Multiple sequence alignment - TraesCS5D01G372700

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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 TraesCS5D01G372700 chr5D 100.000 6028 0 0 1 6028 446410681 446404654 0.000000e+00 11132
1 TraesCS5D01G372700 chr5A 96.277 2337 80 7 3695 6028 564081292 564078960 0.000000e+00 3827
2 TraesCS5D01G372700 chr5A 92.992 1584 53 20 1966 3540 564082836 564081302 0.000000e+00 2257
3 TraesCS5D01G372700 chr5A 89.135 1583 100 31 466 2007 564084303 564082752 0.000000e+00 1905
4 TraesCS5D01G372700 chr5B 94.613 2432 91 14 3610 6028 544336079 544333675 0.000000e+00 3729
5 TraesCS5D01G372700 chr5B 91.961 1331 71 17 714 2017 544339268 544337947 0.000000e+00 1832
6 TraesCS5D01G372700 chr5B 94.891 920 24 15 2713 3613 544337029 544336114 0.000000e+00 1417
7 TraesCS5D01G372700 chr5B 90.837 753 46 12 1966 2714 544338041 544337308 0.000000e+00 987
8 TraesCS5D01G372700 chr5B 79.666 718 47 32 2 686 544339911 544339260 5.580000e-115 425


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 TraesCS5D01G372700 chr5D 446404654 446410681 6027 True 11132 11132 100.000000 1 6028 1 chr5D.!!$R1 6027
1 TraesCS5D01G372700 chr5A 564078960 564084303 5343 True 2663 3827 92.801333 466 6028 3 chr5A.!!$R1 5562
2 TraesCS5D01G372700 chr5B 544333675 544339911 6236 True 1678 3729 90.393600 2 6028 5 chr5B.!!$R1 6026

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
800 884 0.102300 GGCGCACCCCATTTATTGTC 59.898 55.000 10.83 0.0 0.00 3.18 F
936 1024 0.179000 CCCAGGGGAAGATGAAGACG 59.821 60.000 0.00 0.0 37.50 4.18 F
1545 1633 1.085091 CTGTTCTGCCACAGATGCTC 58.915 55.000 0.00 0.0 46.29 4.26 F
2736 3132 1.072806 AGTGTGCAGGAAAGCAGATCA 59.927 47.619 0.00 0.0 46.69 2.92 F
3854 4309 1.227999 TGGAGCAACAGCGCACTTAC 61.228 55.000 11.47 0.0 0.00 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1742 1840 0.679002 GCAAAGCCCTCATCTCAGCA 60.679 55.000 0.00 0.0 0.00 4.41 R
2717 3113 1.527034 TGATCTGCTTTCCTGCACAC 58.473 50.000 0.00 0.0 38.12 3.82 R
3027 3423 3.649502 TGATATCTCCACATGCCAGTCAT 59.350 43.478 3.98 0.0 35.31 3.06 R
3996 4451 0.178961 AAACCCTTGGAGCCAGGAAC 60.179 55.000 0.00 0.0 0.00 3.62 R
5499 5975 0.036294 GAGTCCTTCTTTCCCCGTGG 60.036 60.000 0.00 0.0 0.00 4.94 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
57 58 2.180159 AAATCGCGGCTAGTGGTGGT 62.180 55.000 6.13 0.00 0.00 4.16
58 59 1.324740 AATCGCGGCTAGTGGTGGTA 61.325 55.000 6.13 0.00 0.00 3.25
60 61 2.707849 CGCGGCTAGTGGTGGTAGT 61.708 63.158 0.00 0.00 0.00 2.73
61 62 1.153628 GCGGCTAGTGGTGGTAGTG 60.154 63.158 0.00 0.00 0.00 2.74
62 63 1.515954 CGGCTAGTGGTGGTAGTGG 59.484 63.158 0.00 0.00 0.00 4.00
63 64 1.255667 CGGCTAGTGGTGGTAGTGGT 61.256 60.000 0.00 0.00 0.00 4.16
64 65 0.249398 GGCTAGTGGTGGTAGTGGTG 59.751 60.000 0.00 0.00 0.00 4.17
65 66 0.974383 GCTAGTGGTGGTAGTGGTGT 59.026 55.000 0.00 0.00 0.00 4.16
66 67 1.067071 GCTAGTGGTGGTAGTGGTGTC 60.067 57.143 0.00 0.00 0.00 3.67
67 68 2.526432 CTAGTGGTGGTAGTGGTGTCT 58.474 52.381 0.00 0.00 0.00 3.41
68 69 1.339097 AGTGGTGGTAGTGGTGTCTC 58.661 55.000 0.00 0.00 0.00 3.36
69 70 1.133136 AGTGGTGGTAGTGGTGTCTCT 60.133 52.381 0.00 0.00 0.00 3.10
70 71 1.272769 GTGGTGGTAGTGGTGTCTCTC 59.727 57.143 0.00 0.00 0.00 3.20
71 72 1.147191 TGGTGGTAGTGGTGTCTCTCT 59.853 52.381 0.00 0.00 0.00 3.10
72 73 1.819903 GGTGGTAGTGGTGTCTCTCTC 59.180 57.143 0.00 0.00 0.00 3.20
73 74 1.819903 GTGGTAGTGGTGTCTCTCTCC 59.180 57.143 0.00 0.00 0.00 3.71
74 75 1.711375 TGGTAGTGGTGTCTCTCTCCT 59.289 52.381 0.00 0.00 0.00 3.69
75 76 2.110188 TGGTAGTGGTGTCTCTCTCCTT 59.890 50.000 0.00 0.00 0.00 3.36
76 77 2.756207 GGTAGTGGTGTCTCTCTCCTTC 59.244 54.545 0.00 0.00 0.00 3.46
77 78 2.990740 AGTGGTGTCTCTCTCCTTCT 57.009 50.000 0.00 0.00 0.00 2.85
78 79 2.524306 AGTGGTGTCTCTCTCCTTCTG 58.476 52.381 0.00 0.00 0.00 3.02
79 80 1.548269 GTGGTGTCTCTCTCCTTCTGG 59.452 57.143 0.00 0.00 0.00 3.86
80 81 0.534873 GGTGTCTCTCTCCTTCTGGC 59.465 60.000 0.00 0.00 0.00 4.85
81 82 0.172352 GTGTCTCTCTCCTTCTGGCG 59.828 60.000 0.00 0.00 0.00 5.69
82 83 0.967887 TGTCTCTCTCCTTCTGGCGG 60.968 60.000 0.00 0.00 0.00 6.13
83 84 0.968393 GTCTCTCTCCTTCTGGCGGT 60.968 60.000 0.00 0.00 0.00 5.68
86 87 3.672295 CTCTCCTTCTGGCGGTGGC 62.672 68.421 0.00 0.00 38.90 5.01
382 409 2.679132 AATCGAATCCGGGCGACTCG 62.679 60.000 15.22 10.21 39.56 4.18
405 432 1.433879 CGCCGTGCTCTAGCTACTT 59.566 57.895 3.26 0.00 42.66 2.24
408 435 1.394618 CCGTGCTCTAGCTACTTCCT 58.605 55.000 3.26 0.00 42.66 3.36
409 436 1.335496 CCGTGCTCTAGCTACTTCCTC 59.665 57.143 3.26 0.00 42.66 3.71
410 437 2.294074 CGTGCTCTAGCTACTTCCTCT 58.706 52.381 3.26 0.00 42.66 3.69
421 448 3.617775 GCTACTTCCTCTGGTTCTGTTCC 60.618 52.174 0.00 0.00 0.00 3.62
422 449 1.344763 ACTTCCTCTGGTTCTGTTCCG 59.655 52.381 0.00 0.00 0.00 4.30
423 450 1.618837 CTTCCTCTGGTTCTGTTCCGA 59.381 52.381 0.00 0.00 0.00 4.55
424 451 1.257743 TCCTCTGGTTCTGTTCCGAG 58.742 55.000 0.00 0.00 0.00 4.63
425 452 0.390472 CCTCTGGTTCTGTTCCGAGC 60.390 60.000 0.00 0.00 0.00 5.03
426 453 0.734253 CTCTGGTTCTGTTCCGAGCG 60.734 60.000 0.00 0.00 0.00 5.03
427 454 1.176619 TCTGGTTCTGTTCCGAGCGA 61.177 55.000 0.00 0.00 0.00 4.93
429 456 1.446272 GGTTCTGTTCCGAGCGAGG 60.446 63.158 0.00 0.00 0.00 4.63
430 457 1.446272 GTTCTGTTCCGAGCGAGGG 60.446 63.158 0.73 0.00 0.00 4.30
431 458 1.605451 TTCTGTTCCGAGCGAGGGA 60.605 57.895 0.73 0.00 0.00 4.20
432 459 1.595993 TTCTGTTCCGAGCGAGGGAG 61.596 60.000 0.73 0.00 34.45 4.30
433 460 2.035155 TGTTCCGAGCGAGGGAGA 59.965 61.111 0.73 0.00 34.45 3.71
434 461 1.595993 CTGTTCCGAGCGAGGGAGAA 61.596 60.000 0.73 0.00 34.45 2.87
435 462 1.139947 GTTCCGAGCGAGGGAGAAG 59.860 63.158 0.73 0.00 34.45 2.85
436 463 2.052690 TTCCGAGCGAGGGAGAAGG 61.053 63.158 0.73 0.00 34.45 3.46
437 464 3.532155 CCGAGCGAGGGAGAAGGG 61.532 72.222 0.00 0.00 0.00 3.95
438 465 3.532155 CGAGCGAGGGAGAAGGGG 61.532 72.222 0.00 0.00 0.00 4.79
439 466 2.042843 GAGCGAGGGAGAAGGGGA 60.043 66.667 0.00 0.00 0.00 4.81
440 467 1.458588 GAGCGAGGGAGAAGGGGAT 60.459 63.158 0.00 0.00 0.00 3.85
441 468 0.178958 GAGCGAGGGAGAAGGGGATA 60.179 60.000 0.00 0.00 0.00 2.59
442 469 0.264955 AGCGAGGGAGAAGGGGATAA 59.735 55.000 0.00 0.00 0.00 1.75
445 472 2.896039 CGAGGGAGAAGGGGATAAGAT 58.104 52.381 0.00 0.00 0.00 2.40
457 484 3.902467 GGGGATAAGATAACCCTCTTCGT 59.098 47.826 0.00 0.00 42.86 3.85
509 554 1.641577 CGGGTTCGGTTCAGATTCTC 58.358 55.000 0.00 0.00 0.00 2.87
510 555 1.739371 CGGGTTCGGTTCAGATTCTCC 60.739 57.143 0.00 0.00 0.00 3.71
511 556 1.641577 GGTTCGGTTCAGATTCTCCG 58.358 55.000 6.06 6.06 43.65 4.63
512 557 1.000145 GTTCGGTTCAGATTCTCCGC 59.000 55.000 7.28 0.00 42.28 5.54
513 558 0.457853 TTCGGTTCAGATTCTCCGCG 60.458 55.000 0.00 0.00 42.28 6.46
515 560 2.174319 GGTTCAGATTCTCCGCGGC 61.174 63.158 23.51 5.81 0.00 6.53
516 561 1.153549 GTTCAGATTCTCCGCGGCT 60.154 57.895 23.51 8.61 0.00 5.52
517 562 0.741221 GTTCAGATTCTCCGCGGCTT 60.741 55.000 23.51 4.19 0.00 4.35
521 566 2.045926 ATTCTCCGCGGCTTTGCT 60.046 55.556 23.51 0.00 0.00 3.91
536 581 2.148916 TTGCTGTGAGATTCGTTCGT 57.851 45.000 0.00 0.00 0.00 3.85
539 584 1.057847 GCTGTGAGATTCGTTCGTTCG 59.942 52.381 0.00 0.00 0.00 3.95
540 585 1.649171 CTGTGAGATTCGTTCGTTCGG 59.351 52.381 2.85 0.00 0.00 4.30
542 587 1.647702 GTGAGATTCGTTCGTTCGGTC 59.352 52.381 2.85 2.69 0.00 4.79
543 588 1.266466 GAGATTCGTTCGTTCGGTCC 58.734 55.000 2.85 0.00 0.00 4.46
550 597 2.353610 TTCGTTCGGTCCCTAGGGC 61.354 63.158 24.42 17.58 34.68 5.19
566 613 2.750237 GCGGGCGGGTTCTTCAAT 60.750 61.111 0.00 0.00 0.00 2.57
578 625 2.817844 GTTCTTCAATGGGTTTAGCCGT 59.182 45.455 0.00 0.00 38.44 5.68
579 626 3.985019 TCTTCAATGGGTTTAGCCGTA 57.015 42.857 0.00 0.00 38.44 4.02
598 645 0.397564 ACCGTACGTTTGGGGATGTT 59.602 50.000 15.21 0.00 0.00 2.71
608 655 2.268920 GGGATGTTCCGCTGCTGA 59.731 61.111 0.00 0.00 37.43 4.26
609 656 1.153086 GGGATGTTCCGCTGCTGAT 60.153 57.895 0.00 0.00 37.43 2.90
610 657 0.106708 GGGATGTTCCGCTGCTGATA 59.893 55.000 0.00 0.00 37.43 2.15
611 658 1.221414 GGATGTTCCGCTGCTGATAC 58.779 55.000 0.00 0.00 0.00 2.24
612 659 1.202580 GGATGTTCCGCTGCTGATACT 60.203 52.381 0.00 0.00 0.00 2.12
613 660 1.863454 GATGTTCCGCTGCTGATACTG 59.137 52.381 0.00 0.00 0.00 2.74
614 661 0.894835 TGTTCCGCTGCTGATACTGA 59.105 50.000 0.00 0.00 0.00 3.41
615 662 1.482182 TGTTCCGCTGCTGATACTGAT 59.518 47.619 0.00 0.00 0.00 2.90
616 663 2.693074 TGTTCCGCTGCTGATACTGATA 59.307 45.455 0.00 0.00 0.00 2.15
690 752 1.905922 GCGGTTTCTGTCAGCTCAGC 61.906 60.000 0.00 0.00 35.63 4.26
704 766 2.059541 GCTCAGCCCGTATCGATTTAC 58.940 52.381 1.71 0.00 0.00 2.01
710 772 3.190953 AGCCCGTATCGATTTACTCTAGC 59.809 47.826 1.71 0.00 0.00 3.42
711 773 3.744987 CCCGTATCGATTTACTCTAGCG 58.255 50.000 1.71 0.00 0.00 4.26
736 798 0.672401 TCCGCCTGGTTTCGATTCAC 60.672 55.000 0.00 0.00 36.30 3.18
765 839 4.080582 TCCTGTTTCAGTTCCAGTTTCAGA 60.081 41.667 0.00 0.00 0.00 3.27
783 857 2.856222 AGATGATTTCTGAATCCCGGC 58.144 47.619 0.00 0.00 40.79 6.13
788 862 3.969250 TTCTGAATCCCGGCGCACC 62.969 63.158 10.83 0.00 0.00 5.01
795 869 4.805768 CCCGGCGCACCCCATTTA 62.806 66.667 10.83 0.00 0.00 1.40
800 884 0.102300 GGCGCACCCCATTTATTGTC 59.898 55.000 10.83 0.00 0.00 3.18
801 885 0.814457 GCGCACCCCATTTATTGTCA 59.186 50.000 0.30 0.00 0.00 3.58
805 889 3.243168 CGCACCCCATTTATTGTCATCAG 60.243 47.826 0.00 0.00 0.00 2.90
820 904 8.945481 ATTGTCATCAGTTGTTCAAATTTTGA 57.055 26.923 7.74 7.74 38.04 2.69
821 905 8.768957 TTGTCATCAGTTGTTCAAATTTTGAA 57.231 26.923 18.29 18.29 46.68 2.69
858 942 2.237143 TCTCACCCTGCTCGATTTCAAT 59.763 45.455 0.00 0.00 0.00 2.57
873 958 1.538047 TCAATTTGCTCTGCAGGGAC 58.462 50.000 20.53 9.58 40.61 4.46
936 1024 0.179000 CCCAGGGGAAGATGAAGACG 59.821 60.000 0.00 0.00 37.50 4.18
1446 1534 2.651361 CTGTTCGAGTCGCTGGGT 59.349 61.111 7.92 0.00 0.00 4.51
1545 1633 1.085091 CTGTTCTGCCACAGATGCTC 58.915 55.000 0.00 0.00 46.29 4.26
1547 1635 1.742880 TTCTGCCACAGATGCTCGC 60.743 57.895 0.00 0.00 40.39 5.03
1548 1636 3.561213 CTGCCACAGATGCTCGCG 61.561 66.667 0.00 0.00 32.44 5.87
1575 1663 5.073144 TGTTGTTAAGATCCTCAAGAACCCT 59.927 40.000 8.27 0.00 0.00 4.34
1635 1723 2.551270 AGCATTGTTCAGGTCCCTCTA 58.449 47.619 0.00 0.00 0.00 2.43
1675 1765 8.316946 TCAATATTTGCATTGTAATTGAACCCA 58.683 29.630 0.00 0.00 37.23 4.51
1742 1840 4.040217 TGGCATGATTACCTTGCTTGTTTT 59.960 37.500 0.00 0.00 43.25 2.43
1799 1900 5.769662 AGTTTCTTATGTGTTCAGCCATTCA 59.230 36.000 0.00 0.00 0.00 2.57
1812 1913 3.067742 CAGCCATTCAGGTCCATCATTTC 59.932 47.826 0.00 0.00 40.61 2.17
1814 1915 3.703052 GCCATTCAGGTCCATCATTTCTT 59.297 43.478 0.00 0.00 40.61 2.52
1854 1956 8.723942 AGGTAGTTGAATGATTTGTAGTCATC 57.276 34.615 0.00 0.00 35.35 2.92
1879 1981 8.081025 TCGCATGCATCATTAATTGCTATAAAA 58.919 29.630 19.57 0.00 39.60 1.52
1880 1982 8.701540 CGCATGCATCATTAATTGCTATAAAAA 58.298 29.630 19.57 0.00 39.60 1.94
1980 2092 5.304778 TCAGCAGTTTGTAATAACAGAGCA 58.695 37.500 0.00 0.00 36.83 4.26
1981 2093 5.179368 TCAGCAGTTTGTAATAACAGAGCAC 59.821 40.000 0.00 0.00 36.83 4.40
1982 2094 4.455877 AGCAGTTTGTAATAACAGAGCACC 59.544 41.667 0.00 0.00 36.83 5.01
1983 2095 4.455877 GCAGTTTGTAATAACAGAGCACCT 59.544 41.667 0.00 0.00 36.83 4.00
1996 2108 3.313526 CAGAGCACCTGTTATGTAATGGC 59.686 47.826 0.00 0.00 38.10 4.40
1997 2109 3.200825 AGAGCACCTGTTATGTAATGGCT 59.799 43.478 0.00 0.00 0.00 4.75
1998 2110 3.282021 AGCACCTGTTATGTAATGGCTG 58.718 45.455 0.00 0.00 0.00 4.85
1999 2111 2.223572 GCACCTGTTATGTAATGGCTGC 60.224 50.000 0.00 0.00 0.00 5.25
2000 2112 3.282021 CACCTGTTATGTAATGGCTGCT 58.718 45.455 0.00 0.00 0.00 4.24
2001 2113 3.313526 CACCTGTTATGTAATGGCTGCTC 59.686 47.826 0.00 0.00 0.00 4.26
2002 2114 3.054434 ACCTGTTATGTAATGGCTGCTCA 60.054 43.478 0.00 0.00 0.00 4.26
2003 2115 3.947196 CCTGTTATGTAATGGCTGCTCAA 59.053 43.478 0.00 0.00 0.00 3.02
2004 2116 4.201950 CCTGTTATGTAATGGCTGCTCAAC 60.202 45.833 0.00 0.00 0.00 3.18
2005 2117 4.331108 TGTTATGTAATGGCTGCTCAACA 58.669 39.130 0.00 0.00 0.00 3.33
2018 2130 5.839262 CTGCTCAACAGTTCGTAATAACA 57.161 39.130 0.00 0.00 41.86 2.41
2019 2131 5.839262 TGCTCAACAGTTCGTAATAACAG 57.161 39.130 0.00 0.00 0.00 3.16
2020 2132 5.534407 TGCTCAACAGTTCGTAATAACAGA 58.466 37.500 0.00 0.00 0.00 3.41
2021 2133 5.633601 TGCTCAACAGTTCGTAATAACAGAG 59.366 40.000 0.00 0.00 0.00 3.35
2022 2134 5.634020 GCTCAACAGTTCGTAATAACAGAGT 59.366 40.000 0.00 0.00 0.00 3.24
2137 2253 2.028203 TGCTTCACACTGCTAGTATGCA 60.028 45.455 0.00 0.00 41.05 3.96
2174 2290 8.985315 TCTGCTGGAAATTCAGACAATATATT 57.015 30.769 0.00 0.00 36.93 1.28
2506 2622 8.330466 TGTAAATTTGACAAGGTAGGTACATG 57.670 34.615 0.00 0.00 0.00 3.21
2531 2647 5.456548 TTGTGAAATTGATGCAGTGACAT 57.543 34.783 0.00 0.00 0.00 3.06
2572 2688 7.381408 GCTATAGTGATGTTTGTGCTTCGTATA 59.619 37.037 0.84 0.00 0.00 1.47
2688 2804 8.513139 TGGGTCATCCACAAAAGGTATATATA 57.487 34.615 0.00 0.00 41.46 0.86
2689 2805 9.122954 TGGGTCATCCACAAAAGGTATATATAT 57.877 33.333 0.00 0.00 41.46 0.86
2717 3113 8.282455 TCCTTTCATAGTAACTCACTGTCTAG 57.718 38.462 0.00 0.00 38.24 2.43
2735 3131 1.818642 AGTGTGCAGGAAAGCAGATC 58.181 50.000 0.00 0.00 46.69 2.75
2736 3132 1.072806 AGTGTGCAGGAAAGCAGATCA 59.927 47.619 0.00 0.00 46.69 2.92
2738 3134 2.490903 GTGTGCAGGAAAGCAGATCAAT 59.509 45.455 0.00 0.00 46.69 2.57
2739 3135 2.490509 TGTGCAGGAAAGCAGATCAATG 59.509 45.455 0.00 0.00 46.69 2.82
2740 3136 1.475280 TGCAGGAAAGCAGATCAATGC 59.525 47.619 0.00 0.00 46.88 3.56
2821 3217 7.122948 GTGTACTGAAATCTTCTCTCTTCCCTA 59.877 40.741 0.00 0.00 0.00 3.53
2929 3325 3.769739 ACACCTTCAGCATCTGTTGTA 57.230 42.857 0.00 0.00 32.61 2.41
3027 3423 6.683360 TCAAATCAGCAGCATTTGAAGTCAAA 60.683 34.615 15.28 8.82 43.89 2.69
3472 3868 7.965107 CAGGTGATTCTCATAACTTTTAGTTGC 59.035 37.037 2.45 0.00 39.11 4.17
3473 3869 6.961554 GGTGATTCTCATAACTTTTAGTTGCG 59.038 38.462 2.45 0.00 39.11 4.85
3474 3870 7.148474 GGTGATTCTCATAACTTTTAGTTGCGA 60.148 37.037 2.45 0.00 39.11 5.10
3496 3909 5.578336 CGAGTCATCTTGCTGAATTAACTCA 59.422 40.000 0.00 0.00 0.00 3.41
3497 3910 6.454848 CGAGTCATCTTGCTGAATTAACTCAC 60.455 42.308 0.00 0.00 0.00 3.51
3636 4088 9.875691 GTTTAGATAAAAAGAAGGGCAATTCAT 57.124 29.630 4.75 0.00 0.00 2.57
3641 4093 3.967332 AAGAAGGGCAATTCATGTTGG 57.033 42.857 4.75 0.00 0.00 3.77
3789 4241 7.312154 TGAACAAACCATGTATGTAAAGATGC 58.688 34.615 0.00 0.00 42.99 3.91
3791 4243 7.408756 ACAAACCATGTATGTAAAGATGCAT 57.591 32.000 0.00 0.00 41.63 3.96
3792 4244 7.259882 ACAAACCATGTATGTAAAGATGCATG 58.740 34.615 2.46 10.08 42.75 4.06
3793 4245 5.443185 ACCATGTATGTAAAGATGCATGC 57.557 39.130 11.82 11.82 42.15 4.06
3794 4246 4.888823 ACCATGTATGTAAAGATGCATGCA 59.111 37.500 25.04 25.04 45.15 3.96
3854 4309 1.227999 TGGAGCAACAGCGCACTTAC 61.228 55.000 11.47 0.00 0.00 2.34
3996 4451 2.606725 CAGAGTGAAAGCCGCTATCAAG 59.393 50.000 0.00 0.00 35.38 3.02
4209 4664 1.077716 AAGGCCCATGCTCGTAACC 60.078 57.895 0.00 0.00 37.74 2.85
4515 4970 3.649073 ACGGCAAATGAACTTTTAAGGC 58.351 40.909 0.00 0.00 0.00 4.35
4619 5074 5.008019 AGCAATCTGTTTATACCTGCAATCG 59.992 40.000 0.00 0.00 0.00 3.34
4672 5127 0.944386 GCTGATTTGTGTGTGTCCGT 59.056 50.000 0.00 0.00 0.00 4.69
4868 5323 0.748005 CCCCTTGCAGGTAATCCACG 60.748 60.000 0.00 0.00 31.93 4.94
5152 5615 7.385267 ACGATGTATACTAGGTCTCGATTACT 58.615 38.462 4.17 0.00 0.00 2.24
5234 5697 2.035449 GGTGGTGGTTGTTTTAGCCTTC 59.965 50.000 0.00 0.00 0.00 3.46
5273 5736 3.394874 CTCGTCGTGGTGCGTGTG 61.395 66.667 0.00 0.00 42.13 3.82
5274 5737 4.934942 TCGTCGTGGTGCGTGTGG 62.935 66.667 0.00 0.00 42.13 4.17
5297 5760 7.119846 GTGGTTGTGTATTAGAAGAAGAATGCT 59.880 37.037 0.00 0.00 0.00 3.79
5425 5889 9.823647 ATGATCTTTGATGTTACTACCTACTTG 57.176 33.333 0.00 0.00 0.00 3.16
5427 5891 9.088512 GATCTTTGATGTTACTACCTACTTGTG 57.911 37.037 0.00 0.00 0.00 3.33
5428 5892 6.872020 TCTTTGATGTTACTACCTACTTGTGC 59.128 38.462 0.00 0.00 0.00 4.57
5429 5893 5.995565 TGATGTTACTACCTACTTGTGCT 57.004 39.130 0.00 0.00 0.00 4.40
5430 5894 6.354794 TGATGTTACTACCTACTTGTGCTT 57.645 37.500 0.00 0.00 0.00 3.91
5431 5895 6.163476 TGATGTTACTACCTACTTGTGCTTG 58.837 40.000 0.00 0.00 0.00 4.01
5432 5896 4.312443 TGTTACTACCTACTTGTGCTTGC 58.688 43.478 0.00 0.00 0.00 4.01
5433 5897 2.474410 ACTACCTACTTGTGCTTGCC 57.526 50.000 0.00 0.00 0.00 4.52
5434 5898 1.003233 ACTACCTACTTGTGCTTGCCC 59.997 52.381 0.00 0.00 0.00 5.36
5435 5899 1.003118 CTACCTACTTGTGCTTGCCCA 59.997 52.381 0.00 0.00 0.00 5.36
5436 5900 0.250901 ACCTACTTGTGCTTGCCCAG 60.251 55.000 0.00 0.00 0.00 4.45
5437 5901 0.036732 CCTACTTGTGCTTGCCCAGA 59.963 55.000 0.00 0.00 0.00 3.86
5438 5902 1.545428 CCTACTTGTGCTTGCCCAGAA 60.545 52.381 0.00 0.00 0.00 3.02
5499 5975 5.001232 TGCTCTCTTTACATGGGTAAACAC 58.999 41.667 0.00 0.00 42.86 3.32
5580 6056 8.076178 ACACATTTCACTACAGTAGAAAAATGC 58.924 33.333 28.98 0.00 40.54 3.56
5731 6207 2.579201 GCGCTGTAGAGGAAGCCA 59.421 61.111 0.00 0.00 35.98 4.75
5889 6366 2.687700 ACATGTGAGACCTGATCAGC 57.312 50.000 17.76 4.68 0.00 4.26
5925 6402 1.920325 TGAGAGGGCTGAACCTGGG 60.920 63.158 0.00 0.00 42.10 4.45
5926 6403 1.920835 GAGAGGGCTGAACCTGGGT 60.921 63.158 0.00 0.00 42.10 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.033448 CCTGCGGTAACCAAGCCA 59.967 61.111 0.00 0.00 0.00 4.75
22 23 2.161410 CGATTTGAATTCGAACTGGGCA 59.839 45.455 10.38 0.00 0.00 5.36
57 58 3.562393 CCAGAAGGAGAGAGACACCACTA 60.562 52.174 0.00 0.00 36.89 2.74
58 59 2.524306 CAGAAGGAGAGAGACACCACT 58.476 52.381 0.00 0.00 0.00 4.00
60 61 1.930251 CCAGAAGGAGAGAGACACCA 58.070 55.000 0.00 0.00 36.89 4.17
61 62 0.534873 GCCAGAAGGAGAGAGACACC 59.465 60.000 0.00 0.00 36.89 4.16
62 63 0.172352 CGCCAGAAGGAGAGAGACAC 59.828 60.000 0.00 0.00 36.74 3.67
63 64 0.967887 CCGCCAGAAGGAGAGAGACA 60.968 60.000 0.00 0.00 36.74 3.41
64 65 0.968393 ACCGCCAGAAGGAGAGAGAC 60.968 60.000 0.00 0.00 36.74 3.36
65 66 0.967887 CACCGCCAGAAGGAGAGAGA 60.968 60.000 0.00 0.00 36.74 3.10
66 67 1.515020 CACCGCCAGAAGGAGAGAG 59.485 63.158 0.00 0.00 36.74 3.20
67 68 1.984570 CCACCGCCAGAAGGAGAGA 60.985 63.158 0.00 0.00 36.74 3.10
68 69 2.581354 CCACCGCCAGAAGGAGAG 59.419 66.667 0.00 0.00 36.74 3.20
69 70 3.706373 GCCACCGCCAGAAGGAGA 61.706 66.667 0.00 0.00 36.74 3.71
73 74 4.697756 TTCCGCCACCGCCAGAAG 62.698 66.667 0.00 0.00 0.00 2.85
74 75 4.697756 CTTCCGCCACCGCCAGAA 62.698 66.667 0.00 0.00 0.00 3.02
76 77 4.697756 TTCTTCCGCCACCGCCAG 62.698 66.667 0.00 0.00 0.00 4.85
77 78 4.697756 CTTCTTCCGCCACCGCCA 62.698 66.667 0.00 0.00 0.00 5.69
86 87 2.279517 CGATCCGCCCTTCTTCCG 60.280 66.667 0.00 0.00 0.00 4.30
183 195 3.490759 CGGCAGGCACTTACAGCG 61.491 66.667 0.00 0.00 34.60 5.18
327 350 1.301677 GCGAGTTTGCTTCCCTCTGG 61.302 60.000 0.00 0.00 0.00 3.86
384 411 3.126074 TAGCTAGAGCACGGCGCAG 62.126 63.158 10.83 8.25 46.13 5.18
385 412 3.138128 TAGCTAGAGCACGGCGCA 61.138 61.111 10.83 0.00 46.13 6.09
386 413 2.615262 AAGTAGCTAGAGCACGGCGC 62.615 60.000 6.90 0.00 45.16 6.53
387 414 0.592754 GAAGTAGCTAGAGCACGGCG 60.593 60.000 4.80 4.80 45.16 6.46
388 415 0.249114 GGAAGTAGCTAGAGCACGGC 60.249 60.000 4.01 0.00 45.16 5.68
389 416 1.335496 GAGGAAGTAGCTAGAGCACGG 59.665 57.143 4.01 0.00 45.16 4.94
392 419 2.024846 ACCAGAGGAAGTAGCTAGAGCA 60.025 50.000 4.01 0.00 45.16 4.26
396 423 4.020543 ACAGAACCAGAGGAAGTAGCTAG 58.979 47.826 0.00 0.00 0.00 3.42
405 432 1.257743 CTCGGAACAGAACCAGAGGA 58.742 55.000 0.00 0.00 0.00 3.71
408 435 1.176619 TCGCTCGGAACAGAACCAGA 61.177 55.000 0.00 0.00 0.00 3.86
409 436 0.734253 CTCGCTCGGAACAGAACCAG 60.734 60.000 0.00 0.00 0.00 4.00
410 437 1.289066 CTCGCTCGGAACAGAACCA 59.711 57.895 0.00 0.00 0.00 3.67
421 448 3.532155 CCCCTTCTCCCTCGCTCG 61.532 72.222 0.00 0.00 0.00 5.03
422 449 0.178958 TATCCCCTTCTCCCTCGCTC 60.179 60.000 0.00 0.00 0.00 5.03
423 450 0.264955 TTATCCCCTTCTCCCTCGCT 59.735 55.000 0.00 0.00 0.00 4.93
424 451 0.682292 CTTATCCCCTTCTCCCTCGC 59.318 60.000 0.00 0.00 0.00 5.03
425 452 2.383442 TCTTATCCCCTTCTCCCTCG 57.617 55.000 0.00 0.00 0.00 4.63
426 453 4.532916 GGTTATCTTATCCCCTTCTCCCTC 59.467 50.000 0.00 0.00 0.00 4.30
427 454 4.504382 GGTTATCTTATCCCCTTCTCCCT 58.496 47.826 0.00 0.00 0.00 4.20
429 456 4.504382 AGGGTTATCTTATCCCCTTCTCC 58.496 47.826 0.00 0.00 45.37 3.71
435 462 3.902467 ACGAAGAGGGTTATCTTATCCCC 59.098 47.826 0.00 0.00 39.63 4.81
436 463 5.335504 CGTACGAAGAGGGTTATCTTATCCC 60.336 48.000 10.44 0.00 39.63 3.85
437 464 5.697826 CGTACGAAGAGGGTTATCTTATCC 58.302 45.833 10.44 0.00 39.63 2.59
438 465 5.152804 GCGTACGAAGAGGGTTATCTTATC 58.847 45.833 21.65 0.00 39.63 1.75
439 466 4.022503 GGCGTACGAAGAGGGTTATCTTAT 60.023 45.833 21.65 0.00 39.63 1.73
440 467 3.316308 GGCGTACGAAGAGGGTTATCTTA 59.684 47.826 21.65 0.00 39.63 2.10
441 468 2.100418 GGCGTACGAAGAGGGTTATCTT 59.900 50.000 21.65 0.00 42.23 2.40
442 469 1.680207 GGCGTACGAAGAGGGTTATCT 59.320 52.381 21.65 0.00 0.00 1.98
509 554 4.093952 CTCACAGCAAAGCCGCGG 62.094 66.667 24.05 24.05 36.85 6.46
510 555 1.915614 AATCTCACAGCAAAGCCGCG 61.916 55.000 0.00 0.00 36.85 6.46
511 556 0.179179 GAATCTCACAGCAAAGCCGC 60.179 55.000 0.00 0.00 0.00 6.53
512 557 0.095935 CGAATCTCACAGCAAAGCCG 59.904 55.000 0.00 0.00 0.00 5.52
513 558 1.160137 ACGAATCTCACAGCAAAGCC 58.840 50.000 0.00 0.00 0.00 4.35
515 560 2.476619 ACGAACGAATCTCACAGCAAAG 59.523 45.455 0.14 0.00 0.00 2.77
516 561 2.479837 ACGAACGAATCTCACAGCAAA 58.520 42.857 0.14 0.00 0.00 3.68
517 562 2.148916 ACGAACGAATCTCACAGCAA 57.851 45.000 0.14 0.00 0.00 3.91
521 566 1.001048 ACCGAACGAACGAATCTCACA 60.001 47.619 0.14 0.00 35.09 3.58
550 597 2.406616 CCATTGAAGAACCCGCCCG 61.407 63.158 0.00 0.00 0.00 6.13
578 625 1.265236 ACATCCCCAAACGTACGGTA 58.735 50.000 21.06 0.00 0.00 4.02
579 626 0.397564 AACATCCCCAAACGTACGGT 59.602 50.000 21.06 11.03 0.00 4.83
598 645 1.266989 CGTATCAGTATCAGCAGCGGA 59.733 52.381 0.00 0.00 0.00 5.54
602 649 2.398498 GTGGCGTATCAGTATCAGCAG 58.602 52.381 0.00 0.00 0.00 4.24
603 650 1.068588 GGTGGCGTATCAGTATCAGCA 59.931 52.381 0.00 0.00 0.00 4.41
604 651 1.784525 GGTGGCGTATCAGTATCAGC 58.215 55.000 0.00 0.00 0.00 4.26
605 652 1.930817 GCGGTGGCGTATCAGTATCAG 60.931 57.143 0.00 0.00 0.00 2.90
606 653 0.031585 GCGGTGGCGTATCAGTATCA 59.968 55.000 0.00 0.00 0.00 2.15
608 655 0.462375 TTGCGGTGGCGTATCAGTAT 59.538 50.000 0.00 0.00 44.10 2.12
609 656 0.179121 CTTGCGGTGGCGTATCAGTA 60.179 55.000 0.00 0.00 44.10 2.74
610 657 1.447838 CTTGCGGTGGCGTATCAGT 60.448 57.895 0.00 0.00 44.10 3.41
611 658 2.813179 GCTTGCGGTGGCGTATCAG 61.813 63.158 0.00 0.00 44.10 2.90
612 659 2.817834 GCTTGCGGTGGCGTATCA 60.818 61.111 0.00 0.00 44.10 2.15
613 660 2.511600 AGCTTGCGGTGGCGTATC 60.512 61.111 0.00 0.00 44.10 2.24
614 661 2.511600 GAGCTTGCGGTGGCGTAT 60.512 61.111 0.00 0.00 44.10 3.06
615 662 3.523087 TTGAGCTTGCGGTGGCGTA 62.523 57.895 0.00 0.00 44.10 4.42
616 663 4.927782 TTGAGCTTGCGGTGGCGT 62.928 61.111 0.00 0.00 44.10 5.68
690 752 3.744987 CGCTAGAGTAAATCGATACGGG 58.255 50.000 0.00 0.00 0.00 5.28
704 766 2.025441 GCGGACAGAGCGCTAGAG 59.975 66.667 11.50 5.68 0.00 2.43
710 772 3.883744 AAACCAGGCGGACAGAGCG 62.884 63.158 2.43 0.00 35.59 5.03
711 773 2.032681 AAACCAGGCGGACAGAGC 59.967 61.111 2.43 0.00 35.59 4.09
736 798 2.951642 TGGAACTGAAACAGGAAGCAAG 59.048 45.455 0.00 0.00 35.51 4.01
765 839 1.597742 CGCCGGGATTCAGAAATCAT 58.402 50.000 2.18 0.00 42.66 2.45
783 857 2.687425 TGATGACAATAAATGGGGTGCG 59.313 45.455 0.00 0.00 0.00 5.34
788 862 6.923012 TGAACAACTGATGACAATAAATGGG 58.077 36.000 0.00 0.00 0.00 4.00
789 863 8.815141 TTTGAACAACTGATGACAATAAATGG 57.185 30.769 0.00 0.00 32.56 3.16
795 869 8.945481 TCAAAATTTGAACAACTGATGACAAT 57.055 26.923 5.87 0.00 36.59 2.71
821 905 5.131142 AGGGTGAGATCGATCCATAGTTTTT 59.869 40.000 21.66 0.00 0.00 1.94
828 912 0.683973 GCAGGGTGAGATCGATCCAT 59.316 55.000 21.66 4.15 0.00 3.41
843 927 3.128242 AGAGCAAATTGAAATCGAGCAGG 59.872 43.478 0.00 0.00 0.00 4.85
858 942 3.249805 TGGTCCCTGCAGAGCAAA 58.750 55.556 17.39 0.00 41.08 3.68
999 1087 1.745489 GGCCGTGGTGGACTTCATC 60.745 63.158 0.00 0.00 45.46 2.92
1068 1156 2.464459 GGCGATCTTGTTGAGGGCG 61.464 63.158 0.00 0.00 0.00 6.13
1446 1534 2.234661 CTGGACATACCTGTTCTGCTCA 59.765 50.000 0.00 0.00 39.86 4.26
1545 1633 0.247145 GGATCTTAACAACACGCGCG 60.247 55.000 30.96 30.96 0.00 6.86
1547 1635 2.333926 TGAGGATCTTAACAACACGCG 58.666 47.619 3.53 3.53 34.92 6.01
1548 1636 3.994392 TCTTGAGGATCTTAACAACACGC 59.006 43.478 0.00 0.00 34.92 5.34
1635 1723 7.683578 TGCAAATATTGATATAGGAGAGCAGT 58.316 34.615 0.00 0.00 0.00 4.40
1742 1840 0.679002 GCAAAGCCCTCATCTCAGCA 60.679 55.000 0.00 0.00 0.00 4.41
1812 1913 6.287589 ACTACCTAGACCATGTTCTGAAAG 57.712 41.667 2.51 0.00 0.00 2.62
1814 1915 5.778241 TCAACTACCTAGACCATGTTCTGAA 59.222 40.000 2.51 0.00 0.00 3.02
1854 1956 7.800015 TTTATAGCAATTAATGATGCATGCG 57.200 32.000 14.09 0.00 44.95 4.73
1880 1982 9.656323 TCCCATGATACTACTAATCACTAGTTT 57.344 33.333 0.00 0.00 41.35 2.66
1882 1984 9.303116 CTTCCCATGATACTACTAATCACTAGT 57.697 37.037 0.00 0.00 43.58 2.57
1883 1985 8.744652 CCTTCCCATGATACTACTAATCACTAG 58.255 40.741 0.00 0.00 36.24 2.57
1884 1986 8.453681 TCCTTCCCATGATACTACTAATCACTA 58.546 37.037 0.00 0.00 36.24 2.74
1885 1987 7.306013 TCCTTCCCATGATACTACTAATCACT 58.694 38.462 0.00 0.00 36.24 3.41
1886 1988 7.540474 TCCTTCCCATGATACTACTAATCAC 57.460 40.000 0.00 0.00 36.24 3.06
1887 1989 7.256332 GCTTCCTTCCCATGATACTACTAATCA 60.256 40.741 0.00 0.00 37.73 2.57
1888 1990 7.100409 GCTTCCTTCCCATGATACTACTAATC 58.900 42.308 0.00 0.00 0.00 1.75
1890 1992 5.903010 TGCTTCCTTCCCATGATACTACTAA 59.097 40.000 0.00 0.00 0.00 2.24
1980 2092 3.054434 TGAGCAGCCATTACATAACAGGT 60.054 43.478 0.00 0.00 0.00 4.00
1981 2093 3.544684 TGAGCAGCCATTACATAACAGG 58.455 45.455 0.00 0.00 0.00 4.00
1982 2094 4.395854 TGTTGAGCAGCCATTACATAACAG 59.604 41.667 0.00 0.00 0.00 3.16
1983 2095 4.331108 TGTTGAGCAGCCATTACATAACA 58.669 39.130 0.00 0.00 0.00 2.41
1984 2096 4.913376 CTGTTGAGCAGCCATTACATAAC 58.087 43.478 0.00 0.00 38.52 1.89
1997 2109 5.534407 TCTGTTATTACGAACTGTTGAGCA 58.466 37.500 0.00 0.00 32.01 4.26
1998 2110 5.634020 ACTCTGTTATTACGAACTGTTGAGC 59.366 40.000 0.00 0.00 32.01 4.26
1999 2111 7.272948 GGTACTCTGTTATTACGAACTGTTGAG 59.727 40.741 0.00 0.00 32.01 3.02
2000 2112 7.040201 AGGTACTCTGTTATTACGAACTGTTGA 60.040 37.037 0.00 0.00 32.01 3.18
2001 2113 7.061905 CAGGTACTCTGTTATTACGAACTGTTG 59.938 40.741 0.00 0.00 34.60 3.33
2002 2114 7.088905 CAGGTACTCTGTTATTACGAACTGTT 58.911 38.462 0.00 0.00 34.60 3.16
2003 2115 6.618811 CAGGTACTCTGTTATTACGAACTGT 58.381 40.000 0.00 0.00 34.60 3.55
2018 2130 5.823045 GCAGCCATTAAATAACAGGTACTCT 59.177 40.000 0.00 0.00 34.60 3.24
2019 2131 5.823045 AGCAGCCATTAAATAACAGGTACTC 59.177 40.000 0.00 0.00 34.60 2.59
2020 2132 5.755849 AGCAGCCATTAAATAACAGGTACT 58.244 37.500 0.00 0.00 43.88 2.73
2021 2133 5.588648 TGAGCAGCCATTAAATAACAGGTAC 59.411 40.000 0.00 0.00 0.00 3.34
2022 2134 5.750524 TGAGCAGCCATTAAATAACAGGTA 58.249 37.500 0.00 0.00 0.00 3.08
2137 2253 3.870538 TCCAGCAGAAATAGATGCCAT 57.129 42.857 0.00 0.00 43.60 4.40
2429 2545 4.331968 TGAAAGACGCAACCAAATATCCT 58.668 39.130 0.00 0.00 0.00 3.24
2506 2622 4.090930 GTCACTGCATCAATTTCACAATGC 59.909 41.667 0.00 0.00 43.71 3.56
2554 2670 7.478520 ACCTATTATACGAAGCACAAACATC 57.521 36.000 0.00 0.00 0.00 3.06
2572 2688 2.078392 CACGCACCGGTTTTACCTATT 58.922 47.619 2.97 0.00 35.66 1.73
2689 2805 9.256228 AGACAGTGAGTTACTATGAAAGGAATA 57.744 33.333 0.00 0.00 37.60 1.75
2690 2806 8.140112 AGACAGTGAGTTACTATGAAAGGAAT 57.860 34.615 0.00 0.00 37.60 3.01
2691 2807 7.540474 AGACAGTGAGTTACTATGAAAGGAA 57.460 36.000 0.00 0.00 37.60 3.36
2717 3113 1.527034 TGATCTGCTTTCCTGCACAC 58.473 50.000 0.00 0.00 38.12 3.82
2739 3135 7.970061 TGAGTTATAATGCTTCATGAACAAAGC 59.030 33.333 3.38 7.12 46.37 3.51
2740 3136 9.844790 TTGAGTTATAATGCTTCATGAACAAAG 57.155 29.630 3.38 0.00 0.00 2.77
2741 3137 9.624697 GTTGAGTTATAATGCTTCATGAACAAA 57.375 29.630 3.38 2.28 0.00 2.83
3027 3423 3.649502 TGATATCTCCACATGCCAGTCAT 59.350 43.478 3.98 0.00 35.31 3.06
3472 3868 5.578336 TGAGTTAATTCAGCAAGATGACTCG 59.422 40.000 0.00 0.00 0.00 4.18
3473 3869 6.593382 AGTGAGTTAATTCAGCAAGATGACTC 59.407 38.462 0.16 0.00 0.00 3.36
3474 3870 6.471146 AGTGAGTTAATTCAGCAAGATGACT 58.529 36.000 0.16 0.00 0.00 3.41
3484 3897 7.439655 GGGCAAGTATAGAGTGAGTTAATTCAG 59.560 40.741 0.16 0.00 0.00 3.02
3496 3909 6.717289 TGTGTAAATTGGGCAAGTATAGAGT 58.283 36.000 0.00 0.00 0.00 3.24
3497 3910 7.624360 TTGTGTAAATTGGGCAAGTATAGAG 57.376 36.000 0.00 0.00 0.00 2.43
3540 3954 7.760131 AAATCGTTACTGCGCTTTACTATTA 57.240 32.000 9.73 0.00 30.06 0.98
3541 3955 6.657836 AAATCGTTACTGCGCTTTACTATT 57.342 33.333 9.73 1.11 30.06 1.73
3603 4017 8.401709 GCCCTTCTTTTTATCTAAACTCATCAG 58.598 37.037 0.00 0.00 0.00 2.90
3610 4024 9.875691 ATGAATTGCCCTTCTTTTTATCTAAAC 57.124 29.630 0.00 0.00 0.00 2.01
3613 4027 8.593945 ACATGAATTGCCCTTCTTTTTATCTA 57.406 30.769 0.00 0.00 0.00 1.98
3614 4028 7.486407 ACATGAATTGCCCTTCTTTTTATCT 57.514 32.000 0.00 0.00 0.00 1.98
3615 4029 7.064966 CCAACATGAATTGCCCTTCTTTTTATC 59.935 37.037 0.00 0.00 0.00 1.75
3616 4030 6.880529 CCAACATGAATTGCCCTTCTTTTTAT 59.119 34.615 0.00 0.00 0.00 1.40
3617 4031 6.183361 ACCAACATGAATTGCCCTTCTTTTTA 60.183 34.615 0.00 0.00 0.00 1.52
3618 4032 5.065235 CCAACATGAATTGCCCTTCTTTTT 58.935 37.500 0.00 0.00 0.00 1.94
3619 4033 4.102996 ACCAACATGAATTGCCCTTCTTTT 59.897 37.500 0.00 0.00 0.00 2.27
3620 4034 3.647590 ACCAACATGAATTGCCCTTCTTT 59.352 39.130 0.00 0.00 0.00 2.52
3621 4035 3.242011 ACCAACATGAATTGCCCTTCTT 58.758 40.909 0.00 0.00 0.00 2.52
3622 4036 2.893424 ACCAACATGAATTGCCCTTCT 58.107 42.857 0.00 0.00 0.00 2.85
3623 4037 4.799564 TTACCAACATGAATTGCCCTTC 57.200 40.909 0.00 0.00 0.00 3.46
3725 4177 5.021033 ACACAGCATTTTTCCATGTGAAA 57.979 34.783 10.32 5.55 43.02 2.69
3775 4227 8.187354 CAATTTTGCATGCATCTTTACATACA 57.813 30.769 23.37 0.00 0.00 2.29
3793 4245 2.549329 GTGCTTTGGGAAGGCAATTTTG 59.451 45.455 0.00 0.00 33.34 2.44
3794 4246 2.487086 GGTGCTTTGGGAAGGCAATTTT 60.487 45.455 0.00 0.00 33.34 1.82
3824 4279 1.946768 TGTTGCTCCACAGTTGTTAGC 59.053 47.619 8.65 8.65 35.90 3.09
3830 4285 2.546494 GCGCTGTTGCTCCACAGTT 61.546 57.895 0.00 0.00 45.31 3.16
3862 4317 2.690840 ACTCCTACAGGAAACAGGTGT 58.309 47.619 0.00 0.00 44.91 4.16
3873 4328 5.518128 CAGAATTCGACATGAACTCCTACAG 59.482 44.000 0.00 0.00 40.00 2.74
3996 4451 0.178961 AAACCCTTGGAGCCAGGAAC 60.179 55.000 0.00 0.00 0.00 3.62
4209 4664 1.482593 AGCCCCAGACTTCATAACTCG 59.517 52.381 0.00 0.00 0.00 4.18
4221 4676 4.337304 TGAGCTCCCAGCCCCAGA 62.337 66.667 12.15 0.00 43.77 3.86
4360 4815 2.383527 CGAAACTCGCCAGCCTGAC 61.384 63.158 0.00 0.00 31.14 3.51
4515 4970 2.134789 AGGAACTGGCCAGCAATAAG 57.865 50.000 33.06 8.68 37.18 1.73
4619 5074 5.047660 ACTGTAGTTCTTCAGACATGGAGAC 60.048 44.000 12.12 0.00 41.00 3.36
4751 5206 2.060567 TTGCTGCTTCCTCCAGTGCT 62.061 55.000 0.00 0.00 32.93 4.40
4781 5236 1.334160 TTCTGACGGCTGGTTCTGTA 58.666 50.000 0.00 0.00 0.00 2.74
4853 5308 0.319083 ACGACGTGGATTACCTGCAA 59.681 50.000 3.97 0.00 37.04 4.08
5152 5615 4.770531 ACCACTACTACTGACTTGCATACA 59.229 41.667 0.00 0.00 0.00 2.29
5234 5697 5.796813 AGTGTTCGAGAAAAGAAAACGAAG 58.203 37.500 0.00 0.00 42.09 3.79
5273 5736 7.334421 TCAGCATTCTTCTTCTAATACACAACC 59.666 37.037 0.00 0.00 0.00 3.77
5274 5737 8.256611 TCAGCATTCTTCTTCTAATACACAAC 57.743 34.615 0.00 0.00 0.00 3.32
5297 5760 3.807631 AACAGCAAGCGCCGTCTCA 62.808 57.895 2.29 0.00 39.83 3.27
5315 5778 2.360801 GCAAACTCCACACAAGGCTAAA 59.639 45.455 0.00 0.00 0.00 1.85
5428 5892 3.068590 TGAAAAGAAAGCTTCTGGGCAAG 59.931 43.478 0.00 0.00 40.59 4.01
5429 5893 3.030291 TGAAAAGAAAGCTTCTGGGCAA 58.970 40.909 0.00 0.00 40.59 4.52
5430 5894 2.624838 CTGAAAAGAAAGCTTCTGGGCA 59.375 45.455 0.00 0.00 40.59 5.36
5431 5895 2.625314 ACTGAAAAGAAAGCTTCTGGGC 59.375 45.455 0.00 0.00 40.59 5.36
5432 5896 3.885297 TCACTGAAAAGAAAGCTTCTGGG 59.115 43.478 0.00 0.00 40.59 4.45
5433 5897 5.067023 ACTTCACTGAAAAGAAAGCTTCTGG 59.933 40.000 0.00 0.00 40.59 3.86
5434 5898 6.129053 ACTTCACTGAAAAGAAAGCTTCTG 57.871 37.500 0.00 0.00 40.59 3.02
5435 5899 7.716998 TGATACTTCACTGAAAAGAAAGCTTCT 59.283 33.333 0.00 0.00 43.15 2.85
5436 5900 7.865707 TGATACTTCACTGAAAAGAAAGCTTC 58.134 34.615 0.00 0.00 31.82 3.86
5437 5901 7.716998 TCTGATACTTCACTGAAAAGAAAGCTT 59.283 33.333 0.00 0.00 35.37 3.74
5438 5902 7.172361 GTCTGATACTTCACTGAAAAGAAAGCT 59.828 37.037 0.00 0.00 0.00 3.74
5499 5975 0.036294 GAGTCCTTCTTTCCCCGTGG 60.036 60.000 0.00 0.00 0.00 4.94
5580 6056 1.270785 TGTATGTGAGTGTGGGTGCTG 60.271 52.381 0.00 0.00 0.00 4.41
5766 6242 2.917227 TGTCGCAGGAGCTCACCA 60.917 61.111 17.19 0.00 39.10 4.17


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

AutoCloner maintained by Alex Coulton.