Multiple sequence alignment - TraesCS2D01G175200

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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 TraesCS2D01G175200 chr2D 100.000 6714 0 0 1 6714 118561301 118554588 0.000000e+00 12399.0
1 TraesCS2D01G175200 chr2A 94.279 3391 125 21 2623 5980 120469100 120465746 0.000000e+00 5123.0
2 TraesCS2D01G175200 chr2A 94.076 1958 59 23 691 2621 120471059 120469132 0.000000e+00 2920.0
3 TraesCS2D01G175200 chr2A 88.543 707 69 10 1 699 120472058 120471356 0.000000e+00 846.0
4 TraesCS2D01G175200 chr2A 85.914 717 42 24 6002 6714 120465525 120464864 0.000000e+00 710.0
5 TraesCS2D01G175200 chr2B 95.420 2358 79 12 2745 5076 170390499 170392853 0.000000e+00 3729.0
6 TraesCS2D01G175200 chr2B 93.435 1904 73 24 742 2621 170388112 170389987 0.000000e+00 2776.0
7 TraesCS2D01G175200 chr2B 95.296 744 25 1 5202 5935 170392867 170393610 0.000000e+00 1171.0
8 TraesCS2D01G175200 chr2B 82.796 744 56 24 5975 6709 170393607 170394287 3.470000e-167 599.0
9 TraesCS2D01G175200 chr2B 94.318 88 4 1 2622 2709 170390020 170390106 4.220000e-27 134.0
10 TraesCS2D01G175200 chr2B 76.720 189 42 2 1 188 503979575 503979762 3.310000e-18 104.0
11 TraesCS2D01G175200 chr1D 78.405 301 58 6 1 298 227645464 227645168 8.890000e-44 189.0
12 TraesCS2D01G175200 chr1D 79.755 163 24 8 311 466 463842434 463842594 7.120000e-20 110.0
13 TraesCS2D01G175200 chr1D 76.119 201 45 3 303 500 57313575 57313775 1.190000e-17 102.0
14 TraesCS2D01G175200 chr4D 75.817 306 65 8 1 302 415131517 415131217 5.430000e-31 147.0
15 TraesCS2D01G175200 chr4D 76.786 168 26 8 305 466 450150449 450150609 1.550000e-11 82.4
16 TraesCS2D01G175200 chr3A 73.150 473 87 29 3 446 713307323 713306862 4.220000e-27 134.0
17 TraesCS2D01G175200 chr5D 72.245 490 108 21 1 477 424913458 424912984 7.070000e-25 126.0
18 TraesCS2D01G175200 chr7D 77.021 235 42 12 311 537 26765021 26764791 2.540000e-24 124.0
19 TraesCS2D01G175200 chr1A 76.712 219 47 4 85 301 550954814 550955030 1.180000e-22 119.0
20 TraesCS2D01G175200 chr1A 74.634 205 44 6 303 500 56594368 56594571 4.310000e-12 84.2
21 TraesCS2D01G175200 chr5A 73.754 301 71 7 1 299 467387698 467387404 1.980000e-20 111.0
22 TraesCS2D01G175200 chr3D 77.528 178 33 7 14 188 56878607 56878780 4.280000e-17 100.0
23 TraesCS2D01G175200 chr1B 77.500 160 25 9 306 460 199549077 199548924 1.200000e-12 86.1
24 TraesCS2D01G175200 chr4B 91.111 45 4 0 433 477 49029650 49029606 2.020000e-05 62.1


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 TraesCS2D01G175200 chr2D 118554588 118561301 6713 True 12399.00 12399 100.000 1 6714 1 chr2D.!!$R1 6713
1 TraesCS2D01G175200 chr2A 120464864 120472058 7194 True 2399.75 5123 90.703 1 6714 4 chr2A.!!$R1 6713
2 TraesCS2D01G175200 chr2B 170388112 170394287 6175 False 1681.80 3729 92.253 742 6709 5 chr2B.!!$F2 5967

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
537 545 0.036952 TTCTTCTTGAGGAGGCTGCG 60.037 55.0 0.00 0.00 0.00 5.18 F
548 556 1.002366 GAGGCTGCGTGAGTTATGTG 58.998 55.0 0.00 0.00 0.00 3.21 F
2371 2717 0.954452 ACAGGTTGCAACTTAGCAGC 59.046 50.0 27.64 10.31 46.54 5.25 F
2938 3679 0.031449 GCGATCCACTAGTCCAGCTC 59.969 60.0 0.00 0.00 0.00 4.09 F
3139 3897 0.324614 AGGGTTGTGCACGATCATCA 59.675 50.0 19.09 0.00 0.00 3.07 F
5071 5853 1.037493 AAGGTTTGTTCGGCCCTTTC 58.963 50.0 0.00 0.00 33.55 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2371 2717 0.300491 CGGTTCATTCGGTGTATGCG 59.700 55.000 0.00 0.00 0.0 4.73 R
2387 2733 2.035066 ACTTCTTGCACTTACGTACGGT 59.965 45.455 21.06 4.91 0.0 4.83 R
4071 4849 4.202070 GCTCTGACAGTGATACCCTTAGAC 60.202 50.000 8.69 0.00 0.0 2.59 R
4690 5472 2.893489 AGATGCACAAAGAAAAGGACCC 59.107 45.455 0.00 0.00 0.0 4.46 R
5138 5920 2.167900 AGGGAAGTTATGCGTCAGGTAC 59.832 50.000 0.00 0.00 0.0 3.34 R
6658 7655 0.583438 CGCAATCATCCACGGCTAAG 59.417 55.000 0.00 0.00 0.0 2.18 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
22 23 1.994507 GCACTAGAGCGAGCCGAAGA 61.995 60.000 0.00 0.00 0.00 2.87
53 54 2.427245 ATCGCCTCTCCTTCACCGG 61.427 63.158 0.00 0.00 0.00 5.28
73 74 2.035449 GGAGTTGGGCCAAACTTGTTAC 59.965 50.000 26.62 13.08 40.48 2.50
82 83 5.394333 GGGCCAAACTTGTTACAGTAAACAA 60.394 40.000 4.39 2.54 44.81 2.83
83 84 5.517411 GGCCAAACTTGTTACAGTAAACAAC 59.483 40.000 0.00 0.00 42.78 3.32
108 109 0.533032 AGTCGTTCTGCTAAGGCCTC 59.467 55.000 5.23 0.00 37.74 4.70
132 133 2.281070 CCAGCGCACCAGAACAGT 60.281 61.111 11.47 0.00 0.00 3.55
141 142 2.870435 GCACCAGAACAGTAACCATCGT 60.870 50.000 0.00 0.00 0.00 3.73
142 143 3.399330 CACCAGAACAGTAACCATCGTT 58.601 45.455 0.00 0.00 35.90 3.85
195 196 8.547481 TCCAATCTATAGACACACCTATGAAA 57.453 34.615 4.10 0.00 32.15 2.69
236 237 1.425066 AGCAGATCCACCAAAGACCAA 59.575 47.619 0.00 0.00 0.00 3.67
238 239 2.862541 CAGATCCACCAAAGACCAACA 58.137 47.619 0.00 0.00 0.00 3.33
239 240 2.554032 CAGATCCACCAAAGACCAACAC 59.446 50.000 0.00 0.00 0.00 3.32
243 244 1.136110 CCACCAAAGACCAACACCAAC 59.864 52.381 0.00 0.00 0.00 3.77
259 260 4.899457 ACACCAACCGAATCCTATGAGATA 59.101 41.667 0.00 0.00 0.00 1.98
276 277 2.950309 AGATACGCCGTAGACACTCATT 59.050 45.455 2.44 0.00 0.00 2.57
281 282 1.993370 GCCGTAGACACTCATTCACAC 59.007 52.381 0.00 0.00 0.00 3.82
301 302 1.139095 CCCTCCAACGACGCTAGAC 59.861 63.158 0.00 0.00 0.00 2.59
314 315 3.366739 CTAGACGGCGGGGTGAACC 62.367 68.421 13.24 0.00 39.11 3.62
327 328 4.610333 GGGGTGAACCTTATTCCATCTTT 58.390 43.478 0.00 0.00 40.03 2.52
335 336 4.104897 ACCTTATTCCATCTTTAGGGAGCC 59.895 45.833 0.00 0.00 36.79 4.70
336 337 4.104738 CCTTATTCCATCTTTAGGGAGCCA 59.895 45.833 0.00 0.00 36.79 4.75
352 353 2.432628 CACCACCGCCTCGTCTTC 60.433 66.667 0.00 0.00 0.00 2.87
355 356 2.050350 CCACCGCCTCGTCTTCCTA 61.050 63.158 0.00 0.00 0.00 2.94
359 360 0.801067 CCGCCTCGTCTTCCTAAACG 60.801 60.000 0.00 0.00 40.17 3.60
371 372 5.522824 GTCTTCCTAAACGAGACACAAACTT 59.477 40.000 0.00 0.00 39.59 2.66
376 377 6.540914 TCCTAAACGAGACACAAACTTCAAAT 59.459 34.615 0.00 0.00 0.00 2.32
416 417 1.388065 CGGAGCAAGATCTCTCCCGT 61.388 60.000 19.80 0.00 44.61 5.28
447 449 4.451150 GTCACCGCGCCTCCATGA 62.451 66.667 0.00 0.00 0.00 3.07
452 454 3.536917 CGCGCCTCCATGACCCTA 61.537 66.667 0.00 0.00 0.00 3.53
460 462 2.757124 CCATGACCCTAGGGCCACC 61.757 68.421 28.88 14.69 39.32 4.61
461 463 2.000701 CATGACCCTAGGGCCACCA 61.001 63.158 28.88 19.71 40.13 4.17
478 480 1.285373 ACCAGAGATGAGGTAGACCGT 59.715 52.381 0.00 0.00 42.08 4.83
480 482 2.644676 CAGAGATGAGGTAGACCGTCA 58.355 52.381 0.40 0.00 42.08 4.35
485 487 1.139947 GAGGTAGACCGTCAGCAGC 59.860 63.158 0.40 0.00 42.08 5.25
486 488 1.595993 GAGGTAGACCGTCAGCAGCA 61.596 60.000 0.40 0.00 42.08 4.41
488 490 1.446272 GTAGACCGTCAGCAGCACC 60.446 63.158 0.40 0.00 0.00 5.01
490 492 1.468506 TAGACCGTCAGCAGCACCAA 61.469 55.000 0.40 0.00 0.00 3.67
503 505 3.303135 ACCAACGCGAGGCAGAGA 61.303 61.111 15.93 0.00 0.00 3.10
512 514 1.740718 GCGAGGCAGAGAAAACCCTAG 60.741 57.143 0.00 0.00 0.00 3.02
513 515 1.740718 CGAGGCAGAGAAAACCCTAGC 60.741 57.143 0.00 0.00 0.00 3.42
514 516 1.557371 GAGGCAGAGAAAACCCTAGCT 59.443 52.381 0.00 0.00 0.00 3.32
537 545 0.036952 TTCTTCTTGAGGAGGCTGCG 60.037 55.000 0.00 0.00 0.00 5.18
543 551 1.758440 TTGAGGAGGCTGCGTGAGTT 61.758 55.000 0.00 0.00 0.00 3.01
548 556 1.002366 GAGGCTGCGTGAGTTATGTG 58.998 55.000 0.00 0.00 0.00 3.21
549 557 1.021390 AGGCTGCGTGAGTTATGTGC 61.021 55.000 0.00 0.00 0.00 4.57
551 559 1.021390 GCTGCGTGAGTTATGTGCCT 61.021 55.000 0.00 0.00 0.00 4.75
556 564 1.920574 CGTGAGTTATGTGCCTCTTCG 59.079 52.381 0.00 0.00 0.00 3.79
565 573 1.277842 TGTGCCTCTTCGGATTAGCAA 59.722 47.619 0.00 0.00 33.16 3.91
567 575 1.831106 TGCCTCTTCGGATTAGCAAGA 59.169 47.619 0.00 0.00 33.16 3.02
568 576 2.435805 TGCCTCTTCGGATTAGCAAGAT 59.564 45.455 0.00 0.00 33.16 2.40
569 577 3.641436 TGCCTCTTCGGATTAGCAAGATA 59.359 43.478 0.00 0.00 33.16 1.98
574 582 6.295011 CCTCTTCGGATTAGCAAGATATCTGT 60.295 42.308 5.86 0.00 33.16 3.41
661 669 9.425248 AAAATATCATGTTCTCTCTCTCTCTCT 57.575 33.333 0.00 0.00 0.00 3.10
662 670 9.425248 AAATATCATGTTCTCTCTCTCTCTCTT 57.575 33.333 0.00 0.00 0.00 2.85
699 707 5.385198 ACACATGTAACAACCCTGAAGAAT 58.615 37.500 0.00 0.00 0.00 2.40
700 708 5.241506 ACACATGTAACAACCCTGAAGAATG 59.758 40.000 0.00 0.00 0.00 2.67
701 709 5.241506 CACATGTAACAACCCTGAAGAATGT 59.758 40.000 0.00 0.00 0.00 2.71
702 710 6.429692 CACATGTAACAACCCTGAAGAATGTA 59.570 38.462 0.00 0.00 0.00 2.29
703 711 7.001674 ACATGTAACAACCCTGAAGAATGTAA 58.998 34.615 0.00 0.00 0.00 2.41
704 712 6.870971 TGTAACAACCCTGAAGAATGTAAC 57.129 37.500 0.00 0.00 0.00 2.50
705 713 6.597562 TGTAACAACCCTGAAGAATGTAACT 58.402 36.000 0.00 0.00 0.00 2.24
706 714 6.708949 TGTAACAACCCTGAAGAATGTAACTC 59.291 38.462 0.00 0.00 0.00 3.01
707 715 4.652822 ACAACCCTGAAGAATGTAACTCC 58.347 43.478 0.00 0.00 0.00 3.85
708 716 4.104102 ACAACCCTGAAGAATGTAACTCCA 59.896 41.667 0.00 0.00 0.00 3.86
712 1024 6.314917 ACCCTGAAGAATGTAACTCCAAAAT 58.685 36.000 0.00 0.00 0.00 1.82
725 1037 9.844257 TGTAACTCCAAAATTCCATTTGAAATT 57.156 25.926 1.56 0.00 41.73 1.82
925 1242 1.305297 TGACCACCTCCGCATCTCT 60.305 57.895 0.00 0.00 0.00 3.10
1331 1662 1.412710 TGCTAGGGGATGCTAAAGTCG 59.587 52.381 0.00 0.00 0.00 4.18
1385 1716 3.245797 CTCGAATCTGTGTGTGTACTGG 58.754 50.000 0.00 0.00 0.00 4.00
1390 1721 5.288712 CGAATCTGTGTGTGTACTGGATAAC 59.711 44.000 0.00 0.00 0.00 1.89
1394 1725 5.303333 TCTGTGTGTGTACTGGATAACTTGA 59.697 40.000 0.00 0.00 0.00 3.02
1397 1728 5.756347 GTGTGTGTACTGGATAACTTGACAA 59.244 40.000 0.00 0.00 0.00 3.18
1401 1732 7.642586 GTGTGTACTGGATAACTTGACAAAAAC 59.357 37.037 0.00 0.00 0.00 2.43
1622 1960 7.332557 TGTTGTTGTCCCGAGTATATTTACAT 58.667 34.615 0.00 0.00 0.00 2.29
1677 2015 4.082625 TGCCATACTCAACTGCAGAATTTG 60.083 41.667 23.35 14.86 0.00 2.32
1745 2083 8.634335 TGATTGTTTAGAAACCTGAATCATGA 57.366 30.769 0.00 0.00 35.61 3.07
1749 2087 8.272545 TGTTTAGAAACCTGAATCATGATCTG 57.727 34.615 9.06 6.82 38.11 2.90
1847 2187 2.218953 TATTCCATCAACTCGTCGCC 57.781 50.000 0.00 0.00 0.00 5.54
1888 2228 7.287005 TCCACTACACTTACTTTATCGATGGAT 59.713 37.037 8.54 0.00 36.65 3.41
1889 2229 8.573885 CCACTACACTTACTTTATCGATGGATA 58.426 37.037 8.54 0.00 34.00 2.59
1890 2230 9.961265 CACTACACTTACTTTATCGATGGATAA 57.039 33.333 8.54 6.10 42.04 1.75
1893 2233 8.833231 ACACTTACTTTATCGATGGATAATGG 57.167 34.615 20.22 14.32 42.95 3.16
1894 2234 8.647796 ACACTTACTTTATCGATGGATAATGGA 58.352 33.333 20.22 13.34 42.95 3.41
2072 2412 1.615392 GCTCATTGCCTTTGTCAGGTT 59.385 47.619 0.00 0.00 46.07 3.50
2138 2478 4.774726 ACTCATGCTCTATACAGGTATGGG 59.225 45.833 2.25 0.00 0.00 4.00
2143 2483 4.833380 TGCTCTATACAGGTATGGGAAGTC 59.167 45.833 2.25 0.00 0.00 3.01
2306 2647 8.394971 TCAACACTAATGACTGATGATTTTGT 57.605 30.769 0.00 0.00 0.00 2.83
2371 2717 0.954452 ACAGGTTGCAACTTAGCAGC 59.046 50.000 27.64 10.31 46.54 5.25
2387 2733 1.006086 CAGCGCATACACCGAATGAA 58.994 50.000 11.47 0.00 0.00 2.57
2390 2736 0.300491 CGCATACACCGAATGAACCG 59.700 55.000 0.00 0.00 0.00 4.44
2488 2835 9.967451 TTGGGGAAAAGTTCTTTTATTTTCTTT 57.033 25.926 9.99 0.00 40.88 2.52
2563 2910 5.936956 ACTGAATGACTGAAGGAAGATGAAC 59.063 40.000 0.00 0.00 0.00 3.18
2564 2911 5.248640 TGAATGACTGAAGGAAGATGAACC 58.751 41.667 0.00 0.00 0.00 3.62
2573 2920 6.292923 TGAAGGAAGATGAACCGAACTAAAA 58.707 36.000 0.00 0.00 0.00 1.52
2589 2936 6.758886 CGAACTAAAATTCTAGAGTGAGGCAT 59.241 38.462 0.00 0.00 0.00 4.40
2611 2958 6.128063 GCATTAGGCTAAGGCAGATATGAAAG 60.128 42.308 32.05 0.00 44.19 2.62
2621 2968 4.263243 GGCAGATATGAAAGTCCATAGGCT 60.263 45.833 0.00 0.00 33.08 4.58
2623 2970 6.352565 GGCAGATATGAAAGTCCATAGGCTAT 60.353 42.308 0.00 0.00 33.08 2.97
2625 2972 7.580302 GCAGATATGAAAGTCCATAGGCTATGA 60.580 40.741 31.17 16.76 38.45 2.15
2647 3025 7.470935 TGAAAAATCCATGTGATCTGTTCAT 57.529 32.000 0.00 0.00 36.54 2.57
2653 3031 7.981102 ATCCATGTGATCTGTTCATCTTATG 57.019 36.000 0.00 0.00 36.54 1.90
2660 3038 6.038714 GTGATCTGTTCATCTTATGGAAACCC 59.961 42.308 0.00 0.00 36.54 4.11
2782 3523 9.320295 TCCCAGAAAGGAATTGTTACAATATTT 57.680 29.630 11.23 11.99 41.22 1.40
2805 3546 7.994425 TTTGAGTTTAGTTGGATGCTAATGA 57.006 32.000 0.00 0.00 0.00 2.57
2835 3576 3.984732 GCTTGCCCCACTCCCCTT 61.985 66.667 0.00 0.00 0.00 3.95
2839 3580 1.863155 TTGCCCCACTCCCCTTCATC 61.863 60.000 0.00 0.00 0.00 2.92
2914 3655 0.812014 TTGTCACGAGGCGCTTTTGA 60.812 50.000 7.64 3.78 0.00 2.69
2925 3666 1.803289 GCTTTTGAGGGTGCGATCC 59.197 57.895 0.00 0.00 0.00 3.36
2926 3667 0.960364 GCTTTTGAGGGTGCGATCCA 60.960 55.000 0.00 0.00 0.00 3.41
2927 3668 0.804989 CTTTTGAGGGTGCGATCCAC 59.195 55.000 5.94 5.94 43.90 4.02
2928 3669 0.400213 TTTTGAGGGTGCGATCCACT 59.600 50.000 12.27 0.00 44.08 4.00
2929 3670 1.271856 TTTGAGGGTGCGATCCACTA 58.728 50.000 12.27 0.00 44.08 2.74
2930 3671 0.824109 TTGAGGGTGCGATCCACTAG 59.176 55.000 12.27 0.00 44.08 2.57
2931 3672 0.324368 TGAGGGTGCGATCCACTAGT 60.324 55.000 12.27 0.00 44.08 2.57
2932 3673 0.386113 GAGGGTGCGATCCACTAGTC 59.614 60.000 12.27 5.41 44.08 2.59
2933 3674 1.043673 AGGGTGCGATCCACTAGTCC 61.044 60.000 12.27 6.72 44.08 3.85
2934 3675 1.327690 GGGTGCGATCCACTAGTCCA 61.328 60.000 12.27 0.00 44.08 4.02
2935 3676 0.103208 GGTGCGATCCACTAGTCCAG 59.897 60.000 12.27 0.00 44.08 3.86
2936 3677 0.528684 GTGCGATCCACTAGTCCAGC 60.529 60.000 0.00 0.00 41.35 4.85
2937 3678 0.684479 TGCGATCCACTAGTCCAGCT 60.684 55.000 0.00 0.00 0.00 4.24
2938 3679 0.031449 GCGATCCACTAGTCCAGCTC 59.969 60.000 0.00 0.00 0.00 4.09
2939 3680 0.671251 CGATCCACTAGTCCAGCTCC 59.329 60.000 0.00 0.00 0.00 4.70
3064 3820 2.749044 CAATGCCAGGCGTCAGCT 60.749 61.111 6.62 0.00 44.37 4.24
3115 3871 2.033757 CTTGGTGCAGAGCTGGCT 59.966 61.111 8.30 0.00 0.00 4.75
3139 3897 0.324614 AGGGTTGTGCACGATCATCA 59.675 50.000 19.09 0.00 0.00 3.07
3171 3929 3.894427 AGTGGCATGTGTTTGTATTTGGA 59.106 39.130 0.00 0.00 0.00 3.53
3476 4252 8.239038 GCATATAGCCATAGTCAGGTATCTAA 57.761 38.462 0.00 0.00 37.23 2.10
3687 4464 9.559732 CTGGATTAATATGAACAGTGGTGAATA 57.440 33.333 0.00 0.00 0.00 1.75
3736 4514 5.483937 TCTTCCAGTTAGAAGTCAATGCCTA 59.516 40.000 1.56 0.00 43.17 3.93
3747 4525 7.042335 AGAAGTCAATGCCTAACTGTACATAC 58.958 38.462 0.00 0.00 0.00 2.39
3749 4527 7.655521 AGTCAATGCCTAACTGTACATACTA 57.344 36.000 0.00 0.00 0.00 1.82
3996 4774 6.489603 TCTGGAATAATTTTGGCTTCAGGTA 58.510 36.000 0.00 0.00 0.00 3.08
4041 4819 1.602771 GTGGGGGCTAGAGGTTGAC 59.397 63.158 0.00 0.00 0.00 3.18
4071 4849 2.969628 AACAAGTAGATGAGGCTCGG 57.030 50.000 10.42 0.00 0.00 4.63
4230 5008 6.406370 TGTCAGTAAGCTATTATTGCTGTGT 58.594 36.000 1.46 0.00 40.15 3.72
4661 5443 3.576982 TGGTATCGTTCCAGTCAGTTTCT 59.423 43.478 0.00 0.00 0.00 2.52
4690 5472 7.995488 AGGTAATTGAATCCTTCTATTGTCTGG 59.005 37.037 6.76 0.00 36.18 3.86
4926 5708 6.259893 AGGTCAGTATATCATGTATGGAGCT 58.740 40.000 0.00 0.00 0.00 4.09
4930 5712 7.875041 GTCAGTATATCATGTATGGAGCTGTTT 59.125 37.037 0.00 0.00 0.00 2.83
5063 5845 1.206115 GGCGTGCAAAGGTTTGTTCG 61.206 55.000 4.45 9.66 40.24 3.95
5071 5853 1.037493 AAGGTTTGTTCGGCCCTTTC 58.963 50.000 0.00 0.00 33.55 2.62
5075 5857 2.159014 GGTTTGTTCGGCCCTTTCTTTT 60.159 45.455 0.00 0.00 0.00 2.27
5076 5858 3.527533 GTTTGTTCGGCCCTTTCTTTTT 58.472 40.909 0.00 0.00 0.00 1.94
5079 5861 5.538849 TTGTTCGGCCCTTTCTTTTTAAT 57.461 34.783 0.00 0.00 0.00 1.40
5080 5862 4.877282 TGTTCGGCCCTTTCTTTTTAATG 58.123 39.130 0.00 0.00 0.00 1.90
5082 5864 4.776795 TCGGCCCTTTCTTTTTAATGTC 57.223 40.909 0.00 0.00 0.00 3.06
5143 5925 4.699925 TTGAACTGCAACCTAAGTACCT 57.300 40.909 0.00 0.00 0.00 3.08
5144 5926 4.002906 TGAACTGCAACCTAAGTACCTG 57.997 45.455 0.00 0.00 0.00 4.00
5145 5927 3.644265 TGAACTGCAACCTAAGTACCTGA 59.356 43.478 0.00 0.00 0.00 3.86
5146 5928 3.679824 ACTGCAACCTAAGTACCTGAC 57.320 47.619 0.00 0.00 0.00 3.51
5162 5944 3.081804 CCTGACGCATAACTTCCCTTTT 58.918 45.455 0.00 0.00 0.00 2.27
5541 6324 3.183237 ACTGTCGCGTCTTAATTTTGC 57.817 42.857 5.77 0.00 0.00 3.68
5584 6367 0.249955 TCAGATGCACGATCTTGCCA 59.750 50.000 20.28 9.72 39.64 4.92
5701 6484 0.591170 CCGGTGCAACGATTGAAAGT 59.409 50.000 28.95 0.00 38.12 2.66
5731 6514 2.812358 AAACGGGCAATTCAAACTCC 57.188 45.000 0.00 0.00 0.00 3.85
5741 6524 5.273944 GCAATTCAAACTCCGGATACAATC 58.726 41.667 3.57 0.00 0.00 2.67
5776 6559 5.294306 TCGAAATAATGAAGGTCATGCAGTC 59.706 40.000 0.00 0.00 37.15 3.51
5791 6574 2.983592 GTCGTGCCACCCCCTTTG 60.984 66.667 0.00 0.00 0.00 2.77
5936 6729 9.294030 GATGCAAGATTTTACTAAACCTTGATG 57.706 33.333 18.28 3.45 35.24 3.07
5937 6730 7.090173 TGCAAGATTTTACTAAACCTTGATGC 58.910 34.615 18.28 10.12 35.24 3.91
5970 6763 4.923942 ATCGGCAGCGCATCCCTG 62.924 66.667 11.47 0.00 0.00 4.45
5977 6770 3.830192 GCGCATCCCTGCCTTTGG 61.830 66.667 0.30 0.00 46.07 3.28
5980 6773 1.306296 GCATCCCTGCCTTTGGGTA 59.694 57.895 0.00 0.00 44.84 3.69
5981 6774 0.324275 GCATCCCTGCCTTTGGGTAA 60.324 55.000 0.00 0.00 44.84 2.85
5982 6775 1.689258 GCATCCCTGCCTTTGGGTAAT 60.689 52.381 0.00 0.00 44.84 1.89
5983 6776 2.034124 CATCCCTGCCTTTGGGTAATG 58.966 52.381 0.00 0.00 44.84 1.90
5984 6777 1.080638 TCCCTGCCTTTGGGTAATGT 58.919 50.000 0.00 0.00 44.84 2.71
5985 6778 1.431243 TCCCTGCCTTTGGGTAATGTT 59.569 47.619 0.00 0.00 44.84 2.71
5986 6779 2.650322 TCCCTGCCTTTGGGTAATGTTA 59.350 45.455 0.00 0.00 44.84 2.41
5995 6788 5.400886 CCTTTGGGTAATGTTATATGGGGGT 60.401 44.000 0.00 0.00 0.00 4.95
6000 6793 7.838241 TGGGTAATGTTATATGGGGGTAAATT 58.162 34.615 0.00 0.00 0.00 1.82
6002 6795 8.809066 GGGTAATGTTATATGGGGGTAAATTTC 58.191 37.037 0.00 0.00 0.00 2.17
6008 6801 7.558444 TGTTATATGGGGGTAAATTTCACTGTC 59.442 37.037 0.00 0.00 0.00 3.51
6012 6805 4.018779 TGGGGGTAAATTTCACTGTCTAGG 60.019 45.833 0.00 0.00 0.00 3.02
6077 7069 5.245531 TGGACCATGCTACTTGTAAAAGAG 58.754 41.667 0.00 0.00 0.00 2.85
6079 7071 5.351740 GGACCATGCTACTTGTAAAAGAGAC 59.648 44.000 0.00 0.00 0.00 3.36
6080 7072 4.929808 ACCATGCTACTTGTAAAAGAGACG 59.070 41.667 0.00 0.00 0.00 4.18
6111 7103 7.731720 CGTACACCACGTTATAAAATCAGAAA 58.268 34.615 0.00 0.00 45.82 2.52
6113 7105 7.972832 ACACCACGTTATAAAATCAGAAAGA 57.027 32.000 0.00 0.00 0.00 2.52
6118 7110 9.651718 CCACGTTATAAAATCAGAAAGAATAGC 57.348 33.333 0.00 0.00 0.00 2.97
6188 7182 1.825622 GCAGCCCAATAGGAGCCAC 60.826 63.158 0.00 0.00 38.24 5.01
6200 7194 2.716217 AGGAGCCACTGTTATGAAAGC 58.284 47.619 0.00 0.00 0.00 3.51
6201 7195 1.398390 GGAGCCACTGTTATGAAAGCG 59.602 52.381 0.00 0.00 0.00 4.68
6203 7197 2.742053 GAGCCACTGTTATGAAAGCGAA 59.258 45.455 0.00 0.00 0.00 4.70
6204 7198 2.484264 AGCCACTGTTATGAAAGCGAAC 59.516 45.455 0.00 0.00 0.00 3.95
6205 7199 2.724839 GCCACTGTTATGAAAGCGAACG 60.725 50.000 0.00 0.00 0.00 3.95
6206 7200 2.495939 CACTGTTATGAAAGCGAACGC 58.504 47.619 11.31 11.31 42.33 4.84
6207 7201 2.096466 CACTGTTATGAAAGCGAACGCA 60.096 45.455 20.66 0.69 44.88 5.24
6208 7202 2.742053 ACTGTTATGAAAGCGAACGCAT 59.258 40.909 20.66 6.54 44.88 4.73
6209 7203 3.181520 ACTGTTATGAAAGCGAACGCATC 60.182 43.478 20.66 17.21 44.88 3.91
6210 7204 2.095213 TGTTATGAAAGCGAACGCATCC 59.905 45.455 20.66 9.32 44.88 3.51
6211 7205 2.309528 TATGAAAGCGAACGCATCCT 57.690 45.000 20.66 13.01 44.88 3.24
6212 7206 1.453155 ATGAAAGCGAACGCATCCTT 58.547 45.000 20.66 8.42 44.88 3.36
6214 7208 0.517316 GAAAGCGAACGCATCCTTGT 59.483 50.000 20.66 0.00 44.88 3.16
6216 7210 1.298859 AAGCGAACGCATCCTTGTCC 61.299 55.000 20.66 0.00 44.88 4.02
6217 7211 3.081133 CGAACGCATCCTTGTCCG 58.919 61.111 0.00 0.00 0.00 4.79
6219 7213 1.413767 CGAACGCATCCTTGTCCGAG 61.414 60.000 0.00 0.00 0.00 4.63
6220 7214 1.079127 AACGCATCCTTGTCCGAGG 60.079 57.895 0.00 0.00 38.20 4.63
6221 7215 2.892425 CGCATCCTTGTCCGAGGC 60.892 66.667 0.00 0.00 36.71 4.70
6223 7217 1.078143 GCATCCTTGTCCGAGGCTT 60.078 57.895 0.00 0.00 36.71 4.35
6224 7218 0.678048 GCATCCTTGTCCGAGGCTTT 60.678 55.000 0.00 0.00 36.71 3.51
6225 7219 1.373570 CATCCTTGTCCGAGGCTTTC 58.626 55.000 0.00 0.00 36.71 2.62
6226 7220 0.984230 ATCCTTGTCCGAGGCTTTCA 59.016 50.000 0.00 0.00 36.71 2.69
6227 7221 0.984230 TCCTTGTCCGAGGCTTTCAT 59.016 50.000 0.00 0.00 36.71 2.57
6228 7222 1.089920 CCTTGTCCGAGGCTTTCATG 58.910 55.000 0.00 0.00 0.00 3.07
6229 7223 1.089920 CTTGTCCGAGGCTTTCATGG 58.910 55.000 0.00 0.00 0.00 3.66
6230 7224 0.960364 TTGTCCGAGGCTTTCATGGC 60.960 55.000 0.00 0.00 0.00 4.40
6242 7236 3.248363 GCTTTCATGGCCACTTTGAAAAC 59.752 43.478 25.56 20.23 38.49 2.43
6244 7238 2.676748 TCATGGCCACTTTGAAAACCT 58.323 42.857 8.16 0.00 0.00 3.50
6272 7266 4.424626 TGTTATTTTTGTCAAACAGCGCA 58.575 34.783 11.47 0.00 0.00 6.09
6309 7304 5.982465 AATGCACGTTTAACTGCAAAAAT 57.018 30.435 19.76 6.83 46.18 1.82
6317 7312 6.920758 ACGTTTAACTGCAAAAATGAGCAATA 59.079 30.769 12.52 0.00 40.73 1.90
6385 7380 2.355132 AGACACGGTAGATGCGTAGAAG 59.645 50.000 0.00 0.00 0.00 2.85
6422 7417 2.441164 TGGCCGCCACTTTGTTGT 60.441 55.556 8.43 0.00 0.00 3.32
6423 7418 2.027460 GGCCGCCACTTTGTTGTG 59.973 61.111 3.91 0.00 37.66 3.33
6424 7419 2.658268 GCCGCCACTTTGTTGTGC 60.658 61.111 0.00 0.00 36.68 4.57
6425 7420 2.804167 CCGCCACTTTGTTGTGCA 59.196 55.556 0.00 0.00 36.68 4.57
6426 7421 1.363443 CCGCCACTTTGTTGTGCAT 59.637 52.632 0.00 0.00 36.68 3.96
6427 7422 0.940519 CCGCCACTTTGTTGTGCATG 60.941 55.000 0.00 0.00 36.68 4.06
6428 7423 0.248990 CGCCACTTTGTTGTGCATGT 60.249 50.000 0.00 0.00 36.68 3.21
6542 7537 1.303799 AACGCTCCATGAAGCAGCAG 61.304 55.000 4.32 0.00 42.62 4.24
6585 7580 1.979693 AGGCCGAGACTGTCTGACC 60.980 63.158 16.28 12.93 0.00 4.02
6600 7595 5.224888 TGTCTGACCGTCAAATGTTACTAC 58.775 41.667 5.17 0.00 0.00 2.73
6603 7598 5.924254 TCTGACCGTCAAATGTTACTACTTG 59.076 40.000 2.19 0.00 0.00 3.16
6604 7599 4.449743 TGACCGTCAAATGTTACTACTTGC 59.550 41.667 0.00 0.00 0.00 4.01
6605 7600 4.638304 ACCGTCAAATGTTACTACTTGCT 58.362 39.130 0.00 0.00 0.00 3.91
6606 7601 5.786311 ACCGTCAAATGTTACTACTTGCTA 58.214 37.500 0.00 0.00 0.00 3.49
6609 7604 6.183360 CCGTCAAATGTTACTACTTGCTACTG 60.183 42.308 0.00 0.00 0.00 2.74
6610 7605 6.183360 CGTCAAATGTTACTACTTGCTACTGG 60.183 42.308 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.010574 CGTCTTCGGCTCGCTCTAG 60.011 63.158 0.00 0.00 0.00 2.43
8 9 4.484258 GCGTCTTCGGCTCGCTCT 62.484 66.667 0.00 0.00 45.29 4.09
27 28 2.583593 GAGAGGCGATGACGGTGC 60.584 66.667 0.00 0.00 40.15 5.01
32 33 0.179097 GGTGAAGGAGAGGCGATGAC 60.179 60.000 0.00 0.00 0.00 3.06
53 54 2.691011 TGTAACAAGTTTGGCCCAACTC 59.309 45.455 21.64 10.04 0.00 3.01
57 58 2.445682 ACTGTAACAAGTTTGGCCCA 57.554 45.000 0.00 0.00 0.00 5.36
73 74 5.236478 AGAACGACTTCATGGTTGTTTACTG 59.764 40.000 8.57 0.00 42.03 2.74
82 83 3.589988 CTTAGCAGAACGACTTCATGGT 58.410 45.455 0.00 0.00 0.00 3.55
83 84 2.932614 CCTTAGCAGAACGACTTCATGG 59.067 50.000 0.00 0.00 0.00 3.66
108 109 2.591429 TGGTGCGCTGGTCTTGTG 60.591 61.111 9.73 0.00 0.00 3.33
142 143 9.920133 CCTTTCGATCTATATTTCTCTTCATCA 57.080 33.333 0.00 0.00 0.00 3.07
178 179 5.575606 CGTTCGTTTTCATAGGTGTGTCTAT 59.424 40.000 0.00 0.00 0.00 1.98
195 196 2.299521 TGGACCCAATTTTCGTTCGTT 58.700 42.857 0.00 0.00 0.00 3.85
236 237 3.104512 TCTCATAGGATTCGGTTGGTGT 58.895 45.455 0.00 0.00 0.00 4.16
238 239 4.022242 CGTATCTCATAGGATTCGGTTGGT 60.022 45.833 0.00 0.00 34.47 3.67
239 240 4.486090 CGTATCTCATAGGATTCGGTTGG 58.514 47.826 0.00 0.00 34.47 3.77
243 244 2.478031 CGGCGTATCTCATAGGATTCGG 60.478 54.545 0.00 0.00 37.12 4.30
259 260 0.885879 TGAATGAGTGTCTACGGCGT 59.114 50.000 19.64 19.64 0.00 5.68
276 277 3.228017 TCGTTGGAGGGCGTGTGA 61.228 61.111 0.00 0.00 0.00 3.58
281 282 4.124351 TAGCGTCGTTGGAGGGCG 62.124 66.667 0.00 0.00 0.00 6.13
301 302 1.078001 AATAAGGTTCACCCCGCCG 60.078 57.895 0.00 0.00 36.42 6.46
314 315 5.066593 GTGGCTCCCTAAAGATGGAATAAG 58.933 45.833 0.00 0.00 0.00 1.73
335 336 2.432628 GAAGACGAGGCGGTGGTG 60.433 66.667 0.00 0.00 0.00 4.17
336 337 2.776370 TAGGAAGACGAGGCGGTGGT 62.776 60.000 0.00 0.00 0.00 4.16
352 353 5.728351 TTGAAGTTTGTGTCTCGTTTAGG 57.272 39.130 0.00 0.00 0.00 2.69
355 356 7.483691 GTGTTATTTGAAGTTTGTGTCTCGTTT 59.516 33.333 0.00 0.00 0.00 3.60
359 360 8.682128 TTTGTGTTATTTGAAGTTTGTGTCTC 57.318 30.769 0.00 0.00 0.00 3.36
376 377 6.917533 TCCGTTTTTAGGTGTTTTTGTGTTA 58.082 32.000 0.00 0.00 0.00 2.41
430 432 4.451150 TCATGGAGGCGCGGTGAC 62.451 66.667 8.83 0.00 0.00 3.67
436 438 2.423446 CTAGGGTCATGGAGGCGC 59.577 66.667 0.00 0.00 34.52 6.53
447 449 1.902818 ATCTCTGGTGGCCCTAGGGT 61.903 60.000 28.96 1.65 37.65 4.34
452 454 1.692042 CCTCATCTCTGGTGGCCCT 60.692 63.158 0.00 0.00 0.00 5.19
460 462 2.616376 CTGACGGTCTACCTCATCTCTG 59.384 54.545 9.88 0.00 0.00 3.35
461 463 2.925724 CTGACGGTCTACCTCATCTCT 58.074 52.381 9.88 0.00 0.00 3.10
478 480 4.600576 TCGCGTTGGTGCTGCTGA 62.601 61.111 5.77 0.00 0.00 4.26
485 487 3.114616 CTCTGCCTCGCGTTGGTG 61.115 66.667 18.60 13.17 0.00 4.17
486 488 2.377628 TTTCTCTGCCTCGCGTTGGT 62.378 55.000 18.60 0.00 0.00 3.67
488 490 0.110644 GTTTTCTCTGCCTCGCGTTG 60.111 55.000 5.77 0.00 0.00 4.10
490 492 1.668151 GGTTTTCTCTGCCTCGCGT 60.668 57.895 5.77 0.00 0.00 6.01
532 534 1.021390 AGGCACATAACTCACGCAGC 61.021 55.000 0.00 0.00 0.00 5.25
533 535 1.002366 GAGGCACATAACTCACGCAG 58.998 55.000 0.00 0.00 33.95 5.18
537 545 2.094182 TCCGAAGAGGCACATAACTCAC 60.094 50.000 0.00 0.00 40.77 3.51
543 551 2.698274 TGCTAATCCGAAGAGGCACATA 59.302 45.455 0.00 0.00 40.77 2.29
548 556 2.604046 TCTTGCTAATCCGAAGAGGC 57.396 50.000 0.00 0.00 40.77 4.70
549 557 6.098679 CAGATATCTTGCTAATCCGAAGAGG 58.901 44.000 1.33 0.00 42.97 3.69
551 559 6.656632 ACAGATATCTTGCTAATCCGAAGA 57.343 37.500 1.33 0.00 0.00 2.87
639 647 9.913310 TTTAAGAGAGAGAGAGAGAACATGATA 57.087 33.333 0.00 0.00 0.00 2.15
699 707 9.844257 AATTTCAAATGGAATTTTGGAGTTACA 57.156 25.926 0.00 0.00 46.10 2.41
701 709 9.844257 ACAATTTCAAATGGAATTTTGGAGTTA 57.156 25.926 0.00 0.00 46.10 2.24
702 710 8.750515 ACAATTTCAAATGGAATTTTGGAGTT 57.249 26.923 0.00 0.00 46.10 3.01
703 711 8.750515 AACAATTTCAAATGGAATTTTGGAGT 57.249 26.923 0.00 0.00 46.10 3.85
732 1044 9.816787 ACCTATTAGGGTCTGTTTGATTTAAAA 57.183 29.630 14.26 0.00 40.58 1.52
733 1045 9.816787 AACCTATTAGGGTCTGTTTGATTTAAA 57.183 29.630 14.26 0.00 40.58 1.52
754 1066 6.771749 TGTTTTTCTGGTTATTTCCGAACCTA 59.228 34.615 6.15 0.00 45.63 3.08
925 1242 1.226974 GCGACGGCTATTGCAGAGA 60.227 57.895 6.27 0.00 41.91 3.10
1296 1626 3.181487 CCCTAGCAAATGTCGGAAATTGG 60.181 47.826 0.00 0.00 0.00 3.16
1331 1662 2.097396 CGCGTATCAACATCGAATCACC 60.097 50.000 0.00 0.00 0.00 4.02
1385 1716 8.406172 ACACATGTTGTTTTTGTCAAGTTATC 57.594 30.769 0.00 0.00 33.09 1.75
1390 1721 7.026562 TGAGTACACATGTTGTTTTTGTCAAG 58.973 34.615 0.00 0.00 39.91 3.02
1394 1725 5.105957 TGCTGAGTACACATGTTGTTTTTGT 60.106 36.000 0.00 0.00 39.91 2.83
1397 1728 4.498009 GCTGCTGAGTACACATGTTGTTTT 60.498 41.667 0.00 0.00 39.91 2.43
1401 1732 1.127397 CGCTGCTGAGTACACATGTTG 59.873 52.381 0.00 0.00 0.00 3.33
1622 1960 8.698210 ACTAATTGGTACTCCGTATTTGACATA 58.302 33.333 0.00 0.00 36.30 2.29
1677 2015 8.494016 AGGAATGAAGTAGCACAAATAAGTAC 57.506 34.615 0.00 0.00 0.00 2.73
1716 2054 9.739276 TGATTCAGGTTTCTAAACAATCATACT 57.261 29.630 12.29 0.00 40.63 2.12
1745 2083 4.922206 TCTGCAGGACAAAAATACCAGAT 58.078 39.130 15.13 0.00 0.00 2.90
1749 2087 5.453567 AAGTTCTGCAGGACAAAAATACC 57.546 39.130 26.95 0.00 0.00 2.73
2018 2358 3.890756 AGTGGAACAAGCATTCATCACAA 59.109 39.130 0.00 0.00 44.16 3.33
2072 2412 5.601729 AGCTGGATGATCACATAAAGAGAGA 59.398 40.000 0.00 0.00 36.82 3.10
2138 2478 5.579564 AGTATAGAGTGGTTTCCGACTTC 57.420 43.478 0.00 0.00 0.00 3.01
2143 2483 4.730949 TCCAAGTATAGAGTGGTTTCCG 57.269 45.455 0.00 0.00 33.88 4.30
2306 2647 2.091541 GCCATGTTGCTAAGCTTACCA 58.908 47.619 0.86 0.00 0.00 3.25
2371 2717 0.300491 CGGTTCATTCGGTGTATGCG 59.700 55.000 0.00 0.00 0.00 4.73
2387 2733 2.035066 ACTTCTTGCACTTACGTACGGT 59.965 45.455 21.06 4.91 0.00 4.83
2390 2736 5.218139 ACTGTACTTCTTGCACTTACGTAC 58.782 41.667 0.00 0.00 0.00 3.67
2488 2835 9.725206 AGGACAAAAGTATAGAATAAGAGGGTA 57.275 33.333 0.00 0.00 0.00 3.69
2532 2879 3.624861 CCTTCAGTCATTCAGTGTATGCC 59.375 47.826 4.93 0.00 0.00 4.40
2563 2910 5.520649 GCCTCACTCTAGAATTTTAGTTCGG 59.479 44.000 3.17 0.95 33.36 4.30
2564 2911 6.100004 TGCCTCACTCTAGAATTTTAGTTCG 58.900 40.000 3.17 0.00 33.36 3.95
2573 2920 4.230455 AGCCTAATGCCTCACTCTAGAAT 58.770 43.478 0.00 0.00 42.71 2.40
2589 2936 6.464465 GGACTTTCATATCTGCCTTAGCCTAA 60.464 42.308 0.00 0.00 38.69 2.69
2611 2958 6.491403 ACATGGATTTTTCATAGCCTATGGAC 59.509 38.462 11.69 0.00 36.81 4.02
2621 2968 8.578448 TGAACAGATCACATGGATTTTTCATA 57.422 30.769 0.00 0.00 36.00 2.15
2623 2970 6.897706 TGAACAGATCACATGGATTTTTCA 57.102 33.333 0.00 5.21 36.00 2.69
2625 2972 7.713734 AGATGAACAGATCACATGGATTTTT 57.286 32.000 0.00 0.00 41.93 1.94
2647 3025 4.941263 CAGAATGTTCGGGTTTCCATAAGA 59.059 41.667 0.00 0.00 0.00 2.10
2690 3068 1.483827 TCCAGTCTGAGGATGTGATGC 59.516 52.381 0.00 0.00 0.00 3.91
2750 3491 8.490311 TGTAACAATTCCTTTCTGGGAAATTTT 58.510 29.630 0.00 0.00 46.73 1.82
2782 3523 6.092122 CGTCATTAGCATCCAACTAAACTCAA 59.908 38.462 0.00 0.00 33.54 3.02
2819 3560 1.867595 ATGAAGGGGAGTGGGGCAAG 61.868 60.000 0.00 0.00 0.00 4.01
2835 3576 0.607620 TGATCACAGTGCACGGATGA 59.392 50.000 24.13 21.04 0.00 2.92
2839 3580 1.328680 GCTATTGATCACAGTGCACGG 59.671 52.381 15.82 15.82 0.00 4.94
2884 3625 0.171231 TCGTGACAAGGAGCGATCTG 59.829 55.000 0.00 0.00 0.00 2.90
2914 3655 1.043673 GGACTAGTGGATCGCACCCT 61.044 60.000 0.00 0.00 0.00 4.34
2925 3666 0.324738 TGGAGGGAGCTGGACTAGTG 60.325 60.000 0.00 0.00 0.00 2.74
2926 3667 0.639392 ATGGAGGGAGCTGGACTAGT 59.361 55.000 0.00 0.00 0.00 2.57
2927 3668 1.415659 CAATGGAGGGAGCTGGACTAG 59.584 57.143 0.00 0.00 0.00 2.57
2928 3669 1.500474 CAATGGAGGGAGCTGGACTA 58.500 55.000 0.00 0.00 0.00 2.59
2929 3670 1.277580 CCAATGGAGGGAGCTGGACT 61.278 60.000 0.00 0.00 0.00 3.85
2930 3671 1.225704 CCAATGGAGGGAGCTGGAC 59.774 63.158 0.00 0.00 0.00 4.02
2931 3672 1.229951 ACCAATGGAGGGAGCTGGA 60.230 57.895 6.16 0.00 0.00 3.86
2932 3673 1.077212 CACCAATGGAGGGAGCTGG 60.077 63.158 6.16 0.00 0.00 4.85
2933 3674 0.393537 GTCACCAATGGAGGGAGCTG 60.394 60.000 6.16 0.00 0.00 4.24
2934 3675 0.842030 TGTCACCAATGGAGGGAGCT 60.842 55.000 6.16 0.00 0.00 4.09
2935 3676 0.038166 TTGTCACCAATGGAGGGAGC 59.962 55.000 6.16 0.00 0.00 4.70
2936 3677 1.352352 AGTTGTCACCAATGGAGGGAG 59.648 52.381 6.16 0.00 32.11 4.30
2937 3678 1.444933 AGTTGTCACCAATGGAGGGA 58.555 50.000 6.16 0.00 32.11 4.20
2938 3679 2.162681 GAAGTTGTCACCAATGGAGGG 58.837 52.381 6.16 0.00 32.11 4.30
2939 3680 3.146104 AGAAGTTGTCACCAATGGAGG 57.854 47.619 6.16 0.00 32.11 4.30
2964 3720 3.070576 GCCATGCCCTTCCACCAC 61.071 66.667 0.00 0.00 0.00 4.16
3074 3830 3.014623 TGAGCCTCATCTTGAATTGCAG 58.985 45.455 0.00 0.00 0.00 4.41
3115 3871 0.907704 ATCGTGCACAACCCTAGGGA 60.908 55.000 35.38 7.81 38.96 4.20
3139 3897 2.573462 ACACATGCCACTATTCTCCTGT 59.427 45.455 0.00 0.00 0.00 4.00
3171 3929 1.049289 GGGAGGTAGAAGCCCGACAT 61.049 60.000 0.00 0.00 31.06 3.06
3199 3957 8.606830 AGAGGGAGAAATAGTTCTACAAAACAT 58.393 33.333 16.58 0.00 45.49 2.71
3687 4464 9.277783 GAATCAATGTCCTTATTGCTAGTACAT 57.722 33.333 0.00 0.00 37.83 2.29
3688 4465 8.486210 AGAATCAATGTCCTTATTGCTAGTACA 58.514 33.333 0.00 0.00 37.83 2.90
3689 4466 8.894768 AGAATCAATGTCCTTATTGCTAGTAC 57.105 34.615 0.00 0.00 37.83 2.73
3736 4514 8.094548 TGACAAGCTGAAATAGTATGTACAGTT 58.905 33.333 0.33 0.00 30.76 3.16
3747 4525 7.496920 TGGATTAGTGATGACAAGCTGAAATAG 59.503 37.037 0.00 0.00 0.00 1.73
3749 4527 6.182627 TGGATTAGTGATGACAAGCTGAAAT 58.817 36.000 0.00 0.00 0.00 2.17
3888 4666 6.068010 ACATACAAAAGAACCACCATGAAGA 58.932 36.000 0.00 0.00 0.00 2.87
3996 4774 7.020827 TGTCTCTTCATCAAGGAAATAAGGT 57.979 36.000 0.00 0.00 0.00 3.50
4071 4849 4.202070 GCTCTGACAGTGATACCCTTAGAC 60.202 50.000 8.69 0.00 0.00 2.59
4193 4971 5.001232 GCTTACTGACATACAACTTTCCCA 58.999 41.667 0.00 0.00 0.00 4.37
4230 5008 8.977412 TCTGTCATGGTCTTTCTATGTATGTAA 58.023 33.333 0.00 0.00 36.58 2.41
4243 5025 6.365970 AAGTTATCTGTCTGTCATGGTCTT 57.634 37.500 0.00 0.00 0.00 3.01
4690 5472 2.893489 AGATGCACAAAGAAAAGGACCC 59.107 45.455 0.00 0.00 0.00 4.46
4926 5708 6.491745 TGCCATAACTATTCCACTTTGAAACA 59.508 34.615 0.00 0.00 0.00 2.83
4930 5712 4.947388 GGTGCCATAACTATTCCACTTTGA 59.053 41.667 0.00 0.00 0.00 2.69
5063 5845 3.055385 GGGGACATTAAAAAGAAAGGGCC 60.055 47.826 0.00 0.00 34.99 5.80
5071 5853 7.902087 TCAAAATAGGTGGGGACATTAAAAAG 58.098 34.615 0.00 0.00 46.14 2.27
5075 5857 7.456269 ACAAATCAAAATAGGTGGGGACATTAA 59.544 33.333 0.00 0.00 46.14 1.40
5076 5858 6.957020 ACAAATCAAAATAGGTGGGGACATTA 59.043 34.615 0.00 0.00 46.14 1.90
5079 5861 4.746466 ACAAATCAAAATAGGTGGGGACA 58.254 39.130 0.00 0.00 38.70 4.02
5080 5862 6.661805 TCTTACAAATCAAAATAGGTGGGGAC 59.338 38.462 0.00 0.00 0.00 4.46
5082 5864 7.660030 ATCTTACAAATCAAAATAGGTGGGG 57.340 36.000 0.00 0.00 0.00 4.96
5138 5920 2.167900 AGGGAAGTTATGCGTCAGGTAC 59.832 50.000 0.00 0.00 0.00 3.34
5139 5921 2.463752 AGGGAAGTTATGCGTCAGGTA 58.536 47.619 0.00 0.00 0.00 3.08
5140 5922 1.276622 AGGGAAGTTATGCGTCAGGT 58.723 50.000 0.00 0.00 0.00 4.00
5141 5923 2.403252 AAGGGAAGTTATGCGTCAGG 57.597 50.000 0.00 0.00 0.00 3.86
5142 5924 3.127030 GGAAAAGGGAAGTTATGCGTCAG 59.873 47.826 0.00 0.00 0.00 3.51
5143 5925 3.078837 GGAAAAGGGAAGTTATGCGTCA 58.921 45.455 0.00 0.00 0.00 4.35
5144 5926 3.078837 TGGAAAAGGGAAGTTATGCGTC 58.921 45.455 0.00 0.00 0.00 5.19
5145 5927 3.149005 TGGAAAAGGGAAGTTATGCGT 57.851 42.857 0.00 0.00 0.00 5.24
5146 5928 3.947834 AGATGGAAAAGGGAAGTTATGCG 59.052 43.478 0.00 0.00 0.00 4.73
5162 5944 7.345691 TCAGGTGATAAAGCATAAAAGATGGA 58.654 34.615 0.00 0.00 0.00 3.41
5521 6303 2.095919 GGCAAAATTAAGACGCGACAGT 60.096 45.455 15.93 0.78 0.00 3.55
5541 6324 1.614413 GATACGTTCCAGGAGCCTAGG 59.386 57.143 3.67 3.67 0.00 3.02
5584 6367 1.272147 GCAGGGATTTTGTCCTCCTGT 60.272 52.381 9.08 0.00 46.91 4.00
5687 6470 2.151202 TCCTCCACTTTCAATCGTTGC 58.849 47.619 0.00 0.00 0.00 4.17
5689 6472 4.559862 ATCTCCTCCACTTTCAATCGTT 57.440 40.909 0.00 0.00 0.00 3.85
5701 6484 1.281419 TGCCCGTTTAATCTCCTCCA 58.719 50.000 0.00 0.00 0.00 3.86
5731 6514 5.347635 TCGACAGAAAGTTTGATTGTATCCG 59.652 40.000 0.00 0.00 0.00 4.18
5776 6559 1.606313 ATTCAAAGGGGGTGGCACG 60.606 57.895 12.17 0.00 0.00 5.34
5788 6571 8.306038 CAAGTTAGGTTGATTCATCCATTCAAA 58.694 33.333 14.68 0.90 31.66 2.69
5791 6574 7.253422 CACAAGTTAGGTTGATTCATCCATTC 58.747 38.462 14.68 5.62 0.00 2.67
5936 6729 0.654683 GATGCGACATCTCAGTTGGC 59.345 55.000 11.15 0.00 0.00 4.52
5937 6730 0.926155 CGATGCGACATCTCAGTTGG 59.074 55.000 14.85 0.00 0.00 3.77
5970 6763 4.526650 CCCCATATAACATTACCCAAAGGC 59.473 45.833 0.00 0.00 36.11 4.35
5971 6764 5.083821 CCCCCATATAACATTACCCAAAGG 58.916 45.833 0.00 0.00 40.04 3.11
5977 6770 9.369672 TGAAATTTACCCCCATATAACATTACC 57.630 33.333 0.00 0.00 0.00 2.85
5980 6773 8.923270 CAGTGAAATTTACCCCCATATAACATT 58.077 33.333 0.00 0.00 0.00 2.71
5981 6774 8.065007 ACAGTGAAATTTACCCCCATATAACAT 58.935 33.333 0.00 0.00 0.00 2.71
5982 6775 7.415086 ACAGTGAAATTTACCCCCATATAACA 58.585 34.615 0.00 0.00 0.00 2.41
5983 6776 7.778382 AGACAGTGAAATTTACCCCCATATAAC 59.222 37.037 0.00 0.00 0.00 1.89
5984 6777 7.878495 AGACAGTGAAATTTACCCCCATATAA 58.122 34.615 0.00 0.00 0.00 0.98
5985 6778 7.460214 AGACAGTGAAATTTACCCCCATATA 57.540 36.000 0.00 0.00 0.00 0.86
5986 6779 6.341408 AGACAGTGAAATTTACCCCCATAT 57.659 37.500 0.00 0.00 0.00 1.78
5995 6788 8.375506 ACTGAACATCCTAGACAGTGAAATTTA 58.624 33.333 0.00 0.00 39.76 1.40
6000 6793 5.540337 AGAACTGAACATCCTAGACAGTGAA 59.460 40.000 0.00 0.00 40.82 3.18
6002 6795 5.167121 CAGAACTGAACATCCTAGACAGTG 58.833 45.833 0.00 0.00 40.82 3.66
6008 6801 5.039984 CGATCACAGAACTGAACATCCTAG 58.960 45.833 8.87 0.00 0.00 3.02
6012 6805 3.849911 TCCGATCACAGAACTGAACATC 58.150 45.455 8.87 5.81 0.00 3.06
6092 7084 9.651718 GCTATTCTTTCTGATTTTATAACGTGG 57.348 33.333 0.00 0.00 0.00 4.94
6111 7103 8.969260 TCATCAAACATCTACAATGCTATTCT 57.031 30.769 0.00 0.00 0.00 2.40
6113 7105 7.519488 CGCTCATCAAACATCTACAATGCTATT 60.519 37.037 0.00 0.00 0.00 1.73
6118 7110 4.260907 CCCGCTCATCAAACATCTACAATG 60.261 45.833 0.00 0.00 0.00 2.82
6121 7113 2.905075 CCCGCTCATCAAACATCTACA 58.095 47.619 0.00 0.00 0.00 2.74
6134 7126 1.476845 TAAACTGACAGGCCCGCTCA 61.477 55.000 7.51 0.00 0.00 4.26
6188 7182 2.873170 TGCGTTCGCTTTCATAACAG 57.127 45.000 17.63 0.00 0.00 3.16
6200 7194 1.413767 CTCGGACAAGGATGCGTTCG 61.414 60.000 0.00 0.00 0.00 3.95
6201 7195 1.084370 CCTCGGACAAGGATGCGTTC 61.084 60.000 0.00 0.00 38.87 3.95
6203 7197 2.579201 CCTCGGACAAGGATGCGT 59.421 61.111 0.00 0.00 38.87 5.24
6204 7198 2.859273 AAGCCTCGGACAAGGATGCG 62.859 60.000 0.00 0.00 38.87 4.73
6205 7199 0.678048 AAAGCCTCGGACAAGGATGC 60.678 55.000 0.00 0.00 38.87 3.91
6206 7200 1.339055 TGAAAGCCTCGGACAAGGATG 60.339 52.381 0.00 0.00 38.87 3.51
6207 7201 0.984230 TGAAAGCCTCGGACAAGGAT 59.016 50.000 0.00 0.00 38.87 3.24
6208 7202 0.984230 ATGAAAGCCTCGGACAAGGA 59.016 50.000 0.00 0.00 38.87 3.36
6209 7203 1.089920 CATGAAAGCCTCGGACAAGG 58.910 55.000 0.00 0.00 39.62 3.61
6210 7204 1.089920 CCATGAAAGCCTCGGACAAG 58.910 55.000 0.00 0.00 0.00 3.16
6211 7205 0.960364 GCCATGAAAGCCTCGGACAA 60.960 55.000 0.00 0.00 0.00 3.18
6212 7206 1.377202 GCCATGAAAGCCTCGGACA 60.377 57.895 0.00 0.00 0.00 4.02
6220 7214 2.818130 TTCAAAGTGGCCATGAAAGC 57.182 45.000 16.20 0.00 30.60 3.51
6221 7215 3.809279 GGTTTTCAAAGTGGCCATGAAAG 59.191 43.478 24.69 10.05 42.20 2.62
6223 7217 3.037549 AGGTTTTCAAAGTGGCCATGAA 58.962 40.909 9.72 12.97 0.00 2.57
6224 7218 2.676748 AGGTTTTCAAAGTGGCCATGA 58.323 42.857 9.72 5.95 0.00 3.07
6225 7219 3.473923 AAGGTTTTCAAAGTGGCCATG 57.526 42.857 9.72 2.84 0.00 3.66
6226 7220 4.502105 AAAAGGTTTTCAAAGTGGCCAT 57.498 36.364 9.72 0.00 0.00 4.40
6227 7221 3.990959 AAAAGGTTTTCAAAGTGGCCA 57.009 38.095 0.00 0.00 0.00 5.36
6270 7264 5.108027 CGTGCATTTACAGGTTTTAAAGTGC 60.108 40.000 0.00 0.00 0.00 4.40
6272 7266 6.139048 ACGTGCATTTACAGGTTTTAAAGT 57.861 33.333 0.00 0.00 35.21 2.66
6309 7304 5.425577 TTTAACACTGCGTTTATTGCTCA 57.574 34.783 0.00 0.00 39.14 4.26
6317 7312 4.364415 TTGCTCTTTTAACACTGCGTTT 57.636 36.364 0.00 0.00 39.14 3.60
6385 7380 3.058914 CCACTCGAGTCACATGGAAAAAC 60.059 47.826 16.96 0.00 31.69 2.43
6413 7408 5.125417 GGACCATATACATGCACAACAAAGT 59.875 40.000 0.00 0.00 0.00 2.66
6414 7409 5.125257 TGGACCATATACATGCACAACAAAG 59.875 40.000 0.00 0.00 0.00 2.77
6415 7410 5.012893 TGGACCATATACATGCACAACAAA 58.987 37.500 0.00 0.00 0.00 2.83
6419 7414 3.550820 GGTGGACCATATACATGCACAA 58.449 45.455 0.00 0.00 35.64 3.33
6420 7415 2.158682 GGGTGGACCATATACATGCACA 60.159 50.000 0.00 0.00 39.85 4.57
6421 7416 2.158682 TGGGTGGACCATATACATGCAC 60.159 50.000 0.00 0.00 46.80 4.57
6422 7417 2.131023 TGGGTGGACCATATACATGCA 58.869 47.619 0.00 0.00 46.80 3.96
6423 7418 2.949177 TGGGTGGACCATATACATGC 57.051 50.000 0.00 0.00 46.80 4.06
6520 7515 1.159285 CTGCTTCATGGAGCGTTTGA 58.841 50.000 21.10 2.01 45.64 2.69
6542 7537 6.816640 TGAATCTACCTGTAGTAACAACATGC 59.183 38.462 4.36 0.00 34.49 4.06
6557 7552 1.063567 AGTCTCGGCCTGAATCTACCT 60.064 52.381 0.00 0.00 0.00 3.08
6585 7580 6.183360 CCAGTAGCAAGTAGTAACATTTGACG 60.183 42.308 0.00 0.00 0.00 4.35
6658 7655 0.583438 CGCAATCATCCACGGCTAAG 59.417 55.000 0.00 0.00 0.00 2.18


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

AutoCloner maintained by Alex Coulton.