Multiple sequence alignment - TraesCS2A01G411500

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 TraesCS2A01G411500 chr2A 100.000 1862 0 0 1495 3356 669558247 669556386 0.000000e+00 3439.0
1 TraesCS2A01G411500 chr2A 100.000 1169 0 0 1 1169 669559741 669558573 0.000000e+00 2159.0
2 TraesCS2A01G411500 chr2D 93.089 1881 93 18 1498 3356 523738401 523736536 0.000000e+00 2719.0
3 TraesCS2A01G411500 chr2D 93.157 1169 51 14 4 1167 523739984 523738840 0.000000e+00 1688.0
4 TraesCS2A01G411500 chr2B 92.632 1208 73 10 1510 2712 618666579 618665383 0.000000e+00 1724.0
5 TraesCS2A01G411500 chr2B 93.819 453 20 7 688 1139 618667467 618667022 0.000000e+00 675.0
6 TraesCS2A01G411500 chr2B 89.294 411 30 7 2729 3133 618665322 618664920 1.390000e-138 503.0
7 TraesCS2A01G411500 chr2B 91.579 95 8 0 3262 3356 618664884 618664790 7.560000e-27 132.0
8 TraesCS2A01G411500 chr5A 85.375 253 34 1 1599 1848 692062520 692062268 3.320000e-65 259.0
9 TraesCS2A01G411500 chr5A 81.641 256 44 1 1600 1852 692058246 692057991 3.390000e-50 209.0
10 TraesCS2A01G411500 chr4B 85.375 253 34 1 1599 1848 654466161 654465909 3.320000e-65 259.0
11 TraesCS2A01G411500 chr4B 82.745 255 41 1 1597 1848 654453590 654453336 1.210000e-54 224.0
12 TraesCS2A01G411500 chr4D 84.980 253 35 1 1599 1848 507119692 507119944 1.550000e-63 254.0
13 TraesCS2A01G411500 chr4D 81.746 252 43 1 1600 1848 507124901 507125152 1.220000e-49 207.0
14 TraesCS2A01G411500 chr1D 92.157 51 3 1 1598 1648 298574169 298574120 1.670000e-08 71.3


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 TraesCS2A01G411500 chr2A 669556386 669559741 3355 True 2799.0 3439 100.000 1 3356 2 chr2A.!!$R1 3355
1 TraesCS2A01G411500 chr2D 523736536 523739984 3448 True 2203.5 2719 93.123 4 3356 2 chr2D.!!$R1 3352
2 TraesCS2A01G411500 chr2B 618664790 618667467 2677 True 758.5 1724 91.831 688 3356 4 chr2B.!!$R1 2668

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
540 545 0.390340 TTCCACTAGCAAGCGAGCAG 60.39 55.0 6.21 4.33 36.85 4.24 F
1889 2025 0.250467 ATCCGCCATACCTCATGCAC 60.25 55.0 0.00 0.00 32.84 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 2178 0.179056 AGGTAACAGTGCGTGCTTGT 60.179 50.000 0.0 0.0 41.41 3.16 R
2931 3124 1.337074 ACATTTTGGACATTGCCGCAG 60.337 47.619 0.0 0.0 0.00 5.18 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
49 50 8.857216 AGATGACGTCGTGTTAAGTTTATTTAG 58.143 33.333 16.54 0.00 0.00 1.85
129 130 7.171630 AGATGTAAACCGAGAACACTCTTAT 57.828 36.000 0.00 0.00 29.54 1.73
130 131 7.612677 AGATGTAAACCGAGAACACTCTTATT 58.387 34.615 0.00 0.00 29.54 1.40
131 132 8.746530 AGATGTAAACCGAGAACACTCTTATTA 58.253 33.333 0.00 0.00 29.54 0.98
132 133 8.928270 ATGTAAACCGAGAACACTCTTATTAG 57.072 34.615 0.00 0.00 29.54 1.73
133 134 7.889469 TGTAAACCGAGAACACTCTTATTAGT 58.111 34.615 0.00 0.00 29.54 2.24
134 135 8.025445 TGTAAACCGAGAACACTCTTATTAGTC 58.975 37.037 0.00 0.00 29.54 2.59
135 136 5.579564 ACCGAGAACACTCTTATTAGTCC 57.420 43.478 0.00 0.00 29.54 3.85
136 137 4.401837 ACCGAGAACACTCTTATTAGTCCC 59.598 45.833 0.00 0.00 29.54 4.46
137 138 4.645588 CCGAGAACACTCTTATTAGTCCCT 59.354 45.833 0.00 0.00 29.54 4.20
138 139 5.127356 CCGAGAACACTCTTATTAGTCCCTT 59.873 44.000 0.00 0.00 29.54 3.95
139 140 6.320672 CCGAGAACACTCTTATTAGTCCCTTA 59.679 42.308 0.00 0.00 29.54 2.69
142 143 8.611051 AGAACACTCTTATTAGTCCCTTACAT 57.389 34.615 0.00 0.00 0.00 2.29
145 146 9.449719 AACACTCTTATTAGTCCCTTACATTTG 57.550 33.333 0.00 0.00 0.00 2.32
220 221 2.202690 CCACAGCAATGCGCATGG 60.203 61.111 26.09 23.37 46.13 3.66
239 242 3.571590 TGGCATCACCTGGTTAAGTTTT 58.428 40.909 0.00 0.00 40.22 2.43
283 286 5.620206 TGTTCACTAATCAGTTGTGATGGT 58.380 37.500 0.00 0.00 43.04 3.55
299 304 5.413523 TGTGATGGTGAGAGACAATTTGATG 59.586 40.000 2.79 0.00 0.00 3.07
338 343 6.533723 AGAAATTCGTTATCTTATCACACGCA 59.466 34.615 0.00 0.00 0.00 5.24
354 359 0.807275 CGCAGCTCGATTCATGTGGA 60.807 55.000 0.00 0.00 41.67 4.02
387 392 2.222819 GCGGAGTGCAAAAACTAGATCG 60.223 50.000 0.00 0.00 45.45 3.69
437 442 2.325484 TGTCACGGGATGTATGGCTAT 58.675 47.619 0.00 0.00 0.00 2.97
540 545 0.390340 TTCCACTAGCAAGCGAGCAG 60.390 55.000 6.21 4.33 36.85 4.24
572 577 4.942852 TGTGCACCAAATTAACTGGAAAG 58.057 39.130 15.69 3.70 37.40 2.62
586 591 2.490903 CTGGAAAGTTGGAGGCTTGATG 59.509 50.000 0.00 0.00 0.00 3.07
616 621 4.624024 TGAGCTAACCGAAAACGACATTAG 59.376 41.667 0.00 0.00 0.00 1.73
642 647 5.386958 ACGCTTTTCAGAGTGATACACTA 57.613 39.130 4.36 0.00 45.44 2.74
643 648 5.162075 ACGCTTTTCAGAGTGATACACTAC 58.838 41.667 4.36 0.07 45.44 2.73
644 649 4.563184 CGCTTTTCAGAGTGATACACTACC 59.437 45.833 4.36 0.00 45.44 3.18
645 650 5.622460 CGCTTTTCAGAGTGATACACTACCT 60.622 44.000 4.36 0.00 45.44 3.08
655 660 5.352569 AGTGATACACTACCTGTACGTACAC 59.647 44.000 24.10 10.93 43.46 2.90
656 661 5.352569 GTGATACACTACCTGTACGTACACT 59.647 44.000 24.10 14.20 38.22 3.55
657 662 5.352293 TGATACACTACCTGTACGTACACTG 59.648 44.000 24.10 19.12 38.22 3.66
658 663 2.816087 ACACTACCTGTACGTACACTGG 59.184 50.000 24.10 24.55 41.82 4.00
670 675 4.868067 ACGTACACTGGTTAGAAACTCAG 58.132 43.478 0.00 0.00 36.43 3.35
684 689 0.824595 ACTCAGGCATGCAAGCAACA 60.825 50.000 21.36 0.00 35.83 3.33
752 757 3.417275 CTAGACGCTGGCTCACCCG 62.417 68.421 0.00 0.00 35.87 5.28
792 797 1.854939 TCCCCTGGCATGATCATCTTT 59.145 47.619 4.86 0.00 0.00 2.52
795 800 1.340248 CCTGGCATGATCATCTTTGCC 59.660 52.381 24.95 24.95 42.28 4.52
807 812 1.599518 CTTTGCCTGCACGTACCCA 60.600 57.895 0.00 0.00 0.00 4.51
830 835 1.783031 GCGGCTCTTCAGATGCATGG 61.783 60.000 2.46 0.00 0.00 3.66
832 837 1.595466 GGCTCTTCAGATGCATGGAG 58.405 55.000 2.46 0.00 0.00 3.86
861 866 6.616947 GGAGAAGTGATGTAAGATATCTCCG 58.383 44.000 5.51 0.00 41.46 4.63
865 870 2.832129 TGATGTAAGATATCTCCGCCCC 59.168 50.000 5.51 0.00 0.00 5.80
866 871 2.696526 TGTAAGATATCTCCGCCCCT 57.303 50.000 5.51 0.00 0.00 4.79
867 872 2.526432 TGTAAGATATCTCCGCCCCTC 58.474 52.381 5.51 0.00 0.00 4.30
871 876 3.564347 ATATCTCCGCCCCTCCCCC 62.564 68.421 0.00 0.00 0.00 5.40
885 890 3.787001 CCCCCTCGCACTCCCTTC 61.787 72.222 0.00 0.00 0.00 3.46
941 946 1.818060 ACACACAACAGAAGCAAAGCA 59.182 42.857 0.00 0.00 0.00 3.91
942 947 2.230992 ACACACAACAGAAGCAAAGCAA 59.769 40.909 0.00 0.00 0.00 3.91
968 973 3.198068 CTGTGAGTGCACTTTGTACACT 58.802 45.455 26.52 3.53 42.10 3.55
969 974 2.935849 TGTGAGTGCACTTTGTACACTG 59.064 45.455 26.52 0.00 39.86 3.66
970 975 2.936498 GTGAGTGCACTTTGTACACTGT 59.064 45.455 22.65 0.00 39.86 3.55
973 978 2.936498 AGTGCACTTTGTACACTGTCAC 59.064 45.455 15.25 8.09 38.54 3.67
1036 1041 1.725557 GGTGATCGCTACGCTCCTGA 61.726 60.000 6.18 0.00 0.00 3.86
1889 2025 0.250467 ATCCGCCATACCTCATGCAC 60.250 55.000 0.00 0.00 32.84 4.57
1893 2029 2.016961 CCATACCTCATGCACGCAC 58.983 57.895 0.00 0.00 32.84 5.34
1894 2030 1.637934 CATACCTCATGCACGCACG 59.362 57.895 0.00 0.00 0.00 5.34
1895 2031 2.173669 ATACCTCATGCACGCACGC 61.174 57.895 0.00 0.00 0.00 5.34
1928 2064 4.286032 TGACTGGCTATTTGAAGTACCACT 59.714 41.667 0.00 0.00 0.00 4.00
1949 2086 5.232626 CACTACGTACTTGTTGTGTGCTTTA 59.767 40.000 0.00 0.00 39.62 1.85
1953 2090 6.557110 ACGTACTTGTTGTGTGCTTTAATTT 58.443 32.000 0.00 0.00 0.00 1.82
1955 2092 6.910433 CGTACTTGTTGTGTGCTTTAATTTCT 59.090 34.615 0.00 0.00 0.00 2.52
2035 2176 2.746362 ACTTCTCCAGGTTCTACGTACG 59.254 50.000 15.01 15.01 0.00 3.67
2036 2177 2.479566 TCTCCAGGTTCTACGTACGT 57.520 50.000 25.98 25.98 0.00 3.57
2037 2178 3.610040 TCTCCAGGTTCTACGTACGTA 57.390 47.619 25.41 25.41 0.00 3.57
2038 2179 3.262420 TCTCCAGGTTCTACGTACGTAC 58.738 50.000 23.60 16.71 0.00 3.67
2291 2432 6.114187 TGTAGTCTGTTTGAATGGTCTCAT 57.886 37.500 0.00 0.00 34.56 2.90
2319 2460 4.511826 GTGATGCTATACTTTGGTACTGGC 59.488 45.833 0.00 0.00 0.00 4.85
2336 2477 5.505173 ACTGGCATTGCACTATTTGTATC 57.495 39.130 11.39 0.00 0.00 2.24
2342 2483 5.904080 GCATTGCACTATTTGTATCGACTTC 59.096 40.000 3.15 0.00 0.00 3.01
2360 2503 6.480981 TCGACTTCCCTACTTTTGTAACTTTG 59.519 38.462 0.00 0.00 34.06 2.77
2374 2517 5.120399 TGTAACTTTGCGAGAGGAGAAAAA 58.880 37.500 0.00 0.00 0.00 1.94
2413 2556 1.160329 GGCAACCCTAGCATGCTACG 61.160 60.000 23.52 18.57 39.94 3.51
2420 2563 2.296190 CCCTAGCATGCTACGTGATACA 59.704 50.000 23.52 1.85 0.00 2.29
2434 2577 2.655474 GTGATACACGTCGCCGATTATC 59.345 50.000 0.00 0.00 37.88 1.75
2502 2645 7.865706 AAGCAAACGATATTGAGAACCTTAT 57.134 32.000 0.00 0.00 31.84 1.73
2534 2677 5.941948 AAACTAATTCTACCACACACAGC 57.058 39.130 0.00 0.00 0.00 4.40
2554 2697 5.413213 ACAGCAGTACACACAACTTAACAAA 59.587 36.000 0.00 0.00 0.00 2.83
2767 2954 7.690256 ACTGTCCCTCTGTTGTAAATTAGATT 58.310 34.615 0.00 0.00 0.00 2.40
2842 3034 8.567221 CATCAAATCGAGTTTCGTCAAATAAAC 58.433 33.333 0.00 0.00 41.35 2.01
2892 3085 8.804688 TGTAATTTTACAAATTGTAGTGGCAC 57.195 30.769 10.29 10.29 40.43 5.01
2931 3124 4.041321 ACTGTAGAGTTACCCCTTGGAAAC 59.959 45.833 0.00 0.00 34.81 2.78
2944 3137 1.212751 GGAAACTGCGGCAATGTCC 59.787 57.895 4.69 4.69 0.00 4.02
3048 3243 4.799564 TTTAGGGAATGATGTGGTTTGC 57.200 40.909 0.00 0.00 0.00 3.68
3094 3290 1.344438 TCAACCGCTCCTAGCCATATG 59.656 52.381 0.00 0.00 38.18 1.78
3104 3300 6.202379 CGCTCCTAGCCATATGATCAATATTG 59.798 42.308 9.29 9.29 38.18 1.90
3189 3387 0.107945 GCAAAAACAGTTGCCACCCA 60.108 50.000 0.00 0.00 46.69 4.51
3208 3406 6.721208 CCACCCAGCTTATACCATTGAAATAT 59.279 38.462 0.00 0.00 0.00 1.28
3212 3410 9.685276 CCCAGCTTATACCATTGAAATATCATA 57.315 33.333 0.00 0.00 34.96 2.15
3299 3504 3.763897 ACCGATAGCTTCAAAGGCAAAAT 59.236 39.130 0.00 0.00 0.00 1.82
3336 3541 4.164030 TCATGTGTGAGGTATTGCCAGTAT 59.836 41.667 0.00 0.00 40.61 2.12
3341 3546 4.716784 TGTGAGGTATTGCCAGTATTCTCT 59.283 41.667 0.00 0.00 40.61 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.776107 TCTTTTGACAAAATGTGAACCATACA 58.224 30.769 13.55 0.00 31.97 2.29
1 2 8.702438 CATCTTTTGACAAAATGTGAACCATAC 58.298 33.333 13.55 0.00 31.97 2.39
2 3 8.637099 TCATCTTTTGACAAAATGTGAACCATA 58.363 29.630 13.55 0.00 31.97 2.74
19 20 5.324739 ACTTAACACGACGTCATCTTTTG 57.675 39.130 17.16 4.73 0.00 2.44
129 130 8.943594 ATGGTAAAACAAATGTAAGGGACTAA 57.056 30.769 0.00 0.00 38.49 2.24
130 131 8.943594 AATGGTAAAACAAATGTAAGGGACTA 57.056 30.769 0.00 0.00 38.49 2.59
180 181 7.552330 GTGGGAATGGTGTTAAAATTGCATAAT 59.448 33.333 0.00 0.00 0.00 1.28
185 186 4.636249 TGTGGGAATGGTGTTAAAATTGC 58.364 39.130 0.00 0.00 0.00 3.56
193 194 1.619827 CATTGCTGTGGGAATGGTGTT 59.380 47.619 2.99 0.00 44.13 3.32
220 221 6.586082 CACAATAAAACTTAACCAGGTGATGC 59.414 38.462 0.00 0.00 0.00 3.91
227 230 6.128849 GCATGTGCACAATAAAACTTAACCAG 60.129 38.462 25.72 0.00 41.59 4.00
283 286 5.049198 GCAGTCAACATCAAATTGTCTCTCA 60.049 40.000 0.00 0.00 0.00 3.27
299 304 5.689819 ACGAATTTCTAATGTGCAGTCAAC 58.310 37.500 0.00 0.00 0.00 3.18
330 335 0.108662 ATGAATCGAGCTGCGTGTGA 60.109 50.000 0.00 0.00 41.80 3.58
335 340 0.807275 TCCACATGAATCGAGCTGCG 60.807 55.000 0.00 0.00 42.69 5.18
338 343 0.817654 TCGTCCACATGAATCGAGCT 59.182 50.000 0.00 0.00 0.00 4.09
379 384 1.337384 TGGTGCATGGCCGATCTAGT 61.337 55.000 0.00 0.00 0.00 2.57
387 392 2.894919 GTTGGATGGTGCATGGCC 59.105 61.111 0.00 0.00 0.00 5.36
437 442 2.988859 TCCGGTTCCCTACCTAGCTATA 59.011 50.000 0.00 0.00 45.40 1.31
452 457 6.479972 TCATAGATATCACTTTGTCCGGTT 57.520 37.500 0.00 0.00 0.00 4.44
455 460 5.871524 CCCATCATAGATATCACTTTGTCCG 59.128 44.000 5.32 0.00 0.00 4.79
456 461 6.176183 CCCCATCATAGATATCACTTTGTCC 58.824 44.000 5.32 0.00 0.00 4.02
463 468 4.502259 GCGATCCCCCATCATAGATATCAC 60.502 50.000 5.32 0.00 0.00 3.06
464 469 3.643320 GCGATCCCCCATCATAGATATCA 59.357 47.826 5.32 0.00 0.00 2.15
572 577 1.377202 TCGCCATCAAGCCTCCAAC 60.377 57.895 0.00 0.00 0.00 3.77
586 591 0.389426 TTCGGTTAGCTCAAGTCGCC 60.389 55.000 0.00 0.00 0.00 5.54
616 621 5.286558 GTGTATCACTCTGAAAAGCGTACTC 59.713 44.000 0.00 0.00 0.00 2.59
641 646 4.905429 TCTAACCAGTGTACGTACAGGTA 58.095 43.478 29.51 20.14 34.73 3.08
642 647 3.754965 TCTAACCAGTGTACGTACAGGT 58.245 45.455 28.02 26.82 36.61 4.00
643 648 4.771590 TTCTAACCAGTGTACGTACAGG 57.228 45.455 28.02 26.19 36.78 4.00
644 649 5.766222 AGTTTCTAACCAGTGTACGTACAG 58.234 41.667 28.02 18.62 36.78 2.74
645 650 5.299028 TGAGTTTCTAACCAGTGTACGTACA 59.701 40.000 24.10 24.10 0.00 2.90
655 660 2.421424 GCATGCCTGAGTTTCTAACCAG 59.579 50.000 6.36 0.00 32.75 4.00
656 661 2.224744 TGCATGCCTGAGTTTCTAACCA 60.225 45.455 16.68 0.00 0.00 3.67
657 662 2.436417 TGCATGCCTGAGTTTCTAACC 58.564 47.619 16.68 0.00 0.00 2.85
658 663 3.671702 GCTTGCATGCCTGAGTTTCTAAC 60.672 47.826 16.68 0.00 0.00 2.34
670 675 2.431260 CGGTGTTGCTTGCATGCC 60.431 61.111 20.65 7.86 0.00 4.40
792 797 4.673298 CGTGGGTACGTGCAGGCA 62.673 66.667 6.26 0.00 44.99 4.75
807 812 4.135153 ATCTGAAGAGCCGCGCGT 62.135 61.111 29.95 11.62 0.00 6.01
813 818 1.134159 ACTCCATGCATCTGAAGAGCC 60.134 52.381 0.00 0.00 0.00 4.70
830 835 6.761099 TCTTACATCACTTCTCCTGTACTC 57.239 41.667 0.00 0.00 0.00 2.59
832 837 9.073475 AGATATCTTACATCACTTCTCCTGTAC 57.927 37.037 0.00 0.00 0.00 2.90
871 876 0.760945 ATAGGGAAGGGAGTGCGAGG 60.761 60.000 0.00 0.00 0.00 4.63
872 877 1.996798 TATAGGGAAGGGAGTGCGAG 58.003 55.000 0.00 0.00 0.00 5.03
873 878 2.464796 TTATAGGGAAGGGAGTGCGA 57.535 50.000 0.00 0.00 0.00 5.10
875 880 4.349930 TGGTATTTATAGGGAAGGGAGTGC 59.650 45.833 0.00 0.00 0.00 4.40
876 881 5.221864 GGTGGTATTTATAGGGAAGGGAGTG 60.222 48.000 0.00 0.00 0.00 3.51
877 882 4.912133 GGTGGTATTTATAGGGAAGGGAGT 59.088 45.833 0.00 0.00 0.00 3.85
878 883 4.288887 GGGTGGTATTTATAGGGAAGGGAG 59.711 50.000 0.00 0.00 0.00 4.30
885 890 2.986728 AGCCTGGGTGGTATTTATAGGG 59.013 50.000 0.00 0.00 38.35 3.53
941 946 0.107017 AAGTGCACTCACAGGCTGTT 60.107 50.000 21.95 0.00 45.49 3.16
942 947 0.107017 AAAGTGCACTCACAGGCTGT 60.107 50.000 21.95 15.88 45.49 4.40
968 973 0.965866 AGCTAGCTACGCCAGTGACA 60.966 55.000 17.69 0.00 0.00 3.58
969 974 1.002251 CTAGCTAGCTACGCCAGTGAC 60.002 57.143 20.67 0.00 0.00 3.67
970 975 1.309950 CTAGCTAGCTACGCCAGTGA 58.690 55.000 20.67 0.00 0.00 3.41
973 978 4.955089 GCTAGCTAGCTACGCCAG 57.045 61.111 33.71 13.36 45.62 4.85
1036 1041 3.071747 GTGAAGAAGAGAAGGTTCAGGGT 59.928 47.826 0.00 0.00 29.71 4.34
1896 2032 2.287977 ATAGCCAGTCATGCATGCAT 57.712 45.000 27.46 27.46 37.08 3.96
1908 2044 4.804139 CGTAGTGGTACTTCAAATAGCCAG 59.196 45.833 0.00 0.00 0.00 4.85
1928 2064 6.847956 ATTAAAGCACACAACAAGTACGTA 57.152 33.333 0.00 0.00 0.00 3.57
1953 2090 8.461222 CACATAAAAACCAGCAGATGATTAAGA 58.539 33.333 0.00 0.00 0.00 2.10
1955 2092 8.028354 CACACATAAAAACCAGCAGATGATTAA 58.972 33.333 0.00 0.00 0.00 1.40
2035 2176 1.193874 GGTAACAGTGCGTGCTTGTAC 59.806 52.381 0.00 0.00 0.00 2.90
2036 2177 1.069513 AGGTAACAGTGCGTGCTTGTA 59.930 47.619 0.00 0.00 41.41 2.41
2037 2178 0.179056 AGGTAACAGTGCGTGCTTGT 60.179 50.000 0.00 0.00 41.41 3.16
2038 2179 0.235665 CAGGTAACAGTGCGTGCTTG 59.764 55.000 0.00 0.00 41.41 4.01
2129 2270 2.113860 TGAGCACTCTGGCAATAACC 57.886 50.000 0.00 0.00 35.83 2.85
2264 2405 4.397420 ACCATTCAAACAGACTACATGCA 58.603 39.130 0.00 0.00 0.00 3.96
2291 2432 5.339008 ACCAAAGTATAGCATCACGAGAA 57.661 39.130 0.00 0.00 0.00 2.87
2319 2460 6.422223 GGAAGTCGATACAAATAGTGCAATG 58.578 40.000 0.00 0.00 0.00 2.82
2336 2477 6.656003 CAAAGTTACAAAAGTAGGGAAGTCG 58.344 40.000 0.00 0.00 0.00 4.18
2342 2483 4.753107 TCTCGCAAAGTTACAAAAGTAGGG 59.247 41.667 0.00 0.00 0.00 3.53
2360 2503 1.729517 GTGCTCTTTTTCTCCTCTCGC 59.270 52.381 0.00 0.00 0.00 5.03
2374 2517 3.494048 GCCAGCTATCATACAAGTGCTCT 60.494 47.826 0.00 0.00 0.00 4.09
2434 2577 8.114290 TGAGCTCGACTTTAAATTAATAAAGCG 58.886 33.333 9.64 12.50 43.53 4.68
2455 2598 1.287146 AGGAATGGCTGGAAATGAGCT 59.713 47.619 0.00 0.00 36.63 4.09
2465 2608 2.096496 CGTTTGCTTAGAGGAATGGCTG 59.904 50.000 0.00 0.00 0.00 4.85
2502 2645 7.776030 TGTGGTAGAATTAGTTTTCCAGTTCAA 59.224 33.333 0.00 0.00 0.00 2.69
2523 2666 0.539518 TGTGTACTGCTGTGTGTGGT 59.460 50.000 6.48 0.00 0.00 4.16
2534 2677 9.997482 AATTAGTTTGTTAAGTTGTGTGTACTG 57.003 29.630 0.00 0.00 0.00 2.74
2554 2697 5.823045 GGACGGGAAGAAATGATCAATTAGT 59.177 40.000 0.00 0.00 0.00 2.24
2767 2954 6.778821 TGATCCCATCTGTTTTCTCAAAGTA 58.221 36.000 0.00 0.00 0.00 2.24
2773 2960 5.006386 AGTGTTGATCCCATCTGTTTTCTC 58.994 41.667 0.00 0.00 0.00 2.87
2780 2972 5.242393 AGTTTGAAAGTGTTGATCCCATCTG 59.758 40.000 0.00 0.00 0.00 2.90
2818 3010 7.631822 TGTTTATTTGACGAAACTCGATTTGA 58.368 30.769 2.59 0.00 43.74 2.69
2866 3059 8.911662 GTGCCACTACAATTTGTAAAATTACAG 58.088 33.333 10.32 1.20 43.77 2.74
2886 3079 9.574641 ACAGTTATGTTTACACGAATGTGCCAC 62.575 40.741 0.00 0.00 43.11 5.01
2892 3085 8.462143 ACTCTACAGTTATGTTTACACGAATG 57.538 34.615 0.00 0.00 41.01 2.67
2931 3124 1.337074 ACATTTTGGACATTGCCGCAG 60.337 47.619 0.00 0.00 0.00 5.18
3025 3220 5.484998 AGCAAACCACATCATTCCCTAAAAT 59.515 36.000 0.00 0.00 0.00 1.82
3035 3230 5.316167 TCTAAGTTGAGCAAACCACATCAT 58.684 37.500 0.00 0.00 39.85 2.45
3094 3290 6.949352 AGTTGGGATGACACAATATTGATC 57.051 37.500 22.16 17.34 41.64 2.92
3104 3300 3.740115 ACAAGTGTAGTTGGGATGACAC 58.260 45.455 4.63 0.00 42.01 3.67
3214 3412 9.810870 CCTAGGAGTATAGAAGTACCAAATAGT 57.189 37.037 1.05 0.00 0.00 2.12
3299 3504 5.863965 TCACACATGACTTTTATGGTGAGA 58.136 37.500 0.00 0.00 34.17 3.27


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

AutoCloner maintained by Alex Coulton.