Multiple sequence alignment - TraesCS2A01G449400

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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 TraesCS2A01G449400 chr2A 100.000 3233 0 0 1 3233 699387128 699383896 0.000000e+00 5971.0
1 TraesCS2A01G449400 chr2B 89.220 3284 199 70 18 3233 667130457 667127261 0.000000e+00 3960.0
2 TraesCS2A01G449400 chr2D 89.759 1494 74 31 872 2343 558734331 558732895 0.000000e+00 1838.0
3 TraesCS2A01G449400 chr2D 91.923 520 32 5 259 773 558734872 558734358 0.000000e+00 719.0
4 TraesCS2A01G449400 chr2D 79.651 172 21 10 16 179 344313317 344313482 9.480000e-21 111.0
5 TraesCS2A01G449400 chr3D 77.908 851 114 46 2434 3229 231133590 231132759 2.270000e-126 462.0
6 TraesCS2A01G449400 chr3D 76.906 892 132 50 2390 3229 46962281 46961412 3.830000e-119 438.0
7 TraesCS2A01G449400 chr3D 77.723 606 75 35 2665 3229 562531374 562530788 1.870000e-82 316.0
8 TraesCS2A01G449400 chr3D 80.428 327 35 19 2841 3152 349640394 349640706 4.200000e-54 222.0
9 TraesCS2A01G449400 chr7D 76.979 821 114 39 2433 3217 6568217 6568998 1.810000e-107 399.0
10 TraesCS2A01G449400 chr7D 81.818 121 18 4 1 119 236014146 236014264 7.380000e-17 99.0
11 TraesCS2A01G449400 chr4A 75.743 841 139 42 2433 3229 738818786 738817967 2.370000e-96 363.0
12 TraesCS2A01G449400 chr3A 77.545 668 99 32 2602 3229 738042524 738041868 3.970000e-94 355.0
13 TraesCS2A01G449400 chr3A 77.888 606 73 36 2665 3229 697637497 697636912 1.450000e-83 320.0
14 TraesCS2A01G449400 chr3A 76.911 641 98 29 2631 3229 742861097 742860465 5.200000e-83 318.0
15 TraesCS2A01G449400 chr3A 84.615 104 16 0 16 119 672444875 672444978 1.590000e-18 104.0
16 TraesCS2A01G449400 chr5D 77.778 513 90 21 2413 2914 1494408 1493909 8.770000e-76 294.0
17 TraesCS2A01G449400 chr5D 77.043 514 90 24 2413 2914 1529578 1529081 1.480000e-68 270.0
18 TraesCS2A01G449400 chr5D 78.066 424 74 18 2413 2827 1505860 1505447 1.930000e-62 250.0
19 TraesCS2A01G449400 chr7A 80.488 410 56 14 2838 3228 1315283 1314879 3.150000e-75 292.0
20 TraesCS2A01G449400 chr3B 77.694 399 58 24 2759 3142 749772407 749772025 7.020000e-52 215.0
21 TraesCS2A01G449400 chr3B 76.875 320 45 19 2935 3229 42168089 42167774 1.550000e-33 154.0
22 TraesCS2A01G449400 chr6D 73.253 744 126 56 2439 3147 9065648 9066353 1.520000e-48 204.0
23 TraesCS2A01G449400 chr4B 79.412 170 23 10 16 179 77660048 77660211 3.410000e-20 110.0
24 TraesCS2A01G449400 chr5A 79.012 162 26 8 1 157 652669975 652670133 1.590000e-18 104.0
25 TraesCS2A01G449400 chr4D 82.114 123 18 4 16 136 390861924 390862044 5.710000e-18 102.0
26 TraesCS2A01G449400 chr4D 80.282 142 21 6 16 152 448500820 448500681 2.050000e-17 100.0
27 TraesCS2A01G449400 chr4D 79.720 143 21 7 16 152 448468047 448467907 2.650000e-16 97.1


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 TraesCS2A01G449400 chr2A 699383896 699387128 3232 True 5971.0 5971 100.000 1 3233 1 chr2A.!!$R1 3232
1 TraesCS2A01G449400 chr2B 667127261 667130457 3196 True 3960.0 3960 89.220 18 3233 1 chr2B.!!$R1 3215
2 TraesCS2A01G449400 chr2D 558732895 558734872 1977 True 1278.5 1838 90.841 259 2343 2 chr2D.!!$R1 2084
3 TraesCS2A01G449400 chr3D 231132759 231133590 831 True 462.0 462 77.908 2434 3229 1 chr3D.!!$R2 795
4 TraesCS2A01G449400 chr3D 46961412 46962281 869 True 438.0 438 76.906 2390 3229 1 chr3D.!!$R1 839
5 TraesCS2A01G449400 chr3D 562530788 562531374 586 True 316.0 316 77.723 2665 3229 1 chr3D.!!$R3 564
6 TraesCS2A01G449400 chr7D 6568217 6568998 781 False 399.0 399 76.979 2433 3217 1 chr7D.!!$F1 784
7 TraesCS2A01G449400 chr4A 738817967 738818786 819 True 363.0 363 75.743 2433 3229 1 chr4A.!!$R1 796
8 TraesCS2A01G449400 chr3A 738041868 738042524 656 True 355.0 355 77.545 2602 3229 1 chr3A.!!$R2 627
9 TraesCS2A01G449400 chr3A 697636912 697637497 585 True 320.0 320 77.888 2665 3229 1 chr3A.!!$R1 564
10 TraesCS2A01G449400 chr3A 742860465 742861097 632 True 318.0 318 76.911 2631 3229 1 chr3A.!!$R3 598
11 TraesCS2A01G449400 chr6D 9065648 9066353 705 False 204.0 204 73.253 2439 3147 1 chr6D.!!$F1 708

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
136 137 0.107361 TCTGATGCGAGGTAGACCGA 60.107 55.0 0.00 0.00 42.08 4.69 F
366 382 0.169672 CCGACTTCTACTTTCGCCGA 59.830 55.0 0.00 0.00 0.00 5.54 F
1463 1510 0.236187 TGCGTTCCGTTTATGTGCAC 59.764 50.0 10.75 10.75 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1622 1674 0.994247 AGATGCAGGATCACCCACAA 59.006 50.000 4.52 0.0 37.41 3.33 R
2163 2215 0.455633 GGTGCGAGCAATGCAAGAAG 60.456 55.000 8.35 0.0 45.23 2.85 R
3064 3222 1.553248 ACTATACTTTGCGCACTGGGA 59.447 47.619 11.12 0.0 0.00 4.37 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
22 23 5.135508 GACATCACTACCAGTACACAACT 57.864 43.478 0.00 0.00 39.81 3.16
27 28 4.056050 CACTACCAGTACACAACTCCAAC 58.944 47.826 0.00 0.00 35.76 3.77
31 32 2.878406 CCAGTACACAACTCCAACCAAG 59.122 50.000 0.00 0.00 35.76 3.61
35 36 0.307760 CACAACTCCAACCAAGACGC 59.692 55.000 0.00 0.00 0.00 5.19
36 37 0.818040 ACAACTCCAACCAAGACGCC 60.818 55.000 0.00 0.00 0.00 5.68
77 78 4.316823 AGTCCCTCCTGCCGGTGA 62.317 66.667 1.90 0.00 0.00 4.02
93 94 1.074926 TGAGGGGCTGAGATCCTCC 60.075 63.158 15.52 0.00 44.73 4.30
106 107 4.864334 CCTCCGCACCTCCATGGC 62.864 72.222 6.96 0.00 40.22 4.40
107 108 4.864334 CTCCGCACCTCCATGGCC 62.864 72.222 6.96 0.00 40.22 5.36
130 131 0.760567 AGGCCATCTGATGCGAGGTA 60.761 55.000 12.17 0.00 0.00 3.08
136 137 0.107361 TCTGATGCGAGGTAGACCGA 60.107 55.000 0.00 0.00 42.08 4.69
138 139 1.009900 GATGCGAGGTAGACCGACG 60.010 63.158 13.92 13.92 42.08 5.12
160 167 1.554583 GGCGGGAGGAGAAAGAAGGT 61.555 60.000 0.00 0.00 0.00 3.50
166 173 3.827302 GGGAGGAGAAAGAAGGTTTTTCC 59.173 47.826 0.00 0.00 35.62 3.13
191 202 3.844090 GAGGAGGAGAGCCCGTGC 61.844 72.222 0.00 0.00 40.87 5.34
208 219 1.787155 GTGCTAGCATGGACGTTATCG 59.213 52.381 22.51 0.00 43.34 2.92
240 251 5.237815 TGCTTAGTACTGATGTTGACTTGG 58.762 41.667 5.39 0.00 0.00 3.61
290 306 3.581024 ACAATGTTCACATGCATGGTC 57.419 42.857 29.41 16.30 36.56 4.02
357 373 1.035139 TTATCCGGCCCGACTTCTAC 58.965 55.000 3.71 0.00 0.00 2.59
366 382 0.169672 CCGACTTCTACTTTCGCCGA 59.830 55.000 0.00 0.00 0.00 5.54
370 386 1.549170 ACTTCTACTTTCGCCGATGGT 59.451 47.619 0.00 0.00 0.00 3.55
405 421 0.321298 ACTTTGCCGTCCGCTGTTAT 60.321 50.000 0.00 0.00 38.78 1.89
406 422 1.066716 ACTTTGCCGTCCGCTGTTATA 60.067 47.619 0.00 0.00 38.78 0.98
407 423 2.004017 CTTTGCCGTCCGCTGTTATAA 58.996 47.619 0.00 0.00 38.78 0.98
408 424 1.361793 TTGCCGTCCGCTGTTATAAC 58.638 50.000 8.75 8.75 38.78 1.89
486 506 7.284489 TGGTAGGCCAATCATGAATACTTTAAC 59.716 37.037 5.01 0.00 42.83 2.01
558 580 0.948678 TGTGCTAAAAGTTGACCCGC 59.051 50.000 0.00 0.00 0.00 6.13
704 727 0.456221 ATACCTCCACGCTCGAAGTG 59.544 55.000 12.27 12.27 39.19 3.16
762 786 4.829064 TTTTTCTCAACCATCGACAAGG 57.171 40.909 0.00 0.00 0.00 3.61
807 831 6.466308 AAGCAAAACAAGAAAACAAGTGAC 57.534 33.333 0.00 0.00 0.00 3.67
826 850 1.652563 GCGAACCACCTCCAACAAC 59.347 57.895 0.00 0.00 0.00 3.32
840 864 3.442273 TCCAACAACTCTCCAACAAACAC 59.558 43.478 0.00 0.00 0.00 3.32
1242 1285 2.027625 GGAGGTGAAACTGGACGCG 61.028 63.158 3.53 3.53 36.74 6.01
1324 1367 1.082766 TCCAAGGGATGCAGGAGGA 59.917 57.895 0.00 0.00 0.00 3.71
1329 1372 1.153349 GGGATGCAGGAGGAACGTC 60.153 63.158 0.00 0.00 0.00 4.34
1397 1440 4.246458 GTCAAGAGCACGAAAGAGGTAAT 58.754 43.478 0.00 0.00 31.14 1.89
1398 1441 4.691216 GTCAAGAGCACGAAAGAGGTAATT 59.309 41.667 0.00 0.00 31.14 1.40
1399 1442 5.867716 GTCAAGAGCACGAAAGAGGTAATTA 59.132 40.000 0.00 0.00 31.14 1.40
1400 1443 6.367969 GTCAAGAGCACGAAAGAGGTAATTAA 59.632 38.462 0.00 0.00 31.14 1.40
1444 1491 7.616313 TGAAAAGTGAAAACCACCTTGTAAAT 58.384 30.769 0.00 0.00 46.87 1.40
1450 1497 3.636282 AACCACCTTGTAAATGCGTTC 57.364 42.857 0.00 0.00 0.00 3.95
1456 1503 3.814283 ACCTTGTAAATGCGTTCCGTTTA 59.186 39.130 0.00 0.00 34.58 2.01
1457 1504 4.456566 ACCTTGTAAATGCGTTCCGTTTAT 59.543 37.500 0.00 0.00 37.28 1.40
1463 1510 0.236187 TGCGTTCCGTTTATGTGCAC 59.764 50.000 10.75 10.75 0.00 4.57
1610 1662 3.056107 CCCTCTCACAAATTCGTCCTGTA 60.056 47.826 0.00 0.00 0.00 2.74
1611 1663 4.383118 CCCTCTCACAAATTCGTCCTGTAT 60.383 45.833 0.00 0.00 0.00 2.29
1612 1664 4.806247 CCTCTCACAAATTCGTCCTGTATC 59.194 45.833 0.00 0.00 0.00 2.24
1613 1665 5.394663 CCTCTCACAAATTCGTCCTGTATCT 60.395 44.000 0.00 0.00 0.00 1.98
1614 1666 6.183360 CCTCTCACAAATTCGTCCTGTATCTA 60.183 42.308 0.00 0.00 0.00 1.98
1615 1667 7.348080 TCTCACAAATTCGTCCTGTATCTAT 57.652 36.000 0.00 0.00 0.00 1.98
1616 1668 7.203218 TCTCACAAATTCGTCCTGTATCTATG 58.797 38.462 0.00 0.00 0.00 2.23
1617 1669 6.873997 TCACAAATTCGTCCTGTATCTATGT 58.126 36.000 0.00 0.00 0.00 2.29
1618 1670 7.327975 TCACAAATTCGTCCTGTATCTATGTT 58.672 34.615 0.00 0.00 0.00 2.71
1619 1671 7.822334 TCACAAATTCGTCCTGTATCTATGTTT 59.178 33.333 0.00 0.00 0.00 2.83
1620 1672 8.450964 CACAAATTCGTCCTGTATCTATGTTTT 58.549 33.333 0.00 0.00 0.00 2.43
1621 1673 9.010029 ACAAATTCGTCCTGTATCTATGTTTTT 57.990 29.630 0.00 0.00 0.00 1.94
1671 1723 8.371770 TGATACGTGCACATGCTAATTAATTA 57.628 30.769 18.64 7.66 42.66 1.40
1809 1861 1.395954 CACTGCATCATCGACAAGGTG 59.604 52.381 0.00 0.00 0.00 4.00
1842 1894 1.139734 CATCGTGGAGGAGACGGTG 59.860 63.158 0.00 0.00 41.20 4.94
1917 1969 4.942852 CAGAGGTTGCAGAGGTTATAGAG 58.057 47.826 0.00 0.00 0.00 2.43
1998 2050 3.411418 CTACTCGCACCCGTCGCAT 62.411 63.158 0.00 0.00 35.54 4.73
2027 2079 3.175240 CGACAGCTTCTCGCCGTG 61.175 66.667 0.00 0.00 40.39 4.94
2085 2137 2.446227 TACGGTGGTGGTGGTGGT 60.446 61.111 0.00 0.00 0.00 4.16
2086 2138 2.047213 CTACGGTGGTGGTGGTGGTT 62.047 60.000 0.00 0.00 0.00 3.67
2087 2139 0.762082 TACGGTGGTGGTGGTGGTTA 60.762 55.000 0.00 0.00 0.00 2.85
2129 2181 1.553248 TGGCTGTGGGTCATACAGTAC 59.447 52.381 6.95 0.00 45.60 2.73
2131 2183 1.203994 GCTGTGGGTCATACAGTACGT 59.796 52.381 6.95 0.00 45.60 3.57
2303 2356 8.644216 TCTAAATAAGAACACCACTGAACTACA 58.356 33.333 0.00 0.00 0.00 2.74
2311 2364 1.202582 CCACTGAACTACACTCTCCGG 59.797 57.143 0.00 0.00 0.00 5.14
2335 2388 8.056571 CGGTTTTATTTATTTTTGCAAACACGA 58.943 29.630 12.39 0.00 0.00 4.35
2367 2420 4.081476 TGCATGTCGATATATCAGAAGGGG 60.081 45.833 13.11 0.00 0.00 4.79
2368 2421 4.160439 GCATGTCGATATATCAGAAGGGGA 59.840 45.833 13.11 0.00 0.00 4.81
2369 2422 5.337571 GCATGTCGATATATCAGAAGGGGAA 60.338 44.000 13.11 0.00 0.00 3.97
2400 2453 3.537580 TGTACAAGGGTGTGAACACTTC 58.462 45.455 12.99 6.48 45.73 3.01
2431 2484 9.672086 AATTTTCGAACATTTTACTGAAATCGA 57.328 25.926 3.70 0.00 35.79 3.59
2432 2485 8.708075 TTTTCGAACATTTTACTGAAATCGAG 57.292 30.769 0.00 0.00 35.79 4.04
2433 2486 7.646446 TTCGAACATTTTACTGAAATCGAGA 57.354 32.000 0.00 0.00 35.79 4.04
2434 2487 7.646446 TCGAACATTTTACTGAAATCGAGAA 57.354 32.000 0.00 0.00 35.79 2.87
2435 2488 8.251750 TCGAACATTTTACTGAAATCGAGAAT 57.748 30.769 0.00 0.00 35.79 2.40
2436 2489 9.361315 TCGAACATTTTACTGAAATCGAGAATA 57.639 29.630 0.00 0.00 35.79 1.75
3064 3222 3.055719 CCAAACGGGTGCGATGCT 61.056 61.111 0.00 0.00 0.00 3.79
3065 3223 2.480555 CAAACGGGTGCGATGCTC 59.519 61.111 0.00 0.00 0.00 4.26
3220 3395 6.072838 CCATGATGTACCATCAGAAGCAATAC 60.073 42.308 12.02 0.00 0.00 1.89
3230 3405 3.138283 TCAGAAGCAATACCCCCATTAGG 59.862 47.826 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.021456 TGGAGTTGTGTACTGGTAGTGATG 60.021 45.833 0.00 0.00 37.17 3.07
3 4 4.157246 TGGAGTTGTGTACTGGTAGTGAT 58.843 43.478 0.00 0.00 37.17 3.06
4 5 3.568443 TGGAGTTGTGTACTGGTAGTGA 58.432 45.455 0.00 0.00 37.17 3.41
5 6 4.056050 GTTGGAGTTGTGTACTGGTAGTG 58.944 47.826 0.00 0.00 37.17 2.74
6 7 3.070590 GGTTGGAGTTGTGTACTGGTAGT 59.929 47.826 0.00 0.00 37.17 2.73
7 8 3.070446 TGGTTGGAGTTGTGTACTGGTAG 59.930 47.826 0.00 0.00 37.17 3.18
8 9 3.039743 TGGTTGGAGTTGTGTACTGGTA 58.960 45.455 0.00 0.00 37.17 3.25
9 10 1.841277 TGGTTGGAGTTGTGTACTGGT 59.159 47.619 0.00 0.00 37.17 4.00
10 11 2.631160 TGGTTGGAGTTGTGTACTGG 57.369 50.000 0.00 0.00 37.17 4.00
11 12 3.560068 GTCTTGGTTGGAGTTGTGTACTG 59.440 47.826 0.00 0.00 37.17 2.74
12 13 3.740141 CGTCTTGGTTGGAGTTGTGTACT 60.740 47.826 0.00 0.00 40.71 2.73
13 14 2.542595 CGTCTTGGTTGGAGTTGTGTAC 59.457 50.000 0.00 0.00 0.00 2.90
14 15 2.828877 CGTCTTGGTTGGAGTTGTGTA 58.171 47.619 0.00 0.00 0.00 2.90
15 16 1.663695 CGTCTTGGTTGGAGTTGTGT 58.336 50.000 0.00 0.00 0.00 3.72
16 17 0.307760 GCGTCTTGGTTGGAGTTGTG 59.692 55.000 0.00 0.00 0.00 3.33
22 23 1.595929 GTTCGGCGTCTTGGTTGGA 60.596 57.895 6.85 0.00 0.00 3.53
27 28 0.320073 TGTTAGGTTCGGCGTCTTGG 60.320 55.000 6.85 0.00 0.00 3.61
31 32 3.058777 TCATTTTTGTTAGGTTCGGCGTC 60.059 43.478 6.85 1.15 0.00 5.19
35 36 5.086058 CGATGTCATTTTTGTTAGGTTCGG 58.914 41.667 0.00 0.00 0.00 4.30
36 37 5.086058 CCGATGTCATTTTTGTTAGGTTCG 58.914 41.667 0.00 0.00 0.00 3.95
72 73 2.801631 GGATCTCAGCCCCTCACCG 61.802 68.421 0.00 0.00 0.00 4.94
75 76 1.074926 GGAGGATCTCAGCCCCTCA 60.075 63.158 12.49 0.00 46.28 3.86
77 78 2.123077 CGGAGGATCTCAGCCCCT 60.123 66.667 0.00 0.00 33.73 4.79
86 87 1.070445 CATGGAGGTGCGGAGGATC 59.930 63.158 0.00 0.00 0.00 3.36
93 94 4.738998 TTGGGCCATGGAGGTGCG 62.739 66.667 18.40 0.00 40.61 5.34
106 107 1.731433 CGCATCAGATGGCCTTTGGG 61.731 60.000 12.54 0.00 0.00 4.12
107 108 0.749091 TCGCATCAGATGGCCTTTGG 60.749 55.000 12.54 0.00 0.00 3.28
109 110 0.465097 CCTCGCATCAGATGGCCTTT 60.465 55.000 12.54 0.00 0.00 3.11
119 120 1.712018 CGTCGGTCTACCTCGCATCA 61.712 60.000 0.00 0.00 0.00 3.07
120 121 1.009900 CGTCGGTCTACCTCGCATC 60.010 63.158 0.00 0.00 0.00 3.91
138 139 4.840005 CTTTCTCCTCCCGCCGGC 62.840 72.222 19.07 19.07 0.00 6.13
139 140 2.579684 CTTCTTTCTCCTCCCGCCGG 62.580 65.000 0.00 0.00 0.00 6.13
144 145 3.827302 GGAAAAACCTTCTTTCTCCTCCC 59.173 47.826 0.00 0.00 33.99 4.30
166 173 0.468029 GCTCTCCTCCTCCTCCTCAG 60.468 65.000 0.00 0.00 0.00 3.35
208 219 1.927174 CAGTACTAAGCATGGACGCAC 59.073 52.381 0.00 0.00 0.00 5.34
210 221 2.579207 TCAGTACTAAGCATGGACGC 57.421 50.000 0.00 0.00 0.00 5.19
212 223 5.292101 GTCAACATCAGTACTAAGCATGGAC 59.708 44.000 0.00 0.00 0.00 4.02
255 266 7.915397 TGTGAACATTGTAAAGAAGAAGAAAGC 59.085 33.333 0.00 0.00 0.00 3.51
256 267 9.956720 ATGTGAACATTGTAAAGAAGAAGAAAG 57.043 29.630 0.00 0.00 31.37 2.62
257 268 9.734620 CATGTGAACATTGTAAAGAAGAAGAAA 57.265 29.630 0.00 0.00 33.61 2.52
326 342 3.508402 GGGCCGGATAAAAACAGAGAAAA 59.492 43.478 5.05 0.00 0.00 2.29
342 358 0.459759 GAAAGTAGAAGTCGGGCCGG 60.460 60.000 27.98 7.65 0.00 6.13
357 373 2.485122 GGCAACCATCGGCGAAAG 59.515 61.111 15.93 11.13 0.00 2.62
405 421 2.350007 GCGATCAGCGGTGTTTTTGTTA 60.350 45.455 15.22 0.00 41.29 2.41
406 422 1.599419 GCGATCAGCGGTGTTTTTGTT 60.599 47.619 15.22 0.00 41.29 2.83
407 423 0.040425 GCGATCAGCGGTGTTTTTGT 60.040 50.000 15.22 0.00 41.29 2.83
408 424 2.712077 GCGATCAGCGGTGTTTTTG 58.288 52.632 15.22 6.22 41.29 2.44
467 487 7.067372 TCTGCTGGTTAAAGTATTCATGATTGG 59.933 37.037 0.00 0.00 0.00 3.16
486 506 3.190849 CGTGCCATCGTCTGCTGG 61.191 66.667 0.00 0.00 34.40 4.85
581 603 1.298859 GGTTGGGCTGTCGTGTGATC 61.299 60.000 0.00 0.00 0.00 2.92
704 727 0.510359 GATCGATCCACTTCGCATGC 59.490 55.000 14.76 7.91 38.97 4.06
762 786 0.323629 TTGAGTCGGGGTTCACATCC 59.676 55.000 0.00 0.00 0.00 3.51
786 810 4.720946 GCGTCACTTGTTTTCTTGTTTTGC 60.721 41.667 0.00 0.00 0.00 3.68
795 819 1.062880 TGGTTCGCGTCACTTGTTTTC 59.937 47.619 5.77 0.00 0.00 2.29
796 820 1.088306 TGGTTCGCGTCACTTGTTTT 58.912 45.000 5.77 0.00 0.00 2.43
807 831 1.890041 TTGTTGGAGGTGGTTCGCG 60.890 57.895 0.00 0.00 0.00 5.87
826 850 1.676006 GGGTGTGTGTTTGTTGGAGAG 59.324 52.381 0.00 0.00 0.00 3.20
860 884 2.056906 GCTTCAGGTGTGAGGTGGGT 62.057 60.000 0.00 0.00 32.32 4.51
861 885 1.302832 GCTTCAGGTGTGAGGTGGG 60.303 63.158 0.00 0.00 32.32 4.61
862 886 1.302832 GGCTTCAGGTGTGAGGTGG 60.303 63.158 0.00 0.00 32.32 4.61
1032 1075 1.374758 CGTCTTCAGCTCCACCACC 60.375 63.158 0.00 0.00 0.00 4.61
1033 1076 1.374758 CCGTCTTCAGCTCCACCAC 60.375 63.158 0.00 0.00 0.00 4.16
1034 1077 3.059982 CCGTCTTCAGCTCCACCA 58.940 61.111 0.00 0.00 0.00 4.17
1125 1168 2.205074 ACAGAAACTGAGAAGCACGTG 58.795 47.619 12.28 12.28 35.18 4.49
1133 1176 5.643379 ACAAAGCAAAACAGAAACTGAGA 57.357 34.783 5.76 0.00 35.18 3.27
1205 1248 2.985847 GAACCCCTGCAGCACACC 60.986 66.667 8.66 0.00 0.00 4.16
1242 1285 2.955881 CGTCACCTTCCCTGACCCC 61.956 68.421 0.00 0.00 35.54 4.95
1324 1367 2.019984 GGGAGGTATGTACTCGACGTT 58.980 52.381 0.00 0.00 35.82 3.99
1329 1372 1.038280 GTGGGGGAGGTATGTACTCG 58.962 60.000 0.00 0.00 35.82 4.18
1356 1399 4.800023 TGACCTCGGTGATTATCTCCTTA 58.200 43.478 10.97 0.00 0.00 2.69
1399 1442 9.434420 CTTTTCAGATAGAGAGATTGTCTGTTT 57.566 33.333 0.00 0.00 37.96 2.83
1400 1443 8.592809 ACTTTTCAGATAGAGAGATTGTCTGTT 58.407 33.333 0.00 0.00 37.96 3.16
1450 1497 3.489059 GGATGAATGGTGCACATAAACGG 60.489 47.826 20.43 0.00 39.40 4.44
1456 1503 2.537633 AAGGGATGAATGGTGCACAT 57.462 45.000 20.43 7.56 43.07 3.21
1457 1504 2.307496 AAAGGGATGAATGGTGCACA 57.693 45.000 20.43 5.24 0.00 4.57
1463 1510 2.143876 ACGGGAAAAGGGATGAATGG 57.856 50.000 0.00 0.00 0.00 3.16
1589 1641 3.045601 ACAGGACGAATTTGTGAGAGG 57.954 47.619 2.13 0.00 0.00 3.69
1619 1671 2.079170 TGCAGGATCACCCACAAAAA 57.921 45.000 0.00 0.00 37.41 1.94
1620 1672 2.170166 GATGCAGGATCACCCACAAAA 58.830 47.619 0.00 0.00 37.41 2.44
1621 1673 1.355381 AGATGCAGGATCACCCACAAA 59.645 47.619 4.52 0.00 37.41 2.83
1622 1674 0.994247 AGATGCAGGATCACCCACAA 59.006 50.000 4.52 0.00 37.41 3.33
1623 1675 1.878211 TAGATGCAGGATCACCCACA 58.122 50.000 4.52 0.00 37.41 4.17
1624 1676 2.105477 ACATAGATGCAGGATCACCCAC 59.895 50.000 4.52 0.00 37.41 4.61
1625 1677 2.411583 ACATAGATGCAGGATCACCCA 58.588 47.619 4.52 0.00 37.41 4.51
1626 1678 3.144506 CAACATAGATGCAGGATCACCC 58.855 50.000 4.52 0.00 36.73 4.61
1627 1679 4.077300 TCAACATAGATGCAGGATCACC 57.923 45.455 4.52 0.00 32.86 4.02
1628 1680 5.347093 CGTATCAACATAGATGCAGGATCAC 59.653 44.000 4.52 0.00 32.86 3.06
1629 1681 5.011023 ACGTATCAACATAGATGCAGGATCA 59.989 40.000 4.52 0.00 32.86 2.92
1630 1682 5.347093 CACGTATCAACATAGATGCAGGATC 59.653 44.000 0.00 0.00 31.85 3.36
1631 1683 5.233225 CACGTATCAACATAGATGCAGGAT 58.767 41.667 0.00 0.00 31.85 3.24
1632 1684 4.620982 CACGTATCAACATAGATGCAGGA 58.379 43.478 0.00 0.00 31.85 3.86
1633 1685 3.185188 GCACGTATCAACATAGATGCAGG 59.815 47.826 0.00 0.00 31.09 4.85
1634 1686 3.803778 TGCACGTATCAACATAGATGCAG 59.196 43.478 0.00 0.00 34.05 4.41
1635 1687 3.555547 GTGCACGTATCAACATAGATGCA 59.444 43.478 0.00 0.00 35.53 3.96
1636 1688 3.555547 TGTGCACGTATCAACATAGATGC 59.444 43.478 13.13 0.00 31.26 3.91
1637 1689 5.673029 CATGTGCACGTATCAACATAGATG 58.327 41.667 12.10 0.81 0.00 2.90
1671 1723 6.309009 CAGCGTAAATATCTGCATTAGTCGAT 59.691 38.462 0.00 0.00 0.00 3.59
1795 1847 1.135139 CGTCTCCACCTTGTCGATGAT 59.865 52.381 0.00 0.00 0.00 2.45
1809 1861 4.796231 ATGCGCACCGTCGTCTCC 62.796 66.667 14.90 0.00 0.00 3.71
1842 1894 4.068599 CCTCTTTCTTCTTCTTCACCACC 58.931 47.826 0.00 0.00 0.00 4.61
1904 1956 7.039784 CCTTGATCTTCTCCTCTATAACCTCTG 60.040 44.444 0.00 0.00 0.00 3.35
1909 1961 6.780522 ACCTCCTTGATCTTCTCCTCTATAAC 59.219 42.308 0.00 0.00 0.00 1.89
1910 1962 6.780031 CACCTCCTTGATCTTCTCCTCTATAA 59.220 42.308 0.00 0.00 0.00 0.98
1911 1963 6.310941 CACCTCCTTGATCTTCTCCTCTATA 58.689 44.000 0.00 0.00 0.00 1.31
1912 1964 5.147032 CACCTCCTTGATCTTCTCCTCTAT 58.853 45.833 0.00 0.00 0.00 1.98
1913 1965 4.541705 CACCTCCTTGATCTTCTCCTCTA 58.458 47.826 0.00 0.00 0.00 2.43
1914 1966 3.373830 CACCTCCTTGATCTTCTCCTCT 58.626 50.000 0.00 0.00 0.00 3.69
1915 1967 2.433970 CCACCTCCTTGATCTTCTCCTC 59.566 54.545 0.00 0.00 0.00 3.71
1916 1968 2.225753 ACCACCTCCTTGATCTTCTCCT 60.226 50.000 0.00 0.00 0.00 3.69
1917 1969 2.093235 CACCACCTCCTTGATCTTCTCC 60.093 54.545 0.00 0.00 0.00 3.71
2027 2079 3.479127 TAACCACCACCACCACCGC 62.479 63.158 0.00 0.00 0.00 5.68
2034 2086 1.003349 CCATAACCGTAACCACCACCA 59.997 52.381 0.00 0.00 0.00 4.17
2085 2137 2.694628 ACCGTAGCCATGACCGTAATAA 59.305 45.455 0.00 0.00 0.00 1.40
2086 2138 2.034939 CACCGTAGCCATGACCGTAATA 59.965 50.000 0.00 0.00 0.00 0.98
2087 2139 1.117150 ACCGTAGCCATGACCGTAAT 58.883 50.000 0.00 0.00 0.00 1.89
2163 2215 0.455633 GGTGCGAGCAATGCAAGAAG 60.456 55.000 8.35 0.00 45.23 2.85
2303 2356 7.662897 TGCAAAAATAAATAAAACCGGAGAGT 58.337 30.769 9.46 0.00 0.00 3.24
2347 2400 6.935240 TTTCCCCTTCTGATATATCGACAT 57.065 37.500 8.19 0.00 0.00 3.06
2369 2422 5.125739 TCACACCCTTGTACATTTCGTTTTT 59.874 36.000 0.00 0.00 33.30 1.94
2618 2717 7.095910 TCATGCATTTCAAATAATGTCCGTTT 58.904 30.769 0.00 0.00 37.72 3.60
2623 2722 8.867112 AGTGATCATGCATTTCAAATAATGTC 57.133 30.769 10.00 0.00 37.72 3.06
3008 3151 7.056635 TGGATGGCCTGTTTTTAAAATTTTCA 58.943 30.769 6.72 0.00 34.31 2.69
3029 3187 4.195334 GCCGGCCCATGTCTGGAT 62.195 66.667 18.11 0.00 46.37 3.41
3064 3222 1.553248 ACTATACTTTGCGCACTGGGA 59.447 47.619 11.12 0.00 0.00 4.37
3065 3223 2.024176 ACTATACTTTGCGCACTGGG 57.976 50.000 11.12 2.73 0.00 4.45
3068 3231 5.047943 CCTCCTATACTATACTTTGCGCACT 60.048 44.000 11.12 0.00 0.00 4.40
3070 3234 4.831155 ACCTCCTATACTATACTTTGCGCA 59.169 41.667 5.66 5.66 0.00 6.09
3149 3315 3.866703 TTACCCACCAATGTCAAGTGA 57.133 42.857 3.31 0.00 33.21 3.41
3150 3316 6.773976 AATATTACCCACCAATGTCAAGTG 57.226 37.500 0.00 0.00 0.00 3.16
3151 3317 7.234577 ACAAAATATTACCCACCAATGTCAAGT 59.765 33.333 0.00 0.00 0.00 3.16
3152 3318 7.610865 ACAAAATATTACCCACCAATGTCAAG 58.389 34.615 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.