Multiple sequence alignment - TraesCS4D01G217600

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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 TraesCS4D01G217600 chr4D 100.000 2989 0 0 1 2989 372978681 372975693 0.000000e+00 5520.0
1 TraesCS4D01G217600 chr4D 100.000 177 0 0 3306 3482 372975376 372975200 9.320000e-86 327.0
2 TraesCS4D01G217600 chr4D 88.439 173 20 0 3306 3478 391712552 391712724 3.520000e-50 209.0
3 TraesCS4D01G217600 chr4D 87.931 174 19 2 3306 3478 474915569 474915397 1.640000e-48 204.0
4 TraesCS4D01G217600 chr4D 96.610 59 1 1 2725 2783 337522473 337522416 2.860000e-16 97.1
5 TraesCS4D01G217600 chr4D 95.238 42 2 0 657 698 504090795 504090754 2.240000e-07 67.6
6 TraesCS4D01G217600 chr4B 88.048 2167 132 55 624 2724 458126704 458124599 0.000000e+00 2449.0
7 TraesCS4D01G217600 chr4B 94.157 599 27 4 1 595 458127299 458126705 0.000000e+00 905.0
8 TraesCS4D01G217600 chr4B 89.615 260 17 5 2723 2978 464535556 464535809 4.340000e-84 322.0
9 TraesCS4D01G217600 chr4B 97.561 41 1 0 658 698 806779 806739 1.730000e-08 71.3
10 TraesCS4D01G217600 chr4A 88.487 1381 70 55 1350 2697 91619177 91620501 0.000000e+00 1587.0
11 TraesCS4D01G217600 chr4A 89.266 708 50 15 624 1313 91618484 91619183 0.000000e+00 863.0
12 TraesCS4D01G217600 chr4A 92.013 601 34 5 1 595 91617892 91618484 0.000000e+00 832.0
13 TraesCS4D01G217600 chr4A 89.888 178 16 2 3306 3482 587157474 587157298 9.720000e-56 228.0
14 TraesCS4D01G217600 chr6D 93.810 210 10 2 2781 2989 438812753 438812546 2.610000e-81 313.0
15 TraesCS4D01G217600 chr6D 86.989 269 25 9 2726 2989 81391616 81391879 9.450000e-76 294.0
16 TraesCS4D01G217600 chr6D 89.593 221 11 10 2775 2989 97586814 97586600 1.590000e-68 270.0
17 TraesCS4D01G217600 chr6D 90.751 173 15 1 3306 3478 438812256 438812085 2.700000e-56 230.0
18 TraesCS4D01G217600 chr6D 97.561 41 1 0 657 697 16236747 16236707 1.730000e-08 71.3
19 TraesCS4D01G217600 chr6D 95.122 41 2 0 658 698 39676415 39676455 8.070000e-07 65.8
20 TraesCS4D01G217600 chr6D 92.857 42 3 0 656 697 110874372 110874331 1.040000e-05 62.1
21 TraesCS4D01G217600 chr6D 94.872 39 2 0 658 696 325727795 325727757 1.040000e-05 62.1
22 TraesCS4D01G217600 chr3D 94.949 198 6 3 2775 2970 278066765 278066960 1.210000e-79 307.0
23 TraesCS4D01G217600 chr3D 93.333 210 11 2 2781 2989 455599461 455599668 1.210000e-79 307.0
24 TraesCS4D01G217600 chr3D 91.329 173 14 1 3306 3478 455599796 455599967 5.810000e-58 235.0
25 TraesCS4D01G217600 chr3D 88.235 170 20 0 3306 3475 483187886 483188055 1.640000e-48 204.0
26 TraesCS4D01G217600 chr3D 88.189 127 12 2 2781 2906 368851448 368851572 7.790000e-32 148.0
27 TraesCS4D01G217600 chr3D 98.148 54 1 0 2725 2778 455599380 455599433 1.030000e-15 95.3
28 TraesCS4D01G217600 chr3D 96.429 56 2 0 2727 2782 25700424 25700369 3.700000e-15 93.5
29 TraesCS4D01G217600 chr7D 94.792 192 7 2 2781 2971 461925305 461925116 2.630000e-76 296.0
30 TraesCS4D01G217600 chr7D 91.083 157 12 2 3324 3480 627411832 627411678 9.790000e-51 211.0
31 TraesCS4D01G217600 chr7D 100.000 41 0 0 658 698 595026561 595026521 3.730000e-10 76.8
32 TraesCS4D01G217600 chr7B 90.323 217 17 3 2775 2989 473692113 473692327 7.360000e-72 281.0
33 TraesCS4D01G217600 chr7B 85.075 268 30 9 2725 2989 572392215 572392475 7.410000e-67 265.0
34 TraesCS4D01G217600 chr5D 89.017 173 18 1 3306 3478 103995775 103995604 2.720000e-51 213.0
35 TraesCS4D01G217600 chr5D 88.824 170 19 0 3306 3475 162498910 162499079 3.520000e-50 209.0
36 TraesCS4D01G217600 chr5D 96.429 56 2 0 2725 2780 52126535 52126590 3.700000e-15 93.5
37 TraesCS4D01G217600 chr5D 95.238 42 2 0 657 698 119763075 119763116 2.240000e-07 67.6
38 TraesCS4D01G217600 chr5D 95.238 42 2 0 657 698 122198430 122198471 2.240000e-07 67.6
39 TraesCS4D01G217600 chr5D 95.122 41 2 0 657 697 122198515 122198475 8.070000e-07 65.8
40 TraesCS4D01G217600 chr7A 82.126 207 30 6 2786 2989 199431992 199431790 1.660000e-38 171.0
41 TraesCS4D01G217600 chr7A 95.652 46 1 1 653 698 136344762 136344718 4.820000e-09 73.1
42 TraesCS4D01G217600 chr6A 100.000 41 0 0 657 697 16471529 16471489 3.730000e-10 76.8
43 TraesCS4D01G217600 chr6A 95.238 42 2 0 656 697 135230187 135230146 2.240000e-07 67.6
44 TraesCS4D01G217600 chr5B 97.561 41 1 0 657 697 134917767 134917807 1.730000e-08 71.3
45 TraesCS4D01G217600 chr1B 100.000 37 0 0 661 697 37577522 37577486 6.240000e-08 69.4
46 TraesCS4D01G217600 chr5A 95.238 42 2 0 657 698 688764046 688764005 2.240000e-07 67.6
47 TraesCS4D01G217600 chr5A 89.796 49 5 0 658 706 626510419 626510371 2.900000e-06 63.9
48 TraesCS4D01G217600 chr1D 100.000 36 0 0 663 698 471863320 471863355 2.240000e-07 67.6
49 TraesCS4D01G217600 chr1D 95.000 40 2 0 658 697 3978478 3978517 2.900000e-06 63.9
50 TraesCS4D01G217600 chr1D 91.111 45 3 1 654 698 78965912 78965869 3.750000e-05 60.2
51 TraesCS4D01G217600 chr1D 92.683 41 3 0 658 698 365743741 365743701 3.750000e-05 60.2
52 TraesCS4D01G217600 chrUn 97.297 37 1 0 658 694 479897952 479897988 2.900000e-06 63.9
53 TraesCS4D01G217600 chr1A 95.000 40 2 0 658 697 96488592 96488553 2.900000e-06 63.9


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 TraesCS4D01G217600 chr4D 372975200 372978681 3481 True 2923.500000 5520 100.0000 1 3482 2 chr4D.!!$R4 3481
1 TraesCS4D01G217600 chr4B 458124599 458127299 2700 True 1677.000000 2449 91.1025 1 2724 2 chr4B.!!$R2 2723
2 TraesCS4D01G217600 chr4A 91617892 91620501 2609 False 1094.000000 1587 89.9220 1 2697 3 chr4A.!!$F1 2696
3 TraesCS4D01G217600 chr6D 438812085 438812753 668 True 271.500000 313 92.2805 2781 3478 2 chr6D.!!$R5 697
4 TraesCS4D01G217600 chr3D 455599380 455599967 587 False 212.433333 307 94.2700 2725 3478 3 chr3D.!!$F4 753

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
599 609 0.178876 TGGAGTGAGGTGGGGATGAA 60.179 55.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2570 2668 0.108585 ACAAGTACACAGTGCCCAGG 59.891 55.0 0.0 0.0 0.0 4.45 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
28 29 1.705337 CGGTTGCATGGGCGTTCTAG 61.705 60.000 0.00 0.00 45.35 2.43
33 34 0.179468 GCATGGGCGTTCTAGGGTTA 59.821 55.000 0.00 0.00 0.00 2.85
86 90 4.635223 TCAACCAGACTCAGTTTGATCTG 58.365 43.478 0.00 0.00 34.64 2.90
188 193 1.334329 CGTTTGTTTGGTACGCCCTTC 60.334 52.381 0.00 0.00 0.00 3.46
199 204 3.128068 GGTACGCCCTTCCACAATAAAAG 59.872 47.826 0.00 0.00 0.00 2.27
262 271 4.704057 TCATGTTAACACTGCATGCCAATA 59.296 37.500 16.68 0.00 39.64 1.90
263 272 5.184671 TCATGTTAACACTGCATGCCAATAA 59.815 36.000 16.68 4.94 39.64 1.40
278 287 3.491104 GCCAATAAGACGTAGGTCAGAGG 60.491 52.174 17.27 11.72 45.92 3.69
279 288 3.491104 CCAATAAGACGTAGGTCAGAGGC 60.491 52.174 17.27 0.00 45.92 4.70
280 289 1.760192 TAAGACGTAGGTCAGAGGCC 58.240 55.000 17.27 0.00 45.92 5.19
281 290 0.251653 AAGACGTAGGTCAGAGGCCA 60.252 55.000 17.27 0.00 45.92 5.36
282 291 0.966370 AGACGTAGGTCAGAGGCCAC 60.966 60.000 17.27 0.00 45.92 5.01
283 292 1.228769 ACGTAGGTCAGAGGCCACA 60.229 57.895 5.01 0.00 0.00 4.17
312 321 4.410400 CCCACTTGTCCTCCGGCC 62.410 72.222 0.00 0.00 0.00 6.13
381 390 7.467623 GTCCTTTGTCAAGACTGCAATAATAG 58.532 38.462 1.53 0.00 30.57 1.73
531 541 5.180680 ACCGAAGTTATAACCTTGAAACTGC 59.819 40.000 12.05 0.00 32.69 4.40
535 545 4.154195 AGTTATAACCTTGAAACTGCGCAG 59.846 41.667 34.89 34.89 31.20 5.18
572 582 3.846360 ACTGCAATGACTAGTTCGTACC 58.154 45.455 0.00 0.00 0.00 3.34
595 605 0.475632 AATGTGGAGTGAGGTGGGGA 60.476 55.000 0.00 0.00 0.00 4.81
596 606 0.253347 ATGTGGAGTGAGGTGGGGAT 60.253 55.000 0.00 0.00 0.00 3.85
597 607 1.200760 TGTGGAGTGAGGTGGGGATG 61.201 60.000 0.00 0.00 0.00 3.51
598 608 0.909610 GTGGAGTGAGGTGGGGATGA 60.910 60.000 0.00 0.00 0.00 2.92
599 609 0.178876 TGGAGTGAGGTGGGGATGAA 60.179 55.000 0.00 0.00 0.00 2.57
600 610 1.216990 GGAGTGAGGTGGGGATGAAT 58.783 55.000 0.00 0.00 0.00 2.57
601 611 2.293519 TGGAGTGAGGTGGGGATGAATA 60.294 50.000 0.00 0.00 0.00 1.75
602 612 2.104963 GGAGTGAGGTGGGGATGAATAC 59.895 54.545 0.00 0.00 0.00 1.89
603 613 2.771943 GAGTGAGGTGGGGATGAATACA 59.228 50.000 0.00 0.00 0.00 2.29
604 614 2.774234 AGTGAGGTGGGGATGAATACAG 59.226 50.000 0.00 0.00 0.00 2.74
605 615 2.505819 GTGAGGTGGGGATGAATACAGT 59.494 50.000 0.00 0.00 0.00 3.55
606 616 3.054361 GTGAGGTGGGGATGAATACAGTT 60.054 47.826 0.00 0.00 0.00 3.16
607 617 3.054434 TGAGGTGGGGATGAATACAGTTG 60.054 47.826 0.00 0.00 0.00 3.16
608 618 3.189606 AGGTGGGGATGAATACAGTTGA 58.810 45.455 0.00 0.00 0.00 3.18
609 619 3.591527 AGGTGGGGATGAATACAGTTGAA 59.408 43.478 0.00 0.00 0.00 2.69
610 620 4.230502 AGGTGGGGATGAATACAGTTGAAT 59.769 41.667 0.00 0.00 0.00 2.57
611 621 4.956075 GGTGGGGATGAATACAGTTGAATT 59.044 41.667 0.00 0.00 0.00 2.17
612 622 5.422012 GGTGGGGATGAATACAGTTGAATTT 59.578 40.000 0.00 0.00 0.00 1.82
613 623 6.070824 GGTGGGGATGAATACAGTTGAATTTT 60.071 38.462 0.00 0.00 0.00 1.82
614 624 7.123547 GGTGGGGATGAATACAGTTGAATTTTA 59.876 37.037 0.00 0.00 0.00 1.52
615 625 8.190784 GTGGGGATGAATACAGTTGAATTTTAG 58.809 37.037 0.00 0.00 0.00 1.85
616 626 7.893302 TGGGGATGAATACAGTTGAATTTTAGT 59.107 33.333 0.00 0.00 0.00 2.24
617 627 8.406297 GGGGATGAATACAGTTGAATTTTAGTC 58.594 37.037 0.00 0.00 0.00 2.59
618 628 8.406297 GGGATGAATACAGTTGAATTTTAGTCC 58.594 37.037 0.00 0.00 0.00 3.85
619 629 8.956426 GGATGAATACAGTTGAATTTTAGTCCA 58.044 33.333 0.00 0.00 0.00 4.02
646 656 1.330829 GACAACTTAGCAATAGCCGGC 59.669 52.381 21.89 21.89 43.56 6.13
661 671 1.962100 GCCGGCCTCTAGTACATACTT 59.038 52.381 18.11 0.00 37.73 2.24
663 673 2.557490 CCGGCCTCTAGTACATACTTCC 59.443 54.545 0.00 0.00 37.73 3.46
667 677 4.471548 GCCTCTAGTACATACTTCCTCCA 58.528 47.826 0.00 0.00 37.73 3.86
702 712 1.154225 CGTTTTGCAAGCTAGGGCG 60.154 57.895 0.00 0.00 44.37 6.13
714 724 1.138464 GCTAGGGCGGCTAAAGTTAGT 59.862 52.381 9.56 0.00 33.32 2.24
746 756 2.950309 GTCAGGATAAGAGCGACCACTA 59.050 50.000 0.00 0.00 0.00 2.74
748 758 2.034812 CAGGATAAGAGCGACCACTACC 59.965 54.545 0.00 0.00 0.00 3.18
777 787 1.340697 GGGGACAGGAAACGGCTAATT 60.341 52.381 0.00 0.00 0.00 1.40
896 907 5.216622 ACCCCAGAGCTCATATAAGTAACA 58.783 41.667 17.77 0.00 0.00 2.41
934 945 7.197703 TGCGAAAATAGATCACGTATACTTCA 58.802 34.615 0.56 0.00 0.00 3.02
937 948 8.682895 CGAAAATAGATCACGTATACTTCACAG 58.317 37.037 0.56 0.00 0.00 3.66
947 972 0.320421 TACTTCACAGCCCACTTCGC 60.320 55.000 0.00 0.00 0.00 4.70
948 973 1.302033 CTTCACAGCCCACTTCGCT 60.302 57.895 0.00 0.00 36.91 4.93
956 981 2.048222 CCACTTCGCTCCTCGCAA 60.048 61.111 0.00 0.00 39.08 4.85
962 987 0.884704 TTCGCTCCTCGCAAAAGCTT 60.885 50.000 0.00 0.00 39.08 3.74
967 992 1.731160 CTCCTCGCAAAAGCTTCTCTG 59.269 52.381 0.00 0.00 0.00 3.35
970 995 1.869767 CTCGCAAAAGCTTCTCTGTGT 59.130 47.619 0.00 0.00 0.00 3.72
1010 1035 1.094073 ACAGCAGCAATGAGATCGGC 61.094 55.000 0.00 0.00 0.00 5.54
1137 1166 2.557059 TACGTGCATGGGAGAGCGTG 62.557 60.000 11.36 0.00 34.38 5.34
1165 1194 7.680062 GCTTACTAGCAAATCGATATGGATTC 58.320 38.462 12.69 2.89 46.95 2.52
1166 1195 7.463383 GCTTACTAGCAAATCGATATGGATTCG 60.463 40.741 12.69 3.94 46.95 3.34
1168 1197 6.223852 ACTAGCAAATCGATATGGATTCGTT 58.776 36.000 12.69 3.59 35.65 3.85
1169 1198 6.706270 ACTAGCAAATCGATATGGATTCGTTT 59.294 34.615 12.69 3.62 35.65 3.60
1170 1199 5.751680 AGCAAATCGATATGGATTCGTTTG 58.248 37.500 12.69 9.50 38.76 2.93
1173 1202 6.472163 GCAAATCGATATGGATTCGTTTGTTT 59.528 34.615 12.69 0.00 38.43 2.83
1174 1203 7.513505 GCAAATCGATATGGATTCGTTTGTTTG 60.514 37.037 12.69 7.39 38.43 2.93
1175 1204 4.904116 TCGATATGGATTCGTTTGTTTGC 58.096 39.130 0.00 0.00 37.82 3.68
1176 1205 3.718864 CGATATGGATTCGTTTGTTTGCG 59.281 43.478 0.00 0.00 32.08 4.85
1183 1212 0.303493 TCGTTTGTTTGCGAGTGCTC 59.697 50.000 0.00 0.00 43.34 4.26
1184 1213 0.304705 CGTTTGTTTGCGAGTGCTCT 59.695 50.000 0.00 0.00 43.34 4.09
1204 1233 1.926561 TGGAGCTGATCGATTTCGTG 58.073 50.000 0.00 0.00 40.80 4.35
1209 1238 2.007049 GCTGATCGATTTCGTGGTGGT 61.007 52.381 0.00 0.00 40.80 4.16
1218 1247 1.978455 TTCGTGGTGGTCTTGCAGGT 61.978 55.000 0.00 0.00 0.00 4.00
1260 1289 1.317613 TGCGAGTCCAAGTTTTGCAT 58.682 45.000 0.00 0.00 0.00 3.96
1314 1363 2.636768 GCAATCTTGCGGTTTTAGCT 57.363 45.000 0.00 0.00 45.11 3.32
1315 1364 2.519963 GCAATCTTGCGGTTTTAGCTC 58.480 47.619 0.00 0.00 45.11 4.09
1316 1365 2.162408 GCAATCTTGCGGTTTTAGCTCT 59.838 45.455 0.00 0.00 45.11 4.09
1319 1368 3.402628 TCTTGCGGTTTTAGCTCTCTT 57.597 42.857 0.00 0.00 35.28 2.85
1320 1369 3.740115 TCTTGCGGTTTTAGCTCTCTTT 58.260 40.909 0.00 0.00 35.28 2.52
1321 1370 3.746492 TCTTGCGGTTTTAGCTCTCTTTC 59.254 43.478 0.00 0.00 35.28 2.62
1322 1371 3.402628 TGCGGTTTTAGCTCTCTTTCT 57.597 42.857 0.00 0.00 35.28 2.52
1323 1372 3.326747 TGCGGTTTTAGCTCTCTTTCTC 58.673 45.455 0.00 0.00 35.28 2.87
1324 1373 3.006967 TGCGGTTTTAGCTCTCTTTCTCT 59.993 43.478 0.00 0.00 35.28 3.10
1325 1374 3.615056 GCGGTTTTAGCTCTCTTTCTCTC 59.385 47.826 0.00 0.00 0.00 3.20
1326 1375 4.177783 CGGTTTTAGCTCTCTTTCTCTCC 58.822 47.826 0.00 0.00 0.00 3.71
1327 1376 4.509616 GGTTTTAGCTCTCTTTCTCTCCC 58.490 47.826 0.00 0.00 0.00 4.30
1328 1377 4.177783 GTTTTAGCTCTCTTTCTCTCCCG 58.822 47.826 0.00 0.00 0.00 5.14
1330 1379 0.324275 AGCTCTCTTTCTCTCCCGCT 60.324 55.000 0.00 0.00 0.00 5.52
1331 1380 0.179113 GCTCTCTTTCTCTCCCGCTG 60.179 60.000 0.00 0.00 0.00 5.18
1333 1382 0.251832 TCTCTTTCTCTCCCGCTGGT 60.252 55.000 0.00 0.00 0.00 4.00
1334 1383 0.174617 CTCTTTCTCTCCCGCTGGTC 59.825 60.000 0.00 0.00 0.00 4.02
1335 1384 1.153745 CTTTCTCTCCCGCTGGTCG 60.154 63.158 0.00 0.00 38.08 4.79
1337 1386 0.970937 TTTCTCTCCCGCTGGTCGAT 60.971 55.000 0.00 0.00 41.67 3.59
1338 1387 1.667154 TTCTCTCCCGCTGGTCGATG 61.667 60.000 0.00 0.00 41.67 3.84
1339 1388 3.781770 CTCTCCCGCTGGTCGATGC 62.782 68.421 0.00 0.00 41.67 3.91
1340 1389 4.147449 CTCCCGCTGGTCGATGCA 62.147 66.667 0.00 0.00 41.67 3.96
1341 1390 3.451556 CTCCCGCTGGTCGATGCAT 62.452 63.158 0.00 0.00 41.67 3.96
1342 1391 3.274586 CCCGCTGGTCGATGCATG 61.275 66.667 2.46 0.00 41.67 4.06
1343 1392 3.945434 CCGCTGGTCGATGCATGC 61.945 66.667 11.82 11.82 41.67 4.06
1344 1393 3.197092 CGCTGGTCGATGCATGCA 61.197 61.111 25.04 25.04 41.67 3.96
1345 1394 2.713770 GCTGGTCGATGCATGCAG 59.286 61.111 26.69 13.62 0.00 4.41
1346 1395 2.110967 GCTGGTCGATGCATGCAGT 61.111 57.895 26.69 14.02 0.00 4.40
1426 1475 7.763172 AGTTAGATTGTTAGATTGAGCTTCG 57.237 36.000 0.00 0.00 0.00 3.79
1428 1477 7.819900 AGTTAGATTGTTAGATTGAGCTTCGTT 59.180 33.333 0.00 0.00 0.00 3.85
1430 1479 7.066374 AGATTGTTAGATTGAGCTTCGTTTC 57.934 36.000 0.00 0.00 0.00 2.78
1431 1480 6.650807 AGATTGTTAGATTGAGCTTCGTTTCA 59.349 34.615 0.00 0.00 0.00 2.69
1432 1481 5.845985 TGTTAGATTGAGCTTCGTTTCAG 57.154 39.130 0.00 0.00 0.00 3.02
1433 1482 5.297547 TGTTAGATTGAGCTTCGTTTCAGT 58.702 37.500 0.00 0.00 0.00 3.41
1435 1484 4.739046 AGATTGAGCTTCGTTTCAGTTG 57.261 40.909 0.00 0.00 0.00 3.16
1436 1485 4.380531 AGATTGAGCTTCGTTTCAGTTGA 58.619 39.130 0.00 0.00 0.00 3.18
1437 1486 4.816385 AGATTGAGCTTCGTTTCAGTTGAA 59.184 37.500 0.00 0.00 0.00 2.69
1439 1488 6.650807 AGATTGAGCTTCGTTTCAGTTGAATA 59.349 34.615 0.00 0.00 33.54 1.75
1440 1489 6.612247 TTGAGCTTCGTTTCAGTTGAATAA 57.388 33.333 0.00 0.00 33.54 1.40
1443 1492 5.942872 AGCTTCGTTTCAGTTGAATAATGG 58.057 37.500 0.00 0.00 33.54 3.16
1444 1493 4.558860 GCTTCGTTTCAGTTGAATAATGGC 59.441 41.667 0.00 0.00 33.54 4.40
1445 1494 4.695217 TCGTTTCAGTTGAATAATGGCC 57.305 40.909 0.00 0.00 33.54 5.36
1446 1495 4.331968 TCGTTTCAGTTGAATAATGGCCT 58.668 39.130 3.32 0.00 33.54 5.19
1448 1497 4.675146 CGTTTCAGTTGAATAATGGCCTGG 60.675 45.833 3.32 0.00 33.54 4.45
1449 1498 4.314522 TTCAGTTGAATAATGGCCTGGA 57.685 40.909 3.32 0.00 0.00 3.86
1450 1499 3.620488 TCAGTTGAATAATGGCCTGGAC 58.380 45.455 3.32 0.00 0.00 4.02
1451 1500 3.266772 TCAGTTGAATAATGGCCTGGACT 59.733 43.478 3.32 0.00 0.00 3.85
1452 1501 3.379372 CAGTTGAATAATGGCCTGGACTG 59.621 47.826 3.32 3.47 0.00 3.51
1453 1502 3.266772 AGTTGAATAATGGCCTGGACTGA 59.733 43.478 3.32 0.00 0.00 3.41
1454 1503 4.016444 GTTGAATAATGGCCTGGACTGAA 58.984 43.478 3.32 0.00 0.00 3.02
1464 1537 2.630580 GCCTGGACTGAAGTAGATAGGG 59.369 54.545 0.00 0.00 0.00 3.53
1531 1604 1.779569 AGTAACTGACGCTCGTTTGG 58.220 50.000 0.00 0.00 0.00 3.28
1757 1838 8.407064 TCTTCTATCTATCTGAACCGAAAAGAC 58.593 37.037 0.00 0.00 0.00 3.01
1778 1859 1.226746 GGACAGGAGGAAAACACGTG 58.773 55.000 15.48 15.48 0.00 4.49
1781 1862 0.878523 CAGGAGGAAAACACGTGCGA 60.879 55.000 17.22 0.00 0.00 5.10
1801 1882 4.367450 CGATTTCCCTTTTGTTTGCTTCA 58.633 39.130 0.00 0.00 0.00 3.02
1808 1889 4.025813 CCCTTTTGTTTGCTTCATTTGACG 60.026 41.667 0.00 0.00 0.00 4.35
1810 1891 5.063312 CCTTTTGTTTGCTTCATTTGACGTT 59.937 36.000 0.00 0.00 0.00 3.99
1833 1914 1.908299 CCAAAAGGCCCCACAGACC 60.908 63.158 0.00 0.00 0.00 3.85
1883 1964 0.525668 CGAGATGACACGCCACCTAC 60.526 60.000 0.00 0.00 0.00 3.18
1968 2049 2.764737 ATGGGCAGATGGCTCCCTG 61.765 63.158 6.34 0.00 44.86 4.45
2030 2111 2.946762 GCACACGCTCCTCCAAAC 59.053 61.111 0.00 0.00 34.30 2.93
2034 2115 1.166531 ACACGCTCCTCCAAACAAGC 61.167 55.000 0.00 0.00 0.00 4.01
2129 2214 3.292936 AACGTCGTCCTGTCGCCT 61.293 61.111 0.00 0.00 32.10 5.52
2136 2221 0.673644 CGTCCTGTCGCCTCCATTTT 60.674 55.000 0.00 0.00 0.00 1.82
2137 2222 1.087501 GTCCTGTCGCCTCCATTTTC 58.912 55.000 0.00 0.00 0.00 2.29
2208 2293 0.185901 TTGCAGGGAAGAAAGCACCT 59.814 50.000 0.00 0.00 36.62 4.00
2221 2306 2.338620 CACCTCCGTCGCACTCAA 59.661 61.111 0.00 0.00 0.00 3.02
2389 2486 2.758207 TTCCCGGGGAACAAGTGCA 61.758 57.895 24.64 0.00 36.71 4.57
2537 2635 2.032924 GGAAATAATGTGGTAGGCGTGC 59.967 50.000 0.00 0.00 0.00 5.34
2560 2658 4.326766 CGTGGTGGTGCGGCAAAG 62.327 66.667 3.23 0.00 0.00 2.77
2561 2659 4.645921 GTGGTGGTGCGGCAAAGC 62.646 66.667 3.23 6.71 37.71 3.51
2571 2669 2.946762 GGCAAAGCCGCGATATCC 59.053 61.111 8.23 0.00 39.62 2.59
2572 2670 1.598130 GGCAAAGCCGCGATATCCT 60.598 57.895 8.23 0.00 39.62 3.24
2573 2671 1.571460 GCAAAGCCGCGATATCCTG 59.429 57.895 8.23 0.00 0.00 3.86
2574 2672 1.845809 GCAAAGCCGCGATATCCTGG 61.846 60.000 8.23 0.22 0.00 4.45
2575 2673 1.071471 AAAGCCGCGATATCCTGGG 59.929 57.895 8.23 4.06 0.00 4.45
2576 2674 3.537206 AAGCCGCGATATCCTGGGC 62.537 63.158 8.23 15.14 44.07 5.36
2577 2675 4.314440 GCCGCGATATCCTGGGCA 62.314 66.667 8.23 0.00 43.23 5.36
2578 2676 2.357517 CCGCGATATCCTGGGCAC 60.358 66.667 8.23 0.00 0.00 5.01
2579 2677 2.737180 CGCGATATCCTGGGCACT 59.263 61.111 0.00 0.00 0.00 4.40
2580 2678 1.665916 CGCGATATCCTGGGCACTG 60.666 63.158 0.00 0.00 0.00 3.66
2584 2682 1.686587 CGATATCCTGGGCACTGTGTA 59.313 52.381 9.86 0.00 0.00 2.90
2588 2686 0.396435 TCCTGGGCACTGTGTACTTG 59.604 55.000 9.86 0.00 0.00 3.16
2589 2687 0.108585 CCTGGGCACTGTGTACTTGT 59.891 55.000 9.86 0.00 0.00 3.16
2612 2710 3.713826 CCAGTTTGGTGGTATAGTGGT 57.286 47.619 0.00 0.00 31.35 4.16
2613 2711 4.829872 CCAGTTTGGTGGTATAGTGGTA 57.170 45.455 0.00 0.00 31.35 3.25
2636 2735 1.003545 CGGCATATTGCTGTACTGCAC 60.004 52.381 24.99 13.93 44.43 4.57
2639 2738 2.223340 GCATATTGCTGTACTGCACACC 60.223 50.000 24.99 9.80 43.20 4.16
2701 2801 3.926616 AGTCAAAGGACATACTGGAACG 58.073 45.455 0.00 0.00 46.80 3.95
2745 2845 9.925268 GACATGGCAAATTTGATAATTTTGATC 57.075 29.630 22.31 0.00 40.97 2.92
2849 2974 0.100682 CACAGATAGGCGCTACACGT 59.899 55.000 7.64 0.00 46.11 4.49
2857 2982 2.809601 CGCTACACGTCTGGCCAC 60.810 66.667 0.00 0.00 36.87 5.01
2858 2983 2.342279 GCTACACGTCTGGCCACA 59.658 61.111 0.00 0.00 0.00 4.17
2859 2984 1.301401 GCTACACGTCTGGCCACAA 60.301 57.895 0.00 0.00 0.00 3.33
2871 2996 4.920112 CCACAACGTCGCACCCCA 62.920 66.667 0.00 0.00 0.00 4.96
2913 3039 0.036010 AATGTGCAGCGCCTAAGAGT 60.036 50.000 2.29 0.00 0.00 3.24
3334 3460 3.499929 ATACGGATGCGACGCTGGG 62.500 63.158 22.08 10.00 34.00 4.45
3388 3514 1.004918 GTGTAGTGTGGCGCCTTCT 60.005 57.895 29.70 23.05 0.00 2.85
3403 3529 3.469863 TTCTTGTCGGGCGCCACTT 62.470 57.895 30.85 0.00 0.00 3.16
3409 3535 0.109919 GTCGGGCGCCACTTAAAAAG 60.110 55.000 30.85 7.24 0.00 2.27
3442 3568 7.093945 TGGGTGAAATATTTTTAGAGGCAGTTC 60.094 37.037 1.43 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 3.056821 GCAAAGAAATGACCTGGTAACCC 60.057 47.826 0.00 0.00 0.00 4.11
33 34 3.565307 TGAAGCAAAGAAATGACCTGGT 58.435 40.909 0.00 0.00 0.00 4.00
128 132 1.259142 CCACCTGCATGCATGGGAAA 61.259 55.000 27.64 2.28 0.00 3.13
262 271 0.251653 TGGCCTCTGACCTACGTCTT 60.252 55.000 3.32 0.00 39.94 3.01
263 272 0.966370 GTGGCCTCTGACCTACGTCT 60.966 60.000 3.32 0.00 39.94 4.18
278 287 0.809636 GGGTGCAGTTTTGTTGTGGC 60.810 55.000 0.00 0.00 0.00 5.01
279 288 0.534412 TGGGTGCAGTTTTGTTGTGG 59.466 50.000 0.00 0.00 0.00 4.17
280 289 1.204467 AGTGGGTGCAGTTTTGTTGTG 59.796 47.619 0.00 0.00 0.00 3.33
281 290 1.555967 AGTGGGTGCAGTTTTGTTGT 58.444 45.000 0.00 0.00 0.00 3.32
282 291 2.270047 CAAGTGGGTGCAGTTTTGTTG 58.730 47.619 0.00 0.00 0.00 3.33
283 292 1.899142 ACAAGTGGGTGCAGTTTTGTT 59.101 42.857 0.00 0.00 0.00 2.83
381 390 3.407424 TCACAGGGAGCATGCATATAC 57.593 47.619 21.98 0.00 0.00 1.47
531 541 7.594824 GCAGTAATGTTATGATAAAACTGCG 57.405 36.000 18.69 0.00 46.08 5.18
541 551 9.098355 GAACTAGTCATTGCAGTAATGTTATGA 57.902 33.333 10.66 5.60 45.17 2.15
572 582 3.282021 CCCACCTCACTCCACATTTATG 58.718 50.000 0.00 0.00 0.00 1.90
601 611 9.403583 TCTACTTTTGGACTAAAATTCAACTGT 57.596 29.630 0.00 0.00 37.61 3.55
602 612 9.665264 GTCTACTTTTGGACTAAAATTCAACTG 57.335 33.333 0.00 0.00 37.61 3.16
603 613 9.403583 TGTCTACTTTTGGACTAAAATTCAACT 57.596 29.630 0.00 0.00 37.61 3.16
606 616 9.403583 AGTTGTCTACTTTTGGACTAAAATTCA 57.596 29.630 0.00 0.00 37.61 2.57
610 620 8.833493 GCTAAGTTGTCTACTTTTGGACTAAAA 58.167 33.333 4.99 0.00 44.73 1.52
611 621 7.988599 TGCTAAGTTGTCTACTTTTGGACTAAA 59.011 33.333 4.99 0.00 44.73 1.85
612 622 7.502696 TGCTAAGTTGTCTACTTTTGGACTAA 58.497 34.615 4.99 0.00 44.73 2.24
613 623 7.058023 TGCTAAGTTGTCTACTTTTGGACTA 57.942 36.000 4.99 0.00 44.73 2.59
614 624 5.925509 TGCTAAGTTGTCTACTTTTGGACT 58.074 37.500 4.99 0.00 44.73 3.85
615 625 6.613755 TTGCTAAGTTGTCTACTTTTGGAC 57.386 37.500 4.99 0.00 44.73 4.02
616 626 7.119262 GCTATTGCTAAGTTGTCTACTTTTGGA 59.881 37.037 4.99 0.00 46.09 3.53
617 627 7.244192 GCTATTGCTAAGTTGTCTACTTTTGG 58.756 38.462 4.99 0.00 46.09 3.28
618 628 7.244192 GGCTATTGCTAAGTTGTCTACTTTTG 58.756 38.462 4.99 1.34 40.65 2.44
619 629 6.092259 CGGCTATTGCTAAGTTGTCTACTTTT 59.908 38.462 4.99 0.00 40.65 2.27
620 630 5.581085 CGGCTATTGCTAAGTTGTCTACTTT 59.419 40.000 4.99 0.00 40.65 2.66
621 631 5.109903 CGGCTATTGCTAAGTTGTCTACTT 58.890 41.667 5.05 5.05 41.97 2.24
622 632 4.441634 CCGGCTATTGCTAAGTTGTCTACT 60.442 45.833 0.00 0.00 37.83 2.57
646 656 5.712917 GGATGGAGGAAGTATGTACTAGAGG 59.287 48.000 0.00 0.00 34.99 3.69
661 671 7.132805 ACGATCTTATATTATGGGATGGAGGA 58.867 38.462 0.00 0.00 0.00 3.71
663 673 9.672673 AAAACGATCTTATATTATGGGATGGAG 57.327 33.333 0.00 0.00 0.00 3.86
667 677 8.862325 TGCAAAACGATCTTATATTATGGGAT 57.138 30.769 0.00 0.00 0.00 3.85
702 712 9.090692 TGACGTTTATAATCACTAACTTTAGCC 57.909 33.333 0.00 0.00 34.09 3.93
714 724 6.861572 CGCTCTTATCCTGACGTTTATAATCA 59.138 38.462 0.00 0.00 0.00 2.57
748 758 3.130340 CGTTTCCTGTCCCCATATTTTGG 59.870 47.826 0.00 0.00 46.00 3.28
762 772 1.539388 TGTGCAATTAGCCGTTTCCTG 59.461 47.619 0.00 0.00 44.83 3.86
764 774 2.529151 CATGTGCAATTAGCCGTTTCC 58.471 47.619 0.00 0.00 44.83 3.13
934 945 2.925170 AGGAGCGAAGTGGGCTGT 60.925 61.111 0.00 0.00 41.72 4.40
956 981 3.584733 AGGGAAACACAGAGAAGCTTT 57.415 42.857 0.00 0.00 0.00 3.51
962 987 0.034896 GCGGAAGGGAAACACAGAGA 59.965 55.000 0.00 0.00 0.00 3.10
1010 1035 1.227089 CAATGGGAGAGACCGAGCG 60.227 63.158 0.00 0.00 40.11 5.03
1123 1148 2.821366 CCACACGCTCTCCCATGC 60.821 66.667 0.00 0.00 0.00 4.06
1158 1187 2.552315 ACTCGCAAACAAACGAATCCAT 59.448 40.909 0.00 0.00 37.94 3.41
1165 1194 0.304705 AGAGCACTCGCAAACAAACG 59.695 50.000 0.00 0.00 42.27 3.60
1166 1195 2.111756 CAAGAGCACTCGCAAACAAAC 58.888 47.619 0.00 0.00 42.27 2.93
1168 1197 0.662619 CCAAGAGCACTCGCAAACAA 59.337 50.000 0.00 0.00 42.27 2.83
1169 1198 0.179059 TCCAAGAGCACTCGCAAACA 60.179 50.000 0.00 0.00 42.27 2.83
1170 1199 0.514691 CTCCAAGAGCACTCGCAAAC 59.485 55.000 0.00 0.00 42.27 2.93
1183 1212 2.283617 CACGAAATCGATCAGCTCCAAG 59.716 50.000 10.16 0.00 43.02 3.61
1184 1213 2.270923 CACGAAATCGATCAGCTCCAA 58.729 47.619 10.16 0.00 43.02 3.53
1204 1233 1.518903 GCTTCACCTGCAAGACCACC 61.519 60.000 0.00 0.00 34.07 4.61
1209 1238 0.250467 GTCCTGCTTCACCTGCAAGA 60.250 55.000 0.00 0.00 40.13 3.02
1260 1289 0.476338 TTGAGGCAAGTGCTTACCCA 59.524 50.000 2.85 0.00 41.70 4.51
1313 1362 0.459489 CCAGCGGGAGAGAAAGAGAG 59.541 60.000 0.00 0.00 35.59 3.20
1314 1363 0.251832 ACCAGCGGGAGAGAAAGAGA 60.252 55.000 10.86 0.00 38.05 3.10
1315 1364 0.174617 GACCAGCGGGAGAGAAAGAG 59.825 60.000 10.86 0.00 38.05 2.85
1316 1365 1.595993 CGACCAGCGGGAGAGAAAGA 61.596 60.000 10.86 0.00 38.05 2.52
1319 1368 1.379977 ATCGACCAGCGGGAGAGAA 60.380 57.895 10.86 0.00 41.33 2.87
1320 1369 2.121538 CATCGACCAGCGGGAGAGA 61.122 63.158 10.86 6.03 41.33 3.10
1321 1370 2.415010 CATCGACCAGCGGGAGAG 59.585 66.667 10.86 0.00 41.33 3.20
1322 1371 3.838271 GCATCGACCAGCGGGAGA 61.838 66.667 10.86 9.10 41.33 3.71
1323 1372 3.451556 ATGCATCGACCAGCGGGAG 62.452 63.158 10.86 3.14 41.33 4.30
1324 1373 3.469970 ATGCATCGACCAGCGGGA 61.470 61.111 10.86 0.00 41.33 5.14
1325 1374 3.274586 CATGCATCGACCAGCGGG 61.275 66.667 0.00 0.00 41.33 6.13
1326 1375 3.945434 GCATGCATCGACCAGCGG 61.945 66.667 14.21 0.00 41.33 5.52
1327 1376 3.164390 CTGCATGCATCGACCAGCG 62.164 63.158 22.97 1.63 42.69 5.18
1328 1377 2.044832 GACTGCATGCATCGACCAGC 62.045 60.000 22.97 0.00 0.00 4.85
1330 1379 0.741927 CAGACTGCATGCATCGACCA 60.742 55.000 22.97 0.00 0.00 4.02
1331 1380 0.742281 ACAGACTGCATGCATCGACC 60.742 55.000 22.97 8.67 0.00 4.79
1333 1382 1.733912 GAAACAGACTGCATGCATCGA 59.266 47.619 22.97 0.00 0.00 3.59
1334 1383 1.736126 AGAAACAGACTGCATGCATCG 59.264 47.619 22.97 13.40 0.00 3.84
1335 1384 5.496133 AATAGAAACAGACTGCATGCATC 57.504 39.130 22.97 19.43 0.00 3.91
1337 1386 3.691118 GGAATAGAAACAGACTGCATGCA 59.309 43.478 21.29 21.29 0.00 3.96
1338 1387 3.944015 AGGAATAGAAACAGACTGCATGC 59.056 43.478 11.82 11.82 0.00 4.06
1339 1388 5.181009 TCAGGAATAGAAACAGACTGCATG 58.819 41.667 1.25 0.00 0.00 4.06
1340 1389 5.426689 TCAGGAATAGAAACAGACTGCAT 57.573 39.130 1.25 0.00 0.00 3.96
1341 1390 4.890158 TCAGGAATAGAAACAGACTGCA 57.110 40.909 1.25 0.00 0.00 4.41
1342 1391 6.428159 TCTTTTCAGGAATAGAAACAGACTGC 59.572 38.462 1.25 0.00 34.94 4.40
1343 1392 7.969536 TCTTTTCAGGAATAGAAACAGACTG 57.030 36.000 0.00 0.00 34.94 3.51
1344 1393 7.993183 TGTTCTTTTCAGGAATAGAAACAGACT 59.007 33.333 13.89 0.00 39.09 3.24
1345 1394 8.154649 TGTTCTTTTCAGGAATAGAAACAGAC 57.845 34.615 13.89 5.76 39.09 3.51
1346 1395 8.210946 TCTGTTCTTTTCAGGAATAGAAACAGA 58.789 33.333 23.33 23.33 39.09 3.41
1421 1470 4.558860 GCCATTATTCAACTGAAACGAAGC 59.441 41.667 0.00 0.00 37.61 3.86
1426 1475 4.462483 TCCAGGCCATTATTCAACTGAAAC 59.538 41.667 5.01 0.00 37.61 2.78
1428 1477 4.016444 GTCCAGGCCATTATTCAACTGAA 58.984 43.478 5.01 0.00 38.56 3.02
1430 1479 3.379372 CAGTCCAGGCCATTATTCAACTG 59.621 47.826 5.01 3.16 0.00 3.16
1431 1480 3.266772 TCAGTCCAGGCCATTATTCAACT 59.733 43.478 5.01 0.00 0.00 3.16
1432 1481 3.620488 TCAGTCCAGGCCATTATTCAAC 58.380 45.455 5.01 0.00 0.00 3.18
1433 1482 4.263905 ACTTCAGTCCAGGCCATTATTCAA 60.264 41.667 5.01 0.00 0.00 2.69
1435 1484 3.891049 ACTTCAGTCCAGGCCATTATTC 58.109 45.455 5.01 0.00 0.00 1.75
1436 1485 4.721776 TCTACTTCAGTCCAGGCCATTATT 59.278 41.667 5.01 0.00 0.00 1.40
1437 1486 4.298626 TCTACTTCAGTCCAGGCCATTAT 58.701 43.478 5.01 0.00 0.00 1.28
1439 1488 2.551270 TCTACTTCAGTCCAGGCCATT 58.449 47.619 5.01 0.00 0.00 3.16
1440 1489 2.254152 TCTACTTCAGTCCAGGCCAT 57.746 50.000 5.01 0.00 0.00 4.40
1443 1492 2.630580 CCCTATCTACTTCAGTCCAGGC 59.369 54.545 0.00 0.00 0.00 4.85
1444 1493 3.917300 ACCCTATCTACTTCAGTCCAGG 58.083 50.000 0.00 0.00 0.00 4.45
1445 1494 4.521256 GCTACCCTATCTACTTCAGTCCAG 59.479 50.000 0.00 0.00 0.00 3.86
1446 1495 4.079385 TGCTACCCTATCTACTTCAGTCCA 60.079 45.833 0.00 0.00 0.00 4.02
1448 1497 5.378332 TCTGCTACCCTATCTACTTCAGTC 58.622 45.833 0.00 0.00 0.00 3.51
1449 1498 5.390087 TCTGCTACCCTATCTACTTCAGT 57.610 43.478 0.00 0.00 0.00 3.41
1450 1499 6.909550 AATCTGCTACCCTATCTACTTCAG 57.090 41.667 0.00 0.00 0.00 3.02
1451 1500 6.267928 GGAAATCTGCTACCCTATCTACTTCA 59.732 42.308 0.00 0.00 0.00 3.02
1452 1501 6.495526 AGGAAATCTGCTACCCTATCTACTTC 59.504 42.308 0.00 0.00 0.00 3.01
1453 1502 6.268847 CAGGAAATCTGCTACCCTATCTACTT 59.731 42.308 0.00 0.00 36.60 2.24
1454 1503 5.777732 CAGGAAATCTGCTACCCTATCTACT 59.222 44.000 0.00 0.00 36.60 2.57
1757 1838 0.949105 CGTGTTTTCCTCCTGTCCGG 60.949 60.000 0.00 0.00 0.00 5.14
1778 1859 2.754472 AGCAAACAAAAGGGAAATCGC 58.246 42.857 0.00 0.00 0.00 4.58
1781 1862 6.827762 TCAAATGAAGCAAACAAAAGGGAAAT 59.172 30.769 0.00 0.00 0.00 2.17
1801 1882 3.739830 GCCTTTTGGTGGAAACGTCAAAT 60.740 43.478 0.00 0.00 42.99 2.32
1808 1889 1.051556 TGGGGCCTTTTGGTGGAAAC 61.052 55.000 0.84 0.00 42.99 2.78
1810 1891 1.458588 GTGGGGCCTTTTGGTGGAA 60.459 57.895 0.84 0.00 42.99 3.53
1833 1914 2.132996 ATGAGGCCGAGAGCTCTGG 61.133 63.158 23.91 20.67 43.05 3.86
1883 1964 2.223900 TGGAGATACGATCTGCTTGCTG 60.224 50.000 14.12 0.00 46.53 4.41
1968 2049 2.700773 GGAGCGTGTTGGGCCAATC 61.701 63.158 23.95 15.06 0.00 2.67
2129 2214 2.281831 TGCCGCGGTGAAAATGGA 60.282 55.556 28.70 0.00 0.00 3.41
2203 2288 3.858868 TTGAGTGCGACGGAGGTGC 62.859 63.158 0.00 0.00 0.00 5.01
2238 2323 1.059098 TTCAGACACAGTGGCAGGAT 58.941 50.000 9.73 0.00 0.00 3.24
2559 2657 4.008933 GCCCAGGATATCGCGGCT 62.009 66.667 6.13 0.00 36.65 5.52
2560 2658 4.314440 TGCCCAGGATATCGCGGC 62.314 66.667 6.13 15.78 40.16 6.53
2561 2659 2.357517 GTGCCCAGGATATCGCGG 60.358 66.667 6.13 0.00 0.00 6.46
2562 2660 1.665916 CAGTGCCCAGGATATCGCG 60.666 63.158 0.00 0.00 0.00 5.87
2565 2663 2.700897 AGTACACAGTGCCCAGGATATC 59.299 50.000 0.00 0.00 0.00 1.63
2566 2664 2.764269 AGTACACAGTGCCCAGGATAT 58.236 47.619 0.00 0.00 0.00 1.63
2569 2667 0.396435 CAAGTACACAGTGCCCAGGA 59.604 55.000 0.00 0.00 0.00 3.86
2570 2668 0.108585 ACAAGTACACAGTGCCCAGG 59.891 55.000 0.00 0.00 0.00 4.45
2571 2669 1.202639 TCACAAGTACACAGTGCCCAG 60.203 52.381 0.00 0.00 33.44 4.45
2572 2670 0.833949 TCACAAGTACACAGTGCCCA 59.166 50.000 0.00 0.00 33.44 5.36
2573 2671 1.226746 GTCACAAGTACACAGTGCCC 58.773 55.000 0.00 0.00 33.44 5.36
2574 2672 1.226746 GGTCACAAGTACACAGTGCC 58.773 55.000 0.00 3.41 33.44 5.01
2575 2673 1.867233 CTGGTCACAAGTACACAGTGC 59.133 52.381 0.00 0.00 33.44 4.40
2576 2674 3.179443 ACTGGTCACAAGTACACAGTG 57.821 47.619 0.00 0.00 37.74 3.66
2577 2675 3.906720 AACTGGTCACAAGTACACAGT 57.093 42.857 0.00 0.00 40.55 3.55
2578 2676 3.312421 CCAAACTGGTCACAAGTACACAG 59.688 47.826 0.00 0.00 31.35 3.66
2579 2677 3.275143 CCAAACTGGTCACAAGTACACA 58.725 45.455 0.00 0.00 31.35 3.72
2580 2678 3.963383 CCAAACTGGTCACAAGTACAC 57.037 47.619 0.00 0.00 31.35 2.90
2607 2705 1.157870 GCAATATGCCGCGTACCACT 61.158 55.000 4.92 0.00 37.42 4.00
2608 2706 1.157870 AGCAATATGCCGCGTACCAC 61.158 55.000 4.92 0.00 46.52 4.16
2609 2707 1.145156 AGCAATATGCCGCGTACCA 59.855 52.632 4.92 0.00 46.52 3.25
2610 2708 1.157870 ACAGCAATATGCCGCGTACC 61.158 55.000 4.92 0.00 46.52 3.34
2612 2710 1.067974 AGTACAGCAATATGCCGCGTA 59.932 47.619 4.92 0.00 46.52 4.42
2613 2711 0.179084 AGTACAGCAATATGCCGCGT 60.179 50.000 4.92 0.00 46.52 6.01
2636 2735 2.699768 ATGCCATTTCGCACCGGTG 61.700 57.895 30.66 30.66 42.70 4.94
2639 2738 2.580326 GCATGCCATTTCGCACCG 60.580 61.111 6.36 0.00 42.70 4.94
2667 2766 5.530915 TGTCCTTTGACTACAGAAACAATGG 59.469 40.000 0.00 0.00 42.28 3.16
2706 2806 2.017049 GCCATGTCCATCAGTAACCAC 58.983 52.381 0.00 0.00 0.00 4.16
2778 2878 1.673009 TCGGGCGCCACTAAAAAGG 60.673 57.895 30.85 5.10 0.00 3.11
2779 2879 1.231958 TGTCGGGCGCCACTAAAAAG 61.232 55.000 30.85 8.33 0.00 2.27
2807 2932 0.581529 CGTTGCACAGTGTAGTGTGG 59.418 55.000 18.52 1.81 46.73 4.17
2849 2974 4.228567 TGCGACGTTGTGGCCAGA 62.229 61.111 5.11 0.00 36.46 3.86
2857 2982 3.041940 GTCTGGGGTGCGACGTTG 61.042 66.667 0.00 0.00 0.00 4.10
2858 2983 3.231736 AGTCTGGGGTGCGACGTT 61.232 61.111 0.00 0.00 35.38 3.99
2859 2984 3.991051 CAGTCTGGGGTGCGACGT 61.991 66.667 0.00 0.00 35.38 4.34
2871 2996 9.167311 CATTGACTAGTAATTTTTAGGCAGTCT 57.833 33.333 0.00 0.00 36.35 3.24
2913 3039 2.104967 ACTGTATAGTGTGGCGCCTAA 58.895 47.619 29.70 13.28 35.34 2.69
3317 3443 4.201679 CCCAGCGTCGCATCCGTA 62.202 66.667 21.09 0.00 35.54 4.02
3388 3514 0.818445 TTTTAAGTGGCGCCCGACAA 60.818 50.000 26.77 10.38 33.39 3.18
3403 3529 3.586470 TTCACCCAGCTGACCTTTTTA 57.414 42.857 17.39 0.00 0.00 1.52
3409 3535 5.405935 AAAAATATTTCACCCAGCTGACC 57.594 39.130 17.39 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.