Multiple sequence alignment - TraesCS2B01G228300

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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 TraesCS2B01G228300 chr2B 100.000 3323 0 0 1 3323 222121931 222125253 0.000000e+00 6137.0
1 TraesCS2B01G228300 chr2B 96.552 116 4 0 1 116 212572926 212573041 3.380000e-45 193.0
2 TraesCS2B01G228300 chr2D 89.021 1257 107 15 114 1361 174245699 174246933 0.000000e+00 1528.0
3 TraesCS2B01G228300 chr2D 93.804 920 34 8 1359 2263 174246960 174247871 0.000000e+00 1362.0
4 TraesCS2B01G228300 chr2D 88.386 508 55 3 2268 2774 174248135 174248639 2.830000e-170 608.0
5 TraesCS2B01G228300 chr2D 88.732 355 31 5 2976 3323 174249383 174249735 3.060000e-115 425.0
6 TraesCS2B01G228300 chr2D 81.720 93 15 2 2623 2714 354956662 354956753 3.550000e-10 76.8
7 TraesCS2B01G228300 chr2A 87.987 1257 115 22 114 1361 173797405 173798634 0.000000e+00 1452.0
8 TraesCS2B01G228300 chr2A 91.657 863 34 15 1359 2215 173798661 173799491 0.000000e+00 1160.0
9 TraesCS2B01G228300 chr2A 87.885 520 57 5 2258 2776 173840082 173840596 1.020000e-169 606.0
10 TraesCS2B01G228300 chr2A 88.136 354 35 3 2976 3323 173841335 173841687 6.630000e-112 414.0
11 TraesCS2B01G228300 chr7D 83.303 557 87 5 175 726 595869663 595869108 2.960000e-140 508.0
12 TraesCS2B01G228300 chr7D 95.833 120 3 2 1 120 477407779 477407896 3.380000e-45 193.0
13 TraesCS2B01G228300 chr7D 76.678 283 55 4 2377 2651 14781412 14781691 2.670000e-31 147.0
14 TraesCS2B01G228300 chr5D 82.529 601 79 16 167 753 72615574 72614986 3.830000e-139 505.0
15 TraesCS2B01G228300 chr5D 82.847 548 83 8 175 715 486225581 486226124 6.450000e-132 481.0
16 TraesCS2B01G228300 chr5D 97.414 116 3 0 1 116 438062207 438062322 7.270000e-47 198.0
17 TraesCS2B01G228300 chr5D 96.552 116 4 0 1 116 425455071 425455186 3.380000e-45 193.0
18 TraesCS2B01G228300 chrUn 81.636 599 98 6 176 762 68800673 68801271 1.390000e-133 486.0
19 TraesCS2B01G228300 chr3A 82.003 589 91 9 178 753 111881114 111880528 1.390000e-133 486.0
20 TraesCS2B01G228300 chr3B 81.802 577 91 12 160 726 828756710 828757282 3.880000e-129 472.0
21 TraesCS2B01G228300 chr6A 81.494 589 94 9 179 753 592431295 592431882 1.400000e-128 470.0
22 TraesCS2B01G228300 chr6A 96.552 116 4 0 1 116 591340669 591340784 3.380000e-45 193.0
23 TraesCS2B01G228300 chr6D 81.145 594 97 9 175 754 335600224 335600816 2.340000e-126 462.0
24 TraesCS2B01G228300 chr6D 97.391 115 3 0 1 115 331252273 331252387 2.620000e-46 196.0
25 TraesCS2B01G228300 chr6D 96.552 116 4 0 1 116 435748724 435748839 3.380000e-45 193.0
26 TraesCS2B01G228300 chr1B 97.479 119 3 0 1 119 143086626 143086744 1.560000e-48 204.0
27 TraesCS2B01G228300 chr1B 96.552 116 4 0 1 116 685735436 685735321 3.380000e-45 193.0
28 TraesCS2B01G228300 chr5B 84.000 100 13 3 2603 2702 487246687 487246591 3.530000e-15 93.5


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 TraesCS2B01G228300 chr2B 222121931 222125253 3322 False 6137.00 6137 100.00000 1 3323 1 chr2B.!!$F2 3322
1 TraesCS2B01G228300 chr2D 174245699 174249735 4036 False 980.75 1528 89.98575 114 3323 4 chr2D.!!$F2 3209
2 TraesCS2B01G228300 chr2A 173797405 173799491 2086 False 1306.00 1452 89.82200 114 2215 2 chr2A.!!$F1 2101
3 TraesCS2B01G228300 chr2A 173840082 173841687 1605 False 510.00 606 88.01050 2258 3323 2 chr2A.!!$F2 1065
4 TraesCS2B01G228300 chr7D 595869108 595869663 555 True 508.00 508 83.30300 175 726 1 chr7D.!!$R1 551
5 TraesCS2B01G228300 chr5D 72614986 72615574 588 True 505.00 505 82.52900 167 753 1 chr5D.!!$R1 586
6 TraesCS2B01G228300 chr5D 486225581 486226124 543 False 481.00 481 82.84700 175 715 1 chr5D.!!$F3 540
7 TraesCS2B01G228300 chrUn 68800673 68801271 598 False 486.00 486 81.63600 176 762 1 chrUn.!!$F1 586
8 TraesCS2B01G228300 chr3A 111880528 111881114 586 True 486.00 486 82.00300 178 753 1 chr3A.!!$R1 575
9 TraesCS2B01G228300 chr3B 828756710 828757282 572 False 472.00 472 81.80200 160 726 1 chr3B.!!$F1 566
10 TraesCS2B01G228300 chr6A 592431295 592431882 587 False 470.00 470 81.49400 179 753 1 chr6A.!!$F2 574
11 TraesCS2B01G228300 chr6D 335600224 335600816 592 False 462.00 462 81.14500 175 754 1 chr6D.!!$F2 579

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
450 465 0.171231 CTGCTCGGATCTGTTCGTCA 59.829 55.0 0.42 0.0 0.0 4.35 F
899 930 0.321564 CAAATGGACCAGTCAGCCGA 60.322 55.0 0.00 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1440 1504 0.301388 GGCAAACGCTGTGCAAAAAG 59.699 50.0 7.72 0.00 44.07 2.27 R
2797 3138 0.031585 CTGAGACCGGTTTGTCGACA 59.968 55.0 15.76 15.76 40.26 4.35 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
23 24 6.350629 TGTGTTAGGGTACTCTAGGTTTTC 57.649 41.667 2.01 0.00 0.00 2.29
24 25 5.840149 TGTGTTAGGGTACTCTAGGTTTTCA 59.160 40.000 2.01 0.00 0.00 2.69
25 26 6.499350 TGTGTTAGGGTACTCTAGGTTTTCAT 59.501 38.462 2.01 0.00 0.00 2.57
26 27 6.817140 GTGTTAGGGTACTCTAGGTTTTCATG 59.183 42.308 2.01 0.00 0.00 3.07
27 28 6.070424 TGTTAGGGTACTCTAGGTTTTCATGG 60.070 42.308 2.01 0.00 0.00 3.66
28 29 4.436079 AGGGTACTCTAGGTTTTCATGGT 58.564 43.478 0.00 0.00 0.00 3.55
29 30 4.470304 AGGGTACTCTAGGTTTTCATGGTC 59.530 45.833 0.00 0.00 0.00 4.02
30 31 4.383880 GGGTACTCTAGGTTTTCATGGTCC 60.384 50.000 0.00 0.00 0.00 4.46
31 32 4.470304 GGTACTCTAGGTTTTCATGGTCCT 59.530 45.833 0.00 0.00 0.00 3.85
32 33 5.045797 GGTACTCTAGGTTTTCATGGTCCTT 60.046 44.000 0.00 0.00 0.00 3.36
33 34 5.584551 ACTCTAGGTTTTCATGGTCCTTT 57.415 39.130 0.00 0.00 0.00 3.11
34 35 5.316987 ACTCTAGGTTTTCATGGTCCTTTG 58.683 41.667 0.00 0.00 0.00 2.77
35 36 5.163088 ACTCTAGGTTTTCATGGTCCTTTGT 60.163 40.000 0.00 0.00 0.00 2.83
36 37 5.070001 TCTAGGTTTTCATGGTCCTTTGTG 58.930 41.667 0.00 0.00 0.00 3.33
37 38 3.642141 AGGTTTTCATGGTCCTTTGTGT 58.358 40.909 0.00 0.00 0.00 3.72
38 39 4.030216 AGGTTTTCATGGTCCTTTGTGTT 58.970 39.130 0.00 0.00 0.00 3.32
39 40 4.469586 AGGTTTTCATGGTCCTTTGTGTTT 59.530 37.500 0.00 0.00 0.00 2.83
40 41 4.570369 GGTTTTCATGGTCCTTTGTGTTTG 59.430 41.667 0.00 0.00 0.00 2.93
41 42 3.451141 TTCATGGTCCTTTGTGTTTGC 57.549 42.857 0.00 0.00 0.00 3.68
42 43 1.336440 TCATGGTCCTTTGTGTTTGCG 59.664 47.619 0.00 0.00 0.00 4.85
43 44 1.066908 CATGGTCCTTTGTGTTTGCGT 59.933 47.619 0.00 0.00 0.00 5.24
44 45 1.178276 TGGTCCTTTGTGTTTGCGTT 58.822 45.000 0.00 0.00 0.00 4.84
45 46 1.546476 TGGTCCTTTGTGTTTGCGTTT 59.454 42.857 0.00 0.00 0.00 3.60
46 47 2.190161 GGTCCTTTGTGTTTGCGTTTC 58.810 47.619 0.00 0.00 0.00 2.78
47 48 2.416162 GGTCCTTTGTGTTTGCGTTTCA 60.416 45.455 0.00 0.00 0.00 2.69
48 49 2.851824 GTCCTTTGTGTTTGCGTTTCAG 59.148 45.455 0.00 0.00 0.00 3.02
49 50 2.490115 TCCTTTGTGTTTGCGTTTCAGT 59.510 40.909 0.00 0.00 0.00 3.41
50 51 2.598192 CCTTTGTGTTTGCGTTTCAGTG 59.402 45.455 0.00 0.00 0.00 3.66
51 52 2.999507 TTGTGTTTGCGTTTCAGTGT 57.000 40.000 0.00 0.00 0.00 3.55
52 53 2.254918 TGTGTTTGCGTTTCAGTGTG 57.745 45.000 0.00 0.00 0.00 3.82
53 54 0.913876 GTGTTTGCGTTTCAGTGTGC 59.086 50.000 0.00 0.00 0.00 4.57
54 55 0.808125 TGTTTGCGTTTCAGTGTGCT 59.192 45.000 0.00 0.00 0.00 4.40
55 56 1.201181 TGTTTGCGTTTCAGTGTGCTT 59.799 42.857 0.00 0.00 0.00 3.91
56 57 1.583404 GTTTGCGTTTCAGTGTGCTTG 59.417 47.619 0.00 0.00 0.00 4.01
57 58 0.808125 TTGCGTTTCAGTGTGCTTGT 59.192 45.000 0.00 0.00 0.00 3.16
58 59 1.657822 TGCGTTTCAGTGTGCTTGTA 58.342 45.000 0.00 0.00 0.00 2.41
59 60 2.010497 TGCGTTTCAGTGTGCTTGTAA 58.990 42.857 0.00 0.00 0.00 2.41
60 61 2.031560 TGCGTTTCAGTGTGCTTGTAAG 59.968 45.455 0.00 0.00 0.00 2.34
61 62 2.602217 GCGTTTCAGTGTGCTTGTAAGG 60.602 50.000 0.00 0.00 0.00 2.69
62 63 2.032030 CGTTTCAGTGTGCTTGTAAGGG 60.032 50.000 0.00 0.00 0.00 3.95
63 64 2.949644 GTTTCAGTGTGCTTGTAAGGGT 59.050 45.455 0.00 0.00 0.00 4.34
64 65 2.543777 TCAGTGTGCTTGTAAGGGTC 57.456 50.000 0.00 0.00 0.00 4.46
65 66 1.765904 TCAGTGTGCTTGTAAGGGTCA 59.234 47.619 0.00 0.00 0.00 4.02
66 67 2.171659 TCAGTGTGCTTGTAAGGGTCAA 59.828 45.455 0.00 0.00 0.00 3.18
67 68 2.290641 CAGTGTGCTTGTAAGGGTCAAC 59.709 50.000 0.00 0.00 0.00 3.18
68 69 2.172717 AGTGTGCTTGTAAGGGTCAACT 59.827 45.455 0.00 0.00 0.00 3.16
69 70 3.389983 AGTGTGCTTGTAAGGGTCAACTA 59.610 43.478 0.00 0.00 0.00 2.24
70 71 3.497262 GTGTGCTTGTAAGGGTCAACTAC 59.503 47.826 0.00 0.00 0.00 2.73
71 72 3.389983 TGTGCTTGTAAGGGTCAACTACT 59.610 43.478 0.00 0.00 0.00 2.57
72 73 4.141574 TGTGCTTGTAAGGGTCAACTACTT 60.142 41.667 0.00 0.00 0.00 2.24
73 74 4.820173 GTGCTTGTAAGGGTCAACTACTTT 59.180 41.667 0.00 0.00 0.00 2.66
74 75 4.819630 TGCTTGTAAGGGTCAACTACTTTG 59.180 41.667 0.00 0.00 36.42 2.77
75 76 4.820173 GCTTGTAAGGGTCAACTACTTTGT 59.180 41.667 0.00 0.00 36.49 2.83
76 77 5.993441 GCTTGTAAGGGTCAACTACTTTGTA 59.007 40.000 0.00 0.00 36.49 2.41
77 78 6.073385 GCTTGTAAGGGTCAACTACTTTGTAC 60.073 42.308 0.00 0.00 36.49 2.90
78 79 6.736110 TGTAAGGGTCAACTACTTTGTACT 57.264 37.500 0.00 0.00 36.49 2.73
79 80 6.518493 TGTAAGGGTCAACTACTTTGTACTG 58.482 40.000 0.00 0.00 36.49 2.74
80 81 5.881923 AAGGGTCAACTACTTTGTACTGA 57.118 39.130 0.00 0.00 36.49 3.41
81 82 6.435292 AAGGGTCAACTACTTTGTACTGAT 57.565 37.500 0.00 0.00 36.49 2.90
82 83 6.435292 AGGGTCAACTACTTTGTACTGATT 57.565 37.500 0.00 0.00 36.49 2.57
83 84 6.465084 AGGGTCAACTACTTTGTACTGATTC 58.535 40.000 0.00 0.00 36.49 2.52
84 85 5.347907 GGGTCAACTACTTTGTACTGATTCG 59.652 44.000 0.00 0.00 36.49 3.34
85 86 5.924825 GGTCAACTACTTTGTACTGATTCGT 59.075 40.000 0.00 0.00 36.49 3.85
86 87 6.128902 GGTCAACTACTTTGTACTGATTCGTG 60.129 42.308 0.00 0.00 36.49 4.35
87 88 6.639686 GTCAACTACTTTGTACTGATTCGTGA 59.360 38.462 0.00 0.00 36.49 4.35
88 89 7.328737 GTCAACTACTTTGTACTGATTCGTGAT 59.671 37.037 0.00 0.00 36.49 3.06
89 90 8.517056 TCAACTACTTTGTACTGATTCGTGATA 58.483 33.333 0.00 0.00 36.49 2.15
90 91 9.302345 CAACTACTTTGTACTGATTCGTGATAT 57.698 33.333 0.00 0.00 0.00 1.63
91 92 8.858003 ACTACTTTGTACTGATTCGTGATATG 57.142 34.615 0.00 0.00 0.00 1.78
92 93 8.683615 ACTACTTTGTACTGATTCGTGATATGA 58.316 33.333 0.00 0.00 0.00 2.15
93 94 9.516314 CTACTTTGTACTGATTCGTGATATGAA 57.484 33.333 0.00 0.00 0.00 2.57
94 95 8.948631 ACTTTGTACTGATTCGTGATATGAAT 57.051 30.769 0.00 0.00 36.60 2.57
95 96 8.820933 ACTTTGTACTGATTCGTGATATGAATG 58.179 33.333 1.29 0.00 34.21 2.67
96 97 8.940768 TTTGTACTGATTCGTGATATGAATGA 57.059 30.769 1.29 0.00 34.21 2.57
97 98 8.940768 TTGTACTGATTCGTGATATGAATGAA 57.059 30.769 1.29 0.00 34.21 2.57
98 99 8.940768 TGTACTGATTCGTGATATGAATGAAA 57.059 30.769 1.29 0.00 34.21 2.69
99 100 9.377312 TGTACTGATTCGTGATATGAATGAAAA 57.623 29.630 1.29 0.00 34.21 2.29
138 139 3.712907 TAGCCGCCGCCTCCTTTT 61.713 61.111 0.00 0.00 34.57 2.27
146 147 1.079405 CGCCTCCTTTTCCACGCTA 60.079 57.895 0.00 0.00 0.00 4.26
147 148 0.672401 CGCCTCCTTTTCCACGCTAA 60.672 55.000 0.00 0.00 0.00 3.09
148 149 1.751437 GCCTCCTTTTCCACGCTAAT 58.249 50.000 0.00 0.00 0.00 1.73
150 151 2.711542 CCTCCTTTTCCACGCTAATGT 58.288 47.619 0.00 0.00 0.00 2.71
171 172 0.482446 TTTTCACCTCCCATGGCACT 59.518 50.000 6.09 0.00 0.00 4.40
194 201 3.147595 CGGTCCGCCTCATCTCCA 61.148 66.667 0.00 0.00 0.00 3.86
195 202 2.721167 CGGTCCGCCTCATCTCCAA 61.721 63.158 0.00 0.00 0.00 3.53
397 411 0.674581 ATCGTCAGTGTGCATGTGGG 60.675 55.000 0.00 0.00 0.00 4.61
450 465 0.171231 CTGCTCGGATCTGTTCGTCA 59.829 55.000 0.42 0.00 0.00 4.35
502 518 5.699097 GATCCTTCTGATCTACGCTACTT 57.301 43.478 0.00 0.00 45.46 2.24
510 526 7.803279 TCTGATCTACGCTACTTTTCATCTA 57.197 36.000 0.00 0.00 0.00 1.98
544 560 2.324014 CTGGTGCGCTGGCCCTATAA 62.324 60.000 9.73 0.00 38.85 0.98
633 654 3.583276 ATGACGACGGCGCCTTTGA 62.583 57.895 25.91 5.59 42.48 2.69
652 673 5.804692 TTGACTCGCTTCAGTTTTTGTAA 57.195 34.783 0.00 0.00 0.00 2.41
662 683 6.528014 TTCAGTTTTTGTAATCGTCGCTAA 57.472 33.333 0.00 0.00 0.00 3.09
679 700 4.887655 TCGCTAAGTGGTCTATGAATCTGA 59.112 41.667 0.00 0.00 0.00 3.27
731 759 6.074088 CGTTGTACTGCCAAGATGAATAGATC 60.074 42.308 0.00 0.00 0.00 2.75
741 769 8.612619 GCCAAGATGAATAGATCGAAAGTTTTA 58.387 33.333 0.00 0.00 0.00 1.52
895 926 4.695455 ACGAAATACAAATGGACCAGTCAG 59.305 41.667 0.00 0.00 0.00 3.51
899 930 0.321564 CAAATGGACCAGTCAGCCGA 60.322 55.000 0.00 0.00 0.00 5.54
904 935 3.222354 GACCAGTCAGCCGAACGGT 62.222 63.158 14.63 0.00 37.65 4.83
935 966 1.373435 CAAACGGTCTGGCCCAGTA 59.627 57.895 11.27 0.00 32.61 2.74
1016 1048 4.547367 CCCGATCCTTCCACCCGC 62.547 72.222 0.00 0.00 0.00 6.13
1017 1049 3.470888 CCGATCCTTCCACCCGCT 61.471 66.667 0.00 0.00 0.00 5.52
1018 1050 2.131709 CCGATCCTTCCACCCGCTA 61.132 63.158 0.00 0.00 0.00 4.26
1132 1164 1.220206 CTCGATGCACCAGCTTCCT 59.780 57.895 0.00 0.00 40.70 3.36
1172 1204 1.006102 CCGCGGTCTCACTGTTCTT 60.006 57.895 19.50 0.00 0.00 2.52
1210 1242 0.957395 GCTGTAGCTTGAAGCAGGCA 60.957 55.000 20.45 13.08 45.56 4.75
1425 1489 1.210234 TCGACCACATGGCATTCATCT 59.790 47.619 0.00 0.00 39.32 2.90
1426 1490 2.433970 TCGACCACATGGCATTCATCTA 59.566 45.455 0.00 0.00 39.32 1.98
1427 1491 3.071457 TCGACCACATGGCATTCATCTAT 59.929 43.478 0.00 0.00 39.32 1.98
1428 1492 3.817084 CGACCACATGGCATTCATCTATT 59.183 43.478 0.00 0.00 39.32 1.73
1429 1493 4.276678 CGACCACATGGCATTCATCTATTT 59.723 41.667 0.00 0.00 39.32 1.40
1430 1494 5.221106 CGACCACATGGCATTCATCTATTTT 60.221 40.000 0.00 0.00 39.32 1.82
1431 1495 6.549433 ACCACATGGCATTCATCTATTTTT 57.451 33.333 0.00 0.00 39.32 1.94
1550 1614 0.040067 GCCGGTGAGTTTGCTGAAAG 60.040 55.000 1.90 0.00 0.00 2.62
1698 1770 5.630680 CCATTTGTTAAACTACAGCTTGCAG 59.369 40.000 0.00 0.00 0.00 4.41
1720 1792 6.537566 CAGTCAATTTCTTGTTCGGTCTATG 58.462 40.000 0.00 0.00 33.87 2.23
1737 1809 4.153117 GTCTATGTTGACTGTGGCAAAGAG 59.847 45.833 12.68 0.00 34.39 2.85
1743 1815 3.360867 TGACTGTGGCAAAGAGGAAAAA 58.639 40.909 12.68 0.00 0.00 1.94
1889 1961 6.861055 AGTAAACGTTTTGCAACTATGAATGG 59.139 34.615 20.19 0.00 0.00 3.16
2088 2160 1.675641 GGTGCTGGCTCCATTTCGT 60.676 57.895 8.56 0.00 0.00 3.85
2098 2170 0.537188 TCCATTTCGTGAGGAGGCTC 59.463 55.000 5.78 5.78 0.00 4.70
2108 2180 3.682718 CGTGAGGAGGCTCAAACCATAAT 60.683 47.826 17.69 0.00 34.88 1.28
2110 2182 4.706962 GTGAGGAGGCTCAAACCATAATTT 59.293 41.667 17.69 0.00 34.88 1.82
2147 2225 3.984508 TTTTTGATCCGCAAACCGTAA 57.015 38.095 0.00 0.00 45.64 3.18
2166 2244 9.940166 AACCGTAAAACAATTGTTCTAAGTAAG 57.060 29.630 23.47 12.35 37.25 2.34
2222 2300 4.328983 ACGTAAACGAAGATTACATGCCAG 59.671 41.667 9.86 0.00 44.40 4.85
2236 2314 1.750193 TGCCAGAAAATAGAAGGCCG 58.250 50.000 0.00 0.00 44.60 6.13
2237 2315 0.382158 GCCAGAAAATAGAAGGCCGC 59.618 55.000 0.00 0.00 39.42 6.53
2238 2316 0.657840 CCAGAAAATAGAAGGCCGCG 59.342 55.000 0.00 0.00 0.00 6.46
2247 2326 0.824759 AGAAGGCCGCGTAAGAGATT 59.175 50.000 4.92 0.00 40.82 2.40
2250 2329 1.688772 AGGCCGCGTAAGAGATTCTA 58.311 50.000 4.92 0.00 40.82 2.10
2259 2338 5.396947 CGCGTAAGAGATTCTAGCTAGTTTG 59.603 44.000 20.10 4.40 40.82 2.93
2260 2339 6.267070 GCGTAAGAGATTCTAGCTAGTTTGT 58.733 40.000 20.10 7.72 43.02 2.83
2261 2340 6.197468 GCGTAAGAGATTCTAGCTAGTTTGTG 59.803 42.308 20.10 0.00 43.02 3.33
2262 2341 7.473366 CGTAAGAGATTCTAGCTAGTTTGTGA 58.527 38.462 20.10 0.00 43.02 3.58
2305 2644 1.410850 AATGTCCGATCTGGCCCGAT 61.411 55.000 9.74 9.74 37.80 4.18
2321 2660 3.621461 GCCCGATAAAGGACCTTTGAGAA 60.621 47.826 26.72 9.48 35.21 2.87
2339 2678 5.105063 TGAGAATTTGTGTCGCTAGATCTG 58.895 41.667 5.18 0.00 0.00 2.90
2346 2685 1.135139 TGTCGCTAGATCTGTTGGCTC 59.865 52.381 5.18 2.31 0.00 4.70
2366 2705 4.677584 CTCTCTTTGGATCTTGGTAGTCG 58.322 47.826 0.00 0.00 0.00 4.18
2382 2721 4.826183 GGTAGTCGGTGTATCTATCAAGGT 59.174 45.833 0.00 0.00 0.00 3.50
2415 2754 2.158534 TGGCTATTGGTGTGGTGACTTT 60.159 45.455 0.00 0.00 0.00 2.66
2474 2813 3.715638 TTCTCTAACTCTCTGGACCGA 57.284 47.619 0.00 0.00 0.00 4.69
2483 2822 1.114627 CTCTGGACCGATGGTGATGA 58.885 55.000 0.00 0.00 35.25 2.92
2498 2837 3.755378 GGTGATGAATTGCAAGTCTGTCT 59.245 43.478 25.47 9.48 0.00 3.41
2509 2848 1.185618 AGTCTGTCTTGCGTGGGCTA 61.186 55.000 0.00 0.00 40.82 3.93
2521 2860 1.077787 TGGGCTAATGCTCCAACCG 60.078 57.895 0.00 0.00 39.40 4.44
2539 2878 2.351726 ACCGATGTTTCTTTAGCGATGC 59.648 45.455 0.00 0.00 0.00 3.91
2540 2879 2.286418 CCGATGTTTCTTTAGCGATGCC 60.286 50.000 0.00 0.00 0.00 4.40
2541 2880 2.609459 CGATGTTTCTTTAGCGATGCCT 59.391 45.455 0.00 0.00 0.00 4.75
2542 2881 3.802139 CGATGTTTCTTTAGCGATGCCTA 59.198 43.478 0.00 0.00 0.00 3.93
2543 2882 4.084849 CGATGTTTCTTTAGCGATGCCTAG 60.085 45.833 0.00 0.00 0.00 3.02
2544 2883 3.531538 TGTTTCTTTAGCGATGCCTAGG 58.468 45.455 3.67 3.67 0.00 3.02
2552 2891 1.765314 AGCGATGCCTAGGTCTCATTT 59.235 47.619 11.31 0.00 0.00 2.32
2620 2959 1.654220 CGTTTGCAGGTGTCCCTTG 59.346 57.895 0.00 0.00 39.89 3.61
2664 3004 1.593196 TTTCAAGCTTCCACGGACAG 58.407 50.000 0.00 0.00 0.00 3.51
2674 3014 1.082117 CCACGGACAGCGTACAATCC 61.082 60.000 0.00 0.00 0.00 3.01
2678 3018 0.454600 GGACAGCGTACAATCCGAGA 59.545 55.000 0.00 0.00 0.00 4.04
2684 3024 3.678072 CAGCGTACAATCCGAGAAAGAAA 59.322 43.478 0.00 0.00 0.00 2.52
2695 3035 9.760660 CAATCCGAGAAAGAAAAATGTTAGTAG 57.239 33.333 0.00 0.00 0.00 2.57
2757 3098 2.665649 TGACGGTGCATAGTACCAAG 57.334 50.000 5.18 0.00 38.11 3.61
2758 3099 1.206132 TGACGGTGCATAGTACCAAGG 59.794 52.381 5.18 0.00 38.11 3.61
2759 3100 0.539986 ACGGTGCATAGTACCAAGGG 59.460 55.000 5.18 0.00 38.11 3.95
2760 3101 0.539986 CGGTGCATAGTACCAAGGGT 59.460 55.000 5.18 0.00 38.11 4.34
2761 3102 1.742411 CGGTGCATAGTACCAAGGGTG 60.742 57.143 5.18 0.00 38.11 4.61
2762 3103 1.379527 GTGCATAGTACCAAGGGTGC 58.620 55.000 0.00 0.00 38.59 5.01
2763 3104 0.254747 TGCATAGTACCAAGGGTGCC 59.745 55.000 0.00 0.00 39.11 5.01
2764 3105 0.465642 GCATAGTACCAAGGGTGCCC 60.466 60.000 0.00 0.00 39.11 5.36
2765 3106 0.179056 CATAGTACCAAGGGTGCCCG 60.179 60.000 0.98 0.00 39.11 6.13
2766 3107 1.342672 ATAGTACCAAGGGTGCCCGG 61.343 60.000 0.00 0.00 39.11 5.73
2767 3108 2.752036 TAGTACCAAGGGTGCCCGGT 62.752 60.000 10.88 10.88 39.11 5.28
2768 3109 2.855014 TACCAAGGGTGCCCGGTT 60.855 61.111 11.26 0.00 41.95 4.44
2769 3110 1.538382 TACCAAGGGTGCCCGGTTA 60.538 57.895 11.26 0.00 41.95 2.85
2770 3111 1.132554 TACCAAGGGTGCCCGGTTAA 61.133 55.000 11.26 0.00 41.95 2.01
2771 3112 1.000145 CCAAGGGTGCCCGGTTAAT 60.000 57.895 0.00 0.00 41.95 1.40
2772 3113 1.035385 CCAAGGGTGCCCGGTTAATC 61.035 60.000 0.00 0.00 41.95 1.75
2773 3114 1.078001 AAGGGTGCCCGGTTAATCG 60.078 57.895 0.00 0.00 41.95 3.34
2781 3122 2.893404 CGGTTAATCGGGTGGCCG 60.893 66.667 0.00 0.00 0.00 6.13
2797 3138 1.525442 CCGGTTAATCGGGAAGCCT 59.475 57.895 19.83 0.00 45.78 4.58
2805 3146 1.541310 ATCGGGAAGCCTGTCGACAA 61.541 55.000 20.49 1.01 34.40 3.18
2816 3157 0.031585 TGTCGACAAACCGGTCTCAG 59.968 55.000 17.62 0.01 35.63 3.35
2821 3162 1.374252 CAAACCGGTCTCAGGGACG 60.374 63.158 8.04 0.00 45.35 4.79
2822 3163 1.532316 AAACCGGTCTCAGGGACGA 60.532 57.895 8.04 0.00 45.35 4.20
2823 3164 1.117142 AAACCGGTCTCAGGGACGAA 61.117 55.000 8.04 0.00 45.35 3.85
2824 3165 1.813728 AACCGGTCTCAGGGACGAAC 61.814 60.000 8.04 0.00 45.35 3.95
2825 3166 2.273179 CCGGTCTCAGGGACGAACA 61.273 63.158 0.00 0.00 45.35 3.18
2826 3167 1.605058 CCGGTCTCAGGGACGAACAT 61.605 60.000 0.00 0.00 45.35 2.71
2827 3168 1.100510 CGGTCTCAGGGACGAACATA 58.899 55.000 0.00 0.00 45.35 2.29
2828 3169 1.202268 CGGTCTCAGGGACGAACATAC 60.202 57.143 0.00 0.00 45.35 2.39
2829 3170 1.136500 GGTCTCAGGGACGAACATACC 59.864 57.143 0.00 0.00 45.35 2.73
2830 3171 1.822990 GTCTCAGGGACGAACATACCA 59.177 52.381 0.00 0.00 35.07 3.25
2831 3172 2.232941 GTCTCAGGGACGAACATACCAA 59.767 50.000 0.00 0.00 35.07 3.67
2832 3173 2.496070 TCTCAGGGACGAACATACCAAG 59.504 50.000 0.00 0.00 0.00 3.61
2833 3174 2.496070 CTCAGGGACGAACATACCAAGA 59.504 50.000 0.00 0.00 0.00 3.02
2834 3175 2.232941 TCAGGGACGAACATACCAAGAC 59.767 50.000 0.00 0.00 0.00 3.01
2835 3176 2.028476 CAGGGACGAACATACCAAGACA 60.028 50.000 0.00 0.00 0.00 3.41
2836 3177 2.838202 AGGGACGAACATACCAAGACAT 59.162 45.455 0.00 0.00 0.00 3.06
2837 3178 2.936498 GGGACGAACATACCAAGACATG 59.064 50.000 0.00 0.00 0.00 3.21
2845 3186 4.567318 CCAAGACATGGCCTAGGC 57.433 61.111 26.55 26.55 43.80 3.93
2866 3207 4.405671 TCGTCCCGCGAGAGACCT 62.406 66.667 8.23 0.00 45.68 3.85
2867 3208 2.513204 CGTCCCGCGAGAGACCTA 60.513 66.667 8.23 0.00 44.77 3.08
2868 3209 2.821688 CGTCCCGCGAGAGACCTAC 61.822 68.421 8.23 0.00 44.77 3.18
2869 3210 2.124403 TCCCGCGAGAGACCTACC 60.124 66.667 8.23 0.00 0.00 3.18
2870 3211 2.124236 CCCGCGAGAGACCTACCT 60.124 66.667 8.23 0.00 0.00 3.08
2871 3212 1.753463 CCCGCGAGAGACCTACCTT 60.753 63.158 8.23 0.00 0.00 3.50
2872 3213 1.726533 CCCGCGAGAGACCTACCTTC 61.727 65.000 8.23 0.00 0.00 3.46
2873 3214 0.748729 CCGCGAGAGACCTACCTTCT 60.749 60.000 8.23 0.00 0.00 2.85
2874 3215 1.474677 CCGCGAGAGACCTACCTTCTA 60.475 57.143 8.23 0.00 0.00 2.10
2875 3216 1.868498 CGCGAGAGACCTACCTTCTAG 59.132 57.143 0.00 0.00 0.00 2.43
2876 3217 2.483363 CGCGAGAGACCTACCTTCTAGA 60.483 54.545 0.00 0.00 0.00 2.43
2877 3218 3.543665 GCGAGAGACCTACCTTCTAGAA 58.456 50.000 4.81 4.81 0.00 2.10
2878 3219 3.562557 GCGAGAGACCTACCTTCTAGAAG 59.437 52.174 23.31 23.31 38.14 2.85
2879 3220 4.683942 GCGAGAGACCTACCTTCTAGAAGA 60.684 50.000 30.17 13.02 40.79 2.87
2880 3221 5.617252 CGAGAGACCTACCTTCTAGAAGAT 58.383 45.833 30.17 18.94 40.79 2.40
2881 3222 6.742082 GCGAGAGACCTACCTTCTAGAAGATA 60.742 46.154 30.17 19.05 40.79 1.98
2882 3223 7.218614 CGAGAGACCTACCTTCTAGAAGATAA 58.781 42.308 30.17 15.31 40.79 1.75
2883 3224 7.172019 CGAGAGACCTACCTTCTAGAAGATAAC 59.828 44.444 30.17 16.50 40.79 1.89
2884 3225 7.874252 AGAGACCTACCTTCTAGAAGATAACA 58.126 38.462 30.17 11.34 40.79 2.41
2885 3226 7.776500 AGAGACCTACCTTCTAGAAGATAACAC 59.224 40.741 30.17 17.37 40.79 3.32
2886 3227 7.411808 AGACCTACCTTCTAGAAGATAACACA 58.588 38.462 30.17 0.02 40.79 3.72
2887 3228 8.062536 AGACCTACCTTCTAGAAGATAACACAT 58.937 37.037 30.17 10.24 40.79 3.21
2888 3229 8.611051 ACCTACCTTCTAGAAGATAACACATT 57.389 34.615 30.17 5.74 40.79 2.71
2889 3230 8.478877 ACCTACCTTCTAGAAGATAACACATTG 58.521 37.037 30.17 13.67 40.79 2.82
2890 3231 8.696374 CCTACCTTCTAGAAGATAACACATTGA 58.304 37.037 30.17 0.00 40.79 2.57
2891 3232 9.522804 CTACCTTCTAGAAGATAACACATTGAC 57.477 37.037 30.17 0.00 40.79 3.18
2892 3233 7.036220 ACCTTCTAGAAGATAACACATTGACG 58.964 38.462 30.17 12.65 40.79 4.35
2893 3234 7.036220 CCTTCTAGAAGATAACACATTGACGT 58.964 38.462 30.17 0.00 40.79 4.34
2894 3235 8.188799 CCTTCTAGAAGATAACACATTGACGTA 58.811 37.037 30.17 0.00 40.79 3.57
2895 3236 8.906636 TTCTAGAAGATAACACATTGACGTAC 57.093 34.615 0.00 0.00 0.00 3.67
2896 3237 8.047413 TCTAGAAGATAACACATTGACGTACA 57.953 34.615 0.00 0.00 0.00 2.90
2897 3238 8.517056 TCTAGAAGATAACACATTGACGTACAA 58.483 33.333 0.00 0.00 42.95 2.41
2898 3239 7.582435 AGAAGATAACACATTGACGTACAAG 57.418 36.000 0.00 0.00 42.02 3.16
2899 3240 7.152645 AGAAGATAACACATTGACGTACAAGT 58.847 34.615 0.00 0.00 42.02 3.16
2900 3241 7.656137 AGAAGATAACACATTGACGTACAAGTT 59.344 33.333 0.00 0.00 42.02 2.66
2901 3242 8.821147 AAGATAACACATTGACGTACAAGTTA 57.179 30.769 0.00 1.48 42.02 2.24
2902 3243 8.462143 AGATAACACATTGACGTACAAGTTAG 57.538 34.615 0.00 0.00 42.02 2.34
2903 3244 5.917541 AACACATTGACGTACAAGTTAGG 57.082 39.130 0.00 0.00 42.02 2.69
2904 3245 5.204409 ACACATTGACGTACAAGTTAGGA 57.796 39.130 0.00 0.00 42.02 2.94
2905 3246 5.603596 ACACATTGACGTACAAGTTAGGAA 58.396 37.500 0.00 0.00 42.02 3.36
2947 3288 6.127786 GGTCTAGGTAAACATCTTGACGTACT 60.128 42.308 0.00 0.00 36.89 2.73
2949 3290 7.907563 GTCTAGGTAAACATCTTGACGTACTAC 59.092 40.741 0.00 0.00 0.00 2.73
2951 3292 7.928307 AGGTAAACATCTTGACGTACTACTA 57.072 36.000 0.00 0.00 0.00 1.82
2952 3293 7.756558 AGGTAAACATCTTGACGTACTACTAC 58.243 38.462 0.00 0.00 0.00 2.73
2953 3294 7.391554 AGGTAAACATCTTGACGTACTACTACA 59.608 37.037 0.00 0.00 0.00 2.74
2954 3295 8.186821 GGTAAACATCTTGACGTACTACTACAT 58.813 37.037 0.00 0.00 0.00 2.29
2958 3299 9.731819 AACATCTTGACGTACTACTACATATTG 57.268 33.333 0.00 0.00 0.00 1.90
2959 3300 8.900781 ACATCTTGACGTACTACTACATATTGT 58.099 33.333 0.00 0.00 0.00 2.71
2960 3301 9.731819 CATCTTGACGTACTACTACATATTGTT 57.268 33.333 0.00 0.00 0.00 2.83
2984 3978 2.289010 ACGGTTAGTAAACACCCTTCCG 60.289 50.000 0.00 1.11 37.34 4.30
3119 4117 4.325119 ACTGCATATTGATGAGATCCTGC 58.675 43.478 0.00 0.00 34.73 4.85
3144 4142 7.336931 GCTGGAGGAGTTAGAATTGTTGAAATA 59.663 37.037 0.00 0.00 0.00 1.40
3200 4198 5.469421 GTCCAGATCATGAGTTTGATGGATC 59.531 44.000 0.09 0.00 37.22 3.36
3203 4204 6.649973 CCAGATCATGAGTTTGATGGATCTAC 59.350 42.308 0.09 0.00 36.48 2.59
3209 4210 8.048514 TCATGAGTTTGATGGATCTACATTGAA 58.951 33.333 0.00 0.00 0.00 2.69
3248 4249 5.001232 GCAAGTGAGTGTAATTCTGGGTAA 58.999 41.667 0.00 0.00 0.00 2.85
3251 4252 7.499232 GCAAGTGAGTGTAATTCTGGGTAATAT 59.501 37.037 0.00 0.00 0.00 1.28
3265 4266 7.732996 TCTGGGTAATATACTTTAAGAGCCAC 58.267 38.462 0.00 0.00 0.00 5.01
3266 4267 6.518493 TGGGTAATATACTTTAAGAGCCACG 58.482 40.000 0.00 0.00 0.00 4.94
3284 4285 4.759782 CCACGTCTCTCCAATTATCTTGT 58.240 43.478 0.00 0.00 0.00 3.16
3315 4316 1.602377 GTGTTTCCTTGACCAACCTCG 59.398 52.381 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.350629 TGAAAACCTAGAGTACCCTAACAC 57.649 41.667 0.00 0.00 0.00 3.32
2 3 6.070424 CCATGAAAACCTAGAGTACCCTAACA 60.070 42.308 0.00 0.00 0.00 2.41
4 5 6.027482 ACCATGAAAACCTAGAGTACCCTAA 58.973 40.000 0.00 0.00 0.00 2.69
5 6 5.596763 ACCATGAAAACCTAGAGTACCCTA 58.403 41.667 0.00 0.00 0.00 3.53
6 7 4.436079 ACCATGAAAACCTAGAGTACCCT 58.564 43.478 0.00 0.00 0.00 4.34
7 8 4.383880 GGACCATGAAAACCTAGAGTACCC 60.384 50.000 0.00 0.00 0.00 3.69
8 9 4.470304 AGGACCATGAAAACCTAGAGTACC 59.530 45.833 0.00 0.00 0.00 3.34
9 10 5.678955 AGGACCATGAAAACCTAGAGTAC 57.321 43.478 0.00 0.00 0.00 2.73
10 11 6.043938 ACAAAGGACCATGAAAACCTAGAGTA 59.956 38.462 0.00 0.00 32.06 2.59
11 12 5.163088 ACAAAGGACCATGAAAACCTAGAGT 60.163 40.000 0.00 0.00 32.06 3.24
12 13 5.182001 CACAAAGGACCATGAAAACCTAGAG 59.818 44.000 0.00 0.00 32.06 2.43
13 14 5.070001 CACAAAGGACCATGAAAACCTAGA 58.930 41.667 0.00 0.00 32.06 2.43
14 15 4.827284 ACACAAAGGACCATGAAAACCTAG 59.173 41.667 0.00 0.00 32.06 3.02
15 16 4.798882 ACACAAAGGACCATGAAAACCTA 58.201 39.130 0.00 0.00 32.06 3.08
16 17 3.642141 ACACAAAGGACCATGAAAACCT 58.358 40.909 0.00 0.00 0.00 3.50
17 18 4.400529 AACACAAAGGACCATGAAAACC 57.599 40.909 0.00 0.00 0.00 3.27
18 19 4.033932 GCAAACACAAAGGACCATGAAAAC 59.966 41.667 0.00 0.00 0.00 2.43
19 20 4.187694 GCAAACACAAAGGACCATGAAAA 58.812 39.130 0.00 0.00 0.00 2.29
20 21 3.736433 CGCAAACACAAAGGACCATGAAA 60.736 43.478 0.00 0.00 0.00 2.69
21 22 2.223688 CGCAAACACAAAGGACCATGAA 60.224 45.455 0.00 0.00 0.00 2.57
22 23 1.336440 CGCAAACACAAAGGACCATGA 59.664 47.619 0.00 0.00 0.00 3.07
23 24 1.066908 ACGCAAACACAAAGGACCATG 59.933 47.619 0.00 0.00 0.00 3.66
24 25 1.398692 ACGCAAACACAAAGGACCAT 58.601 45.000 0.00 0.00 0.00 3.55
25 26 1.178276 AACGCAAACACAAAGGACCA 58.822 45.000 0.00 0.00 0.00 4.02
26 27 2.190161 GAAACGCAAACACAAAGGACC 58.810 47.619 0.00 0.00 0.00 4.46
27 28 2.851824 CTGAAACGCAAACACAAAGGAC 59.148 45.455 0.00 0.00 0.00 3.85
28 29 2.490115 ACTGAAACGCAAACACAAAGGA 59.510 40.909 0.00 0.00 0.00 3.36
29 30 2.598192 CACTGAAACGCAAACACAAAGG 59.402 45.455 0.00 0.00 0.00 3.11
30 31 3.059306 CACACTGAAACGCAAACACAAAG 59.941 43.478 0.00 0.00 0.00 2.77
31 32 2.983136 CACACTGAAACGCAAACACAAA 59.017 40.909 0.00 0.00 0.00 2.83
32 33 2.590073 CACACTGAAACGCAAACACAA 58.410 42.857 0.00 0.00 0.00 3.33
33 34 1.730772 GCACACTGAAACGCAAACACA 60.731 47.619 0.00 0.00 0.00 3.72
34 35 0.913876 GCACACTGAAACGCAAACAC 59.086 50.000 0.00 0.00 0.00 3.32
35 36 0.808125 AGCACACTGAAACGCAAACA 59.192 45.000 0.00 0.00 0.00 2.83
36 37 1.583404 CAAGCACACTGAAACGCAAAC 59.417 47.619 0.00 0.00 0.00 2.93
37 38 1.201181 ACAAGCACACTGAAACGCAAA 59.799 42.857 0.00 0.00 0.00 3.68
38 39 0.808125 ACAAGCACACTGAAACGCAA 59.192 45.000 0.00 0.00 0.00 4.85
39 40 1.657822 TACAAGCACACTGAAACGCA 58.342 45.000 0.00 0.00 0.00 5.24
40 41 2.602217 CCTTACAAGCACACTGAAACGC 60.602 50.000 0.00 0.00 0.00 4.84
41 42 2.032030 CCCTTACAAGCACACTGAAACG 60.032 50.000 0.00 0.00 0.00 3.60
42 43 2.949644 ACCCTTACAAGCACACTGAAAC 59.050 45.455 0.00 0.00 0.00 2.78
43 44 3.211045 GACCCTTACAAGCACACTGAAA 58.789 45.455 0.00 0.00 0.00 2.69
44 45 2.171659 TGACCCTTACAAGCACACTGAA 59.828 45.455 0.00 0.00 0.00 3.02
45 46 1.765904 TGACCCTTACAAGCACACTGA 59.234 47.619 0.00 0.00 0.00 3.41
46 47 2.254546 TGACCCTTACAAGCACACTG 57.745 50.000 0.00 0.00 0.00 3.66
47 48 2.172717 AGTTGACCCTTACAAGCACACT 59.827 45.455 0.00 0.00 0.00 3.55
48 49 2.572290 AGTTGACCCTTACAAGCACAC 58.428 47.619 0.00 0.00 0.00 3.82
49 50 3.389983 AGTAGTTGACCCTTACAAGCACA 59.610 43.478 0.00 0.00 0.00 4.57
50 51 4.004196 AGTAGTTGACCCTTACAAGCAC 57.996 45.455 0.00 0.00 0.00 4.40
51 52 4.699925 AAGTAGTTGACCCTTACAAGCA 57.300 40.909 0.00 0.00 0.00 3.91
52 53 4.820173 ACAAAGTAGTTGACCCTTACAAGC 59.180 41.667 0.00 0.00 39.87 4.01
53 54 7.170998 CAGTACAAAGTAGTTGACCCTTACAAG 59.829 40.741 0.00 0.00 39.87 3.16
54 55 6.987992 CAGTACAAAGTAGTTGACCCTTACAA 59.012 38.462 0.00 0.00 39.87 2.41
55 56 6.324512 TCAGTACAAAGTAGTTGACCCTTACA 59.675 38.462 0.00 0.00 39.87 2.41
56 57 6.752168 TCAGTACAAAGTAGTTGACCCTTAC 58.248 40.000 0.00 0.00 39.87 2.34
57 58 6.982160 TCAGTACAAAGTAGTTGACCCTTA 57.018 37.500 0.00 0.00 39.87 2.69
58 59 5.881923 TCAGTACAAAGTAGTTGACCCTT 57.118 39.130 0.00 0.00 39.87 3.95
59 60 6.435292 AATCAGTACAAAGTAGTTGACCCT 57.565 37.500 0.00 0.00 39.87 4.34
60 61 5.347907 CGAATCAGTACAAAGTAGTTGACCC 59.652 44.000 0.00 0.00 39.87 4.46
61 62 5.924825 ACGAATCAGTACAAAGTAGTTGACC 59.075 40.000 0.00 0.00 39.87 4.02
62 63 6.639686 TCACGAATCAGTACAAAGTAGTTGAC 59.360 38.462 0.00 0.00 39.87 3.18
63 64 6.741109 TCACGAATCAGTACAAAGTAGTTGA 58.259 36.000 0.00 0.00 39.87 3.18
64 65 7.582435 ATCACGAATCAGTACAAAGTAGTTG 57.418 36.000 0.00 0.00 43.43 3.16
65 66 9.302345 CATATCACGAATCAGTACAAAGTAGTT 57.698 33.333 0.00 0.00 0.00 2.24
66 67 8.683615 TCATATCACGAATCAGTACAAAGTAGT 58.316 33.333 0.00 0.00 0.00 2.73
67 68 9.516314 TTCATATCACGAATCAGTACAAAGTAG 57.484 33.333 0.00 0.00 0.00 2.57
69 70 8.820933 CATTCATATCACGAATCAGTACAAAGT 58.179 33.333 0.00 0.00 30.65 2.66
70 71 9.034544 TCATTCATATCACGAATCAGTACAAAG 57.965 33.333 0.00 0.00 30.65 2.77
71 72 8.940768 TCATTCATATCACGAATCAGTACAAA 57.059 30.769 0.00 0.00 30.65 2.83
72 73 8.940768 TTCATTCATATCACGAATCAGTACAA 57.059 30.769 0.00 0.00 30.65 2.41
73 74 8.940768 TTTCATTCATATCACGAATCAGTACA 57.059 30.769 0.00 0.00 30.65 2.90
111 112 1.791662 CGGCGGCTACGTGATTTTT 59.208 52.632 7.61 0.00 43.45 1.94
112 113 2.746803 GCGGCGGCTACGTGATTTT 61.747 57.895 9.78 0.00 43.45 1.82
156 157 1.377725 GTCAGTGCCATGGGAGGTG 60.378 63.158 15.13 11.47 0.00 4.00
157 158 2.959484 CGTCAGTGCCATGGGAGGT 61.959 63.158 15.13 0.00 0.00 3.85
158 159 2.124983 CGTCAGTGCCATGGGAGG 60.125 66.667 15.13 6.17 0.00 4.30
289 302 4.279671 CAGTCTCGCCTTCCTGAATAGTAT 59.720 45.833 0.00 0.00 0.00 2.12
291 304 2.428890 CAGTCTCGCCTTCCTGAATAGT 59.571 50.000 0.00 0.00 0.00 2.12
397 411 0.249657 GATCCGCTGGAGACACATCC 60.250 60.000 3.76 0.00 40.03 3.51
409 423 2.752354 CTCCATCGAAGATAGATCCGCT 59.248 50.000 0.00 0.00 45.12 5.52
450 465 6.398095 TGAAGACACATGAACATAGACGAAT 58.602 36.000 0.00 0.00 0.00 3.34
510 526 0.108041 ACCAGAACAACAACCGTCGT 60.108 50.000 0.00 0.00 0.00 4.34
544 560 3.372025 GGGAAGTCATTGTGATAAGGCCT 60.372 47.826 0.00 0.00 0.00 5.19
633 654 4.510340 ACGATTACAAAAACTGAAGCGAGT 59.490 37.500 0.00 0.00 0.00 4.18
652 673 3.211865 TCATAGACCACTTAGCGACGAT 58.788 45.455 0.00 0.00 0.00 3.73
662 683 9.911788 AAATTACATTCAGATTCATAGACCACT 57.088 29.630 0.00 0.00 0.00 4.00
895 926 1.514873 CGTACTACCACCGTTCGGC 60.515 63.158 11.32 0.00 0.00 5.54
899 930 0.388659 TGCAACGTACTACCACCGTT 59.611 50.000 0.00 0.00 44.81 4.44
1016 1048 4.737765 GGAGACGACACGTAGTAGTAGTAG 59.262 50.000 0.00 0.00 41.61 2.57
1017 1049 4.399618 AGGAGACGACACGTAGTAGTAGTA 59.600 45.833 0.00 0.00 41.61 1.82
1018 1050 3.194542 AGGAGACGACACGTAGTAGTAGT 59.805 47.826 0.00 0.00 41.61 2.73
1113 1145 1.219124 GGAAGCTGGTGCATCGAGA 59.781 57.895 0.00 0.00 42.74 4.04
1115 1147 1.219124 GAGGAAGCTGGTGCATCGA 59.781 57.895 0.00 0.00 42.74 3.59
1172 1204 3.755628 GCACGCCGTCCTACTCCA 61.756 66.667 0.00 0.00 0.00 3.86
1288 1323 2.514824 GGAATGCCAGGAGACGCC 60.515 66.667 0.00 0.00 0.00 5.68
1310 1345 0.400594 GGCAAACCTGGTGGAGTACT 59.599 55.000 0.00 0.00 37.04 2.73
1377 1441 7.253288 CGACAAGCAAAATTCACCGTATATTTG 60.253 37.037 0.00 0.00 0.00 2.32
1430 1494 4.092675 CGCTGTGCAAAAAGAAAGGAAAAA 59.907 37.500 0.00 0.00 0.00 1.94
1431 1495 3.616379 CGCTGTGCAAAAAGAAAGGAAAA 59.384 39.130 0.00 0.00 0.00 2.29
1440 1504 0.301388 GGCAAACGCTGTGCAAAAAG 59.699 50.000 7.72 0.00 44.07 2.27
1448 1512 2.275380 GGGATTGGGCAAACGCTGT 61.275 57.895 0.00 0.00 0.00 4.40
1698 1770 6.481954 ACATAGACCGAACAAGAAATTGAC 57.518 37.500 0.00 0.00 0.00 3.18
1720 1792 1.967319 TCCTCTTTGCCACAGTCAAC 58.033 50.000 0.00 0.00 0.00 3.18
1889 1961 1.359848 CCTACACACACGATGAAGCC 58.640 55.000 0.00 0.00 0.00 4.35
2088 2160 4.591321 AATTATGGTTTGAGCCTCCTCA 57.409 40.909 0.00 0.00 46.03 3.86
2132 2204 2.973419 TGTTTTACGGTTTGCGGATC 57.027 45.000 0.00 0.00 0.00 3.36
2133 2205 3.926821 ATTGTTTTACGGTTTGCGGAT 57.073 38.095 0.00 0.00 0.00 4.18
2135 2207 3.117046 ACAATTGTTTTACGGTTTGCGG 58.883 40.909 4.92 0.00 0.00 5.69
2193 2271 7.578024 GCATGTAATCTTCGTTTACGTGAATAC 59.422 37.037 16.09 11.18 44.07 1.89
2222 2300 3.192466 TCTTACGCGGCCTTCTATTTTC 58.808 45.455 12.47 0.00 0.00 2.29
2236 2314 6.197468 CACAAACTAGCTAGAATCTCTTACGC 59.803 42.308 27.45 0.00 0.00 4.42
2237 2315 7.473366 TCACAAACTAGCTAGAATCTCTTACG 58.527 38.462 27.45 7.37 0.00 3.18
2238 2316 9.810545 ATTCACAAACTAGCTAGAATCTCTTAC 57.189 33.333 27.45 0.00 0.00 2.34
2247 2326 7.616150 AGAGACCTTATTCACAAACTAGCTAGA 59.384 37.037 27.45 2.96 0.00 2.43
2250 2329 6.351456 GGAGAGACCTTATTCACAAACTAGCT 60.351 42.308 0.00 0.00 35.41 3.32
2305 2644 6.017440 CGACACAAATTCTCAAAGGTCCTTTA 60.017 38.462 16.66 1.70 31.96 1.85
2321 2660 3.935203 CCAACAGATCTAGCGACACAAAT 59.065 43.478 0.00 0.00 0.00 2.32
2339 2678 2.751806 CCAAGATCCAAAGAGAGCCAAC 59.248 50.000 0.00 0.00 0.00 3.77
2346 2685 3.195825 ACCGACTACCAAGATCCAAAGAG 59.804 47.826 0.00 0.00 0.00 2.85
2366 2705 4.672587 TGCTCACCTTGATAGATACACC 57.327 45.455 0.00 0.00 0.00 4.16
2382 2721 3.018856 CCAATAGCCAGACAATTGCTCA 58.981 45.455 5.05 0.00 36.57 4.26
2415 2754 7.040548 TGCATAACAACATTGAAGAAGATGTCA 60.041 33.333 0.00 0.00 35.55 3.58
2474 2813 4.084287 ACAGACTTGCAATTCATCACCAT 58.916 39.130 17.88 0.00 0.00 3.55
2498 2837 1.748879 GGAGCATTAGCCCACGCAA 60.749 57.895 0.00 0.00 43.56 4.85
2509 2848 2.795329 AGAAACATCGGTTGGAGCATT 58.205 42.857 0.00 0.00 37.30 3.56
2521 2860 4.212214 CCTAGGCATCGCTAAAGAAACATC 59.788 45.833 0.00 0.00 0.00 3.06
2539 2878 2.093447 ACCGCTTGAAATGAGACCTAGG 60.093 50.000 7.41 7.41 0.00 3.02
2540 2879 2.932614 CACCGCTTGAAATGAGACCTAG 59.067 50.000 0.00 0.00 0.00 3.02
2541 2880 2.565391 TCACCGCTTGAAATGAGACCTA 59.435 45.455 0.00 0.00 0.00 3.08
2542 2881 1.347707 TCACCGCTTGAAATGAGACCT 59.652 47.619 0.00 0.00 0.00 3.85
2543 2882 1.734465 CTCACCGCTTGAAATGAGACC 59.266 52.381 0.00 0.00 40.92 3.85
2544 2883 2.158449 CACTCACCGCTTGAAATGAGAC 59.842 50.000 7.08 0.00 40.92 3.36
2552 2891 2.930887 GCAATAGTCACTCACCGCTTGA 60.931 50.000 0.00 0.00 0.00 3.02
2597 2936 2.123897 ACACCTGCAAACGCCCTT 60.124 55.556 0.00 0.00 0.00 3.95
2600 2939 3.670377 GGGACACCTGCAAACGCC 61.670 66.667 0.00 0.00 0.00 5.68
2620 2959 5.181690 TGCACTGAACCAACAATAAAGTC 57.818 39.130 0.00 0.00 0.00 3.01
2664 3004 4.657075 TTTTCTTTCTCGGATTGTACGC 57.343 40.909 0.00 0.00 0.00 4.42
2730 3071 2.027192 ACTATGCACCGTCAAAGTGGAT 60.027 45.455 3.44 3.44 46.42 3.41
2773 3114 2.515290 CCGATTAACCGGCCACCC 60.515 66.667 0.00 0.00 43.25 4.61
2781 3122 1.664873 GACAGGCTTCCCGATTAACC 58.335 55.000 0.00 0.00 35.76 2.85
2797 3138 0.031585 CTGAGACCGGTTTGTCGACA 59.968 55.000 15.76 15.76 40.26 4.35
2805 3146 1.532316 TTCGTCCCTGAGACCGGTT 60.532 57.895 9.42 0.00 43.08 4.44
2816 3157 2.754946 TGTCTTGGTATGTTCGTCCC 57.245 50.000 0.00 0.00 0.00 4.46
2851 3192 2.479750 GGTAGGTCTCTCGCGGGAC 61.480 68.421 3.45 11.77 0.00 4.46
2852 3193 2.124403 GGTAGGTCTCTCGCGGGA 60.124 66.667 9.14 9.14 0.00 5.14
2853 3194 1.726533 GAAGGTAGGTCTCTCGCGGG 61.727 65.000 6.13 1.01 0.00 6.13
2854 3195 0.748729 AGAAGGTAGGTCTCTCGCGG 60.749 60.000 6.13 0.00 0.00 6.46
2855 3196 1.868498 CTAGAAGGTAGGTCTCTCGCG 59.132 57.143 0.00 0.00 0.00 5.87
2856 3197 3.196939 TCTAGAAGGTAGGTCTCTCGC 57.803 52.381 0.00 0.00 0.00 5.03
2857 3198 5.026038 TCTTCTAGAAGGTAGGTCTCTCG 57.974 47.826 28.09 3.28 38.88 4.04
2858 3199 7.994334 TGTTATCTTCTAGAAGGTAGGTCTCTC 59.006 40.741 28.09 12.95 35.63 3.20
2859 3200 7.776500 GTGTTATCTTCTAGAAGGTAGGTCTCT 59.224 40.741 28.09 8.11 35.63 3.10
2860 3201 7.556996 TGTGTTATCTTCTAGAAGGTAGGTCTC 59.443 40.741 28.09 19.21 35.63 3.36
2861 3202 7.411808 TGTGTTATCTTCTAGAAGGTAGGTCT 58.588 38.462 28.09 10.08 35.63 3.85
2862 3203 7.642082 TGTGTTATCTTCTAGAAGGTAGGTC 57.358 40.000 28.09 19.42 35.63 3.85
2863 3204 8.478877 CAATGTGTTATCTTCTAGAAGGTAGGT 58.521 37.037 28.09 13.93 35.63 3.08
2864 3205 8.696374 TCAATGTGTTATCTTCTAGAAGGTAGG 58.304 37.037 28.09 7.42 35.63 3.18
2865 3206 9.522804 GTCAATGTGTTATCTTCTAGAAGGTAG 57.477 37.037 28.09 14.06 35.63 3.18
2866 3207 8.188799 CGTCAATGTGTTATCTTCTAGAAGGTA 58.811 37.037 28.09 23.95 38.88 3.08
2867 3208 7.036220 CGTCAATGTGTTATCTTCTAGAAGGT 58.964 38.462 28.09 24.98 38.88 3.50
2868 3209 7.036220 ACGTCAATGTGTTATCTTCTAGAAGG 58.964 38.462 28.09 12.77 38.88 3.46
2869 3210 9.011407 GTACGTCAATGTGTTATCTTCTAGAAG 57.989 37.037 24.10 24.10 39.71 2.85
2870 3211 8.517056 TGTACGTCAATGTGTTATCTTCTAGAA 58.483 33.333 4.81 4.81 0.00 2.10
2871 3212 8.047413 TGTACGTCAATGTGTTATCTTCTAGA 57.953 34.615 0.00 0.00 0.00 2.43
2872 3213 8.683550 TTGTACGTCAATGTGTTATCTTCTAG 57.316 34.615 0.00 0.00 0.00 2.43
2873 3214 8.301720 ACTTGTACGTCAATGTGTTATCTTCTA 58.698 33.333 0.00 0.00 35.35 2.10
2874 3215 7.152645 ACTTGTACGTCAATGTGTTATCTTCT 58.847 34.615 0.00 0.00 35.35 2.85
2875 3216 7.347508 ACTTGTACGTCAATGTGTTATCTTC 57.652 36.000 0.00 0.00 35.35 2.87
2876 3217 7.724305 AACTTGTACGTCAATGTGTTATCTT 57.276 32.000 0.00 0.00 35.35 2.40
2877 3218 7.544566 CCTAACTTGTACGTCAATGTGTTATCT 59.455 37.037 0.00 0.00 35.35 1.98
2878 3219 7.543172 TCCTAACTTGTACGTCAATGTGTTATC 59.457 37.037 0.00 0.00 35.35 1.75
2879 3220 7.380536 TCCTAACTTGTACGTCAATGTGTTAT 58.619 34.615 0.00 0.00 35.35 1.89
2880 3221 6.747125 TCCTAACTTGTACGTCAATGTGTTA 58.253 36.000 0.00 1.87 35.35 2.41
2881 3222 5.603596 TCCTAACTTGTACGTCAATGTGTT 58.396 37.500 0.00 0.77 35.35 3.32
2882 3223 5.204409 TCCTAACTTGTACGTCAATGTGT 57.796 39.130 0.00 0.00 35.35 3.72
2883 3224 5.464057 TGTTCCTAACTTGTACGTCAATGTG 59.536 40.000 0.00 0.00 35.35 3.21
2884 3225 5.603596 TGTTCCTAACTTGTACGTCAATGT 58.396 37.500 0.00 0.00 35.35 2.71
2885 3226 6.533819 TTGTTCCTAACTTGTACGTCAATG 57.466 37.500 0.00 0.00 35.35 2.82
2886 3227 7.548075 CCTATTGTTCCTAACTTGTACGTCAAT 59.452 37.037 0.00 0.00 35.35 2.57
2887 3228 6.869913 CCTATTGTTCCTAACTTGTACGTCAA 59.130 38.462 0.00 0.00 34.61 3.18
2888 3229 6.392354 CCTATTGTTCCTAACTTGTACGTCA 58.608 40.000 0.00 0.00 0.00 4.35
2889 3230 5.290400 GCCTATTGTTCCTAACTTGTACGTC 59.710 44.000 0.00 0.00 0.00 4.34
2890 3231 5.173664 GCCTATTGTTCCTAACTTGTACGT 58.826 41.667 0.00 0.00 0.00 3.57
2891 3232 4.569564 GGCCTATTGTTCCTAACTTGTACG 59.430 45.833 0.00 0.00 0.00 3.67
2892 3233 5.493809 TGGCCTATTGTTCCTAACTTGTAC 58.506 41.667 3.32 0.00 0.00 2.90
2893 3234 5.765576 TGGCCTATTGTTCCTAACTTGTA 57.234 39.130 3.32 0.00 0.00 2.41
2894 3235 4.650972 TGGCCTATTGTTCCTAACTTGT 57.349 40.909 3.32 0.00 0.00 3.16
2895 3236 5.123979 GTCTTGGCCTATTGTTCCTAACTTG 59.876 44.000 3.32 0.00 0.00 3.16
2896 3237 5.222048 TGTCTTGGCCTATTGTTCCTAACTT 60.222 40.000 3.32 0.00 0.00 2.66
2897 3238 4.288626 TGTCTTGGCCTATTGTTCCTAACT 59.711 41.667 3.32 0.00 0.00 2.24
2898 3239 4.585879 TGTCTTGGCCTATTGTTCCTAAC 58.414 43.478 3.32 0.00 0.00 2.34
2899 3240 4.919774 TGTCTTGGCCTATTGTTCCTAA 57.080 40.909 3.32 0.00 0.00 2.69
2900 3241 4.385199 CCATGTCTTGGCCTATTGTTCCTA 60.385 45.833 3.32 0.00 39.09 2.94
2901 3242 3.624777 CATGTCTTGGCCTATTGTTCCT 58.375 45.455 3.32 0.00 0.00 3.36
2902 3243 2.689983 CCATGTCTTGGCCTATTGTTCC 59.310 50.000 3.32 0.00 39.09 3.62
2952 3293 9.545611 GGTGTTTACTAACCGTAAAACAATATG 57.454 33.333 1.44 0.00 46.48 1.78
2953 3294 8.729756 GGGTGTTTACTAACCGTAAAACAATAT 58.270 33.333 1.44 0.00 46.48 1.28
2954 3295 7.936301 AGGGTGTTTACTAACCGTAAAACAATA 59.064 33.333 1.44 0.00 46.48 1.90
2956 3297 6.118852 AGGGTGTTTACTAACCGTAAAACAA 58.881 36.000 1.44 0.00 46.48 2.83
2957 3298 5.679601 AGGGTGTTTACTAACCGTAAAACA 58.320 37.500 0.00 0.00 46.48 2.83
2958 3299 6.293407 GGAAGGGTGTTTACTAACCGTAAAAC 60.293 42.308 0.00 0.00 46.48 2.43
2959 3300 5.762711 GGAAGGGTGTTTACTAACCGTAAAA 59.237 40.000 0.00 0.00 46.48 1.52
2960 3301 5.304778 GGAAGGGTGTTTACTAACCGTAAA 58.695 41.667 0.00 0.00 43.79 2.01
2976 3327 7.555195 CATTTATTTAGTAAACTCCGGAAGGGT 59.445 37.037 5.23 0.00 42.57 4.34
2977 3328 7.012989 CCATTTATTTAGTAAACTCCGGAAGGG 59.987 40.741 5.23 0.00 42.57 3.95
2978 3329 7.555195 ACCATTTATTTAGTAAACTCCGGAAGG 59.445 37.037 5.23 0.00 43.19 3.46
3083 4081 9.836864 ATCAATATGCAGTAGACAAATTACTCA 57.163 29.630 0.00 0.00 0.00 3.41
3088 4086 8.969260 TCTCATCAATATGCAGTAGACAAATT 57.031 30.769 0.00 0.00 32.76 1.82
3119 4117 7.693969 ATTTCAACAATTCTAACTCCTCCAG 57.306 36.000 0.00 0.00 0.00 3.86
3144 4142 8.450578 TTCAACAGACAACTATCAATTCAAGT 57.549 30.769 0.00 0.00 0.00 3.16
3159 4157 5.789521 TCTGGACGATAATTTCAACAGACA 58.210 37.500 0.00 0.00 0.00 3.41
3176 4174 4.774124 TCCATCAAACTCATGATCTGGAC 58.226 43.478 0.00 0.00 37.96 4.02
3220 4221 7.147479 ACCCAGAATTACACTCACTTGCTATAT 60.147 37.037 0.00 0.00 0.00 0.86
3248 4249 6.016108 GGAGAGACGTGGCTCTTAAAGTATAT 60.016 42.308 6.70 0.00 44.92 0.86
3251 4252 3.442977 GGAGAGACGTGGCTCTTAAAGTA 59.557 47.826 6.70 0.00 44.92 2.24
3265 4266 5.046529 CCTGACAAGATAATTGGAGAGACG 58.953 45.833 0.00 0.00 0.00 4.18
3266 4267 6.097554 TCTCCTGACAAGATAATTGGAGAGAC 59.902 42.308 0.00 0.00 42.24 3.36
3284 4285 4.821805 GTCAAGGAAACACAATTCTCCTGA 59.178 41.667 0.00 0.00 38.34 3.86


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

AutoCloner maintained by Alex Coulton.