Multiple sequence alignment - TraesCS4A01G299600

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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 TraesCS4A01G299600 chr4A 100.000 3521 0 0 1 3521 597885889 597889409 0.000000e+00 6503.0
1 TraesCS4A01G299600 chr4A 96.014 552 21 1 1 551 355204727 355205278 0.000000e+00 896.0
2 TraesCS4A01G299600 chr4A 88.929 551 59 2 1049 1598 597848729 597849278 0.000000e+00 678.0
3 TraesCS4A01G299600 chr4A 90.952 210 17 2 3257 3465 597868253 597868461 7.440000e-72 281.0
4 TraesCS4A01G299600 chr4A 83.913 230 17 12 2838 3065 573662913 573662702 5.960000e-48 202.0
5 TraesCS4A01G299600 chr4A 76.457 446 57 27 704 1129 573663333 573662916 7.710000e-47 198.0
6 TraesCS4A01G299600 chr4A 83.636 165 11 9 2727 2887 597867749 597867901 1.320000e-29 141.0
7 TraesCS4A01G299600 chr4A 84.783 138 11 5 3058 3195 573662648 573662521 2.850000e-26 130.0
8 TraesCS4A01G299600 chr4A 87.838 74 6 2 2614 2687 597867692 597867762 2.250000e-12 84.2
9 TraesCS4A01G299600 chr4A 89.831 59 0 2 3062 3119 653076820 653076767 1.750000e-08 71.3
10 TraesCS4A01G299600 chr4D 93.031 2009 124 8 689 2687 5662788 5660786 0.000000e+00 2920.0
11 TraesCS4A01G299600 chr4D 96.687 483 15 1 2993 3475 5660694 5660213 0.000000e+00 802.0
12 TraesCS4A01G299600 chr4D 89.394 198 21 0 3245 3442 5672352 5672155 2.100000e-62 250.0
13 TraesCS4A01G299600 chr4D 77.130 446 54 27 704 1129 29412082 29412499 7.660000e-52 215.0
14 TraesCS4A01G299600 chr4D 85.644 202 13 10 2838 3037 29412502 29412689 7.710000e-47 198.0
15 TraesCS4A01G299600 chr4D 85.405 185 14 7 955 1129 5672829 5672648 2.790000e-41 180.0
16 TraesCS4A01G299600 chr4D 94.681 94 3 2 2725 2816 5660801 5660708 1.020000e-30 145.0
17 TraesCS4A01G299600 chr4D 84.058 138 12 5 3058 3195 29412767 29412894 1.330000e-24 124.0
18 TraesCS4A01G299600 chr4D 91.549 71 3 3 559 628 5662904 5662836 1.040000e-15 95.3
19 TraesCS4A01G299600 chr4D 95.833 48 2 0 3472 3519 338446186 338446233 1.050000e-10 78.7
20 TraesCS4A01G299600 chr4B 93.948 1768 101 4 854 2620 9947785 9946023 0.000000e+00 2667.0
21 TraesCS4A01G299600 chr4B 88.785 214 18 5 3257 3465 9945154 9944942 1.250000e-64 257.0
22 TraesCS4A01G299600 chr4B 85.882 170 13 7 2893 3062 41843987 41844145 1.680000e-38 171.0
23 TraesCS4A01G299600 chr4B 96.809 94 3 0 1036 1129 41843848 41843941 1.310000e-34 158.0
24 TraesCS4A01G299600 chr4B 82.609 138 14 5 3058 3195 41844199 41844326 2.870000e-21 113.0
25 TraesCS4A01G299600 chr4B 82.400 125 12 7 743 865 9947931 9947815 2.240000e-17 100.0
26 TraesCS4A01G299600 chr7A 83.977 1941 236 42 693 2620 708656702 708654824 0.000000e+00 1792.0
27 TraesCS4A01G299600 chr7A 74.131 777 158 31 1655 2418 126196460 126197206 7.440000e-72 281.0
28 TraesCS4A01G299600 chr7A 74.832 596 124 17 1778 2363 126192110 126192689 2.710000e-61 246.0
29 TraesCS4A01G299600 chr7A 77.263 453 64 22 1048 1467 126191383 126191829 2.730000e-56 230.0
30 TraesCS4A01G299600 chr7A 89.394 66 4 3 3056 3119 45855233 45855297 2.910000e-11 80.5
31 TraesCS4A01G299600 chr6D 96.739 552 17 1 1 551 429801176 429801727 0.000000e+00 918.0
32 TraesCS4A01G299600 chr6D 97.826 46 1 0 3474 3519 461518700 461518745 2.910000e-11 80.5
33 TraesCS4A01G299600 chr7D 96.685 543 16 2 11 551 632792551 632792009 0.000000e+00 902.0
34 TraesCS4A01G299600 chr7D 73.174 794 167 33 1651 2430 123455890 123456651 9.760000e-61 244.0
35 TraesCS4A01G299600 chr3D 96.196 552 20 1 1 551 536225576 536226127 0.000000e+00 902.0
36 TraesCS4A01G299600 chr3D 96.029 554 20 1 1 554 543938229 543937678 0.000000e+00 900.0
37 TraesCS4A01G299600 chr3D 97.368 38 1 0 2685 2722 496187969 496187932 8.160000e-07 65.8
38 TraesCS4A01G299600 chr3B 96.022 553 19 2 1 552 5080718 5081268 0.000000e+00 896.0
39 TraesCS4A01G299600 chr3B 95.841 553 20 2 1 552 4225325 4225875 0.000000e+00 891.0
40 TraesCS4A01G299600 chr3B 95.780 545 20 2 10 554 773369746 773369205 0.000000e+00 876.0
41 TraesCS4A01G299600 chr3B 86.486 74 7 2 3449 3519 685228239 685228312 1.050000e-10 78.7
42 TraesCS4A01G299600 chr3B 90.164 61 3 3 3460 3519 811506896 811506838 3.770000e-10 76.8
43 TraesCS4A01G299600 chr5D 95.841 553 19 4 1 551 545673984 545673434 0.000000e+00 891.0
44 TraesCS4A01G299600 chrUn 92.162 370 27 2 3104 3471 52143089 52142720 4.030000e-144 521.0
45 TraesCS4A01G299600 chr6B 85.714 175 13 4 955 1129 625884217 625884055 1.300000e-39 174.0
46 TraesCS4A01G299600 chr6B 85.455 110 9 4 3086 3195 625883165 625883063 1.340000e-19 108.0
47 TraesCS4A01G299600 chr6B 95.918 49 2 0 3471 3519 5681688 5681736 2.910000e-11 80.5
48 TraesCS4A01G299600 chr5A 95.918 49 2 0 3473 3521 392031267 392031219 2.910000e-11 80.5
49 TraesCS4A01G299600 chr5A 95.918 49 2 0 3473 3521 392033259 392033211 2.910000e-11 80.5
50 TraesCS4A01G299600 chr5A 89.655 58 3 3 2110 2166 589329409 589329464 1.750000e-08 71.3
51 TraesCS4A01G299600 chr5A 89.286 56 5 1 2110 2165 589312797 589312851 6.310000e-08 69.4
52 TraesCS4A01G299600 chr2A 91.228 57 5 0 3465 3521 608917964 608918020 1.050000e-10 78.7
53 TraesCS4A01G299600 chr2B 92.593 54 2 2 3467 3519 63860705 63860757 3.770000e-10 76.8
54 TraesCS4A01G299600 chr1A 93.750 48 3 0 2685 2732 517073367 517073414 4.880000e-09 73.1
55 TraesCS4A01G299600 chr5B 85.075 67 8 2 2100 2165 576161948 576162013 2.270000e-07 67.6
56 TraesCS4A01G299600 chr5B 94.872 39 1 1 2678 2716 594906299 594906336 3.800000e-05 60.2
57 TraesCS4A01G299600 chr3A 95.238 42 1 1 2678 2719 1744946 1744986 8.160000e-07 65.8


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 TraesCS4A01G299600 chr4A 597885889 597889409 3520 False 6503.000000 6503 100.000000 1 3521 1 chr4A.!!$F3 3520
1 TraesCS4A01G299600 chr4A 355204727 355205278 551 False 896.000000 896 96.014000 1 551 1 chr4A.!!$F1 550
2 TraesCS4A01G299600 chr4A 597848729 597849278 549 False 678.000000 678 88.929000 1049 1598 1 chr4A.!!$F2 549
3 TraesCS4A01G299600 chr4D 5660213 5662904 2691 True 990.575000 2920 93.987000 559 3475 4 chr4D.!!$R1 2916
4 TraesCS4A01G299600 chr4D 5672155 5672829 674 True 215.000000 250 87.399500 955 3442 2 chr4D.!!$R2 2487
5 TraesCS4A01G299600 chr4B 9944942 9947931 2989 True 1008.000000 2667 88.377667 743 3465 3 chr4B.!!$R1 2722
6 TraesCS4A01G299600 chr7A 708654824 708656702 1878 True 1792.000000 1792 83.977000 693 2620 1 chr7A.!!$R1 1927
7 TraesCS4A01G299600 chr7A 126191383 126197206 5823 False 252.333333 281 75.408667 1048 2418 3 chr7A.!!$F2 1370
8 TraesCS4A01G299600 chr6D 429801176 429801727 551 False 918.000000 918 96.739000 1 551 1 chr6D.!!$F1 550
9 TraesCS4A01G299600 chr7D 632792009 632792551 542 True 902.000000 902 96.685000 11 551 1 chr7D.!!$R1 540
10 TraesCS4A01G299600 chr7D 123455890 123456651 761 False 244.000000 244 73.174000 1651 2430 1 chr7D.!!$F1 779
11 TraesCS4A01G299600 chr3D 536225576 536226127 551 False 902.000000 902 96.196000 1 551 1 chr3D.!!$F1 550
12 TraesCS4A01G299600 chr3D 543937678 543938229 551 True 900.000000 900 96.029000 1 554 1 chr3D.!!$R2 553
13 TraesCS4A01G299600 chr3B 5080718 5081268 550 False 896.000000 896 96.022000 1 552 1 chr3B.!!$F2 551
14 TraesCS4A01G299600 chr3B 4225325 4225875 550 False 891.000000 891 95.841000 1 552 1 chr3B.!!$F1 551
15 TraesCS4A01G299600 chr3B 773369205 773369746 541 True 876.000000 876 95.780000 10 554 1 chr3B.!!$R1 544
16 TraesCS4A01G299600 chr5D 545673434 545673984 550 True 891.000000 891 95.841000 1 551 1 chr5D.!!$R1 550

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
628 631 0.037590 TTGGTCTAACAGCCGGCAAT 59.962 50.0 31.54 16.65 0.0 3.56 F
630 633 0.107654 GGTCTAACAGCCGGCAATCT 60.108 55.0 31.54 12.50 0.0 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2480 7107 0.251634 TGTTGATGTATCCTGCGGCA 59.748 50.000 1.29 1.29 0.0 5.69 R
2538 7165 2.364002 GCAAAAGCTTAAACAGGGGTGA 59.636 45.455 0.00 0.00 0.0 4.02 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
359 361 1.423584 TGGATGGCGGTGTGATCTAT 58.576 50.000 0.00 0.00 0.00 1.98
404 406 5.368145 AGCCTCGACATGATTTATTTGCTA 58.632 37.500 0.00 0.00 0.00 3.49
469 472 3.004734 ACTTTTTGGCTGTGTGCATCTAC 59.995 43.478 0.00 0.00 45.15 2.59
495 498 1.303317 GAGGCCGGGCTTTCTTTCA 60.303 57.895 33.28 0.00 0.00 2.69
510 513 6.694411 GCTTTCTTTCAATGCGATTGTATCAT 59.306 34.615 8.19 0.00 41.02 2.45
628 631 0.037590 TTGGTCTAACAGCCGGCAAT 59.962 50.000 31.54 16.65 0.00 3.56
630 633 0.107654 GGTCTAACAGCCGGCAATCT 60.108 55.000 31.54 12.50 0.00 2.40
631 634 1.138266 GGTCTAACAGCCGGCAATCTA 59.862 52.381 31.54 13.01 0.00 1.98
634 637 2.500098 TCTAACAGCCGGCAATCTAGTT 59.500 45.455 31.54 22.42 0.00 2.24
635 638 1.739067 AACAGCCGGCAATCTAGTTC 58.261 50.000 31.54 0.00 0.00 3.01
636 639 0.613260 ACAGCCGGCAATCTAGTTCA 59.387 50.000 31.54 0.00 0.00 3.18
637 640 1.003118 ACAGCCGGCAATCTAGTTCAA 59.997 47.619 31.54 0.00 0.00 2.69
638 641 2.083774 CAGCCGGCAATCTAGTTCAAA 58.916 47.619 31.54 0.00 0.00 2.69
639 642 2.487762 CAGCCGGCAATCTAGTTCAAAA 59.512 45.455 31.54 0.00 0.00 2.44
640 643 3.057596 CAGCCGGCAATCTAGTTCAAAAA 60.058 43.478 31.54 0.00 0.00 1.94
659 662 4.963815 AAAAACAGCCGGCAATCG 57.036 50.000 31.54 16.35 38.88 3.34
660 663 2.037871 AAAAACAGCCGGCAATCGT 58.962 47.368 31.54 17.07 37.11 3.73
661 664 0.318614 AAAAACAGCCGGCAATCGTG 60.319 50.000 31.54 20.36 37.11 4.35
662 665 1.452145 AAAACAGCCGGCAATCGTGT 61.452 50.000 31.54 21.11 37.11 4.49
663 666 2.128853 AAACAGCCGGCAATCGTGTG 62.129 55.000 31.54 18.75 37.11 3.82
664 667 4.465512 CAGCCGGCAATCGTGTGC 62.466 66.667 31.54 0.00 44.14 4.57
680 683 3.303132 CGTGTGCCTGTTGTAGTTTTCTC 60.303 47.826 0.00 0.00 0.00 2.87
681 684 3.877508 GTGTGCCTGTTGTAGTTTTCTCT 59.122 43.478 0.00 0.00 0.00 3.10
685 688 4.947388 TGCCTGTTGTAGTTTTCTCTGTTT 59.053 37.500 0.00 0.00 0.00 2.83
720 740 2.703798 CCATCGCTGTTTGCCTGGG 61.704 63.158 0.00 0.00 37.35 4.45
741 761 0.890542 TGGACACTGGACAAGCATGC 60.891 55.000 10.51 10.51 0.00 4.06
802 853 2.422803 GGCCATATAACAGCAGGGAACA 60.423 50.000 0.00 0.00 0.00 3.18
805 856 4.464008 CCATATAACAGCAGGGAACACAT 58.536 43.478 0.00 0.00 0.00 3.21
806 857 5.620206 CCATATAACAGCAGGGAACACATA 58.380 41.667 0.00 0.00 0.00 2.29
807 858 5.470098 CCATATAACAGCAGGGAACACATAC 59.530 44.000 0.00 0.00 0.00 2.39
808 859 2.949177 AACAGCAGGGAACACATACA 57.051 45.000 0.00 0.00 0.00 2.29
809 860 2.185004 ACAGCAGGGAACACATACAC 57.815 50.000 0.00 0.00 0.00 2.90
810 861 1.699634 ACAGCAGGGAACACATACACT 59.300 47.619 0.00 0.00 0.00 3.55
811 862 2.106511 ACAGCAGGGAACACATACACTT 59.893 45.455 0.00 0.00 0.00 3.16
816 867 4.326826 CAGGGAACACATACACTTGTCAT 58.673 43.478 0.00 0.00 0.00 3.06
818 869 3.119849 GGGAACACATACACTTGTCATGC 60.120 47.826 0.00 0.00 0.00 4.06
820 871 2.436417 ACACATACACTTGTCATGCCC 58.564 47.619 0.00 0.00 0.00 5.36
823 874 0.618458 ATACACTTGTCATGCCCGGT 59.382 50.000 0.00 0.00 0.00 5.28
830 881 1.220749 GTCATGCCCGGTAGCTCAA 59.779 57.895 0.00 0.00 0.00 3.02
846 897 5.674052 AGCTCAAGTCAGAATCACATAGT 57.326 39.130 0.00 0.00 0.00 2.12
849 900 7.208777 AGCTCAAGTCAGAATCACATAGTATG 58.791 38.462 8.66 8.66 0.00 2.39
1012 1108 3.647367 GTAGGATGGCCTGCTGGA 58.353 61.111 14.77 0.00 46.45 3.86
1034 1136 0.949105 GCAAACTCCGACGATGTGGT 60.949 55.000 0.00 0.00 0.00 4.16
1293 5887 2.197875 GAGGCCGCCTACCTCCTA 59.802 66.667 13.29 0.00 46.81 2.94
1297 5891 2.123425 CCGCCTACCTCCTAGCCA 60.123 66.667 0.00 0.00 0.00 4.75
1527 6121 2.072487 AGCGGACCCATACTGGCAT 61.072 57.895 0.00 0.00 35.79 4.40
1558 6152 3.991536 GAGCCGGTCGAGGTGAAGC 62.992 68.421 1.90 0.00 0.00 3.86
1629 6247 1.603172 GCGTACGAGAAGCTGGCATAT 60.603 52.381 21.65 0.00 0.00 1.78
1844 6468 4.056125 CGCTGACGAGTGCCTCCA 62.056 66.667 0.00 0.00 43.93 3.86
2016 6640 2.283529 GCAGGACCAGGACGAGGAA 61.284 63.158 0.00 0.00 0.00 3.36
2230 6854 4.398044 ACCAGTTCTTGAACGAAATGTTGT 59.602 37.500 7.71 0.00 42.09 3.32
2232 6856 5.220854 CCAGTTCTTGAACGAAATGTTGTCT 60.221 40.000 7.71 0.00 42.09 3.41
2480 7107 0.324943 AGGCGTTACCAAGCAGTGAT 59.675 50.000 0.00 0.00 43.14 3.06
2512 7139 7.716998 AGGATACATCAACATCACCTCAAATAC 59.283 37.037 0.00 0.00 41.41 1.89
2673 7483 0.535780 AGCAGACACCACACCACATG 60.536 55.000 0.00 0.00 0.00 3.21
2675 7485 1.679139 CAGACACCACACCACATGTT 58.321 50.000 0.00 0.00 40.64 2.71
2676 7486 1.334556 CAGACACCACACCACATGTTG 59.665 52.381 0.00 0.00 40.64 3.33
2677 7487 0.030638 GACACCACACCACATGTTGC 59.969 55.000 0.00 0.00 40.64 4.17
2679 7489 1.076412 ACCACACCACATGTTGCCA 60.076 52.632 0.00 0.00 40.64 4.92
2680 7490 0.469705 ACCACACCACATGTTGCCAT 60.470 50.000 0.00 0.00 40.64 4.40
2681 7491 0.680618 CCACACCACATGTTGCCATT 59.319 50.000 0.00 0.00 40.64 3.16
2683 7493 2.298446 CCACACCACATGTTGCCATTAA 59.702 45.455 0.00 0.00 40.64 1.40
2685 7495 3.255395 CACACCACATGTTGCCATTAAGA 59.745 43.478 0.00 0.00 40.64 2.10
2686 7496 3.255642 ACACCACATGTTGCCATTAAGAC 59.744 43.478 0.00 0.00 38.98 3.01
2688 7498 4.082081 CACCACATGTTGCCATTAAGACAT 60.082 41.667 0.00 0.00 33.27 3.06
2689 7499 5.125257 CACCACATGTTGCCATTAAGACATA 59.875 40.000 0.00 0.00 31.92 2.29
2691 7501 6.183360 ACCACATGTTGCCATTAAGACATATG 60.183 38.462 0.00 0.00 31.92 1.78
2694 7504 5.833406 TGTTGCCATTAAGACATATGTGG 57.167 39.130 14.43 8.25 0.00 4.17
2695 7505 5.260424 TGTTGCCATTAAGACATATGTGGT 58.740 37.500 14.43 3.00 0.00 4.16
2696 7506 6.418946 TGTTGCCATTAAGACATATGTGGTA 58.581 36.000 14.43 3.71 0.00 3.25
2698 7508 7.066887 TGTTGCCATTAAGACATATGTGGTAAG 59.933 37.037 14.43 2.32 33.16 2.34
2699 7509 5.530915 TGCCATTAAGACATATGTGGTAAGC 59.469 40.000 14.43 11.39 0.00 3.09
2700 7510 5.530915 GCCATTAAGACATATGTGGTAAGCA 59.469 40.000 14.43 0.00 0.00 3.91
2701 7511 6.039270 GCCATTAAGACATATGTGGTAAGCAA 59.961 38.462 14.43 0.00 0.00 3.91
2702 7512 7.255590 GCCATTAAGACATATGTGGTAAGCAAT 60.256 37.037 14.43 0.53 0.00 3.56
2703 7513 8.632679 CCATTAAGACATATGTGGTAAGCAATT 58.367 33.333 14.43 0.00 0.00 2.32
2709 7519 8.466798 AGACATATGTGGTAAGCAATTTAAACC 58.533 33.333 14.43 0.00 0.00 3.27
2711 7521 8.589338 ACATATGTGGTAAGCAATTTAAACCAA 58.411 29.630 7.78 0.00 41.65 3.67
2712 7522 9.598517 CATATGTGGTAAGCAATTTAAACCAAT 57.401 29.630 0.00 0.00 41.65 3.16
2713 7523 9.816354 ATATGTGGTAAGCAATTTAAACCAATC 57.184 29.630 0.00 0.00 41.65 2.67
2719 7769 8.841300 GGTAAGCAATTTAAACCAATCCAAAAA 58.159 29.630 0.00 0.00 0.00 1.94
2829 7884 4.536090 TGAGAGAAGATTGCCCCTCTAAAA 59.464 41.667 0.00 0.00 36.25 1.52
2831 7886 6.084749 AGAGAAGATTGCCCCTCTAAAAAT 57.915 37.500 0.00 0.00 34.54 1.82
2870 7935 1.134098 AGCCCAACACATCTAATCCCG 60.134 52.381 0.00 0.00 0.00 5.14
2881 7946 1.072489 TCTAATCCCGGCAACACAACA 59.928 47.619 0.00 0.00 0.00 3.33
2907 7972 6.646240 CCAAACAAGGATATGTCAACAAAAGG 59.354 38.462 0.00 0.00 31.81 3.11
2912 7977 4.045334 AGGATATGTCAACAAAAGGGGGAA 59.955 41.667 0.00 0.00 0.00 3.97
2913 7978 4.775253 GGATATGTCAACAAAAGGGGGAAA 59.225 41.667 0.00 0.00 0.00 3.13
2933 7998 4.749245 AATGTGAATCCAACGACTGAAC 57.251 40.909 0.00 0.00 0.00 3.18
2936 8001 3.942115 TGTGAATCCAACGACTGAACAAA 59.058 39.130 0.00 0.00 0.00 2.83
2937 8002 4.396478 TGTGAATCCAACGACTGAACAAAA 59.604 37.500 0.00 0.00 0.00 2.44
2939 8004 5.455525 GTGAATCCAACGACTGAACAAAAAG 59.544 40.000 0.00 0.00 0.00 2.27
2940 8005 3.414549 TCCAACGACTGAACAAAAAGC 57.585 42.857 0.00 0.00 0.00 3.51
2941 8006 2.750166 TCCAACGACTGAACAAAAAGCA 59.250 40.909 0.00 0.00 0.00 3.91
2942 8007 2.851824 CCAACGACTGAACAAAAAGCAC 59.148 45.455 0.00 0.00 0.00 4.40
2943 8008 3.497118 CAACGACTGAACAAAAAGCACA 58.503 40.909 0.00 0.00 0.00 4.57
2944 8009 4.104776 CAACGACTGAACAAAAAGCACAT 58.895 39.130 0.00 0.00 0.00 3.21
2945 8010 4.370364 ACGACTGAACAAAAAGCACATT 57.630 36.364 0.00 0.00 0.00 2.71
2946 8011 4.743493 ACGACTGAACAAAAAGCACATTT 58.257 34.783 0.00 0.00 0.00 2.32
2948 8013 6.326375 ACGACTGAACAAAAAGCACATTTAA 58.674 32.000 0.00 0.00 0.00 1.52
2950 8015 6.252441 CGACTGAACAAAAAGCACATTTAACA 59.748 34.615 0.00 0.00 0.00 2.41
2951 8016 7.201393 CGACTGAACAAAAAGCACATTTAACAA 60.201 33.333 0.00 0.00 0.00 2.83
2953 8018 7.064490 ACTGAACAAAAAGCACATTTAACAAGG 59.936 33.333 0.00 0.00 0.00 3.61
2954 8019 5.733226 ACAAAAAGCACATTTAACAAGGC 57.267 34.783 0.00 0.00 0.00 4.35
2955 8020 4.574421 ACAAAAAGCACATTTAACAAGGCC 59.426 37.500 0.00 0.00 0.00 5.19
2956 8021 4.414337 AAAAGCACATTTAACAAGGCCA 57.586 36.364 5.01 0.00 0.00 5.36
2959 8024 2.068519 GCACATTTAACAAGGCCAAGC 58.931 47.619 5.01 0.00 0.00 4.01
2960 8025 2.547642 GCACATTTAACAAGGCCAAGCA 60.548 45.455 5.01 0.00 0.00 3.91
2961 8026 3.726607 CACATTTAACAAGGCCAAGCAA 58.273 40.909 5.01 0.00 0.00 3.91
2962 8027 4.317488 CACATTTAACAAGGCCAAGCAAT 58.683 39.130 5.01 0.00 0.00 3.56
2963 8028 4.152759 CACATTTAACAAGGCCAAGCAATG 59.847 41.667 5.01 8.10 0.00 2.82
2964 8029 4.040217 ACATTTAACAAGGCCAAGCAATGA 59.960 37.500 5.01 0.00 0.00 2.57
2965 8030 4.679373 TTTAACAAGGCCAAGCAATGAA 57.321 36.364 5.01 0.00 0.00 2.57
2966 8031 2.531522 AACAAGGCCAAGCAATGAAC 57.468 45.000 5.01 0.00 0.00 3.18
2967 8032 1.412079 ACAAGGCCAAGCAATGAACA 58.588 45.000 5.01 0.00 0.00 3.18
2968 8033 1.761784 ACAAGGCCAAGCAATGAACAA 59.238 42.857 5.01 0.00 0.00 2.83
2969 8034 2.170187 ACAAGGCCAAGCAATGAACAAA 59.830 40.909 5.01 0.00 0.00 2.83
2970 8035 3.181452 ACAAGGCCAAGCAATGAACAAAT 60.181 39.130 5.01 0.00 0.00 2.32
2971 8036 3.775261 AGGCCAAGCAATGAACAAATT 57.225 38.095 5.01 0.00 0.00 1.82
2972 8037 4.888326 AGGCCAAGCAATGAACAAATTA 57.112 36.364 5.01 0.00 0.00 1.40
2973 8038 5.226194 AGGCCAAGCAATGAACAAATTAA 57.774 34.783 5.01 0.00 0.00 1.40
2974 8039 5.240121 AGGCCAAGCAATGAACAAATTAAG 58.760 37.500 5.01 0.00 0.00 1.85
2975 8040 4.392754 GGCCAAGCAATGAACAAATTAAGG 59.607 41.667 0.00 0.00 0.00 2.69
2976 8041 4.142838 GCCAAGCAATGAACAAATTAAGGC 60.143 41.667 0.00 0.00 0.00 4.35
2977 8042 4.996122 CCAAGCAATGAACAAATTAAGGCA 59.004 37.500 0.00 0.00 0.00 4.75
2978 8043 5.106987 CCAAGCAATGAACAAATTAAGGCAC 60.107 40.000 0.00 0.00 0.00 5.01
2979 8044 4.568956 AGCAATGAACAAATTAAGGCACC 58.431 39.130 0.00 0.00 0.00 5.01
2980 8045 3.367630 GCAATGAACAAATTAAGGCACCG 59.632 43.478 0.00 0.00 0.00 4.94
2981 8046 4.804108 CAATGAACAAATTAAGGCACCGA 58.196 39.130 0.00 0.00 0.00 4.69
2982 8047 3.907894 TGAACAAATTAAGGCACCGAC 57.092 42.857 0.00 0.00 0.00 4.79
2983 8048 2.554893 TGAACAAATTAAGGCACCGACC 59.445 45.455 0.00 0.00 0.00 4.79
2984 8049 1.161843 ACAAATTAAGGCACCGACCG 58.838 50.000 0.00 0.00 33.69 4.79
2985 8050 1.270947 ACAAATTAAGGCACCGACCGA 60.271 47.619 0.00 0.00 33.69 4.69
2986 8051 1.129811 CAAATTAAGGCACCGACCGAC 59.870 52.381 0.00 0.00 33.69 4.79
2987 8052 0.738412 AATTAAGGCACCGACCGACG 60.738 55.000 0.00 0.00 42.18 5.12
2988 8053 3.919973 TTAAGGCACCGACCGACGC 62.920 63.158 0.00 0.00 41.07 5.19
2991 8056 4.501714 GGCACCGACCGACGCATA 62.502 66.667 0.00 0.00 41.07 3.14
2992 8057 2.507547 GCACCGACCGACGCATAA 60.508 61.111 0.00 0.00 41.07 1.90
2993 8058 2.795389 GCACCGACCGACGCATAAC 61.795 63.158 0.00 0.00 41.07 1.89
2994 8059 1.444724 CACCGACCGACGCATAACA 60.445 57.895 0.00 0.00 41.07 2.41
2995 8060 1.153901 ACCGACCGACGCATAACAG 60.154 57.895 0.00 0.00 41.07 3.16
2996 8061 1.153901 CCGACCGACGCATAACAGT 60.154 57.895 0.00 0.00 41.07 3.55
3043 8108 0.029300 CAACCAAACGTGCTGGAGTG 59.971 55.000 20.76 14.37 37.40 3.51
3171 8285 2.223852 GCGGGAAGACTCACTAATCCTC 60.224 54.545 0.00 0.00 0.00 3.71
3200 8314 9.502091 ACATAGACTCATACTCTGAATACTCTC 57.498 37.037 0.00 0.00 32.14 3.20
3201 8315 9.725019 CATAGACTCATACTCTGAATACTCTCT 57.275 37.037 0.00 0.00 32.14 3.10
3205 8319 9.719355 GACTCATACTCTGAATACTCTCTATCA 57.281 37.037 0.00 0.00 32.14 2.15
3212 8326 8.494433 ACTCTGAATACTCTCTATCAGAAGACT 58.506 37.037 5.90 0.00 45.42 3.24
3255 8435 0.458370 GTGGGCGGCATGTTCAAATC 60.458 55.000 12.47 0.00 0.00 2.17
3374 8554 2.098607 CGGAAGTACTTGCCGTCATCTA 59.901 50.000 25.63 0.00 40.17 1.98
3479 8663 8.788325 TTCAGCAAGATGATGATAATATGAGG 57.212 34.615 0.00 0.00 42.81 3.86
3480 8664 7.336396 TCAGCAAGATGATGATAATATGAGGG 58.664 38.462 0.00 0.00 37.93 4.30
3481 8665 7.037802 TCAGCAAGATGATGATAATATGAGGGT 60.038 37.037 0.00 0.00 37.93 4.34
3482 8666 7.065923 CAGCAAGATGATGATAATATGAGGGTG 59.934 40.741 0.00 0.00 35.45 4.61
3483 8667 6.883217 GCAAGATGATGATAATATGAGGGTGT 59.117 38.462 0.00 0.00 0.00 4.16
3484 8668 7.392673 GCAAGATGATGATAATATGAGGGTGTT 59.607 37.037 0.00 0.00 0.00 3.32
3485 8669 9.293404 CAAGATGATGATAATATGAGGGTGTTT 57.707 33.333 0.00 0.00 0.00 2.83
3486 8670 8.859236 AGATGATGATAATATGAGGGTGTTTG 57.141 34.615 0.00 0.00 0.00 2.93
3487 8671 8.443176 AGATGATGATAATATGAGGGTGTTTGT 58.557 33.333 0.00 0.00 0.00 2.83
3488 8672 9.071276 GATGATGATAATATGAGGGTGTTTGTT 57.929 33.333 0.00 0.00 0.00 2.83
3489 8673 8.821686 TGATGATAATATGAGGGTGTTTGTTT 57.178 30.769 0.00 0.00 0.00 2.83
3490 8674 9.253832 TGATGATAATATGAGGGTGTTTGTTTT 57.746 29.630 0.00 0.00 0.00 2.43
3491 8675 9.736023 GATGATAATATGAGGGTGTTTGTTTTC 57.264 33.333 0.00 0.00 0.00 2.29
3492 8676 8.642935 TGATAATATGAGGGTGTTTGTTTTCA 57.357 30.769 0.00 0.00 0.00 2.69
3493 8677 8.739039 TGATAATATGAGGGTGTTTGTTTTCAG 58.261 33.333 0.00 0.00 0.00 3.02
3494 8678 5.982890 ATATGAGGGTGTTTGTTTTCAGG 57.017 39.130 0.00 0.00 0.00 3.86
3495 8679 2.383855 TGAGGGTGTTTGTTTTCAGGG 58.616 47.619 0.00 0.00 0.00 4.45
3496 8680 2.024846 TGAGGGTGTTTGTTTTCAGGGA 60.025 45.455 0.00 0.00 0.00 4.20
3497 8681 2.361119 GAGGGTGTTTGTTTTCAGGGAC 59.639 50.000 0.00 0.00 0.00 4.46
3498 8682 2.024369 AGGGTGTTTGTTTTCAGGGACT 60.024 45.455 0.00 0.00 43.88 3.85
3499 8683 2.764010 GGGTGTTTGTTTTCAGGGACTT 59.236 45.455 0.00 0.00 34.60 3.01
3500 8684 3.955551 GGGTGTTTGTTTTCAGGGACTTA 59.044 43.478 0.00 0.00 34.60 2.24
3501 8685 4.587262 GGGTGTTTGTTTTCAGGGACTTAT 59.413 41.667 0.00 0.00 34.60 1.73
3502 8686 5.069914 GGGTGTTTGTTTTCAGGGACTTATT 59.930 40.000 0.00 0.00 34.60 1.40
3503 8687 5.983118 GGTGTTTGTTTTCAGGGACTTATTG 59.017 40.000 0.00 0.00 34.60 1.90
3504 8688 5.983118 GTGTTTGTTTTCAGGGACTTATTGG 59.017 40.000 0.00 0.00 34.60 3.16
3505 8689 5.659079 TGTTTGTTTTCAGGGACTTATTGGT 59.341 36.000 0.00 0.00 34.60 3.67
3506 8690 5.782893 TTGTTTTCAGGGACTTATTGGTG 57.217 39.130 0.00 0.00 34.60 4.17
3507 8691 4.798882 TGTTTTCAGGGACTTATTGGTGT 58.201 39.130 0.00 0.00 34.60 4.16
3508 8692 5.942961 TGTTTTCAGGGACTTATTGGTGTA 58.057 37.500 0.00 0.00 34.60 2.90
3509 8693 6.001460 TGTTTTCAGGGACTTATTGGTGTAG 58.999 40.000 0.00 0.00 34.60 2.74
3510 8694 4.837093 TTCAGGGACTTATTGGTGTAGG 57.163 45.455 0.00 0.00 34.60 3.18
3511 8695 3.112263 TCAGGGACTTATTGGTGTAGGG 58.888 50.000 0.00 0.00 34.60 3.53
3512 8696 3.112263 CAGGGACTTATTGGTGTAGGGA 58.888 50.000 0.00 0.00 34.60 4.20
3513 8697 3.113043 AGGGACTTATTGGTGTAGGGAC 58.887 50.000 0.00 0.00 27.25 4.46
3514 8698 3.113043 GGGACTTATTGGTGTAGGGACT 58.887 50.000 0.00 0.00 46.37 3.85
3515 8699 3.522343 GGGACTTATTGGTGTAGGGACTT 59.478 47.826 0.00 0.00 41.75 3.01
3516 8700 4.718276 GGGACTTATTGGTGTAGGGACTTA 59.282 45.833 0.00 0.00 41.75 2.24
3517 8701 5.190330 GGGACTTATTGGTGTAGGGACTTAA 59.810 44.000 0.00 0.00 41.75 1.85
3518 8702 6.296605 GGGACTTATTGGTGTAGGGACTTAAA 60.297 42.308 0.00 0.00 41.75 1.52
3519 8703 7.344134 GGACTTATTGGTGTAGGGACTTAAAT 58.656 38.462 0.00 0.00 41.75 1.40
3520 8704 8.488668 GGACTTATTGGTGTAGGGACTTAAATA 58.511 37.037 0.00 0.00 41.75 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.272480 ACCTGAACTATGGCCCAAACC 60.272 52.381 0.00 0.00 0.00 3.27
359 361 1.147191 AGGTGCGGTAGATCCTATCCA 59.853 52.381 0.00 0.00 0.00 3.41
443 446 2.028658 TGCACACAGCCAAAAAGTCAAA 60.029 40.909 0.00 0.00 44.83 2.69
469 472 4.632974 GCCCGGCCTCTGCATAGG 62.633 72.222 13.70 13.70 40.13 2.57
495 498 9.404348 GATATATCGAGATGATACAATCGCATT 57.596 33.333 2.01 0.00 42.24 3.56
560 563 8.826710 CGCACCATCTTTCTTATCAGTTTAATA 58.173 33.333 0.00 0.00 0.00 0.98
561 564 7.552687 TCGCACCATCTTTCTTATCAGTTTAAT 59.447 33.333 0.00 0.00 0.00 1.40
562 565 6.876789 TCGCACCATCTTTCTTATCAGTTTAA 59.123 34.615 0.00 0.00 0.00 1.52
563 566 6.312918 GTCGCACCATCTTTCTTATCAGTTTA 59.687 38.462 0.00 0.00 0.00 2.01
564 567 5.122396 GTCGCACCATCTTTCTTATCAGTTT 59.878 40.000 0.00 0.00 0.00 2.66
565 568 4.631813 GTCGCACCATCTTTCTTATCAGTT 59.368 41.667 0.00 0.00 0.00 3.16
566 569 4.184629 GTCGCACCATCTTTCTTATCAGT 58.815 43.478 0.00 0.00 0.00 3.41
567 570 4.033358 GTGTCGCACCATCTTTCTTATCAG 59.967 45.833 0.00 0.00 0.00 2.90
568 571 3.932710 GTGTCGCACCATCTTTCTTATCA 59.067 43.478 0.00 0.00 0.00 2.15
569 572 3.932710 TGTGTCGCACCATCTTTCTTATC 59.067 43.478 7.38 0.00 32.73 1.75
570 573 3.937814 TGTGTCGCACCATCTTTCTTAT 58.062 40.909 7.38 0.00 32.73 1.73
571 574 3.394674 TGTGTCGCACCATCTTTCTTA 57.605 42.857 7.38 0.00 32.73 2.10
572 575 2.254546 TGTGTCGCACCATCTTTCTT 57.745 45.000 7.38 0.00 32.73 2.52
573 576 2.027745 AGATGTGTCGCACCATCTTTCT 60.028 45.455 7.38 0.00 32.62 2.52
574 577 2.350522 AGATGTGTCGCACCATCTTTC 58.649 47.619 7.38 0.00 32.62 2.62
584 587 4.212214 AGAAGAAGAACAAAGATGTGTCGC 59.788 41.667 0.00 0.00 40.46 5.19
585 588 5.694006 AGAGAAGAAGAACAAAGATGTGTCG 59.306 40.000 0.00 0.00 40.46 4.35
642 645 0.318614 CACGATTGCCGGCTGTTTTT 60.319 50.000 29.70 4.45 43.93 1.94
643 646 1.285641 CACGATTGCCGGCTGTTTT 59.714 52.632 29.70 7.47 43.93 2.43
644 647 1.896660 ACACGATTGCCGGCTGTTT 60.897 52.632 29.70 11.03 43.93 2.83
645 648 2.281484 ACACGATTGCCGGCTGTT 60.281 55.556 29.70 12.35 43.93 3.16
646 649 3.049674 CACACGATTGCCGGCTGT 61.050 61.111 29.70 20.35 43.93 4.40
647 650 4.465512 GCACACGATTGCCGGCTG 62.466 66.667 29.70 19.61 43.93 4.85
653 656 0.871722 TACAACAGGCACACGATTGC 59.128 50.000 4.67 4.67 42.18 3.56
654 657 2.143122 ACTACAACAGGCACACGATTG 58.857 47.619 0.00 0.00 0.00 2.67
655 658 2.543777 ACTACAACAGGCACACGATT 57.456 45.000 0.00 0.00 0.00 3.34
656 659 2.543777 AACTACAACAGGCACACGAT 57.456 45.000 0.00 0.00 0.00 3.73
657 660 2.319136 AAACTACAACAGGCACACGA 57.681 45.000 0.00 0.00 0.00 4.35
658 661 2.612212 AGAAAACTACAACAGGCACACG 59.388 45.455 0.00 0.00 0.00 4.49
659 662 3.877508 AGAGAAAACTACAACAGGCACAC 59.122 43.478 0.00 0.00 0.00 3.82
660 663 3.876914 CAGAGAAAACTACAACAGGCACA 59.123 43.478 0.00 0.00 0.00 4.57
661 664 3.877508 ACAGAGAAAACTACAACAGGCAC 59.122 43.478 0.00 0.00 0.00 5.01
662 665 4.150897 ACAGAGAAAACTACAACAGGCA 57.849 40.909 0.00 0.00 0.00 4.75
663 666 5.500645 AAACAGAGAAAACTACAACAGGC 57.499 39.130 0.00 0.00 0.00 4.85
664 667 7.083875 TGAAAACAGAGAAAACTACAACAGG 57.916 36.000 0.00 0.00 0.00 4.00
680 683 0.527565 CCAAGGCCGGATGAAAACAG 59.472 55.000 5.05 0.00 0.00 3.16
681 684 0.178975 ACCAAGGCCGGATGAAAACA 60.179 50.000 5.05 0.00 0.00 2.83
685 688 1.202099 TGGTACCAAGGCCGGATGAA 61.202 55.000 13.60 0.00 0.00 2.57
720 740 0.607489 ATGCTTGTCCAGTGTCCAGC 60.607 55.000 0.00 0.00 0.00 4.85
762 782 4.770010 TGGCCCTAAAATGTTTAAGACTGG 59.230 41.667 0.00 0.00 0.00 4.00
802 853 1.678728 CCGGGCATGACAAGTGTATGT 60.679 52.381 0.00 0.00 35.90 2.29
805 856 1.206132 CTACCGGGCATGACAAGTGTA 59.794 52.381 6.32 0.00 0.00 2.90
806 857 0.036388 CTACCGGGCATGACAAGTGT 60.036 55.000 6.32 0.00 0.00 3.55
807 858 1.369091 GCTACCGGGCATGACAAGTG 61.369 60.000 6.32 0.00 0.00 3.16
808 859 1.078426 GCTACCGGGCATGACAAGT 60.078 57.895 6.32 0.00 0.00 3.16
809 860 0.811616 GAGCTACCGGGCATGACAAG 60.812 60.000 6.32 0.00 34.17 3.16
810 861 1.220749 GAGCTACCGGGCATGACAA 59.779 57.895 6.32 0.00 34.17 3.18
811 862 1.549243 TTGAGCTACCGGGCATGACA 61.549 55.000 6.32 0.00 34.17 3.58
816 867 1.888436 CTGACTTGAGCTACCGGGCA 61.888 60.000 6.32 0.00 34.17 5.36
818 869 0.895530 TTCTGACTTGAGCTACCGGG 59.104 55.000 6.32 0.00 0.00 5.73
820 871 3.182967 GTGATTCTGACTTGAGCTACCG 58.817 50.000 0.00 0.00 0.00 4.02
823 874 6.782082 ACTATGTGATTCTGACTTGAGCTA 57.218 37.500 0.00 0.00 0.00 3.32
830 881 6.462207 GGCAGACATACTATGTGATTCTGACT 60.462 42.308 15.15 0.50 45.03 3.41
1012 1108 0.603569 ACATCGTCGGAGTTTGCTCT 59.396 50.000 0.00 0.00 41.38 4.09
1527 6121 3.157252 GGCTCCTCGGGCATGAGA 61.157 66.667 0.00 0.00 38.28 3.27
1593 6211 2.264166 GCCAGCTTCTCAGACGCT 59.736 61.111 0.00 0.00 37.65 5.07
1844 6468 2.281761 CCTTGCCGTCAAGCCACT 60.282 61.111 0.00 0.00 46.38 4.00
1876 6500 0.378962 CTCCCGAAGCTGACGTAGAG 59.621 60.000 11.53 12.15 0.00 2.43
1917 6541 4.823276 GTCTCCATGACCTGCTCG 57.177 61.111 0.00 0.00 39.69 5.03
2016 6640 2.439701 TCGAGGAATCCGCGGACT 60.440 61.111 33.75 23.15 46.27 3.85
2094 6718 1.079819 CGCGTGGGACAAGATCAGT 60.080 57.895 0.00 0.00 44.16 3.41
2205 6829 3.315191 ACATTTCGTTCAAGAACTGGTGG 59.685 43.478 10.83 1.55 39.08 4.61
2230 6854 1.609210 TCCCCATCGACTGCACAGA 60.609 57.895 4.31 0.00 0.00 3.41
2232 6856 2.662596 GTCCCCATCGACTGCACA 59.337 61.111 0.00 0.00 0.00 4.57
2480 7107 0.251634 TGTTGATGTATCCTGCGGCA 59.748 50.000 1.29 1.29 0.00 5.69
2491 7118 5.487433 TCGTATTTGAGGTGATGTTGATGT 58.513 37.500 0.00 0.00 0.00 3.06
2531 7158 4.653801 AGCTTAAACAGGGGTGACAAAAAT 59.346 37.500 0.00 0.00 0.00 1.82
2538 7165 2.364002 GCAAAAGCTTAAACAGGGGTGA 59.636 45.455 0.00 0.00 0.00 4.02
2673 7483 5.835113 ACCACATATGTCTTAATGGCAAC 57.165 39.130 5.07 0.00 32.16 4.17
2675 7485 5.530915 GCTTACCACATATGTCTTAATGGCA 59.469 40.000 5.07 0.00 33.36 4.92
2676 7486 5.530915 TGCTTACCACATATGTCTTAATGGC 59.469 40.000 5.07 7.58 0.00 4.40
2677 7487 7.566760 TTGCTTACCACATATGTCTTAATGG 57.433 36.000 5.07 5.81 0.00 3.16
2683 7493 8.466798 GGTTTAAATTGCTTACCACATATGTCT 58.533 33.333 5.07 0.00 0.00 3.41
2685 7495 8.128322 TGGTTTAAATTGCTTACCACATATGT 57.872 30.769 1.41 1.41 34.13 2.29
2686 7496 8.994429 TTGGTTTAAATTGCTTACCACATATG 57.006 30.769 0.00 0.00 38.53 1.78
2688 7498 8.254508 GGATTGGTTTAAATTGCTTACCACATA 58.745 33.333 0.00 0.00 38.53 2.29
2689 7499 7.102993 GGATTGGTTTAAATTGCTTACCACAT 58.897 34.615 0.00 0.00 38.53 3.21
2691 7501 6.459923 TGGATTGGTTTAAATTGCTTACCAC 58.540 36.000 0.00 0.00 38.53 4.16
2767 7817 2.162681 GAGGAAGGTGATGGTTGTTGG 58.837 52.381 0.00 0.00 0.00 3.77
2829 7884 6.406370 GGCTGGGTGCTTTCTTATTTTTATT 58.594 36.000 0.00 0.00 42.39 1.40
2831 7886 4.221924 GGGCTGGGTGCTTTCTTATTTTTA 59.778 41.667 0.00 0.00 42.39 1.52
2840 7905 1.832167 TGTTGGGCTGGGTGCTTTC 60.832 57.895 0.00 0.00 42.39 2.62
2870 7935 1.999024 CTTGTTTGGTGTTGTGTTGCC 59.001 47.619 0.00 0.00 0.00 4.52
2881 7946 6.723298 TTTGTTGACATATCCTTGTTTGGT 57.277 33.333 0.00 0.00 0.00 3.67
2907 7972 2.163613 GTCGTTGGATTCACATTTCCCC 59.836 50.000 0.00 0.00 0.00 4.81
2912 7977 4.133820 TGTTCAGTCGTTGGATTCACATT 58.866 39.130 0.00 0.00 0.00 2.71
2913 7978 3.738982 TGTTCAGTCGTTGGATTCACAT 58.261 40.909 0.00 0.00 0.00 3.21
2933 7998 4.574013 TGGCCTTGTTAAATGTGCTTTTTG 59.426 37.500 3.32 0.00 0.00 2.44
2936 8001 4.379652 CTTGGCCTTGTTAAATGTGCTTT 58.620 39.130 3.32 0.00 0.00 3.51
2937 8002 3.803368 GCTTGGCCTTGTTAAATGTGCTT 60.803 43.478 3.32 0.00 0.00 3.91
2939 8004 2.068519 GCTTGGCCTTGTTAAATGTGC 58.931 47.619 3.32 0.00 0.00 4.57
2940 8005 3.383620 TGCTTGGCCTTGTTAAATGTG 57.616 42.857 3.32 0.00 0.00 3.21
2941 8006 4.040217 TCATTGCTTGGCCTTGTTAAATGT 59.960 37.500 3.32 0.00 0.00 2.71
2942 8007 4.567971 TCATTGCTTGGCCTTGTTAAATG 58.432 39.130 3.32 7.16 0.00 2.32
2943 8008 4.888326 TCATTGCTTGGCCTTGTTAAAT 57.112 36.364 3.32 0.00 0.00 1.40
2944 8009 4.141846 TGTTCATTGCTTGGCCTTGTTAAA 60.142 37.500 3.32 0.00 0.00 1.52
2945 8010 3.386078 TGTTCATTGCTTGGCCTTGTTAA 59.614 39.130 3.32 0.00 0.00 2.01
2946 8011 2.961741 TGTTCATTGCTTGGCCTTGTTA 59.038 40.909 3.32 0.00 0.00 2.41
2948 8013 1.412079 TGTTCATTGCTTGGCCTTGT 58.588 45.000 3.32 0.00 0.00 3.16
2950 8015 3.775261 ATTTGTTCATTGCTTGGCCTT 57.225 38.095 3.32 0.00 0.00 4.35
2951 8016 3.775261 AATTTGTTCATTGCTTGGCCT 57.225 38.095 3.32 0.00 0.00 5.19
2953 8018 4.142838 GCCTTAATTTGTTCATTGCTTGGC 60.143 41.667 0.00 0.00 0.00 4.52
2954 8019 4.996122 TGCCTTAATTTGTTCATTGCTTGG 59.004 37.500 0.00 0.00 0.00 3.61
2955 8020 5.106987 GGTGCCTTAATTTGTTCATTGCTTG 60.107 40.000 0.00 0.00 0.00 4.01
2956 8021 4.996758 GGTGCCTTAATTTGTTCATTGCTT 59.003 37.500 0.00 0.00 0.00 3.91
2959 8024 4.621034 GTCGGTGCCTTAATTTGTTCATTG 59.379 41.667 0.00 0.00 0.00 2.82
2960 8025 4.321675 GGTCGGTGCCTTAATTTGTTCATT 60.322 41.667 0.00 0.00 0.00 2.57
2961 8026 3.192633 GGTCGGTGCCTTAATTTGTTCAT 59.807 43.478 0.00 0.00 0.00 2.57
2962 8027 2.554893 GGTCGGTGCCTTAATTTGTTCA 59.445 45.455 0.00 0.00 0.00 3.18
2963 8028 2.413634 CGGTCGGTGCCTTAATTTGTTC 60.414 50.000 0.00 0.00 0.00 3.18
2964 8029 1.538075 CGGTCGGTGCCTTAATTTGTT 59.462 47.619 0.00 0.00 0.00 2.83
2965 8030 1.161843 CGGTCGGTGCCTTAATTTGT 58.838 50.000 0.00 0.00 0.00 2.83
2966 8031 1.129811 GTCGGTCGGTGCCTTAATTTG 59.870 52.381 0.00 0.00 0.00 2.32
2967 8032 1.445871 GTCGGTCGGTGCCTTAATTT 58.554 50.000 0.00 0.00 0.00 1.82
2968 8033 0.738412 CGTCGGTCGGTGCCTTAATT 60.738 55.000 0.00 0.00 35.71 1.40
2969 8034 1.153706 CGTCGGTCGGTGCCTTAAT 60.154 57.895 0.00 0.00 35.71 1.40
2970 8035 2.259204 CGTCGGTCGGTGCCTTAA 59.741 61.111 0.00 0.00 35.71 1.85
2971 8036 4.424566 GCGTCGGTCGGTGCCTTA 62.425 66.667 0.00 0.00 40.26 2.69
2974 8039 3.993376 TTATGCGTCGGTCGGTGCC 62.993 63.158 0.00 0.00 40.26 5.01
2975 8040 2.507547 TTATGCGTCGGTCGGTGC 60.508 61.111 0.00 0.00 40.26 5.01
2976 8041 1.410737 CTGTTATGCGTCGGTCGGTG 61.411 60.000 0.00 0.00 40.26 4.94
2977 8042 1.153901 CTGTTATGCGTCGGTCGGT 60.154 57.895 0.00 0.00 40.26 4.69
2978 8043 0.734942 AACTGTTATGCGTCGGTCGG 60.735 55.000 0.00 0.00 40.26 4.79
2979 8044 1.844357 CTAACTGTTATGCGTCGGTCG 59.156 52.381 0.00 0.00 43.12 4.79
2980 8045 2.872370 ACTAACTGTTATGCGTCGGTC 58.128 47.619 0.00 0.00 0.00 4.79
2981 8046 3.733077 GCTACTAACTGTTATGCGTCGGT 60.733 47.826 0.00 0.00 0.00 4.69
2982 8047 2.787680 GCTACTAACTGTTATGCGTCGG 59.212 50.000 0.00 0.00 0.00 4.79
2983 8048 3.692576 AGCTACTAACTGTTATGCGTCG 58.307 45.455 0.00 0.00 0.00 5.12
2984 8049 4.676018 GCTAGCTACTAACTGTTATGCGTC 59.324 45.833 7.70 0.00 0.00 5.19
2985 8050 4.097437 TGCTAGCTACTAACTGTTATGCGT 59.903 41.667 17.23 0.00 0.00 5.24
2986 8051 4.607955 TGCTAGCTACTAACTGTTATGCG 58.392 43.478 17.23 0.00 0.00 4.73
2987 8052 4.446051 GCTGCTAGCTACTAACTGTTATGC 59.554 45.833 17.23 6.49 38.45 3.14
2988 8053 5.592054 TGCTGCTAGCTACTAACTGTTATG 58.408 41.667 17.23 0.00 42.97 1.90
2989 8054 5.737635 GCTGCTGCTAGCTACTAACTGTTAT 60.738 44.000 17.23 0.00 42.97 1.89
2990 8055 4.440250 GCTGCTGCTAGCTACTAACTGTTA 60.440 45.833 17.23 0.00 42.97 2.41
2991 8056 3.677424 GCTGCTGCTAGCTACTAACTGTT 60.677 47.826 17.23 0.00 42.97 3.16
2992 8057 2.159170 GCTGCTGCTAGCTACTAACTGT 60.159 50.000 17.23 0.00 42.97 3.55
2993 8058 2.468831 GCTGCTGCTAGCTACTAACTG 58.531 52.381 17.23 4.39 42.97 3.16
2994 8059 2.880963 GCTGCTGCTAGCTACTAACT 57.119 50.000 17.23 0.00 42.97 2.24
3043 8108 3.553511 GTGTGCTGTGACATACTCTATGC 59.446 47.826 0.00 0.00 39.79 3.14
3171 8285 9.283768 AGTATTCAGAGTATGAGTCTATGTCTG 57.716 37.037 6.75 6.75 39.68 3.51
3200 8314 9.778741 AGAGTATGAGTCTAAGTCTTCTGATAG 57.221 37.037 0.00 0.00 0.00 2.08
3201 8315 9.554395 CAGAGTATGAGTCTAAGTCTTCTGATA 57.446 37.037 0.00 0.00 0.00 2.15
3205 8319 6.964464 TCCAGAGTATGAGTCTAAGTCTTCT 58.036 40.000 0.00 0.00 0.00 2.85
3212 8326 7.284261 CACTTCAGATCCAGAGTATGAGTCTAA 59.716 40.741 0.00 0.00 0.00 2.10
3286 8466 0.036952 AGATGGACCTCGTGCACTTG 60.037 55.000 16.19 7.12 36.59 3.16
3374 8554 2.799917 GCGCAAGGAAGATCGTGTATCT 60.800 50.000 0.30 0.00 42.32 1.98
3475 8659 2.024846 TCCCTGAAAACAAACACCCTCA 60.025 45.455 0.00 0.00 0.00 3.86
3476 8660 2.361119 GTCCCTGAAAACAAACACCCTC 59.639 50.000 0.00 0.00 0.00 4.30
3477 8661 2.024369 AGTCCCTGAAAACAAACACCCT 60.024 45.455 0.00 0.00 0.00 4.34
3478 8662 2.384828 AGTCCCTGAAAACAAACACCC 58.615 47.619 0.00 0.00 0.00 4.61
3479 8663 5.784578 ATAAGTCCCTGAAAACAAACACC 57.215 39.130 0.00 0.00 0.00 4.16
3480 8664 5.983118 CCAATAAGTCCCTGAAAACAAACAC 59.017 40.000 0.00 0.00 0.00 3.32
3481 8665 5.659079 ACCAATAAGTCCCTGAAAACAAACA 59.341 36.000 0.00 0.00 0.00 2.83
3482 8666 5.983118 CACCAATAAGTCCCTGAAAACAAAC 59.017 40.000 0.00 0.00 0.00 2.93
3483 8667 5.659079 ACACCAATAAGTCCCTGAAAACAAA 59.341 36.000 0.00 0.00 0.00 2.83
3484 8668 5.205056 ACACCAATAAGTCCCTGAAAACAA 58.795 37.500 0.00 0.00 0.00 2.83
3485 8669 4.798882 ACACCAATAAGTCCCTGAAAACA 58.201 39.130 0.00 0.00 0.00 2.83
3486 8670 5.414765 CCTACACCAATAAGTCCCTGAAAAC 59.585 44.000 0.00 0.00 0.00 2.43
3487 8671 5.515886 CCCTACACCAATAAGTCCCTGAAAA 60.516 44.000 0.00 0.00 0.00 2.29
3488 8672 4.018779 CCCTACACCAATAAGTCCCTGAAA 60.019 45.833 0.00 0.00 0.00 2.69
3489 8673 3.521937 CCCTACACCAATAAGTCCCTGAA 59.478 47.826 0.00 0.00 0.00 3.02
3490 8674 3.112263 CCCTACACCAATAAGTCCCTGA 58.888 50.000 0.00 0.00 0.00 3.86
3491 8675 3.112263 TCCCTACACCAATAAGTCCCTG 58.888 50.000 0.00 0.00 0.00 4.45
3492 8676 3.113043 GTCCCTACACCAATAAGTCCCT 58.887 50.000 0.00 0.00 0.00 4.20
3493 8677 3.113043 AGTCCCTACACCAATAAGTCCC 58.887 50.000 0.00 0.00 0.00 4.46
3494 8678 4.838904 AAGTCCCTACACCAATAAGTCC 57.161 45.455 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.