Multiple sequence alignment - TraesCS2D01G559300

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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 TraesCS2D01G559300 chr2D 100.000 3413 0 0 1 3413 631950671 631947259 0.000000e+00 6303
1 TraesCS2D01G559300 chr2B 93.252 2934 151 23 522 3413 775338932 775336004 0.000000e+00 4277
2 TraesCS2D01G559300 chr2B 80.208 384 40 13 160 538 775339613 775339261 4.370000e-64 255
3 TraesCS2D01G559300 chr2A 95.515 1873 70 5 641 2510 759820452 759822313 0.000000e+00 2981
4 TraesCS2D01G559300 chr2A 91.257 732 55 9 2457 3184 759822312 759823038 0.000000e+00 989
5 TraesCS2D01G559300 chr1D 85.340 573 65 15 2106 2678 348899036 348899589 2.950000e-160 575


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 TraesCS2D01G559300 chr2D 631947259 631950671 3412 True 6303 6303 100.000 1 3413 1 chr2D.!!$R1 3412
1 TraesCS2D01G559300 chr2B 775336004 775339613 3609 True 2266 4277 86.730 160 3413 2 chr2B.!!$R1 3253
2 TraesCS2D01G559300 chr2A 759820452 759823038 2586 False 1985 2981 93.386 641 3184 2 chr2A.!!$F1 2543
3 TraesCS2D01G559300 chr1D 348899036 348899589 553 False 575 575 85.340 2106 2678 1 chr1D.!!$F1 572

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
595 948 0.169230 ACGCGTTTGACAAACTTGCA 59.831 45.000 24.6 0.0 39.23 4.08 F
1407 1778 2.112297 GGTTTGCAGGTCCACGGA 59.888 61.111 0.0 0.0 0.00 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1602 1973 0.178767 CTTCGAGCATCATGGGACCA 59.821 55.000 0.00 0.0 33.17 4.02 R
2890 3325 1.270465 CGCCTGATATCATCACCTGCA 60.270 52.381 5.72 0.0 35.06 4.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 5.925509 TCTTAAGTGCCATATTGGAGTACC 58.074 41.667 1.63 0.00 40.96 3.34
25 26 5.427157 TCTTAAGTGCCATATTGGAGTACCA 59.573 40.000 1.63 0.00 40.96 3.25
26 27 4.796110 AAGTGCCATATTGGAGTACCAT 57.204 40.909 0.00 0.00 46.34 3.55
27 28 4.090761 AGTGCCATATTGGAGTACCATG 57.909 45.455 0.00 0.00 46.34 3.66
28 29 3.459598 AGTGCCATATTGGAGTACCATGT 59.540 43.478 0.00 0.00 46.34 3.21
29 30 3.565482 GTGCCATATTGGAGTACCATGTG 59.435 47.826 0.00 0.00 46.34 3.21
30 31 3.201930 TGCCATATTGGAGTACCATGTGT 59.798 43.478 0.00 0.00 46.34 3.72
31 32 4.207165 GCCATATTGGAGTACCATGTGTT 58.793 43.478 0.00 0.00 46.34 3.32
32 33 5.104318 TGCCATATTGGAGTACCATGTGTTA 60.104 40.000 0.00 0.00 46.34 2.41
33 34 5.825679 GCCATATTGGAGTACCATGTGTTAA 59.174 40.000 0.00 0.00 46.34 2.01
34 35 6.490040 GCCATATTGGAGTACCATGTGTTAAT 59.510 38.462 0.00 0.00 46.34 1.40
35 36 7.663905 GCCATATTGGAGTACCATGTGTTAATA 59.336 37.037 0.00 0.00 46.34 0.98
36 37 9.567776 CCATATTGGAGTACCATGTGTTAATAA 57.432 33.333 0.00 0.00 46.34 1.40
65 66 9.599866 AATAATCGTTGACATTCTAGTGATCAA 57.400 29.630 0.00 0.00 0.00 2.57
66 67 9.770097 ATAATCGTTGACATTCTAGTGATCAAT 57.230 29.630 0.00 0.00 32.30 2.57
68 69 9.599866 AATCGTTGACATTCTAGTGATCAATAA 57.400 29.630 4.22 0.00 32.30 1.40
69 70 8.996024 TCGTTGACATTCTAGTGATCAATAAA 57.004 30.769 4.22 2.92 32.30 1.40
70 71 9.430623 TCGTTGACATTCTAGTGATCAATAAAA 57.569 29.630 4.22 0.00 32.30 1.52
88 89 9.939802 TCAATAAAAACTACCTTTCTAGTCCTC 57.060 33.333 0.00 0.00 0.00 3.71
89 90 9.163899 CAATAAAAACTACCTTTCTAGTCCTCC 57.836 37.037 0.00 0.00 0.00 4.30
90 91 8.682297 ATAAAAACTACCTTTCTAGTCCTCCT 57.318 34.615 0.00 0.00 0.00 3.69
91 92 6.361768 AAAACTACCTTTCTAGTCCTCCTG 57.638 41.667 0.00 0.00 0.00 3.86
92 93 4.949966 ACTACCTTTCTAGTCCTCCTGA 57.050 45.455 0.00 0.00 0.00 3.86
93 94 4.602107 ACTACCTTTCTAGTCCTCCTGAC 58.398 47.826 0.00 0.00 44.82 3.51
102 103 2.100605 GTCCTCCTGACAACATCACC 57.899 55.000 0.00 0.00 43.85 4.02
103 104 1.347707 GTCCTCCTGACAACATCACCA 59.652 52.381 0.00 0.00 43.85 4.17
104 105 2.054021 TCCTCCTGACAACATCACCAA 58.946 47.619 0.00 0.00 32.37 3.67
105 106 2.441375 TCCTCCTGACAACATCACCAAA 59.559 45.455 0.00 0.00 32.37 3.28
106 107 3.117701 TCCTCCTGACAACATCACCAAAA 60.118 43.478 0.00 0.00 32.37 2.44
107 108 3.828451 CCTCCTGACAACATCACCAAAAT 59.172 43.478 0.00 0.00 32.37 1.82
108 109 4.321452 CCTCCTGACAACATCACCAAAATG 60.321 45.833 0.00 0.00 32.37 2.32
109 110 4.468713 TCCTGACAACATCACCAAAATGA 58.531 39.130 0.00 0.00 32.37 2.57
110 111 4.520111 TCCTGACAACATCACCAAAATGAG 59.480 41.667 0.00 0.00 32.37 2.90
111 112 4.321452 CCTGACAACATCACCAAAATGAGG 60.321 45.833 0.00 0.00 36.46 3.86
112 113 4.468713 TGACAACATCACCAAAATGAGGA 58.531 39.130 0.00 0.00 34.50 3.71
113 114 5.078949 TGACAACATCACCAAAATGAGGAT 58.921 37.500 0.00 0.00 34.50 3.24
114 115 5.539574 TGACAACATCACCAAAATGAGGATT 59.460 36.000 0.00 0.00 34.50 3.01
115 116 6.029346 ACAACATCACCAAAATGAGGATTC 57.971 37.500 0.00 0.00 34.50 2.52
116 117 5.047092 ACAACATCACCAAAATGAGGATTCC 60.047 40.000 0.00 0.00 34.50 3.01
117 118 4.676109 ACATCACCAAAATGAGGATTCCA 58.324 39.130 5.29 0.00 34.50 3.53
118 119 4.463891 ACATCACCAAAATGAGGATTCCAC 59.536 41.667 5.29 0.00 34.50 4.02
119 120 3.430453 TCACCAAAATGAGGATTCCACC 58.570 45.455 5.29 0.00 0.00 4.61
120 121 2.164219 CACCAAAATGAGGATTCCACCG 59.836 50.000 5.29 0.00 34.73 4.94
121 122 2.225017 ACCAAAATGAGGATTCCACCGT 60.225 45.455 5.29 0.00 34.73 4.83
122 123 2.825532 CCAAAATGAGGATTCCACCGTT 59.174 45.455 5.29 1.43 34.73 4.44
123 124 3.258123 CCAAAATGAGGATTCCACCGTTT 59.742 43.478 5.29 7.36 34.73 3.60
124 125 4.461081 CCAAAATGAGGATTCCACCGTTTA 59.539 41.667 5.29 0.00 34.73 2.01
125 126 5.393027 CCAAAATGAGGATTCCACCGTTTAG 60.393 44.000 5.29 2.97 34.73 1.85
126 127 2.396590 TGAGGATTCCACCGTTTAGC 57.603 50.000 5.29 0.00 34.73 3.09
127 128 1.065709 TGAGGATTCCACCGTTTAGCC 60.066 52.381 5.29 0.00 34.73 3.93
128 129 0.988832 AGGATTCCACCGTTTAGCCA 59.011 50.000 5.29 0.00 34.73 4.75
129 130 1.353022 AGGATTCCACCGTTTAGCCAA 59.647 47.619 5.29 0.00 34.73 4.52
130 131 2.164338 GGATTCCACCGTTTAGCCAAA 58.836 47.619 0.00 0.00 0.00 3.28
131 132 2.559231 GGATTCCACCGTTTAGCCAAAA 59.441 45.455 0.00 0.00 0.00 2.44
132 133 3.366985 GGATTCCACCGTTTAGCCAAAAG 60.367 47.826 0.00 0.00 0.00 2.27
133 134 2.642154 TCCACCGTTTAGCCAAAAGA 57.358 45.000 0.00 0.00 0.00 2.52
134 135 2.933573 TCCACCGTTTAGCCAAAAGAA 58.066 42.857 0.00 0.00 0.00 2.52
135 136 3.288964 TCCACCGTTTAGCCAAAAGAAA 58.711 40.909 0.00 0.00 0.00 2.52
136 137 3.067040 TCCACCGTTTAGCCAAAAGAAAC 59.933 43.478 0.00 0.00 0.00 2.78
137 138 3.067601 CCACCGTTTAGCCAAAAGAAACT 59.932 43.478 0.00 0.00 32.13 2.66
138 139 4.276431 CCACCGTTTAGCCAAAAGAAACTA 59.724 41.667 0.00 0.00 32.13 2.24
139 140 5.048294 CCACCGTTTAGCCAAAAGAAACTAT 60.048 40.000 0.00 0.00 32.13 2.12
140 141 6.149807 CCACCGTTTAGCCAAAAGAAACTATA 59.850 38.462 0.00 0.00 32.13 1.31
141 142 7.019418 CACCGTTTAGCCAAAAGAAACTATAC 58.981 38.462 0.00 0.00 32.13 1.47
142 143 6.938596 ACCGTTTAGCCAAAAGAAACTATACT 59.061 34.615 0.00 0.00 32.13 2.12
143 144 7.118825 ACCGTTTAGCCAAAAGAAACTATACTC 59.881 37.037 0.00 0.00 32.13 2.59
144 145 7.333672 CCGTTTAGCCAAAAGAAACTATACTCT 59.666 37.037 0.00 0.00 32.13 3.24
145 146 8.718734 CGTTTAGCCAAAAGAAACTATACTCTT 58.281 33.333 0.00 0.00 33.25 2.85
147 148 8.788325 TTAGCCAAAAGAAACTATACTCTTCC 57.212 34.615 0.00 0.00 30.57 3.46
148 149 7.021998 AGCCAAAAGAAACTATACTCTTCCT 57.978 36.000 0.00 0.00 30.57 3.36
149 150 8.147244 AGCCAAAAGAAACTATACTCTTCCTA 57.853 34.615 0.00 0.00 30.57 2.94
150 151 8.261522 AGCCAAAAGAAACTATACTCTTCCTAG 58.738 37.037 0.00 0.00 30.57 3.02
151 152 7.011576 GCCAAAAGAAACTATACTCTTCCTAGC 59.988 40.741 0.00 0.00 30.57 3.42
152 153 8.041323 CCAAAAGAAACTATACTCTTCCTAGCA 58.959 37.037 0.00 0.00 30.57 3.49
153 154 9.436957 CAAAAGAAACTATACTCTTCCTAGCAA 57.563 33.333 0.00 0.00 30.57 3.91
183 184 9.569122 TTTTACTACTCCCCTTATTTCATATGC 57.431 33.333 0.00 0.00 0.00 3.14
184 185 6.763715 ACTACTCCCCTTATTTCATATGCA 57.236 37.500 0.00 0.00 0.00 3.96
185 186 7.335127 ACTACTCCCCTTATTTCATATGCAT 57.665 36.000 3.79 3.79 0.00 3.96
237 240 9.606631 GTAGAGATTGACCAAGTTTATTGAGAT 57.393 33.333 0.00 0.00 0.00 2.75
319 322 7.535997 GCATATCTCATGTTGTATGCAATGAT 58.464 34.615 22.19 2.72 45.32 2.45
359 362 9.975218 ATTTGGTACTATAGGTGTTGATTTTCT 57.025 29.630 4.43 0.00 0.00 2.52
360 363 9.802039 TTTGGTACTATAGGTGTTGATTTTCTT 57.198 29.630 4.43 0.00 0.00 2.52
361 364 9.444600 TTGGTACTATAGGTGTTGATTTTCTTC 57.555 33.333 4.43 0.00 0.00 2.87
362 365 8.822805 TGGTACTATAGGTGTTGATTTTCTTCT 58.177 33.333 4.43 0.00 0.00 2.85
363 366 9.668497 GGTACTATAGGTGTTGATTTTCTTCTT 57.332 33.333 4.43 0.00 0.00 2.52
366 369 9.442047 ACTATAGGTGTTGATTTTCTTCTTCTG 57.558 33.333 4.43 0.00 0.00 3.02
440 443 2.571653 ACCACATTTCGGAATGGAGAGA 59.428 45.455 20.44 0.00 45.56 3.10
451 454 5.186992 TCGGAATGGAGAGAGTATGAAACAA 59.813 40.000 0.00 0.00 0.00 2.83
452 455 5.292101 CGGAATGGAGAGAGTATGAAACAAC 59.708 44.000 0.00 0.00 0.00 3.32
498 501 9.248291 CATAAATTTTACAGGGTCAATGCATAC 57.752 33.333 0.00 0.00 0.00 2.39
503 506 3.347216 ACAGGGTCAATGCATACACTTC 58.653 45.455 0.00 0.00 0.00 3.01
522 525 8.565896 ACACTTCTGCATAAATTAGTGATCAA 57.434 30.769 0.00 0.00 37.15 2.57
543 893 9.970395 GATCAATGTTTTATAGGATTGATTGCA 57.030 29.630 0.00 0.00 42.75 4.08
564 917 8.978564 TTGCATTTTTCTATTCGCAAATCTAA 57.021 26.923 0.00 0.00 36.50 2.10
565 918 9.585099 TTGCATTTTTCTATTCGCAAATCTAAT 57.415 25.926 0.00 0.00 36.50 1.73
578 931 4.723862 GCAAATCTAATACGAGTGCAAACG 59.276 41.667 11.33 11.33 31.65 3.60
580 933 1.915350 TCTAATACGAGTGCAAACGCG 59.085 47.619 3.53 3.53 38.80 6.01
595 948 0.169230 ACGCGTTTGACAAACTTGCA 59.831 45.000 24.60 0.00 39.23 4.08
600 953 3.481789 GCGTTTGACAAACTTGCACAAAG 60.482 43.478 24.60 10.02 42.07 2.77
1407 1778 2.112297 GGTTTGCAGGTCCACGGA 59.888 61.111 0.00 0.00 0.00 4.69
1479 1850 3.513912 TGGTGGAGATGTACACGAAGAAT 59.486 43.478 0.00 0.00 38.46 2.40
1523 1894 4.467084 GTTCGCCGAGATGCCCCA 62.467 66.667 0.00 0.00 0.00 4.96
1524 1895 3.711814 TTCGCCGAGATGCCCCAA 61.712 61.111 0.00 0.00 0.00 4.12
1599 1970 2.514824 GCCAAGGCCATCGGAGTC 60.515 66.667 5.01 0.00 34.56 3.36
1602 1973 1.604378 CAAGGCCATCGGAGTCCTT 59.396 57.895 5.01 3.33 39.35 3.36
1815 2186 2.904866 GCGCACAGGGTGTTCCAA 60.905 61.111 0.30 0.00 38.24 3.53
1818 2189 1.875963 GCACAGGGTGTTCCAATCG 59.124 57.895 0.00 0.00 38.24 3.34
1848 2219 1.407656 GGCCCGTCATATCCTGGACA 61.408 60.000 0.00 0.00 33.66 4.02
2020 2391 4.323333 CCTGGATATACTTCAGAGCCATGG 60.323 50.000 7.63 7.63 0.00 3.66
2032 2403 0.957395 AGCCATGGCAGACAAGTTCG 60.957 55.000 37.18 0.00 44.88 3.95
2035 2406 2.034879 ATGGCAGACAAGTTCGGCG 61.035 57.895 0.00 0.00 45.69 6.46
2052 2423 2.766400 CGTCGAGCCTGGAGAGGAC 61.766 68.421 0.00 0.00 42.93 3.85
2130 2501 1.079543 GCTGATATCGCGGATGCCT 60.080 57.895 6.13 0.00 38.08 4.75
2161 2532 3.241530 TTCTGGTCTGGCAGGCGT 61.242 61.111 15.73 0.00 0.00 5.68
2178 2549 2.518112 TTGCTTGGCGCCTGTCAA 60.518 55.556 29.70 23.17 37.36 3.18
2196 2567 0.333993 AACTCCATGGCAATGAGGCT 59.666 50.000 6.96 0.00 44.55 4.58
2461 2886 2.783135 TCCTGATGGAAGCACTTGAAC 58.217 47.619 0.00 0.00 39.87 3.18
2556 2986 2.167075 GGCTTGGATGGAAGTGAATTGG 59.833 50.000 0.00 0.00 0.00 3.16
2560 2990 2.225091 TGGATGGAAGTGAATTGGCAGT 60.225 45.455 0.00 0.00 0.00 4.40
2565 2996 3.243367 TGGAAGTGAATTGGCAGTTTTCG 60.243 43.478 0.00 0.00 31.86 3.46
2641 3073 6.595716 GCTATCAATTCTGTACAGGACAAACT 59.404 38.462 22.48 5.63 37.70 2.66
2649 3081 7.166691 TCTGTACAGGACAAACTAGTTATCC 57.833 40.000 22.48 22.88 37.70 2.59
2797 3232 1.289231 ACTAGAGCTCATGGAGTGGGA 59.711 52.381 17.77 0.00 31.39 4.37
2811 3246 4.099266 TGGAGTGGGAAAAACTGTTCAATG 59.901 41.667 0.00 0.00 0.00 2.82
2858 3293 1.407979 CCATTTGGCATCCTCTGAAGC 59.592 52.381 0.00 0.00 34.50 3.86
2859 3294 2.097036 CATTTGGCATCCTCTGAAGCA 58.903 47.619 0.00 0.00 36.94 3.91
2890 3325 1.066573 CAAGAATCGGTCCTGCAGACT 60.067 52.381 17.39 0.00 45.54 3.24
3093 3528 3.422417 TGGTCGATCTTGACGATCTTC 57.578 47.619 0.00 0.00 45.19 2.87
3150 3589 2.234143 TCTATCAGAGCTGGTGATCCG 58.766 52.381 10.76 5.40 36.11 4.18
3171 3610 5.704053 TCCGAATTAAAAACAGACTTCCCTC 59.296 40.000 0.00 0.00 0.00 4.30
3188 3628 4.918588 TCCCTCCAAATTCTTTAGACCAC 58.081 43.478 0.00 0.00 0.00 4.16
3190 3630 4.459337 CCCTCCAAATTCTTTAGACCACAC 59.541 45.833 0.00 0.00 0.00 3.82
3191 3631 4.459337 CCTCCAAATTCTTTAGACCACACC 59.541 45.833 0.00 0.00 0.00 4.16
3199 3639 4.710324 TCTTTAGACCACACCGAACATTT 58.290 39.130 0.00 0.00 0.00 2.32
3222 3662 7.842887 TTAAATGTACCCTTAACCTGCTTTT 57.157 32.000 0.00 0.00 0.00 2.27
3262 3706 4.141801 TGGGTTATGCGCAATCTAACTAGT 60.142 41.667 24.07 5.38 37.09 2.57
3330 3774 2.338809 TGGTCAGTTGATCAGAGGGTT 58.661 47.619 0.00 0.00 30.51 4.11
3336 3780 4.043310 TCAGTTGATCAGAGGGTTTTCCAT 59.957 41.667 0.00 0.00 42.91 3.41
3337 3781 4.157289 CAGTTGATCAGAGGGTTTTCCATG 59.843 45.833 0.00 0.00 42.91 3.66
3348 3792 4.898861 AGGGTTTTCCATGACAGCTAAAAA 59.101 37.500 0.00 0.00 42.91 1.94
3350 3794 5.639082 GGGTTTTCCATGACAGCTAAAAATG 59.361 40.000 0.00 0.00 42.91 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.992217 GGTACTCCAATATGGCACTTAAGAG 59.008 44.000 10.09 1.84 37.47 2.85
3 4 5.702065 TGGTACTCCAATATGGCACTTAA 57.298 39.130 0.00 0.00 41.25 1.85
39 40 9.599866 TTGATCACTAGAATGTCAACGATTATT 57.400 29.630 0.00 0.00 0.00 1.40
40 41 9.770097 ATTGATCACTAGAATGTCAACGATTAT 57.230 29.630 0.00 0.00 32.30 1.28
42 43 9.599866 TTATTGATCACTAGAATGTCAACGATT 57.400 29.630 0.00 0.00 32.30 3.34
43 44 9.599866 TTTATTGATCACTAGAATGTCAACGAT 57.400 29.630 0.00 0.00 32.30 3.73
44 45 8.996024 TTTATTGATCACTAGAATGTCAACGA 57.004 30.769 0.00 0.00 32.30 3.85
62 63 9.939802 GAGGACTAGAAAGGTAGTTTTTATTGA 57.060 33.333 0.00 0.00 33.18 2.57
63 64 9.163899 GGAGGACTAGAAAGGTAGTTTTTATTG 57.836 37.037 0.00 0.00 33.18 1.90
64 65 9.113797 AGGAGGACTAGAAAGGTAGTTTTTATT 57.886 33.333 0.00 0.00 33.18 1.40
65 66 8.541234 CAGGAGGACTAGAAAGGTAGTTTTTAT 58.459 37.037 0.00 0.00 33.18 1.40
66 67 7.731688 TCAGGAGGACTAGAAAGGTAGTTTTTA 59.268 37.037 0.00 0.00 33.18 1.52
67 68 6.557633 TCAGGAGGACTAGAAAGGTAGTTTTT 59.442 38.462 0.00 0.00 33.18 1.94
68 69 6.014413 GTCAGGAGGACTAGAAAGGTAGTTTT 60.014 42.308 0.00 0.00 43.46 2.43
69 70 5.481122 GTCAGGAGGACTAGAAAGGTAGTTT 59.519 44.000 0.00 0.00 43.46 2.66
70 71 5.018149 GTCAGGAGGACTAGAAAGGTAGTT 58.982 45.833 0.00 0.00 43.46 2.24
71 72 4.602107 GTCAGGAGGACTAGAAAGGTAGT 58.398 47.826 0.00 0.00 43.46 2.73
84 85 1.728323 TGGTGATGTTGTCAGGAGGA 58.272 50.000 0.00 0.00 37.56 3.71
85 86 2.566833 TTGGTGATGTTGTCAGGAGG 57.433 50.000 0.00 0.00 37.56 4.30
86 87 4.520111 TCATTTTGGTGATGTTGTCAGGAG 59.480 41.667 0.00 0.00 37.56 3.69
87 88 4.468713 TCATTTTGGTGATGTTGTCAGGA 58.531 39.130 0.00 0.00 37.56 3.86
88 89 4.321452 CCTCATTTTGGTGATGTTGTCAGG 60.321 45.833 0.00 0.00 37.56 3.86
89 90 4.520111 TCCTCATTTTGGTGATGTTGTCAG 59.480 41.667 0.00 0.00 37.56 3.51
90 91 4.468713 TCCTCATTTTGGTGATGTTGTCA 58.531 39.130 0.00 0.00 0.00 3.58
91 92 5.649782 ATCCTCATTTTGGTGATGTTGTC 57.350 39.130 0.00 0.00 0.00 3.18
92 93 5.047092 GGAATCCTCATTTTGGTGATGTTGT 60.047 40.000 0.00 0.00 0.00 3.32
93 94 5.047164 TGGAATCCTCATTTTGGTGATGTTG 60.047 40.000 0.00 0.00 0.00 3.33
94 95 5.047092 GTGGAATCCTCATTTTGGTGATGTT 60.047 40.000 0.00 0.00 0.00 2.71
95 96 4.463891 GTGGAATCCTCATTTTGGTGATGT 59.536 41.667 0.00 0.00 0.00 3.06
96 97 4.142093 GGTGGAATCCTCATTTTGGTGATG 60.142 45.833 0.00 0.00 0.00 3.07
97 98 4.026052 GGTGGAATCCTCATTTTGGTGAT 58.974 43.478 0.00 0.00 0.00 3.06
98 99 3.430453 GGTGGAATCCTCATTTTGGTGA 58.570 45.455 0.00 0.00 0.00 4.02
99 100 2.164219 CGGTGGAATCCTCATTTTGGTG 59.836 50.000 0.00 0.00 0.00 4.17
100 101 2.225017 ACGGTGGAATCCTCATTTTGGT 60.225 45.455 0.00 0.00 0.00 3.67
101 102 2.446435 ACGGTGGAATCCTCATTTTGG 58.554 47.619 0.00 0.00 0.00 3.28
102 103 4.519540 AAACGGTGGAATCCTCATTTTG 57.480 40.909 0.00 0.00 0.00 2.44
103 104 4.157840 GCTAAACGGTGGAATCCTCATTTT 59.842 41.667 0.00 3.13 0.00 1.82
104 105 3.694566 GCTAAACGGTGGAATCCTCATTT 59.305 43.478 0.00 4.68 0.00 2.32
105 106 3.279434 GCTAAACGGTGGAATCCTCATT 58.721 45.455 0.00 0.00 0.00 2.57
106 107 2.421529 GGCTAAACGGTGGAATCCTCAT 60.422 50.000 0.00 0.00 0.00 2.90
107 108 1.065709 GGCTAAACGGTGGAATCCTCA 60.066 52.381 0.00 0.00 0.00 3.86
108 109 1.065709 TGGCTAAACGGTGGAATCCTC 60.066 52.381 0.00 0.00 0.00 3.71
109 110 0.988832 TGGCTAAACGGTGGAATCCT 59.011 50.000 0.00 0.00 0.00 3.24
110 111 1.828979 TTGGCTAAACGGTGGAATCC 58.171 50.000 0.00 0.00 0.00 3.01
111 112 3.504520 TCTTTTGGCTAAACGGTGGAATC 59.495 43.478 0.00 0.00 0.00 2.52
112 113 3.492337 TCTTTTGGCTAAACGGTGGAAT 58.508 40.909 0.00 0.00 0.00 3.01
113 114 2.933573 TCTTTTGGCTAAACGGTGGAA 58.066 42.857 0.00 0.00 0.00 3.53
114 115 2.642154 TCTTTTGGCTAAACGGTGGA 57.358 45.000 0.00 0.00 0.00 4.02
115 116 3.067601 AGTTTCTTTTGGCTAAACGGTGG 59.932 43.478 0.00 0.00 37.99 4.61
116 117 4.301637 AGTTTCTTTTGGCTAAACGGTG 57.698 40.909 0.00 0.00 37.99 4.94
117 118 6.938596 AGTATAGTTTCTTTTGGCTAAACGGT 59.061 34.615 0.00 0.00 37.99 4.83
118 119 7.333672 AGAGTATAGTTTCTTTTGGCTAAACGG 59.666 37.037 0.00 0.00 37.99 4.44
119 120 8.252964 AGAGTATAGTTTCTTTTGGCTAAACG 57.747 34.615 0.00 0.00 37.99 3.60
121 122 9.227777 GGAAGAGTATAGTTTCTTTTGGCTAAA 57.772 33.333 0.00 0.00 33.97 1.85
122 123 8.603304 AGGAAGAGTATAGTTTCTTTTGGCTAA 58.397 33.333 0.00 0.00 33.97 3.09
123 124 8.147244 AGGAAGAGTATAGTTTCTTTTGGCTA 57.853 34.615 0.00 0.00 33.97 3.93
124 125 7.021998 AGGAAGAGTATAGTTTCTTTTGGCT 57.978 36.000 0.00 0.00 33.97 4.75
125 126 7.011576 GCTAGGAAGAGTATAGTTTCTTTTGGC 59.988 40.741 0.00 0.00 33.97 4.52
126 127 8.041323 TGCTAGGAAGAGTATAGTTTCTTTTGG 58.959 37.037 0.00 0.00 33.97 3.28
127 128 9.436957 TTGCTAGGAAGAGTATAGTTTCTTTTG 57.563 33.333 0.00 0.00 33.97 2.44
157 158 9.569122 GCATATGAAATAAGGGGAGTAGTAAAA 57.431 33.333 6.97 0.00 29.06 1.52
158 159 8.719596 TGCATATGAAATAAGGGGAGTAGTAAA 58.280 33.333 6.97 0.00 29.06 2.01
288 291 8.344831 TGCATACAACATGAGATATGCTTTTAC 58.655 33.333 25.60 9.27 46.55 2.01
299 302 8.680039 TCAATATCATTGCATACAACATGAGA 57.320 30.769 0.00 0.00 38.99 3.27
301 304 9.069082 TCATCAATATCATTGCATACAACATGA 57.931 29.630 0.00 0.00 38.99 3.07
341 344 9.442047 ACAGAAGAAGAAAATCAACACCTATAG 57.558 33.333 0.00 0.00 0.00 1.31
350 353 9.847224 ACCTAGTTTACAGAAGAAGAAAATCAA 57.153 29.630 0.00 0.00 0.00 2.57
352 355 9.490379 TGACCTAGTTTACAGAAGAAGAAAATC 57.510 33.333 0.00 0.00 0.00 2.17
354 357 9.675464 TTTGACCTAGTTTACAGAAGAAGAAAA 57.325 29.630 0.00 0.00 0.00 2.29
355 358 9.326413 CTTTGACCTAGTTTACAGAAGAAGAAA 57.674 33.333 0.00 0.00 0.00 2.52
356 359 8.483758 ACTTTGACCTAGTTTACAGAAGAAGAA 58.516 33.333 0.00 0.00 0.00 2.52
357 360 8.019656 ACTTTGACCTAGTTTACAGAAGAAGA 57.980 34.615 0.00 0.00 0.00 2.87
358 361 8.552034 CAACTTTGACCTAGTTTACAGAAGAAG 58.448 37.037 0.00 0.00 33.73 2.85
359 362 8.262227 TCAACTTTGACCTAGTTTACAGAAGAA 58.738 33.333 0.00 0.00 33.73 2.52
360 363 7.788026 TCAACTTTGACCTAGTTTACAGAAGA 58.212 34.615 0.00 0.00 33.73 2.87
373 376 9.139940 AAAGTCAAGCTTTGTCAACTTTGACCT 62.140 37.037 21.08 12.76 45.39 3.85
403 406 9.702726 CGAAATGTGGTCAGTATATAACTTTTG 57.297 33.333 0.00 0.00 35.76 2.44
404 407 8.889717 CCGAAATGTGGTCAGTATATAACTTTT 58.110 33.333 0.00 0.00 35.76 2.27
405 408 8.262227 TCCGAAATGTGGTCAGTATATAACTTT 58.738 33.333 0.00 0.00 35.76 2.66
408 411 8.495949 CATTCCGAAATGTGGTCAGTATATAAC 58.504 37.037 0.00 0.00 37.97 1.89
409 412 7.659799 CCATTCCGAAATGTGGTCAGTATATAA 59.340 37.037 0.00 0.00 40.63 0.98
410 413 7.015779 TCCATTCCGAAATGTGGTCAGTATATA 59.984 37.037 0.00 0.00 40.63 0.86
412 415 5.129650 TCCATTCCGAAATGTGGTCAGTATA 59.870 40.000 0.00 0.00 40.63 1.47
417 420 2.304470 TCTCCATTCCGAAATGTGGTCA 59.696 45.455 0.00 0.00 40.63 4.02
418 421 2.939103 CTCTCCATTCCGAAATGTGGTC 59.061 50.000 0.00 0.00 40.63 4.02
428 431 5.011090 TGTTTCATACTCTCTCCATTCCG 57.989 43.478 0.00 0.00 0.00 4.30
473 476 8.976353 TGTATGCATTGACCCTGTAAAATTTAT 58.024 29.630 3.54 0.00 0.00 1.40
485 488 2.098117 GCAGAAGTGTATGCATTGACCC 59.902 50.000 3.54 0.00 41.77 4.46
498 501 9.447040 CATTGATCACTAATTTATGCAGAAGTG 57.553 33.333 4.82 4.82 36.52 3.16
539 889 8.978564 TTAGATTTGCGAATAGAAAAATGCAA 57.021 26.923 0.00 0.00 40.22 4.08
549 899 6.143919 TGCACTCGTATTAGATTTGCGAATAG 59.856 38.462 0.00 0.00 33.93 1.73
551 901 4.808895 TGCACTCGTATTAGATTTGCGAAT 59.191 37.500 0.00 0.00 33.93 3.34
552 902 4.177783 TGCACTCGTATTAGATTTGCGAA 58.822 39.130 0.00 0.00 33.93 4.70
554 904 4.514545 TTGCACTCGTATTAGATTTGCG 57.485 40.909 0.00 0.00 33.93 4.85
564 917 0.863144 AAACGCGTTTGCACTCGTAT 59.137 45.000 34.36 8.10 43.47 3.06
565 918 0.042880 CAAACGCGTTTGCACTCGTA 60.043 50.000 41.32 0.00 43.47 3.43
578 931 1.623359 TGTGCAAGTTTGTCAAACGC 58.377 45.000 20.04 18.28 45.88 4.84
580 933 3.989831 GCTTTGTGCAAGTTTGTCAAAC 58.010 40.909 18.90 18.90 42.31 2.93
1407 1778 1.963338 GCCGCTCTTGACAAGCTGT 60.963 57.895 10.50 0.00 37.62 4.40
1502 1873 3.188786 GCATCTCGGCGAACGCTT 61.189 61.111 12.13 0.00 43.86 4.68
1523 1894 0.317603 CCACGACACGACGTCTCTTT 60.318 55.000 14.70 0.00 44.76 2.52
1524 1895 1.162181 TCCACGACACGACGTCTCTT 61.162 55.000 14.70 0.00 44.76 2.85
1599 1970 0.816825 CGAGCATCATGGGACCAAGG 60.817 60.000 0.00 0.00 33.17 3.61
1602 1973 0.178767 CTTCGAGCATCATGGGACCA 59.821 55.000 0.00 0.00 33.17 4.02
1848 2219 1.953559 CGAACCCCATGATCATCGTT 58.046 50.000 4.86 8.50 0.00 3.85
2020 2391 2.853914 GACGCCGAACTTGTCTGC 59.146 61.111 0.00 0.00 33.39 4.26
2035 2406 2.419739 GGTCCTCTCCAGGCTCGAC 61.420 68.421 0.00 0.00 40.12 4.20
2043 2414 1.681327 GGCGTAGTGGTCCTCTCCA 60.681 63.158 0.00 0.00 34.85 3.86
2046 2417 2.352032 GCAGGCGTAGTGGTCCTCT 61.352 63.158 0.00 0.00 0.00 3.69
2052 2423 1.815421 GACCATGCAGGCGTAGTGG 60.815 63.158 0.00 0.00 43.14 4.00
2085 2456 1.261480 CGTCCTCTATATGGCCTGCT 58.739 55.000 3.32 0.00 0.00 4.24
2169 2540 2.401766 GCCATGGAGTTGACAGGCG 61.402 63.158 18.40 0.00 31.88 5.52
2178 2549 0.395311 CAGCCTCATTGCCATGGAGT 60.395 55.000 18.40 0.00 0.00 3.85
2281 2652 4.778143 GCCCCAATCGTGCCGACT 62.778 66.667 0.00 0.00 39.18 4.18
2493 2918 9.892130 CAGATAACTGAAATACCTACTTTCCTT 57.108 33.333 0.00 0.00 46.03 3.36
2556 2986 4.618489 CAGAAATCCATTCACGAAAACTGC 59.382 41.667 0.00 0.00 40.72 4.40
2560 2990 4.844998 TGCAGAAATCCATTCACGAAAA 57.155 36.364 0.00 0.00 40.72 2.29
2565 2996 4.340097 TGGATCATGCAGAAATCCATTCAC 59.660 41.667 18.59 0.00 43.06 3.18
2681 3113 3.843027 CAAGGGCTATCAGGAGGATGTAT 59.157 47.826 0.00 0.00 36.72 2.29
2691 3123 6.482898 AGAGCATATATCAAGGGCTATCAG 57.517 41.667 0.00 0.00 34.44 2.90
2722 3155 7.012044 GGACTATGTATGGCTTTCGTTGTATTT 59.988 37.037 0.00 0.00 0.00 1.40
2730 3164 4.322080 TCAGGACTATGTATGGCTTTCG 57.678 45.455 0.00 0.00 0.00 3.46
2786 3221 3.636300 TGAACAGTTTTTCCCACTCCATG 59.364 43.478 0.00 0.00 0.00 3.66
2797 3232 4.330620 CAGCTTGCACATTGAACAGTTTTT 59.669 37.500 0.00 0.00 0.00 1.94
2858 3293 5.220854 GGACCGATTCTTGTAATGGTTCATG 60.221 44.000 0.00 0.00 0.00 3.07
2859 3294 4.881850 GGACCGATTCTTGTAATGGTTCAT 59.118 41.667 0.00 0.00 0.00 2.57
2890 3325 1.270465 CGCCTGATATCATCACCTGCA 60.270 52.381 5.72 0.00 35.06 4.41
2896 3331 4.959723 TCAAATGTCGCCTGATATCATCA 58.040 39.130 5.72 2.12 37.76 3.07
3003 3438 3.274288 GGCGTTGATCCTCTTCAAGAAT 58.726 45.455 0.00 0.00 36.34 2.40
3093 3528 4.989875 ACAGGAATATGAGGGGAGATTG 57.010 45.455 0.00 0.00 0.00 2.67
3127 3562 4.262377 CGGATCACCAGCTCTGATAGATTT 60.262 45.833 3.78 0.00 35.59 2.17
3128 3563 3.257873 CGGATCACCAGCTCTGATAGATT 59.742 47.826 3.78 0.00 35.59 2.40
3130 3565 2.158608 TCGGATCACCAGCTCTGATAGA 60.159 50.000 3.78 4.62 35.59 1.98
3148 3587 5.106277 GGAGGGAAGTCTGTTTTTAATTCGG 60.106 44.000 0.00 0.00 0.00 4.30
3150 3589 6.894339 TGGAGGGAAGTCTGTTTTTAATTC 57.106 37.500 0.00 0.00 0.00 2.17
3171 3610 4.069304 TCGGTGTGGTCTAAAGAATTTGG 58.931 43.478 0.00 0.00 39.63 3.28
3188 3628 5.890424 AGGGTACATTTAAATGTTCGGTG 57.110 39.130 32.58 9.77 46.95 4.94
3190 3630 7.121611 AGGTTAAGGGTACATTTAAATGTTCGG 59.878 37.037 32.58 9.62 46.95 4.30
3191 3631 7.966204 CAGGTTAAGGGTACATTTAAATGTTCG 59.034 37.037 32.58 12.27 46.95 3.95
3199 3639 7.288158 ACAAAAAGCAGGTTAAGGGTACATTTA 59.712 33.333 0.00 0.00 0.00 1.40
3238 3678 2.943033 AGTTAGATTGCGCATAACCCAC 59.057 45.455 22.41 11.82 31.21 4.61
3239 3679 3.275617 AGTTAGATTGCGCATAACCCA 57.724 42.857 22.41 4.33 31.21 4.51
3240 3680 4.377897 ACTAGTTAGATTGCGCATAACCC 58.622 43.478 22.41 6.98 31.21 4.11
3241 3681 5.522460 TCAACTAGTTAGATTGCGCATAACC 59.478 40.000 22.41 9.11 31.21 2.85
3244 3684 7.786178 AAATCAACTAGTTAGATTGCGCATA 57.214 32.000 22.69 2.21 32.69 3.14
3247 3687 7.021196 TGAAAAATCAACTAGTTAGATTGCGC 58.979 34.615 22.69 0.00 32.69 6.09
3298 3742 7.776107 TGATCAACTGACCATTGTTTTGTAAA 58.224 30.769 0.00 0.00 0.00 2.01
3309 3753 2.555664 ACCCTCTGATCAACTGACCAT 58.444 47.619 0.00 0.00 0.00 3.55
3330 3774 4.282957 TGGCATTTTTAGCTGTCATGGAAA 59.717 37.500 0.00 0.00 0.00 3.13
3336 3780 4.870123 ACATTGGCATTTTTAGCTGTCA 57.130 36.364 0.00 0.00 0.00 3.58
3337 3781 4.389687 CCAACATTGGCATTTTTAGCTGTC 59.610 41.667 0.00 0.00 42.21 3.51
3350 3794 6.043359 TGCTTTGCAATTTCCAACATTGGC 62.043 41.667 0.00 0.00 41.20 4.52
3372 3816 2.350804 CGATGTGCAATGGAGAGACTTG 59.649 50.000 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.