Multiple sequence alignment - TraesCS2B01G598500

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2B01G598500 chr2B 100.000 5129 0 0 1 5129 781582807 781577679 0.000000e+00 9472.0
1 TraesCS2B01G598500 chr2B 82.823 914 126 23 738 1630 781540130 781539227 0.000000e+00 789.0
2 TraesCS2B01G598500 chr2B 91.832 453 34 3 3670 4120 781536457 781536006 3.370000e-176 628.0
3 TraesCS2B01G598500 chr2B 82.123 358 48 13 154 501 781540900 781540549 5.020000e-75 292.0
4 TraesCS2B01G598500 chr2B 87.317 205 21 4 2025 2225 781538902 781538699 3.990000e-56 230.0
5 TraesCS2B01G598500 chr2B 84.337 83 12 1 26 108 159971974 159971893 4.260000e-11 80.5
6 TraesCS2B01G598500 chr2D 91.268 2176 146 10 2848 4995 651698636 651700795 0.000000e+00 2926.0
7 TraesCS2B01G598500 chr2D 96.324 1632 53 5 1 1630 651695914 651697540 0.000000e+00 2675.0
8 TraesCS2B01G598500 chr2D 95.251 1116 47 5 1724 2837 651697544 651698655 0.000000e+00 1762.0
9 TraesCS2B01G598500 chr2D 85.422 782 82 13 2858 3639 651723948 651724697 0.000000e+00 784.0
10 TraesCS2B01G598500 chr2D 88.581 578 52 11 3646 4213 651724834 651725407 0.000000e+00 689.0
11 TraesCS2B01G598500 chr2D 84.068 703 99 11 738 1431 651721023 651721721 0.000000e+00 665.0
12 TraesCS2B01G598500 chr2D 84.715 386 45 4 3731 4116 651719712 651720083 1.740000e-99 374.0
13 TraesCS2B01G598500 chr2D 80.622 418 58 18 2425 2834 651717432 651717834 8.350000e-78 302.0
14 TraesCS2B01G598500 chr2D 78.516 256 38 5 4219 4457 547952540 547952795 8.890000e-33 152.0
15 TraesCS2B01G598500 chr2D 80.000 210 30 12 4212 4415 553759036 553759239 1.490000e-30 145.0
16 TraesCS2B01G598500 chr2D 96.250 80 3 0 2231 2310 2461028 2461107 1.160000e-26 132.0
17 TraesCS2B01G598500 chr2D 92.537 67 5 0 658 724 651720917 651720983 4.230000e-16 97.1
18 TraesCS2B01G598500 chr2A 95.402 1631 66 5 1 1630 775978875 775977253 0.000000e+00 2588.0
19 TraesCS2B01G598500 chr2A 92.410 1647 90 12 2858 4475 775976144 775974504 0.000000e+00 2316.0
20 TraesCS2B01G598500 chr2A 96.592 1115 37 1 1724 2837 775977249 775976135 0.000000e+00 1847.0
21 TraesCS2B01G598500 chr2A 82.612 1340 174 29 2848 4153 775942096 775940782 0.000000e+00 1129.0
22 TraesCS2B01G598500 chr2A 80.652 1013 144 36 659 1630 775939984 775938983 0.000000e+00 737.0
23 TraesCS2B01G598500 chr2A 83.863 787 89 18 2858 3639 775937812 775937059 0.000000e+00 715.0
24 TraesCS2B01G598500 chr2A 87.868 577 58 11 3646 4213 775936885 775936312 0.000000e+00 667.0
25 TraesCS2B01G598500 chr2A 84.270 445 42 15 4687 5129 775972498 775972080 4.780000e-110 409.0
26 TraesCS2B01G598500 chr2A 81.303 476 64 18 1764 2225 775938952 775938488 3.770000e-96 363.0
27 TraesCS2B01G598500 chr2A 79.596 446 66 23 2338 2774 775968392 775967963 3.880000e-76 296.0
28 TraesCS2B01G598500 chr2A 80.321 249 32 11 4212 4444 15610796 15611043 6.830000e-39 172.0
29 TraesCS2B01G598500 chr2A 78.327 263 40 6 4211 4456 691115427 691115165 2.470000e-33 154.0
30 TraesCS2B01G598500 chr5D 82.977 1169 170 19 2945 4087 527154988 527153823 0.000000e+00 1029.0
31 TraesCS2B01G598500 chr5D 82.918 843 110 23 738 1562 527157094 527156268 0.000000e+00 728.0
32 TraesCS2B01G598500 chr5D 92.222 90 7 0 2221 2310 197147096 197147185 1.500000e-25 128.0
33 TraesCS2B01G598500 chr5A 82.835 1171 173 21 2945 4093 654167303 654166139 0.000000e+00 1024.0
34 TraesCS2B01G598500 chr5A 82.927 820 109 21 738 1541 654169470 654168666 0.000000e+00 710.0
35 TraesCS2B01G598500 chr5A 81.938 836 126 18 738 1562 654157674 654156853 0.000000e+00 684.0
36 TraesCS2B01G598500 chr5A 86.364 418 54 2 2945 3359 654155534 654155117 2.180000e-123 453.0
37 TraesCS2B01G598500 chr5A 74.344 343 67 15 107 432 654159474 654159136 5.390000e-25 126.0
38 TraesCS2B01G598500 chr5B 82.996 841 112 23 738 1562 663229119 663228294 0.000000e+00 732.0
39 TraesCS2B01G598500 chr5B 84.314 663 76 13 2945 3605 663227021 663226385 1.570000e-174 623.0
40 TraesCS2B01G598500 chr5B 94.253 87 4 1 2222 2308 266503269 266503354 1.160000e-26 132.0
41 TraesCS2B01G598500 chr5B 85.714 105 14 1 1 104 712198211 712198315 5.430000e-20 110.0
42 TraesCS2B01G598500 chr7B 95.122 82 4 0 2227 2308 625725340 625725259 4.170000e-26 130.0
43 TraesCS2B01G598500 chr6B 94.118 85 5 0 2224 2308 240546056 240546140 4.170000e-26 130.0
44 TraesCS2B01G598500 chr1B 94.118 85 5 0 2224 2308 222194511 222194595 4.170000e-26 130.0
45 TraesCS2B01G598500 chr7A 89.216 102 11 0 1 102 299390607 299390506 1.500000e-25 128.0
46 TraesCS2B01G598500 chr3B 92.941 85 5 1 2224 2308 806726618 806726701 6.970000e-24 122.0
47 TraesCS2B01G598500 chr4A 76.887 212 36 10 4212 4422 140974910 140975109 1.950000e-19 108.0
48 TraesCS2B01G598500 chr4A 86.667 90 9 3 21 108 540918860 540918948 4.230000e-16 97.1
49 TraesCS2B01G598500 chr6A 76.068 234 37 13 4212 4427 490489299 490489067 2.530000e-18 104.0
50 TraesCS2B01G598500 chr6D 89.157 83 7 2 26 108 303063274 303063194 9.090000e-18 102.0
51 TraesCS2B01G598500 chr3D 75.745 235 37 14 4212 4427 603404355 603404588 3.270000e-17 100.0
52 TraesCS2B01G598500 chr1D 87.209 86 9 1 21 104 433261103 433261188 4.230000e-16 97.1
53 TraesCS2B01G598500 chr7D 75.325 231 34 16 4237 4447 2870036 2870263 7.070000e-14 89.8
54 TraesCS2B01G598500 chr7D 85.714 84 11 1 26 108 220635573 220635490 2.540000e-13 87.9
55 TraesCS2B01G598500 chr4B 75.500 200 37 9 4224 4422 408984823 408984635 2.540000e-13 87.9
56 TraesCS2B01G598500 chr4B 100.000 29 0 0 4211 4239 161070880 161070852 3.000000e-03 54.7
57 TraesCS2B01G598500 chr4D 87.500 72 5 4 4375 4444 15411353 15411284 4.260000e-11 80.5


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 TraesCS2B01G598500 chr2B 781577679 781582807 5128 True 9472.000000 9472 100.000000 1 5129 1 chr2B.!!$R2 5128
1 TraesCS2B01G598500 chr2B 781536006 781540900 4894 True 484.750000 789 86.023750 154 4120 4 chr2B.!!$R3 3966
2 TraesCS2B01G598500 chr2D 651695914 651700795 4881 False 2454.333333 2926 94.281000 1 4995 3 chr2D.!!$F4 4994
3 TraesCS2B01G598500 chr2D 651717432 651725407 7975 False 485.183333 784 85.990833 658 4213 6 chr2D.!!$F5 3555
4 TraesCS2B01G598500 chr2A 775967963 775978875 10912 True 1491.200000 2588 89.654000 1 5129 5 chr2A.!!$R3 5128
5 TraesCS2B01G598500 chr2A 775936312 775942096 5784 True 722.200000 1129 83.259600 659 4213 5 chr2A.!!$R2 3554
6 TraesCS2B01G598500 chr5D 527153823 527157094 3271 True 878.500000 1029 82.947500 738 4087 2 chr5D.!!$R1 3349
7 TraesCS2B01G598500 chr5A 654166139 654169470 3331 True 867.000000 1024 82.881000 738 4093 2 chr5A.!!$R2 3355
8 TraesCS2B01G598500 chr5A 654155117 654159474 4357 True 421.000000 684 80.882000 107 3359 3 chr5A.!!$R1 3252
9 TraesCS2B01G598500 chr5B 663226385 663229119 2734 True 677.500000 732 83.655000 738 3605 2 chr5B.!!$R1 2867

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
295 308 2.295885 CTGATCCCTCCAAAGATGCAC 58.704 52.381 0.0 0.0 0.00 4.57 F
945 4952 3.001838 CCGAATGTTTGACGTGTCTTGAA 59.998 43.478 0.0 0.0 0.00 2.69 F
1705 6035 0.034616 AAGCTCTGCTTCGTGCTTCT 59.965 50.000 0.0 0.0 46.77 2.85 F
3239 8582 0.182775 ACCCTCTTTTTCACCACGCT 59.817 50.000 0.0 0.0 0.00 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1633 5963 0.322456 AAGCACCAGCAAGCGGATAA 60.322 50.0 9.31 0.0 45.49 1.75 R
2844 8180 0.905357 ACCACAGCTATCACCCAGTC 59.095 55.0 0.00 0.0 0.00 3.51 R
3618 8989 0.527565 ATCAACGATTTGCTGCCACC 59.472 50.0 0.00 0.0 32.17 4.61 R
4935 12294 0.033504 GCTCAACTCTTCCGACACCA 59.966 55.0 0.00 0.0 0.00 4.17 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
38 39 4.764679 TTTTATCTGTGACGCAGCAAAT 57.235 36.364 11.29 2.80 44.66 2.32
63 64 3.620488 TGTCATGGCCTTTGGAGATTAC 58.380 45.455 3.32 0.00 0.00 1.89
134 135 6.108687 CACTAATGCAACTTCTCCTATGACA 58.891 40.000 0.00 0.00 0.00 3.58
173 178 3.387397 CTGCTGCCTTTTTCCTTTTCAG 58.613 45.455 0.00 0.00 0.00 3.02
295 308 2.295885 CTGATCCCTCCAAAGATGCAC 58.704 52.381 0.00 0.00 0.00 4.57
446 462 3.124297 CGAGTCACCTTGAGATTGAAAGC 59.876 47.826 0.00 0.00 0.00 3.51
482 504 8.686334 TGAATCCTTTCTCCTTTACAAATATGC 58.314 33.333 0.00 0.00 32.78 3.14
546 568 8.887264 AGTTCCTACTTCATTTTCTCTAGAGA 57.113 34.615 18.76 18.76 35.27 3.10
547 569 8.966868 AGTTCCTACTTCATTTTCTCTAGAGAG 58.033 37.037 21.34 10.96 43.36 3.20
561 583 5.885352 TCTCTAGAGAGATGAACAACCTGAG 59.115 44.000 18.76 0.00 45.48 3.35
562 584 5.821097 TCTAGAGAGATGAACAACCTGAGA 58.179 41.667 0.00 0.00 0.00 3.27
564 586 5.341872 AGAGAGATGAACAACCTGAGATG 57.658 43.478 0.00 0.00 0.00 2.90
565 587 5.022122 AGAGAGATGAACAACCTGAGATGA 58.978 41.667 0.00 0.00 0.00 2.92
566 588 5.483231 AGAGAGATGAACAACCTGAGATGAA 59.517 40.000 0.00 0.00 0.00 2.57
567 589 6.156602 AGAGAGATGAACAACCTGAGATGAAT 59.843 38.462 0.00 0.00 0.00 2.57
568 590 7.344093 AGAGAGATGAACAACCTGAGATGAATA 59.656 37.037 0.00 0.00 0.00 1.75
569 591 7.271511 AGAGATGAACAACCTGAGATGAATAC 58.728 38.462 0.00 0.00 0.00 1.89
570 592 7.125507 AGAGATGAACAACCTGAGATGAATACT 59.874 37.037 0.00 0.00 0.00 2.12
572 594 8.200792 AGATGAACAACCTGAGATGAATACTAC 58.799 37.037 0.00 0.00 0.00 2.73
574 596 8.589701 TGAACAACCTGAGATGAATACTACTA 57.410 34.615 0.00 0.00 0.00 1.82
576 598 7.349412 ACAACCTGAGATGAATACTACTACC 57.651 40.000 0.00 0.00 0.00 3.18
577 599 6.895756 ACAACCTGAGATGAATACTACTACCA 59.104 38.462 0.00 0.00 0.00 3.25
580 602 7.813331 ACCTGAGATGAATACTACTACCAGTA 58.187 38.462 0.00 0.00 35.54 2.74
581 603 8.449625 ACCTGAGATGAATACTACTACCAGTAT 58.550 37.037 0.00 0.00 42.30 2.12
594 616 7.837689 ACTACTACCAGTATACATGACTTTCCA 59.162 37.037 5.50 0.00 29.08 3.53
595 617 7.676683 ACTACCAGTATACATGACTTTCCAT 57.323 36.000 5.50 0.00 0.00 3.41
597 619 8.204836 ACTACCAGTATACATGACTTTCCATTC 58.795 37.037 5.50 0.00 0.00 2.67
598 620 6.049149 ACCAGTATACATGACTTTCCATTCG 58.951 40.000 5.50 0.00 0.00 3.34
599 621 6.049149 CCAGTATACATGACTTTCCATTCGT 58.951 40.000 5.50 0.00 0.00 3.85
600 622 6.018751 CCAGTATACATGACTTTCCATTCGTG 60.019 42.308 5.50 0.00 35.27 4.35
601 623 6.535150 CAGTATACATGACTTTCCATTCGTGT 59.465 38.462 5.50 2.30 43.07 4.49
603 625 3.738982 ACATGACTTTCCATTCGTGTCA 58.261 40.909 0.00 0.00 37.40 3.58
607 629 6.599244 ACATGACTTTCCATTCGTGTCATAAT 59.401 34.615 0.00 0.00 43.71 1.28
610 632 8.731275 TGACTTTCCATTCGTGTCATAATAAT 57.269 30.769 0.00 0.00 33.45 1.28
611 633 8.611757 TGACTTTCCATTCGTGTCATAATAATG 58.388 33.333 0.00 0.00 33.45 1.90
612 634 8.506168 ACTTTCCATTCGTGTCATAATAATGT 57.494 30.769 0.00 0.00 34.50 2.71
613 635 8.956426 ACTTTCCATTCGTGTCATAATAATGTT 58.044 29.630 0.00 0.00 34.50 2.71
614 636 9.438291 CTTTCCATTCGTGTCATAATAATGTTC 57.562 33.333 0.00 0.00 34.50 3.18
615 637 8.499403 TTCCATTCGTGTCATAATAATGTTCA 57.501 30.769 0.00 0.00 34.50 3.18
616 638 8.499403 TCCATTCGTGTCATAATAATGTTCAA 57.501 30.769 0.00 0.00 34.50 2.69
617 639 8.611757 TCCATTCGTGTCATAATAATGTTCAAG 58.388 33.333 0.00 0.00 34.50 3.02
618 640 8.397906 CCATTCGTGTCATAATAATGTTCAAGT 58.602 33.333 0.00 0.00 34.50 3.16
619 641 9.213819 CATTCGTGTCATAATAATGTTCAAGTG 57.786 33.333 0.00 0.00 34.50 3.16
621 643 6.593770 TCGTGTCATAATAATGTTCAAGTGCT 59.406 34.615 0.00 0.00 34.50 4.40
622 644 6.684131 CGTGTCATAATAATGTTCAAGTGCTG 59.316 38.462 0.00 0.00 34.50 4.41
623 645 6.968904 GTGTCATAATAATGTTCAAGTGCTGG 59.031 38.462 0.00 0.00 34.50 4.85
625 647 7.557358 TGTCATAATAATGTTCAAGTGCTGGAT 59.443 33.333 0.00 0.00 34.50 3.41
626 648 8.408601 GTCATAATAATGTTCAAGTGCTGGATT 58.591 33.333 0.00 0.00 34.50 3.01
631 653 6.839124 AATGTTCAAGTGCTGGATTATTCA 57.161 33.333 0.00 0.00 0.00 2.57
633 655 6.647334 TGTTCAAGTGCTGGATTATTCAAA 57.353 33.333 0.00 0.00 0.00 2.69
634 656 7.230849 TGTTCAAGTGCTGGATTATTCAAAT 57.769 32.000 0.00 0.00 0.00 2.32
635 657 8.347004 TGTTCAAGTGCTGGATTATTCAAATA 57.653 30.769 0.00 0.00 0.00 1.40
636 658 8.801299 TGTTCAAGTGCTGGATTATTCAAATAA 58.199 29.630 0.00 0.00 35.52 1.40
637 659 9.638239 GTTCAAGTGCTGGATTATTCAAATAAA 57.362 29.630 0.00 0.00 34.79 1.40
639 661 9.806203 TCAAGTGCTGGATTATTCAAATAAATG 57.194 29.630 0.00 0.00 34.79 2.32
640 662 8.545420 CAAGTGCTGGATTATTCAAATAAATGC 58.455 33.333 0.00 3.54 34.79 3.56
642 664 6.985645 GTGCTGGATTATTCAAATAAATGCCA 59.014 34.615 0.00 6.96 34.79 4.92
643 665 7.658575 GTGCTGGATTATTCAAATAAATGCCAT 59.341 33.333 11.91 0.00 34.79 4.40
644 666 8.212312 TGCTGGATTATTCAAATAAATGCCATT 58.788 29.630 11.91 0.00 34.79 3.16
645 667 9.709495 GCTGGATTATTCAAATAAATGCCATTA 57.291 29.630 11.91 0.00 34.79 1.90
660 682 6.921486 ATGCCATTATATGCTTTGATTGGA 57.079 33.333 0.00 0.00 0.00 3.53
661 683 6.921486 TGCCATTATATGCTTTGATTGGAT 57.079 33.333 0.00 0.00 0.00 3.41
662 684 6.693466 TGCCATTATATGCTTTGATTGGATG 58.307 36.000 0.00 0.00 0.00 3.51
873 4877 3.785486 TGCTCAAGTGGATTATGAGTCG 58.215 45.455 4.19 0.00 42.00 4.18
945 4952 3.001838 CCGAATGTTTGACGTGTCTTGAA 59.998 43.478 0.00 0.00 0.00 2.69
1179 5186 3.502191 TTTGCGATTGAAAGGTATGCC 57.498 42.857 0.00 0.00 0.00 4.40
1205 5212 7.075851 AGTTTTGGCTTCTTAGTTACCTAGT 57.924 36.000 0.00 0.00 0.00 2.57
1284 5293 6.144854 CCACAAATGTCATACAAACTCTGTG 58.855 40.000 0.00 0.00 39.20 3.66
1325 5334 6.668645 TGCATTATATGGGTAGGTCAAAGTT 58.331 36.000 0.00 0.00 0.00 2.66
1349 5358 9.908152 GTTACAAGCCAGAAATGTTTTTATACT 57.092 29.630 0.00 0.00 0.00 2.12
1630 5960 7.385752 TCGGTCATTTTGGTTTTAGTGTAGTAG 59.614 37.037 0.00 0.00 0.00 2.57
1631 5961 7.303261 GGTCATTTTGGTTTTAGTGTAGTAGC 58.697 38.462 0.00 0.00 0.00 3.58
1632 5962 7.303261 GTCATTTTGGTTTTAGTGTAGTAGCC 58.697 38.462 0.00 0.00 0.00 3.93
1633 5963 7.174426 GTCATTTTGGTTTTAGTGTAGTAGCCT 59.826 37.037 0.00 0.00 0.00 4.58
1634 5964 7.722285 TCATTTTGGTTTTAGTGTAGTAGCCTT 59.278 33.333 0.00 0.00 0.00 4.35
1635 5965 9.005777 CATTTTGGTTTTAGTGTAGTAGCCTTA 57.994 33.333 0.00 0.00 0.00 2.69
1636 5966 9.749340 ATTTTGGTTTTAGTGTAGTAGCCTTAT 57.251 29.630 0.00 0.00 0.00 1.73
1637 5967 8.782339 TTTGGTTTTAGTGTAGTAGCCTTATC 57.218 34.615 0.00 0.00 0.00 1.75
1638 5968 6.881570 TGGTTTTAGTGTAGTAGCCTTATCC 58.118 40.000 0.00 0.00 0.00 2.59
1639 5969 5.981915 GGTTTTAGTGTAGTAGCCTTATCCG 59.018 44.000 0.00 0.00 0.00 4.18
1640 5970 4.843220 TTAGTGTAGTAGCCTTATCCGC 57.157 45.455 0.00 0.00 0.00 5.54
1641 5971 2.946785 AGTGTAGTAGCCTTATCCGCT 58.053 47.619 0.00 0.00 40.45 5.52
1642 5972 3.297736 AGTGTAGTAGCCTTATCCGCTT 58.702 45.455 0.00 0.00 37.79 4.68
1643 5973 3.068307 AGTGTAGTAGCCTTATCCGCTTG 59.932 47.826 0.00 0.00 37.79 4.01
1644 5974 2.223971 TGTAGTAGCCTTATCCGCTTGC 60.224 50.000 0.00 0.00 37.79 4.01
1645 5975 1.123928 AGTAGCCTTATCCGCTTGCT 58.876 50.000 0.00 0.00 37.79 3.91
1646 5976 1.202580 AGTAGCCTTATCCGCTTGCTG 60.203 52.381 0.00 0.00 37.79 4.41
1647 5977 0.106708 TAGCCTTATCCGCTTGCTGG 59.893 55.000 0.00 0.00 37.79 4.85
1648 5978 1.452108 GCCTTATCCGCTTGCTGGT 60.452 57.895 0.00 0.00 0.00 4.00
1649 5979 1.718757 GCCTTATCCGCTTGCTGGTG 61.719 60.000 0.00 0.00 0.00 4.17
1650 5980 1.718757 CCTTATCCGCTTGCTGGTGC 61.719 60.000 0.00 0.00 40.20 5.01
1651 5981 0.745845 CTTATCCGCTTGCTGGTGCT 60.746 55.000 0.00 0.00 40.48 4.40
1652 5982 0.322456 TTATCCGCTTGCTGGTGCTT 60.322 50.000 0.00 0.00 40.48 3.91
1653 5983 0.322456 TATCCGCTTGCTGGTGCTTT 60.322 50.000 0.00 0.00 40.48 3.51
1654 5984 1.870055 ATCCGCTTGCTGGTGCTTTG 61.870 55.000 0.00 0.00 40.48 2.77
1655 5985 2.732094 CGCTTGCTGGTGCTTTGC 60.732 61.111 0.00 0.00 40.48 3.68
1656 5986 2.732658 GCTTGCTGGTGCTTTGCT 59.267 55.556 0.00 0.00 40.48 3.91
1657 5987 1.855213 CGCTTGCTGGTGCTTTGCTA 61.855 55.000 0.00 0.00 40.48 3.49
1658 5988 0.529378 GCTTGCTGGTGCTTTGCTAT 59.471 50.000 0.00 0.00 40.48 2.97
1659 5989 1.468736 GCTTGCTGGTGCTTTGCTATC 60.469 52.381 0.00 0.00 40.48 2.08
1660 5990 1.133790 CTTGCTGGTGCTTTGCTATCC 59.866 52.381 0.00 0.00 40.48 2.59
1661 5991 1.026182 TGCTGGTGCTTTGCTATCCG 61.026 55.000 0.00 0.00 40.48 4.18
1662 5992 0.744414 GCTGGTGCTTTGCTATCCGA 60.744 55.000 0.00 0.00 36.03 4.55
1663 5993 1.737838 CTGGTGCTTTGCTATCCGAA 58.262 50.000 0.00 0.00 0.00 4.30
1664 5994 1.398390 CTGGTGCTTTGCTATCCGAAC 59.602 52.381 0.00 0.00 0.00 3.95
1665 5995 1.003118 TGGTGCTTTGCTATCCGAACT 59.997 47.619 0.00 0.00 0.00 3.01
1666 5996 2.235155 TGGTGCTTTGCTATCCGAACTA 59.765 45.455 0.00 0.00 0.00 2.24
1667 5997 2.608090 GGTGCTTTGCTATCCGAACTAC 59.392 50.000 0.00 0.00 0.00 2.73
1668 5998 2.608090 GTGCTTTGCTATCCGAACTACC 59.392 50.000 0.00 0.00 0.00 3.18
1669 5999 1.859080 GCTTTGCTATCCGAACTACCG 59.141 52.381 0.00 0.00 0.00 4.02
1670 6000 2.737679 GCTTTGCTATCCGAACTACCGT 60.738 50.000 0.00 0.00 0.00 4.83
1671 6001 3.518590 CTTTGCTATCCGAACTACCGTT 58.481 45.455 0.00 0.00 35.68 4.44
1672 6002 2.572191 TGCTATCCGAACTACCGTTG 57.428 50.000 0.00 0.00 32.39 4.10
1673 6003 1.206523 GCTATCCGAACTACCGTTGC 58.793 55.000 0.00 0.00 32.39 4.17
1674 6004 1.202382 GCTATCCGAACTACCGTTGCT 60.202 52.381 0.00 0.00 32.39 3.91
1675 6005 2.033801 GCTATCCGAACTACCGTTGCTA 59.966 50.000 0.00 0.00 32.39 3.49
1676 6006 3.489738 GCTATCCGAACTACCGTTGCTAA 60.490 47.826 0.00 0.00 32.39 3.09
1677 6007 2.352503 TCCGAACTACCGTTGCTAAC 57.647 50.000 0.00 0.00 32.39 2.34
1678 6008 1.888512 TCCGAACTACCGTTGCTAACT 59.111 47.619 0.00 0.00 32.39 2.24
1679 6009 2.095059 TCCGAACTACCGTTGCTAACTC 60.095 50.000 0.00 0.00 32.39 3.01
1680 6010 2.094854 CCGAACTACCGTTGCTAACTCT 60.095 50.000 0.00 0.00 32.39 3.24
1681 6011 2.915463 CGAACTACCGTTGCTAACTCTG 59.085 50.000 0.00 0.00 32.39 3.35
1682 6012 3.365666 CGAACTACCGTTGCTAACTCTGA 60.366 47.826 0.00 0.00 32.39 3.27
1683 6013 4.553323 GAACTACCGTTGCTAACTCTGAA 58.447 43.478 0.00 0.00 32.39 3.02
1684 6014 4.175787 ACTACCGTTGCTAACTCTGAAG 57.824 45.455 0.00 0.00 0.00 3.02
1685 6015 3.825014 ACTACCGTTGCTAACTCTGAAGA 59.175 43.478 0.00 0.00 0.00 2.87
1686 6016 3.746045 ACCGTTGCTAACTCTGAAGAA 57.254 42.857 0.00 0.00 0.00 2.52
1687 6017 4.067972 ACCGTTGCTAACTCTGAAGAAA 57.932 40.909 0.00 0.00 0.00 2.52
1688 6018 4.058817 ACCGTTGCTAACTCTGAAGAAAG 58.941 43.478 0.00 0.00 0.00 2.62
1689 6019 3.120511 CCGTTGCTAACTCTGAAGAAAGC 60.121 47.826 0.00 0.00 35.63 3.51
1690 6020 3.743396 CGTTGCTAACTCTGAAGAAAGCT 59.257 43.478 9.22 0.00 35.89 3.74
1691 6021 4.143221 CGTTGCTAACTCTGAAGAAAGCTC 60.143 45.833 0.00 0.00 35.89 4.09
1692 6022 4.881019 TGCTAACTCTGAAGAAAGCTCT 57.119 40.909 0.00 0.00 35.89 4.09
1693 6023 4.564041 TGCTAACTCTGAAGAAAGCTCTG 58.436 43.478 0.00 0.00 35.89 3.35
1694 6024 3.370672 GCTAACTCTGAAGAAAGCTCTGC 59.629 47.826 0.00 0.00 33.70 4.26
1695 6025 3.767902 AACTCTGAAGAAAGCTCTGCT 57.232 42.857 0.00 0.00 42.56 4.24
1703 6033 4.787871 AAGCTCTGCTTCGTGCTT 57.212 50.000 0.00 0.00 46.77 3.91
1704 6034 2.537863 AAGCTCTGCTTCGTGCTTC 58.462 52.632 0.00 0.00 46.77 3.86
1705 6035 0.034616 AAGCTCTGCTTCGTGCTTCT 59.965 50.000 0.00 0.00 46.77 2.85
1706 6036 0.034616 AGCTCTGCTTCGTGCTTCTT 59.965 50.000 5.00 0.00 43.37 2.52
1707 6037 0.441921 GCTCTGCTTCGTGCTTCTTC 59.558 55.000 5.00 0.00 43.37 2.87
1708 6038 0.712775 CTCTGCTTCGTGCTTCTTCG 59.287 55.000 5.00 0.00 43.37 3.79
1709 6039 1.131420 CTGCTTCGTGCTTCTTCGC 59.869 57.895 5.00 0.00 43.37 4.70
1710 6040 1.287730 CTGCTTCGTGCTTCTTCGCT 61.288 55.000 5.00 0.00 43.37 4.93
1711 6041 0.880278 TGCTTCGTGCTTCTTCGCTT 60.880 50.000 5.00 0.00 43.37 4.68
1712 6042 1.068474 GCTTCGTGCTTCTTCGCTTA 58.932 50.000 0.00 0.00 38.95 3.09
1713 6043 1.661112 GCTTCGTGCTTCTTCGCTTAT 59.339 47.619 0.00 0.00 38.95 1.73
1714 6044 2.094417 GCTTCGTGCTTCTTCGCTTATT 59.906 45.455 0.00 0.00 38.95 1.40
1715 6045 3.782574 GCTTCGTGCTTCTTCGCTTATTC 60.783 47.826 0.00 0.00 38.95 1.75
1716 6046 2.954316 TCGTGCTTCTTCGCTTATTCA 58.046 42.857 0.00 0.00 0.00 2.57
1717 6047 3.322369 TCGTGCTTCTTCGCTTATTCAA 58.678 40.909 0.00 0.00 0.00 2.69
1718 6048 3.932710 TCGTGCTTCTTCGCTTATTCAAT 59.067 39.130 0.00 0.00 0.00 2.57
1719 6049 4.024438 CGTGCTTCTTCGCTTATTCAATG 58.976 43.478 0.00 0.00 0.00 2.82
1722 6052 4.096833 TGCTTCTTCGCTTATTCAATGCAT 59.903 37.500 0.00 0.00 0.00 3.96
1767 6097 2.168521 CTGTCCTTTCCGGCAGAGAATA 59.831 50.000 0.00 0.00 38.45 1.75
1781 6111 6.116126 GGCAGAGAATATCAGTTTTACCAGT 58.884 40.000 0.00 0.00 0.00 4.00
2256 6645 8.047911 TCCGTCCCACAATATAAGATGTTTTTA 58.952 33.333 0.00 0.00 0.00 1.52
2454 7701 8.367660 TGAGTGGTAACTTTCTCTCTCATTAT 57.632 34.615 0.00 0.00 36.52 1.28
2629 7955 7.798596 ACCATTGTGAAATTTGTTTATTGCA 57.201 28.000 0.00 0.00 0.00 4.08
2651 7977 9.959749 TTGCACTTCTTCGAATTTAGTAAAAAT 57.040 25.926 0.00 0.00 0.00 1.82
2761 8097 6.892951 GCGTTCGTACATACTTTAGAAACATG 59.107 38.462 0.00 0.00 0.00 3.21
2833 8169 3.515602 AAAAAGGATGAGAGCTGTGGT 57.484 42.857 0.00 0.00 0.00 4.16
2834 8170 4.640771 AAAAAGGATGAGAGCTGTGGTA 57.359 40.909 0.00 0.00 0.00 3.25
2835 8171 4.640771 AAAAGGATGAGAGCTGTGGTAA 57.359 40.909 0.00 0.00 0.00 2.85
2836 8172 4.851639 AAAGGATGAGAGCTGTGGTAAT 57.148 40.909 0.00 0.00 0.00 1.89
2976 8315 7.718314 AGTGTATATGTGAGTGCATTGATGAAT 59.282 33.333 0.00 0.00 0.00 2.57
3155 8498 8.718102 TTATGAAAGTTTCTGGTATAGTGCTC 57.282 34.615 16.33 0.00 0.00 4.26
3176 8519 1.301401 TGCGGCTGGTGTTACTGTC 60.301 57.895 0.00 0.00 0.00 3.51
3239 8582 0.182775 ACCCTCTTTTTCACCACGCT 59.817 50.000 0.00 0.00 0.00 5.07
3370 8713 2.998772 GTGTGCACAGGTTACACAATG 58.001 47.619 22.40 0.00 45.20 2.82
3405 8776 5.922544 GGGCATGTTGTGATGCTAATTTATC 59.077 40.000 0.00 0.00 46.74 1.75
3424 8795 9.660544 AATTTATCCATCCTAAATTTAGCCTGT 57.339 29.630 18.18 6.64 36.04 4.00
3585 8956 0.535335 TGGATGTAGGTCTTGTCGCC 59.465 55.000 0.00 0.00 0.00 5.54
3608 8979 7.380333 CGCCATCGTCTATTGTGTAAGTATAAA 59.620 37.037 0.00 0.00 0.00 1.40
3618 8989 7.852971 TTGTGTAAGTATAAAAATCCCCTCG 57.147 36.000 0.00 0.00 0.00 4.63
3620 8991 6.070078 TGTGTAAGTATAAAAATCCCCTCGGT 60.070 38.462 0.00 0.00 0.00 4.69
3621 8992 6.259387 GTGTAAGTATAAAAATCCCCTCGGTG 59.741 42.308 0.00 0.00 0.00 4.94
3646 9129 5.680229 GCAGCAAATCGTTGATTCATTAGAG 59.320 40.000 0.00 0.00 36.83 2.43
3668 9213 8.785329 AGAGAACAAAAATCCTAATCTCTGTC 57.215 34.615 0.00 0.00 40.31 3.51
3929 9487 3.997762 TGAACAGTGTAATAAGTGGCGT 58.002 40.909 0.00 0.00 0.00 5.68
4023 9581 2.135933 GGTAGCGGAGAAAATGGATCG 58.864 52.381 0.00 0.00 0.00 3.69
4146 9704 0.380378 GAAACGGTGAGCAGCAAACA 59.620 50.000 0.00 0.00 0.00 2.83
4217 9780 6.647067 GCTGTTCACATATCTGTAATACTCCC 59.353 42.308 0.00 0.00 33.14 4.30
4281 9844 7.499895 AGTCAAACTTTATAAGGTTCGACCAAA 59.500 33.333 21.40 0.84 41.95 3.28
4415 9978 5.567138 AGTTCACAAAGTTTGACTTGAGG 57.433 39.130 22.23 3.05 38.66 3.86
4429 9992 4.336433 TGACTTGAGGCAAAGCTAATATGC 59.664 41.667 5.44 5.44 39.33 3.14
4434 9997 2.883386 AGGCAAAGCTAATATGCAGAGC 59.117 45.455 13.50 0.00 41.80 4.09
4469 10032 1.993370 CGACTACTGTTTACTGCCAGC 59.007 52.381 0.00 0.00 31.76 4.85
4534 10625 5.970592 AGAAAGTTTTTGCTTTTGAGCTCT 58.029 33.333 16.19 0.00 38.64 4.09
4556 10647 6.019748 TCTTGTTGTAGAGGAGAGGAGATTT 58.980 40.000 0.00 0.00 0.00 2.17
4580 10671 1.131826 GTTGCGAACGCGTGCTATT 59.868 52.632 14.98 0.00 45.51 1.73
4582 10673 1.561717 TTGCGAACGCGTGCTATTGT 61.562 50.000 14.98 0.00 45.51 2.71
4592 10683 1.402325 CGTGCTATTGTGACTCCGTGA 60.402 52.381 0.00 0.00 0.00 4.35
4634 10729 2.856000 AGGTGCTCCCTTGGCAGT 60.856 61.111 0.00 0.00 42.73 4.40
4635 10730 2.674380 GGTGCTCCCTTGGCAGTG 60.674 66.667 0.00 0.00 40.54 3.66
4636 10731 2.113986 GTGCTCCCTTGGCAGTGT 59.886 61.111 0.00 0.00 40.54 3.55
4727 12084 0.250166 AGCCACGAGTTAGCCGTTTT 60.250 50.000 0.00 0.00 38.29 2.43
4752 12111 0.537188 CGGTGGCTAGTGTCTTGGAT 59.463 55.000 0.00 0.00 0.00 3.41
4781 12140 1.255882 TTTGCGGCCTGATGTTGATT 58.744 45.000 0.00 0.00 0.00 2.57
4787 12146 2.097825 GGCCTGATGTTGATTTGAGCT 58.902 47.619 0.00 0.00 0.00 4.09
4793 12152 1.702182 TGTTGATTTGAGCTTGGCCA 58.298 45.000 0.00 0.00 0.00 5.36
4840 12199 2.667318 CCGTGCTAGTGTTGTGGCG 61.667 63.158 0.00 0.00 0.00 5.69
4858 12217 0.319211 CGGACGCAACAACTAGGTGA 60.319 55.000 16.48 0.00 36.95 4.02
4860 12219 1.732259 GGACGCAACAACTAGGTGATG 59.268 52.381 16.48 14.76 36.95 3.07
4866 12225 3.317993 GCAACAACTAGGTGATGTTTGGT 59.682 43.478 16.48 0.00 39.21 3.67
4873 12232 1.282157 AGGTGATGTTTGGTAGGGAGC 59.718 52.381 0.00 0.00 0.00 4.70
4877 12236 0.392998 ATGTTTGGTAGGGAGCGCTG 60.393 55.000 18.48 0.00 0.00 5.18
4906 12265 2.441532 TCGGAGTCGGATGGGGTC 60.442 66.667 0.00 0.00 36.95 4.46
4935 12294 2.587753 CGTTGGCGTGGTGTCAGT 60.588 61.111 0.00 0.00 30.83 3.41
5002 12361 1.905354 GCAGCTCTGGCAAGGGTTT 60.905 57.895 0.00 0.00 41.70 3.27
5009 12368 1.757423 CTGGCAAGGGTTTGGGTTGG 61.757 60.000 0.00 0.00 34.79 3.77
5037 12396 0.481128 ACGGAGGTGGAAAATGGGTT 59.519 50.000 0.00 0.00 0.00 4.11
5038 12397 0.887933 CGGAGGTGGAAAATGGGTTG 59.112 55.000 0.00 0.00 0.00 3.77
5088 12447 0.038166 GAGGGTGTGGATTTGGCTCA 59.962 55.000 0.00 0.00 0.00 4.26
5089 12448 0.482446 AGGGTGTGGATTTGGCTCAA 59.518 50.000 0.00 0.00 0.00 3.02
5090 12449 1.077663 AGGGTGTGGATTTGGCTCAAT 59.922 47.619 0.00 0.00 0.00 2.57
5091 12450 1.205417 GGGTGTGGATTTGGCTCAATG 59.795 52.381 0.00 0.00 0.00 2.82
5092 12451 1.404583 GGTGTGGATTTGGCTCAATGC 60.405 52.381 0.00 0.00 41.94 3.56
5094 12453 2.754552 GTGTGGATTTGGCTCAATGCTA 59.245 45.455 3.86 0.00 42.39 3.49
5117 12476 1.139853 GTGCATCCTCAACCTCCTAGG 59.860 57.143 0.82 0.82 42.49 3.02
5121 12480 2.435693 CCTCAACCTCCTAGGGGCG 61.436 68.421 9.46 1.93 40.58 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 1.962807 CTCCAAAGGCCATGACAACAA 59.037 47.619 5.01 0.00 0.00 2.83
134 135 4.702131 CAGCAGCTAAGGACCAGTAAAATT 59.298 41.667 0.00 0.00 0.00 1.82
360 375 5.798132 ACTAATGCTCAGTGAGTCATTTCA 58.202 37.500 30.32 20.18 37.48 2.69
446 462 4.457257 GGAGAAAGGATTCAACAGTTCCAG 59.543 45.833 0.00 0.00 38.06 3.86
501 523 8.921205 AGGAACTTCTAAGTACTTCAGTTACAA 58.079 33.333 25.33 5.61 38.57 2.41
504 526 9.804977 AGTAGGAACTTCTAAGTACTTCAGTTA 57.195 33.333 19.98 8.75 41.75 2.24
538 560 5.885352 TCTCAGGTTGTTCATCTCTCTAGAG 59.115 44.000 13.98 13.98 43.36 2.43
543 565 5.336150 TCATCTCAGGTTGTTCATCTCTC 57.664 43.478 0.00 0.00 0.00 3.20
545 567 7.271511 AGTATTCATCTCAGGTTGTTCATCTC 58.728 38.462 0.00 0.00 0.00 2.75
546 568 7.192852 AGTATTCATCTCAGGTTGTTCATCT 57.807 36.000 0.00 0.00 0.00 2.90
547 569 8.200792 AGTAGTATTCATCTCAGGTTGTTCATC 58.799 37.037 0.00 0.00 0.00 2.92
549 571 7.482169 AGTAGTATTCATCTCAGGTTGTTCA 57.518 36.000 0.00 0.00 0.00 3.18
550 572 7.921745 GGTAGTAGTATTCATCTCAGGTTGTTC 59.078 40.741 0.00 0.00 0.00 3.18
553 575 7.068839 ACTGGTAGTAGTATTCATCTCAGGTTG 59.931 40.741 0.00 0.00 0.00 3.77
555 577 6.674573 ACTGGTAGTAGTATTCATCTCAGGT 58.325 40.000 0.00 0.00 0.00 4.00
567 589 9.347240 GGAAAGTCATGTATACTGGTAGTAGTA 57.653 37.037 4.17 0.00 33.66 1.82
568 590 7.837689 TGGAAAGTCATGTATACTGGTAGTAGT 59.162 37.037 4.17 0.00 33.66 2.73
569 591 8.234136 TGGAAAGTCATGTATACTGGTAGTAG 57.766 38.462 4.17 0.00 33.66 2.57
570 592 8.777578 ATGGAAAGTCATGTATACTGGTAGTA 57.222 34.615 4.17 0.00 34.82 1.82
572 594 7.382488 CGAATGGAAAGTCATGTATACTGGTAG 59.618 40.741 4.17 0.00 0.00 3.18
574 596 6.049149 CGAATGGAAAGTCATGTATACTGGT 58.951 40.000 4.17 0.00 0.00 4.00
576 598 6.535150 ACACGAATGGAAAGTCATGTATACTG 59.465 38.462 4.17 0.58 0.00 2.74
577 599 6.640518 ACACGAATGGAAAGTCATGTATACT 58.359 36.000 4.17 0.00 0.00 2.12
580 602 5.487433 TGACACGAATGGAAAGTCATGTAT 58.513 37.500 0.00 0.00 34.59 2.29
581 603 4.888917 TGACACGAATGGAAAGTCATGTA 58.111 39.130 0.00 0.00 34.59 2.29
585 607 8.611757 CATTATTATGACACGAATGGAAAGTCA 58.388 33.333 0.00 0.00 42.62 3.41
587 609 8.506168 ACATTATTATGACACGAATGGAAAGT 57.494 30.769 0.00 0.00 35.65 2.66
588 610 9.438291 GAACATTATTATGACACGAATGGAAAG 57.562 33.333 0.00 0.00 35.65 2.62
590 612 8.499403 TGAACATTATTATGACACGAATGGAA 57.501 30.769 0.00 0.00 35.65 3.53
591 613 8.499403 TTGAACATTATTATGACACGAATGGA 57.501 30.769 0.00 0.00 35.65 3.41
592 614 8.397906 ACTTGAACATTATTATGACACGAATGG 58.602 33.333 0.00 0.00 35.65 3.16
594 616 7.910162 GCACTTGAACATTATTATGACACGAAT 59.090 33.333 0.00 0.00 35.65 3.34
595 617 7.119116 AGCACTTGAACATTATTATGACACGAA 59.881 33.333 0.00 0.00 35.65 3.85
597 619 6.684131 CAGCACTTGAACATTATTATGACACG 59.316 38.462 0.00 0.00 35.65 4.49
598 620 6.968904 CCAGCACTTGAACATTATTATGACAC 59.031 38.462 0.00 0.00 35.65 3.67
599 621 6.883756 TCCAGCACTTGAACATTATTATGACA 59.116 34.615 0.00 0.00 35.65 3.58
600 622 7.320443 TCCAGCACTTGAACATTATTATGAC 57.680 36.000 0.00 0.00 35.65 3.06
601 623 8.523915 AATCCAGCACTTGAACATTATTATGA 57.476 30.769 0.00 0.00 35.65 2.15
607 629 7.936496 TGAATAATCCAGCACTTGAACATTA 57.064 32.000 0.00 0.00 0.00 1.90
610 632 6.647334 TTTGAATAATCCAGCACTTGAACA 57.353 33.333 0.00 0.00 0.00 3.18
611 633 9.638239 TTTATTTGAATAATCCAGCACTTGAAC 57.362 29.630 0.00 0.00 31.47 3.18
613 635 9.806203 CATTTATTTGAATAATCCAGCACTTGA 57.194 29.630 0.00 0.00 31.47 3.02
614 636 8.545420 GCATTTATTTGAATAATCCAGCACTTG 58.455 33.333 0.00 0.00 31.47 3.16
615 637 7.712205 GGCATTTATTTGAATAATCCAGCACTT 59.288 33.333 0.00 0.00 31.47 3.16
616 638 7.147689 TGGCATTTATTTGAATAATCCAGCACT 60.148 33.333 0.00 0.00 31.47 4.40
617 639 6.985645 TGGCATTTATTTGAATAATCCAGCAC 59.014 34.615 0.00 0.00 31.47 4.40
618 640 7.122138 TGGCATTTATTTGAATAATCCAGCA 57.878 32.000 0.00 0.00 31.47 4.41
619 641 8.611654 AATGGCATTTATTTGAATAATCCAGC 57.388 30.769 6.96 8.60 33.15 4.85
633 655 9.661563 CCAATCAAAGCATATAATGGCATTTAT 57.338 29.630 19.21 12.40 0.00 1.40
634 656 8.868103 TCCAATCAAAGCATATAATGGCATTTA 58.132 29.630 19.21 10.72 0.00 1.40
635 657 7.737869 TCCAATCAAAGCATATAATGGCATTT 58.262 30.769 19.21 8.86 0.00 2.32
636 658 7.305813 TCCAATCAAAGCATATAATGGCATT 57.694 32.000 18.01 18.01 0.00 3.56
637 659 6.921486 TCCAATCAAAGCATATAATGGCAT 57.079 33.333 0.00 0.00 0.00 4.40
639 661 5.579511 GCATCCAATCAAAGCATATAATGGC 59.420 40.000 0.00 0.00 0.00 4.40
640 662 6.693466 TGCATCCAATCAAAGCATATAATGG 58.307 36.000 0.00 0.00 0.00 3.16
642 664 8.129496 TGATGCATCCAATCAAAGCATATAAT 57.871 30.769 23.67 0.00 45.08 1.28
643 665 7.527568 TGATGCATCCAATCAAAGCATATAA 57.472 32.000 23.67 0.00 45.08 0.98
644 666 7.543756 CATGATGCATCCAATCAAAGCATATA 58.456 34.615 23.67 0.00 45.08 0.86
645 667 6.398095 CATGATGCATCCAATCAAAGCATAT 58.602 36.000 23.67 3.00 45.08 1.78
648 670 3.739830 GCATGATGCATCCAATCAAAGCA 60.740 43.478 23.67 1.96 44.26 3.91
662 684 7.864686 TGTGTACTTATTAGAATGCATGATGC 58.135 34.615 11.12 11.12 45.29 3.91
856 4857 6.739112 TCAGATACGACTCATAATCCACTTG 58.261 40.000 0.00 0.00 0.00 3.16
873 4877 8.467598 TCACTGTCATAAGGTTAGTTCAGATAC 58.532 37.037 0.00 0.00 0.00 2.24
945 4952 4.905456 TGCTTATATACCACTACTTGCCCT 59.095 41.667 0.00 0.00 0.00 5.19
1179 5186 5.278964 GGTAACTAAGAAGCCAAAACTCG 57.721 43.478 0.00 0.00 0.00 4.18
1205 5212 4.033009 TGCTTCCTAGATGACATCCAGAA 58.967 43.478 11.92 11.02 0.00 3.02
1284 5293 3.220507 TGCATGCACAAATAGCTTCAC 57.779 42.857 18.46 0.00 0.00 3.18
1580 5909 7.649306 CGAGCAAGGAATTAATGAAATAAAGGG 59.351 37.037 0.00 0.00 0.00 3.95
1630 5960 1.452108 ACCAGCAAGCGGATAAGGC 60.452 57.895 9.31 0.00 0.00 4.35
1631 5961 1.718757 GCACCAGCAAGCGGATAAGG 61.719 60.000 9.31 0.00 41.58 2.69
1632 5962 0.745845 AGCACCAGCAAGCGGATAAG 60.746 55.000 9.31 0.16 45.49 1.73
1633 5963 0.322456 AAGCACCAGCAAGCGGATAA 60.322 50.000 9.31 0.00 45.49 1.75
1634 5964 0.322456 AAAGCACCAGCAAGCGGATA 60.322 50.000 9.31 0.00 45.49 2.59
1635 5965 1.604593 AAAGCACCAGCAAGCGGAT 60.605 52.632 9.31 0.00 45.49 4.18
1636 5966 2.203337 AAAGCACCAGCAAGCGGA 60.203 55.556 9.31 0.00 45.49 5.54
1637 5967 2.049802 CAAAGCACCAGCAAGCGG 60.050 61.111 0.00 2.25 45.49 5.52
1638 5968 1.855213 TAGCAAAGCACCAGCAAGCG 61.855 55.000 0.00 0.00 45.49 4.68
1639 5969 0.529378 ATAGCAAAGCACCAGCAAGC 59.471 50.000 0.00 0.00 45.49 4.01
1640 5970 1.133790 GGATAGCAAAGCACCAGCAAG 59.866 52.381 0.00 0.00 45.49 4.01
1641 5971 1.176527 GGATAGCAAAGCACCAGCAA 58.823 50.000 0.00 0.00 45.49 3.91
1642 5972 1.026182 CGGATAGCAAAGCACCAGCA 61.026 55.000 0.00 0.00 45.49 4.41
1643 5973 0.744414 TCGGATAGCAAAGCACCAGC 60.744 55.000 0.00 0.00 42.56 4.85
1644 5974 1.398390 GTTCGGATAGCAAAGCACCAG 59.602 52.381 0.00 0.00 0.00 4.00
1645 5975 1.003118 AGTTCGGATAGCAAAGCACCA 59.997 47.619 0.00 0.00 0.00 4.17
1646 5976 1.739067 AGTTCGGATAGCAAAGCACC 58.261 50.000 0.00 0.00 0.00 5.01
1647 5977 2.608090 GGTAGTTCGGATAGCAAAGCAC 59.392 50.000 0.00 0.00 0.00 4.40
1648 5978 2.737359 CGGTAGTTCGGATAGCAAAGCA 60.737 50.000 0.00 0.00 0.00 3.91
1649 5979 1.859080 CGGTAGTTCGGATAGCAAAGC 59.141 52.381 0.00 0.00 0.00 3.51
1650 5980 3.160777 ACGGTAGTTCGGATAGCAAAG 57.839 47.619 0.00 0.00 0.00 2.77
1651 5981 3.255725 CAACGGTAGTTCGGATAGCAAA 58.744 45.455 0.00 0.00 38.79 3.68
1652 5982 2.883574 CAACGGTAGTTCGGATAGCAA 58.116 47.619 0.00 0.00 38.79 3.91
1653 5983 1.470285 GCAACGGTAGTTCGGATAGCA 60.470 52.381 0.00 0.00 38.79 3.49
1654 5984 1.202382 AGCAACGGTAGTTCGGATAGC 60.202 52.381 0.00 0.00 38.79 2.97
1655 5985 2.865343 AGCAACGGTAGTTCGGATAG 57.135 50.000 0.00 0.00 38.79 2.08
1656 5986 3.696051 AGTTAGCAACGGTAGTTCGGATA 59.304 43.478 0.00 0.00 38.79 2.59
1657 5987 2.494870 AGTTAGCAACGGTAGTTCGGAT 59.505 45.455 0.00 0.00 38.79 4.18
1658 5988 1.888512 AGTTAGCAACGGTAGTTCGGA 59.111 47.619 0.00 0.00 38.79 4.55
1659 5989 2.094854 AGAGTTAGCAACGGTAGTTCGG 60.095 50.000 0.00 0.00 38.79 4.30
1660 5990 2.915463 CAGAGTTAGCAACGGTAGTTCG 59.085 50.000 0.00 0.00 38.79 3.95
1661 5991 4.170292 TCAGAGTTAGCAACGGTAGTTC 57.830 45.455 0.00 0.00 38.79 3.01
1662 5992 4.280174 TCTTCAGAGTTAGCAACGGTAGTT 59.720 41.667 0.00 0.00 42.15 2.24
1663 5993 3.825014 TCTTCAGAGTTAGCAACGGTAGT 59.175 43.478 0.00 0.00 36.23 2.73
1664 5994 4.436242 TCTTCAGAGTTAGCAACGGTAG 57.564 45.455 0.00 0.00 36.23 3.18
1665 5995 4.859304 TTCTTCAGAGTTAGCAACGGTA 57.141 40.909 0.00 0.00 36.23 4.02
1666 5996 3.746045 TTCTTCAGAGTTAGCAACGGT 57.254 42.857 0.00 0.00 36.23 4.83
1667 5997 3.120511 GCTTTCTTCAGAGTTAGCAACGG 60.121 47.826 0.00 0.00 36.23 4.44
1668 5998 3.743396 AGCTTTCTTCAGAGTTAGCAACG 59.257 43.478 0.00 0.00 34.83 4.10
1669 5999 4.994217 AGAGCTTTCTTCAGAGTTAGCAAC 59.006 41.667 0.00 0.00 34.83 4.17
1670 6000 4.993584 CAGAGCTTTCTTCAGAGTTAGCAA 59.006 41.667 0.00 0.00 34.83 3.91
1671 6001 4.564041 CAGAGCTTTCTTCAGAGTTAGCA 58.436 43.478 0.00 0.00 34.83 3.49
1672 6002 3.370672 GCAGAGCTTTCTTCAGAGTTAGC 59.629 47.826 0.00 0.00 33.56 3.09
1673 6003 4.819769 AGCAGAGCTTTCTTCAGAGTTAG 58.180 43.478 0.00 0.00 33.89 2.34
1674 6004 4.881019 AGCAGAGCTTTCTTCAGAGTTA 57.119 40.909 0.00 0.00 33.89 2.24
1675 6005 3.767902 AGCAGAGCTTTCTTCAGAGTT 57.232 42.857 0.00 0.00 33.89 3.01
1693 6023 1.068474 TAAGCGAAGAAGCACGAAGC 58.932 50.000 0.00 0.00 46.19 3.86
1694 6024 3.367932 TGAATAAGCGAAGAAGCACGAAG 59.632 43.478 0.00 0.00 40.15 3.79
1695 6025 3.322369 TGAATAAGCGAAGAAGCACGAA 58.678 40.909 0.00 0.00 40.15 3.85
1696 6026 2.954316 TGAATAAGCGAAGAAGCACGA 58.046 42.857 0.00 0.00 40.15 4.35
1697 6027 3.722555 TTGAATAAGCGAAGAAGCACG 57.277 42.857 0.00 0.00 40.15 5.34
1698 6028 3.788163 GCATTGAATAAGCGAAGAAGCAC 59.212 43.478 0.00 0.00 40.15 4.40
1699 6029 3.439825 TGCATTGAATAAGCGAAGAAGCA 59.560 39.130 0.00 0.00 40.15 3.91
1700 6030 4.019919 TGCATTGAATAAGCGAAGAAGC 57.980 40.909 0.00 0.00 37.41 3.86
1701 6031 6.260377 TGAATGCATTGAATAAGCGAAGAAG 58.740 36.000 18.59 0.00 0.00 2.85
1702 6032 6.193514 TGAATGCATTGAATAAGCGAAGAA 57.806 33.333 18.59 0.00 0.00 2.52
1703 6033 5.816449 TGAATGCATTGAATAAGCGAAGA 57.184 34.783 18.59 0.00 0.00 2.87
1704 6034 6.141844 GTGATGAATGCATTGAATAAGCGAAG 59.858 38.462 18.59 0.00 34.11 3.79
1705 6035 5.972973 GTGATGAATGCATTGAATAAGCGAA 59.027 36.000 18.59 0.00 34.11 4.70
1706 6036 5.506151 GGTGATGAATGCATTGAATAAGCGA 60.506 40.000 18.59 0.00 34.11 4.93
1707 6037 4.678287 GGTGATGAATGCATTGAATAAGCG 59.322 41.667 18.59 0.00 34.11 4.68
1708 6038 5.839621 AGGTGATGAATGCATTGAATAAGC 58.160 37.500 18.59 12.55 34.11 3.09
1709 6039 6.635641 CGAAGGTGATGAATGCATTGAATAAG 59.364 38.462 18.59 0.00 34.11 1.73
1710 6040 6.095300 ACGAAGGTGATGAATGCATTGAATAA 59.905 34.615 18.59 0.42 34.11 1.40
1711 6041 5.589855 ACGAAGGTGATGAATGCATTGAATA 59.410 36.000 18.59 0.00 34.11 1.75
1712 6042 4.400251 ACGAAGGTGATGAATGCATTGAAT 59.600 37.500 18.59 10.29 34.11 2.57
1713 6043 3.758023 ACGAAGGTGATGAATGCATTGAA 59.242 39.130 18.59 5.18 34.11 2.69
1714 6044 3.346315 ACGAAGGTGATGAATGCATTGA 58.654 40.909 18.59 9.34 34.11 2.57
1715 6045 3.127376 TGACGAAGGTGATGAATGCATTG 59.873 43.478 18.59 0.29 34.11 2.82
1716 6046 3.346315 TGACGAAGGTGATGAATGCATT 58.654 40.909 12.83 12.83 34.11 3.56
1717 6047 2.989909 TGACGAAGGTGATGAATGCAT 58.010 42.857 0.00 0.00 37.47 3.96
1718 6048 2.470983 TGACGAAGGTGATGAATGCA 57.529 45.000 0.00 0.00 0.00 3.96
1719 6049 3.488047 CCATTGACGAAGGTGATGAATGC 60.488 47.826 0.00 0.00 0.00 3.56
1722 6052 2.083774 GCCATTGACGAAGGTGATGAA 58.916 47.619 0.00 0.00 0.00 2.57
2494 7742 8.713708 ACTGATTAGCACTCCTACTATGTATT 57.286 34.615 0.00 0.00 0.00 1.89
2498 7746 6.266558 AGGAACTGATTAGCACTCCTACTATG 59.733 42.308 2.54 0.00 37.18 2.23
2588 7903 3.241067 TGGTACTCAATTAGTGCGGAC 57.759 47.619 0.00 0.00 41.40 4.79
2651 7977 4.212004 GCAGCACGAGCATTTAGATCATAA 59.788 41.667 7.77 0.00 45.49 1.90
2781 8117 8.402472 GGATGTACAAATGGTTGATTCGATTTA 58.598 33.333 0.00 0.00 38.20 1.40
2844 8180 0.905357 ACCACAGCTATCACCCAGTC 59.095 55.000 0.00 0.00 0.00 3.51
2845 8181 2.247699 TACCACAGCTATCACCCAGT 57.752 50.000 0.00 0.00 0.00 4.00
2846 8182 3.845781 ATTACCACAGCTATCACCCAG 57.154 47.619 0.00 0.00 0.00 4.45
2848 8184 5.291905 AGTAATTACCACAGCTATCACCC 57.708 43.478 12.05 0.00 0.00 4.61
2943 8282 8.873215 ATGCACTCACATATACACTAAAGTAC 57.127 34.615 0.00 0.00 0.00 2.73
2956 8295 6.999871 ACCATATTCATCAATGCACTCACATA 59.000 34.615 0.00 0.00 0.00 2.29
2976 8315 7.287005 CAGTCCCACTATCTTTACTACACCATA 59.713 40.741 0.00 0.00 0.00 2.74
3057 8400 8.552296 AGAAGAACAAATCACTCCCTATTACAT 58.448 33.333 0.00 0.00 0.00 2.29
3155 8498 1.301716 AGTAACACCAGCCGCACAG 60.302 57.895 0.00 0.00 0.00 3.66
3176 8519 2.288030 CGGTCCTTGGTATAGCGTTAGG 60.288 54.545 9.91 9.91 0.00 2.69
3370 8713 1.032014 AACATGCCCACACACACTTC 58.968 50.000 0.00 0.00 0.00 3.01
3405 8776 7.651808 CAACATACAGGCTAAATTTAGGATGG 58.348 38.462 23.37 2.65 0.00 3.51
3424 8795 1.919654 TGGGCCCTAGAAAGCAACATA 59.080 47.619 25.70 0.00 0.00 2.29
3530 8901 5.157940 TCTTGAAAAGTCTCTCTCCATGG 57.842 43.478 4.97 4.97 46.34 3.66
3531 8902 5.585445 CCATCTTGAAAAGTCTCTCTCCATG 59.415 44.000 0.00 0.00 46.34 3.66
3608 8979 2.677228 CTGCCACCGAGGGGATTT 59.323 61.111 0.00 0.00 38.09 2.17
3618 8989 0.527565 ATCAACGATTTGCTGCCACC 59.472 50.000 0.00 0.00 32.17 4.61
3620 8991 1.885233 TGAATCAACGATTTGCTGCCA 59.115 42.857 0.00 0.00 31.89 4.92
3621 8992 2.634982 TGAATCAACGATTTGCTGCC 57.365 45.000 0.00 0.00 31.89 4.85
3668 9213 5.560966 ACGCCCTACAAATGAAGTAATTG 57.439 39.130 0.00 0.00 0.00 2.32
3775 9322 4.935808 AGAATGACCGTGATAACCAAAGTC 59.064 41.667 0.00 0.00 32.55 3.01
3929 9487 2.677524 GGCCAGCAACCATGAGCA 60.678 61.111 0.00 0.00 0.00 4.26
4023 9581 5.003804 TCTTGTTCCTCCAAATCTAAGCAC 58.996 41.667 0.00 0.00 0.00 4.40
4146 9704 6.072452 GCAAAAGCTCTTCTACACCTAACAAT 60.072 38.462 0.00 0.00 0.00 2.71
4388 9951 6.861055 TCAAGTCAAACTTTGTGAACTTTGAC 59.139 34.615 13.83 13.83 42.53 3.18
4415 9978 3.976793 TGCTCTGCATATTAGCTTTGC 57.023 42.857 0.00 0.00 37.16 3.68
4429 9992 3.119743 TCGCTCCATTTTCATTTGCTCTG 60.120 43.478 0.00 0.00 0.00 3.35
4434 9997 5.106555 ACAGTAGTCGCTCCATTTTCATTTG 60.107 40.000 0.00 0.00 0.00 2.32
4534 10625 6.270000 TCAAAATCTCCTCTCCTCTACAACAA 59.730 38.462 0.00 0.00 0.00 2.83
4578 10669 1.996292 CGTCATCACGGAGTCACAAT 58.004 50.000 0.00 0.00 41.61 2.71
4580 10671 1.080772 GCGTCATCACGGAGTCACA 60.081 57.895 0.00 0.00 46.80 3.58
4582 10673 2.178273 CGCGTCATCACGGAGTCA 59.822 61.111 0.00 0.00 46.80 3.41
4592 10683 2.261671 GGTCACCAGTCGCGTCAT 59.738 61.111 5.77 0.00 0.00 3.06
4628 10723 2.203139 CACACGGGAACACTGCCA 60.203 61.111 0.00 0.00 30.82 4.92
4631 10726 0.250295 ATCACCACACGGGAACACTG 60.250 55.000 0.00 0.00 41.15 3.66
4632 10727 0.250295 CATCACCACACGGGAACACT 60.250 55.000 0.00 0.00 41.15 3.55
4634 10729 1.072332 CCATCACCACACGGGAACA 59.928 57.895 0.00 0.00 41.15 3.18
4635 10730 1.072505 ACCATCACCACACGGGAAC 59.927 57.895 0.00 0.00 41.15 3.62
4636 10731 1.072332 CACCATCACCACACGGGAA 59.928 57.895 0.00 0.00 41.15 3.97
4727 12084 2.033448 CACTAGCCACCGCCCAAA 59.967 61.111 0.00 0.00 34.57 3.28
4752 12111 1.378514 GGCCGCAAATCTTCCTCCA 60.379 57.895 0.00 0.00 0.00 3.86
4781 12140 4.577677 TGCGGTGGCCAAGCTCAA 62.578 61.111 27.89 11.29 38.85 3.02
4793 12152 4.787280 CTCCCTCCCTCCTGCGGT 62.787 72.222 0.00 0.00 0.00 5.68
4829 12188 4.539083 TGCGTCCGCCACAACACT 62.539 61.111 9.43 0.00 41.09 3.55
4840 12199 1.732259 CATCACCTAGTTGTTGCGTCC 59.268 52.381 0.00 0.00 0.00 4.79
4858 12217 0.392998 CAGCGCTCCCTACCAAACAT 60.393 55.000 7.13 0.00 0.00 2.71
4860 12219 2.399356 GCAGCGCTCCCTACCAAAC 61.399 63.158 7.13 0.00 0.00 2.93
4873 12232 3.119673 ACTCCGAGATATAATGAGCAGCG 60.120 47.826 1.33 0.00 0.00 5.18
4877 12236 3.690139 TCCGACTCCGAGATATAATGAGC 59.310 47.826 1.33 0.00 38.22 4.26
4883 12242 2.356844 CCCCATCCGACTCCGAGATATA 60.357 54.545 1.33 0.00 38.22 0.86
4885 12244 0.251209 CCCCATCCGACTCCGAGATA 60.251 60.000 1.33 0.00 38.22 1.98
4906 12265 3.353836 CCAACGTTCGTGGCCAGG 61.354 66.667 19.57 19.57 0.00 4.45
4935 12294 0.033504 GCTCAACTCTTCCGACACCA 59.966 55.000 0.00 0.00 0.00 4.17
5050 12409 3.525537 CTCGCCTCTATCAACACATTGT 58.474 45.455 0.00 0.00 37.11 2.71
5062 12421 0.325296 AATCCACACCCTCGCCTCTA 60.325 55.000 0.00 0.00 0.00 2.43
5063 12422 1.201429 AAATCCACACCCTCGCCTCT 61.201 55.000 0.00 0.00 0.00 3.69
5091 12450 2.615912 GAGGTTGAGGATGCACAATAGC 59.384 50.000 0.00 0.00 0.00 2.97
5092 12451 3.118112 AGGAGGTTGAGGATGCACAATAG 60.118 47.826 0.00 0.00 0.00 1.73
5094 12453 1.637553 AGGAGGTTGAGGATGCACAAT 59.362 47.619 0.00 0.00 0.00 2.71
5101 12460 0.400670 GCCCCTAGGAGGTTGAGGAT 60.401 60.000 11.48 0.00 31.93 3.24


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

AutoCloner maintained by Alex Coulton.