Multiple sequence alignment - TraesCS3D01G271600

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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 TraesCS3D01G271600 chr3D 100.000 4034 0 0 1 4034 376813309 376817342 0.000000e+00 7450.0
1 TraesCS3D01G271600 chr3D 90.909 55 4 1 3518 3572 571562106 571562053 5.590000e-09 73.1
2 TraesCS3D01G271600 chr3D 90.476 42 4 0 3521 3562 573740550 573740591 5.630000e-04 56.5
3 TraesCS3D01G271600 chr3B 94.479 3170 100 35 571 3691 491367194 491370337 0.000000e+00 4815.0
4 TraesCS3D01G271600 chr3B 87.597 516 50 5 1 511 491366553 491367059 1.620000e-163 586.0
5 TraesCS3D01G271600 chr3B 82.328 232 26 7 3778 3996 228394148 228394377 1.910000e-43 187.0
6 TraesCS3D01G271600 chr3B 93.478 92 5 1 1 91 491362325 491362416 7.030000e-28 135.0
7 TraesCS3D01G271600 chr3B 96.296 81 3 0 512 592 491367109 491367189 2.530000e-27 134.0
8 TraesCS3D01G271600 chr3A 95.949 2518 61 17 962 3464 501221319 501223810 0.000000e+00 4047.0
9 TraesCS3D01G271600 chr3A 92.523 321 12 5 571 890 501220611 501220920 2.210000e-122 449.0
10 TraesCS3D01G271600 chr3A 91.262 206 9 4 3521 3725 501224138 501224335 5.140000e-69 272.0
11 TraesCS3D01G271600 chr3A 97.403 77 2 0 511 587 501220520 501220596 9.100000e-27 132.0
12 TraesCS3D01G271600 chr3A 87.879 99 10 2 414 511 501220361 501220458 9.160000e-22 115.0
13 TraesCS3D01G271600 chr3A 89.412 85 7 2 3694 3777 501224340 501224423 5.510000e-19 106.0
14 TraesCS3D01G271600 chr3A 91.111 45 4 0 3518 3562 15671840 15671796 1.210000e-05 62.1
15 TraesCS3D01G271600 chr7A 85.446 213 27 4 3773 3983 63285770 63285980 6.790000e-53 219.0
16 TraesCS3D01G271600 chr7A 83.182 220 23 4 3778 3984 491333006 491333224 5.320000e-44 189.0
17 TraesCS3D01G271600 chr7A 100.000 38 0 0 3518 3555 733695765 733695802 2.010000e-08 71.3
18 TraesCS3D01G271600 chr7A 100.000 38 0 0 3518 3555 733735168 733735205 2.010000e-08 71.3
19 TraesCS3D01G271600 chr5A 83.190 232 23 4 3775 3991 615919736 615919966 8.840000e-47 198.0
20 TraesCS3D01G271600 chr5D 81.298 262 29 11 3770 4017 40693284 40693539 1.140000e-45 195.0
21 TraesCS3D01G271600 chr5D 80.717 223 25 9 3776 3984 502074993 502075211 1.500000e-34 158.0
22 TraesCS3D01G271600 chr5B 83.333 216 21 6 3774 3977 553188901 553188689 6.890000e-43 185.0
23 TraesCS3D01G271600 chr4D 81.070 243 27 9 3778 4006 20280267 20280030 4.140000e-40 176.0
24 TraesCS3D01G271600 chr1D 84.049 163 21 4 3775 3935 209742335 209742494 6.980000e-33 152.0
25 TraesCS3D01G271600 chr6A 90.698 43 4 0 3518 3560 171768496 171768538 1.570000e-04 58.4
26 TraesCS3D01G271600 chr6A 100.000 29 0 0 222 250 421101690 421101718 2.000000e-03 54.7
27 TraesCS3D01G271600 chr1A 89.130 46 5 0 3518 3563 242063656 242063701 1.570000e-04 58.4


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 TraesCS3D01G271600 chr3D 376813309 376817342 4033 False 7450.0 7450 100.000000 1 4034 1 chr3D.!!$F1 4033
1 TraesCS3D01G271600 chr3B 491366553 491370337 3784 False 1845.0 4815 92.790667 1 3691 3 chr3B.!!$F3 3690
2 TraesCS3D01G271600 chr3A 501220361 501224423 4062 False 853.5 4047 92.404667 414 3777 6 chr3A.!!$F1 3363

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 1053 0.107654 CCCTTCCTTCGCTTCGGATT 60.108 55.0 0.0 0.0 0.00 3.01 F
936 1056 0.107848 TTCCTTCGCTTCGGATTCCC 60.108 55.0 0.0 0.0 0.00 3.97 F
2656 3133 0.032403 GCATCAACAGCCACAGCAAA 59.968 50.0 0.0 0.0 43.56 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1860 2337 0.598419 GAAGTTTGGCCAGTTGCTGC 60.598 55.0 5.11 0.0 40.92 5.25 R
2927 3404 0.824759 GAGCGTCATACTCCCAACCT 59.175 55.0 0.00 0.0 0.00 3.50 R
3940 4729 0.096454 AAGCGCGGTTATTCTTTCGC 59.904 50.0 23.79 0.0 44.04 4.70 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
55 56 1.073964 CAACTGTGACATCCGCTCTG 58.926 55.000 0.00 0.00 0.00 3.35
69 70 1.961277 CTCTGTGGGACAACGCCAC 60.961 63.158 0.00 0.00 44.16 5.01
82 83 1.206578 CGCCACCGTGACAAACATC 59.793 57.895 0.00 0.00 0.00 3.06
111 116 3.214328 ACACCATCTTTCACACACCTTC 58.786 45.455 0.00 0.00 0.00 3.46
112 117 3.117888 ACACCATCTTTCACACACCTTCT 60.118 43.478 0.00 0.00 0.00 2.85
116 121 6.039270 CACCATCTTTCACACACCTTCTAAAA 59.961 38.462 0.00 0.00 0.00 1.52
162 167 0.611714 GACAAGACGGGAAGGCCTTA 59.388 55.000 20.54 0.00 0.00 2.69
181 186 1.785041 ATTCCATTTCGATGGCGGCG 61.785 55.000 0.51 0.51 41.43 6.46
203 208 2.996249 ATCGCCTCACTGTTGATGAT 57.004 45.000 0.00 0.00 0.00 2.45
204 209 2.768253 TCGCCTCACTGTTGATGATT 57.232 45.000 0.00 0.00 0.00 2.57
207 212 2.868583 CGCCTCACTGTTGATGATTAGG 59.131 50.000 0.00 0.00 0.00 2.69
211 216 4.163078 CCTCACTGTTGATGATTAGGGACT 59.837 45.833 0.00 0.00 46.37 3.85
216 221 5.940470 ACTGTTGATGATTAGGGACTGAAAC 59.060 40.000 0.00 0.00 41.52 2.78
254 259 1.274416 ACCTCACCCTACCATCACCAT 60.274 52.381 0.00 0.00 0.00 3.55
258 263 0.326238 ACCCTACCATCACCATCGGT 60.326 55.000 0.00 0.00 35.62 4.69
260 265 1.202651 CCCTACCATCACCATCGGTTC 60.203 57.143 0.00 0.00 31.02 3.62
261 266 1.538204 CCTACCATCACCATCGGTTCG 60.538 57.143 0.00 0.00 31.02 3.95
270 275 1.231221 CCATCGGTTCGGAAACAACA 58.769 50.000 6.59 0.00 37.10 3.33
277 282 1.871676 GTTCGGAAACAACAGGGTCTC 59.128 52.381 0.00 0.00 35.36 3.36
279 284 0.949105 CGGAAACAACAGGGTCTCGG 60.949 60.000 0.00 0.00 0.00 4.63
313 318 1.028905 CAAAGTGGCAAACGAAGGGA 58.971 50.000 0.00 0.00 0.00 4.20
314 319 1.407258 CAAAGTGGCAAACGAAGGGAA 59.593 47.619 0.00 0.00 0.00 3.97
315 320 1.770294 AAGTGGCAAACGAAGGGAAA 58.230 45.000 0.00 0.00 0.00 3.13
316 321 1.770294 AGTGGCAAACGAAGGGAAAA 58.230 45.000 0.00 0.00 0.00 2.29
317 322 1.681264 AGTGGCAAACGAAGGGAAAAG 59.319 47.619 0.00 0.00 0.00 2.27
318 323 1.679153 GTGGCAAACGAAGGGAAAAGA 59.321 47.619 0.00 0.00 0.00 2.52
319 324 1.953686 TGGCAAACGAAGGGAAAAGAG 59.046 47.619 0.00 0.00 0.00 2.85
324 329 1.378646 CGAAGGGAAAAGAGGCCCC 60.379 63.158 0.00 0.00 45.89 5.80
328 333 1.774300 GGGAAAAGAGGCCCCTGAA 59.226 57.895 0.00 0.00 38.45 3.02
350 355 2.962421 CTCACCAGGGAGAAGGTAGATC 59.038 54.545 0.00 0.00 37.05 2.75
352 357 1.288335 ACCAGGGAGAAGGTAGATCGT 59.712 52.381 0.00 0.00 36.07 3.73
354 359 1.604755 CAGGGAGAAGGTAGATCGTCG 59.395 57.143 0.00 0.00 0.00 5.12
357 362 1.310904 GAGAAGGTAGATCGTCGCCT 58.689 55.000 0.00 0.00 0.00 5.52
358 363 1.677052 GAGAAGGTAGATCGTCGCCTT 59.323 52.381 11.15 11.15 38.58 4.35
360 365 0.381089 AAGGTAGATCGTCGCCTTCG 59.619 55.000 7.14 0.00 33.64 3.79
401 406 1.751382 CGGGAGAGAGGAAGGAGGTAC 60.751 61.905 0.00 0.00 0.00 3.34
405 410 2.684374 GAGAGAGGAAGGAGGTACGAAC 59.316 54.545 0.00 0.00 0.00 3.95
408 413 3.508426 AGAGGAAGGAGGTACGAACTTT 58.492 45.455 0.00 0.00 0.00 2.66
411 416 4.154942 AGGAAGGAGGTACGAACTTTACA 58.845 43.478 0.00 0.00 0.00 2.41
412 417 4.776308 AGGAAGGAGGTACGAACTTTACAT 59.224 41.667 0.00 0.00 0.00 2.29
445 451 3.741249 AGACATAGACGCCTCTCGAATA 58.259 45.455 0.00 0.00 41.67 1.75
448 454 4.608951 ACATAGACGCCTCTCGAATAAAC 58.391 43.478 0.00 0.00 41.67 2.01
465 471 6.488683 CGAATAAACCTATTAATTCCCCAGCA 59.511 38.462 0.00 0.00 0.00 4.41
491 497 0.317603 GGATCACCGTGATACCGACG 60.318 60.000 14.09 0.00 37.20 5.12
505 511 2.511659 ACCGACGGCTCTAATATGCTA 58.488 47.619 15.39 0.00 0.00 3.49
506 512 2.228343 ACCGACGGCTCTAATATGCTAC 59.772 50.000 15.39 0.00 0.00 3.58
507 513 2.488545 CCGACGGCTCTAATATGCTACT 59.511 50.000 0.00 0.00 0.00 2.57
508 514 3.493272 CGACGGCTCTAATATGCTACTG 58.507 50.000 0.00 0.00 0.00 2.74
509 515 3.188667 CGACGGCTCTAATATGCTACTGA 59.811 47.826 0.00 0.00 0.00 3.41
646 746 0.817654 GGCAAGCAAGGTATCCCAAC 59.182 55.000 0.00 0.00 0.00 3.77
657 757 1.469335 TATCCCAACGGCGATCTCCC 61.469 60.000 16.62 0.00 0.00 4.30
658 758 3.470888 CCCAACGGCGATCTCCCT 61.471 66.667 16.62 0.00 0.00 4.20
659 759 2.202932 CCAACGGCGATCTCCCTG 60.203 66.667 16.62 0.00 0.00 4.45
683 783 1.944024 CTGGGCGTCAGTAAACAAACA 59.056 47.619 0.00 0.00 38.64 2.83
933 1053 0.107654 CCCTTCCTTCGCTTCGGATT 60.108 55.000 0.00 0.00 0.00 3.01
936 1056 0.107848 TTCCTTCGCTTCGGATTCCC 60.108 55.000 0.00 0.00 0.00 3.97
941 1061 2.731571 CGCTTCGGATTCCCTCCCA 61.732 63.158 0.00 0.00 41.49 4.37
1194 1627 3.607661 GGTCCCTCGATCTCGGGC 61.608 72.222 10.51 6.67 40.41 6.13
1505 1939 1.667830 CTTCCGCTGCCTCGACAAA 60.668 57.895 0.00 0.00 0.00 2.83
1540 1984 4.161295 TGCCCCGCCTTCAGATCG 62.161 66.667 0.00 0.00 0.00 3.69
1552 1996 4.796231 AGATCGACGCACGCCCAC 62.796 66.667 0.00 0.00 42.26 4.61
1645 2107 3.423776 CGTTTCACGTTTGTCTTGTGTGA 60.424 43.478 0.00 0.00 36.74 3.58
1658 2120 4.390297 GTCTTGTGTGATGCTTAAGGAGTC 59.610 45.833 4.29 2.49 0.00 3.36
1670 2135 0.468226 AAGGAGTCACAGCGGAACAA 59.532 50.000 0.00 0.00 0.00 2.83
1709 2174 4.072131 TCTTAAACTACGTACGGTGGAGT 58.928 43.478 21.06 13.56 0.00 3.85
1710 2175 2.997485 AAACTACGTACGGTGGAGTC 57.003 50.000 21.06 0.00 0.00 3.36
1711 2176 1.896220 AACTACGTACGGTGGAGTCA 58.104 50.000 21.06 0.00 0.00 3.41
1712 2177 1.446907 ACTACGTACGGTGGAGTCAG 58.553 55.000 21.06 5.68 0.00 3.51
1713 2178 1.002430 ACTACGTACGGTGGAGTCAGA 59.998 52.381 21.06 0.00 0.00 3.27
1714 2179 1.396301 CTACGTACGGTGGAGTCAGAC 59.604 57.143 21.06 0.00 0.00 3.51
1715 2180 0.535780 ACGTACGGTGGAGTCAGACA 60.536 55.000 21.06 0.00 0.00 3.41
1716 2181 0.109873 CGTACGGTGGAGTCAGACAC 60.110 60.000 7.57 0.00 36.89 3.67
1755 2220 6.430925 TCTCGTGAGATTTGGATCATTTTTGT 59.569 34.615 0.00 0.00 40.84 2.83
1756 2221 6.611381 TCGTGAGATTTGGATCATTTTTGTC 58.389 36.000 0.00 0.00 34.60 3.18
1757 2222 6.206438 TCGTGAGATTTGGATCATTTTTGTCA 59.794 34.615 0.00 0.00 34.60 3.58
1849 2326 0.394192 TCAGGATAAGCATGAGCCGG 59.606 55.000 0.00 0.00 43.56 6.13
1850 2327 1.072159 AGGATAAGCATGAGCCGGC 59.928 57.895 21.89 21.89 43.56 6.13
1851 2328 1.968540 GGATAAGCATGAGCCGGCC 60.969 63.158 26.15 15.80 43.56 6.13
1852 2329 2.281070 ATAAGCATGAGCCGGCCG 60.281 61.111 26.15 21.04 43.56 6.13
1853 2330 2.715532 GATAAGCATGAGCCGGCCGA 62.716 60.000 30.73 10.77 43.56 5.54
1854 2331 2.996168 ATAAGCATGAGCCGGCCGAC 62.996 60.000 30.73 17.62 43.56 4.79
1903 2380 1.099879 AGCGCATGAATTCCCTGCTC 61.100 55.000 21.08 16.03 33.75 4.26
1936 2413 0.671472 CACTGCCTTGTCGATGCTCA 60.671 55.000 0.00 0.00 0.00 4.26
1962 2439 5.188163 TGCAAGGGAAAATGTCAATGATCAT 59.812 36.000 1.18 1.18 0.00 2.45
1975 2452 6.374894 TGTCAATGATCATAGCACACAATTCA 59.625 34.615 9.04 0.00 0.00 2.57
2157 2634 7.645340 GTGTACTATATGCAAAGCCAAAATCAG 59.355 37.037 0.00 0.00 0.00 2.90
2579 3056 6.218295 GCAGAAGCATCATGAAGTCATGCA 62.218 45.833 17.93 6.24 45.55 3.96
2656 3133 0.032403 GCATCAACAGCCACAGCAAA 59.968 50.000 0.00 0.00 43.56 3.68
2927 3404 5.538813 GTGTAGTAGGGTATCCACATGATCA 59.461 44.000 0.00 0.00 34.76 2.92
2971 3448 1.373497 GTGACTGCGGACTCCAGTG 60.373 63.158 0.00 0.00 43.17 3.66
2972 3449 2.433318 GACTGCGGACTCCAGTGC 60.433 66.667 0.00 0.00 43.17 4.40
3177 3656 6.549364 CAGATTGGTACAGATCCTTCTACTCT 59.451 42.308 0.00 0.00 42.39 3.24
3178 3657 6.775629 AGATTGGTACAGATCCTTCTACTCTC 59.224 42.308 0.00 0.00 42.39 3.20
3242 3721 2.113807 AGTCTAGTGATGATGCTGGCA 58.886 47.619 0.00 0.00 0.00 4.92
3382 3861 5.481105 TCGGTTTACCACAGTTTATGTAGG 58.519 41.667 0.00 0.00 41.41 3.18
3564 4315 9.268282 AGTTTACAGAGGGAGTATATCTTTTCA 57.732 33.333 0.00 0.00 0.00 2.69
3597 4349 5.772825 TTGCTTTCAGATGTAGCAACTTT 57.227 34.783 15.84 0.00 46.59 2.66
3598 4350 5.362556 TGCTTTCAGATGTAGCAACTTTC 57.637 39.130 9.02 0.00 41.57 2.62
3599 4351 4.821260 TGCTTTCAGATGTAGCAACTTTCA 59.179 37.500 9.02 0.00 41.57 2.69
3657 4410 0.879765 CTGCCACTGGAGAAAGCAAG 59.120 55.000 0.00 0.00 32.14 4.01
3691 4444 1.455248 TGGAAAATAACGGCCGGAAG 58.545 50.000 31.76 0.90 0.00 3.46
3702 4455 0.391793 GGCCGGAAGTTCTCTCTTGG 60.392 60.000 5.05 0.00 0.00 3.61
3705 4458 1.205893 CCGGAAGTTCTCTCTTGGAGG 59.794 57.143 0.00 0.00 42.10 4.30
3708 4461 3.367910 CGGAAGTTCTCTCTTGGAGGAAG 60.368 52.174 2.25 0.00 42.10 3.46
3720 4473 5.888901 TCTTGGAGGAAGAACTGTAGAGTA 58.111 41.667 0.00 0.00 37.78 2.59
3725 4478 6.497259 TGGAGGAAGAACTGTAGAGTACAAAT 59.503 38.462 0.00 0.00 38.38 2.32
3726 4479 7.016268 TGGAGGAAGAACTGTAGAGTACAAATT 59.984 37.037 0.00 0.00 38.38 1.82
3728 4481 9.274206 GAGGAAGAACTGTAGAGTACAAATTTT 57.726 33.333 0.00 0.00 38.38 1.82
3730 4483 9.665264 GGAAGAACTGTAGAGTACAAATTTTTG 57.335 33.333 0.00 1.56 43.62 2.44
3734 4487 9.997482 GAACTGTAGAGTACAAATTTTTGAACA 57.003 29.630 9.88 4.00 40.55 3.18
3748 4537 5.392767 TTTTGAACAAACCACTACTTGCA 57.607 34.783 0.00 0.00 0.00 4.08
3795 4584 2.959071 GAGCATCTCCACTCGCGC 60.959 66.667 0.00 0.00 0.00 6.86
3796 4585 4.521062 AGCATCTCCACTCGCGCC 62.521 66.667 0.00 0.00 0.00 6.53
3797 4586 4.521062 GCATCTCCACTCGCGCCT 62.521 66.667 0.00 0.00 0.00 5.52
3798 4587 2.279120 CATCTCCACTCGCGCCTC 60.279 66.667 0.00 0.00 0.00 4.70
3799 4588 3.532155 ATCTCCACTCGCGCCTCC 61.532 66.667 0.00 0.00 0.00 4.30
3801 4590 4.069232 CTCCACTCGCGCCTCCAA 62.069 66.667 0.00 0.00 0.00 3.53
3802 4591 4.373116 TCCACTCGCGCCTCCAAC 62.373 66.667 0.00 0.00 0.00 3.77
3803 4592 4.680237 CCACTCGCGCCTCCAACA 62.680 66.667 0.00 0.00 0.00 3.33
3804 4593 2.664851 CACTCGCGCCTCCAACAA 60.665 61.111 0.00 0.00 0.00 2.83
3805 4594 2.357517 ACTCGCGCCTCCAACAAG 60.358 61.111 0.00 0.00 0.00 3.16
3806 4595 3.793144 CTCGCGCCTCCAACAAGC 61.793 66.667 0.00 0.00 0.00 4.01
3824 4613 2.523168 CCCCCAGGGCGTGTTTTT 60.523 61.111 0.00 0.00 35.35 1.94
3860 4649 2.836944 AAAAACTCTAGTCGCGCCC 58.163 52.632 0.00 0.00 0.00 6.13
3861 4650 0.672711 AAAAACTCTAGTCGCGCCCC 60.673 55.000 0.00 0.00 0.00 5.80
3862 4651 1.823169 AAAACTCTAGTCGCGCCCCA 61.823 55.000 0.00 0.00 0.00 4.96
3863 4652 1.823169 AAACTCTAGTCGCGCCCCAA 61.823 55.000 0.00 0.00 0.00 4.12
3864 4653 2.105128 CTCTAGTCGCGCCCCAAG 59.895 66.667 0.00 0.00 0.00 3.61
3865 4654 2.361992 TCTAGTCGCGCCCCAAGA 60.362 61.111 0.00 0.00 0.00 3.02
3866 4655 1.945354 CTCTAGTCGCGCCCCAAGAA 61.945 60.000 0.00 0.00 0.00 2.52
3867 4656 1.810030 CTAGTCGCGCCCCAAGAAC 60.810 63.158 0.00 0.00 0.00 3.01
3868 4657 3.636313 TAGTCGCGCCCCAAGAACG 62.636 63.158 0.00 0.00 0.00 3.95
3874 4663 2.981350 GCCCCAAGAACGCCGAAA 60.981 61.111 0.00 0.00 0.00 3.46
3875 4664 2.340328 GCCCCAAGAACGCCGAAAT 61.340 57.895 0.00 0.00 0.00 2.17
3876 4665 1.800681 CCCCAAGAACGCCGAAATC 59.199 57.895 0.00 0.00 0.00 2.17
3877 4666 1.654023 CCCCAAGAACGCCGAAATCC 61.654 60.000 0.00 0.00 0.00 3.01
3878 4667 1.423845 CCAAGAACGCCGAAATCCG 59.576 57.895 0.00 0.00 38.18 4.18
3879 4668 1.226018 CAAGAACGCCGAAATCCGC 60.226 57.895 0.00 0.00 36.84 5.54
3880 4669 2.396157 AAGAACGCCGAAATCCGCC 61.396 57.895 0.00 0.00 36.84 6.13
3881 4670 4.218478 GAACGCCGAAATCCGCCG 62.218 66.667 0.00 0.00 45.20 6.46
3899 4688 2.041153 GGCTCGGCCCATATTTTGG 58.959 57.895 0.00 0.00 44.06 3.28
3900 4689 1.363807 GCTCGGCCCATATTTTGGC 59.636 57.895 0.00 0.00 44.97 4.52
3904 4693 3.137687 GCCCATATTTTGGCCCGG 58.862 61.111 0.00 0.00 44.97 5.73
3905 4694 3.137687 CCCATATTTTGGCCCGGC 58.862 61.111 0.00 0.00 44.97 6.13
3906 4695 2.727544 CCATATTTTGGCCCGGCG 59.272 61.111 0.00 0.00 39.09 6.46
3907 4696 1.826054 CCATATTTTGGCCCGGCGA 60.826 57.895 9.30 0.00 39.09 5.54
3908 4697 1.178534 CCATATTTTGGCCCGGCGAT 61.179 55.000 9.30 0.00 39.09 4.58
3909 4698 0.240945 CATATTTTGGCCCGGCGATC 59.759 55.000 9.30 0.00 0.00 3.69
3910 4699 0.893727 ATATTTTGGCCCGGCGATCC 60.894 55.000 9.30 9.66 0.00 3.36
3911 4700 2.969300 TATTTTGGCCCGGCGATCCC 62.969 60.000 9.30 5.93 0.00 3.85
3922 4711 4.547367 CGATCCCAGGCCGAACCC 62.547 72.222 0.00 0.00 40.58 4.11
3923 4712 3.090532 GATCCCAGGCCGAACCCT 61.091 66.667 0.00 0.00 40.58 4.34
3948 4737 4.404098 GGGGCTCCGGCGAAAGAA 62.404 66.667 9.30 0.00 39.81 2.52
3949 4738 2.124695 GGGCTCCGGCGAAAGAAT 60.125 61.111 9.30 0.00 39.81 2.40
3950 4739 1.145377 GGGCTCCGGCGAAAGAATA 59.855 57.895 9.30 0.00 39.81 1.75
3951 4740 0.463116 GGGCTCCGGCGAAAGAATAA 60.463 55.000 9.30 0.00 39.81 1.40
3952 4741 0.656259 GGCTCCGGCGAAAGAATAAC 59.344 55.000 9.30 0.00 39.81 1.89
3953 4742 0.656259 GCTCCGGCGAAAGAATAACC 59.344 55.000 9.30 0.00 0.00 2.85
3954 4743 0.928229 CTCCGGCGAAAGAATAACCG 59.072 55.000 9.30 0.00 43.44 4.44
3955 4744 1.085501 TCCGGCGAAAGAATAACCGC 61.086 55.000 9.30 0.00 46.04 5.68
3957 4746 4.263708 GCGAAAGAATAACCGCGC 57.736 55.556 0.00 0.00 38.27 6.86
3958 4747 1.713830 GCGAAAGAATAACCGCGCT 59.286 52.632 5.56 0.00 41.09 5.92
3959 4748 0.096454 GCGAAAGAATAACCGCGCTT 59.904 50.000 5.56 0.00 41.09 4.68
3960 4749 1.797964 CGAAAGAATAACCGCGCTTG 58.202 50.000 5.56 0.00 0.00 4.01
3961 4750 1.529010 CGAAAGAATAACCGCGCTTGG 60.529 52.381 5.56 2.00 0.00 3.61
3962 4751 0.808755 AAAGAATAACCGCGCTTGGG 59.191 50.000 5.56 1.10 0.00 4.12
3963 4752 1.654023 AAGAATAACCGCGCTTGGGC 61.654 55.000 5.56 0.00 0.00 5.36
3964 4753 3.120979 GAATAACCGCGCTTGGGCC 62.121 63.158 5.56 0.00 34.44 5.80
3965 4754 3.929334 AATAACCGCGCTTGGGCCA 62.929 57.895 0.00 0.00 34.44 5.36
3976 4765 3.569210 TGGGCCACCACTGTCAGG 61.569 66.667 0.00 0.00 43.37 3.86
3977 4766 3.570212 GGGCCACCACTGTCAGGT 61.570 66.667 4.39 0.00 40.85 4.00
3999 4788 2.875080 AAAAAGCATCTCGCACGTAC 57.125 45.000 0.00 0.00 46.13 3.67
4000 4789 1.790755 AAAAGCATCTCGCACGTACA 58.209 45.000 0.00 0.00 46.13 2.90
4001 4790 1.068474 AAAGCATCTCGCACGTACAC 58.932 50.000 0.00 0.00 46.13 2.90
4002 4791 1.071019 AAGCATCTCGCACGTACACG 61.071 55.000 0.00 0.00 46.13 4.49
4003 4792 1.513373 GCATCTCGCACGTACACGA 60.513 57.895 9.04 7.21 43.39 4.35
4004 4793 1.730593 GCATCTCGCACGTACACGAC 61.731 60.000 9.04 0.00 43.39 4.34
4005 4794 0.179197 CATCTCGCACGTACACGACT 60.179 55.000 9.04 0.00 43.02 4.18
4006 4795 0.520404 ATCTCGCACGTACACGACTT 59.480 50.000 9.04 0.00 43.02 3.01
4007 4796 0.308684 TCTCGCACGTACACGACTTT 59.691 50.000 9.04 0.00 43.02 2.66
4008 4797 0.701303 CTCGCACGTACACGACTTTC 59.299 55.000 9.04 0.00 43.02 2.62
4009 4798 0.993251 TCGCACGTACACGACTTTCG 60.993 55.000 9.04 4.56 46.93 3.46
4010 4799 1.127225 GCACGTACACGACTTTCGC 59.873 57.895 9.04 0.00 45.12 4.70
4011 4800 1.771044 CACGTACACGACTTTCGCC 59.229 57.895 9.04 0.00 45.12 5.54
4012 4801 1.727022 ACGTACACGACTTTCGCCG 60.727 57.895 9.04 0.00 45.12 6.46
4013 4802 2.767697 GTACACGACTTTCGCCGC 59.232 61.111 0.00 0.00 45.12 6.53
4014 4803 2.431260 TACACGACTTTCGCCGCC 60.431 61.111 0.00 0.00 45.12 6.13
4015 4804 3.210223 TACACGACTTTCGCCGCCA 62.210 57.895 0.00 0.00 45.12 5.69
4016 4805 2.495366 TACACGACTTTCGCCGCCAT 62.495 55.000 0.00 0.00 45.12 4.40
4017 4806 1.807981 CACGACTTTCGCCGCCATA 60.808 57.895 0.00 0.00 45.12 2.74
4018 4807 1.808390 ACGACTTTCGCCGCCATAC 60.808 57.895 0.00 0.00 45.12 2.39
4019 4808 1.807981 CGACTTTCGCCGCCATACA 60.808 57.895 0.00 0.00 31.14 2.29
4020 4809 1.713830 GACTTTCGCCGCCATACAC 59.286 57.895 0.00 0.00 0.00 2.90
4021 4810 2.020836 GACTTTCGCCGCCATACACG 62.021 60.000 0.00 0.00 0.00 4.49
4022 4811 1.807981 CTTTCGCCGCCATACACGA 60.808 57.895 0.00 0.00 0.00 4.35
4023 4812 1.355796 CTTTCGCCGCCATACACGAA 61.356 55.000 0.00 0.00 42.24 3.85
4024 4813 1.628447 TTTCGCCGCCATACACGAAC 61.628 55.000 0.00 0.00 43.48 3.95
4025 4814 2.766875 TTCGCCGCCATACACGAACA 62.767 55.000 0.00 0.00 39.40 3.18
4026 4815 2.782615 GCCGCCATACACGAACAC 59.217 61.111 0.00 0.00 0.00 3.32
4027 4816 3.077705 CCGCCATACACGAACACG 58.922 61.111 0.00 0.00 0.00 4.49
4028 4817 1.444724 CCGCCATACACGAACACGA 60.445 57.895 0.00 0.00 0.00 4.35
4029 4818 1.680105 CCGCCATACACGAACACGAC 61.680 60.000 0.00 0.00 0.00 4.34
4030 4819 0.731514 CGCCATACACGAACACGACT 60.732 55.000 0.00 0.00 0.00 4.18
4031 4820 1.425412 GCCATACACGAACACGACTT 58.575 50.000 0.00 0.00 0.00 3.01
4032 4821 1.796459 GCCATACACGAACACGACTTT 59.204 47.619 0.00 0.00 0.00 2.66
4033 4822 2.159881 GCCATACACGAACACGACTTTC 60.160 50.000 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.667154 CGCCTTGATCCTCCGACTCA 61.667 60.000 0.00 0.00 0.00 3.41
51 52 2.425592 TGGCGTTGTCCCACAGAG 59.574 61.111 0.00 0.00 0.00 3.35
107 112 5.138125 TGCTTCTTGGCATTTTTAGAAGG 57.862 39.130 21.28 8.57 42.33 3.46
135 140 2.249844 TCCCGTCTTGTCCTTGTTTC 57.750 50.000 0.00 0.00 0.00 2.78
181 186 3.521560 TCATCAACAGTGAGGCGATAAC 58.478 45.455 0.00 0.00 37.14 1.89
193 198 5.355350 GGTTTCAGTCCCTAATCATCAACAG 59.645 44.000 0.00 0.00 0.00 3.16
195 200 5.501156 AGGTTTCAGTCCCTAATCATCAAC 58.499 41.667 0.00 0.00 0.00 3.18
196 201 5.779241 AGGTTTCAGTCCCTAATCATCAA 57.221 39.130 0.00 0.00 0.00 2.57
197 202 5.724370 TGTAGGTTTCAGTCCCTAATCATCA 59.276 40.000 0.00 0.00 35.16 3.07
203 208 3.865571 AGGTGTAGGTTTCAGTCCCTAA 58.134 45.455 0.00 0.00 35.16 2.69
204 209 3.555117 AGGTGTAGGTTTCAGTCCCTA 57.445 47.619 0.00 0.00 32.08 3.53
207 212 5.224821 AGTTTAGGTGTAGGTTTCAGTCC 57.775 43.478 0.00 0.00 0.00 3.85
211 216 8.054572 AGGTTTTTAGTTTAGGTGTAGGTTTCA 58.945 33.333 0.00 0.00 0.00 2.69
216 221 6.429078 GGTGAGGTTTTTAGTTTAGGTGTAGG 59.571 42.308 0.00 0.00 0.00 3.18
254 259 0.533308 CCCTGTTGTTTCCGAACCGA 60.533 55.000 0.00 0.00 34.80 4.69
258 263 1.539496 CGAGACCCTGTTGTTTCCGAA 60.539 52.381 0.00 0.00 0.00 4.30
260 265 0.949105 CCGAGACCCTGTTGTTTCCG 60.949 60.000 0.00 0.00 0.00 4.30
261 266 1.235281 GCCGAGACCCTGTTGTTTCC 61.235 60.000 0.00 0.00 0.00 3.13
279 284 2.821679 CTTTGACGGAGGGAAGGGGC 62.822 65.000 0.00 0.00 0.00 5.80
282 287 0.321653 CCACTTTGACGGAGGGAAGG 60.322 60.000 0.00 0.00 0.00 3.46
313 318 1.149101 TGAGTTCAGGGGCCTCTTTT 58.851 50.000 0.00 0.00 0.00 2.27
314 319 0.402121 GTGAGTTCAGGGGCCTCTTT 59.598 55.000 0.00 0.00 0.00 2.52
315 320 1.492993 GGTGAGTTCAGGGGCCTCTT 61.493 60.000 0.00 0.00 0.00 2.85
316 321 1.920835 GGTGAGTTCAGGGGCCTCT 60.921 63.158 0.00 0.00 0.00 3.69
317 322 2.190488 CTGGTGAGTTCAGGGGCCTC 62.190 65.000 0.84 0.00 0.00 4.70
318 323 2.121963 TGGTGAGTTCAGGGGCCT 60.122 61.111 0.84 0.00 0.00 5.19
319 324 2.352805 CTGGTGAGTTCAGGGGCC 59.647 66.667 0.00 0.00 0.00 5.80
324 329 1.277557 CCTTCTCCCTGGTGAGTTCAG 59.722 57.143 10.66 6.83 33.93 3.02
328 333 1.717077 TCTACCTTCTCCCTGGTGAGT 59.283 52.381 10.66 0.24 37.74 3.41
382 387 1.751382 CGTACCTCCTTCCTCTCTCCC 60.751 61.905 0.00 0.00 0.00 4.30
383 388 1.212441 TCGTACCTCCTTCCTCTCTCC 59.788 57.143 0.00 0.00 0.00 3.71
384 389 2.684374 GTTCGTACCTCCTTCCTCTCTC 59.316 54.545 0.00 0.00 0.00 3.20
401 406 9.103048 GTCTATGAAAAACACATGTAAAGTTCG 57.897 33.333 0.00 0.00 0.00 3.95
408 413 9.083080 CGTCTATGTCTATGAAAAACACATGTA 57.917 33.333 0.00 0.00 0.00 2.29
411 416 6.037172 GGCGTCTATGTCTATGAAAAACACAT 59.963 38.462 0.00 0.00 0.00 3.21
412 417 5.350365 GGCGTCTATGTCTATGAAAAACACA 59.650 40.000 0.00 0.00 0.00 3.72
445 451 6.201591 TGATTGCTGGGGAATTAATAGGTTT 58.798 36.000 0.00 0.00 0.00 3.27
448 454 5.634118 TCTGATTGCTGGGGAATTAATAGG 58.366 41.667 0.00 0.00 0.00 2.57
465 471 3.322254 GGTATCACGGTGATCCTCTGATT 59.678 47.826 25.75 3.71 38.26 2.57
491 497 5.098893 CGTGATCAGTAGCATATTAGAGCC 58.901 45.833 0.00 0.00 0.00 4.70
505 511 4.836125 AAAAGAAATGTGCGTGATCAGT 57.164 36.364 0.00 0.00 0.00 3.41
506 512 7.538334 TGATTAAAAAGAAATGTGCGTGATCAG 59.462 33.333 0.00 0.00 0.00 2.90
507 513 7.325821 GTGATTAAAAAGAAATGTGCGTGATCA 59.674 33.333 0.00 0.00 0.00 2.92
508 514 7.460120 CGTGATTAAAAAGAAATGTGCGTGATC 60.460 37.037 0.00 0.00 0.00 2.92
509 515 6.305399 CGTGATTAAAAAGAAATGTGCGTGAT 59.695 34.615 0.00 0.00 0.00 3.06
657 757 2.786539 TTACTGACGCCCAGCAGCAG 62.787 60.000 5.44 0.00 46.81 4.24
658 758 2.390306 TTTACTGACGCCCAGCAGCA 62.390 55.000 5.44 0.00 46.81 4.41
659 759 1.671054 TTTACTGACGCCCAGCAGC 60.671 57.895 5.44 0.00 46.81 5.25
683 783 1.973281 CTTGGATGTGGCCGTGCTT 60.973 57.895 0.00 0.00 0.00 3.91
1115 1544 4.576053 CAGACAGACAGAGAGATAGTCAGG 59.424 50.000 0.00 0.00 34.80 3.86
1119 1552 4.188462 CGACAGACAGACAGAGAGATAGT 58.812 47.826 0.00 0.00 0.00 2.12
1194 1627 3.546714 AACCCCCGCCTCAGAAACG 62.547 63.158 0.00 0.00 0.00 3.60
1505 1939 2.237392 GGCAGGTACCTGTCTGAGATTT 59.763 50.000 36.31 0.00 44.53 2.17
1552 1996 4.497300 CAAGACATTTGGCAGTAATTGGG 58.503 43.478 0.00 0.00 0.00 4.12
1645 2107 1.406069 CCGCTGTGACTCCTTAAGCAT 60.406 52.381 0.00 0.00 33.41 3.79
1658 2120 2.605338 CCTGTGAAATTGTTCCGCTGTG 60.605 50.000 0.00 0.00 32.28 3.66
1670 2135 6.660949 AGTTTAAGAATAGCAGCCTGTGAAAT 59.339 34.615 0.00 0.00 0.00 2.17
1709 2174 5.133941 AGAACAGTAAGTCTGAGTGTCTGA 58.866 41.667 17.83 0.00 46.27 3.27
1710 2175 5.446143 AGAACAGTAAGTCTGAGTGTCTG 57.554 43.478 0.00 12.50 46.27 3.51
1711 2176 4.214545 CGAGAACAGTAAGTCTGAGTGTCT 59.785 45.833 0.00 0.00 46.27 3.41
1712 2177 4.023878 ACGAGAACAGTAAGTCTGAGTGTC 60.024 45.833 0.00 0.00 46.27 3.67
1713 2178 3.884091 ACGAGAACAGTAAGTCTGAGTGT 59.116 43.478 1.79 0.00 46.27 3.55
1714 2179 4.023963 TCACGAGAACAGTAAGTCTGAGTG 60.024 45.833 1.79 0.00 46.27 3.51
1715 2180 4.135306 TCACGAGAACAGTAAGTCTGAGT 58.865 43.478 1.79 0.00 46.27 3.41
1716 2181 4.452795 TCTCACGAGAACAGTAAGTCTGAG 59.547 45.833 1.79 0.00 39.29 3.35
1755 2220 7.924947 CAGCTCAGAGACATATTCTTAATGTGA 59.075 37.037 0.00 0.00 37.69 3.58
1756 2221 7.924947 TCAGCTCAGAGACATATTCTTAATGTG 59.075 37.037 0.00 0.00 37.69 3.21
1757 2222 8.016301 TCAGCTCAGAGACATATTCTTAATGT 57.984 34.615 0.00 0.00 40.23 2.71
1852 2329 4.374702 CAGTTGCTGCGCCGTGTC 62.375 66.667 4.18 0.00 0.00 3.67
1858 2335 4.283403 TTTGGCCAGTTGCTGCGC 62.283 61.111 5.11 0.00 40.92 6.09
1859 2336 2.354074 AAGTTTGGCCAGTTGCTGCG 62.354 55.000 5.11 0.00 40.92 5.18
1860 2337 0.598419 GAAGTTTGGCCAGTTGCTGC 60.598 55.000 5.11 0.00 40.92 5.25
1903 2380 1.666888 GGCAGTGGCTTCATTTGTTCG 60.667 52.381 9.90 0.00 40.87 3.95
1936 2413 3.896888 TCATTGACATTTTCCCTTGCAGT 59.103 39.130 0.00 0.00 0.00 4.40
1962 2439 2.158534 AGGGTTGGTGAATTGTGTGCTA 60.159 45.455 0.00 0.00 0.00 3.49
2157 2634 0.880278 TGTTCTCTGCGCAGTTCACC 60.880 55.000 34.70 20.24 0.00 4.02
2579 3056 2.175202 TGCCTTGGCCATAAAACGAAT 58.825 42.857 6.09 0.00 0.00 3.34
2656 3133 1.530013 GCCTGGCTCTGTGTTTGCAT 61.530 55.000 12.43 0.00 0.00 3.96
2927 3404 0.824759 GAGCGTCATACTCCCAACCT 59.175 55.000 0.00 0.00 0.00 3.50
3597 4349 8.402798 TGCTTATTCTGAGGTGTTAAAAATGA 57.597 30.769 0.00 0.00 0.00 2.57
3598 4350 8.299570 ACTGCTTATTCTGAGGTGTTAAAAATG 58.700 33.333 0.00 0.00 0.00 2.32
3599 4351 8.409358 ACTGCTTATTCTGAGGTGTTAAAAAT 57.591 30.769 0.00 0.00 0.00 1.82
3657 4410 5.989551 ATTTTCCAAAATCACAGCAACAC 57.010 34.783 0.00 0.00 33.54 3.32
3691 4444 4.039852 ACAGTTCTTCCTCCAAGAGAGAAC 59.960 45.833 14.03 14.03 46.50 3.01
3702 4455 8.834749 AAATTTGTACTCTACAGTTCTTCCTC 57.165 34.615 0.00 0.00 40.24 3.71
3708 4461 9.997482 TGTTCAAAAATTTGTACTCTACAGTTC 57.003 29.630 14.12 0.00 40.24 3.01
3720 4473 8.716909 CAAGTAGTGGTTTGTTCAAAAATTTGT 58.283 29.630 5.84 0.00 39.18 2.83
3725 4478 5.784177 TGCAAGTAGTGGTTTGTTCAAAAA 58.216 33.333 0.00 0.00 0.00 1.94
3726 4479 5.392767 TGCAAGTAGTGGTTTGTTCAAAA 57.607 34.783 0.00 0.00 0.00 2.44
3728 4481 4.461081 ACTTGCAAGTAGTGGTTTGTTCAA 59.539 37.500 30.25 0.00 37.52 2.69
3730 4483 4.632538 ACTTGCAAGTAGTGGTTTGTTC 57.367 40.909 30.25 0.00 37.52 3.18
3731 4484 5.416326 TGTTACTTGCAAGTAGTGGTTTGTT 59.584 36.000 31.89 10.55 42.04 2.83
3732 4485 4.944930 TGTTACTTGCAAGTAGTGGTTTGT 59.055 37.500 31.89 11.76 42.04 2.83
3733 4486 5.065988 AGTGTTACTTGCAAGTAGTGGTTTG 59.934 40.000 31.89 6.45 42.04 2.93
3734 4487 5.065988 CAGTGTTACTTGCAAGTAGTGGTTT 59.934 40.000 31.89 17.68 42.04 3.27
3777 4566 2.804167 CGCGAGTGGAGATGCTCT 59.196 61.111 0.00 0.00 0.00 4.09
3778 4567 2.959071 GCGCGAGTGGAGATGCTC 60.959 66.667 12.10 0.00 0.00 4.26
3779 4568 4.521062 GGCGCGAGTGGAGATGCT 62.521 66.667 12.10 0.00 0.00 3.79
3780 4569 4.521062 AGGCGCGAGTGGAGATGC 62.521 66.667 12.10 0.00 0.00 3.91
3781 4570 2.279120 GAGGCGCGAGTGGAGATG 60.279 66.667 12.10 0.00 0.00 2.90
3782 4571 3.532155 GGAGGCGCGAGTGGAGAT 61.532 66.667 12.10 0.00 0.00 2.75
3784 4573 4.069232 TTGGAGGCGCGAGTGGAG 62.069 66.667 12.10 0.00 0.00 3.86
3785 4574 4.373116 GTTGGAGGCGCGAGTGGA 62.373 66.667 12.10 0.00 0.00 4.02
3786 4575 4.680237 TGTTGGAGGCGCGAGTGG 62.680 66.667 12.10 0.00 0.00 4.00
3787 4576 2.664851 TTGTTGGAGGCGCGAGTG 60.665 61.111 12.10 0.00 0.00 3.51
3788 4577 2.357517 CTTGTTGGAGGCGCGAGT 60.358 61.111 12.10 0.00 0.00 4.18
3789 4578 3.793144 GCTTGTTGGAGGCGCGAG 61.793 66.667 12.10 0.00 0.00 5.03
3842 4631 0.672711 GGGGCGCGACTAGAGTTTTT 60.673 55.000 13.91 0.00 0.00 1.94
3843 4632 1.079336 GGGGCGCGACTAGAGTTTT 60.079 57.895 13.91 0.00 0.00 2.43
3844 4633 1.823169 TTGGGGCGCGACTAGAGTTT 61.823 55.000 13.91 0.00 0.00 2.66
3845 4634 2.227089 CTTGGGGCGCGACTAGAGTT 62.227 60.000 13.91 0.00 0.00 3.01
3846 4635 2.678934 TTGGGGCGCGACTAGAGT 60.679 61.111 13.91 0.00 0.00 3.24
3847 4636 1.945354 TTCTTGGGGCGCGACTAGAG 61.945 60.000 13.91 7.34 0.00 2.43
3848 4637 1.980232 TTCTTGGGGCGCGACTAGA 60.980 57.895 13.91 10.06 0.00 2.43
3849 4638 1.810030 GTTCTTGGGGCGCGACTAG 60.810 63.158 13.91 7.49 0.00 2.57
3850 4639 2.263540 GTTCTTGGGGCGCGACTA 59.736 61.111 13.91 0.00 0.00 2.59
3857 4646 2.266376 GATTTCGGCGTTCTTGGGGC 62.266 60.000 6.85 0.00 0.00 5.80
3858 4647 1.654023 GGATTTCGGCGTTCTTGGGG 61.654 60.000 6.85 0.00 0.00 4.96
3859 4648 1.800681 GGATTTCGGCGTTCTTGGG 59.199 57.895 6.85 0.00 0.00 4.12
3860 4649 1.423845 CGGATTTCGGCGTTCTTGG 59.576 57.895 6.85 0.00 34.75 3.61
3861 4650 1.226018 GCGGATTTCGGCGTTCTTG 60.226 57.895 6.85 1.95 39.69 3.02
3862 4651 3.174788 GCGGATTTCGGCGTTCTT 58.825 55.556 6.85 0.00 39.69 2.52
3890 4679 0.240945 GATCGCCGGGCCAAAATATG 59.759 55.000 14.55 0.00 0.00 1.78
3891 4680 0.893727 GGATCGCCGGGCCAAAATAT 60.894 55.000 14.55 0.00 0.00 1.28
3892 4681 1.527380 GGATCGCCGGGCCAAAATA 60.527 57.895 14.55 0.00 0.00 1.40
3893 4682 2.833121 GGATCGCCGGGCCAAAAT 60.833 61.111 14.55 1.83 0.00 1.82
3905 4694 4.547367 GGGTTCGGCCTGGGATCG 62.547 72.222 0.00 0.00 37.43 3.69
3906 4695 3.090532 AGGGTTCGGCCTGGGATC 61.091 66.667 0.00 0.00 37.43 3.36
3907 4696 3.411517 CAGGGTTCGGCCTGGGAT 61.412 66.667 0.00 0.00 37.43 3.85
3931 4720 2.319890 TATTCTTTCGCCGGAGCCCC 62.320 60.000 5.05 0.00 34.57 5.80
3932 4721 0.463116 TTATTCTTTCGCCGGAGCCC 60.463 55.000 5.05 0.00 34.57 5.19
3933 4722 0.656259 GTTATTCTTTCGCCGGAGCC 59.344 55.000 5.05 0.00 34.57 4.70
3934 4723 0.656259 GGTTATTCTTTCGCCGGAGC 59.344 55.000 5.05 0.00 0.00 4.70
3935 4724 0.928229 CGGTTATTCTTTCGCCGGAG 59.072 55.000 5.05 0.00 38.86 4.63
3936 4725 1.085501 GCGGTTATTCTTTCGCCGGA 61.086 55.000 5.05 0.00 42.34 5.14
3937 4726 1.350665 GCGGTTATTCTTTCGCCGG 59.649 57.895 0.00 0.00 42.34 6.13
3938 4727 1.012671 CGCGGTTATTCTTTCGCCG 60.013 57.895 0.00 0.00 44.56 6.46
3939 4728 1.297378 GCGCGGTTATTCTTTCGCC 60.297 57.895 8.83 0.00 44.56 5.54
3940 4729 0.096454 AAGCGCGGTTATTCTTTCGC 59.904 50.000 23.79 0.00 44.04 4.70
3941 4730 1.529010 CCAAGCGCGGTTATTCTTTCG 60.529 52.381 24.58 8.48 0.00 3.46
3942 4731 1.202143 CCCAAGCGCGGTTATTCTTTC 60.202 52.381 24.58 0.00 0.00 2.62
3943 4732 0.808755 CCCAAGCGCGGTTATTCTTT 59.191 50.000 24.58 0.00 0.00 2.52
3944 4733 1.654023 GCCCAAGCGCGGTTATTCTT 61.654 55.000 24.58 5.86 0.00 2.52
3945 4734 2.112815 GCCCAAGCGCGGTTATTCT 61.113 57.895 24.58 0.00 0.00 2.40
3946 4735 2.407616 GCCCAAGCGCGGTTATTC 59.592 61.111 24.58 11.19 0.00 1.75
3947 4736 3.138128 GGCCCAAGCGCGGTTATT 61.138 61.111 24.58 0.00 41.24 1.40
3948 4737 4.418328 TGGCCCAAGCGCGGTTAT 62.418 61.111 24.58 0.00 41.24 1.89
3955 4744 4.954970 ACAGTGGTGGCCCAAGCG 62.955 66.667 0.00 0.00 44.15 4.68
3956 4745 2.985847 GACAGTGGTGGCCCAAGC 60.986 66.667 0.00 0.00 44.15 4.01
3957 4746 1.601759 CTGACAGTGGTGGCCCAAG 60.602 63.158 0.00 0.00 44.15 3.61
3958 4747 2.515398 CTGACAGTGGTGGCCCAA 59.485 61.111 0.00 0.00 44.15 4.12
3959 4748 3.569210 CCTGACAGTGGTGGCCCA 61.569 66.667 0.00 0.00 38.87 5.36
3960 4749 3.570212 ACCTGACAGTGGTGGCCC 61.570 66.667 0.00 0.00 36.30 5.80
3980 4769 2.096417 GTGTACGTGCGAGATGCTTTTT 60.096 45.455 0.00 0.00 46.63 1.94
3981 4770 1.459592 GTGTACGTGCGAGATGCTTTT 59.540 47.619 0.00 0.00 46.63 2.27
3982 4771 1.068474 GTGTACGTGCGAGATGCTTT 58.932 50.000 0.00 0.00 46.63 3.51
3983 4772 1.071019 CGTGTACGTGCGAGATGCTT 61.071 55.000 0.00 0.00 46.63 3.91
3984 4773 1.514228 CGTGTACGTGCGAGATGCT 60.514 57.895 0.00 0.00 46.63 3.79
3985 4774 1.513373 TCGTGTACGTGCGAGATGC 60.513 57.895 0.00 0.00 40.52 3.91
3986 4775 0.179197 AGTCGTGTACGTGCGAGATG 60.179 55.000 10.96 0.00 40.80 2.90
3987 4776 0.520404 AAGTCGTGTACGTGCGAGAT 59.480 50.000 10.96 2.60 40.80 2.75
3988 4777 0.308684 AAAGTCGTGTACGTGCGAGA 59.691 50.000 10.96 4.64 40.80 4.04
3989 4778 0.701303 GAAAGTCGTGTACGTGCGAG 59.299 55.000 10.96 2.40 40.80 5.03
3990 4779 0.993251 CGAAAGTCGTGTACGTGCGA 60.993 55.000 0.00 2.64 40.80 5.10
3991 4780 1.405838 CGAAAGTCGTGTACGTGCG 59.594 57.895 0.00 0.00 40.80 5.34
3992 4781 1.127225 GCGAAAGTCGTGTACGTGC 59.873 57.895 0.00 0.00 42.81 5.34
3993 4782 1.771044 GGCGAAAGTCGTGTACGTG 59.229 57.895 0.00 0.00 42.81 4.49
3994 4783 4.233408 GGCGAAAGTCGTGTACGT 57.767 55.556 4.20 0.00 42.81 3.57
4002 4791 1.713830 GTGTATGGCGGCGAAAGTC 59.286 57.895 12.98 0.00 0.00 3.01
4003 4792 2.098233 CGTGTATGGCGGCGAAAGT 61.098 57.895 12.98 0.00 0.00 2.66
4004 4793 1.355796 TTCGTGTATGGCGGCGAAAG 61.356 55.000 12.98 0.00 39.83 2.62
4005 4794 1.374378 TTCGTGTATGGCGGCGAAA 60.374 52.632 12.98 0.00 39.83 3.46
4006 4795 2.095847 GTTCGTGTATGGCGGCGAA 61.096 57.895 12.98 0.00 40.38 4.70
4007 4796 2.507547 GTTCGTGTATGGCGGCGA 60.508 61.111 12.98 0.00 0.00 5.54
4008 4797 2.811747 TGTTCGTGTATGGCGGCG 60.812 61.111 0.51 0.51 0.00 6.46
4009 4798 2.782615 GTGTTCGTGTATGGCGGC 59.217 61.111 0.00 0.00 0.00 6.53
4010 4799 1.444724 TCGTGTTCGTGTATGGCGG 60.445 57.895 0.00 0.00 38.33 6.13
4011 4800 0.731514 AGTCGTGTTCGTGTATGGCG 60.732 55.000 0.00 0.00 38.33 5.69
4012 4801 1.425412 AAGTCGTGTTCGTGTATGGC 58.575 50.000 0.00 0.00 38.33 4.40
4013 4802 3.700130 GAAAGTCGTGTTCGTGTATGG 57.300 47.619 0.00 0.00 38.33 2.74


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

AutoCloner maintained by Alex Coulton.