Multiple sequence alignment - TraesCS6D01G395600

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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 TraesCS6D01G395600 chr6D 100.000 6734 0 0 1 6734 468101073 468094340 0.000000e+00 12436.0
1 TraesCS6D01G395600 chr6D 90.561 1748 139 18 1844 3576 468059767 468058031 0.000000e+00 2290.0
2 TraesCS6D01G395600 chr6D 85.676 1508 183 21 2075 3571 468170941 468169456 0.000000e+00 1557.0
3 TraesCS6D01G395600 chr6D 86.986 1337 151 14 4320 5641 468168870 468167542 0.000000e+00 1483.0
4 TraesCS6D01G395600 chr6D 89.886 1137 110 5 4320 5454 468057401 468056268 0.000000e+00 1458.0
5 TraesCS6D01G395600 chr6D 86.364 1254 157 11 97 1344 468186124 468184879 0.000000e+00 1356.0
6 TraesCS6D01G395600 chr6D 85.496 1241 152 21 4438 5658 468147033 468145801 0.000000e+00 1269.0
7 TraesCS6D01G395600 chr6D 86.802 1038 136 1 4433 5470 468181998 468180962 0.000000e+00 1157.0
8 TraesCS6D01G395600 chr6D 83.854 929 118 19 932 1846 468060912 468060002 0.000000e+00 856.0
9 TraesCS6D01G395600 chr6D 83.524 874 98 30 98 958 468172428 468171588 0.000000e+00 774.0
10 TraesCS6D01G395600 chr6D 80.716 363 61 7 966 1325 468664369 468664013 2.390000e-69 274.0
11 TraesCS6D01G395600 chr6D 86.224 196 23 4 3925 4118 468057626 468057433 6.840000e-50 209.0
12 TraesCS6D01G395600 chr6D 76.068 234 25 14 3589 3819 468058046 468057841 7.190000e-15 93.5
13 TraesCS6D01G395600 chr6A 96.919 3538 87 11 3206 6734 614164056 614160532 0.000000e+00 5910.0
14 TraesCS6D01G395600 chr6A 88.936 1184 124 4 2029 3207 614165341 614164160 0.000000e+00 1454.0
15 TraesCS6D01G395600 chr6A 87.915 1175 123 14 223 1387 614166594 614165429 0.000000e+00 1365.0
16 TraesCS6D01G395600 chr6B 87.616 1292 140 13 4354 5629 714340799 714339512 0.000000e+00 1482.0
17 TraesCS6D01G395600 chr6B 88.703 1018 112 3 4438 5454 714330687 714329672 0.000000e+00 1240.0
18 TraesCS6D01G395600 chr6B 82.934 1043 126 37 98 1124 714343912 714342906 0.000000e+00 893.0
19 TraesCS6D01G395600 chr6B 84.736 832 117 7 2328 3156 714342889 714342065 0.000000e+00 824.0
20 TraesCS6D01G395600 chr6B 88.498 313 27 3 3837 4141 714341125 714340814 2.970000e-98 370.0
21 TraesCS6D01G395600 chr6B 88.686 274 31 0 562 835 714410825 714410552 1.080000e-87 335.0
22 TraesCS6D01G395600 chr6B 88.933 253 24 2 148 396 714411123 714410871 6.560000e-80 309.0
23 TraesCS6D01G395600 chr6B 83.280 311 43 6 1034 1344 714410549 714410248 1.850000e-70 278.0
24 TraesCS6D01G395600 chr6B 89.595 173 17 1 4140 4311 664448194 664448022 1.140000e-52 219.0
25 TraesCS6D01G395600 chr6B 86.286 175 9 6 3 163 714413137 714412964 6.940000e-40 176.0
26 TraesCS6D01G395600 chr6B 88.430 121 9 5 3711 3829 714341279 714341162 2.530000e-29 141.0
27 TraesCS6D01G395600 chrUn 89.886 1137 109 5 4320 5455 346081819 346080688 0.000000e+00 1458.0
28 TraesCS6D01G395600 chrUn 84.255 1429 176 27 2075 3494 210219170 210217782 0.000000e+00 1347.0
29 TraesCS6D01G395600 chrUn 85.668 1242 147 25 4438 5658 310899428 310900659 0.000000e+00 1279.0
30 TraesCS6D01G395600 chrUn 83.691 1306 160 36 98 1389 210220495 210219229 0.000000e+00 1182.0
31 TraesCS6D01G395600 chrUn 86.239 545 63 10 97 633 75282856 75283396 1.260000e-161 580.0
32 TraesCS6D01G395600 chrUn 86.239 545 63 10 97 633 327314992 327314452 1.260000e-161 580.0
33 TraesCS6D01G395600 chrUn 83.953 592 76 13 754 1344 75283431 75284004 3.550000e-152 549.0
34 TraesCS6D01G395600 chrUn 83.953 592 76 13 754 1344 327314417 327313844 3.550000e-152 549.0
35 TraesCS6D01G395600 chrUn 84.503 342 46 7 989 1325 216380871 216381210 1.400000e-86 331.0
36 TraesCS6D01G395600 chrUn 88.321 274 32 0 562 835 211919251 211919524 5.030000e-86 329.0
37 TraesCS6D01G395600 chrUn 89.683 252 23 2 148 396 211918954 211919205 1.090000e-82 318.0
38 TraesCS6D01G395600 chrUn 77.524 525 102 14 1387 1901 99118203 99117685 1.100000e-77 302.0
39 TraesCS6D01G395600 chrUn 90.576 191 18 0 645 835 479932506 479932316 3.120000e-63 254.0
40 TraesCS6D01G395600 chrUn 78.644 295 53 7 2584 2869 51444028 51444321 3.210000e-43 187.0
41 TraesCS6D01G395600 chrUn 86.755 151 18 1 1389 1539 84241281 84241133 4.180000e-37 167.0
42 TraesCS6D01G395600 chrUn 85.294 136 6 5 3 125 321021226 321021092 1.970000e-25 128.0
43 TraesCS6D01G395600 chrUn 78.916 166 29 4 2713 2872 252683476 252683311 2.570000e-19 108.0
44 TraesCS6D01G395600 chrUn 78.916 166 29 4 2713 2872 260287940 260288105 2.570000e-19 108.0
45 TraesCS6D01G395600 chrUn 85.294 68 9 1 5896 5962 79769872 79769939 1.210000e-07 69.4
46 TraesCS6D01G395600 chr2D 79.905 632 111 13 1389 2005 33253031 33253661 3.700000e-122 449.0
47 TraesCS6D01G395600 chr2D 80.469 512 88 10 1387 1887 577324781 577325291 1.370000e-101 381.0
48 TraesCS6D01G395600 chr2D 90.419 167 14 2 4140 4306 5442186 5442022 1.140000e-52 219.0
49 TraesCS6D01G395600 chr2D 78.261 138 17 7 6207 6342 37515389 37515263 7.240000e-10 76.8
50 TraesCS6D01G395600 chr3B 77.589 647 129 13 1389 2020 828643902 828643257 1.770000e-100 377.0
51 TraesCS6D01G395600 chr3B 76.899 645 134 13 1389 2020 172058961 172058319 1.070000e-92 351.0
52 TraesCS6D01G395600 chr3B 94.767 172 7 2 4141 4312 487497388 487497557 4.000000e-67 267.0
53 TraesCS6D01G395600 chr3B 79.932 294 51 5 1389 1675 763134924 763135216 6.840000e-50 209.0
54 TraesCS6D01G395600 chr3B 79.932 294 52 4 1389 1675 763163896 763164189 6.840000e-50 209.0
55 TraesCS6D01G395600 chr5B 92.442 172 12 1 4141 4312 41990147 41989977 1.880000e-60 244.0
56 TraesCS6D01G395600 chr5B 92.353 170 12 1 4141 4310 514067823 514067991 2.430000e-59 241.0
57 TraesCS6D01G395600 chr5B 91.228 171 12 3 4142 4312 563604260 563604427 5.250000e-56 230.0
58 TraesCS6D01G395600 chr7D 90.698 172 16 0 4141 4312 45146218 45146389 5.250000e-56 230.0
59 TraesCS6D01G395600 chr4B 89.017 173 19 0 4140 4312 544294493 544294665 1.470000e-51 215.0
60 TraesCS6D01G395600 chr7A 81.467 259 39 6 1389 1645 29015893 29016144 3.180000e-48 204.0
61 TraesCS6D01G395600 chr7A 90.476 63 6 0 2810 2872 346004 345942 4.330000e-12 84.2
62 TraesCS6D01G395600 chr1D 79.252 294 52 9 2583 2872 5422297 5422585 5.330000e-46 196.0
63 TraesCS6D01G395600 chr1A 78.912 294 53 9 2583 2872 6902145 6901857 2.480000e-44 191.0
64 TraesCS6D01G395600 chr4A 77.301 326 65 6 1389 1712 702374776 702375094 4.150000e-42 183.0
65 TraesCS6D01G395600 chr4D 84.393 173 18 7 6207 6370 64373355 64373183 1.940000e-35 161.0
66 TraesCS6D01G395600 chr3A 93.846 65 4 0 6317 6381 684694087 684694151 1.550000e-16 99.0


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 TraesCS6D01G395600 chr6D 468094340 468101073 6733 True 12436.000000 12436 100.000000 1 6734 1 chr6D.!!$R1 6733
1 TraesCS6D01G395600 chr6D 468167542 468172428 4886 True 1271.333333 1557 85.395333 98 5641 3 chr6D.!!$R5 5543
2 TraesCS6D01G395600 chr6D 468145801 468147033 1232 True 1269.000000 1269 85.496000 4438 5658 1 chr6D.!!$R2 1220
3 TraesCS6D01G395600 chr6D 468180962 468186124 5162 True 1256.500000 1356 86.583000 97 5470 2 chr6D.!!$R6 5373
4 TraesCS6D01G395600 chr6D 468056268 468060912 4644 True 981.300000 2290 85.318600 932 5454 5 chr6D.!!$R4 4522
5 TraesCS6D01G395600 chr6A 614160532 614166594 6062 True 2909.666667 5910 91.256667 223 6734 3 chr6A.!!$R1 6511
6 TraesCS6D01G395600 chr6B 714329672 714330687 1015 True 1240.000000 1240 88.703000 4438 5454 1 chr6B.!!$R2 1016
7 TraesCS6D01G395600 chr6B 714339512 714343912 4400 True 742.000000 1482 86.442800 98 5629 5 chr6B.!!$R3 5531
8 TraesCS6D01G395600 chr6B 714410248 714413137 2889 True 274.500000 335 86.796250 3 1344 4 chr6B.!!$R4 1341
9 TraesCS6D01G395600 chrUn 346080688 346081819 1131 True 1458.000000 1458 89.886000 4320 5455 1 chrUn.!!$R5 1135
10 TraesCS6D01G395600 chrUn 310899428 310900659 1231 False 1279.000000 1279 85.668000 4438 5658 1 chrUn.!!$F5 1220
11 TraesCS6D01G395600 chrUn 210217782 210220495 2713 True 1264.500000 1347 83.973000 98 3494 2 chrUn.!!$R7 3396
12 TraesCS6D01G395600 chrUn 75282856 75284004 1148 False 564.500000 580 85.096000 97 1344 2 chrUn.!!$F6 1247
13 TraesCS6D01G395600 chrUn 327313844 327314992 1148 True 564.500000 580 85.096000 97 1344 2 chrUn.!!$R8 1247
14 TraesCS6D01G395600 chrUn 211918954 211919524 570 False 323.500000 329 89.002000 148 835 2 chrUn.!!$F7 687
15 TraesCS6D01G395600 chrUn 99117685 99118203 518 True 302.000000 302 77.524000 1387 1901 1 chrUn.!!$R2 514
16 TraesCS6D01G395600 chr2D 33253031 33253661 630 False 449.000000 449 79.905000 1389 2005 1 chr2D.!!$F1 616
17 TraesCS6D01G395600 chr2D 577324781 577325291 510 False 381.000000 381 80.469000 1387 1887 1 chr2D.!!$F2 500
18 TraesCS6D01G395600 chr3B 828643257 828643902 645 True 377.000000 377 77.589000 1389 2020 1 chr3B.!!$R2 631
19 TraesCS6D01G395600 chr3B 172058319 172058961 642 True 351.000000 351 76.899000 1389 2020 1 chr3B.!!$R1 631

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
668 2556 0.687427 TCCTCGATGAGATGGTGGCA 60.687 55.0 0.00 0.00 0.00 4.92 F
1131 3201 0.043334 CCTCCTCCTCCTCCTTCCAA 59.957 60.0 0.00 0.00 0.00 3.53 F
1156 3229 0.044702 ACTCACATGATCCTGGGGGA 59.955 55.0 7.17 0.00 46.81 4.81 F
1254 3327 0.108329 CTACCCGTTCGGCATGAAGT 60.108 55.0 5.66 0.25 37.23 3.01 F
2317 4791 0.528470 GTTCCTCCTGTCGACAGAGG 59.472 60.0 40.21 36.90 46.59 3.69 F
2769 5248 0.598562 CAGACTACGCCTGTGTCAGT 59.401 55.0 0.00 0.00 32.21 3.41 F
4148 7732 0.252974 TGTAGCCACATAGGGGGTGT 60.253 55.0 0.00 0.00 37.34 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1647 3735 0.036577 CAGAGGCTGGAGGACAACTG 60.037 60.000 0.00 0.0 0.00 3.16 R
2992 5486 0.447406 CGCGGATTTTGCACTCATCA 59.553 50.000 0.00 0.0 0.00 3.07 R
3005 5499 1.873591 GCAAGGATACAAATCGCGGAT 59.126 47.619 6.13 0.0 41.41 4.18 R
3167 5682 3.412386 ACAACAAGAACAGTCATAGCCC 58.588 45.455 0.00 0.0 0.00 5.19 R
4144 7728 0.104120 GTCCCTTGCAACCAAACACC 59.896 55.000 0.00 0.0 0.00 4.16 R
4292 7877 0.479378 GGGGGTGTTTGGTTACAGGA 59.521 55.000 0.00 0.0 0.00 3.86 R
5843 9449 0.456221 AGGACGTTAGGATGCAGTCG 59.544 55.000 0.00 0.0 33.04 4.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 64 5.928976 TGATATGTGTTATCACCCCAAGAG 58.071 41.667 1.53 0.00 41.41 2.85
68 71 4.473196 TGTTATCACCCCAAGAGCTCAATA 59.527 41.667 17.77 0.00 0.00 1.90
73 76 2.769095 ACCCCAAGAGCTCAATACTCTC 59.231 50.000 17.77 0.00 43.71 3.20
126 140 6.162777 TGTGTTTTTGGTCCTTCTTTCTTTG 58.837 36.000 0.00 0.00 0.00 2.77
144 158 4.098349 TCTTTGCAGCAACATCTTTGTCTT 59.902 37.500 7.54 0.00 34.06 3.01
288 2163 6.049149 ACTCCATATCGTATGAACACCAAAG 58.951 40.000 6.59 0.00 0.00 2.77
345 2220 2.266055 CGGAGGACAGACCCAAGC 59.734 66.667 0.00 0.00 40.05 4.01
403 2283 1.078918 TTGTCATGCTCGCCTCCTG 60.079 57.895 0.00 0.00 0.00 3.86
433 2317 2.245159 ATGCTACCATCATCACCACG 57.755 50.000 0.00 0.00 0.00 4.94
502 2388 1.227674 CATGGCCCGCCTCTTAGAC 60.228 63.158 7.35 0.00 36.94 2.59
543 2429 7.251281 GTGCAACCTTTCTTATCTTATTGGAC 58.749 38.462 0.00 0.00 31.56 4.02
581 2467 5.405935 TCATTGCTGCTTGACTAGTTAGA 57.594 39.130 0.00 0.00 0.00 2.10
584 2470 4.600692 TGCTGCTTGACTAGTTAGAACA 57.399 40.909 0.00 0.00 0.00 3.18
589 2475 6.531503 TGCTTGACTAGTTAGAACATAGCT 57.468 37.500 0.00 0.00 0.00 3.32
601 2487 7.716998 AGTTAGAACATAGCTGAAATATGTGGG 59.283 37.037 0.00 0.00 41.79 4.61
603 2489 4.796110 ACATAGCTGAAATATGTGGGGT 57.204 40.909 0.00 0.00 41.24 4.95
618 2504 3.388024 TGTGGGGTAAGCTAGCAGATAAG 59.612 47.826 18.83 0.00 0.00 1.73
628 2514 4.578105 AGCTAGCAGATAAGCAACAATTCC 59.422 41.667 18.83 0.00 41.32 3.01
657 2545 0.802222 ATCGCGTGTGTTCCTCGATG 60.802 55.000 5.77 0.00 38.30 3.84
668 2556 0.687427 TCCTCGATGAGATGGTGGCA 60.687 55.000 0.00 0.00 0.00 4.92
737 2629 4.263550 GGAGCCCTTTTAGAAAGAGAAGGT 60.264 45.833 2.15 0.00 37.53 3.50
743 2635 5.278512 CCTTTTAGAAAGAGAAGGTGGCAAC 60.279 44.000 0.00 0.00 35.13 4.17
812 2705 7.857885 GTGTCAACTTTCCTTCTTGACTAATTG 59.142 37.037 10.26 0.00 42.82 2.32
816 2709 9.273016 CAACTTTCCTTCTTGACTAATTGAGTA 57.727 33.333 0.00 0.00 39.06 2.59
927 2823 1.004745 AGCAAAGAATGACGATGGGGT 59.995 47.619 0.00 0.00 0.00 4.95
930 2826 3.065371 GCAAAGAATGACGATGGGGTTAG 59.935 47.826 0.00 0.00 0.00 2.34
945 2841 2.948315 GGGTTAGAGTAGAACCGTCGAT 59.052 50.000 0.00 0.00 46.26 3.59
964 3022 8.186163 CCGTCGATGCTACCAATATATAAGTTA 58.814 37.037 0.00 0.00 0.00 2.24
1021 3079 5.872963 AGCTTTGCATCCATATCATAGACA 58.127 37.500 0.00 0.00 0.00 3.41
1022 3080 5.938710 AGCTTTGCATCCATATCATAGACAG 59.061 40.000 0.00 0.00 0.00 3.51
1026 3084 6.034161 TGCATCCATATCATAGACAGAGTG 57.966 41.667 0.00 0.00 0.00 3.51
1037 3095 1.155042 GACAGAGTGAGCTTGCAAGG 58.845 55.000 27.10 10.68 0.00 3.61
1050 3108 1.661509 GCAAGGGAGCGCAAAACAC 60.662 57.895 11.47 0.00 0.00 3.32
1065 3129 0.823356 AACACACACCAGCATGACCC 60.823 55.000 0.00 0.00 39.69 4.46
1067 3131 2.435663 CACACCAGCATGACCCCA 59.564 61.111 0.00 0.00 39.69 4.96
1072 3136 2.765969 CAGCATGACCCCACCCTT 59.234 61.111 0.00 0.00 39.69 3.95
1073 3137 1.570857 CCAGCATGACCCCACCCTTA 61.571 60.000 0.00 0.00 39.69 2.69
1074 3138 0.107017 CAGCATGACCCCACCCTTAG 60.107 60.000 0.00 0.00 39.69 2.18
1081 3145 0.986550 ACCCCACCCTTAGAATCCCG 60.987 60.000 0.00 0.00 0.00 5.14
1088 3152 1.562475 CCCTTAGAATCCCGTTCCCAA 59.438 52.381 0.00 0.00 37.56 4.12
1091 3155 1.659022 TAGAATCCCGTTCCCAACCA 58.341 50.000 0.00 0.00 37.56 3.67
1093 3157 1.302993 AATCCCGTTCCCAACCACG 60.303 57.895 0.00 0.00 36.12 4.94
1099 3163 2.519780 TTCCCAACCACGGCCAAC 60.520 61.111 2.24 0.00 0.00 3.77
1100 3164 3.063197 TTCCCAACCACGGCCAACT 62.063 57.895 2.24 0.00 0.00 3.16
1104 3168 0.322098 CCAACCACGGCCAACTATCA 60.322 55.000 2.24 0.00 0.00 2.15
1131 3201 0.043334 CCTCCTCCTCCTCCTTCCAA 59.957 60.000 0.00 0.00 0.00 3.53
1136 3206 0.473694 TCCTCCTCCTTCCAACAGCA 60.474 55.000 0.00 0.00 0.00 4.41
1143 3216 1.211703 TCCTTCCAACAGCAACTCACA 59.788 47.619 0.00 0.00 0.00 3.58
1153 3226 1.064906 AGCAACTCACATGATCCTGGG 60.065 52.381 0.00 0.00 0.00 4.45
1156 3229 0.044702 ACTCACATGATCCTGGGGGA 59.955 55.000 7.17 0.00 46.81 4.81
1165 3238 3.341629 CCTGGGGGATGGTGCTGT 61.342 66.667 0.00 0.00 33.58 4.40
1169 3242 1.307647 GGGGGATGGTGCTGTTGAT 59.692 57.895 0.00 0.00 0.00 2.57
1184 3257 3.617284 TGTTGATCAAGATGAGCAGCAT 58.383 40.909 8.80 0.00 46.18 3.79
1199 3272 1.400846 CAGCATCAGATCACACTTGCC 59.599 52.381 0.00 0.00 0.00 4.52
1200 3273 1.003928 AGCATCAGATCACACTTGCCA 59.996 47.619 0.00 0.00 0.00 4.92
1254 3327 0.108329 CTACCCGTTCGGCATGAAGT 60.108 55.000 5.66 0.25 37.23 3.01
1259 3332 0.670546 CGTTCGGCATGAAGTCAGGT 60.671 55.000 0.00 0.00 37.23 4.00
1286 3359 1.152030 TGAGGGCTTCCAGGTCACT 60.152 57.895 0.00 0.00 0.00 3.41
1377 3453 1.992557 AGCAAATCAGGGTGGAGGTAA 59.007 47.619 0.00 0.00 0.00 2.85
1474 3552 1.226686 CGGCCTCTGCATAGCATGAC 61.227 60.000 0.00 0.00 38.13 3.06
1484 3562 2.207590 CATAGCATGACGCACACAGAT 58.792 47.619 0.00 0.00 46.13 2.90
1514 3594 7.372714 AGTCCAAACGACCCAAAAATAAATAC 58.627 34.615 0.00 0.00 43.08 1.89
1567 3655 0.853530 GGGTGGGGCAAATCCTATCT 59.146 55.000 0.00 0.00 34.39 1.98
1570 3658 0.852842 TGGGGCAAATCCTATCTGGG 59.147 55.000 0.00 0.00 36.20 4.45
1620 3708 1.749638 CTCCCTGACCGTACGCTCT 60.750 63.158 10.49 0.00 0.00 4.09
1635 3723 1.414158 GCTCTAGCCATGTAGACCCA 58.586 55.000 0.00 0.00 34.31 4.51
1636 3724 1.974236 GCTCTAGCCATGTAGACCCAT 59.026 52.381 0.00 0.00 34.31 4.00
1638 3726 3.234353 CTCTAGCCATGTAGACCCATCA 58.766 50.000 0.00 0.00 0.00 3.07
1639 3727 3.837146 CTCTAGCCATGTAGACCCATCAT 59.163 47.826 0.00 0.00 0.00 2.45
1640 3728 5.010708 TCTAGCCATGTAGACCCATCATA 57.989 43.478 0.00 0.00 0.00 2.15
1645 3733 6.376248 AGCCATGTAGACCCATCATAAAAAT 58.624 36.000 0.00 0.00 0.00 1.82
1647 3735 6.449698 CCATGTAGACCCATCATAAAAATGC 58.550 40.000 0.00 0.00 0.00 3.56
1648 3736 6.040729 CCATGTAGACCCATCATAAAAATGCA 59.959 38.462 0.00 0.00 0.00 3.96
1649 3737 6.698008 TGTAGACCCATCATAAAAATGCAG 57.302 37.500 0.00 0.00 0.00 4.41
1650 3738 6.186957 TGTAGACCCATCATAAAAATGCAGT 58.813 36.000 0.00 0.00 0.00 4.40
1689 3793 4.579753 GCAGGATAGTCTAAGTACGGAGTT 59.420 45.833 0.00 0.00 37.78 3.01
1692 3797 7.040548 GCAGGATAGTCTAAGTACGGAGTTATT 60.041 40.741 0.00 0.00 37.78 1.40
1705 3810 8.202137 AGTACGGAGTTATTAAGTACATGCATT 58.798 33.333 0.00 0.00 37.78 3.56
1734 3841 1.131126 GCACGGGAGATGAAACACATG 59.869 52.381 0.00 0.00 39.56 3.21
1774 3882 6.716628 ACATCATTTCTGGTAACTCACAATGT 59.283 34.615 0.00 0.00 37.61 2.71
1776 3884 6.533730 TCATTTCTGGTAACTCACAATGTCT 58.466 36.000 0.00 0.00 37.61 3.41
1809 4011 1.136110 CCGCCCCCACAAAAATATGTC 59.864 52.381 0.00 0.00 0.00 3.06
1811 4013 1.136110 GCCCCCACAAAAATATGTCCG 59.864 52.381 0.00 0.00 0.00 4.79
1857 4296 7.132213 CCGCAATCAATTACCTAACATGTTAG 58.868 38.462 30.69 30.69 41.56 2.34
1871 4311 2.107950 TGTTAGGTGCACTACATGGC 57.892 50.000 17.98 0.00 0.00 4.40
1907 4349 5.468540 AGCTACTTGAACTATGTCACACA 57.531 39.130 0.00 0.00 0.00 3.72
1919 4361 0.944386 GTCACACAGCACAACCGAAT 59.056 50.000 0.00 0.00 0.00 3.34
1925 4367 3.568007 ACACAGCACAACCGAATTTACAT 59.432 39.130 0.00 0.00 0.00 2.29
1960 4402 8.798859 AAGTGTTTAATAGACTCATCATGCTT 57.201 30.769 0.00 0.00 28.53 3.91
1971 4413 4.166523 CTCATCATGCTTGCAAAAGACAG 58.833 43.478 0.00 0.00 0.00 3.51
1976 4419 4.038282 TCATGCTTGCAAAAGACAGATGTT 59.962 37.500 0.00 0.00 0.00 2.71
1978 4421 4.362279 TGCTTGCAAAAGACAGATGTTTC 58.638 39.130 0.00 0.00 0.00 2.78
1989 4432 3.866651 ACAGATGTTTCGCTATCTTGCT 58.133 40.909 0.00 0.00 31.53 3.91
2156 4630 7.345653 TCAAGTTTGGAGTAGATCACTGGATAT 59.654 37.037 0.00 0.00 37.72 1.63
2175 4649 1.448540 CACGGCCTTCGAGCTCATT 60.449 57.895 15.40 0.00 42.43 2.57
2189 4663 4.564372 CGAGCTCATTGATATATCCGTTGG 59.436 45.833 15.40 0.03 0.00 3.77
2201 4675 1.454539 CCGTTGGAAAGGGTGAGGT 59.545 57.895 0.00 0.00 46.38 3.85
2223 4697 2.582498 GCATACGGCGCGTTCTCT 60.582 61.111 6.90 0.00 41.54 3.10
2257 4731 6.526674 CAGCCAAAATCAAACCGATTACTTAC 59.473 38.462 0.00 0.00 43.83 2.34
2258 4732 6.433093 AGCCAAAATCAAACCGATTACTTACT 59.567 34.615 0.00 0.00 43.83 2.24
2259 4733 6.526674 GCCAAAATCAAACCGATTACTTACTG 59.473 38.462 0.00 0.00 43.83 2.74
2286 4760 7.678837 AGAATCAAAATATGAAGTTGGGCAAA 58.321 30.769 0.00 0.00 42.54 3.68
2317 4791 0.528470 GTTCCTCCTGTCGACAGAGG 59.472 60.000 40.21 36.90 46.59 3.69
2326 4800 0.798776 GTCGACAGAGGGCAATGTTG 59.201 55.000 11.55 0.00 32.94 3.33
2331 4805 2.821969 GACAGAGGGCAATGTTGTCATT 59.178 45.455 0.00 0.00 44.02 2.57
2540 5017 0.747283 CCCATCAGAGAGCTTGCACC 60.747 60.000 0.00 0.00 0.00 5.01
2550 5027 2.530497 GCTTGCACCGTCGTTCACA 61.530 57.895 0.00 0.00 0.00 3.58
2551 5028 1.564622 CTTGCACCGTCGTTCACAG 59.435 57.895 0.00 0.00 0.00 3.66
2669 5146 1.822990 CTACGAGGTGCTACCCAAGAA 59.177 52.381 0.00 0.00 39.75 2.52
2769 5248 0.598562 CAGACTACGCCTGTGTCAGT 59.401 55.000 0.00 0.00 32.21 3.41
2876 5355 1.901159 CAATGGATGCCAAGGTGGAAA 59.099 47.619 0.00 0.00 40.96 3.13
2992 5486 8.579863 CCTTTGTATTTCTCCTTTTCAGACATT 58.420 33.333 0.00 0.00 0.00 2.71
3004 5498 5.771153 TTTCAGACATTGATGAGTGCAAA 57.229 34.783 0.00 0.00 35.27 3.68
3005 5499 5.771153 TTCAGACATTGATGAGTGCAAAA 57.229 34.783 0.00 0.00 35.27 2.44
3026 5541 1.013596 CCGCGATTTGTATCCTTGCA 58.986 50.000 8.23 0.00 0.00 4.08
3142 5657 3.545124 ATTCCCCGCAACAGCACGA 62.545 57.895 0.00 0.00 0.00 4.35
3167 5682 6.482973 AGTGATTTTGGGTAAGCACAAATTTG 59.517 34.615 16.67 16.67 46.12 2.32
3552 6836 5.485662 AACAGTGCTGAAACTAAACAGAC 57.514 39.130 6.17 0.00 36.38 3.51
3615 6901 2.460669 GAAATGTTTGGAGGCCCAGAT 58.539 47.619 0.00 0.00 44.60 2.90
3654 6940 7.978982 AGTCCAAATTTGAAAGTCTCGATATG 58.021 34.615 19.86 0.00 0.00 1.78
3776 7201 3.445096 GCTGCTGTGAATAGGATTGGTTT 59.555 43.478 0.00 0.00 0.00 3.27
3819 7245 2.238898 AGTAGGGATGGGTGTTTAGTGC 59.761 50.000 0.00 0.00 0.00 4.40
3930 7477 9.712305 AAGTCATATGTGATAGGCTTGTATTAC 57.288 33.333 1.90 0.00 36.60 1.89
4144 7728 4.532126 TCTTATCATGTAGCCACATAGGGG 59.468 45.833 0.00 0.00 43.73 4.79
4148 7732 0.252974 TGTAGCCACATAGGGGGTGT 60.253 55.000 0.00 0.00 37.34 4.16
4169 7753 1.729586 TGGTTGCAAGGGACTAGACT 58.270 50.000 0.00 0.00 38.49 3.24
4231 7815 6.350612 CCAGTAGAGTCTTTTTCTAGTCCCTG 60.351 46.154 0.00 0.00 30.30 4.45
4247 7831 4.233287 AGTCCCTGTAGAATAAGTCCCTCT 59.767 45.833 0.00 0.00 0.00 3.69
4261 7845 4.398319 AGTCCCTCTTGTTTGGTTACATG 58.602 43.478 0.00 0.00 0.00 3.21
4311 7896 0.479378 TCCTGTAACCAAACACCCCC 59.521 55.000 0.00 0.00 0.00 5.40
4316 7901 1.072173 GTAACCAAACACCCCCGTAGT 59.928 52.381 0.00 0.00 0.00 2.73
4390 7975 4.431416 TCAGAAGTGTTGCTCCCTTTTA 57.569 40.909 0.00 0.00 0.00 1.52
4429 8015 8.721478 GCACACAGAATAGTTCTTAGAATTCAA 58.279 33.333 8.44 0.00 38.11 2.69
4856 8443 7.012894 CCGATTCTAGTCTATGAGTTTCTCTGT 59.987 40.741 0.00 0.00 0.00 3.41
5027 8614 7.100458 ACCAGCAAATATACTTTTGGATGAC 57.900 36.000 2.22 0.00 37.13 3.06
5336 8923 6.409704 TGTAACTGAGGATTTGGAGATTCTG 58.590 40.000 0.00 0.00 0.00 3.02
5617 9222 8.732746 ATGTAATGTAACTCATTGAGTAACCC 57.267 34.615 19.27 8.44 42.59 4.11
5618 9223 7.913789 TGTAATGTAACTCATTGAGTAACCCT 58.086 34.615 19.27 6.47 42.59 4.34
5730 9336 6.042666 TGTTTAGTGTATAGGGCATGCATCTA 59.957 38.462 21.36 19.45 31.44 1.98
5786 9392 1.778334 TGACATTGTTCACGAGTCGG 58.222 50.000 18.30 6.08 32.08 4.79
5820 9426 8.528917 AATATGTATGCATGCATCAAAATGAC 57.471 30.769 35.35 24.90 37.82 3.06
5827 9433 1.199789 TGCATCAAAATGACCGACTGC 59.800 47.619 0.00 0.00 34.61 4.40
5828 9434 1.468054 GCATCAAAATGACCGACTGCC 60.468 52.381 0.00 0.00 34.61 4.85
5839 9445 4.735132 GACTGCCTGCACCGCGTA 62.735 66.667 4.92 0.00 0.00 4.42
5843 9449 3.564027 GCCTGCACCGCGTACATC 61.564 66.667 4.92 0.00 0.00 3.06
5844 9450 3.254654 CCTGCACCGCGTACATCG 61.255 66.667 4.92 0.00 43.12 3.84
5894 9500 1.895798 TCTCGAGACTGAATGTTGCCT 59.104 47.619 12.08 0.00 0.00 4.75
6116 9723 6.643360 GTGACTTGTTTTGGTACAGTTTTGTT 59.357 34.615 0.00 0.00 42.39 2.83
6126 9733 2.724358 GTTTTGTTGGCGACGGCG 60.724 61.111 17.16 6.12 41.24 6.46
6129 9736 4.893601 TTGTTGGCGACGGCGTGA 62.894 61.111 21.19 0.00 41.24 4.35
6338 9946 3.519913 ACCCCTACTTTCAACCTCTCATC 59.480 47.826 0.00 0.00 0.00 2.92
6362 9970 9.825972 ATCTTTGTAGACATTTTATCAAACACG 57.174 29.630 0.00 0.00 31.99 4.49
6364 9972 9.445786 CTTTGTAGACATTTTATCAAACACGTT 57.554 29.630 0.00 0.00 0.00 3.99
6372 9980 1.234821 ATCAAACACGTTGGATGCGT 58.765 45.000 0.00 0.00 43.90 5.24
6399 10007 4.925861 GCATCCTCGGCCAGCTCC 62.926 72.222 2.24 0.00 0.00 4.70
6541 10149 1.649815 CGCGAGCTTCGATCTAGGT 59.350 57.895 0.00 0.00 43.74 3.08
6590 10198 0.669318 CACGCACGGATAACACAGGT 60.669 55.000 0.00 0.00 0.00 4.00
6591 10199 0.389426 ACGCACGGATAACACAGGTC 60.389 55.000 0.00 0.00 0.00 3.85
6730 10342 2.048603 GGATGCTTGGCAGGGTGAC 61.049 63.158 0.00 0.00 43.65 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.037641 AGCCAAGGAATGAAAACAAGGC 59.962 45.455 0.00 0.00 39.82 4.35
1 2 3.656559 CAGCCAAGGAATGAAAACAAGG 58.343 45.455 0.00 0.00 0.00 3.61
80 83 6.426633 CACATGAAAGGGCGATAACACATATA 59.573 38.462 0.00 0.00 0.00 0.86
81 84 5.239306 CACATGAAAGGGCGATAACACATAT 59.761 40.000 0.00 0.00 0.00 1.78
82 85 4.574421 CACATGAAAGGGCGATAACACATA 59.426 41.667 0.00 0.00 0.00 2.29
83 86 3.378112 CACATGAAAGGGCGATAACACAT 59.622 43.478 0.00 0.00 0.00 3.21
85 88 2.747446 ACACATGAAAGGGCGATAACAC 59.253 45.455 0.00 0.00 0.00 3.32
86 89 3.066291 ACACATGAAAGGGCGATAACA 57.934 42.857 0.00 0.00 0.00 2.41
87 90 4.434713 AAACACATGAAAGGGCGATAAC 57.565 40.909 0.00 0.00 0.00 1.89
90 104 3.554752 CCAAAAACACATGAAAGGGCGAT 60.555 43.478 0.00 0.00 0.00 4.58
94 108 3.387699 AGGACCAAAAACACATGAAAGGG 59.612 43.478 0.00 0.00 0.00 3.95
126 140 2.294233 TCCAAGACAAAGATGTTGCTGC 59.706 45.455 0.00 0.00 40.74 5.25
198 2070 7.762588 AAGCTTTTACTAGTCACAGTCTCTA 57.237 36.000 0.00 0.00 0.00 2.43
273 2148 5.872617 TCTTCCATACTTTGGTGTTCATACG 59.127 40.000 0.00 0.00 46.52 3.06
288 2163 3.695830 TGTTGGGTCTGTCTTCCATAC 57.304 47.619 0.00 0.00 0.00 2.39
320 2195 0.603569 GTCTGTCCTCCGTGATGTGT 59.396 55.000 0.00 0.00 0.00 3.72
323 2198 1.257750 TGGGTCTGTCCTCCGTGATG 61.258 60.000 0.00 0.00 36.25 3.07
354 2233 3.138283 CCTAGGCCCCAAATACTGAATGA 59.862 47.826 0.00 0.00 0.00 2.57
363 2242 0.709992 TTTGCTCCTAGGCCCCAAAT 59.290 50.000 2.96 0.00 0.00 2.32
502 2388 0.040067 GCACGGCCTTCTTTCTGTTG 60.040 55.000 0.00 0.00 0.00 3.33
543 2429 3.063997 GCAATGATTAGACCGTGACTTGG 59.936 47.826 0.00 0.00 0.00 3.61
581 2467 5.129368 ACCCCACATATTTCAGCTATGTT 57.871 39.130 0.00 0.00 37.64 2.71
584 2470 5.073691 AGCTTACCCCACATATTTCAGCTAT 59.926 40.000 0.00 0.00 33.33 2.97
589 2475 4.165180 TGCTAGCTTACCCCACATATTTCA 59.835 41.667 17.23 0.00 0.00 2.69
595 2481 1.879575 TCTGCTAGCTTACCCCACAT 58.120 50.000 17.23 0.00 0.00 3.21
601 2487 4.442706 TGTTGCTTATCTGCTAGCTTACC 58.557 43.478 17.23 0.00 38.22 2.85
603 2489 6.260936 GGAATTGTTGCTTATCTGCTAGCTTA 59.739 38.462 17.23 4.01 38.22 3.09
618 2504 2.091541 TCGATTGAGGGGAATTGTTGC 58.908 47.619 0.00 0.00 0.00 4.17
628 2514 1.226974 ACACGCGATCGATTGAGGG 60.227 57.895 21.57 16.26 39.41 4.30
657 2545 2.093288 TGATTCTGTCTGCCACCATCTC 60.093 50.000 0.00 0.00 0.00 2.75
668 2556 7.042187 GCATCTTCGTATGATTTGATTCTGTCT 60.042 37.037 0.00 0.00 0.00 3.41
743 2635 2.795329 ACACCTACCATTGCAAGGAAG 58.205 47.619 13.66 9.36 34.34 3.46
759 2651 4.202111 TGCTAAAAGAAAAGCTGGAACACC 60.202 41.667 0.00 0.00 39.53 4.16
812 2705 6.426937 TCCACAAGCTACAAAAGAATGTACTC 59.573 38.462 0.00 0.00 34.75 2.59
816 2709 5.594317 AGTTCCACAAGCTACAAAAGAATGT 59.406 36.000 0.00 0.00 37.32 2.71
927 2823 3.276857 AGCATCGACGGTTCTACTCTAA 58.723 45.455 0.00 0.00 0.00 2.10
930 2826 2.286891 GGTAGCATCGACGGTTCTACTC 60.287 54.545 15.81 4.75 32.49 2.59
964 3022 4.872691 CGTTCAGGCTTATTGAGTCATCTT 59.127 41.667 0.00 0.00 30.26 2.40
975 3033 3.906720 TTAAGCTCCGTTCAGGCTTAT 57.093 42.857 7.32 0.00 44.47 1.73
1021 3079 0.324285 CTCCCTTGCAAGCTCACTCT 59.676 55.000 21.43 0.00 0.00 3.24
1022 3080 1.304509 GCTCCCTTGCAAGCTCACTC 61.305 60.000 21.43 3.69 35.60 3.51
1026 3084 3.808656 GCGCTCCCTTGCAAGCTC 61.809 66.667 21.43 1.18 36.35 4.09
1037 3095 1.299089 GGTGTGTGTTTTGCGCTCC 60.299 57.895 9.73 0.00 0.00 4.70
1050 3108 1.973281 GTGGGGTCATGCTGGTGTG 60.973 63.158 0.00 0.00 0.00 3.82
1065 3129 1.134189 GGAACGGGATTCTAAGGGTGG 60.134 57.143 0.00 0.00 37.48 4.61
1067 3131 1.210538 GGGAACGGGATTCTAAGGGT 58.789 55.000 0.00 0.00 37.48 4.34
1072 3136 1.279846 GTGGTTGGGAACGGGATTCTA 59.720 52.381 0.00 0.00 37.48 2.10
1073 3137 0.037734 GTGGTTGGGAACGGGATTCT 59.962 55.000 0.00 0.00 37.48 2.40
1074 3138 1.303091 CGTGGTTGGGAACGGGATTC 61.303 60.000 0.00 0.00 36.17 2.52
1081 3145 2.519780 TTGGCCGTGGTTGGGAAC 60.520 61.111 0.00 0.00 0.00 3.62
1088 3152 2.102588 GAGTATGATAGTTGGCCGTGGT 59.897 50.000 0.00 0.00 0.00 4.16
1091 3155 2.628657 GAGGAGTATGATAGTTGGCCGT 59.371 50.000 0.00 0.00 0.00 5.68
1093 3157 3.243724 AGGAGGAGTATGATAGTTGGCC 58.756 50.000 0.00 0.00 0.00 5.36
1099 3163 4.325030 GGAGGAGGAGGAGGAGTATGATAG 60.325 54.167 0.00 0.00 0.00 2.08
1100 3164 3.594232 GGAGGAGGAGGAGGAGTATGATA 59.406 52.174 0.00 0.00 0.00 2.15
1104 3168 2.070573 GAGGAGGAGGAGGAGGAGTAT 58.929 57.143 0.00 0.00 0.00 2.12
1131 3201 2.617276 CCAGGATCATGTGAGTTGCTGT 60.617 50.000 6.62 0.00 0.00 4.40
1136 3206 0.921896 CCCCCAGGATCATGTGAGTT 59.078 55.000 6.62 0.00 33.47 3.01
1153 3226 1.747355 CTTGATCAACAGCACCATCCC 59.253 52.381 3.38 0.00 0.00 3.85
1156 3229 3.945921 CTCATCTTGATCAACAGCACCAT 59.054 43.478 3.38 0.00 0.00 3.55
1159 3232 2.745821 TGCTCATCTTGATCAACAGCAC 59.254 45.455 16.94 3.67 0.00 4.40
1184 3257 2.497138 CAACTGGCAAGTGTGATCTGA 58.503 47.619 0.00 0.00 36.51 3.27
1186 3259 1.242076 GCAACTGGCAAGTGTGATCT 58.758 50.000 0.00 0.00 43.97 2.75
1199 3272 2.908073 GCACTTGTCGGGGCAACTG 61.908 63.158 0.00 0.00 0.00 3.16
1200 3273 2.594592 GCACTTGTCGGGGCAACT 60.595 61.111 0.00 0.00 0.00 3.16
1254 3327 1.371183 CCTCACGGAAGCAACCTGA 59.629 57.895 0.00 0.00 0.00 3.86
1259 3332 1.302511 GAAGCCCTCACGGAAGCAA 60.303 57.895 0.00 0.00 0.00 3.91
1286 3359 2.151202 GGATTGAAGGAGTCGTTGCAA 58.849 47.619 2.13 0.00 0.00 4.08
1361 3434 1.561542 CAGCTTACCTCCACCCTGATT 59.438 52.381 0.00 0.00 0.00 2.57
1362 3435 1.207791 CAGCTTACCTCCACCCTGAT 58.792 55.000 0.00 0.00 0.00 2.90
1377 3453 8.074370 GTCCTTTATCGAAAAACTAAAACAGCT 58.926 33.333 0.00 0.00 0.00 4.24
1474 3552 2.412870 TGGACTTGTTATCTGTGTGCG 58.587 47.619 0.00 0.00 0.00 5.34
1484 3562 3.278668 TTGGGTCGTTTGGACTTGTTA 57.721 42.857 0.00 0.00 45.35 2.41
1567 3655 1.271840 GGATGGCAGTGTACTCCCCA 61.272 60.000 7.21 7.21 0.00 4.96
1570 3658 1.475751 CCATGGATGGCAGTGTACTCC 60.476 57.143 5.56 0.00 41.75 3.85
1620 3708 6.508030 TTTTATGATGGGTCTACATGGCTA 57.492 37.500 0.00 0.00 0.00 3.93
1635 3723 5.716228 TGGAGGACAACTGCATTTTTATGAT 59.284 36.000 0.00 0.00 43.13 2.45
1636 3724 5.076182 TGGAGGACAACTGCATTTTTATGA 58.924 37.500 0.00 0.00 43.13 2.15
1645 3733 2.116983 GAGGCTGGAGGACAACTGCA 62.117 60.000 0.00 0.00 46.04 4.41
1647 3735 0.036577 CAGAGGCTGGAGGACAACTG 60.037 60.000 0.00 0.00 0.00 3.16
1648 3736 1.835927 GCAGAGGCTGGAGGACAACT 61.836 60.000 0.00 0.00 36.96 3.16
1649 3737 1.376553 GCAGAGGCTGGAGGACAAC 60.377 63.158 0.00 0.00 36.96 3.32
1650 3738 1.834856 CTGCAGAGGCTGGAGGACAA 61.835 60.000 8.42 0.00 44.36 3.18
1705 3810 3.035363 TCATCTCCCGTGCAGGTTATTA 58.965 45.455 5.57 0.00 38.74 0.98
1718 3823 6.515272 AACAATACATGTGTTTCATCTCCC 57.485 37.500 9.11 0.00 42.99 4.30
1748 3855 7.882791 ACATTGTGAGTTACCAGAAATGATGTA 59.117 33.333 0.00 0.00 31.18 2.29
1765 3873 4.445453 TGCCTTATGCTAGACATTGTGAG 58.555 43.478 0.00 0.00 40.38 3.51
1774 3882 3.914984 GCGGATGCCTTATGCTAGA 57.085 52.632 0.00 0.00 42.00 2.43
1788 3990 1.272760 ACATATTTTTGTGGGGGCGGA 60.273 47.619 0.00 0.00 0.00 5.54
1809 4011 6.277605 GGGGTATTGATAAACAATTTTCCGG 58.722 40.000 0.00 0.00 45.60 5.14
1811 4013 5.751509 GCGGGGTATTGATAAACAATTTTCC 59.248 40.000 0.00 0.00 45.60 3.13
1857 4296 1.217882 GTATCGCCATGTAGTGCACC 58.782 55.000 14.63 0.00 0.00 5.01
1871 4311 7.276658 AGTTCAAGTAGCTTCAAATCTGTATCG 59.723 37.037 0.00 0.00 0.00 2.92
1960 4402 2.618241 AGCGAAACATCTGTCTTTTGCA 59.382 40.909 8.81 0.00 0.00 4.08
1971 4413 5.732288 CAACTAGCAAGATAGCGAAACATC 58.268 41.667 0.00 0.00 40.15 3.06
2052 4513 5.460646 ACAGCTCCGTGTTAAAAATCATTG 58.539 37.500 0.00 0.00 0.00 2.82
2063 4524 8.276252 ACATTAATTAATTACAGCTCCGTGTT 57.724 30.769 8.01 0.00 31.46 3.32
2100 4561 5.122519 TCTGGCTGCATTAATTTACGATCA 58.877 37.500 0.50 0.00 0.00 2.92
2156 4630 1.888436 AATGAGCTCGAAGGCCGTGA 61.888 55.000 9.64 0.00 39.75 4.35
2175 4649 4.656575 TCACCCTTTCCAACGGATATATCA 59.343 41.667 14.60 0.00 0.00 2.15
2189 4663 3.423154 CGCGCACCTCACCCTTTC 61.423 66.667 8.75 0.00 0.00 2.62
2218 4692 3.701205 TTGGCTGCACATAGAAGAGAA 57.299 42.857 0.50 0.00 0.00 2.87
2223 4697 5.229423 GTTTGATTTTGGCTGCACATAGAA 58.771 37.500 0.50 0.00 0.00 2.10
2257 4731 7.490402 GCCCAACTTCATATTTTGATTCTTCAG 59.510 37.037 0.00 0.00 33.34 3.02
2258 4732 7.039152 TGCCCAACTTCATATTTTGATTCTTCA 60.039 33.333 0.00 0.00 33.34 3.02
2259 4733 7.322664 TGCCCAACTTCATATTTTGATTCTTC 58.677 34.615 0.00 0.00 33.34 2.87
2286 4760 3.838903 ACAGGAGGAACGGACTTATCTTT 59.161 43.478 0.00 0.00 0.00 2.52
2326 4800 3.499737 CCAGCCGACGCCAATGAC 61.500 66.667 0.00 0.00 34.57 3.06
2385 4859 1.138036 CCATGAGTTGCCATGCACG 59.862 57.895 0.00 0.00 41.83 5.34
2528 5005 1.618640 GAACGACGGTGCAAGCTCTC 61.619 60.000 0.00 0.00 0.00 3.20
2529 5006 1.664965 GAACGACGGTGCAAGCTCT 60.665 57.895 0.00 0.00 0.00 4.09
2540 5017 3.918258 TTTTTCTCACTGTGAACGACG 57.082 42.857 12.16 0.00 0.00 5.12
2669 5146 3.159347 GGACGCCCCTCGGGTATT 61.159 66.667 0.55 0.00 46.51 1.89
2769 5248 2.195567 GGCACAAGAGCTGTTGCCA 61.196 57.895 22.55 0.00 44.80 4.92
2898 5390 7.331193 GGCGTAAAATTAAAAGAGAGAGTCTGA 59.669 37.037 0.00 0.00 34.84 3.27
2992 5486 0.447406 CGCGGATTTTGCACTCATCA 59.553 50.000 0.00 0.00 0.00 3.07
3004 5498 2.290641 GCAAGGATACAAATCGCGGATT 59.709 45.455 6.13 1.73 41.41 3.01
3005 5499 1.873591 GCAAGGATACAAATCGCGGAT 59.126 47.619 6.13 0.00 41.41 4.18
3142 5657 5.806654 ATTTGTGCTTACCCAAAATCACT 57.193 34.783 0.00 0.00 34.52 3.41
3167 5682 3.412386 ACAACAAGAACAGTCATAGCCC 58.588 45.455 0.00 0.00 0.00 5.19
3552 6836 1.135803 CATTTCGGCACCAGTTAACCG 60.136 52.381 0.88 0.00 46.97 4.44
3588 6872 0.958091 CTCCAAACATTTCGGCACCA 59.042 50.000 0.00 0.00 0.00 4.17
3615 6901 0.997363 TGGACTCTAAGACCGGGAGA 59.003 55.000 6.32 1.64 32.61 3.71
3654 6940 1.379527 CCATGAGTTTAGTTCCGGGC 58.620 55.000 0.00 0.00 0.00 6.13
3776 7201 9.396022 CTACTCCTTCTGCCTCATAAATAAAAA 57.604 33.333 0.00 0.00 0.00 1.94
3819 7245 1.302832 GTGTGAGGAACCCTGGCTG 60.303 63.158 0.00 0.00 31.76 4.85
3930 7477 5.103000 CCGTCTGACTTTATTGGTCACTAG 58.897 45.833 6.21 0.00 38.57 2.57
4144 7728 0.104120 GTCCCTTGCAACCAAACACC 59.896 55.000 0.00 0.00 0.00 4.16
4148 7732 2.441750 AGTCTAGTCCCTTGCAACCAAA 59.558 45.455 0.00 0.00 0.00 3.28
4203 7787 6.660094 GGACTAGAAAAAGACTCTACTGGAGA 59.340 42.308 0.00 0.00 44.45 3.71
4204 7788 6.127563 GGGACTAGAAAAAGACTCTACTGGAG 60.128 46.154 0.00 0.00 46.87 3.86
4206 7790 5.717654 AGGGACTAGAAAAAGACTCTACTGG 59.282 44.000 0.00 0.00 36.02 4.00
4231 7815 6.473758 ACCAAACAAGAGGGACTTATTCTAC 58.526 40.000 0.00 0.00 41.55 2.59
4247 7831 3.603965 AGTCCCCATGTAACCAAACAA 57.396 42.857 0.00 0.00 32.02 2.83
4292 7877 0.479378 GGGGGTGTTTGGTTACAGGA 59.521 55.000 0.00 0.00 0.00 3.86
4311 7896 1.064906 TCCTACCTCAGGGTCACTACG 60.065 57.143 0.00 0.00 45.98 3.51
4316 7901 3.199442 TGATTTCCTACCTCAGGGTCA 57.801 47.619 0.00 0.00 45.98 4.02
4856 8443 2.430248 TGTCATCGAGGCTACCACTA 57.570 50.000 0.00 0.00 0.00 2.74
5336 8923 2.484889 GCGATCCCTGTCAAACTATCC 58.515 52.381 0.00 0.00 0.00 2.59
5616 9221 3.068024 ACATTTGGCAGTAAACACACAGG 59.932 43.478 0.00 0.00 0.00 4.00
5617 9222 4.305989 ACATTTGGCAGTAAACACACAG 57.694 40.909 0.00 0.00 0.00 3.66
5618 9223 5.300539 ACATACATTTGGCAGTAAACACACA 59.699 36.000 0.00 0.00 0.00 3.72
5730 9336 3.508845 ACTTTTGACCAGCCATAGTGT 57.491 42.857 0.00 0.00 0.00 3.55
5780 9386 6.345565 GCATACATATTAACACGTTCCGACTC 60.346 42.308 0.00 0.00 0.00 3.36
5786 9392 6.426327 TGCATGCATACATATTAACACGTTC 58.574 36.000 18.46 0.00 33.67 3.95
5790 9396 8.800231 TTTGATGCATGCATACATATTAACAC 57.200 30.769 32.27 15.66 36.70 3.32
5827 9433 3.254654 CGATGTACGCGGTGCAGG 61.255 66.667 12.47 0.00 30.87 4.85
5828 9434 2.202557 TCGATGTACGCGGTGCAG 60.203 61.111 12.47 0.00 42.26 4.41
5839 9445 1.476891 ACGTTAGGATGCAGTCGATGT 59.523 47.619 0.00 0.00 0.00 3.06
5843 9449 0.456221 AGGACGTTAGGATGCAGTCG 59.544 55.000 0.00 0.00 33.04 4.18
5844 9450 1.471676 CCAGGACGTTAGGATGCAGTC 60.472 57.143 0.00 0.00 0.00 3.51
5894 9500 6.368779 AGTGTACCAGGAAGCTAAAACATA 57.631 37.500 0.00 0.00 0.00 2.29
6126 9733 2.415512 GCTCTAACAAACGGGATGTCAC 59.584 50.000 0.00 0.00 0.00 3.67
6129 9736 2.851263 TGCTCTAACAAACGGGATGT 57.149 45.000 0.00 0.00 0.00 3.06
6162 9769 6.038356 GCATTTGTGACTCCAAATTAGATGG 58.962 40.000 0.00 0.00 41.79 3.51
6187 9794 4.028490 AAATGGCCCGGTCAGCGA 62.028 61.111 0.00 0.00 0.00 4.93
6199 9806 6.741992 TGTTGTAGATGCTCTAACAAATGG 57.258 37.500 0.00 0.00 29.58 3.16
6201 9808 6.430925 TGCTTGTTGTAGATGCTCTAACAAAT 59.569 34.615 0.00 0.00 32.49 2.32
6229 9836 4.023536 GGCGTTTGTGACTCCAAATTAGAA 60.024 41.667 0.00 0.00 36.75 2.10
6338 9946 9.445786 AACGTGTTTGATAAAATGTCTACAAAG 57.554 29.630 0.00 0.00 0.00 2.77
6362 9970 2.677003 CGGTGACCACGCATCCAAC 61.677 63.158 1.11 0.00 0.00 3.77
6364 9972 3.295304 CTCGGTGACCACGCATCCA 62.295 63.158 1.11 0.00 0.00 3.41
6372 9980 2.710902 CGAGGATGCTCGGTGACCA 61.711 63.158 27.02 0.00 42.51 4.02
6590 10198 3.706373 GAGTTGGCCGAGGCTGGA 61.706 66.667 14.33 0.00 41.60 3.86
6709 10321 2.233566 ACCCTGCCAAGCATCCAGA 61.234 57.895 0.00 0.00 38.13 3.86


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

AutoCloner maintained by Alex Coulton.