Multiple sequence alignment - TraesCS3D01G088200

Loading Multiple Alignment...

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 TraesCS3D01G088200 chr3D 100.000 2784 0 0 1 2784 45010647 45013430 0.000000e+00 5142.0
1 TraesCS3D01G088200 chr3D 81.753 1392 137 57 826 2158 44966645 44967978 0.000000e+00 1055.0
2 TraesCS3D01G088200 chr3D 87.037 108 14 0 484 591 476323280 476323173 3.770000e-24 122.0
3 TraesCS3D01G088200 chr3B 85.705 1462 111 40 1088 2515 70120914 70122311 0.000000e+00 1452.0
4 TraesCS3D01G088200 chr3B 91.690 722 43 12 1 718 70118252 70118960 0.000000e+00 985.0
5 TraesCS3D01G088200 chr3B 80.553 1337 119 66 826 2098 70092656 70093915 0.000000e+00 898.0
6 TraesCS3D01G088200 chr3B 81.391 1064 105 36 1761 2781 70123800 70124813 0.000000e+00 782.0
7 TraesCS3D01G088200 chr3B 93.980 299 18 0 1413 1711 70123485 70123783 1.180000e-123 453.0
8 TraesCS3D01G088200 chr3B 90.909 286 17 8 820 1097 70118960 70119244 2.620000e-100 375.0
9 TraesCS3D01G088200 chr3B 95.455 110 3 2 716 824 211111355 211111463 1.020000e-39 174.0
10 TraesCS3D01G088200 chr3B 93.458 107 7 0 717 823 8054768 8054662 2.870000e-35 159.0
11 TraesCS3D01G088200 chr3B 76.440 191 32 5 2143 2332 70095941 70096119 1.060000e-14 91.6
12 TraesCS3D01G088200 chr3A 91.250 880 55 9 1109 1967 56756813 56757691 0.000000e+00 1179.0
13 TraesCS3D01G088200 chr3A 86.982 868 74 18 1131 1967 56734751 56735610 0.000000e+00 941.0
14 TraesCS3D01G088200 chr3A 82.655 467 70 6 1986 2450 56758952 56759409 1.200000e-108 403.0
15 TraesCS3D01G088200 chr3A 85.714 231 24 4 822 1048 56756546 56756771 4.640000e-58 235.0
16 TraesCS3D01G088200 chrUn 80.912 592 66 23 1279 1835 103768761 103768182 9.220000e-115 424.0
17 TraesCS3D01G088200 chrUn 77.622 572 87 26 1295 1834 103726376 103725814 2.690000e-80 309.0
18 TraesCS3D01G088200 chrUn 92.593 108 8 0 716 823 3061877 3061984 3.710000e-34 156.0
19 TraesCS3D01G088200 chr6D 82.783 424 61 10 3 417 95795350 95795770 4.380000e-98 368.0
20 TraesCS3D01G088200 chr6D 88.073 109 13 0 483 591 6830895 6830787 2.250000e-26 130.0
21 TraesCS3D01G088200 chr6B 81.797 434 52 9 14 430 176772514 176772091 3.430000e-89 339.0
22 TraesCS3D01G088200 chr6B 85.172 290 36 6 1546 1835 55597020 55596738 9.750000e-75 291.0
23 TraesCS3D01G088200 chr6B 86.239 109 15 0 483 591 646633859 646633751 4.870000e-23 119.0
24 TraesCS3D01G088200 chr7D 80.899 445 55 14 11 438 39969863 39970294 9.620000e-85 324.0
25 TraesCS3D01G088200 chr7D 92.174 115 9 0 715 829 186412351 186412237 2.220000e-36 163.0
26 TraesCS3D01G088200 chr2D 86.486 296 22 10 27 320 190031468 190031189 2.690000e-80 309.0
27 TraesCS3D01G088200 chr2D 95.327 107 5 0 717 823 388818757 388818863 1.330000e-38 171.0
28 TraesCS3D01G088200 chr2D 86.486 111 15 0 481 591 406142908 406143018 3.770000e-24 122.0
29 TraesCS3D01G088200 chr2A 85.161 310 18 12 27 324 203899076 203898783 2.710000e-75 292.0
30 TraesCS3D01G088200 chr7B 79.310 348 50 15 27 364 186294667 186294332 1.000000e-54 224.0
31 TraesCS3D01G088200 chr7B 90.435 115 11 0 715 829 329359077 329358963 4.800000e-33 152.0
32 TraesCS3D01G088200 chr4D 93.458 107 7 0 717 823 302003485 302003379 2.870000e-35 159.0
33 TraesCS3D01G088200 chr4D 87.719 114 14 0 478 591 463678720 463678833 1.740000e-27 134.0
34 TraesCS3D01G088200 chr1D 92.661 109 8 0 715 823 462713210 462713318 1.030000e-34 158.0
35 TraesCS3D01G088200 chr1D 85.217 115 17 0 483 597 490323183 490323069 4.870000e-23 119.0
36 TraesCS3D01G088200 chr5A 89.076 119 13 0 716 834 395300612 395300494 6.210000e-32 148.0
37 TraesCS3D01G088200 chr7A 86.916 107 14 0 485 591 183321810 183321704 1.350000e-23 121.0
38 TraesCS3D01G088200 chr5B 86.239 109 15 0 483 591 674416183 674416291 4.870000e-23 119.0


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 TraesCS3D01G088200 chr3D 45010647 45013430 2783 False 5142.000000 5142 100.000000 1 2784 1 chr3D.!!$F2 2783
1 TraesCS3D01G088200 chr3D 44966645 44967978 1333 False 1055.000000 1055 81.753000 826 2158 1 chr3D.!!$F1 1332
2 TraesCS3D01G088200 chr3B 70118252 70124813 6561 False 809.400000 1452 88.735000 1 2781 5 chr3B.!!$F3 2780
3 TraesCS3D01G088200 chr3B 70092656 70096119 3463 False 494.800000 898 78.496500 826 2332 2 chr3B.!!$F2 1506
4 TraesCS3D01G088200 chr3A 56734751 56735610 859 False 941.000000 941 86.982000 1131 1967 1 chr3A.!!$F1 836
5 TraesCS3D01G088200 chr3A 56756546 56759409 2863 False 605.666667 1179 86.539667 822 2450 3 chr3A.!!$F2 1628
6 TraesCS3D01G088200 chrUn 103768182 103768761 579 True 424.000000 424 80.912000 1279 1835 1 chrUn.!!$R2 556
7 TraesCS3D01G088200 chrUn 103725814 103726376 562 True 309.000000 309 77.622000 1295 1834 1 chrUn.!!$R1 539

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
710 715 0.108898 CCTCGCAGTTCAGTCTCCAG 60.109 60.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2582 8823 0.166814 GATCAGTGTGGTTTGCTCGC 59.833 55.0 0.0 0.0 0.0 5.03 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
61 62 1.205655 AGCGCAGATCAAGTAGAGCAA 59.794 47.619 11.47 0.00 34.30 3.91
69 70 5.645067 CAGATCAAGTAGAGCAATGGTGAAA 59.355 40.000 0.00 0.00 34.30 2.69
88 89 4.036734 TGAAATTGAGAACACAGCAACTCC 59.963 41.667 0.00 0.00 0.00 3.85
97 98 1.962822 CAGCAACTCCGCAGAAGCA 60.963 57.895 0.00 0.00 42.27 3.91
121 122 2.816672 CGAGATAGAGCAGCCATGACTA 59.183 50.000 0.00 0.00 0.00 2.59
127 128 0.391661 AGCAGCCATGACTAACACCG 60.392 55.000 0.00 0.00 0.00 4.94
178 179 2.490217 CGTGTCTCCTACAGCCCG 59.510 66.667 0.00 0.00 39.29 6.13
248 249 3.603770 CGAATGAAGCGAAAAATCACCAC 59.396 43.478 0.00 0.00 0.00 4.16
268 269 0.389166 GTCGATCAGCCGATCCATCC 60.389 60.000 4.33 0.00 44.55 3.51
272 273 0.540597 ATCAGCCGATCCATCCGAGA 60.541 55.000 0.00 0.00 0.00 4.04
274 275 2.049985 GCCGATCCATCCGAGACG 60.050 66.667 0.00 0.00 0.00 4.18
340 341 2.921435 GGCCTGATCATGGGCTCA 59.079 61.111 21.58 0.00 46.80 4.26
368 369 1.499949 GCTTTGTTGCATACGCGGA 59.500 52.632 12.47 0.00 42.97 5.54
485 488 2.472695 TCTGTTGAGGGGATGAAACG 57.527 50.000 0.00 0.00 0.00 3.60
500 503 1.711060 AAACGTGTGTTGGGCTCGTG 61.711 55.000 0.00 0.00 38.62 4.35
512 515 1.080093 GCTCGTGGTTCGTGGATGA 60.080 57.895 0.00 0.00 40.80 2.92
515 518 0.389757 TCGTGGTTCGTGGATGACAA 59.610 50.000 0.00 0.00 40.80 3.18
517 520 0.517316 GTGGTTCGTGGATGACAAGC 59.483 55.000 0.00 0.00 0.00 4.01
543 546 0.617413 TCCTCCTCCGACGTCTTAGT 59.383 55.000 14.70 0.00 0.00 2.24
544 547 1.015868 CCTCCTCCGACGTCTTAGTC 58.984 60.000 14.70 0.00 37.76 2.59
545 548 1.678123 CCTCCTCCGACGTCTTAGTCA 60.678 57.143 14.70 0.00 40.98 3.41
548 551 4.066490 CTCCTCCGACGTCTTAGTCATAT 58.934 47.826 14.70 0.00 40.98 1.78
549 552 3.813724 TCCTCCGACGTCTTAGTCATATG 59.186 47.826 14.70 0.00 40.98 1.78
550 553 3.058155 CCTCCGACGTCTTAGTCATATGG 60.058 52.174 14.70 3.20 40.98 2.74
551 554 3.812262 TCCGACGTCTTAGTCATATGGA 58.188 45.455 14.70 5.71 40.98 3.41
552 555 3.813724 TCCGACGTCTTAGTCATATGGAG 59.186 47.826 14.70 0.00 40.98 3.86
553 556 3.564644 CCGACGTCTTAGTCATATGGAGT 59.435 47.826 14.70 0.00 40.98 3.85
554 557 4.036498 CCGACGTCTTAGTCATATGGAGTT 59.964 45.833 14.70 0.00 40.98 3.01
555 558 4.970611 CGACGTCTTAGTCATATGGAGTTG 59.029 45.833 14.70 0.00 40.98 3.16
562 565 7.865385 GTCTTAGTCATATGGAGTTGTCAGATC 59.135 40.741 2.13 0.00 0.00 2.75
569 572 8.927411 TCATATGGAGTTGTCAGATCTGAAATA 58.073 33.333 26.70 13.43 41.85 1.40
571 574 6.358974 TGGAGTTGTCAGATCTGAAATACA 57.641 37.500 26.70 17.68 41.85 2.29
581 584 6.531594 TCAGATCTGAAATACAATGACGTGTC 59.468 38.462 23.17 0.00 36.53 3.67
595 598 1.149854 GTGTCCGGGGTGTTTTCCT 59.850 57.895 0.00 0.00 0.00 3.36
611 615 0.550914 TCCTGGAACTTTGGTGCTGT 59.449 50.000 0.00 0.00 0.00 4.40
614 618 2.301346 CTGGAACTTTGGTGCTGTTCT 58.699 47.619 0.00 0.00 39.73 3.01
615 619 2.023673 TGGAACTTTGGTGCTGTTCTG 58.976 47.619 0.00 0.00 39.73 3.02
625 629 0.391228 TGCTGTTCTGAGCCGTACAA 59.609 50.000 0.00 0.00 38.28 2.41
627 631 2.076863 GCTGTTCTGAGCCGTACAATT 58.923 47.619 0.00 0.00 32.35 2.32
673 677 0.179089 CGAAGGCAGAGACCATGAGG 60.179 60.000 0.00 0.00 42.21 3.86
674 678 1.198713 GAAGGCAGAGACCATGAGGA 58.801 55.000 0.00 0.00 38.69 3.71
676 680 1.145819 GGCAGAGACCATGAGGAGC 59.854 63.158 0.00 0.00 38.69 4.70
683 688 1.066573 AGACCATGAGGAGCGAGTTTG 60.067 52.381 0.00 0.00 38.69 2.93
707 712 1.290324 TGCCTCGCAGTTCAGTCTC 59.710 57.895 0.00 0.00 33.32 3.36
708 713 1.446966 GCCTCGCAGTTCAGTCTCC 60.447 63.158 0.00 0.00 0.00 3.71
709 714 1.967535 CCTCGCAGTTCAGTCTCCA 59.032 57.895 0.00 0.00 0.00 3.86
710 715 0.108898 CCTCGCAGTTCAGTCTCCAG 60.109 60.000 0.00 0.00 0.00 3.86
713 718 0.600557 CGCAGTTCAGTCTCCAGTCT 59.399 55.000 0.00 0.00 0.00 3.24
714 719 1.402194 CGCAGTTCAGTCTCCAGTCTC 60.402 57.143 0.00 0.00 0.00 3.36
716 721 2.233431 GCAGTTCAGTCTCCAGTCTCAT 59.767 50.000 0.00 0.00 0.00 2.90
717 722 3.445450 GCAGTTCAGTCTCCAGTCTCATA 59.555 47.826 0.00 0.00 0.00 2.15
718 723 4.676723 GCAGTTCAGTCTCCAGTCTCATAC 60.677 50.000 0.00 0.00 0.00 2.39
719 724 4.704540 CAGTTCAGTCTCCAGTCTCATACT 59.295 45.833 0.00 0.00 39.81 2.12
720 725 5.184864 CAGTTCAGTCTCCAGTCTCATACTT 59.815 44.000 0.00 0.00 35.76 2.24
721 726 5.417580 AGTTCAGTCTCCAGTCTCATACTTC 59.582 44.000 0.00 0.00 35.76 3.01
722 727 5.186256 TCAGTCTCCAGTCTCATACTTCT 57.814 43.478 0.00 0.00 35.76 2.85
723 728 5.575157 TCAGTCTCCAGTCTCATACTTCTT 58.425 41.667 0.00 0.00 35.76 2.52
724 729 5.650266 TCAGTCTCCAGTCTCATACTTCTTC 59.350 44.000 0.00 0.00 35.76 2.87
725 730 4.953579 AGTCTCCAGTCTCATACTTCTTCC 59.046 45.833 0.00 0.00 35.76 3.46
726 731 3.948473 TCTCCAGTCTCATACTTCTTCCG 59.052 47.826 0.00 0.00 35.76 4.30
727 732 3.697045 CTCCAGTCTCATACTTCTTCCGT 59.303 47.826 0.00 0.00 35.76 4.69
728 733 4.087182 TCCAGTCTCATACTTCTTCCGTT 58.913 43.478 0.00 0.00 35.76 4.44
729 734 4.158025 TCCAGTCTCATACTTCTTCCGTTC 59.842 45.833 0.00 0.00 35.76 3.95
730 735 4.425520 CAGTCTCATACTTCTTCCGTTCC 58.574 47.826 0.00 0.00 35.76 3.62
731 736 4.082190 CAGTCTCATACTTCTTCCGTTCCA 60.082 45.833 0.00 0.00 35.76 3.53
732 737 4.712337 AGTCTCATACTTCTTCCGTTCCAT 59.288 41.667 0.00 0.00 33.35 3.41
733 738 5.892119 AGTCTCATACTTCTTCCGTTCCATA 59.108 40.000 0.00 0.00 33.35 2.74
734 739 6.551601 AGTCTCATACTTCTTCCGTTCCATAT 59.448 38.462 0.00 0.00 33.35 1.78
735 740 7.070074 AGTCTCATACTTCTTCCGTTCCATATT 59.930 37.037 0.00 0.00 33.35 1.28
736 741 8.358148 GTCTCATACTTCTTCCGTTCCATATTA 58.642 37.037 0.00 0.00 0.00 0.98
737 742 8.577296 TCTCATACTTCTTCCGTTCCATATTAG 58.423 37.037 0.00 0.00 0.00 1.73
738 743 8.246430 TCATACTTCTTCCGTTCCATATTAGT 57.754 34.615 0.00 0.00 0.00 2.24
739 744 8.701895 TCATACTTCTTCCGTTCCATATTAGTT 58.298 33.333 0.00 0.00 0.00 2.24
740 745 8.765219 CATACTTCTTCCGTTCCATATTAGTTG 58.235 37.037 0.00 0.00 0.00 3.16
741 746 6.708285 ACTTCTTCCGTTCCATATTAGTTGT 58.292 36.000 0.00 0.00 0.00 3.32
742 747 6.817140 ACTTCTTCCGTTCCATATTAGTTGTC 59.183 38.462 0.00 0.00 0.00 3.18
743 748 5.345702 TCTTCCGTTCCATATTAGTTGTCG 58.654 41.667 0.00 0.00 0.00 4.35
744 749 3.450578 TCCGTTCCATATTAGTTGTCGC 58.549 45.455 0.00 0.00 0.00 5.19
745 750 3.131577 TCCGTTCCATATTAGTTGTCGCT 59.868 43.478 0.00 0.00 0.00 4.93
746 751 3.489785 CCGTTCCATATTAGTTGTCGCTC 59.510 47.826 0.00 0.00 0.00 5.03
747 752 4.109766 CGTTCCATATTAGTTGTCGCTCA 58.890 43.478 0.00 0.00 0.00 4.26
748 753 4.565166 CGTTCCATATTAGTTGTCGCTCAA 59.435 41.667 0.00 0.00 0.00 3.02
749 754 5.062934 CGTTCCATATTAGTTGTCGCTCAAA 59.937 40.000 0.00 0.00 37.81 2.69
750 755 6.248631 GTTCCATATTAGTTGTCGCTCAAAC 58.751 40.000 0.00 0.00 37.81 2.93
751 756 4.565166 TCCATATTAGTTGTCGCTCAAACG 59.435 41.667 0.00 0.00 37.81 3.60
752 757 4.260212 CCATATTAGTTGTCGCTCAAACGG 60.260 45.833 0.00 0.00 37.81 4.44
753 758 2.512485 TTAGTTGTCGCTCAAACGGA 57.488 45.000 0.00 0.00 37.81 4.69
754 759 2.736144 TAGTTGTCGCTCAAACGGAT 57.264 45.000 0.00 0.00 37.81 4.18
755 760 1.148310 AGTTGTCGCTCAAACGGATG 58.852 50.000 0.00 0.00 37.81 3.51
756 761 0.865769 GTTGTCGCTCAAACGGATGT 59.134 50.000 0.00 0.00 37.81 3.06
757 762 2.063266 GTTGTCGCTCAAACGGATGTA 58.937 47.619 0.00 0.00 37.81 2.29
758 763 2.665649 TGTCGCTCAAACGGATGTAT 57.334 45.000 0.00 0.00 0.00 2.29
759 764 2.536365 TGTCGCTCAAACGGATGTATC 58.464 47.619 0.00 0.00 0.00 2.24
760 765 2.165641 TGTCGCTCAAACGGATGTATCT 59.834 45.455 0.00 0.00 0.00 1.98
761 766 3.379057 TGTCGCTCAAACGGATGTATCTA 59.621 43.478 0.00 0.00 0.00 1.98
762 767 3.975670 GTCGCTCAAACGGATGTATCTAG 59.024 47.826 0.00 0.00 0.00 2.43
763 768 2.726760 CGCTCAAACGGATGTATCTAGC 59.273 50.000 0.00 0.00 0.00 3.42
764 769 3.717707 GCTCAAACGGATGTATCTAGCA 58.282 45.455 0.00 0.00 0.00 3.49
765 770 3.491267 GCTCAAACGGATGTATCTAGCAC 59.509 47.826 0.00 0.00 0.00 4.40
766 771 4.737946 GCTCAAACGGATGTATCTAGCACT 60.738 45.833 0.00 0.00 0.00 4.40
767 772 4.682787 TCAAACGGATGTATCTAGCACTG 58.317 43.478 0.00 0.00 0.00 3.66
768 773 4.401202 TCAAACGGATGTATCTAGCACTGA 59.599 41.667 0.00 0.00 0.00 3.41
769 774 5.105513 TCAAACGGATGTATCTAGCACTGAA 60.106 40.000 0.00 0.00 0.00 3.02
770 775 5.339008 AACGGATGTATCTAGCACTGAAA 57.661 39.130 0.00 0.00 0.00 2.69
771 776 5.537300 ACGGATGTATCTAGCACTGAAAT 57.463 39.130 0.00 0.00 0.00 2.17
772 777 6.650427 ACGGATGTATCTAGCACTGAAATA 57.350 37.500 0.00 0.00 0.00 1.40
773 778 7.233389 ACGGATGTATCTAGCACTGAAATAT 57.767 36.000 0.00 0.00 0.00 1.28
774 779 7.093354 ACGGATGTATCTAGCACTGAAATATG 58.907 38.462 0.00 0.00 0.00 1.78
775 780 7.093354 CGGATGTATCTAGCACTGAAATATGT 58.907 38.462 0.00 0.00 0.00 2.29
776 781 7.274468 CGGATGTATCTAGCACTGAAATATGTC 59.726 40.741 0.00 0.00 0.00 3.06
777 782 8.310382 GGATGTATCTAGCACTGAAATATGTCT 58.690 37.037 0.00 0.00 0.00 3.41
780 785 9.131791 TGTATCTAGCACTGAAATATGTCTACA 57.868 33.333 0.00 0.00 0.00 2.74
784 789 9.131791 TCTAGCACTGAAATATGTCTACATACA 57.868 33.333 4.98 0.00 41.15 2.29
785 790 9.920133 CTAGCACTGAAATATGTCTACATACAT 57.080 33.333 4.98 0.00 41.15 2.29
787 792 9.265901 AGCACTGAAATATGTCTACATACATTC 57.734 33.333 16.31 16.31 41.15 2.67
788 793 9.045223 GCACTGAAATATGTCTACATACATTCA 57.955 33.333 20.67 20.67 41.08 2.57
796 801 6.588348 TGTCTACATACATTCATTTCAGCG 57.412 37.500 0.00 0.00 0.00 5.18
797 802 6.337356 TGTCTACATACATTCATTTCAGCGA 58.663 36.000 0.00 0.00 0.00 4.93
798 803 6.255670 TGTCTACATACATTCATTTCAGCGAC 59.744 38.462 0.00 0.00 0.00 5.19
799 804 6.255670 GTCTACATACATTCATTTCAGCGACA 59.744 38.462 0.00 0.00 0.00 4.35
800 805 5.878332 ACATACATTCATTTCAGCGACAA 57.122 34.783 0.00 0.00 0.00 3.18
801 806 5.631026 ACATACATTCATTTCAGCGACAAC 58.369 37.500 0.00 0.00 0.00 3.32
802 807 5.412594 ACATACATTCATTTCAGCGACAACT 59.587 36.000 0.00 0.00 0.00 3.16
803 808 6.593770 ACATACATTCATTTCAGCGACAACTA 59.406 34.615 0.00 0.00 0.00 2.24
804 809 5.940192 ACATTCATTTCAGCGACAACTAA 57.060 34.783 0.00 0.00 0.00 2.24
805 810 6.500684 ACATTCATTTCAGCGACAACTAAT 57.499 33.333 0.00 0.00 0.00 1.73
806 811 7.609760 ACATTCATTTCAGCGACAACTAATA 57.390 32.000 0.00 0.00 0.00 0.98
807 812 8.213518 ACATTCATTTCAGCGACAACTAATAT 57.786 30.769 0.00 0.00 0.00 1.28
808 813 8.124823 ACATTCATTTCAGCGACAACTAATATG 58.875 33.333 0.00 0.00 0.00 1.78
809 814 6.603237 TCATTTCAGCGACAACTAATATGG 57.397 37.500 0.00 0.00 0.00 2.74
810 815 6.345298 TCATTTCAGCGACAACTAATATGGA 58.655 36.000 0.00 0.00 0.00 3.41
811 816 6.821160 TCATTTCAGCGACAACTAATATGGAA 59.179 34.615 0.00 0.00 0.00 3.53
812 817 6.417191 TTTCAGCGACAACTAATATGGAAC 57.583 37.500 0.00 0.00 0.00 3.62
853 858 4.030913 AGTCCCTCTCAATCGTGGAATTA 58.969 43.478 0.00 0.00 0.00 1.40
869 884 6.128661 CGTGGAATTATTCAAAGTCAGTCGAA 60.129 38.462 7.29 0.00 0.00 3.71
885 900 1.985116 GAACGAGTCTCCCCAGCCT 60.985 63.158 0.00 0.00 0.00 4.58
890 905 4.767255 GTCTCCCCAGCCTGCGTG 62.767 72.222 0.00 0.00 0.00 5.34
944 967 2.884012 CAAAAACCCAAAAATGCCCCTC 59.116 45.455 0.00 0.00 0.00 4.30
995 1018 4.149046 GCGAGGATATCTTCGTCATGTTTC 59.851 45.833 30.36 13.24 45.55 2.78
1033 1057 2.307934 GTGCACCAACACAAACCAAT 57.692 45.000 5.22 0.00 40.40 3.16
1062 1092 2.662091 AAACACAAGTGAAGCGCGGC 62.662 55.000 8.83 0.00 0.00 6.53
1112 2821 1.954362 TTTGCTTTGTTGGGCGTGCT 61.954 50.000 0.00 0.00 0.00 4.40
1234 2976 2.038269 CCCAATTCCACCGACACCG 61.038 63.158 0.00 0.00 0.00 4.94
1274 3028 4.016706 GTCCGGTGGTGGAGGTGG 62.017 72.222 0.00 0.00 39.14 4.61
1275 3029 4.242586 TCCGGTGGTGGAGGTGGA 62.243 66.667 0.00 0.00 33.05 4.02
1276 3030 3.706373 CCGGTGGTGGAGGTGGAG 61.706 72.222 0.00 0.00 0.00 3.86
1277 3031 3.706373 CGGTGGTGGAGGTGGAGG 61.706 72.222 0.00 0.00 0.00 4.30
1303 3057 3.812019 CCGTCGAGCTACGCCACT 61.812 66.667 3.43 0.00 41.51 4.00
1837 3630 1.674057 CTTCCTTCTGACGTGCCCT 59.326 57.895 0.00 0.00 0.00 5.19
1877 3680 4.020617 CTCCTTCCGGCACCAGCA 62.021 66.667 0.00 0.00 44.61 4.41
1879 3682 3.136123 CCTTCCGGCACCAGCATG 61.136 66.667 0.00 0.00 44.61 4.06
1899 3704 1.209504 GGAGGACCATCATCGGTTTGA 59.790 52.381 0.00 0.00 40.22 2.69
1913 3718 2.223479 CGGTTTGAGGGCATTTATTCCG 60.223 50.000 0.00 0.00 0.00 4.30
1920 3725 1.947456 GGGCATTTATTCCGTCTGACC 59.053 52.381 1.55 0.00 0.00 4.02
1929 3735 2.265589 TCCGTCTGACCGAGCATATA 57.734 50.000 1.55 0.00 0.00 0.86
1932 3741 2.293677 CCGTCTGACCGAGCATATAGTT 59.706 50.000 1.55 0.00 0.00 2.24
1936 3745 5.109903 GTCTGACCGAGCATATAGTTTTGT 58.890 41.667 0.00 0.00 0.00 2.83
1968 3777 4.501071 TCGGTGTGGCTAATTTTCTACTC 58.499 43.478 0.00 0.00 0.00 2.59
1969 3778 3.621715 CGGTGTGGCTAATTTTCTACTCC 59.378 47.826 0.00 0.00 0.00 3.85
1970 3779 3.945921 GGTGTGGCTAATTTTCTACTCCC 59.054 47.826 0.00 0.00 0.00 4.30
1971 3780 4.324331 GGTGTGGCTAATTTTCTACTCCCT 60.324 45.833 0.00 0.00 0.00 4.20
1972 3781 4.876679 GTGTGGCTAATTTTCTACTCCCTC 59.123 45.833 0.00 0.00 0.00 4.30
1973 3782 4.783227 TGTGGCTAATTTTCTACTCCCTCT 59.217 41.667 0.00 0.00 0.00 3.69
1974 3783 5.119694 GTGGCTAATTTTCTACTCCCTCTG 58.880 45.833 0.00 0.00 0.00 3.35
1975 3784 4.783227 TGGCTAATTTTCTACTCCCTCTGT 59.217 41.667 0.00 0.00 0.00 3.41
1976 3785 5.962031 TGGCTAATTTTCTACTCCCTCTGTA 59.038 40.000 0.00 0.00 0.00 2.74
1977 3786 6.127140 TGGCTAATTTTCTACTCCCTCTGTAC 60.127 42.308 0.00 0.00 0.00 2.90
1978 3787 5.978322 GCTAATTTTCTACTCCCTCTGTACG 59.022 44.000 0.00 0.00 0.00 3.67
1979 3788 5.340439 AATTTTCTACTCCCTCTGTACGG 57.660 43.478 0.00 0.00 0.00 4.02
1980 3789 2.431954 TTCTACTCCCTCTGTACGGG 57.568 55.000 0.85 0.00 43.38 5.28
1981 3790 0.549950 TCTACTCCCTCTGTACGGGG 59.450 60.000 10.91 10.91 42.23 5.73
1984 3793 2.043248 TCCCTCTGTACGGGGAGC 60.043 66.667 14.56 0.00 45.84 4.70
2031 3841 4.751767 TTCAAGGTGAATTTGGCAAACT 57.248 36.364 16.00 3.57 30.26 2.66
2032 3842 4.751767 TCAAGGTGAATTTGGCAAACTT 57.248 36.364 16.00 10.62 0.00 2.66
2037 3847 7.232534 TCAAGGTGAATTTGGCAAACTTATAGT 59.767 33.333 16.00 0.00 0.00 2.12
2038 3848 8.519526 CAAGGTGAATTTGGCAAACTTATAGTA 58.480 33.333 16.00 0.00 0.00 1.82
2039 3849 8.823220 AGGTGAATTTGGCAAACTTATAGTAT 57.177 30.769 16.00 0.00 0.00 2.12
2040 3850 9.255029 AGGTGAATTTGGCAAACTTATAGTATT 57.745 29.630 16.00 1.91 0.00 1.89
2063 3873 2.472695 TGCACTAGAAGAAATGGCGT 57.527 45.000 0.00 0.00 0.00 5.68
2094 3905 1.449070 GAAAACCCTAGGCCCGACG 60.449 63.158 2.05 0.00 0.00 5.12
2098 3909 3.072468 CCCTAGGCCCGACGTCAA 61.072 66.667 17.16 0.00 0.00 3.18
2104 5323 2.396157 GGCCCGACGTCAATTGGTC 61.396 63.158 17.16 7.78 0.00 4.02
2111 5330 1.191647 GACGTCAATTGGTCGTGTCAC 59.808 52.381 25.20 12.83 37.92 3.67
2114 5333 1.206578 CAATTGGTCGTGTCACGGC 59.793 57.895 24.33 22.96 46.91 5.68
2131 5350 4.377471 CGATGTGCTGCATTGCTG 57.623 55.556 5.27 10.68 38.06 4.41
2136 5355 2.640346 TGTGCTGCATTGCTGTATTG 57.360 45.000 15.71 0.00 0.00 1.90
2139 5358 3.113322 GTGCTGCATTGCTGTATTGATG 58.887 45.455 15.71 0.00 0.00 3.07
2140 5359 3.018149 TGCTGCATTGCTGTATTGATGA 58.982 40.909 15.71 0.00 0.00 2.92
2141 5360 3.181494 TGCTGCATTGCTGTATTGATGAC 60.181 43.478 15.71 0.00 0.00 3.06
2174 5969 8.554835 TTGTTTGGAGATTGTTCGATGTAATA 57.445 30.769 0.00 0.00 0.00 0.98
2176 5971 9.825109 TGTTTGGAGATTGTTCGATGTAATATA 57.175 29.630 0.00 0.00 0.00 0.86
2182 5978 7.963532 AGATTGTTCGATGTAATATACAGGGT 58.036 34.615 0.00 0.00 42.77 4.34
2214 6010 8.993424 ACATATGATCCAAACTTAAGTAGGAGT 58.007 33.333 25.20 17.25 36.32 3.85
2215 6011 9.838339 CATATGATCCAAACTTAAGTAGGAGTT 57.162 33.333 25.20 15.24 36.32 3.01
2225 6021 7.120923 ACTTAAGTAGGAGTTTGACTTGACA 57.879 36.000 6.26 0.00 35.17 3.58
2228 6024 4.369182 AGTAGGAGTTTGACTTGACAACG 58.631 43.478 0.00 0.00 0.00 4.10
2229 6025 2.561569 AGGAGTTTGACTTGACAACGG 58.438 47.619 0.00 0.00 0.00 4.44
2230 6026 1.002792 GGAGTTTGACTTGACAACGGC 60.003 52.381 0.00 0.00 0.00 5.68
2238 6034 2.170260 CTTGACAACGGCGCGATTGT 62.170 55.000 23.19 23.19 41.70 2.71
2266 6062 5.874810 CCGTTCAATTGATCACTTCCTAGAA 59.125 40.000 9.40 0.00 0.00 2.10
2282 6079 5.107133 TCCTAGAAGCGTTATTTTTCGGAG 58.893 41.667 0.00 0.00 0.00 4.63
2291 6088 5.681543 GCGTTATTTTTCGGAGAATCATTCC 59.318 40.000 0.00 0.00 45.90 3.01
2306 6103 2.167693 TCATTCCCGTAGTCCATGTGTC 59.832 50.000 0.00 0.00 0.00 3.67
2313 6110 2.095415 CGTAGTCCATGTGTCGTCAAGA 60.095 50.000 0.00 0.00 0.00 3.02
2337 6134 4.846779 TGGTTGGTATTGCTTCAAGTTC 57.153 40.909 0.00 0.00 0.00 3.01
2372 6169 2.298610 GCCTACAAGAACTATTGGCCC 58.701 52.381 0.00 0.00 34.36 5.80
2373 6170 2.356741 GCCTACAAGAACTATTGGCCCA 60.357 50.000 0.00 0.00 34.36 5.36
2376 6173 4.580580 CCTACAAGAACTATTGGCCCAATC 59.419 45.833 13.36 0.00 35.54 2.67
2386 6183 2.361104 GCCCAATCGCCCTGTTCA 60.361 61.111 0.00 0.00 0.00 3.18
2404 6201 1.012841 CATCTTCCGCTTTCAGCTCC 58.987 55.000 0.00 0.00 39.60 4.70
2405 6202 0.107459 ATCTTCCGCTTTCAGCTCCC 60.107 55.000 0.00 0.00 39.60 4.30
2406 6203 1.746991 CTTCCGCTTTCAGCTCCCC 60.747 63.158 0.00 0.00 39.60 4.81
2428 6225 2.581216 ACTCCACGTACTCCTTCAGA 57.419 50.000 0.00 0.00 0.00 3.27
2499 8739 1.542915 GCTCTCCAGCTCATTGCAAAA 59.457 47.619 1.71 0.00 45.94 2.44
2507 8747 4.110482 CAGCTCATTGCAAAAGCCTTATC 58.890 43.478 25.26 5.69 45.94 1.75
2542 8783 1.502163 GCATACCATCGCTCACCAGC 61.502 60.000 0.00 0.00 42.96 4.85
2573 8814 2.584835 TGGCCAGCCCATTATACATC 57.415 50.000 0.00 0.00 39.18 3.06
2582 8823 3.254060 CCCATTATACATCGAGGCGAAG 58.746 50.000 0.00 0.00 39.99 3.79
2596 8837 1.082756 CGAAGCGAGCAAACCACAC 60.083 57.895 0.00 0.00 0.00 3.82
2629 8891 1.071857 GGAACCTTCCTGAACGTTCCT 59.928 52.381 24.78 0.00 45.11 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 7.750229 AAATCTGAAGGTACGTATATCGGTA 57.250 36.000 0.00 0.00 44.69 4.02
18 19 7.693120 CGCTCTAAATCTGAAGGTACGTATATC 59.307 40.741 0.00 0.00 0.00 1.63
25 26 3.782046 TGCGCTCTAAATCTGAAGGTAC 58.218 45.455 9.73 0.00 0.00 3.34
61 62 3.890756 TGCTGTGTTCTCAATTTCACCAT 59.109 39.130 0.00 0.00 0.00 3.55
69 70 2.146342 CGGAGTTGCTGTGTTCTCAAT 58.854 47.619 0.00 0.00 0.00 2.57
88 89 2.979151 CTCTATCTCGATTGCTTCTGCG 59.021 50.000 0.00 0.00 43.34 5.18
97 98 2.896044 TCATGGCTGCTCTATCTCGATT 59.104 45.455 0.00 0.00 0.00 3.34
121 122 1.067776 GCTCTAGTGTGCTACGGTGTT 60.068 52.381 0.00 0.00 0.00 3.32
127 128 1.437986 CGGGGCTCTAGTGTGCTAC 59.562 63.158 0.00 0.00 33.63 3.58
178 179 0.385723 CGATTCTACGCTAGTCGCCC 60.386 60.000 6.50 0.00 43.23 6.13
293 294 0.543410 TCTCGTTGCCCCTTGACCTA 60.543 55.000 0.00 0.00 0.00 3.08
338 339 3.386078 TGCAACAAAGCCCAACTAAATGA 59.614 39.130 0.00 0.00 0.00 2.57
340 341 4.622260 ATGCAACAAAGCCCAACTAAAT 57.378 36.364 0.00 0.00 0.00 1.40
368 369 6.426937 AGTCTAATTCATGCAGTTACACGTTT 59.573 34.615 0.00 0.00 0.00 3.60
485 488 1.782028 GAACCACGAGCCCAACACAC 61.782 60.000 0.00 0.00 0.00 3.82
500 503 1.131126 CATGCTTGTCATCCACGAACC 59.869 52.381 0.00 0.00 31.79 3.62
512 515 1.272147 GGAGGAGGAAACCATGCTTGT 60.272 52.381 0.00 0.00 0.00 3.16
515 518 0.909610 TCGGAGGAGGAAACCATGCT 60.910 55.000 0.00 0.00 0.00 3.79
517 520 0.460284 CGTCGGAGGAGGAAACCATG 60.460 60.000 0.00 0.00 0.00 3.66
543 546 6.796785 TTCAGATCTGACAACTCCATATGA 57.203 37.500 25.07 2.82 39.66 2.15
544 547 8.986847 GTATTTCAGATCTGACAACTCCATATG 58.013 37.037 25.07 0.00 39.66 1.78
545 548 8.708378 TGTATTTCAGATCTGACAACTCCATAT 58.292 33.333 25.07 3.93 39.66 1.78
548 551 6.358974 TGTATTTCAGATCTGACAACTCCA 57.641 37.500 25.07 13.51 39.66 3.86
549 552 7.550551 TCATTGTATTTCAGATCTGACAACTCC 59.449 37.037 25.07 11.25 39.66 3.85
550 553 8.386606 GTCATTGTATTTCAGATCTGACAACTC 58.613 37.037 25.07 14.19 39.66 3.01
551 554 7.063898 CGTCATTGTATTTCAGATCTGACAACT 59.936 37.037 25.07 11.91 39.66 3.16
552 555 7.148573 ACGTCATTGTATTTCAGATCTGACAAC 60.149 37.037 25.07 20.85 39.66 3.32
553 556 6.873605 ACGTCATTGTATTTCAGATCTGACAA 59.126 34.615 25.07 23.62 39.66 3.18
554 557 6.311200 CACGTCATTGTATTTCAGATCTGACA 59.689 38.462 25.07 19.28 39.66 3.58
555 558 6.311445 ACACGTCATTGTATTTCAGATCTGAC 59.689 38.462 25.07 14.42 39.66 3.51
562 565 3.062099 CCGGACACGTCATTGTATTTCAG 59.938 47.826 0.00 0.00 38.78 3.02
569 572 2.345991 CCCCGGACACGTCATTGT 59.654 61.111 0.73 0.00 38.78 2.71
571 574 2.047213 AACACCCCGGACACGTCATT 62.047 55.000 0.73 0.00 38.78 2.57
581 584 1.151908 TTCCAGGAAAACACCCCGG 59.848 57.895 0.00 0.00 0.00 5.73
595 598 2.023673 CAGAACAGCACCAAAGTTCCA 58.976 47.619 0.00 0.00 41.86 3.53
597 601 2.287248 GCTCAGAACAGCACCAAAGTTC 60.287 50.000 0.00 0.00 41.37 3.01
611 615 3.585862 GAGTCAATTGTACGGCTCAGAA 58.414 45.455 5.13 0.00 0.00 3.02
614 618 1.621317 TGGAGTCAATTGTACGGCTCA 59.379 47.619 5.13 0.25 0.00 4.26
615 619 2.380084 TGGAGTCAATTGTACGGCTC 57.620 50.000 5.13 6.73 0.00 4.70
653 657 0.809241 CTCATGGTCTCTGCCTTCGC 60.809 60.000 0.00 0.00 0.00 4.70
658 662 1.145819 GCTCCTCATGGTCTCTGCC 59.854 63.158 0.00 0.00 34.23 4.85
669 673 2.347490 GGGCAAACTCGCTCCTCA 59.653 61.111 0.00 0.00 0.00 3.86
695 700 1.615883 TGAGACTGGAGACTGAACTGC 59.384 52.381 0.00 0.00 0.00 4.40
700 705 5.186256 AGAAGTATGAGACTGGAGACTGA 57.814 43.478 0.00 0.00 38.87 3.41
707 712 4.425520 GAACGGAAGAAGTATGAGACTGG 58.574 47.826 0.00 0.00 38.87 4.00
708 713 4.082190 TGGAACGGAAGAAGTATGAGACTG 60.082 45.833 0.00 0.00 38.87 3.51
709 714 4.087182 TGGAACGGAAGAAGTATGAGACT 58.913 43.478 0.00 0.00 41.56 3.24
710 715 4.451629 TGGAACGGAAGAAGTATGAGAC 57.548 45.455 0.00 0.00 0.00 3.36
713 718 8.246430 ACTAATATGGAACGGAAGAAGTATGA 57.754 34.615 0.00 0.00 0.00 2.15
714 719 8.765219 CAACTAATATGGAACGGAAGAAGTATG 58.235 37.037 0.00 0.00 0.00 2.39
716 721 7.844009 ACAACTAATATGGAACGGAAGAAGTA 58.156 34.615 0.00 0.00 0.00 2.24
717 722 6.708285 ACAACTAATATGGAACGGAAGAAGT 58.292 36.000 0.00 0.00 0.00 3.01
718 723 6.019801 CGACAACTAATATGGAACGGAAGAAG 60.020 42.308 0.00 0.00 0.00 2.85
719 724 5.808540 CGACAACTAATATGGAACGGAAGAA 59.191 40.000 0.00 0.00 0.00 2.52
720 725 5.345702 CGACAACTAATATGGAACGGAAGA 58.654 41.667 0.00 0.00 0.00 2.87
721 726 4.025979 GCGACAACTAATATGGAACGGAAG 60.026 45.833 0.00 0.00 0.00 3.46
722 727 3.866910 GCGACAACTAATATGGAACGGAA 59.133 43.478 0.00 0.00 0.00 4.30
723 728 3.131577 AGCGACAACTAATATGGAACGGA 59.868 43.478 0.00 0.00 0.00 4.69
724 729 3.454375 AGCGACAACTAATATGGAACGG 58.546 45.455 0.00 0.00 0.00 4.44
725 730 4.109766 TGAGCGACAACTAATATGGAACG 58.890 43.478 0.00 0.00 0.00 3.95
726 731 6.248631 GTTTGAGCGACAACTAATATGGAAC 58.751 40.000 0.00 0.00 38.29 3.62
727 732 5.062934 CGTTTGAGCGACAACTAATATGGAA 59.937 40.000 0.00 0.00 38.29 3.53
728 733 4.565166 CGTTTGAGCGACAACTAATATGGA 59.435 41.667 0.00 0.00 38.29 3.41
729 734 4.260212 CCGTTTGAGCGACAACTAATATGG 60.260 45.833 0.00 0.00 38.29 2.74
730 735 4.565166 TCCGTTTGAGCGACAACTAATATG 59.435 41.667 0.00 0.00 38.29 1.78
731 736 4.751060 TCCGTTTGAGCGACAACTAATAT 58.249 39.130 0.00 0.00 38.29 1.28
732 737 4.177165 TCCGTTTGAGCGACAACTAATA 57.823 40.909 0.00 0.00 38.29 0.98
733 738 3.034721 TCCGTTTGAGCGACAACTAAT 57.965 42.857 0.00 0.00 38.29 1.73
734 739 2.512485 TCCGTTTGAGCGACAACTAA 57.488 45.000 0.00 0.00 38.29 2.24
735 740 2.288579 ACATCCGTTTGAGCGACAACTA 60.289 45.455 0.00 0.00 38.29 2.24
736 741 1.148310 CATCCGTTTGAGCGACAACT 58.852 50.000 0.00 0.00 38.29 3.16
737 742 0.865769 ACATCCGTTTGAGCGACAAC 59.134 50.000 0.00 0.00 38.29 3.32
738 743 2.442212 TACATCCGTTTGAGCGACAA 57.558 45.000 0.00 0.00 36.65 3.18
739 744 2.165641 AGATACATCCGTTTGAGCGACA 59.834 45.455 0.00 0.00 0.00 4.35
740 745 2.810650 AGATACATCCGTTTGAGCGAC 58.189 47.619 0.00 0.00 0.00 5.19
741 746 3.550233 GCTAGATACATCCGTTTGAGCGA 60.550 47.826 0.00 0.00 0.00 4.93
742 747 2.726760 GCTAGATACATCCGTTTGAGCG 59.273 50.000 0.00 0.00 0.00 5.03
743 748 3.491267 GTGCTAGATACATCCGTTTGAGC 59.509 47.826 0.00 0.00 0.00 4.26
744 749 4.742167 CAGTGCTAGATACATCCGTTTGAG 59.258 45.833 0.00 0.00 0.00 3.02
745 750 4.401202 TCAGTGCTAGATACATCCGTTTGA 59.599 41.667 0.00 0.00 0.00 2.69
746 751 4.682787 TCAGTGCTAGATACATCCGTTTG 58.317 43.478 0.00 0.00 0.00 2.93
747 752 5.339008 TTCAGTGCTAGATACATCCGTTT 57.661 39.130 0.00 0.00 0.00 3.60
748 753 5.339008 TTTCAGTGCTAGATACATCCGTT 57.661 39.130 0.00 0.00 0.00 4.44
749 754 5.537300 ATTTCAGTGCTAGATACATCCGT 57.463 39.130 0.00 0.00 0.00 4.69
750 755 7.093354 ACATATTTCAGTGCTAGATACATCCG 58.907 38.462 0.00 0.00 0.00 4.18
751 756 8.310382 AGACATATTTCAGTGCTAGATACATCC 58.690 37.037 0.00 0.00 0.00 3.51
754 759 9.131791 TGTAGACATATTTCAGTGCTAGATACA 57.868 33.333 0.00 0.00 0.00 2.29
758 763 9.131791 TGTATGTAGACATATTTCAGTGCTAGA 57.868 33.333 5.69 0.00 40.53 2.43
759 764 9.920133 ATGTATGTAGACATATTTCAGTGCTAG 57.080 33.333 5.69 0.00 40.53 3.42
761 766 9.265901 GAATGTATGTAGACATATTTCAGTGCT 57.734 33.333 16.01 0.00 39.16 4.40
762 767 9.045223 TGAATGTATGTAGACATATTTCAGTGC 57.955 33.333 17.95 3.06 39.16 4.40
770 775 8.929746 CGCTGAAATGAATGTATGTAGACATAT 58.070 33.333 5.69 0.00 39.16 1.78
771 776 8.141268 TCGCTGAAATGAATGTATGTAGACATA 58.859 33.333 0.00 0.00 39.16 2.29
772 777 6.986231 TCGCTGAAATGAATGTATGTAGACAT 59.014 34.615 0.08 0.08 41.92 3.06
773 778 6.255670 GTCGCTGAAATGAATGTATGTAGACA 59.744 38.462 0.00 0.00 0.00 3.41
774 779 6.255670 TGTCGCTGAAATGAATGTATGTAGAC 59.744 38.462 0.00 0.00 0.00 2.59
775 780 6.337356 TGTCGCTGAAATGAATGTATGTAGA 58.663 36.000 0.00 0.00 0.00 2.59
776 781 6.588348 TGTCGCTGAAATGAATGTATGTAG 57.412 37.500 0.00 0.00 0.00 2.74
777 782 6.593770 AGTTGTCGCTGAAATGAATGTATGTA 59.406 34.615 0.00 0.00 0.00 2.29
778 783 5.412594 AGTTGTCGCTGAAATGAATGTATGT 59.587 36.000 0.00 0.00 0.00 2.29
779 784 5.872635 AGTTGTCGCTGAAATGAATGTATG 58.127 37.500 0.00 0.00 0.00 2.39
780 785 7.609760 TTAGTTGTCGCTGAAATGAATGTAT 57.390 32.000 0.00 0.00 0.00 2.29
781 786 7.609760 ATTAGTTGTCGCTGAAATGAATGTA 57.390 32.000 0.00 0.00 0.00 2.29
782 787 5.940192 TTAGTTGTCGCTGAAATGAATGT 57.060 34.783 0.00 0.00 0.00 2.71
783 788 7.588854 CCATATTAGTTGTCGCTGAAATGAATG 59.411 37.037 0.00 0.00 0.00 2.67
784 789 7.498900 TCCATATTAGTTGTCGCTGAAATGAAT 59.501 33.333 0.00 0.00 0.00 2.57
785 790 6.821160 TCCATATTAGTTGTCGCTGAAATGAA 59.179 34.615 0.00 0.00 0.00 2.57
786 791 6.345298 TCCATATTAGTTGTCGCTGAAATGA 58.655 36.000 0.00 0.00 0.00 2.57
787 792 6.603237 TCCATATTAGTTGTCGCTGAAATG 57.397 37.500 0.00 0.00 0.00 2.32
788 793 6.597672 TGTTCCATATTAGTTGTCGCTGAAAT 59.402 34.615 0.00 0.00 0.00 2.17
789 794 5.935206 TGTTCCATATTAGTTGTCGCTGAAA 59.065 36.000 0.00 0.00 0.00 2.69
790 795 5.483811 TGTTCCATATTAGTTGTCGCTGAA 58.516 37.500 0.00 0.00 0.00 3.02
791 796 5.079689 TGTTCCATATTAGTTGTCGCTGA 57.920 39.130 0.00 0.00 0.00 4.26
792 797 5.109210 TCTGTTCCATATTAGTTGTCGCTG 58.891 41.667 0.00 0.00 0.00 5.18
793 798 5.127194 TCTCTGTTCCATATTAGTTGTCGCT 59.873 40.000 0.00 0.00 0.00 4.93
794 799 5.348986 TCTCTGTTCCATATTAGTTGTCGC 58.651 41.667 0.00 0.00 0.00 5.19
795 800 6.796426 TCTCTCTGTTCCATATTAGTTGTCG 58.204 40.000 0.00 0.00 0.00 4.35
796 801 7.777095 ACTCTCTCTGTTCCATATTAGTTGTC 58.223 38.462 0.00 0.00 0.00 3.18
797 802 7.726033 ACTCTCTCTGTTCCATATTAGTTGT 57.274 36.000 0.00 0.00 0.00 3.32
798 803 9.743057 CTTACTCTCTCTGTTCCATATTAGTTG 57.257 37.037 0.00 0.00 0.00 3.16
799 804 9.482175 ACTTACTCTCTCTGTTCCATATTAGTT 57.518 33.333 0.00 0.00 0.00 2.24
803 808 9.647918 TGATACTTACTCTCTCTGTTCCATATT 57.352 33.333 0.00 0.00 0.00 1.28
804 809 9.821240 ATGATACTTACTCTCTCTGTTCCATAT 57.179 33.333 0.00 0.00 0.00 1.78
806 811 9.295825 CTATGATACTTACTCTCTCTGTTCCAT 57.704 37.037 0.00 0.00 0.00 3.41
807 812 8.275758 ACTATGATACTTACTCTCTCTGTTCCA 58.724 37.037 0.00 0.00 0.00 3.53
808 813 8.685838 ACTATGATACTTACTCTCTCTGTTCC 57.314 38.462 0.00 0.00 0.00 3.62
809 814 8.780249 GGACTATGATACTTACTCTCTCTGTTC 58.220 40.741 0.00 0.00 0.00 3.18
810 815 7.722285 GGGACTATGATACTTACTCTCTCTGTT 59.278 40.741 0.00 0.00 0.00 3.16
811 816 7.073215 AGGGACTATGATACTTACTCTCTCTGT 59.927 40.741 0.00 0.00 36.02 3.41
812 817 7.458397 AGGGACTATGATACTTACTCTCTCTG 58.542 42.308 0.00 0.00 36.02 3.35
813 818 7.516209 AGAGGGACTATGATACTTACTCTCTCT 59.484 40.741 0.00 0.00 41.55 3.10
814 819 7.686434 AGAGGGACTATGATACTTACTCTCTC 58.314 42.308 0.00 0.00 41.55 3.20
815 820 7.293771 TGAGAGGGACTATGATACTTACTCTCT 59.706 40.741 15.99 0.00 45.19 3.10
816 821 7.455058 TGAGAGGGACTATGATACTTACTCTC 58.545 42.308 0.00 0.00 45.18 3.20
817 822 7.395525 TGAGAGGGACTATGATACTTACTCT 57.604 40.000 0.00 0.00 41.55 3.24
818 823 8.644374 ATTGAGAGGGACTATGATACTTACTC 57.356 38.462 0.00 0.00 41.55 2.59
819 824 7.392113 CGATTGAGAGGGACTATGATACTTACT 59.608 40.741 0.00 0.00 41.55 2.24
820 825 7.175293 ACGATTGAGAGGGACTATGATACTTAC 59.825 40.741 0.00 0.00 41.55 2.34
823 828 5.475220 CACGATTGAGAGGGACTATGATACT 59.525 44.000 0.00 0.00 41.55 2.12
853 858 3.978687 ACTCGTTCGACTGACTTTGAAT 58.021 40.909 0.00 0.00 0.00 2.57
869 884 2.681778 CAGGCTGGGGAGACTCGT 60.682 66.667 6.61 0.00 0.00 4.18
902 921 5.219343 TGATTAGATGATGATTCTGGCGT 57.781 39.130 0.00 0.00 0.00 5.68
944 967 1.410882 GGGAGAGAGAAGGTTGGATCG 59.589 57.143 0.00 0.00 0.00 3.69
1033 1057 5.659463 CTTCACTTGTGTTTTGGAATTGGA 58.341 37.500 0.46 0.00 0.00 3.53
1112 2821 6.183360 GCACGTAGAATAGATAGATCGTAGCA 60.183 42.308 0.00 0.00 0.00 3.49
1274 3028 3.827898 CGACGGAGCCTCCACCTC 61.828 72.222 12.13 0.85 35.91 3.85
1275 3029 4.361971 TCGACGGAGCCTCCACCT 62.362 66.667 12.13 0.00 35.91 4.00
1276 3030 3.827898 CTCGACGGAGCCTCCACC 61.828 72.222 12.13 0.19 35.91 4.61
1303 3057 4.269523 AACAGGAGCTTGCCGGCA 62.270 61.111 29.03 29.03 34.17 5.69
1411 3165 4.479993 GAGATGGGCAGGCTGCGT 62.480 66.667 31.22 20.30 46.21 5.24
1837 3630 0.392998 GGAAGCTTCCTCGCATCCAA 60.393 55.000 33.98 0.00 44.80 3.53
1879 3682 1.209504 TCAAACCGATGATGGTCCTCC 59.790 52.381 0.00 0.00 42.89 4.30
1899 3704 2.421529 GGTCAGACGGAATAAATGCCCT 60.422 50.000 0.00 0.00 0.00 5.19
1913 3718 5.109903 ACAAAACTATATGCTCGGTCAGAC 58.890 41.667 0.00 0.00 0.00 3.51
1920 3725 5.794687 TCACCAACAAAACTATATGCTCG 57.205 39.130 0.00 0.00 0.00 5.03
1929 3735 1.608590 CCGAGCATCACCAACAAAACT 59.391 47.619 0.00 0.00 33.17 2.66
1932 3741 0.950836 CACCGAGCATCACCAACAAA 59.049 50.000 0.00 0.00 33.17 2.83
1936 3745 1.302431 CCACACCGAGCATCACCAA 60.302 57.895 0.00 0.00 33.17 3.67
1977 3786 0.450184 CCAAATTTGTACGCTCCCCG 59.550 55.000 16.73 0.00 44.21 5.73
1978 3787 0.172578 GCCAAATTTGTACGCTCCCC 59.827 55.000 16.73 0.00 0.00 4.81
1979 3788 0.885196 TGCCAAATTTGTACGCTCCC 59.115 50.000 16.73 0.00 0.00 4.30
1980 3789 1.268352 TGTGCCAAATTTGTACGCTCC 59.732 47.619 16.73 8.65 0.00 4.70
1981 3790 2.697431 TGTGCCAAATTTGTACGCTC 57.303 45.000 16.73 13.36 0.00 5.03
1982 3791 2.352617 CCATGTGCCAAATTTGTACGCT 60.353 45.455 16.73 5.08 0.00 5.07
1983 3792 1.991965 CCATGTGCCAAATTTGTACGC 59.008 47.619 16.73 14.39 0.00 4.42
1984 3793 3.567576 TCCATGTGCCAAATTTGTACG 57.432 42.857 16.73 3.22 0.00 3.67
2012 3822 7.378181 ACTATAAGTTTGCCAAATTCACCTTG 58.622 34.615 0.00 0.00 0.00 3.61
2037 3847 7.282224 ACGCCATTTCTTCTAGTGCAATAAATA 59.718 33.333 0.00 0.00 0.00 1.40
2038 3848 6.095440 ACGCCATTTCTTCTAGTGCAATAAAT 59.905 34.615 0.00 0.00 0.00 1.40
2039 3849 5.414454 ACGCCATTTCTTCTAGTGCAATAAA 59.586 36.000 0.00 0.00 0.00 1.40
2040 3850 4.941263 ACGCCATTTCTTCTAGTGCAATAA 59.059 37.500 0.00 0.00 0.00 1.40
2084 3895 1.219664 CCAATTGACGTCGGGCCTA 59.780 57.895 11.62 0.00 0.00 3.93
2094 3905 0.511221 CCGTGACACGACCAATTGAC 59.489 55.000 28.83 0.00 46.05 3.18
2098 3909 2.501223 ATCGCCGTGACACGACCAAT 62.501 55.000 28.83 13.23 46.05 3.16
2104 5323 4.134187 GCACATCGCCGTGACACG 62.134 66.667 21.02 21.02 39.34 4.49
2111 5330 2.277692 CAATGCAGCACATCGCCG 60.278 61.111 0.00 0.00 44.04 6.46
2114 5333 0.728542 TACAGCAATGCAGCACATCG 59.271 50.000 8.35 0.00 38.34 3.84
2123 5342 3.950087 TCGTCATCAATACAGCAATGC 57.050 42.857 0.00 0.00 0.00 3.56
2131 5350 8.394877 TCCAAACAATACATTCGTCATCAATAC 58.605 33.333 0.00 0.00 0.00 1.89
2136 5355 6.662414 TCTCCAAACAATACATTCGTCATC 57.338 37.500 0.00 0.00 0.00 2.92
2139 5358 6.842163 ACAATCTCCAAACAATACATTCGTC 58.158 36.000 0.00 0.00 0.00 4.20
2140 5359 6.817765 ACAATCTCCAAACAATACATTCGT 57.182 33.333 0.00 0.00 0.00 3.85
2141 5360 6.465781 CGAACAATCTCCAAACAATACATTCG 59.534 38.462 0.00 0.00 0.00 3.34
2174 5969 7.353525 TGGATCATATGTTTTCAACCCTGTAT 58.646 34.615 1.90 0.00 0.00 2.29
2176 5971 5.579047 TGGATCATATGTTTTCAACCCTGT 58.421 37.500 1.90 0.00 0.00 4.00
2204 6000 5.981315 CGTTGTCAAGTCAAACTCCTACTTA 59.019 40.000 0.00 0.00 32.35 2.24
2211 6007 1.332904 CGCCGTTGTCAAGTCAAACTC 60.333 52.381 0.00 0.00 0.00 3.01
2212 6008 0.655733 CGCCGTTGTCAAGTCAAACT 59.344 50.000 0.00 0.00 0.00 2.66
2214 6010 1.353804 GCGCCGTTGTCAAGTCAAA 59.646 52.632 0.00 0.00 0.00 2.69
2215 6011 2.876879 CGCGCCGTTGTCAAGTCAA 61.877 57.895 0.00 0.00 0.00 3.18
2217 6013 1.897398 AATCGCGCCGTTGTCAAGTC 61.897 55.000 0.00 0.00 0.00 3.01
2218 6014 1.959226 AATCGCGCCGTTGTCAAGT 60.959 52.632 0.00 0.00 0.00 3.16
2219 6015 1.509787 CAATCGCGCCGTTGTCAAG 60.510 57.895 0.00 0.00 0.00 3.02
2220 6016 2.248135 ACAATCGCGCCGTTGTCAA 61.248 52.632 16.60 0.00 33.53 3.18
2221 6017 2.663520 ACAATCGCGCCGTTGTCA 60.664 55.556 16.60 0.00 33.53 3.58
2238 6034 0.167908 GTGATCAATTGAACGGCGCA 59.832 50.000 13.09 0.00 0.00 6.09
2266 6062 6.436843 AATGATTCTCCGAAAAATAACGCT 57.563 33.333 0.00 0.00 0.00 5.07
2282 6079 3.809832 CACATGGACTACGGGAATGATTC 59.190 47.826 0.00 0.00 0.00 2.52
2291 6088 0.524414 TGACGACACATGGACTACGG 59.476 55.000 0.00 0.00 0.00 4.02
2306 6103 3.063997 GCAATACCAACCATCTCTTGACG 59.936 47.826 0.00 0.00 0.00 4.35
2313 6110 4.666512 ACTTGAAGCAATACCAACCATCT 58.333 39.130 0.00 0.00 0.00 2.90
2372 6169 1.672881 GGAAGATGAACAGGGCGATTG 59.327 52.381 0.00 0.00 0.00 2.67
2373 6170 1.743772 CGGAAGATGAACAGGGCGATT 60.744 52.381 0.00 0.00 0.00 3.34
2376 6173 2.464459 GCGGAAGATGAACAGGGCG 61.464 63.158 0.00 0.00 0.00 6.13
2404 6201 2.068834 AGGAGTACGTGGAGTATGGG 57.931 55.000 0.00 0.00 37.69 4.00
2405 6202 3.021695 TGAAGGAGTACGTGGAGTATGG 58.978 50.000 0.00 0.00 37.69 2.74
2406 6203 3.945921 TCTGAAGGAGTACGTGGAGTATG 59.054 47.826 0.00 0.00 37.69 2.39
2428 6225 6.716628 CCACCATGGTCAGCAAATACTATAAT 59.283 38.462 16.53 0.00 31.35 1.28
2499 8739 2.639839 ACGATTGCTATGGGATAAGGCT 59.360 45.455 0.00 0.00 0.00 4.58
2533 8774 4.082523 TGCCTACCGCTGGTGAGC 62.083 66.667 10.01 11.82 42.37 4.26
2549 8790 2.005370 ATAATGGGCTGGCCATTCTG 57.995 50.000 40.89 0.00 38.59 3.02
2553 8794 2.618816 CGATGTATAATGGGCTGGCCAT 60.619 50.000 28.20 28.20 37.98 4.40
2554 8795 1.271325 CGATGTATAATGGGCTGGCCA 60.271 52.381 26.08 26.08 37.98 5.36
2559 8800 1.066858 CGCCTCGATGTATAATGGGCT 60.067 52.381 5.20 0.00 36.37 5.19
2570 8811 3.326210 GCTCGCTTCGCCTCGATG 61.326 66.667 0.00 0.00 35.23 3.84
2573 8814 3.112075 TTTGCTCGCTTCGCCTCG 61.112 61.111 0.00 0.00 0.00 4.63
2582 8823 0.166814 GATCAGTGTGGTTTGCTCGC 59.833 55.000 0.00 0.00 0.00 5.03
2584 8825 0.798776 CCGATCAGTGTGGTTTGCTC 59.201 55.000 0.00 0.00 0.00 4.26
2596 8837 2.200373 AGGTTCCCAAAACCGATCAG 57.800 50.000 1.52 0.00 44.82 2.90
2618 8880 1.578583 AACGGTTCAGGAACGTTCAG 58.421 50.000 28.24 19.80 42.02 3.02
2619 8881 2.027003 AAACGGTTCAGGAACGTTCA 57.973 45.000 28.24 6.67 42.02 3.18
2629 8891 7.595604 ACAGTAAAAGAAAAGAAAACGGTTCA 58.404 30.769 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.