Multiple sequence alignment - TraesCS5D01G255300

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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 TraesCS5D01G255300 chr5D 100.000 3405 0 0 1 3405 361658326 361661730 0.000000e+00 6288.0
1 TraesCS5D01G255300 chr5A 90.898 1637 93 16 859 2483 462159410 462161002 0.000000e+00 2146.0
2 TraesCS5D01G255300 chr5A 91.973 897 56 7 2515 3403 462161141 462162029 0.000000e+00 1243.0
3 TraesCS5D01G255300 chr5A 92.000 200 9 3 633 828 462159214 462159410 1.200000e-69 274.0
4 TraesCS5D01G255300 chr5B 92.797 1430 93 2 1026 2445 427280877 427282306 0.000000e+00 2061.0
5 TraesCS5D01G255300 chr5B 91.192 965 51 11 2451 3400 427284723 427285668 0.000000e+00 1280.0
6 TraesCS5D01G255300 chr5B 85.955 178 18 4 860 1037 427278115 427278285 2.090000e-42 183.0
7 TraesCS5D01G255300 chr2D 96.892 547 15 1 1 545 620313809 620313263 0.000000e+00 915.0
8 TraesCS5D01G255300 chr2D 82.149 577 68 18 2 567 568076925 568077477 2.390000e-126 462.0
9 TraesCS5D01G255300 chr1D 81.944 576 69 21 2 566 407825713 407826264 4.010000e-124 455.0
10 TraesCS5D01G255300 chr2B 82.851 449 61 10 131 567 680571963 680572407 4.120000e-104 388.0
11 TraesCS5D01G255300 chr3B 84.595 370 46 8 101 461 13868549 13868916 1.160000e-94 357.0
12 TraesCS5D01G255300 chr4A 79.021 143 17 4 63 194 713490936 713491076 6.050000e-13 86.1
13 TraesCS5D01G255300 chr1B 95.238 42 1 1 499 539 525911014 525910973 7.890000e-07 65.8


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 TraesCS5D01G255300 chr5D 361658326 361661730 3404 False 6288.000000 6288 100.000000 1 3405 1 chr5D.!!$F1 3404
1 TraesCS5D01G255300 chr5A 462159214 462162029 2815 False 1221.000000 2146 91.623667 633 3403 3 chr5A.!!$F1 2770
2 TraesCS5D01G255300 chr5B 427278115 427285668 7553 False 1174.666667 2061 89.981333 860 3400 3 chr5B.!!$F1 2540
3 TraesCS5D01G255300 chr2D 620313263 620313809 546 True 915.000000 915 96.892000 1 545 1 chr2D.!!$R1 544
4 TraesCS5D01G255300 chr2D 568076925 568077477 552 False 462.000000 462 82.149000 2 567 1 chr2D.!!$F1 565
5 TraesCS5D01G255300 chr1D 407825713 407826264 551 False 455.000000 455 81.944000 2 566 1 chr1D.!!$F1 564

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
829 845 0.036010 AAGTGGAATCACCTGGAGCG 60.036 55.0 0.00 0.0 44.64 5.03 F
838 854 0.251916 CACCTGGAGCGGGACAATAA 59.748 55.0 0.00 0.0 33.36 1.40 F
1846 4465 0.307760 CACGCTGTTTCAGGTGAACC 59.692 55.0 10.53 0.0 35.92 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2171 4805 0.032403 CATGTTGCACAGTGGTTGGG 59.968 55.000 1.84 0.0 0.00 4.12 R
2175 4809 1.000060 GCAATCATGTTGCACAGTGGT 60.000 47.619 20.83 0.0 44.34 4.16 R
3367 8549 1.115326 AACAGGGGGAAAGCAACTGC 61.115 55.000 0.00 0.0 42.49 4.40 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
58 59 1.141881 CACGGCCGCAGTATTCTCT 59.858 57.895 28.58 0.00 0.00 3.10
132 133 3.693471 CAATTTGCCCCCGCTGCA 61.693 61.111 0.00 0.00 36.84 4.41
308 309 3.127030 GGCGCTAAAACTGAAGCTAACAT 59.873 43.478 7.64 0.00 36.56 2.71
383 392 2.939103 GAGATTCGGTGGAGTGAATTGG 59.061 50.000 0.00 0.00 35.06 3.16
449 458 1.203112 TGTGGTTAATGTGTGGGGCAT 60.203 47.619 0.00 0.00 0.00 4.40
562 574 2.725641 GCCGTTCCCAAGCGTTTT 59.274 55.556 0.00 0.00 0.00 2.43
567 579 1.874872 CGTTCCCAAGCGTTTTCCTAA 59.125 47.619 0.00 0.00 0.00 2.69
568 580 2.486592 CGTTCCCAAGCGTTTTCCTAAT 59.513 45.455 0.00 0.00 0.00 1.73
569 581 3.669557 CGTTCCCAAGCGTTTTCCTAATG 60.670 47.826 0.00 0.00 0.00 1.90
570 582 3.149005 TCCCAAGCGTTTTCCTAATGT 57.851 42.857 0.00 0.00 0.00 2.71
571 583 4.289238 TCCCAAGCGTTTTCCTAATGTA 57.711 40.909 0.00 0.00 0.00 2.29
572 584 4.653868 TCCCAAGCGTTTTCCTAATGTAA 58.346 39.130 0.00 0.00 0.00 2.41
573 585 5.071370 TCCCAAGCGTTTTCCTAATGTAAA 58.929 37.500 0.00 0.00 0.00 2.01
574 586 5.712917 TCCCAAGCGTTTTCCTAATGTAAAT 59.287 36.000 0.00 0.00 0.00 1.40
575 587 6.033966 CCCAAGCGTTTTCCTAATGTAAATC 58.966 40.000 0.00 0.00 0.00 2.17
576 588 6.127730 CCCAAGCGTTTTCCTAATGTAAATCT 60.128 38.462 0.00 0.00 0.00 2.40
577 589 7.312899 CCAAGCGTTTTCCTAATGTAAATCTT 58.687 34.615 0.00 0.00 0.00 2.40
578 590 7.812669 CCAAGCGTTTTCCTAATGTAAATCTTT 59.187 33.333 0.00 0.00 0.00 2.52
579 591 9.191995 CAAGCGTTTTCCTAATGTAAATCTTTT 57.808 29.630 0.00 0.00 0.00 2.27
580 592 9.758651 AAGCGTTTTCCTAATGTAAATCTTTTT 57.241 25.926 0.00 0.00 0.00 1.94
617 629 7.797038 ATTAGTGTAGTGTCGGAAAAAGTTT 57.203 32.000 0.00 0.00 0.00 2.66
618 630 8.891671 ATTAGTGTAGTGTCGGAAAAAGTTTA 57.108 30.769 0.00 0.00 0.00 2.01
619 631 6.594284 AGTGTAGTGTCGGAAAAAGTTTAC 57.406 37.500 0.00 0.00 0.00 2.01
620 632 5.525012 AGTGTAGTGTCGGAAAAAGTTTACC 59.475 40.000 0.00 0.00 0.00 2.85
621 633 4.507388 TGTAGTGTCGGAAAAAGTTTACCG 59.493 41.667 20.79 20.79 45.61 4.02
625 637 2.582446 CGGAAAAAGTTTACCGACGG 57.418 50.000 21.71 13.61 46.94 4.79
626 638 2.134346 CGGAAAAAGTTTACCGACGGA 58.866 47.619 23.38 0.74 46.94 4.69
627 639 2.156310 CGGAAAAAGTTTACCGACGGAG 59.844 50.000 23.38 0.00 46.94 4.63
628 640 2.481568 GGAAAAAGTTTACCGACGGAGG 59.518 50.000 23.38 0.00 37.30 4.30
629 641 2.174363 AAAAGTTTACCGACGGAGGG 57.826 50.000 23.38 0.00 35.02 4.30
630 642 1.341080 AAAGTTTACCGACGGAGGGA 58.659 50.000 23.38 0.00 35.02 4.20
631 643 0.893447 AAGTTTACCGACGGAGGGAG 59.107 55.000 23.38 0.00 35.02 4.30
638 650 0.394080 CCGACGGAGGGAGTAGTTCT 60.394 60.000 8.64 0.00 0.00 3.01
668 680 4.679373 TCCACTGAAGAAGCTGATATCC 57.321 45.455 0.00 0.00 0.00 2.59
672 684 2.630098 CTGAAGAAGCTGATATCCGGGA 59.370 50.000 0.00 0.00 0.00 5.14
675 687 3.760580 AGAAGCTGATATCCGGGAAAG 57.239 47.619 0.00 0.00 0.00 2.62
704 716 2.161410 TCTTCGAATCCACAAATTGCCG 59.839 45.455 0.00 0.00 0.00 5.69
709 721 3.489059 CGAATCCACAAATTGCCGCTTAT 60.489 43.478 0.00 0.00 0.00 1.73
728 740 5.715070 CTTATCTCGTTCCTGTTCAGACTT 58.285 41.667 1.00 0.00 0.00 3.01
757 769 3.118408 TCCATTGAAGTATCCGAGTTGGG 60.118 47.826 0.00 0.00 38.76 4.12
805 821 4.888038 TCGTAGCGCCATATATACGATT 57.112 40.909 19.37 0.00 43.48 3.34
827 843 3.008375 TGAAGAAGTGGAATCACCTGGAG 59.992 47.826 0.00 0.00 44.64 3.86
828 844 1.280421 AGAAGTGGAATCACCTGGAGC 59.720 52.381 0.00 0.00 44.64 4.70
829 845 0.036010 AAGTGGAATCACCTGGAGCG 60.036 55.000 0.00 0.00 44.64 5.03
830 846 1.450312 GTGGAATCACCTGGAGCGG 60.450 63.158 0.00 0.00 37.92 5.52
831 847 2.190578 GGAATCACCTGGAGCGGG 59.809 66.667 0.00 0.00 35.68 6.13
832 848 2.367202 GGAATCACCTGGAGCGGGA 61.367 63.158 0.00 0.00 33.36 5.14
833 849 1.153349 GAATCACCTGGAGCGGGAC 60.153 63.158 0.00 0.00 33.36 4.46
834 850 1.899437 GAATCACCTGGAGCGGGACA 61.899 60.000 0.00 0.00 33.36 4.02
835 851 1.488705 AATCACCTGGAGCGGGACAA 61.489 55.000 0.00 0.00 33.36 3.18
836 852 1.274703 ATCACCTGGAGCGGGACAAT 61.275 55.000 0.00 0.00 33.36 2.71
837 853 0.616395 TCACCTGGAGCGGGACAATA 60.616 55.000 0.00 0.00 33.36 1.90
838 854 0.251916 CACCTGGAGCGGGACAATAA 59.748 55.000 0.00 0.00 33.36 1.40
839 855 0.988832 ACCTGGAGCGGGACAATAAA 59.011 50.000 0.00 0.00 33.36 1.40
840 856 1.564348 ACCTGGAGCGGGACAATAAAT 59.436 47.619 0.00 0.00 33.36 1.40
841 857 2.775384 ACCTGGAGCGGGACAATAAATA 59.225 45.455 0.00 0.00 33.36 1.40
842 858 3.201266 ACCTGGAGCGGGACAATAAATAA 59.799 43.478 0.00 0.00 33.36 1.40
843 859 3.815401 CCTGGAGCGGGACAATAAATAAG 59.185 47.826 0.00 0.00 29.82 1.73
844 860 3.815401 CTGGAGCGGGACAATAAATAAGG 59.185 47.826 0.00 0.00 0.00 2.69
845 861 3.201266 TGGAGCGGGACAATAAATAAGGT 59.799 43.478 0.00 0.00 0.00 3.50
846 862 3.813724 GGAGCGGGACAATAAATAAGGTC 59.186 47.826 0.00 0.00 0.00 3.85
854 870 6.526526 GGACAATAAATAAGGTCCTCTCTCC 58.473 44.000 0.00 0.00 44.99 3.71
855 871 6.327887 GGACAATAAATAAGGTCCTCTCTCCT 59.672 42.308 0.00 0.00 44.99 3.69
856 872 7.368198 ACAATAAATAAGGTCCTCTCTCCTC 57.632 40.000 0.00 0.00 33.09 3.71
857 873 7.136203 ACAATAAATAAGGTCCTCTCTCCTCT 58.864 38.462 0.00 0.00 33.09 3.69
887 903 0.458716 GCCTCCTTATATCTCGGCGC 60.459 60.000 0.00 0.00 0.00 6.53
890 906 1.272490 CTCCTTATATCTCGGCGCCAA 59.728 52.381 28.98 7.25 0.00 4.52
1002 1018 1.153489 CTGACCGCTGACCTCCATG 60.153 63.158 0.00 0.00 0.00 3.66
1003 1019 1.607801 CTGACCGCTGACCTCCATGA 61.608 60.000 0.00 0.00 0.00 3.07
1160 3779 2.738521 CGCGACCCTGTTGGACAG 60.739 66.667 0.00 1.14 45.53 3.51
1314 3933 1.531149 CAAAAGATTGTCGGCGTCACT 59.469 47.619 6.28 0.82 0.00 3.41
1327 3946 1.517257 GTCACTGACGGCCTCATCG 60.517 63.158 0.00 0.00 0.00 3.84
1577 4196 2.271800 GGTGAACCATCGAGACATCAC 58.728 52.381 12.97 12.97 37.14 3.06
1634 4253 4.293648 CACCACACCGGCGTCAGA 62.294 66.667 6.01 0.00 39.03 3.27
1656 4275 1.226717 GCTCGTTCAGCTCTACCCG 60.227 63.158 0.00 0.00 45.83 5.28
1677 4296 1.754234 AAATCCATGCGGGGCAGTC 60.754 57.895 0.00 0.00 43.65 3.51
1694 4313 4.794439 CGTCGCTCATGTCCCGCA 62.794 66.667 0.00 0.00 0.00 5.69
1695 4314 3.188786 GTCGCTCATGTCCCGCAC 61.189 66.667 0.00 0.00 0.00 5.34
1704 4323 2.737376 GTCCCGCACGAGTTGGTC 60.737 66.667 0.00 0.00 0.00 4.02
1705 4324 3.998672 TCCCGCACGAGTTGGTCC 61.999 66.667 0.00 0.00 0.00 4.46
1743 4362 3.358076 CTTCCTCGTGGAGTCCGGC 62.358 68.421 6.29 0.00 44.24 6.13
1778 4397 1.640069 CCGTGCAGCATCATCGAAG 59.360 57.895 0.00 0.00 0.00 3.79
1782 4401 2.550101 GCAGCATCATCGAAGGGGC 61.550 63.158 0.00 0.00 0.00 5.80
1783 4402 1.895707 CAGCATCATCGAAGGGGCC 60.896 63.158 0.00 0.00 0.00 5.80
1787 4406 1.228367 ATCATCGAAGGGGCCATGC 60.228 57.895 4.39 0.00 0.00 4.06
1816 4435 1.153549 GAGATGGAGTGGTGGCGAC 60.154 63.158 0.00 0.00 0.00 5.19
1833 4452 1.548973 GACACTTCACCGTCACGCTG 61.549 60.000 0.00 0.00 32.24 5.18
1846 4465 0.307760 CACGCTGTTTCAGGTGAACC 59.692 55.000 10.53 0.00 35.92 3.62
1876 4495 1.084370 GGAGCTCATTCCGGTGAACG 61.084 60.000 17.19 0.00 43.80 3.95
1930 4549 2.279120 GCTGCCTGTCGATCTCCG 60.279 66.667 0.00 0.00 40.25 4.63
1934 4553 2.105128 CCTGTCGATCTCCGCCAC 59.895 66.667 0.00 0.00 38.37 5.01
1954 4573 1.000396 AACCTCCCTTGCATCAGCC 60.000 57.895 0.00 0.00 41.13 4.85
1962 4581 2.262471 CTTGCATCAGCCGCAACTCC 62.262 60.000 0.00 0.00 44.13 3.85
2010 4632 1.069022 CCCGTTGTGTTGCATTCTCTG 60.069 52.381 0.00 0.00 0.00 3.35
2014 4636 1.236616 TGTGTTGCATTCTCTGGGCG 61.237 55.000 0.00 0.00 0.00 6.13
2025 4647 2.359975 CTGGGCGGTGGTTCTTCC 60.360 66.667 0.00 0.00 0.00 3.46
2031 4653 4.285851 GGTGGTTCTTCCGAGCAG 57.714 61.111 0.00 0.00 39.52 4.24
2037 4659 0.784778 GTTCTTCCGAGCAGACAACG 59.215 55.000 0.00 0.00 0.00 4.10
2046 4668 1.649171 GAGCAGACAACGATGTACACG 59.351 52.381 13.79 13.79 40.74 4.49
2048 4670 1.649171 GCAGACAACGATGTACACGAG 59.351 52.381 19.80 14.68 40.74 4.18
2065 4687 2.872245 ACGAGGGTGCATTATTCGAATG 59.128 45.455 20.87 6.89 35.42 2.67
2121 4743 6.105333 GCTCCCAGATCATCTTATGACATAC 58.895 44.000 0.00 0.00 43.01 2.39
2144 4766 7.559590 ACTGTCATAATCTTCAATGGTAAGC 57.440 36.000 0.00 0.00 0.00 3.09
2169 4803 1.206371 CCGGTACCCTAACTTCCACTG 59.794 57.143 6.25 0.00 0.00 3.66
2170 4804 1.897802 CGGTACCCTAACTTCCACTGT 59.102 52.381 6.25 0.00 0.00 3.55
2171 4805 2.094338 CGGTACCCTAACTTCCACTGTC 60.094 54.545 6.25 0.00 0.00 3.51
2172 4806 2.235650 GGTACCCTAACTTCCACTGTCC 59.764 54.545 0.00 0.00 0.00 4.02
2173 4807 1.359168 ACCCTAACTTCCACTGTCCC 58.641 55.000 0.00 0.00 0.00 4.46
2174 4808 1.358152 CCCTAACTTCCACTGTCCCA 58.642 55.000 0.00 0.00 0.00 4.37
2175 4809 1.702957 CCCTAACTTCCACTGTCCCAA 59.297 52.381 0.00 0.00 0.00 4.12
2176 4810 2.552373 CCCTAACTTCCACTGTCCCAAC 60.552 54.545 0.00 0.00 0.00 3.77
2177 4811 2.552373 CCTAACTTCCACTGTCCCAACC 60.552 54.545 0.00 0.00 0.00 3.77
2178 4812 0.923358 AACTTCCACTGTCCCAACCA 59.077 50.000 0.00 0.00 0.00 3.67
2179 4813 0.182775 ACTTCCACTGTCCCAACCAC 59.817 55.000 0.00 0.00 0.00 4.16
2180 4814 0.474184 CTTCCACTGTCCCAACCACT 59.526 55.000 0.00 0.00 0.00 4.00
2446 5099 3.332034 CAAGAGGTAAGGGTAAACACCG 58.668 50.000 0.00 0.00 36.14 4.94
2454 7512 2.030862 GTAAACACCGACCGCCCA 59.969 61.111 0.00 0.00 0.00 5.36
2483 7541 7.031975 GGATCTTGAAATTCATTTCTCCACAC 58.968 38.462 12.42 2.35 44.85 3.82
2502 7560 4.639310 CACACACTAGTACCTATCGGTTCT 59.361 45.833 0.00 0.00 42.13 3.01
2509 7567 4.091549 AGTACCTATCGGTTCTTTCACCA 58.908 43.478 0.00 0.00 42.13 4.17
2566 7731 9.755122 TTGCCTTAGCTCTTCTATATGTCTATA 57.245 33.333 0.00 0.00 40.80 1.31
2567 7732 9.179909 TGCCTTAGCTCTTCTATATGTCTATAC 57.820 37.037 0.00 0.00 40.80 1.47
2568 7733 8.339714 GCCTTAGCTCTTCTATATGTCTATACG 58.660 40.741 0.00 0.00 35.50 3.06
2569 7734 9.386010 CCTTAGCTCTTCTATATGTCTATACGT 57.614 37.037 0.00 0.00 0.00 3.57
2817 7983 5.924254 CCTGCGGATTTGATACGAAATACTA 59.076 40.000 0.00 0.00 39.52 1.82
2846 8012 3.568007 TCTGTTTTTCCAGGTTCAATCCG 59.432 43.478 0.00 0.00 33.14 4.18
2870 8036 2.242043 CTCCAAGATGGTTTGCTGGTT 58.758 47.619 0.00 0.00 39.03 3.67
2962 8136 2.023501 AGGAGATCTCTTACTGGCCTGT 60.024 50.000 21.81 20.00 0.00 4.00
3017 8191 5.276348 CGCAGTTGGAATGTTTTGAAACTTC 60.276 40.000 7.97 8.46 39.59 3.01
3097 8271 5.126067 GCCACAGTTTATGACCATAGATGT 58.874 41.667 0.00 0.00 0.00 3.06
3130 8304 9.628500 ACTTTGAAGTAACAAGTAAGGAAAGAT 57.372 29.630 0.00 0.00 37.52 2.40
3187 8361 9.431887 GATGTTGTCCTAGAAACAATACACTTA 57.568 33.333 12.08 0.00 39.57 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
232 233 1.141881 CCGATGCTGCGACTAACCT 59.858 57.895 0.00 0.00 0.00 3.50
308 309 2.290896 CCATGGTAGCCACAAGAAGGAA 60.291 50.000 2.57 0.00 35.80 3.36
383 392 3.260128 TCGTCCTCTTCCTACTTTTTCCC 59.740 47.826 0.00 0.00 0.00 3.97
449 458 2.111384 GGAGAGGACTAGAATGCCACA 58.889 52.381 0.00 0.00 0.00 4.17
550 562 3.149005 ACATTAGGAAAACGCTTGGGA 57.851 42.857 0.00 0.00 0.00 4.37
551 563 5.379732 TTTACATTAGGAAAACGCTTGGG 57.620 39.130 0.00 0.00 0.00 4.12
552 564 6.852664 AGATTTACATTAGGAAAACGCTTGG 58.147 36.000 0.00 0.00 0.00 3.61
591 603 9.498176 AAACTTTTTCCGACACTACACTAATAT 57.502 29.630 0.00 0.00 0.00 1.28
592 604 8.891671 AAACTTTTTCCGACACTACACTAATA 57.108 30.769 0.00 0.00 0.00 0.98
593 605 7.797038 AAACTTTTTCCGACACTACACTAAT 57.203 32.000 0.00 0.00 0.00 1.73
594 606 7.224557 GGTAAACTTTTTCCGACACTACACTAA 59.775 37.037 0.00 0.00 0.00 2.24
595 607 6.701400 GGTAAACTTTTTCCGACACTACACTA 59.299 38.462 0.00 0.00 0.00 2.74
596 608 5.525012 GGTAAACTTTTTCCGACACTACACT 59.475 40.000 0.00 0.00 0.00 3.55
597 609 5.741425 GGTAAACTTTTTCCGACACTACAC 58.259 41.667 0.00 0.00 0.00 2.90
598 610 5.989551 GGTAAACTTTTTCCGACACTACA 57.010 39.130 0.00 0.00 0.00 2.74
607 619 2.481568 CCTCCGTCGGTAAACTTTTTCC 59.518 50.000 11.88 0.00 0.00 3.13
608 620 2.481568 CCCTCCGTCGGTAAACTTTTTC 59.518 50.000 11.88 0.00 0.00 2.29
609 621 2.104622 TCCCTCCGTCGGTAAACTTTTT 59.895 45.455 11.88 0.00 0.00 1.94
610 622 1.693606 TCCCTCCGTCGGTAAACTTTT 59.306 47.619 11.88 0.00 0.00 2.27
611 623 1.274447 CTCCCTCCGTCGGTAAACTTT 59.726 52.381 11.88 0.00 0.00 2.66
612 624 0.893447 CTCCCTCCGTCGGTAAACTT 59.107 55.000 11.88 0.00 0.00 2.66
613 625 0.251519 ACTCCCTCCGTCGGTAAACT 60.252 55.000 11.88 0.00 0.00 2.66
614 626 1.403323 CTACTCCCTCCGTCGGTAAAC 59.597 57.143 11.88 0.00 0.00 2.01
615 627 1.004745 ACTACTCCCTCCGTCGGTAAA 59.995 52.381 11.88 0.00 0.00 2.01
616 628 0.620556 ACTACTCCCTCCGTCGGTAA 59.379 55.000 11.88 0.00 0.00 2.85
617 629 0.620556 AACTACTCCCTCCGTCGGTA 59.379 55.000 11.88 0.00 0.00 4.02
618 630 0.679321 GAACTACTCCCTCCGTCGGT 60.679 60.000 11.88 0.00 0.00 4.69
619 631 0.394080 AGAACTACTCCCTCCGTCGG 60.394 60.000 4.39 4.39 0.00 4.79
620 632 1.401199 GAAGAACTACTCCCTCCGTCG 59.599 57.143 0.00 0.00 0.00 5.12
621 633 2.725637 AGAAGAACTACTCCCTCCGTC 58.274 52.381 0.00 0.00 0.00 4.79
622 634 2.903375 AGAAGAACTACTCCCTCCGT 57.097 50.000 0.00 0.00 0.00 4.69
623 635 3.764972 AGAAAGAAGAACTACTCCCTCCG 59.235 47.826 0.00 0.00 0.00 4.63
624 636 5.748670 AAGAAAGAAGAACTACTCCCTCC 57.251 43.478 0.00 0.00 0.00 4.30
625 637 6.167685 GGAAAGAAAGAAGAACTACTCCCTC 58.832 44.000 0.00 0.00 0.00 4.30
626 638 5.607171 TGGAAAGAAAGAAGAACTACTCCCT 59.393 40.000 0.00 0.00 0.00 4.20
627 639 5.701750 GTGGAAAGAAAGAAGAACTACTCCC 59.298 44.000 0.00 0.00 0.00 4.30
628 640 6.425417 CAGTGGAAAGAAAGAAGAACTACTCC 59.575 42.308 0.00 0.00 0.00 3.85
629 641 7.210873 TCAGTGGAAAGAAAGAAGAACTACTC 58.789 38.462 0.00 0.00 0.00 2.59
630 642 7.125792 TCAGTGGAAAGAAAGAAGAACTACT 57.874 36.000 0.00 0.00 0.00 2.57
631 643 7.711339 TCTTCAGTGGAAAGAAAGAAGAACTAC 59.289 37.037 0.00 0.00 38.67 2.73
638 650 5.297776 CAGCTTCTTCAGTGGAAAGAAAGAA 59.702 40.000 8.03 5.66 31.35 2.52
675 687 3.074412 TGTGGATTCGAAGAAGGCTTTC 58.926 45.455 3.35 0.00 45.90 2.62
687 699 0.171007 AGCGGCAATTTGTGGATTCG 59.829 50.000 1.45 0.00 0.00 3.34
688 700 2.368655 AAGCGGCAATTTGTGGATTC 57.631 45.000 1.45 0.00 0.00 2.52
704 716 3.860536 GTCTGAACAGGAACGAGATAAGC 59.139 47.826 1.93 0.00 0.00 3.09
709 721 2.545952 GCAAGTCTGAACAGGAACGAGA 60.546 50.000 1.93 0.00 0.00 4.04
757 769 1.523758 ATCTGTGTTCGTTTCTGGCC 58.476 50.000 0.00 0.00 0.00 5.36
805 821 2.978978 TCCAGGTGATTCCACTTCTTCA 59.021 45.455 0.00 0.00 42.77 3.02
820 836 0.988832 TTTATTGTCCCGCTCCAGGT 59.011 50.000 0.00 0.00 0.00 4.00
827 843 3.813724 GAGGACCTTATTTATTGTCCCGC 59.186 47.826 0.00 0.00 46.80 6.13
828 844 5.070580 AGAGAGGACCTTATTTATTGTCCCG 59.929 44.000 0.00 0.00 46.80 5.14
829 845 6.464607 GGAGAGAGGACCTTATTTATTGTCCC 60.465 46.154 0.00 0.00 46.80 4.46
830 846 6.327887 AGGAGAGAGGACCTTATTTATTGTCC 59.672 42.308 0.00 0.00 46.12 4.02
831 847 7.289084 AGAGGAGAGAGGACCTTATTTATTGTC 59.711 40.741 0.00 0.00 36.57 3.18
832 848 7.070571 CAGAGGAGAGAGGACCTTATTTATTGT 59.929 40.741 0.00 0.00 36.57 2.71
833 849 7.070571 ACAGAGGAGAGAGGACCTTATTTATTG 59.929 40.741 0.00 0.00 36.57 1.90
834 850 7.136203 ACAGAGGAGAGAGGACCTTATTTATT 58.864 38.462 0.00 0.00 36.57 1.40
835 851 6.688554 ACAGAGGAGAGAGGACCTTATTTAT 58.311 40.000 0.00 0.00 36.57 1.40
836 852 6.093617 ACAGAGGAGAGAGGACCTTATTTA 57.906 41.667 0.00 0.00 36.57 1.40
837 853 4.954089 ACAGAGGAGAGAGGACCTTATTT 58.046 43.478 0.00 0.00 36.57 1.40
838 854 4.618378 ACAGAGGAGAGAGGACCTTATT 57.382 45.455 0.00 0.00 36.57 1.40
839 855 4.618378 AACAGAGGAGAGAGGACCTTAT 57.382 45.455 0.00 0.00 36.57 1.73
840 856 4.090090 CAAACAGAGGAGAGAGGACCTTA 58.910 47.826 0.00 0.00 36.57 2.69
841 857 2.903135 CAAACAGAGGAGAGAGGACCTT 59.097 50.000 0.00 0.00 36.57 3.50
842 858 2.158234 ACAAACAGAGGAGAGAGGACCT 60.158 50.000 0.00 0.00 39.41 3.85
843 859 2.028567 CACAAACAGAGGAGAGAGGACC 60.029 54.545 0.00 0.00 0.00 4.46
844 860 2.630580 ACACAAACAGAGGAGAGAGGAC 59.369 50.000 0.00 0.00 0.00 3.85
845 861 2.894126 GACACAAACAGAGGAGAGAGGA 59.106 50.000 0.00 0.00 0.00 3.71
846 862 2.028567 GGACACAAACAGAGGAGAGAGG 60.029 54.545 0.00 0.00 0.00 3.69
847 863 2.352225 CGGACACAAACAGAGGAGAGAG 60.352 54.545 0.00 0.00 0.00 3.20
848 864 1.613925 CGGACACAAACAGAGGAGAGA 59.386 52.381 0.00 0.00 0.00 3.10
849 865 1.937108 GCGGACACAAACAGAGGAGAG 60.937 57.143 0.00 0.00 0.00 3.20
850 866 0.033504 GCGGACACAAACAGAGGAGA 59.966 55.000 0.00 0.00 0.00 3.71
851 867 0.951040 GGCGGACACAAACAGAGGAG 60.951 60.000 0.00 0.00 0.00 3.69
852 868 1.070786 GGCGGACACAAACAGAGGA 59.929 57.895 0.00 0.00 0.00 3.71
853 869 0.951040 GAGGCGGACACAAACAGAGG 60.951 60.000 0.00 0.00 0.00 3.69
854 870 0.951040 GGAGGCGGACACAAACAGAG 60.951 60.000 0.00 0.00 0.00 3.35
855 871 1.070786 GGAGGCGGACACAAACAGA 59.929 57.895 0.00 0.00 0.00 3.41
856 872 0.535102 AAGGAGGCGGACACAAACAG 60.535 55.000 0.00 0.00 0.00 3.16
857 873 0.759959 TAAGGAGGCGGACACAAACA 59.240 50.000 0.00 0.00 0.00 2.83
887 903 0.322456 TCGCCAGTGGGAAGAATTGG 60.322 55.000 12.15 0.00 35.59 3.16
890 906 2.705658 TGATATCGCCAGTGGGAAGAAT 59.294 45.455 12.15 2.87 36.96 2.40
984 1000 1.153489 CATGGAGGTCAGCGGTCAG 60.153 63.158 0.00 0.00 0.00 3.51
985 1001 1.609210 TCATGGAGGTCAGCGGTCA 60.609 57.895 0.00 0.00 0.00 4.02
986 1002 1.153549 GTCATGGAGGTCAGCGGTC 60.154 63.158 0.00 0.00 0.00 4.79
987 1003 2.982130 GTCATGGAGGTCAGCGGT 59.018 61.111 0.00 0.00 0.00 5.68
988 1004 2.202797 CGTCATGGAGGTCAGCGG 60.203 66.667 0.00 0.00 0.00 5.52
989 1005 1.517257 GTCGTCATGGAGGTCAGCG 60.517 63.158 0.00 0.00 0.00 5.18
990 1006 1.517257 CGTCGTCATGGAGGTCAGC 60.517 63.158 0.00 0.00 0.00 4.26
991 1007 0.099613 CTCGTCGTCATGGAGGTCAG 59.900 60.000 0.00 0.00 0.00 3.51
992 1008 1.934220 GCTCGTCGTCATGGAGGTCA 61.934 60.000 0.00 0.00 0.00 4.02
1327 3946 0.946221 CTGTCCTTGTCCAGCGTGAC 60.946 60.000 2.13 2.13 35.77 3.67
1380 3999 2.179517 GGGAGCTCGACAGTGACG 59.820 66.667 7.83 8.75 0.00 4.35
1516 4135 1.290203 CGCGCACTCATAACCATCTT 58.710 50.000 8.75 0.00 0.00 2.40
1556 4175 1.135112 TGATGTCTCGATGGTTCACCG 60.135 52.381 0.00 0.00 39.43 4.94
1562 4181 0.101399 GAGCGTGATGTCTCGATGGT 59.899 55.000 8.47 0.00 35.14 3.55
1577 4196 3.357079 GCAGGGTGTTGTGGAGCG 61.357 66.667 0.00 0.00 0.00 5.03
1629 4248 1.350706 GCTGAACGAGCTGCTCTGAC 61.351 60.000 25.59 16.29 45.21 3.51
1656 4275 4.225703 GCCCCGCATGGATTTGGC 62.226 66.667 0.00 0.00 37.49 4.52
1677 4296 4.794439 TGCGGGACATGAGCGACG 62.794 66.667 0.00 0.00 0.00 5.12
1694 4313 3.513912 TCTGAATATGTGGACCAACTCGT 59.486 43.478 0.00 0.00 0.00 4.18
1695 4314 4.123497 TCTGAATATGTGGACCAACTCG 57.877 45.455 0.00 0.00 0.00 4.18
1704 4323 6.295575 GGAAGTAGGAGGATCTGAATATGTGG 60.296 46.154 0.00 0.00 33.73 4.17
1705 4324 6.496565 AGGAAGTAGGAGGATCTGAATATGTG 59.503 42.308 0.00 0.00 33.73 3.21
1758 4377 3.945434 CGATGATGCTGCACGGCC 61.945 66.667 3.57 0.00 0.00 6.13
1767 4386 1.228367 ATGGCCCCTTCGATGATGC 60.228 57.895 0.00 2.07 0.00 3.91
1787 4406 0.250209 CTCCATCTCAGGGCGAATGG 60.250 60.000 0.00 0.00 0.00 3.16
1792 4411 2.362369 ACCACTCCATCTCAGGGCG 61.362 63.158 0.00 0.00 0.00 6.13
1795 4414 1.222936 GCCACCACTCCATCTCAGG 59.777 63.158 0.00 0.00 0.00 3.86
1854 4473 3.470888 ACCGGAATGAGCTCCCCG 61.471 66.667 23.95 23.95 41.47 5.73
1887 4506 2.494918 CCTAGGAACACGGCCTCG 59.505 66.667 1.05 0.00 43.02 4.63
1894 4513 1.675116 GCGGTCTTTCCCTAGGAACAC 60.675 57.143 11.48 0.00 41.87 3.32
1930 4549 3.056328 GCAAGGGAGGTTCGTGGC 61.056 66.667 0.00 0.00 0.00 5.01
1934 4553 1.372087 GCTGATGCAAGGGAGGTTCG 61.372 60.000 0.00 0.00 39.41 3.95
1962 4581 9.093970 TCCTTGTTTGATACATATGAGTAAACG 57.906 33.333 10.38 4.38 36.44 3.60
2014 4636 0.670854 GTCTGCTCGGAAGAACCACC 60.671 60.000 0.00 0.00 41.32 4.61
2025 4647 1.649171 GTGTACATCGTTGTCTGCTCG 59.351 52.381 1.61 0.00 37.28 5.03
2031 4653 1.068055 ACCCTCGTGTACATCGTTGTC 60.068 52.381 1.61 0.00 37.28 3.18
2037 4659 2.024176 AATGCACCCTCGTGTACATC 57.976 50.000 0.00 0.00 42.39 3.06
2046 4668 4.380531 TCTCATTCGAATAATGCACCCTC 58.619 43.478 10.97 0.00 0.00 4.30
2048 4670 4.083110 CCATCTCATTCGAATAATGCACCC 60.083 45.833 10.97 0.00 0.00 4.61
2121 4743 7.558161 TGCTTACCATTGAAGATTATGACAG 57.442 36.000 0.00 0.00 0.00 3.51
2169 4803 1.034838 TGTTGCACAGTGGTTGGGAC 61.035 55.000 1.84 0.00 28.76 4.46
2170 4804 0.106268 ATGTTGCACAGTGGTTGGGA 60.106 50.000 1.84 0.00 28.76 4.37
2171 4805 0.032403 CATGTTGCACAGTGGTTGGG 59.968 55.000 1.84 0.00 0.00 4.12
2172 4806 1.031235 TCATGTTGCACAGTGGTTGG 58.969 50.000 1.84 0.00 0.00 3.77
2173 4807 3.054166 CAATCATGTTGCACAGTGGTTG 58.946 45.455 1.84 3.79 28.96 3.77
2174 4808 2.546373 GCAATCATGTTGCACAGTGGTT 60.546 45.455 20.83 0.00 44.34 3.67
2175 4809 1.000060 GCAATCATGTTGCACAGTGGT 60.000 47.619 20.83 0.00 44.34 4.16
2176 4810 1.670674 GGCAATCATGTTGCACAGTGG 60.671 52.381 24.50 0.00 46.58 4.00
2177 4811 1.271379 AGGCAATCATGTTGCACAGTG 59.729 47.619 24.50 0.00 46.58 3.66
2178 4812 1.624336 AGGCAATCATGTTGCACAGT 58.376 45.000 24.50 10.63 46.58 3.55
2179 4813 3.853831 TTAGGCAATCATGTTGCACAG 57.146 42.857 24.50 1.21 46.58 3.66
2180 4814 3.510753 ACATTAGGCAATCATGTTGCACA 59.489 39.130 24.50 14.15 46.58 4.57
2446 5099 1.416401 TCAAGATCCTAATGGGCGGTC 59.584 52.381 0.00 0.00 34.39 4.79
2454 7512 9.705103 TGGAGAAATGAATTTCAAGATCCTAAT 57.295 29.630 16.06 0.00 46.50 1.73
2502 7560 3.620488 GGCATGGATAGAAGTGGTGAAA 58.380 45.455 0.00 0.00 0.00 2.69
2509 7567 3.270877 GACAAACGGCATGGATAGAAGT 58.729 45.455 0.00 0.00 0.00 3.01
2568 7733 1.895131 TCTACACAAAGGGGACGGTAC 59.105 52.381 0.00 0.00 0.00 3.34
2569 7734 2.307496 TCTACACAAAGGGGACGGTA 57.693 50.000 0.00 0.00 0.00 4.02
2635 7800 6.705863 AAGCTCTTCAAGTCAAGTTGATTT 57.294 33.333 9.18 8.39 36.34 2.17
2817 7983 5.714806 TGAACCTGGAAAAACAGAAAAGAGT 59.285 36.000 0.00 0.00 40.97 3.24
2846 8012 2.094854 CAGCAAACCATCTTGGAGCTTC 60.095 50.000 0.00 0.00 40.96 3.86
2962 8136 5.791336 AGATATACTGATTTGTGCGAGGA 57.209 39.130 0.00 0.00 0.00 3.71
3017 8191 7.445402 TCAGTTCCTGTCTTTCCAAGAAAATAG 59.555 37.037 0.00 0.00 39.67 1.73
3029 8203 4.965200 AGCTTACTCAGTTCCTGTCTTT 57.035 40.909 0.00 0.00 32.61 2.52
3036 8210 9.216117 TCTTAATTAACAAGCTTACTCAGTTCC 57.784 33.333 0.00 0.00 0.00 3.62
3130 8304 9.223099 CTAATGAGCACATCCAAATGTATATGA 57.777 33.333 0.00 0.00 44.41 2.15
3191 8365 6.775142 TCTCTAGAAATGACGAGAGAATCCAT 59.225 38.462 0.00 0.00 42.44 3.41
3199 8373 7.883391 ATTAAGGTCTCTAGAAATGACGAGA 57.117 36.000 0.00 0.00 0.00 4.04
3367 8549 1.115326 AACAGGGGGAAAGCAACTGC 61.115 55.000 0.00 0.00 42.49 4.40
3369 8551 2.174685 AAAACAGGGGGAAAGCAACT 57.825 45.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.