Multiple sequence alignment - TraesCS5A01G011700

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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 TraesCS5A01G011700 chr5A 100.000 3672 0 0 1 3672 7618251 7621922 0.000000e+00 6782.0
1 TraesCS5A01G011700 chr5A 89.100 1422 138 11 1146 2554 7506237 7504820 0.000000e+00 1751.0
2 TraesCS5A01G011700 chr5D 92.383 2258 111 37 779 3004 9470779 9473007 0.000000e+00 3160.0
3 TraesCS5A01G011700 chr5D 88.919 1471 132 20 1098 2554 9387166 9385713 0.000000e+00 1784.0
4 TraesCS5A01G011700 chr5D 93.379 589 36 3 48 634 9468335 9468922 0.000000e+00 869.0
5 TraesCS5A01G011700 chr5D 90.272 257 14 4 3143 3397 9473247 9473494 3.540000e-85 326.0
6 TraesCS5A01G011700 chr5D 89.700 233 16 2 3439 3671 9473494 9473718 1.290000e-74 291.0
7 TraesCS5A01G011700 chr5D 86.228 167 9 5 620 783 9470517 9470672 6.310000e-38 169.0
8 TraesCS5A01G011700 chr5B 92.737 2203 126 21 832 3024 9416771 9418949 0.000000e+00 3151.0
9 TraesCS5A01G011700 chr5B 87.910 1464 140 18 1134 2583 9334414 9332974 0.000000e+00 1688.0
10 TraesCS5A01G011700 chr5B 90.099 505 33 6 3143 3647 9444337 9444824 1.110000e-179 640.0
11 TraesCS5A01G011700 chr5B 89.881 504 30 9 3146 3646 27841705 27842190 2.410000e-176 628.0
12 TraesCS5A01G011700 chr5B 93.820 356 21 1 45 399 9416388 9416743 5.400000e-148 534.0
13 TraesCS5A01G011700 chr5B 92.174 115 4 2 3022 3136 9419052 9419161 1.370000e-34 158.0
14 TraesCS5A01G011700 chr7A 76.003 1371 285 35 1212 2554 4687629 4686275 0.000000e+00 669.0
15 TraesCS5A01G011700 chr7A 97.059 34 0 1 206 239 428812748 428812716 5.120000e-04 56.5
16 TraesCS5A01G011700 chr4A 75.225 1445 314 33 1211 2627 738815419 738816847 0.000000e+00 645.0
17 TraesCS5A01G011700 chr4B 90.258 503 30 7 3146 3646 605685555 605685070 1.110000e-179 640.0
18 TraesCS5A01G011700 chr7D 75.328 1374 291 36 1211 2554 4877377 4878732 1.870000e-172 616.0
19 TraesCS5A01G011700 chr3D 90.766 444 26 5 3205 3646 548516961 548517391 2.460000e-161 579.0
20 TraesCS5A01G011700 chr7B 78.947 133 25 3 1698 1828 140163970 140164101 1.820000e-13 87.9


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 TraesCS5A01G011700 chr5A 7618251 7621922 3671 False 6782 6782 100.000000 1 3672 1 chr5A.!!$F1 3671
1 TraesCS5A01G011700 chr5A 7504820 7506237 1417 True 1751 1751 89.100000 1146 2554 1 chr5A.!!$R1 1408
2 TraesCS5A01G011700 chr5D 9385713 9387166 1453 True 1784 1784 88.919000 1098 2554 1 chr5D.!!$R1 1456
3 TraesCS5A01G011700 chr5D 9468335 9473718 5383 False 963 3160 90.392400 48 3671 5 chr5D.!!$F1 3623
4 TraesCS5A01G011700 chr5B 9332974 9334414 1440 True 1688 1688 87.910000 1134 2583 1 chr5B.!!$R1 1449
5 TraesCS5A01G011700 chr5B 9416388 9419161 2773 False 1281 3151 92.910333 45 3136 3 chr5B.!!$F3 3091
6 TraesCS5A01G011700 chr7A 4686275 4687629 1354 True 669 669 76.003000 1212 2554 1 chr7A.!!$R1 1342
7 TraesCS5A01G011700 chr4A 738815419 738816847 1428 False 645 645 75.225000 1211 2627 1 chr4A.!!$F1 1416
8 TraesCS5A01G011700 chr7D 4877377 4878732 1355 False 616 616 75.328000 1211 2554 1 chr7D.!!$F1 1343

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
815 2541 0.254178 GTGGGTCATGTCTGCCAGAT 59.746 55.0 0.0 0.0 0.0 2.90 F
1373 3148 0.256752 CATCATGAAGCTCACCCCCA 59.743 55.0 0.0 0.0 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2230 4026 0.108186 TCTGCGCGTCCATGATCTTT 60.108 50.0 8.43 0.0 0.00 2.52 R
2712 4529 0.441533 GCAATGCGATGCGAGGATAG 59.558 55.0 0.00 0.0 36.45 2.08 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
24 25 6.960468 ACATGTGACAGTACATAGTATCTCG 58.040 40.000 0.00 0.00 39.17 4.04
25 26 6.542735 ACATGTGACAGTACATAGTATCTCGT 59.457 38.462 0.00 0.00 39.17 4.18
26 27 6.997239 TGTGACAGTACATAGTATCTCGTT 57.003 37.500 0.00 0.00 0.00 3.85
27 28 7.387119 TGTGACAGTACATAGTATCTCGTTT 57.613 36.000 0.00 0.00 0.00 3.60
28 29 7.823665 TGTGACAGTACATAGTATCTCGTTTT 58.176 34.615 0.00 0.00 0.00 2.43
29 30 8.301720 TGTGACAGTACATAGTATCTCGTTTTT 58.698 33.333 0.00 0.00 0.00 1.94
117 118 2.993937 TCATGCATGCATTCACTCTCA 58.006 42.857 30.32 0.00 33.90 3.27
206 207 9.796120 GTATTGCATAATGTTTTGTTAGGCTTA 57.204 29.630 0.00 0.00 39.02 3.09
279 280 3.003482 CCGTACCGAAACCAACAAATTCA 59.997 43.478 0.00 0.00 0.00 2.57
287 288 7.148490 ACCGAAACCAACAAATTCAAAAAGAAG 60.148 33.333 0.00 0.00 40.15 2.85
430 432 9.405587 GTCCAATTCGAAGATTCATTTTAAACA 57.594 29.630 3.35 0.00 35.04 2.83
462 464 6.786967 TGAAGTAATTCAGTCTACCTACCC 57.213 41.667 0.56 0.00 0.00 3.69
474 476 8.679725 TCAGTCTACCTACCCTGAATATTCTAT 58.320 37.037 16.24 2.50 31.36 1.98
488 490 8.347004 TGAATATTCTATGAAAGGTTGTGCAA 57.653 30.769 16.24 0.00 0.00 4.08
497 499 1.130777 AGGTTGTGCAAATTTGGCCT 58.869 45.000 19.47 2.38 0.00 5.19
499 501 0.587768 GTTGTGCAAATTTGGCCTGC 59.412 50.000 19.47 5.48 36.60 4.85
501 503 1.071128 GTGCAAATTTGGCCTGCCA 59.929 52.632 19.47 6.80 45.63 4.92
505 507 1.469703 GCAAATTTGGCCTGCCATTTC 59.530 47.619 19.47 0.00 46.64 2.17
568 570 1.336755 TGCGCAAACCTTCTTTCCTTC 59.663 47.619 8.16 0.00 0.00 3.46
591 594 6.133356 TCTTACAGGAACCCAAACTTCAAAT 58.867 36.000 0.00 0.00 0.00 2.32
614 617 2.870175 TCCAGCAAAATTTCTCCGGAA 58.130 42.857 5.23 0.00 0.00 4.30
618 621 4.418392 CAGCAAAATTTCTCCGGAATGAG 58.582 43.478 5.23 0.00 0.00 2.90
627 2239 3.380393 TCTCCGGAATGAGGGTAATTCA 58.620 45.455 5.23 0.00 36.03 2.57
628 2240 3.778075 TCTCCGGAATGAGGGTAATTCAA 59.222 43.478 5.23 0.00 36.03 2.69
777 2392 2.015736 AAATGAGCTGAGCCACTACG 57.984 50.000 0.00 0.00 0.00 3.51
815 2541 0.254178 GTGGGTCATGTCTGCCAGAT 59.746 55.000 0.00 0.00 0.00 2.90
852 2595 6.798427 ATGGATGAAGAAGCTGTCTACTAA 57.202 37.500 0.00 0.00 34.56 2.24
880 2623 5.684704 ACACATAGATATCTTGGTGTTGGG 58.315 41.667 24.95 12.84 38.19 4.12
926 2669 4.366586 CTGCCTATCTATCACACACACAG 58.633 47.826 0.00 0.00 0.00 3.66
966 2713 6.480763 TCTCTCTGTCTGTCTCAATCTACTT 58.519 40.000 0.00 0.00 0.00 2.24
1014 2764 2.048023 CACCATGGCGCTGTTCCAT 61.048 57.895 13.04 0.00 44.70 3.41
1023 2773 1.674611 CGCTGTTCCATGACGACGAC 61.675 60.000 0.00 0.00 0.00 4.34
1076 2826 5.957842 GCTAGCTAGCTTAATCTGAGAGA 57.042 43.478 33.71 0.00 45.62 3.10
1077 2827 6.515272 GCTAGCTAGCTTAATCTGAGAGAT 57.485 41.667 33.71 0.00 45.62 2.75
1078 2828 6.555315 GCTAGCTAGCTTAATCTGAGAGATC 58.445 44.000 33.71 3.16 45.62 2.75
1081 2831 4.526262 GCTAGCTTAATCTGAGAGATCCCA 59.474 45.833 7.70 0.00 32.89 4.37
1096 2850 7.987458 TGAGAGATCCCAATGTAACTAATTCAC 59.013 37.037 0.00 0.00 0.00 3.18
1107 2861 6.548321 TGTAACTAATTCACCAAGGGAATGT 58.452 36.000 0.00 0.00 35.28 2.71
1115 2869 3.117474 TCACCAAGGGAATGTGGTTGTTA 60.117 43.478 0.00 0.00 46.17 2.41
1172 2935 2.043652 GGCTGGTGACCATGGCAT 60.044 61.111 13.04 0.00 30.82 4.40
1182 2945 2.709883 CCATGGCATTTCCGGCGTT 61.710 57.895 6.01 0.00 37.80 4.84
1299 3062 2.879462 GGCGGTGCTCGACGTTAG 60.879 66.667 4.33 0.00 42.43 2.34
1300 3063 2.126580 GCGGTGCTCGACGTTAGT 60.127 61.111 4.33 0.00 42.43 2.24
1301 3064 2.434134 GCGGTGCTCGACGTTAGTG 61.434 63.158 4.33 0.00 42.43 2.74
1302 3065 1.800315 CGGTGCTCGACGTTAGTGG 60.800 63.158 0.00 0.00 42.43 4.00
1303 3066 2.092882 GGTGCTCGACGTTAGTGGC 61.093 63.158 0.00 0.00 0.00 5.01
1304 3067 1.372499 GTGCTCGACGTTAGTGGCA 60.372 57.895 0.00 0.73 0.00 4.92
1305 3068 1.080772 TGCTCGACGTTAGTGGCAG 60.081 57.895 0.00 0.00 0.00 4.85
1306 3069 2.445438 GCTCGACGTTAGTGGCAGC 61.445 63.158 0.00 0.00 0.00 5.25
1307 3070 1.080772 CTCGACGTTAGTGGCAGCA 60.081 57.895 0.00 0.00 0.00 4.41
1345 3120 1.003233 GAGCGTGAAGAAGGCCCTT 60.003 57.895 0.00 0.00 40.67 3.95
1373 3148 0.256752 CATCATGAAGCTCACCCCCA 59.743 55.000 0.00 0.00 0.00 4.96
1483 3258 2.185867 GCCATCGTCAACGGCCTA 59.814 61.111 0.00 0.00 40.07 3.93
1564 3339 2.126071 CGCGTCCACACCGAATCT 60.126 61.111 0.00 0.00 0.00 2.40
2060 3853 4.008933 AGAAGACGCGCCAGCCTT 62.009 61.111 5.73 1.65 41.18 4.35
2183 3979 4.673298 ACGCCAACACGATCGGCA 62.673 61.111 20.98 0.00 46.60 5.69
2270 4066 1.221840 GCGGTGGAGGACATCATGT 59.778 57.895 0.00 0.00 0.00 3.21
2293 4098 1.000283 GATGACGGCGAGAGGATGATT 60.000 52.381 16.62 0.00 0.00 2.57
2497 4302 1.075659 GGAGCAGGCCAAGAGGTTT 59.924 57.895 5.01 0.00 37.19 3.27
2649 4460 1.888436 ATCAAGAAGGTGCTCGCCGA 61.888 55.000 0.00 0.00 0.00 5.54
2690 4501 4.812476 TCAACCGCGCCCTCGATG 62.812 66.667 0.00 0.00 38.10 3.84
2702 4519 1.238439 CCTCGATGGTGCAACACTTT 58.762 50.000 6.58 0.00 39.98 2.66
2705 4522 3.063997 CCTCGATGGTGCAACACTTTATC 59.936 47.826 6.58 0.00 39.98 1.75
2706 4523 3.669536 TCGATGGTGCAACACTTTATCA 58.330 40.909 6.58 0.00 39.98 2.15
2707 4524 4.260985 TCGATGGTGCAACACTTTATCAT 58.739 39.130 6.58 0.00 39.98 2.45
2708 4525 5.423886 TCGATGGTGCAACACTTTATCATA 58.576 37.500 6.58 0.00 39.98 2.15
2709 4526 6.054941 TCGATGGTGCAACACTTTATCATAT 58.945 36.000 6.58 0.00 39.98 1.78
2710 4527 7.213678 TCGATGGTGCAACACTTTATCATATA 58.786 34.615 6.58 0.00 39.98 0.86
2712 4529 8.171196 CGATGGTGCAACACTTTATCATATATC 58.829 37.037 6.58 0.00 39.98 1.63
2810 4627 1.470051 AATCCATGTACCCCGTTTGC 58.530 50.000 0.00 0.00 0.00 3.68
2871 4689 3.242518 TGATACTTTGACGCTTCTCACG 58.757 45.455 0.00 0.00 0.00 4.35
2914 4735 3.930634 AACTAGACCTTAAAGTCGCGT 57.069 42.857 5.77 0.00 41.83 6.01
2917 4738 3.753272 ACTAGACCTTAAAGTCGCGTGTA 59.247 43.478 5.77 0.00 41.83 2.90
2922 4743 0.039256 TTAAAGTCGCGTGTAGCCGT 60.039 50.000 5.77 0.00 44.76 5.68
2933 4754 3.845259 TAGCCGTGCCCGTCCATC 61.845 66.667 0.00 0.00 0.00 3.51
3051 5042 5.580661 TGAATGCATGTATACACACAATGC 58.419 37.500 17.58 17.58 37.54 3.56
3063 5054 9.619316 GTATACACACAATGCTAAATTTGAACA 57.381 29.630 0.00 0.00 0.00 3.18
3128 5119 2.530701 AGTAGCTAGTGTGGCAAGACT 58.469 47.619 0.00 0.00 33.74 3.24
3136 5127 4.307032 AGTGTGGCAAGACTATGGAAAT 57.693 40.909 0.00 0.00 0.00 2.17
3137 5128 5.435686 AGTGTGGCAAGACTATGGAAATA 57.564 39.130 0.00 0.00 0.00 1.40
3138 5129 6.006275 AGTGTGGCAAGACTATGGAAATAT 57.994 37.500 0.00 0.00 0.00 1.28
3139 5130 7.136822 AGTGTGGCAAGACTATGGAAATATA 57.863 36.000 0.00 0.00 0.00 0.86
3140 5131 7.220030 AGTGTGGCAAGACTATGGAAATATAG 58.780 38.462 0.00 0.00 36.83 1.31
3141 5132 6.428159 GTGTGGCAAGACTATGGAAATATAGG 59.572 42.308 0.00 0.00 35.43 2.57
3142 5133 6.101150 TGTGGCAAGACTATGGAAATATAGGT 59.899 38.462 0.00 0.00 35.43 3.08
3143 5134 6.998673 GTGGCAAGACTATGGAAATATAGGTT 59.001 38.462 0.00 0.00 35.43 3.50
3144 5135 6.998074 TGGCAAGACTATGGAAATATAGGTTG 59.002 38.462 0.00 0.00 35.43 3.77
3145 5136 6.998673 GGCAAGACTATGGAAATATAGGTTGT 59.001 38.462 0.00 0.00 35.43 3.32
3170 5161 8.904834 GTTTAGTCTAGACATCTAAGGACATGA 58.095 37.037 24.44 0.00 30.46 3.07
3187 5178 6.763355 GGACATGATCCTTATCACATACTGT 58.237 40.000 0.00 0.00 44.79 3.55
3188 5179 7.896811 GGACATGATCCTTATCACATACTGTA 58.103 38.462 0.00 0.00 44.79 2.74
3189 5180 8.535335 GGACATGATCCTTATCACATACTGTAT 58.465 37.037 0.00 0.00 44.79 2.29
3190 5181 9.579768 GACATGATCCTTATCACATACTGTATC 57.420 37.037 0.00 0.00 44.79 2.24
3191 5182 9.093458 ACATGATCCTTATCACATACTGTATCA 57.907 33.333 0.00 0.00 44.79 2.15
3199 5190 9.404348 CTTATCACATACTGTATCATCACTGAC 57.596 37.037 0.00 0.00 33.22 3.51
3206 5197 9.712359 CATACTGTATCATCACTGACATTTTTG 57.288 33.333 0.00 0.00 33.22 2.44
3262 5253 3.119319 TGGGTGGTGCTGGAAATATAGA 58.881 45.455 0.00 0.00 0.00 1.98
3270 5261 4.991687 GTGCTGGAAATATAGAGGCTACAC 59.008 45.833 0.00 0.00 0.00 2.90
3347 5340 9.468532 GAATCAAAGAAACTTATTTGCAGAACT 57.531 29.630 4.96 0.00 38.77 3.01
3348 5341 8.807667 ATCAAAGAAACTTATTTGCAGAACTG 57.192 30.769 4.96 0.00 38.77 3.16
3372 5365 2.806608 AGCTTGCCAAACTCACAATG 57.193 45.000 0.00 0.00 0.00 2.82
3397 5390 9.134055 TGCATTTCTGAACCATTGATATCAATA 57.866 29.630 26.55 12.77 44.10 1.90
3398 5391 9.970395 GCATTTCTGAACCATTGATATCAATAA 57.030 29.630 26.55 16.52 44.10 1.40
3429 5422 8.810990 AATAGGTAGTACTCTATGGCTACATC 57.189 38.462 0.00 0.00 38.53 3.06
3430 5423 5.247084 AGGTAGTACTCTATGGCTACATCG 58.753 45.833 0.00 0.00 38.53 3.84
3431 5424 4.395542 GGTAGTACTCTATGGCTACATCGG 59.604 50.000 0.00 0.00 38.53 4.18
3432 5425 4.368565 AGTACTCTATGGCTACATCGGA 57.631 45.455 0.00 0.00 38.53 4.55
3433 5426 4.726583 AGTACTCTATGGCTACATCGGAA 58.273 43.478 0.00 0.00 38.53 4.30
3434 5427 5.326069 AGTACTCTATGGCTACATCGGAAT 58.674 41.667 0.00 0.00 38.53 3.01
3435 5428 6.482524 AGTACTCTATGGCTACATCGGAATA 58.517 40.000 0.00 0.00 38.53 1.75
3436 5429 7.120051 AGTACTCTATGGCTACATCGGAATAT 58.880 38.462 0.00 0.00 38.53 1.28
3437 5430 6.214191 ACTCTATGGCTACATCGGAATATG 57.786 41.667 0.00 0.00 38.53 1.78
3438 5431 5.717178 ACTCTATGGCTACATCGGAATATGT 59.283 40.000 0.00 0.00 42.62 2.29
3439 5432 6.211584 ACTCTATGGCTACATCGGAATATGTT 59.788 38.462 0.00 0.00 40.52 2.71
3440 5433 6.398095 TCTATGGCTACATCGGAATATGTTG 58.602 40.000 0.00 0.00 40.52 3.33
3441 5434 4.681074 TGGCTACATCGGAATATGTTGA 57.319 40.909 0.00 0.00 40.52 3.18
3442 5435 5.029807 TGGCTACATCGGAATATGTTGAA 57.970 39.130 0.00 0.00 40.52 2.69
3524 5517 2.099098 GACCAATTACATGGGAAAGGCG 59.901 50.000 0.00 0.00 45.18 5.52
3525 5518 1.408702 CCAATTACATGGGAAAGGCGG 59.591 52.381 0.00 0.00 36.79 6.13
3526 5519 2.374184 CAATTACATGGGAAAGGCGGA 58.626 47.619 0.00 0.00 0.00 5.54
3527 5520 2.958355 CAATTACATGGGAAAGGCGGAT 59.042 45.455 0.00 0.00 0.00 4.18
3528 5521 2.341846 TTACATGGGAAAGGCGGATC 57.658 50.000 0.00 0.00 0.00 3.36
3529 5522 0.472471 TACATGGGAAAGGCGGATCC 59.528 55.000 0.00 0.00 34.85 3.36
3530 5523 1.893808 CATGGGAAAGGCGGATCCG 60.894 63.158 30.03 30.03 40.77 4.18
3549 5542 6.389500 ATCCGCGGATGGATAAATCACCAT 62.390 45.833 38.62 10.61 46.95 3.55
3551 5544 3.370978 CGCGGATGGATAAATCACCATAC 59.629 47.826 0.00 0.00 45.41 2.39
3559 5552 8.682936 ATGGATAAATCACCATACAGAAAGAC 57.317 34.615 0.00 0.00 43.89 3.01
3561 5554 6.202954 GGATAAATCACCATACAGAAAGACGG 59.797 42.308 0.00 0.00 0.00 4.79
3637 5630 8.862325 TTCCTTAATTAGAGAGAATTTGCACA 57.138 30.769 0.00 0.00 31.51 4.57
3671 5664 5.008613 CCAGAAAATTTCTTGTCTCGTCCAA 59.991 40.000 5.36 0.00 38.11 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.542735 ACGAGATACTATGTACTGTCACATGT 59.457 38.462 0.00 0.00 39.46 3.21
1 2 6.960468 ACGAGATACTATGTACTGTCACATG 58.040 40.000 10.92 0.00 39.46 3.21
2 3 7.569639 AACGAGATACTATGTACTGTCACAT 57.430 36.000 0.00 7.63 41.88 3.21
3 4 6.997239 AACGAGATACTATGTACTGTCACA 57.003 37.500 0.00 0.00 0.00 3.58
4 5 8.684973 AAAAACGAGATACTATGTACTGTCAC 57.315 34.615 0.00 0.00 0.00 3.67
26 27 4.739587 AGTTACCCCGCAAAAAGAAAAA 57.260 36.364 0.00 0.00 0.00 1.94
27 28 5.771165 AGATAGTTACCCCGCAAAAAGAAAA 59.229 36.000 0.00 0.00 0.00 2.29
28 29 5.318630 AGATAGTTACCCCGCAAAAAGAAA 58.681 37.500 0.00 0.00 0.00 2.52
29 30 4.913784 AGATAGTTACCCCGCAAAAAGAA 58.086 39.130 0.00 0.00 0.00 2.52
30 31 4.510571 GAGATAGTTACCCCGCAAAAAGA 58.489 43.478 0.00 0.00 0.00 2.52
31 32 3.308866 CGAGATAGTTACCCCGCAAAAAG 59.691 47.826 0.00 0.00 0.00 2.27
32 33 3.264104 CGAGATAGTTACCCCGCAAAAA 58.736 45.455 0.00 0.00 0.00 1.94
33 34 2.234414 ACGAGATAGTTACCCCGCAAAA 59.766 45.455 0.00 0.00 0.00 2.44
34 35 1.826720 ACGAGATAGTTACCCCGCAAA 59.173 47.619 0.00 0.00 0.00 3.68
35 36 1.477553 ACGAGATAGTTACCCCGCAA 58.522 50.000 0.00 0.00 0.00 4.85
36 37 1.477553 AACGAGATAGTTACCCCGCA 58.522 50.000 0.00 0.00 31.74 5.69
37 38 2.620585 ACTAACGAGATAGTTACCCCGC 59.379 50.000 0.00 0.00 32.18 6.13
38 39 4.096984 ACAACTAACGAGATAGTTACCCCG 59.903 45.833 10.90 0.00 42.68 5.73
39 40 5.588958 ACAACTAACGAGATAGTTACCCC 57.411 43.478 10.90 0.00 42.68 4.95
40 41 5.809051 CCAACAACTAACGAGATAGTTACCC 59.191 44.000 10.90 0.00 42.68 3.69
41 42 6.624423 TCCAACAACTAACGAGATAGTTACC 58.376 40.000 10.90 0.00 42.68 2.85
42 43 7.533426 TCTCCAACAACTAACGAGATAGTTAC 58.467 38.462 10.90 0.00 42.68 2.50
43 44 7.692460 TCTCCAACAACTAACGAGATAGTTA 57.308 36.000 10.90 0.00 42.68 2.24
46 47 7.759886 TCATTTCTCCAACAACTAACGAGATAG 59.240 37.037 0.00 0.00 30.10 2.08
95 96 3.315191 TGAGAGTGAATGCATGCATGATG 59.685 43.478 32.79 6.09 36.68 3.07
117 118 2.476619 CACGAATCTCAAAGCAACGACT 59.523 45.455 0.00 0.00 0.00 4.18
364 366 7.623278 ACTTGTCCCAATTAATATCCAAATGGT 59.377 33.333 0.00 0.00 36.34 3.55
435 437 9.099454 GGTAGGTAGACTGAATTACTTCAATTG 57.901 37.037 0.00 0.00 40.78 2.32
462 464 7.988737 TGCACAACCTTTCATAGAATATTCAG 58.011 34.615 17.56 7.15 0.00 3.02
474 476 2.941720 GCCAAATTTGCACAACCTTTCA 59.058 40.909 12.92 0.00 0.00 2.69
497 499 3.037549 AGGTCCAAACTTTGAAATGGCA 58.962 40.909 2.87 0.00 32.87 4.92
499 501 6.816136 ACTTTAGGTCCAAACTTTGAAATGG 58.184 36.000 2.87 0.00 0.00 3.16
501 503 7.283807 ACGTACTTTAGGTCCAAACTTTGAAAT 59.716 33.333 2.87 0.00 0.00 2.17
505 507 5.996669 ACGTACTTTAGGTCCAAACTTTG 57.003 39.130 0.00 0.00 0.00 2.77
551 553 5.278512 CCTGTAAGAAGGAAAGAAGGTTTGC 60.279 44.000 0.00 0.00 40.02 3.68
568 570 5.845391 TTTGAAGTTTGGGTTCCTGTAAG 57.155 39.130 0.00 0.00 0.00 2.34
591 594 2.819608 CCGGAGAAATTTTGCTGGAAGA 59.180 45.455 0.00 0.00 34.07 2.87
706 2321 0.756294 TGGCTCACCGAGTTCTTCAA 59.244 50.000 0.00 0.00 39.70 2.69
707 2322 0.318441 CTGGCTCACCGAGTTCTTCA 59.682 55.000 0.00 0.00 39.70 3.02
708 2323 1.016653 GCTGGCTCACCGAGTTCTTC 61.017 60.000 0.00 0.00 39.70 2.87
709 2324 1.004440 GCTGGCTCACCGAGTTCTT 60.004 57.895 0.00 0.00 39.70 2.52
710 2325 1.882989 GAGCTGGCTCACCGAGTTCT 61.883 60.000 16.55 0.00 42.31 3.01
711 2326 1.446966 GAGCTGGCTCACCGAGTTC 60.447 63.158 16.55 0.00 42.31 3.01
712 2327 2.659610 GAGCTGGCTCACCGAGTT 59.340 61.111 16.55 0.00 42.31 3.01
713 2328 3.753434 CGAGCTGGCTCACCGAGT 61.753 66.667 20.39 0.00 42.86 4.18
746 2361 2.421073 CAGCTCATTTTCGGCTTGATGA 59.579 45.455 0.00 0.00 33.74 2.92
747 2362 2.421073 TCAGCTCATTTTCGGCTTGATG 59.579 45.455 0.00 0.00 33.74 3.07
748 2363 2.681848 CTCAGCTCATTTTCGGCTTGAT 59.318 45.455 0.00 0.00 33.74 2.57
760 2375 1.407936 ATCGTAGTGGCTCAGCTCAT 58.592 50.000 0.00 0.00 0.00 2.90
777 2392 0.877071 CATGACCGGCATTGGCTATC 59.123 55.000 0.00 6.19 40.87 2.08
873 2616 6.295688 CCTCCCTATATATACACACCCAACAC 60.296 46.154 0.00 0.00 0.00 3.32
926 2669 3.381272 AGAGAGAGCAGCTTCTGTATGTC 59.619 47.826 10.70 0.00 33.43 3.06
966 2713 0.749049 TCGGTCGATCGAGTAGAGGA 59.251 55.000 18.48 6.81 34.82 3.71
1014 2764 0.387929 AAGAAGGCTTGTCGTCGTCA 59.612 50.000 3.46 0.00 31.83 4.35
1023 2773 4.260948 GCATTATTCGGAGAAGAAGGCTTG 60.261 45.833 16.14 2.95 45.90 4.01
1069 2819 8.206867 TGAATTAGTTACATTGGGATCTCTCAG 58.793 37.037 0.00 0.00 0.00 3.35
1070 2820 7.987458 GTGAATTAGTTACATTGGGATCTCTCA 59.013 37.037 0.00 0.00 0.00 3.27
1073 2823 7.054124 TGGTGAATTAGTTACATTGGGATCTC 58.946 38.462 0.00 0.00 0.00 2.75
1075 2825 7.201821 CCTTGGTGAATTAGTTACATTGGGATC 60.202 40.741 0.00 0.00 0.00 3.36
1076 2826 6.607198 CCTTGGTGAATTAGTTACATTGGGAT 59.393 38.462 0.00 0.00 0.00 3.85
1077 2827 5.949354 CCTTGGTGAATTAGTTACATTGGGA 59.051 40.000 0.00 0.00 0.00 4.37
1078 2828 5.127031 CCCTTGGTGAATTAGTTACATTGGG 59.873 44.000 0.00 0.00 0.00 4.12
1081 2831 7.673926 ACATTCCCTTGGTGAATTAGTTACATT 59.326 33.333 0.00 0.00 30.16 2.71
1096 2850 4.322650 CCATTAACAACCACATTCCCTTGG 60.323 45.833 0.00 0.00 39.00 3.61
1107 2861 7.293828 TGCATATAATCCTCCATTAACAACCA 58.706 34.615 0.00 0.00 30.39 3.67
1115 2869 5.909621 GCACATGCATATAATCCTCCATT 57.090 39.130 0.00 0.00 41.59 3.16
1141 2904 0.677731 CCAGCCCATCTTTGCTCGAA 60.678 55.000 0.00 0.00 35.12 3.71
1142 2905 1.078214 CCAGCCCATCTTTGCTCGA 60.078 57.895 0.00 0.00 35.12 4.04
1143 2906 1.377725 ACCAGCCCATCTTTGCTCG 60.378 57.895 0.00 0.00 35.12 5.03
1172 2935 2.668212 CCTGCTGAACGCCGGAAA 60.668 61.111 5.05 0.00 45.00 3.13
1182 2945 0.329261 CCCCACATCTTTCCTGCTGA 59.671 55.000 0.00 0.00 0.00 4.26
1291 3054 0.735978 TCATGCTGCCACTAACGTCG 60.736 55.000 0.00 0.00 0.00 5.12
1296 3059 1.450134 CCGCTCATGCTGCCACTAA 60.450 57.895 0.00 0.00 36.97 2.24
1297 3060 2.187685 CCGCTCATGCTGCCACTA 59.812 61.111 0.00 0.00 36.97 2.74
1298 3061 4.790962 CCCGCTCATGCTGCCACT 62.791 66.667 0.00 0.00 36.97 4.00
1302 3065 4.783621 TGTCCCCGCTCATGCTGC 62.784 66.667 0.00 0.00 36.97 5.25
1303 3066 2.046023 TTGTCCCCGCTCATGCTG 60.046 61.111 0.00 0.00 36.97 4.41
1304 3067 1.630126 ATCTTGTCCCCGCTCATGCT 61.630 55.000 0.00 0.00 36.97 3.79
1305 3068 1.153086 ATCTTGTCCCCGCTCATGC 60.153 57.895 0.00 0.00 0.00 4.06
1306 3069 0.877649 CGATCTTGTCCCCGCTCATG 60.878 60.000 0.00 0.00 0.00 3.07
1307 3070 1.043116 TCGATCTTGTCCCCGCTCAT 61.043 55.000 0.00 0.00 0.00 2.90
1345 3120 3.056607 TGAGCTTCATGATGACGAACTGA 60.057 43.478 12.54 0.00 0.00 3.41
1564 3339 1.002624 GAAGATGTTGGGGGTGCGA 60.003 57.895 0.00 0.00 0.00 5.10
1896 3683 1.817099 GTGATGAGGCCGCTCTTGG 60.817 63.158 8.34 0.00 0.00 3.61
2230 4026 0.108186 TCTGCGCGTCCATGATCTTT 60.108 50.000 8.43 0.00 0.00 2.52
2270 4066 1.043116 ATCCTCTCGCCGTCATCCAA 61.043 55.000 0.00 0.00 0.00 3.53
2497 4302 1.000486 CTCCTCCGGGTTCTCCTCA 60.000 63.158 0.00 0.00 0.00 3.86
2672 4483 4.514577 ATCGAGGGCGCGGTTGAG 62.515 66.667 8.83 0.00 37.46 3.02
2673 4484 4.812476 CATCGAGGGCGCGGTTGA 62.812 66.667 8.83 0.00 37.46 3.18
2683 4494 1.238439 AAAGTGTTGCACCATCGAGG 58.762 50.000 0.00 0.00 45.67 4.63
2702 4519 6.655003 TGCGATGCGAGGATAGATATATGATA 59.345 38.462 0.00 0.00 0.00 2.15
2705 4522 5.113502 TGCGATGCGAGGATAGATATATG 57.886 43.478 0.00 0.00 0.00 1.78
2706 4523 5.973899 ATGCGATGCGAGGATAGATATAT 57.026 39.130 0.00 0.00 0.00 0.86
2707 4524 5.523369 CAATGCGATGCGAGGATAGATATA 58.477 41.667 0.00 0.00 0.00 0.86
2708 4525 4.366586 CAATGCGATGCGAGGATAGATAT 58.633 43.478 0.00 0.00 0.00 1.63
2709 4526 3.774066 CAATGCGATGCGAGGATAGATA 58.226 45.455 0.00 0.00 0.00 1.98
2710 4527 2.614779 CAATGCGATGCGAGGATAGAT 58.385 47.619 0.00 0.00 0.00 1.98
2712 4529 0.441533 GCAATGCGATGCGAGGATAG 59.558 55.000 0.00 0.00 36.45 2.08
2871 4689 8.811994 AGTTTAAGAATAGAGGATAGAGGATGC 58.188 37.037 0.00 0.00 0.00 3.91
2997 4819 8.766994 ACAATGTAAAGCCACCTGATTAATAT 57.233 30.769 0.00 0.00 0.00 1.28
3002 4824 6.245408 TCTTACAATGTAAAGCCACCTGATT 58.755 36.000 7.30 0.00 0.00 2.57
3008 4830 7.009540 GCATTCATTCTTACAATGTAAAGCCAC 59.990 37.037 7.30 0.00 31.29 5.01
3063 5054 4.978099 CATACTATGCTCCCCATTGAACT 58.022 43.478 0.00 0.00 35.34 3.01
3112 5103 2.168521 TCCATAGTCTTGCCACACTAGC 59.831 50.000 0.00 0.00 0.00 3.42
3113 5104 4.471904 TTCCATAGTCTTGCCACACTAG 57.528 45.455 0.00 0.00 0.00 2.57
3114 5105 4.901197 TTTCCATAGTCTTGCCACACTA 57.099 40.909 0.00 0.00 0.00 2.74
3115 5106 3.788227 TTTCCATAGTCTTGCCACACT 57.212 42.857 0.00 0.00 0.00 3.55
3138 5129 9.186837 CCTTAGATGTCTAGACTAAACAACCTA 57.813 37.037 23.01 9.67 0.00 3.08
3139 5130 7.894364 TCCTTAGATGTCTAGACTAAACAACCT 59.106 37.037 23.01 10.48 0.00 3.50
3140 5131 7.975058 GTCCTTAGATGTCTAGACTAAACAACC 59.025 40.741 23.01 4.38 0.00 3.77
3141 5132 8.521176 TGTCCTTAGATGTCTAGACTAAACAAC 58.479 37.037 23.01 12.01 29.86 3.32
3142 5133 8.645814 TGTCCTTAGATGTCTAGACTAAACAA 57.354 34.615 23.01 10.01 29.86 2.83
3143 5134 8.687242 CATGTCCTTAGATGTCTAGACTAAACA 58.313 37.037 23.01 14.57 29.86 2.83
3144 5135 8.904834 TCATGTCCTTAGATGTCTAGACTAAAC 58.095 37.037 23.01 10.22 29.86 2.01
3145 5136 9.647918 ATCATGTCCTTAGATGTCTAGACTAAA 57.352 33.333 23.01 10.91 29.86 1.85
3180 5171 9.712359 CAAAAATGTCAGTGATGATACAGTATG 57.288 33.333 0.00 0.00 46.00 2.39
3184 5175 6.405065 CCCCAAAAATGTCAGTGATGATACAG 60.405 42.308 0.00 0.00 0.00 2.74
3185 5176 5.418524 CCCCAAAAATGTCAGTGATGATACA 59.581 40.000 0.00 0.00 0.00 2.29
3186 5177 5.652014 TCCCCAAAAATGTCAGTGATGATAC 59.348 40.000 0.00 0.00 0.00 2.24
3187 5178 5.825532 TCCCCAAAAATGTCAGTGATGATA 58.174 37.500 0.00 0.00 0.00 2.15
3188 5179 4.676109 TCCCCAAAAATGTCAGTGATGAT 58.324 39.130 0.00 0.00 0.00 2.45
3189 5180 4.081406 CTCCCCAAAAATGTCAGTGATGA 58.919 43.478 0.00 0.00 0.00 2.92
3190 5181 3.194116 CCTCCCCAAAAATGTCAGTGATG 59.806 47.826 0.00 0.00 0.00 3.07
3191 5182 3.434309 CCTCCCCAAAAATGTCAGTGAT 58.566 45.455 0.00 0.00 0.00 3.06
3199 5190 5.955355 TGTAACTATTCCCTCCCCAAAAATG 59.045 40.000 0.00 0.00 0.00 2.32
3206 5197 4.658901 TCATCTTGTAACTATTCCCTCCCC 59.341 45.833 0.00 0.00 0.00 4.81
3262 5253 6.070194 ACTCAACTATTATTGTGGTGTAGCCT 60.070 38.462 0.00 0.00 38.35 4.58
3270 5261 9.436957 AGTTCAAGTACTCAACTATTATTGTGG 57.563 33.333 15.39 0.00 37.50 4.17
3333 5326 3.065925 GCTAGCCCAGTTCTGCAAATAAG 59.934 47.826 2.29 0.00 0.00 1.73
3341 5334 2.475666 GCAAGCTAGCCCAGTTCTG 58.524 57.895 12.13 0.00 0.00 3.02
3366 5359 5.231702 TCAATGGTTCAGAAATGCATTGTG 58.768 37.500 13.82 13.65 33.71 3.33
3367 5360 5.471556 TCAATGGTTCAGAAATGCATTGT 57.528 34.783 13.82 3.19 32.39 2.71
3368 5361 7.923878 TGATATCAATGGTTCAGAAATGCATTG 59.076 33.333 13.82 0.96 0.00 2.82
3372 5365 9.970395 TTATTGATATCAATGGTTCAGAAATGC 57.030 29.630 32.15 0.00 45.34 3.56
3403 5396 9.245481 GATGTAGCCATAGAGTACTACCTATTT 57.755 37.037 0.00 0.00 35.25 1.40
3404 5397 7.553402 CGATGTAGCCATAGAGTACTACCTATT 59.447 40.741 0.00 0.00 35.25 1.73
3405 5398 7.049133 CGATGTAGCCATAGAGTACTACCTAT 58.951 42.308 0.00 0.00 35.25 2.57
3406 5399 6.404708 CGATGTAGCCATAGAGTACTACCTA 58.595 44.000 0.00 0.00 35.25 3.08
3407 5400 5.247084 CGATGTAGCCATAGAGTACTACCT 58.753 45.833 0.00 0.00 35.25 3.08
3408 5401 4.395542 CCGATGTAGCCATAGAGTACTACC 59.604 50.000 0.00 0.00 35.25 3.18
3409 5402 5.243981 TCCGATGTAGCCATAGAGTACTAC 58.756 45.833 0.00 0.00 36.40 2.73
3410 5403 5.494390 TCCGATGTAGCCATAGAGTACTA 57.506 43.478 0.00 0.00 0.00 1.82
3411 5404 4.368565 TCCGATGTAGCCATAGAGTACT 57.631 45.455 0.00 0.00 0.00 2.73
3412 5405 5.646577 ATTCCGATGTAGCCATAGAGTAC 57.353 43.478 0.00 0.00 0.00 2.73
3413 5406 6.890268 ACATATTCCGATGTAGCCATAGAGTA 59.110 38.462 0.00 0.00 38.29 2.59
3414 5407 5.717178 ACATATTCCGATGTAGCCATAGAGT 59.283 40.000 0.00 0.00 38.29 3.24
3415 5408 6.214191 ACATATTCCGATGTAGCCATAGAG 57.786 41.667 0.00 0.00 38.29 2.43
3416 5409 6.210584 TCAACATATTCCGATGTAGCCATAGA 59.789 38.462 0.00 0.00 39.16 1.98
3417 5410 6.398095 TCAACATATTCCGATGTAGCCATAG 58.602 40.000 0.00 0.00 39.16 2.23
3418 5411 6.353404 TCAACATATTCCGATGTAGCCATA 57.647 37.500 0.00 0.00 39.16 2.74
3419 5412 5.227569 TCAACATATTCCGATGTAGCCAT 57.772 39.130 0.00 0.00 39.16 4.40
3420 5413 4.681074 TCAACATATTCCGATGTAGCCA 57.319 40.909 0.00 0.00 39.16 4.75
3421 5414 4.213482 GGTTCAACATATTCCGATGTAGCC 59.787 45.833 0.00 0.00 39.16 3.93
3422 5415 5.057149 AGGTTCAACATATTCCGATGTAGC 58.943 41.667 0.00 0.00 39.16 3.58
3423 5416 9.923143 TTATAGGTTCAACATATTCCGATGTAG 57.077 33.333 0.00 0.00 39.16 2.74
3425 5418 9.793259 AATTATAGGTTCAACATATTCCGATGT 57.207 29.630 0.00 0.00 41.92 3.06
3459 5452 5.927689 TGCTCATCAGGCATGTTTTAAAAAG 59.072 36.000 1.31 0.00 34.56 2.27
3466 5459 1.180029 GGTGCTCATCAGGCATGTTT 58.820 50.000 0.00 0.00 41.86 2.83
3495 5488 2.677836 CCATGTAATTGGTCCGTGACTG 59.322 50.000 4.41 0.00 32.47 3.51
3496 5489 2.355716 CCCATGTAATTGGTCCGTGACT 60.356 50.000 4.41 0.00 34.77 3.41
3524 5517 2.280628 GATTTATCCATCCGCGGATCC 58.719 52.381 37.10 14.49 42.36 3.36
3525 5518 2.673368 GTGATTTATCCATCCGCGGATC 59.327 50.000 37.10 24.07 42.36 3.36
3527 5520 1.270625 GGTGATTTATCCATCCGCGGA 60.271 52.381 33.12 33.12 40.07 5.54
3528 5521 1.156736 GGTGATTTATCCATCCGCGG 58.843 55.000 22.12 22.12 0.00 6.46
3529 5522 1.877637 TGGTGATTTATCCATCCGCG 58.122 50.000 0.00 0.00 0.00 6.46
3530 5523 4.323417 TGTATGGTGATTTATCCATCCGC 58.677 43.478 0.00 0.00 42.56 5.54
3531 5524 5.793817 TCTGTATGGTGATTTATCCATCCG 58.206 41.667 0.00 0.00 42.56 4.18
3532 5525 7.939039 TCTTTCTGTATGGTGATTTATCCATCC 59.061 37.037 0.00 0.00 42.56 3.51
3537 5530 6.292919 GCCGTCTTTCTGTATGGTGATTTATC 60.293 42.308 0.00 0.00 0.00 1.75
3549 5542 2.080286 GCTCTTGCCGTCTTTCTGTA 57.920 50.000 0.00 0.00 0.00 2.74
3561 5554 1.136147 CATGCACGAAGGCTCTTGC 59.864 57.895 7.74 7.74 44.89 4.01
3572 5565 8.711457 TCTAATGTTGTGATTATATCATGCACG 58.289 33.333 0.00 0.00 42.04 5.34
3646 5639 4.515567 GGACGAGACAAGAAATTTTCTGGT 59.484 41.667 17.29 17.29 46.51 4.00
3647 5640 4.515191 TGGACGAGACAAGAAATTTTCTGG 59.485 41.667 12.27 11.76 40.59 3.86


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

AutoCloner maintained by Alex Coulton.