Multiple sequence alignment - TraesCS2D01G123900

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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 TraesCS2D01G123900 chr2D 100.000 3152 0 0 1 3152 72596085 72592934 0.000000e+00 5821.0
1 TraesCS2D01G123900 chr2D 86.565 1243 75 41 431 1653 72772498 72771328 0.000000e+00 1286.0
2 TraesCS2D01G123900 chr2D 87.296 1102 94 21 1101 2198 23168476 23167417 0.000000e+00 1218.0
3 TraesCS2D01G123900 chr2D 99.662 591 2 0 528 1118 593841049 593841639 0.000000e+00 1081.0
4 TraesCS2D01G123900 chr2D 90.564 763 66 4 1346 2102 72998927 72999689 0.000000e+00 1005.0
5 TraesCS2D01G123900 chr2D 81.404 769 107 25 2379 3114 72770526 72769761 2.090000e-166 595.0
6 TraesCS2D01G123900 chr2D 79.469 716 84 34 2428 3115 72905249 72905929 1.720000e-122 449.0
7 TraesCS2D01G123900 chr2D 92.237 219 10 3 211 429 72772550 72772339 1.420000e-78 303.0
8 TraesCS2D01G123900 chr2D 88.172 93 10 1 111 203 72772778 72772687 3.320000e-20 110.0
9 TraesCS2D01G123900 chrUn 91.137 2753 162 41 428 3152 287774481 287771783 0.000000e+00 3657.0
10 TraesCS2D01G123900 chrUn 91.137 2753 162 41 428 3152 297963606 297960908 0.000000e+00 3657.0
11 TraesCS2D01G123900 chr2B 91.052 1777 106 25 431 2177 110044882 110043129 0.000000e+00 2351.0
12 TraesCS2D01G123900 chr2B 92.812 1113 47 5 1019 2117 109963779 109964872 0.000000e+00 1581.0
13 TraesCS2D01G123900 chr2B 90.347 777 69 4 1346 2116 110370935 110371711 0.000000e+00 1014.0
14 TraesCS2D01G123900 chr2B 90.090 777 71 4 1346 2116 110406395 110407171 0.000000e+00 1003.0
15 TraesCS2D01G123900 chr2B 85.326 552 45 19 428 956 109955752 109956290 3.580000e-149 538.0
16 TraesCS2D01G123900 chr2B 94.096 271 12 2 159 429 110044984 110044718 2.930000e-110 409.0
17 TraesCS2D01G123900 chr2B 85.915 213 22 4 211 420 109955703 109955910 1.470000e-53 220.0
18 TraesCS2D01G123900 chr2B 94.286 70 4 0 952 1021 109961450 109961519 1.200000e-19 108.0
19 TraesCS2D01G123900 chr2A 89.525 1852 121 41 464 2292 71436448 71434647 0.000000e+00 2278.0
20 TraesCS2D01G123900 chr2A 90.170 763 68 5 1346 2102 71587239 71588000 0.000000e+00 987.0
21 TraesCS2D01G123900 chr2A 87.215 219 16 8 211 429 71436528 71436322 4.060000e-59 239.0
22 TraesCS2D01G123900 chr6D 89.535 86 8 1 111 195 161977767 161977852 1.200000e-19 108.0
23 TraesCS2D01G123900 chr3D 83.621 116 18 1 2428 2543 609150033 609149919 1.200000e-19 108.0
24 TraesCS2D01G123900 chr6A 88.372 86 6 3 111 195 221350791 221350873 2.000000e-17 100.0
25 TraesCS2D01G123900 chr6B 87.209 86 7 3 111 195 300718150 300718068 9.310000e-16 95.3
26 TraesCS2D01G123900 chr6B 90.909 66 4 2 48 112 705385422 705385358 1.560000e-13 87.9


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 TraesCS2D01G123900 chr2D 72592934 72596085 3151 True 5821.0 5821 100.0000 1 3152 1 chr2D.!!$R2 3151
1 TraesCS2D01G123900 chr2D 23167417 23168476 1059 True 1218.0 1218 87.2960 1101 2198 1 chr2D.!!$R1 1097
2 TraesCS2D01G123900 chr2D 593841049 593841639 590 False 1081.0 1081 99.6620 528 1118 1 chr2D.!!$F3 590
3 TraesCS2D01G123900 chr2D 72998927 72999689 762 False 1005.0 1005 90.5640 1346 2102 1 chr2D.!!$F2 756
4 TraesCS2D01G123900 chr2D 72769761 72772778 3017 True 573.5 1286 87.0945 111 3114 4 chr2D.!!$R3 3003
5 TraesCS2D01G123900 chr2D 72905249 72905929 680 False 449.0 449 79.4690 2428 3115 1 chr2D.!!$F1 687
6 TraesCS2D01G123900 chrUn 287771783 287774481 2698 True 3657.0 3657 91.1370 428 3152 1 chrUn.!!$R1 2724
7 TraesCS2D01G123900 chrUn 297960908 297963606 2698 True 3657.0 3657 91.1370 428 3152 1 chrUn.!!$R2 2724
8 TraesCS2D01G123900 chr2B 110043129 110044984 1855 True 1380.0 2351 92.5740 159 2177 2 chr2B.!!$R1 2018
9 TraesCS2D01G123900 chr2B 110370935 110371711 776 False 1014.0 1014 90.3470 1346 2116 1 chr2B.!!$F1 770
10 TraesCS2D01G123900 chr2B 110406395 110407171 776 False 1003.0 1003 90.0900 1346 2116 1 chr2B.!!$F2 770
11 TraesCS2D01G123900 chr2B 109961450 109964872 3422 False 844.5 1581 93.5490 952 2117 2 chr2B.!!$F4 1165
12 TraesCS2D01G123900 chr2B 109955703 109956290 587 False 379.0 538 85.6205 211 956 2 chr2B.!!$F3 745
13 TraesCS2D01G123900 chr2A 71434647 71436528 1881 True 1258.5 2278 88.3700 211 2292 2 chr2A.!!$R1 2081
14 TraesCS2D01G123900 chr2A 71587239 71588000 761 False 987.0 987 90.1700 1346 2102 1 chr2A.!!$F1 756

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
54 55 0.028902 AGCGAGCAAACCAACGAAAC 59.971 50.0 0.0 0.0 0.0 2.78 F
97 98 0.108615 CACGATCGCAAACTCCTCCT 60.109 55.0 16.6 0.0 0.0 3.69 F
98 99 0.608640 ACGATCGCAAACTCCTCCTT 59.391 50.0 16.6 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1269 3746 0.461339 GACGCCACGACATAACCCAT 60.461 55.000 0.0 0.0 0.0 4.0 R
2144 4913 0.257905 ATGCCATGCCTGTCACTCAT 59.742 50.000 0.0 0.0 0.0 2.9 R
2251 5026 7.282224 CCTAAATCAGTCGGTTGAATCCATTAA 59.718 37.037 0.0 0.0 0.0 1.4 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 2.750350 AACTTGTGGGGAGAGGCG 59.250 61.111 0.00 0.00 0.00 5.52
18 19 1.841556 AACTTGTGGGGAGAGGCGA 60.842 57.895 0.00 0.00 0.00 5.54
19 20 1.831652 AACTTGTGGGGAGAGGCGAG 61.832 60.000 0.00 0.00 0.00 5.03
20 21 3.003173 TTGTGGGGAGAGGCGAGG 61.003 66.667 0.00 0.00 0.00 4.63
26 27 4.144727 GGAGAGGCGAGGGGAGGA 62.145 72.222 0.00 0.00 0.00 3.71
27 28 2.520741 GAGAGGCGAGGGGAGGAG 60.521 72.222 0.00 0.00 0.00 3.69
28 29 4.150454 AGAGGCGAGGGGAGGAGG 62.150 72.222 0.00 0.00 0.00 4.30
32 33 4.798682 GCGAGGGGAGGAGGGGAA 62.799 72.222 0.00 0.00 0.00 3.97
33 34 2.444895 CGAGGGGAGGAGGGGAAG 60.445 72.222 0.00 0.00 0.00 3.46
34 35 3.010226 CGAGGGGAGGAGGGGAAGA 62.010 68.421 0.00 0.00 0.00 2.87
35 36 1.396594 GAGGGGAGGAGGGGAAGAA 59.603 63.158 0.00 0.00 0.00 2.52
36 37 0.692756 GAGGGGAGGAGGGGAAGAAG 60.693 65.000 0.00 0.00 0.00 2.85
37 38 2.379459 GGGGAGGAGGGGAAGAAGC 61.379 68.421 0.00 0.00 0.00 3.86
38 39 2.736826 GGGAGGAGGGGAAGAAGCG 61.737 68.421 0.00 0.00 0.00 4.68
39 40 1.686110 GGAGGAGGGGAAGAAGCGA 60.686 63.158 0.00 0.00 0.00 4.93
40 41 1.681486 GGAGGAGGGGAAGAAGCGAG 61.681 65.000 0.00 0.00 0.00 5.03
41 42 2.188207 GGAGGGGAAGAAGCGAGC 59.812 66.667 0.00 0.00 0.00 5.03
42 43 2.660064 GGAGGGGAAGAAGCGAGCA 61.660 63.158 0.00 0.00 0.00 4.26
43 44 1.296715 GAGGGGAAGAAGCGAGCAA 59.703 57.895 0.00 0.00 0.00 3.91
44 45 0.321653 GAGGGGAAGAAGCGAGCAAA 60.322 55.000 0.00 0.00 0.00 3.68
45 46 0.606673 AGGGGAAGAAGCGAGCAAAC 60.607 55.000 0.00 0.00 0.00 2.93
46 47 1.587043 GGGGAAGAAGCGAGCAAACC 61.587 60.000 0.00 0.00 0.00 3.27
47 48 0.889186 GGGAAGAAGCGAGCAAACCA 60.889 55.000 0.00 0.00 0.00 3.67
48 49 0.951558 GGAAGAAGCGAGCAAACCAA 59.048 50.000 0.00 0.00 0.00 3.67
49 50 1.335051 GGAAGAAGCGAGCAAACCAAC 60.335 52.381 0.00 0.00 0.00 3.77
50 51 0.307760 AAGAAGCGAGCAAACCAACG 59.692 50.000 0.00 0.00 0.00 4.10
51 52 0.531974 AGAAGCGAGCAAACCAACGA 60.532 50.000 0.00 0.00 0.00 3.85
52 53 0.306533 GAAGCGAGCAAACCAACGAA 59.693 50.000 0.00 0.00 0.00 3.85
53 54 0.736053 AAGCGAGCAAACCAACGAAA 59.264 45.000 0.00 0.00 0.00 3.46
54 55 0.028902 AGCGAGCAAACCAACGAAAC 59.971 50.000 0.00 0.00 0.00 2.78
55 56 0.933047 GCGAGCAAACCAACGAAACC 60.933 55.000 0.00 0.00 0.00 3.27
56 57 0.378962 CGAGCAAACCAACGAAACCA 59.621 50.000 0.00 0.00 0.00 3.67
57 58 1.202200 CGAGCAAACCAACGAAACCAA 60.202 47.619 0.00 0.00 0.00 3.67
58 59 2.190161 GAGCAAACCAACGAAACCAAC 58.810 47.619 0.00 0.00 0.00 3.77
59 60 0.917939 GCAAACCAACGAAACCAACG 59.082 50.000 0.00 0.00 0.00 4.10
60 61 1.467713 GCAAACCAACGAAACCAACGA 60.468 47.619 0.00 0.00 34.70 3.85
61 62 2.178783 CAAACCAACGAAACCAACGAC 58.821 47.619 0.00 0.00 34.70 4.34
62 63 0.374410 AACCAACGAAACCAACGACG 59.626 50.000 0.00 0.00 34.70 5.12
63 64 0.740516 ACCAACGAAACCAACGACGT 60.741 50.000 0.00 0.00 40.64 4.34
64 65 1.207390 CCAACGAAACCAACGACGTA 58.793 50.000 0.00 0.00 38.00 3.57
65 66 1.071305 CCAACGAAACCAACGACGTAC 60.071 52.381 0.00 0.00 38.00 3.67
66 67 1.587490 CAACGAAACCAACGACGTACA 59.413 47.619 0.00 0.00 38.00 2.90
67 68 2.138596 ACGAAACCAACGACGTACAT 57.861 45.000 0.00 0.00 37.22 2.29
68 69 1.788308 ACGAAACCAACGACGTACATG 59.212 47.619 0.00 0.00 37.22 3.21
69 70 2.052891 CGAAACCAACGACGTACATGA 58.947 47.619 0.00 0.00 0.00 3.07
70 71 2.160065 CGAAACCAACGACGTACATGAC 60.160 50.000 0.00 0.00 0.00 3.06
71 72 2.806608 AACCAACGACGTACATGACT 57.193 45.000 0.00 0.00 0.00 3.41
72 73 2.806608 ACCAACGACGTACATGACTT 57.193 45.000 0.00 0.00 0.00 3.01
73 74 3.921119 ACCAACGACGTACATGACTTA 57.079 42.857 0.00 0.00 0.00 2.24
74 75 3.568538 ACCAACGACGTACATGACTTAC 58.431 45.455 0.00 0.00 0.00 2.34
75 76 2.919229 CCAACGACGTACATGACTTACC 59.081 50.000 0.00 0.00 0.00 2.85
76 77 3.567530 CAACGACGTACATGACTTACCA 58.432 45.455 0.00 0.00 0.00 3.25
77 78 4.171005 CAACGACGTACATGACTTACCAT 58.829 43.478 0.00 0.00 0.00 3.55
78 79 4.025015 ACGACGTACATGACTTACCATC 57.975 45.455 0.00 0.00 0.00 3.51
79 80 3.441222 ACGACGTACATGACTTACCATCA 59.559 43.478 0.00 0.00 0.00 3.07
80 81 3.789756 CGACGTACATGACTTACCATCAC 59.210 47.826 0.00 0.00 0.00 3.06
81 82 3.766151 ACGTACATGACTTACCATCACG 58.234 45.455 0.00 0.00 37.70 4.35
82 83 3.441222 ACGTACATGACTTACCATCACGA 59.559 43.478 0.00 0.00 36.40 4.35
83 84 4.097437 ACGTACATGACTTACCATCACGAT 59.903 41.667 0.00 0.00 36.40 3.73
84 85 4.675565 CGTACATGACTTACCATCACGATC 59.324 45.833 0.00 0.00 35.61 3.69
85 86 3.706698 ACATGACTTACCATCACGATCG 58.293 45.455 14.88 14.88 0.00 3.69
86 87 2.203800 TGACTTACCATCACGATCGC 57.796 50.000 16.60 0.00 0.00 4.58
87 88 1.474879 TGACTTACCATCACGATCGCA 59.525 47.619 16.60 1.73 0.00 5.10
88 89 2.094442 TGACTTACCATCACGATCGCAA 60.094 45.455 16.60 3.38 0.00 4.85
89 90 2.927477 GACTTACCATCACGATCGCAAA 59.073 45.455 16.60 0.42 0.00 3.68
90 91 2.671396 ACTTACCATCACGATCGCAAAC 59.329 45.455 16.60 0.00 0.00 2.93
91 92 2.665649 TACCATCACGATCGCAAACT 57.334 45.000 16.60 0.00 0.00 2.66
92 93 1.359848 ACCATCACGATCGCAAACTC 58.640 50.000 16.60 0.00 0.00 3.01
93 94 0.652592 CCATCACGATCGCAAACTCC 59.347 55.000 16.60 0.00 0.00 3.85
94 95 1.645034 CATCACGATCGCAAACTCCT 58.355 50.000 16.60 0.00 0.00 3.69
95 96 1.590238 CATCACGATCGCAAACTCCTC 59.410 52.381 16.60 0.00 0.00 3.71
96 97 0.108804 TCACGATCGCAAACTCCTCC 60.109 55.000 16.60 0.00 0.00 4.30
97 98 0.108615 CACGATCGCAAACTCCTCCT 60.109 55.000 16.60 0.00 0.00 3.69
98 99 0.608640 ACGATCGCAAACTCCTCCTT 59.391 50.000 16.60 0.00 0.00 3.36
99 100 1.002087 ACGATCGCAAACTCCTCCTTT 59.998 47.619 16.60 0.00 0.00 3.11
100 101 2.232941 ACGATCGCAAACTCCTCCTTTA 59.767 45.455 16.60 0.00 0.00 1.85
101 102 2.860735 CGATCGCAAACTCCTCCTTTAG 59.139 50.000 0.26 0.00 0.00 1.85
117 118 6.220881 TCCTTTAGGAGTAGAGATAGGCAT 57.779 41.667 0.00 0.00 39.78 4.40
225 355 5.293079 CAGAGGCAGTATTTCTTTACAGAGC 59.707 44.000 0.00 0.00 0.00 4.09
246 376 2.059541 GAGTATAAATCAGGGCGTCGC 58.940 52.381 9.22 9.22 0.00 5.19
254 384 4.436998 AGGGCGTCGCGAAGGAAG 62.437 66.667 23.12 8.13 0.00 3.46
255 385 4.736896 GGGCGTCGCGAAGGAAGT 62.737 66.667 23.12 0.00 0.00 3.01
351 481 2.983229 AGCTGCATGGACTGTAAGAAG 58.017 47.619 1.02 0.00 37.43 2.85
410 540 7.624360 AAAATATAATGTCCTGCGTTTCTGA 57.376 32.000 0.00 0.00 0.00 3.27
411 541 6.604735 AATATAATGTCCTGCGTTTCTGAC 57.395 37.500 0.00 0.00 0.00 3.51
412 542 1.523758 AATGTCCTGCGTTTCTGACC 58.476 50.000 0.00 0.00 0.00 4.02
413 543 0.687354 ATGTCCTGCGTTTCTGACCT 59.313 50.000 0.00 0.00 0.00 3.85
414 544 1.334160 TGTCCTGCGTTTCTGACCTA 58.666 50.000 0.00 0.00 0.00 3.08
415 545 1.000506 TGTCCTGCGTTTCTGACCTAC 59.999 52.381 0.00 0.00 0.00 3.18
416 546 1.000506 GTCCTGCGTTTCTGACCTACA 59.999 52.381 0.00 0.00 0.00 2.74
417 547 1.899814 TCCTGCGTTTCTGACCTACAT 59.100 47.619 0.00 0.00 0.00 2.29
418 548 2.002586 CCTGCGTTTCTGACCTACATG 58.997 52.381 0.00 0.00 0.00 3.21
419 549 2.002586 CTGCGTTTCTGACCTACATGG 58.997 52.381 0.00 0.00 42.93 3.66
420 550 0.727398 GCGTTTCTGACCTACATGGC 59.273 55.000 0.00 0.00 40.22 4.40
421 551 1.676014 GCGTTTCTGACCTACATGGCT 60.676 52.381 0.00 0.00 40.22 4.75
422 552 2.418197 GCGTTTCTGACCTACATGGCTA 60.418 50.000 0.00 0.00 40.22 3.93
423 553 3.741388 GCGTTTCTGACCTACATGGCTAT 60.741 47.826 0.00 0.00 40.22 2.97
424 554 4.442706 CGTTTCTGACCTACATGGCTATT 58.557 43.478 0.00 0.00 40.22 1.73
425 555 4.876107 CGTTTCTGACCTACATGGCTATTT 59.124 41.667 0.00 0.00 40.22 1.40
426 556 6.046593 CGTTTCTGACCTACATGGCTATTTA 58.953 40.000 0.00 0.00 40.22 1.40
513 646 5.843673 TCTAGCTTCATGGACACTAAGAG 57.156 43.478 0.00 0.00 0.00 2.85
846 1000 1.298859 AAGATTCGCCCACTGTTCGC 61.299 55.000 0.00 0.00 0.00 4.70
1120 3566 2.612972 CGTGCCTCCTAAACTGATGTGT 60.613 50.000 0.00 0.00 0.00 3.72
1211 3684 2.683933 ACGGCCCCGAGTTCTCAT 60.684 61.111 14.44 0.00 42.83 2.90
1269 3746 6.158023 AGTTTTCTCTTCTTGGTTCTCGTA 57.842 37.500 0.00 0.00 0.00 3.43
2332 5107 1.227556 CGGGGCCGTTAGATCTTGG 60.228 63.158 0.00 1.97 34.35 3.61
2377 5152 1.135402 CCGCCTAACACAATTTGCCTC 60.135 52.381 0.00 0.00 0.00 4.70
2446 5404 8.445275 AAAACATCCAAAATAAACCTTGAACC 57.555 30.769 0.00 0.00 0.00 3.62
2545 5503 1.159285 TGAACCTTGAGCGCATTCTG 58.841 50.000 11.47 0.00 0.00 3.02
2558 5518 3.674138 GCGCATTCTGAATGGATTGTTGT 60.674 43.478 26.67 0.00 39.31 3.32
2569 5529 2.224426 TGGATTGTTGTCGTAGCAGGTT 60.224 45.455 0.00 0.00 0.00 3.50
2571 5531 1.588674 TTGTTGTCGTAGCAGGTTGG 58.411 50.000 0.00 0.00 0.00 3.77
2598 5565 4.397832 GAACGGCCGGCCTACCAA 62.398 66.667 41.01 0.00 34.57 3.67
2601 5568 4.708386 CGGCCGGCCTACCAAACA 62.708 66.667 41.01 0.00 34.57 2.83
2683 5655 1.272313 ACTCACGTTGGGACCTAGCTA 60.272 52.381 0.00 0.00 0.00 3.32
2689 5663 2.099427 CGTTGGGACCTAGCTAGAACTC 59.901 54.545 22.70 14.85 0.00 3.01
2969 5955 3.880490 CCATTATCGAAATCCCCGAACAA 59.120 43.478 0.00 0.00 39.62 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.831652 CTCGCCTCTCCCCACAAGTT 61.832 60.000 0.00 0.00 0.00 2.66
1 2 2.203788 TCGCCTCTCCCCACAAGT 60.204 61.111 0.00 0.00 0.00 3.16
2 3 2.581354 CTCGCCTCTCCCCACAAG 59.419 66.667 0.00 0.00 0.00 3.16
3 4 3.003173 CCTCGCCTCTCCCCACAA 61.003 66.667 0.00 0.00 0.00 3.33
9 10 4.144727 TCCTCCCCTCGCCTCTCC 62.145 72.222 0.00 0.00 0.00 3.71
10 11 2.520741 CTCCTCCCCTCGCCTCTC 60.521 72.222 0.00 0.00 0.00 3.20
11 12 4.150454 CCTCCTCCCCTCGCCTCT 62.150 72.222 0.00 0.00 0.00 3.69
15 16 4.798682 TTCCCCTCCTCCCCTCGC 62.799 72.222 0.00 0.00 0.00 5.03
16 17 2.444895 CTTCCCCTCCTCCCCTCG 60.445 72.222 0.00 0.00 0.00 4.63
17 18 0.692756 CTTCTTCCCCTCCTCCCCTC 60.693 65.000 0.00 0.00 0.00 4.30
18 19 1.398234 CTTCTTCCCCTCCTCCCCT 59.602 63.158 0.00 0.00 0.00 4.79
19 20 2.379459 GCTTCTTCCCCTCCTCCCC 61.379 68.421 0.00 0.00 0.00 4.81
20 21 2.736826 CGCTTCTTCCCCTCCTCCC 61.737 68.421 0.00 0.00 0.00 4.30
21 22 1.681486 CTCGCTTCTTCCCCTCCTCC 61.681 65.000 0.00 0.00 0.00 4.30
22 23 1.819905 CTCGCTTCTTCCCCTCCTC 59.180 63.158 0.00 0.00 0.00 3.71
23 24 2.363172 GCTCGCTTCTTCCCCTCCT 61.363 63.158 0.00 0.00 0.00 3.69
24 25 2.185310 TTGCTCGCTTCTTCCCCTCC 62.185 60.000 0.00 0.00 0.00 4.30
25 26 0.321653 TTTGCTCGCTTCTTCCCCTC 60.322 55.000 0.00 0.00 0.00 4.30
26 27 0.606673 GTTTGCTCGCTTCTTCCCCT 60.607 55.000 0.00 0.00 0.00 4.79
27 28 1.587043 GGTTTGCTCGCTTCTTCCCC 61.587 60.000 0.00 0.00 0.00 4.81
28 29 0.889186 TGGTTTGCTCGCTTCTTCCC 60.889 55.000 0.00 0.00 0.00 3.97
29 30 0.951558 TTGGTTTGCTCGCTTCTTCC 59.048 50.000 0.00 0.00 0.00 3.46
30 31 1.660333 CGTTGGTTTGCTCGCTTCTTC 60.660 52.381 0.00 0.00 0.00 2.87
31 32 0.307760 CGTTGGTTTGCTCGCTTCTT 59.692 50.000 0.00 0.00 0.00 2.52
32 33 0.531974 TCGTTGGTTTGCTCGCTTCT 60.532 50.000 0.00 0.00 0.00 2.85
33 34 0.306533 TTCGTTGGTTTGCTCGCTTC 59.693 50.000 0.00 0.00 0.00 3.86
34 35 0.736053 TTTCGTTGGTTTGCTCGCTT 59.264 45.000 0.00 0.00 0.00 4.68
35 36 0.028902 GTTTCGTTGGTTTGCTCGCT 59.971 50.000 0.00 0.00 0.00 4.93
36 37 0.933047 GGTTTCGTTGGTTTGCTCGC 60.933 55.000 0.00 0.00 0.00 5.03
37 38 0.378962 TGGTTTCGTTGGTTTGCTCG 59.621 50.000 0.00 0.00 0.00 5.03
38 39 2.190161 GTTGGTTTCGTTGGTTTGCTC 58.810 47.619 0.00 0.00 0.00 4.26
39 40 1.468395 CGTTGGTTTCGTTGGTTTGCT 60.468 47.619 0.00 0.00 0.00 3.91
40 41 0.917939 CGTTGGTTTCGTTGGTTTGC 59.082 50.000 0.00 0.00 0.00 3.68
41 42 2.178783 GTCGTTGGTTTCGTTGGTTTG 58.821 47.619 0.00 0.00 0.00 2.93
42 43 1.202054 CGTCGTTGGTTTCGTTGGTTT 60.202 47.619 0.00 0.00 0.00 3.27
43 44 0.374410 CGTCGTTGGTTTCGTTGGTT 59.626 50.000 0.00 0.00 0.00 3.67
44 45 0.740516 ACGTCGTTGGTTTCGTTGGT 60.741 50.000 0.00 0.00 32.62 3.67
45 46 1.071305 GTACGTCGTTGGTTTCGTTGG 60.071 52.381 1.78 0.00 37.66 3.77
46 47 1.587490 TGTACGTCGTTGGTTTCGTTG 59.413 47.619 1.78 0.00 37.66 4.10
47 48 1.919918 TGTACGTCGTTGGTTTCGTT 58.080 45.000 1.78 0.00 37.66 3.85
48 49 1.788308 CATGTACGTCGTTGGTTTCGT 59.212 47.619 1.78 0.00 39.74 3.85
49 50 2.052891 TCATGTACGTCGTTGGTTTCG 58.947 47.619 1.78 0.00 0.00 3.46
50 51 3.054878 AGTCATGTACGTCGTTGGTTTC 58.945 45.455 1.78 0.00 0.00 2.78
51 52 3.102052 AGTCATGTACGTCGTTGGTTT 57.898 42.857 1.78 0.00 0.00 3.27
52 53 2.806608 AGTCATGTACGTCGTTGGTT 57.193 45.000 1.78 0.00 0.00 3.67
53 54 2.806608 AAGTCATGTACGTCGTTGGT 57.193 45.000 1.78 0.00 0.00 3.67
54 55 2.919229 GGTAAGTCATGTACGTCGTTGG 59.081 50.000 1.78 0.00 0.00 3.77
55 56 3.567530 TGGTAAGTCATGTACGTCGTTG 58.432 45.455 1.78 0.00 0.00 4.10
56 57 3.921119 TGGTAAGTCATGTACGTCGTT 57.079 42.857 1.78 0.00 0.00 3.85
57 58 3.441222 TGATGGTAAGTCATGTACGTCGT 59.559 43.478 2.21 2.21 0.00 4.34
58 59 3.789756 GTGATGGTAAGTCATGTACGTCG 59.210 47.826 0.00 0.00 0.00 5.12
59 60 3.789756 CGTGATGGTAAGTCATGTACGTC 59.210 47.826 0.00 0.00 33.51 4.34
60 61 3.441222 TCGTGATGGTAAGTCATGTACGT 59.559 43.478 0.00 0.00 36.54 3.57
61 62 4.023739 TCGTGATGGTAAGTCATGTACG 57.976 45.455 0.00 0.00 36.51 3.67
62 63 4.675565 CGATCGTGATGGTAAGTCATGTAC 59.324 45.833 7.03 0.00 34.86 2.90
63 64 4.791734 GCGATCGTGATGGTAAGTCATGTA 60.792 45.833 17.81 0.00 34.86 2.29
64 65 3.706698 CGATCGTGATGGTAAGTCATGT 58.293 45.455 7.03 0.00 34.86 3.21
65 66 2.472861 GCGATCGTGATGGTAAGTCATG 59.527 50.000 17.81 0.00 34.63 3.07
66 67 2.100749 TGCGATCGTGATGGTAAGTCAT 59.899 45.455 17.81 0.00 0.00 3.06
67 68 1.474879 TGCGATCGTGATGGTAAGTCA 59.525 47.619 17.81 0.00 0.00 3.41
68 69 2.203800 TGCGATCGTGATGGTAAGTC 57.796 50.000 17.81 0.00 0.00 3.01
69 70 2.665649 TTGCGATCGTGATGGTAAGT 57.334 45.000 17.81 0.00 0.00 2.24
70 71 2.930040 AGTTTGCGATCGTGATGGTAAG 59.070 45.455 17.81 0.00 0.00 2.34
71 72 2.927477 GAGTTTGCGATCGTGATGGTAA 59.073 45.455 17.81 0.00 0.00 2.85
72 73 2.536365 GAGTTTGCGATCGTGATGGTA 58.464 47.619 17.81 0.00 0.00 3.25
73 74 1.359848 GAGTTTGCGATCGTGATGGT 58.640 50.000 17.81 0.00 0.00 3.55
74 75 0.652592 GGAGTTTGCGATCGTGATGG 59.347 55.000 17.81 0.00 0.00 3.51
75 76 1.590238 GAGGAGTTTGCGATCGTGATG 59.410 52.381 17.81 0.00 0.00 3.07
76 77 1.471676 GGAGGAGTTTGCGATCGTGAT 60.472 52.381 17.81 0.00 0.00 3.06
77 78 0.108804 GGAGGAGTTTGCGATCGTGA 60.109 55.000 17.81 2.49 0.00 4.35
78 79 0.108615 AGGAGGAGTTTGCGATCGTG 60.109 55.000 17.81 0.00 0.00 4.35
79 80 0.608640 AAGGAGGAGTTTGCGATCGT 59.391 50.000 17.81 0.00 0.00 3.73
80 81 1.726853 AAAGGAGGAGTTTGCGATCG 58.273 50.000 11.69 11.69 0.00 3.69
94 95 5.664815 TGCCTATCTCTACTCCTAAAGGA 57.335 43.478 0.00 0.00 43.08 3.36
95 96 5.777732 ACATGCCTATCTCTACTCCTAAAGG 59.222 44.000 0.00 0.00 0.00 3.11
96 97 6.686630 CACATGCCTATCTCTACTCCTAAAG 58.313 44.000 0.00 0.00 0.00 1.85
97 98 5.011125 GCACATGCCTATCTCTACTCCTAAA 59.989 44.000 0.00 0.00 34.31 1.85
98 99 4.524714 GCACATGCCTATCTCTACTCCTAA 59.475 45.833 0.00 0.00 34.31 2.69
99 100 4.082845 GCACATGCCTATCTCTACTCCTA 58.917 47.826 0.00 0.00 34.31 2.94
100 101 2.896685 GCACATGCCTATCTCTACTCCT 59.103 50.000 0.00 0.00 34.31 3.69
101 102 2.630098 TGCACATGCCTATCTCTACTCC 59.370 50.000 0.49 0.00 41.18 3.85
102 103 3.320541 AGTGCACATGCCTATCTCTACTC 59.679 47.826 21.04 0.00 41.18 2.59
103 104 3.303938 AGTGCACATGCCTATCTCTACT 58.696 45.455 21.04 0.00 41.18 2.57
104 105 3.742433 AGTGCACATGCCTATCTCTAC 57.258 47.619 21.04 0.00 41.18 2.59
105 106 3.742327 GCAAGTGCACATGCCTATCTCTA 60.742 47.826 31.40 0.00 41.18 2.43
106 107 2.915349 CAAGTGCACATGCCTATCTCT 58.085 47.619 21.04 0.00 41.18 3.10
107 108 1.332997 GCAAGTGCACATGCCTATCTC 59.667 52.381 31.40 6.80 41.18 2.75
108 109 1.386533 GCAAGTGCACATGCCTATCT 58.613 50.000 31.40 0.00 41.18 1.98
109 110 3.932459 GCAAGTGCACATGCCTATC 57.068 52.632 31.40 8.20 41.18 2.08
140 141 2.168728 ACAGGAGAAAGAATAGCGACCC 59.831 50.000 0.00 0.00 0.00 4.46
141 142 3.528597 ACAGGAGAAAGAATAGCGACC 57.471 47.619 0.00 0.00 0.00 4.79
144 145 6.701841 TGCTTATAACAGGAGAAAGAATAGCG 59.298 38.462 0.00 0.00 0.00 4.26
145 146 8.614469 ATGCTTATAACAGGAGAAAGAATAGC 57.386 34.615 0.00 0.00 0.00 2.97
148 149 9.638176 ATCAATGCTTATAACAGGAGAAAGAAT 57.362 29.630 0.00 0.00 0.00 2.40
207 208 9.731819 TTATACTCGCTCTGTAAAGAAATACTG 57.268 33.333 0.00 0.00 0.00 2.74
225 355 2.316792 CGACGCCCTGATTTATACTCG 58.683 52.381 0.00 0.00 0.00 4.18
246 376 2.828877 TGGTTACACACACTTCCTTCG 58.171 47.619 0.00 0.00 0.00 3.79
389 519 5.057149 GGTCAGAAACGCAGGACATTATAT 58.943 41.667 0.00 0.00 32.00 0.86
390 520 4.161565 AGGTCAGAAACGCAGGACATTATA 59.838 41.667 0.00 0.00 32.00 0.98
391 521 3.055094 AGGTCAGAAACGCAGGACATTAT 60.055 43.478 0.00 0.00 32.00 1.28
392 522 2.301870 AGGTCAGAAACGCAGGACATTA 59.698 45.455 0.00 0.00 32.00 1.90
393 523 1.072331 AGGTCAGAAACGCAGGACATT 59.928 47.619 0.00 0.00 32.00 2.71
394 524 0.687354 AGGTCAGAAACGCAGGACAT 59.313 50.000 0.00 0.00 32.00 3.06
395 525 1.000506 GTAGGTCAGAAACGCAGGACA 59.999 52.381 0.00 0.00 32.00 4.02
396 526 1.000506 TGTAGGTCAGAAACGCAGGAC 59.999 52.381 0.00 0.00 0.00 3.85
397 527 1.334160 TGTAGGTCAGAAACGCAGGA 58.666 50.000 0.00 0.00 0.00 3.86
398 528 2.002586 CATGTAGGTCAGAAACGCAGG 58.997 52.381 0.00 0.00 0.00 4.85
399 529 2.002586 CCATGTAGGTCAGAAACGCAG 58.997 52.381 0.00 0.00 0.00 5.18
400 530 1.943968 GCCATGTAGGTCAGAAACGCA 60.944 52.381 0.00 0.00 40.61 5.24
401 531 0.727398 GCCATGTAGGTCAGAAACGC 59.273 55.000 0.00 0.00 40.61 4.84
402 532 2.386661 AGCCATGTAGGTCAGAAACG 57.613 50.000 0.00 0.00 40.61 3.60
403 533 9.209175 CTATAAATAGCCATGTAGGTCAGAAAC 57.791 37.037 0.00 0.00 40.61 2.78
488 621 6.634805 TCTTAGTGTCCATGAAGCTAGAAAG 58.365 40.000 0.00 0.00 0.00 2.62
492 625 5.843673 TCTCTTAGTGTCCATGAAGCTAG 57.156 43.478 0.00 0.00 0.00 3.42
496 629 8.954950 AAACATATCTCTTAGTGTCCATGAAG 57.045 34.615 0.00 0.00 0.00 3.02
498 631 9.383519 GAAAAACATATCTCTTAGTGTCCATGA 57.616 33.333 0.00 0.00 0.00 3.07
846 1000 0.615850 GGAGAGACCACCAAAGAGGG 59.384 60.000 0.00 0.00 43.89 4.30
1120 3566 1.713647 TCTTACCCCTGCATTCCCAAA 59.286 47.619 0.00 0.00 0.00 3.28
1269 3746 0.461339 GACGCCACGACATAACCCAT 60.461 55.000 0.00 0.00 0.00 4.00
2144 4913 0.257905 ATGCCATGCCTGTCACTCAT 59.742 50.000 0.00 0.00 0.00 2.90
2251 5026 7.282224 CCTAAATCAGTCGGTTGAATCCATTAA 59.718 37.037 0.00 0.00 0.00 1.40
2313 5088 1.682451 CCAAGATCTAACGGCCCCGA 61.682 60.000 14.44 0.00 42.83 5.14
2318 5093 0.861837 CGCATCCAAGATCTAACGGC 59.138 55.000 0.00 0.00 0.00 5.68
2391 5349 2.425312 CTCGATGAGCCTTACACACTCT 59.575 50.000 0.00 0.00 0.00 3.24
2398 5356 4.054671 CCTCAAATCTCGATGAGCCTTAC 58.945 47.826 8.03 0.00 41.36 2.34
2446 5404 6.895040 GCGTTCGATTTAACTTTCATCTACAG 59.105 38.462 0.00 0.00 0.00 2.74
2499 5457 1.144936 CAGGATCAGGGAGTTCGGC 59.855 63.158 0.00 0.00 0.00 5.54
2545 5503 3.063997 CCTGCTACGACAACAATCCATTC 59.936 47.826 0.00 0.00 0.00 2.67
2598 5565 6.720012 AAAAAGAAAAACATGCTTCGTGTT 57.280 29.167 0.00 0.00 44.22 3.32
2622 5589 6.336566 TGGTACTTTTAACTGTCACGTTACA 58.663 36.000 2.08 2.08 0.00 2.41
2673 5645 2.176148 AGGAGGAGTTCTAGCTAGGTCC 59.824 54.545 20.58 21.03 0.00 4.46
2683 5655 3.704061 GAGTTGATAGCAGGAGGAGTTCT 59.296 47.826 0.00 0.00 0.00 3.01
2689 5663 6.716934 TTAGTTAGAGTTGATAGCAGGAGG 57.283 41.667 0.00 0.00 0.00 4.30
2939 5925 4.515567 GGGATTTCGATAATGGTTCACCTC 59.484 45.833 0.00 0.00 36.82 3.85
2941 5927 3.568430 GGGGATTTCGATAATGGTTCACC 59.432 47.826 0.00 0.00 0.00 4.02
3077 6090 7.384932 CCACTTCAATATTTTGTTCAGGTTTCC 59.615 37.037 0.00 0.00 34.32 3.13
3119 6132 9.230122 ACCAAATCTTGAAACTTGAACAAATTT 57.770 25.926 0.00 0.00 0.00 1.82
3121 6134 8.791327 AACCAAATCTTGAAACTTGAACAAAT 57.209 26.923 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.