Multiple sequence alignment - TraesCS2B01G454200

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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 TraesCS2B01G454200 chr2B 100.000 3200 0 0 1 3200 648486054 648482855 0.000000e+00 5910.0
1 TraesCS2B01G454200 chr2A 90.766 2859 154 48 422 3200 686175247 686172419 0.000000e+00 3716.0
2 TraesCS2B01G454200 chr2A 80.542 406 45 19 2 392 686176063 686175677 6.760000e-72 281.0
3 TraesCS2B01G454200 chr2A 93.333 45 3 0 2890 2934 686172785 686172741 2.060000e-07 67.6
4 TraesCS2B01G454200 chr2D 81.274 1319 112 63 630 1867 543322404 543321140 0.000000e+00 942.0
5 TraesCS2B01G454200 chr2D 91.640 311 23 2 2890 3200 543320168 543319861 8.200000e-116 427.0
6 TraesCS2B01G454200 chr2D 90.426 282 18 7 1935 2213 543320936 543320661 2.350000e-96 363.0
7 TraesCS2B01G454200 chr2D 85.761 309 43 1 315 623 543322749 543322442 3.080000e-85 326.0


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 TraesCS2B01G454200 chr2B 648482855 648486054 3199 True 5910.000000 5910 100.000000 1 3200 1 chr2B.!!$R1 3199
1 TraesCS2B01G454200 chr2A 686172419 686176063 3644 True 1354.866667 3716 88.213667 2 3200 3 chr2A.!!$R1 3198
2 TraesCS2B01G454200 chr2D 543319861 543322749 2888 True 514.500000 942 87.275250 315 3200 4 chr2D.!!$R1 2885

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
112 113 0.169230 CAGACTAGACTTGCGAGCGT 59.831 55.0 0.0 0.0 0.00 5.07 F
625 1064 0.178992 AAGCTTGGTGCAAGGCTACA 60.179 50.0 0.0 0.0 45.94 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1590 2125 0.108585 TGTCAAAGCCTCCACACTCC 59.891 55.0 0.0 0.0 0.0 3.85 R
2224 2914 0.883833 CATGACAACCAAGACCAGCC 59.116 55.0 0.0 0.0 0.0 4.85 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
32 33 9.607988 ATTTGTGTATTGATTAGACCGTTCATA 57.392 29.630 0.00 0.00 0.00 2.15
33 34 9.438228 TTTGTGTATTGATTAGACCGTTCATAA 57.562 29.630 0.00 0.00 0.00 1.90
34 35 9.607988 TTGTGTATTGATTAGACCGTTCATAAT 57.392 29.630 0.00 0.00 0.00 1.28
47 48 7.336931 AGACCGTTCATAATATTTTGAAGCTGT 59.663 33.333 18.15 15.19 32.79 4.40
57 58 5.909621 ATTTTGAAGCTGTAGATGCATGT 57.090 34.783 2.46 1.37 0.00 3.21
67 68 2.554806 AGATGCATGTCACATTTGCG 57.445 45.000 2.46 0.00 39.23 4.85
71 72 3.089573 TGCATGTCACATTTGCGAAAA 57.910 38.095 0.00 0.00 39.23 2.29
72 73 3.051327 TGCATGTCACATTTGCGAAAAG 58.949 40.909 0.00 0.00 39.23 2.27
73 74 3.243334 TGCATGTCACATTTGCGAAAAGA 60.243 39.130 0.00 0.00 39.23 2.52
77 78 1.611491 TCACATTTGCGAAAAGACCCC 59.389 47.619 0.00 0.00 0.00 4.95
78 79 1.613437 CACATTTGCGAAAAGACCCCT 59.387 47.619 0.00 0.00 0.00 4.79
79 80 1.886542 ACATTTGCGAAAAGACCCCTC 59.113 47.619 0.00 0.00 0.00 4.30
94 95 2.769663 ACCCCTCGTATGCTAAACATCA 59.230 45.455 0.00 0.00 40.38 3.07
95 96 3.181465 ACCCCTCGTATGCTAAACATCAG 60.181 47.826 0.00 0.00 40.38 2.90
96 97 3.069586 CCCCTCGTATGCTAAACATCAGA 59.930 47.826 0.00 0.00 40.38 3.27
97 98 4.051922 CCCTCGTATGCTAAACATCAGAC 58.948 47.826 0.00 0.00 40.38 3.51
98 99 4.202161 CCCTCGTATGCTAAACATCAGACT 60.202 45.833 0.00 0.00 40.38 3.24
99 100 5.009710 CCCTCGTATGCTAAACATCAGACTA 59.990 44.000 0.00 0.00 40.38 2.59
100 101 6.146216 CCTCGTATGCTAAACATCAGACTAG 58.854 44.000 0.00 0.00 40.38 2.57
101 102 6.017026 CCTCGTATGCTAAACATCAGACTAGA 60.017 42.308 0.00 0.00 40.38 2.43
102 103 6.726230 TCGTATGCTAAACATCAGACTAGAC 58.274 40.000 0.00 0.00 40.38 2.59
103 104 6.542735 TCGTATGCTAAACATCAGACTAGACT 59.457 38.462 0.00 0.00 40.38 3.24
104 105 7.067129 TCGTATGCTAAACATCAGACTAGACTT 59.933 37.037 0.00 0.00 40.38 3.01
105 106 7.166638 CGTATGCTAAACATCAGACTAGACTTG 59.833 40.741 0.00 0.00 40.38 3.16
112 113 0.169230 CAGACTAGACTTGCGAGCGT 59.831 55.000 0.00 0.00 0.00 5.07
120 121 1.807573 CTTGCGAGCGTCTTCCCTC 60.808 63.158 0.00 0.00 0.00 4.30
122 123 2.507324 GCGAGCGTCTTCCCTCAC 60.507 66.667 0.00 0.00 0.00 3.51
130 131 1.797025 GTCTTCCCTCACGTGAAAGG 58.203 55.000 20.49 21.72 0.00 3.11
137 138 4.030913 TCCCTCACGTGAAAGGAATCTAT 58.969 43.478 26.72 0.00 34.35 1.98
172 173 4.395854 CCTTGACTATAGCATTGCACAACA 59.604 41.667 11.91 0.77 0.00 3.33
179 180 3.738830 AGCATTGCACAACACAAGAAT 57.261 38.095 11.91 0.00 0.00 2.40
184 185 5.463061 GCATTGCACAACACAAGAATACTTT 59.537 36.000 3.15 0.00 33.70 2.66
186 187 5.181690 TGCACAACACAAGAATACTTTCC 57.818 39.130 0.00 0.00 33.70 3.13
192 193 4.385825 ACACAAGAATACTTTCCGAGCAA 58.614 39.130 0.00 0.00 33.70 3.91
197 198 0.988832 ATACTTTCCGAGCAACCCCA 59.011 50.000 0.00 0.00 0.00 4.96
199 200 0.988832 ACTTTCCGAGCAACCCCATA 59.011 50.000 0.00 0.00 0.00 2.74
200 201 1.353022 ACTTTCCGAGCAACCCCATAA 59.647 47.619 0.00 0.00 0.00 1.90
274 275 0.395586 GGCCATGCAACACATCCCTA 60.396 55.000 0.00 0.00 36.64 3.53
282 283 4.598022 TGCAACACATCCCTATTCATTGA 58.402 39.130 0.00 0.00 0.00 2.57
283 284 4.641541 TGCAACACATCCCTATTCATTGAG 59.358 41.667 0.00 0.00 0.00 3.02
284 285 4.883585 GCAACACATCCCTATTCATTGAGA 59.116 41.667 0.00 0.00 0.00 3.27
285 286 5.357878 GCAACACATCCCTATTCATTGAGAA 59.642 40.000 0.00 0.00 41.28 2.87
286 287 6.127647 GCAACACATCCCTATTCATTGAGAAA 60.128 38.462 0.00 0.00 40.22 2.52
287 288 7.253422 CAACACATCCCTATTCATTGAGAAAC 58.747 38.462 0.00 0.00 40.22 2.78
288 289 6.484288 ACACATCCCTATTCATTGAGAAACA 58.516 36.000 0.00 0.00 40.22 2.83
289 290 7.121382 ACACATCCCTATTCATTGAGAAACAT 58.879 34.615 0.00 0.00 40.22 2.71
290 291 7.616935 ACACATCCCTATTCATTGAGAAACATT 59.383 33.333 0.00 0.00 40.22 2.71
291 292 8.472413 CACATCCCTATTCATTGAGAAACATTT 58.528 33.333 0.00 0.00 40.22 2.32
292 293 9.699410 ACATCCCTATTCATTGAGAAACATTTA 57.301 29.630 0.00 0.00 40.22 1.40
304 305 6.801575 TGAGAAACATTTAAAAAGTTCCGCT 58.198 32.000 9.10 7.68 0.00 5.52
312 343 8.573035 ACATTTAAAAAGTTCCGCTAAGATGAA 58.427 29.630 0.00 0.00 0.00 2.57
330 361 8.659925 AAGATGAAAATAACACATGCAACAAA 57.340 26.923 0.00 0.00 0.00 2.83
335 366 8.939929 TGAAAATAACACATGCAACAAAGAAAA 58.060 25.926 0.00 0.00 0.00 2.29
343 374 7.596248 ACACATGCAACAAAGAAAATACAGATC 59.404 33.333 0.00 0.00 0.00 2.75
399 430 3.469899 TCATTGCAACATAACGCTCAC 57.530 42.857 0.00 0.00 0.00 3.51
410 441 4.515191 ACATAACGCTCACATGTTGAAACT 59.485 37.500 0.00 0.00 32.21 2.66
417 448 5.034152 GCTCACATGTTGAAACTTTCGAAA 58.966 37.500 10.71 10.71 32.21 3.46
418 449 5.052370 GCTCACATGTTGAAACTTTCGAAAC 60.052 40.000 6.47 0.00 32.21 2.78
419 450 5.336744 TCACATGTTGAAACTTTCGAAACC 58.663 37.500 6.47 0.00 0.00 3.27
424 455 5.981174 TGTTGAAACTTTCGAAACCGATAG 58.019 37.500 6.47 0.00 39.75 2.08
490 929 1.781786 TGAGCCCTTCGAAGCTAGAT 58.218 50.000 19.99 8.99 40.11 1.98
491 930 1.683917 TGAGCCCTTCGAAGCTAGATC 59.316 52.381 19.99 17.16 40.11 2.75
540 979 2.356432 CCCACCATCTTTCATGAGCTCA 60.356 50.000 20.79 20.79 0.00 4.26
545 984 4.008330 CCATCTTTCATGAGCTCAACACT 58.992 43.478 22.50 0.00 0.00 3.55
566 1005 4.221703 ACTTCAGTGAACTTCCTCATCGAT 59.778 41.667 0.08 0.00 0.00 3.59
579 1018 2.556189 CTCATCGATCTTCGGTCTCCAT 59.444 50.000 0.00 0.00 40.88 3.41
591 1030 5.193099 TCGGTCTCCATCATGAGGATATA 57.807 43.478 9.37 0.00 33.95 0.86
592 1031 5.770919 TCGGTCTCCATCATGAGGATATAT 58.229 41.667 9.37 0.00 33.95 0.86
613 1052 2.166459 TGAGTGAGATCCGTAAGCTTGG 59.834 50.000 9.86 2.33 0.00 3.61
625 1064 0.178992 AAGCTTGGTGCAAGGCTACA 60.179 50.000 0.00 0.00 45.94 2.74
633 1072 1.222113 GCAAGGCTACAGGAGGGAC 59.778 63.158 0.00 0.00 0.00 4.46
666 1135 2.438434 GGTTCGAGCACCCATGGG 60.438 66.667 30.23 30.23 42.03 4.00
675 1144 1.746615 CACCCATGGGAGCGAAGTG 60.747 63.158 38.07 19.03 38.96 3.16
676 1145 2.825836 CCCATGGGAGCGAAGTGC 60.826 66.667 28.27 0.00 46.98 4.40
691 1160 1.664965 GTGCACGGTCAGTCTCCAC 60.665 63.158 0.00 0.00 0.00 4.02
697 1166 1.257750 CGGTCAGTCTCCACCATGGA 61.258 60.000 21.47 0.00 45.98 3.41
725 1194 3.028094 TGCCGACCTCCTAAATAGAGT 57.972 47.619 0.00 0.00 0.00 3.24
726 1195 2.693591 TGCCGACCTCCTAAATAGAGTG 59.306 50.000 0.00 0.00 0.00 3.51
754 1232 7.623999 AGGATAAATGAGACATGATACCAGT 57.376 36.000 0.00 0.00 0.00 4.00
755 1233 8.727100 AGGATAAATGAGACATGATACCAGTA 57.273 34.615 0.00 0.00 0.00 2.74
762 1240 5.360999 TGAGACATGATACCAGTAGAGTTGG 59.639 44.000 0.00 0.00 41.60 3.77
806 1284 1.207329 GGATGAGCGAGTAGTTTGGGT 59.793 52.381 0.00 0.00 0.00 4.51
829 1307 3.377172 ACTGGAGTTCTGTTCAAAAACCG 59.623 43.478 0.00 0.00 34.28 4.44
830 1308 3.611970 TGGAGTTCTGTTCAAAAACCGA 58.388 40.909 0.00 0.00 34.28 4.69
831 1309 3.625764 TGGAGTTCTGTTCAAAAACCGAG 59.374 43.478 0.00 0.00 34.28 4.63
875 1364 7.141758 TGGATCTAATCAACTGCTCCTATTT 57.858 36.000 0.00 0.00 0.00 1.40
876 1365 7.577303 TGGATCTAATCAACTGCTCCTATTTT 58.423 34.615 0.00 0.00 0.00 1.82
878 1367 7.040823 GGATCTAATCAACTGCTCCTATTTTGG 60.041 40.741 0.00 0.00 0.00 3.28
882 1373 4.934356 TCAACTGCTCCTATTTTGGGAAT 58.066 39.130 0.00 0.00 31.92 3.01
982 1484 5.140747 ACTTGTAGCAAAACAAACCACAA 57.859 34.783 1.71 0.00 38.81 3.33
991 1493 5.620467 CAAAACAAACCACAAGCAGAAAAG 58.380 37.500 0.00 0.00 0.00 2.27
995 1497 3.782889 AACCACAAGCAGAAAAGTGAC 57.217 42.857 0.00 0.00 33.99 3.67
1063 1577 4.475444 CCGCCTACCTCCTCCCCA 62.475 72.222 0.00 0.00 0.00 4.96
1386 1909 0.822121 GTTCGACCTTTTGCCCCACT 60.822 55.000 0.00 0.00 0.00 4.00
1392 1915 1.524008 CCTTTTGCCCCACTCGAACC 61.524 60.000 0.00 0.00 0.00 3.62
1418 1941 1.676006 CCGTTGTTTGCCACTTCTCTT 59.324 47.619 0.00 0.00 0.00 2.85
1436 1959 2.099263 TCTTCCCTTATCTTCAGCGTCG 59.901 50.000 0.00 0.00 0.00 5.12
1438 1961 0.460311 CCCTTATCTTCAGCGTCGGT 59.540 55.000 0.00 0.00 0.00 4.69
1565 2100 3.427528 GCCATTTATTCATCTGCATTGCG 59.572 43.478 3.84 0.00 0.00 4.85
1590 2125 2.700371 TGATACTGTGATAGGGGCTGTG 59.300 50.000 0.00 0.00 0.00 3.66
1591 2126 1.496060 TACTGTGATAGGGGCTGTGG 58.504 55.000 0.00 0.00 0.00 4.17
1592 2127 0.252696 ACTGTGATAGGGGCTGTGGA 60.253 55.000 0.00 0.00 0.00 4.02
1593 2128 0.467384 CTGTGATAGGGGCTGTGGAG 59.533 60.000 0.00 0.00 0.00 3.86
1594 2129 0.252696 TGTGATAGGGGCTGTGGAGT 60.253 55.000 0.00 0.00 0.00 3.85
1595 2130 0.179000 GTGATAGGGGCTGTGGAGTG 59.821 60.000 0.00 0.00 0.00 3.51
1596 2131 0.252696 TGATAGGGGCTGTGGAGTGT 60.253 55.000 0.00 0.00 0.00 3.55
1720 2258 4.974645 AACAAGGAGATGGTTCTGTGTA 57.025 40.909 0.00 0.00 30.30 2.90
1725 2263 3.100671 GGAGATGGTTCTGTGTACTCCT 58.899 50.000 0.00 0.00 39.20 3.69
1731 2269 4.160329 TGGTTCTGTGTACTCCTCTGAAT 58.840 43.478 0.00 0.00 0.00 2.57
1747 2299 6.608405 TCCTCTGAATTCGGGTACAATTACTA 59.392 38.462 14.33 0.00 0.00 1.82
1879 2433 6.832520 TGTTTGGCTTAGATATTCTTGCAA 57.167 33.333 0.00 0.00 0.00 4.08
1899 2453 4.358851 CAAAAAGGAATTGAGCACGAACA 58.641 39.130 0.00 0.00 0.00 3.18
1908 2462 7.329226 AGGAATTGAGCACGAACATTTTAAATG 59.671 33.333 15.25 15.25 0.00 2.32
1909 2463 7.116233 GGAATTGAGCACGAACATTTTAAATGT 59.884 33.333 16.57 16.57 0.00 2.71
1915 2469 7.524065 AGCACGAACATTTTAAATGTAGTACC 58.476 34.615 21.55 16.78 0.00 3.34
1916 2470 7.173562 AGCACGAACATTTTAAATGTAGTACCA 59.826 33.333 21.55 0.00 0.00 3.25
1917 2471 7.966204 GCACGAACATTTTAAATGTAGTACCAT 59.034 33.333 21.55 6.23 0.00 3.55
1945 2634 7.230747 TCCTTCATTCCATTCTTCTTGTTACA 58.769 34.615 0.00 0.00 0.00 2.41
1994 2683 8.830201 TTCATGTTCATTAATCCTTGTTTTGG 57.170 30.769 0.00 0.00 0.00 3.28
1996 2685 9.083422 TCATGTTCATTAATCCTTGTTTTGGTA 57.917 29.630 0.00 0.00 0.00 3.25
2224 2914 7.255660 GACTGAAGAGTAATACCTATCCAGGTG 60.256 44.444 6.59 0.00 43.64 4.00
2240 2930 1.172812 GGTGGCTGGTCTTGGTTGTC 61.173 60.000 0.00 0.00 0.00 3.18
2360 3098 8.793592 GTTCCTGTTTAAGAAATGGATGTACTT 58.206 33.333 0.00 0.00 0.00 2.24
2441 3180 4.154195 GCACCGTACTGATTGATTCTGTTT 59.846 41.667 0.00 0.00 37.63 2.83
2450 3189 5.716094 TGATTGATTCTGTTTCAGCAATGG 58.284 37.500 0.00 0.00 27.71 3.16
2515 3254 4.825422 TCAGTCTTTGATGATCTGGTGAC 58.175 43.478 0.00 0.00 0.00 3.67
2534 3273 4.622740 GTGACATTTTTAGCCAGCATGTTC 59.377 41.667 0.00 0.00 0.00 3.18
2541 3280 8.772705 CATTTTTAGCCAGCATGTTCTTTTTAA 58.227 29.630 0.00 0.00 0.00 1.52
2542 3281 8.723942 TTTTTAGCCAGCATGTTCTTTTTAAA 57.276 26.923 0.00 0.00 0.00 1.52
2543 3282 8.723942 TTTTAGCCAGCATGTTCTTTTTAAAA 57.276 26.923 0.00 0.00 0.00 1.52
2544 3283 8.723942 TTTAGCCAGCATGTTCTTTTTAAAAA 57.276 26.923 12.62 12.62 0.00 1.94
2572 3311 0.613260 GTGGAGACAGCATGGTGGTA 59.387 55.000 27.32 7.20 44.46 3.25
2574 3313 1.003118 TGGAGACAGCATGGTGGTAAC 59.997 52.381 27.32 15.42 43.62 2.50
2596 3335 3.192422 CCTCCTCTACTGTCTTGAGTGTG 59.808 52.174 0.00 0.00 0.00 3.82
2597 3336 4.075682 CTCCTCTACTGTCTTGAGTGTGA 58.924 47.826 0.00 0.00 0.00 3.58
2599 3338 4.520874 TCCTCTACTGTCTTGAGTGTGAAG 59.479 45.833 0.00 0.00 0.00 3.02
2640 3379 2.846206 AGGGAAGACATCAATGCAGGTA 59.154 45.455 0.00 0.00 0.00 3.08
2684 3423 7.329471 CGCACTCATATACTATATGCACAAAGT 59.671 37.037 10.24 6.43 0.00 2.66
2714 3453 8.400947 TCTTATCAAGCTTAAATTGCACTGATC 58.599 33.333 0.00 0.00 36.92 2.92
2734 3473 6.450545 TGATCACAATCATTCTAGGATCGTC 58.549 40.000 0.00 0.00 36.98 4.20
2769 3510 4.686091 TCATTTCTGTTGAGTAAGTGAGCG 59.314 41.667 0.00 0.00 0.00 5.03
2901 3652 7.070571 ACAAAGGATTACATTCCAAACCTCAAA 59.929 33.333 0.00 0.00 38.32 2.69
2952 3703 9.366216 GGATTACAATTTTACTCAAAATCCACC 57.634 33.333 0.00 0.00 42.29 4.61
2982 3741 8.542497 TTACAAAAGCATCTGTAACGAGTAAT 57.458 30.769 0.00 0.00 34.02 1.89
3000 3759 8.936864 ACGAGTAATCAAAAATACAGAAGGAAG 58.063 33.333 0.00 0.00 0.00 3.46
3042 3801 5.824624 AGTTTCTATGTACATCAATGCCCTG 59.175 40.000 12.68 0.00 0.00 4.45
3056 3815 7.612065 TCAATGCCCTGTTGTACTACTATAT 57.388 36.000 8.88 0.00 0.00 0.86
3057 3816 7.441836 TCAATGCCCTGTTGTACTACTATATG 58.558 38.462 8.88 0.53 0.00 1.78
3064 3823 7.076362 CCTGTTGTACTACTATATGCACTACG 58.924 42.308 8.88 0.00 0.00 3.51
3121 3884 1.912043 AGAAACAGCAGCACCTAGGAT 59.088 47.619 17.98 0.00 0.00 3.24
3143 3906 9.690913 AGGATCATTTCATCTGAATACTTGAAA 57.309 29.630 6.00 6.00 40.99 2.69
3161 3924 7.707104 ACTTGAAAGATCAAACCACTTACAAG 58.293 34.615 0.00 0.00 44.64 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.328146 CGGTCTAATCAATACACAAATGTACAG 58.672 37.037 0.33 0.00 44.11 2.74
6 7 7.915293 TGAACGGTCTAATCAATACACAAAT 57.085 32.000 0.33 0.00 0.00 2.32
24 25 8.826710 TCTACAGCTTCAAAATATTATGAACGG 58.173 33.333 0.00 0.00 32.46 4.44
32 33 8.004087 ACATGCATCTACAGCTTCAAAATATT 57.996 30.769 0.00 0.00 0.00 1.28
33 34 7.283807 TGACATGCATCTACAGCTTCAAAATAT 59.716 33.333 0.00 0.00 0.00 1.28
34 35 6.598850 TGACATGCATCTACAGCTTCAAAATA 59.401 34.615 0.00 0.00 0.00 1.40
35 36 5.416639 TGACATGCATCTACAGCTTCAAAAT 59.583 36.000 0.00 0.00 0.00 1.82
47 48 3.269178 TCGCAAATGTGACATGCATCTA 58.731 40.909 11.23 0.00 40.04 1.98
57 58 1.611491 GGGGTCTTTTCGCAAATGTGA 59.389 47.619 0.00 0.00 0.00 3.58
67 68 2.693267 AGCATACGAGGGGTCTTTTC 57.307 50.000 0.00 0.00 0.00 2.29
71 72 2.463752 TGTTTAGCATACGAGGGGTCT 58.536 47.619 0.00 0.00 0.00 3.85
72 73 2.973694 TGTTTAGCATACGAGGGGTC 57.026 50.000 0.00 0.00 0.00 4.46
73 74 2.769663 TGATGTTTAGCATACGAGGGGT 59.230 45.455 0.00 0.00 38.06 4.95
77 78 6.853872 GTCTAGTCTGATGTTTAGCATACGAG 59.146 42.308 0.00 0.00 38.06 4.18
78 79 6.542735 AGTCTAGTCTGATGTTTAGCATACGA 59.457 38.462 0.00 0.00 38.06 3.43
79 80 6.730175 AGTCTAGTCTGATGTTTAGCATACG 58.270 40.000 0.00 0.00 38.06 3.06
94 95 0.448593 GACGCTCGCAAGTCTAGTCT 59.551 55.000 0.00 0.00 39.48 3.24
95 96 0.448593 AGACGCTCGCAAGTCTAGTC 59.551 55.000 5.01 0.00 44.93 2.59
96 97 0.882474 AAGACGCTCGCAAGTCTAGT 59.118 50.000 6.86 0.00 45.91 2.57
97 98 1.540407 GAAGACGCTCGCAAGTCTAG 58.460 55.000 6.86 0.00 45.91 2.43
98 99 0.170561 GGAAGACGCTCGCAAGTCTA 59.829 55.000 6.86 0.00 45.91 2.59
100 101 2.095252 GGGAAGACGCTCGCAAGTC 61.095 63.158 0.00 0.00 37.63 3.01
101 102 2.048127 GGGAAGACGCTCGCAAGT 60.048 61.111 0.00 0.00 39.48 3.16
102 103 1.807573 GAGGGAAGACGCTCGCAAG 60.808 63.158 0.00 0.00 43.90 4.01
103 104 2.261671 GAGGGAAGACGCTCGCAA 59.738 61.111 0.00 0.00 43.90 4.85
162 163 6.215845 GGAAAGTATTCTTGTGTTGTGCAAT 58.784 36.000 0.00 0.00 35.79 3.56
172 173 3.751698 GGTTGCTCGGAAAGTATTCTTGT 59.248 43.478 0.00 0.00 35.79 3.16
179 180 0.988832 ATGGGGTTGCTCGGAAAGTA 59.011 50.000 0.00 0.00 0.00 2.24
184 185 2.588464 TTTTTATGGGGTTGCTCGGA 57.412 45.000 0.00 0.00 0.00 4.55
214 215 8.693504 CAAGTGTGATTGAAATGTTACAACATC 58.306 33.333 7.99 0.00 39.30 3.06
218 219 6.475076 GTGCAAGTGTGATTGAAATGTTACAA 59.525 34.615 0.00 0.00 31.55 2.41
257 258 3.289836 TGAATAGGGATGTGTTGCATGG 58.710 45.455 0.00 0.00 38.06 3.66
282 283 8.626526 TCTTAGCGGAACTTTTTAAATGTTTCT 58.373 29.630 9.71 9.66 0.00 2.52
283 284 8.791355 TCTTAGCGGAACTTTTTAAATGTTTC 57.209 30.769 9.71 7.36 0.00 2.78
284 285 9.191995 CATCTTAGCGGAACTTTTTAAATGTTT 57.808 29.630 9.71 0.00 0.00 2.83
285 286 8.573035 TCATCTTAGCGGAACTTTTTAAATGTT 58.427 29.630 8.39 8.39 0.00 2.71
286 287 8.106247 TCATCTTAGCGGAACTTTTTAAATGT 57.894 30.769 0.00 0.00 0.00 2.71
287 288 8.964420 TTCATCTTAGCGGAACTTTTTAAATG 57.036 30.769 0.00 0.00 0.00 2.32
288 289 9.974980 TTTTCATCTTAGCGGAACTTTTTAAAT 57.025 25.926 0.00 0.00 0.00 1.40
289 290 9.974980 ATTTTCATCTTAGCGGAACTTTTTAAA 57.025 25.926 0.00 0.00 0.00 1.52
292 293 9.406828 GTTATTTTCATCTTAGCGGAACTTTTT 57.593 29.630 0.00 0.00 0.00 1.94
296 297 6.653320 TGTGTTATTTTCATCTTAGCGGAACT 59.347 34.615 0.00 0.00 0.00 3.01
304 305 9.755804 TTTGTTGCATGTGTTATTTTCATCTTA 57.244 25.926 0.00 0.00 0.00 2.10
361 392 9.531158 TTGCAATGATTATGGATATGTATTCCA 57.469 29.630 0.00 0.00 37.99 3.53
370 401 7.174772 AGCGTTATGTTGCAATGATTATGGATA 59.825 33.333 0.59 0.00 0.00 2.59
399 430 4.593157 TCGGTTTCGAAAGTTTCAACATG 58.407 39.130 11.66 9.27 43.03 3.21
417 448 6.094881 CACAAAAATATGTGTTCCCTATCGGT 59.905 38.462 0.00 0.00 44.46 4.69
418 449 6.494842 CACAAAAATATGTGTTCCCTATCGG 58.505 40.000 0.00 0.00 44.46 4.18
490 929 0.834612 ACGAGTTTGGGGTCAACTGA 59.165 50.000 0.00 0.00 31.78 3.41
491 930 1.333619 CAACGAGTTTGGGGTCAACTG 59.666 52.381 0.00 0.00 31.78 3.16
512 951 1.177401 GAAAGATGGTGGGTTGAGGC 58.823 55.000 0.00 0.00 0.00 4.70
540 979 4.487714 TGAGGAAGTTCACTGAAGTGTT 57.512 40.909 10.14 0.00 45.76 3.32
545 984 4.464244 AGATCGATGAGGAAGTTCACTGAA 59.536 41.667 0.54 0.00 0.00 3.02
559 998 2.052782 TGGAGACCGAAGATCGATGA 57.947 50.000 0.54 0.00 43.74 2.92
566 1005 2.034878 CCTCATGATGGAGACCGAAGA 58.965 52.381 0.00 0.00 37.05 2.87
579 1018 6.545298 CGGATCTCACTCATATATCCTCATGA 59.455 42.308 0.00 0.00 35.06 3.07
591 1030 3.181471 CCAAGCTTACGGATCTCACTCAT 60.181 47.826 0.00 0.00 0.00 2.90
592 1031 2.166459 CCAAGCTTACGGATCTCACTCA 59.834 50.000 0.00 0.00 0.00 3.41
613 1052 1.078143 CCCTCCTGTAGCCTTGCAC 60.078 63.158 0.00 0.00 0.00 4.57
625 1064 0.334676 CCTCTCTCACAGTCCCTCCT 59.665 60.000 0.00 0.00 0.00 3.69
633 1072 2.098934 CGAACCTCATCCTCTCTCACAG 59.901 54.545 0.00 0.00 0.00 3.66
636 1105 2.649190 CTCGAACCTCATCCTCTCTCA 58.351 52.381 0.00 0.00 0.00 3.27
666 1135 2.355837 TGACCGTGCACTTCGCTC 60.356 61.111 16.19 0.00 43.06 5.03
669 1138 1.004277 GAGACTGACCGTGCACTTCG 61.004 60.000 16.19 1.09 0.00 3.79
675 1144 2.048127 GGTGGAGACTGACCGTGC 60.048 66.667 0.00 0.00 0.00 5.34
676 1145 0.390340 CATGGTGGAGACTGACCGTG 60.390 60.000 7.70 7.70 41.65 4.94
679 1148 2.683916 TCCATGGTGGAGACTGACC 58.316 57.895 12.58 0.00 42.67 4.02
697 1166 2.060980 GGAGGTCGGCATGGAGACT 61.061 63.158 0.00 0.00 37.52 3.24
738 1207 5.360999 CCAACTCTACTGGTATCATGTCTCA 59.639 44.000 0.00 0.00 0.00 3.27
741 1210 5.854010 TCCAACTCTACTGGTATCATGTC 57.146 43.478 0.00 0.00 35.30 3.06
754 1232 6.916360 AATGCCTTTCATTTTCCAACTCTA 57.084 33.333 0.00 0.00 42.48 2.43
755 1233 5.813513 AATGCCTTTCATTTTCCAACTCT 57.186 34.783 0.00 0.00 42.48 3.24
806 1284 4.573201 CGGTTTTTGAACAGAACTCCAGTA 59.427 41.667 0.00 0.00 0.00 2.74
829 1307 4.882671 ACATGTTGTGTTGTTCTCACTC 57.117 40.909 0.00 0.00 38.01 3.51
982 1484 2.146342 CATGGTCGTCACTTTTCTGCT 58.854 47.619 0.00 0.00 0.00 4.24
991 1493 0.034896 AGGGACAACATGGTCGTCAC 59.965 55.000 13.12 10.38 38.70 3.67
995 1497 0.391661 CAGGAGGGACAACATGGTCG 60.392 60.000 0.00 0.00 38.70 4.79
1063 1577 0.625683 ATGGGAATCCTGGTGAGGCT 60.626 55.000 0.00 0.00 39.57 4.58
1174 1697 4.148825 CTCGGCCACCTTCCTCGG 62.149 72.222 2.24 0.00 0.00 4.63
1418 1941 0.744874 CCGACGCTGAAGATAAGGGA 59.255 55.000 0.00 0.00 0.00 4.20
1565 2100 1.000955 CCCCTATCACAGTATCACGGC 59.999 57.143 0.00 0.00 0.00 5.68
1590 2125 0.108585 TGTCAAAGCCTCCACACTCC 59.891 55.000 0.00 0.00 0.00 3.85
1591 2126 2.079925 GATGTCAAAGCCTCCACACTC 58.920 52.381 0.00 0.00 0.00 3.51
1592 2127 1.421268 TGATGTCAAAGCCTCCACACT 59.579 47.619 0.00 0.00 0.00 3.55
1593 2128 1.896220 TGATGTCAAAGCCTCCACAC 58.104 50.000 0.00 0.00 0.00 3.82
1594 2129 2.885135 ATGATGTCAAAGCCTCCACA 57.115 45.000 0.00 0.00 0.00 4.17
1595 2130 8.621532 TTATTATATGATGTCAAAGCCTCCAC 57.378 34.615 0.00 0.00 0.00 4.02
1596 2131 9.812347 ATTTATTATATGATGTCAAAGCCTCCA 57.188 29.630 0.00 0.00 0.00 3.86
1720 2258 2.816411 TGTACCCGAATTCAGAGGAGT 58.184 47.619 11.95 5.57 0.00 3.85
1731 2269 8.929260 TCTCAGATATAGTAATTGTACCCGAA 57.071 34.615 0.00 0.00 0.00 4.30
1747 2299 6.930164 GTCATCACAAGCATCTTCTCAGATAT 59.070 38.462 0.00 0.00 37.71 1.63
1879 2433 4.853924 ATGTTCGTGCTCAATTCCTTTT 57.146 36.364 0.00 0.00 0.00 2.27
1908 2462 9.220767 GAATGGAATGAAGGATAATGGTACTAC 57.779 37.037 0.00 0.00 0.00 2.73
1909 2463 9.170890 AGAATGGAATGAAGGATAATGGTACTA 57.829 33.333 0.00 0.00 0.00 1.82
1915 2469 8.910944 ACAAGAAGAATGGAATGAAGGATAATG 58.089 33.333 0.00 0.00 0.00 1.90
1916 2470 9.484806 AACAAGAAGAATGGAATGAAGGATAAT 57.515 29.630 0.00 0.00 0.00 1.28
1917 2471 8.884124 AACAAGAAGAATGGAATGAAGGATAA 57.116 30.769 0.00 0.00 0.00 1.75
1920 2609 7.230747 TGTAACAAGAAGAATGGAATGAAGGA 58.769 34.615 0.00 0.00 0.00 3.36
1994 2683 6.687604 ACCTGATTGCAAAAAGTACCAATAC 58.312 36.000 1.71 0.00 0.00 1.89
1996 2685 5.806654 ACCTGATTGCAAAAAGTACCAAT 57.193 34.783 1.71 0.00 0.00 3.16
1998 2687 5.594725 TGTTACCTGATTGCAAAAAGTACCA 59.405 36.000 1.71 0.00 0.00 3.25
2224 2914 0.883833 CATGACAACCAAGACCAGCC 59.116 55.000 0.00 0.00 0.00 4.85
2240 2930 5.278169 GCAAAGCTACTAATGTCATCCCATG 60.278 44.000 0.00 0.00 0.00 3.66
2360 3098 8.744568 TCACTATTATTTGTCATGCCAATACA 57.255 30.769 0.00 0.00 0.00 2.29
2441 3180 2.487775 ACCCAGTATACCCATTGCTGA 58.512 47.619 0.00 0.00 0.00 4.26
2450 3189 7.399191 TGATCACTATATCCAACCCAGTATACC 59.601 40.741 0.00 0.00 0.00 2.73
2515 3254 6.790285 AAAAGAACATGCTGGCTAAAAATG 57.210 33.333 0.00 0.00 0.00 2.32
2554 3293 1.003118 GTTACCACCATGCTGTCTCCA 59.997 52.381 0.00 0.00 0.00 3.86
2568 3307 4.087182 CAAGACAGTAGAGGAGGTTACCA 58.913 47.826 3.51 0.00 0.00 3.25
2572 3311 3.829601 CACTCAAGACAGTAGAGGAGGTT 59.170 47.826 0.00 0.00 33.76 3.50
2574 3313 3.192422 CACACTCAAGACAGTAGAGGAGG 59.808 52.174 0.00 0.00 33.76 4.30
2596 3335 6.402226 CCTTCGTTATTACCTTTGAGCACTTC 60.402 42.308 0.00 0.00 0.00 3.01
2597 3336 5.411669 CCTTCGTTATTACCTTTGAGCACTT 59.588 40.000 0.00 0.00 0.00 3.16
2599 3338 4.094442 CCCTTCGTTATTACCTTTGAGCAC 59.906 45.833 0.00 0.00 0.00 4.40
2640 3379 5.778862 AGTGCGCAATTTACTTACCAAAAT 58.221 33.333 14.00 0.00 0.00 1.82
2684 3423 9.231297 AGTGCAATTTAAGCTTGATAAGAACTA 57.769 29.630 9.86 0.00 0.00 2.24
2714 3453 8.084684 TCTATTGACGATCCTAGAATGATTGTG 58.915 37.037 5.39 0.00 37.05 3.33
2734 3473 9.903682 ACTCAACAGAAATGACATTTTCTATTG 57.096 29.630 14.46 15.93 45.19 1.90
2811 3552 6.765989 AGCTCACTTTTGTCAACACAAGTATA 59.234 34.615 12.84 5.65 42.86 1.47
2813 3554 4.941263 AGCTCACTTTTGTCAACACAAGTA 59.059 37.500 12.84 3.91 42.86 2.24
2885 3636 7.360113 ACATAAAGTTTGAGGTTTGGAATGT 57.640 32.000 0.00 0.00 0.00 2.71
2938 3689 2.851263 AGTGCGGTGGATTTTGAGTA 57.149 45.000 0.00 0.00 0.00 2.59
2952 3703 3.542712 ACAGATGCTTTTGTAAGTGCG 57.457 42.857 0.00 0.00 33.74 5.34
2982 3741 8.635328 GGTTTTACCTTCCTTCTGTATTTTTGA 58.365 33.333 0.00 0.00 34.73 2.69
3000 3759 6.732154 AGAAACTAAAAAGAGCGGTTTTACC 58.268 36.000 0.00 0.00 34.05 2.85
3007 3766 7.591006 TGTACATAGAAACTAAAAAGAGCGG 57.409 36.000 0.00 0.00 0.00 5.52
3042 3801 6.963796 ACCGTAGTGCATATAGTAGTACAAC 58.036 40.000 2.52 0.00 38.29 3.32


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

AutoCloner maintained by Alex Coulton.