Multiple sequence alignment - TraesCS3A01G455000

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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 TraesCS3A01G455000 chr3A 100.000 2611 0 0 1 2611 692963862 692961252 0.000000e+00 4822
1 TraesCS3A01G455000 chr3D 90.344 1688 80 33 2 1648 556029199 556027554 0.000000e+00 2137
2 TraesCS3A01G455000 chr3D 90.618 469 40 3 1894 2358 556027441 556026973 1.030000e-173 619
3 TraesCS3A01G455000 chr3B 90.517 580 32 10 708 1284 739029704 739029145 0.000000e+00 745
4 TraesCS3A01G455000 chr3B 94.057 488 26 3 1 485 739030404 739029917 0.000000e+00 737
5 TraesCS3A01G455000 chr3B 85.820 677 63 19 1276 1946 739027652 739027003 0.000000e+00 688
6 TraesCS3A01G455000 chr3B 86.645 629 70 8 1991 2611 739027001 739026379 0.000000e+00 684
7 TraesCS3A01G455000 chr3B 92.683 82 6 0 560 641 739029819 739029738 4.560000e-23 119
8 TraesCS3A01G455000 chr1A 82.175 331 59 0 742 1072 256985325 256984995 4.250000e-73 285
9 TraesCS3A01G455000 chr1B 82.692 312 54 0 761 1072 296811244 296810933 7.120000e-71 278
10 TraesCS3A01G455000 chr2B 79.167 312 47 9 761 1072 775373664 775373371 1.580000e-47 200


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 TraesCS3A01G455000 chr3A 692961252 692963862 2610 True 4822.0 4822 100.0000 1 2611 1 chr3A.!!$R1 2610
1 TraesCS3A01G455000 chr3D 556026973 556029199 2226 True 1378.0 2137 90.4810 2 2358 2 chr3D.!!$R1 2356
2 TraesCS3A01G455000 chr3B 739026379 739030404 4025 True 594.6 745 89.9444 1 2611 5 chr3B.!!$R1 2610

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
601 637 0.249741 AGCACAACCACCACTCGTAC 60.25 55.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2266 3877 0.168128 GGATCGCAAGGACAAAACGG 59.832 55.0 0.0 0.0 38.47 4.44 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
229 233 3.889044 GGCGATGACGGAGAGCGA 61.889 66.667 0.00 0.00 40.15 4.93
381 385 3.520862 CCGACCACATGCCCATGC 61.521 66.667 8.11 0.00 42.39 4.06
432 436 1.227380 ATGGAGATCGCCGACAAGC 60.227 57.895 11.16 0.00 0.00 4.01
485 489 4.700365 GGCTGCCGTTTGCCGTTC 62.700 66.667 1.35 0.00 39.71 3.95
547 581 3.808728 TGGACTAGCAGTGCATTATTCC 58.191 45.455 19.20 14.58 41.73 3.01
549 583 4.199310 GGACTAGCAGTGCATTATTCCAA 58.801 43.478 19.20 0.00 36.49 3.53
551 585 5.220931 GGACTAGCAGTGCATTATTCCAAAG 60.221 44.000 19.20 1.37 36.49 2.77
552 586 3.515330 AGCAGTGCATTATTCCAAAGC 57.485 42.857 19.20 0.00 0.00 3.51
553 587 2.167075 AGCAGTGCATTATTCCAAAGCC 59.833 45.455 19.20 0.00 0.00 4.35
554 588 2.167075 GCAGTGCATTATTCCAAAGCCT 59.833 45.455 11.09 0.00 0.00 4.58
555 589 3.368739 GCAGTGCATTATTCCAAAGCCTT 60.369 43.478 11.09 0.00 0.00 4.35
556 590 4.178540 CAGTGCATTATTCCAAAGCCTTG 58.821 43.478 0.00 0.00 0.00 3.61
557 591 3.834231 AGTGCATTATTCCAAAGCCTTGT 59.166 39.130 0.00 0.00 0.00 3.16
558 592 4.082026 AGTGCATTATTCCAAAGCCTTGTC 60.082 41.667 0.00 0.00 0.00 3.18
565 599 2.942804 TCCAAAGCCTTGTCACAATCA 58.057 42.857 0.00 0.00 0.00 2.57
578 614 8.479280 CCTTGTCACAATCAAAAATACTTTTCG 58.521 33.333 0.00 0.00 32.24 3.46
601 637 0.249741 AGCACAACCACCACTCGTAC 60.250 55.000 0.00 0.00 0.00 3.67
630 666 3.310774 GGAGAAATGGACGTGATCATGTG 59.689 47.826 25.03 8.09 0.00 3.21
673 731 0.748005 CCAGGGGATTTGTACCAGCG 60.748 60.000 0.00 0.00 0.00 5.18
677 735 1.473434 GGGGATTTGTACCAGCGAGAG 60.473 57.143 0.00 0.00 0.00 3.20
690 748 4.264638 GAGAGAGAGCTCGCCGGC 62.265 72.222 19.07 19.07 45.98 6.13
1098 1175 0.536687 TCGTCTCCGAACAGGTGAGT 60.537 55.000 0.00 0.00 42.57 3.41
1105 1182 3.858868 GAACAGGTGAGTCCGCGCA 62.859 63.158 8.75 0.00 41.99 6.09
1121 1198 4.803426 CACGCCTGCCCTCTCGAC 62.803 72.222 0.00 0.00 0.00 4.20
1131 1208 3.391382 CTCTCGACCCACACCCCC 61.391 72.222 0.00 0.00 0.00 5.40
1132 1209 4.242586 TCTCGACCCACACCCCCA 62.243 66.667 0.00 0.00 0.00 4.96
1164 1244 2.942710 ACGAACCTAACACACTCGATG 58.057 47.619 0.00 0.00 33.81 3.84
1165 1245 2.295349 ACGAACCTAACACACTCGATGT 59.705 45.455 0.00 0.00 44.81 3.06
1400 2981 2.204244 ATGAACGGGGAGGGGGTT 60.204 61.111 0.00 0.00 0.00 4.11
1443 3024 1.445410 GTGAGCCGCGTGTACATCA 60.445 57.895 4.92 0.00 0.00 3.07
1459 3040 3.518998 CATCGCCGAGGAGGACGT 61.519 66.667 0.00 0.00 45.00 4.34
1607 3188 3.318275 TGGAGATAGCCGACAAGTACATC 59.682 47.826 0.00 0.00 0.00 3.06
1612 3193 3.895232 AGCCGACAAGTACATCTGAAT 57.105 42.857 0.00 0.00 0.00 2.57
1613 3194 3.786635 AGCCGACAAGTACATCTGAATC 58.213 45.455 0.00 0.00 0.00 2.52
1614 3195 3.195610 AGCCGACAAGTACATCTGAATCA 59.804 43.478 0.00 0.00 0.00 2.57
1615 3196 3.553511 GCCGACAAGTACATCTGAATCAG 59.446 47.826 3.38 3.38 0.00 2.90
1648 3234 9.902684 ACTTCATCTTCAGTTATGAATTCTGAT 57.097 29.630 7.05 0.00 44.32 2.90
1654 3240 9.948964 TCTTCAGTTATGAATTCTGATTTCTGA 57.051 29.630 7.05 9.88 44.32 3.27
1686 3273 7.389884 TCTTCAGAGAAATCAAGAGATGTTTGG 59.610 37.037 0.00 0.00 33.90 3.28
1689 3276 8.156820 TCAGAGAAATCAAGAGATGTTTGGTTA 58.843 33.333 0.00 0.00 33.90 2.85
1690 3277 8.786898 CAGAGAAATCAAGAGATGTTTGGTTAA 58.213 33.333 0.00 0.00 33.90 2.01
1691 3278 9.354673 AGAGAAATCAAGAGATGTTTGGTTAAA 57.645 29.630 0.00 0.00 33.90 1.52
1693 3280 9.971922 AGAAATCAAGAGATGTTTGGTTAAAAG 57.028 29.630 0.00 0.00 33.90 2.27
1698 3285 8.744652 TCAAGAGATGTTTGGTTAAAAGTTCAA 58.255 29.630 0.00 0.00 0.00 2.69
1699 3286 9.364989 CAAGAGATGTTTGGTTAAAAGTTCAAA 57.635 29.630 0.00 0.00 0.00 2.69
1700 3287 8.926715 AGAGATGTTTGGTTAAAAGTTCAAAC 57.073 30.769 9.88 9.88 45.17 2.93
1701 3288 7.979537 AGAGATGTTTGGTTAAAAGTTCAAACC 59.020 33.333 13.03 11.54 44.67 3.27
1702 3289 6.754675 AGATGTTTGGTTAAAAGTTCAAACCG 59.245 34.615 13.03 0.00 44.62 4.44
1703 3290 4.626172 TGTTTGGTTAAAAGTTCAAACCGC 59.374 37.500 13.03 7.52 44.62 5.68
1704 3291 4.451629 TTGGTTAAAAGTTCAAACCGCA 57.548 36.364 12.33 2.52 44.62 5.69
1705 3292 4.035278 TGGTTAAAAGTTCAAACCGCAG 57.965 40.909 12.33 0.00 44.62 5.18
1706 3293 2.792674 GGTTAAAAGTTCAAACCGCAGC 59.207 45.455 4.15 0.00 33.85 5.25
1713 3300 0.447406 TTCAAACCGCAGCATCATCG 59.553 50.000 0.00 0.00 0.00 3.84
1718 3305 2.238942 ACCGCAGCATCATCGAATAA 57.761 45.000 0.00 0.00 0.00 1.40
1724 3311 5.292834 CCGCAGCATCATCGAATAAGAATAT 59.707 40.000 0.00 0.00 0.00 1.28
1725 3312 6.183324 CGCAGCATCATCGAATAAGAATATG 58.817 40.000 0.00 0.00 0.00 1.78
1740 3327 9.739276 AATAAGAATATGTTCTCTGTCCAAACA 57.261 29.630 5.07 0.00 43.80 2.83
1742 3329 8.641498 AAGAATATGTTCTCTGTCCAAACAAT 57.359 30.769 5.07 0.00 43.80 2.71
1747 3334 6.861065 TGTTCTCTGTCCAAACAATAAGTC 57.139 37.500 0.00 0.00 34.24 3.01
1752 3339 7.861629 TCTCTGTCCAAACAATAAGTCCATAT 58.138 34.615 0.00 0.00 34.24 1.78
1755 3342 9.559732 TCTGTCCAAACAATAAGTCCATATATG 57.440 33.333 5.68 5.68 34.24 1.78
1823 3410 6.624352 TCTCTTGATCTTGACAAAACCTTG 57.376 37.500 0.00 0.00 38.61 3.61
1824 3411 6.356556 TCTCTTGATCTTGACAAAACCTTGA 58.643 36.000 0.00 0.00 36.33 3.02
1825 3412 6.260936 TCTCTTGATCTTGACAAAACCTTGAC 59.739 38.462 0.00 0.00 36.33 3.18
1826 3413 5.885352 TCTTGATCTTGACAAAACCTTGACA 59.115 36.000 0.00 0.00 35.79 3.58
1829 3416 3.020984 TCTTGACAAAACCTTGACACCC 58.979 45.455 0.00 0.00 37.03 4.61
1830 3417 2.516227 TGACAAAACCTTGACACCCA 57.484 45.000 0.00 0.00 33.23 4.51
1833 3420 2.494073 GACAAAACCTTGACACCCAACA 59.506 45.455 0.00 0.00 36.33 3.33
1834 3421 2.232696 ACAAAACCTTGACACCCAACAC 59.767 45.455 0.00 0.00 36.33 3.32
1835 3422 2.223803 AAACCTTGACACCCAACACA 57.776 45.000 0.00 0.00 0.00 3.72
1836 3423 2.452600 AACCTTGACACCCAACACAT 57.547 45.000 0.00 0.00 0.00 3.21
1837 3424 2.452600 ACCTTGACACCCAACACATT 57.547 45.000 0.00 0.00 0.00 2.71
1838 3425 3.586470 ACCTTGACACCCAACACATTA 57.414 42.857 0.00 0.00 0.00 1.90
1839 3426 3.219281 ACCTTGACACCCAACACATTAC 58.781 45.455 0.00 0.00 0.00 1.89
1841 3428 2.912690 TGACACCCAACACATTACGA 57.087 45.000 0.00 0.00 0.00 3.43
1842 3429 3.410631 TGACACCCAACACATTACGAT 57.589 42.857 0.00 0.00 0.00 3.73
1845 3432 5.306394 TGACACCCAACACATTACGATAAA 58.694 37.500 0.00 0.00 0.00 1.40
1846 3433 5.763698 TGACACCCAACACATTACGATAAAA 59.236 36.000 0.00 0.00 0.00 1.52
1847 3434 6.262496 TGACACCCAACACATTACGATAAAAA 59.738 34.615 0.00 0.00 0.00 1.94
1848 3435 6.674066 ACACCCAACACATTACGATAAAAAG 58.326 36.000 0.00 0.00 0.00 2.27
1849 3436 6.487331 ACACCCAACACATTACGATAAAAAGA 59.513 34.615 0.00 0.00 0.00 2.52
1864 3451 8.836413 ACGATAAAAAGAAAACTTCAGACATGA 58.164 29.630 0.00 0.00 0.00 3.07
1881 3468 5.381174 ACATGAATGTCACCAAGAACATG 57.619 39.130 0.00 0.00 35.87 3.21
1882 3469 4.219070 ACATGAATGTCACCAAGAACATGG 59.781 41.667 0.00 0.00 40.80 3.66
1883 3470 4.097551 TGAATGTCACCAAGAACATGGA 57.902 40.909 3.07 0.00 43.54 3.41
1884 3471 4.665451 TGAATGTCACCAAGAACATGGAT 58.335 39.130 3.07 0.00 43.54 3.41
1886 3473 5.647658 TGAATGTCACCAAGAACATGGATAC 59.352 40.000 3.07 1.95 43.54 2.24
1927 3537 6.719370 TGTTACATTTCACTCCTTGGCTAAAT 59.281 34.615 0.00 0.00 0.00 1.40
1928 3538 7.885922 TGTTACATTTCACTCCTTGGCTAAATA 59.114 33.333 0.00 0.00 0.00 1.40
1943 3553 5.889289 TGGCTAAATAAAACCATGACCTACC 59.111 40.000 0.00 0.00 0.00 3.18
1944 3554 5.008316 GGCTAAATAAAACCATGACCTACCG 59.992 44.000 0.00 0.00 0.00 4.02
1949 3559 1.956629 AACCATGACCTACCGGAGCG 61.957 60.000 9.46 0.00 0.00 5.03
1963 3573 2.540101 CCGGAGCGAAATTACAAGCTAG 59.460 50.000 0.00 0.00 40.39 3.42
1970 3580 6.346096 AGCGAAATTACAAGCTAGTGGATAA 58.654 36.000 0.00 0.00 38.29 1.75
1973 3583 7.640240 GCGAAATTACAAGCTAGTGGATAAAAG 59.360 37.037 0.00 0.00 0.00 2.27
1974 3584 8.122952 CGAAATTACAAGCTAGTGGATAAAAGG 58.877 37.037 0.00 0.00 0.00 3.11
2026 3637 8.093927 TGTGTGTATCTACAAGATCAAACATCA 58.906 33.333 0.00 0.00 38.04 3.07
2028 3639 8.935844 TGTGTATCTACAAGATCAAACATCAAC 58.064 33.333 0.00 0.00 38.04 3.18
2031 3642 9.113838 GTATCTACAAGATCAAACATCAACCAT 57.886 33.333 0.00 0.00 36.20 3.55
2077 3688 4.695928 GCAAAGAACTCTTCCTTAACCGAT 59.304 41.667 0.00 0.00 34.61 4.18
2092 3703 1.006805 CGATCTCCATGCCGACTCC 60.007 63.158 0.00 0.00 0.00 3.85
2164 3775 0.309302 CCACATTGTGCCGTCGAAAA 59.691 50.000 11.41 0.00 31.34 2.29
2233 3844 1.344438 ACGGTGTCTTCTCTCAATGCA 59.656 47.619 0.00 0.00 0.00 3.96
2239 3850 3.268330 GTCTTCTCTCAATGCAGCATCA 58.732 45.455 8.77 0.00 0.00 3.07
2242 3853 4.335594 TCTTCTCTCAATGCAGCATCAATG 59.664 41.667 8.77 3.59 0.00 2.82
2248 3859 4.773013 TCAATGCAGCATCAATGAGAGTA 58.227 39.130 8.77 0.00 0.00 2.59
2251 3862 2.093341 TGCAGCATCAATGAGAGTAGCA 60.093 45.455 0.00 0.00 0.00 3.49
2257 3868 5.303845 AGCATCAATGAGAGTAGCACTGATA 59.696 40.000 0.00 0.00 0.00 2.15
2260 3871 7.604549 CATCAATGAGAGTAGCACTGATATCT 58.395 38.462 3.98 0.00 0.00 1.98
2266 3877 4.586841 AGAGTAGCACTGATATCTGGGTTC 59.413 45.833 12.83 6.68 0.00 3.62
2269 3880 1.139058 GCACTGATATCTGGGTTCCGT 59.861 52.381 12.83 0.00 0.00 4.69
2287 3898 1.535462 CGTTTTGTCCTTGCGATCCTT 59.465 47.619 0.00 0.00 0.00 3.36
2305 3916 1.059584 TTCTCAGCACCACTTCCCCA 61.060 55.000 0.00 0.00 0.00 4.96
2373 3984 7.817418 TCCAATGCTACTTTAGAAAACACTT 57.183 32.000 0.00 0.00 0.00 3.16
2374 3985 8.911918 TCCAATGCTACTTTAGAAAACACTTA 57.088 30.769 0.00 0.00 0.00 2.24
2375 3986 9.344772 TCCAATGCTACTTTAGAAAACACTTAA 57.655 29.630 0.00 0.00 0.00 1.85
2389 4000 9.908152 AGAAAACACTTAAAATAATGGCACTAC 57.092 29.630 0.00 0.00 0.00 2.73
2390 4001 9.685828 GAAAACACTTAAAATAATGGCACTACA 57.314 29.630 0.00 0.00 0.00 2.74
2393 4004 9.638239 AACACTTAAAATAATGGCACTACAATG 57.362 29.630 0.00 0.00 0.00 2.82
2394 4005 9.019656 ACACTTAAAATAATGGCACTACAATGA 57.980 29.630 0.00 0.00 0.00 2.57
2404 4016 6.012658 TGGCACTACAATGAACTCATTTTC 57.987 37.500 2.11 0.00 43.48 2.29
2406 4018 6.209192 TGGCACTACAATGAACTCATTTTCAT 59.791 34.615 2.11 0.00 46.18 2.57
2422 4034 8.641499 TCATTTTCATTGAAATATTAACCGGC 57.359 30.769 12.39 0.00 31.34 6.13
2424 4036 9.097257 CATTTTCATTGAAATATTAACCGGCTT 57.903 29.630 12.39 0.00 31.34 4.35
2432 4044 6.824196 TGAAATATTAACCGGCTTATGTGACA 59.176 34.615 0.00 0.00 0.00 3.58
2433 4045 7.500892 TGAAATATTAACCGGCTTATGTGACAT 59.499 33.333 0.00 2.65 0.00 3.06
2436 4048 2.779755 ACCGGCTTATGTGACATGAA 57.220 45.000 8.61 0.00 0.00 2.57
2442 4055 5.971202 CCGGCTTATGTGACATGAATTTTAC 59.029 40.000 8.61 0.00 0.00 2.01
2459 4072 9.605955 TGAATTTTACGATCATGTTTTACACAG 57.394 29.630 0.00 0.00 39.40 3.66
2470 4083 5.811399 TGTTTTACACAGGAACTCAAGTG 57.189 39.130 0.00 0.00 34.60 3.16
2476 4089 5.455056 ACACAGGAACTCAAGTGTACTAG 57.545 43.478 0.00 0.00 42.84 2.57
2477 4090 4.238514 CACAGGAACTCAAGTGTACTAGC 58.761 47.826 0.00 0.00 34.60 3.42
2478 4091 3.895656 ACAGGAACTCAAGTGTACTAGCA 59.104 43.478 0.00 0.00 34.60 3.49
2479 4092 4.021894 ACAGGAACTCAAGTGTACTAGCAG 60.022 45.833 0.00 0.00 34.60 4.24
2480 4093 4.021894 CAGGAACTCAAGTGTACTAGCAGT 60.022 45.833 0.00 0.00 34.60 4.40
2481 4094 5.183331 CAGGAACTCAAGTGTACTAGCAGTA 59.817 44.000 0.00 0.00 34.60 2.74
2482 4095 5.416326 AGGAACTCAAGTGTACTAGCAGTAG 59.584 44.000 0.00 0.00 30.12 2.57
2483 4096 5.393243 GGAACTCAAGTGTACTAGCAGTAGG 60.393 48.000 0.00 0.00 30.12 3.18
2484 4097 4.919793 ACTCAAGTGTACTAGCAGTAGGA 58.080 43.478 0.00 0.00 30.12 2.94
2486 4099 5.358442 ACTCAAGTGTACTAGCAGTAGGATG 59.642 44.000 0.00 0.00 30.12 3.51
2487 4100 5.506708 TCAAGTGTACTAGCAGTAGGATGA 58.493 41.667 0.00 0.00 30.12 2.92
2488 4101 6.129874 TCAAGTGTACTAGCAGTAGGATGAT 58.870 40.000 0.00 0.00 30.12 2.45
2489 4102 6.607600 TCAAGTGTACTAGCAGTAGGATGATT 59.392 38.462 0.00 0.00 30.12 2.57
2490 4103 7.124298 TCAAGTGTACTAGCAGTAGGATGATTT 59.876 37.037 0.00 0.00 30.12 2.17
2494 4111 7.982354 GTGTACTAGCAGTAGGATGATTTCTTT 59.018 37.037 0.00 0.00 30.12 2.52
2503 4120 5.559148 AGGATGATTTCTTTCGCTAGGAT 57.441 39.130 0.00 0.00 0.00 3.24
2512 4129 3.068307 TCTTTCGCTAGGATAGAAGTGCC 59.932 47.826 0.00 0.00 42.77 5.01
2516 4133 4.149598 TCGCTAGGATAGAAGTGCCAATA 58.850 43.478 0.00 0.00 42.77 1.90
2518 4135 4.021894 CGCTAGGATAGAAGTGCCAATACT 60.022 45.833 0.00 0.00 42.77 2.12
2528 4145 7.472334 AGAAGTGCCAATACTCATTTCATTT 57.528 32.000 0.00 0.00 33.21 2.32
2531 4148 7.338800 AGTGCCAATACTCATTTCATTTAGG 57.661 36.000 0.00 0.00 0.00 2.69
2535 4152 7.395772 TGCCAATACTCATTTCATTTAGGAACA 59.604 33.333 0.00 0.00 0.00 3.18
2536 4153 8.416329 GCCAATACTCATTTCATTTAGGAACAT 58.584 33.333 0.00 0.00 0.00 2.71
2537 4154 9.740239 CCAATACTCATTTCATTTAGGAACATG 57.260 33.333 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 92 1.666872 AGGAGAAACGTTTCCGCCG 60.667 57.895 31.87 0.00 38.54 6.46
381 385 4.087892 CTGGTGGGGCGTGGAGAG 62.088 72.222 0.00 0.00 0.00 3.20
432 436 2.756829 CTGATGGCTAGCTCAGATGTG 58.243 52.381 23.16 2.77 41.13 3.21
486 490 4.742201 TCTTCAGCTGTCGCCGGC 62.742 66.667 19.07 19.07 43.73 6.13
499 533 0.929615 GCGAGATGCTCTGCTTCTTC 59.070 55.000 8.89 2.61 41.89 2.87
528 562 5.731686 GCTTTGGAATAATGCACTGCTAGTC 60.732 44.000 1.98 0.00 0.00 2.59
532 566 2.167075 GGCTTTGGAATAATGCACTGCT 59.833 45.455 1.98 0.00 0.00 4.24
533 567 2.167075 AGGCTTTGGAATAATGCACTGC 59.833 45.455 0.00 0.00 0.00 4.40
534 568 4.178540 CAAGGCTTTGGAATAATGCACTG 58.821 43.478 0.00 0.00 0.00 3.66
535 569 3.834231 ACAAGGCTTTGGAATAATGCACT 59.166 39.130 13.65 0.00 38.66 4.40
536 570 4.176271 GACAAGGCTTTGGAATAATGCAC 58.824 43.478 13.65 0.00 38.66 4.57
537 571 3.831333 TGACAAGGCTTTGGAATAATGCA 59.169 39.130 13.65 0.00 38.66 3.96
538 572 4.176271 GTGACAAGGCTTTGGAATAATGC 58.824 43.478 13.65 0.00 38.66 3.56
539 573 5.389859 TGTGACAAGGCTTTGGAATAATG 57.610 39.130 13.65 0.00 38.66 1.90
541 575 5.538053 TGATTGTGACAAGGCTTTGGAATAA 59.462 36.000 13.65 5.59 38.66 1.40
544 578 3.295093 TGATTGTGACAAGGCTTTGGAA 58.705 40.909 13.65 0.00 38.66 3.53
546 580 3.731652 TTGATTGTGACAAGGCTTTGG 57.268 42.857 13.65 0.00 38.66 3.28
547 581 6.607735 ATTTTTGATTGTGACAAGGCTTTG 57.392 33.333 7.07 7.07 40.24 2.77
549 583 7.054491 AGTATTTTTGATTGTGACAAGGCTT 57.946 32.000 3.74 0.00 0.00 4.35
551 585 7.713764 AAAGTATTTTTGATTGTGACAAGGC 57.286 32.000 3.74 0.00 31.62 4.35
578 614 1.226746 GAGTGGTGGTTGTGCTGTAC 58.773 55.000 0.00 0.00 0.00 2.90
601 637 3.563808 TCACGTCCATTTCTCCACTTTTG 59.436 43.478 0.00 0.00 0.00 2.44
645 681 0.482446 AAATCCCCTGGACAAGTGCA 59.518 50.000 0.00 0.00 32.98 4.57
673 731 4.264638 GCCGGCGAGCTCTCTCTC 62.265 72.222 12.58 0.00 37.19 3.20
699 757 3.038280 CTCTCCATCGGCCTCTCG 58.962 66.667 0.00 0.00 0.00 4.04
1110 1187 3.311110 GTGTGGGTCGAGAGGGCA 61.311 66.667 0.00 0.00 0.00 5.36
1131 1208 1.206578 GTTCGTTCATGGTGGCGTG 59.793 57.895 0.00 0.00 0.00 5.34
1132 1209 1.964373 GGTTCGTTCATGGTGGCGT 60.964 57.895 0.00 0.00 0.00 5.68
1134 1211 1.467342 GTTAGGTTCGTTCATGGTGGC 59.533 52.381 0.00 0.00 0.00 5.01
1164 1244 3.550275 TGCGCAAACTGTAATATCGAGAC 59.450 43.478 8.16 0.00 0.00 3.36
1165 1245 3.776340 TGCGCAAACTGTAATATCGAGA 58.224 40.909 8.16 0.00 0.00 4.04
1400 2981 1.748122 GTACCTCTCCGCCGTGAGA 60.748 63.158 5.81 5.71 39.04 3.27
1440 3021 2.556459 CGTCCTCCTCGGCGATGAT 61.556 63.158 11.27 0.00 35.30 2.45
1443 3024 3.210528 GACGTCCTCCTCGGCGAT 61.211 66.667 11.27 0.00 36.55 4.58
1607 3188 3.909776 TGAAGTTTGCTGCTGATTCAG 57.090 42.857 9.40 9.40 37.15 3.02
1612 3193 3.479489 TGAAGATGAAGTTTGCTGCTGA 58.521 40.909 0.00 0.00 0.00 4.26
1613 3194 3.252701 ACTGAAGATGAAGTTTGCTGCTG 59.747 43.478 0.00 0.00 0.00 4.41
1614 3195 3.484407 ACTGAAGATGAAGTTTGCTGCT 58.516 40.909 0.00 0.00 0.00 4.24
1615 3196 3.911661 ACTGAAGATGAAGTTTGCTGC 57.088 42.857 0.00 0.00 0.00 5.25
1674 3261 9.366216 GTTTGAACTTTTAACCAAACATCTCTT 57.634 29.630 0.00 0.00 44.42 2.85
1686 3273 3.440228 TGCTGCGGTTTGAACTTTTAAC 58.560 40.909 0.00 0.00 0.00 2.01
1689 3276 2.100584 TGATGCTGCGGTTTGAACTTTT 59.899 40.909 0.00 0.00 0.00 2.27
1690 3277 1.680735 TGATGCTGCGGTTTGAACTTT 59.319 42.857 0.00 0.00 0.00 2.66
1691 3278 1.317613 TGATGCTGCGGTTTGAACTT 58.682 45.000 0.00 0.00 0.00 2.66
1693 3280 1.791555 CGATGATGCTGCGGTTTGAAC 60.792 52.381 0.00 0.00 0.00 3.18
1695 3282 0.390998 TCGATGATGCTGCGGTTTGA 60.391 50.000 0.00 0.00 0.00 2.69
1698 3285 2.238942 TATTCGATGATGCTGCGGTT 57.761 45.000 0.00 0.00 0.00 4.44
1699 3286 2.138320 CTTATTCGATGATGCTGCGGT 58.862 47.619 0.00 0.00 0.00 5.68
1700 3287 2.407090 TCTTATTCGATGATGCTGCGG 58.593 47.619 0.00 0.00 0.00 5.69
1701 3288 4.658713 ATTCTTATTCGATGATGCTGCG 57.341 40.909 0.00 0.00 0.00 5.18
1702 3289 7.069852 ACATATTCTTATTCGATGATGCTGC 57.930 36.000 0.00 0.00 0.00 5.25
1703 3290 8.933807 AGAACATATTCTTATTCGATGATGCTG 58.066 33.333 0.00 0.00 42.91 4.41
1704 3291 9.149225 GAGAACATATTCTTATTCGATGATGCT 57.851 33.333 0.00 0.00 45.60 3.79
1705 3292 9.149225 AGAGAACATATTCTTATTCGATGATGC 57.851 33.333 0.00 0.00 45.60 3.91
1724 3311 5.763204 GGACTTATTGTTTGGACAGAGAACA 59.237 40.000 0.00 0.00 37.04 3.18
1725 3312 5.763204 TGGACTTATTGTTTGGACAGAGAAC 59.237 40.000 0.00 0.00 37.04 3.01
1742 3329 9.945904 TTGTTGTTACACACATATATGGACTTA 57.054 29.630 16.96 0.77 34.43 2.24
1755 3342 9.225201 CTGCATCATAATATTGTTGTTACACAC 57.775 33.333 0.00 0.00 32.98 3.82
1795 3382 8.699130 AGGTTTTGTCAAGATCAAGAGAAATTT 58.301 29.630 9.48 0.00 28.90 1.82
1796 3383 8.242729 AGGTTTTGTCAAGATCAAGAGAAATT 57.757 30.769 9.48 0.09 28.90 1.82
1804 3391 5.163561 GGTGTCAAGGTTTTGTCAAGATCAA 60.164 40.000 0.00 0.00 34.86 2.57
1806 3393 4.261614 GGGTGTCAAGGTTTTGTCAAGATC 60.262 45.833 0.00 0.00 34.86 2.75
1807 3394 3.636764 GGGTGTCAAGGTTTTGTCAAGAT 59.363 43.478 0.00 0.00 34.86 2.40
1808 3395 3.020984 GGGTGTCAAGGTTTTGTCAAGA 58.979 45.455 0.00 0.00 34.86 3.02
1823 3410 5.866335 TTTATCGTAATGTGTTGGGTGTC 57.134 39.130 0.00 0.00 0.00 3.67
1824 3411 6.487331 TCTTTTTATCGTAATGTGTTGGGTGT 59.513 34.615 0.00 0.00 0.00 4.16
1825 3412 6.904498 TCTTTTTATCGTAATGTGTTGGGTG 58.096 36.000 0.00 0.00 0.00 4.61
1826 3413 7.513371 TTCTTTTTATCGTAATGTGTTGGGT 57.487 32.000 0.00 0.00 0.00 4.51
1838 3425 8.836413 TCATGTCTGAAGTTTTCTTTTTATCGT 58.164 29.630 0.00 0.00 40.61 3.73
1839 3426 9.663904 TTCATGTCTGAAGTTTTCTTTTTATCG 57.336 29.630 0.00 0.00 40.61 2.92
1864 3451 5.569355 TGTATCCATGTTCTTGGTGACATT 58.431 37.500 0.00 0.00 42.32 2.71
1912 3522 5.975693 TGGTTTTATTTAGCCAAGGAGTG 57.024 39.130 0.00 0.00 0.00 3.51
1919 3529 5.889289 GGTAGGTCATGGTTTTATTTAGCCA 59.111 40.000 0.00 0.00 35.28 4.75
1927 3537 2.093341 GCTCCGGTAGGTCATGGTTTTA 60.093 50.000 0.00 0.00 39.05 1.52
1928 3538 1.339727 GCTCCGGTAGGTCATGGTTTT 60.340 52.381 0.00 0.00 39.05 2.43
1943 3553 3.000322 CACTAGCTTGTAATTTCGCTCCG 60.000 47.826 0.00 0.00 34.14 4.63
1944 3554 3.309954 CCACTAGCTTGTAATTTCGCTCC 59.690 47.826 0.00 0.00 34.14 4.70
1949 3559 8.957466 ACCTTTTATCCACTAGCTTGTAATTTC 58.043 33.333 0.00 0.00 0.00 2.17
1963 3573 3.245122 TGACCCTTGGACCTTTTATCCAC 60.245 47.826 0.00 0.00 46.09 4.02
1970 3580 1.455822 TCCATGACCCTTGGACCTTT 58.544 50.000 0.00 0.00 38.35 3.11
1973 3583 1.843851 TGTATCCATGACCCTTGGACC 59.156 52.381 0.00 0.00 45.71 4.46
1974 3584 3.644966 TTGTATCCATGACCCTTGGAC 57.355 47.619 0.00 0.00 45.71 4.02
2026 3637 3.685550 CGGATTCCTTCAGCCTAATGGTT 60.686 47.826 0.30 0.00 35.27 3.67
2028 3639 2.498167 CGGATTCCTTCAGCCTAATGG 58.502 52.381 0.30 0.00 0.00 3.16
2031 3642 3.780624 GCGGATTCCTTCAGCCTAA 57.219 52.632 0.30 0.00 39.36 2.69
2164 3775 0.898789 TCCGAGTCGAAAGCCCTTCT 60.899 55.000 15.64 0.00 31.20 2.85
2233 3844 3.450096 TCAGTGCTACTCTCATTGATGCT 59.550 43.478 0.00 0.00 0.00 3.79
2239 3850 5.245751 CCCAGATATCAGTGCTACTCTCATT 59.754 44.000 5.32 0.00 0.00 2.57
2242 3853 4.148838 ACCCAGATATCAGTGCTACTCTC 58.851 47.826 5.32 0.00 0.00 3.20
2248 3859 1.414181 CGGAACCCAGATATCAGTGCT 59.586 52.381 5.32 0.00 0.00 4.40
2251 3862 4.261801 CAAAACGGAACCCAGATATCAGT 58.738 43.478 5.32 0.00 0.00 3.41
2257 3868 1.423921 AGGACAAAACGGAACCCAGAT 59.576 47.619 0.00 0.00 0.00 2.90
2260 3871 1.394618 CAAGGACAAAACGGAACCCA 58.605 50.000 0.00 0.00 0.00 4.51
2266 3877 0.168128 GGATCGCAAGGACAAAACGG 59.832 55.000 0.00 0.00 38.47 4.44
2269 3880 3.074412 GAGAAGGATCGCAAGGACAAAA 58.926 45.455 0.00 0.00 38.47 2.44
2287 3898 1.059584 TTGGGGAAGTGGTGCTGAGA 61.060 55.000 0.00 0.00 0.00 3.27
2305 3916 0.899720 TCGGCGGTCCTAAAGATGTT 59.100 50.000 7.21 0.00 0.00 2.71
2373 3984 9.237187 TGAGTTCATTGTAGTGCCATTATTTTA 57.763 29.630 0.00 0.00 0.00 1.52
2374 3985 8.121305 TGAGTTCATTGTAGTGCCATTATTTT 57.879 30.769 0.00 0.00 0.00 1.82
2375 3986 7.701539 TGAGTTCATTGTAGTGCCATTATTT 57.298 32.000 0.00 0.00 0.00 1.40
2377 3988 7.886629 AATGAGTTCATTGTAGTGCCATTAT 57.113 32.000 6.56 0.00 44.22 1.28
2378 3989 7.701539 AAATGAGTTCATTGTAGTGCCATTA 57.298 32.000 8.04 0.00 45.06 1.90
2379 3990 6.594788 AAATGAGTTCATTGTAGTGCCATT 57.405 33.333 8.04 0.00 45.06 3.16
2381 3992 5.534278 TGAAAATGAGTTCATTGTAGTGCCA 59.466 36.000 8.04 0.00 45.06 4.92
2382 3993 6.012658 TGAAAATGAGTTCATTGTAGTGCC 57.987 37.500 8.04 0.00 45.06 5.01
2404 4016 8.349245 TCACATAAGCCGGTTAATATTTCAATG 58.651 33.333 1.90 0.00 0.00 2.82
2406 4018 7.337184 TGTCACATAAGCCGGTTAATATTTCAA 59.663 33.333 1.90 0.00 0.00 2.69
2414 4026 4.209307 TCATGTCACATAAGCCGGTTAA 57.791 40.909 1.90 0.00 0.00 2.01
2419 4031 5.676744 CGTAAAATTCATGTCACATAAGCCG 59.323 40.000 0.00 0.00 0.00 5.52
2420 4032 6.781138 TCGTAAAATTCATGTCACATAAGCC 58.219 36.000 0.00 0.00 0.00 4.35
2433 4045 9.605955 CTGTGTAAAACATGATCGTAAAATTCA 57.394 29.630 0.00 0.00 38.39 2.57
2436 4048 8.330466 TCCTGTGTAAAACATGATCGTAAAAT 57.670 30.769 0.00 0.00 38.39 1.82
2442 4055 5.408299 TGAGTTCCTGTGTAAAACATGATCG 59.592 40.000 0.00 0.00 38.39 3.69
2453 4066 5.048224 GCTAGTACACTTGAGTTCCTGTGTA 60.048 44.000 0.00 0.00 42.61 2.90
2455 4068 4.238514 GCTAGTACACTTGAGTTCCTGTG 58.761 47.826 0.00 0.00 36.59 3.66
2459 4072 4.522722 ACTGCTAGTACACTTGAGTTCC 57.477 45.455 0.00 0.00 0.00 3.62
2465 4078 5.836821 TCATCCTACTGCTAGTACACTTG 57.163 43.478 0.00 0.00 0.00 3.16
2470 4083 7.380065 CGAAAGAAATCATCCTACTGCTAGTAC 59.620 40.741 0.00 0.00 0.00 2.73
2476 4089 3.873952 AGCGAAAGAAATCATCCTACTGC 59.126 43.478 0.00 0.00 0.00 4.40
2477 4090 5.694006 CCTAGCGAAAGAAATCATCCTACTG 59.306 44.000 0.00 0.00 0.00 2.74
2478 4091 5.598830 TCCTAGCGAAAGAAATCATCCTACT 59.401 40.000 0.00 0.00 0.00 2.57
2479 4092 5.844004 TCCTAGCGAAAGAAATCATCCTAC 58.156 41.667 0.00 0.00 0.00 3.18
2480 4093 6.672266 ATCCTAGCGAAAGAAATCATCCTA 57.328 37.500 0.00 0.00 0.00 2.94
2481 4094 5.559148 ATCCTAGCGAAAGAAATCATCCT 57.441 39.130 0.00 0.00 0.00 3.24
2482 4095 6.692486 TCTATCCTAGCGAAAGAAATCATCC 58.308 40.000 0.00 0.00 0.00 3.51
2483 4096 7.870445 ACTTCTATCCTAGCGAAAGAAATCATC 59.130 37.037 0.00 0.00 0.00 2.92
2484 4097 7.655328 CACTTCTATCCTAGCGAAAGAAATCAT 59.345 37.037 0.00 0.00 0.00 2.45
2486 4099 6.074034 GCACTTCTATCCTAGCGAAAGAAATC 60.074 42.308 0.00 0.00 0.00 2.17
2487 4100 5.755861 GCACTTCTATCCTAGCGAAAGAAAT 59.244 40.000 0.00 0.00 0.00 2.17
2488 4101 5.109903 GCACTTCTATCCTAGCGAAAGAAA 58.890 41.667 0.00 0.00 0.00 2.52
2489 4102 4.441634 GGCACTTCTATCCTAGCGAAAGAA 60.442 45.833 0.00 0.00 0.00 2.52
2490 4103 3.068307 GGCACTTCTATCCTAGCGAAAGA 59.932 47.826 0.00 0.00 0.00 2.52
2494 4111 2.067365 TGGCACTTCTATCCTAGCGA 57.933 50.000 0.00 0.00 0.00 4.93
2503 4120 8.579850 AAATGAAATGAGTATTGGCACTTCTA 57.420 30.769 0.00 0.00 0.00 2.10
2516 4133 9.246670 TCATTCATGTTCCTAAATGAAATGAGT 57.753 29.630 2.52 0.00 43.86 3.41
2548 4165 7.362747 CCCACAAGACTTCTCGTAAGTATACTT 60.363 40.741 21.35 21.35 39.85 2.24
2565 4182 2.289195 TGTATCAACCGTCCCACAAGAC 60.289 50.000 0.00 0.00 0.00 3.01
2571 4188 2.675603 CGTCATTGTATCAACCGTCCCA 60.676 50.000 0.00 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.