Multiple sequence alignment - TraesCS3D01G225600

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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 TraesCS3D01G225600 chr3D 100.000 7954 0 0 1 7954 307226153 307234106 0.000000e+00 14689
1 TraesCS3D01G225600 chr3B 95.543 6058 167 49 13 6016 414027229 414021221 0.000000e+00 9596
2 TraesCS3D01G225600 chr3B 96.954 1346 35 4 6091 7435 414021230 414019890 0.000000e+00 2254
3 TraesCS3D01G225600 chr3B 90.086 232 11 5 7734 7954 414019418 414019188 2.810000e-74 291
4 TraesCS3D01G225600 chr3B 93.789 161 10 0 7449 7609 414019629 414019469 7.970000e-60 243
5 TraesCS3D01G225600 chr3A 93.894 2686 87 42 44 2688 426873459 426870810 0.000000e+00 3980
6 TraesCS3D01G225600 chr3A 95.443 1580 62 9 3721 5297 426867689 426866117 0.000000e+00 2510
7 TraesCS3D01G225600 chr3A 97.482 1231 24 2 6205 7435 426865340 426864117 0.000000e+00 2095
8 TraesCS3D01G225600 chr3A 93.439 945 54 5 2782 3724 426870811 426869873 0.000000e+00 1395
9 TraesCS3D01G225600 chr3A 89.788 803 44 13 5335 6131 426866116 426865346 0.000000e+00 994
10 TraesCS3D01G225600 chr3A 95.010 521 23 2 7436 7954 426864090 426863571 0.000000e+00 815
11 TraesCS3D01G225600 chr3A 91.753 97 8 0 2687 2783 532855334 532855430 1.390000e-27 135
12 TraesCS3D01G225600 chr1A 83.095 420 71 0 2077 2496 577469417 577469836 4.500000e-102 383
13 TraesCS3D01G225600 chr1A 77.507 369 77 5 2131 2496 566012981 566012616 4.830000e-52 217
14 TraesCS3D01G225600 chr1A 77.850 307 50 13 3191 3494 577471079 577471370 2.950000e-39 174
15 TraesCS3D01G225600 chr1A 87.963 108 13 0 7629 7736 498162256 498162149 2.330000e-25 128
16 TraesCS3D01G225600 chr1B 81.384 419 78 0 2077 2495 669158895 669159313 7.640000e-90 342
17 TraesCS3D01G225600 chr1B 79.479 307 45 14 3191 3494 669160210 669160501 1.350000e-47 202
18 TraesCS3D01G225600 chr1D 77.057 401 85 6 2100 2496 471622406 471622009 2.890000e-54 224
19 TraesCS3D01G225600 chr1D 78.859 298 47 13 3200 3494 480890684 480890968 3.790000e-43 187
20 TraesCS3D01G225600 chr7B 93.269 104 7 0 7629 7732 445020280 445020177 3.840000e-33 154
21 TraesCS3D01G225600 chr2D 93.069 101 7 0 2685 2785 82095180 82095080 1.790000e-31 148
22 TraesCS3D01G225600 chr2D 92.857 98 6 1 2690 2786 382456174 382456077 2.990000e-29 141
23 TraesCS3D01G225600 chr5B 90.000 100 10 0 2687 2786 705615822 705615723 6.480000e-26 130
24 TraesCS3D01G225600 chr4D 90.722 97 9 0 2687 2783 454429024 454429120 6.480000e-26 130
25 TraesCS3D01G225600 chr5A 88.182 110 10 3 2676 2783 660796787 660796679 2.330000e-25 128
26 TraesCS3D01G225600 chr5A 89.109 101 11 0 2687 2787 9653194 9653294 8.380000e-25 126
27 TraesCS3D01G225600 chr6D 88.462 104 12 0 7629 7732 128921623 128921726 8.380000e-25 126
28 TraesCS3D01G225600 chr6D 87.156 109 11 3 7629 7736 459064845 459064739 3.900000e-23 121
29 TraesCS3D01G225600 chr7D 88.350 103 12 0 7630 7732 484366909 484367011 3.010000e-24 124
30 TraesCS3D01G225600 chr4A 87.736 106 9 4 7629 7732 615207235 615207132 3.900000e-23 121
31 TraesCS3D01G225600 chr4A 85.437 103 15 0 7630 7732 706248802 706248700 3.040000e-19 108
32 TraesCS3D01G225600 chr2B 87.500 104 13 0 7629 7732 92976494 92976391 3.900000e-23 121


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 TraesCS3D01G225600 chr3D 307226153 307234106 7953 False 14689.000000 14689 100.0000 1 7954 1 chr3D.!!$F1 7953
1 TraesCS3D01G225600 chr3B 414019188 414027229 8041 True 3096.000000 9596 94.0930 13 7954 4 chr3B.!!$R1 7941
2 TraesCS3D01G225600 chr3A 426863571 426873459 9888 True 1964.833333 3980 94.1760 44 7954 6 chr3A.!!$R1 7910
3 TraesCS3D01G225600 chr1A 577469417 577471370 1953 False 278.500000 383 80.4725 2077 3494 2 chr1A.!!$F1 1417
4 TraesCS3D01G225600 chr1B 669158895 669160501 1606 False 272.000000 342 80.4315 2077 3494 2 chr1B.!!$F1 1417

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
707 763 0.336737 GAGGAGGAGGAGGAACAGGA 59.663 60.000 0.00 0.00 0.00 3.86 F
906 967 0.934901 CGTGTGTCTGACCGTGTCTG 60.935 60.000 5.17 5.42 33.15 3.51 F
1575 1636 0.743688 ACATGCAAAAGTTGACCGCA 59.256 45.000 0.00 0.00 36.95 5.69 F
1593 1654 1.203523 GCATTCTGTGACCTCGAGAGT 59.796 52.381 15.71 10.28 0.00 3.24 F
2861 3587 1.208293 GCTGGTTGGGTAGAGAAGAGG 59.792 57.143 0.00 0.00 0.00 3.69 F
3080 3807 2.806244 CCTTGTGGTGGTAGTCTTTTCG 59.194 50.000 0.00 0.00 0.00 3.46 F
3081 3808 3.463944 CTTGTGGTGGTAGTCTTTTCGT 58.536 45.455 0.00 0.00 0.00 3.85 F
3791 6753 5.049198 TCTGCTTCTGTGTGAAAAGCTAATG 60.049 40.000 7.71 0.00 44.45 1.90 F
4953 7916 3.847780 ACTGACTAGGACACTCTCTACCT 59.152 47.826 0.00 0.00 36.65 3.08 F
5772 8745 0.032416 ACCTAGGACTACACCGCCAT 60.032 55.000 17.98 0.00 34.73 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1542 1603 0.524816 GCATGTGAATTGCGAGCTGG 60.525 55.000 0.00 0.0 0.00 4.85 R
2818 3543 3.937814 TGGCACTAGTTGGTACAGATTG 58.062 45.455 0.00 0.0 42.39 2.67 R
3057 3784 2.112279 AAGACTACCACCACAAGGGA 57.888 50.000 0.00 0.0 41.15 4.20 R
3080 3807 3.057245 GGAGATGCTCCTTTTTGGTTGAC 60.057 47.826 6.23 0.0 46.41 3.18 R
3999 6961 1.741706 ACAATGCCTGAGATGCTTTCG 59.258 47.619 0.00 0.0 0.00 3.46 R
4950 7913 1.881973 CAGCACTGCATAAACACAGGT 59.118 47.619 3.30 0.0 0.00 4.00 R
4951 7914 1.881973 ACAGCACTGCATAAACACAGG 59.118 47.619 3.30 0.0 0.00 4.00 R
5484 8451 0.597377 GCTGCCAACTGAAAAACCCG 60.597 55.000 0.00 0.0 0.00 5.28 R
6071 9045 1.076332 CAACCAGCCTAACAGTACGC 58.924 55.000 0.00 0.0 0.00 4.42 R
7683 10905 0.036732 TGGCGATTCCAAGAAGTGCT 59.963 50.000 0.00 0.0 43.21 4.40 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
32 33 9.734984 TCGGGAAATTAGAGAAGAGTAATTTTT 57.265 29.630 0.00 0.00 38.41 1.94
97 99 1.299165 CGAGCTCCGTGGTTATCCG 60.299 63.158 8.47 0.00 36.30 4.18
234 240 4.893608 TCATCGGAGTGAGAATTCAAACA 58.106 39.130 8.44 2.23 34.49 2.83
239 245 5.642063 TCGGAGTGAGAATTCAAACAATACC 59.358 40.000 8.44 6.99 34.49 2.73
262 271 7.466804 ACCAGTCCAAAAATAGATTAGAACCA 58.533 34.615 0.00 0.00 0.00 3.67
263 272 8.116026 ACCAGTCCAAAAATAGATTAGAACCAT 58.884 33.333 0.00 0.00 0.00 3.55
264 273 9.627123 CCAGTCCAAAAATAGATTAGAACCATA 57.373 33.333 0.00 0.00 0.00 2.74
275 286 6.376248 AGATTAGAACCATAACAATGGCCAT 58.624 36.000 14.09 14.09 45.47 4.40
426 451 5.276820 GGGCGCATCAGCATTAAATAAAAAC 60.277 40.000 10.83 0.00 42.27 2.43
434 459 5.288472 CAGCATTAAATAAAAACGGGTCAGC 59.712 40.000 0.00 0.00 0.00 4.26
466 501 1.168714 AACCTGAAGCGAGAAATGGC 58.831 50.000 0.00 0.00 0.00 4.40
481 521 2.989253 GGCTTCCAACCAACCCCG 60.989 66.667 0.00 0.00 0.00 5.73
615 665 1.999634 AAACACACTGCCTGCCTCCT 62.000 55.000 0.00 0.00 0.00 3.69
616 666 2.046507 CACACTGCCTGCCTCCTC 60.047 66.667 0.00 0.00 0.00 3.71
617 667 2.203907 ACACTGCCTGCCTCCTCT 60.204 61.111 0.00 0.00 0.00 3.69
618 668 2.289532 ACACTGCCTGCCTCCTCTC 61.290 63.158 0.00 0.00 0.00 3.20
619 669 2.686835 ACTGCCTGCCTCCTCTCC 60.687 66.667 0.00 0.00 0.00 3.71
632 682 2.045242 TCTCCTCTCCACCCGTCG 60.045 66.667 0.00 0.00 0.00 5.12
638 688 2.361357 CTCCACCCGTCGTCCTCT 60.361 66.667 0.00 0.00 0.00 3.69
639 689 2.360852 TCCACCCGTCGTCCTCTC 60.361 66.667 0.00 0.00 0.00 3.20
640 690 2.361357 CCACCCGTCGTCCTCTCT 60.361 66.667 0.00 0.00 0.00 3.10
641 691 2.408241 CCACCCGTCGTCCTCTCTC 61.408 68.421 0.00 0.00 0.00 3.20
642 692 1.377463 CACCCGTCGTCCTCTCTCT 60.377 63.158 0.00 0.00 0.00 3.10
648 703 1.805120 CGTCGTCCTCTCTCTCTCTCC 60.805 61.905 0.00 0.00 0.00 3.71
707 763 0.336737 GAGGAGGAGGAGGAACAGGA 59.663 60.000 0.00 0.00 0.00 3.86
723 779 3.724478 ACAGGAGAGAGAGAGAGAGAGA 58.276 50.000 0.00 0.00 0.00 3.10
804 860 4.856607 CTCCCTTCGTCGCCTCGC 62.857 72.222 0.00 0.00 0.00 5.03
905 966 1.359117 CGTGTGTCTGACCGTGTCT 59.641 57.895 5.17 0.00 33.15 3.41
906 967 0.934901 CGTGTGTCTGACCGTGTCTG 60.935 60.000 5.17 5.42 33.15 3.51
929 990 4.974721 AGGCGGGCTTGGTGTTGG 62.975 66.667 0.00 0.00 0.00 3.77
935 996 1.441311 GGCTTGGTGTTGGTGTTGG 59.559 57.895 0.00 0.00 0.00 3.77
936 997 1.326951 GGCTTGGTGTTGGTGTTGGT 61.327 55.000 0.00 0.00 0.00 3.67
979 1040 3.155167 GCCGAGGAGATTCCGGGT 61.155 66.667 0.00 0.00 42.75 5.28
1118 1179 2.260743 GCTGCTCCTTTGCCTTGC 59.739 61.111 0.00 0.00 0.00 4.01
1381 1442 1.204941 CGTCCACGATCTTTTCCCTCT 59.795 52.381 0.00 0.00 43.02 3.69
1382 1443 2.426024 CGTCCACGATCTTTTCCCTCTA 59.574 50.000 0.00 0.00 43.02 2.43
1384 1445 4.277672 CGTCCACGATCTTTTCCCTCTATA 59.722 45.833 0.00 0.00 43.02 1.31
1386 1447 6.150641 CGTCCACGATCTTTTCCCTCTATATA 59.849 42.308 0.00 0.00 43.02 0.86
1387 1448 7.309012 CGTCCACGATCTTTTCCCTCTATATAA 60.309 40.741 0.00 0.00 43.02 0.98
1388 1449 8.532819 GTCCACGATCTTTTCCCTCTATATAAT 58.467 37.037 0.00 0.00 0.00 1.28
1389 1450 8.750298 TCCACGATCTTTTCCCTCTATATAATC 58.250 37.037 0.00 0.00 0.00 1.75
1390 1451 8.754080 CCACGATCTTTTCCCTCTATATAATCT 58.246 37.037 0.00 0.00 0.00 2.40
1391 1452 9.579768 CACGATCTTTTCCCTCTATATAATCTG 57.420 37.037 0.00 0.00 0.00 2.90
1392 1453 9.535170 ACGATCTTTTCCCTCTATATAATCTGA 57.465 33.333 0.00 0.00 0.00 3.27
1416 1477 7.919621 TGATGAATCTCTATATGATCATGTCGC 59.080 37.037 18.72 0.00 0.00 5.19
1542 1603 6.480981 TGTAATTTGGCGCTCCTTTACTATAC 59.519 38.462 7.64 0.00 30.89 1.47
1575 1636 0.743688 ACATGCAAAAGTTGACCGCA 59.256 45.000 0.00 0.00 36.95 5.69
1593 1654 1.203523 GCATTCTGTGACCTCGAGAGT 59.796 52.381 15.71 10.28 0.00 3.24
1832 1899 4.862641 AATACTGGTTGTAGCTTCCCAT 57.137 40.909 0.00 0.00 34.24 4.00
2329 2397 7.255491 TGACATTGTTGAGATCAAGCATATC 57.745 36.000 0.00 0.00 36.39 1.63
2506 2668 6.014070 ACATTCACACTGGTAGGTAACATACA 60.014 38.462 0.00 0.00 41.41 2.29
2643 3339 1.602377 GCTTATGGTTGGTGCCGTATC 59.398 52.381 0.00 0.00 30.81 2.24
2705 3413 7.293299 TGACATATACTCCCTCTGATCCAAAAT 59.707 37.037 0.00 0.00 0.00 1.82
2760 3485 2.158449 CCTTAGTTCAAAGCTGCGACAG 59.842 50.000 0.00 2.92 34.12 3.51
2818 3543 9.334693 CTGAAGTTATTGAGTTCATAGCAAAAC 57.665 33.333 0.00 0.00 44.52 2.43
2861 3587 1.208293 GCTGGTTGGGTAGAGAAGAGG 59.792 57.143 0.00 0.00 0.00 3.69
2948 3674 3.343941 TTGTAGGCATTAGGTGGTGAC 57.656 47.619 0.00 0.00 0.00 3.67
2987 3713 4.447724 TCTTTCATAGAGTGCGTGTTGTTC 59.552 41.667 0.00 0.00 0.00 3.18
3057 3784 7.850193 ACATATTTGCTGGTTCAAATGGTATT 58.150 30.769 10.84 0.00 43.95 1.89
3061 3788 3.245586 TGCTGGTTCAAATGGTATTCCCT 60.246 43.478 0.00 0.00 0.00 4.20
3080 3807 2.806244 CCTTGTGGTGGTAGTCTTTTCG 59.194 50.000 0.00 0.00 0.00 3.46
3081 3808 3.463944 CTTGTGGTGGTAGTCTTTTCGT 58.536 45.455 0.00 0.00 0.00 3.85
3537 4312 5.178067 GCATTCTCTTGGTTGAATTTTGGTG 59.822 40.000 0.00 0.00 31.35 4.17
3729 6691 7.993183 TCATTTTCCCCACAGATCTTATAGAAC 59.007 37.037 0.00 0.00 0.00 3.01
3791 6753 5.049198 TCTGCTTCTGTGTGAAAAGCTAATG 60.049 40.000 7.71 0.00 44.45 1.90
3937 6899 9.717942 AAATCTATGCTACATAGAATCTTGACC 57.282 33.333 18.38 0.00 34.67 4.02
4425 7388 5.852738 TGAGAAAGAAAGAGCTGATTTCG 57.147 39.130 12.88 0.00 40.75 3.46
4949 7912 5.093849 GTCTACTGACTAGGACACTCTCT 57.906 47.826 0.00 0.00 39.94 3.10
4950 7913 6.224665 GTCTACTGACTAGGACACTCTCTA 57.775 45.833 0.00 0.00 39.94 2.43
4951 7914 6.044682 GTCTACTGACTAGGACACTCTCTAC 58.955 48.000 0.00 0.00 39.94 2.59
4953 7916 3.847780 ACTGACTAGGACACTCTCTACCT 59.152 47.826 0.00 0.00 36.65 3.08
4954 7917 4.196193 CTGACTAGGACACTCTCTACCTG 58.804 52.174 0.00 0.00 34.42 4.00
5484 8451 8.390354 GCTGGGCAAAAATTAAACTGAATTATC 58.610 33.333 0.00 0.00 0.00 1.75
5513 8480 2.957680 TCAGTTGGCAGCTGAAAATTCA 59.042 40.909 28.50 7.04 39.70 2.57
5530 8497 9.734620 TGAAAATTCAGTTTGTAGAATTGACTG 57.265 29.630 0.00 0.00 42.02 3.51
5591 8558 6.577427 CGGTTAACTGAAAATCCGAAGAAAAG 59.423 38.462 8.90 0.00 40.29 2.27
5772 8745 0.032416 ACCTAGGACTACACCGCCAT 60.032 55.000 17.98 0.00 34.73 4.40
5854 8827 0.108992 CACGGCCTTACTAGCGTTCA 60.109 55.000 0.00 0.00 0.00 3.18
6014 8988 4.516323 GAGCATAAAATTTGGGCCATGTT 58.484 39.130 7.26 1.98 0.00 2.71
6015 8989 4.263435 AGCATAAAATTTGGGCCATGTTG 58.737 39.130 7.26 0.00 0.00 3.33
6023 8997 1.984026 GGGCCATGTTGGAGTTGGG 60.984 63.158 4.39 0.00 40.96 4.12
6071 9045 6.382869 AGAACATTGAAGTCAACTTTCCTG 57.617 37.500 10.66 2.25 38.86 3.86
6072 9046 4.574599 ACATTGAAGTCAACTTTCCTGC 57.425 40.909 0.00 0.00 38.86 4.85
6089 9063 0.682852 TGCGTACTGTTAGGCTGGTT 59.317 50.000 0.00 0.00 39.42 3.67
6172 9146 5.420725 ACCTGATAGTTGATTAGTGCACA 57.579 39.130 21.04 0.00 0.00 4.57
6452 9426 2.639839 ACAGGTGCTTTCTAGTCCATGT 59.360 45.455 0.00 0.00 0.00 3.21
6562 9536 3.502211 CCAGTTCTGCCTTACGAAAATGT 59.498 43.478 0.00 0.00 0.00 2.71
7022 9997 1.329292 CCAACGAAACAGCGAGAAACA 59.671 47.619 0.00 0.00 34.83 2.83
7049 10024 1.384191 GATCAAGCTTGGGTGGGGT 59.616 57.895 25.73 0.00 0.00 4.95
7051 10026 0.251787 ATCAAGCTTGGGTGGGGTTC 60.252 55.000 25.73 0.00 0.00 3.62
7265 10240 1.183549 TTTCTAGGGCGAGGAGACAC 58.816 55.000 0.00 0.00 0.00 3.67
7423 10398 6.478512 AATCAGTGGCTTCTGGTTTTAAAA 57.521 33.333 0.00 0.00 35.55 1.52
7462 10684 3.378427 GGACGGCAATTTCATCTTAGCTT 59.622 43.478 0.00 0.00 0.00 3.74
7469 10691 5.515626 GCAATTTCATCTTAGCTTGCTGAAG 59.484 40.000 5.26 5.65 36.83 3.02
7624 10846 6.798544 TCTATCTACTCCCTCCATTCCTAA 57.201 41.667 0.00 0.00 0.00 2.69
7628 10850 6.289482 TCTACTCCCTCCATTCCTAATGTA 57.711 41.667 0.00 0.00 37.18 2.29
7630 10852 5.157770 ACTCCCTCCATTCCTAATGTAGA 57.842 43.478 0.00 0.00 37.18 2.59
7631 10853 4.902448 ACTCCCTCCATTCCTAATGTAGAC 59.098 45.833 0.00 0.00 37.18 2.59
7634 10856 5.602978 TCCCTCCATTCCTAATGTAGACTTC 59.397 44.000 0.00 0.00 37.18 3.01
7649 10871 3.476552 AGACTTCGAAAAATGCCACTGA 58.523 40.909 0.00 0.00 0.00 3.41
7700 10922 2.349886 CAGTAGCACTTCTTGGAATCGC 59.650 50.000 0.00 0.00 0.00 4.58
7782 11011 4.518249 GCAGTCTTATCCCACTTTTAGCT 58.482 43.478 0.00 0.00 0.00 3.32
7865 11094 5.050490 CGATTGTTCTACAACCAGGATAGG 58.950 45.833 0.00 0.00 41.40 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.734984 ATTACTCTTCTCTAATTTCCCGAAAAA 57.265 29.630 0.00 0.00 33.56 1.94
3 4 9.734984 AATTACTCTTCTCTAATTTCCCGAAAA 57.265 29.630 0.00 0.00 33.56 2.29
4 5 9.734984 AAATTACTCTTCTCTAATTTCCCGAAA 57.265 29.630 0.00 0.00 30.15 3.46
5 6 9.734984 AAAATTACTCTTCTCTAATTTCCCGAA 57.265 29.630 0.00 0.00 33.39 4.30
6 7 9.734984 AAAAATTACTCTTCTCTAATTTCCCGA 57.265 29.630 0.00 0.00 33.39 5.14
32 33 3.181429 ACTCTCCTCCAAAATCCTGCAAA 60.181 43.478 0.00 0.00 0.00 3.68
35 36 2.797177 ACTCTCCTCCAAAATCCTGC 57.203 50.000 0.00 0.00 0.00 4.85
36 37 7.283354 GGTTAATTACTCTCCTCCAAAATCCTG 59.717 40.741 0.00 0.00 0.00 3.86
37 38 7.347252 GGTTAATTACTCTCCTCCAAAATCCT 58.653 38.462 0.00 0.00 0.00 3.24
40 41 5.589050 GCGGTTAATTACTCTCCTCCAAAAT 59.411 40.000 0.00 0.00 0.00 1.82
41 42 4.939439 GCGGTTAATTACTCTCCTCCAAAA 59.061 41.667 0.00 0.00 0.00 2.44
42 43 4.224370 AGCGGTTAATTACTCTCCTCCAAA 59.776 41.667 0.00 0.00 0.00 3.28
97 99 1.333619 TGCGTGAAACTTTTCTCCTGC 59.666 47.619 3.48 3.18 38.02 4.85
154 160 8.525316 GGAATGGATATCATGACATTTATTGCA 58.475 33.333 9.80 0.00 35.99 4.08
175 181 2.977169 CGTTTGCGGTGTTTTAGGAATG 59.023 45.455 0.00 0.00 0.00 2.67
204 210 1.812922 CACTCCGATGAGCCAGTGC 60.813 63.158 0.00 0.00 42.74 4.40
262 271 3.822735 CTCGATTCCATGGCCATTGTTAT 59.177 43.478 17.92 10.88 0.00 1.89
263 272 3.213506 CTCGATTCCATGGCCATTGTTA 58.786 45.455 17.92 6.18 0.00 2.41
264 273 2.026641 CTCGATTCCATGGCCATTGTT 58.973 47.619 17.92 5.07 0.00 2.83
266 275 0.313043 GCTCGATTCCATGGCCATTG 59.687 55.000 17.92 13.90 0.00 2.82
275 286 2.026729 TGGTGGTTTATGCTCGATTCCA 60.027 45.455 0.00 0.00 0.00 3.53
426 451 3.068691 TCCTCCTTCGCTGACCCG 61.069 66.667 0.00 0.00 0.00 5.28
434 459 0.321671 TCAGGTTTGCTCCTCCTTCG 59.678 55.000 0.00 0.00 35.37 3.79
466 501 1.303317 CCTCGGGGTTGGTTGGAAG 60.303 63.158 0.00 0.00 0.00 3.46
615 665 2.045242 CGACGGGTGGAGAGGAGA 60.045 66.667 0.00 0.00 0.00 3.71
616 666 2.361357 ACGACGGGTGGAGAGGAG 60.361 66.667 0.00 0.00 0.00 3.69
617 667 2.360852 GACGACGGGTGGAGAGGA 60.361 66.667 0.00 0.00 0.00 3.71
618 668 3.450115 GGACGACGGGTGGAGAGG 61.450 72.222 0.00 0.00 0.00 3.69
619 669 2.361357 AGGACGACGGGTGGAGAG 60.361 66.667 0.00 0.00 0.00 3.20
632 682 2.104963 GAGAGGGAGAGAGAGAGAGGAC 59.895 59.091 0.00 0.00 0.00 3.85
638 688 4.105697 GGGAATAAGAGAGGGAGAGAGAGA 59.894 50.000 0.00 0.00 0.00 3.10
639 689 4.106341 AGGGAATAAGAGAGGGAGAGAGAG 59.894 50.000 0.00 0.00 0.00 3.20
640 690 4.058731 AGGGAATAAGAGAGGGAGAGAGA 58.941 47.826 0.00 0.00 0.00 3.10
641 691 4.407365 GAGGGAATAAGAGAGGGAGAGAG 58.593 52.174 0.00 0.00 0.00 3.20
642 692 3.141272 GGAGGGAATAAGAGAGGGAGAGA 59.859 52.174 0.00 0.00 0.00 3.10
707 763 2.703007 GGCTCTCTCTCTCTCTCTCTCT 59.297 54.545 0.00 0.00 0.00 3.10
774 830 2.045242 GGGAGGGCGGGAAAACTC 60.045 66.667 0.00 0.00 0.00 3.01
775 831 2.138453 GAAGGGAGGGCGGGAAAACT 62.138 60.000 0.00 0.00 0.00 2.66
776 832 1.677966 GAAGGGAGGGCGGGAAAAC 60.678 63.158 0.00 0.00 0.00 2.43
777 833 2.761160 GAAGGGAGGGCGGGAAAA 59.239 61.111 0.00 0.00 0.00 2.29
905 966 4.697756 CAAGCCCGCCTCCGAACA 62.698 66.667 0.00 0.00 36.29 3.18
929 990 4.279043 GGGCGGCAACACCAACAC 62.279 66.667 12.47 0.00 42.08 3.32
1389 1450 9.453325 CGACATGATCATATAGAGATTCATCAG 57.547 37.037 8.15 0.00 0.00 2.90
1390 1451 7.919621 GCGACATGATCATATAGAGATTCATCA 59.080 37.037 8.15 0.00 0.00 3.07
1391 1452 8.136800 AGCGACATGATCATATAGAGATTCATC 58.863 37.037 8.15 0.00 0.00 2.92
1392 1453 8.009622 AGCGACATGATCATATAGAGATTCAT 57.990 34.615 8.15 0.00 0.00 2.57
1393 1454 7.401955 AGCGACATGATCATATAGAGATTCA 57.598 36.000 8.15 0.00 0.00 2.57
1394 1455 6.917477 GGAGCGACATGATCATATAGAGATTC 59.083 42.308 8.15 0.00 33.60 2.52
1396 1457 6.128486 AGGAGCGACATGATCATATAGAGAT 58.872 40.000 8.15 0.00 33.60 2.75
1397 1458 5.504853 AGGAGCGACATGATCATATAGAGA 58.495 41.667 8.15 0.00 33.60 3.10
1398 1459 5.833406 AGGAGCGACATGATCATATAGAG 57.167 43.478 8.15 0.00 33.60 2.43
1399 1460 5.948758 AGAAGGAGCGACATGATCATATAGA 59.051 40.000 8.15 0.00 33.60 1.98
1400 1461 6.206395 AGAAGGAGCGACATGATCATATAG 57.794 41.667 8.15 0.00 33.60 1.31
1401 1462 5.163713 CGAGAAGGAGCGACATGATCATATA 60.164 44.000 8.15 0.00 33.60 0.86
1416 1477 4.122143 AGAAGATGAAAGCGAGAAGGAG 57.878 45.455 0.00 0.00 0.00 3.69
1542 1603 0.524816 GCATGTGAATTGCGAGCTGG 60.525 55.000 0.00 0.00 0.00 4.85
1575 1636 2.752354 CAGACTCTCGAGGTCACAGAAT 59.248 50.000 25.85 9.72 36.29 2.40
1832 1899 9.438228 TGGACGACATGTAAAATAACTAATCAA 57.562 29.630 0.00 0.00 0.00 2.57
1972 2040 4.927049 AGTGATCAATGGACCATCAGTTT 58.073 39.130 7.63 0.00 27.57 2.66
2329 2397 4.339530 TCTCTTCTCGATGGAGGTAACATG 59.660 45.833 4.78 0.00 40.85 3.21
2643 3339 5.231265 TGAATATGCTAGCGATACCGTAG 57.769 43.478 10.77 0.00 38.24 3.51
2705 3413 6.094881 ACTTTAGTTCAAAGCTGCAACACTTA 59.905 34.615 1.02 0.00 46.50 2.24
2818 3543 3.937814 TGGCACTAGTTGGTACAGATTG 58.062 45.455 0.00 0.00 42.39 2.67
2861 3587 6.426587 AGTGATGGGCATATATTTATCACCC 58.573 40.000 16.78 0.00 43.15 4.61
2948 3674 8.213679 TCTATGAAAGAAAATCTATCCTGGTGG 58.786 37.037 0.00 0.00 0.00 4.61
3057 3784 2.112279 AAGACTACCACCACAAGGGA 57.888 50.000 0.00 0.00 41.15 4.20
3061 3788 3.118702 TGACGAAAAGACTACCACCACAA 60.119 43.478 0.00 0.00 0.00 3.33
3080 3807 3.057245 GGAGATGCTCCTTTTTGGTTGAC 60.057 47.826 6.23 0.00 46.41 3.18
3081 3808 3.157087 GGAGATGCTCCTTTTTGGTTGA 58.843 45.455 6.23 0.00 46.41 3.18
3174 3948 4.836825 ACATATGGCCATAGTATCAGCAC 58.163 43.478 28.58 0.00 0.00 4.40
3729 6691 2.159198 GGTGCTGTGCTCCCATAAAATG 60.159 50.000 0.00 0.00 36.35 2.32
3791 6753 5.858581 GTCAAAGTGATGGTTTGCAGATTAC 59.141 40.000 0.00 0.00 35.29 1.89
3937 6899 2.475864 CTCCTACCGAGAACGATACGAG 59.524 54.545 0.00 0.00 41.63 4.18
3999 6961 1.741706 ACAATGCCTGAGATGCTTTCG 59.258 47.619 0.00 0.00 0.00 3.46
4073 7036 7.141363 AGAAAAACATGCATGAGTAACAAGTC 58.859 34.615 32.75 15.14 0.00 3.01
4425 7388 5.121454 TGCATTGGGAAATTTATGCGAAAAC 59.879 36.000 15.42 0.00 44.77 2.43
4794 7757 4.320494 CCATTGGTGTAGTCTTTGAGCAAC 60.320 45.833 0.00 0.00 0.00 4.17
4946 7909 3.372206 GCACTGCATAAACACAGGTAGAG 59.628 47.826 0.00 0.00 0.00 2.43
4947 7910 3.007940 AGCACTGCATAAACACAGGTAGA 59.992 43.478 3.30 0.00 0.00 2.59
4948 7911 3.125829 CAGCACTGCATAAACACAGGTAG 59.874 47.826 3.30 0.00 0.00 3.18
4949 7912 3.073678 CAGCACTGCATAAACACAGGTA 58.926 45.455 3.30 0.00 0.00 3.08
4950 7913 1.881973 CAGCACTGCATAAACACAGGT 59.118 47.619 3.30 0.00 0.00 4.00
4951 7914 1.881973 ACAGCACTGCATAAACACAGG 59.118 47.619 3.30 0.00 0.00 4.00
4953 7916 2.948315 TCAACAGCACTGCATAAACACA 59.052 40.909 3.30 0.00 0.00 3.72
4954 7917 3.624326 TCAACAGCACTGCATAAACAC 57.376 42.857 3.30 0.00 0.00 3.32
5250 8214 5.102313 GGTTTGTTTCACCTTCTTGTCAAG 58.898 41.667 6.21 6.21 0.00 3.02
5484 8451 0.597377 GCTGCCAACTGAAAAACCCG 60.597 55.000 0.00 0.00 0.00 5.28
5513 8480 5.209818 TCGGTCAGTCAATTCTACAAACT 57.790 39.130 0.00 0.00 0.00 2.66
5591 8558 1.460504 GCCTAAACCCTACAAGGTGC 58.539 55.000 0.00 0.00 40.05 5.01
5663 8630 1.153369 GCATGCGCCCTAGTCTCAA 60.153 57.895 4.18 0.00 0.00 3.02
5981 8955 6.198966 CCAAATTTTATGCTCGCTATTTGGTC 59.801 38.462 17.51 0.00 43.28 4.02
6014 8988 1.133513 AGTTGCATGAACCCAACTCCA 60.134 47.619 9.77 0.00 46.22 3.86
6015 8989 1.270550 CAGTTGCATGAACCCAACTCC 59.729 52.381 11.96 0.00 46.22 3.85
6023 8997 3.921119 TCCACATTCAGTTGCATGAAC 57.079 42.857 4.90 0.00 41.76 3.18
6071 9045 1.076332 CAACCAGCCTAACAGTACGC 58.924 55.000 0.00 0.00 0.00 4.42
6072 9046 1.722011 CCAACCAGCCTAACAGTACG 58.278 55.000 0.00 0.00 0.00 3.67
6172 9146 7.288560 AGAGAATCAGTAAATCCTGCATCAAT 58.711 34.615 0.00 0.00 37.82 2.57
6185 9159 5.717178 AGGTAGACTGCAAGAGAATCAGTAA 59.283 40.000 0.00 0.00 40.74 2.24
6188 9162 4.431809 CAGGTAGACTGCAAGAGAATCAG 58.568 47.826 0.00 0.00 40.97 2.90
6452 9426 5.018539 ACCAGCTAAGCACGTATATCAAA 57.981 39.130 0.00 0.00 0.00 2.69
6562 9536 5.316167 GGTCATATGTATCCTTCATGCCAA 58.684 41.667 1.90 0.00 0.00 4.52
7003 9977 2.730183 TGTTTCTCGCTGTTTCGTTG 57.270 45.000 0.00 0.00 0.00 4.10
7022 9997 0.883833 CAAGCTTGATCCGCCACTTT 59.116 50.000 22.31 0.00 0.00 2.66
7049 10024 1.231958 CGCTGTAAACCTTGCGGGAA 61.232 55.000 2.42 0.00 43.97 3.97
7051 10026 2.867472 CGCTGTAAACCTTGCGGG 59.133 61.111 0.00 0.00 43.97 6.13
7077 10052 2.037847 ATCAAACCCTGGGCTGCC 59.962 61.111 14.08 11.05 0.00 4.85
7078 10053 3.010413 GCATCAAACCCTGGGCTGC 62.010 63.158 14.08 10.56 0.00 5.25
7079 10054 0.901580 AAGCATCAAACCCTGGGCTG 60.902 55.000 14.08 10.96 36.56 4.85
7080 10055 0.704076 TAAGCATCAAACCCTGGGCT 59.296 50.000 14.08 0.00 37.59 5.19
7081 10056 1.410153 CATAAGCATCAAACCCTGGGC 59.590 52.381 14.08 0.00 0.00 5.36
7265 10240 2.812658 AGCATTCCTTCCTTTCCCTTG 58.187 47.619 0.00 0.00 0.00 3.61
7370 10345 2.566952 GTGGCAATTATCACCTGCAC 57.433 50.000 0.00 0.00 37.83 4.57
7440 10443 2.945668 AGCTAAGATGAAATTGCCGTCC 59.054 45.455 0.00 0.00 0.00 4.79
7441 10444 4.346129 CAAGCTAAGATGAAATTGCCGTC 58.654 43.478 0.00 0.00 0.00 4.79
7462 10684 1.372004 GCAACATTGCGCTTCAGCA 60.372 52.632 9.73 0.00 45.11 4.41
7561 10783 3.195041 TGAAGCGTTCTCTTCACCG 57.805 52.632 2.43 0.00 45.21 4.94
7624 10846 5.003804 AGTGGCATTTTTCGAAGTCTACAT 58.996 37.500 0.00 0.00 0.00 2.29
7628 10850 3.476552 TCAGTGGCATTTTTCGAAGTCT 58.523 40.909 0.00 0.00 0.00 3.24
7630 10852 4.647424 TTTCAGTGGCATTTTTCGAAGT 57.353 36.364 0.00 0.00 0.00 3.01
7631 10853 5.107375 CCATTTTCAGTGGCATTTTTCGAAG 60.107 40.000 0.00 0.00 0.00 3.79
7634 10856 4.650545 CCATTTTCAGTGGCATTTTTCG 57.349 40.909 0.00 0.00 0.00 3.46
7649 10871 6.628185 TGCAAACTTTGAAAAATGCCATTTT 58.372 28.000 9.57 9.57 43.83 1.82
7683 10905 0.036732 TGGCGATTCCAAGAAGTGCT 59.963 50.000 0.00 0.00 43.21 4.40
7686 10908 2.859165 TTCTGGCGATTCCAAGAAGT 57.141 45.000 0.00 0.00 46.01 3.01
7687 10909 3.691118 TGAATTCTGGCGATTCCAAGAAG 59.309 43.478 7.05 0.00 46.01 2.85
7692 10914 2.749076 CACTTGAATTCTGGCGATTCCA 59.251 45.455 7.05 0.00 44.18 3.53
7700 10922 9.865321 ATTTGATAAATGTCACTTGAATTCTGG 57.135 29.630 7.05 2.08 0.00 3.86
7756 10978 1.115467 AGTGGGATAAGACTGCCTCG 58.885 55.000 0.00 0.00 0.00 4.63
7782 11011 2.268762 TGCTTTGGAGTATGTGTGCA 57.731 45.000 0.00 0.00 0.00 4.57
7865 11094 6.890268 ACCTACACAAAATTCTCCCTAAATCC 59.110 38.462 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.