Multiple sequence alignment - TraesCS1D01G039500

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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 TraesCS1D01G039500 chr1D 100.000 4404 0 0 1 4404 19021441 19025844 0.000000e+00 8133.0
1 TraesCS1D01G039500 chr1D 86.714 2958 297 55 453 3341 19003113 19000183 0.000000e+00 3197.0
2 TraesCS1D01G039500 chr1D 86.365 2655 290 40 858 3473 19021005 19018384 0.000000e+00 2832.0
3 TraesCS1D01G039500 chr1D 94.886 352 4 1 3662 4013 19034176 19034513 5.010000e-149 538.0
4 TraesCS1D01G039500 chr1D 89.756 205 15 4 457 656 19043302 19043505 1.570000e-64 257.0
5 TraesCS1D01G039500 chr1D 97.959 49 1 0 284 332 19043041 19043089 7.850000e-13 86.1
6 TraesCS1D01G039500 chr1B 93.618 3165 164 21 501 3657 28483160 28486294 0.000000e+00 4691.0
7 TraesCS1D01G039500 chr1B 85.795 3013 315 62 527 3472 28309047 28306081 0.000000e+00 3088.0
8 TraesCS1D01G039500 chr1B 86.127 2941 313 55 563 3473 28325169 28322294 0.000000e+00 3083.0
9 TraesCS1D01G039500 chr1B 85.250 2678 319 53 837 3473 28376022 28373380 0.000000e+00 2687.0
10 TraesCS1D01G039500 chr1B 87.415 2344 254 29 1089 3402 28445634 28443302 0.000000e+00 2656.0
11 TraesCS1D01G039500 chr1B 92.800 250 13 4 459 708 28448108 28448352 1.510000e-94 357.0
12 TraesCS1D01G039500 chr1B 86.222 225 7 5 284 499 28453836 28454045 5.730000e-54 222.0
13 TraesCS1D01G039500 chr1B 87.050 139 10 7 151 284 28452384 28452519 2.740000e-32 150.0
14 TraesCS1D01G039500 chr1B 87.129 101 4 1 284 375 28495935 28496035 6.020000e-19 106.0
15 TraesCS1D01G039500 chr1B 96.000 50 2 0 17 66 28452208 28452257 1.020000e-11 82.4
16 TraesCS1D01G039500 chr1B 94.872 39 2 0 26 64 28446249 28446287 1.320000e-05 62.1
17 TraesCS1D01G039500 chr1A 92.039 2839 176 25 841 3659 20935346 20938154 0.000000e+00 3945.0
18 TraesCS1D01G039500 chr1A 85.757 2668 288 58 858 3473 20932688 20930061 0.000000e+00 2737.0
19 TraesCS1D01G039500 chr1A 94.545 110 6 0 3550 3659 20940564 20940673 2.110000e-38 171.0
20 TraesCS1D01G039500 chr5B 85.059 2791 313 62 855 3597 641822012 641824746 0.000000e+00 2748.0
21 TraesCS1D01G039500 chr5B 87.423 485 27 14 290 761 641818314 641817851 1.080000e-145 527.0
22 TraesCS1D01G039500 chr5B 93.651 126 7 1 160 284 641819985 641819860 2.090000e-43 187.0
23 TraesCS1D01G039500 chr5B 96.000 50 2 0 17 66 641820223 641820174 1.020000e-11 82.4
24 TraesCS1D01G039500 chr2D 85.432 2636 325 45 985 3595 481599547 481602148 0.000000e+00 2686.0
25 TraesCS1D01G039500 chr2A 85.140 2638 336 40 982 3589 624359486 624362097 0.000000e+00 2649.0
26 TraesCS1D01G039500 chr2B 85.019 2630 343 39 982 3589 564920750 564923350 0.000000e+00 2627.0
27 TraesCS1D01G039500 chr2B 94.482 743 34 6 3662 4404 620599116 620599851 0.000000e+00 1138.0
28 TraesCS1D01G039500 chr2B 95.170 352 15 2 3662 4013 620604287 620604636 4.980000e-154 555.0
29 TraesCS1D01G039500 chr5A 93.674 743 39 7 3662 4404 380821327 380820593 0.000000e+00 1105.0
30 TraesCS1D01G039500 chr5A 93.872 359 19 3 3662 4019 380816157 380815801 5.010000e-149 538.0
31 TraesCS1D01G039500 chr7A 85.014 734 84 14 3662 4392 193071878 193071168 0.000000e+00 723.0
32 TraesCS1D01G039500 chr7A 87.535 353 35 5 3662 4013 193535281 193534937 2.470000e-107 399.0
33 TraesCS1D01G039500 chr7A 87.252 353 36 5 3662 4013 193061015 193060671 1.150000e-105 394.0
34 TraesCS1D01G039500 chr7B 96.307 352 11 2 3662 4013 88297473 88297822 1.060000e-160 577.0
35 TraesCS1D01G039500 chr7B 94.462 325 17 1 4080 4404 88292717 88293040 2.370000e-137 499.0
36 TraesCS1D01G039500 chr7B 90.452 199 10 5 3884 4082 88283916 88284105 2.030000e-63 254.0


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 TraesCS1D01G039500 chr1D 19021441 19025844 4403 False 8133.000000 8133 100.000 1 4404 1 chr1D.!!$F1 4403
1 TraesCS1D01G039500 chr1D 19000183 19003113 2930 True 3197.000000 3197 86.714 453 3341 1 chr1D.!!$R1 2888
2 TraesCS1D01G039500 chr1D 19018384 19021005 2621 True 2832.000000 2832 86.365 858 3473 1 chr1D.!!$R2 2615
3 TraesCS1D01G039500 chr1B 28483160 28486294 3134 False 4691.000000 4691 93.618 501 3657 1 chr1B.!!$F1 3156
4 TraesCS1D01G039500 chr1B 28306081 28309047 2966 True 3088.000000 3088 85.795 527 3472 1 chr1B.!!$R1 2945
5 TraesCS1D01G039500 chr1B 28322294 28325169 2875 True 3083.000000 3083 86.127 563 3473 1 chr1B.!!$R2 2910
6 TraesCS1D01G039500 chr1B 28373380 28376022 2642 True 2687.000000 2687 85.250 837 3473 1 chr1B.!!$R3 2636
7 TraesCS1D01G039500 chr1B 28443302 28445634 2332 True 2656.000000 2656 87.415 1089 3402 1 chr1B.!!$R4 2313
8 TraesCS1D01G039500 chr1A 20930061 20932688 2627 True 2737.000000 2737 85.757 858 3473 1 chr1A.!!$R1 2615
9 TraesCS1D01G039500 chr1A 20935346 20940673 5327 False 2058.000000 3945 93.292 841 3659 2 chr1A.!!$F1 2818
10 TraesCS1D01G039500 chr5B 641822012 641824746 2734 False 2748.000000 2748 85.059 855 3597 1 chr5B.!!$F1 2742
11 TraesCS1D01G039500 chr5B 641817851 641820223 2372 True 265.466667 527 92.358 17 761 3 chr5B.!!$R1 744
12 TraesCS1D01G039500 chr2D 481599547 481602148 2601 False 2686.000000 2686 85.432 985 3595 1 chr2D.!!$F1 2610
13 TraesCS1D01G039500 chr2A 624359486 624362097 2611 False 2649.000000 2649 85.140 982 3589 1 chr2A.!!$F1 2607
14 TraesCS1D01G039500 chr2B 564920750 564923350 2600 False 2627.000000 2627 85.019 982 3589 1 chr2B.!!$F1 2607
15 TraesCS1D01G039500 chr2B 620599116 620599851 735 False 1138.000000 1138 94.482 3662 4404 1 chr2B.!!$F2 742
16 TraesCS1D01G039500 chr5A 380820593 380821327 734 True 1105.000000 1105 93.674 3662 4404 1 chr5A.!!$R2 742
17 TraesCS1D01G039500 chr7A 193071168 193071878 710 True 723.000000 723 85.014 3662 4392 1 chr7A.!!$R2 730

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
94 120 0.177836 ACATCGCCATCCATCGTGAA 59.822 50.000 0.0 0.0 0.0 3.18 F
401 2042 0.445436 CCTCGTCATGTGCAAGCTTC 59.555 55.000 0.0 0.0 0.0 3.86 F
554 2197 0.970427 TCGCTATGGAGTCACAGGCA 60.970 55.000 0.0 0.0 0.0 4.75 F
1336 3134 1.140589 CGTCAAGGAGAGCAGCGAT 59.859 57.895 0.0 0.0 0.0 4.58 F
2468 4316 1.494824 ACGACTTCTACAACAACGGC 58.505 50.000 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 3803 0.673644 AAAGAACCATGGACGCGAGG 60.674 55.000 21.47 8.96 0.00 4.63 R
2192 4040 2.734079 GAGCGCATACCTATCTTGCTTC 59.266 50.000 11.47 0.00 34.23 3.86 R
2468 4316 2.157738 CCAGAGAGGTTTGAAGGCAAG 58.842 52.381 0.00 0.00 35.04 4.01 R
3255 5103 0.324614 TCCTTGAGGCATTCGAGCAA 59.675 50.000 0.00 0.00 36.17 3.91 R
4065 8453 0.248458 CAGAACAAACACCACACGCC 60.248 55.000 0.00 0.00 0.00 5.68 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 0.465287 TGCACACTTGACTCTGCTCA 59.535 50.000 0.00 0.00 0.00 4.26
62 63 1.146637 CACTTGACTCTGCTCAGTGC 58.853 55.000 0.00 0.00 43.25 4.40
74 100 1.642037 CTCAGTGCACATCCGCTTGG 61.642 60.000 21.04 0.00 0.00 3.61
86 112 2.537560 CGCTTGGACATCGCCATCC 61.538 63.158 0.00 0.00 37.86 3.51
87 113 1.451927 GCTTGGACATCGCCATCCA 60.452 57.895 0.00 0.00 43.42 3.41
88 114 0.820891 GCTTGGACATCGCCATCCAT 60.821 55.000 2.70 0.00 44.49 3.41
89 115 1.233019 CTTGGACATCGCCATCCATC 58.767 55.000 2.70 0.00 44.49 3.51
91 117 1.069765 GGACATCGCCATCCATCGT 59.930 57.895 0.00 0.00 34.87 3.73
92 118 1.224069 GGACATCGCCATCCATCGTG 61.224 60.000 0.00 0.00 34.87 4.35
93 119 0.249447 GACATCGCCATCCATCGTGA 60.249 55.000 0.00 0.00 0.00 4.35
94 120 0.177836 ACATCGCCATCCATCGTGAA 59.822 50.000 0.00 0.00 0.00 3.18
95 121 0.583438 CATCGCCATCCATCGTGAAC 59.417 55.000 0.00 0.00 0.00 3.18
96 122 0.875908 ATCGCCATCCATCGTGAACG 60.876 55.000 0.00 0.00 41.45 3.95
99 125 1.518352 CCATCCATCGTGAACGCGA 60.518 57.895 15.93 12.54 45.32 5.87
120 202 5.075448 CGATCGCAAGCATGTTTATACATC 58.925 41.667 0.26 0.00 43.07 3.06
122 204 3.247411 TCGCAAGCATGTTTATACATCGG 59.753 43.478 0.00 0.00 43.07 4.18
124 206 4.495679 CGCAAGCATGTTTATACATCGGTT 60.496 41.667 0.00 2.63 43.07 4.44
126 208 5.676079 GCAAGCATGTTTATACATCGGTTGT 60.676 40.000 23.71 0.00 43.07 3.32
128 210 7.468441 CAAGCATGTTTATACATCGGTTGTTA 58.532 34.615 19.67 0.00 43.07 2.41
129 211 7.246674 AGCATGTTTATACATCGGTTGTTAG 57.753 36.000 0.00 0.00 43.07 2.34
130 212 6.821665 AGCATGTTTATACATCGGTTGTTAGT 59.178 34.615 0.00 0.00 43.07 2.24
133 215 6.699366 TGTTTATACATCGGTTGTTAGTGGA 58.301 36.000 0.00 0.00 39.87 4.02
134 216 6.591062 TGTTTATACATCGGTTGTTAGTGGAC 59.409 38.462 0.00 0.00 39.87 4.02
135 217 4.811969 ATACATCGGTTGTTAGTGGACA 57.188 40.909 0.00 0.00 39.87 4.02
136 218 3.695830 ACATCGGTTGTTAGTGGACAT 57.304 42.857 0.00 0.00 33.74 3.06
137 219 3.334691 ACATCGGTTGTTAGTGGACATG 58.665 45.455 0.00 0.00 33.74 3.21
141 223 4.647611 TCGGTTGTTAGTGGACATGATTT 58.352 39.130 0.00 0.00 0.00 2.17
143 225 5.180492 TCGGTTGTTAGTGGACATGATTTTC 59.820 40.000 0.00 0.00 0.00 2.29
146 242 7.084486 GGTTGTTAGTGGACATGATTTTCTTC 58.916 38.462 0.00 0.00 0.00 2.87
147 243 6.817765 TGTTAGTGGACATGATTTTCTTCC 57.182 37.500 0.00 0.00 0.00 3.46
153 249 8.059798 AGTGGACATGATTTTCTTCCATAAAG 57.940 34.615 0.00 0.00 38.60 1.85
154 250 7.123247 AGTGGACATGATTTTCTTCCATAAAGG 59.877 37.037 0.00 0.00 38.60 3.11
207 304 7.677454 GAAATGATTTCCTGGAAATTGCTTT 57.323 32.000 29.80 25.87 41.56 3.51
211 308 9.743581 AATGATTTCCTGGAAATTGCTTTATTT 57.256 25.926 29.80 9.73 41.56 1.40
224 321 4.600032 TGCTTTATTTGCATCGCATACAG 58.400 39.130 0.00 0.00 38.76 2.74
233 330 2.220363 GCATCGCATACAGACAGTCATG 59.780 50.000 2.66 0.00 0.00 3.07
236 333 1.645034 GCATACAGACAGTCATGCGT 58.355 50.000 8.22 0.63 34.96 5.24
305 1942 2.949106 CCTGCCAAGTCAAGTGCG 59.051 61.111 0.00 0.00 0.00 5.34
309 1946 2.546494 GCCAAGTCAAGTGCGCACT 61.546 57.895 36.44 36.44 44.94 4.40
312 1949 1.217001 CAAGTCAAGTGCGCACTACA 58.783 50.000 40.76 27.50 41.58 2.74
373 2014 2.590575 AGACCACGTGCAAACCGG 60.591 61.111 10.91 0.00 0.00 5.28
374 2015 2.589442 GACCACGTGCAAACCGGA 60.589 61.111 9.46 0.00 0.00 5.14
375 2016 2.124653 ACCACGTGCAAACCGGAA 60.125 55.556 9.46 0.00 0.00 4.30
376 2017 1.512156 GACCACGTGCAAACCGGAAT 61.512 55.000 9.46 0.00 0.00 3.01
379 2020 1.063469 CCACGTGCAAACCGGAATATC 59.937 52.381 9.46 0.00 0.00 1.63
401 2042 0.445436 CCTCGTCATGTGCAAGCTTC 59.555 55.000 0.00 0.00 0.00 3.86
413 2054 5.522456 TGTGCAAGCTTCAAGTTCAAATAG 58.478 37.500 0.00 0.00 0.00 1.73
427 2070 7.645058 AGTTCAAATAGAATATGTGGGGTTG 57.355 36.000 0.00 0.00 38.76 3.77
428 2071 6.607198 AGTTCAAATAGAATATGTGGGGTTGG 59.393 38.462 0.00 0.00 38.76 3.77
429 2072 6.086011 TCAAATAGAATATGTGGGGTTGGT 57.914 37.500 0.00 0.00 0.00 3.67
430 2073 6.126409 TCAAATAGAATATGTGGGGTTGGTC 58.874 40.000 0.00 0.00 0.00 4.02
431 2074 4.724279 ATAGAATATGTGGGGTTGGTCC 57.276 45.455 0.00 0.00 0.00 4.46
432 2075 2.573463 AGAATATGTGGGGTTGGTCCT 58.427 47.619 0.00 0.00 36.25 3.85
433 2076 2.926329 AGAATATGTGGGGTTGGTCCTT 59.074 45.455 0.00 0.00 36.25 3.36
434 2077 2.826674 ATATGTGGGGTTGGTCCTTG 57.173 50.000 0.00 0.00 36.25 3.61
461 2104 7.804129 GTCGCACCACACAAAATAAAATACTAA 59.196 33.333 0.00 0.00 0.00 2.24
499 2142 6.628919 TTGTCCATGAATCATTAGCAGATG 57.371 37.500 0.00 0.00 0.00 2.90
519 2162 3.935993 CAACTCCCGTTGTCCAGAT 57.064 52.632 0.00 0.00 44.27 2.90
554 2197 0.970427 TCGCTATGGAGTCACAGGCA 60.970 55.000 0.00 0.00 0.00 4.75
668 2342 2.108700 CGCTTGTTTGAAACGTTCCAG 58.891 47.619 0.00 0.00 0.00 3.86
699 2375 8.163516 CGACAATACGACACATGTTTACATTAA 58.836 33.333 0.00 0.00 32.80 1.40
700 2376 9.982291 GACAATACGACACATGTTTACATTAAT 57.018 29.630 0.00 0.00 33.61 1.40
770 2468 1.730547 GGAACGCACAAGCACATGC 60.731 57.895 0.00 0.00 42.27 4.06
791 2489 3.307242 GCTGGATGACACGATTAACACTC 59.693 47.826 0.00 0.00 0.00 3.51
793 2491 4.494484 TGGATGACACGATTAACACTCAG 58.506 43.478 0.00 0.00 0.00 3.35
817 2539 2.109126 GCATGTGAGAACTCGGCCC 61.109 63.158 0.00 0.00 0.00 5.80
937 2685 1.198713 CCAAGAAGAGCTAGCCTCCA 58.801 55.000 12.13 0.00 41.74 3.86
1042 2822 8.305317 TCTAGCTTACTTGTTTTCCTACTTCTC 58.695 37.037 0.00 0.00 0.00 2.87
1048 2828 4.689612 TGTTTTCCTACTTCTCTGCACT 57.310 40.909 0.00 0.00 0.00 4.40
1336 3134 1.140589 CGTCAAGGAGAGCAGCGAT 59.859 57.895 0.00 0.00 0.00 4.58
1470 3268 8.012241 GCTCATCAGGTACGAATTTATTGAATC 58.988 37.037 0.00 0.00 0.00 2.52
1473 3271 9.655769 CATCAGGTACGAATTTATTGAATCAAG 57.344 33.333 1.10 0.00 0.00 3.02
1521 3361 5.416639 TGCGTCTCTTGGTTATGTAAGTCTA 59.583 40.000 0.00 0.00 0.00 2.59
1853 3701 2.025037 TCCAGATGGCAGCAAGGTTAAT 60.025 45.455 5.19 0.00 34.44 1.40
1861 3709 2.798009 CAAGGTTAATGCCGCCGG 59.202 61.111 0.00 0.00 0.00 6.13
1884 3732 1.882625 TTCAAGATCGCCGGCATCG 60.883 57.895 28.98 10.81 0.00 3.84
1904 3752 2.636830 GAGCATGGCTTCTTTGAGCTA 58.363 47.619 0.00 0.00 39.88 3.32
2192 4040 2.452813 CGACCCGTTGATGAAGCCG 61.453 63.158 0.00 0.00 0.00 5.52
2468 4316 1.494824 ACGACTTCTACAACAACGGC 58.505 50.000 0.00 0.00 0.00 5.68
2624 4472 2.362077 GGAGCAACACAACCAAGATGTT 59.638 45.455 0.00 0.00 37.02 2.71
2627 4475 5.278957 GGAGCAACACAACCAAGATGTTAAT 60.279 40.000 0.00 0.00 34.84 1.40
3134 4982 3.395702 TGCCGGTCATACCCGCTT 61.396 61.111 1.90 0.00 46.71 4.68
3255 5103 2.100631 GGCAAGCACATAGACGCGT 61.101 57.895 13.85 13.85 0.00 6.01
3290 5138 1.450312 GGAGTGGAATGGTGAGCCG 60.450 63.158 0.00 0.00 37.67 5.52
3308 5156 1.600663 CCGCTACCTATCTGCTGAACG 60.601 57.143 0.00 0.00 0.00 3.95
3328 5177 6.811665 TGAACGACGTATGAGAAATTGAAGAT 59.188 34.615 0.00 0.00 0.00 2.40
3356 5206 7.663081 AGATAGTGTGCTTCAGATTTCAAAGAA 59.337 33.333 0.00 0.00 0.00 2.52
3477 5335 8.729805 TTGTTGCCAAAAATTTCAACTAGATT 57.270 26.923 16.76 0.00 39.44 2.40
3659 8046 1.952990 CATGCCATTGCCATTACGGTA 59.047 47.619 0.00 0.00 36.97 4.02
3660 8047 1.384525 TGCCATTGCCATTACGGTAC 58.615 50.000 0.00 0.00 36.97 3.34
3695 8082 1.344438 TGAAGACTGAGGCACAACGAT 59.656 47.619 0.00 0.00 0.00 3.73
3912 8300 0.776080 TTCTTCCCCTTCCCCAAGCT 60.776 55.000 0.00 0.00 0.00 3.74
3913 8301 1.208165 TCTTCCCCTTCCCCAAGCTC 61.208 60.000 0.00 0.00 0.00 4.09
3914 8302 1.151587 TTCCCCTTCCCCAAGCTCT 60.152 57.895 0.00 0.00 0.00 4.09
3944 8332 1.077285 TGATCCAGACCTCGGCGTA 60.077 57.895 6.85 0.00 0.00 4.42
3996 8384 5.826586 TCTCTCGAGTTCAAGCAATAGATC 58.173 41.667 13.13 0.00 0.00 2.75
4004 8392 2.628178 TCAAGCAATAGATCGATCCCGT 59.372 45.455 21.66 6.34 37.05 5.28
4021 8409 3.779183 TCCCGTGGGTAACAATTGGTATA 59.221 43.478 6.46 0.00 39.74 1.47
4052 8440 1.151474 TTCATCTTCCCCCACCCCA 60.151 57.895 0.00 0.00 0.00 4.96
4083 8471 1.711060 CGGCGTGTGGTGTTTGTTCT 61.711 55.000 0.00 0.00 0.00 3.01
4089 8477 1.750780 TGGTGTTTGTTCTGCGGCA 60.751 52.632 1.29 1.29 0.00 5.69
4114 8502 2.193536 GGCGGTGGAGCACTTGTTT 61.194 57.895 0.00 0.00 39.27 2.83
4132 8520 2.149803 TTGGGTGCGATTCGAGTCGT 62.150 55.000 27.63 0.00 43.27 4.34
4154 8543 1.735198 GTCGGTTGGTCGCGAATCA 60.735 57.895 12.06 10.17 0.00 2.57
4223 8612 0.673644 GAACGACACCATGGACCAGG 60.674 60.000 21.47 0.00 0.00 4.45
4258 8647 1.153997 GGAGACGAAGACGACCAGC 60.154 63.158 0.00 0.00 42.66 4.85
4261 8650 3.612371 GACGAAGACGACCAGCGCT 62.612 63.158 2.64 2.64 46.04 5.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.403583 ACTGTATCTTTGGAAGAAACAAGTAAA 57.596 29.630 0.00 0.00 41.63 2.01
1 2 8.974060 ACTGTATCTTTGGAAGAAACAAGTAA 57.026 30.769 0.00 0.00 41.63 2.24
2 3 8.429641 AGACTGTATCTTTGGAAGAAACAAGTA 58.570 33.333 0.00 0.00 41.63 2.24
4 5 7.442364 TGAGACTGTATCTTTGGAAGAAACAAG 59.558 37.037 3.90 0.00 41.63 3.16
6 7 6.706270 GTGAGACTGTATCTTTGGAAGAAACA 59.294 38.462 3.90 0.00 41.63 2.83
7 8 6.931840 AGTGAGACTGTATCTTTGGAAGAAAC 59.068 38.462 3.90 0.00 41.63 2.78
8 9 7.067496 AGTGAGACTGTATCTTTGGAAGAAA 57.933 36.000 3.90 0.00 41.63 2.52
9 10 6.672266 AGTGAGACTGTATCTTTGGAAGAA 57.328 37.500 3.90 0.00 41.63 2.52
10 11 6.495181 AGAAGTGAGACTGTATCTTTGGAAGA 59.505 38.462 3.90 0.00 38.00 2.87
11 12 6.696411 AGAAGTGAGACTGTATCTTTGGAAG 58.304 40.000 3.90 0.00 38.00 3.46
12 13 6.672266 AGAAGTGAGACTGTATCTTTGGAA 57.328 37.500 3.90 0.00 38.00 3.53
13 14 6.459066 CAAGAAGTGAGACTGTATCTTTGGA 58.541 40.000 3.90 0.00 38.00 3.53
14 15 5.641209 CCAAGAAGTGAGACTGTATCTTTGG 59.359 44.000 3.90 6.46 38.00 3.28
15 16 6.146837 CACCAAGAAGTGAGACTGTATCTTTG 59.853 42.308 3.90 1.92 40.34 2.77
58 59 1.672356 GTCCAAGCGGATGTGCACT 60.672 57.895 19.41 3.19 45.33 4.40
62 63 2.009108 CGATGTCCAAGCGGATGTG 58.991 57.895 0.00 0.00 45.33 3.21
69 95 0.820891 ATGGATGGCGATGTCCAAGC 60.821 55.000 7.10 0.00 46.78 4.01
74 100 0.249447 TCACGATGGATGGCGATGTC 60.249 55.000 0.00 0.00 0.00 3.06
89 115 2.018670 CTTGCGATCGCGTTCACG 59.981 61.111 32.64 11.17 45.51 4.35
91 117 2.100031 ATGCTTGCGATCGCGTTCA 61.100 52.632 32.64 27.38 45.51 3.18
92 118 1.649348 CATGCTTGCGATCGCGTTC 60.649 57.895 32.64 23.19 45.51 3.95
93 119 1.911293 AACATGCTTGCGATCGCGTT 61.911 50.000 32.64 25.09 45.51 4.84
94 120 1.911293 AAACATGCTTGCGATCGCGT 61.911 50.000 32.64 21.04 45.51 6.01
95 121 0.026156 TAAACATGCTTGCGATCGCG 59.974 50.000 32.64 21.44 45.51 5.87
96 122 2.389713 ATAAACATGCTTGCGATCGC 57.610 45.000 32.48 32.48 42.35 4.58
99 125 4.083855 CCGATGTATAAACATGCTTGCGAT 60.084 41.667 0.00 0.00 46.49 4.58
120 202 5.181245 AGAAAATCATGTCCACTAACAACCG 59.819 40.000 0.00 0.00 31.81 4.44
122 204 7.084486 GGAAGAAAATCATGTCCACTAACAAC 58.916 38.462 0.00 0.00 31.81 3.32
124 206 6.303054 TGGAAGAAAATCATGTCCACTAACA 58.697 36.000 0.00 0.00 33.43 2.41
126 208 9.527157 TTTATGGAAGAAAATCATGTCCACTAA 57.473 29.630 1.38 1.11 41.05 2.24
128 210 7.123247 CCTTTATGGAAGAAAATCATGTCCACT 59.877 37.037 1.38 0.00 41.05 4.00
129 211 7.122650 TCCTTTATGGAAGAAAATCATGTCCAC 59.877 37.037 1.38 0.00 42.94 4.02
130 212 7.181361 TCCTTTATGGAAGAAAATCATGTCCA 58.819 34.615 1.82 1.82 42.94 4.02
153 249 9.093970 GCTACATTTGGGTTAATAAAAATGTCC 57.906 33.333 19.84 13.04 45.43 4.02
154 250 9.646427 TGCTACATTTGGGTTAATAAAAATGTC 57.354 29.630 19.84 12.34 45.43 3.06
158 254 8.816894 TCCATGCTACATTTGGGTTAATAAAAA 58.183 29.630 0.00 0.00 0.00 1.94
207 304 4.441792 ACTGTCTGTATGCGATGCAAATA 58.558 39.130 0.00 0.00 43.62 1.40
211 308 1.204467 TGACTGTCTGTATGCGATGCA 59.796 47.619 9.51 0.00 44.86 3.96
233 330 5.725110 AATCAAGAATCTGACATGTACGC 57.275 39.130 0.00 0.00 0.00 4.42
312 1949 7.147976 GGCTTGAAAGATACATTCACACTTTT 58.852 34.615 0.00 0.00 36.57 2.27
373 2014 3.243873 TGCACATGACGAGGGAGATATTC 60.244 47.826 0.00 0.00 0.00 1.75
374 2015 2.700371 TGCACATGACGAGGGAGATATT 59.300 45.455 0.00 0.00 0.00 1.28
375 2016 2.319844 TGCACATGACGAGGGAGATAT 58.680 47.619 0.00 0.00 0.00 1.63
376 2017 1.775385 TGCACATGACGAGGGAGATA 58.225 50.000 0.00 0.00 0.00 1.98
379 2020 1.364626 GCTTGCACATGACGAGGGAG 61.365 60.000 0.00 0.00 0.00 4.30
401 2042 7.645058 ACCCCACATATTCTATTTGAACTTG 57.355 36.000 0.00 0.00 37.52 3.16
413 2054 3.023832 CAAGGACCAACCCCACATATTC 58.976 50.000 0.00 0.00 40.05 1.75
420 2063 2.824880 CGACCAAGGACCAACCCCA 61.825 63.158 0.00 0.00 40.05 4.96
434 2077 3.357166 TTTATTTTGTGTGGTGCGACC 57.643 42.857 0.00 0.00 39.22 4.79
461 2104 5.244402 TCATGGACAATGCTTTCACTTTCAT 59.756 36.000 0.00 0.00 36.11 2.57
519 2162 0.392461 GCGAGTGGGGTTCTGCATTA 60.392 55.000 0.00 0.00 0.00 1.90
520 2163 1.675641 GCGAGTGGGGTTCTGCATT 60.676 57.895 0.00 0.00 0.00 3.56
615 2278 5.220739 GCTTCCACAATGCATGAACTACTAG 60.221 44.000 0.00 0.00 0.00 2.57
624 2293 0.459585 GGCTGCTTCCACAATGCATG 60.460 55.000 0.00 0.00 36.07 4.06
668 2342 5.944049 ACATGTGTCGTATTGTCGATAAC 57.056 39.130 0.00 0.00 41.78 1.89
700 2376 9.719355 TGAGTTATGAAAGTGCAAATCTACTAA 57.281 29.630 0.00 0.00 0.00 2.24
701 2377 9.719355 TTGAGTTATGAAAGTGCAAATCTACTA 57.281 29.630 0.00 0.00 0.00 1.82
702 2378 8.507249 GTTGAGTTATGAAAGTGCAAATCTACT 58.493 33.333 0.00 0.00 0.00 2.57
770 2468 4.494484 TGAGTGTTAATCGTGTCATCCAG 58.506 43.478 0.00 0.00 0.00 3.86
791 2489 1.878088 AGTTCTCACATGCAAGTGCTG 59.122 47.619 17.03 11.90 42.66 4.41
793 2491 1.136141 CGAGTTCTCACATGCAAGTGC 60.136 52.381 17.03 3.41 39.35 4.40
817 2539 3.787001 GGTGCCGGGGAGAAGAGG 61.787 72.222 2.18 0.00 0.00 3.69
937 2685 3.184628 TCAGGTTGGAGATGAAGGTGAT 58.815 45.455 0.00 0.00 0.00 3.06
1042 2822 2.467838 CACTCCATCGTGATAGTGCAG 58.532 52.381 0.00 0.00 37.06 4.41
1048 2828 1.675552 TCTCGCACTCCATCGTGATA 58.324 50.000 0.00 0.00 37.06 2.15
1158 2956 1.617947 AAGATGGCTCCCGGACAGAC 61.618 60.000 0.73 0.00 35.79 3.51
1470 3268 4.749245 AGACTAAATCGTTGTTGGCTTG 57.251 40.909 0.00 0.00 0.00 4.01
1473 3271 5.517770 ACGTATAGACTAAATCGTTGTTGGC 59.482 40.000 0.00 0.00 0.00 4.52
1521 3361 9.522804 ACAACAAATACATACACGAAACAAATT 57.477 25.926 0.00 0.00 0.00 1.82
1697 3545 1.725931 GCGTTGAGAAGTTTGGCGATG 60.726 52.381 0.00 0.00 0.00 3.84
1884 3732 1.461559 AGCTCAAAGAAGCCATGCTC 58.538 50.000 0.00 0.00 43.56 4.26
1955 3803 0.673644 AAAGAACCATGGACGCGAGG 60.674 55.000 21.47 8.96 0.00 4.63
2192 4040 2.734079 GAGCGCATACCTATCTTGCTTC 59.266 50.000 11.47 0.00 34.23 3.86
2468 4316 2.157738 CCAGAGAGGTTTGAAGGCAAG 58.842 52.381 0.00 0.00 35.04 4.01
2624 4472 7.609097 AGCAGATATGAGACCAAGAGAATTA 57.391 36.000 0.00 0.00 0.00 1.40
2627 4475 5.538053 CCTAGCAGATATGAGACCAAGAGAA 59.462 44.000 0.00 0.00 0.00 2.87
2705 4553 4.972733 ATGGCCTGGCACAACGCA 62.973 61.111 22.05 8.32 45.17 5.24
3255 5103 0.324614 TCCTTGAGGCATTCGAGCAA 59.675 50.000 0.00 0.00 36.17 3.91
3290 5138 2.733517 GTCGTTCAGCAGATAGGTAGC 58.266 52.381 0.00 0.00 0.00 3.58
3328 5177 8.846943 TTTGAAATCTGAAGCACACTATCTTA 57.153 30.769 0.00 0.00 0.00 2.10
3356 5206 4.819105 TGTCAACTAAGAACATCCGGAT 57.181 40.909 12.38 12.38 0.00 4.18
3414 5267 8.462811 TGTAAGAGCAAGTTTCAAAACATAACA 58.537 29.630 8.23 0.00 41.30 2.41
3601 7988 3.723260 TGCACGATAGATTTAATGCCGA 58.277 40.909 0.00 0.00 41.38 5.54
3659 8046 1.407656 TTCAGGAAGGCCGTGACAGT 61.408 55.000 0.00 0.00 39.15 3.55
3660 8047 0.671781 CTTCAGGAAGGCCGTGACAG 60.672 60.000 0.00 0.00 39.15 3.51
3695 8082 5.076182 TCTCTTCTCTGCTCTCTTCTTCAA 58.924 41.667 0.00 0.00 0.00 2.69
3878 8266 3.452990 GGGAAGAAGGAAGGTAGGAGAAG 59.547 52.174 0.00 0.00 0.00 2.85
3912 8300 4.503123 GTCTGGATCAGATCGAGAGAGAGA 60.503 50.000 21.95 1.30 43.37 3.10
3913 8301 3.748048 GTCTGGATCAGATCGAGAGAGAG 59.252 52.174 21.95 0.00 43.37 3.20
3914 8302 3.495983 GGTCTGGATCAGATCGAGAGAGA 60.496 52.174 21.95 7.68 43.37 3.10
3944 8332 2.421529 GGATACAAGGATTCCTGGCGTT 60.422 50.000 5.84 0.00 32.13 4.84
3955 8343 4.553678 AGAGAATTACGGGGATACAAGGA 58.446 43.478 0.00 0.00 39.74 3.36
3996 8384 1.668751 CAATTGTTACCCACGGGATCG 59.331 52.381 9.72 0.00 43.02 3.69
4004 8392 6.330514 TGGCTCTATATACCAATTGTTACCCA 59.669 38.462 4.43 0.00 0.00 4.51
4021 8409 3.645687 GGAAGATGAAGGACTGGCTCTAT 59.354 47.826 0.00 0.00 0.00 1.98
4061 8449 2.112297 AAACACCACACGCCGGAT 59.888 55.556 5.05 0.00 0.00 4.18
4064 8452 1.298041 GAACAAACACCACACGCCG 60.298 57.895 0.00 0.00 0.00 6.46
4065 8453 0.248458 CAGAACAAACACCACACGCC 60.248 55.000 0.00 0.00 0.00 5.68
4114 8502 2.149803 AACGACTCGAATCGCACCCA 62.150 55.000 17.16 0.00 46.22 4.51
4132 8520 2.919960 TTCGCGACCAACCGACCAAA 62.920 55.000 9.15 0.00 32.60 3.28
4154 8543 2.199236 GGGATTTTACGAGTCGCGAAT 58.801 47.619 12.06 10.83 44.57 3.34
4211 8600 4.722700 GCGCACCTGGTCCATGGT 62.723 66.667 12.58 7.08 36.96 3.55
4245 8634 2.022129 AAAGCGCTGGTCGTCTTCG 61.022 57.895 12.58 0.00 41.07 3.79
4261 8650 4.690719 ACCGATGCCGCGACCAAA 62.691 61.111 8.23 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.