Multiple sequence alignment - TraesCS1B01G336700

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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 TraesCS1B01G336700 chr1B 100.000 4530 0 0 1 4530 563672418 563676947 0.000000e+00 8366.0
1 TraesCS1B01G336700 chr1D 95.438 3398 146 7 583 3972 416841491 416844887 0.000000e+00 5408.0
2 TraesCS1B01G336700 chr1D 88.966 580 46 9 3968 4530 416845224 416845802 0.000000e+00 701.0
3 TraesCS1B01G336700 chr1D 85.837 233 19 5 1 233 416801588 416801806 7.580000e-58 235.0
4 TraesCS1B01G336700 chr1A 94.890 3405 158 8 583 3972 514135385 514138788 0.000000e+00 5310.0
5 TraesCS1B01G336700 chr1A 90.521 422 33 5 3968 4384 514139142 514139561 6.620000e-153 551.0
6 TraesCS1B01G336700 chr1A 90.054 372 28 4 234 596 514135000 514135371 1.470000e-129 473.0
7 TraesCS1B01G336700 chr1A 84.615 234 24 5 1 234 514132342 514132563 5.900000e-54 222.0
8 TraesCS1B01G336700 chr1A 85.542 166 7 7 4380 4530 514140138 514140301 1.690000e-34 158.0
9 TraesCS1B01G336700 chr7B 77.695 2681 511 70 984 3619 750437747 750440385 0.000000e+00 1557.0
10 TraesCS1B01G336700 chr7B 77.433 2641 507 62 1031 3619 750172393 750174996 0.000000e+00 1493.0
11 TraesCS1B01G336700 chr7B 81.865 1555 270 10 1031 2579 750246470 750248018 0.000000e+00 1299.0
12 TraesCS1B01G336700 chr7B 76.996 526 116 4 1031 1556 750578426 750578946 3.430000e-76 296.0
13 TraesCS1B01G336700 chr7A 76.736 2635 523 59 1034 3619 733063363 733060770 0.000000e+00 1387.0
14 TraesCS1B01G336700 chr7A 81.314 1552 277 9 1037 2583 732936375 732934832 0.000000e+00 1247.0
15 TraesCS1B01G336700 chr7A 75.859 1951 391 59 1715 3619 732922568 732920652 0.000000e+00 920.0
16 TraesCS1B01G336700 chr7A 77.334 1553 334 15 1029 2572 733274094 733275637 0.000000e+00 902.0
17 TraesCS1B01G336700 chr7A 76.732 765 162 12 1029 1791 732923314 732922564 3.260000e-111 412.0
18 TraesCS1B01G336700 chr2A 79.200 1625 305 26 974 2583 77335676 77337282 0.000000e+00 1098.0
19 TraesCS1B01G336700 chr6B 97.436 39 1 0 338 376 646278088 646278126 2.920000e-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 TraesCS1B01G336700 chr1B 563672418 563676947 4529 False 8366.0 8366 100.0000 1 4530 1 chr1B.!!$F1 4529
1 TraesCS1B01G336700 chr1D 416841491 416845802 4311 False 3054.5 5408 92.2020 583 4530 2 chr1D.!!$F2 3947
2 TraesCS1B01G336700 chr1A 514132342 514140301 7959 False 1342.8 5310 89.1244 1 4530 5 chr1A.!!$F1 4529
3 TraesCS1B01G336700 chr7B 750437747 750440385 2638 False 1557.0 1557 77.6950 984 3619 1 chr7B.!!$F3 2635
4 TraesCS1B01G336700 chr7B 750172393 750174996 2603 False 1493.0 1493 77.4330 1031 3619 1 chr7B.!!$F1 2588
5 TraesCS1B01G336700 chr7B 750246470 750248018 1548 False 1299.0 1299 81.8650 1031 2579 1 chr7B.!!$F2 1548
6 TraesCS1B01G336700 chr7B 750578426 750578946 520 False 296.0 296 76.9960 1031 1556 1 chr7B.!!$F4 525
7 TraesCS1B01G336700 chr7A 733060770 733063363 2593 True 1387.0 1387 76.7360 1034 3619 1 chr7A.!!$R2 2585
8 TraesCS1B01G336700 chr7A 732934832 732936375 1543 True 1247.0 1247 81.3140 1037 2583 1 chr7A.!!$R1 1546
9 TraesCS1B01G336700 chr7A 733274094 733275637 1543 False 902.0 902 77.3340 1029 2572 1 chr7A.!!$F1 1543
10 TraesCS1B01G336700 chr7A 732920652 732923314 2662 True 666.0 920 76.2955 1029 3619 2 chr7A.!!$R3 2590
11 TraesCS1B01G336700 chr2A 77335676 77337282 1606 False 1098.0 1098 79.2000 974 2583 1 chr2A.!!$F1 1609

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
593 3068 0.861837 GTGTGTGAAAGAGAGCACGG 59.138 55.000 0.00 0.0 37.83 4.94 F
646 3121 2.030371 CTCTCATAGAGCAGCAGGTCA 58.970 52.381 11.08 0.0 44.60 4.02 F
1086 3570 2.419297 CCTGCTATGTGGAGTCAACCTC 60.419 54.545 0.00 0.0 39.67 3.85 F
2585 5157 1.519455 CAGGTTAGGCTTCCTCGCG 60.519 63.158 0.00 0.0 34.61 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1593 4089 0.970937 TTGTTTTTCCCGCACCACCA 60.971 50.000 0.00 0.00 0.00 4.17 R
1926 4494 2.490509 TGCGACATCTTCCTTTCGAGTA 59.509 45.455 0.00 0.00 33.20 2.59 R
2824 5403 1.840635 AGCTGGTTGGAGAAGGATACC 59.159 52.381 0.00 0.00 37.17 2.73 R
4303 7278 0.039180 TGCAACTCCCTCTAGTCGGA 59.961 55.000 2.92 2.15 0.00 4.55 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
29 30 5.989477 TCTTGGAACATGATTAGTCGGATT 58.011 37.500 0.00 0.00 37.60 3.01
32 33 8.210946 TCTTGGAACATGATTAGTCGGATTATT 58.789 33.333 0.00 0.00 37.60 1.40
41 42 8.684386 TGATTAGTCGGATTATTGCCAAAATA 57.316 30.769 0.00 0.00 0.00 1.40
45 46 6.560711 AGTCGGATTATTGCCAAAATACAAC 58.439 36.000 0.00 0.00 0.00 3.32
52 53 4.386867 TTGCCAAAATACAACGGTGAAA 57.613 36.364 7.88 0.00 0.00 2.69
57 58 5.533482 CCAAAATACAACGGTGAAAATGGA 58.467 37.500 7.88 0.00 0.00 3.41
69 70 4.423732 GTGAAAATGGATGCACATGTACC 58.576 43.478 0.00 0.77 0.00 3.34
74 75 2.710377 TGGATGCACATGTACCAGAAC 58.290 47.619 0.00 0.00 0.00 3.01
76 77 2.679837 GGATGCACATGTACCAGAACTG 59.320 50.000 0.00 0.00 0.00 3.16
78 79 3.701205 TGCACATGTACCAGAACTGAT 57.299 42.857 0.00 0.00 0.00 2.90
79 80 4.019792 TGCACATGTACCAGAACTGATT 57.980 40.909 0.00 0.00 0.00 2.57
80 81 4.397420 TGCACATGTACCAGAACTGATTT 58.603 39.130 0.00 0.00 0.00 2.17
81 82 4.826733 TGCACATGTACCAGAACTGATTTT 59.173 37.500 0.00 0.00 0.00 1.82
82 83 5.301551 TGCACATGTACCAGAACTGATTTTT 59.698 36.000 0.00 0.00 0.00 1.94
165 166 8.378421 GGATTATACTCGTGTGTAAAGTTTGAC 58.622 37.037 10.23 0.00 34.35 3.18
174 175 7.222417 TCGTGTGTAAAGTTTGACGAAGAAATA 59.778 33.333 0.00 0.00 33.24 1.40
295 2734 3.531262 ACGGAAGTTATTTTGTCGTGC 57.469 42.857 0.00 0.00 46.40 5.34
313 2755 5.120208 GTCGTGCAACTTTGTACATGAGTAT 59.880 40.000 11.48 2.47 42.83 2.12
317 2759 6.953743 GTGCAACTTTGTACATGAGTATAACG 59.046 38.462 11.48 0.00 42.35 3.18
390 2833 9.507329 TTTAATTATTTTGCTAAATTGGGTGCA 57.493 25.926 11.32 0.00 35.61 4.57
407 2850 2.420022 GTGCATGTAGACCCATGTTCAC 59.580 50.000 0.00 0.97 43.33 3.18
417 2860 2.158325 ACCCATGTTCACCAAATCCACT 60.158 45.455 0.00 0.00 0.00 4.00
418 2861 2.231964 CCCATGTTCACCAAATCCACTG 59.768 50.000 0.00 0.00 0.00 3.66
420 2863 3.573538 CCATGTTCACCAAATCCACTGAA 59.426 43.478 0.00 0.00 0.00 3.02
452 2895 9.635404 TGTATAAATAATGGAAAGGAACGGAAT 57.365 29.630 0.00 0.00 0.00 3.01
455 2898 7.718334 AAATAATGGAAAGGAACGGAATTCT 57.282 32.000 5.23 0.00 37.48 2.40
477 2920 4.334552 TCAATTTCTGCATTGAGTGGCTA 58.665 39.130 0.00 0.00 38.09 3.93
503 2946 1.656652 CAAGTGGATAAGTGGCTCGG 58.343 55.000 0.00 0.00 0.00 4.63
518 2961 1.271054 GCTCGGTGCATCCCTATGAAT 60.271 52.381 0.00 0.00 42.31 2.57
524 2967 3.181451 GGTGCATCCCTATGAATGAGTGA 60.181 47.826 0.00 0.00 34.84 3.41
562 3009 4.079665 TCGTCACTGACATCGTCTAAAG 57.920 45.455 9.84 0.00 33.15 1.85
573 3020 3.513680 TCGTCTAAAGTGTGTGTGTGT 57.486 42.857 0.00 0.00 0.00 3.72
575 3022 2.927477 CGTCTAAAGTGTGTGTGTGTGT 59.073 45.455 0.00 0.00 0.00 3.72
577 3024 3.682858 GTCTAAAGTGTGTGTGTGTGTGT 59.317 43.478 0.00 0.00 0.00 3.72
579 3026 1.890876 AAGTGTGTGTGTGTGTGTGT 58.109 45.000 0.00 0.00 0.00 3.72
582 3029 1.533299 GTGTGTGTGTGTGTGTGTGAA 59.467 47.619 0.00 0.00 0.00 3.18
593 3068 0.861837 GTGTGTGAAAGAGAGCACGG 59.138 55.000 0.00 0.00 37.83 4.94
646 3121 2.030371 CTCTCATAGAGCAGCAGGTCA 58.970 52.381 11.08 0.00 44.60 4.02
699 3176 4.346418 AGGAGAATACAGCCAGGTATGAAG 59.654 45.833 1.10 0.00 34.32 3.02
722 3199 3.292460 CCCTAGATCCGTGAGTCTCTTT 58.708 50.000 0.65 0.00 0.00 2.52
759 3236 5.794894 TCCTCTTCTTCTGTACAAATCCAC 58.205 41.667 0.00 0.00 0.00 4.02
802 3279 2.818921 AGGCCACTAATGAAATTGCCA 58.181 42.857 5.01 0.00 42.34 4.92
975 3459 9.791820 GTTACAAAACAAGTACACTAATTTGGT 57.208 29.630 14.02 9.61 35.56 3.67
1086 3570 2.419297 CCTGCTATGTGGAGTCAACCTC 60.419 54.545 0.00 0.00 39.67 3.85
1359 3843 2.540769 CGGTGTTGAAATCAAGCGTGTT 60.541 45.455 0.00 0.00 36.39 3.32
1521 4011 5.667539 TTGTGATGGTTGGTTTTGAAGAA 57.332 34.783 0.00 0.00 0.00 2.52
1593 4089 3.758554 GTGTTGTCTCCATAGTTGCCATT 59.241 43.478 0.00 0.00 0.00 3.16
1926 4494 7.835181 AGTAATGGCAGTAGAGTACTCTTAACT 59.165 37.037 29.57 23.52 40.93 2.24
2041 4609 2.704572 ACAGCAAAGCTCTACCATCAC 58.295 47.619 0.00 0.00 36.40 3.06
2390 4962 6.516739 TCCGCATTTACCAAATCATAAACA 57.483 33.333 0.00 0.00 0.00 2.83
2421 4993 6.392625 ACAGCACATAAGTATGTACTCGAT 57.607 37.500 3.69 0.00 44.57 3.59
2517 5089 2.626266 TGACAATCTACGTGACTGGTGT 59.374 45.455 0.00 0.00 0.00 4.16
2585 5157 1.519455 CAGGTTAGGCTTCCTCGCG 60.519 63.158 0.00 0.00 34.61 5.87
2597 5169 2.273370 TCCTCGCGTCTCATTGTAAC 57.727 50.000 5.77 0.00 0.00 2.50
2605 5177 7.358435 CCTCGCGTCTCATTGTAACTTTATATG 60.358 40.741 5.77 0.00 0.00 1.78
2656 5229 8.896744 CAGATCATGAGGTTTCTTAATTTGCTA 58.103 33.333 0.09 0.00 0.00 3.49
2659 5232 8.402798 TCATGAGGTTTCTTAATTTGCTAACA 57.597 30.769 0.00 0.00 0.00 2.41
2764 5343 5.241506 TGTCCAAAACTTGAATGGTGATCTC 59.758 40.000 0.00 0.00 35.66 2.75
2792 5371 7.770366 TGCCATGAAAGCATATCTAATTCAT 57.230 32.000 0.00 0.00 40.37 2.57
2812 5391 4.270084 TCATCACGAACACTTGTTGTCTTC 59.730 41.667 0.00 0.00 37.51 2.87
2824 5403 5.237344 ACTTGTTGTCTTCAGAATTCCTTCG 59.763 40.000 0.65 0.00 36.45 3.79
2833 5412 5.277857 TCAGAATTCCTTCGGTATCCTTC 57.722 43.478 0.65 0.00 36.45 3.46
3050 5629 2.715763 AGTACCAAAGTCCCTCTGGA 57.284 50.000 0.00 0.00 38.75 3.86
3064 5643 4.093011 CCCTCTGGAATATCCCTACTCTG 58.907 52.174 0.00 0.00 35.03 3.35
3148 5751 8.603898 TCCAGACCTTTGAGTTATATCTTACA 57.396 34.615 0.00 0.00 0.00 2.41
3191 5794 6.685403 CCGACGTCATAACATGGTTATTTTTC 59.315 38.462 17.16 0.00 0.00 2.29
3196 5799 7.264947 GTCATAACATGGTTATTTTTCTGGGG 58.735 38.462 0.00 0.00 0.00 4.96
3217 5820 4.437390 GGGCAGATGAATCAACTAACAACG 60.437 45.833 0.00 0.00 0.00 4.10
3259 5865 6.467677 CCGTATCCCATCAGAAGTGATTAAT 58.532 40.000 0.00 0.00 40.84 1.40
3325 5934 7.370383 ACAAATTTAATGTGCTCAAGACGATT 58.630 30.769 0.00 0.00 0.00 3.34
3370 5979 2.812011 ACGGTGTCTTGTTCTATTTGCC 59.188 45.455 0.00 0.00 0.00 4.52
3451 6060 4.683643 TGGAGTTATCGGGATATCATGGA 58.316 43.478 4.83 0.00 0.00 3.41
3667 6276 3.341823 ACTGTTCAATGTGCCTCAGATC 58.658 45.455 0.00 0.00 0.00 2.75
3668 6277 2.681848 CTGTTCAATGTGCCTCAGATCC 59.318 50.000 0.00 0.00 0.00 3.36
3669 6278 1.667724 GTTCAATGTGCCTCAGATCCG 59.332 52.381 0.00 0.00 0.00 4.18
3670 6279 1.194218 TCAATGTGCCTCAGATCCGA 58.806 50.000 0.00 0.00 0.00 4.55
3671 6280 1.134699 TCAATGTGCCTCAGATCCGAC 60.135 52.381 0.00 0.00 0.00 4.79
3672 6281 0.179000 AATGTGCCTCAGATCCGACC 59.821 55.000 0.00 0.00 0.00 4.79
3673 6282 1.690219 ATGTGCCTCAGATCCGACCC 61.690 60.000 0.00 0.00 0.00 4.46
3674 6283 2.038813 TGCCTCAGATCCGACCCA 59.961 61.111 0.00 0.00 0.00 4.51
3675 6284 2.060383 TGCCTCAGATCCGACCCAG 61.060 63.158 0.00 0.00 0.00 4.45
3676 6285 2.818132 CCTCAGATCCGACCCAGC 59.182 66.667 0.00 0.00 0.00 4.85
3733 6344 5.997746 GGAAGGTATGCACATATGAAGCTTA 59.002 40.000 19.97 16.22 0.00 3.09
3779 6390 8.352942 GGAGTCAATTATTGTTTATTAGCTGGG 58.647 37.037 4.77 0.00 0.00 4.45
3796 6407 0.735287 GGGTCGACTTAACGGCTCAC 60.735 60.000 16.46 0.00 38.31 3.51
3813 6424 1.800586 TCACTGTGCTCAATTTCTCGC 59.199 47.619 2.12 0.00 0.00 5.03
3993 6964 8.747538 AATATGTAAATGGAGTAAACTGGTCC 57.252 34.615 0.00 0.00 0.00 4.46
4042 7014 7.953158 ATGTATCATGTGTGAGTATGTAAGC 57.047 36.000 0.00 0.00 37.87 3.09
4047 7019 6.405538 TCATGTGTGAGTATGTAAGCATTCA 58.594 36.000 0.00 0.00 36.58 2.57
4052 7024 8.022550 TGTGTGAGTATGTAAGCATTCATTTTG 58.977 33.333 0.00 0.00 36.58 2.44
4066 7038 6.867816 GCATTCATTTTGATTGAGGTGTTGTA 59.132 34.615 4.14 0.00 31.42 2.41
4081 7053 2.892215 TGTTGTATACCGTGGTCTGACA 59.108 45.455 10.38 0.00 0.00 3.58
4112 7084 5.430007 TCACGTCCATCGGGTTTATAAATT 58.570 37.500 0.31 0.00 44.19 1.82
4121 7093 9.069082 CCATCGGGTTTATAAATTTGGTACATA 57.931 33.333 0.00 0.00 39.30 2.29
4208 7180 7.944729 ATACTATTGACAACTTCCTTGCAAT 57.055 32.000 0.00 0.00 38.75 3.56
4303 7278 7.692460 TCAGATGCATGTGAAACTTAGAAAT 57.308 32.000 23.11 0.00 38.04 2.17
4306 7281 5.295431 TGCATGTGAAACTTAGAAATCCG 57.705 39.130 0.00 0.00 38.04 4.18
4319 7295 3.983821 AGAAATCCGACTAGAGGGAGTT 58.016 45.455 15.68 15.68 42.73 3.01
4349 7325 0.304705 GAAACTGACACACACCTGCG 59.695 55.000 0.00 0.00 0.00 5.18
4370 7346 4.414852 CGTGGCTGACAAATTATCCTTTG 58.585 43.478 0.00 0.00 41.02 2.77
4378 7354 7.265599 TGACAAATTATCCTTTGGAGACCTA 57.734 36.000 2.08 0.00 39.83 3.08
4472 8044 3.589542 CAAAGCTGGGGTGGGGGA 61.590 66.667 0.00 0.00 0.00 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 5.707242 TTCACCGTTGTATTTTGGCAATA 57.293 34.783 0.00 0.00 0.00 1.90
32 33 4.386867 TTTTCACCGTTGTATTTTGGCA 57.613 36.364 0.00 0.00 0.00 4.92
41 42 1.959985 TGCATCCATTTTCACCGTTGT 59.040 42.857 0.00 0.00 0.00 3.32
45 46 2.094597 ACATGTGCATCCATTTTCACCG 60.095 45.455 0.00 0.00 0.00 4.94
52 53 3.650281 TCTGGTACATGTGCATCCATT 57.350 42.857 16.11 0.00 38.20 3.16
57 58 3.701205 TCAGTTCTGGTACATGTGCAT 57.299 42.857 16.11 0.00 38.20 3.96
120 121 4.308526 TCCTATACCATGTTTGTTGGCA 57.691 40.909 0.00 0.00 37.81 4.92
121 122 5.852282 AATCCTATACCATGTTTGTTGGC 57.148 39.130 0.00 0.00 37.81 4.52
125 126 8.867097 ACGAGTATAATCCTATACCATGTTTGT 58.133 33.333 0.00 0.00 40.54 2.83
127 128 8.867097 ACACGAGTATAATCCTATACCATGTTT 58.133 33.333 0.00 0.00 40.54 2.83
128 129 8.304596 CACACGAGTATAATCCTATACCATGTT 58.695 37.037 0.00 0.00 40.54 2.71
129 130 7.450634 ACACACGAGTATAATCCTATACCATGT 59.549 37.037 0.00 0.52 40.54 3.21
130 131 7.827701 ACACACGAGTATAATCCTATACCATG 58.172 38.462 0.00 0.00 40.54 3.66
131 132 9.524496 TTACACACGAGTATAATCCTATACCAT 57.476 33.333 0.00 0.00 40.54 3.55
132 133 8.922931 TTACACACGAGTATAATCCTATACCA 57.077 34.615 0.00 0.00 40.54 3.25
133 134 9.837525 CTTTACACACGAGTATAATCCTATACC 57.162 37.037 0.00 0.00 40.54 2.73
229 230 7.748691 AAATTACAGCTACGAAAAGGGTAAA 57.251 32.000 0.00 0.00 0.00 2.01
264 2703 7.172703 ACAAAATAACTTCCGTAGACTTCTTGG 59.827 37.037 0.00 0.00 0.00 3.61
375 2818 3.694072 GTCTACATGCACCCAATTTAGCA 59.306 43.478 0.00 0.00 41.73 3.49
390 2833 4.380843 TTTGGTGAACATGGGTCTACAT 57.619 40.909 0.00 0.00 0.00 2.29
443 2886 4.082787 TGCAGAAATTGAGAATTCCGTTCC 60.083 41.667 0.65 0.00 37.56 3.62
447 2890 5.643664 TCAATGCAGAAATTGAGAATTCCG 58.356 37.500 0.65 0.00 40.72 4.30
455 2898 3.159472 AGCCACTCAATGCAGAAATTGA 58.841 40.909 0.00 0.00 42.78 2.57
477 2920 3.690460 CCACTTATCCACTTGCTTTCCT 58.310 45.455 0.00 0.00 0.00 3.36
496 2939 1.766059 ATAGGGATGCACCGAGCCA 60.766 57.895 0.00 0.00 44.83 4.75
503 2946 4.077300 TCACTCATTCATAGGGATGCAC 57.923 45.455 0.00 0.00 32.62 4.57
518 2961 6.239217 AGCTGGACAATATGTATTCACTCA 57.761 37.500 0.00 0.00 0.00 3.41
524 2967 5.050490 GTGACGAGCTGGACAATATGTATT 58.950 41.667 1.44 0.00 0.00 1.89
562 3009 1.152510 TCACACACACACACACACAC 58.847 50.000 0.00 0.00 0.00 3.82
573 3020 1.570813 CGTGCTCTCTTTCACACACA 58.429 50.000 0.00 0.00 33.03 3.72
575 3022 0.880278 GCCGTGCTCTCTTTCACACA 60.880 55.000 0.00 0.00 33.03 3.72
577 3024 1.664649 CGCCGTGCTCTCTTTCACA 60.665 57.895 0.00 0.00 33.03 3.58
579 3026 2.738521 GCGCCGTGCTCTCTTTCA 60.739 61.111 0.00 0.00 41.73 2.69
608 3083 1.200484 GAGTCGTCCCACAGAGTTCTC 59.800 57.143 0.00 0.00 0.00 2.87
646 3121 1.439353 CGGTTTGCTCTGTGTGCTGT 61.439 55.000 0.00 0.00 0.00 4.40
699 3176 0.468400 AGACTCACGGATCTAGGGGC 60.468 60.000 0.00 0.00 0.00 5.80
722 3199 3.078305 AGAAGAGGAGGGAAAAGAGGAGA 59.922 47.826 0.00 0.00 0.00 3.71
802 3279 5.775701 TGAGCTTCCAACTCTACTAGAACTT 59.224 40.000 0.00 0.00 35.12 2.66
866 3344 6.821665 ACGCTTTTGTTATAGAAAGGATAGCA 59.178 34.615 0.00 0.00 34.30 3.49
975 3459 4.551702 TTGCTCTTCCTTGTATGTGCTA 57.448 40.909 0.00 0.00 0.00 3.49
1009 3493 2.740714 CGACGGCCTTAACAGCAGC 61.741 63.158 0.00 0.00 0.00 5.25
1086 3570 1.593196 TTTTCAGGCACTCCACTTCG 58.407 50.000 0.00 0.00 34.60 3.79
1359 3843 7.231519 TGAAATATCTCATCGAGCTTCCTTCTA 59.768 37.037 0.00 0.00 0.00 2.10
1593 4089 0.970937 TTGTTTTTCCCGCACCACCA 60.971 50.000 0.00 0.00 0.00 4.17
1857 4425 5.676552 ACCTTTTTGTTTATTTGGTCCCAC 58.323 37.500 0.00 0.00 0.00 4.61
1926 4494 2.490509 TGCGACATCTTCCTTTCGAGTA 59.509 45.455 0.00 0.00 33.20 2.59
2041 4609 8.347771 CACATCAATTATGGTTCTCCTTATGTG 58.652 37.037 0.00 0.00 40.16 3.21
2328 4900 8.964772 GCTATCCATATTTCAATAAGAGCCAAT 58.035 33.333 0.00 0.00 0.00 3.16
2344 4916 7.551974 CGGAATGAATCTTTCTGCTATCCATAT 59.448 37.037 8.47 0.00 0.00 1.78
2390 4962 7.986085 ACATACTTATGTGCTGTTTCTTCTT 57.014 32.000 0.94 0.00 44.66 2.52
2421 4993 3.214328 GACCAAGTTTCTCTGAGCCAAA 58.786 45.455 0.00 0.00 0.00 3.28
2451 5023 2.492088 TCCATGTACCTCACTTCTGTCG 59.508 50.000 0.00 0.00 0.00 4.35
2501 5073 6.354938 TCTTCTATACACCAGTCACGTAGAT 58.645 40.000 0.00 0.00 0.00 1.98
2517 5089 5.104360 ACCATCTTGCCTTGCTTCTTCTATA 60.104 40.000 0.00 0.00 0.00 1.31
2628 5201 7.699812 GCAAATTAAGAAACCTCATGATCTGTC 59.300 37.037 0.00 0.00 0.00 3.51
2632 5205 9.508567 GTTAGCAAATTAAGAAACCTCATGATC 57.491 33.333 0.00 0.00 0.00 2.92
2764 5343 8.827177 AATTAGATATGCTTTCATGGCAAATG 57.173 30.769 0.00 0.00 43.14 2.32
2824 5403 1.840635 AGCTGGTTGGAGAAGGATACC 59.159 52.381 0.00 0.00 37.17 2.73
2833 5412 5.452078 TCAACAATTTTAGCTGGTTGGAG 57.548 39.130 0.00 0.00 39.33 3.86
3012 5591 4.008074 ACTACTGAGTCCATTTGTGTGG 57.992 45.455 0.00 0.00 40.76 4.17
3050 5629 4.497516 ACATGCCTCAGAGTAGGGATATT 58.502 43.478 0.00 0.00 45.10 1.28
3064 5643 6.096001 ACTCATTTCCAAGATAAACATGCCTC 59.904 38.462 0.00 0.00 0.00 4.70
3191 5794 2.431954 AGTTGATTCATCTGCCCCAG 57.568 50.000 0.00 0.00 0.00 4.45
3196 5799 5.283060 ACGTTGTTAGTTGATTCATCTGC 57.717 39.130 7.38 2.20 0.00 4.26
3259 5865 8.959548 ACAAGATGAGTCATGTTTGCAAATATA 58.040 29.630 19.44 8.39 32.75 0.86
3325 5934 1.701031 TTTGTGGGAACTCAGCGGGA 61.701 55.000 0.00 0.00 34.92 5.14
3370 5979 6.671641 GCATCGGATCTTGTTCAATGATATCG 60.672 42.308 0.00 0.00 0.00 2.92
3451 6060 1.741732 GCAGAGCAGGACATGATTCGT 60.742 52.381 0.00 0.00 0.00 3.85
3528 6137 0.833287 CGACCCAACATCCATCCTCT 59.167 55.000 0.00 0.00 0.00 3.69
3667 6276 3.194005 ACAATGTATTAGCTGGGTCGG 57.806 47.619 0.00 0.00 0.00 4.79
3668 6277 5.538118 TCATACAATGTATTAGCTGGGTCG 58.462 41.667 2.67 0.00 0.00 4.79
3669 6278 5.409826 GCTCATACAATGTATTAGCTGGGTC 59.590 44.000 24.46 3.20 0.00 4.46
3670 6279 5.072329 AGCTCATACAATGTATTAGCTGGGT 59.928 40.000 30.21 14.33 35.98 4.51
3671 6280 5.410746 CAGCTCATACAATGTATTAGCTGGG 59.589 44.000 37.38 25.01 44.35 4.45
3672 6281 5.106791 GCAGCTCATACAATGTATTAGCTGG 60.107 44.000 40.72 30.92 46.33 4.85
3674 6283 5.614308 TGCAGCTCATACAATGTATTAGCT 58.386 37.500 27.22 27.22 37.25 3.32
3675 6284 5.929697 TGCAGCTCATACAATGTATTAGC 57.070 39.130 24.38 24.38 0.00 3.09
3676 6285 7.227314 TCCTTTGCAGCTCATACAATGTATTAG 59.773 37.037 9.57 9.57 0.00 1.73
3733 6344 7.394923 TGACTCCAAAAACGGTAATATTTCCAT 59.605 33.333 11.24 0.00 0.00 3.41
3745 6356 7.707774 AAACAATAATTGACTCCAAAAACGG 57.292 32.000 0.00 0.00 35.67 4.44
3779 6390 1.335689 ACAGTGAGCCGTTAAGTCGAC 60.336 52.381 7.70 7.70 0.00 4.20
3796 6407 0.519999 GCGCGAGAAATTGAGCACAG 60.520 55.000 12.10 0.00 0.00 3.66
3875 6486 3.880490 ACTCTTCCTCTGCTATGTAGTCG 59.120 47.826 0.00 0.00 0.00 4.18
3903 6514 1.282157 GTAATGAGTGCCCTGGGAGTT 59.718 52.381 19.27 0.00 0.00 3.01
3911 6524 3.059352 ACTGTGAAGTAATGAGTGCCC 57.941 47.619 0.00 0.00 0.00 5.36
3972 6585 5.310451 GTGGACCAGTTTACTCCATTTACA 58.690 41.667 0.00 0.00 32.68 2.41
3973 6586 4.390909 CGTGGACCAGTTTACTCCATTTAC 59.609 45.833 0.00 0.00 32.68 2.01
3974 6587 4.040706 ACGTGGACCAGTTTACTCCATTTA 59.959 41.667 0.00 0.00 32.68 1.40
3975 6588 3.181448 ACGTGGACCAGTTTACTCCATTT 60.181 43.478 0.00 0.00 32.68 2.32
3993 6964 4.218635 AGATGGAGCACATATAGGTACGTG 59.781 45.833 0.00 0.00 40.72 4.49
4042 7014 8.991243 ATACAACACCTCAATCAAAATGAATG 57.009 30.769 0.00 0.00 0.00 2.67
4047 7019 6.657541 ACGGTATACAACACCTCAATCAAAAT 59.342 34.615 5.01 0.00 33.62 1.82
4052 7024 3.869246 CCACGGTATACAACACCTCAATC 59.131 47.826 5.01 0.00 33.62 2.67
4066 7038 0.179111 CGCATGTCAGACCACGGTAT 60.179 55.000 0.00 0.00 0.00 2.73
4081 7053 1.815421 GATGGACGTGAAGGCGCAT 60.815 57.895 10.83 0.00 34.88 4.73
4270 7242 9.715121 AGTTTCACATGCATCTGAATAATTTTT 57.285 25.926 16.74 0.00 0.00 1.94
4271 7243 9.715121 AAGTTTCACATGCATCTGAATAATTTT 57.285 25.926 16.74 6.18 0.00 1.82
4274 7246 9.399797 TCTAAGTTTCACATGCATCTGAATAAT 57.600 29.630 16.74 9.20 0.00 1.28
4303 7278 0.039180 TGCAACTCCCTCTAGTCGGA 59.961 55.000 2.92 2.15 0.00 4.55
4306 7281 3.402628 TGTTTGCAACTCCCTCTAGTC 57.597 47.619 0.00 0.00 0.00 2.59
4319 7295 5.067023 TGTGTGTCAGTTTCATATGTTTGCA 59.933 36.000 1.90 0.00 0.00 4.08
4349 7325 4.462483 TCCAAAGGATAATTTGTCAGCCAC 59.538 41.667 0.00 0.00 38.28 5.01
4370 7346 1.336609 GGTTGTCGTGTGTAGGTCTCC 60.337 57.143 0.00 0.00 0.00 3.71
4378 7354 1.946768 CCAAATCAGGTTGTCGTGTGT 59.053 47.619 0.00 0.00 0.00 3.72
4441 7998 4.437239 CCAGCTTTGACACCTACTATCAG 58.563 47.826 0.00 0.00 0.00 2.90
4443 8000 3.432326 CCCCAGCTTTGACACCTACTATC 60.432 52.174 0.00 0.00 0.00 2.08
4444 8001 2.505819 CCCCAGCTTTGACACCTACTAT 59.494 50.000 0.00 0.00 0.00 2.12
4446 8003 0.693049 CCCCAGCTTTGACACCTACT 59.307 55.000 0.00 0.00 0.00 2.57
4447 8004 0.400594 ACCCCAGCTTTGACACCTAC 59.599 55.000 0.00 0.00 0.00 3.18
4472 8044 2.376695 ATGCCAGCTTGCCTTATGAT 57.623 45.000 7.41 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.