Multiple sequence alignment - TraesCS2D01G328000

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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 TraesCS2D01G328000 chr2D 100.000 3518 0 0 1441 4958 421144250 421140733 0.000000e+00 6497.0
1 TraesCS2D01G328000 chr2D 100.000 1103 0 0 1 1103 421145690 421144588 0.000000e+00 2037.0
2 TraesCS2D01G328000 chr2D 100.000 28 0 0 45 72 243664295 243664322 9.000000e-03 52.8
3 TraesCS2D01G328000 chr2B 93.523 2918 106 37 1455 4349 493717891 493715034 0.000000e+00 4265.0
4 TraesCS2D01G328000 chr2B 96.388 609 14 1 4350 4958 493714817 493714217 0.000000e+00 996.0
5 TraesCS2D01G328000 chr2B 93.103 319 10 5 785 1103 493718210 493717904 1.630000e-124 457.0
6 TraesCS2D01G328000 chr2B 100.000 37 0 0 747 783 493718234 493718198 8.910000e-08 69.4
7 TraesCS2D01G328000 chr2A 95.309 2494 87 9 2472 4958 567381120 567378650 0.000000e+00 3930.0
8 TraesCS2D01G328000 chr2A 95.150 2474 80 9 2491 4958 547411986 547414425 0.000000e+00 3868.0
9 TraesCS2D01G328000 chr2A 90.313 991 70 17 1449 2432 567382098 567381127 0.000000e+00 1275.0
10 TraesCS2D01G328000 chr2A 89.832 954 71 15 1486 2432 547410135 547411069 0.000000e+00 1201.0
11 TraesCS2D01G328000 chr2A 90.344 901 52 18 237 1103 547409015 547409914 0.000000e+00 1149.0
12 TraesCS2D01G328000 chr2A 91.783 791 49 9 1 786 567383188 567382409 0.000000e+00 1086.0
13 TraesCS2D01G328000 chr2A 95.547 247 11 0 857 1103 567382363 567382117 3.600000e-106 396.0
14 TraesCS2D01G328000 chr2A 93.035 201 14 0 1 201 547408816 547409016 1.350000e-75 294.0
15 TraesCS2D01G328000 chr2A 100.000 28 0 0 45 72 283949389 283949416 9.000000e-03 52.8
16 TraesCS2D01G328000 chr3D 78.981 157 29 4 5 159 38607096 38607250 2.440000e-18 104.0
17 TraesCS2D01G328000 chr7D 92.063 63 5 0 11 73 72433670 72433732 6.840000e-14 89.8
18 TraesCS2D01G328000 chr7A 92.063 63 5 0 11 73 77529291 77529353 6.840000e-14 89.8
19 TraesCS2D01G328000 chr3A 97.561 41 1 0 31 71 22565687 22565647 2.480000e-08 71.3
20 TraesCS2D01G328000 chr7B 100.000 28 0 0 45 72 552568561 552568534 9.000000e-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 TraesCS2D01G328000 chr2D 421140733 421145690 4957 True 4267.00 6497 100.00000 1 4958 2 chr2D.!!$R1 4957
1 TraesCS2D01G328000 chr2B 493714217 493718234 4017 True 1446.85 4265 95.75350 747 4958 4 chr2B.!!$R1 4211
2 TraesCS2D01G328000 chr2A 567378650 567383188 4538 True 1671.75 3930 93.23800 1 4958 4 chr2A.!!$R1 4957
3 TraesCS2D01G328000 chr2A 547408816 547414425 5609 False 1628.00 3868 92.09025 1 4958 4 chr2A.!!$F2 4957

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
76 77 1.609208 GGCTGCTGTTGGAGAAGAAA 58.391 50.0 0.00 0.0 33.10 2.52 F
992 1029 1.907222 CTAAACCACCGTCCCCCTCC 61.907 65.0 0.00 0.0 0.00 4.30 F
2100 2137 0.413832 TGGAGGACTTGACTAGCCCT 59.586 55.0 0.00 0.0 39.83 5.19 F
2877 3838 0.038343 CCCGGCCACAATGTTTTCAG 60.038 55.0 2.24 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1758 1795 0.958876 CGGGCTTGTAGAAACCCACC 60.959 60.0 11.38 0.0 42.97 4.61 R
2450 2505 0.322456 TTCGCTTGCAGGCACCTAAT 60.322 50.0 21.61 0.0 0.00 1.73 R
2949 3910 1.986882 AAGGTTGCAGAAGTCCAAGG 58.013 50.0 0.00 0.0 0.00 3.61 R
4695 5880 0.036010 ATGTCCAGGTTGAGGAAGCG 60.036 55.0 0.00 0.0 36.80 4.68 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
76 77 1.609208 GGCTGCTGTTGGAGAAGAAA 58.391 50.000 0.00 0.00 33.10 2.52
79 80 3.551659 GGCTGCTGTTGGAGAAGAAAAAG 60.552 47.826 0.00 0.00 33.10 2.27
81 82 4.022503 GCTGCTGTTGGAGAAGAAAAAGAT 60.023 41.667 0.00 0.00 33.10 2.40
85 86 5.693555 GCTGTTGGAGAAGAAAAAGATTTGG 59.306 40.000 0.00 0.00 0.00 3.28
132 133 3.006752 CCTAAAGCAGTTTTCAATGCCCA 59.993 43.478 0.00 0.00 43.60 5.36
140 141 5.679638 GCAGTTTTCAATGCCCAGTTATAGG 60.680 44.000 0.00 0.00 36.41 2.57
151 152 2.038557 CCAGTTATAGGGCCGCTGTTAT 59.961 50.000 0.00 0.00 0.00 1.89
309 312 7.649370 AGATAAATCGTGCTATGAATGACAG 57.351 36.000 0.00 0.00 0.00 3.51
386 389 2.811431 TGAACTAAGACCACGCCATTTG 59.189 45.455 0.00 0.00 0.00 2.32
425 429 7.428826 GGAATATTTTTGTTATGCTAGCTGCT 58.571 34.615 17.23 7.57 43.37 4.24
520 524 9.884465 AAAAACAAATTTCAATGTTTCACGAAA 57.116 22.222 6.47 0.00 46.09 3.46
564 568 4.280436 TCACGGGTCATGTTTCTACAAT 57.720 40.909 0.00 0.00 37.91 2.71
609 613 4.097892 ACTCAAAACACACATGGAGGAAAC 59.902 41.667 0.00 0.00 0.00 2.78
614 618 4.654091 ACACACATGGAGGAAACAAAAG 57.346 40.909 0.00 0.00 0.00 2.27
615 619 4.023291 ACACACATGGAGGAAACAAAAGT 58.977 39.130 0.00 0.00 0.00 2.66
635 639 9.282247 CAAAAGTAAATCTGCATGAATAGTGTC 57.718 33.333 0.00 0.00 0.00 3.67
691 695 6.992063 AAACACACTATTCACATCCAGATC 57.008 37.500 0.00 0.00 0.00 2.75
693 697 7.423844 AACACACTATTCACATCCAGATCTA 57.576 36.000 0.00 0.00 0.00 1.98
695 699 8.027524 ACACACTATTCACATCCAGATCTATT 57.972 34.615 0.00 0.00 0.00 1.73
732 739 7.307042 CGCCATGTGTGTTTTGAATTTGATTTA 60.307 33.333 0.00 0.00 0.00 1.40
970 1007 2.569134 GTTCCTCTCGACGCTGCT 59.431 61.111 0.00 0.00 0.00 4.24
986 1023 2.098831 GCTCGCTAAACCACCGTCC 61.099 63.158 0.00 0.00 0.00 4.79
992 1029 1.907222 CTAAACCACCGTCCCCCTCC 61.907 65.000 0.00 0.00 0.00 4.30
1806 1843 2.687566 GAAGGGGAGGAGGGCGAA 60.688 66.667 0.00 0.00 0.00 4.70
1808 1845 3.254035 AAGGGGAGGAGGGCGAAGA 62.254 63.158 0.00 0.00 0.00 2.87
1824 1861 3.537874 GACGACGGGGATGAGGGG 61.538 72.222 0.00 0.00 0.00 4.79
2100 2137 0.413832 TGGAGGACTTGACTAGCCCT 59.586 55.000 0.00 0.00 39.83 5.19
2158 2210 6.377146 AGTGCATCCTTTACGTTGGAATTAAT 59.623 34.615 0.00 0.00 35.81 1.40
2173 2225 8.621286 GTTGGAATTAATATGTTGGGTAGAGTG 58.379 37.037 0.00 0.00 0.00 3.51
2195 2247 7.824672 AGTGAATTGTGAAAGATGATTCCTTC 58.175 34.615 0.00 0.00 0.00 3.46
2199 2251 7.636150 ATTGTGAAAGATGATTCCTTCGAAT 57.364 32.000 0.00 0.00 41.57 3.34
2204 2256 8.830580 GTGAAAGATGATTCCTTCGAATTATGA 58.169 33.333 0.00 0.00 38.88 2.15
2261 2313 2.305635 TGTGGCATGTGTATCCTTCAGT 59.694 45.455 0.00 0.00 0.00 3.41
2265 2317 4.009675 GGCATGTGTATCCTTCAGTTTGA 58.990 43.478 0.00 0.00 0.00 2.69
2269 2321 6.749118 GCATGTGTATCCTTCAGTTTGAAATC 59.251 38.462 0.00 0.00 35.73 2.17
2353 2408 5.041191 ACACCTTTAATCAGCTATCCTGG 57.959 43.478 0.00 0.00 42.05 4.45
2441 2496 3.680920 ATTCCCCTCGTCTCCGGCT 62.681 63.158 0.00 0.00 33.95 5.52
2466 2521 0.680921 TCCATTAGGTGCCTGCAAGC 60.681 55.000 0.00 0.00 35.89 4.01
2599 3545 3.895232 TTGTCCTGACTCTATCCTTGC 57.105 47.619 0.00 0.00 0.00 4.01
2661 3622 6.205658 GTGGTATTTTCTATTCTGCTCCCATC 59.794 42.308 0.00 0.00 0.00 3.51
2709 3670 1.741770 CCAGCGTTACTGCCTGACC 60.742 63.158 0.00 0.00 45.78 4.02
2785 3746 4.438744 CGGTTTTGTCTTTCTGTGCTCTTT 60.439 41.667 0.00 0.00 0.00 2.52
2877 3838 0.038343 CCCGGCCACAATGTTTTCAG 60.038 55.000 2.24 0.00 0.00 3.02
2949 3910 0.318445 CCTTCAAGTGCTTGTGCTGC 60.318 55.000 11.17 0.00 41.16 5.25
2955 3916 2.195411 TGCTTGTGCTGCCTTGGA 59.805 55.556 0.00 0.00 40.48 3.53
3023 3984 0.676782 CGAAGGGCGGGTTTGAAGAT 60.677 55.000 0.00 0.00 36.03 2.40
3024 3985 1.406341 CGAAGGGCGGGTTTGAAGATA 60.406 52.381 0.00 0.00 36.03 1.98
3025 3986 2.014857 GAAGGGCGGGTTTGAAGATAC 58.985 52.381 0.00 0.00 0.00 2.24
3026 3987 0.988832 AGGGCGGGTTTGAAGATACA 59.011 50.000 0.00 0.00 0.00 2.29
3027 3988 1.353022 AGGGCGGGTTTGAAGATACAA 59.647 47.619 0.00 0.00 0.00 2.41
3028 3989 1.471287 GGGCGGGTTTGAAGATACAAC 59.529 52.381 0.00 0.00 0.00 3.32
3029 3990 2.433436 GGCGGGTTTGAAGATACAACT 58.567 47.619 0.00 0.00 0.00 3.16
3030 3991 3.602483 GGCGGGTTTGAAGATACAACTA 58.398 45.455 0.00 0.00 0.00 2.24
3031 3992 3.373130 GGCGGGTTTGAAGATACAACTAC 59.627 47.826 0.00 0.00 0.00 2.73
3048 4009 7.349412 ACAACTACCACCTTCATAGTATCTC 57.651 40.000 0.00 0.00 0.00 2.75
3053 4014 5.141182 ACCACCTTCATAGTATCTCGATGT 58.859 41.667 0.00 0.00 32.35 3.06
3079 4040 1.611519 TGTTTTTACCAAGGAGCCCG 58.388 50.000 0.00 0.00 0.00 6.13
3130 4091 6.986817 TGCTTGGTGCTCTTATACTATCTTTC 59.013 38.462 0.00 0.00 43.37 2.62
3176 4137 8.356533 AGTTTTGCTTTGAAACATGATACAAG 57.643 30.769 0.00 0.00 38.99 3.16
3231 4192 4.438200 GGCGAGAAATCATTTAAAAGCGGA 60.438 41.667 0.00 0.00 0.00 5.54
3476 4442 1.153647 GCCCCACCAAAATAAGCGC 60.154 57.895 0.00 0.00 0.00 5.92
3576 4543 5.009631 TCCAAATGAATGTGGTACCTTGAG 58.990 41.667 14.36 1.76 36.23 3.02
3680 4647 7.654116 TGTTCGCGATATTGGATTCTATTGTTA 59.346 33.333 10.88 0.00 0.00 2.41
3774 4741 2.040145 TCTGGTTGTCAAGATGGATGCA 59.960 45.455 0.00 0.00 0.00 3.96
3924 4891 1.388547 TGATGCGCAAGGAATTACCC 58.611 50.000 17.11 0.00 45.01 3.69
4166 5134 8.406297 TGACCTATTGTATAGCTAATATGCTCG 58.594 37.037 0.00 0.00 42.97 5.03
4204 5172 5.120399 TGTTTGAACATCGTAACTCTGGTT 58.880 37.500 0.00 0.00 35.35 3.67
4210 5178 3.813166 ACATCGTAACTCTGGTTGTTTGG 59.187 43.478 0.00 0.00 36.92 3.28
4215 5183 5.415077 TCGTAACTCTGGTTGTTTGGAAAAA 59.585 36.000 0.00 0.00 36.92 1.94
4291 5259 6.715344 TCGTAAACTTTCCACATACATGAC 57.285 37.500 0.00 0.00 0.00 3.06
4292 5260 6.460781 TCGTAAACTTTCCACATACATGACT 58.539 36.000 0.00 0.00 0.00 3.41
4367 5552 8.031864 TGAATCTAAAAACTGTTGCAGAAAACA 58.968 29.630 2.91 0.00 37.71 2.83
4387 5572 7.410120 AAACAGAGAAATGAGGTTTGACTTT 57.590 32.000 0.00 0.00 31.10 2.66
4388 5573 6.382869 ACAGAGAAATGAGGTTTGACTTTG 57.617 37.500 0.00 0.00 0.00 2.77
4389 5574 5.300286 ACAGAGAAATGAGGTTTGACTTTGG 59.700 40.000 0.00 0.00 0.00 3.28
4390 5575 4.279420 AGAGAAATGAGGTTTGACTTTGGC 59.721 41.667 0.00 0.00 0.00 4.52
4391 5576 3.960102 AGAAATGAGGTTTGACTTTGGCA 59.040 39.130 0.00 0.00 0.00 4.92
4392 5577 4.405358 AGAAATGAGGTTTGACTTTGGCAA 59.595 37.500 0.00 0.00 0.00 4.52
4393 5578 4.751767 AATGAGGTTTGACTTTGGCAAA 57.248 36.364 12.79 12.79 33.22 3.68
4394 5579 4.961438 ATGAGGTTTGACTTTGGCAAAT 57.039 36.364 13.89 3.91 37.54 2.32
4468 5653 3.349927 CAGAAGTTCCTGCATCATTGGA 58.650 45.455 0.00 0.00 0.00 3.53
4695 5880 4.900635 TTTCTCCTTTTGTGCTCTGTTC 57.099 40.909 0.00 0.00 0.00 3.18
4732 5917 6.180472 TGGACATCTCTTATTTCCCTTTCAC 58.820 40.000 0.00 0.00 0.00 3.18
4823 6008 1.464219 GCCATTTTCAAAATGTGCCGG 59.536 47.619 19.35 0.00 0.00 6.13
4896 6081 3.130516 TCAAGTTACTGATAGCCGTCCTG 59.869 47.826 0.00 0.00 0.00 3.86
4899 6084 3.961408 AGTTACTGATAGCCGTCCTGAAT 59.039 43.478 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 5.693555 CCAAATCTTTTTCTTCTCCAACAGC 59.306 40.000 0.00 0.00 0.00 4.40
64 65 5.463392 GCACCAAATCTTTTTCTTCTCCAAC 59.537 40.000 0.00 0.00 0.00 3.77
76 77 4.339814 TGAGTTTTACGGCACCAAATCTTT 59.660 37.500 0.00 0.00 0.00 2.52
79 80 3.907894 TGAGTTTTACGGCACCAAATC 57.092 42.857 0.00 0.00 0.00 2.17
81 82 3.482436 AGATGAGTTTTACGGCACCAAA 58.518 40.909 0.00 0.00 0.00 3.28
85 86 4.675114 CACAAAAGATGAGTTTTACGGCAC 59.325 41.667 0.00 0.00 0.00 5.01
132 133 4.413760 TCTATAACAGCGGCCCTATAACT 58.586 43.478 0.00 0.00 0.00 2.24
140 141 1.801178 GAAGCATCTATAACAGCGGCC 59.199 52.381 0.00 0.00 0.00 6.13
144 145 3.248602 CCGGTTGAAGCATCTATAACAGC 59.751 47.826 0.00 0.00 0.00 4.40
145 146 4.442706 ACCGGTTGAAGCATCTATAACAG 58.557 43.478 0.00 0.00 0.00 3.16
151 152 3.259876 AGTTGTACCGGTTGAAGCATCTA 59.740 43.478 15.04 0.00 0.00 1.98
288 291 8.710835 TTAACTGTCATTCATAGCACGATTTA 57.289 30.769 0.00 0.00 0.00 1.40
294 297 9.503427 GGTTAAATTAACTGTCATTCATAGCAC 57.497 33.333 14.61 0.00 38.68 4.40
309 312 6.964934 CCAGTTCATAGCACGGTTAAATTAAC 59.035 38.462 7.32 7.32 37.94 2.01
373 376 1.067821 TCCAAAACAAATGGCGTGGTC 59.932 47.619 0.00 0.00 37.88 4.02
386 389 8.314021 ACAAAAATATTCCCTCTGATCCAAAAC 58.686 33.333 0.00 0.00 0.00 2.43
428 432 9.520204 CCTGGTATATTTCAGTTGCAAATTTAG 57.480 33.333 0.00 0.00 0.00 1.85
437 441 4.576463 GGAGCACCTGGTATATTTCAGTTG 59.424 45.833 0.00 2.63 0.00 3.16
508 512 9.965824 ACTTATTTCTGAAATTTCGTGAAACAT 57.034 25.926 26.75 19.54 36.15 2.71
546 550 2.943033 GGGATTGTAGAAACATGACCCG 59.057 50.000 0.00 0.00 34.92 5.28
548 552 7.696992 TTTTAGGGATTGTAGAAACATGACC 57.303 36.000 0.00 0.00 34.97 4.02
564 568 7.888021 TGAGTTTAGATTTGCAGATTTTAGGGA 59.112 33.333 0.00 0.00 0.00 4.20
609 613 9.282247 GACACTATTCATGCAGATTTACTTTTG 57.718 33.333 0.00 0.00 0.00 2.44
614 618 9.624697 TTTTTGACACTATTCATGCAGATTTAC 57.375 29.630 0.00 0.00 0.00 2.01
643 647 3.007398 TGGTTTTGTCTTTTTGTGGCACT 59.993 39.130 19.83 0.00 0.00 4.40
644 648 3.330267 TGGTTTTGTCTTTTTGTGGCAC 58.670 40.909 11.55 11.55 0.00 5.01
645 649 3.259374 TCTGGTTTTGTCTTTTTGTGGCA 59.741 39.130 0.00 0.00 0.00 4.92
646 650 3.855858 TCTGGTTTTGTCTTTTTGTGGC 58.144 40.909 0.00 0.00 0.00 5.01
648 652 7.068955 GTGTTTTCTGGTTTTGTCTTTTTGTG 58.931 34.615 0.00 0.00 0.00 3.33
649 653 6.763610 TGTGTTTTCTGGTTTTGTCTTTTTGT 59.236 30.769 0.00 0.00 0.00 2.83
650 654 7.042119 AGTGTGTTTTCTGGTTTTGTCTTTTTG 60.042 33.333 0.00 0.00 0.00 2.44
651 655 6.989759 AGTGTGTTTTCTGGTTTTGTCTTTTT 59.010 30.769 0.00 0.00 0.00 1.94
652 656 6.521162 AGTGTGTTTTCTGGTTTTGTCTTTT 58.479 32.000 0.00 0.00 0.00 2.27
707 714 5.927954 ATCAAATTCAAAACACACATGGC 57.072 34.783 0.00 0.00 0.00 4.40
794 801 4.102210 TCCATGCTCCCAACATTTCAAAAA 59.898 37.500 0.00 0.00 0.00 1.94
795 802 3.645212 TCCATGCTCCCAACATTTCAAAA 59.355 39.130 0.00 0.00 0.00 2.44
796 803 3.237746 TCCATGCTCCCAACATTTCAAA 58.762 40.909 0.00 0.00 0.00 2.69
954 991 2.878429 GAGCAGCGTCGAGAGGAA 59.122 61.111 0.00 0.00 0.00 3.36
1055 1092 1.538876 TGGGTGTGGGAGAAGAGGG 60.539 63.158 0.00 0.00 0.00 4.30
1440 1477 3.157949 GAGGGGGAGGAAGAGGCG 61.158 72.222 0.00 0.00 0.00 5.52
1441 1478 2.770475 GGAGGGGGAGGAAGAGGC 60.770 72.222 0.00 0.00 0.00 4.70
1442 1479 2.040359 GGGAGGGGGAGGAAGAGG 60.040 72.222 0.00 0.00 0.00 3.69
1443 1480 2.040359 GGGGAGGGGGAGGAAGAG 60.040 72.222 0.00 0.00 0.00 2.85
1444 1481 3.707189 GGGGGAGGGGGAGGAAGA 61.707 72.222 0.00 0.00 0.00 2.87
1445 1482 3.711782 AGGGGGAGGGGGAGGAAG 61.712 72.222 0.00 0.00 0.00 3.46
1446 1483 3.707189 GAGGGGGAGGGGGAGGAA 61.707 72.222 0.00 0.00 0.00 3.36
1539 1576 1.214589 GGAGTGCTCGTAGCGGAAA 59.785 57.895 3.08 0.00 46.26 3.13
1755 1792 1.073284 GGCTTGTAGAAACCCACCAGA 59.927 52.381 0.00 0.00 0.00 3.86
1758 1795 0.958876 CGGGCTTGTAGAAACCCACC 60.959 60.000 11.38 0.00 42.97 4.61
1806 1843 2.442272 CCCTCATCCCCGTCGTCT 60.442 66.667 0.00 0.00 0.00 4.18
2146 2198 7.497909 ACTCTACCCAACATATTAATTCCAACG 59.502 37.037 0.00 0.00 0.00 4.10
2158 2210 6.367374 TCACAATTCACTCTACCCAACATA 57.633 37.500 0.00 0.00 0.00 2.29
2173 2225 7.076842 TCGAAGGAATCATCTTTCACAATTC 57.923 36.000 2.35 0.00 40.64 2.17
2195 2247 7.864686 TCAAATGCTCCATAGTTCATAATTCG 58.135 34.615 0.00 0.00 0.00 3.34
2199 2251 9.679661 TTTACTCAAATGCTCCATAGTTCATAA 57.320 29.630 0.00 0.00 0.00 1.90
2204 2256 8.814038 ATCTTTTACTCAAATGCTCCATAGTT 57.186 30.769 0.00 0.00 0.00 2.24
2244 2296 5.627499 TTCAAACTGAAGGATACACATGC 57.373 39.130 0.00 0.00 41.41 4.06
2251 2303 6.655003 GGACTGTGATTTCAAACTGAAGGATA 59.345 38.462 0.00 0.00 37.70 2.59
2353 2408 8.992835 AAGCTAGAATTTCAATTCATTCCAAC 57.007 30.769 13.50 0.00 45.59 3.77
2408 2463 1.947456 GGGAATCGGCGAAAATTAGCT 59.053 47.619 15.93 0.00 0.00 3.32
2450 2505 0.322456 TTCGCTTGCAGGCACCTAAT 60.322 50.000 21.61 0.00 0.00 1.73
2466 2521 0.618458 TTCATCCAGGGTTCCCTTCG 59.382 55.000 7.79 1.73 33.50 3.79
2661 3622 1.063806 GCGGAATCAGGAATCGATCG 58.936 55.000 9.36 9.36 0.00 3.69
2709 3670 0.968901 ATTGCCATCACCACTGCCAG 60.969 55.000 0.00 0.00 0.00 4.85
2785 3746 1.434188 TTGCCCAGGAAGAGAAGACA 58.566 50.000 0.00 0.00 0.00 3.41
2877 3838 4.918810 ACAGGTGAGAACCAAAATTCAC 57.081 40.909 0.00 0.00 39.29 3.18
2949 3910 1.986882 AAGGTTGCAGAAGTCCAAGG 58.013 50.000 0.00 0.00 0.00 3.61
2955 3916 4.532834 TCCAGTAAAAAGGTTGCAGAAGT 58.467 39.130 0.00 0.00 0.00 3.01
3023 3984 7.228108 CGAGATACTATGAAGGTGGTAGTTGTA 59.772 40.741 0.00 0.00 31.58 2.41
3024 3985 6.039493 CGAGATACTATGAAGGTGGTAGTTGT 59.961 42.308 0.00 0.00 31.58 3.32
3025 3986 6.262496 TCGAGATACTATGAAGGTGGTAGTTG 59.738 42.308 0.00 0.00 31.58 3.16
3026 3987 6.363065 TCGAGATACTATGAAGGTGGTAGTT 58.637 40.000 0.00 0.00 31.58 2.24
3027 3988 5.938279 TCGAGATACTATGAAGGTGGTAGT 58.062 41.667 0.00 0.00 33.55 2.73
3028 3989 6.431543 ACATCGAGATACTATGAAGGTGGTAG 59.568 42.308 0.00 0.00 0.00 3.18
3029 3990 6.304624 ACATCGAGATACTATGAAGGTGGTA 58.695 40.000 0.00 0.00 0.00 3.25
3030 3991 5.141182 ACATCGAGATACTATGAAGGTGGT 58.859 41.667 0.00 0.00 0.00 4.16
3031 3992 5.713792 ACATCGAGATACTATGAAGGTGG 57.286 43.478 0.00 0.00 0.00 4.61
3048 4009 9.250624 TCCTTGGTAAAAACAAAATTTACATCG 57.749 29.630 10.31 0.00 42.37 3.84
3053 4014 6.993308 GGGCTCCTTGGTAAAAACAAAATTTA 59.007 34.615 0.00 0.00 0.00 1.40
3079 4040 8.726650 ATTTGAAAAGAACAAAAACAAGCAAC 57.273 26.923 0.00 0.00 39.95 4.17
3091 4052 4.332268 GCACCAAGCAATTTGAAAAGAACA 59.668 37.500 0.00 0.00 44.79 3.18
3149 4110 9.462174 TTGTATCATGTTTCAAAGCAAAACTAG 57.538 29.630 0.00 0.00 37.48 2.57
3231 4192 9.014297 GCCACTCCAATAGTTATATAAGCAAAT 57.986 33.333 0.00 0.00 35.76 2.32
3547 4514 2.498481 ACCACATTCATTTGGAGGCATG 59.502 45.455 0.00 0.00 36.28 4.06
3774 4741 6.837992 ACAATGAAGATATACACGCGTTTTT 58.162 32.000 10.22 0.00 0.00 1.94
3924 4891 4.821805 ACATCACTACCAACAGAAACTTGG 59.178 41.667 0.00 0.00 43.49 3.61
4137 5105 9.319143 GCATATTAGCTATACAATAGGTCAAGG 57.681 37.037 0.00 0.00 0.00 3.61
4166 5134 6.384224 TGTTCAAACATCAATTCTGATCAGC 58.616 36.000 18.36 0.00 40.49 4.26
4236 5204 9.588096 AAAACCAGAAAATCTACTTACTCCAAT 57.412 29.630 0.00 0.00 0.00 3.16
4261 5229 8.095792 TGTATGTGGAAAGTTTACGAAGGATAA 58.904 33.333 0.00 0.00 0.00 1.75
4291 5259 5.358160 TGACCTGTACACATGATCACTAGAG 59.642 44.000 0.00 0.00 0.00 2.43
4292 5260 5.261216 TGACCTGTACACATGATCACTAGA 58.739 41.667 0.00 0.00 0.00 2.43
4367 5552 4.279420 GCCAAAGTCAAACCTCATTTCTCT 59.721 41.667 0.00 0.00 0.00 3.10
4387 5572 6.352016 TCTTTTTACTATGCCAATTTGCCA 57.648 33.333 0.00 0.00 0.00 4.92
4388 5573 6.313658 CCTTCTTTTTACTATGCCAATTTGCC 59.686 38.462 0.00 0.00 0.00 4.52
4389 5574 7.096551 TCCTTCTTTTTACTATGCCAATTTGC 58.903 34.615 0.00 0.00 0.00 3.68
4390 5575 9.487790 TTTCCTTCTTTTTACTATGCCAATTTG 57.512 29.630 0.00 0.00 0.00 2.32
4392 5577 9.710900 CTTTTCCTTCTTTTTACTATGCCAATT 57.289 29.630 0.00 0.00 0.00 2.32
4393 5578 9.088987 TCTTTTCCTTCTTTTTACTATGCCAAT 57.911 29.630 0.00 0.00 0.00 3.16
4394 5579 8.472007 TCTTTTCCTTCTTTTTACTATGCCAA 57.528 30.769 0.00 0.00 0.00 4.52
4695 5880 0.036010 ATGTCCAGGTTGAGGAAGCG 60.036 55.000 0.00 0.00 36.80 4.68
4732 5917 3.189287 GGAACAGCAATGACCAGTACAAG 59.811 47.826 0.00 0.00 0.00 3.16
4896 6081 7.172361 GTCATTTCAGCTATTCAGAGGGTATTC 59.828 40.741 0.00 0.00 0.00 1.75
4899 6084 5.451937 CGTCATTTCAGCTATTCAGAGGGTA 60.452 44.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.