Multiple sequence alignment - TraesCS7A01G387100

Loading Multiple Alignment...

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 TraesCS7A01G387100 chr7A 100.000 3533 0 0 1 3533 563294363 563290831 0.000000e+00 6525.0
1 TraesCS7A01G387100 chr7A 87.183 2364 237 31 604 2932 563247217 563244885 0.000000e+00 2627.0
2 TraesCS7A01G387100 chr7A 88.416 1925 194 20 990 2899 29009261 29007351 0.000000e+00 2292.0
3 TraesCS7A01G387100 chr7A 85.846 2176 225 50 778 2899 28809180 28807034 0.000000e+00 2235.0
4 TraesCS7A01G387100 chr7A 94.757 515 25 2 2995 3508 563271343 563270830 0.000000e+00 800.0
5 TraesCS7A01G387100 chr7A 82.645 121 12 8 771 889 29009494 29009381 8.070000e-17 99.0
6 TraesCS7A01G387100 chr7A 100.000 28 0 0 3506 3533 598764209 598764182 6.000000e-03 52.8
7 TraesCS7A01G387100 chr7D 88.518 2099 200 24 688 2782 497321010 497318949 0.000000e+00 2503.0
8 TraesCS7A01G387100 chr7D 89.103 1092 73 16 4 1075 497360300 497359235 0.000000e+00 1315.0
9 TraesCS7A01G387100 chr7D 90.455 660 31 16 2857 3512 497345665 497345034 0.000000e+00 841.0
10 TraesCS7A01G387100 chr7D 89.688 320 29 4 2480 2797 497345979 497345662 4.250000e-109 405.0
11 TraesCS7A01G387100 chr7B 87.296 2141 219 23 825 2939 525598673 525596560 0.000000e+00 2398.0
12 TraesCS7A01G387100 chr7B 86.813 637 54 13 138 757 525958933 525958310 0.000000e+00 684.0
13 TraesCS7A01G387100 chr7B 89.072 485 35 4 3029 3512 525928282 525927815 1.410000e-163 586.0
14 TraesCS7A01G387100 chr7B 87.945 365 27 6 2684 3033 525941701 525941339 7.060000e-112 414.0
15 TraesCS7A01G387100 chr2D 87.680 1940 203 25 1000 2924 608559379 608557461 0.000000e+00 2226.0
16 TraesCS7A01G387100 chr2D 84.727 2213 230 51 669 2847 608578711 608576573 0.000000e+00 2115.0
17 TraesCS7A01G387100 chr2A 87.098 1961 214 25 1000 2939 740079006 740077064 0.000000e+00 2183.0
18 TraesCS7A01G387100 chr4A 85.491 2171 225 48 771 2884 702328049 702325912 0.000000e+00 2182.0
19 TraesCS7A01G387100 chr1D 85.334 2141 249 43 669 2798 33595451 33597537 0.000000e+00 2154.0
20 TraesCS7A01G387100 chr1A 86.961 1879 221 21 928 2799 32111078 32112939 0.000000e+00 2091.0
21 TraesCS7A01G387100 chrUn 82.514 183 24 5 2723 2899 459694201 459694381 1.700000e-33 154.0
22 TraesCS7A01G387100 chr5D 100.000 28 0 0 3504 3531 476285802 476285829 6.000000e-03 52.8


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 TraesCS7A01G387100 chr7A 563290831 563294363 3532 True 6525.0 6525 100.0000 1 3533 1 chr7A.!!$R4 3532
1 TraesCS7A01G387100 chr7A 563244885 563247217 2332 True 2627.0 2627 87.1830 604 2932 1 chr7A.!!$R2 2328
2 TraesCS7A01G387100 chr7A 28807034 28809180 2146 True 2235.0 2235 85.8460 778 2899 1 chr7A.!!$R1 2121
3 TraesCS7A01G387100 chr7A 29007351 29009494 2143 True 1195.5 2292 85.5305 771 2899 2 chr7A.!!$R6 2128
4 TraesCS7A01G387100 chr7A 563270830 563271343 513 True 800.0 800 94.7570 2995 3508 1 chr7A.!!$R3 513
5 TraesCS7A01G387100 chr7D 497318949 497321010 2061 True 2503.0 2503 88.5180 688 2782 1 chr7D.!!$R1 2094
6 TraesCS7A01G387100 chr7D 497359235 497360300 1065 True 1315.0 1315 89.1030 4 1075 1 chr7D.!!$R2 1071
7 TraesCS7A01G387100 chr7D 497345034 497345979 945 True 623.0 841 90.0715 2480 3512 2 chr7D.!!$R3 1032
8 TraesCS7A01G387100 chr7B 525596560 525598673 2113 True 2398.0 2398 87.2960 825 2939 1 chr7B.!!$R1 2114
9 TraesCS7A01G387100 chr7B 525958310 525958933 623 True 684.0 684 86.8130 138 757 1 chr7B.!!$R4 619
10 TraesCS7A01G387100 chr2D 608557461 608559379 1918 True 2226.0 2226 87.6800 1000 2924 1 chr2D.!!$R1 1924
11 TraesCS7A01G387100 chr2D 608576573 608578711 2138 True 2115.0 2115 84.7270 669 2847 1 chr2D.!!$R2 2178
12 TraesCS7A01G387100 chr2A 740077064 740079006 1942 True 2183.0 2183 87.0980 1000 2939 1 chr2A.!!$R1 1939
13 TraesCS7A01G387100 chr4A 702325912 702328049 2137 True 2182.0 2182 85.4910 771 2884 1 chr4A.!!$R1 2113
14 TraesCS7A01G387100 chr1D 33595451 33597537 2086 False 2154.0 2154 85.3340 669 2798 1 chr1D.!!$F1 2129
15 TraesCS7A01G387100 chr1A 32111078 32112939 1861 False 2091.0 2091 86.9610 928 2799 1 chr1A.!!$F1 1871

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
582 583 0.035598 TTTAAGCAGCTGCACCCGTA 59.964 50.0 38.24 19.24 45.16 4.02 F
1311 1453 0.037232 ACTTCTTCGCCTTCTTCCCG 60.037 55.0 0.00 0.00 0.00 5.14 F
1366 1508 0.463295 CATCGCCTCTGCCATGAACT 60.463 55.0 0.00 0.00 38.23 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2264 2407 0.109412 CACGACCACCTCGAACCTAC 60.109 60.0 0.00 0.0 46.14 3.18 R
2400 2543 1.089481 CCACCGTGTGCGCAAGATAT 61.089 55.0 14.00 0.0 43.02 1.63 R
2892 3097 1.101049 CACGGTGACCAAGTGGCTTT 61.101 55.0 0.74 0.0 39.32 3.51 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
25 26 5.010282 ACCTTTGCTAGAAATCCAACGAAT 58.990 37.500 0.00 0.00 0.00 3.34
28 29 7.175990 ACCTTTGCTAGAAATCCAACGAATTTA 59.824 33.333 0.00 0.00 0.00 1.40
30 31 9.226345 CTTTGCTAGAAATCCAACGAATTTATC 57.774 33.333 0.00 0.00 0.00 1.75
43 44 2.981859 ATTTATCGGCCTTGTCGAGT 57.018 45.000 0.00 0.00 44.58 4.18
66 67 0.740868 TCCGGCAGAAATCAAGCTCG 60.741 55.000 0.00 0.00 0.00 5.03
84 85 1.298859 CGGTGCTTGCTAGGTGTTCC 61.299 60.000 0.00 0.00 0.00 3.62
89 90 0.320374 CTTGCTAGGTGTTCCACGGA 59.680 55.000 0.00 0.00 34.83 4.69
112 113 0.533531 CCACAACTGAGCTCTGTGCA 60.534 55.000 24.82 0.00 45.94 4.57
113 114 1.520494 CACAACTGAGCTCTGTGCAT 58.480 50.000 24.82 11.88 45.94 3.96
120 121 4.778579 ACTGAGCTCTGTGCATGAAATAT 58.221 39.130 23.71 0.00 45.94 1.28
161 162 7.063593 TCTTCAACAAGATCTCTTCGAAGAGC 61.064 42.308 38.78 28.90 41.63 4.09
178 179 2.357034 CGGTGGACGTGAACTGGG 60.357 66.667 0.00 0.00 37.93 4.45
204 205 7.489757 GCAATAAGACCACTAGTTCTACTTCTG 59.510 40.741 0.00 0.92 0.00 3.02
206 207 5.968528 AGACCACTAGTTCTACTTCTGTG 57.031 43.478 0.00 0.00 0.00 3.66
211 212 5.244178 CCACTAGTTCTACTTCTGTGTTCCT 59.756 44.000 0.00 0.00 0.00 3.36
212 213 6.239345 CCACTAGTTCTACTTCTGTGTTCCTT 60.239 42.308 0.00 0.00 0.00 3.36
220 221 7.506114 TCTACTTCTGTGTTCCTTGTTATGTT 58.494 34.615 0.00 0.00 0.00 2.71
221 222 7.990886 TCTACTTCTGTGTTCCTTGTTATGTTT 59.009 33.333 0.00 0.00 0.00 2.83
222 223 6.795399 ACTTCTGTGTTCCTTGTTATGTTTG 58.205 36.000 0.00 0.00 0.00 2.93
228 229 5.518487 GTGTTCCTTGTTATGTTTGTTGGTG 59.482 40.000 0.00 0.00 0.00 4.17
270 271 6.363357 GTGAATAACTGTGTTGAATTTGAGGC 59.637 38.462 0.00 0.00 0.00 4.70
272 273 7.446931 TGAATAACTGTGTTGAATTTGAGGCTA 59.553 33.333 0.00 0.00 0.00 3.93
289 290 4.166539 AGGCTATGGATTGATGAGCTACT 58.833 43.478 0.00 0.00 33.57 2.57
329 330 4.839668 TCTGTGTTTTATTTGTTCCGGG 57.160 40.909 0.00 0.00 0.00 5.73
333 334 6.320672 TCTGTGTTTTATTTGTTCCGGGTTTA 59.679 34.615 0.00 0.00 0.00 2.01
341 342 3.123157 TGTTCCGGGTTTATTTGACGA 57.877 42.857 0.00 0.00 0.00 4.20
376 377 8.525729 ACCCCCTTTGTCTCATAATATAGAAT 57.474 34.615 0.00 0.00 0.00 2.40
378 379 8.605947 CCCCCTTTGTCTCATAATATAGAATGA 58.394 37.037 1.15 1.15 0.00 2.57
473 474 8.729805 AGCAATCTTTCTACCTAGATCTTTTG 57.270 34.615 0.00 0.00 30.95 2.44
530 531 3.002246 TGTTTGTCTGCTGTTCGAATGTC 59.998 43.478 0.00 0.00 0.00 3.06
531 532 1.795768 TGTCTGCTGTTCGAATGTCC 58.204 50.000 0.00 0.00 0.00 4.02
532 533 1.069978 TGTCTGCTGTTCGAATGTCCA 59.930 47.619 0.00 0.00 0.00 4.02
533 534 2.143122 GTCTGCTGTTCGAATGTCCAA 58.857 47.619 0.00 0.00 0.00 3.53
534 535 2.158449 GTCTGCTGTTCGAATGTCCAAG 59.842 50.000 0.00 0.00 0.00 3.61
535 536 2.037121 TCTGCTGTTCGAATGTCCAAGA 59.963 45.455 0.00 0.00 0.00 3.02
536 537 2.414481 CTGCTGTTCGAATGTCCAAGAG 59.586 50.000 0.00 0.00 0.00 2.85
537 538 2.224281 TGCTGTTCGAATGTCCAAGAGT 60.224 45.455 0.00 0.00 0.00 3.24
538 539 2.808543 GCTGTTCGAATGTCCAAGAGTT 59.191 45.455 0.00 0.00 0.00 3.01
539 540 3.251004 GCTGTTCGAATGTCCAAGAGTTT 59.749 43.478 0.00 0.00 0.00 2.66
540 541 4.261197 GCTGTTCGAATGTCCAAGAGTTTT 60.261 41.667 0.00 0.00 0.00 2.43
541 542 5.733373 GCTGTTCGAATGTCCAAGAGTTTTT 60.733 40.000 0.00 0.00 0.00 1.94
581 582 1.228124 TTTAAGCAGCTGCACCCGT 60.228 52.632 38.24 16.73 45.16 5.28
582 583 0.035598 TTTAAGCAGCTGCACCCGTA 59.964 50.000 38.24 19.24 45.16 4.02
584 585 0.035598 TAAGCAGCTGCACCCGTAAA 59.964 50.000 38.24 12.58 45.16 2.01
585 586 0.821711 AAGCAGCTGCACCCGTAAAA 60.822 50.000 38.24 0.00 45.16 1.52
742 785 0.602638 CACTTTCCTGGCAGCGTACA 60.603 55.000 9.56 0.00 0.00 2.90
916 1006 6.829811 CCAACTTACTACTCCTACTAGCTCTT 59.170 42.308 0.00 0.00 0.00 2.85
971 1071 2.716217 AGCTCCACTTCATTAAGCCAC 58.284 47.619 0.00 0.00 36.05 5.01
1173 1315 0.611714 TTCTCCCTAACGTGAAGCCC 59.388 55.000 0.00 0.00 0.00 5.19
1197 1339 1.291588 CCTGCAAGACGAGCTCAGT 59.708 57.895 15.40 12.55 34.07 3.41
1288 1430 2.362369 ATGACGCACTGGGCTAGCT 61.362 57.895 15.72 0.00 41.67 3.32
1290 1432 2.997315 ACGCACTGGGCTAGCTCA 60.997 61.111 18.27 18.27 41.67 4.26
1311 1453 0.037232 ACTTCTTCGCCTTCTTCCCG 60.037 55.000 0.00 0.00 0.00 5.14
1317 1459 2.434359 GCCTTCTTCCCGTCCACG 60.434 66.667 0.00 0.00 39.44 4.94
1366 1508 0.463295 CATCGCCTCTGCCATGAACT 60.463 55.000 0.00 0.00 38.23 3.01
1481 1623 0.821301 TTCATGAACCGCACCAGCAA 60.821 50.000 3.38 0.00 42.27 3.91
1704 1846 3.550431 ATCCGCTCCATCCCCACG 61.550 66.667 0.00 0.00 0.00 4.94
1751 1893 2.391389 CGGCCAAACTTCTCGAGGC 61.391 63.158 13.56 6.83 44.48 4.70
1785 1927 4.250305 AACGCCGGTCTTGTGCCT 62.250 61.111 1.90 0.00 0.00 4.75
1799 1941 5.181245 GTCTTGTGCCTACATATGTTTGTGT 59.819 40.000 14.77 0.00 36.53 3.72
1977 2119 2.159043 CGTGGACTCCATTAGCATGAGT 60.159 50.000 0.00 0.00 35.28 3.41
1980 2122 2.546795 GGACTCCATTAGCATGAGTCCG 60.547 54.545 18.88 0.00 42.06 4.79
2016 2158 2.117156 ATGCCTCGATTGCACCTGC 61.117 57.895 11.45 0.00 42.38 4.85
2019 2161 1.377725 CCTCGATTGCACCTGCCTT 60.378 57.895 0.00 0.00 41.18 4.35
2037 2179 2.540515 CTTTACGTCCGTGATGCTCAT 58.459 47.619 1.98 0.00 0.00 2.90
2079 2221 0.688487 CCAACCCGGAGTACCTCAAA 59.312 55.000 0.73 0.00 36.56 2.69
2181 2323 0.608856 TTTGGATGGTCATGCGCACT 60.609 50.000 14.90 0.00 31.21 4.40
2184 2326 0.657840 GGATGGTCATGCGCACTTAC 59.342 55.000 14.90 11.43 0.00 2.34
2190 2332 0.528924 TCATGCGCACTTACGGTACT 59.471 50.000 14.90 0.00 0.00 2.73
2254 2397 6.928492 GGCCAAGATGTTTGAAGATTTTGTTA 59.072 34.615 0.00 0.00 0.00 2.41
2264 2407 2.073816 AGATTTTGTTAGTGCCGACGG 58.926 47.619 10.29 10.29 0.00 4.79
2289 2432 3.371063 GAGGTGGTCGTGCCGAGA 61.371 66.667 0.00 0.00 41.21 4.04
2367 2510 0.528924 CCGATGAGGTCAACCGTGTA 59.471 55.000 0.00 0.00 42.08 2.90
2400 2543 0.106769 TGAACAAGACTGGCAAGGCA 60.107 50.000 0.00 0.00 31.58 4.75
2544 2687 2.373540 TGAATTAAGTGGACGGACCG 57.626 50.000 13.61 13.61 42.61 4.79
2564 2707 2.508526 GGCTGACACAGAAAGTTCCAT 58.491 47.619 2.81 0.00 32.44 3.41
2573 2716 6.299141 ACACAGAAAGTTCCATGAGTTACAT 58.701 36.000 0.00 0.00 40.17 2.29
2575 2718 8.103305 ACACAGAAAGTTCCATGAGTTACATAT 58.897 33.333 0.00 0.00 37.46 1.78
2580 2723 8.833231 AAAGTTCCATGAGTTACATATATCCG 57.167 34.615 0.00 0.00 37.46 4.18
2805 3004 5.940192 TTGTTATTGTACTCTGCAAGTGG 57.060 39.130 10.59 0.00 39.11 4.00
2852 3057 8.590470 CATCTCGATCAATCAAGAAATATACGG 58.410 37.037 0.00 0.00 0.00 4.02
2854 3059 8.141909 TCTCGATCAATCAAGAAATATACGGTT 58.858 33.333 0.00 0.00 0.00 4.44
2855 3060 9.406828 CTCGATCAATCAAGAAATATACGGTTA 57.593 33.333 0.00 0.00 0.00 2.85
2860 3065 9.321562 TCAATCAAGAAATATACGGTTAACTCC 57.678 33.333 5.42 0.00 0.00 3.85
2892 3097 1.425066 AGGTTTCAAGATGCCAGACCA 59.575 47.619 0.00 0.00 0.00 4.02
2939 3144 8.713708 TTCCCAACTTCCTGTTAATTATTTGA 57.286 30.769 0.00 0.00 37.07 2.69
2940 3145 8.713708 TCCCAACTTCCTGTTAATTATTTGAA 57.286 30.769 0.00 0.00 37.07 2.69
2941 3146 9.148879 TCCCAACTTCCTGTTAATTATTTGAAA 57.851 29.630 0.00 0.00 37.07 2.69
2964 3169 4.017775 ACCATCTATCTGCCAATGCCATAT 60.018 41.667 0.00 0.00 36.33 1.78
3021 3229 0.766131 TACGGGGGCAGAGTTTTGAA 59.234 50.000 0.00 0.00 0.00 2.69
3074 3282 0.389296 TTGCGTCCAACGATCGATGT 60.389 50.000 24.34 3.27 46.05 3.06
3117 3325 5.067413 ACGATCGACAGGTAGTATCATGTTT 59.933 40.000 24.34 0.00 32.49 2.83
3282 3491 1.799258 CTGCTCTGCAACCACAACCC 61.799 60.000 0.00 0.00 38.41 4.11
3284 3493 1.152777 CTCTGCAACCACAACCCCA 60.153 57.895 0.00 0.00 0.00 4.96
3348 3573 9.109393 TGTGAAATTCATTATACCTAGTTCAGC 57.891 33.333 0.00 0.00 0.00 4.26
3349 3574 9.109393 GTGAAATTCATTATACCTAGTTCAGCA 57.891 33.333 0.00 0.00 0.00 4.41
3350 3575 9.851686 TGAAATTCATTATACCTAGTTCAGCAT 57.148 29.630 0.00 0.00 0.00 3.79
3408 3634 4.436332 ACCTTACTTTTCAACTCGTCGTT 58.564 39.130 0.00 0.00 35.88 3.85
3462 3688 1.097547 CCTCATGGTCATTGGCGTCC 61.098 60.000 0.00 0.00 0.00 4.79
3488 3714 0.041386 AACTCCGGCTACTCTCCCTT 59.959 55.000 0.00 0.00 0.00 3.95
3509 3735 3.157881 TGTTGTCGAGATCCAGAAGAGT 58.842 45.455 0.00 0.00 0.00 3.24
3512 3738 3.157881 TGTCGAGATCCAGAAGAGTTGT 58.842 45.455 0.00 0.00 0.00 3.32
3513 3739 3.057245 TGTCGAGATCCAGAAGAGTTGTG 60.057 47.826 0.00 0.00 0.00 3.33
3514 3740 3.191581 GTCGAGATCCAGAAGAGTTGTGA 59.808 47.826 0.00 0.00 0.00 3.58
3515 3741 4.019858 TCGAGATCCAGAAGAGTTGTGAT 58.980 43.478 0.00 0.00 0.00 3.06
3516 3742 5.066634 GTCGAGATCCAGAAGAGTTGTGATA 59.933 44.000 0.00 0.00 0.00 2.15
3517 3743 5.066634 TCGAGATCCAGAAGAGTTGTGATAC 59.933 44.000 0.00 0.00 0.00 2.24
3518 3744 5.255710 AGATCCAGAAGAGTTGTGATACG 57.744 43.478 0.00 0.00 0.00 3.06
3519 3745 4.707448 AGATCCAGAAGAGTTGTGATACGT 59.293 41.667 0.00 0.00 0.00 3.57
3520 3746 4.436242 TCCAGAAGAGTTGTGATACGTC 57.564 45.455 0.00 0.00 0.00 4.34
3521 3747 4.079970 TCCAGAAGAGTTGTGATACGTCT 58.920 43.478 0.00 0.00 0.00 4.18
3522 3748 4.156190 TCCAGAAGAGTTGTGATACGTCTC 59.844 45.833 0.00 0.00 0.00 3.36
3523 3749 4.416620 CAGAAGAGTTGTGATACGTCTCC 58.583 47.826 0.00 0.00 0.00 3.71
3524 3750 4.079970 AGAAGAGTTGTGATACGTCTCCA 58.920 43.478 0.00 0.00 0.00 3.86
3525 3751 4.523173 AGAAGAGTTGTGATACGTCTCCAA 59.477 41.667 0.00 0.00 0.00 3.53
3526 3752 4.175787 AGAGTTGTGATACGTCTCCAAC 57.824 45.455 18.77 18.77 37.26 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.502211 CGTTGGATTTCTAGCAAAGGTGT 59.498 43.478 0.00 0.00 0.00 4.16
1 2 3.751175 TCGTTGGATTTCTAGCAAAGGTG 59.249 43.478 0.00 0.00 0.00 4.00
2 3 4.015872 TCGTTGGATTTCTAGCAAAGGT 57.984 40.909 0.00 0.00 0.00 3.50
19 20 2.350498 CGACAAGGCCGATAAATTCGTT 59.650 45.455 0.00 0.00 46.65 3.85
25 26 2.754946 AACTCGACAAGGCCGATAAA 57.245 45.000 0.00 0.00 35.35 1.40
28 29 1.134560 GAGTAACTCGACAAGGCCGAT 59.865 52.381 0.00 0.00 35.35 4.18
30 31 0.458025 GGAGTAACTCGACAAGGCCG 60.458 60.000 0.00 0.00 0.00 6.13
43 44 2.027192 AGCTTGATTTCTGCCGGAGTAA 60.027 45.455 5.05 0.10 0.00 2.24
66 67 0.250727 TGGAACACCTAGCAAGCACC 60.251 55.000 0.00 0.00 0.00 5.01
84 85 1.197721 GCTCAGTTGTGGAATTCCGTG 59.802 52.381 19.57 11.20 39.43 4.94
89 90 3.144506 CACAGAGCTCAGTTGTGGAATT 58.855 45.455 21.17 0.00 38.76 2.17
120 121 6.768483 TGTTGAAGACTTTCATCAGTATCCA 58.232 36.000 0.00 0.00 42.60 3.41
161 162 2.357034 CCCAGTTCACGTCCACCG 60.357 66.667 0.00 0.00 44.03 4.94
178 179 7.489757 CAGAAGTAGAACTAGTGGTCTTATTGC 59.510 40.741 2.47 0.00 0.00 3.56
193 194 7.441458 ACATAACAAGGAACACAGAAGTAGAAC 59.559 37.037 0.00 0.00 0.00 3.01
204 205 5.518487 CACCAACAAACATAACAAGGAACAC 59.482 40.000 0.00 0.00 0.00 3.32
206 207 4.506288 GCACCAACAAACATAACAAGGAAC 59.494 41.667 0.00 0.00 0.00 3.62
211 212 4.081972 ACAGTGCACCAACAAACATAACAA 60.082 37.500 14.63 0.00 0.00 2.83
212 213 3.445450 ACAGTGCACCAACAAACATAACA 59.555 39.130 14.63 0.00 0.00 2.41
220 221 3.020274 ACATAACACAGTGCACCAACAA 58.980 40.909 14.63 0.00 0.00 2.83
221 222 2.649190 ACATAACACAGTGCACCAACA 58.351 42.857 14.63 0.00 0.00 3.33
222 223 3.708563 AACATAACACAGTGCACCAAC 57.291 42.857 14.63 0.00 0.00 3.77
228 229 3.980646 TCACCAAACATAACACAGTGC 57.019 42.857 0.00 0.00 0.00 4.40
309 310 4.577834 ACCCGGAACAAATAAAACACAG 57.422 40.909 0.73 0.00 0.00 3.66
325 326 2.968675 ACTCTCGTCAAATAAACCCGG 58.031 47.619 0.00 0.00 0.00 5.73
329 330 8.393366 GGGGTATAAAACTCTCGTCAAATAAAC 58.607 37.037 0.00 0.00 0.00 2.01
333 334 5.191124 AGGGGGTATAAAACTCTCGTCAAAT 59.809 40.000 0.00 0.00 32.40 2.32
341 342 5.550403 TGAGACAAAGGGGGTATAAAACTCT 59.450 40.000 0.00 0.00 0.00 3.24
350 351 9.629649 ATTCTATATTATGAGACAAAGGGGGTA 57.370 33.333 0.00 0.00 0.00 3.69
409 410 6.370166 TCAAAACTCACGTACATATGCAATGA 59.630 34.615 13.53 1.31 0.00 2.57
424 425 1.933853 ACAGCAGACGTCAAAACTCAC 59.066 47.619 19.50 0.00 0.00 3.51
464 465 5.505181 TTAGGTGAGAAGGCAAAAGATCT 57.495 39.130 0.00 0.00 0.00 2.75
465 466 6.575162 TTTTAGGTGAGAAGGCAAAAGATC 57.425 37.500 0.00 0.00 0.00 2.75
473 474 5.921962 AATCCAATTTTAGGTGAGAAGGC 57.078 39.130 0.00 0.00 0.00 4.35
547 548 4.082081 TGCTTAAACTCTTGGGCATTCATG 60.082 41.667 0.00 0.00 0.00 3.07
548 549 4.088634 TGCTTAAACTCTTGGGCATTCAT 58.911 39.130 0.00 0.00 0.00 2.57
549 550 3.495331 TGCTTAAACTCTTGGGCATTCA 58.505 40.909 0.00 0.00 0.00 2.57
550 551 3.674410 GCTGCTTAAACTCTTGGGCATTC 60.674 47.826 0.00 0.00 0.00 2.67
551 552 2.232208 GCTGCTTAAACTCTTGGGCATT 59.768 45.455 0.00 0.00 0.00 3.56
552 553 1.821136 GCTGCTTAAACTCTTGGGCAT 59.179 47.619 0.00 0.00 0.00 4.40
553 554 1.202927 AGCTGCTTAAACTCTTGGGCA 60.203 47.619 0.00 0.00 0.00 5.36
554 555 1.200948 CAGCTGCTTAAACTCTTGGGC 59.799 52.381 0.00 0.00 0.00 5.36
555 556 1.200948 GCAGCTGCTTAAACTCTTGGG 59.799 52.381 31.33 0.00 38.21 4.12
584 585 1.029681 ACGCGGCTTCCTTTTCTTTT 58.970 45.000 12.47 0.00 0.00 2.27
585 586 0.310854 CACGCGGCTTCCTTTTCTTT 59.689 50.000 12.47 0.00 0.00 2.52
742 785 4.892379 TCGCGCGCGCTTACGTAT 62.892 61.111 45.97 0.00 42.83 3.06
892 964 7.771826 AGAAGAGCTAGTAGGAGTAGTAAGTTG 59.228 40.741 0.00 0.00 0.00 3.16
916 1006 1.370609 CGGAGAGCAACGAGTAGAGA 58.629 55.000 0.00 0.00 0.00 3.10
971 1071 2.328099 GCAAAGGAGGTGTGAGGCG 61.328 63.158 0.00 0.00 0.00 5.52
1173 1315 0.872021 GCTCGTCTTGCAGGTATCCG 60.872 60.000 0.00 0.00 0.00 4.18
1288 1430 3.139077 GGAAGAAGGCGAAGAAGTTTGA 58.861 45.455 0.00 0.00 0.00 2.69
1290 1432 2.505405 GGGAAGAAGGCGAAGAAGTTT 58.495 47.619 0.00 0.00 0.00 2.66
1366 1508 1.669760 GCCACGTGAATCCAACGGA 60.670 57.895 19.30 0.00 35.55 4.69
1481 1623 2.032528 CACCAGTGCCACGACCAT 59.967 61.111 0.00 0.00 0.00 3.55
1500 1642 3.499737 GTGCCAAGGATGACGCCG 61.500 66.667 0.00 0.00 0.00 6.46
1704 1846 0.460811 CGTAGTTAGTTTCCGGCCCC 60.461 60.000 0.00 0.00 0.00 5.80
1740 1882 1.446907 CTTGCATTGCCTCGAGAAGT 58.553 50.000 15.71 0.00 0.00 3.01
1751 1893 1.355971 GTTGGCATCAGCTTGCATTG 58.644 50.000 12.28 0.00 44.59 2.82
1785 1927 3.997681 CCACCGTGACACAAACATATGTA 59.002 43.478 9.21 0.00 30.84 2.29
1851 1993 0.608856 TGAACATGGCGGCAATGTCT 60.609 50.000 22.54 12.98 37.27 3.41
1977 2119 0.250684 TGAGAAGCCATTTGTGCGGA 60.251 50.000 0.00 0.00 0.00 5.54
1980 2122 2.602878 CATGTGAGAAGCCATTTGTGC 58.397 47.619 0.00 0.00 0.00 4.57
2016 2158 1.278238 GAGCATCACGGACGTAAAGG 58.722 55.000 0.00 0.00 33.17 3.11
2037 2179 1.154093 CAACGAGTCGCTTAGCCGA 60.154 57.895 13.59 1.55 34.40 5.54
2079 2221 0.109873 CAGACTCGGTAGCGTCGTTT 60.110 55.000 14.79 5.58 37.20 3.60
2181 2323 1.345089 TGGAGCTTTGCAGTACCGTAA 59.655 47.619 0.00 0.00 0.00 3.18
2184 2326 0.798776 CTTGGAGCTTTGCAGTACCG 59.201 55.000 0.00 0.00 0.00 4.02
2254 2397 2.968206 GAACCTACCGTCGGCACT 59.032 61.111 12.28 0.00 0.00 4.40
2264 2407 0.109412 CACGACCACCTCGAACCTAC 60.109 60.000 0.00 0.00 46.14 3.18
2283 2426 1.604278 ACAAGAGCAAAGTTTCTCGGC 59.396 47.619 8.48 0.06 34.66 5.54
2289 2432 3.874392 AAGCACACAAGAGCAAAGTTT 57.126 38.095 0.00 0.00 33.43 2.66
2367 2510 7.102346 CAGTCTTGTTCAGATTCTCCATTAGT 58.898 38.462 0.00 0.00 32.60 2.24
2400 2543 1.089481 CCACCGTGTGCGCAAGATAT 61.089 55.000 14.00 0.00 43.02 1.63
2544 2687 1.967319 TGGAACTTTCTGTGTCAGCC 58.033 50.000 0.00 0.00 0.00 4.85
2700 2870 1.335145 ACCGGCCTGCTACGTATATT 58.665 50.000 0.00 0.00 0.00 1.28
2800 2999 1.167851 CATGCATTCGTCACCCACTT 58.832 50.000 0.00 0.00 0.00 3.16
2803 3002 2.045708 GGCATGCATTCGTCACCCA 61.046 57.895 21.36 0.00 0.00 4.51
2805 3004 2.045708 TGGGCATGCATTCGTCACC 61.046 57.895 21.36 9.23 0.00 4.02
2892 3097 1.101049 CACGGTGACCAAGTGGCTTT 61.101 55.000 0.74 0.00 39.32 3.51
2939 3144 2.961062 GGCATTGGCAGATAGATGGTTT 59.039 45.455 5.17 0.00 43.71 3.27
2940 3145 2.091720 TGGCATTGGCAGATAGATGGTT 60.092 45.455 9.11 0.00 43.71 3.67
2941 3146 1.496001 TGGCATTGGCAGATAGATGGT 59.504 47.619 9.11 0.00 43.71 3.55
2964 3169 4.026744 CCTGGACTCAAGAGATGGAACTA 58.973 47.826 3.73 0.00 0.00 2.24
3021 3229 7.384115 CGATCACCTAATTATGTAATGTCCGTT 59.616 37.037 0.00 0.00 0.00 4.44
3074 3282 6.019075 CGATCGTTCCTTCATTTGCTAATACA 60.019 38.462 7.03 0.00 0.00 2.29
3117 3325 9.502091 ACTTTAATTAAGCTGTGTTCATACTCA 57.498 29.630 0.00 0.00 37.37 3.41
3206 3414 3.389329 AGACATATAGGGGTGTGCTCTTG 59.611 47.826 0.00 0.00 0.00 3.02
3282 3491 5.312079 TGAAAATAGGGGTTTGCAAATTGG 58.688 37.500 16.21 0.00 0.00 3.16
3284 3493 9.752228 AAATATGAAAATAGGGGTTTGCAAATT 57.248 25.926 16.21 2.42 30.71 1.82
3341 3566 8.997323 GCTCATTTTATCTGTATATGCTGAACT 58.003 33.333 4.59 0.00 0.00 3.01
3342 3567 8.997323 AGCTCATTTTATCTGTATATGCTGAAC 58.003 33.333 4.59 0.00 0.00 3.18
3344 3569 9.645059 GTAGCTCATTTTATCTGTATATGCTGA 57.355 33.333 3.02 3.02 0.00 4.26
3345 3570 9.428097 TGTAGCTCATTTTATCTGTATATGCTG 57.572 33.333 0.00 0.00 0.00 4.41
3351 3576 9.764363 TTCGAATGTAGCTCATTTTATCTGTAT 57.236 29.630 11.18 0.00 45.49 2.29
3352 3577 9.764363 ATTCGAATGTAGCTCATTTTATCTGTA 57.236 29.630 10.50 0.00 45.49 2.74
3353 3578 8.668510 ATTCGAATGTAGCTCATTTTATCTGT 57.331 30.769 10.50 0.00 45.49 3.41
3381 3606 6.857964 CGACGAGTTGAAAAGTAAGGTAGTTA 59.142 38.462 0.00 0.00 0.00 2.24
3408 3634 4.339530 GCGCATAGGTCATCTATATCTCCA 59.660 45.833 0.30 0.00 36.59 3.86
3484 3710 1.550524 TCTGGATCTCGACAACAAGGG 59.449 52.381 0.00 0.00 0.00 3.95
3488 3714 3.157881 ACTCTTCTGGATCTCGACAACA 58.842 45.455 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.