Multiple sequence alignment - TraesCS7D01G470100

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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 TraesCS7D01G470100 chr7D 100.000 4790 0 0 1 4790 583110145 583105356 0.000000e+00 8846.0
1 TraesCS7D01G470100 chr7B 93.170 2372 101 23 764 3098 650668033 650665686 0.000000e+00 3426.0
2 TraesCS7D01G470100 chr7B 89.387 848 42 15 3166 4000 650665676 650664864 0.000000e+00 1024.0
3 TraesCS7D01G470100 chr7B 88.023 526 53 5 7 524 650668836 650668313 8.810000e-172 614.0
4 TraesCS7D01G470100 chr7A 95.286 1103 41 6 1998 3098 674875539 674874446 0.000000e+00 1738.0
5 TraesCS7D01G470100 chr7A 92.683 697 28 9 764 1457 674877185 674876509 0.000000e+00 983.0
6 TraesCS7D01G470100 chr7A 88.046 870 49 19 3184 3999 674874430 674873562 0.000000e+00 979.0
7 TraesCS7D01G470100 chr7A 85.009 527 56 11 7 524 674878368 674877856 9.190000e-142 514.0
8 TraesCS7D01G470100 chr7A 90.244 369 21 5 1507 1865 674876143 674875780 7.260000e-128 468.0
9 TraesCS7D01G470100 chr7A 94.048 84 2 3 1863 1944 674875623 674875541 1.810000e-24 124.0
10 TraesCS7D01G470100 chr3D 91.460 808 46 11 4002 4790 515975670 515976473 0.000000e+00 1088.0
11 TraesCS7D01G470100 chr3D 90.238 799 59 8 4010 4790 429786278 429785481 0.000000e+00 1026.0
12 TraesCS7D01G470100 chr3D 93.548 62 2 2 3099 3159 565635686 565635746 1.840000e-14 91.6
13 TraesCS7D01G470100 chr2D 91.310 794 50 6 4015 4790 644013197 644013989 0.000000e+00 1066.0
14 TraesCS7D01G470100 chr2D 90.729 809 45 12 4012 4790 56634534 56633726 0.000000e+00 1051.0
15 TraesCS7D01G470100 chr2D 83.619 525 53 14 2167 2679 644361795 644362298 3.380000e-126 462.0
16 TraesCS7D01G470100 chr2D 80.377 637 65 26 2155 2752 635948171 635948786 3.430000e-116 429.0
17 TraesCS7D01G470100 chr2D 85.443 316 24 14 3179 3477 635949256 635949566 4.660000e-80 309.0
18 TraesCS7D01G470100 chr2D 75.029 853 116 60 1158 1960 635946321 635947126 6.020000e-79 305.0
19 TraesCS7D01G470100 chr2D 82.558 172 18 6 3428 3597 644362928 644363089 1.800000e-29 141.0
20 TraesCS7D01G470100 chr2B 90.738 799 46 12 4015 4790 742784996 742784203 0.000000e+00 1040.0
21 TraesCS7D01G470100 chr2B 83.043 631 66 19 2066 2662 794047000 794047623 7.060000e-148 534.0
22 TraesCS7D01G470100 chr2B 83.371 445 48 15 3220 3648 794048311 794048745 5.810000e-104 388.0
23 TraesCS7D01G470100 chr2B 88.316 291 16 3 1158 1442 794045775 794046053 2.760000e-87 333.0
24 TraesCS7D01G470100 chr2B 78.066 424 47 21 3194 3603 791477851 791477460 4.820000e-55 226.0
25 TraesCS7D01G470100 chr2B 83.448 145 15 7 1947 2086 794046806 794046946 5.030000e-25 126.0
26 TraesCS7D01G470100 chr2B 84.211 133 12 4 1925 2055 794002909 794003034 2.340000e-23 121.0
27 TraesCS7D01G470100 chr5B 91.877 751 50 9 4048 4790 615399214 615399961 0.000000e+00 1038.0
28 TraesCS7D01G470100 chr5B 93.651 63 2 2 3099 3159 232782785 232782847 5.100000e-15 93.5
29 TraesCS7D01G470100 chr1D 90.633 790 50 8 4020 4790 424637186 424636402 0.000000e+00 1027.0
30 TraesCS7D01G470100 chr1D 90.050 794 57 10 4012 4790 398854332 398855118 0.000000e+00 1009.0
31 TraesCS7D01G470100 chr1D 79.808 624 69 30 2185 2789 490028046 490027461 7.470000e-108 401.0
32 TraesCS7D01G470100 chr1D 83.908 87 8 2 2866 2946 490027001 490026915 1.430000e-10 78.7
33 TraesCS7D01G470100 chr6B 90.355 788 52 11 4012 4790 239770634 239769862 0.000000e+00 1013.0
34 TraesCS7D01G470100 chr6B 89.539 803 55 22 4011 4790 507481793 507480997 0.000000e+00 990.0
35 TraesCS7D01G470100 chr6B 95.000 60 3 0 3099 3158 620179998 620179939 1.420000e-15 95.3
36 TraesCS7D01G470100 chr2A 80.793 656 72 29 2052 2668 761251263 761250623 9.390000e-127 464.0
37 TraesCS7D01G470100 chr2A 80.992 484 60 26 3186 3647 761249933 761249460 5.900000e-94 355.0
38 TraesCS7D01G470100 chr2A 79.043 439 37 17 3171 3597 769498266 769498661 2.860000e-62 250.0
39 TraesCS7D01G470100 chr2A 82.594 293 15 10 1158 1450 761252022 761251766 4.820000e-55 226.0
40 TraesCS7D01G470100 chr4D 90.000 340 15 8 4012 4332 455529867 455529528 5.730000e-114 422.0
41 TraesCS7D01G470100 chr4D 93.548 62 3 1 3099 3159 210459829 210459768 1.840000e-14 91.6
42 TraesCS7D01G470100 chr1A 80.800 500 76 12 2297 2789 588289868 588290354 1.630000e-99 374.0
43 TraesCS7D01G470100 chr1B 80.288 416 31 20 2157 2536 42582857 42583257 2.840000e-67 267.0
44 TraesCS7D01G470100 chr1B 95.000 60 3 0 3096 3155 586290498 586290557 1.420000e-15 95.3
45 TraesCS7D01G470100 chr1B 90.909 66 5 1 3099 3163 448298803 448298738 2.370000e-13 87.9
46 TraesCS7D01G470100 chr5D 95.161 62 1 2 3099 3159 256469526 256469586 3.950000e-16 97.1
47 TraesCS7D01G470100 chr3B 93.548 62 3 1 3099 3159 156865664 156865603 1.840000e-14 91.6
48 TraesCS7D01G470100 chr3A 91.935 62 3 2 3099 3159 676215555 676215615 8.540000e-13 86.1


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 TraesCS7D01G470100 chr7D 583105356 583110145 4789 True 8846.000000 8846 100.000000 1 4790 1 chr7D.!!$R1 4789
1 TraesCS7D01G470100 chr7B 650664864 650668836 3972 True 1688.000000 3426 90.193333 7 4000 3 chr7B.!!$R1 3993
2 TraesCS7D01G470100 chr7A 674873562 674878368 4806 True 801.000000 1738 90.886000 7 3999 6 chr7A.!!$R1 3992
3 TraesCS7D01G470100 chr3D 515975670 515976473 803 False 1088.000000 1088 91.460000 4002 4790 1 chr3D.!!$F1 788
4 TraesCS7D01G470100 chr3D 429785481 429786278 797 True 1026.000000 1026 90.238000 4010 4790 1 chr3D.!!$R1 780
5 TraesCS7D01G470100 chr2D 644013197 644013989 792 False 1066.000000 1066 91.310000 4015 4790 1 chr2D.!!$F1 775
6 TraesCS7D01G470100 chr2D 56633726 56634534 808 True 1051.000000 1051 90.729000 4012 4790 1 chr2D.!!$R1 778
7 TraesCS7D01G470100 chr2D 635946321 635949566 3245 False 347.666667 429 80.283000 1158 3477 3 chr2D.!!$F2 2319
8 TraesCS7D01G470100 chr2D 644361795 644363089 1294 False 301.500000 462 83.088500 2167 3597 2 chr2D.!!$F3 1430
9 TraesCS7D01G470100 chr2B 742784203 742784996 793 True 1040.000000 1040 90.738000 4015 4790 1 chr2B.!!$R1 775
10 TraesCS7D01G470100 chr2B 794045775 794048745 2970 False 345.250000 534 84.544500 1158 3648 4 chr2B.!!$F2 2490
11 TraesCS7D01G470100 chr5B 615399214 615399961 747 False 1038.000000 1038 91.877000 4048 4790 1 chr5B.!!$F2 742
12 TraesCS7D01G470100 chr1D 424636402 424637186 784 True 1027.000000 1027 90.633000 4020 4790 1 chr1D.!!$R1 770
13 TraesCS7D01G470100 chr1D 398854332 398855118 786 False 1009.000000 1009 90.050000 4012 4790 1 chr1D.!!$F1 778
14 TraesCS7D01G470100 chr1D 490026915 490028046 1131 True 239.850000 401 81.858000 2185 2946 2 chr1D.!!$R2 761
15 TraesCS7D01G470100 chr6B 239769862 239770634 772 True 1013.000000 1013 90.355000 4012 4790 1 chr6B.!!$R1 778
16 TraesCS7D01G470100 chr6B 507480997 507481793 796 True 990.000000 990 89.539000 4011 4790 1 chr6B.!!$R2 779
17 TraesCS7D01G470100 chr2A 761249460 761252022 2562 True 348.333333 464 81.459667 1158 3647 3 chr2A.!!$R1 2489

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
638 740 0.108424 CTTTCGAGAGACTGGGCTGG 60.108 60.0 0.0 0.0 41.84 4.85 F
1127 1579 0.038310 TTGGCGGACAGAGAGAGAGA 59.962 55.0 0.0 0.0 0.00 3.10 F
1515 2317 0.249657 ATCTCTTCCATTCCGCTCGC 60.250 55.0 0.0 0.0 0.00 5.03 F
2900 5403 0.392729 AGCTGCCAGAATGCACTCTC 60.393 55.0 0.0 0.0 36.04 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1462 1927 0.191314 CTAGGTTAGGGAGGGGGAGG 59.809 65.0 0.00 0.00 0.00 4.30 R
3114 5638 0.185901 GGAATGGGCTAGGCAATCCA 59.814 55.0 19.14 7.03 33.74 3.41 R
3115 5639 0.185901 TGGAATGGGCTAGGCAATCC 59.814 55.0 19.14 20.00 0.00 3.01 R
4670 7546 0.250234 CCTGGATCAGAAGCCGTTCA 59.750 55.0 0.00 0.00 34.82 3.18 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
72 75 1.792949 GACAAATCGTGACTGTCGCTT 59.207 47.619 18.17 5.07 30.96 4.68
151 154 1.226974 CCTATGCTGACGTGGACGG 60.227 63.158 0.00 0.00 44.95 4.79
174 177 0.456221 CGAGGGCACGACTAGACAAT 59.544 55.000 0.00 0.00 35.09 2.71
207 210 7.556996 CACCAAGTAGTGTAGATAGTCTAGGTT 59.443 40.741 0.00 0.00 32.89 3.50
297 305 6.677913 ACATATAAAGCGACATATTTTGGCC 58.322 36.000 0.00 0.00 0.00 5.36
298 306 2.559998 AAAGCGACATATTTTGGCCG 57.440 45.000 0.00 0.00 0.00 6.13
301 309 1.132262 AGCGACATATTTTGGCCGTTG 59.868 47.619 0.00 0.00 0.00 4.10
375 384 1.597663 CGAGCTTAAATTGCCCCTACG 59.402 52.381 0.00 0.00 0.00 3.51
426 436 9.509855 GATATGAATGTCGTATTATGGAGACTC 57.490 37.037 0.00 0.00 34.92 3.36
428 438 8.637196 ATGAATGTCGTATTATGGAGACTCTA 57.363 34.615 1.74 0.00 34.92 2.43
430 440 8.515414 TGAATGTCGTATTATGGAGACTCTATG 58.485 37.037 11.35 0.00 34.92 2.23
436 446 6.923508 CGTATTATGGAGACTCTATGTTTGCA 59.076 38.462 11.35 0.00 35.76 4.08
443 453 5.874810 GGAGACTCTATGTTTGCATACAACA 59.125 40.000 14.07 9.42 34.87 3.33
444 454 6.036517 GGAGACTCTATGTTTGCATACAACAG 59.963 42.308 14.07 13.38 34.87 3.16
456 466 3.649073 CATACAACAGTCACGACCTTCA 58.351 45.455 0.00 0.00 0.00 3.02
464 474 4.162320 ACAGTCACGACCTTCATATCCATT 59.838 41.667 0.00 0.00 0.00 3.16
465 475 4.747108 CAGTCACGACCTTCATATCCATTC 59.253 45.833 0.00 0.00 0.00 2.67
486 496 1.080501 CGGATGACGATCCCCGATG 60.081 63.158 0.00 0.00 45.12 3.84
487 497 1.806461 CGGATGACGATCCCCGATGT 61.806 60.000 0.00 0.00 45.12 3.06
498 508 1.313091 CCCCGATGTGACGACTCTGA 61.313 60.000 0.00 0.00 35.09 3.27
500 510 1.067846 CCCGATGTGACGACTCTGAAA 60.068 52.381 0.00 0.00 35.09 2.69
509 519 2.476997 GACGACTCTGAAAAGTTGCTCC 59.523 50.000 0.00 0.00 34.50 4.70
510 520 1.801178 CGACTCTGAAAAGTTGCTCCC 59.199 52.381 0.00 0.00 0.00 4.30
512 522 3.214328 GACTCTGAAAAGTTGCTCCCAA 58.786 45.455 0.00 0.00 0.00 4.12
524 534 6.260700 AGTTGCTCCCAATTATACCATGTA 57.739 37.500 0.00 0.00 32.75 2.29
525 535 6.299141 AGTTGCTCCCAATTATACCATGTAG 58.701 40.000 0.00 0.00 32.75 2.74
526 536 6.101150 AGTTGCTCCCAATTATACCATGTAGA 59.899 38.462 0.00 0.00 32.75 2.59
527 537 5.865085 TGCTCCCAATTATACCATGTAGAC 58.135 41.667 0.00 0.00 0.00 2.59
528 538 5.368230 TGCTCCCAATTATACCATGTAGACA 59.632 40.000 0.00 0.00 0.00 3.41
529 539 6.126623 TGCTCCCAATTATACCATGTAGACAA 60.127 38.462 0.00 0.00 0.00 3.18
530 540 6.942576 GCTCCCAATTATACCATGTAGACAAT 59.057 38.462 0.00 0.00 0.00 2.71
531 541 7.448469 GCTCCCAATTATACCATGTAGACAATT 59.552 37.037 0.00 0.00 0.00 2.32
532 542 9.354673 CTCCCAATTATACCATGTAGACAATTT 57.645 33.333 0.00 0.00 0.00 1.82
565 657 4.782019 AACACAACACAGACACAAACAT 57.218 36.364 0.00 0.00 0.00 2.71
572 674 6.540551 ACAACACAGACACAAACATGTACATA 59.459 34.615 8.32 0.00 31.24 2.29
579 681 7.746034 CAGACACAAACATGTACATACATTCAC 59.254 37.037 8.32 0.00 43.99 3.18
588 690 9.109393 ACATGTACATACATTCACTCCATTAAC 57.891 33.333 8.32 0.00 43.99 2.01
607 709 1.545759 CGTACACACGCACATCCTAG 58.454 55.000 0.00 0.00 42.05 3.02
608 710 1.278238 GTACACACGCACATCCTAGC 58.722 55.000 0.00 0.00 0.00 3.42
609 711 1.135083 GTACACACGCACATCCTAGCT 60.135 52.381 0.00 0.00 0.00 3.32
614 716 3.922850 CACACGCACATCCTAGCTATATG 59.077 47.826 12.44 12.44 0.00 1.78
616 718 4.464244 ACACGCACATCCTAGCTATATGAT 59.536 41.667 18.35 8.42 0.00 2.45
619 721 5.039984 CGCACATCCTAGCTATATGATCAC 58.960 45.833 18.35 7.40 0.00 3.06
633 735 3.857549 TGATCACTTTCGAGAGACTGG 57.142 47.619 10.37 0.00 41.84 4.00
636 738 0.605589 CACTTTCGAGAGACTGGGCT 59.394 55.000 10.37 0.00 41.84 5.19
637 739 0.605589 ACTTTCGAGAGACTGGGCTG 59.394 55.000 10.37 0.00 41.84 4.85
638 740 0.108424 CTTTCGAGAGACTGGGCTGG 60.108 60.000 0.00 0.00 41.84 4.85
639 741 0.832135 TTTCGAGAGACTGGGCTGGT 60.832 55.000 0.00 0.00 41.84 4.00
640 742 1.536073 TTCGAGAGACTGGGCTGGTG 61.536 60.000 0.00 0.00 41.84 4.17
649 751 1.152567 TGGGCTGGTGGGTTTTGAG 60.153 57.895 0.00 0.00 0.00 3.02
672 774 3.914984 ACGAAGTCATCACAGGTGG 57.085 52.632 0.00 0.00 29.74 4.61
676 778 1.002430 GAAGTCATCACAGGTGGCTCA 59.998 52.381 0.00 0.00 29.81 4.26
677 779 0.322975 AGTCATCACAGGTGGCTCAC 59.677 55.000 0.00 0.00 0.00 3.51
692 1095 3.264193 TGGCTCACTGTTGATAGGAACAT 59.736 43.478 0.00 0.00 35.32 2.71
704 1107 1.187087 AGGAACATCGACTCCCACTC 58.813 55.000 6.44 0.00 31.50 3.51
711 1114 2.814280 TCGACTCCCACTCAAAGAAC 57.186 50.000 0.00 0.00 0.00 3.01
738 1141 1.485019 CCCCTATGGCCCTATCAGACA 60.485 57.143 0.00 0.00 0.00 3.41
739 1142 1.625818 CCCTATGGCCCTATCAGACAC 59.374 57.143 0.00 0.00 0.00 3.67
792 1237 7.904977 CACATGTTGGTTCTCGACAAATAATAG 59.095 37.037 0.00 0.00 42.57 1.73
802 1247 4.741185 TCGACAAATAATAGTGCGCGTTAT 59.259 37.500 8.43 0.00 0.00 1.89
892 1337 3.906998 TGTCAAATTTTGTGTATGCGGG 58.093 40.909 8.89 0.00 0.00 6.13
985 1430 5.159925 GTCTTTCTTCCTCGGTTACTACAC 58.840 45.833 0.00 0.00 0.00 2.90
1073 1525 1.128188 AGTCTTCCTCCACACCCCAC 61.128 60.000 0.00 0.00 0.00 4.61
1084 1536 4.980476 ACCCCACCCCACCCCATT 62.980 66.667 0.00 0.00 0.00 3.16
1085 1537 4.074408 CCCCACCCCACCCCATTC 62.074 72.222 0.00 0.00 0.00 2.67
1087 1539 4.440829 CCACCCCACCCCATTCCG 62.441 72.222 0.00 0.00 0.00 4.30
1088 1540 4.440829 CACCCCACCCCATTCCGG 62.441 72.222 0.00 0.00 0.00 5.14
1089 1541 4.686437 ACCCCACCCCATTCCGGA 62.686 66.667 0.00 0.00 36.56 5.14
1090 1542 4.123545 CCCCACCCCATTCCGGAC 62.124 72.222 1.83 0.00 36.56 4.79
1100 1552 3.268647 ATTCCGGACCCCCACTCCT 62.269 63.158 1.83 0.00 0.00 3.69
1125 1577 2.092375 TCTATTGGCGGACAGAGAGAGA 60.092 50.000 0.00 0.00 0.00 3.10
1126 1578 1.110442 ATTGGCGGACAGAGAGAGAG 58.890 55.000 0.00 0.00 0.00 3.20
1127 1579 0.038310 TTGGCGGACAGAGAGAGAGA 59.962 55.000 0.00 0.00 0.00 3.10
1142 1595 2.041928 AGAGAGGCCAAGGAGGGG 59.958 66.667 5.01 0.00 38.09 4.79
1456 1921 2.711978 AAAGTAAATCGCCTCCCCTC 57.288 50.000 0.00 0.00 0.00 4.30
1459 1924 0.393448 GTAAATCGCCTCCCCTCCTC 59.607 60.000 0.00 0.00 0.00 3.71
1460 1925 0.763223 TAAATCGCCTCCCCTCCTCC 60.763 60.000 0.00 0.00 0.00 4.30
1461 1926 4.565850 ATCGCCTCCCCTCCTCCC 62.566 72.222 0.00 0.00 0.00 4.30
1509 2311 7.177568 TGCTATGTAGTAGATCTCTTCCATTCC 59.822 40.741 0.00 0.00 31.71 3.01
1515 2317 0.249657 ATCTCTTCCATTCCGCTCGC 60.250 55.000 0.00 0.00 0.00 5.03
1534 2336 2.032204 CGCTTCTCTCTTGCATTATGCC 60.032 50.000 15.06 0.00 44.23 4.40
1536 2338 3.003482 GCTTCTCTCTTGCATTATGCCTG 59.997 47.826 15.06 7.40 44.23 4.85
1539 2341 0.672342 CTCTTGCATTATGCCTGCCC 59.328 55.000 15.06 0.00 44.23 5.36
1541 2343 1.379710 TTGCATTATGCCTGCCCGT 60.380 52.632 15.06 0.00 44.23 5.28
1564 2372 2.564771 TGGATCTGCCATGATTCGTTC 58.435 47.619 0.00 0.00 43.33 3.95
1570 2378 3.369756 TCTGCCATGATTCGTTCGTTAAC 59.630 43.478 0.00 0.00 0.00 2.01
1571 2379 2.417239 TGCCATGATTCGTTCGTTAACC 59.583 45.455 0.00 0.00 31.46 2.85
1706 2562 5.131142 TGCTTTTCCCCTTCCATTTTTAACA 59.869 36.000 0.00 0.00 0.00 2.41
1713 2569 5.066505 CCCCTTCCATTTTTAACATCTCTCG 59.933 44.000 0.00 0.00 0.00 4.04
1752 2629 1.003652 GCATTGCACTGTTTTTGCCAC 60.004 47.619 3.15 0.00 39.39 5.01
1841 2718 7.217200 CCTGGAGATTTCATCGAGGTAATAAA 58.783 38.462 1.80 0.00 37.75 1.40
1842 2719 7.880195 CCTGGAGATTTCATCGAGGTAATAAAT 59.120 37.037 1.80 0.00 37.75 1.40
1915 3163 4.670606 GCAAAGGCGATGCTAACG 57.329 55.556 9.81 0.00 40.64 3.18
2031 3945 3.437741 TCAGATGCATGCAAAGTACTGTG 59.562 43.478 26.68 15.57 0.00 3.66
2039 3953 5.344128 GCATGCAAAGTACTGTGATTCTTTG 59.656 40.000 17.66 6.29 45.13 2.77
2105 4098 6.682423 TGGCCAAATATATATCAAGATGCG 57.318 37.500 0.61 0.00 0.00 4.73
2521 4578 2.981784 CCATCCCATCCCTGTTATCTGA 59.018 50.000 0.00 0.00 0.00 3.27
2662 4722 3.374058 GGTAAGTGAACACATCCATTCCG 59.626 47.826 7.68 0.00 0.00 4.30
2701 4917 8.264347 TCCTCTTGTACATGCATTATAACTGAA 58.736 33.333 0.00 0.00 0.00 3.02
2712 4930 6.321848 CATTATAACTGAATGCTCATGCCA 57.678 37.500 0.00 0.00 38.71 4.92
2764 5258 4.912766 GTCGACGAAATCTGATATCAGTCC 59.087 45.833 27.80 15.83 44.12 3.85
2832 5334 5.710513 TTGCATGGCCATAATAGTCATTC 57.289 39.130 20.30 0.00 0.00 2.67
2868 5371 5.807520 ACGTAGAAGTAGAATGCAGTCAATG 59.192 40.000 17.53 1.08 0.00 2.82
2900 5403 0.392729 AGCTGCCAGAATGCACTCTC 60.393 55.000 0.00 0.00 36.04 3.20
2940 5447 5.106317 TGCAGTTGCTTTACTATGGCTTTAC 60.106 40.000 5.62 0.00 42.66 2.01
3081 5605 6.756542 GCCCAAATATGTTTTTAGTTGCTAGG 59.243 38.462 0.00 0.00 0.00 3.02
3094 5618 4.309933 AGTTGCTAGGAAAATTTGCTTGC 58.690 39.130 21.76 21.76 46.43 4.01
3098 5622 6.284891 TGCTAGGAAAATTTGCTTGCTTAT 57.715 33.333 26.28 0.00 46.40 1.73
3099 5623 6.101332 TGCTAGGAAAATTTGCTTGCTTATG 58.899 36.000 26.28 4.44 46.40 1.90
3102 5626 6.790285 AGGAAAATTTGCTTGCTTATGTTG 57.210 33.333 0.00 0.00 0.00 3.33
3103 5627 6.523840 AGGAAAATTTGCTTGCTTATGTTGA 58.476 32.000 0.00 0.00 0.00 3.18
3104 5628 6.991531 AGGAAAATTTGCTTGCTTATGTTGAA 59.008 30.769 0.00 0.00 0.00 2.69
3107 5631 8.885494 AAAATTTGCTTGCTTATGTTGAAGTA 57.115 26.923 0.00 0.00 0.00 2.24
3114 5638 9.559732 TGCTTGCTTATGTTGAAGTATATATGT 57.440 29.630 0.00 0.00 0.00 2.29
3115 5639 9.817365 GCTTGCTTATGTTGAAGTATATATGTG 57.183 33.333 0.00 0.00 0.00 3.21
3123 5647 7.517320 TGTTGAAGTATATATGTGGATTGCCT 58.483 34.615 0.00 0.00 34.31 4.75
3126 5650 7.331026 TGAAGTATATATGTGGATTGCCTAGC 58.669 38.462 0.00 0.00 34.31 3.42
3127 5651 6.240549 AGTATATATGTGGATTGCCTAGCC 57.759 41.667 0.00 0.00 34.31 3.93
3128 5652 2.887151 ATATGTGGATTGCCTAGCCC 57.113 50.000 0.00 0.00 34.31 5.19
3129 5653 1.517238 TATGTGGATTGCCTAGCCCA 58.483 50.000 0.00 0.00 34.31 5.36
3130 5654 0.855598 ATGTGGATTGCCTAGCCCAT 59.144 50.000 0.00 0.00 34.31 4.00
3131 5655 0.630673 TGTGGATTGCCTAGCCCATT 59.369 50.000 0.00 0.00 34.31 3.16
3132 5656 1.322442 GTGGATTGCCTAGCCCATTC 58.678 55.000 0.00 0.00 34.31 2.67
3133 5657 0.185901 TGGATTGCCTAGCCCATTCC 59.814 55.000 12.21 12.21 34.76 3.01
3134 5658 0.185901 GGATTGCCTAGCCCATTCCA 59.814 55.000 13.40 0.00 34.48 3.53
3135 5659 1.203100 GGATTGCCTAGCCCATTCCAT 60.203 52.381 13.40 0.00 34.48 3.41
3136 5660 2.165998 GATTGCCTAGCCCATTCCATC 58.834 52.381 0.00 0.00 0.00 3.51
3137 5661 0.925558 TTGCCTAGCCCATTCCATCA 59.074 50.000 0.00 0.00 0.00 3.07
3138 5662 0.475475 TGCCTAGCCCATTCCATCAG 59.525 55.000 0.00 0.00 0.00 2.90
3139 5663 0.475906 GCCTAGCCCATTCCATCAGT 59.524 55.000 0.00 0.00 0.00 3.41
3140 5664 1.133668 GCCTAGCCCATTCCATCAGTT 60.134 52.381 0.00 0.00 0.00 3.16
3141 5665 2.856222 CCTAGCCCATTCCATCAGTTC 58.144 52.381 0.00 0.00 0.00 3.01
3142 5666 2.173356 CCTAGCCCATTCCATCAGTTCA 59.827 50.000 0.00 0.00 0.00 3.18
3143 5667 2.431954 AGCCCATTCCATCAGTTCAG 57.568 50.000 0.00 0.00 0.00 3.02
3144 5668 1.918262 AGCCCATTCCATCAGTTCAGA 59.082 47.619 0.00 0.00 0.00 3.27
3145 5669 2.019984 GCCCATTCCATCAGTTCAGAC 58.980 52.381 0.00 0.00 0.00 3.51
3146 5670 2.356535 GCCCATTCCATCAGTTCAGACT 60.357 50.000 0.00 0.00 36.25 3.24
3147 5671 3.875369 GCCCATTCCATCAGTTCAGACTT 60.875 47.826 0.00 0.00 32.54 3.01
3148 5672 4.338879 CCCATTCCATCAGTTCAGACTTT 58.661 43.478 0.00 0.00 32.54 2.66
3149 5673 4.768968 CCCATTCCATCAGTTCAGACTTTT 59.231 41.667 0.00 0.00 32.54 2.27
3150 5674 5.336213 CCCATTCCATCAGTTCAGACTTTTG 60.336 44.000 0.00 0.00 32.54 2.44
3151 5675 5.336213 CCATTCCATCAGTTCAGACTTTTGG 60.336 44.000 0.00 0.00 36.98 3.28
3152 5676 4.437682 TCCATCAGTTCAGACTTTTGGT 57.562 40.909 0.00 0.00 36.97 3.67
3153 5677 4.792068 TCCATCAGTTCAGACTTTTGGTT 58.208 39.130 0.00 0.00 36.97 3.67
3154 5678 4.580167 TCCATCAGTTCAGACTTTTGGTTG 59.420 41.667 0.00 0.00 36.97 3.77
3155 5679 4.293415 CATCAGTTCAGACTTTTGGTTGC 58.707 43.478 0.00 0.00 32.54 4.17
3156 5680 3.620488 TCAGTTCAGACTTTTGGTTGCT 58.380 40.909 0.00 0.00 32.54 3.91
3157 5681 4.016444 TCAGTTCAGACTTTTGGTTGCTT 58.984 39.130 0.00 0.00 32.54 3.91
3158 5682 4.107622 CAGTTCAGACTTTTGGTTGCTTG 58.892 43.478 0.00 0.00 32.54 4.01
3159 5683 3.763897 AGTTCAGACTTTTGGTTGCTTGT 59.236 39.130 0.00 0.00 29.87 3.16
3160 5684 4.220602 AGTTCAGACTTTTGGTTGCTTGTT 59.779 37.500 0.00 0.00 29.87 2.83
3161 5685 4.799564 TCAGACTTTTGGTTGCTTGTTT 57.200 36.364 0.00 0.00 0.00 2.83
3162 5686 5.906113 TCAGACTTTTGGTTGCTTGTTTA 57.094 34.783 0.00 0.00 0.00 2.01
3163 5687 6.463995 TCAGACTTTTGGTTGCTTGTTTAT 57.536 33.333 0.00 0.00 0.00 1.40
3164 5688 6.272318 TCAGACTTTTGGTTGCTTGTTTATG 58.728 36.000 0.00 0.00 0.00 1.90
3245 5805 7.097834 ACTAGTACTAACCATTGTGAAGCTTC 58.902 38.462 19.89 19.89 0.00 3.86
3480 6229 2.410730 GCACGTTGTATGTGTAGTGACC 59.589 50.000 0.00 0.00 37.43 4.02
3501 6250 3.118223 CCTAATCCTGGGGAGAACTGAAC 60.118 52.174 0.00 0.00 34.05 3.18
3617 6387 5.279859 GGTTGCACCTTCTAGTAACCTTAGT 60.280 44.000 0.00 0.00 44.11 2.24
3622 6393 6.517864 GCACCTTCTAGTAACCTTAGTTGTCA 60.518 42.308 0.00 0.00 36.68 3.58
3667 6447 0.892755 CCATGCACTTGGCTGTCAAT 59.107 50.000 0.00 0.00 45.15 2.57
3668 6448 1.135199 CCATGCACTTGGCTGTCAATC 60.135 52.381 0.00 0.00 45.15 2.67
3673 6453 3.118847 TGCACTTGGCTGTCAATCAAAAA 60.119 39.130 0.00 0.00 45.15 1.94
3735 6535 2.086094 TGCTGTGTGGTGCAGATTATG 58.914 47.619 0.00 0.00 36.12 1.90
3737 6537 2.489329 GCTGTGTGGTGCAGATTATGTT 59.511 45.455 0.00 0.00 36.12 2.71
3741 6541 4.002982 GTGTGGTGCAGATTATGTTCTGA 58.997 43.478 10.08 0.00 44.88 3.27
3759 6559 8.408043 TGTTCTGATATCATTTTTGTCCACTT 57.592 30.769 5.72 0.00 0.00 3.16
3818 6645 5.133221 AGGCTACAACTGTGTTGATTTTCT 58.867 37.500 16.04 5.31 39.30 2.52
3849 6677 0.608308 GTAGCAAACCGGGCTTTCCT 60.608 55.000 6.32 0.00 42.62 3.36
3872 6700 4.273969 TGTGAACCGTTCAGACATAAAACC 59.726 41.667 14.35 0.00 41.01 3.27
3901 6730 3.670055 CACTGTCACATGGCGAATTTTTC 59.330 43.478 0.00 0.00 0.00 2.29
3902 6731 3.317711 ACTGTCACATGGCGAATTTTTCA 59.682 39.130 0.00 0.00 0.00 2.69
4000 6830 3.817084 TCATCTGTTTGCTTCAAGGACAG 59.183 43.478 5.48 5.48 35.05 3.51
4001 6831 2.575532 TCTGTTTGCTTCAAGGACAGG 58.424 47.619 9.95 0.00 34.71 4.00
4002 6832 1.000938 CTGTTTGCTTCAAGGACAGGC 60.001 52.381 4.36 0.00 32.06 4.85
4003 6833 1.032014 GTTTGCTTCAAGGACAGGCA 58.968 50.000 0.00 0.00 0.00 4.75
4004 6834 1.000938 GTTTGCTTCAAGGACAGGCAG 60.001 52.381 0.00 0.00 34.37 4.85
4005 6835 0.473755 TTGCTTCAAGGACAGGCAGA 59.526 50.000 0.00 0.00 34.37 4.26
4006 6836 0.473755 TGCTTCAAGGACAGGCAGAA 59.526 50.000 0.00 0.00 0.00 3.02
4007 6837 1.074405 TGCTTCAAGGACAGGCAGAAT 59.926 47.619 0.00 0.00 0.00 2.40
4008 6838 2.165998 GCTTCAAGGACAGGCAGAATT 58.834 47.619 0.00 0.00 0.00 2.17
4018 6848 4.144297 GACAGGCAGAATTAATATGGGCA 58.856 43.478 8.67 0.00 0.00 5.36
4085 6924 1.304381 TTTGAGGGGATGCAGGCAC 60.304 57.895 0.00 0.00 0.00 5.01
4102 6941 1.843368 CACAAAGACCCCAGATGCAT 58.157 50.000 0.00 0.00 0.00 3.96
4155 6996 1.691434 TGAGCAACCATTTTTGACCCC 59.309 47.619 0.00 0.00 0.00 4.95
4166 7007 1.104630 TTTGACCCCACGTTTGGTTC 58.895 50.000 7.17 0.00 42.10 3.62
4207 7053 6.678655 GCGCATATATGATATGGTGTTGCAAT 60.679 38.462 17.10 0.00 0.00 3.56
4227 7073 3.769739 TCTGCATAAGGTGTTGTCACT 57.230 42.857 0.00 0.00 43.41 3.41
4361 7211 4.672899 GCCATTGGCTAAATAGGGGATAA 58.327 43.478 20.66 0.00 46.69 1.75
4365 7215 6.095440 CCATTGGCTAAATAGGGGATAATTCG 59.905 42.308 0.00 0.00 0.00 3.34
4370 7220 3.975168 AATAGGGGATAATTCGTCGGG 57.025 47.619 0.00 0.00 0.00 5.14
4390 7240 2.170607 GGGTTGCTGCTACCAGATCTTA 59.829 50.000 29.25 0.00 41.77 2.10
4414 7277 4.092279 TCTTCATCTTCCTCTGCTTCTGA 58.908 43.478 0.00 0.00 0.00 3.27
4422 7285 1.679336 CCTCTGCTTCTGATGCTGCTT 60.679 52.381 15.38 0.00 0.00 3.91
4432 7307 4.649692 TCTGATGCTGCTTCTTCTTCTTT 58.350 39.130 15.38 0.00 0.00 2.52
4534 7410 3.194116 GTCATTGTCAAATGCCTCCACAT 59.806 43.478 0.00 0.00 42.55 3.21
4611 7487 2.231380 ATCAAAGCCCCACCGGAGT 61.231 57.895 9.46 0.00 0.00 3.85
4670 7546 2.344093 ACCTGAGTGGAGTATGGGTT 57.656 50.000 0.00 0.00 39.71 4.11
4674 7550 3.600388 CTGAGTGGAGTATGGGTTGAAC 58.400 50.000 0.00 0.00 0.00 3.18
4699 7576 5.431765 GCTTCTGATCCAGGATCTTAAACA 58.568 41.667 26.94 8.32 39.56 2.83
4762 7639 4.213564 AGGCTGGAGTGTTTGAGATTAG 57.786 45.455 0.00 0.00 0.00 1.73
4764 7641 4.472833 AGGCTGGAGTGTTTGAGATTAGAT 59.527 41.667 0.00 0.00 0.00 1.98
4776 7653 3.254411 TGAGATTAGATAGCTCCTGTGCG 59.746 47.826 0.00 0.00 38.13 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.590238 GTACTCACAGATGATGCACGC 59.410 52.381 0.00 0.00 33.22 5.34
2 3 1.848608 CGTACTCACAGATGATGCACG 59.151 52.381 0.00 0.00 33.22 5.34
3 4 2.854777 GTCGTACTCACAGATGATGCAC 59.145 50.000 0.00 0.00 33.22 4.57
4 5 2.159240 GGTCGTACTCACAGATGATGCA 60.159 50.000 0.00 0.00 33.22 3.96
13 14 0.468585 AGTGTGGGGTCGTACTCACA 60.469 55.000 10.05 10.05 37.73 3.58
72 75 1.671166 CATGGTGGTCGGACTCACA 59.329 57.895 22.45 13.70 35.74 3.58
151 154 3.736482 CTAGTCGTGCCCTCGTCGC 62.736 68.421 0.00 0.00 0.00 5.19
155 158 0.456221 ATTGTCTAGTCGTGCCCTCG 59.544 55.000 0.00 0.00 0.00 4.63
162 165 0.172803 GGTCGGCATTGTCTAGTCGT 59.827 55.000 0.00 0.00 0.00 4.34
174 177 1.369692 CACTACTTGGTGGTCGGCA 59.630 57.895 0.00 0.00 33.95 5.69
272 280 7.145323 GGCCAAAATATGTCGCTTTATATGTT 58.855 34.615 0.00 0.00 0.00 2.71
277 285 3.630312 ACGGCCAAAATATGTCGCTTTAT 59.370 39.130 2.24 0.00 0.00 1.40
408 418 7.818997 AACATAGAGTCTCCATAATACGACA 57.181 36.000 0.00 0.00 0.00 4.35
410 420 7.145985 GCAAACATAGAGTCTCCATAATACGA 58.854 38.462 0.00 0.00 0.00 3.43
414 424 8.432013 TGTATGCAAACATAGAGTCTCCATAAT 58.568 33.333 0.00 0.00 39.44 1.28
420 430 6.591834 ACTGTTGTATGCAAACATAGAGTCTC 59.408 38.462 0.00 0.00 39.44 3.36
426 436 5.120053 TCGTGACTGTTGTATGCAAACATAG 59.880 40.000 3.03 0.00 39.44 2.23
428 438 3.812609 TCGTGACTGTTGTATGCAAACAT 59.187 39.130 3.03 0.00 40.49 2.71
430 440 3.541711 GTCGTGACTGTTGTATGCAAAC 58.458 45.455 0.00 0.00 36.22 2.93
436 446 4.537135 ATGAAGGTCGTGACTGTTGTAT 57.463 40.909 0.00 0.00 0.00 2.29
443 453 4.499865 CGAATGGATATGAAGGTCGTGACT 60.500 45.833 0.00 0.00 0.00 3.41
444 454 3.736252 CGAATGGATATGAAGGTCGTGAC 59.264 47.826 0.00 0.00 0.00 3.67
456 466 2.817844 TCGTCATCCGTCGAATGGATAT 59.182 45.455 17.50 0.00 41.94 1.63
486 496 2.866762 AGCAACTTTTCAGAGTCGTCAC 59.133 45.455 0.00 0.00 0.00 3.67
487 497 3.123804 GAGCAACTTTTCAGAGTCGTCA 58.876 45.455 0.00 0.00 0.00 4.35
498 508 6.440328 ACATGGTATAATTGGGAGCAACTTTT 59.560 34.615 0.00 0.00 0.00 2.27
500 510 5.518865 ACATGGTATAATTGGGAGCAACTT 58.481 37.500 0.00 0.00 0.00 2.66
541 633 4.277174 TGTTTGTGTCTGTGTTGTGTTTCT 59.723 37.500 0.00 0.00 0.00 2.52
552 644 7.443879 TGAATGTATGTACATGTTTGTGTCTGT 59.556 33.333 18.81 0.00 45.55 3.41
565 657 7.324935 ACGTTAATGGAGTGAATGTATGTACA 58.675 34.615 0.00 0.00 40.98 2.90
572 674 5.407387 GTGTGTACGTTAATGGAGTGAATGT 59.593 40.000 0.00 0.00 0.00 2.71
602 704 7.168905 TCTCGAAAGTGATCATATAGCTAGGA 58.831 38.462 0.00 0.00 0.00 2.94
603 705 7.335673 TCTCTCGAAAGTGATCATATAGCTAGG 59.664 40.741 0.00 0.00 32.62 3.02
607 709 6.801377 CAGTCTCTCGAAAGTGATCATATAGC 59.199 42.308 0.00 0.00 32.62 2.97
608 710 7.304735 CCAGTCTCTCGAAAGTGATCATATAG 58.695 42.308 0.00 0.00 32.62 1.31
609 711 6.207614 CCCAGTCTCTCGAAAGTGATCATATA 59.792 42.308 0.00 0.00 32.62 0.86
614 716 2.737039 GCCCAGTCTCTCGAAAGTGATC 60.737 54.545 0.00 0.00 32.62 2.92
616 718 0.603569 GCCCAGTCTCTCGAAAGTGA 59.396 55.000 0.00 0.00 0.00 3.41
619 721 0.108424 CCAGCCCAGTCTCTCGAAAG 60.108 60.000 0.00 0.00 0.00 2.62
633 735 1.273327 CAATCTCAAAACCCACCAGCC 59.727 52.381 0.00 0.00 0.00 4.85
636 738 2.158740 TCGTCAATCTCAAAACCCACCA 60.159 45.455 0.00 0.00 0.00 4.17
637 739 2.500229 TCGTCAATCTCAAAACCCACC 58.500 47.619 0.00 0.00 0.00 4.61
638 740 3.564225 ACTTCGTCAATCTCAAAACCCAC 59.436 43.478 0.00 0.00 0.00 4.61
639 741 3.813166 GACTTCGTCAATCTCAAAACCCA 59.187 43.478 0.00 0.00 32.09 4.51
640 742 3.813166 TGACTTCGTCAATCTCAAAACCC 59.187 43.478 0.00 0.00 39.78 4.11
649 751 3.369147 CACCTGTGATGACTTCGTCAATC 59.631 47.826 2.65 1.32 45.96 2.67
672 774 3.553511 CGATGTTCCTATCAACAGTGAGC 59.446 47.826 0.00 0.00 39.63 4.26
676 778 4.142138 GGAGTCGATGTTCCTATCAACAGT 60.142 45.833 6.38 0.00 39.63 3.55
677 779 4.363999 GGAGTCGATGTTCCTATCAACAG 58.636 47.826 6.38 0.00 39.63 3.16
692 1095 2.036387 TGTTCTTTGAGTGGGAGTCGA 58.964 47.619 0.00 0.00 0.00 4.20
704 1107 2.122783 TAGGGGCGGAATGTTCTTTG 57.877 50.000 0.00 0.00 0.00 2.77
738 1141 2.831526 ACCACTTGTTTGAAGCTTTGGT 59.168 40.909 8.97 8.97 0.00 3.67
739 1142 3.525268 ACCACTTGTTTGAAGCTTTGG 57.475 42.857 0.00 4.02 0.00 3.28
792 1237 1.060122 GTCAACTGGTATAACGCGCAC 59.940 52.381 5.73 0.00 0.00 5.34
802 1247 8.232412 AGGGATAGTATATTGAGTCAACTGGTA 58.768 37.037 7.96 0.00 0.00 3.25
892 1337 1.685148 GGAAATGACAGATCTGCCCC 58.315 55.000 22.83 12.32 0.00 5.80
900 1345 2.844348 GGTTAGGGAGGGAAATGACAGA 59.156 50.000 0.00 0.00 0.00 3.41
902 1347 1.920351 GGGTTAGGGAGGGAAATGACA 59.080 52.381 0.00 0.00 0.00 3.58
985 1430 4.722700 CACCTTGGCCTCCACCGG 62.723 72.222 3.32 0.00 30.78 5.28
1049 1501 0.321122 GTGTGGAGGAAGACTGGCTG 60.321 60.000 0.00 0.00 0.00 4.85
1073 1525 4.123545 GTCCGGAATGGGGTGGGG 62.124 72.222 5.23 0.00 38.76 4.96
1080 1532 3.015145 AGTGGGGGTCCGGAATGG 61.015 66.667 5.23 0.00 40.09 3.16
1082 1534 2.691252 GGAGTGGGGGTCCGGAAT 60.691 66.667 5.23 0.00 35.24 3.01
1083 1535 3.918328 GAGGAGTGGGGGTCCGGAA 62.918 68.421 5.23 0.00 39.30 4.30
1084 1536 4.393778 GAGGAGTGGGGGTCCGGA 62.394 72.222 0.00 0.00 39.30 5.14
1087 1539 4.026357 AGGGAGGAGTGGGGGTCC 62.026 72.222 0.00 0.00 0.00 4.46
1088 1540 1.591280 TAGAGGGAGGAGTGGGGGTC 61.591 65.000 0.00 0.00 0.00 4.46
1089 1541 0.936863 ATAGAGGGAGGAGTGGGGGT 60.937 60.000 0.00 0.00 0.00 4.95
1090 1542 0.269173 AATAGAGGGAGGAGTGGGGG 59.731 60.000 0.00 0.00 0.00 5.40
1100 1552 0.032515 TCTGTCCGCCAATAGAGGGA 60.033 55.000 0.00 0.00 0.00 4.20
1125 1577 2.041928 CCCCTCCTTGGCCTCTCT 59.958 66.667 3.32 0.00 0.00 3.10
1126 1578 2.923852 ATCCCCCTCCTTGGCCTCTC 62.924 65.000 3.32 0.00 0.00 3.20
1127 1579 2.923852 GATCCCCCTCCTTGGCCTCT 62.924 65.000 3.32 0.00 0.00 3.69
1459 1924 3.382864 TTAGGGAGGGGGAGGGGG 61.383 72.222 0.00 0.00 0.00 5.40
1460 1925 2.039724 GTTAGGGAGGGGGAGGGG 60.040 72.222 0.00 0.00 0.00 4.79
1461 1926 1.309502 TAGGTTAGGGAGGGGGAGGG 61.310 65.000 0.00 0.00 0.00 4.30
1462 1927 0.191314 CTAGGTTAGGGAGGGGGAGG 59.809 65.000 0.00 0.00 0.00 4.30
1509 2311 0.805322 ATGCAAGAGAGAAGCGAGCG 60.805 55.000 0.00 0.00 0.00 5.03
1534 2336 1.817099 GCAGATCCAAGACGGGCAG 60.817 63.158 0.00 0.00 34.36 4.85
1536 2338 2.514824 GGCAGATCCAAGACGGGC 60.515 66.667 0.00 0.00 34.36 6.13
1564 2372 3.682377 GCATTCCCCATTTTTGGTTAACG 59.318 43.478 0.00 0.00 0.00 3.18
1570 2378 4.018484 TCAAAGCATTCCCCATTTTTGG 57.982 40.909 0.00 0.00 0.00 3.28
1571 2379 6.578163 AAATCAAAGCATTCCCCATTTTTG 57.422 33.333 0.00 0.00 0.00 2.44
1706 2562 2.762887 TCAGATTGTGAAGCCGAGAGAT 59.237 45.455 0.00 0.00 29.64 2.75
1752 2629 5.484173 TGCCGCAATTCTGTAATAAGAAG 57.516 39.130 0.00 0.00 39.47 2.85
1915 3163 1.832167 TGGGTGGAAGCAAGGCAAC 60.832 57.895 0.00 0.00 34.77 4.17
2031 3945 4.925646 GCAGGGTGAACAAATCAAAGAATC 59.074 41.667 0.00 0.00 40.50 2.52
2039 3953 1.463674 ATCGGCAGGGTGAACAAATC 58.536 50.000 0.00 0.00 0.00 2.17
2105 4098 7.001099 TCCGGATTTAGGGAGAATGTATAAC 57.999 40.000 0.00 0.00 0.00 1.89
2242 4246 2.299582 CAACAAACCATGGCTTCCATCA 59.700 45.455 13.04 0.00 43.15 3.07
2521 4578 2.304221 TGATCCGGGAATAGGTCGAT 57.696 50.000 0.00 0.00 0.00 3.59
2701 4917 4.383931 AGGATAATCTTGGCATGAGCAT 57.616 40.909 9.09 4.55 44.61 3.79
2832 5334 6.769076 TCTACTTCTACGTTGTTACAGATCG 58.231 40.000 0.00 5.50 0.00 3.69
2868 5371 0.665369 GGCAGCTCAAACACATGTGC 60.665 55.000 25.68 10.61 39.47 4.57
2900 5403 4.494350 ACTGCAACTGAGCAAATACTTG 57.506 40.909 0.00 0.00 45.13 3.16
2940 5447 5.998454 ATAGCACAAGATTTCCTCAATCG 57.002 39.130 0.00 0.00 45.53 3.34
3003 5525 2.487762 TCACGGAAAATGCATCTCCAAC 59.512 45.455 21.63 3.20 0.00 3.77
3012 5534 4.980590 TGTATGTTCATCACGGAAAATGC 58.019 39.130 0.00 0.00 30.44 3.56
3081 5605 7.854534 ACTTCAACATAAGCAAGCAAATTTTC 58.145 30.769 0.00 0.00 0.00 2.29
3098 5622 7.517320 AGGCAATCCACATATATACTTCAACA 58.483 34.615 0.00 0.00 33.74 3.33
3099 5623 7.986085 AGGCAATCCACATATATACTTCAAC 57.014 36.000 0.00 0.00 33.74 3.18
3102 5626 6.763610 GGCTAGGCAATCCACATATATACTTC 59.236 42.308 12.16 0.00 33.74 3.01
3103 5627 6.353082 GGGCTAGGCAATCCACATATATACTT 60.353 42.308 19.14 0.00 33.74 2.24
3104 5628 5.131142 GGGCTAGGCAATCCACATATATACT 59.869 44.000 19.14 0.00 33.74 2.12
3107 5631 3.851976 TGGGCTAGGCAATCCACATATAT 59.148 43.478 19.14 0.00 33.74 0.86
3110 5634 1.517238 TGGGCTAGGCAATCCACATA 58.483 50.000 19.14 0.00 33.74 2.29
3113 5637 1.322442 GAATGGGCTAGGCAATCCAC 58.678 55.000 19.14 4.39 33.74 4.02
3114 5638 0.185901 GGAATGGGCTAGGCAATCCA 59.814 55.000 19.14 7.03 33.74 3.41
3115 5639 0.185901 TGGAATGGGCTAGGCAATCC 59.814 55.000 19.14 20.00 0.00 3.01
3117 5641 1.500303 TGATGGAATGGGCTAGGCAAT 59.500 47.619 19.14 9.87 0.00 3.56
3119 5643 0.475475 CTGATGGAATGGGCTAGGCA 59.525 55.000 19.14 4.76 0.00 4.75
3120 5644 0.475906 ACTGATGGAATGGGCTAGGC 59.524 55.000 8.00 8.00 0.00 3.93
3121 5645 2.173356 TGAACTGATGGAATGGGCTAGG 59.827 50.000 0.00 0.00 0.00 3.02
3123 5647 3.114606 TCTGAACTGATGGAATGGGCTA 58.885 45.455 0.00 0.00 0.00 3.93
3126 5650 3.641434 AGTCTGAACTGATGGAATGGG 57.359 47.619 0.00 0.00 33.32 4.00
3127 5651 5.336213 CCAAAAGTCTGAACTGATGGAATGG 60.336 44.000 4.65 0.00 41.39 3.16
3128 5652 5.242393 ACCAAAAGTCTGAACTGATGGAATG 59.758 40.000 13.68 0.00 41.39 2.67
3129 5653 5.388654 ACCAAAAGTCTGAACTGATGGAAT 58.611 37.500 13.68 0.00 41.39 3.01
3130 5654 4.792068 ACCAAAAGTCTGAACTGATGGAA 58.208 39.130 13.68 0.00 41.39 3.53
3131 5655 4.437682 ACCAAAAGTCTGAACTGATGGA 57.562 40.909 13.68 0.00 41.39 3.41
3132 5656 4.794003 GCAACCAAAAGTCTGAACTGATGG 60.794 45.833 7.83 7.83 43.11 3.51
3133 5657 4.037208 AGCAACCAAAAGTCTGAACTGATG 59.963 41.667 0.00 0.00 35.36 3.07
3134 5658 4.210331 AGCAACCAAAAGTCTGAACTGAT 58.790 39.130 0.00 0.00 35.36 2.90
3135 5659 3.620488 AGCAACCAAAAGTCTGAACTGA 58.380 40.909 0.00 0.00 35.36 3.41
3136 5660 4.107622 CAAGCAACCAAAAGTCTGAACTG 58.892 43.478 0.00 0.00 35.36 3.16
3137 5661 3.763897 ACAAGCAACCAAAAGTCTGAACT 59.236 39.130 0.00 0.00 37.32 3.01
3138 5662 4.110036 ACAAGCAACCAAAAGTCTGAAC 57.890 40.909 0.00 0.00 0.00 3.18
3139 5663 4.799564 AACAAGCAACCAAAAGTCTGAA 57.200 36.364 0.00 0.00 0.00 3.02
3140 5664 4.799564 AAACAAGCAACCAAAAGTCTGA 57.200 36.364 0.00 0.00 0.00 3.27
3141 5665 6.042143 ACATAAACAAGCAACCAAAAGTCTG 58.958 36.000 0.00 0.00 0.00 3.51
3142 5666 6.220726 ACATAAACAAGCAACCAAAAGTCT 57.779 33.333 0.00 0.00 0.00 3.24
3143 5667 6.902224 AACATAAACAAGCAACCAAAAGTC 57.098 33.333 0.00 0.00 0.00 3.01
3144 5668 8.956533 ATAAACATAAACAAGCAACCAAAAGT 57.043 26.923 0.00 0.00 0.00 2.66
3147 5671 9.994432 CAAAATAAACATAAACAAGCAACCAAA 57.006 25.926 0.00 0.00 0.00 3.28
3148 5672 8.616076 CCAAAATAAACATAAACAAGCAACCAA 58.384 29.630 0.00 0.00 0.00 3.67
3149 5673 7.254932 GCCAAAATAAACATAAACAAGCAACCA 60.255 33.333 0.00 0.00 0.00 3.67
3150 5674 7.041440 AGCCAAAATAAACATAAACAAGCAACC 60.041 33.333 0.00 0.00 0.00 3.77
3151 5675 7.798052 CAGCCAAAATAAACATAAACAAGCAAC 59.202 33.333 0.00 0.00 0.00 4.17
3152 5676 7.497249 ACAGCCAAAATAAACATAAACAAGCAA 59.503 29.630 0.00 0.00 0.00 3.91
3153 5677 6.989169 ACAGCCAAAATAAACATAAACAAGCA 59.011 30.769 0.00 0.00 0.00 3.91
3154 5678 7.420184 ACAGCCAAAATAAACATAAACAAGC 57.580 32.000 0.00 0.00 0.00 4.01
3157 5681 9.632807 GTCATACAGCCAAAATAAACATAAACA 57.367 29.630 0.00 0.00 0.00 2.83
3158 5682 9.855021 AGTCATACAGCCAAAATAAACATAAAC 57.145 29.630 0.00 0.00 0.00 2.01
3161 5685 9.899661 AGTAGTCATACAGCCAAAATAAACATA 57.100 29.630 0.00 0.00 34.07 2.29
3162 5686 8.807948 AGTAGTCATACAGCCAAAATAAACAT 57.192 30.769 0.00 0.00 34.07 2.71
3163 5687 8.630054 AAGTAGTCATACAGCCAAAATAAACA 57.370 30.769 0.00 0.00 34.07 2.83
3164 5688 8.182227 GGAAGTAGTCATACAGCCAAAATAAAC 58.818 37.037 0.00 0.00 34.07 2.01
3245 5805 0.838122 AAGAGGTCCCCTGTCACCAG 60.838 60.000 0.00 0.00 38.50 4.00
3480 6229 3.519510 TGTTCAGTTCTCCCCAGGATTAG 59.480 47.826 0.00 0.00 0.00 1.73
3501 6250 3.871006 TGACAACAGCTACAAAGTCACTG 59.129 43.478 0.00 0.00 31.72 3.66
3682 6462 3.568853 AGATTTATCTTCAGGCATGCAGC 59.431 43.478 21.36 2.42 36.67 5.25
3735 6535 9.132521 CAAAGTGGACAAAAATGATATCAGAAC 57.867 33.333 11.78 0.00 0.00 3.01
3737 6537 8.408043 ACAAAGTGGACAAAAATGATATCAGA 57.592 30.769 11.78 0.00 0.00 3.27
3741 6541 9.612066 AACAAACAAAGTGGACAAAAATGATAT 57.388 25.926 0.00 0.00 0.00 1.63
3752 6552 6.141685 CGTATTGCTAAACAAACAAAGTGGAC 59.858 38.462 0.00 0.00 42.86 4.02
3759 6559 9.549509 GATGTAATCGTATTGCTAAACAAACAA 57.450 29.630 0.00 0.00 36.03 2.83
3818 6645 4.036027 CCGGTTTGCTACGACTCTATCTTA 59.964 45.833 0.00 0.00 0.00 2.10
3825 6652 2.098831 GCCCGGTTTGCTACGACTC 61.099 63.158 0.00 0.00 0.00 3.36
3849 6677 4.273969 GGTTTTATGTCTGAACGGTTCACA 59.726 41.667 19.07 16.34 35.46 3.58
3872 6700 1.601162 GCCATGTGACAGTGCAGTTTG 60.601 52.381 4.49 0.00 0.00 2.93
3902 6731 1.675552 AGCAGCTTAAACACGTTGGT 58.324 45.000 0.00 0.00 0.00 3.67
3934 6763 6.256104 TCTCACATTGTTGTTGAAATGCTTTG 59.744 34.615 0.00 0.00 37.30 2.77
4000 6830 5.473066 AACATGCCCATATTAATTCTGCC 57.527 39.130 0.00 0.00 0.00 4.85
4001 6831 5.697633 CCAAACATGCCCATATTAATTCTGC 59.302 40.000 0.00 0.00 0.00 4.26
4002 6832 6.819284 ACCAAACATGCCCATATTAATTCTG 58.181 36.000 0.00 0.00 0.00 3.02
4003 6833 7.436320 AACCAAACATGCCCATATTAATTCT 57.564 32.000 0.00 0.00 0.00 2.40
4004 6834 8.200792 TGTAACCAAACATGCCCATATTAATTC 58.799 33.333 0.00 0.00 0.00 2.17
4005 6835 8.083828 TGTAACCAAACATGCCCATATTAATT 57.916 30.769 0.00 0.00 0.00 1.40
4006 6836 7.667575 TGTAACCAAACATGCCCATATTAAT 57.332 32.000 0.00 0.00 0.00 1.40
4007 6837 7.667575 ATGTAACCAAACATGCCCATATTAA 57.332 32.000 0.00 0.00 38.65 1.40
4008 6838 7.495901 CAATGTAACCAAACATGCCCATATTA 58.504 34.615 0.00 0.00 39.98 0.98
4085 6924 4.978099 ACTATATGCATCTGGGGTCTTTG 58.022 43.478 0.19 0.00 0.00 2.77
4102 6941 3.696045 ACATGCAGGCAACCAAACTATA 58.304 40.909 0.00 0.00 37.17 1.31
4166 7007 3.887868 GCCTAATGCAACGCGGGG 61.888 66.667 12.47 2.29 40.77 5.73
4187 7028 7.381766 GCAGATTGCAACACCATATCATATA 57.618 36.000 0.00 0.00 44.26 0.86
4207 7053 3.769739 AGTGACAACACCTTATGCAGA 57.230 42.857 0.00 0.00 46.99 4.26
4227 7073 7.398047 TGGTAAGCTCACCACTAGTTAGAAATA 59.602 37.037 3.96 0.00 43.76 1.40
4361 7211 1.895020 TAGCAGCAACCCCGACGAAT 61.895 55.000 0.00 0.00 0.00 3.34
4365 7215 2.436115 GGTAGCAGCAACCCCGAC 60.436 66.667 0.00 0.00 0.00 4.79
4370 7220 2.409948 AAGATCTGGTAGCAGCAACC 57.590 50.000 17.20 5.93 37.53 3.77
4390 7240 4.081531 CAGAAGCAGAGGAAGATGAAGAGT 60.082 45.833 0.00 0.00 0.00 3.24
4414 7277 4.009002 GGAGAAAGAAGAAGAAGCAGCAT 58.991 43.478 0.00 0.00 0.00 3.79
4422 7285 6.985653 TGAAGAAGAGGAGAAAGAAGAAGA 57.014 37.500 0.00 0.00 0.00 2.87
4432 7307 3.584406 TGCAGGATTTGAAGAAGAGGAGA 59.416 43.478 0.00 0.00 0.00 3.71
4534 7410 0.392461 GTTGTTAGCTCCGGCCATGA 60.392 55.000 2.24 0.00 39.73 3.07
4670 7546 0.250234 CCTGGATCAGAAGCCGTTCA 59.750 55.000 0.00 0.00 34.82 3.18
4674 7550 1.047002 AGATCCTGGATCAGAAGCCG 58.953 55.000 32.30 0.00 41.12 5.52
4699 7576 4.826183 GGCATTTGGAGCTCTGAAGAATAT 59.174 41.667 14.64 0.00 0.00 1.28
4762 7639 1.068250 GGACCGCACAGGAGCTATC 59.932 63.158 0.00 0.00 45.00 2.08
4764 7641 0.752009 CTAGGACCGCACAGGAGCTA 60.752 60.000 0.00 0.00 45.00 3.32


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

AutoCloner maintained by Alex Coulton.