Multiple sequence alignment - TraesCS6A01G201700

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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 TraesCS6A01G201700 chr6A 100.000 4499 0 0 1 4499 334510286 334514784 0.000000e+00 8309.0
1 TraesCS6A01G201700 chr6A 87.420 469 43 7 1 462 528928213 528927754 3.990000e-145 525.0
2 TraesCS6A01G201700 chr6D 97.055 3531 66 6 860 4384 244542054 244545552 0.000000e+00 5910.0
3 TraesCS6A01G201700 chr6D 95.745 94 2 1 4314 4405 244545552 244545645 2.800000e-32 150.0
4 TraesCS6A01G201700 chr6D 98.000 50 1 0 4450 4499 244545650 244545699 2.230000e-13 87.9
5 TraesCS6A01G201700 chr6B 95.835 3145 84 12 860 4001 334839240 334842340 0.000000e+00 5038.0
6 TraesCS6A01G201700 chr4D 83.462 647 79 12 1 633 401526716 401527348 1.090000e-160 577.0
7 TraesCS6A01G201700 chr4D 83.333 246 31 8 622 864 401527291 401527529 7.580000e-53 219.0
8 TraesCS6A01G201700 chr7D 86.932 528 42 10 1 517 488126021 488125510 6.530000e-158 568.0
9 TraesCS6A01G201700 chr7D 81.550 271 32 6 1 271 436973908 436974160 1.640000e-49 207.0
10 TraesCS6A01G201700 chr7D 87.500 72 7 2 566 637 488125609 488125540 1.040000e-11 82.4
11 TraesCS6A01G201700 chr7D 90.909 55 3 2 806 860 436974187 436974239 6.240000e-09 73.1
12 TraesCS6A01G201700 chr1D 87.872 470 39 11 1 462 466132121 466132580 1.840000e-148 536.0
13 TraesCS6A01G201700 chr2A 86.994 469 41 8 1 462 759297919 759297464 1.120000e-140 510.0
14 TraesCS6A01G201700 chr7B 79.781 549 64 19 1 547 453763872 453764375 5.540000e-94 355.0
15 TraesCS6A01G201700 chr7A 79.417 549 66 24 1 547 487253702 487254205 1.200000e-90 344.0
16 TraesCS6A01G201700 chrUn 79.675 123 13 3 432 543 50990808 50990687 1.340000e-10 78.7
17 TraesCS6A01G201700 chr5A 78.889 90 15 4 257 343 472279752 472279664 1.750000e-04 58.4


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 TraesCS6A01G201700 chr6A 334510286 334514784 4498 False 8309.0 8309 100.000000 1 4499 1 chr6A.!!$F1 4498
1 TraesCS6A01G201700 chr6D 244542054 244545699 3645 False 2049.3 5910 96.933333 860 4499 3 chr6D.!!$F1 3639
2 TraesCS6A01G201700 chr6B 334839240 334842340 3100 False 5038.0 5038 95.835000 860 4001 1 chr6B.!!$F1 3141
3 TraesCS6A01G201700 chr4D 401526716 401527529 813 False 398.0 577 83.397500 1 864 2 chr4D.!!$F1 863
4 TraesCS6A01G201700 chr7D 488125510 488126021 511 True 325.2 568 87.216000 1 637 2 chr7D.!!$R1 636
5 TraesCS6A01G201700 chr7B 453763872 453764375 503 False 355.0 355 79.781000 1 547 1 chr7B.!!$F1 546
6 TraesCS6A01G201700 chr7A 487253702 487254205 503 False 344.0 344 79.417000 1 547 1 chr7A.!!$F1 546

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
478 484 0.245539 ATGTTGCATTGCAGCTCCAC 59.754 50.0 23.27 13.82 40.35 4.02 F
1602 1628 0.108138 CTTTGAGAGGATTCCCGCGT 60.108 55.0 4.92 0.00 37.33 6.01 F
1964 1990 0.719015 AAGGAGGGGAGGATGAGTGA 59.281 55.0 0.00 0.00 0.00 3.41 F
1965 1991 0.948050 AGGAGGGGAGGATGAGTGAT 59.052 55.0 0.00 0.00 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1969 1995 0.119155 TCACTCATCCTCCCCACCTT 59.881 55.000 0.0 0.00 0.0 3.50 R
2739 2765 2.411069 CGCACTTCTGTTCATCTCACTG 59.589 50.000 0.0 0.00 0.0 3.66 R
3261 3287 3.343941 TCACTAATAAGCCCGCAAAGT 57.656 42.857 0.0 0.00 0.0 2.66 R
3913 3940 4.514441 CAGTGCATCTAGTCCATGGAATTC 59.486 45.833 21.5 6.35 0.0 2.17 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
31 32 3.260740 TCTTCGTCTCTAACCTCTCGTC 58.739 50.000 0.00 0.00 0.00 4.20
41 42 0.699399 ACCTCTCGTCCTTCTCCTCA 59.301 55.000 0.00 0.00 0.00 3.86
42 43 1.340600 ACCTCTCGTCCTTCTCCTCAG 60.341 57.143 0.00 0.00 0.00 3.35
53 54 0.975040 TCTCCTCAGGAAGCTCTGCC 60.975 60.000 0.00 0.00 34.91 4.85
141 143 1.136690 GTGATGAAACACTCGCGACA 58.863 50.000 3.71 0.00 37.73 4.35
200 202 1.680735 GATGGTTGCCAGTGTTGTGAA 59.319 47.619 0.00 0.00 36.75 3.18
208 210 1.068748 CCAGTGTTGTGAAGCAGCATC 60.069 52.381 0.00 0.00 40.35 3.91
209 211 1.878088 CAGTGTTGTGAAGCAGCATCT 59.122 47.619 0.00 0.00 40.35 2.90
344 349 2.995482 GCGTTCGACGGTGCTATG 59.005 61.111 8.96 0.00 42.82 2.23
345 350 1.515519 GCGTTCGACGGTGCTATGA 60.516 57.895 8.96 0.00 42.82 2.15
346 351 1.472276 GCGTTCGACGGTGCTATGAG 61.472 60.000 8.96 0.00 42.82 2.90
347 352 1.472276 CGTTCGACGGTGCTATGAGC 61.472 60.000 0.00 0.00 38.82 4.26
348 353 1.141019 TTCGACGGTGCTATGAGCC 59.859 57.895 0.00 0.00 41.51 4.70
389 394 3.055719 CCGGTCCTGCAACGCAAT 61.056 61.111 0.00 0.00 38.41 3.56
478 484 0.245539 ATGTTGCATTGCAGCTCCAC 59.754 50.000 23.27 13.82 40.35 4.02
536 554 1.612950 AGCGACCATGTTTCATTGCAA 59.387 42.857 0.00 0.00 0.00 4.08
552 570 4.015406 AACTCCACCGCGGCATCA 62.015 61.111 28.58 5.68 33.14 3.07
553 571 4.760047 ACTCCACCGCGGCATCAC 62.760 66.667 28.58 0.00 33.14 3.06
563 581 2.742372 GGCATCACGCGACCAAGT 60.742 61.111 15.93 0.00 43.84 3.16
645 663 4.201679 CGGCGACCACCAGCGATA 62.202 66.667 0.00 0.00 0.00 2.92
646 664 2.421739 GGCGACCACCAGCGATAT 59.578 61.111 0.00 0.00 0.00 1.63
647 665 1.227556 GGCGACCACCAGCGATATT 60.228 57.895 0.00 0.00 0.00 1.28
648 666 1.222115 GGCGACCACCAGCGATATTC 61.222 60.000 0.00 0.00 0.00 1.75
649 667 0.529773 GCGACCACCAGCGATATTCA 60.530 55.000 0.00 0.00 0.00 2.57
650 668 1.873903 GCGACCACCAGCGATATTCAT 60.874 52.381 0.00 0.00 0.00 2.57
651 669 2.483876 CGACCACCAGCGATATTCATT 58.516 47.619 0.00 0.00 0.00 2.57
652 670 2.221749 CGACCACCAGCGATATTCATTG 59.778 50.000 0.00 0.00 0.00 2.82
653 671 1.949525 ACCACCAGCGATATTCATTGC 59.050 47.619 0.00 0.00 41.32 3.56
654 672 1.069703 CCACCAGCGATATTCATTGCG 60.070 52.381 0.00 0.00 45.06 4.85
655 673 1.069703 CACCAGCGATATTCATTGCGG 60.070 52.381 0.00 0.00 45.06 5.69
656 674 0.518636 CCAGCGATATTCATTGCGGG 59.481 55.000 2.27 2.27 46.39 6.13
657 675 1.229428 CAGCGATATTCATTGCGGGT 58.771 50.000 0.00 0.00 45.06 5.28
658 676 1.195448 CAGCGATATTCATTGCGGGTC 59.805 52.381 0.00 0.00 45.06 4.46
659 677 0.517316 GCGATATTCATTGCGGGTCC 59.483 55.000 0.00 0.00 31.87 4.46
660 678 1.877637 CGATATTCATTGCGGGTCCA 58.122 50.000 0.00 0.00 0.00 4.02
661 679 1.531149 CGATATTCATTGCGGGTCCAC 59.469 52.381 0.00 0.00 0.00 4.02
662 680 1.880027 GATATTCATTGCGGGTCCACC 59.120 52.381 0.00 0.00 0.00 4.61
663 681 0.916086 TATTCATTGCGGGTCCACCT 59.084 50.000 0.00 0.00 36.97 4.00
664 682 0.394352 ATTCATTGCGGGTCCACCTC 60.394 55.000 0.00 0.00 36.97 3.85
665 683 2.796483 TTCATTGCGGGTCCACCTCG 62.796 60.000 0.00 0.00 36.97 4.63
666 684 3.000819 ATTGCGGGTCCACCTCGA 61.001 61.111 9.89 0.00 36.97 4.04
667 685 3.310860 ATTGCGGGTCCACCTCGAC 62.311 63.158 9.89 3.70 36.97 4.20
669 687 3.771160 GCGGGTCCACCTCGACAT 61.771 66.667 9.89 0.00 36.97 3.06
670 688 2.978824 CGGGTCCACCTCGACATT 59.021 61.111 0.00 0.00 36.97 2.71
676 694 1.003355 CCACCTCGACATTGGCTGT 60.003 57.895 0.00 0.00 42.15 4.40
699 717 4.279043 AAGCGTTTGCCGGCAACC 62.279 61.111 40.36 32.78 44.31 3.77
721 739 0.733150 CGCTCGCCGGATCTATGATA 59.267 55.000 5.05 0.00 0.00 2.15
722 740 1.532090 CGCTCGCCGGATCTATGATAC 60.532 57.143 5.05 0.00 0.00 2.24
723 741 1.532090 GCTCGCCGGATCTATGATACG 60.532 57.143 5.05 5.29 0.00 3.06
724 742 2.007608 CTCGCCGGATCTATGATACGA 58.992 52.381 5.05 0.00 0.00 3.43
726 744 2.354821 TCGCCGGATCTATGATACGATG 59.645 50.000 5.05 5.72 0.00 3.84
727 745 2.541794 CGCCGGATCTATGATACGATGG 60.542 54.545 5.05 0.00 0.00 3.51
728 746 2.688446 GCCGGATCTATGATACGATGGA 59.312 50.000 5.05 0.00 0.00 3.41
731 749 3.547014 CGGATCTATGATACGATGGAGCG 60.547 52.174 6.33 0.00 37.29 5.03
736 754 4.763279 TCTATGATACGATGGAGCGGTTTA 59.237 41.667 0.00 0.00 35.12 2.01
740 758 1.935933 ACGATGGAGCGGTTTATGTC 58.064 50.000 0.00 0.00 35.12 3.06
765 783 2.887360 CAAAAGATGCTGCGGGGG 59.113 61.111 0.00 0.00 0.00 5.40
766 784 3.070576 AAAAGATGCTGCGGGGGC 61.071 61.111 0.00 0.00 0.00 5.80
767 785 3.884704 AAAAGATGCTGCGGGGGCA 62.885 57.895 0.00 0.00 44.05 5.36
777 795 3.524606 CGGGGGCACGACGAGTAT 61.525 66.667 0.00 0.00 35.47 2.12
778 796 2.897972 GGGGGCACGACGAGTATT 59.102 61.111 0.00 0.00 0.00 1.89
820 838 2.273557 GACGGCCTTGATTAAGCGTAA 58.726 47.619 0.00 0.00 34.33 3.18
823 841 2.030457 CGGCCTTGATTAAGCGTAACTG 59.970 50.000 0.00 0.00 32.40 3.16
824 842 3.267483 GGCCTTGATTAAGCGTAACTGA 58.733 45.455 0.00 0.00 32.40 3.41
825 843 3.309954 GGCCTTGATTAAGCGTAACTGAG 59.690 47.826 0.00 0.00 32.40 3.35
829 847 2.235155 TGATTAAGCGTAACTGAGGGCA 59.765 45.455 0.00 0.00 0.00 5.36
873 891 1.467342 GTTATCAACCGCACTGGGAAC 59.533 52.381 0.00 0.00 44.64 3.62
1233 1257 1.074566 CACCTTCTCAGCCTTTCCCTT 59.925 52.381 0.00 0.00 0.00 3.95
1249 1273 0.811616 CCTTCCAATCCTCTTCCGCG 60.812 60.000 0.00 0.00 0.00 6.46
1254 1278 0.179073 CAATCCTCTTCCGCGTCCAT 60.179 55.000 4.92 0.00 0.00 3.41
1364 1390 2.920076 ATCCTCCGCCTCTTCGCTCT 62.920 60.000 0.00 0.00 0.00 4.09
1550 1576 2.815684 TACTCCCGCACCCACCAGAT 62.816 60.000 0.00 0.00 0.00 2.90
1602 1628 0.108138 CTTTGAGAGGATTCCCGCGT 60.108 55.000 4.92 0.00 37.33 6.01
1641 1667 3.956199 CTGCAATGATTGAGGGGTTATGT 59.044 43.478 9.76 0.00 0.00 2.29
1679 1705 2.086869 CGAGGCATTGGACTTGTTCAT 58.913 47.619 0.00 0.00 26.47 2.57
1810 1836 2.671619 GGCGGCCAAGTACTTGCA 60.672 61.111 27.05 0.00 39.16 4.08
1836 1862 1.678360 CAGCCGCGATTGATTTATGC 58.322 50.000 8.23 0.00 0.00 3.14
1950 1976 4.576463 GTGGTCAATGGCTATTGTAAGGAG 59.424 45.833 20.65 0.00 43.33 3.69
1951 1977 4.137543 GGTCAATGGCTATTGTAAGGAGG 58.862 47.826 20.65 0.00 43.33 4.30
1952 1978 4.137543 GTCAATGGCTATTGTAAGGAGGG 58.862 47.826 20.65 0.00 43.33 4.30
1953 1979 3.138283 TCAATGGCTATTGTAAGGAGGGG 59.862 47.826 20.65 0.00 43.33 4.79
1954 1980 2.579624 TGGCTATTGTAAGGAGGGGA 57.420 50.000 0.00 0.00 0.00 4.81
1955 1981 2.408565 TGGCTATTGTAAGGAGGGGAG 58.591 52.381 0.00 0.00 0.00 4.30
1956 1982 1.700186 GGCTATTGTAAGGAGGGGAGG 59.300 57.143 0.00 0.00 0.00 4.30
1957 1983 2.690840 GCTATTGTAAGGAGGGGAGGA 58.309 52.381 0.00 0.00 0.00 3.71
1958 1984 3.252351 GCTATTGTAAGGAGGGGAGGAT 58.748 50.000 0.00 0.00 0.00 3.24
1959 1985 3.008485 GCTATTGTAAGGAGGGGAGGATG 59.992 52.174 0.00 0.00 0.00 3.51
1960 1986 2.961536 TTGTAAGGAGGGGAGGATGA 57.038 50.000 0.00 0.00 0.00 2.92
1961 1987 2.478872 TGTAAGGAGGGGAGGATGAG 57.521 55.000 0.00 0.00 0.00 2.90
1962 1988 1.651770 TGTAAGGAGGGGAGGATGAGT 59.348 52.381 0.00 0.00 0.00 3.41
1963 1989 2.043227 GTAAGGAGGGGAGGATGAGTG 58.957 57.143 0.00 0.00 0.00 3.51
1964 1990 0.719015 AAGGAGGGGAGGATGAGTGA 59.281 55.000 0.00 0.00 0.00 3.41
1965 1991 0.948050 AGGAGGGGAGGATGAGTGAT 59.052 55.000 0.00 0.00 0.00 3.06
1966 1992 1.296523 AGGAGGGGAGGATGAGTGATT 59.703 52.381 0.00 0.00 0.00 2.57
1967 1993 1.419387 GGAGGGGAGGATGAGTGATTG 59.581 57.143 0.00 0.00 0.00 2.67
1968 1994 2.122768 GAGGGGAGGATGAGTGATTGT 58.877 52.381 0.00 0.00 0.00 2.71
1969 1995 3.309296 GAGGGGAGGATGAGTGATTGTA 58.691 50.000 0.00 0.00 0.00 2.41
1970 1996 3.711704 GAGGGGAGGATGAGTGATTGTAA 59.288 47.826 0.00 0.00 0.00 2.41
1971 1997 3.713764 AGGGGAGGATGAGTGATTGTAAG 59.286 47.826 0.00 0.00 0.00 2.34
1972 1998 3.181450 GGGGAGGATGAGTGATTGTAAGG 60.181 52.174 0.00 0.00 0.00 2.69
1973 1999 3.456277 GGGAGGATGAGTGATTGTAAGGT 59.544 47.826 0.00 0.00 0.00 3.50
2078 2104 2.283173 GTGGGGGTTCTGCAAGGG 60.283 66.667 0.00 0.00 0.00 3.95
2173 2199 3.224884 ACAATTTGTTAATTCGGGCCG 57.775 42.857 22.51 22.51 31.63 6.13
2370 2396 6.620678 ACCTAATTTGGTGACATTCAATTCG 58.379 36.000 10.97 0.00 42.32 3.34
2481 2507 9.170734 GATACCTATACATACAGTCCGTTCATA 57.829 37.037 0.00 0.00 0.00 2.15
2607 2633 4.478206 TGACAAGCTATTCAAGGAGAGG 57.522 45.455 0.00 0.00 0.00 3.69
2739 2765 4.545610 TCATTGAAGCCGAAAATGTTGTC 58.454 39.130 0.00 0.00 33.84 3.18
2885 2911 5.016173 TGCTTCTATGCCAAACCAGTTTAT 58.984 37.500 0.00 0.00 0.00 1.40
3063 3089 3.795688 TCTGCAATTCTGGAGAGGTTT 57.204 42.857 0.00 0.00 44.32 3.27
3077 3103 5.014544 TGGAGAGGTTTTCTGAAGATGGAAT 59.985 40.000 0.00 0.00 35.87 3.01
3111 3137 5.006746 GGTGACATCATTGGTTTCTCGTATC 59.993 44.000 0.00 0.00 0.00 2.24
3157 3183 3.020274 GAGGACATCTACACTGCTCTCA 58.980 50.000 0.00 0.00 0.00 3.27
3161 3187 5.068460 AGGACATCTACACTGCTCTCATTAC 59.932 44.000 0.00 0.00 0.00 1.89
3162 3188 5.163509 GGACATCTACACTGCTCTCATTACA 60.164 44.000 0.00 0.00 0.00 2.41
3319 3345 4.808364 TGGCTGAAGAAATTTTTGGAAACG 59.192 37.500 0.00 0.00 0.00 3.60
3450 3476 0.036022 AGAGGAACTGCAGACCAAGC 59.964 55.000 23.35 15.08 41.55 4.01
3464 3490 5.622914 GCAGACCAAGCAATCAAACATATGT 60.623 40.000 1.41 1.41 0.00 2.29
3804 3831 6.049955 TCTTGTCCCACCTAAAGATAACAG 57.950 41.667 0.00 0.00 0.00 3.16
3833 3860 7.425577 ACAACCTTACTTTTACATACCGAAC 57.574 36.000 0.00 0.00 0.00 3.95
3929 3956 3.776969 AGCTGTGAATTCCATGGACTAGA 59.223 43.478 15.91 0.00 0.00 2.43
3973 4000 4.932200 TGACAATTTGCTTTTGGAACGTTT 59.068 33.333 0.46 0.00 0.00 3.60
4064 4091 2.137523 GGGCTTGTTGTGCTCATTTTG 58.862 47.619 0.00 0.00 0.00 2.44
4092 4119 0.040425 CAACACAAGTAACCTGCCGC 60.040 55.000 0.00 0.00 0.00 6.53
4146 4173 8.487028 CAAGGTTGGAAATAGACTAGGAACTAT 58.513 37.037 0.00 0.00 41.70 2.12
4206 4233 3.485394 TGCTTAGCACATGTTCCTTTGA 58.515 40.909 1.39 0.00 31.71 2.69
4247 4274 2.342179 TGTAGTGTGTGTGTGTGTGTG 58.658 47.619 0.00 0.00 0.00 3.82
4248 4275 2.289133 TGTAGTGTGTGTGTGTGTGTGT 60.289 45.455 0.00 0.00 0.00 3.72
4249 4276 1.155889 AGTGTGTGTGTGTGTGTGTG 58.844 50.000 0.00 0.00 0.00 3.82
4250 4277 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
4251 4278 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
4252 4279 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
4253 4280 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
4254 4281 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
4287 4314 7.033530 AGAAACATCCGTTTTGATAACACAA 57.966 32.000 0.00 0.00 45.40 3.33
4360 4387 5.710513 TGACATCCTGTCCAATTTTTCAG 57.289 39.130 4.91 0.00 46.40 3.02
4387 4486 6.535508 GCAGTGAAGTATTTCGAAGTTAGGAT 59.464 38.462 0.00 0.00 36.04 3.24
4405 4504 2.351726 GGATTTCAGACTGCGCGTTAAT 59.648 45.455 8.43 3.42 0.00 1.40
4406 4505 3.181510 GGATTTCAGACTGCGCGTTAATT 60.182 43.478 8.43 0.00 0.00 1.40
4407 4506 2.873170 TTCAGACTGCGCGTTAATTG 57.127 45.000 8.43 1.62 0.00 2.32
4408 4507 2.073117 TCAGACTGCGCGTTAATTGA 57.927 45.000 8.43 4.26 0.00 2.57
4409 4508 1.724623 TCAGACTGCGCGTTAATTGAC 59.275 47.619 8.43 0.00 0.00 3.18
4410 4509 1.076332 AGACTGCGCGTTAATTGACC 58.924 50.000 8.43 0.00 0.00 4.02
4411 4510 1.076332 GACTGCGCGTTAATTGACCT 58.924 50.000 8.43 0.00 0.00 3.85
4412 4511 0.796312 ACTGCGCGTTAATTGACCTG 59.204 50.000 8.43 0.00 0.00 4.00
4413 4512 1.075542 CTGCGCGTTAATTGACCTGA 58.924 50.000 8.43 0.00 0.00 3.86
4414 4513 1.463056 CTGCGCGTTAATTGACCTGAA 59.537 47.619 8.43 0.00 0.00 3.02
4415 4514 1.463056 TGCGCGTTAATTGACCTGAAG 59.537 47.619 8.43 0.00 0.00 3.02
4416 4515 1.730064 GCGCGTTAATTGACCTGAAGA 59.270 47.619 8.43 0.00 0.00 2.87
4417 4516 2.158841 GCGCGTTAATTGACCTGAAGAA 59.841 45.455 8.43 0.00 0.00 2.52
4418 4517 3.364565 GCGCGTTAATTGACCTGAAGAAA 60.365 43.478 8.43 0.00 0.00 2.52
4419 4518 4.778904 CGCGTTAATTGACCTGAAGAAAA 58.221 39.130 0.00 0.00 0.00 2.29
4420 4519 5.209240 CGCGTTAATTGACCTGAAGAAAAA 58.791 37.500 0.00 0.00 0.00 1.94
4421 4520 5.856455 CGCGTTAATTGACCTGAAGAAAAAT 59.144 36.000 0.00 0.00 0.00 1.82
4422 4521 7.018826 CGCGTTAATTGACCTGAAGAAAAATA 58.981 34.615 0.00 0.00 0.00 1.40
4423 4522 7.216317 CGCGTTAATTGACCTGAAGAAAAATAG 59.784 37.037 0.00 0.00 0.00 1.73
4424 4523 7.008357 GCGTTAATTGACCTGAAGAAAAATAGC 59.992 37.037 0.00 0.00 0.00 2.97
4425 4524 7.484959 CGTTAATTGACCTGAAGAAAAATAGCC 59.515 37.037 0.00 0.00 0.00 3.93
4426 4525 5.921962 ATTGACCTGAAGAAAAATAGCCC 57.078 39.130 0.00 0.00 0.00 5.19
4427 4526 4.380843 TGACCTGAAGAAAAATAGCCCA 57.619 40.909 0.00 0.00 0.00 5.36
4428 4527 4.335416 TGACCTGAAGAAAAATAGCCCAG 58.665 43.478 0.00 0.00 0.00 4.45
4429 4528 4.202567 TGACCTGAAGAAAAATAGCCCAGT 60.203 41.667 0.00 0.00 0.00 4.00
4430 4529 4.336280 ACCTGAAGAAAAATAGCCCAGTC 58.664 43.478 0.00 0.00 0.00 3.51
4431 4530 4.043435 ACCTGAAGAAAAATAGCCCAGTCT 59.957 41.667 0.00 0.00 0.00 3.24
4432 4531 5.012893 CCTGAAGAAAAATAGCCCAGTCTT 58.987 41.667 0.00 0.00 0.00 3.01
4433 4532 5.105997 CCTGAAGAAAAATAGCCCAGTCTTG 60.106 44.000 0.00 0.00 0.00 3.02
4434 4533 4.766891 TGAAGAAAAATAGCCCAGTCTTGG 59.233 41.667 0.00 0.00 44.60 3.61
4435 4534 4.388577 AGAAAAATAGCCCAGTCTTGGT 57.611 40.909 0.00 0.00 43.40 3.67
4436 4535 4.336280 AGAAAAATAGCCCAGTCTTGGTC 58.664 43.478 0.00 0.00 43.40 4.02
4437 4536 2.808906 AAATAGCCCAGTCTTGGTCC 57.191 50.000 0.00 0.00 43.40 4.46
4438 4537 1.668826 AATAGCCCAGTCTTGGTCCA 58.331 50.000 0.00 0.00 43.40 4.02
4439 4538 1.668826 ATAGCCCAGTCTTGGTCCAA 58.331 50.000 3.76 3.76 43.40 3.53
4440 4539 1.668826 TAGCCCAGTCTTGGTCCAAT 58.331 50.000 4.34 0.00 43.40 3.16
4441 4540 0.779997 AGCCCAGTCTTGGTCCAATT 59.220 50.000 4.34 0.00 43.40 2.32
4442 4541 1.147817 AGCCCAGTCTTGGTCCAATTT 59.852 47.619 4.34 0.00 43.40 1.82
4443 4542 1.546029 GCCCAGTCTTGGTCCAATTTC 59.454 52.381 4.34 0.00 43.40 2.17
4444 4543 2.875296 CCCAGTCTTGGTCCAATTTCA 58.125 47.619 4.34 0.00 43.40 2.69
4445 4544 3.230134 CCCAGTCTTGGTCCAATTTCAA 58.770 45.455 4.34 0.00 43.40 2.69
4446 4545 3.834231 CCCAGTCTTGGTCCAATTTCAAT 59.166 43.478 4.34 0.00 43.40 2.57
4447 4546 5.016173 CCCAGTCTTGGTCCAATTTCAATA 58.984 41.667 4.34 0.00 43.40 1.90
4448 4547 5.658190 CCCAGTCTTGGTCCAATTTCAATAT 59.342 40.000 4.34 0.00 43.40 1.28
4492 4591 9.251792 TCTTTTGTGTCAAGAATTCATTCATTG 57.748 29.630 8.44 3.22 39.23 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 1.481772 CAGAGCTTCCTGAGGAGAAGG 59.518 57.143 0.00 0.00 40.91 3.46
42 43 4.722700 TTGGGCGGCAGAGCTTCC 62.723 66.667 12.47 0.00 37.29 3.46
53 54 2.044123 ATTCTTTAGGAGCTTGGGCG 57.956 50.000 0.00 0.00 44.37 6.13
141 143 1.729470 CGCCGGAGCATCTCTACAGT 61.729 60.000 5.05 0.00 39.83 3.55
200 202 3.557903 AACACCGCCAGATGCTGCT 62.558 57.895 0.00 0.00 38.05 4.24
341 346 0.237498 CGTCGCGTCATAGGCTCATA 59.763 55.000 5.77 0.00 0.00 2.15
342 347 1.008424 CGTCGCGTCATAGGCTCAT 60.008 57.895 5.77 0.00 0.00 2.90
343 348 2.407616 CGTCGCGTCATAGGCTCA 59.592 61.111 5.77 0.00 0.00 4.26
344 349 2.353607 CCGTCGCGTCATAGGCTC 60.354 66.667 5.77 0.00 0.00 4.70
345 350 3.122250 GACCGTCGCGTCATAGGCT 62.122 63.158 5.77 0.00 32.74 4.58
346 351 2.654404 GACCGTCGCGTCATAGGC 60.654 66.667 5.77 0.00 32.74 3.93
347 352 2.352001 CGACCGTCGCGTCATAGG 60.352 66.667 8.21 6.27 31.14 2.57
348 353 2.402388 ACGACCGTCGCGTCATAG 59.598 61.111 20.67 0.00 45.12 2.23
407 412 2.115052 TTGGGCAGCCGACAACAT 59.885 55.556 5.00 0.00 0.00 2.71
410 415 3.545124 ATCGTTGGGCAGCCGACAA 62.545 57.895 5.00 1.71 32.86 3.18
449 455 1.039856 AATGCAACATTATCGGGGGC 58.960 50.000 0.00 0.00 0.00 5.80
450 456 1.269726 GCAATGCAACATTATCGGGGG 60.270 52.381 0.00 0.00 0.00 5.40
456 462 2.761767 TGGAGCTGCAATGCAACATTAT 59.238 40.909 9.92 0.00 38.41 1.28
458 464 0.970640 TGGAGCTGCAATGCAACATT 59.029 45.000 9.92 0.00 38.41 2.71
478 484 3.386867 GAGCATTGCTTGGTCGCGG 62.387 63.158 13.35 0.00 42.51 6.46
517 534 1.720852 GTTGCAATGAAACATGGTCGC 59.279 47.619 0.59 0.00 0.00 5.19
520 538 2.964464 TGGAGTTGCAATGAAACATGGT 59.036 40.909 6.89 0.00 0.00 3.55
536 554 4.760047 GTGATGCCGCGGTGGAGT 62.760 66.667 28.70 8.35 42.00 3.85
550 568 0.037697 AGCATTACTTGGTCGCGTGA 60.038 50.000 5.77 0.00 0.00 4.35
552 570 2.750815 GAGCATTACTTGGTCGCGT 58.249 52.632 5.77 0.00 42.51 6.01
563 581 2.996444 CTGCTGCGATGGAGCATTA 58.004 52.632 13.36 0.00 45.27 1.90
596 614 2.602878 GTGGAGCTGCAATGAAACATG 58.397 47.619 10.44 0.00 0.00 3.21
628 646 2.971428 AATATCGCTGGTGGTCGCCG 62.971 60.000 0.00 0.00 0.00 6.46
629 647 1.222115 GAATATCGCTGGTGGTCGCC 61.222 60.000 0.00 0.00 0.00 5.54
630 648 0.529773 TGAATATCGCTGGTGGTCGC 60.530 55.000 0.00 0.00 0.00 5.19
631 649 2.154854 ATGAATATCGCTGGTGGTCG 57.845 50.000 0.00 0.00 0.00 4.79
632 650 2.031682 GCAATGAATATCGCTGGTGGTC 60.032 50.000 0.00 0.00 0.00 4.02
633 651 1.949525 GCAATGAATATCGCTGGTGGT 59.050 47.619 0.00 0.00 0.00 4.16
634 652 1.069703 CGCAATGAATATCGCTGGTGG 60.070 52.381 0.00 0.00 0.00 4.61
635 653 1.069703 CCGCAATGAATATCGCTGGTG 60.070 52.381 0.00 0.00 0.00 4.17
636 654 1.229428 CCGCAATGAATATCGCTGGT 58.771 50.000 0.00 0.00 0.00 4.00
637 655 0.518636 CCCGCAATGAATATCGCTGG 59.481 55.000 0.00 0.00 0.00 4.85
638 656 1.195448 GACCCGCAATGAATATCGCTG 59.805 52.381 0.00 0.00 0.00 5.18
639 657 1.512926 GACCCGCAATGAATATCGCT 58.487 50.000 0.00 0.00 0.00 4.93
640 658 0.517316 GGACCCGCAATGAATATCGC 59.483 55.000 0.00 0.00 0.00 4.58
641 659 1.531149 GTGGACCCGCAATGAATATCG 59.469 52.381 0.00 0.00 0.00 2.92
642 660 1.880027 GGTGGACCCGCAATGAATATC 59.120 52.381 1.75 0.00 0.00 1.63
643 661 1.494721 AGGTGGACCCGCAATGAATAT 59.505 47.619 1.75 0.00 38.74 1.28
644 662 0.916086 AGGTGGACCCGCAATGAATA 59.084 50.000 1.75 0.00 38.74 1.75
645 663 0.394352 GAGGTGGACCCGCAATGAAT 60.394 55.000 1.75 0.00 38.74 2.57
646 664 1.002624 GAGGTGGACCCGCAATGAA 60.003 57.895 1.75 0.00 38.74 2.57
647 665 2.668632 GAGGTGGACCCGCAATGA 59.331 61.111 1.75 0.00 38.74 2.57
648 666 2.819595 CGAGGTGGACCCGCAATG 60.820 66.667 1.75 0.00 38.74 2.82
649 667 3.000819 TCGAGGTGGACCCGCAAT 61.001 61.111 1.75 0.00 38.74 3.56
650 668 3.998672 GTCGAGGTGGACCCGCAA 61.999 66.667 1.75 0.00 38.74 4.85
652 670 3.310860 AATGTCGAGGTGGACCCGC 62.311 63.158 0.00 0.00 38.74 6.13
653 671 1.447838 CAATGTCGAGGTGGACCCG 60.448 63.158 0.00 0.00 38.74 5.28
654 672 1.078426 CCAATGTCGAGGTGGACCC 60.078 63.158 3.35 0.00 36.07 4.46
655 673 1.745489 GCCAATGTCGAGGTGGACC 60.745 63.158 12.09 0.00 36.07 4.46
656 674 1.021390 CAGCCAATGTCGAGGTGGAC 61.021 60.000 12.09 4.79 34.05 4.02
657 675 1.296392 CAGCCAATGTCGAGGTGGA 59.704 57.895 12.09 0.00 34.05 4.02
658 676 1.003355 ACAGCCAATGTCGAGGTGG 60.003 57.895 5.89 5.38 37.75 4.61
659 677 1.915614 GCACAGCCAATGTCGAGGTG 61.916 60.000 0.00 0.00 41.41 4.00
660 678 1.672356 GCACAGCCAATGTCGAGGT 60.672 57.895 0.00 0.00 41.41 3.85
661 679 1.376424 AGCACAGCCAATGTCGAGG 60.376 57.895 0.00 0.00 41.41 4.63
662 680 1.792301 CAGCACAGCCAATGTCGAG 59.208 57.895 0.00 0.00 41.41 4.04
663 681 2.327343 GCAGCACAGCCAATGTCGA 61.327 57.895 0.00 0.00 41.41 4.20
664 682 2.132517 TTGCAGCACAGCCAATGTCG 62.133 55.000 0.00 0.00 41.41 4.35
665 683 0.388134 CTTGCAGCACAGCCAATGTC 60.388 55.000 0.00 0.00 41.41 3.06
666 684 1.663739 CTTGCAGCACAGCCAATGT 59.336 52.632 0.00 0.00 45.43 2.71
667 685 1.736645 GCTTGCAGCACAGCCAATG 60.737 57.895 15.04 0.00 41.89 2.82
668 686 2.654877 GCTTGCAGCACAGCCAAT 59.345 55.556 15.04 0.00 41.89 3.16
669 687 3.968568 CGCTTGCAGCACAGCCAA 61.969 61.111 18.29 0.00 42.58 4.52
700 718 4.057428 ATAGATCCGGCGAGCGGC 62.057 66.667 9.30 6.35 42.51 6.53
702 720 0.733150 TATCATAGATCCGGCGAGCG 59.267 55.000 9.30 0.00 0.00 5.03
703 721 1.532090 CGTATCATAGATCCGGCGAGC 60.532 57.143 9.30 0.00 0.00 5.03
721 739 1.480954 AGACATAAACCGCTCCATCGT 59.519 47.619 0.00 0.00 0.00 3.73
722 740 1.860950 CAGACATAAACCGCTCCATCG 59.139 52.381 0.00 0.00 0.00 3.84
723 741 2.866762 GACAGACATAAACCGCTCCATC 59.133 50.000 0.00 0.00 0.00 3.51
724 742 2.501723 AGACAGACATAAACCGCTCCAT 59.498 45.455 0.00 0.00 0.00 3.41
726 744 2.673368 CAAGACAGACATAAACCGCTCC 59.327 50.000 0.00 0.00 0.00 4.70
727 745 2.094417 GCAAGACAGACATAAACCGCTC 59.906 50.000 0.00 0.00 0.00 5.03
728 746 2.076863 GCAAGACAGACATAAACCGCT 58.923 47.619 0.00 0.00 0.00 5.52
731 749 6.072112 TCTTTTGCAAGACAGACATAAACC 57.928 37.500 0.00 0.00 33.80 3.27
764 782 1.135489 TCACAGAATACTCGTCGTGCC 60.135 52.381 0.00 0.00 0.00 5.01
765 783 2.257974 TCACAGAATACTCGTCGTGC 57.742 50.000 0.00 0.00 0.00 5.34
766 784 3.543889 CACATCACAGAATACTCGTCGTG 59.456 47.826 0.00 0.00 0.00 4.35
767 785 3.439129 TCACATCACAGAATACTCGTCGT 59.561 43.478 0.00 0.00 0.00 4.34
769 787 4.355437 CCTCACATCACAGAATACTCGTC 58.645 47.826 0.00 0.00 0.00 4.20
771 789 3.381590 TCCCTCACATCACAGAATACTCG 59.618 47.826 0.00 0.00 0.00 4.18
772 790 4.688021 GTCCCTCACATCACAGAATACTC 58.312 47.826 0.00 0.00 0.00 2.59
774 792 3.130516 TCGTCCCTCACATCACAGAATAC 59.869 47.826 0.00 0.00 0.00 1.89
775 793 3.361786 TCGTCCCTCACATCACAGAATA 58.638 45.455 0.00 0.00 0.00 1.75
776 794 2.179427 TCGTCCCTCACATCACAGAAT 58.821 47.619 0.00 0.00 0.00 2.40
777 795 1.627864 TCGTCCCTCACATCACAGAA 58.372 50.000 0.00 0.00 0.00 3.02
778 796 1.272490 GTTCGTCCCTCACATCACAGA 59.728 52.381 0.00 0.00 0.00 3.41
820 838 1.690219 CCGCCTTATCTGCCCTCAGT 61.690 60.000 0.00 0.00 41.10 3.41
823 841 2.281139 GCCGCCTTATCTGCCCTC 60.281 66.667 0.00 0.00 0.00 4.30
824 842 2.770048 AGCCGCCTTATCTGCCCT 60.770 61.111 0.00 0.00 0.00 5.19
825 843 2.403132 ATCAGCCGCCTTATCTGCCC 62.403 60.000 0.00 0.00 0.00 5.36
829 847 2.548920 GCAGTTATCAGCCGCCTTATCT 60.549 50.000 0.00 0.00 0.00 1.98
873 891 3.136763 CCATTGTTGGGATCTCATCTCG 58.863 50.000 0.00 0.00 39.56 4.04
1080 1104 1.980036 GGGTGTAGGTACCAGTTTGGA 59.020 52.381 15.94 0.00 40.96 3.53
1233 1257 1.515954 GACGCGGAAGAGGATTGGA 59.484 57.895 12.47 0.00 34.13 3.53
1249 1273 3.108288 GCGGGGAGAGGGAATGGAC 62.108 68.421 0.00 0.00 0.00 4.02
1364 1390 1.144716 GGCGAGTGGAGATGCATGA 59.855 57.895 2.46 0.00 0.00 3.07
1461 1487 1.061812 AGGACCATGAGGCTGAGGTAT 60.062 52.381 0.00 0.00 39.06 2.73
1602 1628 1.068588 GCAGCATAGGATACCACGTCA 59.931 52.381 0.00 0.00 37.17 4.35
1641 1667 1.320344 CGTCAATCCTCCCCGTCTCA 61.320 60.000 0.00 0.00 0.00 3.27
1679 1705 0.532573 GTCCGACAGCTCCATCTTCA 59.467 55.000 0.00 0.00 0.00 3.02
1810 1836 0.461870 TCAATCGCGGCTGCATAAGT 60.462 50.000 19.50 0.00 42.97 2.24
1818 1844 1.265095 CAGCATAAATCAATCGCGGCT 59.735 47.619 6.13 0.00 0.00 5.52
1823 1849 4.153117 GCTCCCTACAGCATAAATCAATCG 59.847 45.833 0.00 0.00 39.43 3.34
1836 1862 1.073923 ACAACCCTTTGCTCCCTACAG 59.926 52.381 0.00 0.00 36.00 2.74
1938 1964 4.493618 TCATCCTCCCCTCCTTACAATAG 58.506 47.826 0.00 0.00 0.00 1.73
1950 1976 3.181450 CCTTACAATCACTCATCCTCCCC 60.181 52.174 0.00 0.00 0.00 4.81
1951 1977 3.456277 ACCTTACAATCACTCATCCTCCC 59.544 47.826 0.00 0.00 0.00 4.30
1952 1978 4.446371 CACCTTACAATCACTCATCCTCC 58.554 47.826 0.00 0.00 0.00 4.30
1953 1979 4.446371 CCACCTTACAATCACTCATCCTC 58.554 47.826 0.00 0.00 0.00 3.71
1954 1980 3.200825 CCCACCTTACAATCACTCATCCT 59.799 47.826 0.00 0.00 0.00 3.24
1955 1981 3.545703 CCCACCTTACAATCACTCATCC 58.454 50.000 0.00 0.00 0.00 3.51
1956 1982 3.199946 TCCCCACCTTACAATCACTCATC 59.800 47.826 0.00 0.00 0.00 2.92
1957 1983 3.189606 TCCCCACCTTACAATCACTCAT 58.810 45.455 0.00 0.00 0.00 2.90
1958 1984 2.571653 CTCCCCACCTTACAATCACTCA 59.428 50.000 0.00 0.00 0.00 3.41
1959 1985 2.092914 CCTCCCCACCTTACAATCACTC 60.093 54.545 0.00 0.00 0.00 3.51
1960 1986 1.916181 CCTCCCCACCTTACAATCACT 59.084 52.381 0.00 0.00 0.00 3.41
1961 1987 1.913419 TCCTCCCCACCTTACAATCAC 59.087 52.381 0.00 0.00 0.00 3.06
1962 1988 2.352561 TCCTCCCCACCTTACAATCA 57.647 50.000 0.00 0.00 0.00 2.57
1963 1989 2.777692 TCATCCTCCCCACCTTACAATC 59.222 50.000 0.00 0.00 0.00 2.67
1964 1990 2.780010 CTCATCCTCCCCACCTTACAAT 59.220 50.000 0.00 0.00 0.00 2.71
1965 1991 2.196595 CTCATCCTCCCCACCTTACAA 58.803 52.381 0.00 0.00 0.00 2.41
1966 1992 1.080498 ACTCATCCTCCCCACCTTACA 59.920 52.381 0.00 0.00 0.00 2.41
1967 1993 1.486726 CACTCATCCTCCCCACCTTAC 59.513 57.143 0.00 0.00 0.00 2.34
1968 1994 1.364678 TCACTCATCCTCCCCACCTTA 59.635 52.381 0.00 0.00 0.00 2.69
1969 1995 0.119155 TCACTCATCCTCCCCACCTT 59.881 55.000 0.00 0.00 0.00 3.50
1970 1996 0.344790 ATCACTCATCCTCCCCACCT 59.655 55.000 0.00 0.00 0.00 4.00
1971 1997 0.471617 CATCACTCATCCTCCCCACC 59.528 60.000 0.00 0.00 0.00 4.61
1972 1998 0.179034 GCATCACTCATCCTCCCCAC 60.179 60.000 0.00 0.00 0.00 4.61
1973 1999 1.689243 CGCATCACTCATCCTCCCCA 61.689 60.000 0.00 0.00 0.00 4.96
2078 2104 1.890174 GCATTGTGCACCTTACCCC 59.110 57.895 15.69 0.00 44.26 4.95
2173 2199 8.621532 TTCTCTATATGCCCATAAACACATTC 57.378 34.615 0.00 0.00 0.00 2.67
2370 2396 5.065988 ACATTTGCATAACCCGTCTATCAAC 59.934 40.000 0.00 0.00 0.00 3.18
2481 2507 5.608437 TCCCTTCATCTTGCATAGGTATTCT 59.392 40.000 0.00 0.00 0.00 2.40
2739 2765 2.411069 CGCACTTCTGTTCATCTCACTG 59.589 50.000 0.00 0.00 0.00 3.66
2944 2970 5.193679 GGTCTTCCATAAACCAGCTACATT 58.806 41.667 0.00 0.00 33.11 2.71
3063 3089 7.147655 ACCTCTTTCGATATTCCATCTTCAGAA 60.148 37.037 0.00 0.00 0.00 3.02
3077 3103 5.104941 ACCAATGATGTCACCTCTTTCGATA 60.105 40.000 0.00 0.00 0.00 2.92
3126 3152 6.875726 CAGTGTAGATGTCCTCATTCAAAGAA 59.124 38.462 0.00 0.00 34.06 2.52
3157 3183 9.577110 CTGTCTTGATTTGCATAAACATGTAAT 57.423 29.630 0.00 0.00 0.00 1.89
3161 3187 9.577110 AATACTGTCTTGATTTGCATAAACATG 57.423 29.630 0.00 0.00 0.00 3.21
3162 3188 9.793252 GAATACTGTCTTGATTTGCATAAACAT 57.207 29.630 0.00 0.00 0.00 2.71
3261 3287 3.343941 TCACTAATAAGCCCGCAAAGT 57.656 42.857 0.00 0.00 0.00 2.66
3319 3345 4.902448 AGGATTGTAGTCTTCCCATCTACC 59.098 45.833 0.00 0.00 34.83 3.18
3450 3476 7.975058 TCTGCCAACATTACATATGTTTGATTG 59.025 33.333 14.77 13.17 39.94 2.67
3464 3490 6.374333 GGTAGACAATTCTTCTGCCAACATTA 59.626 38.462 13.19 0.00 43.43 1.90
3913 3940 4.514441 CAGTGCATCTAGTCCATGGAATTC 59.486 45.833 21.50 6.35 0.00 2.17
3973 4000 5.762179 AGTTATTGTGGATCTTCAGGTCA 57.238 39.130 0.00 0.00 0.00 4.02
4064 4091 6.143919 GCAGGTTACTTGTGTTGATTTAAAGC 59.856 38.462 0.00 0.00 0.00 3.51
4092 4119 2.995466 AGTGACATGTCAATTTGGCG 57.005 45.000 29.42 0.00 41.85 5.69
4206 4233 9.628500 ACTACAAAGACAAAAAGGAAGTCTAAT 57.372 29.630 0.00 0.00 41.45 1.73
4247 4274 5.539582 TGTTTCTACTTGAACACACACAC 57.460 39.130 0.00 0.00 33.88 3.82
4248 4275 5.295787 GGATGTTTCTACTTGAACACACACA 59.704 40.000 0.00 0.00 33.88 3.72
4249 4276 5.558273 CGGATGTTTCTACTTGAACACACAC 60.558 44.000 0.00 0.00 33.88 3.82
4250 4277 4.509970 CGGATGTTTCTACTTGAACACACA 59.490 41.667 0.00 0.00 33.88 3.72
4251 4278 4.510340 ACGGATGTTTCTACTTGAACACAC 59.490 41.667 0.00 0.00 33.88 3.82
4252 4279 4.699637 ACGGATGTTTCTACTTGAACACA 58.300 39.130 0.00 0.00 33.88 3.72
4253 4280 5.668558 AACGGATGTTTCTACTTGAACAC 57.331 39.130 0.00 0.00 33.53 3.32
4287 4314 6.455360 TTTTCTGCTCAATTCTTCAACTGT 57.545 33.333 0.00 0.00 0.00 3.55
4360 4387 5.847670 AACTTCGAAATACTTCACTGCTC 57.152 39.130 0.00 0.00 0.00 4.26
4387 4486 2.803386 TCAATTAACGCGCAGTCTGAAA 59.197 40.909 5.73 0.77 0.00 2.69
4405 4504 4.735369 TGGGCTATTTTTCTTCAGGTCAA 58.265 39.130 0.00 0.00 0.00 3.18
4406 4505 4.202567 ACTGGGCTATTTTTCTTCAGGTCA 60.203 41.667 0.00 0.00 0.00 4.02
4407 4506 4.336280 ACTGGGCTATTTTTCTTCAGGTC 58.664 43.478 0.00 0.00 0.00 3.85
4408 4507 4.043435 AGACTGGGCTATTTTTCTTCAGGT 59.957 41.667 0.00 0.00 0.00 4.00
4409 4508 4.593956 AGACTGGGCTATTTTTCTTCAGG 58.406 43.478 0.00 0.00 0.00 3.86
4410 4509 5.105997 CCAAGACTGGGCTATTTTTCTTCAG 60.106 44.000 0.00 0.00 39.30 3.02
4411 4510 4.766891 CCAAGACTGGGCTATTTTTCTTCA 59.233 41.667 0.00 0.00 39.30 3.02
4412 4511 5.316327 CCAAGACTGGGCTATTTTTCTTC 57.684 43.478 0.00 0.00 39.30 2.87
4426 4525 7.121759 ACAGATATTGAAATTGGACCAAGACTG 59.878 37.037 13.43 11.95 0.00 3.51
4427 4526 7.177878 ACAGATATTGAAATTGGACCAAGACT 58.822 34.615 13.43 0.00 0.00 3.24
4428 4527 7.396540 ACAGATATTGAAATTGGACCAAGAC 57.603 36.000 13.43 7.04 0.00 3.01
4429 4528 9.527157 TTAACAGATATTGAAATTGGACCAAGA 57.473 29.630 13.43 0.00 0.00 3.02
4447 4546 9.768662 ACAAAAGAAATGCTCAAATTAACAGAT 57.231 25.926 0.00 0.00 0.00 2.90
4448 4547 9.033481 CACAAAAGAAATGCTCAAATTAACAGA 57.967 29.630 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.