Multiple sequence alignment - TraesCS4A01G432300

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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 TraesCS4A01G432300 chr4A 100.000 4240 0 0 1 4240 703271798 703267559 0.000000e+00 7830.0
1 TraesCS4A01G432300 chr4A 74.505 404 89 14 1115 1511 466926095 466926491 3.390000e-36 163.0
2 TraesCS4A01G432300 chr4A 72.897 321 73 13 1187 1500 499341753 499342066 9.700000e-17 99.0
3 TraesCS4A01G432300 chr7D 90.105 4083 225 79 17 4021 27661389 27657408 0.000000e+00 5136.0
4 TraesCS4A01G432300 chr7D 96.809 188 6 0 4023 4210 27657368 27657181 8.850000e-82 315.0
5 TraesCS4A01G432300 chrUn 86.913 4111 270 113 4 4021 81688335 81692270 0.000000e+00 4364.0
6 TraesCS4A01G432300 chrUn 92.661 218 12 2 4023 4240 81692305 81692518 1.140000e-80 311.0
7 TraesCS4A01G432300 chrUn 75.354 353 19 26 22 335 81685202 81685525 1.610000e-19 108.0
8 TraesCS4A01G432300 chr1B 93.103 203 14 0 4038 4240 110635672 110635874 8.910000e-77 298.0
9 TraesCS4A01G432300 chr1B 92.683 41 3 0 3985 4025 110635639 110635679 4.580000e-05 60.2
10 TraesCS4A01G432300 chr4D 74.257 404 90 13 1115 1511 109911882 109911486 1.580000e-34 158.0
11 TraesCS4A01G432300 chr4D 73.520 321 71 13 1187 1500 85579430 85579743 4.480000e-20 110.0
12 TraesCS4A01G432300 chr4B 74.074 405 89 15 1115 1511 171028470 171028074 7.340000e-33 152.0
13 TraesCS4A01G432300 chr4B 73.209 321 72 13 1187 1500 122520740 122521053 2.090000e-18 104.0
14 TraesCS4A01G432300 chr5D 73.994 323 80 3 1187 1507 489905964 489906284 1.240000e-25 128.0


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 TraesCS4A01G432300 chr4A 703267559 703271798 4239 True 7830.000000 7830 100.000 1 4240 1 chr4A.!!$R1 4239
1 TraesCS4A01G432300 chr7D 27657181 27661389 4208 True 2725.500000 5136 93.457 17 4210 2 chr7D.!!$R1 4193
2 TraesCS4A01G432300 chrUn 81685202 81692518 7316 False 1594.333333 4364 84.976 4 4240 3 chrUn.!!$F1 4236

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
837 4026 0.452184 TCCTCGTCGCAGATTCAGTC 59.548 55.0 0.0 0.0 40.67 3.51 F
1608 4823 0.107800 CTGATCACCCCTGCTCTGTG 60.108 60.0 0.0 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2639 5869 0.694771 TGGAGAATGAGCACAAGCCT 59.305 50.0 0.0 0.0 43.56 4.58 R
3511 6760 0.847983 GCGCGAAATTCACGAGTTCG 60.848 55.0 12.1 4.5 45.28 3.95 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
56 3195 2.023673 CAACAAGAGTGACAGGGCAAA 58.976 47.619 0.00 0.00 0.00 3.68
69 3208 3.132925 CAGGGCAAACATCAAACCAAAG 58.867 45.455 0.00 0.00 0.00 2.77
136 3294 2.097680 CCAATGGGTTTGTCATTGCC 57.902 50.000 10.30 0.00 45.89 4.52
137 3295 1.347050 CCAATGGGTTTGTCATTGCCA 59.653 47.619 10.30 0.00 45.89 4.92
138 3296 2.027007 CCAATGGGTTTGTCATTGCCAT 60.027 45.455 10.30 0.00 45.89 4.40
139 3297 3.559597 CCAATGGGTTTGTCATTGCCATT 60.560 43.478 10.30 0.00 45.89 3.16
140 3298 2.835580 TGGGTTTGTCATTGCCATTG 57.164 45.000 0.00 0.00 0.00 2.82
141 3299 2.045524 TGGGTTTGTCATTGCCATTGT 58.954 42.857 0.00 0.00 0.00 2.71
142 3300 2.036992 TGGGTTTGTCATTGCCATTGTC 59.963 45.455 0.00 0.00 0.00 3.18
143 3301 2.036992 GGGTTTGTCATTGCCATTGTCA 59.963 45.455 0.00 0.00 0.00 3.58
220 3378 9.747293 GATGACACTAATAAACTACTCCTAACC 57.253 37.037 0.00 0.00 0.00 2.85
221 3379 7.765307 TGACACTAATAAACTACTCCTAACCG 58.235 38.462 0.00 0.00 0.00 4.44
222 3380 7.105241 ACACTAATAAACTACTCCTAACCGG 57.895 40.000 0.00 0.00 0.00 5.28
223 3381 6.097412 ACACTAATAAACTACTCCTAACCGGG 59.903 42.308 6.32 0.00 0.00 5.73
224 3382 5.600069 ACTAATAAACTACTCCTAACCGGGG 59.400 44.000 6.32 0.00 40.09 5.73
225 3383 2.629017 AAACTACTCCTAACCGGGGA 57.371 50.000 6.32 1.25 36.45 4.81
226 3384 2.862850 AACTACTCCTAACCGGGGAT 57.137 50.000 6.32 0.00 36.45 3.85
227 3385 2.862850 ACTACTCCTAACCGGGGATT 57.137 50.000 6.32 0.00 36.45 3.01
228 3386 3.979501 ACTACTCCTAACCGGGGATTA 57.020 47.619 6.32 0.56 36.45 1.75
229 3387 4.270317 ACTACTCCTAACCGGGGATTAA 57.730 45.455 6.32 0.00 36.45 1.40
230 3388 4.824276 ACTACTCCTAACCGGGGATTAAT 58.176 43.478 6.32 0.00 36.45 1.40
231 3389 4.837298 ACTACTCCTAACCGGGGATTAATC 59.163 45.833 6.32 6.93 36.45 1.75
232 3390 2.977580 ACTCCTAACCGGGGATTAATCC 59.022 50.000 24.14 24.14 46.41 3.01
261 3419 1.211456 CTCCCTTTCCATCTGCTCCT 58.789 55.000 0.00 0.00 0.00 3.69
262 3420 2.402564 CTCCCTTTCCATCTGCTCCTA 58.597 52.381 0.00 0.00 0.00 2.94
263 3421 2.774234 CTCCCTTTCCATCTGCTCCTAA 59.226 50.000 0.00 0.00 0.00 2.69
357 3519 4.095400 TGAGCTCCCTCCCCCTCC 62.095 72.222 12.15 0.00 37.29 4.30
493 3661 3.775654 CCGGTGAGTGCCCTCCTC 61.776 72.222 0.00 0.00 36.86 3.71
754 3943 4.028993 TCGGGATTTCTGCTAGGTTTTT 57.971 40.909 0.00 0.00 0.00 1.94
837 4026 0.452184 TCCTCGTCGCAGATTCAGTC 59.548 55.000 0.00 0.00 40.67 3.51
908 4097 4.115199 ATTCGGGGTCCTGCCAGC 62.115 66.667 0.00 0.00 39.65 4.85
935 4124 4.610714 GCTCTCCGGGGGCGATTC 62.611 72.222 0.00 0.00 0.00 2.52
972 4161 3.793888 GGACTCCGGCGGGGATTT 61.794 66.667 36.13 10.84 46.04 2.17
973 4162 2.513897 GACTCCGGCGGGGATTTG 60.514 66.667 36.13 14.77 46.04 2.32
1305 4519 2.126031 GTCGTCGACCTCAAGGCC 60.126 66.667 14.60 0.00 39.32 5.19
1511 4725 0.534412 AACATCCTCCTCGTCAGCAG 59.466 55.000 0.00 0.00 0.00 4.24
1518 4732 4.803426 CTCGTCAGCAGGTCGCCC 62.803 72.222 0.00 0.00 44.04 6.13
1598 4813 1.065199 TGATTGACAGCCTGATCACCC 60.065 52.381 0.00 0.00 0.00 4.61
1602 4817 2.124403 CAGCCTGATCACCCCTGC 60.124 66.667 0.00 0.00 0.00 4.85
1603 4818 2.285969 AGCCTGATCACCCCTGCT 60.286 61.111 0.00 0.00 0.00 4.24
1604 4819 2.191641 GCCTGATCACCCCTGCTC 59.808 66.667 0.00 0.00 0.00 4.26
1605 4820 2.373707 GCCTGATCACCCCTGCTCT 61.374 63.158 0.00 0.00 0.00 4.09
1606 4821 1.525923 CCTGATCACCCCTGCTCTG 59.474 63.158 0.00 0.00 0.00 3.35
1607 4822 1.270414 CCTGATCACCCCTGCTCTGT 61.270 60.000 0.00 0.00 0.00 3.41
1608 4823 0.107800 CTGATCACCCCTGCTCTGTG 60.108 60.000 0.00 0.00 0.00 3.66
1609 4824 1.222936 GATCACCCCTGCTCTGTGG 59.777 63.158 0.00 0.00 0.00 4.17
1610 4825 2.883267 GATCACCCCTGCTCTGTGGC 62.883 65.000 0.00 0.00 0.00 5.01
1611 4826 3.644606 CACCCCTGCTCTGTGGCT 61.645 66.667 0.00 0.00 0.00 4.75
1612 4827 3.644606 ACCCCTGCTCTGTGGCTG 61.645 66.667 0.00 0.00 0.00 4.85
1614 4829 4.340246 CCCTGCTCTGTGGCTGCA 62.340 66.667 0.50 0.00 35.30 4.41
1616 4831 2.623915 CCTGCTCTGTGGCTGCAAC 61.624 63.158 0.00 0.00 36.22 4.17
1618 4833 1.152902 TGCTCTGTGGCTGCAACTT 60.153 52.632 8.88 0.00 33.48 2.66
1625 4840 1.024271 GTGGCTGCAACTTGTCAAGA 58.976 50.000 19.53 0.00 0.00 3.02
1626 4841 1.610522 GTGGCTGCAACTTGTCAAGAT 59.389 47.619 19.53 4.39 0.00 2.40
1629 4844 2.035066 GGCTGCAACTTGTCAAGATTGT 59.965 45.455 19.53 0.00 0.00 2.71
1635 4850 4.202050 GCAACTTGTCAAGATTGTTGGTCT 60.202 41.667 19.53 0.00 38.57 3.85
1636 4851 5.679638 GCAACTTGTCAAGATTGTTGGTCTT 60.680 40.000 19.53 0.00 38.57 3.01
1643 4858 6.071108 TGTCAAGATTGTTGGTCTTTTTGGAA 60.071 34.615 0.00 0.00 33.82 3.53
1790 5005 5.183522 CGGGGTTATACTCTACATCCTTCTC 59.816 48.000 0.00 0.00 0.00 2.87
1952 5167 1.326213 ATCCTGGACAGAGGCTCACG 61.326 60.000 18.26 9.85 32.51 4.35
1978 5193 4.180057 GAGCAAGTTCTAGGTGAGACATG 58.820 47.826 0.00 0.00 32.31 3.21
1980 5195 3.929610 GCAAGTTCTAGGTGAGACATGAC 59.070 47.826 0.00 0.00 32.31 3.06
1982 5197 5.728471 CAAGTTCTAGGTGAGACATGACAT 58.272 41.667 0.00 0.00 32.31 3.06
1983 5198 5.590530 AGTTCTAGGTGAGACATGACATC 57.409 43.478 0.00 0.00 32.31 3.06
1984 5199 5.019470 AGTTCTAGGTGAGACATGACATCA 58.981 41.667 0.00 0.00 32.31 3.07
1985 5200 5.660417 AGTTCTAGGTGAGACATGACATCAT 59.340 40.000 0.00 0.00 36.96 2.45
1987 5202 5.453158 TCTAGGTGAGACATGACATCATCT 58.547 41.667 13.91 13.91 38.04 2.90
2028 5251 5.298026 GCTCAGAATTCCATTCCTTTCTACC 59.702 44.000 0.65 0.00 40.13 3.18
2052 5278 7.609146 ACCATATCATTAGCATCATACACAAGG 59.391 37.037 0.00 0.00 0.00 3.61
2074 5300 7.323052 AGGTTAGAAGAGACCTTTGATTCTT 57.677 36.000 0.00 0.00 43.64 2.52
2075 5301 7.164803 AGGTTAGAAGAGACCTTTGATTCTTG 58.835 38.462 0.00 0.00 43.64 3.02
2076 5302 7.016661 AGGTTAGAAGAGACCTTTGATTCTTGA 59.983 37.037 0.00 0.00 43.64 3.02
2081 5307 8.108364 AGAAGAGACCTTTGATTCTTGATGATT 58.892 33.333 0.00 0.00 31.62 2.57
2083 5309 8.961294 AGAGACCTTTGATTCTTGATGATTAG 57.039 34.615 0.00 0.00 0.00 1.73
2103 5329 9.642343 TGATTAGTAGTGTCTATACCTTCATGT 57.358 33.333 0.00 0.00 0.00 3.21
2150 5376 5.738909 AGAGATCAATCAGAATTCGGTTGT 58.261 37.500 17.08 9.11 0.00 3.32
2153 5379 6.846350 AGATCAATCAGAATTCGGTTGTTTC 58.154 36.000 17.08 15.24 0.00 2.78
2168 5394 5.609269 CGGTTGTTTCGTATGCAATTGTTTG 60.609 40.000 7.40 0.00 35.85 2.93
2277 5503 3.263425 TCTGGATTTCTGGTAGAACCACC 59.737 47.826 0.00 0.00 44.79 4.61
2317 5545 1.475682 CTGAATCTTTGCTGGCCCTTC 59.524 52.381 0.00 0.00 0.00 3.46
2337 5566 8.659491 GCCCTTCAATGTTTCTTTTGATAAATC 58.341 33.333 0.00 0.00 32.27 2.17
2350 5579 5.518848 TTGATAAATCACATCCACATGGC 57.481 39.130 0.00 0.00 36.36 4.40
2356 5585 1.281577 TCACATCCACATGGCTGCTTA 59.718 47.619 0.00 0.00 34.82 3.09
2372 5601 7.706159 TGGCTGCTTATTTATTAGTGTTGATG 58.294 34.615 0.00 0.00 0.00 3.07
2373 5602 7.555914 TGGCTGCTTATTTATTAGTGTTGATGA 59.444 33.333 0.00 0.00 0.00 2.92
2374 5603 8.571336 GGCTGCTTATTTATTAGTGTTGATGAT 58.429 33.333 0.00 0.00 0.00 2.45
2453 5683 6.585695 TTTCCAGACCTTACTGTGTAGTAG 57.414 41.667 0.00 0.00 40.33 2.57
2454 5684 5.252586 TCCAGACCTTACTGTGTAGTAGT 57.747 43.478 0.00 0.00 40.33 2.73
2455 5685 6.378661 TCCAGACCTTACTGTGTAGTAGTA 57.621 41.667 0.00 0.00 40.33 1.82
2456 5686 6.176183 TCCAGACCTTACTGTGTAGTAGTAC 58.824 44.000 0.37 0.37 40.33 2.73
2457 5687 5.942236 CCAGACCTTACTGTGTAGTAGTACA 59.058 44.000 6.31 6.31 40.33 2.90
2459 5689 6.877855 CAGACCTTACTGTGTAGTAGTACAGA 59.122 42.308 10.76 8.91 45.46 3.41
2460 5690 7.553402 CAGACCTTACTGTGTAGTAGTACAGAT 59.447 40.741 10.76 2.65 45.46 2.90
2461 5691 7.769970 AGACCTTACTGTGTAGTAGTACAGATC 59.230 40.741 10.76 3.68 45.46 2.75
2477 5707 4.265073 ACAGATCCAGCTGTTAATGGTTC 58.735 43.478 13.81 1.74 46.42 3.62
2497 5727 4.620086 TCCCTTTCTCCTGATGGTAGTA 57.380 45.455 0.00 0.00 34.23 1.82
2498 5728 4.547671 TCCCTTTCTCCTGATGGTAGTAG 58.452 47.826 0.00 0.00 34.23 2.57
2499 5729 4.016479 TCCCTTTCTCCTGATGGTAGTAGT 60.016 45.833 0.00 0.00 34.23 2.73
2511 5741 7.331193 CCTGATGGTAGTAGTTTACAGTTGTTC 59.669 40.741 0.00 0.00 0.00 3.18
2535 5765 3.384467 CCATGTGGGGTTTATTGCCTAAG 59.616 47.826 0.00 0.00 0.00 2.18
2570 5800 1.875576 GCAGAGCATTCCTGGATACGG 60.876 57.143 0.00 0.00 45.15 4.02
2582 5812 1.066918 GATACGGGAACACGCCGAT 59.933 57.895 5.39 0.00 37.37 4.18
2639 5869 4.465446 CTCGGGAGGGAGGAGCCA 62.465 72.222 0.00 0.00 38.95 4.75
2644 5874 2.690510 GAGGGAGGAGCCAGGCTT 60.691 66.667 17.46 0.00 39.88 4.35
2651 5881 2.033141 GAGCCAGGCTTGTGCTCA 59.967 61.111 24.44 0.00 42.38 4.26
2747 5977 2.371259 GGAGGAACCCTGCTCTCCC 61.371 68.421 0.00 0.00 39.84 4.30
2774 6004 0.103937 CCTGCAGATCGTCCTTCTCC 59.896 60.000 17.39 0.00 0.00 3.71
2781 6011 1.313812 ATCGTCCTTCTCCGCGTTCT 61.314 55.000 4.92 0.00 0.00 3.01
2782 6012 1.514443 CGTCCTTCTCCGCGTTCTC 60.514 63.158 4.92 0.00 0.00 2.87
2904 6134 2.365617 AGCTTCTCGTTCTTCTGTTGGA 59.634 45.455 0.00 0.00 0.00 3.53
3093 6326 4.986587 CGAACCCGTCGTCACGCA 62.987 66.667 0.00 0.00 45.29 5.24
3161 6397 2.125106 GACCTGGACATGGCGGTC 60.125 66.667 9.58 9.58 39.14 4.79
3377 6618 5.614668 CGAGACGAGAAGAGATTAGAGATGC 60.615 48.000 0.00 0.00 0.00 3.91
3379 6620 3.233578 CGAGAAGAGATTAGAGATGCGC 58.766 50.000 0.00 0.00 0.00 6.09
3391 6632 1.734477 GATGCGCGTGTCACTGTCT 60.734 57.895 6.97 0.00 0.00 3.41
3404 6651 4.588951 TGTCACTGTCTCTGGTTGTAGAAT 59.411 41.667 0.00 0.00 0.00 2.40
3413 6660 6.586844 GTCTCTGGTTGTAGAATGAGTGTAAC 59.413 42.308 0.00 0.00 0.00 2.50
3433 6680 8.535335 GTGTAACCTGGACATGATGATATATCT 58.465 37.037 13.79 0.00 0.00 1.98
3469 6718 4.021280 AGACTCATAGTAGATCGCCGAGTA 60.021 45.833 0.00 0.00 32.65 2.59
3470 6719 4.834534 ACTCATAGTAGATCGCCGAGTAT 58.165 43.478 0.00 0.00 30.79 2.12
3488 6737 2.706339 ATTTTGTTGCTGGTGCCAAA 57.294 40.000 0.00 0.00 38.71 3.28
3506 6755 5.701029 CCAAATGATGGTGTAAATTTCGC 57.299 39.130 0.00 0.00 44.85 4.70
3511 6760 4.468643 TGATGGTGTAAATTTCGCGTTTC 58.531 39.130 5.77 0.00 0.00 2.78
3581 6830 1.623973 CGGGAAGAGAACCGCGTTTC 61.624 60.000 8.51 8.51 43.96 2.78
3582 6831 1.623973 GGGAAGAGAACCGCGTTTCG 61.624 60.000 10.88 0.00 38.08 3.46
3590 6839 2.432628 CCGCGTTTCGAGCCTCTT 60.433 61.111 4.92 0.00 41.67 2.85
3591 6840 2.027625 CCGCGTTTCGAGCCTCTTT 61.028 57.895 4.92 0.00 41.67 2.52
3593 6842 1.282248 CGCGTTTCGAGCCTCTTTGA 61.282 55.000 0.00 0.00 41.67 2.69
3594 6843 0.865769 GCGTTTCGAGCCTCTTTGAA 59.134 50.000 0.00 0.00 0.00 2.69
3653 6902 5.348164 ACCAGAAATTTGAACGGTTTCTTG 58.652 37.500 0.00 0.00 39.46 3.02
3692 6948 4.210120 CCTTGAAAGAAGTTCAGACGACAG 59.790 45.833 5.50 0.00 46.85 3.51
3723 6979 0.519077 GAAACTTTGCTCTGCCTCGG 59.481 55.000 0.00 0.00 0.00 4.63
3734 6990 4.520846 GCCTCGGTCGCGCATTTG 62.521 66.667 8.75 0.00 0.00 2.32
3850 7106 2.612251 CCTCTCCTCCCTCCCCTC 59.388 72.222 0.00 0.00 0.00 4.30
3851 7107 2.612251 CTCTCCTCCCTCCCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
3853 7109 3.039526 CTCCTCCCTCCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
3854 7110 2.543637 TCCTCCCTCCCCTCCCTT 60.544 66.667 0.00 0.00 0.00 3.95
3855 7111 2.367512 CCTCCCTCCCCTCCCTTG 60.368 72.222 0.00 0.00 0.00 3.61
3884 7140 1.265454 CCCCGTGCTCTCCTAAACCT 61.265 60.000 0.00 0.00 0.00 3.50
3885 7141 0.175989 CCCGTGCTCTCCTAAACCTC 59.824 60.000 0.00 0.00 0.00 3.85
4014 7281 1.219393 CGTTGCTCTTCTCCCCCTC 59.781 63.158 0.00 0.00 0.00 4.30
4211 7516 1.395826 CCTCCCTCTGGAAGCCGTAG 61.396 65.000 0.00 0.00 41.17 3.51
4229 7534 1.004440 GGCTCACTCACGCCTTCTT 60.004 57.895 0.00 0.00 42.98 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 3148 8.988546 TGTTGTTATAATTACTGGTATGCCAT 57.011 30.769 1.83 0.00 45.05 4.40
50 3189 1.872952 GCTTTGGTTTGATGTTTGCCC 59.127 47.619 0.00 0.00 0.00 5.36
56 3195 2.503356 TGGTTTGGCTTTGGTTTGATGT 59.497 40.909 0.00 0.00 0.00 3.06
69 3208 3.591196 TTGCTAATCATGTGGTTTGGC 57.409 42.857 0.00 0.00 0.00 4.52
126 3284 4.038883 TGACAATGACAATGGCAATGACAA 59.961 37.500 11.65 0.00 31.44 3.18
127 3285 3.573110 TGACAATGACAATGGCAATGACA 59.427 39.130 11.65 8.23 31.44 3.58
128 3286 4.177165 TGACAATGACAATGGCAATGAC 57.823 40.909 11.65 5.35 31.44 3.06
129 3287 5.172205 CAATGACAATGACAATGGCAATGA 58.828 37.500 11.65 0.00 38.70 2.57
130 3288 4.932799 ACAATGACAATGACAATGGCAATG 59.067 37.500 12.09 12.09 41.51 2.82
131 3289 5.155278 ACAATGACAATGACAATGGCAAT 57.845 34.783 2.45 0.00 39.73 3.56
132 3290 4.038883 TGACAATGACAATGACAATGGCAA 59.961 37.500 6.83 0.00 39.73 4.52
133 3291 3.573110 TGACAATGACAATGACAATGGCA 59.427 39.130 5.26 5.26 40.80 4.92
134 3292 4.177165 TGACAATGACAATGACAATGGC 57.823 40.909 5.83 2.98 0.00 4.40
135 3293 6.160684 ACAATGACAATGACAATGACAATGG 58.839 36.000 13.21 4.18 30.92 3.16
136 3294 6.864165 TGACAATGACAATGACAATGACAATG 59.136 34.615 7.68 8.78 32.27 2.82
137 3295 6.983984 TGACAATGACAATGACAATGACAAT 58.016 32.000 7.68 0.00 0.00 2.71
138 3296 6.388435 TGACAATGACAATGACAATGACAA 57.612 33.333 7.68 0.00 0.00 3.18
139 3297 6.262720 TCTTGACAATGACAATGACAATGACA 59.737 34.615 7.68 5.04 33.35 3.58
140 3298 6.671190 TCTTGACAATGACAATGACAATGAC 58.329 36.000 7.68 2.60 33.35 3.06
141 3299 6.880942 TCTTGACAATGACAATGACAATGA 57.119 33.333 7.68 6.40 33.35 2.57
142 3300 6.034577 GCATCTTGACAATGACAATGACAATG 59.965 38.462 8.49 6.83 33.35 2.82
143 3301 6.071560 AGCATCTTGACAATGACAATGACAAT 60.072 34.615 8.49 0.00 33.35 2.71
232 3390 1.223763 GAAAGGGAGCCCGGTTAGG 59.776 63.158 0.00 0.00 41.95 2.69
475 3642 4.316823 AGGAGGGCACTCACCGGA 62.317 66.667 19.73 0.00 45.81 5.14
477 3644 3.775654 GGAGGAGGGCACTCACCG 61.776 72.222 19.73 0.00 45.81 4.94
676 3863 3.056304 ACCGCCACGAAATTCAAAATTG 58.944 40.909 0.00 0.00 0.00 2.32
773 3962 0.165944 CAAGCTTTAGCACCCGAACG 59.834 55.000 0.00 0.00 45.16 3.95
779 3968 2.820059 AAAAGGCAAGCTTTAGCACC 57.180 45.000 10.58 2.73 45.16 5.01
801 3990 1.631071 GGAGGAAGAAGAGCAGGGGG 61.631 65.000 0.00 0.00 0.00 5.40
1019 4233 1.342082 CGAGTTGTACTTGCCGTCGG 61.342 60.000 6.99 6.99 0.00 4.79
1239 4453 2.900838 TCGATCTCGAGCCGGACC 60.901 66.667 21.03 0.00 44.22 4.46
1305 4519 0.959372 AGTCCTGGTCCTCGTACACG 60.959 60.000 0.00 0.00 41.45 4.49
1414 4628 0.461961 ATGAGGTACCTGAAGAGCGC 59.538 55.000 22.10 0.00 0.00 5.92
1518 4732 1.227497 GAGCTTGATGGGCGAGGAG 60.227 63.158 0.00 0.00 34.52 3.69
1583 4797 1.222936 CAGGGGTGATCAGGCTGTC 59.777 63.158 15.27 11.73 0.00 3.51
1587 4801 2.191641 GAGCAGGGGTGATCAGGC 59.808 66.667 0.00 0.00 0.00 4.85
1588 4802 1.270414 ACAGAGCAGGGGTGATCAGG 61.270 60.000 0.00 0.00 0.00 3.86
1598 4813 2.281970 TTGCAGCCACAGAGCAGG 60.282 61.111 0.00 0.00 39.72 4.85
1602 4817 0.590195 GACAAGTTGCAGCCACAGAG 59.410 55.000 1.81 0.00 0.00 3.35
1603 4818 0.107263 TGACAAGTTGCAGCCACAGA 60.107 50.000 1.81 0.00 0.00 3.41
1604 4819 0.740149 TTGACAAGTTGCAGCCACAG 59.260 50.000 1.81 0.00 0.00 3.66
1605 4820 0.740149 CTTGACAAGTTGCAGCCACA 59.260 50.000 7.05 0.00 0.00 4.17
1606 4821 1.024271 TCTTGACAAGTTGCAGCCAC 58.976 50.000 14.75 0.00 0.00 5.01
1607 4822 1.985473 ATCTTGACAAGTTGCAGCCA 58.015 45.000 14.75 0.00 0.00 4.75
1608 4823 2.035066 ACAATCTTGACAAGTTGCAGCC 59.965 45.455 20.78 0.00 0.00 4.85
1609 4824 3.360249 ACAATCTTGACAAGTTGCAGC 57.640 42.857 20.78 0.00 0.00 5.25
1610 4825 4.046462 CCAACAATCTTGACAAGTTGCAG 58.954 43.478 20.78 15.84 38.50 4.41
1611 4826 3.446873 ACCAACAATCTTGACAAGTTGCA 59.553 39.130 20.78 0.00 38.50 4.08
1612 4827 4.044426 GACCAACAATCTTGACAAGTTGC 58.956 43.478 20.78 0.00 38.50 4.17
1613 4828 5.505173 AGACCAACAATCTTGACAAGTTG 57.495 39.130 14.75 17.94 39.29 3.16
1614 4829 6.530019 AAAGACCAACAATCTTGACAAGTT 57.470 33.333 14.75 4.00 36.52 2.66
1616 4831 6.256321 CCAAAAAGACCAACAATCTTGACAAG 59.744 38.462 9.03 9.03 36.52 3.16
1618 4833 5.420421 TCCAAAAAGACCAACAATCTTGACA 59.580 36.000 0.00 0.00 36.52 3.58
1625 4840 6.478512 TTAGCTTCCAAAAAGACCAACAAT 57.521 33.333 0.00 0.00 0.00 2.71
1626 4841 5.923733 TTAGCTTCCAAAAAGACCAACAA 57.076 34.783 0.00 0.00 0.00 2.83
1629 4844 6.287525 CCAATTTAGCTTCCAAAAAGACCAA 58.712 36.000 0.00 0.00 0.00 3.67
1635 4850 3.977326 ACCCCCAATTTAGCTTCCAAAAA 59.023 39.130 0.00 0.00 0.00 1.94
1636 4851 3.592865 ACCCCCAATTTAGCTTCCAAAA 58.407 40.909 0.00 0.00 0.00 2.44
1643 4858 3.490060 ATCCAAACCCCCAATTTAGCT 57.510 42.857 0.00 0.00 0.00 3.32
1927 5142 1.326213 CCTCTGTCCAGGATCACGCT 61.326 60.000 0.00 0.00 35.20 5.07
1931 5146 2.907703 GAGCCTCTGTCCAGGATCA 58.092 57.895 0.00 0.00 46.64 2.92
1952 5167 0.741221 CACCTAGAACTTGCTCGGCC 60.741 60.000 0.00 0.00 0.00 6.13
1978 5193 3.826157 TGGTTTCCCAACAAGATGATGTC 59.174 43.478 0.00 0.00 37.98 3.06
1980 5195 3.573538 TGTGGTTTCCCAACAAGATGATG 59.426 43.478 0.00 0.00 44.15 3.07
1982 5197 3.304911 TGTGGTTTCCCAACAAGATGA 57.695 42.857 0.00 0.00 44.15 2.92
1983 5198 3.861886 GCATGTGGTTTCCCAACAAGATG 60.862 47.826 0.00 0.00 44.15 2.90
1984 5199 2.299867 GCATGTGGTTTCCCAACAAGAT 59.700 45.455 0.00 0.00 44.15 2.40
1985 5200 1.686052 GCATGTGGTTTCCCAACAAGA 59.314 47.619 0.00 0.00 44.15 3.02
1987 5202 1.686052 GAGCATGTGGTTTCCCAACAA 59.314 47.619 0.00 0.00 44.15 2.83
2028 5251 8.557592 ACCTTGTGTATGATGCTAATGATATG 57.442 34.615 0.00 0.00 0.00 1.78
2052 5278 8.663911 CATCAAGAATCAAAGGTCTCTTCTAAC 58.336 37.037 0.00 0.00 31.82 2.34
2074 5300 9.862149 TGAAGGTATAGACACTACTAATCATCA 57.138 33.333 0.00 0.00 0.00 3.07
2083 5309 8.900781 TCAGTTACATGAAGGTATAGACACTAC 58.099 37.037 0.00 0.00 0.00 2.73
2103 5329 5.798132 ACATTCTGATCAACAGCTCAGTTA 58.202 37.500 0.00 0.00 45.38 2.24
2190 5416 6.993079 TGACTTAGCAGTGAAGACTTGATAA 58.007 36.000 0.00 0.00 31.22 1.75
2277 5503 9.559958 GATTCAGACTTGTTTATTTGTACCATG 57.440 33.333 0.00 0.00 0.00 3.66
2342 5571 6.039717 ACACTAATAAATAAGCAGCCATGTGG 59.960 38.462 0.00 0.00 38.53 4.17
2372 5601 4.686191 AGGGTGACAGAGATGATGAATC 57.314 45.455 0.00 0.00 35.29 2.52
2373 5602 4.472470 TCAAGGGTGACAGAGATGATGAAT 59.528 41.667 0.00 0.00 0.00 2.57
2374 5603 3.840078 TCAAGGGTGACAGAGATGATGAA 59.160 43.478 0.00 0.00 0.00 2.57
2376 5605 3.900966 TCAAGGGTGACAGAGATGATG 57.099 47.619 0.00 0.00 0.00 3.07
2453 5683 4.770795 ACCATTAACAGCTGGATCTGTAC 58.229 43.478 19.93 0.00 45.77 2.90
2454 5684 5.428253 GAACCATTAACAGCTGGATCTGTA 58.572 41.667 19.93 0.00 45.77 2.74
2456 5686 3.629398 GGAACCATTAACAGCTGGATCTG 59.371 47.826 19.93 9.89 35.36 2.90
2457 5687 3.891049 GGAACCATTAACAGCTGGATCT 58.109 45.455 19.93 1.77 35.36 2.75
2477 5707 4.290942 ACTACTACCATCAGGAGAAAGGG 58.709 47.826 0.00 0.00 38.69 3.95
2497 5727 4.338118 CCACATGGTGAACAACTGTAAACT 59.662 41.667 0.00 0.00 35.23 2.66
2498 5728 4.499019 CCCACATGGTGAACAACTGTAAAC 60.499 45.833 0.00 0.00 35.23 2.01
2499 5729 3.634448 CCCACATGGTGAACAACTGTAAA 59.366 43.478 0.00 0.00 35.23 2.01
2511 5741 1.206849 GGCAATAAACCCCACATGGTG 59.793 52.381 0.00 0.00 39.05 4.17
2543 5773 2.156917 CAGGAATGCTCTGCACAAAGA 58.843 47.619 0.00 0.00 43.04 2.52
2570 5800 1.636340 CGAATCATCGGCGTGTTCC 59.364 57.895 6.85 0.00 45.32 3.62
2582 5812 2.525248 GCAGGAATCGCGCGAATCA 61.525 57.895 39.13 19.96 0.00 2.57
2639 5869 0.694771 TGGAGAATGAGCACAAGCCT 59.305 50.000 0.00 0.00 43.56 4.58
2644 5874 1.375908 GGCGTGGAGAATGAGCACA 60.376 57.895 0.00 0.00 0.00 4.57
2651 5881 2.203070 GCCATCGGCGTGGAGAAT 60.203 61.111 25.53 1.91 42.02 2.40
2723 5953 2.283529 GCAGGGTTCCTCCGACAGA 61.284 63.158 0.00 0.00 37.00 3.41
2747 5977 2.200067 GACGATCTGCAGGAGAATGTG 58.800 52.381 15.13 0.00 33.12 3.21
2804 6034 1.739067 ATAACAAGGCTCCGCAAGAC 58.261 50.000 0.00 0.00 43.02 3.01
2870 6100 2.507102 AAGCTCGGCATCGACACG 60.507 61.111 0.00 0.00 40.88 4.49
2904 6134 2.521224 GGGCTCGTCGGACCCTAT 60.521 66.667 14.24 0.00 40.75 2.57
2936 6166 2.028484 GTGGTGTCGTCGCCTGAA 59.972 61.111 13.33 0.00 43.94 3.02
3133 6369 4.320456 CCAGGTCGTGCTGGTGCT 62.320 66.667 0.00 0.00 40.48 4.40
3194 6430 1.073199 GAGGGTGGTGGACAGGTTG 59.927 63.158 0.00 0.00 0.00 3.77
3195 6431 1.073706 AGAGGGTGGTGGACAGGTT 60.074 57.895 0.00 0.00 0.00 3.50
3268 6504 0.946221 AACAAACTCTGAGCCGCTCG 60.946 55.000 15.58 10.33 32.35 5.03
3274 6510 2.739379 GCTACAGGAACAAACTCTGAGC 59.261 50.000 4.19 0.00 33.19 4.26
3377 6618 1.730902 CCAGAGACAGTGACACGCG 60.731 63.158 3.53 3.53 0.00 6.01
3379 6620 1.202417 ACAACCAGAGACAGTGACACG 60.202 52.381 0.00 0.00 0.00 4.49
3391 6632 5.542635 AGGTTACACTCATTCTACAACCAGA 59.457 40.000 0.00 0.00 37.10 3.86
3404 6651 3.837731 TCATCATGTCCAGGTTACACTCA 59.162 43.478 0.00 0.00 0.00 3.41
3451 6700 6.150318 ACAAAATACTCGGCGATCTACTATG 58.850 40.000 11.27 7.51 0.00 2.23
3469 6718 2.706339 TTTGGCACCAGCAACAAAAT 57.294 40.000 0.00 0.00 44.61 1.82
3470 6719 2.093288 TCATTTGGCACCAGCAACAAAA 60.093 40.909 0.00 0.00 44.61 2.44
3488 6737 4.695217 AACGCGAAATTTACACCATCAT 57.305 36.364 15.93 0.00 0.00 2.45
3506 6755 3.135909 CGAAATTCACGAGTTCGAAACG 58.864 45.455 19.42 19.42 45.32 3.60
3511 6760 0.847983 GCGCGAAATTCACGAGTTCG 60.848 55.000 12.10 4.50 45.28 3.95
3576 6825 2.159653 CCATTCAAAGAGGCTCGAAACG 60.160 50.000 9.22 3.25 0.00 3.60
3581 6830 2.680312 TCTCCATTCAAAGAGGCTCG 57.320 50.000 9.22 0.00 0.00 5.03
3582 6831 4.034975 CGAATTCTCCATTCAAAGAGGCTC 59.965 45.833 6.34 6.34 41.51 4.70
3590 6839 4.393834 TCACCAACGAATTCTCCATTCAA 58.606 39.130 3.52 0.00 41.51 2.69
3591 6840 4.014569 TCACCAACGAATTCTCCATTCA 57.985 40.909 3.52 0.00 41.51 2.57
3593 6842 5.982890 ATTTCACCAACGAATTCTCCATT 57.017 34.783 3.52 0.00 0.00 3.16
3594 6843 5.982890 AATTTCACCAACGAATTCTCCAT 57.017 34.783 3.52 0.00 0.00 3.41
3653 6902 7.433680 TCTTTCAAGGAAAAGGAAAGCAATAC 58.566 34.615 8.15 0.00 44.38 1.89
3723 6979 1.509162 GTTCGACCAAATGCGCGAC 60.509 57.895 12.10 0.88 31.91 5.19
3734 6990 2.358247 ACGGCATGGTGTTCGACC 60.358 61.111 0.00 0.00 46.37 4.79
4213 7518 0.390472 GGGAAGAAGGCGTGAGTGAG 60.390 60.000 0.00 0.00 0.00 3.51
4214 7519 1.671742 GGGAAGAAGGCGTGAGTGA 59.328 57.895 0.00 0.00 0.00 3.41
4215 7520 1.376037 GGGGAAGAAGGCGTGAGTG 60.376 63.158 0.00 0.00 0.00 3.51
4216 7521 1.536662 AGGGGAAGAAGGCGTGAGT 60.537 57.895 0.00 0.00 0.00 3.41
4222 7527 3.409384 AGAGCAGGGGAAGAAGGC 58.591 61.111 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.