Multiple sequence alignment - TraesCS1D01G270800

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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 TraesCS1D01G270800 chr1D 100.000 5802 0 0 1 5802 365549660 365543859 0.000000e+00 10715.0
1 TraesCS1D01G270800 chr1D 100.000 1917 0 0 6264 8180 365543397 365541481 0.000000e+00 3541.0
2 TraesCS1D01G270800 chr1D 86.364 726 80 8 1 720 375943192 375943904 0.000000e+00 774.0
3 TraesCS1D01G270800 chr1D 85.772 745 88 12 1 729 463982188 463982930 0.000000e+00 773.0
4 TraesCS1D01G270800 chr1D 89.292 551 54 2 1 551 470652256 470651711 0.000000e+00 686.0
5 TraesCS1D01G270800 chr1D 86.837 471 59 3 264 731 366007528 366007058 2.620000e-144 523.0
6 TraesCS1D01G270800 chr1D 84.932 438 59 6 291 725 364634445 364634878 3.510000e-118 436.0
7 TraesCS1D01G270800 chr1D 87.791 344 37 2 3 341 23370860 23371203 1.650000e-106 398.0
8 TraesCS1D01G270800 chr1D 86.804 341 38 4 380 714 23371200 23371539 2.790000e-99 374.0
9 TraesCS1D01G270800 chr1D 93.443 61 3 1 6288 6348 14482472 14482531 1.130000e-13 89.8
10 TraesCS1D01G270800 chr1B 94.367 4740 194 42 921 5610 489207554 489202838 0.000000e+00 7206.0
11 TraesCS1D01G270800 chr1B 95.495 999 37 2 6385 7381 489202281 489201289 0.000000e+00 1589.0
12 TraesCS1D01G270800 chr1B 85.637 738 95 8 1 727 639922784 639923521 0.000000e+00 765.0
13 TraesCS1D01G270800 chr1B 95.482 332 8 2 7850 8180 489200415 489200090 2.620000e-144 523.0
14 TraesCS1D01G270800 chr1B 93.725 255 9 2 7571 7825 489200657 489200410 7.750000e-100 375.0
15 TraesCS1D01G270800 chr1B 94.416 197 5 2 736 926 489207774 489207578 1.730000e-76 298.0
16 TraesCS1D01G270800 chr1B 96.364 110 4 0 5693 5802 489202838 489202729 1.810000e-41 182.0
17 TraesCS1D01G270800 chr1B 100.000 28 0 0 7339 7366 32430059 32430032 1.500000e-02 52.8
18 TraesCS1D01G270800 chr1A 91.695 3287 159 42 1602 4809 464804478 464801227 0.000000e+00 4453.0
19 TraesCS1D01G270800 chr1A 89.808 1148 72 12 6332 7473 464798111 464797003 0.000000e+00 1430.0
20 TraesCS1D01G270800 chr1A 94.436 683 28 4 922 1601 464805238 464804563 0.000000e+00 1042.0
21 TraesCS1D01G270800 chr1A 93.178 645 32 10 4800 5440 464801053 464800417 0.000000e+00 937.0
22 TraesCS1D01G270800 chr1A 94.637 578 26 2 7603 8180 464796534 464795962 0.000000e+00 891.0
23 TraesCS1D01G270800 chr1A 91.124 169 11 2 5444 5608 464800318 464800150 8.260000e-55 226.0
24 TraesCS1D01G270800 chr4D 87.603 726 88 2 1 725 446648752 446649476 0.000000e+00 841.0
25 TraesCS1D01G270800 chr4D 87.415 731 86 6 1 730 418385861 418386586 0.000000e+00 835.0
26 TraesCS1D01G270800 chr4D 87.340 703 80 4 1 702 378304804 378305498 0.000000e+00 797.0
27 TraesCS1D01G270800 chr4D 85.635 724 91 7 1 715 52211045 52211764 0.000000e+00 749.0
28 TraesCS1D01G270800 chr2D 87.805 697 80 3 34 725 366055717 366056413 0.000000e+00 811.0
29 TraesCS1D01G270800 chr2D 96.591 88 3 0 5607 5694 643235824 643235911 6.620000e-31 147.0
30 TraesCS1D01G270800 chr2D 94.643 56 3 0 6288 6343 503453864 503453809 4.070000e-13 87.9
31 TraesCS1D01G270800 chr4A 86.443 745 88 12 1 740 697375720 697376456 0.000000e+00 804.0
32 TraesCS1D01G270800 chr4A 94.565 92 4 1 5600 5691 285485457 285485367 3.080000e-29 141.0
33 TraesCS1D01G270800 chr4A 94.643 56 3 0 6289 6344 647342546 647342491 4.070000e-13 87.9
34 TraesCS1D01G270800 chr2A 87.447 701 82 5 1 700 657060368 657061063 0.000000e+00 802.0
35 TraesCS1D01G270800 chr2A 94.565 92 5 0 5604 5695 258406429 258406520 8.560000e-30 143.0
36 TraesCS1D01G270800 chr7D 87.165 709 80 8 1 702 583052451 583051747 0.000000e+00 795.0
37 TraesCS1D01G270800 chr7D 87.464 686 81 4 35 718 31407626 31408308 0.000000e+00 785.0
38 TraesCS1D01G270800 chr7D 86.950 705 79 10 1 694 159005785 159006487 0.000000e+00 780.0
39 TraesCS1D01G270800 chr7D 86.790 704 84 4 1 702 547482654 547483350 0.000000e+00 776.0
40 TraesCS1D01G270800 chr7D 98.077 52 1 0 6288 6339 431874174 431874225 3.140000e-14 91.6
41 TraesCS1D01G270800 chr7B 86.809 705 84 7 1 702 388161312 388160614 0.000000e+00 778.0
42 TraesCS1D01G270800 chr7B 94.681 94 4 1 5604 5696 740996153 740996246 2.380000e-30 145.0
43 TraesCS1D01G270800 chr7B 91.935 62 4 1 6287 6348 174144744 174144804 1.460000e-12 86.1
44 TraesCS1D01G270800 chr3A 85.812 733 98 6 1 730 603921288 603922017 0.000000e+00 773.0
45 TraesCS1D01G270800 chr3A 85.217 230 32 2 1019 1247 631792270 631792498 1.370000e-57 235.0
46 TraesCS1D01G270800 chr3A 91.089 101 7 2 5595 5694 710277872 710277971 1.430000e-27 135.0
47 TraesCS1D01G270800 chr3A 92.647 68 5 0 1871 1938 631818396 631818463 1.880000e-16 99.0
48 TraesCS1D01G270800 chr3A 88.889 72 6 2 6287 6357 314623946 314623876 4.070000e-13 87.9
49 TraesCS1D01G270800 chr3A 94.444 36 2 0 7339 7374 71221314 71221349 1.000000e-03 56.5
50 TraesCS1D01G270800 chr6D 85.812 733 80 13 1 717 341150061 341150785 0.000000e+00 756.0
51 TraesCS1D01G270800 chr6D 85.537 726 92 11 1 723 159381953 159381238 0.000000e+00 747.0
52 TraesCS1D01G270800 chr6D 85.590 687 88 6 44 720 186554300 186553615 0.000000e+00 710.0
53 TraesCS1D01G270800 chr6D 84.859 284 41 2 444 725 377888912 377889195 1.340000e-72 285.0
54 TraesCS1D01G270800 chr6D 91.935 62 5 0 405 466 421798001 421798062 4.070000e-13 87.9
55 TraesCS1D01G270800 chr4B 85.383 732 97 9 1 725 464540273 464541001 0.000000e+00 750.0
56 TraesCS1D01G270800 chr4B 85.180 722 102 4 1 720 558723468 558724186 0.000000e+00 736.0
57 TraesCS1D01G270800 chr4B 88.462 52 6 0 7331 7382 596373461 596373410 6.850000e-06 63.9
58 TraesCS1D01G270800 chr6A 85.097 718 103 4 3 719 519298575 519299289 0.000000e+00 730.0
59 TraesCS1D01G270800 chr6A 100.000 50 0 0 6288 6337 539706733 539706782 8.740000e-15 93.5
60 TraesCS1D01G270800 chr2B 94.624 93 5 0 5607 5699 239852611 239852703 2.380000e-30 145.0
61 TraesCS1D01G270800 chr2B 91.045 67 3 3 6288 6353 16197322 16197258 4.070000e-13 87.9
62 TraesCS1D01G270800 chr5D 93.750 96 5 1 5607 5702 481806190 481806096 8.560000e-30 143.0
63 TraesCS1D01G270800 chr5B 90.179 112 7 4 5603 5712 184285262 184285371 8.560000e-30 143.0
64 TraesCS1D01G270800 chr7A 95.349 86 4 0 5607 5692 96556132 96556217 3.980000e-28 137.0
65 TraesCS1D01G270800 chr3B 92.647 68 5 0 1871 1938 651275606 651275673 1.880000e-16 99.0
66 TraesCS1D01G270800 chr3D 91.176 68 6 0 1871 1938 488269267 488269334 8.740000e-15 93.5
67 TraesCS1D01G270800 chr3D 88.889 72 6 2 6287 6357 197994437 197994367 4.070000e-13 87.9


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 TraesCS1D01G270800 chr1D 365541481 365549660 8179 True 7128.0 10715 100.000000 1 8180 2 chr1D.!!$R3 8179
1 TraesCS1D01G270800 chr1D 375943192 375943904 712 False 774.0 774 86.364000 1 720 1 chr1D.!!$F3 719
2 TraesCS1D01G270800 chr1D 463982188 463982930 742 False 773.0 773 85.772000 1 729 1 chr1D.!!$F4 728
3 TraesCS1D01G270800 chr1D 470651711 470652256 545 True 686.0 686 89.292000 1 551 1 chr1D.!!$R2 550
4 TraesCS1D01G270800 chr1D 23370860 23371539 679 False 386.0 398 87.297500 3 714 2 chr1D.!!$F5 711
5 TraesCS1D01G270800 chr1B 489200090 489207774 7684 True 1695.5 7206 94.974833 736 8180 6 chr1B.!!$R2 7444
6 TraesCS1D01G270800 chr1B 639922784 639923521 737 False 765.0 765 85.637000 1 727 1 chr1B.!!$F1 726
7 TraesCS1D01G270800 chr1A 464795962 464805238 9276 True 1496.5 4453 92.479667 922 8180 6 chr1A.!!$R1 7258
8 TraesCS1D01G270800 chr4D 446648752 446649476 724 False 841.0 841 87.603000 1 725 1 chr4D.!!$F4 724
9 TraesCS1D01G270800 chr4D 418385861 418386586 725 False 835.0 835 87.415000 1 730 1 chr4D.!!$F3 729
10 TraesCS1D01G270800 chr4D 378304804 378305498 694 False 797.0 797 87.340000 1 702 1 chr4D.!!$F2 701
11 TraesCS1D01G270800 chr4D 52211045 52211764 719 False 749.0 749 85.635000 1 715 1 chr4D.!!$F1 714
12 TraesCS1D01G270800 chr2D 366055717 366056413 696 False 811.0 811 87.805000 34 725 1 chr2D.!!$F1 691
13 TraesCS1D01G270800 chr4A 697375720 697376456 736 False 804.0 804 86.443000 1 740 1 chr4A.!!$F1 739
14 TraesCS1D01G270800 chr2A 657060368 657061063 695 False 802.0 802 87.447000 1 700 1 chr2A.!!$F2 699
15 TraesCS1D01G270800 chr7D 583051747 583052451 704 True 795.0 795 87.165000 1 702 1 chr7D.!!$R1 701
16 TraesCS1D01G270800 chr7D 31407626 31408308 682 False 785.0 785 87.464000 35 718 1 chr7D.!!$F1 683
17 TraesCS1D01G270800 chr7D 159005785 159006487 702 False 780.0 780 86.950000 1 694 1 chr7D.!!$F2 693
18 TraesCS1D01G270800 chr7D 547482654 547483350 696 False 776.0 776 86.790000 1 702 1 chr7D.!!$F4 701
19 TraesCS1D01G270800 chr7B 388160614 388161312 698 True 778.0 778 86.809000 1 702 1 chr7B.!!$R1 701
20 TraesCS1D01G270800 chr3A 603921288 603922017 729 False 773.0 773 85.812000 1 730 1 chr3A.!!$F2 729
21 TraesCS1D01G270800 chr6D 341150061 341150785 724 False 756.0 756 85.812000 1 717 1 chr6D.!!$F1 716
22 TraesCS1D01G270800 chr6D 159381238 159381953 715 True 747.0 747 85.537000 1 723 1 chr6D.!!$R1 722
23 TraesCS1D01G270800 chr6D 186553615 186554300 685 True 710.0 710 85.590000 44 720 1 chr6D.!!$R2 676
24 TraesCS1D01G270800 chr4B 464540273 464541001 728 False 750.0 750 85.383000 1 725 1 chr4B.!!$F1 724
25 TraesCS1D01G270800 chr4B 558723468 558724186 718 False 736.0 736 85.180000 1 720 1 chr4B.!!$F2 719
26 TraesCS1D01G270800 chr6A 519298575 519299289 714 False 730.0 730 85.097000 3 719 1 chr6A.!!$F1 716

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
744 816 0.398318 GGGCCGGATGCTCTAATTCT 59.602 55.000 5.05 0.0 37.53 2.40 F
901 979 0.803768 CTCTCCACGAACGGCATCAG 60.804 60.000 0.00 0.0 0.00 2.90 F
2318 2525 0.035439 CGTAGGCAATCACAGGGGTT 60.035 55.000 0.00 0.0 0.00 4.11 F
3757 3989 1.067821 CCTCCTTATCAGTCACGCTCC 59.932 57.143 0.00 0.0 0.00 4.70 F
4422 4688 1.140852 CCGGCTATCCCATGTTTGAGA 59.859 52.381 0.00 0.0 0.00 3.27 F
5340 5813 0.599558 GAGTGCAGCAATTTGGCTCA 59.400 50.000 0.00 0.0 43.68 4.26 F
6330 6903 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2299 2506 0.035439 AACCCCTGTGATTGCCTACG 60.035 55.000 0.00 0.00 0.00 3.51 R
2479 2688 0.809241 GCAATCGGACTGCCAGAGAG 60.809 60.000 0.00 0.00 33.51 3.20 R
4169 4403 0.179056 CACGGTTCTTGTGGGACAGT 60.179 55.000 0.00 0.00 41.80 3.55 R
5309 5782 1.271379 GCTGCACTCCAAGGAGGTTTA 60.271 52.381 19.62 3.35 45.88 2.01 R
6318 6891 1.854939 TCTAATACTCCCTCCGTCCCA 59.145 52.381 0.00 0.00 0.00 4.37 R
6464 8437 0.543277 AGAATCTCAGGCCGCATCAA 59.457 50.000 0.00 0.00 0.00 2.57 R
7673 10483 0.698238 TCCCTGGGGTCATCAACTTG 59.302 55.000 14.00 0.00 36.47 3.16 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
323 354 3.782443 GGGCCGTCGGATGAAGGT 61.782 66.667 17.49 0.00 44.63 3.50
397 428 1.532316 TCCGACGACCAAGACCCTT 60.532 57.895 0.00 0.00 0.00 3.95
447 480 2.754375 GGTCGGAAGGGCAAAGGA 59.246 61.111 0.00 0.00 0.00 3.36
493 545 3.135530 CCCTCCTCCTCCTCAATGTTTAG 59.864 52.174 0.00 0.00 0.00 1.85
553 605 5.642063 GTGGACGAACTATGATCTTTTGGAA 59.358 40.000 0.00 0.00 0.00 3.53
586 650 1.662122 GTTATGTCCGTTTGTAGCCGG 59.338 52.381 0.00 0.00 45.55 6.13
595 659 2.414029 CGTTTGTAGCCGGTCTTACGTA 60.414 50.000 1.90 0.00 0.00 3.57
622 690 2.408368 GCAGCTTAATTTTGTTGTCCGC 59.592 45.455 0.00 0.00 0.00 5.54
631 700 1.880271 TTGTTGTCCGCCGTTTGATA 58.120 45.000 0.00 0.00 0.00 2.15
702 774 4.266265 CGAATATGAGATACGCGAATGCAT 59.734 41.667 15.93 11.93 42.97 3.96
725 797 3.313012 TGATAAATACGAGGGATGCCG 57.687 47.619 0.00 0.00 0.00 5.69
744 816 0.398318 GGGCCGGATGCTCTAATTCT 59.602 55.000 5.05 0.00 37.53 2.40
901 979 0.803768 CTCTCCACGAACGGCATCAG 60.804 60.000 0.00 0.00 0.00 2.90
1294 1408 3.493877 GGATCATCAATTCGTCTCTGCTG 59.506 47.826 0.00 0.00 0.00 4.41
1301 1415 3.902881 ATTCGTCTCTGCTGGAAGAAT 57.097 42.857 13.05 13.05 37.19 2.40
1462 1576 3.511146 AGGCCAAGTAAATCCATGTTGTG 59.489 43.478 5.01 0.00 0.00 3.33
1464 1578 4.461081 GGCCAAGTAAATCCATGTTGTGTA 59.539 41.667 0.00 0.00 0.00 2.90
1490 1604 2.284952 GCCGCATTAACATTTGATTGCC 59.715 45.455 0.00 0.00 0.00 4.52
1597 1712 7.086376 GTGATTCTGATGCAACTGTTATGTTT 58.914 34.615 0.00 0.00 0.00 2.83
1656 1856 2.375174 TGCACCCTACATTTCCAGAAGT 59.625 45.455 0.00 0.00 0.00 3.01
1709 1911 4.664150 AAGAATCTGCAGGCTACTAGAC 57.336 45.455 15.13 0.00 0.00 2.59
1721 1923 4.469945 AGGCTACTAGACAATGTTTAGGCA 59.530 41.667 14.28 2.59 0.00 4.75
1765 1967 5.449177 GCAATTTTACAGCATACTCCTGTCC 60.449 44.000 0.00 0.00 42.22 4.02
2299 2506 3.488047 CGAGCAATGGATGGAATGTTGTC 60.488 47.826 0.00 0.00 0.00 3.18
2318 2525 0.035439 CGTAGGCAATCACAGGGGTT 60.035 55.000 0.00 0.00 0.00 4.11
2479 2688 9.753669 CAATTTTTACACAACTCTTGGTTTTTC 57.246 29.630 0.00 0.00 35.74 2.29
2722 2931 2.043227 GTATCTGGGAGAAGAGGGTGG 58.957 57.143 0.00 0.00 0.00 4.61
2878 3087 8.630278 TTTATCTAAATCTCTACACTTCACGC 57.370 34.615 0.00 0.00 0.00 5.34
2974 3200 1.205055 GGCCTAGTGCTTCCCTTAGT 58.795 55.000 0.00 0.00 40.92 2.24
3485 3717 7.072177 TCATTGGAGACATTATCGTGAAAAC 57.928 36.000 0.00 0.00 42.32 2.43
3496 3728 1.584495 GTGAAAACGGCCATGGGAC 59.416 57.895 15.13 0.00 0.00 4.46
3519 3751 1.483827 CCTAGCCTCTGCACAGATCAA 59.516 52.381 0.00 0.00 41.13 2.57
3528 3760 1.203928 GCACAGATCAATCGAGTCCG 58.796 55.000 0.00 0.00 37.07 4.79
3589 3821 2.158769 TGCAGACATCAACCAGTCTTGT 60.159 45.455 0.00 0.00 42.87 3.16
3642 3874 2.358898 GGTATGCAATGTGCTAACCTGG 59.641 50.000 13.82 0.00 45.31 4.45
3757 3989 1.067821 CCTCCTTATCAGTCACGCTCC 59.932 57.143 0.00 0.00 0.00 4.70
3841 4073 9.907576 CTAATGCTAGCAATAATATTACTTCGC 57.092 33.333 23.54 0.00 0.00 4.70
3879 4111 5.698832 TGCATCAAGTTTTATTGTTCCTCG 58.301 37.500 0.00 0.00 0.00 4.63
3974 4206 9.434420 AAATCACATTTGTTTTGTTCAAGAAGA 57.566 25.926 0.00 0.00 0.00 2.87
4013 4247 5.800438 CGCTTCCTTAAAATTTGAACTAGGC 59.200 40.000 0.00 0.00 0.00 3.93
4152 4386 3.964031 ACCTAATTTGCACTGGACCAAAA 59.036 39.130 0.00 0.00 34.93 2.44
4169 4403 5.495640 ACCAAAATTTTGAACTTCCTTGCA 58.504 33.333 28.44 0.00 40.55 4.08
4186 4420 1.507141 GCACTGTCCCACAAGAACCG 61.507 60.000 0.00 0.00 0.00 4.44
4214 4448 5.332743 AGAATTCTAGCCATTTCCACCAAA 58.667 37.500 6.06 0.00 0.00 3.28
4230 4464 3.189287 CACCAAAGCATCACCTACTGTTC 59.811 47.826 0.00 0.00 0.00 3.18
4292 4558 9.634163 AAAAATAAATCTAAACACGGATCAACC 57.366 29.630 0.00 0.00 0.00 3.77
4320 4586 2.643304 GACCCAGGGAACTCCTACTTTT 59.357 50.000 14.54 0.00 46.12 2.27
4321 4587 2.375509 ACCCAGGGAACTCCTACTTTTG 59.624 50.000 14.54 0.00 46.12 2.44
4322 4588 2.437413 CCAGGGAACTCCTACTTTTGC 58.563 52.381 0.00 0.00 46.12 3.68
4324 4590 3.486383 CAGGGAACTCCTACTTTTGCAA 58.514 45.455 0.00 0.00 46.12 4.08
4325 4591 3.253432 CAGGGAACTCCTACTTTTGCAAC 59.747 47.826 0.00 0.00 46.12 4.17
4327 4593 3.889538 GGGAACTCCTACTTTTGCAACTT 59.110 43.478 0.00 0.00 35.95 2.66
4363 4629 6.601613 CCATTGGGTTAGTTATAGTGAGCAAA 59.398 38.462 0.00 0.00 0.00 3.68
4406 4672 3.554129 GCATAAAATGGGGTTTATCCGGC 60.554 47.826 0.00 0.00 32.53 6.13
4422 4688 1.140852 CCGGCTATCCCATGTTTGAGA 59.859 52.381 0.00 0.00 0.00 3.27
4450 4716 9.429359 GTTGAGACTTGAGATTCTTTCTTGATA 57.571 33.333 0.00 0.00 33.74 2.15
4494 4760 5.367945 TCTATTGAGGGTGGATTGGTTAC 57.632 43.478 0.00 0.00 0.00 2.50
4609 4875 1.804748 GTCCAGGTTTCACGCTTTAGG 59.195 52.381 0.00 0.00 0.00 2.69
4630 4919 1.371558 GACCCTTGGACTTCGCAGT 59.628 57.895 0.00 0.00 35.17 4.40
4661 4950 5.982890 TGGGAAAGAAGAATGAAATGGAC 57.017 39.130 0.00 0.00 0.00 4.02
4699 4988 1.979897 TATTGCAACGCAGCACAATG 58.020 45.000 0.00 0.00 45.61 2.82
4718 5007 1.202639 TGATGGATATGTGACGGCCAC 60.203 52.381 2.24 0.00 45.88 5.01
4763 5052 2.603560 GCCTTACTCGAATGTGTACTGC 59.396 50.000 0.00 0.00 0.00 4.40
4864 5336 7.167535 AGCCAACCAACTTATTAATGCAAATT 58.832 30.769 0.00 0.00 0.00 1.82
5161 5633 7.704578 AGTCTTACACAAGCTCACTATCTTA 57.295 36.000 0.00 0.00 0.00 2.10
5201 5674 7.369607 TGTGTATTGATGAAGTCCACATTTTG 58.630 34.615 0.00 0.00 0.00 2.44
5261 5734 1.696063 CTAATGGTGGCCATCTTGGG 58.304 55.000 18.94 3.86 44.40 4.12
5309 5782 7.824779 GGAAGACTATGGTAAGTTTCATTCACT 59.175 37.037 0.00 0.00 0.00 3.41
5340 5813 0.599558 GAGTGCAGCAATTTGGCTCA 59.400 50.000 0.00 0.00 43.68 4.26
5446 6014 6.716628 GGGTCATATGGATGTGTTCACATAAT 59.283 38.462 16.79 15.13 34.41 1.28
5609 6181 6.925610 TGAAATCCGTACGTACATACTACT 57.074 37.500 24.50 3.29 0.00 2.57
5610 6182 6.948353 TGAAATCCGTACGTACATACTACTC 58.052 40.000 24.50 11.95 0.00 2.59
5611 6183 5.931441 AATCCGTACGTACATACTACTCC 57.069 43.478 24.50 0.00 0.00 3.85
5612 6184 3.728845 TCCGTACGTACATACTACTCCC 58.271 50.000 24.50 0.00 0.00 4.30
5613 6185 3.388024 TCCGTACGTACATACTACTCCCT 59.612 47.826 24.50 0.00 0.00 4.20
5614 6186 3.743396 CCGTACGTACATACTACTCCCTC 59.257 52.174 24.50 0.00 0.00 4.30
5615 6187 3.743396 CGTACGTACATACTACTCCCTCC 59.257 52.174 24.50 0.00 0.00 4.30
5616 6188 2.843701 ACGTACATACTACTCCCTCCG 58.156 52.381 0.00 0.00 0.00 4.63
5617 6189 2.171448 ACGTACATACTACTCCCTCCGT 59.829 50.000 0.00 0.00 0.00 4.69
5618 6190 3.388024 ACGTACATACTACTCCCTCCGTA 59.612 47.826 0.00 0.00 0.00 4.02
5619 6191 4.141711 ACGTACATACTACTCCCTCCGTAA 60.142 45.833 0.00 0.00 0.00 3.18
5620 6192 4.816385 CGTACATACTACTCCCTCCGTAAA 59.184 45.833 0.00 0.00 0.00 2.01
5621 6193 5.049818 CGTACATACTACTCCCTCCGTAAAG 60.050 48.000 0.00 0.00 0.00 1.85
5622 6194 5.121380 ACATACTACTCCCTCCGTAAAGA 57.879 43.478 0.00 0.00 0.00 2.52
5623 6195 5.513233 ACATACTACTCCCTCCGTAAAGAA 58.487 41.667 0.00 0.00 0.00 2.52
5624 6196 5.954150 ACATACTACTCCCTCCGTAAAGAAA 59.046 40.000 0.00 0.00 0.00 2.52
5625 6197 6.610425 ACATACTACTCCCTCCGTAAAGAAAT 59.390 38.462 0.00 0.00 0.00 2.17
5626 6198 7.781693 ACATACTACTCCCTCCGTAAAGAAATA 59.218 37.037 0.00 0.00 0.00 1.40
5627 6199 8.804204 CATACTACTCCCTCCGTAAAGAAATAT 58.196 37.037 0.00 0.00 0.00 1.28
5629 6201 8.773033 ACTACTCCCTCCGTAAAGAAATATAA 57.227 34.615 0.00 0.00 0.00 0.98
5630 6202 8.858094 ACTACTCCCTCCGTAAAGAAATATAAG 58.142 37.037 0.00 0.00 0.00 1.73
5631 6203 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
5632 6204 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
5633 6205 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
5634 6206 6.553852 TCCCTCCGTAAAGAAATATAAGAGCT 59.446 38.462 0.00 0.00 0.00 4.09
5635 6207 7.070821 TCCCTCCGTAAAGAAATATAAGAGCTT 59.929 37.037 0.00 0.00 0.00 3.74
5636 6208 7.715686 CCCTCCGTAAAGAAATATAAGAGCTTT 59.284 37.037 0.00 0.00 33.76 3.51
5637 6209 9.110502 CCTCCGTAAAGAAATATAAGAGCTTTT 57.889 33.333 0.00 0.00 31.85 2.27
5638 6210 9.922305 CTCCGTAAAGAAATATAAGAGCTTTTG 57.078 33.333 0.00 0.00 31.85 2.44
5639 6211 8.889717 TCCGTAAAGAAATATAAGAGCTTTTGG 58.110 33.333 0.00 0.00 31.85 3.28
5640 6212 8.889717 CCGTAAAGAAATATAAGAGCTTTTGGA 58.110 33.333 0.00 0.00 30.71 3.53
5645 6217 9.692325 AAGAAATATAAGAGCTTTTGGATCACT 57.308 29.630 0.00 0.00 31.91 3.41
5652 6224 7.913674 AAGAGCTTTTGGATCACTAAAGTAG 57.086 36.000 14.49 3.53 32.75 2.57
5653 6225 7.010339 AGAGCTTTTGGATCACTAAAGTAGT 57.990 36.000 14.49 0.00 40.28 2.73
5667 6239 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
5668 6240 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
5669 6241 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
5670 6242 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
5685 6257 8.649973 AACGCTCTTATATTTCTTTACAGAGG 57.350 34.615 0.00 0.00 0.00 3.69
5686 6258 7.783042 ACGCTCTTATATTTCTTTACAGAGGT 58.217 34.615 0.00 0.00 0.00 3.85
5687 6259 8.910944 ACGCTCTTATATTTCTTTACAGAGGTA 58.089 33.333 0.00 0.00 0.00 3.08
5688 6260 9.400638 CGCTCTTATATTTCTTTACAGAGGTAG 57.599 37.037 0.00 0.00 0.00 3.18
5782 6355 3.399330 TCTAAAAAGAGGTCAGCGTTGG 58.601 45.455 0.00 0.00 0.00 3.77
6320 6893 8.621286 AGTACAAAGTTGAGACACTTATTTTGG 58.379 33.333 0.00 0.00 35.87 3.28
6321 6894 6.805713 ACAAAGTTGAGACACTTATTTTGGG 58.194 36.000 0.00 0.00 35.87 4.12
6322 6895 6.605594 ACAAAGTTGAGACACTTATTTTGGGA 59.394 34.615 0.00 0.00 35.87 4.37
6324 6897 4.755123 AGTTGAGACACTTATTTTGGGACG 59.245 41.667 0.00 0.00 0.00 4.79
6328 6901 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
6329 6902 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
6330 6903 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
6437 8410 6.566197 ACTGCTACTCTTCAATTTCCTTTG 57.434 37.500 0.00 0.00 0.00 2.77
6440 8413 5.182001 TGCTACTCTTCAATTTCCTTTGCTC 59.818 40.000 0.00 0.00 0.00 4.26
6443 8416 4.453819 ACTCTTCAATTTCCTTTGCTCTCG 59.546 41.667 0.00 0.00 0.00 4.04
6486 8463 2.028658 TGATGCGGCCTGAGATTCTATC 60.029 50.000 0.00 0.00 0.00 2.08
6603 8580 4.819105 TCGACAGAAGGTGGTGATTATT 57.181 40.909 0.00 0.00 0.00 1.40
6731 8708 6.627243 TCGATAAGGGACCATATGTTAATCG 58.373 40.000 1.24 6.70 0.00 3.34
6804 8781 7.991084 TCATGAATCCTTGGATAAGCATAAG 57.009 36.000 2.20 0.00 32.40 1.73
6808 8785 5.573380 ATCCTTGGATAAGCATAAGCAGA 57.427 39.130 0.00 0.00 45.49 4.26
6809 8786 5.573380 TCCTTGGATAAGCATAAGCAGAT 57.427 39.130 0.00 0.00 45.49 2.90
6835 8812 3.087031 AGTGAAATGGAAGGCAGTGATG 58.913 45.455 0.00 0.00 0.00 3.07
6836 8813 2.165030 GTGAAATGGAAGGCAGTGATGG 59.835 50.000 0.00 0.00 0.00 3.51
6837 8814 1.753073 GAAATGGAAGGCAGTGATGGG 59.247 52.381 0.00 0.00 0.00 4.00
6838 8815 1.002069 AATGGAAGGCAGTGATGGGA 58.998 50.000 0.00 0.00 0.00 4.37
6839 8816 0.549950 ATGGAAGGCAGTGATGGGAG 59.450 55.000 0.00 0.00 0.00 4.30
6840 8817 1.225704 GGAAGGCAGTGATGGGAGG 59.774 63.158 0.00 0.00 0.00 4.30
6929 8912 1.123077 AGCGGCACAGAGGATAATGA 58.877 50.000 1.45 0.00 0.00 2.57
7108 9091 1.271840 ATCTTGGCCCTTGCTCGGTA 61.272 55.000 0.00 0.00 37.74 4.02
7304 9287 9.996554 AAAGGAAATAATAAAAGGTCAAGTTGG 57.003 29.630 2.34 0.00 0.00 3.77
7314 9297 1.740025 GGTCAAGTTGGCATGCTACTC 59.260 52.381 18.92 7.47 0.00 2.59
7325 9308 3.370527 GGCATGCTACTCCTCCAAGTTTA 60.371 47.826 18.92 0.00 0.00 2.01
7346 9329 9.596308 AGTTTATGTTTTAGGAATTACACCCTT 57.404 29.630 0.00 0.00 34.11 3.95
7366 9349 7.767198 CACCCTTTGTTCCTAAATATAAGACGA 59.233 37.037 0.00 0.00 0.00 4.20
7438 9727 4.142071 TGCATTTTGCTTGTTCTGGTGTTA 60.142 37.500 0.75 0.00 45.31 2.41
7523 9910 5.414454 TCGCTACAGAAAATAACCTTTGCAT 59.586 36.000 0.00 0.00 0.00 3.96
7558 10243 7.636259 AAAAATGTATCGATGTGTGGTTTTG 57.364 32.000 8.54 0.00 0.00 2.44
7573 10258 5.356751 TGTGGTTTTGCAGATGTATCATACC 59.643 40.000 0.00 0.00 0.00 2.73
7574 10259 5.356751 GTGGTTTTGCAGATGTATCATACCA 59.643 40.000 0.00 0.00 0.00 3.25
7575 10260 5.589855 TGGTTTTGCAGATGTATCATACCAG 59.410 40.000 0.00 0.00 0.00 4.00
7581 10391 7.722949 TGCAGATGTATCATACCAGATATCA 57.277 36.000 5.32 0.00 33.42 2.15
7599 10409 7.841277 CAGATATCAAACAAACTTACATCGTCG 59.159 37.037 5.32 0.00 0.00 5.12
7654 10464 9.482627 CCAGATACAACATCTATCTAGTTTTCC 57.517 37.037 0.00 0.00 31.02 3.13
7656 10466 8.915036 AGATACAACATCTATCTAGTTTTCCGT 58.085 33.333 0.00 0.00 30.51 4.69
7673 10483 5.806654 TTCCGTATACCTAACCATTACCC 57.193 43.478 0.00 0.00 0.00 3.69
7690 10500 0.323725 CCCAAGTTGATGACCCCAGG 60.324 60.000 3.87 0.00 0.00 4.45
7732 10542 5.177326 ACTAAGAAAGAGCAGCTGAAGATG 58.823 41.667 20.43 0.00 34.00 2.90
7733 10543 2.988570 AGAAAGAGCAGCTGAAGATGG 58.011 47.619 20.43 0.00 31.02 3.51
7734 10544 2.570752 AGAAAGAGCAGCTGAAGATGGA 59.429 45.455 20.43 0.00 31.02 3.41
7735 10545 2.695127 AAGAGCAGCTGAAGATGGAG 57.305 50.000 20.43 0.00 31.02 3.86
7836 10646 9.424319 GACTAAGATCAACAATTCAACACTCTA 57.576 33.333 0.00 0.00 0.00 2.43
7837 10647 9.209175 ACTAAGATCAACAATTCAACACTCTAC 57.791 33.333 0.00 0.00 0.00 2.59
7894 10704 1.190323 CTTTGTCACGAGCAAGACGAC 59.810 52.381 0.00 0.00 37.58 4.34
8015 10825 4.860907 ACAAAGCTGAATCGCAAATTGATC 59.139 37.500 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
323 354 1.077716 TCGGAGAGGATGACGAGCA 60.078 57.895 0.00 0.00 0.00 4.26
431 462 1.674651 GGTCCTTTGCCCTTCCGAC 60.675 63.158 0.00 0.00 0.00 4.79
447 480 4.003788 CACCACTTCCTCGCCGGT 62.004 66.667 1.90 0.00 0.00 5.28
528 580 5.046591 TCCAAAAGATCATAGTTCGTCCACT 60.047 40.000 0.00 0.00 0.00 4.00
553 605 5.790593 ACGGACATAACATACTTCACAACT 58.209 37.500 0.00 0.00 0.00 3.16
586 650 2.685100 AGCTGCAAAGGTACGTAAGAC 58.315 47.619 1.02 0.00 43.62 3.01
595 659 5.427378 ACAACAAAATTAAGCTGCAAAGGT 58.573 33.333 1.02 0.00 0.00 3.50
631 700 6.389091 TGTACACGTTGATTTATCCTACGTT 58.611 36.000 13.80 9.99 41.70 3.99
702 774 5.416083 CGGCATCCCTCGTATTTATCATTA 58.584 41.667 0.00 0.00 0.00 1.90
725 797 0.398318 AGAATTAGAGCATCCGGCCC 59.602 55.000 0.00 0.00 46.50 5.80
732 804 4.347292 TGCCTGATCTGAGAATTAGAGCAT 59.653 41.667 0.38 0.00 39.54 3.79
733 805 3.708121 TGCCTGATCTGAGAATTAGAGCA 59.292 43.478 0.38 0.00 38.16 4.26
734 806 4.057432 GTGCCTGATCTGAGAATTAGAGC 58.943 47.826 0.38 0.00 0.00 4.09
744 816 1.205655 CTTTCCTCGTGCCTGATCTGA 59.794 52.381 0.38 0.00 0.00 3.27
842 916 2.283676 GGACTGACGGGGAGGACA 60.284 66.667 0.00 0.00 0.00 4.02
849 923 2.738480 TCGGTTTGGACTGACGGG 59.262 61.111 0.00 0.00 36.26 5.28
901 979 0.373024 CTCGAGACGTTACGGGAGAC 59.627 60.000 6.58 0.00 31.11 3.36
1099 1211 3.145551 GCGGTAGAGGAAGGCGGA 61.146 66.667 0.00 0.00 0.00 5.54
1271 1383 2.474359 GCAGAGACGAATTGATGATCCG 59.526 50.000 0.00 0.00 0.00 4.18
1294 1408 6.591448 GGGTGAATCACAATCAAAATTCTTCC 59.409 38.462 15.86 0.00 35.86 3.46
1301 1415 6.968263 TTACAGGGTGAATCACAATCAAAA 57.032 33.333 15.86 0.00 35.86 2.44
1423 1537 2.031333 GGCCTACCTTCTATACGTGACG 60.031 54.545 2.24 2.24 0.00 4.35
1462 1576 6.055231 TCAAATGTTAATGCGGCATACTAC 57.945 37.500 17.00 14.15 0.00 2.73
1464 1578 5.772825 ATCAAATGTTAATGCGGCATACT 57.227 34.783 17.00 3.98 0.00 2.12
1490 1604 1.276421 CACCTGGACTGGACAAGTAGG 59.724 57.143 0.00 0.00 40.07 3.18
1703 1905 6.476378 AGTGAATGCCTAAACATTGTCTAGT 58.524 36.000 0.00 0.00 40.31 2.57
1709 1911 6.700960 TGAAACAAGTGAATGCCTAAACATTG 59.299 34.615 0.00 0.00 40.31 2.82
1721 1923 5.581126 TGCTCAAACTGAAACAAGTGAAT 57.419 34.783 0.00 0.00 0.00 2.57
1940 2146 6.830873 ATCCAAAATTCTCAGAACCTTCAG 57.169 37.500 0.00 0.00 0.00 3.02
1941 2147 7.461749 ACTATCCAAAATTCTCAGAACCTTCA 58.538 34.615 0.00 0.00 0.00 3.02
2083 2290 3.520290 TCACTAGTTAATCCAGGCACG 57.480 47.619 0.00 0.00 0.00 5.34
2233 2440 8.556194 TGTTTCACATACTAGACATCAAAACAC 58.444 33.333 0.00 0.00 30.48 3.32
2299 2506 0.035439 AACCCCTGTGATTGCCTACG 60.035 55.000 0.00 0.00 0.00 3.51
2479 2688 0.809241 GCAATCGGACTGCCAGAGAG 60.809 60.000 0.00 0.00 33.51 3.20
2678 2887 7.271511 ACTTGACCTGAATGTGCAATTTAAAA 58.728 30.769 0.00 0.00 0.00 1.52
2722 2931 2.417515 GCACCAGCTACAGGAGTACTTC 60.418 54.545 0.00 0.00 37.91 3.01
2878 3087 4.872691 AGAGAGCCGATGTTATTTGAACAG 59.127 41.667 0.00 0.00 33.18 3.16
2953 3163 1.559682 CTAAGGGAAGCACTAGGCCAA 59.440 52.381 5.01 0.00 46.50 4.52
2955 3165 1.139256 GACTAAGGGAAGCACTAGGCC 59.861 57.143 0.00 0.00 46.50 5.19
3247 3479 5.927030 TCTAATTAGCTGTTGCAAAGAACG 58.073 37.500 0.00 0.00 42.74 3.95
3297 3529 2.114616 ACACTGTTTGCCCCATTTGAA 58.885 42.857 0.00 0.00 0.00 2.69
3452 3684 7.650504 CGATAATGTCTCCAATGATTTGCAAAT 59.349 33.333 24.33 24.33 0.00 2.32
3496 3728 2.688666 TGTGCAGAGGCTAGGGGG 60.689 66.667 0.00 0.00 41.91 5.40
3519 3751 2.651455 TCATAACAGTCCGGACTCGAT 58.349 47.619 34.28 22.70 40.20 3.59
3528 3760 5.402398 GCCAAAAGATGTTCATAACAGTCC 58.598 41.667 0.00 0.00 45.95 3.85
3589 3821 0.179234 TCCCAGTTTGCAAGTCGTGA 59.821 50.000 0.00 0.00 0.00 4.35
3757 3989 1.102978 GATGGTCAAATTCCCGGGTG 58.897 55.000 22.86 11.92 0.00 4.61
4013 4247 4.654091 ATAATTCAGGTTTGCATTCCCG 57.346 40.909 4.38 0.00 0.00 5.14
4092 4326 5.280654 ACGACTACCCAACTTCTTTTACA 57.719 39.130 0.00 0.00 0.00 2.41
4152 4386 4.202151 GGACAGTGCAAGGAAGTTCAAAAT 60.202 41.667 5.01 0.00 0.00 1.82
4169 4403 0.179056 CACGGTTCTTGTGGGACAGT 60.179 55.000 0.00 0.00 41.80 3.55
4214 4448 0.608130 TGCGAACAGTAGGTGATGCT 59.392 50.000 0.00 0.00 0.00 3.79
4230 4464 5.116180 TCAAGGGTATAGAAGTTCAATGCG 58.884 41.667 5.50 0.00 0.00 4.73
4266 4506 9.634163 GGTTGATCCGTGTTTAGATTTATTTTT 57.366 29.630 0.00 0.00 0.00 1.94
4292 4558 0.905357 AGTTCCCTGGGTCAATCTCG 59.095 55.000 13.56 0.00 0.00 4.04
4320 4586 5.931146 CCAATGGTTTGCTATTTAAGTTGCA 59.069 36.000 3.12 3.12 0.00 4.08
4321 4587 5.351189 CCCAATGGTTTGCTATTTAAGTTGC 59.649 40.000 0.00 0.00 0.00 4.17
4322 4588 6.463360 ACCCAATGGTTTGCTATTTAAGTTG 58.537 36.000 0.00 0.00 44.75 3.16
4363 4629 2.571202 CCCCCTGTATTTTGCCATTTGT 59.429 45.455 0.00 0.00 0.00 2.83
4406 4672 6.314896 GTCTCAACTTCTCAAACATGGGATAG 59.685 42.308 0.00 0.00 0.00 2.08
4422 4688 7.989741 TCAAGAAAGAATCTCAAGTCTCAACTT 59.010 33.333 0.00 0.00 41.26 2.66
4450 4716 5.533903 AGAATCAAAGTCTGCTGTGAATGTT 59.466 36.000 0.00 0.00 41.86 2.71
4494 4760 0.888736 TGGTGAGGCCACAATTGTCG 60.889 55.000 8.48 2.93 43.61 4.35
4559 4825 2.457366 ACTACAACTACCAGCAGCAC 57.543 50.000 0.00 0.00 0.00 4.40
4609 4875 1.671379 GCGAAGTCCAAGGGTCCAC 60.671 63.158 0.00 0.00 0.00 4.02
4653 4942 4.737054 CCACAGCAAATAGTGTCCATTTC 58.263 43.478 0.00 0.00 33.99 2.17
4688 4977 2.551032 ACATATCCATCATTGTGCTGCG 59.449 45.455 0.00 0.00 0.00 5.18
4699 4988 1.512926 GTGGCCGTCACATATCCATC 58.487 55.000 0.00 0.00 45.39 3.51
4718 5007 6.865834 AGGACTGCCTGATATTCCTAATAG 57.134 41.667 0.00 0.00 44.90 1.73
4864 5336 8.339344 TCAAAAGATTCACAGCATTATTCTCA 57.661 30.769 0.00 0.00 0.00 3.27
4970 5442 5.184864 TGGAAAAATGATTAGTCGGTGCATT 59.815 36.000 0.00 0.00 0.00 3.56
5309 5782 1.271379 GCTGCACTCCAAGGAGGTTTA 60.271 52.381 19.62 3.35 45.88 2.01
5381 5854 9.959749 TTGGATATTTTTCAAACTTCACACTAC 57.040 29.630 0.00 0.00 0.00 2.73
5411 5884 9.111519 ACACATCCATATGACCCACTATTATTA 57.888 33.333 3.65 0.00 36.54 0.98
5414 5887 7.071824 TGAACACATCCATATGACCCACTATTA 59.928 37.037 3.65 0.00 36.54 0.98
5415 5888 5.912149 ACACATCCATATGACCCACTATT 57.088 39.130 3.65 0.00 36.54 1.73
5417 5890 4.719273 TGAACACATCCATATGACCCACTA 59.281 41.667 3.65 0.00 36.54 2.74
5418 5891 3.523157 TGAACACATCCATATGACCCACT 59.477 43.478 3.65 0.00 36.54 4.00
5420 5893 3.265479 TGTGAACACATCCATATGACCCA 59.735 43.478 3.65 0.00 36.21 4.51
5421 5894 3.884895 TGTGAACACATCCATATGACCC 58.115 45.455 3.65 0.00 36.21 4.46
5609 6181 6.553852 AGCTCTTATATTTCTTTACGGAGGGA 59.446 38.462 0.00 0.00 0.00 4.20
5610 6182 6.760291 AGCTCTTATATTTCTTTACGGAGGG 58.240 40.000 0.00 0.00 0.00 4.30
5611 6183 8.664211 AAAGCTCTTATATTTCTTTACGGAGG 57.336 34.615 0.00 0.00 0.00 4.30
5612 6184 9.922305 CAAAAGCTCTTATATTTCTTTACGGAG 57.078 33.333 0.00 0.00 0.00 4.63
5613 6185 8.889717 CCAAAAGCTCTTATATTTCTTTACGGA 58.110 33.333 0.00 0.00 0.00 4.69
5614 6186 8.889717 TCCAAAAGCTCTTATATTTCTTTACGG 58.110 33.333 0.00 0.00 0.00 4.02
5619 6191 9.692325 AGTGATCCAAAAGCTCTTATATTTCTT 57.308 29.630 0.00 0.00 0.00 2.52
5626 6198 9.606631 CTACTTTAGTGATCCAAAAGCTCTTAT 57.393 33.333 10.01 0.00 34.31 1.73
5627 6199 8.594550 ACTACTTTAGTGATCCAAAAGCTCTTA 58.405 33.333 10.01 0.00 37.69 2.10
5628 6200 7.454225 ACTACTTTAGTGATCCAAAAGCTCTT 58.546 34.615 10.01 0.00 37.69 2.85
5629 6201 7.010339 ACTACTTTAGTGATCCAAAAGCTCT 57.990 36.000 10.01 0.00 37.69 4.09
5643 6215 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
5644 6216 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
5659 6231 9.099454 CCTCTGTAAAGAAATATAAGAGCGTTT 57.901 33.333 0.00 0.00 0.00 3.60
5660 6232 8.258708 ACCTCTGTAAAGAAATATAAGAGCGTT 58.741 33.333 0.00 0.00 0.00 4.84
5661 6233 7.783042 ACCTCTGTAAAGAAATATAAGAGCGT 58.217 34.615 0.00 0.00 0.00 5.07
5662 6234 9.400638 CTACCTCTGTAAAGAAATATAAGAGCG 57.599 37.037 0.00 0.00 0.00 5.03
6295 6868 7.860872 CCCAAAATAAGTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
6298 6871 6.918022 GTCCCAAAATAAGTGTCTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
6301 6874 4.755123 CGTCCCAAAATAAGTGTCTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
6304 6877 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
6306 6879 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
6308 6881 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
6310 6883 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
6311 6884 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
6312 6885 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
6313 6886 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
6314 6887 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
6315 6888 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
6316 6889 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
6318 6891 1.854939 TCTAATACTCCCTCCGTCCCA 59.145 52.381 0.00 0.00 0.00 4.37
6320 6893 3.896272 ACATTCTAATACTCCCTCCGTCC 59.104 47.826 0.00 0.00 0.00 4.79
6321 6894 4.796618 GCACATTCTAATACTCCCTCCGTC 60.797 50.000 0.00 0.00 0.00 4.79
6322 6895 3.069729 GCACATTCTAATACTCCCTCCGT 59.930 47.826 0.00 0.00 0.00 4.69
6324 6897 4.141711 TGTGCACATTCTAATACTCCCTCC 60.142 45.833 17.42 0.00 0.00 4.30
6328 6901 6.051717 AGACATGTGCACATTCTAATACTCC 58.948 40.000 29.48 8.99 33.61 3.85
6329 6902 8.648557 TTAGACATGTGCACATTCTAATACTC 57.351 34.615 32.77 19.55 34.70 2.59
6330 6903 9.618890 ATTTAGACATGTGCACATTCTAATACT 57.381 29.630 34.43 26.70 36.73 2.12
6359 8332 4.794762 CCAATGCATTTGTCATACAGAACG 59.205 41.667 9.83 0.00 33.15 3.95
6464 8437 0.543277 AGAATCTCAGGCCGCATCAA 59.457 50.000 0.00 0.00 0.00 2.57
6486 8463 7.504403 AGAAAGACATTATCAGATACCACCAG 58.496 38.462 0.00 0.00 0.00 4.00
6651 8628 5.886992 TCTTGAGTCTGCATGCAAATATTG 58.113 37.500 22.88 9.00 0.00 1.90
6731 8708 2.555757 GCTACCATTCCATCTTCCATGC 59.444 50.000 0.00 0.00 0.00 4.06
6804 8781 4.380233 CCTTCCATTTCACTGACAATCTGC 60.380 45.833 0.00 0.00 0.00 4.26
6808 8785 3.499338 TGCCTTCCATTTCACTGACAAT 58.501 40.909 0.00 0.00 0.00 2.71
6809 8786 2.886523 CTGCCTTCCATTTCACTGACAA 59.113 45.455 0.00 0.00 0.00 3.18
6835 8812 4.563140 TCTGTTGTACATTAACCCTCCC 57.437 45.455 0.00 0.00 0.00 4.30
6836 8813 5.357032 CCATTCTGTTGTACATTAACCCTCC 59.643 44.000 0.00 0.00 0.00 4.30
6837 8814 5.357032 CCCATTCTGTTGTACATTAACCCTC 59.643 44.000 0.00 0.00 0.00 4.30
6838 8815 5.014755 TCCCATTCTGTTGTACATTAACCCT 59.985 40.000 0.00 0.00 0.00 4.34
6839 8816 5.258051 TCCCATTCTGTTGTACATTAACCC 58.742 41.667 0.00 0.00 0.00 4.11
6840 8817 6.601613 TGATCCCATTCTGTTGTACATTAACC 59.398 38.462 0.00 0.00 0.00 2.85
6875 8858 2.930023 GCACTGTGACTCTCATCCTGTG 60.930 54.545 12.86 0.00 0.00 3.66
7304 9287 2.409948 AACTTGGAGGAGTAGCATGC 57.590 50.000 10.51 10.51 0.00 4.06
7325 9308 7.849322 ACAAAGGGTGTAATTCCTAAAACAT 57.151 32.000 0.00 0.00 39.29 2.71
7346 9329 7.656137 GCCAGATCGTCTTATATTTAGGAACAA 59.344 37.037 0.00 0.00 0.00 2.83
7366 9349 7.232534 TGTTCCTAAATGTTTAAACTGCCAGAT 59.767 33.333 18.72 0.67 0.00 2.90
7477 9777 8.663025 AGCGAAATGAGTGCTAAATATCATATG 58.337 33.333 0.00 0.00 37.15 1.78
7490 9877 4.404507 TTTTCTGTAGCGAAATGAGTGC 57.595 40.909 0.00 0.00 33.33 4.40
7498 9885 5.239744 TGCAAAGGTTATTTTCTGTAGCGAA 59.760 36.000 0.00 0.00 0.00 4.70
7534 9921 6.145371 GCAAAACCACACATCGATACATTTTT 59.855 34.615 0.00 0.00 0.00 1.94
7535 9922 5.633182 GCAAAACCACACATCGATACATTTT 59.367 36.000 0.00 0.00 0.00 1.82
7558 10243 8.877779 GTTTGATATCTGGTATGATACATCTGC 58.122 37.037 4.83 0.00 32.51 4.26
7573 10258 7.841277 CGACGATGTAAGTTTGTTTGATATCTG 59.159 37.037 3.98 0.00 0.00 2.90
7574 10259 7.010183 CCGACGATGTAAGTTTGTTTGATATCT 59.990 37.037 3.98 0.00 0.00 1.98
7575 10260 7.117454 CCGACGATGTAAGTTTGTTTGATATC 58.883 38.462 0.00 0.00 0.00 1.63
7581 10391 3.469739 ACCCGACGATGTAAGTTTGTTT 58.530 40.909 0.00 0.00 0.00 2.83
7599 10409 7.416326 CCATCCTGTTTTATTTGTAGCTAACCC 60.416 40.741 0.00 0.00 0.00 4.11
7654 10464 6.165700 ACTTGGGTAATGGTTAGGTATACG 57.834 41.667 0.00 0.00 0.00 3.06
7656 10466 7.752518 TCAACTTGGGTAATGGTTAGGTATA 57.247 36.000 0.00 0.00 0.00 1.47
7673 10483 0.698238 TCCCTGGGGTCATCAACTTG 59.302 55.000 14.00 0.00 36.47 3.16
7836 10646 5.860648 TCCTATTTTGGAAGAAGGGAAGT 57.139 39.130 0.00 0.00 32.39 3.01
7894 10704 0.815615 GCAGAACTAAGGCATCGGGG 60.816 60.000 0.00 0.00 0.00 5.73
7947 10757 4.698575 GGTTCCAGGTTAGCTCTCTTATG 58.301 47.826 0.00 0.00 0.00 1.90
8015 10825 4.735822 CCTTTTCGTCTATTAGAGTCTGCG 59.264 45.833 1.86 0.00 0.00 5.18


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

AutoCloner maintained by Alex Coulton.