Multiple sequence alignment - TraesCS4B01G140700

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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 TraesCS4B01G140700 chr4B 100.000 3810 0 0 330 4139 185208898 185212707 0.000000e+00 7036.0
1 TraesCS4B01G140700 chr4B 95.050 303 15 0 330 632 516868903 516868601 1.040000e-130 477.0
2 TraesCS4B01G140700 chr4B 100.000 103 0 0 1 103 185208569 185208671 1.520000e-44 191.0
3 TraesCS4B01G140700 chr4A 94.540 2454 87 23 695 3112 448540239 448537797 0.000000e+00 3746.0
4 TraesCS4B01G140700 chr4A 97.590 83 2 0 1 83 743301377 743301295 4.310000e-30 143.0
5 TraesCS4B01G140700 chr4A 93.407 91 4 2 1 90 45613167 45613078 2.600000e-27 134.0
6 TraesCS4B01G140700 chr4A 93.846 65 1 3 649 712 448540312 448540250 1.220000e-15 95.3
7 TraesCS4B01G140700 chr4D 93.690 2520 83 34 649 3112 122163591 122166090 0.000000e+00 3703.0
8 TraesCS4B01G140700 chr2B 95.813 1027 43 0 3113 4139 132411259 132410233 0.000000e+00 1659.0
9 TraesCS4B01G140700 chr2B 95.402 435 19 1 3109 3542 132405601 132405167 0.000000e+00 691.0
10 TraesCS4B01G140700 chr2B 95.710 303 13 0 330 632 51101474 51101776 4.810000e-134 488.0
11 TraesCS4B01G140700 chr2B 97.531 81 2 0 1 81 702193273 702193353 5.580000e-29 139.0
12 TraesCS4B01G140700 chr2B 93.478 92 3 2 1 91 600589738 600589827 2.600000e-27 134.0
13 TraesCS4B01G140700 chr7A 88.599 1035 107 9 3108 4139 438252918 438251892 0.000000e+00 1247.0
14 TraesCS4B01G140700 chr7A 94.481 308 16 1 330 636 163350823 163350516 1.350000e-129 473.0
15 TraesCS4B01G140700 chr7A 94.318 88 5 0 1 88 150353308 150353395 7.220000e-28 135.0
16 TraesCS4B01G140700 chr7A 90.909 99 8 1 1 98 243617566 243617468 9.340000e-27 132.0
17 TraesCS4B01G140700 chr5B 87.028 1033 121 13 3113 4139 576543766 576544791 0.000000e+00 1153.0
18 TraesCS4B01G140700 chr3A 90.317 630 51 10 3113 3737 659624553 659625177 0.000000e+00 817.0
19 TraesCS4B01G140700 chr3A 90.141 497 38 11 3109 3599 401469019 401469510 1.620000e-178 636.0
20 TraesCS4B01G140700 chr3A 89.940 497 39 11 3109 3599 401509963 401510454 7.550000e-177 630.0
21 TraesCS4B01G140700 chr3A 89.937 477 36 12 3101 3571 401463724 401464194 4.580000e-169 604.0
22 TraesCS4B01G140700 chr3A 88.934 497 44 11 3109 3599 659630081 659630572 1.650000e-168 603.0
23 TraesCS4B01G140700 chr3A 89.727 477 37 12 3101 3571 401504664 401505134 2.130000e-167 599.0
24 TraesCS4B01G140700 chr3A 92.157 306 22 2 3835 4139 659625145 659625449 8.220000e-117 431.0
25 TraesCS4B01G140700 chr5D 91.699 518 42 1 3622 4139 93846311 93845795 0.000000e+00 717.0
26 TraesCS4B01G140700 chr7B 96.721 305 10 0 330 634 735949072 735948768 3.690000e-140 508.0
27 TraesCS4B01G140700 chr7B 94.318 88 5 0 1 88 675271115 675271202 7.220000e-28 135.0
28 TraesCS4B01G140700 chr6B 95.050 303 12 1 330 632 422971371 422971670 1.350000e-129 473.0
29 TraesCS4B01G140700 chr6B 95.349 86 4 0 1 86 720238336 720238251 2.010000e-28 137.0
30 TraesCS4B01G140700 chr3B 95.578 294 13 0 332 625 221817224 221816931 4.840000e-129 472.0
31 TraesCS4B01G140700 chr3B 94.444 306 17 0 330 635 785308754 785308449 4.840000e-129 472.0
32 TraesCS4B01G140700 chr3B 94.426 305 17 0 330 634 433757805 433758109 1.740000e-128 470.0
33 TraesCS4B01G140700 chr1B 94.444 306 12 2 330 635 1744347 1744647 2.250000e-127 466.0
34 TraesCS4B01G140700 chr7D 77.113 852 142 45 3314 4136 77425036 77424209 1.060000e-120 444.0
35 TraesCS4B01G140700 chr7D 77.279 779 133 38 3374 4130 312549330 312548574 6.400000e-113 418.0
36 TraesCS4B01G140700 chr2D 76.987 843 147 41 3313 4130 551436931 551436111 4.910000e-119 438.0
37 TraesCS4B01G140700 chr1A 77.922 770 119 46 3388 4130 311076960 311076215 2.290000e-117 433.0
38 TraesCS4B01G140700 chr1A 76.190 840 155 40 3313 4130 35492717 35493533 6.440000e-108 401.0
39 TraesCS4B01G140700 chr3D 89.524 105 4 6 1 101 47633923 47633822 4.340000e-25 126.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G140700 chr4B 185208569 185212707 4138 False 3613.50 7036 100.000 1 4139 2 chr4B.!!$F1 4138
1 TraesCS4B01G140700 chr4A 448537797 448540312 2515 True 1920.65 3746 94.193 649 3112 2 chr4A.!!$R3 2463
2 TraesCS4B01G140700 chr4D 122163591 122166090 2499 False 3703.00 3703 93.690 649 3112 1 chr4D.!!$F1 2463
3 TraesCS4B01G140700 chr2B 132410233 132411259 1026 True 1659.00 1659 95.813 3113 4139 1 chr2B.!!$R2 1026
4 TraesCS4B01G140700 chr7A 438251892 438252918 1026 True 1247.00 1247 88.599 3108 4139 1 chr7A.!!$R3 1031
5 TraesCS4B01G140700 chr5B 576543766 576544791 1025 False 1153.00 1153 87.028 3113 4139 1 chr5B.!!$F1 1026
6 TraesCS4B01G140700 chr3A 659624553 659625449 896 False 624.00 817 91.237 3113 4139 2 chr3A.!!$F6 1026
7 TraesCS4B01G140700 chr5D 93845795 93846311 516 True 717.00 717 91.699 3622 4139 1 chr5D.!!$R1 517
8 TraesCS4B01G140700 chr7D 77424209 77425036 827 True 444.00 444 77.113 3314 4136 1 chr7D.!!$R1 822
9 TraesCS4B01G140700 chr7D 312548574 312549330 756 True 418.00 418 77.279 3374 4130 1 chr7D.!!$R2 756
10 TraesCS4B01G140700 chr2D 551436111 551436931 820 True 438.00 438 76.987 3313 4130 1 chr2D.!!$R1 817
11 TraesCS4B01G140700 chr1A 311076215 311076960 745 True 433.00 433 77.922 3388 4130 1 chr1A.!!$R1 742
12 TraesCS4B01G140700 chr1A 35492717 35493533 816 False 401.00 401 76.190 3313 4130 1 chr1A.!!$F1 817

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
623 624 0.032952 AGTTTAGCGCGACTGTTGGA 59.967 50.0 12.10 0.0 0.00 3.53 F
654 655 0.039618 ATCCGGTTGGCCTTTCACAT 59.960 50.0 3.32 0.0 34.14 3.21 F
754 783 0.174845 CGCCGACAAATAGGAGGTCA 59.825 55.0 0.00 0.0 0.00 4.02 F
863 894 0.324275 TTTATGAGCCCAGCCCAACC 60.324 55.0 0.00 0.0 0.00 3.77 F
1908 1998 1.289160 TATCACCCTTGCTGCCTTCT 58.711 50.0 0.00 0.0 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 1998 0.035915 TTGGCACATAACGGCAGCTA 60.036 50.000 0.00 0.00 40.36 3.32 R
2446 2536 4.037565 TGAAACTAGTCTGCAGAAGAACGA 59.962 41.667 20.19 1.69 36.40 3.85 R
2678 2771 3.194116 TGCATGAAAAGGATCCTTCTTGC 59.806 43.478 30.06 30.06 45.70 4.01 R
2799 2894 2.373335 AGCCAGGAGATCAGATACGT 57.627 50.000 0.00 0.00 0.00 3.57 R
3295 3399 2.370445 CCTCCAGAGCAATCCCCGT 61.370 63.158 0.00 0.00 0.00 5.28 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 6.893020 ATAACCTTATTATGGCCTCTAGGG 57.107 41.667 3.32 2.81 35.18 3.53
62 63 6.297068 AATAACCTTATTATGGCCTCTAGGGC 60.297 42.308 15.36 15.36 44.25 5.19
74 75 4.982241 CCTCTAGGGCATATTTCCTTCA 57.018 45.455 0.00 0.00 34.75 3.02
75 76 5.511386 CCTCTAGGGCATATTTCCTTCAT 57.489 43.478 0.00 0.00 34.75 2.57
76 77 5.885465 CCTCTAGGGCATATTTCCTTCATT 58.115 41.667 0.00 0.00 34.75 2.57
77 78 5.942826 CCTCTAGGGCATATTTCCTTCATTC 59.057 44.000 0.00 0.00 34.75 2.67
78 79 5.880901 TCTAGGGCATATTTCCTTCATTCC 58.119 41.667 0.00 0.00 34.75 3.01
79 80 3.849527 AGGGCATATTTCCTTCATTCCC 58.150 45.455 0.00 0.00 0.00 3.97
80 81 2.558359 GGGCATATTTCCTTCATTCCCG 59.442 50.000 0.00 0.00 0.00 5.14
81 82 3.222603 GGCATATTTCCTTCATTCCCGT 58.777 45.455 0.00 0.00 0.00 5.28
82 83 3.004734 GGCATATTTCCTTCATTCCCGTG 59.995 47.826 0.00 0.00 0.00 4.94
83 84 3.550842 GCATATTTCCTTCATTCCCGTGC 60.551 47.826 0.00 0.00 0.00 5.34
84 85 2.514458 ATTTCCTTCATTCCCGTGCT 57.486 45.000 0.00 0.00 0.00 4.40
85 86 3.644966 ATTTCCTTCATTCCCGTGCTA 57.355 42.857 0.00 0.00 0.00 3.49
86 87 2.691409 TTCCTTCATTCCCGTGCTAG 57.309 50.000 0.00 0.00 0.00 3.42
87 88 0.830648 TCCTTCATTCCCGTGCTAGG 59.169 55.000 0.00 0.00 0.00 3.02
94 95 2.125269 CCCGTGCTAGGGTTTCCG 60.125 66.667 8.66 0.00 46.38 4.30
95 96 2.125269 CCGTGCTAGGGTTTCCGG 60.125 66.667 0.00 0.00 38.33 5.14
96 97 2.660802 CGTGCTAGGGTTTCCGGT 59.339 61.111 0.00 0.00 38.33 5.28
97 98 1.740296 CGTGCTAGGGTTTCCGGTG 60.740 63.158 0.00 0.00 38.33 4.94
98 99 1.376812 GTGCTAGGGTTTCCGGTGG 60.377 63.158 0.00 0.00 38.33 4.61
99 100 2.437895 GCTAGGGTTTCCGGTGGC 60.438 66.667 0.00 0.00 38.33 5.01
100 101 2.125269 CTAGGGTTTCCGGTGGCG 60.125 66.667 0.00 0.00 38.33 5.69
101 102 3.675619 CTAGGGTTTCCGGTGGCGG 62.676 68.421 0.00 0.00 38.33 6.13
373 374 3.978193 GTCCATGGGTGGGTGGCA 61.978 66.667 13.02 0.00 46.06 4.92
374 375 3.660571 TCCATGGGTGGGTGGCAG 61.661 66.667 13.02 0.00 46.06 4.85
375 376 4.764771 CCATGGGTGGGTGGCAGG 62.765 72.222 2.85 0.00 42.11 4.85
376 377 4.764771 CATGGGTGGGTGGCAGGG 62.765 72.222 0.00 0.00 0.00 4.45
412 413 4.517934 CGGGGCGTAGGAGGAGGA 62.518 72.222 0.00 0.00 0.00 3.71
413 414 2.522193 GGGGCGTAGGAGGAGGAG 60.522 72.222 0.00 0.00 0.00 3.69
414 415 2.601868 GGGCGTAGGAGGAGGAGA 59.398 66.667 0.00 0.00 0.00 3.71
415 416 1.529713 GGGCGTAGGAGGAGGAGAG 60.530 68.421 0.00 0.00 0.00 3.20
416 417 1.529713 GGCGTAGGAGGAGGAGAGG 60.530 68.421 0.00 0.00 0.00 3.69
417 418 1.532728 GCGTAGGAGGAGGAGAGGA 59.467 63.158 0.00 0.00 0.00 3.71
418 419 0.536460 GCGTAGGAGGAGGAGAGGAG 60.536 65.000 0.00 0.00 0.00 3.69
419 420 1.133363 CGTAGGAGGAGGAGAGGAGA 58.867 60.000 0.00 0.00 0.00 3.71
420 421 1.071699 CGTAGGAGGAGGAGAGGAGAG 59.928 61.905 0.00 0.00 0.00 3.20
421 422 2.414612 GTAGGAGGAGGAGAGGAGAGA 58.585 57.143 0.00 0.00 0.00 3.10
422 423 1.522900 AGGAGGAGGAGAGGAGAGAG 58.477 60.000 0.00 0.00 0.00 3.20
423 424 1.222567 GGAGGAGGAGAGGAGAGAGT 58.777 60.000 0.00 0.00 0.00 3.24
424 425 1.133792 GGAGGAGGAGAGGAGAGAGTG 60.134 61.905 0.00 0.00 0.00 3.51
425 426 0.258774 AGGAGGAGAGGAGAGAGTGC 59.741 60.000 0.00 0.00 0.00 4.40
426 427 1.101049 GGAGGAGAGGAGAGAGTGCG 61.101 65.000 0.00 0.00 0.00 5.34
427 428 1.077068 AGGAGAGGAGAGAGTGCGG 60.077 63.158 0.00 0.00 0.00 5.69
428 429 2.781158 GGAGAGGAGAGAGTGCGGC 61.781 68.421 0.00 0.00 0.00 6.53
429 430 3.119709 GAGAGGAGAGAGTGCGGCG 62.120 68.421 0.51 0.51 0.00 6.46
430 431 4.863925 GAGGAGAGAGTGCGGCGC 62.864 72.222 27.44 27.44 0.00 6.53
477 478 3.206957 GGGCGCCCGAAATACACC 61.207 66.667 33.60 2.25 0.00 4.16
478 479 3.569690 GGCGCCCGAAATACACCG 61.570 66.667 18.11 0.00 0.00 4.94
479 480 4.232248 GCGCCCGAAATACACCGC 62.232 66.667 0.00 0.00 34.50 5.68
480 481 3.920553 CGCCCGAAATACACCGCG 61.921 66.667 0.00 0.00 0.00 6.46
481 482 4.232248 GCCCGAAATACACCGCGC 62.232 66.667 0.00 0.00 0.00 6.86
482 483 3.920553 CCCGAAATACACCGCGCG 61.921 66.667 25.67 25.67 0.00 6.86
483 484 3.920553 CCGAAATACACCGCGCGG 61.921 66.667 44.88 44.88 42.03 6.46
494 495 3.645975 CGCGCGGGACAGTGTTTT 61.646 61.111 24.84 0.00 0.00 2.43
495 496 2.251371 GCGCGGGACAGTGTTTTC 59.749 61.111 8.83 0.00 0.00 2.29
496 497 2.549282 CGCGGGACAGTGTTTTCG 59.451 61.111 0.00 3.40 0.00 3.46
497 498 1.952133 CGCGGGACAGTGTTTTCGA 60.952 57.895 14.87 0.00 0.00 3.71
498 499 1.568025 GCGGGACAGTGTTTTCGAC 59.432 57.895 14.87 5.70 0.00 4.20
499 500 1.838568 GCGGGACAGTGTTTTCGACC 61.839 60.000 14.87 3.49 0.00 4.79
500 501 1.554042 CGGGACAGTGTTTTCGACCG 61.554 60.000 0.00 1.87 0.00 4.79
501 502 1.568025 GGACAGTGTTTTCGACCGC 59.432 57.895 0.00 0.00 0.00 5.68
502 503 1.200839 GACAGTGTTTTCGACCGCG 59.799 57.895 0.00 0.00 39.35 6.46
503 504 2.127758 CAGTGTTTTCGACCGCGC 60.128 61.111 0.00 0.00 37.46 6.86
504 505 3.698463 AGTGTTTTCGACCGCGCG 61.698 61.111 25.67 25.67 37.46 6.86
516 517 3.192230 CGCGCGCCCAACTCATTA 61.192 61.111 27.72 0.00 0.00 1.90
517 518 2.534019 CGCGCGCCCAACTCATTAT 61.534 57.895 27.72 0.00 0.00 1.28
518 519 1.218875 CGCGCGCCCAACTCATTATA 61.219 55.000 27.72 0.00 0.00 0.98
519 520 0.512952 GCGCGCCCAACTCATTATAG 59.487 55.000 23.24 0.00 0.00 1.31
520 521 0.512952 CGCGCCCAACTCATTATAGC 59.487 55.000 0.00 0.00 0.00 2.97
521 522 0.512952 GCGCCCAACTCATTATAGCG 59.487 55.000 0.00 0.00 44.54 4.26
522 523 0.512952 CGCCCAACTCATTATAGCGC 59.487 55.000 0.00 0.00 35.33 5.92
523 524 0.512952 GCCCAACTCATTATAGCGCG 59.487 55.000 0.00 0.00 0.00 6.86
524 525 1.865865 CCCAACTCATTATAGCGCGT 58.134 50.000 8.43 0.00 0.00 6.01
525 526 1.526887 CCCAACTCATTATAGCGCGTG 59.473 52.381 8.43 0.00 0.00 5.34
526 527 2.201732 CCAACTCATTATAGCGCGTGT 58.798 47.619 8.43 0.00 0.00 4.49
527 528 2.033747 CCAACTCATTATAGCGCGTGTG 60.034 50.000 8.43 0.00 0.00 3.82
528 529 2.579207 ACTCATTATAGCGCGTGTGT 57.421 45.000 8.43 0.57 0.00 3.72
529 530 2.460918 ACTCATTATAGCGCGTGTGTC 58.539 47.619 8.43 0.00 0.00 3.67
530 531 1.448308 CTCATTATAGCGCGTGTGTCG 59.552 52.381 8.43 0.00 43.12 4.35
531 532 1.197055 CATTATAGCGCGTGTGTCGT 58.803 50.000 8.43 0.00 42.13 4.34
532 533 1.586578 CATTATAGCGCGTGTGTCGTT 59.413 47.619 8.43 0.00 42.13 3.85
533 534 1.700523 TTATAGCGCGTGTGTCGTTT 58.299 45.000 8.43 0.00 42.13 3.60
534 535 1.700523 TATAGCGCGTGTGTCGTTTT 58.299 45.000 8.43 0.00 42.13 2.43
535 536 0.863144 ATAGCGCGTGTGTCGTTTTT 59.137 45.000 8.43 0.00 42.13 1.94
536 537 0.042880 TAGCGCGTGTGTCGTTTTTG 60.043 50.000 8.43 0.00 42.13 2.44
537 538 2.901303 GCGCGTGTGTCGTTTTTGC 61.901 57.895 8.43 0.00 42.13 3.68
538 539 2.613528 CGCGTGTGTCGTTTTTGCG 61.614 57.895 0.00 0.00 42.13 4.85
539 540 2.901303 GCGTGTGTCGTTTTTGCGC 61.901 57.895 0.00 0.00 42.13 6.09
540 541 2.613528 CGTGTGTCGTTTTTGCGCG 61.614 57.895 0.00 0.00 34.52 6.86
541 542 2.649349 TGTGTCGTTTTTGCGCGC 60.649 55.556 27.26 27.26 0.00 6.86
542 543 3.383601 GTGTCGTTTTTGCGCGCC 61.384 61.111 30.77 11.85 0.00 6.53
543 544 4.615834 TGTCGTTTTTGCGCGCCC 62.616 61.111 30.77 10.12 0.00 6.13
583 584 4.128982 CGCGCGCGCTAAAACAGA 62.129 61.111 45.97 0.00 39.32 3.41
584 585 2.570838 GCGCGCGCTAAAACAGAC 60.571 61.111 44.38 14.45 38.26 3.51
585 586 3.011760 GCGCGCGCTAAAACAGACT 62.012 57.895 44.38 0.00 38.26 3.24
586 587 1.680105 GCGCGCGCTAAAACAGACTA 61.680 55.000 44.38 0.00 38.26 2.59
587 588 0.711670 CGCGCGCTAAAACAGACTAA 59.288 50.000 30.48 0.00 0.00 2.24
588 589 1.323534 CGCGCGCTAAAACAGACTAAT 59.676 47.619 30.48 0.00 0.00 1.73
589 590 2.222729 CGCGCGCTAAAACAGACTAATT 60.223 45.455 30.48 0.00 0.00 1.40
590 591 3.723835 CGCGCGCTAAAACAGACTAATTT 60.724 43.478 30.48 0.00 0.00 1.82
591 592 3.538392 GCGCGCTAAAACAGACTAATTTG 59.462 43.478 26.67 0.00 0.00 2.32
592 593 3.538392 CGCGCTAAAACAGACTAATTTGC 59.462 43.478 5.56 0.00 0.00 3.68
593 594 3.538392 GCGCTAAAACAGACTAATTTGCG 59.462 43.478 0.00 14.06 37.02 4.85
594 595 4.088648 CGCTAAAACAGACTAATTTGCGG 58.911 43.478 11.93 0.00 33.82 5.69
595 596 3.851969 GCTAAAACAGACTAATTTGCGGC 59.148 43.478 0.00 0.00 0.00 6.53
596 597 2.611974 AAACAGACTAATTTGCGGCG 57.388 45.000 0.51 0.51 0.00 6.46
597 598 0.168128 AACAGACTAATTTGCGGCGC 59.832 50.000 27.44 27.44 0.00 6.53
598 599 1.296867 CAGACTAATTTGCGGCGCG 60.297 57.895 28.09 14.11 0.00 6.86
599 600 2.022762 GACTAATTTGCGGCGCGG 59.977 61.111 28.09 11.08 0.00 6.46
600 601 4.174129 ACTAATTTGCGGCGCGGC 62.174 61.111 30.55 30.55 0.00 6.53
619 620 3.031660 GCTAGTTTAGCGCGACTGT 57.968 52.632 12.10 2.65 42.62 3.55
620 621 1.347320 GCTAGTTTAGCGCGACTGTT 58.653 50.000 12.10 0.00 42.62 3.16
621 622 1.059264 GCTAGTTTAGCGCGACTGTTG 59.941 52.381 12.10 12.47 42.62 3.33
622 623 1.654105 CTAGTTTAGCGCGACTGTTGG 59.346 52.381 12.10 7.45 0.00 3.77
623 624 0.032952 AGTTTAGCGCGACTGTTGGA 59.967 50.000 12.10 0.00 0.00 3.53
624 625 0.438830 GTTTAGCGCGACTGTTGGAG 59.561 55.000 12.10 0.00 0.00 3.86
625 626 0.315886 TTTAGCGCGACTGTTGGAGA 59.684 50.000 12.10 0.00 0.00 3.71
626 627 0.530744 TTAGCGCGACTGTTGGAGAT 59.469 50.000 12.10 0.00 0.00 2.75
627 628 0.179137 TAGCGCGACTGTTGGAGATG 60.179 55.000 12.10 0.00 0.00 2.90
628 629 3.084579 CGCGACTGTTGGAGATGC 58.915 61.111 0.00 0.00 0.00 3.91
629 630 1.446792 CGCGACTGTTGGAGATGCT 60.447 57.895 0.00 0.00 0.00 3.79
630 631 1.416813 CGCGACTGTTGGAGATGCTC 61.417 60.000 0.00 0.00 0.00 4.26
631 632 0.108424 GCGACTGTTGGAGATGCTCT 60.108 55.000 0.00 0.00 0.00 4.09
632 633 1.135139 GCGACTGTTGGAGATGCTCTA 59.865 52.381 0.00 0.00 0.00 2.43
633 634 2.417379 GCGACTGTTGGAGATGCTCTAA 60.417 50.000 0.00 0.00 0.00 2.10
634 635 3.443037 CGACTGTTGGAGATGCTCTAAG 58.557 50.000 0.00 0.00 31.92 2.18
635 636 3.129462 CGACTGTTGGAGATGCTCTAAGA 59.871 47.826 0.00 0.00 31.92 2.10
636 637 4.202101 CGACTGTTGGAGATGCTCTAAGAT 60.202 45.833 0.00 0.00 31.92 2.40
637 638 5.275067 ACTGTTGGAGATGCTCTAAGATC 57.725 43.478 0.00 0.00 31.92 2.75
638 639 4.100808 ACTGTTGGAGATGCTCTAAGATCC 59.899 45.833 0.00 0.00 31.92 3.36
639 640 3.068732 TGTTGGAGATGCTCTAAGATCCG 59.931 47.826 0.00 0.00 31.92 4.18
640 641 2.242926 TGGAGATGCTCTAAGATCCGG 58.757 52.381 0.00 0.00 0.00 5.14
641 642 2.243810 GGAGATGCTCTAAGATCCGGT 58.756 52.381 0.00 0.00 0.00 5.28
642 643 2.630580 GGAGATGCTCTAAGATCCGGTT 59.369 50.000 0.00 0.00 0.00 4.44
643 644 3.553922 GGAGATGCTCTAAGATCCGGTTG 60.554 52.174 0.00 0.00 0.00 3.77
644 645 2.366916 AGATGCTCTAAGATCCGGTTGG 59.633 50.000 0.00 0.00 0.00 3.77
645 646 0.178068 TGCTCTAAGATCCGGTTGGC 59.822 55.000 0.00 0.00 34.14 4.52
646 647 0.533085 GCTCTAAGATCCGGTTGGCC 60.533 60.000 0.00 0.00 34.14 5.36
647 648 1.123928 CTCTAAGATCCGGTTGGCCT 58.876 55.000 3.32 0.00 34.14 5.19
648 649 1.486726 CTCTAAGATCCGGTTGGCCTT 59.513 52.381 3.32 1.77 34.03 4.35
649 650 1.913419 TCTAAGATCCGGTTGGCCTTT 59.087 47.619 3.32 0.00 32.54 3.11
650 651 2.093128 TCTAAGATCCGGTTGGCCTTTC 60.093 50.000 3.32 0.00 32.54 2.62
651 652 0.404040 AAGATCCGGTTGGCCTTTCA 59.596 50.000 3.32 0.00 34.14 2.69
652 653 0.322546 AGATCCGGTTGGCCTTTCAC 60.323 55.000 3.32 0.00 34.14 3.18
653 654 0.608035 GATCCGGTTGGCCTTTCACA 60.608 55.000 3.32 0.00 34.14 3.58
654 655 0.039618 ATCCGGTTGGCCTTTCACAT 59.960 50.000 3.32 0.00 34.14 3.21
714 743 6.973229 ATTTTCACAAGCTTTGATATTGGC 57.027 33.333 0.00 0.00 0.00 4.52
731 760 2.804167 CAGGTTTTGGCGTGTGCA 59.196 55.556 0.00 0.00 45.35 4.57
748 777 1.400142 TGCAATTCGCCGACAAATAGG 59.600 47.619 0.00 0.00 41.33 2.57
754 783 0.174845 CGCCGACAAATAGGAGGTCA 59.825 55.000 0.00 0.00 0.00 4.02
755 784 1.653151 GCCGACAAATAGGAGGTCAC 58.347 55.000 0.00 0.00 0.00 3.67
771 800 3.584848 AGGTCACAGTTCTTTGGATAGCT 59.415 43.478 0.00 0.00 0.00 3.32
773 802 4.393371 GGTCACAGTTCTTTGGATAGCTTC 59.607 45.833 0.00 0.00 0.00 3.86
861 892 2.548464 AATTTATGAGCCCAGCCCAA 57.452 45.000 0.00 0.00 0.00 4.12
863 894 0.324275 TTTATGAGCCCAGCCCAACC 60.324 55.000 0.00 0.00 0.00 3.77
864 895 1.505151 TTATGAGCCCAGCCCAACCA 61.505 55.000 0.00 0.00 0.00 3.67
1200 1233 5.867716 GTCCGCACTACAAGAATAAGAGAAA 59.132 40.000 0.00 0.00 0.00 2.52
1395 1437 7.505585 TCATCTTTATGTGGGTGAGTTTCTTTT 59.494 33.333 0.00 0.00 34.50 2.27
1400 1442 3.694072 TGTGGGTGAGTTTCTTTTGTCTG 59.306 43.478 0.00 0.00 0.00 3.51
1537 1608 3.587061 TGAATTTAGGACAAGGAGCAGGA 59.413 43.478 0.00 0.00 0.00 3.86
1569 1640 8.673626 TTAAGTAAGACATTACGAGTTTACGG 57.326 34.615 0.00 0.00 45.01 4.02
1664 1740 6.041637 ACAAACTGACCCCCTTTTCTAAAATC 59.958 38.462 0.00 0.00 0.00 2.17
1833 1923 3.695830 AGACCATGCTTTTAAGACCGA 57.304 42.857 0.00 0.00 0.00 4.69
1908 1998 1.289160 TATCACCCTTGCTGCCTTCT 58.711 50.000 0.00 0.00 0.00 2.85
2264 2354 3.629398 GCAATATAAGCAGTGCCTCAGTT 59.371 43.478 12.58 1.18 0.00 3.16
2279 2369 5.880332 TGCCTCAGTTGTATTACATCTTTCC 59.120 40.000 4.93 0.00 0.00 3.13
2419 2509 2.987282 TTCGCTTGCACGAGCTTCCA 62.987 55.000 6.36 0.00 44.00 3.53
2446 2536 2.907458 AGGCCACCATTTTCTAGCTT 57.093 45.000 5.01 0.00 0.00 3.74
2530 2620 7.279981 TGCACAACCTGTCAATATAACATAGTC 59.720 37.037 0.00 0.00 0.00 2.59
2678 2771 9.807921 ATGTAGTAAATTTATAATGGGGGAGTG 57.192 33.333 0.31 0.00 0.00 3.51
2799 2894 0.178967 TTCAGCATTTGCCTGGTCCA 60.179 50.000 0.00 0.00 43.38 4.02
2882 2977 9.008965 TGTTGCAACTTAGTGTATCATATTTGT 57.991 29.630 28.61 0.00 0.00 2.83
2936 3039 9.905713 ATACTATATTGATTTGGACACTTGTGT 57.094 29.630 6.06 6.06 0.00 3.72
3037 3140 8.782339 ATTTGATTTCCCATGTTGATCTTTTC 57.218 30.769 0.00 0.00 0.00 2.29
3155 3258 0.390492 TGAAGATCCGATCGCTGCAT 59.610 50.000 10.32 0.00 0.00 3.96
3633 3768 0.984230 AAGGTTCATCTCCTTGGCGA 59.016 50.000 0.00 0.00 42.79 5.54
4106 4251 1.261480 GAGAGCAGGACAGACAGGAA 58.739 55.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 9.004231 CCCTAGAGGCCATAATAAGGTTATTAT 57.996 37.037 5.01 8.56 43.52 1.28
36 37 8.388656 CCCTAGAGGCCATAATAAGGTTATTA 57.611 38.462 5.01 4.96 39.25 0.98
37 38 7.272144 CCCTAGAGGCCATAATAAGGTTATT 57.728 40.000 5.01 0.84 37.19 1.40
38 39 6.893020 CCCTAGAGGCCATAATAAGGTTAT 57.107 41.667 5.01 0.00 0.00 1.89
53 54 4.982241 TGAAGGAAATATGCCCTAGAGG 57.018 45.455 0.00 0.00 39.47 3.69
54 55 5.942826 GGAATGAAGGAAATATGCCCTAGAG 59.057 44.000 0.00 0.00 31.36 2.43
55 56 5.222130 GGGAATGAAGGAAATATGCCCTAGA 60.222 44.000 0.00 0.00 31.36 2.43
56 57 5.012893 GGGAATGAAGGAAATATGCCCTAG 58.987 45.833 0.00 0.00 31.36 3.02
57 58 4.506625 CGGGAATGAAGGAAATATGCCCTA 60.507 45.833 0.00 0.00 31.36 3.53
58 59 3.751893 CGGGAATGAAGGAAATATGCCCT 60.752 47.826 0.00 0.00 0.00 5.19
59 60 2.558359 CGGGAATGAAGGAAATATGCCC 59.442 50.000 0.00 0.00 0.00 5.36
60 61 3.004734 CACGGGAATGAAGGAAATATGCC 59.995 47.826 0.00 0.00 0.00 4.40
61 62 3.550842 GCACGGGAATGAAGGAAATATGC 60.551 47.826 0.00 0.00 0.00 3.14
62 63 3.885297 AGCACGGGAATGAAGGAAATATG 59.115 43.478 0.00 0.00 0.00 1.78
63 64 4.170468 AGCACGGGAATGAAGGAAATAT 57.830 40.909 0.00 0.00 0.00 1.28
64 65 3.644966 AGCACGGGAATGAAGGAAATA 57.355 42.857 0.00 0.00 0.00 1.40
65 66 2.514458 AGCACGGGAATGAAGGAAAT 57.486 45.000 0.00 0.00 0.00 2.17
66 67 2.355716 CCTAGCACGGGAATGAAGGAAA 60.356 50.000 0.00 0.00 0.00 3.13
67 68 1.209504 CCTAGCACGGGAATGAAGGAA 59.790 52.381 0.00 0.00 0.00 3.36
68 69 0.830648 CCTAGCACGGGAATGAAGGA 59.169 55.000 0.00 0.00 0.00 3.36
69 70 3.386543 CCTAGCACGGGAATGAAGG 57.613 57.895 0.00 0.00 0.00 3.46
78 79 2.125269 CCGGAAACCCTAGCACGG 60.125 66.667 0.00 0.00 35.01 4.94
79 80 1.740296 CACCGGAAACCCTAGCACG 60.740 63.158 9.46 0.00 0.00 5.34
80 81 1.376812 CCACCGGAAACCCTAGCAC 60.377 63.158 9.46 0.00 0.00 4.40
81 82 3.074281 CCACCGGAAACCCTAGCA 58.926 61.111 9.46 0.00 0.00 3.49
82 83 2.437895 GCCACCGGAAACCCTAGC 60.438 66.667 9.46 0.00 0.00 3.42
83 84 2.125269 CGCCACCGGAAACCCTAG 60.125 66.667 9.46 0.00 0.00 3.02
358 359 4.764771 CCTGCCACCCACCCATGG 62.765 72.222 4.14 4.14 46.81 3.66
359 360 4.764771 CCCTGCCACCCACCCATG 62.765 72.222 0.00 0.00 0.00 3.66
395 396 4.517934 TCCTCCTCCTACGCCCCG 62.518 72.222 0.00 0.00 0.00 5.73
396 397 2.522193 CTCCTCCTCCTACGCCCC 60.522 72.222 0.00 0.00 0.00 5.80
397 398 1.529713 CTCTCCTCCTCCTACGCCC 60.530 68.421 0.00 0.00 0.00 6.13
398 399 1.529713 CCTCTCCTCCTCCTACGCC 60.530 68.421 0.00 0.00 0.00 5.68
399 400 0.536460 CTCCTCTCCTCCTCCTACGC 60.536 65.000 0.00 0.00 0.00 4.42
400 401 1.071699 CTCTCCTCTCCTCCTCCTACG 59.928 61.905 0.00 0.00 0.00 3.51
401 402 2.372172 CTCTCTCCTCTCCTCCTCCTAC 59.628 59.091 0.00 0.00 0.00 3.18
402 403 2.021441 ACTCTCTCCTCTCCTCCTCCTA 60.021 54.545 0.00 0.00 0.00 2.94
403 404 1.275002 ACTCTCTCCTCTCCTCCTCCT 60.275 57.143 0.00 0.00 0.00 3.69
404 405 1.133792 CACTCTCTCCTCTCCTCCTCC 60.134 61.905 0.00 0.00 0.00 4.30
405 406 1.750682 GCACTCTCTCCTCTCCTCCTC 60.751 61.905 0.00 0.00 0.00 3.71
406 407 0.258774 GCACTCTCTCCTCTCCTCCT 59.741 60.000 0.00 0.00 0.00 3.69
407 408 1.101049 CGCACTCTCTCCTCTCCTCC 61.101 65.000 0.00 0.00 0.00 4.30
408 409 1.101049 CCGCACTCTCTCCTCTCCTC 61.101 65.000 0.00 0.00 0.00 3.71
409 410 1.077068 CCGCACTCTCTCCTCTCCT 60.077 63.158 0.00 0.00 0.00 3.69
410 411 2.781158 GCCGCACTCTCTCCTCTCC 61.781 68.421 0.00 0.00 0.00 3.71
411 412 2.804856 GCCGCACTCTCTCCTCTC 59.195 66.667 0.00 0.00 0.00 3.20
412 413 3.137459 CGCCGCACTCTCTCCTCT 61.137 66.667 0.00 0.00 0.00 3.69
413 414 4.863925 GCGCCGCACTCTCTCCTC 62.864 72.222 3.15 0.00 0.00 3.71
460 461 3.206957 GGTGTATTTCGGGCGCCC 61.207 66.667 36.69 36.69 0.00 6.13
461 462 3.569690 CGGTGTATTTCGGGCGCC 61.570 66.667 21.18 21.18 0.00 6.53
462 463 4.232248 GCGGTGTATTTCGGGCGC 62.232 66.667 0.00 0.00 0.00 6.53
463 464 3.920553 CGCGGTGTATTTCGGGCG 61.921 66.667 0.00 0.00 37.56 6.13
465 466 3.920553 CGCGCGGTGTATTTCGGG 61.921 66.667 24.84 0.00 41.28 5.14
466 467 3.920553 CCGCGCGGTGTATTTCGG 61.921 66.667 39.71 11.06 0.00 4.30
467 468 3.920553 CCCGCGCGGTGTATTTCG 61.921 66.667 43.12 24.12 0.00 3.46
468 469 2.509786 TCCCGCGCGGTGTATTTC 60.510 61.111 43.12 0.00 0.00 2.17
469 470 2.816520 GTCCCGCGCGGTGTATTT 60.817 61.111 43.12 0.00 0.00 1.40
470 471 4.071875 TGTCCCGCGCGGTGTATT 62.072 61.111 43.12 0.00 0.00 1.89
471 472 4.508128 CTGTCCCGCGCGGTGTAT 62.508 66.667 43.12 0.00 0.00 2.29
477 478 3.573489 GAAAACACTGTCCCGCGCG 62.573 63.158 25.67 25.67 0.00 6.86
478 479 2.251371 GAAAACACTGTCCCGCGC 59.749 61.111 0.00 0.00 0.00 6.86
479 480 1.952133 TCGAAAACACTGTCCCGCG 60.952 57.895 0.00 0.00 0.00 6.46
480 481 1.568025 GTCGAAAACACTGTCCCGC 59.432 57.895 0.00 0.00 0.00 6.13
481 482 1.554042 CGGTCGAAAACACTGTCCCG 61.554 60.000 0.00 0.00 0.00 5.14
482 483 1.838568 GCGGTCGAAAACACTGTCCC 61.839 60.000 0.00 0.00 0.00 4.46
483 484 1.568025 GCGGTCGAAAACACTGTCC 59.432 57.895 0.00 0.00 0.00 4.02
484 485 1.200839 CGCGGTCGAAAACACTGTC 59.799 57.895 0.00 0.00 38.10 3.51
485 486 2.877974 GCGCGGTCGAAAACACTGT 61.878 57.895 8.83 0.00 38.10 3.55
486 487 2.127758 GCGCGGTCGAAAACACTG 60.128 61.111 8.83 0.00 38.10 3.66
487 488 3.698463 CGCGCGGTCGAAAACACT 61.698 61.111 24.84 0.00 38.10 3.55
499 500 1.218875 TATAATGAGTTGGGCGCGCG 61.219 55.000 28.44 28.44 0.00 6.86
500 501 0.512952 CTATAATGAGTTGGGCGCGC 59.487 55.000 25.94 25.94 0.00 6.86
501 502 0.512952 GCTATAATGAGTTGGGCGCG 59.487 55.000 0.00 0.00 0.00 6.86
502 503 0.512952 CGCTATAATGAGTTGGGCGC 59.487 55.000 0.00 0.00 35.13 6.53
503 504 0.512952 GCGCTATAATGAGTTGGGCG 59.487 55.000 0.00 0.00 43.21 6.13
504 505 0.512952 CGCGCTATAATGAGTTGGGC 59.487 55.000 5.56 0.00 0.00 5.36
505 506 1.526887 CACGCGCTATAATGAGTTGGG 59.473 52.381 5.73 0.00 0.00 4.12
506 507 2.033747 CACACGCGCTATAATGAGTTGG 60.034 50.000 5.73 0.00 0.00 3.77
507 508 2.603110 ACACACGCGCTATAATGAGTTG 59.397 45.455 5.73 0.00 0.00 3.16
508 509 2.858344 GACACACGCGCTATAATGAGTT 59.142 45.455 5.73 0.00 0.00 3.01
509 510 2.460918 GACACACGCGCTATAATGAGT 58.539 47.619 5.73 0.00 0.00 3.41
510 511 1.448308 CGACACACGCGCTATAATGAG 59.552 52.381 5.73 0.00 34.51 2.90
511 512 1.202211 ACGACACACGCGCTATAATGA 60.202 47.619 5.73 0.00 46.94 2.57
512 513 1.197055 ACGACACACGCGCTATAATG 58.803 50.000 5.73 0.00 46.94 1.90
513 514 1.917273 AACGACACACGCGCTATAAT 58.083 45.000 5.73 0.00 46.94 1.28
514 515 1.700523 AAACGACACACGCGCTATAA 58.299 45.000 5.73 0.00 46.94 0.98
515 516 1.700523 AAAACGACACACGCGCTATA 58.299 45.000 5.73 0.00 46.94 1.31
516 517 0.863144 AAAAACGACACACGCGCTAT 59.137 45.000 5.73 0.00 46.94 2.97
517 518 0.042880 CAAAAACGACACACGCGCTA 60.043 50.000 5.73 0.00 46.94 4.26
518 519 1.297304 CAAAAACGACACACGCGCT 60.297 52.632 5.73 0.00 46.94 5.92
519 520 2.901303 GCAAAAACGACACACGCGC 61.901 57.895 5.73 0.00 46.94 6.86
520 521 2.613528 CGCAAAAACGACACACGCG 61.614 57.895 3.53 3.53 46.94 6.01
521 522 2.901303 GCGCAAAAACGACACACGC 61.901 57.895 0.30 0.00 46.94 5.34
523 524 2.901303 GCGCGCAAAAACGACACAC 61.901 57.895 29.10 0.00 34.06 3.82
524 525 2.649349 GCGCGCAAAAACGACACA 60.649 55.556 29.10 0.00 34.06 3.72
525 526 3.383601 GGCGCGCAAAAACGACAC 61.384 61.111 34.42 7.22 37.24 3.67
526 527 4.615834 GGGCGCGCAAAAACGACA 62.616 61.111 34.42 0.00 39.73 4.35
567 568 1.680105 TAGTCTGTTTTAGCGCGCGC 61.680 55.000 45.10 45.10 42.33 6.86
568 569 0.711670 TTAGTCTGTTTTAGCGCGCG 59.288 50.000 28.44 28.44 0.00 6.86
569 570 3.385079 AATTAGTCTGTTTTAGCGCGC 57.615 42.857 26.66 26.66 0.00 6.86
570 571 3.538392 GCAAATTAGTCTGTTTTAGCGCG 59.462 43.478 0.00 0.00 0.00 6.86
571 572 3.538392 CGCAAATTAGTCTGTTTTAGCGC 59.462 43.478 0.00 0.00 34.98 5.92
572 573 4.088648 CCGCAAATTAGTCTGTTTTAGCG 58.911 43.478 0.00 0.00 40.95 4.26
573 574 3.851969 GCCGCAAATTAGTCTGTTTTAGC 59.148 43.478 0.00 0.00 0.00 3.09
574 575 4.088648 CGCCGCAAATTAGTCTGTTTTAG 58.911 43.478 0.00 0.00 0.00 1.85
575 576 3.668491 GCGCCGCAAATTAGTCTGTTTTA 60.668 43.478 3.15 0.00 0.00 1.52
576 577 2.920647 GCGCCGCAAATTAGTCTGTTTT 60.921 45.455 3.15 0.00 0.00 2.43
577 578 1.401018 GCGCCGCAAATTAGTCTGTTT 60.401 47.619 3.15 0.00 0.00 2.83
578 579 0.168128 GCGCCGCAAATTAGTCTGTT 59.832 50.000 3.15 0.00 0.00 3.16
579 580 1.794222 GCGCCGCAAATTAGTCTGT 59.206 52.632 3.15 0.00 0.00 3.41
580 581 1.296867 CGCGCCGCAAATTAGTCTG 60.297 57.895 10.75 0.00 0.00 3.51
581 582 2.461110 CCGCGCCGCAAATTAGTCT 61.461 57.895 10.75 0.00 0.00 3.24
582 583 2.022762 CCGCGCCGCAAATTAGTC 59.977 61.111 10.75 0.00 0.00 2.59
583 584 4.174129 GCCGCGCCGCAAATTAGT 62.174 61.111 15.97 0.00 0.00 2.24
602 603 1.654105 CCAACAGTCGCGCTAAACTAG 59.346 52.381 5.56 4.46 0.00 2.57
603 604 1.270274 TCCAACAGTCGCGCTAAACTA 59.730 47.619 5.56 0.00 0.00 2.24
604 605 0.032952 TCCAACAGTCGCGCTAAACT 59.967 50.000 5.56 3.20 0.00 2.66
605 606 0.438830 CTCCAACAGTCGCGCTAAAC 59.561 55.000 5.56 0.45 0.00 2.01
606 607 0.315886 TCTCCAACAGTCGCGCTAAA 59.684 50.000 5.56 0.00 0.00 1.85
607 608 0.530744 ATCTCCAACAGTCGCGCTAA 59.469 50.000 5.56 0.00 0.00 3.09
608 609 0.179137 CATCTCCAACAGTCGCGCTA 60.179 55.000 5.56 0.00 0.00 4.26
609 610 1.446792 CATCTCCAACAGTCGCGCT 60.447 57.895 5.56 0.00 0.00 5.92
610 611 3.084579 CATCTCCAACAGTCGCGC 58.915 61.111 0.00 0.00 0.00 6.86
611 612 1.416813 GAGCATCTCCAACAGTCGCG 61.417 60.000 0.00 0.00 0.00 5.87
612 613 2.378028 GAGCATCTCCAACAGTCGC 58.622 57.895 0.00 0.00 0.00 5.19
624 625 2.760374 CCAACCGGATCTTAGAGCATC 58.240 52.381 9.46 0.00 0.00 3.91
625 626 1.202698 GCCAACCGGATCTTAGAGCAT 60.203 52.381 9.46 0.00 0.00 3.79
626 627 0.178068 GCCAACCGGATCTTAGAGCA 59.822 55.000 9.46 0.00 0.00 4.26
627 628 0.533085 GGCCAACCGGATCTTAGAGC 60.533 60.000 9.46 0.00 0.00 4.09
628 629 1.123928 AGGCCAACCGGATCTTAGAG 58.876 55.000 9.46 0.00 42.76 2.43
629 630 1.580059 AAGGCCAACCGGATCTTAGA 58.420 50.000 9.46 0.00 42.76 2.10
630 631 2.289565 GAAAGGCCAACCGGATCTTAG 58.710 52.381 9.46 0.00 42.76 2.18
631 632 1.631388 TGAAAGGCCAACCGGATCTTA 59.369 47.619 9.46 0.00 42.76 2.10
632 633 0.404040 TGAAAGGCCAACCGGATCTT 59.596 50.000 9.46 0.84 42.76 2.40
633 634 0.322546 GTGAAAGGCCAACCGGATCT 60.323 55.000 9.46 0.00 42.76 2.75
634 635 0.608035 TGTGAAAGGCCAACCGGATC 60.608 55.000 9.46 0.00 42.76 3.36
635 636 0.039618 ATGTGAAAGGCCAACCGGAT 59.960 50.000 9.46 0.00 42.76 4.18
636 637 0.608035 GATGTGAAAGGCCAACCGGA 60.608 55.000 9.46 0.00 42.76 5.14
637 638 1.883021 GATGTGAAAGGCCAACCGG 59.117 57.895 5.01 0.00 42.76 5.28
638 639 1.501741 CGATGTGAAAGGCCAACCG 59.498 57.895 5.01 0.00 42.76 4.44
639 640 1.212751 GCGATGTGAAAGGCCAACC 59.787 57.895 5.01 0.00 0.00 3.77
640 641 0.598065 AAGCGATGTGAAAGGCCAAC 59.402 50.000 5.01 0.00 0.00 3.77
641 642 0.881118 GAAGCGATGTGAAAGGCCAA 59.119 50.000 5.01 0.00 0.00 4.52
642 643 0.036732 AGAAGCGATGTGAAAGGCCA 59.963 50.000 5.01 0.00 0.00 5.36
643 644 1.135575 CAAGAAGCGATGTGAAAGGCC 60.136 52.381 0.00 0.00 0.00 5.19
644 645 1.730446 GCAAGAAGCGATGTGAAAGGC 60.730 52.381 0.00 0.00 0.00 4.35
645 646 2.253392 GCAAGAAGCGATGTGAAAGG 57.747 50.000 0.00 0.00 0.00 3.11
714 743 0.249405 ATTGCACACGCCAAAACCTG 60.249 50.000 0.00 0.00 37.32 4.00
731 760 2.093128 ACCTCCTATTTGTCGGCGAATT 60.093 45.455 12.92 0.00 31.52 2.17
748 777 3.935828 GCTATCCAAAGAACTGTGACCTC 59.064 47.826 0.00 0.00 0.00 3.85
771 800 4.708386 AAATCGGCCACGCGGGAA 62.708 61.111 11.66 0.00 40.01 3.97
773 802 4.174129 GAAAATCGGCCACGCGGG 62.174 66.667 12.47 6.05 40.69 6.13
843 874 1.689258 GGTTGGGCTGGGCTCATAAAT 60.689 52.381 0.00 0.00 39.47 1.40
847 878 2.172229 AATGGTTGGGCTGGGCTCAT 62.172 55.000 0.00 0.00 39.47 2.90
861 892 6.390504 TGTTATCCCTACTCTATGGAATGGT 58.609 40.000 0.00 0.00 0.00 3.55
863 894 7.015682 ACACTGTTATCCCTACTCTATGGAATG 59.984 40.741 0.00 0.00 0.00 2.67
864 895 7.076446 ACACTGTTATCCCTACTCTATGGAAT 58.924 38.462 0.00 0.00 0.00 3.01
914 945 9.691362 TCTTTTTATTGGATAAAGTTCTTGCAC 57.309 29.630 0.00 0.00 36.23 4.57
1018 1049 1.893919 GCGAGAGGCAAGAGGGAAGT 61.894 60.000 0.00 0.00 42.87 3.01
1061 1092 7.135089 GGTTCAGGAGAGATTTAACTGAAAC 57.865 40.000 6.95 6.06 46.11 2.78
1221 1254 4.700365 CGTCGTCGGCAGCACAGA 62.700 66.667 0.00 0.00 0.00 3.41
1423 1494 2.996631 ACCACTGATTCATGAGCTTCC 58.003 47.619 0.00 0.00 0.00 3.46
1537 1608 6.694447 TCGTAATGTCTTACTTAAGCCAGTT 58.306 36.000 1.29 0.00 35.98 3.16
1541 1612 7.592439 AAACTCGTAATGTCTTACTTAAGCC 57.408 36.000 1.29 0.00 35.98 4.35
1569 1640 1.197055 CAACGCTCAATGCATGATGC 58.803 50.000 11.12 11.12 45.29 3.91
1664 1740 4.122046 TCTCGGAATCATAACATGCACAG 58.878 43.478 0.00 0.00 0.00 3.66
1750 1826 6.911484 CGGTAACAAACTGCAAATAAGAAG 57.089 37.500 0.00 0.00 0.00 2.85
1833 1923 6.183361 TGAGCAGGCCATGTATAGATAAAAGT 60.183 38.462 5.01 0.00 0.00 2.66
1908 1998 0.035915 TTGGCACATAACGGCAGCTA 60.036 50.000 0.00 0.00 40.36 3.32
2279 2369 5.218139 AGCGAGCTGAAAAAGAGAAAAATG 58.782 37.500 0.00 0.00 0.00 2.32
2419 2509 5.653255 AGAAAATGGTGGCCTATGATAGT 57.347 39.130 3.32 0.00 0.00 2.12
2446 2536 4.037565 TGAAACTAGTCTGCAGAAGAACGA 59.962 41.667 20.19 1.69 36.40 3.85
2530 2620 4.579454 AATTTTGGATCTCCATGCATCG 57.421 40.909 0.00 0.00 46.97 3.84
2557 2647 4.253685 TCATTCTTCATCCGACTCCAAAC 58.746 43.478 0.00 0.00 0.00 2.93
2662 2753 4.871871 TCTTGCACTCCCCCATTATAAA 57.128 40.909 0.00 0.00 0.00 1.40
2678 2771 3.194116 TGCATGAAAAGGATCCTTCTTGC 59.806 43.478 30.06 30.06 45.70 4.01
2721 2815 6.238484 CCCCACGCTAAGAGAGATTTAAATTG 60.238 42.308 1.43 0.00 0.00 2.32
2799 2894 2.373335 AGCCAGGAGATCAGATACGT 57.627 50.000 0.00 0.00 0.00 3.57
2882 2977 7.992033 CCATCAAAATATTTCAAGGGGCATTAA 59.008 33.333 0.10 0.00 0.00 1.40
2936 3039 3.780294 ACAGACATTAGGCTGAATGGGTA 59.220 43.478 5.17 0.00 40.50 3.69
3155 3258 5.648960 GGGTTTGAATTAACTGAATCCCGTA 59.351 40.000 0.00 0.00 0.00 4.02
3248 3352 2.639065 GGGTCATCATAACTGGCGAAA 58.361 47.619 0.00 0.00 0.00 3.46
3295 3399 2.370445 CCTCCAGAGCAATCCCCGT 61.370 63.158 0.00 0.00 0.00 5.28
3633 3768 4.498520 CGGCACCAGATCTCGCGT 62.499 66.667 5.77 0.00 0.00 6.01
4106 4251 4.264532 ACATGGTCCCTGAAATCCTCAAAT 60.265 41.667 0.54 0.00 32.17 2.32


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

AutoCloner maintained by Alex Coulton.