Multiple sequence alignment - TraesCS2B01G033300

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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 TraesCS2B01G033300 chr2B 100.000 3497 0 0 556 4052 16040630 16037134 0.000000e+00 6458.0
1 TraesCS2B01G033300 chr2B 91.803 366 22 2 1565 1930 16005902 16006259 1.680000e-138 503.0
2 TraesCS2B01G033300 chr2B 100.000 149 0 0 1 149 16041185 16041037 3.990000e-70 276.0
3 TraesCS2B01G033300 chr2B 98.658 149 2 0 1 149 170769663 170769515 8.640000e-67 265.0
4 TraesCS2B01G033300 chr2B 92.697 178 10 2 556 732 554729380 554729205 1.870000e-63 254.0
5 TraesCS2B01G033300 chr2B 91.620 179 11 4 556 732 672037858 672038034 1.130000e-60 244.0
6 TraesCS2B01G033300 chr2B 92.523 107 7 1 744 849 16005638 16005744 7.010000e-33 152.0
7 TraesCS2B01G033300 chr2D 90.977 3347 187 40 744 4052 10819384 10816115 0.000000e+00 4401.0
8 TraesCS2B01G033300 chr2A 92.753 2401 143 13 744 3137 11331821 11334197 0.000000e+00 3441.0
9 TraesCS2B01G033300 chr2A 89.828 580 45 6 744 1317 11368370 11367799 0.000000e+00 732.0
10 TraesCS2B01G033300 chr2A 78.986 138 27 2 3764 3900 84365057 84365193 4.310000e-15 93.5
11 TraesCS2B01G033300 chr4B 79.793 579 93 20 3323 3898 548766479 548765922 2.270000e-107 399.0
12 TraesCS2B01G033300 chr4B 77.536 552 95 17 3277 3825 131469813 131470338 5.090000e-79 305.0
13 TraesCS2B01G033300 chr4B 97.987 149 3 0 1 149 604543693 604543545 4.020000e-65 259.0
14 TraesCS2B01G033300 chr4B 91.620 179 11 3 556 732 604543382 604543206 1.130000e-60 244.0
15 TraesCS2B01G033300 chr7D 78.080 625 111 17 3279 3900 96505040 96504439 4.950000e-99 372.0
16 TraesCS2B01G033300 chr5D 77.607 652 110 26 3260 3900 130459971 130459345 2.980000e-96 363.0
17 TraesCS2B01G033300 chr5B 77.778 585 103 18 3298 3876 142551565 142551002 6.490000e-88 335.0
18 TraesCS2B01G033300 chr5B 98.621 145 2 0 1 145 418023241 418023385 1.450000e-64 257.0
19 TraesCS2B01G033300 chr4D 78.198 555 88 20 3287 3837 137024892 137025417 1.400000e-84 324.0
20 TraesCS2B01G033300 chr4D 81.572 369 59 8 3259 3623 130456547 130456910 3.060000e-76 296.0
21 TraesCS2B01G033300 chr4D 79.494 395 67 9 3298 3681 68485344 68485735 6.680000e-68 268.0
22 TraesCS2B01G033300 chr6B 94.886 176 5 3 556 729 695846459 695846632 5.160000e-69 272.0
23 TraesCS2B01G033300 chr6B 90.385 52 5 0 2050 2101 14838289 14838238 7.270000e-08 69.4
24 TraesCS2B01G033300 chr1D 98.658 149 2 0 1 149 253148443 253148591 8.640000e-67 265.0
25 TraesCS2B01G033300 chr7B 97.987 149 3 0 1 149 625711643 625711495 4.020000e-65 259.0
26 TraesCS2B01G033300 chr7B 97.315 149 4 0 1 149 14094592 14094444 1.870000e-63 254.0
27 TraesCS2B01G033300 chr7B 92.135 178 11 2 556 732 625711331 625711156 8.700000e-62 248.0
28 TraesCS2B01G033300 chr7B 75.481 416 82 13 3487 3900 50980606 50980209 6.920000e-43 185.0
29 TraesCS2B01G033300 chr3D 97.987 149 3 0 1 149 437962180 437962032 4.020000e-65 259.0
30 TraesCS2B01G033300 chr3D 80.229 349 64 5 3277 3623 120316673 120317018 1.450000e-64 257.0
31 TraesCS2B01G033300 chr3D 92.697 178 10 2 556 732 437961884 437961709 1.870000e-63 254.0
32 TraesCS2B01G033300 chr3D 91.667 180 10 5 556 733 512691626 512691450 1.130000e-60 244.0
33 TraesCS2B01G033300 chr3D 80.952 105 20 0 3703 3807 504722301 504722197 2.600000e-12 84.2
34 TraesCS2B01G033300 chr1B 97.987 149 3 0 1 149 450050104 450050252 4.020000e-65 259.0
35 TraesCS2B01G033300 chr1B 97.315 149 4 0 1 149 25886746 25886598 1.870000e-63 254.0
36 TraesCS2B01G033300 chr1B 91.620 179 11 3 556 732 25886273 25886097 1.130000e-60 244.0
37 TraesCS2B01G033300 chr1B 91.573 178 12 2 556 732 450050415 450050590 4.050000e-60 243.0
38 TraesCS2B01G033300 chr1B 83.486 218 34 2 3684 3900 440747896 440747680 6.870000e-48 202.0
39 TraesCS2B01G033300 chr6D 83.721 215 30 5 3683 3896 451757095 451757305 8.880000e-47 198.0
40 TraesCS2B01G033300 chr3B 79.358 218 30 4 3685 3902 117953517 117953315 5.460000e-29 139.0
41 TraesCS2B01G033300 chr6A 85.075 67 8 2 3742 3807 448667624 448667559 2.610000e-07 67.6


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 TraesCS2B01G033300 chr2B 16037134 16041185 4051 True 3367.0 6458 100.0000 1 4052 2 chr2B.!!$R3 4051
1 TraesCS2B01G033300 chr2B 16005638 16006259 621 False 327.5 503 92.1630 744 1930 2 chr2B.!!$F2 1186
2 TraesCS2B01G033300 chr2D 10816115 10819384 3269 True 4401.0 4401 90.9770 744 4052 1 chr2D.!!$R1 3308
3 TraesCS2B01G033300 chr2A 11331821 11334197 2376 False 3441.0 3441 92.7530 744 3137 1 chr2A.!!$F1 2393
4 TraesCS2B01G033300 chr2A 11367799 11368370 571 True 732.0 732 89.8280 744 1317 1 chr2A.!!$R1 573
5 TraesCS2B01G033300 chr4B 548765922 548766479 557 True 399.0 399 79.7930 3323 3898 1 chr4B.!!$R1 575
6 TraesCS2B01G033300 chr4B 131469813 131470338 525 False 305.0 305 77.5360 3277 3825 1 chr4B.!!$F1 548
7 TraesCS2B01G033300 chr7D 96504439 96505040 601 True 372.0 372 78.0800 3279 3900 1 chr7D.!!$R1 621
8 TraesCS2B01G033300 chr5D 130459345 130459971 626 True 363.0 363 77.6070 3260 3900 1 chr5D.!!$R1 640
9 TraesCS2B01G033300 chr5B 142551002 142551565 563 True 335.0 335 77.7780 3298 3876 1 chr5B.!!$R1 578
10 TraesCS2B01G033300 chr4D 137024892 137025417 525 False 324.0 324 78.1980 3287 3837 1 chr4D.!!$F3 550
11 TraesCS2B01G033300 chr1B 25886097 25886746 649 True 249.0 254 94.4675 1 732 2 chr1B.!!$R2 731

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
955 960 1.100510 TGCCACCACTACTAGTAGCG 58.899 55.000 26.54 18.6 36.66 4.26 F
1194 1211 1.299165 CGCCGATGGTAACTCCTCG 60.299 63.158 0.00 0.0 36.95 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1791 1808 0.109597 CAAAGCCATCACCAACGAGC 60.110 55.0 0.00 0.0 0.00 5.03 R
3122 3152 0.037605 GCCGGGAATATACAGACGGG 60.038 60.0 2.18 0.0 41.46 5.28 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
34 35 3.193903 GGAGGAGCTTACGTTTCTCTCTT 59.806 47.826 0.00 0.00 0.00 2.85
48 49 2.043349 TCTTCGGGGCCATCTCGA 60.043 61.111 4.39 5.27 0.00 4.04
80 81 2.806244 CGGTGAAGAAACGGTGAAGATT 59.194 45.455 0.00 0.00 0.00 2.40
709 711 8.704849 TCAGATCCTGAATTTCTTACCAAAAA 57.295 30.769 0.00 0.00 37.57 1.94
725 727 5.847670 CCAAAAAGGTCAAAACACGAAAA 57.152 34.783 0.00 0.00 0.00 2.29
732 734 3.868661 GGTCAAAACACGAAAATTTGCCT 59.131 39.130 0.00 0.00 34.77 4.75
733 735 5.044558 GGTCAAAACACGAAAATTTGCCTA 58.955 37.500 0.00 0.00 34.77 3.93
734 736 5.694458 GGTCAAAACACGAAAATTTGCCTAT 59.306 36.000 0.00 0.00 34.77 2.57
735 737 6.864165 GGTCAAAACACGAAAATTTGCCTATA 59.136 34.615 0.00 0.00 34.77 1.31
736 738 7.544217 GGTCAAAACACGAAAATTTGCCTATAT 59.456 33.333 0.00 0.00 34.77 0.86
737 739 9.562583 GTCAAAACACGAAAATTTGCCTATATA 57.437 29.630 0.00 0.00 34.77 0.86
738 740 9.562583 TCAAAACACGAAAATTTGCCTATATAC 57.437 29.630 0.00 0.00 34.77 1.47
739 741 8.520258 CAAAACACGAAAATTTGCCTATATACG 58.480 33.333 0.00 0.00 0.00 3.06
740 742 7.542534 AACACGAAAATTTGCCTATATACGA 57.457 32.000 0.00 0.00 0.00 3.43
741 743 7.724305 ACACGAAAATTTGCCTATATACGAT 57.276 32.000 0.00 0.00 0.00 3.73
742 744 7.572759 ACACGAAAATTTGCCTATATACGATG 58.427 34.615 0.00 0.00 0.00 3.84
783 786 1.327460 CATAATCAACCCGCACGTGAG 59.673 52.381 22.23 17.30 0.00 3.51
791 794 1.421410 CCCGCACGTGAGCTGATAAC 61.421 60.000 22.23 0.00 0.00 1.89
921 926 2.292455 CCATTCCCAACCCCAATCTTCT 60.292 50.000 0.00 0.00 0.00 2.85
922 927 2.899303 TTCCCAACCCCAATCTTCTC 57.101 50.000 0.00 0.00 0.00 2.87
939 944 2.588877 CCCGTCATCACCGATGCC 60.589 66.667 0.00 0.00 39.63 4.40
955 960 1.100510 TGCCACCACTACTAGTAGCG 58.899 55.000 26.54 18.60 36.66 4.26
981 986 2.845752 TTCACCACCGTAGCGCCATC 62.846 60.000 2.29 0.00 0.00 3.51
982 987 4.157120 ACCACCGTAGCGCCATCC 62.157 66.667 2.29 0.00 0.00 3.51
983 988 4.155733 CCACCGTAGCGCCATCCA 62.156 66.667 2.29 0.00 0.00 3.41
984 989 2.108976 CACCGTAGCGCCATCCAT 59.891 61.111 2.29 0.00 0.00 3.41
1063 1071 3.347590 TCCTCCCGCTCCTCCTCA 61.348 66.667 0.00 0.00 0.00 3.86
1194 1211 1.299165 CGCCGATGGTAACTCCTCG 60.299 63.158 0.00 0.00 36.95 4.63
1324 1341 2.513204 TCCTCCTCGACTACGCCG 60.513 66.667 0.00 0.00 39.58 6.46
1803 1820 4.096003 CCCGGGCTCGTTGGTGAT 62.096 66.667 8.08 0.00 33.95 3.06
1809 1826 1.244019 GGCTCGTTGGTGATGGCTTT 61.244 55.000 0.00 0.00 0.00 3.51
1811 1828 1.238439 CTCGTTGGTGATGGCTTTGT 58.762 50.000 0.00 0.00 0.00 2.83
1941 1958 1.289380 GTCGGTGTTCTTCCTCGCT 59.711 57.895 0.00 0.00 0.00 4.93
2035 2052 1.451927 GCGTGCATCCCCAAGATCA 60.452 57.895 0.00 0.00 30.59 2.92
2469 2486 4.735132 TACCTGCAGGCGCACGAC 62.735 66.667 33.06 0.00 45.36 4.34
2569 2586 3.310035 AAGCTCGCCTCCTCCTCCT 62.310 63.158 0.00 0.00 0.00 3.69
2570 2587 3.223589 GCTCGCCTCCTCCTCCTC 61.224 72.222 0.00 0.00 0.00 3.71
2571 2588 2.520741 CTCGCCTCCTCCTCCTCC 60.521 72.222 0.00 0.00 0.00 4.30
2628 2645 1.083209 CTCGTCGTCGTCGTCAACA 60.083 57.895 11.41 0.00 38.33 3.33
2673 2690 2.203337 TGCAACTTCGGGCTGCTT 60.203 55.556 0.00 0.00 37.00 3.91
2694 2711 2.755876 ATCGAGCTGCTCACGGGA 60.756 61.111 27.46 17.15 0.00 5.14
2739 2756 4.329545 GTGGCGCCCAAGGTCAGA 62.330 66.667 26.77 0.00 34.18 3.27
2745 2762 1.613630 GCCCAAGGTCAGAGAGGGA 60.614 63.158 0.00 0.00 42.25 4.20
2760 2777 2.579738 GGAAGGCTCCACGAGGTC 59.420 66.667 0.00 0.00 41.96 3.85
2778 2795 4.457496 ATCGACCCCACGCTGCTG 62.457 66.667 0.00 0.00 0.00 4.41
2939 2962 1.892819 ATGCACCTCGTCAGGGACAG 61.893 60.000 0.00 0.00 45.53 3.51
2947 2970 3.016971 TCAGGGACAGCATGGGGG 61.017 66.667 0.00 0.00 43.62 5.40
3063 3089 0.384309 TCCCGTGATGCATAGACGAC 59.616 55.000 25.02 3.43 35.05 4.34
3122 3152 0.737715 CAGTGTAGAGTGAAGCCCGC 60.738 60.000 0.00 0.00 0.00 6.13
3123 3153 1.448013 GTGTAGAGTGAAGCCCGCC 60.448 63.158 0.00 0.00 0.00 6.13
3124 3154 2.187163 GTAGAGTGAAGCCCGCCC 59.813 66.667 0.00 0.00 0.00 6.13
3125 3155 3.458163 TAGAGTGAAGCCCGCCCG 61.458 66.667 0.00 0.00 0.00 6.13
3139 3169 0.388134 CGCCCGTCTGTATATTCCCG 60.388 60.000 0.00 0.00 0.00 5.14
3210 3257 1.537202 AGTGCTCACAAGAATTTCGCC 59.463 47.619 2.63 0.00 0.00 5.54
3212 3259 0.517316 GCTCACAAGAATTTCGCCGT 59.483 50.000 0.00 0.00 0.00 5.68
3267 3314 5.639506 CCTTATTGTCATGATAGTAAGGGCG 59.360 44.000 30.41 15.50 37.85 6.13
3271 3318 4.466827 TGTCATGATAGTAAGGGCGTCTA 58.533 43.478 0.00 0.00 0.00 2.59
3275 3322 2.158769 TGATAGTAAGGGCGTCTACGGA 60.159 50.000 4.49 0.00 40.23 4.69
3315 3362 3.032609 GCATCCGTCCGCGATCAG 61.033 66.667 8.23 0.00 41.33 2.90
3318 3365 1.526225 ATCCGTCCGCGATCAGAGA 60.526 57.895 8.23 0.00 41.33 3.10
3398 3446 5.365403 TTTTCACAACAACTCGAACAACT 57.635 34.783 0.00 0.00 0.00 3.16
3494 3542 7.267128 TGTACATAAAACCGGACGATATTTCT 58.733 34.615 9.46 0.00 0.00 2.52
3556 3606 1.955080 CTATACTCCACGGTGACCTCC 59.045 57.143 10.28 0.00 0.00 4.30
3596 3650 1.668101 GGTGGCTCCTCCTACGTCAG 61.668 65.000 0.00 0.00 35.26 3.51
3609 3663 4.980805 GTCAGCGTTGCCCGACCA 62.981 66.667 0.00 0.00 39.56 4.02
3630 3699 2.636412 CGTCAGAGTCGGGCTTGGA 61.636 63.158 0.00 0.00 0.00 3.53
3642 3711 2.125106 CTTGGAGCGGTGGTAGGC 60.125 66.667 0.00 0.00 0.00 3.93
3664 3733 3.426568 GTGTCGCTGCAGGGCTTC 61.427 66.667 25.01 17.02 0.00 3.86
3665 3734 4.704833 TGTCGCTGCAGGGCTTCC 62.705 66.667 25.01 12.94 0.00 3.46
3810 3880 2.742372 GCGGTCGTGTGAGGCATT 60.742 61.111 0.00 0.00 0.00 3.56
3844 3914 2.203771 GGCGATCTCGGTGAGGGAT 61.204 63.158 1.34 0.00 44.30 3.85
3873 3943 0.686441 CCGTACCTCACCATCTCCCA 60.686 60.000 0.00 0.00 0.00 4.37
3877 3947 0.415429 ACCTCACCATCTCCCAGTCT 59.585 55.000 0.00 0.00 0.00 3.24
3912 3982 2.880890 GACGCTTGGATGGCTTCATAAT 59.119 45.455 2.60 0.00 0.00 1.28
3923 3993 3.055819 TGGCTTCATAATATCGAGGAGGC 60.056 47.826 0.00 0.00 0.00 4.70
3946 4016 5.100259 CGGCGGAGATGACGTAATAATAAT 58.900 41.667 0.00 0.00 0.00 1.28
3967 4037 9.858247 AATAATGTTGCAGTCGTTATTATTACG 57.142 29.630 19.92 0.00 36.12 3.18
3976 4046 7.043590 GCAGTCGTTATTATTACGTCACTGAAT 60.044 37.037 21.19 0.00 42.04 2.57
4002 4072 6.267496 TCTCGTCTCATTCTCACACATAAA 57.733 37.500 0.00 0.00 0.00 1.40
4003 4073 6.687604 TCTCGTCTCATTCTCACACATAAAA 58.312 36.000 0.00 0.00 0.00 1.52
4038 4108 9.891828 GTTGATGTAATTTCTGTGTTCATACAA 57.108 29.630 0.00 0.00 35.69 2.41
4048 4118 3.435327 TGTGTTCATACAATGTTCGGCTC 59.565 43.478 0.00 0.00 35.69 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.415200 GTAAGCTCCTCCGATCCCTT 58.585 55.000 0.00 0.00 0.00 3.95
34 35 2.917751 GGATCGAGATGGCCCCGA 60.918 66.667 0.00 4.54 36.72 5.14
80 81 2.780693 CTCCACTCTCCCCCTCCA 59.219 66.667 0.00 0.00 0.00 3.86
597 598 4.473520 CACAGCCTACCGCCAGGG 62.474 72.222 3.06 0.00 43.47 4.45
668 669 5.965922 GGATCTGATCCCGTTTGAATTTTT 58.034 37.500 23.45 0.00 43.88 1.94
683 684 8.884124 TTTTGGTAAGAAATTCAGGATCTGAT 57.116 30.769 0.00 0.00 40.39 2.90
703 704 5.847670 TTTTCGTGTTTTGACCTTTTTGG 57.152 34.783 0.00 0.00 42.93 3.28
704 705 7.201224 GCAAATTTTCGTGTTTTGACCTTTTTG 60.201 33.333 0.00 0.00 33.24 2.44
709 711 3.868661 GGCAAATTTTCGTGTTTTGACCT 59.131 39.130 0.00 0.00 33.22 3.85
724 726 6.349973 CGATGCATCGTATATAGGCAAATT 57.650 37.500 35.19 0.00 44.74 1.82
725 727 5.973651 CGATGCATCGTATATAGGCAAAT 57.026 39.130 35.19 0.00 44.74 2.32
739 741 0.604780 CCCCAGATCCACGATGCATC 60.605 60.000 17.10 17.10 0.00 3.91
740 742 1.453235 CCCCAGATCCACGATGCAT 59.547 57.895 0.00 0.00 0.00 3.96
741 743 2.745308 CCCCCAGATCCACGATGCA 61.745 63.158 0.00 0.00 0.00 3.96
742 744 2.111878 CCCCCAGATCCACGATGC 59.888 66.667 0.00 0.00 0.00 3.91
749 751 2.711009 TGATTATGTGTCCCCCAGATCC 59.289 50.000 0.00 0.00 0.00 3.36
783 786 5.997385 TCTTCGTTTCTTTTGGTTATCAGC 58.003 37.500 0.00 0.00 0.00 4.26
791 794 3.735746 GCATGGTTCTTCGTTTCTTTTGG 59.264 43.478 0.00 0.00 0.00 3.28
890 895 2.504175 GGTTGGGAATGGTGAGCTAGTA 59.496 50.000 0.00 0.00 0.00 1.82
891 896 1.282157 GGTTGGGAATGGTGAGCTAGT 59.718 52.381 0.00 0.00 0.00 2.57
892 897 1.408822 GGGTTGGGAATGGTGAGCTAG 60.409 57.143 0.00 0.00 0.00 3.42
893 898 0.623723 GGGTTGGGAATGGTGAGCTA 59.376 55.000 0.00 0.00 0.00 3.32
921 926 2.499205 GCATCGGTGATGACGGGA 59.501 61.111 10.81 0.00 42.09 5.14
922 927 2.588877 GGCATCGGTGATGACGGG 60.589 66.667 10.81 0.00 42.09 5.28
939 944 2.422479 TGCTTCGCTACTAGTAGTGGTG 59.578 50.000 32.76 26.54 42.33 4.17
955 960 1.130561 GCTACGGTGGTGAATTGCTTC 59.869 52.381 0.00 0.00 0.00 3.86
971 976 1.146041 TGGACATGGATGGCGCTAC 59.854 57.895 7.64 0.00 36.40 3.58
1003 1008 3.391665 GAGGAGACATGGGCGGTGG 62.392 68.421 0.00 0.00 0.00 4.61
1004 1009 2.187946 GAGGAGACATGGGCGGTG 59.812 66.667 0.00 0.00 0.00 4.94
1005 1010 3.083997 GGAGGAGACATGGGCGGT 61.084 66.667 0.00 0.00 0.00 5.68
1006 1011 4.227134 CGGAGGAGACATGGGCGG 62.227 72.222 0.00 0.00 0.00 6.13
1007 1012 4.899239 GCGGAGGAGACATGGGCG 62.899 72.222 0.00 0.00 0.00 6.13
1130 1147 4.468689 GGAAGGGGAACGGGAGCG 62.469 72.222 0.00 0.00 0.00 5.03
1173 1190 1.588139 GGAGTTACCATCGGCGTCG 60.588 63.158 1.15 1.15 38.79 5.12
1194 1211 0.041982 AGGAGAGGTGGAAGAGGGAC 59.958 60.000 0.00 0.00 0.00 4.46
1239 1256 3.973267 GAGCGTGAGGGTGAGCGTC 62.973 68.421 0.00 0.00 34.34 5.19
1300 1317 1.997256 TAGTCGAGGAGGAGGGAGGC 61.997 65.000 0.00 0.00 0.00 4.70
1302 1319 0.533308 CGTAGTCGAGGAGGAGGGAG 60.533 65.000 0.00 0.00 39.71 4.30
1667 1684 1.077716 TCCACCTCGATCGCTCTCA 60.078 57.895 11.09 0.00 0.00 3.27
1786 1803 4.096003 ATCACCAACGAGCCCGGG 62.096 66.667 19.09 19.09 40.78 5.73
1791 1808 0.109597 CAAAGCCATCACCAACGAGC 60.110 55.000 0.00 0.00 0.00 5.03
1800 1817 2.918345 GCCGTGCACAAAGCCATCA 61.918 57.895 18.64 0.00 44.83 3.07
1941 1958 4.717629 CAGAACGAGACCGCCGCA 62.718 66.667 0.00 0.00 39.95 5.69
2247 2264 3.379445 TTCGGGTGCGAGACCTCC 61.379 66.667 4.25 0.00 45.33 4.30
2420 2437 3.344215 CCAGCTCGATGGCGATGC 61.344 66.667 0.00 0.00 46.80 3.91
2558 2575 2.041405 GGGTGGAGGAGGAGGAGG 60.041 72.222 0.00 0.00 0.00 4.30
2638 2655 2.029073 CACCACGTCCTGCTCGTT 59.971 61.111 0.00 0.00 39.55 3.85
2640 2657 2.734723 CACACCACGTCCTGCTCG 60.735 66.667 0.00 0.00 0.00 5.03
2673 2690 1.431036 CGTGAGCAGCTCGATCAGA 59.569 57.895 17.81 0.00 41.69 3.27
2694 2711 4.643387 GGGTTCTGGTGCCGCAGT 62.643 66.667 0.00 0.00 0.00 4.40
2736 2753 1.904032 GTGGAGCCTTCCCTCTCTG 59.096 63.158 0.00 0.00 43.33 3.35
2739 2756 1.684049 CTCGTGGAGCCTTCCCTCT 60.684 63.158 0.00 0.00 43.33 3.69
2745 2762 1.901085 GATGACCTCGTGGAGCCTT 59.099 57.895 11.17 0.00 37.04 4.35
2947 2970 0.532417 ATCTCGATCTTGCTGCTGCC 60.532 55.000 13.47 0.00 38.71 4.85
3063 3089 1.914051 GCATACGGATGATCATCGTCG 59.086 52.381 25.60 24.78 38.69 5.12
3095 3125 6.926272 GGGCTTCACTCTACACTGAATATTAG 59.074 42.308 0.00 0.00 0.00 1.73
3122 3152 0.037605 GCCGGGAATATACAGACGGG 60.038 60.000 2.18 0.00 41.46 5.28
3123 3153 0.966920 AGCCGGGAATATACAGACGG 59.033 55.000 2.18 0.00 43.81 4.79
3124 3154 1.611977 TCAGCCGGGAATATACAGACG 59.388 52.381 2.18 0.00 0.00 4.18
3125 3155 3.746045 TTCAGCCGGGAATATACAGAC 57.254 47.619 2.18 0.00 0.00 3.51
3139 3169 1.734117 GTGCGCACCAAATTCAGCC 60.734 57.895 30.12 0.00 0.00 4.85
3234 3281 8.109634 ACTATCATGACAATAAGGGAACAAACT 58.890 33.333 0.00 0.00 0.00 2.66
3235 3282 8.281212 ACTATCATGACAATAAGGGAACAAAC 57.719 34.615 0.00 0.00 0.00 2.93
3236 3283 9.967451 TTACTATCATGACAATAAGGGAACAAA 57.033 29.630 0.00 0.00 0.00 2.83
3244 3291 6.223852 ACGCCCTTACTATCATGACAATAAG 58.776 40.000 0.00 6.17 0.00 1.73
3267 3314 1.117150 TATGGGTTGCCTCCGTAGAC 58.883 55.000 0.00 0.00 0.00 2.59
3271 3318 2.525105 AATTTATGGGTTGCCTCCGT 57.475 45.000 0.00 0.00 0.00 4.69
3275 3322 4.281657 GAGAGGAAATTTATGGGTTGCCT 58.718 43.478 0.00 0.00 0.00 4.75
3311 3358 3.625314 GGACTGGTCCCTCTCTGAT 57.375 57.895 8.48 0.00 43.94 2.90
3341 3388 2.586792 GGATGGCGTCCTTCTGCT 59.413 61.111 18.69 0.00 44.16 4.24
3523 3573 6.205464 CCGTGGAGTATAGGATAGTTTACGAA 59.795 42.308 0.00 0.00 0.00 3.85
3556 3606 1.065928 CTAGCCCGGCGTGACTTAG 59.934 63.158 6.01 0.00 0.00 2.18
3579 3633 2.052690 GCTGACGTAGGAGGAGCCA 61.053 63.158 0.00 0.00 40.02 4.75
3668 3737 4.154347 CTGCAGTCGGGAGGCCTC 62.154 72.222 25.59 25.59 32.40 4.70
3673 3742 3.672295 GAAGCCCTGCAGTCGGGAG 62.672 68.421 13.60 0.00 44.90 4.30
3674 3743 3.706373 GAAGCCCTGCAGTCGGGA 61.706 66.667 13.60 0.00 44.90 5.14
3675 3744 4.785453 GGAAGCCCTGCAGTCGGG 62.785 72.222 13.81 9.24 44.89 5.14
3676 3745 4.785453 GGGAAGCCCTGCAGTCGG 62.785 72.222 13.81 8.89 41.34 4.79
3678 3747 4.785453 CCGGGAAGCCCTGCAGTC 62.785 72.222 13.81 3.00 42.67 3.51
3680 3749 4.479993 CTCCGGGAAGCCCTGCAG 62.480 72.222 6.78 6.78 42.67 4.41
3711 3781 3.448194 CGGAGAGGATCATCCGCA 58.552 61.111 17.02 0.00 44.42 5.69
3760 3830 4.789075 CCCACGTACTCGGTGGCG 62.789 72.222 11.71 3.65 41.85 5.69
3770 3840 3.976490 CTCTCCCCCAGCCCACGTA 62.976 68.421 0.00 0.00 0.00 3.57
3808 3878 2.699768 CGCCGCCACCAATGACAAT 61.700 57.895 0.00 0.00 0.00 2.71
3844 3914 0.681887 TGAGGTACGGCGAGGAATGA 60.682 55.000 16.62 0.00 0.00 2.57
3873 3943 1.749638 CGTCTCCACCGCCTAGACT 60.750 63.158 0.00 0.00 37.97 3.24
3877 3947 3.129502 CGTCGTCTCCACCGCCTA 61.130 66.667 0.00 0.00 0.00 3.93
3912 3982 4.574271 TCCGCCGCCTCCTCGATA 62.574 66.667 0.00 0.00 0.00 2.92
3923 3993 2.410785 TTATTACGTCATCTCCGCCG 57.589 50.000 0.00 0.00 0.00 6.46
3946 4016 5.862860 TGACGTAATAATAACGACTGCAACA 59.137 36.000 2.27 0.00 42.90 3.33
3967 4037 6.367422 AGAATGAGACGAGAAAATTCAGTGAC 59.633 38.462 0.00 0.00 31.15 3.67
3976 4046 4.944048 TGTGTGAGAATGAGACGAGAAAA 58.056 39.130 0.00 0.00 0.00 2.29
4025 4095 3.436704 AGCCGAACATTGTATGAACACAG 59.563 43.478 0.00 0.00 34.61 3.66
4026 4096 3.407698 AGCCGAACATTGTATGAACACA 58.592 40.909 0.00 0.00 34.61 3.72


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

AutoCloner maintained by Alex Coulton.