Multiple sequence alignment - TraesCS6A01G096500

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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 TraesCS6A01G096500 chr6A 100.000 9505 0 0 1 9505 63777216 63767712 0.000000e+00 17553.0
1 TraesCS6A01G096500 chr6A 91.986 287 19 4 2 288 214153028 214153310 5.350000e-107 399.0
2 TraesCS6A01G096500 chr6D 96.887 3726 91 14 689 4410 52827743 52824039 0.000000e+00 6215.0
3 TraesCS6A01G096500 chr6D 97.336 1952 30 2 4416 6345 52823990 52822039 0.000000e+00 3297.0
4 TraesCS6A01G096500 chr6D 97.587 1699 36 4 7456 9152 52820991 52819296 0.000000e+00 2905.0
5 TraesCS6A01G096500 chr6D 97.919 961 20 0 6347 7307 52821956 52820996 0.000000e+00 1664.0
6 TraesCS6A01G096500 chr6D 93.578 654 35 4 1 652 52862216 52861568 0.000000e+00 968.0
7 TraesCS6A01G096500 chr6D 97.635 296 6 1 9211 9505 52819166 52818871 3.060000e-139 507.0
8 TraesCS6A01G096500 chr6B 94.473 3709 121 26 391 4063 119986594 119982934 0.000000e+00 5637.0
9 TraesCS6A01G096500 chr6B 96.679 1957 36 5 4417 6345 119982335 119980380 0.000000e+00 3227.0
10 TraesCS6A01G096500 chr6B 97.810 959 19 2 6350 7307 119980263 119979306 0.000000e+00 1653.0
11 TraesCS6A01G096500 chr6B 97.072 888 24 2 7461 8347 119979296 119978410 0.000000e+00 1495.0
12 TraesCS6A01G096500 chr6B 95.588 816 32 3 8346 9160 119978438 119977626 0.000000e+00 1304.0
13 TraesCS6A01G096500 chr6B 97.443 352 9 0 4059 4410 119982736 119982385 1.370000e-167 601.0
14 TraesCS6A01G096500 chr6B 91.870 369 10 8 9157 9505 119977574 119977206 1.840000e-136 497.0
15 TraesCS6A01G096500 chr6B 98.160 163 1 2 7296 7456 28503631 28503793 5.620000e-72 283.0
16 TraesCS6A01G096500 chr6B 99.363 157 0 1 7300 7456 212540812 212540657 5.620000e-72 283.0
17 TraesCS6A01G096500 chr1D 94.444 288 13 3 1 288 61625648 61625932 3.150000e-119 440.0
18 TraesCS6A01G096500 chr1D 93.056 288 16 4 1 288 61833037 61833320 1.480000e-112 418.0
19 TraesCS6A01G096500 chr1D 92.123 292 19 4 1 292 61853655 61853942 8.890000e-110 409.0
20 TraesCS6A01G096500 chr1D 92.361 288 19 3 1 288 269807492 269807208 3.200000e-109 407.0
21 TraesCS6A01G096500 chr3D 91.205 307 23 4 1 306 331189434 331189737 1.910000e-111 414.0
22 TraesCS6A01G096500 chr2B 92.388 289 18 3 1 288 161403875 161404160 8.890000e-110 409.0
23 TraesCS6A01G096500 chr2B 74.459 231 43 11 295 520 441104143 441104362 1.700000e-12 86.1
24 TraesCS6A01G096500 chr5B 91.582 297 20 5 1 297 262368292 262368583 1.150000e-108 405.0
25 TraesCS6A01G096500 chr5B 98.750 160 1 1 7297 7456 471854202 471854360 5.620000e-72 283.0
26 TraesCS6A01G096500 chr5A 100.000 157 0 0 7300 7456 464473876 464473720 3.360000e-74 291.0
27 TraesCS6A01G096500 chr5A 84.706 85 13 0 428 512 660875662 660875746 1.700000e-12 86.1
28 TraesCS6A01G096500 chr1B 99.359 156 1 0 7301 7456 664059137 664059292 5.620000e-72 283.0
29 TraesCS6A01G096500 chr7A 97.561 164 2 2 7295 7456 24466163 24466326 7.270000e-71 279.0
30 TraesCS6A01G096500 chr4A 97.561 164 2 2 7295 7456 338745695 338745858 7.270000e-71 279.0
31 TraesCS6A01G096500 chr4A 73.750 160 37 4 374 530 605023670 605023513 3.710000e-04 58.4
32 TraesCS6A01G096500 chr3B 98.137 161 2 1 7296 7456 620206765 620206924 7.270000e-71 279.0
33 TraesCS6A01G096500 chr3A 97.006 167 1 3 7291 7456 437863548 437863711 2.610000e-70 278.0


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 TraesCS6A01G096500 chr6A 63767712 63777216 9504 True 17553.000000 17553 100.000000 1 9505 1 chr6A.!!$R1 9504
1 TraesCS6A01G096500 chr6D 52818871 52827743 8872 True 2917.600000 6215 97.472800 689 9505 5 chr6D.!!$R2 8816
2 TraesCS6A01G096500 chr6D 52861568 52862216 648 True 968.000000 968 93.578000 1 652 1 chr6D.!!$R1 651
3 TraesCS6A01G096500 chr6B 119977206 119986594 9388 True 2059.142857 5637 95.847857 391 9505 7 chr6B.!!$R2 9114

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
142 143 0.178068 TGGAGTAGCCGATCCTTTGC 59.822 55.000 0.93 0.00 40.66 3.68 F
322 323 0.661020 CGTGTTTGTCTTTCGGGCTT 59.339 50.000 0.00 0.00 0.00 4.35 F
1266 1271 0.406361 ACTCACTCGTCTCCCCTCTT 59.594 55.000 0.00 0.00 0.00 2.85 F
1558 1596 0.478072 ACATGGAGTGGTTTGCAGGA 59.522 50.000 0.00 0.00 0.00 3.86 F
1586 1624 0.577269 GAGTAACGCGATGATGCACC 59.423 55.000 15.93 0.00 34.15 5.01 F
3111 3150 1.028330 TGCTACATGCCTGCAGAAGC 61.028 55.000 17.39 11.96 42.00 3.86 F
3414 3454 1.417145 TGCAAAATTCCTTTGGCTGCT 59.583 42.857 0.00 0.00 44.03 4.24 F
4410 4653 2.875933 GCACTTTACTACTTGTGCCACA 59.124 45.455 0.00 0.00 46.84 4.17 F
5138 5445 0.761802 GTCAGGATGGGGATCACCTC 59.238 60.000 16.81 10.08 40.03 3.85 F
5146 5453 1.363246 GGGGATCACCTCCTATTCCC 58.637 60.000 6.79 0.00 44.28 3.97 F
6781 7208 1.251527 TTCTGGAGGAGGTGAGCGAC 61.252 60.000 0.00 0.00 0.00 5.19 F
7403 7831 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74 F
7405 7833 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1266 1271 0.914644 CTCCTCCCCATCTGAGCAAA 59.085 55.000 0.00 0.00 0.00 3.68 R
1586 1624 0.959372 CTTGCCACCTCCTTCTGCAG 60.959 60.000 7.63 7.63 32.88 4.41 R
3092 3131 1.028330 GCTTCTGCAGGCATGTAGCA 61.028 55.000 15.13 0.00 41.68 3.49 R
3111 3150 1.382522 ATTACACCCAATGCTCTGCG 58.617 50.000 0.00 0.00 0.00 5.18 R
3206 3246 4.244066 TGCCGGTTGAAAATTGATTCATG 58.756 39.130 1.90 0.00 38.98 3.07 R
4576 4862 0.528017 CTCGTAGCCTTGCTCACAGA 59.472 55.000 0.00 0.00 40.44 3.41 R
4850 5157 4.877378 ACATCTTGAACAAATGTGGCAT 57.123 36.364 0.00 0.00 32.58 4.40 R
6309 6623 0.933097 GCAGTGTATCATGTGCGAGG 59.067 55.000 0.00 0.00 0.00 4.63 R
6781 7208 0.533491 CATCAAACCACATGCCTGGG 59.467 55.000 7.24 0.08 35.34 4.45 R
6942 7369 7.254522 GGCACTGGCAAATGTATCAAATAAATG 60.255 37.037 0.00 0.00 43.71 2.32 R
8313 8742 0.390472 GACCTCTGGGCAGACGAAAG 60.390 60.000 0.00 0.00 35.63 2.62 R
8451 8880 0.513820 GCAGCTTTACGTTTACCGCA 59.486 50.000 0.00 0.00 41.42 5.69 R
8853 9284 0.842635 AATGGCTCCCAGTGAGGATC 59.157 55.000 0.00 0.00 41.73 3.36 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
29 30 4.580167 TCACTAAGCACTTTGAGCAACAAT 59.420 37.500 0.00 0.00 38.36 2.71
46 47 6.094603 AGCAACAATCTCATCAACAATACCTC 59.905 38.462 0.00 0.00 0.00 3.85
47 48 6.127925 GCAACAATCTCATCAACAATACCTCA 60.128 38.462 0.00 0.00 0.00 3.86
62 63 7.526918 ACAATACCTCATCCCCTTTTAATAGG 58.473 38.462 5.04 5.04 34.92 2.57
133 134 1.819288 TGAAGAGTCTTGGAGTAGCCG 59.181 52.381 10.90 0.00 40.66 5.52
142 143 0.178068 TGGAGTAGCCGATCCTTTGC 59.822 55.000 0.93 0.00 40.66 3.68
271 272 9.930693 TGTTGTTATTAATTACCAAAATCACCC 57.069 29.630 2.35 0.00 0.00 4.61
272 273 9.930693 GTTGTTATTAATTACCAAAATCACCCA 57.069 29.630 2.35 0.00 0.00 4.51
274 275 9.315363 TGTTATTAATTACCAAAATCACCCAGT 57.685 29.630 2.35 0.00 0.00 4.00
287 288 2.371841 TCACCCAGTGATTAGTTGCACT 59.628 45.455 0.00 0.00 45.62 4.40
295 296 6.818644 CCAGTGATTAGTTGCACTATTACACT 59.181 38.462 15.48 15.48 43.06 3.55
296 297 7.334421 CCAGTGATTAGTTGCACTATTACACTT 59.666 37.037 16.94 8.70 43.06 3.16
297 298 8.383619 CAGTGATTAGTTGCACTATTACACTTC 58.616 37.037 16.94 4.03 43.06 3.01
322 323 0.661020 CGTGTTTGTCTTTCGGGCTT 59.339 50.000 0.00 0.00 0.00 4.35
339 340 1.804748 GCTTCGGTCCTCAAATTCGTT 59.195 47.619 0.00 0.00 0.00 3.85
442 443 4.851558 CGTATGCGATGACGAGATTTGATA 59.148 41.667 0.00 0.00 41.60 2.15
483 484 1.535462 CAAGGGTTCAACGGTGATGAC 59.465 52.381 2.76 0.00 32.48 3.06
486 487 1.542547 GGGTTCAACGGTGATGACTGT 60.543 52.381 2.76 0.00 44.08 3.55
497 498 1.608717 GATGACTGTGGCTCGAGGGT 61.609 60.000 15.58 0.00 0.00 4.34
498 499 1.892819 ATGACTGTGGCTCGAGGGTG 61.893 60.000 15.58 0.00 0.00 4.61
501 502 3.655810 CTGTGGCTCGAGGGTGCTC 62.656 68.421 15.58 0.00 33.30 4.26
523 524 2.045438 TTAGGGGCACGTGCATGG 60.045 61.111 38.60 3.87 44.36 3.66
543 544 3.011144 TGGAGGCTTTTGGGTTATCATCA 59.989 43.478 0.00 0.00 0.00 3.07
567 568 3.806949 AGGTCAAGCCAACTCCAATAA 57.193 42.857 0.00 0.00 40.61 1.40
570 571 4.079253 GGTCAAGCCAACTCCAATAAAGA 58.921 43.478 0.00 0.00 37.17 2.52
573 574 4.766891 TCAAGCCAACTCCAATAAAGAAGG 59.233 41.667 0.00 0.00 0.00 3.46
575 576 3.076032 AGCCAACTCCAATAAAGAAGGGT 59.924 43.478 0.00 0.00 0.00 4.34
617 619 3.485346 TTCCGGTGGTGGAAGTGGC 62.485 63.158 0.00 0.00 43.01 5.01
671 673 8.726068 AGTTTTTATTTTGTTTGAGGTGTTTGG 58.274 29.630 0.00 0.00 0.00 3.28
672 674 8.508062 GTTTTTATTTTGTTTGAGGTGTTTGGT 58.492 29.630 0.00 0.00 0.00 3.67
673 675 9.720769 TTTTTATTTTGTTTGAGGTGTTTGGTA 57.279 25.926 0.00 0.00 0.00 3.25
674 676 9.892130 TTTTATTTTGTTTGAGGTGTTTGGTAT 57.108 25.926 0.00 0.00 0.00 2.73
675 677 9.892130 TTTATTTTGTTTGAGGTGTTTGGTATT 57.108 25.926 0.00 0.00 0.00 1.89
676 678 9.892130 TTATTTTGTTTGAGGTGTTTGGTATTT 57.108 25.926 0.00 0.00 0.00 1.40
679 681 8.879342 TTTGTTTGAGGTGTTTGGTATTTATG 57.121 30.769 0.00 0.00 0.00 1.90
680 682 7.825331 TGTTTGAGGTGTTTGGTATTTATGA 57.175 32.000 0.00 0.00 0.00 2.15
681 683 8.415950 TGTTTGAGGTGTTTGGTATTTATGAT 57.584 30.769 0.00 0.00 0.00 2.45
682 684 9.521841 TGTTTGAGGTGTTTGGTATTTATGATA 57.478 29.630 0.00 0.00 0.00 2.15
758 762 8.579682 AAAAGAAAATTGTACACAGATTCTGC 57.420 30.769 13.64 0.00 34.37 4.26
907 911 2.967076 CTGGTTCGCACGCACACT 60.967 61.111 0.00 0.00 0.00 3.55
1149 1153 2.654079 CCTCCGACTCAAGCAGGCT 61.654 63.158 0.00 0.00 0.00 4.58
1222 1226 2.929477 GTAACCGACCCCACCCCA 60.929 66.667 0.00 0.00 0.00 4.96
1266 1271 0.406361 ACTCACTCGTCTCCCCTCTT 59.594 55.000 0.00 0.00 0.00 2.85
1401 1407 2.352421 CCCAAATGCAGCTCTTTCAGTG 60.352 50.000 0.00 0.00 0.00 3.66
1558 1596 0.478072 ACATGGAGTGGTTTGCAGGA 59.522 50.000 0.00 0.00 0.00 3.86
1586 1624 0.577269 GAGTAACGCGATGATGCACC 59.423 55.000 15.93 0.00 34.15 5.01
1603 1641 2.752358 CTGCAGAAGGAGGTGGCA 59.248 61.111 8.42 0.00 0.00 4.92
1702 1740 2.031012 CTTGGCACCGAGTCTGCA 59.969 61.111 6.69 0.00 36.27 4.41
1856 1894 5.902613 TCGGCTTTTTGAGATGATGAAAT 57.097 34.783 0.00 0.00 0.00 2.17
1885 1923 2.926838 GTTTCAGATCGAGGAAGACAGC 59.073 50.000 0.00 0.00 0.00 4.40
2106 2144 6.149973 GCTGATTATTGCATAGCAGGTAATGA 59.850 38.462 13.00 7.07 40.61 2.57
2159 2197 7.616528 TGGGTATTCATCATAATGAGACAGA 57.383 36.000 0.00 0.00 42.72 3.41
2392 2430 3.009916 ACTGGAGAACCATGCTGAGAAAT 59.990 43.478 0.00 0.00 45.87 2.17
2428 2466 4.024387 TGACGTCAAAAGGTGATAAACTGC 60.024 41.667 17.62 0.00 38.90 4.40
2692 2730 6.636562 ACCGAGTATAGAGGTGAGTAATTG 57.363 41.667 0.00 0.00 36.81 2.32
2712 2750 7.954666 AATTGTTTATGGTAACTGCTGGTAT 57.045 32.000 0.00 0.00 37.61 2.73
2749 2787 8.360325 TCTAATATACAATGTACTGTTTGCCG 57.640 34.615 0.00 0.00 0.00 5.69
2996 3035 3.517296 TTCACTGCCCCAAAGAACATA 57.483 42.857 0.00 0.00 0.00 2.29
3082 3121 5.183530 TGTAGTGGAGTAGGCTGTACTTA 57.816 43.478 0.00 0.00 0.00 2.24
3092 3131 4.428294 AGGCTGTACTTACATGATGCAT 57.572 40.909 0.00 0.00 35.36 3.96
3111 3150 1.028330 TGCTACATGCCTGCAGAAGC 61.028 55.000 17.39 11.96 42.00 3.86
3140 3179 5.823045 AGCATTGGGTGTAATTACTCTTAGC 59.177 40.000 16.33 12.59 0.00 3.09
3354 3394 4.876107 GTCGGTCATGACTGGTTATCATTT 59.124 41.667 29.87 0.00 38.23 2.32
3414 3454 1.417145 TGCAAAATTCCTTTGGCTGCT 59.583 42.857 0.00 0.00 44.03 4.24
3559 3599 8.380867 TCATGAAGGCTGAAGATGTTATATCAT 58.619 33.333 0.00 0.00 0.00 2.45
3560 3600 9.011095 CATGAAGGCTGAAGATGTTATATCATT 57.989 33.333 0.00 0.00 0.00 2.57
3679 3719 5.105997 GCCAAAATCACTCACTGCTCTATTT 60.106 40.000 0.00 0.00 0.00 1.40
3751 3791 7.934120 GCTTGTCCACATAGTCTAAATAATCCT 59.066 37.037 0.00 0.00 0.00 3.24
4017 4057 8.788325 AATCTGTGGTACTAGAAATAACAACC 57.212 34.615 0.00 0.00 0.00 3.77
4179 4422 5.349543 GCATAAGAAAATCTTGGCCAACTTG 59.650 40.000 16.05 5.32 37.29 3.16
4183 4426 3.967332 AAATCTTGGCCAACTTGGATG 57.033 42.857 16.05 2.77 40.96 3.51
4410 4653 2.875933 GCACTTTACTACTTGTGCCACA 59.124 45.455 0.00 0.00 46.84 4.17
4412 4655 4.378459 GCACTTTACTACTTGTGCCACATC 60.378 45.833 0.00 0.00 46.84 3.06
4414 4657 5.238432 CACTTTACTACTTGTGCCACATCAA 59.762 40.000 0.00 0.00 0.00 2.57
4457 4743 7.758076 TGATTCTTGATTTGTCAATGCAATCTC 59.242 33.333 0.00 0.00 0.00 2.75
4777 5084 9.893305 ACAACAATTTTCTAGTATAAACACAGC 57.107 29.630 0.00 0.00 0.00 4.40
5138 5445 0.761802 GTCAGGATGGGGATCACCTC 59.238 60.000 16.81 10.08 40.03 3.85
5146 5453 1.363246 GGGGATCACCTCCTATTCCC 58.637 60.000 6.79 0.00 44.28 3.97
5582 5890 2.099446 CCGTATGGCAAAACCGCG 59.901 61.111 0.00 0.00 43.94 6.46
5970 6278 5.045432 ACCTCCTTTGATTACCCATTCGTTA 60.045 40.000 0.00 0.00 0.00 3.18
6101 6409 1.388547 TGCTATTCATTGTTCCCGCC 58.611 50.000 0.00 0.00 0.00 6.13
6252 6560 5.954752 TGGCCAAACAGGTAAATTATGATCA 59.045 36.000 0.61 0.00 40.61 2.92
6309 6623 4.750098 TCAGTCTTTCACGTTCCAATTCTC 59.250 41.667 0.00 0.00 0.00 2.87
6389 6816 7.762382 ACTGCTAAATTCTAATGTAAGCAACC 58.238 34.615 0.00 0.00 0.00 3.77
6395 6822 6.759497 ATTCTAATGTAAGCAACCAAGGAC 57.241 37.500 0.00 0.00 0.00 3.85
6446 6873 3.838565 TCTTGTTTCATTAGGTTGCCCA 58.161 40.909 0.00 0.00 0.00 5.36
6626 7053 8.691661 ATTGTAAGTAAATCTGTGACACCTTT 57.308 30.769 2.45 3.49 0.00 3.11
6745 7172 2.843701 ACTCAAACAGAAGACCAGCTG 58.156 47.619 6.78 6.78 38.10 4.24
6781 7208 1.251527 TTCTGGAGGAGGTGAGCGAC 61.252 60.000 0.00 0.00 0.00 5.19
6921 7348 7.784470 AGTTAACTTTCCACTCACTATCTCT 57.216 36.000 1.12 0.00 0.00 3.10
6942 7369 9.860898 ATCTCTGCAAAAATAAATTCACTTACC 57.139 29.630 0.00 0.00 0.00 2.85
7163 7590 5.245751 TGGAATTGCACACACCATCTTTAAT 59.754 36.000 0.00 0.00 0.00 1.40
7205 7633 7.044798 GCATGATAATAGTTGATCTAGGGGAC 58.955 42.308 0.00 0.00 31.67 4.46
7332 7760 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
7333 7761 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
7334 7762 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
7335 7763 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
7336 7764 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
7342 7770 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
7343 7771 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
7344 7772 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
7345 7773 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
7348 7776 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
7360 7788 4.785453 GCGCAGGGTCCAGGGAAG 62.785 72.222 0.30 0.00 0.00 3.46
7361 7789 4.101448 CGCAGGGTCCAGGGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
7362 7790 3.732849 GCAGGGTCCAGGGAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
7363 7791 2.204151 CAGGGTCCAGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
7364 7792 2.125225 AGGGTCCAGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
7365 7793 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
7366 7794 3.400054 GGTCCAGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
7367 7795 2.284405 GTCCAGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
7368 7796 2.284405 TCCAGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
7369 7797 3.400054 CCAGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
7370 7798 2.606519 CAGGGAAGGGTCCGACCA 60.607 66.667 19.43 0.00 46.04 4.02
7371 7799 2.606826 AGGGAAGGGTCCGACCAC 60.607 66.667 19.43 8.70 46.04 4.16
7372 7800 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
7373 7801 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
7374 7802 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
7375 7803 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
7376 7804 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
7377 7805 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
7378 7806 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
7388 7816 4.996788 ACCACTTTGGGTCTATAGTACG 57.003 45.455 0.00 0.00 43.37 3.67
7389 7817 3.131755 ACCACTTTGGGTCTATAGTACGC 59.868 47.826 0.00 6.13 43.37 4.42
7390 7818 3.131577 CCACTTTGGGTCTATAGTACGCA 59.868 47.826 13.98 13.98 37.94 5.24
7391 7819 4.360563 CACTTTGGGTCTATAGTACGCAG 58.639 47.826 16.00 11.29 40.36 5.18
7392 7820 3.181478 ACTTTGGGTCTATAGTACGCAGC 60.181 47.826 16.00 2.07 40.36 5.25
7393 7821 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
7394 7822 1.133575 TGGGTCTATAGTACGCAGCCT 60.134 52.381 13.98 0.00 35.18 4.58
7395 7823 1.962100 GGGTCTATAGTACGCAGCCTT 59.038 52.381 0.00 0.00 0.00 4.35
7396 7824 2.364647 GGGTCTATAGTACGCAGCCTTT 59.635 50.000 0.00 0.00 0.00 3.11
7397 7825 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
7398 7826 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
7399 7827 2.626743 TCTATAGTACGCAGCCTTTCCC 59.373 50.000 0.00 0.00 0.00 3.97
7400 7828 1.497161 ATAGTACGCAGCCTTTCCCT 58.503 50.000 0.00 0.00 0.00 4.20
7401 7829 2.148446 TAGTACGCAGCCTTTCCCTA 57.852 50.000 0.00 0.00 0.00 3.53
7402 7830 0.535797 AGTACGCAGCCTTTCCCTAC 59.464 55.000 0.00 0.00 0.00 3.18
7403 7831 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
7404 7832 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
7405 7833 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
7406 7834 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
7407 7835 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
7408 7836 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
7409 7837 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
7410 7838 3.690460 CAGCCTTTCCCTACATTTCTGT 58.310 45.455 0.00 0.00 39.49 3.41
7411 7839 4.843728 CAGCCTTTCCCTACATTTCTGTA 58.156 43.478 0.00 0.00 36.79 2.74
7412 7840 5.253330 CAGCCTTTCCCTACATTTCTGTAA 58.747 41.667 0.00 0.00 37.41 2.41
7413 7841 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
7414 7842 5.250774 AGCCTTTCCCTACATTTCTGTAAGA 59.749 40.000 0.00 0.00 44.68 2.10
7426 7854 3.685139 TCTGTAAGAGGCTGTTTCCAG 57.315 47.619 0.90 9.48 38.67 3.86
7427 7855 2.303022 TCTGTAAGAGGCTGTTTCCAGG 59.697 50.000 17.71 5.83 38.67 4.45
7428 7856 2.303022 CTGTAAGAGGCTGTTTCCAGGA 59.697 50.000 0.90 0.00 35.89 3.86
7429 7857 2.038557 TGTAAGAGGCTGTTTCCAGGAC 59.961 50.000 0.90 0.00 39.22 3.85
7430 7858 1.439543 AAGAGGCTGTTTCCAGGACT 58.560 50.000 0.00 0.00 39.22 3.85
7431 7859 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
7432 7860 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
7433 7861 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
7434 7862 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
7435 7863 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
7436 7864 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
7437 7865 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
7438 7866 1.566703 TGTTTCCAGGACTTGAACCCA 59.433 47.619 0.00 0.00 0.00 4.51
7439 7867 2.176798 TGTTTCCAGGACTTGAACCCAT 59.823 45.455 0.00 0.00 0.00 4.00
7440 7868 2.558359 GTTTCCAGGACTTGAACCCATG 59.442 50.000 0.00 0.00 0.00 3.66
7441 7869 1.741028 TCCAGGACTTGAACCCATGA 58.259 50.000 0.00 0.00 0.00 3.07
7442 7870 1.351017 TCCAGGACTTGAACCCATGAC 59.649 52.381 0.00 0.00 0.00 3.06
7443 7871 1.614317 CCAGGACTTGAACCCATGACC 60.614 57.143 0.00 0.00 34.29 4.02
7444 7872 1.352352 CAGGACTTGAACCCATGACCT 59.648 52.381 0.00 0.00 40.96 3.85
7445 7873 1.630878 AGGACTTGAACCCATGACCTC 59.369 52.381 0.00 0.00 37.82 3.85
7446 7874 1.351017 GGACTTGAACCCATGACCTCA 59.649 52.381 0.00 0.00 32.45 3.86
7447 7875 2.025887 GGACTTGAACCCATGACCTCAT 60.026 50.000 0.00 0.00 36.96 2.90
7694 8123 7.064016 CAGAGTTTCATTTCAGAGTAACTAGCC 59.936 40.741 0.00 0.00 0.00 3.93
7772 8201 4.413495 TTTGTTGCTGGTAGAAATACGC 57.587 40.909 0.00 0.00 0.00 4.42
7773 8202 3.328382 TGTTGCTGGTAGAAATACGCT 57.672 42.857 0.00 0.00 0.00 5.07
7790 8219 8.959734 AAATACGCTTGAATAAAGGTTGTAAC 57.040 30.769 0.00 0.00 36.30 2.50
8313 8742 1.474143 GCAGGATGTACCAGGCTCTTC 60.474 57.143 0.00 0.00 42.04 2.87
8337 8766 1.533033 TCTGCCCAGAGGTCGACAA 60.533 57.895 18.91 0.00 34.57 3.18
8513 8942 5.653255 AACAAGAGGTATAAGGGATGCAT 57.347 39.130 0.00 0.00 0.00 3.96
8545 8974 7.023575 GCCACTTCTGTTACAATGAAATACTG 58.976 38.462 0.00 0.00 0.00 2.74
8585 9015 3.297134 TTGCTCCCTTCATTATCCACC 57.703 47.619 0.00 0.00 0.00 4.61
8712 9143 0.599204 GTGACTCGGTTGAAAGGCGA 60.599 55.000 0.00 0.00 0.00 5.54
8713 9144 0.105224 TGACTCGGTTGAAAGGCGAA 59.895 50.000 0.00 0.00 0.00 4.70
8791 9222 3.258372 ACTTTTCTGAGCACGTCCTATCA 59.742 43.478 0.00 0.00 0.00 2.15
8800 9231 0.385751 ACGTCCTATCATCTGGCACG 59.614 55.000 0.00 0.00 35.05 5.34
8846 9277 3.181480 GGAGCTACAGTTTCTAGCCTGAG 60.181 52.174 9.87 5.52 37.88 3.35
8852 9283 1.552792 AGTTTCTAGCCTGAGACTGGC 59.447 52.381 10.81 10.81 46.61 4.85
8986 9417 1.350319 CCAACGTGTGACCACAACG 59.650 57.895 17.06 17.06 43.77 4.10
9079 9510 2.310647 GTTTGGATTTGGGGAGTAGGGA 59.689 50.000 0.00 0.00 0.00 4.20
9090 9521 1.002274 AGTAGGGAGCTGGGTGGAG 59.998 63.158 0.00 0.00 0.00 3.86
9119 9550 0.615331 TTAGGAGTGCAAGGCAGAGG 59.385 55.000 0.00 0.00 40.08 3.69
9144 9575 5.063060 GGTCACTGTGTCAAATTACCGATAC 59.937 44.000 7.79 0.00 0.00 2.24
9152 9583 5.473846 TGTCAAATTACCGATACCAAGCAAA 59.526 36.000 0.00 0.00 0.00 3.68
9153 9584 6.151985 TGTCAAATTACCGATACCAAGCAAAT 59.848 34.615 0.00 0.00 0.00 2.32
9154 9585 6.472163 GTCAAATTACCGATACCAAGCAAATG 59.528 38.462 0.00 0.00 0.00 2.32
9155 9586 6.375736 TCAAATTACCGATACCAAGCAAATGA 59.624 34.615 0.00 0.00 0.00 2.57
9175 9660 5.975693 TGACTGTTTGAACTCTGGTTTTT 57.024 34.783 0.00 0.00 35.58 1.94
9190 9675 7.286775 ACTCTGGTTTTTATTTGCCTTCTTACA 59.713 33.333 0.00 0.00 0.00 2.41
9202 9687 0.680921 TTCTTACATGCTGGCTGGGC 60.681 55.000 0.00 0.00 0.00 5.36
9212 9697 2.685999 GGCTGGGCCCTCTTGATT 59.314 61.111 25.70 0.00 44.06 2.57
9213 9698 1.922821 GGCTGGGCCCTCTTGATTA 59.077 57.895 25.70 0.00 44.06 1.75
9214 9699 0.480252 GGCTGGGCCCTCTTGATTAT 59.520 55.000 25.70 0.00 44.06 1.28
9215 9700 1.546548 GGCTGGGCCCTCTTGATTATC 60.547 57.143 25.70 0.00 44.06 1.75
9254 9758 2.497138 CAACTGCAAGAGGACACATGA 58.503 47.619 0.00 0.00 37.43 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.540617 TGTTGCTCAAAGTGCTTAGTGA 58.459 40.909 0.00 0.00 0.00 3.41
29 30 4.103153 GGGGATGAGGTATTGTTGATGAGA 59.897 45.833 0.00 0.00 0.00 3.27
46 47 5.397360 AGCCAATCCTATTAAAAGGGGATG 58.603 41.667 0.00 0.00 38.42 3.51
47 48 5.686535 AGCCAATCCTATTAAAAGGGGAT 57.313 39.130 0.00 0.00 39.91 3.85
62 63 3.054361 TGAGTCCCTTAGGAAAGCCAATC 60.054 47.826 0.00 0.00 46.38 2.67
133 134 6.469782 TCAAAATATCAAGGGCAAAGGATC 57.530 37.500 0.00 0.00 0.00 3.36
266 267 2.778299 GTGCAACTAATCACTGGGTGA 58.222 47.619 2.80 2.80 46.90 4.02
287 288 7.924412 AGACAAACACGAAGAAGAAGTGTAATA 59.076 33.333 0.74 0.00 46.91 0.98
295 296 4.033587 CCGAAAGACAAACACGAAGAAGAA 59.966 41.667 0.00 0.00 0.00 2.52
296 297 3.554324 CCGAAAGACAAACACGAAGAAGA 59.446 43.478 0.00 0.00 0.00 2.87
297 298 3.303132 CCCGAAAGACAAACACGAAGAAG 60.303 47.826 0.00 0.00 0.00 2.85
322 323 1.000060 ACGAACGAATTTGAGGACCGA 60.000 47.619 0.00 0.00 0.00 4.69
339 340 1.475280 CCCTTGACTATGTCCGAACGA 59.525 52.381 0.00 0.00 0.00 3.85
442 443 5.957771 TGAATAGACCTAAAGCACCTGAT 57.042 39.130 0.00 0.00 0.00 2.90
483 484 3.655810 GAGCACCCTCGAGCCACAG 62.656 68.421 6.99 0.00 0.00 3.66
497 498 1.295423 GTGCCCCTAAGAACGAGCA 59.705 57.895 0.00 0.00 0.00 4.26
498 499 1.810030 CGTGCCCCTAAGAACGAGC 60.810 63.158 0.00 0.00 38.27 5.03
501 502 2.388232 GCACGTGCCCCTAAGAACG 61.388 63.158 30.12 0.00 41.64 3.95
523 524 4.462483 TGTTGATGATAACCCAAAAGCCTC 59.538 41.667 0.00 0.00 0.00 4.70
543 544 1.064017 TGGAGTTGGCTTGACCTTGTT 60.064 47.619 0.00 0.00 40.22 2.83
617 619 1.536284 GGTAGCTGGATCGACGAAAGG 60.536 57.143 0.00 0.00 0.00 3.11
758 762 8.893727 TGAGTTCCTCAAAAGAAGAGTAAAAAG 58.106 33.333 0.00 0.00 37.57 2.27
796 800 0.681564 GCCCGAGTCCTCTCAAGAGA 60.682 60.000 8.62 1.68 44.74 3.10
1149 1153 2.347490 GTCTTCTTGGAGGCGGCA 59.653 61.111 13.08 0.00 0.00 5.69
1222 1226 2.040544 CAAATGGCGAGCGAGGGTT 61.041 57.895 0.00 0.00 0.00 4.11
1266 1271 0.914644 CTCCTCCCCATCTGAGCAAA 59.085 55.000 0.00 0.00 0.00 3.68
1303 1308 2.305927 GGACAGGATCTCCTTGGTGAAA 59.694 50.000 0.00 0.00 46.09 2.69
1401 1407 1.339055 TGCAGATACAGTTCCACAGCC 60.339 52.381 0.00 0.00 0.00 4.85
1558 1596 2.582498 GCGTTACTCGGCTGCGAT 60.582 61.111 0.00 0.00 40.26 4.58
1572 1610 3.197790 GCAGGTGCATCATCGCGT 61.198 61.111 5.77 0.00 41.59 6.01
1586 1624 0.959372 CTTGCCACCTCCTTCTGCAG 60.959 60.000 7.63 7.63 32.88 4.41
1590 1628 1.151810 TCCCTTGCCACCTCCTTCT 60.152 57.895 0.00 0.00 0.00 2.85
1603 1641 0.980423 AGCGCTTCTTCTTCTCCCTT 59.020 50.000 2.64 0.00 0.00 3.95
1799 1837 2.936919 TGTTCCACTGCTGAGTCAAT 57.063 45.000 0.00 0.00 0.00 2.57
1856 1894 3.141460 TCCTCGATCTGAAACCCCCTATA 59.859 47.826 0.00 0.00 0.00 1.31
1885 1923 2.403252 ACAAGAGAAATGGCCCGTAG 57.597 50.000 0.00 0.00 0.00 3.51
1969 2007 4.087892 CTGGAGCAGGACCGTGGG 62.088 72.222 0.00 0.00 0.00 4.61
2106 2144 4.030216 AGGTTTTGACTGTGATTTTGGGT 58.970 39.130 0.00 0.00 0.00 4.51
2159 2197 7.391148 ACAAACTGTGTAAGATGAAACAACT 57.609 32.000 0.00 0.00 39.29 3.16
2200 2238 6.561070 TGCATTGATTAAGGTACTATAGGGGT 59.439 38.462 4.43 0.00 38.49 4.95
2392 2430 6.017934 CCTTTTGACGTCATCTTCTGAAGAAA 60.018 38.462 22.68 11.33 41.63 2.52
2428 2466 8.481974 TGATTAGATTTGGAAAAATGTGCATG 57.518 30.769 0.00 0.00 0.00 4.06
2536 2574 6.599638 AGAAACTAGAAAATGCACTGTATCCC 59.400 38.462 0.00 0.00 0.00 3.85
2692 2730 7.852971 TGTAATACCAGCAGTTACCATAAAC 57.147 36.000 0.00 0.00 0.00 2.01
2738 2776 2.902705 AGAACACTCGGCAAACAGTA 57.097 45.000 0.00 0.00 0.00 2.74
2749 2787 4.558538 AGCACAACATTGAAGAACACTC 57.441 40.909 0.00 0.00 0.00 3.51
2963 3002 5.374154 TGGGGCAGTGAATCCCTAATAAATA 59.626 40.000 14.88 0.00 42.25 1.40
2996 3035 3.320826 AGCATTTGGGTTTTTCGCTACTT 59.679 39.130 0.00 0.00 0.00 2.24
3082 3121 1.611977 GGCATGTAGCATGCATCATGT 59.388 47.619 33.76 15.49 40.31 3.21
3092 3131 1.028330 GCTTCTGCAGGCATGTAGCA 61.028 55.000 15.13 0.00 41.68 3.49
3111 3150 1.382522 ATTACACCCAATGCTCTGCG 58.617 50.000 0.00 0.00 0.00 5.18
3206 3246 4.244066 TGCCGGTTGAAAATTGATTCATG 58.756 39.130 1.90 0.00 38.98 3.07
4017 4057 8.277018 ACAAACGACTTTTAACAAAACCAAAAG 58.723 29.630 0.00 4.87 42.36 2.27
4410 4653 9.798994 GAATCACAAAATCTAAATGCTCTTGAT 57.201 29.630 0.00 0.00 0.00 2.57
4412 4655 9.635520 AAGAATCACAAAATCTAAATGCTCTTG 57.364 29.630 0.00 0.00 0.00 3.02
4414 4657 9.017509 TCAAGAATCACAAAATCTAAATGCTCT 57.982 29.630 0.00 0.00 0.00 4.09
4457 4743 1.867233 ACGCAAACAGCTCAGTTACAG 59.133 47.619 0.00 0.00 42.61 2.74
4576 4862 0.528017 CTCGTAGCCTTGCTCACAGA 59.472 55.000 0.00 0.00 40.44 3.41
4850 5157 4.877378 ACATCTTGAACAAATGTGGCAT 57.123 36.364 0.00 0.00 32.58 4.40
4981 5288 6.473778 CACCGATGTCACTTGAGAATAACTAG 59.526 42.308 0.00 0.00 0.00 2.57
5138 5445 7.546250 ACTATAACTGATGTCTGGGAATAGG 57.454 40.000 0.00 0.00 0.00 2.57
5146 5453 8.409371 ACAGTGTCATACTATAACTGATGTCTG 58.591 37.037 8.02 0.00 40.54 3.51
5582 5890 5.869753 ATGCATCTTTGTGTACTTGAGTC 57.130 39.130 0.00 0.00 0.00 3.36
6101 6409 6.851222 ATTCAATAGCCAGAAGTTATGTCG 57.149 37.500 0.00 0.00 0.00 4.35
6252 6560 9.283768 GAAAAATGGGTGGAAATTTTAATCAGT 57.716 29.630 0.00 0.00 35.47 3.41
6260 6574 4.821260 GTGCAGAAAAATGGGTGGAAATTT 59.179 37.500 0.00 0.00 0.00 1.82
6309 6623 0.933097 GCAGTGTATCATGTGCGAGG 59.067 55.000 0.00 0.00 0.00 4.63
6395 6822 8.365210 GTTGTAAGCACATCGAACAAAATATTG 58.635 33.333 0.00 0.00 37.24 1.90
6446 6873 6.409349 GCACTTAGGTGGTATTTCCTTATCCT 60.409 42.308 7.15 0.00 43.18 3.24
6626 7053 5.059161 CACTCATCTCAAGTTTTGACAGGA 58.941 41.667 0.00 0.00 35.46 3.86
6745 7172 6.239176 CCTCCAGAAGTTGATACAGTCTATCC 60.239 46.154 0.00 0.00 0.00 2.59
6781 7208 0.533491 CATCAAACCACATGCCTGGG 59.467 55.000 7.24 0.08 35.34 4.45
6942 7369 7.254522 GGCACTGGCAAATGTATCAAATAAATG 60.255 37.037 0.00 0.00 43.71 2.32
7205 7633 4.082733 TCTGGAAGCCGTAATCTATCGATG 60.083 45.833 8.54 0.00 0.00 3.84
7310 7738 0.763986 ATGCACCAGGTTGCCCTTTT 60.764 50.000 10.46 0.00 42.25 2.27
7311 7739 1.152269 ATGCACCAGGTTGCCCTTT 60.152 52.632 10.46 0.00 42.25 3.11
7312 7740 1.909781 CATGCACCAGGTTGCCCTT 60.910 57.895 10.46 0.00 42.25 3.95
7313 7741 1.788518 TACATGCACCAGGTTGCCCT 61.789 55.000 10.46 0.00 42.25 5.19
7314 7742 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
7315 7743 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
7316 7744 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
7317 7745 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
7318 7746 3.558674 GAGCTACATGCACCAGGTT 57.441 52.632 0.00 0.00 45.94 3.50
7343 7771 4.785453 CTTCCCTGGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
7344 7772 4.101448 CCTTCCCTGGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
7345 7773 3.732849 CCCTTCCCTGGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
7346 7774 2.204151 ACCCTTCCCTGGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
7347 7775 2.125225 GACCCTTCCCTGGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
7348 7776 3.015753 GGACCCTTCCCTGGACCC 61.016 72.222 0.00 0.00 35.57 4.46
7349 7777 3.400054 CGGACCCTTCCCTGGACC 61.400 72.222 0.00 0.00 38.99 4.46
7350 7778 2.284405 TCGGACCCTTCCCTGGAC 60.284 66.667 0.00 0.00 38.99 4.02
7351 7779 2.284405 GTCGGACCCTTCCCTGGA 60.284 66.667 0.00 0.00 38.99 3.86
7352 7780 3.400054 GGTCGGACCCTTCCCTGG 61.400 72.222 16.55 0.00 38.99 4.45
7353 7781 2.606519 TGGTCGGACCCTTCCCTG 60.607 66.667 23.81 0.00 38.99 4.45
7354 7782 2.606826 GTGGTCGGACCCTTCCCT 60.607 66.667 23.81 0.00 38.99 4.20
7355 7783 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
7356 7784 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
7357 7785 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
7358 7786 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
7359 7787 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
7360 7788 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
7361 7789 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
7362 7790 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
7367 7795 3.131755 GCGTACTATAGACCCAAAGTGGT 59.868 47.826 6.78 0.00 42.79 4.16
7368 7796 3.131577 TGCGTACTATAGACCCAAAGTGG 59.868 47.826 6.78 0.00 37.25 4.00
7369 7797 4.360563 CTGCGTACTATAGACCCAAAGTG 58.639 47.826 6.78 0.00 0.00 3.16
7370 7798 3.181478 GCTGCGTACTATAGACCCAAAGT 60.181 47.826 6.78 0.00 0.00 2.66
7371 7799 3.381949 GCTGCGTACTATAGACCCAAAG 58.618 50.000 6.78 0.00 0.00 2.77
7372 7800 2.101917 GGCTGCGTACTATAGACCCAAA 59.898 50.000 6.78 0.00 0.00 3.28
7373 7801 1.684983 GGCTGCGTACTATAGACCCAA 59.315 52.381 6.78 0.00 0.00 4.12
7374 7802 1.133575 AGGCTGCGTACTATAGACCCA 60.134 52.381 6.78 0.00 0.00 4.51
7375 7803 1.618487 AGGCTGCGTACTATAGACCC 58.382 55.000 6.78 0.00 0.00 4.46
7376 7804 3.552478 GGAAAGGCTGCGTACTATAGACC 60.552 52.174 6.78 0.00 0.00 3.85
7377 7805 3.552478 GGGAAAGGCTGCGTACTATAGAC 60.552 52.174 6.78 0.00 0.00 2.59
7378 7806 2.626743 GGGAAAGGCTGCGTACTATAGA 59.373 50.000 6.78 0.00 0.00 1.98
7379 7807 2.628657 AGGGAAAGGCTGCGTACTATAG 59.371 50.000 0.00 0.00 0.00 1.31
7380 7808 2.674420 AGGGAAAGGCTGCGTACTATA 58.326 47.619 0.00 0.00 0.00 1.31
7381 7809 1.497161 AGGGAAAGGCTGCGTACTAT 58.503 50.000 0.00 0.00 0.00 2.12
7382 7810 1.753073 GTAGGGAAAGGCTGCGTACTA 59.247 52.381 0.00 0.00 34.81 1.82
7383 7811 0.535797 GTAGGGAAAGGCTGCGTACT 59.464 55.000 0.00 0.00 34.81 2.73
7384 7812 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
7385 7813 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
7386 7814 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
7387 7815 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
7388 7816 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
7389 7817 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
7390 7818 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
7391 7819 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
7392 7820 6.116126 CCTCTTACAGAAATGTAGGGAAAGG 58.884 44.000 0.00 0.00 0.00 3.11
7393 7821 5.586643 GCCTCTTACAGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
7394 7822 5.250774 AGCCTCTTACAGAAATGTAGGGAAA 59.749 40.000 0.00 0.00 0.00 3.13
7395 7823 4.783227 AGCCTCTTACAGAAATGTAGGGAA 59.217 41.667 0.00 0.00 0.00 3.97
7396 7824 4.162320 CAGCCTCTTACAGAAATGTAGGGA 59.838 45.833 0.00 0.00 0.00 4.20
7397 7825 4.080863 ACAGCCTCTTACAGAAATGTAGGG 60.081 45.833 0.00 0.66 0.00 3.53
7398 7826 5.091261 ACAGCCTCTTACAGAAATGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
7399 7827 6.092807 GGAAACAGCCTCTTACAGAAATGTAG 59.907 42.308 0.00 0.00 0.00 2.74
7400 7828 5.938125 GGAAACAGCCTCTTACAGAAATGTA 59.062 40.000 0.00 0.00 0.00 2.29
7401 7829 4.762251 GGAAACAGCCTCTTACAGAAATGT 59.238 41.667 0.00 0.00 0.00 2.71
7402 7830 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
7403 7831 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
7404 7832 4.431416 TGGAAACAGCCTCTTACAGAAA 57.569 40.909 0.00 0.00 35.01 2.52
7418 7846 1.566703 TGGGTTCAAGTCCTGGAAACA 59.433 47.619 0.00 0.00 32.36 2.83
7419 7847 2.358322 TGGGTTCAAGTCCTGGAAAC 57.642 50.000 0.00 0.00 0.00 2.78
7420 7848 2.445145 TCATGGGTTCAAGTCCTGGAAA 59.555 45.455 0.00 0.00 0.00 3.13
7421 7849 2.061848 TCATGGGTTCAAGTCCTGGAA 58.938 47.619 0.00 0.00 0.00 3.53
7422 7850 1.351017 GTCATGGGTTCAAGTCCTGGA 59.649 52.381 0.00 0.00 0.00 3.86
7423 7851 1.614317 GGTCATGGGTTCAAGTCCTGG 60.614 57.143 0.00 0.00 0.00 4.45
7424 7852 1.352352 AGGTCATGGGTTCAAGTCCTG 59.648 52.381 0.00 0.00 0.00 3.86
7425 7853 1.630878 GAGGTCATGGGTTCAAGTCCT 59.369 52.381 0.00 0.00 0.00 3.85
7426 7854 1.351017 TGAGGTCATGGGTTCAAGTCC 59.649 52.381 0.00 0.00 0.00 3.85
7427 7855 2.859165 TGAGGTCATGGGTTCAAGTC 57.141 50.000 0.00 0.00 0.00 3.01
7442 7870 8.875803 CAAATAAAATGAATTGTGACCATGAGG 58.124 33.333 0.00 0.00 42.21 3.86
7443 7871 8.875803 CCAAATAAAATGAATTGTGACCATGAG 58.124 33.333 0.00 0.00 0.00 2.90
7444 7872 8.373981 ACCAAATAAAATGAATTGTGACCATGA 58.626 29.630 0.00 0.00 0.00 3.07
7445 7873 8.550710 ACCAAATAAAATGAATTGTGACCATG 57.449 30.769 0.00 0.00 0.00 3.66
7446 7874 9.001542 CAACCAAATAAAATGAATTGTGACCAT 57.998 29.630 0.00 0.00 0.00 3.55
7447 7875 8.206867 TCAACCAAATAAAATGAATTGTGACCA 58.793 29.630 0.00 0.00 0.00 4.02
7448 7876 8.600449 TCAACCAAATAAAATGAATTGTGACC 57.400 30.769 0.00 0.00 0.00 4.02
7449 7877 8.223100 GCTCAACCAAATAAAATGAATTGTGAC 58.777 33.333 0.00 0.00 0.00 3.67
7450 7878 7.930325 TGCTCAACCAAATAAAATGAATTGTGA 59.070 29.630 0.00 0.00 0.00 3.58
7451 7879 8.085720 TGCTCAACCAAATAAAATGAATTGTG 57.914 30.769 0.00 0.00 0.00 3.33
7452 7880 7.095102 GCTGCTCAACCAAATAAAATGAATTGT 60.095 33.333 0.00 0.00 0.00 2.71
7453 7881 7.238571 GCTGCTCAACCAAATAAAATGAATTG 58.761 34.615 0.00 0.00 0.00 2.32
7454 7882 6.091169 CGCTGCTCAACCAAATAAAATGAATT 59.909 34.615 0.00 0.00 0.00 2.17
7459 7887 4.519540 ACGCTGCTCAACCAAATAAAAT 57.480 36.364 0.00 0.00 0.00 1.82
7673 8102 6.874134 GTCAGGCTAGTTACTCTGAAATGAAA 59.126 38.462 4.21 0.00 37.90 2.69
7694 8123 7.925483 TCAAGGTTTGGTTATTCAAAATGTCAG 59.075 33.333 0.00 0.00 38.21 3.51
7772 8201 8.339714 TCGAAACAGTTACAACCTTTATTCAAG 58.660 33.333 0.00 0.00 0.00 3.02
7773 8202 8.211116 TCGAAACAGTTACAACCTTTATTCAA 57.789 30.769 0.00 0.00 0.00 2.69
8246 8675 4.653801 TGGATATCCCACGAGAAGAAATCA 59.346 41.667 19.34 0.00 40.82 2.57
8313 8742 0.390472 GACCTCTGGGCAGACGAAAG 60.390 60.000 0.00 0.00 35.63 2.62
8337 8766 1.546476 CCACTCGGCAGACTTCTTAGT 59.454 52.381 0.00 0.00 37.31 2.24
8451 8880 0.513820 GCAGCTTTACGTTTACCGCA 59.486 50.000 0.00 0.00 41.42 5.69
8513 8942 2.698274 TGTAACAGAAGTGGCAGAGTGA 59.302 45.455 0.00 0.00 0.00 3.41
8545 8974 1.864669 TTGGGGCTCCATTTCATTCC 58.135 50.000 5.88 0.00 43.63 3.01
8585 9015 8.883731 AGACGGTTTTATCAGTAAAGAATGATG 58.116 33.333 0.00 0.00 36.81 3.07
8712 9143 5.819901 TGGCTTCAATTTGAAACGGATTTTT 59.180 32.000 12.62 0.00 35.73 1.94
8713 9144 5.363939 TGGCTTCAATTTGAAACGGATTTT 58.636 33.333 12.62 0.00 35.73 1.82
8852 9283 1.406065 ATGGCTCCCAGTGAGGATCG 61.406 60.000 0.00 0.00 41.73 3.69
8853 9284 0.842635 AATGGCTCCCAGTGAGGATC 59.157 55.000 0.00 0.00 41.73 3.36
8986 9417 3.938963 TGTTTCACTGTGAACAACCTCTC 59.061 43.478 21.95 6.88 35.89 3.20
9079 9510 3.654143 TGCATGCTCCACCCAGCT 61.654 61.111 20.33 0.00 40.39 4.24
9119 9550 2.482721 CGGTAATTTGACACAGTGACCC 59.517 50.000 7.81 0.00 0.00 4.46
9144 9575 4.685924 AGTTCAAACAGTCATTTGCTTGG 58.314 39.130 0.00 0.00 39.08 3.61
9152 9583 6.530019 AAAAACCAGAGTTCAAACAGTCAT 57.470 33.333 0.00 0.00 34.19 3.06
9153 9584 5.975693 AAAAACCAGAGTTCAAACAGTCA 57.024 34.783 0.00 0.00 34.19 3.41
9154 9585 8.807581 CAAATAAAAACCAGAGTTCAAACAGTC 58.192 33.333 0.00 0.00 34.19 3.51
9155 9586 7.277760 GCAAATAAAAACCAGAGTTCAAACAGT 59.722 33.333 0.00 0.00 34.19 3.55
9175 9660 3.381272 GCCAGCATGTAAGAAGGCAAATA 59.619 43.478 0.00 0.00 41.63 1.40
9202 9687 9.790344 AATGAAATCAGTAGATAATCAAGAGGG 57.210 33.333 0.00 0.00 35.29 4.30
9214 9699 7.970061 GCAGTTGCATAAAATGAAATCAGTAGA 59.030 33.333 0.00 0.00 35.88 2.59
9215 9700 8.112099 GCAGTTGCATAAAATGAAATCAGTAG 57.888 34.615 0.00 0.00 35.88 2.57
9254 9758 4.116747 TGCACGTTTTTGAAACCAGATT 57.883 36.364 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.