Multiple sequence alignment - TraesCS5B01G190800

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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 TraesCS5B01G190800 chr5B 100.000 5920 0 0 1 5920 344623290 344617371 0.000000e+00 10933.0
1 TraesCS5B01G190800 chr5B 100.000 431 0 0 6273 6703 344617018 344616588 0.000000e+00 797.0
2 TraesCS5B01G190800 chr5B 84.647 241 29 5 2737 2971 212395751 212395513 4.040000e-57 233.0
3 TraesCS5B01G190800 chr5B 88.288 111 9 2 2623 2733 212395768 212395662 5.460000e-26 130.0
4 TraesCS5B01G190800 chr5A 94.415 3635 130 24 2234 5822 395911172 395914779 0.000000e+00 5520.0
5 TraesCS5B01G190800 chr5A 88.142 2201 155 48 78 2200 395908896 395911068 0.000000e+00 2521.0
6 TraesCS5B01G190800 chr5A 87.703 431 18 4 6273 6703 395915017 395915412 2.830000e-128 470.0
7 TraesCS5B01G190800 chr5A 84.404 218 30 3 2757 2971 225599618 225599834 1.890000e-50 211.0
8 TraesCS5B01G190800 chr5D 95.353 2539 97 10 3310 5830 301579384 301576849 0.000000e+00 4015.0
9 TraesCS5B01G190800 chr5D 90.576 1581 76 35 1 1541 301582949 301581402 0.000000e+00 2026.0
10 TraesCS5B01G190800 chr5D 92.721 1099 32 14 2239 3311 301580557 301579481 0.000000e+00 1543.0
11 TraesCS5B01G190800 chr5D 89.222 668 44 15 1547 2202 301581317 301580666 0.000000e+00 809.0
12 TraesCS5B01G190800 chr5D 96.835 316 5 3 6388 6703 301576526 301576216 2.140000e-144 523.0
13 TraesCS5B01G190800 chr5D 84.647 241 29 6 2737 2971 201664562 201664324 4.040000e-57 233.0
14 TraesCS5B01G190800 chr4D 83.613 238 31 5 2740 2971 119237678 119237443 4.070000e-52 217.0
15 TraesCS5B01G190800 chr4D 86.047 86 6 3 1105 1190 459920266 459920187 3.330000e-13 87.9
16 TraesCS5B01G190800 chr7D 82.716 243 35 4 2737 2973 312572707 312572948 6.810000e-50 209.0
17 TraesCS5B01G190800 chr7D 77.994 359 42 14 2623 2978 351590027 351589703 2.470000e-44 191.0
18 TraesCS5B01G190800 chr7D 97.619 42 1 0 1106 1147 461650893 461650934 9.320000e-09 73.1
19 TraesCS5B01G190800 chr7B 82.305 243 36 5 2737 2973 303163508 303163749 3.170000e-48 204.0
20 TraesCS5B01G190800 chr7B 77.684 354 42 15 2623 2971 354251292 354251613 1.480000e-41 182.0
21 TraesCS5B01G190800 chr2D 82.041 245 36 5 2737 2975 633322589 633322831 1.140000e-47 202.0
22 TraesCS5B01G190800 chr2D 85.897 78 5 3 1105 1182 588509294 588509223 2.000000e-10 78.7
23 TraesCS5B01G190800 chr2D 100.000 28 0 0 3213 3240 249879447 249879474 1.200000e-02 52.8
24 TraesCS5B01G190800 chr7A 77.994 359 42 14 2623 2978 398933299 398932975 2.470000e-44 191.0
25 TraesCS5B01G190800 chr7A 87.963 108 10 1 2623 2730 341443367 341443471 2.540000e-24 124.0
26 TraesCS5B01G190800 chr2B 91.892 111 6 1 2623 2733 275317147 275317040 1.160000e-32 152.0
27 TraesCS5B01G190800 chr2B 100.000 28 0 0 3213 3240 338733740 338733767 1.200000e-02 52.8
28 TraesCS5B01G190800 chr3A 85.047 107 13 1 2625 2731 555535193 555535296 9.190000e-19 106.0
29 TraesCS5B01G190800 chr2A 85.542 83 6 3 1105 1187 777559680 777559756 1.550000e-11 82.4
30 TraesCS5B01G190800 chr6B 83.721 86 8 3 1105 1190 377866619 377866540 7.210000e-10 76.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G190800 chr5B 344616588 344623290 6702 True 5865.0 10933 100.000000 1 6703 2 chr5B.!!$R2 6702
1 TraesCS5B01G190800 chr5A 395908896 395915412 6516 False 2837.0 5520 90.086667 78 6703 3 chr5A.!!$F2 6625
2 TraesCS5B01G190800 chr5D 301576216 301582949 6733 True 1783.2 4015 92.941400 1 6703 5 chr5D.!!$R2 6702

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
462 472 0.671781 CTCGGAGTTGAAGCCACCAG 60.672 60.0 0.0 0.0 0.00 4.00 F
1381 1457 0.236711 CACCTGCGTTTCTCAGCTTG 59.763 55.0 0.0 0.0 0.00 4.01 F
1757 1950 0.032540 CAGAGCCCAACAACAAAGCC 59.967 55.0 0.0 0.0 0.00 4.35 F
2608 2880 0.171231 CCGACACTGCTCTCGATTGA 59.829 55.0 0.0 0.0 31.24 2.57 F
4137 4533 0.325296 TGAGACCAAGGGCTATCGGT 60.325 55.0 0.0 0.0 0.00 4.69 F
4787 5189 0.597568 TTTTGCCGTTGCTGATCCAG 59.402 50.0 0.0 0.0 38.71 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1738 1927 0.032540 GGCTTTGTTGTTGGGCTCTG 59.967 55.000 0.00 0.0 0.00 3.35 R
2586 2858 1.658686 ATCGAGAGCAGTGTCGGGTC 61.659 60.000 2.26 0.0 39.87 4.46 R
3434 3829 0.531753 TTGCGCTGAACTGTACTGCA 60.532 50.000 9.73 0.0 33.57 4.41 R
4143 4539 0.179084 TCCCATCTTCATCGGCGAAC 60.179 55.000 15.93 0.0 0.00 3.95 R
5508 5913 0.901124 CTCCAGCTGCTTGTCCTAGT 59.099 55.000 8.66 0.0 0.00 2.57 R
5744 6161 1.143684 AGGCCACATATACCCAAGCAG 59.856 52.381 5.01 0.0 0.00 4.24 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
27 28 3.308904 GGGGGTTTCAATACCTTAGCACT 60.309 47.826 0.00 0.00 38.30 4.40
28 29 3.694566 GGGGTTTCAATACCTTAGCACTG 59.305 47.826 0.00 0.00 38.30 3.66
30 31 5.493809 GGGTTTCAATACCTTAGCACTGTA 58.506 41.667 0.00 0.00 38.30 2.74
39 40 2.290323 CCTTAGCACTGTACCAAGCCTT 60.290 50.000 0.00 0.00 0.00 4.35
109 110 2.939460 AGAATGCGGCATTTAACACC 57.061 45.000 27.24 14.38 33.90 4.16
129 130 4.646945 CACCCTTGTCTCTCTCTTGCTATA 59.353 45.833 0.00 0.00 0.00 1.31
195 196 4.142138 CCACTCTAGATTGGACACCACTAC 60.142 50.000 21.64 0.00 33.41 2.73
278 281 4.261197 GCAATAGCTTCAACTAATTCCGGG 60.261 45.833 0.00 0.00 37.91 5.73
295 298 2.017049 CGGGCAGAGGAAGTATTTTGG 58.983 52.381 0.00 0.00 0.00 3.28
358 361 3.117131 ACTCTTGGTTTTTCAGGGATGGT 60.117 43.478 0.00 0.00 0.00 3.55
359 362 4.105697 ACTCTTGGTTTTTCAGGGATGGTA 59.894 41.667 0.00 0.00 0.00 3.25
360 363 4.662278 TCTTGGTTTTTCAGGGATGGTAG 58.338 43.478 0.00 0.00 0.00 3.18
361 364 4.105697 TCTTGGTTTTTCAGGGATGGTAGT 59.894 41.667 0.00 0.00 0.00 2.73
369 372 8.534496 GTTTTTCAGGGATGGTAGTACTAACTA 58.466 37.037 18.57 6.08 37.15 2.24
378 381 6.906157 TGGTAGTACTAACTAGTTTGCACT 57.094 37.500 21.42 21.42 38.89 4.40
419 425 7.437713 AGAAGTCAATACCTTATCACCATGA 57.562 36.000 0.00 0.00 0.00 3.07
422 428 9.778741 GAAGTCAATACCTTATCACCATGAATA 57.221 33.333 0.00 0.00 0.00 1.75
449 459 1.141881 CGGAACCATGGTCTCGGAG 59.858 63.158 20.07 9.03 0.00 4.63
461 471 1.118965 TCTCGGAGTTGAAGCCACCA 61.119 55.000 4.69 0.00 0.00 4.17
462 472 0.671781 CTCGGAGTTGAAGCCACCAG 60.672 60.000 0.00 0.00 0.00 4.00
474 488 0.691078 GCCACCAGGAGGGAGATACA 60.691 60.000 4.89 0.00 41.15 2.29
490 504 2.485266 TACATCAGCATGGTACGTCG 57.515 50.000 0.00 0.00 36.16 5.12
502 516 1.153842 TACGTCGACATGGCAGCAG 60.154 57.895 17.16 0.00 0.00 4.24
505 519 1.374631 GTCGACATGGCAGCAGACA 60.375 57.895 11.55 0.00 37.03 3.41
690 705 6.959639 TTAAAAAGGCATCATCCATACTCC 57.040 37.500 0.00 0.00 0.00 3.85
692 707 5.912149 AAAAGGCATCATCCATACTCCTA 57.088 39.130 0.00 0.00 0.00 2.94
693 708 5.912149 AAAGGCATCATCCATACTCCTAA 57.088 39.130 0.00 0.00 0.00 2.69
694 709 4.899352 AGGCATCATCCATACTCCTAAC 57.101 45.455 0.00 0.00 0.00 2.34
695 710 3.584848 AGGCATCATCCATACTCCTAACC 59.415 47.826 0.00 0.00 0.00 2.85
696 711 3.584848 GGCATCATCCATACTCCTAACCT 59.415 47.826 0.00 0.00 0.00 3.50
697 712 4.042187 GGCATCATCCATACTCCTAACCTT 59.958 45.833 0.00 0.00 0.00 3.50
698 713 5.248477 GGCATCATCCATACTCCTAACCTTA 59.752 44.000 0.00 0.00 0.00 2.69
699 714 6.402222 GCATCATCCATACTCCTAACCTTAG 58.598 44.000 0.00 0.00 0.00 2.18
812 832 6.706055 GACGACAGTCATTCTTGTAAATGA 57.294 37.500 0.41 0.00 46.32 2.57
973 1003 1.135112 TCAATGCGCACACGATACTCT 60.135 47.619 14.90 0.00 43.93 3.24
1065 1098 1.813337 GAGCGAGCTGGAAGGAAGC 60.813 63.158 0.84 0.00 41.15 3.86
1069 1105 1.296715 GAGCTGGAAGGAAGCGGAA 59.703 57.895 0.00 0.00 45.59 4.30
1210 1278 1.068921 GCCTCTGCTTCCTCGGATC 59.931 63.158 0.00 0.00 33.53 3.36
1287 1360 1.515521 CTGCTTCCGTCCAAACACCC 61.516 60.000 0.00 0.00 0.00 4.61
1324 1397 2.666619 CGGTGAAGAACTTGCAATGCTC 60.667 50.000 6.82 0.00 0.00 4.26
1381 1457 0.236711 CACCTGCGTTTCTCAGCTTG 59.763 55.000 0.00 0.00 0.00 4.01
1382 1458 0.886490 ACCTGCGTTTCTCAGCTTGG 60.886 55.000 0.00 0.00 35.23 3.61
1395 1471 2.158534 TCAGCTTGGGTTTGCCTTCTTA 60.159 45.455 0.00 0.00 34.45 2.10
1423 1505 3.867493 CGCTTGCTCATTCAGATTCAGTA 59.133 43.478 0.00 0.00 0.00 2.74
1424 1506 4.025896 CGCTTGCTCATTCAGATTCAGTAG 60.026 45.833 0.00 0.00 0.00 2.57
1425 1507 5.114780 GCTTGCTCATTCAGATTCAGTAGA 58.885 41.667 0.00 0.00 0.00 2.59
1426 1508 5.759273 GCTTGCTCATTCAGATTCAGTAGAT 59.241 40.000 0.00 0.00 0.00 1.98
1446 1532 3.088789 TGGACTTCTCTCCTAGGACAC 57.911 52.381 7.62 0.00 0.00 3.67
1467 1553 2.178912 TTGGTTCCGGTCATTGTCTC 57.821 50.000 0.00 0.00 0.00 3.36
1468 1554 1.052617 TGGTTCCGGTCATTGTCTCA 58.947 50.000 0.00 0.00 0.00 3.27
1470 1556 2.280628 GGTTCCGGTCATTGTCTCATC 58.719 52.381 0.00 0.00 0.00 2.92
1471 1557 1.927174 GTTCCGGTCATTGTCTCATCG 59.073 52.381 0.00 0.00 0.00 3.84
1472 1558 0.459899 TCCGGTCATTGTCTCATCGG 59.540 55.000 0.00 0.00 37.61 4.18
1473 1559 0.459899 CCGGTCATTGTCTCATCGGA 59.540 55.000 0.00 0.00 38.42 4.55
1475 1561 2.483714 CCGGTCATTGTCTCATCGGATT 60.484 50.000 0.00 0.00 38.42 3.01
1477 1563 3.535561 GGTCATTGTCTCATCGGATTGT 58.464 45.455 0.00 0.00 0.00 2.71
1478 1564 3.310774 GGTCATTGTCTCATCGGATTGTG 59.689 47.826 0.00 0.00 0.00 3.33
1584 1754 9.584008 ACGAAGAAAGGGACAGAGTATATTATA 57.416 33.333 0.00 0.00 0.00 0.98
1713 1891 4.494091 TGGGACATTCTTTTGCCAAAAA 57.506 36.364 3.91 0.00 34.17 1.94
1738 1927 4.059008 CAAGCTAGAACTTGCGAACTTC 57.941 45.455 0.00 0.00 40.53 3.01
1757 1950 0.032540 CAGAGCCCAACAACAAAGCC 59.967 55.000 0.00 0.00 0.00 4.35
1896 2092 3.374988 CCACGACAGGTACGACTACATTA 59.625 47.826 0.00 0.00 34.70 1.90
1976 2172 2.681778 CTCGTGCTGGAGAGGGGT 60.682 66.667 0.00 0.00 36.08 4.95
1979 2175 2.607750 GTGCTGGAGAGGGGTGGA 60.608 66.667 0.00 0.00 0.00 4.02
2078 2274 2.948720 GCAGGCCTTCGTCTCCACT 61.949 63.158 0.00 0.00 0.00 4.00
2164 2360 2.187946 CCGGGCTAGCTCAAGGTG 59.812 66.667 16.47 0.00 0.00 4.00
2184 2381 3.597255 TGCCAATGCATTGTTATGGTTG 58.403 40.909 31.87 18.03 44.23 3.77
2185 2382 3.007723 TGCCAATGCATTGTTATGGTTGT 59.992 39.130 31.87 0.00 44.23 3.32
2187 2384 3.371591 CCAATGCATTGTTATGGTTGTGC 59.628 43.478 31.87 0.00 36.06 4.57
2202 2399 4.397103 TGGTTGTGCATCATCATTCTTCTC 59.603 41.667 0.00 0.00 0.00 2.87
2203 2400 4.639310 GGTTGTGCATCATCATTCTTCTCT 59.361 41.667 0.00 0.00 0.00 3.10
2204 2401 5.220815 GGTTGTGCATCATCATTCTTCTCTC 60.221 44.000 0.00 0.00 0.00 3.20
2206 2403 5.116882 TGTGCATCATCATTCTTCTCTCTG 58.883 41.667 0.00 0.00 0.00 3.35
2207 2404 5.117584 GTGCATCATCATTCTTCTCTCTGT 58.882 41.667 0.00 0.00 0.00 3.41
2210 2407 7.279536 GTGCATCATCATTCTTCTCTCTGTTTA 59.720 37.037 0.00 0.00 0.00 2.01
2218 2443 6.974932 TTCTTCTCTCTGTTTATGCATGAC 57.025 37.500 10.16 8.72 0.00 3.06
2228 2453 5.767269 TGTTTATGCATGACAAACGTGAAT 58.233 33.333 10.16 0.00 37.51 2.57
2234 2459 2.753989 TGACAAACGTGAATGCAGTG 57.246 45.000 0.00 0.00 0.00 3.66
2236 2461 2.421775 TGACAAACGTGAATGCAGTGTT 59.578 40.909 0.00 0.00 0.00 3.32
2237 2462 3.623510 TGACAAACGTGAATGCAGTGTTA 59.376 39.130 0.00 0.00 0.00 2.41
2241 2510 2.566913 ACGTGAATGCAGTGTTACCAA 58.433 42.857 0.00 0.00 0.00 3.67
2423 2693 2.434336 CTGCCACCCTAGCAATGTAGTA 59.566 50.000 0.00 0.00 40.35 1.82
2424 2694 2.169769 TGCCACCCTAGCAATGTAGTAC 59.830 50.000 0.00 0.00 37.28 2.73
2425 2695 2.434702 GCCACCCTAGCAATGTAGTACT 59.565 50.000 0.00 0.00 0.00 2.73
2503 2775 8.090214 AGCAACTGTTCTTAATATGCACAAAAT 58.910 29.630 0.00 0.00 34.89 1.82
2504 2776 9.352784 GCAACTGTTCTTAATATGCACAAAATA 57.647 29.630 0.00 0.00 32.80 1.40
2509 2781 9.347934 TGTTCTTAATATGCACAAAATAAACCG 57.652 29.630 0.00 0.00 0.00 4.44
2510 2782 9.349145 GTTCTTAATATGCACAAAATAAACCGT 57.651 29.630 0.00 0.00 0.00 4.83
2513 2785 9.997482 CTTAATATGCACAAAATAAACCGTAGT 57.003 29.630 0.00 0.00 0.00 2.73
2514 2786 9.991388 TTAATATGCACAAAATAAACCGTAGTC 57.009 29.630 0.00 0.00 0.00 2.59
2563 2835 6.786122 AGTACTAAGATTACCCTGCCAAAAA 58.214 36.000 0.00 0.00 0.00 1.94
2608 2880 0.171231 CCGACACTGCTCTCGATTGA 59.829 55.000 0.00 0.00 31.24 2.57
2676 2948 8.896722 AGTCTTGTCCCTTAATTAGAGTCTTA 57.103 34.615 0.00 0.00 0.00 2.10
2677 2949 9.322769 AGTCTTGTCCCTTAATTAGAGTCTTAA 57.677 33.333 0.00 0.00 0.00 1.85
2678 2950 9.939802 GTCTTGTCCCTTAATTAGAGTCTTAAA 57.060 33.333 0.00 0.00 0.00 1.52
2712 2984 6.354130 AGCAAGTTTGTTAGGAAAGAGTACA 58.646 36.000 0.00 0.00 0.00 2.90
2749 3021 5.794687 TGTATTCATCATCAAACGTGGAC 57.205 39.130 0.00 0.00 0.00 4.02
2755 3027 5.977635 TCATCATCAAACGTGGACTCTTAT 58.022 37.500 0.00 0.00 0.00 1.73
2765 3037 9.968743 CAAACGTGGACTCTTATTTAATTAGAC 57.031 33.333 0.00 0.00 0.00 2.59
2797 3069 9.476202 GTTGATTAAGCAAGTTTGTTAGGAAAT 57.524 29.630 6.36 0.00 0.00 2.17
2873 3145 3.243234 CGGTCAAGTCCTGTCTGCTATAG 60.243 52.174 0.00 0.00 0.00 1.31
2954 3227 5.820947 CCGCTTTAGTAATTTGGGTATGTCT 59.179 40.000 0.00 0.00 0.00 3.41
3043 3316 2.955614 ACAATGAGTACCTGCGTACAC 58.044 47.619 4.96 0.00 46.25 2.90
3066 3339 1.891919 GCACTCGTGGGCAACTTGA 60.892 57.895 6.88 0.00 0.00 3.02
3067 3340 1.237285 GCACTCGTGGGCAACTTGAT 61.237 55.000 6.88 0.00 0.00 2.57
3136 3412 1.202710 TCGGCTTTGGTAGTGCAAAGA 60.203 47.619 0.57 0.00 39.91 2.52
3171 3447 5.208463 TGACAGTAACACATGCTCTGTTA 57.792 39.130 3.87 3.87 39.08 2.41
3313 3708 9.844790 TTTGAACAGCAGAAATGTCTTATATTG 57.155 29.630 0.00 0.00 28.78 1.90
3324 3719 9.823647 GAAATGTCTTATATTGAGGAACAGAGA 57.176 33.333 0.00 0.00 0.00 3.10
3434 3829 3.105283 AGCCCAAGAGATAACCGTAACT 58.895 45.455 0.00 0.00 0.00 2.24
3656 4051 8.818860 ACCTGATACTTACATACCTTGTGTTTA 58.181 33.333 0.00 0.00 39.48 2.01
3928 4323 1.347707 CAGCTGGAGACCCTAACAACA 59.652 52.381 5.57 0.00 0.00 3.33
3971 4366 4.060900 AGTGTGCACAAGATAGTGTTCAG 58.939 43.478 23.59 0.00 41.52 3.02
3986 4381 2.076863 GTTCAGCTCGCAACAAGGTAT 58.923 47.619 0.00 0.00 0.00 2.73
3988 4383 3.165058 TCAGCTCGCAACAAGGTATAG 57.835 47.619 0.00 0.00 0.00 1.31
4061 4456 9.557338 CTACAACAGAAAGTGTAGATACTACAC 57.443 37.037 25.16 25.16 45.89 2.90
4070 4466 6.782298 GTGTAGATACTACACAGCGATAGA 57.218 41.667 26.60 0.00 45.13 1.98
4105 4501 6.092748 CCCTTTTTCAATAACATGAACTCCG 58.907 40.000 0.00 0.00 38.95 4.63
4109 4505 7.447374 TTTTCAATAACATGAACTCCGATGT 57.553 32.000 0.00 0.00 38.95 3.06
4137 4533 0.325296 TGAGACCAAGGGCTATCGGT 60.325 55.000 0.00 0.00 0.00 4.69
4143 4539 1.202533 CCAAGGGCTATCGGTGTACAG 60.203 57.143 0.00 0.00 0.00 2.74
4146 4542 1.755380 AGGGCTATCGGTGTACAGTTC 59.245 52.381 0.00 0.00 0.00 3.01
4155 4551 1.670674 GGTGTACAGTTCGCCGATGAA 60.671 52.381 0.00 0.00 0.00 2.57
4158 4554 2.165641 TGTACAGTTCGCCGATGAAGAT 59.834 45.455 0.00 0.00 0.00 2.40
4193 4589 1.748493 GGCACTCCTCAACAACAACAA 59.252 47.619 0.00 0.00 0.00 2.83
4194 4590 2.223572 GGCACTCCTCAACAACAACAAG 60.224 50.000 0.00 0.00 0.00 3.16
4200 4596 5.163195 ACTCCTCAACAACAACAAGGATAGT 60.163 40.000 0.00 0.00 35.65 2.12
4203 4599 5.180117 CCTCAACAACAACAAGGATAGTGAG 59.820 44.000 0.00 0.00 0.00 3.51
4206 4602 6.650807 TCAACAACAACAAGGATAGTGAGATC 59.349 38.462 0.00 0.00 0.00 2.75
4210 4606 5.595885 ACAACAAGGATAGTGAGATCATCG 58.404 41.667 0.00 0.00 0.00 3.84
4218 4614 3.961477 AGTGAGATCATCGTCTCTTCG 57.039 47.619 0.00 0.00 43.96 3.79
4419 4815 3.511934 AGACTGTCGGAATAACTGAAGCT 59.488 43.478 1.52 0.00 35.49 3.74
4464 4860 2.306847 GGTTTTGGCCAGTCTGAAGAA 58.693 47.619 5.11 0.00 0.00 2.52
4579 4979 6.127814 CCACAAGATTCAGATTGCACTGTATT 60.128 38.462 4.42 0.00 38.79 1.89
4787 5189 0.597568 TTTTGCCGTTGCTGATCCAG 59.402 50.000 0.00 0.00 38.71 3.86
5116 5518 2.429971 TGCTCATCTGACTCCTGATGAC 59.570 50.000 9.81 8.39 46.18 3.06
5140 5545 4.651045 GCTGGATATGAAATGGAAAGGGTT 59.349 41.667 0.00 0.00 0.00 4.11
5261 5666 0.616371 GCACTACCATGGTGGGTGTA 59.384 55.000 33.23 15.60 43.37 2.90
5426 5831 9.696917 AGAACATAACTTTCTTATTTGGCAAAG 57.303 29.630 18.61 4.92 28.36 2.77
5508 5913 4.159879 GGAGTGAAGATCTTAAGGGAACGA 59.840 45.833 8.25 0.00 0.00 3.85
5516 5921 4.038271 TCTTAAGGGAACGACTAGGACA 57.962 45.455 1.85 0.00 0.00 4.02
5651 6056 8.546083 AGACATTCTAGGAGTTTCATCTGTAT 57.454 34.615 0.00 0.00 0.00 2.29
5668 6073 9.201989 TCATCTGTATCCAGTAACTATTTGTCT 57.798 33.333 0.00 0.00 39.82 3.41
5728 6144 9.672086 CATCTTTCTTATAAGTAGAGTTCGAGG 57.328 37.037 12.19 0.00 0.00 4.63
5744 6161 3.042560 GGCACAGCCCAGTTGAAC 58.957 61.111 0.00 0.00 44.06 3.18
5750 6167 0.313043 CAGCCCAGTTGAACTGCTTG 59.687 55.000 19.45 12.42 44.63 4.01
5751 6168 0.825010 AGCCCAGTTGAACTGCTTGG 60.825 55.000 19.45 15.76 44.63 3.61
5759 6176 4.943705 CAGTTGAACTGCTTGGGTATATGT 59.056 41.667 12.89 0.00 39.62 2.29
5760 6177 4.943705 AGTTGAACTGCTTGGGTATATGTG 59.056 41.667 0.00 0.00 0.00 3.21
5761 6178 3.884895 TGAACTGCTTGGGTATATGTGG 58.115 45.455 0.00 0.00 0.00 4.17
5773 6190 5.847265 TGGGTATATGTGGCCTAATCTTACA 59.153 40.000 3.32 0.00 0.00 2.41
5776 6193 6.823689 GGTATATGTGGCCTAATCTTACATGG 59.176 42.308 3.32 0.00 34.22 3.66
5805 6222 7.809806 GGTTTGATAAAACATCTTCCAGAACTG 59.190 37.037 7.99 0.00 34.46 3.16
5848 6339 8.994429 TGGTGCAAATACAATATACCAAAAAG 57.006 30.769 0.00 0.00 34.12 2.27
5850 6341 9.816354 GGTGCAAATACAATATACCAAAAAGAT 57.184 29.630 0.00 0.00 0.00 2.40
5886 6377 9.643693 CAACTCAGAAAATATAAAGCAAACCAT 57.356 29.630 0.00 0.00 0.00 3.55
5904 6395 7.566709 CAAACCATTGTGCTGAAACTTTATTC 58.433 34.615 0.00 0.00 0.00 1.75
5910 6401 6.258230 TGTGCTGAAACTTTATTCCATCAG 57.742 37.500 0.00 0.00 37.83 2.90
5914 6405 5.728898 GCTGAAACTTTATTCCATCAGCGAG 60.729 44.000 9.48 0.00 46.83 5.03
6319 6810 7.601856 ACGGATTACATGTTGTGATCATTTTT 58.398 30.769 2.30 0.00 42.90 1.94
6329 6820 8.815141 TGTTGTGATCATTTTTACTGAAATGG 57.185 30.769 0.00 0.00 43.74 3.16
6367 6858 2.592102 ACCATCATTCAACAGTGCCT 57.408 45.000 0.00 0.00 0.00 4.75
6370 6861 4.012374 ACCATCATTCAACAGTGCCTAAG 58.988 43.478 0.00 0.00 0.00 2.18
6378 6869 4.744570 TCAACAGTGCCTAAGAGATAACG 58.255 43.478 0.00 0.00 0.00 3.18
6381 6872 5.502153 ACAGTGCCTAAGAGATAACGTAG 57.498 43.478 0.00 0.00 0.00 3.51
6383 6874 3.952323 AGTGCCTAAGAGATAACGTAGCA 59.048 43.478 0.00 0.00 0.00 3.49
6384 6875 4.043073 GTGCCTAAGAGATAACGTAGCAC 58.957 47.826 0.00 0.00 0.00 4.40
6584 7075 7.664552 AATCAAAATAATGGAAGATGAGGCA 57.335 32.000 0.00 0.00 0.00 4.75
6585 7076 7.664552 ATCAAAATAATGGAAGATGAGGCAA 57.335 32.000 0.00 0.00 0.00 4.52
6586 7077 7.479352 TCAAAATAATGGAAGATGAGGCAAA 57.521 32.000 0.00 0.00 0.00 3.68
6646 7137 7.362401 CCCATAGTTCCATGTCAAGAAGAAAAG 60.362 40.741 0.00 0.00 0.00 2.27
6654 7145 5.095691 TGTCAAGAAGAAAAGATTGCGAC 57.904 39.130 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 4.480115 AGATAACCAGGATCGACATACCA 58.520 43.478 0.00 0.00 0.00 3.25
109 110 4.261994 GGCTATAGCAAGAGAGAGACAAGG 60.262 50.000 25.53 0.00 44.36 3.61
173 174 4.707448 AGTAGTGGTGTCCAATCTAGAGTG 59.293 45.833 13.23 13.23 34.18 3.51
195 196 4.320057 GCAGAACAGATTTGAACTGACCAG 60.320 45.833 14.48 0.00 38.55 4.00
266 269 1.580059 TCCTCTGCCCGGAATTAGTT 58.420 50.000 0.73 0.00 0.00 2.24
278 281 5.940470 TCTTCTTCCAAAATACTTCCTCTGC 59.060 40.000 0.00 0.00 0.00 4.26
333 336 5.183904 CCATCCCTGAAAAACCAAGAGTTAG 59.816 44.000 0.00 0.00 37.88 2.34
358 361 8.344446 TCATCAGTGCAAACTAGTTAGTACTA 57.656 34.615 8.92 0.00 34.99 1.82
359 362 7.228314 TCATCAGTGCAAACTAGTTAGTACT 57.772 36.000 8.92 10.17 34.99 2.73
360 363 7.599245 AGTTCATCAGTGCAAACTAGTTAGTAC 59.401 37.037 8.92 8.08 34.99 2.73
361 364 7.598869 CAGTTCATCAGTGCAAACTAGTTAGTA 59.401 37.037 8.92 0.00 34.99 1.82
369 372 2.880890 GTCCAGTTCATCAGTGCAAACT 59.119 45.455 0.00 0.00 0.00 2.66
378 381 5.304357 TGACTTCTTGTAGTCCAGTTCATCA 59.696 40.000 0.00 0.00 43.11 3.07
419 425 5.694995 ACCATGGTTCCGATGAAGATTATT 58.305 37.500 13.00 0.00 0.00 1.40
422 428 3.200825 AGACCATGGTTCCGATGAAGATT 59.799 43.478 20.85 0.00 0.00 2.40
449 459 1.303643 CCCTCCTGGTGGCTTCAAC 60.304 63.158 9.33 0.00 0.00 3.18
461 471 2.783379 TGCTGATGTATCTCCCTCCT 57.217 50.000 0.00 0.00 0.00 3.69
462 472 2.027377 CCATGCTGATGTATCTCCCTCC 60.027 54.545 0.00 0.00 0.00 4.30
474 488 0.815095 TGTCGACGTACCATGCTGAT 59.185 50.000 11.62 0.00 0.00 2.90
490 504 0.801251 GAAGTGTCTGCTGCCATGTC 59.199 55.000 0.00 0.00 0.00 3.06
522 536 2.030213 CGTGCTGCTTGCTATCTTCTTC 59.970 50.000 0.00 0.00 43.37 2.87
664 679 8.257306 GGAGTATGGATGATGCCTTTTTAAAAA 58.743 33.333 12.62 12.62 0.00 1.94
665 680 7.619302 AGGAGTATGGATGATGCCTTTTTAAAA 59.381 33.333 0.00 0.00 0.00 1.52
666 681 7.125391 AGGAGTATGGATGATGCCTTTTTAAA 58.875 34.615 0.00 0.00 0.00 1.52
667 682 6.672593 AGGAGTATGGATGATGCCTTTTTAA 58.327 36.000 0.00 0.00 0.00 1.52
668 683 6.266131 AGGAGTATGGATGATGCCTTTTTA 57.734 37.500 0.00 0.00 0.00 1.52
670 685 4.803329 AGGAGTATGGATGATGCCTTTT 57.197 40.909 0.00 0.00 0.00 2.27
678 693 7.635089 GCAAACTAAGGTTAGGAGTATGGATGA 60.635 40.741 1.94 0.00 34.90 2.92
685 700 5.829062 TTGGCAAACTAAGGTTAGGAGTA 57.171 39.130 0.00 0.00 34.90 2.59
688 703 6.130569 TCTTTTTGGCAAACTAAGGTTAGGA 58.869 36.000 19.14 5.06 34.90 2.94
689 704 6.399639 TCTTTTTGGCAAACTAAGGTTAGG 57.600 37.500 19.14 3.05 34.90 2.69
690 705 8.194769 TCTTTCTTTTTGGCAAACTAAGGTTAG 58.805 33.333 19.14 14.62 34.90 2.34
692 707 6.941857 TCTTTCTTTTTGGCAAACTAAGGTT 58.058 32.000 19.14 0.00 37.24 3.50
693 708 6.538945 TCTTTCTTTTTGGCAAACTAAGGT 57.461 33.333 19.14 0.00 0.00 3.50
694 709 7.841915 TTTCTTTCTTTTTGGCAAACTAAGG 57.158 32.000 19.14 11.91 0.00 2.69
695 710 9.706846 CATTTTCTTTCTTTTTGGCAAACTAAG 57.293 29.630 13.10 14.37 0.00 2.18
696 711 8.180920 GCATTTTCTTTCTTTTTGGCAAACTAA 58.819 29.630 13.10 4.50 0.00 2.24
697 712 7.552330 AGCATTTTCTTTCTTTTTGGCAAACTA 59.448 29.630 13.10 2.97 0.00 2.24
698 713 6.375174 AGCATTTTCTTTCTTTTTGGCAAACT 59.625 30.769 13.10 0.00 0.00 2.66
699 714 6.469915 CAGCATTTTCTTTCTTTTTGGCAAAC 59.530 34.615 13.10 0.00 0.00 2.93
734 749 3.310307 GCACCCGCCCAATTGGTT 61.310 61.111 22.91 0.00 36.04 3.67
756 771 9.621629 TTTCCAGTTTTCTTATGTTTCTCTGTA 57.378 29.630 0.00 0.00 0.00 2.74
812 832 3.507713 CCCACACCACCACCCCTT 61.508 66.667 0.00 0.00 0.00 3.95
1065 1098 1.519455 CGGTGGCTCTAGCTTTCCG 60.519 63.158 14.36 14.36 41.70 4.30
1069 1105 1.677966 TCGACGGTGGCTCTAGCTT 60.678 57.895 0.00 0.00 41.70 3.74
1238 1307 1.202758 AGAAACACGGACAGCATGGAA 60.203 47.619 0.00 0.00 43.62 3.53
1276 1349 1.603739 GGAGCAGGGGTGTTTGGAC 60.604 63.158 0.00 0.00 0.00 4.02
1287 1360 2.581354 CGGGAAGAGTGGAGCAGG 59.419 66.667 0.00 0.00 0.00 4.85
1324 1397 1.813092 CGAGCAATCAATCTCCCAGGG 60.813 57.143 0.00 0.00 0.00 4.45
1381 1457 3.259902 CGACTAGTAAGAAGGCAAACCC 58.740 50.000 0.00 0.00 36.11 4.11
1382 1458 2.671888 GCGACTAGTAAGAAGGCAAACC 59.328 50.000 0.00 0.00 0.00 3.27
1395 1471 2.493675 TCTGAATGAGCAAGCGACTAGT 59.506 45.455 0.00 0.00 0.00 2.57
1423 1505 3.529734 TGTCCTAGGAGAGAAGTCCATCT 59.470 47.826 13.15 0.00 39.34 2.90
1424 1506 3.634910 GTGTCCTAGGAGAGAAGTCCATC 59.365 52.174 13.15 0.00 39.34 3.51
1425 1507 3.270960 AGTGTCCTAGGAGAGAAGTCCAT 59.729 47.826 13.15 0.00 39.34 3.41
1426 1508 2.650322 AGTGTCCTAGGAGAGAAGTCCA 59.350 50.000 13.15 0.41 39.34 4.02
1446 1532 2.484264 GAGACAATGACCGGAACCAAAG 59.516 50.000 9.46 2.89 0.00 2.77
1492 1582 6.597832 AGTGCATGGTCCTCTATCTATTAC 57.402 41.667 0.00 0.00 0.00 1.89
1545 1636 7.387122 GTCCCTTTCTTCGTGTACTCTATTTTT 59.613 37.037 0.00 0.00 0.00 1.94
1584 1754 4.777463 ACAGGTACGCCTTTTTATAGCAT 58.223 39.130 0.00 0.00 44.18 3.79
1585 1755 4.210724 ACAGGTACGCCTTTTTATAGCA 57.789 40.909 0.00 0.00 44.18 3.49
1713 1891 3.386768 TCGCAAGTTCTAGCTTGTTCT 57.613 42.857 10.60 0.00 45.47 3.01
1738 1927 0.032540 GGCTTTGTTGTTGGGCTCTG 59.967 55.000 0.00 0.00 0.00 3.35
1757 1950 6.676950 TGTTCCATACTGTTTGTTATTGCTG 58.323 36.000 0.00 0.00 0.00 4.41
1934 2130 3.498397 CCTTGTACTTGAGCGACAATGTT 59.502 43.478 0.00 0.00 37.88 2.71
2150 2346 0.394899 ATTGGCACCTTGAGCTAGCC 60.395 55.000 12.13 3.49 45.41 3.93
2153 2349 2.872408 GCATTGGCACCTTGAGCTA 58.128 52.632 0.00 0.00 40.72 3.32
2164 2360 3.371591 CACAACCATAACAATGCATTGGC 59.628 43.478 35.85 0.00 41.96 4.52
2176 2373 6.604396 AGAAGAATGATGATGCACAACCATAA 59.396 34.615 0.00 0.00 0.00 1.90
2178 2375 4.954202 AGAAGAATGATGATGCACAACCAT 59.046 37.500 0.00 0.00 0.00 3.55
2179 2376 4.338012 AGAAGAATGATGATGCACAACCA 58.662 39.130 0.00 0.00 0.00 3.67
2184 2381 5.117584 ACAGAGAGAAGAATGATGATGCAC 58.882 41.667 0.00 0.00 0.00 4.57
2185 2382 5.354842 ACAGAGAGAAGAATGATGATGCA 57.645 39.130 0.00 0.00 0.00 3.96
2187 2384 8.283992 GCATAAACAGAGAGAAGAATGATGATG 58.716 37.037 0.00 0.00 0.00 3.07
2202 2399 4.847757 CACGTTTGTCATGCATAAACAGAG 59.152 41.667 18.80 13.63 36.19 3.35
2203 2400 4.513318 TCACGTTTGTCATGCATAAACAGA 59.487 37.500 18.80 14.07 36.19 3.41
2204 2401 4.782156 TCACGTTTGTCATGCATAAACAG 58.218 39.130 18.80 14.51 36.19 3.16
2206 2403 5.443170 GCATTCACGTTTGTCATGCATAAAC 60.443 40.000 11.83 11.83 38.94 2.01
2207 2404 4.620609 GCATTCACGTTTGTCATGCATAAA 59.379 37.500 0.00 0.00 38.94 1.40
2210 2407 2.030096 TGCATTCACGTTTGTCATGCAT 60.030 40.909 11.02 0.00 41.56 3.96
2218 2443 3.242903 TGGTAACACTGCATTCACGTTTG 60.243 43.478 0.00 0.00 46.17 2.93
2234 2459 8.107399 ACCTAAGCTAACTTGATTTTGGTAAC 57.893 34.615 0.00 0.00 36.57 2.50
2236 2461 9.796180 TTTACCTAAGCTAACTTGATTTTGGTA 57.204 29.630 0.00 0.00 36.57 3.25
2237 2462 8.700439 TTTACCTAAGCTAACTTGATTTTGGT 57.300 30.769 0.00 0.00 36.57 3.67
2266 2535 5.920903 TGCATAGACTGAATCATGACATGA 58.079 37.500 20.09 20.09 44.55 3.07
2463 2733 2.295349 CAGTTGCTTGCTGTCCATTTCT 59.705 45.455 0.00 0.00 0.00 2.52
2491 2763 7.859325 AGACTACGGTTTATTTTGTGCATAT 57.141 32.000 0.00 0.00 0.00 1.78
2492 2764 8.658609 GTTAGACTACGGTTTATTTTGTGCATA 58.341 33.333 0.00 0.00 0.00 3.14
2503 2775 4.081406 TGAGCTGGTTAGACTACGGTTTA 58.919 43.478 0.00 0.00 0.00 2.01
2504 2776 2.895404 TGAGCTGGTTAGACTACGGTTT 59.105 45.455 0.00 0.00 0.00 3.27
2505 2777 2.522185 TGAGCTGGTTAGACTACGGTT 58.478 47.619 0.00 0.00 0.00 4.44
2506 2778 2.211250 TGAGCTGGTTAGACTACGGT 57.789 50.000 0.00 0.00 0.00 4.83
2507 2779 3.587797 TTTGAGCTGGTTAGACTACGG 57.412 47.619 0.00 0.00 0.00 4.02
2508 2780 5.869888 AGAAATTTGAGCTGGTTAGACTACG 59.130 40.000 0.00 0.00 0.00 3.51
2509 2781 6.314152 GGAGAAATTTGAGCTGGTTAGACTAC 59.686 42.308 0.00 0.00 0.00 2.73
2510 2782 6.407202 GGAGAAATTTGAGCTGGTTAGACTA 58.593 40.000 0.00 0.00 0.00 2.59
2511 2783 5.249420 GGAGAAATTTGAGCTGGTTAGACT 58.751 41.667 0.00 0.00 0.00 3.24
2512 2784 4.396478 GGGAGAAATTTGAGCTGGTTAGAC 59.604 45.833 0.00 0.00 0.00 2.59
2513 2785 4.567747 GGGGAGAAATTTGAGCTGGTTAGA 60.568 45.833 0.00 0.00 0.00 2.10
2514 2786 3.696548 GGGGAGAAATTTGAGCTGGTTAG 59.303 47.826 0.00 0.00 0.00 2.34
2586 2858 1.658686 ATCGAGAGCAGTGTCGGGTC 61.659 60.000 2.26 0.00 39.87 4.46
2608 2880 6.377146 GTCCACATAACAATAAGGTCATGGTT 59.623 38.462 0.00 0.00 0.00 3.67
2676 2948 9.313118 CCTAACAAACTTGCTTAATCAACTTTT 57.687 29.630 0.00 0.00 0.00 2.27
2677 2949 8.691797 TCCTAACAAACTTGCTTAATCAACTTT 58.308 29.630 0.00 0.00 0.00 2.66
2678 2950 8.232913 TCCTAACAAACTTGCTTAATCAACTT 57.767 30.769 0.00 0.00 0.00 2.66
2765 3037 7.440523 ACAAACTTGCTTAATCAACTAGGAG 57.559 36.000 0.00 0.00 0.00 3.69
2797 3069 8.794335 ATACGATATCTGAGCTGATTGTACTA 57.206 34.615 0.00 0.00 0.00 1.82
2932 3204 7.625828 ACAGACATACCCAAATTACTAAAGC 57.374 36.000 0.00 0.00 0.00 3.51
3009 3282 5.852282 ACTCATTGTTAAAAACACTGCCT 57.148 34.783 5.53 0.00 41.97 4.75
3043 3316 2.267351 TTGCCCACGAGTGCCAATG 61.267 57.895 0.00 0.00 0.00 2.82
3136 3412 4.202524 TGTTACTGTCAGGGCCAGTTATTT 60.203 41.667 6.18 0.00 42.83 1.40
3171 3447 9.903682 CAACATGAAATTTAATTCTGTGAGAGT 57.096 29.630 0.00 0.00 0.00 3.24
3313 3708 7.708752 CCTTCAATAATACACTCTCTGTTCCTC 59.291 40.741 0.00 0.00 33.91 3.71
3324 3719 5.815581 TGTTGCCTCCTTCAATAATACACT 58.184 37.500 0.00 0.00 0.00 3.55
3333 3728 4.543590 TTTGTTTTGTTGCCTCCTTCAA 57.456 36.364 0.00 0.00 0.00 2.69
3434 3829 0.531753 TTGCGCTGAACTGTACTGCA 60.532 50.000 9.73 0.00 33.57 4.41
3619 4014 7.864108 TGTAAGTATCAGGTTTGATGGAATG 57.136 36.000 0.48 0.00 43.76 2.67
3656 4051 1.001378 GCACGAAGCTGTTGTTCCAAT 60.001 47.619 0.00 0.00 41.15 3.16
3906 4301 0.835971 TGTTAGGGTCTCCAGCTGCA 60.836 55.000 8.66 0.00 34.83 4.41
3928 4323 1.599047 CGTGAAGCAGGACCCTCAT 59.401 57.895 0.00 0.00 0.00 2.90
3971 4366 0.938008 GGCTATACCTTGTTGCGAGC 59.062 55.000 0.00 0.00 34.51 5.03
4007 4402 6.479972 TCTAGACTGTTTTGGAAGAGAACA 57.520 37.500 0.00 0.00 31.04 3.18
4008 4403 7.971183 ATTCTAGACTGTTTTGGAAGAGAAC 57.029 36.000 0.00 0.00 31.04 3.01
4061 4456 3.579709 GGTACATGATGGTCTATCGCTG 58.420 50.000 0.00 0.00 38.71 5.18
4062 4457 2.563179 GGGTACATGATGGTCTATCGCT 59.437 50.000 0.00 0.00 38.71 4.93
4063 4458 2.563179 AGGGTACATGATGGTCTATCGC 59.437 50.000 0.00 0.00 38.71 4.58
4064 4459 4.873746 AAGGGTACATGATGGTCTATCG 57.126 45.455 0.00 0.00 38.71 2.92
4065 4460 7.054124 TGAAAAAGGGTACATGATGGTCTATC 58.946 38.462 0.00 0.00 36.29 2.08
4070 4466 7.453126 TGTTATTGAAAAAGGGTACATGATGGT 59.547 33.333 0.00 0.00 0.00 3.55
4105 4501 2.366533 TGGTCTCAGTCGTCCTACATC 58.633 52.381 0.00 0.00 0.00 3.06
4109 4505 1.616187 CCCTTGGTCTCAGTCGTCCTA 60.616 57.143 0.00 0.00 0.00 2.94
4137 4533 1.542472 TCTTCATCGGCGAACTGTACA 59.458 47.619 15.93 0.00 0.00 2.90
4143 4539 0.179084 TCCCATCTTCATCGGCGAAC 60.179 55.000 15.93 0.00 0.00 3.95
4146 4542 0.598680 GTCTCCCATCTTCATCGGCG 60.599 60.000 0.00 0.00 0.00 6.46
4155 4551 0.326048 CCTGGTGGAGTCTCCCATCT 60.326 60.000 16.60 0.00 38.16 2.90
4158 4554 2.607750 GCCTGGTGGAGTCTCCCA 60.608 66.667 16.60 7.02 35.03 4.37
4193 4589 5.241403 AGAGACGATGATCTCACTATCCT 57.759 43.478 5.63 0.00 46.51 3.24
4194 4590 5.390461 CGAAGAGACGATGATCTCACTATCC 60.390 48.000 5.63 0.00 46.51 2.59
4200 4596 1.950216 CCCGAAGAGACGATGATCTCA 59.050 52.381 5.63 0.00 46.51 3.27
4203 4599 1.866063 GCACCCGAAGAGACGATGATC 60.866 57.143 0.00 0.00 35.09 2.92
4206 4602 0.389817 TTGCACCCGAAGAGACGATG 60.390 55.000 0.00 0.00 35.09 3.84
4210 4606 0.804989 CCAATTGCACCCGAAGAGAC 59.195 55.000 0.00 0.00 0.00 3.36
4245 4641 1.751927 CCCAATCCCACTGAGCAGC 60.752 63.158 0.00 0.00 0.00 5.25
4248 4644 2.440980 GGCCCAATCCCACTGAGC 60.441 66.667 0.00 0.00 0.00 4.26
4419 4815 1.003839 GGCCTCGATGAACACACCA 60.004 57.895 0.00 0.00 0.00 4.17
4618 5018 7.328277 TCAATAACTTATGTTGCATACCCAC 57.672 36.000 4.33 0.00 37.59 4.61
4787 5189 5.853936 TGATAGGAATGTAGTATGGTGCAC 58.146 41.667 8.80 8.80 0.00 4.57
5095 5497 2.743553 TCATCAGGAGTCAGATGAGCA 58.256 47.619 18.33 3.20 44.04 4.26
5116 5518 3.254166 CCCTTTCCATTTCATATCCAGCG 59.746 47.826 0.00 0.00 0.00 5.18
5261 5666 1.553704 GTCGACCACCTTCCCTACATT 59.446 52.381 3.51 0.00 0.00 2.71
5508 5913 0.901124 CTCCAGCTGCTTGTCCTAGT 59.099 55.000 8.66 0.00 0.00 2.57
5516 5921 2.808919 TCTACTACACTCCAGCTGCTT 58.191 47.619 8.66 0.00 0.00 3.91
5651 6056 7.634671 TCATACGAGACAAATAGTTACTGGA 57.365 36.000 0.00 0.00 0.00 3.86
5728 6144 1.656441 CAGTTCAACTGGGCTGTGC 59.344 57.895 9.96 0.00 42.35 4.57
5737 6154 4.943705 CACATATACCCAAGCAGTTCAACT 59.056 41.667 0.00 0.00 0.00 3.16
5739 6156 4.269183 CCACATATACCCAAGCAGTTCAA 58.731 43.478 0.00 0.00 0.00 2.69
5744 6161 1.143684 AGGCCACATATACCCAAGCAG 59.856 52.381 5.01 0.00 0.00 4.24
5750 6167 6.368779 TGTAAGATTAGGCCACATATACCC 57.631 41.667 5.01 0.00 0.00 3.69
5751 6168 6.823689 CCATGTAAGATTAGGCCACATATACC 59.176 42.308 5.01 0.00 0.00 2.73
5759 6176 3.721575 ACCATCCATGTAAGATTAGGCCA 59.278 43.478 5.01 0.00 0.00 5.36
5760 6177 4.373156 ACCATCCATGTAAGATTAGGCC 57.627 45.455 0.00 0.00 0.00 5.19
5761 6178 5.827797 TCAAACCATCCATGTAAGATTAGGC 59.172 40.000 0.00 0.00 0.00 3.93
5773 6190 7.399765 TGGAAGATGTTTTATCAAACCATCCAT 59.600 33.333 5.79 0.00 41.60 3.41
5776 6193 8.055279 TCTGGAAGATGTTTTATCAAACCATC 57.945 34.615 0.20 2.07 38.67 3.51
5822 6313 9.598517 CTTTTTGGTATATTGTATTTGCACCAT 57.401 29.630 0.00 0.00 34.73 3.55
5858 6349 9.860898 GGTTTGCTTTATATTTTCTGAGTTGAT 57.139 29.630 0.00 0.00 0.00 2.57
5859 6350 8.855110 TGGTTTGCTTTATATTTTCTGAGTTGA 58.145 29.630 0.00 0.00 0.00 3.18
5860 6351 9.643693 ATGGTTTGCTTTATATTTTCTGAGTTG 57.356 29.630 0.00 0.00 0.00 3.16
5862 6353 9.643693 CAATGGTTTGCTTTATATTTTCTGAGT 57.356 29.630 0.00 0.00 0.00 3.41
5863 6354 9.643693 ACAATGGTTTGCTTTATATTTTCTGAG 57.356 29.630 0.00 0.00 36.22 3.35
5864 6355 9.421806 CACAATGGTTTGCTTTATATTTTCTGA 57.578 29.630 0.00 0.00 36.22 3.27
5878 6369 2.825205 AGTTTCAGCACAATGGTTTGC 58.175 42.857 0.00 0.00 36.22 3.68
5886 6377 6.647334 TGATGGAATAAAGTTTCAGCACAA 57.353 33.333 0.00 0.00 0.00 3.33
6281 6772 4.075682 TGTAATCCGTTGAATTCCTTGCA 58.924 39.130 2.27 0.00 0.00 4.08
6283 6774 6.194796 ACATGTAATCCGTTGAATTCCTTG 57.805 37.500 0.00 0.00 0.00 3.61
6284 6775 6.208599 ACAACATGTAATCCGTTGAATTCCTT 59.791 34.615 0.00 0.00 42.03 3.36
6289 6780 6.374053 TGATCACAACATGTAATCCGTTGAAT 59.626 34.615 0.00 2.18 42.03 2.57
6319 6810 9.219603 CAGATTTTCTGTAGTTCCATTTCAGTA 57.780 33.333 0.00 0.00 39.58 2.74
6352 6843 4.890158 TCTCTTAGGCACTGTTGAATGA 57.110 40.909 0.00 0.00 41.52 2.57
6354 6845 5.812642 CGTTATCTCTTAGGCACTGTTGAAT 59.187 40.000 0.00 0.00 41.52 2.57
6378 6869 2.955614 ACTATTGGACACACGTGCTAC 58.044 47.619 17.22 6.69 33.94 3.58
6381 6872 2.413837 AGAACTATTGGACACACGTGC 58.586 47.619 17.22 0.00 0.00 5.34
6383 6874 4.380655 GCTCTAGAACTATTGGACACACGT 60.381 45.833 0.00 0.00 0.00 4.49
6384 6875 4.106197 GCTCTAGAACTATTGGACACACG 58.894 47.826 0.00 0.00 0.00 4.49
6584 7075 7.148205 GCCTTATTTGATCAAATGGCATGTTTT 60.148 33.333 35.33 17.92 43.62 2.43
6585 7076 6.316890 GCCTTATTTGATCAAATGGCATGTTT 59.683 34.615 35.33 18.47 43.62 2.83
6586 7077 5.818857 GCCTTATTTGATCAAATGGCATGTT 59.181 36.000 35.33 19.01 43.62 2.71
6646 7137 3.975035 GTCTTGGAAACTTTGTCGCAATC 59.025 43.478 0.00 0.00 0.00 2.67
6654 7145 4.829492 AGGAATGGAGTCTTGGAAACTTTG 59.171 41.667 0.00 0.00 0.00 2.77


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

AutoCloner maintained by Alex Coulton.