Multiple sequence alignment - TraesCS5A01G502000

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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 TraesCS5A01G502000 chr5A 100.000 3684 0 0 1 3684 667108017 667104334 0.000000e+00 6804.0
1 TraesCS5A01G502000 chr5A 100.000 255 0 0 3891 4145 667104127 667103873 4.850000e-129 472.0
2 TraesCS5A01G502000 chr5A 83.486 109 17 1 738 846 546393933 546393826 2.640000e-17 100.0
3 TraesCS5A01G502000 chr5A 93.103 58 3 1 797 854 454722164 454722220 2.660000e-12 84.2
4 TraesCS5A01G502000 chr4B 93.580 1542 59 11 841 2346 621440985 621439448 0.000000e+00 2263.0
5 TraesCS5A01G502000 chr4B 90.045 1326 64 36 2371 3664 621439455 621438166 0.000000e+00 1655.0
6 TraesCS5A01G502000 chr4B 81.618 544 49 19 2 525 621443039 621442527 1.790000e-108 403.0
7 TraesCS5A01G502000 chr4B 88.936 235 24 2 3907 4139 621438058 621437824 5.240000e-74 289.0
8 TraesCS5A01G502000 chr4B 91.743 109 5 2 547 655 621441146 621441042 9.280000e-32 148.0
9 TraesCS5A01G502000 chr4D 93.101 1551 54 18 841 2346 486775622 486774080 0.000000e+00 2222.0
10 TraesCS5A01G502000 chr4D 88.527 1351 85 38 2371 3684 486774087 486772770 0.000000e+00 1572.0
11 TraesCS5A01G502000 chr4D 82.292 576 37 26 1 546 486776464 486775924 4.920000e-119 438.0
12 TraesCS5A01G502000 chr4D 87.755 196 8 6 554 744 486775800 486775616 9.020000e-52 215.0
13 TraesCS5A01G502000 chr6D 86.239 109 10 3 742 846 319685724 319685617 3.390000e-21 113.0
14 TraesCS5A01G502000 chr1B 85.088 114 10 4 742 849 483294028 483293916 4.380000e-20 110.0
15 TraesCS5A01G502000 chr1D 100.000 49 0 0 801 849 348120818 348120770 1.590000e-14 91.6
16 TraesCS5A01G502000 chr2B 86.420 81 9 2 2720 2799 27736262 27736183 2.050000e-13 87.9
17 TraesCS5A01G502000 chr2B 85.185 81 10 2 2726 2805 727221526 727221447 9.550000e-12 82.4
18 TraesCS5A01G502000 chr2B 97.222 36 1 0 2767 2802 17439052 17439017 1.240000e-05 62.1
19 TraesCS5A01G502000 chr2A 85.714 77 7 3 778 850 718362231 718362307 1.240000e-10 78.7
20 TraesCS5A01G502000 chr5B 83.951 81 9 3 778 854 582585156 582585236 1.600000e-09 75.0
21 TraesCS5A01G502000 chr3B 84.810 79 7 5 778 852 12765784 12765861 1.600000e-09 75.0
22 TraesCS5A01G502000 chr3B 84.810 79 7 5 778 852 13065007 13065084 1.600000e-09 75.0
23 TraesCS5A01G502000 chr3B 84.932 73 7 3 778 846 54325935 54326007 2.070000e-08 71.3
24 TraesCS5A01G502000 chr3B 92.000 50 4 0 803 852 82070293 82070244 2.070000e-08 71.3
25 TraesCS5A01G502000 chr3B 91.667 48 4 0 740 787 190468006 190467959 2.670000e-07 67.6
26 TraesCS5A01G502000 chr6B 95.455 44 2 0 739 782 156263627 156263584 2.070000e-08 71.3
27 TraesCS5A01G502000 chr3A 95.455 44 2 0 739 782 696285059 696285016 2.070000e-08 71.3
28 TraesCS5A01G502000 chr7D 91.837 49 4 0 2753 2801 446996541 446996493 7.440000e-08 69.4
29 TraesCS5A01G502000 chr7B 95.349 43 2 0 740 782 379839635 379839677 7.440000e-08 69.4
30 TraesCS5A01G502000 chr7B 91.837 49 4 0 2753 2801 464343647 464343599 7.440000e-08 69.4
31 TraesCS5A01G502000 chr7A 91.837 49 4 0 2753 2801 498229490 498229442 7.440000e-08 69.4
32 TraesCS5A01G502000 chr4A 91.837 49 4 0 739 787 715876486 715876438 7.440000e-08 69.4
33 TraesCS5A01G502000 chr4A 91.667 48 4 0 740 787 589110538 589110491 2.670000e-07 67.6
34 TraesCS5A01G502000 chr2D 91.111 45 2 2 2762 2805 598728664 598728621 4.470000e-05 60.2


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 TraesCS5A01G502000 chr5A 667103873 667108017 4144 True 3638.00 6804 100.00000 1 4145 2 chr5A.!!$R2 4144
1 TraesCS5A01G502000 chr4B 621437824 621443039 5215 True 951.60 2263 89.18440 2 4139 5 chr4B.!!$R1 4137
2 TraesCS5A01G502000 chr4D 486772770 486776464 3694 True 1111.75 2222 87.91875 1 3684 4 chr4D.!!$R1 3683

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
161 167 0.092351 GTACATACGCACACACGCAC 59.908 55.0 0.00 0.0 36.19 5.34 F
726 2260 0.106519 TCCTAGGGGTGCCTACGTAC 60.107 60.0 9.46 0.0 0.00 3.67 F
2251 3829 0.881118 TCTTGACAAAGCGGCCAATC 59.119 50.0 2.24 0.0 33.06 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2094 3644 1.226211 CGTACGTACCCAGAGCACG 60.226 63.158 19.67 3.67 41.32 5.34 R
2281 3859 0.391528 GGAATTTTGCATGGGCGCTT 60.392 50.000 7.64 0.00 45.35 4.68 R
3934 5543 0.037232 CACGACAGTTCCTCCTTCCC 60.037 60.000 0.00 0.00 0.00 3.97 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
17 18 4.849329 GACCGACCGTAGCGCCAG 62.849 72.222 2.29 0.00 0.00 4.85
19 20 4.849329 CCGACCGTAGCGCCAGTC 62.849 72.222 2.29 5.14 0.00 3.51
20 21 3.812019 CGACCGTAGCGCCAGTCT 61.812 66.667 2.29 0.00 0.00 3.24
42 48 2.573009 TGATTCTCCAATCACTGCCTGA 59.427 45.455 0.00 0.00 42.99 3.86
52 58 1.911357 TCACTGCCTGATCTGGAACAT 59.089 47.619 21.91 0.00 38.20 2.71
53 59 2.014857 CACTGCCTGATCTGGAACATG 58.985 52.381 21.91 7.20 38.20 3.21
54 60 1.632409 ACTGCCTGATCTGGAACATGT 59.368 47.619 21.91 3.63 38.20 3.21
55 61 2.840038 ACTGCCTGATCTGGAACATGTA 59.160 45.455 21.91 0.00 38.20 2.29
71 77 2.202690 TACAAGTCGGCGCCATCG 60.203 61.111 28.98 13.22 39.07 3.84
88 94 2.225382 TCGTCCTCTGGTCCATGTTA 57.775 50.000 0.00 0.00 0.00 2.41
122 128 2.612221 GCCACTTTCAGCGTAACTACCT 60.612 50.000 0.00 0.00 0.00 3.08
123 129 3.367703 GCCACTTTCAGCGTAACTACCTA 60.368 47.826 0.00 0.00 0.00 3.08
124 130 4.171754 CCACTTTCAGCGTAACTACCTAC 58.828 47.826 0.00 0.00 0.00 3.18
146 152 4.033776 GCCAGCCCAGCAGGTACA 62.034 66.667 0.00 0.00 37.53 2.90
147 153 3.001514 CCAGCCCAGCAGGTACAT 58.998 61.111 0.00 0.00 38.26 2.29
152 158 1.520192 CCCAGCAGGTACATACGCA 59.480 57.895 0.00 0.00 0.00 5.24
153 159 0.810031 CCCAGCAGGTACATACGCAC 60.810 60.000 0.00 0.00 0.00 5.34
154 160 0.108377 CCAGCAGGTACATACGCACA 60.108 55.000 0.00 0.00 0.00 4.57
155 161 0.999406 CAGCAGGTACATACGCACAC 59.001 55.000 0.00 0.00 0.00 3.82
156 162 0.606096 AGCAGGTACATACGCACACA 59.394 50.000 0.00 0.00 0.00 3.72
157 163 0.719465 GCAGGTACATACGCACACAC 59.281 55.000 0.00 0.00 0.00 3.82
158 164 0.989164 CAGGTACATACGCACACACG 59.011 55.000 0.00 0.00 39.50 4.49
159 165 0.734942 AGGTACATACGCACACACGC 60.735 55.000 0.00 0.00 36.19 5.34
160 166 1.009903 GGTACATACGCACACACGCA 61.010 55.000 0.00 0.00 36.19 5.24
161 167 0.092351 GTACATACGCACACACGCAC 59.908 55.000 0.00 0.00 36.19 5.34
177 183 1.357258 GCACGCTGACTGACCATCTG 61.357 60.000 0.00 0.00 0.00 2.90
314 337 5.590259 GTGGTGCATATCATTAGTCCAACTT 59.410 40.000 0.00 0.00 0.00 2.66
315 338 6.765989 GTGGTGCATATCATTAGTCCAACTTA 59.234 38.462 0.00 0.00 0.00 2.24
316 339 6.992123 TGGTGCATATCATTAGTCCAACTTAG 59.008 38.462 0.00 0.00 0.00 2.18
317 340 6.073003 GGTGCATATCATTAGTCCAACTTAGC 60.073 42.308 0.00 0.00 0.00 3.09
318 341 6.708054 GTGCATATCATTAGTCCAACTTAGCT 59.292 38.462 0.00 0.00 0.00 3.32
319 342 7.872993 GTGCATATCATTAGTCCAACTTAGCTA 59.127 37.037 0.00 0.00 0.00 3.32
320 343 8.090831 TGCATATCATTAGTCCAACTTAGCTAG 58.909 37.037 0.00 0.00 0.00 3.42
365 388 0.546267 ACACAGGAGACCTCATGCCT 60.546 55.000 11.09 0.00 44.38 4.75
375 398 2.361483 TCATGCCTTGCCACGCAT 60.361 55.556 0.00 0.00 46.47 4.73
380 403 0.679321 TGCCTTGCCACGCATCAATA 60.679 50.000 0.00 0.00 38.76 1.90
415 455 7.128234 TCCACACATGATATCATCTCAAGAA 57.872 36.000 15.49 0.00 33.61 2.52
417 457 8.215736 TCCACACATGATATCATCTCAAGAAAT 58.784 33.333 15.49 0.00 33.61 2.17
418 458 9.498176 CCACACATGATATCATCTCAAGAAATA 57.502 33.333 15.49 0.00 33.61 1.40
429 474 9.739276 ATCATCTCAAGAAATAAAAGGTACACA 57.261 29.630 0.00 0.00 0.00 3.72
451 496 7.765819 ACACATGATACATATTGATATGGGTCG 59.234 37.037 13.83 4.63 43.38 4.79
452 497 7.981225 CACATGATACATATTGATATGGGTCGA 59.019 37.037 13.83 0.00 43.38 4.20
455 500 8.078060 TGATACATATTGATATGGGTCGACAT 57.922 34.615 18.91 5.79 43.38 3.06
456 501 7.981225 TGATACATATTGATATGGGTCGACATG 59.019 37.037 18.91 10.41 43.38 3.21
457 502 6.114187 ACATATTGATATGGGTCGACATGT 57.886 37.500 18.91 11.05 43.38 3.21
505 554 5.981174 ACCTCTCTAGACCTATCTATACGC 58.019 45.833 0.00 0.00 36.81 4.42
511 560 6.096036 TCTAGACCTATCTATACGCACGTAC 58.904 44.000 4.84 0.00 36.81 3.67
512 561 4.635223 AGACCTATCTATACGCACGTACA 58.365 43.478 4.84 0.00 31.46 2.90
513 562 5.243981 AGACCTATCTATACGCACGTACAT 58.756 41.667 4.84 1.34 31.46 2.29
514 563 6.401394 AGACCTATCTATACGCACGTACATA 58.599 40.000 4.84 2.39 31.46 2.29
526 575 3.711086 CACGTACATAGCAGAGATGCTT 58.289 45.455 8.20 0.00 43.52 3.91
527 576 4.793028 GCACGTACATAGCAGAGATGCTTA 60.793 45.833 8.20 0.00 43.52 3.09
528 577 5.465051 CACGTACATAGCAGAGATGCTTAT 58.535 41.667 8.20 0.00 43.52 1.73
529 578 6.612306 CACGTACATAGCAGAGATGCTTATA 58.388 40.000 8.20 0.00 43.52 0.98
533 582 6.907853 ACATAGCAGAGATGCTTATACTGA 57.092 37.500 8.20 0.00 43.52 3.41
538 587 7.537596 AGCAGAGATGCTTATACTGACTTAT 57.462 36.000 0.00 0.00 43.52 1.73
540 589 8.519526 AGCAGAGATGCTTATACTGACTTATAC 58.480 37.037 0.00 0.00 43.52 1.47
541 590 8.519526 GCAGAGATGCTTATACTGACTTATACT 58.480 37.037 0.00 0.00 0.00 2.12
579 2111 3.100817 GTGCTATACTTGTGCATTTGCG 58.899 45.455 0.00 0.00 45.83 4.85
580 2112 3.006247 TGCTATACTTGTGCATTTGCGA 58.994 40.909 0.00 0.00 45.83 5.10
604 2136 1.927838 GCTAAGCTAGTTCCACGAAGC 59.072 52.381 0.00 0.00 33.88 3.86
605 2137 2.417515 GCTAAGCTAGTTCCACGAAGCT 60.418 50.000 0.00 0.00 41.75 3.74
606 2138 3.181489 GCTAAGCTAGTTCCACGAAGCTA 60.181 47.826 7.08 0.00 40.01 3.32
607 2139 3.512033 AAGCTAGTTCCACGAAGCTAG 57.488 47.619 7.08 0.00 40.01 3.42
608 2140 1.562017 GCTAGTTCCACGAAGCTAGC 58.438 55.000 6.62 6.62 46.02 3.42
626 2158 4.504689 GCTAGCTCCTTCCTTCATATGCTT 60.505 45.833 7.70 0.00 0.00 3.91
668 2200 9.852091 ACTACACAAAGTTATACTAGTAGCAAC 57.148 33.333 16.83 16.83 32.98 4.17
719 2253 0.910088 AGTGAGTTCCTAGGGGTGCC 60.910 60.000 9.46 0.00 0.00 5.01
721 2255 0.714180 TGAGTTCCTAGGGGTGCCTA 59.286 55.000 9.46 0.00 0.00 3.93
723 2257 0.686769 AGTTCCTAGGGGTGCCTACG 60.687 60.000 9.46 0.00 0.00 3.51
726 2260 0.106519 TCCTAGGGGTGCCTACGTAC 60.107 60.000 9.46 0.00 0.00 3.67
744 2278 3.257624 CGTACCCTCCAAACTGAGTTACT 59.742 47.826 0.00 0.00 0.00 2.24
745 2279 4.617762 CGTACCCTCCAAACTGAGTTACTC 60.618 50.000 5.27 5.27 0.00 2.59
746 2280 2.638363 ACCCTCCAAACTGAGTTACTCC 59.362 50.000 10.10 0.00 0.00 3.85
748 2282 2.907042 CCTCCAAACTGAGTTACTCCCT 59.093 50.000 10.10 0.00 0.00 4.20
749 2283 3.055747 CCTCCAAACTGAGTTACTCCCTC 60.056 52.174 10.10 0.00 0.00 4.30
750 2284 2.904434 TCCAAACTGAGTTACTCCCTCC 59.096 50.000 10.10 0.00 0.00 4.30
751 2285 2.353803 CCAAACTGAGTTACTCCCTCCG 60.354 54.545 10.10 0.00 0.00 4.63
752 2286 2.299297 CAAACTGAGTTACTCCCTCCGT 59.701 50.000 10.10 0.00 0.00 4.69
753 2287 3.446442 AACTGAGTTACTCCCTCCGTA 57.554 47.619 10.10 0.00 0.00 4.02
754 2288 3.446442 ACTGAGTTACTCCCTCCGTAA 57.554 47.619 10.10 0.00 0.00 3.18
755 2289 3.771216 ACTGAGTTACTCCCTCCGTAAA 58.229 45.455 10.10 0.00 0.00 2.01
756 2290 3.509184 ACTGAGTTACTCCCTCCGTAAAC 59.491 47.826 10.10 0.00 0.00 2.01
757 2291 3.762823 CTGAGTTACTCCCTCCGTAAACT 59.237 47.826 10.10 0.00 0.00 2.66
758 2292 4.922206 TGAGTTACTCCCTCCGTAAACTA 58.078 43.478 10.10 0.00 0.00 2.24
759 2293 5.324409 TGAGTTACTCCCTCCGTAAACTAA 58.676 41.667 10.10 0.00 0.00 2.24
760 2294 5.954150 TGAGTTACTCCCTCCGTAAACTAAT 59.046 40.000 10.10 0.00 0.00 1.73
761 2295 7.118723 TGAGTTACTCCCTCCGTAAACTAATA 58.881 38.462 10.10 0.00 0.00 0.98
762 2296 7.781693 TGAGTTACTCCCTCCGTAAACTAATAT 59.218 37.037 10.10 0.00 0.00 1.28
763 2297 9.289782 GAGTTACTCCCTCCGTAAACTAATATA 57.710 37.037 0.00 0.00 0.00 0.86
764 2298 9.646522 AGTTACTCCCTCCGTAAACTAATATAA 57.353 33.333 0.00 0.00 0.00 0.98
768 2302 9.993454 ACTCCCTCCGTAAACTAATATAAAATC 57.007 33.333 0.00 0.00 0.00 2.17
769 2303 9.136952 CTCCCTCCGTAAACTAATATAAAATCG 57.863 37.037 0.00 0.00 0.00 3.34
770 2304 8.641541 TCCCTCCGTAAACTAATATAAAATCGT 58.358 33.333 0.00 0.00 0.00 3.73
771 2305 9.264719 CCCTCCGTAAACTAATATAAAATCGTT 57.735 33.333 0.00 0.00 0.00 3.85
836 2370 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
837 2371 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
838 2372 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
839 2373 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
840 2374 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
841 2375 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
842 2376 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
843 2377 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
844 2378 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
845 2379 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
846 2380 6.907853 ATATTAGTTTACGGAGGGAGTACC 57.092 41.667 0.00 0.00 40.67 3.34
847 2381 2.610438 AGTTTACGGAGGGAGTACCA 57.390 50.000 0.00 0.00 43.89 3.25
848 2382 2.893424 AGTTTACGGAGGGAGTACCAA 58.107 47.619 0.00 0.00 43.89 3.67
849 2383 3.242011 AGTTTACGGAGGGAGTACCAAA 58.758 45.455 0.00 0.00 43.89 3.28
860 2394 1.886542 GAGTACCAAACAAAGGCTGGG 59.113 52.381 0.00 0.00 34.31 4.45
1132 2679 4.181010 CCATCTCCGGTGGCCAGG 62.181 72.222 5.11 4.79 0.00 4.45
1134 2681 2.040464 ATCTCCGGTGGCCAGGAT 60.040 61.111 13.86 6.71 35.75 3.24
1159 2706 4.980805 TCGCCGCAACCACACTCC 62.981 66.667 0.00 0.00 0.00 3.85
1534 3081 3.583276 CTCAACCACGCCGCCTACA 62.583 63.158 0.00 0.00 0.00 2.74
1566 3113 4.880537 CGCTCCATCGGCTTCGCT 62.881 66.667 0.00 0.00 0.00 4.93
2113 3663 1.515736 GTGCTCTGGGTACGTACGC 60.516 63.158 29.83 29.83 39.33 4.42
2118 3668 3.290567 TGGGTACGTACGCAGCAT 58.709 55.556 33.74 0.00 43.04 3.79
2141 3695 7.306399 GCATGCATATTATCAAGAGCAACAAAC 60.306 37.037 14.21 0.00 35.45 2.93
2220 3798 2.803956 TCACGCCTACTACTTTTGTTGC 59.196 45.455 0.00 0.00 0.00 4.17
2226 3804 5.557388 GCCTACTACTTTTGTTGCGATAAC 58.443 41.667 0.00 0.00 0.00 1.89
2251 3829 0.881118 TCTTGACAAAGCGGCCAATC 59.119 50.000 2.24 0.00 33.06 2.67
2278 3856 6.647895 ACGTAGCACTTTTAAAAAGCTAGCTA 59.352 34.615 24.15 17.96 38.35 3.32
2279 3857 7.148623 ACGTAGCACTTTTAAAAAGCTAGCTAG 60.149 37.037 24.15 16.84 38.35 3.42
2347 3925 7.042797 AGTTCCGAATCATTTTAATGGATGG 57.957 36.000 2.85 1.52 37.03 3.51
2348 3926 5.452078 TCCGAATCATTTTAATGGATGGC 57.548 39.130 2.85 0.00 37.03 4.40
2349 3927 5.139727 TCCGAATCATTTTAATGGATGGCT 58.860 37.500 2.85 0.00 37.03 4.75
2350 3928 6.303054 TCCGAATCATTTTAATGGATGGCTA 58.697 36.000 2.85 0.00 37.03 3.93
2351 3929 6.430925 TCCGAATCATTTTAATGGATGGCTAG 59.569 38.462 2.85 0.00 37.03 3.42
2352 3930 6.207417 CCGAATCATTTTAATGGATGGCTAGT 59.793 38.462 2.85 0.00 37.03 2.57
2353 3931 7.390440 CCGAATCATTTTAATGGATGGCTAGTA 59.610 37.037 2.85 0.00 37.03 1.82
2354 3932 8.446273 CGAATCATTTTAATGGATGGCTAGTAG 58.554 37.037 2.85 0.00 37.03 2.57
2355 3933 9.289782 GAATCATTTTAATGGATGGCTAGTAGT 57.710 33.333 0.00 0.00 37.03 2.73
2356 3934 8.854614 ATCATTTTAATGGATGGCTAGTAGTC 57.145 34.615 0.00 0.00 37.03 2.59
2357 3935 7.801104 TCATTTTAATGGATGGCTAGTAGTCA 58.199 34.615 6.97 6.97 37.03 3.41
2358 3936 7.933577 TCATTTTAATGGATGGCTAGTAGTCAG 59.066 37.037 10.75 0.00 33.24 3.51
2359 3937 6.808321 TTTAATGGATGGCTAGTAGTCAGT 57.192 37.500 10.75 0.00 30.91 3.41
2360 3938 6.808321 TTAATGGATGGCTAGTAGTCAGTT 57.192 37.500 10.75 5.40 30.91 3.16
2361 3939 7.907841 TTAATGGATGGCTAGTAGTCAGTTA 57.092 36.000 10.75 4.53 30.91 2.24
2362 3940 5.793030 ATGGATGGCTAGTAGTCAGTTAC 57.207 43.478 10.75 0.00 30.91 2.50
2363 3941 4.868268 TGGATGGCTAGTAGTCAGTTACT 58.132 43.478 10.75 0.00 42.62 2.24
2364 3942 6.009908 TGGATGGCTAGTAGTCAGTTACTA 57.990 41.667 10.75 0.00 39.80 1.82
2679 4260 0.854853 CGATCACCGACACGTACGTC 60.855 60.000 19.94 7.54 41.76 4.34
3003 4584 2.125952 CTGTCGTGCGAGATGGCA 60.126 61.111 0.00 0.00 41.45 4.92
3049 4630 3.474570 GGAGGTGCTCCGCCTGAT 61.475 66.667 19.13 0.00 45.19 2.90
3050 4631 2.202987 GAGGTGCTCCGCCTGATG 60.203 66.667 1.45 0.00 45.19 3.07
3052 4633 2.821366 GGTGCTCCGCCTGATGTG 60.821 66.667 0.00 0.00 0.00 3.21
3071 4652 1.228245 GCTCTGGCCACAGGTTTGA 60.228 57.895 10.31 0.00 44.99 2.69
3072 4653 0.610232 GCTCTGGCCACAGGTTTGAT 60.610 55.000 10.31 0.00 44.99 2.57
3073 4654 1.457346 CTCTGGCCACAGGTTTGATC 58.543 55.000 0.00 0.00 44.99 2.92
3075 4656 1.303236 TGGCCACAGGTTTGATCGG 60.303 57.895 0.00 0.00 0.00 4.18
3077 4658 2.700773 GCCACAGGTTTGATCGGCC 61.701 63.158 0.00 0.00 34.09 6.13
3078 4659 1.002134 CCACAGGTTTGATCGGCCT 60.002 57.895 0.00 0.00 0.00 5.19
3079 4660 1.026718 CCACAGGTTTGATCGGCCTC 61.027 60.000 0.00 0.00 0.00 4.70
3080 4661 1.079127 ACAGGTTTGATCGGCCTCG 60.079 57.895 0.00 0.00 37.82 4.63
3081 4662 2.125106 AGGTTTGATCGGCCTCGC 60.125 61.111 0.00 0.00 36.13 5.03
3082 4663 3.202706 GGTTTGATCGGCCTCGCC 61.203 66.667 0.00 0.00 46.75 5.54
3093 4674 4.435436 CCTCGCCGTGTGCTGCTA 62.435 66.667 0.00 0.00 38.05 3.49
3096 4677 2.180769 CGCCGTGTGCTGCTAGTA 59.819 61.111 0.00 0.00 38.05 1.82
3097 4678 1.874019 CGCCGTGTGCTGCTAGTAG 60.874 63.158 3.05 3.05 38.05 2.57
3098 4679 1.215647 GCCGTGTGCTGCTAGTAGT 59.784 57.895 9.73 0.00 36.87 2.73
3100 4681 1.939838 GCCGTGTGCTGCTAGTAGTTT 60.940 52.381 9.73 0.00 36.87 2.66
3103 4684 2.917971 CGTGTGCTGCTAGTAGTTTCTC 59.082 50.000 9.73 1.63 0.00 2.87
3104 4685 2.917971 GTGTGCTGCTAGTAGTTTCTCG 59.082 50.000 9.73 0.00 0.00 4.04
3105 4686 2.557056 TGTGCTGCTAGTAGTTTCTCGT 59.443 45.455 9.73 0.00 0.00 4.18
3106 4687 3.754850 TGTGCTGCTAGTAGTTTCTCGTA 59.245 43.478 9.73 0.00 0.00 3.43
3107 4688 4.142665 TGTGCTGCTAGTAGTTTCTCGTAG 60.143 45.833 9.73 0.00 0.00 3.51
3108 4689 4.008330 TGCTGCTAGTAGTTTCTCGTAGT 58.992 43.478 9.73 0.00 0.00 2.73
3110 4691 4.496175 GCTGCTAGTAGTTTCTCGTAGTCC 60.496 50.000 9.73 0.00 0.00 3.85
3111 4692 3.944015 TGCTAGTAGTTTCTCGTAGTCCC 59.056 47.826 0.00 0.00 0.00 4.46
3112 4693 3.002144 GCTAGTAGTTTCTCGTAGTCCCG 59.998 52.174 0.00 0.00 0.00 5.14
3113 4694 3.064900 AGTAGTTTCTCGTAGTCCCGT 57.935 47.619 0.00 0.00 0.00 5.28
3114 4695 2.746362 AGTAGTTTCTCGTAGTCCCGTG 59.254 50.000 0.00 0.00 0.00 4.94
3115 4696 1.901591 AGTTTCTCGTAGTCCCGTGA 58.098 50.000 0.00 0.00 0.00 4.35
3158 4747 3.886123 AGTGAATAATTAAGCTGCCGGT 58.114 40.909 1.90 0.00 0.00 5.28
3178 4767 0.247379 GTAAAATGTACGTGCGCCGG 60.247 55.000 19.73 0.00 42.24 6.13
3194 4783 4.486503 GGGCCCAGCTCAGCTCAG 62.487 72.222 19.95 0.00 36.40 3.35
3195 4784 3.715097 GGCCCAGCTCAGCTCAGT 61.715 66.667 0.00 0.00 36.40 3.41
3196 4785 2.436292 GCCCAGCTCAGCTCAGTG 60.436 66.667 0.00 0.00 36.40 3.66
3197 4786 3.067091 CCCAGCTCAGCTCAGTGT 58.933 61.111 0.00 0.00 36.40 3.55
3198 4787 1.374190 CCCAGCTCAGCTCAGTGTT 59.626 57.895 0.00 0.00 36.40 3.32
3199 4788 0.250640 CCCAGCTCAGCTCAGTGTTT 60.251 55.000 0.00 0.00 36.40 2.83
3200 4789 0.873054 CCAGCTCAGCTCAGTGTTTG 59.127 55.000 0.00 0.00 36.40 2.93
3201 4790 0.873054 CAGCTCAGCTCAGTGTTTGG 59.127 55.000 0.00 0.00 36.40 3.28
3202 4791 0.471617 AGCTCAGCTCAGTGTTTGGT 59.528 50.000 0.00 0.00 30.62 3.67
3203 4792 1.133976 AGCTCAGCTCAGTGTTTGGTT 60.134 47.619 0.00 0.00 30.62 3.67
3204 4793 1.265365 GCTCAGCTCAGTGTTTGGTTC 59.735 52.381 0.00 0.00 0.00 3.62
3205 4794 2.564771 CTCAGCTCAGTGTTTGGTTCA 58.435 47.619 0.00 0.00 0.00 3.18
3221 4810 7.610305 TGTTTGGTTCAGAGTTTCTTTCTAACT 59.390 33.333 0.00 0.00 38.49 2.24
3232 4821 7.697691 AGTTTCTTTCTAACTTGTGTGATGTG 58.302 34.615 0.00 0.00 32.06 3.21
3233 4822 7.552687 AGTTTCTTTCTAACTTGTGTGATGTGA 59.447 33.333 0.00 0.00 32.06 3.58
3234 4823 8.345565 GTTTCTTTCTAACTTGTGTGATGTGAT 58.654 33.333 0.00 0.00 0.00 3.06
3235 4824 7.425577 TCTTTCTAACTTGTGTGATGTGATG 57.574 36.000 0.00 0.00 0.00 3.07
3236 4825 6.992123 TCTTTCTAACTTGTGTGATGTGATGT 59.008 34.615 0.00 0.00 0.00 3.06
3237 4826 6.544038 TTCTAACTTGTGTGATGTGATGTG 57.456 37.500 0.00 0.00 0.00 3.21
3238 4827 5.610398 TCTAACTTGTGTGATGTGATGTGT 58.390 37.500 0.00 0.00 0.00 3.72
3239 4828 6.754193 TCTAACTTGTGTGATGTGATGTGTA 58.246 36.000 0.00 0.00 0.00 2.90
3250 4839 7.224557 TGTGATGTGATGTGTATGCTATGTAAC 59.775 37.037 0.00 0.00 0.00 2.50
3366 4971 3.003275 ACCGTTGCTTGTCATGTGTAAAG 59.997 43.478 0.00 0.00 0.00 1.85
3399 5004 2.966309 GCTTTTGGGTCGCACTCCG 61.966 63.158 0.00 0.00 38.61 4.63
3408 5013 4.662961 CGCACTCCGACCACAGCA 62.663 66.667 0.00 0.00 40.02 4.41
3409 5014 2.280797 GCACTCCGACCACAGCAA 60.281 61.111 0.00 0.00 0.00 3.91
3419 5024 3.249917 CGACCACAGCAAAACAGTTTTT 58.750 40.909 8.65 0.00 35.15 1.94
3473 5079 1.963515 GGCAGAGTTTTCATGGTTGGT 59.036 47.619 0.00 0.00 0.00 3.67
3477 5083 4.875536 GCAGAGTTTTCATGGTTGGTTTTT 59.124 37.500 0.00 0.00 0.00 1.94
3562 5171 2.000701 TGGGGACGGCATGAGGAAT 61.001 57.895 0.00 0.00 0.00 3.01
3639 5248 0.933509 GCGAGTTCGACACTTGACGT 60.934 55.000 15.14 0.00 39.12 4.34
3646 5255 1.069090 GACACTTGACGTGAGGGCA 59.931 57.895 0.00 0.00 46.81 5.36
3653 5262 4.316823 ACGTGAGGGCAGGGAGGA 62.317 66.667 0.00 0.00 34.31 3.71
3660 5269 3.086600 GGCAGGGAGGAGAGGTGG 61.087 72.222 0.00 0.00 0.00 4.61
3664 5273 3.695825 GGGAGGAGAGGTGGGGGA 61.696 72.222 0.00 0.00 0.00 4.81
3665 5274 2.365768 GGAGGAGAGGTGGGGGAC 60.366 72.222 0.00 0.00 0.00 4.46
3667 5276 4.400251 AGGAGAGGTGGGGGACGG 62.400 72.222 0.00 0.00 0.00 4.79
3670 5279 4.250170 AGAGGTGGGGGACGGTGT 62.250 66.667 0.00 0.00 0.00 4.16
3912 5521 1.048724 CGACCATAGAGGGGAAGGCA 61.049 60.000 0.00 0.00 43.89 4.75
3915 5524 0.695803 CCATAGAGGGGAAGGCAGGT 60.696 60.000 0.00 0.00 0.00 4.00
3926 5535 3.499737 GGCAGGTGATTGGTCGCG 61.500 66.667 0.00 0.00 35.69 5.87
3927 5536 2.742372 GCAGGTGATTGGTCGCGT 60.742 61.111 5.77 0.00 35.69 6.01
3934 5543 2.047274 ATTGGTCGCGTGTGAGGG 60.047 61.111 5.77 0.00 0.00 4.30
3943 5554 2.660064 CGTGTGAGGGGGAAGGAGG 61.660 68.421 0.00 0.00 0.00 4.30
3951 5562 1.597461 GGGGAAGGAGGAACTGTCG 59.403 63.158 0.00 0.00 41.55 4.35
3952 5563 1.192803 GGGGAAGGAGGAACTGTCGT 61.193 60.000 0.00 0.00 41.55 4.34
3965 5576 0.320771 CTGTCGTGGGTGGAGAAAGG 60.321 60.000 0.00 0.00 0.00 3.11
4005 5616 2.577644 CAATGCACGCACGATGGC 60.578 61.111 0.00 0.00 0.00 4.40
4031 5642 2.103094 GGATGTTGATGGACCGATGAGA 59.897 50.000 0.00 0.00 0.00 3.27
4047 5658 1.214175 TGAGAGTGGTCTTTTTGGGCA 59.786 47.619 0.00 0.00 30.97 5.36
4104 5715 6.267699 CCCCATTTAGAAAAGGAACTCAAACT 59.732 38.462 0.00 0.00 38.49 2.66
4115 5726 6.225981 AGGAACTCAAACTTGCTCAAAAAT 57.774 33.333 0.00 0.00 0.00 1.82
4116 5727 6.044682 AGGAACTCAAACTTGCTCAAAAATG 58.955 36.000 0.00 0.00 0.00 2.32
4129 5740 0.755686 AAAAATGAGTTTGGGCGGCA 59.244 45.000 12.47 0.00 0.00 5.69
4136 5747 4.794648 TTTGGGCGGCAGATCGGG 62.795 66.667 12.47 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 48 3.861840 CCGACTTGTACATGTTCCAGAT 58.138 45.455 14.90 0.00 0.00 2.90
52 58 1.447140 GATGGCGCCGACTTGTACA 60.447 57.895 23.90 0.00 0.00 2.90
53 59 2.514013 CGATGGCGCCGACTTGTAC 61.514 63.158 23.90 5.50 0.00 2.90
54 60 2.202690 CGATGGCGCCGACTTGTA 60.203 61.111 23.90 1.41 0.00 2.41
55 61 4.373116 ACGATGGCGCCGACTTGT 62.373 61.111 23.90 15.76 42.48 3.16
71 77 5.105756 CCATTTTTAACATGGACCAGAGGAC 60.106 44.000 4.21 0.00 43.70 3.85
75 81 6.553100 AGAAACCATTTTTAACATGGACCAGA 59.447 34.615 16.06 0.00 43.70 3.86
76 82 6.646240 CAGAAACCATTTTTAACATGGACCAG 59.354 38.462 16.06 0.00 43.70 4.00
77 83 6.520272 CAGAAACCATTTTTAACATGGACCA 58.480 36.000 16.06 0.00 43.70 4.02
88 94 5.096443 TGAAAGTGGCAGAAACCATTTTT 57.904 34.783 5.65 1.70 46.19 1.94
122 128 3.402681 GCTGGGCTGGCTGGAGTA 61.403 66.667 0.00 0.00 0.00 2.59
124 130 4.798344 CTGCTGGGCTGGCTGGAG 62.798 72.222 0.00 1.75 0.00 3.86
146 152 3.773630 GCGTGCGTGTGTGCGTAT 61.774 61.111 0.00 0.00 37.81 3.06
147 153 4.934942 AGCGTGCGTGTGTGCGTA 62.935 61.111 0.00 0.00 37.81 4.42
152 158 2.961721 CAGTCAGCGTGCGTGTGT 60.962 61.111 0.00 0.00 0.00 3.72
153 159 2.658268 TCAGTCAGCGTGCGTGTG 60.658 61.111 0.00 0.00 0.00 3.82
154 160 2.658593 GTCAGTCAGCGTGCGTGT 60.659 61.111 0.00 0.00 0.00 4.49
155 161 3.406361 GGTCAGTCAGCGTGCGTG 61.406 66.667 0.00 0.00 0.00 5.34
156 162 3.226429 ATGGTCAGTCAGCGTGCGT 62.226 57.895 0.00 0.00 0.00 5.24
157 163 2.433145 ATGGTCAGTCAGCGTGCG 60.433 61.111 0.00 0.00 0.00 5.34
158 164 1.079543 AGATGGTCAGTCAGCGTGC 60.080 57.895 0.00 0.00 0.00 5.34
159 165 0.738762 CCAGATGGTCAGTCAGCGTG 60.739 60.000 0.00 0.00 0.00 5.34
160 166 0.900182 TCCAGATGGTCAGTCAGCGT 60.900 55.000 0.00 0.00 36.34 5.07
161 167 0.463204 ATCCAGATGGTCAGTCAGCG 59.537 55.000 0.00 0.00 36.34 5.18
317 340 2.213513 GGGGAGCCTGGCTAGCTAG 61.214 68.421 23.44 20.50 41.75 3.42
318 341 1.369061 TAGGGGAGCCTGGCTAGCTA 61.369 60.000 23.44 7.83 41.75 3.32
319 342 2.716203 TAGGGGAGCCTGGCTAGCT 61.716 63.158 23.44 0.00 45.23 3.32
320 343 2.122813 TAGGGGAGCCTGGCTAGC 60.123 66.667 23.44 10.25 39.88 3.42
365 388 2.094338 TGCAATTATTGATGCGTGGCAA 60.094 40.909 9.36 0.00 45.47 4.52
375 398 6.094193 TGTGTGGATTTGTGCAATTATTGA 57.906 33.333 9.36 0.00 0.00 2.57
380 403 4.603989 TCATGTGTGGATTTGTGCAATT 57.396 36.364 0.00 0.00 0.00 2.32
422 462 9.330063 CCCATATCAATATGTATCATGTGTACC 57.670 37.037 8.73 0.00 38.73 3.34
425 465 7.765819 CGACCCATATCAATATGTATCATGTGT 59.234 37.037 8.73 0.00 38.73 3.72
426 466 7.981225 TCGACCCATATCAATATGTATCATGTG 59.019 37.037 8.73 0.00 38.73 3.21
429 474 8.078060 TGTCGACCCATATCAATATGTATCAT 57.922 34.615 14.12 0.00 38.73 2.45
435 480 7.765819 ACATACATGTCGACCCATATCAATATG 59.234 37.037 14.12 8.26 35.87 1.78
447 492 3.241868 GCGTGTTAACATACATGTCGACC 60.242 47.826 14.12 0.00 40.80 4.79
451 496 3.482923 CGGTGCGTGTTAACATACATGTC 60.483 47.826 12.26 6.63 40.80 3.06
452 497 2.413796 CGGTGCGTGTTAACATACATGT 59.586 45.455 12.26 2.69 44.20 3.21
455 500 2.435533 TCGGTGCGTGTTAACATACA 57.564 45.000 12.26 10.28 0.00 2.29
456 501 2.035176 CGATCGGTGCGTGTTAACATAC 60.035 50.000 12.26 11.11 0.00 2.39
457 502 2.159407 TCGATCGGTGCGTGTTAACATA 60.159 45.455 16.41 0.00 0.00 2.29
561 2090 5.030295 CCTTTCGCAAATGCACAAGTATAG 58.970 41.667 6.18 0.00 42.21 1.31
568 2097 1.242989 TAGCCTTTCGCAAATGCACA 58.757 45.000 6.18 0.00 42.21 4.57
579 2111 2.930682 CGTGGAACTAGCTTAGCCTTTC 59.069 50.000 0.00 1.03 31.75 2.62
580 2112 2.565834 TCGTGGAACTAGCTTAGCCTTT 59.434 45.455 0.00 0.00 31.75 3.11
604 2136 4.888326 AGCATATGAAGGAAGGAGCTAG 57.112 45.455 6.97 0.00 0.00 3.42
605 2137 4.744867 GCAAGCATATGAAGGAAGGAGCTA 60.745 45.833 6.97 0.00 0.00 3.32
606 2138 3.818180 CAAGCATATGAAGGAAGGAGCT 58.182 45.455 6.97 0.00 0.00 4.09
607 2139 2.292845 GCAAGCATATGAAGGAAGGAGC 59.707 50.000 6.97 0.00 0.00 4.70
608 2140 3.548770 TGCAAGCATATGAAGGAAGGAG 58.451 45.455 6.97 0.00 0.00 3.69
626 2158 9.462174 CTTTGTGTAGTTAATTCATTCTTTGCA 57.538 29.630 0.00 0.00 0.00 4.08
667 2199 7.139287 TGATCTACTACTCCTACTTGCTAGT 57.861 40.000 6.00 6.00 38.44 2.57
668 2200 9.899661 ATATGATCTACTACTCCTACTTGCTAG 57.100 37.037 0.00 0.00 0.00 3.42
673 2205 9.332502 CGCATATATGATCTACTACTCCTACTT 57.667 37.037 17.10 0.00 0.00 2.24
719 2253 2.824341 ACTCAGTTTGGAGGGTACGTAG 59.176 50.000 0.00 0.00 39.27 3.51
721 2255 1.713297 ACTCAGTTTGGAGGGTACGT 58.287 50.000 0.00 0.00 39.27 3.57
723 2257 4.322574 GGAGTAACTCAGTTTGGAGGGTAC 60.323 50.000 0.00 0.00 39.27 3.34
726 2260 2.027100 GGGAGTAACTCAGTTTGGAGGG 60.027 54.545 0.00 0.00 39.27 4.30
744 2278 8.641541 ACGATTTTATATTAGTTTACGGAGGGA 58.358 33.333 0.00 0.00 0.00 4.20
745 2279 8.822652 ACGATTTTATATTAGTTTACGGAGGG 57.177 34.615 0.00 0.00 0.00 4.30
810 2344 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
811 2345 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
812 2346 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
813 2347 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
814 2348 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
815 2349 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
816 2350 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
817 2351 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
818 2352 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
819 2353 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
820 2354 8.518702 GGTACTCCCTCCGTAAACTAATATAAG 58.481 40.741 0.00 0.00 0.00 1.73
821 2355 8.004215 TGGTACTCCCTCCGTAAACTAATATAA 58.996 37.037 0.00 0.00 0.00 0.98
822 2356 7.526041 TGGTACTCCCTCCGTAAACTAATATA 58.474 38.462 0.00 0.00 0.00 0.86
823 2357 6.376248 TGGTACTCCCTCCGTAAACTAATAT 58.624 40.000 0.00 0.00 0.00 1.28
824 2358 5.765510 TGGTACTCCCTCCGTAAACTAATA 58.234 41.667 0.00 0.00 0.00 0.98
825 2359 4.613437 TGGTACTCCCTCCGTAAACTAAT 58.387 43.478 0.00 0.00 0.00 1.73
826 2360 4.046286 TGGTACTCCCTCCGTAAACTAA 57.954 45.455 0.00 0.00 0.00 2.24
827 2361 3.737559 TGGTACTCCCTCCGTAAACTA 57.262 47.619 0.00 0.00 0.00 2.24
828 2362 2.610438 TGGTACTCCCTCCGTAAACT 57.390 50.000 0.00 0.00 0.00 2.66
829 2363 3.244181 TGTTTGGTACTCCCTCCGTAAAC 60.244 47.826 0.00 0.00 0.00 2.01
830 2364 2.971330 TGTTTGGTACTCCCTCCGTAAA 59.029 45.455 0.00 0.00 0.00 2.01
831 2365 2.607499 TGTTTGGTACTCCCTCCGTAA 58.393 47.619 0.00 0.00 0.00 3.18
832 2366 2.307496 TGTTTGGTACTCCCTCCGTA 57.693 50.000 0.00 0.00 0.00 4.02
833 2367 1.426751 TTGTTTGGTACTCCCTCCGT 58.573 50.000 0.00 0.00 0.00 4.69
834 2368 2.423577 CTTTGTTTGGTACTCCCTCCG 58.576 52.381 0.00 0.00 0.00 4.63
835 2369 2.791655 CCTTTGTTTGGTACTCCCTCC 58.208 52.381 0.00 0.00 0.00 4.30
836 2370 2.160205 GCCTTTGTTTGGTACTCCCTC 58.840 52.381 0.00 0.00 0.00 4.30
837 2371 1.780919 AGCCTTTGTTTGGTACTCCCT 59.219 47.619 0.00 0.00 0.00 4.20
838 2372 1.886542 CAGCCTTTGTTTGGTACTCCC 59.113 52.381 0.00 0.00 0.00 4.30
839 2373 1.886542 CCAGCCTTTGTTTGGTACTCC 59.113 52.381 0.00 0.00 0.00 3.85
840 2374 1.886542 CCCAGCCTTTGTTTGGTACTC 59.113 52.381 0.00 0.00 0.00 2.59
841 2375 1.995376 CCCAGCCTTTGTTTGGTACT 58.005 50.000 0.00 0.00 0.00 2.73
842 2376 0.317160 GCCCAGCCTTTGTTTGGTAC 59.683 55.000 0.00 0.00 0.00 3.34
843 2377 1.175983 CGCCCAGCCTTTGTTTGGTA 61.176 55.000 0.00 0.00 0.00 3.25
844 2378 2.498056 CGCCCAGCCTTTGTTTGGT 61.498 57.895 0.00 0.00 0.00 3.67
845 2379 2.339712 CGCCCAGCCTTTGTTTGG 59.660 61.111 0.00 0.00 0.00 3.28
846 2380 2.339712 CCGCCCAGCCTTTGTTTG 59.660 61.111 0.00 0.00 0.00 2.93
847 2381 3.615709 GCCGCCCAGCCTTTGTTT 61.616 61.111 0.00 0.00 0.00 2.83
860 2394 3.431725 CTCTGGTTTTCCCGCCGC 61.432 66.667 0.00 0.00 39.73 6.53
890 2424 4.097418 ACTAGAGAATTGCACTAGTGGGT 58.903 43.478 23.95 0.00 45.45 4.51
967 2501 2.509336 AGCGAAGATTCACCGGCG 60.509 61.111 0.00 0.00 0.00 6.46
1101 2648 4.115199 ATGGCCGGGAGCAAGGTC 62.115 66.667 2.18 0.00 46.50 3.85
1142 2689 4.980805 GGAGTGTGGTTGCGGCGA 62.981 66.667 12.98 0.00 0.00 5.54
1534 3081 2.045926 GCGGTGGAACATGAGGCT 60.046 61.111 0.00 0.00 44.52 4.58
1566 3113 3.390521 CAGTAGGGCCCGTGCTCA 61.391 66.667 18.44 0.00 41.98 4.26
2094 3644 1.226211 CGTACGTACCCAGAGCACG 60.226 63.158 19.67 3.67 41.32 5.34
2113 3663 5.622770 TGCTCTTGATAATATGCATGCTG 57.377 39.130 20.33 0.00 0.00 4.41
2115 3665 5.765176 TGTTGCTCTTGATAATATGCATGC 58.235 37.500 11.82 11.82 0.00 4.06
2116 3666 7.703197 TGTTTGTTGCTCTTGATAATATGCATG 59.297 33.333 10.16 0.00 0.00 4.06
2117 3667 7.703621 GTGTTTGTTGCTCTTGATAATATGCAT 59.296 33.333 3.79 3.79 0.00 3.96
2118 3668 7.028962 GTGTTTGTTGCTCTTGATAATATGCA 58.971 34.615 0.00 0.00 0.00 3.96
2125 3679 6.449635 AAGTTGTGTTTGTTGCTCTTGATA 57.550 33.333 0.00 0.00 0.00 2.15
2130 3684 5.405269 GTGAAAAAGTTGTGTTTGTTGCTCT 59.595 36.000 0.00 0.00 0.00 4.09
2141 3695 3.309410 GCCATGTTGGTGAAAAAGTTGTG 59.691 43.478 0.00 0.00 40.46 3.33
2220 3798 6.628856 CCGCTTTGTCAAGATTATTGTTATCG 59.371 38.462 0.00 0.00 30.57 2.92
2226 3804 3.119531 TGGCCGCTTTGTCAAGATTATTG 60.120 43.478 0.00 0.00 30.57 1.90
2251 3829 6.086371 GCTAGCTTTTTAAAAGTGCTACGTTG 59.914 38.462 22.57 17.19 33.70 4.10
2278 3856 2.175035 ATTTTGCATGGGCGCTTGCT 62.175 50.000 32.05 16.30 45.35 3.91
2279 3857 1.300266 AATTTTGCATGGGCGCTTGC 61.300 50.000 28.03 28.03 45.35 4.01
2280 3858 0.722848 GAATTTTGCATGGGCGCTTG 59.277 50.000 7.64 11.77 45.35 4.01
2281 3859 0.391528 GGAATTTTGCATGGGCGCTT 60.392 50.000 7.64 0.00 45.35 4.68
2286 3864 1.676615 GCTGGTGGAATTTTGCATGGG 60.677 52.381 0.00 0.00 0.00 4.00
2357 3935 6.209788 GCTCTATCCATTAGGCAGTAGTAACT 59.790 42.308 0.00 0.00 35.91 2.24
2358 3936 6.015350 TGCTCTATCCATTAGGCAGTAGTAAC 60.015 42.308 0.00 0.00 32.54 2.50
2359 3937 6.015350 GTGCTCTATCCATTAGGCAGTAGTAA 60.015 42.308 0.00 0.00 35.86 2.24
2360 3938 5.477291 GTGCTCTATCCATTAGGCAGTAGTA 59.523 44.000 0.00 0.00 35.86 1.82
2361 3939 4.282195 GTGCTCTATCCATTAGGCAGTAGT 59.718 45.833 0.00 0.00 35.86 2.73
2362 3940 4.526262 AGTGCTCTATCCATTAGGCAGTAG 59.474 45.833 0.00 0.00 36.66 2.57
2363 3941 4.281941 CAGTGCTCTATCCATTAGGCAGTA 59.718 45.833 0.00 0.00 36.47 2.74
2364 3942 3.070734 CAGTGCTCTATCCATTAGGCAGT 59.929 47.826 0.00 0.00 37.83 4.40
2365 3943 3.556633 CCAGTGCTCTATCCATTAGGCAG 60.557 52.174 0.00 0.00 35.86 4.85
2366 3944 2.369860 CCAGTGCTCTATCCATTAGGCA 59.630 50.000 0.00 0.00 34.05 4.75
2367 3945 2.289945 CCCAGTGCTCTATCCATTAGGC 60.290 54.545 0.00 0.00 33.74 3.93
2368 3946 2.975489 ACCCAGTGCTCTATCCATTAGG 59.025 50.000 0.00 0.00 0.00 2.69
2369 3947 3.389329 ACACCCAGTGCTCTATCCATTAG 59.611 47.826 0.00 0.00 36.98 1.73
2370 3948 3.384168 ACACCCAGTGCTCTATCCATTA 58.616 45.455 0.00 0.00 36.98 1.90
2371 3949 2.200081 ACACCCAGTGCTCTATCCATT 58.800 47.619 0.00 0.00 36.98 3.16
2372 3950 1.885049 ACACCCAGTGCTCTATCCAT 58.115 50.000 0.00 0.00 36.98 3.41
2373 3951 2.543037 TACACCCAGTGCTCTATCCA 57.457 50.000 0.00 0.00 36.98 3.41
2374 3952 3.906720 TTTACACCCAGTGCTCTATCC 57.093 47.619 0.00 0.00 36.98 2.59
2586 4167 1.593750 GATCAGCGCCTGCAGGTAG 60.594 63.158 32.81 26.39 46.23 3.18
2955 4536 4.477975 GACAGGTCGACGCCGGAG 62.478 72.222 5.05 3.72 36.24 4.63
3054 4635 1.457346 GATCAAACCTGTGGCCAGAG 58.543 55.000 22.89 22.89 41.50 3.35
3055 4636 0.321564 CGATCAAACCTGTGGCCAGA 60.322 55.000 5.11 2.89 41.50 3.86
3056 4637 1.308069 CCGATCAAACCTGTGGCCAG 61.308 60.000 5.11 0.00 38.50 4.85
3057 4638 1.303236 CCGATCAAACCTGTGGCCA 60.303 57.895 0.00 0.00 0.00 5.36
3060 4641 1.002134 AGGCCGATCAAACCTGTGG 60.002 57.895 0.00 0.00 30.82 4.17
3062 4643 1.079127 CGAGGCCGATCAAACCTGT 60.079 57.895 0.00 0.00 38.22 4.00
3064 4645 2.125106 GCGAGGCCGATCAAACCT 60.125 61.111 0.00 0.00 38.22 3.50
3065 4646 3.202706 GGCGAGGCCGATCAAACC 61.203 66.667 0.00 0.00 39.62 3.27
3080 4661 0.389948 AACTACTAGCAGCACACGGC 60.390 55.000 0.00 0.00 45.30 5.68
3081 4662 1.993370 GAAACTACTAGCAGCACACGG 59.007 52.381 0.00 0.00 0.00 4.94
3082 4663 2.917971 GAGAAACTACTAGCAGCACACG 59.082 50.000 0.00 0.00 0.00 4.49
3083 4664 2.917971 CGAGAAACTACTAGCAGCACAC 59.082 50.000 0.00 0.00 0.00 3.82
3085 4666 3.219052 ACGAGAAACTACTAGCAGCAC 57.781 47.619 0.00 0.00 0.00 4.40
3086 4667 4.008330 ACTACGAGAAACTACTAGCAGCA 58.992 43.478 0.00 0.00 0.00 4.41
3087 4668 4.496175 GGACTACGAGAAACTACTAGCAGC 60.496 50.000 0.00 0.00 0.00 5.25
3089 4670 3.944015 GGGACTACGAGAAACTACTAGCA 59.056 47.826 0.00 0.00 0.00 3.49
3090 4671 3.002144 CGGGACTACGAGAAACTACTAGC 59.998 52.174 0.00 0.00 35.47 3.42
3091 4672 4.033817 CACGGGACTACGAGAAACTACTAG 59.966 50.000 0.00 0.00 37.61 2.57
3092 4673 3.935203 CACGGGACTACGAGAAACTACTA 59.065 47.826 0.00 0.00 37.61 1.82
3093 4674 2.746362 CACGGGACTACGAGAAACTACT 59.254 50.000 0.00 0.00 37.61 2.57
3096 4677 1.538950 GTCACGGGACTACGAGAAACT 59.461 52.381 11.49 0.00 40.99 2.66
3097 4678 1.727213 CGTCACGGGACTACGAGAAAC 60.727 57.143 17.19 0.00 42.05 2.78
3098 4679 0.518636 CGTCACGGGACTACGAGAAA 59.481 55.000 17.19 0.00 42.05 2.52
3100 4681 1.004560 ACGTCACGGGACTACGAGA 60.005 57.895 17.19 0.00 42.05 4.04
3103 4684 3.256936 TCACGTCACGGGACTACG 58.743 61.111 17.19 5.98 42.05 3.51
3112 4693 3.802418 AAGCACGGGGTCACGTCAC 62.802 63.158 0.00 0.00 46.75 3.67
3113 4694 3.509137 GAAGCACGGGGTCACGTCA 62.509 63.158 0.00 0.00 46.75 4.35
3114 4695 2.737376 GAAGCACGGGGTCACGTC 60.737 66.667 0.00 0.00 46.75 4.34
3158 4747 0.439214 CGGCGCACGTACATTTTACA 59.561 50.000 10.83 0.00 37.93 2.41
3178 4767 3.715097 ACTGAGCTGAGCTGGGCC 61.715 66.667 13.71 0.00 39.88 5.80
3181 4770 0.873054 CAAACACTGAGCTGAGCTGG 59.127 55.000 13.71 7.11 39.88 4.85
3190 4779 4.878397 AGAAACTCTGAACCAAACACTGAG 59.122 41.667 0.00 0.00 36.30 3.35
3191 4780 4.843728 AGAAACTCTGAACCAAACACTGA 58.156 39.130 0.00 0.00 0.00 3.41
3192 4781 5.567138 AAGAAACTCTGAACCAAACACTG 57.433 39.130 0.00 0.00 0.00 3.66
3193 4782 5.946377 AGAAAGAAACTCTGAACCAAACACT 59.054 36.000 0.00 0.00 0.00 3.55
3194 4783 6.196079 AGAAAGAAACTCTGAACCAAACAC 57.804 37.500 0.00 0.00 0.00 3.32
3195 4784 7.610305 AGTTAGAAAGAAACTCTGAACCAAACA 59.390 33.333 0.00 0.00 31.56 2.83
3196 4785 7.986562 AGTTAGAAAGAAACTCTGAACCAAAC 58.013 34.615 0.00 0.00 31.56 2.93
3197 4786 8.458843 CAAGTTAGAAAGAAACTCTGAACCAAA 58.541 33.333 0.00 0.00 36.17 3.28
3198 4787 7.610305 ACAAGTTAGAAAGAAACTCTGAACCAA 59.390 33.333 0.00 0.00 36.17 3.67
3199 4788 7.065803 CACAAGTTAGAAAGAAACTCTGAACCA 59.934 37.037 0.00 0.00 36.17 3.67
3200 4789 7.065923 ACACAAGTTAGAAAGAAACTCTGAACC 59.934 37.037 0.00 0.00 36.17 3.62
3201 4790 7.905493 CACACAAGTTAGAAAGAAACTCTGAAC 59.095 37.037 0.00 0.00 36.17 3.18
3202 4791 7.822334 TCACACAAGTTAGAAAGAAACTCTGAA 59.178 33.333 0.00 0.00 36.17 3.02
3203 4792 7.327975 TCACACAAGTTAGAAAGAAACTCTGA 58.672 34.615 0.00 0.00 36.17 3.27
3204 4793 7.539712 TCACACAAGTTAGAAAGAAACTCTG 57.460 36.000 0.00 0.00 36.17 3.35
3205 4794 7.770897 ACATCACACAAGTTAGAAAGAAACTCT 59.229 33.333 0.00 0.00 36.17 3.24
3221 4810 4.325972 AGCATACACATCACATCACACAA 58.674 39.130 0.00 0.00 0.00 3.33
3232 4821 6.210796 TGGTACGTTACATAGCATACACATC 58.789 40.000 0.00 0.00 0.00 3.06
3233 4822 6.151663 TGGTACGTTACATAGCATACACAT 57.848 37.500 0.00 0.00 0.00 3.21
3234 4823 5.579564 TGGTACGTTACATAGCATACACA 57.420 39.130 0.00 0.00 0.00 3.72
3235 4824 6.210796 TGATGGTACGTTACATAGCATACAC 58.789 40.000 3.13 0.00 40.06 2.90
3236 4825 6.394025 TGATGGTACGTTACATAGCATACA 57.606 37.500 3.13 1.98 40.06 2.29
3237 4826 5.862323 CCTGATGGTACGTTACATAGCATAC 59.138 44.000 3.13 0.00 40.06 2.39
3238 4827 5.537295 ACCTGATGGTACGTTACATAGCATA 59.463 40.000 3.13 0.00 46.43 3.14
3239 4828 4.344102 ACCTGATGGTACGTTACATAGCAT 59.656 41.667 2.75 2.75 46.43 3.79
3250 4839 1.272490 ACACTCACACCTGATGGTACG 59.728 52.381 0.00 0.00 46.60 3.67
3366 4971 0.459411 AAAGCCAAAACACGTGCACC 60.459 50.000 17.22 0.00 0.00 5.01
3419 5024 3.534357 TCAGGAGGCCATAAAAACCAA 57.466 42.857 5.01 0.00 0.00 3.67
3432 5037 4.582240 GCCATTCCTTTAAGATTCAGGAGG 59.418 45.833 0.00 0.00 38.00 4.30
3473 5079 9.581289 TTTCCAGGTATCTAATGTTCAGAAAAA 57.419 29.630 0.00 0.00 0.00 1.94
3639 5248 2.366167 CTCTCCTCCCTGCCCTCA 59.634 66.667 0.00 0.00 0.00 3.86
3646 5255 3.700350 CCCCCACCTCTCCTCCCT 61.700 72.222 0.00 0.00 0.00 4.20
3653 5262 4.250170 ACACCGTCCCCCACCTCT 62.250 66.667 0.00 0.00 0.00 3.69
3664 5273 4.057428 GAGCAGCTCCGACACCGT 62.057 66.667 11.84 0.00 0.00 4.83
3665 5274 3.362399 ATGAGCAGCTCCGACACCG 62.362 63.158 20.16 0.00 0.00 4.94
3890 5499 1.620819 CCTTCCCCTCTATGGTCGATG 59.379 57.143 0.00 0.00 0.00 3.84
3891 5500 2.016905 CCTTCCCCTCTATGGTCGAT 57.983 55.000 0.00 0.00 0.00 3.59
3892 5501 0.759436 GCCTTCCCCTCTATGGTCGA 60.759 60.000 0.00 0.00 0.00 4.20
3893 5502 1.048724 TGCCTTCCCCTCTATGGTCG 61.049 60.000 0.00 0.00 0.00 4.79
3894 5503 0.761802 CTGCCTTCCCCTCTATGGTC 59.238 60.000 0.00 0.00 0.00 4.02
3895 5504 0.695803 CCTGCCTTCCCCTCTATGGT 60.696 60.000 0.00 0.00 0.00 3.55
3896 5505 0.695803 ACCTGCCTTCCCCTCTATGG 60.696 60.000 0.00 0.00 0.00 2.74
3897 5506 0.471617 CACCTGCCTTCCCCTCTATG 59.528 60.000 0.00 0.00 0.00 2.23
3898 5507 0.343372 TCACCTGCCTTCCCCTCTAT 59.657 55.000 0.00 0.00 0.00 1.98
3899 5508 0.343372 ATCACCTGCCTTCCCCTCTA 59.657 55.000 0.00 0.00 0.00 2.43
3900 5509 0.551131 AATCACCTGCCTTCCCCTCT 60.551 55.000 0.00 0.00 0.00 3.69
3901 5510 0.394899 CAATCACCTGCCTTCCCCTC 60.395 60.000 0.00 0.00 0.00 4.30
3902 5511 1.693640 CAATCACCTGCCTTCCCCT 59.306 57.895 0.00 0.00 0.00 4.79
3903 5512 1.380380 CCAATCACCTGCCTTCCCC 60.380 63.158 0.00 0.00 0.00 4.81
3904 5513 0.681243 GACCAATCACCTGCCTTCCC 60.681 60.000 0.00 0.00 0.00 3.97
3905 5514 1.026718 CGACCAATCACCTGCCTTCC 61.027 60.000 0.00 0.00 0.00 3.46
3912 5521 1.667830 CACACGCGACCAATCACCT 60.668 57.895 15.93 0.00 0.00 4.00
3915 5524 1.374125 CCTCACACGCGACCAATCA 60.374 57.895 15.93 0.00 0.00 2.57
3926 5535 0.840722 TTCCTCCTTCCCCCTCACAC 60.841 60.000 0.00 0.00 0.00 3.82
3927 5536 0.840722 GTTCCTCCTTCCCCCTCACA 60.841 60.000 0.00 0.00 0.00 3.58
3934 5543 0.037232 CACGACAGTTCCTCCTTCCC 60.037 60.000 0.00 0.00 0.00 3.97
3943 5554 0.391597 TTCTCCACCCACGACAGTTC 59.608 55.000 0.00 0.00 0.00 3.01
3951 5562 2.372172 TCTTTCTCCTTTCTCCACCCAC 59.628 50.000 0.00 0.00 0.00 4.61
3952 5563 2.639839 CTCTTTCTCCTTTCTCCACCCA 59.360 50.000 0.00 0.00 0.00 4.51
3965 5576 6.696411 TGTTCTTCTTCATCCTCTCTTTCTC 58.304 40.000 0.00 0.00 0.00 2.87
4005 5616 1.767759 GGTCCATCAACATCCAAGGG 58.232 55.000 0.00 0.00 0.00 3.95
4007 5618 2.401583 TCGGTCCATCAACATCCAAG 57.598 50.000 0.00 0.00 0.00 3.61
4031 5642 3.037549 TCAAATGCCCAAAAAGACCACT 58.962 40.909 0.00 0.00 0.00 4.00
4039 5650 3.323403 CCTTACTGGTCAAATGCCCAAAA 59.677 43.478 0.00 0.00 0.00 2.44
4075 5686 5.837829 AGTTCCTTTTCTAAATGGGGCATA 58.162 37.500 7.34 0.00 34.81 3.14
4083 5694 8.011844 AGCAAGTTTGAGTTCCTTTTCTAAAT 57.988 30.769 0.00 0.00 0.00 1.40
4086 5697 6.119536 TGAGCAAGTTTGAGTTCCTTTTCTA 58.880 36.000 0.00 0.00 0.00 2.10
4092 5703 5.659440 TTTTTGAGCAAGTTTGAGTTCCT 57.341 34.783 0.00 0.00 0.00 3.36
4104 5715 3.465871 GCCCAAACTCATTTTTGAGCAA 58.534 40.909 2.98 0.00 39.35 3.91
4115 5726 1.377202 GATCTGCCGCCCAAACTCA 60.377 57.895 0.00 0.00 0.00 3.41
4116 5727 2.464459 CGATCTGCCGCCCAAACTC 61.464 63.158 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.