Multiple sequence alignment - TraesCS3D01G540800

Loading Multiple Alignment...

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 TraesCS3D01G540800 chr3D 100.000 3008 0 0 1 3008 612271489 612274496 0.000000e+00 5555.0
1 TraesCS3D01G540800 chr3A 88.813 2503 128 44 1 2440 746916473 746918886 0.000000e+00 2931.0
2 TraesCS3D01G540800 chr3A 90.485 536 51 0 2472 3007 746918952 746919487 0.000000e+00 708.0
3 TraesCS3D01G540800 chr3B 89.822 2024 120 35 372 2354 826726581 826724603 0.000000e+00 2518.0
4 TraesCS3D01G540800 chr3B 83.774 1097 92 35 18 1044 826737470 826736390 0.000000e+00 961.0
5 TraesCS3D01G540800 chr3B 89.855 345 29 5 1 342 826727782 826727441 3.560000e-119 438.0
6 TraesCS3D01G540800 chr4D 80.635 630 112 8 1024 1651 476875290 476875911 2.100000e-131 479.0
7 TraesCS3D01G540800 chr4B 80.476 630 113 8 1024 1651 601098918 601099539 9.760000e-130 473.0
8 TraesCS3D01G540800 chr4A 80.063 632 116 8 1022 1651 683616980 683617603 7.600000e-126 460.0
9 TraesCS3D01G540800 chr4A 94.737 38 1 1 2448 2485 726289394 726289358 1.160000e-04 58.4
10 TraesCS3D01G540800 chr7D 81.061 264 44 5 1079 1339 433876845 433876585 3.930000e-49 206.0
11 TraesCS3D01G540800 chr7B 80.534 262 49 2 1079 1339 451290187 451289927 1.830000e-47 200.0
12 TraesCS3D01G540800 chr7B 81.871 171 20 10 2470 2635 706120534 706120698 1.880000e-27 134.0
13 TraesCS3D01G540800 chr7A 80.534 262 49 2 1079 1339 484525552 484525292 1.830000e-47 200.0
14 TraesCS3D01G540800 chr6A 83.854 192 31 0 1158 1349 464538720 464538529 1.840000e-42 183.0
15 TraesCS3D01G540800 chr6A 91.566 83 4 2 2560 2642 376486978 376486899 8.810000e-21 111.0
16 TraesCS3D01G540800 chr5B 81.006 179 31 2 2472 2650 710199438 710199613 4.040000e-29 139.0
17 TraesCS3D01G540800 chr5D 80.347 173 30 3 2472 2643 556848535 556848366 8.750000e-26 128.0
18 TraesCS3D01G540800 chr6D 92.771 83 3 2 2560 2642 265898802 265898723 1.890000e-22 117.0
19 TraesCS3D01G540800 chr6B 90.476 84 5 2 2560 2643 413389337 413389257 1.140000e-19 108.0
20 TraesCS3D01G540800 chr2D 83.333 120 16 3 2512 2630 427126735 427126851 1.140000e-19 108.0
21 TraesCS3D01G540800 chr1D 81.188 101 17 2 2515 2614 75884867 75884768 2.490000e-11 80.5
22 TraesCS3D01G540800 chr1A 100.000 28 0 0 2453 2480 530256831 530256804 5.000000e-03 52.8


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 TraesCS3D01G540800 chr3D 612271489 612274496 3007 False 5555.0 5555 100.0000 1 3008 1 chr3D.!!$F1 3007
1 TraesCS3D01G540800 chr3A 746916473 746919487 3014 False 1819.5 2931 89.6490 1 3007 2 chr3A.!!$F1 3006
2 TraesCS3D01G540800 chr3B 826724603 826727782 3179 True 1478.0 2518 89.8385 1 2354 2 chr3B.!!$R2 2353
3 TraesCS3D01G540800 chr3B 826736390 826737470 1080 True 961.0 961 83.7740 18 1044 1 chr3B.!!$R1 1026
4 TraesCS3D01G540800 chr4D 476875290 476875911 621 False 479.0 479 80.6350 1024 1651 1 chr4D.!!$F1 627
5 TraesCS3D01G540800 chr4B 601098918 601099539 621 False 473.0 473 80.4760 1024 1651 1 chr4B.!!$F1 627
6 TraesCS3D01G540800 chr4A 683616980 683617603 623 False 460.0 460 80.0630 1022 1651 1 chr4A.!!$F1 629

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
943 1854 0.108804 ACGGGCTTACTGATGACACG 60.109 55.0 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2440 3396 0.034756 TCCCATTATGACCGGCATCG 59.965 55.0 13.58 5.59 38.44 3.84 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
42 43 1.076632 TTGGGGCTTCACAACGGTT 60.077 52.632 0.00 0.00 0.00 4.44
91 92 1.406341 GCAAAGGCGTGGACCTATGTA 60.406 52.381 0.00 0.00 39.93 2.29
345 352 5.010933 AGAAGAAGTGATTCCGTAGAGTCA 58.989 41.667 0.00 0.00 36.48 3.41
377 1214 3.328050 TGAAAGAAGGAAGGAGGGAAGAC 59.672 47.826 0.00 0.00 0.00 3.01
386 1223 4.141597 GGAAGGAGGGAAGACTAAGAATGG 60.142 50.000 0.00 0.00 0.00 3.16
414 1255 0.891904 GGGGTGCGTGGTGTGTTAAT 60.892 55.000 0.00 0.00 0.00 1.40
430 1271 4.988540 GTGTTAATGTGTGAGCTGTGAGTA 59.011 41.667 0.00 0.00 0.00 2.59
433 1274 1.408969 TGTGTGAGCTGTGAGTACCA 58.591 50.000 0.00 0.00 0.00 3.25
449 1290 5.104527 TGAGTACCATTTAGAGGGTTGGATG 60.105 44.000 0.00 0.00 41.02 3.51
541 1400 8.973835 TTTTAGTCATTGTCTTTTCGTTTTGT 57.026 26.923 0.00 0.00 0.00 2.83
570 1429 6.185852 TGCAATCATTCATACTCACAAGTG 57.814 37.500 0.00 0.00 36.92 3.16
673 1559 9.502091 AATGCTTACCATACATATTATGTCGTT 57.498 29.630 12.50 1.99 43.67 3.85
674 1560 8.896320 TGCTTACCATACATATTATGTCGTTT 57.104 30.769 12.50 0.47 43.67 3.60
675 1561 9.332502 TGCTTACCATACATATTATGTCGTTTT 57.667 29.630 12.50 0.00 43.67 2.43
830 1718 4.745125 AGCATTCATAATTGAGGACGTACG 59.255 41.667 15.01 15.01 32.27 3.67
868 1769 6.096705 AGAGATTATTCCTGACTGACTGACTG 59.903 42.308 0.00 0.00 0.00 3.51
871 1774 2.666272 TCCTGACTGACTGACTGACT 57.334 50.000 0.00 0.00 0.00 3.41
912 1823 5.957842 TCTCAAAGACAAGAGAGAGAGAC 57.042 43.478 0.00 0.00 36.05 3.36
913 1824 4.454161 TCTCAAAGACAAGAGAGAGAGACG 59.546 45.833 0.00 0.00 36.05 4.18
926 1837 5.632959 AGAGAGAGACGATGAAACTAAACG 58.367 41.667 0.00 0.00 0.00 3.60
940 1851 3.858247 ACTAAACGGGCTTACTGATGAC 58.142 45.455 0.00 0.00 0.00 3.06
941 1852 2.851263 AAACGGGCTTACTGATGACA 57.149 45.000 0.00 0.00 0.00 3.58
942 1853 2.094762 AACGGGCTTACTGATGACAC 57.905 50.000 0.00 0.00 0.00 3.67
943 1854 0.108804 ACGGGCTTACTGATGACACG 60.109 55.000 0.00 0.00 0.00 4.49
945 1856 1.202417 CGGGCTTACTGATGACACGAT 60.202 52.381 0.00 0.00 0.00 3.73
946 1857 2.034179 CGGGCTTACTGATGACACGATA 59.966 50.000 0.00 0.00 0.00 2.92
949 1860 4.430007 GGCTTACTGATGACACGATAACA 58.570 43.478 0.00 0.00 0.00 2.41
950 1861 4.267928 GGCTTACTGATGACACGATAACAC 59.732 45.833 0.00 0.00 0.00 3.32
953 1864 3.849911 ACTGATGACACGATAACACCTG 58.150 45.455 0.00 0.00 0.00 4.00
954 1865 2.604914 CTGATGACACGATAACACCTGC 59.395 50.000 0.00 0.00 0.00 4.85
955 1866 2.233676 TGATGACACGATAACACCTGCT 59.766 45.455 0.00 0.00 0.00 4.24
956 1867 2.831685 TGACACGATAACACCTGCTT 57.168 45.000 0.00 0.00 0.00 3.91
961 1881 3.684788 ACACGATAACACCTGCTTGATTC 59.315 43.478 0.00 0.00 0.00 2.52
976 1896 6.390987 GCTTGATTCTTGAAGCAATTTCAG 57.609 37.500 13.30 4.23 46.01 3.02
994 1914 1.408340 CAGTCTCTCATGGCGATGACT 59.592 52.381 7.38 1.19 37.64 3.41
1003 1923 0.107268 TGGCGATGACTGATGGATGG 59.893 55.000 0.00 0.00 0.00 3.51
1008 1928 3.332919 CGATGACTGATGGATGGGATTC 58.667 50.000 0.00 0.00 0.00 2.52
1009 1929 2.916702 TGACTGATGGATGGGATTCG 57.083 50.000 0.00 0.00 0.00 3.34
1016 1936 3.331591 TGATGGATGGGATTCGGATTGAT 59.668 43.478 0.00 0.00 0.00 2.57
1017 1937 4.535692 TGATGGATGGGATTCGGATTGATA 59.464 41.667 0.00 0.00 0.00 2.15
1051 1971 4.008933 GTGGGGAGCTGCTCGTGT 62.009 66.667 22.25 0.00 0.00 4.49
1318 2238 0.649475 CGTAGACGGTGTAGACGAGG 59.351 60.000 0.00 0.00 35.59 4.63
1654 2574 2.282040 GTCAGCTTGCCTGCCAGT 60.282 61.111 0.00 0.00 41.50 4.00
1655 2575 1.003355 GTCAGCTTGCCTGCCAGTA 60.003 57.895 0.00 0.00 41.50 2.74
1656 2576 1.003355 TCAGCTTGCCTGCCAGTAC 60.003 57.895 0.00 0.00 41.50 2.73
1657 2577 2.046892 AGCTTGCCTGCCAGTACG 60.047 61.111 0.00 0.00 0.00 3.67
1658 2578 3.127533 GCTTGCCTGCCAGTACGG 61.128 66.667 0.00 0.06 38.11 4.02
1728 2663 0.036388 GTCGATGCACCAGGAAAGGA 60.036 55.000 0.00 0.00 0.00 3.36
1898 2833 4.514569 CGGCATTTTCGACGGGCG 62.515 66.667 0.00 0.00 42.72 6.13
1929 2869 0.322008 GGGATGAATGGATCGGCTCC 60.322 60.000 0.00 0.00 45.19 4.70
2027 2973 1.528824 CCGGAATGGATGTGAGGCT 59.471 57.895 0.00 0.00 42.00 4.58
2030 2976 0.466922 GGAATGGATGTGAGGCTGGG 60.467 60.000 0.00 0.00 0.00 4.45
2056 3002 3.296709 CTTGCTACGGCCGGTCACT 62.297 63.158 31.76 10.73 37.74 3.41
2077 3023 0.586319 CACGACCGCTTCAACACAAT 59.414 50.000 0.00 0.00 0.00 2.71
2081 3027 2.474526 CGACCGCTTCAACACAATCATC 60.475 50.000 0.00 0.00 0.00 2.92
2101 3047 3.221389 CTGCCATCGCCATTGGGG 61.221 66.667 13.38 13.38 40.85 4.96
2239 3187 0.599991 CGGGCTTGGTTTCTTTTGGC 60.600 55.000 0.00 0.00 0.00 4.52
2240 3188 0.467804 GGGCTTGGTTTCTTTTGGCA 59.532 50.000 0.00 0.00 0.00 4.92
2241 3189 1.541015 GGGCTTGGTTTCTTTTGGCAG 60.541 52.381 0.00 0.00 0.00 4.85
2242 3190 1.220529 GCTTGGTTTCTTTTGGCAGC 58.779 50.000 0.00 0.00 0.00 5.25
2259 3209 4.129380 GGCAGCCAAAAGTTTGAGAAATT 58.871 39.130 6.55 0.00 40.55 1.82
2275 3225 5.769662 TGAGAAATTTGGTTATGTCTGCAGT 59.230 36.000 14.67 0.00 0.00 4.40
2289 3239 3.441244 GCAGTGGCAAAAATAGGGC 57.559 52.632 0.00 0.00 40.72 5.19
2294 3244 2.562738 AGTGGCAAAAATAGGGCTCAAC 59.437 45.455 0.00 0.00 0.00 3.18
2299 3249 4.380973 GGCAAAAATAGGGCTCAACTCTTC 60.381 45.833 0.00 0.00 0.00 2.87
2304 3254 4.917906 ATAGGGCTCAACTCTTCTTTGT 57.082 40.909 0.00 0.00 0.00 2.83
2307 3257 5.048846 AGGGCTCAACTCTTCTTTGTTTA 57.951 39.130 0.00 0.00 0.00 2.01
2312 3262 6.039382 GGCTCAACTCTTCTTTGTTTAGGAAA 59.961 38.462 0.00 0.00 0.00 3.13
2313 3263 6.913132 GCTCAACTCTTCTTTGTTTAGGAAAC 59.087 38.462 0.00 0.00 41.73 2.78
2356 3312 7.393234 ACATCTCAAAATCGACCTTCCAAAATA 59.607 33.333 0.00 0.00 0.00 1.40
2357 3313 7.377766 TCTCAAAATCGACCTTCCAAAATAG 57.622 36.000 0.00 0.00 0.00 1.73
2358 3314 6.374333 TCTCAAAATCGACCTTCCAAAATAGG 59.626 38.462 0.00 0.00 37.56 2.57
2407 3363 4.079253 AGACAAATAATCACACCACACCC 58.921 43.478 0.00 0.00 0.00 4.61
2423 3379 1.600636 CCCGCAAACTCAAGCAGGA 60.601 57.895 0.00 0.00 29.68 3.86
2424 3380 1.576421 CCGCAAACTCAAGCAGGAC 59.424 57.895 0.00 0.00 0.00 3.85
2427 3383 1.312815 GCAAACTCAAGCAGGACAGT 58.687 50.000 0.00 0.00 0.00 3.55
2436 3392 1.876849 AGCAGGACAGTCATGAGGAT 58.123 50.000 19.41 0.00 27.97 3.24
2440 3396 3.529533 CAGGACAGTCATGAGGATGAAC 58.470 50.000 9.74 0.00 40.39 3.18
2443 3399 3.181471 GGACAGTCATGAGGATGAACGAT 60.181 47.826 2.17 0.00 40.39 3.73
2446 3402 1.869767 GTCATGAGGATGAACGATGCC 59.130 52.381 0.00 0.00 40.39 4.40
2447 3403 0.863799 CATGAGGATGAACGATGCCG 59.136 55.000 0.00 0.00 42.50 5.69
2458 3414 0.250295 ACGATGCCGGTCATAATGGG 60.250 55.000 1.90 0.00 40.78 4.00
2460 3416 1.523758 GATGCCGGTCATAATGGGAC 58.476 55.000 1.90 0.00 35.05 4.46
2462 3418 1.796017 TGCCGGTCATAATGGGACTA 58.204 50.000 1.90 0.00 35.61 2.59
2464 3420 2.301870 TGCCGGTCATAATGGGACTATC 59.698 50.000 1.90 0.00 35.61 2.08
2466 3422 3.055094 GCCGGTCATAATGGGACTATCAT 60.055 47.826 1.90 0.00 35.61 2.45
2467 3423 4.161565 GCCGGTCATAATGGGACTATCATA 59.838 45.833 1.90 0.00 35.61 2.15
2470 3426 6.325028 CCGGTCATAATGGGACTATCATAGAT 59.675 42.308 0.00 0.00 35.61 1.98
2514 3504 8.704668 TCATGTCATGGTAAATGATGTAGTAGT 58.295 33.333 12.90 0.00 0.00 2.73
2545 3535 6.675413 ATGCATAACAATAAATGAGGCCAT 57.325 33.333 5.01 0.00 33.66 4.40
2549 3539 9.306777 TGCATAACAATAAATGAGGCCATTATA 57.693 29.630 5.01 0.00 41.84 0.98
2561 3551 9.759473 AATGAGGCCATTATAATAACAAGCTAT 57.241 29.630 5.01 0.00 40.95 2.97
2643 3633 9.206690 CTAGTATATGATACCTCCCATTGTGAT 57.793 37.037 0.00 0.00 0.00 3.06
2644 3634 7.855375 AGTATATGATACCTCCCATTGTGATG 58.145 38.462 0.00 0.00 0.00 3.07
2653 3643 1.747355 CCCATTGTGATGAGCCTGAAC 59.253 52.381 0.00 0.00 35.16 3.18
2659 3649 0.250234 TGATGAGCCTGAACGGAAGG 59.750 55.000 0.00 0.00 37.91 3.46
2665 3655 1.975680 AGCCTGAACGGAAGGTTAAGA 59.024 47.619 2.75 0.00 39.19 2.10
2666 3656 2.074576 GCCTGAACGGAAGGTTAAGAC 58.925 52.381 2.75 0.00 39.19 3.01
2670 3660 4.377897 CTGAACGGAAGGTTAAGACTTGT 58.622 43.478 0.00 0.00 39.19 3.16
2675 3665 3.497262 CGGAAGGTTAAGACTTGTCCAAC 59.503 47.826 0.00 2.88 0.00 3.77
2695 3685 5.244626 CCAACTGGAAACAAAGAAGATGGAT 59.755 40.000 0.00 0.00 42.06 3.41
2724 3714 2.738135 GCGCAATGCCCGTAAAATAAT 58.262 42.857 0.30 0.00 37.76 1.28
2755 3745 9.256477 TGTCTAATTAATGCCTATTAACTGTCG 57.744 33.333 0.00 0.00 40.51 4.35
2817 3807 0.103208 GATGACTACCACTCTGGGCG 59.897 60.000 0.00 0.00 43.37 6.13
2849 3839 3.259876 AGGAGCACATGCATGAAAAATGT 59.740 39.130 32.75 7.43 45.16 2.71
2852 3842 5.461078 GGAGCACATGCATGAAAAATGTATC 59.539 40.000 32.75 19.01 45.16 2.24
2881 3871 1.151677 ACAAGGTTAGGCCCCTCCA 60.152 57.895 0.00 0.00 38.26 3.86
2891 3881 1.295292 AGGCCCCTCCAATAAGAGAGA 59.705 52.381 0.00 0.00 35.82 3.10
2905 3895 1.905922 GAGAGAAGCAACAGCGGCAC 61.906 60.000 1.45 0.00 0.00 5.01
2929 3919 2.281484 GGCTTGTTCTGGCGGTGA 60.281 61.111 0.00 0.00 0.00 4.02
2935 3925 0.973632 TGTTCTGGCGGTGATAGTGT 59.026 50.000 0.00 0.00 0.00 3.55
2937 3927 2.563620 TGTTCTGGCGGTGATAGTGTTA 59.436 45.455 0.00 0.00 0.00 2.41
2941 3931 3.259876 TCTGGCGGTGATAGTGTTAGTTT 59.740 43.478 0.00 0.00 0.00 2.66
2951 3941 8.038944 GGTGATAGTGTTAGTTTTGTGATCCTA 58.961 37.037 0.00 0.00 0.00 2.94
2953 3943 8.258007 TGATAGTGTTAGTTTTGTGATCCTAGG 58.742 37.037 0.82 0.82 0.00 3.02
2958 3948 4.828072 AGTTTTGTGATCCTAGGACCTC 57.172 45.455 15.42 9.69 0.00 3.85
2967 3957 5.244178 GTGATCCTAGGACCTCGATGTAATT 59.756 44.000 15.42 0.00 0.00 1.40
2972 3962 8.258850 TCCTAGGACCTCGATGTAATTTTTAT 57.741 34.615 7.62 0.00 0.00 1.40
2997 3987 9.683069 ATTAAGCTATGTGACAAACAAAGAAAG 57.317 29.630 0.00 0.00 43.61 2.62
3007 3997 7.432252 GTGACAAACAAAGAAAGTACAATGAGG 59.568 37.037 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.246737 GCCCCAACTTGAGAGCTTGG 61.247 60.000 0.00 0.00 35.55 3.61
12 13 0.251077 AGCCCCAACTTGAGAGCTTG 60.251 55.000 0.00 0.00 0.00 4.01
42 43 1.971149 AGGTGGTGAGGATGATGGAA 58.029 50.000 0.00 0.00 0.00 3.53
109 110 1.154197 GGTTTGACCGGAGTGCTTAC 58.846 55.000 9.46 0.00 0.00 2.34
377 1214 1.212935 CCCACCCTGTCCCATTCTTAG 59.787 57.143 0.00 0.00 0.00 2.18
414 1255 1.408969 TGGTACTCACAGCTCACACA 58.591 50.000 0.00 0.00 0.00 3.72
430 1271 3.197983 TCCATCCAACCCTCTAAATGGT 58.802 45.455 0.00 0.00 36.04 3.55
433 1274 5.230759 AGATCTCCATCCAACCCTCTAAAT 58.769 41.667 0.00 0.00 0.00 1.40
449 1290 3.553302 GCCTTTCTAGCCGTTAGATCTCC 60.553 52.174 0.00 0.00 38.19 3.71
477 1318 5.047188 GGCCACCCAAAATATGTTTAATCG 58.953 41.667 0.00 0.00 0.00 3.34
541 1400 7.828712 TGTGAGTATGAATGATTGCAAAATGA 58.171 30.769 1.71 0.00 0.00 2.57
680 1566 8.966868 GGATTTTGTCCTGTCCATATTTTCTAA 58.033 33.333 0.00 0.00 44.16 2.10
681 1567 8.519799 GGATTTTGTCCTGTCCATATTTTCTA 57.480 34.615 0.00 0.00 44.16 2.10
682 1568 7.410120 GGATTTTGTCCTGTCCATATTTTCT 57.590 36.000 0.00 0.00 44.16 2.52
733 1620 4.730657 CAACTTGATGTCTTGCCAATCTC 58.269 43.478 0.00 0.00 0.00 2.75
830 1718 7.278868 CAGGAATAATCTCTTGTCTTGGTGTAC 59.721 40.741 0.00 0.00 0.00 2.90
868 1769 5.998363 AGAAATTCAGGGTAAACAGTGAGTC 59.002 40.000 0.00 0.00 0.00 3.36
871 1774 5.935945 TGAGAAATTCAGGGTAAACAGTGA 58.064 37.500 0.00 0.00 0.00 3.41
912 1823 3.930848 AGTAAGCCCGTTTAGTTTCATCG 59.069 43.478 0.00 0.00 0.00 3.84
913 1824 4.933400 TCAGTAAGCCCGTTTAGTTTCATC 59.067 41.667 0.00 0.00 0.00 2.92
926 1837 2.604046 ATCGTGTCATCAGTAAGCCC 57.396 50.000 0.00 0.00 0.00 5.19
940 1851 3.935203 AGAATCAAGCAGGTGTTATCGTG 59.065 43.478 0.00 0.00 0.00 4.35
941 1852 4.207891 AGAATCAAGCAGGTGTTATCGT 57.792 40.909 0.00 0.00 0.00 3.73
942 1853 4.631377 TCAAGAATCAAGCAGGTGTTATCG 59.369 41.667 0.00 0.00 0.00 2.92
943 1854 6.500684 TTCAAGAATCAAGCAGGTGTTATC 57.499 37.500 0.00 0.00 0.00 1.75
945 1856 4.216257 GCTTCAAGAATCAAGCAGGTGTTA 59.784 41.667 0.00 0.00 43.87 2.41
946 1857 3.005155 GCTTCAAGAATCAAGCAGGTGTT 59.995 43.478 0.00 0.00 43.87 3.32
953 1864 5.924825 ACTGAAATTGCTTCAAGAATCAAGC 59.075 36.000 5.49 0.00 43.54 4.01
954 1865 7.368833 AGACTGAAATTGCTTCAAGAATCAAG 58.631 34.615 5.49 0.00 43.54 3.02
955 1866 7.230108 AGAGACTGAAATTGCTTCAAGAATCAA 59.770 33.333 2.07 2.07 43.54 2.57
956 1867 6.713903 AGAGACTGAAATTGCTTCAAGAATCA 59.286 34.615 0.00 0.00 43.54 2.57
961 1881 5.936686 TGAGAGACTGAAATTGCTTCAAG 57.063 39.130 0.00 0.00 43.54 3.02
969 1889 3.616956 TCGCCATGAGAGACTGAAATT 57.383 42.857 0.00 0.00 0.00 1.82
976 1896 1.406898 TCAGTCATCGCCATGAGAGAC 59.593 52.381 0.00 3.96 39.86 3.36
994 1914 2.710471 TCAATCCGAATCCCATCCATCA 59.290 45.455 0.00 0.00 0.00 3.07
1003 1923 8.608844 ACTACTGAAAATATCAATCCGAATCC 57.391 34.615 0.00 0.00 37.67 3.01
1008 1928 5.107453 GCCGACTACTGAAAATATCAATCCG 60.107 44.000 0.00 0.00 37.67 4.18
1009 1929 5.107453 CGCCGACTACTGAAAATATCAATCC 60.107 44.000 0.00 0.00 37.67 3.01
1016 1936 2.417651 CCACCGCCGACTACTGAAAATA 60.418 50.000 0.00 0.00 0.00 1.40
1017 1937 1.674817 CCACCGCCGACTACTGAAAAT 60.675 52.381 0.00 0.00 0.00 1.82
1303 2223 2.488820 GGCCTCGTCTACACCGTC 59.511 66.667 0.00 0.00 0.00 4.79
1306 2226 1.139095 CTTCGGCCTCGTCTACACC 59.861 63.158 0.00 0.00 37.69 4.16
1318 2238 0.103208 AGATCGTCATGACCTTCGGC 59.897 55.000 20.03 4.99 0.00 5.54
1659 2579 2.430582 CCGGTTTTGCATGGCGTG 60.431 61.111 1.31 1.31 0.00 5.34
1660 2580 4.356442 GCCGGTTTTGCATGGCGT 62.356 61.111 1.90 0.00 37.81 5.68
1670 2590 1.302511 AAGTGCTGATCGCCGGTTT 60.303 52.632 1.90 0.00 38.05 3.27
1684 2609 5.107065 CGATCATCATGTCATCCATCAAGTG 60.107 44.000 0.00 0.00 0.00 3.16
1687 2612 4.202388 ACCGATCATCATGTCATCCATCAA 60.202 41.667 0.00 0.00 0.00 2.57
1688 2613 3.325716 ACCGATCATCATGTCATCCATCA 59.674 43.478 0.00 0.00 0.00 3.07
1689 2614 3.931468 GACCGATCATCATGTCATCCATC 59.069 47.826 0.00 0.00 0.00 3.51
1690 2615 3.615834 CGACCGATCATCATGTCATCCAT 60.616 47.826 5.43 0.00 0.00 3.41
1728 2663 1.831290 GCCCACCCCCATTTCTTTCTT 60.831 52.381 0.00 0.00 0.00 2.52
1910 2850 3.239861 GAGCCGATCCATTCATCCC 57.760 57.895 0.00 0.00 0.00 3.85
1929 2869 0.820226 TAGCTAGCTGCACAGGACAG 59.180 55.000 27.68 0.00 45.94 3.51
2027 2973 3.960136 TAGCAAGTTGCCCGCCCA 61.960 61.111 24.02 0.29 46.52 5.36
2030 2976 3.799755 CCGTAGCAAGTTGCCCGC 61.800 66.667 24.02 13.10 46.52 6.13
2056 3002 0.102663 TGTGTTGAAGCGGTCGTGTA 59.897 50.000 0.00 0.00 0.00 2.90
2077 3023 4.916293 GGCGATGGCAGGCGATGA 62.916 66.667 15.44 0.00 42.47 2.92
2081 3027 4.260355 CAATGGCGATGGCAGGCG 62.260 66.667 1.01 8.02 42.43 5.52
2101 3047 2.363359 GCAATCTGATCCCAATCCCAAC 59.637 50.000 0.00 0.00 0.00 3.77
2239 3187 5.585844 ACCAAATTTCTCAAACTTTTGGCTG 59.414 36.000 11.54 0.00 46.54 4.85
2240 3188 5.744171 ACCAAATTTCTCAAACTTTTGGCT 58.256 33.333 11.54 0.00 46.54 4.75
2241 3189 6.435430 AACCAAATTTCTCAAACTTTTGGC 57.565 33.333 11.54 0.00 46.54 4.52
2247 3195 7.147976 GCAGACATAACCAAATTTCTCAAACT 58.852 34.615 0.00 0.00 0.00 2.66
2248 3196 6.922957 TGCAGACATAACCAAATTTCTCAAAC 59.077 34.615 0.00 0.00 0.00 2.93
2259 3209 1.202867 TGCCACTGCAGACATAACCAA 60.203 47.619 23.35 0.00 44.23 3.67
2275 3225 2.825532 GAGTTGAGCCCTATTTTTGCCA 59.174 45.455 0.00 0.00 0.00 4.92
2289 3239 8.214721 AGTTTCCTAAACAAAGAAGAGTTGAG 57.785 34.615 5.42 0.00 43.79 3.02
2323 3279 8.842358 AAGGTCGATTTTGAGATGTAAAAGTA 57.158 30.769 0.00 0.00 31.31 2.24
2332 3288 6.840780 ATTTTGGAAGGTCGATTTTGAGAT 57.159 33.333 0.00 0.00 0.00 2.75
2380 3336 8.303876 GGTGTGGTGTGATTATTTGTCTATTTT 58.696 33.333 0.00 0.00 0.00 1.82
2388 3344 2.415357 GCGGGTGTGGTGTGATTATTTG 60.415 50.000 0.00 0.00 0.00 2.32
2395 3351 2.115911 GTTTGCGGGTGTGGTGTGA 61.116 57.895 0.00 0.00 0.00 3.58
2407 3363 0.236711 CTGTCCTGCTTGAGTTTGCG 59.763 55.000 0.00 0.00 0.00 4.85
2423 3379 3.790091 CATCGTTCATCCTCATGACTGT 58.210 45.455 0.00 0.00 38.86 3.55
2424 3380 2.543012 GCATCGTTCATCCTCATGACTG 59.457 50.000 0.00 0.00 38.86 3.51
2427 3383 1.538849 CGGCATCGTTCATCCTCATGA 60.539 52.381 0.00 0.00 37.24 3.07
2436 3392 2.209273 CATTATGACCGGCATCGTTCA 58.791 47.619 13.58 3.73 41.77 3.18
2440 3396 0.034756 TCCCATTATGACCGGCATCG 59.965 55.000 13.58 5.59 38.44 3.84
2443 3399 1.796017 TAGTCCCATTATGACCGGCA 58.204 50.000 0.00 0.00 33.09 5.69
2446 3402 6.775594 TCTATGATAGTCCCATTATGACCG 57.224 41.667 0.00 0.00 33.09 4.79
2447 3403 9.427821 ACTATCTATGATAGTCCCATTATGACC 57.572 37.037 12.79 0.00 33.09 4.02
2492 3482 9.982651 ACATACTACTACATCATTTACCATGAC 57.017 33.333 0.00 0.00 0.00 3.06
2521 3511 7.779754 ATGGCCTCATTTATTGTTATGCATA 57.220 32.000 3.32 1.16 0.00 3.14
2626 3616 3.406764 GCTCATCACAATGGGAGGTATC 58.593 50.000 0.00 0.00 35.13 2.24
2643 3633 1.344065 TAACCTTCCGTTCAGGCTCA 58.656 50.000 0.00 0.00 40.77 4.26
2644 3634 2.028385 TCTTAACCTTCCGTTCAGGCTC 60.028 50.000 0.00 0.00 40.77 4.70
2653 3643 3.396260 TGGACAAGTCTTAACCTTCCG 57.604 47.619 0.00 0.00 0.00 4.30
2659 3649 5.355910 TGTTTCCAGTTGGACAAGTCTTAAC 59.644 40.000 0.00 1.27 45.39 2.01
2665 3655 4.340617 TCTTTGTTTCCAGTTGGACAAGT 58.659 39.130 0.00 0.00 45.39 3.16
2666 3656 4.981806 TCTTTGTTTCCAGTTGGACAAG 57.018 40.909 0.00 2.05 45.39 3.16
2670 3660 4.584325 CCATCTTCTTTGTTTCCAGTTGGA 59.416 41.667 0.00 0.00 43.73 3.53
2675 3665 4.381292 GGCATCCATCTTCTTTGTTTCCAG 60.381 45.833 0.00 0.00 0.00 3.86
2695 3685 2.699768 GGCATTGCGCTAGTTGGCA 61.700 57.895 9.73 1.85 41.91 4.92
2741 3731 2.544267 GGTCATGCGACAGTTAATAGGC 59.456 50.000 0.00 0.00 44.54 3.93
2743 3733 2.794910 CCGGTCATGCGACAGTTAATAG 59.205 50.000 0.00 0.00 44.54 1.73
2749 3739 1.153568 CATCCGGTCATGCGACAGT 60.154 57.895 0.00 0.00 44.54 3.55
2754 3744 0.655733 GTTTACCATCCGGTCATGCG 59.344 55.000 0.00 0.00 44.71 4.73
2755 3745 1.745232 TGTTTACCATCCGGTCATGC 58.255 50.000 0.00 0.00 44.71 4.06
2786 3776 3.259625 TGGTAGTCATCATCGTTGAACCA 59.740 43.478 11.28 11.28 36.07 3.67
2817 3807 2.124529 GTGCTCCTAAGGGCCAGC 60.125 66.667 6.18 6.00 34.27 4.85
2829 3819 5.172591 CGATACATTTTTCATGCATGTGCTC 59.827 40.000 25.43 14.38 42.66 4.26
2849 3839 3.861276 ACCTTGTCGATGACAACGATA 57.139 42.857 11.15 5.77 45.88 2.92
2852 3842 2.666508 CCTAACCTTGTCGATGACAACG 59.333 50.000 8.21 7.53 45.88 4.10
2881 3871 3.265791 CCGCTGTTGCTTCTCTCTTATT 58.734 45.455 0.00 0.00 36.97 1.40
2891 3881 3.649986 GACGTGCCGCTGTTGCTT 61.650 61.111 0.00 0.00 36.97 3.91
2905 3895 3.777925 CAGAACAAGCCGCCGACG 61.778 66.667 0.00 0.00 39.67 5.12
2913 3903 1.009829 CTATCACCGCCAGAACAAGC 58.990 55.000 0.00 0.00 0.00 4.01
2925 3915 6.879458 AGGATCACAAAACTAACACTATCACC 59.121 38.462 0.00 0.00 0.00 4.02
2929 3919 8.258708 GTCCTAGGATCACAAAACTAACACTAT 58.741 37.037 16.27 0.00 0.00 2.12
2935 3925 5.105473 CGAGGTCCTAGGATCACAAAACTAA 60.105 44.000 24.20 0.00 0.00 2.24
2937 3927 3.195825 CGAGGTCCTAGGATCACAAAACT 59.804 47.826 24.20 2.95 0.00 2.66
2941 3931 2.820728 TCGAGGTCCTAGGATCACAA 57.179 50.000 24.20 0.00 0.00 3.33
2951 3941 8.837389 GCTTAATAAAAATTACATCGAGGTCCT 58.163 33.333 5.75 0.00 0.00 3.85
2972 3962 8.682710 ACTTTCTTTGTTTGTCACATAGCTTAA 58.317 29.630 0.00 0.00 35.11 1.85


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

AutoCloner maintained by Alex Coulton.