Multiple sequence alignment - TraesCS1A01G212000

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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 TraesCS1A01G212000 chr1A 100.000 2996 0 0 1 2996 374691656 374688661 0.000000e+00 5533.0
1 TraesCS1A01G212000 chr1A 80.299 335 57 4 1671 1996 375468981 375469315 8.300000e-61 244.0
2 TraesCS1A01G212000 chr1A 87.634 186 23 0 1481 1666 375113130 375112945 1.810000e-52 217.0
3 TraesCS1A01G212000 chr1D 90.852 1596 91 26 1421 2996 300326358 300324798 0.000000e+00 2087.0
4 TraesCS1A01G212000 chr1D 92.712 1427 51 24 1 1417 300327790 300326407 0.000000e+00 2010.0
5 TraesCS1A01G212000 chr1D 79.104 335 61 4 1671 1996 300859830 300860164 3.890000e-54 222.0
6 TraesCS1A01G212000 chr1D 87.234 188 23 1 1480 1666 300718827 300718640 2.340000e-51 213.0
7 TraesCS1A01G212000 chr1B 89.109 1414 75 34 21 1410 405527030 405525672 0.000000e+00 1685.0
8 TraesCS1A01G212000 chr1B 91.753 1152 55 16 1416 2558 405525615 405524495 0.000000e+00 1565.0
9 TraesCS1A01G212000 chr1B 87.417 453 42 8 2556 2996 405524430 405523981 9.580000e-140 507.0
10 TraesCS1A01G212000 chr1B 80.299 335 57 4 1671 1996 406037242 406037576 8.300000e-61 244.0
11 TraesCS1A01G212000 chr1B 87.097 186 24 0 1481 1666 405905985 405905800 8.410000e-51 211.0
12 TraesCS1A01G212000 chr1B 88.608 79 9 0 1121 1199 405673634 405673556 2.460000e-16 97.1
13 TraesCS1A01G212000 chr6D 78.812 505 89 13 1508 1997 15551133 15550632 1.040000e-84 324.0
14 TraesCS1A01G212000 chr6D 77.579 504 99 10 1507 1997 15640543 15641045 2.920000e-75 292.0
15 TraesCS1A01G212000 chr6D 86.066 122 17 0 1293 1414 15640251 15640372 6.740000e-27 132.0
16 TraesCS1A01G212000 chrUn 78.373 504 84 17 1508 1990 319197530 319197031 1.350000e-78 303.0
17 TraesCS1A01G212000 chr6B 77.273 506 97 14 1507 1997 27669232 27669734 6.320000e-72 281.0
18 TraesCS1A01G212000 chr6B 85.938 128 13 4 1293 1417 27668940 27669065 6.740000e-27 132.0
19 TraesCS1A01G212000 chr5A 88.652 141 16 0 1526 1666 694759690 694759830 3.970000e-39 172.0
20 TraesCS1A01G212000 chr4B 88.652 141 16 0 1526 1666 659330243 659330103 3.970000e-39 172.0
21 TraesCS1A01G212000 chr3D 91.379 116 6 3 1297 1410 391736 391623 4.000000e-34 156.0
22 TraesCS1A01G212000 chr3A 90.351 114 11 0 1297 1410 9110405 9110518 1.860000e-32 150.0
23 TraesCS1A01G212000 chr3B 88.618 123 9 4 1297 1417 5802830 5802711 8.660000e-31 145.0
24 TraesCS1A01G212000 chr3B 89.655 116 8 3 1297 1410 6117725 6117838 8.660000e-31 145.0
25 TraesCS1A01G212000 chr3B 100.000 30 0 0 1 30 562922492 562922463 4.170000e-04 56.5
26 TraesCS1A01G212000 chr6A 86.066 122 17 0 1293 1414 16337905 16338026 6.740000e-27 132.0


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 TraesCS1A01G212000 chr1A 374688661 374691656 2995 True 5533.000000 5533 100.000000 1 2996 1 chr1A.!!$R1 2995
1 TraesCS1A01G212000 chr1D 300324798 300327790 2992 True 2048.500000 2087 91.782000 1 2996 2 chr1D.!!$R2 2995
2 TraesCS1A01G212000 chr1B 405523981 405527030 3049 True 1252.333333 1685 89.426333 21 2996 3 chr1B.!!$R3 2975
3 TraesCS1A01G212000 chr6D 15550632 15551133 501 True 324.000000 324 78.812000 1508 1997 1 chr6D.!!$R1 489
4 TraesCS1A01G212000 chr6D 15640251 15641045 794 False 212.000000 292 81.822500 1293 1997 2 chr6D.!!$F1 704
5 TraesCS1A01G212000 chr6B 27668940 27669734 794 False 206.500000 281 81.605500 1293 1997 2 chr6B.!!$F1 704

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
931 958 0.320247 CAGACCAGAGTCCACAGCAC 60.32 60.0 0.0 0.0 44.72 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2841 3049 0.039074 AAGCACGAGAACAGGAGACG 60.039 55.0 0.0 0.0 0.0 4.18 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
53 54 6.416750 CCACTAACACTTCGGTTTCATTTTTC 59.583 38.462 0.00 0.00 32.29 2.29
97 98 2.559440 GCTGATTGGCTAAGGTGAGAG 58.441 52.381 0.00 0.00 0.00 3.20
98 99 2.169352 GCTGATTGGCTAAGGTGAGAGA 59.831 50.000 0.00 0.00 0.00 3.10
99 100 3.369892 GCTGATTGGCTAAGGTGAGAGAA 60.370 47.826 0.00 0.00 0.00 2.87
141 144 3.922171 TGAGGGGTTTGTTTGCAAATT 57.078 38.095 16.21 0.00 45.11 1.82
155 158 5.559148 TTGCAAATTTGAAGTGGGGTTAT 57.441 34.783 22.31 0.00 0.00 1.89
158 161 5.163258 TGCAAATTTGAAGTGGGGTTATGTT 60.163 36.000 22.31 0.00 0.00 2.71
173 177 4.773149 GGTTATGTTCTATCCTCGGATCCT 59.227 45.833 10.75 0.00 36.17 3.24
179 183 4.388577 TCTATCCTCGGATCCTGATCAA 57.611 45.455 10.75 0.00 39.54 2.57
202 206 4.312443 ACGGTCAAAAACGACATATGACT 58.688 39.130 10.38 0.00 40.12 3.41
204 208 4.387559 CGGTCAAAAACGACATATGACTGA 59.612 41.667 10.38 0.00 45.75 3.41
222 226 6.834107 TGACTGATACATCATCATCACCAAT 58.166 36.000 0.00 0.00 42.82 3.16
278 285 0.458669 AGACGGGCGGTAACTGTATG 59.541 55.000 0.00 0.00 0.00 2.39
338 347 0.842635 AGCCACCCAGAGGATCAATC 59.157 55.000 0.00 0.00 37.82 2.67
339 348 0.533755 GCCACCCAGAGGATCAATCG 60.534 60.000 0.00 0.00 37.82 3.34
340 349 1.123077 CCACCCAGAGGATCAATCGA 58.877 55.000 0.00 0.00 37.82 3.59
341 350 1.696336 CCACCCAGAGGATCAATCGAT 59.304 52.381 0.00 0.00 37.82 3.59
342 351 2.549563 CCACCCAGAGGATCAATCGATG 60.550 54.545 0.00 0.00 37.82 3.84
351 360 1.058837 GATCAATCGATGCGATGCGAG 59.941 52.381 13.71 0.00 46.30 5.03
375 384 9.434420 GAGGATGAATTATCACTCTAGAAATGG 57.566 37.037 0.00 0.00 38.69 3.16
397 406 2.693069 GGATACGATGATTGCCTCCAG 58.307 52.381 0.00 0.00 0.00 3.86
412 421 3.201290 CCTCCAGAGTTCCATTGATTCG 58.799 50.000 0.00 0.00 0.00 3.34
413 422 3.118629 CCTCCAGAGTTCCATTGATTCGA 60.119 47.826 0.00 0.00 0.00 3.71
414 423 4.118410 CTCCAGAGTTCCATTGATTCGAG 58.882 47.826 0.00 0.00 0.00 4.04
416 425 3.369892 CCAGAGTTCCATTGATTCGAGGT 60.370 47.826 0.00 0.00 0.00 3.85
417 426 3.620374 CAGAGTTCCATTGATTCGAGGTG 59.380 47.826 0.00 0.00 0.00 4.00
418 427 2.939103 GAGTTCCATTGATTCGAGGTGG 59.061 50.000 0.00 0.00 0.00 4.61
420 429 3.200825 AGTTCCATTGATTCGAGGTGGAT 59.799 43.478 7.01 0.00 38.64 3.41
421 430 3.198409 TCCATTGATTCGAGGTGGATG 57.802 47.619 0.00 0.00 34.23 3.51
422 431 1.605710 CCATTGATTCGAGGTGGATGC 59.394 52.381 0.00 0.00 31.59 3.91
423 432 2.569059 CATTGATTCGAGGTGGATGCT 58.431 47.619 0.00 0.00 0.00 3.79
424 433 3.494924 CCATTGATTCGAGGTGGATGCTA 60.495 47.826 0.00 0.00 31.59 3.49
425 434 4.321718 CATTGATTCGAGGTGGATGCTAT 58.678 43.478 0.00 0.00 0.00 2.97
438 447 4.034048 GTGGATGCTATTAGTTTCCGTGTG 59.966 45.833 8.57 0.00 0.00 3.82
484 497 2.818274 GGCGATGGTGGGTCGTTC 60.818 66.667 0.00 0.00 40.98 3.95
485 498 3.186047 GCGATGGTGGGTCGTTCG 61.186 66.667 0.00 0.00 40.98 3.95
486 499 2.260434 CGATGGTGGGTCGTTCGT 59.740 61.111 0.00 0.00 34.56 3.85
487 500 1.804326 CGATGGTGGGTCGTTCGTC 60.804 63.158 0.00 0.00 34.56 4.20
583 596 2.869101 TCGAAATCATCAACACCCCA 57.131 45.000 0.00 0.00 0.00 4.96
584 597 3.147553 TCGAAATCATCAACACCCCAA 57.852 42.857 0.00 0.00 0.00 4.12
585 598 2.817258 TCGAAATCATCAACACCCCAAC 59.183 45.455 0.00 0.00 0.00 3.77
586 599 2.094752 CGAAATCATCAACACCCCAACC 60.095 50.000 0.00 0.00 0.00 3.77
587 600 1.937191 AATCATCAACACCCCAACCC 58.063 50.000 0.00 0.00 0.00 4.11
670 683 2.640302 ATAGCGGCCGAGATGCGAT 61.640 57.895 33.48 9.57 44.57 4.58
680 693 5.088739 GGCCGAGATGCGATTTTTATAATG 58.911 41.667 0.00 0.00 44.57 1.90
931 958 0.320247 CAGACCAGAGTCCACAGCAC 60.320 60.000 0.00 0.00 44.72 4.40
932 959 0.760567 AGACCAGAGTCCACAGCACA 60.761 55.000 0.00 0.00 44.72 4.57
933 960 0.320247 GACCAGAGTCCACAGCACAG 60.320 60.000 0.00 0.00 37.00 3.66
934 961 1.670406 CCAGAGTCCACAGCACAGC 60.670 63.158 0.00 0.00 0.00 4.40
935 962 1.070275 CAGAGTCCACAGCACAGCA 59.930 57.895 0.00 0.00 0.00 4.41
945 972 3.360340 GCACAGCAGAGCACCACC 61.360 66.667 0.00 0.00 0.00 4.61
958 985 0.611714 CACCACCACTACTACCACCC 59.388 60.000 0.00 0.00 0.00 4.61
959 986 0.546027 ACCACCACTACTACCACCCC 60.546 60.000 0.00 0.00 0.00 4.95
960 987 1.269703 CCACCACTACTACCACCCCC 61.270 65.000 0.00 0.00 0.00 5.40
1005 1035 3.796764 AGCTTAGCTGAAGATGGCC 57.203 52.632 5.70 0.00 37.57 5.36
1027 1057 0.179124 GCTACTCTCTGTCAAGGCCG 60.179 60.000 0.00 0.00 0.00 6.13
1061 1091 4.894203 GCTTGCTGCCGCGTATGC 62.894 66.667 4.92 6.43 39.65 3.14
1209 1239 2.513897 GGTACGTGCCTGCCCATC 60.514 66.667 16.23 0.00 0.00 3.51
1210 1240 2.890474 GTACGTGCCTGCCCATCG 60.890 66.667 0.00 0.00 0.00 3.84
1211 1241 3.071837 TACGTGCCTGCCCATCGA 61.072 61.111 0.00 0.00 0.00 3.59
1221 1251 4.838152 CCCATCGAGCCGTGTGGG 62.838 72.222 18.19 18.19 42.96 4.61
1239 1269 0.171903 GGTGCTTTTGATGCAGCGAT 59.828 50.000 0.00 0.00 46.39 4.58
1257 1287 3.303001 GCGATTGCTCTCTGTTCTAATGC 60.303 47.826 0.00 0.00 38.39 3.56
1277 1307 2.393764 CCGTTGCTCAATTTGGTTCAC 58.606 47.619 0.00 0.00 0.00 3.18
1281 1311 0.388520 GCTCAATTTGGTTCACCGGC 60.389 55.000 0.00 0.00 39.43 6.13
1442 1533 3.093717 AGTACACTGTACTGCACACAC 57.906 47.619 19.19 0.00 32.33 3.82
1450 1541 4.039245 ACTGTACTGCACACACTTATCAGT 59.961 41.667 0.00 0.00 40.60 3.41
1471 1567 5.088141 GTCATCAGTGTGTTGACTTCTTG 57.912 43.478 9.79 0.00 41.46 3.02
1472 1568 3.561310 TCATCAGTGTGTTGACTTCTTGC 59.439 43.478 0.00 0.00 0.00 4.01
1635 1756 1.743252 GGGGCTCAACGAGAAGCTG 60.743 63.158 0.00 0.00 0.00 4.24
1669 1790 1.144057 ATCGACATCCAGTTCCGGC 59.856 57.895 0.00 0.00 0.00 6.13
1689 1810 2.116125 GTGCCCTGCAACTTCCCT 59.884 61.111 0.00 0.00 41.47 4.20
1935 2068 1.109323 AGAAGCTGGTGGCCAACAAC 61.109 55.000 26.68 21.64 43.05 3.32
2083 2220 3.077556 CCCCTCTGCTGGCTACGT 61.078 66.667 0.00 0.00 0.00 3.57
2084 2221 1.756950 CCCCTCTGCTGGCTACGTA 60.757 63.158 0.00 0.00 0.00 3.57
2085 2222 1.437986 CCCTCTGCTGGCTACGTAC 59.562 63.158 0.00 0.00 0.00 3.67
2086 2223 1.320344 CCCTCTGCTGGCTACGTACA 61.320 60.000 0.00 0.00 0.00 2.90
2229 2367 4.481870 GCATGTGTGGGAAATGCG 57.518 55.556 0.00 0.00 37.55 4.73
2235 2373 2.440247 GTGGGAAATGCGGGAGGG 60.440 66.667 0.00 0.00 0.00 4.30
2306 2444 2.832129 ACATGAGATGACACTACCGGTT 59.168 45.455 15.04 0.00 0.00 4.44
2312 2450 4.817517 AGATGACACTACCGGTTTGTAAG 58.182 43.478 15.04 5.99 0.00 2.34
2323 2461 3.005367 CCGGTTTGTAAGCAAATCCAAGT 59.995 43.478 0.00 0.00 45.11 3.16
2324 2462 4.500716 CCGGTTTGTAAGCAAATCCAAGTT 60.501 41.667 0.00 0.00 45.11 2.66
2325 2463 5.278561 CCGGTTTGTAAGCAAATCCAAGTTA 60.279 40.000 0.00 0.00 45.11 2.24
2484 2624 2.814280 ATATAAAGAGACGGGCCGTG 57.186 50.000 39.41 6.59 41.37 4.94
2498 2638 2.202298 CGTGGCCGAAACGAATGC 60.202 61.111 8.34 0.00 43.68 3.56
2530 2670 7.342284 TCTCCTAGAATTACAACTCTAAGGTGG 59.658 40.741 0.00 0.00 37.20 4.61
2594 2801 3.845781 TGGAGAAGATGATTGTAGGCC 57.154 47.619 0.00 0.00 0.00 5.19
2809 3017 2.305928 CCATATTCCAAATCCGCACCA 58.694 47.619 0.00 0.00 0.00 4.17
2813 3021 0.958091 TTCCAAATCCGCACCAAGTG 59.042 50.000 0.00 0.00 36.51 3.16
2830 3038 3.111853 AGTGTCGACATTTGAAGAGCA 57.888 42.857 23.12 0.00 0.00 4.26
2841 3049 2.359230 AAGAGCAAGTGAGCCGCC 60.359 61.111 0.00 0.00 34.23 6.13
2868 3076 2.975851 CTGTTCTCGTGCTTGCATTTTC 59.024 45.455 0.00 0.00 0.00 2.29
2869 3077 1.971962 GTTCTCGTGCTTGCATTTTCG 59.028 47.619 0.00 0.00 0.00 3.46
2883 3091 2.610219 TTTTCGCAATGACACATCCG 57.390 45.000 0.00 0.00 0.00 4.18
2893 3101 5.523916 GCAATGACACATCCGAGTTATACTT 59.476 40.000 0.00 0.00 0.00 2.24
2894 3102 6.700081 GCAATGACACATCCGAGTTATACTTA 59.300 38.462 0.00 0.00 0.00 2.24
2896 3104 9.908152 CAATGACACATCCGAGTTATACTTATA 57.092 33.333 0.00 0.00 0.00 0.98
2926 3135 9.177608 TCATAACTTGCAAAAGACTGCTTATAT 57.822 29.630 0.00 0.00 43.07 0.86
2931 3140 8.960591 ACTTGCAAAAGACTGCTTATATTATGT 58.039 29.630 0.00 0.00 43.07 2.29
2932 3141 9.229784 CTTGCAAAAGACTGCTTATATTATGTG 57.770 33.333 0.00 0.00 43.07 3.21
2937 3146 5.784177 AGACTGCTTATATTATGTGACGGG 58.216 41.667 0.00 0.00 0.00 5.28
2982 3201 2.783135 TGAACCAGCTCCAAGATTGAC 58.217 47.619 0.00 0.00 0.00 3.18
2984 3203 0.976641 ACCAGCTCCAAGATTGACGA 59.023 50.000 0.00 0.00 0.00 4.20
2988 3207 3.441572 CCAGCTCCAAGATTGACGATTTT 59.558 43.478 0.00 0.00 0.00 1.82
2989 3208 4.409570 CAGCTCCAAGATTGACGATTTTG 58.590 43.478 0.00 0.00 31.42 2.44
2991 3210 3.762779 CTCCAAGATTGACGATTTTGCC 58.237 45.455 0.00 0.00 30.52 4.52
2992 3211 3.420893 TCCAAGATTGACGATTTTGCCT 58.579 40.909 0.00 0.00 30.52 4.75
2994 3213 3.428045 CCAAGATTGACGATTTTGCCTCC 60.428 47.826 0.00 0.00 30.52 4.30
2995 3214 3.071874 AGATTGACGATTTTGCCTCCA 57.928 42.857 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 7.329588 AGAAAAATGAAACCGAAGTGTTAGT 57.670 32.000 0.00 0.00 0.00 2.24
97 98 8.900781 TCATTCTTTTCATCCATCTTCATCTTC 58.099 33.333 0.00 0.00 0.00 2.87
98 99 8.818622 TCATTCTTTTCATCCATCTTCATCTT 57.181 30.769 0.00 0.00 0.00 2.40
99 100 7.502895 CCTCATTCTTTTCATCCATCTTCATCT 59.497 37.037 0.00 0.00 0.00 2.90
141 144 5.491078 AGGATAGAACATAACCCCACTTCAA 59.509 40.000 0.00 0.00 0.00 2.69
155 158 3.595190 TCAGGATCCGAGGATAGAACA 57.405 47.619 5.98 0.00 34.60 3.18
158 161 4.388577 TTGATCAGGATCCGAGGATAGA 57.611 45.455 14.16 4.49 37.02 1.98
173 177 3.374367 TGTCGTTTTTGACCGTTTGATCA 59.626 39.130 0.00 0.00 38.11 2.92
179 183 4.753107 AGTCATATGTCGTTTTTGACCGTT 59.247 37.500 1.90 0.00 37.91 4.44
278 285 1.067213 ACAAAATATGGGCACGCAACC 60.067 47.619 0.00 0.00 0.00 3.77
311 320 2.674380 CTGGGTGGCTGCAAGTCC 60.674 66.667 0.50 0.00 38.23 3.85
338 347 0.940991 TTCATCCTCGCATCGCATCG 60.941 55.000 0.00 0.00 0.00 3.84
339 348 1.436600 ATTCATCCTCGCATCGCATC 58.563 50.000 0.00 0.00 0.00 3.91
340 349 1.888215 AATTCATCCTCGCATCGCAT 58.112 45.000 0.00 0.00 0.00 4.73
341 350 2.524569 TAATTCATCCTCGCATCGCA 57.475 45.000 0.00 0.00 0.00 5.10
342 351 2.995939 TGATAATTCATCCTCGCATCGC 59.004 45.455 0.00 0.00 32.09 4.58
351 360 7.148507 CGCCATTTCTAGAGTGATAATTCATCC 60.149 40.741 8.36 0.00 33.56 3.51
375 384 1.071605 GAGGCAATCATCGTATCCGC 58.928 55.000 0.00 0.00 0.00 5.54
397 406 2.939103 CCACCTCGAATCAATGGAACTC 59.061 50.000 0.00 0.00 31.69 3.01
412 421 4.058817 CGGAAACTAATAGCATCCACCTC 58.941 47.826 11.08 0.00 0.00 3.85
413 422 3.454812 ACGGAAACTAATAGCATCCACCT 59.545 43.478 11.08 0.00 0.00 4.00
414 423 3.560068 CACGGAAACTAATAGCATCCACC 59.440 47.826 11.08 0.00 0.00 4.61
416 425 4.188462 CACACGGAAACTAATAGCATCCA 58.812 43.478 11.08 0.00 0.00 3.41
417 426 3.560068 CCACACGGAAACTAATAGCATCC 59.440 47.826 2.77 2.77 0.00 3.51
418 427 4.189231 ACCACACGGAAACTAATAGCATC 58.811 43.478 0.00 0.00 35.59 3.91
420 429 3.688694 ACCACACGGAAACTAATAGCA 57.311 42.857 0.00 0.00 35.59 3.49
421 430 5.583457 ACAATACCACACGGAAACTAATAGC 59.417 40.000 0.00 0.00 35.59 2.97
422 431 6.814644 TCACAATACCACACGGAAACTAATAG 59.185 38.462 0.00 0.00 35.59 1.73
423 432 6.699366 TCACAATACCACACGGAAACTAATA 58.301 36.000 0.00 0.00 35.59 0.98
424 433 5.553123 TCACAATACCACACGGAAACTAAT 58.447 37.500 0.00 0.00 35.59 1.73
425 434 4.958509 TCACAATACCACACGGAAACTAA 58.041 39.130 0.00 0.00 35.59 2.24
438 447 1.583054 GCCAGGTCGATCACAATACC 58.417 55.000 0.00 0.00 0.00 2.73
796 823 2.430367 GTCACCCTCACCCACCAC 59.570 66.667 0.00 0.00 0.00 4.16
848 875 2.050442 CAGGCAAAACGAACGGCC 60.050 61.111 0.00 0.00 46.77 6.13
849 876 2.729491 GCAGGCAAAACGAACGGC 60.729 61.111 0.00 0.00 0.00 5.68
850 877 1.231958 TAGGCAGGCAAAACGAACGG 61.232 55.000 0.00 0.00 0.00 4.44
851 878 0.802494 ATAGGCAGGCAAAACGAACG 59.198 50.000 0.00 0.00 0.00 3.95
852 879 4.428615 TTTATAGGCAGGCAAAACGAAC 57.571 40.909 0.00 0.00 0.00 3.95
853 880 5.883673 ACTATTTATAGGCAGGCAAAACGAA 59.116 36.000 0.00 0.00 34.69 3.85
854 881 5.433526 ACTATTTATAGGCAGGCAAAACGA 58.566 37.500 0.00 0.00 34.69 3.85
931 958 0.671781 GTAGTGGTGGTGCTCTGCTG 60.672 60.000 0.00 0.00 0.00 4.41
932 959 0.833834 AGTAGTGGTGGTGCTCTGCT 60.834 55.000 0.00 0.00 0.00 4.24
933 960 0.895530 TAGTAGTGGTGGTGCTCTGC 59.104 55.000 0.00 0.00 0.00 4.26
934 961 1.204941 GGTAGTAGTGGTGGTGCTCTG 59.795 57.143 0.00 0.00 0.00 3.35
935 962 1.203137 TGGTAGTAGTGGTGGTGCTCT 60.203 52.381 0.00 0.00 0.00 4.09
945 972 0.902531 CACTGGGGGTGGTAGTAGTG 59.097 60.000 0.00 0.00 41.90 2.74
958 985 2.282462 GTCAGGGTTGCCACTGGG 60.282 66.667 0.00 0.00 35.47 4.45
959 986 1.152777 TTGTCAGGGTTGCCACTGG 60.153 57.895 0.00 0.00 35.47 4.00
960 987 1.174712 CCTTGTCAGGGTTGCCACTG 61.175 60.000 0.00 0.00 36.36 3.66
996 1026 1.069935 GAGTAGCCCGGCCATCTTC 59.930 63.158 5.55 0.00 0.00 2.87
1005 1035 0.457851 CCTTGACAGAGAGTAGCCCG 59.542 60.000 0.00 0.00 0.00 6.13
1207 1237 4.760047 GCACCCACACGGCTCGAT 62.760 66.667 1.50 0.00 33.26 3.59
1209 1239 4.988598 AAGCACCCACACGGCTCG 62.989 66.667 0.00 0.00 36.76 5.03
1210 1240 2.193536 AAAAGCACCCACACGGCTC 61.194 57.895 0.00 0.00 36.76 4.70
1211 1241 2.123897 AAAAGCACCCACACGGCT 60.124 55.556 0.00 0.00 40.14 5.52
1213 1243 0.039256 CATCAAAAGCACCCACACGG 60.039 55.000 0.00 0.00 37.81 4.94
1214 1244 0.664166 GCATCAAAAGCACCCACACG 60.664 55.000 0.00 0.00 0.00 4.49
1216 1246 0.675083 CTGCATCAAAAGCACCCACA 59.325 50.000 0.00 0.00 37.02 4.17
1217 1247 0.668401 GCTGCATCAAAAGCACCCAC 60.668 55.000 0.00 0.00 39.31 4.61
1220 1250 0.171903 ATCGCTGCATCAAAAGCACC 59.828 50.000 0.00 0.00 39.47 5.01
1221 1251 1.652124 CAATCGCTGCATCAAAAGCAC 59.348 47.619 0.00 0.00 39.47 4.40
1222 1252 1.985334 CAATCGCTGCATCAAAAGCA 58.015 45.000 0.00 0.00 39.47 3.91
1239 1269 2.028112 ACGGCATTAGAACAGAGAGCAA 60.028 45.455 0.00 0.00 0.00 3.91
1257 1287 2.393764 GTGAACCAAATTGAGCAACGG 58.606 47.619 0.00 0.00 0.00 4.44
1277 1307 3.496131 GCATGTACACCACGCCGG 61.496 66.667 0.00 0.00 42.50 6.13
1281 1311 2.739704 CGCCTGCATGTACACCACG 61.740 63.158 0.00 0.00 0.00 4.94
1417 1447 5.474189 TGTGTGCAGTACAGTGTACTATACA 59.526 40.000 30.58 29.96 40.69 2.29
1431 1522 4.864704 TGACTGATAAGTGTGTGCAGTA 57.135 40.909 0.00 0.00 39.68 2.74
1435 1526 4.092529 CACTGATGACTGATAAGTGTGTGC 59.907 45.833 0.00 0.00 38.40 4.57
1442 1533 6.400579 GTCAACACACTGATGACTGATAAG 57.599 41.667 5.62 0.00 43.88 1.73
1450 1541 3.561310 GCAAGAAGTCAACACACTGATGA 59.439 43.478 0.00 0.00 0.00 2.92
1471 1567 1.398390 CCGTATCTGAAAGCACAAGGC 59.602 52.381 0.00 0.00 45.30 4.35
1472 1568 2.416547 CACCGTATCTGAAAGCACAAGG 59.583 50.000 0.00 0.00 0.00 3.61
1615 1736 2.125512 CTTCTCGTTGAGCCCCGG 60.126 66.667 0.00 0.00 0.00 5.73
1689 1810 1.704628 TGGAAGTTGATCTTGAGGCCA 59.295 47.619 5.01 0.00 36.40 5.36
1935 2068 2.819595 CAGTTGGCCGGGATGACG 60.820 66.667 2.18 0.00 0.00 4.35
2060 2197 4.106925 CCAGCAGAGGGGCCAGAC 62.107 72.222 4.39 0.00 0.00 3.51
2083 2220 1.067364 TCGGCCGAGCGATTAATTGTA 59.933 47.619 27.28 0.00 0.00 2.41
2084 2221 0.179094 TCGGCCGAGCGATTAATTGT 60.179 50.000 27.28 0.00 0.00 2.71
2085 2222 1.126846 GATCGGCCGAGCGATTAATTG 59.873 52.381 33.87 0.00 0.00 2.32
2086 2223 1.429463 GATCGGCCGAGCGATTAATT 58.571 50.000 33.87 13.42 0.00 1.40
2132 2270 4.272489 CTCCTTGATCCCAAGCAAATACA 58.728 43.478 0.00 0.00 46.42 2.29
2133 2271 3.067320 GCTCCTTGATCCCAAGCAAATAC 59.933 47.826 0.00 0.00 46.42 1.89
2134 2272 3.053395 AGCTCCTTGATCCCAAGCAAATA 60.053 43.478 8.57 0.00 46.42 1.40
2135 2273 2.105766 GCTCCTTGATCCCAAGCAAAT 58.894 47.619 0.00 0.00 46.42 2.32
2141 2279 0.826715 CTCGAGCTCCTTGATCCCAA 59.173 55.000 8.47 0.00 0.00 4.12
2279 2417 5.240844 CGGTAGTGTCATCTCATGTATGGTA 59.759 44.000 9.80 0.04 0.00 3.25
2498 2638 7.987649 AGAGTTGTAATTCTAGGAGAGTAACG 58.012 38.462 0.00 0.00 0.00 3.18
2530 2670 1.172812 AGGTCAAAGCCGGAGCAAAC 61.173 55.000 5.05 0.00 43.56 2.93
2584 2791 3.247006 TCTCGACAAAGGCCTACAATC 57.753 47.619 5.16 0.28 0.00 2.67
2594 2801 6.143118 GGATCTTTCGTCATATCTCGACAAAG 59.857 42.308 0.00 0.00 35.34 2.77
2731 2938 2.434185 TCGGCGCAACCATGACTC 60.434 61.111 10.83 0.00 39.03 3.36
2735 2942 1.135315 CTTTCTCGGCGCAACCATG 59.865 57.895 10.83 0.00 39.03 3.66
2761 2968 1.412079 TGGGTTGGATGGCATAATGC 58.588 50.000 0.00 0.00 44.08 3.56
2809 3017 3.466836 TGCTCTTCAAATGTCGACACTT 58.533 40.909 22.71 14.53 0.00 3.16
2813 3021 3.494626 TCACTTGCTCTTCAAATGTCGAC 59.505 43.478 9.11 9.11 33.90 4.20
2830 3038 4.070552 GGAGACGGCGGCTCACTT 62.071 66.667 40.17 8.41 34.07 3.16
2841 3049 0.039074 AAGCACGAGAACAGGAGACG 60.039 55.000 0.00 0.00 0.00 4.18
2850 3058 1.662876 GCGAAAATGCAAGCACGAGAA 60.663 47.619 0.00 0.00 34.15 2.87
2868 3076 1.078709 AACTCGGATGTGTCATTGCG 58.921 50.000 0.00 0.00 0.00 4.85
2869 3077 5.050490 AGTATAACTCGGATGTGTCATTGC 58.950 41.667 0.00 0.00 0.00 3.56
2894 3102 9.143631 GCAGTCTTTTGCAAGTTATGAAAATAT 57.856 29.630 0.00 0.00 43.53 1.28
2896 3104 7.212274 AGCAGTCTTTTGCAAGTTATGAAAAT 58.788 30.769 0.00 0.00 46.47 1.82
2898 3106 6.147864 AGCAGTCTTTTGCAAGTTATGAAA 57.852 33.333 0.00 0.00 46.47 2.69
2900 3108 5.772825 AAGCAGTCTTTTGCAAGTTATGA 57.227 34.783 0.00 0.00 46.47 2.15
2904 3112 9.793252 CATAATATAAGCAGTCTTTTGCAAGTT 57.207 29.630 0.00 0.00 46.47 2.66
2905 3113 8.960591 ACATAATATAAGCAGTCTTTTGCAAGT 58.039 29.630 0.00 0.00 46.47 3.16
2915 3124 4.929808 CCCCGTCACATAATATAAGCAGTC 59.070 45.833 0.00 0.00 0.00 3.51
2918 3127 4.280436 CCCCCGTCACATAATATAAGCA 57.720 45.455 0.00 0.00 0.00 3.91
2945 3154 4.196193 GGTTCATCCGTTATGATGGAACA 58.804 43.478 2.02 0.00 44.13 3.18
2950 3159 3.470709 AGCTGGTTCATCCGTTATGATG 58.529 45.455 0.00 0.00 44.13 3.07
2965 3184 0.976641 TCGTCAATCTTGGAGCTGGT 59.023 50.000 0.00 0.00 0.00 4.00
2968 3187 3.119708 GCAAAATCGTCAATCTTGGAGCT 60.120 43.478 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.