Multiple sequence alignment - TraesCS2A01G285400

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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 TraesCS2A01G285400 chr2A 100.000 4164 0 0 1 4164 481805780 481809943 0.000000e+00 7690.0
1 TraesCS2A01G285400 chr2D 93.122 3911 185 26 285 4164 359938657 359942514 0.000000e+00 5655.0
2 TraesCS2A01G285400 chr2D 89.971 349 35 0 3816 4164 353164376 353164028 6.350000e-123 451.0
3 TraesCS2A01G285400 chr2D 91.026 234 21 0 3 236 359938424 359938657 2.420000e-82 316.0
4 TraesCS2A01G285400 chr2B 92.965 3909 203 26 301 4164 426149297 426145416 0.000000e+00 5629.0
5 TraesCS2A01G285400 chr2B 88.994 318 35 0 1 318 426149625 426149308 1.090000e-105 394.0
6 TraesCS2A01G285400 chr2B 80.620 129 21 3 3316 3441 89331077 89330950 3.430000e-16 97.1
7 TraesCS2A01G285400 chr4D 89.888 356 29 7 3810 4160 82127587 82127234 6.350000e-123 451.0
8 TraesCS2A01G285400 chr7D 89.802 353 33 3 3813 4164 480459920 480459570 2.280000e-122 449.0
9 TraesCS2A01G285400 chr7D 89.296 355 35 2 3813 4164 378578242 378577888 3.820000e-120 442.0
10 TraesCS2A01G285400 chr7D 89.655 348 33 3 3813 4158 239760976 239761322 1.370000e-119 440.0
11 TraesCS2A01G285400 chr7D 88.920 352 39 0 3813 4164 310715528 310715879 6.390000e-118 435.0
12 TraesCS2A01G285400 chr6D 89.518 353 36 1 3813 4164 404619289 404618937 2.950000e-121 446.0
13 TraesCS2A01G285400 chr6B 82.857 105 18 0 3337 3441 644538 644434 1.230000e-15 95.3
14 TraesCS2A01G285400 chr5B 93.333 45 2 1 3363 3407 439695518 439695475 9.660000e-07 65.8
15 TraesCS2A01G285400 chr3A 76.522 115 24 1 3324 3438 501028567 501028678 4.500000e-05 60.2


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 TraesCS2A01G285400 chr2A 481805780 481809943 4163 False 7690.0 7690 100.0000 1 4164 1 chr2A.!!$F1 4163
1 TraesCS2A01G285400 chr2D 359938424 359942514 4090 False 2985.5 5655 92.0740 3 4164 2 chr2D.!!$F1 4161
2 TraesCS2A01G285400 chr2B 426145416 426149625 4209 True 3011.5 5629 90.9795 1 4164 2 chr2B.!!$R2 4163

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
416 448 0.179018 ATAGAGCCCAACGCCAATCC 60.179 55.0 0.0 0.0 38.78 3.01 F
1266 1315 1.182385 ATCTCGATCCTCCCCTTCGC 61.182 60.0 0.0 0.0 33.08 4.70 F
1518 1572 0.110373 CTTTAGCGTGCCGTTGTTCC 60.110 55.0 0.0 0.0 0.00 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1518 1572 0.581529 CCGCTGCATATAACCGTGTG 59.418 55.000 0.00 0.0 0.00 3.82 R
2201 2272 1.129064 GCAATTGCGAAAAATGGGCAG 59.871 47.619 15.87 0.0 38.04 4.85 R
3487 3583 0.539438 ATGGACATTTGCCACACGGT 60.539 50.000 0.00 0.0 38.44 4.83 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
58 59 6.648310 TGTCATCTTGAAACTCTGATTGAGAC 59.352 38.462 0.00 0.00 45.39 3.36
127 128 2.012937 ACAATCATTGGCAATTGCGG 57.987 45.000 23.48 13.00 43.26 5.69
140 141 3.586843 TTGCGGGGAAGTATGCAAT 57.413 47.368 0.00 0.00 41.95 3.56
161 162 6.683610 GCAATGATAGCATCCCTTTTAAGCAA 60.684 38.462 0.00 0.00 32.35 3.91
163 164 5.509498 TGATAGCATCCCTTTTAAGCAACT 58.491 37.500 0.00 0.00 0.00 3.16
164 165 5.357878 TGATAGCATCCCTTTTAAGCAACTG 59.642 40.000 0.00 0.00 0.00 3.16
166 167 4.347607 AGCATCCCTTTTAAGCAACTGAT 58.652 39.130 0.00 0.00 0.00 2.90
260 261 5.574891 TTGCTACTCTTGCTTTGACAAAA 57.425 34.783 1.62 0.00 0.00 2.44
262 263 4.397730 TGCTACTCTTGCTTTGACAAAACA 59.602 37.500 1.62 0.69 0.00 2.83
267 268 6.038356 ACTCTTGCTTTGACAAAACAATCAG 58.962 36.000 15.20 15.24 0.00 2.90
272 273 4.746115 GCTTTGACAAAACAATCAGCATCA 59.254 37.500 1.62 0.00 35.21 3.07
279 280 2.211250 ACAATCAGCATCAGCCTTGT 57.789 45.000 0.00 0.00 43.56 3.16
280 281 3.354948 ACAATCAGCATCAGCCTTGTA 57.645 42.857 0.00 0.00 43.56 2.41
290 291 2.447443 TCAGCCTTGTAGTCGAGTGAT 58.553 47.619 2.10 0.00 0.00 3.06
299 328 6.183360 CCTTGTAGTCGAGTGATACAATCTCA 60.183 42.308 2.10 0.00 38.39 3.27
310 339 9.553064 GAGTGATACAATCTCATGAAAGGTATT 57.447 33.333 0.00 0.00 0.00 1.89
331 363 3.168035 TGCTTTTAAGATCTTGCCCCA 57.832 42.857 18.47 5.98 0.00 4.96
332 364 3.505386 TGCTTTTAAGATCTTGCCCCAA 58.495 40.909 18.47 0.66 0.00 4.12
336 368 5.680665 GCTTTTAAGATCTTGCCCCAATCTG 60.681 44.000 18.47 0.00 30.35 2.90
349 381 3.650942 CCCCAATCTGTATTAGCACCCTA 59.349 47.826 0.00 0.00 0.00 3.53
401 433 1.065491 AGTTGGCCACGCATCAATAGA 60.065 47.619 3.88 0.00 0.00 1.98
414 446 1.064758 TCAATAGAGCCCAACGCCAAT 60.065 47.619 0.00 0.00 38.78 3.16
415 447 1.334869 CAATAGAGCCCAACGCCAATC 59.665 52.381 0.00 0.00 38.78 2.67
416 448 0.179018 ATAGAGCCCAACGCCAATCC 60.179 55.000 0.00 0.00 38.78 3.01
509 542 7.974504 ACTTTGAAGAAGAATCTAGGGTTACA 58.025 34.615 0.00 0.00 33.77 2.41
524 557 5.454966 AGGGTTACACTTGACCATTTTCTT 58.545 37.500 0.00 0.00 37.68 2.52
601 634 6.959311 CGTTACGAATTTCTTATTGGACAAGG 59.041 38.462 0.00 0.00 0.00 3.61
665 698 4.398319 AGGTGTTGGTCGAAAATCTTCAT 58.602 39.130 0.00 0.00 0.00 2.57
696 729 6.770746 TCTGAGTAGTGTAGTACCAATTCC 57.229 41.667 0.00 0.00 0.00 3.01
711 744 1.474330 ATTCCGGGCCTTCAATTCAC 58.526 50.000 0.84 0.00 0.00 3.18
793 829 1.752498 TCGCCATTCTTTAGTAGCGGA 59.248 47.619 2.14 0.00 43.50 5.54
848 887 4.157840 GGGTCAAACTGGCGAGAAATAAAT 59.842 41.667 1.44 0.00 0.00 1.40
1212 1261 1.228154 GGACTTCACCACGCCCTTT 60.228 57.895 0.00 0.00 0.00 3.11
1266 1315 1.182385 ATCTCGATCCTCCCCTTCGC 61.182 60.000 0.00 0.00 33.08 4.70
1518 1572 0.110373 CTTTAGCGTGCCGTTGTTCC 60.110 55.000 0.00 0.00 0.00 3.62
1691 1745 8.862085 CCCTTTTGTTCTGTTTACCCTTTTATA 58.138 33.333 0.00 0.00 0.00 0.98
1774 1828 4.700700 TGAAGAGATCTGTGCATGTATGG 58.299 43.478 0.00 0.00 0.00 2.74
1960 2016 2.478134 GTCAGATACATTGCATCGCTCC 59.522 50.000 0.00 0.00 0.00 4.70
2059 2115 6.481976 ACATGTCAGTTTGTCATTACGAAGAA 59.518 34.615 0.00 0.00 29.30 2.52
2066 2122 9.103048 CAGTTTGTCATTACGAAGAATTAACAC 57.897 33.333 0.00 0.00 29.30 3.32
2067 2123 8.832521 AGTTTGTCATTACGAAGAATTAACACA 58.167 29.630 0.00 0.00 29.30 3.72
2068 2124 9.607285 GTTTGTCATTACGAAGAATTAACACAT 57.393 29.630 0.00 0.00 29.30 3.21
2127 2198 3.650950 GGGCTCAGGGTCCTTGCA 61.651 66.667 11.88 0.00 36.61 4.08
2179 2250 1.836802 AGGGAGGAAATCACTCTGAGC 59.163 52.381 4.19 0.00 36.81 4.26
2201 2272 4.647964 CCAGTGTGTTGCGATGTTTATAC 58.352 43.478 0.00 0.00 0.00 1.47
2338 2409 2.229675 TCGCAGACCATTGCAGATAG 57.770 50.000 0.00 0.00 44.28 2.08
2343 2414 4.036027 CGCAGACCATTGCAGATAGAAAAT 59.964 41.667 0.00 0.00 44.28 1.82
2345 2416 6.565435 CGCAGACCATTGCAGATAGAAAATAG 60.565 42.308 0.00 0.00 44.28 1.73
2698 2769 3.740397 GCGCACATCCAGCAGCAA 61.740 61.111 0.30 0.00 33.78 3.91
2893 2976 3.451004 GGCGTGGCAATGCATCCA 61.451 61.111 7.78 0.27 40.34 3.41
2933 3016 2.713770 CTGCGTGGCTGATGATGC 59.286 61.111 0.00 0.00 0.00 3.91
2953 3036 2.643272 CAGCAGCAGCAACACCAG 59.357 61.111 3.17 0.00 45.49 4.00
2956 3039 2.643272 CAGCAGCAACACCAGCAG 59.357 61.111 0.00 0.00 0.00 4.24
2963 3046 3.292936 AACACCAGCAGCAGCAGC 61.293 61.111 3.17 0.46 45.49 5.25
2964 3047 4.574271 ACACCAGCAGCAGCAGCA 62.574 61.111 12.92 0.00 45.49 4.41
2965 3048 4.039357 CACCAGCAGCAGCAGCAC 62.039 66.667 12.92 0.00 45.49 4.40
3045 3128 1.980772 GCAGCTCAAATGGGCAGGT 60.981 57.895 8.17 0.00 0.00 4.00
3088 3171 2.357836 CAGGCTGCTGGGGAACAT 59.642 61.111 0.00 0.00 0.00 2.71
3265 3354 3.508744 AAGAGCACCAAACAAACAGTG 57.491 42.857 0.00 0.00 0.00 3.66
3308 3397 2.096248 GTTCATCCCCGCAAATGGTTA 58.904 47.619 0.00 0.00 0.00 2.85
3317 3406 2.606108 CGCAAATGGTTAGCTTTTCCC 58.394 47.619 0.00 0.00 0.00 3.97
3332 3423 2.270352 TTCCCAAATGAAGTGCGACT 57.730 45.000 0.00 0.00 0.00 4.18
3361 3457 0.745845 CGCTGCACTCTGGCCTTAAT 60.746 55.000 3.32 0.00 0.00 1.40
3380 3476 7.095649 GCCTTAATATTTTTCGATGGCAATTCC 60.096 37.037 0.00 0.00 37.91 3.01
3391 3487 2.596346 TGGCAATTCCAGTCACACAAT 58.404 42.857 0.00 0.00 40.72 2.71
3406 3502 8.291740 CAGTCACACAATGATGACAATTTCTAA 58.708 33.333 18.99 0.00 46.34 2.10
3414 3510 8.736742 CAATGATGACAATTTCTAATAACACGC 58.263 33.333 0.00 0.00 0.00 5.34
3415 3511 6.781138 TGATGACAATTTCTAATAACACGCC 58.219 36.000 0.00 0.00 0.00 5.68
3441 3537 9.271738 CGCAAGTTTTTGTCAAAAATAAAATGT 57.728 25.926 22.78 4.94 41.85 2.71
3469 3565 4.630069 GTCTAACGTGTGGCATTTATCAGT 59.370 41.667 0.00 0.00 0.00 3.41
3470 3566 5.121768 GTCTAACGTGTGGCATTTATCAGTT 59.878 40.000 0.00 0.00 0.00 3.16
3471 3567 4.846779 AACGTGTGGCATTTATCAGTTT 57.153 36.364 0.00 0.00 0.00 2.66
3506 3602 0.539438 ACCGTGTGGCAAATGTCCAT 60.539 50.000 0.00 0.00 39.70 3.41
3521 3623 0.107643 TCCATGGACACTTCAACGCA 59.892 50.000 11.44 0.00 0.00 5.24
3524 3626 0.108585 ATGGACACTTCAACGCACCT 59.891 50.000 0.00 0.00 0.00 4.00
3554 3656 3.181505 CGCAAACCAACACTAAACTGTGA 60.182 43.478 1.47 0.00 40.12 3.58
3556 3658 4.798387 GCAAACCAACACTAAACTGTGAAG 59.202 41.667 1.47 0.00 40.12 3.02
3623 3725 1.789576 GCCCTCCCAAAACCCTCTCA 61.790 60.000 0.00 0.00 0.00 3.27
3624 3726 1.002857 CCCTCCCAAAACCCTCTCAT 58.997 55.000 0.00 0.00 0.00 2.90
3629 3731 2.983192 TCCCAAAACCCTCTCATGTACA 59.017 45.455 0.00 0.00 0.00 2.90
3671 3773 0.595588 TTTGGCGTCGCATTCATGTT 59.404 45.000 20.50 0.00 0.00 2.71
3689 3796 0.675083 TTGGTTTAGAGCGGACGTGA 59.325 50.000 0.00 0.00 0.00 4.35
3690 3797 0.038892 TGGTTTAGAGCGGACGTGAC 60.039 55.000 0.00 0.00 0.00 3.67
3691 3798 0.735287 GGTTTAGAGCGGACGTGACC 60.735 60.000 0.00 0.00 0.00 4.02
3708 3815 2.124983 CGGCCACTACAGCATGCT 60.125 61.111 16.30 16.30 42.53 3.79
3831 3938 0.918983 TTCCGATGATGGGCTTCCTT 59.081 50.000 0.00 0.00 0.00 3.36
3836 3943 4.349636 TCCGATGATGGGCTTCCTTAAATA 59.650 41.667 0.00 0.00 0.00 1.40
3838 3945 5.308825 CGATGATGGGCTTCCTTAAATACT 58.691 41.667 0.00 0.00 0.00 2.12
3851 3958 7.235935 TCCTTAAATACTCGAGGTCTTTGAA 57.764 36.000 18.41 3.37 0.00 2.69
3883 3990 2.228822 GGATGCACACCCACTTAGTTTG 59.771 50.000 0.00 0.00 0.00 2.93
3886 3993 4.359434 TGCACACCCACTTAGTTTGATA 57.641 40.909 0.00 0.00 0.00 2.15
3922 4029 6.723298 ACACTTATAGCTCTTAGTGCATCT 57.277 37.500 15.69 0.00 41.22 2.90
3946 4053 4.508551 TGCATGTCAATCCATACTCCTT 57.491 40.909 0.00 0.00 0.00 3.36
3967 4074 6.778559 TCCTTGCATTGATATCAATTGATGGA 59.221 34.615 27.59 23.62 43.48 3.41
3991 4098 1.077501 CCATGGCCCGTTGATCAGT 60.078 57.895 0.00 0.00 0.00 3.41
4001 4108 2.182014 CGTTGATCAGTTGCGTCGATA 58.818 47.619 0.00 0.00 0.00 2.92
4027 4136 6.318900 TGAGACTTTCTTCCTTTTTGTCTTCC 59.681 38.462 0.00 0.00 34.07 3.46
4028 4137 6.427441 AGACTTTCTTCCTTTTTGTCTTCCT 58.573 36.000 0.00 0.00 30.33 3.36
4061 4170 5.768662 TCTCTACCACCGTATTCTATTCCAG 59.231 44.000 0.00 0.00 0.00 3.86
4070 4179 5.864474 CCGTATTCTATTCCAGTCATAGTGC 59.136 44.000 0.00 0.00 0.00 4.40
4071 4180 6.294787 CCGTATTCTATTCCAGTCATAGTGCT 60.295 42.308 0.00 0.00 0.00 4.40
4072 4181 7.094334 CCGTATTCTATTCCAGTCATAGTGCTA 60.094 40.741 0.00 0.00 0.00 3.49
4073 4182 8.462811 CGTATTCTATTCCAGTCATAGTGCTAT 58.537 37.037 0.00 0.00 0.00 2.97
4078 4187 9.533831 TCTATTCCAGTCATAGTGCTATATTCA 57.466 33.333 0.00 0.00 0.00 2.57
4081 4190 7.781324 TCCAGTCATAGTGCTATATTCATGA 57.219 36.000 0.00 0.00 0.00 3.07
4082 4191 7.606349 TCCAGTCATAGTGCTATATTCATGAC 58.394 38.462 0.00 4.72 41.51 3.06
4140 4262 6.801862 GCTGAAGCACGTTAAAAAGTATGAAT 59.198 34.615 0.00 0.00 41.59 2.57
4160 4282 0.037975 CAATTGCTTGGCTGACACCC 60.038 55.000 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 3.059982 TGAGCAAGGGGACTCACG 58.940 61.111 0.00 0.00 42.68 4.35
102 103 5.107182 CGCAATTGCCAATGATTGTAAACAA 60.107 36.000 24.24 0.00 37.79 2.83
112 113 0.902048 TTCCCCGCAATTGCCAATGA 60.902 50.000 24.24 12.78 37.91 2.57
140 141 5.357878 CAGTTGCTTAAAAGGGATGCTATCA 59.642 40.000 0.00 0.00 0.00 2.15
161 162 2.563179 ACTGCCAAGAACGAGTATCAGT 59.437 45.455 0.00 0.00 33.17 3.41
163 164 4.014406 TCTACTGCCAAGAACGAGTATCA 58.986 43.478 0.00 0.00 33.17 2.15
164 165 4.634184 TCTACTGCCAAGAACGAGTATC 57.366 45.455 0.00 0.00 0.00 2.24
166 167 5.401531 AAATCTACTGCCAAGAACGAGTA 57.598 39.130 0.00 0.00 0.00 2.59
247 248 4.502016 TGCTGATTGTTTTGTCAAAGCAA 58.498 34.783 24.14 24.14 43.93 3.91
260 261 2.211250 ACAAGGCTGATGCTGATTGT 57.789 45.000 0.00 0.00 39.59 2.71
262 263 3.539604 GACTACAAGGCTGATGCTGATT 58.460 45.455 0.00 0.00 39.59 2.57
267 268 1.134965 ACTCGACTACAAGGCTGATGC 60.135 52.381 0.00 0.00 38.76 3.91
272 273 3.353557 TGTATCACTCGACTACAAGGCT 58.646 45.455 0.00 0.00 0.00 4.58
279 280 7.568199 TTCATGAGATTGTATCACTCGACTA 57.432 36.000 0.00 0.00 33.93 2.59
280 281 6.456795 TTCATGAGATTGTATCACTCGACT 57.543 37.500 0.00 0.00 33.93 4.18
290 291 8.579850 AAGCAAATACCTTTCATGAGATTGTA 57.420 30.769 0.00 0.00 0.00 2.41
310 339 3.505386 TGGGGCAAGATCTTAAAAGCAA 58.495 40.909 7.86 0.00 0.00 3.91
331 363 3.651423 GGGGTAGGGTGCTAATACAGATT 59.349 47.826 0.00 0.00 0.00 2.40
332 364 3.248888 GGGGTAGGGTGCTAATACAGAT 58.751 50.000 0.00 0.00 0.00 2.90
336 368 1.708341 TCGGGGTAGGGTGCTAATAC 58.292 55.000 0.00 0.00 0.00 1.89
349 381 0.539669 CTTTGCCCTTTCTTCGGGGT 60.540 55.000 0.00 0.00 44.25 4.95
416 448 4.560856 CTCGCTCGAAGGCTCCCG 62.561 72.222 3.27 3.27 0.00 5.14
465 498 7.518188 TCAAAGTTAAGAGGTTCCAAGAAGAT 58.482 34.615 0.00 0.00 0.00 2.40
488 521 7.234782 TCAAGTGTAACCCTAGATTCTTCTTCA 59.765 37.037 0.00 0.00 37.80 3.02
509 542 5.634118 TCATGGAGAAGAAAATGGTCAAGT 58.366 37.500 0.00 0.00 0.00 3.16
611 644 6.763355 TGCAATTGGTGGTGTAATTTATTGT 58.237 32.000 7.72 0.00 0.00 2.71
620 653 2.881734 TGGATTGCAATTGGTGGTGTA 58.118 42.857 14.33 0.00 0.00 2.90
665 698 3.832490 ACTACACTACTCAGATGCAACCA 59.168 43.478 0.00 0.00 0.00 3.67
696 729 1.508088 GCAGTGAATTGAAGGCCCG 59.492 57.895 0.00 0.00 0.00 6.13
711 744 4.621068 TCGCAAAAGAGAAATATGGCAG 57.379 40.909 0.00 0.00 0.00 4.85
793 829 9.671279 CCTTTTAGGAAATTTGAGGCATTTATT 57.329 29.630 0.00 0.00 37.67 1.40
848 887 3.393278 CCCGTCTCCCCATTTATCCTTTA 59.607 47.826 0.00 0.00 0.00 1.85
1185 1234 2.258726 GGTGAAGTCCGGGTTGCAC 61.259 63.158 0.00 5.05 0.00 4.57
1266 1315 3.470567 GCACGAAGACGACGGCTG 61.471 66.667 2.63 0.00 42.66 4.85
1391 1440 2.648102 CTAAGTCGCGACGCCGAG 60.648 66.667 31.56 22.18 37.99 4.63
1518 1572 0.581529 CCGCTGCATATAACCGTGTG 59.418 55.000 0.00 0.00 0.00 3.82
1691 1745 5.139727 TCTGAACATTTTGTCCAGGAACAT 58.860 37.500 0.00 0.00 0.00 2.71
1692 1746 4.531854 TCTGAACATTTTGTCCAGGAACA 58.468 39.130 0.00 0.00 0.00 3.18
1798 1852 5.939296 TGACATGAGTCTATCAATTGTTGCA 59.061 36.000 5.13 0.00 45.20 4.08
1960 2016 6.922980 TTTCAACAACGAAGTACTAGATCG 57.077 37.500 12.70 12.70 45.00 3.69
2026 2082 4.211164 TGACAAACTGACATGTTCGACATC 59.789 41.667 0.00 0.00 36.53 3.06
2179 2250 3.829886 ATAAACATCGCAACACACTGG 57.170 42.857 0.00 0.00 0.00 4.00
2201 2272 1.129064 GCAATTGCGAAAAATGGGCAG 59.871 47.619 15.87 0.00 38.04 4.85
2343 2414 8.058235 TCTCTCTAGAGTGGTACTGTAGTACTA 58.942 40.741 19.21 12.04 44.23 1.82
2345 2416 7.111247 TCTCTCTAGAGTGGTACTGTAGTAC 57.889 44.000 19.21 12.61 41.35 2.73
2659 2730 2.957489 CGCACGTTGTCCGACACA 60.957 61.111 0.00 0.00 40.70 3.72
2893 2976 1.448540 CGCGGAAGGATCAAGCTGT 60.449 57.895 0.00 0.00 0.00 4.40
2916 2999 2.048312 CTGCATCATCAGCCACGCAG 62.048 60.000 0.00 0.00 40.68 5.18
2917 3000 2.046120 TGCATCATCAGCCACGCA 60.046 55.556 0.00 0.00 0.00 5.24
2933 3016 2.050351 GTGTTGCTGCTGCTGCTG 60.050 61.111 27.67 16.73 40.48 4.41
2947 3030 4.574271 TGCTGCTGCTGCTGGTGT 62.574 61.111 27.67 0.00 40.48 4.16
2963 3046 3.738246 CTGCTGCTGCTGCTGGTG 61.738 66.667 27.67 13.98 40.48 4.17
3141 3224 3.435186 GCTCCCTCCTTTGTGCGC 61.435 66.667 0.00 0.00 0.00 6.09
3142 3225 2.032528 TGCTCCCTCCTTTGTGCG 59.967 61.111 0.00 0.00 0.00 5.34
3226 3315 4.825422 TCTTACATCCAAGCAGAGTTCAG 58.175 43.478 0.00 0.00 0.00 3.02
3308 3397 2.288395 CGCACTTCATTTGGGAAAAGCT 60.288 45.455 0.00 0.00 0.00 3.74
3317 3406 1.792367 TGACGAGTCGCACTTCATTTG 59.208 47.619 13.59 0.00 0.00 2.32
3355 3451 7.925483 TGGAATTGCCATCGAAAAATATTAAGG 59.075 33.333 0.00 0.00 43.33 2.69
3380 3476 6.675026 AGAAATTGTCATCATTGTGTGACTG 58.325 36.000 18.58 0.00 43.87 3.51
3391 3487 6.456315 CGGCGTGTTATTAGAAATTGTCATCA 60.456 38.462 0.00 0.00 0.00 3.07
3406 3502 2.223618 ACAAAAACTTGCGGCGTGTTAT 60.224 40.909 9.37 2.45 0.00 1.89
3414 3510 8.732227 CATTTTATTTTTGACAAAAACTTGCGG 58.268 29.630 24.49 11.97 42.57 5.69
3415 3511 9.271738 ACATTTTATTTTTGACAAAAACTTGCG 57.728 25.926 24.49 15.11 42.57 4.85
3444 3540 4.390603 TGATAAATGCCACACGTTAGACAC 59.609 41.667 0.00 0.00 0.00 3.67
3446 3542 4.630069 ACTGATAAATGCCACACGTTAGAC 59.370 41.667 0.00 0.00 0.00 2.59
3447 3543 4.827692 ACTGATAAATGCCACACGTTAGA 58.172 39.130 0.00 0.00 0.00 2.10
3477 3573 0.816421 GCCACACGGTGTTAGGTGTT 60.816 55.000 11.82 0.00 44.49 3.32
3487 3583 0.539438 ATGGACATTTGCCACACGGT 60.539 50.000 0.00 0.00 38.44 4.83
3506 3602 0.813610 CAGGTGCGTTGAAGTGTCCA 60.814 55.000 0.00 0.00 0.00 4.02
3516 3618 1.169661 TGCGGAATTTCAGGTGCGTT 61.170 50.000 0.00 0.00 0.00 4.84
3521 3623 1.698506 TGGTTTGCGGAATTTCAGGT 58.301 45.000 0.00 0.00 0.00 4.00
3524 3626 2.428890 AGTGTTGGTTTGCGGAATTTCA 59.571 40.909 0.00 0.00 0.00 2.69
3554 3656 1.227734 CCGGACGTCCACAAACCTT 60.228 57.895 32.80 0.00 35.14 3.50
3556 3658 1.957695 GTCCGGACGTCCACAAACC 60.958 63.158 32.80 11.13 35.14 3.27
3608 3710 2.983192 TGTACATGAGAGGGTTTTGGGA 59.017 45.455 0.00 0.00 0.00 4.37
3623 3725 1.412710 ACGATTGGAGCGGATGTACAT 59.587 47.619 8.43 8.43 0.00 2.29
3624 3726 0.821517 ACGATTGGAGCGGATGTACA 59.178 50.000 0.00 0.00 0.00 2.90
3629 3731 2.203070 GGCACGATTGGAGCGGAT 60.203 61.111 0.00 0.00 0.00 4.18
3659 3761 3.126858 GCTCTAAACCAACATGAATGCGA 59.873 43.478 0.00 0.00 0.00 5.10
3671 3773 0.038892 GTCACGTCCGCTCTAAACCA 60.039 55.000 0.00 0.00 0.00 3.67
3689 3796 2.268920 CATGCTGTAGTGGCCGGT 59.731 61.111 1.90 0.00 0.00 5.28
3690 3797 3.204827 GCATGCTGTAGTGGCCGG 61.205 66.667 11.37 0.00 0.00 6.13
3691 3798 2.124983 AGCATGCTGTAGTGGCCG 60.125 61.111 21.98 0.00 0.00 6.13
3692 3799 2.117156 CCAGCATGCTGTAGTGGCC 61.117 63.158 38.22 0.00 42.15 5.36
3693 3800 2.768492 GCCAGCATGCTGTAGTGGC 61.768 63.158 38.22 32.19 46.49 5.01
3723 3830 4.690719 ACGCCGCCGGTTGAATGA 62.691 61.111 4.45 0.00 39.22 2.57
3812 3919 0.918983 AAGGAAGCCCATCATCGGAA 59.081 50.000 0.00 0.00 33.88 4.30
3831 3938 6.367969 GCTTGTTCAAAGACCTCGAGTATTTA 59.632 38.462 12.31 0.00 37.81 1.40
3836 3943 2.158957 TGCTTGTTCAAAGACCTCGAGT 60.159 45.455 12.31 0.00 0.00 4.18
3838 3945 2.613026 TGCTTGTTCAAAGACCTCGA 57.387 45.000 0.00 0.00 0.00 4.04
3851 3958 1.067516 GTGTGCATCCAACTTGCTTGT 59.932 47.619 0.00 0.00 40.77 3.16
3922 4029 3.947196 GGAGTATGGATTGACATGCAACA 59.053 43.478 0.00 1.58 39.78 3.33
3946 4053 6.963083 TGTCCATCAATTGATATCAATGCA 57.037 33.333 27.46 18.41 45.06 3.96
3967 4074 1.077501 CAACGGGCCATGGAGATGT 60.078 57.895 18.40 4.60 0.00 3.06
3991 4098 4.371855 AGAAAGTCTCATATCGACGCAA 57.628 40.909 0.00 0.00 36.53 4.85
4001 4108 7.013750 GGAAGACAAAAAGGAAGAAAGTCTCAT 59.986 37.037 0.00 0.00 34.10 2.90
4027 4136 9.790389 GAATACGGTGGTAGAGATTAATATGAG 57.210 37.037 0.00 0.00 30.81 2.90
4028 4137 9.529823 AGAATACGGTGGTAGAGATTAATATGA 57.470 33.333 0.00 0.00 30.81 2.15
4061 4170 7.411264 CGCAAGTCATGAATATAGCACTATGAC 60.411 40.741 13.20 0.00 42.72 3.06
4078 4187 2.032550 GCAATACATGAGCGCAAGTCAT 59.967 45.455 11.47 7.59 38.18 3.06
4079 4188 1.398041 GCAATACATGAGCGCAAGTCA 59.602 47.619 11.47 4.96 41.68 3.41
4080 4189 1.593070 CGCAATACATGAGCGCAAGTC 60.593 52.381 11.47 0.00 45.14 3.01
4081 4190 0.374758 CGCAATACATGAGCGCAAGT 59.625 50.000 11.47 3.36 45.14 3.16
4082 4191 3.138296 CGCAATACATGAGCGCAAG 57.862 52.632 11.47 0.00 45.14 4.01
4140 4262 0.961019 GGTGTCAGCCAAGCAATTGA 59.039 50.000 10.34 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.