Multiple sequence alignment - TraesCS4A01G368500

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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 TraesCS4A01G368500 chr4A 100.000 2351 0 0 1 2351 641358589 641360939 0.000000e+00 4342.0
1 TraesCS4A01G368500 chr4A 97.500 40 1 0 1645 1684 641360147 641360186 4.190000e-08 69.4
2 TraesCS4A01G368500 chr4A 97.500 40 1 0 1559 1598 641360233 641360272 4.190000e-08 69.4
3 TraesCS4A01G368500 chr5D 85.355 1509 133 25 878 2351 531203188 531201733 0.000000e+00 1482.0
4 TraesCS4A01G368500 chr5D 90.135 892 50 14 885 1763 531254594 531253728 0.000000e+00 1125.0
5 TraesCS4A01G368500 chr5D 92.149 242 17 2 1 240 531254832 531254591 8.050000e-90 340.0
6 TraesCS4A01G368500 chr5D 87.302 189 21 1 1 189 531203379 531203194 1.830000e-51 213.0
7 TraesCS4A01G368500 chr5A 98.459 649 9 1 240 888 46628884 46628237 0.000000e+00 1142.0
8 TraesCS4A01G368500 chr5A 98.457 648 9 1 240 887 327912038 327911392 0.000000e+00 1140.0
9 TraesCS4A01G368500 chr1B 98.607 646 8 1 240 885 360276165 360275521 0.000000e+00 1142.0
10 TraesCS4A01G368500 chr6B 98.454 647 10 0 240 886 672861835 672861189 0.000000e+00 1140.0
11 TraesCS4A01G368500 chr6A 98.454 647 10 0 240 886 59816391 59815745 0.000000e+00 1140.0
12 TraesCS4A01G368500 chr7A 98.297 646 10 1 240 885 200067249 200067893 0.000000e+00 1131.0
13 TraesCS4A01G368500 chr2A 97.903 620 12 1 266 885 724051674 724052292 0.000000e+00 1072.0
14 TraesCS4A01G368500 chr2B 96.965 626 18 1 261 886 210251608 210252232 0.000000e+00 1050.0
15 TraesCS4A01G368500 chr1D 94.737 646 32 1 240 885 81729158 81729801 0.000000e+00 1003.0
16 TraesCS4A01G368500 chr5B 88.175 778 44 12 878 1639 670246701 670245956 0.000000e+00 883.0
17 TraesCS4A01G368500 chr5B 86.860 723 45 24 885 1590 670304958 670305647 0.000000e+00 763.0
18 TraesCS4A01G368500 chr5B 86.722 723 46 23 885 1590 670138796 670138107 0.000000e+00 758.0
19 TraesCS4A01G368500 chr5B 92.308 182 11 1 1 182 670246894 670246716 3.000000e-64 255.0
20 TraesCS4A01G368500 chr5B 88.950 181 13 3 1406 1586 670136659 670136486 1.410000e-52 217.0
21 TraesCS4A01G368500 chr5B 92.199 141 8 1 2 142 670304780 670304917 1.840000e-46 196.0
22 TraesCS4A01G368500 chr5B 85.211 142 7 4 1 142 670138964 670138837 1.470000e-27 134.0


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 TraesCS4A01G368500 chr4A 641358589 641360939 2350 False 1493.600000 4342 98.333333 1 2351 3 chr4A.!!$F1 2350
1 TraesCS4A01G368500 chr5D 531201733 531203379 1646 True 847.500000 1482 86.328500 1 2351 2 chr5D.!!$R1 2350
2 TraesCS4A01G368500 chr5D 531253728 531254832 1104 True 732.500000 1125 91.142000 1 1763 2 chr5D.!!$R2 1762
3 TraesCS4A01G368500 chr5A 46628237 46628884 647 True 1142.000000 1142 98.459000 240 888 1 chr5A.!!$R1 648
4 TraesCS4A01G368500 chr5A 327911392 327912038 646 True 1140.000000 1140 98.457000 240 887 1 chr5A.!!$R2 647
5 TraesCS4A01G368500 chr1B 360275521 360276165 644 True 1142.000000 1142 98.607000 240 885 1 chr1B.!!$R1 645
6 TraesCS4A01G368500 chr6B 672861189 672861835 646 True 1140.000000 1140 98.454000 240 886 1 chr6B.!!$R1 646
7 TraesCS4A01G368500 chr6A 59815745 59816391 646 True 1140.000000 1140 98.454000 240 886 1 chr6A.!!$R1 646
8 TraesCS4A01G368500 chr7A 200067249 200067893 644 False 1131.000000 1131 98.297000 240 885 1 chr7A.!!$F1 645
9 TraesCS4A01G368500 chr2A 724051674 724052292 618 False 1072.000000 1072 97.903000 266 885 1 chr2A.!!$F1 619
10 TraesCS4A01G368500 chr2B 210251608 210252232 624 False 1050.000000 1050 96.965000 261 886 1 chr2B.!!$F1 625
11 TraesCS4A01G368500 chr1D 81729158 81729801 643 False 1003.000000 1003 94.737000 240 885 1 chr1D.!!$F1 645
12 TraesCS4A01G368500 chr5B 670245956 670246894 938 True 569.000000 883 90.241500 1 1639 2 chr5B.!!$R2 1638
13 TraesCS4A01G368500 chr5B 670304780 670305647 867 False 479.500000 763 89.529500 2 1590 2 chr5B.!!$F1 1588
14 TraesCS4A01G368500 chr5B 670136486 670138964 2478 True 369.666667 758 86.961000 1 1590 3 chr5B.!!$R1 1589

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
150 155 0.5925 ATGCACGTACGCTCGAGATG 60.593 55.0 18.75 10.24 34.7 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1636 1672 0.036388 AATACGTGCACAGGACCAGG 60.036 55.0 18.64 0.0 0.0 4.45 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
74 76 1.179174 TGGAGGACTGGACGTGTCTG 61.179 60.000 0.00 0.00 35.04 3.51
112 117 7.730084 TCTCAAAGTCTCAATGGTCCATATAG 58.270 38.462 4.33 5.94 0.00 1.31
113 118 7.345653 TCTCAAAGTCTCAATGGTCCATATAGT 59.654 37.037 4.33 0.00 0.00 2.12
114 119 8.547481 TCAAAGTCTCAATGGTCCATATAGTA 57.453 34.615 4.33 0.00 0.00 1.82
117 122 8.554490 AAGTCTCAATGGTCCATATAGTACTT 57.446 34.615 4.33 12.65 0.00 2.24
150 155 0.592500 ATGCACGTACGCTCGAGATG 60.593 55.000 18.75 10.24 34.70 2.90
158 163 0.818445 ACGCTCGAGATGGATACGGT 60.818 55.000 18.75 0.00 42.51 4.83
207 212 7.425577 TGAATTCATAGGCGTGAAGATAATG 57.574 36.000 3.38 0.00 41.05 1.90
229 234 3.399330 TGGAACTCCACGCTAGAAAAAG 58.601 45.455 0.00 0.00 42.01 2.27
233 238 3.665190 ACTCCACGCTAGAAAAAGGAAG 58.335 45.455 0.00 0.00 0.00 3.46
234 239 3.323979 ACTCCACGCTAGAAAAAGGAAGA 59.676 43.478 0.00 0.00 0.00 2.87
235 240 4.020128 ACTCCACGCTAGAAAAAGGAAGAT 60.020 41.667 0.00 0.00 0.00 2.40
236 241 5.187186 ACTCCACGCTAGAAAAAGGAAGATA 59.813 40.000 0.00 0.00 0.00 1.98
237 242 6.045072 TCCACGCTAGAAAAAGGAAGATAA 57.955 37.500 0.00 0.00 0.00 1.75
238 243 6.650120 TCCACGCTAGAAAAAGGAAGATAAT 58.350 36.000 0.00 0.00 0.00 1.28
605 610 5.186215 GGTTCAAGACTATCCTAGATAGGGC 59.814 48.000 14.43 7.35 43.79 5.19
692 697 5.163923 GCAATGCAAGAGTTTTTAGGAATGC 60.164 40.000 0.00 0.00 0.00 3.56
876 881 2.481568 GCAAATCTTTTGCCTTGCTTCC 59.518 45.455 12.74 0.00 40.76 3.46
980 1001 0.966920 ACCCACTACTCTTCACCACG 59.033 55.000 0.00 0.00 0.00 4.94
993 1014 1.966451 ACCACGCAAAGTAGCTGCC 60.966 57.895 0.00 0.00 36.40 4.85
1017 1038 4.575973 ATGGCCTGCGCTCCATCC 62.576 66.667 18.93 9.76 38.65 3.51
1021 1042 4.147449 CCTGCGCTCCATCCACGA 62.147 66.667 9.73 0.00 0.00 4.35
1242 1263 2.156504 CAGTGAATCGTGTCAGACTTGC 59.843 50.000 1.31 0.00 0.00 4.01
1251 1272 2.096713 GTGTCAGACTTGCATGTTCGTC 60.097 50.000 6.70 0.00 0.00 4.20
1418 1448 1.588404 CGTGTATTCCAAGCAGCTACG 59.412 52.381 0.00 0.00 0.00 3.51
1422 1452 1.922570 ATTCCAAGCAGCTACGTACG 58.077 50.000 15.01 15.01 0.00 3.67
1437 1467 6.538742 AGCTACGTACGTACTAAGTTCCAATA 59.461 38.462 23.60 0.77 0.00 1.90
1523 1553 2.981560 GCGTTGTGGAGGCATGGTG 61.982 63.158 0.00 0.00 38.95 4.17
1586 1620 3.548616 CGTATTGTACGCGTCCCTTGATA 60.549 47.826 18.63 4.33 45.81 2.15
1591 1627 2.795175 ACGCGTCCCTTGATATGTAG 57.205 50.000 5.58 0.00 0.00 2.74
1621 1657 0.037790 TCATGACACGAACGCCATGA 60.038 50.000 16.72 16.72 41.90 3.07
1636 1672 1.026718 CATGACGGCCCTGGTTCTTC 61.027 60.000 0.00 0.00 0.00 2.87
1638 1674 2.529389 ACGGCCCTGGTTCTTCCT 60.529 61.111 0.00 0.00 37.07 3.36
1639 1675 2.045926 CGGCCCTGGTTCTTCCTG 60.046 66.667 0.00 0.00 37.07 3.86
1644 1680 2.778899 CCTGGTTCTTCCTGGTCCT 58.221 57.895 0.00 0.00 46.28 3.85
1646 1682 1.059913 CTGGTTCTTCCTGGTCCTGT 58.940 55.000 0.00 0.00 37.07 4.00
1647 1683 0.764890 TGGTTCTTCCTGGTCCTGTG 59.235 55.000 0.00 0.00 37.07 3.66
1648 1684 0.606673 GGTTCTTCCTGGTCCTGTGC 60.607 60.000 0.00 0.00 0.00 4.57
1649 1685 0.108585 GTTCTTCCTGGTCCTGTGCA 59.891 55.000 0.00 0.00 0.00 4.57
1650 1686 0.108585 TTCTTCCTGGTCCTGTGCAC 59.891 55.000 10.75 10.75 0.00 4.57
1654 1690 0.902984 TCCTGGTCCTGTGCACGTAT 60.903 55.000 13.13 0.00 0.00 3.06
1655 1691 0.036388 CCTGGTCCTGTGCACGTATT 60.036 55.000 13.13 0.00 0.00 1.89
1656 1692 1.078709 CTGGTCCTGTGCACGTATTG 58.921 55.000 13.13 0.00 0.00 1.90
1658 1694 1.619332 TGGTCCTGTGCACGTATTGTA 59.381 47.619 13.13 0.00 0.00 2.41
1668 1704 3.334078 CGTATTGTACGCGTCCCTT 57.666 52.632 18.63 1.94 45.81 3.95
1670 1706 1.467883 CGTATTGTACGCGTCCCTTGA 60.468 52.381 18.63 0.00 45.81 3.02
1672 1708 3.548616 CGTATTGTACGCGTCCCTTGATA 60.549 47.826 18.63 4.33 45.81 2.15
1673 1709 3.746045 ATTGTACGCGTCCCTTGATAT 57.254 42.857 18.63 0.00 0.00 1.63
1674 1710 2.502213 TGTACGCGTCCCTTGATATG 57.498 50.000 18.63 0.00 0.00 1.78
1676 1712 2.950975 TGTACGCGTCCCTTGATATGTA 59.049 45.455 18.63 0.00 0.00 2.29
1677 1713 2.795175 ACGCGTCCCTTGATATGTAG 57.205 50.000 5.58 0.00 0.00 2.74
1678 1714 2.304092 ACGCGTCCCTTGATATGTAGA 58.696 47.619 5.58 0.00 0.00 2.59
1679 1715 2.691526 ACGCGTCCCTTGATATGTAGAA 59.308 45.455 5.58 0.00 0.00 2.10
1798 1836 0.260230 ATCGCCTTCCTCTCCTCTGA 59.740 55.000 0.00 0.00 0.00 3.27
1849 1887 1.078759 GATTCCACACAGTCCGAGCG 61.079 60.000 0.00 0.00 0.00 5.03
1892 1932 4.778415 CCTCTGCGGTCGTCGGTG 62.778 72.222 0.00 0.00 39.69 4.94
1961 2001 7.759433 ACTGTTGGAAAATTAGGCGATTTATTG 59.241 33.333 3.00 0.00 0.00 1.90
1976 2016 9.474920 GGCGATTTATTGATGATTAATTTGGAA 57.525 29.630 0.00 0.00 0.00 3.53
2016 2056 9.941664 TTAAAACAACAATTACAATGCATTTGG 57.058 25.926 9.83 1.80 39.80 3.28
2061 2105 5.018149 ACATCATGAACAACATCATCCCAA 58.982 37.500 0.00 0.00 37.96 4.12
2064 2108 5.968254 TCATGAACAACATCATCCCAAATG 58.032 37.500 0.00 0.00 37.96 2.32
2066 2110 5.136816 TGAACAACATCATCCCAAATGTG 57.863 39.130 0.00 0.00 36.28 3.21
2067 2111 4.021280 TGAACAACATCATCCCAAATGTGG 60.021 41.667 0.00 0.00 45.53 4.17
2092 2136 6.237861 GCGACAACCATAATTAGAGTCTTGAC 60.238 42.308 0.00 0.00 0.00 3.18
2146 2191 6.804677 AGATGAAGTAATTGTTGTTGTTGCA 58.195 32.000 0.00 0.00 0.00 4.08
2165 2210 2.603652 GCAAAGGCGATGTTGTTAACGT 60.604 45.455 0.26 0.00 0.00 3.99
2180 2225 1.011333 AACGTCGTTGTTGGTGAAGG 58.989 50.000 10.39 0.00 0.00 3.46
2185 2230 1.826487 GTTGTTGGTGAAGGCCGGT 60.826 57.895 1.90 0.00 0.00 5.28
2189 2234 2.589157 TTGGTGAAGGCCGGTCGAT 61.589 57.895 1.90 0.00 0.00 3.59
2193 2238 2.203070 GAAGGCCGGTCGATGCAT 60.203 61.111 1.90 0.00 0.00 3.96
2202 2247 3.584834 CCGGTCGATGCATATGTTGATA 58.415 45.455 0.00 0.00 0.00 2.15
2210 2255 3.787785 TGCATATGTTGATAACGACGGT 58.212 40.909 4.29 0.00 33.40 4.83
2217 2262 0.738063 TGATAACGACGGTGCGCAAT 60.738 50.000 14.00 0.00 33.86 3.56
2264 2309 2.539547 CCCGTGATAAAGAATGCAAGCG 60.540 50.000 0.00 0.00 0.00 4.68
2300 2345 4.923281 GCTTGCCAAAAACATAATTCGTCT 59.077 37.500 0.00 0.00 0.00 4.18
2323 2368 0.680921 CCCCGTGCAAGGATCACAAT 60.681 55.000 21.23 0.00 34.27 2.71
2337 2382 0.890683 CACAATGGCAAGAGGTTCCC 59.109 55.000 0.00 0.00 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 11 6.758886 CCACCTAACTGAAATGATCTGTCTAC 59.241 42.308 0.00 0.00 39.07 2.59
44 46 0.255033 AGTCCTCCATTAAACGGGGC 59.745 55.000 0.00 0.00 0.00 5.80
49 51 3.000727 CACGTCCAGTCCTCCATTAAAC 58.999 50.000 0.00 0.00 0.00 2.01
74 76 3.557903 TTGAGAGCCAGTGCCCAGC 62.558 63.158 0.00 0.00 38.69 4.85
112 117 1.292061 TCACGTGGTGCAACAAGTAC 58.708 50.000 22.98 0.98 39.98 2.73
113 118 1.870402 CATCACGTGGTGCAACAAGTA 59.130 47.619 22.98 11.89 39.98 2.24
114 119 0.662619 CATCACGTGGTGCAACAAGT 59.337 50.000 18.05 18.05 39.98 3.16
117 122 3.029810 GCATCACGTGGTGCAACA 58.970 55.556 41.09 11.18 40.94 3.33
142 147 1.871676 TCGAACCGTATCCATCTCGAG 59.128 52.381 5.93 5.93 32.10 4.04
150 155 0.101939 GGGACAGTCGAACCGTATCC 59.898 60.000 0.00 0.00 0.00 2.59
158 163 1.117142 AAAGGGACGGGACAGTCGAA 61.117 55.000 0.00 0.00 41.81 3.71
229 234 4.691216 GGAATACTCGCCACATTATCTTCC 59.309 45.833 0.00 0.00 0.00 3.46
233 238 2.412089 GCGGAATACTCGCCACATTATC 59.588 50.000 0.00 0.00 46.55 1.75
234 239 2.413837 GCGGAATACTCGCCACATTAT 58.586 47.619 0.00 0.00 46.55 1.28
235 240 1.860676 GCGGAATACTCGCCACATTA 58.139 50.000 0.00 0.00 46.55 1.90
236 241 2.690326 GCGGAATACTCGCCACATT 58.310 52.632 0.00 0.00 46.55 2.71
237 242 4.438346 GCGGAATACTCGCCACAT 57.562 55.556 0.00 0.00 46.55 3.21
707 712 5.840693 TCCTTTATCCTAGCAGTGATCATGA 59.159 40.000 0.00 0.00 0.00 3.07
904 911 5.717178 AGCTCGCCTCTATTTATAGATGGAA 59.283 40.000 14.31 5.70 38.60 3.53
980 1001 1.442688 GCAACGGCAGCTACTTTGC 60.443 57.895 13.47 13.47 40.72 3.68
1017 1038 3.499737 GCGGCCACCTTCATCGTG 61.500 66.667 2.24 0.00 0.00 4.35
1021 1042 2.124151 GATGGCGGCCACCTTCAT 60.124 61.111 26.48 7.13 35.80 2.57
1242 1263 1.581912 GCATGCGCAGACGAACATG 60.582 57.895 18.32 7.71 43.93 3.21
1251 1272 2.330372 ACAGTTCTGGCATGCGCAG 61.330 57.895 22.81 22.81 41.24 5.18
1418 1448 7.223387 CCAACCATATTGGAACTTAGTACGTAC 59.777 40.741 18.10 18.10 40.96 3.67
1422 1452 7.392393 ACAACCAACCATATTGGAACTTAGTAC 59.608 37.037 12.55 0.00 40.96 2.73
1437 1467 4.219725 GGTGCTTATTACACAACCAACCAT 59.780 41.667 0.00 0.00 39.87 3.55
1481 1511 0.391130 ATGCACGTATGTTCGCCTGT 60.391 50.000 0.00 0.00 0.00 4.00
1523 1553 3.851976 AACGAGACTCACTGTACCATC 57.148 47.619 2.82 0.00 0.00 3.51
1586 1620 5.882557 GTGTCATGATGGAAAACCTCTACAT 59.117 40.000 0.00 0.00 0.00 2.29
1591 1627 3.334691 TCGTGTCATGATGGAAAACCTC 58.665 45.455 0.00 0.00 0.00 3.85
1621 1657 2.529389 AGGAAGAACCAGGGCCGT 60.529 61.111 0.00 0.00 42.04 5.68
1627 1663 1.059913 ACAGGACCAGGAAGAACCAG 58.940 55.000 0.00 0.00 42.04 4.00
1636 1672 0.036388 AATACGTGCACAGGACCAGG 60.036 55.000 18.64 0.00 0.00 4.45
1638 1674 0.394938 ACAATACGTGCACAGGACCA 59.605 50.000 18.64 0.00 0.00 4.02
1639 1675 1.997606 GTACAATACGTGCACAGGACC 59.002 52.381 18.64 0.00 0.00 4.46
1640 1676 1.652124 CGTACAATACGTGCACAGGAC 59.348 52.381 18.64 6.59 46.41 3.85
1641 1677 1.985334 CGTACAATACGTGCACAGGA 58.015 50.000 18.64 6.87 46.41 3.86
1654 1690 2.166870 ACATATCAAGGGACGCGTACAA 59.833 45.455 25.30 5.62 0.00 2.41
1655 1691 1.752498 ACATATCAAGGGACGCGTACA 59.248 47.619 25.30 1.92 0.00 2.90
1656 1692 2.503920 ACATATCAAGGGACGCGTAC 57.496 50.000 14.70 14.70 0.00 3.67
1658 1694 2.304092 TCTACATATCAAGGGACGCGT 58.696 47.619 13.85 13.85 0.00 6.01
1662 1698 7.496263 GGAAGAAACTTCTACATATCAAGGGAC 59.504 40.741 10.58 0.00 36.28 4.46
1663 1699 7.403231 AGGAAGAAACTTCTACATATCAAGGGA 59.597 37.037 10.58 0.00 36.28 4.20
1665 1701 7.713073 GGAGGAAGAAACTTCTACATATCAAGG 59.287 40.741 10.58 0.00 36.28 3.61
1666 1702 7.713073 GGGAGGAAGAAACTTCTACATATCAAG 59.287 40.741 10.58 0.00 36.28 3.02
1667 1703 7.365652 GGGGAGGAAGAAACTTCTACATATCAA 60.366 40.741 10.58 0.00 36.28 2.57
1668 1704 6.099845 GGGGAGGAAGAAACTTCTACATATCA 59.900 42.308 10.58 0.00 36.28 2.15
1670 1706 5.070580 CGGGGAGGAAGAAACTTCTACATAT 59.929 44.000 10.58 0.00 36.28 1.78
1672 1708 3.197983 CGGGGAGGAAGAAACTTCTACAT 59.802 47.826 10.58 0.00 36.28 2.29
1673 1709 2.565834 CGGGGAGGAAGAAACTTCTACA 59.434 50.000 10.58 0.00 36.28 2.74
1674 1710 2.093606 CCGGGGAGGAAGAAACTTCTAC 60.094 54.545 10.58 5.95 45.00 2.59
1676 1712 0.984995 CCGGGGAGGAAGAAACTTCT 59.015 55.000 10.58 0.00 45.00 2.85
1677 1713 0.677098 GCCGGGGAGGAAGAAACTTC 60.677 60.000 2.18 0.00 45.00 3.01
1678 1714 1.379146 GCCGGGGAGGAAGAAACTT 59.621 57.895 2.18 0.00 45.00 2.66
1679 1715 1.846124 TGCCGGGGAGGAAGAAACT 60.846 57.895 2.18 0.00 45.00 2.66
1703 1739 1.522130 GGTGTTGGACGTCGGTTGT 60.522 57.895 9.92 0.00 0.00 3.32
1817 1855 2.589492 GGAATCGCCGCGACAGATG 61.589 63.158 19.45 0.00 39.18 2.90
1818 1856 2.279517 GGAATCGCCGCGACAGAT 60.280 61.111 19.45 6.38 39.18 2.90
1882 1922 0.108520 TAGATTTGGCACCGACGACC 60.109 55.000 0.00 0.00 0.00 4.79
1885 1925 0.460284 AGCTAGATTTGGCACCGACG 60.460 55.000 0.00 0.00 32.40 5.12
1892 1932 0.457443 GGTTGGCAGCTAGATTTGGC 59.543 55.000 0.24 1.26 40.02 4.52
1896 1936 2.821969 CAGTTTGGTTGGCAGCTAGATT 59.178 45.455 0.24 0.00 0.00 2.40
1932 1972 4.865776 TCGCCTAATTTTCCAACAGTTTG 58.134 39.130 0.00 0.00 0.00 2.93
1933 1973 5.722021 ATCGCCTAATTTTCCAACAGTTT 57.278 34.783 0.00 0.00 0.00 2.66
1934 1974 5.722021 AATCGCCTAATTTTCCAACAGTT 57.278 34.783 0.00 0.00 0.00 3.16
1935 1975 5.722021 AAATCGCCTAATTTTCCAACAGT 57.278 34.783 0.00 0.00 0.00 3.55
1936 1976 7.973388 TCAATAAATCGCCTAATTTTCCAACAG 59.027 33.333 0.00 0.00 31.50 3.16
1937 1977 7.831753 TCAATAAATCGCCTAATTTTCCAACA 58.168 30.769 0.00 0.00 31.50 3.33
1938 1978 8.755018 CATCAATAAATCGCCTAATTTTCCAAC 58.245 33.333 0.00 0.00 31.50 3.77
1939 1979 8.690884 TCATCAATAAATCGCCTAATTTTCCAA 58.309 29.630 0.00 0.00 31.50 3.53
1940 1980 8.231692 TCATCAATAAATCGCCTAATTTTCCA 57.768 30.769 0.00 0.00 31.50 3.53
1941 1981 9.696917 AATCATCAATAAATCGCCTAATTTTCC 57.303 29.630 0.00 0.00 31.50 3.13
2005 2045 3.772932 AGTATGTTCGCCAAATGCATTG 58.227 40.909 13.82 7.26 41.33 2.82
2029 2073 6.141560 TGTTGTTCATGATGTTTAGTGCAA 57.858 33.333 0.00 0.00 0.00 4.08
2061 2105 5.189928 TCTAATTATGGTTGTCGCCACATT 58.810 37.500 0.00 0.00 41.94 2.71
2064 2108 4.189231 ACTCTAATTATGGTTGTCGCCAC 58.811 43.478 0.00 0.00 41.94 5.01
2066 2110 4.694339 AGACTCTAATTATGGTTGTCGCC 58.306 43.478 0.00 0.00 0.00 5.54
2067 2111 5.810587 TCAAGACTCTAATTATGGTTGTCGC 59.189 40.000 0.00 0.00 0.00 5.19
2092 2136 4.342352 TCGTATGTGCGCTATGATCTAG 57.658 45.455 9.73 0.00 0.00 2.43
2139 2184 1.135915 ACAACATCGCCTTTGCAACAA 59.864 42.857 0.00 0.00 37.32 2.83
2146 2191 2.096614 CGACGTTAACAACATCGCCTTT 60.097 45.455 6.39 0.00 40.27 3.11
2165 2210 1.890041 CGGCCTTCACCAACAACGA 60.890 57.895 0.00 0.00 0.00 3.85
2180 2225 0.235665 CAACATATGCATCGACCGGC 59.764 55.000 0.19 0.00 0.00 6.13
2185 2230 4.381566 CGTCGTTATCAACATATGCATCGA 59.618 41.667 0.19 0.00 0.00 3.59
2189 2234 3.553917 CACCGTCGTTATCAACATATGCA 59.446 43.478 1.58 0.00 0.00 3.96
2193 2238 2.186891 CGCACCGTCGTTATCAACATA 58.813 47.619 0.00 0.00 0.00 2.29
2202 2247 1.494189 GTTATTGCGCACCGTCGTT 59.506 52.632 11.12 0.00 0.00 3.85
2217 2262 4.693532 CTGCAAGGTCAGGCGTTA 57.306 55.556 0.00 0.00 0.00 3.18
2251 2296 1.210155 GCGACCGCTTGCATTCTTT 59.790 52.632 7.19 0.00 38.26 2.52
2271 2316 0.869454 TGTTTTTGGCAAGCGCTTCG 60.869 50.000 22.21 16.70 38.60 3.79
2300 2345 1.198094 TGATCCTTGCACGGGGAGAA 61.198 55.000 9.71 0.00 34.89 2.87


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

AutoCloner maintained by Alex Coulton.