Multiple sequence alignment - TraesCS2B01G199500

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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 TraesCS2B01G199500 chr2B 100.000 9919 0 0 1 9919 177658471 177648553 0.000000e+00 18318.0
1 TraesCS2B01G199500 chr2B 86.646 659 59 12 4125 4756 44139283 44139939 0.000000e+00 702.0
2 TraesCS2B01G199500 chr2B 87.769 605 50 13 4125 4706 317239548 317238945 0.000000e+00 686.0
3 TraesCS2B01G199500 chr2B 87.000 100 9 4 3321 3418 51720442 51720539 1.050000e-19 110.0
4 TraesCS2B01G199500 chr2B 90.244 82 7 1 9830 9910 132352065 132352146 1.360000e-18 106.0
5 TraesCS2B01G199500 chr2B 84.000 75 8 3 9757 9831 232350881 232350951 1.790000e-07 69.4
6 TraesCS2B01G199500 chr2A 97.847 3484 43 9 3922 7382 130807473 130803999 0.000000e+00 5989.0
7 TraesCS2B01G199500 chr2A 95.360 2586 65 20 1 2564 130811651 130809099 0.000000e+00 4060.0
8 TraesCS2B01G199500 chr2A 96.983 2088 47 9 7384 9459 130803947 130801864 0.000000e+00 3493.0
9 TraesCS2B01G199500 chr2A 96.982 1226 26 5 2547 3765 130808663 130807442 0.000000e+00 2049.0
10 TraesCS2B01G199500 chr2A 89.311 421 35 5 9505 9918 130801771 130801354 4.110000e-143 520.0
11 TraesCS2B01G199500 chr2A 95.679 162 7 0 3764 3925 272428812 272428973 2.750000e-65 261.0
12 TraesCS2B01G199500 chr2A 93.023 172 10 2 1672 1842 317953165 317953335 5.950000e-62 250.0
13 TraesCS2B01G199500 chr2A 78.528 163 32 3 2984 3146 694149277 694149118 4.900000e-18 104.0
14 TraesCS2B01G199500 chr2A 84.706 85 8 4 3325 3405 175553401 175553318 8.260000e-11 80.5
15 TraesCS2B01G199500 chr2A 79.167 120 18 6 3325 3439 116230292 116230175 1.070000e-09 76.8
16 TraesCS2B01G199500 chr2D 97.073 2904 64 13 877 3765 124882475 124879578 0.000000e+00 4872.0
17 TraesCS2B01G199500 chr2D 98.659 2386 25 4 5000 7382 124878372 124875991 0.000000e+00 4222.0
18 TraesCS2B01G199500 chr2D 97.790 2081 35 4 7384 9461 124875939 124873867 0.000000e+00 3578.0
19 TraesCS2B01G199500 chr2D 95.889 1119 17 5 3922 5018 124879609 124878498 0.000000e+00 1784.0
20 TraesCS2B01G199500 chr2D 92.677 874 31 12 1 864 124883684 124882834 0.000000e+00 1229.0
21 TraesCS2B01G199500 chr2D 85.452 653 70 12 4125 4755 423469227 423468578 0.000000e+00 656.0
22 TraesCS2B01G199500 chr2D 94.152 171 9 1 1672 1842 268894465 268894296 9.880000e-65 259.0
23 TraesCS2B01G199500 chr2D 93.491 169 10 1 1674 1842 512768134 512768301 5.950000e-62 250.0
24 TraesCS2B01G199500 chr2D 80.583 309 44 11 3144 3440 2259397 2259701 3.610000e-54 224.0
25 TraesCS2B01G199500 chr2D 92.079 101 5 1 9509 9609 124873605 124873508 1.340000e-28 139.0
26 TraesCS2B01G199500 chr2D 83.750 80 7 6 9756 9834 571556159 571556085 4.970000e-08 71.3
27 TraesCS2B01G199500 chr7D 87.577 652 56 12 4125 4755 421832665 421832018 0.000000e+00 732.0
28 TraesCS2B01G199500 chr7D 79.848 263 44 7 1973 2234 566566775 566566521 6.120000e-42 183.0
29 TraesCS2B01G199500 chr7D 90.625 96 9 0 9824 9919 232366218 232366313 2.910000e-25 128.0
30 TraesCS2B01G199500 chr7D 90.625 96 9 0 9824 9919 428175373 428175468 2.910000e-25 128.0
31 TraesCS2B01G199500 chr7D 84.762 105 14 2 2982 3085 227658247 227658144 4.900000e-18 104.0
32 TraesCS2B01G199500 chr7D 77.907 172 31 6 3188 3356 32450295 32450462 6.340000e-17 100.0
33 TraesCS2B01G199500 chr7D 92.857 70 2 2 9762 9831 204247274 204247208 2.280000e-16 99.0
34 TraesCS2B01G199500 chr7D 76.821 151 29 5 6395 6545 115035599 115035743 8.260000e-11 80.5
35 TraesCS2B01G199500 chr7D 100.000 35 0 0 2685 2719 256343847 256343813 2.310000e-06 65.8
36 TraesCS2B01G199500 chr7D 100.000 35 0 0 2685 2719 544754786 544754820 2.310000e-06 65.8
37 TraesCS2B01G199500 chr5D 87.615 654 50 13 4125 4756 271901794 271902438 0.000000e+00 730.0
38 TraesCS2B01G199500 chr5D 92.982 171 11 1 1672 1842 299073411 299073580 2.140000e-61 248.0
39 TraesCS2B01G199500 chr5D 84.000 75 8 2 9757 9831 449506431 449506501 1.790000e-07 69.4
40 TraesCS2B01G199500 chr5D 100.000 35 0 0 2685 2719 888290 888256 2.310000e-06 65.8
41 TraesCS2B01G199500 chr5D 83.562 73 8 2 9759 9831 481284609 481284541 2.310000e-06 65.8
42 TraesCS2B01G199500 chr5D 100.000 35 0 0 2685 2719 533763585 533763551 2.310000e-06 65.8
43 TraesCS2B01G199500 chr5D 82.667 75 9 2 9757 9831 299400749 299400819 8.320000e-06 63.9
44 TraesCS2B01G199500 chr5D 97.059 34 0 1 6587 6619 359051121 359051088 1.000000e-03 56.5
45 TraesCS2B01G199500 chr5D 94.595 37 1 1 9758 9793 476941109 476941073 1.000000e-03 56.5
46 TraesCS2B01G199500 chr6A 86.260 655 59 15 4125 4755 9194834 9195481 0.000000e+00 682.0
47 TraesCS2B01G199500 chr6A 86.517 89 12 0 9830 9918 23628748 23628660 2.280000e-16 99.0
48 TraesCS2B01G199500 chr6A 85.870 92 12 1 9829 9919 133757432 133757523 8.200000e-16 97.1
49 TraesCS2B01G199500 chr3A 87.171 608 53 10 4125 4710 13012375 13011771 0.000000e+00 667.0
50 TraesCS2B01G199500 chr3A 92.529 174 12 1 1672 1845 609951128 609950956 2.140000e-61 248.0
51 TraesCS2B01G199500 chr3A 87.912 91 10 1 9830 9919 16144032 16144122 1.360000e-18 106.0
52 TraesCS2B01G199500 chr3A 94.118 68 4 0 3754 3821 625554296 625554229 4.900000e-18 104.0
53 TraesCS2B01G199500 chr3A 91.803 61 5 0 3854 3914 625554229 625554169 1.780000e-12 86.1
54 TraesCS2B01G199500 chr3A 82.759 87 10 4 6525 6611 714645368 714645287 1.380000e-08 73.1
55 TraesCS2B01G199500 chr3A 97.059 34 1 0 6580 6613 404557193 404557160 3.870000e-04 58.4
56 TraesCS2B01G199500 chr3A 100.000 28 0 0 6587 6614 675317201 675317174 1.800000e-02 52.8
57 TraesCS2B01G199500 chr4B 94.083 169 9 1 1674 1842 386210235 386210402 1.280000e-63 255.0
58 TraesCS2B01G199500 chr4B 90.217 92 8 1 9829 9919 80677471 80677562 1.750000e-22 119.0
59 TraesCS2B01G199500 chr4B 86.022 93 9 4 9830 9919 211973377 211973286 8.200000e-16 97.1
60 TraesCS2B01G199500 chr4B 86.905 84 10 1 9828 9910 459945095 459945012 1.060000e-14 93.5
61 TraesCS2B01G199500 chr4B 91.111 45 4 0 9758 9802 643783857 643783901 2.990000e-05 62.1
62 TraesCS2B01G199500 chr7A 92.982 171 9 2 1672 1842 503442487 503442320 7.690000e-61 246.0
63 TraesCS2B01G199500 chr5B 79.098 244 48 3 1967 2209 584253355 584253596 2.220000e-36 165.0
64 TraesCS2B01G199500 chr5B 83.333 90 9 5 647 735 549002189 549002105 2.970000e-10 78.7
65 TraesCS2B01G199500 chr5B 87.324 71 2 2 9761 9831 29336629 29336692 3.840000e-09 75.0
66 TraesCS2B01G199500 chr4D 88.043 92 10 1 9825 9915 31817571 31817480 3.790000e-19 108.0
67 TraesCS2B01G199500 chr4D 82.418 91 15 1 9827 9916 497646663 497646573 2.970000e-10 78.7
68 TraesCS2B01G199500 chr4D 78.740 127 17 8 6488 6612 30747868 30747750 1.070000e-09 76.8
69 TraesCS2B01G199500 chr4D 87.500 64 7 1 9824 9886 72840686 72840749 1.380000e-08 73.1
70 TraesCS2B01G199500 chr4D 84.000 75 8 2 9757 9831 47533272 47533202 1.790000e-07 69.4
71 TraesCS2B01G199500 chr4D 100.000 28 0 0 9828 9855 325364977 325365004 1.800000e-02 52.8
72 TraesCS2B01G199500 chr6B 86.458 96 13 0 9824 9919 719923439 719923534 1.360000e-18 106.0
73 TraesCS2B01G199500 chr6B 84.211 95 11 4 3327 3418 411544723 411544630 1.370000e-13 89.8
74 TraesCS2B01G199500 chr6B 77.622 143 29 3 2984 3123 716226288 716226430 6.380000e-12 84.2
75 TraesCS2B01G199500 chr3B 87.912 91 10 1 9830 9919 146553580 146553490 1.360000e-18 106.0
76 TraesCS2B01G199500 chr3B 80.328 122 21 3 2981 3100 298196684 298196804 1.370000e-13 89.8
77 TraesCS2B01G199500 chr3B 96.774 31 1 0 3763 3793 765390427 765390397 1.800000e-02 52.8
78 TraesCS2B01G199500 chr1B 87.097 93 11 1 9828 9919 520878565 520878657 4.900000e-18 104.0
79 TraesCS2B01G199500 chr7B 83.333 114 15 4 3325 3435 336001893 336001781 1.760000e-17 102.0
80 TraesCS2B01G199500 chr7B 87.640 89 10 1 9830 9918 634628388 634628475 1.760000e-17 102.0
81 TraesCS2B01G199500 chr7B 85.870 92 12 1 9829 9919 13310360 13310269 8.200000e-16 97.1
82 TraesCS2B01G199500 chr7B 79.054 148 25 6 2972 3116 688168579 688168435 8.200000e-16 97.1
83 TraesCS2B01G199500 chr7B 76.250 160 26 10 3237 3390 427092342 427092189 3.840000e-09 75.0
84 TraesCS2B01G199500 chr1D 89.024 82 8 1 9835 9915 52606559 52606640 6.340000e-17 100.0
85 TraesCS2B01G199500 chr1D 84.615 91 13 1 9830 9919 86209922 86210012 1.370000e-13 89.8
86 TraesCS2B01G199500 chr1D 90.000 70 3 2 9762 9831 107217892 107217957 4.940000e-13 87.9
87 TraesCS2B01G199500 chr1D 84.211 76 8 2 9756 9831 192592179 192592250 4.970000e-08 71.3
88 TraesCS2B01G199500 chr1D 83.784 74 8 3 9758 9831 463248109 463248178 6.430000e-07 67.6
89 TraesCS2B01G199500 chr1D 100.000 35 0 0 2685 2719 367276558 367276524 2.310000e-06 65.8
90 TraesCS2B01G199500 chr1A 84.783 92 13 1 9828 9918 586330371 586330280 3.820000e-14 91.6
91 TraesCS2B01G199500 chrUn 86.420 81 11 0 9830 9910 401611670 401611590 1.370000e-13 89.8
92 TraesCS2B01G199500 chrUn 85.366 82 11 1 9830 9910 401612135 401612054 6.380000e-12 84.2
93 TraesCS2B01G199500 chr3D 89.655 58 5 1 9830 9886 542797505 542797562 1.380000e-08 73.1
94 TraesCS2B01G199500 chr3D 100.000 35 0 0 2685 2719 82259833 82259799 2.310000e-06 65.8
95 TraesCS2B01G199500 chr6D 100.000 35 0 0 2685 2719 117194784 117194818 2.310000e-06 65.8
96 TraesCS2B01G199500 chr6D 80.952 84 11 5 6538 6621 152261636 152261558 2.990000e-05 62.1
97 TraesCS2B01G199500 chr6D 81.944 72 12 1 9828 9898 373052641 373052712 1.080000e-04 60.2
98 TraesCS2B01G199500 chr6D 77.119 118 17 6 6499 6613 472134451 472134561 1.080000e-04 60.2
99 TraesCS2B01G199500 chr6D 100.000 28 0 0 9828 9855 447069091 447069118 1.800000e-02 52.8


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 TraesCS2B01G199500 chr2B 177648553 177658471 9918 True 18318.000000 18318 100.0000 1 9919 1 chr2B.!!$R1 9918
1 TraesCS2B01G199500 chr2B 44139283 44139939 656 False 702.000000 702 86.6460 4125 4756 1 chr2B.!!$F1 631
2 TraesCS2B01G199500 chr2B 317238945 317239548 603 True 686.000000 686 87.7690 4125 4706 1 chr2B.!!$R2 581
3 TraesCS2B01G199500 chr2A 130801354 130811651 10297 True 3222.200000 5989 95.2966 1 9918 5 chr2A.!!$R4 9917
4 TraesCS2B01G199500 chr2D 124873508 124883684 10176 True 2637.333333 4872 95.6945 1 9609 6 chr2D.!!$R4 9608
5 TraesCS2B01G199500 chr2D 423468578 423469227 649 True 656.000000 656 85.4520 4125 4755 1 chr2D.!!$R2 630
6 TraesCS2B01G199500 chr7D 421832018 421832665 647 True 732.000000 732 87.5770 4125 4755 1 chr7D.!!$R4 630
7 TraesCS2B01G199500 chr5D 271901794 271902438 644 False 730.000000 730 87.6150 4125 4756 1 chr5D.!!$F1 631
8 TraesCS2B01G199500 chr6A 9194834 9195481 647 False 682.000000 682 86.2600 4125 4755 1 chr6A.!!$F1 630
9 TraesCS2B01G199500 chr3A 13011771 13012375 604 True 667.000000 667 87.1710 4125 4710 1 chr3A.!!$R1 585

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
28 29 0.527817 CGGGACCAACGTATGAGCTC 60.528 60.000 6.82 6.82 0.00 4.09 F
537 550 0.610687 CTCCCTCCTGCTCGTTTTCT 59.389 55.000 0.00 0.00 0.00 2.52 F
1110 1475 2.202878 AGCCGCGTCGTGCATTAT 60.203 55.556 4.92 0.00 46.97 1.28 F
2196 2562 0.179073 CGACGCCAGGAATTGAGGAT 60.179 55.000 0.00 0.00 0.00 3.24 F
3783 4616 1.061131 CACTAGTAAGCATGCACGTGC 59.939 52.381 33.11 33.11 45.38 5.34 F
3918 4751 0.394899 AAGGCTAGGGATGCAAGTGC 60.395 55.000 0.00 0.00 42.50 4.40 F
3921 4754 1.134098 GGCTAGGGATGCAAGTGCTTA 60.134 52.381 4.69 0.00 42.66 3.09 F
5657 6668 1.202330 CTCCTGCTCCTCATCCTTGT 58.798 55.000 0.00 0.00 0.00 3.16 F
7348 8363 0.037975 CTTTTGTCCTGCCATGGTGC 60.038 55.000 14.67 0.00 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1110 1475 0.245539 CCTCGGCGTCTTCCAAGTAA 59.754 55.000 6.85 0.0 0.00 2.24 R
2196 2562 0.739462 CCGTTCTATCGGCAGTTGCA 60.739 55.000 6.43 0.0 43.96 4.08 R
2892 3717 1.079819 CGCACACTCGAGTCCCATT 60.080 57.895 16.96 0.0 0.00 3.16 R
3786 4619 0.107945 TGCGTATGGCTACACATGCA 60.108 50.000 0.00 0.0 44.05 3.96 R
5154 6165 0.469917 ATTGCCCATACGAGGTCCAG 59.530 55.000 0.00 0.0 0.00 3.86 R
5657 6668 8.156820 TGAGAATAAGAGGTGATGAAAACTTCA 58.843 33.333 0.00 0.0 45.01 3.02 R
6032 7043 5.369404 TGGCTTCTGATAAGATGGTATGGAA 59.631 40.000 0.00 0.0 0.00 3.53 R
7381 8396 5.870706 TGGATGTTTACCTATCACACAACA 58.129 37.500 0.00 0.0 0.00 3.33 R
9334 10407 0.105224 TTCGCAACTTCTTCGGGACA 59.895 50.000 0.00 0.0 0.00 4.02 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
19 20 2.094762 AATTTCTCTCGGGACCAACG 57.905 50.000 0.00 0.00 0.00 4.10
28 29 0.527817 CGGGACCAACGTATGAGCTC 60.528 60.000 6.82 6.82 0.00 4.09
116 126 5.389642 AGAAACGCATAACATATGACACG 57.610 39.130 10.38 8.08 0.00 4.49
119 129 4.772046 ACGCATAACATATGACACGAAC 57.228 40.909 10.38 0.00 0.00 3.95
170 181 0.773014 TCATCCCATAGGTGCCATGG 59.227 55.000 7.63 7.63 42.30 3.66
187 198 1.024271 TGGCACAGCTGTTCTTGAAC 58.976 50.000 18.94 6.56 0.00 3.18
188 199 1.312815 GGCACAGCTGTTCTTGAACT 58.687 50.000 18.94 0.00 0.00 3.01
189 200 1.678101 GGCACAGCTGTTCTTGAACTT 59.322 47.619 18.94 0.00 0.00 2.66
190 201 2.099756 GGCACAGCTGTTCTTGAACTTT 59.900 45.455 18.94 0.00 0.00 2.66
191 202 3.429410 GGCACAGCTGTTCTTGAACTTTT 60.429 43.478 18.94 0.00 0.00 2.27
192 203 4.176271 GCACAGCTGTTCTTGAACTTTTT 58.824 39.130 18.94 0.00 0.00 1.94
356 369 2.997986 GCGATACAGAGAAACCCGAAAA 59.002 45.455 0.00 0.00 0.00 2.29
428 441 4.179599 CTCCCCTCCCCTCCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
537 550 0.610687 CTCCCTCCTGCTCGTTTTCT 59.389 55.000 0.00 0.00 0.00 2.52
995 1360 2.754946 TTGTTTAGTACTCCGGGCTG 57.245 50.000 0.00 0.00 0.00 4.85
1000 1365 4.791069 GTACTCCGGGCTGGGGGA 62.791 72.222 18.55 4.55 45.67 4.81
1110 1475 2.202878 AGCCGCGTCGTGCATTAT 60.203 55.556 4.92 0.00 46.97 1.28
1141 1506 3.374402 CCGAGGGCGTGTCTCACT 61.374 66.667 0.00 0.00 35.23 3.41
1206 1571 2.338500 GTCGTGTCAGAGGATTTCCAC 58.662 52.381 0.00 0.00 38.89 4.02
1338 1703 4.037927 CCCTCACCTCAAGTAATTCCCTA 58.962 47.826 0.00 0.00 0.00 3.53
1339 1704 4.473559 CCCTCACCTCAAGTAATTCCCTAA 59.526 45.833 0.00 0.00 0.00 2.69
1599 1964 6.985013 TGTTAGACTGTAATGCGAAAATACG 58.015 36.000 0.00 0.00 0.00 3.06
2044 2410 7.921786 AATAGCAGAATTTTTAAAAAGCCCC 57.078 32.000 17.72 7.60 0.00 5.80
2196 2562 0.179073 CGACGCCAGGAATTGAGGAT 60.179 55.000 0.00 0.00 0.00 3.24
2308 2674 1.682257 GAGGGAAGCAGGCAAGTCT 59.318 57.895 0.00 0.00 0.00 3.24
2542 2911 7.822161 ATGCAAAATTATAGTATGACCAGCA 57.178 32.000 0.00 0.00 0.00 4.41
2543 2912 7.822161 TGCAAAATTATAGTATGACCAGCAT 57.178 32.000 0.00 0.00 41.08 3.79
2544 2913 8.236585 TGCAAAATTATAGTATGACCAGCATT 57.763 30.769 0.00 0.00 38.44 3.56
2695 3518 7.441157 CACTCACTAAGATAAATTTGGCCGATA 59.559 37.037 0.00 0.00 0.00 2.92
2792 3616 7.064229 TGACTGAAAATTTGGTAAGGTAGGTT 58.936 34.615 0.00 0.00 0.00 3.50
2819 3643 5.533528 GGACACAAACAAAACATACCCTAGT 59.466 40.000 0.00 0.00 0.00 2.57
2823 3647 8.315482 ACACAAACAAAACATACCCTAGTTTTT 58.685 29.630 0.00 0.00 43.26 1.94
2906 3731 1.993370 GAACGAAATGGGACTCGAGTG 59.007 52.381 25.58 8.33 38.43 3.51
2924 3749 5.756833 TCGAGTGTGCGAGAGAAGTATTATA 59.243 40.000 0.00 0.00 35.01 0.98
2975 3800 5.261209 TCAACCTGTGGAAATTTTGACTG 57.739 39.130 0.00 0.00 0.00 3.51
3168 3993 8.123130 ACCTATTAGGGCATGTCATAGTATAGT 58.877 37.037 14.26 0.00 40.58 2.12
3652 4484 8.481314 ACTCTGTCAGCTATCTTGATTCATTTA 58.519 33.333 0.00 0.00 0.00 1.40
3765 4598 8.044060 TGAATTATGTGTCCTTTTCTCATCAC 57.956 34.615 0.00 0.00 0.00 3.06
3766 4599 7.884877 TGAATTATGTGTCCTTTTCTCATCACT 59.115 33.333 0.00 0.00 0.00 3.41
3767 4600 9.383519 GAATTATGTGTCCTTTTCTCATCACTA 57.616 33.333 0.00 0.00 0.00 2.74
3768 4601 8.954950 ATTATGTGTCCTTTTCTCATCACTAG 57.045 34.615 0.00 0.00 0.00 2.57
3769 4602 5.808366 TGTGTCCTTTTCTCATCACTAGT 57.192 39.130 0.00 0.00 0.00 2.57
3770 4603 6.911250 TGTGTCCTTTTCTCATCACTAGTA 57.089 37.500 0.00 0.00 0.00 1.82
3771 4604 7.297936 TGTGTCCTTTTCTCATCACTAGTAA 57.702 36.000 0.00 0.00 0.00 2.24
3772 4605 7.378966 TGTGTCCTTTTCTCATCACTAGTAAG 58.621 38.462 0.00 0.00 0.00 2.34
3773 4606 6.311690 GTGTCCTTTTCTCATCACTAGTAAGC 59.688 42.308 0.00 0.00 0.00 3.09
3774 4607 6.014584 TGTCCTTTTCTCATCACTAGTAAGCA 60.015 38.462 0.00 0.00 0.00 3.91
3775 4608 7.044798 GTCCTTTTCTCATCACTAGTAAGCAT 58.955 38.462 0.00 0.00 0.00 3.79
3776 4609 7.010923 GTCCTTTTCTCATCACTAGTAAGCATG 59.989 40.741 0.00 0.00 0.00 4.06
3777 4610 6.238320 CCTTTTCTCATCACTAGTAAGCATGC 60.238 42.308 10.51 10.51 0.00 4.06
3778 4611 5.343307 TTCTCATCACTAGTAAGCATGCA 57.657 39.130 21.98 0.00 0.00 3.96
3779 4612 4.686972 TCTCATCACTAGTAAGCATGCAC 58.313 43.478 21.98 10.48 0.00 4.57
3780 4613 3.447742 TCATCACTAGTAAGCATGCACG 58.552 45.455 21.98 3.52 0.00 5.34
3781 4614 3.119137 TCATCACTAGTAAGCATGCACGT 60.119 43.478 21.98 7.14 0.00 4.49
3782 4615 2.606108 TCACTAGTAAGCATGCACGTG 58.394 47.619 21.98 12.28 0.00 4.49
3783 4616 1.061131 CACTAGTAAGCATGCACGTGC 59.939 52.381 33.11 33.11 45.38 5.34
3797 4630 2.934277 CGTGCAATGCATGTGTAGC 58.066 52.632 18.55 0.49 41.91 3.58
3798 4631 0.523968 CGTGCAATGCATGTGTAGCC 60.524 55.000 18.55 0.00 41.91 3.93
3799 4632 0.527113 GTGCAATGCATGTGTAGCCA 59.473 50.000 12.38 0.00 41.91 4.75
3800 4633 1.135527 GTGCAATGCATGTGTAGCCAT 59.864 47.619 12.38 0.00 41.91 4.40
3801 4634 2.358582 GTGCAATGCATGTGTAGCCATA 59.641 45.455 12.38 0.00 41.91 2.74
3802 4635 2.358582 TGCAATGCATGTGTAGCCATAC 59.641 45.455 2.72 0.00 31.71 2.39
3803 4636 2.602933 GCAATGCATGTGTAGCCATACG 60.603 50.000 0.00 0.00 34.39 3.06
3804 4637 1.229428 ATGCATGTGTAGCCATACGC 58.771 50.000 0.00 0.00 41.81 4.42
3821 4654 9.456147 AGCCATACGCAATAAATATATAAACCA 57.544 29.630 0.00 0.00 41.38 3.67
3822 4655 9.716507 GCCATACGCAATAAATATATAAACCAG 57.283 33.333 0.00 0.00 37.47 4.00
3844 4677 9.357161 ACCAGTAATCAAAATAAAGGTAACACA 57.643 29.630 0.00 0.00 41.41 3.72
3852 4685 9.004717 TCAAAATAAAGGTAACACATTCGATCA 57.995 29.630 0.00 0.00 41.41 2.92
3853 4686 9.061610 CAAAATAAAGGTAACACATTCGATCAC 57.938 33.333 0.00 0.00 41.41 3.06
3854 4687 6.920569 ATAAAGGTAACACATTCGATCACC 57.079 37.500 0.00 0.00 41.41 4.02
3855 4688 3.973206 AGGTAACACATTCGATCACCA 57.027 42.857 0.00 0.00 41.41 4.17
3856 4689 4.280436 AGGTAACACATTCGATCACCAA 57.720 40.909 0.00 0.00 41.41 3.67
3857 4690 4.647611 AGGTAACACATTCGATCACCAAA 58.352 39.130 0.00 0.00 41.41 3.28
3858 4691 4.454504 AGGTAACACATTCGATCACCAAAC 59.545 41.667 0.00 0.00 41.41 2.93
3859 4692 4.214545 GGTAACACATTCGATCACCAAACA 59.785 41.667 0.00 0.00 0.00 2.83
3860 4693 4.909696 AACACATTCGATCACCAAACAA 57.090 36.364 0.00 0.00 0.00 2.83
3861 4694 4.488126 ACACATTCGATCACCAAACAAG 57.512 40.909 0.00 0.00 0.00 3.16
3862 4695 3.882888 ACACATTCGATCACCAAACAAGT 59.117 39.130 0.00 0.00 0.00 3.16
3863 4696 4.024048 ACACATTCGATCACCAAACAAGTC 60.024 41.667 0.00 0.00 0.00 3.01
3864 4697 4.024133 CACATTCGATCACCAAACAAGTCA 60.024 41.667 0.00 0.00 0.00 3.41
3865 4698 4.761739 ACATTCGATCACCAAACAAGTCAT 59.238 37.500 0.00 0.00 0.00 3.06
3866 4699 5.241506 ACATTCGATCACCAAACAAGTCATT 59.758 36.000 0.00 0.00 0.00 2.57
3867 4700 6.429692 ACATTCGATCACCAAACAAGTCATTA 59.570 34.615 0.00 0.00 0.00 1.90
3868 4701 6.869315 TTCGATCACCAAACAAGTCATTAA 57.131 33.333 0.00 0.00 0.00 1.40
3869 4702 6.480524 TCGATCACCAAACAAGTCATTAAG 57.519 37.500 0.00 0.00 0.00 1.85
3870 4703 5.088739 CGATCACCAAACAAGTCATTAAGC 58.911 41.667 0.00 0.00 0.00 3.09
3871 4704 5.334802 CGATCACCAAACAAGTCATTAAGCA 60.335 40.000 0.00 0.00 0.00 3.91
3872 4705 5.843673 TCACCAAACAAGTCATTAAGCAA 57.156 34.783 0.00 0.00 0.00 3.91
3873 4706 6.214191 TCACCAAACAAGTCATTAAGCAAA 57.786 33.333 0.00 0.00 0.00 3.68
3874 4707 6.815089 TCACCAAACAAGTCATTAAGCAAAT 58.185 32.000 0.00 0.00 0.00 2.32
3875 4708 6.922957 TCACCAAACAAGTCATTAAGCAAATC 59.077 34.615 0.00 0.00 0.00 2.17
3876 4709 6.925165 CACCAAACAAGTCATTAAGCAAATCT 59.075 34.615 0.00 0.00 0.00 2.40
3877 4710 7.115378 CACCAAACAAGTCATTAAGCAAATCTC 59.885 37.037 0.00 0.00 0.00 2.75
3878 4711 7.147312 CCAAACAAGTCATTAAGCAAATCTCA 58.853 34.615 0.00 0.00 0.00 3.27
3879 4712 7.652909 CCAAACAAGTCATTAAGCAAATCTCAA 59.347 33.333 0.00 0.00 0.00 3.02
3880 4713 9.199982 CAAACAAGTCATTAAGCAAATCTCAAT 57.800 29.630 0.00 0.00 0.00 2.57
3881 4714 8.752766 AACAAGTCATTAAGCAAATCTCAATG 57.247 30.769 0.00 0.00 0.00 2.82
3882 4715 7.889469 ACAAGTCATTAAGCAAATCTCAATGT 58.111 30.769 0.00 0.00 0.00 2.71
3883 4716 8.025445 ACAAGTCATTAAGCAAATCTCAATGTC 58.975 33.333 0.00 0.00 0.00 3.06
3884 4717 7.093322 AGTCATTAAGCAAATCTCAATGTCC 57.907 36.000 0.00 0.00 0.00 4.02
3885 4718 6.660521 AGTCATTAAGCAAATCTCAATGTCCA 59.339 34.615 0.00 0.00 0.00 4.02
3886 4719 7.177216 AGTCATTAAGCAAATCTCAATGTCCAA 59.823 33.333 0.00 0.00 0.00 3.53
3887 4720 7.274250 GTCATTAAGCAAATCTCAATGTCCAAC 59.726 37.037 0.00 0.00 0.00 3.77
3888 4721 6.647334 TTAAGCAAATCTCAATGTCCAACA 57.353 33.333 0.00 0.00 0.00 3.33
3889 4722 5.534207 AAGCAAATCTCAATGTCCAACAA 57.466 34.783 0.00 0.00 0.00 2.83
3890 4723 4.874970 AGCAAATCTCAATGTCCAACAAC 58.125 39.130 0.00 0.00 0.00 3.32
3891 4724 3.989817 GCAAATCTCAATGTCCAACAACC 59.010 43.478 0.00 0.00 0.00 3.77
3892 4725 4.229096 CAAATCTCAATGTCCAACAACCG 58.771 43.478 0.00 0.00 0.00 4.44
3893 4726 2.920724 TCTCAATGTCCAACAACCGA 57.079 45.000 0.00 0.00 0.00 4.69
3894 4727 3.201353 TCTCAATGTCCAACAACCGAA 57.799 42.857 0.00 0.00 0.00 4.30
3895 4728 3.546724 TCTCAATGTCCAACAACCGAAA 58.453 40.909 0.00 0.00 0.00 3.46
3896 4729 3.563808 TCTCAATGTCCAACAACCGAAAG 59.436 43.478 0.00 0.00 0.00 2.62
3897 4730 3.546724 TCAATGTCCAACAACCGAAAGA 58.453 40.909 0.00 0.00 0.00 2.52
3898 4731 3.948473 TCAATGTCCAACAACCGAAAGAA 59.052 39.130 0.00 0.00 0.00 2.52
3899 4732 4.399618 TCAATGTCCAACAACCGAAAGAAA 59.600 37.500 0.00 0.00 0.00 2.52
3900 4733 4.993029 ATGTCCAACAACCGAAAGAAAA 57.007 36.364 0.00 0.00 0.00 2.29
3901 4734 4.364415 TGTCCAACAACCGAAAGAAAAG 57.636 40.909 0.00 0.00 0.00 2.27
3902 4735 3.129638 TGTCCAACAACCGAAAGAAAAGG 59.870 43.478 0.00 0.00 0.00 3.11
3903 4736 2.100087 TCCAACAACCGAAAGAAAAGGC 59.900 45.455 0.00 0.00 0.00 4.35
3904 4737 2.100749 CCAACAACCGAAAGAAAAGGCT 59.899 45.455 0.00 0.00 0.00 4.58
3905 4738 3.316868 CCAACAACCGAAAGAAAAGGCTA 59.683 43.478 0.00 0.00 0.00 3.93
3906 4739 4.537015 CAACAACCGAAAGAAAAGGCTAG 58.463 43.478 0.00 0.00 0.00 3.42
3907 4740 3.146847 ACAACCGAAAGAAAAGGCTAGG 58.853 45.455 0.00 0.00 0.00 3.02
3908 4741 2.488153 CAACCGAAAGAAAAGGCTAGGG 59.512 50.000 0.00 0.00 0.00 3.53
3909 4742 1.982958 ACCGAAAGAAAAGGCTAGGGA 59.017 47.619 0.00 0.00 0.00 4.20
3910 4743 2.576648 ACCGAAAGAAAAGGCTAGGGAT 59.423 45.455 0.00 0.00 0.00 3.85
3911 4744 2.945668 CCGAAAGAAAAGGCTAGGGATG 59.054 50.000 0.00 0.00 0.00 3.51
3912 4745 2.356069 CGAAAGAAAAGGCTAGGGATGC 59.644 50.000 0.00 0.00 0.00 3.91
3913 4746 3.356290 GAAAGAAAAGGCTAGGGATGCA 58.644 45.455 0.00 0.00 0.00 3.96
3914 4747 3.456380 AAGAAAAGGCTAGGGATGCAA 57.544 42.857 0.00 0.00 0.00 4.08
3915 4748 3.010200 AGAAAAGGCTAGGGATGCAAG 57.990 47.619 0.00 0.00 0.00 4.01
3916 4749 2.310052 AGAAAAGGCTAGGGATGCAAGT 59.690 45.455 0.00 0.00 0.00 3.16
3917 4750 2.134789 AAAGGCTAGGGATGCAAGTG 57.865 50.000 0.00 0.00 0.00 3.16
3918 4751 0.394899 AAGGCTAGGGATGCAAGTGC 60.395 55.000 0.00 0.00 42.50 4.40
3919 4752 1.225704 GGCTAGGGATGCAAGTGCT 59.774 57.895 4.69 0.00 42.66 4.40
3920 4753 0.394899 GGCTAGGGATGCAAGTGCTT 60.395 55.000 4.69 0.00 42.66 3.91
3921 4754 1.134098 GGCTAGGGATGCAAGTGCTTA 60.134 52.381 4.69 0.00 42.66 3.09
3922 4755 2.643551 GCTAGGGATGCAAGTGCTTAA 58.356 47.619 4.69 0.00 42.66 1.85
3923 4756 3.016736 GCTAGGGATGCAAGTGCTTAAA 58.983 45.455 4.69 0.00 42.66 1.52
3924 4757 3.443681 GCTAGGGATGCAAGTGCTTAAAA 59.556 43.478 4.69 0.00 42.66 1.52
3925 4758 4.082245 GCTAGGGATGCAAGTGCTTAAAAA 60.082 41.667 4.69 0.00 42.66 1.94
4047 4880 2.170166 GCACCCAACTGGATTGAATGA 58.830 47.619 0.00 0.00 41.23 2.57
4683 5549 3.553917 CGTTTTGCAAATTTCCGTTTCCT 59.446 39.130 13.65 0.00 0.00 3.36
4757 5624 1.837439 TGCTCCATTTCATCCCTACGT 59.163 47.619 0.00 0.00 0.00 3.57
4981 5848 6.139679 TCCCTTGTGACTATCATTTTCCTT 57.860 37.500 0.00 0.00 0.00 3.36
5023 6034 1.407656 TTTCGACCACCTGTCAGGCT 61.408 55.000 19.40 3.48 44.71 4.58
5657 6668 1.202330 CTCCTGCTCCTCATCCTTGT 58.798 55.000 0.00 0.00 0.00 3.16
6032 7043 1.377725 CCGAAGCCCACAAGCAGAT 60.378 57.895 0.00 0.00 34.23 2.90
6404 7415 8.204160 TCAGAAAAGTCAACTTCTCTATGTTCA 58.796 33.333 0.00 0.00 31.33 3.18
6569 7580 1.682323 GGTTACGTTTGCCCTTTTGGA 59.318 47.619 0.00 0.00 44.07 3.53
6570 7581 2.101082 GGTTACGTTTGCCCTTTTGGAA 59.899 45.455 0.00 0.00 44.07 3.53
6571 7582 3.243941 GGTTACGTTTGCCCTTTTGGAAT 60.244 43.478 0.00 0.00 44.07 3.01
6572 7583 4.022155 GGTTACGTTTGCCCTTTTGGAATA 60.022 41.667 0.00 0.00 44.07 1.75
6699 7710 6.811253 TTCTCCGCAAGTGTATGTTTTTAT 57.189 33.333 0.00 0.00 0.00 1.40
6700 7711 7.908827 TTCTCCGCAAGTGTATGTTTTTATA 57.091 32.000 0.00 0.00 0.00 0.98
7100 8113 9.336171 AGATAAGAGAACAAAATCTCAATAGCC 57.664 33.333 7.04 0.00 46.73 3.93
7278 8293 3.750371 TGTTAGTACAAGCAGGTGCATT 58.250 40.909 4.48 0.00 45.16 3.56
7348 8363 0.037975 CTTTTGTCCTGCCATGGTGC 60.038 55.000 14.67 0.00 0.00 5.01
7371 8386 5.297776 GCTGGTATGACAATAATTCTGCTGT 59.702 40.000 0.00 0.00 0.00 4.40
7375 8390 8.028354 TGGTATGACAATAATTCTGCTGTTTTG 58.972 33.333 0.00 0.00 0.00 2.44
7376 8391 6.956299 ATGACAATAATTCTGCTGTTTTGC 57.044 33.333 0.00 0.00 0.00 3.68
7377 8392 6.088016 TGACAATAATTCTGCTGTTTTGCT 57.912 33.333 0.00 0.00 0.00 3.91
7381 8396 9.143631 GACAATAATTCTGCTGTTTTGCTAAAT 57.856 29.630 0.00 0.00 0.00 1.40
7382 8397 8.928733 ACAATAATTCTGCTGTTTTGCTAAATG 58.071 29.630 0.00 0.00 0.00 2.32
7843 8913 5.712152 ATGATTGTTCCAGGTGAAAACTC 57.288 39.130 0.00 0.00 33.94 3.01
7905 8975 3.515502 AGATTGGATCAAGAGTCGTTGGA 59.484 43.478 0.00 0.00 0.00 3.53
7936 9006 2.664402 AGGAAGCCAGATGTGTTGTT 57.336 45.000 0.00 0.00 0.00 2.83
7951 9021 4.062991 GTGTTGTTGAGAATACCTTCGGT 58.937 43.478 0.00 0.00 40.16 4.69
7993 9063 5.809001 ACTTGATAACATGACATCCACTGT 58.191 37.500 0.00 0.00 42.15 3.55
8231 9301 6.578163 ACTGAGACTAGTTTAACTGAGACC 57.422 41.667 8.00 0.00 0.00 3.85
8589 9659 5.023452 TCTGTTCAACTGATAAGGGCTCTA 58.977 41.667 0.00 0.00 0.00 2.43
8630 9700 3.706086 AGCAAACATTATTAGCAAGGGGG 59.294 43.478 0.00 0.00 0.00 5.40
8752 9825 2.908940 GCGGCCAAGGGATGATGG 60.909 66.667 2.24 0.00 0.00 3.51
8984 10057 3.525800 AGATATGGTAATGCAACCCCC 57.474 47.619 5.11 0.00 38.90 5.40
8988 10061 1.001887 GGTAATGCAACCCCCGTGA 60.002 57.895 0.00 0.00 33.02 4.35
9246 10319 8.747538 AGTTTCCTTTTGCTAAACTAGAAGAA 57.252 30.769 0.00 0.00 40.65 2.52
9247 10320 9.355916 AGTTTCCTTTTGCTAAACTAGAAGAAT 57.644 29.630 0.00 0.00 40.65 2.40
9248 10321 9.967346 GTTTCCTTTTGCTAAACTAGAAGAATT 57.033 29.630 0.00 0.00 31.83 2.17
9334 10407 3.096852 TGGTGATCGTCCTCTACATGTT 58.903 45.455 2.30 0.00 0.00 2.71
9335 10408 3.119137 TGGTGATCGTCCTCTACATGTTG 60.119 47.826 2.30 1.19 0.00 3.33
9337 10410 4.106197 GTGATCGTCCTCTACATGTTGTC 58.894 47.826 2.30 0.00 0.00 3.18
9386 10470 1.455383 CCCCTCCTGTGTTGTGCAAC 61.455 60.000 8.01 8.01 41.50 4.17
9459 10543 3.520691 CCATCCCATGGTCTCATCATT 57.479 47.619 11.73 0.00 45.54 2.57
9461 10545 3.572682 CCATCCCATGGTCTCATCATTTG 59.427 47.826 11.73 0.00 45.54 2.32
9462 10546 4.212716 CATCCCATGGTCTCATCATTTGT 58.787 43.478 11.73 0.00 0.00 2.83
9463 10547 3.623703 TCCCATGGTCTCATCATTTGTG 58.376 45.455 11.73 0.00 0.00 3.33
9466 10550 3.193903 CCATGGTCTCATCATTTGTGCAA 59.806 43.478 2.57 0.00 0.00 4.08
9467 10551 3.921119 TGGTCTCATCATTTGTGCAAC 57.079 42.857 0.00 0.00 37.35 4.17
9480 10564 1.003118 TGTGCAACACCTATCCCTGTC 59.997 52.381 0.00 0.00 45.67 3.51
9481 10565 0.618458 TGCAACACCTATCCCTGTCC 59.382 55.000 0.00 0.00 0.00 4.02
9482 10566 0.107165 GCAACACCTATCCCTGTCCC 60.107 60.000 0.00 0.00 0.00 4.46
9483 10567 1.285280 CAACACCTATCCCTGTCCCA 58.715 55.000 0.00 0.00 0.00 4.37
9493 10634 0.695462 CCCTGTCCCATCCTCCATGA 60.695 60.000 0.00 0.00 33.80 3.07
9505 10646 1.631405 CTCCATGAAAACCCTTGGCA 58.369 50.000 0.00 0.00 32.99 4.92
9613 10918 2.369394 GAGCAGATTCCGATTTTGGGT 58.631 47.619 0.00 0.00 0.00 4.51
9622 10927 3.437213 TCCGATTTTGGGTGTAGAGAGA 58.563 45.455 0.00 0.00 0.00 3.10
9623 10928 3.835978 TCCGATTTTGGGTGTAGAGAGAA 59.164 43.478 0.00 0.00 0.00 2.87
9627 10932 6.151144 CCGATTTTGGGTGTAGAGAGAAAAAT 59.849 38.462 0.00 0.00 0.00 1.82
9635 10942 7.664318 TGGGTGTAGAGAGAAAAATTTTAGGTC 59.336 37.037 3.34 0.00 0.00 3.85
9688 10995 5.733373 GCAATCAGTTCTCGAACAAAAAGGT 60.733 40.000 11.90 0.00 43.47 3.50
9779 11086 8.692710 CACATACATACTCCCTCTGTAAACTAA 58.307 37.037 0.00 0.00 0.00 2.24
9839 11149 7.278461 TCTGAAAGATCTTATACTTCCTCCG 57.722 40.000 8.75 0.00 38.67 4.63
9842 11152 6.040616 TGAAAGATCTTATACTTCCTCCGTCC 59.959 42.308 8.75 0.00 0.00 4.79
9843 11153 4.073549 AGATCTTATACTTCCTCCGTCCG 58.926 47.826 0.00 0.00 0.00 4.79
9855 11165 2.354403 CCTCCGTCCGGAAATACTTGTT 60.354 50.000 5.23 0.00 44.66 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.527817 CGAGCTCATACGTTGGTCCC 60.528 60.000 15.40 0.00 0.00 4.46
28 29 3.617540 TGAACAACAAATGGTAGCACG 57.382 42.857 0.00 0.00 0.00 5.34
89 96 6.027131 GTCATATGTTATGCGTTTCTTGCAA 58.973 36.000 0.00 0.00 46.87 4.08
92 99 5.672426 CGTGTCATATGTTATGCGTTTCTTG 59.328 40.000 1.90 0.00 0.00 3.02
95 102 5.383984 TCGTGTCATATGTTATGCGTTTC 57.616 39.130 1.90 0.00 0.00 2.78
99 106 3.484285 TCGTTCGTGTCATATGTTATGCG 59.516 43.478 1.90 2.67 0.00 4.73
100 107 5.383984 TTCGTTCGTGTCATATGTTATGC 57.616 39.130 1.90 0.00 0.00 3.14
139 149 3.744940 ATGGGATGAGTTGTTCCATGT 57.255 42.857 0.00 0.00 36.90 3.21
170 181 3.427161 AAAGTTCAAGAACAGCTGTGC 57.573 42.857 22.49 20.13 43.47 4.57
286 297 7.973944 GTGAAAAGTGTCAAGGTTTTCTTATGT 59.026 33.333 13.46 0.00 39.74 2.29
289 300 7.696992 AGTGAAAAGTGTCAAGGTTTTCTTA 57.303 32.000 13.46 0.00 39.74 2.10
426 439 3.775654 GAGGCGGACAGGTGGGAG 61.776 72.222 0.00 0.00 0.00 4.30
798 817 4.642429 ACTTGAGATTAACGTGGAAAGCT 58.358 39.130 0.00 0.00 0.00 3.74
872 891 1.615424 TTCTCGGGGAAGAAGGGGG 60.615 63.158 0.00 0.00 31.71 5.40
1000 1365 1.079405 CGGTACCAACAGGACGCAT 60.079 57.895 13.54 0.00 0.00 4.73
1110 1475 0.245539 CCTCGGCGTCTTCCAAGTAA 59.754 55.000 6.85 0.00 0.00 2.24
1383 1748 9.899661 AACAATAACAGATGGTAATGCTTAGTA 57.100 29.630 0.00 0.00 0.00 1.82
1599 1964 3.485947 TTGACATACTTTGCCATTCGC 57.514 42.857 0.00 0.00 38.31 4.70
2044 2410 1.468520 CGTTGGCCCAGATAACACTTG 59.531 52.381 0.00 0.00 0.00 3.16
2196 2562 0.739462 CCGTTCTATCGGCAGTTGCA 60.739 55.000 6.43 0.00 43.96 4.08
2527 2896 6.099701 ACTGTTCCAATGCTGGTCATACTATA 59.900 38.462 0.00 0.00 43.97 1.31
2534 2903 2.363306 AACTGTTCCAATGCTGGTCA 57.637 45.000 0.00 0.00 43.97 4.02
2543 2912 9.703892 CCATATTATTGTTTGAAACTGTTCCAA 57.296 29.630 9.69 0.00 32.28 3.53
2544 2913 8.865090 ACCATATTATTGTTTGAAACTGTTCCA 58.135 29.630 9.69 0.00 32.28 3.53
2670 3493 5.741011 TCGGCCAAATTTATCTTAGTGAGT 58.259 37.500 2.24 0.00 0.00 3.41
2695 3518 7.765695 TCTCTAGTTCATTTTTCTTGCCAAT 57.234 32.000 0.00 0.00 0.00 3.16
2792 3616 5.187967 AGGGTATGTTTTGTTTGTGTCCAAA 59.812 36.000 0.00 0.00 38.22 3.28
2892 3717 1.079819 CGCACACTCGAGTCCCATT 60.080 57.895 16.96 0.00 0.00 3.16
2906 3731 8.085720 TCACTACTATAATACTTCTCTCGCAC 57.914 38.462 0.00 0.00 0.00 5.34
2924 3749 5.125097 CGGTGTAGTTCCTGTTATCACTACT 59.875 44.000 9.17 0.00 41.46 2.57
3415 4245 5.674933 AAGAGCAAGTATAATAAAGCGCC 57.325 39.130 2.29 0.00 0.00 6.53
3652 4484 4.890581 AGACGGTAATAGATCTTCAGCAGT 59.109 41.667 0.00 0.00 0.00 4.40
3776 4609 3.454574 CACATGCATTGCACGTGC 58.545 55.556 33.11 33.11 45.10 5.34
3778 4611 0.168788 GCTACACATGCATTGCACGT 59.831 50.000 14.66 9.40 43.04 4.49
3779 4612 0.523968 GGCTACACATGCATTGCACG 60.524 55.000 14.66 8.59 43.04 5.34
3780 4613 0.527113 TGGCTACACATGCATTGCAC 59.473 50.000 14.66 0.00 43.04 4.57
3781 4614 1.476477 ATGGCTACACATGCATTGCA 58.524 45.000 14.72 14.72 44.86 4.08
3782 4615 2.602933 CGTATGGCTACACATGCATTGC 60.603 50.000 0.00 0.46 33.73 3.56
3783 4616 2.602933 GCGTATGGCTACACATGCATTG 60.603 50.000 0.00 1.69 39.11 2.82
3784 4617 1.603802 GCGTATGGCTACACATGCATT 59.396 47.619 0.00 0.00 39.11 3.56
3785 4618 1.229428 GCGTATGGCTACACATGCAT 58.771 50.000 0.00 0.00 39.11 3.96
3786 4619 0.107945 TGCGTATGGCTACACATGCA 60.108 50.000 0.00 0.00 44.05 3.96
3787 4620 1.013596 TTGCGTATGGCTACACATGC 58.986 50.000 0.00 0.00 44.05 4.06
3788 4621 5.416862 TTTATTGCGTATGGCTACACATG 57.583 39.130 0.00 0.00 44.05 3.21
3789 4622 7.921786 ATATTTATTGCGTATGGCTACACAT 57.078 32.000 0.00 0.00 44.05 3.21
3795 4628 9.456147 TGGTTTATATATTTATTGCGTATGGCT 57.544 29.630 0.00 0.00 44.05 4.75
3796 4629 9.716507 CTGGTTTATATATTTATTGCGTATGGC 57.283 33.333 0.00 0.00 43.96 4.40
3818 4651 9.357161 TGTGTTACCTTTATTTTGATTACTGGT 57.643 29.630 0.00 0.00 0.00 4.00
3826 4659 9.004717 TGATCGAATGTGTTACCTTTATTTTGA 57.995 29.630 0.00 0.00 0.00 2.69
3827 4660 9.061610 GTGATCGAATGTGTTACCTTTATTTTG 57.938 33.333 0.00 0.00 0.00 2.44
3828 4661 8.241367 GGTGATCGAATGTGTTACCTTTATTTT 58.759 33.333 0.00 0.00 0.00 1.82
3829 4662 7.392113 TGGTGATCGAATGTGTTACCTTTATTT 59.608 33.333 0.00 0.00 0.00 1.40
3830 4663 6.882140 TGGTGATCGAATGTGTTACCTTTATT 59.118 34.615 0.00 0.00 0.00 1.40
3831 4664 6.411376 TGGTGATCGAATGTGTTACCTTTAT 58.589 36.000 0.00 0.00 0.00 1.40
3832 4665 5.795972 TGGTGATCGAATGTGTTACCTTTA 58.204 37.500 0.00 0.00 0.00 1.85
3833 4666 4.647611 TGGTGATCGAATGTGTTACCTTT 58.352 39.130 0.00 0.00 0.00 3.11
3834 4667 4.280436 TGGTGATCGAATGTGTTACCTT 57.720 40.909 0.00 0.00 0.00 3.50
3835 4668 3.973206 TGGTGATCGAATGTGTTACCT 57.027 42.857 0.00 0.00 0.00 3.08
3836 4669 4.214545 TGTTTGGTGATCGAATGTGTTACC 59.785 41.667 0.00 0.00 0.00 2.85
3837 4670 5.351233 TGTTTGGTGATCGAATGTGTTAC 57.649 39.130 0.00 0.00 0.00 2.50
3838 4671 5.529430 ACTTGTTTGGTGATCGAATGTGTTA 59.471 36.000 0.00 0.00 0.00 2.41
3839 4672 4.338118 ACTTGTTTGGTGATCGAATGTGTT 59.662 37.500 0.00 0.00 0.00 3.32
3840 4673 3.882888 ACTTGTTTGGTGATCGAATGTGT 59.117 39.130 0.00 0.00 0.00 3.72
3841 4674 4.024133 TGACTTGTTTGGTGATCGAATGTG 60.024 41.667 0.00 0.00 0.00 3.21
3842 4675 4.133820 TGACTTGTTTGGTGATCGAATGT 58.866 39.130 0.00 0.00 0.00 2.71
3843 4676 4.747540 TGACTTGTTTGGTGATCGAATG 57.252 40.909 0.00 0.00 0.00 2.67
3844 4677 5.964958 AATGACTTGTTTGGTGATCGAAT 57.035 34.783 0.00 0.00 0.00 3.34
3845 4678 6.567701 GCTTAATGACTTGTTTGGTGATCGAA 60.568 38.462 0.00 0.00 0.00 3.71
3846 4679 5.106712 GCTTAATGACTTGTTTGGTGATCGA 60.107 40.000 0.00 0.00 0.00 3.59
3847 4680 5.088739 GCTTAATGACTTGTTTGGTGATCG 58.911 41.667 0.00 0.00 0.00 3.69
3848 4681 6.012658 TGCTTAATGACTTGTTTGGTGATC 57.987 37.500 0.00 0.00 0.00 2.92
3849 4682 6.403866 TTGCTTAATGACTTGTTTGGTGAT 57.596 33.333 0.00 0.00 0.00 3.06
3850 4683 5.843673 TTGCTTAATGACTTGTTTGGTGA 57.156 34.783 0.00 0.00 0.00 4.02
3851 4684 6.925165 AGATTTGCTTAATGACTTGTTTGGTG 59.075 34.615 0.00 0.00 0.00 4.17
3852 4685 7.054491 AGATTTGCTTAATGACTTGTTTGGT 57.946 32.000 0.00 0.00 0.00 3.67
3853 4686 7.147312 TGAGATTTGCTTAATGACTTGTTTGG 58.853 34.615 0.00 0.00 0.00 3.28
3854 4687 8.578308 TTGAGATTTGCTTAATGACTTGTTTG 57.422 30.769 0.00 0.00 0.00 2.93
3864 4697 7.230849 TGTTGGACATTGAGATTTGCTTAAT 57.769 32.000 0.00 0.00 33.49 1.40
3865 4698 6.647334 TGTTGGACATTGAGATTTGCTTAA 57.353 33.333 0.00 0.00 0.00 1.85
3866 4699 6.446318 GTTGTTGGACATTGAGATTTGCTTA 58.554 36.000 0.00 0.00 0.00 3.09
3867 4700 5.291971 GTTGTTGGACATTGAGATTTGCTT 58.708 37.500 0.00 0.00 0.00 3.91
3868 4701 4.262164 GGTTGTTGGACATTGAGATTTGCT 60.262 41.667 0.00 0.00 0.00 3.91
3869 4702 3.989817 GGTTGTTGGACATTGAGATTTGC 59.010 43.478 0.00 0.00 0.00 3.68
3870 4703 4.023279 TCGGTTGTTGGACATTGAGATTTG 60.023 41.667 0.00 0.00 0.00 2.32
3871 4704 4.141287 TCGGTTGTTGGACATTGAGATTT 58.859 39.130 0.00 0.00 0.00 2.17
3872 4705 3.750371 TCGGTTGTTGGACATTGAGATT 58.250 40.909 0.00 0.00 0.00 2.40
3873 4706 3.417069 TCGGTTGTTGGACATTGAGAT 57.583 42.857 0.00 0.00 0.00 2.75
3874 4707 2.920724 TCGGTTGTTGGACATTGAGA 57.079 45.000 0.00 0.00 0.00 3.27
3875 4708 3.563808 TCTTTCGGTTGTTGGACATTGAG 59.436 43.478 0.00 0.00 0.00 3.02
3876 4709 3.546724 TCTTTCGGTTGTTGGACATTGA 58.453 40.909 0.00 0.00 0.00 2.57
3877 4710 3.980646 TCTTTCGGTTGTTGGACATTG 57.019 42.857 0.00 0.00 0.00 2.82
3878 4711 4.993029 TTTCTTTCGGTTGTTGGACATT 57.007 36.364 0.00 0.00 0.00 2.71
3879 4712 4.202111 CCTTTTCTTTCGGTTGTTGGACAT 60.202 41.667 0.00 0.00 0.00 3.06
3880 4713 3.129638 CCTTTTCTTTCGGTTGTTGGACA 59.870 43.478 0.00 0.00 0.00 4.02
3881 4714 3.702330 CCTTTTCTTTCGGTTGTTGGAC 58.298 45.455 0.00 0.00 0.00 4.02
3882 4715 2.100087 GCCTTTTCTTTCGGTTGTTGGA 59.900 45.455 0.00 0.00 0.00 3.53
3883 4716 2.100749 AGCCTTTTCTTTCGGTTGTTGG 59.899 45.455 0.00 0.00 0.00 3.77
3884 4717 3.436700 AGCCTTTTCTTTCGGTTGTTG 57.563 42.857 0.00 0.00 0.00 3.33
3885 4718 3.568430 CCTAGCCTTTTCTTTCGGTTGTT 59.432 43.478 0.00 0.00 0.00 2.83
3886 4719 3.146847 CCTAGCCTTTTCTTTCGGTTGT 58.853 45.455 0.00 0.00 0.00 3.32
3887 4720 2.488153 CCCTAGCCTTTTCTTTCGGTTG 59.512 50.000 0.00 0.00 0.00 3.77
3888 4721 2.374170 TCCCTAGCCTTTTCTTTCGGTT 59.626 45.455 0.00 0.00 0.00 4.44
3889 4722 1.982958 TCCCTAGCCTTTTCTTTCGGT 59.017 47.619 0.00 0.00 0.00 4.69
3890 4723 2.781681 TCCCTAGCCTTTTCTTTCGG 57.218 50.000 0.00 0.00 0.00 4.30
3891 4724 2.356069 GCATCCCTAGCCTTTTCTTTCG 59.644 50.000 0.00 0.00 0.00 3.46
3892 4725 3.356290 TGCATCCCTAGCCTTTTCTTTC 58.644 45.455 0.00 0.00 0.00 2.62
3893 4726 3.456380 TGCATCCCTAGCCTTTTCTTT 57.544 42.857 0.00 0.00 0.00 2.52
3894 4727 3.245407 ACTTGCATCCCTAGCCTTTTCTT 60.245 43.478 0.00 0.00 0.00 2.52
3895 4728 2.310052 ACTTGCATCCCTAGCCTTTTCT 59.690 45.455 0.00 0.00 0.00 2.52
3896 4729 2.424956 CACTTGCATCCCTAGCCTTTTC 59.575 50.000 0.00 0.00 0.00 2.29
3897 4730 2.450476 CACTTGCATCCCTAGCCTTTT 58.550 47.619 0.00 0.00 0.00 2.27
3898 4731 1.957113 GCACTTGCATCCCTAGCCTTT 60.957 52.381 0.00 0.00 41.59 3.11
3899 4732 0.394899 GCACTTGCATCCCTAGCCTT 60.395 55.000 0.00 0.00 41.59 4.35
3900 4733 1.225704 GCACTTGCATCCCTAGCCT 59.774 57.895 0.00 0.00 41.59 4.58
3901 4734 0.394899 AAGCACTTGCATCCCTAGCC 60.395 55.000 3.62 0.00 45.16 3.93
3902 4735 2.332063 TAAGCACTTGCATCCCTAGC 57.668 50.000 3.62 0.00 45.16 3.42
3903 4736 5.643379 TTTTTAAGCACTTGCATCCCTAG 57.357 39.130 3.62 0.00 45.16 3.02
3945 4778 9.749340 AGATGCCATTTTCATATTATGATGAGA 57.251 29.630 7.19 0.00 39.39 3.27
4683 5549 7.245292 TGGAAAGGGAGAGGAAATATGAAAAA 58.755 34.615 0.00 0.00 0.00 1.94
4757 5624 2.722094 ACAGCTTGAACTTGGTGTGAA 58.278 42.857 0.00 0.00 42.30 3.18
4981 5848 3.295585 TTATGGCTAGGAAATGCAGCA 57.704 42.857 0.00 0.00 37.02 4.41
5100 6111 9.087871 AGCAACTAGATATCAATATCACTGAGT 57.912 33.333 5.32 6.83 41.21 3.41
5154 6165 0.469917 ATTGCCCATACGAGGTCCAG 59.530 55.000 0.00 0.00 0.00 3.86
5657 6668 8.156820 TGAGAATAAGAGGTGATGAAAACTTCA 58.843 33.333 0.00 0.00 45.01 3.02
6032 7043 5.369404 TGGCTTCTGATAAGATGGTATGGAA 59.631 40.000 0.00 0.00 0.00 3.53
6680 7691 7.586300 GTGCTATATAAAAACATACACTTGCGG 59.414 37.037 0.00 0.00 0.00 5.69
6682 7693 7.586300 CGGTGCTATATAAAAACATACACTTGC 59.414 37.037 0.00 0.00 0.00 4.01
6687 7698 9.203421 CTCATCGGTGCTATATAAAAACATACA 57.797 33.333 0.00 0.00 0.00 2.29
7348 8363 6.932356 ACAGCAGAATTATTGTCATACCAG 57.068 37.500 0.00 0.00 0.00 4.00
7371 8386 7.283625 ACCTATCACACAACATTTAGCAAAA 57.716 32.000 0.00 0.00 0.00 2.44
7375 8390 7.812648 TGTTTACCTATCACACAACATTTAGC 58.187 34.615 0.00 0.00 0.00 3.09
7376 8391 9.988350 GATGTTTACCTATCACACAACATTTAG 57.012 33.333 0.00 0.00 35.50 1.85
7377 8392 8.952278 GGATGTTTACCTATCACACAACATTTA 58.048 33.333 0.00 0.00 35.50 1.40
7381 8396 5.870706 TGGATGTTTACCTATCACACAACA 58.129 37.500 0.00 0.00 0.00 3.33
7382 8397 5.938125 ACTGGATGTTTACCTATCACACAAC 59.062 40.000 0.00 0.00 0.00 3.32
7767 8837 7.381744 GCAACTTGCAGAAGTAACTTTTAAG 57.618 36.000 8.97 0.00 41.87 1.85
7843 8913 4.678509 TTTAGCTGGCATACACGAAAAG 57.321 40.909 0.00 0.00 0.00 2.27
7905 8975 8.099537 CACATCTGGCTTCCTTTCTATATGTAT 58.900 37.037 0.00 0.00 0.00 2.29
7951 9021 2.092103 AGTTGCCTAGTTTGGACACCAA 60.092 45.455 0.00 0.00 42.29 3.67
8214 9284 3.163467 AGGCGGTCTCAGTTAAACTAGT 58.837 45.455 0.00 0.00 0.00 2.57
8312 9382 4.646945 TCAGTCAAACTAAACATTTGCCCA 59.353 37.500 0.00 0.00 37.05 5.36
8537 9607 0.453282 CATTGCAGTTCTGTTCCGCG 60.453 55.000 0.00 0.00 0.00 6.46
8589 9659 8.427276 TGTTTGCTCATCATCATCTATAGAAGT 58.573 33.333 6.52 0.00 0.00 3.01
8630 9700 1.768077 AGCATCACCCTCCCTAGGC 60.768 63.158 2.05 0.00 42.14 3.93
8752 9825 0.593263 GTTGCACTGCTGTTCAGCAC 60.593 55.000 21.30 13.48 46.76 4.40
8819 9892 5.263968 TCCCTAATACTCTTTGCTTCTCG 57.736 43.478 0.00 0.00 0.00 4.04
8984 10057 3.260128 AGACCTAGTAAAACCCCTTCACG 59.740 47.826 0.00 0.00 0.00 4.35
8988 10061 2.836372 CGGAGACCTAGTAAAACCCCTT 59.164 50.000 0.00 0.00 0.00 3.95
9246 10319 3.883830 TGCAGACCAAACAACAACAAT 57.116 38.095 0.00 0.00 0.00 2.71
9247 10320 3.883830 ATGCAGACCAAACAACAACAA 57.116 38.095 0.00 0.00 0.00 2.83
9248 10321 3.883830 AATGCAGACCAAACAACAACA 57.116 38.095 0.00 0.00 0.00 3.33
9334 10407 0.105224 TTCGCAACTTCTTCGGGACA 59.895 50.000 0.00 0.00 0.00 4.02
9335 10408 1.223187 TTTCGCAACTTCTTCGGGAC 58.777 50.000 0.00 0.00 0.00 4.46
9337 10410 1.804151 TCATTTCGCAACTTCTTCGGG 59.196 47.619 0.00 0.00 0.00 5.14
9386 10470 3.565764 TCAGGATGCCAGAAATAGGTG 57.434 47.619 0.00 0.00 34.76 4.00
9395 10479 2.027377 ACTTCAGAGTTCAGGATGCCAG 60.027 50.000 0.00 0.00 34.76 4.85
9449 10533 3.254166 AGGTGTTGCACAAATGATGAGAC 59.746 43.478 1.61 0.00 35.86 3.36
9456 10540 3.091545 AGGGATAGGTGTTGCACAAATG 58.908 45.455 1.61 0.00 35.86 2.32
9459 10543 1.423541 ACAGGGATAGGTGTTGCACAA 59.576 47.619 1.61 0.00 35.86 3.33
9461 10545 1.679032 GGACAGGGATAGGTGTTGCAC 60.679 57.143 0.00 0.00 0.00 4.57
9462 10546 0.618458 GGACAGGGATAGGTGTTGCA 59.382 55.000 0.00 0.00 0.00 4.08
9463 10547 0.107165 GGGACAGGGATAGGTGTTGC 60.107 60.000 0.00 0.00 0.00 4.17
9480 10564 1.288932 AGGGTTTTCATGGAGGATGGG 59.711 52.381 0.00 0.00 32.26 4.00
9481 10565 2.762327 CAAGGGTTTTCATGGAGGATGG 59.238 50.000 0.00 0.00 32.26 3.51
9482 10566 2.762327 CCAAGGGTTTTCATGGAGGATG 59.238 50.000 0.00 0.00 34.82 3.51
9483 10567 2.889756 GCCAAGGGTTTTCATGGAGGAT 60.890 50.000 0.00 0.00 34.82 3.24
9493 10634 0.471591 TGATGGCTGCCAAGGGTTTT 60.472 50.000 27.24 6.97 36.95 2.43
9627 10932 8.730680 GTGAGATGCTCTATTTTTGACCTAAAA 58.269 33.333 0.00 0.00 36.51 1.52
9635 10942 5.645067 TGACCTGTGAGATGCTCTATTTTTG 59.355 40.000 0.00 0.00 0.00 2.44
9688 10995 2.289569 GCTGCATTTCCCCAATTCAACA 60.290 45.455 0.00 0.00 0.00 3.33
9749 11056 4.160439 ACAGAGGGAGTATGTATGTGTGTG 59.840 45.833 0.00 0.00 0.00 3.82
9815 11125 6.834451 ACGGAGGAAGTATAAGATCTTTCAGA 59.166 38.462 14.36 0.00 0.00 3.27
9818 11128 6.448852 GGACGGAGGAAGTATAAGATCTTTC 58.551 44.000 14.36 4.37 0.00 2.62
9833 11143 1.479323 CAAGTATTTCCGGACGGAGGA 59.521 52.381 13.64 7.39 46.06 3.71
9837 11147 4.435425 TGATAACAAGTATTTCCGGACGG 58.565 43.478 1.83 3.96 0.00 4.79


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

AutoCloner maintained by Alex Coulton.