Multiple sequence alignment - TraesCS5B01G406800

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 TraesCS5B01G406800 chr5B 100.000 4245 0 0 1 4245 582892325 582888081 0.000000e+00 7840.0
1 TraesCS5B01G406800 chr5B 98.936 94 1 0 1 94 341507951 341508044 7.300000e-38 169.0
2 TraesCS5B01G406800 chr5B 86.076 79 11 0 997 1075 411932010 411931932 7.560000e-13 86.1
3 TraesCS5B01G406800 chr5A 91.211 3368 197 47 334 3657 594965024 594961712 0.000000e+00 4488.0
4 TraesCS5B01G406800 chr5A 89.703 437 37 5 3808 4242 594961563 594961133 6.200000e-153 551.0
5 TraesCS5B01G406800 chr5A 90.837 251 13 5 101 344 594965939 594965692 1.140000e-85 327.0
6 TraesCS5B01G406800 chr5A 83.019 106 17 1 997 1101 451480977 451480872 1.260000e-15 95.3
7 TraesCS5B01G406800 chr5A 100.000 31 0 0 4147 4177 688713119 688713089 1.650000e-04 58.4
8 TraesCS5B01G406800 chr5D 91.599 1845 103 28 94 1905 475512426 475510601 0.000000e+00 2501.0
9 TraesCS5B01G406800 chr5D 94.800 1000 22 13 2674 3657 475509844 475508859 0.000000e+00 1531.0
10 TraesCS5B01G406800 chr5D 93.497 815 47 5 1894 2707 475510654 475509845 0.000000e+00 1206.0
11 TraesCS5B01G406800 chr5D 89.011 364 24 2 3883 4245 475508620 475508272 1.810000e-118 436.0
12 TraesCS5B01G406800 chr5D 88.333 240 13 4 3676 3901 475508868 475508630 1.500000e-69 274.0
13 TraesCS5B01G406800 chr5D 86.726 113 13 2 3999 4109 475508620 475508508 1.600000e-24 124.0
14 TraesCS5B01G406800 chr5D 83.019 106 17 1 997 1101 351007372 351007267 1.260000e-15 95.3
15 TraesCS5B01G406800 chr2B 100.000 94 0 0 1 94 164092144 164092051 1.570000e-39 174.0
16 TraesCS5B01G406800 chr2B 98.936 94 1 0 1 94 131603697 131603790 7.300000e-38 169.0
17 TraesCS5B01G406800 chr1B 100.000 94 0 0 1 94 670408157 670408250 1.570000e-39 174.0
18 TraesCS5B01G406800 chr1A 100.000 94 0 0 1 94 579777745 579777838 1.570000e-39 174.0
19 TraesCS5B01G406800 chr4A 97.872 94 2 0 1 94 718418210 718418303 3.400000e-36 163.0
20 TraesCS5B01G406800 chr3B 97.872 94 2 0 1 94 32380360 32380267 3.400000e-36 163.0
21 TraesCS5B01G406800 chr3B 92.857 42 2 1 4147 4187 430241211 430241252 4.580000e-05 60.2
22 TraesCS5B01G406800 chr6B 96.809 94 3 0 1 94 51769819 51769726 1.580000e-34 158.0
23 TraesCS5B01G406800 chr3A 96.809 94 3 0 1 94 84033330 84033423 1.580000e-34 158.0


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 TraesCS5B01G406800 chr5B 582888081 582892325 4244 True 7840.000000 7840 100.000000 1 4245 1 chr5B.!!$R2 4244
1 TraesCS5B01G406800 chr5A 594961133 594965939 4806 True 1788.666667 4488 90.583667 101 4242 3 chr5A.!!$R3 4141
2 TraesCS5B01G406800 chr5D 475508272 475512426 4154 True 1012.000000 2501 90.661000 94 4245 6 chr5D.!!$R2 4151

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
43 44 0.109913 AAAGAACAGACCCGGGGTTC 59.890 55.0 27.92 26.39 40.84 3.62 F
1581 2310 0.318699 ATATCATCACCGGTGCGTCG 60.319 55.0 30.25 16.67 0.00 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1620 2349 0.112995 AAGGCACATGTGTGGATGGT 59.887 50.0 26.01 3.46 45.72 3.55 R
3252 4026 0.885196 TTAGCATTGCCGAACCAACC 59.115 50.0 4.70 0.00 0.00 3.77 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 4.926207 CCTAACCCTACCACACGC 57.074 61.111 0.00 0.00 0.00 5.34
18 19 1.219935 CCTAACCCTACCACACGCC 59.780 63.158 0.00 0.00 0.00 5.68
19 20 1.219935 CTAACCCTACCACACGCCC 59.780 63.158 0.00 0.00 0.00 6.13
20 21 1.535930 TAACCCTACCACACGCCCA 60.536 57.895 0.00 0.00 0.00 5.36
21 22 1.829523 TAACCCTACCACACGCCCAC 61.830 60.000 0.00 0.00 0.00 4.61
22 23 4.404098 CCCTACCACACGCCCACC 62.404 72.222 0.00 0.00 0.00 4.61
23 24 3.319198 CCTACCACACGCCCACCT 61.319 66.667 0.00 0.00 0.00 4.00
24 25 1.985662 CCTACCACACGCCCACCTA 60.986 63.158 0.00 0.00 0.00 3.08
25 26 1.546589 CCTACCACACGCCCACCTAA 61.547 60.000 0.00 0.00 0.00 2.69
26 27 0.322322 CTACCACACGCCCACCTAAA 59.678 55.000 0.00 0.00 0.00 1.85
27 28 0.322322 TACCACACGCCCACCTAAAG 59.678 55.000 0.00 0.00 0.00 1.85
28 29 1.373435 CCACACGCCCACCTAAAGA 59.627 57.895 0.00 0.00 0.00 2.52
29 30 0.250553 CCACACGCCCACCTAAAGAA 60.251 55.000 0.00 0.00 0.00 2.52
30 31 0.872388 CACACGCCCACCTAAAGAAC 59.128 55.000 0.00 0.00 0.00 3.01
31 32 0.470766 ACACGCCCACCTAAAGAACA 59.529 50.000 0.00 0.00 0.00 3.18
32 33 1.156736 CACGCCCACCTAAAGAACAG 58.843 55.000 0.00 0.00 0.00 3.16
33 34 1.053424 ACGCCCACCTAAAGAACAGA 58.947 50.000 0.00 0.00 0.00 3.41
34 35 1.270678 ACGCCCACCTAAAGAACAGAC 60.271 52.381 0.00 0.00 0.00 3.51
35 36 1.822506 GCCCACCTAAAGAACAGACC 58.177 55.000 0.00 0.00 0.00 3.85
36 37 1.613520 GCCCACCTAAAGAACAGACCC 60.614 57.143 0.00 0.00 0.00 4.46
37 38 1.338769 CCCACCTAAAGAACAGACCCG 60.339 57.143 0.00 0.00 0.00 5.28
38 39 1.338769 CCACCTAAAGAACAGACCCGG 60.339 57.143 0.00 0.00 0.00 5.73
39 40 0.981943 ACCTAAAGAACAGACCCGGG 59.018 55.000 22.25 22.25 0.00 5.73
40 41 0.252197 CCTAAAGAACAGACCCGGGG 59.748 60.000 27.92 12.73 0.00 5.73
41 42 0.981943 CTAAAGAACAGACCCGGGGT 59.018 55.000 27.92 21.21 39.44 4.95
42 43 1.350019 CTAAAGAACAGACCCGGGGTT 59.650 52.381 27.92 19.62 35.25 4.11
43 44 0.109913 AAAGAACAGACCCGGGGTTC 59.890 55.000 27.92 26.39 40.84 3.62
44 45 1.775934 AAGAACAGACCCGGGGTTCC 61.776 60.000 27.69 8.64 41.32 3.62
45 46 3.254617 AACAGACCCGGGGTTCCC 61.255 66.667 27.92 7.81 41.09 3.97
83 84 3.578272 CGGCCGACGGAGAGAGAG 61.578 72.222 24.07 0.00 39.42 3.20
84 85 3.213402 GGCCGACGGAGAGAGAGG 61.213 72.222 20.50 0.00 0.00 3.69
85 86 3.213402 GCCGACGGAGAGAGAGGG 61.213 72.222 20.50 0.00 0.00 4.30
86 87 2.590645 CCGACGGAGAGAGAGGGA 59.409 66.667 8.64 0.00 0.00 4.20
87 88 1.077644 CCGACGGAGAGAGAGGGAA 60.078 63.158 8.64 0.00 0.00 3.97
88 89 1.378124 CCGACGGAGAGAGAGGGAAC 61.378 65.000 8.64 0.00 0.00 3.62
138 139 8.781196 GTTAGTGGATCGTAGATGTGATTACTA 58.219 37.037 0.00 0.00 45.12 1.82
148 159 9.500864 CGTAGATGTGATTACTATGATCAGATG 57.499 37.037 0.09 0.00 37.56 2.90
150 161 7.849160 AGATGTGATTACTATGATCAGATGGG 58.151 38.462 0.09 0.00 37.56 4.00
171 182 4.995487 GGGTAGATAGGGATAAAAGTTGCG 59.005 45.833 0.00 0.00 0.00 4.85
202 213 2.266055 GGAGTTGACGGGGAGCAG 59.734 66.667 0.00 0.00 0.00 4.24
203 214 2.435059 GAGTTGACGGGGAGCAGC 60.435 66.667 0.00 0.00 0.00 5.25
204 215 3.240134 GAGTTGACGGGGAGCAGCA 62.240 63.158 0.00 0.00 0.00 4.41
220 231 4.347607 AGCAGCAAACTCCCTCAAAATAT 58.652 39.130 0.00 0.00 0.00 1.28
339 353 6.206634 TCATGGGTTGTGAAAACTGTATTCTC 59.793 38.462 0.00 0.00 0.00 2.87
341 355 4.083484 GGGTTGTGAAAACTGTATTCTCCG 60.083 45.833 0.00 0.00 0.00 4.63
347 1042 4.748102 TGAAAACTGTATTCTCCGTGTCAC 59.252 41.667 0.00 0.00 0.00 3.67
355 1050 4.337060 TCCGTGTCACTCGTGCCG 62.337 66.667 0.65 0.00 0.00 5.69
487 1188 4.676018 CCAAATACAACACGGGTAAAAACG 59.324 41.667 0.00 0.00 0.00 3.60
520 1221 1.270907 AACAGGAGATTCACCGCTCT 58.729 50.000 0.00 0.00 0.00 4.09
527 1228 3.265791 GAGATTCACCGCTCTGTTCAAT 58.734 45.455 0.00 0.00 0.00 2.57
529 1230 4.074970 AGATTCACCGCTCTGTTCAATTT 58.925 39.130 0.00 0.00 0.00 1.82
689 1412 1.144936 CCATCTCCCACTTCTCCGC 59.855 63.158 0.00 0.00 0.00 5.54
756 1479 2.427753 GGCCTCCTATCGCCCAAG 59.572 66.667 0.00 0.00 39.39 3.61
760 1483 0.760945 CCTCCTATCGCCCAAGACCT 60.761 60.000 0.00 0.00 0.00 3.85
847 1570 3.528370 CCGACTCCGCCGATCCTT 61.528 66.667 0.00 0.00 0.00 3.36
971 1694 0.790814 CGCCAAGACTCGACCTTTTC 59.209 55.000 0.00 0.00 0.00 2.29
1320 2049 2.598394 GGCAGGCAGCTGACCAAA 60.598 61.111 18.28 0.00 44.79 3.28
1335 2064 3.387947 AAACTCGTCCCCGCCGAT 61.388 61.111 0.00 0.00 33.27 4.18
1368 2097 2.561885 CTGTTCGTCTCGCCGTCT 59.438 61.111 0.00 0.00 0.00 4.18
1371 2100 2.981909 TTCGTCTCGCCGTCTGGT 60.982 61.111 0.00 0.00 37.67 4.00
1428 2157 2.639286 GGTTTGCTGTCGGTGCTG 59.361 61.111 0.00 0.00 0.00 4.41
1431 2160 4.560743 TTGCTGTCGGTGCTGGCA 62.561 61.111 0.00 0.00 0.00 4.92
1446 2175 3.785859 GCATCTGGGGTCGGCTCA 61.786 66.667 0.00 0.00 0.00 4.26
1578 2307 3.586430 TGATATCATCACCGGTGCG 57.414 52.632 30.25 22.07 33.59 5.34
1581 2310 0.318699 ATATCATCACCGGTGCGTCG 60.319 55.000 30.25 16.67 0.00 5.12
1623 2352 2.048597 GATGTGTCGACCGCACCA 60.049 61.111 14.12 2.36 36.14 4.17
1624 2353 1.447838 GATGTGTCGACCGCACCAT 60.448 57.895 14.12 7.23 36.14 3.55
1641 2370 0.448990 CATCCACACATGTGCCTTCG 59.551 55.000 25.68 8.18 44.34 3.79
1773 2502 0.313672 GCGTCAAGGCATTGTTTGGA 59.686 50.000 11.36 0.00 37.68 3.53
1872 2601 4.729918 GCTGCTGGGGTGGTGAGG 62.730 72.222 0.00 0.00 0.00 3.86
1905 2634 3.677648 CTTGGTGGTGCTGCTGGC 61.678 66.667 0.00 0.00 42.22 4.85
1923 2652 2.745492 GTGGTGAGGCAGAGCAGC 60.745 66.667 0.00 0.00 0.00 5.25
1926 2655 4.756458 GTGAGGCAGAGCAGCGCT 62.756 66.667 2.64 2.64 43.88 5.92
2034 2763 0.599991 TTGCTGCTGTGACTGTACCG 60.600 55.000 0.00 0.00 0.00 4.02
2082 2811 0.103208 CGAGGTCCATCCCTTCGAAG 59.897 60.000 18.51 18.51 34.03 3.79
2121 2850 2.835156 TGATGTTGGTGACCGGATTCTA 59.165 45.455 9.46 0.00 0.00 2.10
2168 2897 4.629200 CAGTCTTCCATGAGTAGCAGTTTC 59.371 45.833 0.00 0.00 0.00 2.78
2176 2905 4.193826 TGAGTAGCAGTTTCCTGTGATC 57.806 45.455 0.00 0.00 41.02 2.92
2178 2907 4.180057 GAGTAGCAGTTTCCTGTGATCTG 58.820 47.826 0.00 0.00 41.02 2.90
2235 2964 4.993705 TTCATATATTTTCCGGGAGCCT 57.006 40.909 0.00 0.00 0.00 4.58
2295 3024 4.754114 GTCCTTCAGGTATGATGATTCAGC 59.246 45.833 0.00 0.00 34.73 4.26
2410 3139 3.141398 GTTCATCAAGAGAGTTGTGGCA 58.859 45.455 0.00 0.00 0.00 4.92
2471 3200 5.641155 AGGGTAGTGGCTTCTATTTGTTTT 58.359 37.500 0.00 0.00 0.00 2.43
2480 3209 5.419542 GCTTCTATTTGTTTTCATTCCCCC 58.580 41.667 0.00 0.00 0.00 5.40
2490 3219 6.561294 TGTTTTCATTCCCCCTCTTATTTCT 58.439 36.000 0.00 0.00 0.00 2.52
2495 3224 7.480760 TCATTCCCCCTCTTATTTCTTTTTG 57.519 36.000 0.00 0.00 0.00 2.44
2508 3237 6.607735 ATTTCTTTTTGTTGTTGGCATGAG 57.392 33.333 0.00 0.00 0.00 2.90
2511 3240 6.214191 TCTTTTTGTTGTTGGCATGAGTTA 57.786 33.333 0.00 0.00 0.00 2.24
2515 3244 9.206870 CTTTTTGTTGTTGGCATGAGTTATAAT 57.793 29.630 0.00 0.00 0.00 1.28
2607 3336 1.302033 CTTTGTGCTCGAGCCACCT 60.302 57.895 33.23 0.00 41.18 4.00
2745 3517 8.862325 AACTGTTGAACCTCATATGTAATGAA 57.138 30.769 1.90 0.00 0.00 2.57
2746 3518 8.498054 ACTGTTGAACCTCATATGTAATGAAG 57.502 34.615 1.90 0.00 0.00 3.02
2747 3519 7.554118 ACTGTTGAACCTCATATGTAATGAAGG 59.446 37.037 1.90 3.54 0.00 3.46
2748 3520 7.402054 TGTTGAACCTCATATGTAATGAAGGT 58.598 34.615 1.90 4.20 33.85 3.50
2749 3521 8.544622 TGTTGAACCTCATATGTAATGAAGGTA 58.455 33.333 10.93 0.00 32.89 3.08
2842 3614 2.097110 ACTCACTGGTCCACTGGTAA 57.903 50.000 0.00 0.00 0.00 2.85
2862 3634 4.322057 AAATTGGTGGTCCATAAGAGCT 57.678 40.909 0.00 0.00 43.91 4.09
2989 3763 1.607251 GGCTACGTGTTTGTGCTAGGT 60.607 52.381 0.00 0.00 0.00 3.08
3040 3814 2.496899 ACTGGTATGCCAAACCTCTG 57.503 50.000 3.43 0.00 45.51 3.35
3060 3834 2.171237 TGTGGAGGATACCTGCTTGATG 59.829 50.000 10.34 0.00 42.66 3.07
3172 3946 1.883084 GCTTCGATACTGGCCACCG 60.883 63.158 0.00 3.28 0.00 4.94
3196 3970 8.477709 CCGTCGAAAATAACAGATACAATCTAC 58.522 37.037 0.00 0.00 37.58 2.59
3390 4168 2.421619 CCTGGCTGACTCTCAGTTTTC 58.578 52.381 1.37 0.00 45.94 2.29
3465 4243 2.056906 AAAGGTCTGGCTCGCCTGTT 62.057 55.000 9.65 0.00 36.57 3.16
3605 4395 5.359860 CCTGTTCCTTGTAGAGTTTTGGTTT 59.640 40.000 0.00 0.00 0.00 3.27
3634 4424 4.854399 TGAATCCGACATGTTTGTTTGAC 58.146 39.130 0.00 0.00 35.79 3.18
3635 4425 4.336713 TGAATCCGACATGTTTGTTTGACA 59.663 37.500 0.00 0.00 35.79 3.58
3648 4438 4.399004 TGTTTGACAAAGGAAACCATGG 57.601 40.909 11.19 11.19 32.13 3.66
3649 4439 3.130633 GTTTGACAAAGGAAACCATGGC 58.869 45.455 13.04 0.00 0.00 4.40
3650 4440 1.337118 TGACAAAGGAAACCATGGCC 58.663 50.000 13.04 5.04 0.00 5.36
3651 4441 1.337118 GACAAAGGAAACCATGGCCA 58.663 50.000 13.04 8.56 0.00 5.36
3652 4442 1.691434 GACAAAGGAAACCATGGCCAA 59.309 47.619 10.96 0.00 0.00 4.52
3653 4443 2.302733 GACAAAGGAAACCATGGCCAAT 59.697 45.455 10.96 0.00 0.00 3.16
3654 4444 2.710471 ACAAAGGAAACCATGGCCAATT 59.290 40.909 10.96 1.10 0.00 2.32
3655 4445 3.138098 ACAAAGGAAACCATGGCCAATTT 59.862 39.130 10.96 11.38 0.00 1.82
3656 4446 4.143543 CAAAGGAAACCATGGCCAATTTT 58.856 39.130 10.96 9.60 0.00 1.82
3657 4447 4.451891 AAGGAAACCATGGCCAATTTTT 57.548 36.364 10.96 9.19 0.00 1.94
3658 4448 5.574970 AAGGAAACCATGGCCAATTTTTA 57.425 34.783 10.96 0.00 0.00 1.52
3659 4449 5.777526 AGGAAACCATGGCCAATTTTTAT 57.222 34.783 10.96 0.00 0.00 1.40
3660 4450 6.138391 AGGAAACCATGGCCAATTTTTATT 57.862 33.333 10.96 0.00 0.00 1.40
3661 4451 6.551085 AGGAAACCATGGCCAATTTTTATTT 58.449 32.000 10.96 3.77 0.00 1.40
3662 4452 7.009550 AGGAAACCATGGCCAATTTTTATTTT 58.990 30.769 10.96 0.00 0.00 1.82
3663 4453 7.508636 AGGAAACCATGGCCAATTTTTATTTTT 59.491 29.630 10.96 0.00 0.00 1.94
3664 4454 8.797438 GGAAACCATGGCCAATTTTTATTTTTA 58.203 29.630 10.96 0.00 0.00 1.52
3691 4481 2.588027 AACGGCCAATTTTGAAACGT 57.412 40.000 2.24 0.00 34.76 3.99
3793 4591 8.730680 GTGAGTTGTTGGTAAGAAATGATATGT 58.269 33.333 0.00 0.00 0.00 2.29
3794 4592 9.952030 TGAGTTGTTGGTAAGAAATGATATGTA 57.048 29.630 0.00 0.00 0.00 2.29
3863 4685 3.744238 TTAGCAGTACACTTGACAGCA 57.256 42.857 0.00 0.00 32.18 4.41
3914 4764 4.151157 GCCTGTTGTTGATTTTGATCTTGC 59.849 41.667 0.00 0.00 0.00 4.01
3925 4775 8.890124 TGATTTTGATCTTGCATTCAAAGAAA 57.110 26.923 15.31 6.44 41.42 2.52
3929 4779 9.814899 TTTTGATCTTGCATTCAAAGAAACTTA 57.185 25.926 15.31 2.69 41.42 2.24
4144 4995 8.255111 TGATCCTTGCTAAAAGATCTATGAGA 57.745 34.615 0.00 0.00 36.82 3.27
4203 5055 6.545298 AGATCAAAAGAAAGACTCAAGCTTGT 59.455 34.615 25.19 7.87 0.00 3.16
4217 5069 3.560636 AGCTTGTATCCATTAGCCGTT 57.439 42.857 0.00 0.00 34.19 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.219935 GGCGTGTGGTAGGGTTAGG 59.780 63.158 0.00 0.00 0.00 2.69
1 2 1.219935 GGGCGTGTGGTAGGGTTAG 59.780 63.158 0.00 0.00 0.00 2.34
2 3 1.535930 TGGGCGTGTGGTAGGGTTA 60.536 57.895 0.00 0.00 0.00 2.85
3 4 2.850130 TGGGCGTGTGGTAGGGTT 60.850 61.111 0.00 0.00 0.00 4.11
4 5 3.633116 GTGGGCGTGTGGTAGGGT 61.633 66.667 0.00 0.00 0.00 4.34
5 6 4.404098 GGTGGGCGTGTGGTAGGG 62.404 72.222 0.00 0.00 0.00 3.53
6 7 1.546589 TTAGGTGGGCGTGTGGTAGG 61.547 60.000 0.00 0.00 0.00 3.18
7 8 0.322322 TTTAGGTGGGCGTGTGGTAG 59.678 55.000 0.00 0.00 0.00 3.18
8 9 0.322322 CTTTAGGTGGGCGTGTGGTA 59.678 55.000 0.00 0.00 0.00 3.25
9 10 1.072505 CTTTAGGTGGGCGTGTGGT 59.927 57.895 0.00 0.00 0.00 4.16
10 11 0.250553 TTCTTTAGGTGGGCGTGTGG 60.251 55.000 0.00 0.00 0.00 4.17
11 12 0.872388 GTTCTTTAGGTGGGCGTGTG 59.128 55.000 0.00 0.00 0.00 3.82
12 13 0.470766 TGTTCTTTAGGTGGGCGTGT 59.529 50.000 0.00 0.00 0.00 4.49
13 14 1.156736 CTGTTCTTTAGGTGGGCGTG 58.843 55.000 0.00 0.00 0.00 5.34
14 15 1.053424 TCTGTTCTTTAGGTGGGCGT 58.947 50.000 0.00 0.00 0.00 5.68
15 16 1.439679 GTCTGTTCTTTAGGTGGGCG 58.560 55.000 0.00 0.00 0.00 6.13
16 17 1.613520 GGGTCTGTTCTTTAGGTGGGC 60.614 57.143 0.00 0.00 0.00 5.36
17 18 1.338769 CGGGTCTGTTCTTTAGGTGGG 60.339 57.143 0.00 0.00 0.00 4.61
18 19 1.338769 CCGGGTCTGTTCTTTAGGTGG 60.339 57.143 0.00 0.00 0.00 4.61
19 20 1.338769 CCCGGGTCTGTTCTTTAGGTG 60.339 57.143 14.18 0.00 0.00 4.00
20 21 0.981943 CCCGGGTCTGTTCTTTAGGT 59.018 55.000 14.18 0.00 0.00 3.08
21 22 0.252197 CCCCGGGTCTGTTCTTTAGG 59.748 60.000 21.85 0.00 0.00 2.69
22 23 0.981943 ACCCCGGGTCTGTTCTTTAG 59.018 55.000 21.85 0.95 0.00 1.85
23 24 1.348696 GAACCCCGGGTCTGTTCTTTA 59.651 52.381 25.48 0.00 33.12 1.85
24 25 0.109913 GAACCCCGGGTCTGTTCTTT 59.890 55.000 25.48 2.54 33.12 2.52
25 26 1.759236 GAACCCCGGGTCTGTTCTT 59.241 57.895 25.48 2.87 33.12 2.52
26 27 2.222013 GGAACCCCGGGTCTGTTCT 61.222 63.158 29.03 6.66 38.68 3.01
27 28 2.350134 GGAACCCCGGGTCTGTTC 59.650 66.667 25.02 25.02 33.12 3.18
66 67 3.578272 CTCTCTCTCCGTCGGCCG 61.578 72.222 22.12 22.12 0.00 6.13
67 68 3.213402 CCTCTCTCTCCGTCGGCC 61.213 72.222 6.34 0.00 0.00 6.13
68 69 3.213402 CCCTCTCTCTCCGTCGGC 61.213 72.222 6.34 0.00 0.00 5.54
69 70 1.077644 TTCCCTCTCTCTCCGTCGG 60.078 63.158 4.39 4.39 0.00 4.79
70 71 1.378124 GGTTCCCTCTCTCTCCGTCG 61.378 65.000 0.00 0.00 0.00 5.12
71 72 1.378124 CGGTTCCCTCTCTCTCCGTC 61.378 65.000 0.00 0.00 34.38 4.79
72 73 1.378778 CGGTTCCCTCTCTCTCCGT 60.379 63.158 0.00 0.00 34.38 4.69
73 74 2.122167 CCGGTTCCCTCTCTCTCCG 61.122 68.421 0.00 0.00 38.05 4.63
74 75 2.428085 GCCGGTTCCCTCTCTCTCC 61.428 68.421 1.90 0.00 0.00 3.71
75 76 2.776913 CGCCGGTTCCCTCTCTCTC 61.777 68.421 1.90 0.00 0.00 3.20
76 77 2.756283 CGCCGGTTCCCTCTCTCT 60.756 66.667 1.90 0.00 0.00 3.10
77 78 2.348888 TTCGCCGGTTCCCTCTCTC 61.349 63.158 1.90 0.00 0.00 3.20
78 79 2.283676 TTCGCCGGTTCCCTCTCT 60.284 61.111 1.90 0.00 0.00 3.10
79 80 2.125633 GTTCGCCGGTTCCCTCTC 60.126 66.667 1.90 0.00 0.00 3.20
80 81 3.703127 GGTTCGCCGGTTCCCTCT 61.703 66.667 1.90 0.00 0.00 3.69
81 82 3.325201 ATGGTTCGCCGGTTCCCTC 62.325 63.158 1.90 0.00 41.18 4.30
82 83 3.327404 ATGGTTCGCCGGTTCCCT 61.327 61.111 1.90 0.00 41.18 4.20
83 84 3.131478 CATGGTTCGCCGGTTCCC 61.131 66.667 1.90 0.00 41.18 3.97
84 85 2.359478 ACATGGTTCGCCGGTTCC 60.359 61.111 1.90 1.14 41.18 3.62
85 86 2.867472 CACATGGTTCGCCGGTTC 59.133 61.111 1.90 0.00 41.18 3.62
86 87 3.361977 GCACATGGTTCGCCGGTT 61.362 61.111 1.90 0.00 41.18 4.44
87 88 4.634703 TGCACATGGTTCGCCGGT 62.635 61.111 1.90 0.00 41.18 5.28
88 89 4.101790 GTGCACATGGTTCGCCGG 62.102 66.667 13.17 0.00 41.18 6.13
89 90 3.313007 CTGTGCACATGGTTCGCCG 62.313 63.158 22.00 0.69 41.18 6.46
90 91 2.562912 CTGTGCACATGGTTCGCC 59.437 61.111 22.00 0.00 37.92 5.54
91 92 2.260869 ACCTGTGCACATGGTTCGC 61.261 57.895 25.91 0.00 0.00 4.70
92 93 1.165907 ACACCTGTGCACATGGTTCG 61.166 55.000 27.85 22.02 30.72 3.95
138 139 5.558856 TCCCTATCTACCCATCTGATCAT 57.441 43.478 0.00 0.00 0.00 2.45
148 159 4.995487 CGCAACTTTTATCCCTATCTACCC 59.005 45.833 0.00 0.00 0.00 3.69
150 161 5.054477 TGCGCAACTTTTATCCCTATCTAC 58.946 41.667 8.16 0.00 0.00 2.59
171 182 3.495001 GTCAACTCCTGTACAGTTTCTGC 59.505 47.826 21.18 2.93 34.37 4.26
202 213 5.077134 AGCAATATTTTGAGGGAGTTTGC 57.923 39.130 0.00 0.00 38.71 3.68
203 214 6.747280 CGTAAGCAATATTTTGAGGGAGTTTG 59.253 38.462 0.00 0.00 34.60 2.93
204 215 6.657541 TCGTAAGCAATATTTTGAGGGAGTTT 59.342 34.615 0.00 0.00 34.60 2.66
220 231 6.342111 TGTTATATCCACACATCGTAAGCAA 58.658 36.000 0.00 0.00 37.18 3.91
269 283 7.696992 AAACAGATGGTAACCGAATTGTTAT 57.303 32.000 0.00 0.00 33.58 1.89
284 298 0.454957 CGAGGCGCAAAAACAGATGG 60.455 55.000 10.83 0.00 0.00 3.51
347 1042 3.062909 TAAATCGAATTTTCCGGCACGAG 59.937 43.478 0.00 0.00 43.93 4.18
355 1050 9.721933 GACGAAAAACAATAAATCGAATTTTCC 57.278 29.630 0.00 0.00 37.27 3.13
383 1078 5.484173 TTTTTACAGTCACTGTGCTGAAG 57.516 39.130 27.15 10.81 45.01 3.02
427 1123 3.990469 GCGATTGTGACTCTTCTGAAAGA 59.010 43.478 0.00 0.00 44.68 2.52
428 1124 3.742882 TGCGATTGTGACTCTTCTGAAAG 59.257 43.478 0.00 0.00 0.00 2.62
429 1125 3.494626 GTGCGATTGTGACTCTTCTGAAA 59.505 43.478 0.00 0.00 0.00 2.69
430 1126 3.059884 GTGCGATTGTGACTCTTCTGAA 58.940 45.455 0.00 0.00 0.00 3.02
487 1188 3.117888 TCTCCTGTTATTTGGGCCATCTC 60.118 47.826 7.26 0.00 0.00 2.75
543 1244 1.609210 CCCCAACTTGGCCGGATTT 60.609 57.895 5.05 0.00 35.79 2.17
545 1264 4.759205 GCCCCAACTTGGCCGGAT 62.759 66.667 5.05 0.00 43.33 4.18
581 1300 5.414360 GCCAGGATTTTGGAGATCTTTTTC 58.586 41.667 0.00 0.00 40.87 2.29
760 1483 2.525877 GCCGGTGCCTAGGGGATA 60.526 66.667 11.72 0.00 33.58 2.59
847 1570 0.105658 CAGGGGATCTAGGGTTCGGA 60.106 60.000 0.00 0.00 0.00 4.55
1263 1989 4.666253 TTGGTGGGGCTGCTGCTC 62.666 66.667 15.64 11.63 39.42 4.26
1264 1990 4.673375 CTTGGTGGGGCTGCTGCT 62.673 66.667 15.64 0.00 39.59 4.24
1368 2097 2.642254 ATCCGCCTTCGTCGAACCA 61.642 57.895 2.90 0.00 0.00 3.67
1371 2100 1.153901 GTCATCCGCCTTCGTCGAA 60.154 57.895 7.57 7.57 0.00 3.71
1398 2127 4.344865 AAACCCACCGCCAGCGAT 62.345 61.111 14.67 0.00 42.83 4.58
1413 2142 3.286751 GCCAGCACCGACAGCAAA 61.287 61.111 0.00 0.00 0.00 3.68
1428 2157 4.554036 GAGCCGACCCCAGATGCC 62.554 72.222 0.00 0.00 0.00 4.40
1431 2160 2.765807 CCTGAGCCGACCCCAGAT 60.766 66.667 0.00 0.00 0.00 2.90
1617 2346 1.503091 CACATGTGTGGATGGTGCG 59.497 57.895 18.03 0.00 42.10 5.34
1620 2349 0.112995 AAGGCACATGTGTGGATGGT 59.887 50.000 26.01 3.46 45.72 3.55
1622 2351 0.448990 CGAAGGCACATGTGTGGATG 59.551 55.000 26.01 10.80 45.72 3.51
1623 2352 1.308069 GCGAAGGCACATGTGTGGAT 61.308 55.000 26.01 10.96 45.72 3.41
1624 2353 1.965930 GCGAAGGCACATGTGTGGA 60.966 57.895 26.01 0.00 45.72 4.02
1702 2431 2.062971 CTACCAAGCAAGGCCATCAT 57.937 50.000 5.01 0.00 0.00 2.45
1905 2634 2.433838 CTGCTCTGCCTCACCACG 60.434 66.667 0.00 0.00 0.00 4.94
1923 2652 4.099170 GCAGCACCAAGAGCAGCG 62.099 66.667 0.00 0.00 34.87 5.18
1926 2655 2.981909 GCAGCAGCACCAAGAGCA 60.982 61.111 0.00 0.00 41.58 4.26
2034 2763 1.423161 AGGGAGGATTTATGGAGCAGC 59.577 52.381 0.00 0.00 0.00 5.25
2121 2850 1.823610 GTTAACTGTACCCTCTCGGCT 59.176 52.381 0.00 0.00 33.26 5.52
2168 2897 1.274447 TCAGCAGACACAGATCACAGG 59.726 52.381 0.00 0.00 0.00 4.00
2176 2905 0.604511 TGCACCATCAGCAGACACAG 60.605 55.000 0.00 0.00 37.02 3.66
2178 2907 2.028420 TATGCACCATCAGCAGACAC 57.972 50.000 0.00 0.00 46.36 3.67
2235 2964 6.239008 GGAAGATCACAATGTCCAAAACTTGA 60.239 38.462 0.00 0.00 0.00 3.02
2352 3081 0.826062 GCCCAATGCCTGCAGTAAAT 59.174 50.000 13.81 0.00 0.00 1.40
2357 3086 1.378911 TGTAGCCCAATGCCTGCAG 60.379 57.895 6.78 6.78 42.71 4.41
2401 3130 2.912025 CCGCCCTTTGCCACAACT 60.912 61.111 0.00 0.00 36.24 3.16
2410 3139 2.902457 AACGATGTCCCCGCCCTTT 61.902 57.895 0.00 0.00 0.00 3.11
2471 3200 7.016296 ACAAAAAGAAATAAGAGGGGGAATGA 58.984 34.615 0.00 0.00 0.00 2.57
2480 3209 7.769272 TGCCAACAACAAAAAGAAATAAGAG 57.231 32.000 0.00 0.00 0.00 2.85
2490 3219 9.202273 GATTATAACTCATGCCAACAACAAAAA 57.798 29.630 0.00 0.00 0.00 1.94
2495 3224 8.810427 CAAATGATTATAACTCATGCCAACAAC 58.190 33.333 9.65 0.00 33.69 3.32
2607 3336 4.535781 CCACTGGGTCCATTTCATAATCA 58.464 43.478 0.00 0.00 0.00 2.57
2742 3514 8.839343 CAAATATGTCAGCACATTATACCTTCA 58.161 33.333 0.00 0.00 40.66 3.02
2745 3517 8.623903 CAACAAATATGTCAGCACATTATACCT 58.376 33.333 0.00 0.00 40.66 3.08
2746 3518 7.379529 GCAACAAATATGTCAGCACATTATACC 59.620 37.037 0.00 0.00 40.66 2.73
2747 3519 8.131100 AGCAACAAATATGTCAGCACATTATAC 58.869 33.333 0.00 0.00 40.66 1.47
2748 3520 8.224389 AGCAACAAATATGTCAGCACATTATA 57.776 30.769 0.00 0.00 40.66 0.98
2749 3521 7.104043 AGCAACAAATATGTCAGCACATTAT 57.896 32.000 0.00 0.00 40.66 1.28
2862 3634 8.565896 ACTTGCTTTATGATCAAGTCATGTAA 57.434 30.769 0.00 0.00 46.85 2.41
2914 3686 7.875041 ACAACTGATCAATATGTATACTCCAGC 59.125 37.037 4.17 0.00 0.00 4.85
2989 3763 3.181511 CGAAGCTGTTGTTTCTGTTGTCA 60.182 43.478 0.00 0.00 32.31 3.58
3040 3814 2.171448 ACATCAAGCAGGTATCCTCCAC 59.829 50.000 0.00 0.00 0.00 4.02
3060 3834 5.794894 TGTCCTGGAAATTAGTCTCAAGAC 58.205 41.667 0.00 1.79 45.08 3.01
3172 3946 9.229784 TCGTAGATTGTATCTGTTATTTTCGAC 57.770 33.333 0.00 0.00 40.51 4.20
3196 3970 2.096335 CACATCATGGTCAATGTGGTCG 59.904 50.000 14.49 0.00 45.75 4.79
3252 4026 0.885196 TTAGCATTGCCGAACCAACC 59.115 50.000 4.70 0.00 0.00 3.77
3295 4070 2.680221 GCAGCAGAGGTCATCAGTGATT 60.680 50.000 1.86 0.00 36.60 2.57
3465 4243 1.687563 CTGCCATGGATGCTCATTCA 58.312 50.000 18.40 0.00 0.00 2.57
3605 4395 4.753516 AACATGTCGGATTCAGATGGTA 57.246 40.909 0.00 0.00 0.00 3.25
3634 4424 3.421919 AATTGGCCATGGTTTCCTTTG 57.578 42.857 14.67 0.00 0.00 2.77
3635 4425 4.451891 AAAATTGGCCATGGTTTCCTTT 57.548 36.364 14.67 5.60 0.00 3.11
3652 4442 9.814507 GGCCGTTTCGAAAATAAAAATAAAAAT 57.185 25.926 13.10 0.00 0.00 1.82
3653 4443 8.823818 TGGCCGTTTCGAAAATAAAAATAAAAA 58.176 25.926 13.10 0.00 0.00 1.94
3654 4444 8.361592 TGGCCGTTTCGAAAATAAAAATAAAA 57.638 26.923 13.10 0.00 0.00 1.52
3655 4445 7.941795 TGGCCGTTTCGAAAATAAAAATAAA 57.058 28.000 13.10 0.00 0.00 1.40
3656 4446 7.941795 TTGGCCGTTTCGAAAATAAAAATAA 57.058 28.000 13.10 0.00 0.00 1.40
3657 4447 8.535690 AATTGGCCGTTTCGAAAATAAAAATA 57.464 26.923 13.10 0.00 0.00 1.40
3658 4448 7.428282 AATTGGCCGTTTCGAAAATAAAAAT 57.572 28.000 13.10 7.71 0.00 1.82
3659 4449 6.846325 AATTGGCCGTTTCGAAAATAAAAA 57.154 29.167 13.10 5.67 0.00 1.94
3660 4450 6.846325 AAATTGGCCGTTTCGAAAATAAAA 57.154 29.167 13.10 4.62 0.00 1.52
3661 4451 6.479001 TCAAAATTGGCCGTTTCGAAAATAAA 59.521 30.769 13.10 3.91 0.00 1.40
3662 4452 5.983720 TCAAAATTGGCCGTTTCGAAAATAA 59.016 32.000 13.10 4.32 0.00 1.40
3663 4453 5.529791 TCAAAATTGGCCGTTTCGAAAATA 58.470 33.333 13.10 0.00 0.00 1.40
3664 4454 4.372656 TCAAAATTGGCCGTTTCGAAAAT 58.627 34.783 13.10 0.00 0.00 1.82
3665 4455 3.782046 TCAAAATTGGCCGTTTCGAAAA 58.218 36.364 13.10 0.00 0.00 2.29
3666 4456 3.438297 TCAAAATTGGCCGTTTCGAAA 57.562 38.095 6.47 6.47 0.00 3.46
3667 4457 3.438297 TTCAAAATTGGCCGTTTCGAA 57.562 38.095 0.00 0.15 0.00 3.71
3668 4458 3.117046 GTTTCAAAATTGGCCGTTTCGA 58.883 40.909 0.00 0.00 0.00 3.71
3669 4459 2.097637 CGTTTCAAAATTGGCCGTTTCG 60.098 45.455 0.00 0.00 0.00 3.46
3670 4460 2.861335 ACGTTTCAAAATTGGCCGTTTC 59.139 40.909 0.00 0.00 0.00 2.78
3671 4461 2.605366 CACGTTTCAAAATTGGCCGTTT 59.395 40.909 0.00 0.00 0.00 3.60
3672 4462 2.197577 CACGTTTCAAAATTGGCCGTT 58.802 42.857 0.00 0.00 0.00 4.44
3673 4463 1.135333 ACACGTTTCAAAATTGGCCGT 59.865 42.857 0.00 0.00 0.00 5.68
3674 4464 1.784283 GACACGTTTCAAAATTGGCCG 59.216 47.619 0.00 0.00 0.00 6.13
3691 4481 3.195610 AGAACATCGCCTGTGATAAGACA 59.804 43.478 0.00 0.00 38.39 3.41
3793 4591 9.555727 AACATACTAAAAGCTGAAAAGTCACTA 57.444 29.630 0.00 0.00 0.00 2.74
3794 4592 8.345565 CAACATACTAAAAGCTGAAAAGTCACT 58.654 33.333 0.00 0.00 0.00 3.41
3832 4654 6.787085 AGTGTACTGCTAAACAAACATCTC 57.213 37.500 0.00 0.00 29.66 2.75
3863 4685 6.620733 GCACATATTTTGTACTCGCTCAGTTT 60.621 38.462 0.00 0.00 36.57 2.66
3876 4698 4.202243 ACAACAGGCAAGCACATATTTTGT 60.202 37.500 0.00 0.00 39.91 2.83
3892 4714 5.291178 TGCAAGATCAAAATCAACAACAGG 58.709 37.500 0.00 0.00 34.07 4.00
3893 4715 7.170151 TGAATGCAAGATCAAAATCAACAACAG 59.830 33.333 0.00 0.00 34.07 3.16
3925 4775 8.292448 CACATACTTGCTCAAACAAAGATAAGT 58.708 33.333 0.00 0.00 31.77 2.24
3929 4779 6.882610 TCACATACTTGCTCAAACAAAGAT 57.117 33.333 0.00 0.00 0.00 2.40
3935 4785 5.886960 ATCCTTCACATACTTGCTCAAAC 57.113 39.130 0.00 0.00 0.00 2.93
3991 4841 2.925563 GCACAGAAGCACATATTTTGCC 59.074 45.455 2.94 0.00 41.18 4.52
4047 4897 8.814038 ATCCTTTGTATACTTGCTCAAAAGAT 57.186 30.769 4.17 0.00 30.85 2.40
4066 4916 6.891908 ACAATTGACAGCTACCATAATCCTTT 59.108 34.615 13.59 0.00 0.00 3.11
4076 4926 5.689383 TCTTTGAACAATTGACAGCTACC 57.311 39.130 13.59 0.00 0.00 3.18
4109 4960 3.488778 AGCAAGGATCATAAGCTCAGG 57.511 47.619 1.84 0.00 0.00 3.86
4144 4995 1.069906 GTTTTGACAGAAGCACGCGAT 60.070 47.619 15.93 0.00 0.00 4.58
4150 5001 5.581126 AGTTCAATGTTTTGACAGAAGCA 57.419 34.783 0.00 0.00 41.50 3.91
4203 5055 5.741011 AGAAGAAACAACGGCTAATGGATA 58.259 37.500 0.00 0.00 0.00 2.59
4217 5069 3.008049 GGAGGGCTGTCTTAGAAGAAACA 59.992 47.826 0.00 0.00 36.68 2.83


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

AutoCloner maintained by Alex Coulton.