Multiple sequence alignment - TraesCS4A01G103600

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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 TraesCS4A01G103600 chr4A 100.000 4883 0 0 1 4883 117276547 117281429 0.000000e+00 9018.0
1 TraesCS4A01G103600 chr4D 95.553 2923 95 17 1354 4260 348312907 348310004 0.000000e+00 4645.0
2 TraesCS4A01G103600 chr4D 96.117 515 15 3 825 1339 348313506 348312997 0.000000e+00 835.0
3 TraesCS4A01G103600 chr4D 87.158 584 38 9 4304 4883 348306530 348305980 3.210000e-176 628.0
4 TraesCS4A01G103600 chr4B 95.724 1754 65 5 826 2578 428469990 428468246 0.000000e+00 2815.0
5 TraesCS4A01G103600 chr4B 93.838 1704 70 15 2579 4271 428468207 428466528 0.000000e+00 2532.0
6 TraesCS4A01G103600 chr4B 87.983 233 17 7 4483 4711 428466301 428466076 1.040000e-66 265.0
7 TraesCS4A01G103600 chr4B 90.000 140 9 2 4280 4414 428466459 428466320 5.020000e-40 176.0
8 TraesCS4A01G103600 chr7A 98.506 803 9 2 1 800 644039048 644039850 0.000000e+00 1413.0
9 TraesCS4A01G103600 chr7A 95.301 532 24 1 1 532 516991977 516992507 0.000000e+00 843.0
10 TraesCS4A01G103600 chr2B 98.506 803 8 3 2 800 554723482 554724284 0.000000e+00 1413.0
11 TraesCS4A01G103600 chr2B 92.768 802 27 11 1 800 759755383 759756155 0.000000e+00 1131.0
12 TraesCS4A01G103600 chr2B 96.642 536 17 1 1 535 573817338 573816803 0.000000e+00 889.0
13 TraesCS4A01G103600 chr2B 95.693 534 21 1 1 532 140782695 140783228 0.000000e+00 857.0
14 TraesCS4A01G103600 chr2B 96.947 262 4 2 541 800 140783208 140783467 2.090000e-118 436.0
15 TraesCS4A01G103600 chr3B 92.643 802 27 11 1 800 753817954 753818725 0.000000e+00 1125.0
16 TraesCS4A01G103600 chr3B 91.199 784 35 13 22 800 12308538 12307784 0.000000e+00 1035.0
17 TraesCS4A01G103600 chr1B 92.643 802 27 11 1 800 679687683 679688454 0.000000e+00 1125.0
18 TraesCS4A01G103600 chr5B 91.021 813 39 14 1 809 539436368 539435586 0.000000e+00 1066.0
19 TraesCS4A01G103600 chr7B 94.403 536 29 1 1 535 226421757 226421222 0.000000e+00 822.0
20 TraesCS4A01G103600 chr2A 96.512 258 7 1 545 800 770969983 770969726 4.520000e-115 425.0
21 TraesCS4A01G103600 chr2A 88.312 77 9 0 4700 4776 45481649 45481573 5.200000e-15 93.5
22 TraesCS4A01G103600 chr5A 91.781 73 6 0 4705 4777 474816617 474816545 8.650000e-18 102.0
23 TraesCS4A01G103600 chr5A 100.000 28 0 0 4468 4495 340626348 340626375 9.000000e-03 52.8
24 TraesCS4A01G103600 chr5D 92.857 70 4 1 4709 4777 371786436 371786367 3.110000e-17 100.0
25 TraesCS4A01G103600 chr7D 90.541 74 7 0 4700 4773 165657867 165657940 1.120000e-16 99.0
26 TraesCS4A01G103600 chr6B 90.541 74 7 0 4700 4773 139885294 139885221 1.120000e-16 99.0
27 TraesCS4A01G103600 chr1A 87.209 86 11 0 4700 4785 27362021 27361936 1.120000e-16 99.0
28 TraesCS4A01G103600 chr6D 90.000 70 6 1 4693 4761 155601959 155602028 6.730000e-14 89.8
29 TraesCS4A01G103600 chr6A 90.000 70 6 1 4693 4761 209391339 209391408 6.730000e-14 89.8


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 TraesCS4A01G103600 chr4A 117276547 117281429 4882 False 9018.0 9018 100.000000 1 4883 1 chr4A.!!$F1 4882
1 TraesCS4A01G103600 chr4D 348305980 348313506 7526 True 2036.0 4645 92.942667 825 4883 3 chr4D.!!$R1 4058
2 TraesCS4A01G103600 chr4B 428466076 428469990 3914 True 1447.0 2815 91.886250 826 4711 4 chr4B.!!$R1 3885
3 TraesCS4A01G103600 chr7A 644039048 644039850 802 False 1413.0 1413 98.506000 1 800 1 chr7A.!!$F2 799
4 TraesCS4A01G103600 chr7A 516991977 516992507 530 False 843.0 843 95.301000 1 532 1 chr7A.!!$F1 531
5 TraesCS4A01G103600 chr2B 554723482 554724284 802 False 1413.0 1413 98.506000 2 800 1 chr2B.!!$F1 798
6 TraesCS4A01G103600 chr2B 759755383 759756155 772 False 1131.0 1131 92.768000 1 800 1 chr2B.!!$F2 799
7 TraesCS4A01G103600 chr2B 573816803 573817338 535 True 889.0 889 96.642000 1 535 1 chr2B.!!$R1 534
8 TraesCS4A01G103600 chr2B 140782695 140783467 772 False 646.5 857 96.320000 1 800 2 chr2B.!!$F3 799
9 TraesCS4A01G103600 chr3B 753817954 753818725 771 False 1125.0 1125 92.643000 1 800 1 chr3B.!!$F1 799
10 TraesCS4A01G103600 chr3B 12307784 12308538 754 True 1035.0 1035 91.199000 22 800 1 chr3B.!!$R1 778
11 TraesCS4A01G103600 chr1B 679687683 679688454 771 False 1125.0 1125 92.643000 1 800 1 chr1B.!!$F1 799
12 TraesCS4A01G103600 chr5B 539435586 539436368 782 True 1066.0 1066 91.021000 1 809 1 chr5B.!!$R1 808
13 TraesCS4A01G103600 chr7B 226421222 226421757 535 True 822.0 822 94.403000 1 535 1 chr7B.!!$R1 534

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
819 834 0.035056 CAAGGGAAATGAGCCTCGGT 60.035 55.000 0.0 0.0 0.00 4.69 F
943 958 0.566136 CGTGATACGTTGCTACAGCG 59.434 55.000 0.0 2.2 43.29 5.18 F
1350 1365 0.600255 GGCGGAATGTAGGATGACGG 60.600 60.000 0.0 0.0 0.00 4.79 F
2997 3129 1.697982 AGGGTAAGGCGACACTCTTTT 59.302 47.619 0.0 0.0 0.00 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2709 2841 0.753867 TGGCTTGGTTAGTGTCACGA 59.246 50.000 0.00 0.0 0.00 4.35 R
2933 3065 2.694628 TGAATTGTTTGCCTGACTGCTT 59.305 40.909 0.00 0.0 0.00 3.91 R
3316 3449 2.037251 GACTCCTTGCAACAGTACCTGA 59.963 50.000 6.32 0.0 35.18 3.86 R
4457 8059 0.104304 CCCTCCGTCCAAGTAATCCG 59.896 60.000 0.00 0.0 0.00 4.18 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
87 88 7.496346 AATACTCTGGAATACTGTTCCTTCA 57.504 36.000 6.17 0.00 39.31 3.02
800 815 1.324736 GCACGTGCATGCTTACTAGTC 59.675 52.381 34.52 0.00 42.62 2.59
801 816 2.606108 CACGTGCATGCTTACTAGTCA 58.394 47.619 20.33 0.00 0.00 3.41
802 817 2.993220 CACGTGCATGCTTACTAGTCAA 59.007 45.455 20.33 0.00 0.00 3.18
803 818 3.061295 CACGTGCATGCTTACTAGTCAAG 59.939 47.826 20.33 3.31 0.00 3.02
806 821 2.837591 TGCATGCTTACTAGTCAAGGGA 59.162 45.455 20.33 0.00 0.00 4.20
809 824 4.884164 GCATGCTTACTAGTCAAGGGAAAT 59.116 41.667 11.37 0.00 0.00 2.17
810 825 5.220931 GCATGCTTACTAGTCAAGGGAAATG 60.221 44.000 11.37 0.00 0.00 2.32
811 826 5.755409 TGCTTACTAGTCAAGGGAAATGA 57.245 39.130 0.00 0.00 0.00 2.57
812 827 5.734720 TGCTTACTAGTCAAGGGAAATGAG 58.265 41.667 0.00 0.00 0.00 2.90
813 828 4.572795 GCTTACTAGTCAAGGGAAATGAGC 59.427 45.833 0.00 0.00 0.00 4.26
814 829 3.636153 ACTAGTCAAGGGAAATGAGCC 57.364 47.619 0.00 0.00 0.00 4.70
815 830 3.185455 ACTAGTCAAGGGAAATGAGCCT 58.815 45.455 0.00 0.00 0.00 4.58
816 831 2.797177 AGTCAAGGGAAATGAGCCTC 57.203 50.000 0.00 0.00 0.00 4.70
817 832 1.065854 AGTCAAGGGAAATGAGCCTCG 60.066 52.381 0.00 0.00 0.00 4.63
818 833 0.253044 TCAAGGGAAATGAGCCTCGG 59.747 55.000 0.00 0.00 0.00 4.63
819 834 0.035056 CAAGGGAAATGAGCCTCGGT 60.035 55.000 0.00 0.00 0.00 4.69
820 835 1.209504 CAAGGGAAATGAGCCTCGGTA 59.790 52.381 0.00 0.00 0.00 4.02
821 836 1.807814 AGGGAAATGAGCCTCGGTAT 58.192 50.000 0.00 0.00 0.00 2.73
822 837 2.127708 AGGGAAATGAGCCTCGGTATT 58.872 47.619 0.00 0.00 0.00 1.89
823 838 2.104963 AGGGAAATGAGCCTCGGTATTC 59.895 50.000 0.00 0.00 0.00 1.75
837 852 4.693283 TCGGTATTCGAGATTGATGCTTT 58.307 39.130 0.00 0.00 43.74 3.51
838 853 5.116180 TCGGTATTCGAGATTGATGCTTTT 58.884 37.500 0.00 0.00 43.74 2.27
839 854 5.584649 TCGGTATTCGAGATTGATGCTTTTT 59.415 36.000 0.00 0.00 43.74 1.94
912 927 0.976641 TAGATAGCTGGGGCCGAATG 59.023 55.000 0.00 0.00 39.73 2.67
943 958 0.566136 CGTGATACGTTGCTACAGCG 59.434 55.000 0.00 2.20 43.29 5.18
961 976 1.878102 GCGTGTCAGTGAAACCCATCT 60.878 52.381 7.90 0.00 37.80 2.90
962 977 2.069273 CGTGTCAGTGAAACCCATCTC 58.931 52.381 7.90 0.00 37.80 2.75
1048 1063 1.388065 CCGGAGAGATGTCGAGGCTT 61.388 60.000 0.00 0.00 0.00 4.35
1121 1136 1.134280 CGATCTCAGTGGCATTTCCCT 60.134 52.381 0.00 0.00 0.00 4.20
1215 1230 2.384653 GAAGGTAGCTCCCGCATCCC 62.385 65.000 0.00 0.00 39.10 3.85
1272 1287 7.640852 TCTCTCGTATGCTAGTCTGTTTATTC 58.359 38.462 0.00 0.00 0.00 1.75
1348 1363 1.139058 AGTGGCGGAATGTAGGATGAC 59.861 52.381 0.00 0.00 0.00 3.06
1350 1365 0.600255 GGCGGAATGTAGGATGACGG 60.600 60.000 0.00 0.00 0.00 4.79
1462 1552 2.900122 ACGTTTGGAATGCGAATCAG 57.100 45.000 0.00 0.00 0.00 2.90
1618 1708 4.166144 AGGAGGTATTGGGTTGGATTACAG 59.834 45.833 0.00 0.00 0.00 2.74
1661 1751 6.772716 GCAAGGATGACCATTTTATCTCCTTA 59.227 38.462 0.00 0.00 39.09 2.69
1662 1752 7.285401 GCAAGGATGACCATTTTATCTCCTTAA 59.715 37.037 0.00 0.00 39.09 1.85
1745 1835 5.185056 TGATTCCTGTATGTGACTTTCGAGA 59.815 40.000 0.00 0.00 0.00 4.04
2440 2534 4.636206 CAGGAGTCTACAATTGGGTTTAGC 59.364 45.833 10.83 0.00 0.00 3.09
2477 2571 8.457238 AAAGAAATAGCCTTTTAGGATAGCAG 57.543 34.615 0.00 0.00 39.95 4.24
2482 2576 4.518249 AGCCTTTTAGGATAGCAGTTGAC 58.482 43.478 0.00 0.00 37.67 3.18
2489 2583 4.767578 AGGATAGCAGTTGACATGTGAT 57.232 40.909 1.15 0.00 0.00 3.06
2933 3065 4.009675 CCTTCGGTGGAATCATTTGAGAA 58.990 43.478 0.00 0.00 0.00 2.87
2997 3129 1.697982 AGGGTAAGGCGACACTCTTTT 59.302 47.619 0.00 0.00 0.00 2.27
2999 3131 3.325716 AGGGTAAGGCGACACTCTTTTTA 59.674 43.478 0.00 0.00 0.00 1.52
3000 3132 4.019591 AGGGTAAGGCGACACTCTTTTTAT 60.020 41.667 0.00 0.00 0.00 1.40
3001 3133 4.331992 GGGTAAGGCGACACTCTTTTTATC 59.668 45.833 0.00 0.00 0.00 1.75
3002 3134 4.933400 GGTAAGGCGACACTCTTTTTATCA 59.067 41.667 0.00 0.00 0.00 2.15
3178 3310 4.964262 ACTATTGACCATGCAAATCCCAAT 59.036 37.500 0.00 0.18 0.00 3.16
3189 3321 7.228906 CCATGCAAATCCCAATAAATGCAATAA 59.771 33.333 2.13 0.00 45.63 1.40
3203 3336 2.578021 TGCAATAAGGAGAAGAAGCCCT 59.422 45.455 0.00 0.00 0.00 5.19
3274 3407 6.598064 TGAGATCCATAATGCAGCTATTGATG 59.402 38.462 8.92 0.00 0.00 3.07
3316 3449 5.606348 TGTTTTTGCTGTTTGGGTCTATT 57.394 34.783 0.00 0.00 0.00 1.73
3395 3528 2.616960 TGTGCGGCACTAACTATGAAG 58.383 47.619 30.81 0.00 35.11 3.02
3414 3547 4.520492 TGAAGCTCCTCCATTTGAAAACTC 59.480 41.667 0.00 0.00 0.00 3.01
3438 3571 1.404035 CAGGTAATACTTTTGGGCGGC 59.596 52.381 0.00 0.00 0.00 6.53
3643 3777 5.547465 CCATGCGGGTTATTCAGTAATCTA 58.453 41.667 0.00 0.00 0.00 1.98
3699 3834 2.119495 TCAACCTAGGATCTGAAGCCC 58.881 52.381 17.98 0.00 0.00 5.19
3727 3862 3.665871 CGCATGTGATAGAGATGTGTACG 59.334 47.826 0.00 0.00 32.42 3.67
3807 3946 0.108585 TCAACCTGGACCTTGTGCTC 59.891 55.000 0.00 0.00 0.00 4.26
3989 4132 0.810426 TGGTGCGTTTGAACTGCGTA 60.810 50.000 6.34 0.00 33.37 4.42
4022 4165 2.676121 CGCATTGTTGGGCTGGGA 60.676 61.111 0.00 0.00 0.00 4.37
4039 4182 4.273235 GCTGGGAAAATTTTGAGGTTGTTG 59.727 41.667 8.47 0.00 0.00 3.33
4044 4187 5.526846 GGAAAATTTTGAGGTTGTTGCATCA 59.473 36.000 8.47 0.00 0.00 3.07
4062 4205 5.533528 TGCATCATCCATTTGGTTCTAGATG 59.466 40.000 0.00 0.00 36.34 2.90
4119 4262 5.364735 TGCTGAGAAGATATGTGGAGAATGA 59.635 40.000 0.00 0.00 0.00 2.57
4137 4288 9.028185 GGAGAATGAATGCAAAGAAATATGTTC 57.972 33.333 0.00 0.00 0.00 3.18
4157 4308 6.946340 TGTTCTTCATTGGCTCTCAGTATTA 58.054 36.000 0.00 0.00 0.00 0.98
4158 4309 7.044181 TGTTCTTCATTGGCTCTCAGTATTAG 58.956 38.462 0.00 0.00 0.00 1.73
4159 4310 6.798427 TCTTCATTGGCTCTCAGTATTAGT 57.202 37.500 0.00 0.00 0.00 2.24
4160 4311 7.898014 TCTTCATTGGCTCTCAGTATTAGTA 57.102 36.000 0.00 0.00 0.00 1.82
4209 4360 3.884091 CTGGTAATAGTAGGAGCGTCTGT 59.116 47.826 0.00 0.00 0.00 3.41
4219 4370 1.560860 GAGCGTCTGTGACTGGCAAC 61.561 60.000 0.00 0.00 0.00 4.17
4233 4387 1.067916 GCAACAACTTGGCACCCAG 59.932 57.895 0.00 0.00 33.81 4.45
4235 4389 2.133641 AACAACTTGGCACCCAGGC 61.134 57.895 0.00 0.00 44.50 4.85
4260 4414 7.795859 CAAAGGCAATTTGTTGTTTATTCGAT 58.204 30.769 5.67 0.00 42.84 3.59
4262 4416 5.348451 AGGCAATTTGTTGTTTATTCGATGC 59.652 36.000 0.00 0.00 0.00 3.91
4336 7867 2.207590 GCGATGCTTCATCAGTCATCA 58.792 47.619 7.47 0.00 40.54 3.07
4381 7981 7.690952 AAACCCTTATATCTGCACGTAAAAA 57.309 32.000 0.00 0.00 0.00 1.94
4390 7990 2.973224 CTGCACGTAAAAACATCAGCAC 59.027 45.455 0.00 0.00 0.00 4.40
4419 8019 4.456911 CAGTAAAACAGCAGATGTCACCAT 59.543 41.667 0.00 0.00 43.00 3.55
4453 8055 5.665812 AGTCCTGCAAGTAATATTACCTCCA 59.334 40.000 19.74 13.35 34.19 3.86
4457 8059 5.876357 TGCAAGTAATATTACCTCCATCCC 58.124 41.667 19.74 3.74 34.19 3.85
4490 8092 3.615155 ACGGAGGGAGTACTACTACAAC 58.385 50.000 4.77 0.00 27.88 3.32
4491 8093 3.265479 ACGGAGGGAGTACTACTACAACT 59.735 47.826 4.77 0.00 27.88 3.16
4513 8115 0.462789 TTCCTTAACGAGATCGGGGC 59.537 55.000 7.22 0.00 44.95 5.80
4655 8258 6.262496 ACTTTACTTGGTTAAGGCAAGACTTC 59.738 38.462 0.00 0.00 38.26 3.01
4656 8259 3.487372 ACTTGGTTAAGGCAAGACTTCC 58.513 45.455 0.00 0.00 38.26 3.46
4663 8266 5.475564 GGTTAAGGCAAGACTTCCATAAACA 59.524 40.000 0.00 0.00 32.02 2.83
4731 8335 8.637986 TCTTAAATGTAAGATGTTTTGGCAGTT 58.362 29.630 0.84 0.00 40.68 3.16
4773 8377 8.848474 AACATCTTATATTAATGAACGGAGGG 57.152 34.615 0.00 0.00 0.00 4.30
4785 8389 3.758554 TGAACGGAGGGTGTAGTAAGTAC 59.241 47.826 0.00 0.00 0.00 2.73
4789 8393 4.460731 ACGGAGGGTGTAGTAAGTACTTTC 59.539 45.833 14.49 8.92 37.73 2.62
4811 8415 9.311916 CTTTCAAATAAGAGTCGAATGATCTCT 57.688 33.333 0.00 0.00 39.79 3.10
4825 8429 4.508551 TGATCTCTATTTGGTGTGCCAT 57.491 40.909 0.00 0.00 45.56 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
673 686 6.581919 CACAATGTTTGATGTCGCTCAAATTA 59.418 34.615 9.72 4.96 44.48 1.40
800 815 0.035056 ACCGAGGCTCATTTCCCTTG 60.035 55.000 15.95 0.00 33.21 3.61
801 816 1.580059 TACCGAGGCTCATTTCCCTT 58.420 50.000 15.95 0.00 0.00 3.95
802 817 1.807814 ATACCGAGGCTCATTTCCCT 58.192 50.000 15.95 0.00 0.00 4.20
803 818 2.495084 GAATACCGAGGCTCATTTCCC 58.505 52.381 15.95 0.00 0.00 3.97
815 830 4.322080 AAGCATCAATCTCGAATACCGA 57.678 40.909 0.00 0.00 46.35 4.69
816 831 5.409643 AAAAGCATCAATCTCGAATACCG 57.590 39.130 0.00 0.00 40.25 4.02
837 852 4.092675 GCTTTGCAACTAAGCACACAAAAA 59.907 37.500 15.16 0.00 45.61 1.94
838 853 3.616379 GCTTTGCAACTAAGCACACAAAA 59.384 39.130 15.16 0.00 45.61 2.44
839 854 3.186119 GCTTTGCAACTAAGCACACAAA 58.814 40.909 15.16 0.00 45.61 2.83
840 855 2.808244 GCTTTGCAACTAAGCACACAA 58.192 42.857 15.16 0.00 45.61 3.33
854 869 2.683362 GGTCATAGTTAGTGGGCTTTGC 59.317 50.000 0.00 0.00 0.00 3.68
943 958 2.069273 CGAGATGGGTTTCACTGACAC 58.931 52.381 0.00 0.00 0.00 3.67
961 976 2.106131 CGATGCGAATGGACCCGA 59.894 61.111 0.00 0.00 0.00 5.14
962 977 1.762222 GAACGATGCGAATGGACCCG 61.762 60.000 0.00 0.00 0.00 5.28
969 984 0.174845 TTCGGGAGAACGATGCGAAT 59.825 50.000 0.00 0.00 45.39 3.34
1028 1043 2.122167 GCCTCGACATCTCTCCGGT 61.122 63.158 0.00 0.00 0.00 5.28
1121 1136 2.020720 GAAGAGACGAGAGGATGCAGA 58.979 52.381 0.00 0.00 0.00 4.26
1215 1230 2.070262 TCACGAGAATCACAGCACAG 57.930 50.000 0.00 0.00 33.17 3.66
1272 1287 2.026522 CTAGACCTCGCCGGAGAAG 58.973 63.158 9.83 5.69 43.27 2.85
1348 1363 3.198068 CCTCAATGAACTACATGGTCCG 58.802 50.000 0.00 0.00 39.39 4.79
1350 1365 5.760253 CCATACCTCAATGAACTACATGGTC 59.240 44.000 0.00 0.00 39.39 4.02
1462 1552 8.704234 CAGCACTATCTCGTATTTTAGGATTTC 58.296 37.037 0.00 0.00 0.00 2.17
1661 1751 7.290110 TGACTCGGTATCATGATCATAACTT 57.710 36.000 12.53 0.00 0.00 2.66
1662 1752 6.901081 TGACTCGGTATCATGATCATAACT 57.099 37.500 12.53 0.00 0.00 2.24
1721 1811 5.185056 TCTCGAAAGTCACATACAGGAATCA 59.815 40.000 0.00 0.00 0.00 2.57
1858 1950 2.409064 TGGGAAGGACCACTCAGTTA 57.591 50.000 0.00 0.00 41.20 2.24
2112 2204 8.700644 CAGTAGAAGTGTTACTGAAATGTACAC 58.299 37.037 0.00 0.00 46.98 2.90
2477 2571 5.459762 CACAAAACAAGGATCACATGTCAAC 59.540 40.000 0.00 0.00 0.00 3.18
2482 2576 4.589216 ACCACAAAACAAGGATCACATG 57.411 40.909 0.00 0.00 0.00 3.21
2489 2583 3.366396 TGCCTTAACCACAAAACAAGGA 58.634 40.909 2.91 0.00 38.42 3.36
2709 2841 0.753867 TGGCTTGGTTAGTGTCACGA 59.246 50.000 0.00 0.00 0.00 4.35
2933 3065 2.694628 TGAATTGTTTGCCTGACTGCTT 59.305 40.909 0.00 0.00 0.00 3.91
3158 3290 5.954153 TTATTGGGATTTGCATGGTCAAT 57.046 34.783 0.00 0.00 0.00 2.57
3178 3310 5.594317 GGGCTTCTTCTCCTTATTGCATTTA 59.406 40.000 0.00 0.00 0.00 1.40
3247 3380 7.173032 TCAATAGCTGCATTATGGATCTCAAT 58.827 34.615 1.02 0.00 0.00 2.57
3316 3449 2.037251 GACTCCTTGCAACAGTACCTGA 59.963 50.000 6.32 0.00 35.18 3.86
3395 3528 5.882557 TGATAGAGTTTTCAAATGGAGGAGC 59.117 40.000 0.00 0.00 0.00 4.70
3414 3547 4.755123 CCGCCCAAAAGTATTACCTGATAG 59.245 45.833 0.00 0.00 0.00 2.08
3438 3571 0.541863 ATCCTGGCTAACAAGGACCG 59.458 55.000 0.00 0.00 31.94 4.79
3643 3777 5.046376 TGACACACACATGATAAGACCTGAT 60.046 40.000 0.00 0.00 0.00 2.90
3699 3834 1.066136 CTCTATCACATGCGCCGATG 58.934 55.000 4.18 5.40 0.00 3.84
3727 3862 7.373493 CCATAATAAATCAGGTTGAATGGAGC 58.627 38.462 0.00 0.00 34.57 4.70
3807 3946 0.951558 AAACCTGCAACCTAAGCACG 59.048 50.000 0.00 0.00 37.02 5.34
3989 4132 7.359933 CCAACAATGCGTGTATTTTTAAGCAAT 60.360 33.333 0.00 0.00 40.60 3.56
4022 4165 6.205270 GGATGATGCAACAACCTCAAAATTTT 59.795 34.615 14.94 0.00 31.45 1.82
4039 4182 5.564259 GCATCTAGAACCAAATGGATGATGC 60.564 44.000 20.79 20.79 39.86 3.91
4044 4187 5.378230 TCAGCATCTAGAACCAAATGGAT 57.622 39.130 6.42 0.00 38.94 3.41
4062 4205 2.744202 CGTTAATGCCCAGGATATCAGC 59.256 50.000 4.83 2.44 0.00 4.26
4119 4262 9.158233 CCAATGAAGAACATATTTCTTTGCATT 57.842 29.630 11.63 12.90 38.73 3.56
4137 4288 7.492524 TGTACTAATACTGAGAGCCAATGAAG 58.507 38.462 0.00 0.00 32.00 3.02
4185 4336 4.023878 CAGACGCTCCTACTATTACCAGTC 60.024 50.000 0.00 0.00 0.00 3.51
4188 4339 3.630769 CACAGACGCTCCTACTATTACCA 59.369 47.826 0.00 0.00 0.00 3.25
4209 4360 0.682532 TGCCAAGTTGTTGCCAGTCA 60.683 50.000 1.45 0.00 31.64 3.41
4219 4370 1.684386 TTTGCCTGGGTGCCAAGTTG 61.684 55.000 0.00 0.00 30.80 3.16
4223 4374 2.523902 CCTTTGCCTGGGTGCCAA 60.524 61.111 0.00 0.00 30.80 4.52
4226 4377 2.115734 AATTGCCTTTGCCTGGGTGC 62.116 55.000 0.00 0.00 36.33 5.01
4227 4378 0.397564 AAATTGCCTTTGCCTGGGTG 59.602 50.000 0.00 0.00 36.33 4.61
4228 4379 0.397564 CAAATTGCCTTTGCCTGGGT 59.602 50.000 0.00 0.00 37.98 4.51
4233 4387 5.687770 ATAAACAACAAATTGCCTTTGCC 57.312 34.783 8.35 0.00 46.81 4.52
4236 4390 7.571059 GCATCGAATAAACAACAAATTGCCTTT 60.571 33.333 0.00 0.00 39.66 3.11
4262 4416 9.793245 GCTATGTACTATAACGCAAATAAGTTG 57.207 33.333 0.00 0.00 40.50 3.16
4318 7849 2.548904 GGCTGATGACTGATGAAGCATC 59.451 50.000 0.00 0.00 40.88 3.91
4336 7867 1.839994 TCTCTTGGATTTGGATCGGCT 59.160 47.619 0.00 0.00 32.84 5.52
4381 7981 4.558226 TTTACTGATGGAGTGCTGATGT 57.442 40.909 0.00 0.00 35.96 3.06
4390 7990 4.940046 ACATCTGCTGTTTTACTGATGGAG 59.060 41.667 12.48 0.00 42.94 3.86
4436 8036 5.247564 TCCGGGATGGAGGTAATATTACTTG 59.752 44.000 21.86 4.34 43.74 3.16
4453 8055 0.756903 CCGTCCAAGTAATCCGGGAT 59.243 55.000 2.97 2.97 35.11 3.85
4457 8059 0.104304 CCCTCCGTCCAAGTAATCCG 59.896 60.000 0.00 0.00 0.00 4.18
4474 8076 6.422333 AGGAAGTAGTTGTAGTAGTACTCCC 58.578 44.000 5.96 0.00 34.07 4.30
4490 8092 3.004524 CCCCGATCTCGTTAAGGAAGTAG 59.995 52.174 0.00 0.00 37.74 2.57
4491 8093 2.954318 CCCCGATCTCGTTAAGGAAGTA 59.046 50.000 0.00 0.00 37.74 2.24
4575 8178 2.624838 CTGCTCATCCACCAGTGTTTTT 59.375 45.455 0.00 0.00 0.00 1.94
4636 8239 3.486383 TGGAAGTCTTGCCTTAACCAAG 58.514 45.455 1.19 5.23 40.72 3.61
4703 8307 9.132521 CTGCCAAAACATCTTACATTTAAGAAG 57.867 33.333 5.46 4.15 45.52 2.85
4753 8357 8.365647 ACTACACCCTCCGTTCATTAATATAAG 58.634 37.037 0.00 0.00 0.00 1.73
4770 8374 9.939802 CTTATTTGAAAGTACTTACTACACCCT 57.060 33.333 8.92 0.00 34.99 4.34
4771 8375 9.933723 TCTTATTTGAAAGTACTTACTACACCC 57.066 33.333 8.92 0.00 34.99 4.61
4785 8389 9.311916 AGAGATCATTCGACTCTTATTTGAAAG 57.688 33.333 0.00 0.00 37.69 2.62
4801 8405 4.883585 TGGCACACCAAATAGAGATCATTC 59.116 41.667 0.00 0.00 45.37 2.67
4825 8429 9.932207 TGCTTTTACTAGTATGTAGTTTTAGCA 57.068 29.630 2.79 6.01 34.04 3.49


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

AutoCloner maintained by Alex Coulton.