Multiple sequence alignment - TraesCS4B01G163700

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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 TraesCS4B01G163700 chr4B 100.000 8442 0 0 1 8442 335945415 335936974 0.000000e+00 15590
1 TraesCS4B01G163700 chr4B 92.238 773 51 8 7677 8442 330774265 330773495 0.000000e+00 1086
2 TraesCS4B01G163700 chr4B 92.098 772 52 7 7678 8442 27782409 27781640 0.000000e+00 1079
3 TraesCS4B01G163700 chr4B 86.772 567 60 8 2765 3319 335942471 335941908 1.200000e-172 617
4 TraesCS4B01G163700 chr4B 86.772 567 60 8 2945 3508 335942651 335942097 1.200000e-172 617
5 TraesCS4B01G163700 chr4B 86.975 476 59 1 3490 3962 335941455 335940980 4.490000e-147 532
6 TraesCS4B01G163700 chr4B 86.975 476 59 1 3961 4436 335941926 335941454 4.490000e-147 532
7 TraesCS4B01G163700 chr4B 81.941 371 53 12 2765 3124 335942291 335941924 1.380000e-77 302
8 TraesCS4B01G163700 chr4B 81.892 370 55 10 3125 3492 335942651 335942292 1.380000e-77 302
9 TraesCS4B01G163700 chr4B 91.875 160 12 1 437 596 335969205 335969363 1.100000e-53 222
10 TraesCS4B01G163700 chr4B 84.404 218 11 6 724 941 335969208 335969014 8.650000e-45 193
11 TraesCS4B01G163700 chr4A 96.137 7558 233 28 134 7674 345843444 345835929 0.000000e+00 12285
12 TraesCS4B01G163700 chr4A 87.080 565 62 9 2765 3319 345840664 345840101 5.560000e-176 628
13 TraesCS4B01G163700 chr4A 85.640 578 68 8 2943 3517 345840846 345840281 2.030000e-165 593
14 TraesCS4B01G163700 chr4A 87.815 476 55 1 3961 4436 345840119 345839647 9.570000e-154 555
15 TraesCS4B01G163700 chr4A 87.421 477 55 3 3490 3962 345839648 345839173 2.070000e-150 544
16 TraesCS4B01G163700 chr4A 91.418 268 18 5 729 996 345845005 345844743 6.230000e-96 363
17 TraesCS4B01G163700 chr4A 81.941 371 53 12 2765 3124 345840484 345840117 1.380000e-77 302
18 TraesCS4B01G163700 chr4A 81.501 373 55 12 3123 3492 345840846 345840485 2.300000e-75 294
19 TraesCS4B01G163700 chr4A 93.082 159 10 1 438 596 345845007 345845164 1.830000e-56 231
20 TraesCS4B01G163700 chr4D 97.533 6567 136 11 166 6727 271205059 271211604 0.000000e+00 11206
21 TraesCS4B01G163700 chr4D 97.592 955 18 2 6720 7674 271216124 271217073 0.000000e+00 1631
22 TraesCS4B01G163700 chr4D 87.125 567 58 11 2765 3319 271207827 271208390 5.560000e-176 628
23 TraesCS4B01G163700 chr4D 86.643 569 61 8 2943 3508 271207645 271208201 4.330000e-172 616
24 TraesCS4B01G163700 chr4D 87.315 473 57 1 3961 4433 271208372 271208841 9.640000e-149 538
25 TraesCS4B01G163700 chr4D 87.315 473 57 1 3490 3959 271208843 271209315 9.640000e-149 538
26 TraesCS4B01G163700 chr4D 93.040 273 16 3 724 996 271203172 271203441 6.140000e-106 396
27 TraesCS4B01G163700 chr4D 83.019 371 49 12 2765 3124 271208007 271208374 2.940000e-84 324
28 TraesCS4B01G163700 chr4D 81.720 372 56 10 3123 3492 271207645 271208006 4.950000e-77 300
29 TraesCS4B01G163700 chr4D 93.373 166 10 1 437 602 271203175 271203011 2.350000e-60 244
30 TraesCS4B01G163700 chr4D 86.772 189 22 3 1 188 271204726 271204912 3.090000e-49 207
31 TraesCS4B01G163700 chr3B 94.703 774 34 4 7676 8442 726423503 726422730 0.000000e+00 1195
32 TraesCS4B01G163700 chr1B 93.694 777 43 3 7672 8442 67114719 67113943 0.000000e+00 1158
33 TraesCS4B01G163700 chr7B 93.411 774 44 4 7676 8442 697872314 697873087 0.000000e+00 1140
34 TraesCS4B01G163700 chr7B 92.784 776 43 11 7678 8442 527881275 527882048 0.000000e+00 1110
35 TraesCS4B01G163700 chr5B 92.674 778 48 7 7672 8442 180711579 180710804 0.000000e+00 1112
36 TraesCS4B01G163700 chr6B 92.308 780 49 9 7670 8442 704392610 704391835 0.000000e+00 1098
37 TraesCS4B01G163700 chr2B 91.742 775 55 7 7675 8442 24649818 24650590 0.000000e+00 1068
38 TraesCS4B01G163700 chr5D 96.970 66 2 0 223 288 88472041 88471976 2.490000e-20 111


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 TraesCS4B01G163700 chr4B 335936974 335945415 8441 True 15590.000000 15590 100.000000 1 8442 1 chr4B.!!$R3 8441
1 TraesCS4B01G163700 chr4B 330773495 330774265 770 True 1086.000000 1086 92.238000 7677 8442 1 chr4B.!!$R2 765
2 TraesCS4B01G163700 chr4B 27781640 27782409 769 True 1079.000000 1079 92.098000 7678 8442 1 chr4B.!!$R1 764
3 TraesCS4B01G163700 chr4B 335940980 335942651 1671 True 483.666667 617 85.221167 2765 4436 6 chr4B.!!$R5 1671
4 TraesCS4B01G163700 chr4A 345835929 345843444 7515 True 12285.000000 12285 96.137000 134 7674 1 chr4A.!!$R1 7540
5 TraesCS4B01G163700 chr4A 345839173 345845005 5832 True 468.428571 628 86.116571 729 4436 7 chr4A.!!$R2 3707
6 TraesCS4B01G163700 chr4D 271203172 271211604 8432 False 1639.222222 11206 87.831333 1 6727 9 chr4D.!!$F2 6726
7 TraesCS4B01G163700 chr4D 271216124 271217073 949 False 1631.000000 1631 97.592000 6720 7674 1 chr4D.!!$F1 954
8 TraesCS4B01G163700 chr3B 726422730 726423503 773 True 1195.000000 1195 94.703000 7676 8442 1 chr3B.!!$R1 766
9 TraesCS4B01G163700 chr1B 67113943 67114719 776 True 1158.000000 1158 93.694000 7672 8442 1 chr1B.!!$R1 770
10 TraesCS4B01G163700 chr7B 697872314 697873087 773 False 1140.000000 1140 93.411000 7676 8442 1 chr7B.!!$F2 766
11 TraesCS4B01G163700 chr7B 527881275 527882048 773 False 1110.000000 1110 92.784000 7678 8442 1 chr7B.!!$F1 764
12 TraesCS4B01G163700 chr5B 180710804 180711579 775 True 1112.000000 1112 92.674000 7672 8442 1 chr5B.!!$R1 770
13 TraesCS4B01G163700 chr6B 704391835 704392610 775 True 1098.000000 1098 92.308000 7670 8442 1 chr6B.!!$R1 772
14 TraesCS4B01G163700 chr2B 24649818 24650590 772 False 1068.000000 1068 91.742000 7675 8442 1 chr2B.!!$F1 767

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
212 1938 2.162681 AGGCGTTGGATCTTTTTCCAG 58.837 47.619 0.00 0.0 46.22 3.86 F
1035 2762 1.329256 AGGTCTTGTACAGTGTCGCT 58.671 50.000 0.00 0.0 0.00 4.93 F
1501 3228 0.107508 CCCTGCTGTGGATAGTGTGG 60.108 60.000 0.00 0.0 0.00 4.17 F
1872 3599 0.811915 CTATAGACCGGCCAGGATCG 59.188 60.000 18.74 0.0 45.00 3.69 F
4465 6192 1.421268 TCATCAACAGTCCAGTGCCTT 59.579 47.619 0.00 0.0 0.00 4.35 F
6264 7999 0.041312 CTGTTTGTGCCCGAAAGTCG 60.041 55.000 0.00 0.0 40.07 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1305 3032 0.036388 TCAGCACCTCCCGTTCATTC 60.036 55.000 0.00 0.0 0.00 2.67 R
2763 4490 0.112995 TTTGGGCAATGCACTCTCCT 59.887 50.000 9.57 0.0 30.56 3.69 R
4465 6192 5.422012 TCAGGTCATCAGAGTGCTTGTTATA 59.578 40.000 0.00 0.0 0.00 0.98 R
4642 6369 2.366266 ACAAAATTCACTGCACATGCCT 59.634 40.909 0.49 0.0 41.18 4.75 R
7315 9055 0.323999 TCCTACTCCGTAGCAGGCAA 60.324 55.000 0.00 0.0 35.06 4.52 R
7626 9378 0.041663 AAAACGCAACGTCATCACCG 60.042 50.000 0.00 0.0 39.99 4.94 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
32 1588 4.334203 TCTTCTCATTACAGAGAGACGCTC 59.666 45.833 0.00 0.00 44.78 5.03
62 1618 5.728637 ATGTACTCGCCAATGAGATGATA 57.271 39.130 0.00 0.00 39.35 2.15
64 1620 4.340950 TGTACTCGCCAATGAGATGATACA 59.659 41.667 0.00 0.00 39.35 2.29
65 1621 4.613925 ACTCGCCAATGAGATGATACAT 57.386 40.909 0.00 0.00 39.35 2.29
67 1623 5.718146 ACTCGCCAATGAGATGATACATAG 58.282 41.667 0.00 0.00 39.35 2.23
68 1624 5.244851 ACTCGCCAATGAGATGATACATAGT 59.755 40.000 0.00 0.00 39.35 2.12
69 1625 5.714047 TCGCCAATGAGATGATACATAGTC 58.286 41.667 0.00 0.00 0.00 2.59
70 1626 4.560427 CGCCAATGAGATGATACATAGTCG 59.440 45.833 0.00 0.00 0.00 4.18
71 1627 5.619981 CGCCAATGAGATGATACATAGTCGA 60.620 44.000 0.00 0.00 0.00 4.20
114 1670 3.129287 GCGATGATGGGTGTGAATCTTTT 59.871 43.478 0.00 0.00 0.00 2.27
116 1672 4.395854 CGATGATGGGTGTGAATCTTTTGA 59.604 41.667 0.00 0.00 0.00 2.69
117 1673 5.106197 CGATGATGGGTGTGAATCTTTTGAA 60.106 40.000 0.00 0.00 0.00 2.69
212 1938 2.162681 AGGCGTTGGATCTTTTTCCAG 58.837 47.619 0.00 0.00 46.22 3.86
571 2298 5.756195 TGTTGTTTCTCTGGTTCAGATTG 57.244 39.130 0.00 0.00 39.92 2.67
714 2441 3.429410 GGCATTAGCTTGTTGGATTGTCC 60.429 47.826 0.00 0.00 41.70 4.02
1035 2762 1.329256 AGGTCTTGTACAGTGTCGCT 58.671 50.000 0.00 0.00 0.00 4.93
1065 2792 3.679738 CCATTTGGCGGTGCGGTT 61.680 61.111 0.00 0.00 0.00 4.44
1158 2885 1.699634 CAGGGGGTTCTCAAGACAAGA 59.300 52.381 0.00 0.00 0.00 3.02
1191 2918 4.405116 AAACATTGCTGTGAATGGTGTT 57.595 36.364 0.00 0.00 37.60 3.32
1387 3114 2.196742 TATCTCAACCATGGAGGCCT 57.803 50.000 21.47 3.86 43.14 5.19
1412 3139 1.649271 GGGGATGGGAAGATGCCTGT 61.649 60.000 0.00 0.00 34.33 4.00
1501 3228 0.107508 CCCTGCTGTGGATAGTGTGG 60.108 60.000 0.00 0.00 0.00 4.17
1633 3360 1.558294 ATCTGAGAGATGCTGGCAACA 59.442 47.619 0.00 0.00 37.75 3.33
1719 3446 4.406456 TGGGCTCTAATTGTGACAATGTT 58.594 39.130 12.09 0.22 0.00 2.71
1872 3599 0.811915 CTATAGACCGGCCAGGATCG 59.188 60.000 18.74 0.00 45.00 3.69
2118 3845 8.153479 ACCAAAATTTTACTGAAGCAAATTCC 57.847 30.769 2.44 0.00 37.08 3.01
2375 4102 4.827284 GGAACAGGAAGATGTCAAGGAAAA 59.173 41.667 0.00 0.00 31.50 2.29
2540 4267 7.082602 GTCAATGATCACATGGATATTTCTGC 58.917 38.462 0.00 0.00 38.52 4.26
2701 4428 3.543680 AGGATTCCACGGTGAATACTG 57.456 47.619 10.28 0.00 42.94 2.74
2740 4467 7.309377 GGGAACATGATGTTTCTTTCAATCAGA 60.309 37.037 15.67 0.00 41.28 3.27
2755 4482 8.961294 TTTCAATCAGACACCAAAAATTCAAT 57.039 26.923 0.00 0.00 0.00 2.57
2763 4490 5.728471 ACACCAAAAATTCAATGTGTGACA 58.272 33.333 0.00 0.00 35.39 3.58
4465 6192 1.421268 TCATCAACAGTCCAGTGCCTT 59.579 47.619 0.00 0.00 0.00 4.35
4500 6227 4.220602 TCTGATGACCTGAAAGACGATTCA 59.779 41.667 0.00 0.00 37.70 2.57
4697 6424 8.044574 TCATATTCATCAATTTCAGGGGACTA 57.955 34.615 0.00 0.00 40.21 2.59
4884 6618 2.249139 ACCTTAGAGAAGTTCCGTGCT 58.751 47.619 0.00 0.00 0.00 4.40
4966 6700 1.123077 CTGGGATGTAGCTGCACCTA 58.877 55.000 6.66 7.87 0.00 3.08
5154 6888 3.819337 AGAGCACAGTCGTGAGTACTTTA 59.181 43.478 0.00 0.00 46.80 1.85
5186 6920 4.956700 TGTTAGAGAGTCGGATGGAGAAAT 59.043 41.667 0.00 0.00 0.00 2.17
5340 7074 1.581447 GCAGCAGGTTAGTTGCCAC 59.419 57.895 0.00 0.00 42.48 5.01
5663 7397 6.954487 AGAGTTTGGAAAAATAACGTCCTT 57.046 33.333 0.00 0.00 32.28 3.36
6022 7757 8.432805 TCTTTTCTCCAACTACAGAAGATTCTT 58.567 33.333 0.00 0.00 34.74 2.52
6052 7787 5.517770 GCCTGAAGAATTGCATATGTTTGTC 59.482 40.000 4.29 0.00 0.00 3.18
6056 7791 9.199982 CTGAAGAATTGCATATGTTTGTCTTTT 57.800 29.630 4.29 0.00 0.00 2.27
6094 7829 2.675032 GCAAGCTGCCCCTAAAATGTTC 60.675 50.000 0.00 0.00 37.42 3.18
6264 7999 0.041312 CTGTTTGTGCCCGAAAGTCG 60.041 55.000 0.00 0.00 40.07 4.18
6552 8287 3.777106 TGAGGACAGTGCTGAAGAATT 57.223 42.857 0.00 0.00 0.00 2.17
6622 8358 3.430333 AACCACCGTTGTTTGACATTC 57.570 42.857 0.00 0.00 0.00 2.67
6996 8736 1.264020 GTGAAGTTGCTGTGAATCGCA 59.736 47.619 0.00 0.00 0.00 5.10
7023 8763 6.772716 GGTGAATACCAAATCATACATGTCCT 59.227 38.462 0.00 0.00 46.71 3.85
7089 8829 1.244697 GGAGCAGGTCTGTCTGTCGA 61.245 60.000 0.00 0.00 37.12 4.20
7115 8855 9.525409 AGTTTTCTGATTCTTGACTTGAATTTG 57.475 29.630 0.00 0.00 34.67 2.32
7230 8970 2.872557 CAGTCTGGGCACAATGCG 59.127 61.111 0.00 0.00 46.21 4.73
7315 9055 4.431416 TGTCATAACCTGTTGTGTTCCT 57.569 40.909 6.65 0.00 34.03 3.36
7593 9345 7.920738 ACTAGAACAACAAGACAAGAATTCAC 58.079 34.615 8.44 0.00 0.00 3.18
7626 9378 3.594453 TCCTGTTGGATTGGATGCC 57.406 52.632 0.00 0.00 37.46 4.40
7788 9540 1.579429 GGTCGTTTTTCTGCGCCAT 59.421 52.632 4.18 0.00 0.00 4.40
7869 9621 2.358737 GTCAGGGGTTGCCACTCG 60.359 66.667 0.00 0.00 33.28 4.18
8001 9755 2.357034 CGCACCGCAGTTACTGGT 60.357 61.111 14.63 1.24 36.10 4.00
8057 9812 2.754658 GAGGGGAGAAGGCGACGA 60.755 66.667 0.00 0.00 0.00 4.20
8148 9903 2.740714 GCCTGCGCGTTGAAGGTAG 61.741 63.158 8.43 0.00 33.34 3.18
8206 9963 1.617947 CCCCTTCCTCCCTGTTCGAG 61.618 65.000 0.00 0.00 0.00 4.04
8261 10018 4.537533 CGATGCGTCGGCGTTTCG 62.538 66.667 20.66 18.45 44.00 3.46
8262 10019 3.475774 GATGCGTCGGCGTTTCGT 61.476 61.111 12.58 0.00 44.10 3.85
8276 10038 1.291184 TTTCGTCGCGGAGTCGTCTA 61.291 55.000 6.13 0.00 38.89 2.59
8412 10177 0.243636 CTCCCGGTTTGTTTGATGCC 59.756 55.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.836007 TCTCTGTAATGAGAAGATCTGGCTAA 59.164 38.462 0.00 0.00 39.80 3.09
3 4 5.301551 TCTCTCTGTAATGAGAAGATCTGGC 59.698 44.000 0.00 0.00 41.85 4.85
8 9 4.887071 AGCGTCTCTCTGTAATGAGAAGAT 59.113 41.667 9.39 1.38 41.85 2.40
10 11 4.497340 GGAGCGTCTCTCTGTAATGAGAAG 60.497 50.000 6.78 0.00 41.85 2.85
11 12 3.378742 GGAGCGTCTCTCTGTAATGAGAA 59.621 47.826 6.78 0.00 41.85 2.87
12 13 2.946329 GGAGCGTCTCTCTGTAATGAGA 59.054 50.000 6.78 0.00 41.60 3.27
13 14 2.034053 GGGAGCGTCTCTCTGTAATGAG 59.966 54.545 6.78 0.00 41.60 2.90
14 15 2.025155 GGGAGCGTCTCTCTGTAATGA 58.975 52.381 6.78 0.00 41.60 2.57
17 18 1.030488 CGGGGAGCGTCTCTCTGTAA 61.030 60.000 7.23 0.00 41.60 2.41
18 19 1.451567 CGGGGAGCGTCTCTCTGTA 60.452 63.158 7.23 0.00 41.60 2.74
20 21 2.752238 ACGGGGAGCGTCTCTCTG 60.752 66.667 12.32 12.32 42.66 3.35
32 1588 1.520787 GGCGAGTACATTGACGGGG 60.521 63.158 0.00 0.00 0.00 5.73
62 1618 4.547905 CGCCGCCGTCGACTATGT 62.548 66.667 14.70 0.00 38.10 2.29
81 1637 3.490793 ATCATCGCTGTCTCCGCCG 62.491 63.158 0.00 0.00 0.00 6.46
95 1651 6.669125 TTTCAAAAGATTCACACCCATCAT 57.331 33.333 0.00 0.00 0.00 2.45
114 1670 1.505807 CGCAACATCCGCCATTTCA 59.494 52.632 0.00 0.00 0.00 2.69
116 1672 1.531739 AACCGCAACATCCGCCATTT 61.532 50.000 0.00 0.00 0.00 2.32
117 1673 0.678366 TAACCGCAACATCCGCCATT 60.678 50.000 0.00 0.00 0.00 3.16
212 1938 2.368221 CCTCTGTCCCTCTGATGGATTC 59.632 54.545 4.94 0.00 33.65 2.52
285 2011 9.185192 ACGTCGCCACTTACTTATTATTTATAC 57.815 33.333 0.00 0.00 0.00 1.47
287 2013 7.922278 TGACGTCGCCACTTACTTATTATTTAT 59.078 33.333 11.62 0.00 0.00 1.40
288 2014 7.257003 TGACGTCGCCACTTACTTATTATTTA 58.743 34.615 11.62 0.00 0.00 1.40
289 2015 6.101332 TGACGTCGCCACTTACTTATTATTT 58.899 36.000 11.62 0.00 0.00 1.40
290 2016 5.653507 TGACGTCGCCACTTACTTATTATT 58.346 37.500 11.62 0.00 0.00 1.40
291 2017 5.252969 TGACGTCGCCACTTACTTATTAT 57.747 39.130 11.62 0.00 0.00 1.28
292 2018 4.700268 TGACGTCGCCACTTACTTATTA 57.300 40.909 11.62 0.00 0.00 0.98
487 2214 0.443869 CACGATCCAAGCAAGAACCG 59.556 55.000 0.00 0.00 0.00 4.44
654 2381 2.124570 CACCTTGGCAGGATCGGG 60.125 66.667 9.53 0.00 44.19 5.14
714 2441 3.868077 CCTGCTGAGAATCCGAACTTTAG 59.132 47.826 0.00 0.00 0.00 1.85
795 2522 5.068987 CCTCAAAACTCCAACCAATTCTTCA 59.931 40.000 0.00 0.00 0.00 3.02
1035 2762 1.552023 CCAAATGGGTGGAATGGACCA 60.552 52.381 0.00 0.00 41.65 4.02
1065 2792 2.549329 CTGCTGCACAACAACTATGTCA 59.451 45.455 0.00 0.00 39.40 3.58
1158 2885 4.074970 CAGCAATGTTTACCACCTTCTCT 58.925 43.478 0.00 0.00 0.00 3.10
1191 2918 0.179004 ACATGTGAAACCCGGCTTCA 60.179 50.000 11.93 11.93 34.36 3.02
1304 3031 1.026718 CAGCACCTCCCGTTCATTCC 61.027 60.000 0.00 0.00 0.00 3.01
1305 3032 0.036388 TCAGCACCTCCCGTTCATTC 60.036 55.000 0.00 0.00 0.00 2.67
1306 3033 0.620556 ATCAGCACCTCCCGTTCATT 59.379 50.000 0.00 0.00 0.00 2.57
1387 3114 0.920763 ATCTTCCCATCCCCAGCACA 60.921 55.000 0.00 0.00 0.00 4.57
1412 3139 3.153130 CTCTGTCTTGAGACTGTCCTCA 58.847 50.000 12.00 5.15 44.99 3.86
1633 3360 4.463050 TTGTGGTTTCCCCTTGATTACT 57.537 40.909 0.00 0.00 0.00 2.24
2118 3845 2.428890 TGTGGTTGTGCTAAAAGTTGGG 59.571 45.455 0.00 0.00 0.00 4.12
2281 4008 4.097437 AGCCAATGAGTTACATTCAGCATG 59.903 41.667 0.00 0.00 46.01 4.06
2290 4017 3.264193 AGACCATCAGCCAATGAGTTACA 59.736 43.478 0.00 0.00 42.53 2.41
2375 4102 5.171339 AGAACTATGATTTGACAGTGGCT 57.829 39.130 0.00 0.00 0.00 4.75
2540 4267 2.226200 TGATCATTTGCAACAGTGTCCG 59.774 45.455 0.00 0.00 0.00 4.79
2701 4428 3.953612 TCATGTTCCCCATAGCATGTTTC 59.046 43.478 0.00 0.00 39.54 2.78
2740 4467 5.728471 TGTCACACATTGAATTTTTGGTGT 58.272 33.333 0.00 0.00 39.83 4.16
2755 4482 1.051008 ATGCACTCTCCTGTCACACA 58.949 50.000 0.00 0.00 0.00 3.72
2763 4490 0.112995 TTTGGGCAATGCACTCTCCT 59.887 50.000 9.57 0.00 30.56 3.69
4465 6192 5.422012 TCAGGTCATCAGAGTGCTTGTTATA 59.578 40.000 0.00 0.00 0.00 0.98
4642 6369 2.366266 ACAAAATTCACTGCACATGCCT 59.634 40.909 0.49 0.00 41.18 4.75
4726 6453 4.997565 ACACATACAATATTGCAGGCAAC 58.002 39.130 15.48 0.00 38.88 4.17
4884 6618 6.479990 CGTTTCTTATCAATGACTGCTCCATA 59.520 38.462 0.00 0.00 0.00 2.74
4966 6700 0.466963 GAAACCATCCCCCGTACGAT 59.533 55.000 18.76 0.00 0.00 3.73
5144 6878 8.603898 TCTAACAGGAATGGATAAAGTACTCA 57.396 34.615 0.00 0.00 0.00 3.41
5154 6888 3.639094 CCGACTCTCTAACAGGAATGGAT 59.361 47.826 0.00 0.00 0.00 3.41
5186 6920 7.363705 CCATCATCTTTGCACTGGGTTTATTTA 60.364 37.037 0.00 0.00 0.00 1.40
5340 7074 6.527023 GCAAATCAAGTGTGATGATGAAAGAG 59.473 38.462 6.84 0.00 44.02 2.85
5598 7332 8.877779 CCACTTTTCATTTAACACAAAATGTCA 58.122 29.630 8.65 0.00 42.31 3.58
6022 7757 4.811969 ATGCAATTCTTCAGGCATTTGA 57.188 36.364 0.00 0.00 43.97 2.69
6052 7787 5.629097 TGCTGCAAAAATTCACACAAAAAG 58.371 33.333 0.00 0.00 0.00 2.27
6056 7791 3.063725 GCTTGCTGCAAAAATTCACACAA 59.936 39.130 16.74 0.00 42.31 3.33
6094 7829 7.378181 AGGCCATAAGAACAAACACAATTAAG 58.622 34.615 5.01 0.00 0.00 1.85
6552 8287 3.439857 ACTAAATTCAGCAGCCTCCAA 57.560 42.857 0.00 0.00 0.00 3.53
6622 8358 5.163774 GGAGCTCTTCTGATAACTGCAAAAG 60.164 44.000 14.64 0.00 0.00 2.27
6996 8736 6.672593 ACATGTATGATTTGGTATTCACCCT 58.327 36.000 0.00 0.00 45.11 4.34
7023 8763 1.469703 CCGATTCACAAGAGCATGCAA 59.530 47.619 21.98 3.36 0.00 4.08
7089 8829 9.525409 CAAATTCAAGTCAAGAATCAGAAAACT 57.475 29.630 0.00 0.00 34.78 2.66
7115 8855 5.277828 GGTCAAGGTACAAAACACACTGATC 60.278 44.000 0.00 0.00 0.00 2.92
7154 8894 2.248248 CAGGTGTTGTAGTCCTCCTGA 58.752 52.381 0.00 0.00 43.28 3.86
7230 8970 1.298863 CATTGCTGTGCGCCATAGC 60.299 57.895 17.43 17.43 46.31 2.97
7315 9055 0.323999 TCCTACTCCGTAGCAGGCAA 60.324 55.000 0.00 0.00 35.06 4.52
7452 9201 2.854777 CTCGTACAGACTATGTTGCTGC 59.145 50.000 0.00 0.00 39.96 5.25
7453 9202 2.854777 GCTCGTACAGACTATGTTGCTG 59.145 50.000 0.00 0.00 39.96 4.41
7454 9203 2.478031 CGCTCGTACAGACTATGTTGCT 60.478 50.000 0.00 0.00 39.96 3.91
7593 9345 8.859236 ATCCAACAGGATTACTTGATGATATG 57.141 34.615 0.00 0.00 39.09 1.78
7608 9360 0.394216 CGGCATCCAATCCAACAGGA 60.394 55.000 0.00 0.00 35.50 3.86
7626 9378 0.041663 AAAACGCAACGTCATCACCG 60.042 50.000 0.00 0.00 39.99 4.94
7699 9451 1.215647 GTCGAGATGGTGAACGCCT 59.784 57.895 5.99 0.00 0.00 5.52
7788 9540 1.303074 ACACTCGCCTCGTCCTACA 60.303 57.895 0.00 0.00 0.00 2.74
8001 9755 2.552599 TGAAATGCGAGTGGGTTGTA 57.447 45.000 0.00 0.00 0.00 2.41
8057 9812 2.050350 TCGATTCTTCCGCCTCCGT 61.050 57.895 0.00 0.00 0.00 4.69
8148 9903 1.406970 GCGAGAGTTGTAGCGAGCAC 61.407 60.000 0.00 0.00 0.00 4.40
8206 9963 2.809119 TCTATGAATCTCGAGCGAGGAC 59.191 50.000 18.57 11.09 42.20 3.85
8259 10016 2.125952 TAGACGACTCCGCGACGA 60.126 61.111 8.23 0.00 39.95 4.20
8261 10018 0.576328 CTAGTAGACGACTCCGCGAC 59.424 60.000 8.23 0.00 39.81 5.19
8262 10019 1.150567 GCTAGTAGACGACTCCGCGA 61.151 60.000 8.23 0.00 39.81 5.87
8289 10051 1.827789 GAAACTGCCCAGTGCCACA 60.828 57.895 1.07 0.00 41.58 4.17
8335 10100 0.107214 CCGGACAGGCATAACCACAT 60.107 55.000 0.00 0.00 43.14 3.21
8388 10153 1.065345 TCAAACAAACCGGGAGACACA 60.065 47.619 6.32 0.00 0.00 3.72
8412 10177 3.658757 AACACCAATTCGAACCAATGG 57.341 42.857 15.62 15.62 0.00 3.16


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

AutoCloner maintained by Alex Coulton.