Multiple sequence alignment - TraesCS6B01G066300

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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 TraesCS6B01G066300 chr6B 100.000 3334 0 0 1 3334 44103839 44107172 0.000000e+00 6157
1 TraesCS6B01G066300 chr6B 96.000 125 5 0 2566 2690 470914823 470914947 1.570000e-48 204
2 TraesCS6B01G066300 chrUn 87.725 2607 177 60 1 2584 94821671 94824157 0.000000e+00 2909
3 TraesCS6B01G066300 chrUn 94.281 647 24 6 2681 3326 94824222 94824856 0.000000e+00 977
4 TraesCS6B01G066300 chr6A 90.146 1776 93 38 833 2584 25635965 25637682 0.000000e+00 2235
5 TraesCS6B01G066300 chr6A 94.962 655 27 5 2681 3334 25637747 25638396 0.000000e+00 1022
6 TraesCS6B01G066300 chr6A 85.827 508 40 11 2 496 25635050 25635538 8.250000e-141 510
7 TraesCS6B01G066300 chr7B 91.241 685 37 11 160 838 225821326 225821993 0.000000e+00 911
8 TraesCS6B01G066300 chr7B 97.458 118 3 0 2572 2689 517095190 517095073 5.640000e-48 202
9 TraesCS6B01G066300 chr7B 92.029 138 8 3 2566 2702 226219656 226219521 1.220000e-44 191
10 TraesCS6B01G066300 chr2D 91.228 684 39 8 160 838 583715294 583714627 0.000000e+00 911
11 TraesCS6B01G066300 chr2D 94.531 128 6 1 2562 2689 520503943 520503817 2.620000e-46 196
12 TraesCS6B01G066300 chr4B 98.319 119 2 0 2571 2689 612251211 612251093 3.370000e-50 209
13 TraesCS6B01G066300 chr4B 93.893 131 7 1 2570 2699 545032682 545032812 2.620000e-46 196
14 TraesCS6B01G066300 chr3B 97.500 120 3 0 2570 2689 630881441 630881560 4.360000e-49 206
15 TraesCS6B01G066300 chr3B 96.032 126 3 2 2565 2689 545060684 545060808 1.570000e-48 204
16 TraesCS6B01G066300 chr1B 92.593 135 8 2 2566 2699 459759414 459759281 3.390000e-45 193


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 TraesCS6B01G066300 chr6B 44103839 44107172 3333 False 6157.000000 6157 100.000000 1 3334 1 chr6B.!!$F1 3333
1 TraesCS6B01G066300 chrUn 94821671 94824856 3185 False 1943.000000 2909 91.003000 1 3326 2 chrUn.!!$F1 3325
2 TraesCS6B01G066300 chr6A 25635050 25638396 3346 False 1255.666667 2235 90.311667 2 3334 3 chr6A.!!$F1 3332
3 TraesCS6B01G066300 chr7B 225821326 225821993 667 False 911.000000 911 91.241000 160 838 1 chr7B.!!$F1 678
4 TraesCS6B01G066300 chr2D 583714627 583715294 667 True 911.000000 911 91.228000 160 838 1 chr2D.!!$R2 678

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
970 1180 0.179045 CCGACCCACCATCATCCTTC 60.179 60.0 0.0 0.0 0.0 3.46 F
1037 1247 0.038310 CCTTCCAGAACCTTCCACCC 59.962 60.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2256 2498 0.324943 TCAGCCTGCAAAGTAGGACC 59.675 55.0 5.28 0.0 37.52 4.46 R
2439 2681 0.803117 CGGTTACAGCTCTCGTCTCA 59.197 55.0 0.00 0.0 0.00 3.27 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
37 38 3.751018 TAGAGAGGCCGGCCAGGA 61.751 66.667 45.13 23.49 45.00 3.86
38 39 3.311511 TAGAGAGGCCGGCCAGGAA 62.312 63.158 45.13 24.34 45.00 3.36
92 99 7.484035 AGTTCTTGTGTACAAAAGCTAAGAG 57.516 36.000 19.40 0.00 35.15 2.85
149 163 0.901580 TTCTTCGGGTCGGCTTACCT 60.902 55.000 7.76 0.00 39.65 3.08
242 256 3.715628 GGCAACTGGGCAATTGTATAG 57.284 47.619 7.40 5.49 42.77 1.31
246 260 4.640201 GCAACTGGGCAATTGTATAGAAGA 59.360 41.667 7.40 0.00 0.00 2.87
250 264 5.824624 ACTGGGCAATTGTATAGAAGATGTG 59.175 40.000 7.40 0.00 0.00 3.21
273 287 3.118075 TCTTGTCCTTGATGGTGTTGTGA 60.118 43.478 0.00 0.00 37.07 3.58
313 328 4.218635 TGTGTTTGTGTGAGTGCCTTTTTA 59.781 37.500 0.00 0.00 0.00 1.52
333 348 8.450578 TTTTTATCTTCAGAGTTTCTCTTGCA 57.549 30.769 0.00 0.00 38.99 4.08
334 349 8.627208 TTTTATCTTCAGAGTTTCTCTTGCAT 57.373 30.769 0.00 0.00 38.99 3.96
393 412 6.841601 AGCAGGCAGGTCTATCATTTAATTA 58.158 36.000 0.00 0.00 0.00 1.40
395 414 7.946776 AGCAGGCAGGTCTATCATTTAATTATT 59.053 33.333 0.00 0.00 0.00 1.40
441 461 6.455360 TGAACTTCTGCATCCCAATATTTC 57.545 37.500 0.00 0.00 0.00 2.17
448 468 7.664552 TCTGCATCCCAATATTTCTTTGATT 57.335 32.000 0.00 0.00 0.00 2.57
599 635 5.375956 TCCAGAATAGGAGTATAGGACAGGT 59.624 44.000 0.00 0.00 32.77 4.00
600 636 6.565314 TCCAGAATAGGAGTATAGGACAGGTA 59.435 42.308 0.00 0.00 32.77 3.08
601 637 6.660094 CCAGAATAGGAGTATAGGACAGGTAC 59.340 46.154 0.00 0.00 0.00 3.34
619 655 3.995048 GGTACTAGCTTGTCTTGAACACC 59.005 47.826 3.45 1.17 37.70 4.16
758 968 2.588620 AGGGAAAATAAACACCGCACA 58.411 42.857 0.00 0.00 0.00 4.57
848 1058 9.169592 TGTAACAGGAGTAATAAACAATAAGGC 57.830 33.333 0.00 0.00 0.00 4.35
876 1086 7.754091 AAATGGGGAAAATGGAATATTCTGT 57.246 32.000 14.95 1.79 0.00 3.41
968 1178 0.620410 TTCCGACCCACCATCATCCT 60.620 55.000 0.00 0.00 0.00 3.24
970 1180 0.179045 CCGACCCACCATCATCCTTC 60.179 60.000 0.00 0.00 0.00 3.46
971 1181 0.179045 CGACCCACCATCATCCTTCC 60.179 60.000 0.00 0.00 0.00 3.46
972 1182 0.179045 GACCCACCATCATCCTTCCG 60.179 60.000 0.00 0.00 0.00 4.30
973 1183 1.149174 CCCACCATCATCCTTCCGG 59.851 63.158 0.00 0.00 0.00 5.14
974 1184 1.526917 CCACCATCATCCTTCCGGC 60.527 63.158 0.00 0.00 0.00 6.13
1037 1247 0.038310 CCTTCCAGAACCTTCCACCC 59.962 60.000 0.00 0.00 0.00 4.61
1063 1273 2.204151 CCCACCCTCAACCCTCCT 60.204 66.667 0.00 0.00 0.00 3.69
1065 1275 2.301738 CCACCCTCAACCCTCCTCC 61.302 68.421 0.00 0.00 0.00 4.30
1068 1278 2.685380 CCTCAACCCTCCTCCGCT 60.685 66.667 0.00 0.00 0.00 5.52
1255 1468 2.500369 CGTCCACACGTACGTCCG 60.500 66.667 19.94 11.26 41.42 4.79
1264 1477 4.112341 GTACGTCCGCGAGCCACT 62.112 66.667 8.23 0.00 42.00 4.00
1321 1535 2.837498 CAAAAGTTTGGCCCTTTCAGG 58.163 47.619 0.00 0.00 34.59 3.86
1359 1573 8.327941 GCTGATTAGCCTCATACAATATTTCA 57.672 34.615 0.00 0.00 44.33 2.69
1404 1619 8.570488 TGTCAATTGATCCATGTGATATTAAGC 58.430 33.333 12.12 0.00 32.41 3.09
1412 1627 5.066375 TCCATGTGATATTAAGCACTGCAAC 59.934 40.000 3.30 0.00 42.60 4.17
1414 1629 5.801350 TGTGATATTAAGCACTGCAACTC 57.199 39.130 3.30 0.00 42.60 3.01
1422 1637 3.904136 AGCACTGCAACTCATGTTTAC 57.096 42.857 3.30 0.00 33.52 2.01
1423 1638 3.213506 AGCACTGCAACTCATGTTTACA 58.786 40.909 3.30 0.00 33.52 2.41
1424 1639 3.631686 AGCACTGCAACTCATGTTTACAA 59.368 39.130 3.30 0.00 33.52 2.41
1425 1640 4.279169 AGCACTGCAACTCATGTTTACAAT 59.721 37.500 3.30 0.00 33.52 2.71
1429 1644 6.696583 CACTGCAACTCATGTTTACAATCAAA 59.303 34.615 0.00 0.00 33.52 2.69
1444 1662 9.832445 TTTACAATCAAAAGTTACAGTCTCTCT 57.168 29.630 0.00 0.00 0.00 3.10
1445 1663 9.832445 TTACAATCAAAAGTTACAGTCTCTCTT 57.168 29.630 0.00 0.00 0.00 2.85
1492 1721 8.920509 ATTACATTGGTTAAATTAAACTCGGC 57.079 30.769 2.26 0.00 0.00 5.54
1608 1837 3.334583 TCAACTGTCCAGGTAATCAGC 57.665 47.619 0.00 0.00 0.00 4.26
1612 1842 2.499289 ACTGTCCAGGTAATCAGCTCAG 59.501 50.000 0.00 0.00 31.39 3.35
1623 1853 1.449956 CAGCTCAGCCCTGCTCTTC 60.450 63.158 0.00 0.00 36.40 2.87
1632 1862 1.471684 GCCCTGCTCTTCATTCTTGTG 59.528 52.381 0.00 0.00 0.00 3.33
1665 1900 2.479275 GTCTCTAACTGAAACCGGTTGC 59.521 50.000 23.08 21.10 35.05 4.17
1676 1911 2.639286 CGGTTGCCACTGCTGTTC 59.361 61.111 0.00 0.00 38.71 3.18
1681 1916 1.265365 GTTGCCACTGCTGTTCTTCTC 59.735 52.381 0.00 0.00 38.71 2.87
1708 1943 3.057019 TCATTTCGACTGCATATACCGC 58.943 45.455 0.00 0.00 0.00 5.68
1801 2036 2.812011 GCAAAATACTCCTGACACCGTT 59.188 45.455 0.00 0.00 0.00 4.44
1807 2042 1.338769 ACTCCTGACACCGTTTATGGC 60.339 52.381 0.00 0.00 0.00 4.40
1809 2044 0.802494 CCTGACACCGTTTATGGCAC 59.198 55.000 0.00 0.00 29.89 5.01
1822 2057 1.812686 ATGGCACTGCTGCTGGTTTG 61.813 55.000 11.29 1.82 43.66 2.93
1996 2231 3.323691 CCATGTACATGATAACCGAGGGA 59.676 47.826 32.72 0.00 41.20 4.20
2008 2243 1.702957 ACCGAGGGAATGAAAGTTGGA 59.297 47.619 0.00 0.00 0.00 3.53
2019 2254 5.536497 ATGAAAGTTGGAGGGAAGGTATT 57.464 39.130 0.00 0.00 0.00 1.89
2034 2269 6.296259 GGGAAGGTATTGACAAGGAGAACTAA 60.296 42.308 0.00 0.00 0.00 2.24
2038 2273 6.270231 AGGTATTGACAAGGAGAACTAACACT 59.730 38.462 0.00 0.00 0.00 3.55
2054 2289 8.467402 AACTAACACTGAGTGAAGAATAATCG 57.533 34.615 20.97 0.00 36.96 3.34
2136 2373 0.325933 TGCAGAGGAGGGTGATTGTG 59.674 55.000 0.00 0.00 0.00 3.33
2145 2382 0.257039 GGGTGATTGTGCCTCCAGAT 59.743 55.000 0.00 0.00 0.00 2.90
2188 2427 1.832998 AGGGCGAGATACCGGTAAAAA 59.167 47.619 20.22 0.00 0.00 1.94
2213 2452 5.006386 CCCTCAGTTTCTGCTAGTTTGATT 58.994 41.667 0.00 0.00 0.00 2.57
2214 2453 5.106396 CCCTCAGTTTCTGCTAGTTTGATTG 60.106 44.000 0.00 0.00 0.00 2.67
2227 2469 3.504906 AGTTTGATTGTGCATCTGAGTGG 59.495 43.478 0.00 0.00 32.34 4.00
2237 2479 3.181468 TGCATCTGAGTGGATTCAGCTAG 60.181 47.826 0.00 0.00 43.39 3.42
2256 2498 9.249457 TCAGCTAGTGATGAGTTATTTAATTCG 57.751 33.333 0.00 0.00 33.24 3.34
2257 2499 8.491152 CAGCTAGTGATGAGTTATTTAATTCGG 58.509 37.037 0.00 0.00 0.00 4.30
2350 2592 4.606961 AGTTGACCATTTTTGCTTACACG 58.393 39.130 0.00 0.00 0.00 4.49
2399 2641 5.243730 TGAAGCTTCACAAATTTTAGAGGGG 59.756 40.000 25.16 0.00 31.01 4.79
2403 2645 5.772521 CTTCACAAATTTTAGAGGGGTGTG 58.227 41.667 0.00 0.00 36.96 3.82
2407 2649 6.834451 TCACAAATTTTAGAGGGGTGTGTTTA 59.166 34.615 0.00 0.00 36.96 2.01
2408 2650 7.507616 TCACAAATTTTAGAGGGGTGTGTTTAT 59.492 33.333 0.00 0.00 36.96 1.40
2417 2659 9.675464 TTAGAGGGGTGTGTTTATTTTATACAG 57.325 33.333 0.00 0.00 0.00 2.74
2509 2751 6.627243 TGGATATATATCGAAACGTTGGGAG 58.373 40.000 15.06 0.00 33.52 4.30
2584 2826 3.771216 TCTAACAAGTACTCCCTCCGTT 58.229 45.455 0.00 0.00 0.00 4.44
2585 2827 4.154942 TCTAACAAGTACTCCCTCCGTTT 58.845 43.478 0.00 0.00 0.00 3.60
2586 2828 2.833631 ACAAGTACTCCCTCCGTTTG 57.166 50.000 0.00 0.00 0.00 2.93
2587 2829 1.346722 ACAAGTACTCCCTCCGTTTGG 59.653 52.381 0.00 0.00 0.00 3.28
2588 2830 1.621814 CAAGTACTCCCTCCGTTTGGA 59.378 52.381 0.00 0.00 43.88 3.53
2590 2832 2.547990 AGTACTCCCTCCGTTTGGAAT 58.452 47.619 0.00 0.00 45.87 3.01
2592 2834 4.098894 AGTACTCCCTCCGTTTGGAATTA 58.901 43.478 0.00 0.00 45.87 1.40
2593 2835 3.345508 ACTCCCTCCGTTTGGAATTAC 57.654 47.619 0.00 0.00 45.87 1.89
2594 2836 2.910977 ACTCCCTCCGTTTGGAATTACT 59.089 45.455 0.00 0.00 45.87 2.24
2595 2837 3.055312 ACTCCCTCCGTTTGGAATTACTC 60.055 47.826 0.00 0.00 45.87 2.59
2597 2839 2.354403 CCCTCCGTTTGGAATTACTCGT 60.354 50.000 0.00 0.00 45.87 4.18
2599 2841 2.928116 CTCCGTTTGGAATTACTCGTCC 59.072 50.000 0.00 0.00 45.87 4.79
2600 2842 2.299582 TCCGTTTGGAATTACTCGTCCA 59.700 45.455 0.00 0.00 42.85 4.02
2607 2849 6.494893 TTGGAATTACTCGTCCAAGAAATG 57.505 37.500 1.01 0.00 46.58 2.32
2608 2850 5.800296 TGGAATTACTCGTCCAAGAAATGA 58.200 37.500 0.00 0.00 41.02 2.57
2610 2852 6.884295 TGGAATTACTCGTCCAAGAAATGAAT 59.116 34.615 0.00 0.00 41.02 2.57
2611 2853 7.148255 TGGAATTACTCGTCCAAGAAATGAATG 60.148 37.037 0.00 0.00 41.02 2.67
2612 2854 7.148239 GGAATTACTCGTCCAAGAAATGAATGT 60.148 37.037 0.00 0.00 33.79 2.71
2613 2855 8.786826 AATTACTCGTCCAAGAAATGAATGTA 57.213 30.769 0.00 0.00 0.00 2.29
2614 2856 8.964476 ATTACTCGTCCAAGAAATGAATGTAT 57.036 30.769 0.00 0.00 0.00 2.29
2620 2862 8.642432 TCGTCCAAGAAATGAATGTATCTAGAT 58.358 33.333 10.73 10.73 0.00 1.98
2621 2863 8.706936 CGTCCAAGAAATGAATGTATCTAGATG 58.293 37.037 15.79 0.00 0.00 2.90
2622 2864 9.553064 GTCCAAGAAATGAATGTATCTAGATGT 57.447 33.333 15.79 0.00 0.00 3.06
2664 2906 9.218440 ACATCCATTTTTATCCATTTTTGTGAC 57.782 29.630 0.00 0.00 0.00 3.67
2665 2907 9.217278 CATCCATTTTTATCCATTTTTGTGACA 57.783 29.630 0.00 0.00 0.00 3.58
2666 2908 9.790344 ATCCATTTTTATCCATTTTTGTGACAA 57.210 25.926 0.00 0.00 0.00 3.18
2667 2909 9.270640 TCCATTTTTATCCATTTTTGTGACAAG 57.729 29.630 0.00 0.00 0.00 3.16
2668 2910 9.054922 CCATTTTTATCCATTTTTGTGACAAGT 57.945 29.630 0.00 0.00 0.00 3.16
2674 2916 9.921637 TTATCCATTTTTGTGACAAGTAATTCC 57.078 29.630 0.00 0.00 0.00 3.01
2675 2917 6.442952 TCCATTTTTGTGACAAGTAATTCCG 58.557 36.000 0.00 0.00 0.00 4.30
2676 2918 6.263392 TCCATTTTTGTGACAAGTAATTCCGA 59.737 34.615 0.00 0.00 0.00 4.55
2677 2919 6.920758 CCATTTTTGTGACAAGTAATTCCGAA 59.079 34.615 0.00 0.00 0.00 4.30
2678 2920 7.598493 CCATTTTTGTGACAAGTAATTCCGAAT 59.402 33.333 0.00 0.00 0.00 3.34
2679 2921 7.922505 TTTTTGTGACAAGTAATTCCGAATG 57.077 32.000 0.00 0.00 0.00 2.67
2858 3100 3.428452 CCATTGTGATGTCAGCATGTTCC 60.428 47.826 0.00 0.00 37.40 3.62
2892 3134 1.335132 GGTCCTCAGGGCCGTTGATA 61.335 60.000 0.00 0.00 0.00 2.15
2908 3150 7.201785 GGCCGTTGATATCCTGAAATAAAAGAA 60.202 37.037 0.00 0.00 0.00 2.52
2909 3151 8.352942 GCCGTTGATATCCTGAAATAAAAGAAT 58.647 33.333 0.00 0.00 0.00 2.40
2966 3209 6.128007 GGTGCTAGCAGCTTAGTTTTTGATTA 60.128 38.462 33.89 0.00 42.97 1.75
2971 3214 6.003950 AGCAGCTTAGTTTTTGATTAGGACA 58.996 36.000 0.00 0.00 0.00 4.02
2972 3215 6.660949 AGCAGCTTAGTTTTTGATTAGGACAT 59.339 34.615 0.00 0.00 0.00 3.06
3020 3265 8.347771 GGTTTTAGTTTGTTACCCAGAAACTAG 58.652 37.037 0.00 0.00 41.09 2.57
3130 3376 5.865085 TGCTGATAAACAAGTAACCAGACT 58.135 37.500 0.00 0.00 0.00 3.24
3169 3415 5.458452 TGTTGCTTTTAAACTGCTGAATTCG 59.542 36.000 11.94 0.00 0.00 3.34
3177 3423 4.630894 AACTGCTGAATTCGTGAAACAA 57.369 36.364 0.04 0.00 35.74 2.83
3198 3444 5.242171 ACAACAATGAGAACATGCATCTTGA 59.758 36.000 0.00 0.00 36.79 3.02
3322 3568 7.611855 AGAAAACATACATCTTTACTCCCAAGG 59.388 37.037 0.00 0.00 0.00 3.61
3329 3575 9.990868 ATACATCTTTACTCCCAAGGTTTAAAT 57.009 29.630 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 1.391485 CTATATCAATGACGCTGCCGC 59.609 52.381 0.00 0.00 38.22 6.53
92 99 8.325997 GGGTCGAAAACGTGCATATATATAATC 58.674 37.037 0.00 0.00 0.00 1.75
104 111 2.664436 CCTCGGGTCGAAAACGTGC 61.664 63.158 0.00 0.00 34.74 5.34
124 138 3.479269 CGACCCGAAGAACAGCGC 61.479 66.667 0.00 0.00 0.00 5.92
129 143 0.738762 GGTAAGCCGACCCGAAGAAC 60.739 60.000 0.00 0.00 32.88 3.01
149 163 5.737318 TCTATTTCCCCCTCCATTAGATCA 58.263 41.667 0.00 0.00 0.00 2.92
232 246 8.607459 GGACAAGACACATCTTCTATACAATTG 58.393 37.037 3.24 3.24 43.69 2.32
234 248 8.083828 AGGACAAGACACATCTTCTATACAAT 57.916 34.615 0.00 0.00 43.69 2.71
242 256 4.394300 CCATCAAGGACAAGACACATCTTC 59.606 45.833 0.00 0.00 40.96 2.87
246 260 3.181440 ACACCATCAAGGACAAGACACAT 60.181 43.478 0.00 0.00 41.22 3.21
250 264 3.003689 CACAACACCATCAAGGACAAGAC 59.996 47.826 0.00 0.00 41.22 3.01
273 287 3.167485 ACACATTCCTGCCATTCACAAT 58.833 40.909 0.00 0.00 0.00 2.71
313 328 5.415077 CCAATGCAAGAGAAACTCTGAAGAT 59.585 40.000 1.97 0.00 40.28 2.40
353 368 0.994247 TGCTCACATCCATTCAGGGT 59.006 50.000 0.00 0.00 38.24 4.34
441 461 5.234972 GCACTTCCAACCAAGAAAATCAAAG 59.765 40.000 0.00 0.00 0.00 2.77
448 468 4.751767 AATTGCACTTCCAACCAAGAAA 57.248 36.364 0.00 0.00 0.00 2.52
497 530 1.762708 AACAGTGAAGGTGGTGGTTG 58.237 50.000 0.00 0.00 0.00 3.77
499 532 1.684869 CCAAACAGTGAAGGTGGTGGT 60.685 52.381 0.00 0.00 0.00 4.16
599 635 3.570975 TCGGTGTTCAAGACAAGCTAGTA 59.429 43.478 0.00 0.00 40.65 1.82
600 636 2.364324 TCGGTGTTCAAGACAAGCTAGT 59.636 45.455 0.00 0.00 40.65 2.57
601 637 3.026630 TCGGTGTTCAAGACAAGCTAG 57.973 47.619 0.00 0.00 40.65 3.42
630 666 6.205464 ACAGATTGTGGTATTTGTGACAAGAG 59.795 38.462 0.00 0.00 32.12 2.85
635 673 9.691362 AAAAATACAGATTGTGGTATTTGTGAC 57.309 29.630 9.69 0.00 44.88 3.67
758 968 3.451141 ACAATGTTCGCAAACCACATT 57.549 38.095 0.00 0.00 40.94 2.71
838 1048 6.882768 TTCCCCATTTTATGCCTTATTGTT 57.117 33.333 0.00 0.00 0.00 2.83
839 1049 6.882768 TTTCCCCATTTTATGCCTTATTGT 57.117 33.333 0.00 0.00 0.00 2.71
840 1050 7.229106 CCATTTTCCCCATTTTATGCCTTATTG 59.771 37.037 0.00 0.00 0.00 1.90
882 1092 2.355310 CCATAAACGGTAGGGTGCAGAA 60.355 50.000 0.00 0.00 0.00 3.02
883 1093 1.208535 CCATAAACGGTAGGGTGCAGA 59.791 52.381 0.00 0.00 0.00 4.26
974 1184 3.174265 GAGGAGGAGGCATGGGGG 61.174 72.222 0.00 0.00 0.00 5.40
1044 1254 4.048470 GAGGGTTGAGGGTGGGGC 62.048 72.222 0.00 0.00 0.00 5.80
1046 1256 2.204151 AGGAGGGTTGAGGGTGGG 60.204 66.667 0.00 0.00 0.00 4.61
1047 1257 2.301738 GGAGGAGGGTTGAGGGTGG 61.302 68.421 0.00 0.00 0.00 4.61
1068 1278 4.507916 CTCGGAGGAGGAGCGGGA 62.508 72.222 0.00 0.00 36.61 5.14
1262 1475 4.351054 CAAGGGCGCAGGGGAAGT 62.351 66.667 10.83 0.00 0.00 3.01
1319 1533 1.346062 TCAGCTTCAGAGTTCAGCCT 58.654 50.000 0.00 0.00 33.73 4.58
1321 1535 3.309410 GCTAATCAGCTTCAGAGTTCAGC 59.691 47.826 0.00 0.00 44.93 4.26
1375 1590 3.959293 TCACATGGATCAATTGACAGCT 58.041 40.909 11.07 0.00 0.00 4.24
1404 1619 5.761003 TGATTGTAAACATGAGTTGCAGTG 58.239 37.500 0.00 0.00 38.17 3.66
1412 1627 9.950680 ACTGTAACTTTTGATTGTAAACATGAG 57.049 29.630 0.00 0.00 0.00 2.90
1414 1629 9.950680 AGACTGTAACTTTTGATTGTAAACATG 57.049 29.630 0.00 0.00 0.00 3.21
1422 1637 9.657121 GAAAAGAGAGACTGTAACTTTTGATTG 57.343 33.333 0.00 0.00 39.67 2.67
1423 1638 8.841300 GGAAAAGAGAGACTGTAACTTTTGATT 58.159 33.333 0.00 0.00 39.67 2.57
1424 1639 7.993183 TGGAAAAGAGAGACTGTAACTTTTGAT 59.007 33.333 0.00 0.25 39.67 2.57
1425 1640 7.335627 TGGAAAAGAGAGACTGTAACTTTTGA 58.664 34.615 0.00 0.00 39.67 2.69
1429 1644 7.067496 TCATGGAAAAGAGAGACTGTAACTT 57.933 36.000 0.00 0.00 0.00 2.66
1492 1721 3.104470 CTCACATCAGATCACTCGAACG 58.896 50.000 0.00 0.00 0.00 3.95
1501 1730 3.881688 CCCAATGGTTCTCACATCAGATC 59.118 47.826 0.00 0.00 0.00 2.75
1608 1837 1.209990 AGAATGAAGAGCAGGGCTGAG 59.790 52.381 0.00 0.00 39.88 3.35
1612 1842 1.471684 CACAAGAATGAAGAGCAGGGC 59.528 52.381 0.00 0.00 0.00 5.19
1623 1853 4.063689 ACTGAAGAGTGAGCACAAGAATG 58.936 43.478 3.19 0.00 0.00 2.67
1659 1894 1.447317 AAGAACAGCAGTGGCAACCG 61.447 55.000 0.00 0.00 44.61 4.44
1661 1896 1.265365 GAGAAGAACAGCAGTGGCAAC 59.735 52.381 0.00 0.00 44.61 4.17
1665 1900 2.149578 CCTTGAGAAGAACAGCAGTGG 58.850 52.381 0.00 0.00 0.00 4.00
1676 1911 4.377841 GCAGTCGAAATGAACCTTGAGAAG 60.378 45.833 3.17 0.00 0.00 2.85
1681 1916 3.837213 ATGCAGTCGAAATGAACCTTG 57.163 42.857 3.17 0.00 0.00 3.61
1807 2042 2.337532 GCCAAACCAGCAGCAGTG 59.662 61.111 0.00 0.00 0.00 3.66
1809 2044 4.712425 GCGCCAAACCAGCAGCAG 62.712 66.667 0.00 0.00 32.54 4.24
1822 2057 0.388294 ATCTTAGTTCCTACCGCGCC 59.612 55.000 0.00 0.00 0.00 6.53
1996 2231 3.903530 ACCTTCCCTCCAACTTTCATT 57.096 42.857 0.00 0.00 0.00 2.57
2008 2243 3.803340 TCTCCTTGTCAATACCTTCCCT 58.197 45.455 0.00 0.00 0.00 4.20
2019 2254 4.649674 ACTCAGTGTTAGTTCTCCTTGTCA 59.350 41.667 0.00 0.00 0.00 3.58
2034 2269 4.223032 ACCCGATTATTCTTCACTCAGTGT 59.777 41.667 4.28 0.00 34.79 3.55
2038 2273 4.819105 ACACCCGATTATTCTTCACTCA 57.181 40.909 0.00 0.00 0.00 3.41
2145 2382 2.043801 CCCCTTTTTCCCATAACCCAGA 59.956 50.000 0.00 0.00 0.00 3.86
2188 2427 4.137543 CAAACTAGCAGAAACTGAGGGTT 58.862 43.478 2.81 1.61 40.28 4.11
2189 2428 3.391296 TCAAACTAGCAGAAACTGAGGGT 59.609 43.478 2.81 0.00 32.44 4.34
2190 2429 4.008074 TCAAACTAGCAGAAACTGAGGG 57.992 45.455 2.81 0.00 32.44 4.30
2202 2441 4.394300 ACTCAGATGCACAATCAAACTAGC 59.606 41.667 0.00 0.00 37.81 3.42
2213 2452 2.938314 GCTGAATCCACTCAGATGCACA 60.938 50.000 4.81 0.00 44.82 4.57
2214 2453 1.669779 GCTGAATCCACTCAGATGCAC 59.330 52.381 4.81 0.00 44.82 4.57
2237 2479 7.787725 AGGACCGAATTAAATAACTCATCAC 57.212 36.000 0.00 0.00 0.00 3.06
2256 2498 0.324943 TCAGCCTGCAAAGTAGGACC 59.675 55.000 5.28 0.00 37.52 4.46
2257 2499 2.012673 CATCAGCCTGCAAAGTAGGAC 58.987 52.381 5.28 0.00 37.52 3.85
2321 2563 3.853671 GCAAAAATGGTCAACTATCTGCG 59.146 43.478 0.00 0.00 0.00 5.18
2322 2564 5.064441 AGCAAAAATGGTCAACTATCTGC 57.936 39.130 0.00 0.00 0.00 4.26
2350 2592 5.817816 CAGGTACCTCATCAGTATTTTCCAC 59.182 44.000 12.84 0.00 0.00 4.02
2439 2681 0.803117 CGGTTACAGCTCTCGTCTCA 59.197 55.000 0.00 0.00 0.00 3.27
2440 2682 1.062880 CTCGGTTACAGCTCTCGTCTC 59.937 57.143 0.00 0.00 0.00 3.36
2441 2683 1.088306 CTCGGTTACAGCTCTCGTCT 58.912 55.000 0.00 0.00 0.00 4.18
2442 2684 1.085091 TCTCGGTTACAGCTCTCGTC 58.915 55.000 0.00 0.00 0.00 4.20
2483 2725 5.810587 CCCAACGTTTCGATATATATCCAGG 59.189 44.000 15.61 8.93 0.00 4.45
2489 2731 4.281435 TGCCTCCCAACGTTTCGATATATA 59.719 41.667 0.00 0.00 0.00 0.86
2509 2751 1.396648 ACAAAACGCAAAAGCTTTGCC 59.603 42.857 13.54 5.89 42.10 4.52
2584 2826 6.234920 TCATTTCTTGGACGAGTAATTCCAA 58.765 36.000 3.17 3.17 39.62 3.53
2585 2827 5.800296 TCATTTCTTGGACGAGTAATTCCA 58.200 37.500 0.00 0.00 0.00 3.53
2586 2828 6.737254 TTCATTTCTTGGACGAGTAATTCC 57.263 37.500 0.00 0.00 0.00 3.01
2587 2829 7.752695 ACATTCATTTCTTGGACGAGTAATTC 58.247 34.615 0.00 0.00 0.00 2.17
2588 2830 7.687941 ACATTCATTTCTTGGACGAGTAATT 57.312 32.000 0.00 0.00 0.00 1.40
2590 2832 8.258007 AGATACATTCATTTCTTGGACGAGTAA 58.742 33.333 0.00 0.00 0.00 2.24
2592 2834 6.644347 AGATACATTCATTTCTTGGACGAGT 58.356 36.000 0.00 0.00 0.00 4.18
2593 2835 8.138074 TCTAGATACATTCATTTCTTGGACGAG 58.862 37.037 0.00 0.00 0.00 4.18
2594 2836 8.007405 TCTAGATACATTCATTTCTTGGACGA 57.993 34.615 0.00 0.00 0.00 4.20
2595 2837 8.706936 CATCTAGATACATTCATTTCTTGGACG 58.293 37.037 4.54 0.00 0.00 4.79
2638 2880 9.218440 GTCACAAAAATGGATAAAAATGGATGT 57.782 29.630 0.00 0.00 0.00 3.06
2639 2881 9.217278 TGTCACAAAAATGGATAAAAATGGATG 57.783 29.630 0.00 0.00 0.00 3.51
2642 2884 9.054922 ACTTGTCACAAAAATGGATAAAAATGG 57.945 29.630 0.00 0.00 0.00 3.16
2648 2890 9.921637 GGAATTACTTGTCACAAAAATGGATAA 57.078 29.630 0.00 0.00 0.00 1.75
2649 2891 8.240682 CGGAATTACTTGTCACAAAAATGGATA 58.759 33.333 0.00 0.00 0.00 2.59
2650 2892 7.040062 TCGGAATTACTTGTCACAAAAATGGAT 60.040 33.333 0.00 0.00 0.00 3.41
2651 2893 6.263392 TCGGAATTACTTGTCACAAAAATGGA 59.737 34.615 0.00 0.00 0.00 3.41
2652 2894 6.442952 TCGGAATTACTTGTCACAAAAATGG 58.557 36.000 0.00 0.00 0.00 3.16
2653 2895 7.922505 TTCGGAATTACTTGTCACAAAAATG 57.077 32.000 0.00 0.00 0.00 2.32
2654 2896 7.598493 CCATTCGGAATTACTTGTCACAAAAAT 59.402 33.333 0.00 0.00 0.00 1.82
2655 2897 6.920758 CCATTCGGAATTACTTGTCACAAAAA 59.079 34.615 0.00 0.00 0.00 1.94
2656 2898 6.263392 TCCATTCGGAATTACTTGTCACAAAA 59.737 34.615 0.00 0.00 38.83 2.44
2657 2899 5.765677 TCCATTCGGAATTACTTGTCACAAA 59.234 36.000 0.00 0.00 38.83 2.83
2658 2900 5.309638 TCCATTCGGAATTACTTGTCACAA 58.690 37.500 0.00 0.00 38.83 3.33
2659 2901 4.900684 TCCATTCGGAATTACTTGTCACA 58.099 39.130 0.00 0.00 38.83 3.58
2660 2902 4.332819 CCTCCATTCGGAATTACTTGTCAC 59.667 45.833 0.00 0.00 42.21 3.67
2661 2903 4.513442 CCTCCATTCGGAATTACTTGTCA 58.487 43.478 0.00 0.00 42.21 3.58
2662 2904 3.877508 CCCTCCATTCGGAATTACTTGTC 59.122 47.826 0.00 0.00 42.21 3.18
2663 2905 3.521937 TCCCTCCATTCGGAATTACTTGT 59.478 43.478 0.00 0.00 42.21 3.16
2664 2906 4.130118 CTCCCTCCATTCGGAATTACTTG 58.870 47.826 0.00 0.00 42.21 3.16
2665 2907 3.780850 ACTCCCTCCATTCGGAATTACTT 59.219 43.478 0.00 0.00 42.21 2.24
2666 2908 3.385115 ACTCCCTCCATTCGGAATTACT 58.615 45.455 0.00 0.00 42.21 2.24
2667 2909 3.840124 ACTCCCTCCATTCGGAATTAC 57.160 47.619 0.00 0.00 42.21 1.89
2668 2910 5.961398 TTTACTCCCTCCATTCGGAATTA 57.039 39.130 0.00 0.00 42.21 1.40
2669 2911 4.855298 TTTACTCCCTCCATTCGGAATT 57.145 40.909 0.00 0.00 42.21 2.17
2670 2912 4.855298 TTTTACTCCCTCCATTCGGAAT 57.145 40.909 0.00 0.00 42.21 3.01
2671 2913 4.473559 AGATTTTACTCCCTCCATTCGGAA 59.526 41.667 0.00 0.00 42.21 4.30
2672 2914 4.037927 AGATTTTACTCCCTCCATTCGGA 58.962 43.478 0.00 0.00 39.79 4.55
2673 2915 4.423625 AGATTTTACTCCCTCCATTCGG 57.576 45.455 0.00 0.00 0.00 4.30
2674 2916 6.817184 TCTTAGATTTTACTCCCTCCATTCG 58.183 40.000 0.00 0.00 0.00 3.34
2677 2919 9.676129 TCTAATCTTAGATTTTACTCCCTCCAT 57.324 33.333 13.00 0.00 34.99 3.41
2678 2920 9.502035 TTCTAATCTTAGATTTTACTCCCTCCA 57.498 33.333 13.00 0.00 39.36 3.86
2679 2921 9.990360 CTTCTAATCTTAGATTTTACTCCCTCC 57.010 37.037 13.00 0.00 39.36 4.30
2858 3100 4.191544 TGAGGACCTTTAAATGAGCATCG 58.808 43.478 0.00 0.00 38.61 3.84
3009 3253 9.401058 ACTAATTTTCATCATCTAGTTTCTGGG 57.599 33.333 0.00 0.00 0.00 4.45
3093 3338 8.984891 TGTTTATCAGCATTGGAATAAGTTTG 57.015 30.769 0.00 0.00 0.00 2.93
3124 3370 7.479980 CAACAGAGATCTTAGTTCTAGTCTGG 58.520 42.308 9.90 0.00 0.00 3.86
3169 3415 5.042593 TGCATGTTCTCATTGTTGTTTCAC 58.957 37.500 0.00 0.00 31.15 3.18
3177 3423 5.250982 TCTCAAGATGCATGTTCTCATTGT 58.749 37.500 2.46 0.00 31.15 2.71
3198 3444 7.684529 AGTGATTGAGAACAAGGTATCTTTCT 58.315 34.615 0.00 0.00 39.46 2.52


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

AutoCloner maintained by Alex Coulton.