Multiple sequence alignment - TraesCS2D01G153700

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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 TraesCS2D01G153700 chr2D 100.000 3163 0 0 1 3163 96748452 96751614 0.000000e+00 5842.0
1 TraesCS2D01G153700 chr2D 96.691 2025 38 18 514 2530 96679186 96681189 0.000000e+00 3341.0
2 TraesCS2D01G153700 chr2D 88.279 401 31 11 2553 2949 96683041 96683429 1.720000e-127 466.0
3 TraesCS2D01G153700 chr2D 84.556 259 31 8 128 379 96678826 96679082 6.770000e-62 248.0
4 TraesCS2D01G153700 chr2D 87.047 193 25 0 2967 3159 96683663 96683855 5.310000e-53 219.0
5 TraesCS2D01G153700 chr2D 88.976 127 14 0 1150 1276 95772687 95772813 1.170000e-34 158.0
6 TraesCS2D01G153700 chr2D 95.082 61 3 0 1216 1276 96774906 96774966 2.600000e-16 97.1
7 TraesCS2D01G153700 chr2D 97.826 46 1 0 416 461 96679086 96679131 2.620000e-11 80.5
8 TraesCS2D01G153700 chr2A 91.043 2166 130 22 403 2553 95157409 95159525 0.000000e+00 2867.0
9 TraesCS2D01G153700 chr2A 90.909 2024 119 21 403 2408 95272117 95274093 0.000000e+00 2658.0
10 TraesCS2D01G153700 chr2A 88.614 404 34 8 2553 2949 95159578 95159976 6.140000e-132 481.0
11 TraesCS2D01G153700 chr2A 77.313 789 166 12 1381 2163 95259753 95260534 1.340000e-123 453.0
12 TraesCS2D01G153700 chr2A 85.106 282 29 11 2675 2949 95277289 95277564 3.110000e-70 276.0
13 TraesCS2D01G153700 chr2A 87.709 179 22 0 2985 3163 95277812 95277990 3.200000e-50 209.0
14 TraesCS2D01G153700 chr2A 85.535 159 15 6 2398 2553 95274257 95274410 3.270000e-35 159.0
15 TraesCS2D01G153700 chr2B 87.587 2167 172 47 409 2553 147829451 147831542 0.000000e+00 2422.0
16 TraesCS2D01G153700 chr2B 87.587 2167 172 47 409 2553 147869204 147871295 0.000000e+00 2422.0
17 TraesCS2D01G153700 chr2B 93.184 1203 70 7 1353 2553 148037099 148038291 0.000000e+00 1757.0
18 TraesCS2D01G153700 chr2B 87.161 1106 98 24 232 1318 148035915 148036995 0.000000e+00 1216.0
19 TraesCS2D01G153700 chr2B 89.055 402 34 8 2553 2949 147831595 147831991 1.020000e-134 490.0
20 TraesCS2D01G153700 chr2B 86.861 411 35 9 2553 2949 147871348 147871753 8.050000e-121 444.0
21 TraesCS2D01G153700 chr2B 86.747 249 27 4 2704 2949 148038531 148038776 4.020000e-69 272.0
22 TraesCS2D01G153700 chr2B 87.791 172 16 5 2553 2720 148038348 148038518 2.490000e-46 196.0
23 TraesCS2D01G153700 chr2B 87.500 120 10 3 96 214 148035475 148035590 1.980000e-27 134.0
24 TraesCS2D01G153700 chr2B 92.500 80 6 0 16 95 148035369 148035448 7.170000e-22 115.0
25 TraesCS2D01G153700 chrUn 76.991 791 167 13 1381 2164 17365105 17365887 3.750000e-119 438.0
26 TraesCS2D01G153700 chr6D 78.412 718 94 29 578 1279 409871809 409872481 8.170000e-111 411.0
27 TraesCS2D01G153700 chr6B 75.703 391 57 18 400 784 616380318 616380676 9.080000e-36 161.0


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 TraesCS2D01G153700 chr2D 96748452 96751614 3162 False 5842.0 5842 100.000000 1 3163 1 chr2D.!!$F2 3162
1 TraesCS2D01G153700 chr2D 96678826 96683855 5029 False 870.9 3341 90.879800 128 3159 5 chr2D.!!$F4 3031
2 TraesCS2D01G153700 chr2A 95157409 95159976 2567 False 1674.0 2867 89.828500 403 2949 2 chr2A.!!$F2 2546
3 TraesCS2D01G153700 chr2A 95272117 95277990 5873 False 825.5 2658 87.314750 403 3163 4 chr2A.!!$F3 2760
4 TraesCS2D01G153700 chr2A 95259753 95260534 781 False 453.0 453 77.313000 1381 2163 1 chr2A.!!$F1 782
5 TraesCS2D01G153700 chr2B 147829451 147831991 2540 False 1456.0 2422 88.321000 409 2949 2 chr2B.!!$F1 2540
6 TraesCS2D01G153700 chr2B 147869204 147871753 2549 False 1433.0 2422 87.224000 409 2949 2 chr2B.!!$F2 2540
7 TraesCS2D01G153700 chr2B 148035369 148038776 3407 False 615.0 1757 89.147167 16 2949 6 chr2B.!!$F3 2933
8 TraesCS2D01G153700 chrUn 17365105 17365887 782 False 438.0 438 76.991000 1381 2164 1 chrUn.!!$F1 783
9 TraesCS2D01G153700 chr6D 409871809 409872481 672 False 411.0 411 78.412000 578 1279 1 chr6D.!!$F1 701

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
82 83 0.246635 ACGACCAGCTTTACGATGCT 59.753 50.0 9.58 0.0 40.54 3.79 F
283 617 0.464036 ACGTGTGGCTTGTCTTCAGA 59.536 50.0 0.00 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1148 1519 2.478872 AGGGCAGGAATAGCTGTAGA 57.521 50.000 0.0 0.0 0.0 2.59 R
2386 2841 6.648725 TGTTTGTTACGGGTTTGATTTTTG 57.351 33.333 0.0 0.0 0.0 2.44 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
58 59 2.560504 TCGCAACACAATCAAGACACT 58.439 42.857 0.00 0.00 0.00 3.55
79 80 2.884827 GGTAACGACCAGCTTTACGAT 58.115 47.619 9.58 1.73 46.12 3.73
82 83 0.246635 ACGACCAGCTTTACGATGCT 59.753 50.000 9.58 0.00 40.54 3.79
124 151 7.364762 CGGCATCCCTATATAAGGTGAAGTTAT 60.365 40.741 0.00 0.00 44.90 1.89
174 201 4.129380 TCAACAAGATCACAAGACACCTG 58.871 43.478 0.00 0.00 0.00 4.00
214 241 6.206048 TGTTCATACGTGAGAGAACAACTAGA 59.794 38.462 18.17 2.11 42.65 2.43
225 252 5.947566 AGAGAACAACTAGAAGGAGTAGGAC 59.052 44.000 0.00 0.00 0.00 3.85
228 255 5.725325 ACAACTAGAAGGAGTAGGACAAC 57.275 43.478 0.00 0.00 0.00 3.32
229 256 4.527427 ACAACTAGAAGGAGTAGGACAACC 59.473 45.833 0.00 0.00 0.00 3.77
234 568 4.232091 AGAAGGAGTAGGACAACCTTTCA 58.768 43.478 0.00 0.00 45.36 2.69
249 583 4.162640 TCACCGCGTGAAATCTCG 57.837 55.556 4.92 0.83 39.78 4.04
264 598 5.596772 TGAAATCTCGTACCTGGATCATACA 59.403 40.000 0.00 0.00 0.00 2.29
271 605 1.207089 ACCTGGATCATACACGTGTGG 59.793 52.381 30.83 21.55 34.19 4.17
282 616 0.583438 CACGTGTGGCTTGTCTTCAG 59.417 55.000 7.58 0.00 0.00 3.02
283 617 0.464036 ACGTGTGGCTTGTCTTCAGA 59.536 50.000 0.00 0.00 0.00 3.27
297 631 7.523709 GCTTGTCTTCAGATGGAATTGGTTTTA 60.524 37.037 0.00 0.00 34.32 1.52
315 649 8.288217 TGGTTTTAAATTTTACATGTTCGCTC 57.712 30.769 2.30 0.00 0.00 5.03
334 668 2.917971 CTCTTCTTCGGACGCTTGTAAG 59.082 50.000 0.00 0.00 0.00 2.34
380 715 5.353394 TGGCTACAGAATTCGGAGTAATT 57.647 39.130 12.79 0.00 0.00 1.40
381 716 6.474140 TGGCTACAGAATTCGGAGTAATTA 57.526 37.500 12.79 0.00 0.00 1.40
382 717 6.513180 TGGCTACAGAATTCGGAGTAATTAG 58.487 40.000 12.79 3.85 0.00 1.73
401 736 2.795329 AGGTGGTGTATTTGGCTCAAG 58.205 47.619 0.00 0.00 0.00 3.02
404 739 4.076394 GGTGGTGTATTTGGCTCAAGTTA 58.924 43.478 0.00 0.00 0.00 2.24
423 758 8.579006 TCAAGTTATCACATGCAAGAAATTCTT 58.421 29.630 1.80 1.80 37.14 2.52
478 813 5.186797 AGACTAGCTAGAGACAAAACTGCAT 59.813 40.000 27.45 0.00 0.00 3.96
483 818 4.094146 GCTAGAGACAAAACTGCATCCTTC 59.906 45.833 0.00 0.00 0.00 3.46
484 819 3.416156 AGAGACAAAACTGCATCCTTCC 58.584 45.455 0.00 0.00 0.00 3.46
485 820 2.489722 GAGACAAAACTGCATCCTTCCC 59.510 50.000 0.00 0.00 0.00 3.97
487 822 2.893489 GACAAAACTGCATCCTTCCCTT 59.107 45.455 0.00 0.00 0.00 3.95
488 823 4.079253 GACAAAACTGCATCCTTCCCTTA 58.921 43.478 0.00 0.00 0.00 2.69
490 825 4.202567 ACAAAACTGCATCCTTCCCTTAGA 60.203 41.667 0.00 0.00 0.00 2.10
491 826 4.870021 AAACTGCATCCTTCCCTTAGAT 57.130 40.909 0.00 0.00 0.00 1.98
494 829 3.390639 ACTGCATCCTTCCCTTAGATGAG 59.609 47.826 3.51 1.63 39.84 2.90
496 831 2.551938 GCATCCTTCCCTTAGATGAGCC 60.552 54.545 3.51 0.00 39.84 4.70
498 833 2.119495 TCCTTCCCTTAGATGAGCCAC 58.881 52.381 0.00 0.00 0.00 5.01
500 835 2.420687 CCTTCCCTTAGATGAGCCACAC 60.421 54.545 0.00 0.00 0.00 3.82
501 836 0.824109 TCCCTTAGATGAGCCACACG 59.176 55.000 0.00 0.00 0.00 4.49
502 837 0.824109 CCCTTAGATGAGCCACACGA 59.176 55.000 0.00 0.00 0.00 4.35
506 841 3.068165 CCTTAGATGAGCCACACGATACA 59.932 47.826 0.00 0.00 0.00 2.29
507 842 4.441495 CCTTAGATGAGCCACACGATACAA 60.441 45.833 0.00 0.00 0.00 2.41
508 843 3.827008 AGATGAGCCACACGATACAAT 57.173 42.857 0.00 0.00 0.00 2.71
509 844 4.142609 AGATGAGCCACACGATACAATT 57.857 40.909 0.00 0.00 0.00 2.32
510 845 5.276461 AGATGAGCCACACGATACAATTA 57.724 39.130 0.00 0.00 0.00 1.40
511 846 5.858381 AGATGAGCCACACGATACAATTAT 58.142 37.500 0.00 0.00 0.00 1.28
512 847 5.928839 AGATGAGCCACACGATACAATTATC 59.071 40.000 0.00 0.00 0.00 1.75
565 907 1.112113 GGACATTACCCTCGCTCTCA 58.888 55.000 0.00 0.00 0.00 3.27
634 977 6.252655 GCACACGATACAAATTATCAAAACCC 59.747 38.462 0.00 0.00 0.00 4.11
641 984 9.659830 GATACAAATTATCAAAACCCATCGTAC 57.340 33.333 0.00 0.00 0.00 3.67
748 1095 1.746861 CGCCATGCATGTTCCCTCTTA 60.747 52.381 24.58 0.00 0.00 2.10
777 1126 1.818060 GCCACAACCTAACATGCATGA 59.182 47.619 32.75 10.86 0.00 3.07
857 1215 1.892819 CGGGACACAGGCTCATCAGT 61.893 60.000 0.00 0.00 0.00 3.41
867 1226 3.128242 CAGGCTCATCAGTTTGGATCAAC 59.872 47.826 0.00 0.00 0.00 3.18
872 1231 5.627735 GCTCATCAGTTTGGATCAACCTAGA 60.628 44.000 0.00 0.00 39.86 2.43
873 1232 5.734720 TCATCAGTTTGGATCAACCTAGAC 58.265 41.667 0.00 0.00 39.86 2.59
874 1233 5.485353 TCATCAGTTTGGATCAACCTAGACT 59.515 40.000 0.00 0.00 39.86 3.24
875 1234 6.667848 TCATCAGTTTGGATCAACCTAGACTA 59.332 38.462 0.00 0.00 39.86 2.59
944 1306 3.456644 TCCATCTTCGTCCTCTCTCTAGT 59.543 47.826 0.00 0.00 0.00 2.57
945 1307 3.813166 CCATCTTCGTCCTCTCTCTAGTC 59.187 52.174 0.00 0.00 0.00 2.59
946 1308 4.444306 CCATCTTCGTCCTCTCTCTAGTCT 60.444 50.000 0.00 0.00 0.00 3.24
947 1309 4.395959 TCTTCGTCCTCTCTCTAGTCTC 57.604 50.000 0.00 0.00 0.00 3.36
948 1310 4.028131 TCTTCGTCCTCTCTCTAGTCTCT 58.972 47.826 0.00 0.00 0.00 3.10
949 1311 5.202765 TCTTCGTCCTCTCTCTAGTCTCTA 58.797 45.833 0.00 0.00 0.00 2.43
950 1312 5.657745 TCTTCGTCCTCTCTCTAGTCTCTAA 59.342 44.000 0.00 0.00 0.00 2.10
1148 1519 4.021925 GGCGCTCACCCTGGACTT 62.022 66.667 7.64 0.00 0.00 3.01
1487 1933 1.632589 GCATTCCAAACTTCCCCAGT 58.367 50.000 0.00 0.00 37.30 4.00
2378 2833 9.725019 TGAGATGTGACTGTCAAAGTATATTTT 57.275 29.630 12.81 0.00 40.07 1.82
2386 2841 9.118236 GACTGTCAAAGTATATTTTGTTTGCTC 57.882 33.333 17.29 6.54 40.07 4.26
2416 3045 5.067936 TCAAACCCGTAACAAACATGTTGAT 59.932 36.000 12.82 4.12 33.59 2.57
2485 3122 7.230849 TGAAACAATGAAACATATCTTGCCT 57.769 32.000 0.00 0.00 0.00 4.75
2555 4972 1.972872 GGTGCAGGACCATAATGGAG 58.027 55.000 6.15 0.00 45.34 3.86
2556 4973 1.312815 GTGCAGGACCATAATGGAGC 58.687 55.000 0.00 0.00 40.96 4.70
2560 5041 2.811873 GCAGGACCATAATGGAGCGAAT 60.812 50.000 0.00 0.00 40.96 3.34
2563 5044 3.885297 AGGACCATAATGGAGCGAATTTG 59.115 43.478 0.00 0.00 40.96 2.32
2716 7952 3.501062 GGCCTGGTCAACTAGTTTGTAAC 59.499 47.826 5.07 2.31 36.49 2.50
2756 7992 1.568612 CGAGCAGCGGCAAGAAAAGA 61.569 55.000 12.44 0.00 44.61 2.52
2757 7993 0.167689 GAGCAGCGGCAAGAAAAGAG 59.832 55.000 12.44 0.00 44.61 2.85
2765 8002 4.279420 AGCGGCAAGAAAAGAGAAAAGAAT 59.721 37.500 1.45 0.00 0.00 2.40
2819 8067 1.092348 CACTGGTGCACCATGATGAG 58.908 55.000 37.66 26.26 46.46 2.90
2824 8072 1.474077 GGTGCACCATGATGAGTTTCC 59.526 52.381 31.23 0.00 35.64 3.13
2876 8129 2.222886 CACCCGACACCAACATTAACA 58.777 47.619 0.00 0.00 0.00 2.41
2915 8168 1.151777 CGCAGTGTCAACCTGTTCGT 61.152 55.000 0.00 0.00 32.41 3.85
2940 8193 3.796717 TGTAAGATTATGCTCTTCGTGCG 59.203 43.478 0.00 0.00 36.82 5.34
2942 8195 2.464865 AGATTATGCTCTTCGTGCGTC 58.535 47.619 0.00 0.00 0.00 5.19
2949 8202 1.930817 GCTCTTCGTGCGTCTTCTTGA 60.931 52.381 0.00 0.00 0.00 3.02
2952 8205 4.166523 CTCTTCGTGCGTCTTCTTGATTA 58.833 43.478 0.00 0.00 0.00 1.75
2953 8206 4.166523 TCTTCGTGCGTCTTCTTGATTAG 58.833 43.478 0.00 0.00 0.00 1.73
2954 8207 2.876091 TCGTGCGTCTTCTTGATTAGG 58.124 47.619 0.00 0.00 0.00 2.69
2955 8208 1.927174 CGTGCGTCTTCTTGATTAGGG 59.073 52.381 0.00 0.00 0.00 3.53
2957 8210 3.428452 CGTGCGTCTTCTTGATTAGGGTA 60.428 47.826 0.00 0.00 0.00 3.69
2958 8211 4.694339 GTGCGTCTTCTTGATTAGGGTAT 58.306 43.478 0.00 0.00 0.00 2.73
2960 8213 4.404394 TGCGTCTTCTTGATTAGGGTATCA 59.596 41.667 0.00 0.00 32.87 2.15
2961 8214 4.985409 GCGTCTTCTTGATTAGGGTATCAG 59.015 45.833 0.00 0.00 36.03 2.90
2962 8215 5.533482 CGTCTTCTTGATTAGGGTATCAGG 58.467 45.833 0.00 0.00 36.03 3.86
2963 8216 5.302059 CGTCTTCTTGATTAGGGTATCAGGA 59.698 44.000 0.00 0.00 38.43 3.86
2971 8446 2.332063 AGGGTATCAGGACATTTGCG 57.668 50.000 0.00 0.00 0.00 4.85
2975 8450 0.254462 TATCAGGACATTTGCGGGCA 59.746 50.000 0.00 0.00 0.00 5.36
2978 8453 1.001020 AGGACATTTGCGGGCATCA 60.001 52.632 0.00 0.00 0.00 3.07
2982 8457 1.315257 ACATTTGCGGGCATCAGGAC 61.315 55.000 0.00 0.00 0.00 3.85
2992 8467 1.908340 GCATCAGGACTGCCTCCACT 61.908 60.000 0.59 0.00 44.80 4.00
3035 8510 2.488891 CCACTCAAAACCATCTCCCACA 60.489 50.000 0.00 0.00 0.00 4.17
3072 8547 0.039074 GCGATCATACCTCCACTCCG 60.039 60.000 0.00 0.00 0.00 4.63
3085 8560 2.283529 ACTCCGCGACCCACATTCT 61.284 57.895 8.23 0.00 0.00 2.40
3097 8572 0.392998 CACATTCTTGCCGGCCTAGT 60.393 55.000 26.77 11.10 0.00 2.57
3100 8575 2.196997 ATTCTTGCCGGCCTAGTGCA 62.197 55.000 26.77 10.18 43.89 4.57
3135 8610 0.395586 TGGAGCCGGCATTAAAGCAT 60.396 50.000 31.54 3.33 35.83 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.009829 CGCCATTGCTAACTCCTGTC 58.990 55.000 0.00 0.00 34.43 3.51
2 3 1.718757 GGCGCCATTGCTAACTCCTG 61.719 60.000 24.80 0.00 34.43 3.86
5 6 0.308993 GATGGCGCCATTGCTAACTC 59.691 55.000 40.56 23.71 36.70 3.01
6 7 0.394216 TGATGGCGCCATTGCTAACT 60.394 50.000 40.56 19.56 36.70 2.24
7 8 0.455410 TTGATGGCGCCATTGCTAAC 59.545 50.000 40.56 26.93 36.70 2.34
8 9 1.180907 TTTGATGGCGCCATTGCTAA 58.819 45.000 40.56 27.40 36.70 3.09
9 10 1.337703 GATTTGATGGCGCCATTGCTA 59.662 47.619 40.56 25.86 36.70 3.49
10 11 0.103572 GATTTGATGGCGCCATTGCT 59.896 50.000 40.56 25.40 36.70 3.91
11 12 0.103572 AGATTTGATGGCGCCATTGC 59.896 50.000 40.56 29.07 36.70 3.56
12 13 2.620115 ACTAGATTTGATGGCGCCATTG 59.380 45.455 40.56 21.72 36.70 2.82
13 14 2.936202 ACTAGATTTGATGGCGCCATT 58.064 42.857 40.56 26.49 36.70 3.16
14 15 2.645838 ACTAGATTTGATGGCGCCAT 57.354 45.000 41.16 41.16 39.69 4.40
15 16 2.418368 AACTAGATTTGATGGCGCCA 57.582 45.000 34.80 34.80 0.00 5.69
16 17 5.005779 CGATATAACTAGATTTGATGGCGCC 59.994 44.000 22.73 22.73 0.00 6.53
17 18 5.500931 GCGATATAACTAGATTTGATGGCGC 60.501 44.000 0.00 0.00 0.00 6.53
18 19 5.576774 TGCGATATAACTAGATTTGATGGCG 59.423 40.000 0.00 0.00 0.00 5.69
71 72 6.417044 AGCGTACTAATAACAGCATCGTAAAG 59.583 38.462 0.00 0.00 0.00 1.85
77 78 4.148348 CCGAAGCGTACTAATAACAGCATC 59.852 45.833 0.00 0.00 0.00 3.91
79 80 3.441163 CCGAAGCGTACTAATAACAGCA 58.559 45.455 0.00 0.00 0.00 4.41
82 83 3.507103 TGCCGAAGCGTACTAATAACA 57.493 42.857 0.00 0.00 44.31 2.41
124 151 8.792633 CCAATTGAGTTTGTCTAGAATTTACCA 58.207 33.333 7.12 0.00 0.00 3.25
131 158 7.338196 TGTTGAACCAATTGAGTTTGTCTAGAA 59.662 33.333 7.12 0.00 0.00 2.10
132 159 6.826231 TGTTGAACCAATTGAGTTTGTCTAGA 59.174 34.615 7.12 0.00 0.00 2.43
133 160 7.026631 TGTTGAACCAATTGAGTTTGTCTAG 57.973 36.000 7.12 0.00 0.00 2.43
174 201 3.980646 TGAACAATGTGGTTACAGCAC 57.019 42.857 0.00 0.00 46.05 4.40
214 241 3.072622 GGTGAAAGGTTGTCCTACTCCTT 59.927 47.826 0.00 0.00 44.35 3.36
225 252 3.725819 TCACGCGGTGAAAGGTTG 58.274 55.556 12.47 0.00 39.78 3.77
234 568 0.457337 GGTACGAGATTTCACGCGGT 60.457 55.000 12.47 0.00 37.39 5.68
249 583 3.444916 CACACGTGTATGATCCAGGTAC 58.555 50.000 22.90 0.00 30.42 3.34
264 598 0.464036 TCTGAAGACAAGCCACACGT 59.536 50.000 0.00 0.00 0.00 4.49
271 605 3.760684 ACCAATTCCATCTGAAGACAAGC 59.239 43.478 0.00 0.00 36.14 4.01
297 631 6.797033 CGAAGAAGAGCGAACATGTAAAATTT 59.203 34.615 0.00 0.00 0.00 1.82
304 638 1.272490 TCCGAAGAAGAGCGAACATGT 59.728 47.619 0.00 0.00 0.00 3.21
306 640 1.732732 CGTCCGAAGAAGAGCGAACAT 60.733 52.381 0.00 0.00 0.00 2.71
311 645 1.444553 AAGCGTCCGAAGAAGAGCG 60.445 57.895 0.00 0.00 0.00 5.03
315 649 2.942710 TCTTACAAGCGTCCGAAGAAG 58.057 47.619 0.00 0.00 0.00 2.85
334 668 3.000727 AGACGTCATTTCGTGGGAATTC 58.999 45.455 19.50 0.00 44.21 2.17
380 715 3.329520 ACTTGAGCCAAATACACCACCTA 59.670 43.478 0.00 0.00 0.00 3.08
381 716 2.108250 ACTTGAGCCAAATACACCACCT 59.892 45.455 0.00 0.00 0.00 4.00
382 717 2.514803 ACTTGAGCCAAATACACCACC 58.485 47.619 0.00 0.00 0.00 4.61
404 739 9.932207 TGAAAATAAGAATTTCTTGCATGTGAT 57.068 25.926 19.60 2.82 37.29 3.06
461 796 4.633565 GGAAGGATGCAGTTTTGTCTCTAG 59.366 45.833 0.00 0.00 0.00 2.43
462 797 4.565652 GGGAAGGATGCAGTTTTGTCTCTA 60.566 45.833 0.00 0.00 0.00 2.43
463 798 3.416156 GGAAGGATGCAGTTTTGTCTCT 58.584 45.455 0.00 0.00 0.00 3.10
464 799 2.489722 GGGAAGGATGCAGTTTTGTCTC 59.510 50.000 0.00 0.00 0.00 3.36
478 813 2.119495 GTGGCTCATCTAAGGGAAGGA 58.881 52.381 0.00 0.00 0.00 3.36
483 818 0.824109 TCGTGTGGCTCATCTAAGGG 59.176 55.000 0.00 0.00 0.00 3.95
484 819 2.898729 ATCGTGTGGCTCATCTAAGG 57.101 50.000 0.00 0.00 0.00 2.69
485 820 4.307443 TGTATCGTGTGGCTCATCTAAG 57.693 45.455 0.00 0.00 0.00 2.18
487 822 4.937201 ATTGTATCGTGTGGCTCATCTA 57.063 40.909 0.00 0.00 0.00 1.98
488 823 3.827008 ATTGTATCGTGTGGCTCATCT 57.173 42.857 0.00 0.00 0.00 2.90
490 825 5.610398 TGATAATTGTATCGTGTGGCTCAT 58.390 37.500 0.00 0.00 39.29 2.90
491 826 5.017294 TGATAATTGTATCGTGTGGCTCA 57.983 39.130 0.00 0.00 39.29 4.26
494 829 5.741982 GGTTTTGATAATTGTATCGTGTGGC 59.258 40.000 0.00 0.00 39.29 5.01
496 831 8.909708 ATTGGTTTTGATAATTGTATCGTGTG 57.090 30.769 0.00 0.00 39.29 3.82
500 835 9.801873 AGGAAATTGGTTTTGATAATTGTATCG 57.198 29.630 0.00 0.00 39.29 2.92
506 841 8.435982 TGGTTCAGGAAATTGGTTTTGATAATT 58.564 29.630 0.00 0.00 0.00 1.40
507 842 7.877612 GTGGTTCAGGAAATTGGTTTTGATAAT 59.122 33.333 0.00 0.00 0.00 1.28
508 843 7.213678 GTGGTTCAGGAAATTGGTTTTGATAA 58.786 34.615 0.00 0.00 0.00 1.75
509 844 6.515862 CGTGGTTCAGGAAATTGGTTTTGATA 60.516 38.462 0.00 0.00 0.00 2.15
510 845 5.610398 GTGGTTCAGGAAATTGGTTTTGAT 58.390 37.500 0.00 0.00 0.00 2.57
511 846 4.440802 CGTGGTTCAGGAAATTGGTTTTGA 60.441 41.667 0.00 0.00 0.00 2.69
512 847 3.801594 CGTGGTTCAGGAAATTGGTTTTG 59.198 43.478 0.00 0.00 0.00 2.44
565 907 5.770162 CAGTTCTGTTCTTTTATTGGGGACT 59.230 40.000 0.00 0.00 0.00 3.85
634 977 3.123804 GTGGCATCAAGTAGGTACGATG 58.876 50.000 0.00 0.00 38.61 3.84
641 984 0.462047 GTCGGGTGGCATCAAGTAGG 60.462 60.000 0.00 0.00 0.00 3.18
665 1008 1.815866 CCCATTTCCCCGTTGATGC 59.184 57.895 0.00 0.00 0.00 3.91
748 1095 3.946558 TGTTAGGTTGTGGCGTTTAAGTT 59.053 39.130 0.00 0.00 0.00 2.66
874 1233 9.976511 GTGTTGTGCAGGTCTATTTATAGTATA 57.023 33.333 0.00 0.00 0.00 1.47
875 1234 7.931948 GGTGTTGTGCAGGTCTATTTATAGTAT 59.068 37.037 0.00 0.00 0.00 2.12
944 1306 3.901844 ACAGGCCGGCTTATATTTAGAGA 59.098 43.478 28.56 0.00 0.00 3.10
945 1307 4.273148 ACAGGCCGGCTTATATTTAGAG 57.727 45.455 28.56 5.73 0.00 2.43
946 1308 4.222145 CCTACAGGCCGGCTTATATTTAGA 59.778 45.833 28.56 0.00 0.00 2.10
947 1309 4.504858 CCTACAGGCCGGCTTATATTTAG 58.495 47.826 28.56 15.74 0.00 1.85
948 1310 4.546829 CCTACAGGCCGGCTTATATTTA 57.453 45.455 28.56 7.28 0.00 1.40
949 1311 3.418684 CCTACAGGCCGGCTTATATTT 57.581 47.619 28.56 6.43 0.00 1.40
1148 1519 2.478872 AGGGCAGGAATAGCTGTAGA 57.521 50.000 0.00 0.00 0.00 2.59
2386 2841 6.648725 TGTTTGTTACGGGTTTGATTTTTG 57.351 33.333 0.00 0.00 0.00 2.44
2394 2849 4.985538 TCAACATGTTTGTTACGGGTTT 57.014 36.364 8.77 0.00 44.24 3.27
2549 4966 1.329913 GCCCCCAAATTCGCTCCATT 61.330 55.000 0.00 0.00 0.00 3.16
2553 4970 2.885113 GTGCCCCCAAATTCGCTC 59.115 61.111 0.00 0.00 0.00 5.03
2555 4972 4.794439 GCGTGCCCCCAAATTCGC 62.794 66.667 0.00 0.00 37.17 4.70
2556 4973 2.817470 CTTGCGTGCCCCCAAATTCG 62.817 60.000 0.00 0.00 0.00 3.34
2560 5041 3.222855 CACTTGCGTGCCCCCAAA 61.223 61.111 0.00 0.00 33.82 3.28
2639 5124 7.712797 ACTTATTCGGACTGTTTGTTCAAAAT 58.287 30.769 0.00 0.00 0.00 1.82
2689 7896 2.269940 ACTAGTTGACCAGGCCTTCAT 58.730 47.619 0.00 0.00 0.00 2.57
2716 7952 2.855180 CCAGAAACATGCAAAGTAGCG 58.145 47.619 0.00 0.00 37.31 4.26
2750 7986 7.899841 GTGCAACAACAATTCTTTTCTCTTTTC 59.100 33.333 0.00 0.00 36.32 2.29
2756 7992 8.770438 TTTTAGTGCAACAACAATTCTTTTCT 57.230 26.923 0.00 0.00 41.43 2.52
2915 8168 4.805719 CACGAAGAGCATAATCTTACAGCA 59.194 41.667 0.00 0.00 39.63 4.41
2940 8193 6.098409 TGTCCTGATACCCTAATCAAGAAGAC 59.902 42.308 0.00 0.00 35.51 3.01
2942 8195 6.485830 TGTCCTGATACCCTAATCAAGAAG 57.514 41.667 0.00 0.00 35.51 2.85
2949 8202 4.389374 CGCAAATGTCCTGATACCCTAAT 58.611 43.478 0.00 0.00 0.00 1.73
2952 8205 1.134098 CCGCAAATGTCCTGATACCCT 60.134 52.381 0.00 0.00 0.00 4.34
2953 8206 1.308998 CCGCAAATGTCCTGATACCC 58.691 55.000 0.00 0.00 0.00 3.69
2954 8207 1.308998 CCCGCAAATGTCCTGATACC 58.691 55.000 0.00 0.00 0.00 2.73
2955 8208 0.663153 GCCCGCAAATGTCCTGATAC 59.337 55.000 0.00 0.00 0.00 2.24
2957 8210 0.396139 ATGCCCGCAAATGTCCTGAT 60.396 50.000 0.00 0.00 0.00 2.90
2958 8211 1.001020 ATGCCCGCAAATGTCCTGA 60.001 52.632 0.00 0.00 0.00 3.86
2960 8213 1.001020 TGATGCCCGCAAATGTCCT 60.001 52.632 0.00 0.00 0.00 3.85
2961 8214 1.434696 CTGATGCCCGCAAATGTCC 59.565 57.895 0.00 0.00 0.00 4.02
2962 8215 1.031571 TCCTGATGCCCGCAAATGTC 61.032 55.000 0.00 0.00 0.00 3.06
2963 8216 1.001020 TCCTGATGCCCGCAAATGT 60.001 52.632 0.00 0.00 0.00 2.71
2982 8457 0.389948 GGACGTGTAAGTGGAGGCAG 60.390 60.000 0.00 0.00 0.00 4.85
2992 8467 2.436795 CGCATTGTCGGACGTGTAA 58.563 52.632 12.82 0.00 0.00 2.41
3035 8510 2.959484 CGTGGGAGATGGTGCAGGT 61.959 63.158 0.00 0.00 0.00 4.00
3072 8547 2.877691 GGCAAGAATGTGGGTCGC 59.122 61.111 0.00 0.00 0.00 5.19
3079 8554 0.392998 CACTAGGCCGGCAAGAATGT 60.393 55.000 30.85 14.37 0.00 2.71
3085 8560 3.318384 TCTGCACTAGGCCGGCAA 61.318 61.111 30.85 15.16 43.89 4.52
3142 8617 3.114616 CGTGAGGTGCTCTTGGCG 61.115 66.667 0.00 0.00 45.43 5.69


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

AutoCloner maintained by Alex Coulton.