Multiple sequence alignment - TraesCS2D01G431000

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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 TraesCS2D01G431000 chr2D 100.000 3070 0 0 1 3070 543431122 543428053 0.000000e+00 5670
1 TraesCS2D01G431000 chr2D 87.069 116 13 2 1851 1965 331179447 331179561 2.480000e-26 130
2 TraesCS2D01G431000 chr2A 90.893 2295 127 37 3 2246 686216361 686214098 0.000000e+00 3005
3 TraesCS2D01G431000 chr2A 85.039 635 38 24 2348 2946 686214044 686213431 7.330000e-166 593
4 TraesCS2D01G431000 chr2A 86.207 116 14 2 1851 1965 438300511 438300625 1.160000e-24 124
5 TraesCS2D01G431000 chr2B 90.957 2256 109 43 1 2219 648654802 648652605 0.000000e+00 2948
6 TraesCS2D01G431000 chr2B 83.867 781 42 32 2342 3070 648652454 648651706 0.000000e+00 667
7 TraesCS2D01G431000 chr2B 86.207 116 14 2 1851 1965 399708194 399708308 1.160000e-24 124
8 TraesCS2D01G431000 chr4A 83.946 299 35 8 1042 1339 494074879 494074593 1.080000e-69 274
9 TraesCS2D01G431000 chr4B 78.981 314 40 6 1038 1351 71705445 71705732 1.120000e-44 191
10 TraesCS2D01G431000 chr5D 84.545 110 17 0 1856 1965 70520861 70520752 3.240000e-20 110
11 TraesCS2D01G431000 chr5A 84.545 110 17 0 1856 1965 60413600 60413491 3.240000e-20 110


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 TraesCS2D01G431000 chr2D 543428053 543431122 3069 True 5670.0 5670 100.000 1 3070 1 chr2D.!!$R1 3069
1 TraesCS2D01G431000 chr2A 686213431 686216361 2930 True 1799.0 3005 87.966 3 2946 2 chr2A.!!$R1 2943
2 TraesCS2D01G431000 chr2B 648651706 648654802 3096 True 1807.5 2948 87.412 1 3070 2 chr2B.!!$R1 3069

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
940 972 0.108019 ACTCCCAACCAAACCGAGAC 59.892 55.0 0.00 0.00 0.0 3.36 F
974 1006 0.175302 CGAGCCAAGATCTGCAGAGT 59.825 55.0 22.96 9.12 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1802 1854 0.107508 CTTGCACCCACGGAGATGAT 60.108 55.0 0.00 0.0 0.0 2.45 R
2341 2469 0.179094 ATCCGCGGCGTTGAATCTTA 60.179 50.0 23.51 0.0 0.0 2.10 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 0.755079 AGATATGCCAGCTCTCGCAA 59.245 50.000 3.92 0.00 38.75 4.85
97 98 1.700186 GAGGTGGTGGGAAAGTTCTCT 59.300 52.381 0.00 0.00 0.00 3.10
185 186 9.884636 TTAAATACAGACAATATCATATCCCCG 57.115 33.333 0.00 0.00 0.00 5.73
204 205 2.104928 CGCGATAGTGCTGCTGGA 59.895 61.111 0.00 0.00 41.13 3.86
235 237 8.980596 AGGAAATAATGGTGCTTTTTATCATGA 58.019 29.630 0.00 0.00 0.00 3.07
244 246 6.705825 GGTGCTTTTTATCATGACCAACTTTT 59.294 34.615 0.00 0.00 0.00 2.27
299 301 4.873129 CAGGACGTCCATCGCCCG 62.873 72.222 35.00 11.06 46.48 6.13
347 349 0.109272 AGACACAGGACACATACGCG 60.109 55.000 3.53 3.53 0.00 6.01
391 396 0.251033 TTCTGCCTGCTTGTGATGCT 60.251 50.000 0.00 0.00 0.00 3.79
492 497 3.118223 TCATTATCACACCGCATTGGGTA 60.118 43.478 0.00 0.00 44.64 3.69
493 498 2.319136 TATCACACCGCATTGGGTAC 57.681 50.000 0.00 0.00 44.64 3.34
494 499 0.618458 ATCACACCGCATTGGGTACT 59.382 50.000 0.00 0.00 44.64 2.73
530 537 2.042162 CCCCCTAATTGCTATGCCTCAT 59.958 50.000 0.00 0.00 0.00 2.90
533 540 4.018960 CCCCTAATTGCTATGCCTCATACT 60.019 45.833 0.00 0.00 0.00 2.12
657 689 9.239002 CAAATTTGTATTTTGTACGACCTTCAA 57.761 29.630 10.15 0.00 31.63 2.69
658 690 8.791355 AATTTGTATTTTGTACGACCTTCAAC 57.209 30.769 0.00 0.00 0.00 3.18
697 729 7.534085 TTTTTGTAACAGTGTGAGACTACAG 57.466 36.000 0.00 0.00 31.73 2.74
698 730 6.459670 TTTGTAACAGTGTGAGACTACAGA 57.540 37.500 0.00 0.00 31.73 3.41
702 734 3.567397 ACAGTGTGAGACTACAGAGGTT 58.433 45.455 0.00 0.00 31.73 3.50
712 744 5.087323 AGACTACAGAGGTTTTCAGATCCA 58.913 41.667 0.00 0.00 0.00 3.41
713 745 5.544176 AGACTACAGAGGTTTTCAGATCCAA 59.456 40.000 0.00 0.00 0.00 3.53
714 746 6.043243 AGACTACAGAGGTTTTCAGATCCAAA 59.957 38.462 0.00 0.00 0.00 3.28
715 747 5.998363 ACTACAGAGGTTTTCAGATCCAAAC 59.002 40.000 4.79 4.79 32.94 2.93
716 748 4.792068 ACAGAGGTTTTCAGATCCAAACA 58.208 39.130 12.44 0.00 35.01 2.83
717 749 4.823989 ACAGAGGTTTTCAGATCCAAACAG 59.176 41.667 12.44 4.72 35.01 3.16
718 750 5.065914 CAGAGGTTTTCAGATCCAAACAGA 58.934 41.667 12.44 0.00 35.01 3.41
719 751 5.180868 CAGAGGTTTTCAGATCCAAACAGAG 59.819 44.000 12.44 0.34 35.01 3.35
755 787 9.274065 GATTAGACCGTTCATTCATGTAAAAAC 57.726 33.333 0.00 0.00 0.00 2.43
773 805 4.622701 AAACTGTGAAGCTGACACTTTC 57.377 40.909 19.93 0.00 38.81 2.62
778 810 5.294552 ACTGTGAAGCTGACACTTTCTAAAC 59.705 40.000 19.93 0.00 38.81 2.01
781 813 5.965918 GTGAAGCTGACACTTTCTAAACAAC 59.034 40.000 14.47 0.00 35.66 3.32
785 817 4.033587 GCTGACACTTTCTAAACAACGACA 59.966 41.667 0.00 0.00 0.00 4.35
787 819 5.172934 TGACACTTTCTAAACAACGACAGT 58.827 37.500 0.00 0.00 0.00 3.55
829 861 2.461739 GGGAATCCAGGGGGCTACC 61.462 68.421 0.09 0.00 39.11 3.18
866 898 4.100035 ACCATCATTGACTCGCATCTTCTA 59.900 41.667 0.00 0.00 0.00 2.10
940 972 0.108019 ACTCCCAACCAAACCGAGAC 59.892 55.000 0.00 0.00 0.00 3.36
974 1006 0.175302 CGAGCCAAGATCTGCAGAGT 59.825 55.000 22.96 9.12 0.00 3.24
1771 1818 5.708697 CCTTACCCACGGTAAATTTCTTTCT 59.291 40.000 4.89 0.00 45.92 2.52
1776 1823 5.009210 CCCACGGTAAATTTCTTTCTTCACA 59.991 40.000 0.00 0.00 0.00 3.58
1777 1824 6.294508 CCCACGGTAAATTTCTTTCTTCACAT 60.295 38.462 0.00 0.00 0.00 3.21
1793 1840 6.057533 TCTTCACATATCCAATAACAGCAGG 58.942 40.000 0.00 0.00 0.00 4.85
1796 1848 6.233434 TCACATATCCAATAACAGCAGGATC 58.767 40.000 0.00 0.00 41.03 3.36
1802 1854 5.076182 TCCAATAACAGCAGGATCAACAAA 58.924 37.500 0.00 0.00 0.00 2.83
1803 1855 5.716228 TCCAATAACAGCAGGATCAACAAAT 59.284 36.000 0.00 0.00 0.00 2.32
1804 1856 6.038356 CCAATAACAGCAGGATCAACAAATC 58.962 40.000 0.00 0.00 0.00 2.17
1805 1857 6.350361 CCAATAACAGCAGGATCAACAAATCA 60.350 38.462 0.00 0.00 0.00 2.57
1808 1860 4.597004 ACAGCAGGATCAACAAATCATCT 58.403 39.130 0.00 0.00 0.00 2.90
1809 1861 4.639310 ACAGCAGGATCAACAAATCATCTC 59.361 41.667 0.00 0.00 0.00 2.75
1814 1880 3.313526 GGATCAACAAATCATCTCCGTGG 59.686 47.826 0.00 0.00 0.00 4.94
1837 1903 3.057946 GTGCAAGGATCTGACTTGGTTTC 60.058 47.826 10.88 0.00 44.16 2.78
1943 2009 3.127533 GCGATGCTGGTGGTGACC 61.128 66.667 0.00 0.00 43.48 4.02
2075 2147 1.805945 CGGGCACGTCTGACTTAGC 60.806 63.158 0.00 6.81 34.81 3.09
2138 2217 1.063174 GGTTCGCAATCTGTCTGATGC 59.937 52.381 0.00 0.00 35.21 3.91
2230 2309 1.273606 CAGACTCCACTTCGTCCACAT 59.726 52.381 0.00 0.00 0.00 3.21
2240 2324 6.093495 TCCACTTCGTCCACATCATTTTTATC 59.907 38.462 0.00 0.00 0.00 1.75
2246 2330 6.093495 TCGTCCACATCATTTTTATCTGTTCC 59.907 38.462 0.00 0.00 0.00 3.62
2248 2332 7.253422 GTCCACATCATTTTTATCTGTTCCTG 58.747 38.462 0.00 0.00 0.00 3.86
2257 2380 9.410556 CATTTTTATCTGTTCCTGAAATCGTTT 57.589 29.630 0.00 0.00 0.00 3.60
2265 2388 7.860373 TCTGTTCCTGAAATCGTTTATTTTGTG 59.140 33.333 0.00 0.00 37.93 3.33
2270 2393 7.433719 TCCTGAAATCGTTTATTTTGTGTGTTG 59.566 33.333 0.00 0.00 37.93 3.33
2273 2396 6.820470 AATCGTTTATTTTGTGTGTTGTGG 57.180 33.333 0.00 0.00 0.00 4.17
2278 2401 0.969149 TTTTGTGTGTTGTGGGTGCA 59.031 45.000 0.00 0.00 0.00 4.57
2279 2402 0.244994 TTTGTGTGTTGTGGGTGCAC 59.755 50.000 8.80 8.80 0.00 4.57
2287 2415 0.250858 TTGTGGGTGCACATGGAGAG 60.251 55.000 20.43 0.00 34.76 3.20
2290 2418 0.994247 TGGGTGCACATGGAGAGATT 59.006 50.000 20.43 0.00 0.00 2.40
2295 2423 2.094894 GTGCACATGGAGAGATTTCGTG 59.905 50.000 13.17 0.00 0.00 4.35
2296 2424 1.667724 GCACATGGAGAGATTTCGTGG 59.332 52.381 0.00 0.00 0.00 4.94
2301 2429 1.303309 GGAGAGATTTCGTGGCATGG 58.697 55.000 6.90 0.00 0.00 3.66
2305 2433 1.474077 GAGATTTCGTGGCATGGCTTT 59.526 47.619 21.08 0.00 0.00 3.51
2309 2437 1.865788 TTCGTGGCATGGCTTTGAGC 61.866 55.000 21.08 3.11 41.46 4.26
2317 2445 3.808656 GGCTTTGAGCTGAGCGGC 61.809 66.667 0.00 0.00 41.99 6.53
2321 2449 2.504461 CTTTGAGCTGAGCGGCGTTG 62.504 60.000 9.37 0.00 37.29 4.10
2326 2454 4.012895 CTGAGCGGCGTTGCGTTT 62.013 61.111 9.37 0.00 40.67 3.60
2338 2466 3.727518 CGTTGCGTTTCGATGTGATAAA 58.272 40.909 0.00 0.00 0.00 1.40
2339 2467 3.773549 CGTTGCGTTTCGATGTGATAAAG 59.226 43.478 0.00 0.00 0.00 1.85
2340 2468 4.088648 GTTGCGTTTCGATGTGATAAAGG 58.911 43.478 0.00 0.00 0.00 3.11
2341 2469 3.331150 TGCGTTTCGATGTGATAAAGGT 58.669 40.909 0.00 0.00 0.00 3.50
2342 2470 4.496360 TGCGTTTCGATGTGATAAAGGTA 58.504 39.130 0.00 0.00 0.00 3.08
2343 2471 4.930405 TGCGTTTCGATGTGATAAAGGTAA 59.070 37.500 0.00 0.00 0.00 2.85
2391 2519 2.222796 CGTGATGAAACTGCCATGTACG 60.223 50.000 0.00 0.00 0.00 3.67
2392 2520 1.737236 TGATGAAACTGCCATGTACGC 59.263 47.619 0.00 0.00 0.00 4.42
2393 2521 0.726827 ATGAAACTGCCATGTACGCG 59.273 50.000 3.53 3.53 0.00 6.01
2394 2522 1.226018 GAAACTGCCATGTACGCGC 60.226 57.895 5.73 0.00 0.00 6.86
2395 2523 2.879942 GAAACTGCCATGTACGCGCG 62.880 60.000 30.96 30.96 0.00 6.86
2496 2640 2.482336 CACAATACAGTGCGCCAACTAA 59.518 45.455 4.18 0.00 32.04 2.24
2500 2665 1.675552 ACAGTGCGCCAACTAAAGTT 58.324 45.000 4.18 0.00 39.12 2.66
2501 2666 2.021457 ACAGTGCGCCAACTAAAGTTT 58.979 42.857 4.18 0.00 35.83 2.66
2502 2667 2.425668 ACAGTGCGCCAACTAAAGTTTT 59.574 40.909 4.18 0.00 35.83 2.43
2503 2668 3.119280 ACAGTGCGCCAACTAAAGTTTTT 60.119 39.130 4.18 0.00 35.83 1.94
2531 2696 4.379499 GCACAAAATAGAAAACTCGGGAGG 60.379 45.833 0.00 0.00 0.00 4.30
2533 2698 4.042435 ACAAAATAGAAAACTCGGGAGGGA 59.958 41.667 0.00 0.00 0.00 4.20
2639 2816 0.976641 CTGTGCAGAGGTCAAGGGTA 59.023 55.000 2.14 0.00 0.00 3.69
2658 2835 2.537560 GGCATCCGCACCGATTGAG 61.538 63.158 0.00 0.00 41.24 3.02
2666 2847 1.002900 CGCACCGATTGAGTTGTTTGT 60.003 47.619 0.00 0.00 0.00 2.83
2684 2865 9.379811 GTTGTTTGTGCCATTATTATTGTTTTG 57.620 29.630 0.00 0.00 0.00 2.44
2686 2867 9.113838 TGTTTGTGCCATTATTATTGTTTTGTT 57.886 25.926 0.00 0.00 0.00 2.83
2687 2868 9.943163 GTTTGTGCCATTATTATTGTTTTGTTT 57.057 25.926 0.00 0.00 0.00 2.83
2857 3051 1.218230 GCGCCCAATCTCATCTCGTC 61.218 60.000 0.00 0.00 0.00 4.20
2858 3052 0.103026 CGCCCAATCTCATCTCGTCA 59.897 55.000 0.00 0.00 0.00 4.35
2859 3053 1.576356 GCCCAATCTCATCTCGTCAC 58.424 55.000 0.00 0.00 0.00 3.67
2860 3054 1.845266 CCCAATCTCATCTCGTCACG 58.155 55.000 0.00 0.00 0.00 4.35
2890 3084 1.670406 CCCAGCAGTGCAGTGAGAC 60.670 63.158 25.76 7.62 0.00 3.36
2896 3092 0.578683 CAGTGCAGTGAGACAACACG 59.421 55.000 16.94 0.00 44.35 4.49
2946 3146 4.327680 CTCCTCCCACCTCTTTTACTTTG 58.672 47.826 0.00 0.00 0.00 2.77
2947 3147 2.820197 CCTCCCACCTCTTTTACTTTGC 59.180 50.000 0.00 0.00 0.00 3.68
2948 3148 3.486383 CTCCCACCTCTTTTACTTTGCA 58.514 45.455 0.00 0.00 0.00 4.08
2949 3149 3.888930 CTCCCACCTCTTTTACTTTGCAA 59.111 43.478 0.00 0.00 0.00 4.08
2950 3150 4.479158 TCCCACCTCTTTTACTTTGCAAT 58.521 39.130 0.00 0.00 0.00 3.56
2955 3169 7.713073 CCCACCTCTTTTACTTTGCAATTTTTA 59.287 33.333 0.00 0.00 0.00 1.52
2956 3170 9.103861 CCACCTCTTTTACTTTGCAATTTTTAA 57.896 29.630 0.00 0.00 0.00 1.52
2981 3195 9.788960 AATTATTTTCTCGAATGAAAGTAAGGC 57.211 29.630 15.42 0.00 39.59 4.35
2983 3197 3.261981 TCTCGAATGAAAGTAAGGCCC 57.738 47.619 0.00 0.00 0.00 5.80
2984 3198 2.838202 TCTCGAATGAAAGTAAGGCCCT 59.162 45.455 0.00 0.00 0.00 5.19
2985 3199 2.939103 CTCGAATGAAAGTAAGGCCCTG 59.061 50.000 0.00 0.00 0.00 4.45
2987 3201 2.379005 GAATGAAAGTAAGGCCCTGGG 58.621 52.381 8.86 8.86 0.00 4.45
3056 3273 1.763770 CCATGGATGGGGGCTACTC 59.236 63.158 5.56 0.00 44.31 2.59
3057 3274 1.372683 CATGGATGGGGGCTACTCG 59.627 63.158 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 167 4.424626 CGTCGGGGATATGATATTGTCTG 58.575 47.826 0.00 0.00 0.00 3.51
185 186 2.233654 CCAGCAGCACTATCGCGTC 61.234 63.158 5.77 0.00 36.85 5.19
202 203 3.137360 AGCACCATTATTTCCTCTCCTCC 59.863 47.826 0.00 0.00 0.00 4.30
204 205 4.870021 AAGCACCATTATTTCCTCTCCT 57.130 40.909 0.00 0.00 0.00 3.69
244 246 7.503991 CGTGCGTTTCTATTCTACACTAAAAA 58.496 34.615 0.00 0.00 0.00 1.94
249 251 2.921754 GCGTGCGTTTCTATTCTACACT 59.078 45.455 0.00 0.00 0.00 3.55
299 301 3.933861 AAGTCAACTATGGGGATGGAC 57.066 47.619 0.00 0.00 0.00 4.02
359 364 3.355378 CAGGCAGAAGAGAGAGAGAGAA 58.645 50.000 0.00 0.00 0.00 2.87
370 375 1.817357 CATCACAAGCAGGCAGAAGA 58.183 50.000 0.00 0.00 0.00 2.87
371 376 0.170561 GCATCACAAGCAGGCAGAAG 59.829 55.000 0.00 0.00 0.00 2.85
372 377 0.251033 AGCATCACAAGCAGGCAGAA 60.251 50.000 0.00 0.00 0.00 3.02
391 396 6.349528 GGGTTTTCTTTAAGCCGTTATTGCTA 60.350 38.462 0.00 0.00 38.34 3.49
500 505 3.856900 AGCAATTAGGGGGTTTCTTTGT 58.143 40.909 0.00 0.00 0.00 2.83
508 513 1.425448 GAGGCATAGCAATTAGGGGGT 59.575 52.381 0.00 0.00 0.00 4.95
514 519 6.173427 TGTGAGTATGAGGCATAGCAATTA 57.827 37.500 0.00 0.00 0.00 1.40
515 520 5.039920 TGTGAGTATGAGGCATAGCAATT 57.960 39.130 0.00 0.00 0.00 2.32
517 522 4.080919 ACTTGTGAGTATGAGGCATAGCAA 60.081 41.667 0.00 0.00 33.32 3.91
518 523 3.452264 ACTTGTGAGTATGAGGCATAGCA 59.548 43.478 0.00 0.00 33.32 3.49
519 524 4.054671 GACTTGTGAGTATGAGGCATAGC 58.945 47.826 0.00 0.00 35.88 2.97
530 537 3.517901 CTGTTATGGGGGACTTGTGAGTA 59.482 47.826 0.00 0.00 35.88 2.59
533 540 2.344592 ACTGTTATGGGGGACTTGTGA 58.655 47.619 0.00 0.00 0.00 3.58
630 658 8.622157 TGAAGGTCGTACAAAATACAAATTTGA 58.378 29.630 24.64 8.78 39.56 2.69
631 659 8.789881 TGAAGGTCGTACAAAATACAAATTTG 57.210 30.769 16.67 16.67 42.18 2.32
632 660 9.240159 GTTGAAGGTCGTACAAAATACAAATTT 57.760 29.630 0.00 0.00 36.87 1.82
633 661 8.626526 AGTTGAAGGTCGTACAAAATACAAATT 58.373 29.630 0.00 0.00 0.00 1.82
634 662 8.161699 AGTTGAAGGTCGTACAAAATACAAAT 57.838 30.769 0.00 0.00 0.00 2.32
635 663 7.517101 CGAGTTGAAGGTCGTACAAAATACAAA 60.517 37.037 0.00 0.00 0.00 2.83
636 664 6.074195 CGAGTTGAAGGTCGTACAAAATACAA 60.074 38.462 0.00 0.00 0.00 2.41
637 665 5.403166 CGAGTTGAAGGTCGTACAAAATACA 59.597 40.000 0.00 0.00 0.00 2.29
638 666 5.164022 CCGAGTTGAAGGTCGTACAAAATAC 60.164 44.000 0.00 0.00 34.27 1.89
678 710 4.519730 ACCTCTGTAGTCTCACACTGTTAC 59.480 45.833 0.00 0.00 36.43 2.50
690 722 5.407407 TGGATCTGAAAACCTCTGTAGTC 57.593 43.478 0.00 0.00 0.00 2.59
697 729 5.308825 TCTCTGTTTGGATCTGAAAACCTC 58.691 41.667 13.15 0.00 35.80 3.85
698 730 5.310409 TCTCTGTTTGGATCTGAAAACCT 57.690 39.130 13.15 0.00 35.80 3.50
702 734 6.038603 CACTGTTTCTCTGTTTGGATCTGAAA 59.961 38.462 0.00 0.00 0.00 2.69
712 744 5.998363 GTCTAATCCCACTGTTTCTCTGTTT 59.002 40.000 0.00 0.00 0.00 2.83
713 745 5.513267 GGTCTAATCCCACTGTTTCTCTGTT 60.513 44.000 0.00 0.00 0.00 3.16
714 746 4.020128 GGTCTAATCCCACTGTTTCTCTGT 60.020 45.833 0.00 0.00 0.00 3.41
715 747 4.508662 GGTCTAATCCCACTGTTTCTCTG 58.491 47.826 0.00 0.00 0.00 3.35
716 748 3.195825 CGGTCTAATCCCACTGTTTCTCT 59.804 47.826 0.00 0.00 0.00 3.10
717 749 3.056035 ACGGTCTAATCCCACTGTTTCTC 60.056 47.826 0.00 0.00 0.00 2.87
718 750 2.904434 ACGGTCTAATCCCACTGTTTCT 59.096 45.455 0.00 0.00 0.00 2.52
719 751 3.329929 ACGGTCTAATCCCACTGTTTC 57.670 47.619 0.00 0.00 0.00 2.78
755 787 5.294306 TGTTTAGAAAGTGTCAGCTTCACAG 59.706 40.000 17.48 0.00 38.16 3.66
781 813 0.530650 AGATATGCGCCCAACTGTCG 60.531 55.000 4.18 0.00 0.00 4.35
785 817 0.546122 TTGGAGATATGCGCCCAACT 59.454 50.000 4.18 0.00 35.27 3.16
787 819 2.158623 AGAATTGGAGATATGCGCCCAA 60.159 45.455 14.57 14.57 42.16 4.12
829 861 1.644786 GATGGTGGTCGCTTTTCGGG 61.645 60.000 0.00 0.00 39.05 5.14
866 898 2.448931 TGGAAACGGGGTGAGGGT 60.449 61.111 0.00 0.00 0.00 4.34
974 1006 2.108157 GTGTGTGGTCGCCTGTGA 59.892 61.111 0.00 0.00 0.00 3.58
1740 1787 2.837199 TACCGTGGGTAAGGGGATCCT 61.837 57.143 12.58 0.00 40.37 3.24
1771 1818 6.000246 TCCTGCTGTTATTGGATATGTGAA 58.000 37.500 0.00 0.00 0.00 3.18
1776 1823 6.604171 TGTTGATCCTGCTGTTATTGGATAT 58.396 36.000 0.00 0.00 39.19 1.63
1777 1824 6.000246 TGTTGATCCTGCTGTTATTGGATA 58.000 37.500 0.00 0.00 39.19 2.59
1785 1832 5.014858 AGATGATTTGTTGATCCTGCTGTT 58.985 37.500 0.00 0.00 0.00 3.16
1789 1836 3.003068 CGGAGATGATTTGTTGATCCTGC 59.997 47.826 0.00 0.00 0.00 4.85
1793 1840 3.313526 CCCACGGAGATGATTTGTTGATC 59.686 47.826 0.00 0.00 0.00 2.92
1796 1848 2.162208 CACCCACGGAGATGATTTGTTG 59.838 50.000 0.00 0.00 0.00 3.33
1802 1854 0.107508 CTTGCACCCACGGAGATGAT 60.108 55.000 0.00 0.00 0.00 2.45
1803 1855 1.296392 CTTGCACCCACGGAGATGA 59.704 57.895 0.00 0.00 0.00 2.92
1804 1856 1.746615 CCTTGCACCCACGGAGATG 60.747 63.158 0.00 0.00 32.32 2.90
1805 1857 1.274703 ATCCTTGCACCCACGGAGAT 61.275 55.000 0.00 0.00 41.99 2.75
1808 1860 1.918293 AGATCCTTGCACCCACGGA 60.918 57.895 0.00 0.00 42.77 4.69
1809 1861 1.746615 CAGATCCTTGCACCCACGG 60.747 63.158 0.00 0.00 0.00 4.94
1814 1880 1.271597 ACCAAGTCAGATCCTTGCACC 60.272 52.381 5.04 0.00 38.36 5.01
1837 1903 0.967380 GCCCCTGAAACCCAGACATG 60.967 60.000 0.00 0.00 45.78 3.21
1943 2009 4.554363 CGGTGCTCGCCCTCGTAG 62.554 72.222 0.00 0.00 36.96 3.51
2003 2069 2.347114 CCCATCGGCATCGGCATA 59.653 61.111 0.00 0.00 43.71 3.14
2030 2102 1.226603 GGACACACTAGCTACGGCG 60.227 63.158 4.80 4.80 44.37 6.46
2138 2217 6.204882 ACAATCTTTCTTCTTCTTTACACGGG 59.795 38.462 0.00 0.00 0.00 5.28
2230 2309 8.335532 ACGATTTCAGGAACAGATAAAAATGA 57.664 30.769 0.00 0.00 0.00 2.57
2240 2324 7.647715 ACACAAAATAAACGATTTCAGGAACAG 59.352 33.333 0.00 0.00 36.71 3.16
2246 2330 8.049592 CACAACACACAAAATAAACGATTTCAG 58.950 33.333 0.00 0.00 36.71 3.02
2248 2332 7.334009 CCACAACACACAAAATAAACGATTTC 58.666 34.615 0.00 0.00 36.71 2.17
2257 2380 2.760650 TGCACCCACAACACACAAAATA 59.239 40.909 0.00 0.00 0.00 1.40
2259 2382 0.969149 TGCACCCACAACACACAAAA 59.031 45.000 0.00 0.00 0.00 2.44
2270 2393 0.254178 ATCTCTCCATGTGCACCCAC 59.746 55.000 15.69 0.00 42.40 4.61
2273 2396 1.667724 CGAAATCTCTCCATGTGCACC 59.332 52.381 15.69 0.00 0.00 5.01
2278 2401 1.278985 TGCCACGAAATCTCTCCATGT 59.721 47.619 0.00 0.00 0.00 3.21
2279 2402 2.028420 TGCCACGAAATCTCTCCATG 57.972 50.000 0.00 0.00 0.00 3.66
2287 2415 1.202114 TCAAAGCCATGCCACGAAATC 59.798 47.619 0.00 0.00 0.00 2.17
2290 2418 1.865788 GCTCAAAGCCATGCCACGAA 61.866 55.000 0.00 0.00 34.48 3.85
2295 2423 1.807886 CTCAGCTCAAAGCCATGCC 59.192 57.895 0.00 0.00 43.77 4.40
2296 2424 1.139095 GCTCAGCTCAAAGCCATGC 59.861 57.895 0.00 0.00 43.77 4.06
2301 2429 4.157958 CGCCGCTCAGCTCAAAGC 62.158 66.667 0.00 2.79 42.84 3.51
2309 2437 3.911155 GAAACGCAACGCCGCTCAG 62.911 63.158 0.00 0.00 0.00 3.35
2317 2445 3.362281 TTATCACATCGAAACGCAACG 57.638 42.857 0.00 0.00 0.00 4.10
2321 2449 5.290158 TCTTACCTTTATCACATCGAAACGC 59.710 40.000 0.00 0.00 0.00 4.84
2322 2450 6.880822 TCTTACCTTTATCACATCGAAACG 57.119 37.500 0.00 0.00 0.00 3.60
2323 2451 8.879759 TGAATCTTACCTTTATCACATCGAAAC 58.120 33.333 0.00 0.00 0.00 2.78
2324 2452 9.443323 TTGAATCTTACCTTTATCACATCGAAA 57.557 29.630 0.00 0.00 0.00 3.46
2325 2453 8.879759 GTTGAATCTTACCTTTATCACATCGAA 58.120 33.333 0.00 0.00 0.00 3.71
2326 2454 7.222031 CGTTGAATCTTACCTTTATCACATCGA 59.778 37.037 0.00 0.00 0.00 3.59
2338 2466 1.082117 CGCGGCGTTGAATCTTACCT 61.082 55.000 15.36 0.00 0.00 3.08
2339 2467 1.347221 CGCGGCGTTGAATCTTACC 59.653 57.895 15.36 0.00 0.00 2.85
2340 2468 1.079875 TCCGCGGCGTTGAATCTTAC 61.080 55.000 23.51 0.00 0.00 2.34
2341 2469 0.179094 ATCCGCGGCGTTGAATCTTA 60.179 50.000 23.51 0.00 0.00 2.10
2342 2470 1.429148 GATCCGCGGCGTTGAATCTT 61.429 55.000 23.51 0.00 0.00 2.40
2343 2471 1.883084 GATCCGCGGCGTTGAATCT 60.883 57.895 23.51 0.00 0.00 2.40
2393 2521 1.698714 ATTTACTGTAACCGCGCCGC 61.699 55.000 0.00 0.00 0.00 6.53
2394 2522 1.558741 TATTTACTGTAACCGCGCCG 58.441 50.000 0.00 0.00 0.00 6.46
2395 2523 2.286025 CCTTATTTACTGTAACCGCGCC 59.714 50.000 0.00 0.00 0.00 6.53
2409 2537 2.427095 GGAGCATTTGCCGTCCTTATTT 59.573 45.455 0.00 0.00 43.38 1.40
2502 2667 6.205784 CGAGTTTTCTATTTTGTGCCTCAAA 58.794 36.000 0.97 0.97 43.24 2.69
2503 2668 5.278266 CCGAGTTTTCTATTTTGTGCCTCAA 60.278 40.000 0.00 0.00 0.00 3.02
2504 2669 4.215399 CCGAGTTTTCTATTTTGTGCCTCA 59.785 41.667 0.00 0.00 0.00 3.86
2505 2670 4.379499 CCCGAGTTTTCTATTTTGTGCCTC 60.379 45.833 0.00 0.00 0.00 4.70
2506 2671 3.506067 CCCGAGTTTTCTATTTTGTGCCT 59.494 43.478 0.00 0.00 0.00 4.75
2507 2672 3.504520 TCCCGAGTTTTCTATTTTGTGCC 59.495 43.478 0.00 0.00 0.00 5.01
2508 2673 4.379499 CCTCCCGAGTTTTCTATTTTGTGC 60.379 45.833 0.00 0.00 0.00 4.57
2509 2674 4.156008 CCCTCCCGAGTTTTCTATTTTGTG 59.844 45.833 0.00 0.00 0.00 3.33
2510 2675 4.042435 TCCCTCCCGAGTTTTCTATTTTGT 59.958 41.667 0.00 0.00 0.00 2.83
2511 2676 4.585879 TCCCTCCCGAGTTTTCTATTTTG 58.414 43.478 0.00 0.00 0.00 2.44
2512 2677 4.844884 CTCCCTCCCGAGTTTTCTATTTT 58.155 43.478 0.00 0.00 0.00 1.82
2513 2678 3.370633 GCTCCCTCCCGAGTTTTCTATTT 60.371 47.826 0.00 0.00 32.11 1.40
2514 2679 2.170817 GCTCCCTCCCGAGTTTTCTATT 59.829 50.000 0.00 0.00 32.11 1.73
2531 2696 2.767505 TCTTGTTCTTTTCTCCGCTCC 58.232 47.619 0.00 0.00 0.00 4.70
2533 2698 3.809905 ACTTCTTGTTCTTTTCTCCGCT 58.190 40.909 0.00 0.00 0.00 5.52
2639 2816 2.514592 CAATCGGTGCGGATGCCT 60.515 61.111 0.00 0.00 41.78 4.75
2684 2865 2.684374 GGACGGAGGAGAGAGAGTAAAC 59.316 54.545 0.00 0.00 0.00 2.01
2686 2867 2.171027 GAGGACGGAGGAGAGAGAGTAA 59.829 54.545 0.00 0.00 0.00 2.24
2687 2868 1.764134 GAGGACGGAGGAGAGAGAGTA 59.236 57.143 0.00 0.00 0.00 2.59
2688 2869 0.544697 GAGGACGGAGGAGAGAGAGT 59.455 60.000 0.00 0.00 0.00 3.24
2913 3109 0.614979 TGGGAGGAGGAGGAGAAACG 60.615 60.000 0.00 0.00 0.00 3.60
2955 3169 9.788960 GCCTTACTTTCATTCGAGAAAATAATT 57.211 29.630 2.73 0.00 37.09 1.40
2956 3170 8.406297 GGCCTTACTTTCATTCGAGAAAATAAT 58.594 33.333 0.00 0.00 37.09 1.28
2960 3174 4.457949 GGGCCTTACTTTCATTCGAGAAAA 59.542 41.667 0.84 0.00 37.09 2.29
2961 3175 4.007659 GGGCCTTACTTTCATTCGAGAAA 58.992 43.478 0.84 0.57 36.21 2.52
2964 3178 2.939103 CAGGGCCTTACTTTCATTCGAG 59.061 50.000 1.32 0.00 0.00 4.04
2967 3181 2.379005 CCCAGGGCCTTACTTTCATTC 58.621 52.381 1.32 0.00 0.00 2.67
3021 3235 4.516195 GCGAGCGACCCCTCCTTC 62.516 72.222 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.