Multiple sequence alignment - TraesCS2D01G394900

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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 TraesCS2D01G394900 chr2D 100.000 4450 0 0 1 4450 506166913 506162464 0.000000e+00 8218.0
1 TraesCS2D01G394900 chr2B 94.517 2061 77 17 715 2744 593677355 593675300 0.000000e+00 3147.0
2 TraesCS2D01G394900 chr2B 89.829 1750 87 25 2741 4448 593675266 593673566 0.000000e+00 2161.0
3 TraesCS2D01G394900 chr2B 87.294 606 43 18 1 599 593677940 593677362 0.000000e+00 662.0
4 TraesCS2D01G394900 chr2B 87.147 389 40 7 2271 2654 601732133 601732516 2.460000e-117 433.0
5 TraesCS2D01G394900 chr2B 95.181 83 4 0 564 646 140765930 140766012 1.000000e-26 132.0
6 TraesCS2D01G394900 chr2B 94.118 51 2 1 655 704 256952511 256952561 4.770000e-10 76.8
7 TraesCS2D01G394900 chr2A 95.964 1561 51 8 715 2266 650657323 650655766 0.000000e+00 2523.0
8 TraesCS2D01G394900 chr2A 94.765 745 36 3 2741 3482 650654537 650653793 0.000000e+00 1157.0
9 TraesCS2D01G394900 chr2A 88.048 912 55 19 3527 4388 650653780 650652873 0.000000e+00 1031.0
10 TraesCS2D01G394900 chr2A 89.881 504 22 12 2259 2744 650655063 650654571 4.890000e-174 621.0
11 TraesCS2D01G394900 chr2A 83.280 622 48 19 1 599 650657918 650657330 5.100000e-144 521.0
12 TraesCS2D01G394900 chr2A 85.294 170 22 3 2292 2460 80262282 80262449 5.920000e-39 172.0
13 TraesCS2D01G394900 chr2A 80.663 181 32 3 2460 2639 80262766 80262944 2.160000e-28 137.0
14 TraesCS2D01G394900 chr2A 96.000 50 1 1 655 703 437970553 437970602 3.690000e-11 80.5
15 TraesCS2D01G394900 chr7D 86.780 295 33 6 2353 2646 562395877 562395588 1.540000e-84 324.0
16 TraesCS2D01G394900 chr7D 95.238 84 4 0 563 646 600055728 600055645 2.790000e-27 134.0
17 TraesCS2D01G394900 chr7D 89.041 73 8 0 2272 2344 562396248 562396176 1.700000e-14 91.6
18 TraesCS2D01G394900 chr4B 95.238 84 4 0 563 646 638118088 638118005 2.790000e-27 134.0
19 TraesCS2D01G394900 chr4B 92.593 81 6 0 564 644 63757301 63757221 2.810000e-22 117.0
20 TraesCS2D01G394900 chr3B 95.238 84 4 0 563 646 710589997 710590080 2.790000e-27 134.0
21 TraesCS2D01G394900 chr5B 95.181 83 4 0 564 646 248393994 248393912 1.000000e-26 132.0
22 TraesCS2D01G394900 chr1D 95.181 83 4 0 564 646 317429450 317429532 1.000000e-26 132.0
23 TraesCS2D01G394900 chr1D 91.765 85 7 0 563 647 64328806 64328722 7.820000e-23 119.0
24 TraesCS2D01G394900 chr1D 94.118 51 0 3 655 703 104573379 104573428 1.720000e-09 75.0
25 TraesCS2D01G394900 chr1D 94.000 50 2 1 655 703 317429577 317429626 1.720000e-09 75.0
26 TraesCS2D01G394900 chr6B 93.258 89 5 1 558 646 225525363 225525450 3.610000e-26 130.0
27 TraesCS2D01G394900 chr6B 86.598 97 13 0 548 644 202124746 202124842 1.690000e-19 108.0
28 TraesCS2D01G394900 chr6D 94.048 84 5 0 563 646 319689597 319689514 1.300000e-25 128.0
29 TraesCS2D01G394900 chr6D 94.000 50 2 1 655 703 4632416 4632465 1.720000e-09 75.0
30 TraesCS2D01G394900 chr1B 91.209 91 8 0 556 646 425360375 425360285 1.680000e-24 124.0
31 TraesCS2D01G394900 chr1B 96.000 50 1 1 655 703 429586249 429586298 3.690000e-11 80.5
32 TraesCS2D01G394900 chr1A 90.217 92 8 1 555 646 391672919 391672829 7.820000e-23 119.0
33 TraesCS2D01G394900 chr1A 94.000 50 2 1 655 703 257557139 257557188 1.720000e-09 75.0
34 TraesCS2D01G394900 chr7A 90.000 90 8 1 556 644 539714932 539715021 1.010000e-21 115.0
35 TraesCS2D01G394900 chr5D 93.878 49 3 0 655 703 236423553 236423601 1.720000e-09 75.0
36 TraesCS2D01G394900 chr4A 88.333 60 4 3 655 712 594666511 594666453 7.990000e-08 69.4


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 TraesCS2D01G394900 chr2D 506162464 506166913 4449 True 8218.0 8218 100.000000 1 4450 1 chr2D.!!$R1 4449
1 TraesCS2D01G394900 chr2B 593673566 593677940 4374 True 1990.0 3147 90.546667 1 4448 3 chr2B.!!$R1 4447
2 TraesCS2D01G394900 chr2A 650652873 650657918 5045 True 1170.6 2523 90.387600 1 4388 5 chr2A.!!$R1 4387
3 TraesCS2D01G394900 chr7D 562395588 562396248 660 True 207.8 324 87.910500 2272 2646 2 chr7D.!!$R2 374

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
609 651 0.038892 GCTGTTGCCTTGTGACCATG 60.039 55.000 0.00 0.0 0.00 3.66 F
670 712 0.103876 AAAGACCCTTCCTGGACCCT 60.104 55.000 0.00 0.0 38.35 4.34 F
1065 1112 0.822164 AAACGTACCGCTGCTATCCT 59.178 50.000 0.00 0.0 0.00 3.24 F
1367 1414 0.896226 AGACCTTAGGCTGAACGACC 59.104 55.000 0.00 0.0 0.00 4.79 F
2624 3684 1.300620 CGTTCCTGCAGACCGAACA 60.301 57.895 24.68 0.0 36.51 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2269 3035 0.240145 GTTGCGAACAGGGCCTAAAC 59.760 55.000 5.28 0.67 0.00 2.01 R
2420 3479 1.691434 GGTCCCAAACCTTTTGCATGA 59.309 47.619 0.00 0.00 45.45 3.07 R
2679 3754 0.537371 GGCAACACCAGTAAGGCTGT 60.537 55.000 0.00 0.00 43.55 4.40 R
2770 3882 2.356069 GCAGCCTATAGAAAAGTGGCAC 59.644 50.000 10.29 10.29 45.42 5.01 R
4267 5425 0.184211 TGATGATGGATGGGTGCTGG 59.816 55.000 0.00 0.00 0.00 4.85 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
155 158 0.613260 TTCCTATGCAACTCGGTGCT 59.387 50.000 8.55 0.00 45.17 4.40
192 210 1.385528 GGTTGTATACCCGCCAAAGG 58.614 55.000 0.00 0.00 41.43 3.11
193 211 1.340308 GGTTGTATACCCGCCAAAGGT 60.340 52.381 0.00 0.00 41.43 3.50
194 212 2.439409 GTTGTATACCCGCCAAAGGTT 58.561 47.619 0.00 0.00 38.89 3.50
195 213 3.608796 GTTGTATACCCGCCAAAGGTTA 58.391 45.455 0.00 0.00 38.89 2.85
196 214 4.201657 GTTGTATACCCGCCAAAGGTTAT 58.798 43.478 0.00 0.00 38.89 1.89
197 215 5.367302 GTTGTATACCCGCCAAAGGTTATA 58.633 41.667 0.00 0.00 38.89 0.98
198 216 5.829062 TGTATACCCGCCAAAGGTTATAT 57.171 39.130 0.00 0.00 38.89 0.86
199 217 6.931790 TGTATACCCGCCAAAGGTTATATA 57.068 37.500 0.00 0.00 38.89 0.86
200 218 6.700352 TGTATACCCGCCAAAGGTTATATAC 58.300 40.000 0.00 0.00 38.89 1.47
234 268 9.715121 AAAAAGAGAATTAGGTTGTATACGTGA 57.285 29.630 0.00 0.00 0.00 4.35
235 269 8.928270 AAAGAGAATTAGGTTGTATACGTGAG 57.072 34.615 0.00 0.00 0.00 3.51
309 343 4.019174 ACAAATGCCAAGATAGGGTTCAG 58.981 43.478 0.00 0.00 0.00 3.02
341 375 8.242053 GCATTTGATAGATGAATCTGGTTATGG 58.758 37.037 2.99 0.00 37.76 2.74
398 432 9.371136 CAGTTGATTTAAGTCATTGCTAGTCTA 57.629 33.333 1.06 0.00 0.00 2.59
578 620 2.941583 GGGAAGGGGAGCCTTGGT 60.942 66.667 0.00 0.00 0.00 3.67
581 623 3.185203 AAGGGGAGCCTTGGTGCA 61.185 61.111 0.00 0.00 0.00 4.57
585 627 2.431683 GGAGCCTTGGTGCAGTGA 59.568 61.111 0.00 0.00 0.00 3.41
589 631 2.648059 GAGCCTTGGTGCAGTGATAAT 58.352 47.619 0.00 0.00 0.00 1.28
599 641 1.747355 GCAGTGATAATGCTGTTGCCT 59.253 47.619 0.00 0.00 40.59 4.75
600 642 2.165030 GCAGTGATAATGCTGTTGCCTT 59.835 45.455 0.00 0.00 40.59 4.35
601 643 3.766151 CAGTGATAATGCTGTTGCCTTG 58.234 45.455 0.00 0.00 38.71 3.61
603 645 3.192001 AGTGATAATGCTGTTGCCTTGTG 59.808 43.478 0.00 0.00 38.71 3.33
604 646 3.191162 GTGATAATGCTGTTGCCTTGTGA 59.809 43.478 0.00 0.00 38.71 3.58
605 647 3.191162 TGATAATGCTGTTGCCTTGTGAC 59.809 43.478 0.00 0.00 38.71 3.67
606 648 0.675633 AATGCTGTTGCCTTGTGACC 59.324 50.000 0.00 0.00 38.71 4.02
607 649 0.467844 ATGCTGTTGCCTTGTGACCA 60.468 50.000 0.00 0.00 38.71 4.02
608 650 0.467844 TGCTGTTGCCTTGTGACCAT 60.468 50.000 0.00 0.00 38.71 3.55
609 651 0.038892 GCTGTTGCCTTGTGACCATG 60.039 55.000 0.00 0.00 0.00 3.66
610 652 1.608055 CTGTTGCCTTGTGACCATGA 58.392 50.000 0.00 0.00 0.00 3.07
611 653 1.538512 CTGTTGCCTTGTGACCATGAG 59.461 52.381 0.00 0.00 0.00 2.90
612 654 0.883833 GTTGCCTTGTGACCATGAGG 59.116 55.000 0.00 0.00 42.21 3.86
622 664 4.617875 CCATGAGGTCACGGGTTC 57.382 61.111 0.00 0.00 0.00 3.62
623 665 1.447838 CCATGAGGTCACGGGTTCG 60.448 63.158 0.00 0.00 43.02 3.95
624 666 1.589630 CATGAGGTCACGGGTTCGA 59.410 57.895 0.00 0.00 40.11 3.71
625 667 0.458543 CATGAGGTCACGGGTTCGAG 60.459 60.000 0.00 0.00 40.11 4.04
626 668 0.898789 ATGAGGTCACGGGTTCGAGT 60.899 55.000 0.00 0.00 40.11 4.18
627 669 1.212229 GAGGTCACGGGTTCGAGTC 59.788 63.158 0.00 0.00 40.11 3.36
628 670 2.210341 GAGGTCACGGGTTCGAGTCC 62.210 65.000 0.82 0.82 40.11 3.85
629 671 2.273912 GGTCACGGGTTCGAGTCCT 61.274 63.158 8.28 0.00 40.11 3.85
630 672 1.080705 GTCACGGGTTCGAGTCCTG 60.081 63.158 13.65 13.65 40.11 3.86
631 673 2.261671 CACGGGTTCGAGTCCTGG 59.738 66.667 17.72 9.36 40.11 4.45
632 674 2.116772 ACGGGTTCGAGTCCTGGA 59.883 61.111 17.72 0.00 40.11 3.86
633 675 1.532316 ACGGGTTCGAGTCCTGGAA 60.532 57.895 17.72 0.00 40.11 3.53
634 676 1.117142 ACGGGTTCGAGTCCTGGAAA 61.117 55.000 17.72 0.00 40.11 3.13
635 677 0.669625 CGGGTTCGAGTCCTGGAAAC 60.670 60.000 0.00 0.00 39.00 2.78
636 678 0.395312 GGGTTCGAGTCCTGGAAACA 59.605 55.000 8.95 0.00 36.84 2.83
649 691 2.750948 TGGAAACAGTCTCTTGCGTAC 58.249 47.619 0.00 0.00 35.01 3.67
650 692 2.101750 TGGAAACAGTCTCTTGCGTACA 59.898 45.455 0.00 0.00 35.01 2.90
651 693 3.128349 GGAAACAGTCTCTTGCGTACAA 58.872 45.455 0.00 0.00 0.00 2.41
652 694 3.558418 GGAAACAGTCTCTTGCGTACAAA 59.442 43.478 0.00 0.00 34.74 2.83
653 695 4.034742 GGAAACAGTCTCTTGCGTACAAAA 59.965 41.667 0.00 0.00 34.74 2.44
654 696 4.795970 AACAGTCTCTTGCGTACAAAAG 57.204 40.909 0.00 0.00 34.74 2.27
655 697 4.054780 ACAGTCTCTTGCGTACAAAAGA 57.945 40.909 6.96 6.96 34.74 2.52
657 699 3.790212 GTCTCTTGCGTACAAAAGACC 57.210 47.619 1.64 0.00 44.67 3.85
658 700 2.479275 GTCTCTTGCGTACAAAAGACCC 59.521 50.000 1.64 0.00 44.67 4.46
659 701 2.367567 TCTCTTGCGTACAAAAGACCCT 59.632 45.455 3.67 0.00 34.74 4.34
660 702 3.139077 CTCTTGCGTACAAAAGACCCTT 58.861 45.455 3.67 0.00 34.74 3.95
661 703 3.135994 TCTTGCGTACAAAAGACCCTTC 58.864 45.455 3.67 0.00 34.74 3.46
662 704 1.886886 TGCGTACAAAAGACCCTTCC 58.113 50.000 0.00 0.00 0.00 3.46
663 705 1.418637 TGCGTACAAAAGACCCTTCCT 59.581 47.619 0.00 0.00 0.00 3.36
664 706 1.804748 GCGTACAAAAGACCCTTCCTG 59.195 52.381 0.00 0.00 0.00 3.86
665 707 2.423577 CGTACAAAAGACCCTTCCTGG 58.576 52.381 0.00 0.00 0.00 4.45
666 708 2.038033 CGTACAAAAGACCCTTCCTGGA 59.962 50.000 0.00 0.00 38.35 3.86
667 709 2.658807 ACAAAAGACCCTTCCTGGAC 57.341 50.000 0.00 0.00 38.35 4.02
668 710 1.145119 ACAAAAGACCCTTCCTGGACC 59.855 52.381 0.00 0.00 38.35 4.46
669 711 0.778083 AAAAGACCCTTCCTGGACCC 59.222 55.000 0.00 0.00 38.35 4.46
670 712 0.103876 AAAGACCCTTCCTGGACCCT 60.104 55.000 0.00 0.00 38.35 4.34
671 713 0.842467 AAGACCCTTCCTGGACCCTG 60.842 60.000 0.00 0.00 38.35 4.45
672 714 2.936032 ACCCTTCCTGGACCCTGC 60.936 66.667 0.00 0.00 38.35 4.85
673 715 4.101448 CCCTTCCTGGACCCTGCG 62.101 72.222 0.00 0.00 38.35 5.18
674 716 4.785453 CCTTCCTGGACCCTGCGC 62.785 72.222 0.00 0.00 38.35 6.09
675 717 4.020617 CTTCCTGGACCCTGCGCA 62.021 66.667 10.98 10.98 0.00 6.09
676 718 3.551496 CTTCCTGGACCCTGCGCAA 62.551 63.158 13.05 0.00 0.00 4.85
677 719 3.551496 TTCCTGGACCCTGCGCAAG 62.551 63.158 13.05 4.91 43.44 4.01
695 737 4.111016 CGGGAGCTACGTGCACGA 62.111 66.667 42.94 25.37 45.94 4.35
696 738 2.202623 GGGAGCTACGTGCACGAG 60.203 66.667 42.94 32.43 45.94 4.18
697 739 2.202623 GGAGCTACGTGCACGAGG 60.203 66.667 42.94 31.80 45.94 4.63
698 740 2.881352 GAGCTACGTGCACGAGGC 60.881 66.667 42.94 37.88 45.94 4.70
699 741 3.343788 GAGCTACGTGCACGAGGCT 62.344 63.158 39.69 39.69 45.96 4.58
700 742 3.181967 GCTACGTGCACGAGGCTG 61.182 66.667 42.94 25.89 45.15 4.85
701 743 3.181967 CTACGTGCACGAGGCTGC 61.182 66.667 42.94 0.61 45.15 5.25
702 744 4.735132 TACGTGCACGAGGCTGCC 62.735 66.667 42.94 11.65 45.15 4.85
713 755 2.588027 GAGGCTGCCTCTACACTTAC 57.412 55.000 35.51 11.59 46.41 2.34
759 801 6.957853 TGGATCATCCCTTCATGTATGTAT 57.042 37.500 0.00 0.00 35.03 2.29
807 854 8.421002 AGTTTGCAAAATACTTCACACCTTAAT 58.579 29.630 14.67 0.00 0.00 1.40
815 862 4.559153 ACTTCACACCTTAATGCAAATGC 58.441 39.130 0.00 0.00 42.50 3.56
816 863 3.591196 TCACACCTTAATGCAAATGCC 57.409 42.857 2.46 0.00 41.18 4.40
838 885 5.380043 CCCATATCTGCAGGTTAATCTTGT 58.620 41.667 15.13 0.00 0.00 3.16
860 907 5.932303 TGTTTAACTCTGTTCCTGTGATAGC 59.068 40.000 0.00 0.00 0.00 2.97
866 913 1.915489 TGTTCCTGTGATAGCCATGGT 59.085 47.619 14.67 2.69 0.00 3.55
910 957 7.504238 TGTGGTCCTTTTTCATTCTTAGCTTAA 59.496 33.333 0.00 0.00 0.00 1.85
953 1000 4.587262 TGCCACAGTAGTTAGTTTCTCTCA 59.413 41.667 0.00 0.00 0.00 3.27
1008 1055 6.691508 ACCCAAATTTTCTCTTATGCAGTTC 58.308 36.000 0.00 0.00 0.00 3.01
1065 1112 0.822164 AAACGTACCGCTGCTATCCT 59.178 50.000 0.00 0.00 0.00 3.24
1071 1118 1.670406 CCGCTGCTATCCTGCATCC 60.670 63.158 0.00 0.00 42.48 3.51
1142 1189 1.818642 AGCAGTGCTGGAATCTGAAC 58.181 50.000 18.98 0.00 37.57 3.18
1165 1212 9.827411 GAACTGTATTTAACCATCTTTCTGAAC 57.173 33.333 0.00 0.00 0.00 3.18
1211 1258 3.434596 GGAAGGTGGTGACAAAGGTAAGT 60.435 47.826 0.00 0.00 46.06 2.24
1212 1259 4.202388 GGAAGGTGGTGACAAAGGTAAGTA 60.202 45.833 0.00 0.00 46.06 2.24
1332 1379 2.672961 TGATCGTCTGGGTAAAGCTG 57.327 50.000 0.00 0.00 0.00 4.24
1341 1388 3.054361 TCTGGGTAAAGCTGAAATCCTCC 60.054 47.826 0.00 0.00 0.00 4.30
1365 1412 3.132289 CCATTAGACCTTAGGCTGAACGA 59.868 47.826 0.00 0.00 0.00 3.85
1367 1414 0.896226 AGACCTTAGGCTGAACGACC 59.104 55.000 0.00 0.00 0.00 4.79
1402 1452 7.953158 TTGTTGACTTTAATCACTCTGAGAG 57.047 36.000 12.44 8.15 35.52 3.20
1592 1642 4.535526 TGTGCTATGAGTGAACTTGCTA 57.464 40.909 0.00 0.00 0.00 3.49
1621 1671 7.220030 TGCTCTCTTCAGTTGAAAAGTATTCT 58.780 34.615 0.00 0.00 33.07 2.40
1772 1823 3.513912 ACACGACTGATTTCCTGGACATA 59.486 43.478 0.00 0.00 0.00 2.29
1803 1854 4.507710 CAAAGCCATGTCAGTAGCTAGAA 58.492 43.478 0.00 0.00 34.49 2.10
1827 1878 6.223120 AGTTTGCACTAAAACCCATTCATTC 58.777 36.000 0.00 0.00 40.26 2.67
1839 1890 6.371595 ACCCATTCATTCTTTTTGCCATTA 57.628 33.333 0.00 0.00 0.00 1.90
1840 1891 6.172630 ACCCATTCATTCTTTTTGCCATTAC 58.827 36.000 0.00 0.00 0.00 1.89
1842 1893 6.171921 CCATTCATTCTTTTTGCCATTACCA 58.828 36.000 0.00 0.00 0.00 3.25
1843 1894 6.824704 CCATTCATTCTTTTTGCCATTACCAT 59.175 34.615 0.00 0.00 0.00 3.55
1844 1895 7.201661 CCATTCATTCTTTTTGCCATTACCATG 60.202 37.037 0.00 0.00 0.00 3.66
1845 1896 6.357579 TCATTCTTTTTGCCATTACCATGT 57.642 33.333 0.00 0.00 0.00 3.21
1846 1897 6.397272 TCATTCTTTTTGCCATTACCATGTC 58.603 36.000 0.00 0.00 0.00 3.06
1945 2001 2.071778 TGGCAGCTTGGAGAAAACTT 57.928 45.000 0.00 0.00 0.00 2.66
2073 2129 5.798132 AGCATTATTGAGACAGACTGTGAA 58.202 37.500 14.14 3.34 0.00 3.18
2177 2233 6.554334 TGAAGGTATGTGTTTTACTCTTGC 57.446 37.500 0.00 0.00 0.00 4.01
2216 2272 4.907010 TGAATGTGATTGCGTTTTACGTTC 59.093 37.500 0.00 0.00 44.73 3.95
2246 2302 5.806654 ACAAATTTATTGTTCCTGCCTGT 57.193 34.783 0.00 0.00 0.00 4.00
2266 3032 6.000219 CCTGTCATAGGTTTTATAGCTGCAT 59.000 40.000 1.02 0.00 42.00 3.96
2267 3033 6.148480 CCTGTCATAGGTTTTATAGCTGCATC 59.852 42.308 1.02 0.00 42.00 3.91
2269 3035 6.707608 TGTCATAGGTTTTATAGCTGCATCTG 59.292 38.462 1.02 0.00 35.80 2.90
2358 3416 5.469579 TGGGGTGCTAGTATAAACCTATGA 58.530 41.667 0.00 0.00 33.02 2.15
2361 3419 6.295180 GGGGTGCTAGTATAAACCTATGAGAC 60.295 46.154 0.00 0.00 33.02 3.36
2420 3479 5.015178 TGGTTCACAGGAAAGGAATTAGGAT 59.985 40.000 0.00 0.00 34.13 3.24
2515 3574 1.768684 TTTTCCTGTGCCTCGCCTCT 61.769 55.000 0.00 0.00 0.00 3.69
2550 3610 1.965754 AAGAGCTCCCGGCAGATGTC 61.966 60.000 10.93 0.00 44.79 3.06
2572 3632 6.488683 TGTCTTATTTCCCGTGAAATCAAAGT 59.511 34.615 9.21 0.00 45.87 2.66
2624 3684 1.300620 CGTTCCTGCAGACCGAACA 60.301 57.895 24.68 0.00 36.51 3.18
2646 3706 7.198306 ACACTACTTCCGTAAAATTTTCCTG 57.802 36.000 6.72 0.00 0.00 3.86
2650 3725 8.152898 ACTACTTCCGTAAAATTTTCCTGTACT 58.847 33.333 6.72 0.00 0.00 2.73
2664 3739 5.319043 TCCTGTACTTTTCCTCCACAATT 57.681 39.130 0.00 0.00 0.00 2.32
2674 3749 4.177537 TCCTCCACAATTCCTTCAAACA 57.822 40.909 0.00 0.00 0.00 2.83
2678 3753 5.507985 CCTCCACAATTCCTTCAAACAGAAC 60.508 44.000 0.00 0.00 31.61 3.01
2679 3754 4.952957 TCCACAATTCCTTCAAACAGAACA 59.047 37.500 0.00 0.00 31.61 3.18
2770 3882 6.573664 TTCAAAGTATTGTTGGACATCCTG 57.426 37.500 0.00 0.00 37.79 3.86
2857 3972 3.265221 TGGCAATCTTCAGATCAAGAGGT 59.735 43.478 0.00 0.00 35.83 3.85
3059 4174 2.551912 AACGCGCCAGAAAACAGGG 61.552 57.895 5.73 0.00 0.00 4.45
3110 4225 3.489738 GCAAGAAAGAAGCAGAAGCACAA 60.490 43.478 0.00 0.00 45.49 3.33
3139 4254 7.114953 GGTAGTTTCTGCTATTTTTCAAACTGC 59.885 37.037 5.35 4.07 35.42 4.40
3202 4319 5.891451 AGTTAAACCTTTCAAGTTCAGTGC 58.109 37.500 0.00 0.00 0.00 4.40
3205 4322 5.343307 AAACCTTTCAAGTTCAGTGCATT 57.657 34.783 0.00 0.00 0.00 3.56
3207 4324 3.953612 ACCTTTCAAGTTCAGTGCATTCA 59.046 39.130 0.00 0.00 0.00 2.57
3236 4354 7.823799 ACAAATTCCGGATGCTAAAATGATTTT 59.176 29.630 4.15 8.35 36.67 1.82
3275 4393 9.797473 GTGCAAAGACTAAATTTAATTTGAAGC 57.203 29.630 22.20 12.89 33.82 3.86
3322 4442 8.922058 TCTGTAAGAAGACACGATATTTAACC 57.078 34.615 0.00 0.00 42.31 2.85
3422 4542 0.575390 CGAAGTTCAACGCGTTCACT 59.425 50.000 23.92 22.80 0.00 3.41
3437 4557 3.057174 CGTTCACTGGAAAGAGCTACTCT 60.057 47.826 0.00 0.00 43.37 3.24
3504 4624 2.029244 CGCAATCGAACACGCTATCTTT 59.971 45.455 0.00 0.00 38.10 2.52
3583 4703 0.037326 TCGTCTGAATCAGCACACCC 60.037 55.000 5.18 0.00 0.00 4.61
3712 4833 6.017192 TGGTATTCTGTTCCAGTCTAGTCTT 58.983 40.000 0.00 0.00 32.61 3.01
3717 4838 7.397892 TTCTGTTCCAGTCTAGTCTTATCAG 57.602 40.000 0.00 0.00 32.61 2.90
3723 4844 5.717178 TCCAGTCTAGTCTTATCAGTTGCTT 59.283 40.000 0.00 0.00 0.00 3.91
3730 4851 5.241662 AGTCTTATCAGTTGCTTTCAGACC 58.758 41.667 0.00 0.00 31.55 3.85
3732 4853 2.957402 ATCAGTTGCTTTCAGACCCA 57.043 45.000 0.00 0.00 0.00 4.51
3740 4862 3.765381 TGCTTTCAGACCCATGATTCAA 58.235 40.909 0.00 0.00 0.00 2.69
3743 4865 5.246656 TGCTTTCAGACCCATGATTCAAAAT 59.753 36.000 0.00 0.00 0.00 1.82
3776 4898 7.445121 AGTAGGAAATCAAAGCGATGATGATA 58.555 34.615 7.86 0.00 39.90 2.15
3783 4905 6.476243 TCAAAGCGATGATGATATGACATG 57.524 37.500 0.00 0.00 0.00 3.21
3792 4914 7.224167 CGATGATGATATGACATGAACTATGGG 59.776 40.741 0.00 0.00 41.25 4.00
3797 4919 1.138859 TGACATGAACTATGGGCCTCG 59.861 52.381 4.53 0.00 41.25 4.63
3812 4951 1.377725 CTCGGTGGCAGGCAAGATT 60.378 57.895 0.00 0.00 0.00 2.40
3813 4952 0.962356 CTCGGTGGCAGGCAAGATTT 60.962 55.000 0.00 0.00 0.00 2.17
3838 4977 1.551908 GGCAATCAATGTTGGGCCCA 61.552 55.000 24.45 24.45 35.63 5.36
3839 4978 0.324285 GCAATCAATGTTGGGCCCAA 59.676 50.000 34.07 34.07 0.00 4.12
3854 4993 1.094785 CCCAACATTAAGCCACCGAG 58.905 55.000 0.00 0.00 0.00 4.63
3865 5004 1.810532 CCACCGAGAGTCTGGCTAC 59.189 63.158 0.00 0.00 0.00 3.58
3872 5011 3.132289 CCGAGAGTCTGGCTACCATAAAA 59.868 47.826 0.00 0.00 30.82 1.52
3938 5079 8.491134 TGATTAAAGTAGGCCAACAGTATATGT 58.509 33.333 5.01 0.00 46.97 2.29
3939 5080 8.677148 ATTAAAGTAGGCCAACAGTATATGTG 57.323 34.615 5.01 0.00 43.00 3.21
3957 5098 3.519579 TGTGTGTTGTTTGGCAATGAAG 58.480 40.909 0.00 0.00 39.55 3.02
4002 5143 1.071567 GTGCTTCGGCGTCAGTAGAC 61.072 60.000 6.85 0.23 45.37 2.59
4052 5198 2.844946 TCTTTTGACCTGCGATGACAA 58.155 42.857 0.00 0.00 0.00 3.18
4074 5220 3.899052 AAGTCCATGGCATCAAAATGG 57.101 42.857 6.96 0.00 41.93 3.16
4079 5225 3.569277 TCCATGGCATCAAAATGGTATCG 59.431 43.478 6.96 0.00 41.41 2.92
4137 5286 0.679505 TCTGTCACTGAACTTCCCGG 59.320 55.000 0.00 0.00 0.00 5.73
4142 5291 0.320771 CACTGAACTTCCCGGGTCTG 60.321 60.000 22.86 16.59 0.00 3.51
4194 5351 0.179000 CTACTTGGCCTAGCTGGGTG 59.821 60.000 18.47 8.29 36.00 4.61
4200 5357 2.674220 GCCTAGCTGGGTGGCTCTT 61.674 63.158 18.47 0.00 43.05 2.85
4214 5371 3.507622 GTGGCTCTTGGTATTGAAAGCTT 59.492 43.478 0.00 0.00 0.00 3.74
4216 5373 3.129462 GGCTCTTGGTATTGAAAGCTTCC 59.871 47.826 0.00 0.00 0.00 3.46
4218 5375 3.343617 TCTTGGTATTGAAAGCTTCCGG 58.656 45.455 0.00 0.00 0.00 5.14
4219 5376 3.008594 TCTTGGTATTGAAAGCTTCCGGA 59.991 43.478 0.00 0.00 0.00 5.14
4220 5377 3.644966 TGGTATTGAAAGCTTCCGGAT 57.355 42.857 4.15 0.00 0.00 4.18
4236 5393 4.129380 TCCGGATGCAAGTGAAATGATAG 58.871 43.478 0.00 0.00 0.00 2.08
4267 5425 1.676967 CAGGGTCTTTGCTCAGCCC 60.677 63.158 0.00 0.00 39.60 5.19
4355 5528 2.027751 GGTACTCCGGCGCAGATC 59.972 66.667 10.83 0.00 0.00 2.75
4399 5572 2.693591 TCCATGGATCGAACCTGTACTC 59.306 50.000 11.44 0.00 0.00 2.59
4431 5604 2.182181 TGCACTAGCCGATGCATGC 61.182 57.895 11.82 11.82 46.63 4.06
4448 5621 1.365293 TGCTCCATGGATCCATAGGG 58.635 55.000 26.87 23.29 34.91 3.53
4449 5622 1.366319 GCTCCATGGATCCATAGGGT 58.634 55.000 26.87 2.44 34.91 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
155 158 4.323417 CAACCTAATTGTCTGGCAGTACA 58.677 43.478 15.27 14.16 33.20 2.90
230 264 7.484007 ACAAATACGAACTATAGTCAACTCACG 59.516 37.037 5.70 6.54 0.00 4.35
273 307 4.597075 TGGCATTTGTAGGCAGATATAGGA 59.403 41.667 0.00 0.00 36.56 2.94
279 313 3.370840 TCTTGGCATTTGTAGGCAGAT 57.629 42.857 0.00 0.00 42.75 2.90
309 343 5.533903 AGATTCATCTATCAAATGCCACACC 59.466 40.000 0.00 0.00 34.85 4.16
371 405 7.335422 AGACTAGCAATGACTTAAATCAACTGG 59.665 37.037 0.00 0.00 30.82 4.00
398 432 9.396022 CTGGATCAGTTTATTGTTAGTATGGTT 57.604 33.333 0.00 0.00 0.00 3.67
578 620 1.473677 GGCAACAGCATTATCACTGCA 59.526 47.619 0.00 0.00 42.15 4.41
581 623 3.192001 CACAAGGCAACAGCATTATCACT 59.808 43.478 0.00 0.00 41.41 3.41
585 627 2.493278 GGTCACAAGGCAACAGCATTAT 59.507 45.455 0.00 0.00 41.41 1.28
589 631 0.467844 ATGGTCACAAGGCAACAGCA 60.468 50.000 0.00 0.00 41.41 4.41
606 648 0.458543 CTCGAACCCGTGACCTCATG 60.459 60.000 0.00 0.00 37.05 3.07
607 649 0.898789 ACTCGAACCCGTGACCTCAT 60.899 55.000 0.00 0.00 37.05 2.90
608 650 1.521450 GACTCGAACCCGTGACCTCA 61.521 60.000 0.00 0.00 37.05 3.86
609 651 1.212229 GACTCGAACCCGTGACCTC 59.788 63.158 0.00 0.00 37.05 3.85
610 652 2.273912 GGACTCGAACCCGTGACCT 61.274 63.158 0.00 0.00 39.62 3.85
611 653 2.260743 GGACTCGAACCCGTGACC 59.739 66.667 0.00 0.00 37.08 4.02
612 654 1.080705 CAGGACTCGAACCCGTGAC 60.081 63.158 4.92 0.00 37.05 3.67
613 655 2.273179 CCAGGACTCGAACCCGTGA 61.273 63.158 4.92 0.00 37.05 4.35
614 656 1.812686 TTCCAGGACTCGAACCCGTG 61.813 60.000 0.00 0.64 37.05 4.94
615 657 1.117142 TTTCCAGGACTCGAACCCGT 61.117 55.000 0.00 0.00 37.05 5.28
616 658 0.669625 GTTTCCAGGACTCGAACCCG 60.670 60.000 0.00 0.00 37.07 5.28
617 659 0.395312 TGTTTCCAGGACTCGAACCC 59.605 55.000 0.00 0.12 0.00 4.11
618 660 1.070289 ACTGTTTCCAGGACTCGAACC 59.930 52.381 0.00 0.64 43.36 3.62
619 661 2.036089 AGACTGTTTCCAGGACTCGAAC 59.964 50.000 0.00 0.00 43.36 3.95
620 662 2.296471 GAGACTGTTTCCAGGACTCGAA 59.704 50.000 0.00 0.00 43.36 3.71
621 663 1.887198 GAGACTGTTTCCAGGACTCGA 59.113 52.381 0.00 0.00 43.36 4.04
622 664 1.889829 AGAGACTGTTTCCAGGACTCG 59.110 52.381 0.00 0.00 43.94 4.18
623 665 3.658709 CAAGAGACTGTTTCCAGGACTC 58.341 50.000 0.00 0.00 43.36 3.36
624 666 2.224402 GCAAGAGACTGTTTCCAGGACT 60.224 50.000 0.00 0.00 43.36 3.85
625 667 2.147150 GCAAGAGACTGTTTCCAGGAC 58.853 52.381 0.00 0.00 43.36 3.85
626 668 1.270305 CGCAAGAGACTGTTTCCAGGA 60.270 52.381 0.00 0.00 41.29 3.86
627 669 1.151668 CGCAAGAGACTGTTTCCAGG 58.848 55.000 0.00 0.00 41.29 4.45
628 670 1.871080 ACGCAAGAGACTGTTTCCAG 58.129 50.000 0.00 0.00 42.62 3.86
629 671 2.101750 TGTACGCAAGAGACTGTTTCCA 59.898 45.455 0.00 0.00 43.62 3.53
630 672 2.750948 TGTACGCAAGAGACTGTTTCC 58.249 47.619 0.00 0.00 43.62 3.13
631 673 4.789095 TTTGTACGCAAGAGACTGTTTC 57.211 40.909 0.00 0.00 43.62 2.78
632 674 4.873827 TCTTTTGTACGCAAGAGACTGTTT 59.126 37.500 3.05 0.00 39.81 2.83
633 675 4.439057 TCTTTTGTACGCAAGAGACTGTT 58.561 39.130 3.05 0.00 39.81 3.16
634 676 4.054780 TCTTTTGTACGCAAGAGACTGT 57.945 40.909 3.05 0.00 39.81 3.55
638 680 2.367567 AGGGTCTTTTGTACGCAAGAGA 59.632 45.455 6.77 0.00 41.61 3.10
639 681 2.767505 AGGGTCTTTTGTACGCAAGAG 58.232 47.619 6.77 0.00 37.95 2.85
640 682 2.922740 AGGGTCTTTTGTACGCAAGA 57.077 45.000 3.05 3.05 43.62 3.02
642 684 2.158726 AGGAAGGGTCTTTTGTACGCAA 60.159 45.455 0.00 0.00 32.57 4.85
643 685 1.418637 AGGAAGGGTCTTTTGTACGCA 59.581 47.619 0.00 0.00 32.57 5.24
644 686 1.804748 CAGGAAGGGTCTTTTGTACGC 59.195 52.381 0.00 0.00 0.00 4.42
645 687 2.038033 TCCAGGAAGGGTCTTTTGTACG 59.962 50.000 0.00 0.00 38.24 3.67
646 688 3.409570 GTCCAGGAAGGGTCTTTTGTAC 58.590 50.000 0.00 0.00 38.24 2.90
647 689 2.374170 GGTCCAGGAAGGGTCTTTTGTA 59.626 50.000 0.00 0.00 38.24 2.41
648 690 1.145119 GGTCCAGGAAGGGTCTTTTGT 59.855 52.381 0.00 0.00 38.24 2.83
649 691 1.547901 GGGTCCAGGAAGGGTCTTTTG 60.548 57.143 0.00 0.00 38.24 2.44
650 692 0.778083 GGGTCCAGGAAGGGTCTTTT 59.222 55.000 0.00 0.00 38.24 2.27
651 693 0.103876 AGGGTCCAGGAAGGGTCTTT 60.104 55.000 0.00 0.00 38.24 2.52
652 694 0.842467 CAGGGTCCAGGAAGGGTCTT 60.842 60.000 0.00 0.00 38.24 3.01
653 695 1.229658 CAGGGTCCAGGAAGGGTCT 60.230 63.158 0.00 0.00 38.24 3.85
654 696 2.972819 GCAGGGTCCAGGAAGGGTC 61.973 68.421 0.00 0.00 38.24 4.46
655 697 2.936032 GCAGGGTCCAGGAAGGGT 60.936 66.667 0.00 0.00 38.24 4.34
656 698 4.101448 CGCAGGGTCCAGGAAGGG 62.101 72.222 0.00 0.00 38.24 3.95
657 699 4.785453 GCGCAGGGTCCAGGAAGG 62.785 72.222 0.30 0.00 39.47 3.46
658 700 3.551496 TTGCGCAGGGTCCAGGAAG 62.551 63.158 11.31 0.00 0.00 3.46
659 701 3.551496 CTTGCGCAGGGTCCAGGAA 62.551 63.158 12.39 0.00 0.00 3.36
660 702 4.020617 CTTGCGCAGGGTCCAGGA 62.021 66.667 12.39 0.00 0.00 3.86
669 711 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
672 714 4.796231 ACGTAGCTCCCGCTTGCG 62.796 66.667 8.14 8.14 46.47 4.85
673 715 3.188786 CACGTAGCTCCCGCTTGC 61.189 66.667 5.69 0.00 46.47 4.01
674 716 3.188786 GCACGTAGCTCCCGCTTG 61.189 66.667 5.69 0.00 46.47 4.01
675 717 3.691342 TGCACGTAGCTCCCGCTT 61.691 61.111 10.54 0.00 46.47 4.68
678 720 4.111016 TCGTGCACGTAGCTCCCG 62.111 66.667 35.74 10.21 45.94 5.14
679 721 2.202623 CTCGTGCACGTAGCTCCC 60.203 66.667 35.74 0.00 45.94 4.30
680 722 2.202623 CCTCGTGCACGTAGCTCC 60.203 66.667 35.74 0.00 45.94 4.70
681 723 2.881352 GCCTCGTGCACGTAGCTC 60.881 66.667 35.74 20.56 45.94 4.09
682 724 3.374402 AGCCTCGTGCACGTAGCT 61.374 61.111 35.85 35.85 45.94 3.32
683 725 3.181967 CAGCCTCGTGCACGTAGC 61.182 66.667 35.74 34.44 44.83 3.58
684 726 3.181967 GCAGCCTCGTGCACGTAG 61.182 66.667 35.74 28.59 43.41 3.51
685 727 4.735132 GGCAGCCTCGTGCACGTA 62.735 66.667 35.74 22.18 45.93 3.57
695 737 0.818296 CGTAAGTGTAGAGGCAGCCT 59.182 55.000 16.12 16.12 36.03 4.58
696 738 3.347411 CGTAAGTGTAGAGGCAGCC 57.653 57.895 1.84 1.84 0.00 4.85
710 752 9.661563 AATGATTAATTAGTCCAGTTCACGTAA 57.338 29.630 5.61 0.00 0.00 3.18
711 753 9.093970 CAATGATTAATTAGTCCAGTTCACGTA 57.906 33.333 5.61 0.00 0.00 3.57
712 754 7.065803 CCAATGATTAATTAGTCCAGTTCACGT 59.934 37.037 5.61 0.00 0.00 4.49
713 755 7.279981 TCCAATGATTAATTAGTCCAGTTCACG 59.720 37.037 5.61 0.00 0.00 4.35
807 854 1.684450 CTGCAGATATGGGCATTTGCA 59.316 47.619 8.42 2.31 44.36 4.08
815 862 5.380043 ACAAGATTAACCTGCAGATATGGG 58.620 41.667 17.39 0.00 0.00 4.00
816 863 6.949352 AACAAGATTAACCTGCAGATATGG 57.051 37.500 17.39 0.19 0.00 2.74
838 885 5.012664 TGGCTATCACAGGAACAGAGTTAAA 59.987 40.000 0.00 0.00 0.00 1.52
860 907 8.402472 ACAATACAATAATTACGAACACCATGG 58.598 33.333 11.19 11.19 0.00 3.66
866 913 7.825270 AGGACCACAATACAATAATTACGAACA 59.175 33.333 0.00 0.00 0.00 3.18
953 1000 7.587037 AGCATATGCAAACTACACCAAATAT 57.413 32.000 28.62 0.00 45.16 1.28
968 1015 3.855255 TGGGTTAGCTAAGCATATGCA 57.145 42.857 30.78 19.01 45.16 3.96
1008 1055 1.614903 TGGTAACCATATCCCGCGTAG 59.385 52.381 4.92 0.00 0.00 3.51
1132 1179 8.738645 AGATGGTTAAATACAGTTCAGATTCC 57.261 34.615 0.00 0.00 0.00 3.01
1165 1212 4.039124 AGGTGTGGCTGGAAAATGTAAAAG 59.961 41.667 0.00 0.00 0.00 2.27
1171 1218 0.604578 CCAGGTGTGGCTGGAAAATG 59.395 55.000 0.00 0.00 43.08 2.32
1277 1324 5.459762 CGGCATTATTACTGCATTGGAAAAG 59.540 40.000 8.11 0.00 41.47 2.27
1332 1379 5.638530 AAGGTCTAATGGAGGAGGATTTC 57.361 43.478 0.00 0.00 0.00 2.17
1341 1388 4.698575 GTTCAGCCTAAGGTCTAATGGAG 58.301 47.826 0.00 0.00 0.00 3.86
1365 1412 9.686683 ATTAAAGTCAACAATATGAAGCTAGGT 57.313 29.630 0.00 0.00 0.00 3.08
1592 1642 6.529220 ACTTTTCAACTGAAGAGAGCAGTAT 58.471 36.000 14.90 0.00 45.27 2.12
1772 1823 2.301346 GACATGGCTTTGGGATTCGAT 58.699 47.619 0.00 0.00 0.00 3.59
1803 1854 5.806654 ATGAATGGGTTTTAGTGCAAACT 57.193 34.783 0.00 0.00 36.93 2.66
1839 1890 8.514594 CACAAAGTTATCAGTTATTGACATGGT 58.485 33.333 0.00 0.00 38.99 3.55
1840 1891 7.485913 GCACAAAGTTATCAGTTATTGACATGG 59.514 37.037 0.00 0.00 38.99 3.66
1842 1893 8.340618 AGCACAAAGTTATCAGTTATTGACAT 57.659 30.769 0.00 0.00 38.99 3.06
1843 1894 7.744087 AGCACAAAGTTATCAGTTATTGACA 57.256 32.000 0.00 0.00 38.99 3.58
1844 1895 9.151471 TCTAGCACAAAGTTATCAGTTATTGAC 57.849 33.333 0.00 0.00 38.99 3.18
1845 1896 9.371136 CTCTAGCACAAAGTTATCAGTTATTGA 57.629 33.333 0.00 0.00 40.85 2.57
1846 1897 9.155975 ACTCTAGCACAAAGTTATCAGTTATTG 57.844 33.333 0.00 0.00 0.00 1.90
1903 1959 8.137437 GCCAAGTTACACAAGCATATTAATGAT 58.863 33.333 0.00 0.00 34.84 2.45
1904 1960 7.121907 TGCCAAGTTACACAAGCATATTAATGA 59.878 33.333 0.00 0.00 34.84 2.57
1927 1983 4.278419 TCTTAAAGTTTTCTCCAAGCTGCC 59.722 41.667 0.00 0.00 0.00 4.85
1945 2001 7.254658 CGTGGTTAAGCAAGAGAAGTTTCTTAA 60.255 37.037 14.34 0.00 37.73 1.85
2073 2129 0.398318 GAGGAGGTGCAAAGTCCACT 59.602 55.000 11.73 1.47 33.78 4.00
2177 2233 6.623486 TCACATTCAGCAACTATGATTTTGG 58.377 36.000 0.00 0.00 0.00 3.28
2246 2302 6.830912 ACAGATGCAGCTATAAAACCTATGA 58.169 36.000 3.06 0.00 0.00 2.15
2266 3032 0.321298 GCGAACAGGGCCTAAACAGA 60.321 55.000 5.28 0.00 0.00 3.41
2267 3033 0.605319 TGCGAACAGGGCCTAAACAG 60.605 55.000 5.28 0.00 0.00 3.16
2269 3035 0.240145 GTTGCGAACAGGGCCTAAAC 59.760 55.000 5.28 0.67 0.00 2.01
2358 3416 5.148502 TCTACTTCCCTTGTTTCTCTGTCT 58.851 41.667 0.00 0.00 0.00 3.41
2361 3419 7.445402 TGATTTTCTACTTCCCTTGTTTCTCTG 59.555 37.037 0.00 0.00 0.00 3.35
2420 3479 1.691434 GGTCCCAAACCTTTTGCATGA 59.309 47.619 0.00 0.00 45.45 3.07
2646 3706 5.768164 TGAAGGAATTGTGGAGGAAAAGTAC 59.232 40.000 0.00 0.00 0.00 2.73
2650 3725 5.423610 TGTTTGAAGGAATTGTGGAGGAAAA 59.576 36.000 0.00 0.00 0.00 2.29
2664 3739 2.092429 AGGCTGTGTTCTGTTTGAAGGA 60.092 45.455 0.00 0.00 35.01 3.36
2674 3749 1.768870 ACACCAGTAAGGCTGTGTTCT 59.231 47.619 2.04 0.00 43.55 3.01
2678 3753 0.593128 GCAACACCAGTAAGGCTGTG 59.407 55.000 0.80 0.80 43.55 3.66
2679 3754 0.537371 GGCAACACCAGTAAGGCTGT 60.537 55.000 0.00 0.00 43.55 4.40
2770 3882 2.356069 GCAGCCTATAGAAAAGTGGCAC 59.644 50.000 10.29 10.29 45.42 5.01
2857 3972 7.504924 AACTTTGGTTCATCTTCAACGATAA 57.495 32.000 0.00 0.00 0.00 1.75
3059 4174 3.859386 CACTTGAACCAAACACAAGCTTC 59.141 43.478 0.00 0.00 42.93 3.86
3110 4225 9.529325 GTTTGAAAAATAGCAGAAACTACCTTT 57.471 29.630 0.00 0.00 0.00 3.11
3139 4254 8.939201 TTCAGTAGAGAAAAAGAGCATATGAG 57.061 34.615 6.97 0.00 0.00 2.90
3171 4288 9.529325 GAACTTGAAAGGTTTAACTTGCTAAAT 57.471 29.630 0.00 0.00 0.00 1.40
3202 4319 4.107622 GCATCCGGAATTTGTCTTGAATG 58.892 43.478 9.01 0.00 0.00 2.67
3205 4322 3.071874 AGCATCCGGAATTTGTCTTGA 57.928 42.857 9.01 0.00 0.00 3.02
3207 4324 5.975693 TTTTAGCATCCGGAATTTGTCTT 57.024 34.783 9.01 0.00 0.00 3.01
3268 4386 7.882791 TGTCATACAGAATTAGGAAGCTTCAAA 59.117 33.333 27.02 19.87 0.00 2.69
3271 4389 8.443953 AATGTCATACAGAATTAGGAAGCTTC 57.556 34.615 18.54 18.54 0.00 3.86
3275 4393 9.388506 ACAGAAATGTCATACAGAATTAGGAAG 57.611 33.333 0.00 0.00 0.00 3.46
3322 4442 7.803659 TGAATAGAAATCAGCGACTACGATTAG 59.196 37.037 0.00 0.00 42.66 1.73
3389 4509 3.576982 TGAACTTCGGCTCTTCCTTCTTA 59.423 43.478 0.00 0.00 0.00 2.10
3437 4557 1.359848 GCAGTAGCTAGCGCTTCAAA 58.640 50.000 18.68 0.00 46.47 2.69
3504 4624 3.493699 CGGTAACCAGACAACTTCCAAGA 60.494 47.826 0.00 0.00 0.00 3.02
3599 4719 6.634035 GCTAAACCGTTTATCACTTCGTTTTT 59.366 34.615 4.19 0.00 0.00 1.94
3712 4833 4.019411 TCATGGGTCTGAAAGCAACTGATA 60.019 41.667 0.00 0.00 0.00 2.15
3717 4838 3.507233 TGAATCATGGGTCTGAAAGCAAC 59.493 43.478 0.00 0.00 0.00 4.17
3723 4844 6.267242 TCACAATTTTGAATCATGGGTCTGAA 59.733 34.615 0.00 0.00 0.00 3.02
3730 4851 8.400947 CCTACTAGTCACAATTTTGAATCATGG 58.599 37.037 0.00 0.00 0.00 3.66
3732 4853 9.739276 TTCCTACTAGTCACAATTTTGAATCAT 57.261 29.630 0.00 0.00 0.00 2.45
3740 4862 8.515414 GCTTTGATTTCCTACTAGTCACAATTT 58.485 33.333 0.00 0.00 0.00 1.82
3743 4865 5.637810 CGCTTTGATTTCCTACTAGTCACAA 59.362 40.000 0.00 0.00 0.00 3.33
3776 4898 2.224378 CGAGGCCCATAGTTCATGTCAT 60.224 50.000 0.00 0.00 32.21 3.06
3783 4905 1.146263 CCACCGAGGCCCATAGTTC 59.854 63.158 0.00 0.00 0.00 3.01
3819 4958 1.221566 GGGCCCAACATTGATTGCC 59.778 57.895 19.95 9.82 36.82 4.52
3838 4977 2.567615 AGACTCTCGGTGGCTTAATGTT 59.432 45.455 0.00 0.00 0.00 2.71
3839 4978 2.093973 CAGACTCTCGGTGGCTTAATGT 60.094 50.000 0.00 0.00 0.00 2.71
3840 4979 2.544685 CAGACTCTCGGTGGCTTAATG 58.455 52.381 0.00 0.00 0.00 1.90
3841 4980 1.482593 CCAGACTCTCGGTGGCTTAAT 59.517 52.381 0.00 0.00 0.00 1.40
3872 5011 2.980233 GCACGCTGGCAGGTCTTT 60.980 61.111 17.64 0.00 0.00 2.52
3875 5014 3.965539 ATCAGCACGCTGGCAGGTC 62.966 63.158 17.64 0.00 43.75 3.85
3877 5016 1.450134 TAATCAGCACGCTGGCAGG 60.450 57.895 17.64 9.00 43.75 4.85
3879 5018 0.740868 GAGTAATCAGCACGCTGGCA 60.741 55.000 18.47 0.94 43.75 4.92
3880 5019 0.740868 TGAGTAATCAGCACGCTGGC 60.741 55.000 18.47 7.30 43.75 4.85
3881 5020 1.394917 GTTGAGTAATCAGCACGCTGG 59.605 52.381 18.47 1.04 43.75 4.85
3938 5079 2.548875 GCTTCATTGCCAAACAACACA 58.451 42.857 0.00 0.00 42.27 3.72
3939 5080 1.522258 CGCTTCATTGCCAAACAACAC 59.478 47.619 0.00 0.00 42.27 3.32
3957 5098 3.470567 CAGAACGACGACAGCCGC 61.471 66.667 0.00 0.00 43.32 6.53
4002 5143 5.425630 TCTTCATCAGTGGATCAATCACAG 58.574 41.667 0.00 0.00 37.58 3.66
4052 5198 4.041938 ACCATTTTGATGCCATGGACTTTT 59.958 37.500 18.40 0.00 40.10 2.27
4074 5220 3.511699 TGTCACAATCAGTCAGCGATAC 58.488 45.455 0.00 0.00 0.00 2.24
4079 5225 5.808042 ATTACATGTCACAATCAGTCAGC 57.192 39.130 0.00 0.00 0.00 4.26
4137 5286 4.449405 GCTCTTGTTTCTTCAGTACAGACC 59.551 45.833 0.00 0.00 0.00 3.85
4142 5291 3.997681 GGGAGCTCTTGTTTCTTCAGTAC 59.002 47.826 14.64 0.00 0.00 2.73
4194 5351 3.129462 GGAAGCTTTCAATACCAAGAGCC 59.871 47.826 0.00 0.00 0.00 4.70
4200 5357 3.278574 CATCCGGAAGCTTTCAATACCA 58.721 45.455 9.01 0.00 0.00 3.25
4214 5371 2.488204 TCATTTCACTTGCATCCGGA 57.512 45.000 6.61 6.61 0.00 5.14
4216 5373 4.024556 GGACTATCATTTCACTTGCATCCG 60.025 45.833 0.00 0.00 0.00 4.18
4218 5375 4.553547 GCGGACTATCATTTCACTTGCATC 60.554 45.833 0.00 0.00 0.00 3.91
4219 5376 3.313526 GCGGACTATCATTTCACTTGCAT 59.686 43.478 0.00 0.00 0.00 3.96
4220 5377 2.677836 GCGGACTATCATTTCACTTGCA 59.322 45.455 0.00 0.00 0.00 4.08
4236 5393 3.917760 CCCTGGATCTCGGCGGAC 61.918 72.222 7.21 0.00 0.00 4.79
4267 5425 0.184211 TGATGATGGATGGGTGCTGG 59.816 55.000 0.00 0.00 0.00 4.85
4355 5528 0.459899 TGCATCGGCCTAGTACACAG 59.540 55.000 0.00 0.00 40.13 3.66
4399 5572 2.355599 TGCACAAATTTGCGCCGG 60.356 55.556 24.29 0.00 46.20 6.13
4415 5588 1.226686 GGAGCATGCATCGGCTAGTG 61.227 60.000 21.98 0.00 41.22 2.74
4416 5589 1.070445 GGAGCATGCATCGGCTAGT 59.930 57.895 21.98 0.00 41.22 2.57
4417 5590 1.070275 TGGAGCATGCATCGGCTAG 59.930 57.895 21.98 0.00 41.22 3.42


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

AutoCloner maintained by Alex Coulton.