Multiple sequence alignment - TraesCS4B01G304500

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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 TraesCS4B01G304500 chr4B 100.000 4482 0 0 1 4482 592818382 592822863 0.000000e+00 8277.0
1 TraesCS4B01G304500 chr4A 93.045 3609 144 57 1 3543 678216615 678220182 0.000000e+00 5175.0
2 TraesCS4B01G304500 chr4A 88.329 754 56 17 3543 4290 678220465 678221192 0.000000e+00 876.0
3 TraesCS4B01G304500 chr4A 95.238 42 1 1 1739 1779 678218257 678218298 1.040000e-06 65.8
4 TraesCS4B01G304500 chr4D 92.519 3382 139 43 845 4200 470506391 470509684 0.000000e+00 4739.0
5 TraesCS4B01G304500 chr4D 94.125 817 25 8 1 802 470505480 470506288 0.000000e+00 1221.0
6 TraesCS4B01G304500 chr4D 89.848 197 14 4 4289 4482 470509788 470509981 9.630000e-62 248.0
7 TraesCS4B01G304500 chr5A 88.172 186 22 0 1402 1587 462145388 462145573 5.840000e-54 222.0
8 TraesCS4B01G304500 chr5B 87.027 185 24 0 1402 1586 427238991 427239175 4.540000e-50 209.0
9 TraesCS4B01G304500 chr5D 87.931 174 21 0 1413 1586 361606659 361606832 5.880000e-49 206.0
10 TraesCS4B01G304500 chr2D 85.455 165 21 2 1425 1586 557795286 557795122 7.710000e-38 169.0
11 TraesCS4B01G304500 chr2B 84.848 165 22 2 1425 1586 666089795 666089631 3.590000e-36 163.0
12 TraesCS4B01G304500 chr2B 84.848 165 22 2 1425 1586 666096233 666096069 3.590000e-36 163.0
13 TraesCS4B01G304500 chr2A 84.242 165 23 2 1425 1586 698134340 698134176 1.670000e-34 158.0


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 TraesCS4B01G304500 chr4B 592818382 592822863 4481 False 8277.000000 8277 100.000 1 4482 1 chr4B.!!$F1 4481
1 TraesCS4B01G304500 chr4A 678216615 678221192 4577 False 2038.933333 5175 92.204 1 4290 3 chr4A.!!$F1 4289
2 TraesCS4B01G304500 chr4D 470505480 470509981 4501 False 2069.333333 4739 92.164 1 4482 3 chr4D.!!$F1 4481

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
26 27 0.110486 ACGATGTCAGCCAAAACCCT 59.890 50.0 0.00 0.0 0.00 4.34 F
1060 1151 0.108804 CACACGCCGATCAGTACCTT 60.109 55.0 0.00 0.0 0.00 3.50 F
1095 1186 1.865865 GTACTGTGTGTGTCACCTGG 58.134 55.0 0.00 0.0 45.61 4.45 F
2299 2432 1.359459 CGTTTTAGGGCGAGCACTCC 61.359 60.0 1.89 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2021 2151 2.097038 GCAGAACACTCGCTGCGAT 61.097 57.895 26.15 10.72 46.66 4.58 R
2299 2432 1.066002 CATTAGCATGAAACCCGCTGG 59.934 52.381 0.00 0.00 37.20 4.85 R
2560 2704 1.883275 TGGTCGCCCTAACAAAATGTG 59.117 47.619 0.00 0.00 0.00 3.21 R
3918 4360 0.099968 TGTGTACGCGGTATGCTCTC 59.900 55.000 12.47 0.00 43.27 3.20 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
26 27 0.110486 ACGATGTCAGCCAAAACCCT 59.890 50.000 0.00 0.00 0.00 4.34
259 271 1.295792 GAAAGACGGATGCGCCATAA 58.704 50.000 6.51 0.00 35.94 1.90
260 272 1.873591 GAAAGACGGATGCGCCATAAT 59.126 47.619 6.51 0.00 35.94 1.28
262 274 2.831685 AGACGGATGCGCCATAATAA 57.168 45.000 6.51 0.00 35.94 1.40
264 276 1.463444 GACGGATGCGCCATAATAACC 59.537 52.381 6.51 0.00 35.94 2.85
265 277 1.071699 ACGGATGCGCCATAATAACCT 59.928 47.619 6.51 0.00 35.94 3.50
311 323 0.518355 CGGCGCGTAGTTGAATTGTG 60.518 55.000 8.43 0.00 0.00 3.33
344 360 0.179062 AGAAGGAGGTCGATGCATGC 60.179 55.000 11.82 11.82 0.00 4.06
417 441 3.181462 CCTTCATATGACTGCACTAGCCA 60.181 47.826 4.48 0.00 41.13 4.75
472 496 5.027293 TGCAGTGATGCTGTAGATGTATT 57.973 39.130 0.00 0.00 46.64 1.89
479 504 3.457234 TGCTGTAGATGTATTTGAGGCG 58.543 45.455 0.00 0.00 0.00 5.52
502 527 6.327934 CGTTGAGCTAGCTTAGGTTAGTTTA 58.672 40.000 20.42 0.00 36.51 2.01
577 602 1.215382 CTAGTGCTAGGTGCGTGCA 59.785 57.895 0.00 0.00 46.63 4.57
589 614 3.952675 CGTGCACAAAGCTGGCGT 61.953 61.111 18.64 0.00 45.94 5.68
686 711 2.203470 TAATTTGACCGTTCCCCCAC 57.797 50.000 0.00 0.00 0.00 4.61
687 712 0.541063 AATTTGACCGTTCCCCCACC 60.541 55.000 0.00 0.00 0.00 4.61
688 713 2.435120 ATTTGACCGTTCCCCCACCC 62.435 60.000 0.00 0.00 0.00 4.61
802 828 3.056607 CCATTGGGCCAAGTTTTCAGTAG 60.057 47.826 25.16 4.03 0.00 2.57
803 829 3.586470 TTGGGCCAAGTTTTCAGTAGA 57.414 42.857 16.66 0.00 0.00 2.59
804 830 3.140325 TGGGCCAAGTTTTCAGTAGAG 57.860 47.619 2.13 0.00 0.00 2.43
805 831 2.441750 TGGGCCAAGTTTTCAGTAGAGT 59.558 45.455 2.13 0.00 0.00 3.24
806 832 3.649023 TGGGCCAAGTTTTCAGTAGAGTA 59.351 43.478 2.13 0.00 0.00 2.59
819 845 8.644318 TTTCAGTAGAGTATATTTTTCCTCGC 57.356 34.615 0.00 0.00 0.00 5.03
903 994 4.446413 GGACGCGTCCCCGTTGAT 62.446 66.667 41.88 1.89 43.94 2.57
974 1065 2.286121 TGGTGATGGTCCCCTCCC 60.286 66.667 0.00 0.00 0.00 4.30
1060 1151 0.108804 CACACGCCGATCAGTACCTT 60.109 55.000 0.00 0.00 0.00 3.50
1069 1160 2.271800 GATCAGTACCTTTGTCGCTGG 58.728 52.381 0.00 0.00 32.04 4.85
1095 1186 1.865865 GTACTGTGTGTGTCACCTGG 58.134 55.000 0.00 0.00 45.61 4.45
1126 1217 4.508128 TTGTCGATCTCCGGCCGC 62.508 66.667 22.85 4.27 43.37 6.53
1637 1759 5.981315 TGCCCTACTCGATTTTATCTTTACG 59.019 40.000 0.00 0.00 0.00 3.18
1930 2059 4.938575 TCCCCTTTTGCTATAAGAACCA 57.061 40.909 0.00 0.00 0.00 3.67
1978 2108 5.221244 GCTAATGTTCAAACTCACAACCCTT 60.221 40.000 0.00 0.00 0.00 3.95
1986 2116 4.918810 AACTCACAACCCTTTTCACATC 57.081 40.909 0.00 0.00 0.00 3.06
2008 2138 3.215975 CCCCTTTTGTTGTAAGAACCGA 58.784 45.455 0.00 0.00 0.00 4.69
2017 2147 6.627395 TGTTGTAAGAACCGATCAACAATT 57.373 33.333 6.57 0.00 43.02 2.32
2021 2151 2.422597 AGAACCGATCAACAATTGCGA 58.577 42.857 5.05 2.74 0.00 5.10
2079 2209 3.010584 CCTCTCTTTCCATTCCCCTTTGA 59.989 47.826 0.00 0.00 0.00 2.69
2104 2234 5.895636 ATCCGCAAGAACATGTTATTTCA 57.104 34.783 15.55 0.00 43.02 2.69
2178 2309 5.291858 TGCAAGTTCAATCGTATCAGATGAC 59.708 40.000 0.00 0.00 0.00 3.06
2261 2393 7.396339 TCTCTCAAGCTCCTATTGTGTTAGTAA 59.604 37.037 0.00 0.00 0.00 2.24
2299 2432 1.359459 CGTTTTAGGGCGAGCACTCC 61.359 60.000 1.89 0.00 0.00 3.85
2341 2474 5.012239 TGCTCCAACTCAGCATATTTCTTT 58.988 37.500 0.00 0.00 42.09 2.52
2350 2483 3.947834 CAGCATATTTCTTTCGGTTCCCT 59.052 43.478 0.00 0.00 0.00 4.20
2465 2609 2.258726 GGTTCGCCTGGTTGGACAC 61.259 63.158 0.00 0.00 38.35 3.67
2493 2637 2.616969 CCTCACTGGTTCAACCGTG 58.383 57.895 19.57 19.57 42.58 4.94
2514 2658 6.029607 CGTGTGATTCAAATAAATGAGTGGG 58.970 40.000 0.00 0.00 0.00 4.61
2522 2666 7.572523 TCAAATAAATGAGTGGGTGATCATC 57.427 36.000 0.00 0.00 35.11 2.92
2704 2848 0.321122 CTTTCGCCAGCTCCTTCACT 60.321 55.000 0.00 0.00 0.00 3.41
2719 2863 3.325135 CCTTCACTTTCCCACAGTACTCT 59.675 47.826 0.00 0.00 0.00 3.24
2732 2876 4.453478 CACAGTACTCTACCTCGTGTAACA 59.547 45.833 0.00 0.00 35.74 2.41
2957 3101 4.129737 CCGTCGACGCCATGGTCT 62.130 66.667 31.73 0.00 38.18 3.85
3019 3164 8.011673 CGTACGTGCTATGCTACTTAGTTTATA 58.988 37.037 7.22 0.00 0.00 0.98
3020 3165 9.669353 GTACGTGCTATGCTACTTAGTTTATAA 57.331 33.333 0.00 0.00 0.00 0.98
3113 3259 5.284079 GTTTCTATATAAGAACGGCGTCCA 58.716 41.667 15.17 0.00 44.02 4.02
3428 3579 5.220777 CCTTTGTACGTGAAACTGTGAATGT 60.221 40.000 0.00 0.00 31.75 2.71
3449 3600 1.219124 CGACTGTACCCTGCATGCT 59.781 57.895 20.33 0.00 0.00 3.79
3633 4073 1.302366 CATGCACACAGACACACAGT 58.698 50.000 0.00 0.00 0.00 3.55
3657 4097 3.503363 GCTGTGTGTCTTGAATCCATTCA 59.497 43.478 0.00 0.00 44.42 2.57
3658 4098 4.614535 GCTGTGTGTCTTGAATCCATTCAC 60.615 45.833 1.28 0.00 45.63 3.18
3659 4099 4.459330 TGTGTGTCTTGAATCCATTCACA 58.541 39.130 1.28 0.00 45.63 3.58
3660 4100 4.516321 TGTGTGTCTTGAATCCATTCACAG 59.484 41.667 1.28 4.02 45.63 3.66
3661 4101 4.756642 GTGTGTCTTGAATCCATTCACAGA 59.243 41.667 1.28 5.97 45.63 3.41
3662 4102 5.413833 GTGTGTCTTGAATCCATTCACAGAT 59.586 40.000 1.28 0.00 45.63 2.90
3663 4103 6.005823 TGTGTCTTGAATCCATTCACAGATT 58.994 36.000 1.28 0.00 45.63 2.40
3664 4104 6.149973 TGTGTCTTGAATCCATTCACAGATTC 59.850 38.462 1.28 5.92 45.63 2.52
3682 4122 3.988379 TTCACATGCTTCTGTTTCACC 57.012 42.857 0.00 0.00 0.00 4.02
3683 4123 2.929641 TCACATGCTTCTGTTTCACCA 58.070 42.857 0.00 0.00 0.00 4.17
3690 4130 2.507484 CTTCTGTTTCACCATGAGGCA 58.493 47.619 0.00 0.00 39.06 4.75
3746 4186 0.833287 GGGATGAACAGAGCTAGCCA 59.167 55.000 12.13 0.70 0.00 4.75
3882 4324 2.223409 CGAATAATGCATGTGCTGTGCT 60.223 45.455 0.00 0.00 42.92 4.40
3915 4357 0.240945 GTTTCAGGGTTCATGCACGG 59.759 55.000 0.00 0.00 0.00 4.94
3918 4360 2.047274 AGGGTTCATGCACGGTCG 60.047 61.111 0.00 0.00 0.00 4.79
3919 4361 2.047655 GGGTTCATGCACGGTCGA 60.048 61.111 0.00 0.00 0.00 4.20
3928 4370 1.589196 GCACGGTCGAGAGCATACC 60.589 63.158 3.15 0.00 0.00 2.73
3950 4392 3.571571 GCGTACACAGACAACATGAGTA 58.428 45.455 0.00 0.00 0.00 2.59
3957 4399 7.233389 ACACAGACAACATGAGTAGTATTCT 57.767 36.000 0.00 0.00 0.00 2.40
3998 4440 1.619827 TGACCGGGAAATAGTTGTCGT 59.380 47.619 6.32 0.00 0.00 4.34
4010 4452 2.304401 TTGTCGTTGCGTAGGCGTG 61.304 57.895 2.53 0.00 44.10 5.34
4044 4491 4.697300 GCTTGTTGCACTTGTGTTATTG 57.303 40.909 2.61 0.00 42.31 1.90
4048 4495 4.919206 TGTTGCACTTGTGTTATTGTGAG 58.081 39.130 2.61 0.00 32.72 3.51
4126 4573 7.972832 TTCTTTGAAGGAAACGTGTATATGT 57.027 32.000 0.00 0.00 0.00 2.29
4129 4576 7.442969 TCTTTGAAGGAAACGTGTATATGTTGT 59.557 33.333 0.00 0.00 36.21 3.32
4132 4579 8.604640 TGAAGGAAACGTGTATATGTTGTTAA 57.395 30.769 0.00 0.00 36.21 2.01
4290 4766 5.915196 GTGCTTTGTACTTCTGGTGAATTTC 59.085 40.000 0.00 0.00 0.00 2.17
4291 4767 5.827797 TGCTTTGTACTTCTGGTGAATTTCT 59.172 36.000 0.00 0.00 0.00 2.52
4292 4768 6.145535 GCTTTGTACTTCTGGTGAATTTCTG 58.854 40.000 0.00 0.00 0.00 3.02
4293 4769 6.633500 TTTGTACTTCTGGTGAATTTCTGG 57.367 37.500 0.00 0.00 0.00 3.86
4294 4770 5.304686 TGTACTTCTGGTGAATTTCTGGT 57.695 39.130 0.00 0.00 0.00 4.00
4295 4771 5.063204 TGTACTTCTGGTGAATTTCTGGTG 58.937 41.667 0.00 0.00 0.00 4.17
4296 4772 4.437682 ACTTCTGGTGAATTTCTGGTGA 57.562 40.909 0.00 0.00 0.00 4.02
4297 4773 4.792068 ACTTCTGGTGAATTTCTGGTGAA 58.208 39.130 0.00 0.00 0.00 3.18
4298 4774 5.388654 ACTTCTGGTGAATTTCTGGTGAAT 58.611 37.500 0.00 0.00 31.56 2.57
4299 4775 5.835280 ACTTCTGGTGAATTTCTGGTGAATT 59.165 36.000 0.00 0.00 31.56 2.17
4300 4776 6.324770 ACTTCTGGTGAATTTCTGGTGAATTT 59.675 34.615 0.00 0.00 31.56 1.82
4416 4895 9.701355 CAATTAAAATATTTAAGCCCTTTTGCG 57.299 29.630 0.01 0.00 36.02 4.85
4432 4911 2.171341 TGCGTACTTGGTTGCATGTA 57.829 45.000 0.00 0.00 31.31 2.29
4437 4916 4.433615 CGTACTTGGTTGCATGTAGAGAT 58.566 43.478 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.681175 GCAAGGGTTTTGGCTGACAT 59.319 50.000 0.00 0.00 0.00 3.06
26 27 0.875059 TGTGTGTTGTTGTGTCGCAA 59.125 45.000 0.00 0.00 34.16 4.85
121 123 5.774690 ACAAGCATTCACCCTCTGAAAATAA 59.225 36.000 0.00 0.00 42.37 1.40
259 271 5.581085 GTGACATCTCGCTACAAAAGGTTAT 59.419 40.000 0.00 0.00 0.00 1.89
260 272 4.927425 GTGACATCTCGCTACAAAAGGTTA 59.073 41.667 0.00 0.00 0.00 2.85
262 274 3.244078 TGTGACATCTCGCTACAAAAGGT 60.244 43.478 0.00 0.00 0.00 3.50
264 276 4.627035 TCATGTGACATCTCGCTACAAAAG 59.373 41.667 0.00 0.00 0.00 2.27
265 277 4.565022 TCATGTGACATCTCGCTACAAAA 58.435 39.130 0.00 0.00 0.00 2.44
311 323 1.246737 CCTTCTCCTTGGCCACTTGC 61.247 60.000 3.88 0.00 40.16 4.01
344 360 0.943673 TGTGCTGTGATTTCACCGTG 59.056 50.000 8.16 0.00 45.88 4.94
417 441 3.860968 ACGTAGGAGTACTGGCTAGAT 57.139 47.619 3.17 0.00 0.00 1.98
472 496 0.321671 AAGCTAGCTCAACGCCTCAA 59.678 50.000 19.65 0.00 40.39 3.02
479 504 6.757478 CCTAAACTAACCTAAGCTAGCTCAAC 59.243 42.308 19.65 0.00 0.00 3.18
577 602 1.007038 CATGCAACGCCAGCTTTGT 60.007 52.632 10.13 0.00 0.00 2.83
589 614 2.748251 CGCCCGGGTAACATGCAA 60.748 61.111 24.63 0.00 39.74 4.08
802 828 4.868067 TCGAGGCGAGGAAAAATATACTC 58.132 43.478 0.00 0.00 0.00 2.59
803 829 4.931661 TCGAGGCGAGGAAAAATATACT 57.068 40.909 0.00 0.00 0.00 2.12
804 830 4.626172 GGATCGAGGCGAGGAAAAATATAC 59.374 45.833 0.00 0.00 39.91 1.47
805 831 4.322499 GGGATCGAGGCGAGGAAAAATATA 60.322 45.833 0.00 0.00 39.91 0.86
806 832 3.557264 GGGATCGAGGCGAGGAAAAATAT 60.557 47.826 0.00 0.00 39.91 1.28
819 845 1.044611 GAGAAGGGAAGGGATCGAGG 58.955 60.000 0.00 0.00 0.00 4.63
902 993 1.143073 GCCACTTCGGGGAAGGAATAT 59.857 52.381 9.89 0.00 43.25 1.28
903 994 0.544697 GCCACTTCGGGGAAGGAATA 59.455 55.000 9.89 0.00 43.25 1.75
974 1065 3.227276 CGGACGGAGGGAGGGATG 61.227 72.222 0.00 0.00 0.00 3.51
1095 1186 5.285651 AGATCGACAAGACAAGCTAATAGC 58.714 41.667 3.66 3.66 42.84 2.97
1126 1217 2.348998 GCCTGTGAGTGTGAGGGG 59.651 66.667 0.00 0.00 0.00 4.79
1423 1519 2.364317 CTCCGCTTCCTCCTCCCA 60.364 66.667 0.00 0.00 0.00 4.37
1672 1795 2.182014 CATCATTGCGATGCACACAAG 58.818 47.619 9.26 0.00 44.95 3.16
1695 1818 4.914128 GGTTGAAACCCCGTCCTT 57.086 55.556 0.36 0.00 43.43 3.36
1781 1910 6.705302 AGACACTTGAGAGATGCTAAAATCA 58.295 36.000 0.00 0.00 0.00 2.57
1930 2059 3.481009 CTCGTTGAGAGCGTTGACT 57.519 52.632 0.00 0.00 40.54 3.41
1978 2108 3.379452 ACAACAAAAGGGGGATGTGAAA 58.621 40.909 0.00 0.00 0.00 2.69
1986 2116 2.295070 CGGTTCTTACAACAAAAGGGGG 59.705 50.000 0.00 0.00 0.00 5.40
2021 2151 2.097038 GCAGAACACTCGCTGCGAT 61.097 57.895 26.15 10.72 46.66 4.58
2079 2209 7.995289 TGAAATAACATGTTCTTGCGGATATT 58.005 30.769 15.85 3.00 0.00 1.28
2104 2234 7.332678 GCCTTTTCATTCATTAGTTGCTCAATT 59.667 33.333 0.00 0.00 0.00 2.32
2261 2393 5.705609 AACGCTCCTACATGACAAAAATT 57.294 34.783 0.00 0.00 0.00 1.82
2299 2432 1.066002 CATTAGCATGAAACCCGCTGG 59.934 52.381 0.00 0.00 37.20 4.85
2350 2483 7.136119 CGGTTCTTACAGATAGCAAACAAAAA 58.864 34.615 0.00 0.00 0.00 1.94
2489 2633 6.029607 CCACTCATTTATTTGAATCACACGG 58.970 40.000 0.00 0.00 0.00 4.94
2493 2637 7.156876 TCACCCACTCATTTATTTGAATCAC 57.843 36.000 0.00 0.00 0.00 3.06
2544 2688 7.533426 ACAAAATGTGAGAGAGCATAATCAAC 58.467 34.615 0.00 0.00 0.00 3.18
2554 2698 3.372206 CGCCCTAACAAAATGTGAGAGAG 59.628 47.826 0.00 0.00 30.00 3.20
2558 2702 2.161609 GGTCGCCCTAACAAAATGTGAG 59.838 50.000 0.00 0.00 0.00 3.51
2560 2704 1.883275 TGGTCGCCCTAACAAAATGTG 59.117 47.619 0.00 0.00 0.00 3.21
2673 2817 3.845259 CGAAAGGGGATCGGCCGA 61.845 66.667 33.12 33.12 36.68 5.54
2704 2848 3.087031 CGAGGTAGAGTACTGTGGGAAA 58.913 50.000 0.00 0.00 0.00 3.13
2957 3101 5.514500 ACCTTTAGGCTGAAGGAATACAA 57.486 39.130 36.37 0.00 45.25 2.41
3019 3164 8.275187 TCCATCACCTTATACTCCATGTAATT 57.725 34.615 0.00 0.00 34.45 1.40
3020 3165 7.734865 TCTCCATCACCTTATACTCCATGTAAT 59.265 37.037 0.00 0.00 34.45 1.89
3113 3259 1.078214 CGATGCCATCACCACCACT 60.078 57.895 5.40 0.00 0.00 4.00
3404 3555 4.868450 TTCACAGTTTCACGTACAAAGG 57.132 40.909 0.00 0.00 0.00 3.11
3428 3579 0.246360 CATGCAGGGTACAGTCGTCA 59.754 55.000 0.00 0.00 0.00 4.35
3449 3600 0.909610 CTCTGGACTGGGCAAGGGTA 60.910 60.000 0.00 0.00 0.00 3.69
3483 3635 9.685828 GAGCTAGTTATCTTGTCCTAGTATTTG 57.314 37.037 0.00 0.00 31.58 2.32
3484 3636 9.649316 AGAGCTAGTTATCTTGTCCTAGTATTT 57.351 33.333 0.00 0.00 31.58 1.40
3486 3638 9.729281 GTAGAGCTAGTTATCTTGTCCTAGTAT 57.271 37.037 0.00 0.00 31.58 2.12
3487 3639 8.712103 TGTAGAGCTAGTTATCTTGTCCTAGTA 58.288 37.037 0.00 0.00 31.58 1.82
3576 4016 0.442310 GAATGCATGCACACGTACGT 59.558 50.000 25.37 16.72 0.00 3.57
3633 4073 2.929641 TGGATTCAAGACACACAGCAA 58.070 42.857 0.00 0.00 0.00 3.91
3658 4098 5.152097 GTGAAACAGAAGCATGTGAATCTG 58.848 41.667 13.82 13.82 43.79 2.90
3659 4099 4.217118 GGTGAAACAGAAGCATGTGAATCT 59.783 41.667 0.00 0.00 39.98 2.40
3660 4100 4.022935 TGGTGAAACAGAAGCATGTGAATC 60.023 41.667 0.00 0.00 39.98 2.52
3661 4101 3.890756 TGGTGAAACAGAAGCATGTGAAT 59.109 39.130 0.00 0.00 39.98 2.57
3662 4102 3.286353 TGGTGAAACAGAAGCATGTGAA 58.714 40.909 0.00 0.00 39.98 3.18
3663 4103 2.929641 TGGTGAAACAGAAGCATGTGA 58.070 42.857 0.00 0.00 39.98 3.58
3664 4104 3.571571 CATGGTGAAACAGAAGCATGTG 58.428 45.455 6.67 0.00 43.79 3.21
3682 4122 3.129502 CACACGGCCTGCCTCATG 61.130 66.667 6.60 4.67 0.00 3.07
3683 4123 4.415150 CCACACGGCCTGCCTCAT 62.415 66.667 6.60 0.00 0.00 2.90
3690 4130 1.192146 ACAGATGTACCACACGGCCT 61.192 55.000 0.00 0.00 34.57 5.19
3746 4186 1.103803 CAATCATTCTGCTGCCTGCT 58.896 50.000 0.00 0.00 43.37 4.24
3882 4324 2.290367 CCTGAAACGCACATTTCTGTCA 59.710 45.455 6.64 0.00 39.02 3.58
3887 4329 2.034053 TGAACCCTGAAACGCACATTTC 59.966 45.455 0.00 0.00 38.77 2.17
3915 4357 0.656786 GTACGCGGTATGCTCTCGAC 60.657 60.000 12.47 0.00 43.27 4.20
3918 4360 0.099968 TGTGTACGCGGTATGCTCTC 59.900 55.000 12.47 0.00 43.27 3.20
3919 4361 0.100682 CTGTGTACGCGGTATGCTCT 59.899 55.000 12.47 0.00 43.27 4.09
3928 4370 1.386748 CTCATGTTGTCTGTGTACGCG 59.613 52.381 3.53 3.53 0.00 6.01
3950 4392 8.007742 TGGAATCTCTAGCCTCTAAAGAATACT 58.992 37.037 0.00 0.00 0.00 2.12
3957 4399 6.183361 GGTCAATGGAATCTCTAGCCTCTAAA 60.183 42.308 0.00 0.00 0.00 1.85
3998 4440 0.317799 TTTACCTCACGCCTACGCAA 59.682 50.000 0.00 0.00 45.53 4.85
4010 4452 2.989166 GCAACAAGCAGCAATTTACCTC 59.011 45.455 0.00 0.00 44.79 3.85
4033 4478 3.990469 AGAGACGCTCACAATAACACAAG 59.010 43.478 9.09 0.00 32.06 3.16
4044 4491 2.329379 CACCTACAAAGAGACGCTCAC 58.671 52.381 9.09 0.00 32.06 3.51
4048 4495 2.457080 GGCACCTACAAAGAGACGC 58.543 57.895 0.00 0.00 0.00 5.19
4072 4519 8.697846 AGAAAGTGCATTTATGAAATCATGTG 57.302 30.769 6.17 4.13 37.15 3.21
4126 4573 5.685599 GCCCGGGTATCATCTAGTTTAACAA 60.686 44.000 24.63 0.00 0.00 2.83
4129 4576 3.006110 CGCCCGGGTATCATCTAGTTTAA 59.994 47.826 24.63 0.00 0.00 1.52
4132 4579 0.966920 CGCCCGGGTATCATCTAGTT 59.033 55.000 24.63 0.00 0.00 2.24
4261 4737 3.149196 CCAGAAGTACAAAGCACCACAT 58.851 45.455 0.00 0.00 0.00 3.21
4264 4740 2.171659 TCACCAGAAGTACAAAGCACCA 59.828 45.455 0.00 0.00 0.00 4.17
4390 4866 9.701355 CGCAAAAGGGCTTAAATATTTTAATTG 57.299 29.630 5.91 3.28 0.00 2.32
4394 4870 8.741841 AGTACGCAAAAGGGCTTAAATATTTTA 58.258 29.630 5.91 0.00 0.00 1.52
4396 4872 7.165460 AGTACGCAAAAGGGCTTAAATATTT 57.835 32.000 5.89 5.89 0.00 1.40
4416 4895 7.843490 TTTATCTCTACATGCAACCAAGTAC 57.157 36.000 0.00 0.00 0.00 2.73
4418 4897 9.113838 CTTATTTATCTCTACATGCAACCAAGT 57.886 33.333 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.