Multiple sequence alignment - TraesCS2D01G455200

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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 TraesCS2D01G455200 chr2D 100.000 3487 0 0 1 3487 563290659 563294145 0.000000e+00 6440
1 TraesCS2D01G455200 chr2B 88.073 3144 205 84 419 3487 673924191 673927239 0.000000e+00 3572
2 TraesCS2D01G455200 chr2B 88.916 406 38 5 3 407 673923812 673924211 8.690000e-136 494
3 TraesCS2D01G455200 chr2A 88.562 2177 135 55 1205 3320 703698917 703701040 0.000000e+00 2536
4 TraesCS2D01G455200 chr2A 88.630 387 16 2 512 876 703698119 703698499 2.470000e-121 446
5 TraesCS2D01G455200 chr2A 88.391 379 31 4 27 403 703697703 703698070 8.880000e-121 444
6 TraesCS2D01G455200 chr2A 94.382 89 4 1 3400 3487 703701121 703701209 6.070000e-28 135
7 TraesCS2D01G455200 chr2A 93.846 65 4 0 3339 3403 703701035 703701099 7.970000e-17 99


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 TraesCS2D01G455200 chr2D 563290659 563294145 3486 False 6440 6440 100.0000 1 3487 1 chr2D.!!$F1 3486
1 TraesCS2D01G455200 chr2B 673923812 673927239 3427 False 2033 3572 88.4945 3 3487 2 chr2B.!!$F1 3484
2 TraesCS2D01G455200 chr2A 703697703 703701209 3506 False 732 2536 90.7622 27 3487 5 chr2A.!!$F1 3460

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
52 53 0.188342 ACAATGCCAACCCTTCCAGT 59.812 50.0 0.0 0.0 0.0 4.00 F
1424 1548 0.250124 TGCCTGTGTCTTTGGTACGG 60.250 55.0 0.0 0.0 0.0 4.02 F
2049 2202 0.248215 GTGATTTCGCCGCATGAAGG 60.248 55.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 2190 0.729140 GTTTTCACCTTCATGCGGCG 60.729 55.0 0.51 0.51 0.0 6.46 R
2292 2458 0.036010 ATGTCCCCTCTGCTCAAACG 60.036 55.0 0.00 0.00 0.0 3.60 R
3081 3312 0.036388 TTCAACATCGACCAGAGCCC 60.036 55.0 0.00 0.00 0.0 5.19 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
24 25 6.688578 TCTCGTCTTTATTTACAGTCTGCTT 58.311 36.000 0.00 0.00 0.00 3.91
25 26 7.152645 TCTCGTCTTTATTTACAGTCTGCTTT 58.847 34.615 0.00 0.00 0.00 3.51
29 30 7.018235 GTCTTTATTTACAGTCTGCTTTGCTC 58.982 38.462 0.00 0.00 0.00 4.26
39 40 0.599558 TGCTTTGCTCTGGACAATGC 59.400 50.000 7.25 7.25 44.22 3.56
41 42 1.250328 CTTTGCTCTGGACAATGCCA 58.750 50.000 0.00 0.00 36.30 4.92
44 45 0.895100 TGCTCTGGACAATGCCAACC 60.895 55.000 0.00 0.00 37.52 3.77
45 46 1.598701 GCTCTGGACAATGCCAACCC 61.599 60.000 0.00 0.00 37.52 4.11
50 51 0.541764 GGACAATGCCAACCCTTCCA 60.542 55.000 0.00 0.00 0.00 3.53
52 53 0.188342 ACAATGCCAACCCTTCCAGT 59.812 50.000 0.00 0.00 0.00 4.00
60 61 2.616510 CCAACCCTTCCAGTGAGTGATC 60.617 54.545 0.00 0.00 0.00 2.92
61 62 0.898320 ACCCTTCCAGTGAGTGATCG 59.102 55.000 0.00 0.00 0.00 3.69
82 84 1.077787 GGCATGGGGTTGTCGATGA 60.078 57.895 0.00 0.00 0.00 2.92
85 87 0.391130 CATGGGGTTGTCGATGACGT 60.391 55.000 0.00 0.00 40.69 4.34
162 164 2.616510 CCTTGGTTGGGTCTCTCATGTC 60.617 54.545 0.00 0.00 0.00 3.06
182 184 2.432874 TCGTGTCCTTTGGAGTTTCTCA 59.567 45.455 0.00 0.00 29.39 3.27
198 200 6.122964 AGTTTCTCACTTTTCCTTTGCTAGT 58.877 36.000 0.00 0.00 27.32 2.57
221 223 5.124297 GTGGTGCCTTGTATTACGGTTTAAT 59.876 40.000 0.00 0.00 0.00 1.40
223 225 6.315891 TGGTGCCTTGTATTACGGTTTAATAC 59.684 38.462 6.79 6.79 39.55 1.89
229 231 8.606602 CCTTGTATTACGGTTTAATACAACCTC 58.393 37.037 18.48 0.00 46.65 3.85
261 263 4.755266 TCCAACCCTCTAGATGTTTAGC 57.245 45.455 5.33 0.00 0.00 3.09
312 314 7.692460 TCTTGTACTCCACTTAGTATTTCGA 57.308 36.000 0.00 0.00 34.59 3.71
383 385 5.560953 GCTTCCAGAAATATATTCACGTGGC 60.561 44.000 17.00 0.46 0.00 5.01
384 386 5.290493 TCCAGAAATATATTCACGTGGCT 57.710 39.130 17.00 5.85 0.00 4.75
385 387 6.413783 TCCAGAAATATATTCACGTGGCTA 57.586 37.500 17.00 8.05 0.00 3.93
386 388 7.004555 TCCAGAAATATATTCACGTGGCTAT 57.995 36.000 17.00 14.55 0.00 2.97
387 389 6.873605 TCCAGAAATATATTCACGTGGCTATG 59.126 38.462 17.00 2.25 0.00 2.23
388 390 6.650807 CCAGAAATATATTCACGTGGCTATGT 59.349 38.462 17.00 8.48 0.00 2.29
389 391 7.148573 CCAGAAATATATTCACGTGGCTATGTC 60.149 40.741 17.00 11.47 0.00 3.06
390 392 6.874134 AGAAATATATTCACGTGGCTATGTCC 59.126 38.462 17.00 7.27 0.00 4.02
391 393 6.360370 AATATATTCACGTGGCTATGTCCT 57.640 37.500 17.00 0.00 0.00 3.85
392 394 2.604046 ATTCACGTGGCTATGTCCTC 57.396 50.000 17.00 0.00 0.00 3.71
393 395 1.557099 TTCACGTGGCTATGTCCTCT 58.443 50.000 17.00 0.00 0.00 3.69
394 396 1.557099 TCACGTGGCTATGTCCTCTT 58.443 50.000 17.00 0.00 0.00 2.85
395 397 1.204704 TCACGTGGCTATGTCCTCTTG 59.795 52.381 17.00 0.00 0.00 3.02
396 398 1.066858 CACGTGGCTATGTCCTCTTGT 60.067 52.381 7.95 0.00 0.00 3.16
397 399 2.165641 CACGTGGCTATGTCCTCTTGTA 59.834 50.000 7.95 0.00 0.00 2.41
398 400 2.829720 ACGTGGCTATGTCCTCTTGTAA 59.170 45.455 0.00 0.00 0.00 2.41
399 401 3.259876 ACGTGGCTATGTCCTCTTGTAAA 59.740 43.478 0.00 0.00 0.00 2.01
400 402 3.617263 CGTGGCTATGTCCTCTTGTAAAC 59.383 47.826 0.00 0.00 0.00 2.01
401 403 4.620803 CGTGGCTATGTCCTCTTGTAAACT 60.621 45.833 0.00 0.00 0.00 2.66
402 404 5.246307 GTGGCTATGTCCTCTTGTAAACTT 58.754 41.667 0.00 0.00 0.00 2.66
403 405 5.705905 GTGGCTATGTCCTCTTGTAAACTTT 59.294 40.000 0.00 0.00 0.00 2.66
404 406 6.206829 GTGGCTATGTCCTCTTGTAAACTTTT 59.793 38.462 0.00 0.00 0.00 2.27
405 407 6.775629 TGGCTATGTCCTCTTGTAAACTTTTT 59.224 34.615 0.00 0.00 0.00 1.94
444 447 8.966868 TGTCCTCTTGTAAACTTTCTTGAAAAT 58.033 29.630 0.00 0.00 0.00 1.82
749 779 2.939353 GGCCCCACCAGTAAGGGT 60.939 66.667 0.00 0.00 43.89 4.34
1021 1067 1.152839 GACTCCTCCTCCTCCTCCG 60.153 68.421 0.00 0.00 0.00 4.63
1203 1322 4.421479 CTCGTCAGCTCCGGCGTT 62.421 66.667 6.01 0.00 44.37 4.84
1411 1535 1.885850 GTCCGTCGTGTTTGCCTGT 60.886 57.895 0.00 0.00 0.00 4.00
1417 1541 1.400494 GTCGTGTTTGCCTGTGTCTTT 59.600 47.619 0.00 0.00 0.00 2.52
1422 1546 2.685897 TGTTTGCCTGTGTCTTTGGTAC 59.314 45.455 0.00 0.00 0.00 3.34
1423 1547 1.588674 TTGCCTGTGTCTTTGGTACG 58.411 50.000 0.00 0.00 0.00 3.67
1424 1548 0.250124 TGCCTGTGTCTTTGGTACGG 60.250 55.000 0.00 0.00 0.00 4.02
1425 1549 0.953960 GCCTGTGTCTTTGGTACGGG 60.954 60.000 0.00 0.00 42.49 5.28
1426 1550 0.953960 CCTGTGTCTTTGGTACGGGC 60.954 60.000 0.00 0.00 34.38 6.13
1482 1613 0.876342 CGGAGCTGGTATTTCTCGGC 60.876 60.000 0.00 0.00 35.63 5.54
1487 1618 1.287425 CTGGTATTTCTCGGCGGAAC 58.713 55.000 7.21 0.00 0.00 3.62
1570 1702 9.302345 CTCCAGAAAAGAAAAGAAAAAGGTTAC 57.698 33.333 0.00 0.00 0.00 2.50
1613 1745 2.224769 TGCTAGGACAAACAAGGGAAGG 60.225 50.000 0.00 0.00 0.00 3.46
1624 1756 4.547367 GGGAAGGGATCGGTGCGG 62.547 72.222 0.00 0.00 0.00 5.69
1676 1808 1.825622 GGGCTATTGGTGCAGAGGC 60.826 63.158 0.00 0.00 41.68 4.70
1788 1920 6.127403 GCTTAATTACGGTCACGATTTCATC 58.873 40.000 0.00 0.00 44.60 2.92
1818 1950 1.438651 CATGTGGTGTGGAGTTACCG 58.561 55.000 0.00 0.00 42.61 4.02
1847 1979 7.473027 TTTTTCTCTACAAAGTTACTGACCG 57.527 36.000 0.00 0.00 0.00 4.79
1934 2073 4.019411 TCTGATAGATGCCAAAGGTGTTCA 60.019 41.667 0.00 0.00 0.00 3.18
1956 2095 1.537202 CCCACTGCTTTACTGCTGTTC 59.463 52.381 0.09 0.00 41.89 3.18
1969 2108 1.557443 GCTGTTCGTTCCGTCTGGTG 61.557 60.000 0.00 0.00 36.30 4.17
1978 2126 1.078426 CCGTCTGGTGGATGGGTTC 60.078 63.158 0.00 0.00 45.09 3.62
1983 2131 1.496857 TCTGGTGGATGGGTTCAACAA 59.503 47.619 0.00 0.00 29.48 2.83
1991 2139 4.119136 GGATGGGTTCAACAAAAACTGTG 58.881 43.478 0.00 0.00 38.67 3.66
2012 2160 2.296190 GGCTTTTTGTGTAGGGTCCTTG 59.704 50.000 0.00 0.00 0.00 3.61
2013 2161 2.296190 GCTTTTTGTGTAGGGTCCTTGG 59.704 50.000 0.00 0.00 0.00 3.61
2019 2167 1.422402 GTGTAGGGTCCTTGGGTTTCA 59.578 52.381 0.00 0.00 0.00 2.69
2037 2190 7.656948 TGGGTTTCATTTTGAGATTGTGATTTC 59.343 33.333 0.00 0.00 0.00 2.17
2040 2193 5.401550 TCATTTTGAGATTGTGATTTCGCC 58.598 37.500 0.00 0.00 0.00 5.54
2049 2202 0.248215 GTGATTTCGCCGCATGAAGG 60.248 55.000 0.00 0.00 0.00 3.46
2067 2220 7.682021 GCATGAAGGTGAAAACTATATGGTTCC 60.682 40.741 4.79 2.42 0.00 3.62
2073 2226 6.433093 GGTGAAAACTATATGGTTCCTTGTGT 59.567 38.462 4.79 0.00 0.00 3.72
2151 2314 7.962918 ACGATCTTTCACTAATTGCATGTTTAC 59.037 33.333 0.00 0.00 0.00 2.01
2159 2322 2.884663 TTGCATGTTTACCGCTAACG 57.115 45.000 0.00 0.00 39.67 3.18
2171 2334 3.078837 ACCGCTAACGAACATTTCCATT 58.921 40.909 0.00 0.00 43.93 3.16
2229 2395 3.987868 TGACTAGTTCGTTGAGTGATTGC 59.012 43.478 0.00 0.00 0.00 3.56
2289 2455 6.203723 GCATACACTGAGATTAACCTGAATCC 59.796 42.308 0.00 0.00 36.63 3.01
2292 2458 6.410540 ACACTGAGATTAACCTGAATCCTTC 58.589 40.000 0.00 0.00 36.63 3.46
2298 2464 6.472887 AGATTAACCTGAATCCTTCGTTTGA 58.527 36.000 0.00 0.00 36.63 2.69
2499 2674 1.294659 CGGCTGACAGTGCTCCTTTC 61.295 60.000 3.99 0.00 0.00 2.62
2546 2729 0.393077 ACCACCACCGTCAGAAGAAG 59.607 55.000 0.00 0.00 0.00 2.85
2777 2970 1.139058 CGGCTATTGGGAGTTACTGCT 59.861 52.381 3.53 0.00 0.00 4.24
2785 3008 0.324943 GGAGTTACTGCTGCTTCCCA 59.675 55.000 0.00 0.00 0.00 4.37
2793 3016 2.438075 CTGCTTCCCAGGCTCTGC 60.438 66.667 0.00 0.00 37.93 4.26
2848 3071 4.985538 AGTAGTTGTTGGTGAATGGTGAT 58.014 39.130 0.00 0.00 0.00 3.06
2849 3072 4.761739 AGTAGTTGTTGGTGAATGGTGATG 59.238 41.667 0.00 0.00 0.00 3.07
2850 3073 2.892852 AGTTGTTGGTGAATGGTGATGG 59.107 45.455 0.00 0.00 0.00 3.51
2995 3222 3.447634 TTGCGAGTTGTGCGTGTGC 62.448 57.895 0.00 0.00 43.20 4.57
3040 3268 2.122783 TTTGGCCGGTTCTCCTTATG 57.877 50.000 1.90 0.00 0.00 1.90
3048 3276 3.947834 CCGGTTCTCCTTATGAATTTGCT 59.052 43.478 0.00 0.00 0.00 3.91
3049 3277 5.123227 CCGGTTCTCCTTATGAATTTGCTA 58.877 41.667 0.00 0.00 0.00 3.49
3050 3278 5.588648 CCGGTTCTCCTTATGAATTTGCTAA 59.411 40.000 0.00 0.00 0.00 3.09
3052 3280 7.444183 CCGGTTCTCCTTATGAATTTGCTAATA 59.556 37.037 0.00 0.00 0.00 0.98
3088 3319 6.611613 TCCTAATGAATATACAGGGCTCTG 57.388 41.667 13.44 13.44 46.10 3.35
3104 3335 3.191371 GGCTCTGGTCGATGTTGAAAAAT 59.809 43.478 0.00 0.00 0.00 1.82
3111 3342 6.898041 TGGTCGATGTTGAAAAATCTAACTG 58.102 36.000 0.00 0.00 0.00 3.16
3124 3355 9.122613 GAAAAATCTAACTGAAAAGACTGATGC 57.877 33.333 0.00 0.00 0.00 3.91
3129 3360 3.418995 ACTGAAAAGACTGATGCTGCAT 58.581 40.909 16.20 16.20 0.00 3.96
3132 3363 3.057806 TGAAAAGACTGATGCTGCATGTG 60.058 43.478 21.53 14.11 0.00 3.21
3134 3365 2.195741 AGACTGATGCTGCATGTGTT 57.804 45.000 21.53 0.88 0.00 3.32
3135 3366 2.082231 AGACTGATGCTGCATGTGTTC 58.918 47.619 21.53 10.46 0.00 3.18
3136 3367 1.131883 GACTGATGCTGCATGTGTTCC 59.868 52.381 21.53 4.79 0.00 3.62
3137 3368 1.170442 CTGATGCTGCATGTGTTCCA 58.830 50.000 21.53 9.45 0.00 3.53
3222 3453 2.127232 GCTCGCAACGGTGAAAGC 60.127 61.111 3.55 8.38 32.14 3.51
3231 3462 2.832931 CGGTGAAAGCTCTCACTGG 58.167 57.895 19.59 8.90 45.31 4.00
3232 3463 1.294659 CGGTGAAAGCTCTCACTGGC 61.295 60.000 19.59 3.25 45.31 4.85
3233 3464 0.250467 GGTGAAAGCTCTCACTGGCA 60.250 55.000 19.26 0.00 44.33 4.92
3234 3465 1.612726 GGTGAAAGCTCTCACTGGCAT 60.613 52.381 19.26 0.00 44.33 4.40
3236 3467 1.348696 TGAAAGCTCTCACTGGCATGA 59.651 47.619 0.00 0.00 0.00 3.07
3237 3468 2.026542 TGAAAGCTCTCACTGGCATGAT 60.027 45.455 0.00 0.00 0.00 2.45
3244 3480 2.436911 TCTCACTGGCATGATAGCACAT 59.563 45.455 0.00 0.00 35.83 3.21
3253 3489 4.143030 GGCATGATAGCACATACACGATTC 60.143 45.833 0.00 0.00 35.83 2.52
3264 3500 4.159693 ACATACACGATTCTGGAACTAGCA 59.840 41.667 0.00 0.00 0.00 3.49
3267 3503 2.668457 CACGATTCTGGAACTAGCACAC 59.332 50.000 0.00 0.00 0.00 3.82
3298 3534 1.371183 CGGCTGGACAAGTGGAAGA 59.629 57.895 0.00 0.00 0.00 2.87
3299 3535 0.250295 CGGCTGGACAAGTGGAAGAA 60.250 55.000 0.00 0.00 0.00 2.52
3300 3536 1.528129 GGCTGGACAAGTGGAAGAAG 58.472 55.000 0.00 0.00 0.00 2.85
3396 3632 2.029380 CCGGAAACAGAAACCATTTCCC 60.029 50.000 0.00 0.00 45.78 3.97
3411 3672 1.639722 TTCCCCGATCTCTGTTGACA 58.360 50.000 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.268825 AGCAGACTGTAAATAAAGACGAGA 57.731 37.500 3.99 0.00 0.00 4.04
1 2 6.952935 AAGCAGACTGTAAATAAAGACGAG 57.047 37.500 3.99 0.00 0.00 4.18
17 18 1.597742 TTGTCCAGAGCAAAGCAGAC 58.402 50.000 0.00 0.00 0.00 3.51
20 21 0.599558 GCATTGTCCAGAGCAAAGCA 59.400 50.000 0.00 0.00 39.45 3.91
24 25 0.961019 GTTGGCATTGTCCAGAGCAA 59.039 50.000 0.00 0.00 37.44 3.91
25 26 0.895100 GGTTGGCATTGTCCAGAGCA 60.895 55.000 0.00 0.00 37.44 4.26
29 30 0.890683 GAAGGGTTGGCATTGTCCAG 59.109 55.000 0.00 0.00 37.44 3.86
39 40 0.764890 TCACTCACTGGAAGGGTTGG 59.235 55.000 0.00 0.00 39.54 3.77
41 42 1.276421 CGATCACTCACTGGAAGGGTT 59.724 52.381 0.00 0.00 39.54 4.11
44 45 2.482664 CCATCGATCACTCACTGGAAGG 60.483 54.545 0.00 0.00 39.30 3.46
45 46 2.819115 CCATCGATCACTCACTGGAAG 58.181 52.381 0.00 0.00 42.29 3.46
50 51 1.202615 CCATGCCATCGATCACTCACT 60.203 52.381 0.00 0.00 0.00 3.41
52 53 0.107268 CCCATGCCATCGATCACTCA 59.893 55.000 0.00 0.00 0.00 3.41
60 61 2.472059 CGACAACCCCATGCCATCG 61.472 63.158 0.00 0.00 0.00 3.84
61 62 0.466189 ATCGACAACCCCATGCCATC 60.466 55.000 0.00 0.00 0.00 3.51
82 84 3.389002 AGTAAACACCCAAGGAGTTACGT 59.611 43.478 0.00 0.00 35.59 3.57
85 87 5.633655 TGAAGTAAACACCCAAGGAGTTA 57.366 39.130 0.00 0.00 35.59 2.24
162 164 2.544267 GTGAGAAACTCCAAAGGACACG 59.456 50.000 0.00 0.00 0.00 4.49
182 184 2.623416 GCACCACTAGCAAAGGAAAAGT 59.377 45.455 0.00 0.00 0.00 2.66
198 200 2.863132 AACCGTAATACAAGGCACCA 57.137 45.000 0.00 0.00 0.00 4.17
229 231 0.609131 AGGGTTGGATGAAGCAACCG 60.609 55.000 0.10 0.00 46.75 4.44
261 263 1.068610 CACGGTGTAAATGGCAACCAG 60.069 52.381 6.15 1.91 36.75 4.00
310 312 4.518217 CAAGCAAACACACTAGAAACTCG 58.482 43.478 0.00 0.00 0.00 4.18
312 314 3.632145 CCCAAGCAAACACACTAGAAACT 59.368 43.478 0.00 0.00 0.00 2.66
339 341 1.945394 CTAGCCAGATGGACAATGCAC 59.055 52.381 2.18 0.00 37.39 4.57
412 414 5.584551 AAGTTTACAAGAGGACATTCCCT 57.415 39.130 0.00 0.00 37.19 4.20
413 415 6.004574 AGAAAGTTTACAAGAGGACATTCCC 58.995 40.000 0.00 0.00 37.19 3.97
414 416 7.228706 TCAAGAAAGTTTACAAGAGGACATTCC 59.771 37.037 0.00 0.00 36.58 3.01
415 417 8.154649 TCAAGAAAGTTTACAAGAGGACATTC 57.845 34.615 0.00 0.00 0.00 2.67
416 418 8.519799 TTCAAGAAAGTTTACAAGAGGACATT 57.480 30.769 0.00 0.00 0.00 2.71
417 419 8.519799 TTTCAAGAAAGTTTACAAGAGGACAT 57.480 30.769 0.00 0.00 0.00 3.06
444 447 6.475727 GCTTTACATGTCACTCGCTTAATCTA 59.524 38.462 0.00 0.00 0.00 1.98
446 449 5.292101 AGCTTTACATGTCACTCGCTTAATC 59.708 40.000 0.00 0.00 0.00 1.75
448 451 4.566004 AGCTTTACATGTCACTCGCTTAA 58.434 39.130 0.00 0.00 0.00 1.85
449 452 4.188247 AGCTTTACATGTCACTCGCTTA 57.812 40.909 0.00 0.00 0.00 3.09
453 456 5.597813 AGAAAAGCTTTACATGTCACTCG 57.402 39.130 13.10 0.00 0.00 4.18
641 671 2.951458 CGTCCGCCCTTTGTTTCC 59.049 61.111 0.00 0.00 0.00 3.13
1005 1051 2.520741 GCGGAGGAGGAGGAGGAG 60.521 72.222 0.00 0.00 0.00 3.69
1006 1052 4.144727 GGCGGAGGAGGAGGAGGA 62.145 72.222 0.00 0.00 0.00 3.71
1007 1053 4.150454 AGGCGGAGGAGGAGGAGG 62.150 72.222 0.00 0.00 0.00 4.30
1203 1322 2.867855 GCACACCAGGTCGTCCTCA 61.868 63.158 0.00 0.00 43.07 3.86
1411 1535 2.344500 CGGCCCGTACCAAAGACA 59.656 61.111 0.00 0.00 0.00 3.41
1482 1613 4.219033 CGGTCAAAATTTCTCTTGTTCCG 58.781 43.478 0.00 2.58 36.12 4.30
1487 1618 2.584791 CGGCGGTCAAAATTTCTCTTG 58.415 47.619 0.00 0.00 0.00 3.02
1527 1658 2.825836 GAATCAGGCCGGCACTGG 60.826 66.667 31.68 18.62 36.62 4.00
1570 1702 4.799949 CACCAAGAAACGAATGGCATTATG 59.200 41.667 13.65 11.29 37.77 1.90
1624 1756 1.613925 AGAAGAAAAGGGAAAAGCGCC 59.386 47.619 2.29 0.00 0.00 6.53
1626 1758 4.837896 AGAAGAAGAAAAGGGAAAAGCG 57.162 40.909 0.00 0.00 0.00 4.68
1627 1759 7.549134 TGAAAAAGAAGAAGAAAAGGGAAAAGC 59.451 33.333 0.00 0.00 0.00 3.51
1635 1767 7.117379 GCCCATCATGAAAAAGAAGAAGAAAAG 59.883 37.037 0.00 0.00 0.00 2.27
1676 1808 1.371758 CACGACACAGACGACAGGG 60.372 63.158 0.00 0.00 34.70 4.45
1818 1950 8.774586 TCAGTAACTTTGTAGAGAAAAATCAGC 58.225 33.333 0.00 0.00 0.00 4.26
1847 1979 3.069443 CAGCTAAGTCTCTCCTGAATCCC 59.931 52.174 0.00 0.00 0.00 3.85
1888 2027 7.515586 AGAAGCTCTGATGATGATAATCCAAA 58.484 34.615 0.00 0.00 0.00 3.28
1889 2028 7.075851 AGAAGCTCTGATGATGATAATCCAA 57.924 36.000 0.00 0.00 0.00 3.53
1890 2029 6.683312 AGAAGCTCTGATGATGATAATCCA 57.317 37.500 0.00 0.00 0.00 3.41
1934 2073 1.352352 ACAGCAGTAAAGCAGTGGGAT 59.648 47.619 0.00 0.00 32.71 3.85
1969 2108 4.119136 CACAGTTTTTGTTGAACCCATCC 58.881 43.478 0.00 0.00 38.16 3.51
1974 2122 3.245518 AGCCACAGTTTTTGTTGAACC 57.754 42.857 0.00 0.00 38.16 3.62
1983 2131 4.382577 CCCTACACAAAAAGCCACAGTTTT 60.383 41.667 0.00 0.00 0.00 2.43
1991 2139 2.287977 AGGACCCTACACAAAAAGCC 57.712 50.000 0.00 0.00 0.00 4.35
2012 2160 7.148755 CGAAATCACAATCTCAAAATGAAACCC 60.149 37.037 0.00 0.00 0.00 4.11
2013 2161 7.619982 GCGAAATCACAATCTCAAAATGAAACC 60.620 37.037 0.00 0.00 0.00 3.27
2019 2167 4.414852 CGGCGAAATCACAATCTCAAAAT 58.585 39.130 0.00 0.00 0.00 1.82
2037 2190 0.729140 GTTTTCACCTTCATGCGGCG 60.729 55.000 0.51 0.51 0.00 6.46
2040 2193 5.296780 ACCATATAGTTTTCACCTTCATGCG 59.703 40.000 0.00 0.00 0.00 4.73
2049 2202 7.448748 ACACAAGGAACCATATAGTTTTCAC 57.551 36.000 0.00 0.00 0.00 3.18
2067 2220 4.141287 TCCACTCCAAACCAATACACAAG 58.859 43.478 0.00 0.00 0.00 3.16
2073 2226 3.849574 TGATCCTCCACTCCAAACCAATA 59.150 43.478 0.00 0.00 0.00 1.90
2116 2272 8.857216 CAATTAGTGAAAGATCGTACTACGTTT 58.143 33.333 8.42 2.45 43.14 3.60
2151 2314 3.757745 AATGGAAATGTTCGTTAGCGG 57.242 42.857 0.00 0.00 38.89 5.52
2159 2322 5.467035 TTCCCTCACAAATGGAAATGTTC 57.533 39.130 0.00 0.00 35.29 3.18
2171 2334 3.907474 TCTTATCACACCTTCCCTCACAA 59.093 43.478 0.00 0.00 0.00 3.33
2229 2395 2.238521 ACCAGTAAACACATGGCTTGG 58.761 47.619 5.31 0.00 37.64 3.61
2267 2433 7.496346 AAGGATTCAGGTTAATCTCAGTGTA 57.504 36.000 0.00 0.00 36.34 2.90
2289 2455 0.321671 TCCCCTCTGCTCAAACGAAG 59.678 55.000 0.00 0.00 0.00 3.79
2292 2458 0.036010 ATGTCCCCTCTGCTCAAACG 60.036 55.000 0.00 0.00 0.00 3.60
2298 2464 3.842923 CGCGATGTCCCCTCTGCT 61.843 66.667 0.00 0.00 0.00 4.24
2520 2695 4.602259 ACGGTGGTGGTGCTGACG 62.602 66.667 0.00 0.00 0.00 4.35
2521 2696 2.665185 GACGGTGGTGGTGCTGAC 60.665 66.667 0.00 0.00 0.00 3.51
2525 2708 1.961277 CTTCTGACGGTGGTGGTGC 60.961 63.158 0.00 0.00 0.00 5.01
2536 2719 7.172703 TCGGTAATTTTCTTTCCTTCTTCTGAC 59.827 37.037 0.00 0.00 0.00 3.51
2546 2729 2.745821 AGCGGTCGGTAATTTTCTTTCC 59.254 45.455 0.00 0.00 0.00 3.13
2761 2954 3.370527 GGAAGCAGCAGTAACTCCCAATA 60.371 47.826 0.00 0.00 0.00 1.90
2777 2970 2.932194 AGCAGAGCCTGGGAAGCA 60.932 61.111 0.00 0.00 31.21 3.91
2785 3008 8.586879 AAGAAAAATAATTAAGAGCAGAGCCT 57.413 30.769 0.00 0.00 0.00 4.58
2822 3045 5.639506 CACCATTCACCAACAACTACTAGAG 59.360 44.000 0.00 0.00 0.00 2.43
2823 3046 5.305902 TCACCATTCACCAACAACTACTAGA 59.694 40.000 0.00 0.00 0.00 2.43
2824 3047 5.547465 TCACCATTCACCAACAACTACTAG 58.453 41.667 0.00 0.00 0.00 2.57
2825 3048 5.554437 TCACCATTCACCAACAACTACTA 57.446 39.130 0.00 0.00 0.00 1.82
2826 3049 4.431416 TCACCATTCACCAACAACTACT 57.569 40.909 0.00 0.00 0.00 2.57
2848 3071 1.817087 TAAACCTACCACCACCACCA 58.183 50.000 0.00 0.00 0.00 4.17
2849 3072 2.553685 CCTTAAACCTACCACCACCACC 60.554 54.545 0.00 0.00 0.00 4.61
2850 3073 2.107031 ACCTTAAACCTACCACCACCAC 59.893 50.000 0.00 0.00 0.00 4.16
2908 3134 1.880027 GTCACCCACATGTCAGTTTCC 59.120 52.381 0.00 0.00 0.00 3.13
2937 3163 4.458989 GCTGATACATGGGTGAAAAAGTCA 59.541 41.667 0.00 0.00 0.00 3.41
2995 3222 2.432628 GCCTCCTCCGTCAACACG 60.433 66.667 0.00 0.00 46.29 4.49
3066 3297 5.249393 ACCAGAGCCCTGTATATTCATTAGG 59.751 44.000 0.00 0.00 38.74 2.69
3069 3300 4.262635 CGACCAGAGCCCTGTATATTCATT 60.263 45.833 0.00 0.00 38.74 2.57
3070 3301 3.259374 CGACCAGAGCCCTGTATATTCAT 59.741 47.826 0.00 0.00 38.74 2.57
3071 3302 2.628178 CGACCAGAGCCCTGTATATTCA 59.372 50.000 0.00 0.00 38.74 2.57
3072 3303 2.891580 TCGACCAGAGCCCTGTATATTC 59.108 50.000 0.00 0.00 38.74 1.75
3073 3304 2.958818 TCGACCAGAGCCCTGTATATT 58.041 47.619 0.00 0.00 38.74 1.28
3074 3305 2.677542 TCGACCAGAGCCCTGTATAT 57.322 50.000 0.00 0.00 38.74 0.86
3075 3306 2.239400 CATCGACCAGAGCCCTGTATA 58.761 52.381 0.00 0.00 38.74 1.47
3076 3307 1.043816 CATCGACCAGAGCCCTGTAT 58.956 55.000 0.00 0.00 38.74 2.29
3077 3308 0.324368 ACATCGACCAGAGCCCTGTA 60.324 55.000 0.00 0.00 38.74 2.74
3078 3309 1.194781 AACATCGACCAGAGCCCTGT 61.195 55.000 0.00 0.00 38.74 4.00
3079 3310 0.742281 CAACATCGACCAGAGCCCTG 60.742 60.000 0.00 0.00 40.09 4.45
3080 3311 0.904865 TCAACATCGACCAGAGCCCT 60.905 55.000 0.00 0.00 0.00 5.19
3081 3312 0.036388 TTCAACATCGACCAGAGCCC 60.036 55.000 0.00 0.00 0.00 5.19
3082 3313 1.808411 TTTCAACATCGACCAGAGCC 58.192 50.000 0.00 0.00 0.00 4.70
3083 3314 3.896648 TTTTTCAACATCGACCAGAGC 57.103 42.857 0.00 0.00 0.00 4.09
3084 3315 5.869753 AGATTTTTCAACATCGACCAGAG 57.130 39.130 0.00 0.00 0.00 3.35
3088 3319 7.129109 TCAGTTAGATTTTTCAACATCGACC 57.871 36.000 0.00 0.00 0.00 4.79
3104 3335 4.692625 GCAGCATCAGTCTTTTCAGTTAGA 59.307 41.667 0.00 0.00 0.00 2.10
3111 3342 3.057736 ACACATGCAGCATCAGTCTTTTC 60.058 43.478 4.38 0.00 0.00 2.29
3222 3453 2.159000 TGTGCTATCATGCCAGTGAGAG 60.159 50.000 0.00 2.27 39.74 3.20
3230 3461 2.754472 TCGTGTATGTGCTATCATGCC 58.246 47.619 0.00 0.00 31.24 4.40
3231 3462 4.687948 AGAATCGTGTATGTGCTATCATGC 59.312 41.667 0.00 0.00 0.00 4.06
3232 3463 5.119743 CCAGAATCGTGTATGTGCTATCATG 59.880 44.000 0.00 0.00 0.00 3.07
3233 3464 5.011023 TCCAGAATCGTGTATGTGCTATCAT 59.989 40.000 0.00 0.00 0.00 2.45
3234 3465 4.340950 TCCAGAATCGTGTATGTGCTATCA 59.659 41.667 0.00 0.00 0.00 2.15
3236 3467 4.937201 TCCAGAATCGTGTATGTGCTAT 57.063 40.909 0.00 0.00 0.00 2.97
3237 3468 4.159693 AGTTCCAGAATCGTGTATGTGCTA 59.840 41.667 0.00 0.00 0.00 3.49
3244 3480 3.508402 TGTGCTAGTTCCAGAATCGTGTA 59.492 43.478 0.00 0.00 0.00 2.90
3253 3489 3.895232 AGTATGGTGTGCTAGTTCCAG 57.105 47.619 0.00 0.00 33.33 3.86
3264 3500 0.390735 GCCGTCGGAAAGTATGGTGT 60.391 55.000 17.49 0.00 0.00 4.16
3267 3503 0.810031 CCAGCCGTCGGAAAGTATGG 60.810 60.000 17.49 8.42 0.00 2.74
3300 3536 1.339055 TGTGACACCTCCAGCTTATGC 60.339 52.381 2.45 0.00 40.05 3.14
3396 3632 3.599343 TGGAAATGTCAACAGAGATCGG 58.401 45.455 0.00 0.00 0.00 4.18
3411 3672 7.148540 CGATTTGATTTGATGTTGCTTGGAAAT 60.149 33.333 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.