Multiple sequence alignment - TraesCS1B01G145500

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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 TraesCS1B01G145500 chr1B 100.000 7273 0 0 1 7273 199569505 199576777 0.000000e+00 13431.0
1 TraesCS1B01G145500 chr1B 94.180 756 37 3 379 1134 199549107 199549855 0.000000e+00 1146.0
2 TraesCS1B01G145500 chr1B 93.801 371 22 1 9 379 199544828 199545197 2.290000e-154 556.0
3 TraesCS1B01G145500 chr1B 80.000 355 61 7 382 730 69573029 69573379 3.370000e-63 254.0
4 TraesCS1B01G145500 chr1B 79.552 357 68 3 383 734 330838156 330837800 4.360000e-62 250.0
5 TraesCS1B01G145500 chr1B 82.759 116 14 6 3546 3657 60062566 60062679 1.670000e-16 99.0
6 TraesCS1B01G145500 chr1B 85.294 68 10 0 3655 3722 60062635 60062702 3.640000e-08 71.3
7 TraesCS1B01G145500 chr1B 93.617 47 1 1 3653 3699 199573117 199573161 1.310000e-07 69.4
8 TraesCS1B01G145500 chr1B 93.617 47 1 1 3613 3657 199573157 199573203 1.310000e-07 69.4
9 TraesCS1B01G145500 chr1D 96.549 3477 83 10 3827 7273 139539164 139535695 0.000000e+00 5722.0
10 TraesCS1B01G145500 chr1D 95.143 2244 76 14 1614 3850 139541588 139539371 0.000000e+00 3509.0
11 TraesCS1B01G145500 chr1D 92.903 1240 74 7 383 1617 139543970 139542740 0.000000e+00 1790.0
12 TraesCS1B01G145500 chr1D 95.833 168 6 1 4 170 465772000 465772167 3.340000e-68 270.0
13 TraesCS1B01G145500 chr1D 87.940 199 21 3 183 379 473257651 473257848 1.580000e-56 231.0
14 TraesCS1B01G145500 chr1D 95.918 49 0 1 3611 3657 139539571 139539523 2.180000e-10 78.7
15 TraesCS1B01G145500 chr1A 97.376 3011 74 4 3857 6864 151774325 151777333 0.000000e+00 5118.0
16 TraesCS1B01G145500 chr1A 93.599 2687 134 23 380 3052 151770678 151773340 0.000000e+00 3975.0
17 TraesCS1B01G145500 chr1A 95.957 371 15 0 3161 3531 151773340 151773710 2.900000e-168 603.0
18 TraesCS1B01G145500 chr1A 90.820 305 17 2 6980 7273 151777423 151777727 1.470000e-106 398.0
19 TraesCS1B01G145500 chr1A 96.407 167 5 1 8 173 292328445 292328279 2.590000e-69 274.0
20 TraesCS1B01G145500 chr1A 93.233 133 6 2 3729 3858 151774155 151774287 7.450000e-45 193.0
21 TraesCS1B01G145500 chr1A 93.701 127 6 1 3533 3657 151773795 151773921 9.630000e-44 189.0
22 TraesCS1B01G145500 chr1A 93.396 106 4 1 3655 3760 151773877 151773979 3.510000e-33 154.0
23 TraesCS1B01G145500 chr5D 81.948 349 56 5 388 730 536239866 536239519 9.230000e-74 289.0
24 TraesCS1B01G145500 chr5D 86.842 76 10 0 3655 3730 351472599 351472524 1.300000e-12 86.1
25 TraesCS1B01G145500 chr5D 84.615 91 8 5 3571 3657 351472643 351472555 1.300000e-12 86.1
26 TraesCS1B01G145500 chr2A 81.579 342 57 4 393 730 729831291 729830952 2.000000e-70 278.0
27 TraesCS1B01G145500 chr7D 96.407 167 5 1 8 173 135515896 135515730 2.590000e-69 274.0
28 TraesCS1B01G145500 chr6D 96.407 167 5 1 5 170 276766379 276766545 2.590000e-69 274.0
29 TraesCS1B01G145500 chr6D 80.057 351 65 3 383 729 59782845 59783194 9.360000e-64 255.0
30 TraesCS1B01G145500 chr4D 96.407 167 5 1 8 173 434286113 434285947 2.590000e-69 274.0
31 TraesCS1B01G145500 chr4D 94.828 174 8 1 1 173 164679962 164679789 3.340000e-68 270.0
32 TraesCS1B01G145500 chr6A 95.833 168 6 1 4 170 612026555 612026722 3.340000e-68 270.0
33 TraesCS1B01G145500 chr6A 90.816 196 16 2 185 379 219704495 219704689 2.010000e-65 261.0
34 TraesCS1B01G145500 chrUn 95.808 167 6 1 8 173 70622459 70622293 1.200000e-67 268.0
35 TraesCS1B01G145500 chr6B 79.508 366 69 5 383 744 43319864 43319501 9.360000e-64 255.0
36 TraesCS1B01G145500 chr6B 88.542 192 21 1 184 374 25531800 25531991 1.580000e-56 231.0
37 TraesCS1B01G145500 chr6B 82.609 115 16 4 3546 3657 163547654 163547541 1.670000e-16 99.0
38 TraesCS1B01G145500 chr6B 85.294 68 10 0 3655 3722 163547585 163547518 3.640000e-08 71.3
39 TraesCS1B01G145500 chr4A 88.517 209 19 5 183 389 494799725 494799930 1.570000e-61 248.0
40 TraesCS1B01G145500 chr4A 87.745 204 21 4 188 389 436189386 436189587 1.220000e-57 235.0
41 TraesCS1B01G145500 chr3B 87.317 205 22 4 177 379 241658728 241658526 1.580000e-56 231.0
42 TraesCS1B01G145500 chr3B 88.000 200 18 5 183 379 278451945 278452141 1.580000e-56 231.0
43 TraesCS1B01G145500 chr3D 87.192 203 22 4 189 389 388729771 388729971 2.040000e-55 228.0
44 TraesCS1B01G145500 chr2B 100.000 33 0 0 3625 3657 736912440 736912472 2.190000e-05 62.1
45 TraesCS1B01G145500 chr2B 80.000 80 16 0 3655 3734 736912428 736912507 7.880000e-05 60.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G145500 chr1B 199569505 199576777 7272 False 4523.266667 13431 95.744667 1 7273 3 chr1B.!!$F4 7272
1 TraesCS1B01G145500 chr1B 199544828 199549855 5027 False 851.000000 1146 93.990500 9 1134 2 chr1B.!!$F3 1125
2 TraesCS1B01G145500 chr1D 139535695 139543970 8275 True 2774.925000 5722 95.128250 383 7273 4 chr1D.!!$R1 6890
3 TraesCS1B01G145500 chr1A 151770678 151777727 7049 False 1518.571429 5118 94.011714 380 7273 7 chr1A.!!$F1 6893

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
501 4412 0.179205 GACGATTGCTGTTCTGCTGC 60.179 55.000 0.00 0.00 41.65 5.25 F
1223 5145 0.389948 GACTCGCTTGGGTGATTCGT 60.390 55.000 0.00 0.00 0.00 3.85 F
1677 6756 1.539496 GCATAATTGGTCGCCGGTCTA 60.539 52.381 1.90 0.00 0.00 2.59 F
3492 8574 0.811281 GCCTACATTTCAGTGGCCAC 59.189 55.000 29.22 29.22 37.81 5.01 F
3669 8835 0.041090 ATTGTGTGGAATGGGGGTCC 59.959 55.000 0.00 0.00 35.55 4.46 F
4293 9935 0.941542 TGGCTACCGAAATTATGCGC 59.058 50.000 0.00 0.00 0.00 6.09 F
4475 10117 1.302832 CAGCGAGAAAGGGCAGGTT 60.303 57.895 0.00 0.00 0.00 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2216 7296 0.179073 CGGCATCCCAGATCGACTTT 60.179 55.0 0.00 0.00 0.00 2.66 R
2646 7728 1.297664 CCTACGAGTGTCTACGGGAG 58.702 60.0 0.00 0.00 0.00 4.30 R
3669 8835 0.815213 CCACATGGGCTGGTACATCG 60.815 60.0 0.00 0.00 38.20 3.84 R
4293 9935 2.812591 GCATAAGCTCATCATGACCCAG 59.187 50.0 0.00 0.00 37.91 4.45 R
4736 10378 3.005554 CAATGTTGTAGCCTCAGAGGTG 58.994 50.0 18.37 0.99 37.80 4.00 R
5834 11476 0.537188 CCACAGTCTCTGGGCGTAAT 59.463 55.0 1.90 0.00 32.80 1.89 R
6359 12002 0.257328 TGTTTCAGCCTGGTTGTCCA 59.743 50.0 10.46 3.40 42.05 4.02 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
37 38 8.062065 AGTTGAAGAGTACTCTCATTAGAAGG 57.938 38.462 25.34 0.00 42.66 3.46
46 47 1.207089 CTCATTAGAAGGTGGGCACGA 59.793 52.381 0.00 0.00 0.00 4.35
73 74 2.094762 ATCCGTTCTTCCTCCGTTTG 57.905 50.000 0.00 0.00 0.00 2.93
85 86 2.135933 CTCCGTTTGTTCTTCGCTCTT 58.864 47.619 0.00 0.00 0.00 2.85
92 93 3.942130 TGTTCTTCGCTCTTCTCATCA 57.058 42.857 0.00 0.00 0.00 3.07
115 116 5.633830 TCTTTTTCATCCAATGAGCTCAC 57.366 39.130 20.97 0.00 40.94 3.51
146 147 6.723298 TCAATCTCTTCTTCCATAGACTCC 57.277 41.667 0.00 0.00 30.90 3.85
170 171 8.321353 TCCTGCAAAATATTAGTCTCTTCTTGA 58.679 33.333 0.00 0.00 0.00 3.02
182 183 7.961325 AGTCTCTTCTTGAACTTCTTTCATC 57.039 36.000 0.00 0.00 43.99 2.92
187 188 8.383318 TCTTCTTGAACTTCTTTCATCGATTT 57.617 30.769 0.00 0.00 43.99 2.17
213 214 5.991328 TTCTGGATATAAGCTTTCTTGCG 57.009 39.130 3.20 0.00 38.13 4.85
214 215 5.023533 TCTGGATATAAGCTTTCTTGCGT 57.976 39.130 3.20 0.00 38.13 5.24
237 238 3.444034 CCGAAGTAGAGATCCAACTGACA 59.556 47.826 0.00 0.00 0.00 3.58
244 245 4.274147 AGAGATCCAACTGACATACGAGT 58.726 43.478 0.00 0.00 0.00 4.18
326 327 4.081185 GGGCCCCCGTTTGCATTG 62.081 66.667 12.23 0.00 0.00 2.82
359 360 9.265862 AGTCCCAAAATCACATATATTCCAAAA 57.734 29.630 0.00 0.00 0.00 2.44
395 4306 9.487790 GTAAATTTTTGATGGATTTGTCCTTGA 57.512 29.630 0.00 0.00 0.00 3.02
416 4327 3.726557 TGGATTTGCTCAGATCTGGTT 57.273 42.857 22.42 1.73 0.00 3.67
501 4412 0.179205 GACGATTGCTGTTCTGCTGC 60.179 55.000 0.00 0.00 41.65 5.25
506 4417 1.153107 TGCTGTTCTGCTGCACTGT 60.153 52.632 0.00 0.00 45.14 3.55
539 4450 3.444742 TCTTAGCATAACGACTTCCCGAA 59.555 43.478 0.00 0.00 0.00 4.30
584 4495 1.073373 CTCCGGCGAGGGATAGAGA 59.927 63.158 9.30 0.00 41.52 3.10
650 4561 5.353400 CGTTGCTAGACGGTATATGGATCTA 59.647 44.000 0.00 0.00 39.27 1.98
786 4706 3.879932 AAGTCTTAAAGAACAGCGTGC 57.120 42.857 0.00 0.00 0.00 5.34
839 4759 3.675467 AAACAGAAACGAAGTGAGCAC 57.325 42.857 0.00 0.00 45.00 4.40
840 4760 2.604046 ACAGAAACGAAGTGAGCACT 57.396 45.000 0.00 0.00 45.00 4.40
841 4761 3.728076 ACAGAAACGAAGTGAGCACTA 57.272 42.857 3.21 0.00 45.00 2.74
842 4762 3.643763 ACAGAAACGAAGTGAGCACTAG 58.356 45.455 3.21 4.28 45.00 2.57
843 4763 3.318275 ACAGAAACGAAGTGAGCACTAGA 59.682 43.478 3.21 0.00 45.00 2.43
1223 5145 0.389948 GACTCGCTTGGGTGATTCGT 60.390 55.000 0.00 0.00 0.00 3.85
1228 5150 1.794222 CTTGGGTGATTCGTTCGGC 59.206 57.895 0.00 0.00 0.00 5.54
1320 5242 3.260632 GTGGGTTTACCTACTTCCCGTAA 59.739 47.826 8.04 0.00 43.32 3.18
1354 5277 2.386249 GATCGTACGTTGGATCTCTGC 58.614 52.381 16.05 0.00 36.86 4.26
1382 5305 3.751518 GGGTCTTAGGTGCTTCTTTTGA 58.248 45.455 0.00 0.00 0.00 2.69
1478 5402 7.274033 CAGCAAAGTTCACATTGTTGGTATATG 59.726 37.037 4.41 0.00 33.96 1.78
1573 5497 5.804639 TGTGCTTTACCATCACTAGATTGT 58.195 37.500 0.00 0.00 34.75 2.71
1594 5518 6.552859 TGTCAGTTAATTGAATCAAAGCGA 57.447 33.333 1.77 0.00 0.00 4.93
1597 5521 7.591057 TGTCAGTTAATTGAATCAAAGCGAAAG 59.409 33.333 1.77 0.00 0.00 2.62
1642 6721 9.659830 ATTGTTTGACTCGTTTGTATTTTAGTC 57.340 29.630 0.00 0.00 35.13 2.59
1666 6745 8.338259 GTCTGTACTTGAACTATGCATAATTGG 58.662 37.037 4.92 0.00 0.00 3.16
1677 6756 1.539496 GCATAATTGGTCGCCGGTCTA 60.539 52.381 1.90 0.00 0.00 2.59
1691 6770 3.119955 GCCGGTCTAAAATTGAGTTGGAC 60.120 47.826 1.90 0.00 36.16 4.02
1693 6772 3.991773 CGGTCTAAAATTGAGTTGGACGA 59.008 43.478 0.00 0.00 37.35 4.20
1736 6815 3.887716 GCATGGAATTAGCCAAGATCACT 59.112 43.478 0.00 0.00 42.16 3.41
1950 7029 8.926092 AGAAGTAGGAAGTTTAAGCAAATTCT 57.074 30.769 0.00 0.00 0.00 2.40
2005 7084 4.082125 GACAAGGACAACCATGGAATTCT 58.918 43.478 21.47 4.05 38.95 2.40
2119 7198 2.846206 TCCTGCAATATTCCTGTGGACT 59.154 45.455 0.00 0.00 0.00 3.85
2149 7228 6.264067 AGGCACATTTGATAAAGGAGATAAGC 59.736 38.462 0.00 0.00 0.00 3.09
2150 7229 6.039717 GGCACATTTGATAAAGGAGATAAGCA 59.960 38.462 0.00 0.00 0.00 3.91
2216 7296 2.545742 CCAACATCTCGATATGGTGCGA 60.546 50.000 20.28 0.00 42.20 5.10
2577 7657 6.181190 AGGTAGAGGCAAAACTAGGAATTTC 58.819 40.000 0.00 0.00 0.00 2.17
2626 7708 7.593644 TGCTTTTTCTAAAGGCTCGTATTTTTC 59.406 33.333 7.59 0.00 40.90 2.29
2738 7820 8.226819 TGAGTCGATTATGTTCTAACATCTCT 57.773 34.615 11.45 3.73 46.10 3.10
2744 7826 9.899226 CGATTATGTTCTAACATCTCTACATGA 57.101 33.333 11.45 0.00 46.10 3.07
2964 8046 4.767578 ACATTGCCATAGATGTCTCTGT 57.232 40.909 0.00 0.00 31.07 3.41
3069 8151 6.014584 ACGTATGTTGGATGAATCTGCCTATA 60.015 38.462 0.00 0.00 0.00 1.31
3213 8295 7.765695 AACATGAGAAACATTATCTTGGTGT 57.234 32.000 0.00 0.00 37.07 4.16
3306 8388 5.178067 GTGATTTTCATTTCCTTGGCACTTG 59.822 40.000 0.00 0.00 0.00 3.16
3412 8494 6.273260 AGGTATAGTTATGATGACCATGGCTT 59.727 38.462 13.04 2.83 36.71 4.35
3445 8527 8.790718 GTTTAGGCACATCTATGATGATTCATT 58.209 33.333 13.63 0.00 42.61 2.57
3492 8574 0.811281 GCCTACATTTCAGTGGCCAC 59.189 55.000 29.22 29.22 37.81 5.01
3575 8740 1.122849 CAAACACTGTTGCGCATGAC 58.877 50.000 12.75 8.38 0.00 3.06
3631 8797 2.290514 ACTGTGTGGAATGGGTCTGATG 60.291 50.000 0.00 0.00 0.00 3.07
3669 8835 0.041090 ATTGTGTGGAATGGGGGTCC 59.959 55.000 0.00 0.00 35.55 4.46
3737 9107 6.804783 CCCAAGCACCGTTAAGTTTTAATAAG 59.195 38.462 0.00 0.00 0.00 1.73
3828 9201 2.755655 ACGAGGGAGCATATTATCCGAG 59.244 50.000 0.00 0.00 36.38 4.63
3865 9506 5.532406 TCTTTCCTTGCCATGTAGAATATGC 59.468 40.000 0.00 0.00 0.00 3.14
4001 9643 2.232208 CACCCTTGGGAAATTCTTGAGC 59.768 50.000 13.39 0.00 0.00 4.26
4247 9889 3.055094 GGACATCCAGGCAGAAGAAAGTA 60.055 47.826 0.00 0.00 35.64 2.24
4293 9935 0.941542 TGGCTACCGAAATTATGCGC 59.058 50.000 0.00 0.00 0.00 6.09
4475 10117 1.302832 CAGCGAGAAAGGGCAGGTT 60.303 57.895 0.00 0.00 0.00 3.50
5030 10672 1.630369 TGCCTTCTTGTATGCAGTCCT 59.370 47.619 0.00 0.00 0.00 3.85
5295 10937 3.959495 AAATGGATCACCTGGTATGCT 57.041 42.857 0.00 0.00 37.04 3.79
5393 11035 8.620116 AACATTTTTGACCCTAATTTTGATGG 57.380 30.769 0.00 0.00 0.00 3.51
5507 11149 7.065204 GGTATCACTAAGAAAAAGGCTCTTGAG 59.935 40.741 0.00 0.00 34.90 3.02
5619 11261 4.640771 ACTGGACTTGCTCCTGAAATTA 57.359 40.909 4.63 0.00 39.84 1.40
5784 11426 3.139397 ACCTGATGGTGGGAACAAAAGTA 59.861 43.478 0.00 0.00 46.51 2.24
5785 11427 4.148838 CCTGATGGTGGGAACAAAAGTAA 58.851 43.478 0.00 0.00 46.06 2.24
5834 11476 2.094182 GCCTCTTGATCGTCACAACCTA 60.094 50.000 0.00 0.00 0.00 3.08
5947 11589 3.799917 GCTGCCTACTTTTGTGTTGCATT 60.800 43.478 0.00 0.00 33.44 3.56
5961 11603 4.324402 GTGTTGCATTATGCTAGTTGTTGC 59.676 41.667 18.44 0.00 45.31 4.17
6038 11680 3.124578 TGGCAAATTTTTCAGGCCTTC 57.875 42.857 0.00 0.00 44.85 3.46
6233 11875 3.256960 GAGGCCCACCCACTTCCA 61.257 66.667 0.00 0.00 36.11 3.53
6304 11946 9.856488 AATGTATCACTGTTGTACTTAGTGTAG 57.144 33.333 17.86 2.22 41.82 2.74
6347 11989 8.682936 ACTAACAGAAATGTGAGAAATCTTGT 57.317 30.769 0.00 0.00 0.00 3.16
6359 12002 9.921637 TGTGAGAAATCTTGTAACTTTGTTTTT 57.078 25.926 0.00 0.00 0.00 1.94
6400 12043 7.246171 ACAATGAGTAGCTTTCTCCTTTCTA 57.754 36.000 13.52 0.00 0.00 2.10
6468 12111 4.432712 GTTCTTGGAAGCAAAGCTCAAAA 58.567 39.130 0.00 0.00 38.25 2.44
6566 12210 5.011840 TGTGCAATCCATTCCAATTCTGAAA 59.988 36.000 0.00 0.00 0.00 2.69
6568 12212 6.596497 GTGCAATCCATTCCAATTCTGAAATT 59.404 34.615 0.00 0.00 35.43 1.82
6569 12213 7.765360 GTGCAATCCATTCCAATTCTGAAATTA 59.235 33.333 0.00 0.00 33.27 1.40
6570 12214 7.765360 TGCAATCCATTCCAATTCTGAAATTAC 59.235 33.333 0.00 0.00 33.27 1.89
6626 12270 1.832998 TCTGCTATCATGTGTCAGCCA 59.167 47.619 0.00 0.00 32.97 4.75
6735 12383 4.011023 GTTCCTCTTTCCTAGCCCTTTTC 58.989 47.826 0.00 0.00 0.00 2.29
6745 12393 1.739067 AGCCCTTTTCGTACATGCTC 58.261 50.000 0.00 0.00 0.00 4.26
7060 12749 7.439157 TCATTTTGTCATTCAGTTCTAGTGG 57.561 36.000 0.00 0.00 0.00 4.00
7064 12753 3.265791 GTCATTCAGTTCTAGTGGCAGG 58.734 50.000 0.00 0.00 0.00 4.85
7150 12850 9.553064 TGATCAGCCTATTCTTTCTAAGATTTC 57.447 33.333 0.00 0.00 37.38 2.17
7193 12893 3.950397 TCCGCATGACCTGAAGTAAATT 58.050 40.909 0.00 0.00 0.00 1.82
7201 12901 7.702348 GCATGACCTGAAGTAAATTAACCATTC 59.298 37.037 0.00 0.00 0.00 2.67
7266 12966 1.203065 GTTCAAGCTGTGCTGTTTGC 58.797 50.000 0.00 0.00 39.62 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.832769 AGTACTCTTCAACTCATACCTTTCTC 58.167 38.462 0.00 0.00 0.00 2.87
1 2 7.672239 AGAGTACTCTTCAACTCATACCTTTCT 59.328 37.037 20.00 0.00 43.74 2.52
2 3 7.832769 AGAGTACTCTTCAACTCATACCTTTC 58.167 38.462 20.00 0.00 43.74 2.62
3 4 7.451877 TGAGAGTACTCTTCAACTCATACCTTT 59.548 37.037 25.86 0.00 43.74 3.11
4 5 6.948886 TGAGAGTACTCTTCAACTCATACCTT 59.051 38.462 25.86 0.00 43.74 3.50
5 6 6.486056 TGAGAGTACTCTTCAACTCATACCT 58.514 40.000 25.86 0.00 43.74 3.08
6 7 6.761099 TGAGAGTACTCTTCAACTCATACC 57.239 41.667 25.86 9.47 43.74 2.73
7 8 9.944663 CTAATGAGAGTACTCTTCAACTCATAC 57.055 37.037 25.86 9.96 43.74 2.39
13 14 7.757624 CACCTTCTAATGAGAGTACTCTTCAAC 59.242 40.741 25.86 13.78 42.99 3.18
37 38 1.538419 GGATTAGCTACTCGTGCCCAC 60.538 57.143 5.13 0.00 0.00 4.61
46 47 3.637694 GGAGGAAGAACGGATTAGCTACT 59.362 47.826 0.00 0.00 0.00 2.57
73 74 4.681744 AGATGATGAGAAGAGCGAAGAAC 58.318 43.478 0.00 0.00 0.00 3.01
85 86 7.201794 GCTCATTGGATGAAAAAGATGATGAGA 60.202 37.037 12.24 0.00 40.00 3.27
92 93 5.713389 TGTGAGCTCATTGGATGAAAAAGAT 59.287 36.000 21.47 0.00 39.11 2.40
115 116 7.627298 ATGGAAGAAGAGATTGATGAAACTG 57.373 36.000 0.00 0.00 0.00 3.16
146 147 9.766277 GTTCAAGAAGAGACTAATATTTTGCAG 57.234 33.333 0.00 0.00 0.00 4.41
207 208 1.817357 TCTCTACTTCGGACGCAAGA 58.183 50.000 9.64 0.24 43.62 3.02
213 214 3.695060 TCAGTTGGATCTCTACTTCGGAC 59.305 47.826 0.00 0.00 29.24 4.79
214 215 3.695060 GTCAGTTGGATCTCTACTTCGGA 59.305 47.826 0.00 0.00 29.24 4.55
244 245 1.454847 GGTGGTGGGTTGTGCTCAA 60.455 57.895 0.00 0.00 0.00 3.02
279 280 3.659089 GATACACCACGGCGTGCCT 62.659 63.158 33.15 17.83 37.25 4.75
283 284 2.577059 CAGGATACACCACGGCGT 59.423 61.111 6.77 6.77 42.04 5.68
285 286 2.189521 CCCAGGATACACCACGGC 59.810 66.667 0.00 0.00 42.04 5.68
312 313 0.175531 GGAATCAATGCAAACGGGGG 59.824 55.000 0.00 0.00 0.00 5.40
326 327 5.665916 ATGTGATTTTGGGACTTGGAATC 57.334 39.130 0.00 0.00 0.00 2.52
395 4306 3.947612 ACCAGATCTGAGCAAATCCAT 57.052 42.857 24.62 0.00 0.00 3.41
490 4401 0.590195 GGAACAGTGCAGCAGAACAG 59.410 55.000 0.00 0.00 0.00 3.16
501 4412 3.432326 GCTAAGACCCCATAGGAACAGTG 60.432 52.174 0.00 0.00 39.89 3.66
506 4417 4.039973 CGTTATGCTAAGACCCCATAGGAA 59.960 45.833 0.00 0.00 39.89 3.36
539 4450 9.314321 CCGAACAAATCTTATTGTAGTAGACAT 57.686 33.333 0.00 0.00 42.49 3.06
670 4582 6.230472 TCAGTCATAGTACAACAAACAGCAT 58.770 36.000 0.00 0.00 0.00 3.79
673 4585 7.946655 TCTTCAGTCATAGTACAACAAACAG 57.053 36.000 0.00 0.00 0.00 3.16
730 4645 9.883142 AACACACATTTCCTTTTCTTTGATTAA 57.117 25.926 0.00 0.00 0.00 1.40
786 4706 9.474920 TTTTGTTAGAGCAATTTGATAAAGTGG 57.525 29.630 0.00 0.00 36.99 4.00
839 4759 7.866393 TCTTGTCTTTCCGTTTTTCTACTCTAG 59.134 37.037 0.00 0.00 0.00 2.43
840 4760 7.719483 TCTTGTCTTTCCGTTTTTCTACTCTA 58.281 34.615 0.00 0.00 0.00 2.43
841 4761 6.579865 TCTTGTCTTTCCGTTTTTCTACTCT 58.420 36.000 0.00 0.00 0.00 3.24
842 4762 6.839820 TCTTGTCTTTCCGTTTTTCTACTC 57.160 37.500 0.00 0.00 0.00 2.59
843 4763 7.120138 TGTTTCTTGTCTTTCCGTTTTTCTACT 59.880 33.333 0.00 0.00 0.00 2.57
919 4839 0.840722 GGTGGAAGGAAGAGGGTGGA 60.841 60.000 0.00 0.00 0.00 4.02
1223 5145 3.117794 CCTCGAATAAACATACGCCGAA 58.882 45.455 0.00 0.00 0.00 4.30
1228 5150 4.607955 TCAGCTCCTCGAATAAACATACG 58.392 43.478 0.00 0.00 0.00 3.06
1320 5242 1.079127 CGATCCGTTCCAGCACCTT 60.079 57.895 0.00 0.00 0.00 3.50
1354 5277 1.153823 CACCTAAGACCCGACGCTG 60.154 63.158 0.00 0.00 0.00 5.18
1382 5305 3.446873 CAGCCTCAGACAGATCACTAAGT 59.553 47.826 0.00 0.00 0.00 2.24
1478 5402 3.571401 CCAATGGAGATGATTAGGGCAAC 59.429 47.826 0.00 0.00 0.00 4.17
1573 5497 6.582295 GCTTTCGCTTTGATTCAATTAACTGA 59.418 34.615 0.00 0.00 0.00 3.41
1642 6721 8.213518 ACCAATTATGCATAGTTCAAGTACAG 57.786 34.615 11.21 0.00 0.00 2.74
1666 6745 2.344025 ACTCAATTTTAGACCGGCGAC 58.656 47.619 9.30 1.53 0.00 5.19
1677 6756 6.834168 ATAACCATCGTCCAACTCAATTTT 57.166 33.333 0.00 0.00 0.00 1.82
1691 6770 6.423604 TGCAGTAACATGACATATAACCATCG 59.576 38.462 0.00 0.00 0.00 3.84
2005 7084 8.416329 AGAGAGGACGTTTTTACTAACTTTACA 58.584 33.333 0.00 0.00 0.00 2.41
2115 7194 1.559682 TCAAATGTGCCTAGGGAGTCC 59.440 52.381 11.72 0.00 0.00 3.85
2119 7198 4.476846 TCCTTTATCAAATGTGCCTAGGGA 59.523 41.667 11.72 4.36 0.00 4.20
2149 7228 6.170846 AGATAGTTAACCCGGTTAGGATTG 57.829 41.667 9.96 0.00 45.00 2.67
2150 7229 6.408891 CCAAGATAGTTAACCCGGTTAGGATT 60.409 42.308 9.96 0.00 45.00 3.01
2216 7296 0.179073 CGGCATCCCAGATCGACTTT 60.179 55.000 0.00 0.00 0.00 2.66
2626 7708 8.947115 ACGGGAGTATTCAAGAAAATTTAGAAG 58.053 33.333 0.00 0.00 44.60 2.85
2646 7728 1.297664 CCTACGAGTGTCTACGGGAG 58.702 60.000 0.00 0.00 0.00 4.30
2688 7770 9.774742 CAAGATAGTTAACCAGTTTAAGAATGC 57.225 33.333 0.88 0.00 29.89 3.56
2701 7783 9.530633 AACATAATCGACTCAAGATAGTTAACC 57.469 33.333 0.88 0.00 0.00 2.85
2738 7820 9.997172 ATCCCAGATAGACTTATGTATCATGTA 57.003 33.333 0.00 0.00 34.25 2.29
2744 7826 6.267635 AGCCATCCCAGATAGACTTATGTAT 58.732 40.000 0.00 0.00 0.00 2.29
2964 8046 9.170734 CATCTTATCTCCTTTCTCAAATGTGAA 57.829 33.333 0.00 0.00 31.88 3.18
3069 8151 2.081462 GCAGCTTACAACCGGTTACAT 58.919 47.619 21.79 11.28 0.00 2.29
3172 8254 6.998074 TCTCATGTTAGTCAAGTCACCAAAAT 59.002 34.615 0.00 0.00 0.00 1.82
3213 8295 9.987272 GAAAAAGAAGTACACCTAGGTAAAGTA 57.013 33.333 15.80 10.31 0.00 2.24
3306 8388 2.551459 GCCATTGAGATCCACTACATGC 59.449 50.000 0.00 0.00 0.00 4.06
3412 8494 7.936496 TCATAGATGTGCCTAAACAAATCAA 57.064 32.000 0.00 0.00 36.84 2.57
3445 8527 7.227873 TCTTGTTATTAGTGGATCACAAACCA 58.772 34.615 0.00 0.00 36.74 3.67
3651 8817 1.462928 GGACCCCCATTCCACACAA 59.537 57.895 0.00 0.00 32.82 3.33
3669 8835 0.815213 CCACATGGGCTGGTACATCG 60.815 60.000 0.00 0.00 38.20 3.84
3828 9201 4.978580 GCAAGGAAAGAAACTGATGTGAAC 59.021 41.667 0.00 0.00 0.00 3.18
4293 9935 2.812591 GCATAAGCTCATCATGACCCAG 59.187 50.000 0.00 0.00 37.91 4.45
4475 10117 8.259049 CACGGATAGTGGTTTCAAATAAGTTA 57.741 34.615 0.00 0.00 46.77 2.24
4614 10256 6.305272 TCTGTCTGCTAAATCCTTTGAGAT 57.695 37.500 0.00 0.00 0.00 2.75
4736 10378 3.005554 CAATGTTGTAGCCTCAGAGGTG 58.994 50.000 18.37 0.99 37.80 4.00
4901 10543 5.962433 ACATAGTCGCGCAAGGTATATAAT 58.038 37.500 8.75 0.00 38.28 1.28
5000 10642 5.124457 GCATACAAGAAGGCAAGAATGAGAA 59.876 40.000 0.00 0.00 0.00 2.87
5030 10672 3.159472 TCCGCTAAACTGTCCAGAGTAA 58.841 45.455 0.40 0.00 0.00 2.24
5295 10937 5.876651 AAGTGGTAGATGCATGATGAGTA 57.123 39.130 2.46 0.00 0.00 2.59
5424 11066 8.519799 AGAAAACAAACCTACAGAATGAAGAA 57.480 30.769 0.00 0.00 39.69 2.52
5619 11261 7.759489 TGCTTACCTCAATGTGAAAATAAGT 57.241 32.000 0.00 0.00 0.00 2.24
5834 11476 0.537188 CCACAGTCTCTGGGCGTAAT 59.463 55.000 1.90 0.00 32.80 1.89
5947 11589 9.529325 CAGTAATAGTAAGCAACAACTAGCATA 57.471 33.333 0.00 0.00 32.01 3.14
5985 11627 4.402793 CCTATACCTGTACACAGAACAGCT 59.597 45.833 10.96 0.00 46.59 4.24
5992 11634 3.637229 CCACTCCCTATACCTGTACACAG 59.363 52.174 2.23 2.23 43.40 3.66
6038 11680 8.383619 CCAGAATCAACTTTTGTATACTTCTCG 58.616 37.037 4.17 0.00 0.00 4.04
6233 11875 2.244695 TGTACCACAGACCGAATGACT 58.755 47.619 0.00 0.00 0.00 3.41
6304 11946 9.924650 TCTGTTAGTTAACCTTTCTCATCTTAC 57.075 33.333 0.88 0.00 35.37 2.34
6347 11989 5.725362 CCTGGTTGTCCAAAAACAAAGTTA 58.275 37.500 0.00 0.00 43.81 2.24
6359 12002 0.257328 TGTTTCAGCCTGGTTGTCCA 59.743 50.000 10.46 3.40 42.05 4.02
6400 12043 1.067516 GTGGCACAAGCACAAACATCT 59.932 47.619 13.86 0.00 44.16 2.90
6429 12072 5.757886 CAAGAACGATTTTCTTGCCACTTA 58.242 37.500 12.49 0.00 45.76 2.24
6468 12111 9.671279 TGTATCAAACTATGAAGATGACACATT 57.329 29.630 0.00 0.00 42.54 2.71
6609 12253 3.123157 AGATGGCTGACACATGATAGC 57.877 47.619 0.00 3.24 35.49 2.97
6626 12270 6.792473 TGGTGGGACATTATATGAGGTTAGAT 59.208 38.462 0.00 0.00 44.52 1.98
6716 12364 2.027100 ACGAAAAGGGCTAGGAAAGAGG 60.027 50.000 0.00 0.00 0.00 3.69
6735 12383 5.464965 AATAAAAACGAGGAGCATGTACG 57.535 39.130 0.00 0.00 0.00 3.67
6745 12393 9.849166 ACCATAATACAACAAATAAAAACGAGG 57.151 29.630 0.00 0.00 0.00 4.63
6918 12568 8.815565 TTCTTGGTCACCTGCAAATATAAATA 57.184 30.769 0.00 0.00 0.00 1.40
6920 12570 7.716799 ATTCTTGGTCACCTGCAAATATAAA 57.283 32.000 0.00 0.00 0.00 1.40
6921 12571 8.995027 ATATTCTTGGTCACCTGCAAATATAA 57.005 30.769 0.00 0.00 0.00 0.98
6922 12572 8.995027 AATATTCTTGGTCACCTGCAAATATA 57.005 30.769 0.00 0.00 0.00 0.86
6924 12574 7.178274 ACAAATATTCTTGGTCACCTGCAAATA 59.822 33.333 0.00 0.00 0.00 1.40
6931 12590 7.690256 AGAGTAACAAATATTCTTGGTCACCT 58.310 34.615 0.00 0.00 26.71 4.00
7150 12850 3.855689 AAGAAATTTGGACGCCTGATG 57.144 42.857 0.00 0.00 0.00 3.07
7193 12893 9.923143 CTATTATCAAGATGGTACGAATGGTTA 57.077 33.333 0.00 0.00 0.00 2.85
7201 12901 9.314321 AGTCAAAACTATTATCAAGATGGTACG 57.686 33.333 0.00 0.00 32.59 3.67
7232 12932 6.042777 CAGCTTGAACACTCGATTATCCTAA 58.957 40.000 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.