Multiple sequence alignment - TraesCS7B01G264800

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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 TraesCS7B01G264800 chr7B 100.000 3509 0 0 1 3509 485432204 485428696 0.000000e+00 6481.0
1 TraesCS7B01G264800 chr7B 97.727 44 1 0 422 465 63142413 63142370 3.760000e-10 76.8
2 TraesCS7B01G264800 chr7B 89.474 57 2 3 410 465 700180657 700180710 6.290000e-08 69.4
3 TraesCS7B01G264800 chr7D 94.381 3061 108 35 491 3509 462282749 462279711 0.000000e+00 4641.0
4 TraesCS7B01G264800 chr7D 93.911 427 25 1 1 427 462283178 462282753 0.000000e+00 643.0
5 TraesCS7B01G264800 chr7A 90.643 2052 93 52 886 2902 537662373 537664360 0.000000e+00 2634.0
6 TraesCS7B01G264800 chr7A 90.632 427 28 8 2 424 537661403 537661821 1.100000e-154 556.0
7 TraesCS7B01G264800 chr7A 90.244 369 10 11 491 842 537661828 537662187 3.190000e-125 459.0
8 TraesCS7B01G264800 chr7A 80.475 589 44 29 2957 3509 537664543 537665096 5.490000e-103 385.0
9 TraesCS7B01G264800 chr6A 91.139 79 7 0 1654 1732 219561955 219561877 1.330000e-19 108.0
10 TraesCS7B01G264800 chr6D 89.873 79 8 0 1654 1732 160429236 160429158 6.200000e-18 102.0
11 TraesCS7B01G264800 chrUn 88.608 79 9 0 1654 1732 453960257 453960335 2.880000e-16 97.1
12 TraesCS7B01G264800 chrUn 88.608 79 9 0 1654 1732 466322493 466322571 2.880000e-16 97.1
13 TraesCS7B01G264800 chrUn 95.652 46 2 0 423 468 240888589 240888544 1.350000e-09 75.0
14 TraesCS7B01G264800 chrUn 97.674 43 1 0 423 465 268935311 268935353 1.350000e-09 75.0
15 TraesCS7B01G264800 chr6B 88.608 79 9 0 1654 1732 290596916 290596838 2.880000e-16 97.1
16 TraesCS7B01G264800 chr6B 88.608 79 9 0 1654 1732 290628474 290628396 2.880000e-16 97.1
17 TraesCS7B01G264800 chr4A 97.727 44 1 0 422 465 732398800 732398757 3.760000e-10 76.8
18 TraesCS7B01G264800 chr3B 97.778 45 0 1 422 465 144278411 144278455 3.760000e-10 76.8
19 TraesCS7B01G264800 chr3B 89.286 56 4 1 410 465 581708907 581708854 6.290000e-08 69.4
20 TraesCS7B01G264800 chr3B 87.097 62 4 3 407 468 750315563 750315506 2.260000e-07 67.6
21 TraesCS7B01G264800 chr3D 92.157 51 4 0 414 464 73725561 73725611 4.860000e-09 73.1


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 TraesCS7B01G264800 chr7B 485428696 485432204 3508 True 6481.0 6481 100.0000 1 3509 1 chr7B.!!$R2 3508
1 TraesCS7B01G264800 chr7D 462279711 462283178 3467 True 2642.0 4641 94.1460 1 3509 2 chr7D.!!$R1 3508
2 TraesCS7B01G264800 chr7A 537661403 537665096 3693 False 1008.5 2634 87.9985 2 3509 4 chr7A.!!$F1 3507

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
483 488 0.173255 AGCGCGCAATTTTATTGGCT 59.827 45.0 35.10 3.94 0.00 4.75 F
566 574 0.248215 CGTACGTACCACCGGTCATC 60.248 60.0 19.67 0.00 37.09 2.92 F
859 891 0.257616 CCTCCCTCTCTCTCTCGGTT 59.742 60.0 0.00 0.00 0.00 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1540 1725 0.179065 TGATCCTCATCTTGGCTGCG 60.179 55.0 0.0 0.0 0.00 5.18 R
1757 1942 0.966920 ACTCCTACCAAGTGACCACG 59.033 55.0 0.0 0.0 36.20 4.94 R
2807 3010 1.086696 ACGATTCCCAATGAACAGCG 58.913 50.0 0.0 0.0 35.31 5.18 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 4.681025 TGACGATTACAAACCACGAACTAC 59.319 41.667 0.00 0.00 0.00 2.73
79 80 4.619973 ACGATTACAAACCACGAACTACA 58.380 39.130 0.00 0.00 0.00 2.74
80 81 4.445385 ACGATTACAAACCACGAACTACAC 59.555 41.667 0.00 0.00 0.00 2.90
102 103 2.038033 CCCTACAAGGAGAACGTGGAAA 59.962 50.000 0.00 0.00 37.67 3.13
267 272 1.893137 AGTGATGCTAGACGAACCACA 59.107 47.619 0.00 0.00 0.00 4.17
340 345 6.942532 TTAGGAAATCATTGTGGCACTATC 57.057 37.500 19.83 5.19 0.00 2.08
351 356 1.000274 TGGCACTATCGATCACATCCG 60.000 52.381 0.00 0.00 0.00 4.18
424 429 0.521291 TGAGCTAAGCGCGCAATTTT 59.479 45.000 35.10 21.00 45.63 1.82
427 432 2.715997 GAGCTAAGCGCGCAATTTTATG 59.284 45.455 35.10 15.98 45.59 1.90
428 433 1.187921 GCTAAGCGCGCAATTTTATGC 59.812 47.619 35.10 20.85 42.94 3.14
429 434 1.780860 CTAAGCGCGCAATTTTATGCC 59.219 47.619 35.10 0.00 43.47 4.40
430 435 1.139226 AAGCGCGCAATTTTATGCCG 61.139 50.000 35.10 0.00 43.47 5.69
431 436 1.585002 GCGCGCAATTTTATGCCGA 60.585 52.632 29.10 0.00 43.47 5.54
432 437 1.136872 GCGCGCAATTTTATGCCGAA 61.137 50.000 29.10 0.00 43.47 4.30
433 438 1.263776 CGCGCAATTTTATGCCGAAA 58.736 45.000 8.75 0.00 43.47 3.46
434 439 1.651138 CGCGCAATTTTATGCCGAAAA 59.349 42.857 8.75 0.00 43.47 2.29
435 440 2.091277 CGCGCAATTTTATGCCGAAAAA 59.909 40.909 8.75 0.00 43.47 1.94
436 441 3.658695 GCGCAATTTTATGCCGAAAAAG 58.341 40.909 0.30 0.00 43.47 2.27
437 442 3.483411 GCGCAATTTTATGCCGAAAAAGG 60.483 43.478 0.30 0.00 43.47 3.11
454 459 3.509659 GCTTTCGCCCCGCTTTAT 58.490 55.556 0.00 0.00 0.00 1.40
455 460 2.697819 GCTTTCGCCCCGCTTTATA 58.302 52.632 0.00 0.00 0.00 0.98
456 461 1.235724 GCTTTCGCCCCGCTTTATAT 58.764 50.000 0.00 0.00 0.00 0.86
457 462 2.419667 GCTTTCGCCCCGCTTTATATA 58.580 47.619 0.00 0.00 0.00 0.86
458 463 3.007635 GCTTTCGCCCCGCTTTATATAT 58.992 45.455 0.00 0.00 0.00 0.86
459 464 4.186159 GCTTTCGCCCCGCTTTATATATA 58.814 43.478 0.00 0.00 0.00 0.86
460 465 4.632688 GCTTTCGCCCCGCTTTATATATAA 59.367 41.667 0.81 0.81 0.00 0.98
461 466 5.122711 GCTTTCGCCCCGCTTTATATATAAA 59.877 40.000 15.47 15.47 0.00 1.40
471 476 5.203358 CTTTATATATAAAGCAGCGCGCA 57.797 39.130 35.10 12.17 46.13 6.09
472 477 5.599359 TTTATATATAAAGCAGCGCGCAA 57.401 34.783 35.10 10.94 46.13 4.85
473 478 5.794687 TTATATATAAAGCAGCGCGCAAT 57.205 34.783 35.10 15.87 46.13 3.56
474 479 4.685169 ATATATAAAGCAGCGCGCAATT 57.315 36.364 35.10 22.56 46.13 2.32
475 480 2.842208 TATAAAGCAGCGCGCAATTT 57.158 40.000 35.10 28.67 46.13 1.82
476 481 1.994916 ATAAAGCAGCGCGCAATTTT 58.005 40.000 35.10 27.84 46.13 1.82
477 482 2.620779 TAAAGCAGCGCGCAATTTTA 57.379 40.000 35.10 26.85 46.13 1.52
478 483 1.994916 AAAGCAGCGCGCAATTTTAT 58.005 40.000 35.10 7.55 46.13 1.40
479 484 1.994916 AAGCAGCGCGCAATTTTATT 58.005 40.000 35.10 14.34 46.13 1.40
480 485 1.270971 AGCAGCGCGCAATTTTATTG 58.729 45.000 35.10 20.69 46.13 1.90
481 486 0.298411 GCAGCGCGCAATTTTATTGG 59.702 50.000 35.10 9.62 41.79 3.16
482 487 0.298411 CAGCGCGCAATTTTATTGGC 59.702 50.000 35.10 0.00 0.00 4.52
483 488 0.173255 AGCGCGCAATTTTATTGGCT 59.827 45.000 35.10 3.94 0.00 4.75
484 489 0.572125 GCGCGCAATTTTATTGGCTC 59.428 50.000 29.10 0.00 0.00 4.70
485 490 1.906757 CGCGCAATTTTATTGGCTCA 58.093 45.000 8.75 0.00 0.00 4.26
486 491 1.847999 CGCGCAATTTTATTGGCTCAG 59.152 47.619 8.75 0.00 0.00 3.35
487 492 1.589779 GCGCAATTTTATTGGCTCAGC 59.410 47.619 0.30 0.00 0.00 4.26
488 493 1.847999 CGCAATTTTATTGGCTCAGCG 59.152 47.619 0.00 0.00 36.62 5.18
489 494 1.589779 GCAATTTTATTGGCTCAGCGC 59.410 47.619 0.00 0.00 38.13 5.92
509 514 2.359900 CCTCAGCCACAAACTATGGAC 58.640 52.381 0.00 0.00 39.87 4.02
519 524 5.292765 CACAAACTATGGACGATGAGCTAT 58.707 41.667 0.00 0.00 0.00 2.97
538 546 8.750298 TGAGCTATTTAGTACATAGGATTAGCC 58.250 37.037 5.66 0.00 0.00 3.93
559 567 1.291184 GGCCAAACGTACGTACCACC 61.291 60.000 23.12 16.91 0.00 4.61
565 573 0.960364 ACGTACGTACCACCGGTCAT 60.960 55.000 21.41 0.00 37.09 3.06
566 574 0.248215 CGTACGTACCACCGGTCATC 60.248 60.000 19.67 0.00 37.09 2.92
776 792 1.152138 TTCCCCGCCGATCTAGCTA 59.848 57.895 0.00 0.00 0.00 3.32
796 812 0.915364 ATCCCTTTCCTGTGCTCTCC 59.085 55.000 0.00 0.00 0.00 3.71
797 813 0.473694 TCCCTTTCCTGTGCTCTCCA 60.474 55.000 0.00 0.00 0.00 3.86
833 857 5.395103 GCTACCTCTCTGTGAAAGTGATCAT 60.395 44.000 0.00 0.00 0.00 2.45
855 887 0.261696 AAGGCCTCCCTCTCTCTCTC 59.738 60.000 5.23 0.00 41.90 3.20
856 888 1.528309 GGCCTCCCTCTCTCTCTCG 60.528 68.421 0.00 0.00 0.00 4.04
857 889 1.528309 GCCTCCCTCTCTCTCTCGG 60.528 68.421 0.00 0.00 0.00 4.63
858 890 1.919771 CCTCCCTCTCTCTCTCGGT 59.080 63.158 0.00 0.00 0.00 4.69
859 891 0.257616 CCTCCCTCTCTCTCTCGGTT 59.742 60.000 0.00 0.00 0.00 4.44
881 913 3.200605 TCCTTTATAAAAGGGACCCGACC 59.799 47.826 16.38 0.00 36.02 4.79
1175 1353 2.313234 CTTTTGTGATCAGCAACAGCG 58.687 47.619 0.00 0.00 0.00 5.18
1304 1482 9.610705 TCTTTCTCAGTTCTATATGTACTACGT 57.389 33.333 0.00 0.00 0.00 3.57
1386 1568 1.481772 TGTGCATCAGATGATCGGTGA 59.518 47.619 15.12 0.00 31.21 4.02
1793 1986 7.455638 TGGTAGGAGTACAAGTTAGTTAATGGT 59.544 37.037 0.00 0.00 0.00 3.55
1795 1988 6.171213 AGGAGTACAAGTTAGTTAATGGTGC 58.829 40.000 0.00 0.00 0.00 5.01
1811 2004 3.132925 TGGTGCAACGGTAACTAACTTC 58.867 45.455 0.00 0.00 38.12 3.01
1895 2088 4.545706 GCGATGATGGCCACCGGA 62.546 66.667 8.16 0.00 0.00 5.14
1922 2115 3.747976 GCCACGGATGTTGGTGCC 61.748 66.667 0.00 0.00 32.85 5.01
1923 2116 2.282110 CCACGGATGTTGGTGCCA 60.282 61.111 0.00 0.00 32.85 4.92
2123 2316 2.355481 GTCGTCGTCACCACCACC 60.355 66.667 0.00 0.00 0.00 4.61
2206 2399 0.545309 TGGAGCAAGAGCCCTACTGT 60.545 55.000 0.00 0.00 43.56 3.55
2381 2577 3.220110 TCTGATCTATCCACCACGGTAC 58.780 50.000 0.00 0.00 35.57 3.34
2525 2721 8.656849 GTGATTCGTTTGTGTGTAAGATAAGAT 58.343 33.333 0.00 0.00 0.00 2.40
2582 2779 4.682563 AGAAACAAGGAGAGATCAGAGGA 58.317 43.478 0.00 0.00 0.00 3.71
2583 2780 4.711355 AGAAACAAGGAGAGATCAGAGGAG 59.289 45.833 0.00 0.00 0.00 3.69
2659 2861 3.240884 CACTGTGAGATCGAGTGAGTTG 58.759 50.000 0.32 0.00 39.64 3.16
2687 2890 3.486383 AGTAGCTAGCTTTTTGTTGCCA 58.514 40.909 24.88 0.00 0.00 4.92
2766 2969 3.064207 GCTCGAACCATTTGTACTGTGA 58.936 45.455 0.00 0.00 0.00 3.58
2807 3010 2.403252 AGACCGGACCATGAAATGTC 57.597 50.000 9.46 0.00 44.81 3.06
2870 3073 7.662604 TGCATGATTATATGTCAGTGATGAC 57.337 36.000 0.00 1.44 39.15 3.06
2902 3105 3.640000 GTCAGCGCGCACAGTGTT 61.640 61.111 35.10 7.55 0.00 3.32
2903 3106 2.028337 TCAGCGCGCACAGTGTTA 59.972 55.556 35.10 4.49 0.00 2.41
2904 3107 1.592939 TCAGCGCGCACAGTGTTAA 60.593 52.632 35.10 3.70 0.00 2.01
2905 3108 1.438710 CAGCGCGCACAGTGTTAAC 60.439 57.895 35.10 0.00 0.00 2.01
2943 3299 5.891451 ACCCGAGAAGCTTAATTAATTTGC 58.109 37.500 5.91 11.17 0.00 3.68
2944 3300 4.970003 CCCGAGAAGCTTAATTAATTTGCG 59.030 41.667 5.91 3.83 0.00 4.85
2945 3301 5.220777 CCCGAGAAGCTTAATTAATTTGCGA 60.221 40.000 5.91 0.00 0.00 5.10
2946 3302 5.677178 CCGAGAAGCTTAATTAATTTGCGAC 59.323 40.000 5.91 10.27 0.00 5.19
2947 3303 5.677178 CGAGAAGCTTAATTAATTTGCGACC 59.323 40.000 5.91 6.56 0.00 4.79
2948 3304 5.891451 AGAAGCTTAATTAATTTGCGACCC 58.109 37.500 5.91 4.58 0.00 4.46
2949 3305 4.287238 AGCTTAATTAATTTGCGACCCG 57.713 40.909 5.91 0.00 0.00 5.28
2950 3306 3.942748 AGCTTAATTAATTTGCGACCCGA 59.057 39.130 5.91 0.00 0.00 5.14
2951 3307 4.035208 AGCTTAATTAATTTGCGACCCGAG 59.965 41.667 5.91 0.00 0.00 4.63
2952 3308 4.034742 GCTTAATTAATTTGCGACCCGAGA 59.965 41.667 5.91 0.00 0.00 4.04
2953 3309 5.448089 GCTTAATTAATTTGCGACCCGAGAA 60.448 40.000 5.91 0.00 0.00 2.87
2954 3310 4.616181 AATTAATTTGCGACCCGAGAAG 57.384 40.909 0.00 0.00 0.00 2.85
2955 3311 1.365699 TAATTTGCGACCCGAGAAGC 58.634 50.000 0.00 0.00 0.00 3.86
2956 3312 0.321653 AATTTGCGACCCGAGAAGCT 60.322 50.000 0.00 0.00 0.00 3.74
2957 3313 0.321653 ATTTGCGACCCGAGAAGCTT 60.322 50.000 0.00 0.00 0.00 3.74
2958 3314 0.319083 TTTGCGACCCGAGAAGCTTA 59.681 50.000 0.00 0.00 0.00 3.09
2959 3315 0.319083 TTGCGACCCGAGAAGCTTAA 59.681 50.000 0.00 0.00 0.00 1.85
2960 3316 0.535335 TGCGACCCGAGAAGCTTAAT 59.465 50.000 0.00 0.00 0.00 1.40
2961 3317 1.066430 TGCGACCCGAGAAGCTTAATT 60.066 47.619 0.00 0.00 0.00 1.40
2962 3318 2.166870 TGCGACCCGAGAAGCTTAATTA 59.833 45.455 0.00 0.00 0.00 1.40
2963 3319 3.192466 GCGACCCGAGAAGCTTAATTAA 58.808 45.455 0.00 0.00 0.00 1.40
2964 3320 3.808174 GCGACCCGAGAAGCTTAATTAAT 59.192 43.478 0.00 0.00 0.00 1.40
2965 3321 4.272748 GCGACCCGAGAAGCTTAATTAATT 59.727 41.667 0.00 5.89 0.00 1.40
2966 3322 5.220796 GCGACCCGAGAAGCTTAATTAATTT 60.221 40.000 5.91 0.00 0.00 1.82
2967 3323 6.192360 CGACCCGAGAAGCTTAATTAATTTG 58.808 40.000 5.91 1.60 0.00 2.32
2990 3346 4.968812 TGCACATACTGAATTGTGGATG 57.031 40.909 5.33 0.00 42.72 3.51
3011 3367 2.099141 TGCTAGTAGCTTTGCACAGG 57.901 50.000 22.34 0.00 42.97 4.00
3016 3372 3.492102 AGTAGCTTTGCACAGGAAAGA 57.508 42.857 13.99 0.00 33.01 2.52
3194 3553 2.685897 ACAAAAGTTACACATGCCACGT 59.314 40.909 0.00 0.00 0.00 4.49
3286 3669 3.689347 ACACTGAAATGCTATCAGGCAA 58.311 40.909 15.21 0.00 46.81 4.52
3308 3693 1.463444 GCGTTTGTGGCGAACTTATCT 59.537 47.619 0.00 0.00 0.00 1.98
3327 3712 8.567948 ACTTATCTCACAAACAACCAAACATAG 58.432 33.333 0.00 0.00 0.00 2.23
3339 3724 6.165577 CAACCAAACATAGCCAAGCTAATTT 58.834 36.000 0.00 2.49 44.62 1.82
3397 3785 3.942115 CAGATCTTCTGTAGTGTCCTCGA 59.058 47.826 0.00 0.00 39.58 4.04
3440 3833 9.619316 CCACGTTGAAAGTTCATAATAATTTGA 57.381 29.630 0.00 0.00 37.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 2.165845 CTCCTTGTAGGGGTGTAGTTCG 59.834 54.545 0.00 0.00 35.59 3.95
78 79 0.974383 ACGTTCTCCTTGTAGGGGTG 59.026 55.000 0.00 0.00 37.09 4.61
79 80 0.974383 CACGTTCTCCTTGTAGGGGT 59.026 55.000 0.00 0.00 37.09 4.95
80 81 0.249398 CCACGTTCTCCTTGTAGGGG 59.751 60.000 0.00 0.00 37.13 4.79
102 103 0.841289 TTTGGTGGAGTTTCCCGAGT 59.159 50.000 0.00 0.00 35.03 4.18
267 272 4.735132 ACGTACACGCATGCGCCT 62.735 61.111 38.15 25.32 44.43 5.52
304 309 8.879759 CAATGATTTCCTAAACTCGCTTACTAA 58.120 33.333 0.00 0.00 0.00 2.24
340 345 0.645355 CGGTTGTTCGGATGTGATCG 59.355 55.000 0.00 0.00 0.00 3.69
351 356 7.435784 GGTCTTCTTAGATCTATTCGGTTGTTC 59.564 40.741 2.58 0.00 31.86 3.18
394 399 3.002791 CGCTTAGCTCATCAAACCTTCA 58.997 45.455 1.76 0.00 0.00 3.02
438 443 6.730960 TTTATATATAAAGCGGGGCGAAAG 57.269 37.500 12.90 0.00 0.00 2.62
439 444 6.730960 CTTTATATATAAAGCGGGGCGAAA 57.269 37.500 25.10 1.66 41.69 3.46
450 455 5.599359 TTGCGCGCTGCTTTATATATAAA 57.401 34.783 33.29 15.47 46.63 1.40
451 456 5.794687 ATTGCGCGCTGCTTTATATATAA 57.205 34.783 33.29 13.46 46.63 0.98
452 457 5.794687 AATTGCGCGCTGCTTTATATATA 57.205 34.783 33.29 3.26 46.63 0.86
453 458 4.685169 AATTGCGCGCTGCTTTATATAT 57.315 36.364 33.29 6.80 46.63 0.86
454 459 4.481930 AAATTGCGCGCTGCTTTATATA 57.518 36.364 33.29 4.14 46.63 0.86
455 460 3.354089 AAATTGCGCGCTGCTTTATAT 57.646 38.095 33.29 9.35 46.63 0.86
456 461 2.842208 AAATTGCGCGCTGCTTTATA 57.158 40.000 33.29 5.92 46.63 0.98
457 462 1.994916 AAAATTGCGCGCTGCTTTAT 58.005 40.000 33.29 12.47 46.63 1.40
458 463 2.620779 TAAAATTGCGCGCTGCTTTA 57.379 40.000 33.29 25.37 46.63 1.85
459 464 1.994916 ATAAAATTGCGCGCTGCTTT 58.005 40.000 33.29 26.34 46.63 3.51
460 465 1.655099 CAATAAAATTGCGCGCTGCTT 59.345 42.857 33.29 20.75 46.63 3.91
461 466 1.270971 CAATAAAATTGCGCGCTGCT 58.729 45.000 33.29 13.84 46.63 4.24
462 467 0.298411 CCAATAAAATTGCGCGCTGC 59.702 50.000 33.29 15.63 46.70 5.25
463 468 0.298411 GCCAATAAAATTGCGCGCTG 59.702 50.000 33.29 18.78 0.00 5.18
464 469 0.173255 AGCCAATAAAATTGCGCGCT 59.827 45.000 33.29 14.40 0.00 5.92
465 470 0.572125 GAGCCAATAAAATTGCGCGC 59.428 50.000 27.26 27.26 0.00 6.86
466 471 1.847999 CTGAGCCAATAAAATTGCGCG 59.152 47.619 0.00 0.00 0.00 6.86
467 472 1.589779 GCTGAGCCAATAAAATTGCGC 59.410 47.619 0.00 0.00 0.00 6.09
468 473 1.847999 CGCTGAGCCAATAAAATTGCG 59.152 47.619 0.00 0.00 35.22 4.85
469 474 1.589779 GCGCTGAGCCAATAAAATTGC 59.410 47.619 0.00 0.00 40.81 3.56
482 487 3.889134 TTGTGGCTGAGGCGCTGAG 62.889 63.158 20.31 1.53 39.38 3.35
483 488 3.474486 TTTGTGGCTGAGGCGCTGA 62.474 57.895 20.31 6.62 39.38 4.26
484 489 2.979676 TTTGTGGCTGAGGCGCTG 60.980 61.111 20.31 0.00 39.38 5.18
485 490 2.111999 TAGTTTGTGGCTGAGGCGCT 62.112 55.000 20.31 2.74 39.38 5.92
486 491 1.026718 ATAGTTTGTGGCTGAGGCGC 61.027 55.000 13.06 13.06 39.81 6.53
487 492 0.729116 CATAGTTTGTGGCTGAGGCG 59.271 55.000 0.35 0.00 39.81 5.52
488 493 1.098050 CCATAGTTTGTGGCTGAGGC 58.902 55.000 0.00 0.00 37.82 4.70
489 494 2.359900 GTCCATAGTTTGTGGCTGAGG 58.640 52.381 0.00 0.00 36.66 3.86
519 524 5.012768 GGCCTGGCTAATCCTATGTACTAAA 59.987 44.000 19.68 0.00 35.26 1.85
538 546 0.319727 TGGTACGTACGTTTGGCCTG 60.320 55.000 27.92 0.00 0.00 4.85
559 567 3.812577 TGTAGCACACAGATGACCG 57.187 52.632 0.00 0.00 31.89 4.79
776 792 1.283321 GGAGAGCACAGGAAAGGGATT 59.717 52.381 0.00 0.00 0.00 3.01
796 812 2.441750 AGAGGTAGCTAGAGAGAGGGTG 59.558 54.545 0.00 0.00 0.00 4.61
797 813 2.709397 GAGAGGTAGCTAGAGAGAGGGT 59.291 54.545 0.00 0.00 0.00 4.34
833 857 1.011595 AGAGAGAGGGAGGCCTTGTA 58.988 55.000 6.77 0.00 0.00 2.41
855 887 3.949754 GGGTCCCTTTTATAAAGGAACCG 59.050 47.826 19.55 3.95 46.03 4.44
857 889 4.637534 GTCGGGTCCCTTTTATAAAGGAAC 59.362 45.833 17.57 11.43 39.81 3.62
858 890 4.324486 GGTCGGGTCCCTTTTATAAAGGAA 60.324 45.833 17.57 0.00 39.81 3.36
859 891 3.200605 GGTCGGGTCCCTTTTATAAAGGA 59.799 47.826 17.57 5.61 39.81 3.36
1144 1322 6.038356 GCTGATCACAAAAGGGAACAATATG 58.962 40.000 0.00 0.00 0.00 1.78
1147 1325 3.896888 TGCTGATCACAAAAGGGAACAAT 59.103 39.130 0.00 0.00 0.00 2.71
1175 1353 2.820037 GCTGTTGTCGCTAGGGCC 60.820 66.667 1.02 0.00 34.44 5.80
1300 1478 5.786311 AGTGACCAAGCAAACTAATACGTA 58.214 37.500 0.00 0.00 0.00 3.57
1301 1479 4.638304 AGTGACCAAGCAAACTAATACGT 58.362 39.130 0.00 0.00 0.00 3.57
1302 1480 5.607119 AAGTGACCAAGCAAACTAATACG 57.393 39.130 0.00 0.00 0.00 3.06
1303 1481 7.078228 CAGAAAGTGACCAAGCAAACTAATAC 58.922 38.462 0.00 0.00 0.00 1.89
1304 1482 6.206634 CCAGAAAGTGACCAAGCAAACTAATA 59.793 38.462 0.00 0.00 0.00 0.98
1386 1568 3.589988 GTCGAGAACACACTGGATGATT 58.410 45.455 0.00 0.00 0.00 2.57
1393 1575 2.365068 CGGCGTCGAGAACACACTG 61.365 63.158 1.44 0.00 39.00 3.66
1540 1725 0.179065 TGATCCTCATCTTGGCTGCG 60.179 55.000 0.00 0.00 0.00 5.18
1757 1942 0.966920 ACTCCTACCAAGTGACCACG 59.033 55.000 0.00 0.00 36.20 4.94
1793 1986 1.794116 GCGAAGTTAGTTACCGTTGCA 59.206 47.619 0.00 0.00 0.00 4.08
1795 1988 2.665052 GGAGCGAAGTTAGTTACCGTTG 59.335 50.000 0.00 0.00 0.00 4.10
1811 2004 4.481112 GCCATGCAAACCGGAGCG 62.481 66.667 9.46 0.00 0.00 5.03
1958 2151 4.265056 ACCTTCGGTGGGTGCACC 62.265 66.667 28.57 28.57 41.68 5.01
2094 2287 3.681835 GACGACCGGTGGCTCTGT 61.682 66.667 14.63 0.00 0.00 3.41
2102 2295 3.969802 GTGGTGACGACGACCGGT 61.970 66.667 6.92 6.92 43.93 5.28
2115 2308 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
2116 2309 3.814906 TGGTGGTGGTGGTGGTGG 61.815 66.667 0.00 0.00 0.00 4.61
2339 2535 2.230025 AGTCTCTCGAGTGTTCCATGTG 59.770 50.000 13.13 0.00 0.00 3.21
2340 2536 2.490115 GAGTCTCTCGAGTGTTCCATGT 59.510 50.000 13.13 0.00 0.00 3.21
2396 2592 2.492484 ACTGTCTAACGGACTAAGGCAG 59.508 50.000 1.84 1.84 46.11 4.85
2525 2721 6.157820 TCTCTAGATCTCTCTCTTTCTCACCA 59.842 42.308 0.00 0.00 32.66 4.17
2631 2831 2.802247 CTCGATCTCACAGTGTTTGCAA 59.198 45.455 0.00 0.00 0.00 4.08
2659 2861 6.546972 ACAAAAAGCTAGCTACTCAAACTC 57.453 37.500 19.70 0.00 0.00 3.01
2766 2969 9.468532 GGTCTTTCGGTATTTATTATTACGAGT 57.531 33.333 0.00 0.00 0.00 4.18
2807 3010 1.086696 ACGATTCCCAATGAACAGCG 58.913 50.000 0.00 0.00 35.31 5.18
2870 3073 3.300009 CGCTGACAAAAACTAAAGCAGG 58.700 45.455 0.00 0.00 0.00 4.85
2902 3105 5.845103 TCGGGTCGCATATGATAAAAGTTA 58.155 37.500 6.97 0.00 0.00 2.24
2903 3106 4.699637 TCGGGTCGCATATGATAAAAGTT 58.300 39.130 6.97 0.00 0.00 2.66
2904 3107 4.038763 TCTCGGGTCGCATATGATAAAAGT 59.961 41.667 6.97 0.00 0.00 2.66
2905 3108 4.556233 TCTCGGGTCGCATATGATAAAAG 58.444 43.478 6.97 0.00 0.00 2.27
2943 3299 5.986004 AATTAATTAAGCTTCTCGGGTCG 57.014 39.130 0.00 0.00 0.00 4.79
2944 3300 7.316544 TCAAATTAATTAAGCTTCTCGGGTC 57.683 36.000 0.00 0.00 0.00 4.46
2945 3301 7.682021 GCATCAAATTAATTAAGCTTCTCGGGT 60.682 37.037 0.00 0.00 0.00 5.28
2946 3302 6.638468 GCATCAAATTAATTAAGCTTCTCGGG 59.362 38.462 0.00 0.00 0.00 5.14
2947 3303 7.166473 GTGCATCAAATTAATTAAGCTTCTCGG 59.834 37.037 0.00 0.00 0.00 4.63
2948 3304 7.697710 TGTGCATCAAATTAATTAAGCTTCTCG 59.302 33.333 0.00 0.00 0.00 4.04
2949 3305 8.915871 TGTGCATCAAATTAATTAAGCTTCTC 57.084 30.769 0.00 0.00 0.00 2.87
2953 3309 9.740239 CAGTATGTGCATCAAATTAATTAAGCT 57.260 29.630 0.01 0.00 0.00 3.74
2954 3310 9.734620 TCAGTATGTGCATCAAATTAATTAAGC 57.265 29.630 0.01 4.43 37.40 3.09
2960 3316 9.356433 CACAATTCAGTATGTGCATCAAATTAA 57.644 29.630 0.00 0.00 40.32 1.40
2961 3317 7.975058 CCACAATTCAGTATGTGCATCAAATTA 59.025 33.333 0.00 0.00 44.32 1.40
2962 3318 6.814644 CCACAATTCAGTATGTGCATCAAATT 59.185 34.615 0.00 0.00 44.32 1.82
2963 3319 6.153170 TCCACAATTCAGTATGTGCATCAAAT 59.847 34.615 0.00 0.00 44.32 2.32
2964 3320 5.476254 TCCACAATTCAGTATGTGCATCAAA 59.524 36.000 0.00 0.00 44.32 2.69
2965 3321 5.008980 TCCACAATTCAGTATGTGCATCAA 58.991 37.500 0.00 0.00 44.32 2.57
2966 3322 4.587891 TCCACAATTCAGTATGTGCATCA 58.412 39.130 0.00 0.00 44.32 3.07
2967 3323 5.297527 TCATCCACAATTCAGTATGTGCATC 59.702 40.000 0.00 0.00 44.32 3.91
2976 3332 5.108187 ACTAGCATCATCCACAATTCAGT 57.892 39.130 0.00 0.00 0.00 3.41
2990 3346 2.611292 CCTGTGCAAAGCTACTAGCATC 59.389 50.000 10.73 0.00 45.56 3.91
3011 3367 5.573146 CGATGGAAAGTTATGCCTTCTTTC 58.427 41.667 7.94 7.94 43.30 2.62
3016 3372 2.024414 GGCGATGGAAAGTTATGCCTT 58.976 47.619 0.00 0.00 38.00 4.35
3095 3454 6.833416 TGATACCCCATCTAAGGTTTGAAATG 59.167 38.462 0.00 0.00 37.59 2.32
3194 3553 9.391006 AGAATACAAGTGAAAGAAACACACTAA 57.609 29.630 0.00 0.00 42.81 2.24
3236 3616 1.563111 TAACTATGTTGCTACGGCGC 58.437 50.000 6.90 0.00 42.25 6.53
3267 3649 3.129988 GCTTTGCCTGATAGCATTTCAGT 59.870 43.478 8.99 0.00 43.64 3.41
3286 3669 1.301423 TAAGTTCGCCACAAACGCTT 58.699 45.000 0.00 0.00 0.00 4.68
3308 3693 3.701542 TGGCTATGTTTGGTTGTTTGTGA 59.298 39.130 0.00 0.00 0.00 3.58
3327 3712 8.451908 TCCTTAGATCTAAAAATTAGCTTGGC 57.548 34.615 15.85 0.00 0.00 4.52
3359 3744 8.146412 CAGAAGATCTGTGTGTCAATATATGGA 58.854 37.037 0.00 0.00 39.58 3.41
3440 3833 1.826024 CTCTACATGAAGGGCGGCT 59.174 57.895 9.56 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.