Multiple sequence alignment - TraesCS4B01G271000

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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 TraesCS4B01G271000 chr4B 100.000 3595 0 0 1 3595 547092683 547096277 0.000000e+00 6639.0
1 TraesCS4B01G271000 chr4D 93.316 1930 62 21 432 2324 441104917 441106816 0.000000e+00 2787.0
2 TraesCS4B01G271000 chr4D 92.601 838 44 14 2316 3144 441106967 441107795 0.000000e+00 1188.0
3 TraesCS4B01G271000 chr4D 89.153 378 18 10 3138 3498 441107822 441108193 1.970000e-122 449.0
4 TraesCS4B01G271000 chr4D 93.502 277 9 3 12 279 441104492 441104768 1.550000e-108 403.0
5 TraesCS4B01G271000 chr4D 88.268 179 16 5 2438 2615 122202102 122202276 3.640000e-50 209.0
6 TraesCS4B01G271000 chr4D 86.813 182 19 5 2435 2615 69179556 69179733 7.870000e-47 198.0
7 TraesCS4B01G271000 chr4D 90.667 150 12 2 298 447 441104754 441104901 7.870000e-47 198.0
8 TraesCS4B01G271000 chr4D 95.238 105 5 0 3491 3595 441109166 441109270 2.220000e-37 167.0
9 TraesCS4B01G271000 chr4A 88.981 2178 92 56 298 2406 26467161 26465063 0.000000e+00 2556.0
10 TraesCS4B01G271000 chr4A 92.500 280 15 1 6 279 26467426 26467147 2.600000e-106 396.0
11 TraesCS4B01G271000 chr4A 87.079 178 19 4 2438 2615 448512983 448512810 7.870000e-47 198.0
12 TraesCS4B01G271000 chr4A 77.812 320 63 7 1296 1611 26413808 26413493 1.320000e-44 191.0
13 TraesCS4B01G271000 chr2A 80.645 620 109 11 1290 1902 29989774 29990389 1.510000e-128 470.0
14 TraesCS4B01G271000 chr2D 80.323 620 111 11 1290 1902 27837050 27837665 3.270000e-125 459.0
15 TraesCS4B01G271000 chr2B 80.000 620 113 11 1290 1902 44159064 44159679 7.080000e-122 448.0
16 TraesCS4B01G271000 chr3A 77.248 545 111 11 1291 1827 170811690 170812229 1.250000e-79 307.0
17 TraesCS4B01G271000 chr3A 93.750 48 3 0 2774 2821 513903033 513902986 4.980000e-09 73.1
18 TraesCS4B01G271000 chr3D 77.206 544 110 13 1291 1827 157443377 157442841 4.510000e-79 305.0
19 TraesCS4B01G271000 chr3D 87.293 181 18 5 2436 2615 588164409 588164233 6.090000e-48 202.0
20 TraesCS4B01G271000 chr3D 87.151 179 18 5 2438 2615 557813854 557813680 7.870000e-47 198.0
21 TraesCS4B01G271000 chr3D 82.716 81 11 3 2941 3019 82363946 82363867 6.440000e-08 69.4
22 TraesCS4B01G271000 chr1D 87.709 179 17 4 2438 2615 413416515 413416341 1.690000e-48 204.0
23 TraesCS4B01G271000 chr5A 87.640 178 17 5 2438 2614 578233465 578233638 6.090000e-48 202.0
24 TraesCS4B01G271000 chr5A 100.000 29 0 0 2794 2822 117191432 117191460 2.000000e-03 54.7
25 TraesCS4B01G271000 chrUn 86.243 189 18 8 2433 2618 83299848 83300031 7.870000e-47 198.0
26 TraesCS4B01G271000 chr7D 85.938 64 9 0 1632 1695 501116721 501116784 6.440000e-08 69.4
27 TraesCS4B01G271000 chr7D 90.196 51 4 1 2935 2984 101560521 101560471 8.330000e-07 65.8
28 TraesCS4B01G271000 chr5D 100.000 34 0 0 2789 2822 346843165 346843132 3.000000e-06 63.9
29 TraesCS4B01G271000 chr3B 97.059 34 0 1 2935 2967 575300179 575300212 5.010000e-04 56.5
30 TraesCS4B01G271000 chr7B 94.118 34 2 0 1626 1659 530441513 530441546 6.000000e-03 52.8


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 TraesCS4B01G271000 chr4B 547092683 547096277 3594 False 6639.000000 6639 100.000000 1 3595 1 chr4B.!!$F1 3594
1 TraesCS4B01G271000 chr4D 441104492 441109270 4778 False 865.333333 2787 92.412833 12 3595 6 chr4D.!!$F3 3583
2 TraesCS4B01G271000 chr4A 26465063 26467426 2363 True 1476.000000 2556 90.740500 6 2406 2 chr4A.!!$R3 2400
3 TraesCS4B01G271000 chr2A 29989774 29990389 615 False 470.000000 470 80.645000 1290 1902 1 chr2A.!!$F1 612
4 TraesCS4B01G271000 chr2D 27837050 27837665 615 False 459.000000 459 80.323000 1290 1902 1 chr2D.!!$F1 612
5 TraesCS4B01G271000 chr2B 44159064 44159679 615 False 448.000000 448 80.000000 1290 1902 1 chr2B.!!$F1 612
6 TraesCS4B01G271000 chr3A 170811690 170812229 539 False 307.000000 307 77.248000 1291 1827 1 chr3A.!!$F1 536
7 TraesCS4B01G271000 chr3D 157442841 157443377 536 True 305.000000 305 77.206000 1291 1827 1 chr3D.!!$R2 536

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
313 329 0.396435 TAATGGCGGGTATCAGCTGG 59.604 55.0 15.13 0.0 0.00 4.85 F
923 1028 1.136690 TCGCCGCATCGCTATTTAAG 58.863 50.0 0.00 0.0 0.00 1.85 F
1905 2020 0.690762 GGCCAGACCTTCACCAACTA 59.309 55.0 0.00 0.0 34.51 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1882 1997 1.299976 GGTGAAGGTCTGGCCGAAT 59.700 57.895 0.0 0.00 43.70 3.34 R
2431 2741 0.464452 GGACGGAGGGAGTACATTGG 59.536 60.000 0.0 0.00 0.00 3.16 R
3522 4864 1.372623 GGACGTGGTCTCCGAACAC 60.373 63.158 0.0 2.04 45.71 3.32 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
55 56 4.104776 CGCAAAGCAAAAGAGTTTCTTCA 58.895 39.130 0.00 0.00 35.27 3.02
135 142 8.053355 AGAAAAACTAATCCTCCCGTAAATCAT 58.947 33.333 0.00 0.00 0.00 2.45
144 151 4.141959 CCTCCCGTAAATCATGCCAAAATT 60.142 41.667 0.00 0.00 0.00 1.82
154 161 8.782137 AAATCATGCCAAAATTACCTACCTAT 57.218 30.769 0.00 0.00 0.00 2.57
208 221 1.479323 CTAACCGCTAGTACCTGCCAA 59.521 52.381 2.66 0.00 0.00 4.52
279 295 2.871096 TTCTTGGCGGGTATCAGTTT 57.129 45.000 0.00 0.00 0.00 2.66
280 296 2.871096 TCTTGGCGGGTATCAGTTTT 57.129 45.000 0.00 0.00 0.00 2.43
281 297 3.149005 TCTTGGCGGGTATCAGTTTTT 57.851 42.857 0.00 0.00 0.00 1.94
308 324 4.774660 TTTTAGGTAATGGCGGGTATCA 57.225 40.909 0.00 0.00 0.00 2.15
309 325 4.345859 TTTAGGTAATGGCGGGTATCAG 57.654 45.455 0.00 0.00 0.00 2.90
310 326 0.396811 AGGTAATGGCGGGTATCAGC 59.603 55.000 0.00 0.00 0.00 4.26
311 327 0.396811 GGTAATGGCGGGTATCAGCT 59.603 55.000 0.00 0.00 0.00 4.24
312 328 1.512926 GTAATGGCGGGTATCAGCTG 58.487 55.000 7.63 7.63 0.00 4.24
313 329 0.396435 TAATGGCGGGTATCAGCTGG 59.604 55.000 15.13 0.00 0.00 4.85
348 364 3.521796 GCGGCTCAATCCAAGGGC 61.522 66.667 0.00 0.00 0.00 5.19
353 369 4.794648 TCAATCCAAGGGCCCGCG 62.795 66.667 18.44 11.76 0.00 6.46
367 383 4.054455 CGCGTCGTGGTTCGGTTG 62.054 66.667 0.00 0.00 40.32 3.77
459 510 3.134792 GACTCAGAGCGGCCGAGA 61.135 66.667 33.48 18.92 0.00 4.04
501 552 3.148279 GCCTCCGGATGGTCGAGT 61.148 66.667 3.57 0.00 36.30 4.18
536 587 5.977731 TGATCGAAATGTTAATGCTCATCG 58.022 37.500 0.00 0.00 0.00 3.84
609 696 7.335627 TGATCCCAAATGATTAAGACGTACTT 58.664 34.615 0.00 0.00 42.04 2.24
676 763 3.225104 TGCTTGCCAGAGAAGAAAATGT 58.775 40.909 0.00 0.00 0.00 2.71
682 769 6.271488 TGCCAGAGAAGAAAATGTAAATGG 57.729 37.500 0.00 0.00 0.00 3.16
686 774 8.037166 GCCAGAGAAGAAAATGTAAATGGAAAT 58.963 33.333 0.00 0.00 0.00 2.17
806 911 2.108157 GTGCATGGCATGGCATGG 59.892 61.111 44.47 32.20 41.91 3.66
833 938 2.967507 TTAAGGCGCTGGGTGCAACA 62.968 55.000 7.64 0.00 41.25 3.33
923 1028 1.136690 TCGCCGCATCGCTATTTAAG 58.863 50.000 0.00 0.00 0.00 1.85
1210 1317 2.679837 GGTAAGTGACGATCCACGACTA 59.320 50.000 0.00 0.00 45.77 2.59
1241 1348 3.023946 TGCGTATTTGCATTGCACTTT 57.976 38.095 11.66 1.66 40.62 2.66
1423 1532 4.320456 CAGTGCGACCAGGGCAGT 62.320 66.667 0.00 0.00 44.52 4.40
1905 2020 0.690762 GGCCAGACCTTCACCAACTA 59.309 55.000 0.00 0.00 34.51 2.24
2030 2166 9.178758 CATTTGGGAACTTAAGTAAGATTAGCT 57.821 33.333 8.92 0.00 37.08 3.32
2031 2167 8.561738 TTTGGGAACTTAAGTAAGATTAGCTG 57.438 34.615 8.92 0.00 37.08 4.24
2130 2269 0.814010 GATCAATTACCCGCCGTGCT 60.814 55.000 0.00 0.00 0.00 4.40
2293 2438 7.776030 TGGTTTCTGACTTTGACCAGTTAAATA 59.224 33.333 0.00 0.00 35.58 1.40
2308 2453 5.004630 CAGTTAAATAAATGCATGTGCGTGG 59.995 40.000 0.00 0.00 45.83 4.94
2379 2685 4.307432 AGTGTGGTCTGAAGTAAACGATG 58.693 43.478 0.00 0.00 0.00 3.84
2408 2718 5.176958 GGATCACTACGTTATTACATGTGCC 59.823 44.000 9.11 0.00 0.00 5.01
2421 2731 3.149196 ACATGTGCCTAAAGTGTCCTTG 58.851 45.455 0.00 0.00 0.00 3.61
2422 2732 3.181445 ACATGTGCCTAAAGTGTCCTTGA 60.181 43.478 0.00 0.00 0.00 3.02
2423 2733 3.126001 TGTGCCTAAAGTGTCCTTGAG 57.874 47.619 0.00 0.00 0.00 3.02
2424 2734 2.438021 TGTGCCTAAAGTGTCCTTGAGT 59.562 45.455 0.00 0.00 28.10 3.41
2425 2735 3.067833 GTGCCTAAAGTGTCCTTGAGTC 58.932 50.000 0.00 0.00 28.10 3.36
2431 2741 3.372660 AAGTGTCCTTGAGTCGAGAAC 57.627 47.619 9.14 0.00 0.00 3.01
2446 2756 2.159085 CGAGAACCAATGTACTCCCTCC 60.159 54.545 0.00 0.00 0.00 4.30
2447 2757 1.831736 AGAACCAATGTACTCCCTCCG 59.168 52.381 0.00 0.00 0.00 4.63
2450 2760 0.464452 CCAATGTACTCCCTCCGTCC 59.536 60.000 0.00 0.00 0.00 4.79
2461 2771 3.112263 TCCCTCCGTCCATGAATAAGTT 58.888 45.455 0.00 0.00 0.00 2.66
2462 2772 3.118408 TCCCTCCGTCCATGAATAAGTTG 60.118 47.826 0.00 0.00 0.00 3.16
2463 2773 3.370527 CCCTCCGTCCATGAATAAGTTGT 60.371 47.826 0.00 0.00 0.00 3.32
2464 2774 4.141801 CCCTCCGTCCATGAATAAGTTGTA 60.142 45.833 0.00 0.00 0.00 2.41
2465 2775 4.809426 CCTCCGTCCATGAATAAGTTGTAC 59.191 45.833 0.00 0.00 0.00 2.90
2467 2777 6.045072 TCCGTCCATGAATAAGTTGTACTT 57.955 37.500 0.00 0.00 41.97 2.24
2469 2779 6.070995 TCCGTCCATGAATAAGTTGTACTTCT 60.071 38.462 0.00 0.00 39.51 2.85
2470 2780 7.123098 TCCGTCCATGAATAAGTTGTACTTCTA 59.877 37.037 0.00 0.00 39.51 2.10
2471 2781 7.926555 CCGTCCATGAATAAGTTGTACTTCTAT 59.073 37.037 0.00 0.00 39.51 1.98
2644 2954 5.676079 GCAATTTAATGCGGCTGAAACTCTA 60.676 40.000 0.00 0.00 36.45 2.43
2658 2968 6.595716 GCTGAAACTCTAAATATGTGACCACT 59.404 38.462 1.62 0.00 0.00 4.00
2732 3043 1.065926 AGCGATCTGATGCACCTGAAA 60.066 47.619 12.37 0.00 0.00 2.69
2735 3046 3.005554 CGATCTGATGCACCTGAAACTT 58.994 45.455 0.00 0.00 0.00 2.66
2752 3063 7.337689 CCTGAAACTTTGAATATGTGATGGAGA 59.662 37.037 0.00 0.00 0.00 3.71
2806 3117 7.803279 AAATTAAGATAAGCCCTCTAAACCG 57.197 36.000 0.00 0.00 0.00 4.44
2811 3122 5.429130 AGATAAGCCCTCTAAACCGAAAAG 58.571 41.667 0.00 0.00 0.00 2.27
2814 3125 2.027100 AGCCCTCTAAACCGAAAAGGAG 60.027 50.000 0.00 0.00 45.00 3.69
2829 3140 2.950990 AGGAGGGAGTAACAGATGGT 57.049 50.000 0.00 0.00 0.00 3.55
2841 3152 1.899814 ACAGATGGTTCCGCTCAACTA 59.100 47.619 0.00 0.00 0.00 2.24
2843 3154 2.673368 CAGATGGTTCCGCTCAACTAAC 59.327 50.000 0.00 0.00 0.00 2.34
2850 3161 2.883574 TCCGCTCAACTAACGTAATGG 58.116 47.619 0.00 0.00 0.00 3.16
2869 3180 2.294979 GGTTGGACCTTTTGAACTCGT 58.705 47.619 0.00 0.00 34.73 4.18
2912 3224 7.595819 TCTTTTCATGTTTGGATACCACTTT 57.404 32.000 0.00 0.00 30.78 2.66
2933 3245 8.028354 CACTTTTCATATTATTGGCACTCACAA 58.972 33.333 0.00 0.00 0.00 3.33
3075 3388 2.501261 GGTACACAGGGACAAAAGACC 58.499 52.381 0.00 0.00 0.00 3.85
3088 3401 3.066203 ACAAAAGACCACGAATGTTGGAC 59.934 43.478 0.00 0.00 0.00 4.02
3089 3402 1.892209 AAGACCACGAATGTTGGACC 58.108 50.000 0.00 0.00 0.00 4.46
3090 3403 1.056660 AGACCACGAATGTTGGACCT 58.943 50.000 0.00 0.00 0.00 3.85
3091 3404 1.156736 GACCACGAATGTTGGACCTG 58.843 55.000 0.00 0.00 0.00 4.00
3115 3428 5.641209 GCCCTTTATGCATAGTCATAGACAG 59.359 44.000 6.50 0.00 34.60 3.51
3144 3457 6.422400 TCGCAAATCACTTTTGAATAAAACCC 59.578 34.615 2.42 0.00 46.36 4.11
3145 3458 6.347321 CGCAAATCACTTTTGAATAAAACCCC 60.347 38.462 2.42 0.00 46.36 4.95
3187 3534 3.696051 CCTCCAATCCAATCAATTGTCGT 59.304 43.478 5.13 0.00 36.06 4.34
3251 3598 9.847706 CTATGATAATTATTATCGATCGGAGGG 57.152 37.037 16.41 0.00 43.90 4.30
3255 3602 6.862469 AATTATTATCGATCGGAGGGGTAA 57.138 37.500 16.41 7.94 0.00 2.85
3268 3615 4.275936 CGGAGGGGTAAATAAAATCAGCAG 59.724 45.833 0.00 0.00 0.00 4.24
3369 3716 3.427503 GGCGTGCTGTGCAGTTTTATAAT 60.428 43.478 0.00 0.00 40.08 1.28
3370 3717 3.543494 GCGTGCTGTGCAGTTTTATAATG 59.457 43.478 0.00 0.00 40.08 1.90
3371 3718 4.722194 CGTGCTGTGCAGTTTTATAATGT 58.278 39.130 0.00 0.00 40.08 2.71
3373 3720 5.283717 CGTGCTGTGCAGTTTTATAATGTTC 59.716 40.000 0.00 0.00 40.08 3.18
3374 3721 6.381801 GTGCTGTGCAGTTTTATAATGTTCT 58.618 36.000 0.00 0.00 40.08 3.01
3376 3723 6.862608 TGCTGTGCAGTTTTATAATGTTCTTG 59.137 34.615 0.00 0.00 33.32 3.02
3377 3724 7.083858 GCTGTGCAGTTTTATAATGTTCTTGA 58.916 34.615 0.00 0.00 0.00 3.02
3379 3726 9.630098 CTGTGCAGTTTTATAATGTTCTTGAAT 57.370 29.630 0.00 0.00 0.00 2.57
3522 4864 3.125316 CCCGGAAAAATCACTCTCGAAAG 59.875 47.826 0.73 0.00 0.00 2.62
3526 4868 5.277345 CGGAAAAATCACTCTCGAAAGTGTT 60.277 40.000 18.04 7.69 45.57 3.32
3544 4886 3.680786 CGGAGACCACGTCCTGCA 61.681 66.667 0.00 0.00 32.18 4.41
3557 4899 0.471591 TCCTGCAAGTTTTGGGCCAT 60.472 50.000 7.26 0.00 0.00 4.40
3559 4901 0.680618 CTGCAAGTTTTGGGCCATCA 59.319 50.000 7.26 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.066215 CCATGCACACACTAGTAGCCA 60.066 52.381 0.00 0.00 0.00 4.75
1 2 1.656652 CCATGCACACACTAGTAGCC 58.343 55.000 0.00 0.00 0.00 3.93
2 3 1.009829 GCCATGCACACACTAGTAGC 58.990 55.000 0.00 0.00 0.00 3.58
3 4 2.274437 CTGCCATGCACACACTAGTAG 58.726 52.381 0.00 0.00 33.79 2.57
4 5 1.623311 ACTGCCATGCACACACTAGTA 59.377 47.619 0.00 0.00 33.79 1.82
34 35 4.027377 CGTGAAGAAACTCTTTTGCTTTGC 60.027 41.667 0.00 0.00 36.73 3.68
55 56 3.782046 CTCGGTTGATTGGAATCTACGT 58.218 45.455 0.00 0.00 40.50 3.57
109 110 7.399634 TGATTTACGGGAGGATTAGTTTTTCT 58.600 34.615 0.00 0.00 0.00 2.52
135 142 5.197451 CACCATAGGTAGGTAATTTTGGCA 58.803 41.667 0.00 0.00 37.23 4.92
144 151 5.308759 GGGAATTTAGCACCATAGGTAGGTA 59.691 44.000 0.00 0.00 37.23 3.08
154 161 1.214424 GGCTAGGGGAATTTAGCACCA 59.786 52.381 8.69 0.00 43.14 4.17
208 221 0.844661 TGTTACTGCCTGGTCCCCAT 60.845 55.000 0.00 0.00 30.82 4.00
218 231 1.837538 TTGCGCTCGTTGTTACTGCC 61.838 55.000 9.73 0.00 0.00 4.85
219 232 0.451135 CTTGCGCTCGTTGTTACTGC 60.451 55.000 9.73 0.00 0.00 4.40
286 302 5.113446 TGATACCCGCCATTACCTAAAAA 57.887 39.130 0.00 0.00 0.00 1.94
287 303 4.710324 CTGATACCCGCCATTACCTAAAA 58.290 43.478 0.00 0.00 0.00 1.52
288 304 3.495453 GCTGATACCCGCCATTACCTAAA 60.495 47.826 0.00 0.00 0.00 1.85
289 305 2.038033 GCTGATACCCGCCATTACCTAA 59.962 50.000 0.00 0.00 0.00 2.69
290 306 1.621814 GCTGATACCCGCCATTACCTA 59.378 52.381 0.00 0.00 0.00 3.08
291 307 0.396811 GCTGATACCCGCCATTACCT 59.603 55.000 0.00 0.00 0.00 3.08
292 308 0.396811 AGCTGATACCCGCCATTACC 59.603 55.000 0.00 0.00 0.00 2.85
293 309 1.512926 CAGCTGATACCCGCCATTAC 58.487 55.000 8.42 0.00 0.00 1.89
294 310 0.396435 CCAGCTGATACCCGCCATTA 59.604 55.000 17.39 0.00 0.00 1.90
295 311 1.149174 CCAGCTGATACCCGCCATT 59.851 57.895 17.39 0.00 0.00 3.16
296 312 2.822637 CCCAGCTGATACCCGCCAT 61.823 63.158 17.39 0.00 0.00 4.40
297 313 3.479203 CCCAGCTGATACCCGCCA 61.479 66.667 17.39 0.00 0.00 5.69
298 314 4.937431 GCCCAGCTGATACCCGCC 62.937 72.222 17.39 0.00 0.00 6.13
299 315 3.866582 AGCCCAGCTGATACCCGC 61.867 66.667 17.39 6.52 37.57 6.13
353 369 2.315386 GCCTCAACCGAACCACGAC 61.315 63.158 0.00 0.00 45.77 4.34
501 552 7.504924 AACATTTCGATCAGAAGTAAACCAA 57.495 32.000 0.00 0.00 40.40 3.67
609 696 1.003839 GGTTCCACTGATCCGTGCA 60.004 57.895 11.47 0.00 33.60 4.57
676 763 2.215196 GCCGCCGACTATTTCCATTTA 58.785 47.619 0.00 0.00 0.00 1.40
682 769 2.590859 GGGGCCGCCGACTATTTC 60.591 66.667 9.05 0.00 0.00 2.17
715 803 2.028883 GCTACGTTTTCGAAGGATTCCG 59.971 50.000 0.00 0.00 43.81 4.30
806 911 0.872881 CCAGCGCCTTAAATGCATGC 60.873 55.000 11.82 11.82 0.00 4.06
807 912 0.249155 CCCAGCGCCTTAAATGCATG 60.249 55.000 2.29 0.00 0.00 4.06
808 913 0.684153 ACCCAGCGCCTTAAATGCAT 60.684 50.000 2.29 0.00 0.00 3.96
809 914 1.304052 ACCCAGCGCCTTAAATGCA 60.304 52.632 2.29 0.00 0.00 3.96
810 915 1.139520 CACCCAGCGCCTTAAATGC 59.860 57.895 2.29 0.00 0.00 3.56
886 991 3.757248 ATTGAGGCACGGGATCGGC 62.757 63.158 0.00 0.00 41.39 5.54
887 992 1.595382 GATTGAGGCACGGGATCGG 60.595 63.158 0.00 0.00 41.39 4.18
888 993 1.951130 CGATTGAGGCACGGGATCG 60.951 63.158 0.00 0.00 43.02 3.69
889 994 2.247437 GCGATTGAGGCACGGGATC 61.247 63.158 0.00 0.00 0.00 3.36
890 995 2.203070 GCGATTGAGGCACGGGAT 60.203 61.111 0.00 0.00 0.00 3.85
891 996 4.467084 GGCGATTGAGGCACGGGA 62.467 66.667 0.00 0.00 36.61 5.14
895 1000 3.173390 GATGCGGCGATTGAGGCAC 62.173 63.158 12.98 0.00 38.36 5.01
896 1001 2.896854 GATGCGGCGATTGAGGCA 60.897 61.111 12.98 0.00 40.06 4.75
1241 1348 2.630592 TACATATCCACGGCGCGCAA 62.631 55.000 34.42 12.62 0.00 4.85
1423 1532 2.282180 GGCTTGCAGTTCGGGGAA 60.282 61.111 0.00 0.00 0.00 3.97
1528 1643 2.360350 ATGTCCAGGTGCTTGCGG 60.360 61.111 0.00 0.00 0.00 5.69
1882 1997 1.299976 GGTGAAGGTCTGGCCGAAT 59.700 57.895 0.00 0.00 43.70 3.34
2030 2166 2.242965 ACTTCCCATCCATGAGAATGCA 59.757 45.455 0.00 0.00 0.00 3.96
2031 2167 2.621998 CACTTCCCATCCATGAGAATGC 59.378 50.000 0.00 0.00 0.00 3.56
2140 2279 2.930385 ATCAGCCGGTCATCGCAAGG 62.930 60.000 1.90 0.00 37.59 3.61
2293 2438 1.469595 GCATACCACGCACATGCATTT 60.470 47.619 0.00 0.00 43.59 2.32
2308 2453 2.030946 GGCACATTCGTGAAGAGCATAC 59.969 50.000 0.00 0.00 46.80 2.39
2379 2685 9.042008 ACATGTAATAACGTAGTGATCCAATTC 57.958 33.333 0.00 0.00 45.00 2.17
2408 2718 4.768130 TCTCGACTCAAGGACACTTTAG 57.232 45.455 0.00 0.00 33.81 1.85
2421 2731 3.429135 GGGAGTACATTGGTTCTCGACTC 60.429 52.174 0.00 0.00 41.01 3.36
2422 2732 2.496470 GGGAGTACATTGGTTCTCGACT 59.504 50.000 0.00 0.00 41.01 4.18
2423 2733 2.496470 AGGGAGTACATTGGTTCTCGAC 59.504 50.000 0.00 0.00 41.01 4.20
2424 2734 2.758979 GAGGGAGTACATTGGTTCTCGA 59.241 50.000 0.00 0.00 41.01 4.04
2425 2735 2.159085 GGAGGGAGTACATTGGTTCTCG 60.159 54.545 0.00 0.00 41.01 4.04
2431 2741 0.464452 GGACGGAGGGAGTACATTGG 59.536 60.000 0.00 0.00 0.00 3.16
2446 2756 8.873215 ATAGAAGTACAACTTATTCATGGACG 57.127 34.615 0.00 0.00 38.80 4.79
2628 2938 5.008019 CACATATTTAGAGTTTCAGCCGCAT 59.992 40.000 0.00 0.00 0.00 4.73
2632 2942 5.880332 TGGTCACATATTTAGAGTTTCAGCC 59.120 40.000 0.00 0.00 0.00 4.85
2633 2943 6.595716 AGTGGTCACATATTTAGAGTTTCAGC 59.404 38.462 3.82 0.00 0.00 4.26
2682 2993 7.093640 TGCAAGGCTTAAGAGAAAATTCATCAT 60.094 33.333 6.67 0.00 0.00 2.45
2718 3029 4.572985 TTCAAAGTTTCAGGTGCATCAG 57.427 40.909 0.00 0.00 0.00 2.90
2732 3043 5.999044 AGCTCTCCATCACATATTCAAAGT 58.001 37.500 0.00 0.00 0.00 2.66
2806 3117 4.019231 ACCATCTGTTACTCCCTCCTTTTC 60.019 45.833 0.00 0.00 0.00 2.29
2811 3122 2.170817 GGAACCATCTGTTACTCCCTCC 59.829 54.545 0.00 0.00 37.29 4.30
2812 3123 2.159085 CGGAACCATCTGTTACTCCCTC 60.159 54.545 0.00 0.00 37.29 4.30
2814 3125 1.742750 GCGGAACCATCTGTTACTCCC 60.743 57.143 0.00 0.00 37.29 4.30
2829 3140 3.255725 CCATTACGTTAGTTGAGCGGAA 58.744 45.455 0.00 0.00 32.75 4.30
2841 3152 4.208746 TCAAAAGGTCCAACCATTACGTT 58.791 39.130 0.00 0.00 41.95 3.99
2843 3154 4.277423 AGTTCAAAAGGTCCAACCATTACG 59.723 41.667 0.00 0.00 41.95 3.18
2850 3161 5.334646 GGAATACGAGTTCAAAAGGTCCAAC 60.335 44.000 0.00 0.00 0.00 3.77
2907 3219 7.537715 TGTGAGTGCCAATAATATGAAAAGTG 58.462 34.615 0.00 0.00 0.00 3.16
2912 3224 8.046708 AGTACTTGTGAGTGCCAATAATATGAA 58.953 33.333 0.00 0.00 39.07 2.57
3016 3329 7.123098 TGCAACATATGAGAAATGAAGGATGTT 59.877 33.333 10.38 0.00 36.88 2.71
3075 3388 1.586154 GGGCAGGTCCAACATTCGTG 61.586 60.000 0.00 0.00 36.21 4.35
3088 3401 3.213206 TGACTATGCATAAAGGGCAGG 57.787 47.619 8.00 0.00 45.68 4.85
3089 3402 5.641209 GTCTATGACTATGCATAAAGGGCAG 59.359 44.000 8.00 0.00 45.68 4.85
3090 3403 5.071653 TGTCTATGACTATGCATAAAGGGCA 59.928 40.000 8.00 5.14 38.36 5.36
3091 3404 5.551233 TGTCTATGACTATGCATAAAGGGC 58.449 41.667 8.00 0.00 33.15 5.19
3115 3428 3.347958 TCAAAAGTGATTTGCGACACC 57.652 42.857 0.00 0.00 46.53 4.16
3144 3457 6.239345 GGAGGGAGTAATATATATTGCCTCGG 60.239 46.154 19.36 0.00 31.37 4.63
3145 3458 6.323996 TGGAGGGAGTAATATATATTGCCTCG 59.676 42.308 19.36 0.00 31.37 4.63
3237 3584 6.669125 TTTATTTACCCCTCCGATCGATAA 57.331 37.500 18.66 6.36 0.00 1.75
3241 3588 5.302360 TGATTTTATTTACCCCTCCGATCG 58.698 41.667 8.51 8.51 0.00 3.69
3245 3592 4.204012 TGCTGATTTTATTTACCCCTCCG 58.796 43.478 0.00 0.00 0.00 4.63
3522 4864 1.372623 GGACGTGGTCTCCGAACAC 60.373 63.158 0.00 2.04 45.71 3.32
3526 4868 3.371063 GCAGGACGTGGTCTCCGA 61.371 66.667 0.00 0.00 32.45 4.55
3544 4886 5.012975 ACAAATATGTGATGGCCCAAAACTT 59.987 36.000 0.00 0.00 38.69 2.66
3557 4899 4.154015 CACAAGGAGCGAACAAATATGTGA 59.846 41.667 0.00 0.00 40.46 3.58
3559 4901 4.072131 ACACAAGGAGCGAACAAATATGT 58.928 39.130 0.00 0.00 43.14 2.29


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

AutoCloner maintained by Alex Coulton.