597166746 597166791 1.470000e-09 75.0
24 TraesCS3D01G341900 chr3A 89.583 48 4 1 3730 3776 672085895 672085942 4.110000e-05 60.2
25 TraesCS3D01G341900 chr3A 97.059 34 1 0 2322 2355 597166746 597166779 1.480000e-04 58.4
26 TraesCS3D01G341900 chr1A 95.556 45 0 2 3737 3780 571345743 571345786 1.900000e-08 71.3
27 TraesCS3D01G341900 chr5D 88.136 59 6 1 3737 3795 548952571 548952514 6.830000e-08 69.4
28 TraesCS3D01G341900 chr4D 93.333 45 2 1 3737 3780 281208544 281208500 8.830000e-07 65.8
29 TraesCS3D01G341900 chr4D 93.182 44 3 0 3737 3780 362116500 362116457 8.830000e-07 65.8
30 TraesCS3D01G341900 chr4D 86.667 60 5 3 3737 3793 17861302 17861243 3.180000e-06 63.9
31 TraesCS3D01G341900 chr7B 93.023 43 3 0 3737 3779 382279260 382279302 3.180000e-06 63.9


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 TraesCS3D01G341900 chr3D 454893721 454897530 3809 True 2380.533333 7036 100.000000 1 3810 3 chr3D.!!$R1 3809
1 TraesCS3D01G341900 chr3B 597782289 597786184 3895 True 880.633333 3694 92.850667 89 3804 6 chr3B.!!$R1 3715
2 TraesCS3D01G341900 chr3A 597165222 597169352 4130 True 699.000000 2161 88.829750 23 3810 8 chr3A.!!$R1 3787

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
817 1113 0.100503 GCATCGCATACACCCCAAAC 59.899 55.0 0.00 0.0 0.00 2.93 F
1141 1481 0.547712 AGCCCAGGCAAGAACCTCTA 60.548 55.0 12.03 0.0 44.88 2.43 F
1269 1609 1.471119 TCTACTTCGGCGACTCCATT 58.529 50.0 10.16 0.0 34.01 3.16 F
1999 2342 0.801251 GTGTGGATGAGCAGAACAGC 59.199 55.0 0.00 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1768 2108 1.032014 GAAACAAACCCAGAGCTGCA 58.968 50.000 1.02 0.0 0.00 4.41 R
1999 2342 1.218316 GTTGTAGACCTGGGCCTCG 59.782 63.158 4.53 0.0 0.00 4.63 R
2627 3014 1.271054 ACATCCCAGTGTTGTCTCTGC 60.271 52.381 0.00 0.0 34.88 4.26 R
3698 4211 1.614903 TGTGGAAGCATGCCTTTTGAG 59.385 47.619 15.66 0.0 31.46 3.02 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
28 29 7.203218 AGAATTCGGAGAAACAAAGAAAAAGG 58.797 34.615 0.00 0.00 45.90 3.11
38 39 4.993905 ACAAAGAAAAAGGTGAAGGAACG 58.006 39.130 0.00 0.00 0.00 3.95
44 45 3.436700 AAAGGTGAAGGAACGCAAAAG 57.563 42.857 0.00 0.00 0.00 2.27
64 65 7.524065 CAAAAGGAATCATTGAAAGAAATGCC 58.476 34.615 0.00 0.00 37.44 4.40
66 67 6.363167 AGGAATCATTGAAAGAAATGCCAA 57.637 33.333 0.00 0.00 37.44 4.52
67 68 6.403878 AGGAATCATTGAAAGAAATGCCAAG 58.596 36.000 0.00 0.00 37.44 3.61
74 75 7.716123 TCATTGAAAGAAATGCCAAGAAAACAT 59.284 29.630 0.00 0.00 37.44 2.71
88 89 6.016943 CCAAGAAAACATAGAAAACCGGTACA 60.017 38.462 8.00 0.00 0.00 2.90
89 90 6.796705 AGAAAACATAGAAAACCGGTACAG 57.203 37.500 8.00 0.00 0.00 2.74
180 195 5.575019 ACACACATAGAAAACCGACAAAAC 58.425 37.500 0.00 0.00 0.00 2.43
351 367 2.564062 CGAGACCCAAGTAGGTACCAAA 59.436 50.000 15.94 0.00 41.42 3.28
542 701 3.437491 CCAAATCCACCATCCTCCATCAT 60.437 47.826 0.00 0.00 0.00 2.45
597 766 2.668457 CTGCTCTGGACGTACATTGTTC 59.332 50.000 0.00 0.00 0.00 3.18
603 772 2.550606 TGGACGTACATTGTTCCTTTGC 59.449 45.455 0.00 0.00 0.00 3.68
680 849 8.034215 ACATTTGCAATCCGATTAAAAGATTGA 58.966 29.630 20.84 7.97 46.33 2.57
697 866 0.660488 TGACACGCACAACCACATTC 59.340 50.000 0.00 0.00 0.00 2.67
732 903 0.973632 TTCGGCTAAGTTGCTCCTCA 59.026 50.000 0.00 0.00 0.00 3.86
768 1064 1.461127 GTTAGCTCTGTGCCAAACTCG 59.539 52.381 0.00 0.00 44.23 4.18
815 1111 0.747644 CTGCATCGCATACACCCCAA 60.748 55.000 0.00 0.00 38.13 4.12
817 1113 0.100503 GCATCGCATACACCCCAAAC 59.899 55.000 0.00 0.00 0.00 2.93
838 1134 4.405548 ACGGAGTAGGTTACAAAGTCTCT 58.594 43.478 0.00 0.00 41.94 3.10
846 1142 6.936968 AGGTTACAAAGTCTCTAATCCTGT 57.063 37.500 0.00 0.00 0.00 4.00
849 1145 6.814146 GGTTACAAAGTCTCTAATCCTGTCAG 59.186 42.308 0.00 0.00 0.00 3.51
876 1172 1.134640 CCACATCATGGGCCAACAATG 60.135 52.381 11.89 16.67 45.95 2.82
879 1175 2.104967 CATCATGGGCCAACAATGAGT 58.895 47.619 11.89 0.00 0.00 3.41
884 1183 3.343941 TGGGCCAACAATGAGTAGTAC 57.656 47.619 2.13 0.00 0.00 2.73
885 1184 2.910319 TGGGCCAACAATGAGTAGTACT 59.090 45.455 2.13 1.37 0.00 2.73
886 1185 3.055385 TGGGCCAACAATGAGTAGTACTC 60.055 47.826 21.35 21.35 45.26 2.59
887 1186 3.532542 GGCCAACAATGAGTAGTACTCC 58.467 50.000 24.32 9.65 44.44 3.85
921 1220 5.945310 AGATAAGGATTTCCATTAGCAGCA 58.055 37.500 0.00 0.00 38.89 4.41
935 1261 2.846371 CAGCACCTCTGCACCTTAC 58.154 57.895 0.00 0.00 46.97 2.34
957 1283 8.867112 TTACTAGTGCAGGAGTATTAATTTCG 57.133 34.615 5.39 0.00 0.00 3.46
1062 1402 7.500227 TGGATCTTTTGCAGAGTTATTATCAGG 59.500 37.037 0.00 0.00 33.87 3.86
1141 1481 0.547712 AGCCCAGGCAAGAACCTCTA 60.548 55.000 12.03 0.00 44.88 2.43
1154 1494 2.735772 CCTCTACCATGGCGCACCT 61.736 63.158 13.04 0.00 36.63 4.00
1171 1511 1.704007 CCTTGCCATCCTCCTCCTCC 61.704 65.000 0.00 0.00 0.00 4.30
1269 1609 1.471119 TCTACTTCGGCGACTCCATT 58.529 50.000 10.16 0.00 34.01 3.16
1662 2002 2.920724 TGTTCATCAACTCGGGAACA 57.079 45.000 0.00 0.00 45.12 3.18
1674 2014 4.141287 ACTCGGGAACAAATGATTTCACA 58.859 39.130 0.00 0.00 0.00 3.58
1768 2108 6.677920 GCGTGCTCATGTCAAGGTAAAATTAT 60.678 38.462 0.00 0.00 0.00 1.28
1773 2113 6.563422 TCATGTCAAGGTAAAATTATGCAGC 58.437 36.000 0.00 0.00 0.00 5.25
1837 2180 9.416284 TCTGTAACATATAGACCACAACTATGA 57.584 33.333 0.00 0.00 33.43 2.15
1999 2342 0.801251 GTGTGGATGAGCAGAACAGC 59.199 55.000 0.00 0.00 0.00 4.40
2175 2519 8.097038 TGTCATGATTCCCAACTTATATCTAGC 58.903 37.037 0.00 0.00 0.00 3.42
2210 2555 7.285629 CACCTCTAAGATCACTAATACTCCACA 59.714 40.741 0.00 0.00 0.00 4.17
2211 2556 8.007742 ACCTCTAAGATCACTAATACTCCACAT 58.992 37.037 0.00 0.00 0.00 3.21
2218 2563 8.709308 AGATCACTAATACTCCACATTAGCTTT 58.291 33.333 0.00 0.00 38.85 3.51
2220 2565 8.079211 TCACTAATACTCCACATTAGCTTTCT 57.921 34.615 0.00 0.00 38.85 2.52
2221 2566 9.197306 TCACTAATACTCCACATTAGCTTTCTA 57.803 33.333 0.00 0.00 38.85 2.10
2239 2584 9.267084 AGCTTTCTATAATTCTGCTTTAGCTAC 57.733 33.333 3.10 0.00 42.66 3.58
2294 2639 9.624373 TCAGAACTAACTATACTGGGTACTTAG 57.376 37.037 0.00 0.00 0.00 2.18
2326 2672 4.900635 AAACACCAAGAAAGCAGTAGTG 57.099 40.909 0.00 0.00 0.00 2.74
2437 2824 7.062322 ACACCAAGATTGCATCATAATCCTAA 58.938 34.615 0.00 0.00 35.62 2.69
2556 2943 5.679734 AGCAGAGTTATCAGTTTGTGTTG 57.320 39.130 0.00 0.00 0.00 3.33
2578 2965 3.814005 TCTTATCGCCCTACCTGTTTC 57.186 47.619 0.00 0.00 0.00 2.78
2627 3014 3.663995 TTGCCATGACAACAGGATTTG 57.336 42.857 0.00 0.00 0.00 2.32
2882 3271 4.079253 ACCTAATGCGTTTGGTTCAATCT 58.921 39.130 17.68 0.00 39.91 2.40
2978 3367 6.039047 CACAATATGGTAAGCTCAGCATTCTT 59.961 38.462 6.91 0.00 37.74 2.52
2981 3370 3.535561 TGGTAAGCTCAGCATTCTTAGC 58.464 45.455 0.00 0.00 39.30 3.09
3026 3517 6.867816 TCAAAGGCATAACATGTGTTTCATTC 59.132 34.615 0.00 0.00 39.31 2.67
3038 3529 9.982291 ACATGTGTTTCATTCGTTATGTTATAC 57.018 29.630 0.00 0.00 35.64 1.47
3041 3532 8.875803 TGTGTTTCATTCGTTATGTTATACTCC 58.124 33.333 1.38 0.00 35.64 3.85
3042 3533 8.875803 GTGTTTCATTCGTTATGTTATACTCCA 58.124 33.333 1.38 0.00 35.64 3.86
3043 3534 9.438228 TGTTTCATTCGTTATGTTATACTCCAA 57.562 29.630 1.38 0.00 35.64 3.53
3092 3583 8.192774 TCAGCATTCTCAGCAATTAATTTAAGG 58.807 33.333 0.00 0.00 0.00 2.69
3123 3614 7.341445 ACTAAAAAGTCAAAGGCATAACACA 57.659 32.000 0.00 0.00 0.00 3.72
3138 3629 3.973206 AACACAGTGATCGGGTTATGA 57.027 42.857 7.81 0.00 0.00 2.15
3145 3636 4.935205 CAGTGATCGGGTTATGAAAACTCA 59.065 41.667 0.00 0.00 0.00 3.41
3196 3693 7.110155 GGAGTAACCATTCTCACCTCAAATAA 58.890 38.462 0.00 0.00 38.79 1.40
3197 3694 7.065923 GGAGTAACCATTCTCACCTCAAATAAC 59.934 40.741 0.00 0.00 38.79 1.89
3198 3695 7.690256 AGTAACCATTCTCACCTCAAATAACT 58.310 34.615 0.00 0.00 0.00 2.24
3199 3696 8.164070 AGTAACCATTCTCACCTCAAATAACTT 58.836 33.333 0.00 0.00 0.00 2.66
3200 3697 7.454260 AACCATTCTCACCTCAAATAACTTC 57.546 36.000 0.00 0.00 0.00 3.01
3201 3698 6.542821 ACCATTCTCACCTCAAATAACTTCA 58.457 36.000 0.00 0.00 0.00 3.02
3355 3868 3.064207 TGCGTACCTCACATTCTGAAAC 58.936 45.455 0.00 0.00 0.00 2.78
3435 3948 3.064931 GTTCACCTACTGTGGCACTAAC 58.935 50.000 19.83 6.57 45.48 2.34
3452 3965 9.923143 TGGCACTAACATATATAACTACATGTC 57.077 33.333 0.00 0.00 31.40 3.06
3551 4064 4.799564 TCAGCATATGTACACACAGACA 57.200 40.909 0.00 0.00 38.30 3.41
3555 4068 5.409520 CAGCATATGTACACACAGACAAAGT 59.590 40.000 0.00 0.00 38.30 2.66
3556 4069 6.589907 CAGCATATGTACACACAGACAAAGTA 59.410 38.462 0.00 0.00 38.30 2.24
3557 4070 7.117667 CAGCATATGTACACACAGACAAAGTAA 59.882 37.037 0.00 0.00 38.30 2.24
3631 4144 5.769662 ACTTCAGGATAGCAACATTCAACAA 59.230 36.000 0.00 0.00 0.00 2.83
3698 4211 1.541588 GGAACACCAGTCATTCAAGGC 59.458 52.381 0.00 0.00 0.00 4.35
3807 4320 8.047310 GGAGTAAATGATAAAAGAGAAGACCCA 58.953 37.037 0.00 0.00 0.00 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.935741 TTCTTTGTTTCTCCGAATTCTTCA 57.064 33.333 3.52 0.00 0.00 3.02
2 3 7.706607 CCTTTTTCTTTGTTTCTCCGAATTCTT 59.293 33.333 3.52 0.00 0.00 2.52
3 4 7.147897 ACCTTTTTCTTTGTTTCTCCGAATTCT 60.148 33.333 3.52 0.00 0.00 2.40
4 5 6.978659 ACCTTTTTCTTTGTTTCTCCGAATTC 59.021 34.615 0.00 0.00 0.00 2.17
5 6 6.756542 CACCTTTTTCTTTGTTTCTCCGAATT 59.243 34.615 0.00 0.00 0.00 2.17
6 7 6.096282 TCACCTTTTTCTTTGTTTCTCCGAAT 59.904 34.615 0.00 0.00 0.00 3.34
7 8 5.416326 TCACCTTTTTCTTTGTTTCTCCGAA 59.584 36.000 0.00 0.00 0.00 4.30
8 9 4.944930 TCACCTTTTTCTTTGTTTCTCCGA 59.055 37.500 0.00 0.00 0.00 4.55
9 10 5.243426 TCACCTTTTTCTTTGTTTCTCCG 57.757 39.130 0.00 0.00 0.00 4.63
10 11 6.042777 CCTTCACCTTTTTCTTTGTTTCTCC 58.957 40.000 0.00 0.00 0.00 3.71
11 12 6.863275 TCCTTCACCTTTTTCTTTGTTTCTC 58.137 36.000 0.00 0.00 0.00 2.87
12 13 6.850752 TCCTTCACCTTTTTCTTTGTTTCT 57.149 33.333 0.00 0.00 0.00 2.52
13 14 6.034577 CGTTCCTTCACCTTTTTCTTTGTTTC 59.965 38.462 0.00 0.00 0.00 2.78
14 15 5.867174 CGTTCCTTCACCTTTTTCTTTGTTT 59.133 36.000 0.00 0.00 0.00 2.83
15 16 5.407502 CGTTCCTTCACCTTTTTCTTTGTT 58.592 37.500 0.00 0.00 0.00 2.83
16 17 4.676986 GCGTTCCTTCACCTTTTTCTTTGT 60.677 41.667 0.00 0.00 0.00 2.83
17 18 3.796717 GCGTTCCTTCACCTTTTTCTTTG 59.203 43.478 0.00 0.00 0.00 2.77
18 19 3.445805 TGCGTTCCTTCACCTTTTTCTTT 59.554 39.130 0.00 0.00 0.00 2.52
19 20 3.020984 TGCGTTCCTTCACCTTTTTCTT 58.979 40.909 0.00 0.00 0.00 2.52
20 21 2.650322 TGCGTTCCTTCACCTTTTTCT 58.350 42.857 0.00 0.00 0.00 2.52
21 22 3.430333 TTGCGTTCCTTCACCTTTTTC 57.570 42.857 0.00 0.00 0.00 2.29
28 29 3.004315 TGATTCCTTTTGCGTTCCTTCAC 59.996 43.478 0.00 0.00 0.00 3.18
38 39 7.019418 GCATTTCTTTCAATGATTCCTTTTGC 58.981 34.615 0.00 0.00 36.39 3.68
44 45 6.400568 TCTTGGCATTTCTTTCAATGATTCC 58.599 36.000 0.00 0.00 36.39 3.01
64 65 6.961576 TGTACCGGTTTTCTATGTTTTCTTG 58.038 36.000 15.04 0.00 0.00 3.02
66 67 6.527423 TCTGTACCGGTTTTCTATGTTTTCT 58.473 36.000 15.04 0.00 0.00 2.52
67 68 6.790285 TCTGTACCGGTTTTCTATGTTTTC 57.210 37.500 15.04 0.00 0.00 2.29
97 110 6.133356 TCATTGGACTTAGAACCTTTGGTTT 58.867 36.000 3.34 0.00 46.95 3.27
150 164 7.280428 TGTCGGTTTTCTATGTGTGTTTCTTTA 59.720 33.333 0.00 0.00 0.00 1.85
159 174 4.037089 GGGTTTTGTCGGTTTTCTATGTGT 59.963 41.667 0.00 0.00 0.00 3.72
180 195 4.457603 TGATTGGTTCAGTTTTCATACGGG 59.542 41.667 0.00 0.00 0.00 5.28
310 326 0.606401 CCTGAAGCGCTTCCCTGAAA 60.606 55.000 39.25 23.02 38.77 2.69
334 350 3.073503 GGAGTTTTGGTACCTACTTGGGT 59.926 47.826 14.36 0.00 42.86 4.51
351 367 2.781595 AATCGAGTTGCGCGGGAGTT 62.782 55.000 8.83 0.00 40.61 3.01
542 701 3.247442 CGACAAACTGTATGCCGACTTA 58.753 45.455 0.00 0.00 0.00 2.24
579 745 3.594603 AGGAACAATGTACGTCCAGAG 57.405 47.619 5.50 0.00 0.00 3.35
584 750 2.834689 CGCAAAGGAACAATGTACGTC 58.165 47.619 0.00 0.00 0.00 4.34
603 772 2.111756 GAAAAAGGATTATGCGCTGCG 58.888 47.619 19.17 19.17 0.00 5.18
612 781 8.477419 ACATTCTTGTTCTGGAAAAAGGATTA 57.523 30.769 11.84 0.00 32.72 1.75
680 849 1.781025 CGGAATGTGGTTGTGCGTGT 61.781 55.000 0.00 0.00 0.00 4.49
697 866 0.247974 CGAACTAGGAGCGTACACGG 60.248 60.000 3.67 0.00 40.23 4.94
732 903 7.093289 ACAGAGCTAACATACAGTATTGTTCCT 60.093 37.037 0.00 8.76 38.76 3.36
768 1064 1.028905 TGGTTACTGTGCAAAGTGGC 58.971 50.000 20.28 11.45 0.00 5.01
815 1111 4.831710 AGAGACTTTGTAACCTACTCCGTT 59.168 41.667 0.00 0.00 0.00 4.44
817 1113 6.506500 TTAGAGACTTTGTAACCTACTCCG 57.493 41.667 0.00 0.00 0.00 4.63
838 1134 5.042463 TGTGGTTGTTTCTGACAGGATTA 57.958 39.130 1.81 0.00 39.94 1.75
884 1183 3.958798 TCCTTATCTTTCTGGGTACGGAG 59.041 47.826 0.00 0.00 32.56 4.63
885 1184 3.985127 TCCTTATCTTTCTGGGTACGGA 58.015 45.455 0.00 0.00 0.00 4.69
886 1185 4.957684 ATCCTTATCTTTCTGGGTACGG 57.042 45.455 0.00 0.00 0.00 4.02
887 1186 5.758784 GGAAATCCTTATCTTTCTGGGTACG 59.241 44.000 0.00 0.00 33.02 3.67
935 1261 6.292381 GCACGAAATTAATACTCCTGCACTAG 60.292 42.308 12.54 0.00 0.00 2.57
1003 1329 9.749340 TCGTTCATATCTTCCTGGAGTATATAA 57.251 33.333 10.71 0.00 0.00 0.98
1154 1494 0.984961 CAGGAGGAGGAGGATGGCAA 60.985 60.000 0.00 0.00 0.00 4.52
1171 1511 3.535962 GAGGAGGAGGAGCGCCAG 61.536 72.222 9.88 0.00 36.29 4.85
1209 1549 0.110486 GCTGGGTTCTCTTGGTGGAA 59.890 55.000 0.00 0.00 0.00 3.53
1269 1609 1.025113 TGTTGTTGCCCGTGTCGAAA 61.025 50.000 0.00 0.00 0.00 3.46
1469 1809 2.431942 CGAAGTTCACCCCCGTCG 60.432 66.667 3.32 0.00 0.00 5.12
1662 2002 7.681939 ACGGTAGTAATGTGTGAAATCATTT 57.318 32.000 0.00 0.00 36.06 2.32
1674 2014 4.454678 TCCTCGATGTACGGTAGTAATGT 58.545 43.478 0.00 0.00 42.82 2.71
1768 2108 1.032014 GAAACAAACCCAGAGCTGCA 58.968 50.000 1.02 0.00 0.00 4.41
1773 2113 3.253432 GCTTGGTAGAAACAAACCCAGAG 59.747 47.826 0.00 0.00 31.68 3.35
1860 2203 1.339438 GCTCCTGCATTCCAGTTCAGA 60.339 52.381 0.00 0.00 40.06 3.27
1999 2342 1.218316 GTTGTAGACCTGGGCCTCG 59.782 63.158 4.53 0.00 0.00 4.63
2175 2519 4.932200 GTGATCTTAGAGGTGTCCACTTTG 59.068 45.833 0.00 0.00 0.00 2.77
2211 2556 9.838339 AGCTAAAGCAGAATTATAGAAAGCTAA 57.162 29.630 4.54 0.00 45.16 3.09
2239 2584 8.687824 AAAACACCAAGAAAGCATATTAATCG 57.312 30.769 0.00 0.00 0.00 3.34
2286 2631 9.059260 TGGTGTTTTTATTCAGAACTAAGTACC 57.941 33.333 0.00 0.00 0.00 3.34
2294 2639 7.491048 TGCTTTCTTGGTGTTTTTATTCAGAAC 59.509 33.333 0.00 0.00 0.00 3.01
2326 2672 9.237846 CTTTCTTGGTGTTTTTATTCAGAACTC 57.762 33.333 0.00 0.00 0.00 3.01
2437 2824 8.815912 ACCATGCTTTAATAATTCTTCTTTGGT 58.184 29.630 0.00 0.00 0.00 3.67
2468 2855 3.937814 TCTAGTTGTACATGGCCAAGTG 58.062 45.455 23.54 14.39 0.00 3.16
2556 2943 3.538634 AACAGGTAGGGCGATAAGAAC 57.461 47.619 0.00 0.00 0.00 3.01
2578 2965 6.201044 CGGTGAGAACTGCTATAATTACAAGG 59.799 42.308 0.00 0.00 0.00 3.61
2627 3014 1.271054 ACATCCCAGTGTTGTCTCTGC 60.271 52.381 0.00 0.00 34.88 4.26
2856 3245 5.769484 TGAACCAAACGCATTAGGTTAAA 57.231 34.783 0.00 0.00 43.94 1.52
2882 3271 5.810074 GCAGACTTCAAGTAAAAGCCAAAAA 59.190 36.000 0.00 0.00 0.00 1.94
2978 3367 7.397221 TGATTTCTTGATCTCCTTTCTTGCTA 58.603 34.615 0.00 0.00 0.00 3.49
2981 3370 8.027771 CCTTTGATTTCTTGATCTCCTTTCTTG 58.972 37.037 0.00 0.00 0.00 3.02
3026 3517 9.917129 TGTACCATATTGGAGTATAACATAACG 57.083 33.333 0.00 0.00 40.96 3.18
3037 3528 6.003950 GCCATATTGTGTACCATATTGGAGT 58.996 40.000 0.00 0.00 40.96 3.85
3038 3529 6.003326 TGCCATATTGTGTACCATATTGGAG 58.997 40.000 0.00 0.00 40.96 3.86
3039 3530 5.946486 TGCCATATTGTGTACCATATTGGA 58.054 37.500 0.00 0.00 40.96 3.53
3040 3531 6.647334 TTGCCATATTGTGTACCATATTGG 57.353 37.500 0.00 0.00 45.02 3.16
3041 3532 6.016024 AGCTTGCCATATTGTGTACCATATTG 60.016 38.462 0.00 0.00 0.00 1.90
3042 3533 6.070656 AGCTTGCCATATTGTGTACCATATT 58.929 36.000 0.00 0.00 0.00 1.28
3043 3534 5.634118 AGCTTGCCATATTGTGTACCATAT 58.366 37.500 0.00 0.00 0.00 1.78
3044 3535 5.047566 AGCTTGCCATATTGTGTACCATA 57.952 39.130 0.00 0.00 0.00 2.74
3045 3536 3.885297 GAGCTTGCCATATTGTGTACCAT 59.115 43.478 0.00 0.00 0.00 3.55
3046 3537 3.278574 GAGCTTGCCATATTGTGTACCA 58.721 45.455 0.00 0.00 0.00 3.25
3047 3538 3.278574 TGAGCTTGCCATATTGTGTACC 58.721 45.455 0.00 0.00 0.00 3.34
3048 3539 3.242870 GCTGAGCTTGCCATATTGTGTAC 60.243 47.826 0.00 0.00 0.00 2.90
3049 3540 2.945008 GCTGAGCTTGCCATATTGTGTA 59.055 45.455 0.00 0.00 0.00 2.90
3092 3583 6.569780 TGCCTTTGACTTTTTAGTTTCCTTC 58.430 36.000 0.00 0.00 0.00 3.46
3123 3614 5.160607 TGAGTTTTCATAACCCGATCACT 57.839 39.130 0.00 0.00 0.00 3.41
3138 3629 5.308237 TCCCTTCTCTAGCTTCTTGAGTTTT 59.692 40.000 0.00 0.00 35.49 2.43
3145 3636 4.421131 TCAGTTCCCTTCTCTAGCTTCTT 58.579 43.478 0.00 0.00 0.00 2.52
3196 3693 7.220030 ACATTCACAAGTTACAGATCTGAAGT 58.780 34.615 29.27 17.12 0.00 3.01
3197 3694 7.664082 ACATTCACAAGTTACAGATCTGAAG 57.336 36.000 29.27 13.03 0.00 3.02
3198 3695 9.154847 CATACATTCACAAGTTACAGATCTGAA 57.845 33.333 29.27 15.31 0.00 3.02
3199 3696 7.765819 CCATACATTCACAAGTTACAGATCTGA 59.234 37.037 29.27 10.06 0.00 3.27
3200 3697 7.765819 TCCATACATTCACAAGTTACAGATCTG 59.234 37.037 21.37 21.37 0.00 2.90
3201 3698 7.851228 TCCATACATTCACAAGTTACAGATCT 58.149 34.615 0.00 0.00 0.00 2.75
3355 3868 5.868801 ACTGTGGTTTGTTTTGAACTCATTG 59.131 36.000 0.00 0.00 0.00 2.82
3575 4088 4.981806 TGACCCTTCAACAAAGAGTTTG 57.018 40.909 0.00 0.00 45.95 2.93
3576 4089 5.993748 TTTGACCCTTCAACAAAGAGTTT 57.006 34.783 0.00 0.00 41.64 2.66
3577 4090 5.621329 CGTTTTGACCCTTCAACAAAGAGTT 60.621 40.000 0.00 0.00 41.64 3.01
3578 4091 4.142469 CGTTTTGACCCTTCAACAAAGAGT 60.142 41.667 0.00 0.00 41.64 3.24
3579 4092 4.351192 CGTTTTGACCCTTCAACAAAGAG 58.649 43.478 0.00 0.00 41.64 2.85
3580 4093 3.428316 GCGTTTTGACCCTTCAACAAAGA 60.428 43.478 0.00 0.00 41.64 2.52
3581 4094 2.857748 GCGTTTTGACCCTTCAACAAAG 59.142 45.455 0.00 0.00 41.64 2.77
3587 4100 1.757682 AAGTGCGTTTTGACCCTTCA 58.242 45.000 0.00 0.00 0.00 3.02
3698 4211 1.614903 TGTGGAAGCATGCCTTTTGAG 59.385 47.619 15.66 0.00 31.46 3.02


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

AutoCloner maintained by Alex Coulton.