Multiple sequence alignment - TraesCS5D01G271000

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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 TraesCS5D01G271000 chr5D 100.000 2591 0 0 1 2591 374657688 374660278 0.000000e+00 4785.0
1 TraesCS5D01G271000 chr5A 89.474 1843 103 29 801 2591 476399322 476401125 0.000000e+00 2244.0
2 TraesCS5D01G271000 chr5A 89.895 475 38 5 280 754 689514382 689514846 1.030000e-168 603.0
3 TraesCS5D01G271000 chr5A 91.489 47 4 0 675 721 484397647 484397693 5.980000e-07 65.8
4 TraesCS5D01G271000 chr5B 91.667 1044 48 16 675 1704 447393752 447394770 0.000000e+00 1410.0
5 TraesCS5D01G271000 chr5B 87.500 568 43 9 134 681 447393032 447393591 4.710000e-177 630.0
6 TraesCS5D01G271000 chr5B 84.110 472 43 18 1857 2306 447395624 447396085 6.630000e-116 427.0
7 TraesCS5D01G271000 chr5B 84.255 235 16 7 2303 2516 447400893 447401127 2.610000e-50 209.0
8 TraesCS5D01G271000 chr1B 89.498 438 41 3 285 721 446948234 446947801 1.360000e-152 549.0
9 TraesCS5D01G271000 chr4D 90.864 405 30 2 350 754 505310019 505310416 1.060000e-148 536.0
10 TraesCS5D01G271000 chr4B 88.144 194 20 1 285 478 6012923 6012733 7.210000e-56 228.0
11 TraesCS5D01G271000 chr4B 82.407 216 24 9 539 746 6012732 6012523 2.650000e-40 176.0
12 TraesCS5D01G271000 chr4A 88.000 75 7 2 428 500 601280254 601280180 1.280000e-13 87.9


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 TraesCS5D01G271000 chr5D 374657688 374660278 2590 False 4785.000000 4785 100.000 1 2591 1 chr5D.!!$F1 2590
1 TraesCS5D01G271000 chr5A 476399322 476401125 1803 False 2244.000000 2244 89.474 801 2591 1 chr5A.!!$F1 1790
2 TraesCS5D01G271000 chr5B 447393032 447396085 3053 False 822.333333 1410 87.759 134 2306 3 chr5B.!!$F2 2172

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
103 104 0.108804 TTTTCCGTGAGCTAGCCGAG 60.109 55.0 12.13 0.32 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1775 2719 0.112995 ACCCACATGTGCTGATTGGT 59.887 50.0 20.81 17.11 0.0 3.67 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
101 102 2.835605 TTTTTCCGTGAGCTAGCCG 58.164 52.632 12.13 8.06 0.00 5.52
102 103 0.319083 TTTTTCCGTGAGCTAGCCGA 59.681 50.000 12.13 0.00 0.00 5.54
103 104 0.108804 TTTTCCGTGAGCTAGCCGAG 60.109 55.000 12.13 0.32 0.00 4.63
104 105 0.963856 TTTCCGTGAGCTAGCCGAGA 60.964 55.000 12.13 5.19 0.00 4.04
105 106 0.963856 TTCCGTGAGCTAGCCGAGAA 60.964 55.000 12.13 10.56 0.00 2.87
106 107 0.963856 TCCGTGAGCTAGCCGAGAAA 60.964 55.000 12.13 0.00 0.00 2.52
107 108 0.108804 CCGTGAGCTAGCCGAGAAAA 60.109 55.000 12.13 0.00 0.00 2.29
108 109 1.671850 CCGTGAGCTAGCCGAGAAAAA 60.672 52.381 12.13 0.00 0.00 1.94
109 110 2.271800 CGTGAGCTAGCCGAGAAAAAT 58.728 47.619 12.13 0.00 0.00 1.82
110 111 3.444916 CGTGAGCTAGCCGAGAAAAATA 58.555 45.455 12.13 0.00 0.00 1.40
111 112 3.863424 CGTGAGCTAGCCGAGAAAAATAA 59.137 43.478 12.13 0.00 0.00 1.40
112 113 4.328983 CGTGAGCTAGCCGAGAAAAATAAA 59.671 41.667 12.13 0.00 0.00 1.40
113 114 5.163893 CGTGAGCTAGCCGAGAAAAATAAAA 60.164 40.000 12.13 0.00 0.00 1.52
114 115 6.456988 CGTGAGCTAGCCGAGAAAAATAAAAT 60.457 38.462 12.13 0.00 0.00 1.82
115 116 6.688813 GTGAGCTAGCCGAGAAAAATAAAATG 59.311 38.462 12.13 0.00 0.00 2.32
116 117 6.136541 AGCTAGCCGAGAAAAATAAAATGG 57.863 37.500 12.13 0.00 0.00 3.16
117 118 5.067805 AGCTAGCCGAGAAAAATAAAATGGG 59.932 40.000 12.13 0.00 0.00 4.00
118 119 4.123497 AGCCGAGAAAAATAAAATGGGC 57.877 40.909 0.00 0.00 38.29 5.36
119 120 2.857748 GCCGAGAAAAATAAAATGGGCG 59.142 45.455 0.00 0.00 0.00 6.13
120 121 3.428316 GCCGAGAAAAATAAAATGGGCGA 60.428 43.478 0.00 0.00 0.00 5.54
121 122 4.351192 CCGAGAAAAATAAAATGGGCGAG 58.649 43.478 0.00 0.00 0.00 5.03
122 123 3.791353 CGAGAAAAATAAAATGGGCGAGC 59.209 43.478 0.00 0.00 0.00 5.03
123 124 4.112634 GAGAAAAATAAAATGGGCGAGCC 58.887 43.478 5.37 5.37 0.00 4.70
124 125 3.513515 AGAAAAATAAAATGGGCGAGCCA 59.486 39.130 16.65 2.66 37.98 4.75
125 126 3.971245 AAAATAAAATGGGCGAGCCAA 57.029 38.095 16.65 4.77 37.98 4.52
126 127 4.486125 AAAATAAAATGGGCGAGCCAAT 57.514 36.364 16.65 7.38 37.98 3.16
127 128 3.457610 AATAAAATGGGCGAGCCAATG 57.542 42.857 16.65 0.00 37.98 2.82
128 129 2.136298 TAAAATGGGCGAGCCAATGA 57.864 45.000 16.65 0.00 37.98 2.57
129 130 0.532115 AAAATGGGCGAGCCAATGAC 59.468 50.000 16.65 0.00 37.98 3.06
130 131 1.656818 AAATGGGCGAGCCAATGACG 61.657 55.000 16.65 0.00 37.98 4.35
131 132 2.535485 AATGGGCGAGCCAATGACGA 62.535 55.000 16.65 0.00 37.98 4.20
132 133 2.892425 GGGCGAGCCAATGACGAG 60.892 66.667 16.65 0.00 37.98 4.18
160 161 1.345410 CGCGTTTTAGGGCATTTTGG 58.655 50.000 0.00 0.00 0.00 3.28
161 162 1.720805 GCGTTTTAGGGCATTTTGGG 58.279 50.000 0.00 0.00 0.00 4.12
165 166 1.567357 TTTAGGGCATTTTGGGGAGC 58.433 50.000 0.00 0.00 0.00 4.70
183 184 4.443621 GGAGCGCTAAATAGGAGAAAAGT 58.556 43.478 11.50 0.00 0.00 2.66
189 190 7.011482 AGCGCTAAATAGGAGAAAAGTACATTG 59.989 37.037 8.99 0.00 0.00 2.82
190 191 7.630924 CGCTAAATAGGAGAAAAGTACATTGG 58.369 38.462 0.00 0.00 0.00 3.16
192 193 7.067008 GCTAAATAGGAGAAAAGTACATTGGCA 59.933 37.037 0.00 0.00 0.00 4.92
218 227 1.063266 AGGAGAAAAACACCCTGGCAA 60.063 47.619 0.00 0.00 0.00 4.52
234 243 3.613661 CAACCCATGCCCAGGTTAT 57.386 52.632 4.07 0.00 44.61 1.89
249 258 4.255301 CAGGTTATAGCCGTACCACAAAA 58.745 43.478 0.00 0.00 34.32 2.44
311 320 0.538057 TCTCAACAAGGCTGGCTTGG 60.538 55.000 36.77 24.69 36.23 3.61
314 323 1.833934 AACAAGGCTGGCTTGGGTG 60.834 57.895 36.77 20.56 36.23 4.61
315 324 3.688159 CAAGGCTGGCTTGGGTGC 61.688 66.667 30.03 0.00 0.00 5.01
337 346 1.058428 TGGCTCTGGATCATGAGGGG 61.058 60.000 0.09 0.00 0.00 4.79
340 349 0.841961 CTCTGGATCATGAGGGGCAA 59.158 55.000 0.09 0.00 0.00 4.52
356 365 2.434884 AATGCACCCTCTCGCGTG 60.435 61.111 5.77 3.13 0.00 5.34
379 388 1.392131 GGGCCCCCTTTTGGAGATT 59.608 57.895 12.23 0.00 44.07 2.40
380 389 0.252696 GGGCCCCCTTTTGGAGATTT 60.253 55.000 12.23 0.00 44.07 2.17
396 418 2.064762 GATTTCGATCCAGAGATGGCG 58.935 52.381 0.00 0.00 30.90 5.69
416 438 1.805945 AAGCCTTAGCGCTTCGTCG 60.806 57.895 18.68 0.00 46.06 5.12
425 447 2.733593 GCTTCGTCGTGCGGTCTT 60.734 61.111 0.00 0.00 41.72 3.01
426 448 2.308039 GCTTCGTCGTGCGGTCTTT 61.308 57.895 0.00 0.00 41.72 2.52
427 449 1.773496 CTTCGTCGTGCGGTCTTTC 59.227 57.895 0.00 0.00 41.72 2.62
428 450 0.663568 CTTCGTCGTGCGGTCTTTCT 60.664 55.000 0.00 0.00 41.72 2.52
467 489 0.593128 ACGCATGTGACTTTTGCCTC 59.407 50.000 14.43 0.00 32.76 4.70
471 493 2.351157 GCATGTGACTTTTGCCTCTGAC 60.351 50.000 0.00 0.00 0.00 3.51
481 503 3.845781 TTGCCTCTGACTGTTTCTCTT 57.154 42.857 0.00 0.00 0.00 2.85
490 512 3.128589 TGACTGTTTCTCTTTGGTGCAAC 59.871 43.478 0.00 0.00 0.00 4.17
510 532 6.073276 TGCAACGAATCAATTCTAATATCCGG 60.073 38.462 0.00 0.00 34.69 5.14
517 539 4.021719 TCAATTCTAATATCCGGGACCGTC 60.022 45.833 10.17 0.00 37.81 4.79
518 540 1.915141 TCTAATATCCGGGACCGTCC 58.085 55.000 9.30 9.30 37.81 4.79
577 600 2.418746 GCCCTAGCTTTCACATCTTCGA 60.419 50.000 0.00 0.00 35.50 3.71
580 603 2.100605 AGCTTTCACATCTTCGACCC 57.899 50.000 0.00 0.00 0.00 4.46
598 621 0.670546 CCTCAAGCATGTTCGTCGGT 60.671 55.000 0.00 0.00 0.00 4.69
600 623 2.540515 CTCAAGCATGTTCGTCGGTAT 58.459 47.619 0.00 0.00 0.00 2.73
619 642 5.998981 CGGTATTGTAATTTAGTGGCCCATA 59.001 40.000 0.00 0.00 0.00 2.74
672 695 6.688578 AGTTTGTTCTCTATTTCGCACTCTA 58.311 36.000 0.00 0.00 0.00 2.43
738 928 4.780275 TCAAATCAATGAAATGCCGACA 57.220 36.364 0.00 0.00 0.00 4.35
775 965 2.296945 AAACTTGCACCCTCTGCCCA 62.297 55.000 0.00 0.00 46.51 5.36
784 974 1.228124 CCTCTGCCCACCGTTTCAA 60.228 57.895 0.00 0.00 0.00 2.69
868 1059 0.469144 TCTTTCCCCTTGGCCACAAC 60.469 55.000 3.88 0.00 32.14 3.32
869 1060 1.458588 TTTCCCCTTGGCCACAACC 60.459 57.895 3.88 0.00 32.14 3.77
870 1061 2.243774 TTTCCCCTTGGCCACAACCA 62.244 55.000 3.88 0.00 38.16 3.67
871 1062 2.917227 CCCCTTGGCCACAACCAC 60.917 66.667 3.88 0.00 40.19 4.16
872 1063 2.123511 CCCTTGGCCACAACCACA 60.124 61.111 3.88 0.00 40.19 4.17
873 1064 1.760086 CCCTTGGCCACAACCACAA 60.760 57.895 3.88 0.00 40.19 3.33
874 1065 1.333636 CCCTTGGCCACAACCACAAA 61.334 55.000 3.88 0.00 40.19 2.83
938 1129 1.541147 CATCTCCATCGCTCTCTCCTC 59.459 57.143 0.00 0.00 0.00 3.71
939 1130 0.843309 TCTCCATCGCTCTCTCCTCT 59.157 55.000 0.00 0.00 0.00 3.69
979 1170 0.679960 TCTCCTTGGATCTCGTCGCA 60.680 55.000 0.00 0.00 0.00 5.10
1586 1795 1.446272 CTGCCGACGGAGAAGAACC 60.446 63.158 20.50 0.00 0.00 3.62
1594 1803 2.828874 CGGAGAAGAACCGTAGAGAC 57.171 55.000 0.00 0.00 44.57 3.36
1596 1805 2.096174 CGGAGAAGAACCGTAGAGACAG 59.904 54.545 0.00 0.00 44.57 3.51
1597 1806 3.345414 GGAGAAGAACCGTAGAGACAGA 58.655 50.000 0.00 0.00 0.00 3.41
1598 1807 3.375922 GGAGAAGAACCGTAGAGACAGAG 59.624 52.174 0.00 0.00 0.00 3.35
1599 1808 2.750712 AGAAGAACCGTAGAGACAGAGC 59.249 50.000 0.00 0.00 0.00 4.09
1600 1809 2.201921 AGAACCGTAGAGACAGAGCA 57.798 50.000 0.00 0.00 0.00 4.26
1601 1810 1.813786 AGAACCGTAGAGACAGAGCAC 59.186 52.381 0.00 0.00 0.00 4.40
1602 1811 1.813786 GAACCGTAGAGACAGAGCACT 59.186 52.381 0.00 0.00 0.00 4.40
1604 1813 0.179150 CCGTAGAGACAGAGCACTGC 60.179 60.000 11.37 4.41 46.95 4.40
1629 1838 1.411977 AGCATGCTCGCTCTCTGTTAT 59.588 47.619 16.30 0.00 37.91 1.89
1630 1839 2.158986 AGCATGCTCGCTCTCTGTTATT 60.159 45.455 16.30 0.00 37.91 1.40
1631 1840 2.611292 GCATGCTCGCTCTCTGTTATTT 59.389 45.455 11.37 0.00 0.00 1.40
1632 1841 3.804325 GCATGCTCGCTCTCTGTTATTTA 59.196 43.478 11.37 0.00 0.00 1.40
1710 1927 5.009010 ACGGTATCCATTGATCAAATTGCTC 59.991 40.000 13.09 2.74 32.18 4.26
1790 2736 0.885879 CTGCACCAATCAGCACATGT 59.114 50.000 0.00 0.00 36.62 3.21
1818 2764 2.724977 TCATCGTCACAGGTGTTCTC 57.275 50.000 0.00 0.00 0.00 2.87
1821 2767 1.687563 TCGTCACAGGTGTTCTCTCA 58.312 50.000 0.00 0.00 0.00 3.27
1828 2774 1.824230 CAGGTGTTCTCTCAGAGAGGG 59.176 57.143 24.74 6.64 42.54 4.30
1830 2776 2.650322 AGGTGTTCTCTCAGAGAGGGTA 59.350 50.000 24.74 10.21 42.54 3.69
1835 2781 6.468543 GTGTTCTCTCAGAGAGGGTAAAAAT 58.531 40.000 24.74 0.00 42.54 1.82
1836 2782 6.592220 GTGTTCTCTCAGAGAGGGTAAAAATC 59.408 42.308 24.74 6.02 42.54 2.17
1847 2793 4.583871 AGGGTAAAAATCTCAGTGCTCAG 58.416 43.478 0.00 0.00 0.00 3.35
1869 2816 0.667792 GGAGCAGTGGTCGTGAGTTC 60.668 60.000 15.76 0.00 0.00 3.01
1878 2825 1.337821 GTCGTGAGTTCGTGATGACC 58.662 55.000 0.00 0.00 0.00 4.02
1954 2901 2.449031 CTAAGTGGCCGGCTGTGACA 62.449 60.000 28.56 12.88 0.00 3.58
1955 2902 2.725203 TAAGTGGCCGGCTGTGACAC 62.725 60.000 28.56 24.15 0.00 3.67
2038 2992 2.466982 CGCCGCGTCTACTCCAGTA 61.467 63.158 4.92 0.00 0.00 2.74
2046 3000 3.251571 CGTCTACTCCAGTAAAACCTGC 58.748 50.000 0.00 0.00 0.00 4.85
2062 3026 2.436824 GCCCGAAAGACCTGAGCC 60.437 66.667 0.00 0.00 0.00 4.70
2065 3029 3.181967 CGAAAGACCTGAGCCGCG 61.182 66.667 0.00 0.00 0.00 6.46
2089 3057 2.507992 CCGAACGAGAGCAGCAGG 60.508 66.667 0.00 0.00 0.00 4.85
2119 3089 3.583086 AGTGCTGTTGGATTACTACCACT 59.417 43.478 0.00 0.00 37.13 4.00
2294 3293 3.555547 TCGCACGATTAACAATCCAGATG 59.444 43.478 0.00 0.00 34.35 2.90
2296 3295 4.591202 GCACGATTAACAATCCAGATGTG 58.409 43.478 0.00 0.00 34.35 3.21
2313 3312 4.740822 GCACATCAAGGGGCCGGT 62.741 66.667 1.90 0.00 0.00 5.28
2341 3340 2.202797 CCGGTCCTCATGCACTCG 60.203 66.667 0.00 0.00 0.00 4.18
2370 3369 6.570672 AAGCTAGGATATTATTCGTCGACA 57.429 37.500 17.16 0.00 0.00 4.35
2384 3383 1.961277 CGACAGAAAACGGCCTGCT 60.961 57.895 0.00 0.00 33.90 4.24
2385 3384 0.669318 CGACAGAAAACGGCCTGCTA 60.669 55.000 0.00 0.00 33.90 3.49
2414 3413 3.220999 CTCCTTGACGTGTCGGCCA 62.221 63.158 2.24 0.00 31.60 5.36
2415 3414 2.280524 CCTTGACGTGTCGGCCAA 60.281 61.111 2.24 0.00 31.60 4.52
2431 3430 1.410737 CCAATCGAGCCGTGTACGTG 61.411 60.000 0.00 0.00 37.74 4.49
2434 3433 1.579964 ATCGAGCCGTGTACGTGTCA 61.580 55.000 0.00 0.00 37.74 3.58
2443 3442 2.059541 GTGTACGTGTCAGCTTCCTTC 58.940 52.381 0.00 0.00 0.00 3.46
2446 3445 3.190744 TGTACGTGTCAGCTTCCTTCTAG 59.809 47.826 0.00 0.00 0.00 2.43
2467 3466 1.748122 ATGCGCCAGCCTCTCAAAG 60.748 57.895 4.18 0.00 44.33 2.77
2506 3513 1.006832 ACGCGGCACTTCATCATTAC 58.993 50.000 12.47 0.00 0.00 1.89
2516 3523 6.018669 GGCACTTCATCATTACACTAAGCTAC 60.019 42.308 0.00 0.00 0.00 3.58
2517 3524 6.758886 GCACTTCATCATTACACTAAGCTACT 59.241 38.462 0.00 0.00 0.00 2.57
2519 3526 9.457110 CACTTCATCATTACACTAAGCTACTAG 57.543 37.037 0.00 0.00 0.00 2.57
2520 3527 9.409918 ACTTCATCATTACACTAAGCTACTAGA 57.590 33.333 0.00 0.00 0.00 2.43
2549 3559 2.032634 TGACGCAACGAGCCAATCC 61.033 57.895 0.00 0.00 41.38 3.01
2559 3569 0.249398 GAGCCAATCCACCACGTACT 59.751 55.000 0.00 0.00 0.00 2.73
2561 3571 0.743345 GCCAATCCACCACGTACTCC 60.743 60.000 0.00 0.00 0.00 3.85
2565 3575 1.933021 ATCCACCACGTACTCCAGAA 58.067 50.000 0.00 0.00 0.00 3.02
2583 3593 3.857093 CAGAAAAACACCGGTTTGAGTTG 59.143 43.478 2.97 0.00 46.20 3.16
2586 3596 4.729227 AAAACACCGGTTTGAGTTGAAT 57.271 36.364 2.97 0.00 46.20 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 0.319083 TCGGCTAGCTCACGGAAAAA 59.681 50.000 15.72 0.00 0.00 1.94
84 85 0.108804 CTCGGCTAGCTCACGGAAAA 60.109 55.000 15.72 0.00 0.00 2.29
85 86 0.963856 TCTCGGCTAGCTCACGGAAA 60.964 55.000 15.72 0.00 0.00 3.13
86 87 0.963856 TTCTCGGCTAGCTCACGGAA 60.964 55.000 15.72 11.89 0.00 4.30
87 88 0.963856 TTTCTCGGCTAGCTCACGGA 60.964 55.000 15.72 6.79 0.00 4.69
88 89 0.108804 TTTTCTCGGCTAGCTCACGG 60.109 55.000 15.72 4.60 0.00 4.94
89 90 1.710013 TTTTTCTCGGCTAGCTCACG 58.290 50.000 15.72 10.15 0.00 4.35
90 91 5.796350 TTTATTTTTCTCGGCTAGCTCAC 57.204 39.130 15.72 0.00 0.00 3.51
91 92 6.183360 CCATTTTATTTTTCTCGGCTAGCTCA 60.183 38.462 15.72 0.00 0.00 4.26
92 93 6.202226 CCATTTTATTTTTCTCGGCTAGCTC 58.798 40.000 15.72 3.82 0.00 4.09
93 94 5.067805 CCCATTTTATTTTTCTCGGCTAGCT 59.932 40.000 15.72 0.00 0.00 3.32
94 95 5.281727 CCCATTTTATTTTTCTCGGCTAGC 58.718 41.667 6.04 6.04 0.00 3.42
95 96 5.281727 GCCCATTTTATTTTTCTCGGCTAG 58.718 41.667 0.00 0.00 0.00 3.42
96 97 4.201970 CGCCCATTTTATTTTTCTCGGCTA 60.202 41.667 0.00 0.00 0.00 3.93
97 98 3.428862 CGCCCATTTTATTTTTCTCGGCT 60.429 43.478 0.00 0.00 0.00 5.52
98 99 2.857748 CGCCCATTTTATTTTTCTCGGC 59.142 45.455 0.00 0.00 0.00 5.54
99 100 4.351192 CTCGCCCATTTTATTTTTCTCGG 58.649 43.478 0.00 0.00 0.00 4.63
100 101 3.791353 GCTCGCCCATTTTATTTTTCTCG 59.209 43.478 0.00 0.00 0.00 4.04
101 102 4.112634 GGCTCGCCCATTTTATTTTTCTC 58.887 43.478 0.00 0.00 0.00 2.87
102 103 3.513515 TGGCTCGCCCATTTTATTTTTCT 59.486 39.130 5.33 0.00 39.18 2.52
103 104 3.855858 TGGCTCGCCCATTTTATTTTTC 58.144 40.909 5.33 0.00 39.18 2.29
104 105 3.971245 TGGCTCGCCCATTTTATTTTT 57.029 38.095 5.33 0.00 39.18 1.94
105 106 3.971245 TTGGCTCGCCCATTTTATTTT 57.029 38.095 5.33 0.00 44.89 1.82
106 107 3.450457 TCATTGGCTCGCCCATTTTATTT 59.550 39.130 5.33 0.00 44.89 1.40
107 108 3.030291 TCATTGGCTCGCCCATTTTATT 58.970 40.909 5.33 0.00 44.89 1.40
108 109 2.362077 GTCATTGGCTCGCCCATTTTAT 59.638 45.455 5.33 0.00 44.89 1.40
109 110 1.748493 GTCATTGGCTCGCCCATTTTA 59.252 47.619 5.33 0.00 44.89 1.52
110 111 0.532115 GTCATTGGCTCGCCCATTTT 59.468 50.000 5.33 0.00 44.89 1.82
111 112 1.656818 CGTCATTGGCTCGCCCATTT 61.657 55.000 5.33 0.00 44.89 2.32
112 113 2.114670 CGTCATTGGCTCGCCCATT 61.115 57.895 5.33 0.00 44.89 3.16
113 114 2.514592 CGTCATTGGCTCGCCCAT 60.515 61.111 5.33 0.00 44.89 4.00
114 115 3.664025 CTCGTCATTGGCTCGCCCA 62.664 63.158 5.33 0.00 43.51 5.36
115 116 2.892425 CTCGTCATTGGCTCGCCC 60.892 66.667 5.33 0.00 34.56 6.13
116 117 2.892425 CCTCGTCATTGGCTCGCC 60.892 66.667 0.00 0.00 0.00 5.54
117 118 3.567797 GCCTCGTCATTGGCTCGC 61.568 66.667 0.00 0.00 45.26 5.03
122 123 2.008268 GCATTGGGCCTCGTCATTGG 62.008 60.000 4.53 0.00 36.11 3.16
123 124 1.434696 GCATTGGGCCTCGTCATTG 59.565 57.895 4.53 0.00 36.11 2.82
124 125 2.114670 CGCATTGGGCCTCGTCATT 61.115 57.895 4.53 0.00 40.31 2.57
125 126 2.514592 CGCATTGGGCCTCGTCAT 60.515 61.111 4.53 0.00 40.31 3.06
130 131 1.928706 TAAAACGCGCATTGGGCCTC 61.929 55.000 18.73 0.00 40.31 4.70
131 132 1.933115 CTAAAACGCGCATTGGGCCT 61.933 55.000 18.73 5.80 40.31 5.19
132 133 1.516169 CTAAAACGCGCATTGGGCC 60.516 57.895 18.73 0.00 40.31 5.80
160 161 3.470645 TTTCTCCTATTTAGCGCTCCC 57.529 47.619 16.34 0.00 0.00 4.30
161 162 4.443621 ACTTTTCTCCTATTTAGCGCTCC 58.556 43.478 16.34 0.00 0.00 4.70
165 166 7.630924 CCAATGTACTTTTCTCCTATTTAGCG 58.369 38.462 0.00 0.00 0.00 4.26
218 227 0.478507 GCTATAACCTGGGCATGGGT 59.521 55.000 0.00 0.00 37.44 4.51
249 258 2.744709 GCCCGTGCGTGTACCATT 60.745 61.111 0.00 0.00 0.00 3.16
259 268 2.112815 GGGTGTAATGAGCCCGTGC 61.113 63.158 0.00 0.00 37.95 5.34
287 296 2.573462 AGCCAGCCTTGTTGAGATTAGA 59.427 45.455 0.00 0.00 0.00 2.10
311 320 4.101448 ATCCAGAGCCACCGCACC 62.101 66.667 0.00 0.00 37.52 5.01
314 323 1.890979 CATGATCCAGAGCCACCGC 60.891 63.158 0.00 0.00 0.00 5.68
315 324 0.249784 CTCATGATCCAGAGCCACCG 60.250 60.000 0.00 0.00 0.00 4.94
337 346 3.869272 CGCGAGAGGGTGCATTGC 61.869 66.667 0.00 0.46 39.50 3.56
359 368 4.759205 CTCCAAAAGGGGGCCCGG 62.759 72.222 17.79 12.16 41.95 5.73
362 371 1.195115 GAAATCTCCAAAAGGGGGCC 58.805 55.000 0.00 0.00 36.91 5.80
379 388 0.755327 TCCGCCATCTCTGGATCGAA 60.755 55.000 0.00 0.00 46.37 3.71
380 389 0.755327 TTCCGCCATCTCTGGATCGA 60.755 55.000 0.00 0.00 46.37 3.59
416 438 0.246635 TCTAGCCAGAAAGACCGCAC 59.753 55.000 0.00 0.00 0.00 5.34
421 443 5.078411 TGTTCATCTCTAGCCAGAAAGAC 57.922 43.478 0.00 0.00 0.00 3.01
422 444 5.946942 ATGTTCATCTCTAGCCAGAAAGA 57.053 39.130 0.00 0.00 0.00 2.52
423 445 6.596888 TGAAATGTTCATCTCTAGCCAGAAAG 59.403 38.462 0.00 0.00 34.08 2.62
424 446 6.372659 GTGAAATGTTCATCTCTAGCCAGAAA 59.627 38.462 0.00 0.00 42.47 2.52
425 447 5.877012 GTGAAATGTTCATCTCTAGCCAGAA 59.123 40.000 0.00 0.00 42.47 3.02
426 448 5.423015 GTGAAATGTTCATCTCTAGCCAGA 58.577 41.667 0.00 0.00 42.47 3.86
427 449 4.269603 CGTGAAATGTTCATCTCTAGCCAG 59.730 45.833 0.00 0.00 42.47 4.85
428 450 4.183865 CGTGAAATGTTCATCTCTAGCCA 58.816 43.478 0.00 0.00 42.47 4.75
462 484 3.470709 CAAAGAGAAACAGTCAGAGGCA 58.529 45.455 0.00 0.00 0.00 4.75
467 489 2.945008 TGCACCAAAGAGAAACAGTCAG 59.055 45.455 0.00 0.00 0.00 3.51
471 493 2.354510 TCGTTGCACCAAAGAGAAACAG 59.645 45.455 0.00 0.00 29.55 3.16
481 503 5.697473 TTAGAATTGATTCGTTGCACCAA 57.303 34.783 0.00 0.00 41.56 3.67
490 512 5.581085 GGTCCCGGATATTAGAATTGATTCG 59.419 44.000 0.73 0.00 41.56 3.34
510 532 2.125269 CCCACATTCGGACGGTCC 60.125 66.667 17.38 17.38 0.00 4.46
517 539 1.746615 CCACAGAGCCCACATTCGG 60.747 63.158 0.00 0.00 0.00 4.30
518 540 0.606401 AACCACAGAGCCCACATTCG 60.606 55.000 0.00 0.00 0.00 3.34
522 544 0.327924 CCATAACCACAGAGCCCACA 59.672 55.000 0.00 0.00 0.00 4.17
577 600 0.670546 CGACGAACATGCTTGAGGGT 60.671 55.000 6.60 0.69 0.00 4.34
580 603 1.990799 TACCGACGAACATGCTTGAG 58.009 50.000 6.60 0.36 0.00 3.02
600 623 7.560368 CCAAAATATGGGCCACTAAATTACAA 58.440 34.615 9.28 0.00 46.27 2.41
619 642 5.712152 CTCTTACAAGAGTTGGCCAAAAT 57.288 39.130 22.47 12.48 45.84 1.82
644 667 8.997621 AGTGCGAAATAGAGAACAAACTATAA 57.002 30.769 0.00 0.00 0.00 0.98
660 683 1.471119 TCCGGAGTAGAGTGCGAAAT 58.529 50.000 0.00 0.00 32.11 2.17
664 687 0.456221 ACAATCCGGAGTAGAGTGCG 59.544 55.000 11.34 0.00 32.72 5.34
798 989 0.179073 CGGATTCATCTGCGGGAGTT 60.179 55.000 0.00 0.00 0.00 3.01
799 990 1.043116 TCGGATTCATCTGCGGGAGT 61.043 55.000 0.00 0.00 33.18 3.85
868 1059 1.542915 AGCTACAGCAAGCATTTGTGG 59.457 47.619 3.70 0.00 45.30 4.17
869 1060 2.030540 ACAGCTACAGCAAGCATTTGTG 60.031 45.455 3.70 0.85 45.30 3.33
870 1061 2.227388 GACAGCTACAGCAAGCATTTGT 59.773 45.455 3.70 4.23 45.30 2.83
871 1062 2.415090 GGACAGCTACAGCAAGCATTTG 60.415 50.000 3.70 1.46 45.30 2.32
872 1063 1.815003 GGACAGCTACAGCAAGCATTT 59.185 47.619 3.70 0.00 45.30 2.32
873 1064 1.004044 AGGACAGCTACAGCAAGCATT 59.996 47.619 3.70 0.00 45.30 3.56
874 1065 0.617413 AGGACAGCTACAGCAAGCAT 59.383 50.000 3.70 0.00 45.30 3.79
938 1129 3.432051 CTGGCCGGCGAGGTAGAAG 62.432 68.421 29.09 3.74 43.70 2.85
939 1130 3.458163 CTGGCCGGCGAGGTAGAA 61.458 66.667 29.09 2.32 43.70 2.10
1504 1713 0.464735 ATCCTCTCGACGACCTCCTG 60.465 60.000 0.00 0.00 0.00 3.86
1569 1778 2.654877 GGTTCTTCTCCGTCGGCA 59.345 61.111 6.34 0.00 0.00 5.69
1586 1795 0.522286 CGCAGTGCTCTGTCTCTACG 60.522 60.000 14.33 7.15 43.05 3.51
1593 1802 2.048409 CTCTGCGCAGTGCTCTGT 60.048 61.111 34.70 0.00 46.63 3.41
1594 1803 3.488978 GCTCTGCGCAGTGCTCTG 61.489 66.667 41.76 24.59 46.63 3.35
1629 1838 6.597672 CCAGCCAGTATTTACACATCAGTAAA 59.402 38.462 0.00 0.00 45.07 2.01
1630 1839 6.112734 CCAGCCAGTATTTACACATCAGTAA 58.887 40.000 0.00 0.00 32.46 2.24
1631 1840 5.396324 CCCAGCCAGTATTTACACATCAGTA 60.396 44.000 0.00 0.00 0.00 2.74
1632 1841 4.517285 CCAGCCAGTATTTACACATCAGT 58.483 43.478 0.00 0.00 0.00 3.41
1686 1903 4.889409 AGCAATTTGATCAATGGATACCGT 59.111 37.500 9.40 0.00 32.67 4.83
1688 1905 5.239306 TCGAGCAATTTGATCAATGGATACC 59.761 40.000 9.40 0.00 31.10 2.73
1689 1906 6.138761 GTCGAGCAATTTGATCAATGGATAC 58.861 40.000 9.40 0.16 31.10 2.24
1710 1927 1.805943 TGCCAAGAACATGACATGTCG 59.194 47.619 21.05 10.04 44.07 4.35
1775 2719 0.112995 ACCCACATGTGCTGATTGGT 59.887 50.000 20.81 17.11 0.00 3.67
1780 2724 2.161855 GATTTGACCCACATGTGCTGA 58.838 47.619 20.81 0.00 0.00 4.26
1786 2732 3.009026 TGACGATGATTTGACCCACATG 58.991 45.455 0.00 0.00 0.00 3.21
1787 2733 3.009723 GTGACGATGATTTGACCCACAT 58.990 45.455 0.00 0.00 0.00 3.21
1788 2734 2.224402 TGTGACGATGATTTGACCCACA 60.224 45.455 0.00 0.00 0.00 4.17
1790 2736 2.615240 CCTGTGACGATGATTTGACCCA 60.615 50.000 0.00 0.00 0.00 4.51
1818 2764 6.105333 CACTGAGATTTTTACCCTCTCTGAG 58.895 44.000 11.16 0.00 37.98 3.35
1821 2767 4.534103 AGCACTGAGATTTTTACCCTCTCT 59.466 41.667 0.00 0.00 37.04 3.10
1828 2774 4.633565 CCCTCTGAGCACTGAGATTTTTAC 59.366 45.833 17.46 0.00 42.20 2.01
1830 2776 3.328931 TCCCTCTGAGCACTGAGATTTTT 59.671 43.478 17.46 0.00 42.20 1.94
1835 2781 3.279646 CTCCCTCTGAGCACTGAGA 57.720 57.895 17.46 0.72 42.20 3.27
1847 2793 2.219325 CTCACGACCACTGCTCCCTC 62.219 65.000 0.00 0.00 0.00 4.30
1869 2816 1.320344 TTCTCCTCCCGGTCATCACG 61.320 60.000 0.00 0.00 0.00 4.35
1878 2825 2.146920 ACCTCTAGTTTCTCCTCCCG 57.853 55.000 0.00 0.00 0.00 5.14
1954 2901 4.988598 CCGCCACGGCTGTTCAGT 62.989 66.667 6.48 0.00 41.17 3.41
1971 2918 3.127533 GTGGTGCCATCTGGTCGC 61.128 66.667 0.00 0.00 37.57 5.19
2038 2992 0.185175 AGGTCTTTCGGGCAGGTTTT 59.815 50.000 0.00 0.00 0.00 2.43
2046 3000 2.125512 CGGCTCAGGTCTTTCGGG 60.126 66.667 0.00 0.00 0.00 5.14
2062 3026 4.394078 TCGTTCGGACAGGACGCG 62.394 66.667 3.53 3.53 36.77 6.01
2065 3029 1.153997 GCTCTCGTTCGGACAGGAC 60.154 63.158 0.00 0.00 0.00 3.85
2089 3057 4.332637 CAACAGCACTGGCCGCAC 62.333 66.667 0.00 0.00 42.56 5.34
2119 3089 1.806247 CGGCTCGCCTACATTCATTCA 60.806 52.381 6.35 0.00 0.00 2.57
2179 3165 1.208535 GGACCGAACATATGTGTCCCA 59.791 52.381 23.92 0.00 39.65 4.37
2294 3293 3.443045 CGGCCCCTTGATGTGCAC 61.443 66.667 10.75 10.75 0.00 4.57
2296 3295 4.740822 ACCGGCCCCTTGATGTGC 62.741 66.667 0.00 0.00 0.00 4.57
2308 3307 4.790861 GGAGAACGTCCGACCGGC 62.791 72.222 0.00 0.00 34.84 6.13
2341 3340 7.429920 CGACGAATAATATCCTAGCTTAGCTTC 59.570 40.741 13.44 0.00 40.44 3.86
2370 3369 1.267121 TCTCTAGCAGGCCGTTTTCT 58.733 50.000 0.00 0.00 0.00 2.52
2384 3383 3.024547 CGTCAAGGAGGTGGATTCTCTA 58.975 50.000 0.00 0.00 0.00 2.43
2385 3384 1.827969 CGTCAAGGAGGTGGATTCTCT 59.172 52.381 0.00 0.00 0.00 3.10
2414 3413 0.455633 GACACGTACACGGCTCGATT 60.456 55.000 6.72 0.00 44.95 3.34
2415 3414 1.136147 GACACGTACACGGCTCGAT 59.864 57.895 6.72 0.00 44.95 3.59
2424 3423 1.961394 AGAAGGAAGCTGACACGTACA 59.039 47.619 0.00 0.00 0.00 2.90
2425 3424 2.726832 AGAAGGAAGCTGACACGTAC 57.273 50.000 0.00 0.00 0.00 3.67
2426 3425 3.439476 GTCTAGAAGGAAGCTGACACGTA 59.561 47.826 0.00 0.00 0.00 3.57
2431 3430 3.194062 GCATGTCTAGAAGGAAGCTGAC 58.806 50.000 0.00 0.00 0.00 3.51
2434 3433 1.472376 GCGCATGTCTAGAAGGAAGCT 60.472 52.381 0.30 0.00 0.00 3.74
2443 3442 1.593750 GAGGCTGGCGCATGTCTAG 60.594 63.158 10.83 0.00 38.10 2.43
2446 3445 2.894387 GAGAGGCTGGCGCATGTC 60.894 66.667 10.83 1.79 38.10 3.06
2467 3466 0.453782 GCCACGTACGCAACATTTCC 60.454 55.000 16.72 0.00 0.00 3.13
2470 3469 1.572447 GTGCCACGTACGCAACATT 59.428 52.632 16.72 0.00 38.13 2.71
2489 3488 2.009774 AGTGTAATGATGAAGTGCCGC 58.990 47.619 0.00 0.00 0.00 6.53
2506 3513 8.812329 CACTTGCTTAATTCTAGTAGCTTAGTG 58.188 37.037 0.00 0.00 38.86 2.74
2516 3523 5.316770 GTTGCGTCACTTGCTTAATTCTAG 58.683 41.667 0.00 0.00 0.00 2.43
2517 3524 4.143200 CGTTGCGTCACTTGCTTAATTCTA 60.143 41.667 0.00 0.00 0.00 2.10
2519 3526 2.902484 CGTTGCGTCACTTGCTTAATTC 59.098 45.455 0.00 0.00 0.00 2.17
2520 3527 2.546368 TCGTTGCGTCACTTGCTTAATT 59.454 40.909 0.00 0.00 0.00 1.40
2522 3529 1.525197 CTCGTTGCGTCACTTGCTTAA 59.475 47.619 0.00 0.00 0.00 1.85
2523 3530 1.136690 CTCGTTGCGTCACTTGCTTA 58.863 50.000 0.00 0.00 0.00 3.09
2549 3559 3.001939 GTGTTTTTCTGGAGTACGTGGTG 59.998 47.826 0.00 0.00 0.00 4.17
2559 3569 2.685897 CTCAAACCGGTGTTTTTCTGGA 59.314 45.455 8.52 0.00 41.92 3.86
2561 3571 3.775661 ACTCAAACCGGTGTTTTTCTG 57.224 42.857 8.52 0.00 41.92 3.02
2565 3575 4.729227 ATTCAACTCAAACCGGTGTTTT 57.271 36.364 8.52 0.00 41.92 2.43


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

AutoCloner maintained by Alex Coulton.