Multiple sequence alignment - TraesCS4A01G022800

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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 TraesCS4A01G022800 chr4A 100.000 8765 0 0 1 8765 16257594 16248830 0.000000e+00 16187.0
1 TraesCS4A01G022800 chr4B 97.186 3021 73 10 2562 5578 563620534 563623546 0.000000e+00 5097.0
2 TraesCS4A01G022800 chr4B 96.456 2596 57 10 5639 8220 563623930 563626504 0.000000e+00 4252.0
3 TraesCS4A01G022800 chr4B 95.496 1954 68 5 1 1954 514590794 514592727 0.000000e+00 3103.0
4 TraesCS4A01G022800 chr4B 86.025 551 36 17 1957 2504 563618940 563619452 3.580000e-153 553.0
5 TraesCS4A01G022800 chr4B 91.818 220 9 5 8552 8765 563626766 563626982 1.850000e-76 298.0
6 TraesCS4A01G022800 chr4D 98.107 2483 45 2 5639 8119 450327420 450329902 0.000000e+00 4324.0
7 TraesCS4A01G022800 chr4D 96.576 2512 82 3 2999 5507 450324097 450326607 0.000000e+00 4159.0
8 TraesCS4A01G022800 chr4D 89.796 392 25 5 8163 8554 450329906 450330282 1.020000e-133 488.0
9 TraesCS4A01G022800 chr4D 87.082 449 31 12 2562 3008 450323344 450323767 4.760000e-132 483.0
10 TraesCS4A01G022800 chr4D 92.032 251 12 4 1977 2225 450323016 450323260 6.510000e-91 346.0
11 TraesCS4A01G022800 chr4D 97.810 137 2 1 8629 8765 450330511 450330646 1.470000e-57 235.0
12 TraesCS4A01G022800 chr4D 98.462 130 2 0 5507 5636 450326957 450327086 6.840000e-56 230.0
13 TraesCS4A01G022800 chr4D 98.182 55 1 0 6542 6596 505744590 505744644 7.240000e-16 97.1
14 TraesCS4A01G022800 chr3A 95.406 1959 70 5 1 1959 435361120 435363058 0.000000e+00 3101.0
15 TraesCS4A01G022800 chr3A 81.674 1959 330 18 1 1954 82462438 82464372 0.000000e+00 1602.0
16 TraesCS4A01G022800 chr1D 95.299 1957 71 6 1 1957 413774670 413772735 0.000000e+00 3085.0
17 TraesCS4A01G022800 chr2B 95.294 1955 73 4 2 1956 677673265 677671330 0.000000e+00 3083.0
18 TraesCS4A01G022800 chr2B 94.890 1957 81 4 1 1957 769097205 769099142 0.000000e+00 3042.0
19 TraesCS4A01G022800 chr2B 85.441 1937 253 18 5872 7802 136622281 136624194 0.000000e+00 1988.0
20 TraesCS4A01G022800 chr2B 81.541 1441 185 48 4297 5700 136620845 136622241 0.000000e+00 1112.0
21 TraesCS4A01G022800 chr2B 77.447 2115 302 87 4233 6238 135690889 135688841 0.000000e+00 1101.0
22 TraesCS4A01G022800 chr2B 85.080 563 83 1 3012 3573 136619559 136620121 2.740000e-159 573.0
23 TraesCS4A01G022800 chr2B 100.000 28 0 0 8620 8647 661179703 661179730 1.600000e-02 52.8
24 TraesCS4A01G022800 chr3B 94.836 1956 79 7 1 1955 659536734 659538668 0.000000e+00 3033.0
25 TraesCS4A01G022800 chr3B 94.479 1793 78 6 1 1791 659534163 659535936 0.000000e+00 2743.0
26 TraesCS4A01G022800 chr3B 83.615 1953 292 13 10 1956 436512574 436510644 0.000000e+00 1808.0
27 TraesCS4A01G022800 chr3B 94.438 881 38 3 1051 1930 542341476 542340606 0.000000e+00 1345.0
28 TraesCS4A01G022800 chr7B 94.694 1960 83 6 1 1959 221310187 221308248 0.000000e+00 3024.0
29 TraesCS4A01G022800 chr7B 85.915 71 9 1 8579 8649 23414513 23414444 3.390000e-09 75.0
30 TraesCS4A01G022800 chr1B 94.992 1897 75 4 1 1896 618010237 618012114 0.000000e+00 2959.0
31 TraesCS4A01G022800 chr2A 84.410 2027 282 24 5872 7888 85598295 85600297 0.000000e+00 1962.0
32 TraesCS4A01G022800 chr2A 82.228 1221 164 34 4297 5507 85596810 85597987 0.000000e+00 1003.0
33 TraesCS4A01G022800 chr2A 76.090 1376 200 63 4233 5544 84551578 84550268 4.530000e-167 599.0
34 TraesCS4A01G022800 chr2A 81.369 789 100 15 3026 3769 85595538 85596324 4.530000e-167 599.0
35 TraesCS4A01G022800 chr2A 84.964 552 75 5 6365 6916 84151811 84151268 3.580000e-153 553.0
36 TraesCS4A01G022800 chr2A 91.626 203 14 2 6060 6261 84549781 84549581 2.410000e-70 278.0
37 TraesCS4A01G022800 chr2A 90.833 120 10 1 5909 6027 84549900 84549781 9.110000e-35 159.0
38 TraesCS4A01G022800 chr2D 84.361 2027 270 29 5872 7888 84763139 84765128 0.000000e+00 1943.0
39 TraesCS4A01G022800 chr2D 80.652 1995 267 70 3772 5700 84761158 84763099 0.000000e+00 1435.0
40 TraesCS4A01G022800 chr2D 81.630 1301 203 15 6359 7657 84921109 84922375 0.000000e+00 1046.0
41 TraesCS4A01G022800 chr2D 85.965 570 78 2 3005 3573 84760338 84760906 7.520000e-170 608.0
42 TraesCS4A01G022800 chr2D 85.584 437 37 10 5828 6261 83820191 83819778 1.350000e-117 435.0
43 TraesCS4A01G022800 chr2D 78.186 463 62 22 5256 5692 83821077 83820628 8.730000e-65 259.0
44 TraesCS4A01G022800 chr2D 86.331 139 8 6 6242 6373 84920935 84921069 3.300000e-29 141.0
45 TraesCS4A01G022800 chr5B 82.017 1963 323 18 1 1958 556964815 556966752 0.000000e+00 1642.0
46 TraesCS4A01G022800 chr5B 83.201 1512 236 12 448 1956 447209950 447211446 0.000000e+00 1369.0
47 TraesCS4A01G022800 chr6B 81.517 1450 246 16 510 1954 290688315 290686883 0.000000e+00 1173.0
48 TraesCS4A01G022800 chr7A 93.520 679 35 5 1276 1954 24336869 24337538 0.000000e+00 1002.0
49 TraesCS4A01G022800 chr6A 88.235 51 4 2 8600 8649 43576226 43576275 9.500000e-05 60.2
50 TraesCS4A01G022800 chr3D 88.235 51 4 2 8600 8649 62526921 62526872 9.500000e-05 60.2


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 TraesCS4A01G022800 chr4A 16248830 16257594 8764 True 16187.000000 16187 100.000000 1 8765 1 chr4A.!!$R1 8764
1 TraesCS4A01G022800 chr4B 514590794 514592727 1933 False 3103.000000 3103 95.496000 1 1954 1 chr4B.!!$F1 1953
2 TraesCS4A01G022800 chr4B 563618940 563626982 8042 False 2550.000000 5097 92.871250 1957 8765 4 chr4B.!!$F2 6808
3 TraesCS4A01G022800 chr4D 450323016 450330646 7630 False 1466.428571 4324 94.266429 1977 8765 7 chr4D.!!$F2 6788
4 TraesCS4A01G022800 chr3A 435361120 435363058 1938 False 3101.000000 3101 95.406000 1 1959 1 chr3A.!!$F2 1958
5 TraesCS4A01G022800 chr3A 82462438 82464372 1934 False 1602.000000 1602 81.674000 1 1954 1 chr3A.!!$F1 1953
6 TraesCS4A01G022800 chr1D 413772735 413774670 1935 True 3085.000000 3085 95.299000 1 1957 1 chr1D.!!$R1 1956
7 TraesCS4A01G022800 chr2B 677671330 677673265 1935 True 3083.000000 3083 95.294000 2 1956 1 chr2B.!!$R2 1954
8 TraesCS4A01G022800 chr2B 769097205 769099142 1937 False 3042.000000 3042 94.890000 1 1957 1 chr2B.!!$F2 1956
9 TraesCS4A01G022800 chr2B 136619559 136624194 4635 False 1224.333333 1988 84.020667 3012 7802 3 chr2B.!!$F3 4790
10 TraesCS4A01G022800 chr2B 135688841 135690889 2048 True 1101.000000 1101 77.447000 4233 6238 1 chr2B.!!$R1 2005
11 TraesCS4A01G022800 chr3B 659534163 659538668 4505 False 2888.000000 3033 94.657500 1 1955 2 chr3B.!!$F1 1954
12 TraesCS4A01G022800 chr3B 436510644 436512574 1930 True 1808.000000 1808 83.615000 10 1956 1 chr3B.!!$R1 1946
13 TraesCS4A01G022800 chr3B 542340606 542341476 870 True 1345.000000 1345 94.438000 1051 1930 1 chr3B.!!$R2 879
14 TraesCS4A01G022800 chr7B 221308248 221310187 1939 True 3024.000000 3024 94.694000 1 1959 1 chr7B.!!$R2 1958
15 TraesCS4A01G022800 chr1B 618010237 618012114 1877 False 2959.000000 2959 94.992000 1 1896 1 chr1B.!!$F1 1895
16 TraesCS4A01G022800 chr2A 85595538 85600297 4759 False 1188.000000 1962 82.669000 3026 7888 3 chr2A.!!$F1 4862
17 TraesCS4A01G022800 chr2A 84151268 84151811 543 True 553.000000 553 84.964000 6365 6916 1 chr2A.!!$R1 551
18 TraesCS4A01G022800 chr2A 84549581 84551578 1997 True 345.333333 599 86.183000 4233 6261 3 chr2A.!!$R2 2028
19 TraesCS4A01G022800 chr2D 84760338 84765128 4790 False 1328.666667 1943 83.659333 3005 7888 3 chr2D.!!$F1 4883
20 TraesCS4A01G022800 chr2D 84920935 84922375 1440 False 593.500000 1046 83.980500 6242 7657 2 chr2D.!!$F2 1415
21 TraesCS4A01G022800 chr2D 83819778 83821077 1299 True 347.000000 435 81.885000 5256 6261 2 chr2D.!!$R1 1005
22 TraesCS4A01G022800 chr5B 556964815 556966752 1937 False 1642.000000 1642 82.017000 1 1958 1 chr5B.!!$F2 1957
23 TraesCS4A01G022800 chr5B 447209950 447211446 1496 False 1369.000000 1369 83.201000 448 1956 1 chr5B.!!$F1 1508
24 TraesCS4A01G022800 chr6B 290686883 290688315 1432 True 1173.000000 1173 81.517000 510 1954 1 chr6B.!!$R1 1444
25 TraesCS4A01G022800 chr7A 24336869 24337538 669 False 1002.000000 1002 93.520000 1276 1954 1 chr7A.!!$F1 678

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
629 631 0.103390 TCGTGGACAAAGTTGCGAGA 59.897 50.000 0.00 0.00 0.00 4.04 F
883 887 0.251787 GGGCTTGGGGTTCTCAACAT 60.252 55.000 0.00 0.00 0.00 2.71 F
2202 4789 0.397941 CCCTCTGGTTGCTGTTCTGA 59.602 55.000 0.00 0.00 0.00 3.27 F
2317 4913 0.104120 GGCGGCTGTTTCCTTTTGTT 59.896 50.000 0.00 0.00 0.00 2.83 F
2416 5013 0.178961 GTTGTGCCTTTCTTCCCCCT 60.179 55.000 0.00 0.00 0.00 4.79 F
2516 5113 0.249073 AGTCACACGCTCACACTGAC 60.249 55.000 0.00 0.00 32.92 3.51 F
2559 5156 0.250553 TTTGCCGTCGATGGGAGTTT 60.251 50.000 24.85 0.00 0.00 2.66 F
2560 5157 0.672401 TTGCCGTCGATGGGAGTTTC 60.672 55.000 24.85 7.72 0.00 2.78 F
2697 6334 2.543777 TAATATTGGGCTCTGGACGC 57.456 50.000 0.00 0.00 0.00 5.19 F
4544 8640 3.004839 TCGTGACAAGGAGAGAGAAACAG 59.995 47.826 0.00 0.00 0.00 3.16 F
5331 9480 2.144482 TTGTTCCGTCGGAGAAGAAC 57.856 50.000 14.79 9.99 46.17 3.01 F
6262 11452 1.750778 GACATGCCCATACCCTTGTTG 59.249 52.381 0.00 0.00 0.00 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1963 4548 0.102481 ATCGTTCGGGATCGTTCAGG 59.898 55.000 0.00 0.00 37.69 3.86 R
2298 4894 0.104120 AACAAAAGGAAACAGCCGCC 59.896 50.000 0.00 0.00 0.00 6.13 R
3731 7755 3.503363 TGCGAGCATGGGAATGAATAATC 59.497 43.478 0.00 0.00 0.00 1.75 R
4514 8598 3.483421 TCTCCTTGTCACGACTCTGTTA 58.517 45.455 0.00 0.00 0.00 2.41 R
4544 8640 0.252742 TCCTCACCTTCTCCTTCCCC 60.253 60.000 0.00 0.00 0.00 4.81 R
4646 8742 3.959535 ATGTCCATTTGCCGTTGAATT 57.040 38.095 0.00 0.00 0.00 2.17 R
4833 8931 2.686915 CAAGGCCCTGAGATCATGAAAC 59.313 50.000 0.00 0.00 0.00 2.78 R
4877 8984 3.053842 AGAACCATTCCATCAGTGCAGAT 60.054 43.478 0.00 0.00 0.00 2.90 R
4890 8997 4.284378 GCATACTTGCTGAGAACCATTC 57.716 45.455 0.00 0.00 45.77 2.67 R
5900 11069 1.053424 TAGTTTCTGGGTTCTGGCGT 58.947 50.000 0.00 0.00 0.00 5.68 R
7427 12680 0.027979 CGGTAGCAATGCACCATTCG 59.972 55.000 20.70 7.89 31.05 3.34 R
8150 13447 0.179065 TCATCAGATTCAGGCAGCCG 60.179 55.000 5.55 0.83 0.00 5.52 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
43 44 4.096382 TCCTTTTCAAGCTTGATATTCGCC 59.904 41.667 28.89 0.00 37.00 5.54
65 66 3.192844 CAGGCCTTCGACTCTGTTAAGTA 59.807 47.826 0.00 0.00 0.00 2.24
127 128 5.500234 CAAGTAAATTCTGGGACTGGATCA 58.500 41.667 0.00 0.00 0.00 2.92
176 177 7.275183 TCGAGGATCATTCTCAATTGTATTGT 58.725 34.615 5.13 0.00 33.17 2.71
215 216 1.375326 GGAAAGGTCTTCGGCAGGT 59.625 57.895 0.00 0.00 0.00 4.00
439 441 1.896122 CGGAGAGGTTACGGGCCTTT 61.896 60.000 0.84 0.00 36.29 3.11
440 442 0.392595 GGAGAGGTTACGGGCCTTTG 60.393 60.000 0.84 0.00 36.29 2.77
441 443 1.002502 AGAGGTTACGGGCCTTTGC 60.003 57.895 0.84 0.00 36.29 3.68
442 444 1.302993 GAGGTTACGGGCCTTTGCA 60.303 57.895 0.84 0.00 40.13 4.08
443 445 1.583495 GAGGTTACGGGCCTTTGCAC 61.583 60.000 0.84 0.00 40.13 4.57
444 446 2.632544 GGTTACGGGCCTTTGCACC 61.633 63.158 0.84 0.00 37.75 5.01
445 447 1.899534 GTTACGGGCCTTTGCACCA 60.900 57.895 0.84 0.00 37.75 4.17
446 448 1.152735 TTACGGGCCTTTGCACCAA 60.153 52.632 0.84 0.00 37.75 3.67
512 514 1.039233 ATCTTGATTTGGGCCGCCTG 61.039 55.000 9.86 0.00 0.00 4.85
536 538 1.088306 AAAGTTTGTCGGCAACACGA 58.912 45.000 0.00 0.00 37.70 4.35
629 631 0.103390 TCGTGGACAAAGTTGCGAGA 59.897 50.000 0.00 0.00 0.00 4.04
691 693 1.578583 CGAACGACCCTTGTCAAGTT 58.421 50.000 11.61 0.00 41.85 2.66
883 887 0.251787 GGGCTTGGGGTTCTCAACAT 60.252 55.000 0.00 0.00 0.00 2.71
895 899 5.506317 GGGTTCTCAACATTGACAAGTTCAG 60.506 44.000 0.00 0.00 34.94 3.02
918 923 2.743718 CTCTCAGGTTGCGGTGGT 59.256 61.111 0.00 0.00 0.00 4.16
1020 1025 0.697658 TGCTTCCACCACCATCATCA 59.302 50.000 0.00 0.00 0.00 3.07
1049 1054 1.292223 CGCGAAGACCCCTTTCTGA 59.708 57.895 0.00 0.00 31.62 3.27
1105 1110 3.397482 ACATTTCTCCGCTCATCTATGC 58.603 45.455 0.00 0.00 0.00 3.14
1118 1123 2.165357 TCTATGCAGCCTCCAAGAGA 57.835 50.000 0.00 0.00 0.00 3.10
1119 1124 2.470990 TCTATGCAGCCTCCAAGAGAA 58.529 47.619 0.00 0.00 0.00 2.87
1120 1125 2.840038 TCTATGCAGCCTCCAAGAGAAA 59.160 45.455 0.00 0.00 0.00 2.52
1205 1215 3.006110 CCACCATTGTTTCTGTTGAGCAT 59.994 43.478 0.00 0.00 0.00 3.79
1264 1275 1.883275 GGTCCATCTCGACGATCTCAT 59.117 52.381 0.00 0.00 33.30 2.90
1291 1302 4.881850 GGACGACATCCTTTGGAAACATAT 59.118 41.667 0.00 0.00 45.22 1.78
1351 3933 2.339769 GCAATACCTAGGGATGGTCCT 58.660 52.381 7.45 0.00 38.88 3.85
1352 3934 2.303311 GCAATACCTAGGGATGGTCCTC 59.697 54.545 7.45 0.00 38.88 3.71
1353 3935 3.863086 CAATACCTAGGGATGGTCCTCT 58.137 50.000 7.45 0.00 38.88 3.69
1354 3936 3.835395 CAATACCTAGGGATGGTCCTCTC 59.165 52.174 7.45 0.00 38.88 3.20
1355 3937 1.319947 ACCTAGGGATGGTCCTCTCA 58.680 55.000 14.81 0.00 38.30 3.27
1356 3938 1.651770 ACCTAGGGATGGTCCTCTCAA 59.348 52.381 14.81 0.00 38.30 3.02
1357 3939 2.324541 CCTAGGGATGGTCCTCTCAAG 58.675 57.143 0.00 0.00 38.30 3.02
1546 4129 3.584848 ACCTCACCTCTTCTACAAATGCT 59.415 43.478 0.00 0.00 0.00 3.79
1563 4146 1.338337 TGCTGCTATACTCGAAGGCTC 59.662 52.381 0.00 0.00 0.00 4.70
1618 4201 1.002544 GGCTAGACACTTCTGCTTGGT 59.997 52.381 0.00 0.00 32.75 3.67
1619 4203 2.551071 GGCTAGACACTTCTGCTTGGTT 60.551 50.000 0.00 0.00 32.75 3.67
1704 4288 0.758734 CCAAGGCGTCCCTCATCATA 59.241 55.000 0.00 0.00 41.90 2.15
1881 4466 1.372838 CCGCATGCCGTGTAATTGGA 61.373 55.000 13.15 0.00 34.38 3.53
1935 4520 4.628963 AATGGATGAGGCAAAGCTTTTT 57.371 36.364 9.53 0.00 0.00 1.94
2057 4642 1.210478 CAAGAACATCGGAGGGGTCAT 59.790 52.381 0.00 0.00 0.00 3.06
2136 4721 2.283676 TTCCTCCGCTCCTCCGTT 60.284 61.111 0.00 0.00 0.00 4.44
2155 4740 1.225855 TGTACGGTTTGCTCTGCTTG 58.774 50.000 0.00 0.00 0.00 4.01
2157 4742 1.234615 TACGGTTTGCTCTGCTTGCC 61.235 55.000 0.00 0.00 0.00 4.52
2174 4761 3.703001 TGCCTCCTCTTTCAGTTAAGG 57.297 47.619 0.00 0.00 0.00 2.69
2175 4762 3.248024 TGCCTCCTCTTTCAGTTAAGGA 58.752 45.455 0.00 0.00 36.50 3.36
2176 4763 3.650942 TGCCTCCTCTTTCAGTTAAGGAA 59.349 43.478 0.00 0.00 37.46 3.36
2183 4770 3.684788 TCTTTCAGTTAAGGAATCGCTGC 59.315 43.478 0.00 0.00 0.00 5.25
2184 4771 2.024176 TCAGTTAAGGAATCGCTGCC 57.976 50.000 0.00 0.00 0.00 4.85
2202 4789 0.397941 CCCTCTGGTTGCTGTTCTGA 59.602 55.000 0.00 0.00 0.00 3.27
2208 4795 3.345808 TTGCTGTTCTGACCGCGC 61.346 61.111 0.00 0.00 38.66 6.86
2230 4817 4.315264 CTTGGGGTTGGGTGGGGG 62.315 72.222 0.00 0.00 0.00 5.40
2259 4846 2.290960 TGGGGTTTTTGGTTGTTTTGGG 60.291 45.455 0.00 0.00 0.00 4.12
2280 4876 2.782615 CGTTTCGGCGGTCCAATC 59.217 61.111 7.21 0.00 0.00 2.67
2313 4909 2.983592 CCGGCGGCTGTTTCCTTT 60.984 61.111 15.42 0.00 0.00 3.11
2314 4910 2.561037 CCGGCGGCTGTTTCCTTTT 61.561 57.895 15.42 0.00 0.00 2.27
2315 4911 1.371635 CGGCGGCTGTTTCCTTTTG 60.372 57.895 7.61 0.00 0.00 2.44
2316 4912 1.739667 GGCGGCTGTTTCCTTTTGT 59.260 52.632 0.00 0.00 0.00 2.83
2317 4913 0.104120 GGCGGCTGTTTCCTTTTGTT 59.896 50.000 0.00 0.00 0.00 2.83
2318 4914 1.487482 GCGGCTGTTTCCTTTTGTTC 58.513 50.000 0.00 0.00 0.00 3.18
2351 4947 1.305930 GCCGGATTCGTGCCTTTCTT 61.306 55.000 5.05 0.00 33.95 2.52
2356 4952 2.355209 GGATTCGTGCCTTTCTTCCTCT 60.355 50.000 0.00 0.00 0.00 3.69
2357 4953 2.457366 TTCGTGCCTTTCTTCCTCTC 57.543 50.000 0.00 0.00 0.00 3.20
2358 4954 1.338107 TCGTGCCTTTCTTCCTCTCA 58.662 50.000 0.00 0.00 0.00 3.27
2363 4960 3.441922 GTGCCTTTCTTCCTCTCATTTCC 59.558 47.826 0.00 0.00 0.00 3.13
2413 5010 0.822121 ACCGTTGTGCCTTTCTTCCC 60.822 55.000 0.00 0.00 0.00 3.97
2416 5013 0.178961 GTTGTGCCTTTCTTCCCCCT 60.179 55.000 0.00 0.00 0.00 4.79
2418 5015 1.000771 GTGCCTTTCTTCCCCCTCC 60.001 63.158 0.00 0.00 0.00 4.30
2421 5018 1.927569 GCCTTTCTTCCCCCTCCTCC 61.928 65.000 0.00 0.00 0.00 4.30
2504 5101 1.290491 GAGAGCAGCAGCAGTCACAC 61.290 60.000 3.17 0.00 45.49 3.82
2505 5102 2.664185 AGCAGCAGCAGTCACACG 60.664 61.111 3.17 0.00 45.49 4.49
2506 5103 4.380628 GCAGCAGCAGTCACACGC 62.381 66.667 0.00 0.00 41.58 5.34
2507 5104 2.664185 CAGCAGCAGTCACACGCT 60.664 61.111 0.00 0.00 39.66 5.07
2508 5105 2.356793 AGCAGCAGTCACACGCTC 60.357 61.111 0.00 0.00 35.96 5.03
2509 5106 2.662857 GCAGCAGTCACACGCTCA 60.663 61.111 0.00 0.00 35.96 4.26
2510 5107 2.947890 GCAGCAGTCACACGCTCAC 61.948 63.158 0.00 0.00 35.96 3.51
2511 5108 1.592400 CAGCAGTCACACGCTCACA 60.592 57.895 0.00 0.00 35.96 3.58
2512 5109 1.592669 AGCAGTCACACGCTCACAC 60.593 57.895 0.00 0.00 31.16 3.82
2516 5113 0.249073 AGTCACACGCTCACACTGAC 60.249 55.000 0.00 0.00 32.92 3.51
2526 5123 0.542938 TCACACTGACAGGGGAGGAG 60.543 60.000 10.07 0.00 0.00 3.69
2527 5124 1.229336 ACACTGACAGGGGAGGAGG 60.229 63.158 10.07 0.00 0.00 4.30
2528 5125 1.079256 CACTGACAGGGGAGGAGGA 59.921 63.158 7.51 0.00 0.00 3.71
2529 5126 0.975040 CACTGACAGGGGAGGAGGAG 60.975 65.000 7.51 0.00 0.00 3.69
2530 5127 1.149782 ACTGACAGGGGAGGAGGAGA 61.150 60.000 7.51 0.00 0.00 3.71
2531 5128 0.264359 CTGACAGGGGAGGAGGAGAT 59.736 60.000 0.00 0.00 0.00 2.75
2532 5129 0.263172 TGACAGGGGAGGAGGAGATC 59.737 60.000 0.00 0.00 0.00 2.75
2537 5134 0.963355 GGGGAGGAGGAGATCGATCG 60.963 65.000 19.33 9.36 0.00 3.69
2540 5137 1.271163 GGAGGAGGAGATCGATCGAGT 60.271 57.143 23.84 13.15 0.00 4.18
2556 5153 1.079127 AGTTTGCCGTCGATGGGAG 60.079 57.895 24.85 0.16 0.00 4.30
2557 5154 1.375523 GTTTGCCGTCGATGGGAGT 60.376 57.895 24.85 0.00 0.00 3.85
2559 5156 0.250553 TTTGCCGTCGATGGGAGTTT 60.251 50.000 24.85 0.00 0.00 2.66
2560 5157 0.672401 TTGCCGTCGATGGGAGTTTC 60.672 55.000 24.85 7.72 0.00 2.78
2634 6270 8.054572 AGGGTTTTGTAGTTTGTAGGTCTAAAA 58.945 33.333 0.00 0.00 0.00 1.52
2635 6271 8.685427 GGGTTTTGTAGTTTGTAGGTCTAAAAA 58.315 33.333 0.00 0.00 0.00 1.94
2672 6308 3.834610 AGGTCAGAAGTACGAAATCACG 58.165 45.455 0.00 0.00 39.31 4.35
2676 6312 4.321217 GTCAGAAGTACGAAATCACGTCAG 59.679 45.833 0.00 0.00 45.32 3.51
2677 6313 4.023450 TCAGAAGTACGAAATCACGTCAGT 60.023 41.667 0.00 0.00 45.32 3.41
2697 6334 2.543777 TAATATTGGGCTCTGGACGC 57.456 50.000 0.00 0.00 0.00 5.19
3218 7196 6.971184 CACTGAAGATTACAAGGCAATCAATC 59.029 38.462 0.00 0.00 35.30 2.67
3468 7446 5.426504 ACTTGATTCTGATGATGAGGACAC 58.573 41.667 0.00 0.00 0.00 3.67
3654 7660 5.069119 AGGTGCATTCAACTCATCGTATCTA 59.931 40.000 0.00 0.00 34.53 1.98
3720 7744 6.683974 TTTAACTGCATGAATAAGAGAGGC 57.316 37.500 0.00 0.00 0.00 4.70
3731 7755 5.011125 TGAATAAGAGAGGCGGGAAATAGAG 59.989 44.000 0.00 0.00 0.00 2.43
3890 7941 6.018262 GCATGATAAATTGCATTGTGCTGAAT 60.018 34.615 0.00 0.00 45.31 2.57
4063 8126 8.800370 TGGAAATGTTAGTCAATATTGCTGTA 57.200 30.769 10.76 0.00 0.00 2.74
4387 8455 6.407412 CCAGAAGATATGCCTACTCAGTTTCA 60.407 42.308 0.00 0.00 0.00 2.69
4514 8598 7.218228 TGTCATGTTCACTATCTTGCATTTT 57.782 32.000 0.00 0.00 0.00 1.82
4544 8640 3.004839 TCGTGACAAGGAGAGAGAAACAG 59.995 47.826 0.00 0.00 0.00 3.16
4877 8984 8.815565 TTGCTTACTTGATAATGGGTTTCATA 57.184 30.769 0.00 0.00 34.44 2.15
4890 8997 3.567164 GGGTTTCATATCTGCACTGATGG 59.433 47.826 0.00 0.00 0.00 3.51
5148 9270 4.202243 TGCATTTTCCTCTGGTCCTTTTTG 60.202 41.667 0.00 0.00 0.00 2.44
5214 9337 9.908152 CTACTGTTTTCTTAATTTTACCCCTTG 57.092 33.333 0.00 0.00 0.00 3.61
5250 9399 9.665264 CTTTGTTCTTTTGTCTACCATTACTTC 57.335 33.333 0.00 0.00 0.00 3.01
5331 9480 2.144482 TTGTTCCGTCGGAGAAGAAC 57.856 50.000 14.79 9.99 46.17 3.01
5807 10976 9.793252 CCCAAATGTTAAGATGTAGATTTTGAG 57.207 33.333 0.00 0.00 0.00 3.02
5900 11069 6.046593 CGTAAGCAATCCCACAGAACTTATA 58.953 40.000 0.00 0.00 0.00 0.98
5975 11164 7.829211 CAGGAAATATTCTTCAAGTTGTCCCTA 59.171 37.037 2.11 0.00 0.00 3.53
6262 11452 1.750778 GACATGCCCATACCCTTGTTG 59.249 52.381 0.00 0.00 0.00 3.33
6288 11478 7.658167 GGACTTCTATTCCTCCAAAGCTAATAC 59.342 40.741 0.00 0.00 0.00 1.89
6892 12145 3.914426 ATGAGTACCGAGCAGGAAAAT 57.086 42.857 5.19 0.00 45.00 1.82
7390 12643 2.066262 GAAAATCCTTCTGTGACGCGA 58.934 47.619 15.93 0.00 0.00 5.87
7485 12738 2.406559 CCCAGAAGAGGAGGATCACAT 58.593 52.381 0.00 0.00 36.25 3.21
7858 13153 7.509141 TTCTTTGCAGTATTTTGTCTGATCA 57.491 32.000 0.00 0.00 34.02 2.92
7891 13187 9.900710 GTGTGGTAGTATGAGAGATATAACAAG 57.099 37.037 0.00 0.00 0.00 3.16
8066 13362 2.869801 GTGAGTCGAACCAATTGTGTGA 59.130 45.455 4.43 0.00 0.00 3.58
8071 13367 3.974401 GTCGAACCAATTGTGTGATGTTG 59.026 43.478 4.43 0.00 0.00 3.33
8131 13428 8.828688 ATTGTTACTCTTAACCTTACTGTCAC 57.171 34.615 0.00 0.00 37.39 3.67
8140 13437 2.002586 CCTTACTGTCACGAGCCATTG 58.997 52.381 0.00 0.00 0.00 2.82
8148 13445 3.262420 GTCACGAGCCATTGTCTATGTT 58.738 45.455 0.00 0.00 31.99 2.71
8150 13447 3.932710 TCACGAGCCATTGTCTATGTTTC 59.067 43.478 0.00 0.00 31.99 2.78
8214 13511 3.155998 GACAAAATCTGAACATCACGCG 58.844 45.455 3.53 3.53 0.00 6.01
8235 13532 3.366171 CGGTGTCATGATGCATTTGTCAA 60.366 43.478 0.00 0.00 0.00 3.18
8242 13539 4.227512 TGATGCATTTGTCAACACTGTC 57.772 40.909 0.00 0.00 0.00 3.51
8248 13545 4.515191 GCATTTGTCAACACTGTCTCCTTA 59.485 41.667 0.00 0.00 0.00 2.69
8303 13600 1.135199 CCAGCTTGTAAATGGCAGCAG 60.135 52.381 0.00 0.00 0.00 4.24
8332 13629 4.156922 CAGAAGTTCAGGAGAGTGATACGT 59.843 45.833 5.50 0.00 0.00 3.57
8333 13630 5.354513 CAGAAGTTCAGGAGAGTGATACGTA 59.645 44.000 5.50 0.00 0.00 3.57
8334 13631 5.354792 AGAAGTTCAGGAGAGTGATACGTAC 59.645 44.000 5.50 0.00 0.00 3.67
8335 13632 3.622163 AGTTCAGGAGAGTGATACGTACG 59.378 47.826 15.01 15.01 0.00 3.67
8346 13643 0.743097 ATACGTACGGAGGGCAGAAC 59.257 55.000 21.06 0.00 0.00 3.01
8352 13649 1.274703 ACGGAGGGCAGAACCATGAT 61.275 55.000 0.00 0.00 42.05 2.45
8370 13667 3.457234 TGATACGTCTGCATTGCTAAGG 58.543 45.455 10.49 6.16 0.00 2.69
8377 13674 3.016736 TCTGCATTGCTAAGGGCTAAAC 58.983 45.455 10.49 0.00 42.39 2.01
8381 13678 4.039730 TGCATTGCTAAGGGCTAAACAAAA 59.960 37.500 10.49 0.00 42.39 2.44
8387 13684 4.279922 GCTAAGGGCTAAACAAAACTTGGA 59.720 41.667 0.00 0.00 38.06 3.53
8389 13686 3.910989 AGGGCTAAACAAAACTTGGAGT 58.089 40.909 0.00 0.00 34.12 3.85
8396 13693 7.709182 GGCTAAACAAAACTTGGAGTTATTTGT 59.291 33.333 5.50 5.50 39.49 2.83
8406 13703 7.981142 ACTTGGAGTTATTTGTAAGTTCCCTA 58.019 34.615 0.00 0.00 0.00 3.53
8407 13704 8.101419 ACTTGGAGTTATTTGTAAGTTCCCTAG 58.899 37.037 0.00 0.00 0.00 3.02
8448 13745 0.043183 TCATCTTCCTCCTCCCAGCA 59.957 55.000 0.00 0.00 0.00 4.41
8449 13746 0.469070 CATCTTCCTCCTCCCAGCAG 59.531 60.000 0.00 0.00 0.00 4.24
8453 13750 0.178891 TTCCTCCTCCCAGCAGTCTT 60.179 55.000 0.00 0.00 0.00 3.01
8454 13751 0.616111 TCCTCCTCCCAGCAGTCTTC 60.616 60.000 0.00 0.00 0.00 2.87
8455 13752 1.621672 CCTCCTCCCAGCAGTCTTCC 61.622 65.000 0.00 0.00 0.00 3.46
8460 13757 1.225704 CCCAGCAGTCTTCCCCATC 59.774 63.158 0.00 0.00 0.00 3.51
8461 13758 1.277580 CCCAGCAGTCTTCCCCATCT 61.278 60.000 0.00 0.00 0.00 2.90
8462 13759 0.179936 CCAGCAGTCTTCCCCATCTC 59.820 60.000 0.00 0.00 0.00 2.75
8486 13783 0.631753 TCCGTCCCTTCATCTCCTCT 59.368 55.000 0.00 0.00 0.00 3.69
8488 13785 0.103937 CGTCCCTTCATCTCCTCTGC 59.896 60.000 0.00 0.00 0.00 4.26
8491 13788 1.045350 CCCTTCATCTCCTCTGCCGA 61.045 60.000 0.00 0.00 0.00 5.54
8574 14066 6.258160 CCCTAAATTACTTGTCGCAGAAATG 58.742 40.000 0.00 0.00 39.69 2.32
8711 14220 5.954296 ATTGATCAAGAAACTGGTGTCTG 57.046 39.130 14.54 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 2.028930 ACTTAACAGAGTCGAAGGCCTG 60.029 50.000 5.69 0.00 36.69 4.85
65 66 5.190528 TGGAGAAGATCAAGCAAATACTCCT 59.809 40.000 0.00 0.00 41.03 3.69
127 128 1.306226 AAGAGCTAAGGAGGGCCGT 60.306 57.895 0.00 0.00 39.96 5.68
215 216 2.090719 AGAAACGGGGAGATGGGATCTA 60.091 50.000 0.00 0.00 40.38 1.98
441 443 2.299582 TCTGGAAATTGGTGCATTGGTG 59.700 45.455 0.00 0.00 0.00 4.17
442 444 2.607499 TCTGGAAATTGGTGCATTGGT 58.393 42.857 0.00 0.00 0.00 3.67
443 445 3.258872 TCTTCTGGAAATTGGTGCATTGG 59.741 43.478 0.00 0.00 0.00 3.16
444 446 4.021719 ACTCTTCTGGAAATTGGTGCATTG 60.022 41.667 0.00 0.00 0.00 2.82
445 447 4.154942 ACTCTTCTGGAAATTGGTGCATT 58.845 39.130 0.00 0.00 0.00 3.56
446 448 3.771216 ACTCTTCTGGAAATTGGTGCAT 58.229 40.909 0.00 0.00 0.00 3.96
512 514 0.741915 TTGCCGACAAACTTTGGGTC 59.258 50.000 6.47 0.00 31.21 4.46
536 538 0.693049 ATCACAAGGGGAACGAAGCT 59.307 50.000 0.00 0.00 0.00 3.74
691 693 1.066215 CCACTTGGGATGTGATCACGA 60.066 52.381 20.54 10.47 40.01 4.35
883 887 0.468226 AGCCCGACTGAACTTGTCAA 59.532 50.000 0.00 0.00 35.22 3.18
895 899 2.435059 GCAACCTGAGAGCCCGAC 60.435 66.667 0.00 0.00 0.00 4.79
918 923 2.434336 CCTCCTTCCATTCATACCACGA 59.566 50.000 0.00 0.00 0.00 4.35
1020 1025 1.079681 TCTTCGCGCCGTTACCAAT 60.080 52.632 0.00 0.00 0.00 3.16
1043 1048 2.564947 GAGCCAAGGAGAGTCTCAGAAA 59.435 50.000 21.53 0.00 31.08 2.52
1049 1054 1.274712 CAAGGAGCCAAGGAGAGTCT 58.725 55.000 0.00 0.00 0.00 3.24
1089 1094 0.316522 GCTGCATAGATGAGCGGAGA 59.683 55.000 0.00 0.00 39.47 3.71
1137 1142 4.704833 GTGCTTGAGCGCCTCCCA 62.705 66.667 2.29 0.00 45.15 4.37
1205 1215 1.409064 AGAGCGAAGAACTGTGTGACA 59.591 47.619 0.00 0.00 0.00 3.58
1291 1302 0.676466 CGAGTATTGCCCACTTGCCA 60.676 55.000 0.00 0.00 0.00 4.92
1351 3933 2.325661 TCCATGGGTGAGACTTGAGA 57.674 50.000 13.02 0.00 0.00 3.27
1352 3934 4.406972 TCTTATCCATGGGTGAGACTTGAG 59.593 45.833 15.30 0.00 0.00 3.02
1353 3935 4.361783 TCTTATCCATGGGTGAGACTTGA 58.638 43.478 15.30 0.00 0.00 3.02
1354 3936 4.760530 TCTTATCCATGGGTGAGACTTG 57.239 45.455 15.30 0.00 0.00 3.16
1355 3937 4.103785 CCATCTTATCCATGGGTGAGACTT 59.896 45.833 21.02 4.38 37.71 3.01
1356 3938 3.649981 CCATCTTATCCATGGGTGAGACT 59.350 47.826 21.02 8.46 37.71 3.24
1357 3939 3.392616 ACCATCTTATCCATGGGTGAGAC 59.607 47.826 21.02 0.00 44.70 3.36
1468 4051 0.397675 TCACAATTTGGCCACCCACA 60.398 50.000 3.88 0.00 41.97 4.17
1546 4129 1.957177 CCAGAGCCTTCGAGTATAGCA 59.043 52.381 0.00 0.00 0.00 3.49
1563 4146 2.967599 TCTCGATGACCAATGACCAG 57.032 50.000 0.00 0.00 0.00 4.00
1618 4201 7.041372 CCAATCTTTAACCGAGTCAAAGAAGAA 60.041 37.037 7.28 0.00 40.58 2.52
1619 4203 6.426937 CCAATCTTTAACCGAGTCAAAGAAGA 59.573 38.462 7.28 2.61 40.58 2.87
1692 4276 2.688446 TGACACGAGTATGATGAGGGAC 59.312 50.000 0.00 0.00 0.00 4.46
1700 4284 6.128309 CCAAATTGTTCATGACACGAGTATGA 60.128 38.462 0.00 0.00 38.18 2.15
1704 4288 4.133820 TCCAAATTGTTCATGACACGAGT 58.866 39.130 0.00 0.00 38.18 4.18
1881 4466 8.738645 AGAGAAAAGAGTTTGTTACAAGTCAT 57.261 30.769 10.70 0.00 0.00 3.06
1959 4544 1.956629 TTCGGGATCGTTCAGGGAGC 61.957 60.000 0.00 0.00 37.69 4.70
1960 4545 0.179108 GTTCGGGATCGTTCAGGGAG 60.179 60.000 0.00 0.00 37.69 4.30
1961 4546 1.895238 GTTCGGGATCGTTCAGGGA 59.105 57.895 0.00 0.00 37.69 4.20
1962 4547 1.518572 CGTTCGGGATCGTTCAGGG 60.519 63.158 0.00 0.00 37.69 4.45
1963 4548 0.102481 ATCGTTCGGGATCGTTCAGG 59.898 55.000 0.00 0.00 37.69 3.86
1964 4549 1.852895 GAATCGTTCGGGATCGTTCAG 59.147 52.381 0.00 0.00 37.69 3.02
1965 4550 1.917273 GAATCGTTCGGGATCGTTCA 58.083 50.000 0.00 0.00 37.69 3.18
2110 4695 2.586357 GCGGAGGAAGACGATGCC 60.586 66.667 0.00 0.00 0.00 4.40
2136 4721 1.225855 CAAGCAGAGCAAACCGTACA 58.774 50.000 0.00 0.00 0.00 2.90
2155 4740 3.983044 TCCTTAACTGAAAGAGGAGGC 57.017 47.619 0.00 0.00 37.43 4.70
2157 4742 4.568760 GCGATTCCTTAACTGAAAGAGGAG 59.431 45.833 0.00 0.00 39.33 3.69
2174 4761 1.078143 AACCAGAGGGCAGCGATTC 60.078 57.895 0.00 0.00 37.90 2.52
2175 4762 1.377725 CAACCAGAGGGCAGCGATT 60.378 57.895 0.00 0.00 37.90 3.34
2176 4763 2.270205 CAACCAGAGGGCAGCGAT 59.730 61.111 0.00 0.00 37.90 4.58
2183 4770 0.397941 TCAGAACAGCAACCAGAGGG 59.602 55.000 0.00 0.00 41.29 4.30
2184 4771 1.517242 GTCAGAACAGCAACCAGAGG 58.483 55.000 0.00 0.00 0.00 3.69
2227 4814 4.695791 AACCCCAGACCCTCCCCC 62.696 72.222 0.00 0.00 0.00 5.40
2228 4815 1.736491 AAAAACCCCAGACCCTCCCC 61.736 60.000 0.00 0.00 0.00 4.81
2229 4816 0.541998 CAAAAACCCCAGACCCTCCC 60.542 60.000 0.00 0.00 0.00 4.30
2230 4817 0.541998 CCAAAAACCCCAGACCCTCC 60.542 60.000 0.00 0.00 0.00 4.30
2231 4818 0.187606 ACCAAAAACCCCAGACCCTC 59.812 55.000 0.00 0.00 0.00 4.30
2232 4819 0.639943 AACCAAAAACCCCAGACCCT 59.360 50.000 0.00 0.00 0.00 4.34
2233 4820 0.756294 CAACCAAAAACCCCAGACCC 59.244 55.000 0.00 0.00 0.00 4.46
2234 4821 1.491668 ACAACCAAAAACCCCAGACC 58.508 50.000 0.00 0.00 0.00 3.85
2235 4822 3.620427 AAACAACCAAAAACCCCAGAC 57.380 42.857 0.00 0.00 0.00 3.51
2236 4823 3.307762 CCAAAACAACCAAAAACCCCAGA 60.308 43.478 0.00 0.00 0.00 3.86
2237 4824 3.013219 CCAAAACAACCAAAAACCCCAG 58.987 45.455 0.00 0.00 0.00 4.45
2238 4825 2.290960 CCCAAAACAACCAAAAACCCCA 60.291 45.455 0.00 0.00 0.00 4.96
2239 4826 2.370349 CCCAAAACAACCAAAAACCCC 58.630 47.619 0.00 0.00 0.00 4.95
2240 4827 2.370349 CCCCAAAACAACCAAAAACCC 58.630 47.619 0.00 0.00 0.00 4.11
2241 4828 2.370349 CCCCCAAAACAACCAAAAACC 58.630 47.619 0.00 0.00 0.00 3.27
2262 4849 3.376914 GATTGGACCGCCGAAACGC 62.377 63.158 0.00 0.00 36.79 4.84
2263 4850 1.693083 GAGATTGGACCGCCGAAACG 61.693 60.000 0.00 0.00 36.79 3.60
2264 4851 1.366854 GGAGATTGGACCGCCGAAAC 61.367 60.000 0.00 0.00 36.79 2.78
2268 4864 4.891727 CCGGAGATTGGACCGCCG 62.892 72.222 0.00 0.00 46.59 6.46
2297 4893 1.371635 CAAAAGGAAACAGCCGCCG 60.372 57.895 0.00 0.00 0.00 6.46
2298 4894 0.104120 AACAAAAGGAAACAGCCGCC 59.896 50.000 0.00 0.00 0.00 6.13
2299 4895 1.487482 GAACAAAAGGAAACAGCCGC 58.513 50.000 0.00 0.00 0.00 6.53
2300 4896 1.269569 GGGAACAAAAGGAAACAGCCG 60.270 52.381 0.00 0.00 0.00 5.52
2301 4897 1.269569 CGGGAACAAAAGGAAACAGCC 60.270 52.381 0.00 0.00 0.00 4.85
2302 4898 1.407618 ACGGGAACAAAAGGAAACAGC 59.592 47.619 0.00 0.00 0.00 4.40
2303 4899 2.223711 CCACGGGAACAAAAGGAAACAG 60.224 50.000 0.00 0.00 0.00 3.16
2304 4900 1.751924 CCACGGGAACAAAAGGAAACA 59.248 47.619 0.00 0.00 0.00 2.83
2305 4901 1.067974 CCCACGGGAACAAAAGGAAAC 59.932 52.381 0.00 0.00 37.50 2.78
2306 4902 1.342175 ACCCACGGGAACAAAAGGAAA 60.342 47.619 9.72 0.00 38.96 3.13
2307 4903 0.259356 ACCCACGGGAACAAAAGGAA 59.741 50.000 9.72 0.00 38.96 3.36
2308 4904 0.179012 GACCCACGGGAACAAAAGGA 60.179 55.000 9.72 0.00 38.96 3.36
2309 4905 1.512156 CGACCCACGGGAACAAAAGG 61.512 60.000 9.72 0.00 38.96 3.11
2310 4906 1.946267 CGACCCACGGGAACAAAAG 59.054 57.895 9.72 0.00 38.96 2.27
2311 4907 4.144418 CGACCCACGGGAACAAAA 57.856 55.556 9.72 0.00 38.96 2.44
2330 4926 1.582610 GAAAGGCACGAATCCGGCAA 61.583 55.000 0.00 0.00 40.78 4.52
2351 4947 0.725133 AGGGAGGGGAAATGAGAGGA 59.275 55.000 0.00 0.00 0.00 3.71
2356 4952 0.850883 AGCCAAGGGAGGGGAAATGA 60.851 55.000 0.00 0.00 0.00 2.57
2357 4953 0.396278 GAGCCAAGGGAGGGGAAATG 60.396 60.000 0.00 0.00 0.00 2.32
2358 4954 1.584717 GGAGCCAAGGGAGGGGAAAT 61.585 60.000 0.00 0.00 0.00 2.17
2363 4960 3.732849 GGTGGAGCCAAGGGAGGG 61.733 72.222 0.00 0.00 37.17 4.30
2384 4981 3.931247 ACAACGGTGGCGGCAGTA 61.931 61.111 13.91 0.00 0.00 2.74
2399 4996 1.767692 GAGGGGGAAGAAAGGCACA 59.232 57.895 0.00 0.00 0.00 4.57
2413 5010 3.628832 AGATAGAAAGGAGGAGGAGGG 57.371 52.381 0.00 0.00 0.00 4.30
2416 5013 4.388118 GGGAGAAGATAGAAAGGAGGAGGA 60.388 50.000 0.00 0.00 0.00 3.71
2418 5015 3.901222 GGGGAGAAGATAGAAAGGAGGAG 59.099 52.174 0.00 0.00 0.00 3.69
2421 5018 3.070878 GCAGGGGAGAAGATAGAAAGGAG 59.929 52.174 0.00 0.00 0.00 3.69
2497 5094 0.249073 GTCAGTGTGAGCGTGTGACT 60.249 55.000 0.00 0.00 35.64 3.41
2499 5096 0.249031 CTGTCAGTGTGAGCGTGTGA 60.249 55.000 0.00 0.00 0.00 3.58
2504 5101 2.047844 CCCCTGTCAGTGTGAGCG 60.048 66.667 0.00 0.00 0.00 5.03
2505 5102 1.294780 CTCCCCTGTCAGTGTGAGC 59.705 63.158 0.00 0.00 0.00 4.26
2506 5103 0.542938 TCCTCCCCTGTCAGTGTGAG 60.543 60.000 0.00 1.85 0.00 3.51
2507 5104 0.542938 CTCCTCCCCTGTCAGTGTGA 60.543 60.000 0.00 0.00 0.00 3.58
2508 5105 1.548357 CCTCCTCCCCTGTCAGTGTG 61.548 65.000 0.00 0.00 0.00 3.82
2509 5106 1.229336 CCTCCTCCCCTGTCAGTGT 60.229 63.158 0.00 0.00 0.00 3.55
2510 5107 0.975040 CTCCTCCTCCCCTGTCAGTG 60.975 65.000 0.00 0.00 0.00 3.66
2511 5108 1.149782 TCTCCTCCTCCCCTGTCAGT 61.150 60.000 0.00 0.00 0.00 3.41
2512 5109 0.264359 ATCTCCTCCTCCCCTGTCAG 59.736 60.000 0.00 0.00 0.00 3.51
2516 5113 0.114168 ATCGATCTCCTCCTCCCCTG 59.886 60.000 0.00 0.00 0.00 4.45
2526 5123 1.492720 GGCAAACTCGATCGATCTCC 58.507 55.000 19.78 11.60 0.00 3.71
2527 5124 1.124462 CGGCAAACTCGATCGATCTC 58.876 55.000 19.78 6.38 0.00 2.75
2528 5125 0.456221 ACGGCAAACTCGATCGATCT 59.544 50.000 19.78 5.73 0.00 2.75
2529 5126 0.847035 GACGGCAAACTCGATCGATC 59.153 55.000 19.78 15.68 0.00 3.69
2530 5127 0.866061 CGACGGCAAACTCGATCGAT 60.866 55.000 19.78 0.94 35.18 3.59
2531 5128 1.513373 CGACGGCAAACTCGATCGA 60.513 57.895 18.32 18.32 35.18 3.59
2532 5129 0.866061 ATCGACGGCAAACTCGATCG 60.866 55.000 9.36 9.36 44.43 3.69
2537 5134 1.079405 TCCCATCGACGGCAAACTC 60.079 57.895 0.00 0.00 0.00 3.01
2540 5137 0.250553 AAACTCCCATCGACGGCAAA 60.251 50.000 0.00 0.00 0.00 3.68
2556 5153 5.768164 TGATCCTACCAGAACAAAAGGAAAC 59.232 40.000 0.00 0.00 39.68 2.78
2557 5154 5.947663 TGATCCTACCAGAACAAAAGGAAA 58.052 37.500 0.00 0.00 39.68 3.13
2559 5156 5.779241 ATGATCCTACCAGAACAAAAGGA 57.221 39.130 0.00 0.00 40.50 3.36
2560 5157 6.840780 AAATGATCCTACCAGAACAAAAGG 57.159 37.500 0.00 0.00 0.00 3.11
2634 6270 5.046591 TCTGACCTCAATAAACCAGTCGATT 60.047 40.000 0.00 0.00 0.00 3.34
2635 6271 4.466370 TCTGACCTCAATAAACCAGTCGAT 59.534 41.667 0.00 0.00 0.00 3.59
2672 6308 4.816925 GTCCAGAGCCCAATATTAACTGAC 59.183 45.833 0.00 0.00 0.00 3.51
2676 6312 2.548480 GCGTCCAGAGCCCAATATTAAC 59.452 50.000 0.00 0.00 0.00 2.01
2677 6313 2.438021 AGCGTCCAGAGCCCAATATTAA 59.562 45.455 0.00 0.00 34.64 1.40
2697 6334 6.071503 ACAACTAGTACACCAAACCTAGCTAG 60.072 42.308 14.20 14.20 32.03 3.42
2755 6392 5.684704 ACGGAGGATAACATCATCACAATT 58.315 37.500 3.55 0.00 41.57 2.32
3218 7196 4.260538 GCTGATAAGTTCATGCCTCTTTCG 60.261 45.833 0.00 0.00 32.72 3.46
3367 7345 6.484288 TCCAACATTGTACAGATCCAATTCT 58.516 36.000 0.00 0.00 0.00 2.40
3468 7446 4.513442 TCCATCTACAAAGGATTGAACCG 58.487 43.478 0.00 0.00 38.94 4.44
3720 7744 7.168219 TGGGAATGAATAATCTCTATTTCCCG 58.832 38.462 11.59 0.00 34.13 5.14
3731 7755 3.503363 TGCGAGCATGGGAATGAATAATC 59.497 43.478 0.00 0.00 0.00 1.75
4514 8598 3.483421 TCTCCTTGTCACGACTCTGTTA 58.517 45.455 0.00 0.00 0.00 2.41
4544 8640 0.252742 TCCTCACCTTCTCCTTCCCC 60.253 60.000 0.00 0.00 0.00 4.81
4646 8742 3.959535 ATGTCCATTTGCCGTTGAATT 57.040 38.095 0.00 0.00 0.00 2.17
4833 8931 2.686915 CAAGGCCCTGAGATCATGAAAC 59.313 50.000 0.00 0.00 0.00 2.78
4877 8984 3.053842 AGAACCATTCCATCAGTGCAGAT 60.054 43.478 0.00 0.00 0.00 2.90
4890 8997 4.284378 GCATACTTGCTGAGAACCATTC 57.716 45.455 0.00 0.00 45.77 2.67
4985 9095 9.706846 CAATCACATTTTCCTTTTCTTTTTGAC 57.293 29.630 0.00 0.00 0.00 3.18
5148 9270 8.438676 AGCATTAAAGTATATGTGTGAGAACC 57.561 34.615 0.00 0.00 0.00 3.62
5250 9399 5.005740 TGTTGGTCAGATTCATCAAGAAGG 58.994 41.667 0.00 0.00 40.15 3.46
5331 9480 7.335171 TGACAATCATCCACTACTTCAGAATTG 59.665 37.037 0.00 0.00 0.00 2.32
5807 10976 6.534793 TGGAAACAGAAGTGAATTGCTTTTTC 59.465 34.615 0.00 0.00 35.01 2.29
5900 11069 1.053424 TAGTTTCTGGGTTCTGGCGT 58.947 50.000 0.00 0.00 0.00 5.68
5975 11164 2.760092 GAGAGTGGATTGAGAGAGCACT 59.240 50.000 0.00 0.00 0.00 4.40
6262 11452 4.495690 AGCTTTGGAGGAATAGAAGTCC 57.504 45.455 0.00 0.00 35.17 3.85
6288 11478 1.512926 CTTGAGTTGTTCAGACCGGG 58.487 55.000 6.32 0.00 37.07 5.73
6892 12145 8.563502 TCTAGTCTTACCAAACTCCTAAGGATA 58.436 37.037 0.00 0.00 0.00 2.59
7390 12643 2.676471 GCCCGTCCAATTGCCTGT 60.676 61.111 0.00 0.00 0.00 4.00
7427 12680 0.027979 CGGTAGCAATGCACCATTCG 59.972 55.000 20.70 7.89 31.05 3.34
7548 12801 2.523015 CGGCAAGCTCAAAATCATCAC 58.477 47.619 0.00 0.00 0.00 3.06
7858 13153 6.427441 TCTCTCATACTACCACACTTCAGAT 58.573 40.000 0.00 0.00 0.00 2.90
7966 13262 0.963962 ACCACATTACCACGACTCGT 59.036 50.000 0.00 0.00 42.36 4.18
7967 13263 2.163010 AGTACCACATTACCACGACTCG 59.837 50.000 0.00 0.00 0.00 4.18
8066 13362 1.202639 TGTTCAGCGGACAGACAACAT 60.203 47.619 0.00 0.00 0.00 2.71
8071 13367 1.583054 AACTTGTTCAGCGGACAGAC 58.417 50.000 0.00 0.00 0.00 3.51
8131 13428 2.285220 CCGAAACATAGACAATGGCTCG 59.715 50.000 0.00 0.00 40.62 5.03
8140 13437 1.009829 CAGGCAGCCGAAACATAGAC 58.990 55.000 5.55 0.00 0.00 2.59
8148 13445 0.543277 ATCAGATTCAGGCAGCCGAA 59.457 50.000 17.47 17.47 0.00 4.30
8150 13447 0.179065 TCATCAGATTCAGGCAGCCG 60.179 55.000 5.55 0.83 0.00 5.52
8214 13511 3.853831 TGACAAATGCATCATGACACC 57.146 42.857 16.78 5.98 0.00 4.16
8235 13532 4.160329 TGAACCTGATAAGGAGACAGTGT 58.840 43.478 1.89 0.00 0.00 3.55
8303 13600 3.576550 ACTCTCCTGAACTTCTGAAGACC 59.423 47.826 23.36 13.90 0.00 3.85
8332 13629 0.616395 TCATGGTTCTGCCCTCCGTA 60.616 55.000 0.00 0.00 36.04 4.02
8333 13630 1.274703 ATCATGGTTCTGCCCTCCGT 61.275 55.000 0.00 0.00 36.04 4.69
8334 13631 0.758734 TATCATGGTTCTGCCCTCCG 59.241 55.000 0.00 0.00 36.04 4.63
8335 13632 1.541233 CGTATCATGGTTCTGCCCTCC 60.541 57.143 0.00 0.00 36.04 4.30
8346 13643 2.216046 AGCAATGCAGACGTATCATGG 58.784 47.619 8.35 0.00 0.00 3.66
8352 13649 1.742411 GCCCTTAGCAATGCAGACGTA 60.742 52.381 8.35 0.00 42.97 3.57
8370 13667 7.709182 ACAAATAACTCCAAGTTTTGTTTAGCC 59.291 33.333 0.00 0.00 36.36 3.93
8377 13674 9.244799 GGAACTTACAAATAACTCCAAGTTTTG 57.755 33.333 0.00 0.95 39.51 2.44
8381 13678 6.849151 AGGGAACTTACAAATAACTCCAAGT 58.151 36.000 0.00 0.00 37.44 3.16
8396 13693 7.277396 CCGTTGGATAATTTCTAGGGAACTTA 58.723 38.462 0.00 0.00 43.67 2.24
8406 13703 3.456277 AGGAGAGCCGTTGGATAATTTCT 59.544 43.478 0.00 0.00 39.96 2.52
8407 13704 3.809905 AGGAGAGCCGTTGGATAATTTC 58.190 45.455 0.00 0.00 39.96 2.17
8448 13745 2.628290 GGAGAAGGAGATGGGGAAGACT 60.628 54.545 0.00 0.00 0.00 3.24
8449 13746 1.765904 GGAGAAGGAGATGGGGAAGAC 59.234 57.143 0.00 0.00 0.00 3.01
8453 13750 0.397254 GACGGAGAAGGAGATGGGGA 60.397 60.000 0.00 0.00 0.00 4.81
8454 13751 1.403687 GGACGGAGAAGGAGATGGGG 61.404 65.000 0.00 0.00 0.00 4.96
8455 13752 1.403687 GGGACGGAGAAGGAGATGGG 61.404 65.000 0.00 0.00 0.00 4.00
8460 13757 1.410882 GATGAAGGGACGGAGAAGGAG 59.589 57.143 0.00 0.00 0.00 3.69
8461 13758 1.007238 AGATGAAGGGACGGAGAAGGA 59.993 52.381 0.00 0.00 0.00 3.36
8462 13759 1.410882 GAGATGAAGGGACGGAGAAGG 59.589 57.143 0.00 0.00 0.00 3.46
8512 13809 1.901948 TGTCCGAGCTCAAGACGGT 60.902 57.895 22.25 0.00 45.71 4.83
8614 14106 3.927142 GTCCGGAATTACTTGTCACAGAG 59.073 47.826 5.23 0.00 0.00 3.35
8672 14179 9.383519 CTTGATCAATACCAGTACAATACAAGT 57.616 33.333 8.96 0.00 0.00 3.16
8673 14180 9.599866 TCTTGATCAATACCAGTACAATACAAG 57.400 33.333 8.96 0.00 0.00 3.16
8674 14181 9.952030 TTCTTGATCAATACCAGTACAATACAA 57.048 29.630 8.96 0.00 0.00 2.41
8675 14182 9.952030 TTTCTTGATCAATACCAGTACAATACA 57.048 29.630 8.96 0.00 0.00 2.29
8691 14200 4.422073 ACAGACACCAGTTTCTTGATCA 57.578 40.909 0.00 0.00 0.00 2.92
8711 14220 9.252962 GGATATTGATGATTTGTTGATCCAAAC 57.747 33.333 0.00 0.00 37.16 2.93


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

AutoCloner maintained by Alex Coulton.