Multiple sequence alignment - TraesCS7A01G104500

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 TraesCS7A01G104500 chr7A 100.000 2317 0 0 1 2317 63574192 63576508 0.000000e+00 4279.0
1 TraesCS7A01G104500 chr7A 96.327 1470 47 5 852 2317 180639864 180638398 0.000000e+00 2409.0
2 TraesCS7A01G104500 chr7A 93.004 1601 41 18 746 2317 42989693 42988135 0.000000e+00 2270.0
3 TraesCS7A01G104500 chr7A 96.166 313 12 0 356 668 180640309 180639997 1.590000e-141 512.0
4 TraesCS7A01G104500 chr7A 86.164 318 28 5 671 988 161732905 161733206 1.720000e-86 329.0
5 TraesCS7A01G104500 chr5A 91.707 1664 76 21 675 2317 592641348 592642970 0.000000e+00 2252.0
6 TraesCS7A01G104500 chr5A 94.643 168 9 0 501 668 592641135 592641302 6.350000e-66 261.0
7 TraesCS7A01G104500 chr5A 83.962 106 6 7 361 466 592641040 592641134 8.820000e-15 91.6
8 TraesCS7A01G104500 chr5B 91.286 1664 83 21 675 2317 75684535 75682913 0.000000e+00 2213.0
9 TraesCS7A01G104500 chr5B 94.643 168 9 0 501 668 75684748 75684581 6.350000e-66 261.0
10 TraesCS7A01G104500 chr5B 83.962 106 6 7 361 466 75684843 75684749 8.820000e-15 91.6
11 TraesCS7A01G104500 chr3B 91.046 1664 87 21 675 2317 110277519 110275897 0.000000e+00 2191.0
12 TraesCS7A01G104500 chr3B 92.899 859 44 10 1464 2317 281743895 281743049 0.000000e+00 1232.0
13 TraesCS7A01G104500 chr3B 94.643 168 9 0 501 668 110277732 110277565 6.350000e-66 261.0
14 TraesCS7A01G104500 chr7D 94.524 1333 58 9 990 2317 32371233 32372555 0.000000e+00 2043.0
15 TraesCS7A01G104500 chr7D 83.176 529 54 20 990 1483 160630067 160630595 3.510000e-123 451.0
16 TraesCS7A01G104500 chr7D 90.938 320 11 5 671 990 32370889 32371190 4.610000e-112 414.0
17 TraesCS7A01G104500 chr7D 94.492 236 13 0 356 591 32349295 32349530 4.700000e-97 364.0
18 TraesCS7A01G104500 chr7D 86.164 318 28 3 671 988 160629721 160630022 1.720000e-86 329.0
19 TraesCS7A01G104500 chr7D 89.535 258 26 1 107 364 32348852 32349108 2.220000e-85 326.0
20 TraesCS7A01G104500 chr7D 94.366 71 4 0 593 663 32370779 32370849 2.430000e-20 110.0
21 TraesCS7A01G104500 chr1B 93.154 1081 63 8 990 2066 41747649 41748722 0.000000e+00 1576.0
22 TraesCS7A01G104500 chr1B 92.332 313 22 1 356 668 41746955 41747265 5.870000e-121 444.0
23 TraesCS7A01G104500 chr1B 89.720 321 14 6 671 991 136919622 136919923 2.160000e-105 392.0
24 TraesCS7A01G104500 chr1B 88.679 318 16 8 674 991 41747310 41747607 1.010000e-98 370.0
25 TraesCS7A01G104500 chr1B 88.519 270 23 5 98 365 41746504 41746767 1.030000e-83 320.0
26 TraesCS7A01G104500 chr1B 90.830 229 19 1 356 584 136918957 136919183 2.890000e-79 305.0
27 TraesCS7A01G104500 chr1B 91.398 93 6 1 578 668 136919488 136919580 2.420000e-25 126.0
28 TraesCS7A01G104500 chr2B 92.144 1082 61 11 990 2066 547410957 547412019 0.000000e+00 1506.0
29 TraesCS7A01G104500 chr2B 89.097 321 16 6 671 991 547410614 547410915 4.670000e-102 381.0
30 TraesCS7A01G104500 chr2B 90.037 271 26 1 396 666 547410301 547410570 1.320000e-92 350.0
31 TraesCS7A01G104500 chr2B 85.161 155 19 3 2166 2317 549452 549299 3.080000e-34 156.0
32 TraesCS7A01G104500 chr4B 85.404 507 61 12 990 1485 423402825 423402321 4.410000e-142 514.0
33 TraesCS7A01G104500 chr3A 85.323 511 56 11 993 1485 745811844 745811335 5.710000e-141 510.0
34 TraesCS7A01G104500 chr6A 84.843 508 61 8 993 1485 412853465 412852959 4.450000e-137 497.0
35 TraesCS7A01G104500 chr6A 84.810 158 20 3 2163 2317 584756685 584756841 3.080000e-34 156.0
36 TraesCS7A01G104500 chr7B 82.543 527 59 13 990 1483 121884812 121885338 1.270000e-117 433.0
37 TraesCS7A01G104500 chr7B 85.358 321 31 3 671 991 121884466 121884770 3.720000e-83 318.0
38 TraesCS7A01G104500 chr7B 80.636 346 47 9 356 682 121884094 121884438 1.370000e-62 250.0
39 TraesCS7A01G104500 chr6B 84.783 414 35 15 1816 2203 197245561 197245150 7.760000e-105 390.0
40 TraesCS7A01G104500 chr6B 89.723 253 24 2 993 1244 197246836 197246585 2.870000e-84 322.0
41 TraesCS7A01G104500 chr2D 84.177 158 21 3 2163 2317 148872945 148873101 1.430000e-32 150.0


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 TraesCS7A01G104500 chr7A 63574192 63576508 2316 False 4279.000000 4279 100.000000 1 2317 1 chr7A.!!$F1 2316
1 TraesCS7A01G104500 chr7A 42988135 42989693 1558 True 2270.000000 2270 93.004000 746 2317 1 chr7A.!!$R1 1571
2 TraesCS7A01G104500 chr7A 180638398 180640309 1911 True 1460.500000 2409 96.246500 356 2317 2 chr7A.!!$R2 1961
3 TraesCS7A01G104500 chr5A 592641040 592642970 1930 False 868.200000 2252 90.104000 361 2317 3 chr5A.!!$F1 1956
4 TraesCS7A01G104500 chr5B 75682913 75684843 1930 True 855.200000 2213 89.963667 361 2317 3 chr5B.!!$R1 1956
5 TraesCS7A01G104500 chr3B 281743049 281743895 846 True 1232.000000 1232 92.899000 1464 2317 1 chr3B.!!$R1 853
6 TraesCS7A01G104500 chr3B 110275897 110277732 1835 True 1226.000000 2191 92.844500 501 2317 2 chr3B.!!$R2 1816
7 TraesCS7A01G104500 chr7D 32370779 32372555 1776 False 855.666667 2043 93.276000 593 2317 3 chr7D.!!$F2 1724
8 TraesCS7A01G104500 chr7D 160629721 160630595 874 False 390.000000 451 84.670000 671 1483 2 chr7D.!!$F3 812
9 TraesCS7A01G104500 chr7D 32348852 32349530 678 False 345.000000 364 92.013500 107 591 2 chr7D.!!$F1 484
10 TraesCS7A01G104500 chr1B 41746504 41748722 2218 False 677.500000 1576 90.671000 98 2066 4 chr1B.!!$F1 1968
11 TraesCS7A01G104500 chr1B 136918957 136919923 966 False 274.333333 392 90.649333 356 991 3 chr1B.!!$F2 635
12 TraesCS7A01G104500 chr2B 547410301 547412019 1718 False 745.666667 1506 90.426000 396 2066 3 chr2B.!!$F1 1670
13 TraesCS7A01G104500 chr4B 423402321 423402825 504 True 514.000000 514 85.404000 990 1485 1 chr4B.!!$R1 495
14 TraesCS7A01G104500 chr3A 745811335 745811844 509 True 510.000000 510 85.323000 993 1485 1 chr3A.!!$R1 492
15 TraesCS7A01G104500 chr6A 412852959 412853465 506 True 497.000000 497 84.843000 993 1485 1 chr6A.!!$R1 492
16 TraesCS7A01G104500 chr7B 121884094 121885338 1244 False 333.666667 433 82.845667 356 1483 3 chr7B.!!$F1 1127
17 TraesCS7A01G104500 chr6B 197245150 197246836 1686 True 356.000000 390 87.253000 993 2203 2 chr6B.!!$R1 1210

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
100 101 0.178912 ACCGTACCCCACTCCTTTCT 60.179 55.0 0.0 0.0 0.0 2.52 F
596 1130 0.239082 GCCCTTACCGTGTTTTTCCG 59.761 55.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1293 2304 2.437281 ACACATCCAATCTAGCTCCCAG 59.563 50.000 0.00 0.0 0.0 4.45 R
2227 3439 2.301870 AGAGAAATAGTGGGTTGCGACA 59.698 45.455 6.39 0.0 0.0 4.35 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
22 23 5.405935 ACCGGTAAAATTACTTAGTCGGT 57.594 39.130 4.49 13.98 37.27 4.69
23 24 5.410924 ACCGGTAAAATTACTTAGTCGGTC 58.589 41.667 4.49 0.00 37.40 4.79
24 25 4.500477 CCGGTAAAATTACTTAGTCGGTCG 59.500 45.833 0.00 0.00 34.16 4.79
25 26 4.027377 CGGTAAAATTACTTAGTCGGTCGC 60.027 45.833 3.55 0.00 34.16 5.19
26 27 4.268644 GGTAAAATTACTTAGTCGGTCGCC 59.731 45.833 3.55 0.00 34.16 5.54
27 28 2.591571 AATTACTTAGTCGGTCGCCC 57.408 50.000 0.00 0.00 0.00 6.13
28 29 1.477553 ATTACTTAGTCGGTCGCCCA 58.522 50.000 0.00 0.00 0.00 5.36
29 30 0.813184 TTACTTAGTCGGTCGCCCAG 59.187 55.000 0.00 0.00 0.00 4.45
30 31 1.033746 TACTTAGTCGGTCGCCCAGG 61.034 60.000 0.00 0.00 0.00 4.45
31 32 3.072468 TTAGTCGGTCGCCCAGGG 61.072 66.667 0.00 0.00 0.00 4.45
57 58 2.631428 CGTGGGCGTTCTGTTGTG 59.369 61.111 0.00 0.00 0.00 3.33
58 59 2.892334 CGTGGGCGTTCTGTTGTGG 61.892 63.158 0.00 0.00 0.00 4.17
59 60 2.904866 TGGGCGTTCTGTTGTGGC 60.905 61.111 0.00 0.00 0.00 5.01
60 61 3.670377 GGGCGTTCTGTTGTGGCC 61.670 66.667 0.00 0.00 43.01 5.36
61 62 2.594592 GGCGTTCTGTTGTGGCCT 60.595 61.111 3.32 0.00 40.59 5.19
62 63 2.617274 GGCGTTCTGTTGTGGCCTC 61.617 63.158 3.32 0.00 40.59 4.70
63 64 2.954753 GCGTTCTGTTGTGGCCTCG 61.955 63.158 3.32 0.00 0.00 4.63
64 65 1.300620 CGTTCTGTTGTGGCCTCGA 60.301 57.895 3.32 0.00 0.00 4.04
65 66 0.670546 CGTTCTGTTGTGGCCTCGAT 60.671 55.000 3.32 0.00 0.00 3.59
66 67 1.079503 GTTCTGTTGTGGCCTCGATC 58.920 55.000 3.32 0.00 0.00 3.69
67 68 0.976641 TTCTGTTGTGGCCTCGATCT 59.023 50.000 3.32 0.00 0.00 2.75
68 69 1.847328 TCTGTTGTGGCCTCGATCTA 58.153 50.000 3.32 0.00 0.00 1.98
69 70 2.388735 TCTGTTGTGGCCTCGATCTAT 58.611 47.619 3.32 0.00 0.00 1.98
70 71 2.362397 TCTGTTGTGGCCTCGATCTATC 59.638 50.000 3.32 0.00 0.00 2.08
71 72 1.412710 TGTTGTGGCCTCGATCTATCC 59.587 52.381 3.32 0.00 0.00 2.59
72 73 1.689273 GTTGTGGCCTCGATCTATCCT 59.311 52.381 3.32 0.00 0.00 3.24
73 74 2.891580 GTTGTGGCCTCGATCTATCCTA 59.108 50.000 3.32 0.00 0.00 2.94
74 75 3.238788 TGTGGCCTCGATCTATCCTAA 57.761 47.619 3.32 0.00 0.00 2.69
75 76 3.572642 TGTGGCCTCGATCTATCCTAAA 58.427 45.455 3.32 0.00 0.00 1.85
76 77 3.964688 TGTGGCCTCGATCTATCCTAAAA 59.035 43.478 3.32 0.00 0.00 1.52
77 78 4.407621 TGTGGCCTCGATCTATCCTAAAAA 59.592 41.667 3.32 0.00 0.00 1.94
78 79 4.991687 GTGGCCTCGATCTATCCTAAAAAG 59.008 45.833 3.32 0.00 0.00 2.27
79 80 3.997681 GGCCTCGATCTATCCTAAAAAGC 59.002 47.826 0.00 0.00 0.00 3.51
80 81 4.503296 GGCCTCGATCTATCCTAAAAAGCA 60.503 45.833 0.00 0.00 0.00 3.91
81 82 5.057149 GCCTCGATCTATCCTAAAAAGCAA 58.943 41.667 0.00 0.00 0.00 3.91
82 83 5.050023 GCCTCGATCTATCCTAAAAAGCAAC 60.050 44.000 0.00 0.00 0.00 4.17
83 84 5.467063 CCTCGATCTATCCTAAAAAGCAACC 59.533 44.000 0.00 0.00 0.00 3.77
84 85 5.047847 TCGATCTATCCTAAAAAGCAACCG 58.952 41.667 0.00 0.00 0.00 4.44
85 86 4.809426 CGATCTATCCTAAAAAGCAACCGT 59.191 41.667 0.00 0.00 0.00 4.83
86 87 5.981315 CGATCTATCCTAAAAAGCAACCGTA 59.019 40.000 0.00 0.00 0.00 4.02
87 88 6.074463 CGATCTATCCTAAAAAGCAACCGTAC 60.074 42.308 0.00 0.00 0.00 3.67
88 89 5.422145 TCTATCCTAAAAAGCAACCGTACC 58.578 41.667 0.00 0.00 0.00 3.34
89 90 2.781923 TCCTAAAAAGCAACCGTACCC 58.218 47.619 0.00 0.00 0.00 3.69
90 91 1.814394 CCTAAAAAGCAACCGTACCCC 59.186 52.381 0.00 0.00 0.00 4.95
91 92 2.506444 CTAAAAAGCAACCGTACCCCA 58.494 47.619 0.00 0.00 0.00 4.96
92 93 1.034356 AAAAAGCAACCGTACCCCAC 58.966 50.000 0.00 0.00 0.00 4.61
93 94 0.184211 AAAAGCAACCGTACCCCACT 59.816 50.000 0.00 0.00 0.00 4.00
94 95 0.250597 AAAGCAACCGTACCCCACTC 60.251 55.000 0.00 0.00 0.00 3.51
95 96 2.046604 GCAACCGTACCCCACTCC 60.047 66.667 0.00 0.00 0.00 3.85
96 97 2.590114 GCAACCGTACCCCACTCCT 61.590 63.158 0.00 0.00 0.00 3.69
100 101 0.178912 ACCGTACCCCACTCCTTTCT 60.179 55.000 0.00 0.00 0.00 2.52
103 104 2.454538 CGTACCCCACTCCTTTCTACT 58.545 52.381 0.00 0.00 0.00 2.57
104 105 3.624777 CGTACCCCACTCCTTTCTACTA 58.375 50.000 0.00 0.00 0.00 1.82
105 106 3.631227 CGTACCCCACTCCTTTCTACTAG 59.369 52.174 0.00 0.00 0.00 2.57
112 113 6.411086 CCCCACTCCTTTCTACTAGTCTCTAT 60.411 46.154 0.00 0.00 0.00 1.98
142 144 3.558829 GGTGATCTGTAGTCGTCGTGATA 59.441 47.826 0.00 0.00 0.00 2.15
158 160 1.006758 TGATAGTTCGACTCCCCACCT 59.993 52.381 0.00 0.00 0.00 4.00
203 205 3.710722 AGGAGCAGCCCACCTTCG 61.711 66.667 3.08 0.00 37.37 3.79
206 208 3.003173 AGCAGCCCACCTTCGCTA 61.003 61.111 0.00 0.00 32.92 4.26
225 227 2.934083 GAAGCAAGCCTTCCTTCGT 58.066 52.632 0.00 0.00 43.39 3.85
237 239 4.320935 GCCTTCCTTCGTGCAATTAAAAGA 60.321 41.667 0.00 0.00 0.00 2.52
238 240 5.768317 CCTTCCTTCGTGCAATTAAAAGAA 58.232 37.500 0.00 0.00 0.00 2.52
239 241 5.858581 CCTTCCTTCGTGCAATTAAAAGAAG 59.141 40.000 0.00 7.72 35.99 2.85
240 242 6.293955 CCTTCCTTCGTGCAATTAAAAGAAGA 60.294 38.462 13.35 2.41 37.78 2.87
291 296 2.594131 CCACGTCCCATGTATCCTCTA 58.406 52.381 0.00 0.00 0.00 2.43
293 298 3.223435 CACGTCCCATGTATCCTCTACT 58.777 50.000 0.00 0.00 0.00 2.57
299 304 6.515200 CGTCCCATGTATCCTCTACTAGTTTG 60.515 46.154 0.00 0.00 0.00 2.93
307 312 0.899720 TCTACTAGTTTGCCCCACCG 59.100 55.000 0.00 0.00 0.00 4.94
506 728 3.655810 CTGCTCGCCTCGGCTTTCT 62.656 63.158 6.35 0.00 39.32 2.52
596 1130 0.239082 GCCCTTACCGTGTTTTTCCG 59.761 55.000 0.00 0.00 0.00 4.30
668 1204 3.827898 CGTCTCGGTGCTCTCCCC 61.828 72.222 0.00 0.00 0.00 4.81
669 1205 3.827898 GTCTCGGTGCTCTCCCCG 61.828 72.222 0.00 0.00 45.55 5.73
722 1297 0.302288 GTCGACGTCATCTCGAGGAG 59.698 60.000 17.16 5.62 40.72 3.69
813 1388 1.028330 TCGTCACGGCCTACTACCTG 61.028 60.000 0.00 0.00 0.00 4.00
814 1389 1.310933 CGTCACGGCCTACTACCTGT 61.311 60.000 0.00 0.00 0.00 4.00
815 1390 0.455005 GTCACGGCCTACTACCTGTC 59.545 60.000 0.00 0.00 0.00 3.51
816 1391 0.330604 TCACGGCCTACTACCTGTCT 59.669 55.000 0.00 0.00 0.00 3.41
817 1392 1.561076 TCACGGCCTACTACCTGTCTA 59.439 52.381 0.00 0.00 0.00 2.59
818 1393 1.674962 CACGGCCTACTACCTGTCTAC 59.325 57.143 0.00 0.00 0.00 2.59
819 1394 1.316651 CGGCCTACTACCTGTCTACC 58.683 60.000 0.00 0.00 0.00 3.18
820 1395 1.133853 CGGCCTACTACCTGTCTACCT 60.134 57.143 0.00 0.00 0.00 3.08
839 1414 2.743928 GTCTCCGGCAGCAACCAG 60.744 66.667 0.00 0.00 0.00 4.00
840 1415 4.704833 TCTCCGGCAGCAACCAGC 62.705 66.667 0.00 0.00 46.19 4.85
1024 1654 3.129502 CGTGGTCCGCCGTCTCTA 61.130 66.667 0.00 0.00 37.67 2.43
1293 2304 4.455917 TTCACCGTTGTTTCGATTGTAC 57.544 40.909 0.00 0.00 0.00 2.90
1603 2663 4.314522 TTGGGGTCATCATGTGTATTGT 57.685 40.909 0.00 0.00 0.00 2.71
1793 2856 4.700213 CCCGTTGTGAATTAGGTCAATCTT 59.300 41.667 0.00 0.00 0.00 2.40
2080 3283 0.597637 CATACTAGGGCGTTGGAGCG 60.598 60.000 0.00 0.00 38.18 5.03
2218 3430 6.307776 TGGTGATTGTATGTCCCTTTGTTTA 58.692 36.000 0.00 0.00 0.00 2.01
2227 3439 9.303116 TGTATGTCCCTTTGTTTATATGTTGTT 57.697 29.630 0.00 0.00 0.00 2.83
2249 3461 3.244422 TGTCGCAACCCACTATTTCTCTT 60.244 43.478 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.405935 ACCGACTAAGTAATTTTACCGGT 57.594 39.130 13.98 13.98 39.85 5.28
1 2 4.500477 CGACCGACTAAGTAATTTTACCGG 59.500 45.833 0.00 0.00 38.53 5.28
2 3 4.027377 GCGACCGACTAAGTAATTTTACCG 60.027 45.833 0.00 0.00 34.19 4.02
3 4 4.268644 GGCGACCGACTAAGTAATTTTACC 59.731 45.833 0.00 0.00 34.19 2.85
4 5 4.268644 GGGCGACCGACTAAGTAATTTTAC 59.731 45.833 0.00 0.00 43.64 2.01
5 6 4.432712 GGGCGACCGACTAAGTAATTTTA 58.567 43.478 0.00 0.00 43.64 1.52
6 7 3.264947 GGGCGACCGACTAAGTAATTTT 58.735 45.455 0.00 0.00 43.64 1.82
7 8 2.897436 GGGCGACCGACTAAGTAATTT 58.103 47.619 0.00 0.00 43.64 1.82
8 9 2.591571 GGGCGACCGACTAAGTAATT 57.408 50.000 0.00 0.00 43.64 1.40
41 42 3.030652 CCACAACAGAACGCCCAC 58.969 61.111 0.00 0.00 0.00 4.61
42 43 2.904866 GCCACAACAGAACGCCCA 60.905 61.111 0.00 0.00 0.00 5.36
43 44 3.670377 GGCCACAACAGAACGCCC 61.670 66.667 0.00 0.00 33.30 6.13
44 45 2.594592 AGGCCACAACAGAACGCC 60.595 61.111 5.01 0.00 40.03 5.68
45 46 2.946762 GAGGCCACAACAGAACGC 59.053 61.111 5.01 0.00 0.00 4.84
46 47 0.670546 ATCGAGGCCACAACAGAACG 60.671 55.000 5.01 0.00 0.00 3.95
47 48 1.079503 GATCGAGGCCACAACAGAAC 58.920 55.000 5.01 0.00 0.00 3.01
48 49 0.976641 AGATCGAGGCCACAACAGAA 59.023 50.000 5.01 0.00 0.00 3.02
49 50 1.847328 TAGATCGAGGCCACAACAGA 58.153 50.000 5.01 0.00 0.00 3.41
50 51 2.546795 GGATAGATCGAGGCCACAACAG 60.547 54.545 5.01 0.00 0.00 3.16
51 52 1.412710 GGATAGATCGAGGCCACAACA 59.587 52.381 5.01 0.00 0.00 3.33
52 53 1.689273 AGGATAGATCGAGGCCACAAC 59.311 52.381 5.01 0.00 0.00 3.32
53 54 2.088104 AGGATAGATCGAGGCCACAA 57.912 50.000 5.01 0.00 0.00 3.33
54 55 2.971901 TAGGATAGATCGAGGCCACA 57.028 50.000 5.01 0.00 0.00 4.17
55 56 4.602340 TTTTAGGATAGATCGAGGCCAC 57.398 45.455 5.01 0.00 0.00 5.01
56 57 4.503296 GCTTTTTAGGATAGATCGAGGCCA 60.503 45.833 5.01 0.00 0.00 5.36
57 58 3.997681 GCTTTTTAGGATAGATCGAGGCC 59.002 47.826 0.00 0.00 0.00 5.19
58 59 4.632153 TGCTTTTTAGGATAGATCGAGGC 58.368 43.478 0.00 0.00 0.00 4.70
59 60 5.467063 GGTTGCTTTTTAGGATAGATCGAGG 59.533 44.000 0.00 0.00 0.00 4.63
60 61 5.175856 CGGTTGCTTTTTAGGATAGATCGAG 59.824 44.000 0.00 0.00 0.00 4.04
61 62 5.047847 CGGTTGCTTTTTAGGATAGATCGA 58.952 41.667 0.00 0.00 0.00 3.59
62 63 4.809426 ACGGTTGCTTTTTAGGATAGATCG 59.191 41.667 0.00 0.00 0.00 3.69
63 64 6.202379 GGTACGGTTGCTTTTTAGGATAGATC 59.798 42.308 0.00 0.00 0.00 2.75
64 65 6.053650 GGTACGGTTGCTTTTTAGGATAGAT 58.946 40.000 0.00 0.00 0.00 1.98
65 66 5.422145 GGTACGGTTGCTTTTTAGGATAGA 58.578 41.667 0.00 0.00 0.00 1.98
66 67 4.573607 GGGTACGGTTGCTTTTTAGGATAG 59.426 45.833 0.00 0.00 0.00 2.08
67 68 4.516323 GGGTACGGTTGCTTTTTAGGATA 58.484 43.478 0.00 0.00 0.00 2.59
68 69 3.349927 GGGTACGGTTGCTTTTTAGGAT 58.650 45.455 0.00 0.00 0.00 3.24
69 70 2.552809 GGGGTACGGTTGCTTTTTAGGA 60.553 50.000 0.00 0.00 0.00 2.94
70 71 1.814394 GGGGTACGGTTGCTTTTTAGG 59.186 52.381 0.00 0.00 0.00 2.69
71 72 2.227149 GTGGGGTACGGTTGCTTTTTAG 59.773 50.000 0.00 0.00 0.00 1.85
72 73 2.158638 AGTGGGGTACGGTTGCTTTTTA 60.159 45.455 0.00 0.00 0.00 1.52
73 74 1.034356 GTGGGGTACGGTTGCTTTTT 58.966 50.000 0.00 0.00 0.00 1.94
74 75 0.184211 AGTGGGGTACGGTTGCTTTT 59.816 50.000 0.00 0.00 0.00 2.27
75 76 0.250597 GAGTGGGGTACGGTTGCTTT 60.251 55.000 0.00 0.00 0.00 3.51
76 77 1.373812 GAGTGGGGTACGGTTGCTT 59.626 57.895 0.00 0.00 0.00 3.91
77 78 2.590114 GGAGTGGGGTACGGTTGCT 61.590 63.158 0.00 0.00 0.00 3.91
78 79 2.046604 GGAGTGGGGTACGGTTGC 60.047 66.667 0.00 0.00 0.00 4.17
79 80 0.399075 AAAGGAGTGGGGTACGGTTG 59.601 55.000 0.00 0.00 0.00 3.77
80 81 0.689055 GAAAGGAGTGGGGTACGGTT 59.311 55.000 0.00 0.00 0.00 4.44
81 82 0.178912 AGAAAGGAGTGGGGTACGGT 60.179 55.000 0.00 0.00 0.00 4.83
82 83 1.479730 GTAGAAAGGAGTGGGGTACGG 59.520 57.143 0.00 0.00 0.00 4.02
83 84 2.454538 AGTAGAAAGGAGTGGGGTACG 58.545 52.381 0.00 0.00 0.00 3.67
84 85 4.608269 ACTAGTAGAAAGGAGTGGGGTAC 58.392 47.826 3.59 0.00 0.00 3.34
85 86 4.543337 AGACTAGTAGAAAGGAGTGGGGTA 59.457 45.833 3.59 0.00 0.00 3.69
86 87 3.337301 AGACTAGTAGAAAGGAGTGGGGT 59.663 47.826 3.59 0.00 0.00 4.95
87 88 3.955551 GAGACTAGTAGAAAGGAGTGGGG 59.044 52.174 3.59 0.00 0.00 4.96
88 89 4.862371 AGAGACTAGTAGAAAGGAGTGGG 58.138 47.826 3.59 0.00 0.00 4.61
89 90 9.802039 ATAATAGAGACTAGTAGAAAGGAGTGG 57.198 37.037 3.59 0.00 0.00 4.00
112 113 7.148188 ACGACGACTACAGATCACCTTTAATAA 60.148 37.037 0.00 0.00 0.00 1.40
122 123 4.439968 ACTATCACGACGACTACAGATCA 58.560 43.478 0.00 0.00 0.00 2.92
129 131 3.914555 GTCGAACTATCACGACGACTA 57.085 47.619 0.00 0.00 46.39 2.59
142 144 0.113776 TACAGGTGGGGAGTCGAACT 59.886 55.000 0.00 0.00 0.00 3.01
199 201 1.663135 GAAGGCTTGCTTCTAGCGAAG 59.337 52.381 3.46 0.00 46.26 3.79
203 205 2.121291 AAGGAAGGCTTGCTTCTAGC 57.879 50.000 25.88 0.00 36.54 3.42
257 262 2.576832 CGTGGGACGGTAGTGGGTT 61.577 63.158 0.00 0.00 38.08 4.11
291 296 2.033602 GCGGTGGGGCAAACTAGT 59.966 61.111 0.00 0.00 0.00 2.57
293 298 2.349755 GAGCGGTGGGGCAAACTA 59.650 61.111 0.00 0.00 34.64 2.24
307 312 1.005156 GGATGGATCAGGAGCGAGC 60.005 63.158 0.00 0.00 0.00 5.03
591 1125 2.674033 TCCTCGTCGAGCCGGAAA 60.674 61.111 17.02 0.00 0.00 3.13
1278 2287 3.120304 GCTCCCAGTACAATCGAAACAAC 60.120 47.826 0.00 0.00 0.00 3.32
1293 2304 2.437281 ACACATCCAATCTAGCTCCCAG 59.563 50.000 0.00 0.00 0.00 4.45
1423 2483 9.878599 AACACGAAATAACTTTCAAACTATGAG 57.121 29.630 0.00 0.00 40.72 2.90
1603 2663 3.084039 GGACTGAACATGATTCAAGCCA 58.916 45.455 0.00 0.00 0.00 4.75
2175 3387 4.656112 CACCAACTCCCCTTGTATATCTCT 59.344 45.833 0.00 0.00 0.00 3.10
2227 3439 2.301870 AGAGAAATAGTGGGTTGCGACA 59.698 45.455 6.39 0.00 0.00 4.35
2249 3461 6.999871 AGATATATGAAATGGTGCATGTGTCA 59.000 34.615 0.00 0.00 30.18 3.58


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

AutoCloner maintained by Alex Coulton.