Multiple sequence alignment - TraesCS5B01G252700

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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 TraesCS5B01G252700 chr5B 100.000 3410 0 0 1 3410 435767036 435770445 0.000000e+00 6298.0
1 TraesCS5B01G252700 chr5D 88.161 2441 156 45 43 2405 367807989 367810374 0.000000e+00 2784.0
2 TraesCS5B01G252700 chr5D 91.102 472 32 6 2784 3253 367811508 367811971 6.210000e-177 630.0
3 TraesCS5B01G252700 chr5D 81.500 200 14 11 2449 2625 367810369 367810568 3.550000e-30 143.0
4 TraesCS5B01G252700 chr5D 95.455 44 2 0 1 44 367799677 367799720 1.700000e-08 71.3
5 TraesCS5B01G252700 chr5A 92.323 1498 84 15 936 2405 469896155 469897649 0.000000e+00 2100.0
6 TraesCS5B01G252700 chr5A 92.381 630 36 11 2787 3410 469898096 469898719 0.000000e+00 887.0
7 TraesCS5B01G252700 chr5A 82.847 857 54 33 2610 3410 469905362 469906181 0.000000e+00 682.0
8 TraesCS5B01G252700 chr5A 82.047 596 59 23 1 563 469895285 469895865 6.670000e-127 464.0
9 TraesCS5B01G252700 chr5A 88.889 171 9 4 595 760 469895862 469896027 5.770000e-48 202.0
10 TraesCS5B01G252700 chr5A 81.095 201 13 14 2449 2625 469897644 469897843 1.650000e-28 137.0
11 TraesCS5B01G252700 chr7A 84.529 976 101 28 469 1422 191919757 191918810 0.000000e+00 920.0


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 TraesCS5B01G252700 chr5B 435767036 435770445 3409 False 6298.000000 6298 100.000 1 3410 1 chr5B.!!$F1 3409
1 TraesCS5B01G252700 chr5D 367807989 367811971 3982 False 1185.666667 2784 86.921 43 3253 3 chr5D.!!$F2 3210
2 TraesCS5B01G252700 chr5A 469895285 469898719 3434 False 758.000000 2100 87.347 1 3410 5 chr5A.!!$F2 3409
3 TraesCS5B01G252700 chr5A 469905362 469906181 819 False 682.000000 682 82.847 2610 3410 1 chr5A.!!$F1 800
4 TraesCS5B01G252700 chr7A 191918810 191919757 947 True 920.000000 920 84.529 469 1422 1 chr7A.!!$R1 953

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
726 790 0.249953 TACGACCAAAGCAAAGCCGA 60.25 50.0 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2420 2557 0.313043 CTCCAACACTGCAAAGCCAG 59.687 55.0 0.0 0.0 38.78 4.85 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
28 30 4.918278 TTGCTGCTTGCTGGGCCA 62.918 61.111 5.85 5.85 43.37 5.36
32 34 2.203669 TGCTTGCTGGGCCAATGT 60.204 55.556 8.04 0.00 0.00 2.71
66 68 4.837093 TCTGATTTTGGATTCTACCGGT 57.163 40.909 13.98 13.98 0.00 5.28
118 120 0.666913 GATAGCGGTAACTGCGGAGA 59.333 55.000 12.26 0.00 40.31 3.71
184 200 3.215975 AGAGGAGGTCGATAAGTAGCAC 58.784 50.000 0.00 0.00 0.00 4.40
186 202 3.215975 AGGAGGTCGATAAGTAGCACTC 58.784 50.000 0.00 0.00 0.00 3.51
205 224 3.944123 CGGAGGATAACGGTGGGA 58.056 61.111 0.00 0.00 0.00 4.37
261 280 1.078143 CTTCTTCTTCGCCTGGGGG 60.078 63.158 11.17 0.78 0.00 5.40
342 384 4.388499 ATTCGGCCGCGGTGTCTT 62.388 61.111 28.70 6.61 0.00 3.01
349 391 4.012895 CGCGGTGTCTTGTGTGGC 62.013 66.667 0.00 0.00 0.00 5.01
350 392 2.591715 GCGGTGTCTTGTGTGGCT 60.592 61.111 0.00 0.00 0.00 4.75
356 401 2.289444 GGTGTCTTGTGTGGCTAGCTAA 60.289 50.000 15.72 0.00 0.00 3.09
372 417 4.918810 AGCTAAGTGGTTTTGAAGTTGG 57.081 40.909 0.00 0.00 0.00 3.77
386 435 2.586648 AGTTGGGGATGAACTGGAAC 57.413 50.000 0.00 0.00 32.30 3.62
393 442 2.437413 GGATGAACTGGAACCTGGAAC 58.563 52.381 0.00 0.00 0.00 3.62
394 443 2.040412 GGATGAACTGGAACCTGGAACT 59.960 50.000 0.00 0.00 0.00 3.01
395 444 2.638480 TGAACTGGAACCTGGAACTG 57.362 50.000 0.00 0.00 0.00 3.16
417 466 2.861147 AGCAACTTGGACTAGAACCC 57.139 50.000 0.00 0.00 0.00 4.11
427 476 4.942944 TGGACTAGAACCCTGTAGAATGA 58.057 43.478 0.00 0.00 0.00 2.57
442 491 5.719563 TGTAGAATGAGTGAGTGATGGGTTA 59.280 40.000 0.00 0.00 0.00 2.85
449 498 3.123804 GTGAGTGATGGGTTAGTATGCG 58.876 50.000 0.00 0.00 0.00 4.73
452 501 4.037565 TGAGTGATGGGTTAGTATGCGTAG 59.962 45.833 0.00 0.00 0.00 3.51
498 555 1.593296 CCCTGAAGGCTTTCTGCTGC 61.593 60.000 10.19 0.00 42.39 5.25
545 602 6.486253 TGCTGCATCTACTAGAAAAAGTTG 57.514 37.500 0.00 0.00 0.00 3.16
566 623 1.281656 CGTGCCTTCGTTTCAACCC 59.718 57.895 0.00 0.00 0.00 4.11
606 665 4.142093 ACACTTCAAACTTCATTTGCAGCT 60.142 37.500 0.00 0.00 43.13 4.24
648 712 6.041296 ACCAATTCAAGTTGAAAATCAGAGCT 59.959 34.615 21.57 0.00 40.12 4.09
649 713 7.231317 ACCAATTCAAGTTGAAAATCAGAGCTA 59.769 33.333 21.57 0.00 40.12 3.32
650 714 7.754027 CCAATTCAAGTTGAAAATCAGAGCTAG 59.246 37.037 21.57 1.25 40.12 3.42
686 750 7.540474 AGACCAGTGACTGAAAATAGTAGAA 57.460 36.000 15.33 0.00 32.44 2.10
706 770 1.354101 TGCCTTCTTTTCCGAGGGTA 58.646 50.000 0.00 0.00 33.06 3.69
707 771 1.913419 TGCCTTCTTTTCCGAGGGTAT 59.087 47.619 0.00 0.00 33.06 2.73
726 790 0.249953 TACGACCAAAGCAAAGCCGA 60.250 50.000 0.00 0.00 0.00 5.54
829 917 2.094545 GCAGAATGAAAATCCAACGCCT 60.095 45.455 0.00 0.00 39.69 5.52
843 931 5.492895 TCCAACGCCTTAAGATGTTCAATA 58.507 37.500 3.36 0.00 0.00 1.90
849 937 8.366671 ACGCCTTAAGATGTTCAATAGTATTC 57.633 34.615 3.36 0.00 0.00 1.75
903 999 9.890629 AATAGTACAAGCAATCATCTGTCTTTA 57.109 29.630 0.00 0.00 0.00 1.85
904 1000 9.890629 ATAGTACAAGCAATCATCTGTCTTTAA 57.109 29.630 0.00 0.00 0.00 1.52
905 1001 8.034058 AGTACAAGCAATCATCTGTCTTTAAC 57.966 34.615 0.00 0.00 0.00 2.01
906 1002 5.931532 ACAAGCAATCATCTGTCTTTAACG 58.068 37.500 0.00 0.00 0.00 3.18
907 1003 5.700832 ACAAGCAATCATCTGTCTTTAACGA 59.299 36.000 0.00 0.00 0.00 3.85
908 1004 6.204688 ACAAGCAATCATCTGTCTTTAACGAA 59.795 34.615 0.00 0.00 0.00 3.85
909 1005 6.992063 AGCAATCATCTGTCTTTAACGAAT 57.008 33.333 0.00 0.00 0.00 3.34
924 1020 7.650504 TCTTTAACGAATACATAAGATGGACGG 59.349 37.037 0.00 0.00 33.60 4.79
929 1025 6.257193 ACGAATACATAAGATGGACGGTTTTC 59.743 38.462 0.00 0.00 33.60 2.29
942 1038 1.282157 CGGTTTTCCCCTCTTGGATCT 59.718 52.381 0.00 0.00 35.39 2.75
959 1055 3.496870 GGATCTGATAAGCCGTTCCCATT 60.497 47.826 0.00 0.00 0.00 3.16
1028 1124 9.206870 GATCCTAGAACTGAATCAATCTTCATC 57.793 37.037 3.96 1.67 34.76 2.92
1111 1233 2.682856 GACTTGTCAGGCACAACTTTCA 59.317 45.455 0.00 0.00 40.29 2.69
1112 1234 2.423538 ACTTGTCAGGCACAACTTTCAC 59.576 45.455 0.00 0.00 40.29 3.18
1118 1240 0.467290 GGCACAACTTTCACAGGGGA 60.467 55.000 0.00 0.00 0.00 4.81
1164 1286 1.264020 GACACAAACGATGCAGAGCAA 59.736 47.619 0.00 0.00 43.62 3.91
1278 1406 2.597805 AGACTCTGCCGGACGTGT 60.598 61.111 5.05 1.01 0.00 4.49
1341 1469 2.491152 CATGCCAATCGTGCACCC 59.509 61.111 12.15 0.00 42.38 4.61
1365 1493 1.078143 CCTCCTCCTTTTCCTGCCG 60.078 63.158 0.00 0.00 0.00 5.69
1467 1598 2.203070 GCGGCGTCTTCCATGGAT 60.203 61.111 17.06 0.00 0.00 3.41
1491 1622 2.649034 GACCACCTCTTCGCGTCA 59.351 61.111 5.77 0.00 0.00 4.35
1614 1745 3.457380 TCCGTGACCTGTACTACCTCTAT 59.543 47.826 0.00 0.00 0.00 1.98
1617 1748 5.454471 CCGTGACCTGTACTACCTCTATAGT 60.454 48.000 0.00 0.00 38.89 2.12
1794 1925 3.612247 CTGCCTGGTGAACCTCGGG 62.612 68.421 0.37 2.25 36.82 5.14
1825 1956 3.405592 GACGGCGCGATGTACTGGA 62.406 63.158 12.10 0.00 0.00 3.86
1827 1958 1.284715 CGGCGCGATGTACTGGATA 59.715 57.895 12.10 0.00 0.00 2.59
1828 1959 0.109272 CGGCGCGATGTACTGGATAT 60.109 55.000 12.10 0.00 0.00 1.63
1884 2015 0.108804 TGGCGTTCGATCTCAAGGAC 60.109 55.000 0.00 0.00 0.00 3.85
1997 2131 0.178929 ACGGAGGTGGAGAAGAAGGT 60.179 55.000 0.00 0.00 0.00 3.50
1998 2132 0.977395 CGGAGGTGGAGAAGAAGGTT 59.023 55.000 0.00 0.00 0.00 3.50
2001 2135 2.106684 GGAGGTGGAGAAGAAGGTTTGT 59.893 50.000 0.00 0.00 0.00 2.83
2277 2414 0.913451 AGGAGGTGAGGCTGCTGAAT 60.913 55.000 0.00 0.00 0.00 2.57
2352 2489 3.107661 CCGTTGGACGTGTACGCC 61.108 66.667 4.06 7.51 44.43 5.68
2394 2531 3.465403 CACTGGCCTCTCCCTCCG 61.465 72.222 3.32 0.00 0.00 4.63
2405 2542 3.787001 CCCTCCGCCAGGTTCCTC 61.787 72.222 0.00 0.00 41.51 3.71
2406 2543 3.787001 CCTCCGCCAGGTTCCTCC 61.787 72.222 0.00 0.00 37.53 4.30
2416 2553 2.030027 AGGTTCCTCCTGACATGACA 57.970 50.000 0.00 0.00 46.19 3.58
2417 2554 1.905215 AGGTTCCTCCTGACATGACAG 59.095 52.381 16.92 16.92 46.19 3.51
2418 2555 1.625818 GGTTCCTCCTGACATGACAGT 59.374 52.381 21.04 0.00 36.30 3.55
2419 2556 2.832129 GGTTCCTCCTGACATGACAGTA 59.168 50.000 21.04 7.29 36.30 2.74
2420 2557 3.368531 GGTTCCTCCTGACATGACAGTAC 60.369 52.174 21.04 11.64 36.30 2.73
2421 2558 3.458044 TCCTCCTGACATGACAGTACT 57.542 47.619 21.04 0.00 36.30 2.73
2422 2559 3.092301 TCCTCCTGACATGACAGTACTG 58.908 50.000 21.44 21.44 36.30 2.74
2423 2560 2.167281 CCTCCTGACATGACAGTACTGG 59.833 54.545 26.12 11.17 36.30 4.00
2424 2561 1.550524 TCCTGACATGACAGTACTGGC 59.449 52.381 26.12 24.45 39.62 4.85
2425 2562 1.552337 CCTGACATGACAGTACTGGCT 59.448 52.381 28.56 9.62 39.96 4.75
2426 2563 2.027745 CCTGACATGACAGTACTGGCTT 60.028 50.000 28.56 20.20 39.96 4.35
2427 2564 3.557898 CCTGACATGACAGTACTGGCTTT 60.558 47.826 28.56 14.03 39.96 3.51
2428 2565 3.402110 TGACATGACAGTACTGGCTTTG 58.598 45.455 28.56 25.30 39.96 2.77
2429 2566 2.154462 ACATGACAGTACTGGCTTTGC 58.846 47.619 28.56 10.03 39.96 3.68
2430 2567 2.153645 CATGACAGTACTGGCTTTGCA 58.846 47.619 28.56 9.27 39.96 4.08
2431 2568 1.882912 TGACAGTACTGGCTTTGCAG 58.117 50.000 28.56 0.00 39.96 4.41
2432 2569 1.140852 TGACAGTACTGGCTTTGCAGT 59.859 47.619 28.56 3.31 39.96 4.40
2433 2570 1.532868 GACAGTACTGGCTTTGCAGTG 59.467 52.381 26.12 0.00 35.21 3.66
2434 2571 1.134098 ACAGTACTGGCTTTGCAGTGT 60.134 47.619 26.12 0.00 33.26 3.55
2435 2572 1.949525 CAGTACTGGCTTTGCAGTGTT 59.050 47.619 15.49 0.00 33.26 3.32
2436 2573 1.949525 AGTACTGGCTTTGCAGTGTTG 59.050 47.619 0.00 0.00 33.26 3.33
2437 2574 1.001378 GTACTGGCTTTGCAGTGTTGG 60.001 52.381 0.00 0.00 33.26 3.77
2438 2575 0.395586 ACTGGCTTTGCAGTGTTGGA 60.396 50.000 0.00 0.00 0.00 3.53
2439 2576 0.313043 CTGGCTTTGCAGTGTTGGAG 59.687 55.000 0.00 0.00 0.00 3.86
2440 2577 1.006922 GGCTTTGCAGTGTTGGAGC 60.007 57.895 0.00 0.00 0.00 4.70
2441 2578 1.370900 GCTTTGCAGTGTTGGAGCG 60.371 57.895 0.00 0.00 0.00 5.03
2442 2579 1.370900 CTTTGCAGTGTTGGAGCGC 60.371 57.895 0.00 0.00 0.00 5.92
2443 2580 2.737932 CTTTGCAGTGTTGGAGCGCC 62.738 60.000 2.29 0.00 0.00 6.53
2444 2581 3.772853 TTGCAGTGTTGGAGCGCCT 62.773 57.895 8.34 0.00 34.31 5.52
2445 2582 2.980233 GCAGTGTTGGAGCGCCTT 60.980 61.111 8.34 0.00 34.31 4.35
2446 2583 2.949106 CAGTGTTGGAGCGCCTTG 59.051 61.111 8.34 0.00 34.31 3.61
2447 2584 1.893808 CAGTGTTGGAGCGCCTTGT 60.894 57.895 8.34 0.00 34.31 3.16
2448 2585 1.893808 AGTGTTGGAGCGCCTTGTG 60.894 57.895 8.34 0.00 34.31 3.33
2449 2586 2.186826 GTGTTGGAGCGCCTTGTGT 61.187 57.895 8.34 0.00 34.31 3.72
2450 2587 1.453015 TGTTGGAGCGCCTTGTGTT 60.453 52.632 8.34 0.00 34.31 3.32
2451 2588 1.282875 GTTGGAGCGCCTTGTGTTC 59.717 57.895 8.34 0.00 34.31 3.18
2452 2589 1.148273 TTGGAGCGCCTTGTGTTCT 59.852 52.632 8.34 0.00 34.31 3.01
2468 2605 6.480524 TGTGTTCTGAATTTCTGATTACGG 57.519 37.500 6.79 0.00 0.00 4.02
2478 2615 1.067142 TCTGATTACGGCTCTGCGTTT 60.067 47.619 0.00 0.00 0.00 3.60
2485 2622 2.174349 GCTCTGCGTTTGCCTTCG 59.826 61.111 0.00 0.00 41.78 3.79
2513 2650 2.674420 TGGTCCAGTATAGGTGTAGGC 58.326 52.381 0.00 0.00 0.00 3.93
2515 2652 2.628657 GGTCCAGTATAGGTGTAGGCAG 59.371 54.545 0.00 0.00 0.00 4.85
2520 2657 3.576118 CAGTATAGGTGTAGGCAGCAGAT 59.424 47.826 0.00 0.00 44.89 2.90
2521 2658 3.576118 AGTATAGGTGTAGGCAGCAGATG 59.424 47.826 0.00 0.00 44.89 2.90
2522 2659 2.159179 TAGGTGTAGGCAGCAGATGA 57.841 50.000 0.00 0.00 44.89 2.92
2523 2660 1.279496 AGGTGTAGGCAGCAGATGAA 58.721 50.000 0.00 0.00 44.89 2.57
2525 2662 1.945394 GGTGTAGGCAGCAGATGAATG 59.055 52.381 0.00 0.00 42.26 2.67
2526 2663 2.420547 GGTGTAGGCAGCAGATGAATGA 60.421 50.000 0.00 0.00 42.26 2.57
2567 2726 8.956533 TGAATGAATTATGGTGTAATTCTCGA 57.043 30.769 16.81 0.00 41.81 4.04
2603 2762 8.574251 AGCAACTGGTTATTGTAACATATTCA 57.426 30.769 2.68 0.00 0.00 2.57
2604 2763 8.677300 AGCAACTGGTTATTGTAACATATTCAG 58.323 33.333 2.68 0.00 0.00 3.02
2638 2854 8.391075 AGTATTTTGTGCACTAAGCTTTTCTA 57.609 30.769 19.41 0.00 45.94 2.10
2639 2855 8.290325 AGTATTTTGTGCACTAAGCTTTTCTAC 58.710 33.333 19.41 9.34 45.94 2.59
2686 3626 9.234827 TGCAAATTCTACCCATGATATATCAAG 57.765 33.333 19.03 14.47 40.69 3.02
2687 3627 9.236006 GCAAATTCTACCCATGATATATCAAGT 57.764 33.333 19.03 17.33 40.69 3.16
2689 3629 9.745018 AAATTCTACCCATGATATATCAAGTGG 57.255 33.333 21.42 21.42 40.69 4.00
2738 3678 0.829182 CCAGAAAACAGGGCAGCCTT 60.829 55.000 12.43 0.00 0.00 4.35
2742 3682 1.000171 GAAAACAGGGCAGCCTTGAAG 60.000 52.381 29.54 4.05 34.05 3.02
2942 3939 3.573491 GGAAGCGGCGGGAAATCG 61.573 66.667 9.78 0.00 0.00 3.34
2980 3977 2.394506 GCCCTCCCATCCCAATCCA 61.395 63.158 0.00 0.00 0.00 3.41
3017 4022 1.272114 GCTCGTCTGATCCGAATCGC 61.272 60.000 0.00 0.00 34.39 4.58
3044 4049 1.153147 GTCCTCGATGCCCCCTTTC 60.153 63.158 0.00 0.00 0.00 2.62
3068 4073 1.302949 CGGAATGCTTTCTCCCCCA 59.697 57.895 11.68 0.00 32.16 4.96
3071 4076 2.422803 CGGAATGCTTTCTCCCCCAATA 60.423 50.000 11.68 0.00 32.16 1.90
3089 4094 0.535335 TATCCTTCTTGTCCGCGCTT 59.465 50.000 5.56 0.00 0.00 4.68
3121 4126 1.818363 GGCGGCTAGGGTTTGTAGC 60.818 63.158 0.00 0.00 41.96 3.58
3128 4133 3.197116 GGCTAGGGTTTGTAGCTACTTGA 59.803 47.826 23.84 8.09 42.27 3.02
3140 4145 1.939838 GCTACTTGACGTGGTTGAGGG 60.940 57.143 0.00 0.00 0.00 4.30
3188 4193 0.461516 GGGCGTCTAGGGTTTGTAGC 60.462 60.000 0.00 0.00 0.00 3.58
3260 4265 4.750098 AGTGTTCGTTGGATTTGACAGTAG 59.250 41.667 0.00 0.00 0.00 2.57
3261 4266 3.496884 TGTTCGTTGGATTTGACAGTAGC 59.503 43.478 0.00 0.00 0.00 3.58
3267 4272 2.025981 TGGATTTGACAGTAGCCTGCAT 60.026 45.455 0.00 0.00 42.81 3.96
3288 4293 7.092079 TGCATTTTTGGTACATGAGAGATTTG 58.908 34.615 0.00 0.00 39.30 2.32
3308 4318 1.746787 GTTTTTGACCGTGGGTTCACT 59.253 47.619 0.00 0.00 41.53 3.41
3309 4319 2.131776 TTTTGACCGTGGGTTCACTT 57.868 45.000 0.00 0.00 41.53 3.16
3389 4413 5.889853 AGCAGAAATTTGGAGATGCTATCAA 59.110 36.000 0.00 0.00 41.90 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 68 0.878523 CGTGACGGCTTCTTCAACCA 60.879 55.000 0.00 0.00 0.00 3.67
111 113 3.695606 GCACTCCAGGTCTCCGCA 61.696 66.667 0.00 0.00 0.00 5.69
118 120 1.376424 CAAGCATCGCACTCCAGGT 60.376 57.895 0.00 0.00 0.00 4.00
205 224 2.406616 CCGCGGCCACAAGCTTAAT 61.407 57.895 14.67 0.00 43.05 1.40
226 245 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
227 246 7.865385 CGAAGAAGAAGAAGAAGAAGAAGAAGA 59.135 37.037 0.00 0.00 0.00 2.87
228 247 7.359181 GCGAAGAAGAAGAAGAAGAAGAAGAAG 60.359 40.741 0.00 0.00 0.00 2.85
230 249 5.923684 GCGAAGAAGAAGAAGAAGAAGAAGA 59.076 40.000 0.00 0.00 0.00 2.87
231 250 5.120053 GGCGAAGAAGAAGAAGAAGAAGAAG 59.880 44.000 0.00 0.00 0.00 2.85
232 251 4.991687 GGCGAAGAAGAAGAAGAAGAAGAA 59.008 41.667 0.00 0.00 0.00 2.52
233 252 4.282195 AGGCGAAGAAGAAGAAGAAGAAGA 59.718 41.667 0.00 0.00 0.00 2.87
261 280 2.095059 ACAGCGGAATCATCAACAAAGC 60.095 45.455 0.00 0.00 0.00 3.51
262 281 3.837213 ACAGCGGAATCATCAACAAAG 57.163 42.857 0.00 0.00 0.00 2.77
263 282 4.759693 ACTTACAGCGGAATCATCAACAAA 59.240 37.500 0.00 0.00 0.00 2.83
264 283 4.323417 ACTTACAGCGGAATCATCAACAA 58.677 39.130 0.00 0.00 0.00 2.83
266 285 4.946784 AACTTACAGCGGAATCATCAAC 57.053 40.909 0.00 0.00 0.00 3.18
267 286 5.705441 AGAAAACTTACAGCGGAATCATCAA 59.295 36.000 0.00 0.00 0.00 2.57
268 287 5.245531 AGAAAACTTACAGCGGAATCATCA 58.754 37.500 0.00 0.00 0.00 3.07
269 288 5.803020 AGAAAACTTACAGCGGAATCATC 57.197 39.130 0.00 0.00 0.00 2.92
270 289 5.705441 TGAAGAAAACTTACAGCGGAATCAT 59.295 36.000 0.00 0.00 0.00 2.45
312 354 1.952102 GCCGAATCCGACACCAGGTA 61.952 60.000 0.00 0.00 38.22 3.08
313 355 2.978824 CCGAATCCGACACCAGGT 59.021 61.111 0.00 0.00 38.22 4.00
335 377 0.035458 AGCTAGCCACACAAGACACC 59.965 55.000 12.13 0.00 0.00 4.16
336 378 2.743636 TAGCTAGCCACACAAGACAC 57.256 50.000 12.13 0.00 0.00 3.67
342 384 1.348064 ACCACTTAGCTAGCCACACA 58.652 50.000 12.13 0.00 0.00 3.72
349 391 5.048713 CCCAACTTCAAAACCACTTAGCTAG 60.049 44.000 0.00 0.00 0.00 3.42
350 392 4.825085 CCCAACTTCAAAACCACTTAGCTA 59.175 41.667 0.00 0.00 0.00 3.32
356 401 2.838637 TCCCCAACTTCAAAACCACT 57.161 45.000 0.00 0.00 0.00 4.00
372 417 0.991920 TCCAGGTTCCAGTTCATCCC 59.008 55.000 0.00 0.00 0.00 3.85
386 435 1.610522 CAAGTTGCTTCCAGTTCCAGG 59.389 52.381 0.00 0.00 0.00 4.45
393 442 3.685139 TCTAGTCCAAGTTGCTTCCAG 57.315 47.619 0.00 0.00 0.00 3.86
394 443 3.496160 GGTTCTAGTCCAAGTTGCTTCCA 60.496 47.826 0.00 0.00 0.00 3.53
395 444 3.075148 GGTTCTAGTCCAAGTTGCTTCC 58.925 50.000 0.00 0.00 0.00 3.46
396 445 3.075148 GGGTTCTAGTCCAAGTTGCTTC 58.925 50.000 0.00 0.00 0.00 3.86
397 446 2.711547 AGGGTTCTAGTCCAAGTTGCTT 59.288 45.455 0.00 0.00 0.00 3.91
398 447 2.039084 CAGGGTTCTAGTCCAAGTTGCT 59.961 50.000 0.00 0.00 0.00 3.91
399 448 2.224548 ACAGGGTTCTAGTCCAAGTTGC 60.225 50.000 0.00 0.00 0.00 4.17
417 466 4.161189 ACCCATCACTCACTCATTCTACAG 59.839 45.833 0.00 0.00 0.00 2.74
427 476 3.181475 CGCATACTAACCCATCACTCACT 60.181 47.826 0.00 0.00 0.00 3.41
442 491 1.747355 ACTAACACGCCTACGCATACT 59.253 47.619 0.00 0.00 45.53 2.12
449 498 1.463444 CAAAGCCACTAACACGCCTAC 59.537 52.381 0.00 0.00 0.00 3.18
452 501 0.666374 AACAAAGCCACTAACACGCC 59.334 50.000 0.00 0.00 0.00 5.68
491 548 3.545724 CATGAACTGGAGCAGCAGA 57.454 52.632 0.00 0.00 34.37 4.26
606 665 3.730215 TGGTTAGAATAGCCCTGCAAA 57.270 42.857 0.00 0.00 41.88 3.68
648 712 5.821470 GTCACTGGTCTAGCATGTACTACTA 59.179 44.000 0.00 0.00 0.00 1.82
649 713 4.641094 GTCACTGGTCTAGCATGTACTACT 59.359 45.833 0.00 0.00 0.00 2.57
650 714 4.641094 AGTCACTGGTCTAGCATGTACTAC 59.359 45.833 0.00 0.00 0.00 2.73
686 750 0.698818 ACCCTCGGAAAAGAAGGCAT 59.301 50.000 0.00 0.00 0.00 4.40
706 770 0.802494 CGGCTTTGCTTTGGTCGTAT 59.198 50.000 0.00 0.00 0.00 3.06
707 771 0.249953 TCGGCTTTGCTTTGGTCGTA 60.250 50.000 0.00 0.00 0.00 3.43
726 790 6.658391 CAGAACAGAATTCCTTCCAAGAGAAT 59.342 38.462 0.65 0.00 32.82 2.40
794 878 8.810652 TTTTCATTCTGCCAAACAAATAGTAC 57.189 30.769 0.00 0.00 0.00 2.73
796 880 7.603784 GGATTTTCATTCTGCCAAACAAATAGT 59.396 33.333 0.00 0.00 0.00 2.12
800 888 5.678583 TGGATTTTCATTCTGCCAAACAAA 58.321 33.333 0.00 0.00 0.00 2.83
843 931 5.148502 CCATCCCCGCCTATATAGAATACT 58.851 45.833 11.53 0.00 0.00 2.12
849 937 2.168521 CACACCATCCCCGCCTATATAG 59.831 54.545 2.46 2.46 0.00 1.31
903 999 5.272283 ACCGTCCATCTTATGTATTCGTT 57.728 39.130 0.00 0.00 0.00 3.85
904 1000 4.931661 ACCGTCCATCTTATGTATTCGT 57.068 40.909 0.00 0.00 0.00 3.85
905 1001 6.292703 GGAAAACCGTCCATCTTATGTATTCG 60.293 42.308 0.00 0.00 37.65 3.34
906 1002 6.017357 GGGAAAACCGTCCATCTTATGTATTC 60.017 42.308 0.00 0.00 39.70 1.75
907 1003 5.826208 GGGAAAACCGTCCATCTTATGTATT 59.174 40.000 0.00 0.00 39.70 1.89
908 1004 5.374071 GGGAAAACCGTCCATCTTATGTAT 58.626 41.667 0.00 0.00 39.70 2.29
909 1005 4.384427 GGGGAAAACCGTCCATCTTATGTA 60.384 45.833 0.00 0.00 39.70 2.29
924 1020 3.721087 TCAGATCCAAGAGGGGAAAAC 57.279 47.619 0.00 0.00 41.12 2.43
929 1025 2.039613 GGCTTATCAGATCCAAGAGGGG 59.960 54.545 0.00 0.00 37.22 4.79
942 1038 3.358111 TTCAATGGGAACGGCTTATCA 57.642 42.857 0.00 0.00 0.00 2.15
959 1055 3.703556 TGACAGAAACAGCCCATTTTTCA 59.296 39.130 0.00 0.00 32.62 2.69
1028 1124 8.283992 CGGAAGGTGCTAGTATATCTATAATCG 58.716 40.741 0.00 0.00 0.00 3.34
1164 1286 1.168714 GATTTTCGGTTGCCTGCTCT 58.831 50.000 0.00 0.00 0.00 4.09
1267 1395 3.171828 ATTGGTGACACGTCCGGCA 62.172 57.895 0.00 0.00 42.67 5.69
1270 1398 2.677003 GCCATTGGTGACACGTCCG 61.677 63.158 4.26 0.00 42.67 4.79
1293 1421 2.187946 CAGGGGTCGCTGATCACC 59.812 66.667 9.07 0.00 0.00 4.02
1341 1469 0.391793 GGAAAAGGAGGAGGTGCTCG 60.392 60.000 0.00 0.00 0.00 5.03
1458 1589 1.682451 GGTCGTCCGGATCCATGGAA 61.682 60.000 20.67 0.00 35.67 3.53
1467 1598 1.975407 GAAGAGGTGGTCGTCCGGA 60.975 63.158 0.00 0.00 36.30 5.14
1491 1622 2.749044 CAGAGCAGGCCGTTGCAT 60.749 61.111 18.35 4.52 46.47 3.96
1815 1946 3.697045 CCTCCTCCGATATCCAGTACATC 59.303 52.174 0.00 0.00 0.00 3.06
1825 1956 0.545548 GCCCCTTCCTCCTCCGATAT 60.546 60.000 0.00 0.00 0.00 1.63
1827 1958 2.446802 GCCCCTTCCTCCTCCGAT 60.447 66.667 0.00 0.00 0.00 4.18
1872 2003 3.928343 GGTCTCGTCCTTGAGATCG 57.072 57.895 0.00 0.00 46.07 3.69
1884 2015 1.787155 CTCAACGTCACAAAGGTCTCG 59.213 52.381 0.00 0.00 0.00 4.04
1956 2090 2.831742 TAGTAGGACAGCGCGGGG 60.832 66.667 13.26 3.67 0.00 5.73
2001 2135 1.059584 TGAAAGGGGCTGTCACCAGA 61.060 55.000 0.00 0.00 41.50 3.86
2010 2144 2.035312 CTGCTGCTGAAAGGGGCT 59.965 61.111 0.00 0.00 0.00 5.19
2107 2241 0.603569 CTGTACTTGAGCGACCACCT 59.396 55.000 0.00 0.00 0.00 4.00
2256 2393 2.686835 AGCAGCCTCACCTCCTCC 60.687 66.667 0.00 0.00 0.00 4.30
2258 2395 0.913451 ATTCAGCAGCCTCACCTCCT 60.913 55.000 0.00 0.00 0.00 3.69
2405 2542 1.552337 AGCCAGTACTGTCATGTCAGG 59.448 52.381 21.18 7.66 39.48 3.86
2406 2543 3.325293 AAGCCAGTACTGTCATGTCAG 57.675 47.619 21.18 16.97 40.80 3.51
2407 2544 3.402110 CAAAGCCAGTACTGTCATGTCA 58.598 45.455 21.18 0.00 0.00 3.58
2408 2545 2.160417 GCAAAGCCAGTACTGTCATGTC 59.840 50.000 21.18 5.55 0.00 3.06
2409 2546 2.154462 GCAAAGCCAGTACTGTCATGT 58.846 47.619 21.18 0.00 0.00 3.21
2410 2547 2.153645 TGCAAAGCCAGTACTGTCATG 58.846 47.619 21.18 12.72 0.00 3.07
2411 2548 2.224621 ACTGCAAAGCCAGTACTGTCAT 60.225 45.455 21.18 0.00 43.86 3.06
2412 2549 1.140852 ACTGCAAAGCCAGTACTGTCA 59.859 47.619 21.18 8.17 43.86 3.58
2413 2550 1.532868 CACTGCAAAGCCAGTACTGTC 59.467 52.381 21.18 9.17 43.85 3.51
2414 2551 1.134098 ACACTGCAAAGCCAGTACTGT 60.134 47.619 21.18 0.80 43.85 3.55
2415 2552 1.597742 ACACTGCAAAGCCAGTACTG 58.402 50.000 16.34 16.34 43.85 2.74
2416 2553 1.949525 CAACACTGCAAAGCCAGTACT 59.050 47.619 0.00 0.00 43.85 2.73
2417 2554 1.001378 CCAACACTGCAAAGCCAGTAC 60.001 52.381 0.00 0.00 43.85 2.73
2418 2555 1.133945 TCCAACACTGCAAAGCCAGTA 60.134 47.619 0.00 0.00 43.85 2.74
2419 2556 0.395586 TCCAACACTGCAAAGCCAGT 60.396 50.000 0.00 0.00 46.47 4.00
2420 2557 0.313043 CTCCAACACTGCAAAGCCAG 59.687 55.000 0.00 0.00 38.78 4.85
2421 2558 1.737355 GCTCCAACACTGCAAAGCCA 61.737 55.000 0.00 0.00 0.00 4.75
2422 2559 1.006922 GCTCCAACACTGCAAAGCC 60.007 57.895 0.00 0.00 0.00 4.35
2423 2560 1.370900 CGCTCCAACACTGCAAAGC 60.371 57.895 0.00 0.00 0.00 3.51
2424 2561 1.370900 GCGCTCCAACACTGCAAAG 60.371 57.895 0.00 0.00 0.00 2.77
2425 2562 2.721231 GCGCTCCAACACTGCAAA 59.279 55.556 0.00 0.00 0.00 3.68
2426 2563 3.286751 GGCGCTCCAACACTGCAA 61.287 61.111 7.64 0.00 0.00 4.08
2427 2564 3.772853 AAGGCGCTCCAACACTGCA 62.773 57.895 7.64 0.00 33.74 4.41
2428 2565 2.980233 AAGGCGCTCCAACACTGC 60.980 61.111 7.64 0.00 33.74 4.40
2429 2566 1.893808 ACAAGGCGCTCCAACACTG 60.894 57.895 7.64 0.00 33.74 3.66
2430 2567 1.893808 CACAAGGCGCTCCAACACT 60.894 57.895 7.64 0.00 33.74 3.55
2431 2568 1.724582 AACACAAGGCGCTCCAACAC 61.725 55.000 7.64 0.00 33.74 3.32
2432 2569 1.444119 GAACACAAGGCGCTCCAACA 61.444 55.000 7.64 0.00 33.74 3.33
2433 2570 1.166531 AGAACACAAGGCGCTCCAAC 61.167 55.000 7.64 0.00 33.74 3.77
2434 2571 1.148273 AGAACACAAGGCGCTCCAA 59.852 52.632 7.64 0.00 33.74 3.53
2435 2572 1.597854 CAGAACACAAGGCGCTCCA 60.598 57.895 7.64 0.00 33.74 3.86
2436 2573 0.884704 TTCAGAACACAAGGCGCTCC 60.885 55.000 7.64 0.00 0.00 4.70
2437 2574 1.160137 ATTCAGAACACAAGGCGCTC 58.840 50.000 7.64 0.00 0.00 5.03
2438 2575 1.609208 AATTCAGAACACAAGGCGCT 58.391 45.000 7.64 0.00 0.00 5.92
2439 2576 2.030805 AGAAATTCAGAACACAAGGCGC 60.031 45.455 0.00 0.00 0.00 6.53
2440 2577 3.250762 TCAGAAATTCAGAACACAAGGCG 59.749 43.478 0.00 0.00 0.00 5.52
2441 2578 4.836125 TCAGAAATTCAGAACACAAGGC 57.164 40.909 0.00 0.00 0.00 4.35
2442 2579 7.017645 CGTAATCAGAAATTCAGAACACAAGG 58.982 38.462 0.00 0.00 0.00 3.61
2443 2580 7.017645 CCGTAATCAGAAATTCAGAACACAAG 58.982 38.462 0.00 0.00 0.00 3.16
2444 2581 6.567701 GCCGTAATCAGAAATTCAGAACACAA 60.568 38.462 0.00 0.00 0.00 3.33
2445 2582 5.106712 GCCGTAATCAGAAATTCAGAACACA 60.107 40.000 0.00 0.00 0.00 3.72
2446 2583 5.122396 AGCCGTAATCAGAAATTCAGAACAC 59.878 40.000 0.00 0.00 0.00 3.32
2447 2584 5.245531 AGCCGTAATCAGAAATTCAGAACA 58.754 37.500 0.00 0.00 0.00 3.18
2448 2585 5.582665 AGAGCCGTAATCAGAAATTCAGAAC 59.417 40.000 0.00 0.00 0.00 3.01
2449 2586 5.582269 CAGAGCCGTAATCAGAAATTCAGAA 59.418 40.000 0.00 0.00 0.00 3.02
2450 2587 5.111989 CAGAGCCGTAATCAGAAATTCAGA 58.888 41.667 0.00 0.00 0.00 3.27
2451 2588 4.260538 GCAGAGCCGTAATCAGAAATTCAG 60.261 45.833 0.00 0.00 0.00 3.02
2452 2589 3.623060 GCAGAGCCGTAATCAGAAATTCA 59.377 43.478 0.00 0.00 0.00 2.57
2468 2605 2.174349 CGAAGGCAAACGCAGAGC 59.826 61.111 0.00 0.00 0.00 4.09
2485 2622 2.368875 CCTATACTGGACCATGACCACC 59.631 54.545 0.00 0.24 33.57 4.61
2513 2650 7.549615 TCAGAAGTAATTCATTCATCTGCTG 57.450 36.000 5.62 0.00 31.87 4.41
2515 2652 8.239314 TGTTTCAGAAGTAATTCATTCATCTGC 58.761 33.333 5.62 0.00 0.00 4.26
2567 2726 7.397192 ACAATAACCAGTTGCTTAAATCTCCAT 59.603 33.333 0.00 0.00 0.00 3.41
2626 2812 5.921408 ACACGAGTGAAGTAGAAAAGCTTAG 59.079 40.000 10.50 0.00 0.00 2.18
2686 3626 2.615240 GCCATTTTCCATTGGTTCCCAC 60.615 50.000 1.86 0.00 35.34 4.61
2687 3627 1.627834 GCCATTTTCCATTGGTTCCCA 59.372 47.619 1.86 0.00 35.34 4.37
2688 3628 1.627834 TGCCATTTTCCATTGGTTCCC 59.372 47.619 1.86 0.00 35.34 3.97
2689 3629 3.415457 TTGCCATTTTCCATTGGTTCC 57.585 42.857 1.86 0.00 35.34 3.62
2690 3630 3.189080 GCTTTGCCATTTTCCATTGGTTC 59.811 43.478 1.86 0.00 35.34 3.62
2691 3631 3.148412 GCTTTGCCATTTTCCATTGGTT 58.852 40.909 1.86 0.00 35.34 3.67
2692 3632 2.781923 GCTTTGCCATTTTCCATTGGT 58.218 42.857 1.86 0.00 35.34 3.67
2713 3653 0.875059 GCCCTGTTTTCTGGACGAAG 59.125 55.000 0.00 0.00 40.71 3.79
2738 3678 7.060421 AGAACTTTGGTGGATCTAAAACTTCA 58.940 34.615 0.00 0.00 0.00 3.02
2742 3682 8.942338 AAAAAGAACTTTGGTGGATCTAAAAC 57.058 30.769 0.45 0.00 32.36 2.43
2785 3775 4.785575 GGCCCAATTAGCCCAACT 57.214 55.556 7.33 0.00 45.16 3.16
2829 3819 2.184579 GGCGGAAGAGGAACGAGG 59.815 66.667 0.00 0.00 0.00 4.63
2858 3850 3.004839 GCCCAAGAGGAACAAGTTCTTTC 59.995 47.826 12.22 10.24 39.45 2.62
2860 3852 2.587522 GCCCAAGAGGAACAAGTTCTT 58.412 47.619 12.22 5.13 39.45 2.52
2992 3989 2.026879 GATCAGACGAGCTCCGCC 59.973 66.667 8.47 0.00 43.32 6.13
3017 4022 1.297967 CATCGAGGACTCACGAGCG 60.298 63.158 0.00 0.00 39.16 5.03
3068 4073 1.139058 AGCGCGGACAAGAAGGATATT 59.861 47.619 8.83 0.00 0.00 1.28
3071 4076 0.741221 GAAGCGCGGACAAGAAGGAT 60.741 55.000 8.83 0.00 0.00 3.24
3089 4094 1.813859 CCGCCGTTACAGATGGAGA 59.186 57.895 0.00 0.00 36.41 3.71
3121 4126 1.337823 CCCCTCAACCACGTCAAGTAG 60.338 57.143 0.00 0.00 0.00 2.57
3128 4133 2.847234 TCAGCCCCTCAACCACGT 60.847 61.111 0.00 0.00 0.00 4.49
3140 4145 2.939103 CCATTACAGCAAGTAGTCAGCC 59.061 50.000 0.00 0.00 33.43 4.85
3188 4193 3.685139 TCCCTCAACTTCAGCAAGTAG 57.315 47.619 0.00 0.00 42.45 2.57
3198 4203 0.678048 GCGCCTCAATCCCTCAACTT 60.678 55.000 0.00 0.00 0.00 2.66
3260 4265 3.193267 TCTCATGTACCAAAAATGCAGGC 59.807 43.478 0.00 0.00 0.00 4.85
3261 4266 4.701651 TCTCTCATGTACCAAAAATGCAGG 59.298 41.667 0.00 0.00 0.00 4.85
3267 4272 9.883142 AAAAACAAATCTCTCATGTACCAAAAA 57.117 25.926 0.00 0.00 0.00 1.94
3288 4293 2.197792 GTGAACCCACGGTCAAAAAC 57.802 50.000 0.00 0.00 33.12 2.43
3308 4318 9.856162 AAGTAACAATCTCTAGTTACCCAAAAA 57.144 29.630 10.74 0.00 46.95 1.94
3309 4319 9.856162 AAAGTAACAATCTCTAGTTACCCAAAA 57.144 29.630 10.74 0.00 46.95 2.44


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

AutoCloner maintained by Alex Coulton.