Multiple sequence alignment - TraesCS4B01G019400

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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 TraesCS4B01G019400 chr4B 100.000 3200 0 0 1 3200 14012153 14015352 0.000000e+00 5910
1 TraesCS4B01G019400 chr4A 94.015 2356 93 14 882 3197 595422683 595425030 0.000000e+00 3526
2 TraesCS4B01G019400 chr4A 87.293 362 40 2 2759 3115 595425357 595425717 2.970000e-110 409
3 TraesCS4B01G019400 chr4A 84.016 244 32 6 617 858 595422450 595422688 8.930000e-56 228
4 TraesCS4B01G019400 chr4D 92.714 2141 129 12 992 3115 7893170 7891040 0.000000e+00 3064
5 TraesCS4B01G019400 chr4D 80.000 485 57 22 5 466 7894376 7893909 3.980000e-84 322
6 TraesCS4B01G019400 chr7B 88.689 1777 150 26 694 2434 594954691 594956452 0.000000e+00 2121
7 TraesCS4B01G019400 chr7B 76.316 266 50 8 48 307 594953707 594953965 2.590000e-26 130
8 TraesCS4B01G019400 chr7D 86.753 1940 184 37 530 2434 550265614 550267515 0.000000e+00 2091
9 TraesCS4B01G019400 chr7D 78.904 602 59 29 2496 3090 550267757 550268297 2.360000e-91 346
10 TraesCS4B01G019400 chr7D 77.068 266 43 11 50 311 550265039 550265290 1.550000e-28 137
11 TraesCS4B01G019400 chr7A 92.538 1434 93 8 1012 2434 635684214 635685644 0.000000e+00 2043
12 TraesCS4B01G019400 chr7A 74.444 270 50 14 48 311 635683129 635683385 7.310000e-17 99


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 TraesCS4B01G019400 chr4B 14012153 14015352 3199 False 5910.000000 5910 100.000000 1 3200 1 chr4B.!!$F1 3199
1 TraesCS4B01G019400 chr4A 595422450 595425717 3267 False 1387.666667 3526 88.441333 617 3197 3 chr4A.!!$F1 2580
2 TraesCS4B01G019400 chr4D 7891040 7894376 3336 True 1693.000000 3064 86.357000 5 3115 2 chr4D.!!$R1 3110
3 TraesCS4B01G019400 chr7B 594953707 594956452 2745 False 1125.500000 2121 82.502500 48 2434 2 chr7B.!!$F1 2386
4 TraesCS4B01G019400 chr7D 550265039 550268297 3258 False 858.000000 2091 80.908333 50 3090 3 chr7D.!!$F1 3040
5 TraesCS4B01G019400 chr7A 635683129 635685644 2515 False 1071.000000 2043 83.491000 48 2434 2 chr7A.!!$F1 2386

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
235 262 0.182775 ATCACCCGTAAAGCCATCCC 59.817 55.000 0.0 0.00 0.00 3.85 F
515 860 1.228245 GAAGCCTGCCTGGTGACAA 60.228 57.895 0.0 0.00 42.06 3.18 F
1014 1721 1.302285 CTGAATGCTCAGGGCCTGT 59.698 57.895 31.6 13.59 44.72 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1665 2377 1.287730 CTTCTCGTGCTGTGACTGCC 61.288 60.000 11.94 2.85 0.0 4.85 R
2183 2895 1.409064 CGAGCTATACTGCCAGTGGAA 59.591 52.381 15.20 0.00 0.0 3.53 R
2838 3754 0.804989 GCTTGTTCATGCGCTAACCT 59.195 50.000 9.73 0.00 0.0 3.50 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
36 37 4.394712 CCCACTCAGACCGGGCAC 62.395 72.222 11.69 0.00 31.89 5.01
71 72 2.436646 CCCATCACCGGTGCTGTC 60.437 66.667 30.67 0.00 0.00 3.51
216 243 1.923395 CCTTGCTCCCCAGTACCCA 60.923 63.158 0.00 0.00 0.00 4.51
235 262 0.182775 ATCACCCGTAAAGCCATCCC 59.817 55.000 0.00 0.00 0.00 3.85
351 407 4.500116 GGACCTGAGCGCGACCTC 62.500 72.222 12.10 8.79 0.00 3.85
355 411 2.101965 CTGAGCGCGACCTCTGAG 59.898 66.667 12.10 0.00 33.99 3.35
357 413 3.821055 GAGCGCGACCTCTGAGCT 61.821 66.667 12.10 0.00 41.29 4.09
360 416 3.137459 CGCGACCTCTGAGCTCCT 61.137 66.667 12.15 0.00 0.00 3.69
363 419 1.599606 GCGACCTCTGAGCTCCTTCA 61.600 60.000 12.15 0.00 0.00 3.02
413 469 3.793559 GGTAACTAGTGCGATTGTGGAT 58.206 45.455 0.00 0.00 0.00 3.41
418 474 7.328737 GGTAACTAGTGCGATTGTGGATATTAG 59.671 40.741 0.00 0.00 0.00 1.73
425 481 6.924060 GTGCGATTGTGGATATTAGAAGTACT 59.076 38.462 0.00 0.00 0.00 2.73
426 482 8.080417 GTGCGATTGTGGATATTAGAAGTACTA 58.920 37.037 0.00 0.00 0.00 1.82
427 483 8.080417 TGCGATTGTGGATATTAGAAGTACTAC 58.920 37.037 0.00 0.00 0.00 2.73
429 485 8.794553 CGATTGTGGATATTAGAAGTACTACCT 58.205 37.037 0.00 0.00 0.00 3.08
432 488 8.693120 TGTGGATATTAGAAGTACTACCTCAG 57.307 38.462 0.00 0.00 0.00 3.35
452 546 3.925913 CAGTTTCAGTCTTCAGAGCTAGC 59.074 47.826 6.62 6.62 0.00 3.42
466 563 3.139397 AGAGCTAGCTGGTACTGGAGTAT 59.861 47.826 24.99 0.00 32.54 2.12
467 564 3.892588 GAGCTAGCTGGTACTGGAGTATT 59.107 47.826 24.99 0.00 32.54 1.89
470 567 5.051153 GCTAGCTGGTACTGGAGTATTTTC 58.949 45.833 7.70 0.00 32.54 2.29
482 680 6.071728 ACTGGAGTATTTTCTTTCTGCAATGG 60.072 38.462 0.00 0.00 0.00 3.16
492 690 4.225942 TCTTTCTGCAATGGGTCTAGTGAT 59.774 41.667 0.00 0.00 0.00 3.06
493 691 4.574674 TTCTGCAATGGGTCTAGTGATT 57.425 40.909 0.00 0.00 0.00 2.57
495 693 5.282055 TCTGCAATGGGTCTAGTGATTAG 57.718 43.478 0.00 0.00 0.00 1.73
497 695 4.769688 TGCAATGGGTCTAGTGATTAGTG 58.230 43.478 0.00 0.00 0.00 2.74
506 851 2.409948 AGTGATTAGTGAAGCCTGCC 57.590 50.000 0.00 0.00 0.00 4.85
515 860 1.228245 GAAGCCTGCCTGGTGACAA 60.228 57.895 0.00 0.00 42.06 3.18
528 873 5.491070 CCTGGTGACAATTATTGAGTGAGA 58.509 41.667 12.28 0.00 42.06 3.27
539 992 9.020813 CAATTATTGAGTGAGATGATGCTTTTG 57.979 33.333 0.00 0.00 0.00 2.44
549 1002 1.345089 TGATGCTTTTGTGGCAATGCT 59.655 42.857 4.82 0.00 43.14 3.79
567 1020 6.032460 GCAATGCTAAAGCGTAAAGTAGTTTG 59.968 38.462 5.77 0.00 45.83 2.93
574 1027 5.030874 AGCGTAAAGTAGTTTGATGTTGC 57.969 39.130 5.77 1.43 0.00 4.17
576 1030 4.846137 GCGTAAAGTAGTTTGATGTTGCAG 59.154 41.667 5.77 0.00 0.00 4.41
577 1031 5.333798 GCGTAAAGTAGTTTGATGTTGCAGA 60.334 40.000 5.77 0.00 0.00 4.26
581 1035 9.118236 GTAAAGTAGTTTGATGTTGCAGATTTC 57.882 33.333 5.77 0.00 0.00 2.17
615 1069 5.391312 TCTTTTATTCTTCTTGCAAGGCC 57.609 39.130 25.73 0.00 0.00 5.19
626 1080 2.219080 TGCAAGGCCATTTCATCTCA 57.781 45.000 5.01 0.00 0.00 3.27
644 1099 4.188462 TCTCACCAACTAGTTGTGTTGTG 58.812 43.478 29.05 26.77 42.09 3.33
653 1108 5.927030 ACTAGTTGTGTTGTGATATTTGCG 58.073 37.500 0.00 0.00 0.00 4.85
654 1109 3.564511 AGTTGTGTTGTGATATTTGCGC 58.435 40.909 0.00 0.00 0.00 6.09
656 1111 3.632855 TGTGTTGTGATATTTGCGCAA 57.367 38.095 21.02 21.02 33.77 4.85
657 1112 3.969899 TGTGTTGTGATATTTGCGCAAA 58.030 36.364 35.19 35.19 37.48 3.68
658 1113 4.363138 TGTGTTGTGATATTTGCGCAAAA 58.637 34.783 36.42 25.19 37.48 2.44
659 1114 4.805719 TGTGTTGTGATATTTGCGCAAAAA 59.194 33.333 36.42 22.87 37.48 1.94
710 1214 6.759497 AACATGTTTAGGGAACTCTAATGC 57.241 37.500 4.92 0.00 43.67 3.56
713 1217 4.261801 TGTTTAGGGAACTCTAATGCTGC 58.738 43.478 0.00 0.00 43.67 5.25
734 1238 6.349973 TGCGAGACTTGATTAAGCTATTTG 57.650 37.500 0.00 0.00 37.43 2.32
737 1241 7.222805 TGCGAGACTTGATTAAGCTATTTGTAG 59.777 37.037 0.00 0.00 37.43 2.74
738 1242 7.559845 CGAGACTTGATTAAGCTATTTGTAGC 58.440 38.462 0.00 0.00 43.12 3.58
764 1268 7.867909 CGCTCTTCTGGTCAATTTCATAGTATA 59.132 37.037 0.00 0.00 0.00 1.47
784 1290 8.997621 AGTATACGTGTGATGTCTGTAAATTT 57.002 30.769 0.00 0.00 0.00 1.82
785 1291 9.431887 AGTATACGTGTGATGTCTGTAAATTTT 57.568 29.630 0.00 0.00 0.00 1.82
786 1292 9.685005 GTATACGTGTGATGTCTGTAAATTTTC 57.315 33.333 0.00 0.00 0.00 2.29
823 1335 8.927411 GGTACACCCTATAAAGTGTTATTCCTA 58.073 37.037 11.52 0.00 44.65 2.94
875 1387 7.230747 TCTGAAATGGGAATTGTTGAGAGTTA 58.769 34.615 0.00 0.00 0.00 2.24
879 1391 7.693969 AATGGGAATTGTTGAGAGTTAAGAG 57.306 36.000 0.00 0.00 0.00 2.85
905 1417 8.903820 GTTGAGATACAGGCTTTTGGTATTATT 58.096 33.333 0.00 0.00 0.00 1.40
941 1454 8.728088 CTTAGTTGTAAGGCTTATGTTGTTTG 57.272 34.615 10.65 0.00 33.18 2.93
945 1458 7.704899 AGTTGTAAGGCTTATGTTGTTTGAAAC 59.295 33.333 10.65 0.14 0.00 2.78
949 1462 2.729360 GCTTATGTTGTTTGAAACGGCC 59.271 45.455 3.37 0.00 32.47 6.13
954 1467 2.428890 TGTTGTTTGAAACGGCCTGAAT 59.571 40.909 0.00 0.00 32.47 2.57
1006 1713 3.578282 TGAAGTACACTCCTGAATGCTCA 59.422 43.478 0.00 0.00 0.00 4.26
1014 1721 1.302285 CTGAATGCTCAGGGCCTGT 59.698 57.895 31.60 13.59 44.72 4.00
1048 1756 8.507249 ACACAGACTTGCATTTAAGAGTAAATC 58.493 33.333 0.00 0.00 37.75 2.17
1071 1783 4.259356 TGATGAGAAGATTGGCAGAACAG 58.741 43.478 0.00 0.00 0.00 3.16
1094 1806 2.509052 TCTTACATTCCCAGATCGCG 57.491 50.000 0.00 0.00 0.00 5.87
1102 1814 1.815421 CCCAGATCGCGTTCCTTGG 60.815 63.158 13.36 14.40 0.00 3.61
1125 1837 7.516027 TGGTACAATTCAAGGAAATGTCCTCG 61.516 42.308 4.43 0.00 46.37 4.63
1452 2164 2.777969 GATCCAAGCACAGGAGCTG 58.222 57.895 0.00 0.00 45.89 4.24
1665 2377 3.008375 TGGAGAGTTGGGATTCTTCACTG 59.992 47.826 0.00 0.00 0.00 3.66
1761 2473 3.934457 AATTTACTGGGTCCTTTTGCG 57.066 42.857 0.00 0.00 0.00 4.85
1959 2671 1.795768 TGCAGAAACGACTGACATCC 58.204 50.000 11.57 0.00 39.94 3.51
2173 2885 2.497792 AATTGGACGGCCATGCTCCA 62.498 55.000 13.08 0.00 45.46 3.86
2183 2895 2.961062 GGCCATGCTCCAACTTGAATAT 59.039 45.455 0.00 0.00 0.00 1.28
2246 2961 0.827507 AAACCATGGTGTGTCTGGCC 60.828 55.000 20.60 0.00 33.12 5.36
2430 3150 0.250234 AAGTTGCGGCTCAGCTGATA 59.750 50.000 18.63 0.00 36.32 2.15
2444 3183 3.107601 AGCTGATAAGAGGCACAGGTTA 58.892 45.455 0.00 0.00 37.75 2.85
2460 3199 6.001460 CACAGGTTAAGTTGAAATGTAGGGA 58.999 40.000 0.00 0.00 0.00 4.20
2613 3521 7.391148 ACGTTTGGCTCATAAACAATAATCT 57.609 32.000 0.00 0.00 37.78 2.40
2615 3523 7.120579 ACGTTTGGCTCATAAACAATAATCTGA 59.879 33.333 0.00 0.00 37.78 3.27
2620 3528 7.611467 TGGCTCATAAACAATAATCTGACACTT 59.389 33.333 0.00 0.00 0.00 3.16
2659 3567 2.795231 ATTCACCCAGTCTCATGTGG 57.205 50.000 0.00 0.00 0.00 4.17
2680 3588 3.950395 GGTTCTGCTTGCAGAAGGATATT 59.050 43.478 30.74 0.00 41.31 1.28
2681 3589 4.400567 GGTTCTGCTTGCAGAAGGATATTT 59.599 41.667 30.74 0.00 41.31 1.40
2682 3590 5.338365 GTTCTGCTTGCAGAAGGATATTTG 58.662 41.667 30.74 1.65 41.31 2.32
2683 3591 4.592942 TCTGCTTGCAGAAGGATATTTGT 58.407 39.130 21.22 0.00 0.00 2.83
2684 3592 5.012239 TCTGCTTGCAGAAGGATATTTGTT 58.988 37.500 21.22 0.00 0.00 2.83
2685 3593 6.179756 TCTGCTTGCAGAAGGATATTTGTTA 58.820 36.000 21.22 0.00 0.00 2.41
2686 3594 6.317140 TCTGCTTGCAGAAGGATATTTGTTAG 59.683 38.462 21.22 0.00 0.00 2.34
2838 3754 3.006940 GCATGAACTGACCATCGGTAAA 58.993 45.455 0.00 0.00 34.28 2.01
2876 3792 1.674962 GCTGGCATCTCAATCAGTTCC 59.325 52.381 0.00 0.00 0.00 3.62
2937 3853 2.360165 CCTGTAAAATGCTCCAGATGCC 59.640 50.000 0.00 0.00 0.00 4.40
2941 3857 0.254178 AAATGCTCCAGATGCCGTCT 59.746 50.000 0.00 0.00 37.80 4.18
2960 3876 7.338196 TGCCGTCTATAATTGAATTTTCCTTCA 59.662 33.333 0.00 0.00 33.42 3.02
2961 3877 7.857885 GCCGTCTATAATTGAATTTTCCTTCAG 59.142 37.037 0.00 0.00 36.55 3.02
3035 4721 6.976636 TCTACGTTCATTGTATGCAATTGA 57.023 33.333 10.34 5.59 42.91 2.57
3036 4722 7.371126 TCTACGTTCATTGTATGCAATTGAA 57.629 32.000 10.34 10.74 42.91 2.69
3039 4725 6.855836 ACGTTCATTGTATGCAATTGAATCT 58.144 32.000 10.34 8.55 42.91 2.40
3051 4737 3.687572 ATTGAATCTTGATGCTCGTGC 57.312 42.857 1.71 1.71 40.20 5.34
3059 4745 4.704833 ATGCTCGTGCCGCTGGTT 62.705 61.111 7.05 0.00 38.71 3.67
3062 4748 3.414700 CTCGTGCCGCTGGTTGAC 61.415 66.667 0.00 0.00 0.00 3.18
3080 4771 5.163713 GGTTGACTTATCTGCATTGGACTTC 60.164 44.000 0.00 0.00 0.00 3.01
3095 4786 2.361438 GGACTTCGACGGTATCATTCCT 59.639 50.000 0.00 0.00 0.00 3.36
3105 4796 4.587684 ACGGTATCATTCCTTTATCGGTCT 59.412 41.667 0.00 0.00 0.00 3.85
3107 4798 6.436532 ACGGTATCATTCCTTTATCGGTCTAT 59.563 38.462 0.00 0.00 0.00 1.98
3122 4813 9.605951 TTATCGGTCTATTTATTTACTACCCCT 57.394 33.333 0.00 0.00 0.00 4.79
3123 4814 7.294017 TCGGTCTATTTATTTACTACCCCTG 57.706 40.000 0.00 0.00 0.00 4.45
3124 4815 6.840705 TCGGTCTATTTATTTACTACCCCTGT 59.159 38.462 0.00 0.00 0.00 4.00
3125 4816 8.004215 TCGGTCTATTTATTTACTACCCCTGTA 58.996 37.037 0.00 0.00 0.00 2.74
3126 4817 8.641541 CGGTCTATTTATTTACTACCCCTGTAA 58.358 37.037 0.00 0.00 0.00 2.41
3140 4831 7.983484 ACTACCCCTGTAAATAAATGTAAGACG 59.017 37.037 0.00 0.00 0.00 4.18
3141 4832 6.714278 ACCCCTGTAAATAAATGTAAGACGT 58.286 36.000 0.00 0.00 0.00 4.34
3142 4833 7.170277 ACCCCTGTAAATAAATGTAAGACGTT 58.830 34.615 0.00 0.00 0.00 3.99
3143 4834 7.666804 ACCCCTGTAAATAAATGTAAGACGTTT 59.333 33.333 0.00 2.63 40.18 3.60
3144 4835 8.517056 CCCCTGTAAATAAATGTAAGACGTTTT 58.483 33.333 2.37 0.00 38.23 2.43
3161 4852 9.760077 AAGACGTTTTAAGACTTCTAAGAATGA 57.240 29.630 5.69 0.00 29.18 2.57
3162 4853 9.413048 AGACGTTTTAAGACTTCTAAGAATGAG 57.587 33.333 3.61 0.00 0.00 2.90
3163 4854 9.408069 GACGTTTTAAGACTTCTAAGAATGAGA 57.592 33.333 0.00 0.00 0.00 3.27
3164 4855 9.760077 ACGTTTTAAGACTTCTAAGAATGAGAA 57.240 29.630 0.00 0.00 31.55 2.87
3172 4863 9.651913 AGACTTCTAAGAATGAGAAATGACTTC 57.348 33.333 0.00 0.00 34.45 3.01
3173 4864 9.429359 GACTTCTAAGAATGAGAAATGACTTCA 57.571 33.333 0.00 0.00 34.45 3.02
3174 4865 9.434420 ACTTCTAAGAATGAGAAATGACTTCAG 57.566 33.333 0.00 0.00 34.45 3.02
3175 4866 9.650539 CTTCTAAGAATGAGAAATGACTTCAGA 57.349 33.333 0.00 0.00 34.45 3.27
3177 4868 9.597170 TCTAAGAATGAGAAATGACTTCAGATG 57.403 33.333 0.00 0.00 36.40 2.90
3178 4869 9.381033 CTAAGAATGAGAAATGACTTCAGATGT 57.619 33.333 0.00 0.00 36.40 3.06
3180 4871 9.730705 AAGAATGAGAAATGACTTCAGATGTAA 57.269 29.630 0.00 0.00 36.40 2.41
3181 4872 9.902684 AGAATGAGAAATGACTTCAGATGTAAT 57.097 29.630 0.00 0.00 36.40 1.89
3184 4875 7.755591 TGAGAAATGACTTCAGATGTAATTGC 58.244 34.615 0.61 0.00 36.40 3.56
3185 4876 7.391275 TGAGAAATGACTTCAGATGTAATTGCA 59.609 33.333 0.00 0.00 36.40 4.08
3186 4877 7.533426 AGAAATGACTTCAGATGTAATTGCAC 58.467 34.615 0.00 0.00 36.40 4.57
3187 4878 6.822667 AATGACTTCAGATGTAATTGCACA 57.177 33.333 0.00 0.00 0.00 4.57
3188 4879 7.400599 AATGACTTCAGATGTAATTGCACAT 57.599 32.000 0.00 0.00 41.83 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.283684 CGCCGCAAACTCCAACCA 61.284 61.111 0.00 0.00 0.00 3.67
1 2 4.038080 CCGCCGCAAACTCCAACC 62.038 66.667 0.00 0.00 0.00 3.77
2 3 4.700365 GCCGCCGCAAACTCCAAC 62.700 66.667 0.00 0.00 34.03 3.77
21 22 4.742201 CGGTGCCCGGTCTGAGTG 62.742 72.222 0.00 0.00 44.15 3.51
34 35 4.864334 GGATCAGCCAGCCCGGTG 62.864 72.222 0.00 0.00 36.97 4.94
98 100 1.750193 TTGGTTCATTCGATGGCTCC 58.250 50.000 0.00 0.00 0.00 4.70
163 175 4.436998 CAGTCGTGGAGGCGGGTC 62.437 72.222 0.00 0.00 0.00 4.46
216 243 0.182775 GGGATGGCTTTACGGGTGAT 59.817 55.000 0.00 0.00 0.00 3.06
264 297 4.200283 GAGCTCGGAGTCAGGCGG 62.200 72.222 6.90 0.00 0.00 6.13
317 373 4.778415 CTCAGGACGTCACCGGCG 62.778 72.222 18.91 0.00 45.55 6.46
342 398 4.863925 GGAGCTCAGAGGTCGCGC 62.864 72.222 20.87 0.00 43.29 6.86
350 406 0.619832 ATGCCCTGAAGGAGCTCAGA 60.620 55.000 17.19 0.00 44.82 3.27
351 407 0.179051 GATGCCCTGAAGGAGCTCAG 60.179 60.000 17.19 4.79 42.19 3.35
355 411 1.227497 CTCGATGCCCTGAAGGAGC 60.227 63.158 0.00 0.48 38.24 4.70
357 413 1.680522 GAGCTCGATGCCCTGAAGGA 61.681 60.000 0.00 0.00 44.23 3.36
360 416 2.052104 TCGAGCTCGATGCCCTGAA 61.052 57.895 33.84 9.60 44.22 3.02
382 438 2.877335 CACTAGTTACCTCGAGCAACC 58.123 52.381 18.96 4.04 0.00 3.77
384 440 1.135489 CGCACTAGTTACCTCGAGCAA 60.135 52.381 6.99 0.00 0.00 3.91
413 469 9.750783 ACTGAAACTGAGGTAGTACTTCTAATA 57.249 33.333 13.04 0.00 39.18 0.98
418 474 6.578163 AGACTGAAACTGAGGTAGTACTTC 57.422 41.667 0.00 5.49 39.18 3.01
425 481 4.021894 GCTCTGAAGACTGAAACTGAGGTA 60.022 45.833 0.00 0.00 0.00 3.08
426 482 3.244044 GCTCTGAAGACTGAAACTGAGGT 60.244 47.826 0.00 0.00 0.00 3.85
427 483 3.006752 AGCTCTGAAGACTGAAACTGAGG 59.993 47.826 0.00 0.00 0.00 3.86
429 485 4.321601 GCTAGCTCTGAAGACTGAAACTGA 60.322 45.833 7.70 0.00 0.00 3.41
430 486 3.925913 GCTAGCTCTGAAGACTGAAACTG 59.074 47.826 7.70 0.00 0.00 3.16
432 488 3.925913 CAGCTAGCTCTGAAGACTGAAAC 59.074 47.826 16.15 0.00 36.19 2.78
452 546 6.092807 GCAGAAAGAAAATACTCCAGTACCAG 59.907 42.308 0.00 0.00 32.72 4.00
466 563 5.241506 CACTAGACCCATTGCAGAAAGAAAA 59.758 40.000 0.00 0.00 0.00 2.29
467 564 4.761739 CACTAGACCCATTGCAGAAAGAAA 59.238 41.667 0.00 0.00 0.00 2.52
470 567 3.942829 TCACTAGACCCATTGCAGAAAG 58.057 45.455 0.00 0.00 0.00 2.62
482 680 4.688021 CAGGCTTCACTAATCACTAGACC 58.312 47.826 0.00 0.00 0.00 3.85
492 690 0.036732 CACCAGGCAGGCTTCACTAA 59.963 55.000 0.00 0.00 43.14 2.24
493 691 0.835971 TCACCAGGCAGGCTTCACTA 60.836 55.000 0.00 0.00 43.14 2.74
495 693 1.968540 GTCACCAGGCAGGCTTCAC 60.969 63.158 0.00 0.00 43.14 3.18
497 695 0.610232 ATTGTCACCAGGCAGGCTTC 60.610 55.000 0.00 0.00 43.14 3.86
506 851 6.820152 TCATCTCACTCAATAATTGTCACCAG 59.180 38.462 0.00 0.00 0.00 4.00
515 860 8.188799 CACAAAAGCATCATCTCACTCAATAAT 58.811 33.333 0.00 0.00 0.00 1.28
528 873 2.027561 AGCATTGCCACAAAAGCATCAT 60.028 40.909 4.70 0.00 40.59 2.45
539 992 2.911819 TTACGCTTTAGCATTGCCAC 57.088 45.000 4.70 0.00 42.21 5.01
549 1002 7.073265 GCAACATCAAACTACTTTACGCTTTA 58.927 34.615 0.00 0.00 0.00 1.85
567 1020 6.674694 ACATGAGTAGAAATCTGCAACATC 57.325 37.500 0.00 0.00 30.86 3.06
605 1059 2.494471 TGAGATGAAATGGCCTTGCAAG 59.506 45.455 19.93 19.93 0.00 4.01
607 1061 1.820519 GTGAGATGAAATGGCCTTGCA 59.179 47.619 3.32 0.59 0.00 4.08
608 1062 1.135721 GGTGAGATGAAATGGCCTTGC 59.864 52.381 3.32 0.00 0.00 4.01
609 1063 2.449464 TGGTGAGATGAAATGGCCTTG 58.551 47.619 3.32 0.00 0.00 3.61
615 1069 6.205464 ACACAACTAGTTGGTGAGATGAAATG 59.795 38.462 33.11 21.33 44.45 2.32
692 1148 3.309954 CGCAGCATTAGAGTTCCCTAAAC 59.690 47.826 0.00 0.00 38.21 2.01
698 1202 2.159170 AGTCTCGCAGCATTAGAGTTCC 60.159 50.000 0.00 0.00 33.96 3.62
710 1214 6.036517 ACAAATAGCTTAATCAAGTCTCGCAG 59.963 38.462 0.00 0.00 34.00 5.18
734 1238 2.301577 ATTGACCAGAAGAGCGCTAC 57.698 50.000 11.50 5.11 0.00 3.58
737 1241 1.806542 TGAAATTGACCAGAAGAGCGC 59.193 47.619 0.00 0.00 0.00 5.92
738 1242 4.872691 ACTATGAAATTGACCAGAAGAGCG 59.127 41.667 0.00 0.00 0.00 5.03
764 1268 6.260050 ACAGAAAATTTACAGACATCACACGT 59.740 34.615 0.00 0.00 0.00 4.49
784 1290 2.922740 GTGTACCACCTCCAACAGAA 57.077 50.000 0.00 0.00 0.00 3.02
812 1324 2.678336 GCAGTGGCAGTAGGAATAACAC 59.322 50.000 0.00 0.00 40.72 3.32
817 1329 0.393537 GCAGCAGTGGCAGTAGGAAT 60.394 55.000 0.00 0.00 44.61 3.01
823 1335 0.107800 CTCATAGCAGCAGTGGCAGT 60.108 55.000 0.00 0.00 44.61 4.40
875 1387 5.006386 CCAAAAGCCTGTATCTCAACTCTT 58.994 41.667 0.00 0.00 0.00 2.85
879 1391 6.759497 AATACCAAAAGCCTGTATCTCAAC 57.241 37.500 0.00 0.00 0.00 3.18
924 1436 5.764131 CCGTTTCAAACAACATAAGCCTTA 58.236 37.500 0.22 0.00 0.00 2.69
927 1439 2.729360 GCCGTTTCAAACAACATAAGCC 59.271 45.455 0.22 0.00 0.00 4.35
941 1454 3.312697 GGACAGAATATTCAGGCCGTTTC 59.687 47.826 16.26 1.91 31.83 2.78
945 1458 1.543429 GGGGACAGAATATTCAGGCCG 60.543 57.143 22.58 6.90 42.42 6.13
977 1491 7.334421 GCATTCAGGAGTGTACTTCAAATTCTA 59.666 37.037 0.00 0.00 0.00 2.10
1009 1716 2.429930 TGTGTAGGCACCACAGGC 59.570 61.111 5.29 0.00 44.65 4.85
1014 1721 0.250295 GCAAGTCTGTGTAGGCACCA 60.250 55.000 0.00 0.00 44.65 4.17
1048 1756 4.259356 TGTTCTGCCAATCTTCTCATCAG 58.741 43.478 0.00 0.00 0.00 2.90
1071 1783 4.386049 CGCGATCTGGGAATGTAAGATAAC 59.614 45.833 0.00 0.00 30.83 1.89
1125 1837 1.731720 GTCCATGACCAGCAGAGAAC 58.268 55.000 0.00 0.00 0.00 3.01
1452 2164 8.214364 AGATTTCTTACCAAGATAGGTTCCATC 58.786 37.037 0.00 0.00 43.08 3.51
1665 2377 1.287730 CTTCTCGTGCTGTGACTGCC 61.288 60.000 11.94 2.85 0.00 4.85
1761 2473 5.938125 TCCTGCTGGATACTTTAACTTGAAC 59.062 40.000 8.48 0.00 37.46 3.18
1902 2614 3.681897 CCTCATGTAGAACAGCAACAGAC 59.318 47.826 0.00 0.00 0.00 3.51
1959 2671 3.577649 TGGAAGACTTCTAGCTTGTCG 57.422 47.619 14.72 0.00 36.01 4.35
2046 2758 5.046807 GGTACTTCTTGCTCCCTTGTTAGTA 60.047 44.000 0.00 0.00 0.00 1.82
2173 2885 4.666512 ACTGCCAGTGGAATATTCAAGTT 58.333 39.130 15.20 0.00 0.00 2.66
2183 2895 1.409064 CGAGCTATACTGCCAGTGGAA 59.591 52.381 15.20 0.00 0.00 3.53
2246 2961 2.163818 TCAACTAAGAAGGTGCACCG 57.836 50.000 29.68 16.82 40.52 4.94
2430 3150 3.857157 TCAACTTAACCTGTGCCTCTT 57.143 42.857 0.00 0.00 0.00 2.85
2444 3183 7.466804 TCAACCTAATCCCTACATTTCAACTT 58.533 34.615 0.00 0.00 0.00 2.66
2460 3199 5.039645 TCCTCTCAAATCCCTCAACCTAAT 58.960 41.667 0.00 0.00 0.00 1.73
2545 3453 9.109393 GGAGAAGCAAACTCAACATTACATATA 57.891 33.333 0.00 0.00 36.26 0.86
2637 3545 4.042809 ACCACATGAGACTGGGTGAATAAA 59.957 41.667 0.00 0.00 33.16 1.40
2680 3588 7.270047 AGTAGCAGAACAGTAACAACTAACAA 58.730 34.615 0.00 0.00 0.00 2.83
2681 3589 6.812998 AGTAGCAGAACAGTAACAACTAACA 58.187 36.000 0.00 0.00 0.00 2.41
2682 3590 7.437267 TGAAGTAGCAGAACAGTAACAACTAAC 59.563 37.037 0.00 0.00 0.00 2.34
2683 3591 7.494211 TGAAGTAGCAGAACAGTAACAACTAA 58.506 34.615 0.00 0.00 0.00 2.24
2684 3592 7.046292 TGAAGTAGCAGAACAGTAACAACTA 57.954 36.000 0.00 0.00 0.00 2.24
2685 3593 5.914033 TGAAGTAGCAGAACAGTAACAACT 58.086 37.500 0.00 0.00 0.00 3.16
2686 3594 6.787085 ATGAAGTAGCAGAACAGTAACAAC 57.213 37.500 0.00 0.00 0.00 3.32
2838 3754 0.804989 GCTTGTTCATGCGCTAACCT 59.195 50.000 9.73 0.00 0.00 3.50
2876 3792 6.949578 ATGGATGCGAAAACAACAAAATAG 57.050 33.333 0.00 0.00 0.00 1.73
2937 3853 9.922305 GACTGAAGGAAAATTCAATTATAGACG 57.078 33.333 0.00 0.00 38.66 4.18
2960 3876 4.511527 CAGACCAATCAATGTGCTAGACT 58.488 43.478 0.00 0.00 0.00 3.24
2961 3877 3.064545 GCAGACCAATCAATGTGCTAGAC 59.935 47.826 0.00 0.00 0.00 2.59
3051 4737 1.009829 GCAGATAAGTCAACCAGCGG 58.990 55.000 0.00 0.00 0.00 5.52
3059 4745 4.081697 TCGAAGTCCAATGCAGATAAGTCA 60.082 41.667 0.00 0.00 0.00 3.41
3060 4746 4.268884 GTCGAAGTCCAATGCAGATAAGTC 59.731 45.833 0.00 0.00 0.00 3.01
3061 4747 4.184629 GTCGAAGTCCAATGCAGATAAGT 58.815 43.478 0.00 0.00 0.00 2.24
3062 4748 3.243877 CGTCGAAGTCCAATGCAGATAAG 59.756 47.826 0.00 0.00 0.00 1.73
3080 4771 3.918591 CCGATAAAGGAATGATACCGTCG 59.081 47.826 0.00 0.00 0.00 5.12
3115 4806 7.983484 ACGTCTTACATTTATTTACAGGGGTAG 59.017 37.037 0.00 0.00 0.00 3.18
3116 4807 7.850193 ACGTCTTACATTTATTTACAGGGGTA 58.150 34.615 0.00 0.00 0.00 3.69
3117 4808 6.714278 ACGTCTTACATTTATTTACAGGGGT 58.286 36.000 0.00 0.00 0.00 4.95
3118 4809 7.619964 AACGTCTTACATTTATTTACAGGGG 57.380 36.000 0.00 0.00 0.00 4.79
3135 4826 9.760077 TCATTCTTAGAAGTCTTAAAACGTCTT 57.240 29.630 2.66 0.00 38.62 3.01
3136 4827 9.413048 CTCATTCTTAGAAGTCTTAAAACGTCT 57.587 33.333 2.91 2.91 40.41 4.18
3137 4828 9.408069 TCTCATTCTTAGAAGTCTTAAAACGTC 57.592 33.333 0.03 0.00 0.00 4.34
3138 4829 9.760077 TTCTCATTCTTAGAAGTCTTAAAACGT 57.240 29.630 0.03 0.00 0.00 3.99
3146 4837 9.651913 GAAGTCATTTCTCATTCTTAGAAGTCT 57.348 33.333 0.03 0.00 34.59 3.24
3147 4838 9.429359 TGAAGTCATTTCTCATTCTTAGAAGTC 57.571 33.333 0.03 0.00 36.71 3.01
3148 4839 9.434420 CTGAAGTCATTTCTCATTCTTAGAAGT 57.566 33.333 0.03 0.00 36.71 3.01
3149 4840 9.650539 TCTGAAGTCATTTCTCATTCTTAGAAG 57.349 33.333 0.03 0.00 36.71 2.85
3151 4842 9.597170 CATCTGAAGTCATTTCTCATTCTTAGA 57.403 33.333 0.00 0.00 36.71 2.10
3152 4843 9.381033 ACATCTGAAGTCATTTCTCATTCTTAG 57.619 33.333 0.00 0.00 36.71 2.18
3154 4845 9.730705 TTACATCTGAAGTCATTTCTCATTCTT 57.269 29.630 0.00 0.00 36.71 2.52
3155 4846 9.902684 ATTACATCTGAAGTCATTTCTCATTCT 57.097 29.630 0.00 0.00 36.71 2.40
3158 4849 8.404000 GCAATTACATCTGAAGTCATTTCTCAT 58.596 33.333 0.00 0.00 36.71 2.90
3159 4850 7.391275 TGCAATTACATCTGAAGTCATTTCTCA 59.609 33.333 0.00 0.00 36.71 3.27
3160 4851 7.695618 GTGCAATTACATCTGAAGTCATTTCTC 59.304 37.037 0.00 0.00 36.71 2.87
3161 4852 7.175467 TGTGCAATTACATCTGAAGTCATTTCT 59.825 33.333 0.00 0.00 36.71 2.52
3162 4853 7.307694 TGTGCAATTACATCTGAAGTCATTTC 58.692 34.615 0.00 0.00 36.29 2.17
3163 4854 7.218228 TGTGCAATTACATCTGAAGTCATTT 57.782 32.000 0.00 0.00 0.00 2.32
3164 4855 6.822667 TGTGCAATTACATCTGAAGTCATT 57.177 33.333 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.