Multiple sequence alignment - TraesCS3D01G217300

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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 TraesCS3D01G217300 chr3D 100.000 4460 0 0 1 4460 295139967 295144426 0.000000e+00 8237.0
1 TraesCS3D01G217300 chr3A 96.546 3474 97 8 937 4405 392799604 392803059 0.000000e+00 5729.0
2 TraesCS3D01G217300 chr3A 97.842 139 3 0 1 139 392781134 392781272 1.600000e-59 241.0
3 TraesCS3D01G217300 chr3A 82.143 140 19 5 540 676 392781826 392781962 1.010000e-21 115.0
4 TraesCS3D01G217300 chr3A 94.366 71 4 0 4390 4460 392803202 392803272 4.720000e-20 110.0
5 TraesCS3D01G217300 chr3B 98.160 2011 37 0 1534 3544 389260682 389262692 0.000000e+00 3509.0
6 TraesCS3D01G217300 chr3B 95.254 885 26 7 3523 4405 389262740 389263610 0.000000e+00 1387.0
7 TraesCS3D01G217300 chr3B 94.432 880 24 9 495 1356 389259809 389260681 0.000000e+00 1330.0
8 TraesCS3D01G217300 chr3B 89.489 352 23 10 1 351 389259142 389259480 2.460000e-117 433.0
9 TraesCS3D01G217300 chr3B 98.182 55 1 0 440 494 389259574 389259628 3.670000e-16 97.1
10 TraesCS3D01G217300 chr3B 94.643 56 2 1 4405 4460 389263730 389263784 7.950000e-13 86.1


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 TraesCS3D01G217300 chr3D 295139967 295144426 4459 False 8237.000000 8237 100.000000 1 4460 1 chr3D.!!$F1 4459
1 TraesCS3D01G217300 chr3A 392799604 392803272 3668 False 2919.500000 5729 95.456000 937 4460 2 chr3A.!!$F2 3523
2 TraesCS3D01G217300 chr3B 389259142 389263784 4642 False 1140.366667 3509 95.026667 1 4460 6 chr3B.!!$F1 4459

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
403 411 0.104120 TGTCACGAGGAACACAGTGG 59.896 55.000 5.31 0.0 35.50 4.00 F
404 412 0.600255 GTCACGAGGAACACAGTGGG 60.600 60.000 5.31 0.0 35.50 4.61 F
553 746 0.623723 TACCCTTGGGTGAAGATGCC 59.376 55.000 20.78 0.0 32.82 4.40 F
1284 1503 1.027255 TTCTCCTCGACTCGCTCCTG 61.027 60.000 0.00 0.0 0.00 3.86 F
2236 2455 0.594602 TGCTGCTCAAGATGCAACAC 59.405 50.000 0.00 0.0 40.13 3.32 F
2799 3018 3.496130 CAGTTGTTTCTGGTGCTCTAGTG 59.504 47.826 0.00 0.0 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1446 1665 0.250553 TGAACCCGTTAGGCACAAGG 60.251 55.000 0.00 0.00 40.58 3.61 R
1788 2007 1.597663 CCGAGTTCCACACAACACTTC 59.402 52.381 0.00 0.00 0.00 3.01 R
2236 2455 5.459107 GCTCATGCATAAGATGAAAAGCAAG 59.541 40.000 0.00 0.00 39.41 4.01 R
3075 3294 0.250038 CATAGTGCTCCATCGTGGGG 60.250 60.000 4.52 2.37 42.32 4.96 R
3228 3447 0.746063 CTGCTCTCTCGGCAATCTCT 59.254 55.000 0.00 0.00 39.30 3.10 R
4326 4613 0.190815 AAAACTGACCTTGCCCCCAT 59.809 50.000 0.00 0.00 0.00 4.00 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
20 21 0.516001 GCGTGATGCCATGAGCTATG 59.484 55.000 0.00 0.00 44.23 2.23
108 109 7.672660 TGTCATAGAAGAGTACCTTTCCTGTTA 59.327 37.037 3.95 0.00 34.68 2.41
165 166 7.385267 TGGCTACCTTTTAGTTCGTAATTACA 58.615 34.615 15.67 0.56 0.00 2.41
174 175 7.795482 TTAGTTCGTAATTACAATGGATGGG 57.205 36.000 15.67 0.00 0.00 4.00
188 189 1.473258 GATGGGTATTGTGCCTTGCA 58.527 50.000 0.00 0.00 35.60 4.08
192 193 2.636893 TGGGTATTGTGCCTTGCATTTT 59.363 40.909 0.00 0.00 41.91 1.82
217 218 2.158682 TGTCCTACCAGAGCTTGCAAAA 60.159 45.455 0.00 0.00 0.00 2.44
299 307 4.280929 GGTTCAACATAGGCACTTTCCTTT 59.719 41.667 0.00 0.00 41.75 3.11
302 310 5.385198 TCAACATAGGCACTTTCCTTTTCT 58.615 37.500 0.00 0.00 41.75 2.52
303 311 5.473504 TCAACATAGGCACTTTCCTTTTCTC 59.526 40.000 0.00 0.00 41.75 2.87
326 334 9.541143 TCTCTCTGAAAACAAAACAAAACTTTT 57.459 25.926 0.00 0.00 0.00 2.27
329 337 7.866729 TCTGAAAACAAAACAAAACTTTTCCC 58.133 30.769 0.00 0.00 32.27 3.97
351 359 1.299468 GGTGGCTGTCGCGATCTAG 60.299 63.158 14.06 12.73 36.88 2.43
353 361 0.661552 GTGGCTGTCGCGATCTAGTA 59.338 55.000 14.06 2.89 36.88 1.82
355 363 1.535896 TGGCTGTCGCGATCTAGTATC 59.464 52.381 14.06 0.00 36.88 2.24
356 364 1.807742 GGCTGTCGCGATCTAGTATCT 59.192 52.381 14.06 0.00 36.88 1.98
357 365 2.226912 GGCTGTCGCGATCTAGTATCTT 59.773 50.000 14.06 0.00 36.88 2.40
358 366 3.436015 GGCTGTCGCGATCTAGTATCTTA 59.564 47.826 14.06 0.00 36.88 2.10
359 367 4.083431 GGCTGTCGCGATCTAGTATCTTAA 60.083 45.833 14.06 0.00 36.88 1.85
360 368 5.392165 GGCTGTCGCGATCTAGTATCTTAAT 60.392 44.000 14.06 0.00 36.88 1.40
361 369 5.509972 GCTGTCGCGATCTAGTATCTTAATG 59.490 44.000 14.06 0.00 0.00 1.90
363 371 6.371389 TGTCGCGATCTAGTATCTTAATGTG 58.629 40.000 14.06 0.00 0.00 3.21
365 373 6.739100 GTCGCGATCTAGTATCTTAATGTGAG 59.261 42.308 14.06 0.00 0.00 3.51
366 374 6.649557 TCGCGATCTAGTATCTTAATGTGAGA 59.350 38.462 3.71 0.00 0.00 3.27
368 376 7.638295 CGCGATCTAGTATCTTAATGTGAGATC 59.362 40.741 0.00 0.00 35.56 2.75
385 393 8.777865 TGTGAGATCTAGTTTTAAAGGTCATG 57.222 34.615 0.00 0.00 0.00 3.07
387 395 8.874816 GTGAGATCTAGTTTTAAAGGTCATGTC 58.125 37.037 0.00 0.00 0.00 3.06
388 396 8.593679 TGAGATCTAGTTTTAAAGGTCATGTCA 58.406 33.333 0.00 0.00 0.00 3.58
389 397 8.779354 AGATCTAGTTTTAAAGGTCATGTCAC 57.221 34.615 0.00 0.00 0.00 3.67
390 398 7.545965 AGATCTAGTTTTAAAGGTCATGTCACG 59.454 37.037 0.00 0.00 0.00 4.35
391 399 6.751157 TCTAGTTTTAAAGGTCATGTCACGA 58.249 36.000 0.00 0.00 0.00 4.35
392 400 5.924475 AGTTTTAAAGGTCATGTCACGAG 57.076 39.130 0.00 0.00 0.00 4.18
393 401 4.755123 AGTTTTAAAGGTCATGTCACGAGG 59.245 41.667 0.00 0.00 0.00 4.63
395 403 4.610605 TTAAAGGTCATGTCACGAGGAA 57.389 40.909 0.00 0.00 0.00 3.36
396 404 2.457366 AAGGTCATGTCACGAGGAAC 57.543 50.000 0.00 0.00 0.00 3.62
397 405 1.338107 AGGTCATGTCACGAGGAACA 58.662 50.000 0.00 0.00 0.00 3.18
398 406 1.000955 AGGTCATGTCACGAGGAACAC 59.999 52.381 0.00 0.00 0.00 3.32
399 407 1.270094 GGTCATGTCACGAGGAACACA 60.270 52.381 0.00 0.00 0.00 3.72
400 408 2.061773 GTCATGTCACGAGGAACACAG 58.938 52.381 0.00 0.00 0.00 3.66
401 409 1.686587 TCATGTCACGAGGAACACAGT 59.313 47.619 0.00 0.00 0.00 3.55
402 410 1.794701 CATGTCACGAGGAACACAGTG 59.205 52.381 0.00 0.00 36.06 3.66
403 411 0.104120 TGTCACGAGGAACACAGTGG 59.896 55.000 5.31 0.00 35.50 4.00
404 412 0.600255 GTCACGAGGAACACAGTGGG 60.600 60.000 5.31 0.00 35.50 4.61
405 413 1.046472 TCACGAGGAACACAGTGGGT 61.046 55.000 5.31 0.00 35.50 4.51
415 423 3.800826 ACAGTGGGTGAAAGTGGAC 57.199 52.632 0.00 0.00 0.00 4.02
416 424 1.213296 ACAGTGGGTGAAAGTGGACT 58.787 50.000 0.00 0.00 0.00 3.85
419 427 2.358898 CAGTGGGTGAAAGTGGACTTTG 59.641 50.000 9.49 0.00 45.37 2.77
420 428 2.241176 AGTGGGTGAAAGTGGACTTTGA 59.759 45.455 9.49 0.00 45.37 2.69
423 431 4.099419 GTGGGTGAAAGTGGACTTTGATTT 59.901 41.667 9.49 0.00 45.37 2.17
425 433 4.501400 GGGTGAAAGTGGACTTTGATTTGG 60.501 45.833 9.49 0.00 45.37 3.28
426 434 4.051237 GTGAAAGTGGACTTTGATTTGGC 58.949 43.478 9.49 0.00 45.37 4.52
427 435 3.069443 TGAAAGTGGACTTTGATTTGGCC 59.931 43.478 9.49 0.00 45.37 5.36
429 437 1.202879 AGTGGACTTTGATTTGGCCGA 60.203 47.619 0.00 0.00 0.00 5.54
430 438 1.818674 GTGGACTTTGATTTGGCCGAT 59.181 47.619 0.00 0.00 0.00 4.18
431 439 2.231235 GTGGACTTTGATTTGGCCGATT 59.769 45.455 0.00 0.00 0.00 3.34
432 440 2.896685 TGGACTTTGATTTGGCCGATTT 59.103 40.909 0.00 0.00 0.00 2.17
434 442 3.306019 GGACTTTGATTTGGCCGATTTGT 60.306 43.478 0.00 0.00 0.00 2.83
435 443 4.306600 GACTTTGATTTGGCCGATTTGTT 58.693 39.130 0.00 0.00 0.00 2.83
438 446 6.284459 ACTTTGATTTGGCCGATTTGTTTAA 58.716 32.000 0.00 0.00 0.00 1.52
511 704 6.366877 GCCGTCTATTTTGTTTGTAGTGAGTA 59.633 38.462 0.00 0.00 0.00 2.59
553 746 0.623723 TACCCTTGGGTGAAGATGCC 59.376 55.000 20.78 0.00 32.82 4.40
561 754 4.356405 TGGGTGAAGATGCCTGTATATG 57.644 45.455 0.00 0.00 0.00 1.78
563 756 4.165950 TGGGTGAAGATGCCTGTATATGTT 59.834 41.667 0.00 0.00 0.00 2.71
608 803 3.521796 GAAAGCCCATGAGCGCCC 61.522 66.667 2.29 0.00 38.01 6.13
764 961 8.724229 TCATGTTCTAGAGTGAAAATTGTCATG 58.276 33.333 0.61 0.00 30.76 3.07
772 969 8.902540 AGAGTGAAAATTGTCATGTAGTGTAA 57.097 30.769 0.61 0.00 0.00 2.41
819 1016 1.804748 TGCTATGCGTACGATCGAGAT 59.195 47.619 24.34 1.27 0.00 2.75
871 1068 8.679100 CGTGAAATGTATATTGGGGTTAAAAGA 58.321 33.333 0.00 0.00 0.00 2.52
902 1099 7.565398 ACATATAGGCTGTTTCCTTTCTCTCTA 59.435 37.037 0.00 0.00 37.66 2.43
1161 1380 3.267860 CAAGCCGATGAGCTCCGC 61.268 66.667 12.15 7.64 44.11 5.54
1284 1503 1.027255 TTCTCCTCGACTCGCTCCTG 61.027 60.000 0.00 0.00 0.00 3.86
1387 1606 1.461091 CGCCCTCTTATCCGCCTACA 61.461 60.000 0.00 0.00 0.00 2.74
1441 1660 6.317391 GGACCTCTTTTATCAGATGAACCAAG 59.683 42.308 0.00 0.00 0.00 3.61
1446 1665 6.375455 TCTTTTATCAGATGAACCAAGAAGGC 59.625 38.462 0.00 0.00 43.14 4.35
1764 1983 6.049149 GTCGGAATTTGGTGATGAGATAAGA 58.951 40.000 0.00 0.00 0.00 2.10
1788 2007 8.254508 AGAAAGTATACTTTGCCTACTCTTCTG 58.745 37.037 30.66 0.00 45.37 3.02
1878 2097 1.659098 CTGGAAACCGATAACGTGCTC 59.341 52.381 0.00 0.00 37.88 4.26
2167 2386 1.108727 TGTGAAAAGTGGGCTGGCTG 61.109 55.000 0.00 0.00 0.00 4.85
2236 2455 0.594602 TGCTGCTCAAGATGCAACAC 59.405 50.000 0.00 0.00 40.13 3.32
2799 3018 3.496130 CAGTTGTTTCTGGTGCTCTAGTG 59.504 47.826 0.00 0.00 0.00 2.74
2883 3102 3.921119 TGTGATCAAGTTGCATGGAAC 57.079 42.857 21.29 21.29 0.00 3.62
3075 3294 6.183360 TGCTGAGTAGTGTCTATGGAATTACC 60.183 42.308 0.00 0.00 39.54 2.85
3078 3297 4.906060 AGTAGTGTCTATGGAATTACCCCC 59.094 45.833 0.00 0.00 38.00 5.40
3154 3373 4.605640 GCTGAGGCTGAATCTCTTATCT 57.394 45.455 0.00 0.00 35.22 1.98
3174 3393 3.911894 TCTATCAGATGCCATTGATCCCA 59.088 43.478 5.88 0.00 35.72 4.37
3228 3447 6.782986 AGCTTGCAGGATACATGGAAATATA 58.217 36.000 0.00 0.00 41.41 0.86
3237 3456 8.270744 AGGATACATGGAAATATAGAGATTGCC 58.729 37.037 0.00 0.00 35.27 4.52
3488 3707 1.967319 ACAACGTGCATTCTGTTCCT 58.033 45.000 0.00 0.00 0.00 3.36
3495 3714 1.820519 TGCATTCTGTTCCTGCAATCC 59.179 47.619 0.00 0.00 42.53 3.01
3600 3887 6.403309 GGCTGATACAAAGTGCTAAGGTAAAC 60.403 42.308 0.00 0.00 0.00 2.01
3779 4066 2.825532 TCGCATATGCTATCCTGCAGTA 59.174 45.455 24.56 0.00 46.71 2.74
3785 4072 6.645827 GCATATGCTATCCTGCAGTATGATAG 59.354 42.308 23.63 23.63 46.71 2.08
3865 4152 8.956446 TCATATACTAGGATGAATTCTGACCA 57.044 34.615 7.05 0.00 0.00 4.02
4006 4293 4.333649 CGTTGATACTGGATTGCTCATGTT 59.666 41.667 0.00 0.00 0.00 2.71
4340 4627 1.076549 GTTCATGGGGGCAAGGTCA 59.923 57.895 0.00 0.00 0.00 4.02
4346 4633 0.469144 TGGGGGCAAGGTCAGTTTTC 60.469 55.000 0.00 0.00 0.00 2.29
4347 4634 0.469144 GGGGGCAAGGTCAGTTTTCA 60.469 55.000 0.00 0.00 0.00 2.69
4348 4635 1.632589 GGGGCAAGGTCAGTTTTCAT 58.367 50.000 0.00 0.00 0.00 2.57
4349 4636 1.970640 GGGGCAAGGTCAGTTTTCATT 59.029 47.619 0.00 0.00 0.00 2.57
4350 4637 2.289010 GGGGCAAGGTCAGTTTTCATTG 60.289 50.000 0.00 0.00 0.00 2.82
4351 4638 2.365293 GGGCAAGGTCAGTTTTCATTGT 59.635 45.455 0.00 0.00 0.00 2.71
4352 4639 3.383761 GGCAAGGTCAGTTTTCATTGTG 58.616 45.455 0.00 0.00 0.00 3.33
4353 4640 2.796593 GCAAGGTCAGTTTTCATTGTGC 59.203 45.455 0.00 0.00 0.00 4.57
4354 4641 3.737663 GCAAGGTCAGTTTTCATTGTGCA 60.738 43.478 0.00 0.00 0.00 4.57
4367 4654 3.384146 TCATTGTGCACACCACTTTTCAT 59.616 39.130 21.56 3.80 44.92 2.57
4408 4853 9.469807 GAGGTTTCAGAACACATCACTATATAG 57.530 37.037 8.27 8.27 37.51 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 9.669353 CTAATTGCATATAACAAGGAACATGAC 57.331 33.333 0.00 0.00 0.00 3.06
108 109 1.874129 TCAAGATGGTACCGTGGGAT 58.126 50.000 12.53 0.00 0.00 3.85
165 166 3.033184 CAAGGCACAATACCCATCCATT 58.967 45.455 0.00 0.00 0.00 3.16
192 193 2.884639 GCAAGCTCTGGTAGGACAAAAA 59.115 45.455 0.00 0.00 0.00 1.94
196 197 1.055849 TTGCAAGCTCTGGTAGGACA 58.944 50.000 0.00 0.00 0.00 4.02
200 201 3.507233 TGGATTTTTGCAAGCTCTGGTAG 59.493 43.478 0.00 0.00 0.00 3.18
240 241 8.871125 CCAGAAATAACACCCAGTAGTAGATAT 58.129 37.037 0.00 0.00 0.00 1.63
241 242 7.842743 ACCAGAAATAACACCCAGTAGTAGATA 59.157 37.037 0.00 0.00 0.00 1.98
242 243 6.672657 ACCAGAAATAACACCCAGTAGTAGAT 59.327 38.462 0.00 0.00 0.00 1.98
243 244 6.021030 ACCAGAAATAACACCCAGTAGTAGA 58.979 40.000 0.00 0.00 0.00 2.59
244 245 6.154706 AGACCAGAAATAACACCCAGTAGTAG 59.845 42.308 0.00 0.00 0.00 2.57
245 246 6.021030 AGACCAGAAATAACACCCAGTAGTA 58.979 40.000 0.00 0.00 0.00 1.82
246 247 4.844655 AGACCAGAAATAACACCCAGTAGT 59.155 41.667 0.00 0.00 0.00 2.73
247 248 5.420409 GAGACCAGAAATAACACCCAGTAG 58.580 45.833 0.00 0.00 0.00 2.57
248 249 4.224370 GGAGACCAGAAATAACACCCAGTA 59.776 45.833 0.00 0.00 0.00 2.74
249 250 3.009143 GGAGACCAGAAATAACACCCAGT 59.991 47.826 0.00 0.00 0.00 4.00
250 251 3.264450 AGGAGACCAGAAATAACACCCAG 59.736 47.826 0.00 0.00 0.00 4.45
251 252 3.009033 CAGGAGACCAGAAATAACACCCA 59.991 47.826 0.00 0.00 0.00 4.51
252 253 3.009143 ACAGGAGACCAGAAATAACACCC 59.991 47.826 0.00 0.00 0.00 4.61
253 254 4.287766 ACAGGAGACCAGAAATAACACC 57.712 45.455 0.00 0.00 0.00 4.16
299 307 9.541143 AAAGTTTTGTTTTGTTTTCAGAGAGAA 57.459 25.926 0.00 0.00 0.00 2.87
302 310 8.769891 GGAAAAGTTTTGTTTTGTTTTCAGAGA 58.230 29.630 5.36 0.00 38.37 3.10
303 311 8.015087 GGGAAAAGTTTTGTTTTGTTTTCAGAG 58.985 33.333 5.36 0.00 38.37 3.35
326 334 3.066190 CGACAGCCACCTACGGGA 61.066 66.667 0.00 0.00 36.25 5.14
329 337 3.411418 ATCGCGACAGCCACCTACG 62.411 63.158 12.93 0.00 41.18 3.51
358 366 9.965902 ATGACCTTTAAAACTAGATCTCACATT 57.034 29.630 0.00 0.00 0.00 2.71
359 367 9.388506 CATGACCTTTAAAACTAGATCTCACAT 57.611 33.333 0.00 0.00 0.00 3.21
360 368 8.375506 ACATGACCTTTAAAACTAGATCTCACA 58.624 33.333 0.00 0.00 0.00 3.58
361 369 8.779354 ACATGACCTTTAAAACTAGATCTCAC 57.221 34.615 0.00 0.00 0.00 3.51
363 371 8.874816 GTGACATGACCTTTAAAACTAGATCTC 58.125 37.037 0.00 0.00 0.00 2.75
365 373 7.544566 TCGTGACATGACCTTTAAAACTAGATC 59.455 37.037 0.00 0.00 0.00 2.75
366 374 7.383687 TCGTGACATGACCTTTAAAACTAGAT 58.616 34.615 0.00 0.00 0.00 1.98
368 376 6.090898 CCTCGTGACATGACCTTTAAAACTAG 59.909 42.308 0.00 0.00 0.00 2.57
370 378 4.755123 CCTCGTGACATGACCTTTAAAACT 59.245 41.667 0.00 0.00 0.00 2.66
371 379 4.753107 TCCTCGTGACATGACCTTTAAAAC 59.247 41.667 0.00 0.00 0.00 2.43
372 380 4.963373 TCCTCGTGACATGACCTTTAAAA 58.037 39.130 0.00 0.00 0.00 1.52
373 381 4.610605 TCCTCGTGACATGACCTTTAAA 57.389 40.909 0.00 0.00 0.00 1.52
375 383 3.322541 TGTTCCTCGTGACATGACCTTTA 59.677 43.478 0.00 0.00 0.00 1.85
376 384 2.104111 TGTTCCTCGTGACATGACCTTT 59.896 45.455 0.00 0.00 0.00 3.11
378 386 1.000955 GTGTTCCTCGTGACATGACCT 59.999 52.381 0.00 0.00 0.00 3.85
379 387 1.270094 TGTGTTCCTCGTGACATGACC 60.270 52.381 0.00 0.00 0.00 4.02
380 388 2.061773 CTGTGTTCCTCGTGACATGAC 58.938 52.381 0.00 0.00 0.00 3.06
381 389 1.686587 ACTGTGTTCCTCGTGACATGA 59.313 47.619 0.00 0.00 0.00 3.07
382 390 1.794701 CACTGTGTTCCTCGTGACATG 59.205 52.381 0.00 0.00 0.00 3.21
383 391 1.270305 CCACTGTGTTCCTCGTGACAT 60.270 52.381 7.08 0.00 0.00 3.06
385 393 0.600255 CCCACTGTGTTCCTCGTGAC 60.600 60.000 7.08 0.00 0.00 3.67
387 395 0.880278 CACCCACTGTGTTCCTCGTG 60.880 60.000 7.08 0.02 40.26 4.35
388 396 1.046472 TCACCCACTGTGTTCCTCGT 61.046 55.000 7.08 0.00 45.61 4.18
389 397 0.105964 TTCACCCACTGTGTTCCTCG 59.894 55.000 7.08 0.00 45.61 4.63
390 398 2.222027 CTTTCACCCACTGTGTTCCTC 58.778 52.381 7.08 0.00 45.61 3.71
391 399 1.564348 ACTTTCACCCACTGTGTTCCT 59.436 47.619 7.08 0.00 45.61 3.36
392 400 1.676006 CACTTTCACCCACTGTGTTCC 59.324 52.381 7.08 0.00 45.61 3.62
393 401 1.676006 CCACTTTCACCCACTGTGTTC 59.324 52.381 7.08 0.00 45.61 3.18
395 403 0.916086 TCCACTTTCACCCACTGTGT 59.084 50.000 7.08 0.00 45.61 3.72
396 404 1.134098 AGTCCACTTTCACCCACTGTG 60.134 52.381 0.00 0.00 46.88 3.66
397 405 1.213296 AGTCCACTTTCACCCACTGT 58.787 50.000 0.00 0.00 0.00 3.55
398 406 2.348411 AAGTCCACTTTCACCCACTG 57.652 50.000 0.00 0.00 30.82 3.66
399 407 2.241176 TCAAAGTCCACTTTCACCCACT 59.759 45.455 1.52 0.00 43.72 4.00
400 408 2.650322 TCAAAGTCCACTTTCACCCAC 58.350 47.619 1.52 0.00 43.72 4.61
401 409 3.593442 ATCAAAGTCCACTTTCACCCA 57.407 42.857 1.52 0.00 43.72 4.51
402 410 4.501400 CCAAATCAAAGTCCACTTTCACCC 60.501 45.833 1.52 0.00 43.72 4.61
403 411 4.620982 CCAAATCAAAGTCCACTTTCACC 58.379 43.478 1.52 0.00 43.72 4.02
404 412 4.051237 GCCAAATCAAAGTCCACTTTCAC 58.949 43.478 1.52 0.00 43.72 3.18
405 413 3.069443 GGCCAAATCAAAGTCCACTTTCA 59.931 43.478 0.00 0.00 43.72 2.69
407 415 2.035832 CGGCCAAATCAAAGTCCACTTT 59.964 45.455 2.24 0.00 46.23 2.66
408 416 1.613437 CGGCCAAATCAAAGTCCACTT 59.387 47.619 2.24 0.00 37.91 3.16
409 417 1.202879 TCGGCCAAATCAAAGTCCACT 60.203 47.619 2.24 0.00 0.00 4.00
410 418 1.243902 TCGGCCAAATCAAAGTCCAC 58.756 50.000 2.24 0.00 0.00 4.02
411 419 2.214376 ATCGGCCAAATCAAAGTCCA 57.786 45.000 2.24 0.00 0.00 4.02
412 420 3.253230 CAAATCGGCCAAATCAAAGTCC 58.747 45.455 2.24 0.00 0.00 3.85
413 421 3.913089 ACAAATCGGCCAAATCAAAGTC 58.087 40.909 2.24 0.00 0.00 3.01
415 423 6.777526 TTAAACAAATCGGCCAAATCAAAG 57.222 33.333 2.24 0.00 0.00 2.77
416 424 7.281100 ACTTTTAAACAAATCGGCCAAATCAAA 59.719 29.630 2.24 0.00 0.00 2.69
418 426 6.284459 ACTTTTAAACAAATCGGCCAAATCA 58.716 32.000 2.24 0.00 0.00 2.57
419 427 6.779115 ACTTTTAAACAAATCGGCCAAATC 57.221 33.333 2.24 0.00 0.00 2.17
420 428 8.716909 CATTACTTTTAAACAAATCGGCCAAAT 58.283 29.630 2.24 0.00 0.00 2.32
423 431 5.635700 GCATTACTTTTAAACAAATCGGCCA 59.364 36.000 2.24 0.00 0.00 5.36
425 433 6.698359 TGCATTACTTTTAAACAAATCGGC 57.302 33.333 0.00 0.00 0.00 5.54
458 471 4.632688 GCACCATGCAAAGCTATTTTTGAT 59.367 37.500 0.00 0.00 44.26 2.57
511 704 7.915397 GGTAAACATAGCATCAAATCAACGAAT 59.085 33.333 0.00 0.00 0.00 3.34
553 746 5.753438 ACTACGGCACATGAAACATATACAG 59.247 40.000 0.00 0.00 0.00 2.74
561 754 0.179225 CGCACTACGGCACATGAAAC 60.179 55.000 0.00 0.00 38.44 2.78
563 756 3.869187 CGCACTACGGCACATGAA 58.131 55.556 0.00 0.00 38.44 2.57
652 848 4.749245 AATGCTAAAAACTGACGTCTGG 57.251 40.909 23.96 15.55 0.00 3.86
764 961 5.195379 CAGCACGACAAGTTTTTACACTAC 58.805 41.667 0.00 0.00 0.00 2.73
772 969 0.248621 GCTGCAGCACGACAAGTTTT 60.249 50.000 33.36 0.00 41.59 2.43
819 1016 0.899720 AAAATCTGAGGTACGCCGGA 59.100 50.000 5.05 0.00 40.50 5.14
879 1076 7.973048 TTAGAGAGAAAGGAAACAGCCTATA 57.027 36.000 0.00 0.00 37.26 1.31
881 1078 6.681729 TTTAGAGAGAAAGGAAACAGCCTA 57.318 37.500 0.00 0.00 37.26 3.93
883 1080 6.635030 TTTTTAGAGAGAAAGGAAACAGCC 57.365 37.500 0.00 0.00 0.00 4.85
1141 1360 3.934684 GAGCTCATCGGCTTGCGC 61.935 66.667 9.40 0.00 43.20 6.09
1142 1361 3.267860 GGAGCTCATCGGCTTGCG 61.268 66.667 17.19 0.00 43.20 4.85
1143 1362 3.267860 CGGAGCTCATCGGCTTGC 61.268 66.667 17.19 0.00 43.20 4.01
1249 1468 4.250305 AAACGTGTCCGGCTGCCT 62.250 61.111 17.92 0.00 38.78 4.75
1284 1503 1.135972 CCGCACTTGCAGTACATGTTC 60.136 52.381 2.30 0.00 42.21 3.18
1422 1641 6.405176 GGCCTTCTTGGTTCATCTGATAAAAG 60.405 42.308 0.00 0.00 38.35 2.27
1427 1646 2.579860 AGGCCTTCTTGGTTCATCTGAT 59.420 45.455 0.00 0.00 38.35 2.90
1446 1665 0.250553 TGAACCCGTTAGGCACAAGG 60.251 55.000 0.00 0.00 40.58 3.61
1451 1670 2.357760 GCGTGAACCCGTTAGGCA 60.358 61.111 0.00 0.00 40.58 4.75
1764 1983 8.135382 TCAGAAGAGTAGGCAAAGTATACTTT 57.865 34.615 22.49 22.49 46.23 2.66
1788 2007 1.597663 CCGAGTTCCACACAACACTTC 59.402 52.381 0.00 0.00 0.00 3.01
2236 2455 5.459107 GCTCATGCATAAGATGAAAAGCAAG 59.541 40.000 0.00 0.00 39.41 4.01
2799 3018 1.665679 CCGCACTTCACATACATGTCC 59.334 52.381 0.00 0.00 39.39 4.02
2883 3102 5.482006 TGAGAATAACCACAGATGAGTGTG 58.518 41.667 0.00 0.00 46.32 3.82
3075 3294 0.250038 CATAGTGCTCCATCGTGGGG 60.250 60.000 4.52 2.37 42.32 4.96
3154 3373 3.911894 TCTGGGATCAATGGCATCTGATA 59.088 43.478 18.60 8.31 32.40 2.15
3174 3393 4.420206 TCGTCCTCCATATGGATGAATCT 58.580 43.478 25.84 0.00 44.05 2.40
3228 3447 0.746063 CTGCTCTCTCGGCAATCTCT 59.254 55.000 0.00 0.00 39.30 3.10
3237 3456 2.582728 ATCTTTCTGCTGCTCTCTCG 57.417 50.000 0.00 0.00 0.00 4.04
3464 3683 3.602390 ACAGAATGCACGTTGTAACAC 57.398 42.857 0.00 0.00 42.53 3.32
3488 3707 0.897401 TGGTGGCATTTCGGATTGCA 60.897 50.000 12.39 0.00 40.66 4.08
3698 3985 2.026905 GCAAGTTCAGGGACCCAACAA 61.027 52.381 14.60 0.00 0.00 2.83
3779 4066 2.487934 GCACATTGCGTCTCCTATCAT 58.512 47.619 0.00 0.00 31.71 2.45
3882 4169 1.811965 TGACCATTTTCACATGCCTCG 59.188 47.619 0.00 0.00 0.00 4.63
3980 4267 3.126831 GAGCAATCCAGTATCAACGGAG 58.873 50.000 0.00 0.00 33.72 4.63
4006 4293 3.772387 TCCCAATTGGACTACAAATGCA 58.228 40.909 26.60 0.00 43.46 3.96
4031 4318 0.883153 TGATCACCTTGCATGCACAC 59.117 50.000 22.58 7.34 0.00 3.82
4264 4551 1.827969 AGAGGATTCAAGGGACAGACG 59.172 52.381 0.00 0.00 0.00 4.18
4317 4604 2.044353 ACCTTGCCCCCATGAACTAATT 59.956 45.455 0.00 0.00 0.00 1.40
4318 4605 1.645919 ACCTTGCCCCCATGAACTAAT 59.354 47.619 0.00 0.00 0.00 1.73
4320 4607 0.623723 GACCTTGCCCCCATGAACTA 59.376 55.000 0.00 0.00 0.00 2.24
4321 4608 1.384191 GACCTTGCCCCCATGAACT 59.616 57.895 0.00 0.00 0.00 3.01
4322 4609 0.967380 CTGACCTTGCCCCCATGAAC 60.967 60.000 0.00 0.00 0.00 3.18
4324 4611 1.434513 AACTGACCTTGCCCCCATGA 61.435 55.000 0.00 0.00 0.00 3.07
4325 4612 0.542702 AAACTGACCTTGCCCCCATG 60.543 55.000 0.00 0.00 0.00 3.66
4326 4613 0.190815 AAAACTGACCTTGCCCCCAT 59.809 50.000 0.00 0.00 0.00 4.00
4327 4614 0.469144 GAAAACTGACCTTGCCCCCA 60.469 55.000 0.00 0.00 0.00 4.96
4330 4617 2.365293 ACAATGAAAACTGACCTTGCCC 59.635 45.455 0.00 0.00 0.00 5.36
4340 4627 2.760092 AGTGGTGTGCACAATGAAAACT 59.240 40.909 23.59 15.02 0.00 2.66
4346 4633 3.162202 TGAAAAGTGGTGTGCACAATG 57.838 42.857 23.59 0.00 0.00 2.82
4347 4634 5.243507 TCATATGAAAAGTGGTGTGCACAAT 59.756 36.000 23.59 10.57 0.00 2.71
4348 4635 4.582240 TCATATGAAAAGTGGTGTGCACAA 59.418 37.500 23.59 3.57 0.00 3.33
4349 4636 4.140536 TCATATGAAAAGTGGTGTGCACA 58.859 39.130 17.42 17.42 0.00 4.57
4350 4637 4.216257 ACTCATATGAAAAGTGGTGTGCAC 59.784 41.667 10.75 10.75 0.00 4.57
4351 4638 4.397420 ACTCATATGAAAAGTGGTGTGCA 58.603 39.130 6.90 0.00 0.00 4.57
4352 4639 6.494893 TTACTCATATGAAAAGTGGTGTGC 57.505 37.500 6.90 0.00 0.00 4.57
4353 4640 6.968904 GCATTACTCATATGAAAAGTGGTGTG 59.031 38.462 6.90 5.45 0.00 3.82
4354 4641 6.658816 TGCATTACTCATATGAAAAGTGGTGT 59.341 34.615 6.90 1.31 0.00 4.16
4367 4654 6.048732 TGAAACCTCAGTGCATTACTCATA 57.951 37.500 0.00 0.00 37.60 2.15
4392 4680 8.753497 TCACTCAGTCTATATAGTGATGTGTT 57.247 34.615 18.95 7.26 42.46 3.32
4408 4853 9.736023 AAAAGAAACAATTTATGTCACTCAGTC 57.264 29.630 0.00 0.00 42.99 3.51
4411 4856 9.515020 GACAAAAGAAACAATTTATGTCACTCA 57.485 29.630 0.00 0.00 42.99 3.41


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

AutoCloner maintained by Alex Coulton.