Multiple sequence alignment - TraesCS6B01G297000

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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 TraesCS6B01G297000 chr6B 100.000 5105 0 0 1 5105 533528195 533533299 0.000000e+00 9428.0
1 TraesCS6B01G297000 chr6D 93.502 4109 165 31 285 4337 347157121 347153059 0.000000e+00 6015.0
2 TraesCS6B01G297000 chr6D 85.106 611 72 9 4436 5029 347137017 347136409 1.570000e-169 606.0
3 TraesCS6B01G297000 chr6D 92.780 277 19 1 1 277 347157701 347157426 2.860000e-107 399.0
4 TraesCS6B01G297000 chr6A 92.227 2097 94 26 993 3064 496234335 496236387 0.000000e+00 2905.0
5 TraesCS6B01G297000 chr6A 90.357 1317 66 28 3106 4408 496236799 496238068 0.000000e+00 1672.0
6 TraesCS6B01G297000 chr6A 86.192 688 66 10 4435 5105 496238143 496238818 0.000000e+00 717.0
7 TraesCS6B01G297000 chr6A 86.687 661 65 15 2 647 496210985 496211637 0.000000e+00 712.0
8 TraesCS6B01G297000 chr6A 77.338 556 89 19 4456 4983 607822082 607822628 1.390000e-75 294.0
9 TraesCS6B01G297000 chr6A 97.872 47 1 0 3061 3107 496236621 496236667 1.180000e-11 82.4
10 TraesCS6B01G297000 chr6A 97.368 38 1 0 804 841 496234231 496234268 1.190000e-06 65.8
11 TraesCS6B01G297000 chr2D 81.337 643 89 17 4464 5086 616436213 616435582 1.280000e-135 494.0
12 TraesCS6B01G297000 chr1B 80.422 664 103 18 4436 5079 322117200 322116544 9.940000e-132 481.0
13 TraesCS6B01G297000 chr1B 74.725 182 26 10 4817 4983 174832805 174832629 4.270000e-06 63.9
14 TraesCS6B01G297000 chr3A 79.666 659 100 17 4438 5080 120354901 120354261 1.300000e-120 444.0
15 TraesCS6B01G297000 chr3A 78.729 362 70 6 4485 4843 83959024 83958667 8.550000e-58 235.0
16 TraesCS6B01G297000 chr1D 80.325 493 83 11 4436 4921 363058211 363058696 1.350000e-95 361.0
17 TraesCS6B01G297000 chr2A 80.435 460 79 8 4471 4921 745735234 745734777 1.760000e-89 340.0
18 TraesCS6B01G297000 chr1A 78.980 490 95 5 4437 4921 371825737 371826223 1.370000e-85 327.0
19 TraesCS6B01G297000 chr5A 76.027 584 89 27 4443 4979 364670067 364669488 6.560000e-64 255.0
20 TraesCS6B01G297000 chr5D 78.610 187 23 7 4810 4979 276262812 276262626 1.940000e-19 108.0
21 TraesCS6B01G297000 chr5D 96.000 50 2 0 4935 4984 508597155 508597106 1.180000e-11 82.4
22 TraesCS6B01G297000 chr2B 84.932 73 9 2 649 720 447750087 447750158 7.090000e-09 73.1


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 TraesCS6B01G297000 chr6B 533528195 533533299 5104 False 9428.00 9428 100.0000 1 5105 1 chr6B.!!$F1 5104
1 TraesCS6B01G297000 chr6D 347153059 347157701 4642 True 3207.00 6015 93.1410 1 4337 2 chr6D.!!$R2 4336
2 TraesCS6B01G297000 chr6D 347136409 347137017 608 True 606.00 606 85.1060 4436 5029 1 chr6D.!!$R1 593
3 TraesCS6B01G297000 chr6A 496234231 496238818 4587 False 1088.44 2905 92.8032 804 5105 5 chr6A.!!$F3 4301
4 TraesCS6B01G297000 chr6A 496210985 496211637 652 False 712.00 712 86.6870 2 647 1 chr6A.!!$F1 645
5 TraesCS6B01G297000 chr6A 607822082 607822628 546 False 294.00 294 77.3380 4456 4983 1 chr6A.!!$F2 527
6 TraesCS6B01G297000 chr2D 616435582 616436213 631 True 494.00 494 81.3370 4464 5086 1 chr2D.!!$R1 622
7 TraesCS6B01G297000 chr1B 322116544 322117200 656 True 481.00 481 80.4220 4436 5079 1 chr1B.!!$R2 643
8 TraesCS6B01G297000 chr3A 120354261 120354901 640 True 444.00 444 79.6660 4438 5080 1 chr3A.!!$R2 642
9 TraesCS6B01G297000 chr5A 364669488 364670067 579 True 255.00 255 76.0270 4443 4979 1 chr5A.!!$R1 536

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
970 1301 0.519961 CTTCGCCCCAACTTTTACCG 59.480 55.000 0.00 0.0 0.0 4.02 F
1632 1983 0.676184 TGAGCTATCCATCCGACTGC 59.324 55.000 0.00 0.0 0.0 4.40 F
2093 2451 0.645496 TAGCCATTCCCTCCCCTACA 59.355 55.000 0.00 0.0 0.0 2.74 F
3678 4412 3.452627 ACTCTCAGGATATCAAAACGGCT 59.547 43.478 4.83 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2022 2380 0.102481 TAAACGGGCTGATCGAGAGC 59.898 55.0 10.14 10.14 35.57 4.09 R
2681 3045 0.968901 TGAGCTACCACCGATTCCGT 60.969 55.0 0.00 0.00 0.00 4.69 R
3779 4513 0.179166 GCAGCACAGAGAGAGAGACG 60.179 60.0 0.00 0.00 0.00 4.18 R
4482 5280 0.104855 GCCATCTCTGTGGTCGCATA 59.895 55.0 0.00 0.00 41.47 3.14 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
149 150 3.356290 GTGGGAATAGCTTGTCCAACAT 58.644 45.455 15.06 0.00 37.73 2.71
165 166 7.004086 TGTCCAACATACTTGAGGAGAATTTT 58.996 34.615 0.00 0.00 33.45 1.82
169 170 9.231297 CCAACATACTTGAGGAGAATTTTCTTA 57.769 33.333 0.00 0.00 37.73 2.10
184 185 7.772757 AGAATTTTCTTACCTCTGGCAGATAAG 59.227 37.037 23.09 23.09 32.55 1.73
191 193 8.109634 TCTTACCTCTGGCAGATAAGAATTTTT 58.890 33.333 26.73 5.90 28.35 1.94
262 264 2.009774 CAGGAGCTTTTGTCCATACCG 58.990 52.381 0.00 0.00 36.43 4.02
263 265 1.065418 AGGAGCTTTTGTCCATACCGG 60.065 52.381 0.00 0.00 36.43 5.28
295 594 4.142160 GGTAAATCCAAATGAGGGCTTCAC 60.142 45.833 0.00 0.00 35.84 3.18
322 622 9.932207 TCATAAGATTCAAAATGTGCAGATTTT 57.068 25.926 24.47 24.47 36.21 1.82
354 654 5.475719 TGTTCACTTTCGTATTGGGACTAG 58.524 41.667 0.00 0.00 0.00 2.57
358 658 6.942976 TCACTTTCGTATTGGGACTAGAAAT 58.057 36.000 0.00 0.00 0.00 2.17
389 689 0.741326 TCTCTACGCTCACCATCTGC 59.259 55.000 0.00 0.00 0.00 4.26
420 720 7.038729 AGGCAGCATAGTAAGAATCTAATGCTA 60.039 37.037 16.51 3.10 41.51 3.49
613 914 8.520119 AGAATAAGTAGAGAGATAGAGGGTCT 57.480 38.462 0.00 0.00 0.00 3.85
616 917 3.914435 AGTAGAGAGATAGAGGGTCTCCC 59.086 52.174 0.00 0.00 45.90 4.30
657 958 1.504359 TTAAAACTCGGTGCTCCACG 58.496 50.000 5.52 0.00 34.83 4.94
659 960 2.319890 AAAACTCGGTGCTCCACGGT 62.320 55.000 5.52 0.00 36.35 4.83
696 997 7.231317 TGCATAATTAGATTCACCCAATTCTCC 59.769 37.037 0.00 0.00 0.00 3.71
703 1004 6.259123 AGATTCACCCAATTCTCCTGAAAAT 58.741 36.000 0.00 0.00 35.63 1.82
785 1086 1.878102 CGTGTGGTAGCAAAAGGAGCT 60.878 52.381 0.00 0.00 45.77 4.09
844 1164 1.304052 AGCGAGAGGAGTCACTGCT 60.304 57.895 0.00 0.00 34.11 4.24
878 1198 4.926238 GGAGACAATGTCAAGTCACAGTAG 59.074 45.833 16.38 0.00 37.23 2.57
954 1285 1.300233 CTCGTAGCCGCCCATCTTC 60.300 63.158 0.00 0.00 0.00 2.87
962 1293 3.140814 GCCCATCTTCGCCCCAAC 61.141 66.667 0.00 0.00 0.00 3.77
966 1297 1.256812 CCATCTTCGCCCCAACTTTT 58.743 50.000 0.00 0.00 0.00 2.27
970 1301 0.519961 CTTCGCCCCAACTTTTACCG 59.480 55.000 0.00 0.00 0.00 4.02
1239 1570 4.154347 CCTGTCCTGCCGCTCCTC 62.154 72.222 0.00 0.00 0.00 3.71
1521 1870 0.882484 TGTCGCAATTCGCACCAAGA 60.882 50.000 1.75 0.00 42.60 3.02
1526 1875 1.130373 GCAATTCGCACCAAGATCGAA 59.870 47.619 0.00 0.00 44.67 3.71
1587 1938 4.954970 CAGCAACAGCCCACGGGT 62.955 66.667 3.54 0.00 37.65 5.28
1602 1953 1.875963 GGGTCGGATTTGTGCACTG 59.124 57.895 19.41 0.00 0.00 3.66
1619 1970 4.342092 TGCACTGTATATTGAGCTGAGCTA 59.658 41.667 7.08 0.00 39.88 3.32
1620 1971 5.011431 TGCACTGTATATTGAGCTGAGCTAT 59.989 40.000 7.08 0.00 39.88 2.97
1621 1972 5.576384 GCACTGTATATTGAGCTGAGCTATC 59.424 44.000 7.08 0.00 39.88 2.08
1622 1973 6.098679 CACTGTATATTGAGCTGAGCTATCC 58.901 44.000 7.08 0.00 39.88 2.59
1632 1983 0.676184 TGAGCTATCCATCCGACTGC 59.324 55.000 0.00 0.00 0.00 4.40
1910 2268 6.926630 ATTCCCAAGGCTATAGTTCTCTAG 57.073 41.667 0.84 0.00 0.00 2.43
1919 2277 7.371936 AGGCTATAGTTCTCTAGTAATTTGCG 58.628 38.462 0.84 0.00 0.00 4.85
1929 2287 9.880157 TTCTCTAGTAATTTGCGGTAATACTTT 57.120 29.630 0.00 0.00 0.00 2.66
1995 2353 2.010145 AACGCTATGCAGTACACCTG 57.990 50.000 0.00 0.00 44.53 4.00
1999 2357 2.348666 CGCTATGCAGTACACCTGTTTC 59.651 50.000 0.00 0.00 43.55 2.78
2001 2359 4.003648 GCTATGCAGTACACCTGTTTCTT 58.996 43.478 0.00 0.00 43.55 2.52
2002 2360 4.455877 GCTATGCAGTACACCTGTTTCTTT 59.544 41.667 0.00 0.00 43.55 2.52
2003 2361 5.048713 GCTATGCAGTACACCTGTTTCTTTT 60.049 40.000 0.00 0.00 43.55 2.27
2004 2362 6.148811 GCTATGCAGTACACCTGTTTCTTTTA 59.851 38.462 0.00 0.00 43.55 1.52
2005 2363 6.560253 ATGCAGTACACCTGTTTCTTTTAG 57.440 37.500 0.00 0.00 43.55 1.85
2006 2364 5.676552 TGCAGTACACCTGTTTCTTTTAGA 58.323 37.500 0.00 0.00 43.55 2.10
2007 2365 6.296026 TGCAGTACACCTGTTTCTTTTAGAT 58.704 36.000 0.00 0.00 43.55 1.98
2008 2366 6.204688 TGCAGTACACCTGTTTCTTTTAGATG 59.795 38.462 0.00 0.00 43.55 2.90
2009 2367 6.204882 GCAGTACACCTGTTTCTTTTAGATGT 59.795 38.462 0.00 0.00 43.55 3.06
2010 2368 7.386848 GCAGTACACCTGTTTCTTTTAGATGTA 59.613 37.037 0.00 0.00 43.55 2.29
2011 2369 8.709646 CAGTACACCTGTTTCTTTTAGATGTAC 58.290 37.037 0.00 0.00 35.26 2.90
2093 2451 0.645496 TAGCCATTCCCTCCCCTACA 59.355 55.000 0.00 0.00 0.00 2.74
2261 2620 4.507710 TGGTGCTAGAGTGTGATTTCATC 58.492 43.478 0.00 0.00 0.00 2.92
2276 2635 5.981915 TGATTTCATCTTATGCTCACTCTCG 59.018 40.000 0.00 0.00 0.00 4.04
2549 2913 5.006386 TCAAAACAAACTTGGCCAATTTGT 58.994 33.333 31.66 31.66 45.95 2.83
2563 2927 6.040729 TGGCCAATTTGTCATTATGTATGGAG 59.959 38.462 0.61 0.00 34.85 3.86
2589 2953 5.929697 TTGCTTGATCTGTACTTCAAGTG 57.070 39.130 22.89 9.97 46.76 3.16
2681 3045 6.310960 CGAAAACGATTGTTGATGTTGGATA 58.689 36.000 0.00 0.00 38.62 2.59
3489 4223 4.787135 TTGTGATGCATATTACCTCCCA 57.213 40.909 0.00 0.00 0.00 4.37
3604 4338 7.408910 TCTGATACACAAATTTGCATGATACG 58.591 34.615 18.12 1.73 0.00 3.06
3659 4393 9.482627 CCTGATACACAAAATATTCCTCTACTC 57.517 37.037 0.00 0.00 0.00 2.59
3678 4412 3.452627 ACTCTCAGGATATCAAAACGGCT 59.547 43.478 4.83 0.00 0.00 5.52
3779 4513 4.647399 ACTAAGGAGTGGTATGCTCTTCTC 59.353 45.833 0.00 0.00 33.41 2.87
3782 4518 2.223618 GGAGTGGTATGCTCTTCTCGTC 60.224 54.545 0.00 0.00 33.73 4.20
3857 4593 9.673454 TTTTGTAGCTGATATATACGTACACTG 57.327 33.333 0.00 0.00 0.00 3.66
3858 4594 8.611654 TTGTAGCTGATATATACGTACACTGA 57.388 34.615 0.00 0.00 0.00 3.41
3995 4731 3.604667 CGCAAACCCCAAGCAGCA 61.605 61.111 0.00 0.00 0.00 4.41
4094 4832 3.802139 CGCCTCGTAGCTGAATAATTTCA 59.198 43.478 0.00 0.00 39.54 2.69
4106 4844 6.502136 TGAATAATTTCATGTTACCGTGCA 57.498 33.333 0.00 0.00 36.94 4.57
4166 4904 6.382608 GTTCCTAAAGCAAAATTCTCCTCAC 58.617 40.000 0.00 0.00 0.00 3.51
4218 4956 1.064389 AGGGAAGCCTGCCAGATTTAC 60.064 52.381 0.00 0.00 34.87 2.01
4235 4973 2.882402 TACGATGCGCGCTGATGTGT 62.882 55.000 33.29 21.89 46.04 3.72
4309 5047 1.277557 GCAAAATGCACAATGGGGGTA 59.722 47.619 0.00 0.00 44.26 3.69
4337 5075 0.179020 CCCGCATAGAGCCCAATCAA 60.179 55.000 0.00 0.00 41.38 2.57
4383 5132 0.667184 CGTTCCATGTTTTGGCCTGC 60.667 55.000 3.32 0.00 46.01 4.85
4386 5135 0.968405 TCCATGTTTTGGCCTGCTTC 59.032 50.000 3.32 0.00 46.01 3.86
4389 5138 1.181098 ATGTTTTGGCCTGCTTCGCT 61.181 50.000 3.32 0.00 0.00 4.93
4395 5144 4.443266 GCCTGCTTCGCTCGGACT 62.443 66.667 0.00 0.00 0.00 3.85
4407 5189 2.282820 CGCTCGGACTTTAAAGCATCTC 59.717 50.000 15.24 5.17 34.39 2.75
4409 5191 3.198872 CTCGGACTTTAAAGCATCTCCC 58.801 50.000 15.24 6.28 0.00 4.30
4415 5197 2.897271 TTAAAGCATCTCCCAGCCAA 57.103 45.000 0.00 0.00 0.00 4.52
4417 5199 0.407139 AAAGCATCTCCCAGCCAAGT 59.593 50.000 0.00 0.00 0.00 3.16
4419 5201 1.817099 GCATCTCCCAGCCAAGTCG 60.817 63.158 0.00 0.00 0.00 4.18
4482 5280 3.127533 GAATGCGGTGCCGAGCTT 61.128 61.111 15.45 3.81 42.83 3.74
4523 5321 1.915614 AAGCTCGCGCATGTCTTTGG 61.916 55.000 8.75 0.00 39.10 3.28
4555 5353 2.619074 GGAGAAATTGGGGTCACCTCTG 60.619 54.545 0.00 0.00 41.11 3.35
4598 5396 2.925170 AGCTTCACCTCACCGCCT 60.925 61.111 0.00 0.00 0.00 5.52
4646 5448 4.329545 AGCTTTTCCTCCCGCGCA 62.330 61.111 8.75 0.00 0.00 6.09
4648 5450 2.870372 CTTTTCCTCCCGCGCAAG 59.130 61.111 8.75 0.67 43.44 4.01
4657 5459 3.036084 CCGCGCAAGTCGACACTT 61.036 61.111 19.50 0.54 44.26 3.16
4684 5486 1.019805 GGTAAGCGGCGCTTCTTCTT 61.020 55.000 45.55 26.89 46.77 2.52
4823 5661 5.833406 TCTAGCTAGATCTATGAGCATGC 57.167 43.478 19.72 10.51 38.73 4.06
4836 5675 0.464452 AGCATGCGGTAGGGTTAGAC 59.536 55.000 13.01 0.00 0.00 2.59
4851 5692 4.080526 GGGTTAGACCTGTGACCATTGTAT 60.081 45.833 0.00 0.00 38.64 2.29
4874 5715 2.347697 TGTACACTGTCGATCTGTGC 57.652 50.000 18.02 11.01 45.63 4.57
4986 5843 3.613910 GCATGTTTGTTGGTGTATGGTCC 60.614 47.826 0.00 0.00 0.00 4.46
4990 5847 4.141459 TGTTTGTTGGTGTATGGTCCTGTA 60.141 41.667 0.00 0.00 0.00 2.74
4991 5848 4.919774 TTGTTGGTGTATGGTCCTGTAT 57.080 40.909 0.00 0.00 0.00 2.29
4992 5849 4.919774 TGTTGGTGTATGGTCCTGTATT 57.080 40.909 0.00 0.00 0.00 1.89
4993 5850 4.584874 TGTTGGTGTATGGTCCTGTATTG 58.415 43.478 0.00 0.00 0.00 1.90
4994 5851 4.287326 TGTTGGTGTATGGTCCTGTATTGA 59.713 41.667 0.00 0.00 0.00 2.57
4995 5852 5.221945 TGTTGGTGTATGGTCCTGTATTGAA 60.222 40.000 0.00 0.00 0.00 2.69
4996 5853 4.839121 TGGTGTATGGTCCTGTATTGAAC 58.161 43.478 0.00 0.00 0.00 3.18
5012 5869 6.828273 TGTATTGAACTTCATGGATTGGTAGG 59.172 38.462 0.00 0.00 0.00 3.18
5049 5906 4.134563 GTGGTAGTGTGTTGAACTCCATT 58.865 43.478 0.00 0.00 31.79 3.16
5084 5945 3.562141 GCATGTTGTTGTGTGGTAGTGTA 59.438 43.478 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.579657 CCGGTGCACCTAGGTGTCA 61.580 63.158 36.31 30.56 46.90 3.58
75 76 2.322081 GCGCAAAGTAGCCCGACAA 61.322 57.895 0.30 0.00 0.00 3.18
96 97 0.390340 CACATGTGGACCCGACTCAG 60.390 60.000 18.51 0.00 0.00 3.35
106 107 2.282391 GCCAGGCACACATGTGGA 60.282 61.111 28.64 0.00 45.72 4.02
149 150 8.314751 CAGAGGTAAGAAAATTCTCCTCAAGTA 58.685 37.037 22.83 0.90 44.61 2.24
169 170 6.488715 AGAAAAATTCTTATCTGCCAGAGGT 58.511 36.000 0.00 0.00 36.36 3.85
262 264 1.388547 TGGATTTACCAGCGAATGCC 58.611 50.000 0.00 0.00 44.64 4.40
278 567 1.704628 TGAGTGAAGCCCTCATTTGGA 59.295 47.619 0.00 0.00 36.14 3.53
295 594 9.582431 AAATCTGCACATTTTGAATCTTATGAG 57.418 29.630 0.00 0.00 0.00 2.90
322 622 4.103365 ACGAAAGTGAACAACAATGCAA 57.897 36.364 0.00 0.00 46.97 4.08
354 654 5.906285 GCGTAGAGAAATCAAGCATCATTTC 59.094 40.000 0.00 0.00 38.70 2.17
358 658 4.115516 GAGCGTAGAGAAATCAAGCATCA 58.884 43.478 0.00 0.00 0.00 3.07
389 689 0.034059 CTTACTATGCTGCCTCGGGG 59.966 60.000 0.00 0.00 0.00 5.73
402 702 9.751542 GCTGAAAGTAGCATTAGATTCTTACTA 57.248 33.333 0.00 0.00 43.17 1.82
420 720 0.814010 AACGCGAAGGTGCTGAAAGT 60.814 50.000 15.93 0.00 35.30 2.66
475 775 9.342308 CAGTGATTTCTAATATTCCCTTTGCTA 57.658 33.333 0.00 0.00 0.00 3.49
483 783 7.882271 AGATGCTCCAGTGATTTCTAATATTCC 59.118 37.037 0.00 0.00 0.00 3.01
577 877 7.668469 TCTCTCTACTTATTCTTGTGTGTACCA 59.332 37.037 0.00 0.00 0.00 3.25
613 914 1.292242 ACTAGAGGATCAAGGCAGGGA 59.708 52.381 0.00 0.00 37.82 4.20
657 958 4.519540 AATTATGCAGTGTGTTTCCACC 57.480 40.909 0.00 0.00 41.09 4.61
659 960 7.392953 TGAATCTAATTATGCAGTGTGTTTCCA 59.607 33.333 0.00 0.00 0.00 3.53
785 1086 4.471548 GGCTGGAATAGGACTAGTACTGA 58.528 47.826 18.50 2.42 0.00 3.41
832 1152 1.002544 GCCAAACTAGCAGTGACTCCT 59.997 52.381 0.00 0.00 0.00 3.69
844 1164 2.224426 ACATTGTCTCCGTGCCAAACTA 60.224 45.455 0.00 0.00 0.00 2.24
891 1211 2.158842 AGCCCATTGTCAAGCTAGCTAG 60.159 50.000 19.70 16.84 32.73 3.42
903 1223 2.039418 TCGCATCTACTAGCCCATTGT 58.961 47.619 0.00 0.00 0.00 2.71
914 1245 3.424326 CGAGACTCGTCGCATCTAC 57.576 57.895 16.83 0.00 34.72 2.59
954 1285 1.797211 TTGCGGTAAAAGTTGGGGCG 61.797 55.000 0.00 0.00 0.00 6.13
1035 1366 3.936203 GAGGTCACGTGGGCCACA 61.936 66.667 34.11 14.37 33.40 4.17
1521 1870 4.471904 TGAACCAAGCAGATAGTTCGAT 57.528 40.909 0.00 0.00 41.17 3.59
1526 1875 2.038557 ACGGTTGAACCAAGCAGATAGT 59.961 45.455 15.58 0.00 41.25 2.12
1587 1938 5.423886 TCAATATACAGTGCACAAATCCGA 58.576 37.500 21.04 2.74 0.00 4.55
1602 1953 6.279882 GGATGGATAGCTCAGCTCAATATAC 58.720 44.000 0.00 0.00 40.44 1.47
1619 1970 0.753262 GTACAGGCAGTCGGATGGAT 59.247 55.000 0.00 0.00 0.00 3.41
1620 1971 0.324368 AGTACAGGCAGTCGGATGGA 60.324 55.000 0.00 0.00 0.00 3.41
1621 1972 0.537188 AAGTACAGGCAGTCGGATGG 59.463 55.000 0.00 0.00 0.00 3.51
1622 1973 1.645034 CAAGTACAGGCAGTCGGATG 58.355 55.000 0.00 0.00 0.00 3.51
1657 2008 2.825205 ACTTGCAAAAGCAATGGTCAC 58.175 42.857 0.00 0.00 0.00 3.67
2002 2360 8.654215 CGAGAGCTGTATTATACGTACATCTAA 58.346 37.037 0.00 0.00 30.97 2.10
2003 2361 8.031277 TCGAGAGCTGTATTATACGTACATCTA 58.969 37.037 0.00 0.00 30.97 1.98
2004 2362 6.872547 TCGAGAGCTGTATTATACGTACATCT 59.127 38.462 0.00 0.00 32.83 2.90
2005 2363 7.058298 TCGAGAGCTGTATTATACGTACATC 57.942 40.000 0.00 0.00 32.13 3.06
2006 2364 7.333672 TGATCGAGAGCTGTATTATACGTACAT 59.666 37.037 0.00 0.00 32.13 2.29
2007 2365 6.647895 TGATCGAGAGCTGTATTATACGTACA 59.352 38.462 0.00 0.00 0.00 2.90
2008 2366 7.058298 TGATCGAGAGCTGTATTATACGTAC 57.942 40.000 0.00 0.00 0.00 3.67
2009 2367 6.183360 GCTGATCGAGAGCTGTATTATACGTA 60.183 42.308 11.13 0.00 33.37 3.57
2010 2368 5.391097 GCTGATCGAGAGCTGTATTATACGT 60.391 44.000 11.13 0.00 33.37 3.57
2011 2369 5.025190 GCTGATCGAGAGCTGTATTATACG 58.975 45.833 11.13 0.00 33.37 3.06
2022 2380 0.102481 TAAACGGGCTGATCGAGAGC 59.898 55.000 10.14 10.14 35.57 4.09
2093 2451 7.506938 TGAAAGGGAATGTTCAGAAGAGAATTT 59.493 33.333 0.00 0.00 30.41 1.82
2187 2545 6.802608 TCTCAAAGAAAGAAGTCGTAACTCA 58.197 36.000 0.00 0.00 33.48 3.41
2193 2551 9.110502 ACTTAATTTCTCAAAGAAAGAAGTCGT 57.889 29.630 17.96 6.47 46.15 4.34
2261 2620 3.617540 ATCGTCGAGAGTGAGCATAAG 57.382 47.619 0.00 0.00 0.00 1.73
2308 2667 5.482908 AGTCTACGACATTCTTTTCATGCT 58.517 37.500 0.00 0.00 34.60 3.79
2403 2762 7.246171 ACTGAAGATGTAGTTGAGGTTATGT 57.754 36.000 0.00 0.00 0.00 2.29
2549 2913 8.750515 TCAAGCAAATTCTCCATACATAATGA 57.249 30.769 0.00 0.00 37.86 2.57
2681 3045 0.968901 TGAGCTACCACCGATTCCGT 60.969 55.000 0.00 0.00 0.00 4.69
2789 3153 2.674563 CTTGTCCGACAACCCCTGCA 62.675 60.000 9.99 0.00 33.96 4.41
3258 3992 8.482128 TGATTGGACTAATTTTCTGGTTTTGTT 58.518 29.630 0.00 0.00 0.00 2.83
3489 4223 2.586792 GAGGGCGAGCACCAATCT 59.413 61.111 0.00 0.00 0.00 2.40
3659 4393 3.557595 GTCAGCCGTTTTGATATCCTGAG 59.442 47.826 0.00 0.00 0.00 3.35
3678 4412 1.948104 CCACGTTTTCAGACCAGTCA 58.052 50.000 0.00 0.00 0.00 3.41
3779 4513 0.179166 GCAGCACAGAGAGAGAGACG 60.179 60.000 0.00 0.00 0.00 4.18
3782 4518 1.175654 TGAGCAGCACAGAGAGAGAG 58.824 55.000 0.00 0.00 0.00 3.20
3855 4591 4.095483 AGACAACAGCAAAGTGAGTTTCAG 59.905 41.667 0.00 0.00 0.00 3.02
3857 4593 4.622701 AGACAACAGCAAAGTGAGTTTC 57.377 40.909 0.00 0.00 0.00 2.78
3858 4594 4.458989 TCAAGACAACAGCAAAGTGAGTTT 59.541 37.500 0.00 0.00 0.00 2.66
3995 4731 2.774809 GGCCTCAGGTTCTCCTTCTATT 59.225 50.000 0.00 0.00 43.07 1.73
4094 4832 4.371786 CAGATACAGATGCACGGTAACAT 58.628 43.478 0.00 0.00 33.45 2.71
4106 4844 4.511527 CACTTCCAGTTGCAGATACAGAT 58.488 43.478 0.00 0.00 0.00 2.90
4218 4956 1.551503 ATACACATCAGCGCGCATCG 61.552 55.000 35.10 21.05 42.12 3.84
4260 4998 7.330946 GCATGTATAGCGTCATAGGATTTTGTA 59.669 37.037 0.00 0.00 0.00 2.41
4300 5038 1.578897 GGCAACCAAATACCCCCATT 58.421 50.000 0.00 0.00 0.00 3.16
4337 5075 0.893727 AATTTCGTCCCGCAAAGGCT 60.894 50.000 0.00 0.00 39.21 4.58
4383 5132 2.066262 TGCTTTAAAGTCCGAGCGAAG 58.934 47.619 16.38 0.00 37.94 3.79
4386 5135 2.271800 AGATGCTTTAAAGTCCGAGCG 58.728 47.619 16.38 0.00 37.94 5.03
4389 5138 2.569853 TGGGAGATGCTTTAAAGTCCGA 59.430 45.455 16.38 9.60 0.00 4.55
4395 5144 2.897271 TGGCTGGGAGATGCTTTAAA 57.103 45.000 0.00 0.00 0.00 1.52
4415 5197 3.231298 GGCCATTCCTAGCCGACT 58.769 61.111 0.00 0.00 39.87 4.18
4419 5201 2.280186 CGTCGGCCATTCCTAGCC 60.280 66.667 2.24 0.00 46.17 3.93
4482 5280 0.104855 GCCATCTCTGTGGTCGCATA 59.895 55.000 0.00 0.00 41.47 3.14
4514 5312 2.554032 CCTGTCGCTTTTCCAAAGACAT 59.446 45.455 0.25 0.00 40.46 3.06
4515 5313 1.946768 CCTGTCGCTTTTCCAAAGACA 59.053 47.619 0.25 0.00 39.21 3.41
4523 5321 3.366374 CCCAATTTCTCCTGTCGCTTTTC 60.366 47.826 0.00 0.00 0.00 2.29
4598 5396 1.765074 GGGTGGTGGCAGGAGTTTA 59.235 57.895 0.00 0.00 0.00 2.01
4646 5448 1.068472 CCTGCTCGTAAGTGTCGACTT 60.068 52.381 17.92 6.19 44.90 3.01
4648 5450 0.240411 ACCTGCTCGTAAGTGTCGAC 59.760 55.000 9.11 9.11 39.48 4.20
4657 5459 2.493030 GCCGCTTACCTGCTCGTA 59.507 61.111 0.00 0.00 0.00 3.43
4684 5486 2.266372 CCATGTACCGCCGACCAA 59.734 61.111 0.00 0.00 0.00 3.67
4823 5661 1.475682 GTCACAGGTCTAACCCTACCG 59.524 57.143 0.00 0.00 39.75 4.02
4836 5675 5.879777 TGTACAATCATACAATGGTCACAGG 59.120 40.000 0.00 0.00 32.07 4.00
4851 5692 4.485163 CACAGATCGACAGTGTACAATCA 58.515 43.478 0.00 0.00 32.54 2.57
4874 5715 6.199154 CACTAGCTACCAGAACATTACATTCG 59.801 42.308 0.00 0.00 0.00 3.34
4930 5781 4.286032 TCACAACTAGCTACCAATCCTTGT 59.714 41.667 0.00 0.00 0.00 3.16
4986 5843 6.764308 ACCAATCCATGAAGTTCAATACAG 57.236 37.500 10.14 0.00 0.00 2.74
4990 5847 6.078456 TCCTACCAATCCATGAAGTTCAAT 57.922 37.500 10.14 0.00 0.00 2.57
4991 5848 5.512942 TCCTACCAATCCATGAAGTTCAA 57.487 39.130 10.14 0.00 0.00 2.69
4992 5849 5.439721 CATCCTACCAATCCATGAAGTTCA 58.560 41.667 8.27 8.27 0.00 3.18
4993 5850 4.276926 GCATCCTACCAATCCATGAAGTTC 59.723 45.833 0.00 0.00 0.00 3.01
4994 5851 4.210331 GCATCCTACCAATCCATGAAGTT 58.790 43.478 0.00 0.00 0.00 2.66
4995 5852 3.202818 TGCATCCTACCAATCCATGAAGT 59.797 43.478 0.00 0.00 0.00 3.01
4996 5853 3.824133 TGCATCCTACCAATCCATGAAG 58.176 45.455 0.00 0.00 0.00 3.02
5012 5869 2.798976 ACCACACAACAACATGCATC 57.201 45.000 0.00 0.00 0.00 3.91
5019 5876 3.437395 TCAACACACTACCACACAACAAC 59.563 43.478 0.00 0.00 0.00 3.32
5049 5906 3.090790 ACAACATGCATGCTACCAATCA 58.909 40.909 26.53 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.