Multiple sequence alignment - TraesCS7D01G386900

Loading Multiple Alignment...

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 TraesCS7D01G386900 chr7D 100.000 6761 0 0 1 6761 500999839 500993079 0.000000e+00 12486.0
1 TraesCS7D01G386900 chr7D 94.295 596 30 4 1 594 628443794 628443201 0.000000e+00 909.0
2 TraesCS7D01G386900 chr7D 93.729 590 30 5 1 588 92713578 92712994 0.000000e+00 878.0
3 TraesCS7D01G386900 chr7A 94.944 5340 175 37 583 5877 567506943 567501654 0.000000e+00 8277.0
4 TraesCS7D01G386900 chr7A 88.611 799 67 9 5962 6757 567500271 567499494 0.000000e+00 950.0
5 TraesCS7D01G386900 chr7A 93.130 131 1 1 5866 5996 567500399 567500277 1.160000e-42 185.0
6 TraesCS7D01G386900 chr7B 95.619 1940 70 11 3088 5022 530002260 530000331 0.000000e+00 3097.0
7 TraesCS7D01G386900 chr7B 92.826 2091 90 22 587 2633 530004927 530002853 0.000000e+00 2976.0
8 TraesCS7D01G386900 chr7B 93.713 1702 68 17 5020 6699 529991197 529989513 0.000000e+00 2514.0
9 TraesCS7D01G386900 chr7B 98.540 411 6 0 2680 3090 530002858 530002448 0.000000e+00 726.0
10 TraesCS7D01G386900 chr7B 96.537 231 8 0 5020 5250 576960253 576960023 3.830000e-102 383.0
11 TraesCS7D01G386900 chr7B 96.537 231 8 0 5020 5250 653964836 653965066 3.830000e-102 383.0
12 TraesCS7D01G386900 chr4D 94.435 593 30 3 1 591 506031498 506030907 0.000000e+00 909.0
13 TraesCS7D01G386900 chr4D 90.441 136 13 0 1049 1184 500342942 500342807 5.390000e-41 180.0
14 TraesCS7D01G386900 chr4D 97.297 37 1 0 4041 4077 57027747 57027783 5.660000e-06 63.9
15 TraesCS7D01G386900 chrUn 94.108 594 30 5 1 591 46247197 46246606 0.000000e+00 898.0
16 TraesCS7D01G386900 chrUn 96.537 231 8 0 5020 5250 242425604 242425834 3.830000e-102 383.0
17 TraesCS7D01G386900 chrUn 96.537 231 8 0 5020 5250 367351498 367351268 3.830000e-102 383.0
18 TraesCS7D01G386900 chrUn 96.537 231 8 0 5020 5250 432439023 432439253 3.830000e-102 383.0
19 TraesCS7D01G386900 chr2D 94.237 590 30 4 1 588 608741189 608741776 0.000000e+00 898.0
20 TraesCS7D01G386900 chr2D 97.297 37 1 0 4041 4077 354810654 354810618 5.660000e-06 63.9
21 TraesCS7D01G386900 chr5D 94.218 588 31 3 1 586 13915968 13916554 0.000000e+00 894.0
22 TraesCS7D01G386900 chr1D 93.729 590 33 4 1 588 464850824 464850237 0.000000e+00 881.0
23 TraesCS7D01G386900 chr1D 97.297 37 1 0 4041 4077 464636389 464636353 5.660000e-06 63.9
24 TraesCS7D01G386900 chr6D 93.559 590 34 4 1 588 446862131 446862718 0.000000e+00 876.0
25 TraesCS7D01G386900 chr6D 97.297 37 1 0 4041 4077 48150796 48150832 5.660000e-06 63.9
26 TraesCS7D01G386900 chr6D 97.297 37 1 0 4041 4077 289621111 289621075 5.660000e-06 63.9
27 TraesCS7D01G386900 chr3D 93.423 593 35 4 1 590 146189504 146188913 0.000000e+00 876.0
28 TraesCS7D01G386900 chr3D 97.297 37 1 0 4041 4077 564628522 564628486 5.660000e-06 63.9
29 TraesCS7D01G386900 chr4A 96.970 231 7 0 5020 5250 406151102 406151332 8.220000e-104 388.0
30 TraesCS7D01G386900 chr1A 96.537 231 8 0 5020 5250 33032529 33032299 3.830000e-102 383.0
31 TraesCS7D01G386900 chr5A 91.034 145 13 0 1040 1184 681010391 681010247 5.350000e-46 196.0
32 TraesCS7D01G386900 chr4B 88.312 154 18 0 1031 1184 643657525 643657372 1.160000e-42 185.0
33 TraesCS7D01G386900 chr2A 97.368 38 1 0 2794 2831 100643887 100643924 1.570000e-06 65.8


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 TraesCS7D01G386900 chr7D 500993079 500999839 6760 True 12486.000000 12486 100.000000 1 6761 1 chr7D.!!$R2 6760
1 TraesCS7D01G386900 chr7D 628443201 628443794 593 True 909.000000 909 94.295000 1 594 1 chr7D.!!$R3 593
2 TraesCS7D01G386900 chr7D 92712994 92713578 584 True 878.000000 878 93.729000 1 588 1 chr7D.!!$R1 587
3 TraesCS7D01G386900 chr7A 567499494 567506943 7449 True 3137.333333 8277 92.228333 583 6757 3 chr7A.!!$R1 6174
4 TraesCS7D01G386900 chr7B 529989513 529991197 1684 True 2514.000000 2514 93.713000 5020 6699 1 chr7B.!!$R1 1679
5 TraesCS7D01G386900 chr7B 530000331 530004927 4596 True 2266.333333 3097 95.661667 587 5022 3 chr7B.!!$R3 4435
6 TraesCS7D01G386900 chr4D 506030907 506031498 591 True 909.000000 909 94.435000 1 591 1 chr4D.!!$R2 590
7 TraesCS7D01G386900 chrUn 46246606 46247197 591 True 898.000000 898 94.108000 1 591 1 chrUn.!!$R1 590
8 TraesCS7D01G386900 chr2D 608741189 608741776 587 False 898.000000 898 94.237000 1 588 1 chr2D.!!$F1 587
9 TraesCS7D01G386900 chr5D 13915968 13916554 586 False 894.000000 894 94.218000 1 586 1 chr5D.!!$F1 585
10 TraesCS7D01G386900 chr1D 464850237 464850824 587 True 881.000000 881 93.729000 1 588 1 chr1D.!!$R2 587
11 TraesCS7D01G386900 chr6D 446862131 446862718 587 False 876.000000 876 93.559000 1 588 1 chr6D.!!$F2 587
12 TraesCS7D01G386900 chr3D 146188913 146189504 591 True 876.000000 876 93.423000 1 590 1 chr3D.!!$R1 589

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
566 571 0.032540 CACCTGGAAAGCCTTGTTGC 59.967 55.000 0.0 0.0 34.31 4.17 F
1375 1411 0.321298 ACTCCCGAACCAAACCATCG 60.321 55.000 0.0 0.0 36.39 3.84 F
2523 2590 1.412079 TGCAGATTGGGTGCTTTTGT 58.588 45.000 0.0 0.0 41.78 2.83 F
3094 3352 2.843701 GGCAACTGGGAGATATGTGAG 58.156 52.381 0.0 0.0 0.00 3.51 F
3733 4024 2.421424 GAGGCGAAGTTACCTAGACGAA 59.579 50.000 0.0 0.0 36.05 3.85 F
5390 5709 0.620556 CCAACTCTGGGTATGTGGCT 59.379 55.000 0.0 0.0 39.30 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2523 2590 0.324943 GAGGAAGCAGCTGTAACCCA 59.675 55.000 16.64 0.00 0.00 4.51 R
2906 2973 3.083349 TCCCATCCAGGCACGAGG 61.083 66.667 0.00 0.00 35.39 4.63 R
3504 3762 0.466543 TGTGTGTGTTTAGCTCCCGT 59.533 50.000 0.00 0.00 0.00 5.28 R
4890 5182 0.392461 GCCGATGGGTAACTTCAGCA 60.392 55.000 0.00 0.00 34.97 4.41 R
5641 5960 1.568612 CCGCCATAATGCAGCCGTAG 61.569 60.000 0.00 0.00 0.00 3.51 R
6303 7941 0.989890 GGGCGTCATATATCGTTCGC 59.010 55.000 10.06 10.06 42.32 4.70 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
20 22 4.077184 AAACGCTCGCCATCGGGA 62.077 61.111 0.00 0.00 38.83 5.14
75 77 2.060980 GCTCGGGAGATGGAGTGGT 61.061 63.158 0.00 0.00 38.80 4.16
165 168 2.122954 GGGAGAGGTGGGAGGTGT 59.877 66.667 0.00 0.00 0.00 4.16
520 525 1.375523 GAAACGTGACTGGGCCGAT 60.376 57.895 0.00 0.00 0.00 4.18
554 559 0.958382 CGGCCGAAAAATCACCTGGA 60.958 55.000 24.07 0.00 0.00 3.86
566 571 0.032540 CACCTGGAAAGCCTTGTTGC 59.967 55.000 0.00 0.00 34.31 4.17
700 709 1.595993 CTCGCCATATCGGGATCGGT 61.596 60.000 0.00 0.00 36.95 4.69
746 755 4.962122 CGCACAGTGCCACGCAAC 62.962 66.667 20.16 0.00 41.47 4.17
761 770 1.202568 CAACGATCGCATCCATCGC 59.797 57.895 16.60 0.00 45.83 4.58
768 777 2.863853 CGCATCCATCGCTCACACG 61.864 63.158 0.00 0.00 0.00 4.49
824 833 2.677836 CTGCCATTTTGAAGCTACGCTA 59.322 45.455 0.00 0.00 38.25 4.26
1219 1246 2.272447 TTGCCTACGCTTTTGCCCC 61.272 57.895 0.00 0.00 43.93 5.80
1220 1247 3.810896 GCCTACGCTTTTGCCCCG 61.811 66.667 0.00 0.00 43.93 5.73
1225 1252 2.791501 TACGCTTTTGCCCCGGTCTC 62.792 60.000 0.00 0.00 43.93 3.36
1226 1253 3.062466 GCTTTTGCCCCGGTCTCC 61.062 66.667 0.00 0.00 40.15 3.71
1230 1257 2.002018 TTTTGCCCCGGTCTCCAGTT 62.002 55.000 0.00 0.00 0.00 3.16
1231 1258 2.406002 TTTGCCCCGGTCTCCAGTTC 62.406 60.000 0.00 0.00 0.00 3.01
1235 1262 2.266055 CCGGTCTCCAGTTCAGCC 59.734 66.667 0.00 0.00 0.00 4.85
1241 1268 4.704833 TCCAGTTCAGCCGCCTGC 62.705 66.667 0.00 0.00 39.00 4.85
1261 1288 0.796312 CATTCCTTGTTCACGACGGG 59.204 55.000 0.00 0.00 0.00 5.28
1335 1371 2.049433 ACTCGACCAAGAACGGCG 60.049 61.111 4.80 4.80 0.00 6.46
1373 1409 2.235891 GAAACTCCCGAACCAAACCAT 58.764 47.619 0.00 0.00 0.00 3.55
1375 1411 0.321298 ACTCCCGAACCAAACCATCG 60.321 55.000 0.00 0.00 36.39 3.84
1393 1429 4.081420 CCATCGTCCCTTCCCTTATATGAG 60.081 50.000 0.00 0.00 0.00 2.90
1640 1687 1.875514 TCGGAGCATGCTATTGATTGC 59.124 47.619 22.74 5.09 35.34 3.56
1646 1693 3.446161 AGCATGCTATTGATTGCTGTGTT 59.554 39.130 21.21 0.00 43.44 3.32
1694 1741 1.701031 TTCCTTGACCCTTGCCGTCA 61.701 55.000 0.00 0.00 38.46 4.35
1771 1820 6.427547 TGTGTTTTACTTCGTTATAGTTGGGG 59.572 38.462 0.00 0.00 0.00 4.96
1772 1821 6.650390 GTGTTTTACTTCGTTATAGTTGGGGA 59.350 38.462 0.00 0.00 0.00 4.81
1901 1962 9.625747 AAAACCATGATAAAAGGTCATTGTTTT 57.374 25.926 17.82 17.82 46.20 2.43
2050 2117 7.607607 ACATCTGCAATAGAAGTTCATAACACA 59.392 33.333 5.50 0.00 39.30 3.72
2268 2335 7.271511 TGTTACCAAGATTTCAGCAAACAAAT 58.728 30.769 0.00 0.00 0.00 2.32
2418 2485 2.483013 GCCAACGATGCTACTGGTATCA 60.483 50.000 0.00 0.00 36.96 2.15
2523 2590 1.412079 TGCAGATTGGGTGCTTTTGT 58.588 45.000 0.00 0.00 41.78 2.83
2906 2973 5.047802 TCTGCAAGGAATTTGGAATCAAGAC 60.048 40.000 0.00 0.00 36.63 3.01
3094 3352 2.843701 GGCAACTGGGAGATATGTGAG 58.156 52.381 0.00 0.00 0.00 3.51
3186 3444 7.850935 ATCTTCAGATGAATTATTGGCCAAT 57.149 32.000 32.59 32.59 32.68 3.16
3329 3587 5.067153 TGAAACAGTGAGGTTACCACAAATG 59.933 40.000 2.54 8.20 37.01 2.32
3365 3623 8.998814 TGAGAATAGAATTGTAATACCTTGGGA 58.001 33.333 0.00 0.00 0.00 4.37
3431 3689 4.582701 TGACCAACTTTGTAAAGGCATG 57.417 40.909 9.00 0.00 40.31 4.06
3504 3762 3.004839 GCTAGAGATGTGTTATCTCGCCA 59.995 47.826 10.31 1.71 46.74 5.69
3531 3821 3.694072 AGCTAAACACACACACACACATT 59.306 39.130 0.00 0.00 0.00 2.71
3620 3911 3.006537 TGACACAAAGGTAGACAGGTAGC 59.993 47.826 0.00 0.00 0.00 3.58
3650 3941 7.867403 TGAACTTTAGATTTTGTTCTGATTGCC 59.133 33.333 0.00 0.00 39.38 4.52
3733 4024 2.421424 GAGGCGAAGTTACCTAGACGAA 59.579 50.000 0.00 0.00 36.05 3.85
4336 4627 7.936496 TTTGAAGAACACTGCATATCCATTA 57.064 32.000 0.00 0.00 0.00 1.90
4651 4942 4.630894 TTGTGAAATGTGTGTTGACTCC 57.369 40.909 0.00 0.00 0.00 3.85
4663 4954 4.081807 TGTGTTGACTCCATCATCTCTCAG 60.082 45.833 0.00 0.00 37.11 3.35
4699 4991 4.661993 TGCTACTACGCAACAGATTTTG 57.338 40.909 0.00 0.00 36.89 2.44
4729 5021 4.078922 TCTGATACTCCTCTGGTCCAGAAT 60.079 45.833 22.08 12.37 40.18 2.40
4890 5182 3.947834 CGGAGGCACAAGATTTTAAGGAT 59.052 43.478 0.00 0.00 0.00 3.24
5068 5360 7.561251 TCCTCAAATCGGAAGTTAATACATCA 58.439 34.615 0.00 0.00 0.00 3.07
5148 5440 2.785258 CGCGCCTTCTTAACAGCC 59.215 61.111 0.00 0.00 0.00 4.85
5188 5480 4.345859 TCCTGAAGTTAATCACGTTGGT 57.654 40.909 0.00 0.00 0.00 3.67
5228 5520 2.108970 GGGTTCGAAGGAGGACTGTAT 58.891 52.381 0.00 0.00 0.00 2.29
5380 5699 7.469260 CGTAATTACCAATTAACCAACTCTGG 58.531 38.462 10.01 0.00 39.27 3.86
5381 5700 7.414762 CGTAATTACCAATTAACCAACTCTGGG 60.415 40.741 10.01 0.00 38.43 4.45
5383 5702 6.451292 TTACCAATTAACCAACTCTGGGTA 57.549 37.500 0.00 0.00 42.68 3.69
5384 5703 5.530176 ACCAATTAACCAACTCTGGGTAT 57.470 39.130 0.00 0.00 44.69 2.73
5385 5704 5.261216 ACCAATTAACCAACTCTGGGTATG 58.739 41.667 0.00 0.00 44.69 2.39
5386 5705 5.222254 ACCAATTAACCAACTCTGGGTATGT 60.222 40.000 0.00 0.00 44.69 2.29
5387 5706 5.125417 CCAATTAACCAACTCTGGGTATGTG 59.875 44.000 0.00 0.00 44.69 3.21
5388 5707 2.879103 AACCAACTCTGGGTATGTGG 57.121 50.000 0.00 0.00 42.68 4.17
5389 5708 1.271926 AACCAACTCTGGGTATGTGGC 60.272 52.381 0.00 0.00 42.68 5.01
5390 5709 0.620556 CCAACTCTGGGTATGTGGCT 59.379 55.000 0.00 0.00 39.30 4.75
5391 5710 1.679944 CCAACTCTGGGTATGTGGCTG 60.680 57.143 0.00 0.00 39.30 4.85
5392 5711 1.003580 CAACTCTGGGTATGTGGCTGT 59.996 52.381 0.00 0.00 0.00 4.40
5393 5712 1.362224 ACTCTGGGTATGTGGCTGTT 58.638 50.000 0.00 0.00 0.00 3.16
5394 5713 1.003580 ACTCTGGGTATGTGGCTGTTG 59.996 52.381 0.00 0.00 0.00 3.33
5395 5714 1.003580 CTCTGGGTATGTGGCTGTTGT 59.996 52.381 0.00 0.00 0.00 3.32
5396 5715 1.003118 TCTGGGTATGTGGCTGTTGTC 59.997 52.381 0.00 0.00 0.00 3.18
5397 5716 1.003580 CTGGGTATGTGGCTGTTGTCT 59.996 52.381 0.00 0.00 0.00 3.41
5398 5717 1.271325 TGGGTATGTGGCTGTTGTCTG 60.271 52.381 0.00 0.00 0.00 3.51
5429 5748 8.854614 AATATTAGCATCTCCAATTCTGTACC 57.145 34.615 0.00 0.00 0.00 3.34
5633 5952 6.636850 GTGCTGTGGTTTAACAACAGAAATAG 59.363 38.462 30.33 9.35 34.15 1.73
5641 5960 9.447040 GGTTTAACAACAGAAATAGTTCAGTTC 57.553 33.333 10.28 0.12 40.38 3.01
5713 6032 2.510613 ACGTTTACAGGTTCAATGGGG 58.489 47.619 0.00 0.00 0.00 4.96
5958 7555 5.532406 ACATTTGGTGTATGGATACTGATGC 59.468 40.000 0.00 0.00 39.91 3.91
5959 7556 5.372343 TTTGGTGTATGGATACTGATGCT 57.628 39.130 0.00 0.00 34.41 3.79
5960 7557 6.493189 TTTGGTGTATGGATACTGATGCTA 57.507 37.500 0.00 0.00 34.41 3.49
5961 7558 6.686484 TTGGTGTATGGATACTGATGCTAT 57.314 37.500 0.00 0.00 34.41 2.97
6086 7723 4.021981 AGCAAACAGATTAACCTTTGGCTC 60.022 41.667 0.00 0.00 0.00 4.70
6176 7814 7.704472 CCAGTAACATGTCTAGTCAGAAATCTC 59.296 40.741 0.00 0.00 30.85 2.75
6187 7825 9.521841 TCTAGTCAGAAATCTCAGAGAAAACTA 57.478 33.333 3.63 5.72 0.00 2.24
6302 7940 5.472478 CAGTGTACAGAGTCCACAGTAAGTA 59.528 44.000 0.00 0.00 0.00 2.24
6303 7941 5.706369 AGTGTACAGAGTCCACAGTAAGTAG 59.294 44.000 0.00 0.00 0.00 2.57
6337 7975 1.602771 GCCCAGAGTGTTAGACCCC 59.397 63.158 0.00 0.00 0.00 4.95
6339 7977 1.614241 CCCAGAGTGTTAGACCCCGG 61.614 65.000 0.00 0.00 0.00 5.73
6376 8014 7.824289 AGTGACAATTGTTATTAGCTCTAAGCA 59.176 33.333 13.36 0.00 45.56 3.91
6382 8020 2.493713 ATTAGCTCTAAGCACGACCG 57.506 50.000 0.00 0.00 45.56 4.79
6401 8039 3.947834 ACCGCCAAATCCTAATCAGAAAG 59.052 43.478 0.00 0.00 0.00 2.62
6402 8040 3.947834 CCGCCAAATCCTAATCAGAAAGT 59.052 43.478 0.00 0.00 0.00 2.66
6425 8064 1.142748 GCGTGTCCTCTCCATCCAG 59.857 63.158 0.00 0.00 0.00 3.86
6458 8097 4.687483 AGCATTTTAAGTTGCTTCACATGC 59.313 37.500 8.06 6.23 46.71 4.06
6467 8106 3.063510 TGCTTCACATGCTAGCTTTCT 57.936 42.857 17.23 0.00 35.93 2.52
6480 8119 3.439857 AGCTTTCTGCACCTTATGGAA 57.560 42.857 0.81 0.00 45.94 3.53
6491 8131 3.252215 CACCTTATGGAAGTTTGTCGCAA 59.748 43.478 0.81 0.00 37.04 4.85
6636 8277 2.158900 ACCACTCCTGAACAGAACACTG 60.159 50.000 3.19 0.00 37.63 3.66
6663 8304 6.589907 ACACACAATTCAAACTGGAAAGAAAC 59.410 34.615 0.00 0.00 0.00 2.78
6664 8305 6.813152 CACACAATTCAAACTGGAAAGAAACT 59.187 34.615 0.00 0.00 0.00 2.66
6665 8306 7.973388 CACACAATTCAAACTGGAAAGAAACTA 59.027 33.333 0.00 0.00 0.00 2.24
6666 8307 8.527810 ACACAATTCAAACTGGAAAGAAACTAA 58.472 29.630 0.00 0.00 0.00 2.24
6739 8381 5.971763 TGTAAAATGGTTGTTTTGCTCACT 58.028 33.333 0.00 0.00 35.54 3.41
6754 8396 4.862823 ACTAGGCTCCTCCCCGGC 62.863 72.222 0.00 0.00 34.51 6.13
6760 8402 3.470888 CTCCTCCCCGGCGACAAT 61.471 66.667 9.30 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 22 1.229951 TCCCCAGCCACTCCATCTT 60.230 57.895 0.00 0.00 0.00 2.40
75 77 1.338136 GCCGATCTCTTCTCCCCCAA 61.338 60.000 0.00 0.00 0.00 4.12
165 168 1.216444 GCTCGCCTGTGATGAGTGA 59.784 57.895 0.00 0.00 32.32 3.41
494 497 2.147387 AGTCACGTTTCCAGGGGCT 61.147 57.895 0.00 0.00 0.00 5.19
504 509 0.536460 AAAATCGGCCCAGTCACGTT 60.536 50.000 0.00 0.00 0.00 3.99
548 553 1.455383 CGCAACAAGGCTTTCCAGGT 61.455 55.000 0.00 0.00 33.74 4.00
746 755 1.372128 TGAGCGATGGATGCGATCG 60.372 57.895 11.69 11.69 46.08 3.69
761 770 1.517257 GCTGATCCGTCCGTGTGAG 60.517 63.158 0.00 0.00 0.00 3.51
768 777 3.746949 CTGGCTGGCTGATCCGTCC 62.747 68.421 2.00 0.00 37.80 4.79
824 833 0.865769 GAGGACAAAACGCATCGTGT 59.134 50.000 0.00 0.00 39.99 4.49
876 891 1.849823 AGGGTGGCAGAGCTTCCTT 60.850 57.895 0.00 0.00 0.00 3.36
877 892 2.204059 AGGGTGGCAGAGCTTCCT 60.204 61.111 0.00 0.00 0.00 3.36
959 984 1.557371 GTGGAAGAGGGAGGAGGAAAG 59.443 57.143 0.00 0.00 0.00 2.62
1219 1246 2.125912 CGGCTGAACTGGAGACCG 60.126 66.667 0.00 0.00 0.00 4.79
1220 1247 2.435059 GCGGCTGAACTGGAGACC 60.435 66.667 0.00 0.00 0.00 3.85
1230 1257 4.802051 GGAATGGCAGGCGGCTGA 62.802 66.667 39.78 22.33 44.01 4.26
1231 1258 4.809496 AGGAATGGCAGGCGGCTG 62.809 66.667 32.81 32.81 44.01 4.85
1235 1262 1.243342 TGAACAAGGAATGGCAGGCG 61.243 55.000 0.00 0.00 0.00 5.52
1241 1268 0.796312 CCGTCGTGAACAAGGAATGG 59.204 55.000 0.00 0.00 0.00 3.16
1261 1288 3.142796 CGTGCTCCGTTTGAAACAC 57.857 52.632 8.93 0.00 0.00 3.32
1282 1309 0.659957 GTTTGCTGATCTGATCCCGC 59.340 55.000 14.71 16.13 0.00 6.13
1335 1371 2.047179 GTCGAACACCCTCCAGGC 60.047 66.667 0.00 0.00 40.58 4.85
1373 1409 4.194678 ACTCATATAAGGGAAGGGACGA 57.805 45.455 0.00 0.00 0.00 4.20
1375 1411 7.365117 CCATGATACTCATATAAGGGAAGGGAC 60.365 44.444 0.00 0.00 34.28 4.46
1393 1429 6.942532 TTATCCTTTCACTTGCCATGATAC 57.057 37.500 0.00 0.00 0.00 2.24
1433 1480 2.141517 CCAGAGAGTGTCAACTGCAAG 58.858 52.381 0.00 0.00 36.52 4.01
1528 1575 2.340328 GGCATCCACAAACCGTCCC 61.340 63.158 0.00 0.00 0.00 4.46
1640 1687 3.357079 GGCCTCACCGCAACACAG 61.357 66.667 0.00 0.00 0.00 3.66
1771 1820 6.724263 TGTTGCATATATCGTCAACCAAATC 58.276 36.000 14.49 0.00 38.32 2.17
1772 1821 6.691754 TGTTGCATATATCGTCAACCAAAT 57.308 33.333 14.49 0.00 38.32 2.32
1882 1939 9.535878 GGTTAACAAAACAATGACCTTTTATCA 57.464 29.630 8.10 0.00 0.00 2.15
1883 1940 9.758651 AGGTTAACAAAACAATGACCTTTTATC 57.241 29.630 8.10 0.00 32.38 1.75
1884 1941 9.541143 CAGGTTAACAAAACAATGACCTTTTAT 57.459 29.630 8.10 0.00 33.99 1.40
1950 2017 7.923414 AGTTTAGTTCAATTTCTTCGGCTAT 57.077 32.000 0.00 0.00 0.00 2.97
2050 2117 8.658619 AGACCTTCATAGCATCAAGATAAGATT 58.341 33.333 0.00 0.00 0.00 2.40
2268 2335 9.034544 CGATAAAGTCAATGATACATGTTCTGA 57.965 33.333 2.30 0.39 0.00 3.27
2418 2485 1.884067 GCTAAGGACAGCTGCAAACCT 60.884 52.381 15.27 14.43 38.57 3.50
2523 2590 0.324943 GAGGAAGCAGCTGTAACCCA 59.675 55.000 16.64 0.00 0.00 4.51
2906 2973 3.083349 TCCCATCCAGGCACGAGG 61.083 66.667 0.00 0.00 35.39 4.63
3072 3140 3.643320 CTCACATATCTCCCAGTTGCCTA 59.357 47.826 0.00 0.00 0.00 3.93
3094 3352 8.691661 TGAATATTTGATTCTTAAGGCCCTAC 57.308 34.615 0.00 0.00 0.00 3.18
3186 3444 4.967084 TCAGTAAGGTTGCAAGGAAGTA 57.033 40.909 0.00 0.00 0.00 2.24
3329 3587 9.534565 TTACAATTCTATTCTCATGCTACTCAC 57.465 33.333 0.00 0.00 0.00 3.51
3431 3689 8.819643 AACTGTTCAGTAAGTAGATTTCAGTC 57.180 34.615 5.87 0.00 32.48 3.51
3504 3762 0.466543 TGTGTGTGTTTAGCTCCCGT 59.533 50.000 0.00 0.00 0.00 5.28
3565 3855 7.726033 AATCAGATAGTCTACTGTCAACCTT 57.274 36.000 9.20 0.00 36.68 3.50
3620 3911 7.930217 TCAGAACAAAATCTAAAGTTCAGTGG 58.070 34.615 0.00 0.00 42.01 4.00
3650 3941 4.836125 AACATACTGTTTGCAGGACTTG 57.164 40.909 0.00 0.00 46.62 3.16
3733 4024 8.734386 GTTATGAATGGAAGAAAGACACTGATT 58.266 33.333 0.00 0.00 0.00 2.57
4336 4627 2.124570 AGCGCGCATCCTTCCAAT 60.125 55.556 35.10 4.83 0.00 3.16
4348 4639 0.792640 AATCAGTCAGAAACAGCGCG 59.207 50.000 0.00 0.00 0.00 6.86
4408 4699 2.672098 ACATGCTCGGGAGAAGTAGAT 58.328 47.619 0.00 0.00 39.18 1.98
4619 4910 7.351223 ACACACATTTCACAAACAAAAACAAG 58.649 30.769 0.00 0.00 0.00 3.16
4663 4954 9.140286 TGCGTAGTAGCATCAAAATATTATCTC 57.860 33.333 0.00 0.00 42.92 2.75
4699 4991 4.410555 ACCAGAGGAGTATCAGATTTTCCC 59.589 45.833 8.56 2.96 36.25 3.97
4890 5182 0.392461 GCCGATGGGTAACTTCAGCA 60.392 55.000 0.00 0.00 34.97 4.41
5068 5360 6.447084 TCCATCTTCCCCTAGTAAGAAACAAT 59.553 38.462 4.19 0.00 35.47 2.71
5148 5440 7.034685 TCAGGATCATTCTGTATGCATTTTG 57.965 36.000 3.54 0.00 34.06 2.44
5228 5520 2.472695 GTGCTGTCCACAGATTGGTA 57.527 50.000 11.04 0.00 46.97 3.25
5326 5618 4.151335 CGGAAACTGTCAAACTGATCAGAG 59.849 45.833 29.27 16.38 33.15 3.35
5380 5699 2.472695 TCAGACAACAGCCACATACC 57.527 50.000 0.00 0.00 0.00 2.73
5381 5700 3.815401 ACTTTCAGACAACAGCCACATAC 59.185 43.478 0.00 0.00 0.00 2.39
5382 5701 4.085357 ACTTTCAGACAACAGCCACATA 57.915 40.909 0.00 0.00 0.00 2.29
5383 5702 2.936202 ACTTTCAGACAACAGCCACAT 58.064 42.857 0.00 0.00 0.00 3.21
5384 5703 2.418368 ACTTTCAGACAACAGCCACA 57.582 45.000 0.00 0.00 0.00 4.17
5385 5704 6.743575 ATATTACTTTCAGACAACAGCCAC 57.256 37.500 0.00 0.00 0.00 5.01
5386 5705 7.065803 GCTAATATTACTTTCAGACAACAGCCA 59.934 37.037 0.00 0.00 0.00 4.75
5387 5706 7.065803 TGCTAATATTACTTTCAGACAACAGCC 59.934 37.037 0.00 0.00 0.00 4.85
5388 5707 7.974675 TGCTAATATTACTTTCAGACAACAGC 58.025 34.615 0.00 0.00 0.00 4.40
5390 5709 9.890629 AGATGCTAATATTACTTTCAGACAACA 57.109 29.630 0.00 0.00 0.00 3.33
5392 5711 9.547753 GGAGATGCTAATATTACTTTCAGACAA 57.452 33.333 0.00 0.00 0.00 3.18
5393 5712 8.704668 TGGAGATGCTAATATTACTTTCAGACA 58.295 33.333 0.00 0.00 0.00 3.41
5394 5713 9.547753 TTGGAGATGCTAATATTACTTTCAGAC 57.452 33.333 0.00 0.00 0.00 3.51
5633 5952 1.726853 ATGCAGCCGTAGAACTGAAC 58.273 50.000 0.00 0.00 34.20 3.18
5641 5960 1.568612 CCGCCATAATGCAGCCGTAG 61.569 60.000 0.00 0.00 0.00 3.51
5713 6032 4.084537 CCATGTCTCGACACACTGTAAAAC 60.085 45.833 1.26 0.00 45.05 2.43
5852 6181 3.586470 ACCCACACACCAACTCATTAA 57.414 42.857 0.00 0.00 0.00 1.40
5954 7551 7.930865 ACTGAGAACAAGGAGAAATATAGCATC 59.069 37.037 0.00 0.00 0.00 3.91
5955 7552 7.800092 ACTGAGAACAAGGAGAAATATAGCAT 58.200 34.615 0.00 0.00 0.00 3.79
5956 7553 7.187824 ACTGAGAACAAGGAGAAATATAGCA 57.812 36.000 0.00 0.00 0.00 3.49
5957 7554 9.601217 TTTACTGAGAACAAGGAGAAATATAGC 57.399 33.333 0.00 0.00 0.00 2.97
5960 7557 9.442047 CTGTTTACTGAGAACAAGGAGAAATAT 57.558 33.333 0.00 0.00 36.64 1.28
5961 7558 8.429641 ACTGTTTACTGAGAACAAGGAGAAATA 58.570 33.333 0.00 0.00 36.64 1.40
6049 7686 8.530269 AATCTGTTTGCTTCAGAAATCAAATC 57.470 30.769 11.34 7.66 43.65 2.17
6086 7723 6.035435 CAGGTTAAACTCGTCTCATCTCATTG 59.965 42.308 0.00 0.00 0.00 2.82
6176 7814 9.330063 TGCAGACCATATTTATAGTTTTCTCTG 57.670 33.333 0.00 0.00 0.00 3.35
6217 7855 7.603784 CCTTGTTTAATTAGCAGGCTGAATTTT 59.396 33.333 20.86 8.43 0.00 1.82
6226 7864 8.184192 CAGTTCATACCTTGTTTAATTAGCAGG 58.816 37.037 0.00 0.00 0.00 4.85
6302 7940 1.402456 GGGCGTCATATATCGTTCGCT 60.402 52.381 15.00 0.00 42.59 4.93
6303 7941 0.989890 GGGCGTCATATATCGTTCGC 59.010 55.000 10.06 10.06 42.32 4.70
6337 7975 4.794439 TCACTCGCATGTCGGCCG 62.794 66.667 22.12 22.12 39.05 6.13
6339 7977 1.361668 ATTGTCACTCGCATGTCGGC 61.362 55.000 9.16 0.00 39.05 5.54
6348 7986 6.893958 AGAGCTAATAACAATTGTCACTCG 57.106 37.500 12.39 2.41 0.00 4.18
6376 8014 1.208535 TGATTAGGATTTGGCGGTCGT 59.791 47.619 0.00 0.00 0.00 4.34
6382 8020 8.293157 GCTATTACTTTCTGATTAGGATTTGGC 58.707 37.037 0.00 0.00 0.00 4.52
6401 8039 3.305471 GGATGGAGAGGACACGCTATTAC 60.305 52.174 0.00 0.00 0.00 1.89
6402 8040 2.891580 GGATGGAGAGGACACGCTATTA 59.108 50.000 0.00 0.00 0.00 0.98
6425 8064 2.423538 ACTTAAAATGCTCGACATGGCC 59.576 45.455 0.00 0.00 39.60 5.36
6458 8097 4.142609 TCCATAAGGTGCAGAAAGCTAG 57.857 45.455 0.00 0.00 45.94 3.42
6467 8106 2.811431 CGACAAACTTCCATAAGGTGCA 59.189 45.455 0.00 0.00 37.01 4.57
6480 8119 3.705604 CCATCAACTTTTGCGACAAACT 58.294 40.909 4.80 0.00 0.00 2.66
6595 8236 6.424207 AGTGGTAAGCGAGAGAAAACTAAAAG 59.576 38.462 0.00 0.00 0.00 2.27
6601 8242 2.994578 GGAGTGGTAAGCGAGAGAAAAC 59.005 50.000 0.00 0.00 0.00 2.43
6606 8247 1.464734 TCAGGAGTGGTAAGCGAGAG 58.535 55.000 0.00 0.00 0.00 3.20
6607 8248 1.544691 GTTCAGGAGTGGTAAGCGAGA 59.455 52.381 0.00 0.00 0.00 4.04
6608 8249 1.272490 TGTTCAGGAGTGGTAAGCGAG 59.728 52.381 0.00 0.00 0.00 5.03
6610 8251 1.272490 TCTGTTCAGGAGTGGTAAGCG 59.728 52.381 0.00 0.00 0.00 4.68
6636 8277 6.329496 TCTTTCCAGTTTGAATTGTGTGTTC 58.671 36.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.