Multiple sequence alignment - TraesCS6B01G372200

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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 TraesCS6B01G372200 chr6B 100.000 4055 0 0 1 4055 645652216 645656270 0.000000e+00 7489.0
1 TraesCS6B01G372200 chr6B 92.384 2626 136 32 718 3313 646010744 646008153 0.000000e+00 3683.0
2 TraesCS6B01G372200 chr6B 86.138 2359 244 38 932 3247 711739854 711737536 0.000000e+00 2468.0
3 TraesCS6B01G372200 chr6B 84.418 1829 239 30 1206 3025 615087996 615086205 0.000000e+00 1757.0
4 TraesCS6B01G372200 chr6B 85.570 1684 208 21 1351 3025 704155640 704153983 0.000000e+00 1731.0
5 TraesCS6B01G372200 chr6D 93.249 3318 175 26 778 4055 428959760 428963068 0.000000e+00 4841.0
6 TraesCS6B01G372200 chr6D 85.356 1673 206 22 1364 3026 461820157 461818514 0.000000e+00 1696.0
7 TraesCS6B01G372200 chr6D 87.883 718 79 5 2356 3066 466524959 466525675 0.000000e+00 837.0
8 TraesCS6B01G372200 chr6A 91.654 3391 177 42 718 4055 573635774 573639111 0.000000e+00 4597.0
9 TraesCS6B01G372200 chr6A 94.807 2253 107 8 1060 3303 574222465 574220214 0.000000e+00 3504.0
10 TraesCS6B01G372200 chr6A 86.834 1876 202 12 1374 3247 613092215 613090383 0.000000e+00 2054.0
11 TraesCS6B01G372200 chr6A 83.589 1822 240 40 1228 3031 135224279 135226059 0.000000e+00 1653.0
12 TraesCS6B01G372200 chr3B 86.642 1894 210 19 1184 3065 197792012 197790150 0.000000e+00 2056.0
13 TraesCS6B01G372200 chr5D 92.308 273 21 0 83 355 480706797 480706525 4.910000e-104 388.0
14 TraesCS6B01G372200 chr5D 88.889 171 18 1 3320 3489 7616582 7616412 4.110000e-50 209.0
15 TraesCS6B01G372200 chr5D 96.774 31 1 0 948 978 24616035 24616005 7.000000e-03 52.8
16 TraesCS6B01G372200 chr5B 92.308 273 21 0 83 355 589121519 589121247 4.910000e-104 388.0
17 TraesCS6B01G372200 chr5A 92.058 277 21 1 79 355 599803975 599803700 4.910000e-104 388.0
18 TraesCS6B01G372200 chr5A 89.820 167 16 1 3322 3487 463602134 463602300 3.170000e-51 213.0
19 TraesCS6B01G372200 chr7D 92.273 220 17 0 136 355 120302480 120302699 3.040000e-81 313.0
20 TraesCS6B01G372200 chr7D 79.357 373 51 22 362 718 171028233 171028595 5.240000e-59 239.0
21 TraesCS6B01G372200 chr2A 82.972 323 26 10 405 719 764331128 764331429 8.640000e-67 265.0
22 TraesCS6B01G372200 chr2A 88.182 220 26 0 136 355 683565170 683565389 3.110000e-66 263.0
23 TraesCS6B01G372200 chr2A 88.482 191 21 1 138 327 513848424 513848614 3.150000e-56 230.0
24 TraesCS6B01G372200 chr2A 85.388 219 27 1 136 349 513850434 513850652 5.280000e-54 222.0
25 TraesCS6B01G372200 chr2A 86.429 140 17 1 570 707 513851076 513851215 7.020000e-33 152.0
26 TraesCS6B01G372200 chr7B 86.547 223 19 7 506 718 747743474 747743253 6.780000e-58 235.0
27 TraesCS6B01G372200 chr7B 86.547 223 19 7 506 718 747767792 747767571 6.780000e-58 235.0
28 TraesCS6B01G372200 chr4D 91.667 168 13 1 3321 3487 258893622 258893455 8.770000e-57 231.0
29 TraesCS6B01G372200 chr2D 91.667 168 13 1 3321 3487 647674638 647674805 8.770000e-57 231.0
30 TraesCS6B01G372200 chr2D 84.186 215 23 7 514 718 352710206 352710419 8.890000e-47 198.0
31 TraesCS6B01G372200 chr3D 90.000 170 16 1 3321 3489 317203427 317203596 6.820000e-53 219.0
32 TraesCS6B01G372200 chr1D 90.058 171 13 4 3321 3489 196608142 196607974 6.820000e-53 219.0
33 TraesCS6B01G372200 chr7A 89.595 173 12 5 3320 3489 504221520 504221351 8.830000e-52 215.0
34 TraesCS6B01G372200 chr3A 78.142 366 47 22 364 719 17271220 17270878 6.870000e-48 202.0
35 TraesCS6B01G372200 chr3A 93.023 43 3 0 119 161 17272130 17272088 3.380000e-06 63.9
36 TraesCS6B01G372200 chr1A 93.878 49 3 0 121 169 543639168 543639120 1.560000e-09 75.0


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 TraesCS6B01G372200 chr6B 645652216 645656270 4054 False 7489.000000 7489 100.000000 1 4055 1 chr6B.!!$F1 4054
1 TraesCS6B01G372200 chr6B 646008153 646010744 2591 True 3683.000000 3683 92.384000 718 3313 1 chr6B.!!$R2 2595
2 TraesCS6B01G372200 chr6B 711737536 711739854 2318 True 2468.000000 2468 86.138000 932 3247 1 chr6B.!!$R4 2315
3 TraesCS6B01G372200 chr6B 615086205 615087996 1791 True 1757.000000 1757 84.418000 1206 3025 1 chr6B.!!$R1 1819
4 TraesCS6B01G372200 chr6B 704153983 704155640 1657 True 1731.000000 1731 85.570000 1351 3025 1 chr6B.!!$R3 1674
5 TraesCS6B01G372200 chr6D 428959760 428963068 3308 False 4841.000000 4841 93.249000 778 4055 1 chr6D.!!$F1 3277
6 TraesCS6B01G372200 chr6D 461818514 461820157 1643 True 1696.000000 1696 85.356000 1364 3026 1 chr6D.!!$R1 1662
7 TraesCS6B01G372200 chr6D 466524959 466525675 716 False 837.000000 837 87.883000 2356 3066 1 chr6D.!!$F2 710
8 TraesCS6B01G372200 chr6A 573635774 573639111 3337 False 4597.000000 4597 91.654000 718 4055 1 chr6A.!!$F2 3337
9 TraesCS6B01G372200 chr6A 574220214 574222465 2251 True 3504.000000 3504 94.807000 1060 3303 1 chr6A.!!$R1 2243
10 TraesCS6B01G372200 chr6A 613090383 613092215 1832 True 2054.000000 2054 86.834000 1374 3247 1 chr6A.!!$R2 1873
11 TraesCS6B01G372200 chr6A 135224279 135226059 1780 False 1653.000000 1653 83.589000 1228 3031 1 chr6A.!!$F1 1803
12 TraesCS6B01G372200 chr3B 197790150 197792012 1862 True 2056.000000 2056 86.642000 1184 3065 1 chr3B.!!$R1 1881
13 TraesCS6B01G372200 chr2A 513848424 513851215 2791 False 201.333333 230 86.766333 136 707 3 chr2A.!!$F3 571

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
571 2885 0.032217 AAGGAGAGAGAGAGGGGCTG 60.032 60.000 0.0 0.00 0.00 4.85 F
698 3014 0.249280 CAAAACAACGTCTTGGGGGC 60.249 55.000 0.0 0.00 0.00 5.80 F
906 3243 0.531532 AAATCTCCGAGCTGCCATCG 60.532 55.000 0.0 4.51 39.86 3.84 F
1634 4060 1.154035 GCCAATACCAACGTGCTGC 60.154 57.895 0.0 0.00 0.00 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1491 3914 1.630878 GTCTGGAGAGGATGGTGGTTT 59.369 52.381 0.00 0.00 0.00 3.27 R
1634 4060 1.741706 CAGTATGCTCCTGGTTGCTTG 59.258 52.381 13.47 5.69 0.00 4.01 R
2598 5037 6.129352 GCAAGTTTGAACTTCGAAATGACATC 60.129 38.462 6.16 0.00 45.65 3.06 R
3368 5859 0.107831 AAGCGTCAGCCCTGTACAAA 59.892 50.000 0.00 0.00 46.67 2.83 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
18 19 3.179925 GCCCACAATCTGCAGATGA 57.820 52.632 29.34 2.79 34.49 2.92
19 20 1.022735 GCCCACAATCTGCAGATGAG 58.977 55.000 29.34 24.81 34.49 2.90
20 21 1.022735 CCCACAATCTGCAGATGAGC 58.977 55.000 29.34 0.00 34.49 4.26
21 22 1.680860 CCCACAATCTGCAGATGAGCA 60.681 52.381 29.34 0.73 43.35 4.26
22 23 2.089201 CCACAATCTGCAGATGAGCAA 58.911 47.619 29.34 0.00 45.13 3.91
23 24 2.490509 CCACAATCTGCAGATGAGCAAA 59.509 45.455 29.34 0.00 45.13 3.68
24 25 3.499048 CACAATCTGCAGATGAGCAAAC 58.501 45.455 29.34 0.00 45.13 2.93
25 26 3.190744 CACAATCTGCAGATGAGCAAACT 59.809 43.478 29.34 8.71 45.13 2.66
26 27 3.439476 ACAATCTGCAGATGAGCAAACTC 59.561 43.478 29.34 0.00 45.13 3.01
27 28 3.630892 ATCTGCAGATGAGCAAACTCT 57.369 42.857 28.21 0.00 45.13 3.24
28 29 3.413846 TCTGCAGATGAGCAAACTCTT 57.586 42.857 13.74 0.00 45.13 2.85
29 30 3.748083 TCTGCAGATGAGCAAACTCTTT 58.252 40.909 13.74 0.00 45.13 2.52
30 31 4.139786 TCTGCAGATGAGCAAACTCTTTT 58.860 39.130 13.74 0.00 45.13 2.27
31 32 4.023450 TCTGCAGATGAGCAAACTCTTTTG 60.023 41.667 13.74 0.00 45.13 2.44
32 33 3.884693 TGCAGATGAGCAAACTCTTTTGA 59.115 39.130 1.29 0.00 44.38 2.69
33 34 4.023450 TGCAGATGAGCAAACTCTTTTGAG 60.023 41.667 1.29 0.00 44.38 3.02
34 35 6.205093 TGCAGATGAGCAAACTCTTTTGAGA 61.205 40.000 1.29 0.00 44.62 3.27
35 36 8.163558 TGCAGATGAGCAAACTCTTTTGAGAC 62.164 42.308 1.29 0.00 44.62 3.36
61 62 6.147864 CTTCAAGAAGGAAAACAATGTCCA 57.852 37.500 1.86 0.00 36.28 4.02
62 63 6.537453 TTCAAGAAGGAAAACAATGTCCAA 57.463 33.333 0.00 0.00 36.28 3.53
63 64 6.147864 TCAAGAAGGAAAACAATGTCCAAG 57.852 37.500 0.00 0.00 36.28 3.61
64 65 5.068987 TCAAGAAGGAAAACAATGTCCAAGG 59.931 40.000 0.00 0.00 36.28 3.61
65 66 4.803452 AGAAGGAAAACAATGTCCAAGGA 58.197 39.130 0.00 0.00 36.28 3.36
66 67 4.584743 AGAAGGAAAACAATGTCCAAGGAC 59.415 41.667 12.30 12.30 44.77 3.85
74 75 2.804090 GTCCAAGGACGTCGTCGC 60.804 66.667 18.61 11.75 41.18 5.19
75 76 4.047059 TCCAAGGACGTCGTCGCC 62.047 66.667 18.61 7.14 41.18 5.54
84 85 4.176851 GTCGTCGCCCTCCGTCTC 62.177 72.222 0.00 0.00 38.35 3.36
90 91 4.131088 GCCCTCCGTCTCCGACAC 62.131 72.222 0.00 0.00 35.63 3.67
91 92 3.450115 CCCTCCGTCTCCGACACC 61.450 72.222 0.00 0.00 35.63 4.16
92 93 2.675423 CCTCCGTCTCCGACACCA 60.675 66.667 0.00 0.00 35.63 4.17
93 94 2.052690 CCTCCGTCTCCGACACCAT 61.053 63.158 0.00 0.00 35.63 3.55
94 95 1.433879 CTCCGTCTCCGACACCATC 59.566 63.158 0.00 0.00 35.63 3.51
95 96 1.001269 TCCGTCTCCGACACCATCT 60.001 57.895 0.00 0.00 35.63 2.90
96 97 1.030488 TCCGTCTCCGACACCATCTC 61.030 60.000 0.00 0.00 35.63 2.75
97 98 1.433879 CGTCTCCGACACCATCTCC 59.566 63.158 0.00 0.00 35.63 3.71
98 99 1.433879 GTCTCCGACACCATCTCCG 59.566 63.158 0.00 0.00 32.09 4.63
99 100 1.001269 TCTCCGACACCATCTCCGT 60.001 57.895 0.00 0.00 0.00 4.69
100 101 1.030488 TCTCCGACACCATCTCCGTC 61.030 60.000 0.00 0.00 0.00 4.79
102 103 2.579787 CGACACCATCTCCGTCGC 60.580 66.667 0.00 0.00 44.99 5.19
103 104 2.579787 GACACCATCTCCGTCGCG 60.580 66.667 0.00 0.00 0.00 5.87
104 105 4.796231 ACACCATCTCCGTCGCGC 62.796 66.667 0.00 0.00 0.00 6.86
158 159 1.152440 ATCCTCGATCGGGGCTTCT 60.152 57.895 29.84 10.63 35.22 2.85
171 172 2.111582 GCTTCTGCCACCTGCTAGC 61.112 63.158 8.10 8.10 42.00 3.42
203 204 2.893398 CCACCTCTGGCTACGACC 59.107 66.667 0.00 0.00 0.00 4.79
243 244 2.168496 CTCCTACAAGGTCGAGGACAA 58.832 52.381 0.00 0.00 36.53 3.18
244 245 1.891150 TCCTACAAGGTCGAGGACAAC 59.109 52.381 0.00 0.00 36.53 3.32
254 255 3.264866 GAGGACAACGACGCCGACT 62.265 63.158 0.00 0.00 39.50 4.18
332 1059 1.813337 GAGAGCCTCGCCTTTGAGC 60.813 63.158 0.00 0.00 34.56 4.26
356 1083 3.227276 CCTCCTGCGACGGCCTAT 61.227 66.667 0.00 0.00 38.85 2.57
357 1084 2.336809 CTCCTGCGACGGCCTATC 59.663 66.667 0.00 0.00 38.85 2.08
358 1085 2.441348 TCCTGCGACGGCCTATCA 60.441 61.111 0.00 0.00 38.85 2.15
360 1087 2.028190 CTGCGACGGCCTATCAGG 59.972 66.667 0.00 0.00 38.85 3.86
487 2801 2.363018 CCAGGGACGAGGAGCAGA 60.363 66.667 0.00 0.00 0.00 4.26
488 2802 2.422231 CCAGGGACGAGGAGCAGAG 61.422 68.421 0.00 0.00 0.00 3.35
489 2803 1.379176 CAGGGACGAGGAGCAGAGA 60.379 63.158 0.00 0.00 0.00 3.10
490 2804 0.754957 CAGGGACGAGGAGCAGAGAT 60.755 60.000 0.00 0.00 0.00 2.75
491 2805 0.754957 AGGGACGAGGAGCAGAGATG 60.755 60.000 0.00 0.00 0.00 2.90
492 2806 1.067250 GGACGAGGAGCAGAGATGC 59.933 63.158 0.00 0.00 0.00 3.91
493 2807 1.670949 GGACGAGGAGCAGAGATGCA 61.671 60.000 2.73 0.00 37.25 3.96
495 2809 1.592131 CGAGGAGCAGAGATGCAGC 60.592 63.158 0.00 0.00 37.25 5.25
496 2810 1.521141 GAGGAGCAGAGATGCAGCA 59.479 57.895 4.07 0.00 37.25 4.41
498 2812 1.524165 GGAGCAGAGATGCAGCAGG 60.524 63.158 4.07 0.00 37.25 4.85
499 2813 1.521141 GAGCAGAGATGCAGCAGGA 59.479 57.895 4.07 0.00 37.25 3.86
505 2819 1.632409 AGAGATGCAGCAGGAGGAAAA 59.368 47.619 4.07 0.00 0.00 2.29
506 2820 2.015587 GAGATGCAGCAGGAGGAAAAG 58.984 52.381 4.07 0.00 0.00 2.27
507 2821 1.632409 AGATGCAGCAGGAGGAAAAGA 59.368 47.619 4.07 0.00 0.00 2.52
526 2840 6.610075 AAAGATCCCTTTTTACATGCACAT 57.390 33.333 0.00 0.00 39.45 3.21
527 2841 7.716799 AAAGATCCCTTTTTACATGCACATA 57.283 32.000 0.00 0.00 39.45 2.29
528 2842 6.699575 AGATCCCTTTTTACATGCACATAC 57.300 37.500 0.00 0.00 0.00 2.39
529 2843 6.186957 AGATCCCTTTTTACATGCACATACA 58.813 36.000 0.00 0.00 0.00 2.29
530 2844 5.637006 TCCCTTTTTACATGCACATACAC 57.363 39.130 0.00 0.00 0.00 2.90
531 2845 4.155099 TCCCTTTTTACATGCACATACACG 59.845 41.667 0.00 0.00 0.00 4.49
532 2846 4.411327 CCTTTTTACATGCACATACACGG 58.589 43.478 0.00 0.00 0.00 4.94
533 2847 4.411327 CTTTTTACATGCACATACACGGG 58.589 43.478 0.00 0.00 0.00 5.28
534 2848 2.772077 TTACATGCACATACACGGGT 57.228 45.000 0.00 0.00 0.00 5.28
535 2849 2.017138 TACATGCACATACACGGGTG 57.983 50.000 0.00 0.00 38.05 4.61
536 2850 0.676466 ACATGCACATACACGGGTGG 60.676 55.000 0.00 0.00 35.58 4.61
537 2851 1.077787 ATGCACATACACGGGTGGG 60.078 57.895 0.00 0.00 35.58 4.61
538 2852 3.131478 GCACATACACGGGTGGGC 61.131 66.667 0.00 0.00 37.62 5.36
539 2853 2.437716 CACATACACGGGTGGGCC 60.438 66.667 0.00 0.00 34.19 5.80
540 2854 2.609610 ACATACACGGGTGGGCCT 60.610 61.111 0.00 0.00 34.45 5.19
541 2855 1.306312 ACATACACGGGTGGGCCTA 60.306 57.895 0.00 0.00 34.45 3.93
542 2856 1.335132 ACATACACGGGTGGGCCTAG 61.335 60.000 0.00 0.00 34.45 3.02
543 2857 2.440817 ATACACGGGTGGGCCTAGC 61.441 63.158 10.28 10.28 34.45 3.42
544 2858 3.908904 TACACGGGTGGGCCTAGCA 62.909 63.158 20.67 0.00 34.45 3.49
545 2859 4.473520 CACGGGTGGGCCTAGCAG 62.474 72.222 20.67 18.50 34.45 4.24
548 2862 3.015145 GGGTGGGCCTAGCAGGAA 61.015 66.667 20.67 0.00 37.67 3.36
549 2863 2.612493 GGGTGGGCCTAGCAGGAAA 61.612 63.158 20.67 0.00 37.67 3.13
550 2864 1.382629 GGTGGGCCTAGCAGGAAAA 59.617 57.895 14.14 0.00 37.67 2.29
551 2865 0.681243 GGTGGGCCTAGCAGGAAAAG 60.681 60.000 14.14 0.00 37.67 2.27
552 2866 0.328258 GTGGGCCTAGCAGGAAAAGA 59.672 55.000 4.53 0.00 37.67 2.52
553 2867 1.072266 TGGGCCTAGCAGGAAAAGAA 58.928 50.000 4.53 0.00 37.67 2.52
554 2868 1.004745 TGGGCCTAGCAGGAAAAGAAG 59.995 52.381 4.53 0.00 37.67 2.85
555 2869 1.683319 GGGCCTAGCAGGAAAAGAAGG 60.683 57.143 0.84 0.00 37.67 3.46
556 2870 1.282157 GGCCTAGCAGGAAAAGAAGGA 59.718 52.381 0.00 0.00 37.67 3.36
557 2871 2.637947 GCCTAGCAGGAAAAGAAGGAG 58.362 52.381 6.40 0.00 37.67 3.69
558 2872 2.237392 GCCTAGCAGGAAAAGAAGGAGA 59.763 50.000 6.40 0.00 37.67 3.71
559 2873 3.681313 GCCTAGCAGGAAAAGAAGGAGAG 60.681 52.174 6.40 0.00 37.67 3.20
560 2874 3.772025 CCTAGCAGGAAAAGAAGGAGAGA 59.228 47.826 0.00 0.00 37.67 3.10
561 2875 3.979101 AGCAGGAAAAGAAGGAGAGAG 57.021 47.619 0.00 0.00 0.00 3.20
562 2876 3.515562 AGCAGGAAAAGAAGGAGAGAGA 58.484 45.455 0.00 0.00 0.00 3.10
563 2877 3.515104 AGCAGGAAAAGAAGGAGAGAGAG 59.485 47.826 0.00 0.00 0.00 3.20
564 2878 3.513515 GCAGGAAAAGAAGGAGAGAGAGA 59.486 47.826 0.00 0.00 0.00 3.10
565 2879 4.381932 GCAGGAAAAGAAGGAGAGAGAGAG 60.382 50.000 0.00 0.00 0.00 3.20
566 2880 4.160252 CAGGAAAAGAAGGAGAGAGAGAGG 59.840 50.000 0.00 0.00 0.00 3.69
567 2881 3.450817 GGAAAAGAAGGAGAGAGAGAGGG 59.549 52.174 0.00 0.00 0.00 4.30
568 2882 2.846665 AAGAAGGAGAGAGAGAGGGG 57.153 55.000 0.00 0.00 0.00 4.79
569 2883 0.261696 AGAAGGAGAGAGAGAGGGGC 59.738 60.000 0.00 0.00 0.00 5.80
570 2884 0.261696 GAAGGAGAGAGAGAGGGGCT 59.738 60.000 0.00 0.00 0.00 5.19
571 2885 0.032217 AAGGAGAGAGAGAGGGGCTG 60.032 60.000 0.00 0.00 0.00 4.85
606 2920 2.072298 GCCATGCAAAAATTAACGCCA 58.928 42.857 0.00 0.00 0.00 5.69
613 2927 0.524414 AAAATTAACGCCAGCGGTCC 59.476 50.000 17.33 0.00 44.69 4.46
666 2980 2.872858 CAGGTCGCTAGGGCTATTTTTC 59.127 50.000 1.02 0.00 36.09 2.29
675 2991 5.278022 GCTAGGGCTATTTTTCTCAAATCCG 60.278 44.000 0.00 0.00 35.22 4.18
676 2992 4.855340 AGGGCTATTTTTCTCAAATCCGA 58.145 39.130 0.00 0.00 0.00 4.55
679 2995 4.029043 GCTATTTTTCTCAAATCCGACGC 58.971 43.478 0.00 0.00 0.00 5.19
688 3004 1.446465 CAAATCCGACGCAAAACAACG 59.554 47.619 0.00 0.00 0.00 4.10
694 3010 3.615099 ACGCAAAACAACGTCTTGG 57.385 47.368 0.00 0.00 38.28 3.61
698 3014 0.249280 CAAAACAACGTCTTGGGGGC 60.249 55.000 0.00 0.00 0.00 5.80
762 3081 3.479370 CTCCTTTTCGAGCTGCCG 58.521 61.111 0.00 0.00 0.00 5.69
787 3122 3.362581 GGAATCAATCCGAGTCGCA 57.637 52.632 7.12 0.00 39.69 5.10
798 3133 2.507102 AGTCGCAGTCCGCAATCG 60.507 61.111 0.00 0.00 42.60 3.34
809 3144 3.929948 GCAATCGAAGCGGCTCCG 61.930 66.667 0.83 0.83 43.09 4.63
889 3226 8.973182 ACAGGTCCTGTTTCAGTTTTAATTAAA 58.027 29.630 19.42 6.54 42.59 1.52
901 3238 6.688813 CAGTTTTAATTAAATCTCCGAGCTGC 59.311 38.462 15.53 0.00 0.00 5.25
902 3239 5.751243 TTTAATTAAATCTCCGAGCTGCC 57.249 39.130 6.54 0.00 0.00 4.85
903 3240 3.281727 AATTAAATCTCCGAGCTGCCA 57.718 42.857 0.00 0.00 0.00 4.92
904 3241 3.498774 ATTAAATCTCCGAGCTGCCAT 57.501 42.857 0.00 0.00 0.00 4.40
906 3243 0.531532 AAATCTCCGAGCTGCCATCG 60.532 55.000 0.00 4.51 39.86 3.84
920 3264 2.047274 ATCGGTGGCAGGAACGTG 60.047 61.111 0.00 0.00 0.00 4.49
1088 3449 6.504279 TCCTGTTCCTTTTCTCCTTTAGGTAT 59.496 38.462 0.00 0.00 36.34 2.73
1106 3467 6.472686 AGGTATAGCTCTTACAAAGTCAGG 57.527 41.667 0.00 0.00 0.00 3.86
1142 3534 5.347012 TCGTGGTCGAATTTAACCTTTTC 57.653 39.130 10.50 0.00 43.34 2.29
1165 3560 4.382470 CGGTGGGGAAATATCAAAATTGCA 60.382 41.667 0.00 0.00 0.00 4.08
1201 3608 9.748708 TGAAAGTATATAATCAAATTTGCAGGC 57.251 29.630 13.54 0.00 0.00 4.85
1491 3914 1.202557 TGATATCGCTGATGCTGCACA 60.203 47.619 3.57 4.59 36.97 4.57
1634 4060 1.154035 GCCAATACCAACGTGCTGC 60.154 57.895 0.00 0.00 0.00 5.25
1866 4292 2.165030 GGCAGTTCATGTCATTCCTTGG 59.835 50.000 0.00 0.00 32.08 3.61
2598 5037 8.682016 GCCGATTATTCAATTCTCGTTTTTATG 58.318 33.333 0.00 0.00 0.00 1.90
3039 5491 2.910319 AGGGGAAATTTTTACTTGGCCC 59.090 45.455 0.00 0.00 0.00 5.80
3042 5494 4.263727 GGGGAAATTTTTACTTGGCCCAAT 60.264 41.667 0.00 0.00 36.03 3.16
3051 5503 1.427368 ACTTGGCCCAATTACTGGTCA 59.573 47.619 0.00 0.00 44.76 4.02
3124 5588 5.159273 TGACAGGAGTTGTTGTATGCATA 57.841 39.130 1.16 1.16 41.05 3.14
3136 5600 9.884465 GTTGTTGTATGCATAGATTAATTCTCC 57.116 33.333 6.67 0.00 35.79 3.71
3139 5604 8.725148 GTTGTATGCATAGATTAATTCTCCCTG 58.275 37.037 6.67 0.00 35.79 4.45
3179 5644 6.727824 ATTTCTGTTTCGAGATTGTACTGG 57.272 37.500 0.00 0.00 0.00 4.00
3181 5646 2.673368 CTGTTTCGAGATTGTACTGGGC 59.327 50.000 0.00 0.00 0.00 5.36
3242 5707 8.610896 TGAAGTATTTTGGCAAATGAAAGTTTG 58.389 29.630 14.29 0.00 41.02 2.93
3270 5735 3.005261 TGTTATTCGTGGCAAATGCTTGT 59.995 39.130 5.25 0.00 41.70 3.16
3306 5771 8.292444 TGTTGTGAAATCCCTAAGATTAATGG 57.708 34.615 0.00 0.00 44.75 3.16
3380 5871 2.723273 GGTGCTTATTTGTACAGGGCT 58.277 47.619 0.00 0.00 0.00 5.19
3395 5886 1.141053 AGGGCTGACGCTTAATTAGGG 59.859 52.381 0.00 0.00 42.27 3.53
3396 5887 1.140252 GGGCTGACGCTTAATTAGGGA 59.860 52.381 0.00 0.00 39.94 4.20
3397 5888 2.210961 GGCTGACGCTTAATTAGGGAC 58.789 52.381 0.00 0.00 39.94 4.46
3437 5928 0.313987 CCGGTGCTTCAGAAAAACCC 59.686 55.000 0.00 0.00 0.00 4.11
3449 5940 8.221100 GCTTCAGAAAAACCCGATTTATTTTTC 58.779 33.333 11.59 11.59 45.95 2.29
3458 5949 5.712917 ACCCGATTTATTTTTCTAAGCACCA 59.287 36.000 0.00 0.00 0.00 4.17
3461 5952 7.312899 CCGATTTATTTTTCTAAGCACCAGTT 58.687 34.615 0.00 0.00 0.00 3.16
3478 5970 3.763897 CCAGTTTAAGCCCTAGCATTGTT 59.236 43.478 0.00 0.00 43.56 2.83
3510 6002 0.111253 CTTGCCCCAAACCTCTGTCT 59.889 55.000 0.00 0.00 0.00 3.41
3532 6024 7.081976 GTCTGCGATACAAACAAAAATTACCT 58.918 34.615 0.00 0.00 0.00 3.08
3582 6076 2.825861 TTACCACAAACCTCCGTCTC 57.174 50.000 0.00 0.00 0.00 3.36
3623 6117 8.500753 TTAAACTAGCCGAACAAATATCATGT 57.499 30.769 0.00 0.00 0.00 3.21
3663 6157 7.496529 ACAATATGATTTACATGAACCGGAG 57.503 36.000 9.46 0.00 39.77 4.63
3668 6162 6.288941 TGATTTACATGAACCGGAGAGTAA 57.711 37.500 9.46 7.03 0.00 2.24
3689 6183 8.428186 AGTAATTCGTCTGTTGAACTAAAACA 57.572 30.769 0.00 0.00 36.19 2.83
3696 6190 9.493206 TCGTCTGTTGAACTAAAACATAAAAAC 57.507 29.630 0.00 0.00 36.95 2.43
3713 6207 3.538634 AAACCCTAAGGCAGACGTATC 57.461 47.619 0.00 0.00 36.11 2.24
3724 6218 3.130633 GCAGACGTATCCATGCAACATA 58.869 45.455 0.00 0.00 38.54 2.29
3725 6219 3.059597 GCAGACGTATCCATGCAACATAC 60.060 47.826 0.00 0.00 38.54 2.39
3737 6231 8.700722 TCCATGCAACATACATAAAATTTGAC 57.299 30.769 0.00 0.00 0.00 3.18
3782 6276 8.344098 ACGATATTTTGTCCGTTCAACTAAAAA 58.656 29.630 0.00 0.00 30.41 1.94
3787 6281 9.804758 ATTTTGTCCGTTCAACTAAAAATTACA 57.195 25.926 0.00 0.00 0.00 2.41
3828 6323 2.106332 GGGCGGTGACCTCGTATG 59.894 66.667 0.00 0.00 0.00 2.39
3873 6369 1.884464 CCATGCCATCGTCGGAGTG 60.884 63.158 0.00 0.00 0.00 3.51
3879 6375 0.811915 CCATCGTCGGAGTGAGAGTT 59.188 55.000 0.00 0.00 0.00 3.01
3881 6377 0.811915 ATCGTCGGAGTGAGAGTTGG 59.188 55.000 0.00 0.00 0.00 3.77
3883 6379 1.666011 GTCGGAGTGAGAGTTGGCA 59.334 57.895 0.00 0.00 0.00 4.92
3898 6394 4.319133 GCATCGAGGCCTTTCCAA 57.681 55.556 11.78 0.00 37.29 3.53
3903 6399 2.764314 CGAGGCCTTTCCAATGGCG 61.764 63.158 6.77 0.00 46.88 5.69
3908 6404 0.965363 GCCTTTCCAATGGCGGAAGA 60.965 55.000 10.14 0.00 45.65 2.87
3986 6482 4.394712 CTTCCTCCCGCGCCTTGT 62.395 66.667 0.00 0.00 0.00 3.16
3997 6493 2.113986 GCCTTGTGCAGGTCCACT 59.886 61.111 0.00 0.00 46.07 4.00
4036 6532 3.330720 CGGGGAGCCCTGTCCTTT 61.331 66.667 6.20 0.00 42.67 3.11
4043 6539 1.068352 AGCCCTGTCCTTTCCCTTGT 61.068 55.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.418995 AGTTTGCTCATCTGCAGATTGT 58.581 40.909 26.70 4.20 44.27 2.71
5 6 3.690139 AGAGTTTGCTCATCTGCAGATTG 59.310 43.478 26.70 21.35 44.27 2.67
7 8 3.630892 AGAGTTTGCTCATCTGCAGAT 57.369 42.857 23.75 23.75 44.27 2.90
8 9 3.413846 AAGAGTTTGCTCATCTGCAGA 57.586 42.857 20.79 20.79 44.27 4.26
9 10 4.023450 TCAAAAGAGTTTGCTCATCTGCAG 60.023 41.667 7.63 7.63 43.30 4.41
10 11 3.884693 TCAAAAGAGTTTGCTCATCTGCA 59.115 39.130 0.00 0.00 43.30 4.41
11 12 4.214971 TCTCAAAAGAGTTTGCTCATCTGC 59.785 41.667 0.00 0.00 43.30 4.26
12 13 5.237996 TGTCTCAAAAGAGTTTGCTCATCTG 59.762 40.000 0.00 0.00 43.30 2.90
13 14 5.238214 GTGTCTCAAAAGAGTTTGCTCATCT 59.762 40.000 0.00 0.00 43.30 2.90
14 15 5.447573 GTGTCTCAAAAGAGTTTGCTCATC 58.552 41.667 0.00 0.00 43.30 2.92
15 16 4.276926 GGTGTCTCAAAAGAGTTTGCTCAT 59.723 41.667 0.00 0.00 43.30 2.90
16 17 3.627577 GGTGTCTCAAAAGAGTTTGCTCA 59.372 43.478 0.00 0.00 43.30 4.26
17 18 3.879892 AGGTGTCTCAAAAGAGTTTGCTC 59.120 43.478 0.00 0.00 43.30 4.26
18 19 3.891049 AGGTGTCTCAAAAGAGTTTGCT 58.109 40.909 0.00 0.00 43.30 3.91
19 20 4.096382 TGAAGGTGTCTCAAAAGAGTTTGC 59.904 41.667 0.00 0.00 43.30 3.68
20 21 5.818136 TGAAGGTGTCTCAAAAGAGTTTG 57.182 39.130 0.00 0.00 44.71 2.93
21 22 6.180472 TCTTGAAGGTGTCTCAAAAGAGTTT 58.820 36.000 0.00 0.00 30.24 2.66
22 23 5.745227 TCTTGAAGGTGTCTCAAAAGAGTT 58.255 37.500 0.00 0.00 30.24 3.01
23 24 5.359194 TCTTGAAGGTGTCTCAAAAGAGT 57.641 39.130 0.00 0.00 30.24 3.24
24 25 5.238214 CCTTCTTGAAGGTGTCTCAAAAGAG 59.762 44.000 18.52 0.00 35.22 2.85
25 26 5.104527 TCCTTCTTGAAGGTGTCTCAAAAGA 60.105 40.000 23.78 2.94 40.81 2.52
26 27 5.126067 TCCTTCTTGAAGGTGTCTCAAAAG 58.874 41.667 23.78 0.00 40.81 2.27
27 28 5.110814 TCCTTCTTGAAGGTGTCTCAAAA 57.889 39.130 23.78 4.00 40.81 2.44
28 29 4.771114 TCCTTCTTGAAGGTGTCTCAAA 57.229 40.909 23.78 4.62 40.81 2.69
29 30 4.771114 TTCCTTCTTGAAGGTGTCTCAA 57.229 40.909 23.78 10.79 40.81 3.02
30 31 4.771114 TTTCCTTCTTGAAGGTGTCTCA 57.229 40.909 23.78 5.87 40.81 3.27
31 32 4.881850 TGTTTTCCTTCTTGAAGGTGTCTC 59.118 41.667 23.78 14.28 40.81 3.36
32 33 4.855340 TGTTTTCCTTCTTGAAGGTGTCT 58.145 39.130 23.78 0.00 40.81 3.41
33 34 5.576447 TTGTTTTCCTTCTTGAAGGTGTC 57.424 39.130 23.78 15.05 40.81 3.67
34 35 5.422012 ACATTGTTTTCCTTCTTGAAGGTGT 59.578 36.000 23.78 17.18 40.81 4.16
35 36 5.906073 ACATTGTTTTCCTTCTTGAAGGTG 58.094 37.500 23.78 16.67 40.81 4.00
36 37 5.069119 GGACATTGTTTTCCTTCTTGAAGGT 59.931 40.000 23.78 6.27 40.81 3.50
37 38 5.068987 TGGACATTGTTTTCCTTCTTGAAGG 59.931 40.000 20.21 20.21 41.35 3.46
38 39 6.147864 TGGACATTGTTTTCCTTCTTGAAG 57.852 37.500 3.55 3.55 32.55 3.02
39 40 6.406849 CCTTGGACATTGTTTTCCTTCTTGAA 60.407 38.462 0.00 0.00 32.55 2.69
40 41 5.068987 CCTTGGACATTGTTTTCCTTCTTGA 59.931 40.000 0.00 0.00 32.55 3.02
41 42 5.068987 TCCTTGGACATTGTTTTCCTTCTTG 59.931 40.000 0.00 0.00 32.55 3.02
42 43 5.069119 GTCCTTGGACATTGTTTTCCTTCTT 59.931 40.000 14.34 0.00 32.55 2.52
43 44 4.584743 GTCCTTGGACATTGTTTTCCTTCT 59.415 41.667 14.34 0.00 32.55 2.85
44 45 4.556699 CGTCCTTGGACATTGTTTTCCTTC 60.557 45.833 18.51 0.00 32.55 3.46
45 46 3.317993 CGTCCTTGGACATTGTTTTCCTT 59.682 43.478 18.51 0.00 32.55 3.36
46 47 2.884639 CGTCCTTGGACATTGTTTTCCT 59.115 45.455 18.51 0.00 32.55 3.36
47 48 2.621526 ACGTCCTTGGACATTGTTTTCC 59.378 45.455 18.51 0.00 0.00 3.13
48 49 3.606153 CGACGTCCTTGGACATTGTTTTC 60.606 47.826 18.51 3.61 0.00 2.29
49 50 2.289547 CGACGTCCTTGGACATTGTTTT 59.710 45.455 18.51 0.00 0.00 2.43
50 51 1.871039 CGACGTCCTTGGACATTGTTT 59.129 47.619 18.51 0.00 0.00 2.83
51 52 1.202604 ACGACGTCCTTGGACATTGTT 60.203 47.619 18.51 0.00 0.00 2.83
52 53 0.391597 ACGACGTCCTTGGACATTGT 59.608 50.000 18.51 11.20 0.00 2.71
53 54 1.068474 GACGACGTCCTTGGACATTG 58.932 55.000 17.25 10.58 0.00 2.82
54 55 0.388134 CGACGACGTCCTTGGACATT 60.388 55.000 21.63 5.72 34.56 2.71
55 56 1.211969 CGACGACGTCCTTGGACAT 59.788 57.895 21.63 4.25 34.56 3.06
56 57 2.640989 CGACGACGTCCTTGGACA 59.359 61.111 21.63 0.00 34.56 4.02
57 58 2.804090 GCGACGACGTCCTTGGAC 60.804 66.667 21.63 9.62 41.98 4.02
58 59 4.047059 GGCGACGACGTCCTTGGA 62.047 66.667 21.63 0.00 41.98 3.53
67 68 4.176851 GAGACGGAGGGCGACGAC 62.177 72.222 0.00 0.00 0.00 4.34
81 82 1.001269 ACGGAGATGGTGTCGGAGA 60.001 57.895 0.00 0.00 0.00 3.71
82 83 1.433879 GACGGAGATGGTGTCGGAG 59.566 63.158 0.00 0.00 0.00 4.63
83 84 3.599584 GACGGAGATGGTGTCGGA 58.400 61.111 0.00 0.00 0.00 4.55
86 87 2.579787 CGCGACGGAGATGGTGTC 60.580 66.667 0.00 0.00 0.00 3.67
87 88 4.796231 GCGCGACGGAGATGGTGT 62.796 66.667 12.10 0.00 0.00 4.16
136 137 4.363990 CCCCGATCGAGGATGGCG 62.364 72.222 18.66 0.00 0.00 5.69
137 138 4.688966 GCCCCGATCGAGGATGGC 62.689 72.222 21.11 16.63 32.80 4.40
138 139 2.441822 GAAGCCCCGATCGAGGATGG 62.442 65.000 21.11 10.13 0.00 3.51
139 140 1.005630 GAAGCCCCGATCGAGGATG 60.006 63.158 21.11 7.12 0.00 3.51
140 141 1.152440 AGAAGCCCCGATCGAGGAT 60.152 57.895 21.11 11.00 0.00 3.24
141 142 2.127869 CAGAAGCCCCGATCGAGGA 61.128 63.158 21.11 0.00 0.00 3.71
193 194 4.371417 AGGGACGGGTCGTAGCCA 62.371 66.667 0.00 0.00 41.37 4.75
215 216 1.153823 CCTTGTAGGAGACGCCGTG 60.154 63.158 0.00 0.00 43.43 4.94
216 217 1.593296 GACCTTGTAGGAGACGCCGT 61.593 60.000 0.00 0.00 43.43 5.68
220 221 0.733729 CCTCGACCTTGTAGGAGACG 59.266 60.000 0.00 3.17 37.67 4.18
223 224 1.835494 TGTCCTCGACCTTGTAGGAG 58.165 55.000 0.00 0.00 40.06 3.69
304 1031 2.748268 GAGGCTCTCGTTGAAGCAG 58.252 57.895 7.40 0.00 0.00 4.24
305 1032 4.996976 GAGGCTCTCGTTGAAGCA 57.003 55.556 7.40 0.00 0.00 3.91
474 2788 1.067250 GCATCTCTGCTCCTCGTCC 59.933 63.158 0.00 0.00 45.32 4.79
487 2801 1.632409 TCTTTTCCTCCTGCTGCATCT 59.368 47.619 1.31 0.00 0.00 2.90
488 2802 2.119801 TCTTTTCCTCCTGCTGCATC 57.880 50.000 1.31 0.00 0.00 3.91
489 2803 2.652590 GATCTTTTCCTCCTGCTGCAT 58.347 47.619 1.31 0.00 0.00 3.96
490 2804 1.340405 GGATCTTTTCCTCCTGCTGCA 60.340 52.381 0.88 0.88 41.78 4.41
491 2805 1.387539 GGATCTTTTCCTCCTGCTGC 58.612 55.000 0.00 0.00 41.78 5.25
492 2806 1.563410 AGGGATCTTTTCCTCCTGCTG 59.437 52.381 0.00 0.00 44.75 4.41
493 2807 1.978361 AGGGATCTTTTCCTCCTGCT 58.022 50.000 0.00 0.00 44.75 4.24
505 2819 6.095440 GTGTATGTGCATGTAAAAAGGGATCT 59.905 38.462 0.00 0.00 0.00 2.75
506 2820 6.265577 GTGTATGTGCATGTAAAAAGGGATC 58.734 40.000 0.00 0.00 0.00 3.36
507 2821 5.163663 CGTGTATGTGCATGTAAAAAGGGAT 60.164 40.000 0.00 0.00 0.00 3.85
510 2824 4.411327 CCGTGTATGTGCATGTAAAAAGG 58.589 43.478 0.00 0.00 0.00 3.11
511 2825 4.083003 ACCCGTGTATGTGCATGTAAAAAG 60.083 41.667 0.00 0.00 0.00 2.27
512 2826 3.821600 ACCCGTGTATGTGCATGTAAAAA 59.178 39.130 0.00 0.00 0.00 1.94
513 2827 3.189495 CACCCGTGTATGTGCATGTAAAA 59.811 43.478 0.00 0.00 0.00 1.52
514 2828 2.744741 CACCCGTGTATGTGCATGTAAA 59.255 45.455 0.00 0.00 0.00 2.01
515 2829 2.351455 CACCCGTGTATGTGCATGTAA 58.649 47.619 0.00 0.00 0.00 2.41
516 2830 1.406205 CCACCCGTGTATGTGCATGTA 60.406 52.381 0.00 0.00 0.00 2.29
517 2831 0.676466 CCACCCGTGTATGTGCATGT 60.676 55.000 0.00 0.00 0.00 3.21
518 2832 1.375853 CCCACCCGTGTATGTGCATG 61.376 60.000 0.00 0.00 0.00 4.06
519 2833 1.077787 CCCACCCGTGTATGTGCAT 60.078 57.895 0.00 0.00 0.00 3.96
520 2834 2.349376 CCCACCCGTGTATGTGCA 59.651 61.111 0.00 0.00 0.00 4.57
521 2835 3.131478 GCCCACCCGTGTATGTGC 61.131 66.667 0.00 0.00 0.00 4.57
522 2836 1.618876 TAGGCCCACCCGTGTATGTG 61.619 60.000 0.00 0.00 39.21 3.21
523 2837 1.306312 TAGGCCCACCCGTGTATGT 60.306 57.895 0.00 0.00 39.21 2.29
524 2838 1.445942 CTAGGCCCACCCGTGTATG 59.554 63.158 0.00 0.00 39.21 2.39
525 2839 2.440817 GCTAGGCCCACCCGTGTAT 61.441 63.158 0.00 0.00 39.21 2.29
526 2840 3.078836 GCTAGGCCCACCCGTGTA 61.079 66.667 0.00 0.00 39.21 2.90
528 2842 4.473520 CTGCTAGGCCCACCCGTG 62.474 72.222 0.00 0.00 39.21 4.94
531 2845 2.150014 TTTTCCTGCTAGGCCCACCC 62.150 60.000 0.00 0.00 34.61 4.61
532 2846 0.681243 CTTTTCCTGCTAGGCCCACC 60.681 60.000 0.00 0.00 34.61 4.61
533 2847 0.328258 TCTTTTCCTGCTAGGCCCAC 59.672 55.000 0.00 0.00 34.61 4.61
534 2848 1.004745 CTTCTTTTCCTGCTAGGCCCA 59.995 52.381 0.00 0.00 34.61 5.36
535 2849 1.683319 CCTTCTTTTCCTGCTAGGCCC 60.683 57.143 0.00 0.00 34.61 5.80
536 2850 1.282157 TCCTTCTTTTCCTGCTAGGCC 59.718 52.381 0.00 0.00 34.61 5.19
537 2851 2.237392 TCTCCTTCTTTTCCTGCTAGGC 59.763 50.000 0.00 0.00 34.61 3.93
538 2852 3.772025 TCTCTCCTTCTTTTCCTGCTAGG 59.228 47.826 0.00 0.00 36.46 3.02
539 2853 4.709397 TCTCTCTCCTTCTTTTCCTGCTAG 59.291 45.833 0.00 0.00 0.00 3.42
540 2854 4.678256 TCTCTCTCCTTCTTTTCCTGCTA 58.322 43.478 0.00 0.00 0.00 3.49
541 2855 3.515104 CTCTCTCTCCTTCTTTTCCTGCT 59.485 47.826 0.00 0.00 0.00 4.24
542 2856 3.513515 TCTCTCTCTCCTTCTTTTCCTGC 59.486 47.826 0.00 0.00 0.00 4.85
543 2857 4.160252 CCTCTCTCTCTCCTTCTTTTCCTG 59.840 50.000 0.00 0.00 0.00 3.86
544 2858 4.352893 CCTCTCTCTCTCCTTCTTTTCCT 58.647 47.826 0.00 0.00 0.00 3.36
545 2859 3.450817 CCCTCTCTCTCTCCTTCTTTTCC 59.549 52.174 0.00 0.00 0.00 3.13
546 2860 3.450817 CCCCTCTCTCTCTCCTTCTTTTC 59.549 52.174 0.00 0.00 0.00 2.29
547 2861 3.449918 CCCCTCTCTCTCTCCTTCTTTT 58.550 50.000 0.00 0.00 0.00 2.27
548 2862 2.892301 GCCCCTCTCTCTCTCCTTCTTT 60.892 54.545 0.00 0.00 0.00 2.52
549 2863 1.342975 GCCCCTCTCTCTCTCCTTCTT 60.343 57.143 0.00 0.00 0.00 2.52
550 2864 0.261696 GCCCCTCTCTCTCTCCTTCT 59.738 60.000 0.00 0.00 0.00 2.85
551 2865 0.261696 AGCCCCTCTCTCTCTCCTTC 59.738 60.000 0.00 0.00 0.00 3.46
552 2866 0.032217 CAGCCCCTCTCTCTCTCCTT 60.032 60.000 0.00 0.00 0.00 3.36
553 2867 0.923729 TCAGCCCCTCTCTCTCTCCT 60.924 60.000 0.00 0.00 0.00 3.69
554 2868 0.755327 GTCAGCCCCTCTCTCTCTCC 60.755 65.000 0.00 0.00 0.00 3.71
555 2869 0.258774 AGTCAGCCCCTCTCTCTCTC 59.741 60.000 0.00 0.00 0.00 3.20
556 2870 0.033208 CAGTCAGCCCCTCTCTCTCT 60.033 60.000 0.00 0.00 0.00 3.10
557 2871 1.042559 CCAGTCAGCCCCTCTCTCTC 61.043 65.000 0.00 0.00 0.00 3.20
558 2872 1.001503 CCAGTCAGCCCCTCTCTCT 59.998 63.158 0.00 0.00 0.00 3.10
559 2873 1.305718 ACCAGTCAGCCCCTCTCTC 60.306 63.158 0.00 0.00 0.00 3.20
560 2874 1.611851 CACCAGTCAGCCCCTCTCT 60.612 63.158 0.00 0.00 0.00 3.10
561 2875 2.664081 CCACCAGTCAGCCCCTCTC 61.664 68.421 0.00 0.00 0.00 3.20
562 2876 2.608988 CCACCAGTCAGCCCCTCT 60.609 66.667 0.00 0.00 0.00 3.69
563 2877 3.721706 CCCACCAGTCAGCCCCTC 61.722 72.222 0.00 0.00 0.00 4.30
566 2880 2.656698 AAAACCCCACCAGTCAGCCC 62.657 60.000 0.00 0.00 0.00 5.19
567 2881 1.152546 AAAACCCCACCAGTCAGCC 60.153 57.895 0.00 0.00 0.00 4.85
568 2882 2.041153 CAAAACCCCACCAGTCAGC 58.959 57.895 0.00 0.00 0.00 4.26
569 2883 1.463553 GGCAAAACCCCACCAGTCAG 61.464 60.000 0.00 0.00 0.00 3.51
570 2884 1.456705 GGCAAAACCCCACCAGTCA 60.457 57.895 0.00 0.00 0.00 3.41
571 2885 0.831711 ATGGCAAAACCCCACCAGTC 60.832 55.000 0.00 0.00 37.83 3.51
613 2927 2.043652 CCATCAGGGGGCACTTGG 60.044 66.667 0.00 0.00 0.00 3.61
625 2939 2.361104 GCGAAACCCAGCCCATCA 60.361 61.111 0.00 0.00 0.00 3.07
644 2958 0.106894 AAATAGCCCTAGCGACCTGC 59.893 55.000 0.00 0.00 46.67 4.85
645 2959 2.622064 AAAATAGCCCTAGCGACCTG 57.378 50.000 0.00 0.00 46.67 4.00
650 2964 5.278022 GGATTTGAGAAAAATAGCCCTAGCG 60.278 44.000 0.00 0.00 46.67 4.26
653 2967 5.820947 GTCGGATTTGAGAAAAATAGCCCTA 59.179 40.000 0.00 0.00 0.00 3.53
654 2968 4.640647 GTCGGATTTGAGAAAAATAGCCCT 59.359 41.667 0.00 0.00 0.00 5.19
666 2980 2.679355 TGTTTTGCGTCGGATTTGAG 57.321 45.000 0.00 0.00 0.00 3.02
676 2992 0.099791 CCCAAGACGTTGTTTTGCGT 59.900 50.000 0.00 0.00 44.50 5.24
679 2995 0.249280 GCCCCCAAGACGTTGTTTTG 60.249 55.000 0.00 0.00 30.95 2.44
714 3030 3.731089 CTGCTGCTTTCATTGGGAAAAA 58.269 40.909 0.00 0.00 44.52 1.94
715 3031 2.548493 GCTGCTGCTTTCATTGGGAAAA 60.548 45.455 8.53 0.00 44.52 2.29
716 3032 1.001181 GCTGCTGCTTTCATTGGGAAA 59.999 47.619 8.53 0.00 43.07 3.13
717 3033 0.604578 GCTGCTGCTTTCATTGGGAA 59.395 50.000 8.53 0.00 36.03 3.97
718 3034 0.540133 TGCTGCTGCTTTCATTGGGA 60.540 50.000 17.00 0.00 40.48 4.37
719 3035 0.108804 CTGCTGCTGCTTTCATTGGG 60.109 55.000 17.00 0.00 40.48 4.12
720 3036 0.736325 GCTGCTGCTGCTTTCATTGG 60.736 55.000 22.10 0.00 40.48 3.16
721 3037 0.038618 TGCTGCTGCTGCTTTCATTG 60.039 50.000 27.67 0.29 40.48 2.82
722 3038 0.243907 CTGCTGCTGCTGCTTTCATT 59.756 50.000 27.67 0.00 40.48 2.57
723 3039 1.883732 CTGCTGCTGCTGCTTTCAT 59.116 52.632 27.67 0.00 40.48 2.57
724 3040 3.351450 CTGCTGCTGCTGCTTTCA 58.649 55.556 27.67 10.41 40.48 2.69
762 3081 2.159085 ACTCGGATTGATTCCTTCGGAC 60.159 50.000 0.00 0.00 42.99 4.79
825 3160 2.615493 GGAAGGACTGCTTTGATTCCGA 60.615 50.000 0.00 0.00 32.97 4.55
886 3222 1.269778 CGATGGCAGCTCGGAGATTTA 60.270 52.381 9.69 0.00 33.89 1.40
889 3226 2.733301 CGATGGCAGCTCGGAGAT 59.267 61.111 9.69 0.00 33.89 2.75
902 3239 2.047274 ACGTTCCTGCCACCGATG 60.047 61.111 0.00 0.00 0.00 3.84
903 3240 2.047274 CACGTTCCTGCCACCGAT 60.047 61.111 0.00 0.00 0.00 4.18
904 3241 4.308458 CCACGTTCCTGCCACCGA 62.308 66.667 0.00 0.00 0.00 4.69
923 3267 1.160137 GCCAGGCCAGATTTATAGCG 58.840 55.000 5.01 0.00 0.00 4.26
1028 3384 3.071602 CACCATATCGAGGGAGGATTTGT 59.928 47.826 7.48 0.00 0.00 2.83
1088 3449 2.903784 TGCCCTGACTTTGTAAGAGCTA 59.096 45.455 0.00 0.00 0.00 3.32
1106 3467 3.059597 CGACCACGAATTCTGATTATGCC 60.060 47.826 3.52 0.00 42.66 4.40
1142 3534 4.119136 GCAATTTTGATATTTCCCCACCG 58.881 43.478 0.00 0.00 0.00 4.94
1438 3861 3.559238 ATGTTGAGCAAAACGTCATCC 57.441 42.857 0.00 0.00 32.47 3.51
1491 3914 1.630878 GTCTGGAGAGGATGGTGGTTT 59.369 52.381 0.00 0.00 0.00 3.27
1634 4060 1.741706 CAGTATGCTCCTGGTTGCTTG 59.258 52.381 13.47 5.69 0.00 4.01
2473 4906 7.466805 TCGCATTCTTCAGAAATGTTAATCAG 58.533 34.615 0.00 0.00 37.61 2.90
2598 5037 6.129352 GCAAGTTTGAACTTCGAAATGACATC 60.129 38.462 6.16 0.00 45.65 3.06
3039 5491 3.011818 TGCAGCTCATGACCAGTAATTG 58.988 45.455 0.00 0.00 0.00 2.32
3042 5494 2.703416 CTTGCAGCTCATGACCAGTAA 58.297 47.619 0.00 0.00 0.00 2.24
3079 5535 1.747325 GCAGCTTGCAACCCCTCAAA 61.747 55.000 0.00 0.00 44.26 2.69
3124 5588 4.790790 AGGTTGACCAGGGAGAATTAATCT 59.209 41.667 2.56 0.00 38.93 2.40
3136 5600 9.423061 CAGAAATAATTTAAAAGGTTGACCAGG 57.577 33.333 2.56 0.00 38.89 4.45
3166 5631 0.249073 CTCGGCCCAGTACAATCTCG 60.249 60.000 0.00 0.00 0.00 4.04
3179 5644 0.470268 ACTCCTTATCCTCCTCGGCC 60.470 60.000 0.00 0.00 0.00 6.13
3181 5646 3.822167 GAGTTACTCCTTATCCTCCTCGG 59.178 52.174 0.00 0.00 0.00 4.63
3242 5707 1.745232 TGCCACGAATAACACATCCC 58.255 50.000 0.00 0.00 0.00 3.85
3270 5735 6.155393 AGGGATTTCACAACAAAAACAAGGTA 59.845 34.615 0.00 0.00 0.00 3.08
3306 5771 1.202698 GCACCTCCATGTCTATGTCCC 60.203 57.143 0.00 0.00 32.21 4.46
3361 5852 3.127030 GTCAGCCCTGTACAAATAAGCAC 59.873 47.826 0.00 0.00 0.00 4.40
3362 5853 3.343617 GTCAGCCCTGTACAAATAAGCA 58.656 45.455 0.00 0.00 0.00 3.91
3363 5854 2.351726 CGTCAGCCCTGTACAAATAAGC 59.648 50.000 0.00 0.00 0.00 3.09
3364 5855 2.351726 GCGTCAGCCCTGTACAAATAAG 59.648 50.000 0.00 0.00 37.42 1.73
3365 5856 2.027561 AGCGTCAGCCCTGTACAAATAA 60.028 45.455 0.00 0.00 46.67 1.40
3366 5857 1.553248 AGCGTCAGCCCTGTACAAATA 59.447 47.619 0.00 0.00 46.67 1.40
3367 5858 0.324943 AGCGTCAGCCCTGTACAAAT 59.675 50.000 0.00 0.00 46.67 2.32
3368 5859 0.107831 AAGCGTCAGCCCTGTACAAA 59.892 50.000 0.00 0.00 46.67 2.83
3369 5860 0.970640 TAAGCGTCAGCCCTGTACAA 59.029 50.000 0.00 0.00 46.67 2.41
3370 5861 0.970640 TTAAGCGTCAGCCCTGTACA 59.029 50.000 0.00 0.00 46.67 2.90
3371 5862 2.311124 ATTAAGCGTCAGCCCTGTAC 57.689 50.000 0.00 0.00 46.67 2.90
3380 5871 3.371965 AGAGGTCCCTAATTAAGCGTCA 58.628 45.455 0.00 0.00 0.00 4.35
3437 5928 8.742554 AAACTGGTGCTTAGAAAAATAAATCG 57.257 30.769 0.00 0.00 0.00 3.34
3449 5940 3.073274 AGGGCTTAAACTGGTGCTTAG 57.927 47.619 0.00 0.00 0.00 2.18
3458 5949 4.662278 TGAACAATGCTAGGGCTTAAACT 58.338 39.130 0.00 0.00 39.59 2.66
3461 5952 4.016444 CCTTGAACAATGCTAGGGCTTAA 58.984 43.478 0.00 0.00 39.59 1.85
3478 5970 0.251165 GGGCAAGTGTTAGGCCTTGA 60.251 55.000 12.58 0.00 46.87 3.02
3510 6002 6.971602 TGAGGTAATTTTTGTTTGTATCGCA 58.028 32.000 0.00 0.00 0.00 5.10
3532 6024 2.037902 TGTATTGCAGACGGAGGTTTGA 59.962 45.455 0.00 0.00 30.09 2.69
3604 6098 6.811954 TGTCTACATGATATTTGTTCGGCTA 58.188 36.000 0.00 0.00 0.00 3.93
3639 6133 7.279615 TCTCCGGTTCATGTAAATCATATTGT 58.720 34.615 0.00 0.00 34.67 2.71
3648 6142 5.808540 CGAATTACTCTCCGGTTCATGTAAA 59.191 40.000 0.00 0.00 0.00 2.01
3655 6149 3.119566 ACAGACGAATTACTCTCCGGTTC 60.120 47.826 0.00 0.00 0.00 3.62
3659 6153 4.092771 TCAACAGACGAATTACTCTCCG 57.907 45.455 0.00 0.00 0.00 4.63
3663 6157 8.545420 TGTTTTAGTTCAACAGACGAATTACTC 58.455 33.333 0.00 0.00 30.49 2.59
3689 6183 4.296621 ACGTCTGCCTTAGGGTTTTTAT 57.703 40.909 0.00 0.00 34.45 1.40
3696 6190 1.410004 TGGATACGTCTGCCTTAGGG 58.590 55.000 0.00 0.00 42.51 3.53
3702 6196 0.657840 GTTGCATGGATACGTCTGCC 59.342 55.000 0.00 0.00 38.05 4.85
3713 6207 8.476657 TGTCAAATTTTATGTATGTTGCATGG 57.523 30.769 0.00 0.00 0.00 3.66
3765 6259 9.635520 TTTTTGTAATTTTTAGTTGAACGGACA 57.364 25.926 0.00 0.00 0.00 4.02
3857 6353 1.037579 TCTCACTCCGACGATGGCAT 61.038 55.000 0.00 0.00 0.00 4.40
3873 6369 4.116878 GCCTCGATGCCAACTCTC 57.883 61.111 0.58 0.00 0.00 3.20
3881 6377 0.383231 CATTGGAAAGGCCTCGATGC 59.617 55.000 5.23 3.83 37.63 3.91
3883 6379 0.753111 GCCATTGGAAAGGCCTCGAT 60.753 55.000 5.23 0.00 45.18 3.59
3970 6466 4.697756 CACAAGGCGCGGGAGGAA 62.698 66.667 8.83 0.00 0.00 3.36
3986 6482 4.329545 GGCCGAAGTGGACCTGCA 62.330 66.667 0.00 0.00 41.58 4.41
4031 6527 0.611714 GCTACCGACAAGGGAAAGGA 59.388 55.000 0.00 0.00 46.96 3.36
4036 6532 2.050350 CCTCGCTACCGACAAGGGA 61.050 63.158 0.00 0.00 46.96 4.20


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

AutoCloner maintained by Alex Coulton.