Multiple sequence alignment - TraesCS2B01G088500

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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 TraesCS2B01G088500 chr2B 100.000 7596 0 0 1 7596 49970582 49978177 0.000000e+00 14028
1 TraesCS2B01G088500 chr2B 98.320 2381 22 1 4419 6781 50151215 50148835 0.000000e+00 4159
2 TraesCS2B01G088500 chr2B 95.719 2336 54 9 922 3255 50153713 50151422 0.000000e+00 3718
3 TraesCS2B01G088500 chr2B 95.132 719 18 9 211 926 50154441 50153737 0.000000e+00 1118
4 TraesCS2B01G088500 chr2B 96.491 171 6 0 1 171 50154609 50154439 4.490000e-72 283
5 TraesCS2B01G088500 chr2B 93.023 129 5 3 5196 5323 518048325 518048450 1.300000e-42 185
6 TraesCS2B01G088500 chr2A 93.147 4319 159 50 916 5192 32513201 32508978 0.000000e+00 6209
7 TraesCS2B01G088500 chr2A 87.303 2032 147 33 5294 7275 32508962 32506992 0.000000e+00 2220
8 TraesCS2B01G088500 chr2A 89.149 470 38 4 389 847 32514038 32513571 2.380000e-159 573
9 TraesCS2B01G088500 chr2A 87.250 400 23 10 1 396 32514494 32514119 1.510000e-116 431
10 TraesCS2B01G088500 chr2D 95.280 2521 79 16 1919 4422 30487625 30485128 0.000000e+00 3960
11 TraesCS2B01G088500 chr2D 91.009 1279 93 12 5318 6591 30484379 30483118 0.000000e+00 1705
12 TraesCS2B01G088500 chr2D 90.769 1040 47 14 916 1951 30488796 30487802 0.000000e+00 1343
13 TraesCS2B01G088500 chr2D 89.220 1039 85 12 6581 7596 30483091 30482057 0.000000e+00 1273
14 TraesCS2B01G088500 chr2D 95.935 738 30 0 4455 5192 30485126 30484389 0.000000e+00 1197
15 TraesCS2B01G088500 chr2D 89.583 864 50 18 1 853 30489978 30489144 0.000000e+00 1061
16 TraesCS2B01G088500 chr2D 93.750 128 6 2 5187 5312 12692230 12692357 2.800000e-44 191
17 TraesCS2B01G088500 chr3A 89.035 1523 123 29 922 2435 632622255 632620768 0.000000e+00 1847
18 TraesCS2B01G088500 chr3A 88.528 1325 114 26 3873 5182 632617712 632616411 0.000000e+00 1570
19 TraesCS2B01G088500 chr3A 87.152 1292 104 23 5315 6580 632616315 632615060 0.000000e+00 1410
20 TraesCS2B01G088500 chr3A 89.984 629 43 8 2933 3554 632619389 632618774 0.000000e+00 795
21 TraesCS2B01G088500 chr3A 83.733 584 68 14 2975 3551 400096537 400095974 1.880000e-145 527
22 TraesCS2B01G088500 chr3A 82.164 499 47 22 2450 2931 632620601 632620128 2.570000e-104 390
23 TraesCS2B01G088500 chr3A 83.333 330 23 18 3583 3888 632618197 632617876 7.510000e-70 276
24 TraesCS2B01G088500 chr3A 90.777 206 17 2 1 205 632623341 632623137 2.700000e-69 274
25 TraesCS2B01G088500 chr3A 90.909 143 12 1 6585 6727 632615010 632614869 2.800000e-44 191
26 TraesCS2B01G088500 chr3B 88.525 1525 132 25 922 2435 651727117 651725625 0.000000e+00 1807
27 TraesCS2B01G088500 chr3B 85.629 1670 127 58 3583 5182 651723109 651721483 0.000000e+00 1650
28 TraesCS2B01G088500 chr3B 87.267 1288 110 21 5315 6580 651721388 651720133 0.000000e+00 1421
29 TraesCS2B01G088500 chr3B 89.348 629 47 8 2931 3552 651724112 651723497 0.000000e+00 773
30 TraesCS2B01G088500 chr3B 84.191 544 63 9 2976 3515 395986652 395986128 2.450000e-139 507
31 TraesCS2B01G088500 chr3B 84.872 390 41 11 2479 2858 651725506 651725125 2.000000e-100 377
32 TraesCS2B01G088500 chr3B 90.345 145 13 1 6583 6727 651720088 651719945 1.010000e-43 189
33 TraesCS2B01G088500 chr3B 90.210 143 12 2 1 142 651728618 651728477 1.300000e-42 185
34 TraesCS2B01G088500 chr3D 88.231 1521 120 29 922 2435 489551623 489550155 0.000000e+00 1762
35 TraesCS2B01G088500 chr3D 86.151 1668 131 51 3583 5182 489547913 489546278 0.000000e+00 1709
36 TraesCS2B01G088500 chr3D 87.974 1239 97 19 5365 6580 489546154 489544945 0.000000e+00 1415
37 TraesCS2B01G088500 chr3D 90.174 631 42 8 2931 3554 489548915 489548298 0.000000e+00 804
38 TraesCS2B01G088500 chr3D 84.076 471 53 10 3081 3548 323244675 323245126 1.170000e-117 435
39 TraesCS2B01G088500 chr3D 82.164 499 47 22 2450 2931 489549988 489549515 2.570000e-104 390
40 TraesCS2B01G088500 chr3D 91.262 206 16 2 1 205 489552691 489552487 5.800000e-71 279
41 TraesCS2B01G088500 chr3D 91.034 145 12 1 6583 6727 489544897 489544754 2.160000e-45 195
42 TraesCS2B01G088500 chr4A 95.385 130 4 2 5184 5312 677435902 677436030 9.990000e-49 206
43 TraesCS2B01G088500 chr6B 95.868 121 5 0 5192 5312 683214110 683214230 6.010000e-46 196
44 TraesCS2B01G088500 chr4B 96.581 117 4 0 5196 5312 16060844 16060960 2.160000e-45 195
45 TraesCS2B01G088500 chr7B 94.355 124 6 1 5195 5317 143329515 143329392 1.010000e-43 189
46 TraesCS2B01G088500 chr5B 91.111 135 10 2 5180 5312 619116594 619116728 1.680000e-41 182
47 TraesCS2B01G088500 chr6D 89.655 145 9 5 5189 5329 178852324 178852182 6.060000e-41 180
48 TraesCS2B01G088500 chr5A 80.097 206 34 5 1 201 617347122 617347325 6.140000e-31 147
49 TraesCS2B01G088500 chr5D 79.710 207 33 7 1 201 494458729 494458932 2.860000e-29 141


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 TraesCS2B01G088500 chr2B 49970582 49978177 7595 False 14028.000000 14028 100.000000 1 7596 1 chr2B.!!$F1 7595
1 TraesCS2B01G088500 chr2B 50148835 50154609 5774 True 2319.500000 4159 96.415500 1 6781 4 chr2B.!!$R1 6780
2 TraesCS2B01G088500 chr2A 32506992 32514494 7502 True 2358.250000 6209 89.212250 1 7275 4 chr2A.!!$R1 7274
3 TraesCS2B01G088500 chr2D 30482057 30489978 7921 True 1756.500000 3960 91.966000 1 7596 6 chr2D.!!$R1 7595
4 TraesCS2B01G088500 chr3A 632614869 632623341 8472 True 844.125000 1847 87.735250 1 6727 8 chr3A.!!$R2 6726
5 TraesCS2B01G088500 chr3A 400095974 400096537 563 True 527.000000 527 83.733000 2975 3551 1 chr3A.!!$R1 576
6 TraesCS2B01G088500 chr3B 651719945 651728618 8673 True 914.571429 1807 88.028000 1 6727 7 chr3B.!!$R2 6726
7 TraesCS2B01G088500 chr3B 395986128 395986652 524 True 507.000000 507 84.191000 2976 3515 1 chr3B.!!$R1 539
8 TraesCS2B01G088500 chr3D 489544754 489552691 7937 True 936.285714 1762 88.141429 1 6727 7 chr3D.!!$R1 6726

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
142 145 1.153823 CGGCCTCGAGTTCGACAAT 60.154 57.895 12.31 0.00 44.22 2.71 F
1176 2145 2.890808 AACTGCGTCAAGACTCAAGA 57.109 45.000 0.00 0.00 0.00 3.02 F
3091 5611 0.465097 CTGGATCCCCATGTCAGTGC 60.465 60.000 9.90 0.00 42.59 4.40 F
3479 6001 1.139853 CCAGAGGAGGACAAGGTATGC 59.860 57.143 0.00 0.00 0.00 3.14 F
3616 6497 1.776710 TAGTGCCCCACCCCTTGTT 60.777 57.895 0.00 0.00 34.49 2.83 F
3922 7206 3.244345 GCAAACCGCATTCATGATTCATG 59.756 43.478 18.71 18.71 40.86 3.07 F
5919 9248 1.597854 CCTTGCTTCCACGCACTGA 60.598 57.895 0.00 0.00 40.09 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 3241 2.271800 GCTAGATGTCCAACTTGACCG 58.728 52.381 0.0 0.0 34.25 4.79 R
3114 5634 2.034221 GCGAGGCCCTTGGAAACT 59.966 61.111 0.0 0.0 0.00 2.66 R
4066 7351 0.320374 TTACCCAGCACAGACCTTCG 59.680 55.000 0.0 0.0 0.00 3.79 R
4770 8085 1.616994 GCAGTTTGGCTATCCCCTGTT 60.617 52.381 0.0 0.0 0.00 3.16 R
5919 9248 7.290014 ACCATTTCAAAAGTTGGTTAGGATTCT 59.710 33.333 0.0 0.0 39.41 2.40 R
6514 9870 1.418334 AGGAGTTCTGTGACTGCTGT 58.582 50.000 0.0 0.0 45.14 4.40 R
6809 10237 0.319813 AGGAACGTAACCGAAACCCG 60.320 55.000 0.0 0.0 37.88 5.28 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
77 78 4.787280 AGGAGGAGGCCGTGGAGG 62.787 72.222 0.00 0.00 44.97 4.30
79 80 3.775654 GAGGAGGCCGTGGAGGTG 61.776 72.222 0.00 0.00 43.70 4.00
142 145 1.153823 CGGCCTCGAGTTCGACAAT 60.154 57.895 12.31 0.00 44.22 2.71
217 220 4.374689 GGTACCTACCTACCTACCTACC 57.625 54.545 4.06 0.00 43.10 3.18
218 221 3.984090 GGTACCTACCTACCTACCTACCT 59.016 52.174 4.06 0.00 43.10 3.08
219 222 5.163390 GGTACCTACCTACCTACCTACCTA 58.837 50.000 4.06 0.00 43.10 3.08
220 223 5.013287 GGTACCTACCTACCTACCTACCTAC 59.987 52.000 4.06 0.00 43.10 3.18
221 224 4.914217 ACCTACCTACCTACCTACCTACT 58.086 47.826 0.00 0.00 0.00 2.57
222 225 5.301141 ACCTACCTACCTACCTACCTACTT 58.699 45.833 0.00 0.00 0.00 2.24
223 226 5.133491 ACCTACCTACCTACCTACCTACTTG 59.867 48.000 0.00 0.00 0.00 3.16
279 815 4.386711 GCAGCCGGGTCTTACTTAATTAT 58.613 43.478 1.27 0.00 0.00 1.28
319 858 2.925966 TGCAATTCAAAGGGAGGGAT 57.074 45.000 0.00 0.00 0.00 3.85
469 1102 5.200368 ACACAGCAAAACTAATTTCTGGG 57.800 39.130 0.00 0.00 36.48 4.45
1170 2139 4.537936 AGAAGAAAAACTGCGTCAAGAC 57.462 40.909 0.00 0.00 0.00 3.01
1171 2140 4.192317 AGAAGAAAAACTGCGTCAAGACT 58.808 39.130 0.00 0.00 0.00 3.24
1172 2141 4.271291 AGAAGAAAAACTGCGTCAAGACTC 59.729 41.667 0.00 0.00 0.00 3.36
1173 2142 3.531538 AGAAAAACTGCGTCAAGACTCA 58.468 40.909 0.00 0.00 0.00 3.41
1174 2143 3.938963 AGAAAAACTGCGTCAAGACTCAA 59.061 39.130 0.00 0.00 0.00 3.02
1175 2144 3.951979 AAAACTGCGTCAAGACTCAAG 57.048 42.857 0.00 0.00 0.00 3.02
1176 2145 2.890808 AACTGCGTCAAGACTCAAGA 57.109 45.000 0.00 0.00 0.00 3.02
2048 3241 1.251251 AGGACAAATGCTTCCTGTGC 58.749 50.000 0.00 0.00 40.98 4.57
2435 3677 6.528423 CACTAGAGATTCGTGAGGTTAGTTTG 59.472 42.308 0.00 0.00 0.00 2.93
2447 3792 6.757947 GTGAGGTTAGTTTGTGTAGTGTTACA 59.242 38.462 0.00 0.00 37.45 2.41
2508 3859 9.730420 TTTTAGTTCACTTTCTTAGATTGTTGC 57.270 29.630 0.00 0.00 0.00 4.17
2644 4008 4.649674 ACGGTATTGTACATCATCTGACCT 59.350 41.667 0.00 0.00 0.00 3.85
2695 4059 2.658285 TGTGAAATGATCCTCATGGGC 58.342 47.619 0.00 0.00 37.15 5.36
2716 4088 5.394005 GGGCACATCAGCAATAACACATTTA 60.394 40.000 0.00 0.00 35.83 1.40
2955 5474 3.244353 ACACTTGATGCTCAGCTGTTACT 60.244 43.478 14.67 0.00 0.00 2.24
2956 5475 4.021104 ACACTTGATGCTCAGCTGTTACTA 60.021 41.667 14.67 0.00 0.00 1.82
2957 5476 4.328440 CACTTGATGCTCAGCTGTTACTAC 59.672 45.833 14.67 3.39 0.00 2.73
3091 5611 0.465097 CTGGATCCCCATGTCAGTGC 60.465 60.000 9.90 0.00 42.59 4.40
3114 5634 5.123820 GCTGATCTTATTGTACCTGTTGCAA 59.876 40.000 0.00 0.00 0.00 4.08
3144 5665 3.710722 CTCGCCTTGCCTCTGGGT 61.711 66.667 0.00 0.00 34.45 4.51
3276 5797 5.512753 TGTTGTTGAAGCTGAAATTAGCA 57.487 34.783 3.15 0.00 46.07 3.49
3479 6001 1.139853 CCAGAGGAGGACAAGGTATGC 59.860 57.143 0.00 0.00 0.00 3.14
3508 6031 4.460263 TCTTTGGTATCTGTGCACAAGTT 58.540 39.130 21.98 10.76 0.00 2.66
3616 6497 1.776710 TAGTGCCCCACCCCTTGTT 60.777 57.895 0.00 0.00 34.49 2.83
3906 7190 6.369615 ACTGCATTCATGAATAAAAGCAAACC 59.630 34.615 23.54 3.24 29.53 3.27
3922 7206 3.244345 GCAAACCGCATTCATGATTCATG 59.756 43.478 18.71 18.71 40.86 3.07
3923 7207 4.426416 CAAACCGCATTCATGATTCATGT 58.574 39.130 22.64 5.39 41.98 3.21
4066 7351 5.760743 GCTCCTTCAGGTTCTCAAATATACC 59.239 44.000 0.00 0.00 36.34 2.73
4104 7389 8.257602 TGGGTAATGCACTACTATTATGAAGA 57.742 34.615 5.17 0.00 0.00 2.87
4133 7424 4.038402 GCTCATGGCAATGGTAATTTAGCT 59.962 41.667 0.00 0.00 41.35 3.32
4167 7461 4.499696 GGCCAATTATATGCCACACAGTTC 60.500 45.833 0.00 0.00 44.70 3.01
4403 7697 4.219944 AGCGGCGAGGTGAATATTCTAATA 59.780 41.667 12.98 0.00 0.00 0.98
4404 7698 5.105310 AGCGGCGAGGTGAATATTCTAATAT 60.105 40.000 12.98 0.00 33.14 1.28
4405 7699 5.581085 GCGGCGAGGTGAATATTCTAATATT 59.419 40.000 12.98 7.50 42.61 1.28
4406 7700 6.755141 GCGGCGAGGTGAATATTCTAATATTA 59.245 38.462 12.98 0.00 40.63 0.98
4407 7701 7.438459 GCGGCGAGGTGAATATTCTAATATTAT 59.562 37.037 12.98 0.00 40.63 1.28
4616 7913 3.380637 TCTCCTAGCTACAACCTTAAGCG 59.619 47.826 0.00 0.00 41.19 4.68
5620 8942 5.397360 TCCAGATCCTCATAAGCACATAGA 58.603 41.667 0.00 0.00 0.00 1.98
5919 9248 1.597854 CCTTGCTTCCACGCACTGA 60.598 57.895 0.00 0.00 40.09 3.41
6481 9837 3.969976 CTCATGGTTCCTATTCTGGAGGA 59.030 47.826 0.00 0.00 41.52 3.71
6482 9838 8.996059 ACCTCATGGTTCCTATTCTGGAGGAA 62.996 46.154 10.55 0.00 46.05 3.36
6514 9870 2.037902 TGCAAGACCTAATTCACGACCA 59.962 45.455 0.00 0.00 0.00 4.02
6811 10239 4.101448 CTCCTGGCCTGGAACCGG 62.101 72.222 29.20 15.70 35.43 5.28
6830 10258 1.001293 GGGTTTCGGTTACGTTCCTCT 59.999 52.381 0.00 0.00 41.85 3.69
6840 10268 7.601856 TCGGTTACGTTCCTCTAGAAATTTTA 58.398 34.615 0.00 0.00 41.85 1.52
6841 10269 8.253113 TCGGTTACGTTCCTCTAGAAATTTTAT 58.747 33.333 0.00 0.00 41.85 1.40
7018 10450 3.229276 TCCATGTAAAATGCTTTGCCG 57.771 42.857 0.00 0.00 0.00 5.69
7022 10454 1.259316 GTAAAATGCTTTGCCGCTCG 58.741 50.000 0.00 0.00 0.00 5.03
7096 10528 9.179909 TCATTAAAGGTCGCTTTATTTTGGATA 57.820 29.630 0.00 0.00 0.00 2.59
7164 10597 3.376546 GGAGTGAAGCAATCATCCTCAAC 59.623 47.826 10.35 0.00 40.97 3.18
7178 10611 4.437682 TCCTCAACCTCAACTTCACAAT 57.562 40.909 0.00 0.00 0.00 2.71
7308 10747 4.418013 TTGCTATCAACGACCAATGTTG 57.582 40.909 0.00 0.00 46.23 3.33
7319 10758 4.154195 ACGACCAATGTTGACTAATGCTTC 59.846 41.667 0.00 0.00 0.00 3.86
7357 10796 6.976934 ACTACAAAACTCAAATTGATGGGT 57.023 33.333 0.00 0.00 34.84 4.51
7369 10808 8.506168 TCAAATTGATGGGTAGTTATCTTGAC 57.494 34.615 0.00 0.00 0.00 3.18
7370 10809 8.106462 TCAAATTGATGGGTAGTTATCTTGACA 58.894 33.333 0.00 0.00 0.00 3.58
7390 10829 9.208022 CTTGACACATCTGACTTAGTTATTGAA 57.792 33.333 0.00 0.00 0.00 2.69
7484 10923 6.320418 TGCAGTCTTCAATATGATGCTTTGAT 59.680 34.615 5.56 0.00 33.47 2.57
7563 11002 7.860649 AAAGGGCATTTCATGGTATATTCAT 57.139 32.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 101 1.227853 GTTGGCCTTGGACGTGTCT 60.228 57.895 3.32 0.00 0.00 3.41
142 145 2.014857 CCGTTCATGTCGAGGTAGAGA 58.985 52.381 12.77 0.00 0.00 3.10
209 212 7.642082 ATCAAGTACACAAGTAGGTAGGTAG 57.358 40.000 0.00 0.00 0.00 3.18
210 213 7.093640 CCAATCAAGTACACAAGTAGGTAGGTA 60.094 40.741 0.00 0.00 0.00 3.08
211 214 6.295688 CCAATCAAGTACACAAGTAGGTAGGT 60.296 42.308 0.00 0.00 0.00 3.08
212 215 6.106673 CCAATCAAGTACACAAGTAGGTAGG 58.893 44.000 0.00 0.00 0.00 3.18
213 216 6.106673 CCCAATCAAGTACACAAGTAGGTAG 58.893 44.000 0.00 0.00 0.00 3.18
214 217 5.570034 GCCCAATCAAGTACACAAGTAGGTA 60.570 44.000 0.00 0.00 0.00 3.08
215 218 4.806286 GCCCAATCAAGTACACAAGTAGGT 60.806 45.833 0.00 0.00 0.00 3.08
216 219 3.689649 GCCCAATCAAGTACACAAGTAGG 59.310 47.826 0.00 0.00 0.00 3.18
217 220 4.579869 AGCCCAATCAAGTACACAAGTAG 58.420 43.478 0.00 0.00 0.00 2.57
218 221 4.634012 AGCCCAATCAAGTACACAAGTA 57.366 40.909 0.00 0.00 0.00 2.24
219 222 3.508845 AGCCCAATCAAGTACACAAGT 57.491 42.857 0.00 0.00 0.00 3.16
220 223 3.375299 GCTAGCCCAATCAAGTACACAAG 59.625 47.826 2.29 0.00 0.00 3.16
221 224 3.009033 AGCTAGCCCAATCAAGTACACAA 59.991 43.478 12.13 0.00 0.00 3.33
222 225 2.571653 AGCTAGCCCAATCAAGTACACA 59.428 45.455 12.13 0.00 0.00 3.72
223 226 3.268023 AGCTAGCCCAATCAAGTACAC 57.732 47.619 12.13 0.00 0.00 2.90
319 858 1.829222 GGGGACGGACAGTATTGAAGA 59.171 52.381 0.00 0.00 0.00 2.87
402 1031 5.799827 AAAACCGGATTGAATCTTGGAAA 57.200 34.783 9.46 0.00 0.00 3.13
469 1102 3.844577 ATCTTGTGCAGATTCACTTGC 57.155 42.857 0.00 0.00 39.47 4.01
690 1342 7.140705 CACAAAATGCAATAGAAGTGAGAACA 58.859 34.615 0.00 0.00 0.00 3.18
919 1876 4.943705 CACCATCTGTAAGCCATTGTAGTT 59.056 41.667 0.00 0.00 0.00 2.24
1062 2019 7.654520 GTCCACAAATAACAATAGATACGGCTA 59.345 37.037 0.00 0.00 0.00 3.93
1171 2140 3.587498 TCCTTCCCTCTCAAACTCTTGA 58.413 45.455 0.00 0.00 39.30 3.02
1172 2141 4.040952 TCTTCCTTCCCTCTCAAACTCTTG 59.959 45.833 0.00 0.00 0.00 3.02
1173 2142 4.235372 TCTTCCTTCCCTCTCAAACTCTT 58.765 43.478 0.00 0.00 0.00 2.85
1174 2143 3.863086 TCTTCCTTCCCTCTCAAACTCT 58.137 45.455 0.00 0.00 0.00 3.24
1175 2144 4.625607 TTCTTCCTTCCCTCTCAAACTC 57.374 45.455 0.00 0.00 0.00 3.01
1176 2145 4.748239 GCTTTCTTCCTTCCCTCTCAAACT 60.748 45.833 0.00 0.00 0.00 2.66
2048 3241 2.271800 GCTAGATGTCCAACTTGACCG 58.728 52.381 0.00 0.00 34.25 4.79
2435 3677 9.997482 TGAAAGAAGAAAAATGTAACACTACAC 57.003 29.630 0.00 0.00 40.84 2.90
2508 3859 4.326826 AGAGTAACCATTGTGTCATGTGG 58.673 43.478 0.00 0.00 37.74 4.17
2695 4059 9.577110 AAGATTAAATGTGTTATTGCTGATGTG 57.423 29.630 0.00 0.00 0.00 3.21
2716 4088 3.950397 TCCGGCTACAACAATGAAGATT 58.050 40.909 0.00 0.00 0.00 2.40
2829 4201 7.609146 TGATAAGCAAAATCAAGACAGTCATCT 59.391 33.333 2.66 0.00 30.52 2.90
2955 5474 7.365741 GTGAAAGCACACACTACTAGTAAGTA 58.634 38.462 3.76 0.00 44.51 2.24
2956 5475 6.214399 GTGAAAGCACACACTACTAGTAAGT 58.786 40.000 3.76 3.11 44.51 2.24
2957 5476 6.692232 GTGAAAGCACACACTACTAGTAAG 57.308 41.667 3.76 2.47 44.51 2.34
3091 5611 6.372659 ACTTGCAACAGGTACAATAAGATCAG 59.627 38.462 0.00 0.00 0.00 2.90
3114 5634 2.034221 GCGAGGCCCTTGGAAACT 59.966 61.111 0.00 0.00 0.00 2.66
3221 5742 3.993081 GGCTGGAATCTGAAGATGATACG 59.007 47.826 0.00 0.00 34.49 3.06
3276 5797 6.170506 TCAAATTAAGTACCTGTGCTTCGAT 58.829 36.000 3.84 0.00 36.85 3.59
3479 6001 5.065218 GTGCACAGATACCAAAGATACAAGG 59.935 44.000 13.17 0.00 0.00 3.61
3508 6031 4.277515 ACTGATACAGCAGCAGAAGAAA 57.722 40.909 0.00 0.00 43.68 2.52
3608 6489 5.862678 TTAGAAGTTCCAAAAACAAGGGG 57.137 39.130 0.00 0.00 0.00 4.79
3616 6497 7.946207 TGTGCAACATATTAGAAGTTCCAAAA 58.054 30.769 0.00 0.00 45.67 2.44
3862 6964 9.632638 AATGCAGTATATTAAAGACACTTCCAT 57.367 29.630 0.00 0.00 0.00 3.41
3906 7190 3.065648 TGTCCACATGAATCATGAATGCG 59.934 43.478 27.86 11.52 43.81 4.73
3922 7206 1.821216 CAACAGGGTATGGTGTCCAC 58.179 55.000 0.00 0.00 42.07 4.02
3923 7207 3.345557 GGCAACAGGGTATGGTGTCCA 62.346 57.143 0.00 0.00 46.02 4.02
4066 7351 0.320374 TTACCCAGCACAGACCTTCG 59.680 55.000 0.00 0.00 0.00 3.79
4078 7363 8.367911 TCTTCATAATAGTAGTGCATTACCCAG 58.632 37.037 15.09 1.65 0.00 4.45
4133 7424 8.443953 GGCATATAATTGGCCAATTAAAACAA 57.556 30.769 40.62 26.85 46.92 2.83
4343 7637 7.012327 CCATAAGCTGATCGAAAGGTTTGAATA 59.988 37.037 17.64 4.05 36.75 1.75
4414 7711 7.390440 CACCACATGAAGGTACTAAGATTGAAA 59.610 37.037 12.96 0.00 38.49 2.69
4616 7913 6.072119 ACAAAGGTTCAACCGGATTAGAATTC 60.072 38.462 9.46 0.00 44.90 2.17
4770 8085 1.616994 GCAGTTTGGCTATCCCCTGTT 60.617 52.381 0.00 0.00 0.00 3.16
5919 9248 7.290014 ACCATTTCAAAAGTTGGTTAGGATTCT 59.710 33.333 0.00 0.00 39.41 2.40
6514 9870 1.418334 AGGAGTTCTGTGACTGCTGT 58.582 50.000 0.00 0.00 45.14 4.40
6809 10237 0.319813 AGGAACGTAACCGAAACCCG 60.320 55.000 0.00 0.00 37.88 5.28
6811 10239 2.445565 AGAGGAACGTAACCGAAACC 57.554 50.000 0.00 0.00 37.88 3.27
6812 10240 4.425577 TCTAGAGGAACGTAACCGAAAC 57.574 45.455 0.00 0.00 37.88 2.78
6840 10268 5.422214 AGACGAAGGTTTGAGGATGTTAT 57.578 39.130 0.00 0.00 0.00 1.89
6841 10269 4.884668 AGACGAAGGTTTGAGGATGTTA 57.115 40.909 0.00 0.00 0.00 2.41
6992 10424 6.090763 GGCAAAGCATTTTACATGGAACTTAC 59.909 38.462 0.00 0.00 35.03 2.34
7002 10434 1.400888 CGAGCGGCAAAGCATTTTACA 60.401 47.619 1.45 0.00 35.03 2.41
7018 10450 2.335712 CCACCAGGAAAAGCCGAGC 61.336 63.158 0.00 0.00 43.43 5.03
7022 10454 2.997315 GGGCCACCAGGAAAAGCC 60.997 66.667 4.39 0.00 43.09 4.35
7096 10528 2.090324 TCTCATGGATGGTCAGGATCCT 60.090 50.000 9.02 9.02 40.26 3.24
7104 10536 5.541845 TCGTGAATAATCTCATGGATGGTC 58.458 41.667 0.00 0.00 34.45 4.02
7108 10540 9.376075 GTGAATATCGTGAATAATCTCATGGAT 57.624 33.333 0.00 0.00 33.81 3.41
7138 10570 1.002069 ATGATTGCTTCACTCCCCCA 58.998 50.000 0.00 0.00 37.11 4.96
7164 10597 7.439157 TGAGTGAATAATTGTGAAGTTGAGG 57.561 36.000 0.00 0.00 0.00 3.86
7295 10734 4.072131 AGCATTAGTCAACATTGGTCGTT 58.928 39.130 0.00 0.00 0.00 3.85
7298 10737 5.886960 AGAAGCATTAGTCAACATTGGTC 57.113 39.130 0.00 0.00 0.00 4.02
7314 10753 8.840833 TGTAGTACAATTGTTTCATAGAAGCA 57.159 30.769 17.78 0.62 0.00 3.91
7357 10796 9.244292 ACTAAGTCAGATGTGTCAAGATAACTA 57.756 33.333 0.00 0.00 0.00 2.24
7462 10901 8.693120 ATGATCAAAGCATCATATTGAAGACT 57.307 30.769 0.00 0.00 40.99 3.24


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

AutoCloner maintained by Alex Coulton.