Multiple sequence alignment - TraesCS6D01G127600

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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 TraesCS6D01G127600 chr6D 100.000 6832 0 0 1 6832 91516263 91523094 0.000000e+00 12617.0
1 TraesCS6D01G127600 chr6B 96.942 6181 133 28 166 6310 175337377 175343537 0.000000e+00 10316.0
2 TraesCS6D01G127600 chr6B 82.353 136 16 6 5980 6114 175709355 175709483 2.010000e-20 111.0
3 TraesCS6D01G127600 chr6B 95.455 44 2 0 124 167 55999810 55999767 3.420000e-08 71.3
4 TraesCS6D01G127600 chr6B 88.235 51 6 0 49 99 175337284 175337334 2.060000e-05 62.1
5 TraesCS6D01G127600 chr6A 94.236 6384 213 73 18 6310 109982433 109988752 0.000000e+00 9607.0
6 TraesCS6D01G127600 chr6A 90.822 523 43 5 6313 6832 468343014 468343534 0.000000e+00 695.0
7 TraesCS6D01G127600 chr6A 80.315 254 18 21 5863 6114 110331196 110331419 5.480000e-36 163.0
8 TraesCS6D01G127600 chr3D 91.778 523 38 4 6313 6832 407812393 407812913 0.000000e+00 723.0
9 TraesCS6D01G127600 chr2A 91.346 520 39 4 6315 6832 716883041 716882526 0.000000e+00 706.0
10 TraesCS6D01G127600 chr5D 90.440 523 46 3 6312 6832 233233713 233233193 0.000000e+00 686.0
11 TraesCS6D01G127600 chr5D 89.286 56 6 0 112 167 374630243 374630298 3.420000e-08 71.3
12 TraesCS6D01G127600 chr7D 90.133 527 47 4 6309 6832 137849810 137850334 0.000000e+00 680.0
13 TraesCS6D01G127600 chr7D 75.833 720 132 33 1780 2482 568953536 568952842 1.840000e-85 327.0
14 TraesCS6D01G127600 chr7D 79.581 382 66 9 2858 3228 568952490 568952110 5.250000e-66 263.0
15 TraesCS6D01G127600 chr7D 85.714 182 26 0 2097 2278 548771557 548771738 6.990000e-45 193.0
16 TraesCS6D01G127600 chr5B 90.057 523 46 4 6312 6832 176590308 176589790 0.000000e+00 673.0
17 TraesCS6D01G127600 chr5B 89.474 57 6 0 112 168 419846426 419846370 9.500000e-09 73.1
18 TraesCS6D01G127600 chr5B 87.931 58 7 0 111 168 406061561 406061618 1.230000e-07 69.4
19 TraesCS6D01G127600 chr1D 89.850 532 43 7 6305 6832 202281908 202282432 0.000000e+00 673.0
20 TraesCS6D01G127600 chr2B 89.734 526 50 3 6310 6832 468890721 468891245 0.000000e+00 669.0
21 TraesCS6D01G127600 chr2D 89.714 525 49 4 6309 6830 52943204 52942682 0.000000e+00 665.0
22 TraesCS6D01G127600 chr2D 93.333 45 3 0 124 168 164992727 164992683 4.420000e-07 67.6
23 TraesCS6D01G127600 chr7B 79.521 376 67 8 2857 3224 625299596 625299223 6.800000e-65 259.0
24 TraesCS6D01G127600 chr7B 78.517 391 68 14 2097 2482 625300329 625299950 6.850000e-60 243.0
25 TraesCS6D01G127600 chr7A 78.772 391 68 15 2097 2482 657720170 657719790 1.470000e-61 248.0
26 TraesCS6D01G127600 chr7A 78.534 382 70 10 2857 3228 657719437 657719058 2.460000e-59 241.0
27 TraesCS6D01G127600 chr7A 89.474 57 6 0 112 168 97021680 97021736 9.500000e-09 73.1
28 TraesCS6D01G127600 chr5A 86.667 60 8 0 111 170 629251154 629251095 4.420000e-07 67.6
29 TraesCS6D01G127600 chr5A 86.667 60 8 0 111 170 629371939 629371998 4.420000e-07 67.6
30 TraesCS6D01G127600 chr1B 93.333 45 3 0 124 168 320588093 320588049 4.420000e-07 67.6
31 TraesCS6D01G127600 chr4D 92.857 42 3 0 52 93 8394129 8394170 2.060000e-05 62.1


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 TraesCS6D01G127600 chr6D 91516263 91523094 6831 False 12617.00 12617 100.0000 1 6832 1 chr6D.!!$F1 6831
1 TraesCS6D01G127600 chr6B 175337284 175343537 6253 False 5189.05 10316 92.5885 49 6310 2 chr6B.!!$F2 6261
2 TraesCS6D01G127600 chr6A 109982433 109988752 6319 False 9607.00 9607 94.2360 18 6310 1 chr6A.!!$F1 6292
3 TraesCS6D01G127600 chr6A 468343014 468343534 520 False 695.00 695 90.8220 6313 6832 1 chr6A.!!$F3 519
4 TraesCS6D01G127600 chr3D 407812393 407812913 520 False 723.00 723 91.7780 6313 6832 1 chr3D.!!$F1 519
5 TraesCS6D01G127600 chr2A 716882526 716883041 515 True 706.00 706 91.3460 6315 6832 1 chr2A.!!$R1 517
6 TraesCS6D01G127600 chr5D 233233193 233233713 520 True 686.00 686 90.4400 6312 6832 1 chr5D.!!$R1 520
7 TraesCS6D01G127600 chr7D 137849810 137850334 524 False 680.00 680 90.1330 6309 6832 1 chr7D.!!$F1 523
8 TraesCS6D01G127600 chr7D 568952110 568953536 1426 True 295.00 327 77.7070 1780 3228 2 chr7D.!!$R1 1448
9 TraesCS6D01G127600 chr5B 176589790 176590308 518 True 673.00 673 90.0570 6312 6832 1 chr5B.!!$R1 520
10 TraesCS6D01G127600 chr1D 202281908 202282432 524 False 673.00 673 89.8500 6305 6832 1 chr1D.!!$F1 527
11 TraesCS6D01G127600 chr2B 468890721 468891245 524 False 669.00 669 89.7340 6310 6832 1 chr2B.!!$F1 522
12 TraesCS6D01G127600 chr2D 52942682 52943204 522 True 665.00 665 89.7140 6309 6830 1 chr2D.!!$R1 521
13 TraesCS6D01G127600 chr7B 625299223 625300329 1106 True 251.00 259 79.0190 2097 3224 2 chr7B.!!$R1 1127
14 TraesCS6D01G127600 chr7A 657719058 657720170 1112 True 244.50 248 78.6530 2097 3228 2 chr7A.!!$R1 1131

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
992 1053 0.321671 TGTTGCCTTCTAGCTCGCTT 59.678 50.000 0.00 0.0 0.00 4.68 F
1017 1078 0.028110 GCATGAATCTTTCGCCGTCC 59.972 55.000 0.00 0.0 0.00 4.79 F
1018 1079 0.301687 CATGAATCTTTCGCCGTCCG 59.698 55.000 0.00 0.0 38.61 4.79 F
1843 1954 1.592669 CTATCCGAACCTGCCTGCG 60.593 63.158 0.00 0.0 0.00 5.18 F
3228 3458 1.076332 GTGTCAGGCGGTATGTCAAC 58.924 55.000 0.00 0.0 0.00 3.18 F
3865 4108 0.251653 AGCCTCTGACGACTTACCCA 60.252 55.000 0.00 0.0 0.00 4.51 F
3922 4165 1.891722 CTTGGCCAACAGGATTGCCC 61.892 60.000 16.05 0.0 43.35 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1843 1954 2.412421 GCAGTTGGCATATAAGCTGC 57.588 50.000 0.00 0.00 43.97 5.25 R
2635 2809 4.148079 TGACCTGCACCAACAATTTGATA 58.852 39.130 2.79 0.00 34.24 2.15 R
2789 2963 4.280789 ACAGTAGGGTATGGATGGAGAA 57.719 45.455 0.00 0.00 0.00 2.87 R
3835 4078 1.138661 GTCAGAGGCTCAATCTCCCAG 59.861 57.143 18.26 0.00 31.96 4.45 R
4708 4953 0.876342 GACGGGACATTCGATGGAGC 60.876 60.000 0.00 0.00 33.60 4.70 R
4887 5132 1.200948 GGCTCTGAATCCAACTGTTGC 59.799 52.381 14.94 2.23 0.00 4.17 R
5890 6142 1.021202 TGCTTTGGTTCCAGTTCACG 58.979 50.000 0.00 0.00 0.00 4.35 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
30 31 9.231297 TGCTGTAGAAAGTAAATAAATTCAGCT 57.769 29.630 0.00 0.00 42.19 4.24
101 106 5.277601 AGACATGACAAATTTAACGTCCG 57.722 39.130 0.00 0.51 0.00 4.79
102 107 4.992319 AGACATGACAAATTTAACGTCCGA 59.008 37.500 0.00 0.00 0.00 4.55
103 108 5.120208 AGACATGACAAATTTAACGTCCGAG 59.880 40.000 0.00 0.00 0.00 4.63
125 155 8.285394 CCGAGATGATAATTTATTTCAGTGGTG 58.715 37.037 0.00 0.00 0.00 4.17
126 156 8.830580 CGAGATGATAATTTATTTCAGTGGTGT 58.169 33.333 0.00 0.00 0.00 4.16
130 160 9.859427 ATGATAATTTATTTCAGTGGTGTTGTG 57.141 29.630 0.00 0.00 0.00 3.33
131 161 8.855110 TGATAATTTATTTCAGTGGTGTTGTGT 58.145 29.630 0.00 0.00 0.00 3.72
132 162 9.691362 GATAATTTATTTCAGTGGTGTTGTGTT 57.309 29.630 0.00 0.00 0.00 3.32
135 165 9.877178 AATTTATTTCAGTGGTGTTGTGTTAAA 57.123 25.926 0.00 0.00 0.00 1.52
137 167 9.706691 TTTATTTCAGTGGTGTTGTGTTAAAAA 57.293 25.926 0.00 0.00 0.00 1.94
138 168 7.589574 ATTTCAGTGGTGTTGTGTTAAAAAC 57.410 32.000 0.00 0.00 0.00 2.43
139 169 5.707242 TCAGTGGTGTTGTGTTAAAAACA 57.293 34.783 0.00 0.00 39.52 2.83
169 199 2.815019 TGGGACAGAGGGAGTAGGA 58.185 57.895 0.00 0.00 0.00 2.94
170 200 0.631753 TGGGACAGAGGGAGTAGGAG 59.368 60.000 0.00 0.00 0.00 3.69
171 201 0.632294 GGGACAGAGGGAGTAGGAGT 59.368 60.000 0.00 0.00 0.00 3.85
172 202 1.851653 GGGACAGAGGGAGTAGGAGTA 59.148 57.143 0.00 0.00 0.00 2.59
173 203 2.447811 GGGACAGAGGGAGTAGGAGTAT 59.552 54.545 0.00 0.00 0.00 2.12
174 204 3.656751 GGGACAGAGGGAGTAGGAGTATA 59.343 52.174 0.00 0.00 0.00 1.47
323 354 4.722526 TGATAGAGAAGAGAGAGGGAGG 57.277 50.000 0.00 0.00 0.00 4.30
324 355 3.397618 TGATAGAGAAGAGAGAGGGAGGG 59.602 52.174 0.00 0.00 0.00 4.30
331 362 2.018086 AGAGAGGGAGGGAGGGAGG 61.018 68.421 0.00 0.00 0.00 4.30
335 366 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
430 461 2.156343 AGAACAGCACCGAGAAGAAC 57.844 50.000 0.00 0.00 0.00 3.01
454 491 1.813192 CACTTCCCTCTCTCTCGCC 59.187 63.158 0.00 0.00 0.00 5.54
490 527 2.097038 GCACAGTAGCACGAGCAGG 61.097 63.158 7.77 0.00 45.49 4.85
496 533 2.714991 TAGCACGAGCAGGCAGGAG 61.715 63.158 7.77 0.00 45.49 3.69
509 565 1.903877 GCAGGAGGCTACAGGAAGCA 61.904 60.000 0.00 0.00 44.64 3.91
692 748 3.746889 CAAAGGCGGCGCATTCCA 61.747 61.111 32.20 0.00 28.96 3.53
802 858 0.527817 CTCGGATCGAAAAGGACCGG 60.528 60.000 0.00 0.00 43.14 5.28
992 1053 0.321671 TGTTGCCTTCTAGCTCGCTT 59.678 50.000 0.00 0.00 0.00 4.68
1016 1077 1.009829 AGCATGAATCTTTCGCCGTC 58.990 50.000 0.00 0.00 0.00 4.79
1017 1078 0.028110 GCATGAATCTTTCGCCGTCC 59.972 55.000 0.00 0.00 0.00 4.79
1018 1079 0.301687 CATGAATCTTTCGCCGTCCG 59.698 55.000 0.00 0.00 38.61 4.79
1099 1163 3.118847 TGCATTTCAGTTGGCAGTTTTCA 60.119 39.130 0.00 0.00 0.00 2.69
1100 1164 4.060205 GCATTTCAGTTGGCAGTTTTCAT 58.940 39.130 0.00 0.00 0.00 2.57
1161 1225 8.579863 CCCATCAACCTATCAATTTATTCTTCC 58.420 37.037 0.00 0.00 0.00 3.46
1690 1800 4.457834 TTTCGCAAGTTCCCTTTTGAAA 57.542 36.364 0.00 0.00 32.75 2.69
1723 1833 4.006319 GCAGCAGTTCTTAGATGGTTCTT 58.994 43.478 0.00 0.00 33.17 2.52
1843 1954 1.592669 CTATCCGAACCTGCCTGCG 60.593 63.158 0.00 0.00 0.00 5.18
1902 2013 5.377358 CGTAAGTTCGGATCGATATAACGT 58.623 41.667 0.00 4.46 35.23 3.99
3123 3353 3.262420 CCCTTCAGAGTTTGTCATACCG 58.738 50.000 0.00 0.00 0.00 4.02
3228 3458 1.076332 GTGTCAGGCGGTATGTCAAC 58.924 55.000 0.00 0.00 0.00 3.18
3283 3513 2.555199 GTGTACATCACATGGAGCTCC 58.445 52.381 26.78 26.78 45.51 4.70
3301 3531 4.723789 AGCTCCTTCCTTATCTTGATTCCA 59.276 41.667 0.00 0.00 0.00 3.53
3402 3645 7.445707 AGAACTTGTTTCAGAACTCCCTAAATC 59.554 37.037 0.00 0.00 36.57 2.17
3484 3727 4.158394 TCTTGCTTGTTTTCTGCTCTGTTT 59.842 37.500 0.00 0.00 0.00 2.83
3492 3735 6.112734 TGTTTTCTGCTCTGTTTTAGTGAGA 58.887 36.000 0.00 0.00 0.00 3.27
3672 3915 1.193874 GTTTGTCACTAAAGGCGGACG 59.806 52.381 0.00 0.00 33.04 4.79
3835 4078 0.606673 GGCAACCAAGGGTGTCTCTC 60.607 60.000 5.96 0.00 35.34 3.20
3865 4108 0.251653 AGCCTCTGACGACTTACCCA 60.252 55.000 0.00 0.00 0.00 4.51
3922 4165 1.891722 CTTGGCCAACAGGATTGCCC 61.892 60.000 16.05 0.00 43.35 5.36
4708 4953 7.040494 TCAAGACAGAAATATCAGCTCTCTTG 58.960 38.462 0.00 0.00 0.00 3.02
4887 5132 4.976116 TCTCATGTTAACTCGTCGCATATG 59.024 41.667 7.22 0.00 0.00 1.78
4904 5149 4.096833 GCATATGCAACAGTTGGATTCAGA 59.903 41.667 23.67 7.90 42.07 3.27
5283 5528 2.536761 TCGTGAAGGTGACCGAATTT 57.463 45.000 0.00 0.00 0.00 1.82
5300 5545 6.070078 ACCGAATTTACTTACCCACCTAATCA 60.070 38.462 0.00 0.00 0.00 2.57
5411 5663 4.695455 GCTGGACATCACTAAGTTTAGCAA 59.305 41.667 0.00 0.00 34.09 3.91
5620 5872 3.941483 GTGTCCACTCTTACATTCATGGG 59.059 47.826 0.00 0.00 0.00 4.00
5890 6142 0.380378 CTGCAGCTCGTCCTAGTCTC 59.620 60.000 0.00 0.00 0.00 3.36
5928 6180 3.381590 AGCACATAGATCAAGTGTAGCGA 59.618 43.478 11.98 0.00 35.75 4.93
5975 6227 9.212641 GTTTATGTCATGCATGTGATATAGACT 57.787 33.333 25.43 7.17 35.89 3.24
6089 6341 0.788391 GACTCTTTACCCGTGTTGCG 59.212 55.000 0.00 0.00 40.95 4.85
6119 6373 5.375417 TGTTTTGGTCATATTCTGTGCAG 57.625 39.130 0.00 0.00 0.00 4.41
6165 6419 5.968254 TGTAACTATTGACGATGTTAGCCA 58.032 37.500 0.00 0.00 0.00 4.75
6297 6551 7.828508 TTAGTTGGAGTTAGTGACTAGTGAA 57.171 36.000 0.00 0.00 39.19 3.18
6299 6553 5.010820 AGTTGGAGTTAGTGACTAGTGAACC 59.989 44.000 0.00 0.00 39.19 3.62
6303 6557 6.722590 TGGAGTTAGTGACTAGTGAACCAATA 59.277 38.462 0.00 0.00 39.19 1.90
6310 6564 8.596781 AGTGACTAGTGAACCAATACTTCTAT 57.403 34.615 0.00 0.00 0.00 1.98
6311 6565 9.036980 AGTGACTAGTGAACCAATACTTCTATT 57.963 33.333 0.00 0.00 0.00 1.73
6312 6566 9.654663 GTGACTAGTGAACCAATACTTCTATTT 57.345 33.333 0.00 0.00 0.00 1.40
6345 6601 1.054978 GGAGGATTACCCGGCCTCTT 61.055 60.000 20.39 0.94 45.87 2.85
6351 6607 2.464796 TTACCCGGCCTCTTCATCTA 57.535 50.000 0.00 0.00 0.00 1.98
6368 6624 0.940126 CTAGACGATGCATGCAACCC 59.060 55.000 26.68 14.91 0.00 4.11
6428 6684 1.471119 TAGGTAGTCTGAAGCCACCG 58.529 55.000 0.00 0.00 34.36 4.94
6436 6692 1.078759 CTGAAGCCACCGTCTTAGCG 61.079 60.000 0.00 0.00 0.00 4.26
6446 6702 2.751259 ACCGTCTTAGCGACAACTATCA 59.249 45.455 0.00 0.00 42.98 2.15
6483 6739 1.141053 GATGAAGGGGTGCCGATAGTT 59.859 52.381 0.00 0.00 0.00 2.24
6572 6830 0.039618 ATACTGGGTTTGGGGCACAG 59.960 55.000 0.00 0.00 42.68 3.66
6669 6931 2.932194 TTGCCAGGCCTCTCTGCT 60.932 61.111 9.64 0.00 33.64 4.24
6793 7055 4.096231 CCGCCATCAATGTGTAAGATGAAA 59.904 41.667 0.00 0.00 41.18 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.755122 ACCCTTAGCTGAATTTATTTACTTTCT 57.245 29.630 0.00 0.00 0.00 2.52
42 43 9.739276 TGTCAGATTTGTAGTGAAATCCTATTT 57.261 29.630 0.00 0.00 41.45 1.40
45 46 8.539544 TGATGTCAGATTTGTAGTGAAATCCTA 58.460 33.333 0.00 0.00 41.45 2.94
46 47 7.397221 TGATGTCAGATTTGTAGTGAAATCCT 58.603 34.615 0.00 0.00 41.45 3.24
47 48 7.615582 TGATGTCAGATTTGTAGTGAAATCC 57.384 36.000 0.00 0.00 41.45 3.01
80 85 5.119588 TCTCGGACGTTAAATTTGTCATGTC 59.880 40.000 0.00 5.92 34.32 3.06
86 91 7.837202 TTATCATCTCGGACGTTAAATTTGT 57.163 32.000 0.00 0.00 0.00 2.83
94 99 8.657074 TGAAATAAATTATCATCTCGGACGTT 57.343 30.769 0.00 0.00 0.00 3.99
99 104 8.285394 CACCACTGAAATAAATTATCATCTCGG 58.715 37.037 0.00 0.00 0.00 4.63
115 145 6.513180 TGTTTTTAACACAACACCACTGAAA 58.487 32.000 0.00 0.00 36.25 2.69
134 164 9.838339 CTCTGTCCCATAATATAAGAGTGTTTT 57.162 33.333 0.00 0.00 0.00 2.43
135 165 8.432805 CCTCTGTCCCATAATATAAGAGTGTTT 58.567 37.037 0.00 0.00 0.00 2.83
137 167 6.498651 CCCTCTGTCCCATAATATAAGAGTGT 59.501 42.308 0.00 0.00 0.00 3.55
138 168 6.726299 TCCCTCTGTCCCATAATATAAGAGTG 59.274 42.308 0.00 0.00 0.00 3.51
139 169 6.875469 TCCCTCTGTCCCATAATATAAGAGT 58.125 40.000 0.00 0.00 0.00 3.24
140 170 6.957020 ACTCCCTCTGTCCCATAATATAAGAG 59.043 42.308 0.00 0.00 0.00 2.85
141 171 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
142 172 7.343316 CCTACTCCCTCTGTCCCATAATATAAG 59.657 44.444 0.00 0.00 0.00 1.73
143 173 7.020270 TCCTACTCCCTCTGTCCCATAATATAA 59.980 40.741 0.00 0.00 0.00 0.98
144 174 6.511445 TCCTACTCCCTCTGTCCCATAATATA 59.489 42.308 0.00 0.00 0.00 0.86
145 175 5.318889 TCCTACTCCCTCTGTCCCATAATAT 59.681 44.000 0.00 0.00 0.00 1.28
146 176 4.673132 TCCTACTCCCTCTGTCCCATAATA 59.327 45.833 0.00 0.00 0.00 0.98
147 177 3.471306 TCCTACTCCCTCTGTCCCATAAT 59.529 47.826 0.00 0.00 0.00 1.28
148 178 2.863238 TCCTACTCCCTCTGTCCCATAA 59.137 50.000 0.00 0.00 0.00 1.90
149 179 2.447429 CTCCTACTCCCTCTGTCCCATA 59.553 54.545 0.00 0.00 0.00 2.74
150 180 1.219213 CTCCTACTCCCTCTGTCCCAT 59.781 57.143 0.00 0.00 0.00 4.00
151 181 0.631753 CTCCTACTCCCTCTGTCCCA 59.368 60.000 0.00 0.00 0.00 4.37
152 182 0.632294 ACTCCTACTCCCTCTGTCCC 59.368 60.000 0.00 0.00 0.00 4.46
153 183 3.887916 ATACTCCTACTCCCTCTGTCC 57.112 52.381 0.00 0.00 0.00 4.02
154 184 5.571791 AGTATACTCCTACTCCCTCTGTC 57.428 47.826 0.00 0.00 0.00 3.51
155 185 5.998128 AAGTATACTCCTACTCCCTCTGT 57.002 43.478 5.70 0.00 30.68 3.41
156 186 7.342284 TGAAAAAGTATACTCCTACTCCCTCTG 59.658 40.741 5.70 0.00 30.68 3.35
157 187 7.420029 TGAAAAAGTATACTCCTACTCCCTCT 58.580 38.462 5.70 0.00 30.68 3.69
158 188 7.657023 TGAAAAAGTATACTCCTACTCCCTC 57.343 40.000 5.70 0.00 30.68 4.30
159 189 6.098552 GCTGAAAAAGTATACTCCTACTCCCT 59.901 42.308 5.70 0.00 30.68 4.20
160 190 6.282167 GCTGAAAAAGTATACTCCTACTCCC 58.718 44.000 5.70 0.00 30.68 4.30
161 191 6.282167 GGCTGAAAAAGTATACTCCTACTCC 58.718 44.000 5.70 0.00 30.68 3.85
162 192 5.978322 CGGCTGAAAAAGTATACTCCTACTC 59.022 44.000 5.70 0.35 30.68 2.59
163 193 5.421374 ACGGCTGAAAAAGTATACTCCTACT 59.579 40.000 5.70 0.00 33.34 2.57
164 194 5.519206 CACGGCTGAAAAAGTATACTCCTAC 59.481 44.000 5.70 0.05 0.00 3.18
165 195 5.186409 ACACGGCTGAAAAAGTATACTCCTA 59.814 40.000 5.70 0.00 0.00 2.94
166 196 4.020485 ACACGGCTGAAAAAGTATACTCCT 60.020 41.667 5.70 0.00 0.00 3.69
167 197 4.251268 ACACGGCTGAAAAAGTATACTCC 58.749 43.478 5.70 0.11 0.00 3.85
168 198 5.865552 TGTACACGGCTGAAAAAGTATACTC 59.134 40.000 5.70 0.00 0.00 2.59
169 199 5.786311 TGTACACGGCTGAAAAAGTATACT 58.214 37.500 0.00 0.00 0.00 2.12
170 200 6.657836 ATGTACACGGCTGAAAAAGTATAC 57.342 37.500 0.00 0.00 0.00 1.47
171 201 6.757947 GGTATGTACACGGCTGAAAAAGTATA 59.242 38.462 0.00 0.00 0.00 1.47
172 202 5.583457 GGTATGTACACGGCTGAAAAAGTAT 59.417 40.000 0.00 0.00 0.00 2.12
173 203 4.931002 GGTATGTACACGGCTGAAAAAGTA 59.069 41.667 0.00 0.00 0.00 2.24
174 204 3.749609 GGTATGTACACGGCTGAAAAAGT 59.250 43.478 0.00 0.00 0.00 2.66
323 354 4.095400 TGCTCCCTCCCTCCCTCC 62.095 72.222 0.00 0.00 0.00 4.30
324 355 2.766229 GTGCTCCCTCCCTCCCTC 60.766 72.222 0.00 0.00 0.00 4.30
331 362 2.997897 ACGAGTGGTGCTCCCTCC 60.998 66.667 14.05 0.00 41.10 4.30
430 461 1.622811 AGAGAGAGGGAAGTGCACTTG 59.377 52.381 35.67 0.00 36.11 3.16
454 491 3.374367 TGTGCTCGTGCTACTAGTTAGAG 59.626 47.826 11.19 4.71 40.48 2.43
490 527 1.153269 GCTTCCTGTAGCCTCCTGC 60.153 63.158 0.00 0.00 41.71 4.85
782 838 0.454600 CGGTCCTTTTCGATCCGAGA 59.545 55.000 0.00 0.00 43.22 4.04
992 1053 2.162208 GGCGAAAGATTCATGCTTGACA 59.838 45.455 1.02 0.00 0.00 3.58
1070 1134 3.118847 TGCCAACTGAAATGCAAAGACAA 60.119 39.130 0.00 0.00 0.00 3.18
1099 1163 6.985117 TGCACAGATTTAAAGCAAGAGAAAT 58.015 32.000 6.19 0.00 31.42 2.17
1100 1164 6.389830 TGCACAGATTTAAAGCAAGAGAAA 57.610 33.333 6.19 0.00 31.42 2.52
1161 1225 7.067372 TGTCAAGAAGCATATAAATCACCCAAG 59.933 37.037 0.00 0.00 0.00 3.61
1211 1275 8.500753 AAACAGTGTCAACAAGTGTATTAGAA 57.499 30.769 0.00 0.00 0.00 2.10
1212 1276 7.985184 AGAAACAGTGTCAACAAGTGTATTAGA 59.015 33.333 0.00 0.00 0.00 2.10
1225 1289 5.941058 TGTAAAGAACCAGAAACAGTGTCAA 59.059 36.000 0.00 0.00 0.00 3.18
1690 1800 2.089980 GAACTGCTGCAAGACATGGAT 58.910 47.619 3.02 0.00 34.07 3.41
1723 1833 7.509546 AGTGTCTTAAAATCTTCAGTTCTGGA 58.490 34.615 0.00 0.00 0.00 3.86
1843 1954 2.412421 GCAGTTGGCATATAAGCTGC 57.588 50.000 0.00 0.00 43.97 5.25
1902 2013 8.092687 GGTACTACTTGGTTCTTGAAACAGATA 58.907 37.037 1.27 0.00 0.00 1.98
2635 2809 4.148079 TGACCTGCACCAACAATTTGATA 58.852 39.130 2.79 0.00 34.24 2.15
2789 2963 4.280789 ACAGTAGGGTATGGATGGAGAA 57.719 45.455 0.00 0.00 0.00 2.87
3064 3284 4.800993 CACGTGGACAAATCTGAGTATCTC 59.199 45.833 7.95 0.00 34.92 2.75
3123 3353 4.941873 ACAGCCTTTACATACTTAGCCAAC 59.058 41.667 0.00 0.00 0.00 3.77
3228 3458 9.809096 ACATCACTATAAGAGATAAACACAGTG 57.191 33.333 0.00 0.00 33.78 3.66
3283 3513 6.405176 GGCAAGTTGGAATCAAGATAAGGAAG 60.405 42.308 4.75 0.00 32.92 3.46
3301 3531 2.754946 TTCGATACTTCGGGCAAGTT 57.245 45.000 0.00 0.00 43.38 2.66
3402 3645 2.227388 GCCAAGTGAAGAAGTGGTGATG 59.773 50.000 0.00 0.00 33.43 3.07
3484 3727 6.818644 GCTACTGAAAACATGGATCTCACTAA 59.181 38.462 0.00 0.00 0.00 2.24
3492 3735 3.436704 CACGTGCTACTGAAAACATGGAT 59.563 43.478 0.82 0.00 0.00 3.41
3835 4078 1.138661 GTCAGAGGCTCAATCTCCCAG 59.861 57.143 18.26 0.00 31.96 4.45
3865 4108 6.944862 GCATAGGGAAAGGAGATGAATACATT 59.055 38.462 0.00 0.00 36.82 2.71
3922 4165 6.387041 TCGTCACTTGTACCATATAAGGAG 57.613 41.667 0.00 0.00 31.98 3.69
4598 4843 1.499007 AGGAAAGCTGGGAGAAAACCA 59.501 47.619 0.00 0.00 36.38 3.67
4708 4953 0.876342 GACGGGACATTCGATGGAGC 60.876 60.000 0.00 0.00 33.60 4.70
4887 5132 1.200948 GGCTCTGAATCCAACTGTTGC 59.799 52.381 14.94 2.23 0.00 4.17
4904 5149 6.253946 AGCTTTGTGGTATATTAGAAGGCT 57.746 37.500 0.00 0.00 29.66 4.58
5283 5528 7.941053 ATTGGTATGATTAGGTGGGTAAGTA 57.059 36.000 0.00 0.00 0.00 2.24
5411 5663 2.751259 TCGCTACGAAGTTCATGGTAGT 59.249 45.455 14.23 2.41 37.78 2.73
5457 5709 2.936032 GGGTCCTCCAACTGGCCT 60.936 66.667 3.32 0.00 35.00 5.19
5532 5784 4.545706 TGCCACGGATCATCGCCC 62.546 66.667 0.00 0.00 0.00 6.13
5620 5872 4.024556 CGAATTCCCTGCAGATTACATGAC 60.025 45.833 17.39 0.00 0.00 3.06
5890 6142 1.021202 TGCTTTGGTTCCAGTTCACG 58.979 50.000 0.00 0.00 0.00 4.35
6089 6341 9.691362 ACAGAATATGACCAAAACAAACATTAC 57.309 29.630 0.00 0.00 0.00 1.89
6119 6373 4.002906 TGTGGAACCAGAACACTATCAC 57.997 45.455 0.00 0.00 36.16 3.06
6312 6566 9.181061 CGGGTAATCCTCCTTTTCTAATAAAAA 57.819 33.333 0.00 0.00 0.00 1.94
6313 6567 7.776500 CCGGGTAATCCTCCTTTTCTAATAAAA 59.224 37.037 0.00 0.00 0.00 1.52
6314 6568 7.284820 CCGGGTAATCCTCCTTTTCTAATAAA 58.715 38.462 0.00 0.00 0.00 1.40
6315 6569 6.689690 GCCGGGTAATCCTCCTTTTCTAATAA 60.690 42.308 2.18 0.00 0.00 1.40
6316 6570 5.221783 GCCGGGTAATCCTCCTTTTCTAATA 60.222 44.000 2.18 0.00 0.00 0.98
6317 6571 4.445879 GCCGGGTAATCCTCCTTTTCTAAT 60.446 45.833 2.18 0.00 0.00 1.73
6318 6572 3.118149 GCCGGGTAATCCTCCTTTTCTAA 60.118 47.826 2.18 0.00 0.00 2.10
6319 6573 2.436911 GCCGGGTAATCCTCCTTTTCTA 59.563 50.000 2.18 0.00 0.00 2.10
6351 6607 0.322816 AAGGGTTGCATGCATCGTCT 60.323 50.000 23.37 17.40 0.00 4.18
6436 6692 6.016108 GGTGGATAGGAGTAGTGATAGTTGTC 60.016 46.154 0.00 0.00 0.00 3.18
6446 6702 4.816048 TCATCAGGTGGATAGGAGTAGT 57.184 45.455 0.00 0.00 33.95 2.73
6483 6739 3.512329 TGTCTGTTTGGTATTAGGCTCGA 59.488 43.478 0.00 0.00 0.00 4.04
6572 6830 2.126424 GAGTGCGTCGGACCAGTC 60.126 66.667 13.70 14.45 0.00 3.51
6669 6931 1.065109 CGTCATGGTGGCGTCGATA 59.935 57.895 0.00 0.00 41.12 2.92
6760 7022 3.978491 GATGGCGGCGGATCTCGA 61.978 66.667 9.78 0.00 42.43 4.04
6793 7055 2.508526 GCTTCTTTGGTGGAGTGATGT 58.491 47.619 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.