Multiple sequence alignment - TraesCS1B01G068100

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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 TraesCS1B01G068100 chr1B 100.000 7216 0 0 1 7216 52902646 52909861 0.000000e+00 13326.0
1 TraesCS1B01G068100 chr1B 81.880 585 80 9 3336 3919 52905630 52906189 3.050000e-128 470.0
2 TraesCS1B01G068100 chr1B 81.880 585 80 9 2985 3544 52905981 52906564 3.050000e-128 470.0
3 TraesCS1B01G068100 chr1B 85.839 459 45 10 6703 7150 52910239 52910688 3.050000e-128 470.0
4 TraesCS1B01G068100 chr1B 86.445 391 39 7 6222 6608 52909817 52910197 4.030000e-112 416.0
5 TraesCS1B01G068100 chr1B 77.412 456 90 9 4603 5056 52906594 52907038 7.180000e-65 259.0
6 TraesCS1B01G068100 chr1B 77.412 456 90 9 3949 4393 52907248 52907701 7.180000e-65 259.0
7 TraesCS1B01G068100 chr1B 92.105 38 2 1 6634 6670 52910198 52910235 1.300000e-02 52.8
8 TraesCS1B01G068100 chr1A 92.116 5492 328 44 1738 7150 32896681 32902146 0.000000e+00 7646.0
9 TraesCS1B01G068100 chr1A 80.808 594 88 9 3336 3928 32897930 32898498 6.640000e-120 442.0
10 TraesCS1B01G068100 chr1A 81.455 550 67 23 320 849 32895380 32895914 1.120000e-112 418.0
11 TraesCS1B01G068100 chr1A 78.462 455 87 5 3949 4393 32899566 32900019 3.290000e-73 287.0
12 TraesCS1B01G068100 chr1A 92.222 180 8 2 12 186 32895030 32895208 4.320000e-62 250.0
13 TraesCS1B01G068100 chr1A 82.648 219 18 11 886 1100 32895988 32896190 7.440000e-40 176.0
14 TraesCS1B01G068100 chr1D 90.963 3364 219 37 1400 4683 34623395 34626753 0.000000e+00 4449.0
15 TraesCS1B01G068100 chr1D 92.012 2003 116 13 4718 6697 34626749 34628730 0.000000e+00 2772.0
16 TraesCS1B01G068100 chr1D 87.030 1118 106 20 297 1401 34622273 34623364 0.000000e+00 1225.0
17 TraesCS1B01G068100 chr1D 80.808 594 88 10 3336 3928 34625037 34625605 6.640000e-120 442.0
18 TraesCS1B01G068100 chr1D 90.674 193 4 6 2 186 34621918 34622104 2.010000e-60 244.0
19 TraesCS1B01G068100 chr1D 79.412 340 66 3 4056 4393 34626750 34627087 3.360000e-58 237.0
20 TraesCS1B01G068100 chr1D 77.481 262 42 14 3088 3333 34626460 34626720 2.710000e-29 141.0
21 TraesCS1B01G068100 chr2A 94.118 102 4 2 1000 1100 36628193 36628293 3.490000e-33 154.0
22 TraesCS1B01G068100 chr2B 94.898 98 3 2 1000 1096 55881137 55881233 1.250000e-32 152.0
23 TraesCS1B01G068100 chr2D 93.137 102 5 2 1000 1100 33718817 33718917 1.620000e-31 148.0
24 TraesCS1B01G068100 chr6A 93.878 98 4 2 1000 1096 76578628 76578724 5.830000e-31 147.0
25 TraesCS1B01G068100 chr3D 91.589 107 8 1 991 1096 614203929 614203823 5.830000e-31 147.0
26 TraesCS1B01G068100 chr3B 92.233 103 8 0 994 1096 823577946 823577844 5.830000e-31 147.0
27 TraesCS1B01G068100 chr3A 91.589 107 8 1 991 1096 750504234 750504128 5.830000e-31 147.0


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 TraesCS1B01G068100 chr1B 52902646 52909861 7215 False 13326.000000 13326 100.000000 1 7216 1 chr1B.!!$F1 7215
1 TraesCS1B01G068100 chr1B 52905630 52910688 5058 False 342.400000 470 83.281857 2985 7150 7 chr1B.!!$F2 4165
2 TraesCS1B01G068100 chr1A 32895030 32902146 7116 False 2122.500000 7646 87.110250 12 7150 4 chr1A.!!$F1 7138
3 TraesCS1B01G068100 chr1A 32897930 32900019 2089 False 364.500000 442 79.635000 3336 4393 2 chr1A.!!$F2 1057
4 TraesCS1B01G068100 chr1D 34621918 34628730 6812 False 1358.571429 4449 85.482857 2 6697 7 chr1D.!!$F1 6695

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
83 85 0.106066 TAATTGCATCCTGGCTGGGG 60.106 55.0 10.79 4.74 36.20 4.96 F
1672 1887 0.387622 CTTGCAATTGGACACCAGCG 60.388 55.0 7.72 0.00 33.81 5.18 F
2132 2375 0.035915 GGAAGCCAGGACTGAAGGAC 60.036 60.0 0.00 0.00 0.00 3.85 F
2834 3077 0.118144 AACTGGAGGGAGAGAAGGCT 59.882 55.0 0.00 0.00 0.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1746 1989 0.035317 AGGCAATCGCTCAGTGTTCA 59.965 50.000 0.00 0.00 38.60 3.18 R
2570 2813 0.583438 CCATCTTAACGCTGGCATCG 59.417 55.000 9.46 9.46 0.00 3.84 R
2958 3201 2.143925 GAAGCTACTTGCCGTTTCAGT 58.856 47.619 0.00 0.00 44.23 3.41 R
7090 8292 1.145571 AGCTCTAGGGAGACGGAGAT 58.854 55.000 0.00 0.00 41.86 2.75 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
83 85 0.106066 TAATTGCATCCTGGCTGGGG 60.106 55.000 10.79 4.74 36.20 4.96
101 103 5.417580 GCTGGGGTGTAAAGTATCAAATGAA 59.582 40.000 0.00 0.00 0.00 2.57
103 105 7.363793 GCTGGGGTGTAAAGTATCAAATGAAAT 60.364 37.037 0.00 0.00 0.00 2.17
105 107 7.093552 TGGGGTGTAAAGTATCAAATGAAATGG 60.094 37.037 0.00 0.00 0.00 3.16
214 249 3.412386 GTGTTTTGGACTGCCTAGTGAT 58.588 45.455 0.00 0.00 37.25 3.06
215 250 3.821033 GTGTTTTGGACTGCCTAGTGATT 59.179 43.478 0.00 0.00 37.25 2.57
217 252 4.892934 TGTTTTGGACTGCCTAGTGATTTT 59.107 37.500 0.00 0.00 37.25 1.82
218 253 5.009610 TGTTTTGGACTGCCTAGTGATTTTC 59.990 40.000 0.00 0.00 37.25 2.29
221 256 2.680339 GGACTGCCTAGTGATTTTCTGC 59.320 50.000 0.00 0.00 37.25 4.26
224 260 2.681848 CTGCCTAGTGATTTTCTGCTGG 59.318 50.000 0.00 0.00 0.00 4.85
227 263 3.370527 GCCTAGTGATTTTCTGCTGGGTA 60.371 47.826 0.00 0.00 32.99 3.69
238 274 1.806542 CTGCTGGGTATGTGTGTGAAC 59.193 52.381 0.00 0.00 0.00 3.18
240 276 2.226330 GCTGGGTATGTGTGTGAACAA 58.774 47.619 0.00 0.00 32.81 2.83
241 277 2.226437 GCTGGGTATGTGTGTGAACAAG 59.774 50.000 0.00 0.00 32.81 3.16
248 284 2.279741 TGTGTGTGAACAAGCTCTGTC 58.720 47.619 0.00 0.00 37.23 3.51
299 380 3.118445 GGAGAGGAAGCAGCTGTCTAAAT 60.118 47.826 16.64 2.60 0.00 1.40
300 381 4.512484 GAGAGGAAGCAGCTGTCTAAATT 58.488 43.478 16.64 1.04 0.00 1.82
301 382 4.916183 AGAGGAAGCAGCTGTCTAAATTT 58.084 39.130 16.64 0.00 0.00 1.82
302 383 5.320277 AGAGGAAGCAGCTGTCTAAATTTT 58.680 37.500 16.64 0.00 0.00 1.82
303 384 5.772169 AGAGGAAGCAGCTGTCTAAATTTTT 59.228 36.000 16.64 0.00 0.00 1.94
384 471 5.220970 GCTTTAACTTGCTACTGACACCAAA 60.221 40.000 0.00 0.00 0.00 3.28
389 476 3.769739 TGCTACTGACACCAAATCTGT 57.230 42.857 0.00 0.00 33.41 3.41
399 486 8.527810 ACTGACACCAAATCTGTAAAAGAAAAA 58.472 29.630 0.00 0.00 38.79 1.94
401 488 7.978975 TGACACCAAATCTGTAAAAGAAAAAGG 59.021 33.333 0.00 0.00 38.79 3.11
405 492 9.599866 ACCAAATCTGTAAAAGAAAAAGGAAAG 57.400 29.630 0.00 0.00 38.79 2.62
407 494 9.816354 CAAATCTGTAAAAGAAAAAGGAAAGGA 57.184 29.630 0.00 0.00 38.79 3.36
443 533 5.099575 GGAAAAAGAAGACGAAAGCACAAA 58.900 37.500 0.00 0.00 0.00 2.83
444 534 5.004440 GGAAAAAGAAGACGAAAGCACAAAC 59.996 40.000 0.00 0.00 0.00 2.93
446 536 6.431198 AAAAGAAGACGAAAGCACAAACTA 57.569 33.333 0.00 0.00 0.00 2.24
498 588 3.636043 AACGTCGTGCACTTGCCG 61.636 61.111 16.19 13.17 41.18 5.69
578 676 0.543174 GGACCCACACCTCAGAGACT 60.543 60.000 0.00 0.00 0.00 3.24
609 707 3.078836 GCCCTGCACCATGCCATT 61.079 61.111 0.00 0.00 44.23 3.16
610 708 2.897207 CCCTGCACCATGCCATTG 59.103 61.111 0.00 0.00 44.23 2.82
624 722 1.171308 CCATTGCCACCACTTCTCTG 58.829 55.000 0.00 0.00 0.00 3.35
709 807 7.830264 GCAGGAACATTGCTACGAAGTATTCA 61.830 42.308 0.00 0.00 44.56 2.57
710 808 9.211900 GCAGGAACATTGCTACGAAGTATTCAA 62.212 40.741 0.00 0.00 44.56 2.69
721 819 3.536570 GAAGTATTCAACTCCTGCTCCC 58.463 50.000 0.00 0.00 46.62 4.30
743 841 2.545810 CCCTTCTCCTCCTGTTCTTCT 58.454 52.381 0.00 0.00 0.00 2.85
780 879 2.094700 CCGTCTCGTTCATCTTCTTCCA 60.095 50.000 0.00 0.00 0.00 3.53
799 898 2.093181 CCAAAGATGACATACGTCCCCA 60.093 50.000 0.00 0.00 41.85 4.96
800 899 3.433598 CCAAAGATGACATACGTCCCCAT 60.434 47.826 0.00 0.00 41.85 4.00
801 900 3.475566 AAGATGACATACGTCCCCATG 57.524 47.619 0.00 0.00 41.85 3.66
809 908 1.034838 TACGTCCCCATGGCAAATGC 61.035 55.000 6.09 0.00 41.14 3.56
884 1004 1.493950 GATCAGCAGGGACGCATTCG 61.494 60.000 0.00 0.00 42.43 3.34
911 1053 3.730761 CTTGTGTGCGCTGGAGGC 61.731 66.667 9.73 0.00 37.64 4.70
953 1095 2.125066 TTGGAGGAAGAGGAGGGGCT 62.125 60.000 0.00 0.00 0.00 5.19
954 1096 1.228920 TGGAGGAAGAGGAGGGGCTA 61.229 60.000 0.00 0.00 0.00 3.93
955 1097 0.471022 GGAGGAAGAGGAGGGGCTAG 60.471 65.000 0.00 0.00 0.00 3.42
956 1098 0.471022 GAGGAAGAGGAGGGGCTAGG 60.471 65.000 0.00 0.00 0.00 3.02
1111 1256 1.325355 AGGTCCGTTCGTCTTCTTCA 58.675 50.000 0.00 0.00 0.00 3.02
1113 1258 1.050767 GTCCGTTCGTCTTCTTCACG 58.949 55.000 0.00 0.00 38.67 4.35
1114 1259 0.662374 TCCGTTCGTCTTCTTCACGC 60.662 55.000 0.00 0.00 37.18 5.34
1144 1289 0.517755 ATACACGCGCCTAGATCTCG 59.482 55.000 5.73 0.00 0.00 4.04
1169 1314 3.508762 CTTGCTTGGCACATCTTTGATC 58.491 45.455 0.00 0.00 38.71 2.92
1175 1320 5.063060 GCTTGGCACATCTTTGATCATTTTC 59.937 40.000 0.00 0.00 39.30 2.29
1177 1322 4.081531 TGGCACATCTTTGATCATTTTCCC 60.082 41.667 0.00 0.00 0.00 3.97
1187 1332 4.335416 TGATCATTTTCCCTGGTCAGAAC 58.665 43.478 0.00 0.00 30.45 3.01
1196 1341 2.507484 CCTGGTCAGAACTTTGCATGA 58.493 47.619 0.00 0.00 0.00 3.07
1208 1353 3.471354 TGCATGATGTCCTGCAGAG 57.529 52.632 17.39 5.49 43.11 3.35
1209 1354 0.616891 TGCATGATGTCCTGCAGAGT 59.383 50.000 17.39 0.00 43.11 3.24
1213 1358 3.340928 CATGATGTCCTGCAGAGTTTGA 58.659 45.455 17.39 0.00 0.00 2.69
1226 1371 5.822519 TGCAGAGTTTGACAAATGAAGTAGT 59.177 36.000 3.49 0.00 0.00 2.73
1227 1372 6.138761 GCAGAGTTTGACAAATGAAGTAGTG 58.861 40.000 3.49 0.00 0.00 2.74
1255 1400 5.698089 CGTATATGGTCAGTTGCTTCATGAT 59.302 40.000 0.00 0.00 0.00 2.45
1259 1404 3.253921 TGGTCAGTTGCTTCATGATTGTG 59.746 43.478 0.00 0.00 0.00 3.33
1261 1406 4.261741 GGTCAGTTGCTTCATGATTGTGTT 60.262 41.667 0.00 0.00 0.00 3.32
1280 1429 4.917415 GTGTTATGGTAGTTGCAGCAAAAG 59.083 41.667 10.11 0.00 0.00 2.27
1285 1434 3.004629 TGGTAGTTGCAGCAAAAGATGTG 59.995 43.478 10.11 0.00 0.00 3.21
1304 1453 5.833406 TGTGCTTTGTATCACCATTATGG 57.167 39.130 10.08 10.08 45.02 2.74
1319 1468 4.648762 CCATTATGGGCCAAGAAACACATA 59.351 41.667 11.89 0.00 32.67 2.29
1325 1474 4.947388 TGGGCCAAGAAACACATAGATTAC 59.053 41.667 2.13 0.00 0.00 1.89
1330 1479 7.148373 GGCCAAGAAACACATAGATTACGTAAA 60.148 37.037 12.81 0.00 0.00 2.01
1353 1502 8.894768 AAAGAAATATAGGCTACATCACTGTC 57.105 34.615 0.00 0.00 36.79 3.51
1368 1517 5.169992 TCACTGTCAGGTGATCATGAAAT 57.830 39.130 0.00 0.00 40.72 2.17
1374 1523 6.798482 TGTCAGGTGATCATGAAATTTATGC 58.202 36.000 0.00 0.00 36.14 3.14
1382 1531 4.862350 TCATGAAATTTATGCATGGCTCG 58.138 39.130 10.16 0.00 39.76 5.03
1401 1550 4.693283 CTCGGGTTAGCAGAAATGTATCA 58.307 43.478 0.00 0.00 0.00 2.15
1403 1552 3.560068 CGGGTTAGCAGAAATGTATCACC 59.440 47.826 0.00 0.00 0.00 4.02
1410 1591 3.181510 GCAGAAATGTATCACCGGTTGAC 60.182 47.826 2.97 3.48 36.92 3.18
1413 1594 3.973206 AATGTATCACCGGTTGACAGA 57.027 42.857 2.97 0.00 36.92 3.41
1426 1607 5.163854 CCGGTTGACAGAAAAGATATGTGAC 60.164 44.000 0.00 0.00 0.00 3.67
1482 1679 9.283768 TGTGCATATATACAGTTAAATTCCCTG 57.716 33.333 0.00 0.00 0.00 4.45
1484 1681 7.393234 TGCATATATACAGTTAAATTCCCTGCC 59.607 37.037 0.00 0.00 0.00 4.85
1506 1703 3.371591 CCAAAAATTGATGCACCATTCGG 59.628 43.478 0.00 0.00 38.77 4.30
1520 1717 2.612212 CCATTCGGGTCGTTAAGGATTG 59.388 50.000 0.50 0.00 0.00 2.67
1524 1721 3.328505 TCGGGTCGTTAAGGATTGAAAC 58.671 45.455 0.50 0.00 0.00 2.78
1525 1722 3.068560 CGGGTCGTTAAGGATTGAAACA 58.931 45.455 0.50 0.00 0.00 2.83
1526 1723 3.687698 CGGGTCGTTAAGGATTGAAACAT 59.312 43.478 0.50 0.00 0.00 2.71
1527 1724 4.871557 CGGGTCGTTAAGGATTGAAACATA 59.128 41.667 0.50 0.00 0.00 2.29
1550 1760 9.113838 CATATACAGAAATTAAGTGGACAAGCT 57.886 33.333 0.00 0.00 0.00 3.74
1566 1776 4.074970 ACAAGCTGAAACCACTTGGATAG 58.925 43.478 1.14 0.00 44.01 2.08
1574 1784 1.004745 ACCACTTGGATAGCAACCCAG 59.995 52.381 1.14 0.00 38.94 4.45
1577 1787 1.340405 ACTTGGATAGCAACCCAGCAG 60.340 52.381 0.00 0.00 36.85 4.24
1578 1788 0.698238 TTGGATAGCAACCCAGCAGT 59.302 50.000 0.00 0.00 36.85 4.40
1598 1813 4.516698 CAGTACTGCTTTGGTCTCAACATT 59.483 41.667 10.54 0.00 31.78 2.71
1610 1825 8.690203 TTGGTCTCAACATTTCTTTAATCAGA 57.310 30.769 0.00 0.00 0.00 3.27
1615 1830 9.436957 TCTCAACATTTCTTTAATCAGAGTACC 57.563 33.333 0.00 0.00 0.00 3.34
1625 1840 9.166173 TCTTTAATCAGAGTACCATGAAACATG 57.834 33.333 0.00 4.94 0.00 3.21
1627 1842 3.609853 TCAGAGTACCATGAAACATGCC 58.390 45.455 0.00 0.00 0.00 4.40
1628 1843 3.008923 TCAGAGTACCATGAAACATGCCA 59.991 43.478 0.00 0.00 0.00 4.92
1668 1883 3.199764 GCACTTGCAATTGGACACC 57.800 52.632 17.38 0.00 41.59 4.16
1669 1884 0.388659 GCACTTGCAATTGGACACCA 59.611 50.000 17.38 0.00 41.59 4.17
1670 1885 1.603678 GCACTTGCAATTGGACACCAG 60.604 52.381 17.38 1.05 41.59 4.00
1672 1887 0.387622 CTTGCAATTGGACACCAGCG 60.388 55.000 7.72 0.00 33.81 5.18
1673 1888 2.126346 GCAATTGGACACCAGCGC 60.126 61.111 7.72 0.00 33.81 5.92
1674 1889 2.568090 CAATTGGACACCAGCGCC 59.432 61.111 2.29 0.00 33.81 6.53
1675 1890 1.973281 CAATTGGACACCAGCGCCT 60.973 57.895 2.29 0.00 33.81 5.52
1676 1891 1.973281 AATTGGACACCAGCGCCTG 60.973 57.895 2.29 1.18 33.81 4.85
1678 1893 2.697147 ATTGGACACCAGCGCCTGTT 62.697 55.000 2.29 0.00 33.81 3.16
1679 1894 3.050275 GGACACCAGCGCCTGTTC 61.050 66.667 2.29 0.00 0.00 3.18
1680 1895 2.031163 GACACCAGCGCCTGTTCT 59.969 61.111 2.29 0.00 0.00 3.01
1681 1896 2.281070 ACACCAGCGCCTGTTCTG 60.281 61.111 2.29 0.00 0.00 3.02
1698 1938 7.670364 CCTGTTCTGAAAATAGGGTTGAATTT 58.330 34.615 8.11 0.00 0.00 1.82
1701 1941 5.949735 TCTGAAAATAGGGTTGAATTTCGC 58.050 37.500 0.00 0.00 33.74 4.70
1705 1945 5.722021 AAATAGGGTTGAATTTCGCTGTT 57.278 34.783 0.00 0.00 31.78 3.16
1713 1953 5.798434 GGTTGAATTTCGCTGTTATGTAACC 59.202 40.000 0.82 0.00 35.37 2.85
1714 1954 6.375377 GTTGAATTTCGCTGTTATGTAACCA 58.625 36.000 0.82 0.00 35.37 3.67
1716 1956 6.607689 TGAATTTCGCTGTTATGTAACCAAG 58.392 36.000 0.82 0.00 35.37 3.61
1723 1963 5.243207 GCTGTTATGTAACCAAGTACCTGT 58.757 41.667 0.82 0.00 35.37 4.00
1727 1967 9.275398 CTGTTATGTAACCAAGTACCTGTTTAA 57.725 33.333 0.82 0.00 35.37 1.52
1729 1969 6.790285 ATGTAACCAAGTACCTGTTTAACG 57.210 37.500 0.00 0.00 0.00 3.18
1738 1978 8.139989 CCAAGTACCTGTTTAACGCTACTATAT 58.860 37.037 0.00 0.00 0.00 0.86
1752 1995 7.524065 ACGCTACTATATTTTTGGTTGAACAC 58.476 34.615 0.00 0.00 0.00 3.32
1814 2057 3.196469 TCAAGTGCATCCTCTTACTCCTG 59.804 47.826 0.00 0.00 0.00 3.86
1835 2078 3.331889 TGGGAGAGGAAGCAGATTCTTTT 59.668 43.478 0.00 0.00 38.07 2.27
1847 2090 2.229784 AGATTCTTTTGCAAAGAGGGCG 59.770 45.455 12.41 0.00 0.00 6.13
2012 2255 5.028549 ACCAGGTTCAGTATTCTATGCTG 57.971 43.478 0.00 0.00 43.29 4.41
2112 2355 5.530543 GGGCTGATGAATAAGAAGAAAGGAG 59.469 44.000 0.00 0.00 0.00 3.69
2117 2360 7.341805 TGATGAATAAGAAGAAAGGAGGGAAG 58.658 38.462 0.00 0.00 0.00 3.46
2125 2368 0.476611 AAAGGAGGGAAGCCAGGACT 60.477 55.000 0.00 0.00 0.00 3.85
2129 2372 0.251634 GAGGGAAGCCAGGACTGAAG 59.748 60.000 0.00 0.00 0.00 3.02
2132 2375 0.035915 GGAAGCCAGGACTGAAGGAC 60.036 60.000 0.00 0.00 0.00 3.85
2143 2386 1.896465 ACTGAAGGACGGAGGAAAGAG 59.104 52.381 0.00 0.00 0.00 2.85
2145 2388 1.893801 TGAAGGACGGAGGAAAGAGTC 59.106 52.381 0.00 0.00 0.00 3.36
2153 2396 0.319900 GAGGAAAGAGTCGTGCAGCA 60.320 55.000 0.00 0.00 0.00 4.41
2384 2627 1.817357 CCAGAGCTTTGATGACAGCA 58.183 50.000 5.68 0.00 0.00 4.41
2414 2657 5.351465 TCTTAAATCTTGTGAAGACGCCATC 59.649 40.000 0.00 0.00 41.01 3.51
2437 2680 0.392193 AGATTGCGGGAACAGCAGAG 60.392 55.000 0.00 0.00 46.01 3.35
2525 2768 8.618702 AGAATATCATGAAAGAGCATGGTAAG 57.381 34.615 0.00 0.00 43.05 2.34
2529 2772 5.559770 TCATGAAAGAGCATGGTAAGTTCA 58.440 37.500 15.57 15.57 44.44 3.18
2531 2774 7.337938 TCATGAAAGAGCATGGTAAGTTCATA 58.662 34.615 20.78 12.11 44.44 2.15
2546 2789 8.831550 GGTAAGTTCATATCAGATTCAGGAAAC 58.168 37.037 0.00 0.00 0.00 2.78
2551 2794 7.666063 TCATATCAGATTCAGGAAACTCTCA 57.334 36.000 0.00 0.00 40.21 3.27
2834 3077 0.118144 AACTGGAGGGAGAGAAGGCT 59.882 55.000 0.00 0.00 0.00 4.58
2835 3078 1.011595 ACTGGAGGGAGAGAAGGCTA 58.988 55.000 0.00 0.00 0.00 3.93
2839 3082 2.176045 GGAGGGAGAGAAGGCTATAGC 58.824 57.143 16.78 16.78 41.14 2.97
2853 3096 2.680805 GCTATAGCAACCAGTGGCTCAA 60.681 50.000 20.01 0.00 41.41 3.02
2854 3097 2.584835 ATAGCAACCAGTGGCTCAAA 57.415 45.000 9.78 0.00 41.41 2.69
2915 3158 3.578282 TGATGAGAGTGCAGTACCTTGAA 59.422 43.478 0.00 0.00 0.00 2.69
2951 3194 4.260538 GCAGAAGAAAGCATAGTCCATTCG 60.261 45.833 0.00 0.00 0.00 3.34
2958 3201 6.599244 AGAAAGCATAGTCCATTCGAATTTCA 59.401 34.615 8.21 0.00 0.00 2.69
2966 3209 4.846137 GTCCATTCGAATTTCACTGAAACG 59.154 41.667 8.21 7.18 34.23 3.60
7090 8292 2.127297 CCCCTCTTCCCCTTCCCA 59.873 66.667 0.00 0.00 0.00 4.37
7102 8304 1.403687 CCTTCCCATCTCCGTCTCCC 61.404 65.000 0.00 0.00 0.00 4.30
7104 8306 0.931468 TTCCCATCTCCGTCTCCCTA 59.069 55.000 0.00 0.00 0.00 3.53
7108 8316 1.243902 CATCTCCGTCTCCCTAGAGC 58.756 60.000 0.00 0.00 40.22 4.09
7134 8342 4.534168 GTTTTGGTTTTTCCTAGCTCGAC 58.466 43.478 0.00 0.00 37.07 4.20
7138 8346 2.619147 GTTTTTCCTAGCTCGACCTCC 58.381 52.381 0.00 0.00 0.00 4.30
7147 8355 3.584868 CTCGACCTCCGCGGGTTTT 62.585 63.158 27.83 7.30 40.06 2.43
7149 8357 2.674084 CGACCTCCGCGGGTTTTTC 61.674 63.158 27.83 13.59 40.06 2.29
7161 8369 2.491675 GGTTTTTCCCATCTCCGTCT 57.508 50.000 0.00 0.00 0.00 4.18
7162 8370 2.357075 GGTTTTTCCCATCTCCGTCTC 58.643 52.381 0.00 0.00 0.00 3.36
7163 8371 2.357075 GTTTTTCCCATCTCCGTCTCC 58.643 52.381 0.00 0.00 0.00 3.71
7164 8372 1.952621 TTTTCCCATCTCCGTCTCCT 58.047 50.000 0.00 0.00 0.00 3.69
7165 8373 2.840640 TTTCCCATCTCCGTCTCCTA 57.159 50.000 0.00 0.00 0.00 2.94
7166 8374 2.366640 TTCCCATCTCCGTCTCCTAG 57.633 55.000 0.00 0.00 0.00 3.02
7167 8375 1.519498 TCCCATCTCCGTCTCCTAGA 58.481 55.000 0.00 0.00 0.00 2.43
7168 8376 2.066592 TCCCATCTCCGTCTCCTAGAT 58.933 52.381 0.00 0.00 0.00 1.98
7169 8377 2.166829 CCCATCTCCGTCTCCTAGATG 58.833 57.143 0.00 0.00 44.03 2.90
7170 8378 2.489985 CCCATCTCCGTCTCCTAGATGT 60.490 54.545 9.88 0.00 43.28 3.06
7171 8379 2.817258 CCATCTCCGTCTCCTAGATGTC 59.183 54.545 9.88 0.00 43.28 3.06
7172 8380 2.642154 TCTCCGTCTCCTAGATGTCC 57.358 55.000 0.00 0.00 29.27 4.02
7173 8381 1.143277 TCTCCGTCTCCTAGATGTCCC 59.857 57.143 0.00 0.00 29.27 4.46
7174 8382 1.144093 CTCCGTCTCCTAGATGTCCCT 59.856 57.143 0.00 0.00 29.27 4.20
7175 8383 1.133761 TCCGTCTCCTAGATGTCCCTG 60.134 57.143 0.00 0.00 29.27 4.45
7176 8384 1.410365 CCGTCTCCTAGATGTCCCTGT 60.410 57.143 0.00 0.00 29.27 4.00
7177 8385 1.950909 CGTCTCCTAGATGTCCCTGTC 59.049 57.143 0.00 0.00 0.00 3.51
7178 8386 2.422235 CGTCTCCTAGATGTCCCTGTCT 60.422 54.545 0.00 0.00 0.00 3.41
7179 8387 2.955660 GTCTCCTAGATGTCCCTGTCTG 59.044 54.545 0.00 0.00 0.00 3.51
7180 8388 1.686052 CTCCTAGATGTCCCTGTCTGC 59.314 57.143 0.00 0.00 0.00 4.26
7181 8389 0.755686 CCTAGATGTCCCTGTCTGCC 59.244 60.000 0.00 0.00 0.00 4.85
7182 8390 1.690845 CCTAGATGTCCCTGTCTGCCT 60.691 57.143 0.00 0.00 0.00 4.75
7183 8391 1.411977 CTAGATGTCCCTGTCTGCCTG 59.588 57.143 0.00 0.00 0.00 4.85
7184 8392 0.546267 AGATGTCCCTGTCTGCCTGT 60.546 55.000 0.00 0.00 0.00 4.00
7185 8393 0.326264 GATGTCCCTGTCTGCCTGTT 59.674 55.000 0.00 0.00 0.00 3.16
7186 8394 0.326264 ATGTCCCTGTCTGCCTGTTC 59.674 55.000 0.00 0.00 0.00 3.18
7187 8395 0.764369 TGTCCCTGTCTGCCTGTTCT 60.764 55.000 0.00 0.00 0.00 3.01
7188 8396 0.398318 GTCCCTGTCTGCCTGTTCTT 59.602 55.000 0.00 0.00 0.00 2.52
7189 8397 1.623811 GTCCCTGTCTGCCTGTTCTTA 59.376 52.381 0.00 0.00 0.00 2.10
7190 8398 2.237392 GTCCCTGTCTGCCTGTTCTTAT 59.763 50.000 0.00 0.00 0.00 1.73
7191 8399 3.451178 GTCCCTGTCTGCCTGTTCTTATA 59.549 47.826 0.00 0.00 0.00 0.98
7192 8400 4.101741 GTCCCTGTCTGCCTGTTCTTATAT 59.898 45.833 0.00 0.00 0.00 0.86
7193 8401 4.101585 TCCCTGTCTGCCTGTTCTTATATG 59.898 45.833 0.00 0.00 0.00 1.78
7194 8402 3.812053 CCTGTCTGCCTGTTCTTATATGC 59.188 47.826 0.00 0.00 0.00 3.14
7195 8403 4.445453 CTGTCTGCCTGTTCTTATATGCA 58.555 43.478 0.00 0.00 0.00 3.96
7196 8404 5.039920 TGTCTGCCTGTTCTTATATGCAT 57.960 39.130 3.79 3.79 0.00 3.96
7197 8405 5.439721 TGTCTGCCTGTTCTTATATGCATT 58.560 37.500 3.54 0.00 0.00 3.56
7198 8406 6.591001 TGTCTGCCTGTTCTTATATGCATTA 58.409 36.000 3.54 0.00 0.00 1.90
7199 8407 7.053498 TGTCTGCCTGTTCTTATATGCATTAA 58.947 34.615 3.54 2.98 0.00 1.40
7200 8408 7.720957 TGTCTGCCTGTTCTTATATGCATTAAT 59.279 33.333 3.54 0.00 0.00 1.40
7201 8409 8.019669 GTCTGCCTGTTCTTATATGCATTAATG 58.980 37.037 3.54 11.27 0.00 1.90
7202 8410 7.175467 TCTGCCTGTTCTTATATGCATTAATGG 59.825 37.037 17.02 0.00 0.00 3.16
7203 8411 6.095377 GCCTGTTCTTATATGCATTAATGGC 58.905 40.000 17.02 9.73 0.00 4.40
7204 8412 6.071728 GCCTGTTCTTATATGCATTAATGGCT 60.072 38.462 17.02 3.34 0.00 4.75
7205 8413 7.121168 GCCTGTTCTTATATGCATTAATGGCTA 59.879 37.037 17.02 5.08 0.00 3.93
7206 8414 9.182214 CCTGTTCTTATATGCATTAATGGCTAT 57.818 33.333 17.02 10.44 0.00 2.97
7214 8422 8.743085 ATATGCATTAATGGCTATACTTCCAG 57.257 34.615 17.02 0.00 35.57 3.86
7215 8423 5.940617 TGCATTAATGGCTATACTTCCAGT 58.059 37.500 17.02 0.00 35.57 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 19 1.000060 CATGTGACAAAACCCAGCCAG 60.000 52.381 0.00 0.00 0.00 4.85
21 23 1.269726 GGTGCATGTGACAAAACCCAG 60.270 52.381 0.00 0.00 0.00 4.45
83 85 7.702348 GCTCCCATTTCATTTGATACTTTACAC 59.298 37.037 0.00 0.00 0.00 2.90
101 103 2.037144 GGAATGAATGCTGCTCCCATT 58.963 47.619 0.00 7.35 35.73 3.16
103 105 0.396139 GGGAATGAATGCTGCTCCCA 60.396 55.000 15.33 4.58 44.53 4.37
105 107 1.030457 CTGGGAATGAATGCTGCTCC 58.970 55.000 0.00 0.00 0.00 4.70
188 223 0.387239 GGCAGTCCAAAACACGCATC 60.387 55.000 0.00 0.00 31.91 3.91
192 227 1.531149 CACTAGGCAGTCCAAAACACG 59.469 52.381 0.00 0.00 30.46 4.49
195 230 5.241728 AGAAAATCACTAGGCAGTCCAAAAC 59.758 40.000 0.00 0.00 30.46 2.43
196 231 5.241506 CAGAAAATCACTAGGCAGTCCAAAA 59.758 40.000 0.00 0.00 30.46 2.44
199 234 3.869912 GCAGAAAATCACTAGGCAGTCCA 60.870 47.826 0.00 0.00 30.46 4.02
214 249 2.884012 CACACACATACCCAGCAGAAAA 59.116 45.455 0.00 0.00 0.00 2.29
215 250 2.105649 TCACACACATACCCAGCAGAAA 59.894 45.455 0.00 0.00 0.00 2.52
217 252 1.347062 TCACACACATACCCAGCAGA 58.653 50.000 0.00 0.00 0.00 4.26
218 253 1.806542 GTTCACACACATACCCAGCAG 59.193 52.381 0.00 0.00 0.00 4.24
221 256 2.226437 GCTTGTTCACACACATACCCAG 59.774 50.000 0.00 0.00 30.32 4.45
224 260 3.187227 CAGAGCTTGTTCACACACATACC 59.813 47.826 0.00 0.00 30.32 2.73
227 263 2.874701 GACAGAGCTTGTTCACACACAT 59.125 45.455 0.00 0.00 41.05 3.21
279 360 4.566426 AATTTAGACAGCTGCTTCCTCT 57.434 40.909 15.27 11.32 0.00 3.69
319 400 9.719355 AAGGTGTTGTTTTGTTCTAAGAAAAAT 57.281 25.926 0.00 0.00 33.70 1.82
327 414 8.514330 AACAGATAAGGTGTTGTTTTGTTCTA 57.486 30.769 0.00 0.00 36.76 2.10
418 505 2.621526 TGCTTTCGTCTTCTTTTTCCCC 59.378 45.455 0.00 0.00 0.00 4.81
419 506 3.066203 TGTGCTTTCGTCTTCTTTTTCCC 59.934 43.478 0.00 0.00 0.00 3.97
420 507 4.287238 TGTGCTTTCGTCTTCTTTTTCC 57.713 40.909 0.00 0.00 0.00 3.13
421 508 5.800438 AGTTTGTGCTTTCGTCTTCTTTTTC 59.200 36.000 0.00 0.00 0.00 2.29
427 517 4.212150 GCTTAGTTTGTGCTTTCGTCTTC 58.788 43.478 0.00 0.00 0.00 2.87
431 521 1.607148 GGGCTTAGTTTGTGCTTTCGT 59.393 47.619 0.00 0.00 0.00 3.85
436 526 0.889186 CCGTGGGCTTAGTTTGTGCT 60.889 55.000 0.00 0.00 0.00 4.40
561 659 2.110188 TCTAAGTCTCTGAGGTGTGGGT 59.890 50.000 4.59 0.00 0.00 4.51
568 666 2.661718 GGGAGGTCTAAGTCTCTGAGG 58.338 57.143 4.59 0.00 0.00 3.86
578 676 2.042230 GGGCTCGGGGAGGTCTAA 60.042 66.667 0.00 0.00 0.00 2.10
609 707 2.431683 GGCAGAGAAGTGGTGGCA 59.568 61.111 0.00 0.00 36.77 4.92
610 708 1.968540 GTGGCAGAGAAGTGGTGGC 60.969 63.158 0.00 0.00 37.28 5.01
624 722 0.175989 GAGCAGTAGGTGGTAGTGGC 59.824 60.000 0.00 0.00 36.87 5.01
691 789 5.812642 AGGAGTTGAATACTTCGTAGCAATG 59.187 40.000 0.00 0.00 37.45 2.82
721 819 0.252927 AGAACAGGAGGAGAAGGGGG 60.253 60.000 0.00 0.00 0.00 5.40
734 832 1.404851 GGCGGAGAGGAAGAAGAACAG 60.405 57.143 0.00 0.00 0.00 3.16
793 892 1.518774 CTGCATTTGCCATGGGGAC 59.481 57.895 15.13 0.00 41.18 4.46
799 898 0.616371 ACATTGCCTGCATTTGCCAT 59.384 45.000 0.00 0.00 41.18 4.40
800 899 0.320858 CACATTGCCTGCATTTGCCA 60.321 50.000 0.00 0.00 41.18 4.92
801 900 1.641123 GCACATTGCCTGCATTTGCC 61.641 55.000 0.00 0.00 37.59 4.52
877 997 1.325640 CAAGACCTGATCACGAATGCG 59.674 52.381 0.00 0.00 44.79 4.73
884 1004 0.792640 CGCACACAAGACCTGATCAC 59.207 55.000 0.00 0.00 0.00 3.06
911 1053 1.296715 CCTCCCTGGTTCACCTTCG 59.703 63.158 0.00 0.00 36.82 3.79
953 1095 3.463585 CCGCCGGTTAGCCACCTA 61.464 66.667 1.90 0.00 44.69 3.08
1102 1247 4.135493 GCGCGGCGTGAAGAAGAC 62.135 66.667 26.40 0.00 0.00 3.01
1128 1273 1.064296 AACGAGATCTAGGCGCGTG 59.936 57.895 13.84 3.01 40.75 5.34
1144 1289 0.316204 AGATGTGCCAAGCAAGCAAC 59.684 50.000 0.00 0.00 43.02 4.17
1169 1314 4.797275 GCAAAGTTCTGACCAGGGAAAATG 60.797 45.833 0.00 0.00 0.00 2.32
1175 1320 1.542915 CATGCAAAGTTCTGACCAGGG 59.457 52.381 0.00 0.00 0.00 4.45
1177 1322 3.504906 ACATCATGCAAAGTTCTGACCAG 59.495 43.478 0.00 0.00 0.00 4.00
1196 1341 2.936919 TGTCAAACTCTGCAGGACAT 57.063 45.000 15.13 0.00 33.88 3.06
1208 1353 6.964934 ACGAAACACTACTTCATTTGTCAAAC 59.035 34.615 0.00 0.00 0.00 2.93
1209 1354 7.079182 ACGAAACACTACTTCATTTGTCAAA 57.921 32.000 0.00 0.00 0.00 2.69
1213 1358 8.879759 CCATATACGAAACACTACTTCATTTGT 58.120 33.333 0.00 0.00 0.00 2.83
1226 1371 4.827692 AGCAACTGACCATATACGAAACA 58.172 39.130 0.00 0.00 0.00 2.83
1227 1372 5.350365 TGAAGCAACTGACCATATACGAAAC 59.650 40.000 0.00 0.00 0.00 2.78
1255 1400 3.481453 TGCTGCAACTACCATAACACAA 58.519 40.909 0.00 0.00 0.00 3.33
1259 1404 5.371115 TCTTTTGCTGCAACTACCATAAC 57.629 39.130 15.72 0.00 0.00 1.89
1261 1406 5.009631 ACATCTTTTGCTGCAACTACCATA 58.990 37.500 15.72 0.00 0.00 2.74
1280 1429 6.441274 CCATAATGGTGATACAAAGCACATC 58.559 40.000 0.00 0.00 43.95 3.06
1285 1434 3.005791 GGCCCATAATGGTGATACAAAGC 59.994 47.826 0.00 0.00 35.17 3.51
1304 1453 4.634443 ACGTAATCTATGTGTTTCTTGGCC 59.366 41.667 0.00 0.00 0.00 5.36
1325 1474 8.916654 CAGTGATGTAGCCTATATTTCTTTACG 58.083 37.037 0.00 0.00 0.00 3.18
1330 1479 7.256119 CCTGACAGTGATGTAGCCTATATTTCT 60.256 40.741 0.00 0.00 0.00 2.52
1353 1502 6.645003 CCATGCATAAATTTCATGATCACCTG 59.355 38.462 16.11 0.00 39.80 4.00
1368 1517 2.571212 CTAACCCGAGCCATGCATAAA 58.429 47.619 0.00 0.00 0.00 1.40
1374 1523 0.107703 TTCTGCTAACCCGAGCCATG 60.108 55.000 0.00 0.00 42.11 3.66
1382 1531 3.560068 CGGTGATACATTTCTGCTAACCC 59.440 47.826 0.00 0.00 0.00 4.11
1401 1550 4.695455 CACATATCTTTTCTGTCAACCGGT 59.305 41.667 0.00 0.00 0.00 5.28
1403 1552 5.444613 CGTCACATATCTTTTCTGTCAACCG 60.445 44.000 0.00 0.00 0.00 4.44
1410 1591 6.963242 CCAAACATCGTCACATATCTTTTCTG 59.037 38.462 0.00 0.00 0.00 3.02
1413 1594 6.429692 TGACCAAACATCGTCACATATCTTTT 59.570 34.615 0.00 0.00 34.14 2.27
1426 1607 2.010145 ATCCGAGTGACCAAACATCG 57.990 50.000 0.00 0.00 0.00 3.84
1477 1674 1.278699 GCATCAATTTTTGGGCAGGGA 59.721 47.619 0.00 0.00 33.53 4.20
1482 1679 2.181954 TGGTGCATCAATTTTTGGGC 57.818 45.000 0.00 0.00 33.80 5.36
1484 1681 3.371591 CCGAATGGTGCATCAATTTTTGG 59.628 43.478 2.42 3.46 0.00 3.28
1506 1703 8.428186 TGTATATGTTTCAATCCTTAACGACC 57.572 34.615 0.00 0.00 0.00 4.79
1508 1705 9.878667 TTCTGTATATGTTTCAATCCTTAACGA 57.121 29.630 0.00 0.00 0.00 3.85
1524 1721 9.113838 AGCTTGTCCACTTAATTTCTGTATATG 57.886 33.333 0.00 0.00 0.00 1.78
1525 1722 9.113838 CAGCTTGTCCACTTAATTTCTGTATAT 57.886 33.333 0.00 0.00 0.00 0.86
1526 1723 8.318412 TCAGCTTGTCCACTTAATTTCTGTATA 58.682 33.333 0.00 0.00 0.00 1.47
1527 1724 7.168219 TCAGCTTGTCCACTTAATTTCTGTAT 58.832 34.615 0.00 0.00 0.00 2.29
1543 1753 2.297701 TCCAAGTGGTTTCAGCTTGTC 58.702 47.619 0.00 0.00 38.24 3.18
1546 1756 3.084786 GCTATCCAAGTGGTTTCAGCTT 58.915 45.455 0.00 0.00 36.34 3.74
1550 1760 3.153919 GGTTGCTATCCAAGTGGTTTCA 58.846 45.455 0.00 0.00 33.21 2.69
1577 1787 5.239525 AGAAATGTTGAGACCAAAGCAGTAC 59.760 40.000 0.00 0.00 33.49 2.73
1578 1788 5.376625 AGAAATGTTGAGACCAAAGCAGTA 58.623 37.500 0.00 0.00 33.49 2.74
1590 1805 9.219603 TGGTACTCTGATTAAAGAAATGTTGAG 57.780 33.333 0.00 0.00 0.00 3.02
1591 1806 9.739276 ATGGTACTCTGATTAAAGAAATGTTGA 57.261 29.630 0.00 0.00 0.00 3.18
1598 1813 9.739276 ATGTTTCATGGTACTCTGATTAAAGAA 57.261 29.630 0.00 0.00 0.00 2.52
1610 1825 4.339247 GCTTATGGCATGTTTCATGGTACT 59.661 41.667 10.98 0.00 41.35 2.73
1625 1840 5.583457 AGAATTGCTGAAATTTGCTTATGGC 59.417 36.000 0.00 0.00 38.64 4.40
1654 1869 1.659233 CGCTGGTGTCCAATTGCAA 59.341 52.632 0.00 0.00 30.80 4.08
1665 1880 1.165907 TTTCAGAACAGGCGCTGGTG 61.166 55.000 7.64 5.30 35.51 4.17
1668 1883 2.096496 CCTATTTTCAGAACAGGCGCTG 59.904 50.000 7.64 6.31 37.52 5.18
1669 1884 2.359900 CCTATTTTCAGAACAGGCGCT 58.640 47.619 7.64 0.00 0.00 5.92
1670 1885 1.401905 CCCTATTTTCAGAACAGGCGC 59.598 52.381 0.00 0.00 0.00 6.53
1672 1887 4.079253 TCAACCCTATTTTCAGAACAGGC 58.921 43.478 0.63 0.00 0.00 4.85
1673 1888 6.840780 ATTCAACCCTATTTTCAGAACAGG 57.159 37.500 0.00 0.00 0.00 4.00
1674 1889 7.538678 CGAAATTCAACCCTATTTTCAGAACAG 59.461 37.037 0.00 0.00 0.00 3.16
1675 1890 7.367285 CGAAATTCAACCCTATTTTCAGAACA 58.633 34.615 0.00 0.00 0.00 3.18
1676 1891 6.308041 GCGAAATTCAACCCTATTTTCAGAAC 59.692 38.462 0.00 0.00 0.00 3.01
1678 1893 5.710099 AGCGAAATTCAACCCTATTTTCAGA 59.290 36.000 0.00 0.00 0.00 3.27
1679 1894 5.801947 CAGCGAAATTCAACCCTATTTTCAG 59.198 40.000 0.00 0.00 0.00 3.02
1680 1895 5.242838 ACAGCGAAATTCAACCCTATTTTCA 59.757 36.000 0.00 0.00 0.00 2.69
1681 1896 5.709966 ACAGCGAAATTCAACCCTATTTTC 58.290 37.500 0.00 0.00 0.00 2.29
1698 1938 4.221262 AGGTACTTGGTTACATAACAGCGA 59.779 41.667 4.27 0.00 34.08 4.93
1701 1941 7.739498 AAACAGGTACTTGGTTACATAACAG 57.261 36.000 6.46 0.00 34.60 3.16
1705 1945 6.368516 GCGTTAAACAGGTACTTGGTTACATA 59.631 38.462 14.48 0.00 34.60 2.29
1713 1953 9.525409 AATATAGTAGCGTTAAACAGGTACTTG 57.475 33.333 17.77 2.98 45.79 3.16
1727 1967 7.389607 AGTGTTCAACCAAAAATATAGTAGCGT 59.610 33.333 0.00 0.00 0.00 5.07
1729 1969 8.726988 TCAGTGTTCAACCAAAAATATAGTAGC 58.273 33.333 0.00 0.00 0.00 3.58
1738 1978 2.750166 TCGCTCAGTGTTCAACCAAAAA 59.250 40.909 0.00 0.00 0.00 1.94
1746 1989 0.035317 AGGCAATCGCTCAGTGTTCA 59.965 50.000 0.00 0.00 38.60 3.18
1752 1995 1.741706 ACATCAAAGGCAATCGCTCAG 59.258 47.619 0.00 0.00 38.60 3.35
1814 2057 3.643199 AAAGAATCTGCTTCCTCTCCC 57.357 47.619 0.00 0.00 34.11 4.30
1835 2078 0.539438 ACATTTCCGCCCTCTTTGCA 60.539 50.000 0.00 0.00 0.00 4.08
1847 2090 4.272748 GGTCGCCTCTTGTAATACATTTCC 59.727 45.833 0.00 0.00 0.00 3.13
2012 2255 2.096248 AGACTGTCATCGTCCTCTTCC 58.904 52.381 10.88 0.00 31.83 3.46
2087 2330 5.192522 TCCTTTCTTCTTATTCATCAGCCCT 59.807 40.000 0.00 0.00 0.00 5.19
2112 2355 1.201429 TCCTTCAGTCCTGGCTTCCC 61.201 60.000 0.00 0.00 0.00 3.97
2117 2360 2.232298 CTCCGTCCTTCAGTCCTGGC 62.232 65.000 0.00 0.00 0.00 4.85
2125 2368 1.893801 GACTCTTTCCTCCGTCCTTCA 59.106 52.381 0.00 0.00 0.00 3.02
2129 2372 0.109226 CACGACTCTTTCCTCCGTCC 60.109 60.000 0.00 0.00 0.00 4.79
2132 2375 0.734253 CTGCACGACTCTTTCCTCCG 60.734 60.000 0.00 0.00 0.00 4.63
2153 2396 0.609131 CATTCTCCTTGTTGGCCGGT 60.609 55.000 1.90 0.00 35.26 5.28
2158 2401 0.597568 TTGCGCATTCTCCTTGTTGG 59.402 50.000 12.75 0.00 37.10 3.77
2344 2587 2.224137 GCCTCATCATCTTCGATCACCA 60.224 50.000 0.00 0.00 0.00 4.17
2384 2627 6.073548 CGTCTTCACAAGATTTAAGAGCAGTT 60.074 38.462 0.00 0.00 40.18 3.16
2390 2633 4.637276 TGGCGTCTTCACAAGATTTAAGA 58.363 39.130 0.00 0.00 40.18 2.10
2437 2680 1.448985 TGCTTGGCTGAACGATAACC 58.551 50.000 0.00 0.00 0.00 2.85
2525 2768 7.984050 TGAGAGTTTCCTGAATCTGATATGAAC 59.016 37.037 0.00 0.00 0.00 3.18
2529 2772 9.995003 GTAATGAGAGTTTCCTGAATCTGATAT 57.005 33.333 0.00 0.00 0.00 1.63
2531 2774 6.983307 CGTAATGAGAGTTTCCTGAATCTGAT 59.017 38.462 0.00 0.00 0.00 2.90
2551 2794 5.005779 GCATCGTTTCTCACATTCTCGTAAT 59.994 40.000 0.00 0.00 0.00 1.89
2570 2813 0.583438 CCATCTTAACGCTGGCATCG 59.417 55.000 9.46 9.46 0.00 3.84
2834 3077 3.712016 TTTGAGCCACTGGTTGCTATA 57.288 42.857 0.00 0.00 38.11 1.31
2835 3078 2.584835 TTTGAGCCACTGGTTGCTAT 57.415 45.000 0.00 0.00 38.11 2.97
2839 3082 3.947910 ATTCATTTGAGCCACTGGTTG 57.052 42.857 0.00 0.00 0.00 3.77
2853 3096 8.571461 TTCTCTAGCTTGTCATTCAATTCATT 57.429 30.769 0.00 0.00 35.35 2.57
2854 3097 7.282675 CCTTCTCTAGCTTGTCATTCAATTCAT 59.717 37.037 0.00 0.00 35.35 2.57
2915 3158 1.632409 TCTTCTGCATGGAAGGAGCTT 59.368 47.619 13.92 0.00 41.94 3.74
2946 3189 3.603770 GCCGTTTCAGTGAAATTCGAATG 59.396 43.478 22.96 12.01 33.97 2.67
2951 3194 3.964909 ACTTGCCGTTTCAGTGAAATTC 58.035 40.909 20.72 12.97 33.97 2.17
2958 3201 2.143925 GAAGCTACTTGCCGTTTCAGT 58.856 47.619 0.00 0.00 44.23 3.41
2966 3209 5.642063 TGTAATACAACAGAAGCTACTTGCC 59.358 40.000 0.00 0.00 44.23 4.52
7090 8292 1.145571 AGCTCTAGGGAGACGGAGAT 58.854 55.000 0.00 0.00 41.86 2.75
7102 8304 5.008712 AGGAAAAACCAAAACGAAGCTCTAG 59.991 40.000 0.00 0.00 42.04 2.43
7104 8306 3.699538 AGGAAAAACCAAAACGAAGCTCT 59.300 39.130 0.00 0.00 42.04 4.09
7108 8316 5.183014 AGCTAGGAAAAACCAAAACGAAG 57.817 39.130 0.00 0.00 42.04 3.79
7147 8355 1.850998 TCTAGGAGACGGAGATGGGAA 59.149 52.381 0.00 0.00 0.00 3.97
7149 8357 2.166829 CATCTAGGAGACGGAGATGGG 58.833 57.143 3.65 0.00 44.94 4.00
7152 8360 2.224917 GGGACATCTAGGAGACGGAGAT 60.225 54.545 0.00 0.00 38.11 2.75
7153 8361 1.143277 GGGACATCTAGGAGACGGAGA 59.857 57.143 0.00 0.00 0.00 3.71
7154 8362 1.144093 AGGGACATCTAGGAGACGGAG 59.856 57.143 0.00 0.00 0.00 4.63
7155 8363 1.133761 CAGGGACATCTAGGAGACGGA 60.134 57.143 0.00 0.00 0.00 4.69
7156 8364 1.323412 CAGGGACATCTAGGAGACGG 58.677 60.000 0.00 0.00 0.00 4.79
7157 8365 1.950909 GACAGGGACATCTAGGAGACG 59.049 57.143 0.00 0.00 0.00 4.18
7158 8366 2.955660 CAGACAGGGACATCTAGGAGAC 59.044 54.545 0.00 0.00 0.00 3.36
7159 8367 2.688214 GCAGACAGGGACATCTAGGAGA 60.688 54.545 0.00 0.00 0.00 3.71
7160 8368 1.686052 GCAGACAGGGACATCTAGGAG 59.314 57.143 0.00 0.00 0.00 3.69
7161 8369 1.689575 GGCAGACAGGGACATCTAGGA 60.690 57.143 0.00 0.00 0.00 2.94
7162 8370 0.755686 GGCAGACAGGGACATCTAGG 59.244 60.000 0.00 0.00 0.00 3.02
7163 8371 1.411977 CAGGCAGACAGGGACATCTAG 59.588 57.143 0.00 0.00 0.00 2.43
7164 8372 1.273267 ACAGGCAGACAGGGACATCTA 60.273 52.381 0.00 0.00 0.00 1.98
7165 8373 0.546267 ACAGGCAGACAGGGACATCT 60.546 55.000 0.00 0.00 0.00 2.90
7166 8374 0.326264 AACAGGCAGACAGGGACATC 59.674 55.000 0.00 0.00 0.00 3.06
7167 8375 0.326264 GAACAGGCAGACAGGGACAT 59.674 55.000 0.00 0.00 0.00 3.06
7168 8376 0.764369 AGAACAGGCAGACAGGGACA 60.764 55.000 0.00 0.00 0.00 4.02
7169 8377 0.398318 AAGAACAGGCAGACAGGGAC 59.602 55.000 0.00 0.00 0.00 4.46
7170 8378 2.024176 TAAGAACAGGCAGACAGGGA 57.976 50.000 0.00 0.00 0.00 4.20
7171 8379 4.384056 CATATAAGAACAGGCAGACAGGG 58.616 47.826 0.00 0.00 0.00 4.45
7172 8380 3.812053 GCATATAAGAACAGGCAGACAGG 59.188 47.826 0.00 0.00 0.00 4.00
7173 8381 4.445453 TGCATATAAGAACAGGCAGACAG 58.555 43.478 0.00 0.00 0.00 3.51
7174 8382 4.486125 TGCATATAAGAACAGGCAGACA 57.514 40.909 0.00 0.00 0.00 3.41
7175 8383 7.496529 TTAATGCATATAAGAACAGGCAGAC 57.503 36.000 0.00 0.00 34.43 3.51
7176 8384 7.175467 CCATTAATGCATATAAGAACAGGCAGA 59.825 37.037 10.11 0.00 34.43 4.26
7177 8385 7.310664 CCATTAATGCATATAAGAACAGGCAG 58.689 38.462 10.11 0.00 34.43 4.85
7178 8386 6.294675 GCCATTAATGCATATAAGAACAGGCA 60.295 38.462 10.11 0.00 35.15 4.75
7179 8387 6.071728 AGCCATTAATGCATATAAGAACAGGC 60.072 38.462 10.11 4.72 35.26 4.85
7180 8388 7.458409 AGCCATTAATGCATATAAGAACAGG 57.542 36.000 10.11 0.00 0.00 4.00
7188 8396 9.836864 CTGGAAGTATAGCCATTAATGCATATA 57.163 33.333 10.11 10.76 32.89 0.86
7189 8397 8.743085 CTGGAAGTATAGCCATTAATGCATAT 57.257 34.615 10.11 11.63 32.89 1.78


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

AutoCloner maintained by Alex Coulton.