Multiple sequence alignment - TraesCS4A01G146700

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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 TraesCS4A01G146700 chr4A 100.000 2680 0 0 1 2680 258638170 258635491 0.000000e+00 4950.0
1 TraesCS4A01G146700 chr4D 94.122 1429 46 6 596 2010 211741699 211740295 0.000000e+00 2139.0
2 TraesCS4A01G146700 chr4D 92.035 226 17 1 137 361 211800483 211800258 1.550000e-82 316.0
3 TraesCS4A01G146700 chr4D 94.527 201 11 0 390 590 211741945 211741745 7.200000e-81 311.0
4 TraesCS4A01G146700 chr4B 94.603 982 39 3 596 1568 316521845 316520869 0.000000e+00 1507.0
5 TraesCS4A01G146700 chr4B 90.123 567 44 9 33 590 316522448 316521885 0.000000e+00 726.0
6 TraesCS4A01G146700 chr4B 93.865 163 9 1 1848 2010 316520403 316520242 7.410000e-61 244.0
7 TraesCS4A01G146700 chr4B 93.805 113 4 3 1630 1741 316520672 316520562 1.650000e-37 167.0
8 TraesCS4A01G146700 chr4B 100.000 34 0 0 1601 1634 316520860 316520827 2.230000e-06 63.9
9 TraesCS4A01G146700 chr2A 93.939 660 38 2 2022 2680 486289050 486289708 0.000000e+00 996.0
10 TraesCS4A01G146700 chr2A 92.802 653 44 3 2029 2680 273294999 273294349 0.000000e+00 942.0
11 TraesCS4A01G146700 chr2D 93.865 652 36 2 2029 2680 236118413 236117766 0.000000e+00 979.0
12 TraesCS4A01G146700 chr6A 93.425 654 41 2 2027 2679 6696335 6695683 0.000000e+00 968.0
13 TraesCS4A01G146700 chrUn 92.988 656 43 3 2026 2680 110768598 110769251 0.000000e+00 953.0
14 TraesCS4A01G146700 chrUn 92.530 656 43 4 2026 2680 352779587 352778937 0.000000e+00 935.0
15 TraesCS4A01G146700 chrUn 92.530 656 43 4 2026 2680 367737647 367738297 0.000000e+00 935.0
16 TraesCS4A01G146700 chr5D 92.413 659 48 2 2022 2680 549467308 549467964 0.000000e+00 939.0
17 TraesCS4A01G146700 chr6B 91.791 670 52 3 2013 2680 39297831 39298499 0.000000e+00 929.0


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 TraesCS4A01G146700 chr4A 258635491 258638170 2679 True 4950.00 4950 100.0000 1 2680 1 chr4A.!!$R1 2679
1 TraesCS4A01G146700 chr4D 211740295 211741945 1650 True 1225.00 2139 94.3245 390 2010 2 chr4D.!!$R2 1620
2 TraesCS4A01G146700 chr4B 316520242 316522448 2206 True 541.58 1507 94.4792 33 2010 5 chr4B.!!$R1 1977
3 TraesCS4A01G146700 chr2A 486289050 486289708 658 False 996.00 996 93.9390 2022 2680 1 chr2A.!!$F1 658
4 TraesCS4A01G146700 chr2A 273294349 273294999 650 True 942.00 942 92.8020 2029 2680 1 chr2A.!!$R1 651
5 TraesCS4A01G146700 chr2D 236117766 236118413 647 True 979.00 979 93.8650 2029 2680 1 chr2D.!!$R1 651
6 TraesCS4A01G146700 chr6A 6695683 6696335 652 True 968.00 968 93.4250 2027 2679 1 chr6A.!!$R1 652
7 TraesCS4A01G146700 chrUn 110768598 110769251 653 False 953.00 953 92.9880 2026 2680 1 chrUn.!!$F1 654
8 TraesCS4A01G146700 chrUn 352778937 352779587 650 True 935.00 935 92.5300 2026 2680 1 chrUn.!!$R1 654
9 TraesCS4A01G146700 chrUn 367737647 367738297 650 False 935.00 935 92.5300 2026 2680 1 chrUn.!!$F2 654
10 TraesCS4A01G146700 chr5D 549467308 549467964 656 False 939.00 939 92.4130 2022 2680 1 chr5D.!!$F1 658
11 TraesCS4A01G146700 chr6B 39297831 39298499 668 False 929.00 929 91.7910 2013 2680 1 chr6B.!!$F1 667

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
494 504 0.033011 TCTTCTCTTCCCTCCTCCGG 60.033 60.0 0.0 0.0 0.0 5.14 F
1359 1418 0.324614 TCATGGATGGTGTGCTCGTT 59.675 50.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1494 1553 0.534203 TCTCCCAAACACAAGCCGAC 60.534 55.000 0.00 0.0 0.00 4.79 R
2484 2766 1.694150 ACTGAAGCAGAGTACAAGGCA 59.306 47.619 0.82 0.0 35.18 4.75 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
17 18 3.057337 GTCCGGGCGTGCCTATAT 58.943 61.111 11.25 0.00 36.10 0.86
18 19 1.080025 GTCCGGGCGTGCCTATATC 60.080 63.158 11.25 0.00 36.10 1.63
19 20 1.228769 TCCGGGCGTGCCTATATCT 60.229 57.895 11.25 0.00 36.10 1.98
20 21 1.079819 CCGGGCGTGCCTATATCTG 60.080 63.158 11.25 0.00 36.10 2.90
21 22 1.666011 CGGGCGTGCCTATATCTGT 59.334 57.895 11.25 0.00 36.10 3.41
22 23 0.388649 CGGGCGTGCCTATATCTGTC 60.389 60.000 11.25 0.00 36.10 3.51
23 24 0.037232 GGGCGTGCCTATATCTGTCC 60.037 60.000 11.25 0.00 36.10 4.02
24 25 0.969894 GGCGTGCCTATATCTGTCCT 59.030 55.000 2.98 0.00 0.00 3.85
25 26 2.168496 GGCGTGCCTATATCTGTCCTA 58.832 52.381 2.98 0.00 0.00 2.94
26 27 2.561419 GGCGTGCCTATATCTGTCCTAA 59.439 50.000 2.98 0.00 0.00 2.69
27 28 3.006537 GGCGTGCCTATATCTGTCCTAAA 59.993 47.826 2.98 0.00 0.00 1.85
28 29 4.322801 GGCGTGCCTATATCTGTCCTAAAT 60.323 45.833 2.98 0.00 0.00 1.40
29 30 5.105473 GGCGTGCCTATATCTGTCCTAAATA 60.105 44.000 2.98 0.00 0.00 1.40
30 31 6.407074 GGCGTGCCTATATCTGTCCTAAATAT 60.407 42.308 2.98 0.00 0.00 1.28
31 32 6.477033 GCGTGCCTATATCTGTCCTAAATATG 59.523 42.308 0.00 0.00 0.00 1.78
41 42 6.817184 TCTGTCCTAAATATGAGCCAAGTAC 58.183 40.000 0.00 0.00 0.00 2.73
42 43 5.925509 TGTCCTAAATATGAGCCAAGTACC 58.074 41.667 0.00 0.00 0.00 3.34
44 45 5.992217 GTCCTAAATATGAGCCAAGTACCAG 59.008 44.000 0.00 0.00 0.00 4.00
45 46 5.903010 TCCTAAATATGAGCCAAGTACCAGA 59.097 40.000 0.00 0.00 0.00 3.86
53 54 1.939838 GCCAAGTACCAGAAGTGTCGG 60.940 57.143 0.00 0.00 0.00 4.79
56 57 0.879765 AGTACCAGAAGTGTCGGTCG 59.120 55.000 0.00 0.00 34.13 4.79
60 61 1.080705 CAGAAGTGTCGGTCGGTCC 60.081 63.158 0.00 0.00 0.00 4.46
83 84 1.002900 ACGTGAGTGTCAAATTTGCCG 60.003 47.619 13.54 9.19 46.97 5.69
84 85 1.262950 CGTGAGTGTCAAATTTGCCGA 59.737 47.619 13.54 0.00 0.00 5.54
87 88 2.948979 TGAGTGTCAAATTTGCCGAGTT 59.051 40.909 13.54 0.00 0.00 3.01
91 92 4.109050 GTGTCAAATTTGCCGAGTTTGAA 58.891 39.130 13.54 0.00 41.77 2.69
93 94 5.918011 GTGTCAAATTTGCCGAGTTTGAATA 59.082 36.000 13.54 0.00 41.77 1.75
94 95 6.586082 GTGTCAAATTTGCCGAGTTTGAATAT 59.414 34.615 13.54 0.00 41.77 1.28
99 100 5.446143 TTTGCCGAGTTTGAATATGTGTT 57.554 34.783 0.00 0.00 0.00 3.32
111 112 7.804614 TTGAATATGTGTTAAATTTGCGTCC 57.195 32.000 0.00 0.00 0.00 4.79
112 113 6.914259 TGAATATGTGTTAAATTTGCGTCCA 58.086 32.000 0.00 0.00 0.00 4.02
113 114 7.371159 TGAATATGTGTTAAATTTGCGTCCAA 58.629 30.769 0.00 0.00 0.00 3.53
122 123 2.166829 ATTTGCGTCCAAATAGTGGCA 58.833 42.857 0.18 0.00 46.83 4.92
127 128 3.513225 CCAAATAGTGGCAGGCCG 58.487 61.111 5.74 0.00 41.72 6.13
139 146 3.061848 AGGCCGCCGAATGTTTGG 61.062 61.111 3.05 0.00 34.66 3.28
144 151 4.128388 GCCGAATGTTTGGGGCGG 62.128 66.667 0.00 0.00 44.47 6.13
150 157 1.548269 GAATGTTTGGGGCGGAAATGA 59.452 47.619 0.00 0.00 0.00 2.57
183 190 7.328737 GGTTCTAGATGCTCTTACAAACCTTA 58.671 38.462 0.00 0.00 0.00 2.69
186 193 7.548097 TCTAGATGCTCTTACAAACCTTAGTG 58.452 38.462 0.00 0.00 0.00 2.74
192 199 2.572209 TACAAACCTTAGTGGGCCAC 57.428 50.000 29.32 29.32 41.11 5.01
207 214 2.589157 CCACGTTAGGAGGCACCCA 61.589 63.158 0.00 0.00 40.05 4.51
208 215 1.373435 CACGTTAGGAGGCACCCAA 59.627 57.895 0.00 0.00 40.05 4.12
209 216 0.250553 CACGTTAGGAGGCACCCAAA 60.251 55.000 0.00 0.00 40.05 3.28
265 275 6.500589 AATGTTAAGGAGGATGCTAAGCTA 57.499 37.500 0.00 0.00 33.13 3.32
292 302 4.015872 ACAAAATTAAGGAGGACGCAGA 57.984 40.909 0.00 0.00 0.00 4.26
303 313 1.098712 GGACGCAGAGATCTCGACCT 61.099 60.000 16.97 3.48 35.72 3.85
365 375 3.740764 GCACAGCTGAAAATTCAAACCCA 60.741 43.478 23.35 0.00 36.64 4.51
396 406 1.278637 GCCGCGCGTATTTATGCTT 59.721 52.632 29.95 0.00 36.10 3.91
443 453 2.146342 TCGAAAAAGAAGCTGCTCCTG 58.854 47.619 1.00 0.00 0.00 3.86
494 504 0.033011 TCTTCTCTTCCCTCCTCCGG 60.033 60.000 0.00 0.00 0.00 5.14
590 600 1.517257 CTGGTAGGTGCTTCGCTCG 60.517 63.158 0.00 0.00 0.00 5.03
591 601 2.886124 GGTAGGTGCTTCGCTCGC 60.886 66.667 0.00 0.00 0.00 5.03
619 669 2.729360 CGAATGCTTGTGTTCTCGTACA 59.271 45.455 0.00 0.00 0.00 2.90
638 688 5.506649 CGTACATTCGGGGATTTTATTTGGG 60.507 44.000 0.00 0.00 0.00 4.12
680 730 3.633065 TGTTTAAGGGGTTCTCGTTTTGG 59.367 43.478 0.00 0.00 0.00 3.28
736 786 3.641437 TTTCGCTTGGACTTGGAATTG 57.359 42.857 0.00 0.00 0.00 2.32
792 842 1.300620 CTCGTGCGGTTCTGTTGGA 60.301 57.895 0.00 0.00 0.00 3.53
799 849 1.202211 GCGGTTCTGTTGGACGTTTTT 60.202 47.619 0.00 0.00 0.00 1.94
851 907 1.735571 CCAAATCGAACCAGGTTACGG 59.264 52.381 18.38 7.48 0.00 4.02
929 985 3.181525 TGCACTGTTTCGCGTGTATATTG 60.182 43.478 5.77 0.00 33.78 1.90
1139 1195 0.674581 CTCATGCTGGCCTTCAACGA 60.675 55.000 3.32 2.58 0.00 3.85
1156 1212 2.046892 ATGCTGCTGGTGACGGTC 60.047 61.111 0.00 0.00 39.64 4.79
1239 1298 2.264794 CACCCCCGCTACAGTCAC 59.735 66.667 0.00 0.00 0.00 3.67
1351 1410 0.536724 TGTCCTCGTCATGGATGGTG 59.463 55.000 0.00 0.00 35.87 4.17
1352 1411 0.537188 GTCCTCGTCATGGATGGTGT 59.463 55.000 0.00 0.00 35.87 4.16
1353 1412 0.536724 TCCTCGTCATGGATGGTGTG 59.463 55.000 0.00 0.00 0.00 3.82
1359 1418 0.324614 TCATGGATGGTGTGCTCGTT 59.675 50.000 0.00 0.00 0.00 3.85
1404 1463 2.885861 CGCTACGCCTCCTTCACT 59.114 61.111 0.00 0.00 0.00 3.41
1494 1553 5.390885 CCAGGTAATCGATTCACACTTGTTG 60.391 44.000 15.25 5.67 0.00 3.33
1581 1640 2.945447 ATGGTTTCATGGTCGCATTG 57.055 45.000 0.00 0.00 31.34 2.82
1582 1641 1.614996 TGGTTTCATGGTCGCATTGT 58.385 45.000 0.00 0.00 0.00 2.71
1583 1642 1.269174 TGGTTTCATGGTCGCATTGTG 59.731 47.619 0.00 0.00 0.00 3.33
1584 1643 1.339711 GTTTCATGGTCGCATTGTGC 58.660 50.000 0.00 0.00 40.69 4.57
1585 1644 1.068333 GTTTCATGGTCGCATTGTGCT 60.068 47.619 0.00 0.00 42.25 4.40
1586 1645 1.246649 TTCATGGTCGCATTGTGCTT 58.753 45.000 0.00 0.00 42.25 3.91
1587 1646 1.246649 TCATGGTCGCATTGTGCTTT 58.753 45.000 0.00 0.00 42.25 3.51
1588 1647 2.431454 TCATGGTCGCATTGTGCTTTA 58.569 42.857 0.00 0.00 42.25 1.85
1589 1648 2.419673 TCATGGTCGCATTGTGCTTTAG 59.580 45.455 0.00 0.00 42.25 1.85
1590 1649 0.521291 TGGTCGCATTGTGCTTTAGC 59.479 50.000 0.10 0.00 42.25 3.09
1634 1693 2.412325 GGAAGATTGCGTGGTGTTAACG 60.412 50.000 0.26 0.00 43.81 3.18
1771 1994 4.486125 TGGTAGATCACTTTGCATGCTA 57.514 40.909 20.33 8.83 0.00 3.49
1817 2040 9.768215 AATAGGGAAAAAGGAATGTTGAGATTA 57.232 29.630 0.00 0.00 0.00 1.75
1864 2139 3.243839 TGAGAAAAGAGCCAATGCAAACC 60.244 43.478 0.00 0.00 41.13 3.27
1875 2150 4.095782 GCCAATGCAAACCGAGAAGTTATA 59.904 41.667 0.00 0.00 37.47 0.98
1876 2151 5.730568 GCCAATGCAAACCGAGAAGTTATAG 60.731 44.000 0.00 0.00 37.47 1.31
1901 2176 6.486320 GGAAATGAAAAGAAAATTTGGGAGCA 59.514 34.615 0.00 0.00 0.00 4.26
1910 2185 6.355747 AGAAAATTTGGGAGCAATTGTTTCA 58.644 32.000 7.40 1.52 0.00 2.69
1923 2198 7.885297 AGCAATTGTTTCAGTAGATTAAAGCA 58.115 30.769 7.40 0.00 0.00 3.91
1958 2233 2.906389 TCAAGGCAGACCAAGAGTACAT 59.094 45.455 0.00 0.00 39.06 2.29
1998 2273 5.278758 GCTTTGCTTACTGGAAACCATGTTA 60.279 40.000 0.00 0.00 32.58 2.41
2010 2285 5.447279 GGAAACCATGTTATGTAGTTGCTCG 60.447 44.000 0.00 0.00 0.00 5.03
2011 2286 2.936498 ACCATGTTATGTAGTTGCTCGC 59.064 45.455 0.00 0.00 0.00 5.03
2019 2294 6.203145 TGTTATGTAGTTGCTCGCTGTAAAAA 59.797 34.615 0.00 0.00 0.00 1.94
2127 2404 8.713708 AGATACAAGGTATACACAGAAGCTAT 57.286 34.615 5.01 0.00 0.00 2.97
2248 2529 2.143122 GTGGCTTCGTGAAGATGTCAA 58.857 47.619 13.60 0.00 39.78 3.18
2327 2608 5.762179 TCCCTCACAAAGTGATAGTCAAT 57.238 39.130 0.00 0.00 41.94 2.57
2570 2852 3.476552 TCAAGTTGCGACCAAAGAAGAT 58.523 40.909 0.00 0.00 31.68 2.40
2611 2893 1.699054 CCGATCATCCAGGCTCCCAA 61.699 60.000 0.00 0.00 0.00 4.12
2622 2904 2.409870 GCTCCCAACCCAATCTGCG 61.410 63.158 0.00 0.00 0.00 5.18
2624 2906 0.609131 CTCCCAACCCAATCTGCGTT 60.609 55.000 0.00 0.00 0.00 4.84
2663 2945 2.420722 CACTCGAGGAGGTAGACTGAAC 59.579 54.545 18.41 0.00 33.35 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.079819 CAGATATAGGCACGCCCGG 60.080 63.158 3.95 0.00 39.21 5.73
3 4 0.388649 GACAGATATAGGCACGCCCG 60.389 60.000 3.95 0.00 39.21 6.13
6 7 3.936372 TTAGGACAGATATAGGCACGC 57.064 47.619 0.00 0.00 0.00 5.34
7 8 7.772166 TCATATTTAGGACAGATATAGGCACG 58.228 38.462 0.00 0.00 0.00 5.34
8 9 7.708752 GCTCATATTTAGGACAGATATAGGCAC 59.291 40.741 0.00 0.00 0.00 5.01
9 10 7.147655 GGCTCATATTTAGGACAGATATAGGCA 60.148 40.741 0.00 0.00 0.00 4.75
10 11 7.147655 TGGCTCATATTTAGGACAGATATAGGC 60.148 40.741 0.00 0.00 0.00 3.93
11 12 8.311395 TGGCTCATATTTAGGACAGATATAGG 57.689 38.462 0.00 0.00 0.00 2.57
12 13 9.814899 CTTGGCTCATATTTAGGACAGATATAG 57.185 37.037 0.00 0.00 0.00 1.31
13 14 9.326489 ACTTGGCTCATATTTAGGACAGATATA 57.674 33.333 0.00 0.00 0.00 0.86
14 15 8.212259 ACTTGGCTCATATTTAGGACAGATAT 57.788 34.615 0.00 0.00 0.00 1.63
15 16 7.618019 ACTTGGCTCATATTTAGGACAGATA 57.382 36.000 0.00 0.00 0.00 1.98
16 17 6.506538 ACTTGGCTCATATTTAGGACAGAT 57.493 37.500 0.00 0.00 0.00 2.90
17 18 5.957771 ACTTGGCTCATATTTAGGACAGA 57.042 39.130 0.00 0.00 0.00 3.41
18 19 5.992217 GGTACTTGGCTCATATTTAGGACAG 59.008 44.000 0.00 0.00 0.00 3.51
19 20 5.427157 TGGTACTTGGCTCATATTTAGGACA 59.573 40.000 0.00 0.00 0.00 4.02
20 21 5.925509 TGGTACTTGGCTCATATTTAGGAC 58.074 41.667 0.00 0.00 0.00 3.85
21 22 5.903010 TCTGGTACTTGGCTCATATTTAGGA 59.097 40.000 0.00 0.00 0.00 2.94
22 23 6.174720 TCTGGTACTTGGCTCATATTTAGG 57.825 41.667 0.00 0.00 0.00 2.69
23 24 7.225538 CACTTCTGGTACTTGGCTCATATTTAG 59.774 40.741 0.00 0.00 0.00 1.85
24 25 7.047891 CACTTCTGGTACTTGGCTCATATTTA 58.952 38.462 0.00 0.00 0.00 1.40
25 26 5.882557 CACTTCTGGTACTTGGCTCATATTT 59.117 40.000 0.00 0.00 0.00 1.40
26 27 5.045578 ACACTTCTGGTACTTGGCTCATATT 60.046 40.000 0.00 0.00 0.00 1.28
27 28 4.471386 ACACTTCTGGTACTTGGCTCATAT 59.529 41.667 0.00 0.00 0.00 1.78
28 29 3.838317 ACACTTCTGGTACTTGGCTCATA 59.162 43.478 0.00 0.00 0.00 2.15
29 30 2.639839 ACACTTCTGGTACTTGGCTCAT 59.360 45.455 0.00 0.00 0.00 2.90
30 31 2.037251 GACACTTCTGGTACTTGGCTCA 59.963 50.000 0.00 0.00 0.00 4.26
31 32 2.689646 GACACTTCTGGTACTTGGCTC 58.310 52.381 0.00 0.00 0.00 4.70
41 42 1.080705 GACCGACCGACACTTCTGG 60.081 63.158 0.00 0.00 0.00 3.86
42 43 1.080705 GGACCGACCGACACTTCTG 60.081 63.158 0.00 0.00 0.00 3.02
53 54 3.360340 ACTCACGTCCGGACCGAC 61.360 66.667 28.52 10.75 0.00 4.79
56 57 2.079020 TTGACACTCACGTCCGGACC 62.079 60.000 28.52 12.33 34.88 4.46
60 61 2.903678 CAAATTTGACACTCACGTCCG 58.096 47.619 13.08 0.00 34.88 4.79
67 68 3.626028 AACTCGGCAAATTTGACACTC 57.374 42.857 23.49 4.64 35.35 3.51
74 75 6.454795 ACACATATTCAAACTCGGCAAATTT 58.545 32.000 0.00 0.00 0.00 1.82
83 84 8.911662 ACGCAAATTTAACACATATTCAAACTC 58.088 29.630 0.00 0.00 0.00 3.01
84 85 8.810652 ACGCAAATTTAACACATATTCAAACT 57.189 26.923 0.00 0.00 0.00 2.66
87 88 7.371159 TGGACGCAAATTTAACACATATTCAA 58.629 30.769 0.00 0.00 0.00 2.69
91 92 9.515020 CTATTTGGACGCAAATTTAACACATAT 57.485 29.630 6.36 0.00 36.35 1.78
93 94 7.328249 CACTATTTGGACGCAAATTTAACACAT 59.672 33.333 6.36 0.00 36.35 3.21
94 95 6.638873 CACTATTTGGACGCAAATTTAACACA 59.361 34.615 6.36 0.00 36.35 3.72
111 112 2.800736 GCGGCCTGCCACTATTTG 59.199 61.111 9.17 0.00 37.76 2.32
120 121 3.747976 AAACATTCGGCGGCCTGC 61.748 61.111 18.34 10.60 45.38 4.85
122 123 3.061848 CCAAACATTCGGCGGCCT 61.062 61.111 18.34 0.00 0.00 5.19
125 126 4.128388 GCCCCAAACATTCGGCGG 62.128 66.667 7.21 0.00 0.00 6.13
127 128 4.128388 CCGCCCCAAACATTCGGC 62.128 66.667 0.00 0.00 38.07 5.54
129 136 0.530288 ATTTCCGCCCCAAACATTCG 59.470 50.000 0.00 0.00 0.00 3.34
131 138 1.638529 TCATTTCCGCCCCAAACATT 58.361 45.000 0.00 0.00 0.00 2.71
133 140 1.414158 TTTCATTTCCGCCCCAAACA 58.586 45.000 0.00 0.00 0.00 2.83
139 146 0.100503 CGGACATTTCATTTCCGCCC 59.899 55.000 0.00 0.00 45.35 6.13
143 150 5.183228 TCTAGAACCGGACATTTCATTTCC 58.817 41.667 9.46 0.00 0.00 3.13
144 151 6.719365 CATCTAGAACCGGACATTTCATTTC 58.281 40.000 9.46 0.00 0.00 2.17
150 157 3.798202 GAGCATCTAGAACCGGACATTT 58.202 45.455 9.46 0.00 0.00 2.32
183 190 2.291043 CCTCCTAACGTGGCCCACT 61.291 63.158 12.94 0.00 31.34 4.00
192 199 1.611519 TTTTTGGGTGCCTCCTAACG 58.388 50.000 0.00 0.00 36.41 3.18
292 302 5.578005 TTTCATTCGTTAGGTCGAGATCT 57.422 39.130 0.00 0.00 40.86 2.75
365 375 4.292178 GCGGCGCCTCTCAGCTAT 62.292 66.667 26.68 0.00 0.00 2.97
418 428 4.540824 GAGCAGCTTCTTTTTCGATTTGT 58.459 39.130 0.00 0.00 0.00 2.83
443 453 2.743179 GGGGGAACGGAGGTGGATC 61.743 68.421 0.00 0.00 0.00 3.36
538 548 2.124507 TACCTTGCAGAGCCCACACC 62.125 60.000 0.00 0.00 0.00 4.16
540 550 1.374947 GTACCTTGCAGAGCCCACA 59.625 57.895 0.00 0.00 0.00 4.17
590 600 0.379669 CACAAGCATTCGGATGGAGC 59.620 55.000 5.68 0.00 33.72 4.70
591 601 1.742761 ACACAAGCATTCGGATGGAG 58.257 50.000 5.68 0.00 33.72 3.86
619 669 3.051727 TCCCCCAAATAAAATCCCCGAAT 60.052 43.478 0.00 0.00 0.00 3.34
680 730 4.513442 TCATAAGCAACTGGATACACACC 58.487 43.478 0.00 0.00 46.17 4.16
792 842 5.233263 CGGAAATTCAAACCATCAAAAACGT 59.767 36.000 0.00 0.00 0.00 3.99
799 849 4.642885 GGATACCGGAAATTCAAACCATCA 59.357 41.667 9.46 0.00 0.00 3.07
929 985 1.900237 ACGCGGTACTAAATGTCGAC 58.100 50.000 12.47 9.11 0.00 4.20
964 1020 2.991250 AGCGGATTAGTGTTGCAGATT 58.009 42.857 0.00 0.00 0.00 2.40
965 1021 2.698855 AGCGGATTAGTGTTGCAGAT 57.301 45.000 0.00 0.00 0.00 2.90
966 1022 2.346803 GAAGCGGATTAGTGTTGCAGA 58.653 47.619 0.00 0.00 0.00 4.26
967 1023 1.398390 GGAAGCGGATTAGTGTTGCAG 59.602 52.381 0.00 0.00 0.00 4.41
968 1024 1.003118 AGGAAGCGGATTAGTGTTGCA 59.997 47.619 0.00 0.00 0.00 4.08
969 1025 1.666189 GAGGAAGCGGATTAGTGTTGC 59.334 52.381 0.00 0.00 0.00 4.17
970 1026 2.280628 GGAGGAAGCGGATTAGTGTTG 58.719 52.381 0.00 0.00 0.00 3.33
971 1027 1.134788 CGGAGGAAGCGGATTAGTGTT 60.135 52.381 0.00 0.00 0.00 3.32
972 1028 0.460311 CGGAGGAAGCGGATTAGTGT 59.540 55.000 0.00 0.00 0.00 3.55
1059 1115 2.125912 GCTGACGCGTCCACTGAT 60.126 61.111 34.34 0.00 0.00 2.90
1139 1195 2.046892 GACCGTCACCAGCAGCAT 60.047 61.111 0.00 0.00 0.00 3.79
1156 1212 4.530857 GGACGACCTCCCGCCATG 62.531 72.222 0.00 0.00 31.83 3.66
1239 1298 2.677524 TCGGGGTAGACACGGTGG 60.678 66.667 13.48 0.00 0.00 4.61
1494 1553 0.534203 TCTCCCAAACACAAGCCGAC 60.534 55.000 0.00 0.00 0.00 4.79
1583 1642 7.275560 CCATAAACCATACAGTTTTGCTAAAGC 59.724 37.037 0.00 0.00 40.38 3.51
1584 1643 8.303876 ACCATAAACCATACAGTTTTGCTAAAG 58.696 33.333 0.00 0.00 40.38 1.85
1585 1644 8.184304 ACCATAAACCATACAGTTTTGCTAAA 57.816 30.769 0.00 0.00 40.38 1.85
1586 1645 7.668052 AGACCATAAACCATACAGTTTTGCTAA 59.332 33.333 0.00 0.00 40.38 3.09
1587 1646 7.120579 CAGACCATAAACCATACAGTTTTGCTA 59.879 37.037 0.00 0.00 40.38 3.49
1588 1647 6.010219 AGACCATAAACCATACAGTTTTGCT 58.990 36.000 0.00 0.00 40.38 3.91
1589 1648 6.092748 CAGACCATAAACCATACAGTTTTGC 58.907 40.000 0.00 0.00 40.38 3.68
1590 1649 6.432783 TCCAGACCATAAACCATACAGTTTTG 59.567 38.462 0.00 0.00 40.38 2.44
1591 1650 6.548321 TCCAGACCATAAACCATACAGTTTT 58.452 36.000 0.00 0.00 40.38 2.43
1592 1651 6.134535 TCCAGACCATAAACCATACAGTTT 57.865 37.500 0.00 0.00 42.47 2.66
1593 1652 5.772393 TCCAGACCATAAACCATACAGTT 57.228 39.130 0.00 0.00 0.00 3.16
1594 1653 5.487488 TCTTCCAGACCATAAACCATACAGT 59.513 40.000 0.00 0.00 0.00 3.55
1595 1654 5.989477 TCTTCCAGACCATAAACCATACAG 58.011 41.667 0.00 0.00 0.00 2.74
1596 1655 6.575244 ATCTTCCAGACCATAAACCATACA 57.425 37.500 0.00 0.00 0.00 2.29
1597 1656 6.238759 GCAATCTTCCAGACCATAAACCATAC 60.239 42.308 0.00 0.00 0.00 2.39
1598 1657 5.827797 GCAATCTTCCAGACCATAAACCATA 59.172 40.000 0.00 0.00 0.00 2.74
1599 1658 4.646492 GCAATCTTCCAGACCATAAACCAT 59.354 41.667 0.00 0.00 0.00 3.55
1771 1994 8.695456 CCCTATTTGTAAACAGGATTAAAGCAT 58.305 33.333 3.30 0.00 31.41 3.79
1784 2007 9.772973 AACATTCCTTTTTCCCTATTTGTAAAC 57.227 29.630 0.00 0.00 0.00 2.01
1817 2040 5.242795 ACTTGTCCAACTATAAAGCACCT 57.757 39.130 0.00 0.00 0.00 4.00
1875 2150 6.712095 GCTCCCAAATTTTCTTTTCATTTCCT 59.288 34.615 0.00 0.00 0.00 3.36
1876 2151 6.486320 TGCTCCCAAATTTTCTTTTCATTTCC 59.514 34.615 0.00 0.00 0.00 3.13
1910 2185 9.959721 TGAACTCCTAAAATGCTTTAATCTACT 57.040 29.630 0.00 0.00 0.00 2.57
1923 2198 5.649831 GTCTGCCTTGATGAACTCCTAAAAT 59.350 40.000 0.00 0.00 0.00 1.82
1929 2204 1.003580 TGGTCTGCCTTGATGAACTCC 59.996 52.381 0.00 0.00 35.27 3.85
1958 2233 3.137484 AGCGTGCAAGCTTATTCGA 57.863 47.368 21.99 0.00 46.80 3.71
1998 2273 4.755123 AGTTTTTACAGCGAGCAACTACAT 59.245 37.500 0.00 0.00 0.00 2.29
2010 2285 4.146564 TCCCAAACCCTAGTTTTTACAGC 58.853 43.478 0.00 0.00 43.82 4.40
2011 2286 6.322969 AGTTTCCCAAACCCTAGTTTTTACAG 59.677 38.462 0.00 0.00 43.82 2.74
2019 2294 1.780919 AGCAGTTTCCCAAACCCTAGT 59.219 47.619 0.00 0.00 42.34 2.57
2127 2404 8.434392 GGGAGGGTGTTAGATAATGTTTATACA 58.566 37.037 0.00 0.00 38.95 2.29
2248 2529 4.982241 TCTCCTCCAAAGATCAACTTGT 57.018 40.909 0.00 0.00 38.98 3.16
2327 2608 2.333926 CTCGTACCAAGCACATCGAAA 58.666 47.619 0.00 0.00 0.00 3.46
2484 2766 1.694150 ACTGAAGCAGAGTACAAGGCA 59.306 47.619 0.82 0.00 35.18 4.75
2591 2873 1.838846 GGGAGCCTGGATGATCGGA 60.839 63.158 0.00 0.00 0.00 4.55
2611 2893 2.301870 TGTTCTCTAACGCAGATTGGGT 59.698 45.455 0.00 0.00 45.92 4.51
2622 2904 2.488545 TGCTCTCTCGGTGTTCTCTAAC 59.511 50.000 0.00 0.00 36.07 2.34
2624 2906 2.085320 GTGCTCTCTCGGTGTTCTCTA 58.915 52.381 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.