Multiple sequence alignment - TraesCS6D01G205100

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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 TraesCS6D01G205100 chr6D 100.000 7399 0 0 1 7399 291141583 291148981 0.000000e+00 13664.0
1 TraesCS6D01G205100 chr6D 81.395 258 46 2 2838 3094 172118062 172117806 7.520000e-50 209.0
2 TraesCS6D01G205100 chr6B 95.536 3965 108 28 2865 6812 451931557 451927645 0.000000e+00 6277.0
3 TraesCS6D01G205100 chr6B 94.057 1935 58 19 84 2008 451934422 451932535 0.000000e+00 2883.0
4 TraesCS6D01G205100 chr6B 91.208 853 57 8 2026 2878 451932406 451931572 0.000000e+00 1144.0
5 TraesCS6D01G205100 chr6B 96.899 129 4 0 6844 6972 451927645 451927517 4.500000e-52 217.0
6 TraesCS6D01G205100 chr6B 93.617 141 7 1 7259 7399 451927410 451927272 7.520000e-50 209.0
7 TraesCS6D01G205100 chr6B 95.556 90 4 0 7120 7209 451927496 451927407 2.150000e-30 145.0
8 TraesCS6D01G205100 chr6A 94.432 2263 74 17 631 2878 432525501 432523276 0.000000e+00 3434.0
9 TraesCS6D01G205100 chr6A 93.720 1640 49 16 2865 4487 432523261 432521659 0.000000e+00 2409.0
10 TraesCS6D01G205100 chr6A 95.652 1334 54 3 4516 5847 432521661 432520330 0.000000e+00 2139.0
11 TraesCS6D01G205100 chr6A 94.310 1160 33 12 5851 7008 432520215 432519087 0.000000e+00 1746.0
12 TraesCS6D01G205100 chr6A 89.126 469 20 13 105 569 432526215 432525774 8.390000e-154 555.0
13 TraesCS6D01G205100 chr6A 97.021 235 6 1 7165 7399 432513889 432513656 1.930000e-105 394.0
14 TraesCS6D01G205100 chr6A 82.824 262 34 8 2837 3092 606785644 606785388 2.690000e-54 224.0
15 TraesCS6D01G205100 chr6A 85.577 208 26 4 2865 3071 173428894 173429098 1.620000e-51 215.0
16 TraesCS6D01G205100 chr6A 95.918 98 4 0 2 99 432526459 432526362 7.680000e-35 159.0
17 TraesCS6D01G205100 chr6A 96.000 50 2 0 7120 7169 432519090 432519041 1.710000e-11 82.4
18 TraesCS6D01G205100 chr3A 86.161 224 25 6 2868 3089 620769899 620769680 3.450000e-58 237.0
19 TraesCS6D01G205100 chr3A 86.957 69 7 2 6940 7007 78190610 78190543 7.960000e-10 76.8
20 TraesCS6D01G205100 chr3D 85.714 224 27 5 2868 3089 477254298 477254078 1.610000e-56 231.0
21 TraesCS6D01G205100 chr3D 86.957 69 6 3 6940 7007 67062996 67062930 2.860000e-09 75.0
22 TraesCS6D01G205100 chr7D 81.227 277 38 11 2838 3108 408019846 408020114 2.090000e-50 211.0
23 TraesCS6D01G205100 chr5D 83.404 235 24 10 2853 3082 135661055 135660831 3.500000e-48 204.0
24 TraesCS6D01G205100 chrUn 95.798 119 5 0 7005 7123 82049479 82049597 7.580000e-45 193.0
25 TraesCS6D01G205100 chr5B 95.798 119 5 0 7004 7122 711834030 711834148 7.580000e-45 193.0
26 TraesCS6D01G205100 chr5B 93.651 126 6 2 6998 7122 450504143 450504267 3.520000e-43 187.0
27 TraesCS6D01G205100 chr1D 95.833 120 3 2 7004 7121 298558571 298558690 7.580000e-45 193.0
28 TraesCS6D01G205100 chr7B 94.309 123 7 0 7001 7123 573939304 573939182 9.800000e-44 189.0
29 TraesCS6D01G205100 chr7B 94.309 123 7 0 7001 7123 573954943 573954821 9.800000e-44 189.0
30 TraesCS6D01G205100 chr3B 93.600 125 8 0 7005 7129 98078124 98078000 3.520000e-43 187.0
31 TraesCS6D01G205100 chr3B 92.366 131 10 0 6992 7122 792568541 792568671 3.520000e-43 187.0
32 TraesCS6D01G205100 chr3B 86.957 69 7 2 6940 7007 111853565 111853498 7.960000e-10 76.8
33 TraesCS6D01G205100 chr4B 91.111 135 10 2 7005 7138 9944460 9944327 1.640000e-41 182.0


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 TraesCS6D01G205100 chr6D 291141583 291148981 7398 False 13664.000000 13664 100.000000 1 7399 1 chr6D.!!$F1 7398
1 TraesCS6D01G205100 chr6B 451927272 451934422 7150 True 1812.500000 6277 94.478833 84 7399 6 chr6B.!!$R1 7315
2 TraesCS6D01G205100 chr6A 432519041 432526459 7418 True 1503.485714 3434 94.165429 2 7169 7 chr6A.!!$R3 7167

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
933 1304 0.238289 CGCATCGCCACAAATATCCC 59.762 55.000 0.00 0.00 0.00 3.85 F
1744 2122 1.004200 AGTTTGGGAACGGGTAGCG 60.004 57.895 0.00 0.00 40.75 4.26 F
1861 2239 0.249031 GCTGGTTGGTTGACTTGTGC 60.249 55.000 0.00 0.00 0.00 4.57 F
2574 3063 1.565288 TGATCATCATGGGTTGGCTCA 59.435 47.619 0.00 0.00 0.00 4.26 F
3726 4292 1.471676 GCCCACGTTCTGTCCTATCAG 60.472 57.143 0.00 0.00 36.85 2.90 F
5241 5821 1.202639 TGTGGACCTGCAGTACTGTTG 60.203 52.381 23.44 15.63 0.00 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1783 2161 0.247185 CGGCCAATGGAAGCAACAAT 59.753 50.000 2.05 0.0 0.00 2.71 R
2672 3167 0.400213 CAACCCCAAGCACCTCAGTA 59.600 55.000 0.00 0.0 0.00 2.74 R
3217 3776 1.104577 TTTTTGGTCAGTCGGCCCAC 61.105 55.000 0.00 0.0 0.00 4.61 R
3913 4489 1.096386 ACGTAAGGCGCAAAACACCA 61.096 50.000 10.83 0.0 46.11 4.17 R
5539 6120 1.268625 GGAATGGTGGGAACGAACAAC 59.731 52.381 0.00 0.0 0.00 3.32 R
7111 7806 0.033011 TGCTCCTCAGTACTCCCTCC 60.033 60.000 0.00 0.0 0.00 4.30 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
117 259 6.897259 TGCTTAAAACACGAGGATGTATAC 57.103 37.500 0.00 0.00 30.75 1.47
122 264 1.133699 ACACGAGGATGTATACCGGGA 60.134 52.381 6.32 0.00 0.00 5.14
150 292 6.063404 TCCAGGTAACACTTAAATTTTCCGT 58.937 36.000 0.00 0.00 41.41 4.69
223 368 5.505654 CGAAATCACATTATACACCTTGCCC 60.506 44.000 0.00 0.00 0.00 5.36
247 393 1.429463 AGATTGTCCTTGAACGCGTC 58.571 50.000 14.44 7.01 0.00 5.19
324 470 4.685169 ATTGACGCCAAACATAGAACTG 57.315 40.909 0.00 0.00 35.67 3.16
347 493 2.180017 CCGGTCGGGTTGTAGACG 59.820 66.667 0.74 0.00 38.20 4.18
348 494 2.505557 CGGTCGGGTTGTAGACGC 60.506 66.667 0.00 0.00 38.20 5.19
349 495 2.652530 GGTCGGGTTGTAGACGCA 59.347 61.111 0.00 0.00 41.00 5.24
350 496 1.445582 GGTCGGGTTGTAGACGCAG 60.446 63.158 0.00 0.00 41.00 5.18
351 497 2.092882 GTCGGGTTGTAGACGCAGC 61.093 63.158 0.00 0.00 41.00 5.25
352 498 3.179265 CGGGTTGTAGACGCAGCG 61.179 66.667 14.82 14.82 41.00 5.18
353 499 3.488090 GGGTTGTAGACGCAGCGC 61.488 66.667 16.61 8.00 40.67 5.92
382 539 1.614241 ATTCGGTTCCTCGGACCAGG 61.614 60.000 4.12 4.12 34.40 4.45
469 626 0.958382 TTAACGCACACAGCCCATCC 60.958 55.000 0.00 0.00 41.38 3.51
502 659 2.111043 CGCCACCATATCCGGCTT 59.889 61.111 0.00 0.00 43.95 4.35
539 696 3.765051 ATCGATGGACCGATCGCT 58.235 55.556 10.32 0.00 45.03 4.93
606 764 2.047274 CGTCCACCGAGCCATGTT 60.047 61.111 0.00 0.00 39.56 2.71
802 1173 1.846124 TCGGGCAGAAGTTTCCCCT 60.846 57.895 5.15 0.00 36.69 4.79
807 1178 0.881796 GCAGAAGTTTCCCCTTTCCG 59.118 55.000 0.00 0.00 0.00 4.30
933 1304 0.238289 CGCATCGCCACAAATATCCC 59.762 55.000 0.00 0.00 0.00 3.85
950 1321 3.847602 CTCCTCCTCCCGCTGCTG 61.848 72.222 0.00 0.00 0.00 4.41
1185 1556 2.356313 CTCTGCGCGTCTGTGGTT 60.356 61.111 8.43 0.00 0.00 3.67
1215 1586 2.591715 GGCGCCTTGTCTGTGTGT 60.592 61.111 22.15 0.00 0.00 3.72
1226 1597 2.004017 GTCTGTGTGTTTCCGTTCACA 58.996 47.619 0.00 0.00 41.37 3.58
1301 1672 1.176527 GGCCTTGTGATTTGCTGCTA 58.823 50.000 0.00 0.00 0.00 3.49
1302 1673 1.545582 GGCCTTGTGATTTGCTGCTAA 59.454 47.619 0.00 0.00 0.00 3.09
1303 1674 2.167075 GGCCTTGTGATTTGCTGCTAAT 59.833 45.455 9.01 9.01 0.00 1.73
1304 1675 3.381272 GGCCTTGTGATTTGCTGCTAATA 59.619 43.478 9.22 0.00 0.00 0.98
1400 1772 7.848076 GACTTGTGTCTAGCTAACTCAGCCC 62.848 52.000 0.00 0.00 44.36 5.19
1461 1833 1.029947 CCACAGGGATACGGGCAAAC 61.030 60.000 0.00 0.00 35.59 2.93
1470 1842 4.443881 GGGATACGGGCAAACTACATACTT 60.444 45.833 0.00 0.00 37.60 2.24
1531 1903 7.432148 TGGAGATGGTCTAGCATTAGTAAAA 57.568 36.000 0.00 0.00 0.00 1.52
1532 1904 7.857456 TGGAGATGGTCTAGCATTAGTAAAAA 58.143 34.615 0.00 0.00 0.00 1.94
1684 2062 1.746220 TCTGCGCCTCTCTTTCTCTAC 59.254 52.381 4.18 0.00 0.00 2.59
1685 2063 1.474478 CTGCGCCTCTCTTTCTCTACA 59.526 52.381 4.18 0.00 0.00 2.74
1744 2122 1.004200 AGTTTGGGAACGGGTAGCG 60.004 57.895 0.00 0.00 40.75 4.26
1783 2161 4.627900 TGATTGTTGCTAATCGTCGCTAAA 59.372 37.500 0.00 0.00 39.39 1.85
1861 2239 0.249031 GCTGGTTGGTTGACTTGTGC 60.249 55.000 0.00 0.00 0.00 4.57
1894 2272 2.350498 CCATTTTGGTACCGCTAGTTCG 59.650 50.000 7.57 0.00 31.35 3.95
1966 2344 5.464722 CGTAGGTATTCGTCACTAAGAGCTA 59.535 44.000 0.00 0.00 29.59 3.32
2052 2539 9.179552 CTATCTATCTCTCAGAAACACAATTCG 57.820 37.037 0.00 0.00 34.46 3.34
2269 2758 1.616865 TGTAGTAAAGGTCACAGCGCT 59.383 47.619 2.64 2.64 0.00 5.92
2357 2846 3.006940 TGTGGATCCGACAAAAGTATGC 58.993 45.455 7.39 0.00 0.00 3.14
2458 2947 4.349503 TGCCGCAGCACCTCCATT 62.350 61.111 0.00 0.00 46.52 3.16
2489 2978 4.931601 CCTACATGGTCATCATTGATACGG 59.068 45.833 0.00 0.00 33.56 4.02
2567 3056 2.364324 GCATGCTTTGATCATCATGGGT 59.636 45.455 23.10 0.00 37.40 4.51
2574 3063 1.565288 TGATCATCATGGGTTGGCTCA 59.435 47.619 0.00 0.00 0.00 4.26
2671 3166 8.947115 GTTTCTGTTAGGCATTACTTCTGTTAT 58.053 33.333 0.00 0.00 0.00 1.89
2672 3167 9.515226 TTTCTGTTAGGCATTACTTCTGTTATT 57.485 29.630 0.00 0.00 0.00 1.40
2733 3228 4.952957 TGACTTCTATCTAACTGCTCAGCT 59.047 41.667 0.00 0.00 0.00 4.24
2830 3325 2.363683 CCTGCTTGAATGGAGACTTCC 58.636 52.381 0.00 0.00 44.31 3.46
2849 3344 6.574350 ACTTCCATGAGAACTAGTAAATCCG 58.426 40.000 0.00 0.00 0.00 4.18
2878 3429 8.525876 CAATGCACGTTCATATTTTGTAGAATG 58.474 33.333 0.00 0.00 34.16 2.67
3217 3776 4.836825 TGGTAAGAGAGAGCAAATTCTGG 58.163 43.478 0.00 0.00 0.00 3.86
3224 3783 1.937546 GAGCAAATTCTGGTGGGCCG 61.938 60.000 0.00 0.00 35.35 6.13
3339 3900 8.192774 TGCCAAATTACAATTGCAAATGAAAAA 58.807 25.926 21.10 11.70 28.27 1.94
3436 3998 5.474876 ACAGAAACTTCCTGATGACATTTCC 59.525 40.000 0.00 0.00 35.69 3.13
3438 4000 3.703001 ACTTCCTGATGACATTTCCGT 57.297 42.857 0.00 0.00 0.00 4.69
3635 4197 7.980099 AGTCTGTATTGTTAAATACCCTCTTCG 59.020 37.037 6.23 0.00 45.15 3.79
3721 4287 1.978455 TTGTGCCCACGTTCTGTCCT 61.978 55.000 0.00 0.00 0.00 3.85
3726 4292 1.471676 GCCCACGTTCTGTCCTATCAG 60.472 57.143 0.00 0.00 36.85 2.90
3734 4300 5.168569 CGTTCTGTCCTATCAGCAGTAAAA 58.831 41.667 0.00 0.00 35.63 1.52
3735 4301 5.637810 CGTTCTGTCCTATCAGCAGTAAAAA 59.362 40.000 0.00 0.00 35.63 1.94
3763 4329 3.576118 ACTGTGCTAGACAATCTGTGACT 59.424 43.478 0.00 0.00 36.21 3.41
3766 4332 4.202253 TGTGCTAGACAATCTGTGACTTGT 60.202 41.667 0.00 0.00 38.26 3.16
3780 4346 4.083003 TGTGACTTGTTTGTGGTCTTTGAC 60.083 41.667 0.00 0.00 0.00 3.18
3913 4489 6.406370 TGCAGCTTACAGTGATATAGTTGTT 58.594 36.000 0.00 0.00 0.00 2.83
3919 4495 7.119262 GCTTACAGTGATATAGTTGTTGGTGTT 59.881 37.037 0.00 0.00 0.00 3.32
3963 4539 8.636213 TGTACTAACTTTCTTTAGCTGTACAGT 58.364 33.333 23.44 12.90 33.02 3.55
4228 4805 6.183360 GCTTATTACCTCGCACACAATTAAGT 60.183 38.462 0.00 0.00 0.00 2.24
4287 4864 6.491403 ACTTTGAATTCTGAATGGTGCTTACT 59.509 34.615 7.05 0.00 0.00 2.24
4487 5064 7.568199 ACTTTACTTTGCATTTGTACTGTCT 57.432 32.000 0.00 0.00 0.00 3.41
4489 5066 7.282224 ACTTTACTTTGCATTTGTACTGTCTCA 59.718 33.333 0.00 0.00 0.00 3.27
4490 5067 5.679734 ACTTTGCATTTGTACTGTCTCAG 57.320 39.130 0.00 0.00 37.52 3.35
4686 5263 2.481568 TCGAATCTGCTTGTTGCTCTTG 59.518 45.455 0.00 0.00 43.37 3.02
4707 5284 6.653320 TCTTGTCGTTATCAAGCCTTGTAATT 59.347 34.615 4.04 0.00 41.13 1.40
4708 5285 6.811253 TGTCGTTATCAAGCCTTGTAATTT 57.189 33.333 4.04 0.00 0.00 1.82
5085 5664 6.588373 TCAACACTTGTTTTGTTCTTTTAGGC 59.412 34.615 0.00 0.00 34.91 3.93
5094 5673 7.651704 TGTTTTGTTCTTTTAGGCAAATCTAGC 59.348 33.333 0.00 0.00 31.99 3.42
5241 5821 1.202639 TGTGGACCTGCAGTACTGTTG 60.203 52.381 23.44 15.63 0.00 3.33
5304 5884 2.512476 TCCTTACCTTTATTCCCCTGGC 59.488 50.000 0.00 0.00 0.00 4.85
5389 5969 2.500098 GACTACAGTACTTGGGGATGCA 59.500 50.000 0.00 0.00 0.00 3.96
5537 6118 1.284657 CACTAGCTCGTGAGGCATTG 58.715 55.000 12.88 0.00 37.06 2.82
5539 6120 1.284657 CTAGCTCGTGAGGCATTGTG 58.715 55.000 0.00 0.00 0.00 3.33
5546 6127 1.660052 CGTGAGGCATTGTGTTGTTCG 60.660 52.381 0.00 0.00 0.00 3.95
5693 6274 7.356089 TCACATATTACCACGTTCTAATCCT 57.644 36.000 0.00 0.00 0.00 3.24
5847 6428 5.958955 CTCTTGAAAGCAAGGGGAAATAAG 58.041 41.667 5.87 0.00 46.67 1.73
5955 6647 3.431411 TTTTCCTGGGATAGCTAGGGA 57.569 47.619 0.00 0.00 32.39 4.20
6017 6709 4.438744 GGTGGTGCTGCTATTTTCATGTAC 60.439 45.833 0.00 0.00 0.00 2.90
6161 6853 9.128107 CAACATGCGTAGTATTTTGAAATCTTT 57.872 29.630 0.00 0.00 41.58 2.52
6162 6854 8.895932 ACATGCGTAGTATTTTGAAATCTTTC 57.104 30.769 0.00 0.00 37.69 2.62
6163 6855 8.511321 ACATGCGTAGTATTTTGAAATCTTTCA 58.489 29.630 1.28 1.28 44.78 2.69
6164 6856 9.507280 CATGCGTAGTATTTTGAAATCTTTCAT 57.493 29.630 6.21 0.00 45.65 2.57
6165 6857 8.894409 TGCGTAGTATTTTGAAATCTTTCATG 57.106 30.769 6.21 0.00 45.65 3.07
6166 6858 8.726068 TGCGTAGTATTTTGAAATCTTTCATGA 58.274 29.630 6.21 0.00 45.65 3.07
6167 6859 9.722056 GCGTAGTATTTTGAAATCTTTCATGAT 57.278 29.630 6.21 6.42 45.65 2.45
6269 6963 3.431055 TTGTTGCTCGGCCACAAG 58.569 55.556 2.24 0.00 38.84 3.16
6635 7329 3.308053 CAGCATCTCTGTACCATCGTTTG 59.692 47.826 0.00 0.00 38.02 2.93
6652 7346 0.948623 TTGGTCTGTTCACATCGCCG 60.949 55.000 0.00 0.00 0.00 6.46
6653 7347 1.374252 GGTCTGTTCACATCGCCGT 60.374 57.895 0.00 0.00 0.00 5.68
6654 7348 0.108992 GGTCTGTTCACATCGCCGTA 60.109 55.000 0.00 0.00 0.00 4.02
6655 7349 1.470979 GGTCTGTTCACATCGCCGTAT 60.471 52.381 0.00 0.00 0.00 3.06
6656 7350 2.268298 GTCTGTTCACATCGCCGTATT 58.732 47.619 0.00 0.00 0.00 1.89
6657 7351 2.671396 GTCTGTTCACATCGCCGTATTT 59.329 45.455 0.00 0.00 0.00 1.40
6658 7352 2.670905 TCTGTTCACATCGCCGTATTTG 59.329 45.455 0.00 0.00 0.00 2.32
6659 7353 2.415168 CTGTTCACATCGCCGTATTTGT 59.585 45.455 0.00 0.00 0.00 2.83
6660 7354 2.413796 TGTTCACATCGCCGTATTTGTC 59.586 45.455 0.00 0.00 0.00 3.18
6661 7355 2.665649 TCACATCGCCGTATTTGTCT 57.334 45.000 0.00 0.00 0.00 3.41
6662 7356 2.267426 TCACATCGCCGTATTTGTCTG 58.733 47.619 0.00 0.00 0.00 3.51
6663 7357 2.094442 TCACATCGCCGTATTTGTCTGA 60.094 45.455 0.00 0.00 0.00 3.27
6664 7358 2.670905 CACATCGCCGTATTTGTCTGAA 59.329 45.455 0.00 0.00 0.00 3.02
6665 7359 3.124466 CACATCGCCGTATTTGTCTGAAA 59.876 43.478 0.00 0.00 0.00 2.69
6666 7360 3.938963 ACATCGCCGTATTTGTCTGAAAT 59.061 39.130 0.00 0.00 0.00 2.17
6667 7361 5.006261 CACATCGCCGTATTTGTCTGAAATA 59.994 40.000 0.00 0.00 0.00 1.40
6668 7362 5.234329 ACATCGCCGTATTTGTCTGAAATAG 59.766 40.000 0.00 0.00 0.00 1.73
6669 7363 5.001237 TCGCCGTATTTGTCTGAAATAGA 57.999 39.130 0.00 0.00 0.00 1.98
6670 7364 5.041287 TCGCCGTATTTGTCTGAAATAGAG 58.959 41.667 0.00 0.00 35.70 2.43
6671 7365 4.804139 CGCCGTATTTGTCTGAAATAGAGT 59.196 41.667 0.00 0.00 35.70 3.24
6672 7366 5.975344 CGCCGTATTTGTCTGAAATAGAGTA 59.025 40.000 0.00 0.00 35.70 2.59
6673 7367 6.074994 CGCCGTATTTGTCTGAAATAGAGTAC 60.075 42.308 0.00 0.00 35.70 2.73
6674 7368 6.755141 GCCGTATTTGTCTGAAATAGAGTACA 59.245 38.462 0.00 0.00 35.70 2.90
6675 7369 7.277098 GCCGTATTTGTCTGAAATAGAGTACAA 59.723 37.037 0.00 0.00 35.70 2.41
6676 7370 8.592998 CCGTATTTGTCTGAAATAGAGTACAAC 58.407 37.037 0.00 0.00 35.70 3.32
6677 7371 9.135843 CGTATTTGTCTGAAATAGAGTACAACA 57.864 33.333 0.00 0.00 35.70 3.33
6773 7468 9.750125 CACTATAATCAAGTAATAGCTGTGTCA 57.250 33.333 0.00 0.00 0.00 3.58
6914 7609 0.103937 AGAGGCTATTGTCTCAGCGC 59.896 55.000 11.34 0.00 46.70 5.92
7010 7705 9.498176 TAGTTCAAACTTGAGTTAAATACTCCC 57.502 33.333 0.00 0.00 44.65 4.30
7017 7712 4.319139 GAGTTAAATACTCCCTCCGTCC 57.681 50.000 0.00 0.00 46.30 4.79
7018 7713 2.692041 AGTTAAATACTCCCTCCGTCCG 59.308 50.000 0.00 0.00 28.23 4.79
7019 7714 2.689983 GTTAAATACTCCCTCCGTCCGA 59.310 50.000 0.00 0.00 0.00 4.55
7020 7715 1.856629 AAATACTCCCTCCGTCCGAA 58.143 50.000 0.00 0.00 0.00 4.30
7021 7716 1.856629 AATACTCCCTCCGTCCGAAA 58.143 50.000 0.00 0.00 0.00 3.46
7022 7717 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
7023 7718 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
7024 7719 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
7025 7720 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
7026 7721 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
7027 7722 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
7028 7723 3.364549 TCCCTCCGTCCGAAAATACTTA 58.635 45.455 0.00 0.00 0.00 2.24
7029 7724 3.962718 TCCCTCCGTCCGAAAATACTTAT 59.037 43.478 0.00 0.00 0.00 1.73
7030 7725 4.038402 TCCCTCCGTCCGAAAATACTTATC 59.962 45.833 0.00 0.00 0.00 1.75
7031 7726 4.202182 CCCTCCGTCCGAAAATACTTATCA 60.202 45.833 0.00 0.00 0.00 2.15
7032 7727 5.510861 CCCTCCGTCCGAAAATACTTATCAT 60.511 44.000 0.00 0.00 0.00 2.45
7033 7728 5.989777 CCTCCGTCCGAAAATACTTATCATT 59.010 40.000 0.00 0.00 0.00 2.57
7034 7729 7.149973 CCTCCGTCCGAAAATACTTATCATTA 58.850 38.462 0.00 0.00 0.00 1.90
7035 7730 7.654520 CCTCCGTCCGAAAATACTTATCATTAA 59.345 37.037 0.00 0.00 0.00 1.40
7036 7731 8.945481 TCCGTCCGAAAATACTTATCATTAAA 57.055 30.769 0.00 0.00 0.00 1.52
7037 7732 9.381033 TCCGTCCGAAAATACTTATCATTAAAA 57.619 29.630 0.00 0.00 0.00 1.52
7086 7781 9.685276 AGTTGTAGATACATCCATTTTCATTCA 57.315 29.630 0.00 0.00 35.89 2.57
7096 7791 9.158233 ACATCCATTTTCATTCATTTTGATGAC 57.842 29.630 0.00 0.00 32.39 3.06
7097 7792 9.157104 CATCCATTTTCATTCATTTTGATGACA 57.843 29.630 0.00 0.00 0.00 3.58
7098 7793 9.727859 ATCCATTTTCATTCATTTTGATGACAA 57.272 25.926 0.00 0.00 0.00 3.18
7099 7794 9.210329 TCCATTTTCATTCATTTTGATGACAAG 57.790 29.630 0.00 0.00 37.32 3.16
7100 7795 8.995220 CCATTTTCATTCATTTTGATGACAAGT 58.005 29.630 0.00 0.00 37.32 3.16
7106 7801 9.142515 TCATTCATTTTGATGACAAGTATTTGC 57.857 29.630 0.00 0.00 37.85 3.68
7107 7802 7.565450 TTCATTTTGATGACAAGTATTTGCG 57.435 32.000 0.00 0.00 37.85 4.85
7108 7803 6.092092 TCATTTTGATGACAAGTATTTGCGG 58.908 36.000 0.00 0.00 37.85 5.69
7109 7804 5.697473 TTTTGATGACAAGTATTTGCGGA 57.303 34.783 0.00 0.00 37.85 5.54
7110 7805 4.678509 TTGATGACAAGTATTTGCGGAC 57.321 40.909 0.00 0.00 37.85 4.79
7111 7806 2.670905 TGATGACAAGTATTTGCGGACG 59.329 45.455 0.00 0.00 37.85 4.79
7112 7807 1.434555 TGACAAGTATTTGCGGACGG 58.565 50.000 0.00 0.00 37.85 4.79
7113 7808 1.001068 TGACAAGTATTTGCGGACGGA 59.999 47.619 0.00 0.00 37.85 4.69
7114 7809 1.659098 GACAAGTATTTGCGGACGGAG 59.341 52.381 0.00 0.00 37.85 4.63
7115 7810 1.006832 CAAGTATTTGCGGACGGAGG 58.993 55.000 0.00 0.00 0.00 4.30
7116 7811 0.107848 AAGTATTTGCGGACGGAGGG 60.108 55.000 0.00 0.00 0.00 4.30
7117 7812 0.974010 AGTATTTGCGGACGGAGGGA 60.974 55.000 0.00 0.00 0.00 4.20
7118 7813 0.529992 GTATTTGCGGACGGAGGGAG 60.530 60.000 0.00 0.00 0.00 4.30
7119 7814 0.974010 TATTTGCGGACGGAGGGAGT 60.974 55.000 0.00 0.00 0.00 3.85
7120 7815 0.974010 ATTTGCGGACGGAGGGAGTA 60.974 55.000 0.00 0.00 0.00 2.59
7121 7816 1.880819 TTTGCGGACGGAGGGAGTAC 61.881 60.000 0.00 0.00 0.00 2.73
7122 7817 2.439883 GCGGACGGAGGGAGTACT 60.440 66.667 0.00 0.00 0.00 2.73
7123 7818 2.772691 GCGGACGGAGGGAGTACTG 61.773 68.421 0.00 0.00 0.00 2.74
7124 7819 1.077930 CGGACGGAGGGAGTACTGA 60.078 63.158 0.00 0.00 0.00 3.41
7216 7911 9.691362 TTTGTCCTAAATCAAACATTCTTAAGC 57.309 29.630 0.00 0.00 0.00 3.09
7217 7912 8.635765 TGTCCTAAATCAAACATTCTTAAGCT 57.364 30.769 0.00 0.00 0.00 3.74
7218 7913 8.514594 TGTCCTAAATCAAACATTCTTAAGCTG 58.485 33.333 0.00 0.53 0.00 4.24
7219 7914 7.970614 GTCCTAAATCAAACATTCTTAAGCTGG 59.029 37.037 0.00 0.00 0.00 4.85
7220 7915 7.888021 TCCTAAATCAAACATTCTTAAGCTGGA 59.112 33.333 0.00 0.00 0.00 3.86
7221 7916 7.970614 CCTAAATCAAACATTCTTAAGCTGGAC 59.029 37.037 0.00 0.00 0.00 4.02
7222 7917 5.904362 ATCAAACATTCTTAAGCTGGACC 57.096 39.130 0.00 0.00 0.00 4.46
7223 7918 3.751175 TCAAACATTCTTAAGCTGGACCG 59.249 43.478 0.00 0.00 0.00 4.79
7224 7919 3.695830 AACATTCTTAAGCTGGACCGA 57.304 42.857 0.00 0.00 0.00 4.69
7225 7920 3.252974 ACATTCTTAAGCTGGACCGAG 57.747 47.619 0.00 0.00 0.00 4.63
7226 7921 2.567615 ACATTCTTAAGCTGGACCGAGT 59.432 45.455 0.00 0.00 0.00 4.18
7227 7922 3.190874 CATTCTTAAGCTGGACCGAGTC 58.809 50.000 0.00 0.00 0.00 3.36
7228 7923 2.217510 TCTTAAGCTGGACCGAGTCT 57.782 50.000 0.00 0.00 32.47 3.24
7229 7924 3.361281 TCTTAAGCTGGACCGAGTCTA 57.639 47.619 0.00 0.00 32.47 2.59
7230 7925 3.899726 TCTTAAGCTGGACCGAGTCTAT 58.100 45.455 0.00 0.00 32.47 1.98
7231 7926 5.045012 TCTTAAGCTGGACCGAGTCTATA 57.955 43.478 0.00 0.00 32.47 1.31
7232 7927 5.443283 TCTTAAGCTGGACCGAGTCTATAA 58.557 41.667 0.00 0.00 32.47 0.98
7233 7928 5.889853 TCTTAAGCTGGACCGAGTCTATAAA 59.110 40.000 0.00 0.00 32.47 1.40
7234 7929 6.379133 TCTTAAGCTGGACCGAGTCTATAAAA 59.621 38.462 0.00 0.00 32.47 1.52
7235 7930 5.416271 AAGCTGGACCGAGTCTATAAAAA 57.584 39.130 0.00 0.00 32.47 1.94
7236 7931 5.615925 AGCTGGACCGAGTCTATAAAAAT 57.384 39.130 0.00 0.00 32.47 1.82
7237 7932 6.726490 AGCTGGACCGAGTCTATAAAAATA 57.274 37.500 0.00 0.00 32.47 1.40
7238 7933 7.304497 AGCTGGACCGAGTCTATAAAAATAT 57.696 36.000 0.00 0.00 32.47 1.28
7239 7934 7.379750 AGCTGGACCGAGTCTATAAAAATATC 58.620 38.462 0.00 0.00 32.47 1.63
7240 7935 7.015292 AGCTGGACCGAGTCTATAAAAATATCA 59.985 37.037 0.00 0.00 32.47 2.15
7241 7936 7.819900 GCTGGACCGAGTCTATAAAAATATCAT 59.180 37.037 4.41 0.00 32.47 2.45
7242 7937 9.712305 CTGGACCGAGTCTATAAAAATATCATT 57.288 33.333 4.41 0.00 32.47 2.57
7243 7938 9.489084 TGGACCGAGTCTATAAAAATATCATTG 57.511 33.333 4.41 0.00 32.47 2.82
7244 7939 8.443937 GGACCGAGTCTATAAAAATATCATTGC 58.556 37.037 4.41 0.00 32.47 3.56
7245 7940 9.209175 GACCGAGTCTATAAAAATATCATTGCT 57.791 33.333 0.00 0.00 0.00 3.91
7246 7941 8.993121 ACCGAGTCTATAAAAATATCATTGCTG 58.007 33.333 0.00 0.00 0.00 4.41
7247 7942 8.993121 CCGAGTCTATAAAAATATCATTGCTGT 58.007 33.333 0.00 0.00 0.00 4.40
7383 8078 6.524101 AACAGAGAGATACTGACCTTTCTC 57.476 41.667 0.00 0.00 38.55 2.87
7391 8086 5.719085 AGATACTGACCTTTCTCACATCTGT 59.281 40.000 0.00 0.00 0.00 3.41
7395 8090 5.305644 ACTGACCTTTCTCACATCTGTAACT 59.694 40.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 8.387354 CGTGTTTTAAGCATGTATAAGTGATGA 58.613 33.333 0.00 0.00 0.00 2.92
117 259 1.411612 GTGTTACCTGGATAGTCCCGG 59.588 57.143 0.00 0.00 45.34 5.73
122 264 9.239551 GGAAAATTTAAGTGTTACCTGGATAGT 57.760 33.333 0.00 0.00 0.00 2.12
223 368 4.084013 ACGCGTTCAAGGACAATCTTAAAG 60.084 41.667 5.58 0.00 0.00 1.85
247 393 6.198966 GTGTGTATTTGCTTCTTTCCTTGTTG 59.801 38.462 0.00 0.00 0.00 3.33
343 489 4.731612 CTGGTCTGCGCTGCGTCT 62.732 66.667 24.04 0.00 0.00 4.18
344 490 4.724602 TCTGGTCTGCGCTGCGTC 62.725 66.667 24.04 15.82 0.00 5.19
345 491 4.731612 CTCTGGTCTGCGCTGCGT 62.732 66.667 24.04 0.00 0.00 5.24
346 492 3.713205 ATCTCTGGTCTGCGCTGCG 62.713 63.158 19.17 19.17 0.00 5.18
347 493 1.427592 GAATCTCTGGTCTGCGCTGC 61.428 60.000 9.73 4.51 0.00 5.25
348 494 1.144565 CGAATCTCTGGTCTGCGCTG 61.145 60.000 9.73 8.88 0.00 5.18
349 495 1.140589 CGAATCTCTGGTCTGCGCT 59.859 57.895 9.73 0.00 0.00 5.92
350 496 1.880340 CCGAATCTCTGGTCTGCGC 60.880 63.158 0.00 0.00 0.00 6.09
351 497 0.108615 AACCGAATCTCTGGTCTGCG 60.109 55.000 0.00 0.00 37.54 5.18
352 498 1.646189 GAACCGAATCTCTGGTCTGC 58.354 55.000 0.00 0.00 37.54 4.26
353 499 1.827969 AGGAACCGAATCTCTGGTCTG 59.172 52.381 0.00 0.00 37.54 3.51
382 539 3.255379 GTAGTGCGCTGCGTAGGC 61.255 66.667 24.04 8.28 40.52 3.93
469 626 1.729517 TGGCGTTATGTGTCACGATTG 59.270 47.619 0.00 0.00 38.76 2.67
502 659 7.737972 TCGATTAAAGAAACAAATCTCCACA 57.262 32.000 0.00 0.00 0.00 4.17
933 1304 3.847602 CAGCAGCGGGAGGAGGAG 61.848 72.222 0.00 0.00 0.00 3.69
954 1325 3.827898 GACCACGCCGAGGAGGAG 61.828 72.222 7.79 0.00 45.00 3.69
1185 1556 3.183259 GCGCCAATTCTACGCCAA 58.817 55.556 0.00 0.00 46.63 4.52
1255 1626 3.056328 GCTGCCTGTTCCCGAACC 61.056 66.667 5.17 0.00 40.46 3.62
1301 1672 2.613691 ACGAGTTGGCGACGATTTATT 58.386 42.857 0.00 0.00 34.83 1.40
1302 1673 2.288961 ACGAGTTGGCGACGATTTAT 57.711 45.000 0.00 0.00 34.83 1.40
1303 1674 1.722464 CAACGAGTTGGCGACGATTTA 59.278 47.619 8.01 0.00 36.95 1.40
1304 1675 0.511221 CAACGAGTTGGCGACGATTT 59.489 50.000 8.01 0.00 36.95 2.17
1400 1772 2.068837 ATGGTTTCATGCAAACGCAG 57.931 45.000 0.00 0.00 44.90 5.18
1461 1833 8.569641 GGTGAATACCTACTGAGAAGTATGTAG 58.430 40.741 7.00 0.00 43.97 2.74
1531 1903 8.863872 AATACATAGTAGAAGCAACCAGTTTT 57.136 30.769 0.00 0.00 0.00 2.43
1532 1904 8.730680 CAAATACATAGTAGAAGCAACCAGTTT 58.269 33.333 0.00 0.00 0.00 2.66
1684 2062 2.715005 CACCACAGCACAACCGTG 59.285 61.111 0.00 0.00 46.56 4.94
1685 2063 3.209097 GCACCACAGCACAACCGT 61.209 61.111 0.00 0.00 0.00 4.83
1783 2161 0.247185 CGGCCAATGGAAGCAACAAT 59.753 50.000 2.05 0.00 0.00 2.71
1861 2239 3.216147 CCAAAATGGTTTCGTGCTAGG 57.784 47.619 0.00 0.00 31.35 3.02
1894 2272 0.730840 GCGTATAACCTGTGGCAACC 59.269 55.000 0.00 0.00 0.00 3.77
2052 2539 5.783111 ACAAGCCAAATGATTGTCTTTACC 58.217 37.500 0.00 0.00 32.72 2.85
2107 2596 1.117150 CGCTAGTGCCTACCCCTAAA 58.883 55.000 0.00 0.00 35.36 1.85
2357 2846 3.054878 GCCATGACAAGAAAACAAGCAG 58.945 45.455 0.00 0.00 0.00 4.24
2458 2947 0.970427 TGACCATGTAGGAGAGCGCA 60.970 55.000 11.47 0.00 41.22 6.09
2489 2978 3.119137 ACAAGACAAAAGAAGTGGGTTGC 60.119 43.478 0.00 0.00 0.00 4.17
2556 3045 3.228453 GAATGAGCCAACCCATGATGAT 58.772 45.455 0.00 0.00 0.00 2.45
2567 3056 1.241165 CAGTGCACTGAATGAGCCAA 58.759 50.000 38.12 0.00 46.59 4.52
2574 3063 5.711506 TCCAAATTCATACAGTGCACTGAAT 59.288 36.000 44.82 31.81 46.59 2.57
2640 3135 6.327279 AGTAATGCCTAACAGAAACAAACC 57.673 37.500 0.00 0.00 0.00 3.27
2671 3166 1.145571 AACCCCAAGCACCTCAGTAA 58.854 50.000 0.00 0.00 0.00 2.24
2672 3167 0.400213 CAACCCCAAGCACCTCAGTA 59.600 55.000 0.00 0.00 0.00 2.74
2673 3168 1.151450 CAACCCCAAGCACCTCAGT 59.849 57.895 0.00 0.00 0.00 3.41
2733 3228 5.582269 CGAAATGATTCCTACTTGAAGCTCA 59.418 40.000 0.00 0.00 32.04 4.26
2795 3290 5.393866 TCAAGCAGGGTAAAATTCTTCCTT 58.606 37.500 0.00 0.00 0.00 3.36
2830 3325 8.755941 CATTGTACGGATTTACTAGTTCTCATG 58.244 37.037 0.00 0.00 0.00 3.07
2849 3344 8.172484 TCTACAAAATATGAACGTGCATTGTAC 58.828 33.333 15.80 0.00 0.00 2.90
2878 3429 2.919666 ACATCAGCGGTGCAATTAAC 57.080 45.000 10.38 0.00 0.00 2.01
3217 3776 1.104577 TTTTTGGTCAGTCGGCCCAC 61.105 55.000 0.00 0.00 0.00 4.61
3386 3947 5.507315 CGGAAACCAGTTTGTAATGCTTCTT 60.507 40.000 0.00 0.00 32.11 2.52
3436 3998 9.329913 CTTCCACAACATAAAGAATAGAAAACG 57.670 33.333 0.00 0.00 0.00 3.60
3753 4319 4.526970 AGACCACAAACAAGTCACAGATT 58.473 39.130 0.00 0.00 32.82 2.40
3763 4329 6.375736 TCATTACTGTCAAAGACCACAAACAA 59.624 34.615 0.00 0.00 0.00 2.83
3766 4332 8.154203 TCTATCATTACTGTCAAAGACCACAAA 58.846 33.333 0.00 0.00 0.00 2.83
3780 4346 7.917505 GTGGCTTTTGGAAATCTATCATTACTG 59.082 37.037 0.00 0.00 0.00 2.74
3834 4400 9.918630 CCAATAAGAAAGTGAACATTCTTCAAT 57.081 29.630 14.87 4.43 41.30 2.57
3913 4489 1.096386 ACGTAAGGCGCAAAACACCA 61.096 50.000 10.83 0.00 46.11 4.17
3919 4495 5.350633 AGTACATATTACGTAAGGCGCAAA 58.649 37.500 14.25 0.00 46.11 3.68
3963 4539 4.335315 CAGTAACAAGTTCAGCCAACAGAA 59.665 41.667 0.00 0.00 37.48 3.02
4228 4805 6.127281 ACAATTTCCATATTTGCAGCTCATGA 60.127 34.615 0.00 0.00 0.00 3.07
4287 4864 5.011943 AGCTTTTAGCAAACCATCATGGAAA 59.988 36.000 11.90 0.00 45.56 3.13
4487 5064 4.790937 TGGCTATGGAATAACAATGCTGA 58.209 39.130 0.00 0.00 0.00 4.26
4489 5066 5.448654 TCTTGGCTATGGAATAACAATGCT 58.551 37.500 0.00 0.00 29.21 3.79
4490 5067 5.772825 TCTTGGCTATGGAATAACAATGC 57.227 39.130 0.00 0.00 29.21 3.56
4535 5112 5.826643 AGAGGCTCATATTAGCTAGCTAGT 58.173 41.667 23.03 22.35 42.37 2.57
4686 5263 6.027749 CCAAATTACAAGGCTTGATAACGAC 58.972 40.000 32.50 0.00 0.00 4.34
4708 5285 9.685276 ACTAAATGAATGTGAATTCTGATACCA 57.315 29.630 7.05 0.00 0.00 3.25
5085 5664 2.481952 GCTATTCAGCCCGCTAGATTTG 59.518 50.000 0.00 0.00 42.37 2.32
5241 5821 3.746492 GGTCGCCCTGAATATATGTCAAC 59.254 47.826 0.00 0.00 0.00 3.18
5537 6118 1.314730 ATGGTGGGAACGAACAACAC 58.685 50.000 0.00 0.00 37.09 3.32
5539 6120 1.268625 GGAATGGTGGGAACGAACAAC 59.731 52.381 0.00 0.00 0.00 3.32
5546 6127 2.025887 AGATCACAGGAATGGTGGGAAC 60.026 50.000 0.00 0.00 36.90 3.62
5719 6300 7.970614 GCAACCAAGAAGATTTAAGAACCTATG 59.029 37.037 0.00 0.00 0.00 2.23
5859 6551 4.129380 TCAAGACCTTGATGTCAACTGTG 58.871 43.478 8.27 0.00 43.90 3.66
5955 6647 7.054124 ACGTCAAAATGATTGATACCTATGGT 58.946 34.615 0.00 0.00 40.16 3.55
6017 6709 7.549134 TGGTGTAGTTCAATAGAAATGCTAGTG 59.451 37.037 0.00 0.00 44.40 2.74
6161 6853 6.117975 TCCTGCAGAAATAGCATATCATGA 57.882 37.500 17.39 0.00 41.82 3.07
6162 6854 7.392494 AATCCTGCAGAAATAGCATATCATG 57.608 36.000 17.39 0.00 41.82 3.07
6163 6855 7.889073 AGAAATCCTGCAGAAATAGCATATCAT 59.111 33.333 17.39 0.00 41.82 2.45
6164 6856 7.229308 AGAAATCCTGCAGAAATAGCATATCA 58.771 34.615 17.39 0.00 41.82 2.15
6165 6857 7.684937 AGAAATCCTGCAGAAATAGCATATC 57.315 36.000 17.39 0.00 41.82 1.63
6166 6858 7.722728 TGAAGAAATCCTGCAGAAATAGCATAT 59.277 33.333 17.39 0.00 41.82 1.78
6167 6859 7.012704 GTGAAGAAATCCTGCAGAAATAGCATA 59.987 37.037 17.39 0.00 41.82 3.14
6269 6963 5.940470 TCAGGAAAGGAAATTGAAGAGCTAC 59.060 40.000 0.00 0.00 0.00 3.58
6422 7116 7.977818 ACTGCCCATATCAATATCTACTTTCA 58.022 34.615 0.00 0.00 0.00 2.69
6635 7329 0.108992 TACGGCGATGTGAACAGACC 60.109 55.000 16.62 0.00 0.00 3.85
6654 7348 9.507329 ACATGTTGTACTCTATTTCAGACAAAT 57.493 29.630 0.00 0.00 0.00 2.32
6655 7349 8.902540 ACATGTTGTACTCTATTTCAGACAAA 57.097 30.769 0.00 0.00 0.00 2.83
6666 7360 9.990360 TTTCAGACAAATACATGTTGTACTCTA 57.010 29.630 2.30 0.00 39.29 2.43
6667 7361 8.902540 TTTCAGACAAATACATGTTGTACTCT 57.097 30.769 2.30 0.00 39.29 3.24
6672 7366 9.507329 ACTCTATTTCAGACAAATACATGTTGT 57.493 29.630 2.30 1.69 41.84 3.32
6678 7372 9.990360 TGTTGTACTCTATTTCAGACAAATACA 57.010 29.630 0.00 0.00 0.00 2.29
6697 7391 2.492088 GGGGGCTGAAATCTTGTTGTAC 59.508 50.000 0.00 0.00 0.00 2.90
6722 7417 5.690097 GCTGTGGACCCTATATTTTGGATGA 60.690 44.000 0.00 0.00 0.00 2.92
6914 7609 6.332630 CAAAGAGGGTAATATTTTGCACCAG 58.667 40.000 7.30 0.00 32.42 4.00
6968 7663 0.461339 ACTAAATACCGGGCAGCACG 60.461 55.000 11.11 11.11 0.00 5.34
7008 7703 2.685850 AAGTATTTTCGGACGGAGGG 57.314 50.000 0.00 0.00 0.00 4.30
7009 7704 4.940463 TGATAAGTATTTTCGGACGGAGG 58.060 43.478 0.00 0.00 0.00 4.30
7010 7705 8.583810 TTAATGATAAGTATTTTCGGACGGAG 57.416 34.615 0.00 0.00 0.00 4.63
7011 7706 8.945481 TTTAATGATAAGTATTTTCGGACGGA 57.055 30.769 0.00 0.00 0.00 4.69
7060 7755 9.685276 TGAATGAAAATGGATGTATCTACAACT 57.315 29.630 0.00 0.00 39.99 3.16
7070 7765 9.158233 GTCATCAAAATGAATGAAAATGGATGT 57.842 29.630 0.00 0.00 43.42 3.06
7071 7766 9.157104 TGTCATCAAAATGAATGAAAATGGATG 57.843 29.630 0.00 0.00 43.42 3.51
7072 7767 9.727859 TTGTCATCAAAATGAATGAAAATGGAT 57.272 25.926 0.00 0.00 43.42 3.41
7073 7768 9.210329 CTTGTCATCAAAATGAATGAAAATGGA 57.790 29.630 0.00 0.00 43.42 3.41
7074 7769 8.995220 ACTTGTCATCAAAATGAATGAAAATGG 58.005 29.630 0.00 0.00 43.42 3.16
7080 7775 9.142515 GCAAATACTTGTCATCAAAATGAATGA 57.857 29.630 0.00 0.00 43.42 2.57
7081 7776 8.105742 CGCAAATACTTGTCATCAAAATGAATG 58.894 33.333 0.00 0.00 43.42 2.67
7082 7777 7.276218 CCGCAAATACTTGTCATCAAAATGAAT 59.724 33.333 0.00 0.00 43.42 2.57
7083 7778 6.585702 CCGCAAATACTTGTCATCAAAATGAA 59.414 34.615 0.00 0.00 43.42 2.57
7084 7779 6.072230 TCCGCAAATACTTGTCATCAAAATGA 60.072 34.615 0.00 0.00 34.91 2.57
7085 7780 6.033831 GTCCGCAAATACTTGTCATCAAAATG 59.966 38.462 0.00 0.00 34.79 2.32
7086 7781 6.092748 GTCCGCAAATACTTGTCATCAAAAT 58.907 36.000 0.00 0.00 34.79 1.82
7087 7782 5.457140 GTCCGCAAATACTTGTCATCAAAA 58.543 37.500 0.00 0.00 34.79 2.44
7088 7783 4.377943 CGTCCGCAAATACTTGTCATCAAA 60.378 41.667 0.00 0.00 34.79 2.69
7089 7784 3.124466 CGTCCGCAAATACTTGTCATCAA 59.876 43.478 0.00 0.00 34.79 2.57
7090 7785 2.670905 CGTCCGCAAATACTTGTCATCA 59.329 45.455 0.00 0.00 34.79 3.07
7091 7786 2.030457 CCGTCCGCAAATACTTGTCATC 59.970 50.000 0.00 0.00 34.79 2.92
7092 7787 2.006888 CCGTCCGCAAATACTTGTCAT 58.993 47.619 0.00 0.00 34.79 3.06
7093 7788 1.001068 TCCGTCCGCAAATACTTGTCA 59.999 47.619 0.00 0.00 34.79 3.58
7094 7789 1.659098 CTCCGTCCGCAAATACTTGTC 59.341 52.381 0.00 0.00 34.79 3.18
7095 7790 1.674817 CCTCCGTCCGCAAATACTTGT 60.675 52.381 0.00 0.00 34.79 3.16
7096 7791 1.006832 CCTCCGTCCGCAAATACTTG 58.993 55.000 0.00 0.00 35.49 3.16
7097 7792 0.107848 CCCTCCGTCCGCAAATACTT 60.108 55.000 0.00 0.00 0.00 2.24
7098 7793 0.974010 TCCCTCCGTCCGCAAATACT 60.974 55.000 0.00 0.00 0.00 2.12
7099 7794 0.529992 CTCCCTCCGTCCGCAAATAC 60.530 60.000 0.00 0.00 0.00 1.89
7100 7795 0.974010 ACTCCCTCCGTCCGCAAATA 60.974 55.000 0.00 0.00 0.00 1.40
7101 7796 0.974010 TACTCCCTCCGTCCGCAAAT 60.974 55.000 0.00 0.00 0.00 2.32
7102 7797 1.607178 TACTCCCTCCGTCCGCAAA 60.607 57.895 0.00 0.00 0.00 3.68
7103 7798 2.036098 TACTCCCTCCGTCCGCAA 59.964 61.111 0.00 0.00 0.00 4.85
7104 7799 2.753043 GTACTCCCTCCGTCCGCA 60.753 66.667 0.00 0.00 0.00 5.69
7105 7800 2.439883 AGTACTCCCTCCGTCCGC 60.440 66.667 0.00 0.00 0.00 5.54
7106 7801 1.077930 TCAGTACTCCCTCCGTCCG 60.078 63.158 0.00 0.00 0.00 4.79
7107 7802 0.752376 CCTCAGTACTCCCTCCGTCC 60.752 65.000 0.00 0.00 0.00 4.79
7108 7803 0.255318 TCCTCAGTACTCCCTCCGTC 59.745 60.000 0.00 0.00 0.00 4.79
7109 7804 0.256464 CTCCTCAGTACTCCCTCCGT 59.744 60.000 0.00 0.00 0.00 4.69
7110 7805 1.104577 GCTCCTCAGTACTCCCTCCG 61.105 65.000 0.00 0.00 0.00 4.63
7111 7806 0.033011 TGCTCCTCAGTACTCCCTCC 60.033 60.000 0.00 0.00 0.00 4.30
7112 7807 1.107945 GTGCTCCTCAGTACTCCCTC 58.892 60.000 0.00 0.00 32.68 4.30
7113 7808 0.409876 TGTGCTCCTCAGTACTCCCT 59.590 55.000 0.00 0.00 36.27 4.20
7114 7809 0.533032 GTGTGCTCCTCAGTACTCCC 59.467 60.000 0.00 0.00 36.27 4.30
7115 7810 1.551452 AGTGTGCTCCTCAGTACTCC 58.449 55.000 0.00 0.00 36.27 3.85
7116 7811 4.993029 ATTAGTGTGCTCCTCAGTACTC 57.007 45.455 0.00 0.00 36.27 2.59
7117 7812 5.746990 AAATTAGTGTGCTCCTCAGTACT 57.253 39.130 0.00 0.00 36.27 2.73
7118 7813 6.872020 TGTAAAATTAGTGTGCTCCTCAGTAC 59.128 38.462 0.00 0.00 35.86 2.73
7119 7814 6.872020 GTGTAAAATTAGTGTGCTCCTCAGTA 59.128 38.462 0.00 0.00 0.00 2.74
7120 7815 5.701290 GTGTAAAATTAGTGTGCTCCTCAGT 59.299 40.000 0.00 0.00 0.00 3.41
7121 7816 5.934625 AGTGTAAAATTAGTGTGCTCCTCAG 59.065 40.000 0.00 0.00 0.00 3.35
7122 7817 5.865085 AGTGTAAAATTAGTGTGCTCCTCA 58.135 37.500 0.00 0.00 0.00 3.86
7123 7818 5.932303 TGAGTGTAAAATTAGTGTGCTCCTC 59.068 40.000 0.00 0.00 0.00 3.71
7124 7819 5.865085 TGAGTGTAAAATTAGTGTGCTCCT 58.135 37.500 0.00 0.00 0.00 3.69
7205 7900 2.567615 ACTCGGTCCAGCTTAAGAATGT 59.432 45.455 6.67 0.00 0.00 2.71
7206 7901 3.118956 AGACTCGGTCCAGCTTAAGAATG 60.119 47.826 6.67 3.90 32.18 2.67
7207 7902 3.100671 AGACTCGGTCCAGCTTAAGAAT 58.899 45.455 6.67 0.00 32.18 2.40
7208 7903 2.526432 AGACTCGGTCCAGCTTAAGAA 58.474 47.619 6.67 0.00 32.18 2.52
7209 7904 2.217510 AGACTCGGTCCAGCTTAAGA 57.782 50.000 6.67 0.00 32.18 2.10
7210 7905 5.769484 TTATAGACTCGGTCCAGCTTAAG 57.231 43.478 0.00 0.00 32.18 1.85
7211 7906 6.534475 TTTTATAGACTCGGTCCAGCTTAA 57.466 37.500 0.00 0.00 32.18 1.85
7212 7907 6.534475 TTTTTATAGACTCGGTCCAGCTTA 57.466 37.500 0.00 0.00 32.18 3.09
7213 7908 5.416271 TTTTTATAGACTCGGTCCAGCTT 57.584 39.130 0.00 0.00 32.18 3.74
7214 7909 5.615925 ATTTTTATAGACTCGGTCCAGCT 57.384 39.130 1.06 0.00 32.18 4.24
7215 7910 7.152645 TGATATTTTTATAGACTCGGTCCAGC 58.847 38.462 1.06 0.00 32.18 4.85
7216 7911 9.712305 AATGATATTTTTATAGACTCGGTCCAG 57.288 33.333 1.06 0.00 32.18 3.86
7217 7912 9.489084 CAATGATATTTTTATAGACTCGGTCCA 57.511 33.333 1.06 0.00 32.18 4.02
7218 7913 8.443937 GCAATGATATTTTTATAGACTCGGTCC 58.556 37.037 1.06 0.00 32.18 4.46
7219 7914 9.209175 AGCAATGATATTTTTATAGACTCGGTC 57.791 33.333 0.00 0.00 0.00 4.79
7220 7915 8.993121 CAGCAATGATATTTTTATAGACTCGGT 58.007 33.333 0.00 0.00 0.00 4.69
7221 7916 8.993121 ACAGCAATGATATTTTTATAGACTCGG 58.007 33.333 0.00 0.00 0.00 4.63
7237 7932 9.676861 ACATATGCTTATATGTACAGCAATGAT 57.323 29.630 21.64 11.46 46.35 2.45
7238 7933 8.938906 CACATATGCTTATATGTACAGCAATGA 58.061 33.333 21.64 10.26 46.35 2.57
7239 7934 8.724229 ACACATATGCTTATATGTACAGCAATG 58.276 33.333 10.35 14.86 46.35 2.82
7240 7935 8.853077 ACACATATGCTTATATGTACAGCAAT 57.147 30.769 10.35 2.69 46.35 3.56
7241 7936 8.558700 CAACACATATGCTTATATGTACAGCAA 58.441 33.333 10.35 0.00 46.35 3.91
7243 7938 8.087982 ACAACACATATGCTTATATGTACAGC 57.912 34.615 11.36 0.00 43.63 4.40
7251 7946 9.845740 ACCAAATCTACAACACATATGCTTATA 57.154 29.630 1.58 0.00 0.00 0.98
7252 7947 8.752005 ACCAAATCTACAACACATATGCTTAT 57.248 30.769 1.58 0.00 0.00 1.73
7253 7948 7.826744 TGACCAAATCTACAACACATATGCTTA 59.173 33.333 1.58 0.00 0.00 3.09
7254 7949 6.658816 TGACCAAATCTACAACACATATGCTT 59.341 34.615 1.58 0.00 0.00 3.91
7255 7950 6.179756 TGACCAAATCTACAACACATATGCT 58.820 36.000 1.58 0.00 0.00 3.79
7256 7951 6.435430 TGACCAAATCTACAACACATATGC 57.565 37.500 1.58 0.00 0.00 3.14
7287 7982 8.908786 AACACATCTCATTTTCAAACTCTCTA 57.091 30.769 0.00 0.00 0.00 2.43
7288 7983 7.500227 TGAACACATCTCATTTTCAAACTCTCT 59.500 33.333 0.00 0.00 0.00 3.10
7293 7988 9.683069 AAGTATGAACACATCTCATTTTCAAAC 57.317 29.630 0.00 0.00 35.21 2.93
7329 8024 4.395959 AAATCGCAAATTGGATGATGCT 57.604 36.364 0.00 0.00 36.67 3.79
7343 8038 5.525745 TCTCTGTTTGTGTTCTTAAATCGCA 59.474 36.000 0.00 0.00 0.00 5.10
7345 8040 7.408132 TCTCTCTGTTTGTGTTCTTAAATCG 57.592 36.000 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.