Multiple sequence alignment - TraesCS6D01G192700

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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 TraesCS6D01G192700 chr6D 100.000 2462 0 0 1 2462 266782327 266784788 0.000000e+00 4547.0
1 TraesCS6D01G192700 chr6D 88.608 79 7 2 423 500 322457503 322457580 7.250000e-16 95.3
2 TraesCS6D01G192700 chr6D 88.571 70 3 1 432 496 87332495 87332564 2.030000e-11 80.5
3 TraesCS6D01G192700 chr6A 93.871 1860 68 13 612 2462 378186803 378188625 0.000000e+00 2761.0
4 TraesCS6D01G192700 chr6A 90.455 220 18 3 214 432 378172070 378172287 1.110000e-73 287.0
5 TraesCS6D01G192700 chr6A 92.647 68 5 0 494 561 378172284 378172351 5.600000e-17 99.0
6 TraesCS6D01G192700 chr6B 94.980 1753 51 21 718 2462 414343638 414345361 0.000000e+00 2715.0
7 TraesCS6D01G192700 chr6B 82.313 441 43 17 1 432 414341068 414341482 1.400000e-92 350.0
8 TraesCS6D01G192700 chr6B 89.344 122 7 2 573 694 414343529 414343644 5.490000e-32 148.0
9 TraesCS6D01G192700 chr7A 93.651 63 3 1 433 495 719588908 719588969 2.610000e-15 93.5
10 TraesCS6D01G192700 chr7A 93.651 63 3 1 433 495 719588969 719588908 2.610000e-15 93.5
11 TraesCS6D01G192700 chr5B 89.474 76 5 2 423 496 232635834 232635908 2.610000e-15 93.5
12 TraesCS6D01G192700 chr5B 89.855 69 4 3 430 495 232635911 232635843 4.360000e-13 86.1
13 TraesCS6D01G192700 chr1A 93.220 59 3 1 410 467 580659380 580659322 4.360000e-13 86.1
14 TraesCS6D01G192700 chr1A 89.706 68 3 1 433 496 111790438 111790505 1.570000e-12 84.2
15 TraesCS6D01G192700 chr3D 88.732 71 3 1 430 495 3821269 3821339 5.640000e-12 82.4


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 TraesCS6D01G192700 chr6D 266782327 266784788 2461 False 4547 4547 100.000 1 2462 1 chr6D.!!$F2 2461
1 TraesCS6D01G192700 chr6A 378186803 378188625 1822 False 2761 2761 93.871 612 2462 1 chr6A.!!$F1 1850
2 TraesCS6D01G192700 chr6B 414341068 414345361 4293 False 1071 2715 88.879 1 2462 3 chr6B.!!$F1 2461

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
290 313 0.391597 TCTTCGGAGGAGCGTTGTTT 59.608 50.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 3665 0.3199 ACCGCAGACACATCACTCAC 60.32 55.0 0.0 0.0 0.0 3.51 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 60 0.893270 TTGTCTGGTTGATTGGGGCG 60.893 55.000 0.00 0.00 0.00 6.13
98 117 4.386867 TCGAAAGAGGATTGTAGCGAAT 57.613 40.909 0.00 0.00 34.84 3.34
116 135 4.874977 GCGAGGACTACAGCGGCC 62.875 72.222 0.00 0.00 0.00 6.13
117 136 3.141488 CGAGGACTACAGCGGCCT 61.141 66.667 0.00 0.00 0.00 5.19
118 137 1.822613 CGAGGACTACAGCGGCCTA 60.823 63.158 0.00 0.00 0.00 3.93
119 138 1.173444 CGAGGACTACAGCGGCCTAT 61.173 60.000 0.00 0.00 0.00 2.57
120 139 1.041437 GAGGACTACAGCGGCCTATT 58.959 55.000 0.00 0.00 0.00 1.73
121 140 2.236766 GAGGACTACAGCGGCCTATTA 58.763 52.381 0.00 0.00 0.00 0.98
122 141 2.626743 GAGGACTACAGCGGCCTATTAA 59.373 50.000 0.00 0.00 0.00 1.40
123 142 3.036091 AGGACTACAGCGGCCTATTAAA 58.964 45.455 0.00 0.00 0.00 1.52
124 143 3.129109 GGACTACAGCGGCCTATTAAAC 58.871 50.000 0.00 0.00 0.00 2.01
125 144 3.431207 GGACTACAGCGGCCTATTAAACA 60.431 47.826 0.00 0.00 0.00 2.83
126 145 4.186159 GACTACAGCGGCCTATTAAACAA 58.814 43.478 0.00 0.00 0.00 2.83
127 146 4.777463 ACTACAGCGGCCTATTAAACAAT 58.223 39.130 0.00 0.00 0.00 2.71
128 147 4.574828 ACTACAGCGGCCTATTAAACAATG 59.425 41.667 0.00 0.00 0.00 2.82
129 148 2.687935 ACAGCGGCCTATTAAACAATGG 59.312 45.455 0.00 0.00 0.00 3.16
130 149 1.681264 AGCGGCCTATTAAACAATGGC 59.319 47.619 0.00 0.00 42.56 4.40
131 150 1.681264 GCGGCCTATTAAACAATGGCT 59.319 47.619 0.00 0.00 42.84 4.75
132 151 2.287608 GCGGCCTATTAAACAATGGCTC 60.288 50.000 0.00 0.00 42.84 4.70
133 152 2.032030 CGGCCTATTAAACAATGGCTCG 60.032 50.000 0.00 0.00 42.84 5.03
134 153 2.293399 GGCCTATTAAACAATGGCTCGG 59.707 50.000 0.00 0.00 42.84 4.63
135 154 2.293399 GCCTATTAAACAATGGCTCGGG 59.707 50.000 0.00 0.00 40.36 5.14
136 155 2.293399 CCTATTAAACAATGGCTCGGGC 59.707 50.000 0.00 0.00 37.82 6.13
137 156 0.738389 ATTAAACAATGGCTCGGGCG 59.262 50.000 0.00 0.00 39.81 6.13
138 157 1.928706 TTAAACAATGGCTCGGGCGC 61.929 55.000 0.00 0.00 39.81 6.53
160 179 1.144057 CCCGGACTCGCTTGCTTAT 59.856 57.895 0.73 0.00 34.56 1.73
163 182 0.460284 CGGACTCGCTTGCTTATGGT 60.460 55.000 0.00 0.00 0.00 3.55
196 218 2.037367 TCCCACCCGTCTCCAGAG 59.963 66.667 0.00 0.00 0.00 3.35
197 219 2.037367 CCCACCCGTCTCCAGAGA 59.963 66.667 0.00 0.00 34.56 3.10
200 222 1.729470 CCACCCGTCTCCAGAGATCG 61.729 65.000 0.00 6.65 39.97 3.69
210 232 4.194720 AGAGATCGTCGTGGCGCC 62.195 66.667 22.73 22.73 0.00 6.53
224 246 3.461773 CGCCGTCCCCATGTCTCT 61.462 66.667 0.00 0.00 0.00 3.10
225 247 2.990479 GCCGTCCCCATGTCTCTT 59.010 61.111 0.00 0.00 0.00 2.85
233 255 1.649664 CCCATGTCTCTTCAAGCTCG 58.350 55.000 0.00 0.00 0.00 5.03
252 274 1.134818 CGATGTTCACCTCCCGATTCA 60.135 52.381 0.00 0.00 0.00 2.57
253 275 2.280628 GATGTTCACCTCCCGATTCAC 58.719 52.381 0.00 0.00 0.00 3.18
255 277 0.739813 GTTCACCTCCCGATTCACCG 60.740 60.000 0.00 0.00 0.00 4.94
264 287 2.965572 CCGATTCACCGGGTAAGTTA 57.034 50.000 6.32 0.00 45.43 2.24
274 297 7.369551 TCACCGGGTAAGTTATGATTATCTT 57.630 36.000 6.32 0.00 0.00 2.40
275 298 7.439381 TCACCGGGTAAGTTATGATTATCTTC 58.561 38.462 6.32 0.00 0.00 2.87
277 300 5.867716 CCGGGTAAGTTATGATTATCTTCGG 59.132 44.000 0.00 0.00 0.00 4.30
279 302 6.807230 CGGGTAAGTTATGATTATCTTCGGAG 59.193 42.308 0.00 0.00 0.00 4.63
280 303 7.097834 GGGTAAGTTATGATTATCTTCGGAGG 58.902 42.308 0.00 0.00 0.00 4.30
281 304 7.039223 GGGTAAGTTATGATTATCTTCGGAGGA 60.039 40.741 0.00 0.00 0.00 3.71
282 305 8.030106 GGTAAGTTATGATTATCTTCGGAGGAG 58.970 40.741 0.00 0.00 0.00 3.69
283 306 6.031751 AGTTATGATTATCTTCGGAGGAGC 57.968 41.667 0.00 0.00 0.00 4.70
285 308 2.307768 TGATTATCTTCGGAGGAGCGT 58.692 47.619 0.00 0.00 0.00 5.07
286 309 2.693591 TGATTATCTTCGGAGGAGCGTT 59.306 45.455 0.00 0.00 0.00 4.84
287 310 2.579207 TTATCTTCGGAGGAGCGTTG 57.421 50.000 0.00 0.00 0.00 4.10
288 311 1.471119 TATCTTCGGAGGAGCGTTGT 58.529 50.000 0.00 0.00 0.00 3.32
289 312 0.608640 ATCTTCGGAGGAGCGTTGTT 59.391 50.000 0.00 0.00 0.00 2.83
290 313 0.391597 TCTTCGGAGGAGCGTTGTTT 59.608 50.000 0.00 0.00 0.00 2.83
291 314 1.202604 TCTTCGGAGGAGCGTTGTTTT 60.203 47.619 0.00 0.00 0.00 2.43
292 315 1.602377 CTTCGGAGGAGCGTTGTTTTT 59.398 47.619 0.00 0.00 0.00 1.94
353 376 8.579850 TGCATTTTGTTAGAAATAGGAGATGT 57.420 30.769 0.00 0.00 0.00 3.06
354 377 8.677300 TGCATTTTGTTAGAAATAGGAGATGTC 58.323 33.333 0.00 0.00 0.00 3.06
355 378 8.897752 GCATTTTGTTAGAAATAGGAGATGTCT 58.102 33.333 0.00 0.00 0.00 3.41
390 413 8.792830 TTTATCGAGGAATCAAAAGTCATTCT 57.207 30.769 0.00 0.00 30.85 2.40
397 420 8.048534 AGGAATCAAAAGTCATTCTGTGTATG 57.951 34.615 0.00 0.00 30.85 2.39
400 423 9.552114 GAATCAAAAGTCATTCTGTGTATGAAG 57.448 33.333 0.00 0.00 34.06 3.02
432 455 7.136822 TGCATGTACTACCTCCATTCTAAAT 57.863 36.000 0.00 0.00 0.00 1.40
433 456 8.257602 TGCATGTACTACCTCCATTCTAAATA 57.742 34.615 0.00 0.00 0.00 1.40
434 457 8.148351 TGCATGTACTACCTCCATTCTAAATAC 58.852 37.037 0.00 0.00 0.00 1.89
436 459 9.915629 CATGTACTACCTCCATTCTAAATACTC 57.084 37.037 0.00 0.00 0.00 2.59
437 460 8.474710 TGTACTACCTCCATTCTAAATACTCC 57.525 38.462 0.00 0.00 0.00 3.85
438 461 6.997942 ACTACCTCCATTCTAAATACTCCC 57.002 41.667 0.00 0.00 0.00 4.30
439 462 6.694611 ACTACCTCCATTCTAAATACTCCCT 58.305 40.000 0.00 0.00 0.00 4.20
440 463 6.783482 ACTACCTCCATTCTAAATACTCCCTC 59.217 42.308 0.00 0.00 0.00 4.30
441 464 5.793967 ACCTCCATTCTAAATACTCCCTCT 58.206 41.667 0.00 0.00 0.00 3.69
442 465 5.604650 ACCTCCATTCTAAATACTCCCTCTG 59.395 44.000 0.00 0.00 0.00 3.35
443 466 5.604650 CCTCCATTCTAAATACTCCCTCTGT 59.395 44.000 0.00 0.00 0.00 3.41
446 469 8.618240 TCCATTCTAAATACTCCCTCTGTAAA 57.382 34.615 0.00 0.00 0.00 2.01
447 470 8.483758 TCCATTCTAAATACTCCCTCTGTAAAC 58.516 37.037 0.00 0.00 0.00 2.01
448 471 8.487028 CCATTCTAAATACTCCCTCTGTAAACT 58.513 37.037 0.00 0.00 0.00 2.66
459 482 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
460 483 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
462 485 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
463 486 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
484 507 6.786103 CGTTTAGCGCTCTTATAATAGTTTGC 59.214 38.462 16.34 2.91 0.00 3.68
485 508 7.516155 CGTTTAGCGCTCTTATAATAGTTTGCA 60.516 37.037 16.34 0.00 0.00 4.08
486 509 5.914085 AGCGCTCTTATAATAGTTTGCAG 57.086 39.130 2.64 0.00 0.00 4.41
487 510 5.601662 AGCGCTCTTATAATAGTTTGCAGA 58.398 37.500 2.64 0.00 0.00 4.26
488 511 5.694006 AGCGCTCTTATAATAGTTTGCAGAG 59.306 40.000 2.64 0.00 0.00 3.35
489 512 5.107298 GCGCTCTTATAATAGTTTGCAGAGG 60.107 44.000 0.00 0.00 0.00 3.69
491 514 6.525629 GCTCTTATAATAGTTTGCAGAGGGA 58.474 40.000 0.42 0.00 0.00 4.20
492 515 6.648725 GCTCTTATAATAGTTTGCAGAGGGAG 59.351 42.308 0.42 0.00 0.00 4.30
493 516 7.676683 TCTTATAATAGTTTGCAGAGGGAGT 57.323 36.000 0.00 0.00 0.00 3.85
494 517 8.777578 TCTTATAATAGTTTGCAGAGGGAGTA 57.222 34.615 0.00 0.00 0.00 2.59
495 518 8.639761 TCTTATAATAGTTTGCAGAGGGAGTAC 58.360 37.037 0.00 0.00 0.00 2.73
513 2469 8.233116 AGGGAGTACAATATAAACTAGCCTACT 58.767 37.037 0.00 0.00 0.00 2.57
548 2504 9.802039 TTGTATTTTGAAATGGAGGTAGTAACT 57.198 29.630 0.00 0.00 0.00 2.24
549 2505 9.802039 TGTATTTTGAAATGGAGGTAGTAACTT 57.198 29.630 0.00 0.00 0.00 2.66
551 2507 8.706322 ATTTTGAAATGGAGGTAGTAACTTGT 57.294 30.769 0.00 0.00 0.00 3.16
552 2508 8.528044 TTTTGAAATGGAGGTAGTAACTTGTT 57.472 30.769 0.00 0.00 0.00 2.83
553 2509 8.528044 TTTGAAATGGAGGTAGTAACTTGTTT 57.472 30.769 0.00 0.00 0.00 2.83
554 2510 9.629878 TTTGAAATGGAGGTAGTAACTTGTTTA 57.370 29.630 0.00 0.00 0.00 2.01
555 2511 9.802039 TTGAAATGGAGGTAGTAACTTGTTTAT 57.198 29.630 0.00 0.00 0.00 1.40
556 2512 9.802039 TGAAATGGAGGTAGTAACTTGTTTATT 57.198 29.630 0.00 0.00 0.00 1.40
560 2516 9.676861 ATGGAGGTAGTAACTTGTTTATTAACC 57.323 33.333 0.00 0.00 33.15 2.85
561 2517 8.883302 TGGAGGTAGTAACTTGTTTATTAACCT 58.117 33.333 0.00 0.00 34.23 3.50
562 2518 9.376075 GGAGGTAGTAACTTGTTTATTAACCTC 57.624 37.037 16.19 16.19 40.64 3.85
563 2519 9.376075 GAGGTAGTAACTTGTTTATTAACCTCC 57.624 37.037 0.00 0.00 38.40 4.30
564 2520 9.109246 AGGTAGTAACTTGTTTATTAACCTCCT 57.891 33.333 0.00 0.00 29.39 3.69
565 2521 9.159364 GGTAGTAACTTGTTTATTAACCTCCTG 57.841 37.037 0.00 0.00 33.15 3.86
566 2522 7.683437 AGTAACTTGTTTATTAACCTCCTGC 57.317 36.000 0.00 0.00 33.15 4.85
567 2523 7.228590 AGTAACTTGTTTATTAACCTCCTGCA 58.771 34.615 0.00 0.00 33.15 4.41
568 2524 6.969993 AACTTGTTTATTAACCTCCTGCAA 57.030 33.333 0.00 0.00 33.15 4.08
569 2525 6.969993 ACTTGTTTATTAACCTCCTGCAAA 57.030 33.333 0.00 0.00 33.15 3.68
570 2526 7.354751 ACTTGTTTATTAACCTCCTGCAAAA 57.645 32.000 0.00 0.00 33.15 2.44
571 2527 7.787028 ACTTGTTTATTAACCTCCTGCAAAAA 58.213 30.769 0.00 0.00 33.15 1.94
608 2564 6.493189 ACCAATGAAAACAAAAGGTATGGT 57.507 33.333 0.00 0.00 0.00 3.55
614 2570 7.266922 TGAAAACAAAAGGTATGGTGTAGTC 57.733 36.000 0.00 0.00 0.00 2.59
739 2696 3.321682 AGTGCTGCATACACCACAAAAAT 59.678 39.130 5.27 0.00 38.87 1.82
749 2706 3.244387 ACACCACAAAAATTACATGGCCC 60.244 43.478 0.00 0.00 33.46 5.80
791 2751 6.205784 TCCTATTTCACTTGCAAAACTTTCG 58.794 36.000 0.00 0.00 0.00 3.46
795 2755 4.014847 TCACTTGCAAAACTTTCGAGTG 57.985 40.909 0.00 1.54 35.55 3.51
798 2761 3.181487 ACTTGCAAAACTTTCGAGTGCAT 60.181 39.130 0.00 0.00 44.13 3.96
807 2770 5.186996 ACTTTCGAGTGCATGTTTCAAAT 57.813 34.783 0.00 0.00 0.00 2.32
962 2925 2.525629 CAAAACCCCACCCACCCC 60.526 66.667 0.00 0.00 0.00 4.95
1018 2981 2.351244 ATGAAGAGCTCGGCGGACA 61.351 57.895 7.21 4.26 0.00 4.02
1449 3412 1.038130 CGTCCAGGAGGTTCGAGGAT 61.038 60.000 0.44 0.00 36.21 3.24
1526 3490 3.650942 TCTAGTCCTTCCTTGCCTGAAAA 59.349 43.478 0.00 0.00 0.00 2.29
1551 3518 1.594862 GGCAGCGTCTATGCAACTTAG 59.405 52.381 0.00 0.00 45.68 2.18
1561 3528 6.238402 CGTCTATGCAACTTAGTACAGAGCTA 60.238 42.308 0.00 0.00 0.00 3.32
1582 3549 3.769739 TCTGTATTGTCAACCACAGCT 57.230 42.857 18.25 0.00 38.60 4.24
1583 3550 4.882842 TCTGTATTGTCAACCACAGCTA 57.117 40.909 18.25 5.75 38.60 3.32
1584 3551 4.566004 TCTGTATTGTCAACCACAGCTAC 58.434 43.478 18.25 4.48 38.60 3.58
1585 3552 4.283467 TCTGTATTGTCAACCACAGCTACT 59.717 41.667 18.25 0.00 38.60 2.57
1586 3553 4.314961 TGTATTGTCAACCACAGCTACTG 58.685 43.478 0.00 0.00 35.97 2.74
1688 3655 2.099141 TCGCCAATCAGAGTTCAAGG 57.901 50.000 0.00 0.00 0.00 3.61
1696 3663 5.292101 CCAATCAGAGTTCAAGGACGATAAC 59.708 44.000 0.00 0.00 0.00 1.89
1698 3665 5.060662 TCAGAGTTCAAGGACGATAACAG 57.939 43.478 0.00 0.00 0.00 3.16
1746 3713 2.093394 TCCAGTCAGGAACAACGACAAA 60.093 45.455 0.00 0.00 45.65 2.83
1816 3786 2.968675 ACGTCCTAATAACACCACAGC 58.031 47.619 0.00 0.00 0.00 4.40
1973 3943 1.252904 ATGCAAGTGTGATGTGGCCC 61.253 55.000 0.00 0.00 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 60 1.977293 ATTCCTCTCTTGCCCGCCTC 61.977 60.000 0.00 0.00 0.00 4.70
72 74 4.698575 GCTACAATCCTCTTTCGATTCCT 58.301 43.478 0.00 0.00 0.00 3.36
90 109 1.065102 TGTAGTCCTCGCATTCGCTAC 59.935 52.381 0.00 0.00 35.30 3.58
98 117 4.129737 GCCGCTGTAGTCCTCGCA 62.130 66.667 0.00 0.00 0.00 5.10
103 122 3.129109 GTTTAATAGGCCGCTGTAGTCC 58.871 50.000 0.00 0.00 0.00 3.85
104 123 3.788937 TGTTTAATAGGCCGCTGTAGTC 58.211 45.455 0.00 0.00 0.00 2.59
105 124 3.899052 TGTTTAATAGGCCGCTGTAGT 57.101 42.857 0.00 0.00 0.00 2.73
116 135 2.032030 CGCCCGAGCCATTGTTTAATAG 60.032 50.000 0.00 0.00 34.57 1.73
117 136 1.944024 CGCCCGAGCCATTGTTTAATA 59.056 47.619 0.00 0.00 34.57 0.98
118 137 0.738389 CGCCCGAGCCATTGTTTAAT 59.262 50.000 0.00 0.00 34.57 1.40
119 138 1.928706 GCGCCCGAGCCATTGTTTAA 61.929 55.000 0.00 0.00 34.57 1.52
120 139 2.403378 GCGCCCGAGCCATTGTTTA 61.403 57.895 0.00 0.00 34.57 2.01
121 140 3.747976 GCGCCCGAGCCATTGTTT 61.748 61.111 0.00 0.00 34.57 2.83
140 159 1.945354 TAAGCAAGCGAGTCCGGGAG 61.945 60.000 0.00 0.00 36.06 4.30
141 160 1.327690 ATAAGCAAGCGAGTCCGGGA 61.328 55.000 0.00 0.00 36.06 5.14
142 161 1.144057 ATAAGCAAGCGAGTCCGGG 59.856 57.895 0.00 0.00 36.06 5.73
143 162 1.154205 CCATAAGCAAGCGAGTCCGG 61.154 60.000 0.00 0.00 36.06 5.14
144 163 0.460284 ACCATAAGCAAGCGAGTCCG 60.460 55.000 0.00 0.00 39.16 4.79
145 164 1.398390 CAACCATAAGCAAGCGAGTCC 59.602 52.381 0.00 0.00 0.00 3.85
160 179 2.036098 CCATGGAGCAGGCAACCA 59.964 61.111 5.56 11.33 38.09 3.67
179 198 1.875422 ATCTCTGGAGACGGGTGGGA 61.875 60.000 2.15 0.00 40.75 4.37
210 232 2.009042 GCTTGAAGAGACATGGGGACG 61.009 57.143 0.00 0.00 0.00 4.79
224 246 2.612972 GGAGGTGAACATCGAGCTTGAA 60.613 50.000 7.99 0.00 0.00 2.69
225 247 1.066858 GGAGGTGAACATCGAGCTTGA 60.067 52.381 6.01 6.01 0.00 3.02
233 255 2.280628 GTGAATCGGGAGGTGAACATC 58.719 52.381 0.00 0.00 0.00 3.06
252 274 6.453092 CGAAGATAATCATAACTTACCCGGT 58.547 40.000 0.00 0.00 0.00 5.28
253 275 5.867716 CCGAAGATAATCATAACTTACCCGG 59.132 44.000 0.00 0.00 29.19 5.73
255 277 7.039223 TCCTCCGAAGATAATCATAACTTACCC 60.039 40.741 0.00 0.00 0.00 3.69
256 278 7.893658 TCCTCCGAAGATAATCATAACTTACC 58.106 38.462 0.00 0.00 0.00 2.85
257 279 7.542824 GCTCCTCCGAAGATAATCATAACTTAC 59.457 40.741 0.00 0.00 0.00 2.34
264 287 2.894126 ACGCTCCTCCGAAGATAATCAT 59.106 45.455 0.00 0.00 0.00 2.45
274 297 3.390003 AAAAACAACGCTCCTCCGA 57.610 47.368 0.00 0.00 0.00 4.55
385 408 7.012044 TGCAAGATGATCTTCATACACAGAATG 59.988 37.037 4.39 0.00 37.20 2.67
390 413 6.117488 ACATGCAAGATGATCTTCATACACA 58.883 36.000 4.39 0.00 37.20 3.72
397 420 6.520272 AGGTAGTACATGCAAGATGATCTTC 58.480 40.000 4.39 0.31 33.78 2.87
400 423 5.221521 TGGAGGTAGTACATGCAAGATGATC 60.222 44.000 6.69 0.00 24.59 2.92
433 456 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
434 457 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
436 459 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
437 460 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
441 464 8.961092 CGCTAAACGCTCTTATATTAGTTTACA 58.039 33.333 0.00 0.00 34.29 2.41
460 483 7.627340 TGCAAACTATTATAAGAGCGCTAAAC 58.373 34.615 11.50 0.00 0.00 2.01
462 485 7.207383 TCTGCAAACTATTATAAGAGCGCTAA 58.793 34.615 11.50 0.00 0.00 3.09
463 486 6.745116 TCTGCAAACTATTATAAGAGCGCTA 58.255 36.000 11.50 0.00 0.00 4.26
465 488 5.107298 CCTCTGCAAACTATTATAAGAGCGC 60.107 44.000 7.03 0.00 0.00 5.92
467 490 6.525629 TCCCTCTGCAAACTATTATAAGAGC 58.474 40.000 7.03 0.00 0.00 4.09
468 491 7.731054 ACTCCCTCTGCAAACTATTATAAGAG 58.269 38.462 5.56 5.56 0.00 2.85
469 492 7.676683 ACTCCCTCTGCAAACTATTATAAGA 57.323 36.000 0.00 0.00 0.00 2.10
470 493 8.421784 TGTACTCCCTCTGCAAACTATTATAAG 58.578 37.037 0.00 0.00 0.00 1.73
471 494 8.313944 TGTACTCCCTCTGCAAACTATTATAA 57.686 34.615 0.00 0.00 0.00 0.98
472 495 7.907841 TGTACTCCCTCTGCAAACTATTATA 57.092 36.000 0.00 0.00 0.00 0.98
473 496 6.808321 TGTACTCCCTCTGCAAACTATTAT 57.192 37.500 0.00 0.00 0.00 1.28
474 497 6.614694 TTGTACTCCCTCTGCAAACTATTA 57.385 37.500 0.00 0.00 0.00 0.98
477 500 6.808321 ATATTGTACTCCCTCTGCAAACTA 57.192 37.500 0.00 0.00 0.00 2.24
478 501 5.700402 ATATTGTACTCCCTCTGCAAACT 57.300 39.130 0.00 0.00 0.00 2.66
481 504 7.195374 AGTTTATATTGTACTCCCTCTGCAA 57.805 36.000 0.00 0.00 0.00 4.08
482 505 6.808321 AGTTTATATTGTACTCCCTCTGCA 57.192 37.500 0.00 0.00 0.00 4.41
483 506 6.869388 GCTAGTTTATATTGTACTCCCTCTGC 59.131 42.308 0.00 0.00 0.00 4.26
484 507 7.233757 AGGCTAGTTTATATTGTACTCCCTCTG 59.766 40.741 0.00 0.00 0.00 3.35
485 508 7.306781 AGGCTAGTTTATATTGTACTCCCTCT 58.693 38.462 0.00 0.00 0.00 3.69
486 509 7.541916 AGGCTAGTTTATATTGTACTCCCTC 57.458 40.000 0.00 0.00 0.00 4.30
487 510 8.233116 AGTAGGCTAGTTTATATTGTACTCCCT 58.767 37.037 0.00 0.00 32.18 4.20
488 511 8.419922 AGTAGGCTAGTTTATATTGTACTCCC 57.580 38.462 0.00 0.00 0.00 4.30
513 2469 9.672086 CTCCATTTCAAAATACAAGACGTTTTA 57.328 29.630 0.00 0.00 0.00 1.52
534 2490 9.676861 GGTTAATAAACAAGTTACTACCTCCAT 57.323 33.333 0.00 0.00 37.34 3.41
608 2564 9.899661 ATAAATTGTTAGGCATTACTGACTACA 57.100 29.630 0.00 0.00 42.87 2.74
614 2570 8.931385 AAAGCATAAATTGTTAGGCATTACTG 57.069 30.769 5.98 0.00 46.91 2.74
791 2751 4.030977 GCATTCGATTTGAAACATGCACTC 59.969 41.667 9.05 0.00 39.06 3.51
795 2755 2.279659 CCGCATTCGATTTGAAACATGC 59.720 45.455 4.70 4.70 40.71 4.06
798 2761 1.539388 AGCCGCATTCGATTTGAAACA 59.461 42.857 0.00 0.00 40.71 2.83
997 2960 3.624300 CGCCGAGCTCTTCATGCG 61.624 66.667 12.85 13.52 39.36 4.73
1018 2981 1.079819 CCAGCTCGATGTCCACGTT 60.080 57.895 0.00 0.00 0.00 3.99
1269 3232 2.125512 ATCTTCTGCGCCACGGTC 60.126 61.111 4.18 0.00 0.00 4.79
1465 3428 3.551846 AGAGAGGAGAACACTAGCTAGC 58.448 50.000 20.91 6.62 0.00 3.42
1466 3429 5.061179 GGTAGAGAGGAGAACACTAGCTAG 58.939 50.000 19.44 19.44 0.00 3.42
1467 3430 4.722781 AGGTAGAGAGGAGAACACTAGCTA 59.277 45.833 0.00 0.00 39.17 3.32
1468 3431 3.526019 AGGTAGAGAGGAGAACACTAGCT 59.474 47.826 0.00 0.00 37.17 3.32
1526 3490 0.321564 TGCATAGACGCTGCCAAGTT 60.322 50.000 0.00 0.00 38.89 2.66
1561 3528 4.292186 AGCTGTGGTTGACAATACAGAT 57.708 40.909 26.64 21.62 42.28 2.90
1582 3549 6.308015 ACCTAAATGCATGGAAGTACAGTA 57.692 37.500 8.47 0.00 0.00 2.74
1583 3550 5.179452 ACCTAAATGCATGGAAGTACAGT 57.821 39.130 8.47 0.00 0.00 3.55
1584 3551 6.582636 TCTACCTAAATGCATGGAAGTACAG 58.417 40.000 8.47 0.00 0.00 2.74
1585 3552 6.382859 TCTCTACCTAAATGCATGGAAGTACA 59.617 38.462 8.47 0.00 0.00 2.90
1586 3553 6.817184 TCTCTACCTAAATGCATGGAAGTAC 58.183 40.000 8.47 0.00 0.00 2.73
1645 3612 7.961283 CGATGTGATTCTGGATTATATGCTTTG 59.039 37.037 0.00 0.00 0.00 2.77
1646 3613 7.361542 GCGATGTGATTCTGGATTATATGCTTT 60.362 37.037 0.00 0.00 0.00 3.51
1688 3655 4.486090 ACACATCACTCACTGTTATCGTC 58.514 43.478 0.00 0.00 0.00 4.20
1696 3663 1.066136 CGCAGACACATCACTCACTG 58.934 55.000 0.00 0.00 0.00 3.66
1698 3665 0.319900 ACCGCAGACACATCACTCAC 60.320 55.000 0.00 0.00 0.00 3.51
1738 3705 7.062956 GGACTTCATTTTCTTTTGTTTGTCGTT 59.937 33.333 0.00 0.00 0.00 3.85
1746 3713 7.069826 TGGATTCTGGACTTCATTTTCTTTTGT 59.930 33.333 0.00 0.00 0.00 2.83
1816 3786 5.459110 GCAAGACATTTGTTATGCCATTG 57.541 39.130 9.30 0.00 35.35 2.82


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

AutoCloner maintained by Alex Coulton.