Multiple sequence alignment - TraesCS1A01G214000

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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 TraesCS1A01G214000 chr1A 100.000 3115 0 0 1 3115 377206890 377210004 0.000000e+00 5753.0
1 TraesCS1A01G214000 chr1A 86.667 105 8 3 1134 1238 22682950 22682852 9.130000e-21 111.0
2 TraesCS1A01G214000 chr1A 100.000 30 0 0 654 683 377207475 377207504 4.340000e-04 56.5
3 TraesCS1A01G214000 chr1A 100.000 30 0 0 586 615 377207543 377207572 4.340000e-04 56.5
4 TraesCS1A01G214000 chr1D 90.418 2463 84 51 746 3115 302690706 302693109 0.000000e+00 3101.0
5 TraesCS1A01G214000 chr1D 95.565 451 13 4 1 445 302689946 302690395 0.000000e+00 715.0
6 TraesCS1A01G214000 chr1D 85.816 282 27 9 449 723 302690437 302690712 1.410000e-73 287.0
7 TraesCS1A01G214000 chr1D 90.909 55 5 0 1131 1185 11789267 11789321 1.200000e-09 75.0
8 TraesCS1A01G214000 chr1D 100.000 30 0 0 654 683 302690569 302690598 4.340000e-04 56.5
9 TraesCS1A01G214000 chr1B 89.394 1914 73 50 758 2588 409598678 409600544 0.000000e+00 2290.0
10 TraesCS1A01G214000 chr1B 87.447 470 17 13 2676 3115 409600589 409601046 1.290000e-138 503.0
11 TraesCS1A01G214000 chr1B 90.347 259 25 0 1584 1842 668439509 668439251 1.070000e-89 340.0
12 TraesCS1A01G214000 chr1B 91.371 197 14 3 463 657 409598408 409598603 1.840000e-67 267.0
13 TraesCS1A01G214000 chr5B 86.072 359 49 1 1548 1906 419524808 419525165 4.870000e-103 385.0
14 TraesCS1A01G214000 chr5B 88.973 263 29 0 1580 1842 458926805 458927067 3.000000e-85 326.0
15 TraesCS1A01G214000 chr2B 90.494 263 25 0 1580 1842 699046148 699046410 6.390000e-92 348.0
16 TraesCS1A01G214000 chr7B 90.114 263 26 0 1580 1842 104245479 104245741 2.970000e-90 342.0
17 TraesCS1A01G214000 chr7B 90.385 52 3 2 1289 1339 714430798 714430748 2.000000e-07 67.6
18 TraesCS1A01G214000 chr4B 89.734 263 26 1 1580 1842 7048819 7049080 4.980000e-88 335.0
19 TraesCS1A01G214000 chr2D 87.189 281 28 3 1562 1842 92835253 92834981 2.330000e-81 313.0
20 TraesCS1A01G214000 chr2D 83.333 108 12 3 1136 1243 114648229 114648330 9.200000e-16 95.3
21 TraesCS1A01G214000 chr3D 90.041 241 15 6 939 1178 68387145 68386913 1.400000e-78 303.0
22 TraesCS1A01G214000 chr5A 89.552 67 7 0 1136 1202 502394924 502394990 5.530000e-13 86.1


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 TraesCS1A01G214000 chr1A 377206890 377210004 3114 False 1955.333333 5753 100.00000 1 3115 3 chr1A.!!$F1 3114
1 TraesCS1A01G214000 chr1D 302689946 302693109 3163 False 1039.875000 3101 92.94975 1 3115 4 chr1D.!!$F2 3114
2 TraesCS1A01G214000 chr1B 409598408 409601046 2638 False 1020.000000 2290 89.40400 463 3115 3 chr1B.!!$F1 2652

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
748 801 0.041238 TGAGAGGAGGGTGATTCCGT 59.959 55.0 0.0 0.0 39.77 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2536 2674 0.193574 TCAGTTCCCAAGGGAGGAGT 59.806 55.0 8.06 0.0 46.06 3.85 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
106 107 6.677913 TCCTTGATCTTTTCGATGTTTTTCC 58.322 36.000 0.00 0.00 30.84 3.13
107 108 6.264292 TCCTTGATCTTTTCGATGTTTTTCCA 59.736 34.615 0.00 0.00 30.84 3.53
158 165 6.859112 AGAAAGAGAGCTATGACACCTTAA 57.141 37.500 0.00 0.00 0.00 1.85
185 192 1.899814 ACGTCTGGCAGATCCAAAGTA 59.100 47.619 21.84 0.00 46.01 2.24
193 200 4.141846 TGGCAGATCCAAAGTAGATGTCTC 60.142 45.833 0.00 0.00 43.21 3.36
211 218 4.274950 TGTCTCACCGTTCTTTCCATTTTC 59.725 41.667 0.00 0.00 0.00 2.29
256 263 1.993948 GAGTCCACCTACCCCCACC 60.994 68.421 0.00 0.00 0.00 4.61
290 297 6.166982 TCGGTTTCCTTTTTCACATTTGTTT 58.833 32.000 0.00 0.00 0.00 2.83
385 392 2.739913 TCGTTATTTTGAGAACTGGCGG 59.260 45.455 0.00 0.00 0.00 6.13
425 432 1.681538 CTTCGGCAGAGTAGAGGCTA 58.318 55.000 0.00 0.00 0.00 3.93
445 452 1.301423 TGTTTCCTTTTCACGACCGG 58.699 50.000 0.00 0.00 0.00 5.28
448 455 1.301423 TTCCTTTTCACGACCGGTTG 58.699 50.000 20.86 20.86 0.00 3.77
449 456 0.533308 TCCTTTTCACGACCGGTTGG 60.533 55.000 25.74 15.35 42.84 3.77
459 504 4.591038 CCGGTTGGTGAAAGGGTT 57.409 55.556 0.00 0.00 0.00 4.11
467 512 0.956633 GGTGAAAGGGTTCGTTTCCC 59.043 55.000 9.58 4.63 44.90 3.97
575 620 9.472361 TCCTAAATCGACCGAGAAAATTAATAG 57.528 33.333 0.00 0.00 0.00 1.73
657 704 6.687958 CGTGTACAGAAATGTTTTTAACGGTT 59.312 34.615 0.00 0.00 0.00 4.44
659 706 9.500864 GTGTACAGAAATGTTTTTAACGGTTAA 57.499 29.630 9.18 9.18 0.00 2.01
678 725 6.989659 GGTTAAATACCATCCGATCTAGACA 58.010 40.000 0.00 0.00 46.92 3.41
679 726 6.867293 GGTTAAATACCATCCGATCTAGACAC 59.133 42.308 0.00 0.00 46.92 3.67
680 727 4.768130 AATACCATCCGATCTAGACACG 57.232 45.455 12.37 12.37 0.00 4.49
681 728 2.343484 ACCATCCGATCTAGACACGA 57.657 50.000 18.58 5.13 0.00 4.35
682 729 2.222886 ACCATCCGATCTAGACACGAG 58.777 52.381 18.58 10.98 0.00 4.18
683 730 1.537638 CCATCCGATCTAGACACGAGG 59.462 57.143 18.58 13.93 0.00 4.63
684 731 2.495084 CATCCGATCTAGACACGAGGA 58.505 52.381 18.58 12.36 0.00 3.71
724 777 2.096318 GCAACGAATAAAACCGAACGGA 60.096 45.455 20.14 0.00 38.96 4.69
727 780 3.248266 ACGAATAAAACCGAACGGAGAG 58.752 45.455 20.14 4.88 38.96 3.20
729 782 4.110482 CGAATAAAACCGAACGGAGAGAT 58.890 43.478 20.14 5.18 38.96 2.75
730 783 4.026804 CGAATAAAACCGAACGGAGAGATG 60.027 45.833 20.14 0.00 38.96 2.90
731 784 4.730949 ATAAAACCGAACGGAGAGATGA 57.269 40.909 20.14 0.00 38.96 2.92
732 785 2.656560 AAACCGAACGGAGAGATGAG 57.343 50.000 20.14 0.00 38.96 2.90
733 786 1.835494 AACCGAACGGAGAGATGAGA 58.165 50.000 20.14 0.00 38.96 3.27
734 787 1.384525 ACCGAACGGAGAGATGAGAG 58.615 55.000 20.14 0.00 38.96 3.20
735 788 0.665835 CCGAACGGAGAGATGAGAGG 59.334 60.000 7.53 0.00 37.50 3.69
736 789 1.669604 CGAACGGAGAGATGAGAGGA 58.330 55.000 0.00 0.00 0.00 3.71
737 790 1.601903 CGAACGGAGAGATGAGAGGAG 59.398 57.143 0.00 0.00 0.00 3.69
738 791 1.953686 GAACGGAGAGATGAGAGGAGG 59.046 57.143 0.00 0.00 0.00 4.30
739 792 0.184933 ACGGAGAGATGAGAGGAGGG 59.815 60.000 0.00 0.00 0.00 4.30
740 793 0.184933 CGGAGAGATGAGAGGAGGGT 59.815 60.000 0.00 0.00 0.00 4.34
741 794 1.703411 GGAGAGATGAGAGGAGGGTG 58.297 60.000 0.00 0.00 0.00 4.61
742 795 1.216678 GGAGAGATGAGAGGAGGGTGA 59.783 57.143 0.00 0.00 0.00 4.02
743 796 2.158325 GGAGAGATGAGAGGAGGGTGAT 60.158 54.545 0.00 0.00 0.00 3.06
744 797 3.575805 GAGAGATGAGAGGAGGGTGATT 58.424 50.000 0.00 0.00 0.00 2.57
745 798 3.573967 GAGAGATGAGAGGAGGGTGATTC 59.426 52.174 0.00 0.00 0.00 2.52
746 799 2.632512 GAGATGAGAGGAGGGTGATTCC 59.367 54.545 0.00 0.00 34.83 3.01
747 800 1.342819 GATGAGAGGAGGGTGATTCCG 59.657 57.143 0.00 0.00 39.77 4.30
748 801 0.041238 TGAGAGGAGGGTGATTCCGT 59.959 55.000 0.00 0.00 39.77 4.69
749 802 1.286849 TGAGAGGAGGGTGATTCCGTA 59.713 52.381 0.00 0.00 39.77 4.02
750 803 2.291996 TGAGAGGAGGGTGATTCCGTAA 60.292 50.000 0.00 0.00 39.77 3.18
751 804 2.101082 GAGAGGAGGGTGATTCCGTAAC 59.899 54.545 0.00 0.00 39.77 2.50
752 805 0.822164 AGGAGGGTGATTCCGTAACG 59.178 55.000 0.00 0.00 39.77 3.18
784 837 2.780595 CACCGGTGCCTTGGAATAG 58.219 57.895 24.02 0.00 0.00 1.73
848 916 2.552315 CCGTCCCAAATAAATCCATCCG 59.448 50.000 0.00 0.00 0.00 4.18
953 1027 2.064014 GACAAAAATCCAAGCTGCAGC 58.936 47.619 31.53 31.53 42.49 5.25
1474 1571 2.359975 CGGTCCTTCCTGGCAACC 60.360 66.667 0.00 0.00 35.26 3.77
1603 1700 3.822192 CCGGACGCGTCATCCTCA 61.822 66.667 37.26 0.00 33.70 3.86
1606 1703 1.736586 GGACGCGTCATCCTCATCT 59.263 57.895 37.26 0.00 33.03 2.90
1675 1775 4.335647 AGCAGCTGGTGGTTCCCG 62.336 66.667 19.45 0.00 30.62 5.14
1702 1802 4.511246 CCGGCCAGGCACCATCAT 62.511 66.667 15.19 0.00 0.00 2.45
1714 1814 2.745308 CCATCATCACCCCCAGCGA 61.745 63.158 0.00 0.00 0.00 4.93
1995 2098 1.218316 CTCCTCTTTTCCCCCGTCG 59.782 63.158 0.00 0.00 0.00 5.12
2036 2139 2.352715 CCTCCCGCAAAATTTGACCTTC 60.353 50.000 10.26 0.00 0.00 3.46
2115 2218 8.898983 AATCAAATGAAGCTGTTTTGTTTTTG 57.101 26.923 13.05 5.15 33.24 2.44
2135 2238 2.685897 TGAGTTTCTTGTTTGAACGGGG 59.314 45.455 0.00 0.00 0.00 5.73
2190 2294 3.063084 GACGAGACGACCTGGGCT 61.063 66.667 0.00 0.00 0.00 5.19
2192 2296 4.135153 CGAGACGACCTGGGCTGG 62.135 72.222 0.00 0.00 0.00 4.85
2193 2297 3.775654 GAGACGACCTGGGCTGGG 61.776 72.222 0.00 0.00 0.00 4.45
2253 2359 1.609072 TGTGTTCTCTGACCTCTGACG 59.391 52.381 0.00 0.00 0.00 4.35
2311 2417 4.782252 TTTATTTACGTGCGGCTGTATC 57.218 40.909 0.00 0.00 0.00 2.24
2339 2445 4.731612 CTCGTGAGCTGCTGCCGT 62.732 66.667 7.01 0.00 40.80 5.68
2378 2484 8.764287 GTTTTTCCATTCATGTTTCGAATTCTT 58.236 29.630 0.00 0.00 30.65 2.52
2381 2487 5.709631 TCCATTCATGTTTCGAATTCTTGGA 59.290 36.000 0.00 3.36 30.65 3.53
2384 2490 6.875948 TTCATGTTTCGAATTCTTGGAAGA 57.124 33.333 0.00 0.00 0.00 2.87
2385 2491 6.241207 TCATGTTTCGAATTCTTGGAAGAC 57.759 37.500 0.00 0.00 34.13 3.01
2387 2493 4.373527 TGTTTCGAATTCTTGGAAGACGA 58.626 39.130 0.00 0.00 34.13 4.20
2399 2505 2.287427 TGGAAGACGAAAGACGACTGTC 60.287 50.000 0.00 0.00 44.76 3.51
2418 2524 3.248043 AGCGGCATTGTTTAGCTGA 57.752 47.368 1.45 0.00 39.47 4.26
2419 2525 1.089920 AGCGGCATTGTTTAGCTGAG 58.910 50.000 1.45 0.00 39.47 3.35
2450 2576 2.045045 CTTCTCCCGGGCAATGCA 60.045 61.111 18.49 0.00 0.00 3.96
2457 2583 2.048023 CCGGGCAATGCATGTGTCT 61.048 57.895 7.79 0.00 0.00 3.41
2474 2608 7.482743 GCATGTGTCTGTCAGTATGTTTTATTG 59.517 37.037 0.00 0.00 37.40 1.90
2479 2613 9.944663 TGTCTGTCAGTATGTTTTATTGTTTTC 57.055 29.630 0.00 0.00 37.40 2.29
2502 2640 9.691362 TTTCTAAAAAGTGGATAAAGCATTGTC 57.309 29.630 0.00 0.00 0.00 3.18
2515 2653 0.452987 CATTGTCCTGGACATTGGCG 59.547 55.000 30.51 16.18 42.40 5.69
2536 2674 2.499205 CGAGGGCGGTGATTAGCA 59.501 61.111 0.00 0.00 34.54 3.49
2593 2755 0.325110 TGAGAGAAGCTGGAGAGGGG 60.325 60.000 0.00 0.00 0.00 4.79
2657 2819 9.322773 CGATCATGAGCATACATAAAGGATAAT 57.677 33.333 12.15 0.00 0.00 1.28
2659 2821 8.272545 TCATGAGCATACATAAAGGATAATGC 57.727 34.615 0.00 0.00 36.79 3.56
2660 2822 6.726258 TGAGCATACATAAAGGATAATGCG 57.274 37.500 0.00 0.00 39.47 4.73
2661 2823 6.463360 TGAGCATACATAAAGGATAATGCGA 58.537 36.000 0.00 0.00 39.47 5.10
2662 2824 7.105588 TGAGCATACATAAAGGATAATGCGAT 58.894 34.615 0.00 0.00 39.47 4.58
2663 2825 7.064966 TGAGCATACATAAAGGATAATGCGATG 59.935 37.037 0.00 0.00 39.47 3.84
2664 2826 7.105588 AGCATACATAAAGGATAATGCGATGA 58.894 34.615 0.00 0.00 39.47 2.92
2665 2827 7.065085 AGCATACATAAAGGATAATGCGATGAC 59.935 37.037 0.00 0.00 39.47 3.06
2666 2828 7.148423 GCATACATAAAGGATAATGCGATGACA 60.148 37.037 0.00 0.00 30.59 3.58
2667 2829 8.886719 CATACATAAAGGATAATGCGATGACAT 58.113 33.333 0.00 0.00 0.00 3.06
2668 2830 7.369803 ACATAAAGGATAATGCGATGACATC 57.630 36.000 5.28 5.28 0.00 3.06
2669 2831 6.936335 ACATAAAGGATAATGCGATGACATCA 59.064 34.615 15.58 0.00 0.00 3.07
2670 2832 5.679734 AAAGGATAATGCGATGACATCAC 57.320 39.130 15.58 6.38 0.00 3.06
2671 2833 3.668447 AGGATAATGCGATGACATCACC 58.332 45.455 15.58 6.24 0.00 4.02
2672 2834 3.071457 AGGATAATGCGATGACATCACCA 59.929 43.478 15.58 11.40 0.00 4.17
2673 2835 4.005650 GGATAATGCGATGACATCACCAT 58.994 43.478 15.58 13.01 0.00 3.55
2674 2836 4.456911 GGATAATGCGATGACATCACCATT 59.543 41.667 23.66 23.66 35.97 3.16
2684 2846 6.260714 CGATGACATCACCATTAGGATGAAAA 59.739 38.462 15.58 0.00 42.73 2.29
2783 2948 0.244994 CGCATATCCCTTCTCCTCCG 59.755 60.000 0.00 0.00 0.00 4.63
2789 2954 4.856607 CCTTCTCCTCCGCGACGC 62.857 72.222 8.23 10.49 0.00 5.19
2802 2977 2.798262 GACGCGCTACAACGACGT 60.798 61.111 5.73 0.00 44.18 4.34
2803 2978 2.761941 GACGCGCTACAACGACGTC 61.762 63.158 5.73 5.18 46.46 4.34
2819 2994 1.536073 CGTCTCCTCTGTGCTTCCCA 61.536 60.000 0.00 0.00 0.00 4.37
2821 2996 1.280421 GTCTCCTCTGTGCTTCCCATT 59.720 52.381 0.00 0.00 0.00 3.16
2822 2997 1.988107 TCTCCTCTGTGCTTCCCATTT 59.012 47.619 0.00 0.00 0.00 2.32
2823 2998 2.089980 CTCCTCTGTGCTTCCCATTTG 58.910 52.381 0.00 0.00 0.00 2.32
2824 2999 1.425066 TCCTCTGTGCTTCCCATTTGT 59.575 47.619 0.00 0.00 0.00 2.83
2825 3000 2.642311 TCCTCTGTGCTTCCCATTTGTA 59.358 45.455 0.00 0.00 0.00 2.41
2826 3001 3.012518 CCTCTGTGCTTCCCATTTGTAG 58.987 50.000 0.00 0.00 0.00 2.74
2862 3047 5.688621 CACTATTACTACGTTGTGTGTGTGT 59.311 40.000 13.03 2.00 0.00 3.72
2864 3049 2.373540 ACTACGTTGTGTGTGTGTGT 57.626 45.000 0.73 0.00 0.00 3.72
2866 3051 1.996898 CTACGTTGTGTGTGTGTGTGT 59.003 47.619 0.00 0.00 0.00 3.72
2887 3072 1.823295 GCTCCGGTCATCTAGGCAA 59.177 57.895 0.00 0.00 0.00 4.52
2888 3073 0.249657 GCTCCGGTCATCTAGGCAAG 60.250 60.000 0.00 0.00 0.00 4.01
2889 3074 0.390860 CTCCGGTCATCTAGGCAAGG 59.609 60.000 0.00 0.00 0.00 3.61
2890 3075 1.227674 CCGGTCATCTAGGCAAGGC 60.228 63.158 0.00 0.00 0.00 4.35
2891 3076 1.522092 CGGTCATCTAGGCAAGGCA 59.478 57.895 0.00 0.00 0.00 4.75
2937 3122 1.449246 CCTCTTTCCTCGCAGCCAG 60.449 63.158 0.00 0.00 0.00 4.85
3022 3217 2.987125 GCGTCCTTGGCCTAGGAA 59.013 61.111 33.70 17.48 45.62 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.159366 CCGATATCGATTTCTCCCGAGG 60.159 54.545 26.32 0.81 43.02 4.63
12 13 1.630148 GCCGATATCGATTTCTCCCG 58.370 55.000 26.32 7.23 43.02 5.14
113 114 1.302192 GTAGGCGGCAAACCAGTCA 60.302 57.895 13.08 0.00 34.57 3.41
114 115 0.887387 TTGTAGGCGGCAAACCAGTC 60.887 55.000 13.08 0.00 34.57 3.51
158 165 0.603569 ATCTGCCAGACGTTCGAAGT 59.396 50.000 0.00 0.00 0.00 3.01
185 192 2.632996 TGGAAAGAACGGTGAGACATCT 59.367 45.455 0.00 0.00 0.00 2.90
193 200 3.067461 TGTGGAAAATGGAAAGAACGGTG 59.933 43.478 0.00 0.00 0.00 4.94
211 218 7.118101 CACCCATTCTCAAAATAATTGTTGTGG 59.882 37.037 5.38 3.20 0.00 4.17
290 297 4.508461 TGACTCGATCGGTTCTAAAACA 57.492 40.909 16.41 2.15 37.10 2.83
364 371 2.739913 CCGCCAGTTCTCAAAATAACGA 59.260 45.455 0.00 0.00 0.00 3.85
385 392 3.581141 AAGGGGAGGGGGTGGACTC 62.581 68.421 0.00 0.00 0.00 3.36
425 432 1.877443 CCGGTCGTGAAAAGGAAACAT 59.123 47.619 0.00 0.00 0.00 2.71
445 452 2.223641 GGAAACGAACCCTTTCACCAAC 60.224 50.000 0.00 0.00 30.42 3.77
448 455 0.956633 GGGAAACGAACCCTTTCACC 59.043 55.000 0.00 0.00 43.65 4.02
459 504 1.064357 GTGCGTGAAAAAGGGAAACGA 59.936 47.619 0.00 0.00 36.38 3.85
467 512 5.260140 TCTAAAAGAACGTGCGTGAAAAAG 58.740 37.500 0.00 0.00 0.00 2.27
495 540 4.201881 GCGGATCTTATTTTTGTACGCCTT 60.202 41.667 0.00 0.00 38.71 4.35
497 542 3.064271 TGCGGATCTTATTTTTGTACGCC 59.936 43.478 0.00 0.00 43.34 5.68
499 544 7.734538 AAATTGCGGATCTTATTTTTGTACG 57.265 32.000 0.00 0.00 0.00 3.67
502 547 9.868277 TCAATAAATTGCGGATCTTATTTTTGT 57.132 25.926 0.00 0.00 37.68 2.83
657 704 5.999600 TCGTGTCTAGATCGGATGGTATTTA 59.000 40.000 16.28 0.00 0.00 1.40
659 706 4.395625 TCGTGTCTAGATCGGATGGTATT 58.604 43.478 16.28 0.00 0.00 1.89
660 707 4.004314 CTCGTGTCTAGATCGGATGGTAT 58.996 47.826 16.28 0.00 0.00 2.73
662 709 2.222886 CTCGTGTCTAGATCGGATGGT 58.777 52.381 16.28 0.00 0.00 3.55
664 711 2.495084 TCCTCGTGTCTAGATCGGATG 58.505 52.381 16.28 9.48 0.00 3.51
665 712 2.932855 TCCTCGTGTCTAGATCGGAT 57.067 50.000 16.28 0.00 0.00 4.18
667 714 2.773487 AGATCCTCGTGTCTAGATCGG 58.227 52.381 16.28 9.55 40.06 4.18
668 715 6.334989 AGTATAGATCCTCGTGTCTAGATCG 58.665 44.000 12.10 12.10 40.06 3.69
669 716 7.277098 GTGAGTATAGATCCTCGTGTCTAGATC 59.723 44.444 0.00 0.00 36.25 2.75
670 717 7.038587 AGTGAGTATAGATCCTCGTGTCTAGAT 60.039 40.741 0.00 0.00 31.05 1.98
671 718 6.268158 AGTGAGTATAGATCCTCGTGTCTAGA 59.732 42.308 0.00 0.00 31.05 2.43
672 719 6.460781 AGTGAGTATAGATCCTCGTGTCTAG 58.539 44.000 0.00 0.00 31.05 2.43
673 720 6.422344 AGTGAGTATAGATCCTCGTGTCTA 57.578 41.667 0.00 0.00 0.00 2.59
674 721 5.298989 AGTGAGTATAGATCCTCGTGTCT 57.701 43.478 0.00 0.00 0.00 3.41
676 723 5.297278 GTGAAGTGAGTATAGATCCTCGTGT 59.703 44.000 0.00 0.00 0.00 4.49
678 725 5.686753 AGTGAAGTGAGTATAGATCCTCGT 58.313 41.667 0.00 0.00 0.00 4.18
679 726 6.434596 CAAGTGAAGTGAGTATAGATCCTCG 58.565 44.000 0.00 0.00 0.00 4.63
680 727 6.183360 TGCAAGTGAAGTGAGTATAGATCCTC 60.183 42.308 0.00 0.00 0.00 3.71
681 728 5.658634 TGCAAGTGAAGTGAGTATAGATCCT 59.341 40.000 0.00 0.00 0.00 3.24
682 729 5.907207 TGCAAGTGAAGTGAGTATAGATCC 58.093 41.667 0.00 0.00 0.00 3.36
683 730 6.020281 CGTTGCAAGTGAAGTGAGTATAGATC 60.020 42.308 0.00 0.00 0.00 2.75
684 731 5.807520 CGTTGCAAGTGAAGTGAGTATAGAT 59.192 40.000 0.00 0.00 0.00 1.98
724 777 3.575805 GAATCACCCTCCTCTCATCTCT 58.424 50.000 0.00 0.00 0.00 3.10
727 780 1.342819 CGGAATCACCCTCCTCTCATC 59.657 57.143 0.00 0.00 34.64 2.92
729 782 0.041238 ACGGAATCACCCTCCTCTCA 59.959 55.000 0.00 0.00 34.64 3.27
730 783 2.068834 TACGGAATCACCCTCCTCTC 57.931 55.000 0.00 0.00 34.64 3.20
731 784 2.108970 GTTACGGAATCACCCTCCTCT 58.891 52.381 0.00 0.00 34.64 3.69
732 785 1.202382 CGTTACGGAATCACCCTCCTC 60.202 57.143 0.00 0.00 34.64 3.71
733 786 0.822164 CGTTACGGAATCACCCTCCT 59.178 55.000 0.00 0.00 34.64 3.69
734 787 0.808847 GCGTTACGGAATCACCCTCC 60.809 60.000 6.94 0.00 34.64 4.30
735 788 0.175073 AGCGTTACGGAATCACCCTC 59.825 55.000 6.94 0.00 34.64 4.30
736 789 1.407979 CTAGCGTTACGGAATCACCCT 59.592 52.381 6.94 0.00 34.64 4.34
737 790 1.406539 TCTAGCGTTACGGAATCACCC 59.593 52.381 6.94 0.00 34.64 4.61
738 791 2.457970 GTCTAGCGTTACGGAATCACC 58.542 52.381 6.94 0.00 0.00 4.02
739 792 2.107178 CGTCTAGCGTTACGGAATCAC 58.893 52.381 6.94 0.00 35.51 3.06
740 793 2.463553 CGTCTAGCGTTACGGAATCA 57.536 50.000 6.94 0.00 35.51 2.57
746 799 1.531912 CTGTTCCGTCTAGCGTTACG 58.468 55.000 0.00 0.00 39.32 3.18
747 800 1.266466 GCTGTTCCGTCTAGCGTTAC 58.734 55.000 5.97 4.45 39.32 2.50
748 801 0.883153 TGCTGTTCCGTCTAGCGTTA 59.117 50.000 5.97 0.00 40.24 3.18
749 802 0.666577 GTGCTGTTCCGTCTAGCGTT 60.667 55.000 5.97 0.00 40.24 4.84
750 803 1.080705 GTGCTGTTCCGTCTAGCGT 60.081 57.895 5.97 0.00 40.24 5.07
751 804 1.805945 GGTGCTGTTCCGTCTAGCG 60.806 63.158 0.00 0.33 40.24 4.26
752 805 1.805945 CGGTGCTGTTCCGTCTAGC 60.806 63.158 0.00 0.00 42.62 3.42
781 834 4.668636 GCACCCTGGTCTACTCTATCTAT 58.331 47.826 0.00 0.00 0.00 1.98
782 835 3.496337 CGCACCCTGGTCTACTCTATCTA 60.496 52.174 0.00 0.00 0.00 1.98
783 836 2.750135 CGCACCCTGGTCTACTCTATCT 60.750 54.545 0.00 0.00 0.00 1.98
784 837 1.609555 CGCACCCTGGTCTACTCTATC 59.390 57.143 0.00 0.00 0.00 2.08
825 885 3.317993 GGATGGATTTATTTGGGACGGTG 59.682 47.826 0.00 0.00 0.00 4.94
826 886 3.562182 GGATGGATTTATTTGGGACGGT 58.438 45.455 0.00 0.00 0.00 4.83
827 887 2.552315 CGGATGGATTTATTTGGGACGG 59.448 50.000 0.00 0.00 0.00 4.79
848 916 1.520787 CTGTAATGCCCGGACGGAC 60.521 63.158 13.13 0.06 37.50 4.79
953 1027 3.869272 GGATTGCTGGAGCGTGCG 61.869 66.667 0.00 0.00 45.83 5.34
1088 1167 4.554036 GCACCTCATCGGCCCTCC 62.554 72.222 0.00 0.00 35.61 4.30
1633 1733 3.086600 CTGCCTCCTGGGGACTCC 61.087 72.222 0.00 0.00 35.12 3.85
1741 1841 4.632458 GAGATCCCGTCGCCGCTC 62.632 72.222 0.00 0.00 0.00 5.03
1995 2098 2.347731 GAGGACAAGGTGACGATTTCC 58.652 52.381 0.00 0.00 0.00 3.13
2061 2164 2.871099 GTCGTCTCTCAGCGAGCA 59.129 61.111 0.00 0.00 39.70 4.26
2115 2218 2.034179 CCCCCGTTCAAACAAGAAACTC 59.966 50.000 0.00 0.00 0.00 3.01
2192 2296 4.416738 GACCTGTGAGCCCCAGCC 62.417 72.222 0.00 0.00 41.25 4.85
2193 2297 3.640407 TGACCTGTGAGCCCCAGC 61.640 66.667 0.00 0.00 40.32 4.85
2194 2298 2.348998 GTGACCTGTGAGCCCCAG 59.651 66.667 0.00 0.00 0.00 4.45
2195 2299 3.249189 GGTGACCTGTGAGCCCCA 61.249 66.667 0.00 0.00 0.00 4.96
2197 2301 1.557269 ATGAGGTGACCTGTGAGCCC 61.557 60.000 9.89 0.00 31.76 5.19
2198 2302 0.326264 AATGAGGTGACCTGTGAGCC 59.674 55.000 9.89 0.00 31.76 4.70
2199 2303 2.079925 GAAATGAGGTGACCTGTGAGC 58.920 52.381 9.89 0.00 31.76 4.26
2200 2304 3.692257 AGAAATGAGGTGACCTGTGAG 57.308 47.619 9.89 0.00 31.76 3.51
2201 2305 4.437682 AAAGAAATGAGGTGACCTGTGA 57.562 40.909 9.89 0.00 31.76 3.58
2203 2307 4.536765 ACAAAAGAAATGAGGTGACCTGT 58.463 39.130 9.89 0.00 31.76 4.00
2253 2359 4.473199 GGAACAAAATTGAAGTCGTAGGC 58.527 43.478 0.00 0.00 0.00 3.93
2341 2447 1.110442 TGGAAAAACACAGCCACAGG 58.890 50.000 0.00 0.00 0.00 4.00
2342 2448 3.181477 TGAATGGAAAAACACAGCCACAG 60.181 43.478 0.00 0.00 32.42 3.66
2343 2449 2.762887 TGAATGGAAAAACACAGCCACA 59.237 40.909 0.00 0.00 32.42 4.17
2347 2453 5.332506 CGAAACATGAATGGAAAAACACAGC 60.333 40.000 0.00 0.00 0.00 4.40
2378 2484 1.679680 ACAGTCGTCTTTCGTCTTCCA 59.320 47.619 0.00 0.00 40.80 3.53
2381 2487 2.859032 GCTGACAGTCGTCTTTCGTCTT 60.859 50.000 3.99 0.00 43.06 3.01
2384 2490 0.660595 CGCTGACAGTCGTCTTTCGT 60.661 55.000 3.99 0.00 43.06 3.85
2385 2491 1.337817 CCGCTGACAGTCGTCTTTCG 61.338 60.000 15.01 3.91 43.06 3.46
2387 2493 1.664965 GCCGCTGACAGTCGTCTTT 60.665 57.895 15.01 0.00 43.06 2.52
2399 2505 0.804364 TCAGCTAAACAATGCCGCTG 59.196 50.000 0.00 0.00 46.94 5.18
2450 2576 8.621532 ACAATAAAACATACTGACAGACACAT 57.378 30.769 10.08 0.00 0.00 3.21
2479 2613 7.756722 CAGGACAATGCTTTATCCACTTTTTAG 59.243 37.037 11.82 0.00 33.33 1.85
2485 2623 3.266772 TCCAGGACAATGCTTTATCCACT 59.733 43.478 11.82 0.00 33.33 4.00
2497 2635 0.327924 TCGCCAATGTCCAGGACAAT 59.672 50.000 26.53 15.87 45.96 2.71
2502 2640 2.825836 GCCTCGCCAATGTCCAGG 60.826 66.667 0.00 0.00 0.00 4.45
2515 2653 2.701163 CTAATCACCGCCCTCGCCTC 62.701 65.000 0.00 0.00 0.00 4.70
2526 2664 1.501582 AGGGAGGAGTGCTAATCACC 58.498 55.000 0.00 0.00 46.81 4.02
2536 2674 0.193574 TCAGTTCCCAAGGGAGGAGT 59.806 55.000 8.06 0.00 46.06 3.85
2593 2755 2.602322 GCGCGCCTTCATCATCTCC 61.602 63.158 23.24 0.00 0.00 3.71
2657 2819 2.433970 TCCTAATGGTGATGTCATCGCA 59.566 45.455 24.11 12.93 41.46 5.10
2658 2820 3.111853 TCCTAATGGTGATGTCATCGC 57.888 47.619 16.60 16.60 39.02 4.58
2659 2821 4.886579 TCATCCTAATGGTGATGTCATCG 58.113 43.478 8.29 0.00 39.47 3.84
2660 2822 7.255381 CCTTTTCATCCTAATGGTGATGTCATC 60.255 40.741 5.83 5.83 39.47 2.92
2661 2823 6.548622 CCTTTTCATCCTAATGGTGATGTCAT 59.451 38.462 0.00 0.00 39.47 3.06
2662 2824 5.887598 CCTTTTCATCCTAATGGTGATGTCA 59.112 40.000 0.00 0.00 39.47 3.58
2663 2825 6.122277 TCCTTTTCATCCTAATGGTGATGTC 58.878 40.000 0.00 0.00 39.47 3.06
2664 2826 6.078456 TCCTTTTCATCCTAATGGTGATGT 57.922 37.500 0.00 0.00 39.47 3.06
2665 2827 7.408756 TTTCCTTTTCATCCTAATGGTGATG 57.591 36.000 0.00 0.00 39.75 3.07
2666 2828 6.097412 GCTTTCCTTTTCATCCTAATGGTGAT 59.903 38.462 0.00 0.00 33.42 3.06
2667 2829 5.418840 GCTTTCCTTTTCATCCTAATGGTGA 59.581 40.000 0.00 0.00 33.42 4.02
2668 2830 5.185635 TGCTTTCCTTTTCATCCTAATGGTG 59.814 40.000 0.00 0.00 33.42 4.17
2669 2831 5.332743 TGCTTTCCTTTTCATCCTAATGGT 58.667 37.500 0.00 0.00 33.42 3.55
2670 2832 5.920193 TGCTTTCCTTTTCATCCTAATGG 57.080 39.130 0.00 0.00 33.42 3.16
2671 2833 6.759827 CCATTGCTTTCCTTTTCATCCTAATG 59.240 38.462 0.00 0.00 0.00 1.90
2672 2834 6.126968 CCCATTGCTTTCCTTTTCATCCTAAT 60.127 38.462 0.00 0.00 0.00 1.73
2673 2835 5.187576 CCCATTGCTTTCCTTTTCATCCTAA 59.812 40.000 0.00 0.00 0.00 2.69
2674 2836 4.711355 CCCATTGCTTTCCTTTTCATCCTA 59.289 41.667 0.00 0.00 0.00 2.94
2684 2846 1.669999 GATGCGCCCATTGCTTTCCT 61.670 55.000 4.18 0.00 38.05 3.36
2747 2912 6.033091 GGATATGCGTTTTCTTTTTGTTACGG 59.967 38.462 0.00 0.00 0.00 4.02
2789 2954 0.520827 GAGGAGACGTCGTTGTAGCG 60.521 60.000 10.46 0.00 0.00 4.26
2802 2977 1.661463 AATGGGAAGCACAGAGGAGA 58.339 50.000 0.00 0.00 0.00 3.71
2803 2978 2.089980 CAAATGGGAAGCACAGAGGAG 58.910 52.381 0.00 0.00 0.00 3.69
2819 2994 3.512724 AGTGCTACGTGGGTACTACAAAT 59.487 43.478 11.03 0.00 41.01 2.32
2821 2996 2.517959 AGTGCTACGTGGGTACTACAA 58.482 47.619 11.03 0.00 41.01 2.41
2822 2997 2.205022 AGTGCTACGTGGGTACTACA 57.795 50.000 11.03 0.00 41.01 2.74
2823 2998 4.907879 AATAGTGCTACGTGGGTACTAC 57.092 45.455 17.82 1.67 35.44 2.73
2824 2999 5.684704 AGTAATAGTGCTACGTGGGTACTA 58.315 41.667 17.79 17.79 36.61 1.82
2825 3000 4.530875 AGTAATAGTGCTACGTGGGTACT 58.469 43.478 15.36 15.36 34.33 2.73
2826 3001 4.907879 AGTAATAGTGCTACGTGGGTAC 57.092 45.455 0.00 0.52 0.00 3.34
2862 3047 3.932580 GATGACCGGAGCGCACACA 62.933 63.158 9.46 2.91 0.00 3.72
2864 3049 2.004808 CTAGATGACCGGAGCGCACA 62.005 60.000 9.46 0.00 0.00 4.57
2866 3051 2.490148 CCTAGATGACCGGAGCGCA 61.490 63.158 9.46 0.17 0.00 6.09
2887 3072 0.969917 TGTGGTGTTTTGTGCTGCCT 60.970 50.000 0.00 0.00 0.00 4.75
2888 3073 0.108424 TTGTGGTGTTTTGTGCTGCC 60.108 50.000 0.00 0.00 0.00 4.85
2889 3074 1.719600 TTTGTGGTGTTTTGTGCTGC 58.280 45.000 0.00 0.00 0.00 5.25
2890 3075 2.094099 GCTTTTGTGGTGTTTTGTGCTG 59.906 45.455 0.00 0.00 0.00 4.41
2891 3076 2.345876 GCTTTTGTGGTGTTTTGTGCT 58.654 42.857 0.00 0.00 0.00 4.40
2932 3117 0.613012 GGGAATTTGCAGTCCTGGCT 60.613 55.000 11.61 0.00 37.33 4.75
2937 3122 1.212751 GCGTGGGAATTTGCAGTCC 59.787 57.895 4.91 4.91 36.32 3.85


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

AutoCloner maintained by Alex Coulton.