Multiple sequence alignment - TraesCS2A01G256900

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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 TraesCS2A01G256900 chr2A 100.000 4360 0 0 1 4360 394021858 394017499 0.000000e+00 8052
1 TraesCS2A01G256900 chr2A 82.635 334 56 2 1 333 536624598 536624930 1.190000e-75 294
2 TraesCS2A01G256900 chr2D 95.207 3714 89 33 696 4358 324594763 324598438 0.000000e+00 5790
3 TraesCS2A01G256900 chr2D 90.973 565 13 7 1 565 324594185 324594711 0.000000e+00 726
4 TraesCS2A01G256900 chr2B 94.748 3694 94 32 696 4360 393464749 393468371 0.000000e+00 5655
5 TraesCS2A01G256900 chr2B 93.493 584 25 3 1 584 393464144 393464714 0.000000e+00 856
6 TraesCS2A01G256900 chr2B 83.533 334 53 2 1 333 472899442 472899774 1.180000e-80 311


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 TraesCS2A01G256900 chr2A 394017499 394021858 4359 True 8052.0 8052 100.0000 1 4360 1 chr2A.!!$R1 4359
1 TraesCS2A01G256900 chr2D 324594185 324598438 4253 False 3258.0 5790 93.0900 1 4358 2 chr2D.!!$F1 4357
2 TraesCS2A01G256900 chr2B 393464144 393468371 4227 False 3255.5 5655 94.1205 1 4360 2 chr2B.!!$F2 4359

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
360 361 0.393820 TTTGTTCTTACCCGGCGTCT 59.606 50.0 6.01 0.0 0.0 4.18 F
1018 1027 0.833287 CATCCGTCATTCCTGGGTCT 59.167 55.0 0.00 0.0 0.0 3.85 F
1948 1973 0.106217 CCCACCCACAACTGAACCTT 60.106 55.0 0.00 0.0 0.0 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1215 1224 0.386113 GCAGGAAGGGCGAGTAGTAG 59.614 60.0 0.0 0.0 0.00 2.57 R
2798 2851 0.320683 CCTGTGAGTGTGGCGATTCA 60.321 55.0 0.0 0.0 0.00 2.57 R
3790 3849 0.981183 AGGTCGGTATGCACCTTTCA 59.019 50.0 0.0 0.0 40.35 2.69 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
254 255 2.363795 ACGGAGGCGATCTTCCCA 60.364 61.111 0.00 0.00 0.00 4.37
329 330 0.743097 GGTCAGCAAAGATCATGGCC 59.257 55.000 0.00 0.00 0.00 5.36
348 349 3.416156 GCCTGAGGAGATGTTTTGTTCT 58.584 45.455 0.65 0.00 0.00 3.01
349 350 3.823304 GCCTGAGGAGATGTTTTGTTCTT 59.177 43.478 0.65 0.00 0.00 2.52
350 351 5.003804 GCCTGAGGAGATGTTTTGTTCTTA 58.996 41.667 0.65 0.00 0.00 2.10
351 352 5.106515 GCCTGAGGAGATGTTTTGTTCTTAC 60.107 44.000 0.65 0.00 0.00 2.34
352 353 5.412904 CCTGAGGAGATGTTTTGTTCTTACC 59.587 44.000 0.00 0.00 0.00 2.85
353 354 5.313712 TGAGGAGATGTTTTGTTCTTACCC 58.686 41.667 0.00 0.00 0.00 3.69
354 355 4.324267 AGGAGATGTTTTGTTCTTACCCG 58.676 43.478 0.00 0.00 0.00 5.28
355 356 3.439129 GGAGATGTTTTGTTCTTACCCGG 59.561 47.826 0.00 0.00 0.00 5.73
356 357 2.817844 AGATGTTTTGTTCTTACCCGGC 59.182 45.455 0.00 0.00 0.00 6.13
357 358 0.945813 TGTTTTGTTCTTACCCGGCG 59.054 50.000 0.00 0.00 0.00 6.46
358 359 0.946528 GTTTTGTTCTTACCCGGCGT 59.053 50.000 6.01 0.00 0.00 5.68
359 360 1.069703 GTTTTGTTCTTACCCGGCGTC 60.070 52.381 6.01 0.00 0.00 5.19
360 361 0.393820 TTTGTTCTTACCCGGCGTCT 59.606 50.000 6.01 0.00 0.00 4.18
392 393 4.082845 TCTTACACTTGAGCTCTGCTAGT 58.917 43.478 16.19 10.00 39.88 2.57
398 399 1.090728 TGAGCTCTGCTAGTGTCTCG 58.909 55.000 16.19 0.00 39.88 4.04
428 429 1.597797 ATCCCTGCGTGTTGCCATTG 61.598 55.000 0.00 0.00 45.60 2.82
479 480 8.917655 GTTAGCTCTATAAAATTTCTAGCCTCG 58.082 37.037 0.00 0.00 0.00 4.63
490 491 1.819288 TCTAGCCTCGTGGACAAGAAG 59.181 52.381 7.92 0.00 34.57 2.85
492 493 1.270907 AGCCTCGTGGACAAGAAGAT 58.729 50.000 7.92 0.00 34.57 2.40
495 496 2.738964 GCCTCGTGGACAAGAAGATACC 60.739 54.545 7.92 0.00 34.57 2.73
566 567 1.438651 TCCGTTCTAGTGCAATGTGC 58.561 50.000 0.00 0.00 45.29 4.57
584 590 5.527511 TGTGCAATGTTCTGTTGTTTTTG 57.472 34.783 0.00 0.00 0.00 2.44
585 591 4.391216 TGTGCAATGTTCTGTTGTTTTTGG 59.609 37.500 0.00 0.00 0.00 3.28
586 592 3.373439 TGCAATGTTCTGTTGTTTTTGGC 59.627 39.130 0.00 0.00 0.00 4.52
587 593 3.242706 GCAATGTTCTGTTGTTTTTGGCC 60.243 43.478 0.00 0.00 0.00 5.36
589 595 3.518634 TGTTCTGTTGTTTTTGGCCTC 57.481 42.857 3.32 0.00 0.00 4.70
591 597 3.130340 TGTTCTGTTGTTTTTGGCCTCTC 59.870 43.478 3.32 0.00 0.00 3.20
593 599 3.631250 TCTGTTGTTTTTGGCCTCTCTT 58.369 40.909 3.32 0.00 0.00 2.85
595 601 4.466015 TCTGTTGTTTTTGGCCTCTCTTTT 59.534 37.500 3.32 0.00 0.00 2.27
631 637 6.615264 CTGATGTCAGATCTTTAACCATGG 57.385 41.667 11.19 11.19 46.59 3.66
632 638 4.883585 TGATGTCAGATCTTTAACCATGGC 59.116 41.667 13.04 0.00 0.00 4.40
633 639 4.299586 TGTCAGATCTTTAACCATGGCA 57.700 40.909 13.04 0.00 0.00 4.92
634 640 4.661222 TGTCAGATCTTTAACCATGGCAA 58.339 39.130 13.04 3.06 0.00 4.52
635 641 5.076182 TGTCAGATCTTTAACCATGGCAAA 58.924 37.500 13.04 11.61 0.00 3.68
636 642 5.716228 TGTCAGATCTTTAACCATGGCAAAT 59.284 36.000 13.04 0.00 0.00 2.32
637 643 6.127647 TGTCAGATCTTTAACCATGGCAAATC 60.128 38.462 13.04 8.09 0.00 2.17
638 644 6.096001 GTCAGATCTTTAACCATGGCAAATCT 59.904 38.462 13.04 10.14 0.00 2.40
639 645 6.095860 TCAGATCTTTAACCATGGCAAATCTG 59.904 38.462 22.67 22.67 33.88 2.90
640 646 5.361857 AGATCTTTAACCATGGCAAATCTGG 59.638 40.000 13.04 3.32 36.09 3.86
671 677 3.772060 GGAGCATCGCAGATTCTTTTT 57.228 42.857 0.00 0.00 45.12 1.94
743 750 4.768968 AGATTAGCTTGCTTGTTTGGTGAT 59.231 37.500 0.00 0.00 0.00 3.06
744 751 2.806608 AGCTTGCTTGTTTGGTGATG 57.193 45.000 0.00 0.00 0.00 3.07
745 752 1.142474 GCTTGCTTGTTTGGTGATGC 58.858 50.000 0.00 0.00 0.00 3.91
746 753 1.269936 GCTTGCTTGTTTGGTGATGCT 60.270 47.619 0.00 0.00 0.00 3.79
747 754 2.030007 GCTTGCTTGTTTGGTGATGCTA 60.030 45.455 0.00 0.00 0.00 3.49
748 755 3.829948 CTTGCTTGTTTGGTGATGCTAG 58.170 45.455 0.00 0.00 0.00 3.42
749 756 1.541147 TGCTTGTTTGGTGATGCTAGC 59.459 47.619 8.10 8.10 0.00 3.42
750 757 1.541147 GCTTGTTTGGTGATGCTAGCA 59.459 47.619 21.85 21.85 31.86 3.49
751 758 2.415090 GCTTGTTTGGTGATGCTAGCAG 60.415 50.000 23.89 5.71 31.86 4.24
752 759 2.857186 TGTTTGGTGATGCTAGCAGA 57.143 45.000 23.89 9.40 0.00 4.26
753 760 2.703416 TGTTTGGTGATGCTAGCAGAG 58.297 47.619 23.89 0.00 0.00 3.35
784 791 1.442526 GGCGATTGAGGTGGCAGATG 61.443 60.000 0.00 0.00 0.00 2.90
801 810 4.803426 GAGTGGAGGCGCAGGTCG 62.803 72.222 10.83 0.00 42.12 4.79
955 964 1.630878 ACAGACCAACCATTCCTCCTC 59.369 52.381 0.00 0.00 0.00 3.71
1018 1027 0.833287 CATCCGTCATTCCTGGGTCT 59.167 55.000 0.00 0.00 0.00 3.85
1063 1072 2.427245 GCGAAGGAGAGCAGCCCTA 61.427 63.158 0.00 0.00 31.36 3.53
1064 1073 1.739049 CGAAGGAGAGCAGCCCTAG 59.261 63.158 0.00 0.00 31.36 3.02
1065 1074 1.445518 GAAGGAGAGCAGCCCTAGC 59.554 63.158 0.00 0.00 40.32 3.42
1066 1075 2.038814 GAAGGAGAGCAGCCCTAGCC 62.039 65.000 0.00 0.00 41.25 3.93
1067 1076 3.555324 GGAGAGCAGCCCTAGCCC 61.555 72.222 0.00 0.00 41.25 5.19
1068 1077 2.445654 GAGAGCAGCCCTAGCCCT 60.446 66.667 0.00 0.00 41.25 5.19
1069 1078 1.152440 GAGAGCAGCCCTAGCCCTA 60.152 63.158 0.00 0.00 41.25 3.53
1070 1079 1.152355 AGAGCAGCCCTAGCCCTAG 60.152 63.158 0.00 0.00 41.25 3.02
1071 1080 2.846754 AGCAGCCCTAGCCCTAGC 60.847 66.667 0.00 0.00 41.25 3.42
1072 1081 3.947459 GCAGCCCTAGCCCTAGCC 61.947 72.222 0.00 0.00 41.25 3.93
1073 1082 3.245346 CAGCCCTAGCCCTAGCCC 61.245 72.222 0.00 0.00 41.25 5.19
1074 1083 3.452919 AGCCCTAGCCCTAGCCCT 61.453 66.667 0.00 0.00 41.25 5.19
1533 1542 7.115805 TGTTCATTCACAAGAGATTGTACGTAC 59.884 37.037 18.90 18.90 33.17 3.67
1578 1587 1.419374 CACGCAGCGAAAGAGTACTT 58.581 50.000 24.65 0.00 38.05 2.24
1679 1692 6.219417 TCATGGAAGAAGATCAAGTCTCTC 57.781 41.667 0.00 0.00 35.67 3.20
1773 1786 5.336372 GCAACCTATAGCCATTGTTTGTTGA 60.336 40.000 13.51 0.00 34.10 3.18
1872 1885 4.711949 CGCAGGCAGCCCTTCACT 62.712 66.667 8.22 0.00 40.33 3.41
1900 1913 3.879892 GCACAAAGAAGAACTTCAGGTCT 59.120 43.478 15.43 0.00 41.84 3.85
1901 1914 5.057149 GCACAAAGAAGAACTTCAGGTCTA 58.943 41.667 15.43 0.00 41.84 2.59
1925 1950 2.318908 AGACTCCATCTCATCTCTGGC 58.681 52.381 0.00 0.00 28.16 4.85
1941 1966 4.603535 GCCTGCCCACCCACAACT 62.604 66.667 0.00 0.00 0.00 3.16
1942 1967 2.598394 CCTGCCCACCCACAACTG 60.598 66.667 0.00 0.00 0.00 3.16
1944 1969 1.152777 CTGCCCACCCACAACTGAA 60.153 57.895 0.00 0.00 0.00 3.02
1945 1970 1.454847 TGCCCACCCACAACTGAAC 60.455 57.895 0.00 0.00 0.00 3.18
1946 1971 2.200337 GCCCACCCACAACTGAACC 61.200 63.158 0.00 0.00 0.00 3.62
1947 1972 1.536676 CCCACCCACAACTGAACCT 59.463 57.895 0.00 0.00 0.00 3.50
1948 1973 0.106217 CCCACCCACAACTGAACCTT 60.106 55.000 0.00 0.00 0.00 3.50
1959 1995 5.010282 ACAACTGAACCTTCTTTTGTCTGT 58.990 37.500 0.00 0.00 31.59 3.41
2076 2112 4.714802 GGCAACTAATTCCCCCATAGTTTT 59.285 41.667 0.00 0.00 37.68 2.43
2086 2122 5.398236 TCCCCCATAGTTTTCAAATTGTCA 58.602 37.500 0.00 0.00 0.00 3.58
2288 2330 3.477198 AGTGCACCACCAGAGGATCTAC 61.477 54.545 14.63 0.00 38.45 2.59
2312 2357 6.988580 ACATGTGTCACAATCATACCATCTAG 59.011 38.462 10.28 0.00 0.00 2.43
2497 2545 4.690748 CAGTGAGTATTTACCACCACAGTG 59.309 45.833 0.00 0.00 44.12 3.66
2569 2618 5.170748 GTGCACCTTCAAAATAATTCCTGG 58.829 41.667 5.22 0.00 0.00 4.45
2659 2708 4.249661 GCTCTGTAAGAACCCTCTTCTTG 58.750 47.826 5.72 0.00 46.34 3.02
2798 2851 2.224378 CCACTATGCTGGTTCCGATGAT 60.224 50.000 0.00 0.00 0.00 2.45
2952 3005 5.130292 CAAGGTTTCTTGTCTCATGCAAT 57.870 39.130 0.00 0.00 43.92 3.56
2969 3022 2.610976 GCAATCTGCCAATTTCACAGCA 60.611 45.455 0.00 0.00 37.42 4.41
3462 3515 7.916450 GCCGTATTTAAATGCAAGGTTGTAATA 59.084 33.333 15.33 0.00 0.00 0.98
3539 3595 4.082026 GCTTGGTGATGAGTATTTGCCTTT 60.082 41.667 0.00 0.00 0.00 3.11
3541 3597 4.406456 TGGTGATGAGTATTTGCCTTTGT 58.594 39.130 0.00 0.00 0.00 2.83
3567 3623 5.175127 TCATCGTTGCAAGCTATAACAGAA 58.825 37.500 0.00 0.00 0.00 3.02
3571 3627 5.805486 TCGTTGCAAGCTATAACAGAACTAG 59.195 40.000 0.00 0.00 0.00 2.57
3639 3698 6.096695 TGAGAAACTAACTTTGCACCAAAAC 58.903 36.000 0.00 0.00 32.75 2.43
3694 3753 7.096551 TCAATTTAGGCAGGTTAAAATTCAGC 58.903 34.615 0.00 0.00 31.05 4.26
3705 3764 6.493458 AGGTTAAAATTCAGCCACTACACATT 59.507 34.615 0.00 0.00 0.00 2.71
3719 3778 3.073274 ACACATTAACTTCTGGAGGCC 57.927 47.619 0.00 0.00 0.00 5.19
3754 3813 3.777106 TGCAACTCTCACCTTCATTCT 57.223 42.857 0.00 0.00 0.00 2.40
3800 3859 1.619654 CACCCAAGATGAAAGGTGCA 58.380 50.000 0.00 0.00 43.02 4.57
3818 3877 2.499693 TGCATACCGACCTTCATGAGAA 59.500 45.455 0.00 0.00 0.00 2.87
3843 3902 4.023739 ACACAAACGAAACAAACTAGCC 57.976 40.909 0.00 0.00 0.00 3.93
3849 3908 2.484264 ACGAAACAAACTAGCCTGCATC 59.516 45.455 0.00 0.00 0.00 3.91
3869 3928 4.066646 TCGGTGTTTGATCTCACAAAGA 57.933 40.909 14.45 8.18 39.83 2.52
4227 4287 1.604278 GCTGACTGAAACTGGTTCCAC 59.396 52.381 2.48 0.00 35.12 4.02
4253 4313 5.741964 GCTCCATGTCGAGAATAATACCCAA 60.742 44.000 3.41 0.00 30.97 4.12
4271 4331 6.909550 ACCCAACATTGTTTATATGTGTGT 57.090 33.333 0.00 0.00 36.41 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 0.454196 TCTCTGCTACGTGCGCAATA 59.546 50.000 14.00 7.12 46.63 1.90
215 216 3.380320 TCTTGGCGTCTTCGAAGATGATA 59.620 43.478 39.02 27.04 43.22 2.15
263 264 3.257127 TCCCCACATTCGAAATTGTTTCC 59.743 43.478 0.00 0.00 36.30 3.13
329 330 5.412904 GGGTAAGAACAAAACATCTCCTCAG 59.587 44.000 0.00 0.00 0.00 3.35
348 349 0.611618 TAACTGGAGACGCCGGGTAA 60.612 55.000 9.06 0.00 42.81 2.85
349 350 0.611618 TTAACTGGAGACGCCGGGTA 60.612 55.000 9.06 3.07 42.81 3.69
353 354 2.295253 AGATTTAACTGGAGACGCCG 57.705 50.000 0.00 0.00 40.66 6.46
354 355 4.329256 GTGTAAGATTTAACTGGAGACGCC 59.671 45.833 0.00 0.00 37.10 5.68
355 356 5.169295 AGTGTAAGATTTAACTGGAGACGC 58.831 41.667 0.00 0.00 0.00 5.19
356 357 6.866770 TCAAGTGTAAGATTTAACTGGAGACG 59.133 38.462 0.00 0.00 0.00 4.18
357 358 7.148557 GCTCAAGTGTAAGATTTAACTGGAGAC 60.149 40.741 9.69 0.00 41.41 3.36
358 359 6.874134 GCTCAAGTGTAAGATTTAACTGGAGA 59.126 38.462 9.69 0.00 41.41 3.71
359 360 6.876257 AGCTCAAGTGTAAGATTTAACTGGAG 59.124 38.462 2.33 2.33 41.68 3.86
360 361 6.769512 AGCTCAAGTGTAAGATTTAACTGGA 58.230 36.000 0.00 0.00 0.00 3.86
398 399 1.303309 CGCAGGGATTTCATGTCCTC 58.697 55.000 1.25 0.00 36.00 3.71
428 429 6.199719 CAGAAGACAATTTGCAAGGAAGAAAC 59.800 38.462 0.00 0.00 0.00 2.78
469 470 1.919240 TCTTGTCCACGAGGCTAGAA 58.081 50.000 0.28 0.00 33.74 2.10
475 476 2.479730 CGGTATCTTCTTGTCCACGAGG 60.480 54.545 0.00 0.00 0.00 4.63
479 480 3.660865 ACAACGGTATCTTCTTGTCCAC 58.339 45.455 0.00 0.00 0.00 4.02
490 491 2.063266 TCACGCAGAAACAACGGTATC 58.937 47.619 0.00 0.00 0.00 2.24
492 493 1.795872 CATCACGCAGAAACAACGGTA 59.204 47.619 0.00 0.00 0.00 4.02
495 496 0.865111 TCCATCACGCAGAAACAACG 59.135 50.000 0.00 0.00 0.00 4.10
539 540 2.811431 TGCACTAGAACGGAAATGGTTG 59.189 45.455 0.00 0.00 0.00 3.77
566 567 4.190772 AGGCCAAAAACAACAGAACATTG 58.809 39.130 5.01 0.00 0.00 2.82
608 614 5.008415 GCCATGGTTAAAGATCTGACATCAG 59.992 44.000 14.67 2.24 45.08 2.90
609 615 4.883585 GCCATGGTTAAAGATCTGACATCA 59.116 41.667 14.67 0.00 0.00 3.07
610 616 4.883585 TGCCATGGTTAAAGATCTGACATC 59.116 41.667 14.67 0.00 0.00 3.06
611 617 4.858850 TGCCATGGTTAAAGATCTGACAT 58.141 39.130 14.67 0.00 0.00 3.06
612 618 4.299586 TGCCATGGTTAAAGATCTGACA 57.700 40.909 14.67 0.00 0.00 3.58
613 619 5.643379 TTTGCCATGGTTAAAGATCTGAC 57.357 39.130 14.67 0.00 0.00 3.51
614 620 6.095860 CAGATTTGCCATGGTTAAAGATCTGA 59.904 38.462 24.63 6.54 34.31 3.27
615 621 6.270815 CAGATTTGCCATGGTTAAAGATCTG 58.729 40.000 20.44 20.44 0.00 2.90
616 622 5.361857 CCAGATTTGCCATGGTTAAAGATCT 59.638 40.000 14.67 12.31 0.00 2.75
617 623 5.594926 CCAGATTTGCCATGGTTAAAGATC 58.405 41.667 14.67 10.46 0.00 2.75
618 624 4.141869 GCCAGATTTGCCATGGTTAAAGAT 60.142 41.667 14.67 5.73 36.43 2.40
619 625 3.195396 GCCAGATTTGCCATGGTTAAAGA 59.805 43.478 14.67 0.00 36.43 2.52
620 626 3.524541 GCCAGATTTGCCATGGTTAAAG 58.475 45.455 14.67 5.18 36.43 1.85
621 627 3.608316 GCCAGATTTGCCATGGTTAAA 57.392 42.857 14.67 15.21 36.43 1.52
645 651 1.838112 ATCTGCGATGCTCCCAAAAA 58.162 45.000 0.00 0.00 0.00 1.94
646 652 1.745087 GAATCTGCGATGCTCCCAAAA 59.255 47.619 0.00 0.00 0.00 2.44
647 653 1.065199 AGAATCTGCGATGCTCCCAAA 60.065 47.619 0.00 0.00 0.00 3.28
648 654 0.543277 AGAATCTGCGATGCTCCCAA 59.457 50.000 0.00 0.00 0.00 4.12
649 655 0.543277 AAGAATCTGCGATGCTCCCA 59.457 50.000 0.36 0.00 0.00 4.37
650 656 1.673168 AAAGAATCTGCGATGCTCCC 58.327 50.000 0.36 0.00 0.00 4.30
651 657 3.772060 AAAAAGAATCTGCGATGCTCC 57.228 42.857 0.36 0.00 0.00 4.70
743 750 2.111384 CTAACCCCTTCTCTGCTAGCA 58.889 52.381 18.22 18.22 0.00 3.49
744 751 2.112190 ACTAACCCCTTCTCTGCTAGC 58.888 52.381 8.10 8.10 0.00 3.42
745 752 2.432510 CCACTAACCCCTTCTCTGCTAG 59.567 54.545 0.00 0.00 0.00 3.42
746 753 2.467880 CCACTAACCCCTTCTCTGCTA 58.532 52.381 0.00 0.00 0.00 3.49
747 754 1.280457 CCACTAACCCCTTCTCTGCT 58.720 55.000 0.00 0.00 0.00 4.24
748 755 0.393132 GCCACTAACCCCTTCTCTGC 60.393 60.000 0.00 0.00 0.00 4.26
749 756 0.108138 CGCCACTAACCCCTTCTCTG 60.108 60.000 0.00 0.00 0.00 3.35
750 757 0.252103 TCGCCACTAACCCCTTCTCT 60.252 55.000 0.00 0.00 0.00 3.10
751 758 0.831307 ATCGCCACTAACCCCTTCTC 59.169 55.000 0.00 0.00 0.00 2.87
752 759 1.065418 CAATCGCCACTAACCCCTTCT 60.065 52.381 0.00 0.00 0.00 2.85
753 760 1.065709 TCAATCGCCACTAACCCCTTC 60.066 52.381 0.00 0.00 0.00 3.46
784 791 4.803426 CGACCTGCGCCTCCACTC 62.803 72.222 4.18 0.00 0.00 3.51
801 810 5.073428 CCCCTAAATCTCCCTGCTAATTTC 58.927 45.833 0.00 0.00 0.00 2.17
1063 1072 4.825679 GGGGTCAGGGCTAGGGCT 62.826 72.222 0.00 0.00 38.73 5.19
1065 1074 4.475444 TCGGGGTCAGGGCTAGGG 62.475 72.222 0.00 0.00 0.00 3.53
1066 1075 3.155167 GTCGGGGTCAGGGCTAGG 61.155 72.222 0.00 0.00 0.00 3.02
1067 1076 3.528370 CGTCGGGGTCAGGGCTAG 61.528 72.222 0.00 0.00 0.00 3.42
1206 1215 3.524606 GAGTAGTAGCCGCCCGCA 61.525 66.667 0.00 0.00 41.38 5.69
1215 1224 0.386113 GCAGGAAGGGCGAGTAGTAG 59.614 60.000 0.00 0.00 0.00 2.57
1389 1398 1.620819 ACCTGCTTGACGATCTTCTGT 59.379 47.619 0.48 0.00 0.00 3.41
1533 1542 3.601356 CGCTGCAGAAGAATGAAATACG 58.399 45.455 20.43 2.18 0.00 3.06
1558 1567 1.009389 AGTACTCTTTCGCTGCGTGC 61.009 55.000 22.48 4.98 38.57 5.34
1559 1568 1.387084 GAAGTACTCTTTCGCTGCGTG 59.613 52.381 22.48 13.16 33.64 5.34
1560 1569 1.000607 TGAAGTACTCTTTCGCTGCGT 60.001 47.619 22.48 3.71 33.64 5.24
1561 1570 1.651138 CTGAAGTACTCTTTCGCTGCG 59.349 52.381 17.25 17.25 33.64 5.18
1562 1571 2.678324 ACTGAAGTACTCTTTCGCTGC 58.322 47.619 0.00 0.00 33.64 5.25
1563 1572 8.373992 GTTTTATACTGAAGTACTCTTTCGCTG 58.626 37.037 0.00 0.00 33.64 5.18
1564 1573 8.086522 TGTTTTATACTGAAGTACTCTTTCGCT 58.913 33.333 0.00 0.00 33.64 4.93
1565 1574 8.236084 TGTTTTATACTGAAGTACTCTTTCGC 57.764 34.615 0.00 0.00 33.64 4.70
1622 1635 4.917385 ACAAGGGAACTGTATGCATGTAA 58.083 39.130 10.16 0.00 42.68 2.41
1623 1636 4.019771 TGACAAGGGAACTGTATGCATGTA 60.020 41.667 10.16 0.00 42.68 2.29
1624 1637 3.244875 TGACAAGGGAACTGTATGCATGT 60.245 43.478 10.16 0.00 42.68 3.21
1679 1692 1.926511 GCATCTGGTTGGTTGCTCCG 61.927 60.000 0.00 0.00 39.52 4.63
1773 1786 2.776536 AGGATGCTTCATCTGGTAGCTT 59.223 45.455 0.00 0.00 40.39 3.74
1872 1885 5.185454 TGAAGTTCTTCTTTGTGCTTCTCA 58.815 37.500 12.74 0.00 36.40 3.27
1900 1913 5.362143 CCAGAGATGAGATGGAGTCTTTGTA 59.638 44.000 0.00 0.00 37.29 2.41
1901 1914 4.161942 CCAGAGATGAGATGGAGTCTTTGT 59.838 45.833 0.00 0.00 37.29 2.83
1925 1950 2.598394 CAGTTGTGGGTGGGCAGG 60.598 66.667 0.00 0.00 0.00 4.85
1938 1963 4.142381 GCACAGACAAAAGAAGGTTCAGTT 60.142 41.667 0.00 0.00 0.00 3.16
1939 1964 3.378427 GCACAGACAAAAGAAGGTTCAGT 59.622 43.478 0.00 0.00 0.00 3.41
1940 1965 3.378112 TGCACAGACAAAAGAAGGTTCAG 59.622 43.478 0.00 0.00 0.00 3.02
1941 1966 3.351740 TGCACAGACAAAAGAAGGTTCA 58.648 40.909 0.00 0.00 0.00 3.18
1942 1967 3.378427 ACTGCACAGACAAAAGAAGGTTC 59.622 43.478 4.31 0.00 0.00 3.62
1944 1969 2.945668 GACTGCACAGACAAAAGAAGGT 59.054 45.455 4.31 0.00 0.00 3.50
1945 1970 3.209410 AGACTGCACAGACAAAAGAAGG 58.791 45.455 4.31 0.00 0.00 3.46
1946 1971 3.060003 CGAGACTGCACAGACAAAAGAAG 60.060 47.826 4.31 0.00 0.00 2.85
1947 1972 2.866156 CGAGACTGCACAGACAAAAGAA 59.134 45.455 4.31 0.00 0.00 2.52
1948 1973 2.473816 CGAGACTGCACAGACAAAAGA 58.526 47.619 4.31 0.00 0.00 2.52
1959 1995 2.029560 GCTATGATCATCCGAGACTGCA 60.030 50.000 12.53 0.00 0.00 4.41
2097 2134 4.893524 TGGACGTCATCAGTTCCTACATAT 59.106 41.667 18.91 0.00 0.00 1.78
2288 2330 6.426025 CCTAGATGGTATGATTGTGACACATG 59.574 42.308 9.55 0.00 0.00 3.21
2312 2357 3.609853 TGTCAATCTACACAATGAGCCC 58.390 45.455 0.00 0.00 0.00 5.19
2569 2618 3.505464 TCGTTTAGCTTCTCTACCTGC 57.495 47.619 0.00 0.00 0.00 4.85
2705 2758 3.820467 TCATGGAGTTGCAGTAAAACAGG 59.180 43.478 0.00 0.00 0.00 4.00
2798 2851 0.320683 CCTGTGAGTGTGGCGATTCA 60.321 55.000 0.00 0.00 0.00 2.57
2952 3005 2.555325 CTCTTGCTGTGAAATTGGCAGA 59.445 45.455 7.95 0.00 36.06 4.26
2969 3022 1.577736 CCCACTCTGGTGATCCTCTT 58.422 55.000 0.00 0.00 45.61 2.85
3462 3515 8.842280 TCATACTTTCCGTGAAACAGTAAAAAT 58.158 29.630 3.75 0.00 35.74 1.82
3498 3552 5.068987 ACCAAGCATTCTTTCAGCTGTTTAA 59.931 36.000 14.67 6.10 38.86 1.52
3499 3553 4.584325 ACCAAGCATTCTTTCAGCTGTTTA 59.416 37.500 14.67 0.00 38.86 2.01
3539 3595 4.764679 ATAGCTTGCAACGATGAAAACA 57.235 36.364 0.00 0.00 0.00 2.83
3541 3597 6.148645 TCTGTTATAGCTTGCAACGATGAAAA 59.851 34.615 0.00 0.00 0.00 2.29
3592 3648 8.050778 TCATAAAATTCTGGGTGTGTAATCAC 57.949 34.615 0.00 0.00 44.08 3.06
3593 3649 8.106462 TCTCATAAAATTCTGGGTGTGTAATCA 58.894 33.333 0.00 0.00 0.00 2.57
3594 3650 8.506168 TCTCATAAAATTCTGGGTGTGTAATC 57.494 34.615 0.00 0.00 0.00 1.75
3595 3651 8.877864 TTCTCATAAAATTCTGGGTGTGTAAT 57.122 30.769 0.00 0.00 0.00 1.89
3639 3698 2.093447 AGAAGACGAATTGGCTGGTAGG 60.093 50.000 0.00 0.00 0.00 3.18
3694 3753 5.178797 CCTCCAGAAGTTAATGTGTAGTGG 58.821 45.833 0.00 0.00 0.00 4.00
3705 3764 9.847224 CTAAATAAAATAGGCCTCCAGAAGTTA 57.153 33.333 9.68 2.78 0.00 2.24
3790 3849 0.981183 AGGTCGGTATGCACCTTTCA 59.019 50.000 0.00 0.00 40.35 2.69
3791 3850 3.855159 AGGTCGGTATGCACCTTTC 57.145 52.632 0.00 0.00 40.35 2.62
3800 3859 5.104941 TGTTGATTCTCATGAAGGTCGGTAT 60.105 40.000 0.00 0.00 35.44 2.73
3818 3877 5.741982 GCTAGTTTGTTTCGTTTGTGTTGAT 59.258 36.000 0.00 0.00 0.00 2.57
3843 3902 2.094894 GTGAGATCAAACACCGATGCAG 59.905 50.000 0.00 0.00 0.00 4.41
3849 3908 4.811555 TTCTTTGTGAGATCAAACACCG 57.188 40.909 12.63 3.50 36.35 4.94
4227 4287 4.926238 GGTATTATTCTCGACATGGAGCTG 59.074 45.833 0.00 0.00 33.98 4.24
4270 4330 5.862924 TTCGTTCTGATCCATCAAAGAAC 57.137 39.130 10.02 10.02 38.02 3.01
4271 4331 6.881065 AGAATTCGTTCTGATCCATCAAAGAA 59.119 34.615 0.00 0.00 36.18 2.52


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

AutoCloner maintained by Alex Coulton.