Multiple sequence alignment - TraesCS3A01G244200

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 TraesCS3A01G244200 chr3A 100.000 4116 0 0 1 4116 457487819 457483704 0.000000e+00 7601.0
1 TraesCS3A01G244200 chr3B 91.742 2979 173 38 390 3336 445595121 445598058 0.000000e+00 4071.0
2 TraesCS3A01G244200 chr3B 91.582 594 26 9 3338 3918 445598140 445598722 0.000000e+00 798.0
3 TraesCS3A01G244200 chr3B 91.593 226 14 1 1 221 445594496 445594721 1.440000e-79 307.0
4 TraesCS3A01G244200 chr3B 90.000 210 7 5 3907 4116 445598745 445598940 4.080000e-65 259.0
5 TraesCS3A01G244200 chr3B 93.269 104 6 1 212 315 445594884 445594986 7.130000e-33 152.0
6 TraesCS3A01G244200 chr3D 91.980 2444 134 32 390 2801 346311118 346313531 0.000000e+00 3371.0
7 TraesCS3A01G244200 chr3D 93.233 1330 57 21 2800 4116 346313692 346315001 0.000000e+00 1927.0
8 TraesCS3A01G244200 chr3D 94.087 389 21 2 1 387 346310686 346311074 1.270000e-164 590.0
9 TraesCS3A01G244200 chr1A 100.000 29 0 0 652 680 482257132 482257160 2.000000e-03 54.7


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 TraesCS3A01G244200 chr3A 457483704 457487819 4115 True 7601.000000 7601 100.0000 1 4116 1 chr3A.!!$R1 4115
1 TraesCS3A01G244200 chr3B 445594496 445598940 4444 False 1117.400000 4071 91.6372 1 4116 5 chr3B.!!$F1 4115
2 TraesCS3A01G244200 chr3D 346310686 346315001 4315 False 1962.666667 3371 93.1000 1 4116 3 chr3D.!!$F1 4115

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
392 599 0.107410 AACACTCACAAGGCCACGAA 60.107 50.0 5.01 0.0 0.00 3.85 F
971 1224 0.179145 TCTTCGATTCGTTCTCCGGC 60.179 55.0 5.89 0.0 37.11 6.13 F
1401 1669 0.243095 GAGTACCTGGACGACACCAC 59.757 60.0 0.00 0.0 35.91 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2008 2310 0.552363 CCATCACCCCACATCATCCA 59.448 55.0 0.0 0.0 0.00 3.41 R
2490 2793 0.034476 TGCAGAGCAGACAGTTGAGG 59.966 55.0 0.0 0.0 33.32 3.86 R
3374 3928 0.453950 CGTCCAACAGTCCTACGACG 60.454 60.0 0.0 0.0 44.28 5.12 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
184 192 9.991388 GAACCGAGATAATGATACTACTCATAC 57.009 37.037 0.00 0.00 34.79 2.39
261 441 1.273327 GGTGTCCAAAATGAAGCTGGG 59.727 52.381 0.00 0.00 0.00 4.45
300 480 2.100749 TGCGGTCATACAGATGGTACTG 59.899 50.000 0.00 0.00 42.78 2.74
315 495 8.820933 CAGATGGTACTGATTGTTTACTGTATG 58.179 37.037 0.00 0.00 39.94 2.39
322 529 8.970691 ACTGATTGTTTACTGTATGCAAAATC 57.029 30.769 0.00 4.41 0.00 2.17
325 532 7.536964 TGATTGTTTACTGTATGCAAAATCGTG 59.463 33.333 0.00 0.00 0.00 4.35
343 550 2.734175 CGTGAAGTATGCGCAGTAGGAA 60.734 50.000 18.32 0.00 0.00 3.36
351 558 3.165058 TGCGCAGTAGGAAATCAGTAG 57.835 47.619 5.66 0.00 0.00 2.57
367 574 9.160496 GAAATCAGTAGAATCACTTCACATTCT 57.840 33.333 0.00 0.00 41.35 2.40
368 575 8.489990 AATCAGTAGAATCACTTCACATTCTG 57.510 34.615 4.73 0.00 39.28 3.02
388 595 2.171659 TGAAGTAACACTCACAAGGCCA 59.828 45.455 5.01 0.00 0.00 5.36
392 599 0.107410 AACACTCACAAGGCCACGAA 60.107 50.000 5.01 0.00 0.00 3.85
443 691 1.227556 GCGCATAACCTCGTCCCAT 60.228 57.895 0.30 0.00 0.00 4.00
626 874 0.976590 AGGTTCTAGGGAGGCGGAAC 60.977 60.000 0.00 0.00 37.79 3.62
812 1060 3.181520 CGTCCGATCCAAAATCAACAGTC 60.182 47.826 0.00 0.00 0.00 3.51
813 1061 3.751175 GTCCGATCCAAAATCAACAGTCA 59.249 43.478 0.00 0.00 0.00 3.41
864 1112 7.808381 TGACGCAAAATTTTATACCGAATGAAA 59.192 29.630 2.44 0.00 0.00 2.69
885 1137 9.778993 ATGAAATGAAATAGAACGAAACATCAG 57.221 29.630 0.00 0.00 0.00 2.90
959 1212 1.395826 CCTCCTCCGCCTTCTTCGAT 61.396 60.000 0.00 0.00 0.00 3.59
962 1215 0.872021 CCTCCGCCTTCTTCGATTCG 60.872 60.000 0.00 0.00 0.00 3.34
968 1221 1.927838 GCCTTCTTCGATTCGTTCTCC 59.072 52.381 5.89 0.00 0.00 3.71
970 1223 2.186076 CTTCTTCGATTCGTTCTCCGG 58.814 52.381 5.89 0.00 37.11 5.14
971 1224 0.179145 TCTTCGATTCGTTCTCCGGC 60.179 55.000 5.89 0.00 37.11 6.13
974 1227 2.585247 GATTCGTTCTCCGGCCCG 60.585 66.667 0.00 0.00 37.11 6.13
1023 1289 0.464013 CGACTCTCTTCCTCGCCCTA 60.464 60.000 0.00 0.00 0.00 3.53
1035 1301 2.345991 GCCCTACAGTGCGTGGAA 59.654 61.111 0.00 0.00 0.00 3.53
1075 1343 3.059982 CCTCGACCAAGCAGTCCA 58.940 61.111 0.00 0.00 32.91 4.02
1088 1356 0.673644 CAGTCCACCGATTTCCGCTT 60.674 55.000 0.00 0.00 36.84 4.68
1114 1382 2.917933 TGTTCCACCATTGATCCGATC 58.082 47.619 1.01 1.01 0.00 3.69
1349 1617 1.667154 CGGGGATCAGCAAGACGAGA 61.667 60.000 0.00 0.00 0.00 4.04
1375 1643 1.124477 GGGAGAGGAAGCGGATGGAT 61.124 60.000 0.00 0.00 0.00 3.41
1400 1668 1.239296 CGAGTACCTGGACGACACCA 61.239 60.000 0.00 0.00 38.33 4.17
1401 1669 0.243095 GAGTACCTGGACGACACCAC 59.757 60.000 0.00 0.00 35.91 4.16
1402 1670 1.183676 AGTACCTGGACGACACCACC 61.184 60.000 0.00 0.00 35.91 4.61
1438 1706 3.267860 CGCGGCTCTGCTGATTCC 61.268 66.667 0.00 0.00 37.02 3.01
1449 1717 1.233019 GCTGATTCCCGTGATGATGG 58.767 55.000 0.00 0.00 0.00 3.51
1450 1718 1.475751 GCTGATTCCCGTGATGATGGT 60.476 52.381 0.00 0.00 0.00 3.55
1451 1719 2.224281 GCTGATTCCCGTGATGATGGTA 60.224 50.000 0.00 0.00 0.00 3.25
1452 1720 3.557898 GCTGATTCCCGTGATGATGGTAT 60.558 47.826 0.00 0.00 0.00 2.73
1453 1721 3.999001 CTGATTCCCGTGATGATGGTATG 59.001 47.826 0.00 0.00 0.00 2.39
1454 1722 2.254546 TTCCCGTGATGATGGTATGC 57.745 50.000 0.00 0.00 0.00 3.14
1455 1723 1.127343 TCCCGTGATGATGGTATGCA 58.873 50.000 0.00 0.00 0.00 3.96
1456 1724 1.202639 TCCCGTGATGATGGTATGCAC 60.203 52.381 0.00 0.00 0.00 4.57
1457 1725 1.229428 CCGTGATGATGGTATGCACC 58.771 55.000 0.00 0.00 46.00 5.01
1505 1791 3.198068 TGGATGCTTCGAATCTGCTAAC 58.802 45.455 0.00 0.00 0.00 2.34
1506 1792 3.118629 TGGATGCTTCGAATCTGCTAACT 60.119 43.478 0.00 0.00 0.00 2.24
1541 1828 9.753674 ATCATTCAAGGTTTAATTTACAGAGGA 57.246 29.630 0.00 0.00 0.00 3.71
1611 1898 8.471609 TGTGATCTGAAATTGACATGCATTTAT 58.528 29.630 0.00 0.00 0.00 1.40
1663 1950 5.630415 ACCTATGCCAGCACTAGAATAAA 57.370 39.130 0.00 0.00 0.00 1.40
1667 1954 6.148480 CCTATGCCAGCACTAGAATAAACATC 59.852 42.308 0.00 0.00 0.00 3.06
1685 1972 6.919775 AACATCTCACAAGTTCCTAGTACT 57.080 37.500 0.00 0.00 0.00 2.73
1686 1973 6.274157 ACATCTCACAAGTTCCTAGTACTG 57.726 41.667 5.39 0.00 0.00 2.74
1689 1976 5.138276 TCTCACAAGTTCCTAGTACTGTGT 58.862 41.667 5.39 10.87 32.01 3.72
1729 2017 7.078228 GCTTATTGCCTGTTATTATTTCTCCG 58.922 38.462 0.00 0.00 35.15 4.63
1766 2054 3.129871 TGGTTAAGTTGCTGCATTTTGC 58.870 40.909 1.84 0.00 45.29 3.68
1788 2076 0.671796 TCAGGATATGGCCGTACGTG 59.328 55.000 15.21 12.61 0.00 4.49
1799 2092 1.066002 GCCGTACGTGGTATGCTTCTA 59.934 52.381 15.21 0.00 0.00 2.10
1800 2093 2.480073 GCCGTACGTGGTATGCTTCTAA 60.480 50.000 15.21 0.00 0.00 2.10
1810 2103 6.183360 CGTGGTATGCTTCTAAAAGTTGCATA 60.183 38.462 0.00 0.00 43.09 3.14
1850 2143 7.003939 GCAAATTGCATTTTCCATTACCTAC 57.996 36.000 13.73 0.00 44.26 3.18
1856 2149 7.385778 TGCATTTTCCATTACCTACTGTAAC 57.614 36.000 0.00 0.00 42.06 2.50
1861 2154 6.995511 TTCCATTACCTACTGTAACATTGC 57.004 37.500 0.00 0.00 42.06 3.56
1866 2159 3.750371 ACCTACTGTAACATTGCTTGCA 58.250 40.909 0.00 0.00 0.00 4.08
1870 2163 3.968649 ACTGTAACATTGCTTGCACAAG 58.031 40.909 6.01 6.01 41.24 3.16
1877 2170 4.444536 ACATTGCTTGCACAAGACATTTT 58.555 34.783 14.44 0.24 40.79 1.82
1878 2171 4.877251 ACATTGCTTGCACAAGACATTTTT 59.123 33.333 14.44 0.00 40.79 1.94
2028 2330 0.846015 GGATGATGTGGGGTGATGGA 59.154 55.000 0.00 0.00 0.00 3.41
2030 2332 1.212688 GATGATGTGGGGTGATGGACA 59.787 52.381 0.00 0.00 0.00 4.02
2032 2334 0.749454 GATGTGGGGTGATGGACAGC 60.749 60.000 0.00 0.00 45.06 4.40
2060 2362 2.515398 CCCTGTCTGTGGTGGCAA 59.485 61.111 0.00 0.00 0.00 4.52
2088 2390 4.786507 TGATCATGCTCTGTTTCAAAACG 58.213 39.130 0.00 0.00 41.74 3.60
2159 2462 2.039879 ACCCTGGTCTTTTACGCAGATT 59.960 45.455 0.00 0.00 31.61 2.40
2176 2479 5.230726 CGCAGATTTTGTCAAATTAGATGGC 59.769 40.000 0.00 0.00 32.35 4.40
2181 2484 7.542130 AGATTTTGTCAAATTAGATGGCGAAAC 59.458 33.333 0.00 0.00 38.28 2.78
2231 2534 9.199982 CTCAAAATTTGTTAGCATCACATTTCT 57.800 29.630 5.56 0.00 29.01 2.52
2238 2541 5.528690 TGTTAGCATCACATTTCTAGGCATC 59.471 40.000 0.00 0.00 0.00 3.91
2264 2567 2.288640 GGCCTCATTTCCAATGCATAGC 60.289 50.000 0.00 0.00 0.00 2.97
2276 2579 6.289834 TCCAATGCATAGCCCAATTATTTTG 58.710 36.000 0.00 0.00 0.00 2.44
2277 2580 6.099413 TCCAATGCATAGCCCAATTATTTTGA 59.901 34.615 0.00 0.00 0.00 2.69
2278 2581 6.766944 CCAATGCATAGCCCAATTATTTTGAA 59.233 34.615 0.00 0.00 0.00 2.69
2327 2630 6.028146 TCTCATGCTGCAATTTACAAACAT 57.972 33.333 6.36 0.00 0.00 2.71
2328 2631 7.155655 TCTCATGCTGCAATTTACAAACATA 57.844 32.000 6.36 0.00 0.00 2.29
2336 2639 8.028938 GCTGCAATTTACAAACATATATAGGGG 58.971 37.037 0.00 0.00 0.00 4.79
2354 2657 2.421529 GGGGTTGAAGTGACAACTGAGT 60.422 50.000 0.00 0.00 46.17 3.41
2453 2756 0.681243 GCCACCAATCAACCCCTCTC 60.681 60.000 0.00 0.00 0.00 3.20
2527 2830 1.466558 GCAACTTCTACTGCTGAAGGC 59.533 52.381 12.60 5.82 43.59 4.35
2546 2851 5.603170 AGGCAACATATGAAAAATCCTGG 57.397 39.130 10.38 0.00 41.41 4.45
2568 2873 3.489785 GTCACACTTTCTTACACCTGTCG 59.510 47.826 0.00 0.00 0.00 4.35
2886 3353 6.714810 TGTTTGATAGCACTATGGACTTTTGT 59.285 34.615 0.00 0.00 0.00 2.83
2904 3372 4.998671 TTGTGAATGCTTTGAGTTGGAA 57.001 36.364 0.00 0.00 0.00 3.53
3266 3738 2.684881 AGTTGACTGAGCACCAAACAAG 59.315 45.455 0.00 0.00 0.00 3.16
3279 3751 4.082245 CACCAAACAAGTCAACTCCAGTTT 60.082 41.667 0.00 0.00 35.83 2.66
3399 3953 1.153628 GGACTGTTGGACGCGCTAT 60.154 57.895 5.73 0.00 0.00 2.97
3412 3966 4.084693 GGACGCGCTATAGAAATACAAACC 60.085 45.833 5.73 0.00 0.00 3.27
3580 4145 1.884579 CTCTCAGCCATGCACAAAAGT 59.115 47.619 0.00 0.00 0.00 2.66
3613 4180 2.276732 TGCCTCTTTTCTGTTGGAGG 57.723 50.000 0.00 0.00 45.71 4.30
3782 4349 4.016444 GGCAAATCACTAAGAATGTCCCA 58.984 43.478 0.00 0.00 0.00 4.37
3798 4365 3.326297 TGTCCCATTGAAATTTCCCAACC 59.674 43.478 15.48 0.00 0.00 3.77
3845 4412 1.993370 GATCAAGTTCAGACCGTTCCG 59.007 52.381 0.00 0.00 0.00 4.30
3860 4427 2.349275 CGTTCCGTTGTTGTGTTGTAGT 59.651 45.455 0.00 0.00 0.00 2.73
3863 4430 3.191669 TCCGTTGTTGTGTTGTAGTGAG 58.808 45.455 0.00 0.00 0.00 3.51
3961 4565 2.552591 GCTGCTGCTATTGATCCATCCT 60.553 50.000 8.53 0.00 36.03 3.24
3968 4572 6.644248 TGCTATTGATCCATCCTGAATTTG 57.356 37.500 0.00 0.00 0.00 2.32
3977 4596 3.879295 CCATCCTGAATTTGCACGAGTAT 59.121 43.478 0.00 0.00 0.00 2.12
3978 4597 5.056480 CCATCCTGAATTTGCACGAGTATA 58.944 41.667 0.00 0.00 0.00 1.47
3979 4598 5.178252 CCATCCTGAATTTGCACGAGTATAG 59.822 44.000 0.00 0.00 0.00 1.31
3980 4599 5.339008 TCCTGAATTTGCACGAGTATAGT 57.661 39.130 0.00 0.00 0.00 2.12
3981 4600 5.109210 TCCTGAATTTGCACGAGTATAGTG 58.891 41.667 0.00 0.00 45.04 2.74
3988 4607 2.783828 CACGAGTATAGTGCTGGAGG 57.216 55.000 0.00 0.00 34.29 4.30
3989 4608 2.025155 CACGAGTATAGTGCTGGAGGT 58.975 52.381 0.00 0.00 34.29 3.85
3990 4609 3.211865 CACGAGTATAGTGCTGGAGGTA 58.788 50.000 0.00 0.00 34.29 3.08
4011 4630 2.125106 CACTGGTAAGCCCGGAGC 60.125 66.667 0.73 4.57 42.95 4.70
4108 4727 5.048643 CACATATTCCTCTAGTGGTACCGAG 60.049 48.000 7.57 7.46 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 55 1.794701 GCTTGCTGGCTTTGCTAAAAC 59.205 47.619 0.00 0.00 0.00 2.43
145 153 4.223320 TCTCGGTTCAAAATGCTTCAAC 57.777 40.909 0.00 0.00 0.00 3.18
184 192 8.740369 CAATTGCTAATCTTGAATTCTTAAGCG 58.260 33.333 7.05 0.00 0.00 4.68
280 460 2.361119 TCAGTACCATCTGTATGACCGC 59.639 50.000 0.00 0.00 34.84 5.68
300 480 7.748683 TCACGATTTTGCATACAGTAAACAATC 59.251 33.333 0.00 0.00 31.28 2.67
315 495 1.840141 GCGCATACTTCACGATTTTGC 59.160 47.619 0.30 0.00 0.00 3.68
322 529 1.200483 CCTACTGCGCATACTTCACG 58.800 55.000 12.24 0.00 0.00 4.35
325 532 4.119862 TGATTTCCTACTGCGCATACTTC 58.880 43.478 12.24 0.98 0.00 3.01
343 550 8.316946 TCAGAATGTGAAGTGATTCTACTGATT 58.683 33.333 0.00 0.00 36.90 2.57
367 574 2.171659 TGGCCTTGTGAGTGTTACTTCA 59.828 45.455 3.32 0.00 0.00 3.02
368 575 2.548480 GTGGCCTTGTGAGTGTTACTTC 59.452 50.000 3.32 0.00 0.00 3.01
376 583 0.180406 AACTTCGTGGCCTTGTGAGT 59.820 50.000 3.32 0.00 0.00 3.41
378 585 2.422597 CATAACTTCGTGGCCTTGTGA 58.577 47.619 3.32 0.00 0.00 3.58
388 595 3.194116 TCGCTCTTAACCCATAACTTCGT 59.806 43.478 0.00 0.00 0.00 3.85
392 599 2.158943 GCCTCGCTCTTAACCCATAACT 60.159 50.000 0.00 0.00 0.00 2.24
443 691 2.499205 CCGCTCAAGGATACGCCA 59.501 61.111 0.00 0.00 46.39 5.69
626 874 2.588856 GGATCTTCCAACCGACCCGG 62.589 65.000 3.58 3.58 44.30 5.73
766 1014 1.746991 GAAAGGGCTCTGGGCTTCG 60.747 63.158 0.00 0.00 41.46 3.79
774 1022 1.893919 GACGGCTGAGAAAGGGCTCT 61.894 60.000 0.00 0.00 35.91 4.09
864 1112 6.676456 GCAGCTGATGTTTCGTTCTATTTCAT 60.676 38.462 20.43 0.00 0.00 2.57
872 1120 0.179215 CGGCAGCTGATGTTTCGTTC 60.179 55.000 20.43 0.00 0.00 3.95
942 1195 0.460311 GAATCGAAGAAGGCGGAGGA 59.540 55.000 0.00 0.00 43.58 3.71
948 1201 1.927838 GGAGAACGAATCGAAGAAGGC 59.072 52.381 10.55 0.00 43.58 4.35
968 1221 4.560856 CTCTTCTCGAGCGGGCCG 62.561 72.222 24.35 24.35 31.99 6.13
970 1223 1.517475 GTTCTCTTCTCGAGCGGGC 60.517 63.158 7.81 0.00 39.70 6.13
971 1224 1.139947 GGTTCTCTTCTCGAGCGGG 59.860 63.158 7.81 0.87 39.70 6.13
974 1227 0.174617 CCCAGGTTCTCTTCTCGAGC 59.825 60.000 7.81 0.00 39.70 5.03
978 1231 0.533032 CGGACCCAGGTTCTCTTCTC 59.467 60.000 0.00 0.00 0.00 2.87
979 1232 1.545706 GCGGACCCAGGTTCTCTTCT 61.546 60.000 0.00 0.00 0.00 2.85
980 1233 1.079057 GCGGACCCAGGTTCTCTTC 60.079 63.158 0.00 0.00 0.00 2.87
981 1234 2.593956 GGCGGACCCAGGTTCTCTT 61.594 63.158 0.00 0.00 0.00 2.85
982 1235 3.003763 GGCGGACCCAGGTTCTCT 61.004 66.667 0.00 0.00 0.00 3.10
1008 1274 0.331954 ACTGTAGGGCGAGGAAGAGA 59.668 55.000 0.00 0.00 0.00 3.10
1023 1289 1.672356 GGAGCATTCCACGCACTGT 60.672 57.895 0.00 0.00 43.45 3.55
1088 1356 3.826157 GGATCAATGGTGGAACAAACAGA 59.174 43.478 0.00 0.00 44.16 3.41
1114 1382 1.264288 GAAGGGCAACACAGAAACGAG 59.736 52.381 0.00 0.00 39.74 4.18
1349 1617 2.364961 CTTCCTCTCCCTCGGGGT 59.635 66.667 0.00 0.00 44.74 4.95
1375 1643 1.246056 CGTCCAGGTACTCGGACCAA 61.246 60.000 21.26 0.00 46.46 3.67
1428 1696 1.871676 CATCATCACGGGAATCAGCAG 59.128 52.381 0.00 0.00 0.00 4.24
1438 1706 1.229428 GGTGCATACCATCATCACGG 58.771 55.000 0.00 0.00 46.71 4.94
1449 1717 2.503920 AGTACGATTCCGGTGCATAC 57.496 50.000 0.00 0.00 40.78 2.39
1450 1718 4.321452 GGATTAGTACGATTCCGGTGCATA 60.321 45.833 0.00 0.00 40.78 3.14
1451 1719 3.554337 GGATTAGTACGATTCCGGTGCAT 60.554 47.826 0.00 0.00 40.78 3.96
1452 1720 2.223876 GGATTAGTACGATTCCGGTGCA 60.224 50.000 0.00 0.00 40.78 4.57
1453 1721 2.035576 AGGATTAGTACGATTCCGGTGC 59.964 50.000 0.00 0.00 40.78 5.01
1454 1722 4.037684 AGAAGGATTAGTACGATTCCGGTG 59.962 45.833 0.00 0.00 40.78 4.94
1455 1723 4.213513 AGAAGGATTAGTACGATTCCGGT 58.786 43.478 0.00 4.32 40.78 5.28
1456 1724 4.277672 TGAGAAGGATTAGTACGATTCCGG 59.722 45.833 10.17 0.00 40.78 5.14
1457 1725 5.434352 TGAGAAGGATTAGTACGATTCCG 57.566 43.478 10.17 0.00 42.50 4.30
1458 1726 5.692654 GCTTGAGAAGGATTAGTACGATTCC 59.307 44.000 8.41 8.41 0.00 3.01
1459 1727 6.508777 AGCTTGAGAAGGATTAGTACGATTC 58.491 40.000 0.00 0.00 0.00 2.52
1460 1728 6.472686 AGCTTGAGAAGGATTAGTACGATT 57.527 37.500 0.00 0.00 0.00 3.34
1461 1729 6.276847 CAAGCTTGAGAAGGATTAGTACGAT 58.723 40.000 22.31 0.00 0.00 3.73
1462 1730 5.394224 CCAAGCTTGAGAAGGATTAGTACGA 60.394 44.000 28.05 0.00 0.00 3.43
1463 1731 4.806247 CCAAGCTTGAGAAGGATTAGTACG 59.194 45.833 28.05 0.90 0.00 3.67
1492 1778 8.248253 TGATAAAGTGTAAGTTAGCAGATTCGA 58.752 33.333 0.00 0.00 0.00 3.71
1611 1898 8.352201 GCTGTATGAATTGCTCCAAATAACATA 58.648 33.333 0.00 0.00 0.00 2.29
1617 1904 5.864418 ATGCTGTATGAATTGCTCCAAAT 57.136 34.783 0.00 0.00 0.00 2.32
1663 1950 5.775701 ACAGTACTAGGAACTTGTGAGATGT 59.224 40.000 0.00 0.00 45.24 3.06
1667 1954 5.455056 ACACAGTACTAGGAACTTGTGAG 57.545 43.478 22.13 7.88 45.24 3.51
1713 2001 5.527582 CCAGTTCCCGGAGAAATAATAACAG 59.472 44.000 0.73 0.00 35.85 3.16
1729 2017 3.577389 CCATCTGGTTCCAGTTCCC 57.423 57.895 17.00 0.00 35.70 3.97
1766 2054 2.288825 ACGTACGGCCATATCCTGAATG 60.289 50.000 21.06 0.00 0.00 2.67
1777 2065 1.890625 AAGCATACCACGTACGGCCA 61.891 55.000 21.06 1.74 0.00 5.36
1810 2103 8.774890 TGCAATTTGCTAATGAATAAACATGT 57.225 26.923 21.19 0.00 45.31 3.21
1850 2143 3.976942 GTCTTGTGCAAGCAATGTTACAG 59.023 43.478 7.03 0.00 38.28 2.74
1856 2149 5.201910 CAAAAATGTCTTGTGCAAGCAATG 58.798 37.500 7.03 4.69 38.28 2.82
1861 2154 4.330620 AGCAACAAAAATGTCTTGTGCAAG 59.669 37.500 5.63 5.63 37.10 4.01
1866 2159 6.212888 AGAGAAGCAACAAAAATGTCTTGT 57.787 33.333 0.00 0.00 38.65 3.16
1870 2163 5.291614 TGCAAAGAGAAGCAACAAAAATGTC 59.708 36.000 0.00 0.00 37.90 3.06
1877 2170 5.163571 TGTTATGTGCAAAGAGAAGCAACAA 60.164 36.000 0.00 0.00 43.20 2.83
1878 2171 4.337836 TGTTATGTGCAAAGAGAAGCAACA 59.662 37.500 0.00 0.00 43.20 3.33
1934 2228 0.811281 GGTCGGATTGGAAAAGCAGG 59.189 55.000 0.00 0.00 0.00 4.85
2008 2310 0.552363 CCATCACCCCACATCATCCA 59.448 55.000 0.00 0.00 0.00 3.41
2011 2313 1.213678 CTGTCCATCACCCCACATCAT 59.786 52.381 0.00 0.00 0.00 2.45
2032 2334 4.814294 GACAGGGCCAGCCGTACG 62.814 72.222 8.69 8.69 36.85 3.67
2044 2346 1.601759 CCTTGCCACCACAGACAGG 60.602 63.158 0.00 0.00 0.00 4.00
2060 2362 3.446442 AACAGAGCATGATCAAACCCT 57.554 42.857 14.38 0.00 0.00 4.34
2112 2414 9.453325 TTTGGTTTTCTTTGAATATAACACGTC 57.547 29.630 0.00 0.00 0.00 4.34
2115 2417 8.984764 GGGTTTGGTTTTCTTTGAATATAACAC 58.015 33.333 0.00 0.00 0.00 3.32
2146 2449 9.393249 TCTAATTTGACAAAATCTGCGTAAAAG 57.607 29.630 4.41 0.00 34.84 2.27
2151 2454 6.324819 CCATCTAATTTGACAAAATCTGCGT 58.675 36.000 4.41 0.00 34.84 5.24
2159 2462 6.325919 AGTTTCGCCATCTAATTTGACAAA 57.674 33.333 2.48 2.48 0.00 2.83
2176 2479 8.508800 AAATAGAGAGTATATTGCGAGTTTCG 57.491 34.615 0.00 0.00 43.89 3.46
2204 2507 9.195411 GAAATGTGATGCTAACAAATTTTGAGA 57.805 29.630 15.81 2.43 35.95 3.27
2209 2512 7.761249 GCCTAGAAATGTGATGCTAACAAATTT 59.239 33.333 0.00 0.00 37.72 1.82
2224 2527 2.880890 GCCATTCGATGCCTAGAAATGT 59.119 45.455 0.00 0.00 0.00 2.71
2238 2541 2.800629 GCATTGGAAATGAGGCCATTCG 60.801 50.000 5.01 0.00 41.84 3.34
2276 2579 8.829612 CAATTAGGCCATTACCATTCAAATTTC 58.170 33.333 5.01 0.00 0.00 2.17
2277 2580 8.328014 ACAATTAGGCCATTACCATTCAAATTT 58.672 29.630 5.01 0.00 0.00 1.82
2278 2581 7.860584 ACAATTAGGCCATTACCATTCAAATT 58.139 30.769 5.01 0.00 0.00 1.82
2327 2630 6.670464 TCAGTTGTCACTTCAACCCCTATATA 59.330 38.462 6.04 0.00 45.90 0.86
2328 2631 5.487488 TCAGTTGTCACTTCAACCCCTATAT 59.513 40.000 6.04 0.00 45.90 0.86
2336 2639 4.272748 GGGTAACTCAGTTGTCACTTCAAC 59.727 45.833 0.00 1.94 45.33 3.18
2453 2756 3.887110 TCCATTTGCTGCATCTTGGATAG 59.113 43.478 18.90 1.63 0.00 2.08
2490 2793 0.034476 TGCAGAGCAGACAGTTGAGG 59.966 55.000 0.00 0.00 33.32 3.86
2527 2830 6.808212 GTGTGACCAGGATTTTTCATATGTTG 59.192 38.462 1.90 0.00 0.00 3.33
2531 2834 7.671398 AGAAAGTGTGACCAGGATTTTTCATAT 59.329 33.333 0.00 0.00 0.00 1.78
2532 2835 7.004086 AGAAAGTGTGACCAGGATTTTTCATA 58.996 34.615 0.00 0.00 0.00 2.15
2546 2851 3.489785 CGACAGGTGTAAGAAAGTGTGAC 59.510 47.826 0.00 0.00 0.00 3.67
2568 2873 6.560253 TTTCAACTCTCCTATTTTGCTCAC 57.440 37.500 0.00 0.00 0.00 3.51
2753 3058 6.005823 AGACCAGAACAATCACATGAAATCA 58.994 36.000 0.00 0.00 0.00 2.57
2886 3353 5.850557 TTTCTTCCAACTCAAAGCATTCA 57.149 34.783 0.00 0.00 0.00 2.57
2975 3447 0.459759 GTGGGTGCGTAGTAAGAGGC 60.460 60.000 0.00 0.00 0.00 4.70
3042 3514 6.758886 CCTACATCCAACACTTATCTGAAGAC 59.241 42.308 0.00 0.00 0.00 3.01
3230 3702 7.632028 GCTCAGTCAACTAGAGAGTAGAGACTA 60.632 44.444 0.00 0.00 38.96 2.59
3363 3917 3.502595 AGTCCTACGACGACCATATGATG 59.497 47.826 3.65 0.00 44.28 3.07
3374 3928 0.453950 CGTCCAACAGTCCTACGACG 60.454 60.000 0.00 0.00 44.28 5.12
3399 3953 7.997107 CGTAGCTGTATGGTTTGTATTTCTA 57.003 36.000 0.00 0.00 0.00 2.10
3522 4087 9.248291 CGCCAAATTAAATTAGACTATGCATTT 57.752 29.630 3.54 0.00 0.00 2.32
3523 4088 8.629158 TCGCCAAATTAAATTAGACTATGCATT 58.371 29.630 3.54 0.00 0.00 3.56
3524 4089 8.165239 TCGCCAAATTAAATTAGACTATGCAT 57.835 30.769 3.79 3.79 0.00 3.96
3613 4180 2.170607 TGGCTAACTAATGGCTCTGTCC 59.829 50.000 0.00 0.00 35.51 4.02
3689 4256 4.608948 CCAGATATGAAGGTACTGGGAC 57.391 50.000 0.00 0.00 42.77 4.46
3747 4314 2.162208 TGATTTGCCTTTCGCTTGCTAG 59.838 45.455 0.00 0.00 38.78 3.42
3782 4349 2.896685 TGCGAGGTTGGGAAATTTCAAT 59.103 40.909 19.49 0.00 0.00 2.57
3798 4365 6.237279 CGGTTTTGTGATTCATAAAATGCGAG 60.237 38.462 19.87 9.47 36.97 5.03
3845 4412 3.537580 TCCCTCACTACAACACAACAAC 58.462 45.455 0.00 0.00 0.00 3.32
3860 4427 0.400213 AAACTGAACGGCATCCCTCA 59.600 50.000 0.00 0.00 0.00 3.86
3863 4430 1.463674 ATGAAACTGAACGGCATCCC 58.536 50.000 0.00 0.00 0.00 3.85
3977 4596 2.826128 CAGTGAACTACCTCCAGCACTA 59.174 50.000 0.00 0.00 35.09 2.74
3978 4597 1.620819 CAGTGAACTACCTCCAGCACT 59.379 52.381 0.00 0.00 37.09 4.40
3979 4598 1.338200 CCAGTGAACTACCTCCAGCAC 60.338 57.143 0.00 0.00 0.00 4.40
3980 4599 0.976641 CCAGTGAACTACCTCCAGCA 59.023 55.000 0.00 0.00 0.00 4.41
3981 4600 0.977395 ACCAGTGAACTACCTCCAGC 59.023 55.000 0.00 0.00 0.00 4.85
3982 4601 3.368531 GCTTACCAGTGAACTACCTCCAG 60.369 52.174 0.00 0.00 0.00 3.86
3983 4602 2.565834 GCTTACCAGTGAACTACCTCCA 59.434 50.000 0.00 0.00 0.00 3.86
3984 4603 2.093606 GGCTTACCAGTGAACTACCTCC 60.094 54.545 0.00 0.00 35.26 4.30
3985 4604 2.093606 GGGCTTACCAGTGAACTACCTC 60.094 54.545 0.00 0.00 39.85 3.85
3986 4605 1.907255 GGGCTTACCAGTGAACTACCT 59.093 52.381 0.00 0.00 39.85 3.08
3987 4606 1.405121 CGGGCTTACCAGTGAACTACC 60.405 57.143 0.00 0.00 40.22 3.18
3988 4607 1.405121 CCGGGCTTACCAGTGAACTAC 60.405 57.143 0.00 0.00 40.22 2.73
3989 4608 0.899720 CCGGGCTTACCAGTGAACTA 59.100 55.000 0.00 0.00 40.22 2.24
3990 4609 0.834687 TCCGGGCTTACCAGTGAACT 60.835 55.000 0.00 0.00 40.22 3.01
4011 4630 2.357517 GACACCTCACAGGCACGG 60.358 66.667 0.00 0.00 39.63 4.94
4080 4699 3.780294 ACCACTAGAGGAATATGTGCCAA 59.220 43.478 13.71 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.