Multiple sequence alignment - TraesCS3D01G021300

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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 TraesCS3D01G021300 chr3D 100.000 5245 0 0 1 5245 7035403 7030159 0.000000e+00 9686.0
1 TraesCS3D01G021300 chr3A 94.248 3842 167 24 511 4323 13349633 13353449 0.000000e+00 5821.0
2 TraesCS3D01G021300 chr3A 95.413 109 4 1 219 326 267070304 267070196 6.980000e-39 172.0
3 TraesCS3D01G021300 chr3B 92.280 3627 207 26 717 4323 8542453 8538880 0.000000e+00 5079.0
4 TraesCS3D01G021300 chr3B 96.012 326 12 1 1 325 8543326 8543001 3.600000e-146 529.0
5 TraesCS3D01G021300 chr3B 91.632 239 17 3 326 563 8542964 8542728 1.410000e-85 327.0
6 TraesCS3D01G021300 chr3B 95.327 107 5 0 220 326 672541608 672541714 2.510000e-38 171.0
7 TraesCS3D01G021300 chr3B 87.387 111 13 1 220 329 7491158 7491048 5.510000e-25 126.0
8 TraesCS3D01G021300 chr2D 92.199 923 68 3 4324 5245 354988107 354987188 0.000000e+00 1303.0
9 TraesCS3D01G021300 chr5D 91.927 929 68 6 4323 5245 176090203 176091130 0.000000e+00 1293.0
10 TraesCS3D01G021300 chr2A 85.008 627 88 4 4362 4985 141536511 141537134 2.670000e-177 632.0
11 TraesCS3D01G021300 chr2A 91.743 109 8 1 219 326 714526701 714526809 3.270000e-32 150.0
12 TraesCS3D01G021300 chr4A 81.575 711 122 7 4539 5243 562173432 562174139 3.520000e-161 579.0
13 TraesCS3D01G021300 chr4A 88.525 122 10 4 346 466 719070773 719070655 1.520000e-30 145.0
14 TraesCS3D01G021300 chr4A 79.464 112 16 6 358 466 470802736 470802843 7.290000e-09 73.1
15 TraesCS3D01G021300 chr1D 90.909 143 12 1 324 466 120036787 120036646 1.930000e-44 191.0
16 TraesCS3D01G021300 chr1D 97.143 105 3 0 225 329 120036922 120036818 1.500000e-40 178.0
17 TraesCS3D01G021300 chr1D 95.413 109 4 1 219 326 181630772 181630664 6.980000e-39 172.0
18 TraesCS3D01G021300 chr7D 96.396 111 4 0 219 329 535408158 535408048 3.230000e-42 183.0
19 TraesCS3D01G021300 chr7D 88.321 137 15 1 324 460 535408017 535407882 4.200000e-36 163.0
20 TraesCS3D01G021300 chr6B 97.196 107 2 1 220 326 716538330 716538435 4.170000e-41 180.0
21 TraesCS3D01G021300 chr7A 95.495 111 5 0 219 329 721122820 721122710 1.500000e-40 178.0
22 TraesCS3D01G021300 chr7A 87.879 66 5 2 402 466 727284573 727284636 2.030000e-09 75.0
23 TraesCS3D01G021300 chr7A 87.879 66 5 2 402 466 727310503 727310566 2.030000e-09 75.0
24 TraesCS3D01G021300 chr1B 94.643 112 6 0 219 330 42172006 42171895 1.940000e-39 174.0
25 TraesCS3D01G021300 chr1B 88.406 138 11 3 330 466 256907225 256907092 1.510000e-35 161.0
26 TraesCS3D01G021300 chr6D 86.667 105 13 1 325 429 333451343 333451446 1.190000e-21 115.0
27 TraesCS3D01G021300 chr2B 95.455 44 2 0 4322 4365 749541243 749541200 2.620000e-08 71.3
28 TraesCS3D01G021300 chr7B 83.784 74 9 2 394 466 615305406 615305477 3.390000e-07 67.6


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 TraesCS3D01G021300 chr3D 7030159 7035403 5244 True 9686.000000 9686 100.000 1 5245 1 chr3D.!!$R1 5244
1 TraesCS3D01G021300 chr3A 13349633 13353449 3816 False 5821.000000 5821 94.248 511 4323 1 chr3A.!!$F1 3812
2 TraesCS3D01G021300 chr3B 8538880 8543326 4446 True 1978.333333 5079 93.308 1 4323 3 chr3B.!!$R2 4322
3 TraesCS3D01G021300 chr2D 354987188 354988107 919 True 1303.000000 1303 92.199 4324 5245 1 chr2D.!!$R1 921
4 TraesCS3D01G021300 chr5D 176090203 176091130 927 False 1293.000000 1293 91.927 4323 5245 1 chr5D.!!$F1 922
5 TraesCS3D01G021300 chr2A 141536511 141537134 623 False 632.000000 632 85.008 4362 4985 1 chr2A.!!$F1 623
6 TraesCS3D01G021300 chr4A 562173432 562174139 707 False 579.000000 579 81.575 4539 5243 1 chr4A.!!$F2 704

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
169 170 0.104304 GCGGGGTATCATCTCGTGTT 59.896 55.000 0.00 0.00 0.00 3.32 F
645 867 0.249531 TACGACAACCGCAGAAGCAA 60.250 50.000 0.00 0.00 43.32 3.91 F
1268 1519 0.392336 TTTGCACAACCTCCATTGCC 59.608 50.000 0.00 0.00 33.86 4.52 F
1478 1731 0.734253 GAGTGCGCACGATGTTCTCT 60.734 55.000 32.94 13.91 36.20 3.10 F
2307 2567 2.061220 CCTGAGCAGTGACCCAAGA 58.939 57.895 0.00 0.00 0.00 3.02 F
3981 4245 0.247736 CAAGAAGGACGTGGCTAGCT 59.752 55.000 15.72 0.00 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1549 1802 0.173708 GGCCGAGTCAATCTCTTCGT 59.826 55.000 0.00 0.00 40.75 3.85 R
2407 2667 0.386838 AGCTCACCTTTTGCTGCAAC 59.613 50.000 15.72 0.71 35.54 4.17 R
3016 3277 2.168521 TGTAAGTACCTCTGCATGGCTC 59.831 50.000 5.87 0.72 0.00 4.70 R
3435 3697 8.729805 TTTTACTCCCTAAACGACACTTAAAA 57.270 30.769 0.00 0.00 0.00 1.52 R
4235 4504 0.114364 ACCACTGGCTTTAAAGGGGG 59.886 55.000 16.78 12.61 41.67 5.40 R
5046 5330 0.537188 AGGCCATGGACTCAGTTACG 59.463 55.000 16.83 0.00 0.00 3.18 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
142 143 1.656818 AACTGCATCCAATTCCCGCG 61.657 55.000 0.00 0.00 0.00 6.46
144 145 2.828549 GCATCCAATTCCCGCGGT 60.829 61.111 26.12 1.61 0.00 5.68
165 166 1.371758 CACGCGGGGTATCATCTCG 60.372 63.158 12.47 0.00 0.00 4.04
169 170 0.104304 GCGGGGTATCATCTCGTGTT 59.896 55.000 0.00 0.00 0.00 3.32
279 281 3.249559 GCGATTCCTTCTTGAAGGCATAG 59.750 47.826 21.16 17.34 39.80 2.23
299 301 6.017852 GCATAGCCTAGGAGTTGTGTATTTTC 60.018 42.308 14.75 0.00 0.00 2.29
303 305 5.163884 GCCTAGGAGTTGTGTATTTTCGTTC 60.164 44.000 14.75 0.00 0.00 3.95
314 316 6.037720 TGTGTATTTTCGTTCATGTTGTGTCT 59.962 34.615 0.00 0.00 0.00 3.41
384 422 1.153647 CGATGGTGTTCGGCTGCTA 60.154 57.895 0.00 0.00 35.50 3.49
385 423 0.739462 CGATGGTGTTCGGCTGCTAA 60.739 55.000 0.00 0.00 35.50 3.09
387 425 2.017049 GATGGTGTTCGGCTGCTAAAT 58.983 47.619 0.00 0.00 0.00 1.40
394 432 2.346099 TCGGCTGCTAAATTTTGCAC 57.654 45.000 20.94 16.94 35.25 4.57
402 440 7.222611 CGGCTGCTAAATTTTGCACTATTAATT 59.777 33.333 20.94 0.00 35.25 1.40
403 441 9.528018 GGCTGCTAAATTTTGCACTATTAATTA 57.472 29.630 20.94 0.00 35.25 1.40
452 490 2.043227 CAGAGGTCAGGGGTTATCCTC 58.957 57.143 0.00 0.00 43.29 3.71
458 496 3.371702 GGTCAGGGGTTATCCTCCTTTTC 60.372 52.174 0.00 0.00 33.94 2.29
459 497 3.265995 GTCAGGGGTTATCCTCCTTTTCA 59.734 47.826 0.00 0.00 33.94 2.69
504 542 4.901881 CGTCATGAAACTAACGTTCCAAAC 59.098 41.667 2.82 0.00 31.66 2.93
560 598 1.749634 ACGAGGACCCGAGATTGTTAG 59.250 52.381 9.04 0.00 0.00 2.34
602 817 2.864343 GCTAGTACACCGGCTTGTAATG 59.136 50.000 13.60 0.32 33.73 1.90
642 864 2.279582 ATCTACGACAACCGCAGAAG 57.720 50.000 0.00 0.00 43.19 2.85
643 865 0.388134 TCTACGACAACCGCAGAAGC 60.388 55.000 0.00 0.00 37.70 3.86
644 866 0.666274 CTACGACAACCGCAGAAGCA 60.666 55.000 0.00 0.00 43.32 3.91
645 867 0.249531 TACGACAACCGCAGAAGCAA 60.250 50.000 0.00 0.00 43.32 3.91
646 868 1.205064 CGACAACCGCAGAAGCAAG 59.795 57.895 0.00 0.00 42.27 4.01
647 869 1.576421 GACAACCGCAGAAGCAAGG 59.424 57.895 0.00 0.00 42.27 3.61
648 870 2.256461 CAACCGCAGAAGCAAGGC 59.744 61.111 0.00 0.00 42.27 4.35
649 871 2.113986 AACCGCAGAAGCAAGGCT 59.886 55.556 0.00 0.00 42.56 4.58
650 872 0.955428 CAACCGCAGAAGCAAGGCTA 60.955 55.000 0.00 0.00 38.25 3.93
651 873 0.674895 AACCGCAGAAGCAAGGCTAG 60.675 55.000 0.00 0.00 38.25 3.42
652 874 1.078848 CCGCAGAAGCAAGGCTAGT 60.079 57.895 0.00 0.00 38.25 2.57
653 875 0.674895 CCGCAGAAGCAAGGCTAGTT 60.675 55.000 0.00 0.00 38.25 2.24
654 876 1.160137 CGCAGAAGCAAGGCTAGTTT 58.840 50.000 0.00 0.00 38.25 2.66
655 877 1.537202 CGCAGAAGCAAGGCTAGTTTT 59.463 47.619 0.00 0.00 38.25 2.43
656 878 2.666619 CGCAGAAGCAAGGCTAGTTTTG 60.667 50.000 0.00 0.00 38.25 2.44
657 879 2.294512 GCAGAAGCAAGGCTAGTTTTGT 59.705 45.455 9.21 0.00 38.25 2.83
658 880 3.854784 GCAGAAGCAAGGCTAGTTTTGTG 60.855 47.826 9.21 0.00 38.25 3.33
659 881 2.294512 AGAAGCAAGGCTAGTTTTGTGC 59.705 45.455 9.21 0.00 38.25 4.57
660 882 1.691196 AGCAAGGCTAGTTTTGTGCA 58.309 45.000 7.72 0.00 36.99 4.57
661 883 1.338020 AGCAAGGCTAGTTTTGTGCAC 59.662 47.619 10.75 10.75 36.99 4.57
739 973 3.111484 TCTCTCTCTCTCTAGCAGGTGA 58.889 50.000 0.00 0.00 0.00 4.02
1188 1439 2.603473 CACGACCCTCCTCACCCA 60.603 66.667 0.00 0.00 0.00 4.51
1220 1471 8.023021 TGGCATACATATATACTCCTTCCATC 57.977 38.462 0.00 0.00 0.00 3.51
1268 1519 0.392336 TTTGCACAACCTCCATTGCC 59.608 50.000 0.00 0.00 33.86 4.52
1280 1533 4.898861 ACCTCCATTGCCAGTTTAAGAAAA 59.101 37.500 0.00 0.00 0.00 2.29
1281 1534 5.365314 ACCTCCATTGCCAGTTTAAGAAAAA 59.635 36.000 0.00 0.00 0.00 1.94
1307 1560 9.513906 AAAAACAATCTTGGGGGTAATTTATTG 57.486 29.630 0.00 0.00 0.00 1.90
1478 1731 0.734253 GAGTGCGCACGATGTTCTCT 60.734 55.000 32.94 13.91 36.20 3.10
1499 1752 4.314440 GACAGTGTGGCCGAGGCA 62.314 66.667 16.65 0.00 44.11 4.75
1752 2005 6.295067 GCCTAGGTGTTGATTGTTTAACCAAT 60.295 38.462 11.31 0.00 37.74 3.16
1779 2036 6.001449 ACTGCATAGTGGCCTATCTAAAAA 57.999 37.500 3.32 0.00 35.34 1.94
1836 2093 5.945784 AGCATATGACTTAGAAGTGGCAAAA 59.054 36.000 6.97 0.00 39.88 2.44
1925 2185 4.514066 ACAATTTCTACCGTGAAGTCAACC 59.486 41.667 0.00 0.00 0.00 3.77
1963 2223 6.294361 ACAAAGTTTCTAGCAAAAACCCTT 57.706 33.333 2.75 0.00 37.33 3.95
2004 2264 6.774170 TGCAGGCATCTAATGATTATCTTGTT 59.226 34.615 0.00 0.00 0.00 2.83
2055 2315 6.663734 CCTCCCTGGTCTGTTAATCTTATTT 58.336 40.000 0.00 0.00 0.00 1.40
2079 2339 8.684386 TTGGTGTCTTTTACTTCACATATTCA 57.316 30.769 0.00 0.00 33.17 2.57
2128 2388 9.744468 TTTTAGAATTTTACTTTGAGACTTGCC 57.256 29.630 0.00 0.00 0.00 4.52
2130 2390 7.588497 AGAATTTTACTTTGAGACTTGCCTT 57.412 32.000 0.00 0.00 0.00 4.35
2137 2397 4.953579 ACTTTGAGACTTGCCTTGGTAAAA 59.046 37.500 0.00 0.00 0.00 1.52
2138 2398 4.911514 TTGAGACTTGCCTTGGTAAAAC 57.088 40.909 0.00 0.00 0.00 2.43
2139 2399 3.892284 TGAGACTTGCCTTGGTAAAACA 58.108 40.909 0.00 0.00 0.00 2.83
2175 2435 7.552687 AGAACTATCGGCAATCTTAAAATCACA 59.447 33.333 0.00 0.00 0.00 3.58
2304 2564 2.149383 AAGCCTGAGCAGTGACCCA 61.149 57.895 0.00 0.00 43.56 4.51
2307 2567 2.061220 CCTGAGCAGTGACCCAAGA 58.939 57.895 0.00 0.00 0.00 3.02
2774 3035 8.764287 CAAATATGCATAAGATCGTGAGTGTAA 58.236 33.333 11.13 0.00 0.00 2.41
3016 3277 3.871594 GAGGAATGTCATAGTTTCACCGG 59.128 47.826 0.00 0.00 0.00 5.28
3039 3300 3.134458 GCCATGCAGAGGTACTTACATC 58.866 50.000 9.48 0.00 41.55 3.06
3140 3401 8.845413 ATCTCTCATTAAGGCAAACATATCTC 57.155 34.615 0.00 0.00 0.00 2.75
3144 3405 9.466497 TCTCATTAAGGCAAACATATCTCTTTT 57.534 29.630 0.00 0.00 0.00 2.27
3414 3676 9.755064 AACAATTTTATCTCTCATTTAACGTCG 57.245 29.630 0.00 0.00 0.00 5.12
3435 3697 7.074502 CGTCGTAAACTGTACTTTCTAGTTCT 58.925 38.462 0.00 0.00 33.82 3.01
3566 3830 1.734163 AGCCAACACGGTAATAGTGC 58.266 50.000 0.00 0.00 42.94 4.40
3585 3849 6.554334 AGTGCGTTCTAAATTGTTGTGTAT 57.446 33.333 0.00 0.00 0.00 2.29
3605 3869 1.005037 CAGTACCAACTGCAGGCGA 60.005 57.895 19.93 0.00 46.28 5.54
3745 4009 3.005205 CTATGGCGCCATAGCAACA 57.995 52.632 46.43 29.37 46.03 3.33
3855 4119 3.288964 ACAAGGTACTCCGTCTCCTATG 58.711 50.000 0.00 0.00 38.49 2.23
3860 4124 3.825014 GGTACTCCGTCTCCTATGCATAA 59.175 47.826 8.00 0.00 0.00 1.90
3935 4199 6.203647 TGTACTATCATAACAACCGACATCG 58.796 40.000 0.00 0.00 39.44 3.84
3936 4200 5.258456 ACTATCATAACAACCGACATCGT 57.742 39.130 0.00 0.00 37.74 3.73
3981 4245 0.247736 CAAGAAGGACGTGGCTAGCT 59.752 55.000 15.72 0.00 0.00 3.32
3982 4246 0.533032 AAGAAGGACGTGGCTAGCTC 59.467 55.000 15.72 3.73 0.00 4.09
3995 4259 0.382515 CTAGCTCCGTGGAGTGCTAC 59.617 60.000 16.88 0.45 43.70 3.58
4000 4264 1.153369 CCGTGGAGTGCTACATGGG 60.153 63.158 13.62 3.00 45.03 4.00
4010 4274 0.988678 GCTACATGGGGGAGAAGGGT 60.989 60.000 0.00 0.00 0.00 4.34
4028 4292 2.567883 TACCACAGGGGAGGAGGCT 61.568 63.158 0.00 0.00 41.15 4.58
4052 4316 3.654201 GCAATCGCCGCCATGATA 58.346 55.556 0.00 0.00 0.00 2.15
4070 4334 4.742012 TGATAGAGGATAGTTGGAGGACC 58.258 47.826 0.00 0.00 0.00 4.46
4078 4342 1.747444 AGTTGGAGGACCATGAACCT 58.253 50.000 9.76 9.76 46.34 3.50
4079 4343 2.915869 AGTTGGAGGACCATGAACCTA 58.084 47.619 9.92 0.00 46.34 3.08
4090 4354 2.578786 CATGAACCTAGCATGCATGGA 58.421 47.619 27.34 12.04 37.00 3.41
4091 4355 3.154710 CATGAACCTAGCATGCATGGAT 58.845 45.455 27.34 19.85 37.00 3.41
4100 4364 0.806868 CATGCATGGATATGGACCGC 59.193 55.000 19.40 0.00 37.47 5.68
4103 4367 1.301637 CATGGATATGGACCGCGCA 60.302 57.895 8.75 0.00 0.00 6.09
4106 4370 0.884259 TGGATATGGACCGCGCATTG 60.884 55.000 8.75 0.00 0.00 2.82
4169 4433 1.826921 GGTCATCTACCTCCGCGGA 60.827 63.158 29.03 29.03 45.75 5.54
4235 4504 2.121538 GCTTTTCCTCGCCCCCATC 61.122 63.158 0.00 0.00 0.00 3.51
4243 4512 3.100514 CGCCCCCATCCCCCTTTA 61.101 66.667 0.00 0.00 0.00 1.85
4251 4520 1.007118 CCATCCCCCTTTAAAGCCAGT 59.993 52.381 9.86 0.00 0.00 4.00
4279 4548 4.446385 GCAACATACGCGTAATCCTGAATA 59.554 41.667 24.55 0.00 0.00 1.75
4437 4709 2.525124 ATGCGGTCCAACTCCACCA 61.525 57.895 0.00 0.00 32.33 4.17
4444 4716 2.100749 GGTCCAACTCCACCACAAAAAG 59.899 50.000 0.00 0.00 32.33 2.27
4505 4787 2.088423 CGCTCCGAATAGAGGCTCTAT 58.912 52.381 27.44 27.44 41.19 1.98
4558 4840 2.990479 GCCCCTCGTCCTCAATGT 59.010 61.111 0.00 0.00 0.00 2.71
4617 4901 4.341502 ACAATGGCGTTGCGGTGC 62.342 61.111 19.02 0.00 41.69 5.01
4639 4923 1.490490 TCCATAGCTCCCACATTGTCC 59.510 52.381 0.00 0.00 0.00 4.02
4645 4929 0.833287 CTCCCACATTGTCCGGAGAT 59.167 55.000 18.71 0.00 43.96 2.75
4797 5081 1.668419 GTGCAAAGACACAGTGGAGT 58.332 50.000 5.31 0.00 40.40 3.85
4818 5102 2.106566 AGAATGTGGTCGATGCTCTCT 58.893 47.619 0.00 0.00 0.00 3.10
4857 5141 3.080641 CATGCCTCCTGGTGGTCA 58.919 61.111 15.72 13.73 35.27 4.02
4935 5219 1.760268 CGAAGAAGCGGCATCTCAGC 61.760 60.000 8.32 1.04 36.06 4.26
5034 5318 1.134560 ACCGAGTATTCGCCACTCTTC 59.865 52.381 1.48 0.00 45.38 2.87
5046 5330 1.920835 ACTCTTCTCCCAGGCCCAC 60.921 63.158 0.00 0.00 0.00 4.61
5088 5372 1.451936 GTTCAGGTGGGTGTGAGCT 59.548 57.895 0.00 0.00 0.00 4.09
5114 5398 3.370527 CGGTCCCAAAGGATCATGTACTT 60.371 47.826 0.00 0.00 44.45 2.24
5180 5465 1.006102 CGAGTTCGTCAAGGCCTGT 60.006 57.895 5.69 0.00 34.11 4.00
5181 5466 0.242825 CGAGTTCGTCAAGGCCTGTA 59.757 55.000 5.69 0.00 34.11 2.74
5187 5472 0.892755 CGTCAAGGCCTGTACCACTA 59.107 55.000 5.69 0.00 0.00 2.74
5197 5482 3.904717 CCTGTACCACTATCCTCTCTGT 58.095 50.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 115 7.255590 CGGGAATTGGATGCAGTTATTTCTATT 60.256 37.037 0.00 0.00 0.00 1.73
142 143 2.028631 GATACCCCGCGTGCTACC 59.971 66.667 4.92 0.00 0.00 3.18
144 145 0.826256 AGATGATACCCCGCGTGCTA 60.826 55.000 4.92 0.00 0.00 3.49
279 281 4.251268 ACGAAAATACACAACTCCTAGGC 58.749 43.478 2.96 0.00 0.00 3.93
299 301 5.590104 TGATACAAGACACAACATGAACG 57.410 39.130 0.00 0.00 0.00 3.95
303 305 8.893219 ATACCTATGATACAAGACACAACATG 57.107 34.615 0.00 0.00 0.00 3.21
314 316 5.326900 TGAGGCCGTATACCTATGATACAA 58.673 41.667 0.00 0.00 37.77 2.41
402 440 4.333372 CACGATGCATGCAGCCATATATTA 59.667 41.667 28.76 0.00 44.83 0.98
403 441 3.128068 CACGATGCATGCAGCCATATATT 59.872 43.478 28.76 7.39 44.83 1.28
404 442 2.681344 CACGATGCATGCAGCCATATAT 59.319 45.455 28.76 8.20 44.83 0.86
438 476 3.537337 TGAAAAGGAGGATAACCCCTGA 58.463 45.455 0.72 0.00 37.09 3.86
440 478 5.348259 TTTTGAAAAGGAGGATAACCCCT 57.652 39.130 0.00 0.00 38.08 4.79
466 504 5.799827 TCATGACGTCCACATCCATATTA 57.200 39.130 14.12 0.00 0.00 0.98
467 505 4.687901 TCATGACGTCCACATCCATATT 57.312 40.909 14.12 0.00 0.00 1.28
470 508 3.009723 GTTTCATGACGTCCACATCCAT 58.990 45.455 14.12 0.00 0.00 3.41
471 509 2.038426 AGTTTCATGACGTCCACATCCA 59.962 45.455 14.12 0.00 0.00 3.41
472 510 2.699954 AGTTTCATGACGTCCACATCC 58.300 47.619 14.12 0.00 0.00 3.51
478 516 3.122445 GGAACGTTAGTTTCATGACGTCC 59.878 47.826 14.12 7.88 46.66 4.79
504 542 0.309922 AGTGACACTACACACCGACG 59.690 55.000 6.24 0.00 42.45 5.12
551 589 3.709653 TGAAGCCGGGATACTAACAATCT 59.290 43.478 2.18 0.00 0.00 2.40
560 598 2.178235 GCCGTTGAAGCCGGGATAC 61.178 63.158 2.18 0.00 45.57 2.24
629 851 1.576421 CCTTGCTTCTGCGGTTGTC 59.424 57.895 0.00 0.00 43.34 3.18
642 864 1.770957 GTGCACAAAACTAGCCTTGC 58.229 50.000 13.17 1.00 0.00 4.01
643 865 1.925946 GCGTGCACAAAACTAGCCTTG 60.926 52.381 18.64 3.45 0.00 3.61
644 866 0.310854 GCGTGCACAAAACTAGCCTT 59.689 50.000 18.64 0.00 0.00 4.35
645 867 0.535102 AGCGTGCACAAAACTAGCCT 60.535 50.000 18.64 0.00 0.00 4.58
646 868 0.110192 GAGCGTGCACAAAACTAGCC 60.110 55.000 18.64 1.05 0.00 3.93
647 869 0.451135 CGAGCGTGCACAAAACTAGC 60.451 55.000 18.64 10.09 0.00 3.42
648 870 0.451135 GCGAGCGTGCACAAAACTAG 60.451 55.000 18.64 9.42 34.15 2.57
649 871 1.567537 GCGAGCGTGCACAAAACTA 59.432 52.632 18.64 0.00 34.15 2.24
650 872 2.327940 GCGAGCGTGCACAAAACT 59.672 55.556 18.64 8.03 34.15 2.66
651 873 3.085010 CGCGAGCGTGCACAAAAC 61.085 61.111 18.64 2.71 34.15 2.43
661 883 0.028242 ACTGAATAGAGACGCGAGCG 59.972 55.000 15.93 16.38 46.03 5.03
1092 1343 1.595382 GGCGTTGATCATCCTCGGG 60.595 63.158 0.00 0.00 0.00 5.14
1188 1439 6.408548 GGAGTATATATGTATGCCATGCCTGT 60.409 42.308 0.00 0.00 34.86 4.00
1220 1471 3.341823 ACAAGCAAAGGTAGATCTGCAG 58.658 45.455 13.14 7.63 37.26 4.41
1281 1534 9.513906 CAATAAATTACCCCCAAGATTGTTTTT 57.486 29.630 0.00 0.00 0.00 1.94
1359 1612 9.895138 AGAAATTGATATGCAGGCTTAAATTTT 57.105 25.926 0.00 0.00 0.00 1.82
1401 1654 2.162608 CCTCCGACCTCTGCTTATATCG 59.837 54.545 0.00 0.00 0.00 2.92
1408 1661 1.680651 CACTCCTCCGACCTCTGCT 60.681 63.158 0.00 0.00 0.00 4.24
1478 1731 3.207547 CTCGGCCACACTGTCGTCA 62.208 63.158 2.24 0.00 0.00 4.35
1499 1752 3.777106 AGTGTGTCCATCAATGTCACT 57.223 42.857 12.98 0.00 34.35 3.41
1549 1802 0.173708 GGCCGAGTCAATCTCTTCGT 59.826 55.000 0.00 0.00 40.75 3.85
1752 2005 4.483950 AGATAGGCCACTATGCAGTTCTA 58.516 43.478 5.01 0.00 39.97 2.10
1779 2036 2.221055 GTCGTTCAAGTCGCACAGAAAT 59.779 45.455 0.00 0.00 0.00 2.17
1874 2133 3.129113 CGATTGAAGGCAAATGGATGTCA 59.871 43.478 0.00 0.00 37.59 3.58
1925 2185 4.468095 ACTTTGTTCTGGAAAACGATCG 57.532 40.909 14.88 14.88 31.58 3.69
1963 2223 8.644216 AGATGCCTGCATATAAAATTCAATGAA 58.356 29.630 4.30 0.00 36.70 2.57
2027 2287 2.868964 TAACAGACCAGGGAGGCTAT 57.131 50.000 0.00 0.00 43.14 2.97
2055 2315 8.684386 TTGAATATGTGAAGTAAAAGACACCA 57.316 30.769 0.00 0.00 33.08 4.17
2079 2339 7.875327 AAGTGTAGTTGTGAAAGTACCATTT 57.125 32.000 0.00 0.00 0.00 2.32
2137 2397 4.840271 CCGATAGTTCTTTTAAGGGGTGT 58.160 43.478 0.00 0.00 0.00 4.16
2138 2398 3.626217 GCCGATAGTTCTTTTAAGGGGTG 59.374 47.826 0.00 0.00 0.00 4.61
2139 2399 3.264964 TGCCGATAGTTCTTTTAAGGGGT 59.735 43.478 0.00 0.00 0.00 4.95
2407 2667 0.386838 AGCTCACCTTTTGCTGCAAC 59.613 50.000 15.72 0.71 35.54 4.17
3016 3277 2.168521 TGTAAGTACCTCTGCATGGCTC 59.831 50.000 5.87 0.72 0.00 4.70
3039 3300 9.632807 TTCTTGAAAATAATTGAATTACACCCG 57.367 29.630 0.00 0.00 0.00 5.28
3435 3697 8.729805 TTTTACTCCCTAAACGACACTTAAAA 57.270 30.769 0.00 0.00 0.00 1.52
3566 3830 6.370593 ACTGCATACACAACAATTTAGAACG 58.629 36.000 0.00 0.00 0.00 3.95
3605 3869 7.093201 CCATTGGGCCTCTTGCATATAATATTT 60.093 37.037 4.53 0.00 43.89 1.40
3730 3994 0.607762 TCTTTGTTGCTATGGCGCCA 60.608 50.000 34.80 34.80 42.25 5.69
3745 4009 4.884668 TGTCCACTCGAATACCTTCTTT 57.115 40.909 0.00 0.00 0.00 2.52
3855 4119 9.090692 AGAAATGCAACATTAATTCACTTATGC 57.909 29.630 0.00 0.00 0.00 3.14
3860 4124 7.660112 TGACAGAAATGCAACATTAATTCACT 58.340 30.769 0.00 0.00 0.00 3.41
3908 4172 8.958119 ATGTCGGTTGTTATGATAGTACATTT 57.042 30.769 0.00 0.00 0.00 2.32
3935 4199 2.925563 CCCCAACTACATTTACGTCGAC 59.074 50.000 5.18 5.18 0.00 4.20
3936 4200 2.824936 TCCCCAACTACATTTACGTCGA 59.175 45.455 0.00 0.00 0.00 4.20
3940 4204 4.998672 TGTTCTTCCCCAACTACATTTACG 59.001 41.667 0.00 0.00 0.00 3.18
3944 4208 5.319043 TCTTGTTCTTCCCCAACTACATT 57.681 39.130 0.00 0.00 0.00 2.71
3948 4212 3.977999 TCCTTCTTGTTCTTCCCCAACTA 59.022 43.478 0.00 0.00 0.00 2.24
3981 4245 1.613317 CCCATGTAGCACTCCACGGA 61.613 60.000 0.00 0.00 0.00 4.69
3982 4246 1.153369 CCCATGTAGCACTCCACGG 60.153 63.158 0.00 0.00 0.00 4.94
3995 4259 0.623324 TGGTACCCTTCTCCCCCATG 60.623 60.000 10.07 0.00 0.00 3.66
4000 4264 1.272554 CCCTGTGGTACCCTTCTCCC 61.273 65.000 10.07 0.00 0.00 4.30
4010 4274 2.040606 GCCTCCTCCCCTGTGGTA 59.959 66.667 0.00 0.00 34.77 3.25
4013 4277 2.608988 ACAGCCTCCTCCCCTGTG 60.609 66.667 0.00 0.00 38.32 3.66
4070 4334 2.578786 TCCATGCATGCTAGGTTCATG 58.421 47.619 21.69 11.76 43.02 3.07
4078 4342 2.355007 CGGTCCATATCCATGCATGCTA 60.355 50.000 21.69 14.41 0.00 3.49
4079 4343 1.612462 CGGTCCATATCCATGCATGCT 60.612 52.381 21.69 12.66 0.00 3.79
4090 4354 0.662619 CAACAATGCGCGGTCCATAT 59.337 50.000 8.83 0.00 0.00 1.78
4091 4355 1.987704 GCAACAATGCGCGGTCCATA 61.988 55.000 8.83 0.00 43.83 2.74
4124 4388 2.612972 CGACCTTGCTATGTTCACCACT 60.613 50.000 0.00 0.00 0.00 4.00
4235 4504 0.114364 ACCACTGGCTTTAAAGGGGG 59.886 55.000 16.78 12.61 41.67 5.40
4240 4509 2.497675 TGTTGCAACCACTGGCTTTAAA 59.502 40.909 26.14 0.00 0.00 1.52
4243 4512 1.122227 ATGTTGCAACCACTGGCTTT 58.878 45.000 26.14 0.00 0.00 3.51
4251 4520 1.509703 TTACGCGTATGTTGCAACCA 58.490 45.000 26.14 14.70 0.00 3.67
4350 4621 8.004801 CCCCATCCCTTCTTTAATATAAAGTGT 58.995 37.037 9.09 0.00 0.00 3.55
4437 4709 8.422566 AGTAGTTAGACTAGTTGCTCTTTTTGT 58.577 33.333 0.00 0.00 30.49 2.83
4444 4716 5.502869 GCGAGAGTAGTTAGACTAGTTGCTC 60.503 48.000 0.00 0.00 34.66 4.26
4558 4840 2.159212 CCATACGTACGATTGTCCACCA 60.159 50.000 24.41 0.00 0.00 4.17
4595 4879 1.729131 CGCAACGCCATTGTGTTCC 60.729 57.895 0.00 0.00 43.13 3.62
4617 4901 3.209410 GACAATGTGGGAGCTATGGAAG 58.791 50.000 0.00 0.00 0.00 3.46
4639 4923 1.249407 GGTAGGGCTGTCTATCTCCG 58.751 60.000 0.00 0.00 0.00 4.63
4645 4929 2.398588 CAAGGATGGTAGGGCTGTCTA 58.601 52.381 0.00 0.00 0.00 2.59
4797 5081 3.291584 AGAGAGCATCGACCACATTCTA 58.708 45.455 0.00 0.00 42.67 2.10
4857 5141 2.281761 CTTGCCAGGCACGGACTT 60.282 61.111 15.89 0.00 38.71 3.01
5034 5318 2.267961 GTTACGTGGGCCTGGGAG 59.732 66.667 4.53 0.00 0.00 4.30
5046 5330 0.537188 AGGCCATGGACTCAGTTACG 59.463 55.000 16.83 0.00 0.00 3.18
5088 5372 0.619255 TGATCCTTTGGGACCGCCTA 60.619 55.000 0.00 0.00 45.43 3.93
5144 5429 1.881602 GACGTGGGCTAGAGACGTT 59.118 57.895 13.37 1.45 45.84 3.99
5180 5465 3.117474 CCAGGACAGAGAGGATAGTGGTA 60.117 52.174 0.00 0.00 0.00 3.25
5181 5466 2.358721 CCAGGACAGAGAGGATAGTGGT 60.359 54.545 0.00 0.00 0.00 4.16
5187 5472 0.712979 TCCACCAGGACAGAGAGGAT 59.287 55.000 0.00 0.00 39.61 3.24


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

AutoCloner maintained by Alex Coulton.