Multiple sequence alignment - TraesCS5A01G416200

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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 TraesCS5A01G416200 chr5A 100.000 2267 0 0 1 2267 605144973 605142707 0.000000e+00 4187.0
1 TraesCS5A01G416200 chr5A 96.662 719 20 3 1551 2267 622284111 622283395 0.000000e+00 1192.0
2 TraesCS5A01G416200 chr5A 96.657 718 17 6 1554 2267 460325399 460324685 0.000000e+00 1186.0
3 TraesCS5A01G416200 chr5A 83.125 160 15 7 227 381 663403755 663403603 3.930000e-28 135.0
4 TraesCS5A01G416200 chr5A 94.872 39 2 0 1552 1590 138091135 138091097 6.760000e-06 62.1
5 TraesCS5A01G416200 chr5D 92.277 1243 76 9 221 1453 483659722 483658490 0.000000e+00 1746.0
6 TraesCS5A01G416200 chr5D 94.886 176 6 3 1 173 483688458 483688283 2.870000e-69 272.0
7 TraesCS5A01G416200 chr5B 90.064 1248 69 22 221 1453 594760726 594759519 0.000000e+00 1567.0
8 TraesCS5A01G416200 chr5B 90.000 170 14 3 7 173 594865538 594865369 1.360000e-52 217.0
9 TraesCS5A01G416200 chr5B 87.059 170 16 4 1982 2145 461635975 461636144 1.070000e-43 187.0
10 TraesCS5A01G416200 chr5B 85.294 170 17 6 1982 2145 639222018 639222185 3.870000e-38 169.0
11 TraesCS5A01G416200 chr5B 84.615 169 21 3 1982 2145 581220006 581220174 1.800000e-36 163.0
12 TraesCS5A01G416200 chr5B 96.000 100 3 1 1458 1556 594759481 594759382 6.480000e-36 161.0
13 TraesCS5A01G416200 chr5B 80.672 119 16 6 54 168 227636207 227636092 4.010000e-13 86.1
14 TraesCS5A01G416200 chr3B 96.783 715 19 3 1555 2267 726124512 726123800 0.000000e+00 1190.0
15 TraesCS5A01G416200 chr4B 83.944 573 78 14 1569 2134 509008460 509009025 9.220000e-149 536.0
16 TraesCS5A01G416200 chr4B 83.624 574 69 19 1554 2119 509522951 509522395 1.200000e-142 516.0
17 TraesCS5A01G416200 chr4B 82.143 168 16 8 221 381 613710698 613710858 5.080000e-27 132.0
18 TraesCS5A01G416200 chr7D 89.015 264 25 4 1542 1804 352085961 352086221 7.810000e-85 324.0
19 TraesCS5A01G416200 chr7D 97.500 40 0 1 1390 1429 261818642 261818680 1.450000e-07 67.6
20 TraesCS5A01G416200 chr2B 85.207 169 18 6 1982 2145 559181215 559181049 1.390000e-37 167.0
21 TraesCS5A01G416200 chr2B 97.368 38 0 1 1391 1428 202180178 202180142 1.880000e-06 63.9
22 TraesCS5A01G416200 chr7B 83.425 181 20 7 1982 2155 703726629 703726452 2.330000e-35 159.0
23 TraesCS5A01G416200 chr7B 92.857 42 3 0 2164 2205 27057908 27057949 6.760000e-06 62.1
24 TraesCS5A01G416200 chr4D 77.857 280 46 13 1981 2257 91072538 91072272 2.330000e-35 159.0
25 TraesCS5A01G416200 chr4D 82.857 175 23 5 1 173 466836424 466836593 1.400000e-32 150.0
26 TraesCS5A01G416200 chr4D 77.739 283 37 16 221 497 483461856 483461594 1.400000e-32 150.0
27 TraesCS5A01G416200 chr4D 84.375 160 13 7 227 381 483449689 483449537 1.810000e-31 147.0
28 TraesCS5A01G416200 chr4D 97.368 38 0 1 1392 1429 384268279 384268243 1.880000e-06 63.9
29 TraesCS5A01G416200 chr6D 82.941 170 24 3 6 173 338400527 338400361 5.050000e-32 148.0
30 TraesCS5A01G416200 chr1D 83.432 169 18 5 6 171 221024950 221025111 5.050000e-32 148.0
31 TraesCS5A01G416200 chr1D 97.436 39 0 1 1390 1428 51933923 51933886 5.230000e-07 65.8
32 TraesCS5A01G416200 chrUn 89.706 68 5 2 6 72 89112366 89112432 4.010000e-13 86.1
33 TraesCS5A01G416200 chrUn 89.706 68 5 2 6 72 89115181 89115247 4.010000e-13 86.1
34 TraesCS5A01G416200 chrUn 89.706 68 5 2 6 72 89308336 89308402 4.010000e-13 86.1
35 TraesCS5A01G416200 chrUn 89.706 68 5 2 6 72 331565731 331565797 4.010000e-13 86.1
36 TraesCS5A01G416200 chr2A 97.561 41 1 0 1554 1594 64793296 64793256 1.120000e-08 71.3
37 TraesCS5A01G416200 chr2A 94.737 38 2 0 1555 1592 304769479 304769516 2.430000e-05 60.2


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 TraesCS5A01G416200 chr5A 605142707 605144973 2266 True 4187 4187 100.000 1 2267 1 chr5A.!!$R3 2266
1 TraesCS5A01G416200 chr5A 622283395 622284111 716 True 1192 1192 96.662 1551 2267 1 chr5A.!!$R4 716
2 TraesCS5A01G416200 chr5A 460324685 460325399 714 True 1186 1186 96.657 1554 2267 1 chr5A.!!$R2 713
3 TraesCS5A01G416200 chr5D 483658490 483659722 1232 True 1746 1746 92.277 221 1453 1 chr5D.!!$R1 1232
4 TraesCS5A01G416200 chr5B 594759382 594760726 1344 True 864 1567 93.032 221 1556 2 chr5B.!!$R3 1335
5 TraesCS5A01G416200 chr3B 726123800 726124512 712 True 1190 1190 96.783 1555 2267 1 chr3B.!!$R1 712
6 TraesCS5A01G416200 chr4B 509008460 509009025 565 False 536 536 83.944 1569 2134 1 chr4B.!!$F1 565
7 TraesCS5A01G416200 chr4B 509522395 509522951 556 True 516 516 83.624 1554 2119 1 chr4B.!!$R1 565

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
743 749 0.588252 CCGTGTGGAAAGAGCACTTG 59.412 55.0 0.0 0.0 37.49 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2034 2098 3.451141 TTCAAACGCATTTTGGAGCTT 57.549 38.095 7.7 0.0 44.3 3.74 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
40 41 8.346476 TGTTTACACATTTTGATGTTACTTGC 57.654 30.769 0.00 0.00 31.37 4.01
41 42 8.194104 TGTTTACACATTTTGATGTTACTTGCT 58.806 29.630 0.00 0.00 31.37 3.91
42 43 9.030301 GTTTACACATTTTGATGTTACTTGCTT 57.970 29.630 0.00 0.00 31.37 3.91
46 47 9.195411 ACACATTTTGATGTTACTTGCTTATTG 57.805 29.630 0.00 0.00 31.37 1.90
47 48 9.195411 CACATTTTGATGTTACTTGCTTATTGT 57.805 29.630 0.00 0.00 31.37 2.71
48 49 9.195411 ACATTTTGATGTTACTTGCTTATTGTG 57.805 29.630 0.00 0.00 0.00 3.33
49 50 9.409312 CATTTTGATGTTACTTGCTTATTGTGA 57.591 29.630 0.00 0.00 0.00 3.58
50 51 9.979578 ATTTTGATGTTACTTGCTTATTGTGAA 57.020 25.926 0.00 0.00 0.00 3.18
51 52 9.979578 TTTTGATGTTACTTGCTTATTGTGAAT 57.020 25.926 0.00 0.00 0.00 2.57
52 53 9.979578 TTTGATGTTACTTGCTTATTGTGAATT 57.020 25.926 0.00 0.00 0.00 2.17
82 83 9.508567 GATTATTGCTTTAGATCACTTTTGTCC 57.491 33.333 0.00 0.00 0.00 4.02
83 84 6.899393 ATTGCTTTAGATCACTTTTGTCCA 57.101 33.333 0.00 0.00 0.00 4.02
84 85 6.707440 TTGCTTTAGATCACTTTTGTCCAA 57.293 33.333 0.00 0.00 0.00 3.53
85 86 6.317789 TGCTTTAGATCACTTTTGTCCAAG 57.682 37.500 0.00 0.00 0.00 3.61
86 87 5.827797 TGCTTTAGATCACTTTTGTCCAAGT 59.172 36.000 0.00 0.00 37.49 3.16
87 88 6.321181 TGCTTTAGATCACTTTTGTCCAAGTT 59.679 34.615 0.00 0.00 34.60 2.66
88 89 6.858478 GCTTTAGATCACTTTTGTCCAAGTTC 59.142 38.462 0.00 0.00 34.60 3.01
89 90 7.468631 GCTTTAGATCACTTTTGTCCAAGTTCA 60.469 37.037 0.00 0.00 34.60 3.18
90 91 5.757850 AGATCACTTTTGTCCAAGTTCAC 57.242 39.130 0.00 0.00 34.60 3.18
91 92 5.192927 AGATCACTTTTGTCCAAGTTCACA 58.807 37.500 0.00 0.00 34.60 3.58
92 93 4.695217 TCACTTTTGTCCAAGTTCACAC 57.305 40.909 0.00 0.00 34.60 3.82
93 94 3.442273 TCACTTTTGTCCAAGTTCACACC 59.558 43.478 0.00 0.00 34.60 4.16
94 95 3.192422 CACTTTTGTCCAAGTTCACACCA 59.808 43.478 0.00 0.00 34.60 4.17
95 96 3.192633 ACTTTTGTCCAAGTTCACACCAC 59.807 43.478 0.00 0.00 32.81 4.16
96 97 2.498644 TTGTCCAAGTTCACACCACA 57.501 45.000 0.00 0.00 0.00 4.17
97 98 2.498644 TGTCCAAGTTCACACCACAA 57.501 45.000 0.00 0.00 0.00 3.33
98 99 3.011566 TGTCCAAGTTCACACCACAAT 57.988 42.857 0.00 0.00 0.00 2.71
99 100 3.360867 TGTCCAAGTTCACACCACAATT 58.639 40.909 0.00 0.00 0.00 2.32
100 101 3.130164 TGTCCAAGTTCACACCACAATTG 59.870 43.478 3.24 3.24 0.00 2.32
101 102 3.130340 GTCCAAGTTCACACCACAATTGT 59.870 43.478 4.92 4.92 0.00 2.71
102 103 3.766591 TCCAAGTTCACACCACAATTGTT 59.233 39.130 8.77 0.00 0.00 2.83
103 104 4.950475 TCCAAGTTCACACCACAATTGTTA 59.050 37.500 8.77 0.00 0.00 2.41
104 105 5.040635 CCAAGTTCACACCACAATTGTTAC 58.959 41.667 8.77 0.00 0.00 2.50
105 106 5.393569 CCAAGTTCACACCACAATTGTTACA 60.394 40.000 8.77 0.00 0.00 2.41
106 107 6.272318 CAAGTTCACACCACAATTGTTACAT 58.728 36.000 8.77 0.00 0.00 2.29
107 108 6.072112 AGTTCACACCACAATTGTTACATC 57.928 37.500 8.77 0.00 0.00 3.06
108 109 5.592282 AGTTCACACCACAATTGTTACATCA 59.408 36.000 8.77 0.00 0.00 3.07
109 110 6.265196 AGTTCACACCACAATTGTTACATCAT 59.735 34.615 8.77 0.00 0.00 2.45
110 111 6.647334 TCACACCACAATTGTTACATCATT 57.353 33.333 8.77 0.00 0.00 2.57
111 112 7.048629 TCACACCACAATTGTTACATCATTT 57.951 32.000 8.77 0.00 0.00 2.32
112 113 6.922407 TCACACCACAATTGTTACATCATTTG 59.078 34.615 8.77 0.00 35.87 2.32
113 114 6.922407 CACACCACAATTGTTACATCATTTGA 59.078 34.615 8.77 0.00 34.69 2.69
114 115 7.599621 CACACCACAATTGTTACATCATTTGAT 59.400 33.333 8.77 0.00 34.69 2.57
115 116 7.814107 ACACCACAATTGTTACATCATTTGATC 59.186 33.333 8.77 0.00 34.69 2.92
116 117 7.813627 CACCACAATTGTTACATCATTTGATCA 59.186 33.333 8.77 0.00 34.69 2.92
117 118 8.366401 ACCACAATTGTTACATCATTTGATCAA 58.634 29.630 8.77 3.38 34.69 2.57
118 119 8.865978 CCACAATTGTTACATCATTTGATCAAG 58.134 33.333 8.77 0.00 34.69 3.02
119 120 9.628746 CACAATTGTTACATCATTTGATCAAGA 57.371 29.630 8.77 4.03 34.69 3.02
124 125 9.628746 TTGTTACATCATTTGATCAAGAACATG 57.371 29.630 8.41 9.57 31.21 3.21
125 126 7.756272 TGTTACATCATTTGATCAAGAACATGC 59.244 33.333 8.41 0.00 31.21 4.06
126 127 6.525578 ACATCATTTGATCAAGAACATGCT 57.474 33.333 8.41 0.00 31.21 3.79
127 128 7.634671 ACATCATTTGATCAAGAACATGCTA 57.365 32.000 8.41 0.00 31.21 3.49
128 129 8.058667 ACATCATTTGATCAAGAACATGCTAA 57.941 30.769 8.41 0.00 31.21 3.09
129 130 8.525316 ACATCATTTGATCAAGAACATGCTAAA 58.475 29.630 8.41 0.00 31.21 1.85
130 131 9.529325 CATCATTTGATCAAGAACATGCTAAAT 57.471 29.630 8.41 0.00 31.21 1.40
175 176 9.073475 ACAACTTTGTTTATCATTTACCTAGCA 57.927 29.630 0.00 0.00 38.47 3.49
176 177 9.559958 CAACTTTGTTTATCATTTACCTAGCAG 57.440 33.333 0.00 0.00 0.00 4.24
177 178 9.515226 AACTTTGTTTATCATTTACCTAGCAGA 57.485 29.630 0.00 0.00 0.00 4.26
178 179 9.167311 ACTTTGTTTATCATTTACCTAGCAGAG 57.833 33.333 0.00 0.00 0.00 3.35
192 193 5.119694 CCTAGCAGAGGTTGTATTCTTTCC 58.880 45.833 0.00 0.00 40.98 3.13
193 194 4.917906 AGCAGAGGTTGTATTCTTTCCT 57.082 40.909 0.00 0.00 0.00 3.36
194 195 5.248380 AGCAGAGGTTGTATTCTTTCCTT 57.752 39.130 0.00 0.00 0.00 3.36
195 196 5.635120 AGCAGAGGTTGTATTCTTTCCTTT 58.365 37.500 0.00 0.00 0.00 3.11
196 197 6.071320 AGCAGAGGTTGTATTCTTTCCTTTT 58.929 36.000 0.00 0.00 0.00 2.27
197 198 6.551227 AGCAGAGGTTGTATTCTTTCCTTTTT 59.449 34.615 0.00 0.00 0.00 1.94
217 218 3.726291 TTTTAGGAAAGTGCAGGTTGC 57.274 42.857 0.00 0.00 45.29 4.17
361 362 4.521130 TGTGACTCTGAGTGAACCATAC 57.479 45.455 16.28 0.00 0.00 2.39
395 396 3.906846 ACCCAAGAGGCCAAGATAGATAG 59.093 47.826 5.01 0.00 40.58 2.08
441 442 3.421844 GGTTTTTGGCAGGTATGTCTCT 58.578 45.455 0.00 0.00 30.13 3.10
443 444 3.350219 TTTTGGCAGGTATGTCTCTCC 57.650 47.619 0.00 0.00 30.13 3.71
503 508 9.526286 GTTTTAATCGAACAAGTAAACTAGAGC 57.474 33.333 0.00 0.00 0.00 4.09
526 531 5.698545 GCATAATCTAACCTGAGCCTAACTG 59.301 44.000 0.00 0.00 0.00 3.16
530 535 6.909550 ATCTAACCTGAGCCTAACTGATAG 57.090 41.667 0.00 0.00 0.00 2.08
532 537 6.065374 TCTAACCTGAGCCTAACTGATAGAG 58.935 44.000 0.00 0.00 33.04 2.43
550 555 3.672808 AGAGCAGGCTCAATGCATATAC 58.327 45.455 22.12 0.00 46.31 1.47
551 556 3.072038 AGAGCAGGCTCAATGCATATACA 59.928 43.478 22.12 0.00 46.31 2.29
622 627 1.142688 AAACCCCATCAGGCAGGACT 61.143 55.000 0.00 0.00 0.00 3.85
664 670 3.371285 GCGCCTAGAAAGTCGAAGAAAAT 59.629 43.478 0.00 0.00 39.69 1.82
681 687 4.876701 TGGAGACAAAAGTGCGCT 57.123 50.000 9.73 0.00 37.44 5.92
726 732 1.724623 CACGTTGTCAACCACTATCCG 59.275 52.381 10.12 0.00 0.00 4.18
730 736 2.448926 TGTCAACCACTATCCGTGTG 57.551 50.000 0.00 0.00 42.20 3.82
743 749 0.588252 CCGTGTGGAAAGAGCACTTG 59.412 55.000 0.00 0.00 37.49 3.16
750 756 3.434984 GTGGAAAGAGCACTTGAGCTTAG 59.565 47.826 0.00 0.00 46.75 2.18
757 763 5.105752 AGAGCACTTGAGCTTAGTATTTCG 58.894 41.667 2.52 0.00 46.75 3.46
787 793 3.149196 ACGCATGGTCAAGATGAAAAGT 58.851 40.909 0.00 0.00 0.00 2.66
1035 1051 0.937304 TGTGCTTCTGCGTCTGTTTC 59.063 50.000 0.00 0.00 43.34 2.78
1044 1060 0.110056 GCGTCTGTTTCGTCGTCCTA 60.110 55.000 0.00 0.00 0.00 2.94
1045 1061 1.879646 CGTCTGTTTCGTCGTCCTAG 58.120 55.000 0.00 0.00 0.00 3.02
1048 1064 1.462283 TCTGTTTCGTCGTCCTAGTCG 59.538 52.381 0.00 0.00 0.00 4.18
1053 1069 2.733671 CGTCGTCCTAGTCGTCGCA 61.734 63.158 9.89 0.00 34.15 5.10
1134 1153 3.300765 GACGTCGACAGGGGTGGT 61.301 66.667 17.16 2.78 0.00 4.16
1209 1228 1.384989 AGATCGCCGATCTGGTCGTT 61.385 55.000 27.51 2.80 46.21 3.85
1236 1255 0.906756 CCTCCAAGAGGCTCAGTCCA 60.907 60.000 18.26 0.00 43.29 4.02
1268 1287 0.904649 CCTCAGCACCACCACTGATA 59.095 55.000 0.00 0.00 41.84 2.15
1332 1354 4.094294 TCATGTATAACTTCAGTTTGCGGC 59.906 41.667 0.00 0.00 39.31 6.53
1377 1399 9.871299 TCGCAAAATAAAAATAAAAGAAAAGCC 57.129 25.926 0.00 0.00 0.00 4.35
1418 1441 2.682856 GAGGGCTGCGTCAATTAATTCA 59.317 45.455 0.00 0.00 0.00 2.57
1429 1452 5.368989 GTCAATTAATTCAGATCGGAGGGT 58.631 41.667 0.00 0.00 0.00 4.34
1436 1459 3.657398 TCAGATCGGAGGGTTGTAGTA 57.343 47.619 0.00 0.00 0.00 1.82
1441 1464 0.097674 CGGAGGGTTGTAGTACGTCG 59.902 60.000 0.00 0.00 0.00 5.12
1453 1476 4.694982 TGTAGTACGTCGATGTTCCAACTA 59.305 41.667 16.79 13.98 0.00 2.24
1454 1477 4.978083 AGTACGTCGATGTTCCAACTAT 57.022 40.909 16.79 0.00 0.00 2.12
1455 1478 4.669318 AGTACGTCGATGTTCCAACTATG 58.331 43.478 16.79 0.00 0.00 2.23
1456 1479 2.268298 ACGTCGATGTTCCAACTATGC 58.732 47.619 3.92 0.00 0.00 3.14
1501 1557 4.002982 TGGAATGTTGATCTCCTGAAACG 58.997 43.478 0.00 0.00 0.00 3.60
1533 1589 4.178540 CGGCCTTGTCTAATCTTCGTAAA 58.821 43.478 0.00 0.00 0.00 2.01
2016 2078 2.900716 TCACATTCGTGGAAGTCACA 57.099 45.000 0.00 0.00 46.36 3.58
2072 2136 6.183359 CGTTTGAATGTAACATTTTCAGAGCG 60.183 38.462 0.00 0.00 31.54 5.03
2198 2265 9.474920 CTTAAAGTTTGCCACAAAAAGATATCA 57.525 29.630 5.32 0.00 0.00 2.15
2199 2266 9.995003 TTAAAGTTTGCCACAAAAAGATATCAT 57.005 25.926 5.32 0.00 0.00 2.45
2200 2267 8.907222 AAAGTTTGCCACAAAAAGATATCATT 57.093 26.923 5.32 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 8.812329 GCAAGTAACATCAAAATGTGTAAACAA 58.188 29.630 0.00 0.00 45.48 2.83
15 16 8.194104 AGCAAGTAACATCAAAATGTGTAAACA 58.806 29.630 0.00 0.00 45.48 2.83
16 17 8.574196 AGCAAGTAACATCAAAATGTGTAAAC 57.426 30.769 0.00 0.00 45.48 2.01
20 21 9.195411 CAATAAGCAAGTAACATCAAAATGTGT 57.805 29.630 0.00 0.00 45.48 3.72
21 22 9.195411 ACAATAAGCAAGTAACATCAAAATGTG 57.805 29.630 0.00 0.00 45.48 3.21
23 24 9.409312 TCACAATAAGCAAGTAACATCAAAATG 57.591 29.630 0.00 0.00 38.93 2.32
24 25 9.979578 TTCACAATAAGCAAGTAACATCAAAAT 57.020 25.926 0.00 0.00 0.00 1.82
25 26 9.979578 ATTCACAATAAGCAAGTAACATCAAAA 57.020 25.926 0.00 0.00 0.00 2.44
26 27 9.979578 AATTCACAATAAGCAAGTAACATCAAA 57.020 25.926 0.00 0.00 0.00 2.69
56 57 9.508567 GGACAAAAGTGATCTAAAGCAATAATC 57.491 33.333 0.00 0.00 0.00 1.75
57 58 9.023962 TGGACAAAAGTGATCTAAAGCAATAAT 57.976 29.630 0.00 0.00 0.00 1.28
58 59 8.402798 TGGACAAAAGTGATCTAAAGCAATAA 57.597 30.769 0.00 0.00 0.00 1.40
59 60 7.994425 TGGACAAAAGTGATCTAAAGCAATA 57.006 32.000 0.00 0.00 0.00 1.90
60 61 6.899393 TGGACAAAAGTGATCTAAAGCAAT 57.101 33.333 0.00 0.00 0.00 3.56
61 62 6.321181 ACTTGGACAAAAGTGATCTAAAGCAA 59.679 34.615 0.00 0.00 38.95 3.91
62 63 5.827797 ACTTGGACAAAAGTGATCTAAAGCA 59.172 36.000 0.00 0.00 38.95 3.91
63 64 6.319141 ACTTGGACAAAAGTGATCTAAAGC 57.681 37.500 0.00 0.00 38.95 3.51
64 65 7.857885 GTGAACTTGGACAAAAGTGATCTAAAG 59.142 37.037 0.00 0.00 40.28 1.85
65 66 7.338196 TGTGAACTTGGACAAAAGTGATCTAAA 59.662 33.333 0.00 0.00 40.28 1.85
66 67 6.826231 TGTGAACTTGGACAAAAGTGATCTAA 59.174 34.615 0.00 0.00 40.28 2.10
67 68 6.260050 GTGTGAACTTGGACAAAAGTGATCTA 59.740 38.462 0.00 0.00 40.28 1.98
68 69 5.066505 GTGTGAACTTGGACAAAAGTGATCT 59.933 40.000 0.00 0.00 40.28 2.75
69 70 5.273944 GTGTGAACTTGGACAAAAGTGATC 58.726 41.667 0.00 0.00 40.28 2.92
70 71 4.097892 GGTGTGAACTTGGACAAAAGTGAT 59.902 41.667 0.00 0.00 40.28 3.06
71 72 3.442273 GGTGTGAACTTGGACAAAAGTGA 59.558 43.478 0.00 0.00 40.28 3.41
72 73 3.192422 TGGTGTGAACTTGGACAAAAGTG 59.808 43.478 0.00 0.00 40.28 3.16
73 74 3.192633 GTGGTGTGAACTTGGACAAAAGT 59.807 43.478 0.00 0.00 42.21 2.66
74 75 3.192422 TGTGGTGTGAACTTGGACAAAAG 59.808 43.478 0.00 0.00 0.00 2.27
75 76 3.157881 TGTGGTGTGAACTTGGACAAAA 58.842 40.909 0.00 0.00 0.00 2.44
76 77 2.796557 TGTGGTGTGAACTTGGACAAA 58.203 42.857 0.00 0.00 0.00 2.83
77 78 2.498644 TGTGGTGTGAACTTGGACAA 57.501 45.000 0.00 0.00 0.00 3.18
78 79 2.498644 TTGTGGTGTGAACTTGGACA 57.501 45.000 0.00 0.00 0.00 4.02
79 80 3.130340 ACAATTGTGGTGTGAACTTGGAC 59.870 43.478 11.07 0.00 0.00 4.02
80 81 3.360867 ACAATTGTGGTGTGAACTTGGA 58.639 40.909 11.07 0.00 0.00 3.53
81 82 3.799281 ACAATTGTGGTGTGAACTTGG 57.201 42.857 11.07 0.00 0.00 3.61
82 83 5.645624 TGTAACAATTGTGGTGTGAACTTG 58.354 37.500 12.82 0.00 0.00 3.16
83 84 5.906113 TGTAACAATTGTGGTGTGAACTT 57.094 34.783 12.82 0.00 0.00 2.66
84 85 5.592282 TGATGTAACAATTGTGGTGTGAACT 59.408 36.000 12.82 0.00 0.00 3.01
85 86 5.826586 TGATGTAACAATTGTGGTGTGAAC 58.173 37.500 12.82 3.27 0.00 3.18
86 87 6.647334 ATGATGTAACAATTGTGGTGTGAA 57.353 33.333 12.82 0.00 0.00 3.18
87 88 6.647334 AATGATGTAACAATTGTGGTGTGA 57.353 33.333 12.82 0.00 0.00 3.58
88 89 6.922407 TCAAATGATGTAACAATTGTGGTGTG 59.078 34.615 12.82 1.95 33.85 3.82
89 90 7.048629 TCAAATGATGTAACAATTGTGGTGT 57.951 32.000 12.82 0.00 33.85 4.16
90 91 7.813627 TGATCAAATGATGTAACAATTGTGGTG 59.186 33.333 12.82 0.88 34.37 4.17
91 92 7.894708 TGATCAAATGATGTAACAATTGTGGT 58.105 30.769 12.82 0.00 34.37 4.16
92 93 8.760103 TTGATCAAATGATGTAACAATTGTGG 57.240 30.769 12.82 0.00 34.37 4.17
93 94 9.628746 TCTTGATCAAATGATGTAACAATTGTG 57.371 29.630 12.82 0.00 34.37 3.33
98 99 9.628746 CATGTTCTTGATCAAATGATGTAACAA 57.371 29.630 9.88 0.00 34.37 2.83
99 100 7.756272 GCATGTTCTTGATCAAATGATGTAACA 59.244 33.333 17.98 14.28 34.37 2.41
100 101 7.972277 AGCATGTTCTTGATCAAATGATGTAAC 59.028 33.333 17.98 10.46 34.37 2.50
101 102 8.058667 AGCATGTTCTTGATCAAATGATGTAA 57.941 30.769 17.98 0.00 34.37 2.41
102 103 7.634671 AGCATGTTCTTGATCAAATGATGTA 57.365 32.000 17.98 1.92 34.37 2.29
103 104 6.525578 AGCATGTTCTTGATCAAATGATGT 57.474 33.333 17.98 3.24 34.37 3.06
104 105 8.920509 TTTAGCATGTTCTTGATCAAATGATG 57.079 30.769 17.98 13.80 34.37 3.07
149 150 9.073475 TGCTAGGTAAATGATAAACAAAGTTGT 57.927 29.630 0.00 0.00 44.72 3.32
150 151 9.559958 CTGCTAGGTAAATGATAAACAAAGTTG 57.440 33.333 0.00 0.00 0.00 3.16
151 152 9.515226 TCTGCTAGGTAAATGATAAACAAAGTT 57.485 29.630 0.00 0.00 0.00 2.66
152 153 9.167311 CTCTGCTAGGTAAATGATAAACAAAGT 57.833 33.333 0.00 0.00 0.00 2.66
153 154 8.616076 CCTCTGCTAGGTAAATGATAAACAAAG 58.384 37.037 0.00 0.00 40.94 2.77
154 155 8.506168 CCTCTGCTAGGTAAATGATAAACAAA 57.494 34.615 0.00 0.00 40.94 2.83
170 171 5.983540 AGGAAAGAATACAACCTCTGCTAG 58.016 41.667 0.00 0.00 0.00 3.42
171 172 6.374417 AAGGAAAGAATACAACCTCTGCTA 57.626 37.500 0.00 0.00 0.00 3.49
172 173 4.917906 AGGAAAGAATACAACCTCTGCT 57.082 40.909 0.00 0.00 0.00 4.24
173 174 5.966742 AAAGGAAAGAATACAACCTCTGC 57.033 39.130 0.00 0.00 0.00 4.26
196 197 4.053469 GCAACCTGCACTTTCCTAAAAA 57.947 40.909 0.00 0.00 44.26 1.94
197 198 3.726291 GCAACCTGCACTTTCCTAAAA 57.274 42.857 0.00 0.00 44.26 1.52
209 210 1.168714 CCCTAAGAAGTGCAACCTGC 58.831 55.000 0.00 0.00 45.29 4.85
210 211 2.568623 ACCCTAAGAAGTGCAACCTG 57.431 50.000 0.00 0.00 37.80 4.00
211 212 4.717279 TTTACCCTAAGAAGTGCAACCT 57.283 40.909 0.00 0.00 37.80 3.50
212 213 5.941647 TGTATTTACCCTAAGAAGTGCAACC 59.058 40.000 0.00 0.00 37.80 3.77
213 214 7.443259 TTGTATTTACCCTAAGAAGTGCAAC 57.557 36.000 0.00 0.00 0.00 4.17
214 215 8.466617 TTTTGTATTTACCCTAAGAAGTGCAA 57.533 30.769 0.00 0.00 0.00 4.08
215 216 8.354426 GTTTTTGTATTTACCCTAAGAAGTGCA 58.646 33.333 0.00 0.00 0.00 4.57
216 217 8.573885 AGTTTTTGTATTTACCCTAAGAAGTGC 58.426 33.333 0.00 0.00 0.00 4.40
255 256 2.323968 TTCAGTTGTGCAGCTGTGTA 57.676 45.000 16.64 0.00 40.07 2.90
347 348 4.202151 TGGATGATCGTATGGTTCACTCAG 60.202 45.833 0.00 0.00 0.00 3.35
361 362 2.549563 CCTCTTGGGTCATGGATGATCG 60.550 54.545 0.00 0.00 38.81 3.69
395 396 1.915078 ATGCAGGACCCACCAGTAGC 61.915 60.000 0.00 0.00 42.04 3.58
418 419 1.201414 GACATACCTGCCAAAAACCGG 59.799 52.381 0.00 0.00 0.00 5.28
463 464 4.549599 CGATTAAAACGATAATGATGGCGC 59.450 41.667 0.00 0.00 0.00 6.53
503 508 7.055667 TCAGTTAGGCTCAGGTTAGATTATG 57.944 40.000 0.00 0.00 0.00 1.90
526 531 2.251409 TGCATTGAGCCTGCTCTATC 57.749 50.000 19.07 11.51 44.83 2.08
530 535 3.188048 GTGTATATGCATTGAGCCTGCTC 59.812 47.826 3.54 12.18 44.83 4.26
532 537 2.880268 TGTGTATATGCATTGAGCCTGC 59.120 45.455 3.54 0.00 44.83 4.85
550 555 1.621107 CCTTGCGCATTAAGCTTGTG 58.379 50.000 12.75 9.20 42.61 3.33
551 556 0.109132 GCCTTGCGCATTAAGCTTGT 60.109 50.000 12.75 0.00 42.61 3.16
568 573 7.948278 ACTTGAATTCGATAGTAGTATTGCC 57.052 36.000 0.04 0.00 37.40 4.52
664 670 1.785041 GCAGCGCACTTTTGTCTCCA 61.785 55.000 11.47 0.00 0.00 3.86
680 686 1.126079 CAAAGCAAAAGAGCACGCAG 58.874 50.000 0.00 0.00 36.85 5.18
681 687 0.737804 TCAAAGCAAAAGAGCACGCA 59.262 45.000 0.00 0.00 36.85 5.24
726 732 1.265365 GCTCAAGTGCTCTTTCCACAC 59.735 52.381 0.00 0.00 35.69 3.82
730 736 3.669536 ACTAAGCTCAAGTGCTCTTTCC 58.330 45.455 0.00 0.00 43.24 3.13
743 749 6.948777 CGTTCTTGTTTCGAAATACTAAGCTC 59.051 38.462 14.69 10.66 0.00 4.09
750 756 4.553429 CCATGCGTTCTTGTTTCGAAATAC 59.447 41.667 14.69 3.21 0.00 1.89
757 763 3.003275 TCTTGACCATGCGTTCTTGTTTC 59.997 43.478 0.00 0.00 0.00 2.78
870 880 8.662781 TTTATAGGCTAAGCATGAACACTAAG 57.337 34.615 0.00 0.00 0.00 2.18
1016 1032 0.937304 GAAACAGACGCAGAAGCACA 59.063 50.000 0.00 0.00 42.27 4.57
1035 1051 2.021106 GCGACGACTAGGACGACG 59.979 66.667 22.49 22.49 46.70 5.12
1044 1060 3.444805 GAGGAGCCTGCGACGACT 61.445 66.667 0.00 0.00 0.00 4.18
1045 1061 4.500116 GGAGGAGCCTGCGACGAC 62.500 72.222 0.00 0.00 0.00 4.34
1268 1287 1.271379 CCGATGAACACCCAAGGTTCT 60.271 52.381 6.80 0.00 43.84 3.01
1332 1354 7.525688 TTGCGAATAGTAATCTCTTGTCTTG 57.474 36.000 0.00 0.00 0.00 3.02
1377 1399 8.095169 AGCCCTCTATACAATTATTAAACTCGG 58.905 37.037 0.00 0.00 0.00 4.63
1397 1419 2.682856 TGAATTAATTGACGCAGCCCTC 59.317 45.455 5.17 0.00 0.00 4.30
1418 1441 2.295885 CGTACTACAACCCTCCGATCT 58.704 52.381 0.00 0.00 0.00 2.75
1429 1452 4.022935 AGTTGGAACATCGACGTACTACAA 60.023 41.667 0.00 0.00 39.30 2.41
1436 1459 2.268298 GCATAGTTGGAACATCGACGT 58.732 47.619 0.00 0.00 39.30 4.34
1441 1464 6.199937 AGAAACATGCATAGTTGGAACATC 57.800 37.500 13.05 7.65 39.30 3.06
1453 1476 1.475751 CCTAGCCGGAGAAACATGCAT 60.476 52.381 5.05 0.00 33.16 3.96
1454 1477 0.107703 CCTAGCCGGAGAAACATGCA 60.108 55.000 5.05 0.00 33.16 3.96
1455 1478 1.440145 GCCTAGCCGGAGAAACATGC 61.440 60.000 5.05 0.00 33.16 4.06
1456 1479 0.815615 GGCCTAGCCGGAGAAACATG 60.816 60.000 5.05 0.00 39.62 3.21
1501 1557 1.092348 GACAAGGCCGGTATTGTTCC 58.908 55.000 22.11 10.80 39.66 3.62
1542 1599 6.542005 TCACACTGCTAGTTCTTTTGATGAAA 59.458 34.615 0.00 0.00 0.00 2.69
2022 2084 7.479291 CGCATTTTGGAGCTTTGATTTTAATTG 59.521 33.333 0.00 0.00 0.00 2.32
2034 2098 3.451141 TTCAAACGCATTTTGGAGCTT 57.549 38.095 7.70 0.00 44.30 3.74


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

AutoCloner maintained by Alex Coulton.