Multiple sequence alignment - TraesCS2B01G482600

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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 TraesCS2B01G482600 chr2B 100.000 2228 0 0 1 2228 680236575 680238802 0.000000e+00 4115.0
1 TraesCS2B01G482600 chr2B 77.049 732 105 37 857 1541 680408829 680409544 1.630000e-96 363.0
2 TraesCS2B01G482600 chr2B 74.961 639 91 45 857 1433 680322376 680323007 1.720000e-56 230.0
3 TraesCS2B01G482600 chr2B 95.181 83 4 0 3 85 680232253 680232335 4.990000e-27 132.0
4 TraesCS2B01G482600 chr2B 78.626 131 23 4 1379 1506 680075176 680075304 5.100000e-12 82.4
5 TraesCS2B01G482600 chr2B 100.000 28 0 0 273 300 378438886 378438859 4.000000e-03 52.8
6 TraesCS2B01G482600 chr2A 92.361 1741 80 22 501 2227 707063841 707065542 0.000000e+00 2429.0
7 TraesCS2B01G482600 chr2A 86.009 436 36 9 97 508 707063316 707063750 5.650000e-121 444.0
8 TraesCS2B01G482600 chr2A 74.668 1054 158 68 707 1699 706919069 706920074 1.260000e-97 366.0
9 TraesCS2B01G482600 chr2A 76.167 621 82 34 870 1440 707168574 707169178 1.310000e-67 267.0
10 TraesCS2B01G482600 chr2A 76.616 526 64 29 882 1367 707222012 707222518 3.700000e-58 235.0
11 TraesCS2B01G482600 chr2A 77.714 175 25 12 1366 1532 706922935 706923103 6.550000e-16 95.3
12 TraesCS2B01G482600 chr2D 93.176 1143 48 8 501 1639 567584212 567585328 0.000000e+00 1652.0
13 TraesCS2B01G482600 chr2D 96.899 516 16 0 1713 2228 567585786 567586301 0.000000e+00 865.0
14 TraesCS2B01G482600 chr2D 89.019 428 20 16 86 508 567575336 567575741 2.550000e-139 505.0
15 TraesCS2B01G482600 chr2D 75.490 816 117 57 670 1433 567594523 567595307 2.760000e-84 322.0
16 TraesCS2B01G482600 chr2D 73.381 1127 168 76 658 1699 567051247 567052326 4.650000e-77 298.0
17 TraesCS2B01G482600 chr2D 74.474 760 118 42 795 1504 567641833 567642566 2.190000e-65 259.0
18 TraesCS2B01G482600 chr2D 88.614 202 13 3 1713 1914 523640680 523640489 1.030000e-58 237.0
19 TraesCS2B01G482600 chr2D 79.545 132 21 4 1379 1508 567057893 567058020 3.050000e-14 89.8
20 TraesCS2B01G482600 chr5D 93.564 202 13 0 1713 1914 526418672 526418471 3.600000e-78 302.0
21 TraesCS2B01G482600 chr4D 92.647 204 15 0 1711 1914 252170393 252170190 6.020000e-76 294.0
22 TraesCS2B01G482600 chr4D 95.181 83 4 0 3 85 261594276 261594358 4.990000e-27 132.0
23 TraesCS2B01G482600 chr1A 92.040 201 16 0 1713 1913 403605600 403605800 1.300000e-72 283.0
24 TraesCS2B01G482600 chr1D 95.181 83 4 0 3 85 57124783 57124865 4.990000e-27 132.0
25 TraesCS2B01G482600 chr1D 93.182 88 5 1 3 89 143030835 143030922 6.460000e-26 128.0
26 TraesCS2B01G482600 chr1D 93.023 86 6 0 2 87 93444350 93444435 2.320000e-25 126.0
27 TraesCS2B01G482600 chrUn 93.182 88 3 3 3 88 24335273 24335187 2.320000e-25 126.0
28 TraesCS2B01G482600 chrUn 92.045 88 6 1 3 89 132045058 132045145 3.000000e-24 122.0
29 TraesCS2B01G482600 chrUn 100.000 28 0 0 1872 1899 336021211 336021238 4.000000e-03 52.8
30 TraesCS2B01G482600 chr5B 93.976 83 5 0 3 85 256521162 256521080 2.320000e-25 126.0
31 TraesCS2B01G482600 chr7B 92.135 89 6 1 2 89 710987814 710987726 8.350000e-25 124.0


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 TraesCS2B01G482600 chr2B 680236575 680238802 2227 False 4115.00 4115 100.0000 1 2228 1 chr2B.!!$F3 2227
1 TraesCS2B01G482600 chr2B 680408829 680409544 715 False 363.00 363 77.0490 857 1541 1 chr2B.!!$F5 684
2 TraesCS2B01G482600 chr2B 680322376 680323007 631 False 230.00 230 74.9610 857 1433 1 chr2B.!!$F4 576
3 TraesCS2B01G482600 chr2A 707063316 707065542 2226 False 1436.50 2429 89.1850 97 2227 2 chr2A.!!$F4 2130
4 TraesCS2B01G482600 chr2A 707168574 707169178 604 False 267.00 267 76.1670 870 1440 1 chr2A.!!$F1 570
5 TraesCS2B01G482600 chr2A 707222012 707222518 506 False 235.00 235 76.6160 882 1367 1 chr2A.!!$F2 485
6 TraesCS2B01G482600 chr2A 706919069 706923103 4034 False 230.65 366 76.1910 707 1699 2 chr2A.!!$F3 992
7 TraesCS2B01G482600 chr2D 567584212 567586301 2089 False 1258.50 1652 95.0375 501 2228 2 chr2D.!!$F6 1727
8 TraesCS2B01G482600 chr2D 567594523 567595307 784 False 322.00 322 75.4900 670 1433 1 chr2D.!!$F4 763
9 TraesCS2B01G482600 chr2D 567051247 567052326 1079 False 298.00 298 73.3810 658 1699 1 chr2D.!!$F1 1041
10 TraesCS2B01G482600 chr2D 567641833 567642566 733 False 259.00 259 74.4740 795 1504 1 chr2D.!!$F5 709

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
27 28 0.24912 CGTGGCCCATCTCTTGTACA 59.751 55.0 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1802 5726 0.463295 CAGGACTGCTGTATGGCTGG 60.463 60.0 0.0 0.0 35.86 4.85 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 2.607750 ACTGAGGTCGTGGCCCAT 60.608 61.111 0.00 0.00 0.00 4.00
18 19 2.187946 CTGAGGTCGTGGCCCATC 59.812 66.667 0.00 0.00 0.00 3.51
19 20 2.284625 TGAGGTCGTGGCCCATCT 60.285 61.111 0.00 0.00 0.00 2.90
20 21 2.303549 CTGAGGTCGTGGCCCATCTC 62.304 65.000 0.00 0.00 0.00 2.75
21 22 2.039624 AGGTCGTGGCCCATCTCT 59.960 61.111 0.00 0.00 0.00 3.10
22 23 1.613630 AGGTCGTGGCCCATCTCTT 60.614 57.895 0.00 0.00 0.00 2.85
23 24 1.450312 GGTCGTGGCCCATCTCTTG 60.450 63.158 0.00 0.00 0.00 3.02
24 25 1.296715 GTCGTGGCCCATCTCTTGT 59.703 57.895 0.00 0.00 0.00 3.16
25 26 0.535335 GTCGTGGCCCATCTCTTGTA 59.465 55.000 0.00 0.00 0.00 2.41
26 27 0.535335 TCGTGGCCCATCTCTTGTAC 59.465 55.000 0.00 0.00 0.00 2.90
27 28 0.249120 CGTGGCCCATCTCTTGTACA 59.751 55.000 0.00 0.00 0.00 2.90
28 29 1.134401 CGTGGCCCATCTCTTGTACAT 60.134 52.381 0.00 0.00 0.00 2.29
29 30 2.565841 GTGGCCCATCTCTTGTACATC 58.434 52.381 0.00 0.00 0.00 3.06
30 31 2.092968 GTGGCCCATCTCTTGTACATCA 60.093 50.000 0.00 0.00 0.00 3.07
31 32 2.779430 TGGCCCATCTCTTGTACATCAT 59.221 45.455 0.00 0.00 0.00 2.45
32 33 3.973305 TGGCCCATCTCTTGTACATCATA 59.027 43.478 0.00 0.00 0.00 2.15
33 34 4.598807 TGGCCCATCTCTTGTACATCATAT 59.401 41.667 0.00 0.00 0.00 1.78
34 35 5.784906 TGGCCCATCTCTTGTACATCATATA 59.215 40.000 0.00 0.00 0.00 0.86
35 36 6.444816 TGGCCCATCTCTTGTACATCATATAT 59.555 38.462 0.00 0.00 0.00 0.86
36 37 7.623278 TGGCCCATCTCTTGTACATCATATATA 59.377 37.037 0.00 0.00 0.00 0.86
37 38 7.928706 GGCCCATCTCTTGTACATCATATATAC 59.071 40.741 0.00 0.00 0.00 1.47
38 39 7.649705 GCCCATCTCTTGTACATCATATATACG 59.350 40.741 0.00 0.00 0.00 3.06
39 40 8.687242 CCCATCTCTTGTACATCATATATACGT 58.313 37.037 0.00 0.00 0.00 3.57
40 41 9.508567 CCATCTCTTGTACATCATATATACGTG 57.491 37.037 0.00 0.00 0.00 4.49
41 42 9.014533 CATCTCTTGTACATCATATATACGTGC 57.985 37.037 0.00 0.00 0.00 5.34
42 43 7.535997 TCTCTTGTACATCATATATACGTGCC 58.464 38.462 0.00 0.00 0.00 5.01
43 44 7.393515 TCTCTTGTACATCATATATACGTGCCT 59.606 37.037 0.00 0.00 0.00 4.75
44 45 7.892609 TCTTGTACATCATATATACGTGCCTT 58.107 34.615 0.00 0.00 0.00 4.35
45 46 8.364894 TCTTGTACATCATATATACGTGCCTTT 58.635 33.333 0.00 0.00 0.00 3.11
46 47 7.883229 TGTACATCATATATACGTGCCTTTG 57.117 36.000 0.00 0.00 0.00 2.77
47 48 5.862924 ACATCATATATACGTGCCTTTGC 57.137 39.130 0.00 0.00 38.26 3.68
56 57 4.177673 TGCCTTTGCACATGAGCA 57.822 50.000 14.17 14.17 44.23 4.26
64 65 0.998669 TGCACATGAGCAATACGTCG 59.001 50.000 15.81 0.00 42.46 5.12
65 66 0.999406 GCACATGAGCAATACGTCGT 59.001 50.000 10.48 2.21 0.00 4.34
66 67 1.267038 GCACATGAGCAATACGTCGTG 60.267 52.381 10.48 0.00 36.04 4.35
67 68 0.999406 ACATGAGCAATACGTCGTGC 59.001 50.000 8.47 13.95 41.22 5.34
68 69 0.998669 CATGAGCAATACGTCGTGCA 59.001 50.000 21.41 6.12 43.42 4.57
69 70 1.393196 CATGAGCAATACGTCGTGCAA 59.607 47.619 21.41 11.93 43.42 4.08
70 71 1.720805 TGAGCAATACGTCGTGCAAT 58.279 45.000 21.41 5.68 43.42 3.56
71 72 2.073056 TGAGCAATACGTCGTGCAATT 58.927 42.857 21.41 5.05 43.42 2.32
72 73 2.482336 TGAGCAATACGTCGTGCAATTT 59.518 40.909 21.41 4.74 43.42 1.82
73 74 3.091417 GAGCAATACGTCGTGCAATTTC 58.909 45.455 21.41 9.46 43.42 2.17
74 75 2.482336 AGCAATACGTCGTGCAATTTCA 59.518 40.909 21.41 0.00 43.42 2.69
75 76 3.058570 AGCAATACGTCGTGCAATTTCAA 60.059 39.130 21.41 0.00 43.42 2.69
76 77 3.057609 GCAATACGTCGTGCAATTTCAAC 59.942 43.478 16.23 0.00 40.58 3.18
77 78 4.215201 CAATACGTCGTGCAATTTCAACA 58.785 39.130 8.47 0.00 0.00 3.33
78 79 2.834574 ACGTCGTGCAATTTCAACAA 57.165 40.000 0.00 0.00 0.00 2.83
79 80 2.446282 ACGTCGTGCAATTTCAACAAC 58.554 42.857 0.00 0.00 0.00 3.32
80 81 2.159503 ACGTCGTGCAATTTCAACAACA 60.160 40.909 0.00 0.00 0.00 3.33
81 82 3.042189 CGTCGTGCAATTTCAACAACAT 58.958 40.909 0.00 0.00 0.00 2.71
82 83 4.215201 CGTCGTGCAATTTCAACAACATA 58.785 39.130 0.00 0.00 0.00 2.29
83 84 4.086524 CGTCGTGCAATTTCAACAACATAC 59.913 41.667 0.00 0.00 0.00 2.39
84 85 4.973051 GTCGTGCAATTTCAACAACATACA 59.027 37.500 0.00 0.00 0.00 2.29
85 86 5.115472 GTCGTGCAATTTCAACAACATACAG 59.885 40.000 0.00 0.00 0.00 2.74
86 87 4.382457 CGTGCAATTTCAACAACATACAGG 59.618 41.667 0.00 0.00 0.00 4.00
87 88 5.288804 GTGCAATTTCAACAACATACAGGT 58.711 37.500 0.00 0.00 0.00 4.00
88 89 6.442952 GTGCAATTTCAACAACATACAGGTA 58.557 36.000 0.00 0.00 0.00 3.08
89 90 6.362283 GTGCAATTTCAACAACATACAGGTAC 59.638 38.462 0.00 0.00 0.00 3.34
90 91 5.861787 GCAATTTCAACAACATACAGGTACC 59.138 40.000 2.73 2.73 0.00 3.34
91 92 6.386654 CAATTTCAACAACATACAGGTACCC 58.613 40.000 8.74 0.00 0.00 3.69
92 93 3.706600 TCAACAACATACAGGTACCCC 57.293 47.619 8.74 0.00 0.00 4.95
93 94 3.253220 TCAACAACATACAGGTACCCCT 58.747 45.455 8.74 0.00 44.02 4.79
94 95 4.427637 TCAACAACATACAGGTACCCCTA 58.572 43.478 8.74 0.00 39.89 3.53
95 96 4.845225 TCAACAACATACAGGTACCCCTAA 59.155 41.667 8.74 0.00 39.89 2.69
96 97 4.831674 ACAACATACAGGTACCCCTAAC 57.168 45.455 8.74 0.00 39.89 2.34
97 98 3.520721 ACAACATACAGGTACCCCTAACC 59.479 47.826 8.74 0.00 39.89 2.85
98 99 2.767972 ACATACAGGTACCCCTAACCC 58.232 52.381 8.74 0.00 39.89 4.11
129 130 3.118445 TGGCTAACACAATGATCGATGGA 60.118 43.478 0.54 0.00 0.00 3.41
143 144 2.832129 TCGATGGAGAGGTACAAAGCTT 59.168 45.455 0.00 0.00 32.30 3.74
154 155 4.000988 GGTACAAAGCTTGGAGAATCGAA 58.999 43.478 8.15 0.00 34.37 3.71
160 161 5.774498 AAGCTTGGAGAATCGAAAGTTTT 57.226 34.783 0.00 0.00 32.03 2.43
250 251 9.456147 TGAAAATAAACTAATTCCTCCGATTCA 57.544 29.630 0.00 0.00 0.00 2.57
294 318 6.712241 AGCGTCAATTAATATGAATCGGAG 57.288 37.500 0.00 0.00 0.00 4.63
313 337 1.371558 GGAGTTCCTGCTTGGTCGT 59.628 57.895 0.00 0.00 37.07 4.34
317 341 1.072331 AGTTCCTGCTTGGTCGTTCAT 59.928 47.619 0.00 0.00 37.07 2.57
330 354 3.791586 TTCATCCATGCGGCCGGA 61.792 61.111 29.38 27.51 35.27 5.14
333 357 1.302431 CATCCATGCGGCCGGAATA 60.302 57.895 27.18 12.83 34.22 1.75
335 359 3.345808 CCATGCGGCCGGAATACG 61.346 66.667 27.18 12.65 43.80 3.06
355 379 0.732880 CTGTGGATCGGTGTGACGAC 60.733 60.000 0.00 0.00 46.64 4.34
362 386 2.927618 CGGTGTGACGACGCTTGTG 61.928 63.158 0.00 0.00 35.47 3.33
393 417 2.766828 CCTTCCCTTCTCAACGGTAGAT 59.233 50.000 0.00 0.00 0.00 1.98
400 424 5.278561 CCCTTCTCAACGGTAGATGATCTAC 60.279 48.000 21.41 21.41 46.50 2.59
406 430 6.589135 TCAACGGTAGATGATCTACTAGTGA 58.411 40.000 26.48 22.32 46.44 3.41
411 435 3.757270 AGATGATCTACTAGTGACCGGG 58.243 50.000 6.32 0.00 0.00 5.73
430 454 1.025113 GGGCAGCGAGTAGGTTTTCC 61.025 60.000 0.00 0.00 41.05 3.13
444 468 4.939474 AGGTTTTCCCGATCGCAAGACTA 61.939 47.826 10.32 0.00 46.83 2.59
538 660 3.064324 GGCATTTGACCCGCTGCT 61.064 61.111 0.00 0.00 35.03 4.24
581 703 1.696884 GGAGACTCCCATCCTTGATCC 59.303 57.143 10.74 0.00 32.51 3.36
619 741 4.678622 ACCGAAGAAACACAAACCAATTC 58.321 39.130 0.00 0.00 0.00 2.17
702 826 6.488006 CGGATTCAAGGACAATAATTCCATCT 59.512 38.462 0.00 0.00 35.33 2.90
804 942 3.210012 AAGGACGGGCCAGCATGTT 62.210 57.895 4.39 0.00 40.02 2.71
839 977 6.155737 CCTACTAGTACTATCCTCCTCTCCTC 59.844 50.000 2.33 0.00 0.00 3.71
958 1162 2.234908 GCCACACAACACTATCTCCTCT 59.765 50.000 0.00 0.00 0.00 3.69
963 1167 5.184096 CACACAACACTATCTCCTCTGTAGT 59.816 44.000 0.00 0.00 0.00 2.73
964 1168 6.374613 CACACAACACTATCTCCTCTGTAGTA 59.625 42.308 0.00 0.00 0.00 1.82
965 1169 6.600032 ACACAACACTATCTCCTCTGTAGTAG 59.400 42.308 0.00 0.00 0.00 2.57
966 1170 6.600032 CACAACACTATCTCCTCTGTAGTAGT 59.400 42.308 0.00 0.00 0.00 2.73
967 1171 7.769507 CACAACACTATCTCCTCTGTAGTAGTA 59.230 40.741 0.00 0.00 0.00 1.82
968 1172 7.769970 ACAACACTATCTCCTCTGTAGTAGTAC 59.230 40.741 0.37 0.37 0.00 2.73
1050 1268 4.662961 CTGGTGGTGCTCGCGTCA 62.663 66.667 5.77 2.39 0.00 4.35
1258 1532 1.741706 CTCATGTGCTGGCTTACAAGG 59.258 52.381 0.00 0.00 0.00 3.61
1321 1615 1.302993 CCGGGAAGGAAAAAGCGGA 60.303 57.895 0.00 0.00 45.00 5.54
1375 4893 3.677148 CGCCTGTATCAACTGTCATCTGT 60.677 47.826 0.00 0.00 0.00 3.41
1376 4894 4.440112 CGCCTGTATCAACTGTCATCTGTA 60.440 45.833 0.00 0.00 0.00 2.74
1377 4895 4.806247 GCCTGTATCAACTGTCATCTGTAC 59.194 45.833 0.00 0.00 0.00 2.90
1511 5047 2.715046 ACTGGTTGCATCATCGATGTT 58.285 42.857 24.09 14.06 41.60 2.71
1514 5050 2.679336 TGGTTGCATCATCGATGTTCTG 59.321 45.455 24.09 19.31 41.60 3.02
1519 5055 4.256110 TGCATCATCGATGTTCTGTTTCT 58.744 39.130 24.09 0.00 41.60 2.52
1563 5099 4.319046 CCAAGTTCAGAGTCGTTCATGTTG 60.319 45.833 0.00 0.00 0.00 3.33
1564 5100 4.060038 AGTTCAGAGTCGTTCATGTTGT 57.940 40.909 0.00 0.00 0.00 3.32
1701 5241 4.165779 GAGTTTTCTTTGTGTGTGTGTGG 58.834 43.478 0.00 0.00 0.00 4.17
1704 5244 1.745232 TCTTTGTGTGTGTGTGGGTC 58.255 50.000 0.00 0.00 0.00 4.46
1705 5245 0.376852 CTTTGTGTGTGTGTGGGTCG 59.623 55.000 0.00 0.00 0.00 4.79
1706 5246 0.321741 TTTGTGTGTGTGTGGGTCGT 60.322 50.000 0.00 0.00 0.00 4.34
1709 5249 2.359967 TGTGTGTGTGGGTCGTGGA 61.360 57.895 0.00 0.00 0.00 4.02
1710 5250 1.070786 GTGTGTGTGGGTCGTGGAT 59.929 57.895 0.00 0.00 0.00 3.41
1711 5251 0.534203 GTGTGTGTGGGTCGTGGATT 60.534 55.000 0.00 0.00 0.00 3.01
1756 5680 6.748333 TTTCATTCAATCAACTAGGAGCAG 57.252 37.500 0.00 0.00 0.00 4.24
1770 5694 1.002544 GGAGCAGTACAGTCCTTTGCT 59.997 52.381 3.43 3.43 46.86 3.91
1857 5781 0.322816 TCTGCCCAAGAACATGGCTC 60.323 55.000 0.00 0.00 45.56 4.70
1965 5889 5.288804 TGAAAAATTTAGCCACTCTTGCAC 58.711 37.500 0.00 0.00 0.00 4.57
1988 5912 7.257722 CACTATGGATTATTTGTGGGTGAAAC 58.742 38.462 0.00 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.607750 ATGGGCCACGACCTCAGT 60.608 61.111 9.28 0.00 0.00 3.41
3 4 1.617947 AAGAGATGGGCCACGACCTC 61.618 60.000 9.28 13.34 0.00 3.85
4 5 1.613630 AAGAGATGGGCCACGACCT 60.614 57.895 9.28 3.47 0.00 3.85
5 6 1.450312 CAAGAGATGGGCCACGACC 60.450 63.158 9.28 0.00 0.00 4.79
6 7 0.535335 TACAAGAGATGGGCCACGAC 59.465 55.000 9.28 3.37 0.00 4.34
7 8 0.535335 GTACAAGAGATGGGCCACGA 59.465 55.000 9.28 0.00 0.00 4.35
8 9 0.249120 TGTACAAGAGATGGGCCACG 59.751 55.000 9.28 0.00 0.00 4.94
9 10 2.092968 TGATGTACAAGAGATGGGCCAC 60.093 50.000 9.28 2.67 0.00 5.01
10 11 2.195727 TGATGTACAAGAGATGGGCCA 58.804 47.619 9.61 9.61 0.00 5.36
11 12 3.498774 ATGATGTACAAGAGATGGGCC 57.501 47.619 0.00 0.00 0.00 5.80
12 13 7.649705 CGTATATATGATGTACAAGAGATGGGC 59.350 40.741 0.00 0.00 0.00 5.36
13 14 8.687242 ACGTATATATGATGTACAAGAGATGGG 58.313 37.037 8.98 0.00 0.00 4.00
14 15 9.508567 CACGTATATATGATGTACAAGAGATGG 57.491 37.037 8.98 0.00 0.00 3.51
15 16 9.014533 GCACGTATATATGATGTACAAGAGATG 57.985 37.037 8.98 0.00 0.00 2.90
16 17 8.191446 GGCACGTATATATGATGTACAAGAGAT 58.809 37.037 8.98 0.00 0.00 2.75
17 18 7.393515 AGGCACGTATATATGATGTACAAGAGA 59.606 37.037 8.98 0.00 0.00 3.10
18 19 7.539436 AGGCACGTATATATGATGTACAAGAG 58.461 38.462 8.98 0.00 0.00 2.85
19 20 7.462571 AGGCACGTATATATGATGTACAAGA 57.537 36.000 8.98 0.00 0.00 3.02
20 21 8.435430 CAAAGGCACGTATATATGATGTACAAG 58.565 37.037 8.98 0.00 0.00 3.16
21 22 7.095397 GCAAAGGCACGTATATATGATGTACAA 60.095 37.037 8.98 0.00 40.72 2.41
22 23 6.367695 GCAAAGGCACGTATATATGATGTACA 59.632 38.462 8.98 0.00 40.72 2.90
23 24 6.762108 GCAAAGGCACGTATATATGATGTAC 58.238 40.000 8.98 0.00 40.72 2.90
24 25 6.961359 GCAAAGGCACGTATATATGATGTA 57.039 37.500 8.98 0.00 40.72 2.29
25 26 5.862924 GCAAAGGCACGTATATATGATGT 57.137 39.130 8.98 0.00 40.72 3.06
45 46 0.998669 CGACGTATTGCTCATGTGCA 59.001 50.000 18.04 18.04 41.65 4.57
46 47 0.999406 ACGACGTATTGCTCATGTGC 59.001 50.000 12.78 12.78 0.00 4.57
47 48 1.267038 GCACGACGTATTGCTCATGTG 60.267 52.381 12.51 0.00 35.74 3.21
48 49 0.999406 GCACGACGTATTGCTCATGT 59.001 50.000 12.51 0.00 35.74 3.21
49 50 0.998669 TGCACGACGTATTGCTCATG 59.001 50.000 18.74 0.00 39.62 3.07
50 51 1.720805 TTGCACGACGTATTGCTCAT 58.279 45.000 18.74 0.00 39.62 2.90
51 52 1.720805 ATTGCACGACGTATTGCTCA 58.279 45.000 18.74 8.51 39.62 4.26
52 53 2.806288 AATTGCACGACGTATTGCTC 57.194 45.000 18.74 0.00 39.62 4.26
53 54 2.482336 TGAAATTGCACGACGTATTGCT 59.518 40.909 18.74 2.04 39.62 3.91
54 55 2.845486 TGAAATTGCACGACGTATTGC 58.155 42.857 12.82 12.82 39.33 3.56
55 56 4.215201 TGTTGAAATTGCACGACGTATTG 58.785 39.130 0.00 0.00 0.00 1.90
56 57 4.475763 TGTTGAAATTGCACGACGTATT 57.524 36.364 0.00 0.00 0.00 1.89
57 58 4.215965 GTTGTTGAAATTGCACGACGTAT 58.784 39.130 0.00 0.00 0.00 3.06
58 59 3.063588 TGTTGTTGAAATTGCACGACGTA 59.936 39.130 0.00 0.00 0.00 3.57
59 60 2.159503 TGTTGTTGAAATTGCACGACGT 60.160 40.909 0.00 0.00 0.00 4.34
60 61 2.445316 TGTTGTTGAAATTGCACGACG 58.555 42.857 0.00 0.00 0.00 5.12
61 62 4.973051 TGTATGTTGTTGAAATTGCACGAC 59.027 37.500 0.00 0.00 0.00 4.34
62 63 5.175090 TGTATGTTGTTGAAATTGCACGA 57.825 34.783 0.00 0.00 0.00 4.35
63 64 4.382457 CCTGTATGTTGTTGAAATTGCACG 59.618 41.667 0.00 0.00 0.00 5.34
64 65 5.288804 ACCTGTATGTTGTTGAAATTGCAC 58.711 37.500 0.00 0.00 0.00 4.57
65 66 5.528043 ACCTGTATGTTGTTGAAATTGCA 57.472 34.783 0.00 0.00 0.00 4.08
66 67 5.861787 GGTACCTGTATGTTGTTGAAATTGC 59.138 40.000 4.06 0.00 0.00 3.56
86 87 1.617804 GCAAAAGGGGGTTAGGGGTAC 60.618 57.143 0.00 0.00 0.00 3.34
87 88 0.705842 GCAAAAGGGGGTTAGGGGTA 59.294 55.000 0.00 0.00 0.00 3.69
88 89 1.077901 AGCAAAAGGGGGTTAGGGGT 61.078 55.000 0.00 0.00 0.00 4.95
89 90 0.614697 CAGCAAAAGGGGGTTAGGGG 60.615 60.000 0.00 0.00 0.00 4.79
90 91 0.614697 CCAGCAAAAGGGGGTTAGGG 60.615 60.000 0.00 0.00 0.00 3.53
91 92 1.257750 GCCAGCAAAAGGGGGTTAGG 61.258 60.000 0.00 0.00 0.00 2.69
92 93 0.251787 AGCCAGCAAAAGGGGGTTAG 60.252 55.000 0.00 0.00 0.00 2.34
93 94 1.077276 TAGCCAGCAAAAGGGGGTTA 58.923 50.000 0.00 0.00 33.78 2.85
94 95 0.189822 TTAGCCAGCAAAAGGGGGTT 59.810 50.000 0.00 0.00 33.78 4.11
95 96 0.541998 GTTAGCCAGCAAAAGGGGGT 60.542 55.000 0.00 0.00 36.24 4.95
96 97 0.541764 TGTTAGCCAGCAAAAGGGGG 60.542 55.000 0.00 0.00 0.00 5.40
97 98 0.603065 GTGTTAGCCAGCAAAAGGGG 59.397 55.000 0.00 0.00 0.00 4.79
98 99 1.327303 TGTGTTAGCCAGCAAAAGGG 58.673 50.000 0.00 0.00 0.00 3.95
129 130 4.621747 CGATTCTCCAAGCTTTGTACCTCT 60.622 45.833 0.00 0.00 0.00 3.69
143 144 9.720769 ACTAATTAGAAAACTTTCGATTCTCCA 57.279 29.630 19.38 0.00 41.92 3.86
160 161 8.621532 ACTGCAGACATTGAAAACTAATTAGA 57.378 30.769 23.35 0.00 0.00 2.10
236 237 8.197439 GGTCAATTAATTTGAATCGGAGGAATT 58.803 33.333 0.00 0.00 45.71 2.17
250 251 5.527582 CGCTACTGCTAGGGTCAATTAATTT 59.472 40.000 0.00 0.00 36.97 1.82
251 252 5.057149 CGCTACTGCTAGGGTCAATTAATT 58.943 41.667 0.00 0.00 36.97 1.40
253 254 3.449737 ACGCTACTGCTAGGGTCAATTAA 59.550 43.478 0.00 0.00 41.18 1.40
254 255 3.028850 ACGCTACTGCTAGGGTCAATTA 58.971 45.455 0.00 0.00 41.18 1.40
255 256 1.831736 ACGCTACTGCTAGGGTCAATT 59.168 47.619 0.00 0.00 41.18 2.32
256 257 1.486211 ACGCTACTGCTAGGGTCAAT 58.514 50.000 0.00 0.00 41.18 2.57
257 258 2.971676 ACGCTACTGCTAGGGTCAA 58.028 52.632 0.00 0.00 41.18 3.18
260 261 1.486211 ATTGACGCTACTGCTAGGGT 58.514 50.000 2.78 2.78 46.19 4.34
261 262 2.604046 AATTGACGCTACTGCTAGGG 57.396 50.000 0.00 0.00 38.59 3.53
262 263 7.090808 TCATATTAATTGACGCTACTGCTAGG 58.909 38.462 0.00 0.00 36.97 3.02
263 264 8.520835 TTCATATTAATTGACGCTACTGCTAG 57.479 34.615 0.00 0.00 36.97 3.42
266 267 6.950428 CGATTCATATTAATTGACGCTACTGC 59.050 38.462 0.00 0.00 0.00 4.40
267 268 7.328493 TCCGATTCATATTAATTGACGCTACTG 59.672 37.037 0.00 0.00 0.00 2.74
269 270 7.201444 CCTCCGATTCATATTAATTGACGCTAC 60.201 40.741 0.00 0.00 0.00 3.58
284 308 1.765314 CAGGAACTCCCTCCGATTCAT 59.235 52.381 0.00 0.00 45.60 2.57
290 314 1.078848 CAAGCAGGAACTCCCTCCG 60.079 63.158 0.00 0.00 45.60 4.63
294 318 1.376037 CGACCAAGCAGGAACTCCC 60.376 63.158 1.83 0.00 41.22 4.30
313 337 2.623094 ATTCCGGCCGCATGGATGAA 62.623 55.000 22.85 16.44 37.49 2.57
317 341 2.110213 GTATTCCGGCCGCATGGA 59.890 61.111 22.85 9.01 37.49 3.41
330 354 0.535335 ACACCGATCCACAGCGTATT 59.465 50.000 0.00 0.00 0.00 1.89
333 357 2.048222 CACACCGATCCACAGCGT 60.048 61.111 0.00 0.00 0.00 5.07
335 359 2.094659 CGTCACACCGATCCACAGC 61.095 63.158 0.00 0.00 0.00 4.40
365 389 0.547712 TGAGAAGGGAAGGGGACAGG 60.548 60.000 0.00 0.00 0.00 4.00
366 390 1.003696 GTTGAGAAGGGAAGGGGACAG 59.996 57.143 0.00 0.00 0.00 3.51
370 394 1.299976 CCGTTGAGAAGGGAAGGGG 59.700 63.158 0.00 0.00 38.71 4.79
393 417 1.133575 CCCCCGGTCACTAGTAGATCA 60.134 57.143 3.59 0.00 0.00 2.92
400 424 4.162690 GCTGCCCCCGGTCACTAG 62.163 72.222 0.00 0.00 0.00 2.57
411 435 1.025113 GGAAAACCTACTCGCTGCCC 61.025 60.000 0.00 0.00 0.00 5.36
430 454 0.030908 GACCCTAGTCTTGCGATCGG 59.969 60.000 18.30 0.00 40.10 4.18
444 468 0.984230 TTTCCAATCTGCTCGACCCT 59.016 50.000 0.00 0.00 0.00 4.34
538 660 5.224821 TGGAAAATGGAAATGTGATTGCA 57.775 34.783 0.00 0.00 35.04 4.08
581 703 4.933400 TCTTCGGTAGATTTTTCCTTTCCG 59.067 41.667 0.00 0.00 38.36 4.30
619 741 0.319900 CCAACCAGTCGAGGTGAGTG 60.320 60.000 0.00 0.00 45.92 3.51
702 826 1.490069 TCGATGGATTGGAATGGAGCA 59.510 47.619 0.00 0.00 0.00 4.26
804 942 6.239829 GGATAGTACTAGTAGGTAGAGGTGCA 60.240 46.154 8.85 0.00 32.41 4.57
901 1054 1.191535 TGGGCTTAGCATCGTGTACT 58.808 50.000 6.53 0.00 0.00 2.73
963 1167 4.999950 GCGGCTCTGGTAATAGTAGTACTA 59.000 45.833 12.38 12.38 34.82 1.82
964 1168 3.819902 GCGGCTCTGGTAATAGTAGTACT 59.180 47.826 8.14 8.14 0.00 2.73
965 1169 3.057666 GGCGGCTCTGGTAATAGTAGTAC 60.058 52.174 0.00 0.00 0.00 2.73
966 1170 3.152341 GGCGGCTCTGGTAATAGTAGTA 58.848 50.000 0.00 0.00 0.00 1.82
967 1171 1.962100 GGCGGCTCTGGTAATAGTAGT 59.038 52.381 0.00 0.00 0.00 2.73
968 1172 2.229302 GAGGCGGCTCTGGTAATAGTAG 59.771 54.545 30.02 0.00 0.00 2.57
1050 1268 2.366167 AGCTCCCTCCCTTCGCAT 60.366 61.111 0.00 0.00 0.00 4.73
1321 1615 4.298332 GAACATGGAAATGAGCAAAACGT 58.702 39.130 0.00 0.00 0.00 3.99
1376 4894 7.923344 CGAGAACATGAACTGGAAATAGATAGT 59.077 37.037 0.00 0.00 0.00 2.12
1377 4895 7.923344 ACGAGAACATGAACTGGAAATAGATAG 59.077 37.037 0.00 0.00 0.00 2.08
1511 5047 6.405278 TGTGATTAGAGTGACAGAAACAGA 57.595 37.500 0.00 0.00 0.00 3.41
1514 5050 7.307455 GGACTTTGTGATTAGAGTGACAGAAAC 60.307 40.741 0.00 0.00 0.00 2.78
1519 5055 4.346709 TGGGACTTTGTGATTAGAGTGACA 59.653 41.667 0.00 0.00 0.00 3.58
1563 5099 2.941428 CAACGAAATTTGCTACCCCAC 58.059 47.619 0.00 0.00 0.00 4.61
1756 5680 3.500014 GACTCGTAGCAAAGGACTGTAC 58.500 50.000 0.00 0.00 0.00 2.90
1802 5726 0.463295 CAGGACTGCTGTATGGCTGG 60.463 60.000 0.00 0.00 35.86 4.85
1857 5781 9.345517 CATGTGAGTAGAAACCAAAATAATGTG 57.654 33.333 0.00 0.00 0.00 3.21
1965 5889 6.379703 TGGTTTCACCCACAAATAATCCATAG 59.620 38.462 0.00 0.00 37.50 2.23
2009 5933 7.962918 ACATGTTAAAATGAACTCGATAAGTGC 59.037 33.333 12.75 0.00 38.58 4.40


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

AutoCloner maintained by Alex Coulton.