Multiple sequence alignment - TraesCS4A01G261600

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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 TraesCS4A01G261600 chr4A 100.000 7273 0 0 1 7273 573892925 573885653 0.000000e+00 13431.0
1 TraesCS4A01G261600 chr4D 97.350 5924 92 15 1 5910 29322487 29328359 0.000000e+00 10009.0
2 TraesCS4A01G261600 chr4D 95.455 748 20 5 5977 6715 29328325 29329067 0.000000e+00 1181.0
3 TraesCS4A01G261600 chr4D 93.182 44 3 0 6063 6106 259053329 259053286 1.690000e-06 65.8
4 TraesCS4A01G261600 chr4D 100.000 35 0 0 6019 6053 259053357 259053323 1.690000e-06 65.8
5 TraesCS4A01G261600 chr4B 96.236 4649 110 25 941 5573 41778037 41782636 0.000000e+00 7555.0
6 TraesCS4A01G261600 chr4B 91.541 1324 64 19 5982 7273 41783066 41784373 0.000000e+00 1781.0
7 TraesCS4A01G261600 chr4B 96.348 356 12 1 5552 5907 41782711 41783065 1.050000e-162 584.0
8 TraesCS4A01G261600 chr4B 89.826 403 28 6 4908 5308 42141373 42141764 8.420000e-139 505.0
9 TraesCS4A01G261600 chr4B 92.049 327 26 0 1 327 41776182 41776508 1.850000e-125 460.0
10 TraesCS4A01G261600 chr4B 81.403 613 52 28 328 915 41777464 41778039 1.860000e-120 444.0
11 TraesCS4A01G261600 chr4B 91.639 299 23 1 5300 5596 42144186 42144484 5.250000e-111 412.0
12 TraesCS4A01G261600 chr4B 88.372 86 9 1 4838 4923 42141272 42141356 1.290000e-17 102.0
13 TraesCS4A01G261600 chr7D 88.930 271 23 1 6930 7200 459743136 459742873 1.960000e-85 327.0
14 TraesCS4A01G261600 chr7D 88.235 272 23 7 6929 7200 270700097 270700359 4.230000e-82 316.0
15 TraesCS4A01G261600 chr7A 83.611 360 48 7 5452 5805 610205449 610205803 1.960000e-85 327.0
16 TraesCS4A01G261600 chr6B 88.028 284 25 4 6932 7215 113783176 113783450 1.960000e-85 327.0
17 TraesCS4A01G261600 chr6B 95.238 42 2 0 6063 6104 15269085 15269044 4.710000e-07 67.6
18 TraesCS4A01G261600 chr5B 88.930 271 22 3 6930 7200 27825038 27825300 1.960000e-85 327.0
19 TraesCS4A01G261600 chr5B 90.789 76 5 2 5901 5976 370194779 370194706 4.640000e-17 100.0
20 TraesCS4A01G261600 chr5B 90.789 76 5 2 5901 5976 370239639 370239566 4.640000e-17 100.0
21 TraesCS4A01G261600 chr5B 94.915 59 2 1 5921 5978 321416922 321416980 2.790000e-14 91.6
22 TraesCS4A01G261600 chr2D 88.321 274 22 7 6929 7202 79687753 79688016 3.270000e-83 320.0
23 TraesCS4A01G261600 chr2A 83.146 356 48 8 5452 5801 238530331 238530680 1.520000e-81 315.0
24 TraesCS4A01G261600 chr6A 88.593 263 22 6 6932 7194 604536767 604537021 5.480000e-81 313.0
25 TraesCS4A01G261600 chr6A 93.750 64 3 1 5914 5976 573510875 573510812 2.160000e-15 95.3
26 TraesCS4A01G261600 chr6A 95.238 42 2 0 6063 6104 142074852 142074893 4.710000e-07 67.6
27 TraesCS4A01G261600 chr6A 100.000 35 0 0 6019 6053 142074824 142074858 1.690000e-06 65.8
28 TraesCS4A01G261600 chr5D 88.148 270 23 3 6932 7201 307096135 307096395 5.480000e-81 313.0
29 TraesCS4A01G261600 chr5D 88.346 266 23 2 6935 7200 447144769 447144512 5.480000e-81 313.0
30 TraesCS4A01G261600 chr7B 87.687 268 25 5 6935 7202 164074329 164074588 9.170000e-79 305.0
31 TraesCS4A01G261600 chr7B 93.750 64 2 2 5914 5976 699186067 699186005 2.160000e-15 95.3
32 TraesCS4A01G261600 chr7B 86.585 82 7 4 5914 5993 267241285 267241206 3.610000e-13 87.9
33 TraesCS4A01G261600 chr1A 92.857 98 2 1 848 945 562001637 562001729 3.540000e-28 137.0
34 TraesCS4A01G261600 chr1A 91.089 101 4 1 848 948 562004867 562004962 1.650000e-26 132.0
35 TraesCS4A01G261600 chr1A 92.593 81 1 1 848 928 561981088 561981163 2.140000e-20 111.0
36 TraesCS4A01G261600 chr1D 91.358 81 2 1 848 928 469030407 469030482 9.980000e-19 106.0
37 TraesCS4A01G261600 chr1D 89.610 77 4 4 5901 5976 351255395 351255322 2.160000e-15 95.3
38 TraesCS4A01G261600 chr1D 96.000 50 2 0 6019 6068 481042124 481042075 1.680000e-11 82.4
39 TraesCS4A01G261600 chr2B 93.939 66 3 1 5914 5978 321689904 321689839 1.670000e-16 99.0
40 TraesCS4A01G261600 chr3D 91.304 69 2 3 5914 5978 450882690 450882758 2.790000e-14 91.6
41 TraesCS4A01G261600 chr6D 95.238 42 2 0 6063 6104 423818549 423818508 4.710000e-07 67.6


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 TraesCS4A01G261600 chr4A 573885653 573892925 7272 True 13431.000000 13431 100.000000 1 7273 1 chr4A.!!$R1 7272
1 TraesCS4A01G261600 chr4D 29322487 29329067 6580 False 5595.000000 10009 96.402500 1 6715 2 chr4D.!!$F1 6714
2 TraesCS4A01G261600 chr4B 41776182 41784373 8191 False 2164.800000 7555 91.515400 1 7273 5 chr4B.!!$F1 7272
3 TraesCS4A01G261600 chr4B 42141272 42144484 3212 False 339.666667 505 89.945667 4838 5596 3 chr4B.!!$F2 758

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
294 295 0.401738 CTGGGAGGCTTTGTGAGGAA 59.598 55.000 0.00 0.0 0.00 3.36 F
422 1379 0.740868 AGGATGTGCCATCGTCAACG 60.741 55.000 8.49 0.0 40.02 4.10 F
1447 2439 0.744771 GATCTCTCGTTTGGGGTGGC 60.745 60.000 0.00 0.0 0.00 5.01 F
2510 3506 2.031870 ACCAAGTTGAGAAGCAAACCC 58.968 47.619 3.87 0.0 38.44 4.11 F
2887 3883 1.888436 TTCCAGTGCCTCTGCCTACG 61.888 60.000 1.15 0.0 42.38 3.51 F
4271 5267 2.376518 AGGATCAAGCAAAAGGTGAGGA 59.623 45.455 0.00 0.0 0.00 3.71 F
5827 9396 1.302832 GCTAGCTGCACTGGTGGTT 60.303 57.895 7.70 0.0 42.31 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2030 3026 1.821136 CTTTCCCTTTCATGGTGAGGC 59.179 52.381 0.0 0.0 0.00 4.70 R
2079 3075 3.009584 TGGTTGCACATGGTTACTGGATA 59.990 43.478 0.0 0.0 0.00 2.59 R
2527 3523 0.459585 TCCGCTTCTCCGATTTTCCG 60.460 55.000 0.0 0.0 0.00 4.30 R
3477 4473 0.178903 TCAGGTACTTCAGGGGTGCT 60.179 55.000 0.0 0.0 34.60 4.40 R
4489 5485 2.092914 CACCCTTATCCACCAGAGGAAC 60.093 54.545 0.0 0.0 41.92 3.62 R
5969 9538 0.685097 TGGCACAGAACACTACTCCC 59.315 55.000 0.0 0.0 0.00 4.30 R
7184 10794 0.408700 ACTGTACTTCCTCCGGTCCT 59.591 55.000 0.0 0.0 0.00 3.85 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
25 26 2.032302 CCACCGAACGACATTGTCAAAA 59.968 45.455 16.61 0.00 32.09 2.44
32 33 2.100087 ACGACATTGTCAAAAACCACCC 59.900 45.455 16.61 0.00 32.09 4.61
62 63 1.954382 GAAGACAAAACTGTGACCCCC 59.046 52.381 0.00 0.00 0.00 5.40
108 109 3.181440 ACATGCCTTCCATCGATACCAAT 60.181 43.478 0.00 0.00 29.71 3.16
111 112 3.118075 TGCCTTCCATCGATACCAATCAA 60.118 43.478 0.00 0.00 31.93 2.57
120 121 2.088423 GATACCAATCAACACCGCCAA 58.912 47.619 0.00 0.00 31.93 4.52
155 156 4.220693 TGTGGAGACCTTATTCCATGTG 57.779 45.455 0.00 0.00 44.74 3.21
293 294 2.069776 CTGGGAGGCTTTGTGAGGA 58.930 57.895 0.00 0.00 0.00 3.71
294 295 0.401738 CTGGGAGGCTTTGTGAGGAA 59.598 55.000 0.00 0.00 0.00 3.36
336 1292 4.592942 ACACACATGAGAGGCACAATTAT 58.407 39.130 0.00 0.00 0.00 1.28
422 1379 0.740868 AGGATGTGCCATCGTCAACG 60.741 55.000 8.49 0.00 40.02 4.10
457 1414 9.515020 AACATCAATGCTATTAATTTTGTACCG 57.485 29.630 0.00 0.00 0.00 4.02
460 1417 8.270080 TCAATGCTATTAATTTTGTACCGTGA 57.730 30.769 0.00 0.00 0.00 4.35
564 1521 2.666508 CCGATTAGGCGATTACCATTCG 59.333 50.000 0.00 0.00 39.55 3.34
612 1569 2.030274 ACCGCTGTAAGAATTGTTTGCC 60.030 45.455 0.00 0.00 34.07 4.52
699 1656 3.134985 GGAACCCTAGATCTCTTCAACCC 59.865 52.174 0.00 0.00 0.00 4.11
748 1728 2.866523 TAACTCATCCCGTCCCGGCT 62.867 60.000 0.00 0.00 46.86 5.52
977 1969 1.388065 CCGGAGCGGTGAGAGAATCT 61.388 60.000 0.00 0.00 46.38 2.40
1012 2004 3.350163 CCCCCATGGAGCCCAAGT 61.350 66.667 15.22 0.00 36.95 3.16
1338 2330 2.746277 GAAACGCCGCTGGTGGAT 60.746 61.111 11.79 1.59 37.55 3.41
1447 2439 0.744771 GATCTCTCGTTTGGGGTGGC 60.745 60.000 0.00 0.00 0.00 5.01
1459 2451 2.409870 GGGTGGCGAATTGCTGGAG 61.410 63.158 0.00 0.00 45.43 3.86
1690 2686 8.565896 TGATGTGCTAATTGTAGTTTTCATCT 57.434 30.769 0.00 0.00 31.52 2.90
1889 2885 5.243283 AGTGCTCATCATTTTGCTTTCTTCT 59.757 36.000 0.00 0.00 0.00 2.85
2030 3026 9.950680 AAATCTTGATAACACAGTAAACAGTTG 57.049 29.630 0.00 0.00 0.00 3.16
2079 3075 4.951715 TGGCAGATCTTGATAATTGCTGTT 59.048 37.500 0.00 0.00 0.00 3.16
2117 3113 3.065371 GCAACCATGACTAATACTGGCAC 59.935 47.826 0.00 0.00 31.72 5.01
2356 3352 2.318908 TGCTGCCTTTCAAGTTTCCAT 58.681 42.857 0.00 0.00 0.00 3.41
2461 3457 6.036953 TGCACAACAACAAATCATTTTCTTCC 59.963 34.615 0.00 0.00 0.00 3.46
2510 3506 2.031870 ACCAAGTTGAGAAGCAAACCC 58.968 47.619 3.87 0.00 38.44 4.11
2887 3883 1.888436 TTCCAGTGCCTCTGCCTACG 61.888 60.000 1.15 0.00 42.38 3.51
4271 5267 2.376518 AGGATCAAGCAAAAGGTGAGGA 59.623 45.455 0.00 0.00 0.00 3.71
4272 5268 3.011032 AGGATCAAGCAAAAGGTGAGGAT 59.989 43.478 0.00 0.00 0.00 3.24
4273 5269 3.379688 GGATCAAGCAAAAGGTGAGGATC 59.620 47.826 0.00 0.00 32.84 3.36
4274 5270 8.981659 GAGGATCAAGCAAAAGGTGAGGATCA 62.982 46.154 0.00 0.00 37.86 2.92
4288 5284 3.693085 TGAGGATCAAGCAAAAGATGAGC 59.307 43.478 0.00 0.00 45.97 4.26
4489 5485 2.029470 GCTAAGGAGACCGATGATCCAG 60.029 54.545 0.00 0.00 35.45 3.86
4768 5764 2.093973 ACTGCCGTACAAGAAGATGAGG 60.094 50.000 0.00 0.00 0.00 3.86
5016 6044 7.526041 TGGTAATGCTGGGTAAGATTATTCAT 58.474 34.615 0.00 0.00 0.00 2.57
5191 6220 6.299805 TGCCATAAGAGATCAACTTGTAGT 57.700 37.500 13.09 0.00 0.00 2.73
5470 8941 1.416401 GTAAGGATGGCCCGATGAGAA 59.584 52.381 0.00 0.00 40.87 2.87
5507 8978 4.957296 ACCACGATGAAGTAAACAGAGTT 58.043 39.130 0.00 0.00 0.00 3.01
5511 8982 6.128902 CCACGATGAAGTAAACAGAGTTGTAC 60.129 42.308 0.00 0.00 36.23 2.90
5827 9396 1.302832 GCTAGCTGCACTGGTGGTT 60.303 57.895 7.70 0.00 42.31 3.67
5845 9414 4.863131 GTGGTTGAGAAACTGGTATAGTCG 59.137 45.833 0.00 0.00 39.18 4.18
5892 9461 2.371841 TCCTGTGTTCTGTGCCAGTAAT 59.628 45.455 2.68 0.00 32.61 1.89
5927 9496 9.883142 ATTATATACTGTACTACTACTCCGTCC 57.117 37.037 0.00 0.00 0.00 4.79
5928 9497 3.274095 ACTGTACTACTACTCCGTCCC 57.726 52.381 0.00 0.00 0.00 4.46
5929 9498 2.573462 ACTGTACTACTACTCCGTCCCA 59.427 50.000 0.00 0.00 0.00 4.37
5930 9499 3.201708 ACTGTACTACTACTCCGTCCCAT 59.798 47.826 0.00 0.00 0.00 4.00
5931 9500 4.410228 ACTGTACTACTACTCCGTCCCATA 59.590 45.833 0.00 0.00 0.00 2.74
5932 9501 5.104360 ACTGTACTACTACTCCGTCCCATAA 60.104 44.000 0.00 0.00 0.00 1.90
5933 9502 5.945310 TGTACTACTACTCCGTCCCATAAT 58.055 41.667 0.00 0.00 0.00 1.28
5934 9503 5.766670 TGTACTACTACTCCGTCCCATAATG 59.233 44.000 0.00 0.00 0.00 1.90
5935 9504 4.801164 ACTACTACTCCGTCCCATAATGT 58.199 43.478 0.00 0.00 0.00 2.71
5936 9505 5.945310 ACTACTACTCCGTCCCATAATGTA 58.055 41.667 0.00 0.00 0.00 2.29
5937 9506 6.002704 ACTACTACTCCGTCCCATAATGTAG 58.997 44.000 0.00 0.00 34.06 2.74
5938 9507 4.801164 ACTACTCCGTCCCATAATGTAGT 58.199 43.478 0.00 0.00 35.68 2.73
5939 9508 4.583489 ACTACTCCGTCCCATAATGTAGTG 59.417 45.833 0.00 0.00 38.04 2.74
5940 9509 3.371965 ACTCCGTCCCATAATGTAGTGT 58.628 45.455 0.00 0.00 0.00 3.55
5941 9510 3.383825 ACTCCGTCCCATAATGTAGTGTC 59.616 47.826 0.00 0.00 0.00 3.67
5942 9511 3.367321 TCCGTCCCATAATGTAGTGTCA 58.633 45.455 0.00 0.00 0.00 3.58
5943 9512 3.770388 TCCGTCCCATAATGTAGTGTCAA 59.230 43.478 0.00 0.00 0.00 3.18
5944 9513 4.223255 TCCGTCCCATAATGTAGTGTCAAA 59.777 41.667 0.00 0.00 0.00 2.69
5945 9514 4.938832 CCGTCCCATAATGTAGTGTCAAAA 59.061 41.667 0.00 0.00 0.00 2.44
5946 9515 5.413213 CCGTCCCATAATGTAGTGTCAAAAA 59.587 40.000 0.00 0.00 0.00 1.94
5967 9536 6.693315 AAAACGTCTTACATTATGGGATGG 57.307 37.500 0.00 0.00 0.00 3.51
5968 9537 5.623956 AACGTCTTACATTATGGGATGGA 57.376 39.130 0.00 0.00 0.00 3.41
5969 9538 5.215252 ACGTCTTACATTATGGGATGGAG 57.785 43.478 0.00 0.00 0.00 3.86
5970 9539 4.040461 ACGTCTTACATTATGGGATGGAGG 59.960 45.833 0.00 0.00 0.00 4.30
5971 9540 4.563580 CGTCTTACATTATGGGATGGAGGG 60.564 50.000 0.00 0.00 0.00 4.30
5972 9541 4.597507 GTCTTACATTATGGGATGGAGGGA 59.402 45.833 0.00 0.00 0.00 4.20
5973 9542 4.846367 TCTTACATTATGGGATGGAGGGAG 59.154 45.833 0.00 0.00 0.00 4.30
5974 9543 3.080660 ACATTATGGGATGGAGGGAGT 57.919 47.619 0.00 0.00 0.00 3.85
5975 9544 4.228237 ACATTATGGGATGGAGGGAGTA 57.772 45.455 0.00 0.00 0.00 2.59
5976 9545 4.171234 ACATTATGGGATGGAGGGAGTAG 58.829 47.826 0.00 0.00 0.00 2.57
5977 9546 4.171234 CATTATGGGATGGAGGGAGTAGT 58.829 47.826 0.00 0.00 0.00 2.73
5978 9547 2.109229 ATGGGATGGAGGGAGTAGTG 57.891 55.000 0.00 0.00 0.00 2.74
5979 9548 0.716591 TGGGATGGAGGGAGTAGTGT 59.283 55.000 0.00 0.00 0.00 3.55
5980 9549 1.080498 TGGGATGGAGGGAGTAGTGTT 59.920 52.381 0.00 0.00 0.00 3.32
6161 9730 2.310327 TAATCGCAGCTCGCATGGGT 62.310 55.000 9.86 0.00 42.60 4.51
6245 9814 2.662596 CCTGCAGTAAGACCGCCA 59.337 61.111 13.81 0.00 0.00 5.69
6333 9902 7.343833 ACCTGTATACCCGATTCTTTTAGAAGA 59.656 37.037 0.00 0.00 37.69 2.87
6416 9985 4.458295 ACCGTATCGTGATCTGTATAAGGG 59.542 45.833 13.72 5.69 30.52 3.95
6478 10047 0.533531 TGCACTCTGCTTGTGACTGG 60.534 55.000 8.13 0.00 45.31 4.00
6535 10104 3.004734 ACCAAAAGAGTTTTCATGCGGAG 59.995 43.478 0.00 0.00 0.00 4.63
6578 10147 0.305617 GGTTCGGTTTTCGTGGTCAC 59.694 55.000 0.00 0.00 40.32 3.67
6691 10282 1.878522 GTGGAGGCAGCGTCGTATG 60.879 63.158 8.97 0.00 0.00 2.39
6913 10504 3.118956 AGCATGCTCTTGTCACTAGGTAC 60.119 47.826 16.30 0.00 0.00 3.34
6933 10525 5.050159 GGTACGTTGGTTCGTTCTTTTGTAT 60.050 40.000 0.00 0.00 43.80 2.29
6940 10532 5.001874 GGTTCGTTCTTTTGTATTCCCTCT 58.998 41.667 0.00 0.00 0.00 3.69
6952 10544 6.062258 TGTATTCCCTCTGGTCCTTTTTAG 57.938 41.667 0.00 0.00 0.00 1.85
6956 10548 4.240323 TCCCTCTGGTCCTTTTTAGTTCT 58.760 43.478 0.00 0.00 0.00 3.01
6961 10553 7.366011 CCCTCTGGTCCTTTTTAGTTCTCATAT 60.366 40.741 0.00 0.00 0.00 1.78
6962 10554 8.705594 CCTCTGGTCCTTTTTAGTTCTCATATA 58.294 37.037 0.00 0.00 0.00 0.86
6989 10589 8.637986 AGATCTATTTGAAGTCAAGCCTAGTAG 58.362 37.037 0.00 0.00 37.15 2.57
7004 10604 4.930405 GCCTAGTAGAGTTTGACCAACTTC 59.070 45.833 0.00 0.00 46.53 3.01
7057 10659 6.986231 TGTGAAATCAATATCAGTAGATGCGT 59.014 34.615 0.00 0.00 35.67 5.24
7190 10800 6.984474 TCTTATATGCAGAGTAAAAAGGACCG 59.016 38.462 0.00 0.00 0.00 4.79
7191 10801 2.178912 TGCAGAGTAAAAAGGACCGG 57.821 50.000 0.00 0.00 0.00 5.28
7216 10826 2.688507 AGTACAGTGATGAAGCAACCG 58.311 47.619 0.00 0.00 0.00 4.44
7259 10869 2.540515 CTCGACCATAGTGCGTTCATT 58.459 47.619 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.808919 TCTTGTGGGTGGTTTTTGACA 58.191 42.857 0.00 0.00 0.00 3.58
25 26 2.241176 TCTTCACTTCTTGTGGGTGGTT 59.759 45.455 0.00 0.00 46.20 3.67
32 33 5.796935 CACAGTTTTGTCTTCACTTCTTGTG 59.203 40.000 0.00 0.00 40.85 3.33
62 63 1.726853 CTTCGGTCTAGGGCAGTTTG 58.273 55.000 0.00 0.00 0.00 2.93
108 109 0.958091 CCTCATTTTGGCGGTGTTGA 59.042 50.000 0.00 0.00 0.00 3.18
111 112 0.179004 TGTCCTCATTTTGGCGGTGT 60.179 50.000 0.00 0.00 0.00 4.16
120 121 4.566488 GGTCTCCACATCTTGTCCTCATTT 60.566 45.833 0.00 0.00 0.00 2.32
265 266 0.851469 AGCCTCCCAGCATTGATGAT 59.149 50.000 2.89 0.00 34.23 2.45
279 280 1.073923 TCCCTTTCCTCACAAAGCCTC 59.926 52.381 0.00 0.00 32.75 4.70
293 294 2.938838 TGTTCATGACGGTTTCCCTTT 58.061 42.857 0.00 0.00 0.00 3.11
294 295 2.621526 GTTGTTCATGACGGTTTCCCTT 59.378 45.455 0.00 0.00 0.00 3.95
336 1292 1.272037 TGAGGATGCACATCTTTGGCA 60.272 47.619 10.30 0.00 42.43 4.92
348 1304 3.584406 ACAGATATACGCTGAGGATGC 57.416 47.619 10.51 0.00 36.86 3.91
404 1361 1.019278 ACGTTGACGATGGCACATCC 61.019 55.000 10.87 0.00 43.40 3.51
472 1429 7.650504 CGATAATCCGGTATGACTACTGAAAAA 59.349 37.037 0.00 0.00 36.48 1.94
564 1521 4.748600 GCTTAATGGTGAGGTATACCGAAC 59.251 45.833 16.31 16.87 41.18 3.95
612 1569 4.377839 TGAGGACAAGATTAAGAGCGAG 57.622 45.455 0.00 0.00 0.00 5.03
1447 2439 2.176273 CCCTCGCTCCAGCAATTCG 61.176 63.158 0.00 0.00 42.21 3.34
1459 2451 2.358737 CCTCACAACCACCCTCGC 60.359 66.667 0.00 0.00 0.00 5.03
2030 3026 1.821136 CTTTCCCTTTCATGGTGAGGC 59.179 52.381 0.00 0.00 0.00 4.70
2079 3075 3.009584 TGGTTGCACATGGTTACTGGATA 59.990 43.478 0.00 0.00 0.00 2.59
2117 3113 7.709947 AGCATATTACATGAATGAAGTGGTTG 58.290 34.615 0.00 0.00 0.00 3.77
2461 3457 1.462616 TCCATGAAAACCATCCTGCG 58.537 50.000 0.00 0.00 31.94 5.18
2527 3523 0.459585 TCCGCTTCTCCGATTTTCCG 60.460 55.000 0.00 0.00 0.00 4.30
2536 3532 1.216710 CTCTGGTGTCCGCTTCTCC 59.783 63.158 0.00 0.00 0.00 3.71
2887 3883 3.064900 AGAACAGGATCAGGAAGCAAC 57.935 47.619 0.00 0.00 0.00 4.17
3477 4473 0.178903 TCAGGTACTTCAGGGGTGCT 60.179 55.000 0.00 0.00 34.60 4.40
3882 4878 4.286032 AGACACTATGGCAGTTCTTACCAA 59.714 41.667 0.00 0.00 36.94 3.67
4271 5267 5.597182 ACCATATGCTCATCTTTTGCTTGAT 59.403 36.000 0.00 0.00 0.00 2.57
4272 5268 4.951715 ACCATATGCTCATCTTTTGCTTGA 59.048 37.500 0.00 0.00 0.00 3.02
4273 5269 5.163591 TGACCATATGCTCATCTTTTGCTTG 60.164 40.000 0.00 0.00 0.00 4.01
4274 5270 4.951715 TGACCATATGCTCATCTTTTGCTT 59.048 37.500 0.00 0.00 0.00 3.91
4275 5271 4.529897 TGACCATATGCTCATCTTTTGCT 58.470 39.130 0.00 0.00 0.00 3.91
4276 5272 4.906065 TGACCATATGCTCATCTTTTGC 57.094 40.909 0.00 0.00 0.00 3.68
4277 5273 7.974482 TCTATGACCATATGCTCATCTTTTG 57.026 36.000 15.31 4.86 0.00 2.44
4278 5274 9.228949 GAATCTATGACCATATGCTCATCTTTT 57.771 33.333 15.31 8.62 0.00 2.27
4279 5275 8.380867 TGAATCTATGACCATATGCTCATCTTT 58.619 33.333 15.31 8.90 0.00 2.52
4280 5276 7.914859 TGAATCTATGACCATATGCTCATCTT 58.085 34.615 15.31 9.05 0.00 2.40
4281 5277 7.492077 TGAATCTATGACCATATGCTCATCT 57.508 36.000 15.31 0.00 0.00 2.90
4282 5278 7.823310 AGTTGAATCTATGACCATATGCTCATC 59.177 37.037 15.31 4.66 0.00 2.92
4283 5279 7.606839 CAGTTGAATCTATGACCATATGCTCAT 59.393 37.037 15.98 15.98 0.00 2.90
4284 5280 6.932960 CAGTTGAATCTATGACCATATGCTCA 59.067 38.462 3.22 3.22 0.00 4.26
4285 5281 6.370994 CCAGTTGAATCTATGACCATATGCTC 59.629 42.308 0.00 0.00 0.00 4.26
4286 5282 6.183361 ACCAGTTGAATCTATGACCATATGCT 60.183 38.462 0.00 0.00 0.00 3.79
4287 5283 6.000219 ACCAGTTGAATCTATGACCATATGC 59.000 40.000 0.00 0.00 0.00 3.14
4288 5284 8.370940 AGTACCAGTTGAATCTATGACCATATG 58.629 37.037 0.00 0.00 0.00 1.78
4489 5485 2.092914 CACCCTTATCCACCAGAGGAAC 60.093 54.545 0.00 0.00 41.92 3.62
4981 6009 1.674441 CAGCATTACCAGACCAGCATG 59.326 52.381 0.00 0.00 0.00 4.06
5033 6061 8.454106 GGCGTGCTAAGAAATTATGATGAATAT 58.546 33.333 0.00 0.00 0.00 1.28
5034 6062 7.443879 TGGCGTGCTAAGAAATTATGATGAATA 59.556 33.333 0.00 0.00 0.00 1.75
5035 6063 6.262944 TGGCGTGCTAAGAAATTATGATGAAT 59.737 34.615 0.00 0.00 0.00 2.57
5036 6064 5.588246 TGGCGTGCTAAGAAATTATGATGAA 59.412 36.000 0.00 0.00 0.00 2.57
5037 6065 5.122519 TGGCGTGCTAAGAAATTATGATGA 58.877 37.500 0.00 0.00 0.00 2.92
5038 6066 5.422666 TGGCGTGCTAAGAAATTATGATG 57.577 39.130 0.00 0.00 0.00 3.07
5039 6067 5.764686 TGATGGCGTGCTAAGAAATTATGAT 59.235 36.000 0.00 0.00 0.00 2.45
5124 6153 9.453572 CACATATTCCATGGCTACAATACTATT 57.546 33.333 6.96 0.00 0.00 1.73
5191 6220 7.039784 CCTTCTCACTTCCACATCCAAATTTTA 60.040 37.037 0.00 0.00 0.00 1.52
5470 8941 4.801330 TCGTGGTCAGATATCACAAAGT 57.199 40.909 5.32 0.00 0.00 2.66
5507 8978 5.992829 TGACTGCCTTTTTCTAATTCGTACA 59.007 36.000 0.00 0.00 0.00 2.90
5511 8982 7.974675 TCTAATGACTGCCTTTTTCTAATTCG 58.025 34.615 0.00 0.00 0.00 3.34
5827 9396 4.202121 GCATCCGACTATACCAGTTTCTCA 60.202 45.833 0.00 0.00 37.72 3.27
5845 9414 2.756760 TCATTTGGAGAGCAAAGCATCC 59.243 45.455 6.38 6.38 37.25 3.51
5920 9489 3.383505 TGACACTACATTATGGGACGGAG 59.616 47.826 0.00 0.00 0.00 4.63
5921 9490 3.367321 TGACACTACATTATGGGACGGA 58.633 45.455 0.00 0.00 0.00 4.69
5922 9491 3.812156 TGACACTACATTATGGGACGG 57.188 47.619 0.00 0.00 0.00 4.79
5923 9492 6.489127 TTTTTGACACTACATTATGGGACG 57.511 37.500 0.00 0.00 0.00 4.79
5943 9512 6.887545 TCCATCCCATAATGTAAGACGTTTTT 59.112 34.615 0.00 0.00 0.00 1.94
5944 9513 6.419791 TCCATCCCATAATGTAAGACGTTTT 58.580 36.000 0.00 0.00 0.00 2.43
5945 9514 5.996644 TCCATCCCATAATGTAAGACGTTT 58.003 37.500 0.00 0.00 0.00 3.60
5946 9515 5.454755 CCTCCATCCCATAATGTAAGACGTT 60.455 44.000 0.00 0.00 0.00 3.99
5947 9516 4.040461 CCTCCATCCCATAATGTAAGACGT 59.960 45.833 0.00 0.00 0.00 4.34
5948 9517 4.563580 CCCTCCATCCCATAATGTAAGACG 60.564 50.000 0.00 0.00 0.00 4.18
5949 9518 4.597507 TCCCTCCATCCCATAATGTAAGAC 59.402 45.833 0.00 0.00 0.00 3.01
5950 9519 4.838403 TCCCTCCATCCCATAATGTAAGA 58.162 43.478 0.00 0.00 0.00 2.10
5951 9520 4.599241 ACTCCCTCCATCCCATAATGTAAG 59.401 45.833 0.00 0.00 0.00 2.34
5952 9521 4.577096 ACTCCCTCCATCCCATAATGTAA 58.423 43.478 0.00 0.00 0.00 2.41
5953 9522 4.228237 ACTCCCTCCATCCCATAATGTA 57.772 45.455 0.00 0.00 0.00 2.29
5954 9523 3.080660 ACTCCCTCCATCCCATAATGT 57.919 47.619 0.00 0.00 0.00 2.71
5955 9524 4.019860 CACTACTCCCTCCATCCCATAATG 60.020 50.000 0.00 0.00 0.00 1.90
5956 9525 4.171234 CACTACTCCCTCCATCCCATAAT 58.829 47.826 0.00 0.00 0.00 1.28
5957 9526 3.051341 ACACTACTCCCTCCATCCCATAA 60.051 47.826 0.00 0.00 0.00 1.90
5958 9527 2.522705 ACACTACTCCCTCCATCCCATA 59.477 50.000 0.00 0.00 0.00 2.74
5959 9528 1.295292 ACACTACTCCCTCCATCCCAT 59.705 52.381 0.00 0.00 0.00 4.00
5960 9529 0.716591 ACACTACTCCCTCCATCCCA 59.283 55.000 0.00 0.00 0.00 4.37
5961 9530 1.763545 GAACACTACTCCCTCCATCCC 59.236 57.143 0.00 0.00 0.00 3.85
5962 9531 2.432510 CAGAACACTACTCCCTCCATCC 59.567 54.545 0.00 0.00 0.00 3.51
5963 9532 3.100671 ACAGAACACTACTCCCTCCATC 58.899 50.000 0.00 0.00 0.00 3.51
5964 9533 2.834549 CACAGAACACTACTCCCTCCAT 59.165 50.000 0.00 0.00 0.00 3.41
5965 9534 2.248248 CACAGAACACTACTCCCTCCA 58.752 52.381 0.00 0.00 0.00 3.86
5966 9535 1.066787 GCACAGAACACTACTCCCTCC 60.067 57.143 0.00 0.00 0.00 4.30
5967 9536 1.066787 GGCACAGAACACTACTCCCTC 60.067 57.143 0.00 0.00 0.00 4.30
5968 9537 0.977395 GGCACAGAACACTACTCCCT 59.023 55.000 0.00 0.00 0.00 4.20
5969 9538 0.685097 TGGCACAGAACACTACTCCC 59.315 55.000 0.00 0.00 0.00 4.30
6333 9902 1.271597 GCCTGATTGGTCTGAGGTGTT 60.272 52.381 0.00 0.00 38.35 3.32
6364 9933 5.643348 TCCTACATGAATGCTACAACAACAG 59.357 40.000 0.00 0.00 0.00 3.16
6416 9985 1.518325 CCAAAATGGCCGGGTTTTTC 58.482 50.000 2.18 0.00 0.00 2.29
6478 10047 2.549754 CACGGAAGATCATAACATGGCC 59.450 50.000 0.00 0.00 0.00 5.36
6535 10104 1.740025 GCCTCCTTACAAGCACATCAC 59.260 52.381 0.00 0.00 0.00 3.06
6654 10232 0.600255 CCGTCGAGACTTTGCCACTT 60.600 55.000 0.00 0.00 0.00 3.16
6655 10233 1.006102 CCGTCGAGACTTTGCCACT 60.006 57.895 0.00 0.00 0.00 4.00
6656 10234 1.300697 ACCGTCGAGACTTTGCCAC 60.301 57.895 0.00 0.00 0.00 5.01
6657 10235 1.300620 CACCGTCGAGACTTTGCCA 60.301 57.895 0.00 0.00 0.00 4.92
6691 10282 6.426025 GGATAGAACCGTGGGACATTTATTAC 59.574 42.308 0.00 0.00 44.52 1.89
6811 10402 1.299541 CCGAAGCGCCAGATAACAAT 58.700 50.000 2.29 0.00 0.00 2.71
6913 10504 4.907582 GGAATACAAAAGAACGAACCAACG 59.092 41.667 0.00 0.00 39.31 4.10
6933 10525 4.663592 AGAACTAAAAAGGACCAGAGGGAA 59.336 41.667 0.00 0.00 38.05 3.97
6961 10553 8.982723 ACTAGGCTTGACTTCAAATAGATCTTA 58.017 33.333 0.00 0.00 35.15 2.10
6962 10554 7.856415 ACTAGGCTTGACTTCAAATAGATCTT 58.144 34.615 0.00 0.00 35.15 2.40
6964 10556 8.634444 TCTACTAGGCTTGACTTCAAATAGATC 58.366 37.037 2.20 0.00 35.15 2.75
6966 10558 7.616150 ACTCTACTAGGCTTGACTTCAAATAGA 59.384 37.037 2.20 0.00 35.15 1.98
6967 10559 7.777095 ACTCTACTAGGCTTGACTTCAAATAG 58.223 38.462 2.20 0.00 35.15 1.73
6968 10560 7.719871 ACTCTACTAGGCTTGACTTCAAATA 57.280 36.000 2.20 0.00 35.15 1.40
6969 10561 6.613153 ACTCTACTAGGCTTGACTTCAAAT 57.387 37.500 2.20 0.00 35.15 2.32
6970 10562 6.420913 AACTCTACTAGGCTTGACTTCAAA 57.579 37.500 2.20 0.00 35.15 2.69
6971 10563 6.041637 TCAAACTCTACTAGGCTTGACTTCAA 59.958 38.462 2.20 0.00 30.41 2.69
6972 10564 5.538813 TCAAACTCTACTAGGCTTGACTTCA 59.461 40.000 2.20 0.00 30.41 3.02
6973 10565 5.865013 GTCAAACTCTACTAGGCTTGACTTC 59.135 44.000 2.20 0.00 42.83 3.01
6974 10566 5.279556 GGTCAAACTCTACTAGGCTTGACTT 60.280 44.000 2.20 0.00 44.14 3.01
6975 10567 4.221041 GGTCAAACTCTACTAGGCTTGACT 59.779 45.833 2.20 0.00 44.14 3.41
6976 10568 4.021368 TGGTCAAACTCTACTAGGCTTGAC 60.021 45.833 2.20 2.31 44.05 3.18
6977 10569 4.157246 TGGTCAAACTCTACTAGGCTTGA 58.843 43.478 2.20 0.00 32.00 3.02
6978 10570 4.537135 TGGTCAAACTCTACTAGGCTTG 57.463 45.455 0.00 0.00 0.00 4.01
7152 10762 8.654230 TCTGCATATAAGAATTGTCTGAAGTC 57.346 34.615 0.00 0.00 33.05 3.01
7184 10794 0.408700 ACTGTACTTCCTCCGGTCCT 59.591 55.000 0.00 0.00 0.00 3.85
7185 10795 0.531200 CACTGTACTTCCTCCGGTCC 59.469 60.000 0.00 0.00 0.00 4.46
7190 10800 3.055819 TGCTTCATCACTGTACTTCCTCC 60.056 47.826 0.00 0.00 0.00 4.30
7191 10801 4.193826 TGCTTCATCACTGTACTTCCTC 57.806 45.455 0.00 0.00 0.00 3.71
7195 10805 3.067106 CGGTTGCTTCATCACTGTACTT 58.933 45.455 0.00 0.00 0.00 2.24
7216 10826 1.588667 CACGCACAACCCTTGCAAC 60.589 57.895 0.00 0.00 40.20 4.17


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

AutoCloner maintained by Alex Coulton.