Multiple sequence alignment - TraesCS7D01G308900

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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 TraesCS7D01G308900 chr7D 100.000 5009 0 0 1 5009 391579317 391584325 0.000000e+00 9250.0
1 TraesCS7D01G308900 chr7D 95.000 200 10 0 4810 5009 182809714 182809515 1.050000e-81 315.0
2 TraesCS7D01G308900 chr7D 100.000 30 0 0 4522 4551 60438317 60438346 7.010000e-04 56.5
3 TraesCS7D01G308900 chr7B 92.736 3703 187 41 131 3783 388168652 388172322 0.000000e+00 5273.0
4 TraesCS7D01G308900 chr7B 92.094 721 33 8 3782 4481 388172416 388173133 0.000000e+00 994.0
5 TraesCS7D01G308900 chr7B 92.565 269 15 2 4545 4813 388173134 388173397 1.020000e-101 381.0
6 TraesCS7D01G308900 chr7B 92.593 135 7 1 1 132 388168384 388168518 1.840000e-44 191.0
7 TraesCS7D01G308900 chr7A 95.206 2065 64 16 1 2046 443390523 443392571 0.000000e+00 3232.0
8 TraesCS7D01G308900 chr7A 96.402 1751 61 1 1973 3723 443392570 443394318 0.000000e+00 2883.0
9 TraesCS7D01G308900 chr7A 90.464 797 39 17 3812 4572 443394320 443395115 0.000000e+00 1016.0
10 TraesCS7D01G308900 chr7A 94.872 234 12 0 4580 4813 443395349 443395582 2.850000e-97 366.0
11 TraesCS7D01G308900 chr7A 91.080 213 17 2 4799 5009 595211369 595211581 2.280000e-73 287.0
12 TraesCS7D01G308900 chr1D 95.500 200 6 1 4810 5009 303303448 303303252 2.910000e-82 316.0
13 TraesCS7D01G308900 chr1D 95.337 193 9 0 4817 5009 50895755 50895563 1.750000e-79 307.0
14 TraesCS7D01G308900 chr1D 87.671 73 9 0 4382 4454 19263740 19263668 8.930000e-13 86.1
15 TraesCS7D01G308900 chr1D 100.000 29 0 0 4522 4550 360443062 360443034 3.000000e-03 54.7
16 TraesCS7D01G308900 chr6D 94.000 200 12 0 4810 5009 460280321 460280122 2.270000e-78 303.0
17 TraesCS7D01G308900 chr6D 93.782 193 12 0 4817 5009 120645886 120645694 1.760000e-74 291.0
18 TraesCS7D01G308900 chr3A 95.288 191 9 0 4817 5007 490628177 490628367 2.270000e-78 303.0
19 TraesCS7D01G308900 chr2B 92.537 201 15 0 4809 5009 90783296 90783496 6.340000e-74 289.0
20 TraesCS7D01G308900 chr2B 94.286 35 2 0 4521 4555 5552931 5552965 3.000000e-03 54.7
21 TraesCS7D01G308900 chr2A 92.500 200 14 1 4810 5009 653368163 653367965 8.210000e-73 285.0
22 TraesCS7D01G308900 chr2A 86.957 69 9 0 4382 4450 386294353 386294421 1.500000e-10 78.7
23 TraesCS7D01G308900 chr2A 94.444 36 2 0 4479 4514 767318783 767318818 7.010000e-04 56.5
24 TraesCS7D01G308900 chr2A 100.000 29 0 0 4522 4550 337716732 337716704 3.000000e-03 54.7
25 TraesCS7D01G308900 chr1B 89.706 68 6 1 4743 4810 457468498 457468564 8.930000e-13 86.1
26 TraesCS7D01G308900 chr1B 100.000 29 0 0 4522 4550 15143665 15143637 3.000000e-03 54.7
27 TraesCS7D01G308900 chr1A 86.301 73 10 0 4382 4454 21039722 21039650 4.160000e-11 80.5
28 TraesCS7D01G308900 chr1A 94.286 35 2 0 4382 4416 299633852 299633818 3.000000e-03 54.7
29 TraesCS7D01G308900 chr4D 92.857 42 3 0 4382 4423 301756309 301756350 1.510000e-05 62.1
30 TraesCS7D01G308900 chr4D 94.286 35 1 1 4521 4554 4484052 4484086 9.000000e-03 52.8
31 TraesCS7D01G308900 chr6A 82.353 68 10 2 4382 4448 464514283 464514349 1.950000e-04 58.4
32 TraesCS7D01G308900 chr6B 100.000 30 0 0 4522 4551 672924273 672924244 7.010000e-04 56.5
33 TraesCS7D01G308900 chr4B 90.476 42 4 0 4382 4423 376157715 376157756 7.010000e-04 56.5
34 TraesCS7D01G308900 chrUn 96.774 31 1 0 4521 4551 62344952 62344922 9.000000e-03 52.8
35 TraesCS7D01G308900 chrUn 96.774 31 1 0 4521 4551 62406292 62406262 9.000000e-03 52.8
36 TraesCS7D01G308900 chrUn 91.892 37 3 0 4382 4418 249263442 249263406 9.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G308900 chr7D 391579317 391584325 5008 False 9250.00 9250 100.000 1 5009 1 chr7D.!!$F2 5008
1 TraesCS7D01G308900 chr7B 388168384 388173397 5013 False 1709.75 5273 92.497 1 4813 4 chr7B.!!$F1 4812
2 TraesCS7D01G308900 chr7A 443390523 443395582 5059 False 1874.25 3232 94.236 1 4813 4 chr7A.!!$F2 4812


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
983 1143 0.736325 CTCTGAAACCCTACGCACCG 60.736 60.0 0.0 0.0 0.00 4.94 F
1273 1434 0.322456 ATGTGGGGTGGTCGTGAATG 60.322 55.0 0.0 0.0 0.00 2.67 F
2299 2556 0.940126 CTATCCCACAAGCGTGCATC 59.060 55.0 0.0 0.0 42.17 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2299 2556 0.321653 AGGCTGAACTAAACAGGGCG 60.322 55.000 0.00 0.0 36.09 6.13 R
2394 2651 3.490348 GCCTGGTGCATATATCCTTGTT 58.510 45.455 0.00 0.0 40.77 2.83 R
4218 4579 0.040958 CGCCTTTTGCACAGTGAGTC 60.041 55.000 4.15 0.0 41.33 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
82 83 4.541705 TCAAACTCTGAAACCCATCCAAA 58.458 39.130 0.00 0.00 0.00 3.28
351 490 2.570442 AAACGCAAAAATCACACCGT 57.430 40.000 0.00 0.00 0.00 4.83
387 526 1.472026 CGGTAATTCGACACCCCGATT 60.472 52.381 6.89 0.00 38.45 3.34
434 574 1.527370 GCTCCCAGCGAAACCCTAT 59.473 57.895 0.00 0.00 0.00 2.57
440 580 1.389555 CAGCGAAACCCTATTTCCCC 58.610 55.000 0.00 0.00 0.00 4.81
605 751 1.733402 CGCCTGCCTCTCCTAGTCTG 61.733 65.000 0.00 0.00 0.00 3.51
606 752 2.026945 GCCTGCCTCTCCTAGTCTGC 62.027 65.000 0.00 0.00 0.00 4.26
607 753 1.732917 CTGCCTCTCCTAGTCTGCG 59.267 63.158 0.00 0.00 0.00 5.18
609 755 3.124686 CCTCTCCTAGTCTGCGCC 58.875 66.667 4.18 0.00 0.00 6.53
744 904 3.122971 GGCTAACCCGCAACCGTC 61.123 66.667 0.00 0.00 0.00 4.79
745 905 2.357760 GCTAACCCGCAACCGTCA 60.358 61.111 0.00 0.00 0.00 4.35
746 906 1.962306 GCTAACCCGCAACCGTCAA 60.962 57.895 0.00 0.00 0.00 3.18
840 1000 2.644555 AATCCATCCCGGCTCGTTCG 62.645 60.000 0.00 0.00 33.14 3.95
983 1143 0.736325 CTCTGAAACCCTACGCACCG 60.736 60.000 0.00 0.00 0.00 4.94
994 1154 2.457743 TACGCACCGAAACCAGCCAT 62.458 55.000 0.00 0.00 0.00 4.40
1136 1296 0.460311 CCTCGGTCTCTGCGGTAATT 59.540 55.000 0.00 0.00 0.00 1.40
1160 1321 0.602905 ACCACCTCGCCTTTTTCTCG 60.603 55.000 0.00 0.00 0.00 4.04
1164 1325 1.337541 ACCTCGCCTTTTTCTCGGTAC 60.338 52.381 0.00 0.00 0.00 3.34
1168 1329 3.469739 TCGCCTTTTTCTCGGTACTTTT 58.530 40.909 0.00 0.00 0.00 2.27
1257 1418 3.148279 GCGTCCCCGAGGAGATGT 61.148 66.667 0.00 0.00 45.21 3.06
1265 1426 1.990060 CGAGGAGATGTGGGGTGGT 60.990 63.158 0.00 0.00 0.00 4.16
1273 1434 0.322456 ATGTGGGGTGGTCGTGAATG 60.322 55.000 0.00 0.00 0.00 2.67
1274 1435 2.033448 TGGGGTGGTCGTGAATGC 59.967 61.111 0.00 0.00 0.00 3.56
1275 1436 3.124921 GGGGTGGTCGTGAATGCG 61.125 66.667 0.00 0.00 0.00 4.73
1305 1466 1.159664 AGGAGCCCCTGACTTCAGT 59.840 57.895 5.53 0.00 42.42 3.41
1369 1530 9.149225 GCTACATGACCAGATTTCTATCTAATG 57.851 37.037 0.00 0.00 39.11 1.90
1370 1531 7.976135 ACATGACCAGATTTCTATCTAATGC 57.024 36.000 0.00 0.00 39.11 3.56
1378 1539 5.762218 AGATTTCTATCTAATGCTGTGCACC 59.238 40.000 15.69 0.00 39.36 5.01
1380 1541 5.869649 TTCTATCTAATGCTGTGCACCTA 57.130 39.130 15.69 0.24 43.04 3.08
1449 1610 3.744530 GCATTACCCCACTCGATAGCTTT 60.745 47.826 0.00 0.00 0.00 3.51
1574 1735 1.755959 TGTGTGATTTTGGCTTGCACT 59.244 42.857 0.00 0.00 0.00 4.40
1612 1773 3.245087 TGTGGTGCACTAATAATGGTGGT 60.245 43.478 17.98 0.00 38.39 4.16
1631 1792 2.620585 GGTGCTATTGGGATTTCAGCTC 59.379 50.000 0.00 0.00 33.38 4.09
1640 1801 2.350522 GGATTTCAGCTCGAGAAAGCA 58.649 47.619 18.75 0.00 45.00 3.91
1667 1828 1.208776 ACTGTGATGATGCAGCAGCTA 59.791 47.619 21.91 9.49 42.74 3.32
1732 1893 2.609491 GCTGTTATGGCATGCATGGATG 60.609 50.000 27.34 21.79 0.00 3.51
1753 1914 7.071447 TGGATGCTGATTTTTCATAATTGGGAT 59.929 33.333 0.00 0.00 0.00 3.85
1773 1934 7.458397 TGGGATACTCACAAGTTACAAGATTT 58.542 34.615 0.00 0.00 36.92 2.17
1801 1963 8.908678 CATTGCATTTGTTACATATGTAGATGC 58.091 33.333 27.31 27.31 36.32 3.91
1805 1967 9.520204 GCATTTGTTACATATGTAGATGCTTTT 57.480 29.630 27.06 9.30 34.88 2.27
1885 2048 1.873698 TTGTCAGTCAAAGGTACGGC 58.126 50.000 0.00 0.00 32.64 5.68
1950 2134 7.989741 CAGATGGATAGACTTGTAGGTTGAAAT 59.010 37.037 0.00 0.00 0.00 2.17
1981 2237 5.127356 AGTCCTTTCCTACTAATGTTCTCCG 59.873 44.000 0.00 0.00 0.00 4.63
2151 2407 7.535139 TCCTTGTTCCATCGACATTATTTTTC 58.465 34.615 0.00 0.00 0.00 2.29
2175 2432 7.432869 TCTGGGTTCACTTAATTTTTGTGATG 58.567 34.615 8.11 0.00 39.92 3.07
2299 2556 0.940126 CTATCCCACAAGCGTGCATC 59.060 55.000 0.00 0.00 42.17 3.91
2324 2581 3.008485 CCTGTTTAGTTCAGCCTTCTCCT 59.992 47.826 0.00 0.00 0.00 3.69
2413 2671 7.566760 TTTGTAACAAGGATATATGCACCAG 57.433 36.000 7.02 0.00 0.00 4.00
2539 2797 6.324042 CGCATAAATATGGCAATATCAGCAA 58.676 36.000 0.00 0.00 34.32 3.91
2622 2880 9.772973 TTTATGCTTTTCAGTGTCTACTTTCTA 57.227 29.630 0.00 0.00 34.07 2.10
2745 3004 2.471103 GCGTGCATTTGAAATTTCTGCG 60.471 45.455 18.64 9.69 35.63 5.18
2886 3145 5.522097 GGGTAATGTTTCCATTAAAATGCCG 59.478 40.000 0.00 0.00 43.36 5.69
2907 3166 7.857569 TGCCGTTATTAAGTATTGAATGCTAC 58.142 34.615 0.00 0.00 0.00 3.58
2945 3204 6.538742 TGAATCTCTTCAACGAAGTCTTTGTT 59.461 34.615 11.82 11.82 45.00 2.83
3010 3269 8.977505 CAAACATATCAAAAACTAAGGTGTTGG 58.022 33.333 0.00 0.00 0.00 3.77
3032 3291 4.458989 GGTATTTTCCTCATCTTGTGTGCA 59.541 41.667 0.00 0.00 0.00 4.57
3247 3506 3.239449 TCAGAAGCTGAGGGTTACTGAA 58.761 45.455 0.00 0.00 35.39 3.02
3316 3575 9.360093 CACTTACTAGCCTATAATTAGCACATC 57.640 37.037 0.00 0.00 0.00 3.06
3574 3833 6.183360 GGTTTTCCTGCTGCAATGTTATCTAT 60.183 38.462 3.02 0.00 36.94 1.98
3586 3845 6.564125 GCAATGTTATCTATGACCGCTTGTAC 60.564 42.308 0.00 0.00 0.00 2.90
3774 4033 1.667724 GTGTGTGTAGATGCATCAGCC 59.332 52.381 27.81 15.01 41.13 4.85
3790 4144 5.242393 GCATCAGCCATATTGTAGAACCATT 59.758 40.000 0.00 0.00 33.58 3.16
3829 4183 3.750371 CACACTTGTTCATGGAGGGTAA 58.250 45.455 0.00 0.00 0.00 2.85
3843 4197 3.000727 GAGGGTAACGTTCCATGTCAAG 58.999 50.000 2.82 0.00 37.60 3.02
3896 4257 2.688446 CCTTGCTGCATCACATCATCTT 59.312 45.455 1.84 0.00 0.00 2.40
3915 4276 6.758416 TCATCTTATGCTCACTTGTGATGTAC 59.242 38.462 3.79 0.00 33.82 2.90
3960 4321 5.666969 TGTTTCAGGAGTTGATTGTTACG 57.333 39.130 0.00 0.00 35.27 3.18
4167 4528 7.618502 TTTGAAATATACGTACTTGTGCCAT 57.381 32.000 0.00 0.00 0.00 4.40
4194 4555 2.678336 GAGGTAGAGAATTTTGGGTGCG 59.322 50.000 0.00 0.00 0.00 5.34
4218 4579 3.803778 GCTTCTGTTTGAACAATTGTGGG 59.196 43.478 12.82 0.00 38.66 4.61
4376 4738 1.135257 TGTTTTGGTGTTGTCGGCAAG 60.135 47.619 0.75 0.00 34.94 4.01
4484 4867 4.508124 GGCTTGTCATAATTGAGTACTCCG 59.492 45.833 20.11 2.33 30.85 4.63
4506 4890 7.276658 TCCGTTTGTTCCATAATATAAGAGCA 58.723 34.615 0.00 0.00 0.00 4.26
4508 4892 8.567948 CCGTTTGTTCCATAATATAAGAGCATT 58.432 33.333 0.00 0.00 0.00 3.56
4521 4905 9.678260 AATATAAGAGCATTTTTGAGACAGAGT 57.322 29.630 0.00 0.00 0.00 3.24
4522 4906 5.938438 AAGAGCATTTTTGAGACAGAGTC 57.062 39.130 0.00 0.00 0.00 3.36
4523 4907 5.226194 AGAGCATTTTTGAGACAGAGTCT 57.774 39.130 0.00 0.00 46.42 3.24
4524 4908 5.619220 AGAGCATTTTTGAGACAGAGTCTT 58.381 37.500 0.70 0.00 43.53 3.01
4525 4909 6.763355 AGAGCATTTTTGAGACAGAGTCTTA 58.237 36.000 0.70 0.00 43.53 2.10
4527 4911 8.535335 AGAGCATTTTTGAGACAGAGTCTTATA 58.465 33.333 0.70 0.00 43.53 0.98
4537 4921 9.853177 TGAGACAGAGTCTTATATTATGAGACA 57.147 33.333 23.13 4.87 45.35 3.41
4558 4947 2.067197 GGGAGTACCTGCTTGTGGT 58.933 57.895 0.00 0.00 41.28 4.16
4604 5219 4.732938 GCAAAGCAGCACATCTCTAAATCC 60.733 45.833 0.00 0.00 0.00 3.01
4685 5300 6.309712 AGATAAATCAATCAATGTCCAGCG 57.690 37.500 0.00 0.00 0.00 5.18
4724 5339 1.728971 CAGTTTTCCAGCGCTCACTAG 59.271 52.381 7.13 0.00 0.00 2.57
4755 5370 7.979537 AGTTCATTCTTAACCAAGGTGTTTTTC 59.020 33.333 0.00 0.00 32.22 2.29
4813 5428 4.437930 GCTTAGTGCAATGACAGCTTAAGG 60.438 45.833 4.29 0.00 42.31 2.69
4814 5429 3.146104 AGTGCAATGACAGCTTAAGGT 57.854 42.857 0.12 0.12 0.00 3.50
4815 5430 4.286297 AGTGCAATGACAGCTTAAGGTA 57.714 40.909 6.90 0.00 0.00 3.08
4816 5431 4.003648 AGTGCAATGACAGCTTAAGGTAC 58.996 43.478 6.90 5.57 0.00 3.34
4818 5433 4.002982 TGCAATGACAGCTTAAGGTACTG 58.997 43.478 6.90 6.93 40.86 2.74
4819 5434 4.003648 GCAATGACAGCTTAAGGTACTGT 58.996 43.478 6.90 10.17 46.92 3.55
4820 5435 4.455877 GCAATGACAGCTTAAGGTACTGTT 59.544 41.667 6.90 0.00 44.40 3.16
4821 5436 5.048713 GCAATGACAGCTTAAGGTACTGTTT 60.049 40.000 6.90 0.67 44.40 2.83
4822 5437 6.373779 CAATGACAGCTTAAGGTACTGTTTG 58.626 40.000 6.90 8.74 44.40 2.93
4823 5438 4.385825 TGACAGCTTAAGGTACTGTTTGG 58.614 43.478 6.90 0.00 44.40 3.28
4824 5439 4.141574 TGACAGCTTAAGGTACTGTTTGGT 60.142 41.667 6.90 0.00 44.40 3.67
4825 5440 4.788679 ACAGCTTAAGGTACTGTTTGGTT 58.211 39.130 6.90 0.00 41.78 3.67
4826 5441 4.820173 ACAGCTTAAGGTACTGTTTGGTTC 59.180 41.667 6.90 0.00 41.78 3.62
4827 5442 4.819630 CAGCTTAAGGTACTGTTTGGTTCA 59.180 41.667 6.90 0.00 40.86 3.18
4828 5443 5.473504 CAGCTTAAGGTACTGTTTGGTTCAT 59.526 40.000 6.90 0.00 40.86 2.57
4829 5444 6.653320 CAGCTTAAGGTACTGTTTGGTTCATA 59.347 38.462 6.90 0.00 40.86 2.15
4830 5445 7.174253 CAGCTTAAGGTACTGTTTGGTTCATAA 59.826 37.037 6.90 0.00 40.86 1.90
4831 5446 7.390718 AGCTTAAGGTACTGTTTGGTTCATAAG 59.609 37.037 5.12 0.00 40.86 1.73
4832 5447 7.174426 GCTTAAGGTACTGTTTGGTTCATAAGT 59.826 37.037 4.29 0.00 40.86 2.24
4833 5448 8.611654 TTAAGGTACTGTTTGGTTCATAAGTC 57.388 34.615 0.00 0.00 40.86 3.01
4834 5449 6.435292 AGGTACTGTTTGGTTCATAAGTCT 57.565 37.500 0.00 0.00 37.18 3.24
4835 5450 6.838382 AGGTACTGTTTGGTTCATAAGTCTT 58.162 36.000 0.00 0.00 37.18 3.01
4836 5451 7.287810 AGGTACTGTTTGGTTCATAAGTCTTT 58.712 34.615 0.00 0.00 37.18 2.52
4837 5452 7.228706 AGGTACTGTTTGGTTCATAAGTCTTTG 59.771 37.037 0.00 0.00 37.18 2.77
4838 5453 6.391227 ACTGTTTGGTTCATAAGTCTTTGG 57.609 37.500 0.00 0.00 0.00 3.28
4839 5454 6.126409 ACTGTTTGGTTCATAAGTCTTTGGA 58.874 36.000 0.00 0.00 0.00 3.53
4840 5455 6.039382 ACTGTTTGGTTCATAAGTCTTTGGAC 59.961 38.462 0.00 0.00 42.41 4.02
4868 5483 6.956102 TTTAGTCCCAACTTATAAGTCCCA 57.044 37.500 18.28 1.06 38.57 4.37
4869 5484 6.956102 TTAGTCCCAACTTATAAGTCCCAA 57.044 37.500 18.28 3.05 38.57 4.12
4870 5485 5.437191 AGTCCCAACTTATAAGTCCCAAG 57.563 43.478 18.28 6.66 38.57 3.61
4871 5486 4.850386 AGTCCCAACTTATAAGTCCCAAGT 59.150 41.667 18.28 5.74 38.57 3.16
4872 5487 5.045797 AGTCCCAACTTATAAGTCCCAAGTC 60.046 44.000 18.28 6.78 38.57 3.01
4873 5488 4.226620 TCCCAACTTATAAGTCCCAAGTCC 59.773 45.833 18.28 0.00 38.57 3.85
4874 5489 4.524053 CCAACTTATAAGTCCCAAGTCCC 58.476 47.826 18.28 0.00 38.57 4.46
4875 5490 4.524053 CAACTTATAAGTCCCAAGTCCCC 58.476 47.826 18.28 0.00 38.57 4.81
4876 5491 3.810623 ACTTATAAGTCCCAAGTCCCCA 58.189 45.455 12.50 0.00 32.86 4.96
4877 5492 4.180723 ACTTATAAGTCCCAAGTCCCCAA 58.819 43.478 12.50 0.00 32.86 4.12
4878 5493 4.604490 ACTTATAAGTCCCAAGTCCCCAAA 59.396 41.667 12.50 0.00 32.86 3.28
4879 5494 5.075344 ACTTATAAGTCCCAAGTCCCCAAAA 59.925 40.000 12.50 0.00 32.86 2.44
4880 5495 2.858787 AAGTCCCAAGTCCCCAAAAA 57.141 45.000 0.00 0.00 0.00 1.94
4881 5496 2.381752 AGTCCCAAGTCCCCAAAAAG 57.618 50.000 0.00 0.00 0.00 2.27
4882 5497 1.573857 AGTCCCAAGTCCCCAAAAAGT 59.426 47.619 0.00 0.00 0.00 2.66
4883 5498 1.961394 GTCCCAAGTCCCCAAAAAGTC 59.039 52.381 0.00 0.00 0.00 3.01
4884 5499 1.133294 TCCCAAGTCCCCAAAAAGTCC 60.133 52.381 0.00 0.00 0.00 3.85
4885 5500 1.338107 CCAAGTCCCCAAAAAGTCCC 58.662 55.000 0.00 0.00 0.00 4.46
4886 5501 1.133167 CCAAGTCCCCAAAAAGTCCCT 60.133 52.381 0.00 0.00 0.00 4.20
4887 5502 2.109304 CCAAGTCCCCAAAAAGTCCCTA 59.891 50.000 0.00 0.00 0.00 3.53
4888 5503 3.154710 CAAGTCCCCAAAAAGTCCCTAC 58.845 50.000 0.00 0.00 0.00 3.18
4889 5504 2.424793 AGTCCCCAAAAAGTCCCTACA 58.575 47.619 0.00 0.00 0.00 2.74
4890 5505 2.993863 AGTCCCCAAAAAGTCCCTACAT 59.006 45.455 0.00 0.00 0.00 2.29
4891 5506 3.089284 GTCCCCAAAAAGTCCCTACATG 58.911 50.000 0.00 0.00 0.00 3.21
4892 5507 2.719705 TCCCCAAAAAGTCCCTACATGT 59.280 45.455 2.69 2.69 0.00 3.21
4893 5508 3.141272 TCCCCAAAAAGTCCCTACATGTT 59.859 43.478 2.30 0.00 0.00 2.71
4894 5509 3.901222 CCCCAAAAAGTCCCTACATGTTT 59.099 43.478 2.30 0.00 0.00 2.83
4895 5510 4.262420 CCCCAAAAAGTCCCTACATGTTTG 60.262 45.833 2.30 0.00 0.00 2.93
4896 5511 4.262420 CCCAAAAAGTCCCTACATGTTTGG 60.262 45.833 2.30 8.41 39.89 3.28
4897 5512 4.343814 CCAAAAAGTCCCTACATGTTTGGT 59.656 41.667 2.30 0.00 37.78 3.67
4898 5513 5.163353 CCAAAAAGTCCCTACATGTTTGGTT 60.163 40.000 2.30 0.00 37.78 3.67
4899 5514 5.784578 AAAAGTCCCTACATGTTTGGTTC 57.215 39.130 2.30 3.85 0.00 3.62
4900 5515 3.434940 AGTCCCTACATGTTTGGTTCC 57.565 47.619 2.30 0.00 0.00 3.62
4901 5516 2.986728 AGTCCCTACATGTTTGGTTCCT 59.013 45.455 2.30 1.09 0.00 3.36
4902 5517 3.081804 GTCCCTACATGTTTGGTTCCTG 58.918 50.000 2.30 0.00 0.00 3.86
4903 5518 2.041081 TCCCTACATGTTTGGTTCCTGG 59.959 50.000 2.30 0.00 0.00 4.45
4904 5519 2.446435 CCTACATGTTTGGTTCCTGGG 58.554 52.381 2.30 0.00 0.00 4.45
4905 5520 2.041081 CCTACATGTTTGGTTCCTGGGA 59.959 50.000 2.30 0.00 0.00 4.37
4906 5521 1.995376 ACATGTTTGGTTCCTGGGAC 58.005 50.000 0.00 0.00 0.00 4.46
4907 5522 1.499007 ACATGTTTGGTTCCTGGGACT 59.501 47.619 4.84 0.00 0.00 3.85
4908 5523 2.091333 ACATGTTTGGTTCCTGGGACTT 60.091 45.455 4.84 0.00 0.00 3.01
4909 5524 3.139397 ACATGTTTGGTTCCTGGGACTTA 59.861 43.478 4.84 0.00 0.00 2.24
4910 5525 3.955524 TGTTTGGTTCCTGGGACTTAA 57.044 42.857 4.84 0.00 0.00 1.85
4911 5526 3.558033 TGTTTGGTTCCTGGGACTTAAC 58.442 45.455 4.84 9.92 0.00 2.01
4912 5527 3.053544 TGTTTGGTTCCTGGGACTTAACA 60.054 43.478 16.45 16.45 0.00 2.41
4913 5528 4.149598 GTTTGGTTCCTGGGACTTAACAT 58.850 43.478 4.84 0.00 0.00 2.71
4914 5529 3.433306 TGGTTCCTGGGACTTAACATG 57.567 47.619 4.84 0.00 0.00 3.21
4915 5530 2.041081 TGGTTCCTGGGACTTAACATGG 59.959 50.000 4.84 0.00 0.00 3.66
4916 5531 2.307686 GGTTCCTGGGACTTAACATGGA 59.692 50.000 4.84 0.00 0.00 3.41
4917 5532 3.344515 GTTCCTGGGACTTAACATGGAC 58.655 50.000 0.00 0.00 0.00 4.02
4918 5533 2.915869 TCCTGGGACTTAACATGGACT 58.084 47.619 0.00 0.00 0.00 3.85
4919 5534 4.069312 TCCTGGGACTTAACATGGACTA 57.931 45.455 0.00 0.00 0.00 2.59
4920 5535 4.431378 TCCTGGGACTTAACATGGACTAA 58.569 43.478 0.00 0.00 0.00 2.24
4921 5536 4.847512 TCCTGGGACTTAACATGGACTAAA 59.152 41.667 0.00 0.00 0.00 1.85
4922 5537 5.311121 TCCTGGGACTTAACATGGACTAAAA 59.689 40.000 0.00 0.00 0.00 1.52
4923 5538 5.648092 CCTGGGACTTAACATGGACTAAAAG 59.352 44.000 0.00 0.00 0.00 2.27
4924 5539 6.442541 TGGGACTTAACATGGACTAAAAGA 57.557 37.500 0.00 0.00 0.00 2.52
4925 5540 6.235664 TGGGACTTAACATGGACTAAAAGAC 58.764 40.000 0.00 0.00 0.00 3.01
4926 5541 5.646793 GGGACTTAACATGGACTAAAAGACC 59.353 44.000 0.00 1.56 0.00 3.85
4927 5542 6.235664 GGACTTAACATGGACTAAAAGACCA 58.764 40.000 0.00 0.74 43.65 4.02
4929 5544 8.044908 GGACTTAACATGGACTAAAAGACCATA 58.955 37.037 9.96 0.00 46.31 2.74
4930 5545 9.614792 GACTTAACATGGACTAAAAGACCATAT 57.385 33.333 9.96 6.06 46.31 1.78
4931 5546 9.975218 ACTTAACATGGACTAAAAGACCATATT 57.025 29.630 9.96 8.42 46.31 1.28
4935 5550 9.747898 AACATGGACTAAAAGACCATATTACAA 57.252 29.630 9.96 0.00 46.31 2.41
4936 5551 9.174166 ACATGGACTAAAAGACCATATTACAAC 57.826 33.333 9.96 0.00 46.31 3.32
4937 5552 9.396022 CATGGACTAAAAGACCATATTACAACT 57.604 33.333 9.96 0.00 46.31 3.16
4947 5562 9.448587 AAGACCATATTACAACTATAAGTCCCT 57.551 33.333 0.00 0.00 0.00 4.20
4948 5563 9.091220 AGACCATATTACAACTATAAGTCCCTC 57.909 37.037 0.00 0.00 0.00 4.30
4949 5564 8.792830 ACCATATTACAACTATAAGTCCCTCA 57.207 34.615 0.00 0.00 0.00 3.86
4950 5565 9.393786 ACCATATTACAACTATAAGTCCCTCAT 57.606 33.333 0.00 0.00 0.00 2.90
4955 5570 8.603898 TTACAACTATAAGTCCCTCATTGAGA 57.396 34.615 15.36 0.00 0.00 3.27
4956 5571 7.118496 ACAACTATAAGTCCCTCATTGAGAG 57.882 40.000 15.36 1.59 44.31 3.20
4957 5572 6.670027 ACAACTATAAGTCCCTCATTGAGAGT 59.330 38.462 15.36 5.07 43.12 3.24
4958 5573 6.969993 ACTATAAGTCCCTCATTGAGAGTC 57.030 41.667 15.36 0.00 43.12 3.36
4959 5574 6.678547 ACTATAAGTCCCTCATTGAGAGTCT 58.321 40.000 15.36 2.18 43.12 3.24
4960 5575 7.129425 ACTATAAGTCCCTCATTGAGAGTCTT 58.871 38.462 15.36 12.94 43.12 3.01
4961 5576 8.282982 ACTATAAGTCCCTCATTGAGAGTCTTA 58.717 37.037 15.36 14.55 43.12 2.10
4962 5577 9.308000 CTATAAGTCCCTCATTGAGAGTCTTAT 57.692 37.037 21.75 21.75 43.12 1.73
4963 5578 6.882768 AAGTCCCTCATTGAGAGTCTTATT 57.117 37.500 15.36 0.00 43.12 1.40
4964 5579 6.882768 AGTCCCTCATTGAGAGTCTTATTT 57.117 37.500 15.36 0.00 43.12 1.40
4965 5580 6.883744 AGTCCCTCATTGAGAGTCTTATTTC 58.116 40.000 15.36 0.00 43.12 2.17
4966 5581 6.441924 AGTCCCTCATTGAGAGTCTTATTTCA 59.558 38.462 15.36 0.00 43.12 2.69
4967 5582 7.127032 AGTCCCTCATTGAGAGTCTTATTTCAT 59.873 37.037 15.36 0.00 43.12 2.57
4968 5583 8.424918 GTCCCTCATTGAGAGTCTTATTTCATA 58.575 37.037 15.36 0.00 43.12 2.15
4969 5584 8.992349 TCCCTCATTGAGAGTCTTATTTCATAA 58.008 33.333 15.36 0.00 43.12 1.90
4970 5585 9.270640 CCCTCATTGAGAGTCTTATTTCATAAG 57.729 37.037 15.36 0.00 43.12 1.73
4971 5586 9.829507 CCTCATTGAGAGTCTTATTTCATAAGT 57.170 33.333 15.36 0.00 43.12 2.24
4981 5596 8.897752 AGTCTTATTTCATAAGTCTCAAATGCC 58.102 33.333 3.93 0.00 42.21 4.40
4982 5597 8.131731 GTCTTATTTCATAAGTCTCAAATGCCC 58.868 37.037 3.93 0.00 42.21 5.36
4983 5598 7.833682 TCTTATTTCATAAGTCTCAAATGCCCA 59.166 33.333 3.93 0.00 42.21 5.36
4984 5599 5.643379 TTTCATAAGTCTCAAATGCCCAC 57.357 39.130 0.00 0.00 0.00 4.61
4985 5600 4.574674 TCATAAGTCTCAAATGCCCACT 57.425 40.909 0.00 0.00 0.00 4.00
4986 5601 4.922206 TCATAAGTCTCAAATGCCCACTT 58.078 39.130 0.00 0.00 0.00 3.16
4987 5602 5.324409 TCATAAGTCTCAAATGCCCACTTT 58.676 37.500 0.00 0.00 0.00 2.66
4988 5603 6.480763 TCATAAGTCTCAAATGCCCACTTTA 58.519 36.000 0.00 0.00 0.00 1.85
4989 5604 6.945435 TCATAAGTCTCAAATGCCCACTTTAA 59.055 34.615 0.00 0.00 0.00 1.52
4990 5605 5.712152 AAGTCTCAAATGCCCACTTTAAG 57.288 39.130 0.00 0.00 0.00 1.85
4991 5606 4.729868 AGTCTCAAATGCCCACTTTAAGT 58.270 39.130 0.00 0.00 0.00 2.24
4992 5607 4.762251 AGTCTCAAATGCCCACTTTAAGTC 59.238 41.667 0.00 0.00 0.00 3.01
4993 5608 4.079253 TCTCAAATGCCCACTTTAAGTCC 58.921 43.478 0.00 0.00 0.00 3.85
4994 5609 3.161866 TCAAATGCCCACTTTAAGTCCC 58.838 45.455 0.00 0.00 0.00 4.46
4995 5610 3.165071 CAAATGCCCACTTTAAGTCCCT 58.835 45.455 0.00 0.00 0.00 4.20
4996 5611 4.043561 TCAAATGCCCACTTTAAGTCCCTA 59.956 41.667 0.00 0.00 0.00 3.53
4997 5612 3.646736 ATGCCCACTTTAAGTCCCTAC 57.353 47.619 0.00 0.00 0.00 3.18
4998 5613 2.340731 TGCCCACTTTAAGTCCCTACA 58.659 47.619 0.00 0.00 0.00 2.74
4999 5614 2.712087 TGCCCACTTTAAGTCCCTACAA 59.288 45.455 0.00 0.00 0.00 2.41
5000 5615 3.244770 TGCCCACTTTAAGTCCCTACAAG 60.245 47.826 0.00 0.00 0.00 3.16
5001 5616 3.244805 GCCCACTTTAAGTCCCTACAAGT 60.245 47.826 0.00 0.00 0.00 3.16
5002 5617 4.576879 CCCACTTTAAGTCCCTACAAGTC 58.423 47.826 0.00 0.00 0.00 3.01
5003 5618 4.565028 CCCACTTTAAGTCCCTACAAGTCC 60.565 50.000 0.00 0.00 0.00 3.85
5004 5619 4.565028 CCACTTTAAGTCCCTACAAGTCCC 60.565 50.000 0.00 0.00 0.00 4.46
5005 5620 4.286291 CACTTTAAGTCCCTACAAGTCCCT 59.714 45.833 0.00 0.00 0.00 4.20
5006 5621 4.531339 ACTTTAAGTCCCTACAAGTCCCTC 59.469 45.833 0.00 0.00 0.00 4.30
5007 5622 1.954035 AAGTCCCTACAAGTCCCTCC 58.046 55.000 0.00 0.00 0.00 4.30
5008 5623 1.094269 AGTCCCTACAAGTCCCTCCT 58.906 55.000 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 2.057922 AGTGGATCCCTGACTTGTTGT 58.942 47.619 9.90 0.00 0.00 3.32
150 289 1.725164 CGAGAAGCCGGTAAGTTGTTC 59.275 52.381 1.90 0.00 0.00 3.18
351 490 6.688385 CGAATTACCGTCGACAGTTATCTTAA 59.312 38.462 17.16 0.59 41.02 1.85
387 526 5.305139 GGCTTTTCGTTGCCTAATTTCTA 57.695 39.130 0.00 0.00 45.26 2.10
434 574 3.020984 GCATAATTGGTTCGAGGGGAAA 58.979 45.455 0.00 0.00 36.14 3.13
440 580 1.003545 CTGCGGCATAATTGGTTCGAG 60.004 52.381 1.75 0.00 0.00 4.04
467 613 1.002087 CTCCGATTTTAGATCCGGGGG 59.998 57.143 0.00 0.00 42.03 5.40
535 681 6.696441 TCTTCTCGAAACTCTAACCCTATC 57.304 41.667 0.00 0.00 0.00 2.08
741 901 1.516386 CGAGTCGGACCCATTGACG 60.516 63.158 4.10 0.00 37.69 4.35
742 902 4.496670 CGAGTCGGACCCATTGAC 57.503 61.111 4.10 0.00 0.00 3.18
983 1143 2.678471 CATTGGGAATGGCTGGTTTC 57.322 50.000 0.00 0.00 35.23 2.78
1136 1296 1.474332 AAAAGGCGAGGTGGTACGGA 61.474 55.000 0.00 0.00 0.00 4.69
1168 1329 4.157656 CGTCCAGCCATTAAAATCCTCAAA 59.842 41.667 0.00 0.00 0.00 2.69
1181 1342 1.512926 GATTTATCGCGTCCAGCCAT 58.487 50.000 5.77 0.00 44.76 4.40
1182 1343 0.531974 GGATTTATCGCGTCCAGCCA 60.532 55.000 5.77 0.00 44.76 4.75
1257 1418 2.033448 GCATTCACGACCACCCCA 59.967 61.111 0.00 0.00 0.00 4.96
1305 1466 3.567585 CCTCATAAGAGCTCTCATCGTCA 59.432 47.826 18.55 0.00 40.68 4.35
1369 1530 0.035458 AGGTTCAGTAGGTGCACAGC 59.965 55.000 20.43 7.79 0.00 4.40
1370 1531 1.070758 ACAGGTTCAGTAGGTGCACAG 59.929 52.381 20.43 2.68 0.00 3.66
1378 1539 7.220683 CACAAAATCAAAACACAGGTTCAGTAG 59.779 37.037 0.00 0.00 35.82 2.57
1380 1541 5.868801 CACAAAATCAAAACACAGGTTCAGT 59.131 36.000 0.00 0.00 35.82 3.41
1449 1610 4.831107 TGTATGCTAGCTTCATGTTGTCA 58.169 39.130 17.23 0.00 0.00 3.58
1574 1735 5.594725 TGCACCACAACAAAACTAATAAGGA 59.405 36.000 0.00 0.00 0.00 3.36
1612 1773 2.170397 TCGAGCTGAAATCCCAATAGCA 59.830 45.455 0.00 0.00 36.87 3.49
1631 1792 4.176271 TCACAGTGTCATATGCTTTCTCG 58.824 43.478 0.00 0.00 0.00 4.04
1640 1801 3.813724 GCTGCATCATCACAGTGTCATAT 59.186 43.478 0.00 0.00 36.26 1.78
1667 1828 3.013648 TGACCCCCTTCTTCCTATACTGT 59.986 47.826 0.00 0.00 0.00 3.55
1732 1893 8.632679 TGAGTATCCCAATTATGAAAAATCAGC 58.367 33.333 0.00 0.00 0.00 4.26
1753 1914 7.744087 ATGCAAATCTTGTAACTTGTGAGTA 57.256 32.000 0.00 0.00 34.21 2.59
1773 1934 7.994194 TCTACATATGTAACAAATGCAATGCA 58.006 30.769 11.44 11.44 44.86 3.96
1885 2048 4.725556 ATACAATGCAGTTATAACCGCG 57.274 40.909 16.88 0.00 35.12 6.46
1950 2134 8.840200 ACATTAGTAGGAAAGGACTTAGATGA 57.160 34.615 0.00 0.00 0.00 2.92
2136 2392 6.659242 AGTGAACCCAGAAAAATAATGTCGAT 59.341 34.615 0.00 0.00 0.00 3.59
2151 2407 6.146021 GCATCACAAAAATTAAGTGAACCCAG 59.854 38.462 10.38 2.92 44.47 4.45
2175 2432 5.119898 TGAATTTGCCATTTTCATAACGTGC 59.880 36.000 0.00 0.00 0.00 5.34
2299 2556 0.321653 AGGCTGAACTAAACAGGGCG 60.322 55.000 0.00 0.00 36.09 6.13
2324 2581 9.692749 TTGGTATCAAATTAAACGCATAAACAA 57.307 25.926 0.00 0.00 0.00 2.83
2394 2651 3.490348 GCCTGGTGCATATATCCTTGTT 58.510 45.455 0.00 0.00 40.77 2.83
2413 2671 6.143919 GCTGTTTAGTTCAAATTACAAGTGCC 59.856 38.462 0.00 0.00 0.00 5.01
2539 2797 9.466497 AGGAATGTGTTAAGATCATACAATTGT 57.534 29.630 16.68 16.68 0.00 2.71
2704 2963 6.674519 GCACGCTCAAGCATTACAACTTATAA 60.675 38.462 2.50 0.00 42.21 0.98
2705 2964 5.220586 GCACGCTCAAGCATTACAACTTATA 60.221 40.000 2.50 0.00 42.21 0.98
2745 3004 9.619316 TGATAACAACACTAAATTAACATGCAC 57.381 29.630 0.00 0.00 0.00 4.57
2907 3166 4.057406 AGAGATTCAGAGAGGCATTTCG 57.943 45.455 0.00 0.00 0.00 3.46
2911 3170 4.680172 CGTTGAAGAGATTCAGAGAGGCAT 60.680 45.833 0.00 0.00 31.87 4.40
2945 3204 4.442893 CCAGGGAGACATACGAGCATTTAA 60.443 45.833 0.00 0.00 0.00 1.52
2985 3244 8.700973 ACCAACACCTTAGTTTTTGATATGTTT 58.299 29.630 0.00 0.00 0.00 2.83
3010 3269 5.048782 TGTGCACACAAGATGAGGAAAATAC 60.049 40.000 17.42 0.00 38.56 1.89
3032 3291 6.324819 CCAAATAGATGCATTCGAACTTTGT 58.675 36.000 0.00 0.00 0.00 2.83
3041 3300 5.603596 TCATTTGCCCAAATAGATGCATTC 58.396 37.500 0.00 0.00 38.84 2.67
3289 3548 8.246430 TGTGCTAATTATAGGCTAGTAAGTGT 57.754 34.615 0.00 0.00 0.00 3.55
3332 3591 1.081242 CCACGCAGACAACAATGGC 60.081 57.895 0.00 0.00 33.34 4.40
3531 3790 2.188817 ACCCAAGAAGAATCTAGCGGT 58.811 47.619 0.00 0.00 33.77 5.68
3574 3833 5.216648 GCAAATAAAAAGTACAAGCGGTCA 58.783 37.500 0.00 0.00 0.00 4.02
3744 4003 5.149273 GCATCTACACACACTTCACATTTG 58.851 41.667 0.00 0.00 0.00 2.32
3774 4033 8.340443 CACAGATCACAATGGTTCTACAATATG 58.660 37.037 0.00 0.00 0.00 1.78
3790 4144 2.102925 TGTGCTCAACTCACAGATCACA 59.897 45.455 0.00 0.00 39.29 3.58
3843 4197 1.671979 TCTAGCCAGCATGCATGTTC 58.328 50.000 26.79 12.06 31.97 3.18
4105 4466 2.432444 TGGCTTTTCCCTAATGTGACG 58.568 47.619 0.00 0.00 0.00 4.35
4167 4528 6.434028 CACCCAAAATTCTCTACCTCAAATGA 59.566 38.462 0.00 0.00 0.00 2.57
4194 4555 4.268405 CCACAATTGTTCAAACAGAAGCAC 59.732 41.667 8.77 0.00 40.50 4.40
4218 4579 0.040958 CGCCTTTTGCACAGTGAGTC 60.041 55.000 4.15 0.00 41.33 3.36
4376 4738 6.050432 TCAATTAATTTGGAATGGAGCATGC 58.950 36.000 10.51 10.51 35.92 4.06
4515 4899 9.295825 CCTCTGTCTCATAATATAAGACTCTGT 57.704 37.037 5.27 0.00 40.07 3.41
4516 4900 8.739039 CCCTCTGTCTCATAATATAAGACTCTG 58.261 40.741 5.27 0.00 40.07 3.35
4517 4901 8.674173 TCCCTCTGTCTCATAATATAAGACTCT 58.326 37.037 5.27 0.00 40.07 3.24
4518 4902 8.871629 TCCCTCTGTCTCATAATATAAGACTC 57.128 38.462 5.27 0.00 40.07 3.36
4520 4904 8.644374 ACTCCCTCTGTCTCATAATATAAGAC 57.356 38.462 0.00 0.00 39.87 3.01
4521 4905 9.742144 GTACTCCCTCTGTCTCATAATATAAGA 57.258 37.037 0.00 0.00 0.00 2.10
4522 4906 8.962679 GGTACTCCCTCTGTCTCATAATATAAG 58.037 40.741 0.00 0.00 0.00 1.73
4523 4907 8.679725 AGGTACTCCCTCTGTCTCATAATATAA 58.320 37.037 0.00 0.00 40.71 0.98
4524 4908 8.110271 CAGGTACTCCCTCTGTCTCATAATATA 58.890 40.741 0.00 0.00 43.86 0.86
4525 4909 6.951198 CAGGTACTCCCTCTGTCTCATAATAT 59.049 42.308 0.00 0.00 43.86 1.28
4527 4911 5.144100 CAGGTACTCCCTCTGTCTCATAAT 58.856 45.833 0.00 0.00 43.86 1.28
4532 4916 1.107945 GCAGGTACTCCCTCTGTCTC 58.892 60.000 0.00 0.00 43.86 3.36
4533 4917 0.707616 AGCAGGTACTCCCTCTGTCT 59.292 55.000 0.00 0.00 43.86 3.41
4534 4918 1.205893 CAAGCAGGTACTCCCTCTGTC 59.794 57.143 0.00 0.00 43.86 3.51
4536 4920 1.066573 CACAAGCAGGTACTCCCTCTG 60.067 57.143 0.00 0.00 43.86 3.35
4537 4921 1.270907 CACAAGCAGGTACTCCCTCT 58.729 55.000 0.00 0.00 43.86 3.69
4558 4947 5.067936 GCACATTTCTAGACCAGACTAGCTA 59.932 44.000 0.00 0.00 39.50 3.32
4604 5219 2.036556 ACGAATTTTGTGCAGCTTCG 57.963 45.000 9.88 9.88 43.10 3.79
4669 5284 1.337728 ACGACGCTGGACATTGATTGA 60.338 47.619 0.00 0.00 0.00 2.57
4672 5287 1.464608 CAAACGACGCTGGACATTGAT 59.535 47.619 0.00 0.00 0.00 2.57
4685 5300 4.614946 ACTGTTACTCCTACACAAACGAC 58.385 43.478 0.00 0.00 0.00 4.34
4724 5339 6.200854 CACCTTGGTTAAGAATGAACTTTTGC 59.799 38.462 0.00 0.00 35.92 3.68
4813 5428 7.227910 TCCAAAGACTTATGAACCAAACAGTAC 59.772 37.037 0.00 0.00 0.00 2.73
4814 5429 7.227910 GTCCAAAGACTTATGAACCAAACAGTA 59.772 37.037 0.00 0.00 40.10 2.74
4815 5430 6.039382 GTCCAAAGACTTATGAACCAAACAGT 59.961 38.462 0.00 0.00 40.10 3.55
4816 5431 6.438763 GTCCAAAGACTTATGAACCAAACAG 58.561 40.000 0.00 0.00 40.10 3.16
4817 5432 6.385649 GTCCAAAGACTTATGAACCAAACA 57.614 37.500 0.00 0.00 40.10 2.83
4843 5458 7.757611 TGGGACTTATAAGTTGGGACTAAAAA 58.242 34.615 18.96 0.00 39.88 1.94
4844 5459 7.332433 TGGGACTTATAAGTTGGGACTAAAA 57.668 36.000 18.96 0.00 39.88 1.52
4845 5460 6.956102 TGGGACTTATAAGTTGGGACTAAA 57.044 37.500 18.96 0.00 39.88 1.85
4846 5461 6.502863 ACTTGGGACTTATAAGTTGGGACTAA 59.497 38.462 18.96 10.32 39.88 2.24
4847 5462 6.027482 ACTTGGGACTTATAAGTTGGGACTA 58.973 40.000 18.96 3.96 39.88 2.59
4848 5463 4.850386 ACTTGGGACTTATAAGTTGGGACT 59.150 41.667 18.96 0.00 39.88 3.85
4849 5464 5.175388 ACTTGGGACTTATAAGTTGGGAC 57.825 43.478 18.96 6.19 39.88 4.46
4850 5465 4.226620 GGACTTGGGACTTATAAGTTGGGA 59.773 45.833 18.96 6.15 39.88 4.37
4851 5466 4.524053 GGACTTGGGACTTATAAGTTGGG 58.476 47.826 18.96 10.37 39.88 4.12
4852 5467 4.524053 GGGACTTGGGACTTATAAGTTGG 58.476 47.826 18.96 10.07 39.88 3.77
4853 5468 4.018779 TGGGGACTTGGGACTTATAAGTTG 60.019 45.833 18.96 9.81 39.88 3.16
4854 5469 4.180723 TGGGGACTTGGGACTTATAAGTT 58.819 43.478 18.96 2.29 39.88 2.66
4855 5470 3.810623 TGGGGACTTGGGACTTATAAGT 58.189 45.455 18.05 18.05 43.16 2.24
4856 5471 4.855298 TTGGGGACTTGGGACTTATAAG 57.145 45.455 11.05 11.05 0.00 1.73
4857 5472 5.602291 TTTTGGGGACTTGGGACTTATAA 57.398 39.130 0.00 0.00 0.00 0.98
4858 5473 5.075344 ACTTTTTGGGGACTTGGGACTTATA 59.925 40.000 0.00 0.00 0.00 0.98
4859 5474 4.140782 ACTTTTTGGGGACTTGGGACTTAT 60.141 41.667 0.00 0.00 0.00 1.73
4860 5475 3.205733 ACTTTTTGGGGACTTGGGACTTA 59.794 43.478 0.00 0.00 0.00 2.24
4861 5476 2.023404 ACTTTTTGGGGACTTGGGACTT 60.023 45.455 0.00 0.00 0.00 3.01
4862 5477 1.573857 ACTTTTTGGGGACTTGGGACT 59.426 47.619 0.00 0.00 0.00 3.85
4863 5478 1.961394 GACTTTTTGGGGACTTGGGAC 59.039 52.381 0.00 0.00 0.00 4.46
4864 5479 1.133294 GGACTTTTTGGGGACTTGGGA 60.133 52.381 0.00 0.00 0.00 4.37
4865 5480 1.338107 GGACTTTTTGGGGACTTGGG 58.662 55.000 0.00 0.00 0.00 4.12
4866 5481 1.133167 AGGGACTTTTTGGGGACTTGG 60.133 52.381 0.00 0.00 27.25 3.61
4867 5482 2.381752 AGGGACTTTTTGGGGACTTG 57.618 50.000 0.00 0.00 27.25 3.16
4868 5483 2.787035 TGTAGGGACTTTTTGGGGACTT 59.213 45.455 0.00 0.00 41.75 3.01
4869 5484 2.424793 TGTAGGGACTTTTTGGGGACT 58.575 47.619 0.00 0.00 41.75 3.85
4870 5485 2.963599 TGTAGGGACTTTTTGGGGAC 57.036 50.000 0.00 0.00 41.75 4.46
4871 5486 2.719705 ACATGTAGGGACTTTTTGGGGA 59.280 45.455 0.00 0.00 41.75 4.81
4872 5487 3.169512 ACATGTAGGGACTTTTTGGGG 57.830 47.619 0.00 0.00 41.75 4.96
4873 5488 4.262420 CCAAACATGTAGGGACTTTTTGGG 60.262 45.833 9.55 0.00 41.75 4.12
4874 5489 4.343814 ACCAAACATGTAGGGACTTTTTGG 59.656 41.667 19.48 17.32 41.75 3.28
4875 5490 5.529581 ACCAAACATGTAGGGACTTTTTG 57.470 39.130 19.48 8.12 41.75 2.44
4876 5491 5.069914 GGAACCAAACATGTAGGGACTTTTT 59.930 40.000 19.48 5.69 41.75 1.94
4877 5492 4.587262 GGAACCAAACATGTAGGGACTTTT 59.413 41.667 19.48 6.31 41.75 2.27
4878 5493 4.141018 AGGAACCAAACATGTAGGGACTTT 60.141 41.667 19.48 6.62 41.75 2.66
4879 5494 3.397955 AGGAACCAAACATGTAGGGACTT 59.602 43.478 19.48 6.91 41.75 3.01
4880 5495 2.986728 AGGAACCAAACATGTAGGGACT 59.013 45.455 19.48 11.76 46.37 3.85
4881 5496 3.081804 CAGGAACCAAACATGTAGGGAC 58.918 50.000 19.48 12.61 0.00 4.46
4882 5497 2.041081 CCAGGAACCAAACATGTAGGGA 59.959 50.000 19.48 0.00 0.00 4.20
4883 5498 2.446435 CCAGGAACCAAACATGTAGGG 58.554 52.381 18.43 15.73 0.00 3.53
4884 5499 2.041081 TCCCAGGAACCAAACATGTAGG 59.959 50.000 14.04 14.04 0.00 3.18
4885 5500 3.081804 GTCCCAGGAACCAAACATGTAG 58.918 50.000 0.00 0.00 0.00 2.74
4886 5501 2.714250 AGTCCCAGGAACCAAACATGTA 59.286 45.455 0.00 0.00 0.00 2.29
4887 5502 1.499007 AGTCCCAGGAACCAAACATGT 59.501 47.619 0.00 0.00 0.00 3.21
4888 5503 2.292828 AGTCCCAGGAACCAAACATG 57.707 50.000 0.00 0.00 0.00 3.21
4889 5504 4.149598 GTTAAGTCCCAGGAACCAAACAT 58.850 43.478 0.00 0.00 0.00 2.71
4890 5505 3.053544 TGTTAAGTCCCAGGAACCAAACA 60.054 43.478 0.00 0.00 0.00 2.83
4891 5506 3.558033 TGTTAAGTCCCAGGAACCAAAC 58.442 45.455 0.00 0.00 0.00 2.93
4892 5507 3.955524 TGTTAAGTCCCAGGAACCAAA 57.044 42.857 0.00 0.00 0.00 3.28
4893 5508 3.499563 CCATGTTAAGTCCCAGGAACCAA 60.500 47.826 0.00 0.00 0.00 3.67
4894 5509 2.041081 CCATGTTAAGTCCCAGGAACCA 59.959 50.000 0.00 0.00 0.00 3.67
4895 5510 2.307686 TCCATGTTAAGTCCCAGGAACC 59.692 50.000 0.00 0.00 0.00 3.62
4896 5511 3.009143 AGTCCATGTTAAGTCCCAGGAAC 59.991 47.826 0.00 0.00 0.00 3.62
4897 5512 3.256704 AGTCCATGTTAAGTCCCAGGAA 58.743 45.455 0.00 0.00 0.00 3.36
4898 5513 2.915869 AGTCCATGTTAAGTCCCAGGA 58.084 47.619 0.00 0.00 0.00 3.86
4899 5514 4.837093 TTAGTCCATGTTAAGTCCCAGG 57.163 45.455 0.00 0.00 0.00 4.45
4900 5515 6.371825 GTCTTTTAGTCCATGTTAAGTCCCAG 59.628 42.308 0.00 0.00 0.00 4.45
4901 5516 6.235664 GTCTTTTAGTCCATGTTAAGTCCCA 58.764 40.000 0.00 0.00 0.00 4.37
4902 5517 5.646793 GGTCTTTTAGTCCATGTTAAGTCCC 59.353 44.000 0.00 0.00 0.00 4.46
4903 5518 6.235664 TGGTCTTTTAGTCCATGTTAAGTCC 58.764 40.000 0.00 0.00 28.55 3.85
4904 5519 7.923414 ATGGTCTTTTAGTCCATGTTAAGTC 57.077 36.000 4.95 0.00 41.46 3.01
4905 5520 9.975218 AATATGGTCTTTTAGTCCATGTTAAGT 57.025 29.630 13.41 0.00 42.62 2.24
4909 5524 9.747898 TTGTAATATGGTCTTTTAGTCCATGTT 57.252 29.630 15.13 15.13 42.62 2.71
4910 5525 9.174166 GTTGTAATATGGTCTTTTAGTCCATGT 57.826 33.333 13.41 6.18 42.62 3.21
4911 5526 9.396022 AGTTGTAATATGGTCTTTTAGTCCATG 57.604 33.333 13.41 0.00 42.62 3.66
4921 5536 9.448587 AGGGACTTATAGTTGTAATATGGTCTT 57.551 33.333 0.00 0.00 27.25 3.01
4922 5537 9.091220 GAGGGACTTATAGTTGTAATATGGTCT 57.909 37.037 0.00 0.00 41.55 3.85
4923 5538 8.867097 TGAGGGACTTATAGTTGTAATATGGTC 58.133 37.037 0.00 0.00 41.55 4.02
4924 5539 8.792830 TGAGGGACTTATAGTTGTAATATGGT 57.207 34.615 0.00 0.00 41.55 3.55
4929 5544 9.213777 TCTCAATGAGGGACTTATAGTTGTAAT 57.786 33.333 10.71 0.00 41.55 1.89
4930 5545 8.603898 TCTCAATGAGGGACTTATAGTTGTAA 57.396 34.615 10.71 0.00 41.55 2.41
4931 5546 7.839705 ACTCTCAATGAGGGACTTATAGTTGTA 59.160 37.037 18.25 0.00 46.72 2.41
4932 5547 6.670027 ACTCTCAATGAGGGACTTATAGTTGT 59.330 38.462 18.25 0.00 46.72 3.32
4933 5548 7.069331 AGACTCTCAATGAGGGACTTATAGTTG 59.931 40.741 18.25 0.00 46.72 3.16
4934 5549 7.129425 AGACTCTCAATGAGGGACTTATAGTT 58.871 38.462 18.25 0.00 46.72 2.24
4935 5550 6.678547 AGACTCTCAATGAGGGACTTATAGT 58.321 40.000 18.25 6.90 46.72 2.12
4936 5551 7.595819 AAGACTCTCAATGAGGGACTTATAG 57.404 40.000 22.51 7.73 41.64 1.31
4939 5554 7.979786 AATAAGACTCTCAATGAGGGACTTA 57.020 36.000 27.68 27.68 45.57 2.24
4940 5555 6.882768 AATAAGACTCTCAATGAGGGACTT 57.117 37.500 25.71 25.71 44.42 3.01
4941 5556 6.441924 TGAAATAAGACTCTCAATGAGGGACT 59.558 38.462 18.25 13.46 46.72 3.85
4942 5557 6.644347 TGAAATAAGACTCTCAATGAGGGAC 58.356 40.000 18.25 11.06 46.72 4.46
4943 5558 6.874278 TGAAATAAGACTCTCAATGAGGGA 57.126 37.500 18.25 0.00 46.72 4.20
4959 5574 7.615365 AGTGGGCATTTGAGACTTATGAAATAA 59.385 33.333 0.00 0.00 36.20 1.40
4960 5575 7.118723 AGTGGGCATTTGAGACTTATGAAATA 58.881 34.615 0.00 0.00 0.00 1.40
4961 5576 5.954150 AGTGGGCATTTGAGACTTATGAAAT 59.046 36.000 0.00 0.00 0.00 2.17
4962 5577 5.324409 AGTGGGCATTTGAGACTTATGAAA 58.676 37.500 0.00 0.00 0.00 2.69
4963 5578 4.922206 AGTGGGCATTTGAGACTTATGAA 58.078 39.130 0.00 0.00 0.00 2.57
4964 5579 4.574674 AGTGGGCATTTGAGACTTATGA 57.425 40.909 0.00 0.00 0.00 2.15
4965 5580 5.649782 AAAGTGGGCATTTGAGACTTATG 57.350 39.130 0.00 0.00 0.00 1.90
4966 5581 6.948309 ACTTAAAGTGGGCATTTGAGACTTAT 59.052 34.615 7.52 0.00 30.26 1.73
4967 5582 6.303839 ACTTAAAGTGGGCATTTGAGACTTA 58.696 36.000 7.52 0.00 30.26 2.24
4968 5583 5.140454 ACTTAAAGTGGGCATTTGAGACTT 58.860 37.500 7.52 0.00 30.26 3.01
4969 5584 4.729868 ACTTAAAGTGGGCATTTGAGACT 58.270 39.130 7.52 0.00 30.26 3.24
4970 5585 4.082733 GGACTTAAAGTGGGCATTTGAGAC 60.083 45.833 7.52 2.89 30.26 3.36
4971 5586 4.079253 GGACTTAAAGTGGGCATTTGAGA 58.921 43.478 7.52 0.00 30.26 3.27
4972 5587 3.193479 GGGACTTAAAGTGGGCATTTGAG 59.807 47.826 0.00 0.00 31.53 3.02
4973 5588 3.161866 GGGACTTAAAGTGGGCATTTGA 58.838 45.455 0.00 0.00 0.00 2.69
4974 5589 3.165071 AGGGACTTAAAGTGGGCATTTG 58.835 45.455 0.00 0.00 27.25 2.32
4975 5590 3.542969 AGGGACTTAAAGTGGGCATTT 57.457 42.857 0.00 0.00 27.25 2.32
4976 5591 3.332485 TGTAGGGACTTAAAGTGGGCATT 59.668 43.478 0.00 0.00 41.75 3.56
4977 5592 2.916934 TGTAGGGACTTAAAGTGGGCAT 59.083 45.455 0.00 0.00 41.75 4.40
4978 5593 2.340731 TGTAGGGACTTAAAGTGGGCA 58.659 47.619 0.00 0.00 41.75 5.36
4979 5594 3.244805 ACTTGTAGGGACTTAAAGTGGGC 60.245 47.826 0.00 0.00 40.03 5.36
4980 5595 4.565028 GGACTTGTAGGGACTTAAAGTGGG 60.565 50.000 0.00 0.00 41.07 4.61
4981 5596 4.565028 GGGACTTGTAGGGACTTAAAGTGG 60.565 50.000 0.00 0.00 41.07 4.00
4982 5597 4.286291 AGGGACTTGTAGGGACTTAAAGTG 59.714 45.833 0.00 0.00 41.07 3.16
4983 5598 4.500452 AGGGACTTGTAGGGACTTAAAGT 58.500 43.478 0.00 0.00 42.79 2.66
4984 5599 4.081031 GGAGGGACTTGTAGGGACTTAAAG 60.081 50.000 0.00 0.00 41.55 1.85
4985 5600 3.842436 GGAGGGACTTGTAGGGACTTAAA 59.158 47.826 0.00 0.00 41.55 1.52
4986 5601 3.078612 AGGAGGGACTTGTAGGGACTTAA 59.921 47.826 0.00 0.00 41.55 1.85
4987 5602 2.658489 AGGAGGGACTTGTAGGGACTTA 59.342 50.000 0.00 0.00 41.55 2.24
4988 5603 1.437547 AGGAGGGACTTGTAGGGACTT 59.562 52.381 0.00 0.00 41.55 3.01
4989 5604 1.094269 AGGAGGGACTTGTAGGGACT 58.906 55.000 0.00 0.00 41.55 3.85
4990 5605 3.713867 AGGAGGGACTTGTAGGGAC 57.286 57.895 0.00 0.00 41.55 4.46



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

AutoCloner maintained by Alex Coulton.