Multiple sequence alignment - TraesCS3A01G156200

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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 TraesCS3A01G156200 chr3A 100.000 8386 0 0 1 8386 150717644 150726029 0.000000e+00 15487
1 TraesCS3A01G156200 chr3B 96.967 4187 80 17 3576 7725 193617583 193621759 0.000000e+00 6985
2 TraesCS3A01G156200 chr3B 97.143 1365 23 3 2216 3579 193615466 193616815 0.000000e+00 2290
3 TraesCS3A01G156200 chr3B 93.246 1140 45 11 575 1694 193614335 193615462 0.000000e+00 1650
4 TraesCS3A01G156200 chr3B 92.542 590 17 8 1 572 193613448 193614028 0.000000e+00 821
5 TraesCS3A01G156200 chr3B 92.745 510 20 7 7882 8386 193622131 193622628 0.000000e+00 721
6 TraesCS3A01G156200 chr3B 94.118 119 7 0 7723 7841 193622031 193622149 1.860000e-41 182
7 TraesCS3A01G156200 chr3D 95.556 3195 99 20 3791 6962 135382168 135385342 0.000000e+00 5073
8 TraesCS3A01G156200 chr3D 93.692 1617 61 16 575 2166 135379155 135380755 0.000000e+00 2383
9 TraesCS3A01G156200 chr3D 98.678 1059 14 0 2395 3453 135381113 135382171 0.000000e+00 1879
10 TraesCS3A01G156200 chr3D 92.025 790 33 12 6960 7725 135385444 135386227 0.000000e+00 1083
11 TraesCS3A01G156200 chr3D 93.537 588 16 9 1 577 135378285 135378861 0.000000e+00 856
12 TraesCS3A01G156200 chr3D 94.444 504 15 5 7886 8386 135386598 135387091 0.000000e+00 763
13 TraesCS3A01G156200 chr3D 95.062 162 7 1 2163 2324 135380835 135380995 3.890000e-63 254
14 TraesCS3A01G156200 chr3D 95.062 81 2 1 2317 2397 135380942 135381020 8.840000e-25 126


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 TraesCS3A01G156200 chr3A 150717644 150726029 8385 False 15487.000000 15487 100.000000 1 8386 1 chr3A.!!$F1 8385
1 TraesCS3A01G156200 chr3B 193613448 193622628 9180 False 2108.166667 6985 94.460167 1 8386 6 chr3B.!!$F1 8385
2 TraesCS3A01G156200 chr3D 135378285 135387091 8806 False 1552.125000 5073 94.757000 1 8386 8 chr3D.!!$F1 8385

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
694 1018 0.107800 CATCTCTCCTGGCTGTGGTG 60.108 60.000 0.00 0.0 0.00 4.17 F
760 1090 0.327259 AGCCTTAAAACTCCCCGACC 59.673 55.000 0.00 0.0 0.00 4.79 F
1876 2244 0.317479 GCACGTATCCGCCCTAGATT 59.683 55.000 0.00 0.0 37.70 2.40 F
1990 2358 1.550327 TGAGTGTTTTGTTGCACCCA 58.450 45.000 0.00 0.0 36.35 4.51 F
2722 3269 1.667724 GCTATGCGTCAGCTTGTTCAT 59.332 47.619 0.00 0.0 45.42 2.57 F
3399 3946 3.118000 CAGGTGAGTTTAGGATAACCCCC 60.118 52.174 0.00 0.0 36.73 5.40 F
3517 4064 4.065088 ACAGTGACGAGTGCATATTTTGT 58.935 39.130 0.00 0.0 0.00 2.83 F
3720 5039 4.593206 AGTTCAGAACTGTATGAAGTGGGA 59.407 41.667 15.41 0.0 37.27 4.37 F
5214 6550 1.774254 TCCTTGGTCAAAGCTCCTTCA 59.226 47.619 0.00 0.0 34.24 3.02 F
6499 7849 0.030638 AACATGCACGTTGTTGAGGC 59.969 50.000 0.00 0.0 36.02 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1597 1963 0.247185 ATGGAGCGGCAACCAATTTG 59.753 50.000 19.30 0.00 39.69 2.32 R
2722 3269 1.422402 GGGTCAGGGTGTCCTTTGTAA 59.578 52.381 0.00 0.00 42.67 2.41 R
3478 4025 0.681733 TGTCACTTGTCAGAGGAGCC 59.318 55.000 0.00 0.00 0.00 4.70 R
3865 5184 8.278408 GCAATATCACTGATACTTGTATGTGTG 58.722 37.037 0.58 12.41 0.00 3.82 R
4240 5572 1.986575 GCCTTCATGCGAACCTGAGC 61.987 60.000 0.00 0.00 0.00 4.26 R
4740 6076 0.250038 TGCTCGCTGCTTTCTTGAGT 60.250 50.000 0.00 0.00 43.37 3.41 R
4950 6286 2.101415 TCAGAGAGTTATCATGCACGGG 59.899 50.000 0.00 0.00 0.00 5.28 R
5239 6575 3.118811 ACCAAACATTTGTGGTGACAAGG 60.119 43.478 0.00 0.00 46.53 3.61 R
7204 8663 1.467734 GCAGATGCTTTGAGTGTCAGG 59.532 52.381 0.00 0.00 38.21 3.86 R
7750 9508 1.229177 TCACTGGCAGACCTAGGCA 60.229 57.895 23.66 0.00 39.41 4.75 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
61 62 0.613853 TCCCGGTCTTTGACGAGGAT 60.614 55.000 0.00 0.00 34.56 3.24
127 128 2.822255 GCCGATTTGCCCGTGCTA 60.822 61.111 0.00 0.00 38.71 3.49
228 229 2.440627 TGGTGTAGCGAGGGAGATAGTA 59.559 50.000 0.00 0.00 0.00 1.82
229 230 3.075884 GGTGTAGCGAGGGAGATAGTAG 58.924 54.545 0.00 0.00 0.00 2.57
230 231 3.496515 GGTGTAGCGAGGGAGATAGTAGT 60.497 52.174 0.00 0.00 0.00 2.73
374 376 8.091449 GGGGTCAGATAGAATAGAATACAGTTG 58.909 40.741 0.00 0.00 0.00 3.16
381 383 6.567602 AGAATAGAATACAGTTGGGCTCTT 57.432 37.500 0.00 0.00 0.00 2.85
507 527 7.742089 CAGAGTTAATTTCGTTTCTGACATGAC 59.258 37.037 0.00 0.00 35.28 3.06
512 532 5.666969 TTTCGTTTCTGACATGACGATTT 57.333 34.783 0.00 0.00 43.09 2.17
513 533 5.666969 TTCGTTTCTGACATGACGATTTT 57.333 34.783 0.00 0.00 43.09 1.82
514 534 5.264060 TCGTTTCTGACATGACGATTTTC 57.736 39.130 0.00 0.00 39.33 2.29
573 593 8.424918 AGAATTGGAGTAGACTGGTTATATGTG 58.575 37.037 0.00 0.00 0.00 3.21
611 935 0.766674 TGTTGCCCCTGTCCTACTGT 60.767 55.000 0.00 0.00 0.00 3.55
658 982 7.360575 ACCACGTGATATACTGAAACTTTTC 57.639 36.000 19.30 0.00 37.69 2.29
693 1017 0.546267 ACATCTCTCCTGGCTGTGGT 60.546 55.000 0.00 0.00 0.00 4.16
694 1018 0.107800 CATCTCTCCTGGCTGTGGTG 60.108 60.000 0.00 0.00 0.00 4.17
695 1019 0.546267 ATCTCTCCTGGCTGTGGTGT 60.546 55.000 0.00 0.00 0.00 4.16
697 1021 2.033141 CTCCTGGCTGTGGTGTGG 59.967 66.667 0.00 0.00 0.00 4.17
698 1022 4.269523 TCCTGGCTGTGGTGTGGC 62.270 66.667 0.00 0.00 0.00 5.01
701 1031 4.584518 TGGCTGTGGTGTGGCTGG 62.585 66.667 0.00 0.00 0.00 4.85
703 1033 3.289834 GCTGTGGTGTGGCTGGTG 61.290 66.667 0.00 0.00 0.00 4.17
758 1088 2.963599 AAAGCCTTAAAACTCCCCGA 57.036 45.000 0.00 0.00 0.00 5.14
759 1089 2.195741 AAGCCTTAAAACTCCCCGAC 57.804 50.000 0.00 0.00 0.00 4.79
760 1090 0.327259 AGCCTTAAAACTCCCCGACC 59.673 55.000 0.00 0.00 0.00 4.79
761 1091 0.327259 GCCTTAAAACTCCCCGACCT 59.673 55.000 0.00 0.00 0.00 3.85
762 1092 1.949079 GCCTTAAAACTCCCCGACCTG 60.949 57.143 0.00 0.00 0.00 4.00
956 1290 4.862823 GCGGTAGCCTCCCTCCCT 62.863 72.222 0.00 0.00 37.42 4.20
957 1291 2.522193 CGGTAGCCTCCCTCCCTC 60.522 72.222 0.00 0.00 0.00 4.30
958 1292 2.122769 GGTAGCCTCCCTCCCTCC 60.123 72.222 0.00 0.00 0.00 4.30
959 1293 2.696893 GTAGCCTCCCTCCCTCCA 59.303 66.667 0.00 0.00 0.00 3.86
1316 1671 6.723131 CGATGATCGTTCAGTATAGGACTA 57.277 41.667 6.68 0.00 33.73 2.59
1401 1756 4.952071 TTCCTAGAGCATTCTGATCTGG 57.048 45.455 5.22 2.28 43.72 3.86
1405 1760 3.773418 AGAGCATTCTGATCTGGATGG 57.227 47.619 19.36 4.96 42.17 3.51
1427 1783 6.342906 TGGTGTATAGTTACAGGGATTTTCG 58.657 40.000 0.00 0.00 38.98 3.46
1480 1836 1.967319 TGCAGGGAAATAGGCGATTC 58.033 50.000 0.00 0.00 0.00 2.52
1481 1837 1.211703 TGCAGGGAAATAGGCGATTCA 59.788 47.619 0.00 0.00 0.00 2.57
1516 1872 7.179460 AGGATGGATATAGGAAATTTGGGTT 57.821 36.000 0.00 0.00 0.00 4.11
1518 1874 6.211384 GGATGGATATAGGAAATTTGGGTTGG 59.789 42.308 0.00 0.00 0.00 3.77
1519 1875 6.098716 TGGATATAGGAAATTTGGGTTGGT 57.901 37.500 0.00 0.00 0.00 3.67
1523 1879 8.803235 GGATATAGGAAATTTGGGTTGGTTATC 58.197 37.037 0.00 0.00 0.00 1.75
1580 1946 2.778299 GTAGTGAGGTGTGGCAATCAA 58.222 47.619 0.00 0.00 0.00 2.57
1597 1963 2.778299 TCAACACTATGTCTGGCCAAC 58.222 47.619 7.01 9.02 0.00 3.77
1698 2064 0.982852 TAGCTACTGCCACCCTGCAT 60.983 55.000 0.00 0.00 41.16 3.96
1709 2075 2.238646 CCACCCTGCATACCTTCTAACA 59.761 50.000 0.00 0.00 0.00 2.41
1715 2081 4.442192 CCTGCATACCTTCTAACACTCTCC 60.442 50.000 0.00 0.00 0.00 3.71
1725 2091 1.789576 AACACTCTCCGCCCCCAAAT 61.790 55.000 0.00 0.00 0.00 2.32
1804 2170 9.895507 ATATAGCTCCTAATGATGGATATCACT 57.104 33.333 4.83 0.00 45.54 3.41
1813 2179 5.541953 TGATGGATATCACTGTCCTTCTG 57.458 43.478 4.83 0.00 38.37 3.02
1814 2180 3.827008 TGGATATCACTGTCCTTCTGC 57.173 47.619 4.83 0.00 33.93 4.26
1815 2181 3.378512 TGGATATCACTGTCCTTCTGCT 58.621 45.455 4.83 0.00 33.93 4.24
1816 2182 3.776969 TGGATATCACTGTCCTTCTGCTT 59.223 43.478 4.83 0.00 33.93 3.91
1817 2183 4.962362 TGGATATCACTGTCCTTCTGCTTA 59.038 41.667 4.83 0.00 33.93 3.09
1859 2227 0.961019 GTCCATCCAACTTGCTTGCA 59.039 50.000 0.00 0.00 0.00 4.08
1876 2244 0.317479 GCACGTATCCGCCCTAGATT 59.683 55.000 0.00 0.00 37.70 2.40
1900 2268 5.043737 TGGGTTTTAGAGTAACACTTGCT 57.956 39.130 0.00 0.00 30.25 3.91
1901 2269 5.442391 TGGGTTTTAGAGTAACACTTGCTT 58.558 37.500 0.00 0.00 30.25 3.91
1902 2270 5.298276 TGGGTTTTAGAGTAACACTTGCTTG 59.702 40.000 0.00 0.00 30.25 4.01
1903 2271 5.212934 GGTTTTAGAGTAACACTTGCTTGC 58.787 41.667 0.00 0.00 0.00 4.01
1904 2272 5.212934 GTTTTAGAGTAACACTTGCTTGCC 58.787 41.667 0.00 0.00 0.00 4.52
1905 2273 2.638480 AGAGTAACACTTGCTTGCCA 57.362 45.000 0.00 0.00 0.00 4.92
1911 2279 4.582656 AGTAACACTTGCTTGCCAATTACA 59.417 37.500 0.00 0.00 32.61 2.41
1990 2358 1.550327 TGAGTGTTTTGTTGCACCCA 58.450 45.000 0.00 0.00 36.35 4.51
2199 2651 3.456277 GGGTAGTGATCAACTCCAATCCT 59.544 47.826 0.00 0.00 40.56 3.24
2207 2659 7.512058 AGTGATCAACTCCAATCCTAGTGATAT 59.488 37.037 0.00 0.00 31.64 1.63
2722 3269 1.667724 GCTATGCGTCAGCTTGTTCAT 59.332 47.619 0.00 0.00 45.42 2.57
3302 3849 4.953667 TCGAGATGCTCTGCAGATATTTT 58.046 39.130 18.63 3.27 43.65 1.82
3399 3946 3.118000 CAGGTGAGTTTAGGATAACCCCC 60.118 52.174 0.00 0.00 36.73 5.40
3449 3996 8.655935 ACTTTAGATCATTTCCTTTTGTGGAT 57.344 30.769 0.00 0.00 35.83 3.41
3517 4064 4.065088 ACAGTGACGAGTGCATATTTTGT 58.935 39.130 0.00 0.00 0.00 2.83
3720 5039 4.593206 AGTTCAGAACTGTATGAAGTGGGA 59.407 41.667 15.41 0.00 37.27 4.37
3991 5320 5.316167 TGTCTGGATTTGTGATGTTTAGCT 58.684 37.500 0.00 0.00 0.00 3.32
4132 5464 5.352846 TGGTACACCATTTATTCACATCGTG 59.647 40.000 0.00 0.00 42.01 4.35
4153 5485 5.005394 CGTGAATTCTATTGGTTAGGTCACG 59.995 44.000 7.05 7.82 43.38 4.35
4216 5548 6.228273 TGCTTTTCGTCTTGTTCTGATAAG 57.772 37.500 0.00 0.00 0.00 1.73
4740 6076 7.836685 AGGATGATCTAGTAACTCAGAGTTCAA 59.163 37.037 19.51 0.00 39.51 2.69
5115 6451 5.107065 CCTGGACTAAAAGCAGAAACTAACG 60.107 44.000 0.00 0.00 0.00 3.18
5214 6550 1.774254 TCCTTGGTCAAAGCTCCTTCA 59.226 47.619 0.00 0.00 34.24 3.02
5239 6575 3.611766 ACAGGTTCCTATGCAGTACAC 57.388 47.619 0.00 0.00 0.00 2.90
5629 6965 1.344763 CAGTCCTCCGAGTTCCAACTT 59.655 52.381 0.00 0.00 39.88 2.66
5679 7015 2.863401 ATCACTAGCAATCGTACGCA 57.137 45.000 11.24 0.00 0.00 5.24
5871 7208 7.323656 GCCATGTGTGAATAATTAAGCGATTAC 59.676 37.037 0.00 0.00 0.00 1.89
5938 7275 1.665735 GCATTTGCGAACCATGTTCGT 60.666 47.619 24.76 7.59 43.24 3.85
5983 7321 5.730550 AGAAAATACAGTTCTCGTGGCATA 58.269 37.500 0.00 0.00 29.04 3.14
6369 7718 8.319143 TGGTTTATCTAACTGTTAAGTTGAGC 57.681 34.615 1.46 0.00 46.30 4.26
6382 7731 8.306680 TGTTAAGTTGAGCTGAAGTAATACAC 57.693 34.615 0.00 0.00 0.00 2.90
6499 7849 0.030638 AACATGCACGTTGTTGAGGC 59.969 50.000 0.00 0.00 36.02 4.70
6512 7862 5.456265 GTTGTTGAGGCATTTCTTCTCTTC 58.544 41.667 0.00 0.00 0.00 2.87
6783 8133 6.491403 ACAGAATTGGAGTACTTGATTTTGCT 59.509 34.615 0.00 0.00 0.00 3.91
6981 8435 5.940192 AACTGCGACACTCATTTTGATTA 57.060 34.783 0.00 0.00 0.00 1.75
7204 8663 4.970003 GCATAAGAATGTATTGTTGCCGTC 59.030 41.667 0.00 0.00 35.38 4.79
7337 8799 7.475015 TGTTCAGAATTTTGACAAGAACAGAG 58.525 34.615 12.05 0.00 38.95 3.35
7442 8908 4.201980 GCATGCAGCAGATGTTGAAGATTA 60.202 41.667 14.21 0.00 44.79 1.75
7618 9095 9.269415 CGGGATTTTATCTTTTGTTACTTTACG 57.731 33.333 0.00 0.00 0.00 3.18
7655 9133 9.541143 TTTCTTTTGATGGGAATTGTAAAGTTC 57.459 29.630 0.00 0.00 0.00 3.01
7679 9157 8.736751 TCGTTAATTTAAGAAAGGTGAAATGC 57.263 30.769 0.00 0.00 0.00 3.56
7681 9159 8.638565 CGTTAATTTAAGAAAGGTGAAATGCTG 58.361 33.333 0.00 0.00 0.00 4.41
7688 9166 4.279420 AGAAAGGTGAAATGCTGGAAGAAC 59.721 41.667 0.00 0.00 34.07 3.01
7704 9182 7.579339 GCTGGAAGAACAATCATATTTTTGGGA 60.579 37.037 0.79 0.00 34.07 4.37
7709 9187 8.206126 AGAACAATCATATTTTTGGGAAAGGT 57.794 30.769 0.79 0.00 0.00 3.50
7810 9568 5.357314 TCAAAAATATTACAATCCCGCGGAA 59.643 36.000 30.73 6.63 34.34 4.30
7832 9590 7.797123 CGGAATAGTACAACAGAAAACAGAAAC 59.203 37.037 0.00 0.00 0.00 2.78
7833 9591 8.617809 GGAATAGTACAACAGAAAACAGAAACA 58.382 33.333 0.00 0.00 0.00 2.83
7836 9594 9.950680 ATAGTACAACAGAAAACAGAAACATTG 57.049 29.630 0.00 0.00 0.00 2.82
7837 9595 6.751888 AGTACAACAGAAAACAGAAACATTGC 59.248 34.615 0.00 0.00 0.00 3.56
7838 9596 5.477510 ACAACAGAAAACAGAAACATTGCA 58.522 33.333 0.00 0.00 0.00 4.08
7839 9597 6.108015 ACAACAGAAAACAGAAACATTGCAT 58.892 32.000 0.00 0.00 0.00 3.96
7840 9598 7.264221 ACAACAGAAAACAGAAACATTGCATA 58.736 30.769 0.00 0.00 0.00 3.14
7841 9599 7.222611 ACAACAGAAAACAGAAACATTGCATAC 59.777 33.333 0.00 0.00 0.00 2.39
7842 9600 5.914635 ACAGAAAACAGAAACATTGCATACG 59.085 36.000 0.00 0.00 0.00 3.06
7843 9601 5.914635 CAGAAAACAGAAACATTGCATACGT 59.085 36.000 0.00 0.00 0.00 3.57
7844 9602 7.075121 CAGAAAACAGAAACATTGCATACGTA 58.925 34.615 0.00 0.00 0.00 3.57
7845 9603 7.589587 CAGAAAACAGAAACATTGCATACGTAA 59.410 33.333 0.00 0.00 0.00 3.18
7846 9604 8.132362 AGAAAACAGAAACATTGCATACGTAAA 58.868 29.630 0.00 0.00 0.00 2.01
7847 9605 8.635877 AAAACAGAAACATTGCATACGTAAAA 57.364 26.923 0.00 0.00 0.00 1.52
7848 9606 8.635877 AAACAGAAACATTGCATACGTAAAAA 57.364 26.923 0.00 0.00 0.00 1.94
7874 9632 5.536554 AAGAGACAGAAACATTGCATACG 57.463 39.130 0.00 0.00 0.00 3.06
7875 9633 4.569943 AGAGACAGAAACATTGCATACGT 58.430 39.130 0.00 0.00 0.00 3.57
7876 9634 5.720202 AGAGACAGAAACATTGCATACGTA 58.280 37.500 0.00 0.00 0.00 3.57
7877 9635 6.163476 AGAGACAGAAACATTGCATACGTAA 58.837 36.000 0.00 0.00 0.00 3.18
7878 9636 6.649141 AGAGACAGAAACATTGCATACGTAAA 59.351 34.615 0.00 0.00 0.00 2.01
7879 9637 7.172532 AGAGACAGAAACATTGCATACGTAAAA 59.827 33.333 0.00 0.00 0.00 1.52
7880 9638 7.644490 AGACAGAAACATTGCATACGTAAAAA 58.356 30.769 0.00 0.00 0.00 1.94
8074 9834 5.128171 CACCAACTACCAATACTACTGGCTA 59.872 44.000 0.00 0.00 37.48 3.93
8080 9840 9.998106 AACTACCAATACTACTGGCTAATATTG 57.002 33.333 0.00 0.00 37.48 1.90
8254 10019 1.079057 GCTCGGTTTCCCCTCTGAC 60.079 63.158 0.00 0.00 0.00 3.51
8282 10047 2.447244 CATCGACTATGGAGGAAGCC 57.553 55.000 0.00 0.00 31.38 4.35
8348 10113 4.037089 ACGGGACCTGTTTGTATTGTTTTC 59.963 41.667 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 0.179023 TGCAGGTCTTGTGCATGTCA 60.179 50.000 0.00 0.00 45.96 3.58
228 229 4.956085 TGTGCATTGTTGTGTCTACTACT 58.044 39.130 0.00 0.00 34.31 2.57
229 230 5.862924 ATGTGCATTGTTGTGTCTACTAC 57.137 39.130 0.00 0.00 33.89 2.73
230 231 6.239908 CAATGTGCATTGTTGTGTCTACTA 57.760 37.500 14.75 0.00 42.32 1.82
349 351 8.091449 CCAACTGTATTCTATTCTATCTGACCC 58.909 40.741 0.00 0.00 0.00 4.46
374 376 0.543749 AGGTATGACAGCAAGAGCCC 59.456 55.000 0.00 0.00 43.56 5.19
417 427 4.729227 TGCAGTACTTCGGATGACAATA 57.271 40.909 0.00 0.00 0.00 1.90
418 428 3.610040 TGCAGTACTTCGGATGACAAT 57.390 42.857 0.00 0.00 0.00 2.71
419 429 3.394674 TTGCAGTACTTCGGATGACAA 57.605 42.857 0.00 0.00 0.00 3.18
489 509 5.862924 AATCGTCATGTCAGAAACGAAAT 57.137 34.783 8.83 0.15 45.93 2.17
497 517 8.777865 ATAAAGAAGAAAATCGTCATGTCAGA 57.222 30.769 0.00 0.00 0.00 3.27
534 554 6.155475 ACTCCAATTCTAGCTCATACTCAC 57.845 41.667 0.00 0.00 0.00 3.51
611 935 2.554462 GAGATGAGATGCTACACCGCTA 59.446 50.000 0.00 0.00 0.00 4.26
664 988 3.431486 CCAGGAGAGATGTAGTGGAAAGC 60.431 52.174 0.00 0.00 0.00 3.51
674 998 0.546267 ACCACAGCCAGGAGAGATGT 60.546 55.000 0.00 0.00 0.00 3.06
693 1017 2.431683 GAGGAAGCACCAGCCACA 59.568 61.111 2.96 0.00 43.56 4.17
694 1018 2.360475 GGAGGAAGCACCAGCCAC 60.360 66.667 2.96 0.00 43.56 5.01
695 1019 3.650950 GGGAGGAAGCACCAGCCA 61.651 66.667 11.57 0.00 43.56 4.75
701 1031 4.373116 TGTCGCGGGAGGAAGCAC 62.373 66.667 6.13 0.00 0.00 4.40
703 1033 3.708220 CTCTGTCGCGGGAGGAAGC 62.708 68.421 6.13 0.00 0.00 3.86
758 1088 4.954118 TGGCGGGTCAGGTCAGGT 62.954 66.667 0.00 0.00 0.00 4.00
759 1089 4.394712 GTGGCGGGTCAGGTCAGG 62.395 72.222 0.00 0.00 0.00 3.86
760 1090 3.302347 GAGTGGCGGGTCAGGTCAG 62.302 68.421 0.00 0.00 0.00 3.51
761 1091 3.311110 GAGTGGCGGGTCAGGTCA 61.311 66.667 0.00 0.00 0.00 4.02
762 1092 4.436998 CGAGTGGCGGGTCAGGTC 62.437 72.222 0.00 0.00 36.03 3.85
866 1196 2.361771 GGTGTACGGGGAGGAGGA 59.638 66.667 0.00 0.00 0.00 3.71
901 1235 1.152943 CGGGGAGGTCGAGATCTGA 60.153 63.158 0.00 0.00 0.00 3.27
957 1291 3.995809 TAAGGGAGGGCGGGAGTGG 62.996 68.421 0.00 0.00 0.00 4.00
958 1292 2.365105 TAAGGGAGGGCGGGAGTG 60.365 66.667 0.00 0.00 0.00 3.51
959 1293 2.041819 CTAAGGGAGGGCGGGAGT 60.042 66.667 0.00 0.00 0.00 3.85
1087 1421 3.820467 CAGATCTCCTCGAGCTTGTAGAT 59.180 47.826 6.99 9.20 35.90 1.98
1296 1634 5.374071 TGCTAGTCCTATACTGAACGATCA 58.626 41.667 0.00 0.00 39.39 2.92
1341 1696 1.933853 GACCGCGAAACTAATCAGCAT 59.066 47.619 8.23 0.00 0.00 3.79
1401 1756 7.170998 CGAAAATCCCTGTAACTATACACCATC 59.829 40.741 0.00 0.00 37.11 3.51
1405 1760 7.222224 CACTCGAAAATCCCTGTAACTATACAC 59.778 40.741 0.00 0.00 37.11 2.90
1480 1836 7.775093 TCCTATATCCATCCTTTCAACACTTTG 59.225 37.037 0.00 0.00 0.00 2.77
1481 1837 7.872138 TCCTATATCCATCCTTTCAACACTTT 58.128 34.615 0.00 0.00 0.00 2.66
1494 1850 6.782494 ACCAACCCAAATTTCCTATATCCATC 59.218 38.462 0.00 0.00 0.00 3.51
1516 1872 6.995427 CCATACCTATGGCTTGGGATAACCA 61.995 48.000 9.83 0.00 46.53 3.67
1518 1874 4.589908 CCATACCTATGGCTTGGGATAAC 58.410 47.826 9.83 0.00 45.92 1.89
1519 1875 4.927267 CCATACCTATGGCTTGGGATAA 57.073 45.455 9.83 0.00 45.92 1.75
1544 1900 6.043012 ACCTCACTACGAGTAGGTATGATAGT 59.957 42.308 14.00 7.08 40.57 2.12
1580 1946 2.949177 TTGTTGGCCAGACATAGTGT 57.051 45.000 17.71 0.00 0.00 3.55
1597 1963 0.247185 ATGGAGCGGCAACCAATTTG 59.753 50.000 19.30 0.00 39.69 2.32
1698 2064 2.097825 GGCGGAGAGTGTTAGAAGGTA 58.902 52.381 0.00 0.00 0.00 3.08
1709 2075 2.998949 GATTTGGGGGCGGAGAGT 59.001 61.111 0.00 0.00 0.00 3.24
1715 2081 1.453015 TTCATCCGATTTGGGGGCG 60.453 57.895 0.00 0.00 38.76 6.13
1725 2091 3.576982 ACAGAAGGTAACAGTTCATCCGA 59.423 43.478 0.00 0.00 41.41 4.55
1778 2144 9.895507 AGTGATATCCATCATTAGGAGCTATAT 57.104 33.333 0.00 0.00 43.03 0.86
1829 2197 4.658063 AGTTGGATGGACGGAACATTTTA 58.342 39.130 0.00 0.00 0.00 1.52
1831 2199 3.154827 AGTTGGATGGACGGAACATTT 57.845 42.857 0.00 0.00 0.00 2.32
1876 2244 5.061179 GCAAGTGTTACTCTAAAACCCAGA 58.939 41.667 0.00 0.00 0.00 3.86
1904 2272 9.492973 AATTCTTCAGGAAAACCAATGTAATTG 57.507 29.630 0.00 0.00 44.48 2.32
1911 2279 7.243604 TGCATAATTCTTCAGGAAAACCAAT 57.756 32.000 0.00 0.00 37.49 3.16
2090 2459 4.021981 TCACATCCTACTTCACTGTGTGAG 60.022 45.833 7.79 9.58 43.69 3.51
2722 3269 1.422402 GGGTCAGGGTGTCCTTTGTAA 59.578 52.381 0.00 0.00 42.67 2.41
3302 3849 3.137544 TCCAGTTTGGAGGCTTCTGTTAA 59.862 43.478 0.00 0.00 42.67 2.01
3399 3946 7.870954 GTCCAAAGGTTAAAATAGACCCAAAAG 59.129 37.037 0.00 0.00 36.57 2.27
3460 4007 4.458989 GGAGCCAAGACACATAATTCACAA 59.541 41.667 0.00 0.00 0.00 3.33
3473 4020 1.346068 ACTTGTCAGAGGAGCCAAGAC 59.654 52.381 5.34 0.00 38.11 3.01
3478 4025 0.681733 TGTCACTTGTCAGAGGAGCC 59.318 55.000 0.00 0.00 0.00 4.70
3600 4919 9.976511 ATGCATCAAAGAAGATACCAAATATTG 57.023 29.630 0.00 0.00 0.00 1.90
3613 4932 9.582431 AAATGAAATCAGTATGCATCAAAGAAG 57.418 29.630 0.19 0.00 34.76 2.85
3614 4933 9.577110 GAAATGAAATCAGTATGCATCAAAGAA 57.423 29.630 0.19 0.00 34.76 2.52
3615 4934 8.963725 AGAAATGAAATCAGTATGCATCAAAGA 58.036 29.630 0.19 0.00 34.76 2.52
3864 5183 9.317936 CAATATCACTGATACTTGTATGTGTGT 57.682 33.333 0.58 9.88 0.00 3.72
3865 5184 8.278408 GCAATATCACTGATACTTGTATGTGTG 58.722 37.037 0.58 12.41 0.00 3.82
4077 5409 6.869315 TCAAATAAGATCAACAAACGTCCA 57.131 33.333 0.00 0.00 0.00 4.02
4132 5464 5.293569 CCACGTGACCTAACCAATAGAATTC 59.706 44.000 19.30 0.00 33.04 2.17
4216 5548 8.504005 AGCAGTAAACAAACACATATTCAGTAC 58.496 33.333 0.00 0.00 0.00 2.73
4229 5561 3.848554 GCGAACCTGAGCAGTAAACAAAC 60.849 47.826 0.00 0.00 0.00 2.93
4230 5562 2.289547 GCGAACCTGAGCAGTAAACAAA 59.710 45.455 0.00 0.00 0.00 2.83
4240 5572 1.986575 GCCTTCATGCGAACCTGAGC 61.987 60.000 0.00 0.00 0.00 4.26
4314 5646 6.486320 TGTTCTCACTGAAATATGAAGCAACA 59.514 34.615 0.00 0.00 36.30 3.33
4740 6076 0.250038 TGCTCGCTGCTTTCTTGAGT 60.250 50.000 0.00 0.00 43.37 3.41
4767 6103 7.168219 ACTGAAGAAGCATAATTACTGTTCCA 58.832 34.615 0.00 0.00 0.00 3.53
4783 6119 5.862323 CCAAGCAAATCATCAACTGAAGAAG 59.138 40.000 0.00 0.00 37.44 2.85
4950 6286 2.101415 TCAGAGAGTTATCATGCACGGG 59.899 50.000 0.00 0.00 0.00 5.28
5115 6451 5.940470 AGAACTGTGAACCATTGAGATTACC 59.060 40.000 0.00 0.00 0.00 2.85
5214 6550 4.307032 ACTGCATAGGAACCTGTTGATT 57.693 40.909 3.36 0.00 0.00 2.57
5239 6575 3.118811 ACCAAACATTTGTGGTGACAAGG 60.119 43.478 0.00 0.00 46.53 3.61
5327 6663 8.391075 TGAAATTTCCCAAGTTCTGTAGTAAG 57.609 34.615 15.48 0.00 37.77 2.34
5629 6965 3.153919 GGTGGTCAAAGCTATGTTTGGA 58.846 45.455 0.00 0.00 37.89 3.53
5658 6994 4.039703 GTGCGTACGATTGCTAGTGATAA 58.960 43.478 21.65 0.00 0.00 1.75
5659 6995 3.624900 GTGCGTACGATTGCTAGTGATA 58.375 45.455 21.65 0.00 0.00 2.15
5759 7096 5.236263 GGTATTTTTGCAAGGGAAACACTTG 59.764 40.000 9.08 9.08 46.15 3.16
6369 7718 7.099764 AGAATGTGTCCAGTGTATTACTTCAG 58.900 38.462 0.00 0.00 37.60 3.02
6382 7731 6.653989 AGGTAAAATCCTAGAATGTGTCCAG 58.346 40.000 0.00 0.00 35.87 3.86
6558 7908 5.238650 ACAAGCTACAGAAACAACATACCAC 59.761 40.000 0.00 0.00 0.00 4.16
6981 8435 6.239120 GCAAGCACCCTTATGATTATGAACAT 60.239 38.462 0.00 0.00 0.00 2.71
7204 8663 1.467734 GCAGATGCTTTGAGTGTCAGG 59.532 52.381 0.00 0.00 38.21 3.86
7337 8799 2.621998 CAATCCCATGAAGCCTGACATC 59.378 50.000 0.00 0.00 0.00 3.06
7519 8995 9.913310 AATTGGGAAAAAGGTAAAAGAAAATGA 57.087 25.926 0.00 0.00 0.00 2.57
7531 9007 4.968719 AGGACAAGAAATTGGGAAAAAGGT 59.031 37.500 0.00 0.00 0.00 3.50
7630 9107 7.865385 CGAACTTTACAATTCCCATCAAAAGAA 59.135 33.333 0.00 0.00 0.00 2.52
7632 9109 7.145323 ACGAACTTTACAATTCCCATCAAAAG 58.855 34.615 0.00 0.00 0.00 2.27
7633 9110 7.045126 ACGAACTTTACAATTCCCATCAAAA 57.955 32.000 0.00 0.00 0.00 2.44
7637 9114 9.634163 AAATTAACGAACTTTACAATTCCCATC 57.366 29.630 0.00 0.00 0.00 3.51
7655 9133 8.638565 CAGCATTTCACCTTTCTTAAATTAACG 58.361 33.333 0.00 0.00 0.00 3.18
7679 9157 7.839907 TCCCAAAAATATGATTGTTCTTCCAG 58.160 34.615 1.43 0.00 0.00 3.86
7681 9159 9.154847 CTTTCCCAAAAATATGATTGTTCTTCC 57.845 33.333 1.43 0.00 0.00 3.46
7688 9166 6.070309 TCCCACCTTTCCCAAAAATATGATTG 60.070 38.462 0.00 0.00 0.00 2.67
7704 9182 3.312736 TGAAAGAAAGCTCCCACCTTT 57.687 42.857 0.00 0.00 35.36 3.11
7709 9187 4.648762 TGAATGTTTGAAAGAAAGCTCCCA 59.351 37.500 0.00 0.00 0.00 4.37
7738 9495 3.589288 AGACCTAGGCAAAGATCCTTTGT 59.411 43.478 9.30 5.03 35.21 2.83
7750 9508 1.229177 TCACTGGCAGACCTAGGCA 60.229 57.895 23.66 0.00 39.41 4.75
7778 9536 9.986833 GGGATTGTAATATTTTTGAAAATGTGC 57.013 29.630 11.02 4.64 38.90 4.57
7810 9568 9.950680 CAATGTTTCTGTTTTCTGTTGTACTAT 57.049 29.630 0.00 0.00 0.00 2.12
7849 9607 6.857964 CGTATGCAATGTTTCTGTCTCTTTTT 59.142 34.615 0.00 0.00 0.00 1.94
7850 9608 6.017109 ACGTATGCAATGTTTCTGTCTCTTTT 60.017 34.615 0.00 0.00 0.00 2.27
7851 9609 5.470098 ACGTATGCAATGTTTCTGTCTCTTT 59.530 36.000 0.00 0.00 0.00 2.52
7852 9610 4.997395 ACGTATGCAATGTTTCTGTCTCTT 59.003 37.500 0.00 0.00 0.00 2.85
7853 9611 4.569943 ACGTATGCAATGTTTCTGTCTCT 58.430 39.130 0.00 0.00 0.00 3.10
7854 9612 4.928661 ACGTATGCAATGTTTCTGTCTC 57.071 40.909 0.00 0.00 0.00 3.36
7855 9613 6.795098 TTTACGTATGCAATGTTTCTGTCT 57.205 33.333 0.00 0.00 0.00 3.41
7856 9614 7.845617 TTTTTACGTATGCAATGTTTCTGTC 57.154 32.000 0.00 0.00 0.00 3.51
7879 9637 7.669427 TGGATATGCAATGTTTCTGTCTTTTT 58.331 30.769 0.00 0.00 0.00 1.94
7880 9638 7.230849 TGGATATGCAATGTTTCTGTCTTTT 57.769 32.000 0.00 0.00 0.00 2.27
7881 9639 6.839124 TGGATATGCAATGTTTCTGTCTTT 57.161 33.333 0.00 0.00 0.00 2.52
7882 9640 6.839124 TTGGATATGCAATGTTTCTGTCTT 57.161 33.333 5.43 0.00 0.00 3.01
7883 9641 6.839124 TTTGGATATGCAATGTTTCTGTCT 57.161 33.333 10.71 0.00 0.00 3.41
7884 9642 8.483307 AATTTTGGATATGCAATGTTTCTGTC 57.517 30.769 10.71 0.00 0.00 3.51
7885 9643 9.369904 GTAATTTTGGATATGCAATGTTTCTGT 57.630 29.630 10.71 0.00 0.00 3.41
7886 9644 9.368674 TGTAATTTTGGATATGCAATGTTTCTG 57.631 29.630 10.71 0.00 0.00 3.02
7887 9645 9.941325 TTGTAATTTTGGATATGCAATGTTTCT 57.059 25.926 10.71 0.00 0.00 2.52
7890 9648 9.723601 AGTTTGTAATTTTGGATATGCAATGTT 57.276 25.926 10.71 10.64 0.00 2.71
7891 9649 9.369904 GAGTTTGTAATTTTGGATATGCAATGT 57.630 29.630 10.71 0.00 0.00 2.71
8080 9840 7.206687 AGCTAAGAGTTGTAGATGCAGAATAC 58.793 38.462 0.00 0.00 0.00 1.89
8254 10019 2.043495 CATAGTCGATGGAGTGCTCG 57.957 55.000 0.00 0.00 36.25 5.03
8348 10113 3.169099 TGGAAAGGACCTTGAGAGAGAG 58.831 50.000 7.72 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.