Multiple sequence alignment - TraesCS6B01G219800

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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 TraesCS6B01G219800 chr6B 100.000 4826 0 0 1 4826 309756673 309751848 0.000000e+00 8913.0
1 TraesCS6B01G219800 chr6B 100.000 2930 0 0 5182 8111 309751492 309748563 0.000000e+00 5411.0
2 TraesCS6B01G219800 chr6B 76.471 255 44 9 6755 6999 129681063 129681311 3.070000e-24 124.0
3 TraesCS6B01G219800 chr6B 81.818 121 20 2 309 429 169177206 169177324 5.180000e-17 100.0
4 TraesCS6B01G219800 chr6D 97.962 2846 49 6 5182 8020 163834954 163837797 0.000000e+00 4926.0
5 TraesCS6B01G219800 chr6D 97.065 2351 38 7 557 2877 163830164 163832513 0.000000e+00 3930.0
6 TraesCS6B01G219800 chr6D 97.113 1940 33 5 2905 4826 163832631 163834565 0.000000e+00 3251.0
7 TraesCS6B01G219800 chr6D 91.880 468 31 5 64 524 163826749 163827216 0.000000e+00 647.0
8 TraesCS6B01G219800 chr6D 95.283 106 2 3 1653 1756 98100063 98099959 1.810000e-36 165.0
9 TraesCS6B01G219800 chr6D 95.050 101 5 0 1651 1751 319691670 319691570 8.430000e-35 159.0
10 TraesCS6B01G219800 chr6D 76.774 310 47 12 6701 6999 57784192 57784487 5.070000e-32 150.0
11 TraesCS6B01G219800 chr6A 96.637 2855 50 9 5182 8011 258140095 258142928 0.000000e+00 4698.0
12 TraesCS6B01G219800 chr6A 96.356 2278 42 6 654 2907 258132407 258134667 0.000000e+00 3709.0
13 TraesCS6B01G219800 chr6A 96.195 1945 39 8 2897 4826 258137856 258139780 0.000000e+00 3149.0
14 TraesCS6B01G219800 chr6A 91.200 375 29 4 190 563 257974399 257974770 2.610000e-139 507.0
15 TraesCS6B01G219800 chr6A 85.000 80 11 1 336 414 9350207 9350128 6.750000e-11 80.5
16 TraesCS6B01G219800 chr7D 76.853 661 96 32 3064 3680 243335272 243334625 3.650000e-83 320.0
17 TraesCS6B01G219800 chr7B 78.107 507 60 23 3064 3528 218820268 218819771 2.880000e-69 274.0
18 TraesCS6B01G219800 chr7B 94.393 107 5 1 1648 1754 134634222 134634117 6.510000e-36 163.0
19 TraesCS6B01G219800 chr7B 92.308 39 1 1 1361 1397 248548812 248548774 4.000000e-03 54.7
20 TraesCS6B01G219800 chr7B 92.308 39 2 1 1361 1399 544725864 544725901 4.000000e-03 54.7
21 TraesCS6B01G219800 chr4B 86.508 252 25 7 2823 3070 21941046 21940800 1.340000e-67 268.0
22 TraesCS6B01G219800 chr4B 86.667 75 6 3 1323 1393 164765017 164765091 6.750000e-11 80.5
23 TraesCS6B01G219800 chr4A 85.333 225 25 4 2846 3070 590664613 590664397 8.190000e-55 226.0
24 TraesCS6B01G219800 chr4D 81.379 290 40 8 2786 3070 11858473 11858753 2.950000e-54 224.0
25 TraesCS6B01G219800 chr4D 94.286 105 6 0 1653 1757 13198378 13198274 2.340000e-35 161.0
26 TraesCS6B01G219800 chr4D 91.743 109 9 0 1653 1761 498045970 498045862 1.410000e-32 152.0
27 TraesCS6B01G219800 chr5B 81.526 249 35 6 2823 3070 53020190 53020428 2.310000e-45 195.0
28 TraesCS6B01G219800 chr5D 79.435 248 42 7 2823 3070 50319433 50319671 5.040000e-37 167.0
29 TraesCS6B01G219800 chr3D 96.939 98 3 0 1653 1750 138076240 138076337 1.810000e-36 165.0
30 TraesCS6B01G219800 chr3D 92.308 39 1 1 1361 1397 450878818 450878780 4.000000e-03 54.7
31 TraesCS6B01G219800 chr5A 76.049 405 45 33 3293 3680 578111178 578110809 6.510000e-36 163.0
32 TraesCS6B01G219800 chr5A 78.516 256 31 13 3111 3361 39733661 39733897 6.560000e-31 147.0
33 TraesCS6B01G219800 chr2A 93.578 109 4 3 1653 1759 101847023 101846916 8.430000e-35 159.0
34 TraesCS6B01G219800 chr2A 92.308 39 1 2 1361 1397 605185349 605185311 4.000000e-03 54.7
35 TraesCS6B01G219800 chr3B 91.358 81 5 2 8030 8108 477623482 477623402 8.610000e-20 110.0
36 TraesCS6B01G219800 chr3B 86.585 82 5 4 446 524 62666023 62666101 1.450000e-12 86.1
37 TraesCS6B01G219800 chr3B 86.301 73 5 4 531 601 373626205 373626136 3.140000e-09 75.0
38 TraesCS6B01G219800 chr1B 87.234 94 11 1 2828 2921 8220882 8220974 1.110000e-18 106.0
39 TraesCS6B01G219800 chr1D 91.026 78 5 1 8036 8111 449986017 449985940 4.000000e-18 104.0
40 TraesCS6B01G219800 chr1A 81.308 107 18 2 2823 2928 189717588 189717693 1.450000e-12 86.1
41 TraesCS6B01G219800 chr7A 97.500 40 1 0 8072 8111 642585989 642586028 1.460000e-07 69.4
42 TraesCS6B01G219800 chr7A 94.444 36 0 1 1361 1394 561598664 561598699 4.000000e-03 54.7
43 TraesCS6B01G219800 chr3A 94.595 37 0 1 1361 1395 107732015 107732051 1.000000e-03 56.5
44 TraesCS6B01G219800 chr2B 94.286 35 1 1 1335 1368 337084236 337084202 1.500000e-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 TraesCS6B01G219800 chr6B 309748563 309756673 8110 True 7162.0 8913 100.000 1 8111 2 chr6B.!!$R1 8110
1 TraesCS6B01G219800 chr6D 163826749 163837797 11048 False 3188.5 4926 96.005 64 8020 4 chr6D.!!$F2 7956
2 TraesCS6B01G219800 chr6A 258132407 258142928 10521 False 3852.0 4698 96.396 654 8011 3 chr6A.!!$F2 7357
3 TraesCS6B01G219800 chr7D 243334625 243335272 647 True 320.0 320 76.853 3064 3680 1 chr7D.!!$R1 616

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
817 3747 0.251787 ATTGCAGGGGAACAGGGTTC 60.252 55.000 0.54 0.54 0.00 3.62 F
1339 4269 0.179000 ATTGCTTGCTACTCCCTCCG 59.821 55.000 0.00 0.00 0.00 4.63 F
2517 5471 1.138859 TGATTGGATGAGTAGGGTGCG 59.861 52.381 0.00 0.00 0.00 5.34 F
2975 9128 0.107017 ACCGCCTCATTTCCATCTGG 60.107 55.000 0.00 0.00 0.00 3.86 F
3282 9458 0.383231 GCAGCAGCTCAACAACAAGT 59.617 50.000 0.00 0.00 37.91 3.16 F
3501 9685 2.147958 GTGCGAGTGGGTTTGTATCAA 58.852 47.619 0.00 0.00 0.00 2.57 F
3692 9890 2.223112 CCATGCTTTCGAGATTGGAACG 60.223 50.000 0.00 0.00 0.00 3.95 F
4596 10812 4.022849 AGGTATTGCTTTTGACTGCTCAAC 60.023 41.667 0.00 0.00 36.06 3.18 F
5914 12185 3.897505 ACTGCCTTGTTTGAGCCTTTTAT 59.102 39.130 0.00 0.00 0.00 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2517 5471 3.066760 GGCACATAAATTACTCCACTGGC 59.933 47.826 0.00 0.0 0.00 4.85 R
2958 9111 1.019673 CACCAGATGGAAATGAGGCG 58.980 55.000 5.72 0.0 38.94 5.52 R
3692 9890 1.181098 ACACCAACCAAGCAGCATCC 61.181 55.000 0.00 0.0 0.00 3.51 R
4781 10997 2.494073 TGAACTGAACGGTTTGCCTTTT 59.506 40.909 0.00 0.0 0.00 2.27 R
5310 11559 5.237779 GTGTTGTCCGGAAATTCTACAAAGA 59.762 40.000 5.23 0.0 32.32 2.52 R
5321 11570 0.834612 ACCTGAGTGTTGTCCGGAAA 59.165 50.000 5.23 0.0 0.00 3.13 R
5452 11723 3.690475 AGGAAACCAGTAACCTAACCG 57.310 47.619 0.00 0.0 0.00 4.44 R
6614 12885 2.936919 TGATTCACTGTGACCAGCTT 57.063 45.000 10.56 0.0 42.81 3.74 R
7615 13888 0.606401 ACTGAACATTCCGGCACCAG 60.606 55.000 0.00 0.5 0.00 4.00 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
17 18 2.434884 CCTCCGCTGCACGTCAAT 60.435 61.111 0.00 0.00 41.42 2.57
18 19 2.743752 CCTCCGCTGCACGTCAATG 61.744 63.158 0.00 0.00 41.42 2.82
19 20 2.029288 CTCCGCTGCACGTCAATGT 61.029 57.895 0.00 0.00 41.42 2.71
20 21 0.735978 CTCCGCTGCACGTCAATGTA 60.736 55.000 0.00 0.00 41.42 2.29
21 22 0.319986 TCCGCTGCACGTCAATGTAA 60.320 50.000 0.00 0.00 41.42 2.41
22 23 0.515127 CCGCTGCACGTCAATGTAAA 59.485 50.000 0.00 0.00 41.42 2.01
23 24 1.464023 CCGCTGCACGTCAATGTAAAG 60.464 52.381 0.00 0.00 41.42 1.85
24 25 1.606606 GCTGCACGTCAATGTAAAGC 58.393 50.000 0.00 0.00 0.00 3.51
25 26 1.069296 GCTGCACGTCAATGTAAAGCA 60.069 47.619 0.00 0.00 32.56 3.91
26 27 2.574322 CTGCACGTCAATGTAAAGCAC 58.426 47.619 0.00 0.00 0.00 4.40
27 28 1.070242 TGCACGTCAATGTAAAGCACG 60.070 47.619 0.00 0.00 36.54 5.34
28 29 1.591248 CACGTCAATGTAAAGCACGC 58.409 50.000 0.00 0.00 33.73 5.34
29 30 1.070242 CACGTCAATGTAAAGCACGCA 60.070 47.619 0.00 0.00 33.73 5.24
30 31 1.600013 ACGTCAATGTAAAGCACGCAA 59.400 42.857 0.00 0.00 33.73 4.85
31 32 2.032302 ACGTCAATGTAAAGCACGCAAA 59.968 40.909 0.00 0.00 33.73 3.68
32 33 3.233578 CGTCAATGTAAAGCACGCAAAT 58.766 40.909 0.00 0.00 0.00 2.32
33 34 3.297979 CGTCAATGTAAAGCACGCAAATC 59.702 43.478 0.00 0.00 0.00 2.17
34 35 3.608073 GTCAATGTAAAGCACGCAAATCC 59.392 43.478 0.00 0.00 0.00 3.01
35 36 2.923020 CAATGTAAAGCACGCAAATCCC 59.077 45.455 0.00 0.00 0.00 3.85
36 37 0.885196 TGTAAAGCACGCAAATCCCC 59.115 50.000 0.00 0.00 0.00 4.81
37 38 0.885196 GTAAAGCACGCAAATCCCCA 59.115 50.000 0.00 0.00 0.00 4.96
38 39 1.476488 GTAAAGCACGCAAATCCCCAT 59.524 47.619 0.00 0.00 0.00 4.00
39 40 0.532115 AAAGCACGCAAATCCCCATC 59.468 50.000 0.00 0.00 0.00 3.51
40 41 0.611618 AAGCACGCAAATCCCCATCA 60.612 50.000 0.00 0.00 0.00 3.07
41 42 0.611618 AGCACGCAAATCCCCATCAA 60.612 50.000 0.00 0.00 0.00 2.57
42 43 0.461135 GCACGCAAATCCCCATCAAT 59.539 50.000 0.00 0.00 0.00 2.57
43 44 1.680735 GCACGCAAATCCCCATCAATA 59.319 47.619 0.00 0.00 0.00 1.90
44 45 2.100584 GCACGCAAATCCCCATCAATAA 59.899 45.455 0.00 0.00 0.00 1.40
45 46 3.243839 GCACGCAAATCCCCATCAATAAT 60.244 43.478 0.00 0.00 0.00 1.28
46 47 4.740334 GCACGCAAATCCCCATCAATAATT 60.740 41.667 0.00 0.00 0.00 1.40
47 48 4.746115 CACGCAAATCCCCATCAATAATTG 59.254 41.667 0.00 0.00 0.00 2.32
48 49 3.742369 CGCAAATCCCCATCAATAATTGC 59.258 43.478 0.00 0.00 38.73 3.56
49 50 3.742369 GCAAATCCCCATCAATAATTGCG 59.258 43.478 0.00 0.00 33.54 4.85
50 51 4.501229 GCAAATCCCCATCAATAATTGCGA 60.501 41.667 0.00 0.00 33.54 5.10
51 52 5.599732 CAAATCCCCATCAATAATTGCGAA 58.400 37.500 0.00 0.00 0.00 4.70
52 53 5.458041 AATCCCCATCAATAATTGCGAAG 57.542 39.130 0.00 0.00 0.00 3.79
53 54 3.221771 TCCCCATCAATAATTGCGAAGG 58.778 45.455 0.00 0.00 0.00 3.46
54 55 2.288395 CCCCATCAATAATTGCGAAGGC 60.288 50.000 0.00 0.00 40.52 4.35
55 56 2.288395 CCCATCAATAATTGCGAAGGCC 60.288 50.000 0.00 0.00 38.85 5.19
56 57 2.605338 CCATCAATAATTGCGAAGGCCG 60.605 50.000 0.00 0.00 38.85 6.13
57 58 1.745232 TCAATAATTGCGAAGGCCGT 58.255 45.000 0.00 0.00 41.15 5.68
58 59 1.400142 TCAATAATTGCGAAGGCCGTG 59.600 47.619 0.00 0.00 41.15 4.94
59 60 0.738389 AATAATTGCGAAGGCCGTGG 59.262 50.000 0.00 0.00 41.15 4.94
60 61 1.101049 ATAATTGCGAAGGCCGTGGG 61.101 55.000 0.00 0.00 41.15 4.61
61 62 2.186602 TAATTGCGAAGGCCGTGGGA 62.187 55.000 0.00 0.00 41.15 4.37
62 63 3.561120 ATTGCGAAGGCCGTGGGAA 62.561 57.895 10.06 10.06 41.15 3.97
65 66 2.046314 CGAAGGCCGTGGGAACAT 60.046 61.111 0.00 0.00 46.14 2.71
66 67 2.398554 CGAAGGCCGTGGGAACATG 61.399 63.158 0.00 0.00 46.14 3.21
72 73 2.350895 CGTGGGAACATGGCTGGA 59.649 61.111 0.00 0.00 46.14 3.86
97 98 3.075148 GTCAAGCAGTAAGGAAACTCCC 58.925 50.000 0.00 0.00 42.68 4.30
112 113 2.358125 CCCGCCGACACATCACAA 60.358 61.111 0.00 0.00 0.00 3.33
132 134 5.643777 CACAAGAGGACATGTTAAACCCTAG 59.356 44.000 0.00 0.00 0.00 3.02
177 179 3.558931 CCATGTTGGCTAGTGGTATCA 57.441 47.619 0.00 0.00 0.00 2.15
210 216 1.565156 GCGACGCCACATCAAGTTCA 61.565 55.000 9.14 0.00 0.00 3.18
212 218 2.267426 CGACGCCACATCAAGTTCATA 58.733 47.619 0.00 0.00 0.00 2.15
286 292 9.859427 CAATTAAAATAAGAAAGATGCACCTCA 57.141 29.630 0.00 0.00 0.00 3.86
309 315 3.997021 CACAGTAGTAGAAGCAAAGGTGG 59.003 47.826 0.00 0.00 0.00 4.61
328 334 3.976704 CCAAATGGGCCAGTACTGA 57.023 52.632 24.68 4.30 0.00 3.41
391 397 1.182667 GGCCCGCCCCATTTATAATC 58.817 55.000 0.00 0.00 0.00 1.75
524 532 1.271325 CCCCCAAAACAGCCCAAAATC 60.271 52.381 0.00 0.00 0.00 2.17
555 3452 2.804986 TGGGCTAAACATGCTGATGA 57.195 45.000 0.00 0.00 33.36 2.92
563 3460 4.923942 ATGCTGATGAGCCGGCCG 62.924 66.667 26.15 21.04 45.57 6.13
817 3747 0.251787 ATTGCAGGGGAACAGGGTTC 60.252 55.000 0.54 0.54 0.00 3.62
821 3751 3.647771 GGGGAACAGGGTTCGGCT 61.648 66.667 3.30 0.00 0.00 5.52
907 3837 1.401905 GGTCGATTTGAATCAGTGGGC 59.598 52.381 4.75 0.00 35.11 5.36
959 3889 5.466728 GCTTGATTCCGATTCTGCTGTAATA 59.533 40.000 0.00 0.00 0.00 0.98
1339 4269 0.179000 ATTGCTTGCTACTCCCTCCG 59.821 55.000 0.00 0.00 0.00 4.63
1341 4271 1.153549 GCTTGCTACTCCCTCCGTG 60.154 63.158 0.00 0.00 0.00 4.94
1362 4292 7.331440 TCCGTGAACAAATATAAGAGCGTTTAA 59.669 33.333 0.00 0.00 0.00 1.52
1365 4295 9.601971 GTGAACAAATATAAGAGCGTTTAAACA 57.398 29.630 18.07 0.00 0.00 2.83
1427 4380 5.934402 TTCTATGGAAGTAGGAGGTGAAC 57.066 43.478 0.00 0.00 0.00 3.18
1589 4542 7.175641 CCCAGACTTGAGAATGTTTGATTAGTT 59.824 37.037 0.00 0.00 0.00 2.24
1796 4750 2.552373 GCCCTGCAGTTACTAACCTGTT 60.552 50.000 13.81 0.00 0.00 3.16
2268 5222 1.671979 TATCAGCTTGGCACTGCATC 58.328 50.000 13.09 0.00 35.04 3.91
2517 5471 1.138859 TGATTGGATGAGTAGGGTGCG 59.861 52.381 0.00 0.00 0.00 5.34
2736 5690 9.528018 CAGATAAGATTTGAGTTAGAAGGAGTC 57.472 37.037 0.00 0.00 0.00 3.36
2954 9107 6.159299 TGAGGAATTGAGATGAGATCAGAC 57.841 41.667 0.00 0.00 0.00 3.51
2958 9111 6.267471 AGGAATTGAGATGAGATCAGACTACC 59.733 42.308 0.00 0.00 0.00 3.18
2975 9128 0.107017 ACCGCCTCATTTCCATCTGG 60.107 55.000 0.00 0.00 0.00 3.86
3112 9277 3.882025 CTGCCCTTCAGCGTCTTC 58.118 61.111 0.00 0.00 35.78 2.87
3163 9328 1.884067 GCTCCCTAACAGCAAGCAACT 60.884 52.381 0.00 0.00 36.82 3.16
3282 9458 0.383231 GCAGCAGCTCAACAACAAGT 59.617 50.000 0.00 0.00 37.91 3.16
3417 9601 4.170062 CAGGCAGCGGCGTTGATG 62.170 66.667 27.88 19.55 42.47 3.07
3501 9685 2.147958 GTGCGAGTGGGTTTGTATCAA 58.852 47.619 0.00 0.00 0.00 2.57
3692 9890 2.223112 CCATGCTTTCGAGATTGGAACG 60.223 50.000 0.00 0.00 0.00 3.95
3797 9995 8.885494 AGATAGATTCAATTGAGTAGTTGCTC 57.115 34.615 8.41 0.72 36.12 4.26
3831 10029 8.347035 AGATTTTGCATCTTTTTCCAAACAATG 58.653 29.630 0.00 0.00 0.00 2.82
3959 10157 8.053355 TCTGATATCAGTAGTTAACTCACAGGA 58.947 37.037 27.80 10.50 44.12 3.86
3960 10158 8.589701 TGATATCAGTAGTTAACTCACAGGAA 57.410 34.615 12.39 0.00 35.76 3.36
3961 10159 9.201989 TGATATCAGTAGTTAACTCACAGGAAT 57.798 33.333 12.39 0.00 35.76 3.01
4092 10294 9.953565 ATTTTGCTAAGTTCCTGTTACAGTATA 57.046 29.630 11.68 0.00 0.00 1.47
4093 10295 9.953565 TTTTGCTAAGTTCCTGTTACAGTATAT 57.046 29.630 11.68 0.00 0.00 0.86
4143 10345 6.575162 ACTTCCTGTGCTGGTAAATTTAAG 57.425 37.500 0.00 0.00 0.00 1.85
4434 10636 8.934023 ACCTCTTATGAAATTTAAGTTCCACA 57.066 30.769 2.68 0.00 0.00 4.17
4503 10705 5.705609 ACCACCAGTAAGTTGCATTTTAG 57.294 39.130 0.00 0.00 0.00 1.85
4596 10812 4.022849 AGGTATTGCTTTTGACTGCTCAAC 60.023 41.667 0.00 0.00 36.06 3.18
4641 10857 4.094442 CCGCTTTAGTTGTCCCTAATGAAC 59.906 45.833 0.00 0.00 0.00 3.18
5452 11723 5.157067 GTGCTGGCATCTAAAAGTTTTCTC 58.843 41.667 3.60 0.00 0.00 2.87
5914 12185 3.897505 ACTGCCTTGTTTGAGCCTTTTAT 59.102 39.130 0.00 0.00 0.00 1.40
6061 12332 7.064609 CCTCATTTTAGAACTTTATCGCTCACA 59.935 37.037 0.00 0.00 0.00 3.58
6079 12350 5.279256 GCTCACAAGCCTTAATTTTAACCCA 60.279 40.000 0.00 0.00 43.10 4.51
6187 12458 8.164070 ACCAAGATACCACAGAATACTTTCTTT 58.836 33.333 0.00 0.00 40.28 2.52
6614 12885 5.947228 AAGAGAAAGCGTGATTTTGATGA 57.053 34.783 0.00 0.00 0.00 2.92
6722 12993 6.315393 AGCATTGTAAGTAAAGTTGTATCCGG 59.685 38.462 0.00 0.00 0.00 5.14
6735 13006 4.074627 TGTATCCGGAAACACAGTCAAA 57.925 40.909 9.01 0.00 0.00 2.69
6787 13058 1.002257 AATGGACTGTCGCATGGCA 60.002 52.632 10.99 0.00 0.00 4.92
6892 13163 3.766591 TGTGGAAACAGTTCACATGGTTT 59.233 39.130 4.13 0.00 44.46 3.27
6941 13212 6.550481 TCAATGGCATGTGTTATCAATGGTAT 59.450 34.615 0.00 0.00 0.00 2.73
6945 13216 5.278463 GGCATGTGTTATCAATGGTATGGTC 60.278 44.000 0.00 0.00 0.00 4.02
7123 13394 4.164294 GTGTGAATGAGCTGATTTGAAGC 58.836 43.478 0.00 0.00 41.15 3.86
7344 13615 4.400567 AGAAAGCTTCAATTAGGCATGTCC 59.599 41.667 0.00 0.00 0.00 4.02
7505 13778 6.241645 AGGATAGTCAAAAGGAAAAGACTGG 58.758 40.000 0.00 0.00 41.14 4.00
7513 13786 2.576615 AGGAAAAGACTGGTGACTTGC 58.423 47.619 0.00 0.00 0.00 4.01
7593 13866 4.289410 TGACATGGATTTTCTCAGAAGGGA 59.711 41.667 0.00 0.00 0.00 4.20
7614 13887 3.993736 GAGTCTTGAAAGAAGAGGTGCTC 59.006 47.826 0.00 0.00 36.68 4.26
7615 13888 3.070748 GTCTTGAAAGAAGAGGTGCTCC 58.929 50.000 0.00 0.00 36.68 4.70
7696 13969 3.737850 CTTCTCTGACAAGGACAAGCTT 58.262 45.455 0.00 0.00 0.00 3.74
7697 13970 3.845781 TCTCTGACAAGGACAAGCTTT 57.154 42.857 0.00 0.00 0.00 3.51
7698 13971 4.156455 TCTCTGACAAGGACAAGCTTTT 57.844 40.909 0.00 0.00 0.00 2.27
7787 14060 7.223582 CAGCTTGTAAGTGTTATACAGAGATGG 59.776 40.741 0.00 0.00 34.92 3.51
7863 14136 7.337942 ACCATCAATTTTGTCATAGAGAAGACC 59.662 37.037 0.00 0.00 33.89 3.85
7892 14165 9.762381 ACACCCTTTACCTATGATAATTTTCAA 57.238 29.630 2.59 0.00 0.00 2.69
8020 14297 2.684374 TGCTATTATGCTGCCAACTGTG 59.316 45.455 0.00 0.00 0.00 3.66
8021 14298 2.945008 GCTATTATGCTGCCAACTGTGA 59.055 45.455 0.00 0.00 0.00 3.58
8022 14299 3.567164 GCTATTATGCTGCCAACTGTGAT 59.433 43.478 0.00 0.00 0.00 3.06
8023 14300 4.037208 GCTATTATGCTGCCAACTGTGATT 59.963 41.667 0.00 0.00 0.00 2.57
8024 14301 5.450965 GCTATTATGCTGCCAACTGTGATTT 60.451 40.000 0.00 0.00 0.00 2.17
8025 14302 4.870123 TTATGCTGCCAACTGTGATTTT 57.130 36.364 0.00 0.00 0.00 1.82
8026 14303 3.756933 ATGCTGCCAACTGTGATTTTT 57.243 38.095 0.00 0.00 0.00 1.94
8044 14321 1.444836 TTTTGTCCTGATAACGCCCG 58.555 50.000 0.00 0.00 0.00 6.13
8045 14322 1.022451 TTTGTCCTGATAACGCCCGC 61.022 55.000 0.00 0.00 0.00 6.13
8046 14323 2.173758 TTGTCCTGATAACGCCCGCA 62.174 55.000 0.00 0.00 0.00 5.69
8047 14324 2.171725 GTCCTGATAACGCCCGCAC 61.172 63.158 0.00 0.00 0.00 5.34
8048 14325 2.125310 CCTGATAACGCCCGCACA 60.125 61.111 0.00 0.00 0.00 4.57
8049 14326 1.523711 CCTGATAACGCCCGCACAT 60.524 57.895 0.00 0.00 0.00 3.21
8050 14327 1.643292 CTGATAACGCCCGCACATG 59.357 57.895 0.00 0.00 0.00 3.21
8051 14328 1.078778 TGATAACGCCCGCACATGT 60.079 52.632 0.00 0.00 0.00 3.21
8052 14329 1.351707 GATAACGCCCGCACATGTG 59.648 57.895 21.83 21.83 0.00 3.21
8053 14330 2.047151 GATAACGCCCGCACATGTGG 62.047 60.000 26.55 16.14 45.02 4.17
8057 14334 2.749839 GCCCGCACATGTGGCTTA 60.750 61.111 26.55 0.00 44.11 3.09
8058 14335 3.051392 GCCCGCACATGTGGCTTAC 62.051 63.158 26.55 9.00 44.11 2.34
8059 14336 1.377202 CCCGCACATGTGGCTTACT 60.377 57.895 26.55 0.00 44.11 2.24
8060 14337 0.107897 CCCGCACATGTGGCTTACTA 60.108 55.000 26.55 0.00 44.11 1.82
8061 14338 1.290203 CCGCACATGTGGCTTACTAG 58.710 55.000 26.55 5.95 39.04 2.57
8062 14339 1.134818 CCGCACATGTGGCTTACTAGA 60.135 52.381 26.55 0.00 39.04 2.43
8063 14340 1.927174 CGCACATGTGGCTTACTAGAC 59.073 52.381 26.55 5.43 0.00 2.59
8064 14341 2.673893 CGCACATGTGGCTTACTAGACA 60.674 50.000 26.55 0.00 36.95 3.41
8065 14342 3.535561 GCACATGTGGCTTACTAGACAT 58.464 45.455 26.55 0.00 42.67 3.06
8066 14343 3.557595 GCACATGTGGCTTACTAGACATC 59.442 47.826 26.55 1.43 42.67 3.06
8067 14344 4.122776 CACATGTGGCTTACTAGACATCC 58.877 47.826 18.51 0.00 42.67 3.51
8068 14345 3.181475 ACATGTGGCTTACTAGACATCCG 60.181 47.826 0.00 0.00 42.67 4.18
8069 14346 2.453521 TGTGGCTTACTAGACATCCGT 58.546 47.619 0.00 0.00 42.67 4.69
8070 14347 2.426024 TGTGGCTTACTAGACATCCGTC 59.574 50.000 0.00 0.00 42.67 4.79
8071 14348 2.029623 TGGCTTACTAGACATCCGTCC 58.970 52.381 0.00 0.00 43.73 4.79
8072 14349 2.029623 GGCTTACTAGACATCCGTCCA 58.970 52.381 0.00 0.00 43.73 4.02
8073 14350 2.223758 GGCTTACTAGACATCCGTCCAC 60.224 54.545 0.00 0.00 43.73 4.02
8074 14351 2.426024 GCTTACTAGACATCCGTCCACA 59.574 50.000 0.00 0.00 43.73 4.17
8075 14352 3.734293 GCTTACTAGACATCCGTCCACAC 60.734 52.174 0.00 0.00 43.73 3.82
8076 14353 1.183549 ACTAGACATCCGTCCACACC 58.816 55.000 0.00 0.00 43.73 4.16
8077 14354 0.100682 CTAGACATCCGTCCACACCG 59.899 60.000 0.00 0.00 43.73 4.94
8078 14355 0.609957 TAGACATCCGTCCACACCGT 60.610 55.000 0.00 0.00 43.73 4.83
8079 14356 1.736645 GACATCCGTCCACACCGTG 60.737 63.158 0.00 0.00 36.02 4.94
8080 14357 2.342279 CATCCGTCCACACCGTGT 59.658 61.111 0.00 0.00 0.00 4.49
8090 14367 3.256936 CACCGTGTGTGGCATGAG 58.743 61.111 0.00 0.00 41.52 2.90
8091 14368 2.669569 ACCGTGTGTGGCATGAGC 60.670 61.111 0.00 0.00 36.21 4.26
8092 14369 2.669229 CCGTGTGTGGCATGAGCA 60.669 61.111 0.00 0.00 44.61 4.26
8093 14370 2.683859 CCGTGTGTGGCATGAGCAG 61.684 63.158 0.00 0.00 44.61 4.24
8094 14371 2.683859 CGTGTGTGGCATGAGCAGG 61.684 63.158 0.00 0.00 44.61 4.85
8095 14372 1.302752 GTGTGTGGCATGAGCAGGA 60.303 57.895 0.00 0.00 44.61 3.86
8096 14373 1.002990 TGTGTGGCATGAGCAGGAG 60.003 57.895 0.00 0.00 44.61 3.69
8097 14374 1.748122 GTGTGGCATGAGCAGGAGG 60.748 63.158 0.00 0.00 44.61 4.30
8098 14375 2.827642 GTGGCATGAGCAGGAGGC 60.828 66.667 0.00 0.00 44.61 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.735978 TACATTGACGTGCAGCGGAG 60.736 55.000 12.18 1.91 46.52 4.63
3 4 0.515127 TTTACATTGACGTGCAGCGG 59.485 50.000 12.18 0.00 46.52 5.52
5 6 1.069296 TGCTTTACATTGACGTGCAGC 60.069 47.619 0.00 0.00 0.00 5.25
6 7 2.574322 GTGCTTTACATTGACGTGCAG 58.426 47.619 0.00 0.00 0.00 4.41
7 8 1.070242 CGTGCTTTACATTGACGTGCA 60.070 47.619 0.00 0.00 0.00 4.57
10 11 1.222300 TGCGTGCTTTACATTGACGT 58.778 45.000 0.00 0.00 32.66 4.34
11 12 2.308347 TTGCGTGCTTTACATTGACG 57.692 45.000 0.00 0.00 0.00 4.35
12 13 3.608073 GGATTTGCGTGCTTTACATTGAC 59.392 43.478 0.00 0.00 0.00 3.18
13 14 3.366883 GGGATTTGCGTGCTTTACATTGA 60.367 43.478 0.00 0.00 0.00 2.57
14 15 2.923020 GGGATTTGCGTGCTTTACATTG 59.077 45.455 0.00 0.00 0.00 2.82
15 16 2.094234 GGGGATTTGCGTGCTTTACATT 60.094 45.455 0.00 0.00 0.00 2.71
16 17 1.476488 GGGGATTTGCGTGCTTTACAT 59.524 47.619 0.00 0.00 0.00 2.29
17 18 0.885196 GGGGATTTGCGTGCTTTACA 59.115 50.000 0.00 0.00 0.00 2.41
18 19 0.885196 TGGGGATTTGCGTGCTTTAC 59.115 50.000 0.00 0.00 0.00 2.01
19 20 1.748493 GATGGGGATTTGCGTGCTTTA 59.252 47.619 0.00 0.00 0.00 1.85
20 21 0.532115 GATGGGGATTTGCGTGCTTT 59.468 50.000 0.00 0.00 0.00 3.51
21 22 0.611618 TGATGGGGATTTGCGTGCTT 60.612 50.000 0.00 0.00 0.00 3.91
22 23 0.611618 TTGATGGGGATTTGCGTGCT 60.612 50.000 0.00 0.00 0.00 4.40
23 24 0.461135 ATTGATGGGGATTTGCGTGC 59.539 50.000 0.00 0.00 0.00 5.34
24 25 4.589216 ATTATTGATGGGGATTTGCGTG 57.411 40.909 0.00 0.00 0.00 5.34
25 26 4.740334 GCAATTATTGATGGGGATTTGCGT 60.740 41.667 9.36 0.00 0.00 5.24
26 27 3.742369 GCAATTATTGATGGGGATTTGCG 59.258 43.478 9.36 0.00 0.00 4.85
27 28 3.742369 CGCAATTATTGATGGGGATTTGC 59.258 43.478 9.36 0.00 0.00 3.68
28 29 5.199024 TCGCAATTATTGATGGGGATTTG 57.801 39.130 9.36 0.00 0.00 2.32
29 30 5.221501 CCTTCGCAATTATTGATGGGGATTT 60.222 40.000 9.36 0.00 31.33 2.17
30 31 4.281688 CCTTCGCAATTATTGATGGGGATT 59.718 41.667 9.36 0.00 31.33 3.01
31 32 3.828451 CCTTCGCAATTATTGATGGGGAT 59.172 43.478 9.36 0.00 31.33 3.85
32 33 3.221771 CCTTCGCAATTATTGATGGGGA 58.778 45.455 9.36 0.00 0.00 4.81
33 34 2.288395 GCCTTCGCAATTATTGATGGGG 60.288 50.000 9.36 6.18 34.03 4.96
34 35 2.288395 GGCCTTCGCAATTATTGATGGG 60.288 50.000 9.36 5.85 36.38 4.00
35 36 2.605338 CGGCCTTCGCAATTATTGATGG 60.605 50.000 9.36 5.54 36.38 3.51
36 37 2.033299 ACGGCCTTCGCAATTATTGATG 59.967 45.455 9.36 0.33 43.89 3.07
37 38 2.033299 CACGGCCTTCGCAATTATTGAT 59.967 45.455 9.36 0.00 43.89 2.57
38 39 1.400142 CACGGCCTTCGCAATTATTGA 59.600 47.619 9.36 0.00 43.89 2.57
39 40 1.533756 CCACGGCCTTCGCAATTATTG 60.534 52.381 0.00 0.00 43.89 1.90
40 41 0.738389 CCACGGCCTTCGCAATTATT 59.262 50.000 0.00 0.00 43.89 1.40
41 42 1.101049 CCCACGGCCTTCGCAATTAT 61.101 55.000 0.00 0.00 43.89 1.28
42 43 1.747367 CCCACGGCCTTCGCAATTA 60.747 57.895 0.00 0.00 43.89 1.40
43 44 3.061848 CCCACGGCCTTCGCAATT 61.062 61.111 0.00 0.00 43.89 2.32
44 45 3.561120 TTCCCACGGCCTTCGCAAT 62.561 57.895 0.00 0.00 43.89 3.56
45 46 4.257654 TTCCCACGGCCTTCGCAA 62.258 61.111 0.00 0.00 43.89 4.85
48 49 2.046314 ATGTTCCCACGGCCTTCG 60.046 61.111 0.00 0.00 45.88 3.79
49 50 2.046285 CCATGTTCCCACGGCCTTC 61.046 63.158 0.00 0.00 0.00 3.46
50 51 2.035626 CCATGTTCCCACGGCCTT 59.964 61.111 0.00 0.00 0.00 4.35
51 52 4.740822 GCCATGTTCCCACGGCCT 62.741 66.667 0.00 0.00 38.67 5.19
52 53 4.740822 AGCCATGTTCCCACGGCC 62.741 66.667 0.00 0.00 46.08 6.13
53 54 3.443045 CAGCCATGTTCCCACGGC 61.443 66.667 0.00 0.00 45.23 5.68
54 55 2.556840 ATCCAGCCATGTTCCCACGG 62.557 60.000 0.00 0.00 0.00 4.94
55 56 1.077501 ATCCAGCCATGTTCCCACG 60.078 57.895 0.00 0.00 0.00 4.94
56 57 0.034186 TGATCCAGCCATGTTCCCAC 60.034 55.000 0.00 0.00 0.00 4.61
57 58 0.256752 CTGATCCAGCCATGTTCCCA 59.743 55.000 0.00 0.00 0.00 4.37
58 59 0.257039 ACTGATCCAGCCATGTTCCC 59.743 55.000 0.00 0.00 34.37 3.97
59 60 1.065199 TGACTGATCCAGCCATGTTCC 60.065 52.381 0.00 0.00 34.37 3.62
60 61 2.408271 TGACTGATCCAGCCATGTTC 57.592 50.000 0.00 0.00 34.37 3.18
61 62 2.719739 CTTGACTGATCCAGCCATGTT 58.280 47.619 0.00 0.00 34.37 2.71
62 63 1.681166 GCTTGACTGATCCAGCCATGT 60.681 52.381 0.00 0.00 37.59 3.21
63 64 1.022735 GCTTGACTGATCCAGCCATG 58.977 55.000 0.00 0.00 37.59 3.66
64 65 0.622136 TGCTTGACTGATCCAGCCAT 59.378 50.000 0.00 0.00 41.85 4.40
65 66 0.035725 CTGCTTGACTGATCCAGCCA 60.036 55.000 0.00 0.00 41.85 4.75
66 67 0.035630 ACTGCTTGACTGATCCAGCC 60.036 55.000 0.00 0.00 41.85 4.85
67 68 2.680312 TACTGCTTGACTGATCCAGC 57.320 50.000 0.00 0.00 42.66 4.85
68 69 3.196469 TCCTTACTGCTTGACTGATCCAG 59.804 47.826 0.00 0.00 37.52 3.86
69 70 3.173151 TCCTTACTGCTTGACTGATCCA 58.827 45.455 0.00 0.00 0.00 3.41
70 71 3.895232 TCCTTACTGCTTGACTGATCC 57.105 47.619 0.00 0.00 0.00 3.36
71 72 5.241662 AGTTTCCTTACTGCTTGACTGATC 58.758 41.667 0.00 0.00 0.00 2.92
72 73 5.234466 AGTTTCCTTACTGCTTGACTGAT 57.766 39.130 0.00 0.00 0.00 2.90
85 86 1.186917 TGTCGGCGGGAGTTTCCTTA 61.187 55.000 7.21 0.00 36.57 2.69
97 98 1.354337 CCTCTTGTGATGTGTCGGCG 61.354 60.000 0.00 0.00 0.00 6.46
112 113 4.436079 ACCTAGGGTTTAACATGTCCTCT 58.564 43.478 14.81 0.14 27.29 3.69
132 134 2.742589 CGAAAGTTCCCTAGCAGAAACC 59.257 50.000 0.00 0.00 0.00 3.27
170 172 7.094631 GTCGCATATACCTTATTGTGATACCA 58.905 38.462 0.00 0.00 31.94 3.25
171 173 6.252869 CGTCGCATATACCTTATTGTGATACC 59.747 42.308 0.00 0.00 31.94 2.73
173 175 5.803461 GCGTCGCATATACCTTATTGTGATA 59.197 40.000 13.44 0.00 31.94 2.15
174 176 4.625742 GCGTCGCATATACCTTATTGTGAT 59.374 41.667 13.44 0.00 31.94 3.06
175 177 3.985279 GCGTCGCATATACCTTATTGTGA 59.015 43.478 13.44 0.00 0.00 3.58
176 178 3.122948 GGCGTCGCATATACCTTATTGTG 59.877 47.826 20.50 0.00 0.00 3.33
177 179 3.243941 TGGCGTCGCATATACCTTATTGT 60.244 43.478 20.50 0.00 0.00 2.71
210 216 8.803235 TGGTACGCTTGAACTCTATTCATATAT 58.197 33.333 0.00 0.00 0.00 0.86
212 218 7.050970 TGGTACGCTTGAACTCTATTCATAT 57.949 36.000 0.00 0.00 0.00 1.78
224 230 3.011119 ACACAAACTTGGTACGCTTGAA 58.989 40.909 0.00 0.00 0.00 2.69
286 292 4.503296 CCACCTTTGCTTCTACTACTGTGT 60.503 45.833 0.00 0.00 0.00 3.72
321 327 1.370064 GGGCCAACACGTCAGTACT 59.630 57.895 4.39 0.00 0.00 2.73
328 334 2.125269 GCTATCGGGCCAACACGT 60.125 61.111 4.39 0.00 0.00 4.49
395 401 1.449601 GGGCCATGTGTCGGTACAG 60.450 63.158 4.39 0.00 35.91 2.74
434 440 2.181777 CTCGTGCTTAGCCTCGCA 59.818 61.111 0.29 0.00 0.00 5.10
495 503 4.416516 GGCTGTTTTGGGGGCTAATATAT 58.583 43.478 0.00 0.00 0.00 0.86
524 532 0.543277 TTAGCCCATCAGCCTGTCTG 59.457 55.000 0.00 0.00 44.21 3.51
597 3521 1.166531 GGCAAAGCACTTCACGGACT 61.167 55.000 0.00 0.00 0.00 3.85
601 3525 1.205064 CGAGGCAAAGCACTTCACG 59.795 57.895 0.00 0.00 0.00 4.35
781 3711 1.029947 AATCCCGATGGCACGAAACC 61.030 55.000 10.33 0.00 35.09 3.27
786 3716 2.823593 TGCAATCCCGATGGCACG 60.824 61.111 2.49 0.00 42.48 5.34
817 3747 1.814169 GCGGAACCCTAGAAAGCCG 60.814 63.158 0.00 0.00 41.51 5.52
821 3751 1.482748 AACCGGCGGAACCCTAGAAA 61.483 55.000 35.78 0.00 33.26 2.52
924 3854 0.733150 GAATCAAGCTAACCGCCACC 59.267 55.000 0.00 0.00 40.39 4.61
959 3889 0.899720 TAGCTGAAAATCCCGTCGGT 59.100 50.000 11.06 0.00 0.00 4.69
1223 4153 2.735823 GCTTCAACCAAGAACTGCAAG 58.264 47.619 0.00 0.00 35.01 4.01
1339 4269 9.601971 TGTTTAAACGCTCTTATATTTGTTCAC 57.398 29.630 13.45 0.00 0.00 3.18
1341 4271 9.821662 AGTGTTTAAACGCTCTTATATTTGTTC 57.178 29.630 25.12 0.00 46.01 3.18
1427 4380 7.618512 TCCGATTAAATATAGTCCCCTTCTAGG 59.381 40.741 0.00 0.00 34.30 3.02
1796 4750 4.219507 TCTGCAAATCAATTAAAAGCCCGA 59.780 37.500 0.00 0.00 0.00 5.14
2268 5222 7.879677 TGACATAAACTATGCAATATCAGAGGG 59.120 37.037 0.00 0.00 39.79 4.30
2517 5471 3.066760 GGCACATAAATTACTCCACTGGC 59.933 47.826 0.00 0.00 0.00 4.85
2551 5505 6.418946 GTGACCTATTTCTCCCTCTTGATTT 58.581 40.000 0.00 0.00 0.00 2.17
2736 5690 5.724328 TGCTGAACTAATTCACTACTCCAG 58.276 41.667 0.00 0.00 40.01 3.86
2954 9107 2.487934 CAGATGGAAATGAGGCGGTAG 58.512 52.381 0.00 0.00 0.00 3.18
2958 9111 1.019673 CACCAGATGGAAATGAGGCG 58.980 55.000 5.72 0.00 38.94 5.52
2975 9128 5.173774 TGAGCACTTGAAAAATGAGACAC 57.826 39.130 0.00 0.00 0.00 3.67
3163 9328 1.202867 TGCTGCTGTTGGGTGTTGATA 60.203 47.619 0.00 0.00 0.00 2.15
3277 9453 5.674525 TCTTCATCTCTTTGTGACACTTGT 58.325 37.500 7.20 0.00 0.00 3.16
3282 9458 4.963318 ACCTCTTCATCTCTTTGTGACA 57.037 40.909 0.00 0.00 0.00 3.58
3692 9890 1.181098 ACACCAACCAAGCAGCATCC 61.181 55.000 0.00 0.00 0.00 3.51
3770 9968 9.678260 AGCAACTACTCAATTGAATCTATCTTT 57.322 29.630 9.88 0.00 0.00 2.52
3797 9995 8.013378 GGAAAAAGATGCAAAATCTCAAACATG 58.987 33.333 0.00 0.00 0.00 3.21
3959 10157 8.568617 ACCTCTACATTGTAGAATCCCTTATT 57.431 34.615 23.19 2.44 0.00 1.40
3960 10158 8.568617 AACCTCTACATTGTAGAATCCCTTAT 57.431 34.615 23.19 5.69 0.00 1.73
3961 10159 7.989947 AACCTCTACATTGTAGAATCCCTTA 57.010 36.000 23.19 3.39 0.00 2.69
4143 10345 5.009210 AGAGGTCATTATGAAGTAGACTCGC 59.991 44.000 0.00 0.00 0.00 5.03
4434 10636 2.579860 AGAGAAGGTCAATTGCCATCCT 59.420 45.455 17.54 11.65 0.00 3.24
4503 10705 8.931385 ATTTGAGAACATGCACAAATATTACC 57.069 30.769 8.48 0.00 39.88 2.85
4596 10812 3.621558 GGAAGGGACCTTACAGAATTGG 58.378 50.000 8.46 0.00 36.89 3.16
4748 10964 7.042051 CCTCAATATAGTAACCAAATGACCACG 60.042 40.741 0.00 0.00 0.00 4.94
4781 10997 2.494073 TGAACTGAACGGTTTGCCTTTT 59.506 40.909 0.00 0.00 0.00 2.27
5310 11559 5.237779 GTGTTGTCCGGAAATTCTACAAAGA 59.762 40.000 5.23 0.00 32.32 2.52
5321 11570 0.834612 ACCTGAGTGTTGTCCGGAAA 59.165 50.000 5.23 0.00 0.00 3.13
5452 11723 3.690475 AGGAAACCAGTAACCTAACCG 57.310 47.619 0.00 0.00 0.00 4.44
5933 12204 7.624344 GCAACAATGTCAACCACTAGATACTTC 60.624 40.741 0.00 0.00 0.00 3.01
6061 12332 8.988546 AAAATTGTGGGTTAAAATTAAGGCTT 57.011 26.923 4.58 4.58 0.00 4.35
6172 12443 6.187727 TCACAGGGAAAGAAAGTATTCTGT 57.812 37.500 0.00 0.00 45.19 3.41
6614 12885 2.936919 TGATTCACTGTGACCAGCTT 57.063 45.000 10.56 0.00 42.81 3.74
6661 12932 1.112113 CTTTCCTCGTAGCCTAGGCA 58.888 55.000 34.70 18.26 44.88 4.75
6722 12993 5.415221 TGGAAACCAATTTGACTGTGTTTC 58.585 37.500 14.63 14.63 40.30 2.78
6735 13006 0.779997 AGAGGGCACTGGAAACCAAT 59.220 50.000 0.00 0.00 30.80 3.16
6787 13058 8.238631 GCAATTTGCTGATTCCAAATTTACATT 58.761 29.630 14.11 0.00 45.53 2.71
6892 13163 4.518970 GCTTTCAGGACCAACAGTTTCATA 59.481 41.667 0.00 0.00 0.00 2.15
7123 13394 2.833631 ACCTGTTTAGTGGAAGGTCG 57.166 50.000 0.00 0.00 38.73 4.79
7240 13511 2.961062 ACCACTCAGCTTTGCAGAAAAT 59.039 40.909 0.00 0.00 0.00 1.82
7243 13514 2.057137 AACCACTCAGCTTTGCAGAA 57.943 45.000 0.00 0.00 0.00 3.02
7344 13615 9.888878 CTAAATGCAACAGGATTATGATTACAG 57.111 33.333 0.00 0.00 0.00 2.74
7505 13778 3.128242 CCTGATTCCATTCAGCAAGTCAC 59.872 47.826 0.00 0.00 41.50 3.67
7513 13786 3.700538 TGAAACCCCTGATTCCATTCAG 58.299 45.455 0.00 0.00 42.31 3.02
7593 13866 3.244387 GGAGCACCTCTTCTTTCAAGACT 60.244 47.826 0.00 0.00 34.13 3.24
7614 13887 1.303236 TGAACATTCCGGCACCAGG 60.303 57.895 0.00 0.00 0.00 4.45
7615 13888 0.606401 ACTGAACATTCCGGCACCAG 60.606 55.000 0.00 0.50 0.00 4.00
7696 13969 3.194968 TGGTTCGCAGTTTTGGGTAAAAA 59.805 39.130 0.00 0.00 37.51 1.94
7697 13970 2.758979 TGGTTCGCAGTTTTGGGTAAAA 59.241 40.909 0.00 0.00 38.34 1.52
7698 13971 2.376109 TGGTTCGCAGTTTTGGGTAAA 58.624 42.857 0.00 0.00 38.34 2.01
7863 14136 2.684001 TCATAGGTAAAGGGTGTGCG 57.316 50.000 0.00 0.00 0.00 5.34
7892 14165 2.084546 GTAGACAAAGCTTCCGGCATT 58.915 47.619 0.00 0.00 44.79 3.56
7894 14167 0.685097 AGTAGACAAAGCTTCCGGCA 59.315 50.000 0.00 0.00 44.79 5.69
7895 14168 1.337823 TGAGTAGACAAAGCTTCCGGC 60.338 52.381 0.00 0.00 42.19 6.13
7896 14169 2.743636 TGAGTAGACAAAGCTTCCGG 57.256 50.000 0.00 0.00 0.00 5.14
7897 14170 5.592054 TCATATGAGTAGACAAAGCTTCCG 58.408 41.667 0.00 0.00 0.00 4.30
7981 14257 2.016604 GCATATGGTCCACGGCTCAAA 61.017 52.381 4.56 0.00 0.00 2.69
8024 14301 1.807742 CGGGCGTTATCAGGACAAAAA 59.192 47.619 0.00 0.00 0.00 1.94
8025 14302 1.444836 CGGGCGTTATCAGGACAAAA 58.555 50.000 0.00 0.00 0.00 2.44
8026 14303 1.022451 GCGGGCGTTATCAGGACAAA 61.022 55.000 0.00 0.00 0.00 2.83
8027 14304 1.448893 GCGGGCGTTATCAGGACAA 60.449 57.895 0.00 0.00 0.00 3.18
8028 14305 2.185867 GCGGGCGTTATCAGGACA 59.814 61.111 0.00 0.00 0.00 4.02
8029 14306 2.171725 GTGCGGGCGTTATCAGGAC 61.172 63.158 0.00 0.00 0.00 3.85
8030 14307 1.966901 ATGTGCGGGCGTTATCAGGA 61.967 55.000 0.00 0.00 0.00 3.86
8031 14308 1.523711 ATGTGCGGGCGTTATCAGG 60.524 57.895 0.00 0.00 0.00 3.86
8032 14309 1.089481 ACATGTGCGGGCGTTATCAG 61.089 55.000 0.00 0.00 0.00 2.90
8033 14310 1.078778 ACATGTGCGGGCGTTATCA 60.079 52.632 0.00 0.00 0.00 2.15
8034 14311 1.351707 CACATGTGCGGGCGTTATC 59.648 57.895 13.94 0.00 0.00 1.75
8035 14312 2.112198 CCACATGTGCGGGCGTTAT 61.112 57.895 20.81 0.00 0.00 1.89
8036 14313 2.744318 CCACATGTGCGGGCGTTA 60.744 61.111 20.81 0.00 0.00 3.18
8041 14318 0.107897 TAGTAAGCCACATGTGCGGG 60.108 55.000 20.81 8.37 0.00 6.13
8042 14319 1.134818 TCTAGTAAGCCACATGTGCGG 60.135 52.381 20.81 9.16 0.00 5.69
8043 14320 1.927174 GTCTAGTAAGCCACATGTGCG 59.073 52.381 20.81 14.27 0.00 5.34
8044 14321 2.972625 TGTCTAGTAAGCCACATGTGC 58.027 47.619 20.81 15.25 0.00 4.57
8045 14322 4.122776 GGATGTCTAGTAAGCCACATGTG 58.877 47.826 19.31 19.31 29.43 3.21
8046 14323 3.181475 CGGATGTCTAGTAAGCCACATGT 60.181 47.826 0.00 0.00 29.43 3.21
8047 14324 3.181475 ACGGATGTCTAGTAAGCCACATG 60.181 47.826 0.00 0.00 29.43 3.21
8048 14325 3.031736 ACGGATGTCTAGTAAGCCACAT 58.968 45.455 3.30 0.00 32.02 3.21
8049 14326 2.426024 GACGGATGTCTAGTAAGCCACA 59.574 50.000 3.30 0.00 42.08 4.17
8050 14327 2.223758 GGACGGATGTCTAGTAAGCCAC 60.224 54.545 3.30 0.00 44.83 5.01
8051 14328 2.029623 GGACGGATGTCTAGTAAGCCA 58.970 52.381 3.30 0.00 44.83 4.75
8052 14329 2.029623 TGGACGGATGTCTAGTAAGCC 58.970 52.381 0.00 0.00 44.83 4.35
8053 14330 2.426024 TGTGGACGGATGTCTAGTAAGC 59.574 50.000 0.00 0.00 44.83 3.09
8054 14331 3.181489 GGTGTGGACGGATGTCTAGTAAG 60.181 52.174 0.00 0.00 44.83 2.34
8055 14332 2.756760 GGTGTGGACGGATGTCTAGTAA 59.243 50.000 0.00 0.00 44.83 2.24
8056 14333 2.372264 GGTGTGGACGGATGTCTAGTA 58.628 52.381 0.00 0.00 44.83 1.82
8057 14334 1.183549 GGTGTGGACGGATGTCTAGT 58.816 55.000 0.00 0.00 44.83 2.57
8058 14335 0.100682 CGGTGTGGACGGATGTCTAG 59.899 60.000 0.00 0.00 44.83 2.43
8059 14336 0.609957 ACGGTGTGGACGGATGTCTA 60.610 55.000 0.00 0.00 44.83 2.59
8060 14337 1.906824 ACGGTGTGGACGGATGTCT 60.907 57.895 0.00 0.00 44.83 3.41
8061 14338 1.736645 CACGGTGTGGACGGATGTC 60.737 63.158 0.00 0.00 44.72 3.06
8062 14339 2.342279 CACGGTGTGGACGGATGT 59.658 61.111 0.00 0.00 35.23 3.06
8063 14340 2.027073 CACACGGTGTGGACGGATG 61.027 63.158 29.07 5.15 44.27 3.51
8064 14341 2.342279 CACACGGTGTGGACGGAT 59.658 61.111 29.07 0.00 44.27 4.18
8074 14351 2.669569 GCTCATGCCACACACGGT 60.670 61.111 0.00 0.00 0.00 4.83
8075 14352 2.669229 TGCTCATGCCACACACGG 60.669 61.111 0.00 0.00 38.71 4.94
8076 14353 2.683859 CCTGCTCATGCCACACACG 61.684 63.158 0.00 0.00 38.71 4.49
8077 14354 1.302752 TCCTGCTCATGCCACACAC 60.303 57.895 0.00 0.00 38.71 3.82
8078 14355 1.002990 CTCCTGCTCATGCCACACA 60.003 57.895 0.00 0.00 38.71 3.72
8079 14356 1.748122 CCTCCTGCTCATGCCACAC 60.748 63.158 0.00 0.00 38.71 3.82
8080 14357 2.672908 CCTCCTGCTCATGCCACA 59.327 61.111 0.00 0.00 38.71 4.17
8081 14358 2.827642 GCCTCCTGCTCATGCCAC 60.828 66.667 0.00 0.00 38.71 5.01
8082 14359 3.332385 TGCCTCCTGCTCATGCCA 61.332 61.111 0.00 0.00 42.00 4.92
8083 14360 2.516460 CTGCCTCCTGCTCATGCC 60.516 66.667 0.00 0.00 42.00 4.40
8084 14361 3.210528 GCTGCCTCCTGCTCATGC 61.211 66.667 0.00 0.00 42.00 4.06
8085 14362 2.516460 GGCTGCCTCCTGCTCATG 60.516 66.667 12.43 0.00 42.00 3.07
8086 14363 4.172512 CGGCTGCCTCCTGCTCAT 62.173 66.667 17.92 0.00 42.00 2.90
8088 14365 4.828925 GTCGGCTGCCTCCTGCTC 62.829 72.222 17.92 0.00 42.00 4.26


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

AutoCloner maintained by Alex Coulton.