Multiple sequence alignment - TraesCS5A01G186400

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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 TraesCS5A01G186400 chr5A 100.000 5318 0 0 1 5318 387409724 387404407 0.000000e+00 9821.0
1 TraesCS5A01G186400 chr5D 93.053 2850 124 29 186 2995 294428933 294426118 0.000000e+00 4098.0
2 TraesCS5A01G186400 chr5D 95.155 1486 59 11 3001 4479 294425950 294424471 0.000000e+00 2333.0
3 TraesCS5A01G186400 chr5D 92.788 832 36 11 4478 5300 294424433 294423617 0.000000e+00 1182.0
4 TraesCS5A01G186400 chr5D 93.711 159 9 1 1 158 294430871 294430713 2.480000e-58 237.0
5 TraesCS5A01G186400 chr5B 91.808 2527 111 37 2821 5318 335949801 335947342 0.000000e+00 3432.0
6 TraesCS5A01G186400 chr5B 92.760 1837 62 17 991 2784 335951610 335949802 0.000000e+00 2590.0
7 TraesCS5A01G186400 chr4D 81.379 145 26 1 470 614 400792140 400791997 3.370000e-22 117.0
8 TraesCS5A01G186400 chr7B 73.220 295 58 14 292 570 412814723 412815012 2.640000e-13 87.9
9 TraesCS5A01G186400 chr2A 80.851 94 15 3 729 822 579703860 579703950 2.660000e-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 TraesCS5A01G186400 chr5A 387404407 387409724 5317 True 9821.0 9821 100.00000 1 5318 1 chr5A.!!$R1 5317
1 TraesCS5A01G186400 chr5D 294423617 294430871 7254 True 1962.5 4098 93.67675 1 5300 4 chr5D.!!$R1 5299
2 TraesCS5A01G186400 chr5B 335947342 335951610 4268 True 3011.0 3432 92.28400 991 5318 2 chr5B.!!$R1 4327

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
895 2650 0.031585 CGTCCAAACAGGTCGTCTCA 59.968 55.000 0.0 0.0 42.79 3.27 F
923 2678 0.249741 CGGGTGTTTTGAGAGTCCGT 60.250 55.000 0.0 0.0 0.00 4.69 F
1619 3419 0.615827 AGGGCTTGGCAGGGATTTTC 60.616 55.000 0.0 0.0 0.00 2.29 F
1715 3545 0.808755 GTGAAACTTATGCCCACCGG 59.191 55.000 0.0 0.0 0.00 5.28 F
1843 3674 1.066286 AGTGCTCTGCTGAACTGGATC 60.066 52.381 0.0 0.0 0.00 3.36 F
2301 4133 1.203162 TCATTGCATTCTTGGGGGTGT 60.203 47.619 0.0 0.0 0.00 4.16 F
2438 4270 1.848388 TCCTGATGCAAGGGACATGAT 59.152 47.619 0.0 0.0 37.96 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1772 3602 0.106719 TTCCCCAAGAATCCCATCGC 60.107 55.000 0.0 0.0 0.0 4.58 R
1856 3687 0.753867 TTTACACTCCTGTCGCCACA 59.246 50.000 0.0 0.0 0.0 4.17 R
3615 5615 1.212616 GCGTACATGAGCAGCTAAGG 58.787 55.000 0.0 0.0 0.0 2.69 R
3816 5816 1.202651 ACGACAGTTGAAAGAGTGGGG 60.203 52.381 0.0 0.0 0.0 4.96 R
3888 5889 5.452777 GTTGGCTCACTCAAAACATACTTC 58.547 41.667 0.0 0.0 0.0 3.01 R
3978 5979 4.537015 GCGTTGTTTTTAGCATCTGAAGT 58.463 39.130 0.0 0.0 0.0 3.01 R
4503 6544 3.310774 CGCTTACATCCTTCCAGAACATG 59.689 47.826 0.0 0.0 0.0 3.21 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
24 26 5.009010 CCATCTACTATTGCACCCAATGAAC 59.991 44.000 0.00 0.00 41.58 3.18
25 27 4.188462 TCTACTATTGCACCCAATGAACG 58.812 43.478 0.00 0.00 41.58 3.95
49 51 6.693545 CGAGGTTTGATTCTCTACATGTCTAC 59.306 42.308 0.00 0.00 0.00 2.59
61 63 8.478066 TCTCTACATGTCTACGTAGGTAGTTTA 58.522 37.037 24.05 14.45 45.22 2.01
115 117 4.795268 CGAGAGCTATATCGGCTAAACAA 58.205 43.478 7.41 0.00 40.40 2.83
142 144 2.512476 AGTTTGGTTGTGGTCTTAGGGT 59.488 45.455 0.00 0.00 0.00 4.34
148 150 4.031611 GGTTGTGGTCTTAGGGTATCTCT 58.968 47.826 0.00 0.00 0.00 3.10
159 1891 9.091220 GTCTTAGGGTATCTCTAACACCATTAT 57.909 37.037 0.00 0.00 33.78 1.28
184 1916 0.902984 ACGGACACACTATCTGCCCA 60.903 55.000 0.00 0.00 0.00 5.36
191 1923 0.465705 CACTATCTGCCCACGGACAT 59.534 55.000 0.00 0.00 32.77 3.06
207 1961 0.755698 ACATAGATGCGGGAGTCGGT 60.756 55.000 0.00 0.00 39.69 4.69
228 1982 5.313712 GGTCATCCAACGTATCCCATAAAT 58.686 41.667 0.00 0.00 0.00 1.40
244 1998 2.075355 AAATGTCCGCCCAGGTCCAA 62.075 55.000 0.00 0.00 41.99 3.53
272 2026 6.392353 TTTCATTTCAAACGCATAGCAATG 57.608 33.333 0.00 0.00 36.09 2.82
312 2066 2.285602 GCAATACGACACATGCCTAACG 60.286 50.000 0.00 0.00 32.73 3.18
341 2095 1.027357 GTGGATTACCGACCGAGCTA 58.973 55.000 0.00 0.00 39.42 3.32
377 2131 4.965200 AGTAGGGAGGTTGATATTGCTC 57.035 45.455 0.00 0.00 0.00 4.26
378 2132 3.648545 AGTAGGGAGGTTGATATTGCTCC 59.351 47.826 0.00 0.00 0.00 4.70
413 2167 2.173669 GCATGGACGACGATGGTGG 61.174 63.158 11.26 0.00 33.80 4.61
417 2171 2.104331 GACGACGATGGTGGCGAT 59.896 61.111 0.00 0.00 0.00 4.58
482 2236 0.827368 TTGCCGCCCTTCTTTTTGTT 59.173 45.000 0.00 0.00 0.00 2.83
487 2241 0.599991 GCCCTTCTTTTTGTTGGCCG 60.600 55.000 0.00 0.00 32.74 6.13
504 2258 1.512694 CGCCCCATCTTTTGCCTTC 59.487 57.895 0.00 0.00 0.00 3.46
505 2259 1.250154 CGCCCCATCTTTTGCCTTCA 61.250 55.000 0.00 0.00 0.00 3.02
570 2324 1.479709 CGGACACCTTCTCCAGATCT 58.520 55.000 0.00 0.00 0.00 2.75
596 2350 4.845580 CGCCGGCTCCAGCAGATT 62.846 66.667 26.68 0.00 44.36 2.40
597 2351 2.899339 GCCGGCTCCAGCAGATTC 60.899 66.667 22.15 0.00 44.36 2.52
599 2353 1.222936 CCGGCTCCAGCAGATTCTT 59.777 57.895 0.03 0.00 44.36 2.52
603 2357 2.484417 CGGCTCCAGCAGATTCTTGTAT 60.484 50.000 0.03 0.00 44.36 2.29
643 2397 0.949105 GCGAAAAGTGCGAGAAGGGA 60.949 55.000 0.00 0.00 0.00 4.20
649 2403 1.522580 GTGCGAGAAGGGAGGATGC 60.523 63.158 0.00 0.00 0.00 3.91
748 2503 0.389025 GTTTTTGTGTGGGCTGAGGG 59.611 55.000 0.00 0.00 0.00 4.30
750 2505 0.467290 TTTTGTGTGGGCTGAGGGTC 60.467 55.000 0.00 0.00 0.00 4.46
767 2522 1.163554 GTCTCGGAGTCCTACGTGTT 58.836 55.000 7.77 0.00 38.28 3.32
768 2523 2.350522 GTCTCGGAGTCCTACGTGTTA 58.649 52.381 7.77 0.00 38.28 2.41
777 2532 0.737219 CCTACGTGTTAGAGGTCCGG 59.263 60.000 0.00 0.00 0.00 5.14
784 2539 1.006758 TGTTAGAGGTCCGGACTCCAT 59.993 52.381 32.52 18.59 35.58 3.41
798 2553 2.037687 CCATGCAAAGCCCCCTGA 59.962 61.111 0.00 0.00 0.00 3.86
806 2561 1.066645 CAAAGCCCCCTGATTTGCTTC 60.067 52.381 0.00 0.00 42.85 3.86
814 2569 1.669795 CCTGATTTGCTTCCGGTTTGC 60.670 52.381 0.00 5.18 0.00 3.68
853 2608 3.190535 GGACTCGTTGCCAACAAATACAT 59.809 43.478 8.51 0.00 37.58 2.29
857 2612 2.352617 CGTTGCCAACAAATACATGCCT 60.353 45.455 8.51 0.00 37.58 4.75
863 2618 4.321601 GCCAACAAATACATGCCTGTGTTA 60.322 41.667 4.73 0.00 35.87 2.41
868 2623 5.163622 ACAAATACATGCCTGTGTTAGATGC 60.164 40.000 4.73 0.00 35.87 3.91
877 2632 1.535028 TGTGTTAGATGCCTTGCAACG 59.465 47.619 0.00 0.00 43.62 4.10
881 2636 0.323302 TAGATGCCTTGCAACGTCCA 59.677 50.000 0.00 0.00 43.62 4.02
886 2641 0.594796 GCCTTGCAACGTCCAAACAG 60.595 55.000 0.00 0.00 0.00 3.16
895 2650 0.031585 CGTCCAAACAGGTCGTCTCA 59.968 55.000 0.00 0.00 42.79 3.27
899 2654 4.214061 TCCAAACAGGTCGTCTCAGACG 62.214 54.545 21.74 21.74 46.11 4.18
907 2662 2.430921 GTCTCAGACGTGTGCGGG 60.431 66.667 8.02 1.06 43.45 6.13
908 2663 2.910479 TCTCAGACGTGTGCGGGT 60.910 61.111 8.02 0.00 43.45 5.28
909 2664 2.734723 CTCAGACGTGTGCGGGTG 60.735 66.667 8.02 0.00 43.45 4.61
917 2672 1.433053 CGTGTGCGGGTGTTTTGAGA 61.433 55.000 0.00 0.00 0.00 3.27
918 2673 0.307760 GTGTGCGGGTGTTTTGAGAG 59.692 55.000 0.00 0.00 0.00 3.20
923 2678 0.249741 CGGGTGTTTTGAGAGTCCGT 60.250 55.000 0.00 0.00 0.00 4.69
924 2679 1.000060 CGGGTGTTTTGAGAGTCCGTA 60.000 52.381 0.00 0.00 0.00 4.02
946 2701 5.904362 ATTGGAGATGACCTTAGCAAAAC 57.096 39.130 0.00 0.00 0.00 2.43
995 2750 6.374417 AGCTCTGTTTTTCTAGGGTCATTA 57.626 37.500 0.00 0.00 0.00 1.90
1001 2756 9.120538 TCTGTTTTTCTAGGGTCATTATTATGC 57.879 33.333 0.00 0.00 0.00 3.14
1140 2909 3.494048 CGAAGGCAGGAGAGCTTATGAAT 60.494 47.826 0.00 0.00 34.17 2.57
1438 3238 5.660864 TGGGTTCTTGGAGTTTGAAGATTTT 59.339 36.000 0.00 0.00 0.00 1.82
1464 3264 0.953960 CCTTTAGAGGGCGTGCGTTT 60.954 55.000 0.00 0.00 39.55 3.60
1471 3271 2.804931 GGCGTGCGTTTTGATGGC 60.805 61.111 0.00 0.00 0.00 4.40
1533 3333 3.190878 CCGTGCTTGGCAGGAATC 58.809 61.111 12.77 0.00 45.68 2.52
1561 3361 1.906574 TGGTTCCAAATCGAGCTAGGT 59.093 47.619 0.00 0.00 0.00 3.08
1619 3419 0.615827 AGGGCTTGGCAGGGATTTTC 60.616 55.000 0.00 0.00 0.00 2.29
1621 3421 1.512694 GCTTGGCAGGGATTTTCGG 59.487 57.895 0.00 0.00 0.00 4.30
1699 3529 2.817258 CCGGTAAAAATTGCAGGAGTGA 59.183 45.455 0.00 0.00 32.75 3.41
1700 3530 3.254657 CCGGTAAAAATTGCAGGAGTGAA 59.745 43.478 0.00 0.00 32.75 3.18
1701 3531 4.261825 CCGGTAAAAATTGCAGGAGTGAAA 60.262 41.667 0.00 0.00 32.75 2.69
1702 3532 4.679654 CGGTAAAAATTGCAGGAGTGAAAC 59.320 41.667 0.00 0.00 0.00 2.78
1715 3545 0.808755 GTGAAACTTATGCCCACCGG 59.191 55.000 0.00 0.00 0.00 5.28
1772 3602 4.414852 CTTGGTGAATGATTAGTTTGCGG 58.585 43.478 0.00 0.00 0.00 5.69
1843 3674 1.066286 AGTGCTCTGCTGAACTGGATC 60.066 52.381 0.00 0.00 0.00 3.36
1856 3687 6.032956 TGAACTGGATCGTGTAACTATTGT 57.967 37.500 0.00 0.00 31.75 2.71
1880 3711 3.512329 TGGCGACAGGAGTGTAAATTAGA 59.488 43.478 0.00 0.00 36.88 2.10
1947 3778 6.763610 GGAAGATGTTATAGGACACTTTCTGG 59.236 42.308 0.00 0.00 31.30 3.86
2101 3933 1.406539 GCATGGATGGCGAAATTGTCT 59.593 47.619 0.00 0.00 0.00 3.41
2204 4036 2.609002 TGCTTTGCTACATGACGCATAG 59.391 45.455 18.85 18.85 37.96 2.23
2301 4133 1.203162 TCATTGCATTCTTGGGGGTGT 60.203 47.619 0.00 0.00 0.00 4.16
2381 4213 9.571810 GTTGTTTATTATGACAATTCATGAGCA 57.428 29.630 0.00 0.00 42.79 4.26
2430 4262 2.295885 GTCCTGAATCCTGATGCAAGG 58.704 52.381 0.00 0.00 38.84 3.61
2438 4270 1.848388 TCCTGATGCAAGGGACATGAT 59.152 47.619 0.00 0.00 37.96 2.45
2456 4288 7.148755 GGACATGATATTTTGTGCAAGTTGAAC 60.149 37.037 7.08 7.08 34.68 3.18
2517 4350 8.902540 TGTTCATTACATTTGAGTAGAGTTGT 57.097 30.769 0.00 0.00 0.00 3.32
2671 4504 2.742589 GGACTAGGTTGTGCTAAACTGC 59.257 50.000 0.00 0.00 0.00 4.40
2675 4508 5.238583 ACTAGGTTGTGCTAAACTGCTAAG 58.761 41.667 0.00 0.00 0.00 2.18
2680 4513 5.120363 GGTTGTGCTAAACTGCTAAGAGTAC 59.880 44.000 2.76 0.00 0.00 2.73
2728 4561 5.891551 GGGGCTTGGTATTTGATAAAGAAGA 59.108 40.000 0.00 0.00 0.00 2.87
2765 4598 5.294356 TGGAACGTGATGGTAGTATTATGC 58.706 41.667 0.00 0.00 0.00 3.14
2773 4606 6.425114 GTGATGGTAGTATTATGCAAGTCCTG 59.575 42.308 0.00 0.00 0.00 3.86
2792 4625 3.314357 CCTGGTGCATCATATTGTGTCTG 59.686 47.826 0.00 0.00 0.00 3.51
2911 4744 5.675684 TGCCTGACTACTCATTGACAATA 57.324 39.130 0.00 0.00 0.00 1.90
2980 4813 7.652300 TGTGTGTTTTAGTCATCTCATGTAC 57.348 36.000 0.00 0.00 0.00 2.90
3046 5041 2.101249 CCAATTGTGAGTTGTTGGCACT 59.899 45.455 4.43 0.00 35.21 4.40
3057 5053 6.700960 TGAGTTGTTGGCACTGATTAATTTTG 59.299 34.615 0.00 0.00 0.00 2.44
3097 5093 5.941647 TCCCTATAAGTTAGTTTGTTGGTGC 59.058 40.000 0.00 0.00 0.00 5.01
3174 5171 3.758554 GCAATGAGAACAGGGCTAGAAAA 59.241 43.478 0.00 0.00 0.00 2.29
3176 5173 5.105595 GCAATGAGAACAGGGCTAGAAAAAT 60.106 40.000 0.00 0.00 0.00 1.82
3220 5217 8.227791 TGAACTTTTCATCGAATAGTAAGTTGC 58.772 33.333 15.86 10.50 33.93 4.17
3225 5222 6.647212 TCATCGAATAGTAAGTTGCACAAG 57.353 37.500 0.00 0.00 0.00 3.16
3262 5259 9.601217 TTACATAGAGATGAGTTTTTAAGAGCC 57.399 33.333 0.00 0.00 36.48 4.70
3361 5358 4.444022 GGCTTCACTGGTCATCTCATACAT 60.444 45.833 0.00 0.00 0.00 2.29
3378 5375 8.801299 TCTCATACATTGTGGCTTATTTTTCAA 58.199 29.630 0.00 0.00 0.00 2.69
3595 5595 6.428159 TGATAGTTGAGCTCCACTTTCTTTTC 59.572 38.462 27.13 15.80 0.00 2.29
3596 5596 4.526970 AGTTGAGCTCCACTTTCTTTTCA 58.473 39.130 14.48 0.00 0.00 2.69
3606 5606 6.680810 TCCACTTTCTTTTCATGCTTGTATG 58.319 36.000 0.00 0.00 0.00 2.39
3615 5615 9.109393 TCTTTTCATGCTTGTATGTATAGTTCC 57.891 33.333 0.00 0.00 0.00 3.62
3814 5814 8.929746 GTTTGATTTTCCATCTGATTCCTTTTC 58.070 33.333 0.00 0.00 0.00 2.29
3815 5815 7.174107 TGATTTTCCATCTGATTCCTTTTCC 57.826 36.000 0.00 0.00 0.00 3.13
3816 5816 6.155049 TGATTTTCCATCTGATTCCTTTTCCC 59.845 38.462 0.00 0.00 0.00 3.97
3834 5834 1.897560 CCCCCACTCTTTCAACTGTC 58.102 55.000 0.00 0.00 0.00 3.51
3888 5889 3.002656 CAGGTGCTAAATATGAACTGCCG 59.997 47.826 0.00 0.00 0.00 5.69
4194 6196 4.382160 GTGCTACTGTAAACACGAGTCTTC 59.618 45.833 0.00 0.00 0.00 2.87
4195 6197 4.277672 TGCTACTGTAAACACGAGTCTTCT 59.722 41.667 0.00 0.00 0.00 2.85
4196 6198 5.221130 GCTACTGTAAACACGAGTCTTCTT 58.779 41.667 0.00 0.00 0.00 2.52
4280 6282 9.203421 TGATATAAGTTGAAGTATGGCAATACG 57.797 33.333 5.57 0.00 43.03 3.06
4297 6299 6.143919 GGCAATACGTTTCAGAAAGGAAAAAG 59.856 38.462 20.03 8.36 38.41 2.27
4398 6400 3.142162 TGCCCATGCATTGCCTCG 61.142 61.111 13.83 0.00 44.23 4.63
4503 6544 4.701765 ACAAGATATCTGGTGATGCTGAC 58.298 43.478 12.20 0.00 34.32 3.51
4553 6595 5.336055 CCATGCTACTATAGTACTGGAGTGC 60.336 48.000 18.45 17.22 0.00 4.40
4555 6597 5.446860 TGCTACTATAGTACTGGAGTGCTT 58.553 41.667 17.41 0.00 41.24 3.91
4564 6606 2.044946 GGAGTGCTTCCCCGCAAT 60.045 61.111 0.00 0.00 42.32 3.56
4603 6650 6.166279 AGTACTGAGTGTTACATGTTCATGG 58.834 40.000 2.30 0.00 0.00 3.66
4653 6700 1.308998 ACAGAGGCCAAGTGTTTTCG 58.691 50.000 5.01 0.00 0.00 3.46
4758 6805 8.578308 TCTGAAGAAACATGCTATTTTTGTTG 57.422 30.769 0.00 0.00 34.04 3.33
4886 6954 6.822667 TCTGACAACAAAATGCACATCTAT 57.177 33.333 0.00 0.00 0.00 1.98
4888 6956 6.430616 TCTGACAACAAAATGCACATCTATGA 59.569 34.615 0.00 0.00 0.00 2.15
4967 7036 2.499693 TGAGATAGGCACGGTGAATTGA 59.500 45.455 13.29 0.00 0.00 2.57
5062 7133 1.880027 GCGGTGACCTCTGATTTTTGT 59.120 47.619 0.00 0.00 0.00 2.83
5081 7152 4.385358 TGTGCGCTAGATTACATTCTGA 57.615 40.909 9.73 0.00 0.00 3.27
5096 7167 6.949352 ACATTCTGATTACATGGCTAAAGG 57.051 37.500 0.00 0.00 0.00 3.11
5098 7169 7.573710 ACATTCTGATTACATGGCTAAAGGTA 58.426 34.615 0.00 0.00 0.00 3.08
5122 7193 5.640147 TGAAACCTGAACCACCTATGAATT 58.360 37.500 0.00 0.00 0.00 2.17
5180 7251 0.878416 TGCACATGAACGTTAAGCCC 59.122 50.000 0.00 0.00 0.00 5.19
5259 7330 4.157105 TGCTCCATCTTGTGAATCATGTTG 59.843 41.667 0.00 0.00 0.00 3.33
5311 7382 4.756084 GAAGCAGCTTCTGTTACACATT 57.244 40.909 25.51 0.00 37.49 2.71
5312 7383 4.470462 GAAGCAGCTTCTGTTACACATTG 58.530 43.478 25.51 0.00 37.49 2.82
5314 7385 3.885297 AGCAGCTTCTGTTACACATTGTT 59.115 39.130 0.00 0.00 33.43 2.83
5315 7386 4.023707 AGCAGCTTCTGTTACACATTGTTC 60.024 41.667 0.00 0.00 33.43 3.18
5317 7388 5.733091 GCAGCTTCTGTTACACATTGTTCAA 60.733 40.000 0.00 0.00 33.43 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 26 5.655488 AGACATGTAGAGAATCAAACCTCG 58.345 41.667 0.00 0.00 37.82 4.63
25 27 6.693545 CGTAGACATGTAGAGAATCAAACCTC 59.306 42.308 0.00 0.00 37.82 3.85
82 84 1.610363 TAGCTCTCGCTAGTGATGGG 58.390 55.000 6.42 2.57 46.79 4.00
115 117 4.230745 AGACCACAACCAAACTTACAGT 57.769 40.909 0.00 0.00 0.00 3.55
142 144 9.976511 CCGTTTTAGATAATGGTGTTAGAGATA 57.023 33.333 0.00 0.00 30.93 1.98
148 150 7.118101 GTGTGTCCGTTTTAGATAATGGTGTTA 59.882 37.037 0.00 0.00 35.94 2.41
159 1891 4.491676 GCAGATAGTGTGTCCGTTTTAGA 58.508 43.478 0.00 0.00 0.00 2.10
166 1898 0.460284 GTGGGCAGATAGTGTGTCCG 60.460 60.000 0.00 0.00 43.14 4.79
184 1916 0.755698 ACTCCCGCATCTATGTCCGT 60.756 55.000 0.00 0.00 0.00 4.69
191 1923 0.467474 ATGACCGACTCCCGCATCTA 60.467 55.000 0.00 0.00 36.84 1.98
207 1961 5.935945 ACATTTATGGGATACGTTGGATGA 58.064 37.500 0.00 0.00 37.60 2.92
228 1982 3.948719 GTTGGACCTGGGCGGACA 61.949 66.667 0.00 0.00 36.31 4.02
244 1998 5.348451 GCTATGCGTTTGAAATGAAATTGGT 59.652 36.000 0.48 0.00 36.10 3.67
272 2026 1.136446 GCGTGAATGTCAACGTACCAC 60.136 52.381 0.00 0.00 0.00 4.16
306 2060 1.553248 TCCACAACCTCCATCGTTAGG 59.447 52.381 0.00 0.00 38.93 2.69
309 2063 2.879103 AATCCACAACCTCCATCGTT 57.121 45.000 0.00 0.00 0.00 3.85
312 2066 2.169769 TCGGTAATCCACAACCTCCATC 59.830 50.000 0.00 0.00 33.34 3.51
341 2095 3.022406 CCCTACTTCTACGCTACCAAGT 58.978 50.000 0.00 0.00 33.63 3.16
348 2102 2.100989 CAACCTCCCTACTTCTACGCT 58.899 52.381 0.00 0.00 0.00 5.07
391 2145 1.695893 CCATCGTCGTCCATGCACAC 61.696 60.000 0.00 0.00 0.00 3.82
396 2150 2.173669 GCCACCATCGTCGTCCATG 61.174 63.158 0.00 0.00 0.00 3.66
482 2236 2.679642 CAAAAGATGGGGCGGCCA 60.680 61.111 30.95 16.32 0.00 5.36
487 2241 0.247460 GTGAAGGCAAAAGATGGGGC 59.753 55.000 0.00 0.00 0.00 5.80
504 2258 3.365265 GCCCGCCACCTCAAAGTG 61.365 66.667 0.00 0.00 37.51 3.16
505 2259 3.133365 AAGCCCGCCACCTCAAAGT 62.133 57.895 0.00 0.00 0.00 2.66
534 2288 1.136305 TCCGCCTGGAAGATTAACTCG 59.864 52.381 0.00 0.00 42.85 4.18
596 2350 0.180171 CCGCATGGACCCATACAAGA 59.820 55.000 0.55 0.00 37.49 3.02
597 2351 0.107214 ACCGCATGGACCCATACAAG 60.107 55.000 0.55 0.00 39.21 3.16
599 2353 1.223211 CACCGCATGGACCCATACA 59.777 57.895 0.55 0.00 39.21 2.29
650 2404 4.520846 GCGCTCCAATCGCCGTTG 62.521 66.667 0.00 0.00 46.18 4.10
667 2421 1.384191 CAAAACCCCTCCCCCTCTG 59.616 63.158 0.00 0.00 0.00 3.35
701 2456 0.611618 AGCCCGTGCATTTGGATCAA 60.612 50.000 4.33 0.00 41.13 2.57
704 2459 1.656818 CGAAGCCCGTGCATTTGGAT 61.657 55.000 4.33 0.00 41.13 3.41
726 2481 1.067516 CTCAGCCCACACAAAAACCAG 59.932 52.381 0.00 0.00 0.00 4.00
727 2482 1.110442 CTCAGCCCACACAAAAACCA 58.890 50.000 0.00 0.00 0.00 3.67
730 2485 0.032615 ACCCTCAGCCCACACAAAAA 60.033 50.000 0.00 0.00 0.00 1.94
748 2503 1.163554 AACACGTAGGACTCCGAGAC 58.836 55.000 1.33 0.00 0.00 3.36
750 2505 2.608546 CTCTAACACGTAGGACTCCGAG 59.391 54.545 0.00 0.00 0.00 4.63
767 2522 0.755698 GCATGGAGTCCGGACCTCTA 60.756 60.000 30.82 23.10 0.00 2.43
768 2523 2.060980 GCATGGAGTCCGGACCTCT 61.061 63.158 30.82 13.25 0.00 3.69
777 2532 2.054453 GGGGGCTTTGCATGGAGTC 61.054 63.158 0.00 0.00 0.00 3.36
784 2539 2.364353 CAAATCAGGGGGCTTTGCA 58.636 52.632 0.00 0.00 0.00 4.08
798 2553 0.240945 CTCGCAAACCGGAAGCAAAT 59.759 50.000 9.46 0.00 37.59 2.32
806 2561 0.945265 TCCGTTTACTCGCAAACCGG 60.945 55.000 0.00 0.00 35.42 5.28
814 2569 0.457166 TCCGCATGTCCGTTTACTCG 60.457 55.000 0.00 0.00 0.00 4.18
853 2608 1.825090 CAAGGCATCTAACACAGGCA 58.175 50.000 0.00 0.00 0.00 4.75
857 2612 1.535028 CGTTGCAAGGCATCTAACACA 59.465 47.619 6.16 0.00 38.76 3.72
863 2618 0.537143 TTGGACGTTGCAAGGCATCT 60.537 50.000 18.61 0.00 38.76 2.90
868 2623 0.030638 CCTGTTTGGACGTTGCAAGG 59.969 55.000 17.21 17.21 38.35 3.61
877 2632 1.340248 TCTGAGACGACCTGTTTGGAC 59.660 52.381 0.00 0.00 39.71 4.02
891 2646 2.910479 ACCCGCACACGTCTGAGA 60.910 61.111 0.00 0.00 37.70 3.27
892 2647 2.734723 CACCCGCACACGTCTGAG 60.735 66.667 0.00 0.00 37.70 3.35
895 2650 1.450669 AAAACACCCGCACACGTCT 60.451 52.632 0.00 0.00 37.70 4.18
899 2654 0.307760 CTCTCAAAACACCCGCACAC 59.692 55.000 0.00 0.00 0.00 3.82
900 2655 0.107410 ACTCTCAAAACACCCGCACA 60.107 50.000 0.00 0.00 0.00 4.57
907 2662 4.312443 TCCAATACGGACTCTCAAAACAC 58.688 43.478 0.00 0.00 39.64 3.32
908 2663 4.282449 TCTCCAATACGGACTCTCAAAACA 59.718 41.667 0.00 0.00 39.64 2.83
909 2664 4.817517 TCTCCAATACGGACTCTCAAAAC 58.182 43.478 0.00 0.00 39.64 2.43
917 2672 3.033659 AGGTCATCTCCAATACGGACT 57.966 47.619 0.00 0.00 39.64 3.85
918 2673 3.821421 AAGGTCATCTCCAATACGGAC 57.179 47.619 0.00 0.00 39.64 4.79
923 2678 5.584649 CGTTTTGCTAAGGTCATCTCCAATA 59.415 40.000 0.00 0.00 0.00 1.90
924 2679 4.396166 CGTTTTGCTAAGGTCATCTCCAAT 59.604 41.667 0.00 0.00 0.00 3.16
946 2701 2.679837 AGCAAGACAATATGGCTCAACG 59.320 45.455 0.00 0.00 31.94 4.10
976 2731 9.125026 AGCATAATAATGACCCTAGAAAAACAG 57.875 33.333 0.00 0.00 34.84 3.16
1106 2875 4.539726 TCCTGCCTTCGTTTATAGGAGTA 58.460 43.478 0.00 0.00 33.13 2.59
1123 2892 1.530293 CGCATTCATAAGCTCTCCTGC 59.470 52.381 0.00 0.00 0.00 4.85
1140 2909 1.967319 AGAAAGGAACAGAAAGCGCA 58.033 45.000 11.47 0.00 0.00 6.09
1408 3208 2.200373 ACTCCAAGAACCCAATTCCG 57.800 50.000 0.00 0.00 38.16 4.30
1464 3264 0.529773 GACGCCATCTACGCCATCAA 60.530 55.000 0.00 0.00 0.00 2.57
1471 3271 0.992072 CACAACTGACGCCATCTACG 59.008 55.000 0.00 0.00 0.00 3.51
1554 3354 5.763876 AACTCAACTTGGATAACCTAGCT 57.236 39.130 0.40 0.00 41.46 3.32
1561 3361 8.458573 ACACACAAATAACTCAACTTGGATAA 57.541 30.769 0.00 0.00 0.00 1.75
1708 3538 2.046314 ATTCAGTTCGCCGGTGGG 60.046 61.111 16.49 2.85 0.00 4.61
1709 3539 2.398554 CCATTCAGTTCGCCGGTGG 61.399 63.158 16.49 0.67 0.00 4.61
1710 3540 2.398554 CCCATTCAGTTCGCCGGTG 61.399 63.158 9.28 9.28 0.00 4.94
1711 3541 1.910580 ATCCCATTCAGTTCGCCGGT 61.911 55.000 1.90 0.00 0.00 5.28
1712 3542 1.153168 ATCCCATTCAGTTCGCCGG 60.153 57.895 0.00 0.00 0.00 6.13
1713 3543 0.461870 TGATCCCATTCAGTTCGCCG 60.462 55.000 0.00 0.00 0.00 6.46
1714 3544 1.972872 ATGATCCCATTCAGTTCGCC 58.027 50.000 0.00 0.00 0.00 5.54
1715 3545 3.129287 ACAAATGATCCCATTCAGTTCGC 59.871 43.478 0.00 0.00 41.84 4.70
1716 3546 4.970662 ACAAATGATCCCATTCAGTTCG 57.029 40.909 0.00 0.00 41.84 3.95
1772 3602 0.106719 TTCCCCAAGAATCCCATCGC 60.107 55.000 0.00 0.00 0.00 4.58
1843 3674 2.091588 GTCGCCACACAATAGTTACACG 59.908 50.000 0.00 0.00 0.00 4.49
1856 3687 0.753867 TTTACACTCCTGTCGCCACA 59.246 50.000 0.00 0.00 0.00 4.17
1947 3778 6.417191 TCACCAAACTATGATTAACGAAGC 57.583 37.500 0.00 0.00 0.00 3.86
2301 4133 8.762645 ACCTTCAAGATACAGAGATGTTAATCA 58.237 33.333 0.00 0.00 35.03 2.57
2430 4262 6.389091 TCAACTTGCACAAAATATCATGTCC 58.611 36.000 0.00 0.00 0.00 4.02
2438 4270 6.201226 TCAGTGTTCAACTTGCACAAAATA 57.799 33.333 0.00 0.00 36.83 1.40
2456 4288 4.872691 CCTGTATAGTTCCAGCTTTCAGTG 59.127 45.833 0.00 0.00 0.00 3.66
2680 4513 9.357652 CCCACAGAATTGTTCAAAACATAATAG 57.642 33.333 0.00 0.00 41.79 1.73
2728 4561 2.844122 GTTCCAAACGTCACTTGCTT 57.156 45.000 0.00 0.00 0.00 3.91
2748 4581 6.425114 CAGGACTTGCATAATACTACCATCAC 59.575 42.308 0.00 0.00 0.00 3.06
2765 4598 3.949754 ACAATATGATGCACCAGGACTTG 59.050 43.478 0.00 0.00 0.00 3.16
2773 4606 4.395854 TCAACAGACACAATATGATGCACC 59.604 41.667 0.00 0.00 0.00 5.01
2812 4645 7.226523 GTGGCAAGAACTAAAAATTCCACAAAT 59.773 33.333 0.00 0.00 40.65 2.32
2952 4785 8.314021 ACATGAGATGACTAAAACACACATAGA 58.686 33.333 0.00 0.00 0.00 1.98
2980 4813 9.181061 TGGACATAATATTTGATCCATGCTATG 57.819 33.333 9.17 0.00 31.30 2.23
3025 5020 2.101249 AGTGCCAACAACTCACAATTGG 59.899 45.455 10.83 0.00 43.78 3.16
3174 5171 9.845740 AAGTTCACCTTTAAATTTTAAGGCATT 57.154 25.926 27.79 16.07 43.84 3.56
3176 5173 9.674068 AAAAGTTCACCTTTAAATTTTAAGGCA 57.326 25.926 27.79 16.41 42.62 4.75
3195 5192 8.227791 TGCAACTTACTATTCGATGAAAAGTTC 58.772 33.333 9.23 6.80 34.43 3.01
3211 5208 3.821033 GGAACATCCTTGTGCAACTTACT 59.179 43.478 0.00 0.00 35.83 2.24
3213 5210 4.098914 AGGAACATCCTTGTGCAACTTA 57.901 40.909 0.00 0.00 46.91 2.24
3220 5217 8.642432 TCTCTATGTAATAGGAACATCCTTGTG 58.358 37.037 3.90 0.00 46.91 3.33
3225 5222 9.030452 ACTCATCTCTATGTAATAGGAACATCC 57.970 37.037 0.00 0.00 46.94 3.51
3239 5236 8.498054 TTGGCTCTTAAAAACTCATCTCTATG 57.502 34.615 0.00 0.00 0.00 2.23
3271 5268 2.017049 AGACAAAAGACAAACAGCGCT 58.983 42.857 2.64 2.64 0.00 5.92
3274 5271 3.304293 GTGCAAGACAAAAGACAAACAGC 59.696 43.478 0.00 0.00 0.00 4.40
3326 5323 7.630082 TGACCAGTGAAGCCTTAATAAGTATT 58.370 34.615 0.00 0.00 0.00 1.89
3331 5328 6.070251 TGAGATGACCAGTGAAGCCTTAATAA 60.070 38.462 0.00 0.00 0.00 1.40
3336 5333 1.980765 TGAGATGACCAGTGAAGCCTT 59.019 47.619 0.00 0.00 0.00 4.35
3361 5358 8.093307 TCTGCATAATTGAAAAATAAGCCACAA 58.907 29.630 0.00 0.00 0.00 3.33
3378 5375 6.109359 ACTTTCTTCGTAGCTTCTGCATAAT 58.891 36.000 0.00 0.00 42.74 1.28
3518 5515 4.217767 ACACACGACAGAAGCATAAGAGTA 59.782 41.667 0.00 0.00 0.00 2.59
3525 5522 2.533266 AAGACACACGACAGAAGCAT 57.467 45.000 0.00 0.00 0.00 3.79
3571 5571 6.428159 TGAAAAGAAAGTGGAGCTCAACTATC 59.572 38.462 24.24 14.72 0.00 2.08
3572 5572 6.299141 TGAAAAGAAAGTGGAGCTCAACTAT 58.701 36.000 24.24 10.62 0.00 2.12
3583 5583 6.449698 ACATACAAGCATGAAAAGAAAGTGG 58.550 36.000 0.00 0.00 0.00 4.00
3595 5595 7.118390 GCTAAGGGAACTATACATACAAGCATG 59.882 40.741 0.00 0.00 42.68 4.06
3596 5596 7.016661 AGCTAAGGGAACTATACATACAAGCAT 59.983 37.037 0.00 0.00 42.68 3.79
3606 5606 4.939052 TGAGCAGCTAAGGGAACTATAC 57.061 45.455 0.00 0.00 42.68 1.47
3615 5615 1.212616 GCGTACATGAGCAGCTAAGG 58.787 55.000 0.00 0.00 0.00 2.69
3815 5815 1.878102 CGACAGTTGAAAGAGTGGGGG 60.878 57.143 0.00 0.00 0.00 5.40
3816 5816 1.202651 ACGACAGTTGAAAGAGTGGGG 60.203 52.381 0.00 0.00 0.00 4.96
3888 5889 5.452777 GTTGGCTCACTCAAAACATACTTC 58.547 41.667 0.00 0.00 0.00 3.01
3978 5979 4.537015 GCGTTGTTTTTAGCATCTGAAGT 58.463 39.130 0.00 0.00 0.00 3.01
4194 6196 9.595823 TTCTAACCCATAACGAAGATTTCTAAG 57.404 33.333 0.00 0.00 0.00 2.18
4195 6197 9.947433 TTTCTAACCCATAACGAAGATTTCTAA 57.053 29.630 0.00 0.00 0.00 2.10
4196 6198 9.374838 GTTTCTAACCCATAACGAAGATTTCTA 57.625 33.333 0.00 0.00 0.00 2.10
4280 6282 7.492524 ACATTCTCCTTTTTCCTTTCTGAAAC 58.507 34.615 0.00 0.00 34.13 2.78
4398 6400 6.647895 ACATTCCTCAATTTGCATTCTCAAAC 59.352 34.615 0.00 0.00 38.58 2.93
4503 6544 3.310774 CGCTTACATCCTTCCAGAACATG 59.689 47.826 0.00 0.00 0.00 3.21
4603 6650 8.099364 TCTCTTAATTTGAACCAACATCAGAC 57.901 34.615 0.00 0.00 0.00 3.51
4653 6700 0.029834 CGCCAATAATCAGTGCTGCC 59.970 55.000 0.00 0.00 0.00 4.85
4744 6791 6.667414 TCCTACCCATTCAACAAAAATAGCAT 59.333 34.615 0.00 0.00 0.00 3.79
4758 6805 4.200092 GTTTCTGGATGTCCTACCCATTC 58.800 47.826 0.09 0.00 36.82 2.67
4886 6954 3.801307 ATGCCCTGCAGAATATCATCA 57.199 42.857 17.39 1.22 43.65 3.07
4888 6956 5.509832 TCTTATGCCCTGCAGAATATCAT 57.490 39.130 17.39 12.34 43.65 2.45
5062 7133 6.512297 TGTAATCAGAATGTAATCTAGCGCA 58.488 36.000 11.47 0.00 37.40 6.09
5081 7152 7.582667 GGTTTCATACCTTTAGCCATGTAAT 57.417 36.000 0.00 0.00 44.10 1.89
5096 7167 5.741011 TCATAGGTGGTTCAGGTTTCATAC 58.259 41.667 0.00 0.00 0.00 2.39
5098 7169 4.927267 TCATAGGTGGTTCAGGTTTCAT 57.073 40.909 0.00 0.00 0.00 2.57
5122 7193 7.396055 AGGAACCGGAATTAAATTGAAGATTCA 59.604 33.333 9.46 0.00 34.92 2.57
5259 7330 1.075450 AGGTGGGGTCGGTATCTCC 60.075 63.158 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.