Multiple sequence alignment - TraesCS7B01G207800

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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 TraesCS7B01G207800 chr7B 100.000 2988 0 0 1 2988 380539030 380536043 0.000000e+00 5518
1 TraesCS7B01G207800 chr7B 79.696 527 80 16 2479 2984 643203121 643202601 3.660000e-94 355
2 TraesCS7B01G207800 chr7B 79.206 529 83 15 2478 2985 712853301 712852779 2.850000e-90 342
3 TraesCS7B01G207800 chr7B 79.600 500 75 16 2479 2957 636429909 636430402 1.720000e-87 333
4 TraesCS7B01G207800 chr7D 94.753 1963 81 8 378 2325 386360015 386358060 0.000000e+00 3035
5 TraesCS7B01G207800 chr7D 93.467 398 14 3 1 389 386360457 386360063 5.550000e-162 580
6 TraesCS7B01G207800 chr7A 93.225 1963 83 11 378 2323 434740918 434738989 0.000000e+00 2843
7 TraesCS7B01G207800 chr7A 95.373 389 13 3 3 389 434741351 434740966 5.470000e-172 614
8 TraesCS7B01G207800 chr4D 81.749 526 71 15 2479 2984 443713327 443712807 1.660000e-112 416
9 TraesCS7B01G207800 chr6D 81.644 523 74 16 2479 2984 455635394 455635911 5.960000e-112 414
10 TraesCS7B01G207800 chr2D 81.369 526 73 15 2479 2985 571067264 571067783 3.590000e-109 405
11 TraesCS7B01G207800 chr1D 81.369 526 73 16 2479 2984 461901024 461900504 3.590000e-109 405
12 TraesCS7B01G207800 chr1D 78.585 523 90 11 2479 2984 13008989 13009506 2.870000e-85 326
13 TraesCS7B01G207800 chr6B 80.819 537 77 15 2469 2984 679676930 679677461 6.000000e-107 398
14 TraesCS7B01G207800 chr6B 79.619 525 83 13 2479 2984 41109054 41109573 3.660000e-94 355
15 TraesCS7B01G207800 chr1B 80.989 526 75 13 2479 2984 629923302 629922782 7.760000e-106 394
16 TraesCS7B01G207800 chr1B 80.228 526 78 13 2479 2984 635437056 635436537 3.640000e-99 372
17 TraesCS7B01G207800 chr1B 77.927 521 90 13 2484 2984 429922805 429923320 4.840000e-78 302
18 TraesCS7B01G207800 chr4B 80.798 526 76 13 2479 2984 588581738 588582258 3.610000e-104 388
19 TraesCS7B01G207800 chr4B 79.732 523 84 13 2479 2984 100844405 100843888 2.830000e-95 359
20 TraesCS7B01G207800 chr4B 75.518 531 104 16 2478 2988 497226171 497226695 1.380000e-58 237
21 TraesCS7B01G207800 chr2B 79.278 526 82 16 2481 2985 263697700 263697181 2.850000e-90 342
22 TraesCS7B01G207800 chr2A 76.870 575 93 29 2416 2960 605306620 605306056 3.770000e-74 289


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 TraesCS7B01G207800 chr7B 380536043 380539030 2987 True 5518.0 5518 100.000 1 2988 1 chr7B.!!$R1 2987
1 TraesCS7B01G207800 chr7B 643202601 643203121 520 True 355.0 355 79.696 2479 2984 1 chr7B.!!$R2 505
2 TraesCS7B01G207800 chr7B 712852779 712853301 522 True 342.0 342 79.206 2478 2985 1 chr7B.!!$R3 507
3 TraesCS7B01G207800 chr7D 386358060 386360457 2397 True 1807.5 3035 94.110 1 2325 2 chr7D.!!$R1 2324
4 TraesCS7B01G207800 chr7A 434738989 434741351 2362 True 1728.5 2843 94.299 3 2323 2 chr7A.!!$R1 2320
5 TraesCS7B01G207800 chr4D 443712807 443713327 520 True 416.0 416 81.749 2479 2984 1 chr4D.!!$R1 505
6 TraesCS7B01G207800 chr6D 455635394 455635911 517 False 414.0 414 81.644 2479 2984 1 chr6D.!!$F1 505
7 TraesCS7B01G207800 chr2D 571067264 571067783 519 False 405.0 405 81.369 2479 2985 1 chr2D.!!$F1 506
8 TraesCS7B01G207800 chr1D 461900504 461901024 520 True 405.0 405 81.369 2479 2984 1 chr1D.!!$R1 505
9 TraesCS7B01G207800 chr1D 13008989 13009506 517 False 326.0 326 78.585 2479 2984 1 chr1D.!!$F1 505
10 TraesCS7B01G207800 chr6B 679676930 679677461 531 False 398.0 398 80.819 2469 2984 1 chr6B.!!$F2 515
11 TraesCS7B01G207800 chr6B 41109054 41109573 519 False 355.0 355 79.619 2479 2984 1 chr6B.!!$F1 505
12 TraesCS7B01G207800 chr1B 629922782 629923302 520 True 394.0 394 80.989 2479 2984 1 chr1B.!!$R1 505
13 TraesCS7B01G207800 chr1B 635436537 635437056 519 True 372.0 372 80.228 2479 2984 1 chr1B.!!$R2 505
14 TraesCS7B01G207800 chr1B 429922805 429923320 515 False 302.0 302 77.927 2484 2984 1 chr1B.!!$F1 500
15 TraesCS7B01G207800 chr4B 588581738 588582258 520 False 388.0 388 80.798 2479 2984 1 chr4B.!!$F2 505
16 TraesCS7B01G207800 chr4B 100843888 100844405 517 True 359.0 359 79.732 2479 2984 1 chr4B.!!$R1 505
17 TraesCS7B01G207800 chr4B 497226171 497226695 524 False 237.0 237 75.518 2478 2988 1 chr4B.!!$F1 510
18 TraesCS7B01G207800 chr2B 263697181 263697700 519 True 342.0 342 79.278 2481 2985 1 chr2B.!!$R1 504
19 TraesCS7B01G207800 chr2A 605306056 605306620 564 True 289.0 289 76.870 2416 2960 1 chr2A.!!$R1 544

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
539 610 0.570272 GGCGTCAAAACTTGTTTGCG 59.43 50.0 0.0 6.62 34.54 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2515 2603 0.179043 TTTAGCGGCTGTTGTGGTGA 60.179 50.0 13.86 0.0 0.0 4.02 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
78 79 6.229733 TGCCACTAAAGCAAAGCAATTTATT 58.770 32.000 0.00 0.00 37.28 1.40
218 228 3.110358 CAAAACATGGCATATGACTGCG 58.890 45.455 10.60 0.42 43.23 5.18
240 250 4.155826 CGGGCATTGTTCTTTCATTGACTA 59.844 41.667 0.00 0.00 30.38 2.59
293 303 6.204882 CGGTTTCATGAGGTTTCCTTATATCC 59.795 42.308 0.00 0.00 31.76 2.59
325 335 7.559486 TGTCATGTCTGCTCTTGACTAAATAT 58.441 34.615 16.72 0.00 40.64 1.28
326 336 8.695456 TGTCATGTCTGCTCTTGACTAAATATA 58.305 33.333 16.72 0.00 40.64 0.86
327 337 8.973378 GTCATGTCTGCTCTTGACTAAATATAC 58.027 37.037 0.00 0.00 38.55 1.47
491 562 7.145985 AGTTTGATTCTCATTGATATGCATGC 58.854 34.615 11.82 11.82 0.00 4.06
539 610 0.570272 GGCGTCAAAACTTGTTTGCG 59.430 50.000 0.00 6.62 34.54 4.85
693 764 6.127647 TGTGTGAAAGAAGAATCTGCAAAAGT 60.128 34.615 0.00 0.00 35.59 2.66
694 765 7.066887 TGTGTGAAAGAAGAATCTGCAAAAGTA 59.933 33.333 0.00 0.00 35.59 2.24
710 781 7.053498 TGCAAAAGTAGCCTGAATATGTGATA 58.947 34.615 0.00 0.00 0.00 2.15
1128 1199 5.173774 TGTTGCACTCAGATTTTCTTCAC 57.826 39.130 0.00 0.00 0.00 3.18
1527 1598 9.824534 CACCTTAAAACATTATTTTGCAAATCC 57.175 29.630 13.65 0.00 0.00 3.01
1541 1612 9.995003 ATTTTGCAAATCCATAAGTGACTTAAA 57.005 25.926 13.65 0.00 29.35 1.52
1559 1630 7.494298 TGACTTAAAGAAAAATTGTGGGAAAGC 59.506 33.333 0.00 0.00 0.00 3.51
1561 1632 3.385193 AGAAAAATTGTGGGAAAGCGG 57.615 42.857 0.00 0.00 0.00 5.52
1603 1684 8.897752 AGTTAAGATATGAGATGCACCTTTTTC 58.102 33.333 0.00 0.00 0.00 2.29
1604 1685 8.897752 GTTAAGATATGAGATGCACCTTTTTCT 58.102 33.333 0.00 0.00 0.00 2.52
1611 1692 5.829924 TGAGATGCACCTTTTTCTTCTTCTT 59.170 36.000 0.00 0.00 0.00 2.52
1636 1717 2.106566 ACACACAAAAGGGTTGCATGA 58.893 42.857 0.00 0.00 0.00 3.07
1670 1751 6.059787 AGCCAGAGAAGACAATTCTAACAT 57.940 37.500 0.00 0.00 0.00 2.71
1700 1781 9.640963 AGTTATACACTCAGTCAGACAAATAAC 57.359 33.333 2.66 6.09 0.00 1.89
1711 1794 4.003648 CAGACAAATAACCACCTGAGACC 58.996 47.826 0.00 0.00 0.00 3.85
1745 1828 1.890489 TGCTACAGCTCTGTCGGTAAA 59.110 47.619 5.72 0.00 43.74 2.01
1762 1845 9.675464 TGTCGGTAAAAATATTCTGGTCTTAAT 57.325 29.630 0.00 0.00 0.00 1.40
1816 1899 5.004448 TCTAATAGGATCGCTCTCATCGTT 58.996 41.667 0.00 0.00 0.00 3.85
1819 1902 0.598680 GGATCGCTCTCATCGTTGGG 60.599 60.000 0.00 0.00 0.00 4.12
1903 1986 4.432741 GGCAAGACCCTGGGCCTC 62.433 72.222 14.08 3.60 43.09 4.70
1921 2004 0.911769 TCGGAGGGATCATGTGCTTT 59.088 50.000 0.00 0.00 0.00 3.51
1940 2023 1.077787 GTCCATGCGGGGATCACAA 60.078 57.895 0.00 0.00 39.62 3.33
1951 2034 3.027974 GGGATCACAATCGCCTACTAC 57.972 52.381 0.00 0.00 38.56 2.73
1963 2046 1.588824 CCTACTACGTCACCGCCACA 61.589 60.000 0.00 0.00 37.70 4.17
2024 2109 2.353858 CCATGCTTTTGGCCAGTGA 58.646 52.632 5.11 0.00 40.92 3.41
2026 2111 1.070445 CCATGCTTTTGGCCAGTGAAA 59.930 47.619 5.11 2.81 40.92 2.69
2027 2112 2.289819 CCATGCTTTTGGCCAGTGAAAT 60.290 45.455 5.11 0.00 40.92 2.17
2033 2118 5.244851 TGCTTTTGGCCAGTGAAATTATACA 59.755 36.000 5.11 0.00 40.92 2.29
2058 2143 9.298373 CAGTCTGATACTTTCTCCCAGGAGATG 62.298 48.148 17.00 14.51 42.79 2.90
2069 2154 3.593328 TCCCAGGAGATGACCATTCTTTT 59.407 43.478 0.00 0.00 0.00 2.27
2074 2159 4.704057 AGGAGATGACCATTCTTTTCTTGC 59.296 41.667 0.00 0.00 0.00 4.01
2083 2168 5.525012 ACCATTCTTTTCTTGCTTGCTTTTC 59.475 36.000 0.00 0.00 0.00 2.29
2113 2198 4.210537 CGTATCTTTCAGTTTGTGGTTCGT 59.789 41.667 0.00 0.00 0.00 3.85
2119 2204 2.940410 TCAGTTTGTGGTTCGTCCTTTC 59.060 45.455 1.80 0.00 37.07 2.62
2173 2260 3.734463 TCCGACTTGTATCAAAGTTGCA 58.266 40.909 0.00 0.00 40.48 4.08
2191 2278 9.995003 AAAGTTGCACAAAAAGGAATATGATTA 57.005 25.926 0.00 0.00 0.00 1.75
2193 2280 9.807649 AGTTGCACAAAAAGGAATATGATTATC 57.192 29.630 0.00 0.00 0.00 1.75
2274 2361 9.745880 GATGATCTTTCAGCAAATTCATATGTT 57.254 29.630 1.90 0.00 38.18 2.71
2298 2385 9.612620 GTTAATTCTAAATTCTGTCAAGTGGTG 57.387 33.333 0.00 0.00 0.00 4.17
2308 2395 3.814625 TGTCAAGTGGTGTCAAATAGCA 58.185 40.909 0.00 0.00 0.00 3.49
2309 2396 4.397420 TGTCAAGTGGTGTCAAATAGCAT 58.603 39.130 0.00 0.00 0.00 3.79
2325 2412 8.038944 TCAAATAGCATAAAGTAGTCCGAACTT 58.961 33.333 0.00 0.00 38.82 2.66
2326 2413 7.772332 AATAGCATAAAGTAGTCCGAACTTG 57.228 36.000 0.00 0.00 37.26 3.16
2327 2414 4.504858 AGCATAAAGTAGTCCGAACTTGG 58.495 43.478 0.00 0.00 37.26 3.61
2328 2415 4.222145 AGCATAAAGTAGTCCGAACTTGGA 59.778 41.667 0.00 0.00 37.26 3.53
2329 2416 4.933400 GCATAAAGTAGTCCGAACTTGGAA 59.067 41.667 0.00 0.00 40.44 3.53
2330 2417 5.063564 GCATAAAGTAGTCCGAACTTGGAAG 59.936 44.000 0.00 0.00 40.44 3.46
2331 2418 3.679824 AAGTAGTCCGAACTTGGAAGG 57.320 47.619 0.00 0.00 40.44 3.46
2332 2419 1.275573 AGTAGTCCGAACTTGGAAGGC 59.724 52.381 0.00 0.00 40.44 4.35
2333 2420 1.275573 GTAGTCCGAACTTGGAAGGCT 59.724 52.381 0.00 0.00 40.44 4.58
2334 2421 0.765510 AGTCCGAACTTGGAAGGCTT 59.234 50.000 0.00 0.00 40.44 4.35
2335 2422 1.143073 AGTCCGAACTTGGAAGGCTTT 59.857 47.619 0.00 0.00 40.44 3.51
2336 2423 1.535896 GTCCGAACTTGGAAGGCTTTC 59.464 52.381 0.00 0.00 40.44 2.62
2337 2424 1.420138 TCCGAACTTGGAAGGCTTTCT 59.580 47.619 7.14 0.00 34.30 2.52
2338 2425 1.537202 CCGAACTTGGAAGGCTTTCTG 59.463 52.381 7.14 2.50 33.68 3.02
2339 2426 1.068954 CGAACTTGGAAGGCTTTCTGC 60.069 52.381 7.14 0.00 41.94 4.26
2404 2491 9.836864 AAGATCATAGTACAATGCATGTAAAGA 57.163 29.630 0.00 2.74 45.81 2.52
2405 2492 9.265901 AGATCATAGTACAATGCATGTAAAGAC 57.734 33.333 0.00 0.00 45.81 3.01
2406 2493 8.962884 ATCATAGTACAATGCATGTAAAGACA 57.037 30.769 0.00 0.00 45.81 3.41
2407 2494 8.785329 TCATAGTACAATGCATGTAAAGACAA 57.215 30.769 0.00 0.00 45.81 3.18
2408 2495 8.664798 TCATAGTACAATGCATGTAAAGACAAC 58.335 33.333 0.00 0.00 45.81 3.32
2409 2496 6.875948 AGTACAATGCATGTAAAGACAACA 57.124 33.333 0.00 0.00 45.81 3.33
2410 2497 7.270757 AGTACAATGCATGTAAAGACAACAA 57.729 32.000 0.00 0.00 45.81 2.83
2411 2498 7.711846 AGTACAATGCATGTAAAGACAACAAA 58.288 30.769 0.00 0.00 45.81 2.83
2412 2499 8.194104 AGTACAATGCATGTAAAGACAACAAAA 58.806 29.630 0.00 0.00 45.81 2.44
2413 2500 8.977505 GTACAATGCATGTAAAGACAACAAAAT 58.022 29.630 0.00 0.00 45.81 1.82
2425 2512 7.817418 AAGACAACAAAATACTAGCCTTTGA 57.183 32.000 15.10 0.00 34.76 2.69
2426 2513 7.440523 AGACAACAAAATACTAGCCTTTGAG 57.559 36.000 15.10 10.65 34.76 3.02
2430 2517 6.648879 ACAAAATACTAGCCTTTGAGCAAA 57.351 33.333 15.10 0.00 34.76 3.68
2445 2532 0.463620 GCAAAGGAACACCAGCCAAA 59.536 50.000 0.00 0.00 0.00 3.28
2474 2562 9.750125 AGAAATTACAATCAAGACCAAAGAAAC 57.250 29.630 0.00 0.00 0.00 2.78
2476 2564 4.937201 ACAATCAAGACCAAAGAAACCC 57.063 40.909 0.00 0.00 0.00 4.11
2503 2591 2.202960 ACACCAACACCCGTCACG 60.203 61.111 0.00 0.00 0.00 4.35
2515 2603 2.261671 GTCACGTGCCTCCGACAT 59.738 61.111 11.67 0.00 0.00 3.06
2535 2623 0.040425 CACCACAACAGCCGCTAAAC 60.040 55.000 0.00 0.00 0.00 2.01
2536 2624 0.464735 ACCACAACAGCCGCTAAACA 60.465 50.000 0.00 0.00 0.00 2.83
2537 2625 0.665835 CCACAACAGCCGCTAAACAA 59.334 50.000 0.00 0.00 0.00 2.83
2580 2669 2.740055 CTGAGCTTGACGCGGCTT 60.740 61.111 15.80 0.00 45.59 4.35
2653 2747 2.131972 CACCGTTGAACGAATCAGACA 58.868 47.619 20.47 0.00 46.05 3.41
2654 2748 2.736721 CACCGTTGAACGAATCAGACAT 59.263 45.455 20.47 0.00 46.05 3.06
2655 2750 3.924073 CACCGTTGAACGAATCAGACATA 59.076 43.478 20.47 0.00 46.05 2.29
2662 2757 5.178061 TGAACGAATCAGACATAGCAACAT 58.822 37.500 0.00 0.00 33.04 2.71
2687 2792 1.293179 CACGTCAGATCTGGCACCA 59.707 57.895 26.10 2.39 34.22 4.17
2695 2800 3.551496 ATCTGGCACCACCACACGG 62.551 63.158 0.00 0.00 46.36 4.94
2701 2806 1.241315 GCACCACCACACGGCTAAAT 61.241 55.000 0.00 0.00 34.57 1.40
2702 2807 1.946747 GCACCACCACACGGCTAAATA 60.947 52.381 0.00 0.00 34.57 1.40
2707 2812 3.071479 CACCACACGGCTAAATAGTTGT 58.929 45.455 0.00 0.00 34.57 3.32
2708 2813 3.500680 CACCACACGGCTAAATAGTTGTT 59.499 43.478 0.00 0.00 34.57 2.83
2729 2834 2.173356 TGGAGGAAACCATATCTGCCAG 59.827 50.000 0.00 0.00 34.77 4.85
2737 2842 1.667236 CATATCTGCCAGCCACGAAA 58.333 50.000 0.00 0.00 0.00 3.46
2751 2856 1.332375 CACGAAACACGAACCCAACAT 59.668 47.619 0.00 0.00 45.77 2.71
2752 2857 2.544686 CACGAAACACGAACCCAACATA 59.455 45.455 0.00 0.00 45.77 2.29
2753 2858 3.187637 CACGAAACACGAACCCAACATAT 59.812 43.478 0.00 0.00 45.77 1.78
2757 2862 5.560966 AAACACGAACCCAACATATGATC 57.439 39.130 10.38 0.00 0.00 2.92
2759 2864 5.607939 ACACGAACCCAACATATGATCTA 57.392 39.130 10.38 0.00 0.00 1.98
2763 2871 5.104693 ACGAACCCAACATATGATCTACCAA 60.105 40.000 10.38 0.00 0.00 3.67
2777 2885 3.338249 TCTACCAACTTTCAGATGCTGC 58.662 45.455 0.00 0.00 0.00 5.25
2867 2980 1.028330 TCGTCGTAATGGCGGAGTCT 61.028 55.000 0.00 0.00 0.00 3.24
2870 2983 1.135199 GTCGTAATGGCGGAGTCTGAA 60.135 52.381 2.16 0.00 0.00 3.02
2960 3079 1.420430 TCCCAACCATAGGACCGATC 58.580 55.000 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
218 228 4.525912 AGTCAATGAAAGAACAATGCCC 57.474 40.909 0.00 0.00 0.00 5.36
293 303 1.467734 GAGCAGACATGACAAGGCAAG 59.532 52.381 0.00 0.00 0.00 4.01
371 381 5.862924 TTTGTTTAGCTTCAGAATCTCCG 57.137 39.130 0.00 0.00 0.00 4.63
372 382 9.780413 CTAATTTTGTTTAGCTTCAGAATCTCC 57.220 33.333 0.00 0.00 0.00 3.71
431 501 8.313292 CCTTTCCAAAATCTGAAATGGATAACA 58.687 33.333 9.37 0.00 41.36 2.41
432 502 8.314021 ACCTTTCCAAAATCTGAAATGGATAAC 58.686 33.333 9.37 0.00 41.36 1.89
433 503 8.434589 ACCTTTCCAAAATCTGAAATGGATAA 57.565 30.769 9.37 6.99 41.36 1.75
434 504 9.540538 TTACCTTTCCAAAATCTGAAATGGATA 57.459 29.630 9.37 5.46 41.36 2.59
491 562 0.947244 ACAAGGAAAGACGCAGCAAG 59.053 50.000 0.00 0.00 0.00 4.01
498 569 5.689819 CCAGTGAAATAACAAGGAAAGACG 58.310 41.667 0.00 0.00 0.00 4.18
539 610 7.009907 GTGATAAGACGGTATTTACCAAGACAC 59.990 40.741 7.50 0.00 46.80 3.67
693 764 4.532126 CCACCCTATCACATATTCAGGCTA 59.468 45.833 0.00 0.00 0.00 3.93
694 765 3.328931 CCACCCTATCACATATTCAGGCT 59.671 47.826 0.00 0.00 0.00 4.58
710 781 0.834687 TCCAGTACGAAAGCCACCCT 60.835 55.000 0.00 0.00 0.00 4.34
1098 1169 5.483685 AATCTGAGTGCAACAGTACCTTA 57.516 39.130 17.68 2.92 41.43 2.69
1128 1199 9.326413 ACCCTTATTTCAAAATAGTACATCTCG 57.674 33.333 0.00 0.00 32.87 4.04
1156 1227 4.788100 CAGCCGAAAACATCAGTTTAATCG 59.212 41.667 7.73 7.73 46.79 3.34
1199 1270 5.368256 ACTACTCTACAGTAACAACCGTG 57.632 43.478 0.00 0.00 34.53 4.94
1496 1567 8.637986 TGCAAAATAATGTTTTAAGGTGAGAGT 58.362 29.630 0.00 0.00 0.00 3.24
1533 1604 7.494298 GCTTTCCCACAATTTTTCTTTAAGTCA 59.506 33.333 0.00 0.00 0.00 3.41
1539 1610 4.126437 CCGCTTTCCCACAATTTTTCTTT 58.874 39.130 0.00 0.00 0.00 2.52
1540 1611 3.727726 CCGCTTTCCCACAATTTTTCTT 58.272 40.909 0.00 0.00 0.00 2.52
1541 1612 2.547855 GCCGCTTTCCCACAATTTTTCT 60.548 45.455 0.00 0.00 0.00 2.52
1548 1619 1.452145 GAAGTGCCGCTTTCCCACAA 61.452 55.000 0.00 0.00 37.59 3.33
1559 1630 2.336554 CTTCCACAAATGAAGTGCCG 57.663 50.000 0.00 0.00 35.56 5.69
1603 1684 6.261118 CCTTTTGTGTGTTCTCAAGAAGAAG 58.739 40.000 0.00 0.00 44.66 2.85
1604 1685 5.125417 CCCTTTTGTGTGTTCTCAAGAAGAA 59.875 40.000 0.00 0.00 41.81 2.52
1611 1692 2.165437 GCAACCCTTTTGTGTGTTCTCA 59.835 45.455 0.00 0.00 0.00 3.27
1636 1717 6.240894 TGTCTTCTCTGGCTTAATGAAATGT 58.759 36.000 0.00 0.00 0.00 2.71
1670 1751 8.575649 TTGTCTGACTGAGTGTATAACTATCA 57.424 34.615 9.51 0.00 40.07 2.15
1685 1766 4.641396 TCAGGTGGTTATTTGTCTGACTG 58.359 43.478 9.51 0.00 0.00 3.51
1697 1778 1.906574 GACCATGGTCTCAGGTGGTTA 59.093 52.381 33.47 0.00 44.56 2.85
1711 1794 3.181493 GCTGTAGCAATTCCAAGACCATG 60.181 47.826 0.00 0.00 41.59 3.66
1780 1863 7.331934 GCGATCCTATTAGAGCATTCAACAATA 59.668 37.037 0.00 0.00 0.00 1.90
1788 1871 4.769488 TGAGAGCGATCCTATTAGAGCATT 59.231 41.667 0.00 0.00 0.00 3.56
1792 1875 4.634004 ACGATGAGAGCGATCCTATTAGAG 59.366 45.833 0.00 0.00 0.00 2.43
1796 1879 3.305676 CCAACGATGAGAGCGATCCTATT 60.306 47.826 0.00 0.00 0.00 1.73
1816 1899 1.148273 AAGCAGCAACGAGAACCCA 59.852 52.632 0.00 0.00 0.00 4.51
1819 1902 4.522460 GCAAGCAGCAACGAGAAC 57.478 55.556 0.00 0.00 44.79 3.01
1903 1986 1.019673 CAAAGCACATGATCCCTCCG 58.980 55.000 0.00 0.00 0.00 4.63
1921 2004 1.846712 TTGTGATCCCCGCATGGACA 61.847 55.000 0.00 0.00 37.20 4.02
1963 2046 2.187599 GAATTTCGTGTGCCGCTGCT 62.188 55.000 0.70 0.00 38.71 4.24
2000 2083 2.339348 CCAAAAGCATGGCGCACA 59.661 55.556 10.83 5.20 46.13 4.57
2026 2111 8.783660 TGGGAGAAAGTATCAGACTGTATAAT 57.216 34.615 1.59 0.00 38.87 1.28
2027 2112 7.287927 CCTGGGAGAAAGTATCAGACTGTATAA 59.712 40.741 1.59 0.00 38.87 0.98
2033 2118 4.017037 TCTCCTGGGAGAAAGTATCAGACT 60.017 45.833 16.08 0.00 46.89 3.24
2058 2143 4.248691 AGCAAGCAAGAAAAGAATGGTC 57.751 40.909 0.00 0.00 0.00 4.02
2069 2154 3.489059 CGGAACAAGAAAAGCAAGCAAGA 60.489 43.478 0.00 0.00 0.00 3.02
2074 2159 5.613358 AGATACGGAACAAGAAAAGCAAG 57.387 39.130 0.00 0.00 0.00 4.01
2083 2168 6.136071 CACAAACTGAAAGATACGGAACAAG 58.864 40.000 0.00 0.00 37.43 3.16
2113 2198 9.613428 CATGAGTTGTATATAAAGGTGAAAGGA 57.387 33.333 0.00 0.00 0.00 3.36
2119 2204 7.498900 TGCTTCCATGAGTTGTATATAAAGGTG 59.501 37.037 0.00 0.00 0.00 4.00
2191 2278 6.748333 ACAGTGATGAATCAATCAAACGAT 57.252 33.333 0.00 0.00 42.54 3.73
2193 2280 7.167968 ACAAAACAGTGATGAATCAATCAAACG 59.832 33.333 0.00 0.00 42.54 3.60
2274 2361 8.918202 ACACCACTTGACAGAATTTAGAATTA 57.082 30.769 0.00 0.00 0.00 1.40
2276 2363 6.998074 TGACACCACTTGACAGAATTTAGAAT 59.002 34.615 0.00 0.00 0.00 2.40
2298 2385 7.491696 AGTTCGGACTACTTTATGCTATTTGAC 59.508 37.037 0.00 0.00 33.32 3.18
2308 2395 5.731591 CCTTCCAAGTTCGGACTACTTTAT 58.268 41.667 0.00 0.00 34.21 1.40
2309 2396 4.562143 GCCTTCCAAGTTCGGACTACTTTA 60.562 45.833 0.00 0.00 34.21 1.85
2378 2465 9.836864 TCTTTACATGCATTGTACTATGATCTT 57.163 29.630 19.58 4.77 40.53 2.40
2379 2466 9.265901 GTCTTTACATGCATTGTACTATGATCT 57.734 33.333 19.58 1.99 40.53 2.75
2380 2467 9.045223 TGTCTTTACATGCATTGTACTATGATC 57.955 33.333 19.58 5.00 40.53 2.92
2381 2468 8.962884 TGTCTTTACATGCATTGTACTATGAT 57.037 30.769 19.58 8.43 40.53 2.45
2382 2469 8.664798 GTTGTCTTTACATGCATTGTACTATGA 58.335 33.333 19.58 6.68 40.53 2.15
2383 2470 8.450180 TGTTGTCTTTACATGCATTGTACTATG 58.550 33.333 12.29 12.29 40.53 2.23
2384 2471 8.560355 TGTTGTCTTTACATGCATTGTACTAT 57.440 30.769 0.00 0.00 40.53 2.12
2385 2472 7.971183 TGTTGTCTTTACATGCATTGTACTA 57.029 32.000 0.00 0.00 40.53 1.82
2386 2473 6.875948 TGTTGTCTTTACATGCATTGTACT 57.124 33.333 0.00 0.00 40.53 2.73
2387 2474 7.922505 TTTGTTGTCTTTACATGCATTGTAC 57.077 32.000 0.00 0.00 40.53 2.90
2389 2476 8.977505 GTATTTTGTTGTCTTTACATGCATTGT 58.022 29.630 0.00 1.44 42.62 2.71
2390 2477 9.195411 AGTATTTTGTTGTCTTTACATGCATTG 57.805 29.630 0.00 0.00 34.97 2.82
2393 2480 8.020819 GCTAGTATTTTGTTGTCTTTACATGCA 58.979 33.333 0.00 0.00 34.97 3.96
2394 2481 7.484959 GGCTAGTATTTTGTTGTCTTTACATGC 59.515 37.037 0.00 0.00 34.97 4.06
2395 2482 8.730680 AGGCTAGTATTTTGTTGTCTTTACATG 58.269 33.333 0.00 0.00 34.97 3.21
2396 2483 8.863872 AGGCTAGTATTTTGTTGTCTTTACAT 57.136 30.769 0.00 0.00 34.97 2.29
2397 2484 8.685838 AAGGCTAGTATTTTGTTGTCTTTACA 57.314 30.769 0.00 0.00 0.00 2.41
2398 2485 9.394477 CAAAGGCTAGTATTTTGTTGTCTTTAC 57.606 33.333 0.00 0.00 0.00 2.01
2399 2486 9.344772 TCAAAGGCTAGTATTTTGTTGTCTTTA 57.655 29.630 12.33 0.00 34.35 1.85
2400 2487 8.232913 TCAAAGGCTAGTATTTTGTTGTCTTT 57.767 30.769 12.33 0.00 34.35 2.52
2401 2488 7.522236 GCTCAAAGGCTAGTATTTTGTTGTCTT 60.522 37.037 12.33 0.00 34.35 3.01
2402 2489 6.072452 GCTCAAAGGCTAGTATTTTGTTGTCT 60.072 38.462 12.33 0.00 34.35 3.41
2403 2490 6.086871 GCTCAAAGGCTAGTATTTTGTTGTC 58.913 40.000 12.33 0.00 34.35 3.18
2404 2491 5.534654 TGCTCAAAGGCTAGTATTTTGTTGT 59.465 36.000 12.33 0.00 34.35 3.32
2405 2492 6.012658 TGCTCAAAGGCTAGTATTTTGTTG 57.987 37.500 12.33 9.35 34.35 3.33
2406 2493 6.648879 TTGCTCAAAGGCTAGTATTTTGTT 57.351 33.333 12.33 0.00 34.35 2.83
2407 2494 6.648879 TTTGCTCAAAGGCTAGTATTTTGT 57.351 33.333 12.33 0.00 34.35 2.83
2425 2512 0.396974 TTGGCTGGTGTTCCTTTGCT 60.397 50.000 0.00 0.00 34.23 3.91
2426 2513 0.463620 TTTGGCTGGTGTTCCTTTGC 59.536 50.000 0.00 0.00 34.23 3.68
2448 2535 9.750125 GTTTCTTTGGTCTTGATTGTAATTTCT 57.250 29.630 0.00 0.00 0.00 2.52
2449 2536 8.978539 GGTTTCTTTGGTCTTGATTGTAATTTC 58.021 33.333 0.00 0.00 0.00 2.17
2453 2540 6.133356 AGGGTTTCTTTGGTCTTGATTGTAA 58.867 36.000 0.00 0.00 0.00 2.41
2454 2541 5.701224 AGGGTTTCTTTGGTCTTGATTGTA 58.299 37.500 0.00 0.00 0.00 2.41
2455 2542 4.546674 AGGGTTTCTTTGGTCTTGATTGT 58.453 39.130 0.00 0.00 0.00 2.71
2456 2543 5.068987 TCAAGGGTTTCTTTGGTCTTGATTG 59.931 40.000 0.00 0.00 36.65 2.67
2459 2547 4.207165 CTCAAGGGTTTCTTTGGTCTTGA 58.793 43.478 0.00 0.00 38.44 3.02
2466 2554 3.381272 TGTCAAGCTCAAGGGTTTCTTTG 59.619 43.478 0.00 0.00 32.41 2.77
2467 2555 3.381590 GTGTCAAGCTCAAGGGTTTCTTT 59.618 43.478 0.00 0.00 32.41 2.52
2474 2562 0.954452 GTTGGTGTCAAGCTCAAGGG 59.046 55.000 0.00 0.00 32.92 3.95
2476 2564 1.334869 GGTGTTGGTGTCAAGCTCAAG 59.665 52.381 0.00 0.00 32.92 3.02
2512 2600 2.260869 GCGGCTGTTGTGGTGATGT 61.261 57.895 0.00 0.00 0.00 3.06
2515 2603 0.179043 TTTAGCGGCTGTTGTGGTGA 60.179 50.000 13.86 0.00 0.00 4.02
2632 2726 2.132762 GTCTGATTCGTTCAACGGTGT 58.867 47.619 10.69 0.00 42.81 4.16
2633 2727 2.131972 TGTCTGATTCGTTCAACGGTG 58.868 47.619 10.69 0.00 42.81 4.94
2653 2747 0.179084 CGTGTCCGGGATGTTGCTAT 60.179 55.000 0.00 0.00 0.00 2.97
2654 2748 1.216977 CGTGTCCGGGATGTTGCTA 59.783 57.895 0.00 0.00 0.00 3.49
2655 2750 2.047274 CGTGTCCGGGATGTTGCT 60.047 61.111 0.00 0.00 0.00 3.91
2662 2757 1.001269 AGATCTGACGTGTCCGGGA 60.001 57.895 0.00 0.00 38.78 5.14
2687 2792 3.412237 ACAACTATTTAGCCGTGTGGT 57.588 42.857 0.00 0.00 37.67 4.16
2695 2800 5.475564 TGGTTTCCTCCAACAACTATTTAGC 59.524 40.000 0.00 0.00 34.24 3.09
2701 2806 6.414732 CAGATATGGTTTCCTCCAACAACTA 58.585 40.000 0.00 0.00 41.09 2.24
2702 2807 5.256474 CAGATATGGTTTCCTCCAACAACT 58.744 41.667 0.00 0.00 41.09 3.16
2707 2812 2.580322 TGGCAGATATGGTTTCCTCCAA 59.420 45.455 0.00 0.00 41.09 3.53
2708 2813 2.173356 CTGGCAGATATGGTTTCCTCCA 59.827 50.000 9.42 0.00 42.01 3.86
2729 2834 1.716826 TTGGGTTCGTGTTTCGTGGC 61.717 55.000 0.00 0.00 40.80 5.01
2737 2842 4.487714 AGATCATATGTTGGGTTCGTGT 57.512 40.909 1.90 0.00 0.00 4.49
2751 2856 6.988580 CAGCATCTGAAAGTTGGTAGATCATA 59.011 38.462 0.00 0.00 41.99 2.15
2752 2857 5.821470 CAGCATCTGAAAGTTGGTAGATCAT 59.179 40.000 0.00 0.00 41.99 2.45
2753 2858 5.181009 CAGCATCTGAAAGTTGGTAGATCA 58.819 41.667 0.00 0.00 41.99 2.92
2757 2862 2.421424 GGCAGCATCTGAAAGTTGGTAG 59.579 50.000 0.00 0.00 41.99 3.18
2759 2864 1.251251 GGCAGCATCTGAAAGTTGGT 58.749 50.000 0.00 0.00 44.47 3.67
2763 2871 1.203994 GCATTGGCAGCATCTGAAAGT 59.796 47.619 0.00 0.00 40.72 2.66
2777 2885 3.661944 TGCAGGTTATGTTTTGCATTGG 58.338 40.909 0.00 0.00 41.23 3.16
2785 2893 2.752903 GGAACGGATGCAGGTTATGTTT 59.247 45.455 0.00 0.00 0.00 2.83
2787 2895 1.559682 AGGAACGGATGCAGGTTATGT 59.440 47.619 0.00 0.00 0.00 2.29
2793 2902 1.450312 GTCCAGGAACGGATGCAGG 60.450 63.158 0.00 0.00 37.41 4.85
2867 2980 1.472552 CGTGGTGGACTTGTGTCTTCA 60.473 52.381 0.00 0.00 42.54 3.02
2870 2983 0.389391 CTCGTGGTGGACTTGTGTCT 59.611 55.000 0.00 0.00 42.54 3.41
2877 2990 2.660064 GGCATCCTCGTGGTGGACT 61.660 63.158 2.99 0.00 36.30 3.85
2905 3024 1.490490 AGTCTGTTCAAGCAAGGGTGA 59.510 47.619 0.00 0.00 0.00 4.02
2908 3027 1.242076 CCAGTCTGTTCAAGCAAGGG 58.758 55.000 0.00 0.00 0.00 3.95
2960 3079 2.101582 CAGATCCTTCCCTAACGAGGTG 59.898 54.545 0.00 0.00 41.95 4.00


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

AutoCloner maintained by Alex Coulton.