Multiple sequence alignment - TraesCS1A01G173600

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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 TraesCS1A01G173600 chr1A 100.000 3273 0 0 1 3273 309742639 309739367 0.000000e+00 6045.0
1 TraesCS1A01G173600 chr1D 93.781 3071 94 33 1 3021 236274450 236277473 0.000000e+00 4523.0
2 TraesCS1A01G173600 chr1B 93.413 3021 100 44 1 2968 341522285 341525259 0.000000e+00 4385.0
3 TraesCS1A01G173600 chr1B 86.093 151 16 2 3116 3265 341525452 341525598 1.220000e-34 158.0
4 TraesCS1A01G173600 chr1B 88.000 75 8 1 3039 3112 341525318 341525392 1.620000e-13 87.9
5 TraesCS1A01G173600 chr3B 83.007 153 24 2 3113 3264 190398359 190398208 1.580000e-28 137.0
6 TraesCS1A01G173600 chr5D 82.581 155 25 2 3112 3265 41031767 41031920 5.700000e-28 135.0
7 TraesCS1A01G173600 chr6D 79.570 93 16 3 3021 3112 127021953 127021863 2.730000e-06 63.9


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 TraesCS1A01G173600 chr1A 309739367 309742639 3272 True 6045.000000 6045 100.000000 1 3273 1 chr1A.!!$R1 3272
1 TraesCS1A01G173600 chr1D 236274450 236277473 3023 False 4523.000000 4523 93.781000 1 3021 1 chr1D.!!$F1 3020
2 TraesCS1A01G173600 chr1B 341522285 341525598 3313 False 1543.633333 4385 89.168667 1 3265 3 chr1B.!!$F1 3264

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
157 163 0.179086 CCTGTTGTTGGTTTGTGGCC 60.179 55.0 0.00 0.00 0.0 5.36 F
384 391 0.261696 AGGCCAAACAAGGTCTTGGT 59.738 50.0 5.01 5.58 42.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1216 1228 0.587768 CAACGTGAGCTCATGCACAA 59.412 50.000 31.39 0.0 41.12 3.33 R
2360 2432 1.406898 TGCGTGCCTCTGAGATAAGAG 59.593 52.381 6.17 0.0 42.90 2.85 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
157 163 0.179086 CCTGTTGTTGGTTTGTGGCC 60.179 55.000 0.00 0.00 0.00 5.36
167 173 1.970640 GGTTTGTGGCCCTGAGAAAAT 59.029 47.619 0.00 0.00 0.00 1.82
232 238 6.208204 CACCTTCATTTCTCTTGTTTCTCCAT 59.792 38.462 0.00 0.00 0.00 3.41
250 256 9.601217 TTTCTCCATTTCATAGACTAAAGCTAC 57.399 33.333 0.00 0.00 0.00 3.58
259 265 7.708051 TCATAGACTAAAGCTACTAGCAACTG 58.292 38.462 10.73 1.14 45.56 3.16
262 268 7.176589 AGACTAAAGCTACTAGCAACTGAAT 57.823 36.000 10.73 0.00 45.56 2.57
342 349 2.686558 TGCTGCATCGTTTCTTTGTC 57.313 45.000 0.00 0.00 0.00 3.18
353 360 4.876107 TCGTTTCTTTGTCTCTGAAAAGCT 59.124 37.500 0.00 0.00 34.14 3.74
357 364 6.515272 TTCTTTGTCTCTGAAAAGCTGTTT 57.485 33.333 0.00 0.00 34.14 2.83
384 391 0.261696 AGGCCAAACAAGGTCTTGGT 59.738 50.000 5.01 5.58 42.00 3.67
521 528 9.764363 TGCACTAAGAATAGATTTAACATCGAT 57.236 29.630 0.00 0.00 33.15 3.59
531 541 5.520288 AGATTTAACATCGATCACCTTCGTG 59.480 40.000 0.00 0.00 40.03 4.35
594 604 3.321111 TCGCAATACTTCTCCCTATGTCC 59.679 47.826 0.00 0.00 0.00 4.02
783 793 7.563924 TGTTAGAGCCTAGCCTCTTCTATTTTA 59.436 37.037 8.79 0.00 42.07 1.52
784 794 8.422566 GTTAGAGCCTAGCCTCTTCTATTTTAA 58.577 37.037 8.79 0.00 42.07 1.52
790 800 8.422566 GCCTAGCCTCTTCTATTTTAACTTCTA 58.577 37.037 0.00 0.00 0.00 2.10
950 960 3.209410 CTTGAGCCAGACAACTCTTGTT 58.791 45.455 0.00 0.00 45.52 2.83
1216 1228 6.985645 GCTCTGTGATCTTCTGAATTATGTCT 59.014 38.462 0.00 0.00 0.00 3.41
1578 1591 6.698766 GGTTATCCTTTGCTGCTGATTTAATG 59.301 38.462 0.00 0.00 0.00 1.90
1647 1660 3.937079 TGTCACAGATTGCAGCTCATAAG 59.063 43.478 0.00 0.00 0.00 1.73
1766 1779 6.322931 ACCCATTGGAGAAGGTAAGAAATTT 58.677 36.000 3.62 0.00 34.81 1.82
1769 1782 6.437162 CCATTGGAGAAGGTAAGAAATTTCCA 59.563 38.462 14.61 0.00 0.00 3.53
1839 1852 6.264518 GGTAACTGGGAAATCTCAACTTTTGA 59.735 38.462 0.00 0.00 38.17 2.69
1933 1946 7.643123 ACCTACCCAAATTTCATGAGTAATCT 58.357 34.615 0.00 0.00 0.00 2.40
1957 1970 1.399440 GGACACGACAGACTACGCATA 59.601 52.381 0.00 0.00 0.00 3.14
2092 2105 3.647649 CTGCATCCTGACGACCGCA 62.648 63.158 0.00 0.00 32.68 5.69
2097 2110 2.021068 ATCCTGACGACCGCATCCTG 62.021 60.000 0.00 0.00 0.00 3.86
2264 2325 2.363018 CTGCCGAGGACCAGGAGA 60.363 66.667 9.92 0.00 0.00 3.71
2265 2326 2.363018 TGCCGAGGACCAGGAGAG 60.363 66.667 9.92 0.00 0.00 3.20
2276 2337 3.181470 GGACCAGGAGAGCTCATAAGAAC 60.181 52.174 17.77 2.33 0.00 3.01
2277 2338 3.704061 GACCAGGAGAGCTCATAAGAACT 59.296 47.826 17.77 0.00 0.00 3.01
2280 2341 5.721960 ACCAGGAGAGCTCATAAGAACTTAA 59.278 40.000 17.77 0.00 0.00 1.85
2283 2344 6.254589 CAGGAGAGCTCATAAGAACTTAAACG 59.745 42.308 17.77 0.00 0.00 3.60
2284 2345 6.071278 AGGAGAGCTCATAAGAACTTAAACGT 60.071 38.462 17.77 0.00 0.00 3.99
2285 2346 6.035112 GGAGAGCTCATAAGAACTTAAACGTG 59.965 42.308 17.77 0.00 0.00 4.49
2360 2432 0.172803 CTGCTGCTGCCCATCTTTTC 59.827 55.000 13.47 0.00 38.71 2.29
2364 2436 2.444421 CTGCTGCCCATCTTTTCTCTT 58.556 47.619 0.00 0.00 0.00 2.85
2382 2456 0.179100 TTATCTCAGAGGCACGCAGC 60.179 55.000 0.00 0.00 44.65 5.25
2400 2474 2.032549 CAGCGGCTGTTATGCATCTTAC 60.033 50.000 21.60 0.62 34.04 2.34
2401 2475 2.158900 AGCGGCTGTTATGCATCTTACT 60.159 45.455 0.19 0.00 34.04 2.24
2432 2506 5.107298 GCTATCGCAATCCTGAATTCTGTAC 60.107 44.000 7.05 0.00 35.78 2.90
2451 2525 2.823593 TCATTGCCCGTGCCATCG 60.824 61.111 0.00 0.00 36.33 3.84
2521 2603 3.988379 TGCAATTCCAAGGATATTCGC 57.012 42.857 0.00 2.10 0.00 4.70
2522 2604 3.554934 TGCAATTCCAAGGATATTCGCT 58.445 40.909 0.00 0.00 0.00 4.93
2523 2605 4.713553 TGCAATTCCAAGGATATTCGCTA 58.286 39.130 0.00 0.00 0.00 4.26
2524 2606 4.756642 TGCAATTCCAAGGATATTCGCTAG 59.243 41.667 0.00 0.00 0.00 3.42
2525 2607 4.378874 GCAATTCCAAGGATATTCGCTAGC 60.379 45.833 4.06 4.06 0.00 3.42
2526 2608 3.402628 TTCCAAGGATATTCGCTAGCC 57.597 47.619 9.66 0.00 36.04 3.93
2532 2614 3.996480 AGGATATTCGCTAGCCTTTGAC 58.004 45.455 9.66 0.00 43.95 3.18
2533 2615 2.731976 GGATATTCGCTAGCCTTTGACG 59.268 50.000 9.66 0.00 32.83 4.35
2534 2616 2.218953 TATTCGCTAGCCTTTGACGG 57.781 50.000 9.66 0.00 0.00 4.79
2535 2617 0.462047 ATTCGCTAGCCTTTGACGGG 60.462 55.000 9.66 0.00 0.00 5.28
2536 2618 1.823169 TTCGCTAGCCTTTGACGGGT 61.823 55.000 9.66 0.00 38.53 5.28
2537 2619 1.810030 CGCTAGCCTTTGACGGGTC 60.810 63.158 9.66 0.00 36.04 4.46
2538 2620 1.449778 GCTAGCCTTTGACGGGTCC 60.450 63.158 2.29 0.00 36.04 4.46
2539 2621 1.980052 CTAGCCTTTGACGGGTCCA 59.020 57.895 0.00 0.00 36.04 4.02
2540 2622 0.108138 CTAGCCTTTGACGGGTCCAG 60.108 60.000 0.00 0.00 36.04 3.86
2541 2623 1.550130 TAGCCTTTGACGGGTCCAGG 61.550 60.000 8.96 8.96 36.04 4.45
2542 2624 3.157680 CCTTTGACGGGTCCAGGT 58.842 61.111 6.15 0.00 0.00 4.00
2543 2625 1.003718 CCTTTGACGGGTCCAGGTC 60.004 63.158 5.57 5.57 0.00 3.85
2544 2626 1.374252 CTTTGACGGGTCCAGGTCG 60.374 63.158 7.56 0.00 35.95 4.79
2545 2627 1.812686 CTTTGACGGGTCCAGGTCGA 61.813 60.000 7.56 3.66 35.95 4.20
2546 2628 1.401318 TTTGACGGGTCCAGGTCGAA 61.401 55.000 9.75 9.75 35.95 3.71
2547 2629 1.401318 TTGACGGGTCCAGGTCGAAA 61.401 55.000 7.56 0.00 35.95 3.46
2548 2630 1.080025 GACGGGTCCAGGTCGAAAG 60.080 63.158 0.00 0.00 0.00 2.62
2552 2634 0.036294 GGGTCCAGGTCGAAAGAAGG 60.036 60.000 0.00 0.00 45.01 3.46
2555 2638 0.178915 TCCAGGTCGAAAGAAGGGGA 60.179 55.000 0.00 0.00 45.01 4.81
2556 2639 0.690762 CCAGGTCGAAAGAAGGGGAA 59.309 55.000 0.00 0.00 45.01 3.97
2557 2640 1.073284 CCAGGTCGAAAGAAGGGGAAA 59.927 52.381 0.00 0.00 45.01 3.13
2563 2646 2.160205 CGAAAGAAGGGGAAAAGGGAC 58.840 52.381 0.00 0.00 0.00 4.46
2569 2652 0.323451 AGGGGAAAAGGGACGCATTC 60.323 55.000 0.00 0.00 0.00 2.67
2573 2656 1.064060 GGAAAAGGGACGCATTCATCG 59.936 52.381 9.30 0.00 0.00 3.84
2574 2657 1.064060 GAAAAGGGACGCATTCATCGG 59.936 52.381 0.00 0.00 0.00 4.18
2580 2663 1.202371 GGACGCATTCATCGGACACTA 60.202 52.381 0.00 0.00 0.00 2.74
2654 2739 0.460311 CTCTAGACATTCGCCCGGTT 59.540 55.000 0.00 0.00 0.00 4.44
2673 2758 3.966543 CCCCACGCCCCTGTTCTT 61.967 66.667 0.00 0.00 0.00 2.52
2694 2779 0.528924 TGCAGTATCGTAACGTGCCT 59.471 50.000 0.00 0.00 32.99 4.75
2751 2838 3.692101 ACAGGTGATTGACAACGAAACAA 59.308 39.130 0.00 0.00 41.74 2.83
2915 3002 7.231519 TCTGTAGAGAAAACAGACTCAGATTCA 59.768 37.037 1.92 0.00 46.38 2.57
2984 3071 1.205064 CGCGCTCTTTCAACCAGTG 59.795 57.895 5.56 0.00 0.00 3.66
3015 3102 3.038788 TGCAGAGCACATTTCGACTTA 57.961 42.857 0.00 0.00 31.71 2.24
3021 3108 6.238211 GCAGAGCACATTTCGACTTACATTAT 60.238 38.462 0.00 0.00 0.00 1.28
3022 3109 7.677276 GCAGAGCACATTTCGACTTACATTATT 60.677 37.037 0.00 0.00 0.00 1.40
3023 3110 8.177663 CAGAGCACATTTCGACTTACATTATTT 58.822 33.333 0.00 0.00 0.00 1.40
3024 3111 8.730680 AGAGCACATTTCGACTTACATTATTTT 58.269 29.630 0.00 0.00 0.00 1.82
3025 3112 9.341899 GAGCACATTTCGACTTACATTATTTTT 57.658 29.630 0.00 0.00 0.00 1.94
3074 3161 6.869388 TCAAAAGGTTTAAACATTAATCCCGC 59.131 34.615 17.71 0.00 31.98 6.13
3078 3166 4.496840 GGTTTAAACATTAATCCCGCCTCG 60.497 45.833 19.57 0.00 0.00 4.63
3080 3168 0.544697 AACATTAATCCCGCCTCGGT 59.455 50.000 4.47 0.00 46.80 4.69
3085 3173 4.040706 ACATTAATCCCGCCTCGGTATAAA 59.959 41.667 4.47 0.00 46.80 1.40
3087 3175 2.762535 ATCCCGCCTCGGTATAAATG 57.237 50.000 4.47 0.00 46.80 2.32
3095 3183 3.433615 GCCTCGGTATAAATGAGATGCAC 59.566 47.826 0.00 0.00 31.31 4.57
3100 3188 5.523552 TCGGTATAAATGAGATGCACACAAG 59.476 40.000 0.00 0.00 0.00 3.16
3112 3200 3.481453 TGCACACAAGCATAACCAAGTA 58.519 40.909 0.00 0.00 40.11 2.24
3114 3202 3.666902 GCACACAAGCATAACCAAGTACG 60.667 47.826 0.00 0.00 0.00 3.67
3115 3203 2.482721 ACACAAGCATAACCAAGTACGC 59.517 45.455 0.00 0.00 0.00 4.42
3116 3204 2.081462 ACAAGCATAACCAAGTACGCC 58.919 47.619 0.00 0.00 0.00 5.68
3118 3206 3.055675 ACAAGCATAACCAAGTACGCCTA 60.056 43.478 0.00 0.00 0.00 3.93
3119 3207 3.899052 AGCATAACCAAGTACGCCTAA 57.101 42.857 0.00 0.00 0.00 2.69
3120 3208 3.793559 AGCATAACCAAGTACGCCTAAG 58.206 45.455 0.00 0.00 0.00 2.18
3123 3267 2.358939 AACCAAGTACGCCTAAGACG 57.641 50.000 0.00 0.00 0.00 4.18
3142 3286 1.340600 CGTAGGAGGGCCAATCCAAAA 60.341 52.381 24.07 9.61 39.47 2.44
3160 3304 7.715266 TCCAAAAATCATGTTGTCATCCATA 57.285 32.000 0.00 0.00 31.15 2.74
3161 3305 8.308851 TCCAAAAATCATGTTGTCATCCATAT 57.691 30.769 0.00 0.00 31.15 1.78
3166 3310 9.425248 AAAATCATGTTGTCATCCATATTAGGT 57.575 29.630 0.00 0.00 31.15 3.08
3196 3340 3.203086 TTGCCGTGGCCTCCAATCA 62.203 57.895 8.69 0.00 41.09 2.57
3201 3345 1.408127 CCGTGGCCTCCAATCATGTAA 60.408 52.381 3.32 0.00 34.18 2.41
3202 3346 1.942657 CGTGGCCTCCAATCATGTAAG 59.057 52.381 3.32 0.00 34.18 2.34
3209 3353 3.209410 CTCCAATCATGTAAGCACCTCC 58.791 50.000 0.00 0.00 0.00 4.30
3215 3359 3.592059 TCATGTAAGCACCTCCGTAAAC 58.408 45.455 0.00 0.00 0.00 2.01
3216 3360 3.007074 TCATGTAAGCACCTCCGTAAACA 59.993 43.478 0.00 0.00 0.00 2.83
3217 3361 3.034721 TGTAAGCACCTCCGTAAACAG 57.965 47.619 0.00 0.00 0.00 3.16
3218 3362 2.629137 TGTAAGCACCTCCGTAAACAGA 59.371 45.455 0.00 0.00 0.00 3.41
3219 3363 3.259876 TGTAAGCACCTCCGTAAACAGAT 59.740 43.478 0.00 0.00 0.00 2.90
3220 3364 4.463539 TGTAAGCACCTCCGTAAACAGATA 59.536 41.667 0.00 0.00 0.00 1.98
3221 3365 4.755266 AAGCACCTCCGTAAACAGATAT 57.245 40.909 0.00 0.00 0.00 1.63
3222 3366 4.323553 AGCACCTCCGTAAACAGATATC 57.676 45.455 0.00 0.00 0.00 1.63
3223 3367 3.704566 AGCACCTCCGTAAACAGATATCA 59.295 43.478 5.32 0.00 0.00 2.15
3235 3380 7.277760 CGTAAACAGATATCAATTCTCCACACA 59.722 37.037 5.32 0.00 0.00 3.72
3265 3410 4.025015 ACGATCATAAACGAAGCGTACT 57.975 40.909 0.00 0.00 39.99 2.73
3266 3411 5.007039 AGACGATCATAAACGAAGCGTACTA 59.993 40.000 0.00 0.00 39.99 1.82
3267 3412 5.203370 ACGATCATAAACGAAGCGTACTAG 58.797 41.667 0.00 0.00 39.99 2.57
3268 3413 5.203370 CGATCATAAACGAAGCGTACTAGT 58.797 41.667 0.00 0.00 39.99 2.57
3269 3414 5.113678 CGATCATAAACGAAGCGTACTAGTG 59.886 44.000 5.39 0.00 39.99 2.74
3270 3415 4.100529 TCATAAACGAAGCGTACTAGTGC 58.899 43.478 5.39 2.60 39.99 4.40
3271 3416 2.427232 AAACGAAGCGTACTAGTGCA 57.573 45.000 11.70 0.00 39.99 4.57
3272 3417 2.649331 AACGAAGCGTACTAGTGCAT 57.351 45.000 11.70 0.00 39.99 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.086869 ACGATGGATGTGCAGGAAAAG 58.913 47.619 0.00 0.00 0.00 2.27
103 104 2.560105 AGCTTCAGTCCCAAGAATTTGC 59.440 45.455 0.00 0.00 32.79 3.68
232 238 8.750298 AGTTGCTAGTAGCTTTAGTCTATGAAA 58.250 33.333 22.34 1.50 42.97 2.69
342 349 3.381272 TGAACCCAAACAGCTTTTCAGAG 59.619 43.478 0.00 0.00 0.00 3.35
353 360 1.573108 TTTGGCCTTGAACCCAAACA 58.427 45.000 3.32 0.00 43.95 2.83
357 364 1.118838 CTTGTTTGGCCTTGAACCCA 58.881 50.000 3.32 0.00 0.00 4.51
424 431 7.226523 TGCTCGTTTACAGCACATATGATAAAT 59.773 33.333 10.38 0.00 42.09 1.40
425 432 6.536941 TGCTCGTTTACAGCACATATGATAAA 59.463 34.615 10.38 3.77 42.09 1.40
521 528 3.442273 AAGTTTTTCTTGCACGAAGGTGA 59.558 39.130 5.72 0.00 46.09 4.02
783 793 3.197983 CGGATTTGGGAGAGGTAGAAGTT 59.802 47.826 0.00 0.00 0.00 2.66
784 794 2.766828 CGGATTTGGGAGAGGTAGAAGT 59.233 50.000 0.00 0.00 0.00 3.01
790 800 1.004394 GAAACCGGATTTGGGAGAGGT 59.996 52.381 9.46 0.00 0.00 3.85
950 960 3.871006 CGAAATATGCCACTCAGTTGCTA 59.129 43.478 2.04 0.00 0.00 3.49
1216 1228 0.587768 CAACGTGAGCTCATGCACAA 59.412 50.000 31.39 0.00 41.12 3.33
1657 1670 2.829023 TGGGACCTTAGACTGTAAGGG 58.171 52.381 14.87 2.51 46.31 3.95
1660 1673 5.131475 ACTTGTTTGGGACCTTAGACTGTAA 59.869 40.000 0.00 0.00 0.00 2.41
1766 1779 3.621268 CGGCTTAATCGTTCAAGAATGGA 59.379 43.478 2.47 0.00 0.00 3.41
1769 1782 3.606687 ACCGGCTTAATCGTTCAAGAAT 58.393 40.909 0.00 0.00 0.00 2.40
1792 1805 3.432252 CGAAGTTTCCACTGCTTAATCGT 59.568 43.478 0.00 0.00 31.60 3.73
1851 1864 6.954616 TGCATGTTCATTTTATTGCTCTTG 57.045 33.333 0.00 0.00 0.00 3.02
1880 1893 4.778534 AGGACTGAAATGATGCAAACAG 57.221 40.909 0.00 0.00 0.00 3.16
1933 1946 2.734670 CGTAGTCTGTCGTGTCCAAAA 58.265 47.619 0.00 0.00 0.00 2.44
1957 1970 1.782028 GAAAACGAGGCAACAGGCGT 61.782 55.000 0.00 0.00 46.16 5.68
2092 2105 1.527370 GTTAAGGGAGGCGCAGGAT 59.473 57.895 10.83 0.00 0.00 3.24
2218 2231 1.560866 CCTGCTCCTCTTCCTTGGCT 61.561 60.000 0.00 0.00 0.00 4.75
2242 2279 3.672295 CTGGTCCTCGGCAGCTTCC 62.672 68.421 0.00 0.00 0.00 3.46
2248 2285 2.363018 CTCTCCTGGTCCTCGGCA 60.363 66.667 0.00 0.00 0.00 5.69
2250 2287 2.043450 AGCTCTCCTGGTCCTCGG 60.043 66.667 0.00 0.00 0.00 4.63
2264 2325 7.149973 TGTACACGTTTAAGTTCTTATGAGCT 58.850 34.615 0.00 0.00 35.21 4.09
2265 2326 7.342318 TGTACACGTTTAAGTTCTTATGAGC 57.658 36.000 0.00 0.00 0.00 4.26
2276 2337 7.647907 ATGTAGGTTCTTGTACACGTTTAAG 57.352 36.000 0.00 0.00 32.05 1.85
2277 2338 8.140628 TGTATGTAGGTTCTTGTACACGTTTAA 58.859 33.333 0.00 0.00 32.05 1.52
2280 2341 6.088016 TGTATGTAGGTTCTTGTACACGTT 57.912 37.500 0.00 0.00 32.05 3.99
2283 2344 7.201410 CGAACATGTATGTAGGTTCTTGTACAC 60.201 40.741 0.00 0.00 40.80 2.90
2284 2345 6.809689 CGAACATGTATGTAGGTTCTTGTACA 59.190 38.462 0.00 0.00 40.80 2.90
2285 2346 6.810182 ACGAACATGTATGTAGGTTCTTGTAC 59.190 38.462 0.00 0.00 40.80 2.90
2360 2432 1.406898 TGCGTGCCTCTGAGATAAGAG 59.593 52.381 6.17 0.00 42.90 2.85
2364 2436 1.439228 GCTGCGTGCCTCTGAGATA 59.561 57.895 6.17 0.00 35.15 1.98
2382 2456 2.032549 GCAGTAAGATGCATAACAGCCG 60.033 50.000 0.00 0.00 45.77 5.52
2432 2506 2.440796 ATGGCACGGGCAATGAGG 60.441 61.111 13.89 0.00 42.43 3.86
2451 2525 0.462047 CTGCTACCATTCACGGGACC 60.462 60.000 0.00 0.00 0.00 4.46
2455 2529 4.019919 CAAATTCTGCTACCATTCACGG 57.980 45.455 0.00 0.00 0.00 4.94
2521 2603 0.108138 CTGGACCCGTCAAAGGCTAG 60.108 60.000 0.00 0.00 0.00 3.42
2522 2604 1.550130 CCTGGACCCGTCAAAGGCTA 61.550 60.000 0.00 0.00 31.22 3.93
2523 2605 2.750350 CTGGACCCGTCAAAGGCT 59.250 61.111 0.00 0.00 0.00 4.58
2524 2606 2.359975 CCTGGACCCGTCAAAGGC 60.360 66.667 0.00 0.00 31.22 4.35
2525 2607 1.003718 GACCTGGACCCGTCAAAGG 60.004 63.158 0.00 12.10 39.50 3.11
2526 2608 1.374252 CGACCTGGACCCGTCAAAG 60.374 63.158 0.00 0.00 0.00 2.77
2527 2609 1.401318 TTCGACCTGGACCCGTCAAA 61.401 55.000 0.00 0.00 0.00 2.69
2528 2610 1.401318 TTTCGACCTGGACCCGTCAA 61.401 55.000 0.00 0.00 0.00 3.18
2529 2611 1.812686 CTTTCGACCTGGACCCGTCA 61.813 60.000 0.00 0.00 0.00 4.35
2530 2612 1.080025 CTTTCGACCTGGACCCGTC 60.080 63.158 0.00 0.00 0.00 4.79
2531 2613 1.117142 TTCTTTCGACCTGGACCCGT 61.117 55.000 0.00 0.00 0.00 5.28
2532 2614 0.389948 CTTCTTTCGACCTGGACCCG 60.390 60.000 0.00 0.88 0.00 5.28
2533 2615 0.036294 CCTTCTTTCGACCTGGACCC 60.036 60.000 0.00 0.00 0.00 4.46
2534 2616 0.036294 CCCTTCTTTCGACCTGGACC 60.036 60.000 0.00 0.00 0.00 4.46
2535 2617 0.036294 CCCCTTCTTTCGACCTGGAC 60.036 60.000 0.00 0.00 0.00 4.02
2536 2618 0.178915 TCCCCTTCTTTCGACCTGGA 60.179 55.000 0.00 0.00 0.00 3.86
2537 2619 0.690762 TTCCCCTTCTTTCGACCTGG 59.309 55.000 0.00 0.00 0.00 4.45
2538 2620 2.561478 TTTCCCCTTCTTTCGACCTG 57.439 50.000 0.00 0.00 0.00 4.00
2539 2621 2.224793 CCTTTTCCCCTTCTTTCGACCT 60.225 50.000 0.00 0.00 0.00 3.85
2540 2622 2.160205 CCTTTTCCCCTTCTTTCGACC 58.840 52.381 0.00 0.00 0.00 4.79
2541 2623 2.160205 CCCTTTTCCCCTTCTTTCGAC 58.840 52.381 0.00 0.00 0.00 4.20
2542 2624 2.059490 TCCCTTTTCCCCTTCTTTCGA 58.941 47.619 0.00 0.00 0.00 3.71
2543 2625 2.160205 GTCCCTTTTCCCCTTCTTTCG 58.840 52.381 0.00 0.00 0.00 3.46
2544 2626 2.160205 CGTCCCTTTTCCCCTTCTTTC 58.840 52.381 0.00 0.00 0.00 2.62
2545 2627 1.822062 GCGTCCCTTTTCCCCTTCTTT 60.822 52.381 0.00 0.00 0.00 2.52
2546 2628 0.251209 GCGTCCCTTTTCCCCTTCTT 60.251 55.000 0.00 0.00 0.00 2.52
2547 2629 1.379146 GCGTCCCTTTTCCCCTTCT 59.621 57.895 0.00 0.00 0.00 2.85
2548 2630 0.323451 ATGCGTCCCTTTTCCCCTTC 60.323 55.000 0.00 0.00 0.00 3.46
2552 2634 1.405463 GATGAATGCGTCCCTTTTCCC 59.595 52.381 0.00 0.00 0.00 3.97
2555 2638 1.094785 CCGATGAATGCGTCCCTTTT 58.905 50.000 0.00 0.00 0.00 2.27
2556 2639 0.251916 TCCGATGAATGCGTCCCTTT 59.748 50.000 0.00 0.00 0.00 3.11
2557 2640 0.462047 GTCCGATGAATGCGTCCCTT 60.462 55.000 0.00 0.00 0.00 3.95
2563 2646 3.384668 AGAATAGTGTCCGATGAATGCG 58.615 45.455 0.00 0.00 0.00 4.73
2569 2652 4.437239 AGCAAGAAGAATAGTGTCCGATG 58.563 43.478 0.00 0.00 0.00 3.84
2573 2656 6.809630 AAAAGAGCAAGAAGAATAGTGTCC 57.190 37.500 0.00 0.00 0.00 4.02
2612 2695 9.965902 AGAGTTTGAATTGTCTTCTAATACCAT 57.034 29.630 0.00 0.00 0.00 3.55
2658 2743 1.672356 CAGAAGAACAGGGGCGTGG 60.672 63.158 0.00 0.00 0.00 4.94
2659 2744 2.328099 GCAGAAGAACAGGGGCGTG 61.328 63.158 0.00 0.00 0.00 5.34
2660 2745 2.032681 GCAGAAGAACAGGGGCGT 59.967 61.111 0.00 0.00 0.00 5.68
2661 2746 2.032528 TGCAGAAGAACAGGGGCG 59.967 61.111 0.00 0.00 0.00 6.13
2662 2747 0.324943 TACTGCAGAAGAACAGGGGC 59.675 55.000 23.35 0.00 38.25 5.80
2663 2748 2.739932 CGATACTGCAGAAGAACAGGGG 60.740 54.545 23.35 0.00 38.25 4.79
2664 2749 2.093973 ACGATACTGCAGAAGAACAGGG 60.094 50.000 23.35 1.93 38.25 4.45
2665 2750 3.238108 ACGATACTGCAGAAGAACAGG 57.762 47.619 23.35 3.44 38.25 4.00
2673 2758 1.468565 GGCACGTTACGATACTGCAGA 60.469 52.381 23.35 4.31 0.00 4.26
2722 2807 1.625315 TGTCAATCACCTGTCTCCTGG 59.375 52.381 0.00 0.00 35.86 4.45
2764 2851 2.688507 CGTGCAGCTCTCTTCCTTTTA 58.311 47.619 0.00 0.00 0.00 1.52
2984 3071 0.098905 TGCTCTGCACGTAGACGATC 59.901 55.000 9.41 0.54 43.39 3.69
3025 3112 9.504708 TGAGTAATAAAACACCCTTTTATCGAA 57.495 29.630 0.00 0.00 34.53 3.71
3026 3113 9.504708 TTGAGTAATAAAACACCCTTTTATCGA 57.495 29.630 0.00 0.00 34.53 3.59
3031 3118 8.764558 ACCTTTTGAGTAATAAAACACCCTTTT 58.235 29.630 0.00 0.00 0.00 2.27
3032 3119 8.313944 ACCTTTTGAGTAATAAAACACCCTTT 57.686 30.769 0.00 0.00 0.00 3.11
3033 3120 7.907841 ACCTTTTGAGTAATAAAACACCCTT 57.092 32.000 0.00 0.00 0.00 3.95
3034 3121 7.907841 AACCTTTTGAGTAATAAAACACCCT 57.092 32.000 0.00 0.00 0.00 4.34
3074 3161 4.449068 GTGTGCATCTCATTTATACCGAGG 59.551 45.833 0.00 0.00 0.00 4.63
3078 3166 5.066375 TGCTTGTGTGCATCTCATTTATACC 59.934 40.000 0.00 0.00 38.12 2.73
3095 3183 2.159572 GGCGTACTTGGTTATGCTTGTG 60.160 50.000 0.00 0.00 0.00 3.33
3100 3188 3.554731 GTCTTAGGCGTACTTGGTTATGC 59.445 47.826 0.00 0.00 0.00 3.14
3112 3200 0.750911 CCCTCCTACGTCTTAGGCGT 60.751 60.000 17.77 17.77 46.72 5.68
3114 3202 1.740905 GCCCTCCTACGTCTTAGGC 59.259 63.158 0.00 0.00 46.72 3.93
3116 3204 1.481871 TTGGCCCTCCTACGTCTTAG 58.518 55.000 0.00 0.00 0.00 2.18
3118 3206 0.831307 GATTGGCCCTCCTACGTCTT 59.169 55.000 0.00 0.00 0.00 3.01
3119 3207 1.049289 GGATTGGCCCTCCTACGTCT 61.049 60.000 13.07 0.00 0.00 4.18
3120 3208 1.335132 TGGATTGGCCCTCCTACGTC 61.335 60.000 19.30 0.00 34.97 4.34
3123 3267 2.525105 TTTTGGATTGGCCCTCCTAC 57.475 50.000 19.30 0.00 34.97 3.18
3133 3277 6.874664 TGGATGACAACATGATTTTTGGATTG 59.125 34.615 0.00 0.00 36.82 2.67
3160 3304 5.944007 ACGGCAAGAGACATTTTTACCTAAT 59.056 36.000 0.00 0.00 0.00 1.73
3161 3305 5.180492 CACGGCAAGAGACATTTTTACCTAA 59.820 40.000 0.00 0.00 0.00 2.69
3164 3308 3.365969 CCACGGCAAGAGACATTTTTACC 60.366 47.826 0.00 0.00 0.00 2.85
3165 3309 3.821841 CCACGGCAAGAGACATTTTTAC 58.178 45.455 0.00 0.00 0.00 2.01
3166 3310 2.227865 GCCACGGCAAGAGACATTTTTA 59.772 45.455 2.36 0.00 41.49 1.52
3167 3311 1.000274 GCCACGGCAAGAGACATTTTT 60.000 47.619 2.36 0.00 41.49 1.94
3168 3312 0.598065 GCCACGGCAAGAGACATTTT 59.402 50.000 2.36 0.00 41.49 1.82
3176 3320 2.819984 GATTGGAGGCCACGGCAAGA 62.820 60.000 10.83 0.00 44.11 3.02
3179 3323 2.982643 ATGATTGGAGGCCACGGCA 61.983 57.895 10.83 0.00 44.11 5.69
3196 3340 3.259876 TCTGTTTACGGAGGTGCTTACAT 59.740 43.478 0.00 0.00 0.00 2.29
3201 3345 3.704566 TGATATCTGTTTACGGAGGTGCT 59.295 43.478 3.98 0.00 34.27 4.40
3202 3346 4.054780 TGATATCTGTTTACGGAGGTGC 57.945 45.455 3.98 0.00 34.27 5.01
3209 3353 7.277760 TGTGTGGAGAATTGATATCTGTTTACG 59.722 37.037 3.98 0.00 0.00 3.18
3215 3359 7.563888 ACAATGTGTGGAGAATTGATATCTG 57.436 36.000 3.98 0.00 35.67 2.90
3216 3360 9.685276 TTTACAATGTGTGGAGAATTGATATCT 57.315 29.630 3.98 0.00 35.67 1.98
3217 3361 9.941664 CTTTACAATGTGTGGAGAATTGATATC 57.058 33.333 0.00 0.00 35.67 1.63
3218 3362 9.685276 TCTTTACAATGTGTGGAGAATTGATAT 57.315 29.630 0.00 0.00 35.67 1.63
3219 3363 8.946085 GTCTTTACAATGTGTGGAGAATTGATA 58.054 33.333 0.00 0.00 35.67 2.15
3220 3364 7.361201 CGTCTTTACAATGTGTGGAGAATTGAT 60.361 37.037 0.00 0.00 35.67 2.57
3221 3365 6.073276 CGTCTTTACAATGTGTGGAGAATTGA 60.073 38.462 0.00 0.00 35.67 2.57
3222 3366 6.073276 TCGTCTTTACAATGTGTGGAGAATTG 60.073 38.462 0.00 0.00 37.33 2.32
3223 3367 5.995282 TCGTCTTTACAATGTGTGGAGAATT 59.005 36.000 0.00 0.00 29.06 2.17
3235 3380 7.399523 GCTTCGTTTATGATCGTCTTTACAAT 58.600 34.615 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.