Multiple sequence alignment - TraesCS6A01G054400

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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 TraesCS6A01G054400 chr6A 100.000 3489 0 0 1 3489 28329603 28326115 0.000000e+00 6444
1 TraesCS6A01G054400 chr6A 92.308 533 37 4 1 532 580277267 580277796 0.000000e+00 754
2 TraesCS6A01G054400 chr6A 73.034 1157 260 40 795 1928 34029211 34030338 9.210000e-96 361
3 TraesCS6A01G054400 chr6A 75.765 392 81 13 807 1193 30137002 30136620 5.950000e-43 185
4 TraesCS6A01G054400 chr6B 94.048 2520 97 24 600 3098 49280924 49278437 0.000000e+00 3773
5 TraesCS6A01G054400 chr6B 92.326 2515 122 29 599 3098 49409424 49406966 0.000000e+00 3509
6 TraesCS6A01G054400 chr6B 92.612 379 18 4 3118 3489 49406981 49406606 1.430000e-148 536
7 TraesCS6A01G054400 chr6B 91.495 388 15 9 3118 3489 49278452 49278067 5.160000e-143 518
8 TraesCS6A01G054400 chr2A 93.058 533 34 3 1 532 698952106 698952636 0.000000e+00 776
9 TraesCS6A01G054400 chr7A 92.803 528 31 5 7 533 666167399 666166878 0.000000e+00 758
10 TraesCS6A01G054400 chr7B 90.926 529 44 4 1 526 739410655 739411182 0.000000e+00 708
11 TraesCS6A01G054400 chr4B 88.785 535 56 4 1 531 34537314 34537848 0.000000e+00 652
12 TraesCS6A01G054400 chr5B 88.346 532 56 5 1 531 18689956 18690482 4.910000e-178 634
13 TraesCS6A01G054400 chr3B 83.266 496 71 11 44 532 58141307 58141797 2.470000e-121 446
14 TraesCS6A01G054400 chr3B 82.828 495 75 10 44 532 58198358 58198848 5.350000e-118 435
15 TraesCS6A01G054400 chr1B 81.453 523 82 15 9 523 539599748 539600263 6.970000e-112 414


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 TraesCS6A01G054400 chr6A 28326115 28329603 3488 True 6444.0 6444 100.0000 1 3489 1 chr6A.!!$R1 3488
1 TraesCS6A01G054400 chr6A 580277267 580277796 529 False 754.0 754 92.3080 1 532 1 chr6A.!!$F2 531
2 TraesCS6A01G054400 chr6A 34029211 34030338 1127 False 361.0 361 73.0340 795 1928 1 chr6A.!!$F1 1133
3 TraesCS6A01G054400 chr6B 49278067 49280924 2857 True 2145.5 3773 92.7715 600 3489 2 chr6B.!!$R1 2889
4 TraesCS6A01G054400 chr6B 49406606 49409424 2818 True 2022.5 3509 92.4690 599 3489 2 chr6B.!!$R2 2890
5 TraesCS6A01G054400 chr2A 698952106 698952636 530 False 776.0 776 93.0580 1 532 1 chr2A.!!$F1 531
6 TraesCS6A01G054400 chr7A 666166878 666167399 521 True 758.0 758 92.8030 7 533 1 chr7A.!!$R1 526
7 TraesCS6A01G054400 chr7B 739410655 739411182 527 False 708.0 708 90.9260 1 526 1 chr7B.!!$F1 525
8 TraesCS6A01G054400 chr4B 34537314 34537848 534 False 652.0 652 88.7850 1 531 1 chr4B.!!$F1 530
9 TraesCS6A01G054400 chr5B 18689956 18690482 526 False 634.0 634 88.3460 1 531 1 chr5B.!!$F1 530
10 TraesCS6A01G054400 chr1B 539599748 539600263 515 False 414.0 414 81.4530 9 523 1 chr1B.!!$F1 514

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
553 570 0.529773 TTCGGATCATGTGGTAGCGC 60.530 55.0 0.0 0.0 0.0 5.92 F
1144 1172 0.038618 CGTGTTCGTCATCCACCTGA 60.039 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1537 1565 0.672342 GGTGTCGGTATCACGGCTAT 59.328 55.0 0.0 0.0 39.61 2.97 R
3061 3114 0.232303 GTCACACGCCTTCAACTTCG 59.768 55.0 0.0 0.0 0.00 3.79 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
39 40 4.162320 CCAATCACCTAGGCAAGAGAACTA 59.838 45.833 9.30 0.00 0.00 2.24
101 102 1.134007 CCTGTGCTAGATCCCATGCAA 60.134 52.381 0.00 0.00 37.17 4.08
131 132 7.286546 TCATGTTCTTGAAAAACCAATACTGGA 59.713 33.333 0.00 0.00 46.92 3.86
141 142 9.391006 GAAAAACCAATACTGGATGTATGTCTA 57.609 33.333 0.00 0.00 46.92 2.59
163 164 1.889530 GCGAGTGAACCCTAGCCAGT 61.890 60.000 0.00 0.00 0.00 4.00
276 277 1.807755 CGCAGTCACATCATCCGGATT 60.808 52.381 16.19 0.00 32.57 3.01
297 298 0.962356 GTAGGTCCCGAACTCGACCA 60.962 60.000 11.29 0.00 43.02 4.02
311 312 2.678934 ACCACGAAGCTCCGCCTA 60.679 61.111 0.00 0.00 0.00 3.93
357 360 1.689352 CCGATCAACAACGTACCGGC 61.689 60.000 0.00 0.00 0.00 6.13
429 444 1.065926 TGAGCCTGACGCAATCAATCT 60.066 47.619 0.00 0.00 41.38 2.40
480 497 1.005215 CAGGGAAAGCCAGGTCTCAAT 59.995 52.381 0.00 0.00 35.15 2.57
526 543 2.904434 AGGAAAGAAACCCTAGCGAGAA 59.096 45.455 0.00 0.00 0.00 2.87
533 550 0.531200 ACCCTAGCGAGAAGGAAACG 59.469 55.000 0.00 0.00 36.08 3.60
534 551 0.531200 CCCTAGCGAGAAGGAAACGT 59.469 55.000 0.00 0.00 36.08 3.99
535 552 1.067071 CCCTAGCGAGAAGGAAACGTT 60.067 52.381 0.00 0.00 36.08 3.99
536 553 2.260481 CCTAGCGAGAAGGAAACGTTC 58.740 52.381 0.00 0.00 36.08 3.95
537 554 1.912110 CTAGCGAGAAGGAAACGTTCG 59.088 52.381 0.00 0.00 0.00 3.95
538 555 0.666577 AGCGAGAAGGAAACGTTCGG 60.667 55.000 0.00 0.00 0.00 4.30
539 556 0.665369 GCGAGAAGGAAACGTTCGGA 60.665 55.000 0.00 0.00 0.00 4.55
540 557 1.992170 CGAGAAGGAAACGTTCGGAT 58.008 50.000 0.00 0.00 0.00 4.18
541 558 1.918609 CGAGAAGGAAACGTTCGGATC 59.081 52.381 0.00 0.00 0.00 3.36
542 559 2.670229 CGAGAAGGAAACGTTCGGATCA 60.670 50.000 0.00 0.00 0.00 2.92
543 560 3.522553 GAGAAGGAAACGTTCGGATCAT 58.477 45.455 0.00 0.00 0.00 2.45
544 561 3.262420 AGAAGGAAACGTTCGGATCATG 58.738 45.455 0.00 0.00 0.00 3.07
545 562 2.762535 AGGAAACGTTCGGATCATGT 57.237 45.000 0.00 0.00 0.00 3.21
546 563 2.346803 AGGAAACGTTCGGATCATGTG 58.653 47.619 0.00 0.00 0.00 3.21
547 564 1.396996 GGAAACGTTCGGATCATGTGG 59.603 52.381 0.00 0.00 0.00 4.17
548 565 2.073816 GAAACGTTCGGATCATGTGGT 58.926 47.619 0.00 0.00 0.00 4.16
549 566 3.255725 GAAACGTTCGGATCATGTGGTA 58.744 45.455 0.00 0.00 0.00 3.25
550 567 2.579207 ACGTTCGGATCATGTGGTAG 57.421 50.000 0.00 0.00 0.00 3.18
551 568 1.209128 CGTTCGGATCATGTGGTAGC 58.791 55.000 0.00 0.00 0.00 3.58
552 569 1.209128 GTTCGGATCATGTGGTAGCG 58.791 55.000 0.00 0.00 0.00 4.26
553 570 0.529773 TTCGGATCATGTGGTAGCGC 60.530 55.000 0.00 0.00 0.00 5.92
554 571 1.227234 CGGATCATGTGGTAGCGCA 60.227 57.895 11.47 11.06 0.00 6.09
555 572 1.217585 CGGATCATGTGGTAGCGCAG 61.218 60.000 11.47 6.47 0.00 5.18
570 587 4.067913 CAGCGGCCGCCCAAATTT 62.068 61.111 44.47 23.67 43.17 1.82
571 588 4.067913 AGCGGCCGCCCAAATTTG 62.068 61.111 44.47 11.40 43.17 2.32
596 613 2.408022 GCGTCGGCGAGTATCACT 59.592 61.111 16.53 0.00 41.33 3.41
597 614 1.654743 GCGTCGGCGAGTATCACTC 60.655 63.158 16.53 0.00 41.71 3.51
625 647 2.808906 AGTGGTAGGGAATGGAAAGC 57.191 50.000 0.00 0.00 0.00 3.51
626 648 2.279173 AGTGGTAGGGAATGGAAAGCT 58.721 47.619 0.00 0.00 0.00 3.74
628 650 1.340991 TGGTAGGGAATGGAAAGCTGC 60.341 52.381 0.00 0.00 0.00 5.25
629 651 1.017387 GTAGGGAATGGAAAGCTGCG 58.983 55.000 0.00 0.00 0.00 5.18
630 652 0.908910 TAGGGAATGGAAAGCTGCGA 59.091 50.000 0.00 0.00 0.00 5.10
693 717 2.495084 GGATCGTGGGCTTAAATCTCC 58.505 52.381 0.00 0.00 0.00 3.71
762 786 1.217882 GTCCACTTCACTTCACACCG 58.782 55.000 0.00 0.00 0.00 4.94
916 944 1.079819 CTCGTCTGCCGTCAATGGT 60.080 57.895 0.00 0.00 37.94 3.55
990 1018 4.312152 AACCCTCCCCTCGTCGGT 62.312 66.667 0.00 0.00 0.00 4.69
1038 1066 0.966920 ACTTCGTACCCACACTGGAG 59.033 55.000 0.00 0.00 40.96 3.86
1040 1068 0.178955 TTCGTACCCACACTGGAGGA 60.179 55.000 0.00 0.00 40.96 3.71
1144 1172 0.038618 CGTGTTCGTCATCCACCTGA 60.039 55.000 0.00 0.00 0.00 3.86
1251 1279 3.774599 GATCATGGTCCACGGGGCC 62.775 68.421 0.00 4.10 0.00 5.80
1297 1325 2.364970 CAGCATTTCCAGGTGGTTTTGA 59.635 45.455 0.00 0.00 36.34 2.69
1311 1339 2.762327 GGTTTTGATGGTGGCAGATGAT 59.238 45.455 0.00 0.00 0.00 2.45
1329 1357 5.938710 AGATGATGATTATGACATGCAGGAC 59.061 40.000 4.84 0.00 0.00 3.85
1824 1861 3.450817 TCATGTGGACATCAGTTATCGGT 59.549 43.478 0.00 0.00 33.61 4.69
1928 1965 9.461312 TGAAAGTGTCTTTATTGCAGGTAATAT 57.539 29.630 0.00 0.00 0.00 1.28
1935 1972 9.003658 GTCTTTATTGCAGGTAATATAGCATGT 57.996 33.333 0.00 0.00 36.80 3.21
2036 2076 3.253188 ACTGGTTGATGGAATTGTGTTCG 59.747 43.478 0.00 0.00 0.00 3.95
2149 2190 5.400485 GTCATTCTGCAATGTTCTGTTTGAC 59.600 40.000 0.00 0.00 40.47 3.18
2383 2425 5.070770 TGACACATTGTTTGCTTTGACTT 57.929 34.783 0.00 0.00 0.00 3.01
2384 2426 6.201226 TGACACATTGTTTGCTTTGACTTA 57.799 33.333 0.00 0.00 0.00 2.24
2385 2427 6.804677 TGACACATTGTTTGCTTTGACTTAT 58.195 32.000 0.00 0.00 0.00 1.73
2386 2428 7.264221 TGACACATTGTTTGCTTTGACTTATT 58.736 30.769 0.00 0.00 0.00 1.40
2387 2429 7.222417 TGACACATTGTTTGCTTTGACTTATTG 59.778 33.333 0.00 0.00 0.00 1.90
2388 2430 7.041107 ACACATTGTTTGCTTTGACTTATTGT 58.959 30.769 0.00 0.00 0.00 2.71
2595 2638 7.942341 ACTACCATTTCTCAAGTACCAAATTGA 59.058 33.333 0.00 0.00 34.41 2.57
2731 2775 5.050490 GCTTGACACTGTGAGAGTAAAAGA 58.950 41.667 15.86 0.00 31.73 2.52
2773 2817 9.253832 TGACCAATGGAAGTGTGAATTAATAAT 57.746 29.630 6.16 0.00 0.00 1.28
2806 2850 2.843730 TCCCTTGCTTGAGGCTTATACA 59.156 45.455 0.00 0.00 42.39 2.29
2878 2922 6.183361 CCCATGGTTCCCTTTATAATGCATTT 60.183 38.462 18.75 8.19 0.00 2.32
2966 3014 2.445845 TACCCCATGAGCCCCTCG 60.446 66.667 0.00 0.00 32.35 4.63
2974 3022 1.480212 ATGAGCCCCTCGTGTGTCAA 61.480 55.000 0.00 0.00 32.35 3.18
2996 3044 9.665264 GTCAACTGTTCTTTTAATTAACCTCTG 57.335 33.333 0.00 0.00 0.00 3.35
3021 3069 6.092396 GCTCAGATCAGATGTAGCCAATATTG 59.908 42.308 8.58 8.58 0.00 1.90
3023 3071 5.938710 CAGATCAGATGTAGCCAATATTGCT 59.061 40.000 10.11 12.57 42.81 3.91
3024 3072 7.038799 TCAGATCAGATGTAGCCAATATTGCTA 60.039 37.037 10.11 11.66 40.23 3.49
3025 3073 7.278203 CAGATCAGATGTAGCCAATATTGCTAG 59.722 40.741 10.11 0.00 41.70 3.42
3073 3126 4.434520 AGCTAGTATTCGAAGTTGAAGGC 58.565 43.478 3.35 2.42 0.00 4.35
3098 3151 6.964934 CGTGTGACTAAACTAAAAGTTGCTTT 59.035 34.615 0.00 0.00 38.66 3.51
3099 3152 7.483691 CGTGTGACTAAACTAAAAGTTGCTTTT 59.516 33.333 10.99 10.99 44.46 2.27
3100 3153 9.135843 GTGTGACTAAACTAAAAGTTGCTTTTT 57.864 29.630 11.39 0.00 40.23 1.94
3127 3180 7.817418 TTTGTATCAGAGCCAAACTAAAAGT 57.183 32.000 0.00 0.00 0.00 2.66
3128 3181 7.817418 TTGTATCAGAGCCAAACTAAAAGTT 57.183 32.000 0.00 0.00 40.80 2.66
3129 3182 7.202016 TGTATCAGAGCCAAACTAAAAGTTG 57.798 36.000 0.00 0.00 38.66 3.16
3130 3183 4.568152 TCAGAGCCAAACTAAAAGTTGC 57.432 40.909 0.00 0.00 38.66 4.17
3131 3184 4.207165 TCAGAGCCAAACTAAAAGTTGCT 58.793 39.130 4.78 4.78 39.30 3.91
3132 3185 4.644685 TCAGAGCCAAACTAAAAGTTGCTT 59.355 37.500 6.21 0.00 37.52 3.91
3184 3237 4.397481 TGTCTAGTGATGCTGAAGATGG 57.603 45.455 0.00 0.00 0.00 3.51
3204 3257 2.609002 GGTTCAACTTTGCAGCTTTTGG 59.391 45.455 0.00 0.00 0.00 3.28
3207 3260 2.158928 TCAACTTTGCAGCTTTTGGCAT 60.159 40.909 0.00 0.00 44.79 4.40
3270 3330 9.614792 GAGACATACAAAAGTTATACTCCCAAT 57.385 33.333 0.00 0.00 0.00 3.16
3296 3356 7.893302 TGGGTTTTCCTGAATGAATAGTACAAT 59.107 33.333 0.00 0.00 40.46 2.71
3371 3440 2.795973 TGCGATGCAGCAATGAGC 59.204 55.556 1.53 3.39 45.06 4.26
3420 3489 0.328258 GCTTGGCTTGGTCCCTCTAA 59.672 55.000 0.00 0.00 0.00 2.10
3424 3493 0.984995 GGCTTGGTCCCTCTAAGTGT 59.015 55.000 0.00 0.00 37.05 3.55
3440 3509 2.046892 GTCATGCACCGGTCAGCT 60.047 61.111 16.94 1.49 0.00 4.24
3481 3550 7.769220 AGGAAATAATCACTCAATTTGCTCAG 58.231 34.615 0.00 0.00 36.83 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 9.823647 CTCTGGAAGATAATTTATACACTGTGT 57.176 33.333 18.51 18.51 45.62 3.72
101 102 6.773976 TTGGTTTTTCAAGAACATGAGAGT 57.226 33.333 0.00 0.00 0.00 3.24
131 132 4.501571 GGTTCACTCGCCATAGACATACAT 60.502 45.833 0.00 0.00 0.00 2.29
141 142 1.522569 GCTAGGGTTCACTCGCCAT 59.477 57.895 0.00 0.00 0.00 4.40
185 186 1.999634 AATGAAGATGAGGCCCCGGG 62.000 60.000 15.80 15.80 0.00 5.73
276 277 1.021390 GTCGAGTTCGGGACCTACGA 61.021 60.000 1.26 0.00 40.29 3.43
311 312 3.306019 GGGTTCGAAAAAGTCATGGCATT 60.306 43.478 0.00 0.00 0.00 3.56
357 360 2.679349 GCTTCTAGGGTTCCTGCAAGAG 60.679 54.545 9.54 0.00 34.07 2.85
429 444 0.034767 TTCCCTAGTCCTTCGCTCGA 60.035 55.000 0.00 0.00 0.00 4.04
480 497 3.592814 CGATCTAGGTCGCCGCCA 61.593 66.667 13.32 0.00 34.56 5.69
526 543 2.346803 CACATGATCCGAACGTTTCCT 58.653 47.619 0.46 0.00 0.00 3.36
533 550 1.209128 CGCTACCACATGATCCGAAC 58.791 55.000 0.00 0.00 0.00 3.95
534 551 0.529773 GCGCTACCACATGATCCGAA 60.530 55.000 0.00 0.00 0.00 4.30
535 552 1.067416 GCGCTACCACATGATCCGA 59.933 57.895 0.00 0.00 0.00 4.55
536 553 1.217585 CTGCGCTACCACATGATCCG 61.218 60.000 9.73 0.00 0.00 4.18
537 554 1.502163 GCTGCGCTACCACATGATCC 61.502 60.000 9.73 0.00 0.00 3.36
538 555 1.825285 CGCTGCGCTACCACATGATC 61.825 60.000 9.88 0.00 0.00 2.92
539 556 1.884464 CGCTGCGCTACCACATGAT 60.884 57.895 9.88 0.00 0.00 2.45
540 557 2.509111 CGCTGCGCTACCACATGA 60.509 61.111 9.88 0.00 0.00 3.07
541 558 3.566853 CCGCTGCGCTACCACATG 61.567 66.667 18.00 0.00 0.00 3.21
553 570 4.067913 AAATTTGGGCGGCCGCTG 62.068 61.111 45.23 11.42 41.60 5.18
554 571 4.067913 CAAATTTGGGCGGCCGCT 62.068 61.111 45.23 26.44 41.60 5.52
579 596 1.654743 GAGTGATACTCGCCGACGC 60.655 63.158 0.00 0.00 35.28 5.19
580 597 1.009900 GGAGTGATACTCGCCGACG 60.010 63.158 3.17 0.00 45.96 5.12
581 598 0.739561 AAGGAGTGATACTCGCCGAC 59.260 55.000 3.17 0.00 45.96 4.79
582 599 1.471119 AAAGGAGTGATACTCGCCGA 58.529 50.000 3.17 0.00 45.96 5.54
583 600 2.295253 AAAAGGAGTGATACTCGCCG 57.705 50.000 3.17 0.00 45.96 6.46
623 645 2.584261 ATCCATTCGCAGTCGCAGCT 62.584 55.000 0.00 0.00 38.40 4.24
625 647 0.855349 GTATCCATTCGCAGTCGCAG 59.145 55.000 0.00 0.00 38.40 5.18
626 648 0.174617 TGTATCCATTCGCAGTCGCA 59.825 50.000 0.00 0.00 38.40 5.10
628 650 4.030641 CGATAATGTATCCATTCGCAGTCG 59.969 45.833 0.00 0.00 41.50 4.18
629 651 4.923871 ACGATAATGTATCCATTCGCAGTC 59.076 41.667 0.00 0.00 41.50 3.51
630 652 4.686091 CACGATAATGTATCCATTCGCAGT 59.314 41.667 0.00 0.00 41.50 4.40
650 672 3.815401 CCTGAAAATAGATTAGGCCCACG 59.185 47.826 0.00 0.00 0.00 4.94
713 737 7.342284 CCCACGATATCTAATACTCCTACCAAT 59.658 40.741 0.34 0.00 0.00 3.16
714 738 6.662234 CCCACGATATCTAATACTCCTACCAA 59.338 42.308 0.34 0.00 0.00 3.67
715 739 6.185511 CCCACGATATCTAATACTCCTACCA 58.814 44.000 0.34 0.00 0.00 3.25
716 740 5.067544 GCCCACGATATCTAATACTCCTACC 59.932 48.000 0.34 0.00 0.00 3.18
717 741 5.067544 GGCCCACGATATCTAATACTCCTAC 59.932 48.000 0.34 0.00 0.00 3.18
718 742 5.198965 GGCCCACGATATCTAATACTCCTA 58.801 45.833 0.34 0.00 0.00 2.94
762 786 2.182030 CCCTCGTTCCTCTCGTGC 59.818 66.667 0.00 0.00 0.00 5.34
916 944 2.725312 GGTCGGAGATGAGGCAGCA 61.725 63.158 0.00 0.00 40.67 4.41
990 1018 1.067142 CGAGGACCCATGTCGAAGAAA 60.067 52.381 0.00 0.00 42.73 2.52
1119 1147 1.080093 GATGACGAACACGAGGCCA 60.080 57.895 5.01 0.00 0.00 5.36
1212 1240 5.102953 TCCTGTTCAGATGTCCCATTAAG 57.897 43.478 1.00 0.00 0.00 1.85
1274 1302 0.542702 AACCACCTGGAAATGCTGGG 60.543 55.000 0.00 0.00 38.94 4.45
1297 1325 5.008331 GTCATAATCATCATCTGCCACCAT 58.992 41.667 0.00 0.00 0.00 3.55
1311 1339 3.812262 CCTGTCCTGCATGTCATAATCA 58.188 45.455 0.00 0.00 0.00 2.57
1537 1565 0.672342 GGTGTCGGTATCACGGCTAT 59.328 55.000 0.00 0.00 39.61 2.97
1629 1657 3.002759 CGCAGAAGTCTATCACGATGAGA 59.997 47.826 0.00 0.00 0.00 3.27
1824 1861 5.718607 TGACTCAAGATGAATCAGGAAGAGA 59.281 40.000 10.89 0.00 26.54 3.10
1928 1965 6.530019 TCTGAGATGTGTAAAGACATGCTA 57.470 37.500 0.00 0.00 36.67 3.49
1929 1966 5.411831 TCTGAGATGTGTAAAGACATGCT 57.588 39.130 0.00 0.00 36.67 3.79
2036 2076 6.194796 TGTTAGCTTAACATGAAAGGATGC 57.805 37.500 0.00 0.00 43.23 3.91
2187 2228 6.421501 GCTGTGTATCTCATTCTCATCTTGAG 59.578 42.308 0.00 0.00 45.59 3.02
2188 2229 6.097981 AGCTGTGTATCTCATTCTCATCTTGA 59.902 38.462 0.00 0.00 0.00 3.02
2189 2230 6.282167 AGCTGTGTATCTCATTCTCATCTTG 58.718 40.000 0.00 0.00 0.00 3.02
2191 2232 6.482898 AAGCTGTGTATCTCATTCTCATCT 57.517 37.500 0.00 0.00 0.00 2.90
2192 2233 7.516470 CGAAAAGCTGTGTATCTCATTCTCATC 60.516 40.741 0.00 0.00 0.00 2.92
2193 2234 6.257411 CGAAAAGCTGTGTATCTCATTCTCAT 59.743 38.462 0.00 0.00 0.00 2.90
2194 2235 5.578336 CGAAAAGCTGTGTATCTCATTCTCA 59.422 40.000 0.00 0.00 0.00 3.27
2195 2236 5.807520 TCGAAAAGCTGTGTATCTCATTCTC 59.192 40.000 0.00 0.00 0.00 2.87
2196 2237 5.724328 TCGAAAAGCTGTGTATCTCATTCT 58.276 37.500 0.00 0.00 0.00 2.40
2197 2238 6.091441 ACTTCGAAAAGCTGTGTATCTCATTC 59.909 38.462 0.00 0.00 35.81 2.67
2198 2239 5.934625 ACTTCGAAAAGCTGTGTATCTCATT 59.065 36.000 0.00 0.00 35.81 2.57
2211 2252 7.851822 TTTCATGTAATCAACTTCGAAAAGC 57.148 32.000 0.00 0.00 35.81 3.51
2306 2348 2.364324 GCTTGTCCTACACCATATCGGA 59.636 50.000 0.00 0.00 38.63 4.55
2308 2350 3.735237 AGCTTGTCCTACACCATATCG 57.265 47.619 0.00 0.00 0.00 2.92
2309 2351 6.817184 TCTTAAGCTTGTCCTACACCATATC 58.183 40.000 9.86 0.00 0.00 1.63
2385 2427 9.838975 CACATGTTTCTACAAGCATAATAACAA 57.161 29.630 0.00 0.00 37.91 2.83
2386 2428 9.008965 ACACATGTTTCTACAAGCATAATAACA 57.991 29.630 0.00 0.00 37.91 2.41
2387 2429 9.840427 AACACATGTTTCTACAAGCATAATAAC 57.160 29.630 0.00 0.00 37.91 1.89
2388 2430 9.838975 CAACACATGTTTCTACAAGCATAATAA 57.161 29.630 0.00 0.00 37.91 1.40
2747 2791 8.642935 TTATTAATTCACACTTCCATTGGTCA 57.357 30.769 1.86 0.00 0.00 4.02
2777 2821 1.614903 CTCAAGCAAGGGATTGTGCAA 59.385 47.619 0.00 0.00 43.42 4.08
2878 2922 8.447833 CACTAAACAATCGGCTTTGATAAAGTA 58.552 33.333 4.34 0.00 40.64 2.24
2966 3014 9.016623 GGTTAATTAAAAGAACAGTTGACACAC 57.983 33.333 0.00 0.00 0.00 3.82
2974 3022 7.719633 TGAGCAGAGGTTAATTAAAAGAACAGT 59.280 33.333 0.00 0.00 0.00 3.55
2996 3044 3.465742 TTGGCTACATCTGATCTGAGC 57.534 47.619 8.37 5.85 0.00 4.26
3046 3099 7.012515 CCTTCAACTTCGAATACTAGCTCTCTA 59.987 40.741 0.00 0.00 0.00 2.43
3061 3114 0.232303 GTCACACGCCTTCAACTTCG 59.768 55.000 0.00 0.00 0.00 3.79
3073 3126 6.044512 AGCAACTTTTAGTTTAGTCACACG 57.955 37.500 0.00 0.00 36.03 4.49
3101 3154 8.691797 ACTTTTAGTTTGGCTCTGATACAAAAA 58.308 29.630 8.01 0.30 36.05 1.94
3102 3155 8.232913 ACTTTTAGTTTGGCTCTGATACAAAA 57.767 30.769 8.01 0.00 36.05 2.44
3103 3156 7.817418 ACTTTTAGTTTGGCTCTGATACAAA 57.183 32.000 3.66 3.66 0.00 2.83
3104 3157 7.648142 CAACTTTTAGTTTGGCTCTGATACAA 58.352 34.615 0.00 0.00 36.03 2.41
3105 3158 6.293955 GCAACTTTTAGTTTGGCTCTGATACA 60.294 38.462 0.00 0.00 36.03 2.29
3106 3159 6.072452 AGCAACTTTTAGTTTGGCTCTGATAC 60.072 38.462 0.00 0.00 33.78 2.24
3107 3160 6.003950 AGCAACTTTTAGTTTGGCTCTGATA 58.996 36.000 0.00 0.00 33.78 2.15
3108 3161 4.829492 AGCAACTTTTAGTTTGGCTCTGAT 59.171 37.500 0.00 0.00 33.78 2.90
3109 3162 4.207165 AGCAACTTTTAGTTTGGCTCTGA 58.793 39.130 0.00 0.00 33.78 3.27
3110 3163 4.574599 AGCAACTTTTAGTTTGGCTCTG 57.425 40.909 0.00 0.00 33.78 3.35
3111 3164 6.709018 TTAAGCAACTTTTAGTTTGGCTCT 57.291 33.333 5.28 1.16 36.73 4.09
3112 3165 6.923508 ACATTAAGCAACTTTTAGTTTGGCTC 59.076 34.615 5.28 0.00 36.73 4.70
3113 3166 6.816136 ACATTAAGCAACTTTTAGTTTGGCT 58.184 32.000 0.00 0.00 38.57 4.75
3114 3167 7.011016 ACAACATTAAGCAACTTTTAGTTTGGC 59.989 33.333 0.00 0.00 36.03 4.52
3115 3168 8.419076 ACAACATTAAGCAACTTTTAGTTTGG 57.581 30.769 0.00 0.00 36.03 3.28
3155 3208 5.316167 TCAGCATCACTAGACAAAACCAAT 58.684 37.500 0.00 0.00 0.00 3.16
3184 3237 2.030823 GCCAAAAGCTGCAAAGTTGAAC 59.969 45.455 1.02 0.00 38.99 3.18
3204 3257 6.813152 AGCTTCACCATTTGTGTAAATTATGC 59.187 34.615 0.00 0.00 45.61 3.14
3207 3260 9.853555 CATTAGCTTCACCATTTGTGTAAATTA 57.146 29.630 0.00 0.00 45.61 1.40
3270 3330 6.785076 TGTACTATTCATTCAGGAAAACCCA 58.215 36.000 0.00 0.00 37.41 4.51
3296 3356 7.865385 GCAAGTAATACCATCAGTCAAACAAAA 59.135 33.333 0.00 0.00 0.00 2.44
3371 3440 5.723672 TTGGTAGAACCTAGACTGAACAG 57.276 43.478 0.00 0.00 39.58 3.16
3424 3493 2.046988 CAGCTGACCGGTGCATGA 60.047 61.111 14.63 0.00 33.91 3.07
3440 3509 8.877864 ATTATTTCCTACAAGTCCAATTCACA 57.122 30.769 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.