Multiple sequence alignment - TraesCS2A01G469300

Loading Multiple Alignment...

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 TraesCS2A01G469300 chr2A 100.000 6657 0 0 1 6657 712793751 712800407 0.000000e+00 12294.0
1 TraesCS2A01G469300 chr2A 78.700 554 81 21 1214 1762 712794844 712795365 1.070000e-87 335.0
2 TraesCS2A01G469300 chr2A 78.700 554 81 21 1094 1615 712794964 712795512 1.070000e-87 335.0
3 TraesCS2A01G469300 chr2A 92.982 57 3 1 1600 1655 712795084 712795140 1.540000e-11 82.4
4 TraesCS2A01G469300 chr2D 92.193 4816 213 39 1 4750 574387060 574391778 0.000000e+00 6660.0
5 TraesCS2A01G469300 chr2D 91.741 1005 73 5 4838 5840 574391789 574392785 0.000000e+00 1387.0
6 TraesCS2A01G469300 chr2D 84.597 409 49 6 6237 6637 574393379 574393781 1.740000e-105 394.0
7 TraesCS2A01G469300 chr2D 78.378 555 78 20 1215 1762 574388146 574388665 8.330000e-84 322.0
8 TraesCS2A01G469300 chr2D 77.656 546 78 24 1093 1604 574388267 574388802 6.530000e-75 292.0
9 TraesCS2A01G469300 chr2D 91.667 60 4 1 1334 1393 574388650 574388708 1.540000e-11 82.4
10 TraesCS2A01G469300 chr2D 92.857 56 3 1 1600 1654 574388388 574388443 5.530000e-11 80.5
11 TraesCS2A01G469300 chr2B 94.948 2890 120 15 2018 4889 690590612 690593493 0.000000e+00 4505.0
12 TraesCS2A01G469300 chr2B 91.427 1458 76 22 570 2014 690589072 690590493 0.000000e+00 1954.0
13 TraesCS2A01G469300 chr2B 92.557 833 47 10 5352 6181 690593494 690594314 0.000000e+00 1181.0
14 TraesCS2A01G469300 chr2B 91.979 374 10 4 1 373 690588414 690588768 2.140000e-139 507.0
15 TraesCS2A01G469300 chr2B 78.080 552 76 25 1215 1762 690589599 690590109 2.330000e-79 307.0
16 TraesCS2A01G469300 chr2B 77.982 545 74 27 1093 1601 690589708 690590242 3.900000e-77 300.0
17 TraesCS2A01G469300 chr2B 93.333 60 3 1 1334 1393 690590094 690590152 3.310000e-13 87.9
18 TraesCS2A01G469300 chr2B 92.982 57 3 1 1600 1655 690589829 690589885 1.540000e-11 82.4
19 TraesCS2A01G469300 chr2B 100.000 38 0 0 6620 6657 690594349 690594386 3.330000e-08 71.3
20 TraesCS2A01G469300 chr2B 76.692 133 21 5 6063 6187 690671809 690671939 1.550000e-06 65.8
21 TraesCS2A01G469300 chr2B 96.875 32 1 0 6237 6268 690672004 690672035 3.000000e-03 54.7
22 TraesCS2A01G469300 chr5D 94.444 36 2 0 6188 6223 490942315 490942280 1.000000e-03 56.5
23 TraesCS2A01G469300 chr3B 96.970 33 1 0 6191 6223 159560913 159560881 1.000000e-03 56.5
24 TraesCS2A01G469300 chr1B 100.000 28 0 0 6193 6220 626047693 626047720 1.200000e-02 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G469300 chr2A 712793751 712800407 6656 False 12294.000000 12294 100.000000 1 6657 1 chr2A.!!$F1 6656
1 TraesCS2A01G469300 chr2A 712794844 712795512 668 False 250.800000 335 83.460667 1094 1762 3 chr2A.!!$F2 668
2 TraesCS2A01G469300 chr2D 574387060 574393781 6721 False 1316.842857 6660 87.012714 1 6637 7 chr2D.!!$F1 6636
3 TraesCS2A01G469300 chr2B 690588414 690594386 5972 False 999.511111 4505 90.365333 1 6657 9 chr2B.!!$F1 6656

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
870 1052 0.105760 ATCTCCATCCTGCGGTCTCT 60.106 55.000 0.00 0.00 0.00 3.10 F
1768 1966 1.075226 TTCTATGGCGCCTCCTCCT 60.075 57.895 29.70 7.67 35.26 3.69 F
1780 1978 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69 F
2348 2661 1.241165 TCTGCCTTGCACACAGATTG 58.759 50.000 8.11 0.00 35.58 2.67 F
2601 2917 1.755179 ACACAGTTTTGCTCAGTGCT 58.245 45.000 0.00 0.00 43.37 4.40 F
4413 4740 2.184020 TACCCTGCGTGCTTCATGCT 62.184 55.000 11.64 0.00 45.53 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1768 1966 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71 R
2878 3199 0.251922 AGGGCATGTGAGCACCAAAT 60.252 50.000 0.00 0.00 39.23 2.32 R
3498 3825 2.370281 TCGTGCAGCTTTCTTCTAGG 57.630 50.000 0.00 0.00 0.00 3.02 R
4186 4513 0.400594 ACCACTACTCTGGCCAAACC 59.599 55.000 7.01 0.00 34.20 3.27 R
4505 4832 4.274214 GCAAGTGATGAATGCATAGCACTA 59.726 41.667 18.11 3.01 43.04 2.74 R
5658 5995 0.602905 CCACCAACCGACCTCTTCAC 60.603 60.000 0.00 0.00 0.00 3.18 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
220 222 2.621998 CCAGAAATGATGATGGTGCCTC 59.378 50.000 0.00 0.00 0.00 4.70
262 264 4.519540 ACATGCCAACATTTACTTGGTC 57.480 40.909 0.00 0.00 40.46 4.02
280 282 3.506455 TGGTCGTTTTCTTTGTGGTTTCA 59.494 39.130 0.00 0.00 0.00 2.69
400 422 6.147864 TGCATGCCTAGTTTCCATTTATTC 57.852 37.500 16.68 0.00 0.00 1.75
401 423 5.655974 TGCATGCCTAGTTTCCATTTATTCA 59.344 36.000 16.68 0.00 0.00 2.57
448 603 1.744320 AAACAAAGCCCTGCCCGTTC 61.744 55.000 0.00 0.00 0.00 3.95
449 604 2.597217 CAAAGCCCTGCCCGTTCA 60.597 61.111 0.00 0.00 0.00 3.18
450 605 2.197324 AAAGCCCTGCCCGTTCAA 59.803 55.556 0.00 0.00 0.00 2.69
458 613 1.845809 CTGCCCGTTCAACAGCTCAC 61.846 60.000 1.55 0.00 0.00 3.51
468 623 2.882876 CAGCTCACTGGCAATGGC 59.117 61.111 0.00 0.00 40.48 4.40
517 672 1.070105 TTGTTCCGTTCAGGGGACG 59.930 57.895 0.00 0.00 41.52 4.79
565 720 5.961843 CACATGAATTTAGTCGATTGCACTC 59.038 40.000 0.00 0.00 0.00 3.51
592 747 1.327764 GAAGACATCAAACGGATCGCC 59.672 52.381 0.00 0.00 32.57 5.54
605 760 0.652592 GATCGCCGTCACATGAAAGG 59.347 55.000 0.00 0.00 0.00 3.11
611 766 1.006086 CGTCACATGAAAGGCGCATA 58.994 50.000 10.83 0.00 0.00 3.14
612 767 1.004610 CGTCACATGAAAGGCGCATAG 60.005 52.381 10.83 0.00 0.00 2.23
616 771 2.938451 CACATGAAAGGCGCATAGAGAA 59.062 45.455 10.83 0.00 0.00 2.87
621 776 6.318648 ACATGAAAGGCGCATAGAGAAAATTA 59.681 34.615 10.83 0.00 0.00 1.40
622 777 6.751514 TGAAAGGCGCATAGAGAAAATTAA 57.248 33.333 10.83 0.00 0.00 1.40
623 778 6.551736 TGAAAGGCGCATAGAGAAAATTAAC 58.448 36.000 10.83 0.00 0.00 2.01
648 803 3.057386 CACATCAAAAGTGCAGCACCATA 60.057 43.478 22.41 4.09 34.49 2.74
649 804 3.765511 ACATCAAAAGTGCAGCACCATAT 59.234 39.130 22.41 6.30 34.49 1.78
674 846 4.537135 AATAGACATCACAAGTCCACGT 57.463 40.909 0.00 0.00 36.68 4.49
870 1052 0.105760 ATCTCCATCCTGCGGTCTCT 60.106 55.000 0.00 0.00 0.00 3.10
964 1146 2.520968 CCCAAATCCCGATCCCCC 59.479 66.667 0.00 0.00 0.00 5.40
979 1165 1.384643 CCCCTAACCCTAGCCAGCT 60.385 63.158 0.00 0.00 0.00 4.24
982 1168 1.501582 CCTAACCCTAGCCAGCTTCT 58.498 55.000 0.00 0.00 0.00 2.85
1039 1225 4.816984 TCTCCCTCGGCCTCGACC 62.817 72.222 0.00 0.00 40.88 4.79
1051 1237 4.377708 TCGACCTCGACGACCCGA 62.378 66.667 0.00 0.24 44.22 5.14
1766 1964 1.300233 CGTTCTATGGCGCCTCCTC 60.300 63.158 29.70 11.92 35.26 3.71
1767 1965 1.069935 GTTCTATGGCGCCTCCTCC 59.930 63.158 29.70 7.42 35.26 4.30
1768 1966 1.075226 TTCTATGGCGCCTCCTCCT 60.075 57.895 29.70 7.67 35.26 3.69
1769 1967 1.115930 TTCTATGGCGCCTCCTCCTC 61.116 60.000 29.70 0.00 35.26 3.71
1770 1968 2.524394 TATGGCGCCTCCTCCTCC 60.524 66.667 29.70 0.00 35.26 4.30
1771 1969 3.088090 TATGGCGCCTCCTCCTCCT 62.088 63.158 29.70 3.34 35.26 3.69
1774 1972 4.851214 GCGCCTCCTCCTCCTCCT 62.851 72.222 0.00 0.00 0.00 3.69
1775 1973 2.520741 CGCCTCCTCCTCCTCCTC 60.521 72.222 0.00 0.00 0.00 3.71
1776 1974 2.123033 GCCTCCTCCTCCTCCTCC 60.123 72.222 0.00 0.00 0.00 4.30
1777 1975 2.710826 GCCTCCTCCTCCTCCTCCT 61.711 68.421 0.00 0.00 0.00 3.69
1778 1976 1.541672 CCTCCTCCTCCTCCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
1779 1977 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1780 1978 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
1794 1992 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1940 2138 1.738099 CGAGGTGAGGGAAACGCTG 60.738 63.158 0.00 0.00 0.00 5.18
1961 2159 5.649831 GCTGGTCTCTATTTGTGGAATTTCT 59.350 40.000 0.00 0.00 0.00 2.52
1965 2163 7.174946 TGGTCTCTATTTGTGGAATTTCTGTTC 59.825 37.037 0.00 0.00 0.00 3.18
2033 2346 6.488006 GTGATTAATTATCTCCACATGCCTGT 59.512 38.462 0.00 0.00 33.15 4.00
2034 2347 6.487668 TGATTAATTATCTCCACATGCCTGTG 59.512 38.462 14.53 14.53 41.80 3.66
2048 2361 5.124457 ACATGCCTGTGTAAATCAGTGAATC 59.876 40.000 0.00 0.00 33.22 2.52
2056 2369 7.977904 TGTGTAAATCAGTGAATCTATTGCTG 58.022 34.615 0.00 0.00 0.00 4.41
2057 2370 7.066163 TGTGTAAATCAGTGAATCTATTGCTGG 59.934 37.037 0.00 0.00 0.00 4.85
2090 2403 9.453572 TCCATAGAAATATGCATAGTTGATTCC 57.546 33.333 22.99 8.96 0.00 3.01
2098 2411 6.932356 ATGCATAGTTGATTCCTTGTGTAG 57.068 37.500 0.00 0.00 0.00 2.74
2100 2413 5.874810 TGCATAGTTGATTCCTTGTGTAGTC 59.125 40.000 0.00 0.00 0.00 2.59
2101 2414 6.109359 GCATAGTTGATTCCTTGTGTAGTCT 58.891 40.000 0.00 0.00 0.00 3.24
2102 2415 7.093509 TGCATAGTTGATTCCTTGTGTAGTCTA 60.094 37.037 0.00 0.00 0.00 2.59
2110 2423 9.121658 TGATTCCTTGTGTAGTCTACTAGTATG 57.878 37.037 11.28 0.00 0.00 2.39
2143 2456 5.472148 TGAATGAACAATGGAAATGCTGAC 58.528 37.500 0.00 0.00 0.00 3.51
2144 2457 5.244402 TGAATGAACAATGGAAATGCTGACT 59.756 36.000 0.00 0.00 0.00 3.41
2145 2458 4.771590 TGAACAATGGAAATGCTGACTC 57.228 40.909 0.00 0.00 0.00 3.36
2153 2466 7.039504 ACAATGGAAATGCTGACTCTATTTGTT 60.040 33.333 0.00 0.00 0.00 2.83
2169 2482 4.590400 TTTGTTCAATTTTGTGGCAACG 57.410 36.364 0.00 0.00 42.51 4.10
2209 2522 4.962995 ACATAACCAGGTAGTGTAGCATCT 59.037 41.667 7.80 0.00 0.00 2.90
2241 2554 6.780457 AAACATACCTTCAGAAATCATGGG 57.220 37.500 0.00 0.00 0.00 4.00
2246 2559 5.399052 ACCTTCAGAAATCATGGGATCAT 57.601 39.130 0.00 0.00 31.88 2.45
2331 2644 9.696917 CAAAAACAGCTGAAATTTACCTAATCT 57.303 29.630 23.35 0.00 0.00 2.40
2348 2661 1.241165 TCTGCCTTGCACACAGATTG 58.759 50.000 8.11 0.00 35.58 2.67
2354 2667 3.305539 GCCTTGCACACAGATTGATTTCA 60.306 43.478 0.00 0.00 0.00 2.69
2395 2708 3.519510 CCCTCCTAGACCAGACATTTTCA 59.480 47.826 0.00 0.00 0.00 2.69
2398 2711 3.582647 TCCTAGACCAGACATTTTCAGCA 59.417 43.478 0.00 0.00 0.00 4.41
2402 2715 6.259608 CCTAGACCAGACATTTTCAGCATAAG 59.740 42.308 0.00 0.00 0.00 1.73
2403 2716 5.809001 AGACCAGACATTTTCAGCATAAGA 58.191 37.500 0.00 0.00 0.00 2.10
2409 2722 7.754027 CCAGACATTTTCAGCATAAGAAGAAAG 59.246 37.037 0.00 0.00 32.29 2.62
2420 2733 8.131100 CAGCATAAGAAGAAAGAAACAGTTTCA 58.869 33.333 24.85 4.39 42.10 2.69
2458 2771 8.312564 TGCTTGATGAACAATGATTAAAATCCA 58.687 29.630 0.41 0.00 37.88 3.41
2601 2917 1.755179 ACACAGTTTTGCTCAGTGCT 58.245 45.000 0.00 0.00 43.37 4.40
2643 2959 2.545731 GCTAGAGCAAACTGCCTCTAC 58.454 52.381 0.00 0.00 46.52 2.59
2671 2988 7.724490 AAAAATCTTTTCCTAGCCTAAGCAT 57.276 32.000 0.00 0.00 43.56 3.79
2696 3013 9.846248 ATTTCAGAGAAATTATGTAAACAGCAC 57.154 29.630 0.00 0.00 0.00 4.40
2769 3086 5.104193 ACCTGCTTCATTTCTCTGGTGATAT 60.104 40.000 0.00 0.00 31.03 1.63
2962 3283 9.745880 GAATTATTCATGCTGAAATGTTCTCAT 57.254 29.630 0.00 0.00 40.12 2.90
3222 3544 9.410556 GTGCTCAAACAAATTTTATGTAGACAT 57.589 29.630 0.08 0.08 40.22 3.06
3281 3603 4.266029 GCATTGACAACATCGGCAATAAAG 59.734 41.667 0.00 0.00 30.45 1.85
3282 3604 5.401550 CATTGACAACATCGGCAATAAAGT 58.598 37.500 0.00 0.00 30.45 2.66
3283 3605 5.446143 TTGACAACATCGGCAATAAAGTT 57.554 34.783 0.00 0.00 0.00 2.66
3450 3777 3.243501 TGACTCAATCAACAAGCAAAGCC 60.244 43.478 0.00 0.00 33.02 4.35
3498 3825 5.006649 GTCAAATTCTGTTGCTTCAAAACCC 59.993 40.000 0.00 0.00 0.00 4.11
3655 3982 3.876274 TCAAGAAGAGACAGGAATCCG 57.124 47.619 0.00 0.00 0.00 4.18
3682 4009 5.007430 CACAAGTATATGCAGAAGAAGCCTG 59.993 44.000 0.00 0.00 34.88 4.85
3686 4013 6.696411 AGTATATGCAGAAGAAGCCTGTATC 58.304 40.000 0.00 0.00 37.90 2.24
3844 4171 3.368323 CCAGCAGACAAAAACCAACAGTT 60.368 43.478 0.00 0.00 41.81 3.16
4076 4403 3.775316 ACTTCCGAGGGAAATGAGTACAT 59.225 43.478 0.00 0.00 41.54 2.29
4156 4483 6.714810 TCTTGGTAGTGTCATTTGCTAATTGT 59.285 34.615 0.00 0.00 0.00 2.71
4161 4488 7.326063 GGTAGTGTCATTTGCTAATTGTTGTTC 59.674 37.037 0.00 0.00 0.00 3.18
4186 4513 3.596214 TGCTTCTTTTTAGTAGGAGCCG 58.404 45.455 0.00 0.00 42.52 5.52
4342 4669 3.126453 AGGATGGCAGGAAGGTAAGAAT 58.874 45.455 0.00 0.00 0.00 2.40
4413 4740 2.184020 TACCCTGCGTGCTTCATGCT 62.184 55.000 11.64 0.00 45.53 3.79
4505 4832 3.149981 GCCTTCTAGCCACTTCTGTTTT 58.850 45.455 0.00 0.00 0.00 2.43
4538 4865 6.976349 TGCATTCATCACTTGCTTCATTAATC 59.024 34.615 0.00 0.00 37.28 1.75
4612 4939 5.334105 GCCGTGATGCCTATAAACAATACAG 60.334 44.000 0.00 0.00 0.00 2.74
4697 5024 8.902540 TTATTCTGTGCTCATATATCCGTTTT 57.097 30.769 0.00 0.00 0.00 2.43
4750 5079 2.435372 TTTATCCGCCATTCTGCCTT 57.565 45.000 0.00 0.00 0.00 4.35
4753 5082 2.664402 ATCCGCCATTCTGCCTTATT 57.336 45.000 0.00 0.00 0.00 1.40
4829 5163 9.007901 GGATTGTTTATTCTATAGCTTCAGCAT 57.992 33.333 0.75 0.00 45.16 3.79
4898 5232 1.753073 GGGATGATTGTTTGGCTCCTG 59.247 52.381 0.00 0.00 0.00 3.86
4899 5233 1.135721 GGATGATTGTTTGGCTCCTGC 59.864 52.381 0.00 0.00 38.76 4.85
5003 5338 8.310382 AGCTATCCAGATTCACTACATGTAATC 58.690 37.037 7.06 8.78 0.00 1.75
5008 5343 7.981789 TCCAGATTCACTACATGTAATCTTGTC 59.018 37.037 15.76 7.10 36.73 3.18
5031 5366 4.650131 CGGAGTAAGAAAAGTAGGGAGGAT 59.350 45.833 0.00 0.00 0.00 3.24
5067 5402 6.320164 GGATGCTTACCGTAGATATGATCTCT 59.680 42.308 0.00 0.00 40.76 3.10
5111 5446 3.325293 ACATGTTGTCTGCCAGACTAG 57.675 47.619 24.29 12.23 45.27 2.57
5112 5447 2.027745 ACATGTTGTCTGCCAGACTAGG 60.028 50.000 24.29 14.74 45.27 3.02
5122 5457 4.081420 TCTGCCAGACTAGGTGAGATTTTC 60.081 45.833 0.00 0.00 0.00 2.29
5123 5458 3.840666 TGCCAGACTAGGTGAGATTTTCT 59.159 43.478 0.00 0.00 0.00 2.52
5132 5467 2.238395 GGTGAGATTTTCTCTGCTCCCT 59.762 50.000 6.13 0.00 43.73 4.20
5137 5472 1.901591 TTTTCTCTGCTCCCTTGCTG 58.098 50.000 0.00 0.00 0.00 4.41
5142 5477 0.034767 TCTGCTCCCTTGCTGAATGG 60.035 55.000 0.00 0.00 37.83 3.16
5154 5489 3.559069 TGCTGAATGGGGAGAATTGATC 58.441 45.455 0.00 0.00 0.00 2.92
5170 5505 3.988976 TGATCTGGTTCTCCTTTCCAG 57.011 47.619 4.30 4.30 46.94 3.86
5181 5516 3.582998 TCCTTTCCAGGCAAGGATATG 57.417 47.619 16.19 0.00 44.17 1.78
5187 5522 1.149174 AGGCAAGGATATGTGGGCG 59.851 57.895 0.00 0.00 0.00 6.13
5216 5551 4.874970 AGCATTGAACAAACTTGCTTAGG 58.125 39.130 7.89 0.00 40.58 2.69
5276 5611 6.434172 TGCTAAGCAAGGCTAGAATTTAGCC 61.434 44.000 21.55 21.55 46.14 3.93
5306 5641 5.350633 AGATTCAAACAAACCACACATGTG 58.649 37.500 24.25 24.25 45.23 3.21
5308 5643 5.644977 TTCAAACAAACCACACATGTGTA 57.355 34.783 30.11 8.86 42.83 2.90
5309 5644 5.843673 TCAAACAAACCACACATGTGTAT 57.156 34.783 30.11 18.78 42.83 2.29
5310 5645 6.944234 TCAAACAAACCACACATGTGTATA 57.056 33.333 30.11 3.29 42.83 1.47
5325 5660 5.159273 TGTGTATATGTGATGGTGTGTGT 57.841 39.130 0.00 0.00 0.00 3.72
5334 5669 3.572255 GTGATGGTGTGTGTTATTTGGGT 59.428 43.478 0.00 0.00 0.00 4.51
5349 5684 5.581350 ATTTGGGTTCCATGGAAATGTTT 57.419 34.783 28.64 9.67 35.75 2.83
5350 5685 6.694445 ATTTGGGTTCCATGGAAATGTTTA 57.306 33.333 28.64 12.88 35.75 2.01
5385 5721 8.511604 TTGGTCAATCAATCCTAGAATCTTTC 57.488 34.615 0.00 0.00 0.00 2.62
5401 5737 8.341892 AGAATCTTTCCTGGAAGTGATAAAAC 57.658 34.615 19.95 14.13 0.00 2.43
5407 5743 4.104102 TCCTGGAAGTGATAAAACCAGTGT 59.896 41.667 0.00 0.00 44.33 3.55
5440 5777 0.171007 GTGATGCCAACGGGTCAATG 59.829 55.000 0.00 0.00 36.17 2.82
5442 5779 0.679640 GATGCCAACGGGTCAATGGA 60.680 55.000 0.00 0.00 36.27 3.41
5445 5782 0.894835 GCCAACGGGTCAATGGAAAT 59.105 50.000 0.00 0.00 36.27 2.17
5469 5806 5.450818 ACCTTATTCCCTTCACTGCATTA 57.549 39.130 0.00 0.00 0.00 1.90
5490 5827 7.872993 GCATTATTGGTACTGCTATCTGACTAA 59.127 37.037 0.00 0.00 34.63 2.24
5578 5915 2.290323 GGAAGGTTCTGCTAGAGCCAAA 60.290 50.000 16.96 0.00 46.66 3.28
5658 5995 0.453390 GCCAAAAGGAAGCGATGAGG 59.547 55.000 0.00 0.00 0.00 3.86
5659 5996 1.826385 CCAAAAGGAAGCGATGAGGT 58.174 50.000 0.00 0.00 0.00 3.85
5660 5997 1.470098 CCAAAAGGAAGCGATGAGGTG 59.530 52.381 0.00 0.00 0.00 4.00
5730 6067 6.534634 AGAGGTCACTGTAATTAGTTGCTTT 58.465 36.000 0.00 0.00 0.00 3.51
5818 6155 7.500892 TGTCAATATGAACACACTACAACCTTT 59.499 33.333 0.00 0.00 0.00 3.11
5847 6184 7.040961 TCGAAACCCTTCTTTGTTATTAAGGTG 60.041 37.037 0.00 0.00 37.40 4.00
5850 6187 7.939784 ACCCTTCTTTGTTATTAAGGTGATC 57.060 36.000 0.00 0.00 37.40 2.92
5853 6190 6.821665 CCTTCTTTGTTATTAAGGTGATCCGA 59.178 38.462 0.00 0.00 39.05 4.55
5856 6193 6.596497 TCTTTGTTATTAAGGTGATCCGAACC 59.404 38.462 0.00 0.00 39.05 3.62
5872 6209 3.001939 CCGAACCACTCAACTGTGTAAAC 59.998 47.826 0.00 0.00 36.30 2.01
5873 6210 3.869246 CGAACCACTCAACTGTGTAAACT 59.131 43.478 0.00 0.00 36.30 2.66
5874 6211 4.260212 CGAACCACTCAACTGTGTAAACTG 60.260 45.833 0.00 0.00 36.30 3.16
5875 6212 2.943033 ACCACTCAACTGTGTAAACTGC 59.057 45.455 0.00 0.00 36.30 4.40
5891 6228 1.414919 ACTGCTGTTGTTAAGGGACGA 59.585 47.619 0.00 0.00 0.00 4.20
5904 6241 3.110178 GACGAAAGGACGGGCGTG 61.110 66.667 0.00 0.00 37.07 5.34
5939 6277 5.415065 TGGAGGTGATGGATAGGACATTAT 58.585 41.667 0.00 0.00 0.00 1.28
5962 6300 4.586421 TGGGTCTTAATGCATGTTTTGTGA 59.414 37.500 0.00 0.00 0.00 3.58
5998 6336 8.534954 TCCTTTATACTCTGCAGTATGTAAGT 57.465 34.615 14.67 11.02 44.33 2.24
6188 6821 7.826744 ACAAACATCAACCACCACTAAAATTTT 59.173 29.630 8.75 8.75 0.00 1.82
6189 6822 9.319143 CAAACATCAACCACCACTAAAATTTTA 57.681 29.630 10.16 10.16 0.00 1.52
6191 6824 9.892130 AACATCAACCACCACTAAAATTTTAAA 57.108 25.926 11.62 0.00 0.00 1.52
6192 6825 9.892130 ACATCAACCACCACTAAAATTTTAAAA 57.108 25.926 11.62 2.51 0.00 1.52
6256 6904 3.480470 ACCTTCACATGGAGAAACACTG 58.520 45.455 0.00 0.00 0.00 3.66
6268 6916 1.126846 GAAACACTGAAGCCGTCATCG 59.873 52.381 0.00 0.00 35.07 3.84
6281 6929 1.135972 CGTCATCGGCCTTGACAAAAG 60.136 52.381 26.13 12.51 42.90 2.27
6282 6930 1.880027 GTCATCGGCCTTGACAAAAGT 59.120 47.619 23.53 0.00 42.43 2.66
6301 6949 2.840651 AGTACCTCCACCATTTCTCCAG 59.159 50.000 0.00 0.00 0.00 3.86
6305 6953 2.622452 CCTCCACCATTTCTCCAGCATT 60.622 50.000 0.00 0.00 0.00 3.56
6308 6956 3.094572 CCACCATTTCTCCAGCATTCTT 58.905 45.455 0.00 0.00 0.00 2.52
6310 6958 3.760151 CACCATTTCTCCAGCATTCTTCA 59.240 43.478 0.00 0.00 0.00 3.02
6326 6974 7.816031 AGCATTCTTCACCAATATTTTGAACAG 59.184 33.333 5.49 0.00 34.60 3.16
6330 6978 6.265196 TCTTCACCAATATTTTGAACAGCTGT 59.735 34.615 15.25 15.25 34.60 4.40
6415 7063 3.054139 TGTTTTGATAGCCTGAGATGCCT 60.054 43.478 0.00 0.00 0.00 4.75
6419 7067 0.686224 ATAGCCTGAGATGCCTGCTC 59.314 55.000 0.00 0.00 33.63 4.26
6420 7068 0.688749 TAGCCTGAGATGCCTGCTCA 60.689 55.000 0.00 0.00 39.90 4.26
6438 7087 3.619929 GCTCAATGAAAAACCATCCATGC 59.380 43.478 0.00 0.00 0.00 4.06
6446 7095 5.105392 TGAAAAACCATCCATGCCTTCATAC 60.105 40.000 0.00 0.00 0.00 2.39
6453 7102 1.670811 CCATGCCTTCATACAACGACC 59.329 52.381 0.00 0.00 0.00 4.79
6463 7112 3.071892 TCATACAACGACCTGGGAACTTT 59.928 43.478 0.00 0.00 0.00 2.66
6474 7123 2.658548 GGAACTTTCCCCCAAGCTG 58.341 57.895 0.00 0.00 41.62 4.24
6475 7124 0.112412 GGAACTTTCCCCCAAGCTGA 59.888 55.000 0.00 0.00 41.62 4.26
6476 7125 1.272704 GGAACTTTCCCCCAAGCTGAT 60.273 52.381 0.00 0.00 41.62 2.90
6477 7126 2.025321 GGAACTTTCCCCCAAGCTGATA 60.025 50.000 0.00 0.00 41.62 2.15
6478 7127 2.808906 ACTTTCCCCCAAGCTGATAC 57.191 50.000 0.00 0.00 0.00 2.24
6480 7129 0.254747 TTTCCCCCAAGCTGATACCG 59.745 55.000 0.00 0.00 0.00 4.02
6481 7130 0.912487 TTCCCCCAAGCTGATACCGT 60.912 55.000 0.00 0.00 0.00 4.83
6490 7140 2.108168 AGCTGATACCGTGGAAGCTAA 58.892 47.619 7.88 0.00 42.25 3.09
6491 7141 2.700897 AGCTGATACCGTGGAAGCTAAT 59.299 45.455 7.88 0.00 42.25 1.73
6496 7146 6.872020 GCTGATACCGTGGAAGCTAATAATTA 59.128 38.462 0.00 0.00 0.00 1.40
6498 7148 9.436957 CTGATACCGTGGAAGCTAATAATTAAT 57.563 33.333 0.00 0.00 0.00 1.40
6499 7149 9.214957 TGATACCGTGGAAGCTAATAATTAATG 57.785 33.333 0.00 0.00 0.00 1.90
6503 7153 7.717875 ACCGTGGAAGCTAATAATTAATGCTAA 59.282 33.333 9.56 0.08 33.28 3.09
6543 7199 3.565516 GATTGCCGGTTCTTTTGAAGTC 58.434 45.455 1.90 0.00 39.39 3.01
6548 7204 3.609409 GCCGGTTCTTTTGAAGTCATCAC 60.609 47.826 1.90 0.00 39.39 3.06
6557 7213 5.689383 TTTGAAGTCATCACCACTTTAGC 57.311 39.130 0.00 0.00 37.92 3.09
6559 7215 4.910195 TGAAGTCATCACCACTTTAGCAT 58.090 39.130 0.00 0.00 34.10 3.79
6582 7238 4.431661 CGTTAGACGGTAAGAAAGGAGT 57.568 45.455 0.00 0.00 38.08 3.85
6608 7264 1.139163 CAAACCGTGCAAAAGCATCC 58.861 50.000 0.00 0.00 0.00 3.51
6609 7265 0.033366 AAACCGTGCAAAAGCATCCC 59.967 50.000 0.00 0.00 0.00 3.85
6616 7272 0.810648 GCAAAAGCATCCCGATGACA 59.189 50.000 8.89 0.00 41.20 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
220 222 1.916777 ACTGGTACAACGGGAGGGG 60.917 63.158 0.00 0.00 38.70 4.79
262 264 6.248210 GCAAATTTGAAACCACAAAGAAAACG 59.752 34.615 22.31 0.00 41.87 3.60
400 422 5.181811 TCTGGTGCAAATGATACTTTCTGTG 59.818 40.000 0.00 0.00 0.00 3.66
401 423 5.316167 TCTGGTGCAAATGATACTTTCTGT 58.684 37.500 0.00 0.00 0.00 3.41
448 603 0.242825 CCATTGCCAGTGAGCTGTTG 59.757 55.000 0.00 0.00 41.02 3.33
449 604 1.530013 GCCATTGCCAGTGAGCTGTT 61.530 55.000 0.00 0.00 41.02 3.16
450 605 1.975407 GCCATTGCCAGTGAGCTGT 60.975 57.895 0.00 0.00 41.02 4.40
461 616 0.461135 CAGTACCATTGGGCCATTGC 59.539 55.000 20.40 9.12 37.90 3.56
462 617 1.851304 ACAGTACCATTGGGCCATTG 58.149 50.000 19.18 19.18 37.90 2.82
463 618 2.310349 TGTACAGTACCATTGGGCCATT 59.690 45.455 7.26 0.00 37.90 3.16
464 619 1.919654 TGTACAGTACCATTGGGCCAT 59.080 47.619 7.26 0.00 37.90 4.40
465 620 1.003812 GTGTACAGTACCATTGGGCCA 59.996 52.381 0.00 0.00 37.90 5.36
466 621 1.680860 GGTGTACAGTACCATTGGGCC 60.681 57.143 7.78 0.00 38.12 5.80
467 622 1.280998 AGGTGTACAGTACCATTGGGC 59.719 52.381 7.78 0.00 40.74 5.36
468 623 3.263425 AGAAGGTGTACAGTACCATTGGG 59.737 47.826 7.78 0.00 40.74 4.12
469 624 4.253685 CAGAAGGTGTACAGTACCATTGG 58.746 47.826 8.30 0.00 40.74 3.16
470 625 4.690748 CACAGAAGGTGTACAGTACCATTG 59.309 45.833 8.30 0.00 42.75 2.82
500 655 2.738480 CGTCCCCTGAACGGAACA 59.262 61.111 0.00 0.00 36.51 3.18
517 672 1.096416 TTGTTGTGTTGTTCCGGACC 58.904 50.000 1.83 0.00 0.00 4.46
518 673 2.923605 TTTGTTGTGTTGTTCCGGAC 57.076 45.000 1.83 0.00 0.00 4.79
520 675 4.032331 GTGAAATTTGTTGTGTTGTTCCGG 59.968 41.667 0.00 0.00 0.00 5.14
521 676 4.623167 TGTGAAATTTGTTGTGTTGTTCCG 59.377 37.500 0.00 0.00 0.00 4.30
553 708 2.789203 GACGCCGAGTGCAATCGAC 61.789 63.158 35.37 24.82 45.56 4.20
565 720 0.093026 GTTTGATGTCTTCGACGCCG 59.907 55.000 0.00 0.00 34.95 6.46
592 747 1.004610 CTATGCGCCTTTCATGTGACG 60.005 52.381 4.18 0.00 0.00 4.35
605 760 4.956184 GTGACGTTAATTTTCTCTATGCGC 59.044 41.667 0.00 0.00 0.00 6.09
611 766 8.621286 ACTTTTGATGTGACGTTAATTTTCTCT 58.379 29.630 0.00 0.00 0.00 3.10
612 767 8.682016 CACTTTTGATGTGACGTTAATTTTCTC 58.318 33.333 0.00 0.00 37.60 2.87
616 771 6.269315 TGCACTTTTGATGTGACGTTAATTT 58.731 32.000 0.00 0.00 37.60 1.82
621 776 2.541588 GCTGCACTTTTGATGTGACGTT 60.542 45.455 0.00 0.00 37.60 3.99
622 777 1.002468 GCTGCACTTTTGATGTGACGT 60.002 47.619 0.00 0.00 37.60 4.34
623 778 1.002576 TGCTGCACTTTTGATGTGACG 60.003 47.619 0.00 0.00 37.60 4.35
648 803 5.882557 GTGGACTTGTGATGTCTATTTCCAT 59.117 40.000 0.00 0.00 33.34 3.41
649 804 5.245531 GTGGACTTGTGATGTCTATTTCCA 58.754 41.667 0.00 0.00 35.04 3.53
674 846 4.895854 GCCGTGCGTTTCTACCTA 57.104 55.556 0.00 0.00 0.00 3.08
692 865 5.388225 AATTCGTGTGAAATTTGTTGTGC 57.612 34.783 0.00 0.00 37.71 4.57
934 1116 1.290732 GATTTGGGGGAATGGAGGGAA 59.709 52.381 0.00 0.00 0.00 3.97
964 1146 1.414550 GGAGAAGCTGGCTAGGGTTAG 59.585 57.143 0.00 0.00 0.00 2.34
1005 1191 2.856988 AAGGAGGGGGCCGTGAAA 60.857 61.111 0.00 0.00 0.00 2.69
1766 1964 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1767 1965 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
1768 1966 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1769 1967 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1770 1968 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
1771 1969 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1772 1970 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1773 1971 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
1774 1972 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1775 1973 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1776 1974 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
1777 1975 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1778 1976 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1779 1977 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
1780 1978 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1794 1992 2.439104 GGTGCTGCCCTAGGAGGAG 61.439 68.421 11.48 12.13 37.67 3.69
1940 2138 7.174946 TGAACAGAAATTCCACAAATAGAGACC 59.825 37.037 0.00 0.00 0.00 3.85
2033 2346 7.337938 TCCAGCAATAGATTCACTGATTTACA 58.662 34.615 0.00 0.00 0.00 2.41
2034 2347 7.792374 TCCAGCAATAGATTCACTGATTTAC 57.208 36.000 0.00 0.00 0.00 2.01
2080 2393 9.175312 CTAGTAGACTACACAAGGAATCAACTA 57.825 37.037 14.95 0.00 0.00 2.24
2083 2396 9.696572 ATACTAGTAGACTACACAAGGAATCAA 57.303 33.333 14.95 0.00 0.00 2.57
2084 2397 9.121658 CATACTAGTAGACTACACAAGGAATCA 57.878 37.037 14.95 0.00 0.00 2.57
2126 2439 7.039504 ACAAATAGAGTCAGCATTTCCATTGTT 60.040 33.333 0.00 0.00 0.00 2.83
2130 2443 6.660521 TGAACAAATAGAGTCAGCATTTCCAT 59.339 34.615 0.00 0.00 0.00 3.41
2143 2456 7.566709 GTTGCCACAAAATTGAACAAATAGAG 58.433 34.615 0.00 0.00 0.00 2.43
2144 2457 6.199908 CGTTGCCACAAAATTGAACAAATAGA 59.800 34.615 0.00 0.00 0.00 1.98
2145 2458 6.019156 ACGTTGCCACAAAATTGAACAAATAG 60.019 34.615 0.00 0.91 0.00 1.73
2153 2466 4.602995 GAACTACGTTGCCACAAAATTGA 58.397 39.130 0.00 0.00 0.00 2.57
2169 2482 7.629130 TGGTTATGTGTACAAAAACGAACTAC 58.371 34.615 0.00 0.00 30.89 2.73
2174 2487 5.124645 ACCTGGTTATGTGTACAAAAACGA 58.875 37.500 0.00 0.00 30.89 3.85
2176 2489 7.012610 ACACTACCTGGTTATGTGTACAAAAAC 59.987 37.037 22.35 2.41 39.65 2.43
2187 2500 5.537300 AGATGCTACACTACCTGGTTATG 57.463 43.478 3.84 6.56 0.00 1.90
2188 2501 6.611785 TCTAGATGCTACACTACCTGGTTAT 58.388 40.000 3.84 0.00 0.00 1.89
2190 2503 4.868268 TCTAGATGCTACACTACCTGGTT 58.132 43.478 3.84 0.00 0.00 3.67
2191 2504 4.521536 TCTAGATGCTACACTACCTGGT 57.478 45.455 4.05 4.05 0.00 4.00
2224 2537 4.868172 TGATCCCATGATTTCTGAAGGT 57.132 40.909 0.00 0.00 0.00 3.50
2331 2644 1.913778 ATCAATCTGTGTGCAAGGCA 58.086 45.000 0.00 0.00 35.60 4.75
2348 2661 7.646922 GGAAACAGCAGATGATATTGTGAAATC 59.353 37.037 0.00 0.00 0.00 2.17
2354 2667 5.121380 AGGGAAACAGCAGATGATATTGT 57.879 39.130 0.00 0.00 0.00 2.71
2395 2708 8.225603 TGAAACTGTTTCTTTCTTCTTATGCT 57.774 30.769 27.75 0.00 40.32 3.79
2458 2771 7.608376 TGTCATGGATCAAAATTGCAATTGAAT 59.392 29.630 24.74 17.26 38.88 2.57
2567 2883 2.279318 TGTTTACCGACGTGCGCA 60.279 55.556 5.66 5.66 39.11 6.09
2568 2884 2.169327 GTGTTTACCGACGTGCGC 59.831 61.111 0.00 0.00 39.11 6.09
2575 2891 3.271729 TGAGCAAAACTGTGTTTACCGA 58.728 40.909 0.00 0.00 0.00 4.69
2601 2917 9.891828 CTAGCAAATGAAGTGTGTTAAATAACA 57.108 29.630 1.96 1.96 43.32 2.41
2671 2988 8.845227 TGTGCTGTTTACATAATTTCTCTGAAA 58.155 29.630 0.00 0.00 0.00 2.69
2769 3086 9.797642 ATCCACATAATAACAGAATGCTGATAA 57.202 29.630 8.02 0.00 45.17 1.75
2789 3106 7.514721 AGAAAGTAGTTAAAGGTTCATCCACA 58.485 34.615 0.00 0.00 39.02 4.17
2878 3199 0.251922 AGGGCATGTGAGCACCAAAT 60.252 50.000 0.00 0.00 39.23 2.32
2969 3290 9.484326 CAAGCTAAACAAAACACATTTTTAACC 57.516 29.630 0.00 0.00 35.79 2.85
3222 3544 3.852578 AGGGAGCTAAAGGAAAAGGATCA 59.147 43.478 0.00 0.00 0.00 2.92
3281 3603 8.696410 TCTCAAAGGAAAAACATAACAACAAC 57.304 30.769 0.00 0.00 0.00 3.32
3282 3604 9.145865 GTTCTCAAAGGAAAAACATAACAACAA 57.854 29.630 0.00 0.00 0.00 2.83
3283 3605 7.762159 GGTTCTCAAAGGAAAAACATAACAACA 59.238 33.333 0.00 0.00 0.00 3.33
3450 3777 7.202526 ACATTGGTGTAGATTTTGTTGTCTTG 58.797 34.615 0.00 0.00 36.63 3.02
3498 3825 2.370281 TCGTGCAGCTTTCTTCTAGG 57.630 50.000 0.00 0.00 0.00 3.02
3655 3982 5.728898 GCTTCTTCTGCATATACTTGTGCAC 60.729 44.000 10.75 10.75 43.96 4.57
3682 4009 5.734498 CAGATTTACTGTTTTGCTGCGATAC 59.266 40.000 3.80 3.80 41.30 2.24
3686 4013 4.145876 TCAGATTTACTGTTTTGCTGCG 57.854 40.909 0.00 0.00 45.86 5.18
3844 4171 2.693074 GTGAAACCTTGGAGCCAGAAAA 59.307 45.455 0.00 0.00 0.00 2.29
4076 4403 8.429641 ACCTGTAGTTCAGATTTTCTTCTACAA 58.570 33.333 0.00 0.00 46.27 2.41
4156 4483 8.962679 TCCTACTAAAAAGAAGCAAAAGAACAA 58.037 29.630 0.00 0.00 0.00 2.83
4161 4488 6.382608 GGCTCCTACTAAAAAGAAGCAAAAG 58.617 40.000 0.00 0.00 0.00 2.27
4186 4513 0.400594 ACCACTACTCTGGCCAAACC 59.599 55.000 7.01 0.00 34.20 3.27
4505 4832 4.274214 GCAAGTGATGAATGCATAGCACTA 59.726 41.667 18.11 3.01 43.04 2.74
4538 4865 7.934457 AGACATAAACCTGCAGCAATAATAAG 58.066 34.615 8.66 0.00 0.00 1.73
4612 4939 9.167311 TCAGAATAGAGAAGCATTTTACCTTTC 57.833 33.333 0.00 0.00 0.00 2.62
4750 5079 9.393786 AGAAGTTCATTTCCTAGGGCTATAATA 57.606 33.333 9.46 0.00 0.00 0.98
4753 5082 7.691993 AAGAAGTTCATTTCCTAGGGCTATA 57.308 36.000 9.46 0.00 0.00 1.31
4829 5163 7.565398 ACTGATTTATCTTCTCCTAGCTTACCA 59.435 37.037 0.00 0.00 0.00 3.25
4898 5232 2.618053 TCAGCTTAGGTTTTAGAGCGC 58.382 47.619 0.00 0.00 39.99 5.92
4899 5233 5.607119 TTTTCAGCTTAGGTTTTAGAGCG 57.393 39.130 0.00 0.00 39.99 5.03
4996 5330 8.095169 ACTTTTCTTACTCCGACAAGATTACAT 58.905 33.333 0.00 0.00 31.15 2.29
5003 5338 5.047519 TCCCTACTTTTCTTACTCCGACAAG 60.048 44.000 0.00 0.00 0.00 3.16
5008 5343 4.021916 TCCTCCCTACTTTTCTTACTCCG 58.978 47.826 0.00 0.00 0.00 4.63
5031 5366 4.162698 ACGGTAAGCATCCAACTGGTAATA 59.837 41.667 0.00 0.00 36.34 0.98
5099 5434 2.836636 ATCTCACCTAGTCTGGCAGA 57.163 50.000 14.43 14.43 0.00 4.26
5101 5436 3.840666 AGAAAATCTCACCTAGTCTGGCA 59.159 43.478 0.00 0.00 0.00 4.92
5111 5446 2.238395 AGGGAGCAGAGAAAATCTCACC 59.762 50.000 9.82 7.09 45.73 4.02
5112 5447 3.625649 AGGGAGCAGAGAAAATCTCAC 57.374 47.619 9.82 1.96 45.73 3.51
5122 5457 1.380524 CATTCAGCAAGGGAGCAGAG 58.619 55.000 0.00 0.00 36.85 3.35
5123 5458 0.034767 CCATTCAGCAAGGGAGCAGA 60.035 55.000 0.00 0.00 35.24 4.26
5132 5467 3.454719 TCAATTCTCCCCATTCAGCAA 57.545 42.857 0.00 0.00 0.00 3.91
5137 5472 4.176120 ACCAGATCAATTCTCCCCATTC 57.824 45.455 0.00 0.00 29.93 2.67
5170 5505 1.898574 CCGCCCACATATCCTTGCC 60.899 63.158 0.00 0.00 0.00 4.52
5181 5516 0.381801 CAATGCTCATAACCGCCCAC 59.618 55.000 0.00 0.00 0.00 4.61
5187 5522 5.119125 GCAAGTTTGTTCAATGCTCATAACC 59.881 40.000 3.37 0.00 34.29 2.85
5281 5616 5.126869 ACATGTGTGGTTTGTTTGAATCTCA 59.873 36.000 0.00 0.00 0.00 3.27
5306 5641 8.128582 CCAAATAACACACACCATCACATATAC 58.871 37.037 0.00 0.00 0.00 1.47
5308 5643 6.096705 CCCAAATAACACACACCATCACATAT 59.903 38.462 0.00 0.00 0.00 1.78
5309 5644 5.417266 CCCAAATAACACACACCATCACATA 59.583 40.000 0.00 0.00 0.00 2.29
5310 5645 4.220382 CCCAAATAACACACACCATCACAT 59.780 41.667 0.00 0.00 0.00 3.21
5325 5660 6.694445 AACATTTCCATGGAACCCAAATAA 57.306 33.333 27.04 10.17 36.95 1.40
5334 5669 9.844257 ATGTTTTTCTTAAACATTTCCATGGAA 57.156 25.926 23.63 23.63 45.52 3.53
5349 5684 8.869109 AGGATTGATTGACCAATGTTTTTCTTA 58.131 29.630 0.00 0.00 36.93 2.10
5350 5685 7.738847 AGGATTGATTGACCAATGTTTTTCTT 58.261 30.769 0.00 0.00 36.93 2.52
5363 5698 7.228308 CCAGGAAAGATTCTAGGATTGATTGAC 59.772 40.741 0.00 0.00 0.00 3.18
5373 5708 5.683876 TCACTTCCAGGAAAGATTCTAGG 57.316 43.478 2.72 0.00 0.00 3.02
5385 5721 4.398319 ACACTGGTTTTATCACTTCCAGG 58.602 43.478 12.95 5.74 46.71 4.45
5420 5757 1.305219 ATTGACCCGTTGGCATCACG 61.305 55.000 4.77 4.77 33.59 4.35
5431 5768 6.238925 GGAATAAGGTTATTTCCATTGACCCG 60.239 42.308 0.00 0.00 33.72 5.28
5435 5772 8.119246 TGAAGGGAATAAGGTTATTTCCATTGA 58.881 33.333 18.33 7.53 46.83 2.57
5440 5777 6.183360 GCAGTGAAGGGAATAAGGTTATTTCC 60.183 42.308 10.76 10.76 45.42 3.13
5442 5779 6.252995 TGCAGTGAAGGGAATAAGGTTATTT 58.747 36.000 0.00 0.00 33.72 1.40
5445 5782 4.919774 TGCAGTGAAGGGAATAAGGTTA 57.080 40.909 0.00 0.00 0.00 2.85
5469 5806 7.796054 ACATTTAGTCAGATAGCAGTACCAAT 58.204 34.615 0.00 0.00 0.00 3.16
5578 5915 1.474332 TTGCCGTAGAAGAACCCCGT 61.474 55.000 0.00 0.00 0.00 5.28
5658 5995 0.602905 CCACCAACCGACCTCTTCAC 60.603 60.000 0.00 0.00 0.00 3.18
5659 5996 1.752198 CCACCAACCGACCTCTTCA 59.248 57.895 0.00 0.00 0.00 3.02
5660 5997 1.671379 GCCACCAACCGACCTCTTC 60.671 63.158 0.00 0.00 0.00 2.87
5691 6028 2.436173 GACCTCTTCTCTATTGTGGGGG 59.564 54.545 0.00 0.00 0.00 5.40
5692 6029 3.107601 TGACCTCTTCTCTATTGTGGGG 58.892 50.000 0.00 0.00 0.00 4.96
5693 6030 3.772025 AGTGACCTCTTCTCTATTGTGGG 59.228 47.826 0.00 0.00 0.00 4.61
5818 6155 2.721425 ACAAAGAAGGGTTTCGACCA 57.279 45.000 0.00 0.00 38.38 4.02
5847 6184 2.069273 CACAGTTGAGTGGTTCGGATC 58.931 52.381 0.00 0.00 35.88 3.36
5850 6187 2.519377 TACACAGTTGAGTGGTTCGG 57.481 50.000 0.00 0.00 43.72 4.30
5853 6190 3.377172 GCAGTTTACACAGTTGAGTGGTT 59.623 43.478 0.00 0.00 43.72 3.67
5856 6193 3.623060 ACAGCAGTTTACACAGTTGAGTG 59.377 43.478 0.00 0.00 44.93 3.51
5872 6209 2.163818 TCGTCCCTTAACAACAGCAG 57.836 50.000 0.00 0.00 0.00 4.24
5873 6210 2.623878 TTCGTCCCTTAACAACAGCA 57.376 45.000 0.00 0.00 0.00 4.41
5874 6211 2.225727 CCTTTCGTCCCTTAACAACAGC 59.774 50.000 0.00 0.00 0.00 4.40
5875 6212 3.497262 GTCCTTTCGTCCCTTAACAACAG 59.503 47.826 0.00 0.00 0.00 3.16
5891 6228 2.841160 GCAAACACGCCCGTCCTTT 61.841 57.895 0.00 0.00 0.00 3.11
5904 6241 4.096984 CCATCACCTCCATAAAGAGCAAAC 59.903 45.833 0.00 0.00 32.17 2.93
5939 6277 4.586421 TCACAAAACATGCATTAAGACCCA 59.414 37.500 0.00 0.00 0.00 4.51
5998 6336 8.653338 GCGTTGAACTACTGATATTAACTCAAA 58.347 33.333 0.00 0.00 0.00 2.69
6011 6349 1.783284 TCAGCTGCGTTGAACTACTG 58.217 50.000 9.47 0.00 0.00 2.74
6235 6868 3.136443 TCAGTGTTTCTCCATGTGAAGGT 59.864 43.478 0.00 0.00 0.00 3.50
6239 6887 3.141398 GCTTCAGTGTTTCTCCATGTGA 58.859 45.455 0.00 0.00 0.00 3.58
6245 6893 1.149148 GACGGCTTCAGTGTTTCTCC 58.851 55.000 0.00 0.00 0.00 3.71
6268 6916 2.160205 GGAGGTACTTTTGTCAAGGCC 58.840 52.381 0.00 0.00 41.55 5.19
6271 6919 3.815809 TGGTGGAGGTACTTTTGTCAAG 58.184 45.455 0.00 0.00 41.55 3.02
6272 6920 3.935818 TGGTGGAGGTACTTTTGTCAA 57.064 42.857 0.00 0.00 41.55 3.18
6273 6921 4.447138 AATGGTGGAGGTACTTTTGTCA 57.553 40.909 0.00 0.00 41.55 3.58
6274 6922 5.070685 AGAAATGGTGGAGGTACTTTTGTC 58.929 41.667 0.00 0.00 41.55 3.18
6275 6923 5.061721 AGAAATGGTGGAGGTACTTTTGT 57.938 39.130 0.00 0.00 41.55 2.83
6276 6924 4.459337 GGAGAAATGGTGGAGGTACTTTTG 59.541 45.833 0.00 0.00 41.55 2.44
6281 6929 2.681097 GCTGGAGAAATGGTGGAGGTAC 60.681 54.545 0.00 0.00 0.00 3.34
6282 6930 1.559682 GCTGGAGAAATGGTGGAGGTA 59.440 52.381 0.00 0.00 0.00 3.08
6301 6949 7.412237 GCTGTTCAAAATATTGGTGAAGAATGC 60.412 37.037 12.77 9.73 37.15 3.56
6305 6953 6.265196 ACAGCTGTTCAAAATATTGGTGAAGA 59.735 34.615 15.25 11.32 37.15 2.87
6308 6956 7.517614 TTACAGCTGTTCAAAATATTGGTGA 57.482 32.000 27.06 0.00 37.15 4.02
6310 6958 7.867403 CAGTTTACAGCTGTTCAAAATATTGGT 59.133 33.333 27.06 0.00 37.15 3.67
6326 6974 6.089417 GGAAATATGTTGCAACAGTTTACAGC 59.911 38.462 31.04 22.79 43.04 4.40
6330 6978 6.656632 TGGGAAATATGTTGCAACAGTTTA 57.343 33.333 33.44 22.74 43.04 2.01
6339 6987 5.117584 TCAATGCAATGGGAAATATGTTGC 58.882 37.500 1.05 0.00 43.93 4.17
6370 7018 5.931724 CAGCGGGATTAAAAACAAAAGGATT 59.068 36.000 0.00 0.00 0.00 3.01
6377 7025 5.661458 TCAAAACAGCGGGATTAAAAACAA 58.339 33.333 0.00 0.00 0.00 2.83
6380 7028 6.096695 GCTATCAAAACAGCGGGATTAAAAA 58.903 36.000 0.00 0.00 0.00 1.94
6383 7031 3.630312 GGCTATCAAAACAGCGGGATTAA 59.370 43.478 0.00 0.00 38.73 1.40
6415 7063 4.823157 CATGGATGGTTTTTCATTGAGCA 58.177 39.130 0.00 0.00 0.00 4.26
6419 7067 4.210724 AGGCATGGATGGTTTTTCATTG 57.789 40.909 0.00 0.00 0.00 2.82
6420 7068 4.286549 TGAAGGCATGGATGGTTTTTCATT 59.713 37.500 0.00 0.00 0.00 2.57
6438 7087 1.553248 TCCCAGGTCGTTGTATGAAGG 59.447 52.381 0.00 0.00 0.00 3.46
6446 7095 1.235724 GGAAAGTTCCCAGGTCGTTG 58.764 55.000 0.00 0.00 41.62 4.10
6463 7112 1.306654 ACGGTATCAGCTTGGGGGA 60.307 57.895 0.00 0.00 0.00 4.81
6473 7122 9.214957 CATTAATTATTAGCTTCCACGGTATCA 57.785 33.333 0.00 0.00 0.00 2.15
6474 7123 8.175716 GCATTAATTATTAGCTTCCACGGTATC 58.824 37.037 0.00 0.00 0.00 2.24
6475 7124 7.883311 AGCATTAATTATTAGCTTCCACGGTAT 59.117 33.333 0.00 0.00 29.98 2.73
6476 7125 7.221450 AGCATTAATTATTAGCTTCCACGGTA 58.779 34.615 0.00 0.00 29.98 4.02
6477 7126 6.062095 AGCATTAATTATTAGCTTCCACGGT 58.938 36.000 0.00 0.00 29.98 4.83
6478 7127 6.560253 AGCATTAATTATTAGCTTCCACGG 57.440 37.500 0.00 0.00 29.98 4.94
6522 7172 3.004315 TGACTTCAAAAGAACCGGCAATC 59.996 43.478 0.00 0.00 0.00 2.67
6535 7191 5.129634 TGCTAAAGTGGTGATGACTTCAAA 58.870 37.500 0.00 0.00 35.70 2.69
6543 7199 6.019801 GTCTAACGTATGCTAAAGTGGTGATG 60.020 42.308 0.00 0.00 0.00 3.07
6548 7204 3.795101 CCGTCTAACGTATGCTAAAGTGG 59.205 47.826 0.00 0.00 40.58 4.00
6557 7213 5.883661 TCCTTTCTTACCGTCTAACGTATG 58.116 41.667 0.00 0.00 40.58 2.39
6559 7215 5.003804 ACTCCTTTCTTACCGTCTAACGTA 58.996 41.667 0.00 0.00 40.58 3.57
6571 7227 7.767198 CACGGTTTGGATTATACTCCTTTCTTA 59.233 37.037 10.24 0.00 36.20 2.10
6573 7229 6.113411 CACGGTTTGGATTATACTCCTTTCT 58.887 40.000 10.24 0.00 36.20 2.52
6582 7238 4.739195 GCTTTTGCACGGTTTGGATTATA 58.261 39.130 0.00 0.00 46.58 0.98
6608 7264 3.251479 TCACTGAATTCCTGTCATCGG 57.749 47.619 2.27 0.00 0.00 4.18
6609 7265 5.352293 TGAAATCACTGAATTCCTGTCATCG 59.648 40.000 2.27 0.00 0.00 3.84
6616 7272 7.587037 TGAAAACTGAAATCACTGAATTCCT 57.413 32.000 2.27 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.