Multiple sequence alignment - TraesCS5A01G152800

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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 TraesCS5A01G152800 chr5A 100.000 4400 0 0 1 4400 329995487 329991088 0.000000e+00 8126.0
1 TraesCS5A01G152800 chr5A 78.496 1981 396 25 639 2602 606352909 606350942 0.000000e+00 1271.0
2 TraesCS5A01G152800 chr5A 76.997 1978 416 35 654 2610 73828610 73826651 0.000000e+00 1096.0
3 TraesCS5A01G152800 chr5A 92.000 75 2 2 4127 4201 329991408 329991338 7.790000e-18 102.0
4 TraesCS5A01G152800 chr5D 93.868 4126 213 16 1 4099 246013043 246008931 0.000000e+00 6181.0
5 TraesCS5A01G152800 chr5D 77.298 1991 406 38 639 2607 485060086 485058120 0.000000e+00 1131.0
6 TraesCS5A01G152800 chr5D 87.500 200 22 3 4178 4374 246008950 246008751 1.230000e-55 228.0
7 TraesCS5A01G152800 chr5B 94.572 2745 137 4 1 2744 280650797 280648064 0.000000e+00 4233.0
8 TraesCS5A01G152800 chr5B 91.489 940 64 7 2743 3669 280647982 280647046 0.000000e+00 1279.0
9 TraesCS5A01G152800 chr5B 78.046 1986 404 29 639 2607 596224119 596226089 0.000000e+00 1223.0
10 TraesCS5A01G152800 chr5B 78.152 1959 399 24 639 2580 596824529 596822583 0.000000e+00 1219.0
11 TraesCS5A01G152800 chr5B 77.681 1958 404 32 636 2577 280605600 280603660 0.000000e+00 1164.0
12 TraesCS5A01G152800 chr5B 77.459 1952 394 39 658 2589 596393846 596395771 0.000000e+00 1125.0
13 TraesCS5A01G152800 chr5B 76.558 1958 413 38 673 2607 86246899 86244965 0.000000e+00 1031.0
14 TraesCS5A01G152800 chr5B 81.649 376 59 5 3029 3402 280603525 280603158 1.990000e-78 303.0
15 TraesCS5A01G152800 chr5B 89.423 208 22 0 3638 3845 280647041 280646834 3.370000e-66 263.0
16 TraesCS5A01G152800 chr5B 76.471 306 66 6 396 698 86250340 86250038 1.270000e-35 161.0
17 TraesCS5A01G152800 chr5B 78.095 210 44 2 1 209 280606219 280606011 9.930000e-27 132.0
18 TraesCS5A01G152800 chr4A 76.562 704 147 14 652 1343 739780903 739781600 1.930000e-98 370.0
19 TraesCS5A01G152800 chr4A 82.388 335 59 0 3051 3385 741162664 741162998 4.300000e-75 292.0
20 TraesCS5A01G152800 chr4A 81.791 335 61 0 3051 3385 733993696 733994030 9.320000e-72 281.0
21 TraesCS5A01G152800 chr4A 80.168 358 65 3 3051 3402 713503196 713502839 3.370000e-66 263.0
22 TraesCS5A01G152800 chr4A 80.000 355 68 3 3051 3402 733869601 733869247 4.370000e-65 259.0
23 TraesCS5A01G152800 chr7D 80.168 358 65 3 3051 3402 19052903 19053260 3.370000e-66 263.0
24 TraesCS5A01G152800 chr7D 85.380 171 23 2 3535 3703 454079231 454079061 4.520000e-40 176.0
25 TraesCS5A01G152800 chr7A 80.168 358 65 3 3051 3402 19519114 19519471 3.370000e-66 263.0
26 TraesCS5A01G152800 chr2A 90.196 153 15 0 3536 3688 141506318 141506470 2.680000e-47 200.0
27 TraesCS5A01G152800 chr2A 86.957 161 19 2 3536 3694 79316157 79315997 3.500000e-41 180.0
28 TraesCS5A01G152800 chr4D 88.125 160 18 1 3530 3688 74079510 74079351 5.810000e-44 189.0
29 TraesCS5A01G152800 chr4B 88.889 153 17 0 3536 3688 438375333 438375181 5.810000e-44 189.0
30 TraesCS5A01G152800 chr2D 88.312 154 18 0 3536 3689 410600673 410600826 7.520000e-43 185.0
31 TraesCS5A01G152800 chr6A 86.667 165 20 2 3531 3695 184388332 184388170 9.720000e-42 182.0
32 TraesCS5A01G152800 chr3D 97.959 49 1 0 905 953 8370026 8369978 7.840000e-13 86.1


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 TraesCS5A01G152800 chr5A 329991088 329995487 4399 True 8126.0 8126 100.000000 1 4400 1 chr5A.!!$R2 4399
1 TraesCS5A01G152800 chr5A 606350942 606352909 1967 True 1271.0 1271 78.496000 639 2602 1 chr5A.!!$R4 1963
2 TraesCS5A01G152800 chr5A 73826651 73828610 1959 True 1096.0 1096 76.997000 654 2610 1 chr5A.!!$R1 1956
3 TraesCS5A01G152800 chr5D 246008751 246013043 4292 True 3204.5 6181 90.684000 1 4374 2 chr5D.!!$R2 4373
4 TraesCS5A01G152800 chr5D 485058120 485060086 1966 True 1131.0 1131 77.298000 639 2607 1 chr5D.!!$R1 1968
5 TraesCS5A01G152800 chr5B 280646834 280650797 3963 True 1925.0 4233 91.828000 1 3845 3 chr5B.!!$R4 3844
6 TraesCS5A01G152800 chr5B 596224119 596226089 1970 False 1223.0 1223 78.046000 639 2607 1 chr5B.!!$F1 1968
7 TraesCS5A01G152800 chr5B 596822583 596824529 1946 True 1219.0 1219 78.152000 639 2580 1 chr5B.!!$R1 1941
8 TraesCS5A01G152800 chr5B 596393846 596395771 1925 False 1125.0 1125 77.459000 658 2589 1 chr5B.!!$F2 1931
9 TraesCS5A01G152800 chr5B 86244965 86250340 5375 True 596.0 1031 76.514500 396 2607 2 chr5B.!!$R2 2211
10 TraesCS5A01G152800 chr5B 280603158 280606219 3061 True 533.0 1164 79.141667 1 3402 3 chr5B.!!$R3 3401
11 TraesCS5A01G152800 chr4A 739780903 739781600 697 False 370.0 370 76.562000 652 1343 1 chr4A.!!$F2 691

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
343 344 0.179062 GCCTCCAGCACCTAGACATG 60.179 60.000 0.00 0.0 42.97 3.21 F
1213 4529 0.704551 GTTGCGCGCTTCAGAAAATG 59.295 50.000 33.29 0.0 0.00 2.32 F
2265 5594 1.868498 GCTGCTGCTCATCAGAGATTC 59.132 52.381 8.53 0.0 45.72 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2209 5538 0.957362 TTCACAATGTTGCGATGCCA 59.043 45.000 0.00 0.0 0.00 4.92 R
3112 6556 1.278985 TCCCATGAACAACTCGAGCAT 59.721 47.619 13.61 4.4 0.00 3.79 R
3932 7424 1.969923 TGGTCTTGCCAAAAATGAGGG 59.030 47.619 0.00 0.0 45.94 4.30 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
21 22 3.914312 CTTCTCTAGCAAACCTCACGAA 58.086 45.455 0.00 0.00 0.00 3.85
85 86 5.302059 CGAAATACCAGGACAGATAGGAGAA 59.698 44.000 0.00 0.00 0.00 2.87
93 94 3.637694 GGACAGATAGGAGAACTGGGTAC 59.362 52.174 0.00 0.00 36.17 3.34
214 215 2.951642 CAAGCTTTCAGGTCCAGTTTCA 59.048 45.455 0.00 0.00 0.00 2.69
225 226 3.496870 GGTCCAGTTTCATTCTGTCCAGT 60.497 47.826 0.00 0.00 0.00 4.00
243 244 7.913789 TGTCCAGTTAATAACTCCACAGTAAT 58.086 34.615 2.14 0.00 40.46 1.89
331 332 5.902613 TTGTGAATTTATTCAGCCTCCAG 57.097 39.130 5.44 0.00 46.44 3.86
343 344 0.179062 GCCTCCAGCACCTAGACATG 60.179 60.000 0.00 0.00 42.97 3.21
380 381 3.857038 GCTCAATCCCGGGCGGTA 61.857 66.667 18.49 0.00 0.00 4.02
382 383 1.450211 CTCAATCCCGGGCGGTATT 59.550 57.895 18.49 7.59 0.00 1.89
540 541 8.246180 TCCAACTAGTATAGGAAACTTAACACG 58.754 37.037 8.68 0.00 44.97 4.49
545 546 9.727627 CTAGTATAGGAAACTTAACACGGTTAG 57.272 37.037 0.00 0.00 43.67 2.34
563 564 5.220416 CGGTTAGCAACTCTAAATCTTTCGG 60.220 44.000 0.00 0.00 38.86 4.30
620 621 9.588096 AAATAAGGAATTTAGTGAACTTGGAGT 57.412 29.630 0.00 0.00 35.98 3.85
684 829 4.670896 ACAGTTTGGGGAATTTGACAAG 57.329 40.909 0.00 0.00 0.00 3.16
919 4228 3.354089 AATCTTGTTTGGTTGACGCTG 57.646 42.857 0.00 0.00 0.00 5.18
941 4250 4.684484 AGTTCTAACAAACTCTCCGGTT 57.316 40.909 0.00 0.00 34.37 4.44
1119 4429 2.949644 GGGGGTTTATCCGAATCTTGTG 59.050 50.000 0.00 0.00 37.00 3.33
1200 4516 1.154225 CGGACTTTCCATGTTGCGC 60.154 57.895 0.00 0.00 35.91 6.09
1213 4529 0.704551 GTTGCGCGCTTCAGAAAATG 59.295 50.000 33.29 0.00 0.00 2.32
1725 5048 6.708949 ACATGGACGTGTCTTATAACAAACTT 59.291 34.615 0.00 0.00 0.00 2.66
1909 5235 4.634012 ATACCTGCCACTGTGACTTTTA 57.366 40.909 9.86 0.00 0.00 1.52
2108 5437 6.009931 AGAGGAGGGAATGGATCTGTCTATAT 60.010 42.308 0.00 0.00 0.00 0.86
2140 5469 5.543507 ACCAACAGGTGAAATATTTGCAA 57.456 34.783 5.17 0.00 33.38 4.08
2245 5574 3.435327 TGTGAAGTTATTTGGCTACTGCG 59.565 43.478 0.00 0.00 40.82 5.18
2265 5594 1.868498 GCTGCTGCTCATCAGAGATTC 59.132 52.381 8.53 0.00 45.72 2.52
2478 5807 6.604171 TGATATGGATTTCAGTGCCTGTATT 58.396 36.000 2.68 0.00 32.61 1.89
2627 5966 6.037391 TGTTTTCTCCATCTCGTAAACGTTTT 59.963 34.615 20.19 3.53 40.80 2.43
2646 5985 6.208599 ACGTTTTGATGAGGTCATTATTTGGT 59.791 34.615 0.00 0.00 36.54 3.67
2678 6017 9.323985 TGTAATAAAACGTTGTAACAGGTTAGT 57.676 29.630 0.00 0.00 0.00 2.24
2706 6045 3.201290 GCATCTATAATGATGAGGCCGG 58.799 50.000 0.00 0.00 44.71 6.13
2731 6070 6.127897 GGGGGAATAAAAGCGATCATTATCTG 60.128 42.308 0.00 0.00 0.00 2.90
2799 6226 5.877012 AGATGTAGAACAGTTTACCATGCAG 59.123 40.000 0.00 0.00 0.00 4.41
2801 6228 4.994852 TGTAGAACAGTTTACCATGCAGTC 59.005 41.667 0.00 0.00 0.00 3.51
2802 6229 3.412386 AGAACAGTTTACCATGCAGTCC 58.588 45.455 0.00 0.00 0.00 3.85
2805 6232 2.002586 CAGTTTACCATGCAGTCCTCG 58.997 52.381 0.00 0.00 0.00 4.63
2829 6256 9.083080 TCGACAGTACACATTTTGTATCTAATG 57.917 33.333 0.00 0.00 42.82 1.90
2958 6388 6.694447 AGATTCCAAGTGATTTCCATTTGTG 58.306 36.000 0.00 0.00 39.85 3.33
3025 6468 9.655769 GCATCTATACATACACATTCACAAAAG 57.344 33.333 0.00 0.00 0.00 2.27
3112 6556 6.833933 TGATGTCTATAGCTTTGGAGTACTCA 59.166 38.462 23.91 7.95 0.00 3.41
3294 6738 4.771114 AGAACCAAATCCATCATACCGA 57.229 40.909 0.00 0.00 0.00 4.69
3359 6803 4.452825 AGACCTGATGATCAGCTTGATTG 58.547 43.478 16.81 4.19 42.98 2.67
3402 6846 1.553248 CCTTCCACCTGGTCGTGAATA 59.447 52.381 0.00 0.00 35.68 1.75
3547 6996 5.240844 AGAAAAATTTGTTACTCCCTCCGTG 59.759 40.000 0.00 0.00 0.00 4.94
3559 7008 4.196193 CTCCCTCCGTGCACAAATATAAA 58.804 43.478 18.64 0.00 0.00 1.40
3568 7017 7.867909 TCCGTGCACAAATATAAAATGTTTTGA 59.132 29.630 18.64 0.00 34.13 2.69
3677 7162 9.886132 AACTTAGAACACCTTATATTCGTGAAT 57.114 29.630 0.22 0.22 34.93 2.57
3757 7242 9.383519 GTCTATCCTATGTGTGATTTTTGAAGA 57.616 33.333 0.00 0.00 0.00 2.87
3876 7368 6.268617 TGTGCTAGTGATAGGCTTCTCAATAT 59.731 38.462 0.00 0.00 0.00 1.28
3879 7371 8.870116 TGCTAGTGATAGGCTTCTCAATATTTA 58.130 33.333 0.00 0.00 0.00 1.40
3928 7420 7.734726 CGTTCGAGTAGTTTGATAGTTTTGTTC 59.265 37.037 0.00 0.00 0.00 3.18
3929 7421 8.762426 GTTCGAGTAGTTTGATAGTTTTGTTCT 58.238 33.333 0.00 0.00 0.00 3.01
3930 7422 8.882415 TCGAGTAGTTTGATAGTTTTGTTCTT 57.118 30.769 0.00 0.00 0.00 2.52
3931 7423 9.321562 TCGAGTAGTTTGATAGTTTTGTTCTTT 57.678 29.630 0.00 0.00 0.00 2.52
3932 7424 9.582223 CGAGTAGTTTGATAGTTTTGTTCTTTC 57.418 33.333 0.00 0.00 0.00 2.62
3933 7425 9.880064 GAGTAGTTTGATAGTTTTGTTCTTTCC 57.120 33.333 0.00 0.00 0.00 3.13
3941 7433 8.923270 TGATAGTTTTGTTCTTTCCCTCATTTT 58.077 29.630 0.00 0.00 0.00 1.82
3977 7469 3.332761 TTGCAAACTTTGTACTCAGCG 57.667 42.857 0.00 0.00 0.00 5.18
3993 7485 6.830114 ACTCAGCGATGTAATAACTTAAGC 57.170 37.500 0.00 0.00 0.00 3.09
4032 7525 2.288186 GCAGAGAGCGGGCTAATAAAAC 59.712 50.000 0.00 0.00 0.00 2.43
4033 7526 3.798202 CAGAGAGCGGGCTAATAAAACT 58.202 45.455 0.00 0.00 0.00 2.66
4034 7527 4.192317 CAGAGAGCGGGCTAATAAAACTT 58.808 43.478 0.00 0.00 0.00 2.66
4037 7530 5.123979 AGAGAGCGGGCTAATAAAACTTTTG 59.876 40.000 0.00 0.00 0.00 2.44
4038 7531 3.845178 AGCGGGCTAATAAAACTTTTGC 58.155 40.909 0.00 0.00 0.00 3.68
4079 7574 4.993584 GTGGAATATGGAGCACTGTCTATG 59.006 45.833 0.00 0.00 0.00 2.23
4080 7575 4.655649 TGGAATATGGAGCACTGTCTATGT 59.344 41.667 0.00 0.00 0.00 2.29
4081 7576 5.838521 TGGAATATGGAGCACTGTCTATGTA 59.161 40.000 0.00 0.00 0.00 2.29
4082 7577 6.498303 TGGAATATGGAGCACTGTCTATGTAT 59.502 38.462 0.00 0.00 0.00 2.29
4083 7578 7.016563 TGGAATATGGAGCACTGTCTATGTATT 59.983 37.037 0.00 0.00 0.00 1.89
4084 7579 7.547370 GGAATATGGAGCACTGTCTATGTATTC 59.453 40.741 0.00 0.00 0.00 1.75
4085 7580 7.789202 ATATGGAGCACTGTCTATGTATTCT 57.211 36.000 0.00 0.00 0.00 2.40
4086 7581 8.885693 ATATGGAGCACTGTCTATGTATTCTA 57.114 34.615 0.00 0.00 0.00 2.10
4087 7582 6.392625 TGGAGCACTGTCTATGTATTCTAC 57.607 41.667 0.00 0.00 0.00 2.59
4088 7583 5.891551 TGGAGCACTGTCTATGTATTCTACA 59.108 40.000 0.00 0.00 43.80 2.74
4138 7633 8.601845 TTTATTGCGAATAGTATGCTACATGT 57.398 30.769 2.69 2.69 0.00 3.21
4139 7634 9.699703 TTTATTGCGAATAGTATGCTACATGTA 57.300 29.630 5.25 5.25 0.00 2.29
4140 7635 9.869757 TTATTGCGAATAGTATGCTACATGTAT 57.130 29.630 5.91 0.00 0.00 2.29
4141 7636 8.777865 ATTGCGAATAGTATGCTACATGTATT 57.222 30.769 5.91 0.00 0.00 1.89
4142 7637 9.869757 ATTGCGAATAGTATGCTACATGTATTA 57.130 29.630 5.91 0.00 0.00 0.98
4143 7638 9.699703 TTGCGAATAGTATGCTACATGTATTAA 57.300 29.630 5.91 0.00 0.00 1.40
4144 7639 9.869757 TGCGAATAGTATGCTACATGTATTAAT 57.130 29.630 5.91 3.48 0.00 1.40
4223 7718 5.285401 TGGTTTCCTAGGGATACATGAGAA 58.715 41.667 9.46 0.00 35.79 2.87
4254 7749 6.806739 AGAAATGCAAATACGGTTAGAAAAGC 59.193 34.615 0.00 0.00 0.00 3.51
4255 7750 4.428615 TGCAAATACGGTTAGAAAAGCC 57.571 40.909 0.00 0.00 0.00 4.35
4258 7753 4.155280 GCAAATACGGTTAGAAAAGCCTGA 59.845 41.667 0.00 0.00 0.00 3.86
4260 7755 6.625081 GCAAATACGGTTAGAAAAGCCTGAAT 60.625 38.462 0.00 0.00 0.00 2.57
4261 7756 7.312899 CAAATACGGTTAGAAAAGCCTGAATT 58.687 34.615 0.00 0.00 0.00 2.17
4287 7785 4.415881 TTGCAGAAAAGTAGACAGGACA 57.584 40.909 0.00 0.00 0.00 4.02
4288 7786 3.728845 TGCAGAAAAGTAGACAGGACAC 58.271 45.455 0.00 0.00 0.00 3.67
4290 7788 3.799232 GCAGAAAAGTAGACAGGACACGT 60.799 47.826 0.00 0.00 0.00 4.49
4298 7796 3.194005 AGACAGGACACGTGATGTTTT 57.806 42.857 25.01 12.50 43.56 2.43
4307 7805 5.219226 ACACGTGATGTTTTGTTAACGAA 57.781 34.783 25.01 4.04 38.98 3.85
4329 7827 4.723309 AGTTCATCTTCATGGCTAATCCC 58.277 43.478 0.00 0.00 0.00 3.85
4330 7828 4.166725 AGTTCATCTTCATGGCTAATCCCA 59.833 41.667 0.00 0.00 39.65 4.37
4334 7832 1.959282 CTTCATGGCTAATCCCAAGGC 59.041 52.381 0.00 0.00 38.61 4.35
4353 7851 0.035439 CATGGTTACGGGCTCACCTT 60.035 55.000 0.00 0.00 36.97 3.50
4368 7866 4.455606 CTCACCTTCCCATCTACCAAATC 58.544 47.826 0.00 0.00 0.00 2.17
4374 7872 6.069088 ACCTTCCCATCTACCAAATCACATAA 60.069 38.462 0.00 0.00 0.00 1.90
4375 7873 6.488006 CCTTCCCATCTACCAAATCACATAAG 59.512 42.308 0.00 0.00 0.00 1.73
4376 7874 6.575244 TCCCATCTACCAAATCACATAAGT 57.425 37.500 0.00 0.00 0.00 2.24
4377 7875 7.684317 TCCCATCTACCAAATCACATAAGTA 57.316 36.000 0.00 0.00 0.00 2.24
4378 7876 8.275187 TCCCATCTACCAAATCACATAAGTAT 57.725 34.615 0.00 0.00 0.00 2.12
4379 7877 9.387397 TCCCATCTACCAAATCACATAAGTATA 57.613 33.333 0.00 0.00 0.00 1.47
4391 7889 9.507329 AATCACATAAGTATAATTGTAGCCTGG 57.493 33.333 0.00 0.00 0.00 4.45
4392 7890 8.029782 TCACATAAGTATAATTGTAGCCTGGT 57.970 34.615 0.00 0.00 0.00 4.00
4393 7891 9.150028 TCACATAAGTATAATTGTAGCCTGGTA 57.850 33.333 0.00 0.00 0.00 3.25
4394 7892 9.204570 CACATAAGTATAATTGTAGCCTGGTAC 57.795 37.037 0.00 0.00 0.00 3.34
4395 7893 8.930527 ACATAAGTATAATTGTAGCCTGGTACA 58.069 33.333 5.16 5.16 0.00 2.90
4396 7894 9.204570 CATAAGTATAATTGTAGCCTGGTACAC 57.795 37.037 8.59 0.00 32.53 2.90
4397 7895 6.801718 AGTATAATTGTAGCCTGGTACACA 57.198 37.500 8.59 2.26 32.53 3.72
4398 7896 7.374975 AGTATAATTGTAGCCTGGTACACAT 57.625 36.000 8.59 5.90 32.53 3.21
4399 7897 8.486942 AGTATAATTGTAGCCTGGTACACATA 57.513 34.615 8.59 5.97 32.53 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 1.625818 ACAAGTCTAGGCTCACAAGGG 59.374 52.381 0.00 0.00 0.00 3.95
214 215 7.016153 TGTGGAGTTATTAACTGGACAGAAT 57.984 36.000 13.69 0.00 43.03 2.40
243 244 8.862325 TGACAGCCTATTCAGATTTTCTAAAA 57.138 30.769 0.00 0.00 0.00 1.52
291 292 7.408756 TTCACAATATCTTTGGAAATGGGAG 57.591 36.000 0.00 0.00 0.00 4.30
321 322 0.972983 GTCTAGGTGCTGGAGGCTGA 60.973 60.000 0.00 0.00 42.39 4.26
331 332 2.113860 TTTGGCTCATGTCTAGGTGC 57.886 50.000 0.00 0.00 0.00 5.01
343 344 2.866156 GCCTGAAAAGTTGTTTTGGCTC 59.134 45.455 0.00 0.00 39.77 4.70
380 381 3.632145 GTGAGTTTGTTCAGGTCACCAAT 59.368 43.478 0.00 0.00 32.95 3.16
382 383 2.026729 TGTGAGTTTGTTCAGGTCACCA 60.027 45.455 0.00 0.00 37.35 4.17
540 541 5.447413 GCCGAAAGATTTAGAGTTGCTAACC 60.447 44.000 0.00 0.00 38.76 2.85
545 546 5.561070 GTTAGCCGAAAGATTTAGAGTTGC 58.439 41.667 0.00 0.00 0.00 4.17
578 579 5.976870 TCCTTATTTCTTTAGGGATGGGTCT 59.023 40.000 0.00 0.00 0.00 3.85
620 621 1.073284 GTTCTGCCCTAGTCCCAAACA 59.927 52.381 0.00 0.00 0.00 2.83
684 829 2.224523 TGAAGGTCCAATGTGGTGAGTC 60.225 50.000 0.00 0.00 39.03 3.36
941 4250 1.923395 AAAGACCGGATGGCAGGGA 60.923 57.895 9.46 0.00 39.70 4.20
1165 4481 3.958860 GTGGCACTCACCCCAGCT 61.959 66.667 11.13 0.00 40.39 4.24
1200 4516 4.201851 CCAGTGATACCATTTTCTGAAGCG 60.202 45.833 0.00 0.00 0.00 4.68
1662 4985 2.719798 CGTTGAAATGATGGCGGAATC 58.280 47.619 0.00 0.00 0.00 2.52
1909 5235 3.548745 TGCTAGTGCAGTAATGAGCAT 57.451 42.857 11.80 0.00 45.31 3.79
2046 5375 1.269448 TCGCTGAATCTTTTTGTGGCC 59.731 47.619 0.00 0.00 0.00 5.36
2085 5414 2.885388 AGACAGATCCATTCCCTCCT 57.115 50.000 0.00 0.00 0.00 3.69
2140 5469 7.331026 TCTTCCATCGTGTGAATCTTCTTTAT 58.669 34.615 0.00 0.00 0.00 1.40
2209 5538 0.957362 TTCACAATGTTGCGATGCCA 59.043 45.000 0.00 0.00 0.00 4.92
2245 5574 1.868498 GAATCTCTGATGAGCAGCAGC 59.132 52.381 10.66 0.00 43.95 5.25
2265 5594 8.213679 CCCCTATCCATATATTCATACACAAGG 58.786 40.741 0.00 0.00 0.00 3.61
2478 5807 9.077885 AGTATTTTTGCTAGACCAAAATCTGAA 57.922 29.630 8.50 0.00 42.36 3.02
2627 5966 7.959658 AATTCACCAAATAATGACCTCATCA 57.040 32.000 0.00 0.00 43.13 3.07
2678 6017 8.742777 GGCCTCATCATTATAGATGCATAAAAA 58.257 33.333 0.00 0.00 43.94 1.94
2706 6045 5.946377 AGATAATGATCGCTTTTATTCCCCC 59.054 40.000 0.00 0.00 37.15 5.40
2762 6184 7.834681 ACTGTTCTACATCTAGTGACCATAAGA 59.165 37.037 0.00 0.00 0.00 2.10
2799 6226 4.056050 ACAAAATGTGTACTGTCGAGGAC 58.944 43.478 0.00 0.00 39.29 3.85
2801 6228 6.100004 AGATACAAAATGTGTACTGTCGAGG 58.900 40.000 0.00 0.00 45.51 4.63
2802 6229 8.683550 TTAGATACAAAATGTGTACTGTCGAG 57.316 34.615 0.00 0.00 45.51 4.04
2848 6275 4.931661 AATGGGCTCAATGATTGATGTC 57.068 40.909 8.50 4.72 39.30 3.06
2958 6388 8.181487 TGTATCGATGAAGCTAGTGTTTTTAC 57.819 34.615 8.54 0.00 0.00 2.01
3025 6468 3.202906 TGCCAATATTGACGAGTTAGCC 58.797 45.455 17.23 0.00 0.00 3.93
3112 6556 1.278985 TCCCATGAACAACTCGAGCAT 59.721 47.619 13.61 4.40 0.00 3.79
3359 6803 3.969117 TGACAATGTCAGTTTGCAGAC 57.031 42.857 12.63 0.00 37.67 3.51
3422 6866 9.121517 CTGCAAACATTCTGTAGTTAAATGAAG 57.878 33.333 1.65 0.00 35.03 3.02
3423 6867 8.629158 ACTGCAAACATTCTGTAGTTAAATGAA 58.371 29.630 1.65 0.00 36.48 2.57
3425 6869 9.329913 GTACTGCAAACATTCTGTAGTTAAATG 57.670 33.333 0.00 0.00 39.89 2.32
3426 6870 9.062524 TGTACTGCAAACATTCTGTAGTTAAAT 57.937 29.630 0.00 0.00 39.89 1.40
3427 6871 8.439993 TGTACTGCAAACATTCTGTAGTTAAA 57.560 30.769 0.00 0.00 39.89 1.52
3430 6874 6.710295 TGATGTACTGCAAACATTCTGTAGTT 59.290 34.615 13.87 0.00 39.89 2.24
3431 6875 6.230472 TGATGTACTGCAAACATTCTGTAGT 58.770 36.000 13.87 0.00 41.74 2.73
3432 6876 6.726258 TGATGTACTGCAAACATTCTGTAG 57.274 37.500 13.87 0.00 37.69 2.74
3433 6877 7.686438 AATGATGTACTGCAAACATTCTGTA 57.314 32.000 13.87 0.00 37.69 2.74
3434 6878 6.579666 AATGATGTACTGCAAACATTCTGT 57.420 33.333 13.87 0.00 37.69 3.41
3435 6879 6.864685 ACAAATGATGTACTGCAAACATTCTG 59.135 34.615 13.87 11.25 41.63 3.02
3439 6883 7.093814 ACCATACAAATGATGTACTGCAAACAT 60.094 33.333 12.83 12.83 46.90 2.71
3440 6884 6.208402 ACCATACAAATGATGTACTGCAAACA 59.792 34.615 4.18 4.18 46.90 2.83
3448 6894 9.638239 AAATGAAACACCATACAAATGATGTAC 57.362 29.630 0.00 0.00 46.90 2.90
3587 7036 9.169468 GTTTGTTCACTTGTTTGAGTATGTATG 57.831 33.333 0.00 0.00 0.00 2.39
3593 7042 6.205853 AGTGTGTTTGTTCACTTGTTTGAGTA 59.794 34.615 0.00 0.00 41.33 2.59
3602 7051 5.854338 CACGTTTTAGTGTGTTTGTTCACTT 59.146 36.000 3.25 0.00 43.39 3.16
3671 7156 3.288964 ACTAGTACTCCCTCCATTCACG 58.711 50.000 0.00 0.00 0.00 4.35
3677 7162 4.543337 AGAACCTAACTAGTACTCCCTCCA 59.457 45.833 0.00 0.00 0.00 3.86
3716 7201 2.230994 TAGACAGCAAGAGCCCTGCG 62.231 60.000 0.00 0.00 43.56 5.18
3839 7331 3.118408 TCACTAGCACACCACTCAAACTT 60.118 43.478 0.00 0.00 0.00 2.66
3876 7368 7.341445 ACATGCTAAACAAAACCACTCTAAA 57.659 32.000 0.00 0.00 0.00 1.85
3879 7371 5.505654 CGAACATGCTAAACAAAACCACTCT 60.506 40.000 0.00 0.00 0.00 3.24
3882 7374 4.356289 ACGAACATGCTAAACAAAACCAC 58.644 39.130 0.00 0.00 0.00 4.16
3895 7387 3.427528 TCAAACTACTCGAACGAACATGC 59.572 43.478 0.00 0.00 0.00 4.06
3928 7420 4.309933 GTCTTGCCAAAAATGAGGGAAAG 58.690 43.478 0.00 0.00 38.49 2.62
3929 7421 3.070878 GGTCTTGCCAAAAATGAGGGAAA 59.929 43.478 0.00 0.00 34.71 3.13
3930 7422 2.632512 GGTCTTGCCAAAAATGAGGGAA 59.367 45.455 0.00 0.00 37.17 3.97
3931 7423 2.247358 GGTCTTGCCAAAAATGAGGGA 58.753 47.619 0.00 0.00 37.17 4.20
3932 7424 1.969923 TGGTCTTGCCAAAAATGAGGG 59.030 47.619 0.00 0.00 45.94 4.30
3941 7433 5.686960 GTTTGCAAACAATGGTCTTGCCAA 61.687 41.667 32.21 8.93 43.57 4.52
3977 7469 9.994432 GATGCATATGGCTTAAGTTATTACATC 57.006 33.333 0.00 10.13 45.15 3.06
4032 7525 7.271223 CACCATCGTAAAAGTTGATAGCAAAAG 59.729 37.037 0.00 0.00 35.42 2.27
4033 7526 7.081349 CACCATCGTAAAAGTTGATAGCAAAA 58.919 34.615 0.00 0.00 35.42 2.44
4034 7527 6.348950 CCACCATCGTAAAAGTTGATAGCAAA 60.349 38.462 0.00 0.00 35.42 3.68
4037 7530 4.873827 TCCACCATCGTAAAAGTTGATAGC 59.126 41.667 0.00 0.00 0.00 2.97
4038 7531 6.978343 TTCCACCATCGTAAAAGTTGATAG 57.022 37.500 0.00 0.00 0.00 2.08
4052 7547 3.144506 CAGTGCTCCATATTCCACCATC 58.855 50.000 0.00 0.00 0.00 3.51
4112 7607 9.219603 ACATGTAGCATACTATTCGCAATAAAT 57.780 29.630 0.00 0.00 43.54 1.40
4113 7608 8.601845 ACATGTAGCATACTATTCGCAATAAA 57.398 30.769 0.00 0.00 43.54 1.40
4114 7609 9.869757 ATACATGTAGCATACTATTCGCAATAA 57.130 29.630 11.91 0.00 43.54 1.40
4115 7610 9.869757 AATACATGTAGCATACTATTCGCAATA 57.130 29.630 11.91 0.00 43.54 1.90
4116 7611 8.777865 AATACATGTAGCATACTATTCGCAAT 57.222 30.769 11.91 0.00 43.54 3.56
4117 7612 9.699703 TTAATACATGTAGCATACTATTCGCAA 57.300 29.630 11.91 0.00 43.54 4.85
4118 7613 9.869757 ATTAATACATGTAGCATACTATTCGCA 57.130 29.630 11.91 0.00 43.54 5.10
4163 7658 9.219603 ACATGTAGCATACTATTCGCAATAAAT 57.780 29.630 0.00 0.00 43.54 1.40
4164 7659 8.601845 ACATGTAGCATACTATTCGCAATAAA 57.398 30.769 0.00 0.00 43.54 1.40
4165 7660 9.869757 ATACATGTAGCATACTATTCGCAATAA 57.130 29.630 11.91 0.00 43.54 1.40
4166 7661 9.869757 AATACATGTAGCATACTATTCGCAATA 57.130 29.630 11.91 0.00 43.54 1.90
4167 7662 8.777865 AATACATGTAGCATACTATTCGCAAT 57.222 30.769 11.91 0.00 43.54 3.56
4168 7663 9.699703 TTAATACATGTAGCATACTATTCGCAA 57.300 29.630 11.91 0.00 43.54 4.85
4169 7664 9.869757 ATTAATACATGTAGCATACTATTCGCA 57.130 29.630 11.91 0.00 43.54 5.10
4248 7743 5.697633 TCTGCAATGAAAATTCAGGCTTTTC 59.302 36.000 17.78 3.06 41.08 2.29
4253 7748 5.467735 ACTTTTCTGCAATGAAAATTCAGGC 59.532 36.000 12.64 12.87 42.63 4.85
4254 7749 8.084073 TCTACTTTTCTGCAATGAAAATTCAGG 58.916 33.333 12.64 5.48 42.63 3.86
4255 7750 8.909671 GTCTACTTTTCTGCAATGAAAATTCAG 58.090 33.333 12.64 10.39 42.63 3.02
4258 7753 7.869429 CCTGTCTACTTTTCTGCAATGAAAATT 59.131 33.333 12.64 10.41 42.63 1.82
4260 7755 6.545666 TCCTGTCTACTTTTCTGCAATGAAAA 59.454 34.615 11.92 11.92 41.75 2.29
4261 7756 6.017109 GTCCTGTCTACTTTTCTGCAATGAAA 60.017 38.462 0.00 0.00 34.55 2.69
4287 7785 5.473796 ACTTCGTTAACAAAACATCACGT 57.526 34.783 6.39 0.00 0.00 4.49
4288 7786 5.960683 TGAACTTCGTTAACAAAACATCACG 59.039 36.000 6.39 0.00 0.00 4.35
4290 7788 7.925993 AGATGAACTTCGTTAACAAAACATCA 58.074 30.769 19.39 11.80 34.73 3.07
4307 7805 4.166725 TGGGATTAGCCATGAAGATGAACT 59.833 41.667 0.00 0.00 38.95 3.01
4313 7811 2.423373 GCCTTGGGATTAGCCATGAAGA 60.423 50.000 0.00 0.00 38.95 2.87
4315 7813 1.287442 TGCCTTGGGATTAGCCATGAA 59.713 47.619 0.00 0.00 38.95 2.57
4318 7816 1.481802 CCATGCCTTGGGATTAGCCAT 60.482 52.381 0.00 0.00 42.33 4.40
4329 7827 1.376609 GAGCCCGTAACCATGCCTTG 61.377 60.000 0.00 0.00 0.00 3.61
4330 7828 1.077716 GAGCCCGTAACCATGCCTT 60.078 57.895 0.00 0.00 0.00 4.35
4334 7832 0.035439 AAGGTGAGCCCGTAACCATG 60.035 55.000 0.00 0.00 38.74 3.66
4338 7836 1.078637 GGGAAGGTGAGCCCGTAAC 60.079 63.158 0.00 0.00 38.74 2.50
4353 7851 6.575244 ACTTATGTGATTTGGTAGATGGGA 57.425 37.500 0.00 0.00 0.00 4.37
4368 7866 9.204570 GTACCAGGCTACAATTATACTTATGTG 57.795 37.037 0.00 0.00 0.00 3.21
4374 7872 6.801718 TGTGTACCAGGCTACAATTATACT 57.198 37.500 4.10 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.