Multiple sequence alignment - TraesCS3B01G215800

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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 TraesCS3B01G215800 chr3B 100.000 5285 0 0 1 5285 256788205 256782921 0.000000e+00 9760.0
1 TraesCS3B01G215800 chr3B 98.780 82 1 0 1 82 435957116 435957197 4.270000e-31 147.0
2 TraesCS3B01G215800 chr3B 96.000 50 2 0 3619 3668 256784494 256784445 1.220000e-11 82.4
3 TraesCS3B01G215800 chr3B 96.000 50 2 0 3712 3761 256784587 256784538 1.220000e-11 82.4
4 TraesCS3B01G215800 chr3A 96.306 3790 81 15 200 3959 219801965 219798205 0.000000e+00 6168.0
5 TraesCS3B01G215800 chr3A 93.873 1371 38 19 3938 5285 219798191 219796844 0.000000e+00 2025.0
6 TraesCS3B01G215800 chr3A 92.929 99 6 1 101 199 219802109 219802012 5.520000e-30 143.0
7 TraesCS3B01G215800 chr3A 93.617 94 6 0 1 94 492706611 492706704 1.980000e-29 141.0
8 TraesCS3B01G215800 chr3A 98.000 50 1 0 3712 3761 219798548 219798499 2.620000e-13 87.9
9 TraesCS3B01G215800 chr3A 94.000 50 3 0 3619 3668 219798455 219798406 5.680000e-10 76.8
10 TraesCS3B01G215800 chr3D 96.688 2234 48 10 1375 3604 178535696 178533485 0.000000e+00 3692.0
11 TraesCS3B01G215800 chr3D 92.241 1392 45 16 3938 5285 178533214 178531842 0.000000e+00 1914.0
12 TraesCS3B01G215800 chr3D 94.641 1213 34 10 200 1386 178537888 178536681 0.000000e+00 1851.0
13 TraesCS3B01G215800 chr3D 93.452 168 8 1 3638 3805 178533487 178533323 4.090000e-61 246.0
14 TraesCS3B01G215800 chr3D 100.000 45 0 0 3895 3939 178533295 178533251 3.390000e-12 84.2
15 TraesCS3B01G215800 chr3D 100.000 31 0 0 3731 3761 178533487 178533457 2.060000e-04 58.4
16 TraesCS3B01G215800 chr1B 91.653 2492 176 12 1238 3713 622187222 622184747 0.000000e+00 3421.0
17 TraesCS3B01G215800 chr1B 85.721 2248 270 38 1391 3624 585882356 585884566 0.000000e+00 2326.0
18 TraesCS3B01G215800 chr1B 85.801 662 63 11 3938 4572 622184603 622183946 0.000000e+00 673.0
19 TraesCS3B01G215800 chr1B 85.397 315 35 10 948 1251 622187552 622187238 3.070000e-82 316.0
20 TraesCS3B01G215800 chr1B 83.186 339 39 12 4069 4392 585884753 585885088 1.440000e-75 294.0
21 TraesCS3B01G215800 chr1B 95.506 89 4 0 1 89 570480248 570480160 5.520000e-30 143.0
22 TraesCS3B01G215800 chr1D 91.320 2477 165 21 1238 3692 452341963 452344411 0.000000e+00 3338.0
23 TraesCS3B01G215800 chr1D 85.778 2257 264 42 1391 3624 433516610 433518832 0.000000e+00 2337.0
24 TraesCS3B01G215800 chr1D 86.798 659 50 13 3938 4570 452344741 452345388 0.000000e+00 701.0
25 TraesCS3B01G215800 chr1D 91.589 214 18 0 948 1161 452341601 452341814 4.000000e-76 296.0
26 TraesCS3B01G215800 chr1D 83.283 329 43 7 4069 4385 433519198 433519526 5.180000e-75 292.0
27 TraesCS3B01G215800 chr1D 97.561 82 2 0 1 82 315462311 315462230 1.980000e-29 141.0
28 TraesCS3B01G215800 chr1A 91.466 2449 167 18 1281 3713 547255037 547257459 0.000000e+00 3326.0
29 TraesCS3B01G215800 chr1A 86.783 2005 217 33 1627 3624 532103565 532105528 0.000000e+00 2191.0
30 TraesCS3B01G215800 chr1A 87.215 657 55 14 3938 4570 547257603 547258254 0.000000e+00 721.0
31 TraesCS3B01G215800 chr1A 86.032 315 33 9 948 1251 547254493 547254807 1.420000e-85 327.0
32 TraesCS3B01G215800 chr1A 83.383 337 42 9 4069 4392 532105705 532106040 3.090000e-77 300.0
33 TraesCS3B01G215800 chr1A 89.051 137 15 0 1010 1146 532102433 532102569 2.530000e-38 171.0
34 TraesCS3B01G215800 chr1A 85.455 165 21 3 3761 3924 547257389 547257551 9.100000e-38 169.0
35 TraesCS3B01G215800 chr5B 90.429 606 54 2 1234 1835 239395958 239395353 0.000000e+00 795.0
36 TraesCS3B01G215800 chr5B 85.079 315 36 8 948 1251 239396286 239395972 1.430000e-80 311.0
37 TraesCS3B01G215800 chr5B 96.552 87 3 0 1 87 557060873 557060959 1.530000e-30 145.0
38 TraesCS3B01G215800 chr2B 89.982 569 55 2 1234 1800 184124804 184124236 0.000000e+00 734.0
39 TraesCS3B01G215800 chr2B 83.178 214 25 8 1049 1251 184125033 184124820 9.040000e-43 185.0
40 TraesCS3B01G215800 chr2A 82.857 315 38 11 953 1251 203826104 203825790 8.720000e-68 268.0
41 TraesCS3B01G215800 chr5A 95.455 88 4 0 1 88 382088537 382088624 1.980000e-29 141.0
42 TraesCS3B01G215800 chr4B 97.561 82 2 0 1 82 645456702 645456783 1.980000e-29 141.0
43 TraesCS3B01G215800 chr4B 92.708 96 5 2 1 95 672122125 672122219 2.570000e-28 137.0
44 TraesCS3B01G215800 chr7B 96.471 85 2 1 1 85 2765349 2765266 7.140000e-29 139.0


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 TraesCS3B01G215800 chr3B 256782921 256788205 5284 True 3308.266667 9760 97.333333 1 5285 3 chr3B.!!$R1 5284
1 TraesCS3B01G215800 chr3A 219796844 219802109 5265 True 1700.140000 6168 95.021600 101 5285 5 chr3A.!!$R1 5184
2 TraesCS3B01G215800 chr3D 178531842 178537888 6046 True 1307.600000 3692 96.170333 200 5285 6 chr3D.!!$R1 5085
3 TraesCS3B01G215800 chr1B 622183946 622187552 3606 True 1470.000000 3421 87.617000 948 4572 3 chr1B.!!$R2 3624
4 TraesCS3B01G215800 chr1B 585882356 585885088 2732 False 1310.000000 2326 84.453500 1391 4392 2 chr1B.!!$F1 3001
5 TraesCS3B01G215800 chr1D 452341601 452345388 3787 False 1445.000000 3338 89.902333 948 4570 3 chr1D.!!$F2 3622
6 TraesCS3B01G215800 chr1D 433516610 433519526 2916 False 1314.500000 2337 84.530500 1391 4385 2 chr1D.!!$F1 2994
7 TraesCS3B01G215800 chr1A 547254493 547258254 3761 False 1135.750000 3326 87.542000 948 4570 4 chr1A.!!$F2 3622
8 TraesCS3B01G215800 chr1A 532102433 532106040 3607 False 887.333333 2191 86.405667 1010 4392 3 chr1A.!!$F1 3382
9 TraesCS3B01G215800 chr5B 239395353 239396286 933 True 553.000000 795 87.754000 948 1835 2 chr5B.!!$R1 887
10 TraesCS3B01G215800 chr2B 184124236 184125033 797 True 459.500000 734 86.580000 1049 1800 2 chr2B.!!$R1 751

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
83 84 0.251519 AAAGGACGGAGGGAGTACGT 60.252 55.000 0.0 0.0 44.35 3.57 F
707 759 0.598680 GTGAGAGTTGCGTCACAGCT 60.599 55.000 0.0 0.0 43.38 4.24 F
1868 3708 1.010793 TCTCTCTCTCTCCCTCCCTCT 59.989 57.143 0.0 0.0 0.00 3.69 F
3279 5147 0.036388 TGCTGGAAAGAAGGCTACGG 60.036 55.000 0.0 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2016 3875 0.451783 GAGATTTGCCAATTCCGCGT 59.548 50.0 4.92 0.0 0.00 6.01 R
2481 4340 0.039074 ACAGCGACAAGTTCTCCTCG 60.039 55.0 0.00 0.0 0.00 4.63 R
3565 5435 0.527565 GTGGTTGCATGCCTACCAAG 59.472 55.0 31.64 0.0 43.13 3.61 R
4659 6857 0.872388 GTGTTTCATCCGACACACCC 59.128 55.0 1.35 0.0 43.88 4.61 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
50 51 7.848223 AAGTTTGATTTTCCAAGAAAGTTGG 57.152 32.000 0.00 0.00 40.87 3.77
51 52 7.181569 AGTTTGATTTTCCAAGAAAGTTGGA 57.818 32.000 2.24 2.24 46.08 3.53
59 60 5.367945 TCCAAGAAAGTTGGAAGTACACT 57.632 39.130 3.95 0.00 44.90 3.55
60 61 5.365619 TCCAAGAAAGTTGGAAGTACACTC 58.634 41.667 3.95 0.00 44.90 3.51
61 62 5.130477 TCCAAGAAAGTTGGAAGTACACTCT 59.870 40.000 3.95 0.00 44.90 3.24
62 63 5.823045 CCAAGAAAGTTGGAAGTACACTCTT 59.177 40.000 0.00 0.00 42.06 2.85
63 64 6.318900 CCAAGAAAGTTGGAAGTACACTCTTT 59.681 38.462 0.00 0.00 42.06 2.52
64 65 7.497909 CCAAGAAAGTTGGAAGTACACTCTTTA 59.502 37.037 0.00 0.00 42.06 1.85
65 66 8.889717 CAAGAAAGTTGGAAGTACACTCTTTAA 58.110 33.333 0.00 0.00 30.46 1.52
66 67 9.457436 AAGAAAGTTGGAAGTACACTCTTTAAA 57.543 29.630 0.00 0.00 30.46 1.52
67 68 9.110502 AGAAAGTTGGAAGTACACTCTTTAAAG 57.889 33.333 9.04 9.04 30.46 1.85
68 69 7.803279 AAGTTGGAAGTACACTCTTTAAAGG 57.197 36.000 15.13 8.48 0.00 3.11
69 70 7.133133 AGTTGGAAGTACACTCTTTAAAGGA 57.867 36.000 15.13 1.82 0.00 3.36
70 71 6.990939 AGTTGGAAGTACACTCTTTAAAGGAC 59.009 38.462 15.13 6.27 0.00 3.85
71 72 5.535333 TGGAAGTACACTCTTTAAAGGACG 58.465 41.667 15.13 6.90 0.00 4.79
72 73 4.928020 GGAAGTACACTCTTTAAAGGACGG 59.072 45.833 15.13 5.64 0.00 4.79
73 74 5.279156 GGAAGTACACTCTTTAAAGGACGGA 60.279 44.000 15.13 0.00 0.00 4.69
74 75 5.388408 AGTACACTCTTTAAAGGACGGAG 57.612 43.478 15.13 7.51 0.00 4.63
75 76 3.679824 ACACTCTTTAAAGGACGGAGG 57.320 47.619 15.13 2.85 0.00 4.30
76 77 2.302157 ACACTCTTTAAAGGACGGAGGG 59.698 50.000 15.13 8.51 34.07 4.30
77 78 2.565834 CACTCTTTAAAGGACGGAGGGA 59.434 50.000 15.13 0.00 29.82 4.20
78 79 2.832733 ACTCTTTAAAGGACGGAGGGAG 59.167 50.000 15.13 4.81 0.00 4.30
79 80 2.832733 CTCTTTAAAGGACGGAGGGAGT 59.167 50.000 15.13 0.00 0.00 3.85
80 81 4.021916 CTCTTTAAAGGACGGAGGGAGTA 58.978 47.826 15.13 0.00 0.00 2.59
81 82 3.766051 TCTTTAAAGGACGGAGGGAGTAC 59.234 47.826 15.13 0.00 0.00 2.73
82 83 1.755179 TAAAGGACGGAGGGAGTACG 58.245 55.000 0.00 0.00 0.00 3.67
83 84 0.251519 AAAGGACGGAGGGAGTACGT 60.252 55.000 0.00 0.00 44.35 3.57
84 85 0.251519 AAGGACGGAGGGAGTACGTT 60.252 55.000 0.00 0.00 41.40 3.99
85 86 0.620556 AGGACGGAGGGAGTACGTTA 59.379 55.000 0.00 0.00 41.40 3.18
86 87 0.735471 GGACGGAGGGAGTACGTTAC 59.265 60.000 0.00 0.00 41.40 2.50
87 88 1.680249 GGACGGAGGGAGTACGTTACT 60.680 57.143 0.00 0.00 41.40 2.24
88 89 2.420129 GGACGGAGGGAGTACGTTACTA 60.420 54.545 0.00 0.00 41.40 1.82
89 90 3.471680 GACGGAGGGAGTACGTTACTAT 58.528 50.000 0.00 0.00 41.40 2.12
90 91 3.879892 GACGGAGGGAGTACGTTACTATT 59.120 47.826 0.00 0.00 41.40 1.73
91 92 3.629398 ACGGAGGGAGTACGTTACTATTG 59.371 47.826 0.00 0.00 39.59 1.90
92 93 3.629398 CGGAGGGAGTACGTTACTATTGT 59.371 47.826 0.00 0.00 39.59 2.71
93 94 4.096984 CGGAGGGAGTACGTTACTATTGTT 59.903 45.833 0.00 0.00 39.59 2.83
94 95 5.393461 CGGAGGGAGTACGTTACTATTGTTT 60.393 44.000 0.00 0.00 39.59 2.83
95 96 6.401394 GGAGGGAGTACGTTACTATTGTTTT 58.599 40.000 0.00 0.00 39.59 2.43
96 97 6.875726 GGAGGGAGTACGTTACTATTGTTTTT 59.124 38.462 0.00 0.00 39.59 1.94
292 340 1.935327 CTAGTCCCTATAGCCGCCGC 61.935 65.000 0.00 0.00 0.00 6.53
427 475 7.591006 TTTTCAGGTATAAGCTTTACAGTCG 57.409 36.000 3.20 0.00 0.00 4.18
434 482 2.200373 AGCTTTACAGTCGCCCAATT 57.800 45.000 0.00 0.00 0.00 2.32
435 483 1.812571 AGCTTTACAGTCGCCCAATTG 59.187 47.619 0.00 0.00 0.00 2.32
451 499 4.274705 CCCAATTGTTGCTTAAACCCAAAC 59.725 41.667 4.43 0.00 38.06 2.93
454 502 4.553330 TTGTTGCTTAAACCCAAACCAA 57.447 36.364 0.00 0.00 38.06 3.67
463 511 6.463190 GCTTAAACCCAAACCAATTAACCTCA 60.463 38.462 0.00 0.00 0.00 3.86
465 513 5.545063 AACCCAAACCAATTAACCTCAAG 57.455 39.130 0.00 0.00 0.00 3.02
466 514 4.552674 ACCCAAACCAATTAACCTCAAGT 58.447 39.130 0.00 0.00 0.00 3.16
686 738 1.263484 CTGTTGCTCATGCGATGATCC 59.737 52.381 0.00 0.00 43.34 3.36
707 759 0.598680 GTGAGAGTTGCGTCACAGCT 60.599 55.000 0.00 0.00 43.38 4.24
781 833 7.689953 TTATAGTCGAAAGGTTTAATCGCTC 57.310 36.000 0.00 0.00 36.56 5.03
842 913 6.594159 CCTAACTAATGTTCCAACGATCAAGT 59.406 38.462 0.00 0.00 37.59 3.16
843 914 6.877611 AACTAATGTTCCAACGATCAAGTT 57.122 33.333 0.00 0.00 34.15 2.66
844 915 6.877611 ACTAATGTTCCAACGATCAAGTTT 57.122 33.333 0.00 0.00 30.96 2.66
875 949 3.350219 TCTTTGCTAACTCATGGGGTC 57.650 47.619 0.00 0.00 0.00 4.46
885 959 2.779430 ACTCATGGGGTCAATGCATCTA 59.221 45.455 0.00 0.00 0.00 1.98
929 1003 7.552458 AAGATAAACATGTGTGCGAATCATA 57.448 32.000 0.00 0.00 0.00 2.15
1146 1221 5.542635 ACACTTCAGTTCTGGGTAAGTGATA 59.457 40.000 25.40 1.61 46.29 2.15
1178 1286 8.407064 TCAAGTATAATTCTCTCGTTTCTCTCC 58.593 37.037 0.00 0.00 0.00 3.71
1227 1340 6.861065 ACAATTACTGTGGACACTTTACTG 57.139 37.500 3.91 0.00 36.69 2.74
1251 1364 9.241317 CTGCCATGATAAATGTTTGAATAGTTC 57.759 33.333 0.00 0.00 0.00 3.01
1410 2732 4.774586 TCGCAGTATTTTTGTTTGGTACG 58.225 39.130 0.00 0.00 0.00 3.67
1791 3623 6.016276 GTGTGGTCAAATCTCACAGGTAATTT 60.016 38.462 0.00 0.00 41.33 1.82
1855 3695 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1857 3697 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1860 3700 4.219115 TCTCTCTCTCTCTCTCTCTCTCC 58.781 52.174 0.00 0.00 0.00 3.71
1861 3701 3.309296 TCTCTCTCTCTCTCTCTCTCCC 58.691 54.545 0.00 0.00 0.00 4.30
1862 3702 3.051803 TCTCTCTCTCTCTCTCTCTCCCT 60.052 52.174 0.00 0.00 0.00 4.20
1867 3707 1.421646 CTCTCTCTCTCTCCCTCCCTC 59.578 61.905 0.00 0.00 0.00 4.30
1868 3708 1.010793 TCTCTCTCTCTCCCTCCCTCT 59.989 57.143 0.00 0.00 0.00 3.69
1869 3709 1.421646 CTCTCTCTCTCCCTCCCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
1988 3830 1.272114 GACTATGCAGACGCGCTAGC 61.272 60.000 5.73 4.06 42.97 3.42
2016 3875 7.759489 AGTTACATCTGCTTATGTTGGAAAA 57.241 32.000 9.33 0.00 40.52 2.29
2118 3977 2.158885 GGATCTCCCAGGTGCTAAAGTC 60.159 54.545 0.00 0.00 34.14 3.01
2481 4340 8.739649 AATCTAAACGTAGAAACAGTACTGTC 57.260 34.615 28.04 16.78 39.36 3.51
2755 4614 5.276461 TGATCGGAATGCACAGTACTATT 57.724 39.130 0.00 0.00 0.00 1.73
3279 5147 0.036388 TGCTGGAAAGAAGGCTACGG 60.036 55.000 0.00 0.00 0.00 4.02
3706 5578 5.922544 AGTTACTATGTTTTCAACTACGCGT 59.077 36.000 19.17 19.17 0.00 6.01
3782 5654 5.763698 AGGCTTTTTCACTTGGACTAGTTAC 59.236 40.000 0.00 0.00 0.00 2.50
3893 5765 5.467035 TTTGATGAATTGGTTGGTCCTTC 57.533 39.130 0.00 0.00 37.07 3.46
4319 6496 8.715088 ACGATGTTAGTTAAATTGTGGTACTTC 58.285 33.333 0.00 0.00 0.00 3.01
4599 6797 6.942532 TGTTTCAAACTCAGTTGCTCTTAT 57.057 33.333 1.10 0.00 0.00 1.73
4652 6850 3.935993 GGCTGCACTTCAGTCCTTA 57.064 52.632 0.50 0.00 44.66 2.69
4659 6857 2.876079 GCACTTCAGTCCTTAACCCTGG 60.876 54.545 0.00 0.00 0.00 4.45
4776 6974 5.458779 CCTTTTGAAGTTTGGCTTAAAGACG 59.541 40.000 0.00 0.00 35.96 4.18
4787 6992 3.555518 GCTTAAAGACGAAAAGCACCTG 58.444 45.455 0.00 0.00 43.98 4.00
4791 6996 3.692791 AAGACGAAAAGCACCTGTTTC 57.307 42.857 0.00 0.00 0.00 2.78
4835 7040 8.749354 CAAAGTTAAGCCTAACCAAATATTCCT 58.251 33.333 1.48 0.00 38.59 3.36
4865 7070 1.892209 AAGGTTTTGACGTGGGCTAG 58.108 50.000 0.00 0.00 0.00 3.42
4868 7089 2.071540 GGTTTTGACGTGGGCTAGTAC 58.928 52.381 0.00 0.00 0.00 2.73
4871 7092 0.245539 TTGACGTGGGCTAGTACTGC 59.754 55.000 5.39 7.18 0.00 4.40
4889 7110 2.278596 CTACCGTGTCCGATGCCG 60.279 66.667 0.00 0.00 35.63 5.69
4921 7143 7.288810 TGACTGATTTGTCCAAATTTTAGCT 57.711 32.000 6.70 0.00 40.77 3.32
4922 7144 7.725251 TGACTGATTTGTCCAAATTTTAGCTT 58.275 30.769 6.70 0.00 40.77 3.74
5162 7386 5.408909 CACAATGCTGATCATAGAGGTCATC 59.591 44.000 0.00 0.00 34.33 2.92
5185 7409 0.809636 GCACAAACACCCAAACAGGC 60.810 55.000 0.00 0.00 35.39 4.85
5220 7444 1.289160 ATCCCAGCTCCAGCAAGTAA 58.711 50.000 0.48 0.00 45.16 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 8.729756 CCAACTTTCTTGGAAAATCAAACTTTT 58.270 29.630 0.00 0.00 42.06 2.27
25 26 8.100164 TCCAACTTTCTTGGAAAATCAAACTTT 58.900 29.630 0.00 0.00 44.90 2.66
26 27 7.619965 TCCAACTTTCTTGGAAAATCAAACTT 58.380 30.769 0.00 0.00 44.90 2.66
27 28 7.181569 TCCAACTTTCTTGGAAAATCAAACT 57.818 32.000 0.00 0.00 44.90 2.66
37 38 5.130477 AGAGTGTACTTCCAACTTTCTTGGA 59.870 40.000 0.00 0.00 46.08 3.53
38 39 5.368989 AGAGTGTACTTCCAACTTTCTTGG 58.631 41.667 0.00 0.00 40.87 3.61
39 40 6.927294 AAGAGTGTACTTCCAACTTTCTTG 57.073 37.500 0.00 0.00 0.00 3.02
40 41 9.457436 TTTAAAGAGTGTACTTCCAACTTTCTT 57.543 29.630 0.00 0.00 31.02 2.52
41 42 9.110502 CTTTAAAGAGTGTACTTCCAACTTTCT 57.889 33.333 9.77 0.00 31.02 2.52
42 43 8.343366 CCTTTAAAGAGTGTACTTCCAACTTTC 58.657 37.037 16.98 0.00 31.02 2.62
43 44 8.050930 TCCTTTAAAGAGTGTACTTCCAACTTT 58.949 33.333 16.98 0.00 32.26 2.66
44 45 7.498239 GTCCTTTAAAGAGTGTACTTCCAACTT 59.502 37.037 16.98 0.00 0.00 2.66
45 46 6.990939 GTCCTTTAAAGAGTGTACTTCCAACT 59.009 38.462 16.98 0.00 0.00 3.16
46 47 6.073927 CGTCCTTTAAAGAGTGTACTTCCAAC 60.074 42.308 16.98 0.00 0.00 3.77
47 48 5.987347 CGTCCTTTAAAGAGTGTACTTCCAA 59.013 40.000 16.98 0.00 0.00 3.53
48 49 5.510179 CCGTCCTTTAAAGAGTGTACTTCCA 60.510 44.000 16.98 0.00 0.00 3.53
49 50 4.928020 CCGTCCTTTAAAGAGTGTACTTCC 59.072 45.833 16.98 0.00 0.00 3.46
50 51 5.776744 TCCGTCCTTTAAAGAGTGTACTTC 58.223 41.667 16.98 0.00 0.00 3.01
51 52 5.279356 CCTCCGTCCTTTAAAGAGTGTACTT 60.279 44.000 16.98 0.00 0.00 2.24
52 53 4.220163 CCTCCGTCCTTTAAAGAGTGTACT 59.780 45.833 16.98 0.00 0.00 2.73
53 54 4.492611 CCTCCGTCCTTTAAAGAGTGTAC 58.507 47.826 16.98 5.84 0.00 2.90
54 55 3.512724 CCCTCCGTCCTTTAAAGAGTGTA 59.487 47.826 16.98 0.00 0.00 2.90
55 56 2.302157 CCCTCCGTCCTTTAAAGAGTGT 59.698 50.000 16.98 0.00 0.00 3.55
56 57 2.565834 TCCCTCCGTCCTTTAAAGAGTG 59.434 50.000 16.98 5.33 0.00 3.51
57 58 2.832733 CTCCCTCCGTCCTTTAAAGAGT 59.167 50.000 16.98 0.00 0.00 3.24
58 59 2.832733 ACTCCCTCCGTCCTTTAAAGAG 59.167 50.000 16.98 7.03 0.00 2.85
59 60 2.898662 ACTCCCTCCGTCCTTTAAAGA 58.101 47.619 16.98 0.24 0.00 2.52
60 61 3.428589 CGTACTCCCTCCGTCCTTTAAAG 60.429 52.174 8.32 8.32 0.00 1.85
61 62 2.493278 CGTACTCCCTCCGTCCTTTAAA 59.507 50.000 0.00 0.00 0.00 1.52
62 63 2.094675 CGTACTCCCTCCGTCCTTTAA 58.905 52.381 0.00 0.00 0.00 1.52
63 64 1.004745 ACGTACTCCCTCCGTCCTTTA 59.995 52.381 0.00 0.00 0.00 1.85
64 65 0.251519 ACGTACTCCCTCCGTCCTTT 60.252 55.000 0.00 0.00 0.00 3.11
65 66 0.251519 AACGTACTCCCTCCGTCCTT 60.252 55.000 0.00 0.00 32.95 3.36
66 67 0.620556 TAACGTACTCCCTCCGTCCT 59.379 55.000 0.00 0.00 32.95 3.85
67 68 0.735471 GTAACGTACTCCCTCCGTCC 59.265 60.000 0.00 0.00 32.95 4.79
68 69 1.743996 AGTAACGTACTCCCTCCGTC 58.256 55.000 0.00 0.00 32.47 4.79
69 70 3.567478 ATAGTAACGTACTCCCTCCGT 57.433 47.619 0.00 0.00 40.14 4.69
70 71 3.629398 ACAATAGTAACGTACTCCCTCCG 59.371 47.826 0.00 0.00 40.14 4.63
71 72 5.588958 AACAATAGTAACGTACTCCCTCC 57.411 43.478 0.00 0.00 40.14 4.30
72 73 7.895975 AAAAACAATAGTAACGTACTCCCTC 57.104 36.000 0.00 0.00 40.14 4.30
99 100 0.804364 GCGTGGCATTGAGAACATCA 59.196 50.000 0.00 0.00 35.62 3.07
100 101 1.089920 AGCGTGGCATTGAGAACATC 58.910 50.000 0.00 0.00 0.00 3.06
101 102 0.806868 CAGCGTGGCATTGAGAACAT 59.193 50.000 0.00 0.00 0.00 2.71
102 103 1.855213 GCAGCGTGGCATTGAGAACA 61.855 55.000 0.00 0.00 0.00 3.18
103 104 1.154150 GCAGCGTGGCATTGAGAAC 60.154 57.895 0.00 0.00 0.00 3.01
104 105 1.300971 GAGCAGCGTGGCATTGAGAA 61.301 55.000 0.00 0.00 35.83 2.87
105 106 1.742880 GAGCAGCGTGGCATTGAGA 60.743 57.895 0.00 0.00 35.83 3.27
181 182 3.753434 CTCGACTCGGCAGCAGGT 61.753 66.667 0.00 0.00 0.00 4.00
215 262 1.000739 ATCGGGTCGGGTTGGACTA 59.999 57.895 0.00 0.00 37.12 2.59
239 287 9.197694 CGGTAGACCAGAAGAGATTTATTAATG 57.802 37.037 0.00 0.00 35.14 1.90
241 289 7.208080 GCGGTAGACCAGAAGAGATTTATTAA 58.792 38.462 0.00 0.00 35.14 1.40
427 475 2.224402 TGGGTTTAAGCAACAATTGGGC 60.224 45.455 10.83 12.91 37.07 5.36
434 482 4.762289 ATTGGTTTGGGTTTAAGCAACA 57.238 36.364 0.00 0.00 43.28 3.33
435 483 6.017770 GGTTAATTGGTTTGGGTTTAAGCAAC 60.018 38.462 0.00 0.00 43.28 4.17
451 499 5.236263 GGCACAAAAACTTGAGGTTAATTGG 59.764 40.000 9.51 2.59 38.28 3.16
454 502 4.500716 CCGGCACAAAAACTTGAGGTTAAT 60.501 41.667 0.00 0.00 37.12 1.40
463 511 2.093106 TGTACACCGGCACAAAAACTT 58.907 42.857 0.00 0.00 0.00 2.66
465 513 1.534385 GGTGTACACCGGCACAAAAAC 60.534 52.381 28.55 2.05 42.29 2.43
466 514 0.739561 GGTGTACACCGGCACAAAAA 59.260 50.000 28.55 0.00 42.29 1.94
686 738 1.278172 CTGTGACGCAACTCTCACGG 61.278 60.000 0.00 0.00 39.83 4.94
707 759 3.876914 GACTGACAATGACCACACTTCAA 59.123 43.478 0.00 0.00 0.00 2.69
781 833 6.100004 TCAGAAGAACCGAATTAGCAGTTAG 58.900 40.000 0.00 0.00 0.00 2.34
875 949 5.494632 TCACAAGCAGAATAGATGCATTG 57.505 39.130 0.00 0.00 46.31 2.82
885 959 9.985730 TTATCTTTTGATTTTCACAAGCAGAAT 57.014 25.926 0.00 0.00 40.19 2.40
929 1003 7.738437 AATGTTGGGGATCAATGAATAAGTT 57.262 32.000 0.00 0.00 37.73 2.66
1171 1279 5.854010 ATGTAGCAGTTAATCGGAGAGAA 57.146 39.130 0.00 0.00 43.63 2.87
1227 1340 8.416329 AGGAACTATTCAAACATTTATCATGGC 58.584 33.333 0.00 0.00 36.02 4.40
1251 1364 4.974368 AATCTTCAGAGTCGACTACAGG 57.026 45.455 20.09 8.42 0.00 4.00
1410 2732 8.932945 TGATAGATTCATTGAGACACTACAAC 57.067 34.615 0.00 0.00 0.00 3.32
1791 3623 6.899393 ATTACTCAACAATGAAAGCCAGAA 57.101 33.333 0.00 0.00 34.49 3.02
1855 3695 3.028130 GTTGTTAGAGAGGGAGGGAGAG 58.972 54.545 0.00 0.00 0.00 3.20
1857 3697 3.028130 GAGTTGTTAGAGAGGGAGGGAG 58.972 54.545 0.00 0.00 0.00 4.30
1860 3700 5.483811 GAAAAGAGTTGTTAGAGAGGGAGG 58.516 45.833 0.00 0.00 0.00 4.30
1861 3701 5.247337 AGGAAAAGAGTTGTTAGAGAGGGAG 59.753 44.000 0.00 0.00 0.00 4.30
1862 3702 5.155905 AGGAAAAGAGTTGTTAGAGAGGGA 58.844 41.667 0.00 0.00 0.00 4.20
1867 3707 6.102897 TCCTGAGGAAAAGAGTTGTTAGAG 57.897 41.667 0.00 0.00 0.00 2.43
1868 3708 6.099845 AGTTCCTGAGGAAAAGAGTTGTTAGA 59.900 38.462 16.79 0.00 43.86 2.10
1869 3709 6.203723 CAGTTCCTGAGGAAAAGAGTTGTTAG 59.796 42.308 16.79 0.00 43.86 2.34
1988 3830 6.595326 TCCAACATAAGCAGATGTAACTTCAG 59.405 38.462 4.14 0.00 39.16 3.02
2016 3875 0.451783 GAGATTTGCCAATTCCGCGT 59.548 50.000 4.92 0.00 0.00 6.01
2097 3956 1.840635 ACTTTAGCACCTGGGAGATCC 59.159 52.381 0.00 0.00 0.00 3.36
2118 3977 3.419759 CGAACGCAAACCTCCCCG 61.420 66.667 0.00 0.00 0.00 5.73
2481 4340 0.039074 ACAGCGACAAGTTCTCCTCG 60.039 55.000 0.00 0.00 0.00 4.63
2755 4614 2.092429 GGCCCATGTCTTGAAGGATACA 60.092 50.000 0.00 0.00 41.41 2.29
3054 4920 6.071616 GCACCCTTCACAAATAGGAAATACAA 60.072 38.462 0.00 0.00 33.13 2.41
3279 5147 2.599612 GCCAAATTCTGTTTGCAAACGC 60.600 45.455 31.20 22.94 41.74 4.84
3565 5435 0.527565 GTGGTTGCATGCCTACCAAG 59.472 55.000 31.64 0.00 43.13 3.61
3633 5505 8.616076 GTCTAAGTGAAAAAGCATGCATACTAT 58.384 33.333 21.98 0.00 0.00 2.12
3706 5578 9.938280 ATACTACTAGAACAATAGCACAAAACA 57.062 29.630 0.00 0.00 0.00 2.83
3893 5765 0.240945 GGTTGCCATGTTGAGTTCCG 59.759 55.000 0.00 0.00 0.00 4.30
4319 6496 2.340337 GCTGCAACTTAATGCCCAAAG 58.660 47.619 0.00 0.00 45.83 2.77
4447 6644 1.796017 TCCCGGTATCAGTTGGCATA 58.204 50.000 0.00 0.00 0.00 3.14
4499 6696 5.112686 GGATCTGGATACGATAAGCCAATC 58.887 45.833 0.00 0.00 42.51 2.67
4659 6857 0.872388 GTGTTTCATCCGACACACCC 59.128 55.000 1.35 0.00 43.88 4.61
4776 6974 4.639135 AGAACAGAAACAGGTGCTTTTC 57.361 40.909 0.00 0.00 32.76 2.29
4787 6992 3.375642 GCTCAGCCAAAAGAACAGAAAC 58.624 45.455 0.00 0.00 0.00 2.78
4835 7040 6.537301 CCACGTCAAAACCTTAGCAGATATAA 59.463 38.462 0.00 0.00 0.00 0.98
4865 7070 1.138247 CGGACACGGTAGGCAGTAC 59.862 63.158 0.00 0.00 36.18 2.73
4868 7089 1.226974 CATCGGACACGGTAGGCAG 60.227 63.158 0.00 0.00 41.39 4.85
4871 7092 2.106332 GGCATCGGACACGGTAGG 59.894 66.667 0.00 0.00 41.39 3.18
4876 7097 2.431771 TTCACGGCATCGGACACG 60.432 61.111 0.00 0.00 41.39 4.49
4889 7110 2.485814 GGACAAATCAGTCAGCCTTCAC 59.514 50.000 0.00 0.00 40.29 3.18
4921 7143 5.505181 AAGCTGGAGGAGATAAAACAGAA 57.495 39.130 0.00 0.00 0.00 3.02
4922 7144 5.505181 AAAGCTGGAGGAGATAAAACAGA 57.495 39.130 0.00 0.00 0.00 3.41
4936 7158 4.365514 TGAATTGTCCTGTAAAGCTGGA 57.634 40.909 0.00 0.00 42.01 3.86
5162 7386 1.134580 TGTTTGGGTGTTTGTGCCATG 60.135 47.619 0.00 0.00 0.00 3.66
5185 7409 6.831976 AGCTGGGATATTTCTAGTTAAGGTG 58.168 40.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.