Multiple sequence alignment - TraesCS4A01G404400

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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 TraesCS4A01G404400 chr4A 100.000 3173 0 0 1 3173 678041363 678038191 0.000000e+00 5860.0
1 TraesCS4A01G404400 chr4A 88.397 1422 145 7 999 2406 677988869 677987454 0.000000e+00 1694.0
2 TraesCS4A01G404400 chr4A 88.350 1236 120 12 949 2174 677969556 677968335 0.000000e+00 1463.0
3 TraesCS4A01G404400 chr4A 88.640 1206 116 12 987 2177 677958537 677957338 0.000000e+00 1448.0
4 TraesCS4A01G404400 chr4B 91.194 2612 180 26 595 3173 592195253 592192659 0.000000e+00 3504.0
5 TraesCS4A01G404400 chr4B 87.560 1447 138 16 999 2431 592079602 592078184 0.000000e+00 1637.0
6 TraesCS4A01G404400 chr4B 87.483 1446 141 12 999 2431 592188049 592186631 0.000000e+00 1631.0
7 TraesCS4A01G404400 chr4B 91.254 343 19 5 155 493 592195644 592195309 1.040000e-124 457.0
8 TraesCS4A01G404400 chr4B 75.625 480 104 7 2440 2918 438326387 438325920 3.180000e-55 226.0
9 TraesCS4A01G404400 chr4B 93.204 103 4 3 33 135 592197870 592197771 7.090000e-32 148.0
10 TraesCS4A01G404400 chr4D 93.232 2113 105 16 147 2253 470149433 470147353 0.000000e+00 3075.0
11 TraesCS4A01G404400 chr4D 90.418 1148 97 7 1037 2173 470130302 470129157 0.000000e+00 1498.0
12 TraesCS4A01G404400 chr4D 90.096 1151 105 4 1032 2173 470138336 470137186 0.000000e+00 1485.0
13 TraesCS4A01G404400 chr4D 76.763 482 97 8 2440 2918 354807969 354807500 4.060000e-64 255.0
14 TraesCS4A01G404400 chr4D 86.486 148 17 3 2283 2429 470147359 470147214 3.280000e-35 159.0
15 TraesCS4A01G404400 chr4D 84.259 108 6 6 33 132 470149623 470149519 9.370000e-16 95.3
16 TraesCS4A01G404400 chr7D 78.788 429 90 1 2441 2868 230998626 230998198 1.440000e-73 287.0
17 TraesCS4A01G404400 chr6D 77.778 486 89 12 2426 2906 354835813 354836284 6.700000e-72 281.0
18 TraesCS4A01G404400 chr1D 77.366 486 96 5 2426 2909 364067204 364067677 3.120000e-70 276.0
19 TraesCS4A01G404400 chr2A 76.424 509 102 13 2425 2917 263527130 263527636 3.140000e-65 259.0
20 TraesCS4A01G404400 chr3A 78.345 411 74 13 2437 2844 741622231 741621833 5.250000e-63 252.0
21 TraesCS4A01G404400 chr5B 76.139 461 102 4 2449 2908 425177912 425177459 5.290000e-58 235.0
22 TraesCS4A01G404400 chr2B 77.285 361 71 10 2565 2919 448137988 448138343 5.370000e-48 202.0
23 TraesCS4A01G404400 chr6A 80.451 266 38 9 2454 2705 574224251 574223986 1.160000e-44 191.0


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 TraesCS4A01G404400 chr4A 678038191 678041363 3172 True 5860.000000 5860 100.000000 1 3173 1 chr4A.!!$R4 3172
1 TraesCS4A01G404400 chr4A 677987454 677988869 1415 True 1694.000000 1694 88.397000 999 2406 1 chr4A.!!$R3 1407
2 TraesCS4A01G404400 chr4A 677968335 677969556 1221 True 1463.000000 1463 88.350000 949 2174 1 chr4A.!!$R2 1225
3 TraesCS4A01G404400 chr4A 677957338 677958537 1199 True 1448.000000 1448 88.640000 987 2177 1 chr4A.!!$R1 1190
4 TraesCS4A01G404400 chr4B 592078184 592079602 1418 True 1637.000000 1637 87.560000 999 2431 1 chr4B.!!$R2 1432
5 TraesCS4A01G404400 chr4B 592186631 592188049 1418 True 1631.000000 1631 87.483000 999 2431 1 chr4B.!!$R3 1432
6 TraesCS4A01G404400 chr4B 592192659 592197870 5211 True 1369.666667 3504 91.884000 33 3173 3 chr4B.!!$R4 3140
7 TraesCS4A01G404400 chr4D 470129157 470130302 1145 True 1498.000000 1498 90.418000 1037 2173 1 chr4D.!!$R2 1136
8 TraesCS4A01G404400 chr4D 470137186 470138336 1150 True 1485.000000 1485 90.096000 1032 2173 1 chr4D.!!$R3 1141
9 TraesCS4A01G404400 chr4D 470147214 470149623 2409 True 1109.766667 3075 87.992333 33 2429 3 chr4D.!!$R4 2396
10 TraesCS4A01G404400 chr2A 263527130 263527636 506 False 259.000000 259 76.424000 2425 2917 1 chr2A.!!$F1 492

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
346 2504 0.040692 GTCGTGAGCCGTCGCATATA 60.041 55.0 0.00 0.0 37.52 0.86 F
1028 3195 0.035458 ACAACTGCTAGTGCCAGTCC 59.965 55.0 2.46 0.0 38.71 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1572 3748 0.824759 AGTACGTCTTGGATGGCTCC 59.175 55.0 0.0 0.0 42.45 4.70 R
2858 5082 0.039618 AAGGCGTTTGGATGGATGGT 59.960 50.0 0.0 0.0 0.00 3.55 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
135 144 8.766000 TTATTAGACAAGCTTTCGTTGTGATA 57.234 30.769 0.00 0.00 38.26 2.15
137 146 5.597813 AGACAAGCTTTCGTTGTGATAAG 57.402 39.130 0.00 0.00 38.26 1.73
141 150 5.938125 ACAAGCTTTCGTTGTGATAAGGTAT 59.062 36.000 0.00 0.00 36.76 2.73
142 151 6.128282 ACAAGCTTTCGTTGTGATAAGGTATG 60.128 38.462 0.00 0.00 36.76 2.39
145 154 5.220605 GCTTTCGTTGTGATAAGGTATGGAC 60.221 44.000 0.00 0.00 0.00 4.02
157 2315 8.453681 TGATAAGGTATGGACTATGGAGAACTA 58.546 37.037 0.00 0.00 0.00 2.24
168 2326 4.974645 ATGGAGAACTAGTGGTTGTTGA 57.025 40.909 0.00 0.00 38.41 3.18
173 2331 4.398319 AGAACTAGTGGTTGTTGATTGGG 58.602 43.478 0.00 0.00 38.41 4.12
320 2478 4.154918 GGTCAATGAACAAGTGACATCCTC 59.845 45.833 17.40 3.61 42.81 3.71
339 2497 3.664223 GACTCGGTCGTGAGCCGTC 62.664 68.421 3.64 5.87 46.12 4.79
345 2503 1.299165 GTCGTGAGCCGTCGCATAT 60.299 57.895 0.00 0.00 37.52 1.78
346 2504 0.040692 GTCGTGAGCCGTCGCATATA 60.041 55.000 0.00 0.00 37.52 0.86
347 2505 0.879090 TCGTGAGCCGTCGCATATAT 59.121 50.000 0.00 0.00 37.52 0.86
348 2506 2.078392 TCGTGAGCCGTCGCATATATA 58.922 47.619 0.00 0.00 37.52 0.86
358 2516 8.319143 AGCCGTCGCATATATAAAACTAAAAT 57.681 30.769 0.00 0.00 37.52 1.82
411 2569 8.311395 TGAAGGATATCAGATGTTTGTCTAGT 57.689 34.615 4.83 0.00 0.00 2.57
413 2571 9.685828 GAAGGATATCAGATGTTTGTCTAGTAC 57.314 37.037 4.83 0.00 0.00 2.73
414 2572 7.877003 AGGATATCAGATGTTTGTCTAGTACG 58.123 38.462 4.83 0.00 0.00 3.67
415 2573 7.720074 AGGATATCAGATGTTTGTCTAGTACGA 59.280 37.037 4.83 0.00 0.00 3.43
448 2610 4.093998 AGTTTGCTCAGAATACTTCATGCG 59.906 41.667 0.00 0.00 0.00 4.73
510 2672 5.008811 GTCAGTGACTCAGTGTACAGTACTT 59.991 44.000 16.26 0.00 36.33 2.24
535 2698 6.550938 TGAGTGTGATTTATGATGAGAGGT 57.449 37.500 0.00 0.00 0.00 3.85
567 2730 6.005198 AGGGGAATATTGTACGTCAAACAAA 58.995 36.000 6.48 0.00 40.05 2.83
622 2787 1.484653 TCCAGCGGCATACAAGTATGT 59.515 47.619 18.44 0.00 43.57 2.29
675 2840 7.550906 GGAGGAGTACATTATTGGCATTATCTC 59.449 40.741 0.00 0.00 0.00 2.75
711 2876 1.532868 GAACAAGCAGACGCAATCACT 59.467 47.619 0.00 0.00 42.27 3.41
715 2880 1.649664 AGCAGACGCAATCACTCATC 58.350 50.000 0.00 0.00 42.27 2.92
717 2882 0.299895 CAGACGCAATCACTCATCGC 59.700 55.000 0.00 0.00 0.00 4.58
728 2893 6.238211 GCAATCACTCATCGCTAACTGTTTAT 60.238 38.462 0.00 0.00 0.00 1.40
729 2894 7.677276 GCAATCACTCATCGCTAACTGTTTATT 60.677 37.037 0.00 0.00 0.00 1.40
730 2895 8.817100 CAATCACTCATCGCTAACTGTTTATTA 58.183 33.333 0.00 0.00 0.00 0.98
744 2909 7.058023 ACTGTTTATTAGGTGTGTACTGACA 57.942 36.000 0.00 0.00 0.00 3.58
780 2945 6.698380 TCCTTTATGTTGACTCACCTACTTC 58.302 40.000 0.00 0.00 0.00 3.01
793 2959 8.418597 ACTCACCTACTTCTAATTTGTCTACA 57.581 34.615 0.00 0.00 0.00 2.74
846 3012 3.971305 TCACTAGTTTTTCTCTGGGGTCA 59.029 43.478 0.00 0.00 0.00 4.02
862 3028 2.553028 GGGTCAAGCTTCACATCTTCCA 60.553 50.000 1.96 0.00 0.00 3.53
922 3088 2.836372 ACAAGCTCTCATCACCATCTGA 59.164 45.455 0.00 0.00 0.00 3.27
924 3090 2.749600 AGCTCTCATCACCATCTGAGT 58.250 47.619 0.00 0.00 39.87 3.41
926 3092 2.168106 GCTCTCATCACCATCTGAGTGT 59.832 50.000 0.00 0.00 39.87 3.55
956 3123 0.962356 AGGGCATCCAAGAAACAGCG 60.962 55.000 0.00 0.00 34.83 5.18
1025 3192 2.005451 GATCACAACTGCTAGTGCCAG 58.995 52.381 0.00 0.00 38.71 4.85
1026 3193 0.758734 TCACAACTGCTAGTGCCAGT 59.241 50.000 0.00 0.00 38.71 4.00
1027 3194 1.151668 CACAACTGCTAGTGCCAGTC 58.848 55.000 2.46 0.00 38.71 3.51
1028 3195 0.035458 ACAACTGCTAGTGCCAGTCC 59.965 55.000 2.46 0.00 38.71 3.85
1029 3196 1.016130 CAACTGCTAGTGCCAGTCCG 61.016 60.000 2.46 0.00 38.71 4.79
1030 3197 2.172483 AACTGCTAGTGCCAGTCCGG 62.172 60.000 0.00 0.00 38.71 5.14
1200 3376 4.424566 TACTTCGTCCACGGCGGC 62.425 66.667 13.24 0.00 40.29 6.53
1437 3613 2.515757 TTGCTGCTGGCGACACAA 60.516 55.556 0.00 0.00 45.43 3.33
1864 4040 4.015084 GACCAAGTACTACCTAGTGCTCA 58.985 47.826 0.00 0.00 46.34 4.26
2043 4219 4.121669 ATCGCGCTCGTGCTCTGT 62.122 61.111 5.56 0.00 36.97 3.41
2078 4254 1.264557 CTCCTACATGTACGGCGAGAG 59.735 57.143 16.62 0.54 0.00 3.20
2183 4365 0.112412 AACCCTTGAAGACCGGCAAT 59.888 50.000 0.00 0.00 0.00 3.56
2189 4371 1.821216 TGAAGACCGGCAATTTCTCC 58.179 50.000 0.00 0.00 0.00 3.71
2204 4395 3.887621 TTCTCCATGCCTGTAGTGTAC 57.112 47.619 0.00 0.00 0.00 2.90
2259 4453 7.331934 TGAACAAGAGTAGAGTAACATGCATTC 59.668 37.037 0.00 0.00 0.00 2.67
2292 4486 5.266733 TGTTTCGTTCTAGGTAACACAGT 57.733 39.130 0.00 0.00 41.41 3.55
2357 4557 4.036734 TCAGAAATGTTCACTTCTTGCACC 59.963 41.667 0.00 0.00 29.29 5.01
2376 4576 2.895404 ACCGAGTACAGTACAACATGGT 59.105 45.455 13.37 9.39 0.00 3.55
2535 4739 2.740826 ACCGAACGACCATTGCCG 60.741 61.111 0.00 0.00 0.00 5.69
2537 4741 3.118454 CGAACGACCATTGCCGCT 61.118 61.111 0.00 0.00 0.00 5.52
2556 4761 4.919653 TCAGAATGAGCTGCCGAC 57.080 55.556 0.00 0.00 42.56 4.79
2557 4762 1.974543 TCAGAATGAGCTGCCGACA 59.025 52.632 0.00 0.00 42.56 4.35
2559 4764 0.671472 CAGAATGAGCTGCCGACACA 60.671 55.000 0.00 0.00 39.69 3.72
2562 4767 2.395988 AATGAGCTGCCGACACACCA 62.396 55.000 0.00 0.00 0.00 4.17
2580 4785 2.134287 ACTGTCGCCGCTCCCATAT 61.134 57.895 0.00 0.00 0.00 1.78
2582 4787 2.430921 GTCGCCGCTCCCATATCG 60.431 66.667 0.00 0.00 0.00 2.92
2585 4790 1.300620 CGCCGCTCCCATATCGAAA 60.301 57.895 0.00 0.00 0.00 3.46
2594 4799 0.884704 CCATATCGAAACCGGCCTGG 60.885 60.000 0.00 11.48 46.41 4.45
2596 4801 1.978455 ATATCGAAACCGGCCTGGCA 61.978 55.000 22.05 0.00 43.94 4.92
2597 4802 1.978455 TATCGAAACCGGCCTGGCAT 61.978 55.000 22.05 5.04 43.94 4.40
2643 4860 2.125673 CACGTGCCCCTAAGACCG 60.126 66.667 0.82 0.00 0.00 4.79
2668 4885 1.729470 CCAGAGCCGTAGTCATCGCT 61.729 60.000 0.00 0.00 0.00 4.93
2688 4905 5.183713 TCGCTGTTGAATCCTTGAATTGATT 59.816 36.000 0.00 0.00 34.02 2.57
2705 4922 3.486383 TGATTTGAAGAACCTGACACCC 58.514 45.455 0.00 0.00 0.00 4.61
2713 4930 1.940613 GAACCTGACACCCAATATCGC 59.059 52.381 0.00 0.00 0.00 4.58
2744 4961 4.002906 TGCACGACAAGAAATCCTAACT 57.997 40.909 0.00 0.00 0.00 2.24
2746 4963 4.819630 TGCACGACAAGAAATCCTAACTTT 59.180 37.500 0.00 0.00 0.00 2.66
2761 4978 3.249189 TTTGCCGCCCTGAGGAGT 61.249 61.111 0.00 0.00 33.47 3.85
2770 4987 1.490574 CCCTGAGGAGTTGGTAGGAG 58.509 60.000 0.00 0.00 33.47 3.69
2782 4999 3.398318 TGGTAGGAGTCTATGCCAGAA 57.602 47.619 2.46 0.00 34.17 3.02
2786 5003 4.591072 GGTAGGAGTCTATGCCAGAATTCT 59.409 45.833 0.88 0.88 40.38 2.40
2804 5021 4.610605 TTCTGTCTAATTCGTCCCAACA 57.389 40.909 0.00 0.00 0.00 3.33
2805 5022 4.188247 TCTGTCTAATTCGTCCCAACAG 57.812 45.455 0.00 0.00 35.20 3.16
2827 5051 0.915364 GAACTTGAGGAGGGCTGGAT 59.085 55.000 0.00 0.00 0.00 3.41
2846 5070 2.431954 TCCCGGAAGACTAACTCGAT 57.568 50.000 0.73 0.00 0.00 3.59
2854 5078 5.344884 GGAAGACTAACTCGATGAAGAAGG 58.655 45.833 0.00 0.00 0.00 3.46
2855 5079 4.993029 AGACTAACTCGATGAAGAAGGG 57.007 45.455 0.00 0.00 0.00 3.95
2856 5080 4.345854 AGACTAACTCGATGAAGAAGGGT 58.654 43.478 0.00 0.00 0.00 4.34
2858 5082 4.087182 ACTAACTCGATGAAGAAGGGTCA 58.913 43.478 0.00 0.00 0.00 4.02
2865 5089 1.741028 TGAAGAAGGGTCACCATCCA 58.259 50.000 0.00 0.00 40.13 3.41
2877 5101 0.039618 ACCATCCATCCAAACGCCTT 59.960 50.000 0.00 0.00 0.00 4.35
2881 5105 2.406616 CCATCCAAACGCCTTCCCG 61.407 63.158 0.00 0.00 0.00 5.14
2882 5106 2.045340 ATCCAAACGCCTTCCCGG 60.045 61.111 0.00 0.00 0.00 5.73
2883 5107 2.902457 ATCCAAACGCCTTCCCGGT 61.902 57.895 0.00 0.00 34.25 5.28
2901 5125 3.771479 CCGGTAAGGACTAAAACCCTACT 59.229 47.826 0.00 0.00 45.00 2.57
2912 5136 8.756927 GGACTAAAACCCTACTTATCTACAAGT 58.243 37.037 0.00 0.00 41.56 3.16
2931 5155 5.613358 AAGTCGGAGCTTTTATTGACTTG 57.387 39.130 12.33 0.00 43.02 3.16
2933 5157 4.691216 AGTCGGAGCTTTTATTGACTTGAC 59.309 41.667 0.00 0.00 33.15 3.18
2934 5158 3.678072 TCGGAGCTTTTATTGACTTGACG 59.322 43.478 0.00 0.00 0.00 4.35
2976 5202 8.565896 TGCAAACATCTCATTGTAAAGATAGT 57.434 30.769 0.00 0.00 31.10 2.12
3006 5232 7.914537 AAAGACAGCAGAAGTTAATTTTTCG 57.085 32.000 0.00 0.00 0.00 3.46
3078 5304 2.286833 CGACTTCTCCGTGCAAAGAAAA 59.713 45.455 2.16 0.00 31.45 2.29
3155 5381 2.023414 TATTCTACCTGCACGGGCCG 62.023 60.000 27.06 27.06 40.13 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 1.876156 AGCGAAACAAAGGAGAAGCAG 59.124 47.619 0.00 0.00 0.00 4.24
44 45 1.873591 GAGCGAAACAAAGGAGAAGCA 59.126 47.619 0.00 0.00 0.00 3.91
45 46 2.147150 AGAGCGAAACAAAGGAGAAGC 58.853 47.619 0.00 0.00 0.00 3.86
135 144 6.551601 CACTAGTTCTCCATAGTCCATACCTT 59.448 42.308 0.00 0.00 29.77 3.50
137 146 5.244178 CCACTAGTTCTCCATAGTCCATACC 59.756 48.000 0.00 0.00 29.77 2.73
141 150 4.332683 ACCACTAGTTCTCCATAGTCCA 57.667 45.455 0.00 0.00 29.77 4.02
142 151 4.466726 ACAACCACTAGTTCTCCATAGTCC 59.533 45.833 0.00 0.00 36.18 3.85
145 154 6.037786 TCAACAACCACTAGTTCTCCATAG 57.962 41.667 0.00 0.00 36.18 2.23
157 2315 3.075283 TCCATACCCAATCAACAACCACT 59.925 43.478 0.00 0.00 0.00 4.00
168 2326 2.040009 CTCCCGCGTCCATACCCAAT 62.040 60.000 4.92 0.00 0.00 3.16
374 2532 9.618890 ATCTGATATCCTTCATTTCGAAAAGAA 57.381 29.630 22.83 22.83 37.01 2.52
376 2534 8.834465 ACATCTGATATCCTTCATTTCGAAAAG 58.166 33.333 15.66 10.98 31.71 2.27
380 2538 7.770433 ACAAACATCTGATATCCTTCATTTCGA 59.230 33.333 0.00 0.00 0.00 3.71
381 2539 7.923888 ACAAACATCTGATATCCTTCATTTCG 58.076 34.615 0.00 0.00 0.00 3.46
382 2540 9.118300 AGACAAACATCTGATATCCTTCATTTC 57.882 33.333 0.00 0.00 0.00 2.17
440 2602 2.489329 ACTGTTTGAATCCCGCATGAAG 59.511 45.455 0.00 0.00 0.00 3.02
448 2610 2.351738 CCGCAGAAACTGTTTGAATCCC 60.352 50.000 11.03 0.00 33.43 3.85
497 2659 7.704578 ATCACACTCATAAGTACTGTACACT 57.295 36.000 19.27 8.88 33.25 3.55
510 2672 8.255111 ACCTCTCATCATAAATCACACTCATA 57.745 34.615 0.00 0.00 0.00 2.15
535 2698 4.944930 CGTACAATATTCCCCTGGTTTCAA 59.055 41.667 0.00 0.00 0.00 2.69
545 2708 8.643752 CAAATTTGTTTGACGTACAATATTCCC 58.356 33.333 10.15 0.00 38.36 3.97
582 2745 6.860023 GCTGGATATTTTCCTGATCGAATTTG 59.140 38.462 0.00 0.00 45.68 2.32
589 2752 2.485814 GCCGCTGGATATTTTCCTGATC 59.514 50.000 4.57 0.00 45.68 2.92
593 2756 2.664402 ATGCCGCTGGATATTTTCCT 57.336 45.000 0.00 0.00 45.68 3.36
644 2809 5.070446 TGCCAATAATGTACTCCTCCTACTG 59.930 44.000 0.00 0.00 0.00 2.74
650 2815 7.276658 CGAGATAATGCCAATAATGTACTCCTC 59.723 40.741 0.00 0.00 0.00 3.71
651 2816 7.099764 CGAGATAATGCCAATAATGTACTCCT 58.900 38.462 0.00 0.00 0.00 3.69
652 2817 6.183360 GCGAGATAATGCCAATAATGTACTCC 60.183 42.308 0.00 0.00 0.00 3.85
675 2840 4.721226 GCTTGTTCTACTATTTGTCACGCG 60.721 45.833 3.53 3.53 0.00 6.01
711 2876 6.533723 CACACCTAATAAACAGTTAGCGATGA 59.466 38.462 0.00 0.00 0.00 2.92
715 2880 6.810182 AGTACACACCTAATAAACAGTTAGCG 59.190 38.462 0.00 0.00 0.00 4.26
717 2882 9.136952 GTCAGTACACACCTAATAAACAGTTAG 57.863 37.037 0.00 0.00 0.00 2.34
728 2893 4.219944 GGAGACATGTCAGTACACACCTAA 59.780 45.833 27.02 0.00 38.78 2.69
729 2894 3.762288 GGAGACATGTCAGTACACACCTA 59.238 47.826 27.02 0.00 38.78 3.08
730 2895 2.563179 GGAGACATGTCAGTACACACCT 59.437 50.000 27.02 2.52 38.78 4.00
744 2909 5.488919 TCAACATAAAGGAAGGAGGAGACAT 59.511 40.000 0.00 0.00 0.00 3.06
824 2990 3.971305 TGACCCCAGAGAAAAACTAGTGA 59.029 43.478 0.00 0.00 0.00 3.41
846 3012 2.617532 GGAGCTGGAAGATGTGAAGCTT 60.618 50.000 0.00 0.00 44.00 3.74
862 3028 5.104109 TGTTGCAAGGGTTTATATAGGAGCT 60.104 40.000 0.00 0.00 0.00 4.09
922 3088 1.289231 TGCCCTCTCTATCCTCACACT 59.711 52.381 0.00 0.00 0.00 3.55
924 3090 2.603021 GATGCCCTCTCTATCCTCACA 58.397 52.381 0.00 0.00 0.00 3.58
926 3092 1.505098 TGGATGCCCTCTCTATCCTCA 59.495 52.381 0.00 0.00 40.77 3.86
956 3123 6.337853 CAAGTATGCTTGTACTGCTACTTC 57.662 41.667 14.75 7.87 45.18 3.01
1029 3196 3.936772 TTCTTGCATGGCCGGACCC 62.937 63.158 3.83 0.00 37.83 4.46
1030 3197 2.361104 TTCTTGCATGGCCGGACC 60.361 61.111 3.83 6.37 39.84 4.46
1110 3286 1.686325 ATATGACCAGCGGCGAAGGT 61.686 55.000 21.04 21.04 38.63 3.50
1263 3439 4.409342 CGGAAGATGGAGACGCAG 57.591 61.111 0.00 0.00 0.00 5.18
1572 3748 0.824759 AGTACGTCTTGGATGGCTCC 59.175 55.000 0.00 0.00 42.45 4.70
2078 4254 1.377856 GCCTTCTTCTGCTGGACCC 60.378 63.158 0.00 0.00 0.00 4.46
2135 4317 0.974383 GAGGTCTCCGGTTTTCCTCA 59.026 55.000 22.42 0.00 42.72 3.86
2183 4365 3.838317 AGTACACTACAGGCATGGAGAAA 59.162 43.478 19.38 0.00 40.16 2.52
2233 4424 6.096673 TGCATGTTACTCTACTCTTGTTCA 57.903 37.500 0.00 0.00 0.00 3.18
2259 4453 2.482721 AGAACGAAACAATGCCTTACGG 59.517 45.455 0.00 0.00 0.00 4.02
2266 4460 5.049954 TGTGTTACCTAGAACGAAACAATGC 60.050 40.000 0.00 0.00 32.32 3.56
2276 4470 7.441458 ACTTGATTTCACTGTGTTACCTAGAAC 59.559 37.037 7.79 0.00 0.00 3.01
2292 4486 5.316167 ACTCAATGGTAGCACTTGATTTCA 58.684 37.500 15.37 0.00 0.00 2.69
2357 4557 7.972277 AGTAATAACCATGTTGTACTGTACTCG 59.028 37.037 17.98 3.38 0.00 4.18
2431 4633 9.698309 CTTTATAATACATGTGATCCTTCTCGT 57.302 33.333 9.11 0.00 0.00 4.18
2432 4634 9.914131 TCTTTATAATACATGTGATCCTTCTCG 57.086 33.333 9.11 0.00 0.00 4.04
2447 4651 8.609176 TGCACTTCCGTTGAATCTTTATAATAC 58.391 33.333 0.00 0.00 0.00 1.89
2471 4675 9.777575 ATTTTTATTATGCTTGAATTGCTTTGC 57.222 25.926 0.00 0.00 0.00 3.68
2509 4713 1.361271 GTCGTTCGGTGGTCTGTGA 59.639 57.895 0.00 0.00 0.00 3.58
2512 4716 0.320421 AATGGTCGTTCGGTGGTCTG 60.320 55.000 0.00 0.00 0.00 3.51
2513 4717 0.320421 CAATGGTCGTTCGGTGGTCT 60.320 55.000 0.00 0.00 0.00 3.85
2535 4739 1.703438 CGGCAGCTCATTCTGACAGC 61.703 60.000 0.00 0.00 42.21 4.40
2537 4741 0.390340 GTCGGCAGCTCATTCTGACA 60.390 55.000 0.00 0.00 42.21 3.58
2550 4755 2.108157 GACAGTGGTGTGTCGGCA 59.892 61.111 0.00 0.00 37.69 5.69
2556 4761 4.969196 AGCGGCGACAGTGGTGTG 62.969 66.667 12.98 0.00 36.88 3.82
2557 4762 4.664677 GAGCGGCGACAGTGGTGT 62.665 66.667 12.98 0.00 40.71 4.16
2562 4767 2.088674 GATATGGGAGCGGCGACAGT 62.089 60.000 12.98 0.00 0.00 3.55
2580 4785 3.561120 AATGCCAGGCCGGTTTCGA 62.561 57.895 9.64 0.00 39.00 3.71
2582 4787 2.212900 GACAATGCCAGGCCGGTTTC 62.213 60.000 9.64 0.00 36.97 2.78
2594 4799 1.349627 CGGCTGTCATCGACAATGC 59.650 57.895 0.00 0.00 42.26 3.56
2596 4801 1.153369 CCCGGCTGTCATCGACAAT 60.153 57.895 0.00 0.00 42.26 2.71
2597 4802 1.822114 TTCCCGGCTGTCATCGACAA 61.822 55.000 0.00 0.00 42.26 3.18
2643 4860 4.162690 CTACGGCTCTGGGGTGCC 62.163 72.222 0.00 0.00 45.53 5.01
2668 4885 8.640651 TCTTCAAATCAATTCAAGGATTCAACA 58.359 29.630 0.00 0.00 32.81 3.33
2688 4905 3.593442 ATTGGGTGTCAGGTTCTTCAA 57.407 42.857 0.00 0.00 0.00 2.69
2737 4954 1.002624 CAGGGCGGCAAAGTTAGGA 60.003 57.895 12.47 0.00 0.00 2.94
2744 4961 2.829384 AACTCCTCAGGGCGGCAAA 61.829 57.895 12.47 0.00 0.00 3.68
2746 4963 4.020617 CAACTCCTCAGGGCGGCA 62.021 66.667 12.47 0.00 0.00 5.69
2761 4978 3.398318 TCTGGCATAGACTCCTACCAA 57.602 47.619 0.00 0.00 0.00 3.67
2782 4999 5.046591 TCTGTTGGGACGAATTAGACAGAAT 60.047 40.000 5.08 0.00 39.06 2.40
2786 5003 4.221924 TCATCTGTTGGGACGAATTAGACA 59.778 41.667 0.00 0.00 0.00 3.41
2804 5021 1.558756 CAGCCCTCCTCAAGTTCATCT 59.441 52.381 0.00 0.00 0.00 2.90
2805 5022 1.407989 CCAGCCCTCCTCAAGTTCATC 60.408 57.143 0.00 0.00 0.00 2.92
2827 5051 2.022195 CATCGAGTTAGTCTTCCGGGA 58.978 52.381 0.00 0.00 0.00 5.14
2846 5070 1.741028 TGGATGGTGACCCTTCTTCA 58.259 50.000 0.00 0.00 35.67 3.02
2854 5078 1.094785 CGTTTGGATGGATGGTGACC 58.905 55.000 0.00 0.00 0.00 4.02
2855 5079 0.451783 GCGTTTGGATGGATGGTGAC 59.548 55.000 0.00 0.00 0.00 3.67
2856 5080 0.679640 GGCGTTTGGATGGATGGTGA 60.680 55.000 0.00 0.00 0.00 4.02
2858 5082 0.039618 AAGGCGTTTGGATGGATGGT 59.960 50.000 0.00 0.00 0.00 3.55
2865 5089 1.555477 TACCGGGAAGGCGTTTGGAT 61.555 55.000 6.32 1.81 46.52 3.41
2877 5101 1.908619 GGGTTTTAGTCCTTACCGGGA 59.091 52.381 6.32 0.00 0.00 5.14
2881 5105 8.316497 AGATAAGTAGGGTTTTAGTCCTTACC 57.684 38.462 0.00 0.00 37.97 2.85
2883 5107 9.995594 TGTAGATAAGTAGGGTTTTAGTCCTTA 57.004 33.333 0.00 0.00 34.75 2.69
2895 5119 4.023021 GCTCCGACTTGTAGATAAGTAGGG 60.023 50.000 15.05 9.31 46.87 3.53
2901 5125 8.255206 TCAATAAAAGCTCCGACTTGTAGATAA 58.745 33.333 0.00 0.00 0.00 1.75
2912 5136 3.678072 CGTCAAGTCAATAAAAGCTCCGA 59.322 43.478 0.00 0.00 0.00 4.55
2931 5155 3.119955 GCATAGTCTTTTGAAACCCCGTC 60.120 47.826 0.00 0.00 0.00 4.79
2933 5157 2.817258 TGCATAGTCTTTTGAAACCCCG 59.183 45.455 0.00 0.00 0.00 5.73
2934 5158 4.864704 TTGCATAGTCTTTTGAAACCCC 57.135 40.909 0.00 0.00 0.00 4.95
2987 5213 9.825972 TCTTTATCGAAAAATTAACTTCTGCTG 57.174 29.630 0.00 0.00 0.00 4.41
3006 5232 7.667219 TCCCATAATTTCTGCCATCTCTTTATC 59.333 37.037 0.00 0.00 0.00 1.75
3078 5304 2.229543 TGCGACGGTAGTGTACTCATTT 59.770 45.455 0.00 0.00 0.00 2.32
3109 5335 2.736978 CTCATCGCAGGTGTACTCATC 58.263 52.381 0.00 0.00 0.00 2.92
3130 5356 3.748048 CCCGTGCAGGTAGAATATCATTG 59.252 47.826 5.57 0.00 38.74 2.82


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

AutoCloner maintained by Alex Coulton.