Multiple sequence alignment - TraesCS7A01G456600

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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 TraesCS7A01G456600 chr7A 100.000 3251 0 0 1 3251 652506381 652509631 0.000000e+00 6004.0
1 TraesCS7A01G456600 chr7D 90.554 2435 153 36 1 2372 566190821 566193241 0.000000e+00 3151.0
2 TraesCS7A01G456600 chr7D 86.335 805 61 24 2469 3249 566197535 566198314 0.000000e+00 832.0
3 TraesCS7A01G456600 chr7D 96.667 60 2 0 2411 2470 566197388 566197447 2.060000e-17 100.0
4 TraesCS7A01G456600 chr7D 98.077 52 1 0 2368 2419 566196927 566196978 1.240000e-14 91.6
5 TraesCS7A01G456600 chr7B 90.062 1449 95 33 762 2195 617827709 617829123 0.000000e+00 1832.0
6 TraesCS7A01G456600 chr7B 86.129 757 72 13 1 741 617826719 617827458 0.000000e+00 785.0
7 TraesCS7A01G456600 chr7B 83.553 152 25 0 2232 2383 56921455 56921304 3.380000e-30 143.0
8 TraesCS7A01G456600 chr4A 84.916 179 25 2 2204 2380 512543362 512543184 2.580000e-41 180.0
9 TraesCS7A01G456600 chr4D 82.682 179 29 2 2204 2380 75046433 75046611 1.210000e-34 158.0
10 TraesCS7A01G456600 chr4D 83.333 150 19 5 405 551 74079505 74079359 2.030000e-27 134.0
11 TraesCS7A01G456600 chr4D 81.579 152 20 5 409 557 13604954 13604808 5.700000e-23 119.0
12 TraesCS7A01G456600 chr4B 83.051 177 27 3 2204 2378 107453156 107453331 1.210000e-34 158.0
13 TraesCS7A01G456600 chrUn 83.553 152 18 5 2200 2349 374044465 374044611 5.660000e-28 135.0
14 TraesCS7A01G456600 chrUn 95.349 43 2 0 917 959 38014705 38014663 5.820000e-08 69.4
15 TraesCS7A01G456600 chrUn 95.349 43 2 0 917 959 342675115 342675073 5.820000e-08 69.4
16 TraesCS7A01G456600 chrUn 95.349 43 2 0 917 959 388617132 388617174 5.820000e-08 69.4
17 TraesCS7A01G456600 chrUn 95.349 43 2 0 917 959 473374678 473374720 5.820000e-08 69.4
18 TraesCS7A01G456600 chr2D 83.893 149 17 5 2203 2349 4324165 4324022 5.660000e-28 135.0
19 TraesCS7A01G456600 chr2D 83.893 149 17 5 2203 2349 4349364 4349221 5.660000e-28 135.0
20 TraesCS7A01G456600 chr2D 83.893 149 17 5 2203 2349 4380889 4380746 5.660000e-28 135.0
21 TraesCS7A01G456600 chr1A 82.993 147 17 6 409 551 155857856 155857714 3.410000e-25 126.0
22 TraesCS7A01G456600 chr6D 82.759 145 20 4 409 551 256728599 256728458 1.220000e-24 124.0
23 TraesCS7A01G456600 chr6D 82.759 145 20 4 409 551 256729396 256729255 1.220000e-24 124.0
24 TraesCS7A01G456600 chr3B 82.432 148 20 5 405 549 738374865 738375009 1.220000e-24 124.0
25 TraesCS7A01G456600 chr2A 82.877 146 18 6 409 551 79316154 79316013 1.220000e-24 124.0
26 TraesCS7A01G456600 chr5A 79.675 123 21 4 838 958 310043361 310043481 5.780000e-13 86.1


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 TraesCS7A01G456600 chr7A 652506381 652509631 3250 False 6004.00 6004 100.00000 1 3251 1 chr7A.!!$F1 3250
1 TraesCS7A01G456600 chr7D 566190821 566198314 7493 False 1043.65 3151 92.90825 1 3249 4 chr7D.!!$F1 3248
2 TraesCS7A01G456600 chr7B 617826719 617829123 2404 False 1308.50 1832 88.09550 1 2195 2 chr7B.!!$F1 2194

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
582 606 0.616395 TTGGTGACCGGGCTAGATGA 60.616 55.0 9.82 0.0 0.0 2.92 F
1292 1570 0.601558 TTTCCTCTCCGTCTCAACCG 59.398 55.0 0.00 0.0 0.0 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1461 1745 0.110644 CTTCAGTTTCTTCGCCACGC 60.111 55.0 0.00 0.00 0.0 5.34 R
2811 7350 0.103208 ACATGAGCCTCGATCGGAAC 59.897 55.0 16.41 4.66 0.0 3.62 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
240 250 2.050350 TCGCCCGATCGGAAAGAGT 61.050 57.895 35.42 0.00 37.50 3.24
241 251 0.749091 TCGCCCGATCGGAAAGAGTA 60.749 55.000 35.42 10.16 37.50 2.59
339 349 1.786579 CAACAACGCAAAAGCTTAGCC 59.213 47.619 15.67 0.17 0.00 3.93
355 365 1.439644 GCCTTTCGCTCTCGATCCT 59.560 57.895 0.00 0.00 45.04 3.24
356 366 0.669077 GCCTTTCGCTCTCGATCCTA 59.331 55.000 0.00 0.00 45.04 2.94
357 367 1.600912 GCCTTTCGCTCTCGATCCTAC 60.601 57.143 0.00 0.00 45.04 3.18
358 368 1.676529 CCTTTCGCTCTCGATCCTACA 59.323 52.381 0.00 0.00 45.04 2.74
372 383 4.652822 GATCCTACACAAGAAACCACCTT 58.347 43.478 0.00 0.00 0.00 3.50
437 450 9.277565 CTCCGTTCACAAATATAAGATGTTTTG 57.722 33.333 0.00 0.00 35.66 2.44
529 553 7.141100 TCCGATTTAGAAAAAGTTTAGCAGG 57.859 36.000 0.00 0.00 0.00 4.85
537 561 6.974965 AGAAAAAGTTTAGCAGGACATCTTG 58.025 36.000 0.00 0.00 0.00 3.02
549 573 5.621422 CAGGACATCTTGTATTTGTGAACG 58.379 41.667 0.00 0.00 0.00 3.95
578 602 1.296056 CGTTTTGGTGACCGGGCTAG 61.296 60.000 9.82 0.00 0.00 3.42
582 606 0.616395 TTGGTGACCGGGCTAGATGA 60.616 55.000 9.82 0.00 0.00 2.92
598 622 5.126061 GCTAGATGAAGCCCAGAATTTTTGA 59.874 40.000 0.00 0.00 36.45 2.69
599 623 6.350445 GCTAGATGAAGCCCAGAATTTTTGAA 60.350 38.462 0.00 0.00 36.45 2.69
600 624 6.423776 AGATGAAGCCCAGAATTTTTGAAA 57.576 33.333 0.00 0.00 0.00 2.69
601 625 6.829849 AGATGAAGCCCAGAATTTTTGAAAA 58.170 32.000 0.00 0.00 0.00 2.29
723 765 3.604582 TGAAATACCATGACATGCGACA 58.395 40.909 10.10 1.78 0.00 4.35
732 774 4.558470 CCATGACATGCGACATGTAAAAAC 59.442 41.667 20.38 11.38 41.78 2.43
741 784 5.460419 TGCGACATGTAAAAACCAAATTCAC 59.540 36.000 0.00 0.00 0.00 3.18
742 785 5.460419 GCGACATGTAAAAACCAAATTCACA 59.540 36.000 0.00 0.00 0.00 3.58
755 798 8.463930 AACCAAATTCACAGACTTTGAGAATA 57.536 30.769 10.28 0.00 43.46 1.75
815 1088 9.513906 TTAACAACCTCATTTCAATGTATCTCA 57.486 29.630 0.00 0.00 37.65 3.27
817 1090 8.218338 ACAACCTCATTTCAATGTATCTCATC 57.782 34.615 0.00 0.00 37.65 2.92
925 1198 3.505480 AAAAATTGCAAATGGAGGCCA 57.495 38.095 5.01 0.00 38.19 5.36
966 1239 2.399396 AGCAATTTTCGTGTGAACGG 57.601 45.000 0.00 0.00 32.71 4.44
967 1240 1.944024 AGCAATTTTCGTGTGAACGGA 59.056 42.857 0.00 0.00 32.71 4.69
969 1242 2.916111 CAATTTTCGTGTGAACGGAGG 58.084 47.619 0.00 0.00 32.71 4.30
996 1271 2.521465 TACCCACCACGGTCGTGT 60.521 61.111 19.94 7.55 44.02 4.49
1105 1383 2.526432 ACGTTCTAGCCTCTTCTCCAA 58.474 47.619 0.00 0.00 0.00 3.53
1106 1384 2.231721 ACGTTCTAGCCTCTTCTCCAAC 59.768 50.000 0.00 0.00 0.00 3.77
1113 1391 6.071984 TCTAGCCTCTTCTCCAACTAATAGG 58.928 44.000 0.00 0.00 0.00 2.57
1116 1394 4.698575 CCTCTTCTCCAACTAATAGGTGC 58.301 47.826 0.00 0.00 29.64 5.01
1124 1402 6.385759 TCTCCAACTAATAGGTGCTATGGAAA 59.614 38.462 0.00 0.00 29.64 3.13
1126 1404 7.406916 TCCAACTAATAGGTGCTATGGAAAAA 58.593 34.615 0.00 0.00 29.64 1.94
1181 1459 2.055042 GCGCTCCTCCTCCTCTTCA 61.055 63.158 0.00 0.00 0.00 3.02
1189 1467 2.158593 CCTCCTCCTCTTCATCCTCGTA 60.159 54.545 0.00 0.00 0.00 3.43
1290 1568 1.669211 CGGTTTCCTCTCCGTCTCAAC 60.669 57.143 0.00 0.00 41.58 3.18
1292 1570 0.601558 TTTCCTCTCCGTCTCAACCG 59.398 55.000 0.00 0.00 0.00 4.44
1296 1574 1.935327 CTCTCCGTCTCAACCGGGAC 61.935 65.000 6.32 1.89 45.51 4.46
1300 1578 1.374252 CGTCTCAACCGGGACCAAG 60.374 63.158 6.32 0.00 0.00 3.61
1301 1579 1.671379 GTCTCAACCGGGACCAAGC 60.671 63.158 6.32 0.00 0.00 4.01
1308 1586 1.078426 CCGGGACCAAGCTAACAGG 60.078 63.158 0.00 0.00 0.00 4.00
1341 1625 2.046023 TGCCGCTGCTGCTGTAAT 60.046 55.556 16.81 0.00 38.71 1.89
1411 1695 2.147387 ACCCTTGCCAGGACGACTT 61.147 57.895 5.14 0.00 44.19 3.01
1445 1729 1.519234 CTTGCAGATCGCGGTGCTA 60.519 57.895 23.17 17.24 46.97 3.49
1450 1734 1.788258 CAGATCGCGGTGCTATCAAT 58.212 50.000 6.13 0.00 33.93 2.57
1451 1735 1.458445 CAGATCGCGGTGCTATCAATG 59.542 52.381 6.13 0.00 33.93 2.82
1453 1737 1.723542 GATCGCGGTGCTATCAATGAG 59.276 52.381 6.13 0.00 32.17 2.90
1456 1740 0.940126 GCGGTGCTATCAATGAGGTG 59.060 55.000 0.00 0.00 0.00 4.00
1457 1741 0.940126 CGGTGCTATCAATGAGGTGC 59.060 55.000 0.00 0.00 0.00 5.01
1460 1744 2.420547 GGTGCTATCAATGAGGTGCTGA 60.421 50.000 6.50 0.00 0.00 4.26
1461 1745 2.871022 GTGCTATCAATGAGGTGCTGAG 59.129 50.000 6.50 0.00 0.00 3.35
1484 1768 1.270839 TGGCGAAGAAACTGAAGGAGG 60.271 52.381 0.00 0.00 0.00 4.30
1485 1769 1.002087 GGCGAAGAAACTGAAGGAGGA 59.998 52.381 0.00 0.00 0.00 3.71
1533 1817 0.249657 ATCTTCTTCATCGGGAGCGC 60.250 55.000 0.00 0.00 0.00 5.92
1588 1875 0.732880 CGTCGACGCTCCAAGACAAT 60.733 55.000 26.59 0.00 33.56 2.71
1589 1876 0.992802 GTCGACGCTCCAAGACAATC 59.007 55.000 0.00 0.00 34.09 2.67
1590 1877 0.601057 TCGACGCTCCAAGACAATCA 59.399 50.000 0.00 0.00 0.00 2.57
1591 1878 0.994995 CGACGCTCCAAGACAATCAG 59.005 55.000 0.00 0.00 0.00 2.90
1592 1879 1.363744 GACGCTCCAAGACAATCAGG 58.636 55.000 0.00 0.00 0.00 3.86
1593 1880 0.674895 ACGCTCCAAGACAATCAGGC 60.675 55.000 0.00 0.00 0.00 4.85
1594 1881 1.699656 CGCTCCAAGACAATCAGGCG 61.700 60.000 0.00 0.00 35.75 5.52
1595 1882 1.372087 GCTCCAAGACAATCAGGCGG 61.372 60.000 0.00 0.00 0.00 6.13
1596 1883 0.745845 CTCCAAGACAATCAGGCGGG 60.746 60.000 0.00 0.00 0.00 6.13
1634 1921 1.381463 AAGGTAGACGCCTCCTCCC 60.381 63.158 0.00 0.00 38.03 4.30
1635 1922 2.043248 GGTAGACGCCTCCTCCCA 60.043 66.667 0.00 0.00 0.00 4.37
1636 1923 1.457831 GGTAGACGCCTCCTCCCAT 60.458 63.158 0.00 0.00 0.00 4.00
1666 1953 0.452784 GCAAGCAGGAACTTTACGCG 60.453 55.000 3.53 3.53 34.60 6.01
1726 2013 0.754957 AGATGCAGAGGGAGGAGTCG 60.755 60.000 0.00 0.00 0.00 4.18
1808 2095 7.051623 GGCCTTCTAGAGATTCTCGATCTATA 58.948 42.308 8.01 0.00 45.17 1.31
1837 2124 5.645929 CGTATCTAGAGTCTAGATGCATGGT 59.354 44.000 36.67 22.46 36.76 3.55
1838 2125 6.819146 CGTATCTAGAGTCTAGATGCATGGTA 59.181 42.308 36.67 22.41 36.76 3.25
1839 2126 7.011016 CGTATCTAGAGTCTAGATGCATGGTAG 59.989 44.444 36.67 24.53 36.76 3.18
1840 2127 5.007034 TCTAGAGTCTAGATGCATGGTAGC 58.993 45.833 23.38 1.98 0.00 3.58
1882 2173 0.729116 GCATGTGCAGATACGCTGTT 59.271 50.000 0.00 0.00 46.62 3.16
1965 2268 8.862325 ACAGATATTATGTTGTTTGGTTCTCA 57.138 30.769 0.00 0.00 0.00 3.27
2120 2426 8.934023 AAGTCACCTGAATTTTCTATTTGGTA 57.066 30.769 0.00 0.00 0.00 3.25
2361 2675 9.794685 TTTATTAATCAATTATCGCAGCAACAA 57.205 25.926 0.00 0.00 0.00 2.83
2433 6855 8.241367 GGGTAGAAATAAACCACATACAACTTG 58.759 37.037 0.00 0.00 0.00 3.16
2588 7102 5.872070 CCTAGAAGTTCACTCTTCCACAATC 59.128 44.000 5.50 0.00 43.17 2.67
2595 7109 2.486982 CACTCTTCCACAATCTGCAAGG 59.513 50.000 0.00 0.00 0.00 3.61
2669 7183 8.494016 AAACTTCTATACAATGACTAGCCAAC 57.506 34.615 0.00 0.00 0.00 3.77
2674 7188 7.145985 TCTATACAATGACTAGCCAACGAATC 58.854 38.462 0.00 0.00 0.00 2.52
2683 7197 7.896811 TGACTAGCCAACGAATCTATGATTAT 58.103 34.615 0.00 0.00 0.00 1.28
2684 7198 9.020731 TGACTAGCCAACGAATCTATGATTATA 57.979 33.333 0.00 0.00 0.00 0.98
2686 7200 9.809096 ACTAGCCAACGAATCTATGATTATATG 57.191 33.333 0.00 0.00 0.00 1.78
2689 7203 9.896645 AGCCAACGAATCTATGATTATATGATT 57.103 29.630 0.00 0.00 0.00 2.57
2731 7245 8.472683 TTCAAATGTTGTGAACCTTGTTTAAG 57.527 30.769 0.00 0.00 30.08 1.85
2734 7248 9.360093 CAAATGTTGTGAACCTTGTTTAAGTTA 57.640 29.630 0.00 0.00 31.80 2.24
2738 7252 9.930693 TGTTGTGAACCTTGTTTAAGTTATTTT 57.069 25.926 0.00 0.00 31.80 1.82
2788 7327 4.067972 TGGTCAACTAACCAGTGTCTTC 57.932 45.455 0.00 0.00 44.40 2.87
2789 7328 3.181458 TGGTCAACTAACCAGTGTCTTCC 60.181 47.826 0.00 0.00 44.40 3.46
2790 7329 3.071167 GGTCAACTAACCAGTGTCTTCCT 59.929 47.826 0.00 0.00 39.27 3.36
2791 7330 4.444449 GGTCAACTAACCAGTGTCTTCCTT 60.444 45.833 0.00 0.00 39.27 3.36
2792 7331 5.123936 GTCAACTAACCAGTGTCTTCCTTT 58.876 41.667 0.00 0.00 34.36 3.11
2793 7332 5.589050 GTCAACTAACCAGTGTCTTCCTTTT 59.411 40.000 0.00 0.00 34.36 2.27
2830 7369 0.103208 GTTCCGATCGAGGCTCATGT 59.897 55.000 18.66 0.00 0.00 3.21
2833 7372 0.387202 CCGATCGAGGCTCATGTTCT 59.613 55.000 18.66 0.00 0.00 3.01
2834 7373 1.601663 CCGATCGAGGCTCATGTTCTC 60.602 57.143 18.66 0.67 0.00 2.87
2837 7376 3.425578 CGAGGCTCATGTTCTCGTT 57.574 52.632 15.95 0.00 43.51 3.85
2838 7377 1.272781 CGAGGCTCATGTTCTCGTTC 58.727 55.000 15.95 1.25 43.51 3.95
2839 7378 1.272781 GAGGCTCATGTTCTCGTTCG 58.727 55.000 10.25 0.00 0.00 3.95
2841 7380 1.000955 AGGCTCATGTTCTCGTTCGTT 59.999 47.619 0.00 0.00 0.00 3.85
2842 7381 1.798813 GGCTCATGTTCTCGTTCGTTT 59.201 47.619 0.00 0.00 0.00 3.60
2843 7382 2.159827 GGCTCATGTTCTCGTTCGTTTC 60.160 50.000 0.00 0.00 0.00 2.78
2844 7383 2.731976 GCTCATGTTCTCGTTCGTTTCT 59.268 45.455 0.00 0.00 0.00 2.52
2845 7384 3.184581 GCTCATGTTCTCGTTCGTTTCTT 59.815 43.478 0.00 0.00 0.00 2.52
2846 7385 4.664389 GCTCATGTTCTCGTTCGTTTCTTC 60.664 45.833 0.00 0.00 0.00 2.87
2847 7386 4.617959 TCATGTTCTCGTTCGTTTCTTCT 58.382 39.130 0.00 0.00 0.00 2.85
2849 7388 5.856986 TCATGTTCTCGTTCGTTTCTTCTAG 59.143 40.000 0.00 0.00 0.00 2.43
2850 7389 5.179045 TGTTCTCGTTCGTTTCTTCTAGT 57.821 39.130 0.00 0.00 0.00 2.57
2851 7390 5.585390 TGTTCTCGTTCGTTTCTTCTAGTT 58.415 37.500 0.00 0.00 0.00 2.24
2853 7392 6.532657 TGTTCTCGTTCGTTTCTTCTAGTTTT 59.467 34.615 0.00 0.00 0.00 2.43
2855 7394 7.158243 TCTCGTTCGTTTCTTCTAGTTTTTC 57.842 36.000 0.00 0.00 0.00 2.29
2856 7395 6.199719 TCTCGTTCGTTTCTTCTAGTTTTTCC 59.800 38.462 0.00 0.00 0.00 3.13
2857 7396 5.234972 TCGTTCGTTTCTTCTAGTTTTTCCC 59.765 40.000 0.00 0.00 0.00 3.97
2982 7521 9.370126 CTTTGTTTCTTACATAGTTTTCACTCG 57.630 33.333 0.00 0.00 36.44 4.18
3002 7550 7.115663 TCACTCGTTTTTCCTTTGTTTTTCTTG 59.884 33.333 0.00 0.00 0.00 3.02
3010 7558 7.899178 TTCCTTTGTTTTTCTTGTTTCTTCC 57.101 32.000 0.00 0.00 0.00 3.46
3016 7564 6.394809 TGTTTTTCTTGTTTCTTCCTGGTTC 58.605 36.000 0.00 0.00 0.00 3.62
3054 7603 9.586435 CCTTTTCTTTTCTTTGTGTCTTAATGT 57.414 29.630 0.00 0.00 0.00 2.71
3097 7647 6.729690 TTCTTGAATTTCACAACCATTCCT 57.270 33.333 0.00 0.00 0.00 3.36
3186 7736 6.106003 TCTTTGTTTCTCTTTTGGAAAAGGC 58.894 36.000 11.10 0.00 44.22 4.35
3200 7750 3.596214 GAAAAGGCTATCACTCAACCGA 58.404 45.455 0.00 0.00 0.00 4.69
3201 7751 2.674796 AAGGCTATCACTCAACCGAC 57.325 50.000 0.00 0.00 0.00 4.79
3249 7799 2.426024 TCTTGATAGACACGTGGCCTAC 59.574 50.000 20.18 10.10 0.00 3.18
3250 7800 2.139323 TGATAGACACGTGGCCTACT 57.861 50.000 20.18 11.61 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 5.586243 GTCCCGTAAGTAACCTTTTTATCCC 59.414 44.000 0.00 0.00 31.89 3.85
240 250 5.383476 GCACTGGAGGTAGGAATAGTAGTA 58.617 45.833 0.00 0.00 0.00 1.82
241 251 4.216708 GCACTGGAGGTAGGAATAGTAGT 58.783 47.826 0.00 0.00 0.00 2.73
350 360 4.287766 AGGTGGTTTCTTGTGTAGGATC 57.712 45.455 0.00 0.00 0.00 3.36
351 361 4.104102 TCAAGGTGGTTTCTTGTGTAGGAT 59.896 41.667 0.00 0.00 41.52 3.24
352 362 3.456644 TCAAGGTGGTTTCTTGTGTAGGA 59.543 43.478 0.00 0.00 41.52 2.94
353 363 3.815401 CTCAAGGTGGTTTCTTGTGTAGG 59.185 47.826 0.00 0.00 41.52 3.18
355 365 3.118038 AGCTCAAGGTGGTTTCTTGTGTA 60.118 43.478 0.00 0.00 41.52 2.90
356 366 2.024414 GCTCAAGGTGGTTTCTTGTGT 58.976 47.619 0.00 0.00 41.52 3.72
357 367 2.301346 AGCTCAAGGTGGTTTCTTGTG 58.699 47.619 0.00 0.00 41.52 3.33
358 368 2.736670 AGCTCAAGGTGGTTTCTTGT 57.263 45.000 0.00 0.00 41.52 3.16
372 383 2.032620 GGGTCGGAGAAGATAAGCTCA 58.967 52.381 0.00 0.00 39.69 4.26
521 545 6.939730 TCACAAATACAAGATGTCCTGCTAAA 59.060 34.615 0.00 0.00 0.00 1.85
529 553 4.693566 TCCCGTTCACAAATACAAGATGTC 59.306 41.667 0.00 0.00 0.00 3.06
537 561 2.081462 CCCACTCCCGTTCACAAATAC 58.919 52.381 0.00 0.00 0.00 1.89
549 573 2.989253 CCAAAACGCCCCACTCCC 60.989 66.667 0.00 0.00 0.00 4.30
578 602 7.495135 TTTTTCAAAAATTCTGGGCTTCATC 57.505 32.000 0.00 0.00 0.00 2.92
695 737 5.475909 GCATGTCATGGTATTTCATCCTGAT 59.524 40.000 14.64 0.00 0.00 2.90
711 753 4.217334 TGGTTTTTACATGTCGCATGTCAT 59.783 37.500 22.74 7.42 33.76 3.06
723 765 9.097257 CAAAGTCTGTGAATTTGGTTTTTACAT 57.903 29.630 11.20 0.00 41.78 2.29
732 774 9.918630 ATTTATTCTCAAAGTCTGTGAATTTGG 57.081 29.630 16.67 9.99 44.35 3.28
812 1085 6.963242 CACGATGTGTAAATTTTCTGGATGAG 59.037 38.462 0.00 0.00 0.00 2.90
815 1088 6.817765 ACACGATGTGTAAATTTTCTGGAT 57.182 33.333 0.00 0.00 45.56 3.41
996 1271 6.720112 AGTTGGCCGTGTATTTATAGACTA 57.280 37.500 0.00 0.00 0.00 2.59
1124 1402 2.793278 GGCAACCTGACATTCGTTTT 57.207 45.000 0.00 0.00 0.00 2.43
1153 1431 1.524863 GGAGGAGCGCGGCTATCTTA 61.525 60.000 8.83 0.00 39.88 2.10
1162 1440 3.132481 GAAGAGGAGGAGGAGCGCG 62.132 68.421 0.00 0.00 0.00 6.86
1181 1459 1.696097 GGCACCATGGGTACGAGGAT 61.696 60.000 18.09 0.00 32.11 3.24
1189 1467 1.542375 AGAAGGAGGCACCATGGGT 60.542 57.895 18.09 0.00 42.04 4.51
1261 1539 3.984200 GAGGAAACCGGCCTCGACG 62.984 68.421 10.43 0.00 42.22 5.12
1273 1551 0.601558 CGGTTGAGACGGAGAGGAAA 59.398 55.000 0.00 0.00 0.00 3.13
1274 1552 2.264124 CGGTTGAGACGGAGAGGAA 58.736 57.895 0.00 0.00 0.00 3.36
1290 1568 1.078426 CCTGTTAGCTTGGTCCCGG 60.078 63.158 0.00 0.00 0.00 5.73
1292 1570 1.378646 GGCCTGTTAGCTTGGTCCC 60.379 63.158 0.00 0.00 0.00 4.46
1296 1574 2.048603 GGCTGGCCTGTTAGCTTGG 61.049 63.158 12.16 0.00 39.80 3.61
1328 1612 1.135286 GTTGGGAATTACAGCAGCAGC 60.135 52.381 0.00 0.00 42.56 5.25
1329 1613 1.474077 GGTTGGGAATTACAGCAGCAG 59.526 52.381 0.00 0.00 0.00 4.24
1341 1625 0.178975 GTGGTGATGGTGGTTGGGAA 60.179 55.000 0.00 0.00 0.00 3.97
1393 1677 0.834687 TAAGTCGTCCTGGCAAGGGT 60.835 55.000 7.48 0.00 44.62 4.34
1411 1695 2.843730 TGCAAGCAGATTTACCTCCCTA 59.156 45.455 0.00 0.00 0.00 3.53
1445 1729 0.251354 ACGCTCAGCACCTCATTGAT 59.749 50.000 0.00 0.00 0.00 2.57
1450 1734 4.687215 GCCACGCTCAGCACCTCA 62.687 66.667 0.00 0.00 0.00 3.86
1456 1740 2.317609 TTTCTTCGCCACGCTCAGC 61.318 57.895 0.00 0.00 0.00 4.26
1457 1741 0.946221 AGTTTCTTCGCCACGCTCAG 60.946 55.000 0.00 0.00 0.00 3.35
1460 1744 0.531974 TTCAGTTTCTTCGCCACGCT 60.532 50.000 0.00 0.00 0.00 5.07
1461 1745 0.110644 CTTCAGTTTCTTCGCCACGC 60.111 55.000 0.00 0.00 0.00 5.34
1468 1752 5.413309 TGATCTCCTCCTTCAGTTTCTTC 57.587 43.478 0.00 0.00 0.00 2.87
1484 1768 2.233922 TGGACGGGACTTTCTTGATCTC 59.766 50.000 0.00 0.00 0.00 2.75
1485 1769 2.234908 CTGGACGGGACTTTCTTGATCT 59.765 50.000 0.00 0.00 0.00 2.75
1582 1869 1.915078 CTTCCCCCGCCTGATTGTCT 61.915 60.000 0.00 0.00 0.00 3.41
1593 1880 4.354162 TTTTCCGCCCTTCCCCCG 62.354 66.667 0.00 0.00 0.00 5.73
1594 1881 2.362503 CTTTTCCGCCCTTCCCCC 60.363 66.667 0.00 0.00 0.00 5.40
1595 1882 2.362503 CCTTTTCCGCCCTTCCCC 60.363 66.667 0.00 0.00 0.00 4.81
1596 1883 1.977009 CACCTTTTCCGCCCTTCCC 60.977 63.158 0.00 0.00 0.00 3.97
1635 1922 2.438392 TCCTGCTTGCTCATGAGATCAT 59.562 45.455 27.04 0.00 36.96 2.45
1636 1923 1.835531 TCCTGCTTGCTCATGAGATCA 59.164 47.619 27.04 12.74 0.00 2.92
1666 1953 2.799540 GATGAACGCGTCGGCCTTC 61.800 63.158 14.44 5.69 35.54 3.46
1678 1965 3.424962 GCTTGTAGAAGTTGCCGATGAAC 60.425 47.826 1.12 0.00 0.00 3.18
1726 2013 1.518903 GGTCCTGCAGCTTGTTCCAC 61.519 60.000 8.66 0.00 0.00 4.02
1808 2095 5.863397 GCATCTAGACTCTAGATACGTACGT 59.137 44.000 25.98 25.98 33.34 3.57
1837 2124 9.431887 CATGCATGCACATATATATAGATGCTA 57.568 33.333 25.37 13.98 36.69 3.49
1838 2125 8.324163 CATGCATGCACATATATATAGATGCT 57.676 34.615 25.37 0.00 36.69 3.79
1867 2156 1.531149 ACACAAACAGCGTATCTGCAC 59.469 47.619 0.00 0.00 46.76 4.57
1874 2163 1.740297 ACCAACACACAAACAGCGTA 58.260 45.000 0.00 0.00 0.00 4.42
1882 2173 1.761784 ACCCTACGTACCAACACACAA 59.238 47.619 0.00 0.00 0.00 3.33
1963 2266 7.494625 GGTCGATGAAGGTAATTAAGAATGTGA 59.505 37.037 0.00 0.00 0.00 3.58
1964 2267 7.254795 GGGTCGATGAAGGTAATTAAGAATGTG 60.255 40.741 0.00 0.00 0.00 3.21
1965 2268 6.766467 GGGTCGATGAAGGTAATTAAGAATGT 59.234 38.462 0.00 0.00 0.00 2.71
2120 2426 6.719829 ACGGAGGGAAAAGAAAAATGACTTAT 59.280 34.615 0.00 0.00 0.00 1.73
2186 2493 6.043411 ACATGGTTAGATAGAGAAAAGCGTC 58.957 40.000 0.00 0.00 0.00 5.19
2304 2618 7.014422 TGGGTTGATAACGTAAGAACCAAATTT 59.986 33.333 16.21 0.00 38.26 1.82
2350 2664 0.605050 TACCATGCTTGTTGCTGCGA 60.605 50.000 0.00 0.00 43.37 5.10
2359 2673 6.821388 AGTTAACTAGAGGATACCATGCTTG 58.179 40.000 6.26 0.00 37.17 4.01
2361 2675 7.439108 AAAGTTAACTAGAGGATACCATGCT 57.561 36.000 8.92 0.00 37.17 3.79
2409 6413 8.293867 TGCAAGTTGTATGTGGTTTATTTCTAC 58.706 33.333 4.48 0.00 0.00 2.59
2441 6863 8.082852 AGCGAGTCACATCGTAATTTTATAGAT 58.917 33.333 0.00 0.00 44.53 1.98
2532 7044 8.994170 TGTGTGTAAGTTTTTATCATCATTCGA 58.006 29.630 0.00 0.00 0.00 3.71
2533 7045 9.773328 ATGTGTGTAAGTTTTTATCATCATTCG 57.227 29.630 0.00 0.00 0.00 3.34
2588 7102 7.262772 ACAATGTCATAAAATCATCCTTGCAG 58.737 34.615 0.00 0.00 0.00 4.41
2803 7342 3.118738 AGCCTCGATCGGAACATACTTTT 60.119 43.478 16.41 0.00 0.00 2.27
2811 7350 0.103208 ACATGAGCCTCGATCGGAAC 59.897 55.000 16.41 4.66 0.00 3.62
2830 7369 7.254218 GGAAAAACTAGAAGAAACGAACGAGAA 60.254 37.037 0.00 0.00 0.00 2.87
2833 7372 5.234972 GGGAAAAACTAGAAGAAACGAACGA 59.765 40.000 0.00 0.00 0.00 3.85
2834 7373 5.438117 GGGAAAAACTAGAAGAAACGAACG 58.562 41.667 0.00 0.00 0.00 3.95
2835 7374 5.278169 GGGGGAAAAACTAGAAGAAACGAAC 60.278 44.000 0.00 0.00 0.00 3.95
2837 7376 4.103627 AGGGGGAAAAACTAGAAGAAACGA 59.896 41.667 0.00 0.00 0.00 3.85
2838 7377 4.395625 AGGGGGAAAAACTAGAAGAAACG 58.604 43.478 0.00 0.00 0.00 3.60
2839 7378 6.726490 AAAGGGGGAAAAACTAGAAGAAAC 57.274 37.500 0.00 0.00 0.00 2.78
2889 7428 9.203421 GTGAAGAAACAGGAAAAGAAAGAAAAA 57.797 29.630 0.00 0.00 0.00 1.94
2890 7429 8.585018 AGTGAAGAAACAGGAAAAGAAAGAAAA 58.415 29.630 0.00 0.00 0.00 2.29
2891 7430 8.028938 CAGTGAAGAAACAGGAAAAGAAAGAAA 58.971 33.333 0.00 0.00 0.00 2.52
2892 7431 7.362920 CCAGTGAAGAAACAGGAAAAGAAAGAA 60.363 37.037 0.00 0.00 0.00 2.52
2893 7432 6.095440 CCAGTGAAGAAACAGGAAAAGAAAGA 59.905 38.462 0.00 0.00 0.00 2.52
2894 7433 6.127619 ACCAGTGAAGAAACAGGAAAAGAAAG 60.128 38.462 0.00 0.00 31.47 2.62
2895 7434 5.714806 ACCAGTGAAGAAACAGGAAAAGAAA 59.285 36.000 0.00 0.00 31.47 2.52
2896 7435 5.261216 ACCAGTGAAGAAACAGGAAAAGAA 58.739 37.500 0.00 0.00 31.47 2.52
2897 7436 4.855340 ACCAGTGAAGAAACAGGAAAAGA 58.145 39.130 0.00 0.00 31.47 2.52
2971 7510 6.020971 ACAAAGGAAAAACGAGTGAAAACT 57.979 33.333 0.00 0.00 0.00 2.66
2982 7521 9.944663 AAGAAACAAGAAAAACAAAGGAAAAAC 57.055 25.926 0.00 0.00 0.00 2.43
3132 7682 7.930865 TCAAAAAGGTACAATGGAAATGGAAAG 59.069 33.333 0.00 0.00 0.00 2.62
3133 7683 7.796054 TCAAAAAGGTACAATGGAAATGGAAA 58.204 30.769 0.00 0.00 0.00 3.13
3178 7728 2.678336 CGGTTGAGTGATAGCCTTTTCC 59.322 50.000 0.00 0.00 0.00 3.13
3186 7736 4.768130 ATATCCGTCGGTTGAGTGATAG 57.232 45.455 11.88 0.00 0.00 2.08
3200 7750 1.333524 CGAACGTCGTGCTATATCCGT 60.334 52.381 0.00 0.00 34.72 4.69
3201 7751 1.315497 CGAACGTCGTGCTATATCCG 58.685 55.000 0.00 0.00 34.72 4.18
3228 7778 1.557099 AGGCCACGTGTCTATCAAGA 58.443 50.000 15.65 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.