Multiple sequence alignment - TraesCS2A01G474400

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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 TraesCS2A01G474400 chr2A 100.000 6449 0 0 1 6449 715427279 715420831 0.000000e+00 11910.0
1 TraesCS2A01G474400 chr2A 84.494 316 37 9 3508 3819 715423032 715422725 1.050000e-77 302.0
2 TraesCS2A01G474400 chr2A 84.494 316 37 9 4248 4555 715423772 715423461 1.050000e-77 302.0
3 TraesCS2A01G474400 chr2A 77.621 496 92 10 2480 2961 692327975 692327485 3.810000e-72 283.0
4 TraesCS2A01G474400 chr2A 91.716 169 13 1 2033 2200 765962677 765962509 3.890000e-57 233.0
5 TraesCS2A01G474400 chr2A 91.124 169 14 1 2033 2200 565216744 565216912 1.810000e-55 228.0
6 TraesCS2A01G474400 chr2D 96.079 4285 106 19 2202 6449 577344786 577340527 0.000000e+00 6926.0
7 TraesCS2A01G474400 chr2D 96.128 1627 42 5 412 2033 577346397 577344787 0.000000e+00 2636.0
8 TraesCS2A01G474400 chr2D 83.529 680 85 15 1365 2032 551704401 551703737 1.540000e-170 610.0
9 TraesCS2A01G474400 chr2D 90.778 347 13 11 1 344 577346729 577346399 4.590000e-121 446.0
10 TraesCS2A01G474400 chr2D 80.242 496 81 9 2480 2961 551821810 551821318 2.210000e-94 357.0
11 TraesCS2A01G474400 chr2D 86.120 317 34 7 3507 3819 577342721 577342411 3.730000e-87 333.0
12 TraesCS2A01G474400 chr2D 85.127 316 35 8 4248 4555 577343487 577343176 4.850000e-81 313.0
13 TraesCS2A01G474400 chr2B 93.763 2854 122 22 3631 6449 694474118 694471286 0.000000e+00 4233.0
14 TraesCS2A01G474400 chr2B 93.671 2607 111 25 3874 6449 694421805 694419222 0.000000e+00 3851.0
15 TraesCS2A01G474400 chr2B 94.237 2169 92 16 3874 6029 694442584 694440436 0.000000e+00 3282.0
16 TraesCS2A01G474400 chr2B 92.521 1658 91 12 2217 3874 694444270 694442646 0.000000e+00 2344.0
17 TraesCS2A01G474400 chr2B 92.410 1660 93 11 2217 3874 694423493 694421865 0.000000e+00 2337.0
18 TraesCS2A01G474400 chr2B 90.072 1672 138 15 385 2032 694477234 694475567 0.000000e+00 2143.0
19 TraesCS2A01G474400 chr2B 91.476 1443 102 13 606 2032 694424958 694423521 0.000000e+00 1964.0
20 TraesCS2A01G474400 chr2B 91.748 1430 91 9 2217 3646 694475539 694474137 0.000000e+00 1962.0
21 TraesCS2A01G474400 chr2B 91.256 1441 109 11 606 2032 694445735 694444298 0.000000e+00 1947.0
22 TraesCS2A01G474400 chr2B 93.617 376 21 3 6076 6449 694440435 694440061 5.650000e-155 558.0
23 TraesCS2A01G474400 chr2B 92.405 316 18 5 1 311 694425894 694425580 4.590000e-121 446.0
24 TraesCS2A01G474400 chr2B 92.089 316 19 5 1 311 694446671 694446357 2.130000e-119 440.0
25 TraesCS2A01G474400 chr2B 90.596 319 21 5 1 311 694477554 694477237 1.290000e-111 414.0
26 TraesCS2A01G474400 chr2B 85.759 316 34 6 3507 3819 694442209 694441902 2.240000e-84 324.0
27 TraesCS2A01G474400 chr2B 85.580 319 34 7 3507 3821 694473486 694473176 2.240000e-84 324.0
28 TraesCS2A01G474400 chr2B 85.127 316 37 5 3507 3819 694421430 694421122 1.350000e-81 315.0
29 TraesCS2A01G474400 chr2B 86.873 259 25 4 3257 3509 694421713 694421458 1.370000e-71 281.0
30 TraesCS2A01G474400 chr2B 86.486 259 26 4 3257 3509 694442492 694442237 6.370000e-70 276.0
31 TraesCS2A01G474400 chr2B 86.486 259 23 6 3965 4219 694422478 694422228 2.290000e-69 274.0
32 TraesCS2A01G474400 chr2B 86.100 259 27 4 3257 3509 694473769 694473514 2.960000e-68 270.0
33 TraesCS2A01G474400 chr2B 86.100 259 24 7 3965 4219 694474524 694474274 1.070000e-67 268.0
34 TraesCS2A01G474400 chr2B 86.100 259 23 7 3965 4219 694443258 694443009 3.830000e-67 267.0
35 TraesCS2A01G474400 chr2B 90.566 53 5 0 531 583 694425005 694424953 3.230000e-08 71.3
36 TraesCS2A01G474400 chr2B 88.679 53 6 0 531 583 694445782 694445730 1.500000e-06 65.8
37 TraesCS2A01G474400 chr5B 81.693 874 128 24 4547 5403 57719021 57718163 0.000000e+00 699.0
38 TraesCS2A01G474400 chr5B 84.783 414 53 7 1369 1775 57722364 57721954 2.160000e-109 407.0
39 TraesCS2A01G474400 chr5B 88.636 220 20 5 5399 5616 57716684 57716468 4.960000e-66 263.0
40 TraesCS2A01G474400 chr5B 88.038 209 20 5 5454 5661 57716471 57716267 6.460000e-60 243.0
41 TraesCS2A01G474400 chr5B 76.699 309 34 15 9 281 582105488 582105182 3.140000e-28 137.0
42 TraesCS2A01G474400 chr5B 84.483 116 14 4 84 196 571205646 571205760 1.900000e-20 111.0
43 TraesCS2A01G474400 chr5D 89.027 565 57 2 4839 5403 464114963 464115522 0.000000e+00 695.0
44 TraesCS2A01G474400 chr5D 83.696 460 72 1 2501 2960 464106921 464107377 1.280000e-116 431.0
45 TraesCS2A01G474400 chr5D 85.407 418 49 7 1366 1775 464111276 464111689 2.150000e-114 424.0
46 TraesCS2A01G474400 chr5D 82.495 457 66 8 2511 2960 474821391 474820942 7.840000e-104 388.0
47 TraesCS2A01G474400 chr5D 76.788 685 96 35 678 1306 474822752 474822075 6.240000e-85 326.0
48 TraesCS2A01G474400 chr5D 88.636 220 19 6 5399 5616 464116982 464117197 4.960000e-66 263.0
49 TraesCS2A01G474400 chr5D 80.693 202 22 11 84 273 464110068 464110264 2.420000e-29 141.0
50 TraesCS2A01G474400 chr5A 87.986 566 61 5 4839 5403 43656383 43655824 0.000000e+00 662.0
51 TraesCS2A01G474400 chr5A 87.633 566 63 5 4839 5403 43742283 43741724 0.000000e+00 651.0
52 TraesCS2A01G474400 chr5A 87.456 566 64 5 4839 5403 43694752 43694193 0.000000e+00 645.0
53 TraesCS2A01G474400 chr5A 85.749 414 49 5 1369 1775 43699836 43699426 4.620000e-116 429.0
54 TraesCS2A01G474400 chr5A 85.301 415 49 7 1369 1775 43659923 43659513 1.000000e-112 418.0
55 TraesCS2A01G474400 chr5A 85.266 414 51 5 1369 1775 43745979 43745569 1.000000e-112 418.0
56 TraesCS2A01G474400 chr5A 79.430 491 67 13 2480 2960 584549912 584550378 3.750000e-82 316.0
57 TraesCS2A01G474400 chr5A 89.202 213 20 3 5399 5610 43612676 43612466 4.960000e-66 263.0
58 TraesCS2A01G474400 chr5A 87.560 209 23 3 5454 5661 43612464 43612258 8.360000e-59 239.0
59 TraesCS2A01G474400 chr7B 82.744 481 68 9 2480 2948 626565899 626565422 1.290000e-111 414.0
60 TraesCS2A01G474400 chr7B 76.774 310 33 20 9 281 626562799 626562492 3.140000e-28 137.0
61 TraesCS2A01G474400 chr4A 96.450 169 5 1 2033 2200 613568695 613568863 1.770000e-70 278.0
62 TraesCS2A01G474400 chr7A 95.858 169 6 1 2033 2200 23351051 23350883 8.240000e-69 272.0
63 TraesCS2A01G474400 chr1A 95.858 169 6 1 2033 2200 570158950 570159118 8.240000e-69 272.0
64 TraesCS2A01G474400 chr6A 95.152 165 7 1 2037 2200 18464790 18464626 6.410000e-65 259.0
65 TraesCS2A01G474400 chr6A 94.340 159 7 2 2033 2189 11769717 11769559 6.460000e-60 243.0
66 TraesCS2A01G474400 chr3A 94.083 169 8 2 2033 2200 652496497 652496330 8.300000e-64 255.0
67 TraesCS2A01G474400 chr3A 92.857 168 11 1 2033 2199 652291524 652291357 6.460000e-60 243.0
68 TraesCS2A01G474400 chr7D 79.710 207 30 8 84 279 570992615 570992820 8.720000e-29 139.0


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 TraesCS2A01G474400 chr2A 715420831 715427279 6448 True 11910.000000 11910 100.000000 1 6449 1 chr2A.!!$R2 6448
1 TraesCS2A01G474400 chr2A 715422725 715423772 1047 True 302.000000 302 84.494000 3508 4555 2 chr2A.!!$R4 1047
2 TraesCS2A01G474400 chr2D 577340527 577346729 6202 True 2130.800000 6926 90.846400 1 6449 5 chr2D.!!$R3 6448
3 TraesCS2A01G474400 chr2D 551703737 551704401 664 True 610.000000 610 83.529000 1365 2032 1 chr2D.!!$R1 667
4 TraesCS2A01G474400 chr2B 694471286 694477554 6268 True 1373.428571 4233 89.137000 1 6449 7 chr2B.!!$R3 6448
5 TraesCS2A01G474400 chr2B 694419222 694425894 6672 True 1192.412500 3851 89.876750 1 6449 8 chr2B.!!$R1 6448
6 TraesCS2A01G474400 chr2B 694440061 694446671 6610 True 1055.977778 3282 90.082667 1 6449 9 chr2B.!!$R2 6448
7 TraesCS2A01G474400 chr5B 57716267 57722364 6097 True 403.000000 699 85.787500 1369 5661 4 chr5B.!!$R2 4292
8 TraesCS2A01G474400 chr5D 464106921 464117197 10276 False 390.800000 695 85.491800 84 5616 5 chr5D.!!$F1 5532
9 TraesCS2A01G474400 chr5D 474820942 474822752 1810 True 357.000000 388 79.641500 678 2960 2 chr5D.!!$R1 2282
10 TraesCS2A01G474400 chr5A 43694193 43694752 559 True 645.000000 645 87.456000 4839 5403 1 chr5A.!!$R1 564
11 TraesCS2A01G474400 chr5A 43655824 43659923 4099 True 540.000000 662 86.643500 1369 5403 2 chr5A.!!$R4 4034
12 TraesCS2A01G474400 chr5A 43741724 43745979 4255 True 534.500000 651 86.449500 1369 5403 2 chr5A.!!$R5 4034
13 TraesCS2A01G474400 chr7B 626562492 626565899 3407 True 275.500000 414 79.759000 9 2948 2 chr7B.!!$R1 2939

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
410 3500 0.679321 TTGTGTGCACTGGTGAAGCA 60.679 50.000 19.41 1.65 35.63 3.91 F
2080 5864 0.109919 GCGGCGACCCTTAAAAACAG 60.110 55.000 12.98 0.00 0.00 3.16 F
2101 5885 1.067821 CTATAGCTGGCTATAGCGGGC 59.932 57.143 26.42 23.96 46.26 6.13 F
2165 5949 1.109323 GGCAACACCCTCAAACAGCT 61.109 55.000 0.00 0.00 0.00 4.24 F
2181 5965 1.153349 GCTATAGCGGGGCCATAGC 60.153 63.158 15.36 15.36 40.10 2.97 F
3484 7345 1.208293 CCAGGAAGTCCAAGGCTACTC 59.792 57.143 0.00 0.00 38.89 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2143 5927 0.033601 TGTTTGAGGGTGTTGCCACT 60.034 50.000 0.00 0.0 41.53 4.00 R
3075 6902 0.250252 TTCTGTTGCTGCGATGGTGA 60.250 50.000 0.00 0.0 0.00 4.02 R
3408 7265 2.807967 TGCACACAGTCACAATTAGCTC 59.192 45.455 0.00 0.0 0.00 4.09 R
4634 10117 3.009026 CGATGACATGACCAATTGACCA 58.991 45.455 7.12 4.6 0.00 4.02 R
4638 10121 2.941064 AGCTCGATGACATGACCAATTG 59.059 45.455 0.00 0.0 0.00 2.32 R
5774 13385 0.034670 GAGCCCATGACAGCTTTCCT 60.035 55.000 0.00 0.0 40.11 3.36 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
87 88 6.541934 TGGTGCAAATTTGAATCATCCATA 57.458 33.333 22.31 0.00 0.00 2.74
102 3168 6.057321 TCATCCATATATGCATGCTCTTGA 57.943 37.500 20.33 6.74 0.00 3.02
106 3172 7.387119 TCCATATATGCATGCTCTTGATTTC 57.613 36.000 20.33 0.00 0.00 2.17
301 3391 1.537638 TGCCGCGACACAAAATTATGT 59.462 42.857 8.23 0.00 0.00 2.29
403 3493 5.175127 TGTATGTATACTTGTGTGCACTGG 58.825 41.667 19.41 7.78 34.41 4.00
404 3494 3.762407 TGTATACTTGTGTGCACTGGT 57.238 42.857 19.41 12.99 0.00 4.00
406 3496 2.928801 ATACTTGTGTGCACTGGTGA 57.071 45.000 19.41 0.00 0.00 4.02
410 3500 0.679321 TTGTGTGCACTGGTGAAGCA 60.679 50.000 19.41 1.65 35.63 3.91
454 3544 1.144936 CCCGCCTCAGCCTTTCTAG 59.855 63.158 0.00 0.00 34.57 2.43
469 3559 4.323485 CCTTTCTAGATACACCCAGCACAA 60.323 45.833 0.00 0.00 0.00 3.33
483 3574 2.526873 ACAACCTCACCTCGCCCT 60.527 61.111 0.00 0.00 0.00 5.19
534 4050 6.466885 AGCCGAAAAGATTAGCTTAGTAGA 57.533 37.500 0.00 0.00 35.24 2.59
578 4094 2.573869 CATCTCTCGTGCCGTGGT 59.426 61.111 0.00 0.00 0.00 4.16
1313 5040 4.471386 TGATAAAGAGGAGGAGTTGAAGGG 59.529 45.833 0.00 0.00 0.00 3.95
1352 5079 3.306472 TTGCCCACAGTTCTTTAGGTT 57.694 42.857 0.00 0.00 0.00 3.50
1494 5223 2.640316 AGGTTCTCTTTCCGTTTGCT 57.360 45.000 0.00 0.00 0.00 3.91
1668 5410 8.972349 CATATCCGCAACATATATGAGTATGTC 58.028 37.037 19.63 7.81 42.79 3.06
1930 5714 5.556915 TCAAACATGTCACTACTAAAGGGG 58.443 41.667 0.00 0.00 0.00 4.79
1936 5720 3.007614 TGTCACTACTAAAGGGGCAGAAC 59.992 47.826 0.00 0.00 38.68 3.01
2035 5819 2.996249 CATCAGTGGAGTGCCTATGT 57.004 50.000 0.00 0.00 34.31 2.29
2036 5820 3.272574 CATCAGTGGAGTGCCTATGTT 57.727 47.619 0.00 0.00 34.31 2.71
2037 5821 3.614092 CATCAGTGGAGTGCCTATGTTT 58.386 45.455 0.00 0.00 34.31 2.83
2038 5822 3.788227 TCAGTGGAGTGCCTATGTTTT 57.212 42.857 0.00 0.00 34.31 2.43
2039 5823 4.901197 TCAGTGGAGTGCCTATGTTTTA 57.099 40.909 0.00 0.00 34.31 1.52
2040 5824 5.235850 TCAGTGGAGTGCCTATGTTTTAA 57.764 39.130 0.00 0.00 34.31 1.52
2041 5825 5.626142 TCAGTGGAGTGCCTATGTTTTAAA 58.374 37.500 0.00 0.00 34.31 1.52
2042 5826 6.245408 TCAGTGGAGTGCCTATGTTTTAAAT 58.755 36.000 0.00 0.00 34.31 1.40
2043 5827 7.398829 TCAGTGGAGTGCCTATGTTTTAAATA 58.601 34.615 0.00 0.00 34.31 1.40
2044 5828 7.552687 TCAGTGGAGTGCCTATGTTTTAAATAG 59.447 37.037 0.00 0.00 34.31 1.73
2045 5829 6.318900 AGTGGAGTGCCTATGTTTTAAATAGC 59.681 38.462 0.00 0.00 34.31 2.97
2046 5830 5.295787 TGGAGTGCCTATGTTTTAAATAGCG 59.704 40.000 0.00 0.00 34.31 4.26
2047 5831 5.277828 GGAGTGCCTATGTTTTAAATAGCGG 60.278 44.000 0.00 0.00 0.00 5.52
2048 5832 4.578928 AGTGCCTATGTTTTAAATAGCGGG 59.421 41.667 0.00 0.00 0.00 6.13
2049 5833 3.316868 TGCCTATGTTTTAAATAGCGGGC 59.683 43.478 12.19 12.19 0.00 6.13
2050 5834 3.568430 GCCTATGTTTTAAATAGCGGGCT 59.432 43.478 11.96 0.00 0.00 5.19
2051 5835 4.758165 GCCTATGTTTTAAATAGCGGGCTA 59.242 41.667 2.42 2.42 0.00 3.93
2052 5836 5.414765 GCCTATGTTTTAAATAGCGGGCTAT 59.585 40.000 7.36 7.36 40.63 2.97
2053 5837 6.622896 GCCTATGTTTTAAATAGCGGGCTATG 60.623 42.308 13.53 0.00 39.03 2.23
2054 5838 5.705609 ATGTTTTAAATAGCGGGCTATGG 57.294 39.130 13.53 0.00 39.03 2.74
2055 5839 3.316868 TGTTTTAAATAGCGGGCTATGGC 59.683 43.478 13.53 0.00 39.03 4.40
2056 5840 2.940994 TTAAATAGCGGGCTATGGCA 57.059 45.000 13.53 0.00 39.03 4.92
2057 5841 3.433306 TTAAATAGCGGGCTATGGCAT 57.567 42.857 13.53 4.88 39.03 4.40
2058 5842 2.292828 AAATAGCGGGCTATGGCATT 57.707 45.000 13.53 2.26 39.03 3.56
2059 5843 2.292828 AATAGCGGGCTATGGCATTT 57.707 45.000 13.53 0.00 39.03 2.32
2060 5844 3.433306 AATAGCGGGCTATGGCATTTA 57.567 42.857 13.53 0.00 39.03 1.40
2061 5845 2.472695 TAGCGGGCTATGGCATTTAG 57.527 50.000 4.78 0.00 40.87 1.85
2062 5846 0.890996 AGCGGGCTATGGCATTTAGC 60.891 55.000 12.79 12.79 41.08 3.09
2071 5855 2.513897 GCATTTAGCGGCGACCCT 60.514 61.111 12.98 0.00 0.00 4.34
2072 5856 2.112815 GCATTTAGCGGCGACCCTT 61.113 57.895 12.98 0.00 0.00 3.95
2073 5857 0.812412 GCATTTAGCGGCGACCCTTA 60.812 55.000 12.98 0.00 0.00 2.69
2074 5858 1.658994 CATTTAGCGGCGACCCTTAA 58.341 50.000 12.98 0.00 0.00 1.85
2075 5859 2.011222 CATTTAGCGGCGACCCTTAAA 58.989 47.619 12.98 7.21 0.00 1.52
2076 5860 2.181954 TTTAGCGGCGACCCTTAAAA 57.818 45.000 12.98 0.00 0.00 1.52
2077 5861 2.181954 TTAGCGGCGACCCTTAAAAA 57.818 45.000 12.98 0.00 0.00 1.94
2078 5862 1.441738 TAGCGGCGACCCTTAAAAAC 58.558 50.000 12.98 0.00 0.00 2.43
2079 5863 0.535553 AGCGGCGACCCTTAAAAACA 60.536 50.000 12.98 0.00 0.00 2.83
2080 5864 0.109919 GCGGCGACCCTTAAAAACAG 60.110 55.000 12.98 0.00 0.00 3.16
2081 5865 0.109919 CGGCGACCCTTAAAAACAGC 60.110 55.000 0.00 0.00 0.00 4.40
2082 5866 1.244816 GGCGACCCTTAAAAACAGCT 58.755 50.000 0.00 0.00 0.00 4.24
2083 5867 2.429478 GGCGACCCTTAAAAACAGCTA 58.571 47.619 0.00 0.00 0.00 3.32
2084 5868 3.014623 GGCGACCCTTAAAAACAGCTAT 58.985 45.455 0.00 0.00 0.00 2.97
2085 5869 4.193865 GGCGACCCTTAAAAACAGCTATA 58.806 43.478 0.00 0.00 0.00 1.31
2086 5870 4.272748 GGCGACCCTTAAAAACAGCTATAG 59.727 45.833 0.00 0.00 0.00 1.31
2087 5871 4.260661 GCGACCCTTAAAAACAGCTATAGC 60.261 45.833 17.33 17.33 42.49 2.97
2101 5885 1.067821 CTATAGCTGGCTATAGCGGGC 59.932 57.143 26.42 23.96 46.26 6.13
2102 5886 3.274250 CTATAGCTGGCTATAGCGGGCT 61.274 54.545 31.15 31.15 46.26 5.19
2103 5887 3.377656 GCTGGCTATAGCGGGCTA 58.622 61.111 24.04 2.42 43.26 3.93
2104 5888 1.901085 GCTGGCTATAGCGGGCTAT 59.099 57.895 24.04 16.61 43.26 2.97
2105 5889 1.112113 GCTGGCTATAGCGGGCTATA 58.888 55.000 24.04 17.02 43.26 1.31
2110 5894 1.676746 CTATAGCGGGCTATAGCGGA 58.323 55.000 26.16 7.19 46.26 5.54
2111 5895 1.604755 CTATAGCGGGCTATAGCGGAG 59.395 57.143 26.16 12.52 46.26 4.63
2112 5896 1.668101 ATAGCGGGCTATAGCGGAGC 61.668 60.000 22.13 22.13 42.31 4.70
2131 5915 3.706994 GCTATAGCGGCAAATTCTACG 57.293 47.619 9.40 0.00 0.00 3.51
2132 5916 3.057734 GCTATAGCGGCAAATTCTACGT 58.942 45.455 9.40 0.00 0.00 3.57
2133 5917 3.120991 GCTATAGCGGCAAATTCTACGTG 60.121 47.826 9.40 0.00 0.00 4.49
2134 5918 2.658373 TAGCGGCAAATTCTACGTGA 57.342 45.000 1.45 0.00 0.00 4.35
2135 5919 1.803334 AGCGGCAAATTCTACGTGAA 58.197 45.000 1.45 0.03 39.24 3.18
2136 5920 2.147958 AGCGGCAAATTCTACGTGAAA 58.852 42.857 1.45 0.00 38.29 2.69
2137 5921 2.747446 AGCGGCAAATTCTACGTGAAAT 59.253 40.909 1.45 0.00 38.29 2.17
2138 5922 3.098636 GCGGCAAATTCTACGTGAAATC 58.901 45.455 0.00 0.00 38.29 2.17
2139 5923 3.425625 GCGGCAAATTCTACGTGAAATCA 60.426 43.478 0.00 0.00 38.29 2.57
2140 5924 4.730613 GCGGCAAATTCTACGTGAAATCAT 60.731 41.667 0.00 0.00 38.29 2.45
2141 5925 5.331902 CGGCAAATTCTACGTGAAATCATT 58.668 37.500 0.00 0.00 38.29 2.57
2142 5926 5.799936 CGGCAAATTCTACGTGAAATCATTT 59.200 36.000 0.00 0.00 38.29 2.32
2143 5927 6.964370 CGGCAAATTCTACGTGAAATCATTTA 59.036 34.615 0.00 0.00 38.29 1.40
2144 5928 7.164171 CGGCAAATTCTACGTGAAATCATTTAG 59.836 37.037 0.00 0.00 38.29 1.85
2145 5929 7.968405 GGCAAATTCTACGTGAAATCATTTAGT 59.032 33.333 0.00 0.00 38.29 2.24
2146 5930 8.788813 GCAAATTCTACGTGAAATCATTTAGTG 58.211 33.333 0.00 0.00 38.29 2.74
2147 5931 9.277565 CAAATTCTACGTGAAATCATTTAGTGG 57.722 33.333 0.00 0.00 38.29 4.00
2148 5932 6.417191 TTCTACGTGAAATCATTTAGTGGC 57.583 37.500 0.00 0.00 0.00 5.01
2149 5933 5.483811 TCTACGTGAAATCATTTAGTGGCA 58.516 37.500 0.00 0.00 0.00 4.92
2150 5934 5.935206 TCTACGTGAAATCATTTAGTGGCAA 59.065 36.000 0.00 0.00 0.00 4.52
2151 5935 4.794169 ACGTGAAATCATTTAGTGGCAAC 58.206 39.130 0.00 0.00 0.00 4.17
2163 5947 2.805897 TGGCAACACCCTCAAACAG 58.194 52.632 0.00 0.00 46.17 3.16
2164 5948 1.363807 GGCAACACCCTCAAACAGC 59.636 57.895 0.00 0.00 0.00 4.40
2165 5949 1.109323 GGCAACACCCTCAAACAGCT 61.109 55.000 0.00 0.00 0.00 4.24
2166 5950 1.604604 GCAACACCCTCAAACAGCTA 58.395 50.000 0.00 0.00 0.00 3.32
2167 5951 2.162681 GCAACACCCTCAAACAGCTAT 58.837 47.619 0.00 0.00 0.00 2.97
2168 5952 3.343617 GCAACACCCTCAAACAGCTATA 58.656 45.455 0.00 0.00 0.00 1.31
2169 5953 3.375299 GCAACACCCTCAAACAGCTATAG 59.625 47.826 0.00 0.00 0.00 1.31
2170 5954 3.268023 ACACCCTCAAACAGCTATAGC 57.732 47.619 17.33 17.33 42.49 2.97
2181 5965 1.153349 GCTATAGCGGGGCCATAGC 60.153 63.158 15.36 15.36 40.10 2.97
2199 5983 6.842163 CCATAGCCGGCTATTTAAAACTATG 58.158 40.000 40.13 28.11 37.16 2.23
2244 6039 1.341080 TGACCATGTCAGCACTCTGA 58.659 50.000 0.00 0.00 46.43 3.27
2439 6236 4.947645 ACATAAAATCCATCGGCCATTTG 58.052 39.130 2.24 0.00 0.00 2.32
3277 7134 6.360370 AGAAGCATTAGGTGACAGTTTAGA 57.640 37.500 0.00 0.00 0.00 2.10
3484 7345 1.208293 CCAGGAAGTCCAAGGCTACTC 59.792 57.143 0.00 0.00 38.89 2.59
4654 10137 5.345702 CAATGGTCAATTGGTCATGTCATC 58.654 41.667 5.42 0.00 41.80 2.92
4691 10179 5.345202 GCGCATATAGTTCATACAGGTGTAC 59.655 44.000 0.30 0.00 32.72 2.90
4786 10274 4.201822 GCTCAGTTCCCGATGTTCAATAAC 60.202 45.833 0.00 0.00 36.07 1.89
5071 10621 6.876789 TGTGTCGTACTTCATGGTAATTGATT 59.123 34.615 0.00 0.00 0.00 2.57
5072 10622 7.148490 TGTGTCGTACTTCATGGTAATTGATTG 60.148 37.037 0.00 0.00 0.00 2.67
5157 10711 3.603532 GACACTGCAGATCATTCCAGAA 58.396 45.455 23.35 0.00 0.00 3.02
5352 10906 0.247736 GTGTGTTCGAGCTCCTGGAT 59.752 55.000 8.47 0.00 0.00 3.41
5429 12467 1.229145 CCCTGGCCCCAAAACATCA 60.229 57.895 0.00 0.00 0.00 3.07
5753 13364 1.583054 GCTTAAGTACGGGATGCCAG 58.417 55.000 3.39 0.00 0.00 4.85
5789 13400 4.589216 TTTTTGAGGAAAGCTGTCATGG 57.411 40.909 6.17 0.00 0.00 3.66
5790 13401 2.205022 TTGAGGAAAGCTGTCATGGG 57.795 50.000 6.17 0.00 0.00 4.00
5791 13402 0.322816 TGAGGAAAGCTGTCATGGGC 60.323 55.000 6.17 0.00 0.00 5.36
5862 13478 1.945394 CAGCCAAAATCAGGAGGATCG 59.055 52.381 0.00 0.00 34.28 3.69
5978 13594 8.122952 AGAGAAATTGTGACAAAGAAAAGTACG 58.877 33.333 0.62 0.00 0.00 3.67
6157 13780 2.087009 GCGGACCTCGAGTTTGACG 61.087 63.158 12.31 9.45 42.43 4.35
6169 13792 2.448582 TTTGACGACAGGGGGTGCT 61.449 57.895 0.00 0.00 0.00 4.40
6323 13949 3.739922 TGGCACCCCCACTAGATG 58.260 61.111 0.00 0.00 39.18 2.90
6435 14061 2.651361 CGAGCCAGTGTCCTCGTT 59.349 61.111 17.49 0.00 44.25 3.85
6441 14067 0.393077 CCAGTGTCCTCGTTGAAGGT 59.607 55.000 0.00 0.00 37.69 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 5.382616 TCAGGAAATCAAGAGCATGCATAT 58.617 37.500 21.98 0.00 0.00 1.78
102 3168 5.935789 CCATTCTTGTGCAAATTCAGGAAAT 59.064 36.000 4.13 0.00 34.41 2.17
106 3172 4.240096 GACCATTCTTGTGCAAATTCAGG 58.760 43.478 0.00 0.00 0.00 3.86
202 3277 6.384015 TGTCTGATCTATCCATTAACAGTGGT 59.616 38.462 0.00 0.00 37.96 4.16
203 3278 6.820335 TGTCTGATCTATCCATTAACAGTGG 58.180 40.000 0.00 0.00 38.11 4.00
212 3289 5.908590 TGATACCCTGTCTGATCTATCCAT 58.091 41.667 0.00 0.00 0.00 3.41
374 3464 9.471084 GTGCACACAAGTATACATACATACATA 57.529 33.333 13.17 0.00 34.42 2.29
403 3493 1.448985 TTGCCCTAACGATGCTTCAC 58.551 50.000 0.08 0.00 0.00 3.18
404 3494 2.192664 TTTGCCCTAACGATGCTTCA 57.807 45.000 0.08 0.00 0.00 3.02
406 3496 2.228822 CACTTTTGCCCTAACGATGCTT 59.771 45.455 0.00 0.00 0.00 3.91
410 3500 2.812011 GACACACTTTTGCCCTAACGAT 59.188 45.455 0.00 0.00 0.00 3.73
454 3544 1.003118 TGAGGTTGTGCTGGGTGTATC 59.997 52.381 0.00 0.00 0.00 2.24
483 3574 2.752358 CCCACCTCTTGCTGAGCA 59.248 61.111 1.40 1.40 41.35 4.26
534 4050 1.512926 CTTGGCACTACTTCACGCTT 58.487 50.000 0.00 0.00 0.00 4.68
890 4439 9.811995 GGCGAAGGTAACAATGATGTATATATA 57.188 33.333 0.00 0.00 39.40 0.86
898 4449 4.433186 TTTGGCGAAGGTAACAATGATG 57.567 40.909 0.00 0.00 41.41 3.07
1341 5068 6.473758 ACTGGTCATTAGGAACCTAAAGAAC 58.526 40.000 20.23 20.23 41.54 3.01
1494 5223 2.375174 AGCACCATTCCTAAAGTGGACA 59.625 45.455 0.00 0.00 35.58 4.02
1758 5503 4.653341 TCACTTGGCATTATATTTTGGGGG 59.347 41.667 0.00 0.00 0.00 5.40
1930 5714 3.423571 CATCAAAAGCGATCAGTTCTGC 58.576 45.455 0.00 0.00 0.00 4.26
1936 5720 1.202222 GCACCCATCAAAAGCGATCAG 60.202 52.381 0.00 0.00 0.00 2.90
2032 5816 4.022329 GCCATAGCCCGCTATTTAAAACAT 60.022 41.667 6.48 0.00 37.16 2.71
2033 5817 3.316868 GCCATAGCCCGCTATTTAAAACA 59.683 43.478 6.48 0.00 37.16 2.83
2034 5818 3.316868 TGCCATAGCCCGCTATTTAAAAC 59.683 43.478 6.48 0.00 37.16 2.43
2035 5819 3.556999 TGCCATAGCCCGCTATTTAAAA 58.443 40.909 6.48 0.00 37.16 1.52
2036 5820 3.216187 TGCCATAGCCCGCTATTTAAA 57.784 42.857 6.48 0.00 37.16 1.52
2037 5821 2.940994 TGCCATAGCCCGCTATTTAA 57.059 45.000 6.48 0.00 37.16 1.52
2038 5822 3.433306 AATGCCATAGCCCGCTATTTA 57.567 42.857 6.48 0.00 37.16 1.40
2039 5823 2.292828 AATGCCATAGCCCGCTATTT 57.707 45.000 6.48 0.00 37.16 1.40
2040 5824 2.292828 AAATGCCATAGCCCGCTATT 57.707 45.000 6.48 0.00 37.16 1.73
2041 5825 2.941415 GCTAAATGCCATAGCCCGCTAT 60.941 50.000 3.31 3.31 39.87 2.97
2042 5826 1.610624 GCTAAATGCCATAGCCCGCTA 60.611 52.381 0.00 0.00 39.87 4.26
2043 5827 0.890996 GCTAAATGCCATAGCCCGCT 60.891 55.000 0.00 0.00 39.87 5.52
2044 5828 1.581447 GCTAAATGCCATAGCCCGC 59.419 57.895 2.08 0.00 39.87 6.13
2045 5829 1.577328 CCGCTAAATGCCATAGCCCG 61.577 60.000 6.85 0.00 42.18 6.13
2046 5830 1.866853 GCCGCTAAATGCCATAGCCC 61.867 60.000 6.85 0.00 42.18 5.19
2047 5831 1.581447 GCCGCTAAATGCCATAGCC 59.419 57.895 6.85 0.00 42.18 3.93
2048 5832 1.207593 CGCCGCTAAATGCCATAGC 59.792 57.895 3.20 3.20 41.85 2.97
2049 5833 0.512952 GTCGCCGCTAAATGCCATAG 59.487 55.000 0.00 0.00 38.78 2.23
2050 5834 0.882927 GGTCGCCGCTAAATGCCATA 60.883 55.000 0.00 0.00 38.78 2.74
2051 5835 2.186826 GGTCGCCGCTAAATGCCAT 61.187 57.895 0.00 0.00 38.78 4.40
2052 5836 2.822255 GGTCGCCGCTAAATGCCA 60.822 61.111 0.00 0.00 38.78 4.92
2053 5837 3.583086 GGGTCGCCGCTAAATGCC 61.583 66.667 0.00 0.00 38.78 4.40
2054 5838 0.812412 TAAGGGTCGCCGCTAAATGC 60.812 55.000 0.00 0.00 38.57 3.56
2055 5839 1.658994 TTAAGGGTCGCCGCTAAATG 58.341 50.000 0.00 0.00 32.78 2.32
2056 5840 2.406596 TTTAAGGGTCGCCGCTAAAT 57.593 45.000 0.00 0.00 32.78 1.40
2057 5841 2.181954 TTTTAAGGGTCGCCGCTAAA 57.818 45.000 0.00 0.00 32.78 1.85
2058 5842 1.805943 GTTTTTAAGGGTCGCCGCTAA 59.194 47.619 0.00 0.00 32.78 3.09
2059 5843 1.270732 TGTTTTTAAGGGTCGCCGCTA 60.271 47.619 0.00 0.00 32.78 4.26
2060 5844 0.535553 TGTTTTTAAGGGTCGCCGCT 60.536 50.000 0.00 0.00 34.93 5.52
2061 5845 0.109919 CTGTTTTTAAGGGTCGCCGC 60.110 55.000 0.00 0.00 0.00 6.53
2062 5846 0.109919 GCTGTTTTTAAGGGTCGCCG 60.110 55.000 0.00 0.00 0.00 6.46
2063 5847 1.244816 AGCTGTTTTTAAGGGTCGCC 58.755 50.000 0.00 0.00 0.00 5.54
2064 5848 4.260661 GCTATAGCTGTTTTTAAGGGTCGC 60.261 45.833 17.75 0.00 38.21 5.19
2065 5849 5.405331 GCTATAGCTGTTTTTAAGGGTCG 57.595 43.478 17.75 0.00 38.21 4.79
2082 5866 1.112113 GCCCGCTATAGCCAGCTATA 58.888 55.000 19.00 16.46 39.65 1.31
2083 5867 0.616111 AGCCCGCTATAGCCAGCTAT 60.616 55.000 26.56 15.98 42.03 2.97
2084 5868 0.039180 TAGCCCGCTATAGCCAGCTA 59.961 55.000 27.41 27.41 43.12 3.32
2085 5869 0.616111 ATAGCCCGCTATAGCCAGCT 60.616 55.000 28.99 28.99 44.68 4.24
2086 5870 1.067821 CTATAGCCCGCTATAGCCAGC 59.932 57.143 23.85 19.96 46.26 4.85
2092 5876 1.676746 CTCCGCTATAGCCCGCTATA 58.323 55.000 19.00 14.20 39.65 1.31
2093 5877 1.668101 GCTCCGCTATAGCCCGCTAT 61.668 60.000 19.00 13.46 41.58 2.97
2094 5878 2.341101 GCTCCGCTATAGCCCGCTA 61.341 63.158 19.00 0.00 37.91 4.26
2095 5879 2.766306 TAGCTCCGCTATAGCCCGCT 62.766 60.000 24.41 24.41 41.02 5.52
2096 5880 2.341101 TAGCTCCGCTATAGCCCGC 61.341 63.158 19.00 17.12 41.02 6.13
2097 5881 3.998156 TAGCTCCGCTATAGCCCG 58.002 61.111 19.00 9.44 41.02 6.13
2104 5888 1.176619 TTGCCGCTATAGCTCCGCTA 61.177 55.000 21.98 13.97 45.55 4.26
2105 5889 2.028125 TTTGCCGCTATAGCTCCGCT 62.028 55.000 21.98 0.00 43.41 5.52
2106 5890 0.951040 ATTTGCCGCTATAGCTCCGC 60.951 55.000 21.98 19.09 39.32 5.54
2107 5891 1.461127 GAATTTGCCGCTATAGCTCCG 59.539 52.381 21.98 10.49 39.32 4.63
2108 5892 2.772287 AGAATTTGCCGCTATAGCTCC 58.228 47.619 21.98 12.84 39.32 4.70
2109 5893 3.365220 CGTAGAATTTGCCGCTATAGCTC 59.635 47.826 21.98 13.79 39.32 4.09
2110 5894 3.243771 ACGTAGAATTTGCCGCTATAGCT 60.244 43.478 21.98 1.45 39.32 3.32
2111 5895 3.057734 ACGTAGAATTTGCCGCTATAGC 58.942 45.455 15.09 15.09 37.78 2.97
2112 5896 4.295870 TCACGTAGAATTTGCCGCTATAG 58.704 43.478 0.00 0.00 0.00 1.31
2113 5897 4.310357 TCACGTAGAATTTGCCGCTATA 57.690 40.909 0.00 0.00 0.00 1.31
2114 5898 3.173668 TCACGTAGAATTTGCCGCTAT 57.826 42.857 0.00 0.00 0.00 2.97
2115 5899 2.658373 TCACGTAGAATTTGCCGCTA 57.342 45.000 0.00 0.00 0.00 4.26
2116 5900 1.803334 TTCACGTAGAATTTGCCGCT 58.197 45.000 0.00 0.00 0.00 5.52
2117 5901 2.604969 TTTCACGTAGAATTTGCCGC 57.395 45.000 0.00 0.00 35.83 6.53
2118 5902 4.335082 TGATTTCACGTAGAATTTGCCG 57.665 40.909 0.00 0.00 35.83 5.69
2119 5903 7.968405 ACTAAATGATTTCACGTAGAATTTGCC 59.032 33.333 0.00 0.00 35.83 4.52
2120 5904 8.788813 CACTAAATGATTTCACGTAGAATTTGC 58.211 33.333 0.00 0.00 35.83 3.68
2121 5905 9.277565 CCACTAAATGATTTCACGTAGAATTTG 57.722 33.333 0.00 0.00 35.83 2.32
2122 5906 7.968405 GCCACTAAATGATTTCACGTAGAATTT 59.032 33.333 0.00 0.00 35.83 1.82
2123 5907 7.120579 TGCCACTAAATGATTTCACGTAGAATT 59.879 33.333 0.00 0.00 35.83 2.17
2124 5908 6.597672 TGCCACTAAATGATTTCACGTAGAAT 59.402 34.615 0.00 0.00 35.83 2.40
2125 5909 5.935206 TGCCACTAAATGATTTCACGTAGAA 59.065 36.000 0.00 0.00 0.00 2.10
2126 5910 5.483811 TGCCACTAAATGATTTCACGTAGA 58.516 37.500 0.00 0.00 0.00 2.59
2127 5911 5.794687 TGCCACTAAATGATTTCACGTAG 57.205 39.130 0.00 0.00 0.00 3.51
2128 5912 5.470437 TGTTGCCACTAAATGATTTCACGTA 59.530 36.000 0.00 0.00 0.00 3.57
2129 5913 4.277174 TGTTGCCACTAAATGATTTCACGT 59.723 37.500 0.00 0.00 0.00 4.49
2130 5914 4.616802 GTGTTGCCACTAAATGATTTCACG 59.383 41.667 0.00 0.00 38.61 4.35
2131 5915 4.923281 GGTGTTGCCACTAAATGATTTCAC 59.077 41.667 0.00 0.00 41.53 3.18
2132 5916 4.021544 GGGTGTTGCCACTAAATGATTTCA 60.022 41.667 0.00 0.00 41.53 2.69
2133 5917 4.220602 AGGGTGTTGCCACTAAATGATTTC 59.779 41.667 0.00 0.00 41.53 2.17
2134 5918 4.159557 AGGGTGTTGCCACTAAATGATTT 58.840 39.130 0.00 0.00 41.53 2.17
2135 5919 3.763897 GAGGGTGTTGCCACTAAATGATT 59.236 43.478 0.00 0.00 41.53 2.57
2136 5920 3.245229 TGAGGGTGTTGCCACTAAATGAT 60.245 43.478 0.00 0.00 41.53 2.45
2137 5921 2.107378 TGAGGGTGTTGCCACTAAATGA 59.893 45.455 0.00 0.00 41.53 2.57
2138 5922 2.513753 TGAGGGTGTTGCCACTAAATG 58.486 47.619 0.00 0.00 41.53 2.32
2139 5923 2.969821 TGAGGGTGTTGCCACTAAAT 57.030 45.000 0.00 0.00 41.53 1.40
2140 5924 2.691011 GTTTGAGGGTGTTGCCACTAAA 59.309 45.455 0.00 0.00 41.53 1.85
2141 5925 2.303175 GTTTGAGGGTGTTGCCACTAA 58.697 47.619 0.00 0.00 41.53 2.24
2142 5926 1.213182 TGTTTGAGGGTGTTGCCACTA 59.787 47.619 0.00 0.00 41.53 2.74
2143 5927 0.033601 TGTTTGAGGGTGTTGCCACT 60.034 50.000 0.00 0.00 41.53 4.00
2144 5928 0.385390 CTGTTTGAGGGTGTTGCCAC 59.615 55.000 0.00 0.00 41.06 5.01
2145 5929 1.391157 GCTGTTTGAGGGTGTTGCCA 61.391 55.000 0.00 0.00 39.65 4.92
2146 5930 1.109323 AGCTGTTTGAGGGTGTTGCC 61.109 55.000 0.00 0.00 0.00 4.52
2147 5931 1.604604 TAGCTGTTTGAGGGTGTTGC 58.395 50.000 0.00 0.00 0.00 4.17
2148 5932 3.375299 GCTATAGCTGTTTGAGGGTGTTG 59.625 47.826 17.75 0.00 38.21 3.33
2149 5933 3.610911 GCTATAGCTGTTTGAGGGTGTT 58.389 45.455 17.75 0.00 38.21 3.32
2150 5934 2.418746 CGCTATAGCTGTTTGAGGGTGT 60.419 50.000 21.98 0.00 39.32 4.16
2151 5935 2.205074 CGCTATAGCTGTTTGAGGGTG 58.795 52.381 21.98 0.00 39.32 4.61
2152 5936 1.139058 CCGCTATAGCTGTTTGAGGGT 59.861 52.381 21.98 0.00 39.32 4.34
2153 5937 1.541233 CCCGCTATAGCTGTTTGAGGG 60.541 57.143 21.98 18.02 39.32 4.30
2154 5938 1.541233 CCCCGCTATAGCTGTTTGAGG 60.541 57.143 21.98 13.33 39.32 3.86
2155 5939 1.871080 CCCCGCTATAGCTGTTTGAG 58.129 55.000 21.98 4.97 39.32 3.02
2156 5940 0.179056 GCCCCGCTATAGCTGTTTGA 60.179 55.000 21.98 0.00 39.32 2.69
2157 5941 1.166531 GGCCCCGCTATAGCTGTTTG 61.167 60.000 21.98 6.39 39.32 2.93
2158 5942 1.148498 GGCCCCGCTATAGCTGTTT 59.852 57.895 21.98 0.00 39.32 2.83
2159 5943 1.418908 ATGGCCCCGCTATAGCTGTT 61.419 55.000 21.98 0.00 39.32 3.16
2160 5944 0.544357 TATGGCCCCGCTATAGCTGT 60.544 55.000 21.98 2.64 39.32 4.40
2161 5945 0.176680 CTATGGCCCCGCTATAGCTG 59.823 60.000 21.98 15.59 41.62 4.24
2162 5946 2.596776 CTATGGCCCCGCTATAGCT 58.403 57.895 21.98 4.48 41.62 3.32
2175 5959 6.430000 ACATAGTTTTAAATAGCCGGCTATGG 59.570 38.462 41.93 23.90 39.03 2.74
2176 5960 7.435068 ACATAGTTTTAAATAGCCGGCTATG 57.565 36.000 41.93 30.89 39.03 2.23
2177 5961 9.216117 CTTACATAGTTTTAAATAGCCGGCTAT 57.784 33.333 37.79 37.79 40.63 2.97
2178 5962 8.423349 TCTTACATAGTTTTAAATAGCCGGCTA 58.577 33.333 36.88 36.88 0.00 3.93
2179 5963 7.226128 GTCTTACATAGTTTTAAATAGCCGGCT 59.774 37.037 34.85 34.85 0.00 5.52
2180 5964 7.011669 TGTCTTACATAGTTTTAAATAGCCGGC 59.988 37.037 21.89 21.89 0.00 6.13
2181 5965 8.333186 GTGTCTTACATAGTTTTAAATAGCCGG 58.667 37.037 0.00 0.00 0.00 6.13
2182 5966 8.054236 CGTGTCTTACATAGTTTTAAATAGCCG 58.946 37.037 0.00 0.00 0.00 5.52
2183 5967 8.333186 CCGTGTCTTACATAGTTTTAAATAGCC 58.667 37.037 0.00 0.00 0.00 3.93
2184 5968 9.090692 TCCGTGTCTTACATAGTTTTAAATAGC 57.909 33.333 0.00 0.00 0.00 2.97
2186 5970 9.926158 TGTCCGTGTCTTACATAGTTTTAAATA 57.074 29.630 0.00 0.00 0.00 1.40
2187 5971 8.836268 TGTCCGTGTCTTACATAGTTTTAAAT 57.164 30.769 0.00 0.00 0.00 1.40
2188 5972 7.927629 ACTGTCCGTGTCTTACATAGTTTTAAA 59.072 33.333 0.00 0.00 0.00 1.52
2189 5973 7.436118 ACTGTCCGTGTCTTACATAGTTTTAA 58.564 34.615 0.00 0.00 0.00 1.52
2190 5974 6.985117 ACTGTCCGTGTCTTACATAGTTTTA 58.015 36.000 0.00 0.00 0.00 1.52
2191 5975 5.850614 ACTGTCCGTGTCTTACATAGTTTT 58.149 37.500 0.00 0.00 0.00 2.43
2192 5976 5.464030 ACTGTCCGTGTCTTACATAGTTT 57.536 39.130 0.00 0.00 0.00 2.66
2193 5977 4.379186 CGACTGTCCGTGTCTTACATAGTT 60.379 45.833 1.55 0.00 32.70 2.24
2194 5978 3.126514 CGACTGTCCGTGTCTTACATAGT 59.873 47.826 1.55 0.00 32.70 2.12
2195 5979 3.681855 CGACTGTCCGTGTCTTACATAG 58.318 50.000 1.55 0.00 32.70 2.23
2196 5980 2.159476 GCGACTGTCCGTGTCTTACATA 60.159 50.000 1.55 0.00 32.70 2.29
2197 5981 1.402456 GCGACTGTCCGTGTCTTACAT 60.402 52.381 1.55 0.00 32.70 2.29
2198 5982 0.039798 GCGACTGTCCGTGTCTTACA 60.040 55.000 1.55 0.00 32.70 2.41
2199 5983 0.240411 AGCGACTGTCCGTGTCTTAC 59.760 55.000 1.55 0.00 32.70 2.34
2244 6039 6.127814 CCACATAAGGACGGTCATATATACGT 60.128 42.308 10.76 8.46 42.88 3.57
2245 6040 6.127814 ACCACATAAGGACGGTCATATATACG 60.128 42.308 10.76 3.08 0.00 3.06
2246 6041 7.033791 CACCACATAAGGACGGTCATATATAC 58.966 42.308 10.76 0.00 0.00 1.47
2247 6042 6.949463 TCACCACATAAGGACGGTCATATATA 59.051 38.462 10.76 0.00 0.00 0.86
2250 6045 3.964688 TCACCACATAAGGACGGTCATAT 59.035 43.478 10.76 5.29 0.00 1.78
2340 6137 9.630098 GAATCTTTCAAGCAAATGTTCTGAATA 57.370 29.630 0.00 0.00 0.00 1.75
2358 6155 7.811236 TGATGATGCAGTTTTTCAGAATCTTTC 59.189 33.333 0.00 0.00 0.00 2.62
2439 6236 5.941948 AAAGGTTGTGTGCTATGTCTTAC 57.058 39.130 0.00 0.00 0.00 2.34
3075 6902 0.250252 TTCTGTTGCTGCGATGGTGA 60.250 50.000 0.00 0.00 0.00 4.02
3277 7134 6.946583 GTGGGAGGGTTCTTCTTAATTACTTT 59.053 38.462 0.00 0.00 0.00 2.66
3356 7213 7.980062 ACAACATTAAACCATTTCAAACCAAC 58.020 30.769 0.00 0.00 0.00 3.77
3408 7265 2.807967 TGCACACAGTCACAATTAGCTC 59.192 45.455 0.00 0.00 0.00 4.09
4634 10117 3.009026 CGATGACATGACCAATTGACCA 58.991 45.455 7.12 4.60 0.00 4.02
4635 10118 3.270027 TCGATGACATGACCAATTGACC 58.730 45.455 7.12 0.00 0.00 4.02
4636 10119 3.242543 GCTCGATGACATGACCAATTGAC 60.243 47.826 7.12 1.29 0.00 3.18
4638 10121 2.941064 AGCTCGATGACATGACCAATTG 59.059 45.455 0.00 0.00 0.00 2.32
4639 10122 3.272574 AGCTCGATGACATGACCAATT 57.727 42.857 0.00 0.00 0.00 2.32
4640 10123 2.996249 AGCTCGATGACATGACCAAT 57.004 45.000 0.00 0.00 0.00 3.16
4641 10124 3.195610 AGTTAGCTCGATGACATGACCAA 59.804 43.478 0.00 0.00 0.00 3.67
4654 10137 1.479420 TATGCGCGCAAGTTAGCTCG 61.479 55.000 39.68 5.64 44.76 5.03
4691 10179 0.583438 CATACGGATTCTGGCGCAAG 59.417 55.000 10.83 7.94 43.44 4.01
4751 10239 4.523173 CGGGAACTGAGCCTTCATACTATA 59.477 45.833 0.00 0.00 36.31 1.31
4786 10274 4.549458 CAGGTTGGTTTTCACTATTGCTG 58.451 43.478 0.00 0.00 0.00 4.41
5157 10711 5.538118 GGGAGGAAATTTTCAACGAACATT 58.462 37.500 11.09 0.00 0.00 2.71
5352 10906 3.686241 GCAGCTTGATGTTGTAGTCATCA 59.314 43.478 4.77 4.77 46.28 3.07
5429 12467 2.094675 GCTATGCACAACCCTGTTGAT 58.905 47.619 13.46 0.33 31.64 2.57
5774 13385 0.034670 GAGCCCATGACAGCTTTCCT 60.035 55.000 0.00 0.00 40.11 3.36
5775 13386 0.322816 TGAGCCCATGACAGCTTTCC 60.323 55.000 0.00 0.00 40.11 3.13
5777 13388 3.994165 ATGAGCCCATGACAGCTTT 57.006 47.368 0.00 0.00 40.11 3.51
5790 13401 3.988379 TCAATAAAATCGGCCATGAGC 57.012 42.857 2.24 0.00 42.60 4.26
5791 13402 5.335426 CCTGATCAATAAAATCGGCCATGAG 60.335 44.000 2.24 0.00 0.00 2.90
5885 13501 6.245408 ACTCATAATCTGGCAAAGTTTACCA 58.755 36.000 7.36 7.36 0.00 3.25
5945 13561 4.188247 TGTCACAATTTCTCTCGGGTAG 57.812 45.455 0.00 0.00 0.00 3.18
5949 13565 5.673337 TTCTTTGTCACAATTTCTCTCGG 57.327 39.130 0.00 0.00 0.00 4.63
5978 13594 2.863137 GCGGCTGCTATATATGAAGAGC 59.137 50.000 11.21 0.00 38.39 4.09
6157 13780 1.282382 TAAGGTTAGCACCCCCTGTC 58.718 55.000 0.00 0.00 45.63 3.51
6279 13904 4.488770 TCCCCTCCAAAATGCTAAACTTT 58.511 39.130 0.00 0.00 0.00 2.66
6335 13961 3.368248 ACCTCCCATTTGTTGATGATGG 58.632 45.455 0.00 0.00 39.99 3.51


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

AutoCloner maintained by Alex Coulton.