Multiple sequence alignment - TraesCS2D01G327100

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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 TraesCS2D01G327100 chr2D 100.000 5866 0 0 1 5866 420520870 420526735 0.000000e+00 10833.0
1 TraesCS2D01G327100 chr2D 80.164 610 96 17 29 617 383561246 383561851 3.250000e-117 433.0
2 TraesCS2D01G327100 chr2D 88.966 290 19 3 5250 5537 628290847 628290569 4.350000e-91 346.0
3 TraesCS2D01G327100 chr2D 93.258 178 12 0 2806 2983 521564193 521564016 4.510000e-66 263.0
4 TraesCS2D01G327100 chr2A 93.874 2530 100 23 2751 5244 569586996 569584486 0.000000e+00 3762.0
5 TraesCS2D01G327100 chr2A 93.367 980 45 8 763 1728 569589244 569588271 0.000000e+00 1432.0
6 TraesCS2D01G327100 chr2A 97.989 547 5 2 2217 2758 569587715 569587170 0.000000e+00 944.0
7 TraesCS2D01G327100 chr2A 95.425 306 8 4 1859 2160 569588003 569587700 3.180000e-132 483.0
8 TraesCS2D01G327100 chr2A 100.000 74 0 0 1784 1857 569588114 569588041 2.850000e-28 137.0
9 TraesCS2D01G327100 chr2A 97.826 46 0 1 5811 5855 569583241 569583196 1.750000e-10 78.7
10 TraesCS2D01G327100 chr2B 92.523 1217 61 12 3868 5062 492957199 492958407 0.000000e+00 1716.0
11 TraesCS2D01G327100 chr2B 95.138 1049 37 10 689 1726 492953884 492954929 0.000000e+00 1642.0
12 TraesCS2D01G327100 chr2B 88.832 976 48 21 2892 3832 492956247 492957196 0.000000e+00 1142.0
13 TraesCS2D01G327100 chr2B 95.760 684 15 8 2267 2944 492955587 492956262 0.000000e+00 1090.0
14 TraesCS2D01G327100 chr2B 88.975 517 38 6 1 516 492953073 492953571 6.460000e-174 621.0
15 TraesCS2D01G327100 chr2B 91.954 174 14 0 513 686 492953679 492953852 1.630000e-60 244.0
16 TraesCS2D01G327100 chr2B 94.839 155 5 1 2114 2265 492955268 492955422 7.600000e-59 239.0
17 TraesCS2D01G327100 chr2B 94.828 116 4 1 1859 1972 492955152 492955267 4.670000e-41 180.0
18 TraesCS2D01G327100 chr2B 89.394 132 11 2 1731 1859 492954985 492955116 4.700000e-36 163.0
19 TraesCS2D01G327100 chr3B 81.923 780 72 38 3816 4547 195352929 195353687 3.910000e-166 595.0
20 TraesCS2D01G327100 chr3B 89.310 290 18 3 5250 5537 201499207 201499485 9.350000e-93 351.0
21 TraesCS2D01G327100 chr3B 93.269 104 7 0 5250 5353 201498664 201498767 2.830000e-33 154.0
22 TraesCS2D01G327100 chr3B 91.667 84 4 2 4620 4700 195360402 195360485 4.800000e-21 113.0
23 TraesCS2D01G327100 chr3B 93.878 49 3 0 3032 3080 183599865 183599913 2.270000e-09 75.0
24 TraesCS2D01G327100 chr6B 83.044 519 79 6 1 515 638936997 638936484 4.140000e-126 462.0
25 TraesCS2D01G327100 chr6B 80.163 615 93 19 35 628 710142929 710142323 3.250000e-117 433.0
26 TraesCS2D01G327100 chr6B 78.737 649 101 24 7 628 710232498 710233136 3.290000e-107 399.0
27 TraesCS2D01G327100 chr5D 82.822 489 74 8 1 483 133539140 133538656 4.200000e-116 429.0
28 TraesCS2D01G327100 chr5D 88.621 290 20 3 5250 5537 6218532 6218254 2.020000e-89 340.0
29 TraesCS2D01G327100 chr5D 88.621 290 20 3 5250 5537 483802107 483801829 2.020000e-89 340.0
30 TraesCS2D01G327100 chr5D 87.241 290 24 3 5250 5537 433387297 433387019 9.490000e-83 318.0
31 TraesCS2D01G327100 chr5D 93.678 174 11 0 2807 2980 537178188 537178361 1.620000e-65 261.0
32 TraesCS2D01G327100 chr5D 91.071 56 2 3 3020 3072 384475723 384475778 8.150000e-09 73.1
33 TraesCS2D01G327100 chr4B 81.044 517 88 8 4 515 610076625 610077136 2.550000e-108 403.0
34 TraesCS2D01G327100 chr4B 96.341 164 6 0 2805 2968 63754004 63753841 2.690000e-68 270.0
35 TraesCS2D01G327100 chr4B 96.296 162 6 0 2807 2968 483266379 483266540 3.480000e-67 267.0
36 TraesCS2D01G327100 chr4B 88.889 81 9 0 3032 3112 68662418 68662498 3.740000e-17 100.0
37 TraesCS2D01G327100 chr6D 81.087 497 87 6 1 492 472366782 472366288 1.980000e-104 390.0
38 TraesCS2D01G327100 chr6D 80.192 520 92 8 1 515 3182937 3183450 4.290000e-101 379.0
39 TraesCS2D01G327100 chr6D 89.310 290 18 3 5250 5537 459928874 459929152 9.350000e-93 351.0
40 TraesCS2D01G327100 chr6D 84.375 160 14 7 1570 1726 390481428 390481277 4.740000e-31 147.0
41 TraesCS2D01G327100 chr1A 88.966 290 19 3 5250 5537 554472929 554472651 4.350000e-91 346.0
42 TraesCS2D01G327100 chr1A 95.758 165 7 0 2804 2968 307400181 307400017 3.480000e-67 267.0
43 TraesCS2D01G327100 chr1A 82.468 154 19 5 1575 1726 483658533 483658680 1.720000e-25 128.0
44 TraesCS2D01G327100 chr7D 88.621 290 20 3 5250 5537 17212407 17212685 2.020000e-89 340.0
45 TraesCS2D01G327100 chr7D 88.477 243 15 3 5297 5537 231542056 231541825 1.240000e-71 281.0
46 TraesCS2D01G327100 chr1D 88.621 290 20 3 5250 5537 254482646 254482924 2.020000e-89 340.0
47 TraesCS2D01G327100 chr1D 87.586 290 23 3 5250 5537 244393060 244393338 2.040000e-84 324.0
48 TraesCS2D01G327100 chr1D 83.893 149 17 5 1578 1726 342174406 342174547 1.030000e-27 135.0
49 TraesCS2D01G327100 chr5B 95.833 168 7 0 2804 2971 539322719 539322886 7.490000e-69 272.0
50 TraesCS2D01G327100 chr3D 96.341 164 6 0 2805 2968 238999577 238999414 2.690000e-68 270.0
51 TraesCS2D01G327100 chr3D 84.138 145 15 6 1584 1726 528183449 528183587 3.690000e-27 134.0
52 TraesCS2D01G327100 chr3D 100.000 35 0 0 702 736 31652429 31652395 1.360000e-06 65.8
53 TraesCS2D01G327100 chr5A 86.758 219 17 2 5250 5467 121715143 121715350 3.530000e-57 233.0
54 TraesCS2D01G327100 chr5A 84.828 145 14 5 1584 1726 18658765 18658627 7.930000e-29 139.0
55 TraesCS2D01G327100 chr4D 84.667 150 16 4 1579 1726 3747591 3747447 6.130000e-30 143.0
56 TraesCS2D01G327100 chr4D 89.333 75 7 1 3033 3107 129756620 129756547 6.260000e-15 93.5
57 TraesCS2D01G327100 chr3A 82.581 155 18 6 1575 1726 68866482 68866630 1.720000e-25 128.0
58 TraesCS2D01G327100 chr3A 89.655 87 4 5 3031 3114 638761262 638761178 8.040000e-19 106.0
59 TraesCS2D01G327100 chrUn 88.000 75 8 1 3033 3107 409550507 409550434 2.910000e-13 87.9
60 TraesCS2D01G327100 chr4A 95.745 47 2 0 3030 3076 455023726 455023772 6.300000e-10 76.8


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 TraesCS2D01G327100 chr2D 420520870 420526735 5865 False 10833.000000 10833 100.000000 1 5866 1 chr2D.!!$F2 5865
1 TraesCS2D01G327100 chr2D 383561246 383561851 605 False 433.000000 433 80.164000 29 617 1 chr2D.!!$F1 588
2 TraesCS2D01G327100 chr2A 569583196 569589244 6048 True 1139.450000 3762 96.413500 763 5855 6 chr2A.!!$R1 5092
3 TraesCS2D01G327100 chr2B 492953073 492958407 5334 False 781.888889 1716 92.471444 1 5062 9 chr2B.!!$F1 5061
4 TraesCS2D01G327100 chr3B 195352929 195353687 758 False 595.000000 595 81.923000 3816 4547 1 chr3B.!!$F2 731
5 TraesCS2D01G327100 chr3B 201498664 201499485 821 False 252.500000 351 91.289500 5250 5537 2 chr3B.!!$F4 287
6 TraesCS2D01G327100 chr6B 638936484 638936997 513 True 462.000000 462 83.044000 1 515 1 chr6B.!!$R1 514
7 TraesCS2D01G327100 chr6B 710142323 710142929 606 True 433.000000 433 80.163000 35 628 1 chr6B.!!$R2 593
8 TraesCS2D01G327100 chr6B 710232498 710233136 638 False 399.000000 399 78.737000 7 628 1 chr6B.!!$F1 621
9 TraesCS2D01G327100 chr4B 610076625 610077136 511 False 403.000000 403 81.044000 4 515 1 chr4B.!!$F3 511
10 TraesCS2D01G327100 chr6D 3182937 3183450 513 False 379.000000 379 80.192000 1 515 1 chr6D.!!$F1 514

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
596 736 0.691078 TCTATGGTGGAGGTGGAGGC 60.691 60.000 0.0 0.0 0.00 4.70 F
1753 1991 0.260230 TTGGGGAAGTTTCAGTGCCA 59.740 50.000 0.0 0.0 0.00 4.92 F
1754 1992 0.482446 TGGGGAAGTTTCAGTGCCAT 59.518 50.000 0.0 0.0 0.00 4.40 F
1991 2363 1.002134 GGCGGTGGGATATGATGGG 60.002 63.158 0.0 0.0 0.00 4.00 F
3643 4430 0.824595 TGCTGTGTGCTGCCTTCATT 60.825 50.000 0.0 0.0 43.37 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1975 2347 0.321919 CAGCCCATCATATCCCACCG 60.322 60.000 0.00 0.0 0.00 4.94 R
3223 4009 0.607217 CATCCCACTGCACAGAAGCA 60.607 55.000 4.31 0.0 43.35 3.91 R
3603 4390 4.646492 GCAACATAGGGAGGTGATGAAAAT 59.354 41.667 0.00 0.0 0.00 1.82 R
3963 4762 1.062587 GCATGGTATTCGTCACAGTGC 59.937 52.381 0.00 0.0 0.00 4.40 R
5353 6224 0.037590 AGTAATGCCCCTTGAACGCA 59.962 50.000 0.00 0.0 36.84 5.24 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
26 27 7.791029 ACACAATCTTGTATTTTTCCAAAGGT 58.209 30.769 0.00 0.00 39.91 3.50
27 28 8.264347 ACACAATCTTGTATTTTTCCAAAGGTT 58.736 29.630 0.00 0.00 39.91 3.50
32 33 3.637229 TGTATTTTTCCAAAGGTTGCCGA 59.363 39.130 0.00 0.00 0.00 5.54
44 46 3.081804 AGGTTGCCGAGGAAAATAACAG 58.918 45.455 0.00 0.00 0.00 3.16
112 114 7.307337 CCCATAATTTTAATTTGAGCCGCAATC 60.307 37.037 0.00 0.00 36.15 2.67
128 130 2.932187 GCAATCCAAAGGTTGTGATGCC 60.932 50.000 0.00 0.00 0.00 4.40
162 164 7.757526 TCCATTAAAGTAATCAACCAACATCG 58.242 34.615 0.00 0.00 0.00 3.84
163 165 6.972328 CCATTAAAGTAATCAACCAACATCGG 59.028 38.462 0.00 0.00 0.00 4.18
164 166 7.362574 CCATTAAAGTAATCAACCAACATCGGT 60.363 37.037 0.00 0.00 42.71 4.69
165 167 8.670135 CATTAAAGTAATCAACCAACATCGGTA 58.330 33.333 0.00 0.00 38.76 4.02
166 168 8.618702 TTAAAGTAATCAACCAACATCGGTAA 57.381 30.769 0.00 0.00 38.76 2.85
167 169 6.737254 AAGTAATCAACCAACATCGGTAAG 57.263 37.500 0.00 0.00 38.76 2.34
168 170 6.045072 AGTAATCAACCAACATCGGTAAGA 57.955 37.500 0.00 0.00 38.76 2.10
169 171 6.106673 AGTAATCAACCAACATCGGTAAGAG 58.893 40.000 0.00 0.00 38.76 2.85
170 172 4.553330 ATCAACCAACATCGGTAAGAGT 57.447 40.909 0.00 0.00 38.76 3.24
171 173 5.670792 ATCAACCAACATCGGTAAGAGTA 57.329 39.130 0.00 0.00 38.76 2.59
172 174 4.813027 TCAACCAACATCGGTAAGAGTAC 58.187 43.478 0.00 0.00 38.76 2.73
173 175 4.525487 TCAACCAACATCGGTAAGAGTACT 59.475 41.667 0.00 0.00 38.76 2.73
197 211 5.970317 ACACCGGTATTTTAGGGAAAAAG 57.030 39.130 6.87 0.00 40.32 2.27
222 236 2.811431 CAAACAACCAGGCTAACATCGA 59.189 45.455 0.00 0.00 0.00 3.59
258 272 3.025978 ACGAATCACCATTGCCAATGAT 58.974 40.909 18.84 0.00 41.46 2.45
427 449 1.202417 TCTCGTCATCGAATGAAGGGC 60.202 52.381 0.00 0.00 45.61 5.19
449 472 6.409349 GGGCCCAAGATTACTTATTGTAGACT 60.409 42.308 19.95 0.00 34.70 3.24
556 693 4.293648 CTGACACCGGCGTGACCA 62.294 66.667 0.00 7.45 43.14 4.02
596 736 0.691078 TCTATGGTGGAGGTGGAGGC 60.691 60.000 0.00 0.00 0.00 4.70
627 767 4.249661 CAGCTAGGTTTTCAGGAGAAGTC 58.750 47.826 0.00 0.00 34.71 3.01
660 800 2.447244 AAAGTCTCGTCTGCTTCCAG 57.553 50.000 0.00 0.00 40.54 3.86
921 1100 2.844966 TCCGTATATCCCAAACCAACCA 59.155 45.455 0.00 0.00 0.00 3.67
926 1105 1.178534 ATCCCAAACCAACCACAGCG 61.179 55.000 0.00 0.00 0.00 5.18
1212 1392 3.445096 GCAGATTTTGTATTGCCCTGTCT 59.555 43.478 0.00 0.00 0.00 3.41
1287 1467 4.808077 CGTCTAGTTAGGCGTAGATTGA 57.192 45.455 5.06 0.00 45.56 2.57
1297 1477 1.858091 CGTAGATTGAAGAGCGGCAT 58.142 50.000 1.45 0.00 0.00 4.40
1370 1552 2.027837 GGTTGGATTCTTTTGGCATGCT 60.028 45.455 18.92 0.00 0.00 3.79
1371 1553 3.256558 GTTGGATTCTTTTGGCATGCTC 58.743 45.455 18.92 8.46 0.00 4.26
1373 1555 2.494471 TGGATTCTTTTGGCATGCTCAG 59.506 45.455 18.92 8.49 0.00 3.35
1374 1556 2.756760 GGATTCTTTTGGCATGCTCAGA 59.243 45.455 18.92 10.69 0.00 3.27
1375 1557 3.383825 GGATTCTTTTGGCATGCTCAGAT 59.616 43.478 18.92 3.09 0.00 2.90
1377 1559 5.068198 GGATTCTTTTGGCATGCTCAGATTA 59.932 40.000 18.92 0.00 0.00 1.75
1378 1560 5.571784 TTCTTTTGGCATGCTCAGATTAG 57.428 39.130 18.92 6.51 0.00 1.73
1379 1561 4.847198 TCTTTTGGCATGCTCAGATTAGA 58.153 39.130 18.92 8.66 0.00 2.10
1380 1562 4.637534 TCTTTTGGCATGCTCAGATTAGAC 59.362 41.667 18.92 0.00 0.00 2.59
1729 1916 9.987272 CAATGATATAGGACTTAGATGTGAACA 57.013 33.333 0.00 0.00 0.00 3.18
1732 1970 9.987272 TGATATAGGACTTAGATGTGAACAATG 57.013 33.333 0.00 0.00 0.00 2.82
1747 1985 4.467795 TGAACAATGTTTGGGGAAGTTTCA 59.532 37.500 0.00 0.00 34.12 2.69
1749 1987 4.030216 ACAATGTTTGGGGAAGTTTCAGT 58.970 39.130 0.00 0.00 34.12 3.41
1750 1988 4.141959 ACAATGTTTGGGGAAGTTTCAGTG 60.142 41.667 0.00 0.00 34.12 3.66
1751 1989 1.754226 TGTTTGGGGAAGTTTCAGTGC 59.246 47.619 0.00 0.00 0.00 4.40
1753 1991 0.260230 TTGGGGAAGTTTCAGTGCCA 59.740 50.000 0.00 0.00 0.00 4.92
1754 1992 0.482446 TGGGGAAGTTTCAGTGCCAT 59.518 50.000 0.00 0.00 0.00 4.40
1757 1995 2.519013 GGGAAGTTTCAGTGCCATCTT 58.481 47.619 0.00 0.00 0.00 2.40
1758 1996 3.561313 GGGGAAGTTTCAGTGCCATCTTA 60.561 47.826 0.00 0.00 0.00 2.10
1759 1997 4.273318 GGGAAGTTTCAGTGCCATCTTAT 58.727 43.478 0.00 0.00 0.00 1.73
1760 1998 4.336713 GGGAAGTTTCAGTGCCATCTTATC 59.663 45.833 0.00 0.00 0.00 1.75
1872 2242 7.606456 TCTGATCTTGTTTAGTGTTATCAACCC 59.394 37.037 0.00 0.00 0.00 4.11
1975 2347 6.936900 ACTATCATTACCATGAACATACAGGC 59.063 38.462 0.00 0.00 42.93 4.85
1991 2363 1.002134 GGCGGTGGGATATGATGGG 60.002 63.158 0.00 0.00 0.00 4.00
1997 2369 2.424812 GGTGGGATATGATGGGCTGTTT 60.425 50.000 0.00 0.00 0.00 2.83
1998 2370 3.181434 GGTGGGATATGATGGGCTGTTTA 60.181 47.826 0.00 0.00 0.00 2.01
2031 2403 9.362151 TCCAATAGTTCCAAACCATTTATATCC 57.638 33.333 0.00 0.00 0.00 2.59
2080 2452 4.502962 CTTTTGGTTTGCTTCAACTTCCA 58.497 39.130 0.00 0.00 0.00 3.53
2164 2536 9.274065 CGTAGGCAAATGTCTTTAATTTTCTAC 57.726 33.333 0.00 0.00 33.41 2.59
2207 2582 1.270826 TCTTGCTTCCAGTCTGTCTCG 59.729 52.381 0.00 0.00 0.00 4.04
2396 2934 7.798596 ATCAGGTTGACAAATATCTGATGTC 57.201 36.000 16.76 1.34 42.90 3.06
2590 3135 1.279271 AGTGTGGGCTGTTGGTCTATC 59.721 52.381 0.00 0.00 0.00 2.08
2612 3157 9.360093 CTATCTGCACCTTAGTACTAATATTGC 57.640 37.037 23.60 23.60 0.00 3.56
2816 3542 2.838202 GGAATCTGTTGTACTCCCTCCA 59.162 50.000 0.00 0.00 0.00 3.86
2910 3636 9.486497 CACTCTAAAATGCATCTACATACATCT 57.514 33.333 0.00 0.00 0.00 2.90
3092 3878 7.602517 TTCAAATTTGAAACAAAACCACGAT 57.397 28.000 27.22 0.00 43.62 3.73
3126 3912 6.183360 TGGAACAGAGGTATACTTCATAGCAC 60.183 42.308 16.46 3.89 39.62 4.40
3128 3914 4.888239 ACAGAGGTATACTTCATAGCACGT 59.112 41.667 16.46 0.00 39.62 4.49
3157 3943 8.960591 AGATCTCAATAATGTTTAGTTTGGGTG 58.039 33.333 0.00 0.00 0.00 4.61
3391 4177 3.595691 CAGGTCGTCTGCTTTCAGT 57.404 52.632 0.00 0.00 41.10 3.41
3503 4289 3.031736 TGGTCCACTAAGAGGCTATGAC 58.968 50.000 0.00 0.00 0.00 3.06
3643 4430 0.824595 TGCTGTGTGCTGCCTTCATT 60.825 50.000 0.00 0.00 43.37 2.57
3963 4762 6.641314 ACCGTAAATCTAAACATATCTCGCTG 59.359 38.462 0.00 0.00 0.00 5.18
3992 4796 1.869767 CGAATACCATGCCAGAGAAGC 59.130 52.381 0.00 0.00 0.00 3.86
4009 4814 7.121168 CCAGAGAAGCACATTAAAAACAGGATA 59.879 37.037 0.00 0.00 0.00 2.59
4063 4872 1.732259 CACCATTTCGTGTCACTAGCC 59.268 52.381 0.65 0.00 0.00 3.93
4071 4880 1.822506 GTGTCACTAGCCTTTTCCCC 58.177 55.000 0.00 0.00 0.00 4.81
4072 4881 1.351350 GTGTCACTAGCCTTTTCCCCT 59.649 52.381 0.00 0.00 0.00 4.79
4073 4882 2.062636 TGTCACTAGCCTTTTCCCCTT 58.937 47.619 0.00 0.00 0.00 3.95
4155 4973 5.059833 GTGTTCTCAGTTTGAGGTTCATCT 58.940 41.667 6.27 0.00 44.39 2.90
4230 5048 9.855021 GTTTTGCATTATTTGAGTATGGTAACT 57.145 29.630 0.00 0.00 37.61 2.24
4255 5073 0.916086 AACATCCACCCCTGCGATTA 59.084 50.000 0.00 0.00 0.00 1.75
4256 5074 0.916086 ACATCCACCCCTGCGATTAA 59.084 50.000 0.00 0.00 0.00 1.40
4257 5075 1.494721 ACATCCACCCCTGCGATTAAT 59.505 47.619 0.00 0.00 0.00 1.40
4258 5076 2.708861 ACATCCACCCCTGCGATTAATA 59.291 45.455 0.00 0.00 0.00 0.98
4294 5112 6.811253 TGAAGTGAACACTAAGTTGTTTGT 57.189 33.333 7.90 0.00 41.51 2.83
4424 5273 3.584848 ACATGGAGATTATGAGGTAGGCC 59.415 47.826 0.00 0.00 0.00 5.19
4583 5442 2.359230 GCACCAGCTCCTGTGACC 60.359 66.667 10.84 0.00 37.91 4.02
4823 5682 1.204941 GACCCTACGCAGACTGTTGAT 59.795 52.381 3.99 0.00 0.00 2.57
4923 5783 7.351981 TGTCTTTCCGATGCATTATTAAATCG 58.648 34.615 0.00 0.00 41.14 3.34
5062 5922 9.941664 CAACTATGAATGGCTATCAAAGTTAAG 57.058 33.333 0.00 0.00 0.00 1.85
5063 5923 9.686683 AACTATGAATGGCTATCAAAGTTAAGT 57.313 29.630 0.00 0.00 0.00 2.24
5064 5924 9.686683 ACTATGAATGGCTATCAAAGTTAAGTT 57.313 29.630 0.00 0.00 0.00 2.66
5119 5979 3.758554 GGCTTGCTTGTTCTCATTTCCTA 59.241 43.478 0.00 0.00 0.00 2.94
5120 5980 4.218417 GGCTTGCTTGTTCTCATTTCCTAA 59.782 41.667 0.00 0.00 0.00 2.69
5121 5981 5.157067 GCTTGCTTGTTCTCATTTCCTAAC 58.843 41.667 0.00 0.00 0.00 2.34
5123 5983 4.985538 TGCTTGTTCTCATTTCCTAACCT 58.014 39.130 0.00 0.00 0.00 3.50
5177 6048 9.699703 GTGAGGGTAAGAAATTGATAGATAGAC 57.300 37.037 0.00 0.00 0.00 2.59
5190 6061 7.767250 TGATAGATAGACGATTCACTTCCAT 57.233 36.000 0.00 0.00 0.00 3.41
5228 6099 9.712305 AGAGTAACCTCATTATAATTTCGGATG 57.288 33.333 10.06 0.11 40.40 3.51
5248 6119 3.084039 TGGAAGATTCAGTTCCACATGC 58.916 45.455 0.29 0.00 46.96 4.06
5282 6153 4.846779 AAACTCACAACCATTTATGCGT 57.153 36.364 0.00 0.00 0.00 5.24
5285 6156 3.568007 ACTCACAACCATTTATGCGTTGT 59.432 39.130 16.85 16.85 44.87 3.32
5286 6157 4.037446 ACTCACAACCATTTATGCGTTGTT 59.963 37.500 18.60 8.94 43.25 2.83
5306 6177 3.414549 TGAGACCGTTTTGTCTTTTGC 57.585 42.857 0.00 0.00 45.41 3.68
5313 6184 2.124122 GTTTTGTCTTTTGCGCCGAAT 58.876 42.857 4.18 0.00 0.00 3.34
5325 6196 7.853929 TCTTTTGCGCCGAATCTATTTATAAAC 59.146 33.333 4.18 0.00 0.00 2.01
5332 6203 6.708949 GCCGAATCTATTTATAAACCACAGGA 59.291 38.462 0.00 0.00 0.00 3.86
5353 6224 1.877443 CGAAACCGGTGAAATCAAGGT 59.123 47.619 8.52 6.13 39.69 3.50
5356 6227 1.234615 ACCGGTGAAATCAAGGTGCG 61.235 55.000 6.12 0.00 37.62 5.34
5416 6820 9.453572 ACATGTGAAAAATGATTAAGAGAGCTA 57.546 29.630 0.00 0.00 34.28 3.32
5428 6832 9.265901 TGATTAAGAGAGCTATATTTGCAAGAC 57.734 33.333 0.00 0.00 0.00 3.01
5435 6839 9.265901 GAGAGCTATATTTGCAAGACAATTAGA 57.734 33.333 0.00 0.00 38.31 2.10
5437 6841 9.265901 GAGCTATATTTGCAAGACAATTAGAGA 57.734 33.333 0.00 0.00 36.33 3.10
5479 6884 1.982958 ACTTAACTGGGGATTCACCGT 59.017 47.619 0.00 0.00 40.11 4.83
5496 6901 5.797051 TCACCGTAAATACTACTTTGGCTT 58.203 37.500 0.00 0.00 0.00 4.35
5532 6937 5.079643 ACAATGGCCTACTTCTTCACATTT 58.920 37.500 3.32 0.00 0.00 2.32
5548 6953 3.560068 CACATTTACCGGAGATAACAGCC 59.440 47.826 9.46 0.00 0.00 4.85
5549 6954 3.199071 ACATTTACCGGAGATAACAGCCA 59.801 43.478 9.46 0.00 0.00 4.75
5564 6969 1.004440 GCCAAACGCTCTCACCTCT 60.004 57.895 0.00 0.00 0.00 3.69
5595 7000 3.235200 AGTTGGGTATAGCTAGGCTCTG 58.765 50.000 0.00 0.00 40.44 3.35
5596 7001 3.117093 AGTTGGGTATAGCTAGGCTCTGA 60.117 47.826 0.00 0.00 40.44 3.27
5618 7023 8.310382 TCTGAACTTTTTGACCATTTTTCTCAA 58.690 29.630 0.00 0.00 0.00 3.02
5630 7035 7.212274 ACCATTTTTCTCAATCTCCAAAACTG 58.788 34.615 0.00 0.00 0.00 3.16
5632 7037 8.092687 CCATTTTTCTCAATCTCCAAAACTGAT 58.907 33.333 0.00 0.00 0.00 2.90
5651 7057 8.830201 AACTGATGTTTTATGCTGCAAAATAA 57.170 26.923 6.36 0.00 31.37 1.40
5655 7061 6.445267 TGTTTTATGCTGCAAAATAACACG 57.555 33.333 6.36 0.00 0.00 4.49
5656 7062 5.403766 TGTTTTATGCTGCAAAATAACACGG 59.596 36.000 6.36 0.00 0.00 4.94
5667 7073 5.616204 GCAAAATAACACGGGAAGTCTACAC 60.616 44.000 0.00 0.00 0.00 2.90
5668 7074 4.877378 AATAACACGGGAAGTCTACACA 57.123 40.909 0.00 0.00 0.00 3.72
5669 7075 4.877378 ATAACACGGGAAGTCTACACAA 57.123 40.909 0.00 0.00 0.00 3.33
5670 7076 3.764237 AACACGGGAAGTCTACACAAT 57.236 42.857 0.00 0.00 0.00 2.71
5671 7077 3.764237 ACACGGGAAGTCTACACAATT 57.236 42.857 0.00 0.00 0.00 2.32
5673 7079 4.563061 ACACGGGAAGTCTACACAATTAC 58.437 43.478 0.00 0.00 0.00 1.89
5675 7081 5.221581 ACACGGGAAGTCTACACAATTACTT 60.222 40.000 0.00 0.00 34.96 2.24
5676 7082 5.347907 CACGGGAAGTCTACACAATTACTTC 59.652 44.000 7.67 7.67 44.51 3.01
5677 7083 5.011329 ACGGGAAGTCTACACAATTACTTCA 59.989 40.000 15.10 0.00 46.18 3.02
5679 7085 6.425721 CGGGAAGTCTACACAATTACTTCAAA 59.574 38.462 15.10 0.00 46.18 2.69
5680 7086 7.041644 CGGGAAGTCTACACAATTACTTCAAAA 60.042 37.037 15.10 0.00 46.18 2.44
5681 7087 8.793592 GGGAAGTCTACACAATTACTTCAAAAT 58.206 33.333 15.10 0.00 46.18 1.82
5682 7088 9.612620 GGAAGTCTACACAATTACTTCAAAATG 57.387 33.333 15.10 0.00 46.18 2.32
5691 7097 8.137437 CACAATTACTTCAAAATGTCACCTTCT 58.863 33.333 0.00 0.00 0.00 2.85
5705 7111 1.275573 ACCTTCTTGAAGGCGTCTACC 59.724 52.381 24.58 0.00 43.80 3.18
5706 7112 1.550976 CCTTCTTGAAGGCGTCTACCT 59.449 52.381 15.43 0.00 43.91 3.08
5718 7124 1.900486 CGTCTACCTCCTTTTCCACCT 59.100 52.381 0.00 0.00 0.00 4.00
5723 7129 1.700186 ACCTCCTTTTCCACCTCACTC 59.300 52.381 0.00 0.00 0.00 3.51
5728 7135 0.771127 TTTTCCACCTCACTCTGGGG 59.229 55.000 0.00 0.00 45.84 4.96
5755 7162 4.833380 CCCTAGTTTCGGATTCCTAGATCA 59.167 45.833 0.30 0.00 30.68 2.92
5760 7167 1.202891 TCGGATTCCTAGATCAGGCGA 60.203 52.381 0.30 2.13 45.10 5.54
5761 7168 1.821753 CGGATTCCTAGATCAGGCGAT 59.178 52.381 0.30 0.00 45.10 4.58
5762 7169 2.416566 CGGATTCCTAGATCAGGCGATG 60.417 54.545 0.30 0.00 45.10 3.84
5763 7170 2.093764 GGATTCCTAGATCAGGCGATGG 60.094 54.545 0.00 0.00 45.10 3.51
5765 7172 1.080230 CCTAGATCAGGCGATGGCG 60.080 63.158 0.00 0.00 41.24 5.69
5766 7173 1.080230 CTAGATCAGGCGATGGCGG 60.080 63.158 0.00 0.00 41.24 6.13
5767 7174 1.810606 CTAGATCAGGCGATGGCGGT 61.811 60.000 0.00 0.00 41.24 5.68
5768 7175 1.806461 TAGATCAGGCGATGGCGGTC 61.806 60.000 0.00 0.00 41.24 4.79
5769 7176 4.241555 ATCAGGCGATGGCGGTCC 62.242 66.667 0.00 0.00 41.24 4.46
5771 7178 4.473520 CAGGCGATGGCGGTCCTT 62.474 66.667 0.00 0.00 41.24 3.36
5772 7179 3.717294 AGGCGATGGCGGTCCTTT 61.717 61.111 0.00 0.00 41.24 3.11
5773 7180 2.750237 GGCGATGGCGGTCCTTTT 60.750 61.111 0.00 0.00 41.24 2.27
5774 7181 2.340328 GGCGATGGCGGTCCTTTTT 61.340 57.895 0.00 0.00 41.24 1.94
5775 7182 1.154035 GCGATGGCGGTCCTTTTTG 60.154 57.895 0.00 0.00 38.16 2.44
5776 7183 1.506262 CGATGGCGGTCCTTTTTGG 59.494 57.895 0.00 0.00 37.10 3.28
5777 7184 0.958382 CGATGGCGGTCCTTTTTGGA 60.958 55.000 0.00 0.00 43.86 3.53
5781 7188 0.538746 GGCGGTCCTTTTTGGAGGAA 60.539 55.000 0.00 0.00 46.95 3.36
5782 7189 1.324383 GCGGTCCTTTTTGGAGGAAA 58.676 50.000 0.00 0.00 46.95 3.13
5783 7190 1.893137 GCGGTCCTTTTTGGAGGAAAT 59.107 47.619 0.00 0.00 46.95 2.17
5784 7191 2.352715 GCGGTCCTTTTTGGAGGAAATG 60.353 50.000 0.00 0.00 46.95 2.32
5785 7192 2.890945 CGGTCCTTTTTGGAGGAAATGT 59.109 45.455 0.00 0.00 46.95 2.71
5786 7193 3.057526 CGGTCCTTTTTGGAGGAAATGTC 60.058 47.826 0.00 0.00 46.95 3.06
5787 7194 4.152647 GGTCCTTTTTGGAGGAAATGTCT 58.847 43.478 0.00 0.00 46.95 3.41
5788 7195 4.588951 GGTCCTTTTTGGAGGAAATGTCTT 59.411 41.667 0.00 0.00 46.95 3.01
5800 7207 7.337689 TGGAGGAAATGTCTTATGTGATCTTTG 59.662 37.037 0.00 0.00 0.00 2.77
5804 7211 7.487189 GGAAATGTCTTATGTGATCTTTGCTTG 59.513 37.037 0.00 0.00 0.00 4.01
5805 7212 7.458409 AATGTCTTATGTGATCTTTGCTTGT 57.542 32.000 0.00 0.00 0.00 3.16
5806 7213 6.882610 TGTCTTATGTGATCTTTGCTTGTT 57.117 33.333 0.00 0.00 0.00 2.83
5808 7215 7.140705 TGTCTTATGTGATCTTTGCTTGTTTG 58.859 34.615 0.00 0.00 0.00 2.93
5809 7216 7.141363 GTCTTATGTGATCTTTGCTTGTTTGT 58.859 34.615 0.00 0.00 0.00 2.83
5810 7217 7.324616 GTCTTATGTGATCTTTGCTTGTTTGTC 59.675 37.037 0.00 0.00 0.00 3.18
5812 7219 3.953612 TGTGATCTTTGCTTGTTTGTCCT 59.046 39.130 0.00 0.00 0.00 3.85
5855 8228 0.253044 TAGCACAGTGGCCTTGGATC 59.747 55.000 3.32 0.00 0.00 3.36
5856 8229 1.303561 GCACAGTGGCCTTGGATCA 60.304 57.895 3.32 0.00 0.00 2.92
5857 8230 0.895100 GCACAGTGGCCTTGGATCAA 60.895 55.000 3.32 0.00 0.00 2.57
5858 8231 1.843368 CACAGTGGCCTTGGATCAAT 58.157 50.000 3.32 0.00 0.00 2.57
5859 8232 1.475280 CACAGTGGCCTTGGATCAATG 59.525 52.381 3.32 0.00 33.43 2.82
5860 8233 0.458669 CAGTGGCCTTGGATCAATGC 59.541 55.000 3.32 0.40 34.98 3.56
5861 8234 1.033746 AGTGGCCTTGGATCAATGCG 61.034 55.000 3.32 0.00 36.20 4.73
5862 8235 1.753848 TGGCCTTGGATCAATGCGG 60.754 57.895 3.32 0.00 36.20 5.69
5863 8236 2.414594 GCCTTGGATCAATGCGGC 59.585 61.111 0.00 0.00 0.00 6.53
5864 8237 2.123428 GCCTTGGATCAATGCGGCT 61.123 57.895 0.00 0.00 32.02 5.52
5865 8238 1.669999 GCCTTGGATCAATGCGGCTT 61.670 55.000 0.00 0.00 32.02 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.234574 GTTATTTTCCTCGGCAACCTTTG 58.765 43.478 0.00 0.00 0.00 2.77
26 27 4.280436 TCTCTGTTATTTTCCTCGGCAA 57.720 40.909 0.00 0.00 0.00 4.52
27 28 3.973206 TCTCTGTTATTTTCCTCGGCA 57.027 42.857 0.00 0.00 0.00 5.69
32 33 8.897752 GTGCTTTGATATCTCTGTTATTTTCCT 58.102 33.333 3.98 0.00 0.00 3.36
44 46 3.559242 GCAGGTCTGTGCTTTGATATCTC 59.441 47.826 3.98 0.00 40.54 2.75
112 114 1.586028 CGGGCATCACAACCTTTGG 59.414 57.895 0.00 0.00 34.12 3.28
128 130 4.955925 TTACTTTAATGGATGTGTGCGG 57.044 40.909 0.00 0.00 0.00 5.69
162 164 6.456795 AATACCGGTGTTAGTACTCTTACC 57.543 41.667 19.93 5.48 0.00 2.85
163 165 9.508567 CTAAAATACCGGTGTTAGTACTCTTAC 57.491 37.037 19.93 0.00 0.00 2.34
164 166 8.686334 CCTAAAATACCGGTGTTAGTACTCTTA 58.314 37.037 19.93 9.41 0.00 2.10
165 167 7.364144 CCCTAAAATACCGGTGTTAGTACTCTT 60.364 40.741 19.93 8.70 0.00 2.85
166 168 6.097412 CCCTAAAATACCGGTGTTAGTACTCT 59.903 42.308 19.93 0.00 0.00 3.24
167 169 6.096846 TCCCTAAAATACCGGTGTTAGTACTC 59.903 42.308 19.93 0.00 0.00 2.59
168 170 5.957774 TCCCTAAAATACCGGTGTTAGTACT 59.042 40.000 19.93 0.00 0.00 2.73
169 171 6.220726 TCCCTAAAATACCGGTGTTAGTAC 57.779 41.667 19.93 0.00 0.00 2.73
170 172 6.865834 TTCCCTAAAATACCGGTGTTAGTA 57.134 37.500 19.93 11.81 0.00 1.82
171 173 5.760484 TTCCCTAAAATACCGGTGTTAGT 57.240 39.130 19.93 11.25 0.00 2.24
172 174 7.391275 TCTTTTTCCCTAAAATACCGGTGTTAG 59.609 37.037 19.93 19.87 35.29 2.34
173 175 7.230027 TCTTTTTCCCTAAAATACCGGTGTTA 58.770 34.615 19.93 11.81 35.29 2.41
197 211 2.691011 TGTTAGCCTGGTTGTTTGGTTC 59.309 45.455 0.00 0.00 0.00 3.62
222 236 3.842923 CGTGCTCTCGGCTCCCAT 61.843 66.667 0.00 0.00 42.39 4.00
258 272 5.473504 TGCAATATCTATCTCGACTGCTACA 59.526 40.000 0.00 0.00 0.00 2.74
449 472 6.758416 CGTCTTCTTCATCATTGGAGAACATA 59.242 38.462 0.00 0.00 41.64 2.29
525 662 2.070650 GTCAGGAGGGGCGGGTAAT 61.071 63.158 0.00 0.00 0.00 1.89
562 699 1.981495 CATAGATCAGTTCCCCCTCCC 59.019 57.143 0.00 0.00 0.00 4.30
596 736 2.781595 AAACCTAGCTGCGACCACCG 62.782 60.000 0.00 0.00 42.21 4.94
642 782 1.543802 CTCTGGAAGCAGACGAGACTT 59.456 52.381 0.00 0.00 0.00 3.01
926 1105 1.493311 CAAGTCGCGGACTGCTTTC 59.507 57.895 6.13 0.00 42.59 2.62
972 1152 1.301953 GTTCGCGGTAGGGTTTGGT 60.302 57.895 6.13 0.00 0.00 3.67
1212 1392 4.336581 CGATCGCCGCCAAATCTA 57.663 55.556 0.26 0.00 0.00 1.98
1263 1443 6.226052 TCAATCTACGCCTAACTAGACGATA 58.774 40.000 0.00 0.00 33.31 2.92
1327 1507 0.457166 CGTAGATCAACCGCCGACAA 60.457 55.000 0.00 0.00 0.00 3.18
1329 1509 0.864797 GACGTAGATCAACCGCCGAC 60.865 60.000 0.00 0.00 0.00 4.79
1477 1662 6.783892 TTGCCTGCAAAAAGTATCAATTTC 57.216 33.333 1.31 0.00 32.44 2.17
1668 1854 4.571176 GGAGATTCGTGTGGGTATTTTCTC 59.429 45.833 0.00 0.00 0.00 2.87
1728 1915 4.370917 CACTGAAACTTCCCCAAACATTG 58.629 43.478 0.00 0.00 0.00 2.82
1729 1916 3.181466 GCACTGAAACTTCCCCAAACATT 60.181 43.478 0.00 0.00 0.00 2.71
1732 1970 1.068588 GGCACTGAAACTTCCCCAAAC 59.931 52.381 0.00 0.00 0.00 2.93
1747 1985 4.641989 GTCAACCAATGATAAGATGGCACT 59.358 41.667 0.00 0.00 40.97 4.40
1749 1987 4.598022 TGTCAACCAATGATAAGATGGCA 58.402 39.130 0.00 0.00 40.97 4.92
1750 1988 5.581126 TTGTCAACCAATGATAAGATGGC 57.419 39.130 0.00 0.00 40.97 4.40
1776 2017 5.333111 GGCGTTGTTTCTCTAGTAGTTGTTG 60.333 44.000 0.00 0.00 0.00 3.33
1781 2022 4.595762 TTGGCGTTGTTTCTCTAGTAGT 57.404 40.909 0.00 0.00 0.00 2.73
1872 2242 3.578688 TCAGATGATCTGTGTTGTGACG 58.421 45.455 20.82 0.00 44.58 4.35
1975 2347 0.321919 CAGCCCATCATATCCCACCG 60.322 60.000 0.00 0.00 0.00 4.94
1991 2363 8.736244 TGGAACTATTGGAAAACTATAAACAGC 58.264 33.333 0.00 0.00 0.00 4.40
1997 2369 9.762381 ATGGTTTGGAACTATTGGAAAACTATA 57.238 29.630 0.00 0.00 30.17 1.31
1998 2370 8.664669 ATGGTTTGGAACTATTGGAAAACTAT 57.335 30.769 0.00 0.00 0.00 2.12
2031 2403 7.201291 CGAACTGATGATAGCATTGTTGTTTTG 60.201 37.037 14.87 4.31 34.20 2.44
2105 2477 7.175467 ACATATGTGGATGCCATTATACAGTTG 59.825 37.037 7.78 0.00 35.28 3.16
2164 2536 8.186178 AGAAACAAAATACTACTATCACTGCG 57.814 34.615 0.00 0.00 0.00 5.18
2194 2569 2.281539 TAACACCGAGACAGACTGGA 57.718 50.000 7.51 0.00 0.00 3.86
2396 2934 2.349590 TGATTGAAGTGGAGTCATGCG 58.650 47.619 0.00 0.00 0.00 4.73
2590 3135 5.701290 GGGCAATATTAGTACTAAGGTGCAG 59.299 44.000 29.82 17.22 34.46 4.41
2795 3521 2.838202 TGGAGGGAGTACAACAGATTCC 59.162 50.000 0.00 0.00 0.00 3.01
2847 3573 2.557056 TGCTCCGTATGTAGTCCATAGC 59.443 50.000 0.00 0.00 36.71 2.97
2910 3636 6.384015 AGAGATTTCACTATGGACCACATACA 59.616 38.462 0.00 0.00 41.03 2.29
3112 3898 7.660208 TGAGATCTACACGTGCTATGAAGTATA 59.340 37.037 17.22 0.00 0.00 1.47
3223 4009 0.607217 CATCCCACTGCACAGAAGCA 60.607 55.000 4.31 0.00 43.35 3.91
3560 4346 8.836268 ACTGGTATACGACAAACTAAAATTGA 57.164 30.769 0.00 0.00 0.00 2.57
3603 4390 4.646492 GCAACATAGGGAGGTGATGAAAAT 59.354 41.667 0.00 0.00 0.00 1.82
3702 4489 8.619683 ATGAAACCCCTAGTACACTATTAAGT 57.380 34.615 0.00 0.00 35.91 2.24
3719 4506 4.838904 AACCTACACTCCTATGAAACCC 57.161 45.455 0.00 0.00 0.00 4.11
3800 4587 4.020543 TGGTAATGCTACAAATTGGGTCC 58.979 43.478 0.00 0.00 0.00 4.46
3801 4588 5.652994 TTGGTAATGCTACAAATTGGGTC 57.347 39.130 0.00 0.00 0.00 4.46
3802 4589 7.912778 ATATTGGTAATGCTACAAATTGGGT 57.087 32.000 0.00 0.00 34.18 4.51
3939 4738 6.400091 GCAGCGAGATATGTTTAGATTTACGG 60.400 42.308 0.00 0.00 0.00 4.02
3948 4747 3.865164 CACAGTGCAGCGAGATATGTTTA 59.135 43.478 0.00 0.00 0.00 2.01
3963 4762 1.062587 GCATGGTATTCGTCACAGTGC 59.937 52.381 0.00 0.00 0.00 4.40
3992 4796 7.201461 GCAAGTGCATATCCTGTTTTTAATGTG 60.201 37.037 0.00 0.00 41.59 3.21
4009 4814 2.283145 AAGAACCAGAGCAAGTGCAT 57.717 45.000 6.00 0.00 45.16 3.96
4052 4861 1.351350 AGGGGAAAAGGCTAGTGACAC 59.649 52.381 0.00 0.00 0.00 3.67
4063 4872 6.655425 CAGACTTAGGTTAAGAAGGGGAAAAG 59.345 42.308 3.04 0.00 39.09 2.27
4071 4880 6.706270 TCAAACAGCAGACTTAGGTTAAGAAG 59.294 38.462 3.04 0.00 39.09 2.85
4072 4881 6.588204 TCAAACAGCAGACTTAGGTTAAGAA 58.412 36.000 3.04 0.00 39.09 2.52
4073 4882 6.169557 TCAAACAGCAGACTTAGGTTAAGA 57.830 37.500 3.04 0.00 39.09 2.10
4124 4942 4.951254 TCAAACTGAGAACACGTGGATTA 58.049 39.130 21.57 0.87 0.00 1.75
4155 4973 7.761038 ACAACACGTATCCAGATGATCTATA 57.239 36.000 0.00 0.00 34.76 1.31
4230 5048 1.230149 AGGGGTGGATGTTGCCCTA 60.230 57.895 0.00 0.00 42.01 3.53
4294 5112 1.369692 CAGGGTGAGCGTGTAACCA 59.630 57.895 0.00 0.00 35.56 3.67
4424 5273 8.686334 ACTGGTATACTGCAAATAAATGGAAAG 58.314 33.333 2.25 0.00 0.00 2.62
4428 5277 7.333528 ACACTGGTATACTGCAAATAAATGG 57.666 36.000 2.25 0.00 0.00 3.16
4769 5628 0.610232 GTGGGAAGCCAGTCTGCAAT 60.610 55.000 0.00 0.00 0.00 3.56
4823 5682 2.037772 GGAGTTCTTGAGTCCAGCTTGA 59.962 50.000 0.00 0.00 45.73 3.02
4923 5783 2.754552 TGATAAACCATTCAGCAGCACC 59.245 45.455 0.00 0.00 0.00 5.01
5062 5922 5.365619 AGACAACCGGACATCCATTATAAC 58.634 41.667 9.46 0.00 35.14 1.89
5063 5923 5.623956 AGACAACCGGACATCCATTATAA 57.376 39.130 9.46 0.00 35.14 0.98
5064 5924 6.495526 TGATAGACAACCGGACATCCATTATA 59.504 38.462 9.46 0.00 35.14 0.98
5065 5925 5.306937 TGATAGACAACCGGACATCCATTAT 59.693 40.000 9.46 0.00 35.14 1.28
5066 5926 4.651962 TGATAGACAACCGGACATCCATTA 59.348 41.667 9.46 0.00 35.14 1.90
5067 5927 3.454447 TGATAGACAACCGGACATCCATT 59.546 43.478 9.46 0.00 35.14 3.16
5068 5928 3.038280 TGATAGACAACCGGACATCCAT 58.962 45.455 9.46 0.00 35.14 3.41
5069 5929 2.462723 TGATAGACAACCGGACATCCA 58.537 47.619 9.46 0.00 35.14 3.41
5070 5930 3.069586 TGATGATAGACAACCGGACATCC 59.930 47.826 9.46 0.00 33.94 3.51
5071 5931 4.038042 TCTGATGATAGACAACCGGACATC 59.962 45.833 9.46 9.94 34.98 3.06
5119 5979 6.718294 AGGTCCAATTTCTTACGATTAGGTT 58.282 36.000 0.00 0.00 0.00 3.50
5120 5980 6.309389 AGGTCCAATTTCTTACGATTAGGT 57.691 37.500 0.00 0.00 0.00 3.08
5121 5981 7.625828 AAAGGTCCAATTTCTTACGATTAGG 57.374 36.000 0.00 0.00 0.00 2.69
5140 6003 8.721133 ATTTCTTACCCTCACAAATAAAAGGT 57.279 30.769 0.00 0.00 0.00 3.50
5152 6015 8.577296 CGTCTATCTATCAATTTCTTACCCTCA 58.423 37.037 0.00 0.00 0.00 3.86
5177 6048 7.464830 ACGATACTTTAATGGAAGTGAATCG 57.535 36.000 16.89 16.89 45.05 3.34
5184 6055 9.460906 GGTTACTCTACGATACTTTAATGGAAG 57.539 37.037 0.00 0.00 0.00 3.46
5214 6085 9.627123 AACTGAATCTTCCATCCGAAATTATAA 57.373 29.630 0.00 0.00 0.00 0.98
5228 6099 3.128242 CAGCATGTGGAACTGAATCTTCC 59.872 47.826 0.00 0.00 38.04 3.46
5238 6109 3.236816 CGTTTTCATCAGCATGTGGAAC 58.763 45.455 0.00 0.00 37.40 3.62
5244 6115 5.565259 GTGAGTTTACGTTTTCATCAGCATG 59.435 40.000 0.00 0.00 37.54 4.06
5245 6116 5.238432 TGTGAGTTTACGTTTTCATCAGCAT 59.762 36.000 0.00 0.00 0.00 3.79
5246 6117 4.572795 TGTGAGTTTACGTTTTCATCAGCA 59.427 37.500 0.00 0.00 0.00 4.41
5248 6119 5.907391 GGTTGTGAGTTTACGTTTTCATCAG 59.093 40.000 0.00 0.00 0.00 2.90
5306 6177 6.347402 CCTGTGGTTTATAAATAGATTCGGCG 60.347 42.308 0.00 0.00 0.00 6.46
5313 6184 7.550196 GGTTTCGTCCTGTGGTTTATAAATAGA 59.450 37.037 0.31 0.00 0.00 1.98
5325 6196 1.959226 CACCGGTTTCGTCCTGTGG 60.959 63.158 2.97 0.00 38.46 4.17
5332 6203 1.877443 CCTTGATTTCACCGGTTTCGT 59.123 47.619 2.97 0.00 33.95 3.85
5353 6224 0.037590 AGTAATGCCCCTTGAACGCA 59.962 50.000 0.00 0.00 36.84 5.24
5380 6783 6.676950 TCATTTTTCACATGTACTCGCAATT 58.323 32.000 0.00 0.00 0.00 2.32
5382 6785 5.681337 TCATTTTTCACATGTACTCGCAA 57.319 34.783 0.00 0.00 0.00 4.85
5532 6937 2.417651 CGTTTGGCTGTTATCTCCGGTA 60.418 50.000 0.00 0.00 0.00 4.02
5548 6953 1.998315 CATCAGAGGTGAGAGCGTTTG 59.002 52.381 0.00 0.00 35.66 2.93
5549 6954 1.620819 ACATCAGAGGTGAGAGCGTTT 59.379 47.619 0.00 0.00 35.66 3.60
5564 6969 3.432186 GCTATACCCAACTCTGCACATCA 60.432 47.826 0.00 0.00 0.00 3.07
5578 6983 3.502356 AGTTCAGAGCCTAGCTATACCC 58.498 50.000 0.00 0.00 39.88 3.69
5582 6987 5.877564 GTCAAAAAGTTCAGAGCCTAGCTAT 59.122 40.000 0.00 0.00 39.88 2.97
5595 7000 9.317936 AGATTGAGAAAAATGGTCAAAAAGTTC 57.682 29.630 0.00 0.00 34.02 3.01
5596 7001 9.317936 GAGATTGAGAAAAATGGTCAAAAAGTT 57.682 29.630 0.00 0.00 34.02 2.66
5630 7035 7.166168 CGTGTTATTTTGCAGCATAAAACATC 58.834 34.615 19.10 14.61 30.64 3.06
5632 7037 5.403766 CCGTGTTATTTTGCAGCATAAAACA 59.596 36.000 15.51 15.48 30.64 2.83
5651 7057 3.764237 AATTGTGTAGACTTCCCGTGT 57.236 42.857 0.00 0.00 0.00 4.49
5655 7061 7.739498 TTTGAAGTAATTGTGTAGACTTCCC 57.261 36.000 11.98 0.00 44.67 3.97
5656 7062 9.612620 CATTTTGAAGTAATTGTGTAGACTTCC 57.387 33.333 11.98 0.00 44.67 3.46
5667 7073 8.971321 CAAGAAGGTGACATTTTGAAGTAATTG 58.029 33.333 0.00 0.00 0.00 2.32
5668 7074 8.912988 TCAAGAAGGTGACATTTTGAAGTAATT 58.087 29.630 5.56 0.00 0.00 1.40
5669 7075 8.463930 TCAAGAAGGTGACATTTTGAAGTAAT 57.536 30.769 5.56 0.00 0.00 1.89
5670 7076 7.873719 TCAAGAAGGTGACATTTTGAAGTAA 57.126 32.000 5.56 0.00 0.00 2.24
5671 7077 7.873719 TTCAAGAAGGTGACATTTTGAAGTA 57.126 32.000 12.60 0.00 32.58 2.24
5705 7111 2.289945 CCAGAGTGAGGTGGAAAAGGAG 60.290 54.545 0.00 0.00 35.67 3.69
5706 7112 1.699634 CCAGAGTGAGGTGGAAAAGGA 59.300 52.381 0.00 0.00 35.67 3.36
5750 7157 3.157217 GACCGCCATCGCCTGATCT 62.157 63.158 0.00 0.00 30.49 2.75
5755 7162 2.764637 AAAAAGGACCGCCATCGCCT 62.765 55.000 0.00 0.00 36.29 5.52
5760 7167 0.611896 CCTCCAAAAAGGACCGCCAT 60.612 55.000 0.00 0.00 43.07 4.40
5761 7168 1.228429 CCTCCAAAAAGGACCGCCA 60.228 57.895 0.00 0.00 43.07 5.69
5762 7169 0.538746 TTCCTCCAAAAAGGACCGCC 60.539 55.000 0.00 0.00 45.20 6.13
5763 7170 1.324383 TTTCCTCCAAAAAGGACCGC 58.676 50.000 0.00 0.00 45.20 5.68
5765 7172 4.152647 AGACATTTCCTCCAAAAAGGACC 58.847 43.478 0.00 0.00 45.20 4.46
5766 7173 5.791336 AAGACATTTCCTCCAAAAAGGAC 57.209 39.130 0.00 0.00 45.20 3.85
5767 7174 7.010160 ACATAAGACATTTCCTCCAAAAAGGA 58.990 34.615 0.00 0.00 46.75 3.36
5768 7175 7.039784 TCACATAAGACATTTCCTCCAAAAAGG 60.040 37.037 0.00 0.00 37.81 3.11
5769 7176 7.885297 TCACATAAGACATTTCCTCCAAAAAG 58.115 34.615 0.00 0.00 0.00 2.27
5770 7177 7.831691 TCACATAAGACATTTCCTCCAAAAA 57.168 32.000 0.00 0.00 0.00 1.94
5771 7178 7.890127 AGATCACATAAGACATTTCCTCCAAAA 59.110 33.333 0.00 0.00 0.00 2.44
5772 7179 7.405292 AGATCACATAAGACATTTCCTCCAAA 58.595 34.615 0.00 0.00 0.00 3.28
5773 7180 6.962182 AGATCACATAAGACATTTCCTCCAA 58.038 36.000 0.00 0.00 0.00 3.53
5774 7181 6.566079 AGATCACATAAGACATTTCCTCCA 57.434 37.500 0.00 0.00 0.00 3.86
5775 7182 7.680588 GCAAAGATCACATAAGACATTTCCTCC 60.681 40.741 0.00 0.00 0.00 4.30
5776 7183 7.066766 AGCAAAGATCACATAAGACATTTCCTC 59.933 37.037 0.00 0.00 0.00 3.71
5777 7184 6.888632 AGCAAAGATCACATAAGACATTTCCT 59.111 34.615 0.00 0.00 0.00 3.36
5778 7185 7.093322 AGCAAAGATCACATAAGACATTTCC 57.907 36.000 0.00 0.00 0.00 3.13
5779 7186 8.025445 ACAAGCAAAGATCACATAAGACATTTC 58.975 33.333 0.00 0.00 0.00 2.17
5780 7187 7.889469 ACAAGCAAAGATCACATAAGACATTT 58.111 30.769 0.00 0.00 0.00 2.32
5781 7188 7.458409 ACAAGCAAAGATCACATAAGACATT 57.542 32.000 0.00 0.00 0.00 2.71
5782 7189 7.458409 AACAAGCAAAGATCACATAAGACAT 57.542 32.000 0.00 0.00 0.00 3.06
5783 7190 6.882610 AACAAGCAAAGATCACATAAGACA 57.117 33.333 0.00 0.00 0.00 3.41
5784 7191 7.141363 ACAAACAAGCAAAGATCACATAAGAC 58.859 34.615 0.00 0.00 0.00 3.01
5785 7192 7.275888 ACAAACAAGCAAAGATCACATAAGA 57.724 32.000 0.00 0.00 0.00 2.10
5786 7193 6.583806 GGACAAACAAGCAAAGATCACATAAG 59.416 38.462 0.00 0.00 0.00 1.73
5787 7194 6.265196 AGGACAAACAAGCAAAGATCACATAA 59.735 34.615 0.00 0.00 0.00 1.90
5788 7195 5.769662 AGGACAAACAAGCAAAGATCACATA 59.230 36.000 0.00 0.00 0.00 2.29
5800 7207 1.268743 GCAGTGACAGGACAAACAAGC 60.269 52.381 0.00 0.00 0.00 4.01
5804 7211 1.268743 GCAAGCAGTGACAGGACAAAC 60.269 52.381 0.00 0.00 0.00 2.93
5805 7212 1.024271 GCAAGCAGTGACAGGACAAA 58.976 50.000 0.00 0.00 0.00 2.83
5806 7213 0.181114 AGCAAGCAGTGACAGGACAA 59.819 50.000 0.00 0.00 0.00 3.18
5808 7215 1.849976 GCAGCAAGCAGTGACAGGAC 61.850 60.000 0.00 0.00 44.79 3.85
5809 7216 1.598962 GCAGCAAGCAGTGACAGGA 60.599 57.895 0.00 0.00 44.79 3.86
5810 7217 2.952245 GCAGCAAGCAGTGACAGG 59.048 61.111 0.00 0.00 44.79 4.00


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

AutoCloner maintained by Alex Coulton.