Multiple sequence alignment - TraesCS1D01G247500

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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 TraesCS1D01G247500 chr1D 100.000 3815 0 0 1 3815 340526258 340522444 0.000000e+00 7046.0
1 TraesCS1D01G247500 chr1A 95.119 2991 103 18 735 3693 440074878 440071899 0.000000e+00 4674.0
2 TraesCS1D01G247500 chr1A 87.737 685 67 13 1 681 440075548 440074877 0.000000e+00 784.0
3 TraesCS1D01G247500 chr1A 91.667 120 5 1 3696 3815 440071834 440071720 1.100000e-35 161.0
4 TraesCS1D01G247500 chr1A 90.698 43 3 1 126 167 477733609 477733651 5.320000e-04 56.5
5 TraesCS1D01G247500 chr1B 95.780 2867 96 10 753 3608 455986196 455983344 0.000000e+00 4601.0
6 TraesCS1D01G247500 chr1B 85.361 485 44 9 3 463 455986662 455986181 9.590000e-131 477.0
7 TraesCS1D01G247500 chr1B 99.167 120 1 0 3696 3815 455983110 455982991 2.310000e-52 217.0
8 TraesCS1D01G247500 chr1B 100.000 28 0 0 140 167 57019498 57019525 7.000000e-03 52.8
9 TraesCS1D01G247500 chr6D 74.675 308 65 8 461 758 99799437 99799133 1.440000e-24 124.0
10 TraesCS1D01G247500 chr7B 85.965 114 13 3 3532 3644 700753233 700753344 6.690000e-23 119.0
11 TraesCS1D01G247500 chr4B 85.714 112 13 3 3534 3644 667029417 667029308 8.660000e-22 115.0
12 TraesCS1D01G247500 chr2B 85.714 112 13 3 3534 3644 9325413 9325304 8.660000e-22 115.0
13 TraesCS1D01G247500 chr6B 86.170 94 10 3 470 561 523878910 523878818 8.720000e-17 99.0
14 TraesCS1D01G247500 chr4A 76.042 192 28 10 581 757 577499987 577500175 2.440000e-12 84.2
15 TraesCS1D01G247500 chr4A 100.000 29 0 0 140 168 583526517 583526489 2.000000e-03 54.7
16 TraesCS1D01G247500 chr7D 100.000 29 0 0 140 168 549514194 549514222 2.000000e-03 54.7
17 TraesCS1D01G247500 chr5A 100.000 28 0 0 3139 3166 609244294 609244267 7.000000e-03 52.8
18 TraesCS1D01G247500 chr3B 88.636 44 3 2 140 183 431583474 431583433 7.000000e-03 52.8
19 TraesCS1D01G247500 chr3A 100.000 28 0 0 140 167 450013252 450013225 7.000000e-03 52.8


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 TraesCS1D01G247500 chr1D 340522444 340526258 3814 True 7046 7046 100.000000 1 3815 1 chr1D.!!$R1 3814
1 TraesCS1D01G247500 chr1A 440071720 440075548 3828 True 1873 4674 91.507667 1 3815 3 chr1A.!!$R1 3814
2 TraesCS1D01G247500 chr1B 455982991 455986662 3671 True 1765 4601 93.436000 3 3815 3 chr1B.!!$R1 3812

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
751 777 0.039798 GCGTCTGTACCGTGTCAAGA 60.040 55.0 0.00 0.00 0.00 3.02 F
2364 2406 0.467474 TAGGCGATGATCGTGTCCCT 60.467 55.0 16.83 15.47 42.81 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2376 2418 0.907486 CATGGAGGCCAGAGTTCAGA 59.093 55.0 5.01 0.0 36.75 3.27 R
3613 3681 0.105760 AGGCCAACAACCATGAACCA 60.106 50.0 5.01 0.0 0.00 3.67 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
24 25 0.321021 TGGTGGCATCAATTGGTTGC 59.679 50.000 19.78 19.78 35.26 4.17
134 135 6.907212 GTGACATAATTCCTGCGTATCAAAAG 59.093 38.462 0.00 0.00 0.00 2.27
135 136 6.038161 TGACATAATTCCTGCGTATCAAAAGG 59.962 38.462 0.00 0.00 0.00 3.11
225 248 2.650322 ACGACAAAGGGACAAACACAT 58.350 42.857 0.00 0.00 0.00 3.21
268 291 5.821516 TTTTAACCATGAACTGAACGTGT 57.178 34.783 0.00 0.00 0.00 4.49
277 300 5.804692 TGAACTGAACGTGTGTAAACAAT 57.195 34.783 0.00 0.00 0.00 2.71
278 301 5.564768 TGAACTGAACGTGTGTAAACAATG 58.435 37.500 0.00 0.00 0.00 2.82
279 302 5.122554 TGAACTGAACGTGTGTAAACAATGT 59.877 36.000 0.00 0.00 0.00 2.71
280 303 5.151632 ACTGAACGTGTGTAAACAATGTC 57.848 39.130 0.00 0.00 0.00 3.06
281 304 4.632251 ACTGAACGTGTGTAAACAATGTCA 59.368 37.500 0.00 0.00 0.00 3.58
282 305 4.899516 TGAACGTGTGTAAACAATGTCAC 58.100 39.130 0.00 0.00 0.00 3.67
287 310 2.032302 TGTGTAAACAATGTCACACGCC 59.968 45.455 19.48 4.43 43.30 5.68
295 318 1.800805 ATGTCACACGCCTTTCTCTG 58.199 50.000 0.00 0.00 0.00 3.35
297 320 1.684450 TGTCACACGCCTTTCTCTGTA 59.316 47.619 0.00 0.00 0.00 2.74
310 333 7.104290 GCCTTTCTCTGTACAAATACTACCTT 58.896 38.462 0.00 0.00 32.00 3.50
311 334 7.278203 GCCTTTCTCTGTACAAATACTACCTTC 59.722 40.741 0.00 0.00 32.00 3.46
398 421 4.141711 TGGAGGGAGTATAACATTCTGCAC 60.142 45.833 0.00 0.00 0.00 4.57
419 444 5.471456 GCACAGAAAGAAAGGAGAATCTCAA 59.529 40.000 12.79 0.00 33.73 3.02
438 463 1.048724 ATCCCATGTCCATCCGACGT 61.049 55.000 0.00 0.00 45.23 4.34
454 479 3.120095 CCGACGTCTCCAAATAAAAACCC 60.120 47.826 14.70 0.00 0.00 4.11
456 481 2.815503 ACGTCTCCAAATAAAAACCCCG 59.184 45.455 0.00 0.00 0.00 5.73
477 502 0.106918 AAAGCGGAACCAACCTGTGA 60.107 50.000 0.00 0.00 0.00 3.58
492 517 5.041191 ACCTGTGATTGGATGATTAGGAC 57.959 43.478 0.00 0.00 0.00 3.85
493 518 4.474651 ACCTGTGATTGGATGATTAGGACA 59.525 41.667 0.00 0.00 0.00 4.02
507 532 7.379059 TGATTAGGACAACAGTGATATCCAT 57.621 36.000 0.09 0.00 31.41 3.41
509 534 8.588472 TGATTAGGACAACAGTGATATCCATAG 58.412 37.037 0.09 0.00 31.41 2.23
528 553 0.178990 GCCCACCAAGGTTCAAGTCT 60.179 55.000 0.00 0.00 34.66 3.24
529 554 1.609208 CCCACCAAGGTTCAAGTCTG 58.391 55.000 0.00 0.00 34.66 3.51
531 556 1.609208 CACCAAGGTTCAAGTCTGGG 58.391 55.000 0.00 0.00 0.00 4.45
546 571 3.019564 GTCTGGGTGCTTGCATTTATCT 58.980 45.455 0.00 0.00 0.00 1.98
548 573 4.640201 GTCTGGGTGCTTGCATTTATCTTA 59.360 41.667 0.00 0.00 0.00 2.10
550 575 5.714333 TCTGGGTGCTTGCATTTATCTTAAA 59.286 36.000 0.00 0.00 0.00 1.52
553 578 7.393216 TGGGTGCTTGCATTTATCTTAAATTT 58.607 30.769 0.00 0.00 0.00 1.82
554 579 8.535335 TGGGTGCTTGCATTTATCTTAAATTTA 58.465 29.630 0.00 0.00 0.00 1.40
555 580 9.546428 GGGTGCTTGCATTTATCTTAAATTTAT 57.454 29.630 0.00 0.00 0.00 1.40
601 626 3.812156 TCAGTGAAAGGAGACGTTTCA 57.188 42.857 8.50 13.13 40.73 2.69
622 648 3.770263 TCGACTACGAGGTGTTTATGG 57.230 47.619 0.00 0.00 43.81 2.74
623 649 3.084039 TCGACTACGAGGTGTTTATGGT 58.916 45.455 0.00 0.00 43.81 3.55
624 650 3.119743 TCGACTACGAGGTGTTTATGGTG 60.120 47.826 0.00 0.00 43.81 4.17
639 665 8.287503 GTGTTTATGGTGTCTTCGTAAAATCTT 58.712 33.333 0.00 0.00 30.40 2.40
672 698 1.667724 CGGCTTTGAGGTGCTCATAAG 59.332 52.381 0.00 0.00 40.39 1.73
676 702 2.787473 TTGAGGTGCTCATAAGGGTG 57.213 50.000 0.00 0.00 40.39 4.61
679 705 1.139853 GAGGTGCTCATAAGGGTGGAG 59.860 57.143 0.00 0.00 0.00 3.86
680 706 0.912486 GGTGCTCATAAGGGTGGAGT 59.088 55.000 0.00 0.00 0.00 3.85
681 707 1.282157 GGTGCTCATAAGGGTGGAGTT 59.718 52.381 0.00 0.00 0.00 3.01
682 708 2.504175 GGTGCTCATAAGGGTGGAGTTA 59.496 50.000 0.00 0.00 0.00 2.24
683 709 3.532542 GTGCTCATAAGGGTGGAGTTAC 58.467 50.000 0.00 0.00 0.00 2.50
684 710 2.167693 TGCTCATAAGGGTGGAGTTACG 59.832 50.000 0.00 0.00 0.00 3.18
685 711 2.167900 GCTCATAAGGGTGGAGTTACGT 59.832 50.000 0.00 0.00 0.00 3.57
686 712 3.782046 CTCATAAGGGTGGAGTTACGTG 58.218 50.000 0.00 0.00 0.00 4.49
687 713 3.167485 TCATAAGGGTGGAGTTACGTGT 58.833 45.455 0.00 0.00 0.00 4.49
688 714 3.056393 TCATAAGGGTGGAGTTACGTGTG 60.056 47.826 0.00 0.00 0.00 3.82
689 715 0.250166 AAGGGTGGAGTTACGTGTGC 60.250 55.000 0.00 0.00 0.00 4.57
690 716 2.025418 GGGTGGAGTTACGTGTGCG 61.025 63.158 0.00 0.00 44.93 5.34
691 717 2.664436 GGTGGAGTTACGTGTGCGC 61.664 63.158 0.00 0.00 42.83 6.09
692 718 1.952133 GTGGAGTTACGTGTGCGCA 60.952 57.895 5.66 5.66 42.83 6.09
693 719 1.005512 TGGAGTTACGTGTGCGCAT 60.006 52.632 15.91 0.00 42.83 4.73
694 720 0.601576 TGGAGTTACGTGTGCGCATT 60.602 50.000 15.91 0.51 42.83 3.56
695 721 0.094730 GGAGTTACGTGTGCGCATTC 59.905 55.000 15.91 9.17 42.83 2.67
696 722 0.787787 GAGTTACGTGTGCGCATTCA 59.212 50.000 15.91 4.58 42.83 2.57
697 723 1.393539 GAGTTACGTGTGCGCATTCAT 59.606 47.619 15.91 2.47 42.83 2.57
698 724 2.601314 GAGTTACGTGTGCGCATTCATA 59.399 45.455 15.91 1.33 42.83 2.15
699 725 2.997303 AGTTACGTGTGCGCATTCATAA 59.003 40.909 15.91 8.20 42.83 1.90
700 726 3.433957 AGTTACGTGTGCGCATTCATAAA 59.566 39.130 15.91 1.26 42.83 1.40
701 727 2.979401 ACGTGTGCGCATTCATAAAA 57.021 40.000 15.91 0.00 42.83 1.52
702 728 3.275400 ACGTGTGCGCATTCATAAAAA 57.725 38.095 15.91 0.00 42.83 1.94
703 729 3.832276 ACGTGTGCGCATTCATAAAAAT 58.168 36.364 15.91 0.00 42.83 1.82
704 730 3.607641 ACGTGTGCGCATTCATAAAAATG 59.392 39.130 15.91 0.00 42.83 2.32
705 731 3.850837 CGTGTGCGCATTCATAAAAATGA 59.149 39.130 15.91 0.00 38.64 2.57
706 732 4.028268 CGTGTGCGCATTCATAAAAATGAG 60.028 41.667 15.91 0.00 38.64 2.90
707 733 4.858692 GTGTGCGCATTCATAAAAATGAGT 59.141 37.500 15.91 0.00 38.64 3.41
708 734 4.858140 TGTGCGCATTCATAAAAATGAGTG 59.142 37.500 15.91 6.53 38.64 3.51
709 735 4.858692 GTGCGCATTCATAAAAATGAGTGT 59.141 37.500 15.91 0.00 39.53 3.55
710 736 6.027131 GTGCGCATTCATAAAAATGAGTGTA 58.973 36.000 15.91 0.00 39.53 2.90
711 737 6.692681 GTGCGCATTCATAAAAATGAGTGTAT 59.307 34.615 15.91 0.00 39.53 2.29
712 738 6.692249 TGCGCATTCATAAAAATGAGTGTATG 59.308 34.615 5.66 3.99 39.53 2.39
713 739 6.345250 GCGCATTCATAAAAATGAGTGTATGC 60.345 38.462 0.30 10.82 39.53 3.14
714 740 7.085797 GCATTCATAAAAATGAGTGTATGCG 57.914 36.000 11.10 0.00 39.53 4.73
715 741 6.345250 GCATTCATAAAAATGAGTGTATGCGC 60.345 38.462 0.00 0.00 39.53 6.09
716 742 5.809719 TCATAAAAATGAGTGTATGCGCA 57.190 34.783 14.96 14.96 0.00 6.09
717 743 6.375945 TCATAAAAATGAGTGTATGCGCAT 57.624 33.333 28.23 28.23 0.00 4.73
718 744 6.794374 TCATAAAAATGAGTGTATGCGCATT 58.206 32.000 30.42 10.67 39.82 3.56
719 745 7.257003 TCATAAAAATGAGTGTATGCGCATTT 58.743 30.769 30.42 15.35 45.81 2.32
720 746 8.401709 TCATAAAAATGAGTGTATGCGCATTTA 58.598 29.630 30.42 17.05 44.11 1.40
721 747 9.184062 CATAAAAATGAGTGTATGCGCATTTAT 57.816 29.630 30.42 18.48 44.11 1.40
726 752 9.825972 AAATGAGTGTATGCGCATTTATATAAC 57.174 29.630 30.42 18.67 43.46 1.89
727 753 7.359262 TGAGTGTATGCGCATTTATATAACC 57.641 36.000 30.42 11.97 0.00 2.85
728 754 6.090223 TGAGTGTATGCGCATTTATATAACCG 59.910 38.462 30.42 0.43 0.00 4.44
729 755 5.019498 GTGTATGCGCATTTATATAACCGC 58.981 41.667 30.42 19.46 41.55 5.68
732 758 4.077063 TGCGCATTTATATAACCGCATG 57.923 40.909 22.66 13.49 45.21 4.06
733 759 2.845967 GCGCATTTATATAACCGCATGC 59.154 45.455 20.54 18.10 40.94 4.06
742 768 0.458889 TAACCGCATGCGTCTGTACC 60.459 55.000 35.55 0.00 37.81 3.34
748 774 0.388006 CATGCGTCTGTACCGTGTCA 60.388 55.000 0.00 0.00 0.00 3.58
750 776 0.318360 TGCGTCTGTACCGTGTCAAG 60.318 55.000 0.00 0.00 0.00 3.02
751 777 0.039798 GCGTCTGTACCGTGTCAAGA 60.040 55.000 0.00 0.00 0.00 3.02
1174 1216 4.493747 CCTTCCTCGGCGTCGTCC 62.494 72.222 10.18 0.00 37.69 4.79
1317 1359 4.021925 GACCCCACCAGCTTCGCT 62.022 66.667 0.00 0.00 40.77 4.93
1815 1857 1.134367 CGCATTCCTCTACTGTTCCGA 59.866 52.381 0.00 0.00 0.00 4.55
1922 1964 2.029073 CAGGAACGACAGGTGCGT 59.971 61.111 0.00 0.00 44.94 5.24
2211 2253 2.983977 CTTCGACGCCGTGTTCACG 61.984 63.158 16.87 16.87 37.05 4.35
2346 2388 3.259876 AGCTTGTCCGGTCATACTTTGTA 59.740 43.478 1.21 0.00 0.00 2.41
2364 2406 0.467474 TAGGCGATGATCGTGTCCCT 60.467 55.000 16.83 15.47 42.81 4.20
2376 2418 2.038426 TCGTGTCCCTGATGTTGTCATT 59.962 45.455 0.00 0.00 35.97 2.57
2439 2481 1.447838 CGCATACGTTCAGGCCACT 60.448 57.895 5.01 0.00 33.53 4.00
2778 2820 1.557099 ACTTCGTGGACCTCATGCTA 58.443 50.000 0.00 0.00 32.54 3.49
2848 2890 1.135689 CCATGCTCGGTAAGTTTGTGC 60.136 52.381 0.00 0.00 0.00 4.57
2849 2891 1.535028 CATGCTCGGTAAGTTTGTGCA 59.465 47.619 0.00 0.00 0.00 4.57
2901 2943 0.532862 CACGGAACTGAGGTTGCTGT 60.533 55.000 0.00 0.00 40.81 4.40
3020 3062 4.630111 GCTGTTATGATCTTGCTCTAGCT 58.370 43.478 3.26 0.00 42.66 3.32
3060 3106 0.242555 GATCAGAGCTAGCTACGGGC 59.757 60.000 19.38 4.54 42.19 6.13
3197 3251 0.682292 TGTGGTCTGTGAACGGCATA 59.318 50.000 0.00 0.00 0.00 3.14
3264 3318 2.411628 TATGTTCCGGGTTGATGTGG 57.588 50.000 0.00 0.00 0.00 4.17
3267 3321 0.879090 GTTCCGGGTTGATGTGGTTC 59.121 55.000 0.00 0.00 0.00 3.62
3273 3327 1.156736 GGTTGATGTGGTTCGAGTGG 58.843 55.000 0.00 0.00 0.00 4.00
3325 3379 0.254178 CCAGGGGGTGTCTTGATGAG 59.746 60.000 0.00 0.00 0.00 2.90
3358 3412 6.609212 AGAGCTAAGTTGTCTTGATCAGGATA 59.391 38.462 11.08 5.43 35.36 2.59
3481 3535 3.889815 CATGACAATTGGAGGAGCCTTA 58.110 45.455 10.83 0.00 37.63 2.69
3548 3616 4.291783 CGTAGCCAGTAATCTTACTCTGC 58.708 47.826 10.83 10.83 41.82 4.26
3608 3676 3.372822 CCAAATGCAGAAATGCCAACATC 59.627 43.478 0.00 0.00 34.62 3.06
3609 3677 3.965379 AATGCAGAAATGCCAACATCA 57.035 38.095 0.00 0.00 34.62 3.07
3610 3678 3.965379 ATGCAGAAATGCCAACATCAA 57.035 38.095 0.00 0.00 34.62 2.57
3611 3679 3.029320 TGCAGAAATGCCAACATCAAC 57.971 42.857 0.00 0.00 34.62 3.18
3612 3680 2.364647 TGCAGAAATGCCAACATCAACA 59.635 40.909 0.00 0.00 34.62 3.33
3613 3681 3.007074 TGCAGAAATGCCAACATCAACAT 59.993 39.130 0.00 0.00 34.62 2.71
3628 3696 4.319139 TCAACATGGTTCATGGTTGTTG 57.681 40.909 11.85 15.02 38.83 3.33
3644 3712 0.467290 GTTGGCCTTGAGGTGAACCA 60.467 55.000 3.32 0.00 38.89 3.67
3645 3713 0.178992 TTGGCCTTGAGGTGAACCAG 60.179 55.000 3.32 0.00 38.89 4.00
3649 3717 2.152016 GCCTTGAGGTGAACCAGTTAC 58.848 52.381 1.62 0.00 38.89 2.50
3650 3718 2.486548 GCCTTGAGGTGAACCAGTTACA 60.487 50.000 1.62 0.00 38.89 2.41
3651 3719 3.403038 CCTTGAGGTGAACCAGTTACAG 58.597 50.000 1.62 0.00 38.89 2.74
3654 3722 5.280011 CCTTGAGGTGAACCAGTTACAGTAT 60.280 44.000 1.62 0.00 38.89 2.12
3658 3728 3.307480 GGTGAACCAGTTACAGTATGCCT 60.307 47.826 0.00 0.00 35.98 4.75
3671 3741 4.080919 ACAGTATGCCTATTGAGTGAAGCA 60.081 41.667 0.00 0.00 42.53 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.737019 CGCAACCAATTGATGCCACC 60.737 55.000 22.43 4.46 38.15 4.61
24 25 8.018677 AGAGTTTGTTGTGATATTGTTAGACG 57.981 34.615 0.00 0.00 0.00 4.18
81 82 7.183433 GCTTAGTATGCTCTTGCTAGTTTTTC 58.817 38.462 0.88 0.00 40.48 2.29
134 135 8.454570 TCCCTCCGTATCAAAATATAAAAACC 57.545 34.615 0.00 0.00 0.00 3.27
135 136 9.117183 ACTCCCTCCGTATCAAAATATAAAAAC 57.883 33.333 0.00 0.00 0.00 2.43
248 271 4.193090 ACACACGTTCAGTTCATGGTTAA 58.807 39.130 0.00 0.00 0.00 2.01
268 291 2.566913 AGGCGTGTGACATTGTTTACA 58.433 42.857 0.00 4.35 0.00 2.41
277 300 0.464036 ACAGAGAAAGGCGTGTGACA 59.536 50.000 0.00 0.00 0.00 3.58
278 301 2.059541 GTACAGAGAAAGGCGTGTGAC 58.940 52.381 0.00 0.00 0.00 3.67
279 302 1.684450 TGTACAGAGAAAGGCGTGTGA 59.316 47.619 0.00 0.00 0.00 3.58
280 303 2.148916 TGTACAGAGAAAGGCGTGTG 57.851 50.000 0.00 0.00 0.00 3.82
281 304 2.902705 TTGTACAGAGAAAGGCGTGT 57.097 45.000 0.00 0.00 0.00 4.49
282 305 4.929808 AGTATTTGTACAGAGAAAGGCGTG 59.070 41.667 0.00 0.00 0.00 5.34
284 307 5.519206 GGTAGTATTTGTACAGAGAAAGGCG 59.481 44.000 0.00 0.00 0.00 5.52
287 310 9.877178 ATGAAGGTAGTATTTGTACAGAGAAAG 57.123 33.333 0.00 0.00 0.00 2.62
375 398 4.037222 TGCAGAATGTTATACTCCCTCCA 58.963 43.478 0.00 0.00 39.31 3.86
398 421 6.318396 GGGATTGAGATTCTCCTTTCTTTCTG 59.682 42.308 11.12 0.00 0.00 3.02
404 427 5.444176 ACATGGGATTGAGATTCTCCTTTC 58.556 41.667 11.12 5.38 0.00 2.62
408 431 3.137176 TGGACATGGGATTGAGATTCTCC 59.863 47.826 11.12 0.00 0.00 3.71
410 433 4.202545 GGATGGACATGGGATTGAGATTCT 60.203 45.833 0.00 0.00 0.00 2.40
411 434 4.077822 GGATGGACATGGGATTGAGATTC 58.922 47.826 0.00 0.00 0.00 2.52
419 444 1.048724 ACGTCGGATGGACATGGGAT 61.049 55.000 0.00 0.00 46.42 3.85
438 463 5.510009 GCTTTTCGGGGTTTTTATTTGGAGA 60.510 40.000 0.00 0.00 0.00 3.71
456 481 1.029681 ACAGGTTGGTTCCGCTTTTC 58.970 50.000 0.00 0.00 0.00 2.29
471 496 5.039920 TGTCCTAATCATCCAATCACAGG 57.960 43.478 0.00 0.00 0.00 4.00
477 502 6.065976 TCACTGTTGTCCTAATCATCCAAT 57.934 37.500 0.00 0.00 0.00 3.16
485 510 7.390027 GCTATGGATATCACTGTTGTCCTAAT 58.610 38.462 4.83 0.00 0.00 1.73
492 517 4.067896 GTGGGCTATGGATATCACTGTTG 58.932 47.826 4.83 0.00 0.00 3.33
493 518 3.073062 GGTGGGCTATGGATATCACTGTT 59.927 47.826 4.83 0.00 0.00 3.16
507 532 1.073284 GACTTGAACCTTGGTGGGCTA 59.927 52.381 0.00 0.00 41.11 3.93
509 534 0.178990 AGACTTGAACCTTGGTGGGC 60.179 55.000 0.00 0.00 41.11 5.36
528 553 5.991933 TTTAAGATAAATGCAAGCACCCA 57.008 34.783 0.00 0.00 0.00 4.51
529 554 7.848223 AAATTTAAGATAAATGCAAGCACCC 57.152 32.000 0.00 0.00 0.00 4.61
587 612 3.662247 AGTCGATGAAACGTCTCCTTT 57.338 42.857 0.00 0.00 34.70 3.11
601 626 3.698040 ACCATAAACACCTCGTAGTCGAT 59.302 43.478 0.00 0.00 45.21 3.59
614 640 7.972832 AGATTTTACGAAGACACCATAAACA 57.027 32.000 0.00 0.00 0.00 2.83
639 665 6.485313 CACCTCAAAGCCGGTATATCATTTTA 59.515 38.462 1.90 0.00 30.91 1.52
642 668 4.389374 CACCTCAAAGCCGGTATATCATT 58.611 43.478 1.90 0.00 30.91 2.57
650 676 2.032681 GAGCACCTCAAAGCCGGT 59.967 61.111 1.90 0.00 0.00 5.28
652 678 1.667724 CTTATGAGCACCTCAAAGCCG 59.332 52.381 0.00 0.00 44.04 5.52
657 683 1.281867 CCACCCTTATGAGCACCTCAA 59.718 52.381 0.00 0.00 44.04 3.02
658 684 0.911769 CCACCCTTATGAGCACCTCA 59.088 55.000 0.00 0.00 44.99 3.86
672 698 2.025418 CGCACACGTAACTCCACCC 61.025 63.158 0.00 0.00 33.53 4.61
676 702 0.094730 GAATGCGCACACGTAACTCC 59.905 55.000 14.90 0.00 42.83 3.85
679 705 3.377434 TTATGAATGCGCACACGTAAC 57.623 42.857 14.90 0.00 42.83 2.50
680 706 4.406001 TTTTATGAATGCGCACACGTAA 57.594 36.364 14.90 18.04 42.83 3.18
681 707 4.406001 TTTTTATGAATGCGCACACGTA 57.594 36.364 14.90 12.82 42.83 3.57
682 708 2.979401 TTTTATGAATGCGCACACGT 57.021 40.000 14.90 13.93 42.83 4.49
683 709 3.850837 TCATTTTTATGAATGCGCACACG 59.149 39.130 14.90 0.00 44.07 4.49
684 710 4.858692 ACTCATTTTTATGAATGCGCACAC 59.141 37.500 14.90 10.84 37.03 3.82
685 711 4.858140 CACTCATTTTTATGAATGCGCACA 59.142 37.500 14.90 7.96 37.03 4.57
686 712 4.858692 ACACTCATTTTTATGAATGCGCAC 59.141 37.500 14.90 0.12 37.03 5.34
687 713 5.058149 ACACTCATTTTTATGAATGCGCA 57.942 34.783 14.96 14.96 37.03 6.09
688 714 6.345250 GCATACACTCATTTTTATGAATGCGC 60.345 38.462 0.00 0.00 37.03 6.09
689 715 7.085797 GCATACACTCATTTTTATGAATGCG 57.914 36.000 6.72 0.00 37.03 4.73
690 716 6.345250 GCGCATACACTCATTTTTATGAATGC 60.345 38.462 0.30 10.36 37.55 3.56
691 717 6.692249 TGCGCATACACTCATTTTTATGAATG 59.308 34.615 5.66 0.00 38.16 2.67
692 718 6.794374 TGCGCATACACTCATTTTTATGAAT 58.206 32.000 5.66 0.00 0.00 2.57
693 719 6.188400 TGCGCATACACTCATTTTTATGAA 57.812 33.333 5.66 0.00 0.00 2.57
694 720 5.809719 TGCGCATACACTCATTTTTATGA 57.190 34.783 5.66 0.00 0.00 2.15
695 721 7.453980 AAATGCGCATACACTCATTTTTATG 57.546 32.000 25.61 0.00 36.16 1.90
700 726 9.825972 GTTATATAAATGCGCATACACTCATTT 57.174 29.630 25.61 14.63 40.77 2.32
701 727 8.450964 GGTTATATAAATGCGCATACACTCATT 58.549 33.333 25.61 14.65 0.00 2.57
702 728 7.201522 CGGTTATATAAATGCGCATACACTCAT 60.202 37.037 25.61 14.16 0.00 2.90
703 729 6.090223 CGGTTATATAAATGCGCATACACTCA 59.910 38.462 25.61 7.54 0.00 3.41
704 730 6.466812 CGGTTATATAAATGCGCATACACTC 58.533 40.000 25.61 9.37 0.00 3.51
705 731 5.163893 GCGGTTATATAAATGCGCATACACT 60.164 40.000 25.61 11.15 0.00 3.55
706 732 5.019498 GCGGTTATATAAATGCGCATACAC 58.981 41.667 25.61 11.85 0.00 2.90
707 733 4.691216 TGCGGTTATATAAATGCGCATACA 59.309 37.500 25.61 14.91 0.00 2.29
708 734 5.211266 TGCGGTTATATAAATGCGCATAC 57.789 39.130 25.61 15.80 0.00 2.39
709 735 5.729176 GCATGCGGTTATATAAATGCGCATA 60.729 40.000 25.61 9.73 39.36 3.14
710 736 4.661125 CATGCGGTTATATAAATGCGCAT 58.339 39.130 19.28 19.28 41.56 4.73
711 737 3.669290 GCATGCGGTTATATAAATGCGCA 60.669 43.478 14.96 14.96 32.04 6.09
712 738 2.845967 GCATGCGGTTATATAAATGCGC 59.154 45.455 0.00 0.00 32.04 6.09
714 740 4.078363 ACGCATGCGGTTATATAAATGC 57.922 40.909 39.95 15.43 44.69 3.56
715 741 5.107104 ACAGACGCATGCGGTTATATAAATG 60.107 40.000 39.95 23.41 44.69 2.32
716 742 4.994852 ACAGACGCATGCGGTTATATAAAT 59.005 37.500 39.95 18.14 44.69 1.40
717 743 4.373527 ACAGACGCATGCGGTTATATAAA 58.626 39.130 39.95 0.00 44.69 1.40
718 744 3.985008 ACAGACGCATGCGGTTATATAA 58.015 40.909 39.95 0.00 44.69 0.98
719 745 3.653539 ACAGACGCATGCGGTTATATA 57.346 42.857 39.95 0.00 44.69 0.86
720 746 2.526304 ACAGACGCATGCGGTTATAT 57.474 45.000 39.95 21.22 44.69 0.86
721 747 2.544277 GGTACAGACGCATGCGGTTATA 60.544 50.000 39.95 24.55 44.69 0.98
722 748 1.567504 GTACAGACGCATGCGGTTAT 58.432 50.000 39.95 25.54 44.69 1.89
723 749 0.458889 GGTACAGACGCATGCGGTTA 60.459 55.000 39.95 22.94 44.69 2.85
724 750 1.740296 GGTACAGACGCATGCGGTT 60.740 57.895 39.95 26.16 44.69 4.44
725 751 2.125673 GGTACAGACGCATGCGGT 60.126 61.111 39.95 29.97 44.69 5.68
726 752 3.254654 CGGTACAGACGCATGCGG 61.255 66.667 39.95 26.21 44.69 5.69
727 753 2.506217 ACGGTACAGACGCATGCG 60.506 61.111 36.79 36.79 46.03 4.73
728 754 1.683790 GACACGGTACAGACGCATGC 61.684 60.000 7.91 7.91 34.00 4.06
729 755 0.388006 TGACACGGTACAGACGCATG 60.388 55.000 0.00 0.00 34.00 4.06
730 756 0.315886 TTGACACGGTACAGACGCAT 59.684 50.000 0.00 0.00 34.00 4.73
731 757 0.318360 CTTGACACGGTACAGACGCA 60.318 55.000 0.00 0.00 34.00 5.24
732 758 0.039798 TCTTGACACGGTACAGACGC 60.040 55.000 0.00 0.00 34.00 5.19
733 759 2.410785 TTCTTGACACGGTACAGACG 57.589 50.000 0.00 0.00 37.36 4.18
1048 1090 1.577922 CGACGTCGGTCTTCTTGGA 59.422 57.895 29.70 0.00 41.16 3.53
1922 1964 4.429212 CGGCGTCGTCCACATCCA 62.429 66.667 0.00 0.00 0.00 3.41
2346 2388 1.758514 AGGGACACGATCATCGCCT 60.759 57.895 7.05 2.18 45.12 5.52
2376 2418 0.907486 CATGGAGGCCAGAGTTCAGA 59.093 55.000 5.01 0.00 36.75 3.27
2424 2466 1.267121 ACTCAGTGGCCTGAACGTAT 58.733 50.000 3.32 0.00 46.79 3.06
2439 2481 1.809619 GAACTGCGCGGCATACTCA 60.810 57.895 18.15 0.00 38.13 3.41
2529 2571 4.830765 GCATACCCGCCAGTCGCA 62.831 66.667 0.00 0.00 37.30 5.10
2751 2793 0.963962 GGTCCACGAAGTACTGGTGA 59.036 55.000 22.38 10.38 41.61 4.02
2778 2820 0.395311 CATTGAGGAGCACATGCCCT 60.395 55.000 12.12 12.12 41.99 5.19
2849 2891 5.003804 CCCTAGTTTACACAATTGAGCTGT 58.996 41.667 13.59 8.90 0.00 4.40
2901 2943 7.450014 ACATAAACTGATACCACAATTTCACCA 59.550 33.333 0.00 0.00 0.00 4.17
3020 3062 1.415672 AACTTCGACCTTCCTGGCCA 61.416 55.000 4.71 4.71 40.22 5.36
3045 3091 1.035932 TTTCGCCCGTAGCTAGCTCT 61.036 55.000 23.26 0.00 40.39 4.09
3129 3175 1.199789 CATTGGACACAACATGACCCG 59.800 52.381 0.00 0.00 41.96 5.28
3197 3251 0.544357 TCCAGTGTCCCAGGATTCGT 60.544 55.000 0.00 0.00 0.00 3.85
3264 3318 0.861837 CACTGTTGCTCCACTCGAAC 59.138 55.000 0.00 0.00 0.00 3.95
3267 3321 1.287730 GCTCACTGTTGCTCCACTCG 61.288 60.000 0.00 0.00 0.00 4.18
3325 3379 2.680339 GACAACTTAGCTCTGAATGGCC 59.320 50.000 0.00 0.00 0.00 5.36
3448 3502 0.767998 TTGTCATGCACCTACCACCA 59.232 50.000 0.00 0.00 0.00 4.17
3548 3616 3.144506 AGCCACACTGAACAAGAATGAG 58.855 45.455 0.00 0.00 0.00 2.90
3608 3676 3.391965 CCAACAACCATGAACCATGTTG 58.608 45.455 15.72 15.72 46.38 3.33
3609 3677 2.224257 GCCAACAACCATGAACCATGTT 60.224 45.455 0.00 0.00 39.94 2.71
3610 3678 1.344114 GCCAACAACCATGAACCATGT 59.656 47.619 0.00 0.00 39.94 3.21
3611 3679 1.338011 GGCCAACAACCATGAACCATG 60.338 52.381 0.00 0.00 41.10 3.66
3612 3680 0.975887 GGCCAACAACCATGAACCAT 59.024 50.000 0.00 0.00 0.00 3.55
3613 3681 0.105760 AGGCCAACAACCATGAACCA 60.106 50.000 5.01 0.00 0.00 3.67
3628 3696 0.178990 AACTGGTTCACCTCAAGGCC 60.179 55.000 0.00 0.00 39.32 5.19
3644 3712 6.791867 TCACTCAATAGGCATACTGTAACT 57.208 37.500 0.00 0.00 0.00 2.24
3645 3713 6.018669 GCTTCACTCAATAGGCATACTGTAAC 60.019 42.308 0.00 0.00 0.00 2.50
3649 3717 4.445453 TGCTTCACTCAATAGGCATACTG 58.555 43.478 0.00 0.00 0.00 2.74
3650 3718 4.760530 TGCTTCACTCAATAGGCATACT 57.239 40.909 0.00 0.00 0.00 2.12
3651 3719 7.126726 CTATTGCTTCACTCAATAGGCATAC 57.873 40.000 12.48 0.00 44.61 2.39
3658 3728 7.764443 GGTCACTAACTATTGCTTCACTCAATA 59.236 37.037 0.00 0.00 35.87 1.90


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

AutoCloner maintained by Alex Coulton.