Multiple sequence alignment - TraesCS6D01G165500

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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 TraesCS6D01G165500 chr6D 100.000 4704 0 0 1 4704 144871277 144875980 0.000000e+00 8687.0
1 TraesCS6D01G165500 chr6D 83.412 211 29 2 4452 4660 53559106 53558900 1.730000e-44 191.0
2 TraesCS6D01G165500 chr6D 100.000 30 0 0 1706 1735 85925798 85925827 6.580000e-04 56.5
3 TraesCS6D01G165500 chr6A 93.589 2059 75 20 50 2082 201047768 201049795 0.000000e+00 3018.0
4 TraesCS6D01G165500 chr6A 95.153 1114 23 3 3292 4403 201085459 201086543 0.000000e+00 1729.0
5 TraesCS6D01G165500 chr6A 90.317 1229 73 24 2077 3295 201084240 201085432 0.000000e+00 1568.0
6 TraesCS6D01G165500 chr6A 89.298 299 18 7 4407 4704 201087274 201087559 3.460000e-96 363.0
7 TraesCS6D01G165500 chr6A 100.000 30 0 0 1705 1734 13808193 13808222 6.580000e-04 56.5
8 TraesCS6D01G165500 chr6A 100.000 29 0 0 1706 1734 374419351 374419323 2.000000e-03 54.7
9 TraesCS6D01G165500 chr6B 97.454 1414 20 4 3292 4704 259077589 259078987 0.000000e+00 2398.0
10 TraesCS6D01G165500 chr6B 92.632 1683 71 21 1620 3295 259075926 259077562 0.000000e+00 2372.0
11 TraesCS6D01G165500 chr6B 92.632 1615 56 27 50 1623 259074174 259075766 0.000000e+00 2265.0
12 TraesCS6D01G165500 chr6B 100.000 29 0 0 1704 1732 57900909 57900937 2.000000e-03 54.7
13 TraesCS6D01G165500 chr4D 83.010 206 25 6 4453 4654 339482252 339482451 1.350000e-40 178.0
14 TraesCS6D01G165500 chr4D 97.959 49 1 0 1 49 139124132 139124180 8.390000e-13 86.1
15 TraesCS6D01G165500 chr4D 100.000 30 0 0 1705 1734 454424375 454424346 6.580000e-04 56.5
16 TraesCS6D01G165500 chr4D 100.000 29 0 0 1706 1734 198483005 198483033 2.000000e-03 54.7
17 TraesCS6D01G165500 chr4B 83.505 194 22 6 4454 4643 419656611 419656798 6.260000e-39 172.0
18 TraesCS6D01G165500 chr3D 82.840 169 24 4 1171 1335 76933444 76933277 3.790000e-31 147.0
19 TraesCS6D01G165500 chr3D 98.077 52 1 0 1 52 90863399 90863450 1.800000e-14 91.6
20 TraesCS6D01G165500 chr3D 100.000 29 0 0 1706 1734 445808506 445808478 2.000000e-03 54.7
21 TraesCS6D01G165500 chr3B 83.230 161 25 2 1176 1335 123472945 123472786 3.790000e-31 147.0
22 TraesCS6D01G165500 chr3B 92.000 50 4 0 4407 4456 636736854 636736805 2.350000e-08 71.3
23 TraesCS6D01G165500 chr3A 82.500 160 23 4 1191 1346 91024901 91024743 8.210000e-28 135.0
24 TraesCS6D01G165500 chr1D 96.774 62 2 0 1041 1102 118888606 118888545 2.320000e-18 104.0
25 TraesCS6D01G165500 chr1D 100.000 51 0 0 1 51 125693560 125693510 1.390000e-15 95.3
26 TraesCS6D01G165500 chr1D 100.000 51 0 0 1 51 486282378 486282428 1.390000e-15 95.3
27 TraesCS6D01G165500 chr1D 98.148 54 0 1 1 53 147001635 147001582 5.010000e-15 93.5
28 TraesCS6D01G165500 chr1D 93.220 59 2 1 1 59 331479125 331479181 8.390000e-13 86.1
29 TraesCS6D01G165500 chr1D 100.000 28 0 0 1704 1731 106956491 106956464 9.000000e-03 52.8
30 TraesCS6D01G165500 chr1A 96.774 62 2 0 1041 1102 130912848 130912787 2.320000e-18 104.0
31 TraesCS6D01G165500 chr7D 98.182 55 1 0 1 55 350502089 350502035 3.870000e-16 97.1
32 TraesCS6D01G165500 chr1B 96.429 56 2 0 1041 1096 180679146 180679091 5.010000e-15 93.5
33 TraesCS6D01G165500 chr1B 96.429 56 2 0 1041 1096 180687313 180687258 5.010000e-15 93.5
34 TraesCS6D01G165500 chr5D 93.548 62 2 2 1 61 551685042 551685102 1.800000e-14 91.6
35 TraesCS6D01G165500 chr2D 98.077 52 1 0 1 52 350668405 350668456 1.800000e-14 91.6
36 TraesCS6D01G165500 chr5A 80.833 120 14 6 4449 4565 593477778 593477891 8.390000e-13 86.1
37 TraesCS6D01G165500 chr2B 83.333 90 9 3 4448 4537 487240145 487240228 1.400000e-10 78.7
38 TraesCS6D01G165500 chr5B 87.879 66 7 1 4449 4514 367209041 367209105 5.050000e-10 76.8
39 TraesCS6D01G165500 chr7A 100.000 29 0 0 1706 1734 522998839 522998811 2.000000e-03 54.7


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 TraesCS6D01G165500 chr6D 144871277 144875980 4703 False 8687 8687 100.000000 1 4704 1 chr6D.!!$F2 4703
1 TraesCS6D01G165500 chr6A 201047768 201049795 2027 False 3018 3018 93.589000 50 2082 1 chr6A.!!$F2 2032
2 TraesCS6D01G165500 chr6A 201084240 201087559 3319 False 1220 1729 91.589333 2077 4704 3 chr6A.!!$F3 2627
3 TraesCS6D01G165500 chr6B 259074174 259078987 4813 False 2345 2398 94.239333 50 4704 3 chr6B.!!$F2 4654

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
147 148 0.250901 AGGTCACTTCACCACCATGC 60.251 55.0 0.00 0.0 39.16 4.06 F
728 779 0.472734 AGCTCTCCACTCACCCTTGT 60.473 55.0 0.00 0.0 0.00 3.16 F
2658 2906 0.609957 TAGTCGGACACGGACATGGT 60.610 55.0 11.27 0.0 41.39 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1434 1506 0.320771 CTGCACCGCTCTAACAACCT 60.321 55.0 0.00 0.0 0.0 3.50 R
2680 2928 0.249868 CTTGCCAAGTCAGACACCGA 60.250 55.0 2.66 0.0 0.0 4.69 R
3788 4071 1.181786 AGCAGAGAGAGCACCACTAC 58.818 55.0 0.00 0.0 0.0 2.73 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
17 18 3.012722 TAACCCGGCCCTTCCTGG 61.013 66.667 0.00 0.00 44.15 4.45
26 27 4.410400 CCTTCCTGGGCGGGTGAC 62.410 72.222 0.00 0.00 0.00 3.67
27 28 3.322466 CTTCCTGGGCGGGTGACT 61.322 66.667 0.00 0.00 0.00 3.41
28 29 3.316573 CTTCCTGGGCGGGTGACTC 62.317 68.421 0.00 0.00 0.00 3.36
31 32 4.087892 CTGGGCGGGTGACTCCAG 62.088 72.222 0.00 0.00 40.46 3.86
32 33 4.954118 TGGGCGGGTGACTCCAGT 62.954 66.667 0.00 0.00 38.11 4.00
33 34 2.682494 GGGCGGGTGACTCCAGTA 60.682 66.667 0.00 0.00 38.11 2.74
34 35 2.722201 GGGCGGGTGACTCCAGTAG 61.722 68.421 0.00 0.00 38.11 2.57
35 36 1.982938 GGCGGGTGACTCCAGTAGT 60.983 63.158 0.00 0.00 42.80 2.73
36 37 1.542187 GGCGGGTGACTCCAGTAGTT 61.542 60.000 0.00 0.00 39.07 2.24
37 38 1.180029 GCGGGTGACTCCAGTAGTTA 58.820 55.000 0.00 0.00 39.07 2.24
38 39 1.755380 GCGGGTGACTCCAGTAGTTAT 59.245 52.381 0.00 0.00 39.07 1.89
39 40 2.954318 GCGGGTGACTCCAGTAGTTATA 59.046 50.000 0.00 0.00 39.07 0.98
40 41 3.573110 GCGGGTGACTCCAGTAGTTATAT 59.427 47.826 0.00 0.00 39.07 0.86
41 42 4.321082 GCGGGTGACTCCAGTAGTTATATC 60.321 50.000 0.00 0.00 39.07 1.63
42 43 4.217983 CGGGTGACTCCAGTAGTTATATCC 59.782 50.000 0.00 0.00 39.07 2.59
43 44 4.527427 GGGTGACTCCAGTAGTTATATCCC 59.473 50.000 0.00 0.00 39.07 3.85
44 45 4.527427 GGTGACTCCAGTAGTTATATCCCC 59.473 50.000 0.00 0.00 39.07 4.81
45 46 5.145564 GTGACTCCAGTAGTTATATCCCCA 58.854 45.833 0.00 0.00 39.07 4.96
46 47 5.601313 GTGACTCCAGTAGTTATATCCCCAA 59.399 44.000 0.00 0.00 39.07 4.12
47 48 5.601313 TGACTCCAGTAGTTATATCCCCAAC 59.399 44.000 0.00 0.00 39.07 3.77
48 49 5.535029 ACTCCAGTAGTTATATCCCCAACA 58.465 41.667 0.00 0.00 33.35 3.33
90 91 4.612943 GACTTCTTCTATCGGGCTACTTG 58.387 47.826 0.00 0.00 0.00 3.16
147 148 0.250901 AGGTCACTTCACCACCATGC 60.251 55.000 0.00 0.00 39.16 4.06
197 198 3.067180 CCTTTGCTTATGTGCCGATGATT 59.933 43.478 0.00 0.00 0.00 2.57
379 380 6.432472 TCATTATTGCAACAATGTCACCTACA 59.568 34.615 25.39 5.41 43.86 2.74
382 383 5.528043 TTGCAACAATGTCACCTACAAAT 57.472 34.783 0.00 0.00 42.70 2.32
425 426 6.011981 ACATTCCCCTTTTCCTACATAGACAA 60.012 38.462 0.00 0.00 0.00 3.18
431 432 6.540189 CCCTTTTCCTACATAGACAATGACAG 59.460 42.308 0.00 0.00 39.07 3.51
550 577 2.678336 GCTACAATGGAGAAAAGGTCGG 59.322 50.000 0.00 0.00 0.00 4.79
728 779 0.472734 AGCTCTCCACTCACCCTTGT 60.473 55.000 0.00 0.00 0.00 3.16
1108 1173 2.694213 AGAAGAAGAAGAAGAAGCCGC 58.306 47.619 0.00 0.00 0.00 6.53
1109 1174 1.735018 GAAGAAGAAGAAGAAGCCGCC 59.265 52.381 0.00 0.00 0.00 6.13
1110 1175 0.980423 AGAAGAAGAAGAAGCCGCCT 59.020 50.000 0.00 0.00 0.00 5.52
1429 1501 2.608090 GCAGCCGGTTTTGATCTAGTAC 59.392 50.000 1.90 0.00 0.00 2.73
1430 1502 3.679083 GCAGCCGGTTTTGATCTAGTACT 60.679 47.826 1.90 0.00 0.00 2.73
1431 1503 3.865745 CAGCCGGTTTTGATCTAGTACTG 59.134 47.826 5.39 0.00 0.00 2.74
1432 1504 3.118738 AGCCGGTTTTGATCTAGTACTGG 60.119 47.826 5.39 1.87 38.11 4.00
1433 1505 3.369157 GCCGGTTTTGATCTAGTACTGGT 60.369 47.826 5.39 0.00 37.53 4.00
1434 1506 4.142093 GCCGGTTTTGATCTAGTACTGGTA 60.142 45.833 5.39 0.00 37.53 3.25
1510 1582 4.640805 TCGTACAAAGATTCAGTTTCGC 57.359 40.909 0.00 0.00 0.00 4.70
1559 1632 6.630413 GCTGATTCTTGTTCTACATAGTGGGA 60.630 42.308 0.00 0.00 0.00 4.37
1627 1863 2.092103 TGGTCCTTTGCTTGTACCACTT 60.092 45.455 0.00 0.00 35.34 3.16
1659 1895 4.574828 ACCATTAACGATGCCAATAGTGAC 59.425 41.667 0.00 0.00 34.25 3.67
1725 1961 9.968870 GAGGTGTCTTATATTACTTTACAGAGG 57.031 37.037 0.00 0.00 0.00 3.69
1726 1962 8.925338 AGGTGTCTTATATTACTTTACAGAGGG 58.075 37.037 0.00 0.00 0.00 4.30
1727 1963 8.921205 GGTGTCTTATATTACTTTACAGAGGGA 58.079 37.037 0.00 0.00 0.00 4.20
2295 2536 6.371548 TCCCGTGATCAATCTAAGAAAAAGTG 59.628 38.462 0.00 0.00 0.00 3.16
2302 2543 7.383102 TCAATCTAAGAAAAAGTGGCTCATC 57.617 36.000 0.00 0.00 0.00 2.92
2315 2556 2.042464 GGCTCATCCCATAGTCTCACA 58.958 52.381 0.00 0.00 0.00 3.58
2316 2557 2.224161 GGCTCATCCCATAGTCTCACAC 60.224 54.545 0.00 0.00 0.00 3.82
2319 2560 4.214310 CTCATCCCATAGTCTCACACTCT 58.786 47.826 0.00 0.00 36.43 3.24
2321 2562 3.739401 TCCCATAGTCTCACACTCTCA 57.261 47.619 0.00 0.00 36.43 3.27
2322 2563 3.357203 TCCCATAGTCTCACACTCTCAC 58.643 50.000 0.00 0.00 36.43 3.51
2323 2564 2.098280 CCCATAGTCTCACACTCTCACG 59.902 54.545 0.00 0.00 36.43 4.35
2431 2673 9.520515 AGGTTTACATATATAGATGCAAAAGGG 57.479 33.333 7.26 0.00 0.00 3.95
2452 2697 5.084519 GGGGGAGAAGAAACCAGTATTTTT 58.915 41.667 0.00 0.00 0.00 1.94
2471 2716 1.927487 TTCAGCTCATGTGGCCAAAT 58.073 45.000 7.24 3.97 0.00 2.32
2491 2736 9.455847 GCCAAATTAGCTTTTATAATGAGAGTG 57.544 33.333 0.00 0.00 0.00 3.51
2509 2754 5.026121 AGAGTGATGATAGAGTGGGAACAA 58.974 41.667 0.00 0.00 46.06 2.83
2557 2802 6.072508 ACGATTGATGTATGCTCTTTGTGTTT 60.073 34.615 0.00 0.00 0.00 2.83
2559 2804 7.201291 CGATTGATGTATGCTCTTTGTGTTTTG 60.201 37.037 0.00 0.00 0.00 2.44
2649 2896 5.573337 ATTACCTAGTGTTAGTCGGACAC 57.427 43.478 11.27 1.18 45.92 3.67
2658 2906 0.609957 TAGTCGGACACGGACATGGT 60.610 55.000 11.27 0.00 41.39 3.55
2693 2941 1.616865 TCGGATTTCGGTGTCTGACTT 59.383 47.619 9.51 0.00 39.77 3.01
2699 2947 0.249868 TCGGTGTCTGACTTGGCAAG 60.250 55.000 25.06 25.06 0.00 4.01
2703 2951 3.679917 CGGTGTCTGACTTGGCAAGATAT 60.680 47.826 32.50 11.53 0.00 1.63
2722 2970 7.230849 AGATATTTTTGGACACAGCAAATGA 57.769 32.000 0.00 0.00 0.00 2.57
2723 2971 7.092716 AGATATTTTTGGACACAGCAAATGAC 58.907 34.615 0.00 0.00 0.00 3.06
2724 2972 4.462508 TTTTTGGACACAGCAAATGACA 57.537 36.364 0.00 0.00 0.00 3.58
2725 2973 4.669206 TTTTGGACACAGCAAATGACAT 57.331 36.364 0.00 0.00 0.00 3.06
2726 2974 4.669206 TTTGGACACAGCAAATGACATT 57.331 36.364 0.00 0.00 0.00 2.71
2727 2975 4.669206 TTGGACACAGCAAATGACATTT 57.331 36.364 7.62 7.62 0.00 2.32
2728 2976 4.669206 TGGACACAGCAAATGACATTTT 57.331 36.364 10.77 0.00 0.00 1.82
2729 2977 5.021033 TGGACACAGCAAATGACATTTTT 57.979 34.783 10.77 0.20 0.00 1.94
2762 3010 5.728351 AATCACATTTGTTATACGGACGG 57.272 39.130 0.00 0.00 0.00 4.79
2769 3017 7.224362 CACATTTGTTATACGGACGGGTATAAA 59.776 37.037 13.86 5.54 43.32 1.40
2770 3018 7.933033 ACATTTGTTATACGGACGGGTATAAAT 59.067 33.333 13.86 7.02 43.32 1.40
2773 3021 6.454795 TGTTATACGGACGGGTATAAATTCC 58.545 40.000 13.86 6.31 43.32 3.01
2779 3027 2.798847 GACGGGTATAAATTCCGACAGC 59.201 50.000 9.30 0.00 45.96 4.40
2792 3040 4.848562 TCCGACAGCGATTCATACTATT 57.151 40.909 0.00 0.00 40.82 1.73
2794 3042 4.277423 TCCGACAGCGATTCATACTATTGA 59.723 41.667 0.00 0.00 40.82 2.57
2797 3045 5.687730 CGACAGCGATTCATACTATTGAGTT 59.312 40.000 0.00 0.00 40.82 3.01
2935 3189 3.248024 CCCCCTTGCATCTAGTATGGTA 58.752 50.000 0.00 0.00 0.00 3.25
2998 3252 5.169992 AGATGATGGTCTTGATGTTGACA 57.830 39.130 0.00 0.00 35.11 3.58
3024 3278 2.968574 TGATGATGAGCTAGAGGAACCC 59.031 50.000 0.00 0.00 0.00 4.11
3213 3467 0.598562 CTACACTGGCTGACGTCACT 59.401 55.000 15.76 0.00 0.00 3.41
3255 3509 9.845740 TGTAATCATGCTACAACCTATACAAAT 57.154 29.630 5.33 0.00 0.00 2.32
3283 3537 7.484993 TCAAAATGATCAACCATTCCTCATT 57.515 32.000 0.00 0.00 37.98 2.57
3295 3549 6.993079 ACCATTCCTCATTTTCTGGTTAAAC 58.007 36.000 0.00 0.00 33.30 2.01
3296 3550 6.782494 ACCATTCCTCATTTTCTGGTTAAACT 59.218 34.615 0.00 0.00 33.30 2.66
3297 3551 7.092716 CCATTCCTCATTTTCTGGTTAAACTG 58.907 38.462 0.00 0.00 0.00 3.16
3298 3552 7.039784 CCATTCCTCATTTTCTGGTTAAACTGA 60.040 37.037 0.00 0.00 0.00 3.41
3299 3553 6.877611 TCCTCATTTTCTGGTTAAACTGAC 57.122 37.500 0.00 0.00 0.00 3.51
3300 3554 6.361433 TCCTCATTTTCTGGTTAAACTGACA 58.639 36.000 0.00 0.00 0.00 3.58
3304 3558 8.684386 TCATTTTCTGGTTAAACTGACATGTA 57.316 30.769 0.00 0.00 0.00 2.29
3305 3559 9.295825 TCATTTTCTGGTTAAACTGACATGTAT 57.704 29.630 0.00 0.00 0.00 2.29
3436 3719 4.473477 ACTAAGGAAGGAGAAACCATCG 57.527 45.455 0.00 0.00 42.04 3.84
3489 3772 1.077212 CCAGCAAGGACCATGGAGG 60.077 63.158 21.47 3.63 41.22 4.30
3946 4229 6.434028 AGTTGTATTATCACCATGCACAGTTT 59.566 34.615 0.00 0.00 0.00 2.66
3963 4246 7.384115 TGCACAGTTTATAATCGGTAAGCTATC 59.616 37.037 0.00 0.00 0.00 2.08
4300 4585 1.471287 ACGATTCTTCATCCGACGTGA 59.529 47.619 0.00 0.00 0.00 4.35
4658 5670 2.464157 AGCTGTGAGGAGTTTGCTAC 57.536 50.000 0.00 0.00 0.00 3.58
4667 5679 2.231721 AGGAGTTTGCTACCGAGACTTC 59.768 50.000 0.00 0.00 0.00 3.01
4668 5680 2.029290 GGAGTTTGCTACCGAGACTTCA 60.029 50.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.012722 CCAGGAAGGGCCGGGTTA 61.013 66.667 2.18 0.00 45.94 2.85
9 10 4.410400 GTCACCCGCCCAGGAAGG 62.410 72.222 0.00 0.00 45.00 3.46
10 11 3.316573 GAGTCACCCGCCCAGGAAG 62.317 68.421 0.00 0.00 45.00 3.46
11 12 3.319198 GAGTCACCCGCCCAGGAA 61.319 66.667 0.00 0.00 45.00 3.36
14 15 4.087892 CTGGAGTCACCCGCCCAG 62.088 72.222 0.00 0.00 40.01 4.45
15 16 3.533079 TACTGGAGTCACCCGCCCA 62.533 63.158 0.00 0.00 38.00 5.36
16 17 2.682494 TACTGGAGTCACCCGCCC 60.682 66.667 0.00 0.00 38.00 6.13
17 18 1.542187 AACTACTGGAGTCACCCGCC 61.542 60.000 0.00 0.00 37.44 6.13
18 19 1.180029 TAACTACTGGAGTCACCCGC 58.820 55.000 0.00 0.00 37.44 6.13
19 20 4.217983 GGATATAACTACTGGAGTCACCCG 59.782 50.000 0.00 0.00 37.44 5.28
20 21 4.527427 GGGATATAACTACTGGAGTCACCC 59.473 50.000 0.00 0.00 37.44 4.61
21 22 4.527427 GGGGATATAACTACTGGAGTCACC 59.473 50.000 0.00 0.00 37.44 4.02
22 23 5.145564 TGGGGATATAACTACTGGAGTCAC 58.854 45.833 0.00 0.00 37.44 3.67
23 24 5.412617 TGGGGATATAACTACTGGAGTCA 57.587 43.478 0.00 0.00 37.44 3.41
24 25 5.601313 TGTTGGGGATATAACTACTGGAGTC 59.399 44.000 0.00 0.00 37.44 3.36
25 26 5.535029 TGTTGGGGATATAACTACTGGAGT 58.465 41.667 0.00 0.00 41.56 3.85
26 27 5.012148 CCTGTTGGGGATATAACTACTGGAG 59.988 48.000 0.00 0.00 0.00 3.86
27 28 4.905456 CCTGTTGGGGATATAACTACTGGA 59.095 45.833 0.00 0.00 0.00 3.86
28 29 4.905456 TCCTGTTGGGGATATAACTACTGG 59.095 45.833 0.00 0.00 35.33 4.00
29 30 5.602978 ACTCCTGTTGGGGATATAACTACTG 59.397 44.000 0.00 0.00 37.25 2.74
30 31 5.789535 ACTCCTGTTGGGGATATAACTACT 58.210 41.667 0.00 0.00 37.25 2.57
31 32 7.793948 ATACTCCTGTTGGGGATATAACTAC 57.206 40.000 0.00 0.00 37.25 2.73
32 33 8.808240 AAATACTCCTGTTGGGGATATAACTA 57.192 34.615 0.00 0.00 37.25 2.24
33 34 7.707467 AAATACTCCTGTTGGGGATATAACT 57.293 36.000 0.00 0.00 37.25 2.24
34 35 7.996644 TCAAAATACTCCTGTTGGGGATATAAC 59.003 37.037 0.00 0.00 37.25 1.89
35 36 8.108378 TCAAAATACTCCTGTTGGGGATATAA 57.892 34.615 0.00 0.00 37.25 0.98
36 37 7.699709 TCAAAATACTCCTGTTGGGGATATA 57.300 36.000 0.00 0.00 37.25 0.86
37 38 6.590656 TCAAAATACTCCTGTTGGGGATAT 57.409 37.500 0.00 0.00 37.25 1.63
38 39 6.590656 ATCAAAATACTCCTGTTGGGGATA 57.409 37.500 0.00 0.00 37.25 2.59
39 40 4.946160 TCAAAATACTCCTGTTGGGGAT 57.054 40.909 0.00 0.00 37.25 3.85
40 41 4.946160 ATCAAAATACTCCTGTTGGGGA 57.054 40.909 0.00 0.00 37.25 4.81
41 42 4.381932 GCAATCAAAATACTCCTGTTGGGG 60.382 45.833 0.00 0.00 40.50 4.96
42 43 4.675146 CGCAATCAAAATACTCCTGTTGGG 60.675 45.833 0.00 0.00 0.00 4.12
43 44 4.155826 TCGCAATCAAAATACTCCTGTTGG 59.844 41.667 0.00 0.00 0.00 3.77
44 45 5.088739 GTCGCAATCAAAATACTCCTGTTG 58.911 41.667 0.00 0.00 0.00 3.33
45 46 4.142902 CGTCGCAATCAAAATACTCCTGTT 60.143 41.667 0.00 0.00 0.00 3.16
46 47 3.370978 CGTCGCAATCAAAATACTCCTGT 59.629 43.478 0.00 0.00 0.00 4.00
47 48 3.616821 TCGTCGCAATCAAAATACTCCTG 59.383 43.478 0.00 0.00 0.00 3.86
48 49 3.617263 GTCGTCGCAATCAAAATACTCCT 59.383 43.478 0.00 0.00 0.00 3.69
147 148 4.817063 CTCATTGTTGCCCGCGCG 62.817 66.667 25.67 25.67 38.08 6.86
197 198 4.201970 GCAAACACAAGTACCAACAGCTAA 60.202 41.667 0.00 0.00 0.00 3.09
303 304 2.680312 ATCATCACAAGCGTGCTAGT 57.320 45.000 0.00 0.00 43.28 2.57
379 380 6.808321 TGTGATGGTAGAGCTAGGTTATTT 57.192 37.500 0.00 0.00 0.00 1.40
382 383 5.304614 GGAATGTGATGGTAGAGCTAGGTTA 59.695 44.000 0.00 0.00 0.00 2.85
425 426 0.401356 TCATGGTGTGTGGCTGTCAT 59.599 50.000 0.00 0.00 0.00 3.06
550 577 3.368236 CCTTTTTCTCGAGACGAATCACC 59.632 47.826 16.36 0.00 34.74 4.02
603 630 8.119226 TGTTTGAAGTGTTTTTCTTTGTTGTTG 58.881 29.630 0.00 0.00 0.00 3.33
728 779 0.259065 TGGCAGGTTGGGTTGTGTTA 59.741 50.000 0.00 0.00 0.00 2.41
849 909 1.715785 GGAGGAGAAGAGGAGATGGG 58.284 60.000 0.00 0.00 0.00 4.00
1108 1173 4.493747 GGACGAGGACGCGGAAGG 62.494 72.222 12.47 0.00 43.96 3.46
1109 1174 4.831307 CGGACGAGGACGCGGAAG 62.831 72.222 12.47 0.00 43.96 3.46
1429 1501 1.549170 ACCGCTCTAACAACCTACCAG 59.451 52.381 0.00 0.00 0.00 4.00
1430 1502 1.274167 CACCGCTCTAACAACCTACCA 59.726 52.381 0.00 0.00 0.00 3.25
1431 1503 2.005560 GCACCGCTCTAACAACCTACC 61.006 57.143 0.00 0.00 0.00 3.18
1432 1504 1.337447 TGCACCGCTCTAACAACCTAC 60.337 52.381 0.00 0.00 0.00 3.18
1433 1505 0.970640 TGCACCGCTCTAACAACCTA 59.029 50.000 0.00 0.00 0.00 3.08
1434 1506 0.320771 CTGCACCGCTCTAACAACCT 60.321 55.000 0.00 0.00 0.00 3.50
1510 1582 3.184581 GTCTCACTAACTGCAACCTTTCG 59.815 47.826 0.00 0.00 0.00 3.46
1559 1632 3.139025 CCCCACATCCTAAAGACCATGAT 59.861 47.826 0.00 0.00 0.00 2.45
1638 1874 4.506288 TCGTCACTATTGGCATCGTTAATG 59.494 41.667 0.00 0.00 38.50 1.90
1659 1895 0.515564 CAAGCTTTACCCGTTGGTCG 59.484 55.000 0.00 0.00 43.06 4.79
1709 1945 9.810870 CCTAGTACTCCCTCTGTAAAGTAATAT 57.189 37.037 0.00 0.00 28.17 1.28
1710 1946 8.785859 ACCTAGTACTCCCTCTGTAAAGTAATA 58.214 37.037 0.00 0.00 0.00 0.98
1711 1947 7.650660 ACCTAGTACTCCCTCTGTAAAGTAAT 58.349 38.462 0.00 0.00 0.00 1.89
1714 1950 5.533333 ACCTAGTACTCCCTCTGTAAAGT 57.467 43.478 0.00 0.00 0.00 2.66
1715 1951 6.631962 CAAACCTAGTACTCCCTCTGTAAAG 58.368 44.000 0.00 0.00 0.00 1.85
1716 1952 5.046807 GCAAACCTAGTACTCCCTCTGTAAA 60.047 44.000 0.00 0.00 0.00 2.01
1717 1953 4.465305 GCAAACCTAGTACTCCCTCTGTAA 59.535 45.833 0.00 0.00 0.00 2.41
1718 1954 4.021916 GCAAACCTAGTACTCCCTCTGTA 58.978 47.826 0.00 0.00 0.00 2.74
1719 1955 2.832733 GCAAACCTAGTACTCCCTCTGT 59.167 50.000 0.00 0.00 0.00 3.41
1720 1956 3.100671 AGCAAACCTAGTACTCCCTCTG 58.899 50.000 0.00 0.00 0.00 3.35
1721 1957 3.476485 AGCAAACCTAGTACTCCCTCT 57.524 47.619 0.00 0.00 0.00 3.69
1722 1958 7.541916 AATATAGCAAACCTAGTACTCCCTC 57.458 40.000 0.00 0.00 0.00 4.30
1723 1959 7.932683 AAATATAGCAAACCTAGTACTCCCT 57.067 36.000 0.00 0.00 0.00 4.20
1724 1960 9.654663 CATAAATATAGCAAACCTAGTACTCCC 57.345 37.037 0.00 0.00 0.00 4.30
1725 1961 9.152595 GCATAAATATAGCAAACCTAGTACTCC 57.847 37.037 0.00 0.00 0.00 3.85
1726 1962 9.706691 TGCATAAATATAGCAAACCTAGTACTC 57.293 33.333 0.00 0.00 34.97 2.59
2223 2464 6.170506 CAAATACACCTACTGGCAGAAAGTA 58.829 40.000 23.66 15.31 36.63 2.24
2295 2536 2.042464 TGTGAGACTATGGGATGAGCC 58.958 52.381 0.00 0.00 0.00 4.70
2302 2543 2.098280 CGTGAGAGTGTGAGACTATGGG 59.902 54.545 0.00 0.00 33.83 4.00
2319 2560 9.074576 ACATAGATTACCTTACATGTATCGTGA 57.925 33.333 6.36 3.34 0.00 4.35
2364 2606 7.257722 CAACACTACAGAACCTCAACAAATTT 58.742 34.615 0.00 0.00 0.00 1.82
2370 2612 3.467803 AGCAACACTACAGAACCTCAAC 58.532 45.455 0.00 0.00 0.00 3.18
2429 2671 4.317530 AAATACTGGTTTCTTCTCCCCC 57.682 45.455 0.00 0.00 0.00 5.40
2452 2697 1.927487 ATTTGGCCACATGAGCTGAA 58.073 45.000 3.88 0.00 0.00 3.02
2453 2698 1.927487 AATTTGGCCACATGAGCTGA 58.073 45.000 3.88 0.00 0.00 4.26
2491 2736 8.738645 ATAACTTTTGTTCCCACTCTATCATC 57.261 34.615 0.00 0.00 42.45 2.92
2535 2780 7.436118 ACAAAACACAAAGAGCATACATCAAT 58.564 30.769 0.00 0.00 0.00 2.57
2576 2823 8.998377 TGAAACAGATTTTCTCGTATTGAATCA 58.002 29.630 0.00 0.00 30.98 2.57
2630 2877 1.808945 CGTGTCCGACTAACACTAGGT 59.191 52.381 0.00 0.00 43.83 3.08
2643 2890 1.301401 ACAACCATGTCCGTGTCCG 60.301 57.895 0.00 0.00 33.41 4.79
2667 2915 1.201647 GACACCGAAATCCGAGTCAGA 59.798 52.381 0.00 0.00 40.38 3.27
2669 2917 1.067846 CAGACACCGAAATCCGAGTCA 60.068 52.381 0.00 0.00 41.89 3.41
2680 2928 0.249868 CTTGCCAAGTCAGACACCGA 60.250 55.000 2.66 0.00 0.00 4.69
2681 2929 0.249868 TCTTGCCAAGTCAGACACCG 60.250 55.000 4.04 0.00 0.00 4.94
2693 2941 4.321899 GCTGTGTCCAAAAATATCTTGCCA 60.322 41.667 0.00 0.00 0.00 4.92
2699 2947 6.867816 TGTCATTTGCTGTGTCCAAAAATATC 59.132 34.615 0.00 0.00 35.97 1.63
2703 2951 4.462508 TGTCATTTGCTGTGTCCAAAAA 57.537 36.364 0.00 0.00 35.97 1.94
2728 2976 5.355596 ACAAATGTGATTTCCTCGCAAAAA 58.644 33.333 0.00 0.00 46.90 1.94
2729 2977 4.942852 ACAAATGTGATTTCCTCGCAAAA 58.057 34.783 0.00 0.00 46.90 2.44
2730 2978 4.582701 ACAAATGTGATTTCCTCGCAAA 57.417 36.364 0.00 0.00 46.90 3.68
2731 2979 4.582701 AACAAATGTGATTTCCTCGCAA 57.417 36.364 0.00 0.00 46.90 4.85
2733 2981 5.901884 CGTATAACAAATGTGATTTCCTCGC 59.098 40.000 0.00 0.00 34.82 5.03
2734 2982 6.256975 TCCGTATAACAAATGTGATTTCCTCG 59.743 38.462 0.00 0.00 0.00 4.63
2735 2983 7.407337 GTCCGTATAACAAATGTGATTTCCTC 58.593 38.462 0.00 0.00 0.00 3.71
2736 2984 6.036735 CGTCCGTATAACAAATGTGATTTCCT 59.963 38.462 0.00 0.00 0.00 3.36
2737 2985 6.189567 CGTCCGTATAACAAATGTGATTTCC 58.810 40.000 0.00 0.00 0.00 3.13
2738 2986 6.189567 CCGTCCGTATAACAAATGTGATTTC 58.810 40.000 0.00 0.00 0.00 2.17
2739 2987 5.065474 CCCGTCCGTATAACAAATGTGATTT 59.935 40.000 0.00 0.00 0.00 2.17
2740 2988 4.573201 CCCGTCCGTATAACAAATGTGATT 59.427 41.667 0.00 0.00 0.00 2.57
2741 2989 4.124238 CCCGTCCGTATAACAAATGTGAT 58.876 43.478 0.00 0.00 0.00 3.06
2742 2990 3.055963 ACCCGTCCGTATAACAAATGTGA 60.056 43.478 0.00 0.00 0.00 3.58
2743 2991 3.264104 ACCCGTCCGTATAACAAATGTG 58.736 45.455 0.00 0.00 0.00 3.21
2762 3010 4.748102 TGAATCGCTGTCGGAATTTATACC 59.252 41.667 0.00 0.00 36.13 2.73
2769 3017 3.735237 AGTATGAATCGCTGTCGGAAT 57.265 42.857 0.00 0.00 36.13 3.01
2770 3018 4.848562 ATAGTATGAATCGCTGTCGGAA 57.151 40.909 0.00 0.00 36.13 4.30
2773 3021 5.215903 ACTCAATAGTATGAATCGCTGTCG 58.784 41.667 0.00 0.00 32.84 4.35
2776 3024 6.346439 GCAGAACTCAATAGTATGAATCGCTG 60.346 42.308 0.00 0.00 33.75 5.18
2779 3027 5.985530 TGGCAGAACTCAATAGTATGAATCG 59.014 40.000 0.00 0.00 33.75 3.34
2811 3059 1.935300 GCAGTTCTACACGGACACCAG 60.935 57.143 0.00 0.00 0.00 4.00
2812 3060 0.032952 GCAGTTCTACACGGACACCA 59.967 55.000 0.00 0.00 0.00 4.17
2920 3168 9.480861 AGAGCTAATTATACCATACTAGATGCA 57.519 33.333 0.00 0.00 0.00 3.96
2921 3169 9.743057 CAGAGCTAATTATACCATACTAGATGC 57.257 37.037 0.00 0.00 0.00 3.91
2922 3170 9.743057 GCAGAGCTAATTATACCATACTAGATG 57.257 37.037 0.00 0.00 0.00 2.90
2923 3171 9.480861 TGCAGAGCTAATTATACCATACTAGAT 57.519 33.333 0.00 0.00 0.00 1.98
2998 3252 2.905085 CCTCTAGCTCATCATCACCCAT 59.095 50.000 0.00 0.00 0.00 4.00
3024 3278 2.349590 TCAACTTCATGTCCATGCTCG 58.650 47.619 2.33 0.00 38.65 5.03
3255 3509 9.033711 TGAGGAATGGTTGATCATTTTGATTAA 57.966 29.630 0.00 0.00 37.20 1.40
3257 3511 7.484993 TGAGGAATGGTTGATCATTTTGATT 57.515 32.000 0.00 0.00 37.20 2.57
3258 3512 7.670605 ATGAGGAATGGTTGATCATTTTGAT 57.329 32.000 0.00 0.00 40.34 2.57
3259 3513 7.484993 AATGAGGAATGGTTGATCATTTTGA 57.515 32.000 0.00 0.00 37.31 2.69
3262 3516 8.038944 CAGAAAATGAGGAATGGTTGATCATTT 58.961 33.333 0.00 5.81 46.91 2.32
3263 3517 7.364408 CCAGAAAATGAGGAATGGTTGATCATT 60.364 37.037 0.00 0.00 41.18 2.57
3264 3518 6.097839 CCAGAAAATGAGGAATGGTTGATCAT 59.902 38.462 0.00 0.00 32.11 2.45
3265 3519 5.419788 CCAGAAAATGAGGAATGGTTGATCA 59.580 40.000 0.00 0.00 0.00 2.92
3274 3528 7.505585 TGTCAGTTTAACCAGAAAATGAGGAAT 59.494 33.333 0.00 0.00 42.25 3.01
3278 3532 7.651808 ACATGTCAGTTTAACCAGAAAATGAG 58.348 34.615 13.69 0.00 42.25 2.90
3280 3534 9.912634 AATACATGTCAGTTTAACCAGAAAATG 57.087 29.630 0.00 2.05 36.09 2.32
3283 3537 9.743057 CAAAATACATGTCAGTTTAACCAGAAA 57.257 29.630 0.00 0.00 0.00 2.52
3295 3549 9.912634 AAGTACCAAAATCAAAATACATGTCAG 57.087 29.630 0.00 0.00 0.00 3.51
3298 3552 8.987890 GCAAAGTACCAAAATCAAAATACATGT 58.012 29.630 2.69 2.69 0.00 3.21
3299 3553 8.986847 TGCAAAGTACCAAAATCAAAATACATG 58.013 29.630 0.00 0.00 0.00 3.21
3300 3554 9.206870 CTGCAAAGTACCAAAATCAAAATACAT 57.793 29.630 0.00 0.00 0.00 2.29
3304 3558 6.203338 CAGCTGCAAAGTACCAAAATCAAAAT 59.797 34.615 0.00 0.00 0.00 1.82
3305 3559 5.523188 CAGCTGCAAAGTACCAAAATCAAAA 59.477 36.000 0.00 0.00 0.00 2.44
3323 3606 1.242076 TCAGGCTTTCTTTCAGCTGC 58.758 50.000 9.47 0.00 37.43 5.25
3436 3719 1.747924 GGCTGCTCTTTGGAATCCTTC 59.252 52.381 0.00 0.00 0.00 3.46
3489 3772 1.507141 CTTTGTATCATCGGCCGCCC 61.507 60.000 23.51 4.39 0.00 6.13
3788 4071 1.181786 AGCAGAGAGAGCACCACTAC 58.818 55.000 0.00 0.00 0.00 2.73
3946 4229 7.611770 AGCACAATGATAGCTTACCGATTATA 58.388 34.615 0.00 0.00 34.37 0.98
3963 4246 9.655769 GATGAAACATACTAACATAGCACAATG 57.344 33.333 0.00 0.00 0.00 2.82
4149 4432 6.945218 ACCAAATGATAAGGCATAAAAGCAA 58.055 32.000 0.00 0.00 35.83 3.91
4300 4585 4.273318 GAGAATCTGCCATTGGGTTACTT 58.727 43.478 4.53 0.00 36.17 2.24
4643 5655 1.544691 TCTCGGTAGCAAACTCCTCAC 59.455 52.381 0.00 0.00 0.00 3.51
4658 5670 4.703645 TCACACTAGAATGAAGTCTCGG 57.296 45.455 0.00 0.00 0.00 4.63
4667 5679 7.468922 TTCGATTAAGCATCACACTAGAATG 57.531 36.000 0.00 0.00 0.00 2.67
4668 5680 7.766278 AGTTTCGATTAAGCATCACACTAGAAT 59.234 33.333 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.