Multiple sequence alignment - TraesCS7A01G309000

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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 TraesCS7A01G309000 chr7A 100.000 7001 0 0 834 7834 437052471 437059471 0.000000e+00 12929.0
1 TraesCS7A01G309000 chr7A 100.000 481 0 0 1 481 437051638 437052118 0.000000e+00 889.0
2 TraesCS7A01G309000 chr7A 97.987 149 2 1 6360 6508 720956427 720956280 2.800000e-64 257.0
3 TraesCS7A01G309000 chr7A 96.753 154 3 2 6366 6519 257420 257269 1.010000e-63 255.0
4 TraesCS7A01G309000 chr7A 96.970 33 1 0 4339 4371 496814482 496814514 1.000000e-03 56.5
5 TraesCS7A01G309000 chr7D 96.605 5567 149 11 834 6368 386914325 386919883 0.000000e+00 9197.0
6 TraesCS7A01G309000 chr7D 95.277 1334 53 7 6508 7834 386919881 386921211 0.000000e+00 2106.0
7 TraesCS7A01G309000 chr7D 83.221 447 27 23 8 441 386913837 386914248 4.470000e-97 366.0
8 TraesCS7A01G309000 chr7B 96.125 4722 118 27 1653 6368 382222687 382227349 0.000000e+00 7646.0
9 TraesCS7A01G309000 chr7B 97.268 732 14 4 6508 7235 382227347 382228076 0.000000e+00 1236.0
10 TraesCS7A01G309000 chr7B 89.437 871 38 12 834 1668 382221786 382222638 0.000000e+00 1050.0
11 TraesCS7A01G309000 chr7B 85.520 442 25 15 43 481 382221330 382221735 7.270000e-115 425.0
12 TraesCS7A01G309000 chr7B 80.589 577 77 16 7236 7809 382240022 382240566 5.660000e-111 412.0
13 TraesCS7A01G309000 chr7B 97.297 37 1 0 4339 4375 104775279 104775243 6.560000e-06 63.9
14 TraesCS7A01G309000 chr3A 98.000 150 2 1 6364 6513 23651164 23651016 7.800000e-65 259.0
15 TraesCS7A01G309000 chr3A 96.732 153 4 1 6362 6514 333860918 333860767 3.630000e-63 254.0
16 TraesCS7A01G309000 chr2B 97.386 153 2 2 6357 6508 704908180 704908331 7.800000e-65 259.0
17 TraesCS7A01G309000 chr5B 97.973 148 3 0 6368 6515 221096834 221096687 2.800000e-64 257.0
18 TraesCS7A01G309000 chr6B 97.351 151 3 1 6358 6508 21171099 21170950 1.010000e-63 255.0
19 TraesCS7A01G309000 chr6B 94.872 39 2 0 4339 4377 21942192 21942154 2.360000e-05 62.1
20 TraesCS7A01G309000 chr6A 97.351 151 2 2 6368 6518 402953624 402953476 1.010000e-63 255.0
21 TraesCS7A01G309000 chr4B 99.291 141 1 0 6368 6508 589253649 589253789 1.010000e-63 255.0
22 TraesCS7A01G309000 chr3B 97.222 36 1 0 4338 4373 766825285 766825320 2.360000e-05 62.1
23 TraesCS7A01G309000 chr3B 91.111 45 3 1 4339 4383 223345268 223345311 8.490000e-05 60.2
24 TraesCS7A01G309000 chr4D 97.143 35 1 0 4339 4373 355714107 355714073 8.490000e-05 60.2
25 TraesCS7A01G309000 chr6D 97.143 35 0 1 4343 4377 168219566 168219533 3.050000e-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 TraesCS7A01G309000 chr7A 437051638 437059471 7833 False 6909.000000 12929 100.0000 1 7834 2 chr7A.!!$F2 7833
1 TraesCS7A01G309000 chr7D 386913837 386921211 7374 False 3889.666667 9197 91.7010 8 7834 3 chr7D.!!$F1 7826
2 TraesCS7A01G309000 chr7B 382221330 382228076 6746 False 2589.250000 7646 92.0875 43 7235 4 chr7B.!!$F2 7192
3 TraesCS7A01G309000 chr7B 382240022 382240566 544 False 412.000000 412 80.5890 7236 7809 1 chr7B.!!$F1 573

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
372 385 1.103398 GTTCCCCCATTGAGGCATCG 61.103 60.000 0.00 0.00 35.39 3.84 F
1115 1131 0.179089 CTCTCATCCACCTCCGCTTG 60.179 60.000 0.00 0.00 0.00 4.01 F
1289 1305 0.248134 CCGAGGTAGAAGTTCTCGCG 60.248 60.000 9.12 9.49 46.08 5.87 F
1405 1457 0.389166 CACCTCGCAGTCTCAACTCC 60.389 60.000 0.00 0.00 31.71 3.85 F
1967 2087 0.396811 CACGGTCCCTTTCTTCAGGT 59.603 55.000 0.00 0.00 30.96 4.00 F
3399 3519 2.160205 GCTGTTTCCCTTGGGTTCTAC 58.840 52.381 5.51 1.37 0.00 2.59 F
4373 4521 3.373565 CACCGGGCTGCCCTTTTC 61.374 66.667 33.39 8.98 42.67 2.29 F
5587 5735 0.177141 CCGCCGAAGAAGGGTATCAA 59.823 55.000 0.00 0.00 0.00 2.57 F
6370 6520 0.729690 GGAGCGAAATCACTTGAGGC 59.270 55.000 0.00 0.00 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1289 1305 0.109226 AAACTAGAGAGGCGCGTGAC 60.109 55.000 7.63 0.00 0.00 3.67 R
1940 2060 1.467342 GAAAGGGACCGTGCATTACAC 59.533 52.381 0.00 0.00 46.45 2.90 R
3154 3274 0.036732 TTGCACGAGGGAAGAAGCAT 59.963 50.000 0.00 0.00 0.00 3.79 R
3155 3275 0.884704 GTTGCACGAGGGAAGAAGCA 60.885 55.000 0.00 0.00 0.00 3.91 R
3589 3709 1.807142 GAGTAAACTGAGGCAAGCCAC 59.193 52.381 14.40 7.79 38.92 5.01 R
4551 4699 1.152984 CAGCCACAGTTGACCCACA 60.153 57.895 0.00 0.00 0.00 4.17 R
6239 6389 0.593128 CGCTTTTCTGGTCTTGGTGG 59.407 55.000 0.00 0.00 0.00 4.61 R
6396 6546 0.178978 GCCAATCCCCTCCAATCCTC 60.179 60.000 0.00 0.00 0.00 3.71 R
7800 8097 0.248498 CAGATCGAAAGTAGCGGCGA 60.248 55.000 12.98 0.00 37.17 5.54 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
28 29 8.761497 GTTTCTTTTGCAGGGTCTAAAAATAAC 58.239 33.333 0.00 0.00 0.00 1.89
29 30 6.674066 TCTTTTGCAGGGTCTAAAAATAACG 58.326 36.000 0.00 0.00 0.00 3.18
30 31 6.263617 TCTTTTGCAGGGTCTAAAAATAACGT 59.736 34.615 0.00 0.00 0.00 3.99
32 33 5.616488 TGCAGGGTCTAAAAATAACGTTC 57.384 39.130 2.82 0.00 0.00 3.95
33 34 5.064558 TGCAGGGTCTAAAAATAACGTTCA 58.935 37.500 2.82 0.00 0.00 3.18
34 35 5.708230 TGCAGGGTCTAAAAATAACGTTCAT 59.292 36.000 2.82 0.00 0.00 2.57
35 36 6.879993 TGCAGGGTCTAAAAATAACGTTCATA 59.120 34.615 2.82 0.00 0.00 2.15
36 37 7.554835 TGCAGGGTCTAAAAATAACGTTCATAT 59.445 33.333 2.82 0.00 0.00 1.78
37 38 9.048446 GCAGGGTCTAAAAATAACGTTCATATA 57.952 33.333 2.82 0.00 0.00 0.86
126 138 8.424274 TGATAATAGTTGTTCATGTGTGCTAG 57.576 34.615 0.00 0.00 0.00 3.42
139 151 7.977904 TCATGTGTGCTAGAATATTTGTCAAG 58.022 34.615 0.00 0.00 0.00 3.02
142 154 8.840833 TGTGTGCTAGAATATTTGTCAAGTAA 57.159 30.769 0.00 0.00 0.00 2.24
250 263 8.379902 GGAAACACACAACAAACATAAAAGAAG 58.620 33.333 0.00 0.00 0.00 2.85
255 268 9.352784 CACACAACAAACATAAAAGAAGAAAGA 57.647 29.630 0.00 0.00 0.00 2.52
256 269 9.921637 ACACAACAAACATAAAAGAAGAAAGAA 57.078 25.926 0.00 0.00 0.00 2.52
363 376 2.360726 GTTCGCCGTTCCCCCATT 60.361 61.111 0.00 0.00 0.00 3.16
372 385 1.103398 GTTCCCCCATTGAGGCATCG 61.103 60.000 0.00 0.00 35.39 3.84
936 952 1.134560 GCCGTCTCGTCCATTTCTACT 59.865 52.381 0.00 0.00 0.00 2.57
966 982 1.475280 CGAGTGGGACGTCCTGAATAA 59.525 52.381 32.52 10.09 36.20 1.40
1060 1076 3.546543 GTCCCCGCGATCCATCCA 61.547 66.667 8.23 0.00 0.00 3.41
1063 1079 3.911698 CCCGCGATCCATCCACGA 61.912 66.667 8.23 0.00 0.00 4.35
1115 1131 0.179089 CTCTCATCCACCTCCGCTTG 60.179 60.000 0.00 0.00 0.00 4.01
1289 1305 0.248134 CCGAGGTAGAAGTTCTCGCG 60.248 60.000 9.12 9.49 46.08 5.87
1405 1457 0.389166 CACCTCGCAGTCTCAACTCC 60.389 60.000 0.00 0.00 31.71 3.85
1636 1688 3.900601 TCTGCCATTTACAAACCCACAAT 59.099 39.130 0.00 0.00 0.00 2.71
1710 1826 7.094508 TCTTGAGTTTTCACTATTGTGCAAA 57.905 32.000 2.09 1.77 43.49 3.68
1751 1869 9.669353 GTGGTATCATCATTTGTTCATTACATC 57.331 33.333 0.00 0.00 36.44 3.06
1877 1997 2.022195 AGATGACATGGACTTGCATGC 58.978 47.619 11.82 11.82 32.40 4.06
1966 2086 0.955919 GCACGGTCCCTTTCTTCAGG 60.956 60.000 0.00 0.00 0.00 3.86
1967 2087 0.396811 CACGGTCCCTTTCTTCAGGT 59.603 55.000 0.00 0.00 30.96 4.00
1999 2119 7.659799 TGCTGTCTGTTAATTCTTGCTTAACTA 59.340 33.333 6.97 0.00 39.00 2.24
2057 2177 3.554752 CCGTGAATGGCATTTGGAAAACT 60.555 43.478 14.93 0.00 0.00 2.66
2075 2195 9.762933 TGGAAAACTTTTAATCAAGAAGGAATG 57.237 29.630 0.00 0.00 0.00 2.67
2121 2241 3.263425 ACATGAAACATTAGACGGGGACT 59.737 43.478 0.00 0.00 0.00 3.85
2212 2332 5.357878 TGCTTTGTGATCTGACAAAAGTCTT 59.642 36.000 11.27 0.00 43.48 3.01
2370 2490 9.295825 ACATTACATTTCCTATCTTGTTGTCAA 57.704 29.630 0.00 0.00 0.00 3.18
2587 2707 7.279615 TGGTCCATTTTGATATCGTTAGACAT 58.720 34.615 0.00 0.00 0.00 3.06
3154 3274 6.012858 ACTTTATCATCCAGGTACTTGGTTGA 60.013 38.462 29.49 29.49 38.59 3.18
3155 3275 6.575244 TTATCATCCAGGTACTTGGTTGAT 57.425 37.500 34.67 34.67 42.64 2.57
3342 3462 6.713903 CCACCATAGAATCATCATTAGCAACT 59.286 38.462 0.00 0.00 0.00 3.16
3344 3464 6.206243 ACCATAGAATCATCATTAGCAACTGC 59.794 38.462 0.00 0.00 42.49 4.40
3399 3519 2.160205 GCTGTTTCCCTTGGGTTCTAC 58.840 52.381 5.51 1.37 0.00 2.59
3589 3709 9.191479 AGTAGATTCGGAGGTAATTATCCATAG 57.809 37.037 6.05 0.00 35.14 2.23
3640 3760 3.679389 AGTATGTCCTTTTCACTGGCTG 58.321 45.455 0.00 0.00 0.00 4.85
3754 3874 4.320494 GCTGTTCCTTTGTCTTGTACATGG 60.320 45.833 8.74 0.00 38.10 3.66
4012 4133 3.745975 ACATTCAAGATTTCGACGCTGAA 59.254 39.130 0.00 0.00 0.00 3.02
4013 4134 3.788434 TTCAAGATTTCGACGCTGAAC 57.212 42.857 0.00 0.00 0.00 3.18
4373 4521 3.373565 CACCGGGCTGCCCTTTTC 61.374 66.667 33.39 8.98 42.67 2.29
4441 4589 5.456548 TGATGCATGTGTGAGAAAACATT 57.543 34.783 2.46 0.00 34.81 2.71
4551 4699 5.726397 TGTTTCGGCATACACATAAGTACT 58.274 37.500 0.00 0.00 0.00 2.73
4642 4790 5.869753 AGTTCTTATACTGTTGCTGCTTG 57.130 39.130 0.00 0.00 0.00 4.01
5249 5397 5.772825 TTTATCTGCTGCTGACAAAAGTT 57.227 34.783 11.54 0.00 0.00 2.66
5341 5489 4.475944 GACAATTTCAAGATCACAACCGG 58.524 43.478 0.00 0.00 0.00 5.28
5541 5689 7.069085 GGGTAACTATGATACTGTGTGGTCTTA 59.931 40.741 0.00 0.00 0.00 2.10
5569 5717 6.852664 ACTGCAGCACATAAAACTTATTACC 58.147 36.000 15.27 0.00 0.00 2.85
5587 5735 0.177141 CCGCCGAAGAAGGGTATCAA 59.823 55.000 0.00 0.00 0.00 2.57
5616 5764 9.866655 TTTATATTCATTACCTCTGCTTTCCAT 57.133 29.630 0.00 0.00 0.00 3.41
5778 5927 4.836825 ACCATGTGGATTACTGAAGTGAG 58.163 43.478 5.96 0.00 38.94 3.51
6097 6247 2.232452 CCTAGTTGGCGATATGCTAGCT 59.768 50.000 17.23 4.07 46.89 3.32
6239 6389 2.682856 TGATAAACCCGCAGATGAAAGC 59.317 45.455 0.00 0.00 0.00 3.51
6365 6515 6.112734 TGTGTTATATGGAGCGAAATCACTT 58.887 36.000 0.00 0.00 0.00 3.16
6366 6516 6.037062 TGTGTTATATGGAGCGAAATCACTTG 59.963 38.462 0.00 0.00 0.00 3.16
6367 6517 6.257849 GTGTTATATGGAGCGAAATCACTTGA 59.742 38.462 0.00 0.00 0.00 3.02
6368 6518 6.479990 TGTTATATGGAGCGAAATCACTTGAG 59.520 38.462 0.00 0.00 0.00 3.02
6369 6519 2.099141 TGGAGCGAAATCACTTGAGG 57.901 50.000 0.00 0.00 0.00 3.86
6370 6520 0.729690 GGAGCGAAATCACTTGAGGC 59.270 55.000 0.00 0.00 0.00 4.70
6371 6521 1.677217 GGAGCGAAATCACTTGAGGCT 60.677 52.381 0.00 0.00 0.00 4.58
6372 6522 2.079925 GAGCGAAATCACTTGAGGCTT 58.920 47.619 0.00 0.00 0.00 4.35
6373 6523 2.485814 GAGCGAAATCACTTGAGGCTTT 59.514 45.455 0.00 0.00 0.00 3.51
6374 6524 2.227388 AGCGAAATCACTTGAGGCTTTG 59.773 45.455 0.00 0.00 0.00 2.77
6375 6525 2.030805 GCGAAATCACTTGAGGCTTTGT 60.031 45.455 0.00 0.00 0.00 2.83
6376 6526 3.550842 GCGAAATCACTTGAGGCTTTGTT 60.551 43.478 0.00 0.00 0.00 2.83
6377 6527 4.222114 CGAAATCACTTGAGGCTTTGTTC 58.778 43.478 0.00 0.00 0.00 3.18
6378 6528 3.904136 AATCACTTGAGGCTTTGTTCG 57.096 42.857 0.00 0.00 0.00 3.95
6379 6529 1.593196 TCACTTGAGGCTTTGTTCGG 58.407 50.000 0.00 0.00 0.00 4.30
6380 6530 1.134220 TCACTTGAGGCTTTGTTCGGT 60.134 47.619 0.00 0.00 0.00 4.69
6381 6531 1.676006 CACTTGAGGCTTTGTTCGGTT 59.324 47.619 0.00 0.00 0.00 4.44
6382 6532 2.875933 CACTTGAGGCTTTGTTCGGTTA 59.124 45.455 0.00 0.00 0.00 2.85
6383 6533 3.314080 CACTTGAGGCTTTGTTCGGTTAA 59.686 43.478 0.00 0.00 0.00 2.01
6384 6534 4.023193 CACTTGAGGCTTTGTTCGGTTAAT 60.023 41.667 0.00 0.00 0.00 1.40
6385 6535 4.215613 ACTTGAGGCTTTGTTCGGTTAATC 59.784 41.667 0.00 0.00 0.00 1.75
6386 6536 3.078837 TGAGGCTTTGTTCGGTTAATCC 58.921 45.455 0.00 0.00 0.00 3.01
6387 6537 3.244770 TGAGGCTTTGTTCGGTTAATCCT 60.245 43.478 0.00 0.00 0.00 3.24
6388 6538 3.344515 AGGCTTTGTTCGGTTAATCCTC 58.655 45.455 0.00 0.00 0.00 3.71
6389 6539 3.009143 AGGCTTTGTTCGGTTAATCCTCT 59.991 43.478 0.00 0.00 0.00 3.69
6390 6540 3.374367 GGCTTTGTTCGGTTAATCCTCTC 59.626 47.826 0.00 0.00 0.00 3.20
6391 6541 3.374367 GCTTTGTTCGGTTAATCCTCTCC 59.626 47.826 0.00 0.00 0.00 3.71
6392 6542 3.622166 TTGTTCGGTTAATCCTCTCCC 57.378 47.619 0.00 0.00 0.00 4.30
6393 6543 1.835531 TGTTCGGTTAATCCTCTCCCC 59.164 52.381 0.00 0.00 0.00 4.81
6394 6544 1.835531 GTTCGGTTAATCCTCTCCCCA 59.164 52.381 0.00 0.00 0.00 4.96
6395 6545 2.237893 GTTCGGTTAATCCTCTCCCCAA 59.762 50.000 0.00 0.00 0.00 4.12
6396 6546 2.116238 TCGGTTAATCCTCTCCCCAAG 58.884 52.381 0.00 0.00 0.00 3.61
6397 6547 2.116238 CGGTTAATCCTCTCCCCAAGA 58.884 52.381 0.00 0.00 0.00 3.02
6405 6555 1.885049 CTCTCCCCAAGAGGATTGGA 58.115 55.000 8.20 0.00 46.73 3.53
6406 6556 1.767681 CTCTCCCCAAGAGGATTGGAG 59.232 57.143 8.20 0.00 46.73 3.86
6407 6557 0.842635 CTCCCCAAGAGGATTGGAGG 59.157 60.000 8.20 7.77 42.06 4.30
6408 6558 0.624500 TCCCCAAGAGGATTGGAGGG 60.625 60.000 8.20 2.36 42.06 4.30
6409 6559 1.925888 CCCAAGAGGATTGGAGGGG 59.074 63.158 8.20 0.00 42.06 4.79
6410 6560 0.624500 CCCAAGAGGATTGGAGGGGA 60.625 60.000 8.20 0.00 42.06 4.81
6411 6561 1.527457 CCAAGAGGATTGGAGGGGAT 58.473 55.000 0.12 0.00 42.06 3.85
6412 6562 1.855599 CCAAGAGGATTGGAGGGGATT 59.144 52.381 0.12 0.00 42.06 3.01
6413 6563 2.423947 CCAAGAGGATTGGAGGGGATTG 60.424 54.545 0.12 0.00 42.06 2.67
6414 6564 1.527457 AGAGGATTGGAGGGGATTGG 58.473 55.000 0.00 0.00 0.00 3.16
6415 6565 0.178978 GAGGATTGGAGGGGATTGGC 60.179 60.000 0.00 0.00 0.00 4.52
6416 6566 0.925720 AGGATTGGAGGGGATTGGCA 60.926 55.000 0.00 0.00 0.00 4.92
6417 6567 0.468771 GGATTGGAGGGGATTGGCAG 60.469 60.000 0.00 0.00 0.00 4.85
6418 6568 0.468771 GATTGGAGGGGATTGGCAGG 60.469 60.000 0.00 0.00 0.00 4.85
6419 6569 1.953100 ATTGGAGGGGATTGGCAGGG 61.953 60.000 0.00 0.00 0.00 4.45
6420 6570 2.696125 GGAGGGGATTGGCAGGGA 60.696 66.667 0.00 0.00 0.00 4.20
6421 6571 2.087461 GGAGGGGATTGGCAGGGAT 61.087 63.158 0.00 0.00 0.00 3.85
6422 6572 1.659035 GGAGGGGATTGGCAGGGATT 61.659 60.000 0.00 0.00 0.00 3.01
6423 6573 0.468771 GAGGGGATTGGCAGGGATTG 60.469 60.000 0.00 0.00 0.00 2.67
6424 6574 1.458209 GGGGATTGGCAGGGATTGG 60.458 63.158 0.00 0.00 0.00 3.16
6425 6575 1.311059 GGGATTGGCAGGGATTGGT 59.689 57.895 0.00 0.00 0.00 3.67
6426 6576 0.325577 GGGATTGGCAGGGATTGGTT 60.326 55.000 0.00 0.00 0.00 3.67
6427 6577 1.114627 GGATTGGCAGGGATTGGTTC 58.885 55.000 0.00 0.00 0.00 3.62
6428 6578 1.619432 GGATTGGCAGGGATTGGTTCA 60.619 52.381 0.00 0.00 0.00 3.18
6429 6579 2.391678 GATTGGCAGGGATTGGTTCAT 58.608 47.619 0.00 0.00 0.00 2.57
6430 6580 3.565307 GATTGGCAGGGATTGGTTCATA 58.435 45.455 0.00 0.00 0.00 2.15
6431 6581 3.686227 TTGGCAGGGATTGGTTCATAT 57.314 42.857 0.00 0.00 0.00 1.78
6432 6582 3.686227 TGGCAGGGATTGGTTCATATT 57.314 42.857 0.00 0.00 0.00 1.28
6433 6583 3.992999 TGGCAGGGATTGGTTCATATTT 58.007 40.909 0.00 0.00 0.00 1.40
6434 6584 4.360889 TGGCAGGGATTGGTTCATATTTT 58.639 39.130 0.00 0.00 0.00 1.82
6435 6585 4.161942 TGGCAGGGATTGGTTCATATTTTG 59.838 41.667 0.00 0.00 0.00 2.44
6436 6586 4.405358 GGCAGGGATTGGTTCATATTTTGA 59.595 41.667 0.00 0.00 0.00 2.69
6437 6587 5.070847 GGCAGGGATTGGTTCATATTTTGAT 59.929 40.000 0.00 0.00 33.34 2.57
6438 6588 6.408434 GGCAGGGATTGGTTCATATTTTGATT 60.408 38.462 0.00 0.00 33.34 2.57
6439 6589 7.049754 GCAGGGATTGGTTCATATTTTGATTT 58.950 34.615 0.00 0.00 33.34 2.17
6440 6590 8.203485 GCAGGGATTGGTTCATATTTTGATTTA 58.797 33.333 0.00 0.00 33.34 1.40
6441 6591 9.754382 CAGGGATTGGTTCATATTTTGATTTAG 57.246 33.333 0.00 0.00 33.34 1.85
6442 6592 9.713684 AGGGATTGGTTCATATTTTGATTTAGA 57.286 29.630 0.00 0.00 33.34 2.10
6448 6598 9.753674 TGGTTCATATTTTGATTTAGAAGAGGT 57.246 29.630 0.00 0.00 33.34 3.85
6458 6608 8.589701 TTGATTTAGAAGAGGTTTAAATCCCC 57.410 34.615 11.50 0.00 40.51 4.81
6459 6609 7.123383 TGATTTAGAAGAGGTTTAAATCCCCC 58.877 38.462 11.50 0.00 40.51 5.40
6460 6610 6.730001 TTTAGAAGAGGTTTAAATCCCCCT 57.270 37.500 0.00 0.00 0.00 4.79
6461 6611 4.864483 AGAAGAGGTTTAAATCCCCCTC 57.136 45.455 12.53 12.53 43.14 4.30
6462 6612 4.183916 AGAAGAGGTTTAAATCCCCCTCA 58.816 43.478 19.38 0.00 44.85 3.86
6463 6613 4.606255 AGAAGAGGTTTAAATCCCCCTCAA 59.394 41.667 19.38 0.00 44.85 3.02
6464 6614 5.075900 AGAAGAGGTTTAAATCCCCCTCAAA 59.924 40.000 19.38 0.00 44.85 2.69
6465 6615 4.673968 AGAGGTTTAAATCCCCCTCAAAC 58.326 43.478 19.38 0.00 44.85 2.93
6466 6616 3.767673 GAGGTTTAAATCCCCCTCAAACC 59.232 47.826 14.63 6.45 45.48 3.27
6467 6617 2.835764 GGTTTAAATCCCCCTCAAACCC 59.164 50.000 3.66 0.00 41.38 4.11
6468 6618 2.835764 GTTTAAATCCCCCTCAAACCCC 59.164 50.000 0.00 0.00 0.00 4.95
6469 6619 2.084121 TAAATCCCCCTCAAACCCCT 57.916 50.000 0.00 0.00 0.00 4.79
6470 6620 1.176182 AAATCCCCCTCAAACCCCTT 58.824 50.000 0.00 0.00 0.00 3.95
6471 6621 0.710588 AATCCCCCTCAAACCCCTTC 59.289 55.000 0.00 0.00 0.00 3.46
6472 6622 0.479589 ATCCCCCTCAAACCCCTTCA 60.480 55.000 0.00 0.00 0.00 3.02
6473 6623 0.703056 TCCCCCTCAAACCCCTTCAA 60.703 55.000 0.00 0.00 0.00 2.69
6474 6624 0.413434 CCCCCTCAAACCCCTTCAAT 59.587 55.000 0.00 0.00 0.00 2.57
6475 6625 1.619704 CCCCCTCAAACCCCTTCAATC 60.620 57.143 0.00 0.00 0.00 2.67
6476 6626 1.619704 CCCCTCAAACCCCTTCAATCC 60.620 57.143 0.00 0.00 0.00 3.01
6477 6627 1.077005 CCCTCAAACCCCTTCAATCCA 59.923 52.381 0.00 0.00 0.00 3.41
6478 6628 2.171003 CCTCAAACCCCTTCAATCCAC 58.829 52.381 0.00 0.00 0.00 4.02
6479 6629 2.225117 CCTCAAACCCCTTCAATCCACT 60.225 50.000 0.00 0.00 0.00 4.00
6480 6630 3.084786 CTCAAACCCCTTCAATCCACTC 58.915 50.000 0.00 0.00 0.00 3.51
6481 6631 1.812571 CAAACCCCTTCAATCCACTCG 59.187 52.381 0.00 0.00 0.00 4.18
6482 6632 0.328258 AACCCCTTCAATCCACTCGG 59.672 55.000 0.00 0.00 0.00 4.63
6497 6647 3.496131 CGGATTCACCCGCAACCG 61.496 66.667 0.00 0.00 43.25 4.44
6498 6648 2.046700 GGATTCACCCGCAACCGA 60.047 61.111 0.00 0.00 36.29 4.69
6499 6649 1.673009 GGATTCACCCGCAACCGAA 60.673 57.895 0.00 0.00 36.29 4.30
6500 6650 1.500396 GATTCACCCGCAACCGAAC 59.500 57.895 0.00 0.00 36.29 3.95
6501 6651 1.228003 ATTCACCCGCAACCGAACA 60.228 52.632 0.00 0.00 36.29 3.18
6502 6652 0.820074 ATTCACCCGCAACCGAACAA 60.820 50.000 0.00 0.00 36.29 2.83
6503 6653 1.440938 TTCACCCGCAACCGAACAAG 61.441 55.000 0.00 0.00 36.29 3.16
6504 6654 2.593436 ACCCGCAACCGAACAAGG 60.593 61.111 0.00 0.00 36.29 3.61
6505 6655 4.038080 CCCGCAACCGAACAAGGC 62.038 66.667 0.00 0.00 36.29 4.35
6506 6656 4.038080 CCGCAACCGAACAAGGCC 62.038 66.667 0.00 0.00 36.29 5.19
6961 7257 2.629617 CAACCCATTTCAGGCAGTCTTT 59.370 45.455 0.00 0.00 0.00 2.52
7154 7450 4.214310 AGACACATGGGTTGTTTGATTCA 58.786 39.130 0.00 0.00 36.00 2.57
7163 7459 9.001542 CATGGGTTGTTTGATTCACATAATTTT 57.998 29.630 0.00 0.00 0.00 1.82
7381 7677 6.484818 AATGTGTTTGCTGGCAAATTTATC 57.515 33.333 21.04 10.32 45.90 1.75
7458 7754 1.486211 CGGACCTCCCATACTTGTCT 58.514 55.000 0.00 0.00 34.14 3.41
7461 7757 2.838202 GGACCTCCCATACTTGTCTCAA 59.162 50.000 0.00 0.00 34.14 3.02
7466 7762 4.315803 CTCCCATACTTGTCTCAAACGTT 58.684 43.478 0.00 0.00 0.00 3.99
7492 7788 2.440065 CTGCCCGGCCATTGCTTA 60.440 61.111 7.03 0.00 37.74 3.09
7527 7823 4.047125 CAACCGGGCTCCCCACAT 62.047 66.667 6.32 0.00 45.83 3.21
7540 7836 1.029947 CCCACATCTACCCCAAACGC 61.030 60.000 0.00 0.00 0.00 4.84
7560 7856 4.021925 GGGCTGACCGGCACTCTT 62.022 66.667 0.00 0.00 40.61 2.85
7570 7866 1.905512 GGCACTCTTCATACCCGGT 59.094 57.895 0.00 0.00 0.00 5.28
7595 7891 3.697190 ATCTAGGGCGGATATGAGGAT 57.303 47.619 0.00 0.00 0.00 3.24
7605 7901 2.172483 ATATGAGGATGCCCGGACGC 62.172 60.000 0.73 0.00 37.58 5.19
7617 7913 2.746277 GGACGCGGGCTTCACATT 60.746 61.111 12.47 0.00 0.00 2.71
7656 7952 2.095853 CCATGCGGTCACACAAATAGAC 59.904 50.000 0.00 0.00 0.00 2.59
7679 7975 3.532155 GTCCGATGAGCGCCTCCT 61.532 66.667 2.29 0.00 39.11 3.69
7783 8080 2.618045 CCCTACCTCGCACCATTTCTTT 60.618 50.000 0.00 0.00 0.00 2.52
7800 8097 3.240302 TCTTTCCCTTTCTCCTCTTCGT 58.760 45.455 0.00 0.00 0.00 3.85
7812 8109 0.456312 CTCTTCGTCGCCGCTACTTT 60.456 55.000 0.00 0.00 0.00 2.66
7816 8113 1.585521 CGTCGCCGCTACTTTCGAT 60.586 57.895 0.00 0.00 33.37 3.59
7821 8118 1.641577 GCCGCTACTTTCGATCTGTT 58.358 50.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.911514 TTAGACCCTGCAAAAGAAACAC 57.088 40.909 0.00 0.00 0.00 3.32
2 3 8.761497 GTTATTTTTAGACCCTGCAAAAGAAAC 58.239 33.333 0.00 0.00 0.00 2.78
3 4 7.650104 CGTTATTTTTAGACCCTGCAAAAGAAA 59.350 33.333 0.00 0.00 0.00 2.52
5 6 6.263617 ACGTTATTTTTAGACCCTGCAAAAGA 59.736 34.615 0.00 0.00 0.00 2.52
6 7 6.443792 ACGTTATTTTTAGACCCTGCAAAAG 58.556 36.000 0.00 0.00 0.00 2.27
207 220 9.803315 GTGTGTTTCCTTCTTCTTTTTCTATTT 57.197 29.630 0.00 0.00 0.00 1.40
208 221 8.966868 TGTGTGTTTCCTTCTTCTTTTTCTATT 58.033 29.630 0.00 0.00 0.00 1.73
209 222 8.519799 TGTGTGTTTCCTTCTTCTTTTTCTAT 57.480 30.769 0.00 0.00 0.00 1.98
229 242 9.352784 TCTTTCTTCTTTTATGTTTGTTGTGTG 57.647 29.630 0.00 0.00 0.00 3.82
250 263 8.683550 TTTTCTCTCTTTTCGGTTTTTCTTTC 57.316 30.769 0.00 0.00 0.00 2.62
324 337 3.151710 CCGGGACCGATGCCTACA 61.152 66.667 13.13 0.00 42.83 2.74
363 376 1.219124 GCTTCAGTCCGATGCCTCA 59.781 57.895 0.00 0.00 38.54 3.86
372 385 2.556287 CGGCGTTTGCTTCAGTCC 59.444 61.111 0.00 0.00 42.25 3.85
883 899 2.202892 CGGAGGGCGCTAAGTTCC 60.203 66.667 7.64 6.73 0.00 3.62
912 928 0.673644 AAATGGACGAGACGGCAAGG 60.674 55.000 0.00 0.00 36.10 3.61
923 939 1.560923 CTCGCCAGTAGAAATGGACG 58.439 55.000 0.00 1.32 40.51 4.79
966 982 1.542547 CGTTTAGCAGTGGGGTTCAGT 60.543 52.381 0.00 0.00 0.00 3.41
1060 1076 0.681564 AGCGAGGAGAGGAATGTCGT 60.682 55.000 0.00 0.00 33.19 4.34
1063 1079 1.859302 AAGAGCGAGGAGAGGAATGT 58.141 50.000 0.00 0.00 0.00 2.71
1148 1164 2.040884 AAGAGCTGGCCCCGGATA 60.041 61.111 0.73 0.00 0.00 2.59
1154 1170 1.452833 GTGATGGAAGAGCTGGCCC 60.453 63.158 0.00 0.00 0.00 5.80
1159 1175 0.252479 CTGCTGGTGATGGAAGAGCT 59.748 55.000 0.00 0.00 0.00 4.09
1289 1305 0.109226 AAACTAGAGAGGCGCGTGAC 60.109 55.000 7.63 0.00 0.00 3.67
1662 1778 6.869695 AGCATCATTTTCATCAAGCATTACA 58.130 32.000 0.00 0.00 0.00 2.41
1710 1826 1.807814 ACCACAAGACTCCTGGAGTT 58.192 50.000 28.90 16.35 43.53 3.01
1751 1869 5.118664 CGTCCTATGTAGTTTTGTCACACAG 59.881 44.000 0.00 0.00 0.00 3.66
1816 1934 5.449107 AATCACTGCAATCATATCCTTGC 57.551 39.130 10.50 10.50 46.19 4.01
1849 1969 5.048504 GCAAGTCCATGTCATCTTTCAGAAA 60.049 40.000 0.00 0.00 0.00 2.52
1940 2060 1.467342 GAAAGGGACCGTGCATTACAC 59.533 52.381 0.00 0.00 46.45 2.90
1956 2076 5.471456 AGACAGCAATAACACCTGAAGAAAG 59.529 40.000 0.00 0.00 0.00 2.62
1966 2086 7.061094 GCAAGAATTAACAGACAGCAATAACAC 59.939 37.037 0.00 0.00 0.00 3.32
1967 2087 7.040478 AGCAAGAATTAACAGACAGCAATAACA 60.040 33.333 0.00 0.00 0.00 2.41
2075 2195 7.598869 TGTGACTGATACAACAGAACAAGATAC 59.401 37.037 0.00 0.00 40.63 2.24
2121 2241 2.894763 AAAGCAGCTGAATGTTTGCA 57.105 40.000 20.43 0.00 38.97 4.08
2370 2490 5.221244 GCCTCACATTGGTAAAGTCTTTGTT 60.221 40.000 8.14 0.00 0.00 2.83
2416 2536 6.672266 ACATTTCTGAACTTCTCTAGTGGA 57.328 37.500 0.00 0.00 37.12 4.02
2496 2616 3.184628 TGGATTCTCCCAGTGAAGACAT 58.815 45.455 0.00 0.00 35.03 3.06
2542 2662 7.900784 TGGACCATCTCAATGTATATCCATAGA 59.099 37.037 0.00 0.00 30.17 1.98
2834 2954 2.038295 GAGCTTACCCCTGATCATGAGG 59.962 54.545 0.09 0.00 0.00 3.86
3154 3274 0.036732 TTGCACGAGGGAAGAAGCAT 59.963 50.000 0.00 0.00 0.00 3.79
3155 3275 0.884704 GTTGCACGAGGGAAGAAGCA 60.885 55.000 0.00 0.00 0.00 3.91
3342 3462 2.238646 AGTCTAAAATCACCCCATCGCA 59.761 45.455 0.00 0.00 0.00 5.10
3344 3464 3.623060 CACAGTCTAAAATCACCCCATCG 59.377 47.826 0.00 0.00 0.00 3.84
3399 3519 5.448632 GGCCTTCAAACCATATGAGTAAACG 60.449 44.000 3.65 0.00 0.00 3.60
3589 3709 1.807142 GAGTAAACTGAGGCAAGCCAC 59.193 52.381 14.40 7.79 38.92 5.01
3640 3760 7.330700 GCTCTATTACCTGTATGAAATCTCAGC 59.669 40.741 0.00 0.00 34.23 4.26
4210 4331 6.500684 AATGAATTACAGCTACAACAGTGG 57.499 37.500 0.00 0.00 0.00 4.00
4551 4699 1.152984 CAGCCACAGTTGACCCACA 60.153 57.895 0.00 0.00 0.00 4.17
4642 4790 2.231964 TCCATGATGTTTCAAAGCTGGC 59.768 45.455 0.00 0.00 34.96 4.85
5341 5489 3.421844 ACCAGGGAGCACATTTACTTTC 58.578 45.455 0.00 0.00 0.00 2.62
5569 5717 2.240493 ATTGATACCCTTCTTCGGCG 57.760 50.000 0.00 0.00 0.00 6.46
5616 5764 4.469945 AGGCACAGCTAGTTACAAGGAATA 59.530 41.667 0.00 0.00 0.00 1.75
5778 5927 4.399934 TGCCCCTTCAATTTATTAACGGAC 59.600 41.667 0.00 0.00 0.00 4.79
6061 6211 5.529800 GCCAACTAGGTTTGAAGTAACTTCA 59.470 40.000 0.00 0.00 43.16 3.02
6097 6247 4.115516 GCATTAGCAATTCAGACTCGAGA 58.884 43.478 21.68 0.00 41.58 4.04
6239 6389 0.593128 CGCTTTTCTGGTCTTGGTGG 59.407 55.000 0.00 0.00 0.00 4.61
6365 6515 3.078837 GGATTAACCGAACAAAGCCTCA 58.921 45.455 0.00 0.00 0.00 3.86
6366 6516 3.344515 AGGATTAACCGAACAAAGCCTC 58.655 45.455 0.00 0.00 44.74 4.70
6367 6517 3.009143 AGAGGATTAACCGAACAAAGCCT 59.991 43.478 0.00 0.00 41.52 4.58
6368 6518 3.344515 AGAGGATTAACCGAACAAAGCC 58.655 45.455 0.00 0.00 44.74 4.35
6369 6519 3.374367 GGAGAGGATTAACCGAACAAAGC 59.626 47.826 0.00 0.00 44.74 3.51
6370 6520 3.939592 GGGAGAGGATTAACCGAACAAAG 59.060 47.826 0.00 0.00 44.74 2.77
6371 6521 3.307904 GGGGAGAGGATTAACCGAACAAA 60.308 47.826 0.00 0.00 44.74 2.83
6372 6522 2.237893 GGGGAGAGGATTAACCGAACAA 59.762 50.000 0.00 0.00 44.74 2.83
6373 6523 1.835531 GGGGAGAGGATTAACCGAACA 59.164 52.381 0.00 0.00 44.74 3.18
6374 6524 1.835531 TGGGGAGAGGATTAACCGAAC 59.164 52.381 0.00 0.00 44.74 3.95
6375 6525 2.257391 TGGGGAGAGGATTAACCGAA 57.743 50.000 0.00 0.00 44.74 4.30
6376 6526 2.116238 CTTGGGGAGAGGATTAACCGA 58.884 52.381 0.00 0.00 44.74 4.69
6377 6527 2.103263 CTCTTGGGGAGAGGATTAACCG 59.897 54.545 0.00 0.00 46.77 4.44
6378 6528 3.847671 CTCTTGGGGAGAGGATTAACC 57.152 52.381 0.00 0.00 46.77 2.85
6387 6537 1.626350 CCTCCAATCCTCTTGGGGAGA 60.626 57.143 5.43 0.00 46.38 3.71
6388 6538 0.842635 CCTCCAATCCTCTTGGGGAG 59.157 60.000 5.43 0.00 42.70 4.30
6389 6539 0.624500 CCCTCCAATCCTCTTGGGGA 60.625 60.000 5.43 0.00 42.70 4.81
6390 6540 1.649271 CCCCTCCAATCCTCTTGGGG 61.649 65.000 0.00 0.00 46.89 4.96
6391 6541 0.624500 TCCCCTCCAATCCTCTTGGG 60.625 60.000 4.28 0.00 39.96 4.12
6392 6542 1.527457 ATCCCCTCCAATCCTCTTGG 58.473 55.000 0.00 0.00 40.87 3.61
6393 6543 2.423947 CCAATCCCCTCCAATCCTCTTG 60.424 54.545 0.00 0.00 0.00 3.02
6394 6544 1.855599 CCAATCCCCTCCAATCCTCTT 59.144 52.381 0.00 0.00 0.00 2.85
6395 6545 1.527457 CCAATCCCCTCCAATCCTCT 58.473 55.000 0.00 0.00 0.00 3.69
6396 6546 0.178978 GCCAATCCCCTCCAATCCTC 60.179 60.000 0.00 0.00 0.00 3.71
6397 6547 0.925720 TGCCAATCCCCTCCAATCCT 60.926 55.000 0.00 0.00 0.00 3.24
6398 6548 0.468771 CTGCCAATCCCCTCCAATCC 60.469 60.000 0.00 0.00 0.00 3.01
6399 6549 0.468771 CCTGCCAATCCCCTCCAATC 60.469 60.000 0.00 0.00 0.00 2.67
6400 6550 1.622499 CCTGCCAATCCCCTCCAAT 59.378 57.895 0.00 0.00 0.00 3.16
6401 6551 2.625460 CCCTGCCAATCCCCTCCAA 61.625 63.158 0.00 0.00 0.00 3.53
6402 6552 2.881491 ATCCCTGCCAATCCCCTCCA 62.881 60.000 0.00 0.00 0.00 3.86
6403 6553 1.659035 AATCCCTGCCAATCCCCTCC 61.659 60.000 0.00 0.00 0.00 4.30
6404 6554 0.468771 CAATCCCTGCCAATCCCCTC 60.469 60.000 0.00 0.00 0.00 4.30
6405 6555 1.622499 CAATCCCTGCCAATCCCCT 59.378 57.895 0.00 0.00 0.00 4.79
6406 6556 1.458209 CCAATCCCTGCCAATCCCC 60.458 63.158 0.00 0.00 0.00 4.81
6407 6557 0.325577 AACCAATCCCTGCCAATCCC 60.326 55.000 0.00 0.00 0.00 3.85
6408 6558 1.114627 GAACCAATCCCTGCCAATCC 58.885 55.000 0.00 0.00 0.00 3.01
6409 6559 1.851304 TGAACCAATCCCTGCCAATC 58.149 50.000 0.00 0.00 0.00 2.67
6410 6560 2.555732 ATGAACCAATCCCTGCCAAT 57.444 45.000 0.00 0.00 0.00 3.16
6411 6561 3.686227 ATATGAACCAATCCCTGCCAA 57.314 42.857 0.00 0.00 0.00 4.52
6412 6562 3.686227 AATATGAACCAATCCCTGCCA 57.314 42.857 0.00 0.00 0.00 4.92
6413 6563 4.405358 TCAAAATATGAACCAATCCCTGCC 59.595 41.667 0.00 0.00 34.30 4.85
6414 6564 5.596836 TCAAAATATGAACCAATCCCTGC 57.403 39.130 0.00 0.00 34.30 4.85
6415 6565 9.754382 CTAAATCAAAATATGAACCAATCCCTG 57.246 33.333 0.00 0.00 42.54 4.45
6416 6566 9.713684 TCTAAATCAAAATATGAACCAATCCCT 57.286 29.630 0.00 0.00 42.54 4.20
6422 6572 9.753674 ACCTCTTCTAAATCAAAATATGAACCA 57.246 29.630 0.00 0.00 42.54 3.67
6432 6582 9.031537 GGGGATTTAAACCTCTTCTAAATCAAA 57.968 33.333 13.07 0.00 41.03 2.69
6433 6583 7.618117 GGGGGATTTAAACCTCTTCTAAATCAA 59.382 37.037 13.07 0.00 41.03 2.57
6434 6584 7.036132 AGGGGGATTTAAACCTCTTCTAAATCA 60.036 37.037 13.07 0.00 41.03 2.57
6435 6585 7.355101 AGGGGGATTTAAACCTCTTCTAAATC 58.645 38.462 6.64 5.58 39.61 2.17
6436 6586 7.298678 AGGGGGATTTAAACCTCTTCTAAAT 57.701 36.000 6.64 0.00 32.28 1.40
6437 6587 6.728411 GAGGGGGATTTAAACCTCTTCTAAA 58.272 40.000 12.97 0.00 44.74 1.85
6438 6588 6.323210 GAGGGGGATTTAAACCTCTTCTAA 57.677 41.667 12.97 0.00 44.74 2.10
6439 6589 5.970501 GAGGGGGATTTAAACCTCTTCTA 57.029 43.478 12.97 0.00 44.74 2.10
6440 6590 4.864483 GAGGGGGATTTAAACCTCTTCT 57.136 45.455 12.97 0.00 44.74 2.85
6444 6594 5.359484 GGGTTTGAGGGGGATTTAAACCTC 61.359 50.000 13.24 13.24 45.86 3.85
6445 6595 3.503412 GGGTTTGAGGGGGATTTAAACCT 60.503 47.826 14.54 0.00 45.86 3.50
6446 6596 2.835764 GGGTTTGAGGGGGATTTAAACC 59.164 50.000 0.00 0.00 45.86 3.27
6447 6597 2.835764 GGGGTTTGAGGGGGATTTAAAC 59.164 50.000 0.00 0.00 0.00 2.01
6448 6598 2.730816 AGGGGTTTGAGGGGGATTTAAA 59.269 45.455 0.00 0.00 0.00 1.52
6449 6599 2.374179 AGGGGTTTGAGGGGGATTTAA 58.626 47.619 0.00 0.00 0.00 1.52
6450 6600 2.084121 AGGGGTTTGAGGGGGATTTA 57.916 50.000 0.00 0.00 0.00 1.40
6451 6601 1.078823 GAAGGGGTTTGAGGGGGATTT 59.921 52.381 0.00 0.00 0.00 2.17
6452 6602 0.710588 GAAGGGGTTTGAGGGGGATT 59.289 55.000 0.00 0.00 0.00 3.01
6453 6603 0.479589 TGAAGGGGTTTGAGGGGGAT 60.480 55.000 0.00 0.00 0.00 3.85
6454 6604 0.703056 TTGAAGGGGTTTGAGGGGGA 60.703 55.000 0.00 0.00 0.00 4.81
6455 6605 0.413434 ATTGAAGGGGTTTGAGGGGG 59.587 55.000 0.00 0.00 0.00 5.40
6456 6606 1.619704 GGATTGAAGGGGTTTGAGGGG 60.620 57.143 0.00 0.00 0.00 4.79
6457 6607 1.077005 TGGATTGAAGGGGTTTGAGGG 59.923 52.381 0.00 0.00 0.00 4.30
6458 6608 2.171003 GTGGATTGAAGGGGTTTGAGG 58.829 52.381 0.00 0.00 0.00 3.86
6459 6609 3.084786 GAGTGGATTGAAGGGGTTTGAG 58.915 50.000 0.00 0.00 0.00 3.02
6460 6610 2.552155 CGAGTGGATTGAAGGGGTTTGA 60.552 50.000 0.00 0.00 0.00 2.69
6461 6611 1.812571 CGAGTGGATTGAAGGGGTTTG 59.187 52.381 0.00 0.00 0.00 2.93
6462 6612 1.271926 CCGAGTGGATTGAAGGGGTTT 60.272 52.381 0.00 0.00 37.49 3.27
6463 6613 0.328258 CCGAGTGGATTGAAGGGGTT 59.672 55.000 0.00 0.00 37.49 4.11
6464 6614 0.546747 TCCGAGTGGATTGAAGGGGT 60.547 55.000 0.00 0.00 40.17 4.95
6465 6615 2.296920 TCCGAGTGGATTGAAGGGG 58.703 57.895 0.00 0.00 40.17 4.79
6481 6631 1.673009 TTCGGTTGCGGGTGAATCC 60.673 57.895 0.00 0.00 0.00 3.01
6482 6632 1.231958 TGTTCGGTTGCGGGTGAATC 61.232 55.000 0.00 0.00 0.00 2.52
6483 6633 0.820074 TTGTTCGGTTGCGGGTGAAT 60.820 50.000 0.00 0.00 0.00 2.57
6484 6634 1.440938 CTTGTTCGGTTGCGGGTGAA 61.441 55.000 0.00 0.00 0.00 3.18
6485 6635 1.890041 CTTGTTCGGTTGCGGGTGA 60.890 57.895 0.00 0.00 0.00 4.02
6486 6636 2.637025 CTTGTTCGGTTGCGGGTG 59.363 61.111 0.00 0.00 0.00 4.61
6487 6637 2.593436 CCTTGTTCGGTTGCGGGT 60.593 61.111 0.00 0.00 0.00 5.28
6488 6638 4.038080 GCCTTGTTCGGTTGCGGG 62.038 66.667 0.00 0.00 0.00 6.13
6489 6639 4.038080 GGCCTTGTTCGGTTGCGG 62.038 66.667 0.00 0.00 0.00 5.69
6490 6640 2.978010 AGGCCTTGTTCGGTTGCG 60.978 61.111 0.00 0.00 0.00 4.85
6491 6641 1.452145 TTCAGGCCTTGTTCGGTTGC 61.452 55.000 0.00 0.00 0.00 4.17
6492 6642 1.001378 CTTTCAGGCCTTGTTCGGTTG 60.001 52.381 0.00 0.00 0.00 3.77
6493 6643 1.133915 TCTTTCAGGCCTTGTTCGGTT 60.134 47.619 0.00 0.00 0.00 4.44
6494 6644 0.472471 TCTTTCAGGCCTTGTTCGGT 59.528 50.000 0.00 0.00 0.00 4.69
6495 6645 1.604604 TTCTTTCAGGCCTTGTTCGG 58.395 50.000 0.00 0.00 0.00 4.30
6496 6646 2.878406 TCTTTCTTTCAGGCCTTGTTCG 59.122 45.455 0.00 0.00 0.00 3.95
6497 6647 4.918810 TTCTTTCTTTCAGGCCTTGTTC 57.081 40.909 0.00 0.00 0.00 3.18
6498 6648 4.895297 TGATTCTTTCTTTCAGGCCTTGTT 59.105 37.500 0.00 0.00 0.00 2.83
6499 6649 4.473444 TGATTCTTTCTTTCAGGCCTTGT 58.527 39.130 0.00 0.00 0.00 3.16
6500 6650 5.458041 TTGATTCTTTCTTTCAGGCCTTG 57.542 39.130 0.00 0.00 0.00 3.61
6501 6651 5.835280 TCTTTGATTCTTTCTTTCAGGCCTT 59.165 36.000 0.00 0.00 0.00 4.35
6502 6652 5.242615 GTCTTTGATTCTTTCTTTCAGGCCT 59.757 40.000 0.00 0.00 0.00 5.19
6503 6653 5.465051 GTCTTTGATTCTTTCTTTCAGGCC 58.535 41.667 0.00 0.00 0.00 5.19
6504 6654 5.010012 TGGTCTTTGATTCTTTCTTTCAGGC 59.990 40.000 0.00 0.00 0.00 4.85
6505 6655 6.639632 TGGTCTTTGATTCTTTCTTTCAGG 57.360 37.500 0.00 0.00 0.00 3.86
6506 6656 7.806960 GTCATGGTCTTTGATTCTTTCTTTCAG 59.193 37.037 0.00 0.00 0.00 3.02
6694 6986 1.415289 TGACTAGATCCCTCGCGTCTA 59.585 52.381 5.77 4.50 0.00 2.59
6961 7257 4.134563 GTTTCTGAAGACAGGGCAACTAA 58.865 43.478 0.00 0.00 43.60 2.24
7098 7394 7.889873 AAAATACCACGGATAAAATCATCCA 57.110 32.000 3.24 0.00 44.16 3.41
7242 7538 5.596836 ATTTATACCCCATTGCAACACAG 57.403 39.130 0.00 0.00 0.00 3.66
7358 7654 6.148150 CAGATAAATTTGCCAGCAAACACATT 59.852 34.615 19.29 13.81 46.80 2.71
7381 7677 2.286772 GGAAAACTTGCCGTGTGTACAG 60.287 50.000 0.00 0.00 0.00 2.74
7412 7708 0.392193 ATGCTCTCAAGGACTTGCCG 60.392 55.000 7.18 1.78 43.43 5.69
7424 7720 1.202428 GGTCCGGTTGTAGATGCTCTC 60.202 57.143 0.00 0.00 0.00 3.20
7480 7776 3.996150 AAATCATCTAAGCAATGGCCG 57.004 42.857 0.00 0.00 42.56 6.13
7483 7779 4.293415 GCCGAAAATCATCTAAGCAATGG 58.707 43.478 0.00 0.00 0.00 3.16
7491 7787 1.562008 TGGGTGGCCGAAAATCATCTA 59.438 47.619 0.00 0.00 0.00 1.98
7492 7788 0.331278 TGGGTGGCCGAAAATCATCT 59.669 50.000 0.00 0.00 0.00 2.90
7527 7823 3.074281 CCAGGCGTTTGGGGTAGA 58.926 61.111 0.00 0.00 34.46 2.59
7549 7845 1.905512 GGGTATGAAGAGTGCCGGT 59.094 57.895 1.90 0.00 0.00 5.28
7560 7856 3.309629 CCCTAGATATGGACCGGGTATGA 60.310 52.174 6.32 0.00 0.00 2.15
7605 7901 2.271800 GTCAGTCTAATGTGAAGCCCG 58.728 52.381 0.00 0.00 0.00 6.13
7611 7907 3.261580 CATTGCGGTCAGTCTAATGTGA 58.738 45.455 0.00 0.00 0.00 3.58
7614 7910 1.331756 GCCATTGCGGTCAGTCTAATG 59.668 52.381 0.00 0.00 36.97 1.90
7617 7913 1.220749 GGCCATTGCGGTCAGTCTA 59.779 57.895 0.00 0.00 40.18 2.59
7656 7952 2.885644 CGCTCATCGGACCAACGG 60.886 66.667 0.00 0.00 33.78 4.44
7659 7955 3.371097 GAGGCGCTCATCGGACCAA 62.371 63.158 7.64 0.00 38.94 3.67
7698 7994 3.257561 CGACATTCCAGAGCGGCG 61.258 66.667 0.51 0.51 33.14 6.46
7709 8005 4.162690 GCTCCCTCGGGCGACATT 62.163 66.667 0.00 0.00 34.68 2.71
7769 8066 2.286365 AAGGGAAAGAAATGGTGCGA 57.714 45.000 0.00 0.00 0.00 5.10
7783 8080 1.174783 CGACGAAGAGGAGAAAGGGA 58.825 55.000 0.00 0.00 0.00 4.20
7800 8097 0.248498 CAGATCGAAAGTAGCGGCGA 60.248 55.000 12.98 0.00 37.17 5.54
7812 8109 0.806102 GCTAGCGGCAAACAGATCGA 60.806 55.000 0.00 0.00 41.35 3.59
7816 8113 2.654289 TCGCTAGCGGCAAACAGA 59.346 55.556 34.76 12.07 41.91 3.41


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

AutoCloner maintained by Alex Coulton.