Multiple sequence alignment - TraesCS6D01G274300

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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 TraesCS6D01G274300 chr6D 100.000 4562 0 0 1 4562 382729326 382724765 0.000000e+00 8425.0
1 TraesCS6D01G274300 chr6A 90.917 4668 261 64 1 4562 524837317 524832707 0.000000e+00 6120.0
2 TraesCS6D01G274300 chr6B 92.225 2328 123 19 2283 4562 572505032 572502715 0.000000e+00 3243.0
3 TraesCS6D01G274300 chr6B 87.305 1859 138 39 3 1804 572545430 572543613 0.000000e+00 2036.0
4 TraesCS6D01G274300 chr6B 88.898 1216 68 27 626 1804 572506703 572505518 0.000000e+00 1435.0
5 TraesCS6D01G274300 chr6B 89.808 1148 69 14 2283 3384 572543127 572541982 0.000000e+00 1428.0
6 TraesCS6D01G274300 chr6B 90.363 799 51 12 3769 4562 572495089 572494312 0.000000e+00 1026.0
7 TraesCS6D01G274300 chr6B 89.776 626 56 7 3 623 572507380 572506758 0.000000e+00 795.0
8 TraesCS6D01G274300 chr6B 94.359 390 22 0 1927 2316 572505490 572505101 2.350000e-167 599.0
9 TraesCS6D01G274300 chr6B 93.846 390 24 0 1927 2316 572543585 572543196 5.080000e-164 588.0
10 TraesCS6D01G274300 chr2A 91.156 147 9 3 2815 2961 114307094 114306952 3.600000e-46 196.0
11 TraesCS6D01G274300 chr2A 78.916 166 24 9 156 317 101882688 101882846 8.070000e-18 102.0
12 TraesCS6D01G274300 chr2A 97.500 40 0 1 2981 3019 114306754 114306715 2.950000e-07 67.6
13 TraesCS6D01G274300 chr1D 77.419 341 67 6 185 522 398557119 398556786 1.290000e-45 195.0
14 TraesCS6D01G274300 chr5A 81.897 232 32 5 4027 4257 639638002 639638224 2.170000e-43 187.0
15 TraesCS6D01G274300 chr5A 79.422 277 46 4 3984 4257 639490875 639491143 7.790000e-43 185.0
16 TraesCS6D01G274300 chr5A 79.422 277 46 4 3984 4257 639565910 639566178 7.790000e-43 185.0
17 TraesCS6D01G274300 chr5A 96.552 58 1 1 3687 3744 619169033 619169089 1.350000e-15 95.3
18 TraesCS6D01G274300 chr5A 94.828 58 2 1 3686 3743 482768158 482768102 6.290000e-14 89.8
19 TraesCS6D01G274300 chr5D 78.623 276 49 5 3985 4257 511451918 511452186 1.690000e-39 174.0
20 TraesCS6D01G274300 chr5D 78.125 128 21 6 133 256 255712966 255712842 1.760000e-09 75.0
21 TraesCS6D01G274300 chr4B 88.710 124 8 5 2804 2927 362712909 362713026 3.680000e-31 147.0
22 TraesCS6D01G274300 chr2B 79.167 168 21 10 156 317 154231664 154231823 2.250000e-18 104.0
23 TraesCS6D01G274300 chr4D 79.085 153 27 5 156 306 41932917 41932768 2.900000e-17 100.0
24 TraesCS6D01G274300 chr2D 92.424 66 4 1 3676 3740 61804612 61804677 4.860000e-15 93.5
25 TraesCS6D01G274300 chr2D 94.915 59 2 1 3688 3746 274856377 274856320 1.750000e-14 91.6
26 TraesCS6D01G274300 chr2D 91.228 57 4 1 2964 3019 288967422 288967366 4.890000e-10 76.8
27 TraesCS6D01G274300 chr3A 96.429 56 1 1 3687 3742 505237242 505237296 1.750000e-14 91.6
28 TraesCS6D01G274300 chr3A 78.571 140 25 5 4088 4226 80432299 80432434 2.260000e-13 87.9
29 TraesCS6D01G274300 chr1B 96.364 55 2 0 3687 3741 411211927 411211873 1.750000e-14 91.6
30 TraesCS6D01G274300 chr7D 91.045 67 3 2 3678 3742 20064764 20064699 2.260000e-13 87.9
31 TraesCS6D01G274300 chr3B 82.653 98 14 3 158 253 245636936 245637032 2.920000e-12 84.2


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 TraesCS6D01G274300 chr6D 382724765 382729326 4561 True 8425.000000 8425 100.000000 1 4562 1 chr6D.!!$R1 4561
1 TraesCS6D01G274300 chr6A 524832707 524837317 4610 True 6120.000000 6120 90.917000 1 4562 1 chr6A.!!$R1 4561
2 TraesCS6D01G274300 chr6B 572502715 572507380 4665 True 1518.000000 3243 91.314500 3 4562 4 chr6B.!!$R2 4559
3 TraesCS6D01G274300 chr6B 572541982 572545430 3448 True 1350.666667 2036 90.319667 3 3384 3 chr6B.!!$R3 3381
4 TraesCS6D01G274300 chr6B 572494312 572495089 777 True 1026.000000 1026 90.363000 3769 4562 1 chr6B.!!$R1 793

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
533 538 0.172352 CTCACTCGGAGTCCTGAAGC 59.828 60.0 7.89 0.0 38.90 3.86 F
1341 1418 0.106918 GTGGTGGTTGGACTTGGACA 60.107 55.0 0.00 0.0 0.00 4.02 F
1363 1440 0.107017 GTGATGGTGGAGGTCATGGG 60.107 60.0 0.00 0.0 0.00 4.00 F
1509 1608 0.615331 TGTGAGCATCCCCACTTCTC 59.385 55.0 0.00 0.0 34.57 2.87 F
3282 3555 0.319986 TTTGTATGTGTGCTCGCCGA 60.320 50.0 0.00 0.0 0.00 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1771 1883 0.036858 AGAGGGAAGCAAACGAGAGC 60.037 55.000 0.00 0.00 0.00 4.09 R
2604 2838 0.040425 GTCGCTTCACCGTTTGCATT 60.040 50.000 0.00 0.00 0.00 3.56 R
3072 3345 1.964448 CTGGACACTCGTGGCACTA 59.036 57.895 16.72 3.47 41.42 2.74 R
3443 3716 2.025155 CCAGCATGTAGTACTCGTCCT 58.975 52.381 0.00 0.00 0.00 3.85 R
4219 4499 0.730840 GCCACAACCAATACTACGCC 59.269 55.000 0.00 0.00 0.00 5.68 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
44 45 6.095860 TGAATCTAATCAGCTTGGTGGATTTG 59.904 38.462 1.98 1.28 33.59 2.32
117 118 1.278637 GAAAGGTCGTTGTGCGTGG 59.721 57.895 0.00 0.00 42.13 4.94
142 143 4.284234 CCAAAGGAAATGAAATGTGACCCT 59.716 41.667 0.00 0.00 0.00 4.34
153 155 7.395190 TGAAATGTGACCCTCAAATTATCAG 57.605 36.000 0.00 0.00 33.37 2.90
163 165 5.067023 CCCTCAAATTATCAGGAAGACAAGC 59.933 44.000 0.00 0.00 0.00 4.01
183 185 2.422127 GCGTTGGCCAAGCTTAGAATTA 59.578 45.455 21.21 0.00 0.00 1.40
188 190 5.065613 TGGCCAAGCTTAGAATTATCCAT 57.934 39.130 0.61 0.00 0.00 3.41
253 257 5.297547 TGCCGATACTATCAAAAGGTGATC 58.702 41.667 0.00 0.00 44.01 2.92
256 260 6.516718 CCGATACTATCAAAAGGTGATCAGT 58.483 40.000 0.00 0.00 44.01 3.41
262 266 6.820656 ACTATCAAAAGGTGATCAGTAAGCTG 59.179 38.462 0.00 0.00 44.01 4.24
332 337 5.320277 CCTCAAAAGTCTTCAATTCCTCCT 58.680 41.667 0.00 0.00 0.00 3.69
338 343 9.103861 CAAAAGTCTTCAATTCCTCCTCTATAC 57.896 37.037 0.00 0.00 0.00 1.47
384 389 1.293498 GCCAAGCTCTTCCAGTCGA 59.707 57.895 0.00 0.00 0.00 4.20
406 411 0.321564 CCACCGAGCAGTTCATCCAA 60.322 55.000 0.00 0.00 0.00 3.53
440 445 2.543777 AACGCTAGAACTTTGGAGCA 57.456 45.000 0.00 0.00 34.49 4.26
461 466 4.503910 CACCAATCATTCTACTCGGAACA 58.496 43.478 0.00 0.00 0.00 3.18
504 509 3.067106 TCTGTTGTCCGCTCAGAATTTC 58.933 45.455 0.00 0.00 35.65 2.17
526 531 1.186267 AACACCCCTCACTCGGAGTC 61.186 60.000 7.89 0.00 42.40 3.36
533 538 0.172352 CTCACTCGGAGTCCTGAAGC 59.828 60.000 7.89 0.00 38.90 3.86
556 561 3.447918 TTATAGAGAGGGAAAACGGCG 57.552 47.619 4.80 4.80 0.00 6.46
557 562 0.464452 ATAGAGAGGGAAAACGGCGG 59.536 55.000 13.24 0.00 0.00 6.13
623 635 1.135972 CCTAATGCTTCGTGTGTGTGC 60.136 52.381 0.00 0.00 0.00 4.57
624 636 1.530720 CTAATGCTTCGTGTGTGTGCA 59.469 47.619 0.00 0.00 38.05 4.57
671 735 6.873997 ACAACTATCATCGTTGGATTCACTA 58.126 36.000 6.96 0.00 44.49 2.74
683 747 6.293081 CGTTGGATTCACTATGATGTTCCATC 60.293 42.308 6.53 0.00 34.87 3.51
737 801 2.702093 ACCTGAGCCATAGGTGCTT 58.298 52.632 3.57 0.00 46.48 3.91
749 813 1.680338 AGGTGCTTCCTGTGTGTTTC 58.320 50.000 0.46 0.00 46.19 2.78
775 839 2.681848 GAGCTGTCATCACCCTCATTTG 59.318 50.000 0.00 0.00 0.00 2.32
777 841 1.747355 CTGTCATCACCCTCATTTGCC 59.253 52.381 0.00 0.00 0.00 4.52
830 895 3.831715 AGCTTCAAATACAGCGGAAAC 57.168 42.857 0.00 0.00 41.24 2.78
907 972 0.251121 TCCCAAGCGCCAATCAAAGA 60.251 50.000 2.29 0.00 0.00 2.52
919 984 4.439700 GCCAATCAAAGACCATCATCACTG 60.440 45.833 0.00 0.00 0.00 3.66
1289 1362 1.993369 GCCATTGGCCGTCAGTTAGC 61.993 60.000 17.28 0.00 44.06 3.09
1297 1374 1.799548 GCCGTCAGTTAGCTAGCTGTC 60.800 57.143 29.65 24.60 36.17 3.51
1341 1418 0.106918 GTGGTGGTTGGACTTGGACA 60.107 55.000 0.00 0.00 0.00 4.02
1357 1434 0.537188 GACATCGTGATGGTGGAGGT 59.463 55.000 13.95 0.00 42.91 3.85
1363 1440 0.107017 GTGATGGTGGAGGTCATGGG 60.107 60.000 0.00 0.00 0.00 4.00
1435 1512 1.216710 GAGGAAGGTGCTGGAGTCG 59.783 63.158 0.00 0.00 0.00 4.18
1474 1551 2.599677 GAGAGGATACGAGACCCCAAT 58.400 52.381 0.00 0.00 46.39 3.16
1478 1555 4.087182 GAGGATACGAGACCCCAATATCA 58.913 47.826 0.00 0.00 46.39 2.15
1498 1575 2.238084 TCTACCCTGACTGTGAGCAT 57.762 50.000 0.00 0.00 0.00 3.79
1501 1600 1.222936 CCCTGACTGTGAGCATCCC 59.777 63.158 0.00 0.00 0.00 3.85
1509 1608 0.615331 TGTGAGCATCCCCACTTCTC 59.385 55.000 0.00 0.00 34.57 2.87
1518 1617 1.674057 CCCACTTCTCCGTCAGCTT 59.326 57.895 0.00 0.00 0.00 3.74
1519 1619 0.895530 CCCACTTCTCCGTCAGCTTA 59.104 55.000 0.00 0.00 0.00 3.09
1523 1623 4.003648 CCACTTCTCCGTCAGCTTATTTT 58.996 43.478 0.00 0.00 0.00 1.82
1584 1696 6.178239 AGTATCAATCGCACAAAGTTTACC 57.822 37.500 0.00 0.00 0.00 2.85
1585 1697 5.703592 AGTATCAATCGCACAAAGTTTACCA 59.296 36.000 0.00 0.00 0.00 3.25
1599 1711 9.520515 ACAAAGTTTACCATGAGAAGATTATGT 57.479 29.630 0.00 0.00 0.00 2.29
1606 1718 9.739276 TTACCATGAGAAGATTATGTTTTCACT 57.261 29.630 0.00 0.00 0.00 3.41
1607 1719 8.048534 ACCATGAGAAGATTATGTTTTCACTG 57.951 34.615 0.00 0.01 0.00 3.66
1608 1720 6.971184 CCATGAGAAGATTATGTTTTCACTGC 59.029 38.462 0.00 0.00 0.00 4.40
1609 1721 6.500684 TGAGAAGATTATGTTTTCACTGCC 57.499 37.500 0.00 0.00 0.00 4.85
1610 1722 5.415701 TGAGAAGATTATGTTTTCACTGCCC 59.584 40.000 0.00 0.00 0.00 5.36
1611 1723 5.574188 AGAAGATTATGTTTTCACTGCCCT 58.426 37.500 0.00 0.00 0.00 5.19
1612 1724 6.012745 AGAAGATTATGTTTTCACTGCCCTT 58.987 36.000 0.00 0.00 0.00 3.95
1613 1725 7.175104 AGAAGATTATGTTTTCACTGCCCTTA 58.825 34.615 0.00 0.00 0.00 2.69
1614 1726 7.836183 AGAAGATTATGTTTTCACTGCCCTTAT 59.164 33.333 0.00 0.00 0.00 1.73
1615 1727 7.338800 AGATTATGTTTTCACTGCCCTTATG 57.661 36.000 0.00 0.00 0.00 1.90
1616 1728 6.891908 AGATTATGTTTTCACTGCCCTTATGT 59.108 34.615 0.00 0.00 0.00 2.29
1625 1737 4.764823 TCACTGCCCTTATGTTTTTACCTG 59.235 41.667 0.00 0.00 0.00 4.00
1628 1740 3.898123 TGCCCTTATGTTTTTACCTGCAA 59.102 39.130 0.00 0.00 0.00 4.08
1653 1765 3.489738 GCACCTCCAATTCGATGATTTGG 60.490 47.826 12.15 12.15 41.59 3.28
1680 1792 6.360947 CGACACGATACTGAAATATCAAGGAG 59.639 42.308 0.00 0.00 34.49 3.69
1681 1793 7.348080 ACACGATACTGAAATATCAAGGAGA 57.652 36.000 0.00 0.00 34.49 3.71
1683 1795 6.360947 CACGATACTGAAATATCAAGGAGACG 59.639 42.308 0.00 0.00 34.49 4.18
1771 1883 3.744660 GGAACCTATCATGGCTGGTAAG 58.255 50.000 0.00 0.00 31.82 2.34
1798 1910 3.193691 CGTTTGCTTCCCTCTCTTCTCTA 59.806 47.826 0.00 0.00 0.00 2.43
1799 1911 4.500127 GTTTGCTTCCCTCTCTTCTCTAC 58.500 47.826 0.00 0.00 0.00 2.59
1824 1936 6.565435 CGCACTTGTGATAATTCAGATCCATC 60.565 42.308 4.79 0.00 30.85 3.51
1882 1995 7.784633 TTTTTCTTTTAGGTTTGCCATTCTG 57.215 32.000 0.00 0.00 37.19 3.02
1935 2048 9.793259 AGAACATTTTATCTGAACTCCTGTTTA 57.207 29.630 0.00 0.00 36.39 2.01
2101 2214 2.497675 GGAGCATCACCTCAAGTACTCA 59.502 50.000 0.00 0.00 36.25 3.41
2232 2345 4.717877 TCTCTTGCCACATCTCTGAAAAA 58.282 39.130 0.00 0.00 0.00 1.94
2235 2348 3.581024 TGCCACATCTCTGAAAAATGC 57.419 42.857 0.00 0.00 0.00 3.56
2274 2388 6.322712 AGTGTCTGCTAATGTTTTGGGTAAAA 59.677 34.615 0.00 0.00 33.57 1.52
2296 2410 7.552848 AAACGATCAAATCTTGTGAAAATCG 57.447 32.000 0.00 0.00 33.42 3.34
2407 2632 4.686554 CCATGCTCTTACCGCTTATCTTAC 59.313 45.833 0.00 0.00 0.00 2.34
2408 2633 4.317671 TGCTCTTACCGCTTATCTTACC 57.682 45.455 0.00 0.00 0.00 2.85
2409 2634 3.702548 TGCTCTTACCGCTTATCTTACCA 59.297 43.478 0.00 0.00 0.00 3.25
2477 2711 6.265196 GCATATTGATGATTCCTTGGTTGGTA 59.735 38.462 0.00 0.00 34.73 3.25
2514 2748 5.933463 TGCTAATTTGGAGCTTTTTCAATGG 59.067 36.000 0.69 0.00 40.76 3.16
2578 2812 4.542662 CACAGAAGGAAGAACAACTGTG 57.457 45.455 0.00 0.00 45.20 3.66
2765 3008 7.048512 ACCAACCAATGTAGTCTAATTAGCTC 58.951 38.462 7.67 3.85 0.00 4.09
2786 3029 5.936956 GCTCATACCCTCAATAATCTTGGAG 59.063 44.000 0.00 0.00 0.00 3.86
2800 3043 5.883875 ATCTTGGAGAGGGAGATAGAGAT 57.116 43.478 0.00 0.00 0.00 2.75
2896 3164 6.964807 AGTGATATGCCTATTTTTGCATCA 57.035 33.333 0.00 0.00 44.58 3.07
2969 3240 9.250246 TGAAAAATAAGTAAATTACAGGGGGAG 57.750 33.333 5.89 0.00 0.00 4.30
3024 3297 9.680315 CCATTTAAGTACAAAATGAAACGGTAA 57.320 29.630 24.35 0.00 43.79 2.85
3031 3304 9.010029 AGTACAAAATGAAACGGTAATTCTCAT 57.990 29.630 0.00 0.00 0.00 2.90
3054 3327 1.875963 GCACTAATGCCGCAAGTGT 59.124 52.632 20.95 7.99 46.97 3.55
3065 3338 5.984233 TGCCGCAAGTGTAATTCTATAAG 57.016 39.130 0.00 0.00 0.00 1.73
3072 3345 6.316390 GCAAGTGTAATTCTATAAGCACCTGT 59.684 38.462 0.00 0.00 0.00 4.00
3093 3366 2.740055 GCCACGAGTGTCCAGCAG 60.740 66.667 2.36 0.00 0.00 4.24
3113 3386 3.686726 CAGGAGCAATAATCGGATTAGCC 59.313 47.826 15.08 10.76 0.00 3.93
3129 3402 6.213138 GGATTAGCCAAGGAAGCATTCAGAT 61.213 44.000 0.00 0.00 41.49 2.90
3186 3459 7.284351 CGACAACTCAGTAAGAAAATTCAGTC 58.716 38.462 0.00 0.00 0.00 3.51
3270 3543 8.504005 ACATCTAACTTCGTTTCCTTTTGTATG 58.496 33.333 0.00 0.00 0.00 2.39
3282 3555 0.319986 TTTGTATGTGTGCTCGCCGA 60.320 50.000 0.00 0.00 0.00 5.54
3337 3610 3.935828 AGCGAAATTTACTGAAGCTCCTC 59.064 43.478 0.00 0.00 0.00 3.71
3366 3639 1.625315 CTCACTCACATTGACTGGGGA 59.375 52.381 0.00 0.00 0.00 4.81
3443 3716 2.029964 GAGCACCGAACCGTTCCA 59.970 61.111 5.67 0.00 0.00 3.53
3558 3831 1.200760 TCACTGCCACTGTGCCCTAT 61.201 55.000 1.29 0.00 34.16 2.57
3670 3943 6.151817 AGGAAGAAAATGATCCTGCAACTTAC 59.848 38.462 0.00 0.00 41.96 2.34
3682 3955 5.003804 CCTGCAACTTACCTACAGAAATGT 58.996 41.667 0.00 0.00 0.00 2.71
3836 4110 2.426738 CAACCAGGAAGACAACTTTGCA 59.573 45.455 0.00 0.00 36.39 4.08
3975 4253 6.412362 AGTTCCTAGATGTATTGCTTCGAT 57.588 37.500 0.00 0.00 0.00 3.59
3976 4254 6.451393 AGTTCCTAGATGTATTGCTTCGATC 58.549 40.000 0.00 0.00 0.00 3.69
3977 4255 5.048153 TCCTAGATGTATTGCTTCGATCG 57.952 43.478 9.36 9.36 0.00 3.69
3978 4256 4.760204 TCCTAGATGTATTGCTTCGATCGA 59.240 41.667 15.15 15.15 0.00 3.59
3981 4259 4.938080 AGATGTATTGCTTCGATCGACTT 58.062 39.130 19.26 3.08 0.00 3.01
3992 4270 2.161808 TCGATCGACTTGTTCACTCTCC 59.838 50.000 15.15 0.00 0.00 3.71
4039 4319 1.005037 TGCTCATTGAAGTCGCCGT 60.005 52.632 0.00 0.00 0.00 5.68
4127 4407 4.056125 CAGTCGAGTGGGCGCTCA 62.056 66.667 5.44 5.44 35.33 4.26
4144 4424 1.175983 TCACGGTTTTCATGGCACCC 61.176 55.000 0.00 0.00 0.00 4.61
4357 4637 2.202932 ATGCCGCAGCCGTAGAAG 60.203 61.111 0.00 0.00 38.69 2.85
4359 4639 4.143333 GCCGCAGCCGTAGAAGGA 62.143 66.667 0.00 0.00 0.00 3.36
4447 4727 1.532007 GAGAGGCCGTAGTCGATGTAG 59.468 57.143 0.00 0.00 39.71 2.74
4448 4728 0.592148 GAGGCCGTAGTCGATGTAGG 59.408 60.000 0.00 0.00 39.71 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 8.206189 CCAATAATTATTCAAATCCACCAAGCT 58.794 33.333 7.76 0.00 0.00 3.74
64 65 8.312669 ACTAGATAAGCATTAGTTCCTTGAGT 57.687 34.615 0.00 0.00 31.76 3.41
107 108 1.098712 TCCTTTGGTCCACGCACAAC 61.099 55.000 0.00 0.00 0.00 3.32
117 118 5.230182 GGTCACATTTCATTTCCTTTGGTC 58.770 41.667 0.00 0.00 0.00 4.02
142 143 5.245531 ACGCTTGTCTTCCTGATAATTTGA 58.754 37.500 0.00 0.00 0.00 2.69
153 155 1.452145 TTGGCCAACGCTTGTCTTCC 61.452 55.000 16.05 0.00 34.44 3.46
163 165 4.261197 GGATAATTCTAAGCTTGGCCAACG 60.261 45.833 16.05 12.18 0.00 4.10
213 216 8.094548 AGTATCGGCATGCTTATAAACTCAATA 58.905 33.333 18.92 0.00 0.00 1.90
222 225 7.549134 CCTTTTGATAGTATCGGCATGCTTATA 59.451 37.037 18.92 12.47 0.00 0.98
232 235 6.516718 ACTGATCACCTTTTGATAGTATCGG 58.483 40.000 5.68 3.37 45.67 4.18
256 260 4.708177 AGAAAGAAACTCAGCACAGCTTA 58.292 39.130 0.00 0.00 36.40 3.09
262 266 7.195839 ACTCAAATAGAAAGAAACTCAGCAC 57.804 36.000 0.00 0.00 0.00 4.40
302 306 3.811083 TGAAGACTTTTGAGGGCGTTTA 58.189 40.909 0.00 0.00 0.00 2.01
306 310 3.366374 GGAATTGAAGACTTTTGAGGGCG 60.366 47.826 0.00 0.00 0.00 6.13
338 343 9.021807 TCTCCGAATATATGAAAGTTAGGTAGG 57.978 37.037 0.00 0.00 0.00 3.18
356 361 0.835941 AGAGCTTGGCATCTCCGAAT 59.164 50.000 12.00 0.00 37.80 3.34
384 389 1.523758 GATGAACTGCTCGGTGGTTT 58.476 50.000 0.00 0.00 0.00 3.27
424 429 2.185004 TGGTGCTCCAAAGTTCTAGC 57.815 50.000 4.68 0.00 41.25 3.42
440 445 4.819105 TGTTCCGAGTAGAATGATTGGT 57.181 40.909 0.00 0.00 0.00 3.67
504 509 2.261671 CGAGTGAGGGGTGTTCGG 59.738 66.667 0.00 0.00 0.00 4.30
526 531 3.637229 TCCCTCTCTATAAACGCTTCAGG 59.363 47.826 0.00 0.00 0.00 3.86
533 538 3.554731 GCCGTTTTCCCTCTCTATAAACG 59.445 47.826 10.43 10.43 46.16 3.60
644 708 2.536365 TCCAACGATGATAGTTGTCGC 58.464 47.619 15.50 0.00 45.31 5.19
656 720 5.760253 GGAACATCATAGTGAATCCAACGAT 59.240 40.000 0.00 0.00 32.61 3.73
737 801 1.475034 GCTCACCAGAAACACACAGGA 60.475 52.381 0.00 0.00 0.00 3.86
744 808 2.104622 TGATGACAGCTCACCAGAAACA 59.895 45.455 0.00 0.00 0.00 2.83
775 839 7.233389 AGAAAGGGAAAGAGAAATAAAAGGC 57.767 36.000 0.00 0.00 0.00 4.35
874 939 1.952296 CTTGGGATTGTGCTGCTATCC 59.048 52.381 15.82 15.82 45.01 2.59
907 972 0.254178 GTGGCTCCAGTGATGATGGT 59.746 55.000 0.00 0.00 39.01 3.55
1286 1359 0.395862 AGAAGCCCGACAGCTAGCTA 60.396 55.000 18.86 0.00 44.11 3.32
1289 1362 1.064946 CGAGAAGCCCGACAGCTAG 59.935 63.158 0.00 0.00 44.11 3.42
1297 1374 1.448540 ATTGCTGACGAGAAGCCCG 60.449 57.895 0.00 0.00 40.06 6.13
1341 1418 1.139654 CATGACCTCCACCATCACGAT 59.860 52.381 0.00 0.00 0.00 3.73
1357 1434 3.785325 TCCTGGATAACAATCACCCATGA 59.215 43.478 0.00 0.00 39.83 3.07
1363 1440 1.940613 GCCGTCCTGGATAACAATCAC 59.059 52.381 0.00 0.00 42.00 3.06
1435 1512 0.727122 CGAACACCTCGTACACGTCC 60.727 60.000 1.19 0.00 42.89 4.79
1463 1540 3.195825 GGGTAGATGATATTGGGGTCTCG 59.804 52.174 0.00 0.00 0.00 4.04
1474 1551 3.891977 GCTCACAGTCAGGGTAGATGATA 59.108 47.826 0.00 0.00 0.00 2.15
1478 1555 2.238084 TGCTCACAGTCAGGGTAGAT 57.762 50.000 0.00 0.00 0.00 1.98
1498 1575 2.283529 GCTGACGGAGAAGTGGGGA 61.284 63.158 0.00 0.00 0.00 4.81
1501 1600 2.969628 ATAAGCTGACGGAGAAGTGG 57.030 50.000 0.00 0.00 0.00 4.00
1584 1696 6.971184 GGCAGTGAAAACATAATCTTCTCATG 59.029 38.462 0.00 0.00 0.00 3.07
1585 1697 6.096001 GGGCAGTGAAAACATAATCTTCTCAT 59.904 38.462 0.00 0.00 0.00 2.90
1599 1711 6.325286 AGGTAAAAACATAAGGGCAGTGAAAA 59.675 34.615 0.00 0.00 0.00 2.29
1600 1712 5.836358 AGGTAAAAACATAAGGGCAGTGAAA 59.164 36.000 0.00 0.00 0.00 2.69
1601 1713 5.242838 CAGGTAAAAACATAAGGGCAGTGAA 59.757 40.000 0.00 0.00 0.00 3.18
1602 1714 4.764823 CAGGTAAAAACATAAGGGCAGTGA 59.235 41.667 0.00 0.00 0.00 3.41
1603 1715 4.618227 GCAGGTAAAAACATAAGGGCAGTG 60.618 45.833 0.00 0.00 0.00 3.66
1604 1716 3.509967 GCAGGTAAAAACATAAGGGCAGT 59.490 43.478 0.00 0.00 0.00 4.40
1605 1717 3.509575 TGCAGGTAAAAACATAAGGGCAG 59.490 43.478 0.00 0.00 0.00 4.85
1606 1718 3.501349 TGCAGGTAAAAACATAAGGGCA 58.499 40.909 0.00 0.00 0.00 5.36
1607 1719 4.529109 TTGCAGGTAAAAACATAAGGGC 57.471 40.909 0.00 0.00 0.00 5.19
1608 1720 5.351189 GCAATTGCAGGTAAAAACATAAGGG 59.649 40.000 25.36 0.00 41.59 3.95
1609 1721 6.407475 GCAATTGCAGGTAAAAACATAAGG 57.593 37.500 25.36 0.00 41.59 2.69
1625 1737 1.202114 TCGAATTGGAGGTGCAATTGC 59.798 47.619 23.69 23.69 42.50 3.56
1628 1740 3.003394 TCATCGAATTGGAGGTGCAAT 57.997 42.857 2.04 0.00 0.00 3.56
1653 1765 6.142480 CCTTGATATTTCAGTATCGTGTCGAC 59.858 42.308 9.11 9.11 33.90 4.20
1680 1792 4.787598 CAAGCCATATTAATGCTTCCGTC 58.212 43.478 8.19 0.00 31.40 4.79
1681 1793 3.004734 GCAAGCCATATTAATGCTTCCGT 59.995 43.478 8.19 0.00 31.40 4.69
1683 1795 4.861102 AGCAAGCCATATTAATGCTTCC 57.139 40.909 8.19 1.15 44.43 3.46
1771 1883 0.036858 AGAGGGAAGCAAACGAGAGC 60.037 55.000 0.00 0.00 0.00 4.09
1772 1884 1.548269 AGAGAGGGAAGCAAACGAGAG 59.452 52.381 0.00 0.00 0.00 3.20
1773 1885 1.633774 AGAGAGGGAAGCAAACGAGA 58.366 50.000 0.00 0.00 0.00 4.04
1774 1886 2.028567 AGAAGAGAGGGAAGCAAACGAG 60.029 50.000 0.00 0.00 0.00 4.18
1775 1887 1.971357 AGAAGAGAGGGAAGCAAACGA 59.029 47.619 0.00 0.00 0.00 3.85
1776 1888 2.028567 AGAGAAGAGAGGGAAGCAAACG 60.029 50.000 0.00 0.00 0.00 3.60
1798 1910 4.572389 GGATCTGAATTATCACAAGTGCGT 59.428 41.667 0.00 0.00 0.00 5.24
1799 1911 4.571984 TGGATCTGAATTATCACAAGTGCG 59.428 41.667 0.00 0.00 0.00 5.34
1824 1936 9.845305 CTTTTAAAACTGAAGTACTTACACTCG 57.155 33.333 8.42 0.70 0.00 4.18
1852 1965 9.845740 ATGGCAAACCTAAAAGAAAAATAACTT 57.154 25.926 0.00 0.00 36.63 2.66
1882 1995 2.031682 GCATGTCTTCCGGAACATATGC 60.032 50.000 28.69 28.69 33.83 3.14
1908 2021 7.678947 ACAGGAGTTCAGATAAAATGTTCTG 57.321 36.000 0.00 0.00 40.58 3.02
2101 2214 1.075601 TGATCTGGCAGTTTTCCCCT 58.924 50.000 15.27 0.00 0.00 4.79
2235 2348 2.874701 CAGACACTGAACCTTGACAAGG 59.125 50.000 29.13 29.13 43.52 3.61
2274 2388 6.241207 ACGATTTTCACAAGATTTGATCGT 57.759 33.333 8.65 8.65 33.53 3.73
2296 2410 5.991933 TTATCAGAGATCCTGGATGCTAC 57.008 43.478 15.25 0.00 43.12 3.58
2407 2632 9.773328 CAATATGTTAACAACTTCATGTAGTGG 57.227 33.333 13.23 5.52 32.02 4.00
2477 2711 9.933723 GCTCCAAATTAGCAAATCCATATAAAT 57.066 29.630 0.00 0.00 39.83 1.40
2514 2748 3.191791 GGCGATAGATCTAGTCCCTTGAC 59.808 52.174 8.70 0.00 39.43 3.18
2578 2812 1.445871 ACGAATAGGGTTTTGCCGAC 58.554 50.000 0.00 0.00 38.44 4.79
2604 2838 0.040425 GTCGCTTCACCGTTTGCATT 60.040 50.000 0.00 0.00 0.00 3.56
2741 2984 7.047891 TGAGCTAATTAGACTACATTGGTTGG 58.952 38.462 16.85 0.00 0.00 3.77
2765 3008 6.471146 CCTCTCCAAGATTATTGAGGGTATG 58.529 44.000 0.00 0.00 37.87 2.39
2808 3051 6.785191 TCAACATTTTCAGTCTCTTTCACAC 58.215 36.000 0.00 0.00 0.00 3.82
2809 3052 7.389803 TTCAACATTTTCAGTCTCTTTCACA 57.610 32.000 0.00 0.00 0.00 3.58
2810 3053 6.416161 GCTTCAACATTTTCAGTCTCTTTCAC 59.584 38.462 0.00 0.00 0.00 3.18
2811 3054 6.498304 GCTTCAACATTTTCAGTCTCTTTCA 58.502 36.000 0.00 0.00 0.00 2.69
2812 3055 5.622856 CGCTTCAACATTTTCAGTCTCTTTC 59.377 40.000 0.00 0.00 0.00 2.62
3019 3290 7.957615 CATTAGTGCTGATATGAGAATTACCG 58.042 38.462 0.00 0.00 0.00 4.02
3072 3345 1.964448 CTGGACACTCGTGGCACTA 59.036 57.895 16.72 3.47 41.42 2.74
3093 3366 3.674997 TGGCTAATCCGATTATTGCTCC 58.325 45.455 10.55 5.20 37.80 4.70
3113 3386 5.352569 ACGAAGTAATCTGAATGCTTCCTTG 59.647 40.000 15.07 6.67 41.94 3.61
3129 3402 2.757262 TGGTTCCTCCTGGACGAAGTAA 60.757 50.000 8.17 0.00 43.06 2.24
3186 3459 9.490379 GGTACAGTAACTGATTAATATTGGGAG 57.510 37.037 0.00 0.00 35.18 4.30
3282 3555 4.479158 TGGAGTACTTTTGATTTGGGCTT 58.521 39.130 0.00 0.00 0.00 4.35
3287 3560 6.715264 AGGTTACCTGGAGTACTTTTGATTTG 59.285 38.462 1.74 0.00 29.57 2.32
3337 3610 4.391216 GTCAATGTGAGTGAGAACCAGATG 59.609 45.833 0.00 0.00 0.00 2.90
3366 3639 8.891720 TGAAACGGTAGTAACAATTTGTTAGTT 58.108 29.630 26.45 19.71 42.13 2.24
3443 3716 2.025155 CCAGCATGTAGTACTCGTCCT 58.975 52.381 0.00 0.00 0.00 3.85
3558 3831 2.161855 GAACCATGGTGATGCAGTCAA 58.838 47.619 20.60 0.00 38.90 3.18
3590 3863 6.994868 TTGTGACTGTTTACAACACAAAAC 57.005 33.333 21.50 5.04 43.24 2.43
3670 3943 5.129485 AGGGAGTACATCACATTTCTGTAGG 59.871 44.000 0.00 0.00 31.63 3.18
3682 3955 3.021695 CACTAACGGAGGGAGTACATCA 58.978 50.000 0.00 0.00 0.00 3.07
3765 4038 6.263168 AGACTTCAAATGTTTTCCTCGTGATT 59.737 34.615 0.00 0.00 0.00 2.57
3975 4253 2.095212 CGATGGAGAGTGAACAAGTCGA 60.095 50.000 0.00 0.00 33.01 4.20
3976 4254 2.254459 CGATGGAGAGTGAACAAGTCG 58.746 52.381 0.00 0.00 33.01 4.18
3977 4255 2.028930 ACCGATGGAGAGTGAACAAGTC 60.029 50.000 0.00 0.00 0.00 3.01
3978 4256 1.971357 ACCGATGGAGAGTGAACAAGT 59.029 47.619 0.00 0.00 0.00 3.16
4110 4390 4.056125 TGAGCGCCCACTCGACTG 62.056 66.667 2.29 0.00 39.68 3.51
4127 4407 1.906333 GGGGTGCCATGAAAACCGT 60.906 57.895 0.00 0.00 34.62 4.83
4144 4424 1.082117 GTGGCTACAACGATGACGGG 61.082 60.000 0.00 0.00 44.46 5.28
4219 4499 0.730840 GCCACAACCAATACTACGCC 59.269 55.000 0.00 0.00 0.00 5.68
4357 4637 2.817423 CGGCGCTCAAGCTGATTCC 61.817 63.158 7.64 0.00 45.94 3.01
4359 4639 2.265739 TCGGCGCTCAAGCTGATT 59.734 55.556 7.64 0.00 46.50 2.57
4376 4656 1.211457 GAGTCACAGCCAGGGATTCAT 59.789 52.381 0.00 0.00 36.47 2.57


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

AutoCloner maintained by Alex Coulton.