Multiple sequence alignment - TraesCS3D01G352100

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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 TraesCS3D01G352100 chr3D 100.000 2939 0 0 628 3566 463083173 463080235 0.000000e+00 5428.0
1 TraesCS3D01G352100 chr3D 100.000 435 0 0 1 435 463083800 463083366 0.000000e+00 804.0
2 TraesCS3D01G352100 chr3D 98.276 58 0 1 3508 3565 467482768 467482824 2.270000e-17 100.0
3 TraesCS3D01G352100 chr3B 93.620 2743 97 30 629 3324 616182067 616184778 0.000000e+00 4024.0
4 TraesCS3D01G352100 chr3B 91.517 389 16 3 45 433 616181650 616182021 1.470000e-143 520.0
5 TraesCS3D01G352100 chr3B 89.080 174 5 5 3329 3489 616184818 616184990 1.680000e-48 204.0
6 TraesCS3D01G352100 chr3A 92.986 2609 106 27 755 3326 606424786 606427354 0.000000e+00 3733.0
7 TraesCS3D01G352100 chr3A 85.533 394 36 17 44 433 606424204 606424580 3.340000e-105 392.0
8 TraesCS3D01G352100 chr3A 90.816 98 6 2 629 726 606424621 606424715 1.040000e-25 128.0
9 TraesCS3D01G352100 chr3A 93.846 65 3 1 3502 3565 573833610 573833546 2.930000e-16 97.1
10 TraesCS3D01G352100 chr3A 96.552 58 1 1 3509 3566 57014482 57014426 1.050000e-15 95.3
11 TraesCS3D01G352100 chr4A 78.442 385 79 4 1466 1848 110379669 110380051 7.640000e-62 248.0
12 TraesCS3D01G352100 chr4B 78.182 385 80 4 1466 1848 438226853 438226471 3.560000e-60 243.0
13 TraesCS3D01G352100 chr4B 96.552 58 2 0 3509 3566 323738531 323738588 2.930000e-16 97.1
14 TraesCS3D01G352100 chr4D 77.403 385 83 4 1466 1848 354146079 354145697 3.580000e-55 226.0
15 TraesCS3D01G352100 chr7B 98.182 55 1 0 3512 3566 599649110 599649056 2.930000e-16 97.1
16 TraesCS3D01G352100 chr6D 96.552 58 1 1 3509 3566 6763315 6763259 1.050000e-15 95.3
17 TraesCS3D01G352100 chr6D 94.915 59 2 1 3508 3566 194803294 194803237 1.360000e-14 91.6
18 TraesCS3D01G352100 chr7A 94.915 59 3 0 3508 3566 35249370 35249312 3.790000e-15 93.5
19 TraesCS3D01G352100 chr7D 89.041 73 5 2 3496 3566 427819059 427819130 1.760000e-13 87.9


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 TraesCS3D01G352100 chr3D 463080235 463083800 3565 True 3116.000000 5428 100.000000 1 3566 2 chr3D.!!$R1 3565
1 TraesCS3D01G352100 chr3B 616181650 616184990 3340 False 1582.666667 4024 91.405667 45 3489 3 chr3B.!!$F1 3444
2 TraesCS3D01G352100 chr3A 606424204 606427354 3150 False 1417.666667 3733 89.778333 44 3326 3 chr3A.!!$F1 3282

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
25 26 0.533308 GGTTTCACCACGGCACAGTA 60.533 55.0 0.0 0.0 38.42 2.74 F
1665 1760 0.104934 ACTATCGGGGCCTCTCCAAT 60.105 55.0 0.0 0.0 36.21 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 1877 0.529378 CAAAATCACTGGCCTCCTGC 59.471 55.0 3.32 0.0 40.16 4.85 R
3449 3634 0.109723 ACCTAAAGCGGAACAGGCAA 59.890 50.0 0.00 0.0 0.00 4.52 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
18 19 3.414486 AAGGAAGGTTTCACCACGG 57.586 52.632 0.00 0.00 41.95 4.94
19 20 0.822121 AAGGAAGGTTTCACCACGGC 60.822 55.000 0.00 0.00 41.95 5.68
20 21 1.527380 GGAAGGTTTCACCACGGCA 60.527 57.895 0.00 0.00 41.95 5.69
21 22 1.652563 GAAGGTTTCACCACGGCAC 59.347 57.895 0.00 0.00 41.95 5.01
22 23 1.077357 AAGGTTTCACCACGGCACA 60.077 52.632 0.00 0.00 41.95 4.57
23 24 1.101049 AAGGTTTCACCACGGCACAG 61.101 55.000 0.00 0.00 41.95 3.66
24 25 1.822186 GGTTTCACCACGGCACAGT 60.822 57.895 0.00 0.00 38.42 3.55
25 26 0.533308 GGTTTCACCACGGCACAGTA 60.533 55.000 0.00 0.00 38.42 2.74
26 27 1.301423 GTTTCACCACGGCACAGTAA 58.699 50.000 0.00 0.00 0.00 2.24
27 28 1.877443 GTTTCACCACGGCACAGTAAT 59.123 47.619 0.00 0.00 0.00 1.89
28 29 3.068560 GTTTCACCACGGCACAGTAATA 58.931 45.455 0.00 0.00 0.00 0.98
29 30 3.404224 TTCACCACGGCACAGTAATAA 57.596 42.857 0.00 0.00 0.00 1.40
30 31 3.620427 TCACCACGGCACAGTAATAAT 57.380 42.857 0.00 0.00 0.00 1.28
31 32 4.739587 TCACCACGGCACAGTAATAATA 57.260 40.909 0.00 0.00 0.00 0.98
32 33 4.689071 TCACCACGGCACAGTAATAATAG 58.311 43.478 0.00 0.00 0.00 1.73
33 34 4.160814 TCACCACGGCACAGTAATAATAGT 59.839 41.667 0.00 0.00 0.00 2.12
34 35 5.360429 TCACCACGGCACAGTAATAATAGTA 59.640 40.000 0.00 0.00 0.00 1.82
35 36 6.044046 CACCACGGCACAGTAATAATAGTAA 58.956 40.000 0.00 0.00 0.00 2.24
36 37 6.535865 CACCACGGCACAGTAATAATAGTAAA 59.464 38.462 0.00 0.00 0.00 2.01
37 38 7.064847 CACCACGGCACAGTAATAATAGTAAAA 59.935 37.037 0.00 0.00 0.00 1.52
38 39 7.607223 ACCACGGCACAGTAATAATAGTAAAAA 59.393 33.333 0.00 0.00 0.00 1.94
76 77 2.362169 AATGCAACAAATACGCCACC 57.638 45.000 0.00 0.00 0.00 4.61
88 89 2.282180 GCCACCGAAGAAAGGCCA 60.282 61.111 5.01 0.00 41.25 5.36
144 146 3.157087 AGCAAACGAGGACATGGAAAAT 58.843 40.909 0.00 0.00 0.00 1.82
168 170 4.996062 CGCAAGCAAATGAAAAGGAAAT 57.004 36.364 0.00 0.00 0.00 2.17
169 171 4.704457 CGCAAGCAAATGAAAAGGAAATG 58.296 39.130 0.00 0.00 0.00 2.32
170 172 4.377635 CGCAAGCAAATGAAAAGGAAATGG 60.378 41.667 0.00 0.00 0.00 3.16
335 365 4.517703 GTCCGTCTCGCCGTCTCG 62.518 72.222 0.00 0.00 0.00 4.04
433 463 0.845102 TCCCTTTCTTCCACCTCCCC 60.845 60.000 0.00 0.00 0.00 4.81
738 777 2.354704 CCCGTGATTCCTAGCAAGTTCA 60.355 50.000 0.00 0.00 0.00 3.18
767 839 2.491693 TCCGGATTTGGTTCAGATTTGC 59.508 45.455 0.00 0.00 0.00 3.68
950 1025 1.930656 ATTAGCACCCACCCTGCCT 60.931 57.895 0.00 0.00 35.01 4.75
951 1026 2.215451 ATTAGCACCCACCCTGCCTG 62.215 60.000 0.00 0.00 35.01 4.85
988 1071 3.374402 CCGACTCGCCACTCACCT 61.374 66.667 0.00 0.00 0.00 4.00
997 1080 4.742201 CACTCACCTGCCGGACGG 62.742 72.222 5.05 6.80 38.57 4.79
1572 1667 0.940126 GCTACATGAATGGGCACTCG 59.060 55.000 0.00 0.00 33.25 4.18
1665 1760 0.104934 ACTATCGGGGCCTCTCCAAT 60.105 55.000 0.00 0.00 36.21 3.16
1782 1877 2.216898 GAGCTCAATTTCTCCATCCCG 58.783 52.381 9.40 0.00 0.00 5.14
1933 2028 4.320057 CGCTTAATGGATCAGGCTTGAATC 60.320 45.833 1.33 1.35 36.78 2.52
1977 2072 1.621992 GAGAGGACGGCATGGATCTA 58.378 55.000 0.00 0.00 0.00 1.98
2258 2353 5.303333 GGGTAAAGGTTTCATGGAAGAACAA 59.697 40.000 0.00 0.00 0.00 2.83
2328 2423 5.830799 TGCCATACATAAGGAGACATGAT 57.169 39.130 0.00 0.00 0.00 2.45
2343 2438 4.472833 AGACATGATAGGGTCTTCAAGCTT 59.527 41.667 0.00 0.00 41.40 3.74
2349 2444 5.663106 TGATAGGGTCTTCAAGCTTACTGAT 59.337 40.000 0.00 0.00 0.00 2.90
2352 2447 3.604582 GGTCTTCAAGCTTACTGATGCT 58.395 45.455 0.00 0.00 41.82 3.79
2538 2633 3.011517 ATGCGCCCTCCTCACCTT 61.012 61.111 4.18 0.00 0.00 3.50
2573 2668 5.221925 ACCTGCTTATGACATAGGTAATGGG 60.222 44.000 5.92 2.79 39.84 4.00
2666 2765 1.949525 ACTGTTGCTGTTGCTTACTGG 59.050 47.619 0.00 0.00 40.48 4.00
2714 2813 7.360101 GCTTTTGCTGAAGATTAGTTCGTTCTA 60.360 37.037 4.17 0.00 43.35 2.10
2767 2866 2.750166 TCGTGTTCTCTTCTCCTAGCAG 59.250 50.000 0.00 0.00 0.00 4.24
2860 2960 4.202212 GGTGGGTTACTGCTCAATTTTTGT 60.202 41.667 0.00 0.00 0.00 2.83
2865 2965 7.885922 TGGGTTACTGCTCAATTTTTGTATCTA 59.114 33.333 0.00 0.00 0.00 1.98
2898 3002 5.723672 TTCTTCTGTTAGTACCAGTCTGG 57.276 43.478 17.88 17.88 45.02 3.86
2927 3034 5.238214 TGCCAAATTTACAATGTTCTTTGCC 59.762 36.000 0.00 0.00 0.00 4.52
2960 3067 7.870509 ATTAATTCAGTGCTTCAGCTTATGA 57.129 32.000 0.00 0.00 42.66 2.15
3030 3137 5.016831 TCCCGATCAGCATACACTATACAT 58.983 41.667 0.00 0.00 0.00 2.29
3096 3220 0.251341 AACTTCCATCTGGCGCCTTT 60.251 50.000 29.70 9.44 34.44 3.11
3098 3222 0.890683 CTTCCATCTGGCGCCTTTTT 59.109 50.000 29.70 6.98 34.44 1.94
3106 3230 2.747446 TCTGGCGCCTTTTTACTGAATC 59.253 45.455 29.70 0.00 0.00 2.52
3107 3231 2.749621 CTGGCGCCTTTTTACTGAATCT 59.250 45.455 29.70 0.00 0.00 2.40
3108 3232 2.747446 TGGCGCCTTTTTACTGAATCTC 59.253 45.455 29.70 0.00 0.00 2.75
3177 3301 6.337185 TCCTCCATCTTACTTACTACTGGA 57.663 41.667 0.00 0.00 0.00 3.86
3180 3304 6.778069 CCTCCATCTTACTTACTACTGGATGA 59.222 42.308 0.00 0.00 33.25 2.92
3238 3376 6.655425 ACACCTAGTTTTTCTATGCCTCTTTC 59.345 38.462 0.00 0.00 0.00 2.62
3292 3430 8.094548 GCCAATCTTTTCTGGGTTTAATAACTT 58.905 33.333 0.00 0.00 34.59 2.66
3326 3464 4.893608 TCAACATAAGCTGTCTTGTGCTA 58.106 39.130 0.00 0.00 42.85 3.49
3368 3541 6.349777 GGATTGTTGATCTCTATCTACTCCGG 60.350 46.154 0.00 0.00 38.30 5.14
3414 3587 5.376625 AGTGAAGTTTCAAGGCAACAGATA 58.623 37.500 0.00 0.00 39.21 1.98
3449 3634 3.181454 ACCTAACAACTGCTGCTTGTACT 60.181 43.478 7.57 0.00 31.43 2.73
3463 3648 0.107831 TGTACTTGCCTGTTCCGCTT 59.892 50.000 0.00 0.00 0.00 4.68
3477 3662 4.222145 TGTTCCGCTTTAGGTTCAGATAGT 59.778 41.667 0.00 0.00 0.00 2.12
3479 3664 5.416271 TCCGCTTTAGGTTCAGATAGTTT 57.584 39.130 0.00 0.00 0.00 2.66
3480 3665 5.175859 TCCGCTTTAGGTTCAGATAGTTTG 58.824 41.667 0.00 0.00 0.00 2.93
3481 3666 4.201822 CCGCTTTAGGTTCAGATAGTTTGC 60.202 45.833 0.00 0.00 0.00 3.68
3482 3667 4.391830 CGCTTTAGGTTCAGATAGTTTGCA 59.608 41.667 0.00 0.00 0.00 4.08
3489 3674 1.922447 TCAGATAGTTTGCACCCCCAT 59.078 47.619 0.00 0.00 0.00 4.00
3490 3675 2.092429 TCAGATAGTTTGCACCCCCATC 60.092 50.000 0.00 0.00 0.00 3.51
3491 3676 1.922447 AGATAGTTTGCACCCCCATCA 59.078 47.619 0.00 0.00 0.00 3.07
3492 3677 2.092212 AGATAGTTTGCACCCCCATCAG 60.092 50.000 0.00 0.00 0.00 2.90
3493 3678 1.367346 TAGTTTGCACCCCCATCAGA 58.633 50.000 0.00 0.00 0.00 3.27
3494 3679 0.038744 AGTTTGCACCCCCATCAGAG 59.961 55.000 0.00 0.00 0.00 3.35
3495 3680 0.251341 GTTTGCACCCCCATCAGAGT 60.251 55.000 0.00 0.00 0.00 3.24
3496 3681 1.004277 GTTTGCACCCCCATCAGAGTA 59.996 52.381 0.00 0.00 0.00 2.59
3497 3682 1.595311 TTGCACCCCCATCAGAGTAT 58.405 50.000 0.00 0.00 0.00 2.12
3498 3683 2.487746 TGCACCCCCATCAGAGTATA 57.512 50.000 0.00 0.00 0.00 1.47
3499 3684 2.329267 TGCACCCCCATCAGAGTATAG 58.671 52.381 0.00 0.00 0.00 1.31
3500 3685 2.330216 GCACCCCCATCAGAGTATAGT 58.670 52.381 0.00 0.00 0.00 2.12
3501 3686 3.116900 TGCACCCCCATCAGAGTATAGTA 60.117 47.826 0.00 0.00 0.00 1.82
3502 3687 3.258622 GCACCCCCATCAGAGTATAGTAC 59.741 52.174 0.00 0.00 0.00 2.73
3503 3688 3.833070 CACCCCCATCAGAGTATAGTACC 59.167 52.174 0.00 0.00 0.00 3.34
3504 3689 3.469771 ACCCCCATCAGAGTATAGTACCA 59.530 47.826 0.00 0.00 0.00 3.25
3505 3690 4.090090 CCCCCATCAGAGTATAGTACCAG 58.910 52.174 0.00 0.00 0.00 4.00
3506 3691 4.090090 CCCCATCAGAGTATAGTACCAGG 58.910 52.174 0.00 0.00 0.00 4.45
3507 3692 4.202684 CCCCATCAGAGTATAGTACCAGGA 60.203 50.000 0.00 0.00 0.00 3.86
3508 3693 4.767928 CCCATCAGAGTATAGTACCAGGAC 59.232 50.000 0.00 0.00 0.00 3.85
3509 3694 5.386060 CCATCAGAGTATAGTACCAGGACA 58.614 45.833 0.00 0.00 0.00 4.02
3510 3695 6.013379 CCATCAGAGTATAGTACCAGGACAT 58.987 44.000 0.00 0.00 0.00 3.06
3511 3696 6.071672 CCATCAGAGTATAGTACCAGGACATG 60.072 46.154 0.00 0.00 0.00 3.21
3512 3697 6.014771 TCAGAGTATAGTACCAGGACATGT 57.985 41.667 0.00 0.00 0.00 3.21
3513 3698 5.828328 TCAGAGTATAGTACCAGGACATGTG 59.172 44.000 1.15 0.00 0.00 3.21
3514 3699 5.010112 CAGAGTATAGTACCAGGACATGTGG 59.990 48.000 1.15 0.07 41.30 4.17
3515 3700 3.641906 AGTATAGTACCAGGACATGTGGC 59.358 47.826 1.15 0.00 38.83 5.01
3516 3701 1.200519 TAGTACCAGGACATGTGGCC 58.799 55.000 1.15 0.00 46.16 5.36
3522 3707 4.519610 GGACATGTGGCCCTGTTT 57.480 55.556 1.15 0.00 37.19 2.83
3523 3708 1.966762 GGACATGTGGCCCTGTTTG 59.033 57.895 1.15 0.00 37.19 2.93
3524 3709 1.535204 GGACATGTGGCCCTGTTTGG 61.535 60.000 1.15 0.00 37.19 3.28
3525 3710 0.539438 GACATGTGGCCCTGTTTGGA 60.539 55.000 1.15 0.00 38.35 3.53
3526 3711 0.114954 ACATGTGGCCCTGTTTGGAT 59.885 50.000 0.00 0.00 38.35 3.41
3527 3712 1.357420 ACATGTGGCCCTGTTTGGATA 59.643 47.619 0.00 0.00 38.35 2.59
3528 3713 1.750778 CATGTGGCCCTGTTTGGATAC 59.249 52.381 0.00 0.00 38.35 2.24
3529 3714 1.072266 TGTGGCCCTGTTTGGATACT 58.928 50.000 0.00 0.00 38.35 2.12
3530 3715 1.004277 TGTGGCCCTGTTTGGATACTC 59.996 52.381 0.00 0.00 38.35 2.59
3531 3716 1.282157 GTGGCCCTGTTTGGATACTCT 59.718 52.381 0.00 0.00 38.35 3.24
3532 3717 2.504175 GTGGCCCTGTTTGGATACTCTA 59.496 50.000 0.00 0.00 38.35 2.43
3533 3718 3.054655 GTGGCCCTGTTTGGATACTCTAA 60.055 47.826 0.00 0.00 38.35 2.10
3534 3719 3.054655 TGGCCCTGTTTGGATACTCTAAC 60.055 47.826 0.00 0.00 38.35 2.34
3535 3720 3.200165 GGCCCTGTTTGGATACTCTAACT 59.800 47.826 0.00 0.00 38.35 2.24
3536 3721 4.443621 GCCCTGTTTGGATACTCTAACTC 58.556 47.826 0.00 0.00 38.35 3.01
3537 3722 4.081087 GCCCTGTTTGGATACTCTAACTCA 60.081 45.833 0.00 0.00 38.35 3.41
3538 3723 5.665459 CCCTGTTTGGATACTCTAACTCAG 58.335 45.833 0.00 0.00 38.35 3.35
3539 3724 5.187967 CCCTGTTTGGATACTCTAACTCAGT 59.812 44.000 0.00 0.00 38.35 3.41
3540 3725 6.295916 CCCTGTTTGGATACTCTAACTCAGTT 60.296 42.308 0.00 0.00 38.35 3.16
3541 3726 7.093465 CCCTGTTTGGATACTCTAACTCAGTTA 60.093 40.741 0.00 0.00 38.35 2.24
3542 3727 7.976734 CCTGTTTGGATACTCTAACTCAGTTAG 59.023 40.741 17.42 17.42 41.36 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.301423 TTACTGTGCCGTGGTGAAAC 58.699 50.000 0.00 0.00 0.00 2.78
8 9 2.264005 ATTACTGTGCCGTGGTGAAA 57.736 45.000 0.00 0.00 0.00 2.69
9 10 3.404224 TTATTACTGTGCCGTGGTGAA 57.596 42.857 0.00 0.00 0.00 3.18
10 11 3.620427 ATTATTACTGTGCCGTGGTGA 57.380 42.857 0.00 0.00 0.00 4.02
11 12 4.439057 ACTATTATTACTGTGCCGTGGTG 58.561 43.478 0.00 0.00 0.00 4.17
12 13 4.748277 ACTATTATTACTGTGCCGTGGT 57.252 40.909 0.00 0.00 0.00 4.16
13 14 7.542534 TTTTACTATTATTACTGTGCCGTGG 57.457 36.000 0.00 0.00 0.00 4.94
39 40 9.373603 TGTTGCATTTCTAGTATGTTACGTATT 57.626 29.630 0.00 0.00 0.00 1.89
40 41 8.936070 TGTTGCATTTCTAGTATGTTACGTAT 57.064 30.769 0.00 0.00 0.00 3.06
41 42 8.760103 TTGTTGCATTTCTAGTATGTTACGTA 57.240 30.769 0.00 0.00 0.00 3.57
42 43 7.661127 TTGTTGCATTTCTAGTATGTTACGT 57.339 32.000 0.00 0.00 0.00 3.57
88 89 2.554032 CTGAAAAGTTGGTCGGCTCATT 59.446 45.455 0.00 0.00 0.00 2.57
144 146 1.500108 CTTTTCATTTGCTTGCGCCA 58.500 45.000 4.18 0.00 34.43 5.69
160 162 7.989416 TTCGTGTAATAACTCCATTTCCTTT 57.011 32.000 0.00 0.00 0.00 3.11
161 163 7.361799 GCTTTCGTGTAATAACTCCATTTCCTT 60.362 37.037 0.00 0.00 0.00 3.36
162 164 6.093633 GCTTTCGTGTAATAACTCCATTTCCT 59.906 38.462 0.00 0.00 0.00 3.36
163 165 6.128117 TGCTTTCGTGTAATAACTCCATTTCC 60.128 38.462 0.00 0.00 0.00 3.13
164 166 6.837992 TGCTTTCGTGTAATAACTCCATTTC 58.162 36.000 0.00 0.00 0.00 2.17
165 167 6.811253 TGCTTTCGTGTAATAACTCCATTT 57.189 33.333 0.00 0.00 0.00 2.32
166 168 7.250569 CAATGCTTTCGTGTAATAACTCCATT 58.749 34.615 0.00 0.00 0.00 3.16
167 169 6.677920 GCAATGCTTTCGTGTAATAACTCCAT 60.678 38.462 0.00 0.00 0.00 3.41
168 170 5.391523 GCAATGCTTTCGTGTAATAACTCCA 60.392 40.000 0.00 0.00 0.00 3.86
169 171 5.028375 GCAATGCTTTCGTGTAATAACTCC 58.972 41.667 0.00 0.00 0.00 3.85
170 172 5.028375 GGCAATGCTTTCGTGTAATAACTC 58.972 41.667 4.82 0.00 0.00 3.01
396 426 1.699930 AAGAGGTGGTTGTGGGGGT 60.700 57.895 0.00 0.00 0.00 4.95
631 661 3.599285 TTTAGCGCGGGTGGAGGTG 62.599 63.158 8.83 0.00 0.00 4.00
632 662 2.400269 TTTTTAGCGCGGGTGGAGGT 62.400 55.000 8.83 0.00 0.00 3.85
633 663 1.029947 ATTTTTAGCGCGGGTGGAGG 61.030 55.000 8.83 0.00 0.00 4.30
634 664 0.808755 AATTTTTAGCGCGGGTGGAG 59.191 50.000 8.83 0.00 0.00 3.86
635 665 0.523966 CAATTTTTAGCGCGGGTGGA 59.476 50.000 8.83 0.00 0.00 4.02
997 1080 3.493303 GAGGTCCTCCCCCATGGC 61.493 72.222 6.09 0.00 0.00 4.40
1650 1745 2.768344 GGATTGGAGAGGCCCCGA 60.768 66.667 0.00 0.00 34.97 5.14
1665 1760 2.124612 CCATGGATGCACTGCGGA 60.125 61.111 5.56 0.00 0.00 5.54
1782 1877 0.529378 CAAAATCACTGGCCTCCTGC 59.471 55.000 3.32 0.00 40.16 4.85
1933 2028 4.885325 TGAATGATTGGATGGTGATGACAG 59.115 41.667 0.00 0.00 0.00 3.51
1977 2072 1.302285 CTTGCTGCTGACAGGGGAT 59.698 57.895 4.26 0.00 44.63 3.85
2223 2318 2.551270 ACCTTTACCCTCTGCTGATCA 58.449 47.619 0.00 0.00 0.00 2.92
2328 2423 4.383118 GCATCAGTAAGCTTGAAGACCCTA 60.383 45.833 9.86 0.00 0.00 3.53
2343 2438 0.318441 GCTCGGGCATAGCATCAGTA 59.682 55.000 0.00 0.00 39.83 2.74
2538 2633 1.334160 TAAGCAGGTCGTTCACTCCA 58.666 50.000 0.00 0.00 0.00 3.86
2573 2668 6.274157 TCACAGACAAGAAAGATAGACCTC 57.726 41.667 0.00 0.00 0.00 3.85
2614 2713 3.782632 GCTAACAGTAGCCCCTTCC 57.217 57.895 0.00 0.00 46.10 3.46
2633 2732 1.527311 GCAACAGTCTCGGAACAAGAC 59.473 52.381 0.00 0.00 0.00 3.01
2714 2813 1.071699 ACACCCGTCACATACAAGCTT 59.928 47.619 0.00 0.00 0.00 3.74
2767 2866 0.684153 ACAGGCCACCCACAATATGC 60.684 55.000 5.01 0.00 0.00 3.14
2873 2973 7.837863 CCAGACTGGTACTAACAGAAGAAATA 58.162 38.462 13.84 0.00 39.24 1.40
2874 2974 6.702329 CCAGACTGGTACTAACAGAAGAAAT 58.298 40.000 13.84 0.00 39.24 2.17
2875 2975 6.097915 CCAGACTGGTACTAACAGAAGAAA 57.902 41.667 13.84 0.00 39.24 2.52
2898 3002 8.587952 AAGAACATTGTAAATTTGGCAAGTAC 57.412 30.769 0.00 5.55 0.00 2.73
2904 3011 5.614449 CGGCAAAGAACATTGTAAATTTGGC 60.614 40.000 23.44 23.44 44.79 4.52
2927 3034 8.948853 TGAAGCACTGAATTAATTTCTTAACG 57.051 30.769 1.43 0.00 35.23 3.18
2960 3067 8.267183 TGGATACAGACATTTACAGTTCATCAT 58.733 33.333 0.00 0.00 46.17 2.45
3030 3137 6.376864 TGTTTTTCAGAGAGACCAACAATTCA 59.623 34.615 0.00 0.00 29.61 2.57
3096 3220 6.169094 CAAGAGCAAGAGGAGATTCAGTAAA 58.831 40.000 0.00 0.00 0.00 2.01
3098 3222 4.382470 GCAAGAGCAAGAGGAGATTCAGTA 60.382 45.833 0.00 0.00 41.58 2.74
3177 3301 6.718454 CCAGGATGCCAAATCTTACTTATCAT 59.282 38.462 0.00 0.00 31.97 2.45
3180 3304 6.266131 TCCAGGATGCCAAATCTTACTTAT 57.734 37.500 0.00 0.00 31.97 1.73
3185 3309 3.053395 AGCTTCCAGGATGCCAAATCTTA 60.053 43.478 21.17 0.00 33.95 2.10
3266 3404 7.611770 AGTTATTAAACCCAGAAAAGATTGGC 58.388 34.615 0.00 0.00 36.15 4.52
3292 3430 5.814188 CAGCTTATGTTGAGCATGAGACTTA 59.186 40.000 5.29 0.00 41.98 2.24
3326 3464 4.289672 ACAATCCACAGTAGAAGACCCATT 59.710 41.667 0.00 0.00 0.00 3.16
3368 3541 9.994432 CACTCATTTCTTGTTTTCCAGATATAC 57.006 33.333 0.00 0.00 0.00 1.47
3379 3552 7.761249 CCTTGAAACTTCACTCATTTCTTGTTT 59.239 33.333 0.00 0.00 36.83 2.83
3449 3634 0.109723 ACCTAAAGCGGAACAGGCAA 59.890 50.000 0.00 0.00 0.00 4.52
3463 3648 4.566907 GGGGTGCAAACTATCTGAACCTAA 60.567 45.833 0.11 0.00 41.71 2.69
3477 3662 1.367346 TACTCTGATGGGGGTGCAAA 58.633 50.000 0.00 0.00 0.00 3.68
3479 3664 2.329267 CTATACTCTGATGGGGGTGCA 58.671 52.381 0.00 0.00 0.00 4.57
3480 3665 2.330216 ACTATACTCTGATGGGGGTGC 58.670 52.381 0.00 0.00 0.00 5.01
3481 3666 3.833070 GGTACTATACTCTGATGGGGGTG 59.167 52.174 0.00 0.00 0.00 4.61
3482 3667 3.469771 TGGTACTATACTCTGATGGGGGT 59.530 47.826 0.00 0.00 0.00 4.95
3489 3674 5.828328 CACATGTCCTGGTACTATACTCTGA 59.172 44.000 0.00 0.00 0.00 3.27
3490 3675 5.010112 CCACATGTCCTGGTACTATACTCTG 59.990 48.000 0.00 0.00 0.00 3.35
3491 3676 5.141182 CCACATGTCCTGGTACTATACTCT 58.859 45.833 0.00 0.00 0.00 3.24
3492 3677 4.262079 GCCACATGTCCTGGTACTATACTC 60.262 50.000 0.00 0.00 0.00 2.59
3493 3678 3.641906 GCCACATGTCCTGGTACTATACT 59.358 47.826 0.00 0.00 0.00 2.12
3494 3679 3.244112 GGCCACATGTCCTGGTACTATAC 60.244 52.174 0.00 0.00 0.00 1.47
3495 3680 2.969950 GGCCACATGTCCTGGTACTATA 59.030 50.000 0.00 0.00 0.00 1.31
3496 3681 1.768870 GGCCACATGTCCTGGTACTAT 59.231 52.381 0.00 0.00 0.00 2.12
3497 3682 1.200519 GGCCACATGTCCTGGTACTA 58.799 55.000 0.00 0.00 0.00 1.82
3498 3683 1.562672 GGGCCACATGTCCTGGTACT 61.563 60.000 4.39 0.00 0.00 2.73
3499 3684 1.077716 GGGCCACATGTCCTGGTAC 60.078 63.158 4.39 0.00 0.00 3.34
3500 3685 1.229820 AGGGCCACATGTCCTGGTA 60.230 57.895 6.18 0.00 0.00 3.25
3501 3686 2.532715 AGGGCCACATGTCCTGGT 60.533 61.111 6.18 0.00 0.00 4.00
3502 3687 2.044650 CAGGGCCACATGTCCTGG 60.045 66.667 19.69 9.80 43.09 4.45
3504 3689 0.540365 CAAACAGGGCCACATGTCCT 60.540 55.000 6.18 0.00 0.00 3.85
3505 3690 1.535204 CCAAACAGGGCCACATGTCC 61.535 60.000 6.18 0.00 0.00 4.02
3506 3691 0.539438 TCCAAACAGGGCCACATGTC 60.539 55.000 6.18 0.00 38.24 3.06
3507 3692 0.114954 ATCCAAACAGGGCCACATGT 59.885 50.000 6.18 2.88 38.24 3.21
3508 3693 1.750778 GTATCCAAACAGGGCCACATG 59.249 52.381 6.18 2.11 38.24 3.21
3509 3694 1.640670 AGTATCCAAACAGGGCCACAT 59.359 47.619 6.18 0.00 38.24 3.21
3510 3695 1.004277 GAGTATCCAAACAGGGCCACA 59.996 52.381 6.18 0.00 38.24 4.17
3511 3696 1.282157 AGAGTATCCAAACAGGGCCAC 59.718 52.381 6.18 0.00 38.24 5.01
3512 3697 1.668826 AGAGTATCCAAACAGGGCCA 58.331 50.000 6.18 0.00 38.24 5.36
3513 3698 3.200165 AGTTAGAGTATCCAAACAGGGCC 59.800 47.826 0.00 0.00 34.84 5.80
3514 3699 4.081087 TGAGTTAGAGTATCCAAACAGGGC 60.081 45.833 0.00 0.00 34.84 5.19
3515 3700 5.187967 ACTGAGTTAGAGTATCCAAACAGGG 59.812 44.000 0.00 0.00 34.84 4.45
3516 3701 6.287589 ACTGAGTTAGAGTATCCAAACAGG 57.712 41.667 0.00 0.00 34.84 4.00
3517 3702 8.740906 TCTAACTGAGTTAGAGTATCCAAACAG 58.259 37.037 26.45 3.66 46.18 3.16
3518 3703 8.645814 TCTAACTGAGTTAGAGTATCCAAACA 57.354 34.615 26.45 4.73 46.18 2.83


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

AutoCloner maintained by Alex Coulton.