Multiple sequence alignment - TraesCS2A01G538600

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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 TraesCS2A01G538600 chr2A 100.000 4309 0 0 1 4309 751418808 751423116 0 7958
1 TraesCS2A01G538600 chr2A 81.808 929 159 8 2387 3308 721989554 721988629 0 771
2 TraesCS2A01G538600 chr2B 92.401 4356 236 52 1 4309 759489677 759493984 0 6122
3 TraesCS2A01G538600 chr2B 81.799 934 161 6 2387 3313 708986913 708985982 0 774
4 TraesCS2A01G538600 chr2D 93.358 3538 191 21 1 3511 619731243 619734763 0 5192
5 TraesCS2A01G538600 chr2D 86.842 874 78 21 3458 4304 619734641 619735504 0 942
6 TraesCS2A01G538600 chr2D 81.974 932 159 7 2389 3313 587166758 587165829 0 782


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 TraesCS2A01G538600 chr2A 751418808 751423116 4308 False 7958 7958 100.000 1 4309 1 chr2A.!!$F1 4308
1 TraesCS2A01G538600 chr2A 721988629 721989554 925 True 771 771 81.808 2387 3308 1 chr2A.!!$R1 921
2 TraesCS2A01G538600 chr2B 759489677 759493984 4307 False 6122 6122 92.401 1 4309 1 chr2B.!!$F1 4308
3 TraesCS2A01G538600 chr2B 708985982 708986913 931 True 774 774 81.799 2387 3313 1 chr2B.!!$R1 926
4 TraesCS2A01G538600 chr2D 619731243 619735504 4261 False 3067 5192 90.100 1 4304 2 chr2D.!!$F1 4303
5 TraesCS2A01G538600 chr2D 587165829 587166758 929 True 782 782 81.974 2389 3313 1 chr2D.!!$R1 924

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
684 715 0.250295 TTGTCGGGCTCTTCCAGTTG 60.250 55.000 0.00 0.00 36.21 3.16 F
1081 1119 1.429021 CCAATGCCGGTGATCAACG 59.571 57.895 26.19 26.19 42.03 4.10 F
1596 1636 1.201647 ACACGACTGTATGAGGAACCG 59.798 52.381 0.00 0.00 0.00 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1596 1636 0.539986 TACAGTTCTCGCCAATCCCC 59.460 55.000 0.0 0.0 0.00 4.81 R
1995 2044 1.142748 CGGCTCCCTGTTGCTCTAG 59.857 63.158 0.0 0.0 0.00 2.43 R
3566 3624 0.901580 AGGGGAAAACAGCATGGCAG 60.902 55.000 0.0 0.0 43.62 4.85 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
186 205 1.135094 CCCACTGGATAGGACAGCAT 58.865 55.000 0.00 0.00 39.55 3.79
187 206 1.202734 CCCACTGGATAGGACAGCATG 60.203 57.143 0.00 0.00 46.00 4.06
285 307 6.801539 TGCATAACAGGAACAAAGAAGTAG 57.198 37.500 0.00 0.00 0.00 2.57
286 308 5.705441 TGCATAACAGGAACAAAGAAGTAGG 59.295 40.000 0.00 0.00 0.00 3.18
334 361 1.336517 CCCAATTTGCTGACACTGCAG 60.337 52.381 13.48 13.48 39.29 4.41
338 365 2.981914 TTTGCTGACACTGCAGGGGG 62.982 60.000 22.46 11.07 39.29 5.40
371 402 1.063417 CCAATGAGGGAATCCAGCCTT 60.063 52.381 0.09 0.00 34.83 4.35
495 526 5.864474 GCATACCAGGACGAAGAAGTATATG 59.136 44.000 0.00 0.00 0.00 1.78
579 610 3.195610 TGGAGCATATGTGACGAAAGAGT 59.804 43.478 4.29 0.00 0.00 3.24
680 711 1.202879 ACATTTTGTCGGGCTCTTCCA 60.203 47.619 0.00 0.00 36.21 3.53
684 715 0.250295 TTGTCGGGCTCTTCCAGTTG 60.250 55.000 0.00 0.00 36.21 3.16
787 820 4.079253 TGGCTTGACCTCTTATTTGGAAC 58.921 43.478 0.00 0.00 40.22 3.62
822 855 2.417924 CCAAGTGAGAAGGATCAGACCG 60.418 54.545 0.00 0.00 34.73 4.79
830 863 4.087182 AGAAGGATCAGACCGTGTAAGAA 58.913 43.478 0.00 0.00 34.73 2.52
912 946 3.971245 AGCTGCCTATAAGTAGATGCC 57.029 47.619 0.00 0.00 0.00 4.40
944 978 2.140717 GAACACTTCATCCCGTTTCGT 58.859 47.619 0.00 0.00 0.00 3.85
1048 1086 4.704103 AGCAGCTCCCCTCCGACA 62.704 66.667 0.00 0.00 0.00 4.35
1081 1119 1.429021 CCAATGCCGGTGATCAACG 59.571 57.895 26.19 26.19 42.03 4.10
1363 1401 2.358898 TGAAAAACCACTGCAGAAGAGC 59.641 45.455 23.35 2.34 0.00 4.09
1367 1405 1.739562 CCACTGCAGAAGAGCGACC 60.740 63.158 23.35 0.00 37.31 4.79
1458 1498 3.955650 AGTAGTACACGCACCATCTTT 57.044 42.857 2.52 0.00 0.00 2.52
1541 1581 5.065731 CCCAAAATGAAGAGTATGAGCTGTC 59.934 44.000 0.00 0.00 0.00 3.51
1592 1632 3.352648 TCATCACACGACTGTATGAGGA 58.647 45.455 0.00 0.00 39.75 3.71
1594 1634 3.570926 TCACACGACTGTATGAGGAAC 57.429 47.619 0.00 0.00 26.14 3.62
1596 1636 1.201647 ACACGACTGTATGAGGAACCG 59.798 52.381 0.00 0.00 0.00 4.44
1608 1648 2.513897 GAACCGGGGATTGGCGAG 60.514 66.667 6.32 0.00 0.00 5.03
1624 1664 2.099621 GCGAGAACTGTACGATACGTG 58.900 52.381 0.00 0.00 41.39 4.49
1655 1695 4.154195 AGCTACATTTTGTCGCTTGGTTAG 59.846 41.667 1.26 0.00 45.48 2.34
1667 1707 3.941483 CGCTTGGTTAGATGGAAACTGAT 59.059 43.478 0.00 0.00 0.00 2.90
1749 1797 9.653287 CAGTACTACATTGAAGGTCATTTTAGA 57.347 33.333 0.00 0.00 0.00 2.10
1750 1798 9.877178 AGTACTACATTGAAGGTCATTTTAGAG 57.123 33.333 0.00 0.00 0.00 2.43
1831 1879 9.913310 TTATGATGTAACATTTCAGTATTGGGA 57.087 29.630 0.00 0.00 0.00 4.37
1835 1883 6.186957 TGTAACATTTCAGTATTGGGAGCAT 58.813 36.000 0.00 0.00 0.00 3.79
1844 1892 4.460382 CAGTATTGGGAGCATTTGTGAAGT 59.540 41.667 0.00 0.00 0.00 3.01
1995 2044 6.403855 GCCTACTCGATATAGATGTCTGGTTC 60.404 46.154 5.61 0.00 0.00 3.62
2032 2081 1.125633 GGGGTCGACCTAAATGGCTA 58.874 55.000 32.52 0.00 40.22 3.93
2090 2139 1.133790 GGACATAGCAAGGCAGCAAAG 59.866 52.381 4.78 0.00 36.85 2.77
2092 2141 2.489329 GACATAGCAAGGCAGCAAAGAA 59.511 45.455 4.78 0.00 36.85 2.52
2176 2225 3.730761 GCAGGTGCCTTCTGTGCG 61.731 66.667 0.00 0.00 34.89 5.34
2203 2252 5.444663 AAATGTTTCCAGCTTCAACTCTC 57.555 39.130 0.00 0.00 0.00 3.20
2316 2365 2.109425 GGTACGGCCTTTCATGAACT 57.891 50.000 7.89 0.00 0.00 3.01
2680 2731 6.299805 TCTTGCAATCCTGAACTACAGTAT 57.700 37.500 0.00 0.00 44.40 2.12
2681 2732 6.108687 TCTTGCAATCCTGAACTACAGTATG 58.891 40.000 0.00 0.00 44.40 2.39
2684 2735 6.108687 TGCAATCCTGAACTACAGTATGAAG 58.891 40.000 0.00 0.00 44.40 3.02
2708 2762 7.324178 AGGTGTAATGTCTGACATAACTCTTC 58.676 38.462 22.53 6.43 37.97 2.87
2710 2764 7.489757 GGTGTAATGTCTGACATAACTCTTCTC 59.510 40.741 22.53 6.63 37.97 2.87
2818 2872 0.771755 GGCCTAGGATTGGGTAAGGG 59.228 60.000 14.75 0.00 0.00 3.95
3188 3242 1.011451 GTGCCAGAGAGCTCGTGAAC 61.011 60.000 17.89 12.51 34.09 3.18
3350 3405 2.613691 AGCACAAAACGATACCTACGG 58.386 47.619 0.00 0.00 34.93 4.02
3364 3419 2.230750 ACCTACGGCAGTTTGTCTCTAC 59.769 50.000 0.00 0.00 0.00 2.59
3419 3474 9.831737 CTTTTGATATGAAAGTACTGAAGTTGG 57.168 33.333 0.00 0.00 31.17 3.77
3459 3514 8.863049 GCTGTTTTGGACAAATTATCTGTAATG 58.137 33.333 0.00 0.00 37.93 1.90
3479 3534 6.727824 AATGTTACTTCCGATCTGAAAGTG 57.272 37.500 12.06 0.51 33.76 3.16
3499 3554 1.919918 GCTGAAGTTGTTGTGTGTTGC 59.080 47.619 0.00 0.00 0.00 4.17
3507 3562 0.598158 GTTGTGTGTTGCCATGCTGG 60.598 55.000 0.00 0.00 41.55 4.85
3524 3579 7.102346 CCATGCTGGTTTGGACAAATTATTAA 58.898 34.615 0.34 0.00 34.81 1.40
3566 3624 1.548986 GTGCTGAAGTTGTTGTGTGC 58.451 50.000 0.00 0.00 0.00 4.57
3596 3654 0.189822 TTTTCCCCTTTCACCCCCAG 59.810 55.000 0.00 0.00 0.00 4.45
3599 3657 0.122435 TCCCCTTTCACCCCCAGTAT 59.878 55.000 0.00 0.00 0.00 2.12
3600 3658 0.258774 CCCCTTTCACCCCCAGTATG 59.741 60.000 0.00 0.00 0.00 2.39
3681 3755 7.321153 AGTAAGGTACTGTATGCTGTTAGTTG 58.679 38.462 0.00 0.00 40.86 3.16
3697 3771 5.221224 TGTTAGTTGGCCATTTGACTTCAAG 60.221 40.000 12.91 0.00 37.15 3.02
3702 3776 3.069443 TGGCCATTTGACTTCAAGTTTCC 59.931 43.478 0.00 0.00 37.15 3.13
3703 3777 3.069443 GGCCATTTGACTTCAAGTTTCCA 59.931 43.478 0.00 0.00 37.15 3.53
3704 3778 4.051237 GCCATTTGACTTCAAGTTTCCAC 58.949 43.478 0.00 0.00 37.15 4.02
3705 3779 4.290155 CCATTTGACTTCAAGTTTCCACG 58.710 43.478 0.00 0.00 37.15 4.94
3706 3780 4.290155 CATTTGACTTCAAGTTTCCACGG 58.710 43.478 0.00 0.00 37.15 4.94
3707 3781 2.702592 TGACTTCAAGTTTCCACGGT 57.297 45.000 0.00 0.00 0.00 4.83
3708 3782 2.285083 TGACTTCAAGTTTCCACGGTG 58.715 47.619 0.00 0.00 0.00 4.94
3709 3783 1.002792 GACTTCAAGTTTCCACGGTGC 60.003 52.381 1.68 0.00 0.00 5.01
3710 3784 0.041312 CTTCAAGTTTCCACGGTGCG 60.041 55.000 1.68 0.00 0.00 5.34
3711 3785 2.051345 CAAGTTTCCACGGTGCGC 60.051 61.111 0.00 0.00 0.00 6.09
3712 3786 2.515057 AAGTTTCCACGGTGCGCA 60.515 55.556 5.66 5.66 0.00 6.09
3713 3787 1.896660 AAGTTTCCACGGTGCGCAT 60.897 52.632 15.91 0.00 0.00 4.73
3714 3788 2.126888 GTTTCCACGGTGCGCATG 60.127 61.111 15.91 12.72 0.00 4.06
3715 3789 2.281139 TTTCCACGGTGCGCATGA 60.281 55.556 15.91 2.65 0.00 3.07
3716 3790 1.894282 TTTCCACGGTGCGCATGAA 60.894 52.632 15.91 9.18 0.00 2.57
3717 3791 1.240641 TTTCCACGGTGCGCATGAAT 61.241 50.000 15.91 0.00 0.00 2.57
3718 3792 1.921045 TTCCACGGTGCGCATGAATG 61.921 55.000 15.91 10.17 0.00 2.67
3719 3793 2.397754 CCACGGTGCGCATGAATGA 61.398 57.895 15.91 0.00 0.00 2.57
3720 3794 1.501292 CACGGTGCGCATGAATGAA 59.499 52.632 15.91 0.00 0.00 2.57
3721 3795 0.794229 CACGGTGCGCATGAATGAAC 60.794 55.000 15.91 0.00 0.00 3.18
3722 3796 0.955428 ACGGTGCGCATGAATGAACT 60.955 50.000 15.91 0.00 0.00 3.01
3723 3797 1.006086 CGGTGCGCATGAATGAACTA 58.994 50.000 15.91 0.00 0.00 2.24
3724 3798 1.267532 CGGTGCGCATGAATGAACTAC 60.268 52.381 15.91 0.00 0.00 2.73
3725 3799 1.737236 GGTGCGCATGAATGAACTACA 59.263 47.619 15.91 0.00 0.00 2.74
3726 3800 2.223112 GGTGCGCATGAATGAACTACAG 60.223 50.000 15.91 0.00 0.00 2.74
3727 3801 2.416547 GTGCGCATGAATGAACTACAGT 59.583 45.455 15.91 0.00 0.00 3.55
3728 3802 3.616821 GTGCGCATGAATGAACTACAGTA 59.383 43.478 15.91 0.00 0.00 2.74
3729 3803 4.271049 GTGCGCATGAATGAACTACAGTAT 59.729 41.667 15.91 0.00 0.00 2.12
3730 3804 4.875536 TGCGCATGAATGAACTACAGTATT 59.124 37.500 5.66 0.00 0.00 1.89
3731 3805 5.353956 TGCGCATGAATGAACTACAGTATTT 59.646 36.000 5.66 0.00 0.00 1.40
3732 3806 5.904080 GCGCATGAATGAACTACAGTATTTC 59.096 40.000 0.30 4.12 0.00 2.17
3733 3807 6.238211 GCGCATGAATGAACTACAGTATTTCT 60.238 38.462 0.30 0.00 0.00 2.52
3739 3813 9.424319 TGAATGAACTACAGTATTTCTCACTTC 57.576 33.333 10.98 9.11 0.00 3.01
3754 3860 1.394917 CACTTCTAATGCTGCGACACC 59.605 52.381 0.00 0.00 0.00 4.16
3779 3885 7.041098 CCTTATCAGCAAGGTTGGACATATAAC 60.041 40.741 0.00 0.00 40.29 1.89
3866 3973 4.021544 TGGAAACAAAATCGAAATGGAGGG 60.022 41.667 0.00 0.00 37.44 4.30
3870 3977 0.254747 AAATCGAAATGGAGGGCGGA 59.745 50.000 0.00 0.00 0.00 5.54
3886 3993 0.179000 CGGAGATGGGGAGGAAACTG 59.821 60.000 0.00 0.00 44.43 3.16
3908 4015 1.971695 CCGAACAGAAACCCCAGGC 60.972 63.158 0.00 0.00 0.00 4.85
4111 4233 4.400961 GCCGTGAGCCTGCCTTCT 62.401 66.667 0.00 0.00 34.35 2.85
4227 4365 2.640302 GCCTCGCCTGTCAGAGTCA 61.640 63.158 0.00 0.00 32.88 3.41
4247 4385 2.080286 TCCTACGCTCAAGTCAAAGC 57.920 50.000 0.00 0.00 35.13 3.51
4270 4408 0.034896 GCCGGAGTCAAAGAAGGTGA 59.965 55.000 5.05 0.00 0.00 4.02
4304 4442 8.918202 TGGAGAAAATAATCGGCTACAAATAT 57.082 30.769 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 1.566211 CCTCTCATGTCCTGTCACCT 58.434 55.000 0.00 0.00 0.00 4.00
285 307 1.705997 ATCCTACGTTCCATGCCCCC 61.706 60.000 0.00 0.00 0.00 5.40
286 308 0.182775 AATCCTACGTTCCATGCCCC 59.817 55.000 0.00 0.00 0.00 5.80
334 361 1.077930 GGAAACTTCGGCTACCCCC 60.078 63.158 0.00 0.00 0.00 5.40
338 365 2.678336 CCTCATTGGAAACTTCGGCTAC 59.322 50.000 0.00 0.00 38.35 3.58
371 402 1.067295 AGGGTGTTGCTTCATGGAGA 58.933 50.000 4.75 0.00 0.00 3.71
495 526 8.778358 CAATTATGAAGTTATCTCTTGGCCTAC 58.222 37.037 3.32 0.00 0.00 3.18
579 610 2.989639 CTCCGGGCCACTCATTCA 59.010 61.111 4.39 0.00 0.00 2.57
639 670 7.750229 ATGTGAATATTCATTTATGTCGCCT 57.250 32.000 20.65 0.00 39.73 5.52
648 679 6.534793 GCCCGACAAAATGTGAATATTCATTT 59.465 34.615 20.65 14.74 43.26 2.32
787 820 0.032678 ACTTGGACAGTGTCTGCTCG 59.967 55.000 22.18 9.47 34.37 5.03
822 855 7.328737 CAGATATAGCGGTATGGTTTCTTACAC 59.671 40.741 17.16 0.00 0.00 2.90
830 863 3.832490 TCTGCAGATATAGCGGTATGGTT 59.168 43.478 13.74 2.10 39.38 3.67
912 946 0.606401 AAGTGTTCCTCCATGGTGCG 60.606 55.000 12.58 3.89 37.07 5.34
944 978 6.535150 CCAATCTCAGTATCTTTACGCAGAAA 59.465 38.462 0.00 0.00 33.32 2.52
1041 1079 2.663196 GGGTGGAGGTTGTCGGAG 59.337 66.667 0.00 0.00 0.00 4.63
1081 1119 0.472471 TCAAGGTTGAGGTGACCCAC 59.528 55.000 0.00 0.00 37.93 4.61
1119 1157 6.007076 TGCTTTGGTAATATCTTCAACCACA 58.993 36.000 0.00 0.00 41.58 4.17
1363 1401 2.678336 GCTCCTAATTTTCCTGTGGTCG 59.322 50.000 0.00 0.00 0.00 4.79
1367 1405 6.994496 TCATCATAGCTCCTAATTTTCCTGTG 59.006 38.462 0.00 0.00 0.00 3.66
1458 1498 2.195411 TGCAGGCAGTTTGCTCCA 59.805 55.556 0.67 0.00 44.28 3.86
1571 1611 3.352648 TCCTCATACAGTCGTGTGATGA 58.647 45.455 0.00 0.00 41.74 2.92
1578 1618 0.815734 CCGGTTCCTCATACAGTCGT 59.184 55.000 0.00 0.00 0.00 4.34
1592 1632 2.598787 TTCTCGCCAATCCCCGGTT 61.599 57.895 0.00 0.00 0.00 4.44
1594 1634 2.513897 GTTCTCGCCAATCCCCGG 60.514 66.667 0.00 0.00 0.00 5.73
1596 1636 0.539986 TACAGTTCTCGCCAATCCCC 59.460 55.000 0.00 0.00 0.00 4.81
1608 1648 2.679837 TCCTCCACGTATCGTACAGTTC 59.320 50.000 0.00 0.00 38.32 3.01
1624 1664 3.010420 GACAAAATGTAGCTGGTCCTCC 58.990 50.000 0.00 0.00 0.00 4.30
1655 1695 9.455847 GCTTCATGTTATTTATCAGTTTCCATC 57.544 33.333 0.00 0.00 0.00 3.51
1667 1707 5.045213 TGGGGACTCAGCTTCATGTTATTTA 60.045 40.000 0.00 0.00 0.00 1.40
1749 1797 4.530710 TTATCTACAACCGACAAGTGCT 57.469 40.909 0.00 0.00 0.00 4.40
1750 1798 5.220605 GGAATTATCTACAACCGACAAGTGC 60.221 44.000 0.00 0.00 0.00 4.40
1829 1877 5.632347 CAGATCAAAACTTCACAAATGCTCC 59.368 40.000 0.00 0.00 0.00 4.70
1831 1879 6.152932 ACAGATCAAAACTTCACAAATGCT 57.847 33.333 0.00 0.00 0.00 3.79
1897 1946 3.288242 CTTGAACATGCACGTTGTGTAC 58.712 45.455 1.34 0.00 35.75 2.90
1909 1958 4.458295 AGGAAACTGAGATGCTTGAACATG 59.542 41.667 0.00 0.00 41.13 3.21
1942 1991 5.941647 GGCCCTGTTACAGATTTACAACTAA 59.058 40.000 14.66 0.00 32.44 2.24
1984 2033 4.180057 CTGTTGCTCTAGAACCAGACATC 58.820 47.826 0.00 0.00 0.00 3.06
1995 2044 1.142748 CGGCTCCCTGTTGCTCTAG 59.857 63.158 0.00 0.00 0.00 2.43
2020 2069 7.523216 GCAGTTGTTAAAACTAGCCATTTAGGT 60.523 37.037 0.00 0.00 40.61 3.08
2032 2081 6.040842 AGGACAATGATGCAGTTGTTAAAACT 59.959 34.615 13.87 7.19 38.57 2.66
2090 2139 7.167801 GTCAGAGAACACGCCTTAGTAATATTC 59.832 40.741 0.00 0.00 0.00 1.75
2092 2141 6.096423 TGTCAGAGAACACGCCTTAGTAATAT 59.904 38.462 0.00 0.00 0.00 1.28
2176 2225 8.515414 AGAGTTGAAGCTGGAAACATTTTATAC 58.485 33.333 8.60 0.00 41.51 1.47
2203 2252 8.461222 TGAGAACCTTGACATTGCTTATATTTG 58.539 33.333 0.00 0.00 0.00 2.32
2316 2365 1.620819 GAGACAGAGTGCCCAAGAAGA 59.379 52.381 0.00 0.00 0.00 2.87
2680 2731 7.004555 AGTTATGTCAGACATTACACCTTCA 57.995 36.000 26.75 4.49 39.73 3.02
2681 2732 7.324178 AGAGTTATGTCAGACATTACACCTTC 58.676 38.462 26.75 18.05 39.73 3.46
2684 2735 7.324178 AGAAGAGTTATGTCAGACATTACACC 58.676 38.462 26.75 19.54 39.73 4.16
2708 2762 7.162082 ACTCCCTGTTTTTAGTACATGAAGAG 58.838 38.462 0.00 0.00 0.00 2.85
2739 2793 7.391833 CCTCCTTACTTCAGTAGCAAAATTTCT 59.608 37.037 0.00 0.00 0.00 2.52
2818 2872 5.098211 GCTCAAATTTCTCATGCTGGTAAC 58.902 41.667 0.00 0.00 0.00 2.50
3188 3242 4.245660 TGTACTTTTCAGGATTCTGCTCG 58.754 43.478 0.00 0.00 40.69 5.03
3350 3405 2.260481 GTAGGCGTAGAGACAAACTGC 58.740 52.381 0.00 0.00 0.00 4.40
3364 3419 1.135083 AGAGATGAACGGTTGTAGGCG 60.135 52.381 0.00 0.00 0.00 5.52
3401 3456 5.296780 CACACACCAACTTCAGTACTTTCAT 59.703 40.000 0.00 0.00 0.00 2.57
3419 3474 2.849880 AACAGCATGACAACACACAC 57.150 45.000 0.00 0.00 39.69 3.82
3459 3514 4.092091 CAGCACTTTCAGATCGGAAGTAAC 59.908 45.833 8.32 5.86 0.00 2.50
3466 3521 2.693069 ACTTCAGCACTTTCAGATCGG 58.307 47.619 0.00 0.00 0.00 4.18
3479 3534 1.919918 GCAACACACAACAACTTCAGC 59.080 47.619 0.00 0.00 0.00 4.26
3548 3606 1.132834 CAGCACACAACAACTTCAGCA 59.867 47.619 0.00 0.00 0.00 4.41
3549 3607 1.831343 CAGCACACAACAACTTCAGC 58.169 50.000 0.00 0.00 0.00 4.26
3566 3624 0.901580 AGGGGAAAACAGCATGGCAG 60.902 55.000 0.00 0.00 43.62 4.85
3620 3678 7.510675 ACATCTTGGATTTCTCCTTACCTAA 57.489 36.000 0.00 0.00 42.59 2.69
3621 3679 8.618240 TTACATCTTGGATTTCTCCTTACCTA 57.382 34.615 0.00 0.00 42.59 3.08
3622 3680 7.510675 TTACATCTTGGATTTCTCCTTACCT 57.489 36.000 0.00 0.00 42.59 3.08
3681 3755 3.069443 TGGAAACTTGAAGTCAAATGGCC 59.931 43.478 0.00 0.00 35.15 5.36
3697 3771 2.123988 TTCATGCGCACCGTGGAAAC 62.124 55.000 14.90 0.00 0.00 2.78
3702 3776 0.794229 GTTCATTCATGCGCACCGTG 60.794 55.000 14.90 7.92 0.00 4.94
3703 3777 0.955428 AGTTCATTCATGCGCACCGT 60.955 50.000 14.90 0.00 0.00 4.83
3704 3778 1.006086 TAGTTCATTCATGCGCACCG 58.994 50.000 14.90 7.41 0.00 4.94
3705 3779 1.737236 TGTAGTTCATTCATGCGCACC 59.263 47.619 14.90 0.00 0.00 5.01
3706 3780 2.416547 ACTGTAGTTCATTCATGCGCAC 59.583 45.455 14.90 0.00 0.00 5.34
3707 3781 2.698803 ACTGTAGTTCATTCATGCGCA 58.301 42.857 14.96 14.96 0.00 6.09
3708 3782 5.409643 AATACTGTAGTTCATTCATGCGC 57.590 39.130 0.00 0.00 0.00 6.09
3709 3783 7.010460 TGAGAAATACTGTAGTTCATTCATGCG 59.990 37.037 24.48 0.00 35.39 4.73
3710 3784 8.119226 GTGAGAAATACTGTAGTTCATTCATGC 58.881 37.037 24.48 9.92 35.39 4.06
3711 3785 9.376075 AGTGAGAAATACTGTAGTTCATTCATG 57.624 33.333 24.48 0.00 35.39 3.07
3712 3786 9.950496 AAGTGAGAAATACTGTAGTTCATTCAT 57.050 29.630 24.48 8.22 35.39 2.57
3713 3787 9.424319 GAAGTGAGAAATACTGTAGTTCATTCA 57.576 33.333 24.48 18.38 35.39 2.57
3714 3788 9.646427 AGAAGTGAGAAATACTGTAGTTCATTC 57.354 33.333 24.48 20.45 35.39 2.67
3719 3793 9.372369 GCATTAGAAGTGAGAAATACTGTAGTT 57.628 33.333 0.00 0.00 0.00 2.24
3720 3794 8.754080 AGCATTAGAAGTGAGAAATACTGTAGT 58.246 33.333 0.00 0.00 0.00 2.73
3721 3795 9.029243 CAGCATTAGAAGTGAGAAATACTGTAG 57.971 37.037 0.00 0.00 0.00 2.74
3722 3796 7.492669 GCAGCATTAGAAGTGAGAAATACTGTA 59.507 37.037 0.00 0.00 29.32 2.74
3723 3797 6.314896 GCAGCATTAGAAGTGAGAAATACTGT 59.685 38.462 0.00 0.00 29.32 3.55
3724 3798 6.509199 CGCAGCATTAGAAGTGAGAAATACTG 60.509 42.308 0.00 0.00 0.00 2.74
3725 3799 5.521735 CGCAGCATTAGAAGTGAGAAATACT 59.478 40.000 0.00 0.00 0.00 2.12
3726 3800 5.520288 TCGCAGCATTAGAAGTGAGAAATAC 59.480 40.000 0.00 0.00 0.00 1.89
3727 3801 5.520288 GTCGCAGCATTAGAAGTGAGAAATA 59.480 40.000 0.00 0.00 0.00 1.40
3728 3802 4.331168 GTCGCAGCATTAGAAGTGAGAAAT 59.669 41.667 0.00 0.00 0.00 2.17
3729 3803 3.679980 GTCGCAGCATTAGAAGTGAGAAA 59.320 43.478 0.00 0.00 0.00 2.52
3730 3804 3.254060 GTCGCAGCATTAGAAGTGAGAA 58.746 45.455 0.00 0.00 0.00 2.87
3731 3805 2.231235 TGTCGCAGCATTAGAAGTGAGA 59.769 45.455 0.00 0.00 0.00 3.27
3732 3806 2.346847 GTGTCGCAGCATTAGAAGTGAG 59.653 50.000 0.00 0.00 0.00 3.51
3733 3807 2.337583 GTGTCGCAGCATTAGAAGTGA 58.662 47.619 0.00 0.00 0.00 3.41
3739 3813 3.457234 TGATAAGGTGTCGCAGCATTAG 58.543 45.455 10.74 0.00 33.95 1.73
3754 3860 7.307396 CGTTATATGTCCAACCTTGCTGATAAG 60.307 40.741 0.00 0.00 0.00 1.73
3779 3885 5.389642 TCTTACTGATTCTAAATTGCGCG 57.610 39.130 0.00 0.00 0.00 6.86
3866 3973 1.153147 GTTTCCTCCCCATCTCCGC 60.153 63.158 0.00 0.00 0.00 5.54
3870 3977 1.840635 GTAGCAGTTTCCTCCCCATCT 59.159 52.381 0.00 0.00 0.00 2.90
3886 3993 0.035739 TGGGGTTTCTGTTCGGTAGC 59.964 55.000 0.00 0.00 0.00 3.58
3892 3999 0.895559 CCTGCCTGGGGTTTCTGTTC 60.896 60.000 0.00 0.00 0.00 3.18
4184 4322 0.817634 CAAAGTTGACTGGACCGCCA 60.818 55.000 0.00 0.00 43.47 5.69
4227 4365 2.622436 GCTTTGACTTGAGCGTAGGAT 58.378 47.619 0.00 0.00 0.00 3.24
4247 4385 1.630148 CTTCTTTGACTCCGGCTACG 58.370 55.000 0.00 0.00 40.55 3.51
4259 4397 5.358922 TCCAAGCATTTTTCACCTTCTTTG 58.641 37.500 0.00 0.00 0.00 2.77
4270 4408 6.313658 GCCGATTATTTTCTCCAAGCATTTTT 59.686 34.615 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.