Multiple sequence alignment - TraesCS5B01G524100

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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 TraesCS5B01G524100 chr5B 100.000 4836 0 0 1 4836 684742710 684747545 0.000000e+00 8931.0
1 TraesCS5B01G524100 chr5B 97.939 1213 25 0 2750 3962 684772708 684771496 0.000000e+00 2102.0
2 TraesCS5B01G524100 chr5B 89.394 528 37 12 4265 4779 684771490 684770969 0.000000e+00 647.0
3 TraesCS5B01G524100 chr5B 79.467 750 146 5 3060 3808 684605225 684605967 4.290000e-145 525.0
4 TraesCS5B01G524100 chr5B 80.506 672 113 14 2249 2906 684879974 684880641 2.600000e-137 499.0
5 TraesCS5B01G524100 chr5B 80.597 670 106 14 2248 2903 684089277 684089936 3.360000e-136 496.0
6 TraesCS5B01G524100 chr5B 78.059 752 148 16 3065 3809 684090036 684090777 4.410000e-125 459.0
7 TraesCS5B01G524100 chr5B 79.300 657 112 16 2248 2903 684611052 684611685 5.750000e-119 438.0
8 TraesCS5B01G524100 chr5B 78.648 651 115 15 2248 2889 684578479 684579114 1.250000e-110 411.0
9 TraesCS5B01G524100 chr5B 81.855 496 79 10 2417 2906 557254071 557253581 1.620000e-109 407.0
10 TraesCS5B01G524100 chr5B 94.853 136 6 1 100 235 105773035 105773169 1.360000e-50 211.0
11 TraesCS5B01G524100 chr5B 93.694 111 2 1 4619 4724 556963222 556963332 1.390000e-35 161.0
12 TraesCS5B01G524100 chr5B 91.667 48 1 2 1392 1439 446357723 446357767 4.040000e-06 63.9
13 TraesCS5B01G524100 chr5B 100.000 32 0 0 3778 3809 684606117 684606148 5.230000e-05 60.2
14 TraesCS5B01G524100 chr5D 94.854 1438 53 7 1534 2953 543270702 543272136 0.000000e+00 2226.0
15 TraesCS5B01G524100 chr5D 96.555 1016 17 4 2985 3992 543272132 543273137 0.000000e+00 1666.0
16 TraesCS5B01G524100 chr5D 90.642 1293 42 26 387 1672 543269572 543270792 0.000000e+00 1644.0
17 TraesCS5B01G524100 chr5D 93.440 747 36 8 4033 4769 543273213 543273956 0.000000e+00 1096.0
18 TraesCS5B01G524100 chr5D 80.239 754 127 11 3057 3809 543236774 543237506 9.150000e-152 547.0
19 TraesCS5B01G524100 chr5D 79.467 750 146 5 3060 3808 543100899 543101641 4.290000e-145 525.0
20 TraesCS5B01G524100 chr5D 79.790 668 115 11 2248 2906 543235972 543236628 7.330000e-128 468.0
21 TraesCS5B01G524100 chr5D 79.429 666 116 17 2248 2903 543213877 543214531 7.380000e-123 451.0
22 TraesCS5B01G524100 chr5D 77.748 755 145 19 3065 3809 542110263 542111004 4.440000e-120 442.0
23 TraesCS5B01G524100 chr5D 81.673 502 92 0 2405 2906 543093080 543093581 7.490000e-113 418.0
24 TraesCS5B01G524100 chr5D 78.295 645 128 9 2248 2889 543068424 543069059 5.830000e-109 405.0
25 TraesCS5B01G524100 chr5D 87.692 130 14 1 234 363 543269381 543269508 3.020000e-32 150.0
26 TraesCS5B01G524100 chr4A 92.598 1432 68 20 1534 2943 625960958 625959543 0.000000e+00 2023.0
27 TraesCS5B01G524100 chr4A 94.970 994 42 4 3004 3992 625959541 625958551 0.000000e+00 1552.0
28 TraesCS5B01G524100 chr4A 91.413 757 28 8 923 1675 625961588 625960865 0.000000e+00 1003.0
29 TraesCS5B01G524100 chr4A 94.444 378 16 3 3982 4355 625958518 625958142 1.170000e-160 577.0
30 TraesCS5B01G524100 chr4A 79.674 797 150 8 3021 3809 626073961 626073169 9.090000e-157 564.0
31 TraesCS5B01G524100 chr4A 90.160 437 27 5 387 812 625966500 625966069 5.470000e-154 555.0
32 TraesCS5B01G524100 chr4A 88.303 436 32 12 4353 4779 625958061 625957636 5.590000e-139 505.0
33 TraesCS5B01G524100 chr4A 79.160 667 122 12 2248 2906 626049102 626048445 3.430000e-121 446.0
34 TraesCS5B01G524100 chr4A 82.822 489 84 0 2418 2906 626074497 626074009 5.750000e-119 438.0
35 TraesCS5B01G524100 chr4A 82.186 494 81 7 2417 2906 695981530 695981040 7.490000e-113 418.0
36 TraesCS5B01G524100 chr4A 91.837 49 4 0 57 105 625972755 625972707 8.690000e-08 69.4
37 TraesCS5B01G524100 chr4A 85.938 64 6 3 1379 1439 697941962 697942025 1.120000e-06 65.8
38 TraesCS5B01G524100 chr6A 82.759 435 35 14 400 809 416959736 416959317 7.700000e-93 351.0
39 TraesCS5B01G524100 chr6A 80.235 425 54 8 400 804 247134395 247134809 4.730000e-75 292.0
40 TraesCS5B01G524100 chr6A 76.038 313 35 19 987 1261 416959162 416958852 5.080000e-25 126.0
41 TraesCS5B01G524100 chr6A 90.323 62 2 2 2942 2999 509276955 509277016 1.440000e-10 78.7
42 TraesCS5B01G524100 chr6A 90.000 60 4 2 2942 2999 104308553 104308494 5.190000e-10 76.8
43 TraesCS5B01G524100 chr1D 78.503 521 101 11 3071 3587 492641184 492640671 1.000000e-86 331.0
44 TraesCS5B01G524100 chr1D 87.342 79 5 5 2925 2999 404066299 404066376 8.620000e-13 86.1
45 TraesCS5B01G524100 chr1D 89.394 66 2 1 2939 2999 15516956 15516891 1.440000e-10 78.7
46 TraesCS5B01G524100 chr1B 78.352 522 100 12 3071 3587 685289409 685288896 4.670000e-85 326.0
47 TraesCS5B01G524100 chr1B 92.754 138 10 0 109 246 277456425 277456288 2.950000e-47 200.0
48 TraesCS5B01G524100 chr1B 90.196 153 13 2 101 252 8823013 8823164 1.060000e-46 198.0
49 TraesCS5B01G524100 chr1A 78.008 532 106 11 3071 3598 591148535 591148011 1.680000e-84 324.0
50 TraesCS5B01G524100 chr1A 90.141 71 4 3 2931 2999 550888598 550888529 6.670000e-14 89.8
51 TraesCS5B01G524100 chr1A 87.500 72 4 4 2942 3008 399497076 399497147 1.440000e-10 78.7
52 TraesCS5B01G524100 chr3B 97.638 127 3 0 109 235 578615446 578615320 8.150000e-53 219.0
53 TraesCS5B01G524100 chr3B 93.431 137 7 2 100 235 747533689 747533824 8.210000e-48 202.0
54 TraesCS5B01G524100 chr7B 95.489 133 6 0 109 241 512769767 512769635 3.790000e-51 213.0
55 TraesCS5B01G524100 chr7B 93.617 141 7 2 96 235 494744412 494744551 4.900000e-50 209.0
56 TraesCS5B01G524100 chr5A 94.815 135 7 0 109 243 658989015 658989149 1.360000e-50 211.0
57 TraesCS5B01G524100 chr6B 94.815 135 5 2 107 241 692233936 692234068 4.900000e-50 209.0
58 TraesCS5B01G524100 chr6B 91.525 59 3 2 2942 2999 504603155 504603098 4.010000e-11 80.5
59 TraesCS5B01G524100 chr6B 93.617 47 1 2 1394 1439 665734353 665734398 8.690000e-08 69.4
60 TraesCS5B01G524100 chr6B 95.238 42 2 0 1398 1439 655780422 655780381 3.120000e-07 67.6
61 TraesCS5B01G524100 chr2A 76.358 313 35 18 987 1261 412387798 412388109 1.090000e-26 132.0
62 TraesCS5B01G524100 chr6D 89.231 65 3 2 2939 2999 406205682 406205746 1.440000e-10 78.7
63 TraesCS5B01G524100 chr4B 95.652 46 1 1 1395 1439 466966723 466966678 6.710000e-09 73.1
64 TraesCS5B01G524100 chr2D 97.561 41 1 0 1399 1439 566134769 566134729 2.410000e-08 71.3
65 TraesCS5B01G524100 chr3D 95.455 44 1 1 1397 1439 465530554 465530597 8.690000e-08 69.4
66 TraesCS5B01G524100 chr4D 93.333 45 3 0 1395 1439 164884040 164884084 3.120000e-07 67.6
67 TraesCS5B01G524100 chr3A 100.000 34 0 0 1406 1439 708819280 708819247 4.040000e-06 63.9


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 TraesCS5B01G524100 chr5B 684742710 684747545 4835 False 8931.0 8931 100.0000 1 4836 1 chr5B.!!$F6 4835
1 TraesCS5B01G524100 chr5B 684770969 684772708 1739 True 1374.5 2102 93.6665 2750 4779 2 chr5B.!!$R2 2029
2 TraesCS5B01G524100 chr5B 684879974 684880641 667 False 499.0 499 80.5060 2249 2906 1 chr5B.!!$F7 657
3 TraesCS5B01G524100 chr5B 684089277 684090777 1500 False 477.5 496 79.3280 2248 3809 2 chr5B.!!$F8 1561
4 TraesCS5B01G524100 chr5B 684611052 684611685 633 False 438.0 438 79.3000 2248 2903 1 chr5B.!!$F5 655
5 TraesCS5B01G524100 chr5B 684578479 684579114 635 False 411.0 411 78.6480 2248 2889 1 chr5B.!!$F4 641
6 TraesCS5B01G524100 chr5B 684605225 684606148 923 False 292.6 525 89.7335 3060 3809 2 chr5B.!!$F9 749
7 TraesCS5B01G524100 chr5D 543269381 543273956 4575 False 1356.4 2226 92.6366 234 4769 5 chr5D.!!$F7 4535
8 TraesCS5B01G524100 chr5D 543100899 543101641 742 False 525.0 525 79.4670 3060 3808 1 chr5D.!!$F4 748
9 TraesCS5B01G524100 chr5D 543235972 543237506 1534 False 507.5 547 80.0145 2248 3809 2 chr5D.!!$F6 1561
10 TraesCS5B01G524100 chr5D 543213877 543214531 654 False 451.0 451 79.4290 2248 2903 1 chr5D.!!$F5 655
11 TraesCS5B01G524100 chr5D 542110263 542111004 741 False 442.0 442 77.7480 3065 3809 1 chr5D.!!$F1 744
12 TraesCS5B01G524100 chr5D 543093080 543093581 501 False 418.0 418 81.6730 2405 2906 1 chr5D.!!$F3 501
13 TraesCS5B01G524100 chr5D 543068424 543069059 635 False 405.0 405 78.2950 2248 2889 1 chr5D.!!$F2 641
14 TraesCS5B01G524100 chr4A 625957636 625961588 3952 True 1132.0 2023 92.3456 923 4779 5 chr4A.!!$R5 3856
15 TraesCS5B01G524100 chr4A 626073169 626074497 1328 True 501.0 564 81.2480 2418 3809 2 chr4A.!!$R6 1391
16 TraesCS5B01G524100 chr4A 626048445 626049102 657 True 446.0 446 79.1600 2248 2906 1 chr4A.!!$R3 658
17 TraesCS5B01G524100 chr6A 416958852 416959736 884 True 238.5 351 79.3985 400 1261 2 chr6A.!!$R2 861
18 TraesCS5B01G524100 chr1D 492640671 492641184 513 True 331.0 331 78.5030 3071 3587 1 chr1D.!!$R2 516
19 TraesCS5B01G524100 chr1B 685288896 685289409 513 True 326.0 326 78.3520 3071 3587 1 chr1B.!!$R2 516
20 TraesCS5B01G524100 chr1A 591148011 591148535 524 True 324.0 324 78.0080 3071 3598 1 chr1A.!!$R2 527

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
862 933 0.032540 CCATGATCCATCGACGCAGA 59.967 55.000 0.00 0.00 0.00 4.26 F
1147 1271 0.036388 TTTCAGGACCATGTCGGCTC 60.036 55.000 0.00 0.00 39.03 4.70 F
1588 1734 0.040058 TCAACAGAATGGGCCTGCAT 59.960 50.000 4.53 0.00 43.62 3.96 F
1950 2162 1.079405 ACCGCTCCACATGGTTACG 60.079 57.895 0.00 0.91 36.34 3.18 F
3620 4011 1.096967 CAATGGCGGTGATGCTAGCA 61.097 55.000 21.85 21.85 34.52 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2013 2225 0.683179 TCGCAAGGCCAGTAGCTAGA 60.683 55.000 5.01 0.00 43.05 2.43 R
2078 2290 1.146485 CCCTGATCAGCAGCCTCAG 59.854 63.158 17.76 9.34 43.50 3.35 R
3462 3850 0.397957 TATAAGCTCCTCGGCCACCA 60.398 55.000 2.24 0.00 0.00 4.17 R
3645 4036 0.687354 AACCAGTTCTGACATCCGCT 59.313 50.000 1.00 0.00 0.00 5.52 R
4795 5336 0.036875 CCCACTCCCTGTTGACCTTC 59.963 60.000 0.00 0.00 0.00 3.46 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
28 29 5.449304 GTGTTCGACACCTAAAGAATTTGG 58.551 41.667 6.82 0.00 43.05 3.28
29 30 5.008316 GTGTTCGACACCTAAAGAATTTGGT 59.992 40.000 6.82 0.00 43.05 3.67
30 31 5.591067 TGTTCGACACCTAAAGAATTTGGTT 59.409 36.000 0.00 0.00 39.63 3.67
31 32 5.682943 TCGACACCTAAAGAATTTGGTTG 57.317 39.130 0.00 0.00 39.63 3.77
32 33 4.023536 TCGACACCTAAAGAATTTGGTTGC 60.024 41.667 0.00 0.00 39.63 4.17
33 34 4.261405 CGACACCTAAAGAATTTGGTTGCA 60.261 41.667 0.00 0.00 39.63 4.08
34 35 4.944048 ACACCTAAAGAATTTGGTTGCAC 58.056 39.130 0.00 0.00 39.63 4.57
35 36 4.649218 ACACCTAAAGAATTTGGTTGCACT 59.351 37.500 0.00 0.00 39.63 4.40
36 37 5.128663 ACACCTAAAGAATTTGGTTGCACTT 59.871 36.000 0.00 0.00 39.63 3.16
37 38 6.048509 CACCTAAAGAATTTGGTTGCACTTT 58.951 36.000 0.00 0.00 39.63 2.66
38 39 6.538381 CACCTAAAGAATTTGGTTGCACTTTT 59.462 34.615 0.00 0.00 39.63 2.27
39 40 7.065683 CACCTAAAGAATTTGGTTGCACTTTTT 59.934 33.333 0.00 0.00 39.63 1.94
40 41 8.261522 ACCTAAAGAATTTGGTTGCACTTTTTA 58.738 29.630 0.00 0.00 39.63 1.52
41 42 9.103861 CCTAAAGAATTTGGTTGCACTTTTTAA 57.896 29.630 0.00 0.00 39.63 1.52
52 53 9.482627 TGGTTGCACTTTTTAATTTATGTAAGG 57.517 29.630 0.00 0.00 0.00 2.69
53 54 9.699703 GGTTGCACTTTTTAATTTATGTAAGGA 57.300 29.630 0.00 0.00 0.00 3.36
80 81 3.905784 ACTAAGAAGTACCGAACCGTTG 58.094 45.455 0.00 0.00 32.84 4.10
81 82 1.505425 AAGAAGTACCGAACCGTTGC 58.495 50.000 0.00 0.00 0.00 4.17
82 83 0.390124 AGAAGTACCGAACCGTTGCA 59.610 50.000 0.00 0.00 0.00 4.08
83 84 1.202557 AGAAGTACCGAACCGTTGCAA 60.203 47.619 0.00 0.00 0.00 4.08
84 85 1.802365 GAAGTACCGAACCGTTGCAAT 59.198 47.619 0.59 0.00 0.00 3.56
85 86 1.153353 AGTACCGAACCGTTGCAATG 58.847 50.000 11.90 11.90 0.00 2.82
86 87 0.453782 GTACCGAACCGTTGCAATGC 60.454 55.000 13.42 0.00 0.00 3.56
87 88 1.579084 TACCGAACCGTTGCAATGCC 61.579 55.000 13.42 3.83 0.00 4.40
88 89 2.642129 CGAACCGTTGCAATGCCA 59.358 55.556 13.42 0.00 0.00 4.92
89 90 1.007964 CGAACCGTTGCAATGCCAA 60.008 52.632 13.42 0.00 0.00 4.52
90 91 0.596083 CGAACCGTTGCAATGCCAAA 60.596 50.000 13.42 0.00 0.00 3.28
91 92 1.139163 GAACCGTTGCAATGCCAAAG 58.861 50.000 13.42 1.84 0.00 2.77
92 93 0.879839 AACCGTTGCAATGCCAAAGC 60.880 50.000 13.42 0.00 40.48 3.51
93 94 2.028733 CCGTTGCAATGCCAAAGCC 61.029 57.895 13.42 0.00 38.69 4.35
94 95 1.005867 CGTTGCAATGCCAAAGCCT 60.006 52.632 5.57 0.00 38.69 4.58
95 96 0.600782 CGTTGCAATGCCAAAGCCTT 60.601 50.000 5.57 0.00 38.69 4.35
96 97 1.596603 GTTGCAATGCCAAAGCCTTT 58.403 45.000 0.59 0.00 38.69 3.11
97 98 1.532437 GTTGCAATGCCAAAGCCTTTC 59.468 47.619 0.59 0.00 38.69 2.62
98 99 0.035176 TGCAATGCCAAAGCCTTTCC 59.965 50.000 1.53 0.00 38.69 3.13
99 100 0.035176 GCAATGCCAAAGCCTTTCCA 59.965 50.000 0.00 0.00 38.69 3.53
100 101 1.339342 GCAATGCCAAAGCCTTTCCAT 60.339 47.619 0.00 0.00 38.69 3.41
101 102 2.876892 GCAATGCCAAAGCCTTTCCATT 60.877 45.455 0.00 6.73 38.69 3.16
102 103 3.619487 GCAATGCCAAAGCCTTTCCATTA 60.619 43.478 10.54 0.00 38.69 1.90
103 104 4.773013 CAATGCCAAAGCCTTTCCATTAT 58.227 39.130 10.54 0.00 38.69 1.28
104 105 5.684552 GCAATGCCAAAGCCTTTCCATTATA 60.685 40.000 10.54 0.00 38.69 0.98
105 106 5.535753 ATGCCAAAGCCTTTCCATTATAC 57.464 39.130 0.00 0.00 38.69 1.47
106 107 4.348486 TGCCAAAGCCTTTCCATTATACA 58.652 39.130 0.00 0.00 38.69 2.29
107 108 4.402155 TGCCAAAGCCTTTCCATTATACAG 59.598 41.667 0.00 0.00 38.69 2.74
108 109 4.402474 GCCAAAGCCTTTCCATTATACAGT 59.598 41.667 0.00 0.00 0.00 3.55
109 110 5.592688 GCCAAAGCCTTTCCATTATACAGTA 59.407 40.000 0.00 0.00 0.00 2.74
110 111 6.459710 GCCAAAGCCTTTCCATTATACAGTAC 60.460 42.308 0.00 0.00 0.00 2.73
111 112 6.828785 CCAAAGCCTTTCCATTATACAGTACT 59.171 38.462 0.00 0.00 0.00 2.73
112 113 7.012421 CCAAAGCCTTTCCATTATACAGTACTC 59.988 40.741 0.00 0.00 0.00 2.59
113 114 6.176014 AGCCTTTCCATTATACAGTACTCC 57.824 41.667 0.00 0.00 0.00 3.85
114 115 5.071923 AGCCTTTCCATTATACAGTACTCCC 59.928 44.000 0.00 0.00 0.00 4.30
115 116 5.071923 GCCTTTCCATTATACAGTACTCCCT 59.928 44.000 0.00 0.00 0.00 4.20
116 117 6.741801 GCCTTTCCATTATACAGTACTCCCTC 60.742 46.154 0.00 0.00 0.00 4.30
117 118 6.239629 CCTTTCCATTATACAGTACTCCCTCC 60.240 46.154 0.00 0.00 0.00 4.30
118 119 5.412617 TCCATTATACAGTACTCCCTCCA 57.587 43.478 0.00 0.00 0.00 3.86
119 120 5.977533 TCCATTATACAGTACTCCCTCCAT 58.022 41.667 0.00 0.00 0.00 3.41
120 121 6.017192 TCCATTATACAGTACTCCCTCCATC 58.983 44.000 0.00 0.00 0.00 3.51
121 122 5.187967 CCATTATACAGTACTCCCTCCATCC 59.812 48.000 0.00 0.00 0.00 3.51
122 123 2.359981 TACAGTACTCCCTCCATCCG 57.640 55.000 0.00 0.00 0.00 4.18
123 124 0.629596 ACAGTACTCCCTCCATCCGA 59.370 55.000 0.00 0.00 0.00 4.55
124 125 1.006758 ACAGTACTCCCTCCATCCGAA 59.993 52.381 0.00 0.00 0.00 4.30
125 126 2.108168 CAGTACTCCCTCCATCCGAAA 58.892 52.381 0.00 0.00 0.00 3.46
126 127 2.500098 CAGTACTCCCTCCATCCGAAAA 59.500 50.000 0.00 0.00 0.00 2.29
127 128 3.134804 CAGTACTCCCTCCATCCGAAAAT 59.865 47.826 0.00 0.00 0.00 1.82
128 129 4.344102 CAGTACTCCCTCCATCCGAAAATA 59.656 45.833 0.00 0.00 0.00 1.40
129 130 3.840124 ACTCCCTCCATCCGAAAATAC 57.160 47.619 0.00 0.00 0.00 1.89
130 131 3.385115 ACTCCCTCCATCCGAAAATACT 58.615 45.455 0.00 0.00 0.00 2.12
131 132 3.780850 ACTCCCTCCATCCGAAAATACTT 59.219 43.478 0.00 0.00 0.00 2.24
132 133 4.130118 CTCCCTCCATCCGAAAATACTTG 58.870 47.826 0.00 0.00 0.00 3.16
133 134 3.521937 TCCCTCCATCCGAAAATACTTGT 59.478 43.478 0.00 0.00 0.00 3.16
134 135 3.877508 CCCTCCATCCGAAAATACTTGTC 59.122 47.826 0.00 0.00 0.00 3.18
135 136 4.513442 CCTCCATCCGAAAATACTTGTCA 58.487 43.478 0.00 0.00 0.00 3.58
136 137 5.126067 CCTCCATCCGAAAATACTTGTCAT 58.874 41.667 0.00 0.00 0.00 3.06
137 138 5.237344 CCTCCATCCGAAAATACTTGTCATC 59.763 44.000 0.00 0.00 0.00 2.92
138 139 5.739959 TCCATCCGAAAATACTTGTCATCA 58.260 37.500 0.00 0.00 0.00 3.07
139 140 6.176896 TCCATCCGAAAATACTTGTCATCAA 58.823 36.000 0.00 0.00 0.00 2.57
140 141 6.657117 TCCATCCGAAAATACTTGTCATCAAA 59.343 34.615 0.00 0.00 32.87 2.69
141 142 7.175816 TCCATCCGAAAATACTTGTCATCAAAA 59.824 33.333 0.00 0.00 32.87 2.44
142 143 7.975616 CCATCCGAAAATACTTGTCATCAAAAT 59.024 33.333 0.00 0.00 32.87 1.82
143 144 8.800972 CATCCGAAAATACTTGTCATCAAAATG 58.199 33.333 0.00 0.00 32.87 2.32
144 145 7.312154 TCCGAAAATACTTGTCATCAAAATGG 58.688 34.615 0.00 0.00 33.42 3.16
145 146 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
146 147 7.273381 CCGAAAATACTTGTCATCAAAATGGAC 59.727 37.037 0.00 0.00 33.42 4.02
147 148 7.807433 CGAAAATACTTGTCATCAAAATGGACA 59.193 33.333 0.00 0.00 33.42 4.02
148 149 9.474920 GAAAATACTTGTCATCAAAATGGACAA 57.525 29.630 0.00 0.00 34.59 3.18
149 150 9.829507 AAAATACTTGTCATCAAAATGGACAAA 57.170 25.926 7.70 0.00 34.98 2.83
150 151 9.829507 AAATACTTGTCATCAAAATGGACAAAA 57.170 25.926 7.70 0.84 34.98 2.44
151 152 9.829507 AATACTTGTCATCAAAATGGACAAAAA 57.170 25.926 7.70 0.55 34.98 1.94
210 211 9.657419 ACATTCCCTTTTATTCATTTTGATGAC 57.343 29.630 0.00 0.00 0.00 3.06
211 212 9.656040 CATTCCCTTTTATTCATTTTGATGACA 57.344 29.630 0.00 0.00 0.00 3.58
213 214 9.709495 TTCCCTTTTATTCATTTTGATGACAAG 57.291 29.630 0.00 0.00 37.32 3.16
214 215 8.869109 TCCCTTTTATTCATTTTGATGACAAGT 58.131 29.630 0.00 0.00 37.32 3.16
222 223 8.741101 TTCATTTTGATGACAAGTATTTTCGG 57.259 30.769 0.00 0.00 37.32 4.30
223 224 8.105097 TCATTTTGATGACAAGTATTTTCGGA 57.895 30.769 0.00 0.00 37.32 4.55
224 225 8.020819 TCATTTTGATGACAAGTATTTTCGGAC 58.979 33.333 0.00 0.00 37.32 4.79
225 226 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
226 227 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
227 228 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
228 229 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
229 230 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
230 231 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
231 232 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
232 233 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
236 237 1.396653 TTTCGGACGGAGGGAGTATC 58.603 55.000 0.00 0.00 0.00 2.24
242 243 2.584236 GACGGAGGGAGTATCTAGCAA 58.416 52.381 0.00 0.00 33.73 3.91
250 251 7.720074 CGGAGGGAGTATCTAGCAATATGTATA 59.280 40.741 0.00 0.00 33.73 1.47
253 254 9.944079 AGGGAGTATCTAGCAATATGTATATGT 57.056 33.333 0.00 0.00 33.73 2.29
319 320 3.008923 TGAGTTGTCAATGATGGCCTACA 59.991 43.478 3.32 4.38 0.00 2.74
331 332 7.671495 ATGATGGCCTACAAAAACAAATTTC 57.329 32.000 3.32 0.00 0.00 2.17
334 335 5.983540 TGGCCTACAAAAACAAATTTCAGT 58.016 33.333 3.32 0.00 0.00 3.41
343 344 7.605691 ACAAAAACAAATTTCAGTGTTCATCCA 59.394 29.630 0.00 0.00 36.97 3.41
351 352 5.947228 TTCAGTGTTCATCCATTCAGAAC 57.053 39.130 0.00 0.00 41.42 3.01
363 364 5.192927 TCCATTCAGAACACTTGTTTCAGT 58.807 37.500 0.00 0.00 38.56 3.41
365 366 5.066375 CCATTCAGAACACTTGTTTCAGTGA 59.934 40.000 7.82 0.00 46.29 3.41
371 388 6.037500 CAGAACACTTGTTTCAGTGATTCAGA 59.962 38.462 7.82 0.00 46.29 3.27
372 389 6.599244 AGAACACTTGTTTCAGTGATTCAGAA 59.401 34.615 7.82 0.00 46.29 3.02
387 404 0.890996 CAGAAGTTCAGGTGGGGTGC 60.891 60.000 5.50 0.00 0.00 5.01
390 407 1.943730 AAGTTCAGGTGGGGTGCCAA 61.944 55.000 0.00 0.00 0.00 4.52
404 445 2.231380 GCCAACCCTCTTCCCTCCA 61.231 63.158 0.00 0.00 0.00 3.86
438 479 3.733960 CGCACGAGACGAGGTCCA 61.734 66.667 0.00 0.00 32.18 4.02
500 542 4.084888 GGCACTTTTCGCGGACGG 62.085 66.667 6.13 0.00 40.63 4.79
501 543 4.736631 GCACTTTTCGCGGACGGC 62.737 66.667 6.13 0.00 40.63 5.68
502 544 3.342627 CACTTTTCGCGGACGGCA 61.343 61.111 6.13 0.00 43.84 5.69
503 545 2.358247 ACTTTTCGCGGACGGCAT 60.358 55.556 6.13 0.00 43.84 4.40
603 662 2.932261 ACAAGGTGACACTTTCTTCCC 58.068 47.619 5.39 0.00 0.00 3.97
628 687 1.286501 TAGTCGCCGCAATGTTCATC 58.713 50.000 0.00 0.00 0.00 2.92
650 709 0.108329 GAATCGAAGCCCTCCGTTGA 60.108 55.000 0.00 0.00 0.00 3.18
721 784 4.292186 TGGTTCAAGAATCCTTCTCTGG 57.708 45.455 0.00 0.00 39.61 3.86
798 868 3.303461 CGATTGCTACTCTACTCCGACTG 60.303 52.174 0.00 0.00 0.00 3.51
862 933 0.032540 CCATGATCCATCGACGCAGA 59.967 55.000 0.00 0.00 0.00 4.26
863 934 1.135046 CATGATCCATCGACGCAGAC 58.865 55.000 0.00 0.00 0.00 3.51
864 935 0.746659 ATGATCCATCGACGCAGACA 59.253 50.000 0.00 0.00 0.00 3.41
865 936 0.179137 TGATCCATCGACGCAGACAC 60.179 55.000 0.00 0.00 0.00 3.67
866 937 1.202973 GATCCATCGACGCAGACACG 61.203 60.000 0.00 0.00 39.50 4.49
867 938 3.545481 CCATCGACGCAGACACGC 61.545 66.667 0.00 0.00 36.19 5.34
868 939 2.804931 CATCGACGCAGACACGCA 60.805 61.111 0.00 0.00 36.19 5.24
869 940 2.504899 ATCGACGCAGACACGCAG 60.505 61.111 0.00 0.00 36.19 5.18
985 1064 0.719465 TTCGAGCGATTCTTTTCGGC 59.281 50.000 0.00 0.00 39.49 5.54
1045 1151 6.553857 TCCAAGGTCTTCTACTCTACTTCTT 58.446 40.000 0.00 0.00 0.00 2.52
1046 1152 6.660094 TCCAAGGTCTTCTACTCTACTTCTTC 59.340 42.308 0.00 0.00 0.00 2.87
1135 1259 0.693622 TACGGGTTGCCATTTCAGGA 59.306 50.000 0.00 0.00 0.00 3.86
1147 1271 0.036388 TTTCAGGACCATGTCGGCTC 60.036 55.000 0.00 0.00 39.03 4.70
1309 1453 3.072468 AGCTACCGGCGCAGGTAA 61.072 61.111 33.78 20.48 45.23 2.85
1310 1454 2.125431 GCTACCGGCGCAGGTAAA 60.125 61.111 33.78 19.54 45.23 2.01
1318 1462 0.743345 GGCGCAGGTAAATCTCCGTT 60.743 55.000 10.83 0.00 0.00 4.44
1410 1556 7.108841 TCTACATATGACTTGTTGGTACTCC 57.891 40.000 10.38 0.00 0.00 3.85
1411 1557 5.099042 ACATATGACTTGTTGGTACTCCC 57.901 43.478 10.38 0.00 0.00 4.30
1412 1558 4.783227 ACATATGACTTGTTGGTACTCCCT 59.217 41.667 10.38 0.00 0.00 4.20
1413 1559 3.983044 ATGACTTGTTGGTACTCCCTC 57.017 47.619 0.00 0.00 0.00 4.30
1414 1560 1.975680 TGACTTGTTGGTACTCCCTCC 59.024 52.381 0.00 0.00 0.00 4.30
1415 1561 0.974383 ACTTGTTGGTACTCCCTCCG 59.026 55.000 0.00 0.00 0.00 4.63
1416 1562 0.974383 CTTGTTGGTACTCCCTCCGT 59.026 55.000 0.00 0.00 0.00 4.69
1417 1563 1.346722 CTTGTTGGTACTCCCTCCGTT 59.653 52.381 0.00 0.00 0.00 4.44
1418 1564 0.971386 TGTTGGTACTCCCTCCGTTC 59.029 55.000 0.00 0.00 0.00 3.95
1419 1565 0.248565 GTTGGTACTCCCTCCGTTCC 59.751 60.000 0.00 0.00 0.00 3.62
1420 1566 1.252904 TTGGTACTCCCTCCGTTCCG 61.253 60.000 0.00 0.00 0.00 4.30
1421 1567 1.379044 GGTACTCCCTCCGTTCCGA 60.379 63.158 0.00 0.00 0.00 4.55
1422 1568 0.754587 GGTACTCCCTCCGTTCCGAT 60.755 60.000 0.00 0.00 0.00 4.18
1423 1569 1.109609 GTACTCCCTCCGTTCCGATT 58.890 55.000 0.00 0.00 0.00 3.34
1424 1570 1.479730 GTACTCCCTCCGTTCCGATTT 59.520 52.381 0.00 0.00 0.00 2.17
1425 1571 1.856629 ACTCCCTCCGTTCCGATTTA 58.143 50.000 0.00 0.00 0.00 1.40
1426 1572 1.479730 ACTCCCTCCGTTCCGATTTAC 59.520 52.381 0.00 0.00 0.00 2.01
1427 1573 1.755380 CTCCCTCCGTTCCGATTTACT 59.245 52.381 0.00 0.00 0.00 2.24
1428 1574 1.753073 TCCCTCCGTTCCGATTTACTC 59.247 52.381 0.00 0.00 0.00 2.59
1430 1576 1.133790 CCTCCGTTCCGATTTACTCGT 59.866 52.381 0.00 0.00 46.18 4.18
1431 1577 2.448219 CTCCGTTCCGATTTACTCGTC 58.552 52.381 0.00 0.00 46.18 4.20
1432 1578 1.186030 CCGTTCCGATTTACTCGTCG 58.814 55.000 0.00 0.00 46.18 5.12
1433 1579 1.466360 CCGTTCCGATTTACTCGTCGT 60.466 52.381 0.00 0.00 46.18 4.34
1434 1580 1.576246 CGTTCCGATTTACTCGTCGTG 59.424 52.381 0.00 0.00 46.18 4.35
1507 1653 0.316522 GATCAGCTCTGCGGATGCTA 59.683 55.000 16.05 8.15 42.84 3.49
1588 1734 0.040058 TCAACAGAATGGGCCTGCAT 59.960 50.000 4.53 0.00 43.62 3.96
1679 1873 2.105477 ACAGACCTCAACAGCAGTGATT 59.895 45.455 0.00 0.00 0.00 2.57
1718 1912 2.245714 CTTCGAAAGCCAGCCTTCGC 62.246 60.000 16.51 0.00 31.99 4.70
1720 1914 2.744768 CGAAAGCCAGCCTTCGCTC 61.745 63.158 10.14 0.00 43.95 5.03
1721 1915 1.376553 GAAAGCCAGCCTTCGCTCT 60.377 57.895 0.00 0.00 43.95 4.09
1808 2002 1.903183 GTAGGTGGCCTCAGTTTCTCT 59.097 52.381 3.32 0.00 34.61 3.10
1887 2099 4.938756 TTGGCAGGGGTGGAGGGT 62.939 66.667 0.00 0.00 0.00 4.34
1950 2162 1.079405 ACCGCTCCACATGGTTACG 60.079 57.895 0.00 0.91 36.34 3.18
2003 2215 2.656069 CCACCTTCGGGACCATCGT 61.656 63.158 0.00 0.00 38.77 3.73
2013 2225 4.329545 ACCATCGTTGCTGCCGGT 62.330 61.111 1.90 0.00 0.00 5.28
2078 2290 4.308265 GACAAGGTGTCTGAGAAGGTAAC 58.692 47.826 1.09 0.00 43.73 2.50
2125 2337 1.586154 CTTTGCCGGCAAGATTCCGT 61.586 55.000 37.88 0.00 45.09 4.69
2370 2647 2.166870 GCCATCATCAACCTTCATGCAA 59.833 45.455 0.00 0.00 0.00 4.08
2415 2731 3.886505 GTGGTTAACCCAGTTTCACATGA 59.113 43.478 21.97 0.00 46.45 3.07
2845 3161 1.508632 CGTTTTGACCGTCATGTCCT 58.491 50.000 1.09 0.00 34.25 3.85
2944 3261 4.036380 CCCCAAAACTATTTGCGATCTACC 59.964 45.833 0.00 0.00 43.73 3.18
3462 3850 2.687418 GATGTCATGATGGGCGGGCT 62.687 60.000 0.00 0.00 0.00 5.19
3620 4011 1.096967 CAATGGCGGTGATGCTAGCA 61.097 55.000 21.85 21.85 34.52 3.49
3645 4036 2.434185 GGCGACCAACATGAGCGA 60.434 61.111 0.00 0.00 0.00 4.93
3846 4237 8.336801 AGTAAATGGTTTTGACAATAGTCCTC 57.663 34.615 0.00 0.00 44.33 3.71
4039 4482 9.739276 ATGGAACTTAAACATGAACTGAATAGA 57.261 29.630 0.00 0.00 0.00 1.98
4109 4555 3.629398 CCCTGGCTATTGTTCTGCTTTAG 59.371 47.826 0.00 0.00 0.00 1.85
4137 4583 7.024340 AGCTTATTAATTGCAGTCACATCAG 57.976 36.000 13.25 0.00 0.00 2.90
4339 4786 0.937304 CCACATAATTCGCCGAGTGG 59.063 55.000 7.90 7.90 40.32 4.00
4440 4970 5.823045 CCCAAAGAAATTAGAAGCCGACTAT 59.177 40.000 0.00 0.00 0.00 2.12
4459 4989 8.450964 CCGACTATAGAAAATCACACACAATTT 58.549 33.333 6.78 0.00 0.00 1.82
4529 5061 2.559998 AAAGAGTGTGGTGTTTTGCG 57.440 45.000 0.00 0.00 0.00 4.85
4553 5085 7.203910 CGTCTTATATCTGTAAAACTCCTGCT 58.796 38.462 0.00 0.00 0.00 4.24
4554 5086 7.707035 CGTCTTATATCTGTAAAACTCCTGCTT 59.293 37.037 0.00 0.00 0.00 3.91
4576 5108 4.481930 TTTTGGAACTCAAGCATGTACG 57.518 40.909 0.00 0.00 36.62 3.67
4597 5130 3.728845 GCAAGATTCTATAACCCGCTCA 58.271 45.455 0.00 0.00 0.00 4.26
4622 5156 4.806640 ACAAATACCATGCCTTTTCCAG 57.193 40.909 0.00 0.00 0.00 3.86
4650 5189 7.520453 CGAATATGGTTTATGTGATCACAAGGG 60.520 40.741 31.00 6.34 45.41 3.95
4712 5253 2.026636 TCCTAGCCGCAAAACCTACATT 60.027 45.455 0.00 0.00 0.00 2.71
4730 5271 1.093159 TTAAGAGAGAGGACGCGACC 58.907 55.000 20.18 20.18 0.00 4.79
4755 5296 2.408050 CAACTGTCAGAAACGAGGAGG 58.592 52.381 6.91 0.00 0.00 4.30
4812 5353 2.638480 TTGAAGGTCAACAGGGAGTG 57.362 50.000 0.00 0.00 30.26 3.51
4813 5354 0.764890 TGAAGGTCAACAGGGAGTGG 59.235 55.000 0.00 0.00 0.00 4.00
4814 5355 0.036875 GAAGGTCAACAGGGAGTGGG 59.963 60.000 0.00 0.00 0.00 4.61
4815 5356 1.427072 AAGGTCAACAGGGAGTGGGG 61.427 60.000 0.00 0.00 0.00 4.96
4816 5357 2.757077 GTCAACAGGGAGTGGGGG 59.243 66.667 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.127491 ACCAAATTCTTTAGGTGTCGAACA 58.873 37.500 0.00 0.00 32.04 3.18
7 8 5.684550 ACCAAATTCTTTAGGTGTCGAAC 57.315 39.130 0.00 0.00 32.04 3.95
8 9 5.506649 GCAACCAAATTCTTTAGGTGTCGAA 60.507 40.000 0.00 0.00 33.93 3.71
9 10 4.023536 GCAACCAAATTCTTTAGGTGTCGA 60.024 41.667 0.00 0.00 33.93 4.20
10 11 4.226761 GCAACCAAATTCTTTAGGTGTCG 58.773 43.478 0.00 0.00 33.93 4.35
11 12 4.982295 GTGCAACCAAATTCTTTAGGTGTC 59.018 41.667 0.00 0.00 33.93 3.67
12 13 4.649218 AGTGCAACCAAATTCTTTAGGTGT 59.351 37.500 0.00 0.00 37.80 4.16
13 14 5.200368 AGTGCAACCAAATTCTTTAGGTG 57.800 39.130 0.00 0.00 37.80 4.00
14 15 5.869649 AAGTGCAACCAAATTCTTTAGGT 57.130 34.783 0.00 0.00 37.80 3.08
15 16 7.552458 AAAAAGTGCAACCAAATTCTTTAGG 57.448 32.000 0.00 0.00 37.80 2.69
26 27 9.482627 CCTTACATAAATTAAAAAGTGCAACCA 57.517 29.630 0.00 0.00 37.80 3.67
27 28 9.699703 TCCTTACATAAATTAAAAAGTGCAACC 57.300 29.630 0.00 0.00 37.80 3.77
58 59 4.615912 GCAACGGTTCGGTACTTCTTAGTA 60.616 45.833 0.00 0.00 35.78 1.82
59 60 3.858503 GCAACGGTTCGGTACTTCTTAGT 60.859 47.826 0.00 0.00 38.44 2.24
60 61 2.665052 GCAACGGTTCGGTACTTCTTAG 59.335 50.000 0.00 0.00 0.00 2.18
61 62 2.035704 TGCAACGGTTCGGTACTTCTTA 59.964 45.455 0.00 0.00 0.00 2.10
62 63 1.202557 TGCAACGGTTCGGTACTTCTT 60.203 47.619 0.00 0.00 0.00 2.52
63 64 0.390124 TGCAACGGTTCGGTACTTCT 59.610 50.000 0.00 0.00 0.00 2.85
64 65 1.219646 TTGCAACGGTTCGGTACTTC 58.780 50.000 0.00 0.00 0.00 3.01
65 66 1.533731 CATTGCAACGGTTCGGTACTT 59.466 47.619 0.00 0.00 0.00 2.24
66 67 1.153353 CATTGCAACGGTTCGGTACT 58.847 50.000 0.00 0.00 0.00 2.73
67 68 0.453782 GCATTGCAACGGTTCGGTAC 60.454 55.000 0.00 0.00 0.00 3.34
68 69 1.579084 GGCATTGCAACGGTTCGGTA 61.579 55.000 11.39 0.00 0.00 4.02
69 70 2.642700 GCATTGCAACGGTTCGGT 59.357 55.556 0.00 0.00 0.00 4.69
70 71 2.126502 GGCATTGCAACGGTTCGG 60.127 61.111 11.39 0.00 0.00 4.30
71 72 0.596083 TTTGGCATTGCAACGGTTCG 60.596 50.000 11.39 0.00 0.00 3.95
72 73 1.139163 CTTTGGCATTGCAACGGTTC 58.861 50.000 11.39 0.00 0.00 3.62
73 74 0.879839 GCTTTGGCATTGCAACGGTT 60.880 50.000 11.39 0.00 38.54 4.44
74 75 1.300853 GCTTTGGCATTGCAACGGT 60.301 52.632 11.39 0.00 38.54 4.83
75 76 2.028733 GGCTTTGGCATTGCAACGG 61.029 57.895 11.39 0.00 40.87 4.44
76 77 0.600782 AAGGCTTTGGCATTGCAACG 60.601 50.000 11.39 0.00 41.08 4.10
77 78 1.532437 GAAAGGCTTTGGCATTGCAAC 59.468 47.619 18.79 0.00 41.81 4.17
78 79 1.542987 GGAAAGGCTTTGGCATTGCAA 60.543 47.619 18.79 0.00 41.81 4.08
79 80 0.035176 GGAAAGGCTTTGGCATTGCA 59.965 50.000 18.79 0.00 41.81 4.08
80 81 0.035176 TGGAAAGGCTTTGGCATTGC 59.965 50.000 18.79 0.00 41.81 3.56
81 82 2.773993 ATGGAAAGGCTTTGGCATTG 57.226 45.000 18.79 0.00 41.81 2.82
82 83 5.424895 TGTATAATGGAAAGGCTTTGGCATT 59.575 36.000 18.79 8.78 44.67 3.56
83 84 4.961730 TGTATAATGGAAAGGCTTTGGCAT 59.038 37.500 18.79 5.89 40.87 4.40
84 85 4.348486 TGTATAATGGAAAGGCTTTGGCA 58.652 39.130 18.79 1.83 40.87 4.92
85 86 4.402474 ACTGTATAATGGAAAGGCTTTGGC 59.598 41.667 18.79 3.48 37.82 4.52
86 87 6.828785 AGTACTGTATAATGGAAAGGCTTTGG 59.171 38.462 18.79 0.00 0.00 3.28
87 88 7.012421 GGAGTACTGTATAATGGAAAGGCTTTG 59.988 40.741 18.79 1.05 0.00 2.77
88 89 7.054751 GGAGTACTGTATAATGGAAAGGCTTT 58.945 38.462 13.25 13.25 0.00 3.51
89 90 6.409349 GGGAGTACTGTATAATGGAAAGGCTT 60.409 42.308 0.00 0.00 0.00 4.35
90 91 5.071923 GGGAGTACTGTATAATGGAAAGGCT 59.928 44.000 0.00 0.00 0.00 4.58
91 92 5.071923 AGGGAGTACTGTATAATGGAAAGGC 59.928 44.000 0.00 0.00 0.00 4.35
92 93 6.239629 GGAGGGAGTACTGTATAATGGAAAGG 60.240 46.154 0.00 0.00 0.00 3.11
93 94 6.326583 TGGAGGGAGTACTGTATAATGGAAAG 59.673 42.308 0.00 0.00 0.00 2.62
94 95 6.206787 TGGAGGGAGTACTGTATAATGGAAA 58.793 40.000 0.00 0.00 0.00 3.13
95 96 5.784023 TGGAGGGAGTACTGTATAATGGAA 58.216 41.667 0.00 0.00 0.00 3.53
96 97 5.412617 TGGAGGGAGTACTGTATAATGGA 57.587 43.478 0.00 0.00 0.00 3.41
97 98 5.187967 GGATGGAGGGAGTACTGTATAATGG 59.812 48.000 0.00 0.00 0.00 3.16
98 99 5.105716 CGGATGGAGGGAGTACTGTATAATG 60.106 48.000 0.00 0.00 0.00 1.90
99 100 5.017490 CGGATGGAGGGAGTACTGTATAAT 58.983 45.833 0.00 0.00 0.00 1.28
100 101 4.105217 TCGGATGGAGGGAGTACTGTATAA 59.895 45.833 0.00 0.00 0.00 0.98
101 102 3.654321 TCGGATGGAGGGAGTACTGTATA 59.346 47.826 0.00 0.00 0.00 1.47
102 103 2.445905 TCGGATGGAGGGAGTACTGTAT 59.554 50.000 0.00 0.00 0.00 2.29
103 104 1.848388 TCGGATGGAGGGAGTACTGTA 59.152 52.381 0.00 0.00 0.00 2.74
104 105 0.629596 TCGGATGGAGGGAGTACTGT 59.370 55.000 0.00 0.00 0.00 3.55
105 106 1.776662 TTCGGATGGAGGGAGTACTG 58.223 55.000 0.00 0.00 0.00 2.74
106 107 2.544844 TTTCGGATGGAGGGAGTACT 57.455 50.000 0.00 0.00 0.00 2.73
107 108 3.840124 ATTTTCGGATGGAGGGAGTAC 57.160 47.619 0.00 0.00 0.00 2.73
108 109 4.553678 AGTATTTTCGGATGGAGGGAGTA 58.446 43.478 0.00 0.00 0.00 2.59
109 110 3.385115 AGTATTTTCGGATGGAGGGAGT 58.615 45.455 0.00 0.00 0.00 3.85
110 111 4.130118 CAAGTATTTTCGGATGGAGGGAG 58.870 47.826 0.00 0.00 0.00 4.30
111 112 3.521937 ACAAGTATTTTCGGATGGAGGGA 59.478 43.478 0.00 0.00 0.00 4.20
112 113 3.877508 GACAAGTATTTTCGGATGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
113 114 4.513442 TGACAAGTATTTTCGGATGGAGG 58.487 43.478 0.00 0.00 0.00 4.30
114 115 5.817296 TGATGACAAGTATTTTCGGATGGAG 59.183 40.000 0.00 0.00 0.00 3.86
115 116 5.739959 TGATGACAAGTATTTTCGGATGGA 58.260 37.500 0.00 0.00 0.00 3.41
116 117 6.435430 TTGATGACAAGTATTTTCGGATGG 57.565 37.500 0.00 0.00 0.00 3.51
117 118 8.800972 CATTTTGATGACAAGTATTTTCGGATG 58.199 33.333 0.00 0.00 37.32 3.51
118 119 7.975616 CCATTTTGATGACAAGTATTTTCGGAT 59.024 33.333 0.00 0.00 37.32 4.18
119 120 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
120 121 7.273381 GTCCATTTTGATGACAAGTATTTTCGG 59.727 37.037 0.00 0.00 37.32 4.30
121 122 7.807433 TGTCCATTTTGATGACAAGTATTTTCG 59.193 33.333 0.00 0.00 37.32 3.46
122 123 9.474920 TTGTCCATTTTGATGACAAGTATTTTC 57.525 29.630 0.00 0.00 37.32 2.29
123 124 9.829507 TTTGTCCATTTTGATGACAAGTATTTT 57.170 25.926 0.00 0.00 37.13 1.82
124 125 9.829507 TTTTGTCCATTTTGATGACAAGTATTT 57.170 25.926 0.00 0.00 37.13 1.40
125 126 9.829507 TTTTTGTCCATTTTGATGACAAGTATT 57.170 25.926 0.00 0.00 37.13 1.89
184 185 9.657419 GTCATCAAAATGAATAAAAGGGAATGT 57.343 29.630 0.00 0.00 43.42 2.71
185 186 9.656040 TGTCATCAAAATGAATAAAAGGGAATG 57.344 29.630 0.00 0.00 43.42 2.67
187 188 9.709495 CTTGTCATCAAAATGAATAAAAGGGAA 57.291 29.630 0.00 0.00 43.42 3.97
188 189 8.869109 ACTTGTCATCAAAATGAATAAAAGGGA 58.131 29.630 0.00 0.00 43.42 4.20
196 197 9.357652 CCGAAAATACTTGTCATCAAAATGAAT 57.642 29.630 0.00 0.00 43.42 2.57
197 198 8.572185 TCCGAAAATACTTGTCATCAAAATGAA 58.428 29.630 0.00 0.00 43.42 2.57
198 199 8.020819 GTCCGAAAATACTTGTCATCAAAATGA 58.979 33.333 0.00 0.00 39.63 2.57
199 200 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
200 201 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
201 202 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
202 203 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
203 204 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
204 205 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
205 206 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
206 207 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
207 208 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
208 209 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
209 210 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
210 211 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
211 212 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
212 213 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
213 214 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
214 215 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
215 216 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
216 217 1.753073 GATACTCCCTCCGTCCGAAAA 59.247 52.381 0.00 0.00 0.00 2.29
217 218 1.064166 AGATACTCCCTCCGTCCGAAA 60.064 52.381 0.00 0.00 0.00 3.46
218 219 0.549950 AGATACTCCCTCCGTCCGAA 59.450 55.000 0.00 0.00 0.00 4.30
219 220 1.347050 CTAGATACTCCCTCCGTCCGA 59.653 57.143 0.00 0.00 0.00 4.55
220 221 1.810959 CTAGATACTCCCTCCGTCCG 58.189 60.000 0.00 0.00 0.00 4.79
221 222 1.202903 TGCTAGATACTCCCTCCGTCC 60.203 57.143 0.00 0.00 0.00 4.79
222 223 2.273538 TGCTAGATACTCCCTCCGTC 57.726 55.000 0.00 0.00 0.00 4.79
223 224 2.750141 TTGCTAGATACTCCCTCCGT 57.250 50.000 0.00 0.00 0.00 4.69
224 225 4.707448 ACATATTGCTAGATACTCCCTCCG 59.293 45.833 0.00 0.00 0.00 4.63
225 226 7.906199 ATACATATTGCTAGATACTCCCTCC 57.094 40.000 0.00 0.00 0.00 4.30
227 228 9.944079 ACATATACATATTGCTAGATACTCCCT 57.056 33.333 0.00 0.00 0.00 4.20
228 229 9.973450 CACATATACATATTGCTAGATACTCCC 57.027 37.037 0.00 0.00 0.00 4.30
279 280 8.092521 ACAACTCAATCTCTTAACATCAACTG 57.907 34.615 0.00 0.00 0.00 3.16
309 310 6.705825 ACTGAAATTTGTTTTTGTAGGCCATC 59.294 34.615 5.01 0.00 0.00 3.51
312 313 5.815222 ACACTGAAATTTGTTTTTGTAGGCC 59.185 36.000 0.00 0.00 0.00 5.19
319 320 8.735692 ATGGATGAACACTGAAATTTGTTTTT 57.264 26.923 0.00 0.00 36.06 1.94
334 335 5.132502 ACAAGTGTTCTGAATGGATGAACA 58.867 37.500 0.00 0.00 44.96 3.18
343 344 6.949352 ATCACTGAAACAAGTGTTCTGAAT 57.051 33.333 4.41 0.00 46.33 2.57
363 364 2.040278 CCCCACCTGAACTTCTGAATCA 59.960 50.000 0.00 0.00 0.00 2.57
364 365 2.040412 ACCCCACCTGAACTTCTGAATC 59.960 50.000 0.00 0.00 0.00 2.52
365 366 2.065799 ACCCCACCTGAACTTCTGAAT 58.934 47.619 0.00 0.00 0.00 2.57
371 388 1.943730 TTGGCACCCCACCTGAACTT 61.944 55.000 0.00 0.00 41.97 2.66
372 389 2.391130 TTGGCACCCCACCTGAACT 61.391 57.895 0.00 0.00 41.97 3.01
387 404 1.685820 GTGGAGGGAAGAGGGTTGG 59.314 63.158 0.00 0.00 0.00 3.77
390 407 1.081277 GAGGTGGAGGGAAGAGGGT 59.919 63.158 0.00 0.00 0.00 4.34
397 438 4.779733 GGGCTCGAGGTGGAGGGA 62.780 72.222 15.58 0.00 34.56 4.20
603 662 1.523711 ATTGCGGCGACTATGTGGG 60.524 57.895 12.98 0.00 0.00 4.61
628 687 1.299468 CGGAGGGCTTCGATTCGAG 60.299 63.158 8.98 5.19 37.14 4.04
650 709 3.094484 TCAAATTAGCCACCCGGATTT 57.906 42.857 0.73 0.00 29.71 2.17
798 868 3.807538 CTGCCATGGCTGTGTCGC 61.808 66.667 35.53 8.82 42.51 5.19
868 939 4.528596 CCTACCTGCCTGCAGTATATAACT 59.471 45.833 17.23 0.00 42.15 2.24
869 940 4.283722 ACCTACCTGCCTGCAGTATATAAC 59.716 45.833 17.23 0.00 42.15 1.89
891 962 2.610374 CTCTGCCTCGTGACTAGACTAC 59.390 54.545 0.00 0.00 0.00 2.73
892 963 2.500504 TCTCTGCCTCGTGACTAGACTA 59.499 50.000 0.00 0.00 0.00 2.59
893 964 1.279558 TCTCTGCCTCGTGACTAGACT 59.720 52.381 0.00 0.00 0.00 3.24
894 965 1.740297 TCTCTGCCTCGTGACTAGAC 58.260 55.000 0.00 0.00 0.00 2.59
1045 1151 2.522367 GGTCACACCGGGGAAAGGA 61.522 63.158 12.96 0.00 0.00 3.36
1046 1152 2.033602 GGTCACACCGGGGAAAGG 59.966 66.667 12.96 0.00 0.00 3.11
1135 1259 3.968837 TACGGGGAGCCGACATGGT 62.969 63.158 0.00 0.00 41.21 3.55
1147 1271 2.107950 TGAATTCAACAGCTACGGGG 57.892 50.000 5.45 0.00 0.00 5.73
1252 1396 4.151417 GCGCGTTGCAAATCACAT 57.849 50.000 8.43 0.00 45.45 3.21
1309 1453 2.094659 CGTGCGAGCAACGGAGATT 61.095 57.895 0.00 0.00 43.91 2.40
1310 1454 2.507102 CGTGCGAGCAACGGAGAT 60.507 61.111 0.00 0.00 43.91 2.75
1420 1566 5.347907 AGAATCAAACCACGACGAGTAAATC 59.652 40.000 0.00 0.00 0.00 2.17
1421 1567 5.235516 AGAATCAAACCACGACGAGTAAAT 58.764 37.500 0.00 0.00 0.00 1.40
1422 1568 4.624015 AGAATCAAACCACGACGAGTAAA 58.376 39.130 0.00 0.00 0.00 2.01
1423 1569 4.247267 AGAATCAAACCACGACGAGTAA 57.753 40.909 0.00 0.00 0.00 2.24
1424 1570 3.928727 AGAATCAAACCACGACGAGTA 57.071 42.857 0.00 0.00 0.00 2.59
1425 1571 2.814280 AGAATCAAACCACGACGAGT 57.186 45.000 0.00 0.00 0.00 4.18
1426 1572 3.059044 CGTAAGAATCAAACCACGACGAG 59.941 47.826 0.00 0.00 43.02 4.18
1427 1573 2.981805 CGTAAGAATCAAACCACGACGA 59.018 45.455 0.00 0.00 43.02 4.20
1428 1574 2.727798 ACGTAAGAATCAAACCACGACG 59.272 45.455 0.00 0.00 43.62 5.12
1429 1575 4.090498 GGTACGTAAGAATCAAACCACGAC 59.910 45.833 0.00 0.00 43.62 4.34
1430 1576 4.236935 GGTACGTAAGAATCAAACCACGA 58.763 43.478 0.00 0.00 43.62 4.35
1431 1577 3.989167 TGGTACGTAAGAATCAAACCACG 59.011 43.478 0.00 0.00 43.62 4.94
1432 1578 5.163794 CCATGGTACGTAAGAATCAAACCAC 60.164 44.000 2.57 0.00 38.28 4.16
1433 1579 4.938832 CCATGGTACGTAAGAATCAAACCA 59.061 41.667 2.57 0.00 39.66 3.67
1434 1580 5.180271 TCCATGGTACGTAAGAATCAAACC 58.820 41.667 12.58 0.00 43.62 3.27
1507 1653 4.876107 CGAACAATGCTACCTGGATTAGTT 59.124 41.667 0.00 0.00 34.89 2.24
1588 1734 0.884704 GACAAGAAGCGGCACCAGAA 60.885 55.000 1.45 0.00 0.00 3.02
1645 1839 0.598562 GGTCTGTGAGACGAGAAGCA 59.401 55.000 0.00 0.00 45.96 3.91
1718 1912 5.096443 AGAGCTGAAGGTTTGGAATAGAG 57.904 43.478 0.00 0.00 0.00 2.43
1720 1914 5.096443 AGAGAGCTGAAGGTTTGGAATAG 57.904 43.478 0.00 0.00 0.00 1.73
1721 1915 4.532126 TGAGAGAGCTGAAGGTTTGGAATA 59.468 41.667 0.00 0.00 0.00 1.75
1887 2099 2.193532 CTTCGACAGGAGCTGGCTA 58.806 57.895 0.00 0.00 37.36 3.93
1950 2162 3.328931 TCCATATCTTGCCCTTCTCCATC 59.671 47.826 0.00 0.00 0.00 3.51
2003 2215 0.970937 AGTAGCTAGACCGGCAGCAA 60.971 55.000 21.34 0.00 40.36 3.91
2013 2225 0.683179 TCGCAAGGCCAGTAGCTAGA 60.683 55.000 5.01 0.00 43.05 2.43
2078 2290 1.146485 CCCTGATCAGCAGCCTCAG 59.854 63.158 17.76 9.34 43.50 3.35
2125 2337 1.188219 AGTTCGCCCAAGAGCTCAGA 61.188 55.000 17.77 2.37 0.00 3.27
2370 2647 2.028930 AGGAAAGAAACGATCGCTGACT 60.029 45.455 16.60 6.94 0.00 3.41
2415 2731 1.490621 GTGAAACGCTGCAAAGCAAT 58.509 45.000 0.00 0.00 38.41 3.56
2944 3261 6.647067 CGCTCTTATATTTCTTTACAGAGGGG 59.353 42.308 0.00 0.00 36.63 4.79
3462 3850 0.397957 TATAAGCTCCTCGGCCACCA 60.398 55.000 2.24 0.00 0.00 4.17
3620 4011 2.594592 GTTGGTCGCCTTGCCACT 60.595 61.111 0.00 0.00 34.02 4.00
3645 4036 0.687354 AACCAGTTCTGACATCCGCT 59.313 50.000 1.00 0.00 0.00 5.52
3846 4237 5.576384 GTCTGTTCAATCTCTTAGCTGTCAG 59.424 44.000 0.00 0.00 0.00 3.51
3935 4329 7.848051 GTCAATTAAATTCTGCTCGTACATCTG 59.152 37.037 0.00 0.00 0.00 2.90
4013 4456 9.739276 TCTATTCAGTTCATGTTTAAGTTCCAT 57.261 29.630 0.00 0.00 0.00 3.41
4039 4482 2.988010 TGTGCTCAGTCACAGAAACT 57.012 45.000 0.00 0.00 41.57 2.66
4109 4555 5.063438 TGTGACTGCAATTAATAAGCTCGTC 59.937 40.000 18.08 18.08 33.35 4.20
4137 4583 9.846248 AATCAACATTCTCAAACATTACTTAGC 57.154 29.630 0.00 0.00 0.00 3.09
4529 5061 8.950208 AAGCAGGAGTTTTACAGATATAAGAC 57.050 34.615 0.00 0.00 0.00 3.01
4554 5086 4.791411 GCGTACATGCTTGAGTTCCAAAAA 60.791 41.667 6.60 0.00 33.76 1.94
4576 5108 3.728845 TGAGCGGGTTATAGAATCTTGC 58.271 45.455 0.00 0.00 0.00 4.01
4597 5130 6.360618 TGGAAAAGGCATGGTATTTGTTTTT 58.639 32.000 0.00 0.00 0.00 1.94
4622 5156 7.477144 TGTGATCACATAAACCATATTCGAC 57.523 36.000 24.56 0.00 36.21 4.20
4698 5239 5.292101 CCTCTCTCTTAATGTAGGTTTTGCG 59.708 44.000 0.00 0.00 0.00 4.85
4712 5253 1.088340 CGGTCGCGTCCTCTCTCTTA 61.088 60.000 19.89 0.00 0.00 2.10
4730 5271 0.042188 CGTTTCTGACAGTTGCACCG 60.042 55.000 1.59 0.00 0.00 4.94
4736 5277 1.270358 GCCTCCTCGTTTCTGACAGTT 60.270 52.381 1.59 0.00 0.00 3.16
4755 5296 2.618559 CCTCTCCGGGTCTATACCTAGC 60.619 59.091 0.00 0.00 45.95 3.42
4790 5331 3.699038 CACTCCCTGTTGACCTTCAAAAA 59.301 43.478 0.00 0.00 38.22 1.94
4791 5332 3.287222 CACTCCCTGTTGACCTTCAAAA 58.713 45.455 0.00 0.00 38.22 2.44
4792 5333 2.422803 CCACTCCCTGTTGACCTTCAAA 60.423 50.000 0.00 0.00 38.22 2.69
4793 5334 1.142870 CCACTCCCTGTTGACCTTCAA 59.857 52.381 0.00 0.00 33.32 2.69
4794 5335 0.764890 CCACTCCCTGTTGACCTTCA 59.235 55.000 0.00 0.00 0.00 3.02
4795 5336 0.036875 CCCACTCCCTGTTGACCTTC 59.963 60.000 0.00 0.00 0.00 3.46
4798 5339 2.757077 CCCCACTCCCTGTTGACC 59.243 66.667 0.00 0.00 0.00 4.02
4799 5340 2.757077 CCCCCACTCCCTGTTGAC 59.243 66.667 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.