Multiple sequence alignment - TraesCS3B01G571400

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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 TraesCS3B01G571400 chr3B 100.000 3603 0 0 1 3603 802997105 803000707 0.000000e+00 6654.0
1 TraesCS3B01G571400 chr3B 90.514 1244 103 9 1447 2678 802929933 802928693 0.000000e+00 1629.0
2 TraesCS3B01G571400 chr3B 74.865 927 204 19 1665 2582 770969755 770968849 9.380000e-106 394.0
3 TraesCS3B01G571400 chr3B 77.563 673 128 17 1922 2584 771533209 771532550 5.640000e-103 385.0
4 TraesCS3B01G571400 chr3B 74.723 902 201 17 1665 2558 771171552 771172434 9.440000e-101 377.0
5 TraesCS3B01G571400 chr3B 90.667 150 10 3 345 494 802932150 802932005 2.840000e-46 196.0
6 TraesCS3B01G571400 chr3B 91.228 114 8 2 494 607 802932055 802931944 1.730000e-33 154.0
7 TraesCS3B01G571400 chr3B 98.039 51 1 0 494 544 802997548 802997598 4.950000e-14 89.8
8 TraesCS3B01G571400 chr3B 98.039 51 1 0 444 494 802997598 802997648 4.950000e-14 89.8
9 TraesCS3B01G571400 chr3D 90.155 2326 158 33 1300 3579 596891247 596888947 0.000000e+00 2961.0
10 TraesCS3B01G571400 chr3D 86.422 626 40 22 618 1230 596891959 596891366 0.000000e+00 643.0
11 TraesCS3B01G571400 chr3D 89.633 463 38 7 35 494 596892544 596892089 6.710000e-162 580.0
12 TraesCS3B01G571400 chr3D 78.149 659 119 19 1922 2569 578243306 578242662 2.610000e-106 396.0
13 TraesCS3B01G571400 chr3D 74.489 929 204 25 1665 2582 577790162 577789256 4.390000e-99 372.0
14 TraesCS3B01G571400 chr3D 73.649 888 184 34 1665 2531 577239466 577240324 7.560000e-77 298.0
15 TraesCS3B01G571400 chr3D 92.500 160 5 2 494 646 596892139 596891980 4.680000e-54 222.0
16 TraesCS3B01G571400 chr3D 86.885 61 7 1 2982 3042 164320952 164320893 2.320000e-07 67.6
17 TraesCS3B01G571400 chr3A 77.424 660 128 16 1880 2530 712553198 712553845 1.220000e-99 374.0
18 TraesCS3B01G571400 chr5A 88.235 51 6 0 2999 3049 448834997 448834947 1.080000e-05 62.1
19 TraesCS3B01G571400 chr2D 81.013 79 11 4 2953 3029 252592294 252592370 3.880000e-05 60.2


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 TraesCS3B01G571400 chr3B 802997105 803000707 3602 False 2277.866667 6654 98.692667 1 3603 3 chr3B.!!$F2 3602
1 TraesCS3B01G571400 chr3B 802928693 802932150 3457 True 659.666667 1629 90.803000 345 2678 3 chr3B.!!$R3 2333
2 TraesCS3B01G571400 chr3B 770968849 770969755 906 True 394.000000 394 74.865000 1665 2582 1 chr3B.!!$R1 917
3 TraesCS3B01G571400 chr3B 771532550 771533209 659 True 385.000000 385 77.563000 1922 2584 1 chr3B.!!$R2 662
4 TraesCS3B01G571400 chr3B 771171552 771172434 882 False 377.000000 377 74.723000 1665 2558 1 chr3B.!!$F1 893
5 TraesCS3B01G571400 chr3D 596888947 596892544 3597 True 1101.500000 2961 89.677500 35 3579 4 chr3D.!!$R4 3544
6 TraesCS3B01G571400 chr3D 578242662 578243306 644 True 396.000000 396 78.149000 1922 2569 1 chr3D.!!$R3 647
7 TraesCS3B01G571400 chr3D 577789256 577790162 906 True 372.000000 372 74.489000 1665 2582 1 chr3D.!!$R2 917
8 TraesCS3B01G571400 chr3D 577239466 577240324 858 False 298.000000 298 73.649000 1665 2531 1 chr3D.!!$F1 866
9 TraesCS3B01G571400 chr3A 712553198 712553845 647 False 374.000000 374 77.424000 1880 2530 1 chr3A.!!$F1 650

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
478 482 0.242825 GTCACCGTTGATCTCACCGA 59.757 55.0 0.0 0.0 33.43 4.69 F
1295 1428 0.040204 CTCCTTTGGCAACCATCCCT 59.960 55.0 0.0 0.0 31.53 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1445 2729 0.541998 TTCTGAGGCCGAGTCAGGAA 60.542 55.000 17.82 9.77 41.62 3.36 R
2628 3941 1.079197 CTATGACACGCCACCTGCA 60.079 57.895 0.00 0.00 41.33 4.41 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
66 67 0.742505 TCGACTTGTGACGTCCACTT 59.257 50.000 14.12 0.07 45.86 3.16
69 70 0.539986 ACTTGTGACGTCCACTTGGT 59.460 50.000 14.12 8.63 45.86 3.67
81 82 3.055719 CTTGGTGGCGAATGGCGT 61.056 61.111 0.00 0.00 44.92 5.68
96 97 4.057615 CGTGATGACGTCCACTCG 57.942 61.111 14.12 14.68 40.91 4.18
105 106 2.504244 GTCCACTCGGAAGCGTCG 60.504 66.667 0.00 0.00 45.20 5.12
132 133 4.142773 TGTGACGGAACACAAAGTTTTCTC 60.143 41.667 9.24 0.00 45.81 2.87
133 134 4.004314 TGACGGAACACAAAGTTTTCTCA 58.996 39.130 0.00 0.00 41.51 3.27
134 135 4.456222 TGACGGAACACAAAGTTTTCTCAA 59.544 37.500 0.00 0.00 41.51 3.02
140 141 7.043656 CGGAACACAAAGTTTTCTCAATAAACC 60.044 37.037 0.00 0.00 41.51 3.27
145 146 7.435192 CACAAAGTTTTCTCAATAAACCTGGTC 59.565 37.037 0.00 0.00 36.40 4.02
148 150 7.654022 AGTTTTCTCAATAAACCTGGTCAAA 57.346 32.000 0.00 0.00 36.40 2.69
152 154 8.885494 TTTCTCAATAAACCTGGTCAAATTTG 57.115 30.769 12.15 12.15 0.00 2.32
203 207 9.838339 GTATCACTATATTATGAAATGGAGGGG 57.162 37.037 0.00 0.00 0.00 4.79
214 218 6.448369 TGAAATGGAGGGGGTATAACTATG 57.552 41.667 0.00 0.00 0.00 2.23
217 221 6.893020 AATGGAGGGGGTATAACTATGATC 57.107 41.667 0.00 0.00 0.00 2.92
218 222 5.363124 TGGAGGGGGTATAACTATGATCA 57.637 43.478 0.00 0.00 0.00 2.92
219 223 5.927465 TGGAGGGGGTATAACTATGATCAT 58.073 41.667 13.81 13.81 0.00 2.45
220 224 5.964477 TGGAGGGGGTATAACTATGATCATC 59.036 44.000 12.53 0.00 0.00 2.92
221 225 5.069251 GGAGGGGGTATAACTATGATCATCG 59.931 48.000 12.53 8.73 0.00 3.84
222 226 5.838955 AGGGGGTATAACTATGATCATCGA 58.161 41.667 12.53 0.00 0.00 3.59
223 227 6.444704 AGGGGGTATAACTATGATCATCGAT 58.555 40.000 12.53 3.17 0.00 3.59
224 228 6.325028 AGGGGGTATAACTATGATCATCGATG 59.675 42.308 19.61 19.61 0.00 3.84
225 229 6.098409 GGGGGTATAACTATGATCATCGATGT 59.902 42.308 24.09 12.20 0.00 3.06
226 230 7.203910 GGGGTATAACTATGATCATCGATGTC 58.796 42.308 24.09 19.60 0.00 3.06
227 231 7.203910 GGGTATAACTATGATCATCGATGTCC 58.796 42.308 24.09 16.77 0.00 4.02
240 244 2.162208 TCGATGTCCACACGTAGTAACC 59.838 50.000 0.00 0.00 41.61 2.85
246 250 4.340666 TGTCCACACGTAGTAACCAGTAAA 59.659 41.667 0.00 0.00 41.61 2.01
315 319 0.802607 GCACGCAGCACCTAGTCTAC 60.803 60.000 0.00 0.00 44.79 2.59
390 394 1.297664 CCCGGTCGACTAGTGACTAG 58.702 60.000 17.61 17.61 39.72 2.57
391 395 1.297664 CCGGTCGACTAGTGACTAGG 58.702 60.000 22.40 17.63 38.30 3.02
395 399 2.015587 GTCGACTAGTGACTAGGGGTG 58.984 57.143 22.40 9.76 38.30 4.61
408 412 3.396611 ACTAGGGGTGCAGGAAACTAAAA 59.603 43.478 0.00 0.00 40.21 1.52
418 422 4.022849 GCAGGAAACTAAAACTGAGCATGT 60.023 41.667 0.00 0.00 40.21 3.21
419 423 5.455392 CAGGAAACTAAAACTGAGCATGTG 58.545 41.667 0.00 0.00 40.21 3.21
471 475 9.915629 ATTATCTTATCTTAGTCACCGTTGATC 57.084 33.333 0.00 0.00 33.11 2.92
472 476 7.589958 ATCTTATCTTAGTCACCGTTGATCT 57.410 36.000 0.00 0.00 33.11 2.75
473 477 7.028926 TCTTATCTTAGTCACCGTTGATCTC 57.971 40.000 0.00 0.00 33.11 2.75
474 478 6.602009 TCTTATCTTAGTCACCGTTGATCTCA 59.398 38.462 0.00 0.00 33.11 3.27
475 479 4.436242 TCTTAGTCACCGTTGATCTCAC 57.564 45.455 0.00 0.00 33.11 3.51
476 480 3.192844 TCTTAGTCACCGTTGATCTCACC 59.807 47.826 0.00 0.00 33.11 4.02
477 481 0.243907 AGTCACCGTTGATCTCACCG 59.756 55.000 0.00 0.00 33.11 4.94
478 482 0.242825 GTCACCGTTGATCTCACCGA 59.757 55.000 0.00 0.00 33.43 4.69
479 483 0.963225 TCACCGTTGATCTCACCGAA 59.037 50.000 0.00 0.00 33.43 4.30
480 484 1.068474 CACCGTTGATCTCACCGAAC 58.932 55.000 0.00 0.00 33.43 3.95
481 485 0.677288 ACCGTTGATCTCACCGAACA 59.323 50.000 0.00 0.00 33.43 3.18
482 486 1.336887 ACCGTTGATCTCACCGAACAG 60.337 52.381 0.00 0.00 33.43 3.16
483 487 1.067846 CCGTTGATCTCACCGAACAGA 60.068 52.381 0.00 0.00 33.43 3.41
484 488 1.986378 CGTTGATCTCACCGAACAGAC 59.014 52.381 0.00 0.00 33.43 3.51
485 489 2.607038 CGTTGATCTCACCGAACAGACA 60.607 50.000 0.00 0.00 33.43 3.41
486 490 3.589988 GTTGATCTCACCGAACAGACAT 58.410 45.455 0.00 0.00 0.00 3.06
487 491 3.236632 TGATCTCACCGAACAGACATG 57.763 47.619 0.00 0.00 0.00 3.21
488 492 2.825532 TGATCTCACCGAACAGACATGA 59.174 45.455 0.00 0.00 0.00 3.07
489 493 2.724977 TCTCACCGAACAGACATGAC 57.275 50.000 0.00 0.00 0.00 3.06
490 494 1.960689 TCTCACCGAACAGACATGACA 59.039 47.619 0.00 0.00 0.00 3.58
491 495 2.364002 TCTCACCGAACAGACATGACAA 59.636 45.455 0.00 0.00 0.00 3.18
492 496 2.476619 CTCACCGAACAGACATGACAAC 59.523 50.000 0.00 0.00 0.00 3.32
493 497 2.102420 TCACCGAACAGACATGACAACT 59.898 45.455 0.00 0.00 0.00 3.16
494 498 3.319689 TCACCGAACAGACATGACAACTA 59.680 43.478 0.00 0.00 0.00 2.24
495 499 4.055360 CACCGAACAGACATGACAACTAA 58.945 43.478 0.00 0.00 0.00 2.24
496 500 4.690748 CACCGAACAGACATGACAACTAAT 59.309 41.667 0.00 0.00 0.00 1.73
497 501 5.179368 CACCGAACAGACATGACAACTAATT 59.821 40.000 0.00 0.00 0.00 1.40
498 502 6.367695 CACCGAACAGACATGACAACTAATTA 59.632 38.462 0.00 0.00 0.00 1.40
499 503 7.064609 CACCGAACAGACATGACAACTAATTAT 59.935 37.037 0.00 0.00 0.00 1.28
500 504 7.277981 ACCGAACAGACATGACAACTAATTATC 59.722 37.037 0.00 0.00 0.00 1.75
501 505 7.492669 CCGAACAGACATGACAACTAATTATCT 59.507 37.037 0.00 0.00 0.00 1.98
502 506 8.873830 CGAACAGACATGACAACTAATTATCTT 58.126 33.333 0.00 0.00 0.00 2.40
588 592 5.935945 TCAAGTTTTGTCAAGGTCCTATCA 58.064 37.500 0.00 0.00 0.00 2.15
590 594 6.486657 TCAAGTTTTGTCAAGGTCCTATCAAG 59.513 38.462 0.00 0.00 0.00 3.02
675 777 5.571784 AGTGCATGTTTGATCGATTCAAT 57.428 34.783 0.00 0.00 43.73 2.57
681 783 8.715088 TGCATGTTTGATCGATTCAATATCTAG 58.285 33.333 0.00 0.00 43.73 2.43
682 784 8.715998 GCATGTTTGATCGATTCAATATCTAGT 58.284 33.333 0.00 0.00 43.73 2.57
692 794 8.285394 TCGATTCAATATCTAGTACGTACCAAC 58.715 37.037 21.80 0.00 0.00 3.77
710 812 2.335316 ACGCCAAGTCCAACAAGTTA 57.665 45.000 0.00 0.00 0.00 2.24
773 883 1.615392 GGTCTGCAACTGGAGCAAATT 59.385 47.619 0.00 0.00 42.17 1.82
774 884 2.819608 GGTCTGCAACTGGAGCAAATTA 59.180 45.455 0.00 0.00 42.17 1.40
778 888 4.158394 TCTGCAACTGGAGCAAATTAATCC 59.842 41.667 0.00 0.00 42.17 3.01
779 889 3.831333 TGCAACTGGAGCAAATTAATCCA 59.169 39.130 6.16 6.16 40.80 3.41
839 954 4.201950 GGCATCTTGGTGTTACATTAGCTG 60.202 45.833 0.00 0.00 0.00 4.24
848 964 7.573710 TGGTGTTACATTAGCTGGAGAAATAT 58.426 34.615 0.00 0.00 0.00 1.28
897 1013 3.244215 TGGAACAAGACACACATCTCTCC 60.244 47.826 0.00 0.00 31.92 3.71
916 1032 5.273208 TCTCCCTATATAAGGCTGGCTAAG 58.727 45.833 3.41 0.00 45.03 2.18
931 1047 2.438392 GGCTAAGGGCTACACTTATGGT 59.562 50.000 0.00 0.00 41.46 3.55
1142 1262 5.577835 TGCAAATTTTATGTAGCATCGACC 58.422 37.500 0.00 0.00 0.00 4.79
1151 1271 7.851387 TTATGTAGCATCGACCATTTGTAAA 57.149 32.000 0.00 0.00 0.00 2.01
1195 1315 4.210724 TCGGTCGATTTCCCAGTAAAAT 57.789 40.909 0.00 0.00 0.00 1.82
1210 1331 7.453126 TCCCAGTAAAATTTGAATAGAAAGCCA 59.547 33.333 0.00 0.00 0.00 4.75
1211 1332 7.545615 CCCAGTAAAATTTGAATAGAAAGCCAC 59.454 37.037 0.00 0.00 0.00 5.01
1212 1333 8.306761 CCAGTAAAATTTGAATAGAAAGCCACT 58.693 33.333 0.00 0.00 0.00 4.00
1224 1346 4.500265 GCCACTGGCTTTCCTTCA 57.500 55.556 13.28 0.00 46.69 3.02
1226 1348 0.813821 GCCACTGGCTTTCCTTCATC 59.186 55.000 13.28 0.00 46.69 2.92
1227 1349 1.467920 CCACTGGCTTTCCTTCATCC 58.532 55.000 0.00 0.00 0.00 3.51
1229 1351 2.363683 CACTGGCTTTCCTTCATCCTC 58.636 52.381 0.00 0.00 0.00 3.71
1242 1364 1.362584 TCATCCTCTTCCTCCACCAGA 59.637 52.381 0.00 0.00 0.00 3.86
1244 1366 3.207549 TCATCCTCTTCCTCCACCAGATA 59.792 47.826 0.00 0.00 0.00 1.98
1254 1376 7.791766 TCTTCCTCCACCAGATATTTCTTCTAT 59.208 37.037 0.00 0.00 0.00 1.98
1258 1391 7.454380 CCTCCACCAGATATTTCTTCTATCTCT 59.546 40.741 0.00 0.00 34.45 3.10
1275 1408 0.112412 TCTTTCTCCACCCTTTGCCC 59.888 55.000 0.00 0.00 0.00 5.36
1282 1415 1.156095 CACCCTTTGCCCCTCCTTT 59.844 57.895 0.00 0.00 0.00 3.11
1284 1417 1.610379 CCCTTTGCCCCTCCTTTGG 60.610 63.158 0.00 0.00 0.00 3.28
1291 1424 1.079073 CCCCTCCTTTGGCAACCAT 59.921 57.895 0.00 0.00 31.53 3.55
1293 1426 0.972471 CCCTCCTTTGGCAACCATCC 60.972 60.000 0.00 0.00 31.53 3.51
1294 1427 0.972471 CCTCCTTTGGCAACCATCCC 60.972 60.000 0.00 0.00 31.53 3.85
1295 1428 0.040204 CTCCTTTGGCAACCATCCCT 59.960 55.000 0.00 0.00 31.53 4.20
1296 1429 1.284785 CTCCTTTGGCAACCATCCCTA 59.715 52.381 0.00 0.00 31.53 3.53
1299 1432 0.780637 TTTGGCAACCATCCCTACCA 59.219 50.000 0.00 0.00 31.53 3.25
1301 1434 1.227383 GGCAACCATCCCTACCAGG 59.773 63.158 0.00 0.00 34.30 4.45
1302 1435 1.453928 GCAACCATCCCTACCAGGC 60.454 63.158 0.00 0.00 32.73 4.85
1303 1436 1.153168 CAACCATCCCTACCAGGCG 60.153 63.158 0.00 0.00 32.73 5.52
1304 1437 1.615424 AACCATCCCTACCAGGCGT 60.615 57.895 0.00 0.00 32.73 5.68
1307 1486 2.838225 ATCCCTACCAGGCGTCCG 60.838 66.667 0.00 0.00 32.73 4.79
1317 1496 4.477975 GGCGTCCGTGTCTCGAGG 62.478 72.222 13.56 0.00 42.86 4.63
1335 1514 4.563524 GAGGACACTCGTTGTTTAATCG 57.436 45.455 0.00 0.00 39.17 3.34
1350 1531 0.879090 AATCGAAGGGGCGTCAAAAC 59.121 50.000 0.00 0.00 0.00 2.43
1378 1559 1.671379 GACCCGAACTTGTGAGCCC 60.671 63.158 0.00 0.00 0.00 5.19
1380 1561 2.359975 CCGAACTTGTGAGCCCCC 60.360 66.667 0.00 0.00 0.00 5.40
1381 1562 2.429930 CGAACTTGTGAGCCCCCA 59.570 61.111 0.00 0.00 0.00 4.96
1383 1564 1.603739 GAACTTGTGAGCCCCCACC 60.604 63.158 0.00 0.00 36.26 4.61
1384 1565 3.146828 AACTTGTGAGCCCCCACCC 62.147 63.158 0.00 0.00 36.26 4.61
1385 1566 3.260100 CTTGTGAGCCCCCACCCT 61.260 66.667 0.00 0.00 36.26 4.34
1386 1567 3.256960 TTGTGAGCCCCCACCCTC 61.257 66.667 0.00 0.00 36.26 4.30
1387 1568 3.810687 TTGTGAGCCCCCACCCTCT 62.811 63.158 0.00 0.00 36.26 3.69
1388 1569 3.403558 GTGAGCCCCCACCCTCTC 61.404 72.222 0.00 0.00 0.00 3.20
1389 1570 4.741239 TGAGCCCCCACCCTCTCC 62.741 72.222 0.00 0.00 0.00 3.71
1390 1571 4.423209 GAGCCCCCACCCTCTCCT 62.423 72.222 0.00 0.00 0.00 3.69
1391 1572 4.423209 AGCCCCCACCCTCTCCTC 62.423 72.222 0.00 0.00 0.00 3.71
1395 1576 3.141488 CCCACCCTCTCCTCGACG 61.141 72.222 0.00 0.00 0.00 5.12
1405 1586 3.129502 CCTCGACGGGCGACACTA 61.130 66.667 0.00 0.00 45.59 2.74
1406 1587 2.478890 CCTCGACGGGCGACACTAT 61.479 63.158 0.00 0.00 45.59 2.12
1409 1590 2.890371 GACGGGCGACACTATGGT 59.110 61.111 0.00 0.00 0.00 3.55
1412 1593 1.226974 CGGGCGACACTATGGTGAG 60.227 63.158 16.98 10.25 45.61 3.51
1415 1596 1.878522 GCGACACTATGGTGAGCCG 60.879 63.158 16.98 15.58 45.61 5.52
1445 2729 2.099921 CGTCTCCGGAGAAATCATGAGT 59.900 50.000 35.18 0.00 39.48 3.41
1449 2733 3.107601 TCCGGAGAAATCATGAGTTCCT 58.892 45.455 27.35 16.94 36.18 3.36
1452 2736 3.868077 CGGAGAAATCATGAGTTCCTGAC 59.132 47.826 27.35 17.50 36.18 3.51
1462 2747 1.216710 GTTCCTGACTCGGCCTCAG 59.783 63.158 12.50 12.50 35.78 3.35
1465 2750 0.324738 TCCTGACTCGGCCTCAGAAT 60.325 55.000 19.43 0.00 37.90 2.40
1468 2753 0.976641 TGACTCGGCCTCAGAATGTT 59.023 50.000 0.00 0.00 37.40 2.71
1475 2760 0.678048 GCCTCAGAATGTTTCCGCCT 60.678 55.000 0.00 0.00 37.40 5.52
1529 2819 8.308207 ACACAAATTAATATTACCGGCAACTTT 58.692 29.630 0.00 0.00 0.00 2.66
1541 2831 3.951680 CCGGCAACTTTTAGATAACCCAT 59.048 43.478 0.00 0.00 0.00 4.00
1543 2833 4.398044 CGGCAACTTTTAGATAACCCATGT 59.602 41.667 0.00 0.00 0.00 3.21
1609 2899 8.907222 ATGCTCCTTAATTGATGTTTTTGTTT 57.093 26.923 0.00 0.00 0.00 2.83
1612 2902 9.045223 GCTCCTTAATTGATGTTTTTGTTTTCT 57.955 29.630 0.00 0.00 0.00 2.52
1620 2910 9.603921 ATTGATGTTTTTGTTTTCTGAATCTGT 57.396 25.926 0.00 0.00 0.00 3.41
1621 2911 9.434420 TTGATGTTTTTGTTTTCTGAATCTGTT 57.566 25.926 0.00 0.00 0.00 3.16
1636 2926 7.939039 TCTGAATCTGTTATCCAAACAAGTTCT 59.061 33.333 12.28 0.00 30.99 3.01
1741 3031 2.874457 GCAACTGTACAAGTCCCGGAAT 60.874 50.000 0.73 0.00 38.56 3.01
1780 3070 4.658786 AACCCGGACCAGGAGGCT 62.659 66.667 0.73 0.00 39.06 4.58
1846 3136 3.379445 GGGCTCGACGAGGTCCAA 61.379 66.667 25.31 0.00 0.00 3.53
2413 3717 2.275418 GGGGCATCGGTGGACAAT 59.725 61.111 0.00 0.00 0.00 2.71
2506 3810 4.439057 AGACGTACATATTCGCCATGTTT 58.561 39.130 0.00 0.00 37.74 2.83
2628 3941 4.110482 GCCGAAAGTCAACGTCTATGTAT 58.890 43.478 0.00 0.00 0.00 2.29
2630 3943 4.026804 CCGAAAGTCAACGTCTATGTATGC 60.027 45.833 0.00 0.00 0.00 3.14
2633 3946 4.046938 AGTCAACGTCTATGTATGCAGG 57.953 45.455 0.00 0.00 0.00 4.85
2680 3996 9.643693 CTTTGCCAGTTGAATAAAAATAGATGT 57.356 29.630 0.00 0.00 0.00 3.06
2718 4034 4.329462 AGCCTATGAACGAATCTTCCTC 57.671 45.455 0.00 0.00 0.00 3.71
2951 4268 3.809905 ACTTCCTTCATCCCGAATTAGC 58.190 45.455 0.00 0.00 31.69 3.09
3091 4435 7.546250 TGTCTAGATCCAGAAGTTTCTTTCT 57.454 36.000 0.00 0.00 37.90 2.52
3155 4499 2.822255 CCCGTGGCGTATGTTGGG 60.822 66.667 0.00 0.00 0.00 4.12
3195 4539 5.491635 TTTGACAACAATTCATCGACACA 57.508 34.783 0.00 0.00 35.85 3.72
3205 4549 6.425114 ACAATTCATCGACACATAGAATAGGC 59.575 38.462 0.00 0.00 0.00 3.93
3206 4550 5.529581 TTCATCGACACATAGAATAGGCA 57.470 39.130 0.00 0.00 0.00 4.75
3255 4599 0.613777 GGAACCTGTCACGGAATCCT 59.386 55.000 0.00 0.00 33.63 3.24
3266 4610 2.766828 CACGGAATCCTCTTAAGGGTCT 59.233 50.000 0.72 0.00 43.56 3.85
3281 4625 2.176798 AGGGTCTGTTTTGATGGGTTGA 59.823 45.455 0.00 0.00 0.00 3.18
3285 4629 4.137543 GTCTGTTTTGATGGGTTGAGAGT 58.862 43.478 0.00 0.00 0.00 3.24
3312 4656 2.190578 GGCATGCTCTTAGCCGGT 59.809 61.111 18.92 0.00 41.51 5.28
3328 4672 1.206132 CCGGTGCTAGGTGTCATGTTA 59.794 52.381 0.00 0.00 0.00 2.41
3333 4677 4.513442 GTGCTAGGTGTCATGTTATGGAA 58.487 43.478 0.00 0.00 0.00 3.53
3350 4694 4.608170 TGGAAGCTCCATAGGGATTTTT 57.392 40.909 0.00 0.00 42.67 1.94
3379 4723 9.575783 TTATTTTTCTATATGCGTTTTTGGACC 57.424 29.630 0.00 0.00 0.00 4.46
3402 4747 6.099701 ACCCTAGAGAATTTGTTTGGCTTTTT 59.900 34.615 0.00 0.00 0.00 1.94
3426 4771 2.610438 TTCGTCTGGTTACCCCTAGT 57.390 50.000 0.00 0.00 0.00 2.57
3439 4785 7.956881 TGGTTACCCCTAGTTTTGGAAAATAAT 59.043 33.333 0.00 0.00 0.00 1.28
3443 4789 7.165485 ACCCCTAGTTTTGGAAAATAATTTGC 58.835 34.615 0.00 0.00 37.38 3.68
3446 4792 7.882791 CCCTAGTTTTGGAAAATAATTTGCCTT 59.117 33.333 2.25 0.00 36.15 4.35
3447 4793 9.936759 CCTAGTTTTGGAAAATAATTTGCCTTA 57.063 29.630 2.25 0.00 36.15 2.69
3567 4916 3.811497 CACATGTTTGCTTCAGAGAGACA 59.189 43.478 0.00 0.00 0.00 3.41
3570 4919 3.872696 TGTTTGCTTCAGAGAGACACAA 58.127 40.909 0.00 0.00 0.00 3.33
3575 4924 3.056304 GCTTCAGAGAGACACAACTGTC 58.944 50.000 0.00 0.00 46.50 3.51
3586 4935 5.162000 GACACAACTGTCCTCTGAAAAAG 57.838 43.478 0.00 0.00 41.06 2.27
3587 4936 4.589908 ACACAACTGTCCTCTGAAAAAGT 58.410 39.130 0.00 0.00 0.00 2.66
3588 4937 5.010282 ACACAACTGTCCTCTGAAAAAGTT 58.990 37.500 0.00 0.00 0.00 2.66
3589 4938 5.476945 ACACAACTGTCCTCTGAAAAAGTTT 59.523 36.000 0.00 0.00 0.00 2.66
3590 4939 6.015434 ACACAACTGTCCTCTGAAAAAGTTTT 60.015 34.615 0.00 0.00 0.00 2.43
3591 4940 6.868339 CACAACTGTCCTCTGAAAAAGTTTTT 59.132 34.615 13.35 13.35 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.161609 GTCGACGCTTCCATCCATTTTT 59.838 45.455 0.00 0.00 0.00 1.94
31 32 1.737793 GTCGACGCTTCCATCCATTTT 59.262 47.619 0.00 0.00 0.00 1.82
32 33 1.066143 AGTCGACGCTTCCATCCATTT 60.066 47.619 10.46 0.00 0.00 2.32
33 34 0.537188 AGTCGACGCTTCCATCCATT 59.463 50.000 10.46 0.00 0.00 3.16
39 40 0.596600 GTCACAAGTCGACGCTTCCA 60.597 55.000 10.46 0.00 0.00 3.53
46 47 2.503256 GTGGACGTCACAAGTCGAC 58.497 57.895 18.91 7.70 45.39 4.20
62 63 2.568090 GCCATTCGCCACCAAGTG 59.432 61.111 0.00 0.00 0.00 3.16
66 67 3.620419 ATCACGCCATTCGCCACCA 62.620 57.895 0.00 0.00 43.23 4.17
69 70 2.106074 GTCATCACGCCATTCGCCA 61.106 57.895 0.00 0.00 43.23 5.69
81 82 0.526211 CTTCCGAGTGGACGTCATCA 59.474 55.000 18.91 3.92 46.45 3.07
90 91 2.473664 AAGTCGACGCTTCCGAGTGG 62.474 60.000 10.46 0.00 39.36 4.00
96 97 2.142641 GTCACAAGTCGACGCTTCC 58.857 57.895 10.46 0.00 0.00 3.46
116 117 8.807581 CAGGTTTATTGAGAAAACTTTGTGTTC 58.192 33.333 0.00 0.00 34.02 3.18
132 133 9.541143 ACTTTACAAATTTGACCAGGTTTATTG 57.459 29.630 24.64 0.00 0.00 1.90
177 179 9.838339 CCCCTCCATTTCATAATATAGTGATAC 57.162 37.037 0.00 0.00 0.00 2.24
178 180 9.003145 CCCCCTCCATTTCATAATATAGTGATA 57.997 37.037 0.00 0.00 0.00 2.15
179 181 7.465563 ACCCCCTCCATTTCATAATATAGTGAT 59.534 37.037 0.00 0.00 0.00 3.06
180 182 6.797540 ACCCCCTCCATTTCATAATATAGTGA 59.202 38.462 0.00 0.00 0.00 3.41
186 190 8.766492 AGTTATACCCCCTCCATTTCATAATA 57.234 34.615 0.00 0.00 0.00 0.98
198 202 5.892119 TCGATGATCATAGTTATACCCCCTC 59.108 44.000 8.54 0.00 0.00 4.30
202 206 7.147897 TGGACATCGATGATCATAGTTATACCC 60.148 40.741 31.33 9.01 0.00 3.69
203 207 7.702772 GTGGACATCGATGATCATAGTTATACC 59.297 40.741 31.33 13.51 0.00 2.73
214 218 2.209838 ACGTGTGGACATCGATGATC 57.790 50.000 31.33 22.06 0.00 2.92
217 221 2.561733 ACTACGTGTGGACATCGATG 57.438 50.000 23.68 23.68 0.00 3.84
218 222 3.181493 GGTTACTACGTGTGGACATCGAT 60.181 47.826 0.00 0.00 0.00 3.59
219 223 2.162208 GGTTACTACGTGTGGACATCGA 59.838 50.000 0.00 0.00 0.00 3.59
220 224 2.095110 TGGTTACTACGTGTGGACATCG 60.095 50.000 0.00 0.00 0.00 3.84
221 225 3.057033 ACTGGTTACTACGTGTGGACATC 60.057 47.826 0.00 0.00 0.00 3.06
222 226 2.895404 ACTGGTTACTACGTGTGGACAT 59.105 45.455 0.00 0.00 0.00 3.06
223 227 2.309613 ACTGGTTACTACGTGTGGACA 58.690 47.619 0.00 0.00 0.00 4.02
224 228 4.503741 TTACTGGTTACTACGTGTGGAC 57.496 45.455 0.00 0.00 0.00 4.02
225 229 4.261994 GGTTTACTGGTTACTACGTGTGGA 60.262 45.833 0.00 0.00 0.00 4.02
226 230 3.989817 GGTTTACTGGTTACTACGTGTGG 59.010 47.826 0.00 0.00 0.00 4.17
227 231 4.619973 TGGTTTACTGGTTACTACGTGTG 58.380 43.478 0.00 0.00 0.00 3.82
240 244 7.485913 CGATTGAAGGAAAATGATGGTTTACTG 59.514 37.037 0.00 0.00 29.31 2.74
246 250 4.094887 CGTCGATTGAAGGAAAATGATGGT 59.905 41.667 0.00 0.00 0.00 3.55
281 285 1.347221 GTGCACGCACGTATTAGCC 59.653 57.895 6.38 0.00 37.19 3.93
315 319 4.092529 CGAGAATGGTTGTTCACATCTCAG 59.907 45.833 7.81 0.00 34.91 3.35
390 394 2.296190 CAGTTTTAGTTTCCTGCACCCC 59.704 50.000 0.00 0.00 0.00 4.95
391 395 3.219281 TCAGTTTTAGTTTCCTGCACCC 58.781 45.455 0.00 0.00 0.00 4.61
395 399 4.022849 ACATGCTCAGTTTTAGTTTCCTGC 60.023 41.667 0.00 0.00 0.00 4.85
408 412 5.503927 ACCTTAAATGATCACATGCTCAGT 58.496 37.500 0.00 0.00 36.79 3.41
418 422 3.130516 ACGAGCTCGACCTTAAATGATCA 59.869 43.478 40.58 0.00 43.02 2.92
419 423 3.707793 ACGAGCTCGACCTTAAATGATC 58.292 45.455 40.58 0.00 43.02 2.92
465 469 3.026630 TGTCTGTTCGGTGAGATCAAC 57.973 47.619 0.00 0.00 0.00 3.18
466 470 3.258123 TCATGTCTGTTCGGTGAGATCAA 59.742 43.478 0.00 0.00 0.00 2.57
467 471 2.825532 TCATGTCTGTTCGGTGAGATCA 59.174 45.455 0.00 0.00 0.00 2.92
468 472 3.182967 GTCATGTCTGTTCGGTGAGATC 58.817 50.000 0.00 0.00 0.00 2.75
469 473 2.562738 TGTCATGTCTGTTCGGTGAGAT 59.437 45.455 0.00 0.00 0.00 2.75
470 474 1.960689 TGTCATGTCTGTTCGGTGAGA 59.039 47.619 0.00 0.00 0.00 3.27
471 475 2.438868 TGTCATGTCTGTTCGGTGAG 57.561 50.000 0.00 0.00 0.00 3.51
472 476 2.102420 AGTTGTCATGTCTGTTCGGTGA 59.898 45.455 0.00 0.00 0.00 4.02
473 477 2.483876 AGTTGTCATGTCTGTTCGGTG 58.516 47.619 0.00 0.00 0.00 4.94
474 478 2.910688 AGTTGTCATGTCTGTTCGGT 57.089 45.000 0.00 0.00 0.00 4.69
475 479 5.862924 AATTAGTTGTCATGTCTGTTCGG 57.137 39.130 0.00 0.00 0.00 4.30
476 480 8.412608 AGATAATTAGTTGTCATGTCTGTTCG 57.587 34.615 0.00 0.00 0.00 3.95
495 499 9.915629 GATCAACGGTGACTAAGATAAGATAAT 57.084 33.333 4.62 0.00 36.31 1.28
496 500 9.132923 AGATCAACGGTGACTAAGATAAGATAA 57.867 33.333 4.62 0.00 36.31 1.75
497 501 8.693120 AGATCAACGGTGACTAAGATAAGATA 57.307 34.615 4.62 0.00 36.31 1.98
498 502 7.285629 TGAGATCAACGGTGACTAAGATAAGAT 59.714 37.037 4.62 0.00 36.31 2.40
499 503 6.602009 TGAGATCAACGGTGACTAAGATAAGA 59.398 38.462 4.62 0.00 36.31 2.10
500 504 6.693545 GTGAGATCAACGGTGACTAAGATAAG 59.306 42.308 4.62 0.00 36.31 1.73
501 505 6.405508 GGTGAGATCAACGGTGACTAAGATAA 60.406 42.308 4.62 0.00 36.31 1.75
502 506 5.067413 GGTGAGATCAACGGTGACTAAGATA 59.933 44.000 4.62 0.00 36.31 1.98
503 507 4.142138 GGTGAGATCAACGGTGACTAAGAT 60.142 45.833 4.62 0.00 36.31 2.40
504 508 3.192844 GGTGAGATCAACGGTGACTAAGA 59.807 47.826 4.62 0.00 36.31 2.10
505 509 3.512680 GGTGAGATCAACGGTGACTAAG 58.487 50.000 4.62 0.00 36.31 2.18
506 510 3.587797 GGTGAGATCAACGGTGACTAA 57.412 47.619 4.62 0.00 36.31 2.24
646 698 6.169419 TCGATCAAACATGCACTTCTTTAG 57.831 37.500 0.00 0.00 0.00 1.85
692 794 1.265905 GGTAACTTGTTGGACTTGGCG 59.734 52.381 0.00 0.00 0.00 5.69
738 848 2.740714 GACCTGCGAACGTGCCATC 61.741 63.158 0.00 0.00 0.00 3.51
773 883 2.308570 AGTGCCACTTGACCATGGATTA 59.691 45.455 21.47 0.37 38.34 1.75
774 884 1.076024 AGTGCCACTTGACCATGGATT 59.924 47.619 21.47 0.00 38.34 3.01
778 888 0.883833 GGAAGTGCCACTTGACCATG 59.116 55.000 16.14 0.00 38.80 3.66
779 889 0.773644 AGGAAGTGCCACTTGACCAT 59.226 50.000 16.14 0.00 38.80 3.55
825 940 9.331282 AGAATATTTCTCCAGCTAATGTAACAC 57.669 33.333 0.00 0.00 34.07 3.32
848 964 4.454504 GCTAACCAGTTCCAAATTCGAGAA 59.545 41.667 0.00 0.00 0.00 2.87
856 972 5.249780 TCCATTAGCTAACCAGTTCCAAA 57.750 39.130 8.70 0.00 0.00 3.28
857 973 4.919774 TCCATTAGCTAACCAGTTCCAA 57.080 40.909 8.70 0.00 0.00 3.53
859 975 4.585879 TGTTCCATTAGCTAACCAGTTCC 58.414 43.478 8.70 0.00 0.00 3.62
897 1013 3.118223 GCCCTTAGCCAGCCTTATATAGG 60.118 52.174 0.00 0.00 40.76 2.57
916 1032 3.626217 GCTTGTTACCATAAGTGTAGCCC 59.374 47.826 0.00 0.00 0.00 5.19
931 1047 3.445450 TGTGCTTTGTTCCTTGCTTGTTA 59.555 39.130 0.00 0.00 0.00 2.41
944 1060 3.426695 GCTCGCTCAAATATGTGCTTTGT 60.427 43.478 2.04 0.00 42.45 2.83
987 1103 4.206477 ACCTCCCATTTTTGCTTAATGC 57.794 40.909 0.00 0.00 43.25 3.56
1120 1240 5.577835 TGGTCGATGCTACATAAAATTTGC 58.422 37.500 0.00 0.00 0.00 3.68
1142 1262 7.692908 ACGTTTTTCAGTCCATTTACAAATG 57.307 32.000 7.56 7.56 44.12 2.32
1151 1271 6.198216 CGATTTGAAAACGTTTTTCAGTCCAT 59.802 34.615 25.86 11.96 39.30 3.41
1210 1331 2.273619 AGAGGATGAAGGAAAGCCAGT 58.726 47.619 0.00 0.00 36.29 4.00
1211 1332 3.277715 GAAGAGGATGAAGGAAAGCCAG 58.722 50.000 0.00 0.00 36.29 4.85
1212 1333 2.025887 GGAAGAGGATGAAGGAAAGCCA 60.026 50.000 0.00 0.00 36.29 4.75
1223 1345 1.871418 TCTGGTGGAGGAAGAGGATG 58.129 55.000 0.00 0.00 0.00 3.51
1224 1346 2.885388 ATCTGGTGGAGGAAGAGGAT 57.115 50.000 0.00 0.00 0.00 3.24
1226 1348 4.657969 AGAAATATCTGGTGGAGGAAGAGG 59.342 45.833 0.00 0.00 33.59 3.69
1227 1349 5.885449 AGAAATATCTGGTGGAGGAAGAG 57.115 43.478 0.00 0.00 33.59 2.85
1229 1351 6.245890 AGAAGAAATATCTGGTGGAGGAAG 57.754 41.667 0.00 0.00 35.59 3.46
1242 1364 8.655901 GGGTGGAGAAAGAGATAGAAGAAATAT 58.344 37.037 0.00 0.00 0.00 1.28
1244 1366 6.676189 AGGGTGGAGAAAGAGATAGAAGAAAT 59.324 38.462 0.00 0.00 0.00 2.17
1254 1376 1.073923 GGCAAAGGGTGGAGAAAGAGA 59.926 52.381 0.00 0.00 0.00 3.10
1258 1391 1.155155 GGGGCAAAGGGTGGAGAAA 59.845 57.895 0.00 0.00 0.00 2.52
1275 1408 0.972471 GGGATGGTTGCCAAAGGAGG 60.972 60.000 0.00 0.00 36.95 4.30
1282 1415 1.570857 CCTGGTAGGGATGGTTGCCA 61.571 60.000 0.00 0.00 35.36 4.92
1284 1417 1.453928 GCCTGGTAGGGATGGTTGC 60.454 63.158 0.00 0.00 35.37 4.17
1286 1419 1.615424 ACGCCTGGTAGGGATGGTT 60.615 57.895 0.00 0.00 35.37 3.67
1287 1420 2.040606 ACGCCTGGTAGGGATGGT 59.959 61.111 0.00 0.00 35.37 3.55
1289 1422 2.822399 GGACGCCTGGTAGGGATG 59.178 66.667 0.00 0.00 35.37 3.51
1291 1424 4.371417 ACGGACGCCTGGTAGGGA 62.371 66.667 0.00 0.00 35.37 4.20
1293 1426 3.352338 GACACGGACGCCTGGTAGG 62.352 68.421 0.00 0.00 38.80 3.18
1294 1427 2.181021 GACACGGACGCCTGGTAG 59.819 66.667 0.00 0.00 0.00 3.18
1295 1428 2.282674 AGACACGGACGCCTGGTA 60.283 61.111 0.00 0.00 0.00 3.25
1296 1429 3.681835 GAGACACGGACGCCTGGT 61.682 66.667 0.00 0.00 0.00 4.00
1299 1432 3.432588 CTCGAGACACGGACGCCT 61.433 66.667 6.58 0.00 42.82 5.52
1301 1434 3.429141 TCCTCGAGACACGGACGC 61.429 66.667 15.71 0.00 42.82 5.19
1302 1435 2.479650 GTCCTCGAGACACGGACG 59.520 66.667 15.71 0.00 45.55 4.79
1317 1496 4.143179 CCCTTCGATTAAACAACGAGTGTC 60.143 45.833 0.00 0.00 40.60 3.67
1322 1501 2.078392 GCCCCTTCGATTAAACAACGA 58.922 47.619 0.00 0.00 0.00 3.85
1335 1514 0.664224 TTTCGTTTTGACGCCCCTTC 59.336 50.000 0.00 0.00 0.00 3.46
1378 1559 3.141488 CGTCGAGGAGAGGGTGGG 61.141 72.222 0.00 0.00 0.00 4.61
1390 1571 2.767445 CCATAGTGTCGCCCGTCGA 61.767 63.158 0.00 0.00 46.29 4.20
1391 1572 2.278596 CCATAGTGTCGCCCGTCG 60.279 66.667 0.00 0.00 40.15 5.12
1392 1573 1.518572 CACCATAGTGTCGCCCGTC 60.519 63.158 0.00 0.00 39.30 4.79
1395 1576 1.521681 GCTCACCATAGTGTCGCCC 60.522 63.158 0.00 0.00 44.83 6.13
1404 1585 3.365291 GACACCGCGGCTCACCATA 62.365 63.158 28.58 0.00 34.57 2.74
1405 1586 4.760047 GACACCGCGGCTCACCAT 62.760 66.667 28.58 0.00 34.57 3.55
1425 2709 3.810310 ACTCATGATTTCTCCGGAGAC 57.190 47.619 33.75 22.19 37.14 3.36
1445 2729 0.541998 TTCTGAGGCCGAGTCAGGAA 60.542 55.000 17.82 9.77 41.62 3.36
1449 2733 0.976641 AACATTCTGAGGCCGAGTCA 59.023 50.000 0.00 0.00 0.00 3.41
1452 2736 1.373570 GGAAACATTCTGAGGCCGAG 58.626 55.000 0.00 0.00 0.00 4.63
1462 2747 3.339141 AGAAGAAGAGGCGGAAACATTC 58.661 45.455 0.00 0.00 0.00 2.67
1465 2750 2.368875 AGAAGAAGAAGAGGCGGAAACA 59.631 45.455 0.00 0.00 0.00 2.83
1468 2753 2.530701 AGAGAAGAAGAAGAGGCGGAA 58.469 47.619 0.00 0.00 0.00 4.30
1501 2790 8.958506 AGTTGCCGGTAATATTAATTTGTGTAA 58.041 29.630 8.64 0.00 0.00 2.41
1520 2810 4.398044 ACATGGGTTATCTAAAAGTTGCCG 59.602 41.667 0.00 0.00 0.00 5.69
1609 2899 8.463930 AACTTGTTTGGATAACAGATTCAGAA 57.536 30.769 0.00 0.00 0.00 3.02
1612 2902 7.719193 TCAGAACTTGTTTGGATAACAGATTCA 59.281 33.333 13.61 0.00 32.67 2.57
1613 2903 8.017946 GTCAGAACTTGTTTGGATAACAGATTC 58.982 37.037 0.00 0.00 0.00 2.52
1614 2904 7.502226 TGTCAGAACTTGTTTGGATAACAGATT 59.498 33.333 0.00 0.00 0.00 2.40
1615 2905 6.998074 TGTCAGAACTTGTTTGGATAACAGAT 59.002 34.615 0.00 0.00 0.00 2.90
1616 2906 6.353323 TGTCAGAACTTGTTTGGATAACAGA 58.647 36.000 0.00 0.00 0.00 3.41
1617 2907 6.618287 TGTCAGAACTTGTTTGGATAACAG 57.382 37.500 0.00 0.00 0.00 3.16
1618 2908 7.581213 AATGTCAGAACTTGTTTGGATAACA 57.419 32.000 0.00 0.00 0.00 2.41
2158 3454 1.339727 GGGTAGACGTTGGCAAGGAAT 60.340 52.381 25.09 14.92 0.00 3.01
2413 3717 1.666553 CTGGTTGTAGTTCCGCGCA 60.667 57.895 8.75 0.00 0.00 6.09
2506 3810 2.289444 CCCTGGCTTCTTGTTCTCGTTA 60.289 50.000 0.00 0.00 0.00 3.18
2628 3941 1.079197 CTATGACACGCCACCTGCA 60.079 57.895 0.00 0.00 41.33 4.41
2630 3943 1.575244 CATCTATGACACGCCACCTG 58.425 55.000 0.00 0.00 0.00 4.00
2633 3946 1.262417 CATGCATCTATGACACGCCAC 59.738 52.381 0.00 0.00 0.00 5.01
2680 3996 1.879380 GGCTACATTGTCACAAGCACA 59.121 47.619 10.56 0.00 34.85 4.57
2785 4102 7.763172 AATGTTCGTTCATTAGTTTTGCAAA 57.237 28.000 8.05 8.05 36.44 3.68
2927 4244 6.497259 AGCTAATTCGGGATGAAGGAAGTATA 59.503 38.462 0.00 0.00 40.65 1.47
2933 4250 2.771943 ACAGCTAATTCGGGATGAAGGA 59.228 45.455 0.00 0.00 40.65 3.36
2951 4268 7.187244 TCGTAGTTAGATAAATCTCCGACAG 57.813 40.000 0.00 0.00 38.32 3.51
3075 4419 8.533569 AAAAATGGTAGAAAGAAACTTCTGGA 57.466 30.769 0.00 0.00 37.65 3.86
3155 4499 2.460757 AAAAAGGCACATGTGATGGC 57.539 45.000 29.80 14.88 42.75 4.40
3176 4520 6.647212 TCTATGTGTCGATGAATTGTTGTC 57.353 37.500 0.00 0.00 0.00 3.18
3190 4534 3.388024 TGGGTCTGCCTATTCTATGTGTC 59.612 47.826 0.00 0.00 34.45 3.67
3193 4537 3.976654 ACATGGGTCTGCCTATTCTATGT 59.023 43.478 0.00 0.00 33.31 2.29
3195 4539 4.220821 CGTACATGGGTCTGCCTATTCTAT 59.779 45.833 0.00 0.00 33.31 1.98
3205 4549 4.920640 ATTACTCTCGTACATGGGTCTG 57.079 45.455 0.00 0.00 0.00 3.51
3206 4550 4.954202 TCAATTACTCTCGTACATGGGTCT 59.046 41.667 0.00 0.00 0.00 3.85
3252 4596 5.514834 CCATCAAAACAGACCCTTAAGAGGA 60.515 44.000 14.70 0.00 46.74 3.71
3255 4599 4.105697 ACCCATCAAAACAGACCCTTAAGA 59.894 41.667 3.36 0.00 0.00 2.10
3266 4610 2.622942 GCACTCTCAACCCATCAAAACA 59.377 45.455 0.00 0.00 0.00 2.83
3312 4656 4.769688 CTTCCATAACATGACACCTAGCA 58.230 43.478 0.00 0.00 0.00 3.49
3315 4659 4.141711 GGAGCTTCCATAACATGACACCTA 60.142 45.833 0.00 0.00 36.28 3.08
3353 4697 9.575783 GGTCCAAAAACGCATATAGAAAAATAA 57.424 29.630 0.00 0.00 0.00 1.40
3354 4698 8.192110 GGGTCCAAAAACGCATATAGAAAAATA 58.808 33.333 0.00 0.00 32.70 1.40
3355 4699 7.039270 GGGTCCAAAAACGCATATAGAAAAAT 58.961 34.615 0.00 0.00 32.70 1.82
3369 4713 6.650427 ACAAATTCTCTAGGGTCCAAAAAC 57.350 37.500 0.00 0.00 0.00 2.43
3370 4714 7.418483 CCAAACAAATTCTCTAGGGTCCAAAAA 60.418 37.037 0.00 0.00 0.00 1.94
3452 4800 6.088824 GTGCCTCTCACAGAAAAACAATATG 58.911 40.000 0.00 0.00 44.98 1.78
3453 4801 6.259550 GTGCCTCTCACAGAAAAACAATAT 57.740 37.500 0.00 0.00 44.98 1.28
3454 4802 5.689383 GTGCCTCTCACAGAAAAACAATA 57.311 39.130 0.00 0.00 44.98 1.90
3455 4803 4.574599 GTGCCTCTCACAGAAAAACAAT 57.425 40.909 0.00 0.00 44.98 2.71
3473 4821 5.860716 GTCTCCATGAGAAGAAAATTTGTGC 59.139 40.000 0.00 0.00 40.59 4.57
3549 4897 3.541996 TGTGTCTCTCTGAAGCAAACA 57.458 42.857 0.00 0.00 0.00 2.83
3567 4916 6.590234 AAAACTTTTTCAGAGGACAGTTGT 57.410 33.333 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.