Multiple sequence alignment - TraesCS6B01G109000

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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 TraesCS6B01G109000 chr6B 100.000 3057 0 0 1 3057 89512689 89515745 0.000000e+00 5646.0
1 TraesCS6B01G109000 chr6B 94.737 76 4 0 1381 1456 89581188 89581263 5.350000e-23 119.0
2 TraesCS6B01G109000 chr6B 93.750 48 3 0 2320 2367 191540537 191540584 4.230000e-09 73.1
3 TraesCS6B01G109000 chr6A 87.787 1744 112 41 842 2549 50034447 50036125 0.000000e+00 1947.0
4 TraesCS6B01G109000 chr6A 91.424 583 37 8 1 576 50032717 50033293 0.000000e+00 787.0
5 TraesCS6B01G109000 chr6A 85.020 247 16 6 577 821 50034133 50034360 6.590000e-57 231.0
6 TraesCS6B01G109000 chr6A 92.053 151 12 0 2554 2704 50036271 50036421 2.390000e-51 213.0
7 TraesCS6B01G109000 chr6A 82.553 235 15 10 2074 2292 50037996 50038220 1.870000e-42 183.0
8 TraesCS6B01G109000 chr6A 83.636 55 9 0 1178 1232 89302740 89302794 6.000000e-03 52.8
9 TraesCS6B01G109000 chrUn 91.030 1349 86 12 867 2194 114968544 114967210 0.000000e+00 1788.0
10 TraesCS6B01G109000 chrUn 84.238 387 33 6 1 364 114969529 114969148 4.850000e-93 351.0
11 TraesCS6B01G109000 chrUn 87.879 231 19 5 593 821 114968892 114968669 2.340000e-66 263.0
12 TraesCS6B01G109000 chr1D 73.544 1013 205 50 1088 2058 62857989 62858980 8.170000e-86 327.0
13 TraesCS6B01G109000 chr1B 73.353 1017 206 52 1088 2058 100308602 100309599 1.770000e-82 316.0
14 TraesCS6B01G109000 chr1B 93.478 46 3 0 2322 2367 250409513 250409468 5.470000e-08 69.4
15 TraesCS6B01G109000 chr3B 91.429 140 12 0 1310 1449 43231969 43232108 3.110000e-45 193.0
16 TraesCS6B01G109000 chr1A 83.444 151 21 4 1088 1236 60956175 60956027 1.480000e-28 137.0
17 TraesCS6B01G109000 chr3A 76.033 242 52 5 1453 1691 121328432 121328194 1.490000e-23 121.0
18 TraesCS6B01G109000 chr7D 81.731 104 13 5 2291 2391 13035049 13035149 7.030000e-12 82.4
19 TraesCS6B01G109000 chr2A 91.379 58 5 0 1179 1236 95259548 95259605 2.530000e-11 80.5
20 TraesCS6B01G109000 chr2B 92.683 41 3 0 2320 2360 13523333 13523373 3.290000e-05 60.2
21 TraesCS6B01G109000 chr2D 90.909 44 3 1 1189 1231 420900987 420900944 1.180000e-04 58.4
22 TraesCS6B01G109000 chr6D 83.636 55 9 0 1178 1232 72405728 72405782 6.000000e-03 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 TraesCS6B01G109000 chr6B 89512689 89515745 3056 False 5646.000000 5646 100.000000 1 3057 1 chr6B.!!$F1 3056
1 TraesCS6B01G109000 chr6A 50032717 50038220 5503 False 672.200000 1947 87.767400 1 2704 5 chr6A.!!$F2 2703
2 TraesCS6B01G109000 chrUn 114967210 114969529 2319 True 800.666667 1788 87.715667 1 2194 3 chrUn.!!$R1 2193
3 TraesCS6B01G109000 chr1D 62857989 62858980 991 False 327.000000 327 73.544000 1088 2058 1 chr1D.!!$F1 970
4 TraesCS6B01G109000 chr1B 100308602 100309599 997 False 316.000000 316 73.353000 1088 2058 1 chr1B.!!$F1 970

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
298 322 0.032952 GTACGTGTGTGCCTCCAAGA 59.967 55.0 0.00 0.0 0.00 3.02 F
808 1692 0.036577 AAGAGCTCGCAGCAACAGAT 60.037 50.0 8.37 0.0 45.56 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1729 2752 0.108804 CGTAGGTGGCGTTCATGTCT 60.109 55.0 0.0 0.0 0.00 3.41 R
2529 3573 0.729690 GCTTCGGCCTCTCATGTTTC 59.270 55.0 0.0 0.0 34.32 2.78 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
62 65 5.816449 TGTTGTACCATTGATGTAGCATG 57.184 39.130 0.00 0.00 0.00 4.06
167 170 2.552743 TGCGAGAGGAGTACATAATCGG 59.447 50.000 0.00 0.00 0.00 4.18
225 249 1.062886 AGGAGGGACGAATGGATGAGA 60.063 52.381 0.00 0.00 0.00 3.27
255 279 1.496429 GTGGTGATGGAGATTGGGGAT 59.504 52.381 0.00 0.00 0.00 3.85
298 322 0.032952 GTACGTGTGTGCCTCCAAGA 59.967 55.000 0.00 0.00 0.00 3.02
323 347 3.117491 TCTCACAGGCAAAAGAGACAG 57.883 47.619 0.00 0.00 32.57 3.51
340 364 3.774766 AGACAGCTCCCACAATACACATA 59.225 43.478 0.00 0.00 0.00 2.29
406 430 9.575783 TTACAAGGAATACAAAACACTTCAAAC 57.424 29.630 0.00 0.00 0.00 2.93
410 434 7.607250 AGGAATACAAAACACTTCAAACACAA 58.393 30.769 0.00 0.00 0.00 3.33
411 435 8.257306 AGGAATACAAAACACTTCAAACACAAT 58.743 29.630 0.00 0.00 0.00 2.71
451 476 6.100668 GTCTCTAGACTTTTGTATGACCACC 58.899 44.000 2.81 0.00 41.65 4.61
461 489 0.742505 TATGACCACCGCCGTTAGAG 59.257 55.000 0.00 0.00 0.00 2.43
464 492 4.832608 CCACCGCCGTTAGAGCCC 62.833 72.222 0.00 0.00 0.00 5.19
487 515 6.815641 CCCTTGAATAGATCTAATGACCATCG 59.184 42.308 6.52 0.00 0.00 3.84
489 517 8.256605 CCTTGAATAGATCTAATGACCATCGAT 58.743 37.037 6.52 0.00 0.00 3.59
493 521 3.507622 AGATCTAATGACCATCGATGCGA 59.492 43.478 20.25 5.82 41.13 5.10
498 526 0.246360 TGACCATCGATGCGACTGTT 59.754 50.000 20.25 0.00 39.18 3.16
504 532 2.724977 TCGATGCGACTGTTCTTCTT 57.275 45.000 0.00 0.00 0.00 2.52
507 535 2.343843 CGATGCGACTGTTCTTCTTGAG 59.656 50.000 0.00 0.00 0.00 3.02
528 556 0.771127 CTCCTTCCTGGTGGGTTGAA 59.229 55.000 8.22 0.00 37.07 2.69
553 581 3.126514 CCATGACACTTTCATCTCTGCAC 59.873 47.826 0.00 0.00 43.68 4.57
559 587 2.476619 ACTTTCATCTCTGCACGTTTCG 59.523 45.455 0.00 0.00 0.00 3.46
567 595 0.179250 CTGCACGTTTCGATTCACGG 60.179 55.000 14.52 6.77 40.84 4.94
571 599 1.012486 ACGTTTCGATTCACGGCTCC 61.012 55.000 14.52 0.00 40.84 4.70
588 1455 4.760047 CCTGCCCCCACGACGAAG 62.760 72.222 0.00 0.00 0.00 3.79
591 1458 4.778143 GCCCCCACGACGAAGCAT 62.778 66.667 0.00 0.00 0.00 3.79
598 1471 2.202932 CGACGAAGCATGGAGGGG 60.203 66.667 0.00 0.00 0.00 4.79
599 1472 2.721167 CGACGAAGCATGGAGGGGA 61.721 63.158 0.00 0.00 0.00 4.81
617 1490 1.456705 AAGTTTGCCCTTTCCGCCA 60.457 52.632 0.00 0.00 0.00 5.69
636 1511 1.960689 CAAAGGGGAAAACACGTCCAT 59.039 47.619 0.00 0.00 36.83 3.41
644 1519 1.956297 AAACACGTCCATTTCGTCCA 58.044 45.000 0.00 0.00 39.55 4.02
653 1528 1.200020 CCATTTCGTCCAAAGGCTGAC 59.800 52.381 0.00 0.00 0.00 3.51
730 1614 1.588404 CAATGGCGCAACGACTAGTAG 59.412 52.381 10.83 0.00 35.04 2.57
731 1615 0.815734 ATGGCGCAACGACTAGTAGT 59.184 50.000 10.83 1.37 35.04 2.73
732 1616 1.452110 TGGCGCAACGACTAGTAGTA 58.548 50.000 10.83 0.00 35.04 1.82
733 1617 1.811965 TGGCGCAACGACTAGTAGTAA 59.188 47.619 10.83 0.00 35.04 2.24
734 1618 2.424601 TGGCGCAACGACTAGTAGTAAT 59.575 45.455 10.83 0.00 35.04 1.89
735 1619 3.627123 TGGCGCAACGACTAGTAGTAATA 59.373 43.478 10.83 0.00 35.04 0.98
736 1620 3.971240 GGCGCAACGACTAGTAGTAATAC 59.029 47.826 10.83 0.00 0.00 1.89
737 1621 4.496341 GGCGCAACGACTAGTAGTAATACA 60.496 45.833 10.83 0.00 0.00 2.29
738 1622 4.669728 GCGCAACGACTAGTAGTAATACAG 59.330 45.833 9.19 1.34 0.00 2.74
739 1623 5.728898 GCGCAACGACTAGTAGTAATACAGT 60.729 44.000 9.19 4.41 0.00 3.55
740 1624 6.510157 GCGCAACGACTAGTAGTAATACAGTA 60.510 42.308 9.19 0.00 0.00 2.74
741 1625 6.843279 CGCAACGACTAGTAGTAATACAGTAC 59.157 42.308 9.19 0.00 33.79 2.73
742 1626 7.464577 CGCAACGACTAGTAGTAATACAGTACA 60.465 40.741 9.19 0.00 35.76 2.90
743 1627 7.850003 GCAACGACTAGTAGTAATACAGTACAG 59.150 40.741 9.19 0.00 35.76 2.74
744 1628 8.877779 CAACGACTAGTAGTAATACAGTACAGT 58.122 37.037 9.19 0.00 35.76 3.55
745 1629 8.417780 ACGACTAGTAGTAATACAGTACAGTG 57.582 38.462 6.87 0.00 35.76 3.66
808 1692 0.036577 AAGAGCTCGCAGCAACAGAT 60.037 50.000 8.37 0.00 45.56 2.90
821 1705 6.038356 GCAGCAACAGATATGCAAATAAACT 58.962 36.000 0.00 0.00 46.22 2.66
822 1706 6.532657 GCAGCAACAGATATGCAAATAAACTT 59.467 34.615 0.00 0.00 46.22 2.66
823 1707 7.701924 GCAGCAACAGATATGCAAATAAACTTA 59.298 33.333 0.00 0.00 46.22 2.24
846 1801 3.971245 GGAGGTCAACTCTGATCACTT 57.029 47.619 0.00 0.00 45.83 3.16
863 1829 3.261643 TCACTTCATGCACATCTACCAGT 59.738 43.478 0.00 0.00 0.00 4.00
903 1869 1.444553 CTGCCGTTGGTCTCGAGAC 60.445 63.158 32.96 32.96 44.04 3.36
922 1888 3.111098 GACCAGTCGACGCGTATAAATT 58.889 45.455 13.97 0.00 0.00 1.82
949 1915 2.254152 TGGCCACACTCTCCTCTATT 57.746 50.000 0.00 0.00 0.00 1.73
984 1950 6.566564 GCTCACAGAAATCAAAAGATCGAACA 60.567 38.462 0.00 0.00 0.00 3.18
985 1951 6.658831 TCACAGAAATCAAAAGATCGAACAC 58.341 36.000 0.00 0.00 0.00 3.32
986 1952 5.561499 CACAGAAATCAAAAGATCGAACACG 59.439 40.000 0.00 0.00 0.00 4.49
987 1953 5.082059 CAGAAATCAAAAGATCGAACACGG 58.918 41.667 0.00 0.00 0.00 4.94
988 1954 4.994852 AGAAATCAAAAGATCGAACACGGA 59.005 37.500 0.00 0.00 0.00 4.69
989 1955 4.928661 AATCAAAAGATCGAACACGGAG 57.071 40.909 0.00 0.00 0.00 4.63
991 1957 3.314553 TCAAAAGATCGAACACGGAGTC 58.685 45.455 0.00 0.00 41.61 3.36
995 1961 1.469308 AGATCGAACACGGAGTCTCAC 59.531 52.381 1.47 0.00 41.61 3.51
999 1965 1.200252 CGAACACGGAGTCTCACAGAT 59.800 52.381 1.47 0.00 41.61 2.90
1027 1993 4.047059 GACGCGTCCTTCACCGGA 62.047 66.667 28.61 0.00 0.00 5.14
1045 2011 3.151022 GGTCTCCTGCCCCTCTCG 61.151 72.222 0.00 0.00 0.00 4.04
1249 2215 2.050144 TCAGGGTCAGCTTCTTTCTGT 58.950 47.619 0.00 0.00 33.48 3.41
1250 2216 2.439507 TCAGGGTCAGCTTCTTTCTGTT 59.560 45.455 0.00 0.00 33.48 3.16
1266 2233 7.258441 TCTTTCTGTTCTATCCGTCTTGTATG 58.742 38.462 0.00 0.00 0.00 2.39
1297 2264 6.017770 TGTCAACAACTTAATCCCAACGTTAG 60.018 38.462 0.00 0.00 0.00 2.34
1323 2323 0.324614 CTGTACAGGGGTGTGATGCA 59.675 55.000 15.49 0.00 0.00 3.96
1660 2683 1.869574 CGACATGGTCACGCTCTCG 60.870 63.158 0.00 0.00 42.43 4.04
1951 2977 4.351938 TACGCGCGCAACAGGACT 62.352 61.111 32.58 9.66 0.00 3.85
2064 3098 5.409826 GCAACAGAGTTAACTAGTGCATTCT 59.590 40.000 19.51 5.90 0.00 2.40
2065 3099 6.590292 GCAACAGAGTTAACTAGTGCATTCTA 59.410 38.462 19.51 0.00 0.00 2.10
2066 3100 7.201478 GCAACAGAGTTAACTAGTGCATTCTAG 60.201 40.741 19.51 9.27 41.99 2.43
2078 3112 4.832266 AGTGCATTCTAGTATCTGCTAGCT 59.168 41.667 17.23 0.00 38.58 3.32
2117 3151 2.639286 CTGCTGCAACCGTGGAAC 59.361 61.111 3.02 0.00 0.00 3.62
2220 3263 2.512692 TTGGTGCATGGAGCTGTTAT 57.487 45.000 17.56 0.00 45.94 1.89
2221 3264 2.512692 TGGTGCATGGAGCTGTTATT 57.487 45.000 17.56 0.00 45.94 1.40
2222 3265 2.806434 TGGTGCATGGAGCTGTTATTT 58.194 42.857 17.56 0.00 45.94 1.40
2223 3266 3.164268 TGGTGCATGGAGCTGTTATTTT 58.836 40.909 17.56 0.00 45.94 1.82
2224 3267 3.056678 TGGTGCATGGAGCTGTTATTTTG 60.057 43.478 17.56 0.00 45.94 2.44
2225 3268 3.193267 GGTGCATGGAGCTGTTATTTTGA 59.807 43.478 9.38 0.00 45.94 2.69
2226 3269 4.321899 GGTGCATGGAGCTGTTATTTTGAA 60.322 41.667 9.38 0.00 45.94 2.69
2227 3270 5.413499 GTGCATGGAGCTGTTATTTTGAAT 58.587 37.500 0.00 0.00 45.94 2.57
2228 3271 5.517770 GTGCATGGAGCTGTTATTTTGAATC 59.482 40.000 0.00 0.00 45.94 2.52
2229 3272 5.419788 TGCATGGAGCTGTTATTTTGAATCT 59.580 36.000 0.00 0.00 45.94 2.40
2230 3273 6.071221 TGCATGGAGCTGTTATTTTGAATCTT 60.071 34.615 0.00 0.00 45.94 2.40
2233 3276 9.211485 CATGGAGCTGTTATTTTGAATCTTTTT 57.789 29.630 0.00 0.00 0.00 1.94
2296 3340 5.836898 TCCACATTATTACGGATGTACTCCT 59.163 40.000 8.96 1.46 42.47 3.69
2299 3343 6.645415 CACATTATTACGGATGTACTCCTTCC 59.355 42.308 8.96 3.27 42.47 3.46
2303 3347 2.517609 GGATGTACTCCTTCCGCCT 58.482 57.895 0.00 0.00 41.29 5.52
2304 3348 0.105039 GGATGTACTCCTTCCGCCTG 59.895 60.000 0.00 0.00 41.29 4.85
2305 3349 1.112113 GATGTACTCCTTCCGCCTGA 58.888 55.000 0.00 0.00 0.00 3.86
2315 3359 3.130340 TCCTTCCGCCTGAAAATATTTGC 59.870 43.478 0.39 0.00 31.06 3.68
2325 3369 6.820152 GCCTGAAAATATTTGCCAGAGAAATT 59.180 34.615 22.49 0.00 0.00 1.82
2339 3383 8.246871 TGCCAGAGAAATTGATATATCTAGACG 58.753 37.037 13.79 0.00 0.00 4.18
2382 3426 8.742554 AATTCATTTTTACTCATTTCCGTGAC 57.257 30.769 0.00 0.00 0.00 3.67
2383 3427 6.869315 TCATTTTTACTCATTTCCGTGACA 57.131 33.333 0.00 0.00 0.00 3.58
2384 3428 6.898041 TCATTTTTACTCATTTCCGTGACAG 58.102 36.000 0.00 0.00 0.00 3.51
2385 3429 5.682943 TTTTTACTCATTTCCGTGACAGG 57.317 39.130 0.00 0.00 0.00 4.00
2401 3445 3.519107 TGACAGGTAATTCTGCATGGAGA 59.481 43.478 13.58 13.58 38.26 3.71
2407 3451 5.663106 AGGTAATTCTGCATGGAGAGAGTAA 59.337 40.000 16.95 2.40 0.00 2.24
2476 3520 4.277476 TGGGATTACAACCATGGATTGAC 58.723 43.478 21.47 12.14 0.00 3.18
2477 3521 4.264128 TGGGATTACAACCATGGATTGACA 60.264 41.667 21.47 11.05 0.00 3.58
2498 3542 8.153221 TGACAAAGTTCTAACCATTATAGGGA 57.847 34.615 0.00 0.00 0.00 4.20
2506 3550 7.857404 TCTAACCATTATAGGGAAGGAGAAG 57.143 40.000 0.00 0.00 0.00 2.85
2512 3556 6.768381 CCATTATAGGGAAGGAGAAGAACAAC 59.232 42.308 0.00 0.00 0.00 3.32
2513 3557 4.846168 ATAGGGAAGGAGAAGAACAACC 57.154 45.455 0.00 0.00 0.00 3.77
2514 3558 1.348036 AGGGAAGGAGAAGAACAACCG 59.652 52.381 0.00 0.00 0.00 4.44
2523 3567 2.037381 AGAAGAACAACCGAGGAGGAAC 59.963 50.000 0.00 0.00 45.00 3.62
2529 3573 0.969894 AACCGAGGAGGAACAGACAG 59.030 55.000 0.00 0.00 45.00 3.51
2536 3580 3.999663 GAGGAGGAACAGACAGAAACATG 59.000 47.826 0.00 0.00 0.00 3.21
2537 3581 3.648067 AGGAGGAACAGACAGAAACATGA 59.352 43.478 0.00 0.00 0.00 3.07
2561 3746 1.404583 GCCGAAGCCGTAAGTTCCTAA 60.405 52.381 0.00 0.00 0.00 2.69
2582 3767 6.649557 CCTAACCAAGTTGTTCGTAGAAATCT 59.350 38.462 1.45 0.00 45.90 2.40
2584 3769 5.607477 ACCAAGTTGTTCGTAGAAATCTCA 58.393 37.500 1.45 0.00 45.90 3.27
2605 3790 6.663523 TCTCATGTGTATTTGTAGTCCTCTCA 59.336 38.462 0.00 0.00 0.00 3.27
2628 3813 2.681064 TCATTGCAGCCCAAGCCC 60.681 61.111 0.00 0.00 41.25 5.19
2640 3825 2.678934 AAGCCCAGCAGCACATGG 60.679 61.111 0.00 0.00 36.27 3.66
2648 3833 2.277737 CAGCACATGGCCCATCCT 59.722 61.111 0.00 0.00 46.50 3.24
2650 3835 0.820891 CAGCACATGGCCCATCCTAC 60.821 60.000 0.00 0.00 46.50 3.18
2680 3865 4.650754 AGGTTGGTCGCTAACAGTATAG 57.349 45.455 7.97 0.00 0.00 1.31
2684 3869 4.365899 TGGTCGCTAACAGTATAGTGTG 57.634 45.455 13.95 4.03 35.42 3.82
2686 3871 4.943093 TGGTCGCTAACAGTATAGTGTGTA 59.057 41.667 13.95 7.85 35.42 2.90
2691 3876 5.173312 CGCTAACAGTATAGTGTGTATGTGC 59.827 44.000 13.95 10.52 0.00 4.57
2704 3889 7.380536 AGTGTGTATGTGCAAATTTTCATGAT 58.619 30.769 0.00 0.00 0.00 2.45
2707 3892 7.871463 TGTGTATGTGCAAATTTTCATGATGAA 59.129 29.630 3.29 3.29 34.03 2.57
2710 3895 9.910511 GTATGTGCAAATTTTCATGATGAAATC 57.089 29.630 20.04 8.83 44.75 2.17
2713 3898 7.608376 TGTGCAAATTTTCATGATGAAATCCAT 59.392 29.630 20.04 9.20 44.75 3.41
2715 3900 8.454894 TGCAAATTTTCATGATGAAATCCATTG 58.545 29.630 20.04 19.79 44.75 2.82
2716 3901 8.670135 GCAAATTTTCATGATGAAATCCATTGA 58.330 29.630 20.04 5.19 44.75 2.57
2717 3902 9.982291 CAAATTTTCATGATGAAATCCATTGAC 57.018 29.630 20.04 0.00 44.75 3.18
2718 3903 9.727859 AAATTTTCATGATGAAATCCATTGACA 57.272 25.926 20.04 3.82 44.75 3.58
2719 3904 9.899661 AATTTTCATGATGAAATCCATTGACAT 57.100 25.926 20.04 5.89 44.75 3.06
2735 3920 9.967451 TCCATTGACATATAGTAAAAGGAACAA 57.033 29.630 0.00 0.00 35.89 2.83
2783 3968 4.371786 CATATGTGGACTGTTCGCTATGT 58.628 43.478 0.76 0.00 0.00 2.29
2784 3969 5.528870 CATATGTGGACTGTTCGCTATGTA 58.471 41.667 0.76 0.00 0.00 2.29
2785 3970 3.945981 TGTGGACTGTTCGCTATGTAA 57.054 42.857 0.76 0.00 0.00 2.41
2786 3971 4.260139 TGTGGACTGTTCGCTATGTAAA 57.740 40.909 0.76 0.00 0.00 2.01
2787 3972 4.633175 TGTGGACTGTTCGCTATGTAAAA 58.367 39.130 0.76 0.00 0.00 1.52
2788 3973 4.449743 TGTGGACTGTTCGCTATGTAAAAC 59.550 41.667 0.76 0.00 0.00 2.43
2790 3975 3.998341 GGACTGTTCGCTATGTAAAACCA 59.002 43.478 0.00 0.00 0.00 3.67
2791 3976 4.453136 GGACTGTTCGCTATGTAAAACCAA 59.547 41.667 0.00 0.00 0.00 3.67
2792 3977 5.123344 GGACTGTTCGCTATGTAAAACCAAT 59.877 40.000 0.00 0.00 0.00 3.16
2793 3978 5.938322 ACTGTTCGCTATGTAAAACCAATG 58.062 37.500 0.00 0.00 0.00 2.82
2807 3992 2.470983 CCAATGGGTTTCGCCATTTT 57.529 45.000 2.63 0.00 39.65 1.82
2810 3995 2.453983 ATGGGTTTCGCCATTTTGTG 57.546 45.000 0.00 0.00 39.65 3.33
2812 3997 1.482593 TGGGTTTCGCCATTTTGTGTT 59.517 42.857 0.00 0.00 39.65 3.32
2813 3998 1.864082 GGGTTTCGCCATTTTGTGTTG 59.136 47.619 0.00 0.00 39.65 3.33
2814 3999 1.260297 GGTTTCGCCATTTTGTGTTGC 59.740 47.619 0.00 0.00 37.17 4.17
2815 4000 2.200899 GTTTCGCCATTTTGTGTTGCT 58.799 42.857 0.00 0.00 0.00 3.91
2817 4002 1.028130 TCGCCATTTTGTGTTGCTCA 58.972 45.000 0.00 0.00 0.00 4.26
2818 4003 1.612950 TCGCCATTTTGTGTTGCTCAT 59.387 42.857 0.00 0.00 0.00 2.90
2820 4005 2.607526 CGCCATTTTGTGTTGCTCATGA 60.608 45.455 0.00 0.00 0.00 3.07
2822 4007 3.998341 GCCATTTTGTGTTGCTCATGAAT 59.002 39.130 0.00 0.00 0.00 2.57
2824 4009 5.231702 CCATTTTGTGTTGCTCATGAATCA 58.768 37.500 0.00 0.00 0.00 2.57
2825 4010 5.872617 CCATTTTGTGTTGCTCATGAATCAT 59.127 36.000 0.00 0.00 0.00 2.45
2826 4011 6.370442 CCATTTTGTGTTGCTCATGAATCATT 59.630 34.615 0.00 0.00 0.00 2.57
2828 4013 5.456548 TTGTGTTGCTCATGAATCATTGT 57.543 34.783 0.00 0.00 0.00 2.71
2829 4014 6.572167 TTGTGTTGCTCATGAATCATTGTA 57.428 33.333 0.00 0.00 0.00 2.41
2830 4015 6.762702 TGTGTTGCTCATGAATCATTGTAT 57.237 33.333 0.00 0.00 0.00 2.29
2832 4017 7.604549 TGTGTTGCTCATGAATCATTGTATTT 58.395 30.769 0.00 0.00 0.00 1.40
2833 4018 8.089597 TGTGTTGCTCATGAATCATTGTATTTT 58.910 29.630 0.00 0.00 0.00 1.82
2834 4019 8.377681 GTGTTGCTCATGAATCATTGTATTTTG 58.622 33.333 0.00 0.00 0.00 2.44
2835 4020 8.305317 TGTTGCTCATGAATCATTGTATTTTGA 58.695 29.630 0.00 0.00 0.00 2.69
2836 4021 8.804743 GTTGCTCATGAATCATTGTATTTTGAG 58.195 33.333 0.00 0.00 35.09 3.02
2837 4022 6.976349 TGCTCATGAATCATTGTATTTTGAGC 59.024 34.615 18.72 18.72 44.89 4.26
2839 4024 6.808829 TCATGAATCATTGTATTTTGAGCCC 58.191 36.000 0.00 0.00 0.00 5.19
2841 4026 4.097741 TGAATCATTGTATTTTGAGCCCCG 59.902 41.667 0.00 0.00 0.00 5.73
2842 4027 1.748493 TCATTGTATTTTGAGCCCCGC 59.252 47.619 0.00 0.00 0.00 6.13
2844 4029 1.917872 TTGTATTTTGAGCCCCGCTT 58.082 45.000 0.00 0.00 39.88 4.68
2845 4030 1.917872 TGTATTTTGAGCCCCGCTTT 58.082 45.000 0.00 0.00 39.88 3.51
2846 4031 1.543802 TGTATTTTGAGCCCCGCTTTG 59.456 47.619 0.00 0.00 39.88 2.77
2847 4032 1.135112 GTATTTTGAGCCCCGCTTTGG 60.135 52.381 0.00 0.00 39.88 3.28
2848 4033 0.831711 ATTTTGAGCCCCGCTTTGGT 60.832 50.000 0.00 0.00 39.88 3.67
2849 4034 0.178987 TTTTGAGCCCCGCTTTGGTA 60.179 50.000 0.00 0.00 39.88 3.25
2850 4035 0.891904 TTTGAGCCCCGCTTTGGTAC 60.892 55.000 0.00 0.00 39.88 3.34
2852 4037 2.033602 AGCCCCGCTTTGGTACAC 59.966 61.111 0.00 0.00 39.29 2.90
2853 4038 3.060000 GCCCCGCTTTGGTACACC 61.060 66.667 0.00 0.00 39.29 4.16
2854 4039 2.360726 CCCCGCTTTGGTACACCC 60.361 66.667 0.00 0.00 39.29 4.61
2880 4065 5.852282 CCCCCTCACAAAACATATAAAGG 57.148 43.478 0.00 0.00 0.00 3.11
2881 4066 4.649218 CCCCCTCACAAAACATATAAAGGG 59.351 45.833 0.00 0.00 41.61 3.95
2883 4068 6.428295 CCCCTCACAAAACATATAAAGGGTA 58.572 40.000 0.00 0.00 40.56 3.69
2885 4070 7.563556 CCCCTCACAAAACATATAAAGGGTAAT 59.436 37.037 0.00 0.00 40.56 1.89
2899 4084 3.816994 AGGGTAATATCGACCTTTTGGC 58.183 45.455 6.69 0.00 45.59 4.52
2900 4085 3.201266 AGGGTAATATCGACCTTTTGGCA 59.799 43.478 6.69 0.00 45.59 4.92
2903 4088 5.068591 GGGTAATATCGACCTTTTGGCAAAT 59.931 40.000 14.29 0.00 45.59 2.32
2904 4089 6.206498 GGTAATATCGACCTTTTGGCAAATC 58.794 40.000 14.29 7.70 45.59 2.17
2905 4090 2.919666 ATCGACCTTTTGGCAAATCG 57.080 45.000 22.03 22.03 45.59 3.34
2907 4092 2.768698 TCGACCTTTTGGCAAATCGTA 58.231 42.857 25.03 14.35 45.59 3.43
2908 4093 3.340034 TCGACCTTTTGGCAAATCGTAT 58.660 40.909 25.03 7.98 45.59 3.06
2910 4095 3.486875 CGACCTTTTGGCAAATCGTATCC 60.487 47.826 20.53 6.65 45.59 2.59
2911 4096 3.426615 ACCTTTTGGCAAATCGTATCCA 58.573 40.909 14.29 0.00 45.59 3.41
2912 4097 3.192633 ACCTTTTGGCAAATCGTATCCAC 59.807 43.478 14.29 0.00 45.59 4.02
2913 4098 3.443681 CCTTTTGGCAAATCGTATCCACT 59.556 43.478 14.29 0.00 0.00 4.00
2914 4099 4.082245 CCTTTTGGCAAATCGTATCCACTT 60.082 41.667 14.29 0.00 0.00 3.16
2915 4100 5.124776 CCTTTTGGCAAATCGTATCCACTTA 59.875 40.000 14.29 0.00 0.00 2.24
2918 4103 4.776349 TGGCAAATCGTATCCACTTACAT 58.224 39.130 0.00 0.00 0.00 2.29
2919 4104 5.919755 TGGCAAATCGTATCCACTTACATA 58.080 37.500 0.00 0.00 0.00 2.29
2921 4106 6.426633 TGGCAAATCGTATCCACTTACATATG 59.573 38.462 0.00 0.00 0.00 1.78
2922 4107 6.426937 GGCAAATCGTATCCACTTACATATGT 59.573 38.462 13.93 13.93 0.00 2.29
2923 4108 7.601130 GGCAAATCGTATCCACTTACATATGTA 59.399 37.037 11.62 11.62 0.00 2.29
2924 4109 9.151471 GCAAATCGTATCCACTTACATATGTAT 57.849 33.333 16.16 4.26 0.00 2.29
2930 4115 9.902196 CGTATCCACTTACATATGTATTGTACA 57.098 33.333 16.16 8.53 43.80 2.90
2943 4128 7.853377 ATGTATTGTACATACGTCAATCGAG 57.147 36.000 0.00 0.00 46.90 4.04
2944 4129 6.788243 TGTATTGTACATACGTCAATCGAGT 58.212 36.000 0.00 0.00 37.05 4.18
2945 4130 7.918643 TGTATTGTACATACGTCAATCGAGTA 58.081 34.615 0.00 0.00 37.05 2.59
2946 4131 8.066000 TGTATTGTACATACGTCAATCGAGTAG 58.934 37.037 0.00 0.00 37.05 2.57
2947 4132 6.426980 TTGTACATACGTCAATCGAGTAGT 57.573 37.500 0.00 0.00 42.86 2.73
2948 4133 7.538303 TTGTACATACGTCAATCGAGTAGTA 57.462 36.000 0.00 0.00 42.86 1.82
2950 4135 5.670149 ACATACGTCAATCGAGTAGTAGG 57.330 43.478 0.00 0.00 42.86 3.18
2951 4136 4.024218 ACATACGTCAATCGAGTAGTAGGC 60.024 45.833 0.00 0.00 42.86 3.93
2952 4137 2.641305 ACGTCAATCGAGTAGTAGGCT 58.359 47.619 0.00 0.00 42.86 4.58
2953 4138 2.613133 ACGTCAATCGAGTAGTAGGCTC 59.387 50.000 0.00 0.00 42.86 4.70
2954 4139 2.031857 CGTCAATCGAGTAGTAGGCTCC 60.032 54.545 0.00 0.00 42.86 4.70
2955 4140 2.031857 GTCAATCGAGTAGTAGGCTCCG 60.032 54.545 0.00 0.00 0.00 4.63
2956 4141 1.948145 CAATCGAGTAGTAGGCTCCGT 59.052 52.381 0.00 0.00 0.00 4.69
2957 4142 1.881591 ATCGAGTAGTAGGCTCCGTC 58.118 55.000 0.00 0.00 0.00 4.79
2958 4143 0.179062 TCGAGTAGTAGGCTCCGTCC 60.179 60.000 0.00 0.00 0.00 4.79
2959 4144 0.179051 CGAGTAGTAGGCTCCGTCCT 60.179 60.000 0.00 0.00 40.21 3.85
2960 4145 1.310904 GAGTAGTAGGCTCCGTCCTG 58.689 60.000 0.00 0.00 37.01 3.86
2962 4147 1.108132 GTAGTAGGCTCCGTCCTGGG 61.108 65.000 0.00 0.00 37.01 4.45
2963 4148 1.578215 TAGTAGGCTCCGTCCTGGGT 61.578 60.000 0.00 0.00 37.01 4.51
2964 4149 1.988406 GTAGGCTCCGTCCTGGGTT 60.988 63.158 0.00 0.00 37.01 4.11
2965 4150 1.684734 TAGGCTCCGTCCTGGGTTC 60.685 63.158 0.00 0.00 37.01 3.62
2967 4152 4.452733 GCTCCGTCCTGGGTTCGG 62.453 72.222 15.69 15.69 44.76 4.30
2968 4153 4.452733 CTCCGTCCTGGGTTCGGC 62.453 72.222 16.56 0.00 43.35 5.54
2982 4472 2.606108 GTTCGGCCCATTCACATTTTC 58.394 47.619 0.00 0.00 0.00 2.29
2987 4477 3.056607 CGGCCCATTCACATTTTCTTCTT 60.057 43.478 0.00 0.00 0.00 2.52
2991 4481 6.293571 GGCCCATTCACATTTTCTTCTTTTTG 60.294 38.462 0.00 0.00 0.00 2.44
2994 4484 6.293571 CCATTCACATTTTCTTCTTTTTGCCC 60.294 38.462 0.00 0.00 0.00 5.36
2999 4489 6.913673 CACATTTTCTTCTTTTTGCCCATTTG 59.086 34.615 0.00 0.00 0.00 2.32
3000 4490 5.497635 TTTTCTTCTTTTTGCCCATTTGC 57.502 34.783 0.00 0.00 0.00 3.68
3001 4491 3.834489 TCTTCTTTTTGCCCATTTGCA 57.166 38.095 0.00 0.00 40.07 4.08
3003 4493 4.716794 TCTTCTTTTTGCCCATTTGCATT 58.283 34.783 0.00 0.00 41.70 3.56
3006 4496 5.435820 TCTTTTTGCCCATTTGCATTTTC 57.564 34.783 0.00 0.00 41.70 2.29
3011 4501 5.848833 TTGCCCATTTGCATTTTCTTTTT 57.151 30.435 0.00 0.00 41.70 1.94
3034 4524 5.352643 TTTTTAGCCTCGAAAAGTACTGC 57.647 39.130 0.00 0.00 0.00 4.40
3035 4525 3.671008 TTAGCCTCGAAAAGTACTGCA 57.329 42.857 0.00 0.00 0.00 4.41
3036 4526 1.797025 AGCCTCGAAAAGTACTGCAC 58.203 50.000 0.00 0.00 0.00 4.57
3037 4527 0.796927 GCCTCGAAAAGTACTGCACC 59.203 55.000 0.00 0.00 0.00 5.01
3038 4528 1.876416 GCCTCGAAAAGTACTGCACCA 60.876 52.381 0.00 0.00 0.00 4.17
3039 4529 2.699954 CCTCGAAAAGTACTGCACCAT 58.300 47.619 0.00 0.00 0.00 3.55
3042 4532 4.466828 CTCGAAAAGTACTGCACCATTTG 58.533 43.478 0.00 0.00 0.00 2.32
3043 4533 3.252215 TCGAAAAGTACTGCACCATTTGG 59.748 43.478 0.00 0.00 42.17 3.28
3044 4534 3.611530 CGAAAAGTACTGCACCATTTGGG 60.612 47.826 0.00 0.00 44.81 4.12
3055 5569 3.685756 GCACCATTTGGGATTCAAACATG 59.314 43.478 0.96 0.00 46.72 3.21
3056 5570 4.803588 GCACCATTTGGGATTCAAACATGT 60.804 41.667 0.96 0.00 46.72 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 65 1.289800 GGTTCTTTCCGAGACGCCAC 61.290 60.000 0.00 0.00 33.02 5.01
225 249 1.492133 CCATCACCACACCCCACTCT 61.492 60.000 0.00 0.00 0.00 3.24
255 279 3.017442 CTCCGGACTATCACTCTCACAA 58.983 50.000 0.00 0.00 0.00 3.33
298 322 5.360714 TGTCTCTTTTGCCTGTGAGAAAATT 59.639 36.000 0.00 0.00 37.32 1.82
323 347 5.897377 AAAACTATGTGTATTGTGGGAGC 57.103 39.130 0.00 0.00 0.00 4.70
426 451 6.100668 GTGGTCATACAAAAGTCTAGAGACC 58.899 44.000 12.71 12.71 45.85 3.85
431 456 3.617263 GCGGTGGTCATACAAAAGTCTAG 59.383 47.826 0.00 0.00 0.00 2.43
438 463 0.250381 AACGGCGGTGGTCATACAAA 60.250 50.000 13.24 0.00 0.00 2.83
451 476 0.462047 ATTCAAGGGCTCTAACGGCG 60.462 55.000 4.80 4.80 0.00 6.46
461 489 5.869579 TGGTCATTAGATCTATTCAAGGGC 58.130 41.667 2.58 0.00 0.00 5.19
464 492 9.085250 CATCGATGGTCATTAGATCTATTCAAG 57.915 37.037 17.96 0.00 0.00 3.02
487 515 2.093467 GCTCAAGAAGAACAGTCGCATC 59.907 50.000 0.00 0.00 0.00 3.91
489 517 1.502231 GCTCAAGAAGAACAGTCGCA 58.498 50.000 0.00 0.00 0.00 5.10
493 521 2.334023 AGGAGGCTCAAGAAGAACAGT 58.666 47.619 17.69 0.00 0.00 3.55
498 526 1.905215 CAGGAAGGAGGCTCAAGAAGA 59.095 52.381 17.69 0.00 0.00 2.87
504 532 1.920325 CCACCAGGAAGGAGGCTCA 60.920 63.158 17.69 0.00 41.47 4.26
507 535 2.539081 AACCCACCAGGAAGGAGGC 61.539 63.158 6.53 0.00 45.99 4.70
536 564 2.533266 ACGTGCAGAGATGAAAGTGT 57.467 45.000 0.00 0.00 0.00 3.55
553 581 1.693083 GGGAGCCGTGAATCGAAACG 61.693 60.000 10.63 10.63 42.86 3.60
571 599 4.760047 CTTCGTCGTGGGGGCAGG 62.760 72.222 0.00 0.00 0.00 4.85
583 1450 1.201429 ACTTCCCCTCCATGCTTCGT 61.201 55.000 0.00 0.00 0.00 3.85
588 1455 1.607801 GGCAAACTTCCCCTCCATGC 61.608 60.000 0.00 0.00 0.00 4.06
589 1456 0.972471 GGGCAAACTTCCCCTCCATG 60.972 60.000 0.00 0.00 38.30 3.66
590 1457 1.388133 GGGCAAACTTCCCCTCCAT 59.612 57.895 0.00 0.00 38.30 3.41
591 1458 2.851045 GGGCAAACTTCCCCTCCA 59.149 61.111 0.00 0.00 38.30 3.86
598 1471 1.289066 GGCGGAAAGGGCAAACTTC 59.711 57.895 0.00 0.00 0.00 3.01
599 1472 1.456705 TGGCGGAAAGGGCAAACTT 60.457 52.632 0.00 0.00 39.78 2.66
610 1483 0.397254 TGTTTTCCCCTTTGGCGGAA 60.397 50.000 0.00 0.00 36.35 4.30
617 1490 2.375014 ATGGACGTGTTTTCCCCTTT 57.625 45.000 0.00 0.00 31.33 3.11
636 1511 0.472471 AGGTCAGCCTTTGGACGAAA 59.528 50.000 0.00 0.00 44.18 3.46
644 1519 0.036306 CGTTGGGTAGGTCAGCCTTT 59.964 55.000 0.00 0.00 44.18 3.11
670 1545 0.465705 GCACTATCTACTGCCCTGCA 59.534 55.000 0.00 0.00 36.92 4.41
686 1561 4.914291 GTGCCACGTTTACTGCAC 57.086 55.556 7.77 7.77 46.09 4.57
730 1614 8.648097 CAAACTGACATCACTGTACTGTATTAC 58.352 37.037 4.96 0.00 35.14 1.89
731 1615 8.581578 TCAAACTGACATCACTGTACTGTATTA 58.418 33.333 4.96 0.00 35.14 0.98
732 1616 7.385205 GTCAAACTGACATCACTGTACTGTATT 59.615 37.037 4.96 0.00 46.22 1.89
733 1617 6.868864 GTCAAACTGACATCACTGTACTGTAT 59.131 38.462 4.96 0.00 46.22 2.29
734 1618 6.213677 GTCAAACTGACATCACTGTACTGTA 58.786 40.000 4.96 0.00 46.22 2.74
735 1619 5.050490 GTCAAACTGACATCACTGTACTGT 58.950 41.667 0.00 0.00 46.22 3.55
736 1620 5.582439 GTCAAACTGACATCACTGTACTG 57.418 43.478 1.92 0.00 46.22 2.74
808 1692 5.747342 ACCTCCGGTAAGTTTATTTGCATA 58.253 37.500 0.00 0.00 32.11 3.14
821 1705 2.297698 TCAGAGTTGACCTCCGGTAA 57.702 50.000 0.00 0.00 41.47 2.85
822 1706 2.291346 TGATCAGAGTTGACCTCCGGTA 60.291 50.000 0.00 0.00 41.47 4.02
823 1707 1.187087 GATCAGAGTTGACCTCCGGT 58.813 55.000 0.00 0.00 41.47 5.28
843 1790 3.988976 ACTGGTAGATGTGCATGAAGT 57.011 42.857 0.00 0.00 0.00 3.01
846 1801 3.261643 ACTGAACTGGTAGATGTGCATGA 59.738 43.478 0.00 0.00 0.00 3.07
863 1829 1.070786 GGTGAACCGGAGCACTGAA 59.929 57.895 23.46 0.00 35.43 3.02
885 1851 1.444553 GTCTCGAGACCAACGGCAG 60.445 63.158 31.24 0.00 39.07 4.85
897 1863 3.785499 CGCGTCGACTGGTCTCGA 61.785 66.667 14.70 0.00 40.37 4.04
903 1869 3.423206 GGTAATTTATACGCGTCGACTGG 59.577 47.826 18.63 7.57 0.00 4.00
906 1872 2.160233 GCGGTAATTTATACGCGTCGAC 60.160 50.000 18.63 5.18 42.66 4.20
922 1888 3.323758 GAGTGTGGCCATGGCGGTA 62.324 63.158 29.90 16.20 43.06 4.02
949 1915 4.402474 TGATTTCTGTGAGCTCGAATAGGA 59.598 41.667 9.64 0.00 0.00 2.94
984 1950 2.621055 GCTCATATCTGTGAGACTCCGT 59.379 50.000 7.99 0.00 46.77 4.69
985 1951 2.350293 CGCTCATATCTGTGAGACTCCG 60.350 54.545 7.99 0.00 46.77 4.63
986 1952 2.030363 CCGCTCATATCTGTGAGACTCC 60.030 54.545 7.99 0.00 46.77 3.85
987 1953 2.881513 TCCGCTCATATCTGTGAGACTC 59.118 50.000 7.99 0.00 46.77 3.36
988 1954 2.884012 CTCCGCTCATATCTGTGAGACT 59.116 50.000 7.99 0.00 46.77 3.24
989 1955 2.030363 CCTCCGCTCATATCTGTGAGAC 60.030 54.545 7.99 0.00 46.77 3.36
990 1956 2.158608 TCCTCCGCTCATATCTGTGAGA 60.159 50.000 7.99 0.00 46.77 3.27
991 1957 2.030363 GTCCTCCGCTCATATCTGTGAG 60.030 54.545 0.03 0.03 46.59 3.51
995 1961 3.782884 CGTCCTCCGCTCATATCTG 57.217 57.895 0.00 0.00 0.00 2.90
1027 1993 2.366570 GAGAGGGGCAGGAGACCT 59.633 66.667 0.00 0.00 45.05 3.85
1029 1995 1.950973 GAACGAGAGGGGCAGGAGAC 61.951 65.000 0.00 0.00 0.00 3.36
1036 2002 4.475135 GGCCAGAACGAGAGGGGC 62.475 72.222 0.00 0.00 43.86 5.80
1045 2011 2.353610 CCCATGCCAAGGCCAGAAC 61.354 63.158 5.01 0.00 41.09 3.01
1200 2166 1.004440 GTGGAAGAAGAGGCGCACT 60.004 57.895 10.83 4.91 0.00 4.40
1249 2215 4.400251 ACGGAACATACAAGACGGATAGAA 59.600 41.667 0.00 0.00 0.00 2.10
1250 2216 3.949754 ACGGAACATACAAGACGGATAGA 59.050 43.478 0.00 0.00 0.00 1.98
1266 2233 4.319984 GGGATTAAGTTGTTGACACGGAAC 60.320 45.833 0.00 0.00 0.00 3.62
1297 2264 0.884704 CACCCCTGTACAGTGCACAC 60.885 60.000 21.04 9.34 0.00 3.82
1323 2323 4.148825 GCGTCCAGGAGCACGGAT 62.149 66.667 0.00 0.00 36.50 4.18
1635 2658 1.447838 GTGACCATGTCGTCGGCAT 60.448 57.895 6.49 6.49 34.95 4.40
1636 2659 2.048597 GTGACCATGTCGTCGGCA 60.049 61.111 0.14 0.14 34.95 5.69
1726 2749 1.672356 GGTGGCGTTCATGTCTGCT 60.672 57.895 0.00 0.00 0.00 4.24
1729 2752 0.108804 CGTAGGTGGCGTTCATGTCT 60.109 55.000 0.00 0.00 0.00 3.41
2078 3112 1.139816 CGCTATTCGTCGAAGCAGCA 61.140 55.000 29.12 5.13 34.98 4.41
2117 3151 6.568869 AGCTGATGAACTACTAGCAGTTTAG 58.431 40.000 9.74 7.59 38.86 1.85
2286 3330 1.112113 TCAGGCGGAAGGAGTACATC 58.888 55.000 0.00 0.00 0.00 3.06
2296 3340 2.828520 TGGCAAATATTTTCAGGCGGAA 59.171 40.909 0.00 0.00 0.00 4.30
2299 3343 3.378112 TCTCTGGCAAATATTTTCAGGCG 59.622 43.478 19.84 14.37 0.00 5.52
2356 3400 9.191995 GTCACGGAAATGAGTAAAAATGAATTT 57.808 29.630 0.00 0.00 0.00 1.82
2357 3401 8.356657 TGTCACGGAAATGAGTAAAAATGAATT 58.643 29.630 0.00 0.00 0.00 2.17
2358 3402 7.881142 TGTCACGGAAATGAGTAAAAATGAAT 58.119 30.769 0.00 0.00 0.00 2.57
2359 3403 7.265647 TGTCACGGAAATGAGTAAAAATGAA 57.734 32.000 0.00 0.00 0.00 2.57
2360 3404 6.072728 CCTGTCACGGAAATGAGTAAAAATGA 60.073 38.462 0.00 0.00 0.00 2.57
2361 3405 6.086222 CCTGTCACGGAAATGAGTAAAAATG 58.914 40.000 0.00 0.00 0.00 2.32
2362 3406 5.768164 ACCTGTCACGGAAATGAGTAAAAAT 59.232 36.000 0.00 0.00 0.00 1.82
2363 3407 5.127491 ACCTGTCACGGAAATGAGTAAAAA 58.873 37.500 0.00 0.00 0.00 1.94
2364 3408 4.710324 ACCTGTCACGGAAATGAGTAAAA 58.290 39.130 0.00 0.00 0.00 1.52
2365 3409 4.345859 ACCTGTCACGGAAATGAGTAAA 57.654 40.909 0.00 0.00 0.00 2.01
2366 3410 5.471556 TTACCTGTCACGGAAATGAGTAA 57.528 39.130 0.00 0.00 0.00 2.24
2367 3411 5.670792 ATTACCTGTCACGGAAATGAGTA 57.329 39.130 0.00 0.00 0.00 2.59
2368 3412 4.553330 ATTACCTGTCACGGAAATGAGT 57.447 40.909 0.00 0.00 0.00 3.41
2369 3413 5.063944 CAGAATTACCTGTCACGGAAATGAG 59.936 44.000 0.00 0.00 0.00 2.90
2370 3414 4.935205 CAGAATTACCTGTCACGGAAATGA 59.065 41.667 0.00 0.00 0.00 2.57
2371 3415 4.437390 GCAGAATTACCTGTCACGGAAATG 60.437 45.833 0.00 0.00 36.57 2.32
2372 3416 3.689649 GCAGAATTACCTGTCACGGAAAT 59.310 43.478 0.00 0.00 36.57 2.17
2373 3417 3.071479 GCAGAATTACCTGTCACGGAAA 58.929 45.455 0.00 0.00 36.57 3.13
2374 3418 2.037902 TGCAGAATTACCTGTCACGGAA 59.962 45.455 0.00 0.00 36.57 4.30
2375 3419 1.621317 TGCAGAATTACCTGTCACGGA 59.379 47.619 0.00 0.00 36.57 4.69
2376 3420 2.093306 TGCAGAATTACCTGTCACGG 57.907 50.000 0.00 0.00 36.57 4.94
2377 3421 2.352651 CCATGCAGAATTACCTGTCACG 59.647 50.000 0.00 0.00 36.57 4.35
2378 3422 3.609853 TCCATGCAGAATTACCTGTCAC 58.390 45.455 0.00 0.00 36.57 3.67
2379 3423 3.519107 TCTCCATGCAGAATTACCTGTCA 59.481 43.478 0.00 0.00 36.57 3.58
2380 3424 4.125703 CTCTCCATGCAGAATTACCTGTC 58.874 47.826 0.00 0.00 36.57 3.51
2381 3425 3.776969 TCTCTCCATGCAGAATTACCTGT 59.223 43.478 0.00 0.00 36.57 4.00
2382 3426 4.141756 ACTCTCTCCATGCAGAATTACCTG 60.142 45.833 0.00 0.00 37.23 4.00
2383 3427 4.036518 ACTCTCTCCATGCAGAATTACCT 58.963 43.478 0.00 0.00 0.00 3.08
2384 3428 4.414337 ACTCTCTCCATGCAGAATTACC 57.586 45.455 0.00 0.00 0.00 2.85
2451 3495 5.963253 TCAATCCATGGTTGTAATCCCAATT 59.037 36.000 12.58 0.00 33.66 2.32
2476 3520 8.272173 TCCTTCCCTATAATGGTTAGAACTTTG 58.728 37.037 0.00 0.00 0.00 2.77
2477 3521 8.401955 TCCTTCCCTATAATGGTTAGAACTTT 57.598 34.615 0.00 0.00 0.00 2.66
2498 3542 2.300437 CTCCTCGGTTGTTCTTCTCCTT 59.700 50.000 0.00 0.00 0.00 3.36
2506 3550 1.343465 TCTGTTCCTCCTCGGTTGTTC 59.657 52.381 0.00 0.00 0.00 3.18
2512 3556 1.257743 TTCTGTCTGTTCCTCCTCGG 58.742 55.000 0.00 0.00 0.00 4.63
2513 3557 2.035961 TGTTTCTGTCTGTTCCTCCTCG 59.964 50.000 0.00 0.00 0.00 4.63
2514 3558 3.753294 TGTTTCTGTCTGTTCCTCCTC 57.247 47.619 0.00 0.00 0.00 3.71
2523 3567 2.354259 GGCCTCTCATGTTTCTGTCTG 58.646 52.381 0.00 0.00 0.00 3.51
2529 3573 0.729690 GCTTCGGCCTCTCATGTTTC 59.270 55.000 0.00 0.00 34.32 2.78
2549 3593 5.332808 CGAACAACTTGGTTAGGAACTTACG 60.333 44.000 0.00 0.00 39.09 3.18
2552 3596 4.520179 ACGAACAACTTGGTTAGGAACTT 58.480 39.130 0.00 0.00 41.75 2.66
2561 3746 5.607477 TGAGATTTCTACGAACAACTTGGT 58.393 37.500 0.00 0.00 0.00 3.67
2582 3767 6.850752 TGAGAGGACTACAAATACACATGA 57.149 37.500 0.00 0.00 0.00 3.07
2584 3769 6.644347 CCTTGAGAGGACTACAAATACACAT 58.356 40.000 0.00 0.00 46.74 3.21
2628 3813 2.758327 ATGGGCCATGTGCTGCTG 60.758 61.111 20.49 0.00 40.92 4.41
2640 3825 1.170919 TACTCTCGCGTAGGATGGGC 61.171 60.000 5.77 0.00 0.00 5.36
2648 3833 1.089920 GACCAACCTACTCTCGCGTA 58.910 55.000 5.77 0.00 0.00 4.42
2650 3835 1.226323 CGACCAACCTACTCTCGCG 60.226 63.158 0.00 0.00 0.00 5.87
2680 3865 7.328982 TCATCATGAAAATTTGCACATACACAC 59.671 33.333 0.00 0.00 0.00 3.82
2743 3928 9.874205 CCACATATGGTTCACTTTATTCAAAAT 57.126 29.630 7.80 0.00 41.64 1.82
2761 3946 4.371786 ACATAGCGAACAGTCCACATATG 58.628 43.478 0.00 0.00 0.00 1.78
2762 3947 4.672587 ACATAGCGAACAGTCCACATAT 57.327 40.909 0.00 0.00 0.00 1.78
2764 3949 4.465632 TTACATAGCGAACAGTCCACAT 57.534 40.909 0.00 0.00 0.00 3.21
2765 3950 3.945981 TTACATAGCGAACAGTCCACA 57.054 42.857 0.00 0.00 0.00 4.17
2766 3951 4.142966 GGTTTTACATAGCGAACAGTCCAC 60.143 45.833 0.00 0.00 0.00 4.02
2767 3952 3.998341 GGTTTTACATAGCGAACAGTCCA 59.002 43.478 0.00 0.00 0.00 4.02
2769 3954 5.600908 TTGGTTTTACATAGCGAACAGTC 57.399 39.130 0.00 0.00 0.00 3.51
2770 3955 5.106317 CCATTGGTTTTACATAGCGAACAGT 60.106 40.000 0.00 0.00 0.00 3.55
2773 3958 4.157105 ACCCATTGGTTTTACATAGCGAAC 59.843 41.667 1.20 0.00 44.75 3.95
2774 3959 4.337145 ACCCATTGGTTTTACATAGCGAA 58.663 39.130 1.20 0.00 44.75 4.70
2775 3960 3.958018 ACCCATTGGTTTTACATAGCGA 58.042 40.909 1.20 0.00 44.75 4.93
2792 3977 1.115467 ACACAAAATGGCGAAACCCA 58.885 45.000 0.00 0.00 39.65 4.51
2793 3978 1.864082 CAACACAAAATGGCGAAACCC 59.136 47.619 0.00 0.00 37.83 4.11
2796 3981 2.159184 TGAGCAACACAAAATGGCGAAA 60.159 40.909 0.00 0.00 0.00 3.46
2797 3982 1.406898 TGAGCAACACAAAATGGCGAA 59.593 42.857 0.00 0.00 0.00 4.70
2798 3983 1.028130 TGAGCAACACAAAATGGCGA 58.972 45.000 0.00 0.00 0.00 5.54
2799 3984 1.722464 CATGAGCAACACAAAATGGCG 59.278 47.619 0.00 0.00 0.00 5.69
2802 3987 6.961359 ATGATTCATGAGCAACACAAAATG 57.039 33.333 0.00 0.00 0.00 2.32
2803 3988 6.932400 ACAATGATTCATGAGCAACACAAAAT 59.068 30.769 0.00 0.00 0.00 1.82
2804 3989 6.282167 ACAATGATTCATGAGCAACACAAAA 58.718 32.000 0.00 0.00 0.00 2.44
2806 3991 5.456548 ACAATGATTCATGAGCAACACAA 57.543 34.783 0.00 0.00 0.00 3.33
2807 3992 6.762702 ATACAATGATTCATGAGCAACACA 57.237 33.333 0.00 0.00 0.00 3.72
2810 3995 8.692110 TCAAAATACAATGATTCATGAGCAAC 57.308 30.769 0.00 0.00 0.00 4.17
2812 3997 6.976349 GCTCAAAATACAATGATTCATGAGCA 59.024 34.615 21.20 0.00 45.98 4.26
2813 3998 6.420008 GGCTCAAAATACAATGATTCATGAGC 59.580 38.462 19.26 19.26 45.97 4.26
2814 3999 6.921857 GGGCTCAAAATACAATGATTCATGAG 59.078 38.462 0.00 2.94 36.59 2.90
2815 4000 6.183360 GGGGCTCAAAATACAATGATTCATGA 60.183 38.462 0.00 0.00 0.00 3.07
2817 4002 5.221303 CGGGGCTCAAAATACAATGATTCAT 60.221 40.000 0.00 0.00 0.00 2.57
2818 4003 4.097741 CGGGGCTCAAAATACAATGATTCA 59.902 41.667 0.00 0.00 0.00 2.57
2820 4005 3.181476 GCGGGGCTCAAAATACAATGATT 60.181 43.478 0.00 0.00 0.00 2.57
2822 4007 1.748493 GCGGGGCTCAAAATACAATGA 59.252 47.619 0.00 0.00 0.00 2.57
2824 4009 2.143876 AGCGGGGCTCAAAATACAAT 57.856 45.000 0.00 0.00 30.62 2.71
2825 4010 1.917872 AAGCGGGGCTCAAAATACAA 58.082 45.000 0.00 0.00 38.25 2.41
2826 4011 1.543802 CAAAGCGGGGCTCAAAATACA 59.456 47.619 0.00 0.00 38.25 2.29
2828 4013 1.181786 CCAAAGCGGGGCTCAAAATA 58.818 50.000 0.00 0.00 38.25 1.40
2829 4014 0.831711 ACCAAAGCGGGGCTCAAAAT 60.832 50.000 0.00 0.00 38.25 1.82
2830 4015 0.178987 TACCAAAGCGGGGCTCAAAA 60.179 50.000 0.00 0.00 38.25 2.44
2832 4017 1.302993 GTACCAAAGCGGGGCTCAA 60.303 57.895 0.00 0.00 38.25 3.02
2833 4018 2.349755 GTACCAAAGCGGGGCTCA 59.650 61.111 0.00 0.00 38.25 4.26
2834 4019 2.038837 GTGTACCAAAGCGGGGCTC 61.039 63.158 0.00 0.00 38.25 4.70
2835 4020 2.033602 GTGTACCAAAGCGGGGCT 59.966 61.111 0.00 0.00 42.56 5.19
2836 4021 3.060000 GGTGTACCAAAGCGGGGC 61.060 66.667 0.00 0.00 40.22 5.80
2837 4022 2.360726 GGGTGTACCAAAGCGGGG 60.361 66.667 3.11 0.00 40.22 5.73
2839 4024 2.360726 GGGGGTGTACCAAAGCGG 60.361 66.667 3.11 0.00 42.91 5.52
2858 4043 4.649218 CCCTTTATATGTTTTGTGAGGGGG 59.351 45.833 0.00 0.00 39.11 5.40
2859 4044 5.269189 ACCCTTTATATGTTTTGTGAGGGG 58.731 41.667 9.67 0.00 45.46 4.79
2860 4045 7.948034 TTACCCTTTATATGTTTTGTGAGGG 57.052 36.000 3.64 3.64 46.37 4.30
2872 4057 9.734984 CCAAAAGGTCGATATTACCCTTTATAT 57.265 33.333 13.92 0.00 44.43 0.86
2873 4058 7.662669 GCCAAAAGGTCGATATTACCCTTTATA 59.337 37.037 13.92 0.00 44.43 0.98
2875 4060 5.824097 GCCAAAAGGTCGATATTACCCTTTA 59.176 40.000 13.92 0.00 44.43 1.85
2878 4063 3.201266 TGCCAAAAGGTCGATATTACCCT 59.799 43.478 4.91 0.00 37.77 4.34
2880 4065 5.570234 TTTGCCAAAAGGTCGATATTACC 57.430 39.130 0.00 0.89 37.27 2.85
2881 4066 5.907391 CGATTTGCCAAAAGGTCGATATTAC 59.093 40.000 5.91 0.00 32.15 1.89
2883 4068 4.398044 ACGATTTGCCAAAAGGTCGATATT 59.602 37.500 16.09 0.00 33.49 1.28
2885 4070 3.340034 ACGATTTGCCAAAAGGTCGATA 58.660 40.909 16.09 0.00 33.49 2.92
2887 4072 1.600023 ACGATTTGCCAAAAGGTCGA 58.400 45.000 16.09 0.00 33.49 4.20
2888 4073 3.486875 GGATACGATTTGCCAAAAGGTCG 60.487 47.826 9.44 9.44 35.11 4.79
2889 4074 3.442273 TGGATACGATTTGCCAAAAGGTC 59.558 43.478 0.00 0.00 42.51 3.85
2891 4076 3.443681 AGTGGATACGATTTGCCAAAAGG 59.556 43.478 0.00 0.00 42.51 3.11
2892 4077 4.701956 AGTGGATACGATTTGCCAAAAG 57.298 40.909 0.00 0.00 42.51 2.27
2893 4078 5.473846 TGTAAGTGGATACGATTTGCCAAAA 59.526 36.000 0.00 0.00 42.51 2.44
2894 4079 5.004448 TGTAAGTGGATACGATTTGCCAAA 58.996 37.500 0.00 0.00 42.51 3.28
2895 4080 4.580868 TGTAAGTGGATACGATTTGCCAA 58.419 39.130 0.00 0.00 42.51 4.52
2896 4081 4.209307 TGTAAGTGGATACGATTTGCCA 57.791 40.909 0.00 0.00 42.51 4.92
2898 4083 7.421530 ACATATGTAAGTGGATACGATTTGC 57.578 36.000 6.56 0.00 42.51 3.68
2904 4089 9.902196 TGTACAATACATATGTAAGTGGATACG 57.098 33.333 23.85 7.69 35.42 3.06
2918 4103 8.562052 ACTCGATTGACGTATGTACAATACATA 58.438 33.333 0.00 4.87 43.81 2.29
2919 4104 7.423199 ACTCGATTGACGTATGTACAATACAT 58.577 34.615 0.00 6.70 44.88 2.29
2921 4106 8.066595 ACTACTCGATTGACGTATGTACAATAC 58.933 37.037 0.00 2.74 43.13 1.89
2922 4107 8.146479 ACTACTCGATTGACGTATGTACAATA 57.854 34.615 0.00 0.00 43.13 1.90
2923 4108 7.024340 ACTACTCGATTGACGTATGTACAAT 57.976 36.000 0.00 10.59 43.13 2.71
2924 4109 6.426980 ACTACTCGATTGACGTATGTACAA 57.573 37.500 0.00 0.00 43.13 2.41
2925 4110 6.201615 CCTACTACTCGATTGACGTATGTACA 59.798 42.308 0.00 0.00 43.13 2.90
2926 4111 6.588552 CCTACTACTCGATTGACGTATGTAC 58.411 44.000 0.00 0.00 43.13 2.90
2927 4112 5.178252 GCCTACTACTCGATTGACGTATGTA 59.822 44.000 0.00 0.00 43.13 2.29
2928 4113 4.024218 GCCTACTACTCGATTGACGTATGT 60.024 45.833 0.00 0.00 43.13 2.29
2930 4115 4.387598 AGCCTACTACTCGATTGACGTAT 58.612 43.478 0.00 0.00 43.13 3.06
2931 4116 3.801698 AGCCTACTACTCGATTGACGTA 58.198 45.455 0.00 0.00 43.13 3.57
2933 4118 2.031857 GGAGCCTACTACTCGATTGACG 60.032 54.545 0.00 0.00 44.09 4.35
2934 4119 2.031857 CGGAGCCTACTACTCGATTGAC 60.032 54.545 0.00 0.00 34.87 3.18
2935 4120 2.219458 CGGAGCCTACTACTCGATTGA 58.781 52.381 0.00 0.00 34.87 2.57
2936 4121 1.948145 ACGGAGCCTACTACTCGATTG 59.052 52.381 0.00 0.00 34.87 2.67
2937 4122 2.220313 GACGGAGCCTACTACTCGATT 58.780 52.381 0.00 0.00 34.87 3.34
2941 4126 1.310904 CAGGACGGAGCCTACTACTC 58.689 60.000 0.00 0.00 36.22 2.59
2943 4128 1.108132 CCCAGGACGGAGCCTACTAC 61.108 65.000 0.00 0.00 36.22 2.73
2944 4129 1.229359 CCCAGGACGGAGCCTACTA 59.771 63.158 0.00 0.00 36.22 1.82
2945 4130 2.042843 CCCAGGACGGAGCCTACT 60.043 66.667 0.00 0.00 36.22 2.57
2946 4131 1.957765 GAACCCAGGACGGAGCCTAC 61.958 65.000 0.00 0.00 36.22 3.18
2947 4132 1.684734 GAACCCAGGACGGAGCCTA 60.685 63.158 0.00 0.00 36.22 3.93
2948 4133 3.003763 GAACCCAGGACGGAGCCT 61.004 66.667 0.00 0.00 39.37 4.58
2962 4147 2.231235 AGAAAATGTGAATGGGCCGAAC 59.769 45.455 0.00 0.00 0.00 3.95
2963 4148 2.524306 AGAAAATGTGAATGGGCCGAA 58.476 42.857 0.00 0.00 0.00 4.30
2964 4149 2.214376 AGAAAATGTGAATGGGCCGA 57.786 45.000 0.00 0.00 0.00 5.54
2965 4150 2.493278 AGAAGAAAATGTGAATGGGCCG 59.507 45.455 0.00 0.00 0.00 6.13
2967 4152 6.661669 CAAAAAGAAGAAAATGTGAATGGGC 58.338 36.000 0.00 0.00 0.00 5.36
2968 4153 6.293571 GGCAAAAAGAAGAAAATGTGAATGGG 60.294 38.462 0.00 0.00 0.00 4.00
2969 4154 6.293571 GGGCAAAAAGAAGAAAATGTGAATGG 60.294 38.462 0.00 0.00 0.00 3.16
2970 4155 6.260493 TGGGCAAAAAGAAGAAAATGTGAATG 59.740 34.615 0.00 0.00 0.00 2.67
2972 4157 5.738909 TGGGCAAAAAGAAGAAAATGTGAA 58.261 33.333 0.00 0.00 0.00 3.18
2973 4158 5.350504 TGGGCAAAAAGAAGAAAATGTGA 57.649 34.783 0.00 0.00 0.00 3.58
2974 4159 6.622833 AATGGGCAAAAAGAAGAAAATGTG 57.377 33.333 0.00 0.00 0.00 3.21
2975 4160 6.459985 GCAAATGGGCAAAAAGAAGAAAATGT 60.460 34.615 0.00 0.00 0.00 2.71
2976 4161 5.916320 GCAAATGGGCAAAAAGAAGAAAATG 59.084 36.000 0.00 0.00 0.00 2.32
2977 4162 5.593502 TGCAAATGGGCAAAAAGAAGAAAAT 59.406 32.000 0.00 0.00 41.65 1.82
3012 4502 4.817464 TGCAGTACTTTTCGAGGCTAAAAA 59.183 37.500 0.00 6.98 0.00 1.94
3017 4507 1.608283 GGTGCAGTACTTTTCGAGGCT 60.608 52.381 0.00 0.00 0.00 4.58
3018 4508 0.796927 GGTGCAGTACTTTTCGAGGC 59.203 55.000 0.00 0.00 0.00 4.70
3019 4509 2.163818 TGGTGCAGTACTTTTCGAGG 57.836 50.000 0.00 0.00 0.00 4.63
3020 4510 4.466828 CAAATGGTGCAGTACTTTTCGAG 58.533 43.478 0.00 0.00 0.00 4.04
3022 4512 3.564511 CCAAATGGTGCAGTACTTTTCG 58.435 45.455 0.00 0.00 0.00 3.46
3023 4513 3.572255 TCCCAAATGGTGCAGTACTTTTC 59.428 43.478 0.00 0.00 34.77 2.29
3024 4514 3.571590 TCCCAAATGGTGCAGTACTTTT 58.428 40.909 0.00 0.00 34.77 2.27
3025 4515 3.237268 TCCCAAATGGTGCAGTACTTT 57.763 42.857 0.00 0.00 34.77 2.66
3026 4516 2.969821 TCCCAAATGGTGCAGTACTT 57.030 45.000 0.00 0.00 34.77 2.24
3028 4518 3.088532 TGAATCCCAAATGGTGCAGTAC 58.911 45.455 0.00 0.00 34.77 2.73
3029 4519 3.448093 TGAATCCCAAATGGTGCAGTA 57.552 42.857 0.00 0.00 34.77 2.74
3030 4520 2.307496 TGAATCCCAAATGGTGCAGT 57.693 45.000 0.00 0.00 34.77 4.40
3031 4521 3.244146 TGTTTGAATCCCAAATGGTGCAG 60.244 43.478 0.00 0.00 45.48 4.41
3033 4523 3.399440 TGTTTGAATCCCAAATGGTGC 57.601 42.857 0.00 0.00 45.48 5.01
3034 4524 4.897140 ACATGTTTGAATCCCAAATGGTG 58.103 39.130 0.00 0.00 45.48 4.17


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

AutoCloner maintained by Alex Coulton.