Multiple sequence alignment - TraesCS5B01G287200

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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 TraesCS5B01G287200 chr5B 100.000 3082 0 0 1 3082 473449828 473446747 0.000000e+00 5692
1 TraesCS5B01G287200 chr5B 85.869 2123 167 58 113 2186 473469049 473467011 0.000000e+00 2135
2 TraesCS5B01G287200 chr5B 83.577 1571 126 56 735 2219 473292441 473290917 0.000000e+00 1351
3 TraesCS5B01G287200 chr5B 84.585 772 90 19 2270 3018 473467002 473466237 0.000000e+00 739
4 TraesCS5B01G287200 chr5B 82.043 646 75 26 991 1618 473626067 473625445 2.120000e-141 512
5 TraesCS5B01G287200 chr5B 96.471 85 2 1 1 85 473469127 473469044 4.140000e-29 139
6 TraesCS5B01G287200 chr5A 84.252 1505 120 44 782 2219 495340326 495338872 0.000000e+00 1358
7 TraesCS5B01G287200 chr5A 88.128 1095 82 15 1139 2201 495359616 495358538 0.000000e+00 1258
8 TraesCS5B01G287200 chr5A 86.097 1007 61 33 114 1082 495360578 495359613 0.000000e+00 1011
9 TraesCS5B01G287200 chr5A 82.395 835 93 19 2263 3078 495357201 495356402 0.000000e+00 678
10 TraesCS5B01G287200 chr5A 89.524 315 22 7 204 509 495399913 495399601 3.730000e-104 388
11 TraesCS5B01G287200 chr5D 86.166 1265 103 33 990 2219 393570154 393568927 0.000000e+00 1301
12 TraesCS5B01G287200 chr5D 88.015 1093 82 21 1139 2202 393608604 393607532 0.000000e+00 1247
13 TraesCS5B01G287200 chr5D 86.687 969 59 37 141 1082 393609526 393608601 0.000000e+00 1011
14 TraesCS5B01G287200 chr5D 83.755 831 100 15 2269 3078 393600756 393599940 0.000000e+00 754
15 TraesCS5B01G287200 chr5D 84.783 644 65 15 1175 1814 393712193 393711579 1.570000e-172 616
16 TraesCS5B01G287200 chr5D 90.354 311 25 2 204 509 393636740 393636430 1.330000e-108 403
17 TraesCS5B01G287200 chr5D 77.435 616 119 17 2476 3082 37637607 37637003 1.760000e-92 350
18 TraesCS5B01G287200 chr1A 79.537 562 100 9 2527 3082 255870885 255870333 1.340000e-103 387
19 TraesCS5B01G287200 chr1A 77.994 618 111 20 2473 3082 490508161 490507561 6.280000e-97 364
20 TraesCS5B01G287200 chr1A 79.744 469 81 12 2622 3082 580565117 580565579 8.240000e-86 327
21 TraesCS5B01G287200 chr1D 77.868 619 115 18 2472 3082 6172974 6173578 6.280000e-97 364
22 TraesCS5B01G287200 chr1B 81.149 435 73 7 2651 3082 289301512 289301084 1.060000e-89 340
23 TraesCS5B01G287200 chr7D 76.006 621 131 17 2472 3082 241893698 241893086 3.860000e-79 305


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 TraesCS5B01G287200 chr5B 473446747 473449828 3081 True 5692.000000 5692 100.000 1 3082 1 chr5B.!!$R2 3081
1 TraesCS5B01G287200 chr5B 473290917 473292441 1524 True 1351.000000 1351 83.577 735 2219 1 chr5B.!!$R1 1484
2 TraesCS5B01G287200 chr5B 473466237 473469127 2890 True 1004.333333 2135 88.975 1 3018 3 chr5B.!!$R4 3017
3 TraesCS5B01G287200 chr5B 473625445 473626067 622 True 512.000000 512 82.043 991 1618 1 chr5B.!!$R3 627
4 TraesCS5B01G287200 chr5A 495338872 495340326 1454 True 1358.000000 1358 84.252 782 2219 1 chr5A.!!$R1 1437
5 TraesCS5B01G287200 chr5A 495356402 495360578 4176 True 982.333333 1258 85.540 114 3078 3 chr5A.!!$R3 2964
6 TraesCS5B01G287200 chr5D 393568927 393570154 1227 True 1301.000000 1301 86.166 990 2219 1 chr5D.!!$R2 1229
7 TraesCS5B01G287200 chr5D 393607532 393609526 1994 True 1129.000000 1247 87.351 141 2202 2 chr5D.!!$R6 2061
8 TraesCS5B01G287200 chr5D 393599940 393600756 816 True 754.000000 754 83.755 2269 3078 1 chr5D.!!$R3 809
9 TraesCS5B01G287200 chr5D 393711579 393712193 614 True 616.000000 616 84.783 1175 1814 1 chr5D.!!$R5 639
10 TraesCS5B01G287200 chr5D 37637003 37637607 604 True 350.000000 350 77.435 2476 3082 1 chr5D.!!$R1 606
11 TraesCS5B01G287200 chr1A 255870333 255870885 552 True 387.000000 387 79.537 2527 3082 1 chr1A.!!$R1 555
12 TraesCS5B01G287200 chr1A 490507561 490508161 600 True 364.000000 364 77.994 2473 3082 1 chr1A.!!$R2 609
13 TraesCS5B01G287200 chr1D 6172974 6173578 604 False 364.000000 364 77.868 2472 3082 1 chr1D.!!$F1 610
14 TraesCS5B01G287200 chr7D 241893086 241893698 612 True 305.000000 305 76.006 2472 3082 1 chr7D.!!$R1 610

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
630 643 0.249405 TTTTTGCTTCTGCTTGGCCG 60.249 50.0 0.0 0.0 40.48 6.13 F
1209 1346 0.249911 ACGTTCTCCTTGCTCGCTTT 60.250 50.0 0.0 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1688 1855 0.035152 TTAGGACTAGGCGTCACCGA 60.035 55.0 0.00 0.0 46.52 4.69 R
2390 3898 0.685097 AGCCTACAAGTTTGCGGAGA 59.315 50.0 5.32 0.0 0.00 3.71 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
31 32 6.959639 TGAGACCAAAGCAAACTAAATTCT 57.040 33.333 0.00 0.00 0.00 2.40
33 34 7.871853 TGAGACCAAAGCAAACTAAATTCTAC 58.128 34.615 0.00 0.00 0.00 2.59
40 41 9.173939 CAAAGCAAACTAAATTCTACTGAACAG 57.826 33.333 0.00 0.00 34.71 3.16
130 131 9.471702 AAACATTAATCACTGAGAGATCCAAAT 57.528 29.630 0.00 0.00 0.00 2.32
139 140 7.391554 TCACTGAGAGATCCAAATTAACAAAGG 59.608 37.037 0.00 0.00 0.00 3.11
183 184 1.446272 GAGCAGGCACGAGGTACAC 60.446 63.158 0.00 0.00 0.00 2.90
237 238 2.232452 AGGAGAACAAGACGACCATCAG 59.768 50.000 0.00 0.00 0.00 2.90
506 507 4.838152 TCCTGCTTGATCGCCGCC 62.838 66.667 0.00 0.00 0.00 6.13
611 624 1.550327 TTGCGTGAGAGAGATCTGGT 58.450 50.000 0.00 0.00 0.00 4.00
630 643 0.249405 TTTTTGCTTCTGCTTGGCCG 60.249 50.000 0.00 0.00 40.48 6.13
644 657 4.049640 GCCGCCGCCATTTGTTGA 62.050 61.111 0.00 0.00 0.00 3.18
745 770 3.644399 GAGGACCGACCGGCTTCAC 62.644 68.421 8.55 0.00 44.74 3.18
749 774 2.432628 CCGACCGGCTTCACAGTC 60.433 66.667 0.00 0.00 0.00 3.51
754 783 2.049156 CGGCTTCACAGTCGCAGA 60.049 61.111 0.00 0.00 42.26 4.26
755 784 1.446792 CGGCTTCACAGTCGCAGAT 60.447 57.895 0.00 0.00 42.26 2.90
759 791 1.354040 CTTCACAGTCGCAGATGGTC 58.646 55.000 0.00 0.00 40.67 4.02
761 793 1.807165 CACAGTCGCAGATGGTCGG 60.807 63.158 0.00 0.00 40.67 4.79
765 797 3.822192 TCGCAGATGGTCGGTCGG 61.822 66.667 0.00 0.00 0.00 4.79
789 829 1.613437 AGTCGGGCTTGGTTTCATTTG 59.387 47.619 0.00 0.00 0.00 2.32
962 1058 3.254411 GGCTACCTAGGGATTGTACGTAC 59.746 52.174 18.90 18.90 0.00 3.67
981 1077 2.109739 GCTCTCGAGAGGACGCTCA 61.110 63.158 36.65 4.58 42.29 4.26
985 1081 1.711060 CTCGAGAGGACGCTCACTCC 61.711 65.000 6.58 0.00 34.56 3.85
986 1082 2.795297 GAGAGGACGCTCACTCCG 59.205 66.667 0.00 0.00 35.01 4.63
1097 1206 1.004320 TGCACCGCGAGTACCAAAT 60.004 52.632 8.23 0.00 0.00 2.32
1209 1346 0.249911 ACGTTCTCCTTGCTCGCTTT 60.250 50.000 0.00 0.00 0.00 3.51
1210 1347 0.440371 CGTTCTCCTTGCTCGCTTTC 59.560 55.000 0.00 0.00 0.00 2.62
1211 1348 0.440371 GTTCTCCTTGCTCGCTTTCG 59.560 55.000 0.00 0.00 0.00 3.46
1212 1349 1.291877 TTCTCCTTGCTCGCTTTCGC 61.292 55.000 0.00 0.00 35.26 4.70
1214 1351 1.294659 CTCCTTGCTCGCTTTCGCTT 61.295 55.000 0.00 0.00 35.26 4.68
1240 1383 5.175856 GCTCATGTACATGTATCCGTCTTTC 59.824 44.000 30.03 7.71 39.72 2.62
1263 1406 4.529897 TCGAGTCCACTAACCTATTGCTA 58.470 43.478 0.00 0.00 0.00 3.49
1292 1441 3.912496 TGGTGATGTCTGGATCGATTT 57.088 42.857 0.00 0.00 0.00 2.17
1331 1480 1.267574 ATCATCTGCCACGTCCACCT 61.268 55.000 0.00 0.00 0.00 4.00
1341 1490 3.063084 GTCCACCTCGCTCTCCGT 61.063 66.667 0.00 0.00 38.35 4.69
1437 1586 1.375908 CCACATCTGGGTCCACGTG 60.376 63.158 9.08 9.08 33.23 4.49
1451 1600 4.680237 CGTGGGCTTCGTGGCTCA 62.680 66.667 1.24 1.24 40.76 4.26
1621 1785 1.419922 CGCCACGAGAAAACATCCG 59.580 57.895 0.00 0.00 0.00 4.18
1624 1788 0.713883 CCACGAGAAAACATCCGTCG 59.286 55.000 0.00 0.00 34.23 5.12
1630 1794 2.927477 GAGAAAACATCCGTCGTATGCA 59.073 45.455 0.00 0.00 0.00 3.96
1631 1795 3.331150 AGAAAACATCCGTCGTATGCAA 58.669 40.909 0.00 0.00 0.00 4.08
1632 1796 3.938963 AGAAAACATCCGTCGTATGCAAT 59.061 39.130 0.00 0.00 0.00 3.56
1633 1797 5.113383 AGAAAACATCCGTCGTATGCAATA 58.887 37.500 0.00 0.00 0.00 1.90
1634 1798 5.758296 AGAAAACATCCGTCGTATGCAATAT 59.242 36.000 0.00 0.00 0.00 1.28
1635 1799 6.926826 AGAAAACATCCGTCGTATGCAATATA 59.073 34.615 0.00 0.00 0.00 0.86
1636 1800 7.602644 AGAAAACATCCGTCGTATGCAATATAT 59.397 33.333 0.00 0.00 0.00 0.86
1637 1801 8.766000 AAAACATCCGTCGTATGCAATATATA 57.234 30.769 0.00 0.00 0.00 0.86
1638 1802 8.942338 AAACATCCGTCGTATGCAATATATAT 57.058 30.769 0.00 0.00 0.00 0.86
1639 1803 7.930513 ACATCCGTCGTATGCAATATATATG 57.069 36.000 0.00 0.00 0.00 1.78
1640 1804 6.420903 ACATCCGTCGTATGCAATATATATGC 59.579 38.462 0.00 10.94 44.08 3.14
1658 1825 3.214697 TGCATAACATTTTCTGGCACG 57.785 42.857 0.00 0.00 0.00 5.34
1659 1826 2.556189 TGCATAACATTTTCTGGCACGT 59.444 40.909 0.00 0.00 0.00 4.49
1662 1829 5.157781 GCATAACATTTTCTGGCACGTTTA 58.842 37.500 0.00 0.00 0.00 2.01
1664 1831 3.262135 ACATTTTCTGGCACGTTTACG 57.738 42.857 0.00 0.00 46.33 3.18
1679 1846 4.631036 CGTTTACGTATGGTTTCCTTTCG 58.369 43.478 0.00 0.00 34.11 3.46
1680 1847 4.150451 CGTTTACGTATGGTTTCCTTTCGT 59.850 41.667 0.00 10.02 38.03 3.85
1688 1855 6.536224 CGTATGGTTTCCTTTCGTATTTACCT 59.464 38.462 0.00 0.00 0.00 3.08
1713 1880 3.589495 GACGCCTAGTCCTAACTTGTT 57.411 47.619 0.00 0.00 43.95 2.83
1716 1887 4.313282 ACGCCTAGTCCTAACTTGTTTTC 58.687 43.478 0.00 0.00 36.92 2.29
1740 1911 9.730420 TTCTTTCTTTCTTTTGTTCTTTATCCG 57.270 29.630 0.00 0.00 0.00 4.18
1769 1940 1.572447 GTCGCGCAAAAGCCACTTA 59.428 52.632 8.75 0.00 0.00 2.24
1796 1967 1.365633 GTGTGCATTTTGCCCCGAA 59.634 52.632 0.00 0.00 44.23 4.30
1826 1997 0.394488 TTTTGCACCCACTTGACGGA 60.394 50.000 0.00 0.00 0.00 4.69
1918 2089 0.329931 TTACCGTTCACATGCCCCAT 59.670 50.000 0.00 0.00 0.00 4.00
1985 2180 2.552591 GGAGGAGCATAGTAGCGTCCTA 60.553 54.545 0.00 0.00 40.12 2.94
2016 2214 0.984995 CCTCCCCTTTCTTCTCGGTT 59.015 55.000 0.00 0.00 0.00 4.44
2028 2239 0.899720 TCTCGGTTATCTTTGCCGGT 59.100 50.000 1.90 0.00 44.97 5.28
2124 2340 3.567164 CCCAATGAAGAGTGATGTATGGC 59.433 47.826 0.00 0.00 0.00 4.40
2151 2369 3.683847 GCAAGGCCATGTATCAGACTCTT 60.684 47.826 10.15 0.00 0.00 2.85
2152 2370 4.521146 CAAGGCCATGTATCAGACTCTTT 58.479 43.478 5.01 0.00 0.00 2.52
2153 2371 5.674525 CAAGGCCATGTATCAGACTCTTTA 58.325 41.667 5.01 0.00 0.00 1.85
2183 2403 8.675705 TTTGAAGTTGATGTATGAGACTGAAA 57.324 30.769 0.00 0.00 0.00 2.69
2206 3682 9.769093 GAAATTGCGACAACTTTGTATACTAAT 57.231 29.630 4.17 0.00 42.43 1.73
2220 3696 9.976255 TTTGTATACTAATCGTGCAATTTACAC 57.024 29.630 4.17 0.00 34.62 2.90
2221 3697 8.705048 TGTATACTAATCGTGCAATTTACACA 57.295 30.769 4.17 0.00 37.93 3.72
2222 3698 8.597227 TGTATACTAATCGTGCAATTTACACAC 58.403 33.333 4.17 0.00 37.93 3.82
2223 3699 5.933187 ACTAATCGTGCAATTTACACACA 57.067 34.783 8.64 0.00 37.93 3.72
2224 3700 5.685841 ACTAATCGTGCAATTTACACACAC 58.314 37.500 8.64 0.00 37.93 3.82
2225 3701 4.560136 AATCGTGCAATTTACACACACA 57.440 36.364 8.64 0.00 37.93 3.72
2226 3702 3.326733 TCGTGCAATTTACACACACAC 57.673 42.857 8.64 0.00 37.93 3.82
2227 3703 2.678336 TCGTGCAATTTACACACACACA 59.322 40.909 8.64 0.00 37.93 3.72
2228 3704 2.781101 CGTGCAATTTACACACACACAC 59.219 45.455 8.64 0.00 37.93 3.82
2229 3705 3.729163 CGTGCAATTTACACACACACACA 60.729 43.478 8.64 0.00 37.93 3.72
2230 3706 3.545873 GTGCAATTTACACACACACACAC 59.454 43.478 0.00 0.00 37.96 3.82
2231 3707 3.191371 TGCAATTTACACACACACACACA 59.809 39.130 0.00 0.00 0.00 3.72
2232 3708 3.545873 GCAATTTACACACACACACACAC 59.454 43.478 0.00 0.00 0.00 3.82
2233 3709 4.727475 CAATTTACACACACACACACACA 58.273 39.130 0.00 0.00 0.00 3.72
2234 3710 3.815337 TTTACACACACACACACACAC 57.185 42.857 0.00 0.00 0.00 3.82
2235 3711 2.457366 TACACACACACACACACACA 57.543 45.000 0.00 0.00 0.00 3.72
2249 3725 3.145286 CACACACACTCTCTCTCTCTCA 58.855 50.000 0.00 0.00 0.00 3.27
2253 3729 3.072330 ACACACTCTCTCTCTCTCACTCA 59.928 47.826 0.00 0.00 0.00 3.41
2254 3730 3.436704 CACACTCTCTCTCTCTCACTCAC 59.563 52.174 0.00 0.00 0.00 3.51
2256 3732 4.202461 ACACTCTCTCTCTCTCACTCACTT 60.202 45.833 0.00 0.00 0.00 3.16
2260 3736 5.630121 TCTCTCTCTCTCACTCACTTCTTT 58.370 41.667 0.00 0.00 0.00 2.52
2262 3738 6.016360 TCTCTCTCTCTCACTCACTTCTTTTG 60.016 42.308 0.00 0.00 0.00 2.44
2265 3741 7.285629 TCTCTCTCTCACTCACTTCTTTTGTAA 59.714 37.037 0.00 0.00 0.00 2.41
2267 3743 8.085296 TCTCTCTCACTCACTTCTTTTGTAATC 58.915 37.037 0.00 0.00 0.00 1.75
2268 3744 7.957002 TCTCTCACTCACTTCTTTTGTAATCT 58.043 34.615 0.00 0.00 0.00 2.40
2275 3751 9.384764 ACTCACTTCTTTTGTAATCTATAAGCC 57.615 33.333 0.00 0.00 0.00 4.35
2350 3858 5.317808 TCCCAAAATCACAGAACGGAAATA 58.682 37.500 0.00 0.00 0.00 1.40
2361 3869 0.323087 ACGGAAATAGGGGCACAACC 60.323 55.000 0.00 0.00 37.93 3.77
2379 3887 1.575922 CGTGAACATGGCCACAGTG 59.424 57.895 8.16 5.14 33.13 3.66
2389 3897 3.749981 CCACAGTGGCTTGGTCAC 58.250 61.111 6.67 0.00 38.58 3.67
2395 3918 1.374758 GTGGCTTGGTCACTCTCCG 60.375 63.158 0.00 0.00 35.05 4.63
2401 3924 0.468226 TTGGTCACTCTCCGCAAACT 59.532 50.000 0.00 0.00 0.00 2.66
2402 3925 0.468226 TGGTCACTCTCCGCAAACTT 59.532 50.000 0.00 0.00 0.00 2.66
2436 3959 5.126061 GGCATGAACCATGAATCTACAAGTT 59.874 40.000 10.77 0.00 43.81 2.66
2441 3964 6.998074 TGAACCATGAATCTACAAGTTCAACT 59.002 34.615 0.00 0.00 40.55 3.16
2552 4081 1.271325 TGAGCAAGATTCGGCCTTTGA 60.271 47.619 0.00 0.00 0.00 2.69
2593 4122 6.534793 ACAGCCAACAAAAACAAGTTTGATAG 59.465 34.615 4.76 0.00 40.29 2.08
2626 4157 5.789643 ATAAACGAAATGGCATATTGGCT 57.210 34.783 0.00 0.00 44.10 4.75
2627 4158 3.441496 AACGAAATGGCATATTGGCTG 57.559 42.857 0.00 0.00 44.10 4.85
2663 4194 4.199310 TGAGACCAAAACTATGCCTATGC 58.801 43.478 0.00 0.00 38.26 3.14
2802 4340 2.076100 CGTGCAACATAGACCACATGT 58.924 47.619 0.00 0.00 38.25 3.21
2812 4350 1.143684 AGACCACATGTGAAGCCAGTT 59.856 47.619 27.46 3.99 0.00 3.16
2818 4356 2.037251 ACATGTGAAGCCAGTTCGTACT 59.963 45.455 0.00 0.00 38.09 2.73
2839 4380 4.953579 ACTACAGAAAAACCTGCAAAGGAA 59.046 37.500 0.00 0.00 37.68 3.36
2860 4402 5.693104 GGAAAAGGGGTTTTACGATTGAAAC 59.307 40.000 0.00 0.00 35.54 2.78
2911 4454 4.401022 CATAATAAGGCAGATGCTCCCAA 58.599 43.478 4.59 0.00 41.70 4.12
2920 4463 5.072741 GGCAGATGCTCCCAATCTTATTAA 58.927 41.667 4.59 0.00 41.70 1.40
2921 4464 5.713861 GGCAGATGCTCCCAATCTTATTAAT 59.286 40.000 4.59 0.00 41.70 1.40
2982 4525 9.319143 GACCATATATATTAGCAACACTCATCC 57.681 37.037 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 9.981114 CAGTGATTAATGTTTTAACCTCCTTTT 57.019 29.630 0.00 0.00 30.33 2.27
93 94 9.362151 TCAGTGATTAATGTTTTAACCTCCTTT 57.638 29.630 0.00 0.00 30.33 3.11
94 95 8.934023 TCAGTGATTAATGTTTTAACCTCCTT 57.066 30.769 0.00 0.00 30.33 3.36
95 96 8.383175 TCTCAGTGATTAATGTTTTAACCTCCT 58.617 33.333 0.00 0.00 30.33 3.69
96 97 8.561738 TCTCAGTGATTAATGTTTTAACCTCC 57.438 34.615 0.00 0.00 30.33 4.30
97 98 9.436957 TCTCTCAGTGATTAATGTTTTAACCTC 57.563 33.333 0.00 0.00 30.33 3.85
98 99 9.965902 ATCTCTCAGTGATTAATGTTTTAACCT 57.034 29.630 0.00 0.00 30.33 3.50
101 102 9.958180 TGGATCTCTCAGTGATTAATGTTTTAA 57.042 29.630 0.00 0.00 0.00 1.52
102 103 9.958180 TTGGATCTCTCAGTGATTAATGTTTTA 57.042 29.630 0.00 0.00 0.00 1.52
103 104 8.868522 TTGGATCTCTCAGTGATTAATGTTTT 57.131 30.769 0.00 0.00 0.00 2.43
104 105 8.868522 TTTGGATCTCTCAGTGATTAATGTTT 57.131 30.769 0.00 0.00 0.00 2.83
105 106 9.471702 AATTTGGATCTCTCAGTGATTAATGTT 57.528 29.630 0.00 0.00 0.00 2.71
109 110 9.958180 TGTTAATTTGGATCTCTCAGTGATTAA 57.042 29.630 0.00 0.00 0.00 1.40
110 111 9.958180 TTGTTAATTTGGATCTCTCAGTGATTA 57.042 29.630 0.00 0.00 0.00 1.75
111 112 8.868522 TTGTTAATTTGGATCTCTCAGTGATT 57.131 30.769 0.00 0.00 0.00 2.57
112 113 8.868522 TTTGTTAATTTGGATCTCTCAGTGAT 57.131 30.769 0.00 0.00 0.00 3.06
130 131 6.096695 GCTTGTGTGTTTCTTCCTTTGTTAA 58.903 36.000 0.00 0.00 0.00 2.01
139 140 3.149436 TGCTTGCTTGTGTGTTTCTTC 57.851 42.857 0.00 0.00 0.00 2.87
185 186 1.302907 AGCCCACCTGAATCCTGATT 58.697 50.000 0.00 0.00 0.00 2.57
188 189 1.821136 GAAAAGCCCACCTGAATCCTG 59.179 52.381 0.00 0.00 0.00 3.86
190 191 2.222227 AGAAAAGCCCACCTGAATCC 57.778 50.000 0.00 0.00 0.00 3.01
191 192 2.893489 ACAAGAAAAGCCCACCTGAATC 59.107 45.455 0.00 0.00 0.00 2.52
192 193 2.962859 ACAAGAAAAGCCCACCTGAAT 58.037 42.857 0.00 0.00 0.00 2.57
193 194 2.452600 ACAAGAAAAGCCCACCTGAA 57.547 45.000 0.00 0.00 0.00 3.02
227 228 2.298446 CTCCTATGATGCTGATGGTCGT 59.702 50.000 0.00 0.00 0.00 4.34
237 238 4.624882 CGATTACTTGCTCTCCTATGATGC 59.375 45.833 0.00 0.00 0.00 3.91
611 624 0.249405 CGGCCAAGCAGAAGCAAAAA 60.249 50.000 2.24 0.00 45.49 1.94
630 643 0.243365 TCACATCAACAAATGGCGGC 59.757 50.000 0.00 0.00 0.00 6.53
632 645 2.918600 CACATCACATCAACAAATGGCG 59.081 45.455 0.00 0.00 0.00 5.69
634 647 5.956642 TCATCACATCACATCAACAAATGG 58.043 37.500 0.00 0.00 0.00 3.16
636 649 6.349860 CCACTCATCACATCACATCAACAAAT 60.350 38.462 0.00 0.00 0.00 2.32
637 650 5.048573 CCACTCATCACATCACATCAACAAA 60.049 40.000 0.00 0.00 0.00 2.83
638 651 4.456566 CCACTCATCACATCACATCAACAA 59.543 41.667 0.00 0.00 0.00 2.83
639 652 4.004982 CCACTCATCACATCACATCAACA 58.995 43.478 0.00 0.00 0.00 3.33
641 654 3.011818 GCCACTCATCACATCACATCAA 58.988 45.455 0.00 0.00 0.00 2.57
642 655 2.635714 GCCACTCATCACATCACATCA 58.364 47.619 0.00 0.00 0.00 3.07
643 656 1.596260 CGCCACTCATCACATCACATC 59.404 52.381 0.00 0.00 0.00 3.06
644 657 1.065926 ACGCCACTCATCACATCACAT 60.066 47.619 0.00 0.00 0.00 3.21
674 692 2.712466 CGTCTATATACACACACGCACG 59.288 50.000 0.00 0.00 0.00 5.34
678 696 1.707117 GCGCGTCTATATACACACACG 59.293 52.381 8.43 0.00 0.00 4.49
726 751 4.493747 GAAGCCGGTCGGTCCTCG 62.494 72.222 11.25 0.00 40.90 4.63
745 770 1.517257 GACCGACCATCTGCGACTG 60.517 63.158 0.00 0.00 0.00 3.51
819 859 2.284263 TTCTGACATGTAGCGCTCAG 57.716 50.000 16.34 14.91 32.86 3.35
904 971 1.136308 CGCTATCGATCGTCTACGCTT 60.136 52.381 15.94 0.00 37.27 4.68
926 997 2.351244 TAGCCCGTGCCTCTCTGTG 61.351 63.158 0.00 0.00 38.69 3.66
938 1012 1.617357 GTACAATCCCTAGGTAGCCCG 59.383 57.143 8.29 0.00 35.12 6.13
962 1058 3.163110 GAGCGTCCTCTCGAGAGCG 62.163 68.421 32.79 29.95 40.75 5.03
981 1077 2.481969 CATTGGTGATGATCGACGGAGT 60.482 50.000 0.00 0.00 40.70 3.85
985 1081 1.202521 TCCCATTGGTGATGATCGACG 60.203 52.381 1.20 0.00 38.03 5.12
986 1082 2.620251 TCCCATTGGTGATGATCGAC 57.380 50.000 1.20 0.00 38.03 4.20
1090 1199 2.304761 AGCGTTCCTGGAGAATTTGGTA 59.695 45.455 0.00 0.00 36.69 3.25
1097 1206 1.906824 ACGGAGCGTTCCTGGAGAA 60.907 57.895 16.80 0.00 41.67 2.87
1209 1346 3.801114 ACATGTACATGAGCTAAGCGA 57.199 42.857 36.36 0.00 41.20 4.93
1210 1347 4.623167 GGATACATGTACATGAGCTAAGCG 59.377 45.833 36.36 11.96 41.20 4.68
1211 1348 4.623167 CGGATACATGTACATGAGCTAAGC 59.377 45.833 36.36 19.61 41.20 3.09
1212 1349 5.773575 ACGGATACATGTACATGAGCTAAG 58.226 41.667 36.36 24.01 41.20 2.18
1214 1351 5.070685 AGACGGATACATGTACATGAGCTA 58.929 41.667 36.36 21.42 41.20 3.32
1240 1383 3.381908 AGCAATAGGTTAGTGGACTCGAG 59.618 47.826 11.84 11.84 0.00 4.04
1263 1406 4.858850 TCCAGACATCACCATTAGCAAAT 58.141 39.130 0.00 0.00 0.00 2.32
1331 1480 0.520404 GTTGTAGTGACGGAGAGCGA 59.480 55.000 0.00 0.00 0.00 4.93
1335 1484 1.174078 TGGCGTTGTAGTGACGGAGA 61.174 55.000 0.00 0.00 40.66 3.71
1341 1490 0.533308 GGTTGGTGGCGTTGTAGTGA 60.533 55.000 0.00 0.00 0.00 3.41
1377 1526 1.617018 CCATGAGAGGCTTGACGGGA 61.617 60.000 0.00 0.00 0.00 5.14
1437 1586 2.743928 CTGTGAGCCACGAAGCCC 60.744 66.667 0.00 0.00 37.14 5.19
1451 1600 0.107945 GCTGGCGATCTTCTTCCTGT 60.108 55.000 0.00 0.00 0.00 4.00
1485 1634 2.604174 CGTGTCGTTGGCCTGGTTC 61.604 63.158 3.32 0.00 0.00 3.62
1632 1796 8.450180 CGTGCCAGAAAATGTTATGCATATATA 58.550 33.333 7.36 0.00 36.67 0.86
1633 1797 7.040478 ACGTGCCAGAAAATGTTATGCATATAT 60.040 33.333 7.36 2.81 36.67 0.86
1634 1798 6.262049 ACGTGCCAGAAAATGTTATGCATATA 59.738 34.615 7.36 0.25 36.67 0.86
1635 1799 5.067674 ACGTGCCAGAAAATGTTATGCATAT 59.932 36.000 7.36 0.00 36.67 1.78
1636 1800 4.397730 ACGTGCCAGAAAATGTTATGCATA 59.602 37.500 1.16 1.16 36.67 3.14
1637 1801 3.193267 ACGTGCCAGAAAATGTTATGCAT 59.807 39.130 3.79 3.79 40.03 3.96
1638 1802 2.556189 ACGTGCCAGAAAATGTTATGCA 59.444 40.909 0.00 0.00 0.00 3.96
1639 1803 3.216147 ACGTGCCAGAAAATGTTATGC 57.784 42.857 0.00 0.00 0.00 3.14
1640 1804 5.282778 CGTAAACGTGCCAGAAAATGTTATG 59.717 40.000 0.00 0.00 34.11 1.90
1658 1825 5.596268 ACGAAAGGAAACCATACGTAAAC 57.404 39.130 0.00 0.00 0.00 2.01
1659 1826 7.903995 AATACGAAAGGAAACCATACGTAAA 57.096 32.000 0.00 0.00 35.27 2.01
1662 1829 6.313658 GGTAAATACGAAAGGAAACCATACGT 59.686 38.462 0.00 0.00 33.99 3.57
1664 1831 7.254218 CGAGGTAAATACGAAAGGAAACCATAC 60.254 40.741 0.00 0.00 0.00 2.39
1675 1842 3.500982 CGTCACCGAGGTAAATACGAAA 58.499 45.455 10.91 0.00 35.63 3.46
1679 1846 1.135721 AGGCGTCACCGAGGTAAATAC 59.864 52.381 0.00 0.00 46.52 1.89
1680 1847 1.477553 AGGCGTCACCGAGGTAAATA 58.522 50.000 0.00 0.00 46.52 1.40
1688 1855 0.035152 TTAGGACTAGGCGTCACCGA 60.035 55.000 0.00 0.00 46.52 4.69
1716 1887 7.647715 TGCGGATAAAGAACAAAAGAAAGAAAG 59.352 33.333 0.00 0.00 0.00 2.62
1734 1905 1.063616 CGACGACTTCTCTGCGGATAA 59.936 52.381 0.00 0.00 0.00 1.75
1740 1911 3.537297 GCGCGACGACTTCTCTGC 61.537 66.667 12.10 0.00 0.00 4.26
1769 1940 1.325943 CAAAATGCACACGCGGTTTTT 59.674 42.857 12.47 6.89 42.97 1.94
1796 1967 2.699846 TGGGTGCAAAATCTGAAAGCTT 59.300 40.909 0.00 0.00 0.00 3.74
1918 2089 2.981914 CTTGCCTTGTCCACTGGCCA 62.982 60.000 4.71 4.71 45.56 5.36
2016 2214 4.214986 TCATCAAAGACCGGCAAAGATA 57.785 40.909 0.00 0.00 0.00 1.98
2045 2259 1.500474 TTGCCCCTGATCTAGTCCAG 58.500 55.000 0.00 7.02 0.00 3.86
2124 2340 4.214971 GTCTGATACATGGCCTTGCTATTG 59.785 45.833 18.17 6.83 0.00 1.90
2153 2371 9.512588 AGTCTCATACATCAACTTCAAAATCTT 57.487 29.630 0.00 0.00 0.00 2.40
2183 2403 7.277098 ACGATTAGTATACAAAGTTGTCGCAAT 59.723 33.333 5.50 0.00 42.35 3.56
2206 3682 2.678336 TGTGTGTGTGTAAATTGCACGA 59.322 40.909 9.49 0.00 39.53 4.35
2219 3695 1.001974 AGAGTGTGTGTGTGTGTGTGT 59.998 47.619 0.00 0.00 0.00 3.72
2220 3696 1.660607 GAGAGTGTGTGTGTGTGTGTG 59.339 52.381 0.00 0.00 0.00 3.82
2221 3697 1.550524 AGAGAGTGTGTGTGTGTGTGT 59.449 47.619 0.00 0.00 0.00 3.72
2222 3698 2.159184 AGAGAGAGTGTGTGTGTGTGTG 60.159 50.000 0.00 0.00 0.00 3.82
2223 3699 2.099921 GAGAGAGAGTGTGTGTGTGTGT 59.900 50.000 0.00 0.00 0.00 3.72
2224 3700 2.360483 AGAGAGAGAGTGTGTGTGTGTG 59.640 50.000 0.00 0.00 0.00 3.82
2225 3701 2.621055 GAGAGAGAGAGTGTGTGTGTGT 59.379 50.000 0.00 0.00 0.00 3.72
2226 3702 2.884012 AGAGAGAGAGAGTGTGTGTGTG 59.116 50.000 0.00 0.00 0.00 3.82
2227 3703 3.146066 GAGAGAGAGAGAGTGTGTGTGT 58.854 50.000 0.00 0.00 0.00 3.72
2228 3704 3.058293 GTGAGAGAGAGAGAGTGTGTGTG 60.058 52.174 0.00 0.00 0.00 3.82
2229 3705 3.146066 GTGAGAGAGAGAGAGTGTGTGT 58.854 50.000 0.00 0.00 0.00 3.72
2230 3706 3.411446 AGTGAGAGAGAGAGAGTGTGTG 58.589 50.000 0.00 0.00 0.00 3.82
2231 3707 3.072330 TGAGTGAGAGAGAGAGAGTGTGT 59.928 47.826 0.00 0.00 0.00 3.72
2232 3708 3.436704 GTGAGTGAGAGAGAGAGAGTGTG 59.563 52.174 0.00 0.00 0.00 3.82
2233 3709 3.327757 AGTGAGTGAGAGAGAGAGAGTGT 59.672 47.826 0.00 0.00 0.00 3.55
2234 3710 3.942829 AGTGAGTGAGAGAGAGAGAGTG 58.057 50.000 0.00 0.00 0.00 3.51
2235 3711 4.287067 AGAAGTGAGTGAGAGAGAGAGAGT 59.713 45.833 0.00 0.00 0.00 3.24
2249 3725 9.384764 GGCTTATAGATTACAAAAGAAGTGAGT 57.615 33.333 0.00 0.00 0.00 3.41
2253 3729 7.011482 CAGCGGCTTATAGATTACAAAAGAAGT 59.989 37.037 0.00 0.00 0.00 3.01
2254 3730 7.348201 CAGCGGCTTATAGATTACAAAAGAAG 58.652 38.462 0.00 0.00 0.00 2.85
2256 3732 5.236478 GCAGCGGCTTATAGATTACAAAAGA 59.764 40.000 0.00 0.00 36.96 2.52
2260 3736 4.066646 TGCAGCGGCTTATAGATTACAA 57.933 40.909 10.92 0.00 41.91 2.41
2262 3738 4.452455 ACAATGCAGCGGCTTATAGATTAC 59.548 41.667 10.92 0.00 41.91 1.89
2265 3741 3.131709 ACAATGCAGCGGCTTATAGAT 57.868 42.857 10.92 0.00 41.91 1.98
2267 3743 3.059597 GTGTACAATGCAGCGGCTTATAG 60.060 47.826 10.92 0.73 41.91 1.31
2268 3744 2.869801 GTGTACAATGCAGCGGCTTATA 59.130 45.455 10.92 0.00 41.91 0.98
2275 3751 2.967459 TCAAAGTGTACAATGCAGCG 57.033 45.000 0.00 0.00 0.00 5.18
2350 3858 2.203294 GTTCACGGTTGTGCCCCT 60.203 61.111 0.00 0.00 46.01 4.79
2361 3869 1.575922 CACTGTGGCCATGTTCACG 59.424 57.895 9.72 0.00 36.74 4.35
2379 3887 2.435059 GCGGAGAGTGACCAAGCC 60.435 66.667 0.00 0.00 0.00 4.35
2386 3894 2.288825 CCTACAAGTTTGCGGAGAGTGA 60.289 50.000 0.00 0.00 0.00 3.41
2389 3897 1.079503 GCCTACAAGTTTGCGGAGAG 58.920 55.000 5.32 0.00 0.00 3.20
2390 3898 0.685097 AGCCTACAAGTTTGCGGAGA 59.315 50.000 5.32 0.00 0.00 3.71
2395 3918 1.068434 TGCCAAAGCCTACAAGTTTGC 59.932 47.619 0.00 0.00 38.69 3.68
2401 3924 1.892474 GGTTCATGCCAAAGCCTACAA 59.108 47.619 0.00 0.00 38.69 2.41
2402 3925 1.202989 TGGTTCATGCCAAAGCCTACA 60.203 47.619 0.00 0.00 38.69 2.74
2436 3959 9.352784 CAAGTGTTGAAAAAGTCATTTAGTTGA 57.647 29.630 0.00 0.00 35.70 3.18
2441 3964 6.634805 TGGCAAGTGTTGAAAAAGTCATTTA 58.365 32.000 0.00 0.00 35.70 1.40
2518 4046 9.888878 CGAATCTTGCTCAATATGAACATATTT 57.111 29.630 14.80 1.41 40.84 1.40
2523 4051 4.035558 GCCGAATCTTGCTCAATATGAACA 59.964 41.667 0.00 0.00 0.00 3.18
2524 4052 4.531332 GCCGAATCTTGCTCAATATGAAC 58.469 43.478 0.00 0.00 0.00 3.18
2525 4053 3.565482 GGCCGAATCTTGCTCAATATGAA 59.435 43.478 0.00 0.00 0.00 2.57
2552 4081 4.535781 TGGCTGTGTGCATCCTAATTATT 58.464 39.130 0.00 0.00 45.15 1.40
2609 4140 1.067364 TGCAGCCAATATGCCATTTCG 59.933 47.619 0.00 0.00 43.18 3.46
2616 4147 3.243201 GGACTTTACTGCAGCCAATATGC 60.243 47.826 15.27 1.49 44.11 3.14
2626 4157 4.093743 TGGTCTCATAGGACTTTACTGCA 58.906 43.478 0.00 0.00 36.55 4.41
2627 4158 4.737855 TGGTCTCATAGGACTTTACTGC 57.262 45.455 0.00 0.00 36.55 4.40
2663 4194 1.597461 GGTCCAACTCCTCCTTCGG 59.403 63.158 0.00 0.00 0.00 4.30
2802 4340 3.151554 TCTGTAGTACGAACTGGCTTCA 58.848 45.455 0.00 0.00 36.36 3.02
2812 4350 4.325028 TGCAGGTTTTTCTGTAGTACGA 57.675 40.909 0.00 0.00 37.12 3.43
2818 4356 5.923733 TTTCCTTTGCAGGTTTTTCTGTA 57.076 34.783 0.00 0.00 41.69 2.74
2839 4380 5.204409 GGTTTCAATCGTAAAACCCCTTT 57.796 39.130 5.85 0.00 45.67 3.11
2860 4402 3.890756 TGGCTATGTAGAAATGGCATTGG 59.109 43.478 14.47 0.00 35.86 3.16
2982 4525 2.621338 AGCATCCAATATGTATCCGCG 58.379 47.619 0.00 0.00 0.00 6.46


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

AutoCloner maintained by Alex Coulton.