Multiple sequence alignment - TraesCS2B01G349100

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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 TraesCS2B01G349100 chr2B 100.000 2540 0 0 1 2540 495907310 495904771 0.000000e+00 4691.0
1 TraesCS2B01G349100 chr2B 91.954 87 7 0 1075 1161 496078632 496078546 3.430000e-24 122.0
2 TraesCS2B01G349100 chr2B 89.130 92 10 0 1070 1161 495952708 495952617 5.740000e-22 115.0
3 TraesCS2B01G349100 chr2B 86.022 93 12 1 1069 1161 496512457 496512366 5.780000e-17 99.0
4 TraesCS2B01G349100 chr2B 84.946 93 13 1 1069 1161 496118195 496118104 2.690000e-15 93.5
5 TraesCS2B01G349100 chr2A 88.352 1760 114 39 842 2540 565348880 565350609 0.000000e+00 2030.0
6 TraesCS2B01G349100 chr2A 89.122 763 42 16 86 834 565348094 565348829 0.000000e+00 911.0
7 TraesCS2B01G349100 chr2A 92.647 68 5 0 2059 2126 483626464 483626397 5.780000e-17 99.0
8 TraesCS2B01G349100 chr2A 91.667 60 4 1 3 61 565347729 565347788 5.820000e-12 82.4
9 TraesCS2B01G349100 chr2D 89.949 1572 79 34 95 1639 423214138 423212619 0.000000e+00 1954.0
10 TraesCS2B01G349100 chr2D 87.273 880 61 17 1706 2540 423212624 423211751 0.000000e+00 957.0
11 TraesCS2B01G349100 chr2D 88.298 94 11 0 1068 1161 423292390 423292297 2.070000e-21 113.0
12 TraesCS2B01G349100 chr2D 89.855 69 7 0 2059 2127 359380299 359380367 3.480000e-14 89.8
13 TraesCS2B01G349100 chr2D 100.000 29 0 0 6 34 423214455 423214427 1.000000e-03 54.7
14 TraesCS2B01G349100 chrUn 89.130 92 10 0 1070 1161 325760222 325760313 5.740000e-22 115.0
15 TraesCS2B01G349100 chr5D 84.286 70 9 2 2059 2127 528137261 528137193 1.630000e-07 67.6
16 TraesCS2B01G349100 chr1D 82.609 69 12 0 2059 2127 267982867 267982935 7.590000e-06 62.1
17 TraesCS2B01G349100 chr6D 92.683 41 1 2 2088 2127 79074793 79074754 9.810000e-05 58.4
18 TraesCS2B01G349100 chr6A 92.500 40 3 0 2088 2127 566441303 566441264 9.810000e-05 58.4
19 TraesCS2B01G349100 chr6A 100.000 29 0 0 2099 2127 493973429 493973401 1.000000e-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 TraesCS2B01G349100 chr2B 495904771 495907310 2539 True 4691.000000 4691 100.000000 1 2540 1 chr2B.!!$R1 2539
1 TraesCS2B01G349100 chr2A 565347729 565350609 2880 False 1007.800000 2030 89.713667 3 2540 3 chr2A.!!$F1 2537
2 TraesCS2B01G349100 chr2D 423211751 423214455 2704 True 988.566667 1954 92.407333 6 2540 3 chr2D.!!$R2 2534

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
336 628 0.178981 AATGTTCTGCCAGGCACACT 60.179 50.0 11.22 0.0 33.79 3.55 F
422 714 0.249280 TGCGCCCATACGACATACTG 60.249 55.0 4.18 0.0 34.06 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1459 1845 0.110486 CCATATGGGTGGTGGTAGCC 59.89 60.0 14.52 0.0 38.69 3.93 R
2017 2423 0.389817 GTTTTGGGAGCCGGATTTGC 60.39 55.0 5.05 0.0 0.00 3.68 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
34 35 4.109050 GGTTTCTCTCATGTCTGATCGTC 58.891 47.826 0.00 0.00 0.00 4.20
37 38 1.673400 CTCTCATGTCTGATCGTCGGT 59.327 52.381 0.00 0.00 0.00 4.69
38 39 2.872858 CTCTCATGTCTGATCGTCGGTA 59.127 50.000 0.00 0.00 0.00 4.02
39 40 3.477530 TCTCATGTCTGATCGTCGGTAT 58.522 45.455 0.00 0.00 0.00 2.73
61 63 3.819902 TGCTCATGTTGTTTGTGATGCTA 59.180 39.130 0.00 0.00 0.00 3.49
62 64 4.161333 GCTCATGTTGTTTGTGATGCTAC 58.839 43.478 0.00 0.00 0.00 3.58
63 65 4.726416 CTCATGTTGTTTGTGATGCTACC 58.274 43.478 0.00 0.00 0.00 3.18
64 66 4.140536 TCATGTTGTTTGTGATGCTACCA 58.859 39.130 0.00 0.00 0.00 3.25
65 67 3.980646 TGTTGTTTGTGATGCTACCAC 57.019 42.857 0.00 0.00 35.23 4.16
66 68 3.550820 TGTTGTTTGTGATGCTACCACT 58.449 40.909 0.00 0.00 35.66 4.00
67 69 4.709250 TGTTGTTTGTGATGCTACCACTA 58.291 39.130 0.00 0.00 35.66 2.74
68 70 5.312895 TGTTGTTTGTGATGCTACCACTAT 58.687 37.500 0.00 0.00 35.66 2.12
69 71 5.181056 TGTTGTTTGTGATGCTACCACTATG 59.819 40.000 0.00 0.00 35.66 2.23
70 72 5.159273 TGTTTGTGATGCTACCACTATGA 57.841 39.130 0.00 0.00 35.66 2.15
71 73 4.935205 TGTTTGTGATGCTACCACTATGAC 59.065 41.667 0.00 0.00 35.66 3.06
72 74 5.178797 GTTTGTGATGCTACCACTATGACT 58.821 41.667 0.00 0.00 35.66 3.41
73 75 4.391405 TGTGATGCTACCACTATGACTG 57.609 45.455 0.00 0.00 35.66 3.51
74 76 4.023291 TGTGATGCTACCACTATGACTGA 58.977 43.478 0.00 0.00 35.66 3.41
75 77 4.098501 TGTGATGCTACCACTATGACTGAG 59.901 45.833 0.00 0.00 35.66 3.35
76 78 3.638627 TGATGCTACCACTATGACTGAGG 59.361 47.826 0.00 0.00 0.00 3.86
77 79 2.388735 TGCTACCACTATGACTGAGGG 58.611 52.381 0.00 0.00 0.00 4.30
78 80 1.689273 GCTACCACTATGACTGAGGGG 59.311 57.143 0.00 0.00 43.79 4.79
79 81 2.320781 CTACCACTATGACTGAGGGGG 58.679 57.143 0.00 0.00 42.33 5.40
256 544 0.245539 TCTTTCGTAGCAAGACCCGG 59.754 55.000 0.00 0.00 0.00 5.73
257 545 0.245539 CTTTCGTAGCAAGACCCGGA 59.754 55.000 0.73 0.00 0.00 5.14
260 552 1.153823 CGTAGCAAGACCCGGAGTG 60.154 63.158 0.73 0.00 0.00 3.51
287 579 9.814507 GACTAGTTGTGTTCTCACGATATATAG 57.185 37.037 0.00 0.00 46.49 1.31
292 584 5.162075 GTGTTCTCACGATATATAGCCACC 58.838 45.833 0.00 0.00 34.79 4.61
307 599 1.541588 GCCACCGAAATCTTCAAGCTT 59.458 47.619 0.00 0.00 0.00 3.74
308 600 2.747446 GCCACCGAAATCTTCAAGCTTA 59.253 45.455 0.00 0.00 0.00 3.09
336 628 0.178981 AATGTTCTGCCAGGCACACT 60.179 50.000 11.22 0.00 33.79 3.55
420 712 0.580104 GTTGCGCCCATACGACATAC 59.420 55.000 4.18 0.00 34.06 2.39
421 713 0.462375 TTGCGCCCATACGACATACT 59.538 50.000 4.18 0.00 34.06 2.12
422 714 0.249280 TGCGCCCATACGACATACTG 60.249 55.000 4.18 0.00 34.06 2.74
423 715 0.249322 GCGCCCATACGACATACTGT 60.249 55.000 0.00 0.00 34.06 3.55
424 716 1.001048 GCGCCCATACGACATACTGTA 60.001 52.381 0.00 0.00 34.06 2.74
430 722 5.509163 GCCCATACGACATACTGTATCACTT 60.509 44.000 0.00 0.00 0.00 3.16
443 735 4.253685 TGTATCACTTAGTTGCTTGCCTC 58.746 43.478 0.00 0.00 0.00 4.70
500 801 4.586618 GCACTGAGCACTGTCGAT 57.413 55.556 0.00 0.00 44.79 3.59
631 943 2.992543 GGCTCGCTCAGACATATCATTC 59.007 50.000 0.00 0.00 0.00 2.67
741 1053 2.435069 TCCTTGTTGTTCACTAACCGGA 59.565 45.455 9.46 0.00 34.49 5.14
834 1146 7.347748 TCTTCACTAGTACCAGGTCTACTATCT 59.652 40.741 0.00 0.00 0.00 1.98
844 1199 2.506444 GTCTACTATCTCCCTCACCCG 58.494 57.143 0.00 0.00 0.00 5.28
867 1222 0.390735 CCCACGTAACTGCCCTGTAC 60.391 60.000 0.00 0.00 0.00 2.90
868 1223 0.606604 CCACGTAACTGCCCTGTACT 59.393 55.000 0.00 0.00 0.00 2.73
869 1224 1.820519 CCACGTAACTGCCCTGTACTA 59.179 52.381 0.00 0.00 0.00 1.82
870 1225 2.429610 CCACGTAACTGCCCTGTACTAT 59.570 50.000 0.00 0.00 0.00 2.12
871 1226 3.633525 CCACGTAACTGCCCTGTACTATA 59.366 47.826 0.00 0.00 0.00 1.31
872 1227 4.498682 CCACGTAACTGCCCTGTACTATAC 60.499 50.000 0.00 0.00 0.00 1.47
873 1228 4.337555 CACGTAACTGCCCTGTACTATACT 59.662 45.833 0.00 0.00 0.00 2.12
963 1318 6.012745 ACACAAGCCTTTCCAAATATTCTCT 58.987 36.000 0.00 0.00 0.00 3.10
979 1334 9.512588 AAATATTCTCTTTGATCGGCATCTAAT 57.487 29.630 0.00 0.00 0.00 1.73
993 1348 3.429085 CATCTAATCAACAAACCAGCGC 58.571 45.455 0.00 0.00 0.00 5.92
995 1350 0.519519 TAATCAACAAACCAGCGCCG 59.480 50.000 2.29 0.00 0.00 6.46
1008 1363 2.124901 CGCCGCCCAATGAAGGTA 60.125 61.111 0.00 0.00 0.00 3.08
1009 1364 1.747367 CGCCGCCCAATGAAGGTAA 60.747 57.895 0.00 0.00 0.00 2.85
1048 1407 2.867624 TCTGCCTGATTTTGAGCACTT 58.132 42.857 0.00 0.00 0.00 3.16
1074 1433 2.741517 GCTCTTGAGCTGAACCTTCTTC 59.258 50.000 14.65 0.00 0.00 2.87
1225 1597 7.021196 CACGTATGTTTACCCTTGAGATTTTG 58.979 38.462 0.00 0.00 0.00 2.44
1228 1600 5.195001 TGTTTACCCTTGAGATTTTGTGC 57.805 39.130 0.00 0.00 0.00 4.57
1259 1632 2.193865 TAACATGGCCGCAAGCGTTG 62.194 55.000 13.80 7.83 45.17 4.10
1278 1661 4.416738 GGTGCAGGGGTGAGCTCC 62.417 72.222 12.15 2.19 34.70 4.70
1320 1703 0.252696 AGGACATGCTGGAGGTGGTA 60.253 55.000 0.00 0.00 0.00 3.25
1384 1767 1.677576 AGAAGTACCACGACGTTCACA 59.322 47.619 0.00 0.00 0.00 3.58
1459 1845 2.202518 CGCCGTACTGGTACCACG 60.203 66.667 11.60 13.48 41.21 4.94
1462 1848 3.281240 CGTACTGGTACCACGGCT 58.719 61.111 11.60 0.00 32.61 5.52
1463 1849 2.481212 CGTACTGGTACCACGGCTA 58.519 57.895 11.60 0.00 32.61 3.93
1465 1851 0.457443 GTACTGGTACCACGGCTACC 59.543 60.000 11.60 7.52 35.13 3.18
1466 1852 0.039472 TACTGGTACCACGGCTACCA 59.961 55.000 11.60 13.50 41.19 3.25
1467 1853 1.217244 CTGGTACCACGGCTACCAC 59.783 63.158 11.60 0.00 39.02 4.16
1550 1936 5.288015 CGCCATCATGTAATTGCCAAATAA 58.712 37.500 0.00 0.00 0.00 1.40
1626 2012 7.335924 TCGGACTATTGGTAAATTGGAAGAAAG 59.664 37.037 0.00 0.00 0.00 2.62
1635 2021 7.777910 TGGTAAATTGGAAGAAAGAAAGAGACA 59.222 33.333 0.00 0.00 0.00 3.41
1640 2026 9.525826 AATTGGAAGAAAGAAAGAGACATATGT 57.474 29.630 8.43 8.43 0.00 2.29
1656 2047 9.846738 GAGACATATGTATACATATACGTCGTC 57.153 37.037 29.38 27.95 45.08 4.20
1684 2075 9.575868 TTGGTCTCCAGTTAGATAGAGTAATAG 57.424 37.037 0.00 0.00 33.81 1.73
1685 2076 8.725256 TGGTCTCCAGTTAGATAGAGTAATAGT 58.275 37.037 0.00 0.00 0.00 2.12
1708 2099 2.234187 GTCGAGAAAAAGCAATCACGC 58.766 47.619 0.00 0.00 31.16 5.34
1730 2121 4.805609 GCATACCCCAGATCTGAATTCCTC 60.806 50.000 24.62 4.67 0.00 3.71
1766 2158 0.248134 CGTACTACGTGCTGCCTCTC 60.248 60.000 0.00 0.00 36.74 3.20
1842 2248 2.395654 GTCTGAAGACGTTGGAGTCAC 58.604 52.381 0.00 0.00 43.24 3.67
1875 2281 1.729517 CATGTAACGGTCAATGCGTCA 59.270 47.619 0.00 0.00 0.00 4.35
1938 2344 1.373748 GCCAGGTCGTTGCGTCTTA 60.374 57.895 0.00 0.00 0.00 2.10
1972 2378 6.127897 CCCACTCTAGCATTTTCGATCTTTTT 60.128 38.462 0.00 0.00 0.00 1.94
2012 2418 4.559862 ACTTTTAGCATCTACAGCCAGT 57.440 40.909 0.00 0.00 0.00 4.00
2032 2438 3.643595 CTGGCAAATCCGGCTCCCA 62.644 63.158 0.00 0.00 37.80 4.37
2059 2465 3.081133 CGGACGCGACCAAGATTG 58.919 61.111 26.33 6.00 0.00 2.67
2064 2470 2.452813 CGCGACCAAGATTGACCGG 61.453 63.158 0.00 0.00 0.00 5.28
2068 2474 1.405526 CGACCAAGATTGACCGGTCAT 60.406 52.381 36.52 25.36 46.84 3.06
2080 2486 4.795469 TGACCGGTCATACCTCATACTTA 58.205 43.478 33.23 5.20 35.66 2.24
2097 2503 2.959030 ACTTAGTGCTATGCATCCGAGA 59.041 45.455 0.19 0.00 41.91 4.04
2130 2536 6.924913 TTCATCCTCTAGATCCATACTTGG 57.075 41.667 0.00 0.00 45.15 3.61
2141 2552 2.079155 CCATACTTGGTGCTATGCGCA 61.079 52.381 14.96 14.96 41.25 6.09
2152 2563 0.578683 CTATGCGCATGTGTCGGAAG 59.421 55.000 32.48 15.26 0.00 3.46
2155 2566 2.047274 CGCATGTGTCGGAAGGGT 60.047 61.111 0.00 0.00 0.00 4.34
2201 2616 3.697747 TCCGCCCGGACGTTTGAT 61.698 61.111 9.94 0.00 39.76 2.57
2211 2626 1.611519 GACGTTTGATGGGGGTTTGA 58.388 50.000 0.00 0.00 0.00 2.69
2212 2627 1.957877 GACGTTTGATGGGGGTTTGAA 59.042 47.619 0.00 0.00 0.00 2.69
2302 2717 5.557891 TTTTGGAGGTGTTTGCAATTTTG 57.442 34.783 0.00 0.00 0.00 2.44
2320 2735 0.991146 TGTGAAAGCTATGGAGGCCA 59.009 50.000 5.01 0.00 38.19 5.36
2348 2763 5.353123 GCCAACTTAAAGTCGTCATAATCCA 59.647 40.000 0.00 0.00 0.00 3.41
2455 2891 7.458409 AACTTGCTCTCAACATCACATAATT 57.542 32.000 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 3.188254 TCACAAACAACATGAGCATACCG 59.812 43.478 0.00 0.00 0.00 4.02
37 38 4.460034 AGCATCACAAACAACATGAGCATA 59.540 37.500 0.00 0.00 0.00 3.14
38 39 3.257375 AGCATCACAAACAACATGAGCAT 59.743 39.130 0.00 0.00 0.00 3.79
39 40 2.624364 AGCATCACAAACAACATGAGCA 59.376 40.909 0.00 0.00 0.00 4.26
61 63 3.324246 CCCCCTCAGTCATAGTGGT 57.676 57.895 0.00 0.00 0.00 4.16
77 79 5.881923 TGTCAATATACTCTAACACCCCC 57.118 43.478 0.00 0.00 0.00 5.40
116 404 9.886132 GTAGTCCGATTACAAATATATTCCCAT 57.114 33.333 0.00 0.00 0.00 4.00
184 472 2.981859 ACGGAAGACTTGTTGACAGT 57.018 45.000 0.00 0.00 0.00 3.55
241 529 1.303888 ACTCCGGGTCTTGCTACGA 60.304 57.895 0.00 0.00 0.00 3.43
242 530 1.153823 CACTCCGGGTCTTGCTACG 60.154 63.158 0.00 0.00 0.00 3.51
256 544 4.299978 GTGAGAACACAACTAGTCCACTC 58.700 47.826 0.00 1.24 45.32 3.51
257 545 3.243434 CGTGAGAACACAACTAGTCCACT 60.243 47.826 0.00 0.00 46.20 4.00
260 552 3.637998 TCGTGAGAACACAACTAGTCC 57.362 47.619 0.00 0.00 46.20 3.85
287 579 1.168714 AGCTTGAAGATTTCGGTGGC 58.831 50.000 0.00 0.00 0.00 5.01
307 599 7.003482 TGCCTGGCAGAACATTGAAATATATA 58.997 34.615 19.30 0.00 33.32 0.86
308 600 5.834742 TGCCTGGCAGAACATTGAAATATAT 59.165 36.000 19.30 0.00 33.32 0.86
336 628 6.433404 ACTCTGTCAAACCTAGAATAGTCGAA 59.567 38.462 0.00 0.00 36.82 3.71
420 712 4.256920 AGGCAAGCAACTAAGTGATACAG 58.743 43.478 0.00 0.00 0.00 2.74
421 713 4.253685 GAGGCAAGCAACTAAGTGATACA 58.746 43.478 0.00 0.00 0.00 2.29
422 714 3.307242 CGAGGCAAGCAACTAAGTGATAC 59.693 47.826 0.00 0.00 0.00 2.24
423 715 3.056107 ACGAGGCAAGCAACTAAGTGATA 60.056 43.478 0.00 0.00 0.00 2.15
424 716 2.289694 ACGAGGCAAGCAACTAAGTGAT 60.290 45.455 0.00 0.00 0.00 3.06
430 722 1.343142 TGAGAACGAGGCAAGCAACTA 59.657 47.619 0.00 0.00 0.00 2.24
443 735 6.523201 GCAAAACCATATTAAGTGTGAGAACG 59.477 38.462 0.00 0.00 0.00 3.95
500 801 0.036388 GGCCGAGATCTGTTGTTCCA 60.036 55.000 0.00 0.00 0.00 3.53
584 890 5.184864 TCAATTGTAGTAATTGCCTGTTGGG 59.815 40.000 5.13 0.00 37.50 4.12
586 892 6.753279 CCATCAATTGTAGTAATTGCCTGTTG 59.247 38.462 5.13 0.00 37.50 3.33
588 894 5.163519 GCCATCAATTGTAGTAATTGCCTGT 60.164 40.000 5.13 0.00 37.50 4.00
589 895 5.068198 AGCCATCAATTGTAGTAATTGCCTG 59.932 40.000 5.13 7.32 37.50 4.85
590 896 5.203528 AGCCATCAATTGTAGTAATTGCCT 58.796 37.500 5.13 0.00 37.50 4.75
591 897 5.520376 AGCCATCAATTGTAGTAATTGCC 57.480 39.130 5.13 0.00 37.50 4.52
592 898 5.207768 CGAGCCATCAATTGTAGTAATTGC 58.792 41.667 5.13 0.00 37.50 3.56
593 899 5.008019 AGCGAGCCATCAATTGTAGTAATTG 59.992 40.000 5.13 6.12 38.60 2.32
594 900 5.126067 AGCGAGCCATCAATTGTAGTAATT 58.874 37.500 5.13 0.00 0.00 1.40
595 901 4.708177 AGCGAGCCATCAATTGTAGTAAT 58.292 39.130 5.13 0.00 0.00 1.89
596 902 4.119862 GAGCGAGCCATCAATTGTAGTAA 58.880 43.478 5.13 0.00 0.00 2.24
597 903 3.132111 TGAGCGAGCCATCAATTGTAGTA 59.868 43.478 5.13 0.00 0.00 1.82
598 904 2.093500 TGAGCGAGCCATCAATTGTAGT 60.093 45.455 5.13 0.00 0.00 2.73
599 905 2.543012 CTGAGCGAGCCATCAATTGTAG 59.457 50.000 5.13 0.00 0.00 2.74
631 943 8.759641 CAGAATACATTAGAAAATGACTCCTCG 58.240 37.037 5.18 0.00 44.50 4.63
741 1053 3.130160 GCGGCAGCAGCTAAGCTT 61.130 61.111 10.66 3.48 43.70 3.74
799 1111 3.695556 GGTACTAGTGAAGACTGGAGACC 59.304 52.174 5.39 0.00 35.08 3.85
844 1199 2.046604 GGCAGTTACGTGGGGTCC 60.047 66.667 0.00 0.00 0.00 4.46
869 1224 7.657761 GCCACTGCTGTTTGTTATATAGAGTAT 59.342 37.037 0.00 0.00 33.53 2.12
870 1225 6.984474 GCCACTGCTGTTTGTTATATAGAGTA 59.016 38.462 0.00 0.00 33.53 2.59
871 1226 5.817816 GCCACTGCTGTTTGTTATATAGAGT 59.182 40.000 0.00 0.00 33.53 3.24
872 1227 5.237344 GGCCACTGCTGTTTGTTATATAGAG 59.763 44.000 0.00 0.00 37.74 2.43
873 1228 5.123227 GGCCACTGCTGTTTGTTATATAGA 58.877 41.667 0.00 0.00 37.74 1.98
963 1318 6.321717 GTTTGTTGATTAGATGCCGATCAAA 58.678 36.000 0.00 0.00 40.35 2.69
979 1334 3.959975 GCGGCGCTGGTTTGTTGA 61.960 61.111 26.86 0.00 0.00 3.18
993 1348 5.335661 GCTATTTATTACCTTCATTGGGCGG 60.336 44.000 0.00 0.00 0.00 6.13
995 1350 6.901081 AGCTATTTATTACCTTCATTGGGC 57.099 37.500 0.00 0.00 0.00 5.36
1074 1433 4.330620 ACAATCTTTTGCTGCAACAACAAG 59.669 37.500 15.72 15.35 36.22 3.16
1155 1523 0.855349 CATGCATACCGTTCGCTCTC 59.145 55.000 0.00 0.00 0.00 3.20
1237 1609 2.404789 CTTGCGGCCATGTTAGCG 59.595 61.111 2.24 0.00 0.00 4.26
1259 1632 3.909086 GAGCTCACCCCTGCACCAC 62.909 68.421 9.40 0.00 0.00 4.16
1278 1661 3.840594 TCGCCGGTTATCCCCACG 61.841 66.667 1.90 0.00 0.00 4.94
1384 1767 1.276421 CACTTCCTCCACCTTGACGAT 59.724 52.381 0.00 0.00 0.00 3.73
1459 1845 0.110486 CCATATGGGTGGTGGTAGCC 59.890 60.000 14.52 0.00 38.69 3.93
1460 1846 3.725754 CCATATGGGTGGTGGTAGC 57.274 57.895 14.52 0.00 34.46 3.58
1550 1936 2.125512 GCGAACTCGGCATCTGGT 60.126 61.111 0.69 0.00 40.23 4.00
1638 2024 5.764686 ACCAAGGACGACGTATATGTATACA 59.235 40.000 8.27 8.27 38.72 2.29
1639 2025 6.148480 AGACCAAGGACGACGTATATGTATAC 59.852 42.308 0.00 0.00 36.15 1.47
1640 2026 6.233434 AGACCAAGGACGACGTATATGTATA 58.767 40.000 0.00 0.00 0.00 1.47
1641 2027 5.068636 AGACCAAGGACGACGTATATGTAT 58.931 41.667 0.00 0.00 0.00 2.29
1642 2028 4.454678 AGACCAAGGACGACGTATATGTA 58.545 43.478 0.00 0.00 0.00 2.29
1643 2029 3.285484 AGACCAAGGACGACGTATATGT 58.715 45.455 0.00 0.00 0.00 2.29
1644 2030 3.304525 GGAGACCAAGGACGACGTATATG 60.305 52.174 0.00 0.00 0.00 1.78
1656 2047 5.205056 ACTCTATCTAACTGGAGACCAAGG 58.795 45.833 0.00 0.00 30.80 3.61
1684 2075 5.015733 CGTGATTGCTTTTTCTCGACATAC 58.984 41.667 0.00 0.00 32.29 2.39
1685 2076 4.435518 GCGTGATTGCTTTTTCTCGACATA 60.436 41.667 0.00 0.00 32.29 2.29
1686 2077 3.667960 GCGTGATTGCTTTTTCTCGACAT 60.668 43.478 0.00 0.00 32.29 3.06
1687 2078 2.349438 GCGTGATTGCTTTTTCTCGACA 60.349 45.455 0.00 0.00 32.29 4.35
1688 2079 2.234187 GCGTGATTGCTTTTTCTCGAC 58.766 47.619 0.00 0.00 32.29 4.20
1695 2086 1.476488 GGGGTATGCGTGATTGCTTTT 59.524 47.619 0.00 0.00 35.36 2.27
1708 2099 4.562347 CGAGGAATTCAGATCTGGGGTATG 60.562 50.000 22.42 3.07 0.00 2.39
1766 2158 1.134280 ACATTCGGAAGCCCAGATCAG 60.134 52.381 0.00 0.00 0.00 2.90
1852 2258 0.861450 GCATTGACCGTTACATGCGC 60.861 55.000 0.00 0.00 0.00 6.09
1853 2259 3.218721 GCATTGACCGTTACATGCG 57.781 52.632 0.00 0.00 0.00 4.73
1875 2281 5.577554 ACGTTTTACATTTTTCTTGCCGTTT 59.422 32.000 0.00 0.00 0.00 3.60
1992 2398 3.873952 GGACTGGCTGTAGATGCTAAAAG 59.126 47.826 0.00 0.00 0.00 2.27
1995 2401 2.432146 CAGGACTGGCTGTAGATGCTAA 59.568 50.000 0.00 0.00 0.00 3.09
2012 2418 2.272146 GAGCCGGATTTGCCAGGA 59.728 61.111 5.05 0.00 35.94 3.86
2017 2423 0.389817 GTTTTGGGAGCCGGATTTGC 60.390 55.000 5.05 0.00 0.00 3.68
2054 2460 2.747177 TGAGGTATGACCGGTCAATCT 58.253 47.619 39.04 31.91 44.90 2.40
2055 2461 3.753294 ATGAGGTATGACCGGTCAATC 57.247 47.619 39.04 30.72 44.90 2.67
2057 2463 3.638860 AGTATGAGGTATGACCGGTCAA 58.361 45.455 39.04 24.95 44.90 3.18
2059 2465 4.826183 ACTAAGTATGAGGTATGACCGGTC 59.174 45.833 28.17 28.17 44.90 4.79
2064 2470 6.809196 GCATAGCACTAAGTATGAGGTATGAC 59.191 42.308 12.44 2.79 40.95 3.06
2068 2474 6.071334 GGATGCATAGCACTAAGTATGAGGTA 60.071 42.308 0.00 0.00 43.04 3.08
2080 2486 1.339610 GAGTCTCGGATGCATAGCACT 59.660 52.381 0.00 2.74 43.04 4.40
2097 2503 8.176105 TGGATCTAGAGGATGAAATATGAGAGT 58.824 37.037 0.00 0.00 34.33 3.24
2193 2608 1.960689 CTTCAAACCCCCATCAAACGT 59.039 47.619 0.00 0.00 0.00 3.99
2201 2616 1.460255 CAGGCTCTTCAAACCCCCA 59.540 57.895 0.00 0.00 0.00 4.96
2211 2626 2.566724 GAGCATCTATAGCCAGGCTCTT 59.433 50.000 20.38 9.84 43.21 2.85
2212 2627 2.178580 GAGCATCTATAGCCAGGCTCT 58.821 52.381 20.38 11.60 43.21 4.09
2302 2717 1.952296 CATGGCCTCCATAGCTTTCAC 59.048 52.381 3.32 0.00 43.15 3.18
2320 2735 3.472652 TGACGACTTTAAGTTGGCACAT 58.527 40.909 16.38 0.00 42.61 3.21
2326 2741 6.961554 GCTTGGATTATGACGACTTTAAGTTG 59.038 38.462 10.56 10.56 35.70 3.16
2348 2763 4.051922 CGAGTCCGCAAAATATAGAGCTT 58.948 43.478 0.00 0.00 0.00 3.74
2415 2830 3.868661 GCAAGTTTCGTTGGTGGATTTTT 59.131 39.130 0.00 0.00 0.00 1.94
2417 2832 2.693074 AGCAAGTTTCGTTGGTGGATTT 59.307 40.909 0.00 0.00 36.79 2.17
2418 2833 2.293399 GAGCAAGTTTCGTTGGTGGATT 59.707 45.455 0.00 0.00 38.25 3.01
2419 2834 1.880027 GAGCAAGTTTCGTTGGTGGAT 59.120 47.619 0.00 0.00 38.25 3.41
2427 2863 3.248602 GTGATGTTGAGAGCAAGTTTCGT 59.751 43.478 0.00 0.00 34.01 3.85
2485 2921 8.675504 TGAACTAAAACCGTTGTTCAATTTCTA 58.324 29.630 11.33 0.00 43.55 2.10
2501 2937 5.548406 TGGAAGAGTAGGCTGAACTAAAAC 58.452 41.667 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.