Multiple sequence alignment - TraesCS7A01G219700

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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 TraesCS7A01G219700 chr7A 100.000 4563 0 0 390 4952 187433856 187429294 0.000000e+00 8427.0
1 TraesCS7A01G219700 chr7A 94.083 338 20 0 4615 4952 187390460 187390123 9.510000e-142 514.0
2 TraesCS7A01G219700 chr7A 85.552 353 51 0 2435 2787 187431721 187431369 2.180000e-98 370.0
3 TraesCS7A01G219700 chr7A 85.552 353 51 0 2525 2877 187431811 187431459 2.180000e-98 370.0
4 TraesCS7A01G219700 chr7A 100.000 170 0 0 1 170 187434245 187434076 1.030000e-81 315.0
5 TraesCS7A01G219700 chr7A 82.018 228 41 0 2435 2662 187431586 187431359 1.410000e-45 195.0
6 TraesCS7A01G219700 chr7D 92.864 2018 114 14 2435 4441 183775958 183777956 0.000000e+00 2902.0
7 TraesCS7A01G219700 chr7D 90.804 1381 117 8 1516 2887 183774989 183776368 0.000000e+00 1838.0
8 TraesCS7A01G219700 chr7D 90.335 807 43 15 644 1422 183774074 183774873 0.000000e+00 1026.0
9 TraesCS7A01G219700 chr7D 88.078 411 46 2 2480 2887 183775913 183776323 7.450000e-133 484.0
10 TraesCS7A01G219700 chr7D 85.714 350 47 1 2435 2781 183776048 183776397 2.820000e-97 366.0
11 TraesCS7A01G219700 chr7D 95.614 114 4 1 4502 4614 183778314 183778427 1.100000e-41 182.0
12 TraesCS7A01G219700 chr7D 93.000 100 5 1 482 579 183752452 183752551 1.440000e-30 145.0
13 TraesCS7A01G219700 chr7D 98.387 62 1 0 390 451 183752405 183752466 5.240000e-20 110.0
14 TraesCS7A01G219700 chr7B 92.259 1731 94 21 638 2340 152491666 152493384 0.000000e+00 2418.0
15 TraesCS7A01G219700 chr7B 93.898 1524 81 6 2480 3997 152493539 152495056 0.000000e+00 2289.0
16 TraesCS7A01G219700 chr7B 84.720 517 73 4 2332 2842 152493436 152493952 3.420000e-141 512.0
17 TraesCS7A01G219700 chr7B 85.552 353 45 3 2435 2781 152493584 152493936 1.010000e-96 364.0
18 TraesCS7A01G219700 chr7B 82.500 320 50 4 2435 2748 152493629 152493948 4.880000e-70 276.0
19 TraesCS7A01G219700 chr7B 81.609 261 40 6 2405 2662 152493697 152493952 5.020000e-50 209.0
20 TraesCS7A01G219700 chr7B 90.683 161 7 5 390 550 152490893 152491045 1.810000e-49 207.0
21 TraesCS7A01G219700 chr4D 93.491 338 21 1 4615 4952 482794653 482794989 7.400000e-138 501.0
22 TraesCS7A01G219700 chr2D 93.433 335 22 0 4615 4949 582829174 582829508 9.570000e-137 497.0
23 TraesCS7A01G219700 chr2D 93.175 337 22 1 4614 4949 582820696 582821032 1.240000e-135 494.0
24 TraesCS7A01G219700 chr2D 93.155 336 22 1 4614 4949 582822482 582822816 4.450000e-135 492.0
25 TraesCS7A01G219700 chr2D 92.582 337 24 1 4615 4950 585619825 585619489 2.680000e-132 483.0
26 TraesCS7A01G219700 chr2D 84.375 160 22 2 4453 4612 574106933 574106777 2.390000e-33 154.0
27 TraesCS7A01G219700 chr2D 93.103 58 3 1 1761 1818 593688609 593688553 3.180000e-12 84.2
28 TraesCS7A01G219700 chr4A 92.941 340 24 0 4613 4952 478872461 478872800 3.440000e-136 496.0
29 TraesCS7A01G219700 chr4A 97.059 34 1 0 4048 4081 603950928 603950895 1.930000e-04 58.4
30 TraesCS7A01G219700 chr6D 92.899 338 23 1 4615 4952 293377661 293377997 1.600000e-134 490.0
31 TraesCS7A01G219700 chr6D 98.485 66 1 0 4485 4550 16885335 16885400 3.130000e-22 117.0
32 TraesCS7A01G219700 chr3D 92.899 338 20 1 4615 4952 280275498 280275165 5.760000e-134 488.0
33 TraesCS7A01G219700 chr3D 95.556 45 2 0 1769 1813 175543163 175543119 6.880000e-09 73.1
34 TraesCS7A01G219700 chr2B 92.090 177 12 2 4437 4612 43679535 43679360 1.060000e-61 248.0
35 TraesCS7A01G219700 chr2B 92.157 51 3 1 1768 1818 720478111 720478062 2.470000e-08 71.3
36 TraesCS7A01G219700 chr2B 93.333 45 3 0 4085 4129 337015411 337015455 3.200000e-07 67.6
37 TraesCS7A01G219700 chr2B 93.333 45 3 0 4085 4129 337035993 337036037 3.200000e-07 67.6
38 TraesCS7A01G219700 chr5A 86.538 156 16 5 4444 4595 482825234 482825388 3.070000e-37 167.0
39 TraesCS7A01G219700 chr5A 95.833 48 1 1 1766 1812 605241817 605241770 5.320000e-10 76.8
40 TraesCS7A01G219700 chr5A 97.436 39 1 0 4091 4129 498529324 498529286 3.200000e-07 67.6
41 TraesCS7A01G219700 chr5B 83.019 159 22 3 4443 4597 458802336 458802493 6.680000e-29 139.0
42 TraesCS7A01G219700 chr5B 83.871 93 14 1 4200 4291 282708042 282707950 2.460000e-13 87.9
43 TraesCS7A01G219700 chrUn 80.240 167 26 4 5 169 39799081 39798920 8.710000e-23 119.0
44 TraesCS7A01G219700 chr3A 97.872 47 1 0 1766 1812 112940946 112940992 1.140000e-11 82.4
45 TraesCS7A01G219700 chr6A 97.727 44 1 0 1766 1809 99787478 99787435 5.320000e-10 76.8
46 TraesCS7A01G219700 chr6A 97.436 39 0 1 4485 4523 17641456 17641493 1.150000e-06 65.8
47 TraesCS7A01G219700 chr1B 93.878 49 3 0 4082 4130 407934406 407934454 1.910000e-09 75.0
48 TraesCS7A01G219700 chr1B 92.453 53 3 1 1766 1817 549520515 549520567 1.910000e-09 75.0
49 TraesCS7A01G219700 chr1B 93.478 46 3 0 4085 4130 561694162 561694117 8.890000e-08 69.4
50 TraesCS7A01G219700 chr6B 93.478 46 3 0 4085 4130 610451272 610451317 8.890000e-08 69.4
51 TraesCS7A01G219700 chr1D 97.436 39 1 0 4091 4129 210519494 210519456 3.200000e-07 67.6
52 TraesCS7A01G219700 chr1D 93.333 45 3 0 4085 4129 492898202 492898246 3.200000e-07 67.6


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 TraesCS7A01G219700 chr7A 187429294 187434245 4951 True 1935.400000 8427 90.624400 1 4952 5 chr7A.!!$R2 4951
1 TraesCS7A01G219700 chr7D 183774074 183778427 4353 False 1133.000000 2902 90.568167 644 4614 6 chr7D.!!$F2 3970
2 TraesCS7A01G219700 chr7B 152490893 152495056 4163 False 896.428571 2418 87.317286 390 3997 7 chr7B.!!$F1 3607
3 TraesCS7A01G219700 chr2D 582820696 582822816 2120 False 493.000000 494 93.165000 4614 4949 2 chr2D.!!$F2 335


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
67 68 0.032117 GGGAAATGGAGGGAAAGGGG 60.032 60.0 0.00 0.0 0.00 4.79 F
139 140 0.094730 CCTTTTCGCTAAAGCCGACG 59.905 55.0 0.00 0.0 41.60 5.12 F
1209 1782 0.094558 GTCGTGTGTGTGTGTGTGTG 59.905 55.0 0.00 0.0 0.00 3.82 F
1355 1928 0.404040 TGCTTCCCGGAACTCCAATT 59.596 50.0 0.73 0.0 35.14 2.32 F
1697 2358 0.515564 GCATACCGCAAACACGAGTT 59.484 50.0 0.00 0.0 41.79 3.01 F
1964 2630 0.674895 AATTCAGTGCGTGCCTCTCC 60.675 55.0 0.00 0.0 0.00 3.71 F
3811 4591 0.037326 TCCTCACCAAGCTAAGCGTG 60.037 55.0 0.00 0.0 37.74 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1106 1673 1.197949 CAGAAGAAGCGAGACGAGTGA 59.802 52.381 0.00 0.0 0.00 3.41 R
1756 2418 1.859302 TTTTTGACACTGGGTTGCCT 58.141 45.000 0.00 0.0 0.00 4.75 R
3151 3931 1.130561 CGGAAGAAGAAAACATCCGCC 59.869 52.381 0.00 0.0 45.41 6.13 R
3205 3985 4.090588 TTGGTCGGCGGGATGGTC 62.091 66.667 7.21 0.0 0.00 4.02 R
3679 4459 2.034879 CAACGCCTCCATTGTCGCT 61.035 57.895 0.00 0.0 0.00 4.93 R
3927 4709 0.178068 ACACCCTCGATACATGCACC 59.822 55.000 0.00 0.0 0.00 5.01 R
4765 7636 1.267261 GATCGGTCGGATCGTGAAGAT 59.733 52.381 10.85 0.0 42.02 2.40 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 3.154473 TCCGGGGAGAGAATGGCG 61.154 66.667 0.00 0.00 0.00 5.69
18 19 4.241555 CCGGGGAGAGAATGGCGG 62.242 72.222 0.00 0.00 0.00 6.13
19 20 4.241555 CGGGGAGAGAATGGCGGG 62.242 72.222 0.00 0.00 0.00 6.13
20 21 2.768344 GGGGAGAGAATGGCGGGA 60.768 66.667 0.00 0.00 0.00 5.14
21 22 2.375345 GGGGAGAGAATGGCGGGAA 61.375 63.158 0.00 0.00 0.00 3.97
22 23 1.147153 GGGAGAGAATGGCGGGAAG 59.853 63.158 0.00 0.00 0.00 3.46
23 24 1.147153 GGAGAGAATGGCGGGAAGG 59.853 63.158 0.00 0.00 0.00 3.46
24 25 1.147153 GAGAGAATGGCGGGAAGGG 59.853 63.158 0.00 0.00 0.00 3.95
25 26 2.517166 GAGAATGGCGGGAAGGGC 60.517 66.667 0.00 0.00 0.00 5.19
26 27 4.489771 AGAATGGCGGGAAGGGCG 62.490 66.667 0.00 0.00 34.76 6.13
35 36 3.798511 GGAAGGGCGGGGGAGAAG 61.799 72.222 0.00 0.00 0.00 2.85
36 37 3.798511 GAAGGGCGGGGGAGAAGG 61.799 72.222 0.00 0.00 0.00 3.46
45 46 4.097361 GGGAGAAGGGGGCGACAC 62.097 72.222 0.00 0.00 0.00 3.67
46 47 3.003763 GGAGAAGGGGGCGACACT 61.004 66.667 0.00 0.00 0.00 3.55
47 48 1.684734 GGAGAAGGGGGCGACACTA 60.685 63.158 0.00 0.00 0.00 2.74
48 49 1.677637 GGAGAAGGGGGCGACACTAG 61.678 65.000 0.00 0.00 0.00 2.57
49 50 1.677637 GAGAAGGGGGCGACACTAGG 61.678 65.000 0.00 0.00 0.00 3.02
50 51 2.687566 AAGGGGGCGACACTAGGG 60.688 66.667 0.00 0.00 0.00 3.53
51 52 3.248248 AAGGGGGCGACACTAGGGA 62.248 63.158 0.00 0.00 0.00 4.20
52 53 2.686106 GGGGGCGACACTAGGGAA 60.686 66.667 0.00 0.00 0.00 3.97
53 54 2.295602 GGGGGCGACACTAGGGAAA 61.296 63.158 0.00 0.00 0.00 3.13
54 55 1.632965 GGGGGCGACACTAGGGAAAT 61.633 60.000 0.00 0.00 0.00 2.17
55 56 0.463833 GGGGCGACACTAGGGAAATG 60.464 60.000 0.00 0.00 0.00 2.32
56 57 0.463833 GGGCGACACTAGGGAAATGG 60.464 60.000 0.00 0.00 0.00 3.16
57 58 0.539986 GGCGACACTAGGGAAATGGA 59.460 55.000 0.00 0.00 0.00 3.41
58 59 1.473434 GGCGACACTAGGGAAATGGAG 60.473 57.143 0.00 0.00 0.00 3.86
59 60 1.473434 GCGACACTAGGGAAATGGAGG 60.473 57.143 0.00 0.00 0.00 4.30
60 61 1.139058 CGACACTAGGGAAATGGAGGG 59.861 57.143 0.00 0.00 0.00 4.30
61 62 2.478292 GACACTAGGGAAATGGAGGGA 58.522 52.381 0.00 0.00 0.00 4.20
62 63 2.844348 GACACTAGGGAAATGGAGGGAA 59.156 50.000 0.00 0.00 0.00 3.97
63 64 3.265489 ACACTAGGGAAATGGAGGGAAA 58.735 45.455 0.00 0.00 0.00 3.13
64 65 3.267031 ACACTAGGGAAATGGAGGGAAAG 59.733 47.826 0.00 0.00 0.00 2.62
65 66 2.853077 ACTAGGGAAATGGAGGGAAAGG 59.147 50.000 0.00 0.00 0.00 3.11
66 67 1.010795 AGGGAAATGGAGGGAAAGGG 58.989 55.000 0.00 0.00 0.00 3.95
67 68 0.032117 GGGAAATGGAGGGAAAGGGG 60.032 60.000 0.00 0.00 0.00 4.79
68 69 0.032117 GGAAATGGAGGGAAAGGGGG 60.032 60.000 0.00 0.00 0.00 5.40
69 70 1.007607 GAAATGGAGGGAAAGGGGGA 58.992 55.000 0.00 0.00 0.00 4.81
70 71 1.361197 GAAATGGAGGGAAAGGGGGAA 59.639 52.381 0.00 0.00 0.00 3.97
71 72 1.010795 AATGGAGGGAAAGGGGGAAG 58.989 55.000 0.00 0.00 0.00 3.46
72 73 0.123266 ATGGAGGGAAAGGGGGAAGA 59.877 55.000 0.00 0.00 0.00 2.87
73 74 0.103608 TGGAGGGAAAGGGGGAAGAA 60.104 55.000 0.00 0.00 0.00 2.52
74 75 1.081481 GGAGGGAAAGGGGGAAGAAA 58.919 55.000 0.00 0.00 0.00 2.52
75 76 1.431633 GGAGGGAAAGGGGGAAGAAAA 59.568 52.381 0.00 0.00 0.00 2.29
76 77 2.526432 GAGGGAAAGGGGGAAGAAAAC 58.474 52.381 0.00 0.00 0.00 2.43
77 78 1.203013 AGGGAAAGGGGGAAGAAAACG 60.203 52.381 0.00 0.00 0.00 3.60
78 79 1.254026 GGAAAGGGGGAAGAAAACGG 58.746 55.000 0.00 0.00 0.00 4.44
79 80 0.601558 GAAAGGGGGAAGAAAACGGC 59.398 55.000 0.00 0.00 0.00 5.68
80 81 1.176619 AAAGGGGGAAGAAAACGGCG 61.177 55.000 4.80 4.80 0.00 6.46
81 82 3.060000 GGGGGAAGAAAACGGCGG 61.060 66.667 13.24 0.00 0.00 6.13
82 83 3.060000 GGGGAAGAAAACGGCGGG 61.060 66.667 13.24 0.00 0.00 6.13
83 84 2.032987 GGGAAGAAAACGGCGGGA 59.967 61.111 13.24 0.00 0.00 5.14
84 85 1.601477 GGGAAGAAAACGGCGGGAA 60.601 57.895 13.24 0.00 0.00 3.97
85 86 0.963856 GGGAAGAAAACGGCGGGAAT 60.964 55.000 13.24 0.00 0.00 3.01
86 87 0.885879 GGAAGAAAACGGCGGGAATT 59.114 50.000 13.24 0.00 0.00 2.17
87 88 1.271379 GGAAGAAAACGGCGGGAATTT 59.729 47.619 13.24 6.90 0.00 1.82
88 89 2.324860 GAAGAAAACGGCGGGAATTTG 58.675 47.619 13.24 0.00 0.00 2.32
89 90 0.601057 AGAAAACGGCGGGAATTTGG 59.399 50.000 13.24 0.00 0.00 3.28
90 91 1.005512 AAAACGGCGGGAATTTGGC 60.006 52.632 13.24 0.00 0.00 4.52
91 92 2.443260 AAAACGGCGGGAATTTGGCC 62.443 55.000 13.24 0.00 43.42 5.36
95 96 4.128388 GCGGGAATTTGGCCGGTG 62.128 66.667 1.90 0.00 0.00 4.94
96 97 2.675075 CGGGAATTTGGCCGGTGT 60.675 61.111 1.90 0.00 0.00 4.16
97 98 2.696759 CGGGAATTTGGCCGGTGTC 61.697 63.158 1.90 0.00 0.00 3.67
98 99 2.696759 GGGAATTTGGCCGGTGTCG 61.697 63.158 1.90 0.00 0.00 4.35
99 100 2.178273 GAATTTGGCCGGTGTCGC 59.822 61.111 1.90 0.00 34.56 5.19
100 101 3.336715 GAATTTGGCCGGTGTCGCC 62.337 63.158 1.90 0.00 34.66 5.54
135 136 4.765611 CGCCTTTTCGCTAAAGCC 57.234 55.556 0.00 0.00 41.60 4.35
136 137 1.226018 CGCCTTTTCGCTAAAGCCG 60.226 57.895 0.00 2.61 41.60 5.52
137 138 1.632046 CGCCTTTTCGCTAAAGCCGA 61.632 55.000 7.21 0.00 44.86 5.54
138 139 0.179197 GCCTTTTCGCTAAAGCCGAC 60.179 55.000 0.00 0.00 41.60 4.79
139 140 0.094730 CCTTTTCGCTAAAGCCGACG 59.905 55.000 0.00 0.00 41.60 5.12
140 141 0.518559 CTTTTCGCTAAAGCCGACGC 60.519 55.000 0.00 0.00 37.06 5.19
141 142 1.903783 TTTTCGCTAAAGCCGACGCC 61.904 55.000 0.00 0.00 37.91 5.68
142 143 4.807039 TCGCTAAAGCCGACGCCC 62.807 66.667 0.00 0.00 37.91 6.13
144 145 4.770874 GCTAAAGCCGACGCCCCA 62.771 66.667 0.00 0.00 34.57 4.96
145 146 2.511600 CTAAAGCCGACGCCCCAG 60.512 66.667 0.00 0.00 34.57 4.45
146 147 4.090588 TAAAGCCGACGCCCCAGG 62.091 66.667 0.00 0.00 34.57 4.45
416 417 7.499563 TCAGCTACCAGAGTAGTACTATTCTTG 59.500 40.741 21.68 20.30 46.60 3.02
422 423 8.852135 ACCAGAGTAGTACTATTCTTGATAAGC 58.148 37.037 24.57 2.95 30.96 3.09
446 447 7.039784 AGCAATAATTTCTGCTAACCACTCAAA 60.040 33.333 11.19 0.00 46.92 2.69
449 450 5.695851 ATTTCTGCTAACCACTCAAACAG 57.304 39.130 0.00 0.00 0.00 3.16
461 462 5.046910 CACTCAAACAGTGTTCTTGTTGT 57.953 39.130 9.40 6.21 46.81 3.32
462 463 5.460646 CACTCAAACAGTGTTCTTGTTGTT 58.539 37.500 9.40 0.00 46.81 2.83
463 464 5.343058 CACTCAAACAGTGTTCTTGTTGTTG 59.657 40.000 9.40 1.30 46.81 3.33
464 465 5.009610 ACTCAAACAGTGTTCTTGTTGTTGT 59.990 36.000 9.40 4.95 34.28 3.32
465 466 5.837437 TCAAACAGTGTTCTTGTTGTTGTT 58.163 33.333 9.40 0.00 34.28 2.83
466 467 5.689514 TCAAACAGTGTTCTTGTTGTTGTTG 59.310 36.000 9.40 0.00 34.28 3.33
554 831 8.174757 TGCCTCAGTATCACCCTATTAGTATTA 58.825 37.037 0.00 0.00 0.00 0.98
594 871 5.488203 AGGATTGCTGGAGATGCTCTTATAT 59.512 40.000 0.00 0.00 0.00 0.86
595 872 6.671340 AGGATTGCTGGAGATGCTCTTATATA 59.329 38.462 0.00 0.00 0.00 0.86
596 873 7.347748 AGGATTGCTGGAGATGCTCTTATATAT 59.652 37.037 0.00 0.00 0.00 0.86
597 874 8.646004 GGATTGCTGGAGATGCTCTTATATATA 58.354 37.037 0.00 0.00 0.00 0.86
753 1300 2.616842 GTCCGTAATATGGCACTTTGGG 59.383 50.000 0.00 0.00 0.00 4.12
845 1392 5.574055 TGCTCTTTCTTAATAACCACGTACG 59.426 40.000 15.01 15.01 0.00 3.67
859 1407 2.096980 CACGTACGACAATAGGAGAGCA 59.903 50.000 24.41 0.00 0.00 4.26
910 1463 1.666209 ATACGTTGGCCCTTGCATGC 61.666 55.000 11.82 11.82 40.13 4.06
937 1490 7.882179 TCATGAATCATGGATTTAGCAAGATG 58.118 34.615 21.58 0.00 41.66 2.90
1097 1664 4.541482 GCGCGCACACCATGGATG 62.541 66.667 29.10 17.07 0.00 3.51
1106 1673 2.237143 CACACCATGGATGTACTCCTGT 59.763 50.000 21.47 5.83 45.21 4.00
1152 1721 1.368641 GCATACGGCACACTCATCAA 58.631 50.000 0.00 0.00 43.97 2.57
1208 1781 1.348538 CGTCGTGTGTGTGTGTGTGT 61.349 55.000 0.00 0.00 0.00 3.72
1209 1782 0.094558 GTCGTGTGTGTGTGTGTGTG 59.905 55.000 0.00 0.00 0.00 3.82
1219 1792 2.668945 TGTGTGTGTGTGACTTGTAACG 59.331 45.455 0.00 0.00 0.00 3.18
1223 1796 2.166870 TGTGTGTGACTTGTAACGGTCT 59.833 45.455 0.00 0.00 34.01 3.85
1226 1799 4.093850 GTGTGTGACTTGTAACGGTCTTTT 59.906 41.667 0.00 0.00 34.01 2.27
1270 1843 5.064692 CAGATTACTGGAGGAGGCAGTCC 62.065 56.522 0.00 0.00 41.87 3.85
1355 1928 0.404040 TGCTTCCCGGAACTCCAATT 59.596 50.000 0.73 0.00 35.14 2.32
1472 2133 5.011635 TGGTCTGAAGCTGAGTGTGTAAATA 59.988 40.000 0.00 0.00 0.00 1.40
1476 2137 7.959651 GTCTGAAGCTGAGTGTGTAAATATTTG 59.040 37.037 11.05 0.00 0.00 2.32
1479 2140 8.629158 TGAAGCTGAGTGTGTAAATATTTGTTT 58.371 29.630 11.05 0.00 0.00 2.83
1480 2141 9.118236 GAAGCTGAGTGTGTAAATATTTGTTTC 57.882 33.333 11.05 1.51 0.00 2.78
1481 2142 7.593825 AGCTGAGTGTGTAAATATTTGTTTCC 58.406 34.615 11.05 0.00 0.00 3.13
1697 2358 0.515564 GCATACCGCAAACACGAGTT 59.484 50.000 0.00 0.00 41.79 3.01
1756 2418 8.774546 ATGTTCAGAGGTCTAATATTCAGAGA 57.225 34.615 0.00 0.00 0.00 3.10
1764 2426 5.301555 GTCTAATATTCAGAGAGGCAACCC 58.698 45.833 0.00 0.00 37.17 4.11
1824 2486 8.905850 GGGAGTAGTATTTAGCATAGTCTATCC 58.094 40.741 0.00 0.00 0.00 2.59
1964 2630 0.674895 AATTCAGTGCGTGCCTCTCC 60.675 55.000 0.00 0.00 0.00 3.71
1972 2638 1.725557 GCGTGCCTCTCCAGACGATA 61.726 60.000 0.00 0.00 33.64 2.92
1977 2643 3.006323 GTGCCTCTCCAGACGATATTGAT 59.994 47.826 0.00 0.00 0.00 2.57
2007 2673 7.415229 AGTTTGTCAAAGGACTACGAAAAATC 58.585 34.615 0.00 0.00 44.61 2.17
2088 2754 4.155462 ACTGCATCACAAGCTGAACATAAG 59.845 41.667 0.00 0.00 35.29 1.73
2099 2765 6.374417 AGCTGAACATAAGTTAAAGGAGGA 57.626 37.500 0.00 0.00 38.30 3.71
2182 2848 2.417719 CAAAAGTTGGAGAGAGACCGG 58.582 52.381 0.00 0.00 0.00 5.28
2196 2862 1.145803 GACCGGAAAAAGTCTCGGTG 58.854 55.000 9.46 0.00 46.71 4.94
2279 2948 5.721480 TGAAGGAGGTTTCTCTGTCATATGA 59.279 40.000 0.00 0.00 39.86 2.15
2291 2960 7.623630 TCTCTGTCATATGAATCAAAAGGTGA 58.376 34.615 7.07 0.00 41.67 4.02
2332 3001 6.942005 AGTATCTGTGTCACATGGATCAAAAA 59.058 34.615 6.03 0.00 0.00 1.94
2454 3183 5.304101 AGGTGAAGATGATCCACATAGAGTC 59.696 44.000 4.62 0.00 39.56 3.36
2466 3195 6.573434 TCCACATAGAGTCACAATGTCATAC 58.427 40.000 0.00 0.00 31.60 2.39
2511 3240 7.801716 TCCCAATAAAGCTACAATGACATAC 57.198 36.000 0.00 0.00 0.00 2.39
2513 3242 7.831690 TCCCAATAAAGCTACAATGACATACAA 59.168 33.333 0.00 0.00 0.00 2.41
2515 3244 8.131100 CCAATAAAGCTACAATGACATACAAGG 58.869 37.037 0.00 0.00 0.00 3.61
2608 3382 3.450817 AGTCACAATGTCATATGGGTCGA 59.549 43.478 2.13 0.00 0.00 4.20
2698 3475 4.127171 AGTTACAATGTCATATGGGTCGC 58.873 43.478 2.13 0.00 0.00 5.19
2795 3575 1.400494 GTCATACGGGTCAAACCATGC 59.600 52.381 0.00 0.00 41.02 4.06
2946 3726 6.650807 CACACATAGAAGGTAAAGAGAAAGCA 59.349 38.462 0.00 0.00 0.00 3.91
2961 3741 7.195839 AGAGAAAGCACAACTTATGAAGAAC 57.804 36.000 0.00 0.00 37.75 3.01
3032 3812 8.442632 TGATAAATATCCAGAAAACAGAGCTG 57.557 34.615 0.00 0.00 31.71 4.24
3096 3876 2.973224 CACTATTGCACGTGTTTCAAGC 59.027 45.455 18.38 0.47 0.00 4.01
3138 3918 4.449131 CATGTTCACTCTCATAGCCACAT 58.551 43.478 0.00 0.00 0.00 3.21
3151 3931 3.996150 AGCCACATGAACAAAAGACAG 57.004 42.857 0.00 0.00 0.00 3.51
3205 3985 4.559502 GGGTCAATGATCACCCCG 57.440 61.111 7.74 0.00 46.13 5.73
3276 4056 1.765314 CGACTCCCTTCCATTCTCCAT 59.235 52.381 0.00 0.00 0.00 3.41
3278 4058 1.765314 ACTCCCTTCCATTCTCCATCG 59.235 52.381 0.00 0.00 0.00 3.84
3695 4475 2.434884 CAGCGACAATGGAGGCGT 60.435 61.111 0.00 0.00 0.00 5.68
3811 4591 0.037326 TCCTCACCAAGCTAAGCGTG 60.037 55.000 0.00 0.00 37.74 5.34
3921 4703 1.063912 GCGCATTCATGAAATGGACGA 59.936 47.619 13.09 0.00 46.73 4.20
3927 4709 6.369005 GCATTCATGAAATGGACGATTCTAG 58.631 40.000 13.09 0.00 46.73 2.43
3943 4725 2.239400 TCTAGGTGCATGTATCGAGGG 58.761 52.381 4.47 0.00 0.00 4.30
3967 4749 7.308951 GGGTGTACTAAATAAATGTGTGCTTGT 60.309 37.037 0.00 0.00 0.00 3.16
4005 4792 5.234752 GTTGATGTTAATTTTGGGGTCACC 58.765 41.667 0.00 0.00 40.81 4.02
4016 4803 3.905493 TGGGGTCACCTTCCATTTAAA 57.095 42.857 0.00 0.00 41.11 1.52
4019 4806 3.762288 GGGGTCACCTTCCATTTAAAGAC 59.238 47.826 0.00 0.00 36.80 3.01
4063 4850 7.136885 TCTTAAGTTATACTTCCTCCATCCCA 58.863 38.462 1.63 0.00 39.51 4.37
4074 4861 5.269554 TCCTCCATCCCAAATTACTTGTT 57.730 39.130 0.00 0.00 32.65 2.83
4082 4869 6.418057 TCCCAAATTACTTGTTGCAGAATT 57.582 33.333 0.00 0.00 32.65 2.17
4094 4881 9.851686 ACTTGTTGCAGAATTAAGATATATCCA 57.148 29.630 9.18 0.00 0.00 3.41
4116 4903 7.264221 TCCATTTTCATGACAAATAATTCCGG 58.736 34.615 12.49 0.00 31.07 5.14
4121 4908 3.613494 TGACAAATAATTCCGGACGGA 57.387 42.857 1.83 9.76 43.52 4.69
4122 4909 3.527533 TGACAAATAATTCCGGACGGAG 58.472 45.455 13.64 3.15 46.06 4.63
4123 4910 2.870411 GACAAATAATTCCGGACGGAGG 59.130 50.000 13.64 0.00 46.06 4.30
4124 4911 2.218603 CAAATAATTCCGGACGGAGGG 58.781 52.381 13.64 0.00 46.06 4.30
4125 4912 1.797320 AATAATTCCGGACGGAGGGA 58.203 50.000 13.64 0.00 46.06 4.20
4126 4913 1.339097 ATAATTCCGGACGGAGGGAG 58.661 55.000 13.64 0.00 46.06 4.30
4127 4914 0.032813 TAATTCCGGACGGAGGGAGT 60.033 55.000 13.64 1.45 46.06 3.85
4128 4915 0.032813 AATTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
4129 4916 0.187851 ATTCCGGACGGAGGGAGTAT 59.812 55.000 13.64 0.61 46.06 2.12
4130 4917 0.466922 TTCCGGACGGAGGGAGTATC 60.467 60.000 13.64 0.00 46.06 2.24
4131 4918 1.152819 CCGGACGGAGGGAGTATCA 60.153 63.158 4.40 0.00 34.77 2.15
4132 4919 1.453762 CCGGACGGAGGGAGTATCAC 61.454 65.000 4.40 0.00 40.51 3.06
4139 4926 5.254901 GACGGAGGGAGTATCACACTATAT 58.745 45.833 0.00 0.00 45.06 0.86
4140 4927 5.010933 ACGGAGGGAGTATCACACTATATG 58.989 45.833 0.00 0.00 45.06 1.78
4228 5016 7.739825 TCTTATTGCCTATCTAAATGTGCTCT 58.260 34.615 0.00 0.00 0.00 4.09
4251 5039 4.631377 TCATTTAATGTGCTTCGTGAGAGG 59.369 41.667 4.77 0.00 43.69 3.69
4305 5093 7.754924 GCTAAGAGCTATGATATGACAACTCTC 59.245 40.741 0.00 0.00 38.45 3.20
4360 5148 7.989826 AGATTTTTGTATAGGTGTCATGCTTC 58.010 34.615 0.00 0.00 0.00 3.86
4376 5164 4.768130 TGCTTCAGATATAGTCCTACGC 57.232 45.455 0.00 0.00 0.00 4.42
4397 5185 3.668447 CGAAGCATTGATACTGCCCTAT 58.332 45.455 0.00 0.00 40.56 2.57
4415 5203 7.619050 TGCCCTATGCTCATTTTAAAATTTCA 58.381 30.769 10.77 9.23 42.00 2.69
4442 5230 9.892130 AAATTAGTGGTTATCTTCTTAGTGGAG 57.108 33.333 0.00 0.00 0.00 3.86
4443 5231 5.941555 AGTGGTTATCTTCTTAGTGGAGG 57.058 43.478 0.00 0.00 0.00 4.30
4444 5232 5.590818 AGTGGTTATCTTCTTAGTGGAGGA 58.409 41.667 0.00 0.00 0.00 3.71
4445 5233 5.659079 AGTGGTTATCTTCTTAGTGGAGGAG 59.341 44.000 0.00 0.00 0.00 3.69
4446 5234 5.422650 GTGGTTATCTTCTTAGTGGAGGAGT 59.577 44.000 0.00 0.00 0.00 3.85
4447 5235 6.023603 TGGTTATCTTCTTAGTGGAGGAGTT 58.976 40.000 0.00 0.00 0.00 3.01
4448 5236 6.500751 TGGTTATCTTCTTAGTGGAGGAGTTT 59.499 38.462 0.00 0.00 0.00 2.66
4449 5237 7.676893 TGGTTATCTTCTTAGTGGAGGAGTTTA 59.323 37.037 0.00 0.00 0.00 2.01
4450 5238 8.198778 GGTTATCTTCTTAGTGGAGGAGTTTAG 58.801 40.741 0.00 0.00 0.00 1.85
4451 5239 8.751242 GTTATCTTCTTAGTGGAGGAGTTTAGT 58.249 37.037 0.00 0.00 0.00 2.24
4452 5240 6.591750 TCTTCTTAGTGGAGGAGTTTAGTG 57.408 41.667 0.00 0.00 0.00 2.74
4453 5241 6.075984 TCTTCTTAGTGGAGGAGTTTAGTGT 58.924 40.000 0.00 0.00 0.00 3.55
4454 5242 7.236529 TCTTCTTAGTGGAGGAGTTTAGTGTA 58.763 38.462 0.00 0.00 0.00 2.90
4455 5243 7.393796 TCTTCTTAGTGGAGGAGTTTAGTGTAG 59.606 40.741 0.00 0.00 0.00 2.74
4456 5244 6.787170 TCTTAGTGGAGGAGTTTAGTGTAGA 58.213 40.000 0.00 0.00 0.00 2.59
4457 5245 6.658391 TCTTAGTGGAGGAGTTTAGTGTAGAC 59.342 42.308 0.00 0.00 0.00 2.59
4458 5246 4.087907 AGTGGAGGAGTTTAGTGTAGACC 58.912 47.826 0.00 0.00 0.00 3.85
4459 5247 3.830755 GTGGAGGAGTTTAGTGTAGACCA 59.169 47.826 0.00 0.00 0.00 4.02
4460 5248 4.282703 GTGGAGGAGTTTAGTGTAGACCAA 59.717 45.833 0.00 0.00 0.00 3.67
4461 5249 4.282703 TGGAGGAGTTTAGTGTAGACCAAC 59.717 45.833 0.00 0.00 0.00 3.77
4462 5250 4.282703 GGAGGAGTTTAGTGTAGACCAACA 59.717 45.833 5.72 0.00 0.00 3.33
4463 5251 5.470047 AGGAGTTTAGTGTAGACCAACAG 57.530 43.478 5.72 0.00 0.00 3.16
4464 5252 4.283722 AGGAGTTTAGTGTAGACCAACAGG 59.716 45.833 5.72 0.00 0.00 4.00
4465 5253 4.562963 GGAGTTTAGTGTAGACCAACAGGG 60.563 50.000 5.72 0.00 44.81 4.45
4466 5254 3.326880 AGTTTAGTGTAGACCAACAGGGG 59.673 47.826 5.72 0.00 42.91 4.79
4472 5260 3.070576 GACCAACAGGGGCCATGC 61.071 66.667 19.71 0.00 39.68 4.06
4497 5285 4.758773 CCCCCTAATTTGTGCATTCATT 57.241 40.909 0.00 0.00 0.00 2.57
4498 5286 4.444536 CCCCCTAATTTGTGCATTCATTG 58.555 43.478 0.00 0.00 0.00 2.82
4499 5287 4.161942 CCCCCTAATTTGTGCATTCATTGA 59.838 41.667 0.00 0.00 0.00 2.57
4500 5288 5.338219 CCCCCTAATTTGTGCATTCATTGAA 60.338 40.000 0.75 0.75 0.00 2.69
4588 5674 1.770324 CCCCCTTCAAGTCTTGGCT 59.230 57.895 12.66 0.00 0.00 4.75
4590 5676 0.322906 CCCCTTCAAGTCTTGGCTCC 60.323 60.000 12.66 0.00 0.00 4.70
4606 5692 1.877443 GCTCCCTCTTACGTTTTGCAA 59.123 47.619 0.00 0.00 0.00 4.08
4666 5753 5.675684 TCCTACACACATGCAAGATCTAA 57.324 39.130 0.00 0.00 0.00 2.10
4685 5772 3.788333 AACATGGTGATGCATAGCAAC 57.212 42.857 0.00 0.00 43.62 4.17
4693 5780 1.069204 GATGCATAGCAACGAGAGGGA 59.931 52.381 0.00 0.00 43.62 4.20
4702 5789 2.678324 CAACGAGAGGGAAGAGTGTTC 58.322 52.381 0.00 0.00 0.00 3.18
4724 5811 1.021390 CACGTACCCTCGTAGACCGT 61.021 60.000 0.00 0.00 42.27 4.83
4765 7636 2.227149 ACGCAGTTGATGTAGTCGTACA 59.773 45.455 0.00 0.00 37.78 2.90
4811 7682 0.599558 CCGAAAGTACGACACCTCCA 59.400 55.000 0.00 0.00 35.09 3.86
4867 7738 2.777832 ACTCTTGATCCAGTTGAGGC 57.222 50.000 0.00 0.00 0.00 4.70
4880 7751 1.258445 TTGAGGCCGAGGGAGAGTTC 61.258 60.000 0.00 0.00 0.00 3.01
4889 7760 0.616111 AGGGAGAGTTCCGTCAGCAT 60.616 55.000 0.00 0.00 45.04 3.79
4903 7774 2.885644 GCATGACGGCGTGACGAT 60.886 61.111 21.19 0.25 37.61 3.73
4950 7821 1.546834 CTTCGCCTAAGCACTACGAC 58.453 55.000 0.00 0.00 39.83 4.34
4951 7822 0.179181 TTCGCCTAAGCACTACGACG 60.179 55.000 0.00 0.00 39.83 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.154473 CGCCATTCTCTCCCCGGA 61.154 66.667 0.73 0.00 0.00 5.14
1 2 4.241555 CCGCCATTCTCTCCCCGG 62.242 72.222 0.00 0.00 0.00 5.73
2 3 4.241555 CCCGCCATTCTCTCCCCG 62.242 72.222 0.00 0.00 0.00 5.73
3 4 2.330924 CTTCCCGCCATTCTCTCCCC 62.331 65.000 0.00 0.00 0.00 4.81
4 5 1.147153 CTTCCCGCCATTCTCTCCC 59.853 63.158 0.00 0.00 0.00 4.30
5 6 1.147153 CCTTCCCGCCATTCTCTCC 59.853 63.158 0.00 0.00 0.00 3.71
6 7 1.147153 CCCTTCCCGCCATTCTCTC 59.853 63.158 0.00 0.00 0.00 3.20
7 8 3.049080 GCCCTTCCCGCCATTCTCT 62.049 63.158 0.00 0.00 0.00 3.10
8 9 2.517166 GCCCTTCCCGCCATTCTC 60.517 66.667 0.00 0.00 0.00 2.87
9 10 4.489771 CGCCCTTCCCGCCATTCT 62.490 66.667 0.00 0.00 0.00 2.40
18 19 3.798511 CTTCTCCCCCGCCCTTCC 61.799 72.222 0.00 0.00 0.00 3.46
19 20 3.798511 CCTTCTCCCCCGCCCTTC 61.799 72.222 0.00 0.00 0.00 3.46
28 29 4.097361 GTGTCGCCCCCTTCTCCC 62.097 72.222 0.00 0.00 0.00 4.30
29 30 1.677637 CTAGTGTCGCCCCCTTCTCC 61.678 65.000 0.00 0.00 0.00 3.71
30 31 1.677637 CCTAGTGTCGCCCCCTTCTC 61.678 65.000 0.00 0.00 0.00 2.87
31 32 1.686110 CCTAGTGTCGCCCCCTTCT 60.686 63.158 0.00 0.00 0.00 2.85
32 33 2.732619 CCCTAGTGTCGCCCCCTTC 61.733 68.421 0.00 0.00 0.00 3.46
33 34 2.687566 CCCTAGTGTCGCCCCCTT 60.688 66.667 0.00 0.00 0.00 3.95
34 35 2.758852 TTTCCCTAGTGTCGCCCCCT 62.759 60.000 0.00 0.00 0.00 4.79
35 36 1.632965 ATTTCCCTAGTGTCGCCCCC 61.633 60.000 0.00 0.00 0.00 5.40
36 37 0.463833 CATTTCCCTAGTGTCGCCCC 60.464 60.000 0.00 0.00 0.00 5.80
37 38 0.463833 CCATTTCCCTAGTGTCGCCC 60.464 60.000 0.00 0.00 0.00 6.13
38 39 0.539986 TCCATTTCCCTAGTGTCGCC 59.460 55.000 0.00 0.00 0.00 5.54
39 40 1.473434 CCTCCATTTCCCTAGTGTCGC 60.473 57.143 0.00 0.00 0.00 5.19
40 41 1.139058 CCCTCCATTTCCCTAGTGTCG 59.861 57.143 0.00 0.00 0.00 4.35
41 42 2.478292 TCCCTCCATTTCCCTAGTGTC 58.522 52.381 0.00 0.00 0.00 3.67
42 43 2.661176 TCCCTCCATTTCCCTAGTGT 57.339 50.000 0.00 0.00 0.00 3.55
43 44 3.372025 CCTTTCCCTCCATTTCCCTAGTG 60.372 52.174 0.00 0.00 0.00 2.74
44 45 2.853077 CCTTTCCCTCCATTTCCCTAGT 59.147 50.000 0.00 0.00 0.00 2.57
45 46 2.175715 CCCTTTCCCTCCATTTCCCTAG 59.824 54.545 0.00 0.00 0.00 3.02
46 47 2.214201 CCCTTTCCCTCCATTTCCCTA 58.786 52.381 0.00 0.00 0.00 3.53
47 48 1.010795 CCCTTTCCCTCCATTTCCCT 58.989 55.000 0.00 0.00 0.00 4.20
48 49 0.032117 CCCCTTTCCCTCCATTTCCC 60.032 60.000 0.00 0.00 0.00 3.97
49 50 0.032117 CCCCCTTTCCCTCCATTTCC 60.032 60.000 0.00 0.00 0.00 3.13
50 51 1.007607 TCCCCCTTTCCCTCCATTTC 58.992 55.000 0.00 0.00 0.00 2.17
51 52 1.362584 CTTCCCCCTTTCCCTCCATTT 59.637 52.381 0.00 0.00 0.00 2.32
52 53 1.010795 CTTCCCCCTTTCCCTCCATT 58.989 55.000 0.00 0.00 0.00 3.16
53 54 0.123266 TCTTCCCCCTTTCCCTCCAT 59.877 55.000 0.00 0.00 0.00 3.41
54 55 0.103608 TTCTTCCCCCTTTCCCTCCA 60.104 55.000 0.00 0.00 0.00 3.86
55 56 1.081481 TTTCTTCCCCCTTTCCCTCC 58.919 55.000 0.00 0.00 0.00 4.30
56 57 2.526432 GTTTTCTTCCCCCTTTCCCTC 58.474 52.381 0.00 0.00 0.00 4.30
57 58 1.203013 CGTTTTCTTCCCCCTTTCCCT 60.203 52.381 0.00 0.00 0.00 4.20
58 59 1.254026 CGTTTTCTTCCCCCTTTCCC 58.746 55.000 0.00 0.00 0.00 3.97
59 60 1.254026 CCGTTTTCTTCCCCCTTTCC 58.746 55.000 0.00 0.00 0.00 3.13
60 61 0.601558 GCCGTTTTCTTCCCCCTTTC 59.398 55.000 0.00 0.00 0.00 2.62
61 62 1.176619 CGCCGTTTTCTTCCCCCTTT 61.177 55.000 0.00 0.00 0.00 3.11
62 63 1.602605 CGCCGTTTTCTTCCCCCTT 60.603 57.895 0.00 0.00 0.00 3.95
63 64 2.033602 CGCCGTTTTCTTCCCCCT 59.966 61.111 0.00 0.00 0.00 4.79
64 65 3.060000 CCGCCGTTTTCTTCCCCC 61.060 66.667 0.00 0.00 0.00 5.40
65 66 3.060000 CCCGCCGTTTTCTTCCCC 61.060 66.667 0.00 0.00 0.00 4.81
66 67 0.963856 ATTCCCGCCGTTTTCTTCCC 60.964 55.000 0.00 0.00 0.00 3.97
67 68 0.885879 AATTCCCGCCGTTTTCTTCC 59.114 50.000 0.00 0.00 0.00 3.46
68 69 2.324860 CAAATTCCCGCCGTTTTCTTC 58.675 47.619 0.00 0.00 0.00 2.87
69 70 1.000394 CCAAATTCCCGCCGTTTTCTT 60.000 47.619 0.00 0.00 0.00 2.52
70 71 0.601057 CCAAATTCCCGCCGTTTTCT 59.399 50.000 0.00 0.00 0.00 2.52
71 72 1.011968 GCCAAATTCCCGCCGTTTTC 61.012 55.000 0.00 0.00 0.00 2.29
72 73 1.005512 GCCAAATTCCCGCCGTTTT 60.006 52.632 0.00 0.00 0.00 2.43
73 74 2.654289 GCCAAATTCCCGCCGTTT 59.346 55.556 0.00 0.00 0.00 3.60
74 75 3.378602 GGCCAAATTCCCGCCGTT 61.379 61.111 0.00 0.00 31.92 4.44
78 79 4.128388 CACCGGCCAAATTCCCGC 62.128 66.667 0.00 0.00 43.05 6.13
79 80 2.675075 ACACCGGCCAAATTCCCG 60.675 61.111 0.00 5.46 43.97 5.14
80 81 2.696759 CGACACCGGCCAAATTCCC 61.697 63.158 0.00 0.00 0.00 3.97
81 82 2.874751 CGACACCGGCCAAATTCC 59.125 61.111 0.00 0.00 0.00 3.01
82 83 2.178273 GCGACACCGGCCAAATTC 59.822 61.111 0.00 0.00 36.06 2.17
120 121 0.094730 CGTCGGCTTTAGCGAAAAGG 59.905 55.000 14.08 2.12 44.13 3.11
121 122 0.518559 GCGTCGGCTTTAGCGAAAAG 60.519 55.000 9.48 9.48 46.29 2.27
122 123 1.494189 GCGTCGGCTTTAGCGAAAA 59.506 52.632 0.00 0.00 43.26 2.29
123 124 2.385091 GGCGTCGGCTTTAGCGAAA 61.385 57.895 12.17 0.00 43.26 3.46
124 125 2.812178 GGCGTCGGCTTTAGCGAA 60.812 61.111 12.17 0.00 43.26 4.70
125 126 4.807039 GGGCGTCGGCTTTAGCGA 62.807 66.667 19.00 0.00 43.26 4.93
127 128 4.770874 TGGGGCGTCGGCTTTAGC 62.771 66.667 19.00 0.90 39.81 3.09
128 129 2.511600 CTGGGGCGTCGGCTTTAG 60.512 66.667 19.00 10.37 39.81 1.85
129 130 4.090588 CCTGGGGCGTCGGCTTTA 62.091 66.667 19.00 4.55 39.81 1.85
422 423 8.081633 TGTTTGAGTGGTTAGCAGAAATTATTG 58.918 33.333 0.00 0.00 0.00 1.90
446 447 4.846779 ACAACAACAACAAGAACACTGT 57.153 36.364 0.00 0.00 0.00 3.55
554 831 4.042187 GCAATCCTCCAGTATACCATTCCT 59.958 45.833 0.00 0.00 0.00 3.36
567 844 0.182061 GCATCTCCAGCAATCCTCCA 59.818 55.000 0.00 0.00 0.00 3.86
568 845 0.473326 AGCATCTCCAGCAATCCTCC 59.527 55.000 0.00 0.00 0.00 4.30
594 871 9.749490 GGCGTTTTACGTACGTATAGTATTATA 57.251 33.333 27.30 7.70 44.73 0.98
595 872 8.286800 TGGCGTTTTACGTACGTATAGTATTAT 58.713 33.333 27.30 0.82 44.73 1.28
596 873 7.584847 GTGGCGTTTTACGTACGTATAGTATTA 59.415 37.037 27.30 9.17 44.73 0.98
597 874 6.413818 GTGGCGTTTTACGTACGTATAGTATT 59.586 38.462 27.30 2.36 44.73 1.89
598 875 5.907391 GTGGCGTTTTACGTACGTATAGTAT 59.093 40.000 27.30 3.14 44.73 2.12
599 876 5.260140 GTGGCGTTTTACGTACGTATAGTA 58.740 41.667 27.30 11.02 44.73 1.82
600 877 4.095610 GTGGCGTTTTACGTACGTATAGT 58.904 43.478 27.30 4.69 44.73 2.12
601 878 3.482110 GGTGGCGTTTTACGTACGTATAG 59.518 47.826 27.30 18.61 44.73 1.31
602 879 3.430931 GGTGGCGTTTTACGTACGTATA 58.569 45.455 27.30 20.25 44.73 1.47
603 880 2.258755 GGTGGCGTTTTACGTACGTAT 58.741 47.619 27.30 6.27 44.73 3.06
622 899 5.937975 ATTCCTTACATGGTTGAATTGGG 57.062 39.130 0.00 0.00 0.00 4.12
845 1392 2.973945 ACCGTTTGCTCTCCTATTGTC 58.026 47.619 0.00 0.00 0.00 3.18
859 1407 1.213094 CGCTGACGACTCAACCGTTT 61.213 55.000 0.00 0.00 43.93 3.60
910 1463 6.489022 TCTTGCTAAATCCATGATTCATGAGG 59.511 38.462 24.93 11.66 43.81 3.86
937 1490 8.484799 CAACAATCATACATATGCATTTCAAGC 58.515 33.333 3.54 0.00 33.76 4.01
956 1509 6.038603 TGGCATAGATTTACTGCTCAACAATC 59.961 38.462 0.00 0.00 36.18 2.67
1026 1589 2.880268 TGAGTGATGGTGTGAAGCAAAG 59.120 45.455 0.00 0.00 0.00 2.77
1097 1664 1.394227 CGAGACGAGTGACAGGAGTAC 59.606 57.143 0.00 0.00 0.00 2.73
1106 1673 1.197949 CAGAAGAAGCGAGACGAGTGA 59.802 52.381 0.00 0.00 0.00 3.41
1152 1721 6.611381 CAATTCGTGTGTGGACAGAAATATT 58.389 36.000 0.00 0.00 30.74 1.28
1208 1781 5.883503 AAACAAAAGACCGTTACAAGTCA 57.116 34.783 5.52 0.00 35.38 3.41
1209 1782 8.739461 CAAATAAACAAAAGACCGTTACAAGTC 58.261 33.333 0.00 0.00 0.00 3.01
1219 1792 7.010923 TGCATCACAACAAATAAACAAAAGACC 59.989 33.333 0.00 0.00 0.00 3.85
1223 1796 6.037610 GGGTGCATCACAACAAATAAACAAAA 59.962 34.615 0.00 0.00 37.92 2.44
1226 1799 4.100035 TGGGTGCATCACAACAAATAAACA 59.900 37.500 0.00 0.00 37.92 2.83
1661 2322 6.321717 CGGTATGCATAGACACAAACAAATT 58.678 36.000 6.67 0.00 0.00 1.82
1756 2418 1.859302 TTTTTGACACTGGGTTGCCT 58.141 45.000 0.00 0.00 0.00 4.75
1854 2519 3.119531 TCAAATTGAACGGGTGATGCATC 60.120 43.478 20.14 20.14 0.00 3.91
1964 2630 7.276438 TGACAAACTTGAGATCAATATCGTCTG 59.724 37.037 0.00 0.00 37.19 3.51
1972 2638 6.774656 AGTCCTTTGACAAACTTGAGATCAAT 59.225 34.615 0.00 0.00 44.33 2.57
1977 2643 5.047847 CGTAGTCCTTTGACAAACTTGAGA 58.952 41.667 0.00 0.00 44.33 3.27
2007 2673 8.888579 ACTTGAGTTTCTTATAATATGGTCCG 57.111 34.615 0.00 0.00 0.00 4.79
2088 2754 4.629092 ACGACAAAGAGTCCTCCTTTAAC 58.371 43.478 0.00 0.00 44.66 2.01
2099 2765 6.464222 TCTTTTGATCCATACGACAAAGAGT 58.536 36.000 0.00 0.00 34.54 3.24
2182 2848 4.392138 CCCATAAGACACCGAGACTTTTTC 59.608 45.833 0.00 0.00 34.20 2.29
2196 2862 1.209621 TGGCACCTACCCCATAAGAC 58.790 55.000 0.00 0.00 0.00 3.01
2304 2973 5.423290 TGATCCATGTGACACAGATACTTCT 59.577 40.000 14.66 0.00 0.00 2.85
2332 3001 4.973168 TCTTGTGCCACAAAGTCTCTATT 58.027 39.130 11.99 0.00 37.69 1.73
2454 3183 2.989909 TCTGGCCTGTATGACATTGTG 58.010 47.619 3.32 0.00 0.00 3.33
2466 3195 3.063510 TCATCTTCTTGTTCTGGCCTG 57.936 47.619 3.32 2.92 0.00 4.85
2511 3240 4.096081 GGATCATCTTCTTGTTCTGCCTTG 59.904 45.833 0.00 0.00 0.00 3.61
2513 3242 3.371380 GGGATCATCTTCTTGTTCTGCCT 60.371 47.826 0.00 0.00 0.00 4.75
2515 3244 3.614092 TGGGATCATCTTCTTGTTCTGC 58.386 45.455 0.00 0.00 0.00 4.26
2608 3382 8.655935 ACTTTATTGGGATCATCTTCTTGTTT 57.344 30.769 0.00 0.00 0.00 2.83
2698 3475 6.976925 GCTTTATTGGGATCATCTTCTTGTTG 59.023 38.462 0.00 0.00 0.00 3.33
2946 3726 5.689383 AATGCACGTTCTTCATAAGTTGT 57.311 34.783 0.00 0.00 0.00 3.32
2961 3741 6.949578 ACATGGAAATTCTAAAAATGCACG 57.050 33.333 0.00 0.00 0.00 5.34
3071 3851 4.123506 TGAAACACGTGCAATAGTGAGAA 58.876 39.130 17.22 5.04 40.56 2.87
3072 3852 3.723260 TGAAACACGTGCAATAGTGAGA 58.277 40.909 17.22 3.45 40.56 3.27
3073 3853 4.457810 CTTGAAACACGTGCAATAGTGAG 58.542 43.478 17.22 7.15 40.56 3.51
3074 3854 3.303725 GCTTGAAACACGTGCAATAGTGA 60.304 43.478 17.22 0.67 40.56 3.41
3075 3855 2.973224 GCTTGAAACACGTGCAATAGTG 59.027 45.455 17.22 14.30 43.46 2.74
3084 3864 1.745232 TCCTGTTGCTTGAAACACGT 58.255 45.000 0.00 0.00 35.16 4.49
3096 3876 1.600636 TGGCTCGCCTTTCCTGTTG 60.601 57.895 9.65 0.00 36.94 3.33
3138 3918 1.879380 CATCCGCCTGTCTTTTGTTCA 59.121 47.619 0.00 0.00 0.00 3.18
3151 3931 1.130561 CGGAAGAAGAAAACATCCGCC 59.869 52.381 0.00 0.00 45.41 6.13
3205 3985 4.090588 TTGGTCGGCGGGATGGTC 62.091 66.667 7.21 0.00 0.00 4.02
3511 4291 2.203877 TTGTACCTCCCCCGCAGT 60.204 61.111 0.00 0.00 0.00 4.40
3679 4459 2.034879 CAACGCCTCCATTGTCGCT 61.035 57.895 0.00 0.00 0.00 4.93
3883 4663 0.179073 GCCGCATCTCACACATACCT 60.179 55.000 0.00 0.00 0.00 3.08
3886 4668 1.882625 GCGCCGCATCTCACACATA 60.883 57.895 3.15 0.00 0.00 2.29
3921 4703 3.259374 CCCTCGATACATGCACCTAGAAT 59.741 47.826 0.00 0.00 0.00 2.40
3927 4709 0.178068 ACACCCTCGATACATGCACC 59.822 55.000 0.00 0.00 0.00 5.01
3943 4725 8.901748 CAACAAGCACACATTTATTTAGTACAC 58.098 33.333 0.00 0.00 0.00 2.90
4005 4792 7.025963 GCATTGAGAGTGTCTTTAAATGGAAG 58.974 38.462 0.00 0.00 29.96 3.46
4052 4839 4.946160 ACAAGTAATTTGGGATGGAGGA 57.054 40.909 0.00 0.00 41.25 3.71
4093 4880 7.044117 CGTCCGGAATTATTTGTCATGAAAATG 60.044 37.037 5.23 7.22 0.00 2.32
4094 4881 6.972328 CGTCCGGAATTATTTGTCATGAAAAT 59.028 34.615 5.23 15.45 0.00 1.82
4099 4886 3.874543 TCCGTCCGGAATTATTTGTCATG 59.125 43.478 5.23 0.00 42.05 3.07
4100 4887 4.127171 CTCCGTCCGGAATTATTTGTCAT 58.873 43.478 5.23 0.00 44.66 3.06
4101 4888 3.527533 CTCCGTCCGGAATTATTTGTCA 58.472 45.455 5.23 0.00 44.66 3.58
4116 4903 1.765230 AGTGTGATACTCCCTCCGTC 58.235 55.000 0.00 0.00 33.17 4.79
4228 5016 4.631377 CCTCTCACGAAGCACATTAAATGA 59.369 41.667 0.00 0.00 0.00 2.57
4334 5122 7.944729 AGCATGACACCTATACAAAAATCTT 57.055 32.000 0.00 0.00 0.00 2.40
4360 5148 3.188667 TGCTTCGCGTAGGACTATATCTG 59.811 47.826 14.82 0.00 0.00 2.90
4376 5164 1.959042 AGGGCAGTATCAATGCTTCG 58.041 50.000 0.00 0.00 43.35 3.79
4422 5210 5.422650 ACTCCTCCACTAAGAAGATAACCAC 59.577 44.000 0.00 0.00 0.00 4.16
4434 5222 5.713861 GGTCTACACTAAACTCCTCCACTAA 59.286 44.000 0.00 0.00 0.00 2.24
4441 5229 4.283722 CCTGTTGGTCTACACTAAACTCCT 59.716 45.833 0.00 0.00 0.00 3.69
4442 5230 4.562963 CCCTGTTGGTCTACACTAAACTCC 60.563 50.000 0.00 0.00 0.00 3.85
4443 5231 4.562963 CCCCTGTTGGTCTACACTAAACTC 60.563 50.000 0.00 0.00 0.00 3.01
4444 5232 3.326880 CCCCTGTTGGTCTACACTAAACT 59.673 47.826 0.00 0.00 0.00 2.66
4445 5233 3.671716 CCCCTGTTGGTCTACACTAAAC 58.328 50.000 0.00 0.00 0.00 2.01
4446 5234 2.039348 GCCCCTGTTGGTCTACACTAAA 59.961 50.000 0.00 0.00 0.00 1.85
4447 5235 1.626825 GCCCCTGTTGGTCTACACTAA 59.373 52.381 0.00 0.00 0.00 2.24
4448 5236 1.272807 GCCCCTGTTGGTCTACACTA 58.727 55.000 0.00 0.00 0.00 2.74
4449 5237 1.489560 GGCCCCTGTTGGTCTACACT 61.490 60.000 0.00 0.00 0.00 3.55
4450 5238 1.002502 GGCCCCTGTTGGTCTACAC 60.003 63.158 0.00 0.00 0.00 2.90
4451 5239 0.844661 ATGGCCCCTGTTGGTCTACA 60.845 55.000 0.00 0.00 0.00 2.74
4452 5240 0.394352 CATGGCCCCTGTTGGTCTAC 60.394 60.000 0.00 0.00 0.00 2.59
4453 5241 1.998530 CATGGCCCCTGTTGGTCTA 59.001 57.895 0.00 0.00 0.00 2.59
4454 5242 2.765969 CATGGCCCCTGTTGGTCT 59.234 61.111 0.00 0.00 0.00 3.85
4455 5243 3.070576 GCATGGCCCCTGTTGGTC 61.071 66.667 0.00 0.00 0.00 4.02
4456 5244 4.702274 GGCATGGCCCCTGTTGGT 62.702 66.667 8.35 0.00 44.06 3.67
4476 5264 4.161942 TCAATGAATGCACAAATTAGGGGG 59.838 41.667 0.00 0.00 0.00 5.40
4477 5265 5.341872 TCAATGAATGCACAAATTAGGGG 57.658 39.130 0.00 0.00 0.00 4.79
4478 5266 6.632909 TCTTCAATGAATGCACAAATTAGGG 58.367 36.000 0.00 0.00 0.00 3.53
4479 5267 8.537049 TTTCTTCAATGAATGCACAAATTAGG 57.463 30.769 0.00 0.00 0.00 2.69
4490 5278 9.635520 AAAGTCTAGCATTTTCTTCAATGAATG 57.364 29.630 0.00 0.00 36.39 2.67
4493 5281 8.950210 CCTAAAGTCTAGCATTTTCTTCAATGA 58.050 33.333 0.00 0.00 36.39 2.57
4494 5282 8.950210 TCCTAAAGTCTAGCATTTTCTTCAATG 58.050 33.333 0.00 0.00 37.23 2.82
4495 5283 9.171877 CTCCTAAAGTCTAGCATTTTCTTCAAT 57.828 33.333 0.00 0.00 0.00 2.57
4496 5284 8.157476 ACTCCTAAAGTCTAGCATTTTCTTCAA 58.843 33.333 0.00 0.00 30.02 2.69
4497 5285 7.680730 ACTCCTAAAGTCTAGCATTTTCTTCA 58.319 34.615 0.00 0.00 30.02 3.02
4498 5286 9.654663 TTACTCCTAAAGTCTAGCATTTTCTTC 57.345 33.333 0.00 0.00 39.55 2.87
4499 5287 9.438228 GTTACTCCTAAAGTCTAGCATTTTCTT 57.562 33.333 0.00 0.00 39.55 2.52
4500 5288 8.817876 AGTTACTCCTAAAGTCTAGCATTTTCT 58.182 33.333 0.00 0.00 39.55 2.52
4547 5632 4.098044 GCAAATTAGTAGGAAAGAAGGGGC 59.902 45.833 0.00 0.00 0.00 5.80
4588 5674 3.243267 GCTTTTGCAAAACGTAAGAGGGA 60.243 43.478 20.46 0.00 46.58 4.20
4606 5692 1.544246 GCGTTCCCCAACAATAGCTTT 59.456 47.619 0.00 0.00 32.14 3.51
4643 5729 4.558226 AGATCTTGCATGTGTGTAGGAA 57.442 40.909 0.00 0.00 30.48 3.36
4650 5737 4.397103 CACCATGTTAGATCTTGCATGTGT 59.603 41.667 24.78 20.84 37.57 3.72
4655 5742 3.628942 GCATCACCATGTTAGATCTTGCA 59.371 43.478 0.00 0.43 31.86 4.08
4666 5753 1.672363 CGTTGCTATGCATCACCATGT 59.328 47.619 0.19 0.00 38.76 3.21
4685 5772 1.474879 GGAGAACACTCTTCCCTCTCG 59.525 57.143 0.00 0.00 34.58 4.04
4702 5789 3.465990 TCTACGAGGGTACGTGGAG 57.534 57.895 0.00 0.00 45.53 3.86
4724 5811 2.658373 TGTCATAACGCTTCCGCTTA 57.342 45.000 0.00 0.00 38.22 3.09
4765 7636 1.267261 GATCGGTCGGATCGTGAAGAT 59.733 52.381 10.85 0.00 42.02 2.40
4803 7674 1.293498 GTGCAGATCGTGGAGGTGT 59.707 57.895 0.00 0.00 0.00 4.16
4811 7682 1.284982 GCTGAACGTGTGCAGATCGT 61.285 55.000 12.25 5.82 39.49 3.73
4867 7738 1.658686 CTGACGGAACTCTCCCTCGG 61.659 65.000 0.00 0.00 38.71 4.63
4889 7760 3.676605 ACCATCGTCACGCCGTCA 61.677 61.111 0.00 0.00 0.00 4.35
4899 7770 4.442706 GGTAACTTCATCATCACCATCGT 58.557 43.478 0.00 0.00 0.00 3.73
4903 7774 2.679639 GCCGGTAACTTCATCATCACCA 60.680 50.000 1.90 0.00 0.00 4.17



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

AutoCloner maintained by Alex Coulton.