Multiple sequence alignment - TraesCS7B01G197900

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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 TraesCS7B01G197900 chr7B 100.000 5794 0 0 1 5794 346679279 346673486 0.000000e+00 10700.0
1 TraesCS7B01G197900 chr7D 95.743 4698 130 33 678 5333 337559887 337555218 0.000000e+00 7504.0
2 TraesCS7B01G197900 chr7D 92.666 709 35 6 1 694 337560607 337559901 0.000000e+00 1005.0
3 TraesCS7B01G197900 chr7D 76.768 297 49 5 5499 5794 437476414 437476137 1.300000e-31 148.0
4 TraesCS7B01G197900 chr7A 96.496 4480 112 20 778 5221 360083114 360078644 0.000000e+00 7361.0
5 TraesCS7B01G197900 chr7A 88.571 560 44 8 227 771 360109863 360109309 0.000000e+00 662.0
6 TraesCS7B01G197900 chr7A 93.277 119 8 0 5215 5333 360078595 360078477 5.970000e-40 176.0
7 TraesCS7B01G197900 chr3B 83.175 422 50 8 5361 5782 548077711 548078111 3.300000e-97 366.0
8 TraesCS7B01G197900 chr3B 82.783 424 50 9 5371 5794 548368050 548368450 1.990000e-94 357.0
9 TraesCS7B01G197900 chr3B 81.840 424 55 8 5371 5794 548548539 548548940 2.590000e-88 337.0
10 TraesCS7B01G197900 chr3B 79.882 338 57 8 5372 5706 479302515 479302844 2.700000e-58 237.0
11 TraesCS7B01G197900 chr3B 79.341 334 55 13 5376 5706 592537008 592537330 7.560000e-54 222.0
12 TraesCS7B01G197900 chr3A 80.876 434 58 10 5361 5794 529620542 529620134 9.370000e-83 318.0
13 TraesCS7B01G197900 chr2D 80.233 344 56 8 5370 5706 308906223 308906561 1.250000e-61 248.0
14 TraesCS7B01G197900 chr2D 79.310 348 62 7 5361 5706 14103408 14103747 9.710000e-58 235.0
15 TraesCS7B01G197900 chr2D 78.070 342 50 13 5457 5794 353255118 353254798 5.920000e-45 193.0
16 TraesCS7B01G197900 chr2D 75.352 426 73 20 5371 5794 455889291 455888896 5.970000e-40 176.0
17 TraesCS7B01G197900 chr2D 76.486 370 58 16 5433 5794 84939224 84938876 2.150000e-39 174.0
18 TraesCS7B01G197900 chr5A 77.672 421 69 17 5375 5794 241137084 241136688 3.490000e-57 233.0
19 TraesCS7B01G197900 chr3D 81.560 282 33 4 5513 5794 421369147 421369409 1.260000e-51 215.0
20 TraesCS7B01G197900 chr2A 78.249 354 64 10 5359 5706 16473628 16473974 1.260000e-51 215.0
21 TraesCS7B01G197900 chr2A 89.524 105 5 2 1572 1673 6501768 6501869 1.690000e-25 128.0
22 TraesCS7B01G197900 chr2B 76.526 426 69 15 5371 5794 536802699 536802303 2.740000e-48 204.0
23 TraesCS7B01G197900 chr1A 91.429 105 6 1 1572 1673 352174093 352174197 2.180000e-29 141.0
24 TraesCS7B01G197900 chr1A 88.889 108 9 1 1568 1672 188150957 188150850 4.710000e-26 130.0
25 TraesCS7B01G197900 chr1A 88.073 109 9 2 1569 1673 188149103 188148995 6.090000e-25 126.0
26 TraesCS7B01G197900 chr4B 87.273 110 11 3 1567 1673 24556001 24555892 7.880000e-24 122.0
27 TraesCS7B01G197900 chr4B 100.000 29 0 0 5155 5183 643774544 643774572 3.000000e-03 54.7
28 TraesCS7B01G197900 chr1D 87.156 109 11 1 1568 1673 128530426 128530318 2.840000e-23 121.0
29 TraesCS7B01G197900 chr1D 85.870 92 12 1 5704 5794 199830560 199830651 4.780000e-16 97.1
30 TraesCS7B01G197900 chr1B 85.345 116 14 1 1566 1678 301273390 301273505 3.670000e-22 117.0
31 TraesCS7B01G197900 chr6B 78.392 199 23 11 5598 5794 648119691 648119511 1.710000e-20 111.0
32 TraesCS7B01G197900 chr5D 94.286 35 2 0 5149 5183 184034762 184034796 3.000000e-03 54.7
33 TraesCS7B01G197900 chr4A 96.875 32 1 0 5155 5186 545111262 545111231 3.000000e-03 54.7
34 TraesCS7B01G197900 chr4A 100.000 28 0 0 5156 5183 576605176 576605149 1.000000e-02 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G197900 chr7B 346673486 346679279 5793 True 10700.0 10700 100.0000 1 5794 1 chr7B.!!$R1 5793
1 TraesCS7B01G197900 chr7D 337555218 337560607 5389 True 4254.5 7504 94.2045 1 5333 2 chr7D.!!$R2 5332
2 TraesCS7B01G197900 chr7A 360078477 360083114 4637 True 3768.5 7361 94.8865 778 5333 2 chr7A.!!$R2 4555
3 TraesCS7B01G197900 chr7A 360109309 360109863 554 True 662.0 662 88.5710 227 771 1 chr7A.!!$R1 544

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
219 220 0.095417 GGACGCACAGAAATCGCTTC 59.905 55.000 0.00 0.00 0.0 3.86 F
1944 1996 0.178068 GAAGCTGTCCCCTCGCAATA 59.822 55.000 0.00 0.00 0.0 1.90 F
1949 2002 1.335132 TGTCCCCTCGCAATAGACCC 61.335 60.000 0.00 0.00 0.0 4.46 F
3058 3154 2.014857 GGCCTGGTAGGTTTCGAAATC 58.985 52.381 14.69 14.02 37.8 2.17 F
4008 4110 2.593436 ACCGTGGGCTTCGTTTGG 60.593 61.111 0.00 0.00 0.0 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2164 2219 0.944386 AGCCACGTTGCAACTACTTG 59.056 50.000 26.09 16.61 0.00 3.16 R
3415 3512 1.136828 ACCTGTTACTTCTGCCCACA 58.863 50.000 0.00 0.00 0.00 4.17 R
3709 3811 5.888691 ACATAATGCAACCGTTGTTATGA 57.111 34.783 26.18 12.66 35.16 2.15 R
4033 4135 1.871772 CTGCAAGGTTCTTCGCAGG 59.128 57.895 16.67 6.07 46.37 4.85 R
5409 5569 0.179076 AGGGTGCTTTGCTGCAAAAC 60.179 50.000 25.93 22.28 45.12 2.43 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
62 63 8.100164 TCAACAGTAAGTATCATCATCAAACCA 58.900 33.333 0.00 0.00 0.00 3.67
71 72 8.777413 AGTATCATCATCAAACCAAACATATCG 58.223 33.333 0.00 0.00 0.00 2.92
81 82 6.481954 AACCAAACATATCGACAGAAAGAC 57.518 37.500 0.00 0.00 0.00 3.01
82 83 4.625742 ACCAAACATATCGACAGAAAGACG 59.374 41.667 0.00 0.00 36.74 4.18
84 85 5.220228 CCAAACATATCGACAGAAAGACGAC 60.220 44.000 0.00 0.00 46.22 4.34
125 126 2.125512 GCCTCGTCGCTGGTGATT 60.126 61.111 6.10 0.00 0.00 2.57
140 141 2.559440 GTGATTGTGGATGAGCTCCTC 58.441 52.381 12.15 11.12 45.21 3.71
166 167 4.814294 GCGTGCAGTAGGGGTCGG 62.814 72.222 0.00 0.00 0.00 4.79
196 197 3.181462 CGGAGATGAGGGATGATTGACAA 60.181 47.826 0.00 0.00 0.00 3.18
213 214 2.808543 GACAAAGAGGACGCACAGAAAT 59.191 45.455 0.00 0.00 0.00 2.17
216 217 0.737715 AGAGGACGCACAGAAATCGC 60.738 55.000 0.00 0.00 0.00 4.58
219 220 0.095417 GGACGCACAGAAATCGCTTC 59.905 55.000 0.00 0.00 0.00 3.86
220 221 1.071605 GACGCACAGAAATCGCTTCT 58.928 50.000 0.00 0.00 45.80 2.85
400 401 3.307059 GGGAATGAGGAATGGATAGGACG 60.307 52.174 0.00 0.00 0.00 4.79
439 440 2.093106 CGTAGTTGGAGTGGCTAGAGT 58.907 52.381 0.00 0.00 0.00 3.24
461 462 2.359900 GCGTGATTTGGAATGAGAGGT 58.640 47.619 0.00 0.00 0.00 3.85
484 485 2.713011 GCTAGATACGTTTCGAAGCGA 58.287 47.619 35.63 21.31 36.44 4.93
487 488 2.937591 AGATACGTTTCGAAGCGAACA 58.062 42.857 35.63 21.59 45.64 3.18
497 498 1.597663 CGAAGCGAACAGTTTTCCACT 59.402 47.619 0.00 0.00 35.35 4.00
498 499 2.031683 CGAAGCGAACAGTTTTCCACTT 59.968 45.455 0.00 0.00 30.92 3.16
499 500 3.618698 GAAGCGAACAGTTTTCCACTTC 58.381 45.455 0.00 4.56 30.92 3.01
500 501 2.639065 AGCGAACAGTTTTCCACTTCA 58.361 42.857 0.00 0.00 30.92 3.02
501 502 2.354821 AGCGAACAGTTTTCCACTTCAC 59.645 45.455 0.00 0.00 30.92 3.18
502 503 2.354821 GCGAACAGTTTTCCACTTCACT 59.645 45.455 0.00 0.00 30.92 3.41
503 504 3.181500 GCGAACAGTTTTCCACTTCACTT 60.181 43.478 0.00 0.00 30.92 3.16
504 505 4.342772 CGAACAGTTTTCCACTTCACTTG 58.657 43.478 0.00 0.00 30.92 3.16
505 506 3.782889 ACAGTTTTCCACTTCACTTGC 57.217 42.857 0.00 0.00 30.92 4.01
594 610 8.741603 TTAGCATTTGGGTAAGTATTTAGGTC 57.258 34.615 0.00 0.00 34.68 3.85
604 620 7.284261 GGGTAAGTATTTAGGTCGAGTTAGAGT 59.716 40.741 0.00 0.00 0.00 3.24
614 630 5.413833 AGGTCGAGTTAGAGTATCAAACGAA 59.586 40.000 0.00 0.00 37.82 3.85
744 791 3.609409 GCAGCAAAAACTTACTCCCTTCG 60.609 47.826 0.00 0.00 0.00 3.79
745 792 3.564225 CAGCAAAAACTTACTCCCTTCGT 59.436 43.478 0.00 0.00 0.00 3.85
760 807 4.222145 TCCCTTCGTGCCATATATTAGACC 59.778 45.833 0.00 0.00 0.00 3.85
771 818 9.420118 TGCCATATATTAGACCTTTTTGACATT 57.580 29.630 0.00 0.00 0.00 2.71
822 869 9.917872 CATTATGAGACCGAATAGTACTATACG 57.082 37.037 15.74 8.63 0.00 3.06
839 886 7.147143 ACTATACGGCATCTACTTGTCATAG 57.853 40.000 0.00 0.00 0.00 2.23
845 892 3.677121 GCATCTACTTGTCATAGCATCCG 59.323 47.826 0.00 0.00 0.00 4.18
851 898 2.602257 TGTCATAGCATCCGTCCAAG 57.398 50.000 0.00 0.00 0.00 3.61
904 951 4.039245 TGGTCTCTGCTAGGTATAACATGC 59.961 45.833 0.00 0.00 0.00 4.06
956 1003 1.337118 GAGGCAAACACCATGGGAAA 58.663 50.000 18.09 0.00 0.00 3.13
1383 1430 4.142534 GGAGGTAAAATCCAGCCGTTTAAC 60.143 45.833 0.00 0.00 36.79 2.01
1463 1510 5.044179 AGGAATTTGATCATCTGGGGTTGTA 60.044 40.000 0.00 0.00 0.00 2.41
1516 1565 6.882610 TGTGAAAAATTGCTCAGACTACAT 57.117 33.333 0.00 0.00 0.00 2.29
1601 1650 5.132502 TCCGTCCGGAATTAGTTATCACTA 58.867 41.667 5.23 0.00 42.05 2.74
1944 1996 0.178068 GAAGCTGTCCCCTCGCAATA 59.822 55.000 0.00 0.00 0.00 1.90
1949 2002 1.335132 TGTCCCCTCGCAATAGACCC 61.335 60.000 0.00 0.00 0.00 4.46
2019 2072 7.148474 GCGTGATTCAAGACTATTTGACCTAAA 60.148 37.037 3.64 0.00 36.84 1.85
2094 2147 2.237392 AGTCCTGTTTCTATGCACCTCC 59.763 50.000 0.00 0.00 0.00 4.30
2164 2219 3.552068 GGGCAAATTTGTACCAGTCACAC 60.552 47.826 19.03 0.00 0.00 3.82
2177 2232 3.242739 CCAGTCACACAAGTAGTTGCAAC 60.243 47.826 22.17 22.17 37.14 4.17
2209 2264 8.802267 TCTAAATCCCATTGTTGTAAAAGAAGG 58.198 33.333 0.00 0.00 0.00 3.46
2239 2294 5.050159 CCAACAACAAATTTAGCTCCTTTGC 60.050 40.000 12.82 0.00 34.08 3.68
2338 2409 4.382470 GGCAGCCCATCTATCTAGTATGTG 60.382 50.000 0.00 0.00 0.00 3.21
2362 2433 4.979335 TGGTTGACTTTGATATGTGTGGA 58.021 39.130 0.00 0.00 0.00 4.02
2366 2437 6.319658 GGTTGACTTTGATATGTGTGGATCAT 59.680 38.462 0.00 0.00 32.27 2.45
2408 2479 5.526111 GTGTCTTGGTTAAAGTTCTGCTACA 59.474 40.000 0.00 0.00 37.18 2.74
2506 2577 4.853468 TGATTCATAAGTGGGCAAGGTA 57.147 40.909 0.00 0.00 0.00 3.08
2615 2686 8.801715 ATCGAAAAAGTAGTACGAGTTTTACA 57.198 30.769 18.23 8.61 36.49 2.41
2686 2757 9.350951 ACTAGTTGGCTACAAAGTTTAATCTTT 57.649 29.630 5.82 5.82 38.54 2.52
2788 2859 7.267128 ACACGGAAAACCAATATACGAGATTA 58.733 34.615 0.00 0.00 0.00 1.75
3058 3154 2.014857 GGCCTGGTAGGTTTCGAAATC 58.985 52.381 14.69 14.02 37.80 2.17
3139 3235 7.377398 TCCTGTGAAATTTTTATGGATGTGTG 58.623 34.615 0.00 0.00 0.00 3.82
3140 3236 7.015098 TCCTGTGAAATTTTTATGGATGTGTGT 59.985 33.333 0.00 0.00 0.00 3.72
3145 3241 8.373981 TGAAATTTTTATGGATGTGTGTGGATT 58.626 29.630 0.00 0.00 0.00 3.01
3415 3512 5.304686 TGACTTGGATACTGACCAAAAGT 57.695 39.130 0.00 0.00 45.05 2.66
3668 3770 5.422145 AGCTTTGCTGAATTTTCTTTGTGT 58.578 33.333 0.00 0.00 37.57 3.72
3687 3789 7.633193 TTGTGTACTTATGTTTGAGGTTTGT 57.367 32.000 0.00 0.00 0.00 2.83
3703 3805 5.419760 GGTTTGTACCTTTTCTCTGTCAC 57.580 43.478 0.00 0.00 41.53 3.67
3709 3811 6.177610 TGTACCTTTTCTCTGTCACTTTGTT 58.822 36.000 0.00 0.00 0.00 2.83
3818 3920 9.054922 GCTTTCTGATATTCTCTTTTGCTCTAT 57.945 33.333 0.00 0.00 0.00 1.98
4008 4110 2.593436 ACCGTGGGCTTCGTTTGG 60.593 61.111 0.00 0.00 0.00 3.28
4181 4283 4.424711 GGGGTGCATGGAAGCCGA 62.425 66.667 0.00 0.00 35.99 5.54
4590 4692 5.237344 CAGTTTGAGTCAGGTAACAGGAAAG 59.763 44.000 8.50 0.00 41.41 2.62
5093 5195 9.117145 GTTTGTCTACATATGTGTTGAAATGTG 57.883 33.333 18.81 0.00 40.76 3.21
5203 5308 5.363101 TGTGATGACTTCTCATTATGGCTC 58.637 41.667 0.00 0.00 37.24 4.70
5225 5385 6.292596 GCTCTGAAAAGAAGGATTAGTATGCG 60.293 42.308 0.00 0.00 0.00 4.73
5333 5493 4.456911 AGGAGCATGTTATGTTGAACTGTG 59.543 41.667 0.00 0.00 0.00 3.66
5334 5494 4.161333 GAGCATGTTATGTTGAACTGTGC 58.839 43.478 0.00 8.29 39.64 4.57
5335 5495 3.822735 AGCATGTTATGTTGAACTGTGCT 59.177 39.130 11.36 11.36 42.14 4.40
5336 5496 4.083110 AGCATGTTATGTTGAACTGTGCTC 60.083 41.667 11.36 0.00 42.72 4.26
5337 5497 4.320421 GCATGTTATGTTGAACTGTGCTCA 60.320 41.667 0.00 0.00 38.00 4.26
5338 5498 5.620654 GCATGTTATGTTGAACTGTGCTCAT 60.621 40.000 0.00 0.00 38.00 2.90
5339 5499 6.384224 CATGTTATGTTGAACTGTGCTCATT 58.616 36.000 0.00 0.00 0.00 2.57
5340 5500 7.529158 CATGTTATGTTGAACTGTGCTCATTA 58.471 34.615 0.00 0.00 0.00 1.90
5341 5501 7.686438 TGTTATGTTGAACTGTGCTCATTAT 57.314 32.000 0.00 0.00 0.00 1.28
5342 5502 7.529158 TGTTATGTTGAACTGTGCTCATTATG 58.471 34.615 0.00 0.00 0.00 1.90
5343 5503 5.571784 ATGTTGAACTGTGCTCATTATGG 57.428 39.130 0.00 0.00 0.00 2.74
5344 5504 4.397420 TGTTGAACTGTGCTCATTATGGT 58.603 39.130 0.00 0.00 0.00 3.55
5345 5505 4.216042 TGTTGAACTGTGCTCATTATGGTG 59.784 41.667 0.00 0.00 0.00 4.17
5346 5506 4.019792 TGAACTGTGCTCATTATGGTGT 57.980 40.909 0.00 0.00 0.00 4.16
5347 5507 4.002982 TGAACTGTGCTCATTATGGTGTC 58.997 43.478 0.00 0.00 0.00 3.67
5348 5508 3.988976 ACTGTGCTCATTATGGTGTCT 57.011 42.857 0.00 0.00 0.00 3.41
5349 5509 4.292186 ACTGTGCTCATTATGGTGTCTT 57.708 40.909 0.00 0.00 0.00 3.01
5350 5510 4.005650 ACTGTGCTCATTATGGTGTCTTG 58.994 43.478 0.00 0.00 0.00 3.02
5351 5511 3.346315 TGTGCTCATTATGGTGTCTTGG 58.654 45.455 0.00 0.00 0.00 3.61
5352 5512 2.684881 GTGCTCATTATGGTGTCTTGGG 59.315 50.000 0.00 0.00 0.00 4.12
5353 5513 1.678101 GCTCATTATGGTGTCTTGGGC 59.322 52.381 0.00 0.00 0.00 5.36
5354 5514 2.301346 CTCATTATGGTGTCTTGGGCC 58.699 52.381 0.00 0.00 0.00 5.80
5355 5515 1.638070 TCATTATGGTGTCTTGGGCCA 59.362 47.619 0.00 0.00 36.64 5.36
5356 5516 1.750778 CATTATGGTGTCTTGGGCCAC 59.249 52.381 5.23 0.00 34.84 5.01
5359 5519 3.580319 GGTGTCTTGGGCCACCCT 61.580 66.667 5.23 0.00 45.70 4.34
5360 5520 2.228480 GGTGTCTTGGGCCACCCTA 61.228 63.158 5.23 0.00 45.70 3.53
5361 5521 1.765074 GTGTCTTGGGCCACCCTAA 59.235 57.895 5.23 0.00 45.70 2.69
5362 5522 0.331616 GTGTCTTGGGCCACCCTAAT 59.668 55.000 5.23 0.00 45.70 1.73
5363 5523 0.623723 TGTCTTGGGCCACCCTAATC 59.376 55.000 5.23 0.00 45.70 1.75
5364 5524 0.919710 GTCTTGGGCCACCCTAATCT 59.080 55.000 5.23 0.00 45.70 2.40
5365 5525 0.918983 TCTTGGGCCACCCTAATCTG 59.081 55.000 5.23 0.00 45.70 2.90
5366 5526 0.625849 CTTGGGCCACCCTAATCTGT 59.374 55.000 5.23 0.00 45.70 3.41
5367 5527 1.843851 CTTGGGCCACCCTAATCTGTA 59.156 52.381 5.23 0.00 45.70 2.74
5368 5528 1.209621 TGGGCCACCCTAATCTGTAC 58.790 55.000 0.00 0.00 45.70 2.90
5369 5529 0.472898 GGGCCACCCTAATCTGTACC 59.527 60.000 4.39 0.00 41.34 3.34
5370 5530 1.508256 GGCCACCCTAATCTGTACCT 58.492 55.000 0.00 0.00 0.00 3.08
5371 5531 2.686119 GGCCACCCTAATCTGTACCTA 58.314 52.381 0.00 0.00 0.00 3.08
5372 5532 2.367894 GGCCACCCTAATCTGTACCTAC 59.632 54.545 0.00 0.00 0.00 3.18
5373 5533 3.306613 GCCACCCTAATCTGTACCTACT 58.693 50.000 0.00 0.00 0.00 2.57
5374 5534 4.477249 GCCACCCTAATCTGTACCTACTA 58.523 47.826 0.00 0.00 0.00 1.82
5375 5535 4.897670 GCCACCCTAATCTGTACCTACTAA 59.102 45.833 0.00 0.00 0.00 2.24
5376 5536 5.543020 GCCACCCTAATCTGTACCTACTAAT 59.457 44.000 0.00 0.00 0.00 1.73
5377 5537 6.723052 GCCACCCTAATCTGTACCTACTAATA 59.277 42.308 0.00 0.00 0.00 0.98
5378 5538 7.234166 GCCACCCTAATCTGTACCTACTAATAA 59.766 40.741 0.00 0.00 0.00 1.40
5379 5539 9.151177 CCACCCTAATCTGTACCTACTAATAAA 57.849 37.037 0.00 0.00 0.00 1.40
5381 5541 9.377238 ACCCTAATCTGTACCTACTAATAAAGG 57.623 37.037 0.00 0.00 38.93 3.11
5382 5542 9.597681 CCCTAATCTGTACCTACTAATAAAGGA 57.402 37.037 0.00 0.00 36.66 3.36
5401 5561 9.726438 ATAAAGGAAATAGGTATTCTTGATCGG 57.274 33.333 0.00 0.00 0.00 4.18
5402 5562 5.552178 AGGAAATAGGTATTCTTGATCGGC 58.448 41.667 0.00 0.00 0.00 5.54
5403 5563 4.695928 GGAAATAGGTATTCTTGATCGGCC 59.304 45.833 0.00 0.00 0.00 6.13
5404 5564 4.974645 AATAGGTATTCTTGATCGGCCA 57.025 40.909 2.24 0.00 0.00 5.36
5405 5565 5.505181 AATAGGTATTCTTGATCGGCCAT 57.495 39.130 2.24 0.00 0.00 4.40
5406 5566 6.620877 AATAGGTATTCTTGATCGGCCATA 57.379 37.500 2.24 0.00 0.00 2.74
5407 5567 4.273148 AGGTATTCTTGATCGGCCATAC 57.727 45.455 2.24 0.00 0.00 2.39
5408 5568 3.904339 AGGTATTCTTGATCGGCCATACT 59.096 43.478 2.24 0.00 0.00 2.12
5409 5569 3.997021 GGTATTCTTGATCGGCCATACTG 59.003 47.826 2.24 0.00 0.00 2.74
5410 5570 3.845781 ATTCTTGATCGGCCATACTGT 57.154 42.857 2.24 0.00 0.00 3.55
5411 5571 3.627395 TTCTTGATCGGCCATACTGTT 57.373 42.857 2.24 0.00 0.00 3.16
5412 5572 3.627395 TCTTGATCGGCCATACTGTTT 57.373 42.857 2.24 0.00 0.00 2.83
5413 5573 3.950397 TCTTGATCGGCCATACTGTTTT 58.050 40.909 2.24 0.00 0.00 2.43
5414 5574 3.689161 TCTTGATCGGCCATACTGTTTTG 59.311 43.478 2.24 0.00 0.00 2.44
5415 5575 1.742831 TGATCGGCCATACTGTTTTGC 59.257 47.619 2.24 0.00 0.00 3.68
5416 5576 1.742831 GATCGGCCATACTGTTTTGCA 59.257 47.619 2.24 0.00 0.00 4.08
5426 5586 0.932399 CTGTTTTGCAGCAAAGCACC 59.068 50.000 27.88 14.89 45.61 5.01
5427 5587 0.461693 TGTTTTGCAGCAAAGCACCC 60.462 50.000 27.88 12.84 45.61 4.61
5428 5588 0.179076 GTTTTGCAGCAAAGCACCCT 60.179 50.000 25.11 0.00 45.61 4.34
5429 5589 1.068434 GTTTTGCAGCAAAGCACCCTA 59.932 47.619 25.11 6.01 45.61 3.53
5430 5590 1.407936 TTTGCAGCAAAGCACCCTAA 58.592 45.000 16.93 0.00 45.61 2.69
5431 5591 1.631405 TTGCAGCAAAGCACCCTAAT 58.369 45.000 4.99 0.00 45.61 1.73
5432 5592 0.889994 TGCAGCAAAGCACCCTAATG 59.110 50.000 0.00 0.00 40.11 1.90
5433 5593 0.890683 GCAGCAAAGCACCCTAATGT 59.109 50.000 0.00 0.00 0.00 2.71
5434 5594 1.273327 GCAGCAAAGCACCCTAATGTT 59.727 47.619 0.00 0.00 0.00 2.71
5435 5595 2.289010 GCAGCAAAGCACCCTAATGTTT 60.289 45.455 0.00 0.00 0.00 2.83
5436 5596 3.803368 GCAGCAAAGCACCCTAATGTTTT 60.803 43.478 0.00 0.00 33.79 2.43
5437 5597 4.379652 CAGCAAAGCACCCTAATGTTTTT 58.620 39.130 0.00 0.00 31.46 1.94
5438 5598 4.211794 CAGCAAAGCACCCTAATGTTTTTG 59.788 41.667 0.00 0.00 31.46 2.44
5439 5599 3.498018 GCAAAGCACCCTAATGTTTTTGG 59.502 43.478 0.00 0.00 31.46 3.28
5440 5600 3.401033 AAGCACCCTAATGTTTTTGGC 57.599 42.857 0.00 0.00 0.00 4.52
5441 5601 2.324541 AGCACCCTAATGTTTTTGGCA 58.675 42.857 0.00 0.00 0.00 4.92
5442 5602 2.703007 AGCACCCTAATGTTTTTGGCAA 59.297 40.909 0.00 0.00 0.00 4.52
5443 5603 3.327464 AGCACCCTAATGTTTTTGGCAAT 59.673 39.130 0.00 0.00 0.00 3.56
5444 5604 3.684305 GCACCCTAATGTTTTTGGCAATC 59.316 43.478 0.00 0.00 0.00 2.67
5445 5605 4.802248 GCACCCTAATGTTTTTGGCAATCA 60.802 41.667 0.00 1.66 0.00 2.57
5446 5606 5.303971 CACCCTAATGTTTTTGGCAATCAA 58.696 37.500 0.00 0.00 0.00 2.57
5447 5607 5.179182 CACCCTAATGTTTTTGGCAATCAAC 59.821 40.000 0.00 8.24 34.67 3.18
5448 5608 4.694982 CCCTAATGTTTTTGGCAATCAACC 59.305 41.667 16.14 0.00 34.67 3.77
5449 5609 5.512921 CCCTAATGTTTTTGGCAATCAACCT 60.513 40.000 16.14 7.30 34.67 3.50
5450 5610 5.409214 CCTAATGTTTTTGGCAATCAACCTG 59.591 40.000 16.14 7.11 34.67 4.00
5451 5611 3.902881 TGTTTTTGGCAATCAACCTGT 57.097 38.095 16.14 0.00 34.67 4.00
5452 5612 5.543507 ATGTTTTTGGCAATCAACCTGTA 57.456 34.783 16.14 3.02 34.67 2.74
5453 5613 4.688021 TGTTTTTGGCAATCAACCTGTAC 58.312 39.130 16.14 0.00 34.67 2.90
5454 5614 4.404073 TGTTTTTGGCAATCAACCTGTACT 59.596 37.500 16.14 0.00 34.67 2.73
5455 5615 5.105146 TGTTTTTGGCAATCAACCTGTACTT 60.105 36.000 16.14 0.00 34.67 2.24
5456 5616 4.846779 TTTGGCAATCAACCTGTACTTC 57.153 40.909 0.00 0.00 34.67 3.01
5457 5617 3.500448 TGGCAATCAACCTGTACTTCA 57.500 42.857 0.00 0.00 0.00 3.02
5458 5618 3.411446 TGGCAATCAACCTGTACTTCAG 58.589 45.455 0.00 0.00 43.27 3.02
5459 5619 3.181445 TGGCAATCAACCTGTACTTCAGT 60.181 43.478 0.00 0.00 42.19 3.41
5460 5620 3.821033 GGCAATCAACCTGTACTTCAGTT 59.179 43.478 0.00 0.00 42.19 3.16
5461 5621 4.278419 GGCAATCAACCTGTACTTCAGTTT 59.722 41.667 0.00 0.00 42.19 2.66
5462 5622 5.221244 GGCAATCAACCTGTACTTCAGTTTT 60.221 40.000 0.00 0.00 42.19 2.43
5463 5623 6.273071 GCAATCAACCTGTACTTCAGTTTTT 58.727 36.000 0.00 0.00 42.19 1.94
5464 5624 7.422399 GCAATCAACCTGTACTTCAGTTTTTA 58.578 34.615 0.00 0.00 42.19 1.52
5465 5625 7.591426 GCAATCAACCTGTACTTCAGTTTTTAG 59.409 37.037 0.00 0.00 42.19 1.85
5466 5626 8.621286 CAATCAACCTGTACTTCAGTTTTTAGT 58.379 33.333 0.00 0.00 42.19 2.24
5467 5627 7.781548 TCAACCTGTACTTCAGTTTTTAGTC 57.218 36.000 0.00 0.00 42.19 2.59
5468 5628 7.332557 TCAACCTGTACTTCAGTTTTTAGTCA 58.667 34.615 0.00 0.00 42.19 3.41
5469 5629 7.494625 TCAACCTGTACTTCAGTTTTTAGTCAG 59.505 37.037 0.00 0.00 42.19 3.51
5470 5630 7.120923 ACCTGTACTTCAGTTTTTAGTCAGA 57.879 36.000 0.00 0.00 42.19 3.27
5471 5631 7.736893 ACCTGTACTTCAGTTTTTAGTCAGAT 58.263 34.615 0.00 0.00 42.19 2.90
5472 5632 8.211629 ACCTGTACTTCAGTTTTTAGTCAGATT 58.788 33.333 0.00 0.00 42.19 2.40
5473 5633 9.057089 CCTGTACTTCAGTTTTTAGTCAGATTT 57.943 33.333 0.00 0.00 42.19 2.17
5477 5637 8.634475 ACTTCAGTTTTTAGTCAGATTTTTGC 57.366 30.769 0.00 0.00 0.00 3.68
5478 5638 8.470002 ACTTCAGTTTTTAGTCAGATTTTTGCT 58.530 29.630 0.00 0.00 0.00 3.91
5479 5639 9.305925 CTTCAGTTTTTAGTCAGATTTTTGCTT 57.694 29.630 0.00 0.00 0.00 3.91
5480 5640 9.651913 TTCAGTTTTTAGTCAGATTTTTGCTTT 57.348 25.926 0.00 0.00 0.00 3.51
5481 5641 9.651913 TCAGTTTTTAGTCAGATTTTTGCTTTT 57.348 25.926 0.00 0.00 0.00 2.27
5482 5642 9.693157 CAGTTTTTAGTCAGATTTTTGCTTTTG 57.307 29.630 0.00 0.00 0.00 2.44
5519 5679 9.684448 TCTAATGTTTTTGTTAATCAATTCGCA 57.316 25.926 0.00 0.00 35.84 5.10
5537 5697 9.988350 CAATTCGCATATTAGTTTTAAGTCAGT 57.012 29.630 0.00 0.00 0.00 3.41
5562 5722 6.493189 TTTTTATTTTGCAGGAAACCCTCT 57.507 33.333 0.00 0.00 0.00 3.69
5563 5723 5.467035 TTTATTTTGCAGGAAACCCTCTG 57.533 39.130 0.00 0.00 0.00 3.35
5564 5724 2.746279 TTTTGCAGGAAACCCTCTGA 57.254 45.000 0.00 0.00 33.11 3.27
5565 5725 2.978156 TTTGCAGGAAACCCTCTGAT 57.022 45.000 0.00 0.00 33.11 2.90
5566 5726 4.380843 TTTTGCAGGAAACCCTCTGATA 57.619 40.909 0.00 0.00 33.11 2.15
5567 5727 4.380843 TTTGCAGGAAACCCTCTGATAA 57.619 40.909 0.00 0.00 33.11 1.75
5568 5728 4.591321 TTGCAGGAAACCCTCTGATAAT 57.409 40.909 0.00 0.00 33.11 1.28
5569 5729 4.591321 TGCAGGAAACCCTCTGATAATT 57.409 40.909 0.00 0.00 33.11 1.40
5570 5730 4.272489 TGCAGGAAACCCTCTGATAATTG 58.728 43.478 0.00 0.00 33.11 2.32
5571 5731 4.018506 TGCAGGAAACCCTCTGATAATTGA 60.019 41.667 0.00 0.00 33.11 2.57
5572 5732 4.578105 GCAGGAAACCCTCTGATAATTGAG 59.422 45.833 0.00 0.00 33.11 3.02
5573 5733 5.749462 CAGGAAACCCTCTGATAATTGAGT 58.251 41.667 0.00 0.00 33.11 3.41
5574 5734 6.183347 CAGGAAACCCTCTGATAATTGAGTT 58.817 40.000 0.00 0.00 33.11 3.01
5575 5735 7.338710 CAGGAAACCCTCTGATAATTGAGTTA 58.661 38.462 0.00 0.00 33.11 2.24
5576 5736 7.829211 CAGGAAACCCTCTGATAATTGAGTTAA 59.171 37.037 0.00 0.00 33.11 2.01
5577 5737 8.560903 AGGAAACCCTCTGATAATTGAGTTAAT 58.439 33.333 0.00 0.00 0.00 1.40
5578 5738 9.847224 GGAAACCCTCTGATAATTGAGTTAATA 57.153 33.333 0.00 0.00 0.00 0.98
5587 5747 9.438291 CTGATAATTGAGTTAATAAACTTGCGG 57.562 33.333 0.00 0.00 46.09 5.69
5588 5748 8.952278 TGATAATTGAGTTAATAAACTTGCGGT 58.048 29.630 0.00 0.00 46.09 5.68
5591 5751 7.675962 ATTGAGTTAATAAACTTGCGGTACA 57.324 32.000 0.00 0.00 46.09 2.90
5592 5752 7.675962 TTGAGTTAATAAACTTGCGGTACAT 57.324 32.000 0.00 0.00 46.09 2.29
5593 5753 8.774890 TTGAGTTAATAAACTTGCGGTACATA 57.225 30.769 0.00 0.00 46.09 2.29
5594 5754 8.951787 TGAGTTAATAAACTTGCGGTACATAT 57.048 30.769 0.00 0.00 46.09 1.78
5595 5755 9.037737 TGAGTTAATAAACTTGCGGTACATATC 57.962 33.333 0.00 0.00 46.09 1.63
5596 5756 8.951787 AGTTAATAAACTTGCGGTACATATCA 57.048 30.769 0.00 0.00 43.60 2.15
5597 5757 9.386010 AGTTAATAAACTTGCGGTACATATCAA 57.614 29.630 0.00 0.00 43.60 2.57
5598 5758 9.991388 GTTAATAAACTTGCGGTACATATCAAA 57.009 29.630 0.00 0.00 32.54 2.69
5601 5761 9.730420 AATAAACTTGCGGTACATATCAAATTC 57.270 29.630 0.00 0.00 0.00 2.17
5602 5762 7.391148 AAACTTGCGGTACATATCAAATTCT 57.609 32.000 0.00 0.00 0.00 2.40
5603 5763 7.391148 AACTTGCGGTACATATCAAATTCTT 57.609 32.000 0.00 0.00 0.00 2.52
5604 5764 7.391148 ACTTGCGGTACATATCAAATTCTTT 57.609 32.000 0.00 0.00 0.00 2.52
5605 5765 7.826690 ACTTGCGGTACATATCAAATTCTTTT 58.173 30.769 0.00 0.00 0.00 2.27
5606 5766 8.303876 ACTTGCGGTACATATCAAATTCTTTTT 58.696 29.630 0.00 0.00 0.00 1.94
5607 5767 9.781834 CTTGCGGTACATATCAAATTCTTTTTA 57.218 29.630 0.00 0.00 0.00 1.52
5684 5844 9.874205 ATATGGAATTTGATTCGAAAAATGTGT 57.126 25.926 0.00 0.00 40.17 3.72
5686 5846 8.741101 TGGAATTTGATTCGAAAAATGTGTAG 57.259 30.769 0.00 0.00 40.17 2.74
5687 5847 8.572185 TGGAATTTGATTCGAAAAATGTGTAGA 58.428 29.630 0.00 0.00 40.17 2.59
5688 5848 9.405587 GGAATTTGATTCGAAAAATGTGTAGAA 57.594 29.630 0.00 0.00 40.17 2.10
5692 5852 9.611284 TTTGATTCGAAAAATGTGTAGAATCTG 57.389 29.630 0.00 0.00 42.37 2.90
5693 5853 8.546597 TGATTCGAAAAATGTGTAGAATCTGA 57.453 30.769 0.00 0.00 42.37 3.27
5694 5854 8.998377 TGATTCGAAAAATGTGTAGAATCTGAA 58.002 29.630 0.00 0.00 42.37 3.02
5695 5855 9.994432 GATTCGAAAAATGTGTAGAATCTGAAT 57.006 29.630 0.00 0.00 40.17 2.57
5778 5938 9.623000 AGGGTGTAACTTTAATAAATAGCGAAT 57.377 29.630 0.00 0.00 36.74 3.34
5779 5939 9.659830 GGGTGTAACTTTAATAAATAGCGAATG 57.340 33.333 0.00 0.00 36.74 2.67
5785 5945 8.603242 ACTTTAATAAATAGCGAATGATCCGT 57.397 30.769 0.00 0.00 0.00 4.69
5786 5946 9.052759 ACTTTAATAAATAGCGAATGATCCGTT 57.947 29.630 0.00 0.00 0.00 4.44
5787 5947 9.878599 CTTTAATAAATAGCGAATGATCCGTTT 57.121 29.630 0.00 0.00 0.00 3.60
5790 5950 8.782533 AATAAATAGCGAATGATCCGTTTTTC 57.217 30.769 0.00 0.00 0.00 2.29
5791 5951 6.436843 AAATAGCGAATGATCCGTTTTTCT 57.563 33.333 0.00 0.00 0.00 2.52
5792 5952 6.436843 AATAGCGAATGATCCGTTTTTCTT 57.563 33.333 0.00 0.00 0.00 2.52
5793 5953 4.766404 AGCGAATGATCCGTTTTTCTTT 57.234 36.364 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.242047 TTGTTGTTCCGTCGATTCCA 57.758 45.000 0.00 0.00 0.00 3.53
62 63 4.557690 CGTCGTCTTTCTGTCGATATGTTT 59.442 41.667 0.00 0.00 38.34 2.83
69 70 1.459975 CTCTCGTCGTCTTTCTGTCGA 59.540 52.381 0.00 0.00 34.21 4.20
71 72 1.536331 ACCTCTCGTCGTCTTTCTGTC 59.464 52.381 0.00 0.00 0.00 3.51
166 167 2.279120 CTCATCTCCGCTCACCGC 60.279 66.667 0.00 0.00 35.03 5.68
196 197 1.714794 CGATTTCTGTGCGTCCTCTT 58.285 50.000 0.00 0.00 0.00 2.85
213 214 1.299648 CCCATCCACCAAGAAGCGA 59.700 57.895 0.00 0.00 0.00 4.93
216 217 3.181526 GAGCCCATCCACCAAGAAG 57.818 57.895 0.00 0.00 0.00 2.85
253 254 3.112709 GAGGCCTTCACGACACGC 61.113 66.667 6.77 0.00 0.00 5.34
400 401 2.426381 ACGTTATCGACTCTTCTTCCCC 59.574 50.000 0.00 0.00 40.62 4.81
439 440 2.358957 CTCTCATTCCAAATCACGCCA 58.641 47.619 0.00 0.00 0.00 5.69
461 462 2.447250 CTTCGAAACGTATCTAGCGCA 58.553 47.619 11.47 0.00 0.00 6.09
484 485 3.763897 AGCAAGTGAAGTGGAAAACTGTT 59.236 39.130 0.00 0.00 39.81 3.16
487 488 3.620488 TGAGCAAGTGAAGTGGAAAACT 58.380 40.909 0.00 0.00 42.60 2.66
497 498 2.224079 GCACGAATCTTGAGCAAGTGAA 59.776 45.455 9.79 0.00 39.38 3.18
498 499 1.800586 GCACGAATCTTGAGCAAGTGA 59.199 47.619 9.79 0.00 39.38 3.41
499 500 1.463034 CGCACGAATCTTGAGCAAGTG 60.463 52.381 9.79 3.26 39.38 3.16
500 501 0.792640 CGCACGAATCTTGAGCAAGT 59.207 50.000 9.79 0.00 39.38 3.16
501 502 1.070821 TCGCACGAATCTTGAGCAAG 58.929 50.000 3.87 3.87 39.71 4.01
502 503 1.460743 CTTCGCACGAATCTTGAGCAA 59.539 47.619 5.87 0.00 33.28 3.91
503 504 1.070821 CTTCGCACGAATCTTGAGCA 58.929 50.000 5.87 0.00 33.28 4.26
504 505 0.247458 GCTTCGCACGAATCTTGAGC 60.247 55.000 5.87 1.19 33.28 4.26
505 506 1.070821 TGCTTCGCACGAATCTTGAG 58.929 50.000 5.87 0.00 31.71 3.02
594 610 6.843711 CGAATTCGTTTGATACTCTAACTCG 58.156 40.000 19.67 0.00 31.54 4.18
614 630 3.791973 TTTTTGTGCCACAAGACGAAT 57.208 38.095 10.58 0.00 39.53 3.34
666 682 7.293535 AGGGCATCTCTAACTCAACCTAAATAT 59.706 37.037 0.00 0.00 0.00 1.28
717 763 4.324267 GGAGTAAGTTTTTGCTGCTAGGA 58.676 43.478 0.00 0.00 35.14 2.94
744 791 8.220755 TGTCAAAAAGGTCTAATATATGGCAC 57.779 34.615 0.00 0.00 0.00 5.01
745 792 8.995027 ATGTCAAAAAGGTCTAATATATGGCA 57.005 30.769 0.00 0.00 0.00 4.92
807 854 7.536895 AGTAGATGCCGTATAGTACTATTCG 57.463 40.000 26.19 26.19 36.51 3.34
810 857 7.881751 TGACAAGTAGATGCCGTATAGTACTAT 59.118 37.037 19.07 19.07 0.00 2.12
822 869 3.999663 GGATGCTATGACAAGTAGATGCC 59.000 47.826 0.00 0.00 0.00 4.40
839 886 1.523154 TTTGGTGCTTGGACGGATGC 61.523 55.000 0.00 0.00 0.00 3.91
863 910 3.370104 ACCATGGTTCTTGGTTTGTTGA 58.630 40.909 13.00 0.00 45.19 3.18
886 933 2.299013 CCCGCATGTTATACCTAGCAGA 59.701 50.000 0.00 0.00 0.00 4.26
887 934 2.612972 CCCCGCATGTTATACCTAGCAG 60.613 54.545 0.00 0.00 0.00 4.24
904 951 0.748005 AATTGCCAGTCGATTCCCCG 60.748 55.000 0.00 0.00 0.00 5.73
956 1003 4.730487 GCACTTGCCCTCTGTGAT 57.270 55.556 0.00 0.00 33.95 3.06
1463 1510 6.585695 TCAACTACAGTTCTTAGTTCCGAT 57.414 37.500 0.00 0.00 37.62 4.18
1735 1787 7.114811 GCACATGTTTTGTCATTAACCTAACAG 59.885 37.037 0.00 0.00 36.00 3.16
1949 2002 4.832608 GTTAGCGTCCTGGCCCCG 62.833 72.222 0.00 0.00 0.00 5.73
2019 2072 6.157994 TGTGTAGCCTCCCTATTATTTCTGTT 59.842 38.462 0.00 0.00 0.00 3.16
2094 2147 7.515684 GCTTAAGATTTGTGCAAGTTTTCTGTG 60.516 37.037 6.67 0.00 0.00 3.66
2164 2219 0.944386 AGCCACGTTGCAACTACTTG 59.056 50.000 26.09 16.61 0.00 3.16
2177 2232 2.643551 ACAATGGGATTTAGAGCCACG 58.356 47.619 0.00 0.00 31.14 4.94
2209 2264 5.278604 AGCTAAATTTGTTGTTGGTTCGAC 58.721 37.500 0.00 0.00 0.00 4.20
2338 2409 5.240623 TCCACACATATCAAAGTCAACCAAC 59.759 40.000 0.00 0.00 0.00 3.77
2366 2437 2.877786 ACACAAACACGATCATGCAGAA 59.122 40.909 0.00 0.00 0.00 3.02
2408 2479 1.204941 GCTCCGAGTGAGTTGTACCAT 59.795 52.381 0.00 0.00 43.48 3.55
2482 2553 4.646492 ACCTTGCCCACTTATGAATCAATC 59.354 41.667 0.00 0.00 0.00 2.67
2506 2577 0.823356 GCCCCACGCCAACATCATAT 60.823 55.000 0.00 0.00 0.00 1.78
2540 2611 6.403866 TGCATGTAGGAACAATTTTCTGTT 57.596 33.333 0.00 0.00 42.23 3.16
2686 2757 7.275779 TGAACATTTAAAAGCAAACAAACGCTA 59.724 29.630 0.00 0.00 37.54 4.26
2957 3053 8.234546 CCAACATAGTGTGGTGTTTAGATTTAC 58.765 37.037 4.07 0.00 44.32 2.01
3058 3154 6.258230 TGTGATTTAGGACAGATTTTGCAG 57.742 37.500 0.00 0.00 0.00 4.41
3186 3282 8.977505 CAAAATCCGTCTGTTTCACAAATTAAT 58.022 29.630 0.00 0.00 0.00 1.40
3375 3472 2.093152 GTCAACGCAACACTATAACCGG 59.907 50.000 0.00 0.00 0.00 5.28
3415 3512 1.136828 ACCTGTTACTTCTGCCCACA 58.863 50.000 0.00 0.00 0.00 4.17
3473 3570 8.298854 ACTGTATCACGTTTAGTTGTGTGTATA 58.701 33.333 0.00 0.00 37.38 1.47
3634 3736 7.468922 AATTCAGCAAAGCTAAAAACAGAAC 57.531 32.000 0.00 0.00 36.40 3.01
3636 3738 7.981225 AGAAAATTCAGCAAAGCTAAAAACAGA 59.019 29.630 0.00 0.00 36.40 3.41
3687 3789 6.411376 TGAACAAAGTGACAGAGAAAAGGTA 58.589 36.000 0.00 0.00 0.00 3.08
3709 3811 5.888691 ACATAATGCAACCGTTGTTATGA 57.111 34.783 26.18 12.66 35.16 2.15
3758 3860 9.853555 ATCGCAATAAATCAGAACAAACATTAA 57.146 25.926 0.00 0.00 0.00 1.40
4008 4110 2.936919 TGGCCTATCCATGTGTCATC 57.063 50.000 3.32 0.00 40.72 2.92
4033 4135 1.871772 CTGCAAGGTTCTTCGCAGG 59.128 57.895 16.67 6.07 46.37 4.85
4181 4283 4.012374 CAAGAAGCCATGTATCACCAAGT 58.988 43.478 0.00 0.00 0.00 3.16
4590 4692 1.909700 TTCCACATCCTCTTTGCCAC 58.090 50.000 0.00 0.00 0.00 5.01
4945 5047 5.292589 CCAAATTGTGGCAGCTGAAATTATC 59.707 40.000 20.43 0.00 41.72 1.75
5199 5304 6.017523 GCATACTAATCCTTCTTTTCAGAGCC 60.018 42.308 0.00 0.00 0.00 4.70
5203 5308 5.277538 GGCGCATACTAATCCTTCTTTTCAG 60.278 44.000 10.83 0.00 0.00 3.02
5304 5464 1.290203 CATAACATGCTCCTCGCGTT 58.710 50.000 5.77 0.00 43.27 4.84
5321 5481 5.012239 ACCATAATGAGCACAGTTCAACAT 58.988 37.500 0.00 0.00 0.00 2.71
5333 5493 1.678101 GCCCAAGACACCATAATGAGC 59.322 52.381 0.00 0.00 0.00 4.26
5334 5494 2.301346 GGCCCAAGACACCATAATGAG 58.699 52.381 0.00 0.00 0.00 2.90
5335 5495 1.638070 TGGCCCAAGACACCATAATGA 59.362 47.619 0.00 0.00 0.00 2.57
5336 5496 1.750778 GTGGCCCAAGACACCATAATG 59.249 52.381 0.00 0.00 35.53 1.90
5337 5497 2.143876 GTGGCCCAAGACACCATAAT 57.856 50.000 0.00 0.00 35.53 1.28
5338 5498 3.662290 GTGGCCCAAGACACCATAA 57.338 52.632 0.00 0.00 35.53 1.90
5350 5510 0.472898 GGTACAGATTAGGGTGGCCC 59.527 60.000 0.00 0.00 45.90 5.80
5351 5511 1.508256 AGGTACAGATTAGGGTGGCC 58.492 55.000 0.00 0.00 0.00 5.36
5352 5512 3.306613 AGTAGGTACAGATTAGGGTGGC 58.693 50.000 0.00 0.00 0.00 5.01
5353 5513 8.716674 TTATTAGTAGGTACAGATTAGGGTGG 57.283 38.462 0.00 0.00 0.00 4.61
5355 5515 9.377238 CCTTTATTAGTAGGTACAGATTAGGGT 57.623 37.037 0.00 0.00 0.00 4.34
5356 5516 9.597681 TCCTTTATTAGTAGGTACAGATTAGGG 57.402 37.037 0.00 0.00 33.15 3.53
5375 5535 9.726438 CCGATCAAGAATACCTATTTCCTTTAT 57.274 33.333 0.00 0.00 0.00 1.40
5376 5536 7.660208 GCCGATCAAGAATACCTATTTCCTTTA 59.340 37.037 0.00 0.00 0.00 1.85
5377 5537 6.486993 GCCGATCAAGAATACCTATTTCCTTT 59.513 38.462 0.00 0.00 0.00 3.11
5378 5538 5.998363 GCCGATCAAGAATACCTATTTCCTT 59.002 40.000 0.00 0.00 0.00 3.36
5379 5539 5.513267 GGCCGATCAAGAATACCTATTTCCT 60.513 44.000 0.00 0.00 0.00 3.36
5380 5540 4.695928 GGCCGATCAAGAATACCTATTTCC 59.304 45.833 0.00 0.00 0.00 3.13
5381 5541 5.305585 TGGCCGATCAAGAATACCTATTTC 58.694 41.667 0.00 0.00 0.00 2.17
5382 5542 5.304686 TGGCCGATCAAGAATACCTATTT 57.695 39.130 0.00 0.00 0.00 1.40
5383 5543 4.974645 TGGCCGATCAAGAATACCTATT 57.025 40.909 0.00 0.00 0.00 1.73
5384 5544 5.721960 AGTATGGCCGATCAAGAATACCTAT 59.278 40.000 0.00 0.00 0.00 2.57
5385 5545 5.047306 CAGTATGGCCGATCAAGAATACCTA 60.047 44.000 0.00 0.00 0.00 3.08
5386 5546 3.904339 AGTATGGCCGATCAAGAATACCT 59.096 43.478 0.00 0.00 0.00 3.08
5387 5547 3.997021 CAGTATGGCCGATCAAGAATACC 59.003 47.826 0.00 0.00 0.00 2.73
5388 5548 4.632153 ACAGTATGGCCGATCAAGAATAC 58.368 43.478 0.00 0.00 43.62 1.89
5389 5549 4.955811 ACAGTATGGCCGATCAAGAATA 57.044 40.909 0.00 0.00 43.62 1.75
5390 5550 3.845781 ACAGTATGGCCGATCAAGAAT 57.154 42.857 0.00 0.00 43.62 2.40
5391 5551 3.627395 AACAGTATGGCCGATCAAGAA 57.373 42.857 0.00 0.00 43.62 2.52
5392 5552 3.627395 AAACAGTATGGCCGATCAAGA 57.373 42.857 0.00 0.00 43.62 3.02
5393 5553 3.731867 GCAAAACAGTATGGCCGATCAAG 60.732 47.826 0.00 0.00 43.62 3.02
5394 5554 2.163412 GCAAAACAGTATGGCCGATCAA 59.837 45.455 0.00 0.00 43.62 2.57
5395 5555 1.742831 GCAAAACAGTATGGCCGATCA 59.257 47.619 0.00 0.00 43.62 2.92
5396 5556 1.742831 TGCAAAACAGTATGGCCGATC 59.257 47.619 0.00 0.00 43.62 3.69
5397 5557 1.745087 CTGCAAAACAGTATGGCCGAT 59.255 47.619 0.00 0.00 43.62 4.18
5398 5558 1.164411 CTGCAAAACAGTATGGCCGA 58.836 50.000 0.00 0.00 43.62 5.54
5399 5559 3.700577 CTGCAAAACAGTATGGCCG 57.299 52.632 0.00 0.00 43.62 6.13
5408 5568 0.461693 GGGTGCTTTGCTGCAAAACA 60.462 50.000 25.93 24.42 45.12 2.83
5409 5569 0.179076 AGGGTGCTTTGCTGCAAAAC 60.179 50.000 25.93 22.28 45.12 2.43
5410 5570 1.407936 TAGGGTGCTTTGCTGCAAAA 58.592 45.000 25.93 11.83 45.12 2.44
5411 5571 1.407936 TTAGGGTGCTTTGCTGCAAA 58.592 45.000 24.68 24.68 45.12 3.68
5412 5572 1.273048 CATTAGGGTGCTTTGCTGCAA 59.727 47.619 11.69 11.69 45.12 4.08
5413 5573 0.889994 CATTAGGGTGCTTTGCTGCA 59.110 50.000 0.00 0.00 41.05 4.41
5414 5574 0.890683 ACATTAGGGTGCTTTGCTGC 59.109 50.000 0.00 0.00 0.00 5.25
5415 5575 3.665745 AAACATTAGGGTGCTTTGCTG 57.334 42.857 0.00 0.00 0.00 4.41
5416 5576 4.379652 CAAAAACATTAGGGTGCTTTGCT 58.620 39.130 0.00 0.00 0.00 3.91
5417 5577 3.498018 CCAAAAACATTAGGGTGCTTTGC 59.502 43.478 0.00 0.00 30.09 3.68
5418 5578 3.498018 GCCAAAAACATTAGGGTGCTTTG 59.502 43.478 0.00 0.00 0.00 2.77
5419 5579 3.135530 TGCCAAAAACATTAGGGTGCTTT 59.864 39.130 0.00 0.00 0.00 3.51
5420 5580 2.703007 TGCCAAAAACATTAGGGTGCTT 59.297 40.909 0.00 0.00 0.00 3.91
5421 5581 2.324541 TGCCAAAAACATTAGGGTGCT 58.675 42.857 0.00 0.00 0.00 4.40
5422 5582 2.829741 TGCCAAAAACATTAGGGTGC 57.170 45.000 0.00 0.00 0.00 5.01
5423 5583 4.892433 TGATTGCCAAAAACATTAGGGTG 58.108 39.130 0.00 0.00 0.00 4.61
5424 5584 5.304778 GTTGATTGCCAAAAACATTAGGGT 58.695 37.500 2.49 0.00 36.36 4.34
5425 5585 4.694982 GGTTGATTGCCAAAAACATTAGGG 59.305 41.667 8.17 0.00 36.36 3.53
5426 5586 5.409214 CAGGTTGATTGCCAAAAACATTAGG 59.591 40.000 8.17 0.00 36.36 2.69
5427 5587 5.990996 ACAGGTTGATTGCCAAAAACATTAG 59.009 36.000 8.17 0.00 36.36 1.73
5428 5588 5.923204 ACAGGTTGATTGCCAAAAACATTA 58.077 33.333 8.17 0.00 36.36 1.90
5429 5589 4.779696 ACAGGTTGATTGCCAAAAACATT 58.220 34.783 8.17 0.00 36.36 2.71
5430 5590 4.420522 ACAGGTTGATTGCCAAAAACAT 57.579 36.364 8.17 0.00 36.36 2.71
5431 5591 3.902881 ACAGGTTGATTGCCAAAAACA 57.097 38.095 8.17 0.00 36.36 2.83
5432 5592 4.944048 AGTACAGGTTGATTGCCAAAAAC 58.056 39.130 0.00 0.00 36.36 2.43
5433 5593 5.127845 TGAAGTACAGGTTGATTGCCAAAAA 59.872 36.000 0.00 0.00 36.36 1.94
5434 5594 4.646945 TGAAGTACAGGTTGATTGCCAAAA 59.353 37.500 0.00 0.00 36.36 2.44
5435 5595 4.211125 TGAAGTACAGGTTGATTGCCAAA 58.789 39.130 0.00 0.00 36.36 3.28
5436 5596 3.820467 CTGAAGTACAGGTTGATTGCCAA 59.180 43.478 0.00 0.00 42.39 4.52
5437 5597 3.411446 CTGAAGTACAGGTTGATTGCCA 58.589 45.455 0.00 0.00 42.39 4.92
5438 5598 3.821033 AACTGAAGTACAGGTTGATTGCC 59.179 43.478 0.00 0.00 45.14 4.52
5451 5611 9.730420 GCAAAAATCTGACTAAAAACTGAAGTA 57.270 29.630 0.00 0.00 0.00 2.24
5452 5612 8.470002 AGCAAAAATCTGACTAAAAACTGAAGT 58.530 29.630 0.00 0.00 0.00 3.01
5453 5613 8.862550 AGCAAAAATCTGACTAAAAACTGAAG 57.137 30.769 0.00 0.00 0.00 3.02
5454 5614 9.651913 AAAGCAAAAATCTGACTAAAAACTGAA 57.348 25.926 0.00 0.00 0.00 3.02
5455 5615 9.651913 AAAAGCAAAAATCTGACTAAAAACTGA 57.348 25.926 0.00 0.00 0.00 3.41
5456 5616 9.693157 CAAAAGCAAAAATCTGACTAAAAACTG 57.307 29.630 0.00 0.00 0.00 3.16
5457 5617 8.390354 GCAAAAGCAAAAATCTGACTAAAAACT 58.610 29.630 0.00 0.00 0.00 2.66
5458 5618 8.174422 TGCAAAAGCAAAAATCTGACTAAAAAC 58.826 29.630 0.00 0.00 0.00 2.43
5459 5619 8.261492 TGCAAAAGCAAAAATCTGACTAAAAA 57.739 26.923 0.00 0.00 0.00 1.94
5460 5620 7.840342 TGCAAAAGCAAAAATCTGACTAAAA 57.160 28.000 0.00 0.00 0.00 1.52
5461 5621 9.539825 TTATGCAAAAGCAAAAATCTGACTAAA 57.460 25.926 0.00 0.00 0.00 1.85
5462 5622 9.539825 TTTATGCAAAAGCAAAAATCTGACTAA 57.460 25.926 0.00 0.00 0.00 2.24
5463 5623 9.539825 TTTTATGCAAAAGCAAAAATCTGACTA 57.460 25.926 0.00 0.00 0.00 2.59
5464 5624 8.436046 TTTTATGCAAAAGCAAAAATCTGACT 57.564 26.923 0.00 0.00 0.00 3.41
5465 5625 9.667989 AATTTTATGCAAAAGCAAAAATCTGAC 57.332 25.926 16.11 0.00 37.08 3.51
5466 5626 9.881529 GAATTTTATGCAAAAGCAAAAATCTGA 57.118 25.926 16.11 0.00 37.08 3.27
5467 5627 9.887406 AGAATTTTATGCAAAAGCAAAAATCTG 57.113 25.926 16.11 0.00 37.08 2.90
5474 5634 9.709495 ACATTAGAGAATTTTATGCAAAAGCAA 57.291 25.926 0.00 0.00 37.08 3.91
5475 5635 9.709495 AACATTAGAGAATTTTATGCAAAAGCA 57.291 25.926 0.00 0.00 37.08 3.91
5493 5653 9.684448 TGCGAATTGATTAACAAAAACATTAGA 57.316 25.926 0.00 0.00 42.03 2.10
5511 5671 9.988350 ACTGACTTAAAACTAATATGCGAATTG 57.012 29.630 0.00 0.00 0.00 2.32
5539 5699 6.098982 TCAGAGGGTTTCCTGCAAAATAAAAA 59.901 34.615 0.00 0.00 45.05 1.94
5540 5700 5.600484 TCAGAGGGTTTCCTGCAAAATAAAA 59.400 36.000 0.00 0.00 45.05 1.52
5541 5701 5.144100 TCAGAGGGTTTCCTGCAAAATAAA 58.856 37.500 0.00 0.00 45.05 1.40
5542 5702 4.735369 TCAGAGGGTTTCCTGCAAAATAA 58.265 39.130 0.00 0.00 45.05 1.40
5543 5703 4.380843 TCAGAGGGTTTCCTGCAAAATA 57.619 40.909 0.00 0.00 45.05 1.40
5544 5704 3.243359 TCAGAGGGTTTCCTGCAAAAT 57.757 42.857 0.00 0.00 45.05 1.82
5545 5705 2.746279 TCAGAGGGTTTCCTGCAAAA 57.254 45.000 0.00 0.00 45.05 2.44
5546 5706 2.978156 ATCAGAGGGTTTCCTGCAAA 57.022 45.000 0.00 0.00 45.05 3.68
5547 5707 4.591321 ATTATCAGAGGGTTTCCTGCAA 57.409 40.909 0.00 0.00 45.05 4.08
5548 5708 4.018506 TCAATTATCAGAGGGTTTCCTGCA 60.019 41.667 0.00 0.00 45.05 4.41
5549 5709 4.526970 TCAATTATCAGAGGGTTTCCTGC 58.473 43.478 0.00 0.00 45.05 4.85
5550 5710 5.749462 ACTCAATTATCAGAGGGTTTCCTG 58.251 41.667 0.00 0.00 45.05 3.86
5552 5712 8.753497 ATTAACTCAATTATCAGAGGGTTTCC 57.247 34.615 0.00 0.00 36.20 3.13
5561 5721 9.438291 CCGCAAGTTTATTAACTCAATTATCAG 57.562 33.333 0.00 0.00 43.74 2.90
5562 5722 8.952278 ACCGCAAGTTTATTAACTCAATTATCA 58.048 29.630 0.00 0.00 43.74 2.15
5565 5725 9.217278 TGTACCGCAAGTTTATTAACTCAATTA 57.783 29.630 0.00 0.00 43.74 1.40
5566 5726 8.101654 TGTACCGCAAGTTTATTAACTCAATT 57.898 30.769 0.00 0.00 43.74 2.32
5567 5727 7.675962 TGTACCGCAAGTTTATTAACTCAAT 57.324 32.000 0.00 0.00 43.74 2.57
5568 5728 7.675962 ATGTACCGCAAGTTTATTAACTCAA 57.324 32.000 0.00 0.00 43.74 3.02
5569 5729 8.951787 ATATGTACCGCAAGTTTATTAACTCA 57.048 30.769 0.00 0.00 43.74 3.41
5570 5730 9.037737 TGATATGTACCGCAAGTTTATTAACTC 57.962 33.333 0.00 0.00 43.74 3.01
5571 5731 8.951787 TGATATGTACCGCAAGTTTATTAACT 57.048 30.769 0.00 0.00 46.44 2.24
5572 5732 9.991388 TTTGATATGTACCGCAAGTTTATTAAC 57.009 29.630 0.00 0.00 34.36 2.01
5575 5735 9.730420 GAATTTGATATGTACCGCAAGTTTATT 57.270 29.630 0.00 0.00 0.00 1.40
5576 5736 9.120538 AGAATTTGATATGTACCGCAAGTTTAT 57.879 29.630 0.00 0.00 0.00 1.40
5577 5737 8.500753 AGAATTTGATATGTACCGCAAGTTTA 57.499 30.769 0.00 0.00 0.00 2.01
5578 5738 7.391148 AGAATTTGATATGTACCGCAAGTTT 57.609 32.000 0.00 0.00 0.00 2.66
5579 5739 7.391148 AAGAATTTGATATGTACCGCAAGTT 57.609 32.000 0.00 0.00 0.00 2.66
5580 5740 7.391148 AAAGAATTTGATATGTACCGCAAGT 57.609 32.000 0.00 0.00 36.60 3.16
5581 5741 8.687824 AAAAAGAATTTGATATGTACCGCAAG 57.312 30.769 0.00 0.00 39.02 4.01
5658 5818 9.874205 ACACATTTTTCGAATCAAATTCCATAT 57.126 25.926 0.00 0.00 35.89 1.78
5660 5820 9.357652 CTACACATTTTTCGAATCAAATTCCAT 57.642 29.630 0.00 0.00 35.89 3.41
5661 5821 8.572185 TCTACACATTTTTCGAATCAAATTCCA 58.428 29.630 0.00 0.00 35.89 3.53
5662 5822 8.964420 TCTACACATTTTTCGAATCAAATTCC 57.036 30.769 0.00 0.00 35.89 3.01
5666 5826 9.611284 CAGATTCTACACATTTTTCGAATCAAA 57.389 29.630 0.00 0.00 39.25 2.69
5667 5827 8.998377 TCAGATTCTACACATTTTTCGAATCAA 58.002 29.630 0.00 0.00 39.25 2.57
5668 5828 8.546597 TCAGATTCTACACATTTTTCGAATCA 57.453 30.769 0.00 0.00 39.25 2.57
5669 5829 9.994432 ATTCAGATTCTACACATTTTTCGAATC 57.006 29.630 0.00 0.00 37.87 2.52
5752 5912 9.623000 ATTCGCTATTTATTAAAGTTACACCCT 57.377 29.630 0.00 0.00 0.00 4.34
5753 5913 9.659830 CATTCGCTATTTATTAAAGTTACACCC 57.340 33.333 0.00 0.00 0.00 4.61
5759 5919 9.052759 ACGGATCATTCGCTATTTATTAAAGTT 57.947 29.630 0.00 0.00 0.00 2.66
5760 5920 8.603242 ACGGATCATTCGCTATTTATTAAAGT 57.397 30.769 0.00 0.00 0.00 2.66
5761 5921 9.878599 AAACGGATCATTCGCTATTTATTAAAG 57.121 29.630 0.00 0.00 0.00 1.85
5764 5924 9.872757 GAAAAACGGATCATTCGCTATTTATTA 57.127 29.630 0.00 0.00 0.00 0.98
5765 5925 8.621286 AGAAAAACGGATCATTCGCTATTTATT 58.379 29.630 0.00 0.00 0.00 1.40
5766 5926 8.154649 AGAAAAACGGATCATTCGCTATTTAT 57.845 30.769 0.00 0.00 0.00 1.40
5767 5927 7.548196 AGAAAAACGGATCATTCGCTATTTA 57.452 32.000 0.00 0.00 0.00 1.40
5768 5928 6.436843 AGAAAAACGGATCATTCGCTATTT 57.563 33.333 0.00 0.00 0.00 1.40
5769 5929 6.436843 AAGAAAAACGGATCATTCGCTATT 57.563 33.333 0.00 0.00 0.00 1.73
5770 5930 6.436843 AAAGAAAAACGGATCATTCGCTAT 57.563 33.333 0.00 0.00 0.00 2.97
5771 5931 5.873179 AAAGAAAAACGGATCATTCGCTA 57.127 34.783 0.00 0.00 0.00 4.26
5772 5932 4.766404 AAAGAAAAACGGATCATTCGCT 57.234 36.364 0.00 0.00 0.00 4.93


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

AutoCloner maintained by Alex Coulton.