Multiple sequence alignment - TraesCS4B01G361900

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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 TraesCS4B01G361900 chr4B 100.000 3499 0 0 543 4041 650960314 650963812 0.000000e+00 6462
1 TraesCS4B01G361900 chr4B 100.000 265 0 0 1 265 650959772 650960036 1.310000e-134 490
2 TraesCS4B01G361900 chr4B 80.000 270 44 9 2758 3021 602448976 602448711 1.480000e-44 191
3 TraesCS4B01G361900 chr5A 92.834 3084 133 43 549 3592 688973154 688976189 0.000000e+00 4390
4 TraesCS4B01G361900 chr5A 93.182 264 12 3 1 261 688972840 688973100 2.280000e-102 383
5 TraesCS4B01G361900 chr5A 88.274 307 24 5 3592 3887 688976291 688976596 1.380000e-94 357
6 TraesCS4B01G361900 chr4D 94.951 1624 50 16 564 2175 504328420 504330023 0.000000e+00 2516
7 TraesCS4B01G361900 chr4D 90.567 1781 79 39 2291 4041 504330066 504331787 0.000000e+00 2276
8 TraesCS4B01G361900 chr4D 95.074 203 10 0 1 203 504327697 504327899 1.810000e-83 320
9 TraesCS4B01G361900 chr4D 79.216 255 47 5 2770 3021 477507107 477506856 5.370000e-39 172
10 TraesCS4B01G361900 chr1B 82.927 1189 170 22 1000 2158 398005998 398007183 0.000000e+00 1040
11 TraesCS4B01G361900 chr1B 88.258 264 31 0 2768 3031 398007499 398007762 2.340000e-82 316
12 TraesCS4B01G361900 chr1D 82.605 1190 172 25 1000 2158 296489213 296490398 0.000000e+00 1018
13 TraesCS4B01G361900 chr1D 89.773 264 27 0 2768 3031 296490704 296490967 5.000000e-89 339
14 TraesCS4B01G361900 chr1A 82.008 1195 170 34 1000 2158 369322660 369323845 0.000000e+00 974
15 TraesCS4B01G361900 chr1A 82.072 502 86 2 1020 1519 243162851 243162352 3.730000e-115 425
16 TraesCS4B01G361900 chr1A 89.272 261 28 0 2768 3028 369324164 369324424 1.080000e-85 327
17 TraesCS4B01G361900 chr6D 80.656 579 106 5 1046 1621 463549388 463548813 1.030000e-120 444
18 TraesCS4B01G361900 chr6B 80.034 596 111 7 1021 1612 706910969 706911560 6.200000e-118 435
19 TraesCS4B01G361900 chr6A 79.630 594 115 5 1022 1612 610203852 610204442 4.830000e-114 422
20 TraesCS4B01G361900 chr6A 80.142 282 49 7 2756 3032 610205963 610206242 1.900000e-48 204
21 TraesCS4B01G361900 chr4A 79.051 253 51 2 2770 3021 684269728 684269477 5.370000e-39 172


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 TraesCS4B01G361900 chr4B 650959772 650963812 4040 False 3476.0 6462 100.000000 1 4041 2 chr4B.!!$F1 4040
1 TraesCS4B01G361900 chr5A 688972840 688976596 3756 False 1710.0 4390 91.430000 1 3887 3 chr5A.!!$F1 3886
2 TraesCS4B01G361900 chr4D 504327697 504331787 4090 False 1704.0 2516 93.530667 1 4041 3 chr4D.!!$F1 4040
3 TraesCS4B01G361900 chr1B 398005998 398007762 1764 False 678.0 1040 85.592500 1000 3031 2 chr1B.!!$F1 2031
4 TraesCS4B01G361900 chr1D 296489213 296490967 1754 False 678.5 1018 86.189000 1000 3031 2 chr1D.!!$F1 2031
5 TraesCS4B01G361900 chr1A 369322660 369324424 1764 False 650.5 974 85.640000 1000 3028 2 chr1A.!!$F1 2028
6 TraesCS4B01G361900 chr6D 463548813 463549388 575 True 444.0 444 80.656000 1046 1621 1 chr6D.!!$R1 575
7 TraesCS4B01G361900 chr6B 706910969 706911560 591 False 435.0 435 80.034000 1021 1612 1 chr6B.!!$F1 591
8 TraesCS4B01G361900 chr6A 610203852 610206242 2390 False 313.0 422 79.886000 1022 3032 2 chr6A.!!$F1 2010

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
963 1136 0.107831 GTGTCACTAACCAGCCACCA 59.892 55.0 0.0 0.0 0.0 4.17 F
965 1138 0.605589 GTCACTAACCAGCCACCACC 60.606 60.0 0.0 0.0 0.0 4.61 F
966 1139 0.766674 TCACTAACCAGCCACCACCT 60.767 55.0 0.0 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2731 3937 0.743345 GACCATCACTTACACCGCCC 60.743 60.000 0.0 0.0 0.00 6.13 R
2746 3952 4.500545 GCACATACCAAAAACACATGACCA 60.501 41.667 0.0 0.0 0.00 4.02 R
3078 4284 0.666913 ATAGTTGGATCGTCGGTCGG 59.333 55.000 0.0 0.0 40.32 4.79 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
28 29 3.120511 GCGTTTTCTGAATGAGTGACCTC 60.121 47.826 0.00 0.00 38.27 3.85
34 35 4.461198 TCTGAATGAGTGACCTCGCTATA 58.539 43.478 0.00 0.00 40.85 1.31
52 53 4.858692 GCTATAAACAACTGCACACAATGG 59.141 41.667 0.00 0.00 0.00 3.16
54 55 1.774110 AACAACTGCACACAATGGGA 58.226 45.000 0.00 0.00 0.00 4.37
62 63 2.004017 GCACACAATGGGAATGCATTG 58.996 47.619 18.59 5.18 42.62 2.82
108 109 0.613260 TGATGCTTTAGTGGGTCGCT 59.387 50.000 0.00 0.00 0.00 4.93
253 257 5.300792 ACCACATCGACAACAAATAGGTTTT 59.699 36.000 0.00 0.00 0.00 2.43
254 258 5.856455 CCACATCGACAACAAATAGGTTTTC 59.144 40.000 0.00 0.00 0.00 2.29
255 259 5.563751 CACATCGACAACAAATAGGTTTTCG 59.436 40.000 7.94 7.94 46.63 3.46
258 262 4.449743 TCGACAACAAATAGGTTTTCGGAG 59.550 41.667 12.71 0.00 45.80 4.63
259 263 4.449743 CGACAACAAATAGGTTTTCGGAGA 59.550 41.667 6.69 0.00 43.48 3.71
260 264 5.049954 CGACAACAAATAGGTTTTCGGAGAA 60.050 40.000 6.69 0.00 43.48 2.87
261 265 6.512091 CGACAACAAATAGGTTTTCGGAGAAA 60.512 38.462 6.69 0.00 43.48 2.52
262 266 6.735130 ACAACAAATAGGTTTTCGGAGAAAG 58.265 36.000 0.00 0.00 45.90 2.62
264 268 7.499895 ACAACAAATAGGTTTTCGGAGAAAGTA 59.500 33.333 0.00 0.00 45.90 2.24
562 726 1.347221 GCGCCGTACATAGTGTTGC 59.653 57.895 0.00 0.00 0.00 4.17
573 737 1.246649 TAGTGTTGCCCAAGTGCATG 58.753 50.000 0.00 0.00 41.70 4.06
747 916 7.942341 AGTTTACATTACCCTTTTGATCTCACA 59.058 33.333 0.00 0.00 0.00 3.58
866 1038 0.900421 GCCCTACATATACCCCCGAC 59.100 60.000 0.00 0.00 0.00 4.79
873 1045 0.829182 ATATACCCCCGACCCACGAC 60.829 60.000 0.00 0.00 45.77 4.34
886 1058 3.063084 ACGACCGTCCTCCTCAGC 61.063 66.667 0.00 0.00 0.00 4.26
921 1094 3.293714 CCACACCGGTGCATGCAA 61.294 61.111 34.26 3.50 43.88 4.08
922 1095 2.050168 CACACCGGTGCATGCAAC 60.050 61.111 34.26 26.17 38.37 4.17
924 1097 4.054825 CACCGGTGCATGCAACCC 62.055 66.667 29.32 22.06 0.00 4.11
925 1098 4.594854 ACCGGTGCATGCAACCCA 62.595 61.111 29.32 0.00 0.00 4.51
926 1099 3.069946 CCGGTGCATGCAACCCAT 61.070 61.111 29.32 0.00 33.39 4.00
957 1130 3.697045 AGCTAGCTAGTGTCACTAACCAG 59.303 47.826 17.69 8.93 29.00 4.00
958 1131 3.735514 GCTAGCTAGTGTCACTAACCAGC 60.736 52.174 21.62 15.09 29.00 4.85
961 1134 2.931320 GCTAGTGTCACTAACCAGCCAC 60.931 54.545 13.63 0.00 29.00 5.01
962 1135 0.396811 AGTGTCACTAACCAGCCACC 59.603 55.000 2.87 0.00 0.00 4.61
963 1136 0.107831 GTGTCACTAACCAGCCACCA 59.892 55.000 0.00 0.00 0.00 4.17
965 1138 0.605589 GTCACTAACCAGCCACCACC 60.606 60.000 0.00 0.00 0.00 4.61
966 1139 0.766674 TCACTAACCAGCCACCACCT 60.767 55.000 0.00 0.00 0.00 4.00
969 1142 1.628846 ACTAACCAGCCACCACCTTAG 59.371 52.381 0.00 0.00 0.00 2.18
970 1143 1.906574 CTAACCAGCCACCACCTTAGA 59.093 52.381 0.00 0.00 0.00 2.10
975 1148 0.838122 AGCCACCACCTTAGACAGCT 60.838 55.000 0.00 0.00 0.00 4.24
977 1150 1.134670 GCCACCACCTTAGACAGCTAG 60.135 57.143 0.00 0.00 0.00 3.42
980 1153 3.024547 CACCACCTTAGACAGCTAGCTA 58.975 50.000 18.86 0.00 0.00 3.32
981 1154 3.025262 ACCACCTTAGACAGCTAGCTAC 58.975 50.000 18.86 14.49 0.00 3.58
984 1157 3.025262 ACCTTAGACAGCTAGCTACACC 58.975 50.000 18.86 6.82 0.00 4.16
985 1158 2.033550 CCTTAGACAGCTAGCTACACCG 59.966 54.545 18.86 7.23 0.00 4.94
987 1160 1.227002 GACAGCTAGCTACACCGGC 60.227 63.158 18.86 2.41 0.00 6.13
988 1161 2.278857 CAGCTAGCTACACCGGCG 60.279 66.667 18.86 0.00 34.52 6.46
989 1162 3.528370 AGCTAGCTACACCGGCGG 61.528 66.667 27.06 27.06 34.52 6.13
1464 1656 3.958147 CTCCAGCGCCAACATCGGT 62.958 63.158 2.29 0.00 38.25 4.69
1527 1719 1.396301 GCCTTCAACAGCAAGATCTCG 59.604 52.381 0.00 0.00 0.00 4.04
1530 1722 3.499918 CCTTCAACAGCAAGATCTCGTTT 59.500 43.478 0.00 0.00 0.00 3.60
1533 1725 2.807967 CAACAGCAAGATCTCGTTTCCA 59.192 45.455 0.00 0.00 0.00 3.53
1539 1731 4.580580 AGCAAGATCTCGTTTCCAAAGTTT 59.419 37.500 0.00 0.00 0.00 2.66
1542 1734 6.291796 GCAAGATCTCGTTTCCAAAGTTTTTG 60.292 38.462 0.00 0.00 0.00 2.44
1866 2228 3.323758 GACGCTGGGCATGGTGGTA 62.324 63.158 0.00 0.00 0.00 3.25
1911 2273 4.386951 TGGACGGCCATCACCACG 62.387 66.667 5.41 0.00 39.92 4.94
2165 3082 5.750067 CCAACGTACCAACAGGTATACATAC 59.250 44.000 5.01 0.00 39.92 2.39
2206 3375 7.064371 TGCATGGATTTTGTACAACAAATATGC 59.936 33.333 24.74 24.74 46.17 3.14
2286 3455 3.000041 TGGCTAGCTAATTTGTCACACG 59.000 45.455 15.72 0.00 0.00 4.49
2315 3484 3.006940 GTGACACTGTGACAGGACAAAA 58.993 45.455 17.92 0.00 35.51 2.44
2371 3542 9.942850 AAAAGAGTTATGGAAAATACCAATTGG 57.057 29.630 23.31 23.31 43.47 3.16
2372 3543 8.893563 AAGAGTTATGGAAAATACCAATTGGA 57.106 30.769 31.22 14.67 43.47 3.53
2373 3544 8.893563 AGAGTTATGGAAAATACCAATTGGAA 57.106 30.769 31.22 7.63 43.47 3.53
2375 3546 8.664669 AGTTATGGAAAATACCAATTGGAACT 57.335 30.769 31.22 20.37 43.47 3.01
2376 3547 8.531146 AGTTATGGAAAATACCAATTGGAACTG 58.469 33.333 31.22 4.18 43.47 3.16
2377 3548 5.146010 TGGAAAATACCAATTGGAACTGC 57.854 39.130 31.22 14.63 36.96 4.40
2378 3549 4.590647 TGGAAAATACCAATTGGAACTGCA 59.409 37.500 31.22 16.81 36.96 4.41
2456 3643 4.593597 GCATGATGCATGGTTTTTCTTG 57.406 40.909 13.36 0.00 44.26 3.02
2457 3644 3.181514 GCATGATGCATGGTTTTTCTTGC 60.182 43.478 13.36 5.09 44.26 4.01
2475 3662 1.611006 TGCCGAATACAGCAAGCAAAA 59.389 42.857 0.00 0.00 35.69 2.44
2479 3666 4.152223 GCCGAATACAGCAAGCAAAATTTT 59.848 37.500 0.00 0.00 0.00 1.82
2496 3683 7.371936 CAAAATTTTAAGTATGGAACGGACCA 58.628 34.615 2.44 5.38 44.41 4.02
2589 3778 1.702401 TGATAAGTGACCAGTGGCCAA 59.298 47.619 7.24 0.00 0.00 4.52
2604 3793 1.901833 GGCCAACATCAAAAGACCCAT 59.098 47.619 0.00 0.00 0.00 4.00
2731 3937 1.610379 CCCCCTCCCCAAAAGCTTG 60.610 63.158 0.00 0.00 0.00 4.01
2746 3952 0.676782 GCTTGGGCGGTGTAAGTGAT 60.677 55.000 0.00 0.00 0.00 3.06
3142 4348 7.921041 ATATATACCAGCAGCCTGTACATAT 57.079 36.000 0.00 0.00 37.38 1.78
3209 4415 2.224719 ACGTATAGGTCATAGCCTCCGT 60.225 50.000 0.00 0.00 39.94 4.69
3337 4543 5.743872 GTGCTAATTATTTAAGCAGTGCACC 59.256 40.000 19.20 0.00 40.47 5.01
3357 4563 2.337583 CGTGGACTGTACTGGTGATTG 58.662 52.381 4.66 0.00 0.00 2.67
3369 4575 2.617308 CTGGTGATTGATCTGCATGGAC 59.383 50.000 0.00 0.00 0.00 4.02
3440 4646 2.797074 CAACACATGTGGTTGCATGA 57.203 45.000 28.64 0.00 46.65 3.07
3441 4647 3.306917 CAACACATGTGGTTGCATGAT 57.693 42.857 28.64 2.30 46.65 2.45
3442 4648 2.990514 CAACACATGTGGTTGCATGATG 59.009 45.455 28.64 5.00 46.65 3.07
3443 4649 1.067425 ACACATGTGGTTGCATGATGC 60.067 47.619 28.64 11.12 46.65 3.91
3444 4650 3.661811 ACACATGTGGTTGCATGATGCA 61.662 45.455 28.64 17.32 46.65 3.96
3445 4651 4.938483 ACACATGTGGTTGCATGATGCAT 61.938 43.478 28.64 0.00 46.65 3.96
3446 4652 6.367999 ACACATGTGGTTGCATGATGCATT 62.368 41.667 28.64 0.00 46.65 3.56
3447 4653 7.073097 ACACATGTGGTTGCATGATGCATTA 62.073 40.000 28.64 4.03 46.65 1.90
3572 4784 3.777522 CTCCTGTTGGTTCCTCTCCTAAT 59.222 47.826 0.00 0.00 34.23 1.73
3573 4785 4.175962 TCCTGTTGGTTCCTCTCCTAATT 58.824 43.478 0.00 0.00 34.23 1.40
3574 4786 5.347124 TCCTGTTGGTTCCTCTCCTAATTA 58.653 41.667 0.00 0.00 34.23 1.40
3794 5117 9.113838 AGTTTTGTAGTATAAGAGGCAATCATG 57.886 33.333 0.00 0.00 0.00 3.07
3809 5132 4.516698 GCAATCATGGTATCTAACACCTGG 59.483 45.833 0.00 0.00 36.96 4.45
3829 5158 7.396339 CACCTGGTCTACTGGCATAGTATAATA 59.604 40.741 0.00 0.00 40.94 0.98
3954 5286 8.483307 ACAAAAGCAATTATTTAGCATCAAGG 57.517 30.769 0.00 0.00 0.00 3.61
3957 5289 8.707938 AAAGCAATTATTTAGCATCAAGGTTC 57.292 30.769 0.00 0.00 0.00 3.62
3960 5292 8.534496 AGCAATTATTTAGCATCAAGGTTCTTT 58.466 29.630 0.00 0.00 0.00 2.52
3971 5306 7.669722 AGCATCAAGGTTCTTTTTATTCCAGTA 59.330 33.333 0.00 0.00 0.00 2.74
4004 5339 0.693049 ACACAGAGGGGTGGTGAATC 59.307 55.000 0.00 0.00 43.08 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 3.804518 TGTGTGCAGTTGTTTATAGCG 57.195 42.857 0.00 0.00 0.00 4.26
34 35 2.106566 TCCCATTGTGTGCAGTTGTTT 58.893 42.857 0.00 0.00 0.00 2.83
52 53 2.023673 TCGAACATCCCAATGCATTCC 58.976 47.619 9.53 0.00 36.26 3.01
54 55 3.289836 TCATCGAACATCCCAATGCATT 58.710 40.909 5.99 5.99 36.26 3.56
62 63 3.743396 GCTCATTACTCATCGAACATCCC 59.257 47.826 0.00 0.00 0.00 3.85
542 546 1.286501 CAACACTATGTACGGCGCAT 58.713 50.000 10.83 5.97 0.00 4.73
543 547 1.355796 GCAACACTATGTACGGCGCA 61.356 55.000 10.83 0.00 0.00 6.09
544 548 1.347221 GCAACACTATGTACGGCGC 59.653 57.895 6.90 0.00 0.00 6.53
545 549 1.426041 GGGCAACACTATGTACGGCG 61.426 60.000 4.80 4.80 39.74 6.46
546 550 0.391927 TGGGCAACACTATGTACGGC 60.392 55.000 0.00 0.00 39.74 5.68
547 551 2.006888 CTTGGGCAACACTATGTACGG 58.993 52.381 0.00 0.00 39.74 4.02
562 726 2.482316 CCAATGTATGCATGCACTTGGG 60.482 50.000 29.64 21.36 35.15 4.12
573 737 3.625764 ACGTATCACCAACCAATGTATGC 59.374 43.478 0.00 0.00 0.00 3.14
638 807 6.837568 CCCAAAACTATCTACCACTCCTACTA 59.162 42.308 0.00 0.00 0.00 1.82
641 810 4.407945 GCCCAAAACTATCTACCACTCCTA 59.592 45.833 0.00 0.00 0.00 2.94
644 813 3.054655 TGGCCCAAAACTATCTACCACTC 60.055 47.826 0.00 0.00 0.00 3.51
648 817 8.879427 ATATTATTGGCCCAAAACTATCTACC 57.121 34.615 0.00 0.00 0.00 3.18
649 818 8.957466 GGATATTATTGGCCCAAAACTATCTAC 58.043 37.037 0.00 0.00 0.00 2.59
650 819 8.113462 GGGATATTATTGGCCCAAAACTATCTA 58.887 37.037 0.00 0.00 40.39 1.98
678 847 1.089481 CGCCCAATGTACGTCTGCAT 61.089 55.000 0.00 0.00 0.00 3.96
747 916 2.279173 AGGGGCTAAGAGTCAAATGGT 58.721 47.619 0.00 0.00 0.00 3.55
812 981 1.566298 GGTCATGGAGGGTTGGAGCT 61.566 60.000 0.00 0.00 0.00 4.09
813 982 1.077429 GGTCATGGAGGGTTGGAGC 60.077 63.158 0.00 0.00 0.00 4.70
814 983 0.543749 GAGGTCATGGAGGGTTGGAG 59.456 60.000 0.00 0.00 0.00 3.86
815 984 0.178876 TGAGGTCATGGAGGGTTGGA 60.179 55.000 0.00 0.00 0.00 3.53
866 1038 3.450115 GAGGAGGACGGTCGTGGG 61.450 72.222 8.23 0.00 0.00 4.61
873 1045 1.374758 GTTGTGCTGAGGAGGACGG 60.375 63.158 0.00 0.00 43.32 4.79
886 1058 4.601794 TGGCTGGGCTGGGTTGTG 62.602 66.667 0.00 0.00 0.00 3.33
921 1094 0.540830 CTAGCTAGGCCTCGATGGGT 60.541 60.000 9.68 3.99 36.00 4.51
922 1095 1.882989 GCTAGCTAGGCCTCGATGGG 61.883 65.000 22.10 0.17 36.00 4.00
924 1097 1.742831 CTAGCTAGCTAGGCCTCGATG 59.257 57.143 34.95 14.13 41.58 3.84
925 1098 2.122783 CTAGCTAGCTAGGCCTCGAT 57.877 55.000 34.95 3.60 41.58 3.59
926 1099 3.635271 CTAGCTAGCTAGGCCTCGA 57.365 57.895 34.95 11.15 41.58 4.04
957 1130 0.902531 TAGCTGTCTAAGGTGGTGGC 59.097 55.000 0.00 0.00 37.17 5.01
958 1131 1.134670 GCTAGCTGTCTAAGGTGGTGG 60.135 57.143 7.70 0.00 37.22 4.61
961 1134 3.024547 TGTAGCTAGCTGTCTAAGGTGG 58.975 50.000 27.68 0.00 37.17 4.61
962 1135 3.181485 GGTGTAGCTAGCTGTCTAAGGTG 60.181 52.174 27.68 0.00 37.17 4.00
963 1136 3.025262 GGTGTAGCTAGCTGTCTAAGGT 58.975 50.000 27.68 0.00 40.55 3.50
965 1138 2.033550 CCGGTGTAGCTAGCTGTCTAAG 59.966 54.545 27.68 13.18 0.00 2.18
966 1139 2.022195 CCGGTGTAGCTAGCTGTCTAA 58.978 52.381 27.68 3.39 0.00 2.10
969 1142 1.227002 GCCGGTGTAGCTAGCTGTC 60.227 63.158 27.68 19.10 0.00 3.51
970 1143 2.893398 GCCGGTGTAGCTAGCTGT 59.107 61.111 27.68 4.38 0.00 4.40
1527 1719 4.116238 TGCCGATCAAAAACTTTGGAAAC 58.884 39.130 0.00 0.00 0.00 2.78
1530 1722 3.056891 GGATGCCGATCAAAAACTTTGGA 60.057 43.478 0.00 0.00 0.00 3.53
1533 1725 4.178545 CAGGATGCCGATCAAAAACTTT 57.821 40.909 0.00 0.00 0.00 2.66
1866 2228 3.482232 GAGCCCGGCCATGTATGCT 62.482 63.158 5.55 0.00 0.00 3.79
2175 3104 4.112716 TGTACAAAATCCATGCATGCAG 57.887 40.909 26.69 16.97 0.00 4.41
2225 3394 8.597662 TGTATGTGTGTTTTAAACTCCTCTAC 57.402 34.615 9.33 7.36 0.00 2.59
2226 3395 9.214957 CATGTATGTGTGTTTTAAACTCCTCTA 57.785 33.333 9.33 0.00 0.00 2.43
2228 3397 7.174253 TCCATGTATGTGTGTTTTAAACTCCTC 59.826 37.037 9.33 3.13 0.00 3.71
2286 3455 2.364324 TGTCACAGTGTCACCCTTCTAC 59.636 50.000 0.00 0.00 0.00 2.59
2456 3643 2.346099 TTTTGCTTGCTGTATTCGGC 57.654 45.000 0.00 0.00 45.37 5.54
2457 3644 5.844301 AAAATTTTGCTTGCTGTATTCGG 57.156 34.783 1.75 0.00 0.00 4.30
2475 3662 6.057321 TCTGGTCCGTTCCATACTTAAAAT 57.943 37.500 0.00 0.00 36.84 1.82
2479 3666 5.424757 CAATTCTGGTCCGTTCCATACTTA 58.575 41.667 0.00 0.00 36.84 2.24
2486 3673 2.396590 TAGCAATTCTGGTCCGTTCC 57.603 50.000 0.00 0.00 34.40 3.62
2496 3683 7.287466 AGTGAGTGATGACTAGATAGCAATTCT 59.713 37.037 0.00 0.00 30.16 2.40
2564 3753 2.744202 CCACTGGTCACTTATCACAAGC 59.256 50.000 0.00 0.00 0.00 4.01
2731 3937 0.743345 GACCATCACTTACACCGCCC 60.743 60.000 0.00 0.00 0.00 6.13
2746 3952 4.500545 GCACATACCAAAAACACATGACCA 60.501 41.667 0.00 0.00 0.00 4.02
3078 4284 0.666913 ATAGTTGGATCGTCGGTCGG 59.333 55.000 0.00 0.00 40.32 4.79
3079 4285 3.489444 CATATAGTTGGATCGTCGGTCG 58.511 50.000 0.00 0.00 41.41 4.79
3080 4286 3.243336 GCATATAGTTGGATCGTCGGTC 58.757 50.000 0.00 0.00 0.00 4.79
3081 4287 2.626266 TGCATATAGTTGGATCGTCGGT 59.374 45.455 0.00 0.00 0.00 4.69
3162 4368 3.450578 ACGTACAAAGTGCCCGTATATG 58.549 45.455 0.00 0.00 0.00 1.78
3209 4415 6.634837 CACAGCAATTAACACACATACGAAAA 59.365 34.615 0.00 0.00 0.00 2.29
3270 4476 3.373830 CCTCTCCTTCTCTTCTCACCAT 58.626 50.000 0.00 0.00 0.00 3.55
3323 4529 0.179043 TCCACGGTGCACTGCTTAAA 60.179 50.000 25.67 4.23 0.00 1.52
3337 4543 2.029380 TCAATCACCAGTACAGTCCACG 60.029 50.000 0.00 0.00 0.00 4.94
3357 4563 5.919141 GCAAATTCATTAGTCCATGCAGATC 59.081 40.000 0.00 0.00 33.00 2.75
3794 5117 4.341520 CCAGTAGACCAGGTGTTAGATACC 59.658 50.000 0.00 0.00 38.52 2.73
3836 5165 1.668047 GCAAGACAAACAGCATGAGGC 60.668 52.381 0.00 0.00 39.69 4.70
3871 5203 6.099701 TGCATGAGTATATTCTGTTGGGTAGT 59.900 38.462 0.00 0.00 0.00 2.73
3944 5276 7.669722 ACTGGAATAAAAAGAACCTTGATGCTA 59.330 33.333 0.00 0.00 0.00 3.49
3957 5289 9.423061 CCAACCTTTGATTACTGGAATAAAAAG 57.577 33.333 10.98 10.98 34.22 2.27
3960 5292 7.177744 GTCCCAACCTTTGATTACTGGAATAAA 59.822 37.037 0.00 0.00 0.00 1.40
3971 5306 3.490348 CTCTGTGTCCCAACCTTTGATT 58.510 45.455 0.00 0.00 0.00 2.57
4004 5339 3.381272 TGAAGGCAAAAACTCTTCTGTGG 59.619 43.478 0.00 0.00 38.10 4.17


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

AutoCloner maintained by Alex Coulton.