Multiple sequence alignment - TraesCS4B01G229300

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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 TraesCS4B01G229300 chr4B 100.000 5445 0 0 1 5445 480065397 480059953 0.000000e+00 10056.0
1 TraesCS4B01G229300 chr4D 96.141 3317 88 17 592 3888 390278957 390275661 0.000000e+00 5380.0
2 TraesCS4B01G229300 chr4D 91.204 1728 73 27 3749 5445 390275722 390274043 0.000000e+00 2276.0
3 TraesCS4B01G229300 chr4D 88.491 530 30 17 14 524 390279562 390279045 3.610000e-171 612.0
4 TraesCS4B01G229300 chr4D 96.296 54 2 0 522 575 390279002 390278949 7.510000e-14 89.8
5 TraesCS4B01G229300 chr4A 96.537 1848 57 4 1201 3045 72031241 72029398 0.000000e+00 3051.0
6 TraesCS4B01G229300 chr4A 91.968 1743 73 26 3749 5445 72028652 72026931 0.000000e+00 2381.0
7 TraesCS4B01G229300 chr4A 96.305 812 28 2 3079 3888 72029402 72028591 0.000000e+00 1332.0
8 TraesCS4B01G229300 chr4A 91.541 331 23 3 14 340 72032568 72032239 8.320000e-123 451.0
9 TraesCS4B01G229300 chr4A 84.416 154 24 0 3722 3875 72028718 72028565 9.450000e-33 152.0
10 TraesCS4B01G229300 chr2D 87.204 211 13 6 5204 5414 11559832 11560028 1.530000e-55 228.0
11 TraesCS4B01G229300 chr2D 86.207 203 16 9 5243 5445 118535013 118534823 5.530000e-50 209.0
12 TraesCS4B01G229300 chrUn 86.391 169 17 3 5204 5372 369330814 369330976 4.330000e-41 180.0


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 TraesCS4B01G229300 chr4B 480059953 480065397 5444 True 10056.00 10056 100.0000 1 5445 1 chr4B.!!$R1 5444
1 TraesCS4B01G229300 chr4D 390274043 390279562 5519 True 2089.45 5380 93.0330 14 5445 4 chr4D.!!$R1 5431
2 TraesCS4B01G229300 chr4A 72026931 72032568 5637 True 1473.40 3051 92.1534 14 5445 5 chr4A.!!$R1 5431

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
381 397 0.039035 AATGAGCCGGGGTTGCTTTA 59.961 50.0 2.18 0.00 39.69 1.85 F
2002 2163 0.248702 GTCGATGCTCCGGAGAAGAC 60.249 60.0 35.69 28.02 0.00 3.01 F
2315 2476 0.378257 ACAAGTTTGACTGTGCTGCG 59.622 50.0 0.00 0.00 0.00 5.18 F
2835 2996 0.991920 TTCCATGTGGGTTCCTCCTC 59.008 55.0 0.00 0.00 38.11 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2315 2476 1.369625 CGACCCAACTGCAGGTATTC 58.630 55.0 19.93 7.49 36.17 1.75 R
3149 3310 0.392998 ACACTATCCAGCTTTGCCCG 60.393 55.0 0.00 0.00 0.00 6.13 R
4004 4246 0.321346 TGCTCTGGATTCTGTTGCGA 59.679 50.0 0.00 0.00 0.00 5.10 R
4672 4932 0.742281 CTGTGAACAGGATCAGGGCG 60.742 60.0 2.35 0.00 40.20 6.13 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
29 30 0.792640 AAGCATTTCTCGTCGTGCAG 59.207 50.000 7.42 0.00 39.94 4.41
205 210 1.595993 GACAGACAGCTAGGCCGTCA 61.596 60.000 9.94 0.00 31.92 4.35
255 270 2.443781 ACCGAGGGTGCTCCACTA 59.556 61.111 7.20 0.00 38.24 2.74
301 316 2.113139 CAGACCAAACGGCCCACT 59.887 61.111 0.00 0.00 0.00 4.00
371 386 1.462616 TGTGAATGGAAATGAGCCGG 58.537 50.000 0.00 0.00 0.00 6.13
381 397 0.039035 AATGAGCCGGGGTTGCTTTA 59.961 50.000 2.18 0.00 39.69 1.85
391 407 0.887387 GGTTGCTTTACCCTGCACGA 60.887 55.000 0.00 0.00 39.05 4.35
435 451 3.050703 CCGAGAGAAACACGGGATG 57.949 57.895 0.00 0.00 46.11 3.51
441 457 0.902531 AGAAACACGGGATGGATCGT 59.097 50.000 0.00 0.00 40.49 3.73
442 458 1.134788 AGAAACACGGGATGGATCGTC 60.135 52.381 0.00 0.00 37.53 4.20
456 476 1.377366 ATCGTCCATCGTCGCTGTCT 61.377 55.000 0.00 0.00 40.80 3.41
457 477 1.869574 CGTCCATCGTCGCTGTCTG 60.870 63.158 0.00 0.00 34.52 3.51
460 480 1.226802 CCATCGTCGCTGTCTGGAG 60.227 63.158 0.00 0.00 0.00 3.86
472 492 3.431905 GCTGTCTGGAGATCACATGATGT 60.432 47.826 0.00 0.00 34.37 3.06
487 507 1.913419 TGATGTAGTTTGACCCCCTCC 59.087 52.381 0.00 0.00 0.00 4.30
520 540 2.414750 CAAACGGGTTGGCACTTCT 58.585 52.632 0.00 0.00 33.18 2.85
556 619 1.599518 AATGACGGCGGCAGTGAAA 60.600 52.632 24.18 0.00 0.00 2.69
575 638 8.926710 CAGTGAAAACAGTTCGTAAATATCTCT 58.073 33.333 0.00 0.00 0.00 3.10
581 644 8.976986 AACAGTTCGTAAATATCTCTACGTTT 57.023 30.769 0.00 0.00 41.26 3.60
582 645 8.612233 ACAGTTCGTAAATATCTCTACGTTTC 57.388 34.615 0.00 4.91 41.26 2.78
583 646 7.699812 ACAGTTCGTAAATATCTCTACGTTTCC 59.300 37.037 0.00 1.51 41.26 3.13
584 647 7.167136 CAGTTCGTAAATATCTCTACGTTTCCC 59.833 40.741 0.00 0.35 41.26 3.97
585 648 6.076981 TCGTAAATATCTCTACGTTTCCCC 57.923 41.667 0.00 0.00 41.26 4.81
586 649 4.913924 CGTAAATATCTCTACGTTTCCCCG 59.086 45.833 0.00 0.00 36.89 5.73
587 650 5.506317 CGTAAATATCTCTACGTTTCCCCGT 60.506 44.000 0.00 0.00 44.50 5.28
588 651 4.581077 AATATCTCTACGTTTCCCCGTC 57.419 45.455 0.00 0.00 42.00 4.79
589 652 1.843368 ATCTCTACGTTTCCCCGTCA 58.157 50.000 0.00 0.00 42.00 4.35
590 653 1.619654 TCTCTACGTTTCCCCGTCAA 58.380 50.000 0.00 0.00 42.00 3.18
591 654 1.962807 TCTCTACGTTTCCCCGTCAAA 59.037 47.619 0.00 0.00 42.00 2.69
592 655 2.364970 TCTCTACGTTTCCCCGTCAAAA 59.635 45.455 0.00 0.00 42.00 2.44
593 656 3.132925 CTCTACGTTTCCCCGTCAAAAA 58.867 45.455 0.00 0.00 42.00 1.94
594 657 3.742385 TCTACGTTTCCCCGTCAAAAAT 58.258 40.909 0.00 0.00 42.00 1.82
595 658 4.892433 TCTACGTTTCCCCGTCAAAAATA 58.108 39.130 0.00 0.00 42.00 1.40
596 659 5.490159 TCTACGTTTCCCCGTCAAAAATAT 58.510 37.500 0.00 0.00 42.00 1.28
597 660 4.690184 ACGTTTCCCCGTCAAAAATATC 57.310 40.909 0.00 0.00 35.95 1.63
598 661 4.329392 ACGTTTCCCCGTCAAAAATATCT 58.671 39.130 0.00 0.00 35.95 1.98
599 662 4.393990 ACGTTTCCCCGTCAAAAATATCTC 59.606 41.667 0.00 0.00 35.95 2.75
600 663 4.634443 CGTTTCCCCGTCAAAAATATCTCT 59.366 41.667 0.00 0.00 0.00 3.10
601 664 5.813672 CGTTTCCCCGTCAAAAATATCTCTA 59.186 40.000 0.00 0.00 0.00 2.43
602 665 6.238022 CGTTTCCCCGTCAAAAATATCTCTAC 60.238 42.308 0.00 0.00 0.00 2.59
603 666 4.940463 TCCCCGTCAAAAATATCTCTACG 58.060 43.478 0.00 0.00 0.00 3.51
604 667 4.403432 TCCCCGTCAAAAATATCTCTACGT 59.597 41.667 0.00 0.00 0.00 3.57
605 668 5.105228 TCCCCGTCAAAAATATCTCTACGTT 60.105 40.000 0.00 0.00 0.00 3.99
852 915 2.889678 TCTCATCTCATCATCTCACGGG 59.110 50.000 0.00 0.00 0.00 5.28
853 916 2.889678 CTCATCTCATCATCTCACGGGA 59.110 50.000 0.00 0.00 0.00 5.14
2002 2163 0.248702 GTCGATGCTCCGGAGAAGAC 60.249 60.000 35.69 28.02 0.00 3.01
2315 2476 0.378257 ACAAGTTTGACTGTGCTGCG 59.622 50.000 0.00 0.00 0.00 5.18
2450 2611 1.085091 CTGAGATGCAGTTCCAGTGC 58.915 55.000 0.00 0.00 44.57 4.40
2703 2864 5.957798 TGCAATTCTTCAAATGTGAGATCC 58.042 37.500 0.00 0.00 34.49 3.36
2743 2904 5.699097 TCTAAAGCACCATGTTACAAACC 57.301 39.130 0.00 0.00 0.00 3.27
2828 2989 2.825532 GCATACACTTTCCATGTGGGTT 59.174 45.455 0.00 0.00 39.52 4.11
2835 2996 0.991920 TTCCATGTGGGTTCCTCCTC 59.008 55.000 0.00 0.00 38.11 3.71
2932 3093 3.694566 ACAGTTTCTTCTGTTTGACCCAC 59.305 43.478 0.00 0.00 44.92 4.61
3056 3217 1.281656 GTTGTGCGGCACTACAACC 59.718 57.895 32.42 13.29 46.69 3.77
3149 3310 4.635765 TCCAGTCATTTAGCACTGCAATAC 59.364 41.667 3.30 0.00 39.03 1.89
3205 3367 8.767085 TGATTTGATTGAATTGAGTTTGAAAGC 58.233 29.630 0.00 0.00 0.00 3.51
3353 3517 3.964031 ACAGTTAAGGGTTCCAAAATGCA 59.036 39.130 0.00 0.00 0.00 3.96
3399 3563 6.545508 TCAAAATGCATATTCTGTTGAGACG 58.454 36.000 0.00 0.00 0.00 4.18
3423 3587 8.537858 ACGAAATCTATTATAATACTCCCACCC 58.462 37.037 0.81 0.00 0.00 4.61
3447 3611 6.405842 CCCTCCAAATACAACTAAAATCTGGC 60.406 42.308 0.00 0.00 0.00 4.85
3490 3654 7.548196 TTAGAGCAATCGAAAATAATTCCGT 57.452 32.000 0.00 0.00 0.00 4.69
4004 4246 1.207329 GAGAACTACCGGCAGATGGTT 59.793 52.381 9.21 0.00 40.96 3.67
4038 4280 1.289231 AGAGCATGGAGGAGGAGTACA 59.711 52.381 0.00 0.00 0.00 2.90
4040 4282 1.195115 GCATGGAGGAGGAGTACACA 58.805 55.000 0.00 0.00 0.00 3.72
4225 4467 4.000928 AGATGTGGGTGTAGAGAGGAAT 57.999 45.455 0.00 0.00 0.00 3.01
4275 4517 2.772691 GCTGCTCCTGAATGCCTGC 61.773 63.158 0.00 0.00 0.00 4.85
4280 4522 1.595466 CTCCTGAATGCCTGCAGATC 58.405 55.000 17.39 7.16 34.06 2.75
4281 4523 0.179065 TCCTGAATGCCTGCAGATCG 60.179 55.000 17.39 0.00 34.06 3.69
4282 4524 1.647629 CTGAATGCCTGCAGATCGC 59.352 57.895 17.39 11.14 42.89 4.58
4283 4525 1.783031 CTGAATGCCTGCAGATCGCC 61.783 60.000 17.39 1.76 41.33 5.54
4303 4549 3.399330 CCGTTGTTGTCCATTAGAGTGT 58.601 45.455 0.00 0.00 0.00 3.55
4381 4627 6.767423 ACTACCCGTTGTTAACTGTTGTTATT 59.233 34.615 7.22 0.00 38.31 1.40
4382 4628 7.930865 ACTACCCGTTGTTAACTGTTGTTATTA 59.069 33.333 7.22 0.00 38.31 0.98
4383 4629 7.748691 ACCCGTTGTTAACTGTTGTTATTAT 57.251 32.000 7.22 0.00 38.31 1.28
4384 4630 8.845413 ACCCGTTGTTAACTGTTGTTATTATA 57.155 30.769 7.22 0.00 38.31 0.98
4423 4670 3.116531 GCGCCGGCGGATATAACC 61.117 66.667 45.81 25.49 40.19 2.85
4527 4787 3.560025 GCCCCATGCTATGCTATAGTTGT 60.560 47.826 0.84 0.00 36.87 3.32
4580 4840 2.003301 GCGTGTCATTTTCTCCTCTCC 58.997 52.381 0.00 0.00 0.00 3.71
4640 4900 3.805385 CTGTTGGCGTGTGCGTTGG 62.805 63.158 0.00 0.00 44.10 3.77
4672 4932 4.738252 GTGGATTTTCTTGTTCGGTTGTTC 59.262 41.667 0.00 0.00 0.00 3.18
4685 4950 0.321653 GTTGTTCGCCCTGATCCTGT 60.322 55.000 0.00 0.00 0.00 4.00
4727 4992 3.708631 CTCCTGTTAGGACATCATGGTCT 59.291 47.826 0.00 0.00 40.06 3.85
4881 5146 6.070824 ACAACATTATTAGCAAGGAAAAGGGG 60.071 38.462 0.00 0.00 0.00 4.79
4886 5151 4.948341 TTAGCAAGGAAAAGGGGAAAAC 57.052 40.909 0.00 0.00 0.00 2.43
4888 5153 3.317406 AGCAAGGAAAAGGGGAAAACAT 58.683 40.909 0.00 0.00 0.00 2.71
4889 5154 3.716353 AGCAAGGAAAAGGGGAAAACATT 59.284 39.130 0.00 0.00 0.00 2.71
4890 5155 4.065088 GCAAGGAAAAGGGGAAAACATTC 58.935 43.478 0.00 0.00 0.00 2.67
4892 5157 5.299949 CAAGGAAAAGGGGAAAACATTCTG 58.700 41.667 0.00 0.00 0.00 3.02
4893 5158 3.903714 AGGAAAAGGGGAAAACATTCTGG 59.096 43.478 0.00 0.00 0.00 3.86
4894 5159 3.901222 GGAAAAGGGGAAAACATTCTGGA 59.099 43.478 0.00 0.00 0.00 3.86
4896 5161 3.903530 AAGGGGAAAACATTCTGGAGT 57.096 42.857 0.00 0.00 0.00 3.85
4897 5162 3.903530 AGGGGAAAACATTCTGGAGTT 57.096 42.857 0.00 0.00 0.00 3.01
4898 5163 3.767711 AGGGGAAAACATTCTGGAGTTC 58.232 45.455 0.00 0.00 0.00 3.01
4899 5164 3.140144 AGGGGAAAACATTCTGGAGTTCA 59.860 43.478 0.00 0.00 0.00 3.18
4966 5240 2.229690 TACCGCGGGAAGTTGTAGGC 62.230 60.000 31.76 0.00 0.00 3.93
5032 5318 4.493350 CAGAAATACTTCCACGTACGTACG 59.507 45.833 38.49 38.49 42.69 3.67
5063 5349 2.060284 TGAAACAAATACGGGTCGTCG 58.940 47.619 0.00 0.00 41.54 5.12
5064 5350 2.061028 GAAACAAATACGGGTCGTCGT 58.939 47.619 0.00 6.49 45.88 4.34
5065 5351 1.701704 AACAAATACGGGTCGTCGTC 58.298 50.000 0.00 0.00 42.82 4.20
5071 5357 0.107703 TACGGGTCGTCGTCTACCAT 60.108 55.000 5.77 0.00 42.82 3.55
5151 5440 4.586472 CGTAGCGATCGACGGCGT 62.586 66.667 21.57 14.65 42.83 5.68
5176 5465 1.365633 GGATGGCGGCTAGAGTCTG 59.634 63.158 11.43 0.00 0.00 3.51
5214 5503 2.742372 GTCGGCTTGCACCACGAT 60.742 61.111 8.72 0.00 37.69 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.688507 GAGAAATGCTTGGTCAGACGA 58.311 47.619 0.00 0.00 0.00 4.20
1 2 1.391485 CGAGAAATGCTTGGTCAGACG 59.609 52.381 0.00 0.00 0.00 4.18
2 3 2.413453 GACGAGAAATGCTTGGTCAGAC 59.587 50.000 0.00 0.00 33.24 3.51
3 4 2.688507 GACGAGAAATGCTTGGTCAGA 58.311 47.619 0.00 0.00 33.24 3.27
4 5 1.391485 CGACGAGAAATGCTTGGTCAG 59.609 52.381 0.00 0.00 32.83 3.51
5 6 1.270094 ACGACGAGAAATGCTTGGTCA 60.270 47.619 0.00 0.00 32.83 4.02
6 7 1.126846 CACGACGAGAAATGCTTGGTC 59.873 52.381 0.00 0.00 31.80 4.02
7 8 1.148310 CACGACGAGAAATGCTTGGT 58.852 50.000 0.00 0.00 31.80 3.67
8 9 0.179215 GCACGACGAGAAATGCTTGG 60.179 55.000 0.00 0.00 35.16 3.61
9 10 0.512518 TGCACGACGAGAAATGCTTG 59.487 50.000 0.00 0.00 38.90 4.01
10 11 0.792640 CTGCACGACGAGAAATGCTT 59.207 50.000 0.00 0.00 38.90 3.91
11 12 1.016130 CCTGCACGACGAGAAATGCT 61.016 55.000 0.00 0.00 38.90 3.79
12 13 1.291877 ACCTGCACGACGAGAAATGC 61.292 55.000 0.00 0.33 38.59 3.56
48 49 6.041423 TGAACTAGTCTGCATTTGATCTGA 57.959 37.500 0.00 0.00 0.00 3.27
65 66 1.565390 ATGCCAGCCAGCCTGAACTA 61.565 55.000 0.00 0.00 44.64 2.24
119 120 7.362662 CCAATAACTTGATAACATAATGCGCT 58.637 34.615 9.73 0.00 34.04 5.92
130 131 5.574891 ACGCAATGCCAATAACTTGATAA 57.425 34.783 0.00 0.00 34.04 1.75
255 270 2.045926 GACGGGGCAGCAATCAGT 60.046 61.111 0.00 0.00 0.00 3.41
301 316 1.403780 GCGAGCGGGTAGAAAGAAAGA 60.404 52.381 0.00 0.00 0.00 2.52
340 355 4.044336 TCCATTCACAACAGCAACAAAG 57.956 40.909 0.00 0.00 0.00 2.77
344 359 4.619973 TCATTTCCATTCACAACAGCAAC 58.380 39.130 0.00 0.00 0.00 4.17
348 363 3.671433 CGGCTCATTTCCATTCACAACAG 60.671 47.826 0.00 0.00 0.00 3.16
350 365 2.415893 CCGGCTCATTTCCATTCACAAC 60.416 50.000 0.00 0.00 0.00 3.32
354 369 0.395586 CCCCGGCTCATTTCCATTCA 60.396 55.000 0.00 0.00 0.00 2.57
358 373 1.304052 CAACCCCGGCTCATTTCCA 60.304 57.895 0.00 0.00 0.00 3.53
381 397 2.203640 TCCACTCTCGTGCAGGGT 60.204 61.111 6.56 0.00 39.86 4.34
391 407 1.678627 CGATCGAACCATCTCCACTCT 59.321 52.381 10.26 0.00 0.00 3.24
405 421 2.019948 TCTCTCGGAAAGACGATCGA 57.980 50.000 24.34 0.00 42.62 3.59
435 451 1.658717 CAGCGACGATGGACGATCC 60.659 63.158 4.91 0.00 45.77 3.36
441 457 1.657751 CTCCAGACAGCGACGATGGA 61.658 60.000 18.40 11.14 37.71 3.41
442 458 1.226802 CTCCAGACAGCGACGATGG 60.227 63.158 18.40 7.49 0.00 3.51
444 460 0.665835 GATCTCCAGACAGCGACGAT 59.334 55.000 0.00 0.00 0.00 3.73
456 476 6.108687 GTCAAACTACATCATGTGATCTCCA 58.891 40.000 0.00 0.00 31.21 3.86
457 477 5.525378 GGTCAAACTACATCATGTGATCTCC 59.475 44.000 0.00 0.00 31.21 3.71
460 480 4.576463 GGGGTCAAACTACATCATGTGATC 59.424 45.833 0.00 0.00 31.21 2.92
472 492 1.652947 GACAGGAGGGGGTCAAACTA 58.347 55.000 0.00 0.00 34.22 2.24
512 532 0.235926 GCGTGAAAGTGAGAAGTGCC 59.764 55.000 0.00 0.00 0.00 5.01
516 536 1.453524 CTCGTGCGTGAAAGTGAGAAG 59.546 52.381 0.00 0.00 0.00 2.85
517 537 1.487482 CTCGTGCGTGAAAGTGAGAA 58.513 50.000 0.00 0.00 0.00 2.87
520 540 0.808060 TTGCTCGTGCGTGAAAGTGA 60.808 50.000 4.84 0.00 43.34 3.41
549 612 8.926710 AGAGATATTTACGAACTGTTTTCACTG 58.073 33.333 0.00 0.00 0.00 3.66
556 619 8.976986 AAACGTAGAGATATTTACGAACTGTT 57.023 30.769 16.24 0.00 43.89 3.16
581 644 4.403432 ACGTAGAGATATTTTTGACGGGGA 59.597 41.667 0.00 0.00 33.32 4.81
582 645 4.690122 ACGTAGAGATATTTTTGACGGGG 58.310 43.478 0.00 0.00 33.32 5.73
583 646 6.311935 TGAAACGTAGAGATATTTTTGACGGG 59.688 38.462 0.00 0.00 33.32 5.28
584 647 7.285783 TGAAACGTAGAGATATTTTTGACGG 57.714 36.000 0.00 0.00 33.32 4.79
585 648 9.755064 ATTTGAAACGTAGAGATATTTTTGACG 57.245 29.630 0.00 0.00 35.10 4.35
594 657 9.392259 TCTCTGACTATTTGAAACGTAGAGATA 57.608 33.333 0.00 0.00 34.80 1.98
595 658 8.282455 TCTCTGACTATTTGAAACGTAGAGAT 57.718 34.615 0.00 0.00 34.80 2.75
596 659 7.606839 TCTCTCTGACTATTTGAAACGTAGAGA 59.393 37.037 6.22 6.22 36.69 3.10
597 660 7.753659 TCTCTCTGACTATTTGAAACGTAGAG 58.246 38.462 0.00 0.00 0.00 2.43
598 661 7.606839 TCTCTCTCTGACTATTTGAAACGTAGA 59.393 37.037 0.00 0.00 0.00 2.59
599 662 7.694784 GTCTCTCTCTGACTATTTGAAACGTAG 59.305 40.741 0.00 0.00 0.00 3.51
600 663 7.174426 TGTCTCTCTCTGACTATTTGAAACGTA 59.826 37.037 0.00 0.00 35.63 3.57
601 664 6.016192 TGTCTCTCTCTGACTATTTGAAACGT 60.016 38.462 0.00 0.00 35.63 3.99
602 665 6.382608 TGTCTCTCTCTGACTATTTGAAACG 58.617 40.000 0.00 0.00 35.63 3.60
603 666 7.328249 CACTGTCTCTCTCTGACTATTTGAAAC 59.672 40.741 0.00 0.00 35.63 2.78
604 667 7.374272 CACTGTCTCTCTCTGACTATTTGAAA 58.626 38.462 0.00 0.00 35.63 2.69
605 668 6.571344 GCACTGTCTCTCTCTGACTATTTGAA 60.571 42.308 0.00 0.00 35.63 2.69
646 709 2.886862 TGTGAGAAAAACGGACGGTA 57.113 45.000 0.00 0.00 0.00 4.02
655 718 3.146066 CCGTCTTCCCATGTGAGAAAAA 58.854 45.455 0.00 0.00 0.00 1.94
693 756 1.868251 GAAGCTACGGACGCGTCAG 60.868 63.158 37.26 35.00 36.20 3.51
695 758 2.943034 CGAAGCTACGGACGCGTC 60.943 66.667 30.67 30.67 33.47 5.19
726 789 0.658536 GTGACGTTCAAAGCAGCAGC 60.659 55.000 0.00 0.00 42.56 5.25
727 790 0.383491 CGTGACGTTCAAAGCAGCAG 60.383 55.000 0.00 0.00 0.00 4.24
728 791 1.641140 CGTGACGTTCAAAGCAGCA 59.359 52.632 0.00 0.00 0.00 4.41
729 792 1.082756 CCGTGACGTTCAAAGCAGC 60.083 57.895 3.64 0.00 0.00 5.25
730 793 1.569493 CCCGTGACGTTCAAAGCAG 59.431 57.895 3.64 0.00 0.00 4.24
776 839 4.863925 GTCGCGGCAGAGGAGCTC 62.864 72.222 5.47 4.71 34.17 4.09
788 851 0.572590 GGAATGAATGTCTCGTCGCG 59.427 55.000 0.00 0.00 0.00 5.87
862 925 4.161565 AGGCCTCGTTTTCTTTTCCTTTTT 59.838 37.500 0.00 0.00 0.00 1.94
868 931 2.596263 CGAGGCCTCGTTTTCTTTTC 57.404 50.000 40.77 8.57 46.99 2.29
879 942 3.462678 GGTCTGTCCCGAGGCCTC 61.463 72.222 23.79 23.79 34.60 4.70
1236 1391 2.454941 GTTGGGAGGGGAGGAGGA 59.545 66.667 0.00 0.00 0.00 3.71
1358 1513 3.975591 ACGGAGGAGTCGTCCCCA 61.976 66.667 22.99 0.00 45.26 4.96
2315 2476 1.369625 CGACCCAACTGCAGGTATTC 58.630 55.000 19.93 7.49 36.17 1.75
2327 2488 1.678627 CAAACATCACAACCGACCCAA 59.321 47.619 0.00 0.00 0.00 4.12
2375 2536 2.499289 TCTGATCAAGTTCCTCTCCAGC 59.501 50.000 0.00 0.00 0.00 4.85
2450 2611 0.971386 AAGAATGGCTGCAACCAAGG 59.029 50.000 13.89 0.00 44.65 3.61
2800 2961 5.585844 CACATGGAAAGTGTATGCAGATGTA 59.414 40.000 0.00 0.00 32.44 2.29
2828 2989 0.979665 CCAAGCAGTTCAGAGGAGGA 59.020 55.000 0.00 0.00 0.00 3.71
2835 2996 4.631377 TGATCGTATTTCCAAGCAGTTCAG 59.369 41.667 0.00 0.00 0.00 3.02
2881 3042 4.403752 CCTAACATGACTGACAGAGATGGA 59.596 45.833 10.08 3.10 0.00 3.41
3056 3217 2.214376 TCCTTATGGCAAAGTGGTGG 57.786 50.000 0.00 0.00 0.00 4.61
3149 3310 0.392998 ACACTATCCAGCTTTGCCCG 60.393 55.000 0.00 0.00 0.00 6.13
3245 3409 8.494016 AAGAAAGATATTCAAGGTTAACTCGG 57.506 34.615 5.42 0.00 0.00 4.63
3353 3517 5.657745 TGATTCTTACATCATGCCCAACATT 59.342 36.000 0.00 0.00 36.64 2.71
3399 3563 9.059023 AGGGGTGGGAGTATTATAATAGATTTC 57.941 37.037 5.39 2.56 0.00 2.17
3423 3587 6.564328 GCCAGATTTTAGTTGTATTTGGAGG 58.436 40.000 0.00 0.00 0.00 4.30
3804 4007 3.986006 AACGGACAGCGGCTTCGA 61.986 61.111 19.27 0.00 35.61 3.71
4004 4246 0.321346 TGCTCTGGATTCTGTTGCGA 59.679 50.000 0.00 0.00 0.00 5.10
4038 4280 1.741770 GCTTCGCCACCTTCGATGT 60.742 57.895 0.00 0.00 35.75 3.06
4040 4282 1.448540 CAGCTTCGCCACCTTCGAT 60.449 57.895 0.00 0.00 35.75 3.59
4248 4490 3.644606 AGGAGCAGCAGGTGGTGG 61.645 66.667 9.50 0.00 43.24 4.61
4275 4517 0.948623 TGGACAACAACGGCGATCTG 60.949 55.000 16.62 10.44 0.00 2.90
4280 4522 1.393539 CTCTAATGGACAACAACGGCG 59.606 52.381 4.80 4.80 0.00 6.46
4281 4523 2.159627 CACTCTAATGGACAACAACGGC 59.840 50.000 0.00 0.00 0.00 5.68
4282 4524 3.399330 ACACTCTAATGGACAACAACGG 58.601 45.455 0.00 0.00 0.00 4.44
4283 4525 6.534059 CATTACACTCTAATGGACAACAACG 58.466 40.000 0.00 0.00 32.77 4.10
4381 4627 2.631545 GTTAGGCCTCCTCCGCTTTATA 59.368 50.000 9.68 0.00 34.61 0.98
4382 4628 1.416772 GTTAGGCCTCCTCCGCTTTAT 59.583 52.381 9.68 0.00 34.61 1.40
4383 4629 0.828677 GTTAGGCCTCCTCCGCTTTA 59.171 55.000 9.68 0.00 34.61 1.85
4384 4630 1.602771 GTTAGGCCTCCTCCGCTTT 59.397 57.895 9.68 0.00 34.61 3.51
4423 4670 4.384846 GCAATGAACTGAAAATGCTGTCAG 59.615 41.667 0.00 0.00 45.59 3.51
4523 4783 2.863739 TCTCATGACGACGATGACAAC 58.136 47.619 0.00 0.00 0.00 3.32
4527 4787 6.503524 TGAAATATTCTCATGACGACGATGA 58.496 36.000 0.00 0.00 0.00 2.92
4629 4889 3.124921 GGGATCCCAACGCACACG 61.125 66.667 26.95 0.00 39.85 4.49
4672 4932 0.742281 CTGTGAACAGGATCAGGGCG 60.742 60.000 2.35 0.00 40.20 6.13
4838 5103 2.258591 CGTGTGAGACTCCCCGTG 59.741 66.667 0.00 0.00 0.00 4.94
4890 5155 2.686915 GCCCATGAATTCTGAACTCCAG 59.313 50.000 7.05 0.00 44.27 3.86
4892 5157 2.424956 GTGCCCATGAATTCTGAACTCC 59.575 50.000 7.05 0.00 0.00 3.85
4893 5158 3.084039 TGTGCCCATGAATTCTGAACTC 58.916 45.455 7.05 0.00 0.00 3.01
4894 5159 3.087031 CTGTGCCCATGAATTCTGAACT 58.913 45.455 7.05 0.00 0.00 3.01
4896 5161 1.820519 GCTGTGCCCATGAATTCTGAA 59.179 47.619 7.05 0.00 0.00 3.02
4897 5162 1.272037 TGCTGTGCCCATGAATTCTGA 60.272 47.619 7.05 0.00 0.00 3.27
4898 5163 1.179152 TGCTGTGCCCATGAATTCTG 58.821 50.000 7.05 2.75 0.00 3.02
4899 5164 1.547372 GTTGCTGTGCCCATGAATTCT 59.453 47.619 7.05 0.00 0.00 2.40
4902 5167 1.206132 CATGTTGCTGTGCCCATGAAT 59.794 47.619 11.37 0.00 38.37 2.57
4910 5175 3.840468 TCAATCAATCATGTTGCTGTGC 58.160 40.909 0.00 0.00 0.00 4.57
4966 5240 4.096833 TGTGGTATTGGTAGTAGCGTGTAG 59.903 45.833 0.00 0.00 0.00 2.74
5032 5318 2.025544 TTTGTTTCATGCGTGCGTAC 57.974 45.000 0.00 0.00 0.00 3.67
5033 5319 2.979401 ATTTGTTTCATGCGTGCGTA 57.021 40.000 0.00 0.00 0.00 4.42
5063 5349 4.322080 TCAACGGATCATGATGGTAGAC 57.678 45.455 14.30 0.00 0.00 2.59
5176 5465 4.500116 GAGCCCGACCTGACGCTC 62.500 72.222 0.00 0.00 40.82 5.03


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

AutoCloner maintained by Alex Coulton.