Multiple sequence alignment - TraesCS2A01G203900

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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 TraesCS2A01G203900 chr2A 100.000 3400 0 0 1 3400 180112119 180115518 0.000000e+00 6279.0
1 TraesCS2A01G203900 chr2A 77.441 297 48 6 3107 3390 104681258 104680968 3.510000e-35 159.0
2 TraesCS2A01G203900 chr2D 91.535 1205 67 16 576 1762 169988309 169987122 0.000000e+00 1628.0
3 TraesCS2A01G203900 chr2D 92.759 1091 52 15 1751 2825 169987105 169986026 0.000000e+00 1552.0
4 TraesCS2A01G203900 chr2D 89.755 449 15 8 79 508 169988753 169988317 2.310000e-151 545.0
5 TraesCS2A01G203900 chr2D 82.623 305 40 6 3085 3376 481063043 481062739 1.210000e-64 257.0
6 TraesCS2A01G203900 chr2D 88.393 112 12 1 3017 3128 169985838 169985728 2.130000e-27 134.0
7 TraesCS2A01G203900 chr2D 98.246 57 1 0 16 72 531750611 531750667 2.160000e-17 100.0
8 TraesCS2A01G203900 chr2D 94.737 57 3 0 16 72 642439945 642440001 4.670000e-14 89.8
9 TraesCS2A01G203900 chr2B 93.803 1065 40 13 1751 2803 227688372 227689422 0.000000e+00 1578.0
10 TraesCS2A01G203900 chr2B 93.718 971 52 7 797 1764 227687393 227688357 0.000000e+00 1447.0
11 TraesCS2A01G203900 chr2B 92.523 321 13 4 135 449 227686633 227686948 1.860000e-122 449.0
12 TraesCS2A01G203900 chr2B 78.378 518 74 24 2892 3390 227689426 227689924 5.510000e-78 302.0
13 TraesCS2A01G203900 chr2B 84.848 231 19 4 576 806 227686999 227687213 5.710000e-53 219.0
14 TraesCS2A01G203900 chr1D 85.172 290 42 1 3097 3385 204986119 204986408 2.570000e-76 296.0
15 TraesCS2A01G203900 chr1D 94.828 58 3 0 16 73 45410881 45410824 1.300000e-14 91.6
16 TraesCS2A01G203900 chr1D 94.545 55 3 0 16 70 45416430 45416376 6.040000e-13 86.1
17 TraesCS2A01G203900 chr6D 83.121 314 47 4 3085 3392 379363393 379363080 7.180000e-72 281.0
18 TraesCS2A01G203900 chr5D 84.848 264 36 2 3085 3344 342593545 342593282 2.600000e-66 263.0
19 TraesCS2A01G203900 chr3A 83.219 292 42 5 3108 3392 685421714 685421423 9.360000e-66 261.0
20 TraesCS2A01G203900 chr3A 96.364 55 2 0 16 70 9461176 9461122 1.300000e-14 91.6
21 TraesCS2A01G203900 chr3A 94.828 58 2 1 17 74 101878994 101879050 4.670000e-14 89.8
22 TraesCS2A01G203900 chr7D 82.215 298 47 4 3108 3400 2407644 2407348 5.630000e-63 252.0
23 TraesCS2A01G203900 chr7D 100.000 29 0 0 2765 2793 169355128 169355100 2.000000e-03 54.7
24 TraesCS2A01G203900 chr5A 82.414 290 34 11 3087 3363 443486544 443486259 1.580000e-58 237.0
25 TraesCS2A01G203900 chr5A 96.364 55 2 0 16 70 563063663 563063609 1.300000e-14 91.6
26 TraesCS2A01G203900 chr4A 81.533 287 42 6 3107 3390 68955139 68954861 3.410000e-55 226.0
27 TraesCS2A01G203900 chr4A 96.364 55 2 0 16 70 550965568 550965622 1.300000e-14 91.6
28 TraesCS2A01G203900 chr1A 98.182 55 1 0 16 70 508290340 508290286 2.790000e-16 97.1
29 TraesCS2A01G203900 chr7A 100.000 29 0 0 2767 2795 198951510 198951538 2.000000e-03 54.7


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 TraesCS2A01G203900 chr2A 180112119 180115518 3399 False 6279.00 6279 100.0000 1 3400 1 chr2A.!!$F1 3399
1 TraesCS2A01G203900 chr2D 169985728 169988753 3025 True 964.75 1628 90.6105 79 3128 4 chr2D.!!$R2 3049
2 TraesCS2A01G203900 chr2B 227686633 227689924 3291 False 799.00 1578 88.6540 135 3390 5 chr2B.!!$F1 3255

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
129 130 0.317160 GGTCAGGTCGATGTGTGTGA 59.683 55.0 0.0 0.0 0.0 3.58 F
1109 1340 0.391263 ACGGTCGAGAGGATTTTGGC 60.391 55.0 0.0 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1757 2048 0.461548 TGCAGGCCAGAATAGTCGAG 59.538 55.0 5.01 0.0 0.0 4.04 R
2944 3278 0.108756 GAGACTGCCCGGTTACTCAC 60.109 60.0 0.00 0.0 0.0 3.51 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
70 71 9.482627 TTGGTAAATTGTTCATATTTCCAACAC 57.517 29.630 0.00 0.00 32.98 3.32
71 72 8.865090 TGGTAAATTGTTCATATTTCCAACACT 58.135 29.630 0.00 0.00 29.74 3.55
75 76 9.691362 AAATTGTTCATATTTCCAACACTACAC 57.309 29.630 0.00 0.00 29.74 2.90
76 77 6.811253 TGTTCATATTTCCAACACTACACC 57.189 37.500 0.00 0.00 0.00 4.16
77 78 5.410132 TGTTCATATTTCCAACACTACACCG 59.590 40.000 0.00 0.00 0.00 4.94
78 79 4.509616 TCATATTTCCAACACTACACCGG 58.490 43.478 0.00 0.00 0.00 5.28
79 80 2.943036 ATTTCCAACACTACACCGGT 57.057 45.000 0.00 0.00 0.00 5.28
80 81 5.187381 TCATATTTCCAACACTACACCGGTA 59.813 40.000 6.87 0.00 0.00 4.02
103 104 0.994995 CGTCATGAGTCGCTCAAAGG 59.005 55.000 12.43 6.83 44.04 3.11
111 112 1.078214 TCGCTCAAAGGCATGGAGG 60.078 57.895 0.00 0.00 0.00 4.30
116 117 0.329261 TCAAAGGCATGGAGGTCAGG 59.671 55.000 0.00 0.00 0.00 3.86
127 128 0.603569 GAGGTCAGGTCGATGTGTGT 59.396 55.000 0.00 0.00 0.00 3.72
128 129 0.318441 AGGTCAGGTCGATGTGTGTG 59.682 55.000 0.00 0.00 0.00 3.82
129 130 0.317160 GGTCAGGTCGATGTGTGTGA 59.683 55.000 0.00 0.00 0.00 3.58
130 131 1.670087 GGTCAGGTCGATGTGTGTGAG 60.670 57.143 0.00 0.00 0.00 3.51
131 132 0.603065 TCAGGTCGATGTGTGTGAGG 59.397 55.000 0.00 0.00 0.00 3.86
132 133 0.603065 CAGGTCGATGTGTGTGAGGA 59.397 55.000 0.00 0.00 0.00 3.71
133 134 0.603569 AGGTCGATGTGTGTGAGGAC 59.396 55.000 0.00 0.00 0.00 3.85
147 148 0.823460 GAGGACTGAGGAAGAGGCTG 59.177 60.000 0.00 0.00 0.00 4.85
191 192 4.080807 AGGAGAGAAGATAGACACGAGACA 60.081 45.833 0.00 0.00 0.00 3.41
278 289 3.151906 AGCTGAGCTGGACCGTTT 58.848 55.556 5.97 0.00 37.57 3.60
305 316 2.825836 GAAGCGGATGCCACCAGG 60.826 66.667 0.00 0.00 44.31 4.45
480 507 4.386867 TGTACAATCTCCGATCACTTCC 57.613 45.455 0.00 0.00 0.00 3.46
489 516 0.921347 CGATCACTTCCGCCTTTACG 59.079 55.000 0.00 0.00 0.00 3.18
507 534 1.332195 CGATCTCCATCCAGCCTGTA 58.668 55.000 0.00 0.00 0.00 2.74
508 535 1.688735 CGATCTCCATCCAGCCTGTAA 59.311 52.381 0.00 0.00 0.00 2.41
509 536 2.301296 CGATCTCCATCCAGCCTGTAAT 59.699 50.000 0.00 0.00 0.00 1.89
510 537 3.672808 GATCTCCATCCAGCCTGTAATG 58.327 50.000 0.00 0.00 0.00 1.90
511 538 2.481441 TCTCCATCCAGCCTGTAATGT 58.519 47.619 0.00 0.00 0.00 2.71
512 539 3.653164 TCTCCATCCAGCCTGTAATGTA 58.347 45.455 0.00 0.00 0.00 2.29
513 540 4.234550 TCTCCATCCAGCCTGTAATGTAT 58.765 43.478 0.00 0.00 0.00 2.29
514 541 4.284490 TCTCCATCCAGCCTGTAATGTATC 59.716 45.833 0.00 0.00 0.00 2.24
515 542 3.973305 TCCATCCAGCCTGTAATGTATCA 59.027 43.478 0.00 0.00 0.00 2.15
516 543 4.411869 TCCATCCAGCCTGTAATGTATCAA 59.588 41.667 0.00 0.00 0.00 2.57
517 544 5.073554 TCCATCCAGCCTGTAATGTATCAAT 59.926 40.000 0.00 0.00 0.00 2.57
518 545 5.182570 CCATCCAGCCTGTAATGTATCAATG 59.817 44.000 0.00 0.00 0.00 2.82
519 546 5.628797 TCCAGCCTGTAATGTATCAATGA 57.371 39.130 0.00 0.00 0.00 2.57
520 547 6.000246 TCCAGCCTGTAATGTATCAATGAA 58.000 37.500 0.00 0.00 0.00 2.57
521 548 5.822519 TCCAGCCTGTAATGTATCAATGAAC 59.177 40.000 0.00 0.00 0.00 3.18
522 549 5.009010 CCAGCCTGTAATGTATCAATGAACC 59.991 44.000 0.00 0.00 0.00 3.62
523 550 5.009010 CAGCCTGTAATGTATCAATGAACCC 59.991 44.000 0.00 0.00 0.00 4.11
524 551 4.887071 GCCTGTAATGTATCAATGAACCCA 59.113 41.667 0.00 0.00 0.00 4.51
525 552 5.221048 GCCTGTAATGTATCAATGAACCCAC 60.221 44.000 0.00 0.00 0.00 4.61
526 553 5.885352 CCTGTAATGTATCAATGAACCCACA 59.115 40.000 0.00 0.00 0.00 4.17
527 554 6.547141 CCTGTAATGTATCAATGAACCCACAT 59.453 38.462 0.00 0.00 0.00 3.21
528 555 7.332213 TGTAATGTATCAATGAACCCACATG 57.668 36.000 0.00 0.00 0.00 3.21
529 556 7.115414 TGTAATGTATCAATGAACCCACATGA 58.885 34.615 0.00 0.00 0.00 3.07
530 557 7.779326 TGTAATGTATCAATGAACCCACATGAT 59.221 33.333 0.00 0.00 36.63 2.45
531 558 6.644248 ATGTATCAATGAACCCACATGATG 57.356 37.500 0.00 0.00 35.28 3.07
541 568 1.671979 CCACATGATGGCACGATTCT 58.328 50.000 0.00 0.00 43.24 2.40
542 569 1.332686 CCACATGATGGCACGATTCTG 59.667 52.381 0.00 0.00 43.24 3.02
543 570 2.011947 CACATGATGGCACGATTCTGT 58.988 47.619 0.00 0.00 0.00 3.41
544 571 2.011947 ACATGATGGCACGATTCTGTG 58.988 47.619 0.00 4.85 42.81 3.66
553 580 3.090312 CACGATTCTGTGCTGTTTACG 57.910 47.619 0.00 0.00 32.31 3.18
554 581 1.459592 ACGATTCTGTGCTGTTTACGC 59.540 47.619 0.00 0.00 0.00 4.42
555 582 1.524986 CGATTCTGTGCTGTTTACGCG 60.525 52.381 3.53 3.53 0.00 6.01
556 583 1.724623 GATTCTGTGCTGTTTACGCGA 59.275 47.619 15.93 0.00 0.00 5.87
557 584 1.136690 TTCTGTGCTGTTTACGCGAG 58.863 50.000 15.93 0.00 0.00 5.03
558 585 1.130613 CTGTGCTGTTTACGCGAGC 59.869 57.895 15.93 12.09 0.00 5.03
576 603 2.738846 GAGCACAAAGACATGTCACGAT 59.261 45.455 27.02 9.25 0.00 3.73
577 604 2.481568 AGCACAAAGACATGTCACGATG 59.518 45.455 27.02 19.84 0.00 3.84
578 605 2.480037 GCACAAAGACATGTCACGATGA 59.520 45.455 27.02 0.00 0.00 2.92
632 659 7.282450 TCTGCAGTAACAGAGTCGATTAAGATA 59.718 37.037 14.67 0.00 41.72 1.98
633 660 7.768240 TGCAGTAACAGAGTCGATTAAGATAA 58.232 34.615 0.00 0.00 0.00 1.75
634 661 7.701078 TGCAGTAACAGAGTCGATTAAGATAAC 59.299 37.037 0.00 0.00 0.00 1.89
635 662 7.916450 GCAGTAACAGAGTCGATTAAGATAACT 59.084 37.037 0.00 0.00 0.00 2.24
636 663 9.440784 CAGTAACAGAGTCGATTAAGATAACTC 57.559 37.037 0.00 0.00 37.27 3.01
637 664 8.623030 AGTAACAGAGTCGATTAAGATAACTCC 58.377 37.037 0.00 0.00 37.63 3.85
644 671 8.239038 AGTCGATTAAGATAACTCCATGAGAA 57.761 34.615 0.00 0.00 33.32 2.87
719 746 6.786967 AGTGGTACTGTGGTAGTAATTAGG 57.213 41.667 0.00 0.00 43.24 2.69
728 770 7.559170 ACTGTGGTAGTAATTAGGAGTAATCGT 59.441 37.037 0.00 0.00 38.04 3.73
748 790 1.538512 TGAAAGGTCGACGTCCACTAG 59.461 52.381 11.73 0.00 0.00 2.57
749 791 1.538950 GAAAGGTCGACGTCCACTAGT 59.461 52.381 11.73 0.00 0.00 2.57
750 792 2.479566 AAGGTCGACGTCCACTAGTA 57.520 50.000 11.73 0.00 0.00 1.82
751 793 2.706339 AGGTCGACGTCCACTAGTAT 57.294 50.000 13.09 0.00 0.00 2.12
752 794 2.286872 AGGTCGACGTCCACTAGTATG 58.713 52.381 13.09 0.00 0.00 2.39
813 1044 4.576873 ACACTACTCATGATGGTCTAGACG 59.423 45.833 16.56 1.97 0.00 4.18
831 1062 1.722677 GTTTCCGTTCCGTGCAACA 59.277 52.632 0.00 0.00 35.74 3.33
972 1203 2.256117 AAGCCGCTCCGCTATAAATT 57.744 45.000 0.00 0.00 38.44 1.82
1029 1260 2.487762 TCGCTTCGCTTCCATTCATTTT 59.512 40.909 0.00 0.00 0.00 1.82
1105 1336 1.477295 GGAGAACGGTCGAGAGGATTT 59.523 52.381 0.00 0.00 0.00 2.17
1109 1340 0.391263 ACGGTCGAGAGGATTTTGGC 60.391 55.000 0.00 0.00 0.00 4.52
1403 1634 2.359975 CCGGTTCCAGTGCCTTCC 60.360 66.667 0.00 0.00 0.00 3.46
1410 1641 3.411517 CAGTGCCTTCCCCGGGAT 61.412 66.667 26.32 0.00 0.00 3.85
1415 1646 4.522975 CCTTCCCCGGGATTGGCC 62.523 72.222 26.32 0.00 0.00 5.36
1432 1663 4.451241 CATGCCGATGGAGGTGAG 57.549 61.111 0.00 0.00 0.00 3.51
1458 1689 1.450134 GCAGTCACCATGGCGATGA 60.450 57.895 13.04 5.42 0.00 2.92
1552 1783 1.532794 CGGAGATGGAGGAGGAGGG 60.533 68.421 0.00 0.00 0.00 4.30
1717 1948 1.880027 CAGCCCAGAAGGTAACAACAC 59.120 52.381 0.00 0.00 38.26 3.32
1732 1966 2.093658 ACAACACCGCCTAATACTCTGG 60.094 50.000 0.00 0.00 0.00 3.86
1757 2048 3.414549 TTCGCCGAGCAATTTAATTCC 57.585 42.857 0.00 0.00 0.00 3.01
1787 2078 1.073897 GGCCTGCAAAGACCAGACT 59.926 57.895 0.00 0.00 32.03 3.24
2122 2413 2.665603 GCAGGCGAGAGGAAGGTT 59.334 61.111 0.00 0.00 0.00 3.50
2164 2455 4.719369 GACGAGCTGAACCGGCGT 62.719 66.667 6.01 0.00 41.21 5.68
2271 2562 3.484547 CGGCGGCCGTTACTGAAC 61.485 66.667 32.14 6.82 42.73 3.18
2284 2576 4.322049 CGTTACTGAACAGAGTTCTCCCAT 60.322 45.833 8.87 0.00 35.06 4.00
2305 2597 0.905357 AACTGAACTCGGGATGGGAG 59.095 55.000 0.00 0.00 37.54 4.30
2308 2600 0.982852 TGAACTCGGGATGGGAGCAT 60.983 55.000 0.00 0.00 34.87 3.79
2506 2804 0.039618 GCCTGGAGACCCCAATTTCA 59.960 55.000 0.00 0.00 46.07 2.69
2531 2829 1.476110 GGAGCCGGGCATGTGTATTAA 60.476 52.381 23.09 0.00 0.00 1.40
2532 2830 2.294074 GAGCCGGGCATGTGTATTAAA 58.706 47.619 23.09 0.00 0.00 1.52
2573 2871 1.031571 TTTCATGGCATCTCGGTGGC 61.032 55.000 0.00 0.00 44.24 5.01
2607 2910 1.923864 CTGTGGTTTTCGTTGTTTGGC 59.076 47.619 0.00 0.00 0.00 4.52
2707 3017 1.947456 AGGTTTGAGAGGAAACAACGC 59.053 47.619 0.00 0.00 37.53 4.84
2741 3051 7.016957 TGGATGATCTAGGATATGCTTCTTTGT 59.983 37.037 0.65 0.00 0.00 2.83
2745 3055 6.798427 TCTAGGATATGCTTCTTTGTGAGT 57.202 37.500 0.65 0.00 0.00 3.41
2776 3086 2.037641 TGAGCACACAACATCTACAGCT 59.962 45.455 0.00 0.00 0.00 4.24
2812 3146 0.031585 GCACCGTGCATCCTATACGA 59.968 55.000 18.79 0.00 44.26 3.43
2835 3169 4.944372 GGGTGCGTCCGCGGATAG 62.944 72.222 33.58 27.77 45.51 2.08
2840 3174 3.108343 CGTCCGCGGATAGTGACT 58.892 61.111 33.58 0.00 0.00 3.41
2841 3175 1.779025 GCGTCCGCGGATAGTGACTA 61.779 60.000 33.58 1.12 38.78 2.59
2843 3177 1.590932 GTCCGCGGATAGTGACTAGA 58.409 55.000 33.58 0.00 0.00 2.43
2885 3219 6.804295 GTGTCCACATTCGAGTATCTCATATC 59.196 42.308 0.00 0.00 0.00 1.63
2887 3221 6.010219 TCCACATTCGAGTATCTCATATCCA 58.990 40.000 0.00 0.00 0.00 3.41
2888 3222 6.665248 TCCACATTCGAGTATCTCATATCCAT 59.335 38.462 0.00 0.00 0.00 3.41
2890 3224 7.147932 CCACATTCGAGTATCTCATATCCATCT 60.148 40.741 0.00 0.00 0.00 2.90
2891 3225 8.897752 CACATTCGAGTATCTCATATCCATCTA 58.102 37.037 0.00 0.00 0.00 1.98
2893 3227 8.897752 CATTCGAGTATCTCATATCCATCTACA 58.102 37.037 0.00 0.00 0.00 2.74
2894 3228 8.499403 TTCGAGTATCTCATATCCATCTACAG 57.501 38.462 0.00 0.00 0.00 2.74
2895 3229 6.540551 TCGAGTATCTCATATCCATCTACAGC 59.459 42.308 0.00 0.00 0.00 4.40
2897 3231 7.467131 CGAGTATCTCATATCCATCTACAGCTG 60.467 44.444 13.48 13.48 0.00 4.24
2898 3232 5.936187 ATCTCATATCCATCTACAGCTGG 57.064 43.478 19.93 0.36 32.83 4.85
2899 3233 5.003096 TCTCATATCCATCTACAGCTGGA 57.997 43.478 19.93 9.06 43.54 3.86
2903 3237 3.766068 ATCCATCTACAGCTGGACATG 57.234 47.619 19.93 13.17 42.38 3.21
2905 3239 1.590932 CATCTACAGCTGGACATGCC 58.409 55.000 19.93 0.00 37.10 4.40
2929 3263 4.404691 GGCACCCTATATGGCTGC 57.595 61.111 10.83 10.83 39.45 5.25
2930 3264 1.672356 GGCACCCTATATGGCTGCG 60.672 63.158 12.12 0.00 39.45 5.18
2931 3265 1.672356 GCACCCTATATGGCTGCGG 60.672 63.158 0.00 0.00 0.00 5.69
2932 3266 1.003355 CACCCTATATGGCTGCGGG 60.003 63.158 6.50 6.50 40.79 6.13
2933 3267 2.224159 ACCCTATATGGCTGCGGGG 61.224 63.158 11.85 9.50 39.27 5.73
2934 3268 2.224159 CCCTATATGGCTGCGGGGT 61.224 63.158 0.00 0.00 0.00 4.95
2935 3269 1.761174 CCTATATGGCTGCGGGGTT 59.239 57.895 0.00 0.00 0.00 4.11
2936 3270 0.321653 CCTATATGGCTGCGGGGTTC 60.322 60.000 0.00 0.00 0.00 3.62
2937 3271 0.670546 CTATATGGCTGCGGGGTTCG 60.671 60.000 0.00 0.00 42.76 3.95
2938 3272 1.404479 TATATGGCTGCGGGGTTCGT 61.404 55.000 0.00 0.00 41.72 3.85
2939 3273 2.660258 ATATGGCTGCGGGGTTCGTC 62.660 60.000 0.00 0.00 41.72 4.20
2949 3283 4.353437 GGTTCGTCCGCGGTGAGT 62.353 66.667 27.15 0.00 38.89 3.41
2950 3284 2.562912 GTTCGTCCGCGGTGAGTA 59.437 61.111 27.15 8.70 38.89 2.59
2951 3285 1.081242 GTTCGTCCGCGGTGAGTAA 60.081 57.895 27.15 10.82 38.89 2.24
2952 3286 1.081242 TTCGTCCGCGGTGAGTAAC 60.081 57.895 27.15 13.94 38.89 2.50
2960 3294 3.066198 GGTGAGTAACCGGGCAGT 58.934 61.111 6.32 0.00 39.81 4.40
2961 3295 1.079336 GGTGAGTAACCGGGCAGTC 60.079 63.158 6.32 5.89 39.81 3.51
2964 3298 0.251653 TGAGTAACCGGGCAGTCTCT 60.252 55.000 6.32 0.00 0.00 3.10
2969 3303 3.518303 AGTAACCGGGCAGTCTCTAAATT 59.482 43.478 6.32 0.00 0.00 1.82
2973 3307 1.927174 CGGGCAGTCTCTAAATTCACG 59.073 52.381 0.00 0.00 0.00 4.35
2980 3314 4.386049 CAGTCTCTAAATTCACGTGTCCAC 59.614 45.833 16.51 1.17 0.00 4.02
2985 3319 1.821216 AATTCACGTGTCCACATCCC 58.179 50.000 16.51 0.00 0.00 3.85
3006 3391 1.268352 CGGGCAAAATCGACAGGAAAA 59.732 47.619 0.00 0.00 0.00 2.29
3007 3392 2.672714 GGGCAAAATCGACAGGAAAAC 58.327 47.619 0.00 0.00 0.00 2.43
3010 3395 3.226347 GCAAAATCGACAGGAAAACGAG 58.774 45.455 0.00 0.00 39.31 4.18
3011 3396 3.810373 CAAAATCGACAGGAAAACGAGG 58.190 45.455 0.00 0.00 39.31 4.63
3012 3397 2.094762 AATCGACAGGAAAACGAGGG 57.905 50.000 0.00 0.00 39.31 4.30
3014 3399 0.316204 TCGACAGGAAAACGAGGGAC 59.684 55.000 0.00 0.00 0.00 4.46
3027 3412 2.810650 CGAGGGACGGACTCTAAATTG 58.189 52.381 0.00 0.00 38.46 2.32
3028 3413 2.426024 CGAGGGACGGACTCTAAATTGA 59.574 50.000 0.00 0.00 38.46 2.57
3058 3443 7.060600 TGATAGCAAAAAGTCATAGTTCACG 57.939 36.000 0.00 0.00 0.00 4.35
3120 3519 1.884235 CGAAGCTTCACCACTTCCTT 58.116 50.000 25.47 0.00 39.29 3.36
3131 3530 2.751837 CTTCCTTGCCGGCCCTTC 60.752 66.667 26.77 0.00 0.00 3.46
3132 3531 3.567579 CTTCCTTGCCGGCCCTTCA 62.568 63.158 26.77 0.09 0.00 3.02
3138 3537 4.678743 GCCGGCCCTTCACCCTTT 62.679 66.667 18.11 0.00 0.00 3.11
3148 3547 0.958382 TTCACCCTTTCGATTGCCGG 60.958 55.000 0.00 0.00 39.14 6.13
3149 3548 2.750237 ACCCTTTCGATTGCCGGC 60.750 61.111 22.73 22.73 39.14 6.13
3150 3549 2.749839 CCCTTTCGATTGCCGGCA 60.750 61.111 29.03 29.03 39.14 5.69
3151 3550 2.485122 CCTTTCGATTGCCGGCAC 59.515 61.111 32.95 18.75 39.14 5.01
3152 3551 2.040544 CCTTTCGATTGCCGGCACT 61.041 57.895 32.95 26.53 39.14 4.40
3153 3552 1.135315 CTTTCGATTGCCGGCACTG 59.865 57.895 32.95 21.85 39.14 3.66
3154 3553 1.577328 CTTTCGATTGCCGGCACTGT 61.577 55.000 32.95 18.96 39.14 3.55
3155 3554 1.169661 TTTCGATTGCCGGCACTGTT 61.170 50.000 32.95 14.84 39.14 3.16
3156 3555 1.851021 TTCGATTGCCGGCACTGTTG 61.851 55.000 32.95 21.33 39.14 3.33
3166 3565 4.162592 CACTGTTGCAGGCTTCCA 57.837 55.556 1.08 0.00 35.51 3.53
3167 3566 1.656441 CACTGTTGCAGGCTTCCAC 59.344 57.895 1.08 0.00 35.51 4.02
3168 3567 1.893808 ACTGTTGCAGGCTTCCACG 60.894 57.895 1.08 0.00 35.51 4.94
3169 3568 2.594303 TGTTGCAGGCTTCCACGG 60.594 61.111 0.00 0.00 0.00 4.94
3170 3569 4.043200 GTTGCAGGCTTCCACGGC 62.043 66.667 0.00 0.00 0.00 5.68
3171 3570 4.577677 TTGCAGGCTTCCACGGCA 62.578 61.111 0.00 0.00 0.00 5.69
3176 3575 4.785453 GGCTTCCACGGCAGGAGG 62.785 72.222 1.31 1.31 39.25 4.30
3196 3595 1.081376 GGGTCGATATCGGAGCGTG 60.081 63.158 24.12 0.00 38.38 5.34
3198 3597 1.081376 GTCGATATCGGAGCGTGGG 60.081 63.158 24.12 0.00 38.38 4.61
3209 3608 4.436998 GCGTGGGAGTCGGACCTG 62.437 72.222 4.14 0.00 0.00 4.00
3212 3611 2.675423 TGGGAGTCGGACCTGTCG 60.675 66.667 4.14 0.00 0.00 4.35
3213 3612 3.450115 GGGAGTCGGACCTGTCGG 61.450 72.222 4.14 0.00 0.00 4.79
3236 3635 2.287909 GGAGGAGAAATCGGAGATGACG 60.288 54.545 0.00 0.00 45.12 4.35
3254 3653 1.766143 CGATGTAGCCCTTCAAGCGC 61.766 60.000 0.00 0.00 34.64 5.92
3272 3671 1.671054 CCGGACAATGCGGTCTTGT 60.671 57.895 0.00 0.00 46.74 3.16
3289 3688 1.360192 GTTTGCGCTTGAGCTTGGT 59.640 52.632 9.73 0.00 39.32 3.67
3293 3692 2.856032 CGCTTGAGCTTGGTCACG 59.144 61.111 1.72 2.20 39.32 4.35
3298 3697 3.482783 GAGCTTGGTCACGCTCGC 61.483 66.667 12.48 0.00 41.70 5.03
3300 3699 3.782244 GCTTGGTCACGCTCGCTG 61.782 66.667 0.00 0.00 0.00 5.18
3328 3727 4.200283 CTCCCGCTCGGACTGCTC 62.200 72.222 10.28 0.00 34.86 4.26
3362 3761 0.384669 GCTGCTTGGCATTGATCCTC 59.615 55.000 0.00 0.00 38.13 3.71
3363 3762 1.758936 CTGCTTGGCATTGATCCTCA 58.241 50.000 0.00 0.00 38.13 3.86
3368 3767 1.588239 TGGCATTGATCCTCAGGAGT 58.412 50.000 0.00 0.00 34.05 3.85
3390 3789 2.892425 GGGCATCTGTCTTCGCCG 60.892 66.667 0.00 0.00 45.85 6.46
3391 3790 2.125512 GGCATCTGTCTTCGCCGT 60.126 61.111 0.00 0.00 34.26 5.68
3392 3791 1.741770 GGCATCTGTCTTCGCCGTT 60.742 57.895 0.00 0.00 34.26 4.44
3393 3792 0.459585 GGCATCTGTCTTCGCCGTTA 60.460 55.000 0.00 0.00 34.26 3.18
3394 3793 1.571919 GCATCTGTCTTCGCCGTTAT 58.428 50.000 0.00 0.00 0.00 1.89
3395 3794 2.545113 GGCATCTGTCTTCGCCGTTATA 60.545 50.000 0.00 0.00 34.26 0.98
3396 3795 3.318017 GCATCTGTCTTCGCCGTTATAT 58.682 45.455 0.00 0.00 0.00 0.86
3397 3796 3.121944 GCATCTGTCTTCGCCGTTATATG 59.878 47.826 0.00 0.00 0.00 1.78
3398 3797 4.299155 CATCTGTCTTCGCCGTTATATGT 58.701 43.478 0.00 0.00 0.00 2.29
3399 3798 3.702330 TCTGTCTTCGCCGTTATATGTG 58.298 45.455 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 9.482627 GTGTTGGAAATATGAACAATTTACCAA 57.517 29.630 0.00 0.00 34.63 3.67
45 46 8.865090 AGTGTTGGAAATATGAACAATTTACCA 58.135 29.630 0.00 0.00 31.62 3.25
49 50 9.691362 GTGTAGTGTTGGAAATATGAACAATTT 57.309 29.630 0.00 0.00 31.62 1.82
50 51 8.303876 GGTGTAGTGTTGGAAATATGAACAATT 58.696 33.333 0.00 0.00 31.62 2.32
51 52 7.361713 CGGTGTAGTGTTGGAAATATGAACAAT 60.362 37.037 0.00 0.00 31.62 2.71
52 53 6.072948 CGGTGTAGTGTTGGAAATATGAACAA 60.073 38.462 0.00 0.00 31.62 2.83
53 54 5.410132 CGGTGTAGTGTTGGAAATATGAACA 59.590 40.000 0.00 0.00 0.00 3.18
54 55 5.163794 CCGGTGTAGTGTTGGAAATATGAAC 60.164 44.000 0.00 0.00 0.00 3.18
55 56 4.938832 CCGGTGTAGTGTTGGAAATATGAA 59.061 41.667 0.00 0.00 0.00 2.57
56 57 4.020039 ACCGGTGTAGTGTTGGAAATATGA 60.020 41.667 6.12 0.00 0.00 2.15
57 58 4.258543 ACCGGTGTAGTGTTGGAAATATG 58.741 43.478 6.12 0.00 0.00 1.78
58 59 4.563140 ACCGGTGTAGTGTTGGAAATAT 57.437 40.909 6.12 0.00 0.00 1.28
59 60 4.621274 GCTACCGGTGTAGTGTTGGAAATA 60.621 45.833 19.93 0.00 45.24 1.40
60 61 2.943036 ACCGGTGTAGTGTTGGAAAT 57.057 45.000 6.12 0.00 0.00 2.17
61 62 2.548493 GCTACCGGTGTAGTGTTGGAAA 60.548 50.000 19.93 0.00 45.24 3.13
62 63 1.001181 GCTACCGGTGTAGTGTTGGAA 59.999 52.381 19.93 0.00 45.24 3.53
63 64 0.604578 GCTACCGGTGTAGTGTTGGA 59.395 55.000 19.93 0.00 45.24 3.53
64 65 0.319083 TGCTACCGGTGTAGTGTTGG 59.681 55.000 19.93 0.00 45.24 3.77
65 66 1.425412 GTGCTACCGGTGTAGTGTTG 58.575 55.000 19.93 0.00 45.24 3.33
66 67 0.038892 CGTGCTACCGGTGTAGTGTT 60.039 55.000 19.93 0.00 45.24 3.32
67 68 1.174712 ACGTGCTACCGGTGTAGTGT 61.175 55.000 19.93 7.61 45.24 3.55
68 69 0.455633 GACGTGCTACCGGTGTAGTG 60.456 60.000 19.93 6.90 45.24 2.74
69 70 0.890542 TGACGTGCTACCGGTGTAGT 60.891 55.000 19.93 10.05 45.24 2.73
70 71 0.454600 ATGACGTGCTACCGGTGTAG 59.545 55.000 19.93 8.99 46.05 2.74
71 72 0.171679 CATGACGTGCTACCGGTGTA 59.828 55.000 19.93 3.82 0.00 2.90
72 73 1.080093 CATGACGTGCTACCGGTGT 60.080 57.895 19.93 5.62 0.00 4.16
73 74 0.802222 CTCATGACGTGCTACCGGTG 60.802 60.000 19.93 8.61 0.00 4.94
74 75 1.248785 ACTCATGACGTGCTACCGGT 61.249 55.000 13.98 13.98 0.00 5.28
75 76 0.525668 GACTCATGACGTGCTACCGG 60.526 60.000 0.00 0.00 0.00 5.28
76 77 0.861866 CGACTCATGACGTGCTACCG 60.862 60.000 0.00 0.00 0.00 4.02
77 78 1.140407 GCGACTCATGACGTGCTACC 61.140 60.000 0.00 0.00 34.17 3.18
78 79 0.179161 AGCGACTCATGACGTGCTAC 60.179 55.000 8.61 0.00 34.17 3.58
79 80 0.098905 GAGCGACTCATGACGTGCTA 59.901 55.000 9.99 0.00 34.17 3.49
80 81 1.153939 GAGCGACTCATGACGTGCT 60.154 57.895 9.83 9.83 34.17 4.40
81 82 1.008875 TTGAGCGACTCATGACGTGC 61.009 55.000 9.78 4.26 40.39 5.34
82 83 1.388093 CTTTGAGCGACTCATGACGTG 59.612 52.381 9.78 0.00 40.39 4.49
83 84 1.670087 CCTTTGAGCGACTCATGACGT 60.670 52.381 9.78 0.00 40.39 4.34
103 104 0.531532 CATCGACCTGACCTCCATGC 60.532 60.000 0.00 0.00 0.00 4.06
111 112 1.670087 CCTCACACACATCGACCTGAC 60.670 57.143 0.00 0.00 0.00 3.51
116 117 1.269723 TCAGTCCTCACACACATCGAC 59.730 52.381 0.00 0.00 0.00 4.20
127 128 0.411452 AGCCTCTTCCTCAGTCCTCA 59.589 55.000 0.00 0.00 0.00 3.86
128 129 0.823460 CAGCCTCTTCCTCAGTCCTC 59.177 60.000 0.00 0.00 0.00 3.71
129 130 0.617249 CCAGCCTCTTCCTCAGTCCT 60.617 60.000 0.00 0.00 0.00 3.85
130 131 0.616111 TCCAGCCTCTTCCTCAGTCC 60.616 60.000 0.00 0.00 0.00 3.85
131 132 1.066502 GTTCCAGCCTCTTCCTCAGTC 60.067 57.143 0.00 0.00 0.00 3.51
132 133 0.980423 GTTCCAGCCTCTTCCTCAGT 59.020 55.000 0.00 0.00 0.00 3.41
133 134 0.251634 GGTTCCAGCCTCTTCCTCAG 59.748 60.000 0.00 0.00 0.00 3.35
191 192 3.816524 CGTCGCTCGCTCCCTCTT 61.817 66.667 0.00 0.00 0.00 2.85
339 350 4.814294 CTCCCAGCCACGTACCGC 62.814 72.222 0.00 0.00 0.00 5.68
340 351 3.064987 CTCTCCCAGCCACGTACCG 62.065 68.421 0.00 0.00 0.00 4.02
341 352 2.893398 CTCTCCCAGCCACGTACC 59.107 66.667 0.00 0.00 0.00 3.34
480 507 1.068588 TGGATGGAGATCGTAAAGGCG 59.931 52.381 0.00 0.00 0.00 5.52
489 516 3.072184 ACATTACAGGCTGGATGGAGATC 59.928 47.826 26.37 0.00 0.00 2.75
507 534 6.041182 CCATCATGTGGGTTCATTGATACATT 59.959 38.462 6.46 0.00 44.79 2.71
508 535 5.537295 CCATCATGTGGGTTCATTGATACAT 59.463 40.000 6.46 0.00 44.79 2.29
509 536 4.888823 CCATCATGTGGGTTCATTGATACA 59.111 41.667 6.46 0.00 44.79 2.29
510 537 5.443185 CCATCATGTGGGTTCATTGATAC 57.557 43.478 6.46 0.00 44.79 2.24
523 550 2.011947 ACAGAATCGTGCCATCATGTG 58.988 47.619 0.00 0.00 0.00 3.21
524 551 2.011947 CACAGAATCGTGCCATCATGT 58.988 47.619 0.00 0.00 0.00 3.21
525 552 2.750301 CACAGAATCGTGCCATCATG 57.250 50.000 0.00 0.00 0.00 3.07
533 560 2.721797 GCGTAAACAGCACAGAATCGTG 60.722 50.000 0.00 1.89 40.00 4.35
534 561 1.459592 GCGTAAACAGCACAGAATCGT 59.540 47.619 0.00 0.00 34.19 3.73
535 562 1.524986 CGCGTAAACAGCACAGAATCG 60.525 52.381 0.00 0.00 34.19 3.34
536 563 1.724623 TCGCGTAAACAGCACAGAATC 59.275 47.619 5.77 0.00 34.19 2.52
537 564 1.726791 CTCGCGTAAACAGCACAGAAT 59.273 47.619 5.77 0.00 34.19 2.40
538 565 1.136690 CTCGCGTAAACAGCACAGAA 58.863 50.000 5.77 0.00 34.19 3.02
539 566 1.282248 GCTCGCGTAAACAGCACAGA 61.282 55.000 5.77 0.00 33.06 3.41
540 567 1.130613 GCTCGCGTAAACAGCACAG 59.869 57.895 5.77 0.00 33.06 3.66
541 568 1.592939 TGCTCGCGTAAACAGCACA 60.593 52.632 14.60 0.00 38.25 4.57
542 569 3.240203 TGCTCGCGTAAACAGCAC 58.760 55.556 14.60 0.00 38.25 4.40
543 570 1.154814 TTGTGCTCGCGTAAACAGCA 61.155 50.000 14.60 14.60 40.90 4.41
544 571 0.041663 TTTGTGCTCGCGTAAACAGC 60.042 50.000 5.77 8.05 0.00 4.40
545 572 1.525197 TCTTTGTGCTCGCGTAAACAG 59.475 47.619 5.77 0.00 0.00 3.16
546 573 1.259507 GTCTTTGTGCTCGCGTAAACA 59.740 47.619 5.77 6.19 0.00 2.83
547 574 1.259507 TGTCTTTGTGCTCGCGTAAAC 59.740 47.619 5.77 3.28 0.00 2.01
548 575 1.573026 TGTCTTTGTGCTCGCGTAAA 58.427 45.000 5.77 0.85 0.00 2.01
549 576 1.459209 CATGTCTTTGTGCTCGCGTAA 59.541 47.619 5.77 0.00 0.00 3.18
550 577 1.067693 CATGTCTTTGTGCTCGCGTA 58.932 50.000 5.77 0.00 0.00 4.42
551 578 0.880278 ACATGTCTTTGTGCTCGCGT 60.880 50.000 5.77 0.00 0.00 6.01
552 579 0.179240 GACATGTCTTTGTGCTCGCG 60.179 55.000 18.83 0.00 0.00 5.87
553 580 0.867746 TGACATGTCTTTGTGCTCGC 59.132 50.000 25.55 0.00 0.00 5.03
554 581 1.136529 CGTGACATGTCTTTGTGCTCG 60.137 52.381 25.55 12.91 0.00 5.03
555 582 2.135139 TCGTGACATGTCTTTGTGCTC 58.865 47.619 25.55 0.00 0.00 4.26
556 583 2.238942 TCGTGACATGTCTTTGTGCT 57.761 45.000 25.55 0.00 0.00 4.40
557 584 2.480037 TCATCGTGACATGTCTTTGTGC 59.520 45.455 25.55 8.69 0.00 4.57
558 585 4.057730 GTCATCGTGACATGTCTTTGTG 57.942 45.455 25.55 18.03 46.22 3.33
576 603 7.094075 ACGAGTAACAGTTTAGATATGGTGTCA 60.094 37.037 0.00 0.00 0.00 3.58
577 604 7.256286 ACGAGTAACAGTTTAGATATGGTGTC 58.744 38.462 0.00 0.00 0.00 3.67
578 605 7.166691 ACGAGTAACAGTTTAGATATGGTGT 57.833 36.000 0.00 0.00 0.00 4.16
579 606 8.186163 TGTACGAGTAACAGTTTAGATATGGTG 58.814 37.037 0.00 0.00 0.00 4.17
580 607 8.284945 TGTACGAGTAACAGTTTAGATATGGT 57.715 34.615 0.00 0.00 0.00 3.55
581 608 9.395707 GATGTACGAGTAACAGTTTAGATATGG 57.604 37.037 0.00 0.00 0.00 2.74
584 611 8.127327 GCAGATGTACGAGTAACAGTTTAGATA 58.873 37.037 0.00 0.00 0.00 1.98
622 649 9.703892 AGAATTCTCATGGAGTTATCTTAATCG 57.296 33.333 0.88 0.00 0.00 3.34
632 659 7.114754 TGCTGATAAAGAATTCTCATGGAGTT 58.885 34.615 8.78 0.00 0.00 3.01
633 660 6.656902 TGCTGATAAAGAATTCTCATGGAGT 58.343 36.000 8.78 0.00 0.00 3.85
634 661 6.205076 CCTGCTGATAAAGAATTCTCATGGAG 59.795 42.308 8.78 6.85 0.00 3.86
635 662 6.060136 CCTGCTGATAAAGAATTCTCATGGA 58.940 40.000 8.78 0.00 0.00 3.41
636 663 5.826737 ACCTGCTGATAAAGAATTCTCATGG 59.173 40.000 8.78 7.75 0.00 3.66
637 664 6.541278 TCACCTGCTGATAAAGAATTCTCATG 59.459 38.462 8.78 0.60 0.00 3.07
644 671 5.769662 TGTTGTTCACCTGCTGATAAAGAAT 59.230 36.000 0.00 0.00 0.00 2.40
650 677 4.203226 TGTTTGTTGTTCACCTGCTGATA 58.797 39.130 0.00 0.00 0.00 2.15
652 679 2.423185 CTGTTTGTTGTTCACCTGCTGA 59.577 45.455 0.00 0.00 0.00 4.26
676 703 5.237344 CCACTACTGTGCTTATGCTTAATCC 59.763 44.000 1.96 0.00 42.54 3.01
699 726 8.525290 TTACTCCTAATTACTACCACAGTACC 57.475 38.462 0.00 0.00 39.52 3.34
703 730 7.861372 CACGATTACTCCTAATTACTACCACAG 59.139 40.741 0.00 0.00 0.00 3.66
704 731 7.557358 TCACGATTACTCCTAATTACTACCACA 59.443 37.037 0.00 0.00 0.00 4.17
705 732 7.934457 TCACGATTACTCCTAATTACTACCAC 58.066 38.462 0.00 0.00 0.00 4.16
707 734 9.460906 CTTTCACGATTACTCCTAATTACTACC 57.539 37.037 0.00 0.00 0.00 3.18
711 738 7.167136 CGACCTTTCACGATTACTCCTAATTAC 59.833 40.741 0.00 0.00 0.00 1.89
719 746 2.844804 CGTCGACCTTTCACGATTACTC 59.155 50.000 10.58 0.00 40.50 2.59
728 770 1.538512 CTAGTGGACGTCGACCTTTCA 59.461 52.381 24.70 5.73 0.00 2.69
748 790 1.906105 TTGGCCGGTGGAGACCATAC 61.906 60.000 1.90 0.00 43.33 2.39
749 791 1.202099 TTTGGCCGGTGGAGACCATA 61.202 55.000 1.90 0.00 43.33 2.74
750 792 2.484287 CTTTGGCCGGTGGAGACCAT 62.484 60.000 1.90 0.00 43.33 3.55
751 793 3.172106 TTTGGCCGGTGGAGACCA 61.172 61.111 1.90 0.00 43.33 4.02
752 794 2.359975 CTTTGGCCGGTGGAGACC 60.360 66.667 1.90 0.00 39.14 3.85
831 1062 3.030652 CCTGCCGCACGTTTTTCT 58.969 55.556 0.00 0.00 0.00 2.52
1052 1283 4.934942 TCACCGTGACCGTGCGTG 62.935 66.667 0.00 0.00 0.00 5.34
1053 1284 4.640855 CTCACCGTGACCGTGCGT 62.641 66.667 0.00 0.00 0.00 5.24
1415 1646 0.812811 CACTCACCTCCATCGGCATG 60.813 60.000 0.00 0.00 0.00 4.06
1439 1670 1.746239 CATCGCCATGGTGACTGCA 60.746 57.895 29.79 8.19 37.47 4.41
1445 1676 2.125147 ACCGTCATCGCCATGGTG 60.125 61.111 19.75 19.75 31.45 4.17
1446 1677 2.125147 CACCGTCATCGCCATGGT 60.125 61.111 14.67 0.00 32.98 3.55
1552 1783 4.880696 CAGATCTTGAAATCAGGAAGTCCC 59.119 45.833 0.00 0.00 35.56 4.46
1592 1823 2.360852 TCCGTCTCCGTGACCCTC 60.361 66.667 1.10 0.00 42.49 4.30
1747 1981 6.486993 GGCCAGAATAGTCGAGGAATTAAATT 59.513 38.462 0.00 0.00 0.00 1.82
1757 2048 0.461548 TGCAGGCCAGAATAGTCGAG 59.538 55.000 5.01 0.00 0.00 4.04
1787 2078 1.606668 AGCGTTCAAGATTCGGCAAAA 59.393 42.857 0.00 0.00 0.00 2.44
2068 2359 1.373873 GGGGTCGTTGAACGTCTCC 60.374 63.158 17.24 17.24 42.43 3.71
2164 2455 0.770499 TGTTGATGAAGGCCTCCACA 59.230 50.000 5.23 7.80 0.00 4.17
2284 2576 0.613260 CCCATCCCGAGTTCAGTTCA 59.387 55.000 0.00 0.00 0.00 3.18
2305 2597 7.468922 AAAAAGAAGTAACTTGCTTTGATGC 57.531 32.000 0.00 0.00 31.53 3.91
2506 2804 2.442643 CATGCCCGGCTCCCAAAT 60.443 61.111 11.61 0.00 0.00 2.32
2573 2871 1.066573 ACCACAGATCGAGCAAAGGAG 60.067 52.381 2.38 0.00 0.00 3.69
2607 2910 1.985447 CTGCCATGTGCTTACGCTGG 61.985 60.000 7.54 0.00 42.00 4.85
2620 2930 1.004745 CAGGTAAACAGACCCTGCCAT 59.995 52.381 0.00 0.00 40.74 4.40
2623 2933 2.427506 CTTCAGGTAAACAGACCCTGC 58.572 52.381 0.00 0.00 44.41 4.85
2664 2974 3.265791 GCTACTTGTTGTCTGATCCCTG 58.734 50.000 0.00 0.00 0.00 4.45
2707 3017 8.675504 GCATATCCTAGATCATCCAAAATTGAG 58.324 37.037 0.00 0.00 0.00 3.02
2741 3051 2.698274 TGTGCTCAGTTGTTCCTACTCA 59.302 45.455 0.00 0.00 0.00 3.41
2745 3055 3.202906 GTTGTGTGCTCAGTTGTTCCTA 58.797 45.455 0.00 0.00 0.00 2.94
2776 3086 4.413928 CCGGATTTGGCAAGTCCA 57.586 55.556 32.62 7.17 44.85 4.02
2798 3108 2.398498 CTGCAGTCGTATAGGATGCAC 58.602 52.381 19.45 2.55 41.65 4.57
2840 3174 9.031537 TGGACACATAGATTTAAAGACTGTCTA 57.968 33.333 11.30 0.00 0.00 2.59
2841 3175 7.819900 GTGGACACATAGATTTAAAGACTGTCT 59.180 37.037 4.06 4.06 0.00 3.41
2843 3177 7.450074 TGTGGACACATAGATTTAAAGACTGT 58.550 34.615 0.13 0.52 36.21 3.55
2857 3191 5.592688 TGAGATACTCGAATGTGGACACATA 59.407 40.000 17.39 2.44 41.10 2.29
2859 3193 3.761752 TGAGATACTCGAATGTGGACACA 59.238 43.478 7.68 7.68 38.36 3.72
2870 3204 6.540551 GCTGTAGATGGATATGAGATACTCGA 59.459 42.308 0.00 0.00 32.35 4.04
2873 3207 7.643569 CAGCTGTAGATGGATATGAGATACT 57.356 40.000 5.25 0.00 0.00 2.12
2887 3221 1.206878 TGGCATGTCCAGCTGTAGAT 58.793 50.000 13.81 0.00 40.72 1.98
2888 3222 2.682631 TGGCATGTCCAGCTGTAGA 58.317 52.632 13.81 0.01 40.72 2.59
2905 3239 2.436417 CCATATAGGGTGCCCGATTTG 58.564 52.381 8.14 10.20 41.95 2.32
2907 3241 0.328258 GCCATATAGGGTGCCCGATT 59.672 55.000 8.14 0.00 41.95 3.34
2916 3250 1.779061 AACCCCGCAGCCATATAGGG 61.779 60.000 0.00 0.00 41.68 3.53
2918 3252 0.670546 CGAACCCCGCAGCCATATAG 60.671 60.000 0.00 0.00 0.00 1.31
2921 3255 3.379865 GACGAACCCCGCAGCCATA 62.380 63.158 0.00 0.00 43.32 2.74
2922 3256 4.778143 GACGAACCCCGCAGCCAT 62.778 66.667 0.00 0.00 43.32 4.40
2932 3266 2.476534 TTACTCACCGCGGACGAACC 62.477 60.000 35.90 0.00 43.93 3.62
2933 3267 1.081242 TTACTCACCGCGGACGAAC 60.081 57.895 35.90 0.00 43.93 3.95
2934 3268 1.081242 GTTACTCACCGCGGACGAA 60.081 57.895 35.90 15.03 43.93 3.85
2935 3269 2.562912 GTTACTCACCGCGGACGA 59.437 61.111 35.90 25.55 43.93 4.20
2936 3270 2.505557 GGTTACTCACCGCGGACG 60.506 66.667 35.90 22.57 35.12 4.79
2943 3277 1.079336 GACTGCCCGGTTACTCACC 60.079 63.158 0.00 0.00 43.16 4.02
2944 3278 0.108756 GAGACTGCCCGGTTACTCAC 60.109 60.000 0.00 0.00 0.00 3.51
2945 3279 0.251653 AGAGACTGCCCGGTTACTCA 60.252 55.000 0.00 0.00 0.00 3.41
2946 3280 1.760192 TAGAGACTGCCCGGTTACTC 58.240 55.000 0.00 2.05 0.00 2.59
2947 3281 2.226962 TTAGAGACTGCCCGGTTACT 57.773 50.000 0.00 0.00 0.00 2.24
2948 3282 3.538634 ATTTAGAGACTGCCCGGTTAC 57.461 47.619 0.00 0.00 0.00 2.50
2949 3283 3.516300 TGAATTTAGAGACTGCCCGGTTA 59.484 43.478 0.00 0.00 0.00 2.85
2950 3284 2.304761 TGAATTTAGAGACTGCCCGGTT 59.695 45.455 0.00 0.00 0.00 4.44
2951 3285 1.906574 TGAATTTAGAGACTGCCCGGT 59.093 47.619 0.00 0.00 0.00 5.28
2952 3286 2.280628 GTGAATTTAGAGACTGCCCGG 58.719 52.381 0.00 0.00 0.00 5.73
2959 3293 4.304110 TGTGGACACGTGAATTTAGAGAC 58.696 43.478 25.01 5.78 0.00 3.36
2960 3294 4.594123 TGTGGACACGTGAATTTAGAGA 57.406 40.909 25.01 0.00 0.00 3.10
2961 3295 4.330074 GGATGTGGACACGTGAATTTAGAG 59.670 45.833 25.01 0.00 0.00 2.43
2964 3298 3.340034 GGGATGTGGACACGTGAATTTA 58.660 45.455 25.01 5.79 0.00 1.40
2969 3303 2.938086 CGGGGATGTGGACACGTGA 61.938 63.158 25.01 0.00 0.00 4.35
2973 3307 4.796495 GCCCGGGGATGTGGACAC 62.796 72.222 25.28 0.00 0.00 3.67
2980 3314 1.453015 TCGATTTTGCCCGGGGATG 60.453 57.895 25.28 7.50 0.00 3.51
2985 3319 0.958382 TTCCTGTCGATTTTGCCCGG 60.958 55.000 0.00 0.00 0.00 5.73
3006 3391 2.140839 ATTTAGAGTCCGTCCCTCGT 57.859 50.000 0.00 0.00 37.94 4.18
3007 3392 2.426024 TCAATTTAGAGTCCGTCCCTCG 59.574 50.000 0.00 0.00 39.52 4.63
3010 3395 6.258068 CAGTTTATCAATTTAGAGTCCGTCCC 59.742 42.308 0.00 0.00 0.00 4.46
3011 3396 7.039882 TCAGTTTATCAATTTAGAGTCCGTCC 58.960 38.462 0.00 0.00 0.00 4.79
3012 3397 8.649973 ATCAGTTTATCAATTTAGAGTCCGTC 57.350 34.615 0.00 0.00 0.00 4.79
3014 3399 8.704234 GCTATCAGTTTATCAATTTAGAGTCCG 58.296 37.037 0.00 0.00 0.00 4.79
3015 3400 9.547753 TGCTATCAGTTTATCAATTTAGAGTCC 57.452 33.333 0.00 0.00 0.00 3.85
3072 3457 5.645497 CCCATATCTAGCTAGAATTTGCCAC 59.355 44.000 26.62 0.00 35.69 5.01
3131 3530 3.051392 GCCGGCAATCGAAAGGGTG 62.051 63.158 24.80 0.00 42.43 4.61
3132 3531 2.750237 GCCGGCAATCGAAAGGGT 60.750 61.111 24.80 0.00 42.43 4.34
3134 3533 2.040544 AGTGCCGGCAATCGAAAGG 61.041 57.895 34.66 0.00 42.43 3.11
3138 3537 2.031919 AACAGTGCCGGCAATCGA 59.968 55.556 34.66 4.50 42.43 3.59
3149 3548 1.656441 GTGGAAGCCTGCAACAGTG 59.344 57.895 0.00 0.00 0.00 3.66
3150 3549 1.893808 CGTGGAAGCCTGCAACAGT 60.894 57.895 0.00 0.00 0.00 3.55
3151 3550 2.620112 CCGTGGAAGCCTGCAACAG 61.620 63.158 0.00 0.00 0.00 3.16
3152 3551 2.594303 CCGTGGAAGCCTGCAACA 60.594 61.111 0.00 0.00 0.00 3.33
3153 3552 4.043200 GCCGTGGAAGCCTGCAAC 62.043 66.667 0.00 0.00 0.00 4.17
3154 3553 4.577677 TGCCGTGGAAGCCTGCAA 62.578 61.111 0.00 0.00 0.00 4.08
3157 3556 3.965539 CTCCTGCCGTGGAAGCCTG 62.966 68.421 0.00 0.00 35.43 4.85
3158 3557 3.710722 CTCCTGCCGTGGAAGCCT 61.711 66.667 0.00 0.00 35.43 4.58
3159 3558 4.785453 CCTCCTGCCGTGGAAGCC 62.785 72.222 0.00 0.00 35.43 4.35
3160 3559 4.021925 ACCTCCTGCCGTGGAAGC 62.022 66.667 0.00 0.00 35.43 3.86
3161 3560 2.046892 CACCTCCTGCCGTGGAAG 60.047 66.667 0.00 0.00 35.43 3.46
3165 3564 4.394712 GACCCACCTCCTGCCGTG 62.395 72.222 0.00 0.00 0.00 4.94
3168 3567 1.122019 ATATCGACCCACCTCCTGCC 61.122 60.000 0.00 0.00 0.00 4.85
3169 3568 0.318762 GATATCGACCCACCTCCTGC 59.681 60.000 0.00 0.00 0.00 4.85
3170 3569 0.598562 CGATATCGACCCACCTCCTG 59.401 60.000 20.50 0.00 43.02 3.86
3171 3570 0.539901 CCGATATCGACCCACCTCCT 60.540 60.000 26.32 0.00 43.02 3.69
3172 3571 0.538977 TCCGATATCGACCCACCTCC 60.539 60.000 26.32 0.00 43.02 4.30
3173 3572 0.882474 CTCCGATATCGACCCACCTC 59.118 60.000 26.32 0.00 43.02 3.85
3176 3575 1.081376 CGCTCCGATATCGACCCAC 60.081 63.158 26.32 9.61 43.02 4.61
3196 3595 3.450115 CCGACAGGTCCGACTCCC 61.450 72.222 0.00 0.00 0.00 4.30
3198 3597 2.408241 CCTCCGACAGGTCCGACTC 61.408 68.421 0.00 0.00 37.53 3.36
3209 3608 0.386113 CCGATTTCTCCTCCTCCGAC 59.614 60.000 0.00 0.00 0.00 4.79
3212 3611 2.074729 TCTCCGATTTCTCCTCCTCC 57.925 55.000 0.00 0.00 0.00 4.30
3213 3612 3.005367 GTCATCTCCGATTTCTCCTCCTC 59.995 52.174 0.00 0.00 0.00 3.71
3362 3761 2.105128 GATGCCCGACGACTCCTG 59.895 66.667 0.00 0.00 0.00 3.86
3363 3762 2.043852 AGATGCCCGACGACTCCT 60.044 61.111 0.00 0.00 0.00 3.69
3368 3767 1.511305 GAAGACAGATGCCCGACGA 59.489 57.895 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.