Multiple sequence alignment - TraesCS7B01G118700

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 TraesCS7B01G118700 chr7B 100.000 2897 0 0 1 2897 138153673 138156569 0.000000e+00 5350
1 TraesCS7B01G118700 chr7D 94.628 2215 67 17 710 2897 171835550 171837739 0.000000e+00 3384
2 TraesCS7B01G118700 chr7D 85.340 573 71 11 2 571 171834855 171835417 5.380000e-162 580
3 TraesCS7B01G118700 chr7D 90.909 242 22 0 2510 2751 171837619 171837860 2.780000e-85 326
4 TraesCS7B01G118700 chr7A 93.742 2221 76 22 710 2897 174890067 174892257 0.000000e+00 3273
5 TraesCS7B01G118700 chr7A 86.364 572 65 10 1 571 174888731 174889290 1.910000e-171 612
6 TraesCS7B01G118700 chr7A 88.843 242 26 1 2510 2751 174892138 174892378 2.180000e-76 296


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 TraesCS7B01G118700 chr7B 138153673 138156569 2896 False 5350.000000 5350 100.000000 1 2897 1 chr7B.!!$F1 2896
1 TraesCS7B01G118700 chr7D 171834855 171837860 3005 False 1430.000000 3384 90.292333 2 2897 3 chr7D.!!$F1 2895
2 TraesCS7B01G118700 chr7A 174888731 174892378 3647 False 1393.666667 3273 89.649667 1 2897 3 chr7A.!!$F1 2896

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
296 300 0.036388 TGGAGTTGCGATTGGAGACC 60.036 55.0 0.0 0.0 0.0 3.85 F
736 1413 0.110486 TGGTGTCTGAAAAGGGGCTC 59.890 55.0 0.0 0.0 0.0 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1836 2522 1.699054 CGGCATCAGATTCTGGGGGA 61.699 60.0 13.59 0.0 31.51 4.81 R
1930 2616 2.432146 TGCTCCATGGACACTAGTCATC 59.568 50.0 11.44 0.0 46.80 2.92 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
38 41 4.000988 CGTGACCAACTTGTTAGCCTAAT 58.999 43.478 0.00 0.00 0.00 1.73
43 46 3.181510 CCAACTTGTTAGCCTAATGTCGC 60.182 47.826 0.00 0.00 0.00 5.19
55 58 2.520465 AATGTCGCATGACCCTCGCA 62.520 55.000 0.00 0.00 44.86 5.10
94 97 4.698304 CCGATAGTTAAGCACTCCCAAAAA 59.302 41.667 0.00 0.00 36.88 1.94
112 115 2.949714 AAAACTGAAGCGATGACACG 57.050 45.000 0.00 0.00 0.00 4.49
118 121 1.352156 GAAGCGATGACACGACACCC 61.352 60.000 0.00 0.00 35.09 4.61
125 128 3.819877 GACACGACACCCACCCACC 62.820 68.421 0.00 0.00 0.00 4.61
126 129 3.867783 CACGACACCCACCCACCA 61.868 66.667 0.00 0.00 0.00 4.17
157 161 5.230942 ACACATACAAGAAGAGGAGAAACG 58.769 41.667 0.00 0.00 0.00 3.60
169 173 5.301555 AGAGGAGAAACGAAGAAAAAGGAG 58.698 41.667 0.00 0.00 0.00 3.69
173 177 5.296035 GGAGAAACGAAGAAAAAGGAGAACA 59.704 40.000 0.00 0.00 0.00 3.18
175 179 4.531659 AACGAAGAAAAAGGAGAACACG 57.468 40.909 0.00 0.00 0.00 4.49
184 188 6.262273 AGAAAAAGGAGAACACGAAGCATTAA 59.738 34.615 0.00 0.00 0.00 1.40
185 189 5.358298 AAAGGAGAACACGAAGCATTAAC 57.642 39.130 0.00 0.00 0.00 2.01
187 191 3.071479 GGAGAACACGAAGCATTAACCA 58.929 45.455 0.00 0.00 0.00 3.67
189 193 4.378459 GGAGAACACGAAGCATTAACCAAG 60.378 45.833 0.00 0.00 0.00 3.61
199 203 2.224161 GCATTAACCAAGGGTGTTGCAA 60.224 45.455 0.00 0.00 36.40 4.08
226 230 4.329545 GCCGAAGCTGTGGTGGGA 62.330 66.667 6.38 0.00 35.50 4.37
253 257 4.776322 TGCTGGAACCGGGCATCG 62.776 66.667 6.32 0.00 38.88 3.84
254 258 4.467084 GCTGGAACCGGGCATCGA 62.467 66.667 6.32 0.00 42.43 3.59
256 260 4.444838 TGGAACCGGGCATCGACG 62.445 66.667 6.32 0.00 42.43 5.12
278 282 1.201998 CGCTTGAACTAGCAGCATGTG 60.202 52.381 8.64 0.00 41.28 3.21
289 293 0.806868 CAGCATGTGGAGTTGCGATT 59.193 50.000 0.00 0.00 43.61 3.34
291 295 0.179156 GCATGTGGAGTTGCGATTGG 60.179 55.000 0.00 0.00 0.00 3.16
295 299 1.079503 GTGGAGTTGCGATTGGAGAC 58.920 55.000 0.00 0.00 0.00 3.36
296 300 0.036388 TGGAGTTGCGATTGGAGACC 60.036 55.000 0.00 0.00 0.00 3.85
300 304 1.375396 TTGCGATTGGAGACCGGTG 60.375 57.895 14.63 0.00 0.00 4.94
323 327 2.125912 ACGAGCGTCAGTGATGCC 60.126 61.111 29.43 20.48 44.75 4.40
326 330 2.125912 AGCGTCAGTGATGCCGAC 60.126 61.111 29.43 9.97 44.75 4.79
354 358 0.687920 TACATTGCTGTGACGGGGAA 59.312 50.000 0.00 0.00 36.79 3.97
363 367 2.818274 GACGGGGAACATGGCGAC 60.818 66.667 0.00 0.00 0.00 5.19
373 377 0.826715 ACATGGCGACTGTAGCTCAT 59.173 50.000 12.54 10.90 34.52 2.90
387 391 1.440893 CTCATGACAGAGCCGGGAG 59.559 63.158 2.18 0.00 0.00 4.30
420 424 1.134965 GTGACCTCGACTTCATGGGAG 60.135 57.143 0.00 0.00 0.00 4.30
426 430 0.460987 CGACTTCATGGGAGGAGCAC 60.461 60.000 0.00 0.00 0.00 4.40
428 432 1.153289 CTTCATGGGAGGAGCACCG 60.153 63.158 0.00 0.00 41.83 4.94
434 438 3.371063 GGAGGAGCACCGACGACA 61.371 66.667 0.00 0.00 41.83 4.35
435 439 2.649034 GAGGAGCACCGACGACAA 59.351 61.111 0.00 0.00 41.83 3.18
452 456 1.531149 ACAATTTCACGACAAGGAGCG 59.469 47.619 0.00 0.00 0.00 5.03
456 460 1.740332 TTCACGACAAGGAGCGGTGA 61.740 55.000 0.00 0.00 0.00 4.02
476 480 2.360475 GCCACACAGGAAGGGAGC 60.360 66.667 0.00 0.00 41.22 4.70
519 523 6.790232 TTTTTCTGTTTGTTTCCATCTCCT 57.210 33.333 0.00 0.00 0.00 3.69
540 544 3.939740 ACTTGCATGGTAGATGGTGAT 57.060 42.857 4.44 0.00 0.00 3.06
563 567 7.446319 TGATCGAAGCAATCAATCCAATTAGAT 59.554 33.333 0.00 0.00 30.37 1.98
577 581 7.067496 TCCAATTAGATGGATCTGTTCCTAC 57.933 40.000 6.35 1.24 44.52 3.18
578 582 6.615316 TCCAATTAGATGGATCTGTTCCTACA 59.385 38.462 6.35 0.00 44.52 2.74
579 583 7.127186 TCCAATTAGATGGATCTGTTCCTACAA 59.873 37.037 6.35 0.00 44.52 2.41
580 584 7.775093 CCAATTAGATGGATCTGTTCCTACAAA 59.225 37.037 6.35 0.00 45.68 2.83
581 585 9.177608 CAATTAGATGGATCTGTTCCTACAAAA 57.822 33.333 6.35 1.35 45.68 2.44
582 586 9.753674 AATTAGATGGATCTGTTCCTACAAAAA 57.246 29.630 6.35 0.00 45.68 1.94
609 613 1.571919 AAATAGACGGATCTGCGTGC 58.428 50.000 0.26 0.00 36.29 5.34
610 614 0.747255 AATAGACGGATCTGCGTGCT 59.253 50.000 0.26 1.99 36.29 4.40
611 615 0.747255 ATAGACGGATCTGCGTGCTT 59.253 50.000 0.26 0.00 36.29 3.91
612 616 0.179137 TAGACGGATCTGCGTGCTTG 60.179 55.000 0.26 0.00 36.29 4.01
617 621 1.493950 GGATCTGCGTGCTTGGATCG 61.494 60.000 12.74 0.00 36.43 3.69
638 642 2.114670 CCACTAGCAATGTGGCCGG 61.115 63.158 0.00 0.00 46.73 6.13
676 680 0.874175 CGACCGGCGCAGATTATTGA 60.874 55.000 10.83 0.00 0.00 2.57
678 682 0.814010 ACCGGCGCAGATTATTGACC 60.814 55.000 10.83 0.00 0.00 4.02
688 692 5.592054 GCAGATTATTGACCTTTTTAGGGC 58.408 41.667 0.00 0.00 37.53 5.19
697 1260 6.553953 TGACCTTTTTAGGGCTTTTCTTTT 57.446 33.333 0.00 0.00 38.00 2.27
706 1269 8.716646 TTTAGGGCTTTTCTTTTTCTTTTCTG 57.283 30.769 0.00 0.00 0.00 3.02
707 1270 6.544928 AGGGCTTTTCTTTTTCTTTTCTGA 57.455 33.333 0.00 0.00 0.00 3.27
708 1271 6.577103 AGGGCTTTTCTTTTTCTTTTCTGAG 58.423 36.000 0.00 0.00 0.00 3.35
736 1413 0.110486 TGGTGTCTGAAAAGGGGCTC 59.890 55.000 0.00 0.00 0.00 4.70
737 1414 0.955919 GGTGTCTGAAAAGGGGCTCG 60.956 60.000 0.00 0.00 0.00 5.03
738 1415 0.955919 GTGTCTGAAAAGGGGCTCGG 60.956 60.000 0.00 0.00 0.00 4.63
739 1416 1.377333 GTCTGAAAAGGGGCTCGGG 60.377 63.158 0.00 0.00 0.00 5.14
740 1417 2.751837 CTGAAAAGGGGCTCGGGC 60.752 66.667 0.00 0.00 37.82 6.13
780 1457 1.338020 CAAAGAAGAAAGGGCTTGCGT 59.662 47.619 0.00 0.00 0.00 5.24
818 1500 1.409427 CCTAATCTCGTGTGACCCTCC 59.591 57.143 0.00 0.00 0.00 4.30
850 1532 1.222115 GGCCGCCGATAGTTAAGCAG 61.222 60.000 0.00 0.00 0.00 4.24
895 1577 2.117206 GCACCCACCCAATCACCA 59.883 61.111 0.00 0.00 0.00 4.17
897 1579 1.971167 CACCCACCCAATCACCACG 60.971 63.158 0.00 0.00 0.00 4.94
912 1594 2.192861 CACGCCCACCACAACACAT 61.193 57.895 0.00 0.00 0.00 3.21
931 1617 2.304221 TCAGGGAGAGGAGAAACGAA 57.696 50.000 0.00 0.00 0.00 3.85
932 1618 2.171840 TCAGGGAGAGGAGAAACGAAG 58.828 52.381 0.00 0.00 0.00 3.79
933 1619 2.171840 CAGGGAGAGGAGAAACGAAGA 58.828 52.381 0.00 0.00 0.00 2.87
934 1620 2.563179 CAGGGAGAGGAGAAACGAAGAA 59.437 50.000 0.00 0.00 0.00 2.52
935 1621 3.006967 CAGGGAGAGGAGAAACGAAGAAA 59.993 47.826 0.00 0.00 0.00 2.52
936 1622 3.646637 AGGGAGAGGAGAAACGAAGAAAA 59.353 43.478 0.00 0.00 0.00 2.29
937 1623 4.102681 AGGGAGAGGAGAAACGAAGAAAAA 59.897 41.667 0.00 0.00 0.00 1.94
938 1624 4.452795 GGGAGAGGAGAAACGAAGAAAAAG 59.547 45.833 0.00 0.00 0.00 2.27
939 1625 4.452795 GGAGAGGAGAAACGAAGAAAAAGG 59.547 45.833 0.00 0.00 0.00 3.11
940 1626 5.291905 AGAGGAGAAACGAAGAAAAAGGA 57.708 39.130 0.00 0.00 0.00 3.36
941 1627 5.681639 AGAGGAGAAACGAAGAAAAAGGAA 58.318 37.500 0.00 0.00 0.00 3.36
942 1628 6.120220 AGAGGAGAAACGAAGAAAAAGGAAA 58.880 36.000 0.00 0.00 0.00 3.13
943 1629 6.602009 AGAGGAGAAACGAAGAAAAAGGAAAA 59.398 34.615 0.00 0.00 0.00 2.29
944 1630 6.561614 AGGAGAAACGAAGAAAAAGGAAAAC 58.438 36.000 0.00 0.00 0.00 2.43
945 1631 5.747197 GGAGAAACGAAGAAAAAGGAAAACC 59.253 40.000 0.00 0.00 0.00 3.27
946 1632 5.657474 AGAAACGAAGAAAAAGGAAAACCC 58.343 37.500 0.00 0.00 0.00 4.11
947 1633 3.703286 ACGAAGAAAAAGGAAAACCCG 57.297 42.857 0.00 0.00 40.87 5.28
948 1634 3.281158 ACGAAGAAAAAGGAAAACCCGA 58.719 40.909 0.00 0.00 40.87 5.14
949 1635 3.695556 ACGAAGAAAAAGGAAAACCCGAA 59.304 39.130 0.00 0.00 40.87 4.30
950 1636 4.201980 ACGAAGAAAAAGGAAAACCCGAAG 60.202 41.667 0.00 0.00 40.87 3.79
951 1637 3.728076 AGAAAAAGGAAAACCCGAAGC 57.272 42.857 0.00 0.00 40.87 3.86
1194 1880 0.115745 AGGAGAACCCTAACCCGTCA 59.884 55.000 0.00 0.00 45.48 4.35
1251 1937 1.324383 GATTCCTCTCCGACTCCTCC 58.676 60.000 0.00 0.00 0.00 4.30
1347 2033 0.812811 TCTACGACGATCCCACCTCG 60.813 60.000 0.00 0.00 41.77 4.63
1836 2522 1.139058 GTATCGTCTGAATGGCCACCT 59.861 52.381 8.16 0.00 0.00 4.00
1907 2593 5.448904 GCTTCTTTGATTGAGCCAGAAGATC 60.449 44.000 10.68 0.00 42.05 2.75
1915 2601 2.562738 TGAGCCAGAAGATCGAGTTTGA 59.437 45.455 0.00 0.00 0.00 2.69
1930 2616 5.869344 TCGAGTTTGAAGGTATGAACATCTG 59.131 40.000 0.00 0.00 0.00 2.90
1975 2664 4.756642 TGAATTGAACTGCTTAGTGGACTG 59.243 41.667 0.00 0.00 0.00 3.51
1982 2671 3.056250 ACTGCTTAGTGGACTGATCAGTG 60.056 47.826 32.50 16.76 42.66 3.66
2123 2812 5.991328 ACATTCATATGTAGCGGAACTTG 57.009 39.130 1.90 0.00 43.12 3.16
2149 2838 8.488668 GGGAGTTATTATACTTACTTTGGACCA 58.511 37.037 0.00 0.00 0.00 4.02
2150 2839 9.895138 GGAGTTATTATACTTACTTTGGACCAA 57.105 33.333 1.69 1.69 0.00 3.67
2161 2850 5.043737 ACTTTGGACCAACTTGTTAGCTA 57.956 39.130 6.36 0.00 0.00 3.32
2522 3212 9.817809 CTTCTTGTAGGCAAATATACTCTGTAA 57.182 33.333 0.00 0.00 33.73 2.41
2629 3319 4.280819 AGCAGCTGGCCTTTTATGAATTA 58.719 39.130 17.12 0.00 46.50 1.40
2679 3371 1.525619 GGTCTTTGTCAACGAGTTCGG 59.474 52.381 6.48 0.00 44.95 4.30
2681 3373 2.218075 GTCTTTGTCAACGAGTTCGGAC 59.782 50.000 6.48 5.41 44.95 4.79
2699 3391 4.758674 TCGGACTATATTTACCAGGACTCG 59.241 45.833 0.00 0.00 0.00 4.18
2700 3392 4.518211 CGGACTATATTTACCAGGACTCGT 59.482 45.833 0.00 0.00 0.00 4.18
2706 3398 8.098912 ACTATATTTACCAGGACTCGTTTTGTT 58.901 33.333 0.00 0.00 0.00 2.83
2788 3503 3.956233 ACTGCAAGCAATATATTGTGCG 58.044 40.909 24.60 21.74 45.62 5.34
2817 3532 7.172703 GGTCTATTGGTATTGGTTATACTGCAC 59.827 40.741 0.00 0.00 39.30 4.57
2833 3548 5.950758 ACTGCACAATTTCAAATACCGTA 57.049 34.783 0.00 0.00 0.00 4.02
2835 3550 6.146898 ACTGCACAATTTCAAATACCGTAAC 58.853 36.000 0.00 0.00 0.00 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 41 3.647649 CTGCGAGGGTCATGCGACA 62.648 63.158 0.00 0.00 44.54 4.35
55 58 2.832201 GGCGGCTACGTAGGACCT 60.832 66.667 23.47 0.00 43.45 3.85
94 97 1.792949 GTCGTGTCATCGCTTCAGTTT 59.207 47.619 0.00 0.00 0.00 2.66
101 104 2.261671 GGGTGTCGTGTCATCGCT 59.738 61.111 0.00 0.00 0.00 4.93
102 105 2.048597 TGGGTGTCGTGTCATCGC 60.049 61.111 0.00 0.00 0.00 4.58
103 106 1.736645 GGTGGGTGTCGTGTCATCG 60.737 63.158 0.00 0.00 0.00 3.84
105 108 2.144078 TGGGTGGGTGTCGTGTCAT 61.144 57.895 0.00 0.00 0.00 3.06
108 111 3.868985 GGTGGGTGGGTGTCGTGT 61.869 66.667 0.00 0.00 0.00 4.49
112 115 4.280019 GGGTGGTGGGTGGGTGTC 62.280 72.222 0.00 0.00 0.00 3.67
118 121 2.520741 GTTGTGGGGTGGTGGGTG 60.521 66.667 0.00 0.00 0.00 4.61
125 128 2.857483 TCTTGTATGTGTTGTGGGGTG 58.143 47.619 0.00 0.00 0.00 4.61
126 129 3.137544 TCTTCTTGTATGTGTTGTGGGGT 59.862 43.478 0.00 0.00 0.00 4.95
157 161 4.035208 TGCTTCGTGTTCTCCTTTTTCTTC 59.965 41.667 0.00 0.00 0.00 2.87
169 173 3.365969 CCCTTGGTTAATGCTTCGTGTTC 60.366 47.826 0.00 0.00 0.00 3.18
173 177 2.159382 CACCCTTGGTTAATGCTTCGT 58.841 47.619 0.00 0.00 31.02 3.85
175 179 3.860754 GCAACACCCTTGGTTAATGCTTC 60.861 47.826 7.19 0.00 34.89 3.86
184 188 1.412343 GTCAATTGCAACACCCTTGGT 59.588 47.619 0.00 0.00 35.62 3.67
185 189 1.411977 TGTCAATTGCAACACCCTTGG 59.588 47.619 0.00 0.00 0.00 3.61
187 191 2.964464 TCATGTCAATTGCAACACCCTT 59.036 40.909 0.00 0.00 0.00 3.95
189 193 2.927871 GCTCATGTCAATTGCAACACCC 60.928 50.000 0.00 0.00 0.00 4.61
226 230 4.488136 TTCCAGCATCCGCGCCAT 62.488 61.111 0.00 0.00 45.49 4.40
234 238 2.124151 ATGCCCGGTTCCAGCATC 60.124 61.111 9.07 0.00 43.58 3.91
238 242 2.511600 GTCGATGCCCGGTTCCAG 60.512 66.667 0.00 0.00 39.14 3.86
241 245 2.884207 GTCGTCGATGCCCGGTTC 60.884 66.667 0.00 0.00 39.14 3.62
246 250 3.554692 CAAGCGTCGTCGATGCCC 61.555 66.667 30.63 9.54 44.75 5.36
253 257 0.985549 CTGCTAGTTCAAGCGTCGTC 59.014 55.000 0.00 0.00 45.85 4.20
254 258 1.009389 GCTGCTAGTTCAAGCGTCGT 61.009 55.000 0.00 0.00 45.85 4.34
256 260 1.061711 CATGCTGCTAGTTCAAGCGTC 59.938 52.381 0.00 0.00 45.85 5.19
262 266 1.625315 ACTCCACATGCTGCTAGTTCA 59.375 47.619 0.00 0.00 0.00 3.18
278 282 1.084370 CGGTCTCCAATCGCAACTCC 61.084 60.000 0.00 0.00 0.00 3.85
315 319 1.667830 CAACACCGTCGGCATCACT 60.668 57.895 12.28 0.00 0.00 3.41
323 327 1.529438 AGCAATGTAACAACACCGTCG 59.471 47.619 0.00 0.00 0.00 5.12
326 330 2.289274 TCACAGCAATGTAACAACACCG 59.711 45.455 0.00 0.00 0.00 4.94
327 331 3.628017 GTCACAGCAATGTAACAACACC 58.372 45.455 0.00 0.00 0.00 4.16
354 358 0.826715 ATGAGCTACAGTCGCCATGT 59.173 50.000 0.00 0.00 34.62 3.21
397 401 1.208052 CCATGAAGTCGAGGTCACCAT 59.792 52.381 0.00 0.00 0.00 3.55
398 402 0.608130 CCATGAAGTCGAGGTCACCA 59.392 55.000 0.00 0.00 0.00 4.17
399 403 0.108138 CCCATGAAGTCGAGGTCACC 60.108 60.000 0.00 0.00 0.00 4.02
420 424 0.442699 GAAATTGTCGTCGGTGCTCC 59.557 55.000 0.00 0.00 0.00 4.70
426 430 1.133407 TGTCGTGAAATTGTCGTCGG 58.867 50.000 0.00 0.00 0.00 4.79
428 432 2.798283 TCCTTGTCGTGAAATTGTCGTC 59.202 45.455 0.00 0.00 0.00 4.20
434 438 1.156736 CCGCTCCTTGTCGTGAAATT 58.843 50.000 0.00 0.00 0.00 1.82
435 439 0.034896 ACCGCTCCTTGTCGTGAAAT 59.965 50.000 0.00 0.00 0.00 2.17
452 456 3.469863 TTCCTGTGTGGCCGTCACC 62.470 63.158 22.33 9.65 45.48 4.02
456 460 3.953775 CCCTTCCTGTGTGGCCGT 61.954 66.667 0.00 0.00 35.26 5.68
459 463 2.360475 GCTCCCTTCCTGTGTGGC 60.360 66.667 0.00 0.00 35.26 5.01
466 470 0.040499 ACTTCTCTCGCTCCCTTCCT 59.960 55.000 0.00 0.00 0.00 3.36
467 471 0.174617 CACTTCTCTCGCTCCCTTCC 59.825 60.000 0.00 0.00 0.00 3.46
476 480 1.540267 AGTCACCTCCACTTCTCTCG 58.460 55.000 0.00 0.00 0.00 4.04
517 521 3.134623 TCACCATCTACCATGCAAGTAGG 59.865 47.826 20.95 12.40 38.20 3.18
518 522 4.406648 TCACCATCTACCATGCAAGTAG 57.593 45.455 17.17 17.17 38.86 2.57
519 523 4.501400 CGATCACCATCTACCATGCAAGTA 60.501 45.833 0.00 0.00 0.00 2.24
540 544 6.016860 CCATCTAATTGGATTGATTGCTTCGA 60.017 38.462 0.83 0.00 39.25 3.71
588 592 2.351726 GCACGCAGATCCGTCTATTTTT 59.648 45.455 0.00 0.00 39.83 1.94
589 593 1.933853 GCACGCAGATCCGTCTATTTT 59.066 47.619 0.00 0.00 39.83 1.82
590 594 1.137086 AGCACGCAGATCCGTCTATTT 59.863 47.619 0.00 0.00 39.83 1.40
591 595 0.747255 AGCACGCAGATCCGTCTATT 59.253 50.000 0.00 0.00 39.83 1.73
592 596 0.747255 AAGCACGCAGATCCGTCTAT 59.253 50.000 0.00 0.00 39.83 1.98
593 597 0.179137 CAAGCACGCAGATCCGTCTA 60.179 55.000 0.00 0.00 39.83 2.59
594 598 1.446792 CAAGCACGCAGATCCGTCT 60.447 57.895 0.00 0.00 39.83 4.18
595 599 2.456119 CCAAGCACGCAGATCCGTC 61.456 63.158 0.00 0.00 39.83 4.79
596 600 2.244117 ATCCAAGCACGCAGATCCGT 62.244 55.000 0.00 0.00 43.11 4.69
597 601 1.493950 GATCCAAGCACGCAGATCCG 61.494 60.000 0.00 0.00 30.97 4.18
598 602 1.493950 CGATCCAAGCACGCAGATCC 61.494 60.000 9.66 0.00 33.13 3.36
599 603 0.807667 ACGATCCAAGCACGCAGATC 60.808 55.000 0.00 6.64 33.34 2.75
600 604 1.086067 CACGATCCAAGCACGCAGAT 61.086 55.000 0.00 0.00 0.00 2.90
601 605 1.737735 CACGATCCAAGCACGCAGA 60.738 57.895 0.00 0.00 0.00 4.26
602 606 2.780643 CACGATCCAAGCACGCAG 59.219 61.111 0.00 0.00 0.00 5.18
603 607 3.422303 GCACGATCCAAGCACGCA 61.422 61.111 0.00 0.00 0.00 5.24
604 608 4.166011 GGCACGATCCAAGCACGC 62.166 66.667 0.00 0.00 0.00 5.34
605 609 2.741985 TGGCACGATCCAAGCACG 60.742 61.111 0.00 0.00 32.18 5.34
606 610 0.391130 TAGTGGCACGATCCAAGCAC 60.391 55.000 12.71 0.00 37.96 4.40
607 611 0.108186 CTAGTGGCACGATCCAAGCA 60.108 55.000 12.71 0.00 37.96 3.91
608 612 1.432270 GCTAGTGGCACGATCCAAGC 61.432 60.000 12.71 11.37 41.35 4.01
609 613 2.682893 GCTAGTGGCACGATCCAAG 58.317 57.895 12.71 5.52 41.35 3.61
610 614 4.932789 GCTAGTGGCACGATCCAA 57.067 55.556 12.71 0.00 41.35 3.53
634 638 1.228063 ATCTCATGCATGGACCGGC 60.228 57.895 25.97 1.14 0.00 6.13
638 642 1.506493 GACCGATCTCATGCATGGAC 58.494 55.000 25.97 13.44 0.00 4.02
663 667 5.273944 CCTAAAAAGGTCAATAATCTGCGC 58.726 41.667 0.00 0.00 0.00 6.09
676 680 7.195374 AGAAAAAGAAAAGCCCTAAAAAGGT 57.805 32.000 0.00 0.00 0.00 3.50
678 682 9.988350 GAAAAGAAAAAGAAAAGCCCTAAAAAG 57.012 29.630 0.00 0.00 0.00 2.27
706 1269 8.624776 CCCTTTTCAGACACCATATTATTTCTC 58.375 37.037 0.00 0.00 0.00 2.87
707 1270 7.561356 CCCCTTTTCAGACACCATATTATTTCT 59.439 37.037 0.00 0.00 0.00 2.52
708 1271 7.684428 GCCCCTTTTCAGACACCATATTATTTC 60.684 40.741 0.00 0.00 0.00 2.17
725 1402 2.035783 AAGCCCGAGCCCCTTTTC 59.964 61.111 0.00 0.00 41.25 2.29
748 1425 2.985896 TCTTCTTTGATAACTGCCCCG 58.014 47.619 0.00 0.00 0.00 5.73
850 1532 1.658114 GGCTCGGTTGTTTTGGGAC 59.342 57.895 0.00 0.00 0.00 4.46
895 1577 1.896660 GATGTGTTGTGGTGGGCGT 60.897 57.895 0.00 0.00 0.00 5.68
897 1579 1.526575 CCTGATGTGTTGTGGTGGGC 61.527 60.000 0.00 0.00 0.00 5.36
912 1594 2.171840 CTTCGTTTCTCCTCTCCCTGA 58.828 52.381 0.00 0.00 0.00 3.86
931 1617 2.034179 CGCTTCGGGTTTTCCTTTTTCT 59.966 45.455 0.00 0.00 40.46 2.52
932 1618 2.033675 TCGCTTCGGGTTTTCCTTTTTC 59.966 45.455 0.00 0.00 40.46 2.29
933 1619 2.025898 TCGCTTCGGGTTTTCCTTTTT 58.974 42.857 0.00 0.00 40.46 1.94
934 1620 1.335810 GTCGCTTCGGGTTTTCCTTTT 59.664 47.619 0.00 0.00 40.46 2.27
935 1621 0.949397 GTCGCTTCGGGTTTTCCTTT 59.051 50.000 0.00 0.00 40.46 3.11
936 1622 1.226030 CGTCGCTTCGGGTTTTCCTT 61.226 55.000 0.00 0.00 40.46 3.36
937 1623 1.666872 CGTCGCTTCGGGTTTTCCT 60.667 57.895 0.00 0.00 40.46 3.36
938 1624 1.665599 TCGTCGCTTCGGGTTTTCC 60.666 57.895 0.00 0.00 39.75 3.13
939 1625 1.490258 GTCGTCGCTTCGGGTTTTC 59.510 57.895 0.00 0.00 0.00 2.29
940 1626 1.957695 GGTCGTCGCTTCGGGTTTT 60.958 57.895 0.00 0.00 0.00 2.43
941 1627 2.356673 GGTCGTCGCTTCGGGTTT 60.357 61.111 0.00 0.00 0.00 3.27
942 1628 4.712425 CGGTCGTCGCTTCGGGTT 62.712 66.667 0.00 0.00 0.00 4.11
1194 1880 2.606826 GGTGGAGGGGACGAGGTT 60.607 66.667 0.00 0.00 0.00 3.50
1227 1913 1.757340 GTCGGAGAGGAATCCCGGT 60.757 63.158 0.00 0.00 43.16 5.28
1251 1937 3.471244 GATGTCGTCGGGCTCCTCG 62.471 68.421 0.00 0.00 0.00 4.63
1305 1991 3.744719 CGAACGAGGCGGGTGAGA 61.745 66.667 0.00 0.00 0.00 3.27
1447 2133 4.778415 CACCTCGACCGTCGGCAG 62.778 72.222 20.35 11.32 40.88 4.85
1836 2522 1.699054 CGGCATCAGATTCTGGGGGA 61.699 60.000 13.59 0.00 31.51 4.81
1907 2593 5.869344 TCAGATGTTCATACCTTCAAACTCG 59.131 40.000 0.00 0.00 0.00 4.18
1915 2601 7.124901 ACACTAGTCATCAGATGTTCATACCTT 59.875 37.037 10.34 0.00 0.00 3.50
1930 2616 2.432146 TGCTCCATGGACACTAGTCATC 59.568 50.000 11.44 0.00 46.80 2.92
2123 2812 8.488668 TGGTCCAAAGTAAGTATAATAACTCCC 58.511 37.037 0.00 0.00 0.00 4.30
2149 2838 8.630054 TCACCAAACATATTAGCTAACAAGTT 57.370 30.769 8.70 3.70 0.00 2.66
2150 2839 8.807948 ATCACCAAACATATTAGCTAACAAGT 57.192 30.769 8.70 0.00 0.00 3.16
2277 2966 9.335891 CTGTTCATCACGTTCAGATATATAGAC 57.664 37.037 0.00 0.00 0.00 2.59
2539 3229 7.870445 ACGGTGTTCAAAATTTTGCAGTATAAT 59.130 29.630 23.36 5.35 38.05 1.28
2629 3319 7.636150 AATCTAAGTGATAATTGCTGCAAGT 57.364 32.000 20.72 20.16 34.45 3.16
2679 3371 7.763071 ACAAAACGAGTCCTGGTAAATATAGTC 59.237 37.037 0.00 0.00 0.00 2.59
2681 3373 8.488651 AACAAAACGAGTCCTGGTAAATATAG 57.511 34.615 0.00 0.00 0.00 1.31
2788 3503 3.965470 AACCAATACCAATAGACCCCC 57.035 47.619 0.00 0.00 0.00 5.40
2842 3557 9.775854 ACATGAATCACATTTTATTTCAAACCA 57.224 25.926 0.00 0.00 37.07 3.67
2863 3578 2.632377 GCCAGCAGCTAGTTAACATGA 58.368 47.619 8.61 0.00 38.99 3.07


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

AutoCloner maintained by Alex Coulton.