Multiple sequence alignment - TraesCS4A01G065600

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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 TraesCS4A01G065600 chr4A 100.000 2747 0 0 1362 4108 63008352 63011098 0.000000e+00 5073
1 TraesCS4A01G065600 chr4A 100.000 1029 0 0 1 1029 63006991 63008019 0.000000e+00 1901
2 TraesCS4A01G065600 chr4A 82.915 638 71 19 1 631 300457827 300457221 1.300000e-149 540
3 TraesCS4A01G065600 chr4B 93.576 2771 122 24 1362 4108 503558478 503561216 0.000000e+00 4080
4 TraesCS4A01G065600 chr4B 90.437 366 27 4 668 1029 503558009 503558370 3.720000e-130 475
5 TraesCS4A01G065600 chr4D 95.213 2235 82 11 1362 3585 405305314 405307534 0.000000e+00 3511
6 TraesCS4A01G065600 chr4D 91.189 454 17 11 3669 4108 405321320 405321764 2.730000e-166 595
7 TraesCS4A01G065600 chr4D 94.017 234 8 2 795 1025 405304972 405305202 2.350000e-92 350
8 TraesCS4A01G065600 chr4D 86.022 93 13 0 3999 4091 32219518 32219610 2.610000e-17 100
9 TraesCS4A01G065600 chr6A 95.246 631 30 0 1 631 597960460 597961090 0.000000e+00 1000
10 TraesCS4A01G065600 chr6A 94.929 631 32 0 1 631 597966755 597967385 0.000000e+00 989
11 TraesCS4A01G065600 chrUn 94.770 631 33 0 1 631 336676891 336676261 0.000000e+00 983
12 TraesCS4A01G065600 chr2A 92.730 564 38 3 70 633 19405305 19404745 0.000000e+00 811
13 TraesCS4A01G065600 chr2A 75.795 975 183 29 2140 3098 147462205 147461268 1.050000e-120 444
14 TraesCS4A01G065600 chr2A 87.611 113 14 0 3996 4108 146786075 146786187 9.270000e-27 132
15 TraesCS4A01G065600 chr2A 94.595 74 3 1 1 74 19407128 19407056 3.360000e-21 113
16 TraesCS4A01G065600 chr5A 89.580 643 60 5 1 642 503063234 503062598 0.000000e+00 809
17 TraesCS4A01G065600 chr3A 88.545 646 64 8 1 643 676846519 676845881 0.000000e+00 774
18 TraesCS4A01G065600 chr7A 88.784 633 64 6 1 632 35542283 35542909 0.000000e+00 769
19 TraesCS4A01G065600 chr6B 82.972 646 81 19 1 630 10038671 10038039 1.290000e-154 556
20 TraesCS4A01G065600 chr2D 87.611 113 14 0 3996 4108 154184124 154184012 9.270000e-27 132
21 TraesCS4A01G065600 chr2B 87.611 113 14 0 3996 4108 211626994 211626882 9.270000e-27 132
22 TraesCS4A01G065600 chr1D 86.022 93 13 0 3999 4091 438368548 438368640 2.610000e-17 100
23 TraesCS4A01G065600 chr1B 86.022 93 13 0 3999 4091 594138226 594138318 2.610000e-17 100
24 TraesCS4A01G065600 chr1A 86.022 93 13 0 3999 4091 535062223 535062315 2.610000e-17 100


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 TraesCS4A01G065600 chr4A 63006991 63011098 4107 False 3487.0 5073 100.0000 1 4108 2 chr4A.!!$F1 4107
1 TraesCS4A01G065600 chr4A 300457221 300457827 606 True 540.0 540 82.9150 1 631 1 chr4A.!!$R1 630
2 TraesCS4A01G065600 chr4B 503558009 503561216 3207 False 2277.5 4080 92.0065 668 4108 2 chr4B.!!$F1 3440
3 TraesCS4A01G065600 chr4D 405304972 405307534 2562 False 1930.5 3511 94.6150 795 3585 2 chr4D.!!$F3 2790
4 TraesCS4A01G065600 chr6A 597960460 597961090 630 False 1000.0 1000 95.2460 1 631 1 chr6A.!!$F1 630
5 TraesCS4A01G065600 chr6A 597966755 597967385 630 False 989.0 989 94.9290 1 631 1 chr6A.!!$F2 630
6 TraesCS4A01G065600 chrUn 336676261 336676891 630 True 983.0 983 94.7700 1 631 1 chrUn.!!$R1 630
7 TraesCS4A01G065600 chr2A 19404745 19407128 2383 True 462.0 811 93.6625 1 633 2 chr2A.!!$R2 632
8 TraesCS4A01G065600 chr2A 147461268 147462205 937 True 444.0 444 75.7950 2140 3098 1 chr2A.!!$R1 958
9 TraesCS4A01G065600 chr5A 503062598 503063234 636 True 809.0 809 89.5800 1 642 1 chr5A.!!$R1 641
10 TraesCS4A01G065600 chr3A 676845881 676846519 638 True 774.0 774 88.5450 1 643 1 chr3A.!!$R1 642
11 TraesCS4A01G065600 chr7A 35542283 35542909 626 False 769.0 769 88.7840 1 632 1 chr7A.!!$F1 631
12 TraesCS4A01G065600 chr6B 10038039 10038671 632 True 556.0 556 82.9720 1 630 1 chr6B.!!$R1 629

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
55 57 0.110295 TACACAGTGGGCATTGCTGT 59.890 50.0 8.82 6.41 43.37 4.40 F
776 2554 0.455633 GAAGAAACGCTCGCCGACTA 60.456 55.0 2.37 0.00 41.02 2.59 F
814 2592 0.604578 TCACGGGTTTTCTACCTCCG 59.395 55.0 0.00 0.00 46.86 4.63 F
1469 3251 0.870307 CACGCCATCGCCTACTACAC 60.870 60.0 0.00 0.00 39.84 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1455 3237 1.299926 GCGGGTGTAGTAGGCGATG 60.300 63.158 0.00 0.0 0.0 3.84 R
2098 3880 0.828022 ATTGAAGATACCGCGGTGGA 59.172 50.000 40.02 23.0 42.0 4.02 R
2347 4138 2.640989 CCGTGTTCACCTCGTCGA 59.359 61.111 0.00 0.0 0.0 4.20 R
3371 5167 0.164647 GCACTGACGCACATCACTTC 59.835 55.000 0.00 0.0 0.0 3.01 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
55 57 0.110295 TACACAGTGGGCATTGCTGT 59.890 50.000 8.82 6.41 43.37 4.40
158 1915 1.417517 TCTGCTTGTGCTCTCCTTTGA 59.582 47.619 0.00 0.00 40.48 2.69
163 1920 4.222810 TGCTTGTGCTCTCCTTTGATACTA 59.777 41.667 0.00 0.00 40.48 1.82
191 1948 4.051237 GGTTGATGAAACAGCAAAAGGAC 58.949 43.478 4.09 0.00 41.39 3.85
192 1949 4.441356 GGTTGATGAAACAGCAAAAGGACA 60.441 41.667 4.09 0.00 41.39 4.02
262 2019 2.806818 GACTGATGCAGATATGTGCTGG 59.193 50.000 23.68 13.58 44.32 4.85
368 2135 5.661312 TGCTCTAAGAGGGAAGCTGTTTATA 59.339 40.000 0.00 0.00 0.00 0.98
396 2163 2.058705 TGTGTGGGTTGGGTGATTAGA 58.941 47.619 0.00 0.00 0.00 2.10
417 2195 6.886178 AGACCCTTTTATCCTTGCTTACTA 57.114 37.500 0.00 0.00 0.00 1.82
445 2223 6.597562 ACAGTCTGGTAGTTTTGGTTTGATA 58.402 36.000 4.53 0.00 0.00 2.15
463 2241 7.094377 GGTTTGATACTGTGATGTAATGGTGTT 60.094 37.037 0.00 0.00 0.00 3.32
476 2254 2.483197 GGTGTTGCCGGGTTTTCGT 61.483 57.895 2.18 0.00 0.00 3.85
577 2355 5.045651 TGCCTCTTTCTCTGGACATTTGATA 60.046 40.000 0.00 0.00 0.00 2.15
666 2444 5.472320 AAAAACGAAAATGAAAAACCGGG 57.528 34.783 6.32 0.00 0.00 5.73
674 2452 2.074729 TGAAAAACCGGGACCACATT 57.925 45.000 6.32 0.00 0.00 2.71
685 2463 1.620822 GACCACATTGGCTGGTTTCT 58.379 50.000 0.90 0.00 42.42 2.52
689 2467 1.815003 CACATTGGCTGGTTTCTCTCC 59.185 52.381 0.00 0.00 0.00 3.71
692 2470 1.434188 TTGGCTGGTTTCTCTCCTGA 58.566 50.000 0.00 0.00 0.00 3.86
693 2471 1.434188 TGGCTGGTTTCTCTCCTGAA 58.566 50.000 0.00 0.00 0.00 3.02
703 2481 3.191539 CTCCTGAAAGCTCCGCGC 61.192 66.667 0.00 0.00 39.57 6.86
720 2498 3.425136 CGCGACAAATGTTGTGCG 58.575 55.556 0.00 17.06 45.52 5.34
745 2523 1.094785 CGCTCCCGAACCATTCATTT 58.905 50.000 0.00 0.00 36.29 2.32
748 2526 3.013921 GCTCCCGAACCATTCATTTGTA 58.986 45.455 0.00 0.00 0.00 2.41
757 2535 5.371115 ACCATTCATTTGTAAACACTCCG 57.629 39.130 0.00 0.00 0.00 4.63
763 2541 6.928979 TCATTTGTAAACACTCCGAAGAAA 57.071 33.333 0.00 0.00 0.00 2.52
764 2542 6.721321 TCATTTGTAAACACTCCGAAGAAAC 58.279 36.000 0.00 0.00 0.00 2.78
776 2554 0.455633 GAAGAAACGCTCGCCGACTA 60.456 55.000 2.37 0.00 41.02 2.59
778 2556 2.506345 GAAACGCTCGCCGACTAGC 61.506 63.158 2.37 0.00 41.02 3.42
784 2562 2.750237 TCGCCGACTAGCTGCTCA 60.750 61.111 4.91 0.00 0.00 4.26
787 2565 2.103143 CCGACTAGCTGCTCACCG 59.897 66.667 4.91 7.94 0.00 4.94
799 2577 1.210413 CTCACCGTCTCACCTCACG 59.790 63.158 0.00 0.00 35.72 4.35
814 2592 0.604578 TCACGGGTTTTCTACCTCCG 59.395 55.000 0.00 0.00 46.86 4.63
832 2610 1.453015 GTGTATTGCGGATGGGGCA 60.453 57.895 0.00 0.00 38.93 5.36
1469 3251 0.870307 CACGCCATCGCCTACTACAC 60.870 60.000 0.00 0.00 39.84 2.90
1770 3552 1.879480 CGGCATCGAGATCTCCGAT 59.121 57.895 17.13 17.89 46.32 4.18
1791 3573 4.410400 CCCCTCTTCACCCACCGC 62.410 72.222 0.00 0.00 0.00 5.68
2058 3840 2.502492 CCCCGAGATCGACATGCCT 61.502 63.158 3.31 0.00 43.02 4.75
2090 3872 4.437587 TCCGACCTCGTCCTCCCC 62.438 72.222 0.00 0.00 37.74 4.81
2098 3880 2.046314 CGTCCTCCCCGCATTTGT 60.046 61.111 0.00 0.00 0.00 2.83
2366 4157 2.737376 GACGAGGTGAACACGGCC 60.737 66.667 0.00 0.00 0.00 6.13
2429 4220 2.356553 GGCACGCACGACAACCTA 60.357 61.111 0.00 0.00 0.00 3.08
2432 4223 1.615107 GCACGCACGACAACCTACTC 61.615 60.000 0.00 0.00 0.00 2.59
3115 4906 1.943116 CTCTCGCAGTAGCCAGCAGT 61.943 60.000 0.00 0.00 37.52 4.40
3118 4909 1.874019 CGCAGTAGCCAGCAGTACG 60.874 63.158 0.00 0.00 37.52 3.67
3142 4933 3.893961 GAAGCCTGGCCCCTGCTTT 62.894 63.158 20.39 0.10 44.83 3.51
3268 5064 2.609459 GTGGATCGACATGGTGATGAAC 59.391 50.000 2.59 2.27 33.36 3.18
3270 5066 3.118298 TGGATCGACATGGTGATGAACAT 60.118 43.478 6.67 0.00 33.36 2.71
3306 5102 7.389053 ACCAAACAAGAAACTGCAAAATAAACA 59.611 29.630 0.00 0.00 0.00 2.83
3334 5130 0.532573 TTGCTAGCTTCCACCTCTCG 59.467 55.000 17.23 0.00 0.00 4.04
3351 5147 0.591659 TCGACAGTCTCGTGGTTCTG 59.408 55.000 0.00 0.00 43.45 3.02
3368 5164 2.742348 TCTGGCGGTAGGATCAAAGTA 58.258 47.619 0.00 0.00 0.00 2.24
3369 5165 3.305720 TCTGGCGGTAGGATCAAAGTAT 58.694 45.455 0.00 0.00 0.00 2.12
3370 5166 3.321111 TCTGGCGGTAGGATCAAAGTATC 59.679 47.826 0.00 0.00 0.00 2.24
3371 5167 2.035449 TGGCGGTAGGATCAAAGTATCG 59.965 50.000 0.00 0.00 0.00 2.92
3372 5168 2.295349 GGCGGTAGGATCAAAGTATCGA 59.705 50.000 0.00 0.00 0.00 3.59
3373 5169 3.243636 GGCGGTAGGATCAAAGTATCGAA 60.244 47.826 0.00 0.00 0.00 3.71
3374 5170 3.982058 GCGGTAGGATCAAAGTATCGAAG 59.018 47.826 0.00 0.00 0.00 3.79
3375 5171 4.499357 GCGGTAGGATCAAAGTATCGAAGT 60.499 45.833 0.00 0.00 0.00 3.01
3441 5242 8.341173 CAATTCATTGCATCTAGGAGTACTTTC 58.659 37.037 0.00 0.00 0.00 2.62
3456 5257 8.478877 AGGAGTACTTTCCAATAACATGAGTAG 58.521 37.037 0.00 0.00 39.84 2.57
3457 5258 8.475639 GGAGTACTTTCCAATAACATGAGTAGA 58.524 37.037 0.00 0.00 37.20 2.59
3500 5301 0.108424 CTAGTGCACAGCAGAGTCCC 60.108 60.000 21.04 0.00 40.08 4.46
3578 5380 0.465097 CAAGATAGCCAGCACCCCTG 60.465 60.000 0.00 0.00 41.41 4.45
3592 5394 1.026718 CCCCTGCCGTTGAACTCATC 61.027 60.000 0.00 0.00 0.00 2.92
3593 5395 0.321564 CCCTGCCGTTGAACTCATCA 60.322 55.000 0.00 0.00 35.85 3.07
3647 5449 2.150837 GTCTTACGACGGCAGCGAC 61.151 63.158 0.00 0.00 0.00 5.19
3750 5560 2.027561 CCCAGTGATTTTGTCCCTACGA 60.028 50.000 0.00 0.00 0.00 3.43
3752 5562 3.000727 CAGTGATTTTGTCCCTACGACC 58.999 50.000 0.00 0.00 41.18 4.79
3762 5572 1.004200 CCTACGACCGGTGGCTTTT 60.004 57.895 14.63 0.00 0.00 2.27
3764 5574 1.004679 TACGACCGGTGGCTTTTCC 60.005 57.895 14.63 0.00 0.00 3.13
3765 5575 2.768503 TACGACCGGTGGCTTTTCCG 62.769 60.000 14.63 9.53 45.42 4.30
3790 5607 0.461163 CGTGCGGTGTAATCCATCCA 60.461 55.000 0.00 0.00 0.00 3.41
3791 5608 1.810031 CGTGCGGTGTAATCCATCCAT 60.810 52.381 0.00 0.00 0.00 3.41
3792 5609 1.873591 GTGCGGTGTAATCCATCCATC 59.126 52.381 0.00 0.00 0.00 3.51
3793 5610 1.202758 TGCGGTGTAATCCATCCATCC 60.203 52.381 0.00 0.00 0.00 3.51
3794 5611 1.202758 GCGGTGTAATCCATCCATCCA 60.203 52.381 0.00 0.00 0.00 3.41
3812 5629 1.299468 ATCGCTTTCCGCTAGCTCG 60.299 57.895 13.93 2.52 36.49 5.03
3848 5665 2.105930 CGTGCAGCCTAGCTCCTC 59.894 66.667 0.00 0.00 36.40 3.71
3869 5686 3.328050 TCCTTCTCTCCTCCAACCTTTTC 59.672 47.826 0.00 0.00 0.00 2.29
3928 5745 2.635229 CTTCCTCGCGCAGGTGCTAT 62.635 60.000 20.54 0.00 43.95 2.97
3929 5746 2.202932 CCTCGCGCAGGTGCTATT 60.203 61.111 8.75 0.00 37.53 1.73
3930 5747 1.067416 CCTCGCGCAGGTGCTATTA 59.933 57.895 8.75 0.00 37.53 0.98
3931 5748 0.319900 CCTCGCGCAGGTGCTATTAT 60.320 55.000 8.75 0.00 37.53 1.28
3962 5779 3.580100 GAGGCGACAGAGCTGCACA 62.580 63.158 1.02 0.00 37.29 4.57
3979 5796 0.320596 ACAAGAGCAGAGCAGAGCAC 60.321 55.000 0.00 0.00 0.00 4.40
3980 5797 1.079956 AAGAGCAGAGCAGAGCACG 60.080 57.895 0.00 0.00 0.00 5.34
3983 5800 3.488978 GCAGAGCAGAGCACGCAG 61.489 66.667 0.00 0.00 0.00 5.18
3986 5803 2.508887 GAGCAGAGCACGCAGAGG 60.509 66.667 0.00 0.00 0.00 3.69
3987 5804 4.079850 AGCAGAGCACGCAGAGGG 62.080 66.667 0.00 0.00 0.00 4.30
3988 5805 4.074526 GCAGAGCACGCAGAGGGA 62.075 66.667 0.00 0.00 0.00 4.20
3989 5806 2.183811 CAGAGCACGCAGAGGGAG 59.816 66.667 0.00 0.00 0.00 4.30
3990 5807 2.036414 AGAGCACGCAGAGGGAGA 59.964 61.111 0.00 0.00 0.00 3.71
3991 5808 2.051518 AGAGCACGCAGAGGGAGAG 61.052 63.158 0.00 0.00 0.00 3.20
3994 5811 3.074999 GCACGCAGAGGGAGAGAGG 62.075 68.421 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 57 2.948979 GTCCAAATCGCCCAACATATGA 59.051 45.455 10.38 0.00 0.00 2.15
158 1915 4.227300 TGTTTCATCAACCCTGCCTAGTAT 59.773 41.667 0.00 0.00 33.97 2.12
163 1920 1.915141 CTGTTTCATCAACCCTGCCT 58.085 50.000 0.00 0.00 33.97 4.75
191 1948 1.274728 CCAGTCCTCAAGTCCTCTGTG 59.725 57.143 0.00 0.00 0.00 3.66
192 1949 1.148027 TCCAGTCCTCAAGTCCTCTGT 59.852 52.381 0.00 0.00 0.00 3.41
262 2019 2.281345 CCTCATCCTGATGCGCCC 60.281 66.667 4.18 0.00 38.65 6.13
368 2135 0.682855 CCAACCCACACACAACCAGT 60.683 55.000 0.00 0.00 0.00 4.00
396 2163 8.582437 GTTTTTAGTAAGCAAGGATAAAAGGGT 58.418 33.333 0.00 0.00 29.79 4.34
417 2195 6.599356 AACCAAAACTACCAGACTGTTTTT 57.401 33.333 0.93 0.00 40.51 1.94
445 2223 2.819608 GGCAACACCATTACATCACAGT 59.180 45.455 0.00 0.00 38.86 3.55
476 2254 3.657398 TCGAGATTACCTACTGTGGGA 57.343 47.619 17.76 0.00 0.00 4.37
577 2355 7.500892 TCCATTACTGCAACATAACGGAAATAT 59.499 33.333 0.00 0.00 0.00 1.28
644 2422 5.063691 GTCCCGGTTTTTCATTTTCGTTTTT 59.936 36.000 0.00 0.00 0.00 1.94
645 2423 4.567558 GTCCCGGTTTTTCATTTTCGTTTT 59.432 37.500 0.00 0.00 0.00 2.43
646 2424 4.114073 GTCCCGGTTTTTCATTTTCGTTT 58.886 39.130 0.00 0.00 0.00 3.60
647 2425 3.491276 GGTCCCGGTTTTTCATTTTCGTT 60.491 43.478 0.00 0.00 0.00 3.85
648 2426 2.034939 GGTCCCGGTTTTTCATTTTCGT 59.965 45.455 0.00 0.00 0.00 3.85
649 2427 2.034812 TGGTCCCGGTTTTTCATTTTCG 59.965 45.455 0.00 0.00 0.00 3.46
650 2428 3.181474 TGTGGTCCCGGTTTTTCATTTTC 60.181 43.478 0.00 0.00 0.00 2.29
651 2429 2.766828 TGTGGTCCCGGTTTTTCATTTT 59.233 40.909 0.00 0.00 0.00 1.82
652 2430 2.389715 TGTGGTCCCGGTTTTTCATTT 58.610 42.857 0.00 0.00 0.00 2.32
653 2431 2.074729 TGTGGTCCCGGTTTTTCATT 57.925 45.000 0.00 0.00 0.00 2.57
654 2432 2.298729 CAATGTGGTCCCGGTTTTTCAT 59.701 45.455 0.00 0.00 0.00 2.57
655 2433 1.683917 CAATGTGGTCCCGGTTTTTCA 59.316 47.619 0.00 0.00 0.00 2.69
656 2434 1.000394 CCAATGTGGTCCCGGTTTTTC 60.000 52.381 0.00 0.00 31.35 2.29
657 2435 1.044611 CCAATGTGGTCCCGGTTTTT 58.955 50.000 0.00 0.00 31.35 1.94
658 2436 1.468506 GCCAATGTGGTCCCGGTTTT 61.469 55.000 0.00 0.00 40.46 2.43
659 2437 1.906333 GCCAATGTGGTCCCGGTTT 60.906 57.895 0.00 0.00 40.46 3.27
660 2438 2.282887 GCCAATGTGGTCCCGGTT 60.283 61.111 0.00 0.00 40.46 4.44
661 2439 3.256960 AGCCAATGTGGTCCCGGT 61.257 61.111 0.00 0.00 40.46 5.28
662 2440 2.751436 CAGCCAATGTGGTCCCGG 60.751 66.667 0.00 0.00 40.46 5.73
663 2441 2.751436 CCAGCCAATGTGGTCCCG 60.751 66.667 0.00 0.00 40.46 5.14
664 2442 2.440599 ACCAGCCAATGTGGTCCC 59.559 61.111 0.00 0.00 45.74 4.46
674 2452 1.434188 TTCAGGAGAGAAACCAGCCA 58.566 50.000 0.00 0.00 0.00 4.75
703 2481 3.425136 CGCACAACATTTGTCGCG 58.575 55.556 15.92 15.92 46.16 5.87
704 2482 2.696521 CGCGCACAACATTTGTCGC 61.697 57.895 8.75 17.94 46.51 5.19
708 2486 2.082366 GCTCCGCGCACAACATTTG 61.082 57.895 8.75 0.00 38.92 2.32
726 2504 1.094785 AAATGAATGGTTCGGGAGCG 58.905 50.000 0.00 0.00 0.00 5.03
733 2511 5.856455 CGGAGTGTTTACAAATGAATGGTTC 59.144 40.000 0.00 0.00 0.00 3.62
738 2516 7.504924 TTCTTCGGAGTGTTTACAAATGAAT 57.495 32.000 0.00 0.00 0.00 2.57
745 2523 2.540931 GCGTTTCTTCGGAGTGTTTACA 59.459 45.455 0.00 0.00 0.00 2.41
748 2526 1.865340 GAGCGTTTCTTCGGAGTGTTT 59.135 47.619 0.00 0.00 0.00 2.83
757 2535 0.455633 TAGTCGGCGAGCGTTTCTTC 60.456 55.000 11.20 0.00 0.00 2.87
763 2541 4.180946 CAGCTAGTCGGCGAGCGT 62.181 66.667 16.50 0.00 45.99 5.07
776 2554 2.653702 GTGAGACGGTGAGCAGCT 59.346 61.111 0.00 0.00 0.00 4.24
778 2556 1.214062 GAGGTGAGACGGTGAGCAG 59.786 63.158 0.00 0.00 0.00 4.24
814 2592 0.823356 ATGCCCCATCCGCAATACAC 60.823 55.000 0.00 0.00 40.22 2.90
1455 3237 1.299926 GCGGGTGTAGTAGGCGATG 60.300 63.158 0.00 0.00 0.00 3.84
1770 3552 4.649705 TGGGTGAAGAGGGGGCGA 62.650 66.667 0.00 0.00 0.00 5.54
1791 3573 1.519455 GGTGTCGAGAAGGATGCCG 60.519 63.158 0.00 0.00 0.00 5.69
2078 3860 3.031417 AAATGCGGGGAGGACGAGG 62.031 63.158 0.00 0.00 0.00 4.63
2098 3880 0.828022 ATTGAAGATACCGCGGTGGA 59.172 50.000 40.02 23.00 42.00 4.02
2347 4138 2.640989 CCGTGTTCACCTCGTCGA 59.359 61.111 0.00 0.00 0.00 4.20
2366 4157 3.775654 GGGTCGTCCTCCCAGCAG 61.776 72.222 0.00 0.00 44.05 4.24
2558 4349 3.705638 CACGTCTGCAGCACGGTG 61.706 66.667 29.20 22.79 41.73 4.94
2777 4568 2.856032 CGCTGCCACGTCTTGAAG 59.144 61.111 0.00 0.00 0.00 3.02
2981 4772 4.728102 TCCGTGGCGTTGGCGTAG 62.728 66.667 0.00 0.00 41.24 3.51
3161 4952 1.379044 CTTCCCACCATGCCACTCC 60.379 63.158 0.00 0.00 0.00 3.85
3165 4956 0.324552 CATTCCTTCCCACCATGCCA 60.325 55.000 0.00 0.00 0.00 4.92
3169 4960 2.109834 TGTGAACATTCCTTCCCACCAT 59.890 45.455 0.00 0.00 0.00 3.55
3211 5007 2.412847 GCTTCCACGTTCCAAATTCTCG 60.413 50.000 0.00 0.00 0.00 4.04
3241 5037 1.613925 ACCATGTCGATCCACGGATAG 59.386 52.381 0.00 0.00 42.82 2.08
3270 5066 1.071542 TCTTGTTTGGTCATCCGCTGA 59.928 47.619 0.00 0.00 36.30 4.26
3306 5102 4.501400 GGTGGAAGCTAGCAACACAAAATT 60.501 41.667 26.69 8.77 33.91 1.82
3334 5130 0.667792 GCCAGAACCACGAGACTGTC 60.668 60.000 0.00 0.00 0.00 3.51
3351 5147 2.295349 TCGATACTTTGATCCTACCGCC 59.705 50.000 0.00 0.00 0.00 6.13
3368 5164 1.067565 ACTGACGCACATCACTTCGAT 60.068 47.619 0.00 0.00 33.27 3.59
3369 5165 0.313987 ACTGACGCACATCACTTCGA 59.686 50.000 0.00 0.00 0.00 3.71
3370 5166 0.436150 CACTGACGCACATCACTTCG 59.564 55.000 0.00 0.00 0.00 3.79
3371 5167 0.164647 GCACTGACGCACATCACTTC 59.835 55.000 0.00 0.00 0.00 3.01
3372 5168 1.560004 CGCACTGACGCACATCACTT 61.560 55.000 0.00 0.00 0.00 3.16
3373 5169 2.023771 CGCACTGACGCACATCACT 61.024 57.895 0.00 0.00 0.00 3.41
3374 5170 2.310233 ACGCACTGACGCACATCAC 61.310 57.895 0.00 0.00 36.19 3.06
3375 5171 2.028925 ACGCACTGACGCACATCA 59.971 55.556 0.00 0.00 36.19 3.07
3481 5282 0.108424 GGGACTCTGCTGTGCACTAG 60.108 60.000 19.41 14.36 33.79 2.57
3500 5301 2.393768 GGCACCACTGCTCACGATG 61.394 63.158 0.00 0.00 43.66 3.84
3578 5380 1.795768 TCACTGATGAGTTCAACGGC 58.204 50.000 0.00 0.00 32.78 5.68
3581 5383 2.096218 GCCGTTCACTGATGAGTTCAAC 60.096 50.000 0.00 0.00 35.83 3.18
3592 5394 3.777925 CGAAGGCGCCGTTCACTG 61.778 66.667 27.09 14.41 0.00 3.66
3593 5395 3.986006 TCGAAGGCGCCGTTCACT 61.986 61.111 27.09 8.38 37.46 3.41
3613 5415 0.246635 AGACCGCAACAAGACGCTAT 59.753 50.000 0.00 0.00 0.00 2.97
3647 5449 4.812476 TGGCGAAGGGACGATGCG 62.812 66.667 0.00 0.00 35.09 4.73
3673 5476 1.734117 GTGCCAAACCGAATGCTGC 60.734 57.895 0.00 0.00 0.00 5.25
3674 5477 1.080569 GGTGCCAAACCGAATGCTG 60.081 57.895 0.00 0.00 39.81 4.41
3694 5504 1.448540 CATGTCTCGCTCCCACCAC 60.449 63.158 0.00 0.00 0.00 4.16
3703 5513 1.153549 GACCTGGACCATGTCTCGC 60.154 63.158 19.47 0.00 32.47 5.03
3765 5575 2.274834 GATTACACCGCACGCACGTC 62.275 60.000 0.00 0.00 0.00 4.34
3766 5576 2.356553 ATTACACCGCACGCACGT 60.357 55.556 0.00 0.00 0.00 4.49
3841 5658 0.261696 GGAGGAGAGAAGGAGGAGCT 59.738 60.000 0.00 0.00 0.00 4.09
3844 5661 1.273324 GGTTGGAGGAGAGAAGGAGGA 60.273 57.143 0.00 0.00 0.00 3.71
3848 5665 3.560239 GGAAAAGGTTGGAGGAGAGAAGG 60.560 52.174 0.00 0.00 0.00 3.46
3928 5745 2.738643 CGCCTCGGAAGCTCAGAAATAA 60.739 50.000 0.00 0.00 0.00 1.40
3929 5746 1.202417 CGCCTCGGAAGCTCAGAAATA 60.202 52.381 0.00 0.00 0.00 1.40
3930 5747 0.460987 CGCCTCGGAAGCTCAGAAAT 60.461 55.000 0.00 0.00 0.00 2.17
3931 5748 1.079819 CGCCTCGGAAGCTCAGAAA 60.080 57.895 0.00 0.00 0.00 2.52
3962 5779 1.079956 CGTGCTCTGCTCTGCTCTT 60.080 57.895 0.00 0.00 0.00 2.85
3979 5796 1.827789 CTCCCTCTCTCCCTCTGCG 60.828 68.421 0.00 0.00 0.00 5.18
3980 5797 0.188342 ATCTCCCTCTCTCCCTCTGC 59.812 60.000 0.00 0.00 0.00 4.26
3983 5800 1.203050 CCTCATCTCCCTCTCTCCCTC 60.203 61.905 0.00 0.00 0.00 4.30
3986 5803 0.856982 TCCCTCATCTCCCTCTCTCC 59.143 60.000 0.00 0.00 0.00 3.71
3987 5804 1.780309 TCTCCCTCATCTCCCTCTCTC 59.220 57.143 0.00 0.00 0.00 3.20
3988 5805 1.919933 TCTCCCTCATCTCCCTCTCT 58.080 55.000 0.00 0.00 0.00 3.10
3989 5806 2.109834 TGATCTCCCTCATCTCCCTCTC 59.890 54.545 0.00 0.00 0.00 3.20
3990 5807 2.151266 TGATCTCCCTCATCTCCCTCT 58.849 52.381 0.00 0.00 0.00 3.69
3991 5808 2.692709 TGATCTCCCTCATCTCCCTC 57.307 55.000 0.00 0.00 0.00 4.30
3994 5811 3.837146 TGCTTATGATCTCCCTCATCTCC 59.163 47.826 0.00 0.00 37.13 3.71


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

AutoCloner maintained by Alex Coulton.