Multiple sequence alignment - TraesCS1B01G213100

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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 TraesCS1B01G213100 chr1B 100.000 4406 0 0 1 4406 386790750 386795155 0.000000e+00 8137
1 TraesCS1B01G213100 chr1D 94.674 3004 118 17 1244 4230 284916865 284919843 0.000000e+00 4623
2 TraesCS1B01G213100 chr1D 93.290 924 46 9 275 1196 284915945 284916854 0.000000e+00 1349
3 TraesCS1B01G213100 chr1D 89.785 186 8 3 98 276 284915650 284915831 1.230000e-55 228
4 TraesCS1B01G213100 chr1A 95.326 2375 87 15 1231 3600 356428284 356430639 0.000000e+00 3749
5 TraesCS1B01G213100 chr1A 92.553 940 53 8 278 1203 356427350 356428286 0.000000e+00 1332
6 TraesCS1B01G213100 chr1A 87.171 608 59 11 3571 4161 356430860 356431465 0.000000e+00 673
7 TraesCS1B01G213100 chr1A 93.939 66 4 0 3489 3554 356430593 356430528 2.800000e-17 100
8 TraesCS1B01G213100 chr7A 85.234 684 77 11 3740 4404 117353598 117352920 0.000000e+00 682
9 TraesCS1B01G213100 chr4D 83.721 688 83 14 3737 4406 293377749 293378425 1.350000e-174 623
10 TraesCS1B01G213100 chr4D 83.556 675 75 21 3737 4406 136961318 136961961 2.270000e-167 599
11 TraesCS1B01G213100 chr4A 83.140 688 94 9 3737 4406 313633604 313634287 3.770000e-170 608
12 TraesCS1B01G213100 chr4B 87.084 511 61 4 3898 4406 391557453 391556946 1.370000e-159 573
13 TraesCS1B01G213100 chr6B 86.312 526 66 5 3883 4406 308488651 308488130 6.400000e-158 568
14 TraesCS1B01G213100 chr7D 82.641 674 83 17 3737 4406 424646775 424647418 2.300000e-157 566
15 TraesCS1B01G213100 chr2D 85.267 543 74 4 3866 4406 624849662 624849124 4.980000e-154 555
16 TraesCS1B01G213100 chr3A 80.917 676 110 13 3740 4404 20743500 20742833 2.350000e-142 516


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 TraesCS1B01G213100 chr1B 386790750 386795155 4405 False 8137.000000 8137 100.000000 1 4406 1 chr1B.!!$F1 4405
1 TraesCS1B01G213100 chr1D 284915650 284919843 4193 False 2066.666667 4623 92.583000 98 4230 3 chr1D.!!$F1 4132
2 TraesCS1B01G213100 chr1A 356427350 356431465 4115 False 1918.000000 3749 91.683333 278 4161 3 chr1A.!!$F1 3883
3 TraesCS1B01G213100 chr7A 117352920 117353598 678 True 682.000000 682 85.234000 3740 4404 1 chr7A.!!$R1 664
4 TraesCS1B01G213100 chr4D 293377749 293378425 676 False 623.000000 623 83.721000 3737 4406 1 chr4D.!!$F2 669
5 TraesCS1B01G213100 chr4D 136961318 136961961 643 False 599.000000 599 83.556000 3737 4406 1 chr4D.!!$F1 669
6 TraesCS1B01G213100 chr4A 313633604 313634287 683 False 608.000000 608 83.140000 3737 4406 1 chr4A.!!$F1 669
7 TraesCS1B01G213100 chr4B 391556946 391557453 507 True 573.000000 573 87.084000 3898 4406 1 chr4B.!!$R1 508
8 TraesCS1B01G213100 chr6B 308488130 308488651 521 True 568.000000 568 86.312000 3883 4406 1 chr6B.!!$R1 523
9 TraesCS1B01G213100 chr7D 424646775 424647418 643 False 566.000000 566 82.641000 3737 4406 1 chr7D.!!$F1 669
10 TraesCS1B01G213100 chr2D 624849124 624849662 538 True 555.000000 555 85.267000 3866 4406 1 chr2D.!!$R1 540
11 TraesCS1B01G213100 chr3A 20742833 20743500 667 True 516.000000 516 80.917000 3740 4404 1 chr3A.!!$R1 664

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
805 934 0.248175 TATATATACGGTGGCGCGCG 60.248 55.0 28.44 28.44 0.00 6.86 F
1352 1490 0.752054 TGGAGAAACGTTACGTGGGT 59.248 50.0 12.23 0.00 39.99 4.51 F
2439 2577 0.252881 TCCTCCTCCTCACCATGCTT 60.253 55.0 0.00 0.00 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2439 2577 1.002624 GGAGGTGACGGCCATGAAA 60.003 57.895 2.24 0.0 0.00 2.69 R
2478 2616 1.682684 GAAGAGGGAGGAGACGGCA 60.683 63.158 0.00 0.0 0.00 5.69 R
4225 4656 0.251341 GGTGGCAAGGTCTTGGATGT 60.251 55.000 12.02 0.0 40.74 3.06 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
43 44 2.940951 GGGGGAGAGGATACGGGA 59.059 66.667 0.00 0.00 46.39 5.14
44 45 1.228925 GGGGGAGAGGATACGGGAG 60.229 68.421 0.00 0.00 46.39 4.30
45 46 1.228925 GGGGAGAGGATACGGGAGG 60.229 68.421 0.00 0.00 46.39 4.30
46 47 1.228925 GGGAGAGGATACGGGAGGG 60.229 68.421 0.00 0.00 46.39 4.30
47 48 1.228925 GGAGAGGATACGGGAGGGG 60.229 68.421 0.00 0.00 46.39 4.79
48 49 1.228925 GAGAGGATACGGGAGGGGG 60.229 68.421 0.00 0.00 46.39 5.40
49 50 1.703966 AGAGGATACGGGAGGGGGA 60.704 63.158 0.00 0.00 46.39 4.81
50 51 1.228925 GAGGATACGGGAGGGGGAG 60.229 68.421 0.00 0.00 46.39 4.30
51 52 2.923568 GGATACGGGAGGGGGAGC 60.924 72.222 0.00 0.00 0.00 4.70
52 53 3.303928 GATACGGGAGGGGGAGCG 61.304 72.222 0.00 0.00 0.00 5.03
53 54 4.936081 ATACGGGAGGGGGAGCGG 62.936 72.222 0.00 0.00 0.00 5.52
65 66 4.144727 GAGCGGGAGGGGAGGAGA 62.145 72.222 0.00 0.00 0.00 3.71
66 67 4.150454 AGCGGGAGGGGAGGAGAG 62.150 72.222 0.00 0.00 0.00 3.20
69 70 4.095400 GGGAGGGGAGGAGAGGCA 62.095 72.222 0.00 0.00 0.00 4.75
70 71 2.445654 GGAGGGGAGGAGAGGCAG 60.446 72.222 0.00 0.00 0.00 4.85
71 72 3.160748 GAGGGGAGGAGAGGCAGC 61.161 72.222 0.00 0.00 0.00 5.25
72 73 4.814041 AGGGGAGGAGAGGCAGCC 62.814 72.222 1.84 1.84 0.00 4.85
74 75 2.771762 GGGAGGAGAGGCAGCCAT 60.772 66.667 15.80 0.38 0.00 4.40
75 76 2.817056 GGGAGGAGAGGCAGCCATC 61.817 68.421 15.80 11.27 0.00 3.51
76 77 2.068821 GGAGGAGAGGCAGCCATCA 61.069 63.158 15.80 0.00 0.00 3.07
77 78 1.446791 GAGGAGAGGCAGCCATCAG 59.553 63.158 15.80 0.00 0.00 2.90
78 79 2.203181 GGAGAGGCAGCCATCAGC 60.203 66.667 15.80 4.96 44.25 4.26
85 86 4.435970 CAGCCATCAGCCCAGCCA 62.436 66.667 0.00 0.00 45.47 4.75
86 87 3.664888 AGCCATCAGCCCAGCCAA 61.665 61.111 0.00 0.00 45.47 4.52
87 88 3.145551 GCCATCAGCCCAGCCAAG 61.146 66.667 0.00 0.00 34.35 3.61
88 89 2.441532 CCATCAGCCCAGCCAAGG 60.442 66.667 0.00 0.00 0.00 3.61
89 90 2.357836 CATCAGCCCAGCCAAGGT 59.642 61.111 0.00 0.00 0.00 3.50
90 91 1.609239 CATCAGCCCAGCCAAGGTA 59.391 57.895 0.00 0.00 0.00 3.08
91 92 0.465097 CATCAGCCCAGCCAAGGTAG 60.465 60.000 0.00 0.00 0.00 3.18
92 93 0.916358 ATCAGCCCAGCCAAGGTAGT 60.916 55.000 0.00 0.00 0.00 2.73
93 94 1.078143 CAGCCCAGCCAAGGTAGTC 60.078 63.158 0.00 0.00 0.00 2.59
94 95 2.272471 GCCCAGCCAAGGTAGTCC 59.728 66.667 0.00 0.00 0.00 3.85
95 96 2.602676 GCCCAGCCAAGGTAGTCCA 61.603 63.158 0.00 0.00 35.89 4.02
96 97 1.299976 CCCAGCCAAGGTAGTCCAC 59.700 63.158 0.00 0.00 35.89 4.02
129 130 6.370718 AGCGGTTAACTATCTTAAACCAACAG 59.629 38.462 5.42 0.00 0.00 3.16
131 132 7.515643 CGGTTAACTATCTTAAACCAACAGTG 58.484 38.462 5.42 0.00 0.00 3.66
135 136 9.616156 TTAACTATCTTAAACCAACAGTGAACA 57.384 29.630 0.00 0.00 0.00 3.18
209 210 6.380079 AAGAAAGAAGGTCATACACATCCT 57.620 37.500 0.00 0.00 0.00 3.24
267 275 3.591527 ACCTCTTTGGGGTGACATATCAA 59.408 43.478 0.00 0.00 41.11 2.57
402 526 2.224548 GGGTTTAGACTCCACTGCACTT 60.225 50.000 0.00 0.00 0.00 3.16
427 553 7.563906 TCATTGTATTACAGTGGATCATGACA 58.436 34.615 16.48 0.00 36.60 3.58
519 647 0.249699 TTATGCGGCAGGACGTATGG 60.250 55.000 9.25 0.00 39.46 2.74
575 704 9.202545 CGTAAGTGTATTTTATAGTTTTTCCGC 57.797 33.333 0.00 0.00 0.00 5.54
655 784 6.405842 CCAGTGGGCTCTTATAAATGTTTTCC 60.406 42.308 0.00 0.00 0.00 3.13
720 849 3.000122 CACAACAAAACACGGAAGCAATG 60.000 43.478 0.00 0.00 0.00 2.82
805 934 0.248175 TATATATACGGTGGCGCGCG 60.248 55.000 28.44 28.44 0.00 6.86
847 984 3.214190 ATCCAACAGCCAGCAGCCA 62.214 57.895 0.00 0.00 45.47 4.75
880 1018 4.916041 TGATTGGAGGAGTGTGAATCTT 57.084 40.909 0.00 0.00 0.00 2.40
938 1076 1.476891 GATAGAGTGAGCCGTTGACCA 59.523 52.381 0.00 0.00 0.00 4.02
949 1087 2.890961 TTGACCACAACGCGCGAA 60.891 55.556 39.36 15.12 0.00 4.70
1199 1337 3.087031 TCACTTCCTTCCTGGTACTACG 58.913 50.000 0.00 0.00 37.07 3.51
1200 1338 3.087031 CACTTCCTTCCTGGTACTACGA 58.913 50.000 0.00 0.00 37.07 3.43
1201 1339 3.128938 CACTTCCTTCCTGGTACTACGAG 59.871 52.174 0.00 0.00 37.07 4.18
1202 1340 3.245193 ACTTCCTTCCTGGTACTACGAGT 60.245 47.826 0.00 0.00 37.07 4.18
1203 1341 2.719739 TCCTTCCTGGTACTACGAGTG 58.280 52.381 0.00 0.00 37.07 3.51
1204 1342 2.040813 TCCTTCCTGGTACTACGAGTGT 59.959 50.000 0.00 0.00 37.07 3.55
1205 1343 2.824341 CCTTCCTGGTACTACGAGTGTT 59.176 50.000 0.00 0.00 0.00 3.32
1206 1344 3.119566 CCTTCCTGGTACTACGAGTGTTC 60.120 52.174 0.00 0.00 0.00 3.18
1207 1345 3.430042 TCCTGGTACTACGAGTGTTCT 57.570 47.619 0.00 0.00 0.00 3.01
1208 1346 3.079578 TCCTGGTACTACGAGTGTTCTG 58.920 50.000 0.00 0.00 0.00 3.02
1209 1347 3.079578 CCTGGTACTACGAGTGTTCTGA 58.920 50.000 0.00 0.00 0.00 3.27
1210 1348 3.695060 CCTGGTACTACGAGTGTTCTGAT 59.305 47.826 0.00 0.00 0.00 2.90
1211 1349 4.880120 CCTGGTACTACGAGTGTTCTGATA 59.120 45.833 0.00 0.00 0.00 2.15
1212 1350 5.356190 CCTGGTACTACGAGTGTTCTGATAA 59.644 44.000 0.00 0.00 0.00 1.75
1213 1351 6.127814 CCTGGTACTACGAGTGTTCTGATAAA 60.128 42.308 0.00 0.00 0.00 1.40
1214 1352 7.218228 TGGTACTACGAGTGTTCTGATAAAA 57.782 36.000 0.00 0.00 0.00 1.52
1215 1353 7.833786 TGGTACTACGAGTGTTCTGATAAAAT 58.166 34.615 0.00 0.00 0.00 1.82
1216 1354 7.972277 TGGTACTACGAGTGTTCTGATAAAATC 59.028 37.037 0.00 0.00 0.00 2.17
1217 1355 8.189460 GGTACTACGAGTGTTCTGATAAAATCT 58.811 37.037 0.00 0.00 0.00 2.40
1218 1356 9.224058 GTACTACGAGTGTTCTGATAAAATCTC 57.776 37.037 0.00 0.00 0.00 2.75
1219 1357 8.057536 ACTACGAGTGTTCTGATAAAATCTCT 57.942 34.615 0.00 0.00 0.00 3.10
1220 1358 9.175312 ACTACGAGTGTTCTGATAAAATCTCTA 57.825 33.333 0.00 0.00 0.00 2.43
1223 1361 8.908903 ACGAGTGTTCTGATAAAATCTCTATCT 58.091 33.333 0.00 0.00 0.00 1.98
1224 1362 9.743057 CGAGTGTTCTGATAAAATCTCTATCTT 57.257 33.333 0.00 0.00 0.00 2.40
1262 1400 9.942850 TTTTTAGTATCAGTTGTCATCATCAGA 57.057 29.630 0.00 0.00 0.00 3.27
1322 1460 4.463209 TGACGAAAACGAGAAAATGATGC 58.537 39.130 0.00 0.00 0.00 3.91
1352 1490 0.752054 TGGAGAAACGTTACGTGGGT 59.248 50.000 12.23 0.00 39.99 4.51
1551 1689 1.984570 CAGGTGCTCCTCTTCGGGA 60.985 63.158 3.81 0.00 43.07 5.14
1650 1788 2.962569 CGCACCTCGTCTTCCTCA 59.037 61.111 0.00 0.00 0.00 3.86
1991 2129 1.967535 CTCTGGTCAGTCTTGCGGA 59.032 57.895 0.00 0.00 0.00 5.54
2133 2271 4.597507 ACAGTCTTCCTTAATTGTCCCTCA 59.402 41.667 0.00 0.00 0.00 3.86
2135 2273 4.846940 AGTCTTCCTTAATTGTCCCTCACT 59.153 41.667 0.00 0.00 0.00 3.41
2162 2300 3.357079 CAGGCGGTGTGCTGGTTC 61.357 66.667 0.00 0.00 45.43 3.62
2192 2330 1.102154 TCGCGCATTGGAATTGGATT 58.898 45.000 8.75 0.00 0.00 3.01
2193 2331 2.293170 TCGCGCATTGGAATTGGATTA 58.707 42.857 8.75 0.00 0.00 1.75
2194 2332 2.685388 TCGCGCATTGGAATTGGATTAA 59.315 40.909 8.75 0.00 0.00 1.40
2195 2333 3.317711 TCGCGCATTGGAATTGGATTAAT 59.682 39.130 8.75 0.00 0.00 1.40
2196 2334 4.517075 TCGCGCATTGGAATTGGATTAATA 59.483 37.500 8.75 0.00 0.00 0.98
2197 2335 5.182950 TCGCGCATTGGAATTGGATTAATAT 59.817 36.000 8.75 0.00 0.00 1.28
2256 2394 3.598715 TCGTCGACGCACAAGGGT 61.599 61.111 32.19 0.00 44.44 4.34
2433 2571 1.755008 CTCCGTCCTCCTCCTCACC 60.755 68.421 0.00 0.00 0.00 4.02
2439 2577 0.252881 TCCTCCTCCTCACCATGCTT 60.253 55.000 0.00 0.00 0.00 3.91
2529 2667 2.654877 CGCACCTACGTCAACCCT 59.345 61.111 0.00 0.00 0.00 4.34
2754 2892 4.457496 CTCGGCACCATCAGCGGT 62.457 66.667 0.00 0.00 41.07 5.68
2940 3078 2.346541 CGACTGGGAGAGCTGCAGA 61.347 63.158 20.43 0.00 0.00 4.26
3255 3393 2.167219 CATCGTGTACCAGCGCCTG 61.167 63.158 2.29 1.18 0.00 4.85
3446 3586 1.348366 TGTATGTACAGGGGCACGTTT 59.652 47.619 0.33 0.00 0.00 3.60
3454 3594 0.678684 AGGGGCACGTTTATTTCCGG 60.679 55.000 0.00 0.00 0.00 5.14
3521 3661 0.944311 CGTCGGGTCACTGGAGTTTG 60.944 60.000 0.00 0.00 0.00 2.93
3526 3666 3.833650 TCGGGTCACTGGAGTTTGTAATA 59.166 43.478 0.00 0.00 0.00 0.98
3557 3697 2.601314 GCGTGTGTAAAGATATGCGTGA 59.399 45.455 0.00 0.00 0.00 4.35
3604 3995 0.179108 GTGTCTATGGCCGTGTCCTC 60.179 60.000 8.05 0.00 0.00 3.71
3609 4000 1.737793 CTATGGCCGTGTCCTCAAAAC 59.262 52.381 8.05 0.00 0.00 2.43
3611 4002 0.179004 TGGCCGTGTCCTCAAAACAT 60.179 50.000 0.00 0.00 0.00 2.71
3623 4014 3.922240 CCTCAAAACATGCAATTCTTCCG 59.078 43.478 0.00 0.00 0.00 4.30
3634 4025 0.517316 ATTCTTCCGTGCACGAAAGC 59.483 50.000 39.10 0.00 43.02 3.51
3641 4032 1.575922 GTGCACGAAAGCTGCATGA 59.424 52.632 0.00 0.00 45.02 3.07
3644 4035 1.270274 TGCACGAAAGCTGCATGAATT 59.730 42.857 1.02 0.00 41.03 2.17
3788 4187 3.369756 ACTTGATATAAACACACGCCACG 59.630 43.478 0.00 0.00 0.00 4.94
3807 4206 1.640210 GACAACACACGCACACACCA 61.640 55.000 0.00 0.00 0.00 4.17
3814 4213 2.026014 CGCACACACCAAAGGCAC 59.974 61.111 0.00 0.00 0.00 5.01
3836 4241 4.234574 CGATACATAGGCGTTGATAGCAA 58.765 43.478 0.00 0.00 36.08 3.91
3864 4279 1.827969 ACCCTAGCACTACAAGAGCAG 59.172 52.381 0.00 0.00 34.13 4.24
3880 4307 3.965258 AGCCGGGAACATGCCACA 61.965 61.111 2.18 0.00 0.00 4.17
3886 4313 1.523154 GGGAACATGCCACAGCGAAA 61.523 55.000 0.00 0.00 44.31 3.46
4073 4501 0.320073 CACCGCCTGTCCGTCTAAAA 60.320 55.000 0.00 0.00 0.00 1.52
4240 4671 1.026718 CCCGACATCCAAGACCTTGC 61.027 60.000 4.31 0.00 39.16 4.01
4260 4691 0.972983 CACCACCTCACCCGAGATCT 60.973 60.000 0.00 0.00 42.34 2.75
4272 4703 1.749334 CGAGATCTGCCACTACCCCC 61.749 65.000 0.00 0.00 0.00 5.40
4275 4706 0.983378 GATCTGCCACTACCCCCACT 60.983 60.000 0.00 0.00 0.00 4.00
4310 4741 4.167597 GGTCCCGCCTTTTTCACA 57.832 55.556 0.00 0.00 0.00 3.58
4311 4742 1.658114 GGTCCCGCCTTTTTCACAC 59.342 57.895 0.00 0.00 0.00 3.82
4316 4747 0.250989 CCGCCTTTTTCACACCCCTA 60.251 55.000 0.00 0.00 0.00 3.53
4319 4750 1.545841 CCTTTTTCACACCCCTAGGC 58.454 55.000 2.05 0.00 36.11 3.93
4320 4751 1.203001 CCTTTTTCACACCCCTAGGCA 60.203 52.381 2.05 0.00 36.11 4.75
4322 4753 0.251165 TTTTCACACCCCTAGGCAGC 60.251 55.000 2.05 0.00 36.11 5.25
4349 4781 3.886001 CCGGGACCCAATAGGCCC 61.886 72.222 12.15 0.00 44.43 5.80
4368 4800 1.247567 CGACAAAACTGGCCTCCATT 58.752 50.000 3.32 0.00 30.82 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.228925 CTCCCGTATCCTCTCCCCC 60.229 68.421 0.00 0.00 0.00 5.40
27 28 1.228925 CCTCCCGTATCCTCTCCCC 60.229 68.421 0.00 0.00 0.00 4.81
28 29 1.228925 CCCTCCCGTATCCTCTCCC 60.229 68.421 0.00 0.00 0.00 4.30
29 30 1.228925 CCCCTCCCGTATCCTCTCC 60.229 68.421 0.00 0.00 0.00 3.71
30 31 1.228925 CCCCCTCCCGTATCCTCTC 60.229 68.421 0.00 0.00 0.00 3.20
31 32 1.703966 TCCCCCTCCCGTATCCTCT 60.704 63.158 0.00 0.00 0.00 3.69
32 33 1.228925 CTCCCCCTCCCGTATCCTC 60.229 68.421 0.00 0.00 0.00 3.71
33 34 2.944271 CTCCCCCTCCCGTATCCT 59.056 66.667 0.00 0.00 0.00 3.24
34 35 2.923568 GCTCCCCCTCCCGTATCC 60.924 72.222 0.00 0.00 0.00 2.59
35 36 3.303928 CGCTCCCCCTCCCGTATC 61.304 72.222 0.00 0.00 0.00 2.24
36 37 4.936081 CCGCTCCCCCTCCCGTAT 62.936 72.222 0.00 0.00 0.00 3.06
48 49 4.144727 TCTCCTCCCCTCCCGCTC 62.145 72.222 0.00 0.00 0.00 5.03
49 50 4.150454 CTCTCCTCCCCTCCCGCT 62.150 72.222 0.00 0.00 0.00 5.52
52 53 4.095400 TGCCTCTCCTCCCCTCCC 62.095 72.222 0.00 0.00 0.00 4.30
53 54 2.445654 CTGCCTCTCCTCCCCTCC 60.446 72.222 0.00 0.00 0.00 4.30
54 55 3.160748 GCTGCCTCTCCTCCCCTC 61.161 72.222 0.00 0.00 0.00 4.30
55 56 4.814041 GGCTGCCTCTCCTCCCCT 62.814 72.222 12.43 0.00 0.00 4.79
57 58 2.771762 ATGGCTGCCTCTCCTCCC 60.772 66.667 21.03 0.00 0.00 4.30
58 59 2.042404 CTGATGGCTGCCTCTCCTCC 62.042 65.000 21.03 1.87 0.00 4.30
59 60 1.446791 CTGATGGCTGCCTCTCCTC 59.553 63.158 21.03 9.14 0.00 3.71
60 61 2.744243 GCTGATGGCTGCCTCTCCT 61.744 63.158 21.03 0.00 38.06 3.69
61 62 2.203181 GCTGATGGCTGCCTCTCC 60.203 66.667 21.03 6.73 38.06 3.71
68 69 3.949885 TTGGCTGGGCTGATGGCTG 62.950 63.158 0.00 0.00 41.46 4.85
69 70 3.657038 CTTGGCTGGGCTGATGGCT 62.657 63.158 0.00 0.00 41.46 4.75
70 71 3.145551 CTTGGCTGGGCTGATGGC 61.146 66.667 0.00 0.00 40.90 4.40
71 72 1.925285 TACCTTGGCTGGGCTGATGG 61.925 60.000 2.53 0.00 0.00 3.51
72 73 0.465097 CTACCTTGGCTGGGCTGATG 60.465 60.000 2.53 0.00 0.00 3.07
73 74 0.916358 ACTACCTTGGCTGGGCTGAT 60.916 55.000 2.53 0.00 0.00 2.90
74 75 1.538876 ACTACCTTGGCTGGGCTGA 60.539 57.895 2.53 0.00 0.00 4.26
75 76 1.078143 GACTACCTTGGCTGGGCTG 60.078 63.158 2.53 0.00 0.00 4.85
76 77 2.301738 GGACTACCTTGGCTGGGCT 61.302 63.158 2.53 0.00 0.00 5.19
77 78 2.272471 GGACTACCTTGGCTGGGC 59.728 66.667 2.53 0.00 0.00 5.36
78 79 1.299976 GTGGACTACCTTGGCTGGG 59.700 63.158 2.53 0.00 37.04 4.45
79 80 1.299976 GGTGGACTACCTTGGCTGG 59.700 63.158 0.00 0.00 46.51 4.85
87 88 0.179108 GCTCATGTCGGTGGACTACC 60.179 60.000 0.00 0.00 46.56 3.18
88 89 0.525668 CGCTCATGTCGGTGGACTAC 60.526 60.000 0.00 0.00 43.79 2.73
89 90 1.663379 CCGCTCATGTCGGTGGACTA 61.663 60.000 17.03 0.00 43.79 2.59
90 91 2.573869 CGCTCATGTCGGTGGACT 59.426 61.111 0.00 0.00 43.79 3.85
91 92 2.509336 CCGCTCATGTCGGTGGAC 60.509 66.667 17.03 0.00 41.85 4.02
209 210 7.293299 ACATACTCCATTCCTCAATCCTCAATA 59.707 37.037 0.00 0.00 0.00 1.90
267 275 5.308825 AGCCGCTTCAGCAACTATTATAAT 58.691 37.500 2.97 2.97 42.21 1.28
369 493 3.320256 AGTCTAAACCCGAAAAGTCGTCT 59.680 43.478 0.00 0.00 46.21 4.18
381 505 1.348036 AGTGCAGTGGAGTCTAAACCC 59.652 52.381 0.00 0.00 0.00 4.11
383 507 3.728845 TGAAGTGCAGTGGAGTCTAAAC 58.271 45.455 0.00 0.00 0.00 2.01
402 526 7.495606 GTGTCATGATCCACTGTAATACAATGA 59.504 37.037 3.17 0.99 24.12 2.57
497 625 2.319136 TACGTCCTGCCGCATAATTT 57.681 45.000 0.00 0.00 0.00 1.82
498 626 2.143122 CATACGTCCTGCCGCATAATT 58.857 47.619 0.00 0.00 0.00 1.40
499 627 1.608025 CCATACGTCCTGCCGCATAAT 60.608 52.381 0.00 0.00 0.00 1.28
502 630 2.108976 CCATACGTCCTGCCGCAT 59.891 61.111 0.00 0.00 0.00 4.73
503 631 4.155733 CCCATACGTCCTGCCGCA 62.156 66.667 0.00 0.00 0.00 5.69
519 647 5.449304 CAGTTATTTTGTCAACTTCGTCCC 58.551 41.667 0.00 0.00 32.72 4.46
677 806 2.820197 GTGGTTGGGAGAATCTTTGACC 59.180 50.000 0.00 0.00 33.73 4.02
720 849 6.773976 TGGAGAATTAACCAATGGATTCAC 57.226 37.500 6.16 3.78 32.93 3.18
739 868 4.045636 CCAACTGGTTCTTTGTTTGGAG 57.954 45.455 0.00 0.00 0.00 3.86
774 903 7.310664 CCACCGTATATATACAAGTCGTTGAT 58.689 38.462 20.24 0.00 37.10 2.57
805 934 2.295349 GGATGGATGCATCAATCACACC 59.705 50.000 34.62 20.69 38.70 4.16
847 984 2.556114 CCTCCAATCAAGGAAGCCACTT 60.556 50.000 0.00 0.00 37.20 3.16
880 1018 0.411848 GGAATTGGGAAGGGGTGGAA 59.588 55.000 0.00 0.00 0.00 3.53
938 1076 1.019278 ATCCAAGATTCGCGCGTTGT 61.019 50.000 30.98 16.73 0.00 3.32
949 1087 5.363939 GAACTCGAATCAGGAATCCAAGAT 58.636 41.667 0.61 1.46 0.00 2.40
1039 1177 2.102109 TACTGCCCGCCGAAACTCAA 62.102 55.000 0.00 0.00 0.00 3.02
1266 1404 9.751542 CCGATCCGCTAATTAATTTCTCTATAT 57.248 33.333 5.91 0.00 0.00 0.86
1267 1405 8.963725 TCCGATCCGCTAATTAATTTCTCTATA 58.036 33.333 5.91 0.00 0.00 1.31
1268 1406 7.837863 TCCGATCCGCTAATTAATTTCTCTAT 58.162 34.615 5.91 0.00 0.00 1.98
1322 1460 2.224209 ACGTTTCTCCAACCACACCTAG 60.224 50.000 0.00 0.00 30.65 3.02
1352 1490 4.687215 GTCTGCAGCTGCGACCCA 62.687 66.667 33.96 19.75 45.83 4.51
1551 1689 2.874861 GCTTGATCTCGATGGCCATGAT 60.875 50.000 26.56 19.77 0.00 2.45
1650 1788 4.021925 GGTGGCGAGGCAGAAGGT 62.022 66.667 0.00 0.00 0.00 3.50
1991 2129 3.256960 AGGTTGCCATGGACGGGT 61.257 61.111 18.40 0.00 0.00 5.28
2051 2189 1.665679 ACGATGTTGATGATGCCGAAC 59.334 47.619 0.00 0.00 0.00 3.95
2192 2330 7.238723 TCATCCAGTACCCCTGCAATTATATTA 59.761 37.037 0.00 0.00 40.06 0.98
2193 2331 5.922960 TCCAGTACCCCTGCAATTATATT 57.077 39.130 0.00 0.00 40.06 1.28
2194 2332 5.551583 TCATCCAGTACCCCTGCAATTATAT 59.448 40.000 0.00 0.00 40.06 0.86
2195 2333 4.910913 TCATCCAGTACCCCTGCAATTATA 59.089 41.667 0.00 0.00 40.06 0.98
2196 2334 3.721575 TCATCCAGTACCCCTGCAATTAT 59.278 43.478 0.00 0.00 40.06 1.28
2197 2335 3.119319 TCATCCAGTACCCCTGCAATTA 58.881 45.455 0.00 0.00 40.06 1.40
2439 2577 1.002624 GGAGGTGACGGCCATGAAA 60.003 57.895 2.24 0.00 0.00 2.69
2478 2616 1.682684 GAAGAGGGAGGAGACGGCA 60.683 63.158 0.00 0.00 0.00 5.69
2754 2892 3.982372 GATCACGCCGAGGACGCAA 62.982 63.158 0.00 0.00 38.29 4.85
3255 3393 3.103911 CGCAGGTTCACGTCGTCC 61.104 66.667 0.00 0.00 0.00 4.79
3521 3661 8.644264 TTTACACACGCGAAGAAAAATATTAC 57.356 30.769 15.93 0.00 0.00 1.89
3526 3666 5.412526 TCTTTACACACGCGAAGAAAAAT 57.587 34.783 15.93 0.00 0.00 1.82
3557 3697 6.296026 AGACACACGCATTTATATACCCAAT 58.704 36.000 0.00 0.00 0.00 3.16
3604 3995 3.120923 GCACGGAAGAATTGCATGTTTTG 60.121 43.478 0.00 0.00 35.47 2.44
3611 4002 0.882484 TCGTGCACGGAAGAATTGCA 60.882 50.000 36.41 12.57 43.89 4.08
3634 4025 1.331756 GTGGACGGCTAATTCATGCAG 59.668 52.381 0.00 0.00 0.00 4.41
3641 4032 3.460648 GCTGAGTGGACGGCTAATT 57.539 52.632 0.00 0.00 38.89 1.40
3731 4122 6.830912 TGCTTCATATATAAAGCTGGACAGT 58.169 36.000 19.23 0.00 46.34 3.55
3732 4123 7.570140 CGTTGCTTCATATATAAAGCTGGACAG 60.570 40.741 19.23 9.42 46.34 3.51
3734 4125 6.423905 TCGTTGCTTCATATATAAAGCTGGAC 59.576 38.462 19.23 14.02 46.34 4.02
3738 4131 8.499162 GTTGATCGTTGCTTCATATATAAAGCT 58.501 33.333 19.23 1.16 46.34 3.74
3788 4187 1.061887 GGTGTGTGCGTGTGTTGTC 59.938 57.895 0.00 0.00 0.00 3.18
3807 4206 1.138266 ACGCCTATGTATCGTGCCTTT 59.862 47.619 0.00 0.00 34.92 3.11
3814 4213 3.833442 TGCTATCAACGCCTATGTATCG 58.167 45.455 0.00 0.00 0.00 2.92
3836 4241 3.503365 TGTAGTGCTAGGGTAGTGTTGT 58.497 45.455 0.00 0.00 0.00 3.32
3864 4279 3.443045 CTGTGGCATGTTCCCGGC 61.443 66.667 0.00 0.00 0.00 6.13
3886 4313 5.144359 GTTCGTCGTATGCAACTTCATTTT 58.856 37.500 0.00 0.00 0.00 1.82
3895 4322 1.009903 CCACGGTTCGTCGTATGCAA 61.010 55.000 0.00 0.00 41.86 4.08
3896 4323 1.444724 CCACGGTTCGTCGTATGCA 60.445 57.895 0.00 0.00 41.86 3.96
3981 4408 2.677848 GGCTCCAGGGGAAACTCC 59.322 66.667 0.00 0.00 35.23 3.85
4061 4489 6.105397 ACCTGTTCTATTTTTAGACGGACA 57.895 37.500 0.00 0.00 0.00 4.02
4225 4656 0.251341 GGTGGCAAGGTCTTGGATGT 60.251 55.000 12.02 0.00 40.74 3.06
4240 4671 1.961180 GATCTCGGGTGAGGTGGTGG 61.961 65.000 0.00 0.00 42.79 4.61
4260 4691 0.988832 CTTTAGTGGGGGTAGTGGCA 59.011 55.000 0.00 0.00 0.00 4.92
4272 4703 3.868077 CCTTTCCGCTCATCTCTTTAGTG 59.132 47.826 0.00 0.00 0.00 2.74
4275 4706 3.118738 GGACCTTTCCGCTCATCTCTTTA 60.119 47.826 0.00 0.00 29.98 1.85
4305 4736 2.602676 GGCTGCCTAGGGGTGTGAA 61.603 63.158 12.43 0.00 34.45 3.18
4306 4737 3.009115 GGCTGCCTAGGGGTGTGA 61.009 66.667 12.43 0.00 34.45 3.58
4349 4781 1.068333 CAATGGAGGCCAGTTTTGTCG 60.068 52.381 5.01 0.00 36.75 4.35


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

AutoCloner maintained by Alex Coulton.