Multiple sequence alignment - TraesCS7B01G365900

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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 TraesCS7B01G365900 chr7B 100.000 3425 0 0 1 3425 629789439 629786015 0.000000e+00 6325
1 TraesCS7B01G365900 chr7B 85.271 129 19 0 5 133 629870033 629869905 2.140000e-27 134
2 TraesCS7B01G365900 chr7D 90.953 2664 128 46 5 2603 572537307 572539922 0.000000e+00 3480
3 TraesCS7B01G365900 chr7D 90.607 511 23 14 2587 3087 572539944 572540439 0.000000e+00 654
4 TraesCS7B01G365900 chr7D 85.387 349 19 3 1826 2173 138312878 138312561 1.970000e-87 333
5 TraesCS7B01G365900 chr7D 89.385 179 5 5 3243 3412 572540528 572540701 2.680000e-51 213
6 TraesCS7B01G365900 chr7A 90.745 2107 103 32 540 2603 661575807 661577864 0.000000e+00 2726
7 TraesCS7B01G365900 chr7A 85.140 821 52 32 2625 3425 661577926 661578696 0.000000e+00 776
8 TraesCS7B01G365900 chr5A 86.961 1066 75 27 1632 2671 328011010 328009983 0.000000e+00 1140
9 TraesCS7B01G365900 chr5A 86.961 1066 75 27 1632 2671 328017251 328016224 0.000000e+00 1140
10 TraesCS7B01G365900 chr5A 92.275 233 17 1 1137 1368 328023120 328022888 2.550000e-86 329
11 TraesCS7B01G365900 chr5A 94.762 210 11 0 1358 1567 328011212 328011003 9.160000e-86 327
12 TraesCS7B01G365900 chr5A 95.238 63 3 0 1505 1567 328017306 328017244 2.170000e-17 100
13 TraesCS7B01G365900 chr1A 86.891 1068 71 36 1633 2671 59587692 59586665 0.000000e+00 1133
14 TraesCS7B01G365900 chr1A 91.422 443 26 4 1137 1567 59588128 59587686 6.330000e-167 597
15 TraesCS7B01G365900 chr6B 81.250 224 35 7 1576 1797 177793962 177794180 1.260000e-39 174
16 TraesCS7B01G365900 chr5D 97.590 83 1 1 1628 1709 49304584 49304666 1.280000e-29 141
17 TraesCS7B01G365900 chr2D 95.000 80 3 1 1628 1706 576403716 576403795 1.290000e-24 124
18 TraesCS7B01G365900 chr2D 95.000 80 3 1 1628 1706 576421624 576421703 1.290000e-24 124
19 TraesCS7B01G365900 chr2D 95.000 80 3 1 1628 1706 576439413 576439492 1.290000e-24 124


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 TraesCS7B01G365900 chr7B 629786015 629789439 3424 True 6325.0 6325 100.0000 1 3425 1 chr7B.!!$R1 3424
1 TraesCS7B01G365900 chr7D 572537307 572540701 3394 False 1449.0 3480 90.3150 5 3412 3 chr7D.!!$F1 3407
2 TraesCS7B01G365900 chr7A 661575807 661578696 2889 False 1751.0 2726 87.9425 540 3425 2 chr7A.!!$F1 2885
3 TraesCS7B01G365900 chr5A 328009983 328011212 1229 True 733.5 1140 90.8615 1358 2671 2 chr5A.!!$R2 1313
4 TraesCS7B01G365900 chr5A 328016224 328017306 1082 True 620.0 1140 91.0995 1505 2671 2 chr5A.!!$R3 1166
5 TraesCS7B01G365900 chr1A 59586665 59588128 1463 True 865.0 1133 89.1565 1137 2671 2 chr1A.!!$R1 1534

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
519 522 0.178816 TCTGAATTTCCCCTCCCCCA 60.179 55.0 0.00 0.0 0.00 4.96 F
2182 2320 0.455295 CAGCAAGGACTCGTCGTCTC 60.455 60.0 7.36 0.0 42.44 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2287 2438 0.030101 CCTCGATCGCAGTCTCTTCC 59.970 60.0 11.09 0.0 0.0 3.46 R
3229 3531 0.393132 GGGAAAGGAGGAGCGAAAGG 60.393 60.0 0.00 0.0 0.0 3.11 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
56 57 7.995289 ACTCAAACATTTGATGTGAACTAACA 58.005 30.769 7.48 0.00 45.26 2.41
115 116 1.679153 CTCCTCCTCTTTCGAGCCTAC 59.321 57.143 0.00 0.00 35.90 3.18
117 118 2.035632 CCTCCTCTTTCGAGCCTACAT 58.964 52.381 0.00 0.00 35.90 2.29
119 120 3.452474 CTCCTCTTTCGAGCCTACATTG 58.548 50.000 0.00 0.00 35.90 2.82
135 136 3.091545 ACATTGGCCAGACAATAAGGTG 58.908 45.455 5.11 0.00 38.94 4.00
147 148 2.215942 ATAAGGTGGGAGGTGCAAAC 57.784 50.000 0.00 0.00 0.00 2.93
148 149 0.250553 TAAGGTGGGAGGTGCAAACG 60.251 55.000 0.00 0.00 0.00 3.60
155 156 1.408266 GGGAGGTGCAAACGTATCCAT 60.408 52.381 0.00 0.00 0.00 3.41
163 165 3.829601 TGCAAACGTATCCATTTTTCCCT 59.170 39.130 0.00 0.00 0.00 4.20
168 170 7.371936 CAAACGTATCCATTTTTCCCTAAACA 58.628 34.615 0.00 0.00 0.00 2.83
177 179 6.426633 CCATTTTTCCCTAAACAATTGGACAC 59.573 38.462 10.83 0.00 0.00 3.67
185 187 8.875168 TCCCTAAACAATTGGACACATTAAAAT 58.125 29.630 10.83 0.00 0.00 1.82
221 224 9.231297 TCCAACTAAATTTTGATACTCAGAAGG 57.769 33.333 6.63 0.00 0.00 3.46
222 225 9.014297 CCAACTAAATTTTGATACTCAGAAGGT 57.986 33.333 6.63 0.00 0.00 3.50
225 228 6.743575 AAATTTTGATACTCAGAAGGTCGG 57.256 37.500 0.00 0.00 0.00 4.79
226 229 4.884668 TTTTGATACTCAGAAGGTCGGT 57.115 40.909 0.00 0.00 0.00 4.69
227 230 3.868757 TTGATACTCAGAAGGTCGGTG 57.131 47.619 0.00 0.00 0.00 4.94
229 232 2.753452 TGATACTCAGAAGGTCGGTGTC 59.247 50.000 0.00 0.00 0.00 3.67
247 250 3.560068 GTGTCGAACCTTTGATGTGAACT 59.440 43.478 0.00 0.00 0.00 3.01
309 312 3.618690 AGTCCGATTCCTCTTTCAAGG 57.381 47.619 0.00 0.00 37.81 3.61
312 315 4.530946 AGTCCGATTCCTCTTTCAAGGTTA 59.469 41.667 0.00 0.00 37.69 2.85
325 328 9.613428 CTCTTTCAAGGTTACATTGGTCATATA 57.387 33.333 9.87 0.00 0.00 0.86
338 341 5.762179 TGGTCATATAATAAGCTGGGAGG 57.238 43.478 0.00 0.00 0.00 4.30
352 355 1.638070 TGGGAGGTGCAAACATATCCA 59.362 47.619 0.00 0.00 35.82 3.41
357 360 5.351458 GGAGGTGCAAACATATCCAAATTC 58.649 41.667 0.00 0.00 34.80 2.17
360 363 4.081198 GGTGCAAACATATCCAAATTCCCA 60.081 41.667 0.00 0.00 0.00 4.37
400 403 0.753848 AACCCCAACGTTTCCACCTG 60.754 55.000 0.00 0.00 0.00 4.00
409 412 2.034558 ACGTTTCCACCTGCATTTTGAG 59.965 45.455 0.00 0.00 0.00 3.02
423 426 4.618489 GCATTTTGAGACAAAAGATGGTCG 59.382 41.667 13.54 0.00 39.01 4.79
440 443 2.357952 GGTCGAACTTGAACCTTTGCTT 59.642 45.455 0.00 0.00 0.00 3.91
443 446 3.442273 TCGAACTTGAACCTTTGCTTTGT 59.558 39.130 0.00 0.00 0.00 2.83
462 465 5.420725 TTGTACTCACATATTGACAGCCT 57.579 39.130 0.00 0.00 33.76 4.58
468 471 6.286758 ACTCACATATTGACAGCCTATTCTG 58.713 40.000 0.00 0.00 39.86 3.02
484 487 7.069578 AGCCTATTCTGTCCTTAAATCTCGTTA 59.930 37.037 0.00 0.00 0.00 3.18
485 488 7.873505 GCCTATTCTGTCCTTAAATCTCGTTAT 59.126 37.037 0.00 0.00 0.00 1.89
486 489 9.765795 CCTATTCTGTCCTTAAATCTCGTTATT 57.234 33.333 0.00 0.00 0.00 1.40
505 508 9.878667 TCGTTATTAATTCTACCACAATCTGAA 57.121 29.630 0.00 0.00 0.00 3.02
511 514 7.410120 AATTCTACCACAATCTGAATTTCCC 57.590 36.000 0.00 0.00 34.83 3.97
512 515 4.855340 TCTACCACAATCTGAATTTCCCC 58.145 43.478 0.00 0.00 0.00 4.81
516 519 3.026694 CACAATCTGAATTTCCCCTCCC 58.973 50.000 0.00 0.00 0.00 4.30
517 520 2.023984 ACAATCTGAATTTCCCCTCCCC 60.024 50.000 0.00 0.00 0.00 4.81
518 521 1.235756 ATCTGAATTTCCCCTCCCCC 58.764 55.000 0.00 0.00 0.00 5.40
519 522 0.178816 TCTGAATTTCCCCTCCCCCA 60.179 55.000 0.00 0.00 0.00 4.96
520 523 0.709992 CTGAATTTCCCCTCCCCCAA 59.290 55.000 0.00 0.00 0.00 4.12
524 527 3.848200 TTTCCCCTCCCCCAAGGCT 62.848 63.158 0.00 0.00 34.88 4.58
527 530 3.097162 CCCTCCCCCAAGGCTACC 61.097 72.222 0.00 0.00 34.88 3.18
551 554 6.465751 CCTTGGTCAGATATAAACCCAGCATA 60.466 42.308 0.00 0.00 31.78 3.14
594 597 2.503356 TGAACAAAACCCCATGTTTGCT 59.497 40.909 6.46 0.00 46.39 3.91
602 605 2.202388 CATGTTTGCTGCGCTCGG 60.202 61.111 9.73 0.00 0.00 4.63
667 677 3.753806 AAAACCCGCAACCCGACGA 62.754 57.895 0.00 0.00 40.02 4.20
812 827 4.531708 CGGCACATTTTCACCGTG 57.468 55.556 0.00 0.00 40.77 4.94
813 828 1.945522 CGGCACATTTTCACCGTGA 59.054 52.632 0.00 0.00 40.77 4.35
1125 1156 0.952280 TCGTCGTGTCTTCTGCTTCT 59.048 50.000 0.00 0.00 0.00 2.85
1221 1252 2.203523 TGCACCACCAGCATGCTT 60.204 55.556 19.98 0.50 40.13 3.91
1284 1321 2.124819 CGGGCTGATGCTTCTGCT 60.125 61.111 24.16 0.00 43.96 4.24
1287 1324 2.772691 GGCTGATGCTTCTGCTGCC 61.773 63.158 24.16 16.47 43.96 4.85
1482 1522 4.020617 CTCAAGAGGGCGGCCACA 62.021 66.667 31.59 7.31 0.00 4.17
1737 1864 2.568612 CGCTTCTCGCACTCCTCA 59.431 61.111 0.00 0.00 39.08 3.86
1770 1897 4.430765 GGCCACGACCACGACGAT 62.431 66.667 0.00 0.00 42.66 3.73
2160 2298 0.832135 AGGACAAGAAGGAGTCGGCA 60.832 55.000 0.00 0.00 35.63 5.69
2178 2316 2.811317 GCCAGCAAGGACTCGTCG 60.811 66.667 0.00 0.00 41.22 5.12
2182 2320 0.455295 CAGCAAGGACTCGTCGTCTC 60.455 60.000 7.36 0.00 42.44 3.36
2196 2334 1.420702 GTCTCTGAGGTCGTCGTCG 59.579 63.158 4.59 0.00 38.55 5.12
2290 2441 4.467084 GCGGGTGATCTGCCGGAA 62.467 66.667 5.05 0.00 41.83 4.30
2291 2442 2.202932 CGGGTGATCTGCCGGAAG 60.203 66.667 5.05 3.22 0.00 3.46
2292 2443 2.721167 CGGGTGATCTGCCGGAAGA 61.721 63.158 16.55 16.55 0.00 2.87
2295 2446 0.179097 GGTGATCTGCCGGAAGAGAC 60.179 60.000 19.37 16.22 0.00 3.36
2296 2447 0.820871 GTGATCTGCCGGAAGAGACT 59.179 55.000 19.37 0.00 0.00 3.24
2306 2470 0.030101 GGAAGAGACTGCGATCGAGG 59.970 60.000 21.57 12.62 0.00 4.63
2324 2489 2.885644 GCGTCGTCGTGCATGGAT 60.886 61.111 5.98 0.00 39.49 3.41
2374 2549 1.132834 TGGATGCATAGCGCTTTGTTG 59.867 47.619 25.42 15.18 43.06 3.33
2377 2552 1.139520 GCATAGCGCTTTGTTGGGG 59.860 57.895 25.42 3.30 37.77 4.96
2439 2614 7.939039 TGAGAAGGTCTAATCAATTGACTGTTT 59.061 33.333 11.07 3.71 0.00 2.83
2480 2664 7.425606 TGTAAATTTGGAGTTTTGCTCTTCTC 58.574 34.615 0.00 0.00 43.62 2.87
2569 2753 3.067461 TCACAAGATGTTTTTCCAACCGG 59.933 43.478 0.00 0.00 0.00 5.28
2589 2856 4.437930 CCGGATGCTGTTTTTGAAGAGATC 60.438 45.833 0.00 0.00 0.00 2.75
2618 2885 3.713858 TGTCATTGTTCAAACCAGCAG 57.286 42.857 0.00 0.00 0.00 4.24
2643 2918 3.929389 GATCGATCGAGCTGGCAC 58.071 61.111 25.17 5.99 0.00 5.01
2672 2947 2.985957 ACAAATGCAGGCAAACAGTT 57.014 40.000 0.00 0.00 0.00 3.16
2681 2956 1.363807 GCAAACAGTTGGAGTGGCC 59.636 57.895 0.00 0.00 35.10 5.36
2816 3095 1.750399 CCAGAGCCCACCCATTTCG 60.750 63.158 0.00 0.00 0.00 3.46
2827 3106 2.202518 CATTTCGCCGCAGCAAGG 60.203 61.111 0.00 0.00 39.83 3.61
2869 3149 1.004560 TCAACAAGAGCTGAGCCGG 60.005 57.895 0.00 0.00 0.00 6.13
2870 3150 2.359230 AACAAGAGCTGAGCCGGC 60.359 61.111 21.89 21.89 35.73 6.13
2891 3171 1.610102 CCGGCTTGATCTGGATCCATC 60.610 57.143 16.63 11.81 37.02 3.51
2925 3205 2.745100 CTGTGCCGCATGTGCTCT 60.745 61.111 0.00 0.00 39.32 4.09
3059 3343 3.785859 ATCATGGCCACGCTCCGT 61.786 61.111 8.16 0.00 42.36 4.69
3102 3395 3.855853 GGCCGAGCTTCCTCCCTC 61.856 72.222 0.00 0.00 34.49 4.30
3103 3396 3.855853 GCCGAGCTTCCTCCCTCC 61.856 72.222 0.00 0.00 34.49 4.30
3104 3397 2.364317 CCGAGCTTCCTCCCTCCA 60.364 66.667 0.00 0.00 34.49 3.86
3105 3398 2.726351 CCGAGCTTCCTCCCTCCAC 61.726 68.421 0.00 0.00 34.49 4.02
3106 3399 1.684049 CGAGCTTCCTCCCTCCACT 60.684 63.158 0.00 0.00 34.49 4.00
3107 3400 1.904032 GAGCTTCCTCCCTCCACTG 59.096 63.158 0.00 0.00 31.68 3.66
3108 3401 2.250741 GAGCTTCCTCCCTCCACTGC 62.251 65.000 0.00 0.00 31.68 4.40
3109 3402 2.993853 CTTCCTCCCTCCACTGCC 59.006 66.667 0.00 0.00 0.00 4.85
3110 3403 3.003173 TTCCTCCCTCCACTGCCG 61.003 66.667 0.00 0.00 0.00 5.69
3238 3540 3.793144 CGCCACTGCCTTTCGCTC 61.793 66.667 0.00 0.00 38.78 5.03
3239 3541 3.435186 GCCACTGCCTTTCGCTCC 61.435 66.667 0.00 0.00 38.78 4.70
3240 3542 2.348998 CCACTGCCTTTCGCTCCT 59.651 61.111 0.00 0.00 38.78 3.69
3241 3543 1.743252 CCACTGCCTTTCGCTCCTC 60.743 63.158 0.00 0.00 38.78 3.71
3272 3574 2.281276 GGCCGTGTCCTTTTCCGT 60.281 61.111 0.00 0.00 0.00 4.69
3314 3625 4.351054 CTTTGCCCCGCTCCAGGT 62.351 66.667 0.00 0.00 0.00 4.00
3342 3653 3.114616 CTCTCGTGCAACCGCCTG 61.115 66.667 0.00 0.00 37.32 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.286800 CCATCTTTGTTTCAAAATGTAGTCGTA 58.713 33.333 0.00 0.00 0.00 3.43
1 2 7.138736 CCATCTTTGTTTCAAAATGTAGTCGT 58.861 34.615 0.00 0.00 0.00 4.34
2 3 7.138736 ACCATCTTTGTTTCAAAATGTAGTCG 58.861 34.615 0.00 0.00 0.00 4.18
3 4 8.755018 CAACCATCTTTGTTTCAAAATGTAGTC 58.245 33.333 0.00 0.00 0.00 2.59
20 21 7.111247 TCAAATGTTTGAGTTCAACCATCTT 57.889 32.000 5.53 1.56 41.88 2.40
82 83 7.064728 CGAAAGAGGAGGAGAAATTAACGAAAT 59.935 37.037 0.00 0.00 0.00 2.17
115 116 2.428171 CCACCTTATTGTCTGGCCAATG 59.572 50.000 7.01 0.00 35.85 2.82
117 118 1.272425 CCCACCTTATTGTCTGGCCAA 60.272 52.381 7.01 0.00 0.00 4.52
119 120 0.623723 TCCCACCTTATTGTCTGGCC 59.376 55.000 0.00 0.00 0.00 5.36
126 127 2.214376 TTGCACCTCCCACCTTATTG 57.786 50.000 0.00 0.00 0.00 1.90
135 136 0.035820 TGGATACGTTTGCACCTCCC 60.036 55.000 0.00 0.00 42.51 4.30
147 148 7.491048 CCAATTGTTTAGGGAAAAATGGATACG 59.509 37.037 4.43 0.00 42.51 3.06
148 149 8.536175 TCCAATTGTTTAGGGAAAAATGGATAC 58.464 33.333 4.43 0.00 0.00 2.24
155 156 6.546428 TGTGTCCAATTGTTTAGGGAAAAA 57.454 33.333 4.43 0.00 0.00 1.94
225 228 3.560068 AGTTCACATCAAAGGTTCGACAC 59.440 43.478 0.00 0.00 0.00 3.67
226 229 3.804036 AGTTCACATCAAAGGTTCGACA 58.196 40.909 0.00 0.00 0.00 4.35
227 230 4.989168 ACTAGTTCACATCAAAGGTTCGAC 59.011 41.667 0.00 0.00 0.00 4.20
229 232 6.422701 TGTTACTAGTTCACATCAAAGGTTCG 59.577 38.462 0.00 0.00 0.00 3.95
272 275 6.847956 TCGGACTTGACGAAATTTAAGAAA 57.152 33.333 5.62 0.00 37.42 2.52
309 312 8.730680 CCCAGCTTATTATATGACCAATGTAAC 58.269 37.037 0.00 0.00 0.00 2.50
312 315 7.090319 TCCCAGCTTATTATATGACCAATGT 57.910 36.000 0.00 0.00 0.00 2.71
325 328 2.171003 GTTTGCACCTCCCAGCTTATT 58.829 47.619 0.00 0.00 0.00 1.40
338 341 5.083533 TGGGAATTTGGATATGTTTGCAC 57.916 39.130 0.00 0.00 0.00 4.57
352 355 7.709149 TTTGTTCAATGGTTTTTGGGAATTT 57.291 28.000 0.00 0.00 0.00 1.82
357 360 6.690194 TTGATTTGTTCAATGGTTTTTGGG 57.310 33.333 0.00 0.00 39.44 4.12
360 363 7.363355 GGGGTTTTGATTTGTTCAATGGTTTTT 60.363 33.333 0.00 0.00 43.73 1.94
400 403 4.618489 CGACCATCTTTTGTCTCAAAATGC 59.382 41.667 7.87 0.00 0.00 3.56
409 412 5.205565 GTTCAAGTTCGACCATCTTTTGTC 58.794 41.667 0.00 0.00 0.00 3.18
423 426 5.891451 AGTACAAAGCAAAGGTTCAAGTTC 58.109 37.500 0.00 0.00 0.00 3.01
440 443 5.420725 AGGCTGTCAATATGTGAGTACAA 57.579 39.130 0.00 0.00 40.84 2.41
443 446 7.069950 ACAGAATAGGCTGTCAATATGTGAGTA 59.930 37.037 0.00 0.00 45.54 2.59
485 488 8.966868 GGGAAATTCAGATTGTGGTAGAATTAA 58.033 33.333 0.00 0.00 37.79 1.40
486 489 7.559897 GGGGAAATTCAGATTGTGGTAGAATTA 59.440 37.037 0.00 0.00 37.79 1.40
487 490 6.381133 GGGGAAATTCAGATTGTGGTAGAATT 59.619 38.462 0.00 0.00 39.74 2.17
493 496 3.564352 GGAGGGGAAATTCAGATTGTGGT 60.564 47.826 0.00 0.00 0.00 4.16
502 505 0.709992 CTTGGGGGAGGGGAAATTCA 59.290 55.000 0.00 0.00 0.00 2.57
505 508 2.636617 GCCTTGGGGGAGGGGAAAT 61.637 63.158 0.00 0.00 37.29 2.17
509 512 3.097162 GTAGCCTTGGGGGAGGGG 61.097 72.222 0.00 0.00 37.29 4.79
510 513 3.097162 GGTAGCCTTGGGGGAGGG 61.097 72.222 0.00 0.00 37.29 4.30
511 514 1.619669 AAGGTAGCCTTGGGGGAGG 60.620 63.158 0.00 0.00 42.96 4.30
512 515 4.171186 AAGGTAGCCTTGGGGGAG 57.829 61.111 0.00 0.00 42.96 4.30
519 522 6.409349 GGTTTATATCTGACCAAGGTAGCCTT 60.409 42.308 0.00 0.00 45.88 4.35
520 523 5.071923 GGTTTATATCTGACCAAGGTAGCCT 59.928 44.000 0.00 0.00 33.87 4.58
524 527 5.163237 GCTGGGTTTATATCTGACCAAGGTA 60.163 44.000 7.99 0.00 35.43 3.08
527 530 4.780815 TGCTGGGTTTATATCTGACCAAG 58.219 43.478 3.25 3.25 37.52 3.61
538 541 7.992608 GGGAATGAATTTTTATGCTGGGTTTAT 59.007 33.333 0.00 0.00 0.00 1.40
551 554 8.412456 GTTCAATGGTTTTGGGAATGAATTTTT 58.588 29.630 0.00 0.00 0.00 1.94
602 605 2.202892 GGTACAGCTACGGCCAGC 60.203 66.667 6.98 6.98 42.12 4.85
673 683 2.102161 GGCAAAATACAGGCGCGG 59.898 61.111 8.83 0.00 0.00 6.46
674 684 1.062525 GAGGCAAAATACAGGCGCG 59.937 57.895 0.00 0.00 35.18 6.86
675 685 0.099436 CAGAGGCAAAATACAGGCGC 59.901 55.000 0.00 0.00 35.18 6.53
676 686 0.099436 GCAGAGGCAAAATACAGGCG 59.901 55.000 0.00 0.00 40.72 5.52
677 687 0.099436 CGCAGAGGCAAAATACAGGC 59.901 55.000 0.00 0.00 41.24 4.85
678 688 0.099436 GCGCAGAGGCAAAATACAGG 59.901 55.000 0.30 0.00 41.24 4.00
679 689 0.247814 CGCGCAGAGGCAAAATACAG 60.248 55.000 8.75 0.00 41.24 2.74
680 690 1.793581 CGCGCAGAGGCAAAATACA 59.206 52.632 8.75 0.00 41.24 2.29
681 691 1.583709 GCGCGCAGAGGCAAAATAC 60.584 57.895 29.10 0.00 41.24 1.89
812 827 1.259840 TATATAAGCGGGGCGGGGTC 61.260 60.000 0.00 0.00 0.00 4.46
813 828 0.619543 ATATATAAGCGGGGCGGGGT 60.620 55.000 0.00 0.00 0.00 4.95
877 892 3.408853 GTAGGTGGGGGTGGGAGC 61.409 72.222 0.00 0.00 0.00 4.70
879 894 2.204029 GTGTAGGTGGGGGTGGGA 60.204 66.667 0.00 0.00 0.00 4.37
886 901 0.527817 GCGAATCTCGTGTAGGTGGG 60.528 60.000 0.00 0.00 42.81 4.61
889 904 1.432251 CGGCGAATCTCGTGTAGGT 59.568 57.895 0.00 0.00 42.81 3.08
890 905 1.944676 GCGGCGAATCTCGTGTAGG 60.945 63.158 12.98 0.00 42.81 3.18
892 907 1.226575 CTGCGGCGAATCTCGTGTA 60.227 57.895 12.98 0.00 42.81 2.90
893 908 2.507102 CTGCGGCGAATCTCGTGT 60.507 61.111 12.98 0.00 42.81 4.49
945 964 2.126071 ACACGCGCACGCTAATCT 60.126 55.556 13.70 0.00 45.53 2.40
1107 1138 1.332178 GAGAAGCAGAAGACACGACG 58.668 55.000 0.00 0.00 0.00 5.12
1108 1139 1.670380 GGGAGAAGCAGAAGACACGAC 60.670 57.143 0.00 0.00 0.00 4.34
1109 1140 0.603569 GGGAGAAGCAGAAGACACGA 59.396 55.000 0.00 0.00 0.00 4.35
1110 1141 0.734253 CGGGAGAAGCAGAAGACACG 60.734 60.000 0.00 0.00 0.00 4.49
1770 1897 2.357034 GAGAAGCGCGGGTTGACA 60.357 61.111 8.83 0.00 0.00 3.58
2160 2298 2.659610 GACGAGTCCTTGCTGGCT 59.340 61.111 0.00 0.00 35.26 4.75
2178 2316 1.420702 CGACGACGACCTCAGAGAC 59.579 63.158 0.00 0.00 42.66 3.36
2182 2320 4.813526 CCGCGACGACGACCTCAG 62.814 72.222 8.23 0.00 42.66 3.35
2283 2434 2.284798 GATCGCAGTCTCTTCCGGCA 62.285 60.000 0.00 0.00 0.00 5.69
2285 2436 1.298713 CGATCGCAGTCTCTTCCGG 60.299 63.158 0.26 0.00 0.00 5.14
2287 2438 0.030101 CCTCGATCGCAGTCTCTTCC 59.970 60.000 11.09 0.00 0.00 3.46
2290 2441 2.485795 GCCCTCGATCGCAGTCTCT 61.486 63.158 11.09 0.00 0.00 3.10
2291 2442 2.026879 GCCCTCGATCGCAGTCTC 59.973 66.667 11.09 0.00 0.00 3.36
2292 2443 3.893763 CGCCCTCGATCGCAGTCT 61.894 66.667 11.09 0.00 38.10 3.24
2306 2470 2.947118 TATCCATGCACGACGACGCC 62.947 60.000 7.30 0.00 43.96 5.68
2339 2504 2.849942 CATCCATCATTGCGTCCCTAA 58.150 47.619 0.00 0.00 0.00 2.69
2374 2549 5.676552 ACAAACCAAATCAGTTAAAACCCC 58.323 37.500 0.00 0.00 0.00 4.95
2377 2552 9.753669 CAAAGAACAAACCAAATCAGTTAAAAC 57.246 29.630 0.00 0.00 0.00 2.43
2439 2614 9.801873 CCAAATTTACAGTCAAGAGAAAAGAAA 57.198 29.630 0.00 0.00 0.00 2.52
2480 2664 0.035056 AACGGCCTTGAGGATTGAGG 60.035 55.000 0.00 0.00 37.39 3.86
2566 2750 2.813754 TCTCTTCAAAAACAGCATCCGG 59.186 45.455 0.00 0.00 0.00 5.14
2569 2753 5.048504 TGTGGATCTCTTCAAAAACAGCATC 60.049 40.000 0.00 0.00 0.00 3.91
2589 2856 4.898829 TTGAACAATGACAAGAGTGTGG 57.101 40.909 0.00 0.00 38.41 4.17
2643 2918 1.609932 CTGCATTTGTAACAGCGCTG 58.390 50.000 34.89 34.89 0.00 5.18
2672 2947 1.562672 GCCCTAGAAAGGCCACTCCA 61.563 60.000 5.01 0.00 45.16 3.86
2681 2956 1.363744 CGTTGCTCTGCCCTAGAAAG 58.636 55.000 0.00 0.00 34.32 2.62
2764 3039 1.144936 GCTAGTGCTAGTGGCTGGG 59.855 63.158 0.00 0.00 42.39 4.45
2805 3084 3.814268 CTGCGGCGAAATGGGTGG 61.814 66.667 12.98 0.00 0.00 4.61
2806 3085 4.481112 GCTGCGGCGAAATGGGTG 62.481 66.667 12.98 0.00 0.00 4.61
2869 3149 1.599240 GATCCAGATCAAGCCGGGC 60.599 63.158 12.11 12.11 37.74 6.13
2870 3150 1.072159 GGATCCAGATCAAGCCGGG 59.928 63.158 6.95 0.00 39.54 5.73
2925 3205 1.593209 GCGCGAATATTCACGGGGA 60.593 57.895 23.16 0.00 41.42 4.81
2946 3226 5.007385 TGGCGTAGGAGTAATTTTCTCTC 57.993 43.478 3.47 0.00 33.06 3.20
3051 3335 4.406173 CTGTCAGCGACGGAGCGT 62.406 66.667 10.75 0.00 41.05 5.07
3087 3380 2.364317 TGGAGGGAGGAAGCTCGG 60.364 66.667 0.00 0.00 0.00 4.63
3088 3381 1.684049 AGTGGAGGGAGGAAGCTCG 60.684 63.158 0.00 0.00 0.00 5.03
3089 3382 1.904032 CAGTGGAGGGAGGAAGCTC 59.096 63.158 0.00 0.00 0.00 4.09
3090 3383 2.297129 GCAGTGGAGGGAGGAAGCT 61.297 63.158 0.00 0.00 0.00 3.74
3091 3384 2.270527 GCAGTGGAGGGAGGAAGC 59.729 66.667 0.00 0.00 0.00 3.86
3092 3385 2.993853 GGCAGTGGAGGGAGGAAG 59.006 66.667 0.00 0.00 0.00 3.46
3093 3386 3.003173 CGGCAGTGGAGGGAGGAA 61.003 66.667 0.00 0.00 0.00 3.36
3115 3408 4.139234 GGAGCGTGTACGGGACCC 62.139 72.222 0.00 0.00 40.23 4.46
3116 3409 4.139234 GGGAGCGTGTACGGGACC 62.139 72.222 6.55 0.00 40.23 4.46
3184 3486 1.635844 CGGCCGGAATTTAAAAAGGC 58.364 50.000 20.10 14.36 43.47 4.35
3185 3487 1.635844 GCGGCCGGAATTTAAAAAGG 58.364 50.000 29.38 0.00 0.00 3.11
3228 3530 1.027255 GGAAAGGAGGAGCGAAAGGC 61.027 60.000 0.00 0.00 44.05 4.35
3229 3531 0.393132 GGGAAAGGAGGAGCGAAAGG 60.393 60.000 0.00 0.00 0.00 3.11
3230 3532 0.393132 GGGGAAAGGAGGAGCGAAAG 60.393 60.000 0.00 0.00 0.00 2.62
3231 3533 1.683441 GGGGAAAGGAGGAGCGAAA 59.317 57.895 0.00 0.00 0.00 3.46
3232 3534 2.298661 GGGGGAAAGGAGGAGCGAA 61.299 63.158 0.00 0.00 0.00 4.70
3233 3535 2.687566 GGGGGAAAGGAGGAGCGA 60.688 66.667 0.00 0.00 0.00 4.93
3234 3536 4.162690 CGGGGGAAAGGAGGAGCG 62.163 72.222 0.00 0.00 0.00 5.03
3235 3537 4.491409 GCGGGGGAAAGGAGGAGC 62.491 72.222 0.00 0.00 0.00 4.70
3236 3538 3.798511 GGCGGGGGAAAGGAGGAG 61.799 72.222 0.00 0.00 0.00 3.69
3314 3625 2.439701 ACGAGAGCGGATCGGGAA 60.440 61.111 11.86 0.00 44.36 3.97


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

AutoCloner maintained by Alex Coulton.