Multiple sequence alignment - TraesCS1A01G137500

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 TraesCS1A01G137500 chr1A 100.000 2519 0 0 1 2519 223442944 223445462 0.000000e+00 4652.0
1 TraesCS1A01G137500 chr1A 83.152 184 31 0 7 190 183344340 183344523 4.310000e-38 169.0
2 TraesCS1A01G137500 chr1D 95.019 2349 82 7 191 2518 160497293 160499627 0.000000e+00 3657.0
3 TraesCS1A01G137500 chr1D 95.789 190 8 0 1 190 160497069 160497258 8.750000e-80 307.0
4 TraesCS1A01G137500 chr1D 81.703 317 57 1 193 508 449289094 449288778 1.920000e-66 263.0
5 TraesCS1A01G137500 chr3A 83.861 316 48 2 194 507 362893686 362894000 5.270000e-77 298.0
6 TraesCS1A01G137500 chrUn 78.997 319 66 1 191 508 121591566 121591884 1.520000e-52 217.0
7 TraesCS1A01G137500 chrUn 78.997 319 66 1 191 508 121809564 121809246 1.520000e-52 217.0
8 TraesCS1A01G137500 chrUn 78.683 319 67 1 191 508 132355810 132355492 7.060000e-51 211.0
9 TraesCS1A01G137500 chrUn 78.370 319 68 1 191 508 133807754 133807436 3.280000e-49 206.0
10 TraesCS1A01G137500 chrUn 83.696 184 30 0 7 190 8436605 8436422 9.260000e-40 174.0
11 TraesCS1A01G137500 chrUn 93.023 86 6 0 1777 1862 50796526 50796611 2.630000e-25 126.0
12 TraesCS1A01G137500 chrUn 93.023 86 6 0 1777 1862 355086394 355086479 2.630000e-25 126.0
13 TraesCS1A01G137500 chr7B 78.481 316 67 1 194 508 495029564 495029249 3.280000e-49 206.0
14 TraesCS1A01G137500 chr7B 92.941 85 6 0 1777 1861 355888563 355888479 9.460000e-25 124.0
15 TraesCS1A01G137500 chr7B 88.710 62 7 0 1777 1838 697543767 697543706 2.690000e-10 76.8
16 TraesCS1A01G137500 chr6B 78.370 319 68 1 191 508 468559868 468560186 3.280000e-49 206.0
17 TraesCS1A01G137500 chr7D 83.684 190 31 0 1 190 311843516 311843705 1.990000e-41 180.0
18 TraesCS1A01G137500 chr7D 82.632 190 33 0 1 190 358532785 358532974 4.310000e-38 169.0
19 TraesCS1A01G137500 chr7D 92.683 82 6 0 1777 1858 350137416 350137497 4.400000e-23 119.0
20 TraesCS1A01G137500 chr4A 85.465 172 23 2 20 190 235274228 235274398 7.160000e-41 178.0
21 TraesCS1A01G137500 chr4A 83.511 188 29 2 3 190 273647440 273647625 9.260000e-40 174.0
22 TraesCS1A01G137500 chr4A 89.535 86 6 2 1777 1861 525736019 525736102 3.430000e-19 106.0
23 TraesCS1A01G137500 chr2A 83.696 184 30 0 7 190 337934872 337934689 9.260000e-40 174.0
24 TraesCS1A01G137500 chr2B 83.069 189 29 3 3 190 386253332 386253518 4.310000e-38 169.0
25 TraesCS1A01G137500 chr2B 82.474 97 12 3 1777 1868 58991873 58991777 2.080000e-11 80.5
26 TraesCS1A01G137500 chr5D 89.412 85 6 1 1777 1861 473051782 473051701 1.230000e-18 104.0
27 TraesCS1A01G137500 chr2D 93.333 45 1 2 691 734 523023998 523023955 5.820000e-07 65.8
28 TraesCS1A01G137500 chr3D 97.222 36 1 0 1827 1862 465465380 465465415 7.520000e-06 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 TraesCS1A01G137500 chr1A 223442944 223445462 2518 False 4652 4652 100.000 1 2519 1 chr1A.!!$F2 2518
1 TraesCS1A01G137500 chr1D 160497069 160499627 2558 False 1982 3657 95.404 1 2518 2 chr1D.!!$F1 2517

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
769 804 0.042131 TATAGGGCCGGTATGAGGGG 59.958 60.0 1.9 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2425 2481 0.52218 ACGGCTAGAACAGTGTCGAG 59.478 55.0 6.78 1.47 0.0 4.04 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
49 50 7.046652 CCATATGCACCTTGAGAGGATATAAG 58.953 42.308 0.00 0.00 46.74 1.73
53 54 5.543790 TGCACCTTGAGAGGATATAAGCATA 59.456 40.000 0.00 0.00 46.74 3.14
88 89 7.180408 ACTTAGTTTGCCTAGGACTAGAAATGA 59.820 37.037 14.75 0.00 35.21 2.57
126 127 1.201414 TCGTTGTGCATCGCTTCTCTA 59.799 47.619 0.00 0.00 0.00 2.43
130 131 4.436050 CGTTGTGCATCGCTTCTCTAAAAT 60.436 41.667 0.00 0.00 0.00 1.82
160 161 6.647334 TTTCATTCCATGCAACAAAGTAGA 57.353 33.333 0.00 0.00 0.00 2.59
202 237 6.524586 GCAAATCTCTTTTACAATTGTCTCCG 59.475 38.462 15.85 3.06 0.00 4.63
206 241 3.991773 TCTTTTACAATTGTCTCCGACCG 59.008 43.478 15.85 0.00 0.00 4.79
211 246 0.388134 AATTGTCTCCGACCGTGACG 60.388 55.000 0.00 0.00 33.81 4.35
222 257 2.049228 GACCGTGACGTCAAGTACTTG 58.951 52.381 26.60 26.60 41.71 3.16
248 283 4.322057 ACTTTTGGAAGACCCTATGCAT 57.678 40.909 3.79 3.79 36.69 3.96
256 291 5.045213 TGGAAGACCCTATGCATCAAACTTA 60.045 40.000 0.19 0.00 35.38 2.24
277 312 9.566432 AACTTAGAATCAAACTCATGTTCTCTT 57.434 29.630 0.00 0.00 34.96 2.85
278 313 9.213799 ACTTAGAATCAAACTCATGTTCTCTTC 57.786 33.333 0.00 0.00 34.96 2.87
291 326 3.945921 TGTTCTCTTCGGTCTATCATCGT 59.054 43.478 0.00 0.00 0.00 3.73
329 364 2.341176 GGTGGTCAACCGTACGCT 59.659 61.111 10.49 0.00 39.81 5.07
330 365 1.586028 GGTGGTCAACCGTACGCTA 59.414 57.895 10.49 0.00 39.81 4.26
331 366 0.174162 GGTGGTCAACCGTACGCTAT 59.826 55.000 10.49 0.00 39.81 2.97
332 367 1.553308 GTGGTCAACCGTACGCTATC 58.447 55.000 10.49 0.00 39.43 2.08
333 368 0.099259 TGGTCAACCGTACGCTATCG 59.901 55.000 10.49 0.00 39.43 2.92
334 369 0.378257 GGTCAACCGTACGCTATCGA 59.622 55.000 10.49 0.00 39.41 3.59
335 370 1.460766 GTCAACCGTACGCTATCGAC 58.539 55.000 10.49 7.66 39.41 4.20
336 371 1.085893 TCAACCGTACGCTATCGACA 58.914 50.000 10.49 0.00 39.41 4.35
337 372 1.186030 CAACCGTACGCTATCGACAC 58.814 55.000 10.49 0.00 39.41 3.67
338 373 1.089920 AACCGTACGCTATCGACACT 58.910 50.000 10.49 0.00 39.41 3.55
339 374 1.089920 ACCGTACGCTATCGACACTT 58.910 50.000 10.49 0.00 39.41 3.16
340 375 1.202110 ACCGTACGCTATCGACACTTG 60.202 52.381 10.49 0.00 39.41 3.16
351 386 1.272784 CGACACTTGTTCGCGTGCTA 61.273 55.000 5.77 0.00 34.58 3.49
375 410 6.627087 ATTAGGAAGAACATCAAGGAGTCA 57.373 37.500 0.00 0.00 0.00 3.41
384 419 0.251386 TCAAGGAGTCAGAGGAGCGT 60.251 55.000 0.00 0.00 0.00 5.07
424 459 4.935205 TCACCTACAATGTGCAAGATACAC 59.065 41.667 0.00 0.00 38.55 2.90
450 485 7.342769 ACTACGTACATGTCTCCATTTGATA 57.657 36.000 0.00 0.00 0.00 2.15
520 555 0.389948 CTCCAAGGTTTCGGAGTCGG 60.390 60.000 0.00 0.00 43.32 4.79
558 593 1.047002 CGGAGAAGGCCTGAGATCAT 58.953 55.000 5.69 0.00 0.00 2.45
560 595 1.000731 GGAGAAGGCCTGAGATCATCG 59.999 57.143 5.69 0.00 0.00 3.84
567 602 2.486191 GGCCTGAGATCATCGAAATGGT 60.486 50.000 0.00 0.00 33.42 3.55
579 614 3.153629 AAATGGTGGTTGGGGGCGA 62.154 57.895 0.00 0.00 0.00 5.54
594 629 1.523758 GGCGAAATGAAGTGGAGTGT 58.476 50.000 0.00 0.00 0.00 3.55
595 630 1.880027 GGCGAAATGAAGTGGAGTGTT 59.120 47.619 0.00 0.00 0.00 3.32
623 658 5.357257 GTTTTGTCTAAGATGCGGATAGGA 58.643 41.667 0.00 0.00 0.00 2.94
643 678 4.964897 AGGATGAATATATGCAGGATCGGA 59.035 41.667 0.00 0.00 0.00 4.55
653 688 2.113986 GGATCGGAATGGGCCAGG 59.886 66.667 13.78 0.93 0.00 4.45
681 716 3.372123 TCCGACGTGGAAGATGCA 58.628 55.556 0.00 0.00 46.38 3.96
682 717 1.897423 TCCGACGTGGAAGATGCAT 59.103 52.632 0.00 0.00 46.38 3.96
683 718 0.460109 TCCGACGTGGAAGATGCATG 60.460 55.000 2.46 0.00 46.38 4.06
687 722 1.028330 ACGTGGAAGATGCATGCAGG 61.028 55.000 26.69 8.24 0.00 4.85
734 769 1.022735 CAGATGTGGGCTGAGAATGC 58.977 55.000 0.00 0.00 35.39 3.56
769 804 0.042131 TATAGGGCCGGTATGAGGGG 59.958 60.000 1.90 0.00 0.00 4.79
772 807 3.087906 GGCCGGTATGAGGGGTGT 61.088 66.667 1.90 0.00 0.00 4.16
775 810 2.189521 CGGTATGAGGGGTGTGGC 59.810 66.667 0.00 0.00 0.00 5.01
796 831 2.157668 CCGAGTCAAGATTTTGTGACCG 59.842 50.000 0.36 4.50 44.30 4.79
797 832 2.411547 CGAGTCAAGATTTTGTGACCGC 60.412 50.000 0.36 0.00 44.30 5.68
801 836 2.807967 TCAAGATTTTGTGACCGCTCAG 59.192 45.455 0.00 0.00 35.73 3.35
804 839 1.197721 GATTTTGTGACCGCTCAGTGG 59.802 52.381 1.44 1.44 39.41 4.00
806 841 3.825160 TTGTGACCGCTCAGTGGCC 62.825 63.158 3.38 0.00 36.54 5.36
809 844 4.681978 GACCGCTCAGTGGCCGTT 62.682 66.667 3.38 0.00 36.54 4.44
810 845 4.250305 ACCGCTCAGTGGCCGTTT 62.250 61.111 3.38 0.00 36.54 3.60
811 846 3.726517 CCGCTCAGTGGCCGTTTG 61.727 66.667 0.00 0.00 0.00 2.93
812 847 2.972505 CGCTCAGTGGCCGTTTGT 60.973 61.111 0.00 0.00 0.00 2.83
813 848 2.639286 GCTCAGTGGCCGTTTGTG 59.361 61.111 0.00 0.00 0.00 3.33
814 849 2.186826 GCTCAGTGGCCGTTTGTGT 61.187 57.895 0.00 0.00 0.00 3.72
815 850 0.882927 GCTCAGTGGCCGTTTGTGTA 60.883 55.000 0.00 0.00 0.00 2.90
817 852 0.753867 TCAGTGGCCGTTTGTGTAGA 59.246 50.000 0.00 0.00 0.00 2.59
887 927 7.671302 TCATATTTATGAGAACCCTAGACAGC 58.329 38.462 0.00 0.00 37.76 4.40
903 943 3.380004 AGACAGCAAAACAAAATGGACGA 59.620 39.130 0.00 0.00 0.00 4.20
931 971 4.737855 TCTTCAAGCCTATGTGTACCTC 57.262 45.455 0.00 0.00 0.00 3.85
935 975 1.112113 AGCCTATGTGTACCTCGGTG 58.888 55.000 0.00 0.00 0.00 4.94
1016 1056 3.187700 GTCGGATGATGCGTAAGAAACT 58.812 45.455 6.18 0.00 43.02 2.66
1044 1084 3.186047 GGAATGGACGCGACGGTG 61.186 66.667 15.93 0.00 0.00 4.94
1130 1170 4.162690 GTCGGGCGGCCAGAAGAT 62.163 66.667 29.19 0.00 28.12 2.40
1140 1180 2.110967 CCAGAAGATGGCAGCCACG 61.111 63.158 19.10 0.87 43.83 4.94
1288 1328 0.325671 ATCTTCCTCTTCCGCCTCCA 60.326 55.000 0.00 0.00 0.00 3.86
1539 1579 8.440833 CAGTAGGTACTGTTGTTGCTTATTAAC 58.559 37.037 8.73 0.00 46.51 2.01
1700 1756 4.374843 TGGCATTATTGTTGCTAGCTTG 57.625 40.909 17.23 0.00 40.03 4.01
1749 1805 0.802222 GTCTTAGTGCGCGATGCTCA 60.802 55.000 12.10 0.00 46.63 4.26
1767 1823 6.855836 ATGCTCAACATAGTTTGGTACAATG 58.144 36.000 0.00 0.00 40.17 2.82
1833 1889 6.543831 AGAAGTTGAACTACAGTTGCTTCAAT 59.456 34.615 20.53 8.51 38.66 2.57
1866 1922 5.121380 TCGGTACAGAGGGAGTAGTTATT 57.879 43.478 0.00 0.00 0.00 1.40
1931 1987 4.859304 TGCCTTACGTTTAAGTCTCTCA 57.141 40.909 0.00 0.00 33.92 3.27
1995 2051 6.547510 GGTAGCTAATCAAATGTCCCAGAAAT 59.452 38.462 0.00 0.00 0.00 2.17
2031 2087 2.012673 CAGCCTACAAGATTGTCAGCC 58.987 52.381 13.34 0.00 42.35 4.85
2132 2188 4.582869 TGCTCTTGCATATGATATGTCCC 58.417 43.478 13.48 0.00 45.31 4.46
2183 2239 7.445121 TCTAGTGAATCATCTGTGTTTCTTGT 58.555 34.615 0.00 0.00 35.84 3.16
2226 2282 2.154854 AGCAGCAACATACGCGATAT 57.845 45.000 15.93 4.03 0.00 1.63
2424 2480 7.441836 TGTAACCTATGTTGATCATATTCGCT 58.558 34.615 0.00 0.00 38.21 4.93
2425 2481 7.598869 TGTAACCTATGTTGATCATATTCGCTC 59.401 37.037 0.00 0.00 38.21 5.03
2427 2483 6.393990 ACCTATGTTGATCATATTCGCTCTC 58.606 40.000 0.00 0.00 38.21 3.20
2443 2499 0.803117 TCTCGACACTGTTCTAGCCG 59.197 55.000 0.00 0.00 0.00 5.52
2480 2536 3.257127 GTCAAGGTCTCTGAGCACTTACT 59.743 47.826 11.52 0.00 31.89 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 7.762382 AGGCAAACTAAGTACAAAATCTATGC 58.238 34.615 0.00 0.00 0.00 3.14
53 54 7.606839 GTCCTAGGCAAACTAAGTACAAAATCT 59.393 37.037 2.96 0.00 0.00 2.40
88 89 7.259290 ACAACGACAAATATTGAGTCTTTGT 57.741 32.000 24.78 24.78 44.58 2.83
106 107 0.038251 AGAGAAGCGATGCACAACGA 60.038 50.000 12.67 0.00 0.00 3.85
107 108 1.629013 TAGAGAAGCGATGCACAACG 58.371 50.000 0.00 0.00 0.00 4.10
160 161 1.237533 TGCAACATGTGAAGCATCGT 58.762 45.000 14.61 0.00 35.19 3.73
202 237 2.049228 CAAGTACTTGACGTCACGGTC 58.951 52.381 28.17 16.06 42.93 4.79
206 241 3.014604 AGCTCAAGTACTTGACGTCAC 57.985 47.619 30.07 17.91 43.90 3.67
211 246 5.989777 TCCAAAAGTAGCTCAAGTACTTGAC 59.010 40.000 30.07 24.85 43.90 3.18
222 257 3.704800 AGGGTCTTCCAAAAGTAGCTC 57.295 47.619 0.00 0.00 38.24 4.09
248 283 9.342308 AGAACATGAGTTTGATTCTAAGTTTGA 57.658 29.630 0.00 0.00 38.30 2.69
256 291 5.641209 CCGAAGAGAACATGAGTTTGATTCT 59.359 40.000 0.00 0.00 38.30 2.40
277 312 3.431922 GGTTTGACGATGATAGACCGA 57.568 47.619 0.00 0.00 0.00 4.69
278 313 2.117137 CGGTTTGACGATGATAGACCG 58.883 52.381 0.00 0.00 41.89 4.79
291 326 0.468214 TGGTTTGGCCATCGGTTTGA 60.468 50.000 6.09 0.00 43.61 2.69
310 345 1.301165 GCGTACGGTTGACCACCTT 60.301 57.895 18.39 0.00 44.69 3.50
323 358 2.525096 CGAACAAGTGTCGATAGCGTAC 59.475 50.000 0.00 1.17 38.98 3.67
327 362 0.294887 CGCGAACAAGTGTCGATAGC 59.705 55.000 0.00 0.00 0.00 2.97
328 363 1.317611 CACGCGAACAAGTGTCGATAG 59.682 52.381 15.93 0.00 33.97 2.08
329 364 1.333115 CACGCGAACAAGTGTCGATA 58.667 50.000 15.93 0.00 33.97 2.92
330 365 1.886861 GCACGCGAACAAGTGTCGAT 61.887 55.000 15.93 0.00 40.26 3.59
331 366 2.582265 GCACGCGAACAAGTGTCGA 61.582 57.895 15.93 0.00 40.26 4.20
332 367 1.272784 TAGCACGCGAACAAGTGTCG 61.273 55.000 15.93 0.00 40.26 4.35
333 368 0.856641 TTAGCACGCGAACAAGTGTC 59.143 50.000 15.93 0.00 40.26 3.67
334 369 1.508632 ATTAGCACGCGAACAAGTGT 58.491 45.000 15.93 0.00 40.26 3.55
335 370 2.594529 AATTAGCACGCGAACAAGTG 57.405 45.000 15.93 0.00 41.01 3.16
336 371 2.671396 CCTAATTAGCACGCGAACAAGT 59.329 45.455 15.93 2.80 0.00 3.16
337 372 2.927477 TCCTAATTAGCACGCGAACAAG 59.073 45.455 15.93 0.00 0.00 3.16
338 373 2.962125 TCCTAATTAGCACGCGAACAA 58.038 42.857 15.93 0.79 0.00 2.83
339 374 2.658373 TCCTAATTAGCACGCGAACA 57.342 45.000 15.93 0.00 0.00 3.18
340 375 3.184541 TCTTCCTAATTAGCACGCGAAC 58.815 45.455 15.93 3.54 0.00 3.95
351 386 7.020827 TGACTCCTTGATGTTCTTCCTAATT 57.979 36.000 0.00 0.00 0.00 1.40
375 410 0.526662 CGACAGGTAAACGCTCCTCT 59.473 55.000 0.00 0.00 30.91 3.69
384 419 3.071479 GGTGAATTCAGCGACAGGTAAA 58.929 45.455 20.86 0.00 34.50 2.01
450 485 3.876309 AGGGTTGAAACAGTACACCAT 57.124 42.857 0.00 0.00 0.00 3.55
520 555 0.946221 GGCATGACGGACATCGGATC 60.946 60.000 0.00 0.00 44.45 3.36
558 593 1.075836 CCCCCAACCACCATTTCGA 59.924 57.895 0.00 0.00 0.00 3.71
560 595 2.645192 CGCCCCCAACCACCATTTC 61.645 63.158 0.00 0.00 0.00 2.17
567 602 0.897863 CTTCATTTCGCCCCCAACCA 60.898 55.000 0.00 0.00 0.00 3.67
579 614 5.061721 ACCCTAAACACTCCACTTCATTT 57.938 39.130 0.00 0.00 0.00 2.32
594 629 4.698304 CCGCATCTTAGACAAAACCCTAAA 59.302 41.667 0.00 0.00 0.00 1.85
595 630 4.020039 TCCGCATCTTAGACAAAACCCTAA 60.020 41.667 0.00 0.00 0.00 2.69
623 658 6.060136 CCATTCCGATCCTGCATATATTCAT 58.940 40.000 0.00 0.00 0.00 2.57
653 688 2.511600 CGTCGGATTCAGCCCACC 60.512 66.667 0.00 0.00 0.00 4.61
661 696 0.931005 GCATCTTCCACGTCGGATTC 59.069 55.000 7.43 0.00 45.80 2.52
662 697 0.249120 TGCATCTTCCACGTCGGATT 59.751 50.000 7.43 0.00 45.80 3.01
674 709 1.651240 GACGTGCCTGCATGCATCTT 61.651 55.000 22.97 7.24 44.30 2.40
675 710 2.045634 ACGTGCCTGCATGCATCT 60.046 55.556 22.97 5.32 44.30 2.90
734 769 2.023414 TATACGGCCGGGCTGACAAG 62.023 60.000 33.58 11.72 38.46 3.16
769 804 1.523758 AAATCTTGACTCGGCCACAC 58.476 50.000 2.24 0.00 0.00 3.82
772 807 1.879380 CACAAAATCTTGACTCGGCCA 59.121 47.619 2.24 0.00 36.33 5.36
775 810 2.157668 CGGTCACAAAATCTTGACTCGG 59.842 50.000 2.04 0.00 41.65 4.63
796 831 0.882927 TACACAAACGGCCACTGAGC 60.883 55.000 2.24 0.00 0.00 4.26
797 832 1.148310 CTACACAAACGGCCACTGAG 58.852 55.000 2.24 0.00 0.00 3.35
801 836 0.877213 ACGTCTACACAAACGGCCAC 60.877 55.000 2.24 0.00 42.99 5.01
804 839 4.019919 TCTATACGTCTACACAAACGGC 57.980 45.455 0.00 0.00 42.99 5.68
806 841 6.630443 GGTACATCTATACGTCTACACAAACG 59.370 42.308 0.00 0.00 44.22 3.60
807 842 7.475015 TGGTACATCTATACGTCTACACAAAC 58.525 38.462 0.00 0.00 0.00 2.93
808 843 7.628769 TGGTACATCTATACGTCTACACAAA 57.371 36.000 0.00 0.00 0.00 2.83
809 844 6.238566 GCTGGTACATCTATACGTCTACACAA 60.239 42.308 0.00 0.00 38.20 3.33
810 845 5.237996 GCTGGTACATCTATACGTCTACACA 59.762 44.000 0.00 0.00 38.20 3.72
811 846 5.469421 AGCTGGTACATCTATACGTCTACAC 59.531 44.000 0.00 0.00 38.20 2.90
812 847 5.618236 AGCTGGTACATCTATACGTCTACA 58.382 41.667 0.00 0.00 38.20 2.74
813 848 5.699915 TGAGCTGGTACATCTATACGTCTAC 59.300 44.000 0.00 0.00 33.65 2.59
814 849 5.861727 TGAGCTGGTACATCTATACGTCTA 58.138 41.667 0.00 0.00 33.65 2.59
815 850 4.715713 TGAGCTGGTACATCTATACGTCT 58.284 43.478 0.00 0.00 33.65 4.18
817 852 6.149640 CAGTATGAGCTGGTACATCTATACGT 59.850 42.308 0.00 0.00 39.69 3.57
887 927 3.067461 TCCAGGTCGTCCATTTTGTTTTG 59.933 43.478 0.51 0.00 35.89 2.44
903 943 3.118112 CACATAGGCTTGAAGATCCAGGT 60.118 47.826 0.00 0.00 0.00 4.00
946 986 1.595093 CCCCCAATTTGAGCACGGTC 61.595 60.000 0.00 0.00 0.00 4.79
947 987 1.606313 CCCCCAATTTGAGCACGGT 60.606 57.895 0.00 0.00 0.00 4.83
1609 1665 3.480470 ACTATGCTGAGCACAACAAACT 58.520 40.909 10.33 0.00 43.04 2.66
1689 1745 2.608016 GCCAAGGAAACAAGCTAGCAAC 60.608 50.000 18.83 1.16 0.00 4.17
1700 1756 2.128771 TATCAGCCAGCCAAGGAAAC 57.871 50.000 0.00 0.00 0.00 2.78
1833 1889 6.072649 TCCCTCTGTACCGAAATATATGTCA 58.927 40.000 3.79 0.00 0.00 3.58
1844 1900 4.785346 ATAACTACTCCCTCTGTACCGA 57.215 45.455 0.00 0.00 0.00 4.69
1995 2051 3.156293 AGGCTGTGACATTGTGCATTAA 58.844 40.909 0.00 0.00 0.00 1.40
2132 2188 2.813754 TGGAAATCTTGGAAAGCACTCG 59.186 45.455 0.00 0.00 45.70 4.18
2183 2239 9.547753 GCTTGTGGATCTTATTATCTCTTAACA 57.452 33.333 0.00 0.00 0.00 2.41
2199 2255 2.223112 CGTATGTTGCTGCTTGTGGATC 60.223 50.000 0.00 0.00 0.00 3.36
2266 2322 8.908786 ATGACCATCTAGTATATTTGGTGTTG 57.091 34.615 0.00 0.00 36.29 3.33
2300 2356 9.685276 AACATAGAGAACATTACATGGAAATGA 57.315 29.630 22.62 6.31 37.68 2.57
2424 2480 0.803117 CGGCTAGAACAGTGTCGAGA 59.197 55.000 0.00 0.00 0.00 4.04
2425 2481 0.522180 ACGGCTAGAACAGTGTCGAG 59.478 55.000 6.78 1.47 0.00 4.04
2427 2483 1.779569 AAACGGCTAGAACAGTGTCG 58.220 50.000 0.00 0.00 0.00 4.35
2443 2499 7.494952 AGAGACCTTGACTTACAACACTTAAAC 59.505 37.037 0.00 0.00 34.56 2.01
2480 2536 1.509463 CTAACGCGTAGGTGGCAGA 59.491 57.895 14.46 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.