Multiple sequence alignment - TraesCS6B01G442700

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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 TraesCS6B01G442700 chr6B 100.000 4450 0 0 1 4450 706187710 706183261 0.000000e+00 8218
1 TraesCS6B01G442700 chr5A 94.796 4477 200 17 1 4450 671914653 671910183 0.000000e+00 6946
2 TraesCS6B01G442700 chr4A 91.880 2537 175 12 1939 4450 28971548 28969018 0.000000e+00 3515
3 TraesCS6B01G442700 chr4A 95.471 1943 83 5 1 1941 28973518 28971579 0.000000e+00 3096
4 TraesCS6B01G442700 chr4A 96.325 653 22 2 1 652 374435018 374435669 0.000000e+00 1072
5 TraesCS6B01G442700 chr3B 91.560 1955 149 11 1 1941 648186244 648184292 0.000000e+00 2682
6 TraesCS6B01G442700 chr3B 89.785 1723 148 15 1939 3642 648184261 648182548 0.000000e+00 2182
7 TraesCS6B01G442700 chr1A 92.881 1194 74 7 1 1185 13269016 13267825 0.000000e+00 1724
8 TraesCS6B01G442700 chr1A 81.298 262 47 2 11 271 250648792 250648532 1.250000e-50 211
9 TraesCS6B01G442700 chr1D 94.057 1060 61 2 1 1059 20333684 20332626 0.000000e+00 1607
10 TraesCS6B01G442700 chr7B 96.733 704 23 0 1 704 304993153 304992450 0.000000e+00 1173
11 TraesCS6B01G442700 chr7A 75.841 803 184 10 3 800 675494267 675495064 2.490000e-107 399
12 TraesCS6B01G442700 chr2D 75.788 793 180 12 14 800 431392367 431391581 1.500000e-104 390
13 TraesCS6B01G442700 chrUn 74.564 802 187 16 7 800 48372796 48372004 7.130000e-88 335
14 TraesCS6B01G442700 chrUn 74.534 805 188 16 4 800 318400794 318401589 7.130000e-88 335


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 TraesCS6B01G442700 chr6B 706183261 706187710 4449 True 8218.0 8218 100.0000 1 4450 1 chr6B.!!$R1 4449
1 TraesCS6B01G442700 chr5A 671910183 671914653 4470 True 6946.0 6946 94.7960 1 4450 1 chr5A.!!$R1 4449
2 TraesCS6B01G442700 chr4A 28969018 28973518 4500 True 3305.5 3515 93.6755 1 4450 2 chr4A.!!$R1 4449
3 TraesCS6B01G442700 chr4A 374435018 374435669 651 False 1072.0 1072 96.3250 1 652 1 chr4A.!!$F1 651
4 TraesCS6B01G442700 chr3B 648182548 648186244 3696 True 2432.0 2682 90.6725 1 3642 2 chr3B.!!$R1 3641
5 TraesCS6B01G442700 chr1A 13267825 13269016 1191 True 1724.0 1724 92.8810 1 1185 1 chr1A.!!$R1 1184
6 TraesCS6B01G442700 chr1D 20332626 20333684 1058 True 1607.0 1607 94.0570 1 1059 1 chr1D.!!$R1 1058
7 TraesCS6B01G442700 chr7B 304992450 304993153 703 True 1173.0 1173 96.7330 1 704 1 chr7B.!!$R1 703
8 TraesCS6B01G442700 chr7A 675494267 675495064 797 False 399.0 399 75.8410 3 800 1 chr7A.!!$F1 797
9 TraesCS6B01G442700 chr2D 431391581 431392367 786 True 390.0 390 75.7880 14 800 1 chr2D.!!$R1 786
10 TraesCS6B01G442700 chrUn 48372004 48372796 792 True 335.0 335 74.5640 7 800 1 chrUn.!!$R1 793
11 TraesCS6B01G442700 chrUn 318400794 318401589 795 False 335.0 335 74.5340 4 800 1 chrUn.!!$F1 796

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
402 404 0.395724 GCATCCCCTCCGGTGAATTT 60.396 55.000 4.76 0.0 0.00 1.82 F
1730 1752 0.409484 AGTAAGCAAGGTTGGGCCAT 59.591 50.000 7.26 0.0 40.61 4.40 F
2196 2251 1.147376 CACCACCACCCGAGAACAA 59.853 57.895 0.00 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1956 2011 0.536687 CTGTGCTATGGCCATCTGGG 60.537 60.0 24.80 12.19 37.74 4.45 R
2645 2707 0.037303 CCCTGATGGAGTGCACAGTT 59.963 55.0 21.04 0.00 35.39 3.16 R
3802 3874 0.252467 AGAGGCAGGTTGTCTAGGCT 60.252 55.0 0.00 0.00 39.79 4.58 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
53 54 5.439721 ACAAGCTGCTATGGTGATTAATCA 58.560 37.500 14.23 14.23 0.00 2.57
86 87 3.054065 AGTGACCAATCCCCTGAAGATTC 60.054 47.826 0.00 0.00 31.56 2.52
325 327 3.004106 GCATGTAGAATCCAGCACAATCC 59.996 47.826 0.00 0.00 0.00 3.01
402 404 0.395724 GCATCCCCTCCGGTGAATTT 60.396 55.000 4.76 0.00 0.00 1.82
630 632 6.921412 TCCCACCTCCAAACATGATTATATT 58.079 36.000 0.00 0.00 0.00 1.28
647 649 8.393259 TGATTATATTTCCATAGATTGCTGGGT 58.607 33.333 0.00 0.00 33.13 4.51
680 682 9.102757 GAATGACATTAGCAAGATCAAGAGTTA 57.897 33.333 0.00 0.00 0.00 2.24
704 706 2.040178 CTGGGGAGGGTATGTACTGAC 58.960 57.143 0.00 0.00 0.00 3.51
707 709 3.046374 GGGGAGGGTATGTACTGACATT 58.954 50.000 0.00 0.00 44.18 2.71
708 710 4.228824 GGGGAGGGTATGTACTGACATTA 58.771 47.826 0.00 0.00 44.18 1.90
709 711 4.283722 GGGGAGGGTATGTACTGACATTAG 59.716 50.000 0.00 0.00 44.18 1.73
710 712 4.262506 GGGAGGGTATGTACTGACATTAGC 60.263 50.000 0.00 0.00 44.18 3.09
711 713 4.344102 GGAGGGTATGTACTGACATTAGCA 59.656 45.833 0.00 0.00 44.18 3.49
712 714 5.163343 GGAGGGTATGTACTGACATTAGCAA 60.163 44.000 0.00 0.00 44.18 3.91
713 715 5.918608 AGGGTATGTACTGACATTAGCAAG 58.081 41.667 0.00 0.00 44.18 4.01
714 716 5.661312 AGGGTATGTACTGACATTAGCAAGA 59.339 40.000 0.00 0.00 44.18 3.02
715 717 6.327626 AGGGTATGTACTGACATTAGCAAGAT 59.672 38.462 0.00 0.00 44.18 2.40
716 718 6.647067 GGGTATGTACTGACATTAGCAAGATC 59.353 42.308 0.00 0.00 44.18 2.75
718 720 7.710907 GGTATGTACTGACATTAGCAAGATCAA 59.289 37.037 0.00 0.00 44.18 2.57
719 721 7.783090 ATGTACTGACATTAGCAAGATCAAG 57.217 36.000 0.00 0.00 44.18 3.02
720 722 6.935167 TGTACTGACATTAGCAAGATCAAGA 58.065 36.000 0.00 0.00 0.00 3.02
866 872 3.920231 TCTTGCTGTGCCAATCTAGAT 57.080 42.857 0.00 0.00 0.00 1.98
1084 1092 3.243636 GGGAGCGGTAATTATCGTCTTCA 60.244 47.826 18.78 0.00 31.21 3.02
1188 1198 4.083862 GGTTCGGCCCGAGCTCTT 62.084 66.667 19.55 0.00 37.27 2.85
1190 1200 1.671379 GTTCGGCCCGAGCTCTTTT 60.671 57.895 13.14 0.00 37.14 2.27
1212 1222 1.021390 AGCAAGCCGATTGAACTCCG 61.021 55.000 0.00 0.00 41.83 4.63
1285 1296 1.561076 AGAGCAAGCATACCATCCACA 59.439 47.619 0.00 0.00 0.00 4.17
1403 1425 0.529378 CCATTTCTCTGTTGCCCTGC 59.471 55.000 0.00 0.00 0.00 4.85
1521 1543 5.716094 TGCACGTGGTATCGCTAATATAAT 58.284 37.500 18.88 0.00 0.00 1.28
1559 1581 5.455392 CATTCCAGACAAACATGTTCACTC 58.545 41.667 12.39 6.76 0.00 3.51
1590 1612 1.876322 CTTATGGCCTGTCTAGCAGC 58.124 55.000 3.32 0.00 43.71 5.25
1690 1712 4.698201 TCCTACAACATCAACAGACCAA 57.302 40.909 0.00 0.00 0.00 3.67
1730 1752 0.409484 AGTAAGCAAGGTTGGGCCAT 59.591 50.000 7.26 0.00 40.61 4.40
1956 2011 3.166657 GCGATGAGATTGACAAGCAAAC 58.833 45.455 6.17 0.00 40.48 2.93
2101 2156 4.154015 TGCATCTTGTTTGGATCAACTACG 59.846 41.667 0.00 0.00 0.00 3.51
2175 2230 4.145807 CCATGGGTTGTTGGTACAGTAAA 58.854 43.478 2.85 0.00 42.39 2.01
2176 2231 4.770010 CCATGGGTTGTTGGTACAGTAAAT 59.230 41.667 2.85 0.00 42.39 1.40
2195 2250 2.825982 CACCACCACCCGAGAACA 59.174 61.111 0.00 0.00 0.00 3.18
2196 2251 1.147376 CACCACCACCCGAGAACAA 59.853 57.895 0.00 0.00 0.00 2.83
2289 2344 2.423538 GCAAACATACACTGATGGGTCC 59.576 50.000 0.00 0.00 0.00 4.46
2311 2366 4.021192 CCCTAAATTTTCAGAGGCAAGCAA 60.021 41.667 0.00 0.00 0.00 3.91
2384 2446 2.715046 GTTTCATCTCAGTGGATGGCA 58.285 47.619 16.71 0.00 42.22 4.92
2452 2514 6.001460 TGAAATTTGTACTTCCATCTTCCGT 58.999 36.000 0.00 0.00 0.00 4.69
2475 2537 1.336240 GCTTGCCCAACTTGACATGTC 60.336 52.381 19.27 19.27 0.00 3.06
2555 2617 3.525537 GTGAGTGACACCATCATACCAG 58.474 50.000 0.84 0.00 43.05 4.00
2613 2675 2.034558 CGCAAACCCTTTCTGAATGTGT 59.965 45.455 0.00 0.00 0.00 3.72
2645 2707 1.195442 TGTCCAATGCCGACCCACTA 61.195 55.000 0.00 0.00 0.00 2.74
2660 2722 2.350522 CCACTAACTGTGCACTCCATC 58.649 52.381 19.41 0.00 44.92 3.51
2747 2809 7.860373 CGACATCATTCAAACACTTTCCTTTTA 59.140 33.333 0.00 0.00 0.00 1.52
2756 2819 4.212716 ACACTTTCCTTTTAGTGGAACCC 58.787 43.478 0.00 0.00 44.68 4.11
2777 2840 4.386761 CCCTACATCCCCATTGAAATCACT 60.387 45.833 0.00 0.00 0.00 3.41
2805 2871 2.374839 TCCATGTCCATTTGTCAGTGGA 59.625 45.455 5.23 5.23 42.03 4.02
2888 2954 0.604073 TCGTCGTTTATGACCCTGCA 59.396 50.000 0.00 0.00 35.40 4.41
3095 3161 3.199727 TCTGCCACTGCCTATACATGAAA 59.800 43.478 0.00 0.00 36.33 2.69
3097 3163 3.947196 TGCCACTGCCTATACATGAAAAG 59.053 43.478 0.00 0.00 36.33 2.27
3230 3296 1.238439 AGTTGCAAATCCCACTCACG 58.762 50.000 0.00 0.00 0.00 4.35
3262 3328 4.651778 TCTTCGGATTGAATGAAACACCT 58.348 39.130 0.00 0.00 35.63 4.00
3278 3344 0.343372 ACCTAGCCCCTGAGGATGAA 59.657 55.000 0.00 0.00 38.24 2.57
3349 3415 2.063266 GGAAACACTCGTATCGCACAA 58.937 47.619 0.00 0.00 0.00 3.33
3379 3445 2.760650 TGTTGTACGAGCTGATGAGGAT 59.239 45.455 0.00 0.00 0.00 3.24
3432 3498 1.531883 CGCTCGAAGCAATTAAAGGGC 60.532 52.381 7.47 0.00 42.58 5.19
3441 3507 2.288518 GCAATTAAAGGGCCGTTTGTCA 60.289 45.455 29.12 15.53 0.00 3.58
3519 3586 7.227512 AGCTTTACTAGATATGGCATTTGTGTC 59.772 37.037 4.78 0.00 0.00 3.67
3521 3588 9.764363 CTTTACTAGATATGGCATTTGTGTCTA 57.236 33.333 4.78 5.82 0.00 2.59
3522 3589 9.764363 TTTACTAGATATGGCATTTGTGTCTAG 57.236 33.333 4.78 15.84 39.50 2.43
3523 3590 6.226787 ACTAGATATGGCATTTGTGTCTAGC 58.773 40.000 20.77 2.91 38.00 3.42
3524 3591 5.039920 AGATATGGCATTTGTGTCTAGCA 57.960 39.130 4.78 0.00 0.00 3.49
3593 3665 6.734137 TGCAAACAAGTTATGACAAACTAGG 58.266 36.000 0.00 3.59 38.76 3.02
3634 3706 6.770286 ACAAGATAGACATGGGGATACATT 57.230 37.500 0.00 0.00 39.74 2.71
3637 3709 7.503566 ACAAGATAGACATGGGGATACATTTTG 59.496 37.037 0.00 0.00 39.74 2.44
3640 3712 2.365293 GACATGGGGATACATTTTGGGC 59.635 50.000 0.00 0.00 39.74 5.36
3665 3737 7.986889 GCCACCAACATTAGATATTTTCCAAAT 59.013 33.333 0.00 0.00 0.00 2.32
3689 3761 5.701224 TGGGCTACCAAATAATTTCCTAGG 58.299 41.667 0.82 0.82 45.87 3.02
3711 3783 6.062095 AGGCAAATATACTATTCCACACCAC 58.938 40.000 0.00 0.00 0.00 4.16
3863 3935 4.568359 CCCTGTGTAGTTCAGAATTCATCG 59.432 45.833 8.44 0.00 35.20 3.84
3945 4017 2.941064 CAATGAGATCGTCATGCCACTT 59.059 45.455 7.99 0.00 45.89 3.16
3979 4051 0.329261 CTCCCATCTGAGCCCAAACA 59.671 55.000 0.00 0.00 0.00 2.83
4024 4096 0.100325 CTCACGGCAAAACACAGCAA 59.900 50.000 0.00 0.00 0.00 3.91
4027 4099 1.932511 CACGGCAAAACACAGCAAAAT 59.067 42.857 0.00 0.00 0.00 1.82
4086 4161 5.070001 CACATGTTTTACCTTCTTCCAGGA 58.930 41.667 0.00 0.00 37.39 3.86
4117 4192 1.062198 TCCAGGAGATCCACATGGCTA 60.062 52.381 13.89 0.00 38.89 3.93
4146 4221 1.689984 TGTGCTTGCATTCACAAGGA 58.310 45.000 16.22 0.51 45.83 3.36
4177 4252 0.693092 GTAGTCCATAGGCCCCACCA 60.693 60.000 0.00 0.00 43.14 4.17
4187 4262 1.645402 GGCCCCACCATGTACCTCAT 61.645 60.000 0.00 0.00 38.86 2.90
4212 4287 1.691434 GACCTGTTTTGCCCATGGAAA 59.309 47.619 15.22 3.57 0.00 3.13
4297 4372 0.843309 TGTGTGTTGGAGGATGGTGT 59.157 50.000 0.00 0.00 0.00 4.16
4329 4404 4.847198 CCTGGCATGGTCATTATATAGCA 58.153 43.478 0.00 0.00 0.00 3.49
4374 4449 6.703165 ACTGATTCTTTCAAATTTTGTGGCTC 59.297 34.615 8.89 2.04 32.78 4.70
4375 4450 6.580788 TGATTCTTTCAAATTTTGTGGCTCA 58.419 32.000 8.89 4.18 0.00 4.26
4378 4453 6.159299 TCTTTCAAATTTTGTGGCTCATGA 57.841 33.333 8.89 0.00 0.00 3.07
4388 4463 3.344215 GCTCATGATGCTCGCGGG 61.344 66.667 6.13 2.60 0.00 6.13
4393 4477 4.819761 TGATGCTCGCGGGACTGC 62.820 66.667 12.03 6.08 0.00 4.40
4423 4507 0.970427 TGGAGCCGCAGAGATACACA 60.970 55.000 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 5.501156 GGGATTGGTCACTCTTTTCTACAT 58.499 41.667 0.00 0.00 0.00 2.29
63 64 1.909302 TCTTCAGGGGATTGGTCACTC 59.091 52.381 0.00 0.00 0.00 3.51
86 87 1.299165 CCATCCTCGTCGCTAACCG 60.299 63.158 0.00 0.00 38.61 4.44
325 327 1.672356 CGCCCTGTTCCTCAAGGTG 60.672 63.158 0.00 0.00 36.34 4.00
402 404 3.450578 GACACCTTCGCCGTTTATATCA 58.549 45.455 0.00 0.00 0.00 2.15
630 632 2.291475 TGCAACCCAGCAATCTATGGAA 60.291 45.455 0.00 0.00 42.46 3.53
641 643 0.242017 GTCATTCAGTGCAACCCAGC 59.758 55.000 0.00 0.00 37.80 4.85
647 649 4.761227 TCTTGCTAATGTCATTCAGTGCAA 59.239 37.500 18.42 18.42 36.59 4.08
680 682 2.318207 AGTACATACCCTCCCCAGTTCT 59.682 50.000 0.00 0.00 0.00 3.01
704 706 7.333921 ACTTTCTGACTCTTGATCTTGCTAATG 59.666 37.037 0.00 0.00 0.00 1.90
706 708 6.763355 ACTTTCTGACTCTTGATCTTGCTAA 58.237 36.000 0.00 0.00 0.00 3.09
707 709 6.352016 ACTTTCTGACTCTTGATCTTGCTA 57.648 37.500 0.00 0.00 0.00 3.49
708 710 5.226194 ACTTTCTGACTCTTGATCTTGCT 57.774 39.130 0.00 0.00 0.00 3.91
709 711 5.468072 TGAACTTTCTGACTCTTGATCTTGC 59.532 40.000 0.00 0.00 0.00 4.01
710 712 7.440556 TCTTGAACTTTCTGACTCTTGATCTTG 59.559 37.037 0.00 0.00 0.00 3.02
711 713 7.440856 GTCTTGAACTTTCTGACTCTTGATCTT 59.559 37.037 0.00 0.00 32.71 2.40
712 714 6.928492 GTCTTGAACTTTCTGACTCTTGATCT 59.072 38.462 0.00 0.00 32.71 2.75
713 715 6.703607 TGTCTTGAACTTTCTGACTCTTGATC 59.296 38.462 13.05 0.00 34.75 2.92
714 716 6.586344 TGTCTTGAACTTTCTGACTCTTGAT 58.414 36.000 13.05 0.00 34.75 2.57
715 717 5.977635 TGTCTTGAACTTTCTGACTCTTGA 58.022 37.500 13.05 0.00 34.75 3.02
716 718 6.045318 TCTGTCTTGAACTTTCTGACTCTTG 58.955 40.000 13.05 5.56 34.75 3.02
718 720 5.860941 TCTGTCTTGAACTTTCTGACTCT 57.139 39.130 13.05 0.00 34.75 3.24
719 721 5.988561 ACATCTGTCTTGAACTTTCTGACTC 59.011 40.000 13.05 0.00 34.75 3.36
720 722 5.923204 ACATCTGTCTTGAACTTTCTGACT 58.077 37.500 13.05 0.00 34.75 3.41
1084 1092 8.085296 TCACAAACCGCAAACTTCAATAATTAT 58.915 29.630 0.00 0.00 0.00 1.28
1128 1137 5.365403 TTTAGTATGGTGCGTGGAAAAAG 57.635 39.130 0.00 0.00 0.00 2.27
1188 1198 4.320935 GGAGTTCAATCGGCTTGCTAAAAA 60.321 41.667 0.00 0.00 34.66 1.94
1190 1200 2.747446 GGAGTTCAATCGGCTTGCTAAA 59.253 45.455 0.00 0.00 34.66 1.85
1196 1206 1.298859 GCACGGAGTTCAATCGGCTT 61.299 55.000 0.00 0.00 41.61 4.35
1212 1222 1.599542 GGGAGCATGTATCTTTCGCAC 59.400 52.381 0.00 0.00 0.00 5.34
1285 1296 4.834534 TGTAATTACACCGTAGCATTGGT 58.165 39.130 14.35 0.00 39.66 3.67
1403 1425 6.369615 TCACAAGGCATGAATATATGTCATCG 59.630 38.462 0.00 5.77 35.16 3.84
1508 1530 6.761242 TGGCGCATTTCTATTATATTAGCGAT 59.239 34.615 10.83 0.00 44.76 4.58
1559 1581 2.012673 GGCCATAAGCTTGTCTGTGAG 58.987 52.381 9.86 0.00 43.05 3.51
1590 1612 1.267806 CCTTGCAGCAGGTACAACTTG 59.732 52.381 3.49 0.00 0.00 3.16
1690 1712 5.140454 ACTAAAGGAGTGCTGAATTGGTTT 58.860 37.500 0.00 0.00 36.87 3.27
1771 1793 5.067805 GGAGAAGTTCTTGGAAAAGCTTCAA 59.932 40.000 6.88 0.00 35.96 2.69
1956 2011 0.536687 CTGTGCTATGGCCATCTGGG 60.537 60.000 24.80 12.19 37.74 4.45
2117 2172 7.910441 AATTGCATTTAGGAAGGTCAATTTG 57.090 32.000 0.00 0.00 33.67 2.32
2119 2174 6.813152 CGAAATTGCATTTAGGAAGGTCAATT 59.187 34.615 0.00 0.00 36.17 2.32
2175 2230 2.525124 TTCTCGGGTGGTGGTGCAT 61.525 57.895 0.00 0.00 0.00 3.96
2176 2231 3.164977 TTCTCGGGTGGTGGTGCA 61.165 61.111 0.00 0.00 0.00 4.57
2195 2250 4.764823 CCAGTCTCTTATAGCTCCGAGATT 59.235 45.833 0.00 0.00 35.26 2.40
2196 2251 4.042311 TCCAGTCTCTTATAGCTCCGAGAT 59.958 45.833 0.00 0.00 35.26 2.75
2201 2256 3.056179 GCCATCCAGTCTCTTATAGCTCC 60.056 52.174 0.00 0.00 0.00 4.70
2289 2344 4.789012 TGCTTGCCTCTGAAAATTTAGG 57.211 40.909 0.96 0.96 0.00 2.69
2452 2514 0.476338 TGTCAAGTTGGGCAAGCCTA 59.524 50.000 11.40 1.12 36.10 3.93
2475 2537 3.181450 ACCAGGAGTGTCTTTTGAGAAGG 60.181 47.826 0.00 0.00 0.00 3.46
2555 2617 5.353956 GTGTCATAAATTTCAAATTGGGGCC 59.646 40.000 0.00 0.00 0.00 5.80
2613 2675 4.065088 GCATTGGACAGAACAGTTGTCTA 58.935 43.478 5.54 0.00 43.44 2.59
2645 2707 0.037303 CCCTGATGGAGTGCACAGTT 59.963 55.000 21.04 0.00 35.39 3.16
2660 2722 1.694133 CCTCCTGGAAGCTAGCCCTG 61.694 65.000 12.13 10.29 34.57 4.45
2747 2809 0.120377 TGGGGATGTAGGGTTCCACT 59.880 55.000 0.00 0.00 36.33 4.00
2756 2819 6.780457 AAAGTGATTTCAATGGGGATGTAG 57.220 37.500 0.00 0.00 0.00 2.74
2805 2871 6.296894 CCATCTGGGAGAATAGCTGGAATAAT 60.297 42.308 0.00 0.00 40.01 1.28
2888 2954 0.916086 TGTATCCGAATGGGCCAACT 59.084 50.000 11.89 0.00 35.24 3.16
2994 3060 3.221964 GTGAGTTGATTCACAATGCCC 57.778 47.619 2.23 0.00 45.32 5.36
3075 3141 3.643199 TTTCATGTATAGGCAGTGGCA 57.357 42.857 20.04 5.37 43.71 4.92
3095 3161 5.499004 TTACTTGACAAGGATAGTGGCTT 57.501 39.130 19.16 0.00 0.00 4.35
3097 3163 6.116126 AGAATTACTTGACAAGGATAGTGGC 58.884 40.000 19.16 1.69 0.00 5.01
3189 3255 1.267806 GTCACCGTCGTAGTTCCTTGA 59.732 52.381 0.00 0.00 0.00 3.02
3200 3266 0.375454 TTTGCAACTTGTCACCGTCG 59.625 50.000 0.00 0.00 0.00 5.12
3230 3296 6.313905 TCATTCAATCCGAAGAGCTTACTTTC 59.686 38.462 0.00 0.00 36.95 2.62
3245 3311 3.381590 GGGCTAGGTGTTTCATTCAATCC 59.618 47.826 0.00 0.00 0.00 3.01
3262 3328 5.930209 AATTAATTCATCCTCAGGGGCTA 57.070 39.130 0.00 0.00 34.39 3.93
3298 3364 9.469097 AGATAAGATAGTCGGCAATAGATTAGT 57.531 33.333 0.00 0.00 0.00 2.24
3306 3372 5.124138 CCTACGAGATAAGATAGTCGGCAAT 59.876 44.000 0.00 0.00 36.74 3.56
3308 3374 4.001652 CCTACGAGATAAGATAGTCGGCA 58.998 47.826 0.00 0.00 36.74 5.69
3379 3445 4.571580 CAGCTTTTGTTTGATTTCCTTGCA 59.428 37.500 0.00 0.00 0.00 4.08
3432 3498 2.422597 TGCCTACAGAATGACAAACGG 58.577 47.619 0.00 0.00 39.69 4.44
3441 3507 5.789643 ACAACAATGTTTGCCTACAGAAT 57.210 34.783 0.00 0.00 35.91 2.40
3519 3586 5.776716 ACATGGGATTAAAATGGGATGCTAG 59.223 40.000 0.00 0.00 0.00 3.42
3521 3588 4.559726 ACATGGGATTAAAATGGGATGCT 58.440 39.130 0.00 0.00 0.00 3.79
3522 3589 4.961438 ACATGGGATTAAAATGGGATGC 57.039 40.909 0.00 0.00 0.00 3.91
3523 3590 6.237887 ACAACATGGGATTAAAATGGGATG 57.762 37.500 0.00 0.00 0.00 3.51
3524 3591 7.986553 TTACAACATGGGATTAAAATGGGAT 57.013 32.000 0.00 0.00 0.00 3.85
3593 3665 3.624326 TGTAACTGCAGCACATGAAAC 57.376 42.857 15.27 1.26 0.00 2.78
3637 3709 5.221441 GGAAAATATCTAATGTTGGTGGCCC 60.221 44.000 0.00 0.00 0.00 5.80
3640 3712 9.889128 AATTTGGAAAATATCTAATGTTGGTGG 57.111 29.630 0.00 0.00 0.00 4.61
3648 3720 8.870116 GGTAGCCCAATTTGGAAAATATCTAAT 58.130 33.333 17.24 0.00 40.96 1.73
3689 3761 6.513393 GCAGTGGTGTGGAATAGTATATTTGC 60.513 42.308 0.00 0.00 0.00 3.68
3696 3768 2.027561 GTGGCAGTGGTGTGGAATAGTA 60.028 50.000 0.00 0.00 0.00 1.82
3711 3783 1.067283 TGTTTGTGTTGGTTGTGGCAG 60.067 47.619 0.00 0.00 0.00 4.85
3795 3867 3.133003 GCAGGTTGTCTAGGCTGAGAATA 59.867 47.826 0.00 0.00 0.00 1.75
3802 3874 0.252467 AGAGGCAGGTTGTCTAGGCT 60.252 55.000 0.00 0.00 39.79 4.58
3863 3935 2.435059 GGTTCGCCTGCTGGAGAC 60.435 66.667 15.51 10.58 41.82 3.36
3929 4001 2.760650 TCTACAAGTGGCATGACGATCT 59.239 45.455 0.00 0.00 0.00 2.75
3945 4017 1.771854 TGGGAGGTTGCAACTTCTACA 59.228 47.619 32.58 28.11 35.57 2.74
3979 4051 8.997323 GCTTTCTAGTTGATATGATGTGCTATT 58.003 33.333 0.00 0.00 0.00 1.73
4024 4096 8.706322 AAGTAATCTTACAACCAACCTGATTT 57.294 30.769 3.15 0.00 36.12 2.17
4086 4161 2.516227 TCTCCTGGAGTGACGAGAAT 57.484 50.000 22.50 0.00 0.00 2.40
4117 4192 0.536260 TGCAAGCACAAGCCAAAAGT 59.464 45.000 0.00 0.00 43.56 2.66
4146 4221 0.538057 TGGACTACGAACCACCGACT 60.538 55.000 0.00 0.00 0.00 4.18
4177 4252 0.264955 AGGTCCCCGATGAGGTACAT 59.735 55.000 0.00 0.00 42.47 2.29
4187 4262 2.114411 GGCAAAACAGGTCCCCGA 59.886 61.111 0.00 0.00 0.00 5.14
4329 4404 4.035102 GTTGGGAGGGAGCCGCTT 62.035 66.667 0.00 0.00 0.00 4.68
4349 4424 6.585416 AGCCACAAAATTTGAAAGAATCAGT 58.415 32.000 13.19 0.00 39.77 3.41
4374 4449 2.107750 AGTCCCGCGAGCATCATG 59.892 61.111 8.23 0.00 33.17 3.07
4375 4450 2.107750 CAGTCCCGCGAGCATCAT 59.892 61.111 8.23 0.00 33.17 2.45
4388 4463 2.452813 CCACATGTACGCGGCAGTC 61.453 63.158 12.47 0.00 0.00 3.51
4393 4477 2.890474 GGCTCCACATGTACGCGG 60.890 66.667 12.47 0.00 0.00 6.46
4423 4507 2.399580 GTACCTAGTTGGCCAGGAGAT 58.600 52.381 15.38 0.00 40.22 2.75
4430 4514 0.459759 GTGAGCGTACCTAGTTGGCC 60.460 60.000 0.00 0.00 40.22 5.36


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

AutoCloner maintained by Alex Coulton.