Multiple sequence alignment - TraesCS3A01G211600

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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 TraesCS3A01G211600 chr3A 100.000 4062 0 0 1 4062 380069301 380065240 0.000000e+00 7502.0
1 TraesCS3A01G211600 chr3D 95.831 2207 49 14 813 3011 289185636 289183465 0.000000e+00 3526.0
2 TraesCS3A01G211600 chr3D 92.355 654 37 3 3080 3720 289183387 289182734 0.000000e+00 918.0
3 TraesCS3A01G211600 chr3D 88.356 146 15 2 3918 4062 289181887 289181743 1.500000e-39 174.0
4 TraesCS3A01G211600 chr3D 97.674 43 1 0 3004 3046 289183430 289183388 1.570000e-09 75.0
5 TraesCS3A01G211600 chr3B 95.185 2222 58 17 813 3011 381843657 381841462 0.000000e+00 3465.0
6 TraesCS3A01G211600 chr3B 89.562 1073 60 13 3004 4042 381841427 381840373 0.000000e+00 1314.0
7 TraesCS3A01G211600 chr3B 91.750 703 49 5 123 816 5958913 5958211 0.000000e+00 968.0
8 TraesCS3A01G211600 chr1A 93.179 821 51 3 1 816 339169753 339170573 0.000000e+00 1201.0
9 TraesCS3A01G211600 chr1A 90.909 44 4 0 3733 3776 178660859 178660902 4.380000e-05 60.2
10 TraesCS3A01G211600 chr2B 93.057 821 51 4 1 816 619954229 619953410 0.000000e+00 1195.0
11 TraesCS3A01G211600 chr2B 88.415 328 33 3 3255 3578 304600970 304601296 1.370000e-104 390.0
12 TraesCS3A01G211600 chr1B 92.843 517 30 5 305 816 362333810 362334324 0.000000e+00 743.0
13 TraesCS3A01G211600 chr5B 83.085 402 48 17 3255 3644 459628973 459629366 8.360000e-92 348.0
14 TraesCS3A01G211600 chrUn 80.963 436 60 23 3254 3676 313152379 313152804 1.410000e-84 324.0
15 TraesCS3A01G211600 chr1D 80.963 436 60 23 3254 3676 263793979 263793554 1.410000e-84 324.0
16 TraesCS3A01G211600 chr1D 80.963 436 60 23 3254 3676 263802349 263801924 1.410000e-84 324.0
17 TraesCS3A01G211600 chr7B 80.493 446 61 21 3195 3623 188390439 188390003 6.550000e-83 318.0
18 TraesCS3A01G211600 chr7B 81.609 87 16 0 3010 3096 219044097 219044183 5.630000e-09 73.1
19 TraesCS3A01G211600 chr7B 88.636 44 4 1 3007 3050 350783774 350783732 7.000000e-03 52.8
20 TraesCS3A01G211600 chr6D 80.734 436 61 23 3254 3676 352307961 352308386 6.550000e-83 318.0
21 TraesCS3A01G211600 chr2D 90.043 231 19 2 589 815 328298466 328298236 3.070000e-76 296.0
22 TraesCS3A01G211600 chr4A 79.464 112 21 2 3009 3119 649540330 649540220 1.210000e-10 78.7
23 TraesCS3A01G211600 chr4A 73.262 187 45 5 3007 3191 549130999 549131182 3.390000e-06 63.9
24 TraesCS3A01G211600 chr7D 93.333 45 3 0 3733 3777 213157692 213157736 2.620000e-07 67.6
25 TraesCS3A01G211600 chr7D 90.909 44 3 1 3748 3791 316527264 316527222 1.580000e-04 58.4
26 TraesCS3A01G211600 chr7D 96.875 32 1 0 3897 3928 315567730 315567699 2.000000e-03 54.7
27 TraesCS3A01G211600 chr6B 87.719 57 6 1 3007 3063 493785274 493785329 9.420000e-07 65.8
28 TraesCS3A01G211600 chr5D 94.444 36 1 1 3897 3932 20392869 20392835 2.000000e-03 54.7
29 TraesCS3A01G211600 chr7A 100.000 28 0 0 3743 3770 197900151 197900178 7.000000e-03 52.8


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 TraesCS3A01G211600 chr3A 380065240 380069301 4061 True 7502.00 7502 100.0000 1 4062 1 chr3A.!!$R1 4061
1 TraesCS3A01G211600 chr3D 289181743 289185636 3893 True 1173.25 3526 93.5540 813 4062 4 chr3D.!!$R1 3249
2 TraesCS3A01G211600 chr3B 381840373 381843657 3284 True 2389.50 3465 92.3735 813 4042 2 chr3B.!!$R2 3229
3 TraesCS3A01G211600 chr3B 5958211 5958913 702 True 968.00 968 91.7500 123 816 1 chr3B.!!$R1 693
4 TraesCS3A01G211600 chr1A 339169753 339170573 820 False 1201.00 1201 93.1790 1 816 1 chr1A.!!$F2 815
5 TraesCS3A01G211600 chr2B 619953410 619954229 819 True 1195.00 1195 93.0570 1 816 1 chr2B.!!$R1 815
6 TraesCS3A01G211600 chr1B 362333810 362334324 514 False 743.00 743 92.8430 305 816 1 chr1B.!!$F1 511

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
453 455 0.033504 GTGGCGGATGTGATATCGGT 59.966 55.000 0.00 0.0 0.00 4.69 F
962 972 0.618968 ATCCTTCTCCTCGGTGGCTT 60.619 55.000 0.00 0.0 35.26 4.35 F
1851 1867 0.679505 AGTCGAGGCTTACTGTTGCA 59.320 50.000 2.97 0.0 0.00 4.08 F
2446 2462 1.133253 CATGGTTTCAGACAGCGCG 59.867 57.895 0.00 0.0 0.00 6.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2209 2225 0.726827 CGGATGTTGCTTGTGCGTAT 59.273 50.000 0.00 0.0 43.34 3.06 R
2933 2966 0.770557 ACAACCCAGGAGTAAGGCCA 60.771 55.000 5.01 0.0 0.00 5.36 R
3051 3126 1.002403 TCGCCTCCCTAATGACCCA 59.998 57.895 0.00 0.0 0.00 4.51 R
3638 3725 1.006998 AGTCATGTCCCTCTCTCTGCT 59.993 52.381 0.00 0.0 0.00 4.24 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
93 94 6.882140 TGAAATCTTTCTTTATGAACCGGCTA 59.118 34.615 0.00 0.00 38.02 3.93
188 189 4.640771 AAGGAGGCAAATAGTGAGACAA 57.359 40.909 0.00 0.00 0.00 3.18
204 205 4.202398 TGAGACAAGAAGAGGTTCAATGCT 60.202 41.667 0.00 0.00 34.82 3.79
240 241 1.422531 GTCCATCAGGGCTCTCTCAT 58.577 55.000 0.00 0.00 36.28 2.90
256 257 6.091441 GCTCTCTCATTGAATTTTGTACGAGT 59.909 38.462 0.00 0.00 0.00 4.18
282 283 1.463444 CTAAACCTACAACACTGCCGC 59.537 52.381 0.00 0.00 0.00 6.53
364 365 1.929836 CGTAGAAGAGGACAATGCAGC 59.070 52.381 0.00 0.00 0.00 5.25
453 455 0.033504 GTGGCGGATGTGATATCGGT 59.966 55.000 0.00 0.00 0.00 4.69
496 498 1.615392 GGTCTCAAACTTGCTGGCAAT 59.385 47.619 8.49 0.00 35.20 3.56
553 555 8.757982 ATAATGTGATTATTGTGGAAGCTCTT 57.242 30.769 0.00 0.00 31.64 2.85
554 556 7.472334 AATGTGATTATTGTGGAAGCTCTTT 57.528 32.000 0.00 0.00 0.00 2.52
638 643 4.885325 GTGATTTCGGGAAGGCCTTATTAA 59.115 41.667 20.54 7.95 0.00 1.40
641 646 4.579647 TTCGGGAAGGCCTTATTAAAGT 57.420 40.909 20.54 0.00 0.00 2.66
674 683 6.352222 CCGGGAATCTAATATGGTAGCTCATT 60.352 42.308 0.00 0.00 0.00 2.57
690 699 3.310774 GCTCATTCGCTAGCTCAAAATGA 59.689 43.478 20.68 20.68 35.62 2.57
712 721 2.224426 ACGTGTTGATCCACCAAGCTTA 60.224 45.455 0.00 0.00 31.47 3.09
744 753 5.424252 ACTCACCTCCGGAATTTATTACTGA 59.576 40.000 5.23 0.00 0.00 3.41
769 778 5.945466 TTTTAACGGACAATGTAAGGGTC 57.055 39.130 0.00 0.00 0.00 4.46
787 796 9.673454 GTAAGGGTCGCATAATTTTAATAAAGG 57.327 33.333 0.00 0.00 0.00 3.11
795 804 9.341899 CGCATAATTTTAATAAAGGTAGCCATC 57.658 33.333 0.00 0.00 0.00 3.51
866 875 3.443052 TGATTTGAAAGGGCATGGTCAT 58.557 40.909 0.00 0.00 0.00 3.06
898 907 0.885596 CGCCCACCCGTAGAACAAAA 60.886 55.000 0.00 0.00 0.00 2.44
899 908 1.320507 GCCCACCCGTAGAACAAAAA 58.679 50.000 0.00 0.00 0.00 1.94
900 909 1.268625 GCCCACCCGTAGAACAAAAAG 59.731 52.381 0.00 0.00 0.00 2.27
901 910 2.853705 CCCACCCGTAGAACAAAAAGA 58.146 47.619 0.00 0.00 0.00 2.52
962 972 0.618968 ATCCTTCTCCTCGGTGGCTT 60.619 55.000 0.00 0.00 35.26 4.35
1014 1027 2.897350 GCGATGGCCCGAAAGAGG 60.897 66.667 0.00 0.00 0.00 3.69
1074 1087 0.814457 CGCTCTACTCCAGCTTCTGT 59.186 55.000 0.00 0.00 34.45 3.41
1215 1228 1.325355 TCTCTCTTCGGTCGGTTGTT 58.675 50.000 0.00 0.00 0.00 2.83
1236 1249 4.963276 TTGTAGGAATTTCGATTGGCTG 57.037 40.909 0.00 0.00 0.00 4.85
1448 1462 5.861787 CGTAATTCAATGTTTGTTCCCTTCC 59.138 40.000 0.00 0.00 0.00 3.46
1451 1465 2.621055 TCAATGTTTGTTCCCTTCCGTG 59.379 45.455 0.00 0.00 0.00 4.94
1452 1466 2.358322 ATGTTTGTTCCCTTCCGTGT 57.642 45.000 0.00 0.00 0.00 4.49
1453 1467 2.131776 TGTTTGTTCCCTTCCGTGTT 57.868 45.000 0.00 0.00 0.00 3.32
1454 1468 2.448453 TGTTTGTTCCCTTCCGTGTTT 58.552 42.857 0.00 0.00 0.00 2.83
1455 1469 2.424246 TGTTTGTTCCCTTCCGTGTTTC 59.576 45.455 0.00 0.00 0.00 2.78
1456 1470 2.421751 TTGTTCCCTTCCGTGTTTCA 57.578 45.000 0.00 0.00 0.00 2.69
1457 1471 2.649531 TGTTCCCTTCCGTGTTTCAT 57.350 45.000 0.00 0.00 0.00 2.57
1458 1472 2.938838 TGTTCCCTTCCGTGTTTCATT 58.061 42.857 0.00 0.00 0.00 2.57
1459 1473 4.088056 TGTTCCCTTCCGTGTTTCATTA 57.912 40.909 0.00 0.00 0.00 1.90
1460 1474 4.658063 TGTTCCCTTCCGTGTTTCATTAT 58.342 39.130 0.00 0.00 0.00 1.28
1461 1475 5.806818 TGTTCCCTTCCGTGTTTCATTATA 58.193 37.500 0.00 0.00 0.00 0.98
1462 1476 5.878116 TGTTCCCTTCCGTGTTTCATTATAG 59.122 40.000 0.00 0.00 0.00 1.31
1463 1477 4.448210 TCCCTTCCGTGTTTCATTATAGC 58.552 43.478 0.00 0.00 0.00 2.97
1464 1478 4.163458 TCCCTTCCGTGTTTCATTATAGCT 59.837 41.667 0.00 0.00 0.00 3.32
1465 1479 5.364446 TCCCTTCCGTGTTTCATTATAGCTA 59.636 40.000 0.00 0.00 0.00 3.32
1466 1480 6.053005 CCCTTCCGTGTTTCATTATAGCTAA 58.947 40.000 0.00 0.00 0.00 3.09
1467 1481 6.018180 CCCTTCCGTGTTTCATTATAGCTAAC 60.018 42.308 0.00 0.00 0.00 2.34
1468 1482 6.537301 CCTTCCGTGTTTCATTATAGCTAACA 59.463 38.462 0.00 0.00 0.00 2.41
1469 1483 7.226720 CCTTCCGTGTTTCATTATAGCTAACAT 59.773 37.037 0.00 0.00 32.10 2.71
1470 1484 7.477144 TCCGTGTTTCATTATAGCTAACATG 57.523 36.000 0.00 3.01 36.16 3.21
1530 1544 8.077386 GGTACCAAAGTATGAAATTTTGTTCGA 58.923 33.333 7.15 0.00 31.55 3.71
1629 1643 7.174426 ACAGTTAGTACCCATTTTGTTTCTAGC 59.826 37.037 0.00 0.00 0.00 3.42
1851 1867 0.679505 AGTCGAGGCTTACTGTTGCA 59.320 50.000 2.97 0.00 0.00 4.08
2187 2203 5.123820 CCATGAGTGTGAATCCGTTTACAAT 59.876 40.000 0.00 0.00 35.86 2.71
2299 2315 4.279982 TCTCAAATGCATTATCAAGCCCA 58.720 39.130 13.39 0.00 0.00 5.36
2416 2432 2.753452 CAACTCTGCAAGCTCCAATGAT 59.247 45.455 0.00 0.00 0.00 2.45
2446 2462 1.133253 CATGGTTTCAGACAGCGCG 59.867 57.895 0.00 0.00 0.00 6.86
2473 2489 7.548427 GGAAATGGGTACTACTAAGTCAGTTTC 59.452 40.741 0.00 0.00 38.80 2.78
2507 2523 1.274167 CATGCACAACCAGGAAGCATT 59.726 47.619 0.00 0.00 42.76 3.56
2597 2613 1.732941 TTATAGTTGCACACCTGGCG 58.267 50.000 0.00 0.00 0.00 5.69
2694 2711 7.502226 TGGTTCATGTCTTATATCCCAACAATC 59.498 37.037 0.00 0.00 0.00 2.67
2788 2805 7.885922 TGTGCTTAATACAATGAGAGGGTTAAA 59.114 33.333 0.00 0.00 0.00 1.52
2863 2888 4.280174 GCATTATCAGGATGTGCCATCTTT 59.720 41.667 12.89 2.57 40.02 2.52
2933 2966 3.529734 TGGTAATATTCCACACACCCCAT 59.470 43.478 0.00 0.00 0.00 4.00
3039 3114 1.348775 GGCCAACCAGCTATCCTCCT 61.349 60.000 0.00 0.00 35.26 3.69
3051 3126 3.181456 GCTATCCTCCTCTGCACAGAATT 60.181 47.826 1.42 0.00 36.94 2.17
3096 3171 1.539827 CCATGGTTTTCGACTTGTCCC 59.460 52.381 2.57 0.00 0.00 4.46
3109 3184 1.393487 TTGTCCCGTCCGAGTTGTCA 61.393 55.000 0.00 0.00 0.00 3.58
3124 3199 1.832883 TGTCACGCCAGCCATTTATT 58.167 45.000 0.00 0.00 0.00 1.40
3126 3201 1.472480 GTCACGCCAGCCATTTATTGT 59.528 47.619 0.00 0.00 0.00 2.71
3137 3212 4.931002 AGCCATTTATTGTGAATGTTGTGC 59.069 37.500 0.00 0.00 33.65 4.57
3201 3276 6.677781 TTTGGTTCTTCTTAGTTGTCACAG 57.322 37.500 0.00 0.00 0.00 3.66
3204 3279 3.402628 TCTTCTTAGTTGTCACAGCCC 57.597 47.619 0.00 0.00 0.00 5.19
3286 3372 3.843422 TGAGGGAATTTTCAAGCCTCAA 58.157 40.909 11.88 1.07 38.99 3.02
3334 3420 5.482878 ACCCTGAAAATTGCATTCTCTGAAT 59.517 36.000 0.00 0.00 0.00 2.57
3339 3425 7.617225 TGAAAATTGCATTCTCTGAATCCAAT 58.383 30.769 4.23 4.23 0.00 3.16
3373 3459 9.991388 CATTAATGTTTGATATTTTTGGCAAGG 57.009 29.630 7.32 0.00 0.00 3.61
3385 3471 0.105246 TGGCAAGGGTTTTGGTCCAT 60.105 50.000 0.00 0.00 0.00 3.41
3388 3474 1.548719 GCAAGGGTTTTGGTCCATACC 59.451 52.381 13.08 13.08 46.98 2.73
3600 3686 5.233902 TCTGTTTGAATTCAAAACAATGGCG 59.766 36.000 30.07 18.04 46.08 5.69
3609 3695 6.917217 TTCAAAACAATGGCGAAAGAATTT 57.083 29.167 0.00 0.00 43.98 1.82
3665 3752 3.100671 GAGAGGGACATGACTTACCTGT 58.899 50.000 0.00 0.00 0.00 4.00
3680 3767 1.705186 ACCTGTCACAGCCCACTTAAT 59.295 47.619 0.00 0.00 0.00 1.40
3709 3797 1.923909 ACCAGGGGTAGCCTTGTCC 60.924 63.158 20.32 0.00 32.11 4.02
3722 4199 0.682855 CTTGTCCTCCTCCTCTCGCT 60.683 60.000 0.00 0.00 0.00 4.93
3739 4230 1.457009 GCTAGTAGGGAGGGTGCTCG 61.457 65.000 0.00 0.00 0.00 5.03
3855 4353 0.460987 CCTCGCTCCCTCACATGTTC 60.461 60.000 0.00 0.00 0.00 3.18
3899 4397 2.356673 GACACCGTCGTGAACCCC 60.357 66.667 0.00 0.00 43.14 4.95
3939 4676 2.765969 CCAGCCCACCTGTCCATT 59.234 61.111 0.00 0.00 40.06 3.16
3947 4684 1.542375 ACCTGTCCATTGGCCCTCT 60.542 57.895 0.00 0.00 0.00 3.69
3986 4723 1.585006 GTCGAAGAACCCGAGCTCA 59.415 57.895 15.40 0.00 39.69 4.26
3992 4729 4.421479 AACCCGAGCTCAGACGCG 62.421 66.667 15.40 3.53 34.40 6.01
4020 4757 0.687757 ATGGCCTCGAGCTCACCTTA 60.688 55.000 15.40 0.00 43.05 2.69
4050 4788 2.750637 ACGGACCTCGCTGTCGAT 60.751 61.111 0.00 0.00 44.56 3.59
4053 4791 1.511305 GGACCTCGCTGTCGATTCA 59.489 57.895 0.00 0.00 44.56 2.57
4055 4793 0.802607 GACCTCGCTGTCGATTCACC 60.803 60.000 0.00 0.00 44.56 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.202493 TGCTATTATGTCATGCAGTCCCAT 60.202 41.667 0.00 0.00 0.00 4.00
39 40 1.335132 GCACCCGATCTCCCCTGTTA 61.335 60.000 0.00 0.00 0.00 2.41
82 83 0.108329 CGTCTGGTTAGCCGGTTCAT 60.108 55.000 1.90 0.00 41.89 2.57
93 94 4.973168 ACATCCATATATTGCGTCTGGTT 58.027 39.130 0.00 0.00 0.00 3.67
152 153 4.263462 TGCCTCCTTTGCCACCATATATAG 60.263 45.833 0.00 0.00 0.00 1.31
188 189 1.625818 ACCGAGCATTGAACCTCTTCT 59.374 47.619 0.00 0.00 0.00 2.85
204 205 1.229082 ACTGGCAGGACCTAACCGA 60.229 57.895 20.34 0.00 40.22 4.69
240 241 5.885881 AGTTGCAACTCGTACAAAATTCAA 58.114 33.333 26.36 0.00 32.86 2.69
256 257 4.201970 GCAGTGTTGTAGGTTTAGTTGCAA 60.202 41.667 0.00 0.00 0.00 4.08
282 283 1.470098 CTTCCTCCATTTGTTCAGCCG 59.530 52.381 0.00 0.00 0.00 5.52
420 422 2.016318 CCGCCACATGCTCTAATTTGA 58.984 47.619 0.00 0.00 38.05 2.69
496 498 9.527157 TGTATCAAAATAGAGTTCAATCCCAAA 57.473 29.630 0.00 0.00 0.00 3.28
538 540 5.772393 TTCCCTAAAGAGCTTCCACAATA 57.228 39.130 0.00 0.00 0.00 1.90
553 555 3.583228 TGAGTGTCCTGAGTTTCCCTAA 58.417 45.455 0.00 0.00 0.00 2.69
554 556 3.254093 TGAGTGTCCTGAGTTTCCCTA 57.746 47.619 0.00 0.00 0.00 3.53
638 643 9.720769 CATATTAGATTCCCGGTTACAATACTT 57.279 33.333 0.00 0.00 0.00 2.24
641 646 8.209802 ACCATATTAGATTCCCGGTTACAATA 57.790 34.615 0.00 0.00 0.00 1.90
674 683 2.411748 CACGTTCATTTTGAGCTAGCGA 59.588 45.455 9.55 0.00 0.00 4.93
690 699 0.951558 GCTTGGTGGATCAACACGTT 59.048 50.000 1.86 0.00 42.23 3.99
712 721 1.983224 CGGAGGTGAGTCCAACCAT 59.017 57.895 2.71 0.00 36.23 3.55
752 761 0.390735 GCGACCCTTACATTGTCCGT 60.391 55.000 0.00 0.00 0.00 4.69
766 775 7.806487 GGCTACCTTTATTAAAATTATGCGACC 59.194 37.037 0.00 0.00 0.00 4.79
769 778 9.341899 GATGGCTACCTTTATTAAAATTATGCG 57.658 33.333 0.00 0.00 0.00 4.73
962 972 0.032813 AGATCCCCTTACGAACCGGA 60.033 55.000 9.46 0.00 0.00 5.14
1168 1181 0.033894 AGGACGGAGAGAGAAGGGTC 60.034 60.000 0.00 0.00 0.00 4.46
1215 1228 3.128589 GCAGCCAATCGAAATTCCTACAA 59.871 43.478 0.00 0.00 0.00 2.41
1236 1249 1.621107 TAGCTGTAAACTACACGCGC 58.379 50.000 5.73 0.00 37.66 6.86
1311 1325 2.662866 AGGATGGCCAAATCTGATGTG 58.337 47.619 10.96 0.56 36.29 3.21
1448 1462 7.224753 AGTCCATGTTAGCTATAATGAAACACG 59.775 37.037 14.69 1.10 33.27 4.49
1451 1465 8.893727 ACAAGTCCATGTTAGCTATAATGAAAC 58.106 33.333 14.69 12.30 0.00 2.78
1452 1466 8.892723 CACAAGTCCATGTTAGCTATAATGAAA 58.107 33.333 14.69 3.66 0.00 2.69
1453 1467 8.046708 ACACAAGTCCATGTTAGCTATAATGAA 58.953 33.333 14.69 0.00 0.00 2.57
1454 1468 7.564793 ACACAAGTCCATGTTAGCTATAATGA 58.435 34.615 14.69 0.00 0.00 2.57
1455 1469 7.792374 ACACAAGTCCATGTTAGCTATAATG 57.208 36.000 0.00 1.72 0.00 1.90
1456 1470 7.201732 GCAACACAAGTCCATGTTAGCTATAAT 60.202 37.037 0.00 0.00 36.92 1.28
1457 1471 6.093495 GCAACACAAGTCCATGTTAGCTATAA 59.907 38.462 0.00 0.00 36.92 0.98
1458 1472 5.584649 GCAACACAAGTCCATGTTAGCTATA 59.415 40.000 0.00 0.00 36.92 1.31
1459 1473 4.396166 GCAACACAAGTCCATGTTAGCTAT 59.604 41.667 0.00 0.00 36.92 2.97
1460 1474 3.751175 GCAACACAAGTCCATGTTAGCTA 59.249 43.478 0.00 0.00 36.92 3.32
1461 1475 2.554032 GCAACACAAGTCCATGTTAGCT 59.446 45.455 0.00 0.00 36.92 3.32
1462 1476 2.293122 TGCAACACAAGTCCATGTTAGC 59.707 45.455 0.00 0.00 36.92 3.09
1463 1477 3.565482 ACTGCAACACAAGTCCATGTTAG 59.435 43.478 0.00 0.00 36.92 2.34
1464 1478 3.550820 ACTGCAACACAAGTCCATGTTA 58.449 40.909 0.00 0.00 36.92 2.41
1465 1479 2.358898 GACTGCAACACAAGTCCATGTT 59.641 45.455 0.00 0.00 39.63 2.71
1466 1480 1.949525 GACTGCAACACAAGTCCATGT 59.050 47.619 0.00 0.00 0.00 3.21
1467 1481 2.224606 AGACTGCAACACAAGTCCATG 58.775 47.619 0.00 0.00 30.94 3.66
1468 1482 2.645838 AGACTGCAACACAAGTCCAT 57.354 45.000 0.00 0.00 30.94 3.41
1469 1483 2.418368 AAGACTGCAACACAAGTCCA 57.582 45.000 0.00 0.00 30.94 4.02
1470 1484 3.782889 AAAAGACTGCAACACAAGTCC 57.217 42.857 0.00 0.00 30.94 3.85
1530 1544 5.694995 TCTGTTTCTCTTGAAAATCCAGGT 58.305 37.500 0.00 0.00 42.94 4.00
1701 1717 5.731591 CGAAAGTACATTTTCTCCCCTACT 58.268 41.667 0.00 0.00 35.42 2.57
1820 1836 0.749049 CCTCGACTCCTCATCATGCA 59.251 55.000 0.00 0.00 0.00 3.96
1866 1882 5.535406 GGAGTTCTAAGATCGAACCTGGATA 59.465 44.000 0.00 0.00 41.19 2.59
1946 1962 7.796958 TGATTCATATATCGTGATGTTCGAC 57.203 36.000 0.00 0.00 40.07 4.20
1947 1963 8.243426 TCATGATTCATATATCGTGATGTTCGA 58.757 33.333 6.36 0.00 42.64 3.71
1978 1994 8.773404 AAAAAGACATACACCTATACACTGAC 57.227 34.615 0.00 0.00 0.00 3.51
2030 2046 9.784531 ATACATATGAGAACTATTGAACCCAAG 57.215 33.333 10.38 0.00 35.48 3.61
2209 2225 0.726827 CGGATGTTGCTTGTGCGTAT 59.273 50.000 0.00 0.00 43.34 3.06
2299 2315 1.680651 CTGGAGACTCCTGCGGACT 60.681 63.158 22.14 0.00 39.21 3.85
2311 2327 3.698040 GGGTTAAGTGATACGTCTGGAGA 59.302 47.826 0.00 0.00 0.00 3.71
2446 2462 5.424573 ACTGACTTAGTAGTACCCATTTCCC 59.575 44.000 0.00 0.00 38.04 3.97
2473 2489 2.063266 GTGCATGCAACATGTTTCCAG 58.937 47.619 24.58 0.00 0.00 3.86
2507 2523 3.942829 CCAGAGAAAATACTGGCACTCA 58.057 45.455 0.00 0.00 45.30 3.41
2555 2571 1.338973 CCACACAGTGCATGAGCTTTT 59.661 47.619 0.00 0.00 42.74 2.27
2556 2572 0.956633 CCACACAGTGCATGAGCTTT 59.043 50.000 0.00 0.00 42.74 3.51
2626 2643 4.114794 CTCCAAACAGGCTTGAACAAAAG 58.885 43.478 1.40 0.00 37.29 2.27
2760 2777 7.136822 ACCCTCTCATTGTATTAAGCACATA 57.863 36.000 0.00 0.00 0.00 2.29
2762 2779 5.435686 ACCCTCTCATTGTATTAAGCACA 57.564 39.130 0.00 0.00 0.00 4.57
2788 2805 6.939730 TGTTACCATTGCCGATACATCATAAT 59.060 34.615 0.00 0.00 0.00 1.28
2832 2857 4.996758 CACATCCTGATAATGCGATAACCA 59.003 41.667 0.00 0.00 0.00 3.67
2863 2888 5.477984 AGCATAACAGAGCCAAAAGAATTCA 59.522 36.000 8.44 0.00 0.00 2.57
2927 2960 1.084842 AGGAGTAAGGCCATGGGGT 59.915 57.895 15.13 0.00 36.17 4.95
2933 2966 0.770557 ACAACCCAGGAGTAAGGCCA 60.771 55.000 5.01 0.00 0.00 5.36
2991 3024 2.863704 GCAACCACAAGCCTGCTAAAAG 60.864 50.000 0.00 0.00 0.00 2.27
3039 3114 2.885135 ATGACCCAATTCTGTGCAGA 57.115 45.000 0.00 0.00 35.27 4.26
3051 3126 1.002403 TCGCCTCCCTAATGACCCA 59.998 57.895 0.00 0.00 0.00 4.51
3096 3171 3.103911 GGCGTGACAACTCGGACG 61.104 66.667 0.00 0.00 34.28 4.79
3109 3184 1.832883 TCACAATAAATGGCTGGCGT 58.167 45.000 0.00 0.00 0.00 5.68
3124 3199 1.876799 CCTTACGGCACAACATTCACA 59.123 47.619 0.00 0.00 0.00 3.58
3334 3420 8.303780 TCAAACATTAATGAAGGCATATTGGA 57.696 30.769 22.16 3.61 33.44 3.53
3616 3703 9.136952 CTGCTTTTCTATGAATTTCCTTTTCTG 57.863 33.333 0.00 0.00 0.00 3.02
3623 3710 7.012232 CCTCTCTCTGCTTTTCTATGAATTTCC 59.988 40.741 0.00 0.00 0.00 3.13
3624 3711 7.012232 CCCTCTCTCTGCTTTTCTATGAATTTC 59.988 40.741 0.00 0.00 0.00 2.17
3625 3712 6.827762 CCCTCTCTCTGCTTTTCTATGAATTT 59.172 38.462 0.00 0.00 0.00 1.82
3630 3717 4.161189 TGTCCCTCTCTCTGCTTTTCTATG 59.839 45.833 0.00 0.00 0.00 2.23
3638 3725 1.006998 AGTCATGTCCCTCTCTCTGCT 59.993 52.381 0.00 0.00 0.00 4.24
3709 3797 1.271163 CCCTACTAGCGAGAGGAGGAG 60.271 61.905 15.23 3.82 31.45 3.69
3722 4199 1.455217 GCGAGCACCCTCCCTACTA 60.455 63.158 0.00 0.00 34.49 1.82
3781 4272 1.585267 TTAACCCGCTCGTCACGCTA 61.585 55.000 0.00 0.00 0.00 4.26
3848 4346 3.133464 CCATGGCGGCGAACATGT 61.133 61.111 29.65 0.00 42.15 3.21
3885 4383 4.289245 CACGGGGTTCACGACGGT 62.289 66.667 0.00 0.00 34.93 4.83
3929 4666 1.542375 AGAGGGCCAATGGACAGGT 60.542 57.895 7.73 0.00 27.52 4.00
3931 4668 1.751927 GCAGAGGGCCAATGGACAG 60.752 63.158 7.73 0.00 36.11 3.51
3939 4676 3.414193 CAGGGATGCAGAGGGCCA 61.414 66.667 6.18 0.00 43.89 5.36
4043 4781 3.330766 GAGTCCGGTGAATCGACAG 57.669 57.895 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.