Multiple sequence alignment - TraesCS1B01G393700

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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 TraesCS1B01G393700 chr1B 100.000 3007 0 0 1 3007 626252575 626249569 0.000000e+00 5553.0
1 TraesCS1B01G393700 chr1B 82.400 125 8 4 541 665 626305931 626305821 2.470000e-16 97.1
2 TraesCS1B01G393700 chr1D 91.615 1610 73 29 1 1569 455805528 455803940 0.000000e+00 2169.0
3 TraesCS1B01G393700 chr1D 85.605 785 45 27 1646 2405 455803821 455803080 0.000000e+00 761.0
4 TraesCS1B01G393700 chr1D 87.582 612 43 10 2396 3007 455802683 455802105 0.000000e+00 678.0
5 TraesCS1B01G393700 chr1A 87.542 1766 99 63 455 2164 549524783 549523083 0.000000e+00 1930.0
6 TraesCS1B01G393700 chr1A 89.799 598 39 6 2415 3007 549522477 549521897 0.000000e+00 747.0
7 TraesCS1B01G393700 chr1A 87.633 469 45 12 1 462 549525270 549524808 1.590000e-147 532.0
8 TraesCS1B01G393700 chr1A 83.733 375 56 3 2638 3007 549500069 549499695 1.720000e-92 350.0
9 TraesCS1B01G393700 chr1A 92.208 231 12 2 2154 2384 549523049 549522825 3.740000e-84 322.0
10 TraesCS1B01G393700 chr1A 78.400 250 27 12 2391 2623 549468908 549468669 1.450000e-28 137.0
11 TraesCS1B01G393700 chr3B 88.319 351 36 4 105 451 139462387 139462736 1.670000e-112 416.0
12 TraesCS1B01G393700 chr3B 80.117 171 25 8 2 172 202815750 202815911 5.270000e-23 119.0
13 TraesCS1B01G393700 chr3D 88.286 350 36 3 105 450 90204501 90204849 6.000000e-112 414.0
14 TraesCS1B01G393700 chr3A 86.932 352 36 5 105 451 106543980 106544326 1.310000e-103 387.0
15 TraesCS1B01G393700 chr2B 89.908 109 10 1 7 115 462776519 462776412 4.040000e-29 139.0
16 TraesCS1B01G393700 chr5D 90.196 102 9 1 1 102 491595550 491595450 6.760000e-27 132.0
17 TraesCS1B01G393700 chr5B 88.785 107 11 1 1 107 629166717 629166612 2.430000e-26 130.0
18 TraesCS1B01G393700 chr2D 89.423 104 10 1 1 104 64722885 64722987 2.430000e-26 130.0
19 TraesCS1B01G393700 chr4B 88.679 106 11 1 1 106 300991072 300990968 8.750000e-26 128.0
20 TraesCS1B01G393700 chr7D 85.470 117 16 1 1 117 182626989 182626874 1.460000e-23 121.0
21 TraesCS1B01G393700 chr7A 97.059 34 1 0 422 455 106812208 106812241 1.160000e-04 58.4


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 TraesCS1B01G393700 chr1B 626249569 626252575 3006 True 5553.000000 5553 100.000000 1 3007 1 chr1B.!!$R1 3006
1 TraesCS1B01G393700 chr1D 455802105 455805528 3423 True 1202.666667 2169 88.267333 1 3007 3 chr1D.!!$R1 3006
2 TraesCS1B01G393700 chr1A 549521897 549525270 3373 True 882.750000 1930 89.295500 1 3007 4 chr1A.!!$R3 3006

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
118 121 0.177141 TATGAGTGGGTTACGCCTGC 59.823 55.000 0.00 0.00 37.43 4.85 F
523 567 1.301795 TGTGCACGCCGTGGATAAA 60.302 52.632 20.07 3.48 36.11 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1219 1308 0.249868 TGCCAACAGTTCAGAGACCG 60.250 55.0 0.0 0.0 0.0 4.79 R
2139 2311 0.107897 ACACACTTTGCCACGACTCA 60.108 50.0 0.0 0.0 0.0 3.41 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
70 71 6.974965 AGATTCTAAAACAAGAGCCAAAGTG 58.025 36.000 0.00 0.00 0.00 3.16
89 90 8.953990 CCAAAGTGTTTTTGAAAAGTAGATACG 58.046 33.333 1.44 0.00 0.00 3.06
118 121 0.177141 TATGAGTGGGTTACGCCTGC 59.823 55.000 0.00 0.00 37.43 4.85
255 259 8.981659 AGGGTTTTAATTTGAGATGAAATAGGG 58.018 33.333 0.00 0.00 0.00 3.53
424 434 6.768078 TCTAAATTAATTCTTTCGTGACCGC 58.232 36.000 0.10 0.00 0.00 5.68
523 567 1.301795 TGTGCACGCCGTGGATAAA 60.302 52.632 20.07 3.48 36.11 1.40
533 577 2.169978 GCCGTGGATAAACCTCCTAGTT 59.830 50.000 0.00 0.00 39.86 2.24
555 603 7.649057 AGTTGTTATAACTGAAGAACAAAGCC 58.351 34.615 16.33 0.00 41.89 4.35
575 623 3.303791 GCCTTTTACCAACAGTCTGAACG 60.304 47.826 6.91 0.00 0.00 3.95
666 716 3.831715 AAGTAGAAATGCTTTGACGCC 57.168 42.857 0.00 0.00 0.00 5.68
709 780 5.705902 ACGCAAGACACTGTTTTAAAAAGT 58.294 33.333 1.31 6.15 43.62 2.66
751 822 4.785453 GAGTTGGCTGGCTCCCGG 62.785 72.222 2.00 0.00 0.00 5.73
926 1006 3.419270 CGAAGCGCTTATAAGTCGAGAAG 59.581 47.826 25.11 13.04 0.00 2.85
1169 1253 7.534085 TCGTATCGAGCATTAACATTTTTCT 57.466 32.000 0.00 0.00 0.00 2.52
1170 1254 7.618442 TCGTATCGAGCATTAACATTTTTCTC 58.382 34.615 0.00 0.00 0.00 2.87
1171 1255 6.846283 CGTATCGAGCATTAACATTTTTCTCC 59.154 38.462 0.00 0.00 0.00 3.71
1172 1256 5.560966 TCGAGCATTAACATTTTTCTCCC 57.439 39.130 0.00 0.00 0.00 4.30
1173 1257 4.398044 TCGAGCATTAACATTTTTCTCCCC 59.602 41.667 0.00 0.00 0.00 4.81
1216 1305 2.028112 GTCACCTACTGACTGAATGCCA 60.028 50.000 0.00 0.00 45.38 4.92
1219 1308 1.945394 CCTACTGACTGAATGCCATGC 59.055 52.381 0.00 0.00 0.00 4.06
1571 1687 4.805744 AGAAGTTCCTCTCGGTACCATAT 58.194 43.478 13.54 0.00 31.44 1.78
1572 1688 5.950023 AGAAGTTCCTCTCGGTACCATATA 58.050 41.667 13.54 0.00 31.44 0.86
1573 1689 6.553857 AGAAGTTCCTCTCGGTACCATATAT 58.446 40.000 13.54 0.00 31.44 0.86
1574 1690 7.696981 AGAAGTTCCTCTCGGTACCATATATA 58.303 38.462 13.54 0.00 31.44 0.86
1588 1704 8.532819 GGTACCATATATACTTTCTTCTCCCTG 58.467 40.741 7.15 0.00 0.00 4.45
1591 1707 8.239478 ACCATATATACTTTCTTCTCCCTGGTA 58.761 37.037 0.00 0.00 0.00 3.25
1594 1745 9.900112 ATATATACTTTCTTCTCCCTGGTACTT 57.100 33.333 0.00 0.00 0.00 2.24
1597 1748 5.622180 ACTTTCTTCTCCCTGGTACTTTTC 58.378 41.667 0.00 0.00 0.00 2.29
1600 1751 4.489737 TCTTCTCCCTGGTACTTTTCTCA 58.510 43.478 0.00 0.00 0.00 3.27
1601 1752 4.905456 TCTTCTCCCTGGTACTTTTCTCAA 59.095 41.667 0.00 0.00 0.00 3.02
1603 1754 4.232091 TCTCCCTGGTACTTTTCTCAACT 58.768 43.478 0.00 0.00 0.00 3.16
1605 1756 3.971305 TCCCTGGTACTTTTCTCAACTGA 59.029 43.478 0.00 0.00 0.00 3.41
1611 1762 5.637810 TGGTACTTTTCTCAACTGATTAGCG 59.362 40.000 0.00 0.00 0.00 4.26
1614 1765 6.229561 ACTTTTCTCAACTGATTAGCGAAC 57.770 37.500 0.00 0.00 0.00 3.95
1617 1768 7.656137 ACTTTTCTCAACTGATTAGCGAACTAA 59.344 33.333 0.00 0.00 42.47 2.24
1622 1773 8.467598 TCTCAACTGATTAGCGAACTAACTAAT 58.532 33.333 0.00 0.00 41.12 1.73
1631 1782 6.079424 AGCGAACTAACTAATCATCTCCTC 57.921 41.667 0.00 0.00 0.00 3.71
1632 1783 5.010213 AGCGAACTAACTAATCATCTCCTCC 59.990 44.000 0.00 0.00 0.00 4.30
1633 1784 5.010213 GCGAACTAACTAATCATCTCCTCCT 59.990 44.000 0.00 0.00 0.00 3.69
1634 1785 6.674066 CGAACTAACTAATCATCTCCTCCTC 58.326 44.000 0.00 0.00 0.00 3.71
1635 1786 6.294286 CGAACTAACTAATCATCTCCTCCTCC 60.294 46.154 0.00 0.00 0.00 4.30
1645 1810 0.560193 CTCCTCCTCCTCCTCCATGA 59.440 60.000 0.00 0.00 0.00 3.07
1646 1811 1.149711 CTCCTCCTCCTCCTCCATGAT 59.850 57.143 0.00 0.00 0.00 2.45
1647 1812 1.132913 TCCTCCTCCTCCTCCATGATG 60.133 57.143 0.00 0.00 0.00 3.07
1648 1813 1.132913 CCTCCTCCTCCTCCATGATGA 60.133 57.143 0.00 0.00 0.00 2.92
1727 1892 3.494332 ACTCTGGTCTACGTTGGTAAGT 58.506 45.455 0.00 0.00 0.00 2.24
1729 1894 4.457257 ACTCTGGTCTACGTTGGTAAGTAC 59.543 45.833 0.00 0.00 0.00 2.73
1731 1896 4.826733 TCTGGTCTACGTTGGTAAGTACAA 59.173 41.667 0.00 0.00 0.00 2.41
1732 1897 5.477984 TCTGGTCTACGTTGGTAAGTACAAT 59.522 40.000 0.00 0.00 0.00 2.71
1786 1951 4.788679 AGATCAAAGGCATGTGATGATCA 58.211 39.130 9.15 0.00 45.52 2.92
1798 1963 4.503910 TGTGATGATCAACGAACTAAGGG 58.496 43.478 0.00 0.00 0.00 3.95
1802 1967 6.592607 GTGATGATCAACGAACTAAGGGTTTA 59.407 38.462 0.00 0.00 38.41 2.01
1818 1983 9.541143 CTAAGGGTTTATTGTGATTTGTTGTTT 57.459 29.630 0.00 0.00 0.00 2.83
1932 2097 3.119424 CGAGGACCTCAAGAAGTTCTACC 60.119 52.174 21.49 3.88 0.00 3.18
1991 2156 1.078848 CCCCGTCAAGAGCAAGAGG 60.079 63.158 0.00 0.00 0.00 3.69
2060 2229 1.448540 CAGGAGGTCGTGATGGTGC 60.449 63.158 0.00 0.00 33.92 5.01
2061 2230 2.125106 GGAGGTCGTGATGGTGCC 60.125 66.667 0.00 0.00 0.00 5.01
2120 2290 1.478105 GGAAATGGCAATGGACTCACC 59.522 52.381 0.00 0.00 39.54 4.02
2139 2311 2.093128 ACCAAGAGTCTTGTTCGGTTGT 60.093 45.455 27.07 15.25 0.00 3.32
2185 2401 9.931210 GTGTGCCTGTTATAAACTGTTATTATC 57.069 33.333 0.00 0.00 32.10 1.75
2261 2499 3.003689 AGAATTGCTTCTTGTTGGTGTCG 59.996 43.478 0.00 0.00 38.63 4.35
2262 2500 1.745232 TTGCTTCTTGTTGGTGTCGT 58.255 45.000 0.00 0.00 0.00 4.34
2263 2501 1.295792 TGCTTCTTGTTGGTGTCGTC 58.704 50.000 0.00 0.00 0.00 4.20
2264 2502 1.134521 TGCTTCTTGTTGGTGTCGTCT 60.135 47.619 0.00 0.00 0.00 4.18
2265 2503 1.261619 GCTTCTTGTTGGTGTCGTCTG 59.738 52.381 0.00 0.00 0.00 3.51
2266 2504 1.867233 CTTCTTGTTGGTGTCGTCTGG 59.133 52.381 0.00 0.00 0.00 3.86
2267 2505 0.828022 TCTTGTTGGTGTCGTCTGGT 59.172 50.000 0.00 0.00 0.00 4.00
2268 2506 0.937304 CTTGTTGGTGTCGTCTGGTG 59.063 55.000 0.00 0.00 0.00 4.17
2269 2507 1.092921 TTGTTGGTGTCGTCTGGTGC 61.093 55.000 0.00 0.00 0.00 5.01
2270 2508 1.522806 GTTGGTGTCGTCTGGTGCA 60.523 57.895 0.00 0.00 0.00 4.57
2271 2509 0.884704 GTTGGTGTCGTCTGGTGCAT 60.885 55.000 0.00 0.00 0.00 3.96
2272 2510 0.884259 TTGGTGTCGTCTGGTGCATG 60.884 55.000 0.00 0.00 0.00 4.06
2273 2511 2.034879 GGTGTCGTCTGGTGCATGG 61.035 63.158 0.00 0.00 0.00 3.66
2274 2512 2.358615 TGTCGTCTGGTGCATGGC 60.359 61.111 0.00 0.00 0.00 4.40
2275 2513 2.046892 GTCGTCTGGTGCATGGCT 60.047 61.111 0.00 0.00 0.00 4.75
2276 2514 1.672356 GTCGTCTGGTGCATGGCTT 60.672 57.895 0.00 0.00 0.00 4.35
2277 2515 1.375908 TCGTCTGGTGCATGGCTTC 60.376 57.895 0.00 0.00 0.00 3.86
2278 2516 2.743752 CGTCTGGTGCATGGCTTCG 61.744 63.158 0.00 0.00 0.00 3.79
2279 2517 1.672356 GTCTGGTGCATGGCTTCGT 60.672 57.895 0.00 0.00 0.00 3.85
2280 2518 1.375908 TCTGGTGCATGGCTTCGTC 60.376 57.895 0.00 0.00 0.00 4.20
2281 2519 1.376424 CTGGTGCATGGCTTCGTCT 60.376 57.895 0.00 0.00 0.00 4.18
2282 2520 1.364626 CTGGTGCATGGCTTCGTCTC 61.365 60.000 0.00 0.00 0.00 3.36
2283 2521 1.078848 GGTGCATGGCTTCGTCTCT 60.079 57.895 0.00 0.00 0.00 3.10
2284 2522 1.086634 GGTGCATGGCTTCGTCTCTC 61.087 60.000 0.00 0.00 0.00 3.20
2315 2553 3.420839 AAGTGAAAGAAAACGCAGTGG 57.579 42.857 0.00 0.00 45.00 4.00
2326 2564 0.598158 ACGCAGTGGCAAGCAAAATG 60.598 50.000 12.79 0.01 42.51 2.32
2358 2596 1.312371 AAATGGGAATGGACGCCACG 61.312 55.000 0.50 0.00 35.80 4.94
2385 2623 1.078214 ACCGTCATGTCATGGGCAG 60.078 57.895 12.90 2.83 0.00 4.85
2389 2627 1.099879 GTCATGTCATGGGCAGAGGC 61.100 60.000 12.90 0.00 40.13 4.70
2390 2628 1.077285 CATGTCATGGGCAGAGGCA 60.077 57.895 4.78 0.00 43.71 4.75
2391 2629 1.077212 ATGTCATGGGCAGAGGCAC 60.077 57.895 0.00 0.00 46.33 5.01
2402 3068 1.227764 AGAGGCACAGCACACACAG 60.228 57.895 0.00 0.00 0.00 3.66
2425 3091 1.148310 CACCGACTGCCTACAAACTG 58.852 55.000 0.00 0.00 0.00 3.16
2469 3135 3.827505 ACAAGGAACATGTGGCTGT 57.172 47.368 0.00 0.00 39.47 4.40
2470 3136 1.321474 ACAAGGAACATGTGGCTGTG 58.679 50.000 0.00 0.00 39.47 3.66
2471 3137 0.599558 CAAGGAACATGTGGCTGTGG 59.400 55.000 0.00 0.00 0.00 4.17
2489 3155 7.124052 GGCTGTGGGGATACTTATACTAGATA 58.876 42.308 0.00 0.00 0.00 1.98
2514 3180 5.844004 ACATATTAGTTAGGCTTGAGGACG 58.156 41.667 0.00 0.00 0.00 4.79
2515 3181 3.821421 ATTAGTTAGGCTTGAGGACGG 57.179 47.619 0.00 0.00 0.00 4.79
2518 3184 0.822164 GTTAGGCTTGAGGACGGCTA 59.178 55.000 0.00 0.00 37.26 3.93
2519 3185 1.206371 GTTAGGCTTGAGGACGGCTAA 59.794 52.381 0.00 0.00 43.30 3.09
2629 3295 8.545229 TTGTATGGAAATTGCATAAGTTTTGG 57.455 30.769 8.75 0.00 32.48 3.28
2769 3436 1.477558 GGCGGTCCATTTCCATCAGAT 60.478 52.381 0.00 0.00 0.00 2.90
2796 3463 2.345991 GTGCTACACCTTCGCCCA 59.654 61.111 0.00 0.00 0.00 5.36
2857 3524 3.072915 TCAACTGGGAGCAAATTGAGAGA 59.927 43.478 0.00 0.00 0.00 3.10
2874 3541 2.834549 AGAGAAACACCTGGACGATCAT 59.165 45.455 0.00 0.00 0.00 2.45
2882 3549 4.199310 CACCTGGACGATCATACCAAAAT 58.801 43.478 0.00 0.00 33.14 1.82
2944 3615 4.071961 TGTGAGCTCTGTAAACATGTGT 57.928 40.909 16.19 0.00 0.00 3.72
2963 3634 3.991773 GTGTTTACCACTTCTGACGCATA 59.008 43.478 0.00 0.00 41.11 3.14
2966 3637 2.094762 ACCACTTCTGACGCATAACC 57.905 50.000 0.00 0.00 0.00 2.85
2985 3656 0.371645 CCATCGTCGCTTTTGAGCTC 59.628 55.000 6.82 6.82 0.00 4.09
2987 3658 0.037326 ATCGTCGCTTTTGAGCTCCA 60.037 50.000 12.15 0.00 0.00 3.86
2990 3661 0.514691 GTCGCTTTTGAGCTCCAGTG 59.485 55.000 12.15 11.15 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 6.867519 TGAAACTAACCCAGACTGATGATA 57.132 37.500 3.32 0.00 0.00 2.15
51 52 7.330700 TCAAAAACACTTTGGCTCTTGTTTTAG 59.669 33.333 15.24 0.00 46.40 1.85
52 53 7.155328 TCAAAAACACTTTGGCTCTTGTTTTA 58.845 30.769 15.24 4.24 46.40 1.52
61 62 6.930731 TCTACTTTTCAAAAACACTTTGGCT 58.069 32.000 0.00 0.00 0.00 4.75
70 71 8.932791 TCTCCATCGTATCTACTTTTCAAAAAC 58.067 33.333 0.00 0.00 0.00 2.43
89 90 2.032620 ACCCACTCATACGTCTCCATC 58.967 52.381 0.00 0.00 0.00 3.51
118 121 1.747325 GAGAGAGCAGCCCAGCCTAG 61.747 65.000 0.00 0.00 34.23 3.02
251 255 5.712917 ACGCATTTTTGTAGGAATTTCCCTA 59.287 36.000 11.92 1.74 37.19 3.53
255 259 5.918011 TGTGACGCATTTTTGTAGGAATTTC 59.082 36.000 0.00 0.00 0.00 2.17
300 304 3.805207 ACTTAGTTTTCTGCACCTTCGT 58.195 40.909 0.00 0.00 0.00 3.85
523 567 8.312564 GTTCTTCAGTTATAACAACTAGGAGGT 58.687 37.037 17.65 0.00 0.00 3.85
533 577 7.817418 AAGGCTTTGTTCTTCAGTTATAACA 57.183 32.000 17.65 0.00 0.00 2.41
555 603 3.560068 AGCGTTCAGACTGTTGGTAAAAG 59.440 43.478 1.59 0.00 0.00 2.27
575 623 1.080569 CAACGGCATTGGGTTCAGC 60.081 57.895 0.00 0.00 34.34 4.26
665 715 0.675083 TGCATCTTGTTGGTTGCTGG 59.325 50.000 0.00 0.00 36.10 4.85
666 716 2.512485 TTGCATCTTGTTGGTTGCTG 57.488 45.000 0.00 0.00 36.10 4.41
709 780 5.935206 TCTCACGGTAAAAGATTTGTGCATA 59.065 36.000 0.00 0.00 0.00 3.14
751 822 0.905357 TTGCTAGAGCCTCCAAGACC 59.095 55.000 0.00 0.00 41.18 3.85
840 919 1.223487 GGGATAGCTTTGTGCCGGA 59.777 57.895 5.05 0.00 44.23 5.14
926 1006 0.668401 GGCATGCAGGTCACAAAAGC 60.668 55.000 21.36 0.00 0.00 3.51
957 1037 1.470098 GTTGTGCAGGTGTGATGATCC 59.530 52.381 0.00 0.00 0.00 3.36
1144 1228 7.970384 AGAAAAATGTTAATGCTCGATACGAA 58.030 30.769 0.00 0.00 34.74 3.85
1171 1255 3.003173 TGCGGTTCTCAGAGGGGG 61.003 66.667 0.00 0.00 0.00 5.40
1172 1256 2.266055 GTGCGGTTCTCAGAGGGG 59.734 66.667 0.00 0.00 0.00 4.79
1173 1257 2.125912 CGTGCGGTTCTCAGAGGG 60.126 66.667 0.00 0.00 0.00 4.30
1216 1305 1.609061 CCAACAGTTCAGAGACCGCAT 60.609 52.381 0.00 0.00 0.00 4.73
1219 1308 0.249868 TGCCAACAGTTCAGAGACCG 60.250 55.000 0.00 0.00 0.00 4.79
1571 1687 8.445361 AAAAGTACCAGGGAGAAGAAAGTATA 57.555 34.615 0.00 0.00 0.00 1.47
1572 1688 6.954352 AAAGTACCAGGGAGAAGAAAGTAT 57.046 37.500 0.00 0.00 0.00 2.12
1573 1689 6.557633 AGAAAAGTACCAGGGAGAAGAAAGTA 59.442 38.462 0.00 0.00 0.00 2.24
1574 1690 5.369993 AGAAAAGTACCAGGGAGAAGAAAGT 59.630 40.000 0.00 0.00 0.00 2.66
1588 1704 5.867716 TCGCTAATCAGTTGAGAAAAGTACC 59.132 40.000 0.00 0.00 0.00 3.34
1591 1707 5.992217 AGTTCGCTAATCAGTTGAGAAAAGT 59.008 36.000 0.00 0.00 0.00 2.66
1594 1745 7.152645 AGTTAGTTCGCTAATCAGTTGAGAAA 58.847 34.615 0.00 0.00 41.24 2.52
1597 1748 8.635877 ATTAGTTAGTTCGCTAATCAGTTGAG 57.364 34.615 0.00 0.00 41.24 3.02
1605 1756 8.184304 AGGAGATGATTAGTTAGTTCGCTAAT 57.816 34.615 0.00 0.00 41.24 1.73
1611 1762 6.780522 AGGAGGAGGAGATGATTAGTTAGTTC 59.219 42.308 0.00 0.00 0.00 3.01
1614 1765 5.714806 GGAGGAGGAGGAGATGATTAGTTAG 59.285 48.000 0.00 0.00 0.00 2.34
1617 1768 3.732204 AGGAGGAGGAGGAGATGATTAGT 59.268 47.826 0.00 0.00 0.00 2.24
1622 1773 0.856982 GGAGGAGGAGGAGGAGATGA 59.143 60.000 0.00 0.00 0.00 2.92
1624 1775 1.149711 CATGGAGGAGGAGGAGGAGAT 59.850 57.143 0.00 0.00 0.00 2.75
1631 1782 2.106166 CCTTTCATCATGGAGGAGGAGG 59.894 54.545 2.65 0.00 0.00 4.30
1632 1783 2.776536 ACCTTTCATCATGGAGGAGGAG 59.223 50.000 13.19 0.00 33.47 3.69
1633 1784 2.507058 CACCTTTCATCATGGAGGAGGA 59.493 50.000 13.19 0.00 33.47 3.71
1634 1785 2.507058 TCACCTTTCATCATGGAGGAGG 59.493 50.000 13.19 0.00 33.47 4.30
1635 1786 3.920231 TCACCTTTCATCATGGAGGAG 57.080 47.619 13.19 6.94 33.47 3.69
1645 1810 5.191426 CACAGAGATCCAATCACCTTTCAT 58.809 41.667 0.00 0.00 0.00 2.57
1646 1811 4.566278 CCACAGAGATCCAATCACCTTTCA 60.566 45.833 0.00 0.00 0.00 2.69
1647 1812 3.944015 CCACAGAGATCCAATCACCTTTC 59.056 47.826 0.00 0.00 0.00 2.62
1648 1813 3.308688 CCCACAGAGATCCAATCACCTTT 60.309 47.826 0.00 0.00 0.00 3.11
1759 1924 7.034685 TCATCACATGCCTTTGATCTTTATG 57.965 36.000 0.00 0.00 29.64 1.90
1761 1926 6.829811 TGATCATCACATGCCTTTGATCTTTA 59.170 34.615 20.20 6.55 41.94 1.85
1765 1930 5.279384 GTTGATCATCACATGCCTTTGATC 58.721 41.667 15.96 15.96 41.83 2.92
1766 1931 4.201980 CGTTGATCATCACATGCCTTTGAT 60.202 41.667 0.00 0.00 32.44 2.57
1767 1932 3.127376 CGTTGATCATCACATGCCTTTGA 59.873 43.478 0.00 0.00 0.00 2.69
1770 1935 2.989909 TCGTTGATCATCACATGCCTT 58.010 42.857 0.00 0.00 0.00 4.35
1771 1936 2.679837 GTTCGTTGATCATCACATGCCT 59.320 45.455 0.00 0.00 0.00 4.75
1772 1937 2.679837 AGTTCGTTGATCATCACATGCC 59.320 45.455 0.00 0.00 0.00 4.40
1773 1938 5.469373 TTAGTTCGTTGATCATCACATGC 57.531 39.130 0.00 0.00 0.00 4.06
1774 1939 5.007039 CCCTTAGTTCGTTGATCATCACATG 59.993 44.000 0.00 0.00 0.00 3.21
1775 1940 5.118990 CCCTTAGTTCGTTGATCATCACAT 58.881 41.667 0.00 0.00 0.00 3.21
1776 1941 4.020573 ACCCTTAGTTCGTTGATCATCACA 60.021 41.667 0.00 0.00 0.00 3.58
1777 1942 4.504858 ACCCTTAGTTCGTTGATCATCAC 58.495 43.478 0.00 0.00 0.00 3.06
1786 1951 7.754851 AATCACAATAAACCCTTAGTTCGTT 57.245 32.000 0.00 0.00 37.88 3.85
1798 1963 7.907563 CCCAACAAACAACAAATCACAATAAAC 59.092 33.333 0.00 0.00 0.00 2.01
1802 1967 4.880696 CCCCAACAAACAACAAATCACAAT 59.119 37.500 0.00 0.00 0.00 2.71
1818 1983 0.482446 AAGAATCCTGCACCCCAACA 59.518 50.000 0.00 0.00 0.00 3.33
1889 2054 3.579302 CCCTTGGCCACCAGGTGA 61.579 66.667 22.37 0.00 35.23 4.02
1932 2097 3.047877 GTTGGCGTCCACCTTCCG 61.048 66.667 0.00 0.00 30.78 4.30
1991 2156 0.528684 CTAGCTAGTGGAAGTGCGCC 60.529 60.000 12.92 0.00 0.00 6.53
2120 2290 3.194861 TCACAACCGAACAAGACTCTTG 58.805 45.455 16.01 16.01 0.00 3.02
2123 2293 2.795470 GACTCACAACCGAACAAGACTC 59.205 50.000 0.00 0.00 0.00 3.36
2134 2306 0.307760 CTTTGCCACGACTCACAACC 59.692 55.000 0.00 0.00 0.00 3.77
2139 2311 0.107897 ACACACTTTGCCACGACTCA 60.108 50.000 0.00 0.00 0.00 3.41
2185 2401 3.245797 CTTCCATCATATCCGTAGCACG 58.754 50.000 2.27 2.27 42.11 5.34
2261 2499 1.639298 GACGAAGCCATGCACCAGAC 61.639 60.000 0.00 0.00 0.00 3.51
2262 2500 1.375908 GACGAAGCCATGCACCAGA 60.376 57.895 0.00 0.00 0.00 3.86
2263 2501 1.364626 GAGACGAAGCCATGCACCAG 61.365 60.000 0.00 0.00 0.00 4.00
2264 2502 1.375908 GAGACGAAGCCATGCACCA 60.376 57.895 0.00 0.00 0.00 4.17
2265 2503 1.078848 AGAGACGAAGCCATGCACC 60.079 57.895 0.00 0.00 0.00 5.01
2266 2504 1.086634 GGAGAGACGAAGCCATGCAC 61.087 60.000 0.00 0.00 0.00 4.57
2267 2505 1.219124 GGAGAGACGAAGCCATGCA 59.781 57.895 0.00 0.00 0.00 3.96
2268 2506 1.522580 GGGAGAGACGAAGCCATGC 60.523 63.158 0.00 0.00 0.00 4.06
2269 2507 1.144936 GGGGAGAGACGAAGCCATG 59.855 63.158 0.00 0.00 0.00 3.66
2270 2508 2.066999 GGGGGAGAGACGAAGCCAT 61.067 63.158 0.00 0.00 0.00 4.40
2271 2509 2.683933 GGGGGAGAGACGAAGCCA 60.684 66.667 0.00 0.00 0.00 4.75
2272 2510 1.962321 GAAGGGGGAGAGACGAAGCC 61.962 65.000 0.00 0.00 0.00 4.35
2273 2511 0.973496 AGAAGGGGGAGAGACGAAGC 60.973 60.000 0.00 0.00 0.00 3.86
2274 2512 1.107945 GAGAAGGGGGAGAGACGAAG 58.892 60.000 0.00 0.00 0.00 3.79
2275 2513 0.408309 TGAGAAGGGGGAGAGACGAA 59.592 55.000 0.00 0.00 0.00 3.85
2276 2514 0.408309 TTGAGAAGGGGGAGAGACGA 59.592 55.000 0.00 0.00 0.00 4.20
2277 2515 1.205893 CTTTGAGAAGGGGGAGAGACG 59.794 57.143 0.00 0.00 0.00 4.18
2278 2516 2.027653 CACTTTGAGAAGGGGGAGAGAC 60.028 54.545 0.00 0.00 37.19 3.36
2279 2517 2.158158 TCACTTTGAGAAGGGGGAGAGA 60.158 50.000 0.00 0.00 36.90 3.10
2280 2518 2.260822 TCACTTTGAGAAGGGGGAGAG 58.739 52.381 0.00 0.00 36.90 3.20
2281 2519 2.415983 TCACTTTGAGAAGGGGGAGA 57.584 50.000 0.00 0.00 36.90 3.71
2282 2520 3.073062 TCTTTCACTTTGAGAAGGGGGAG 59.927 47.826 0.00 0.00 36.90 4.30
2283 2521 3.053077 TCTTTCACTTTGAGAAGGGGGA 58.947 45.455 0.00 0.00 36.90 4.81
2284 2522 3.508845 TCTTTCACTTTGAGAAGGGGG 57.491 47.619 0.00 0.00 36.90 5.40
2315 2553 4.445452 TCATCTTCTCCATTTTGCTTGC 57.555 40.909 0.00 0.00 0.00 4.01
2358 2596 3.179265 CATGACGGTCGCGGTGTC 61.179 66.667 6.13 12.61 0.00 3.67
2385 2623 1.502163 GACTGTGTGTGCTGTGCCTC 61.502 60.000 0.00 0.00 0.00 4.70
2389 2627 1.153188 TGGGACTGTGTGTGCTGTG 60.153 57.895 0.00 0.00 37.18 3.66
2390 2628 1.153168 GTGGGACTGTGTGTGCTGT 60.153 57.895 0.00 0.00 37.18 4.40
2391 2629 1.893808 GGTGGGACTGTGTGTGCTG 60.894 63.158 0.00 0.00 37.18 4.41
2392 2630 2.510906 GGTGGGACTGTGTGTGCT 59.489 61.111 0.00 0.00 37.18 4.40
2394 2632 1.594293 GTCGGTGGGACTGTGTGTG 60.594 63.158 0.00 0.00 42.62 3.82
2402 3068 1.823169 TTGTAGGCAGTCGGTGGGAC 61.823 60.000 0.00 0.00 46.45 4.46
2425 3091 8.517878 TGAAGGTGAATGAGAATTCTGAATTTC 58.482 33.333 14.00 6.99 0.00 2.17
2489 3155 7.309867 CCGTCCTCAAGCCTAACTAATATGTAT 60.310 40.741 0.00 0.00 0.00 2.29
2572 3238 5.411781 AGAATTAGTTACTGCCAAGACTCG 58.588 41.667 0.00 0.00 0.00 4.18
2588 3254 0.462047 ACAAGCGGCCCGAGAATTAG 60.462 55.000 7.68 0.00 0.00 1.73
2629 3295 4.142534 TGTGCATGATTTAAGCTCTTGAGC 60.143 41.667 14.16 14.16 0.00 4.26
2657 3324 1.015109 GCTGATCTGGCATGTCACAG 58.985 55.000 11.08 11.08 36.07 3.66
2796 3463 5.136105 AGGATGTTTTCAAGTTCAGCTTCT 58.864 37.500 0.00 0.00 34.69 2.85
2857 3524 2.569853 TGGTATGATCGTCCAGGTGTTT 59.430 45.455 0.00 0.00 0.00 2.83
2874 3541 7.367285 GCATTTGACACTAACTCATTTTGGTA 58.633 34.615 0.00 0.00 0.00 3.25
2882 3549 4.350368 TCAGGCATTTGACACTAACTCA 57.650 40.909 0.00 0.00 0.00 3.41
2944 3615 3.998341 GGTTATGCGTCAGAAGTGGTAAA 59.002 43.478 0.00 0.00 0.00 2.01
2963 3634 1.156736 CTCAAAAGCGACGATGGGTT 58.843 50.000 0.00 0.00 0.00 4.11


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

AutoCloner maintained by Alex Coulton.