Multiple sequence alignment - TraesCS4A01G406600

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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 TraesCS4A01G406600 chr4A 100.000 4870 0 0 1 4870 679278205 679273336 0.000000e+00 8994.0
1 TraesCS4A01G406600 chr4A 84.430 456 37 5 25 450 679311087 679310636 7.540000e-113 418.0
2 TraesCS4A01G406600 chr4A 100.000 30 0 0 3 32 679311939 679311910 6.810000e-04 56.5
3 TraesCS4A01G406600 chr4D 91.513 4112 193 78 815 4869 472522791 472518779 0.000000e+00 5517.0
4 TraesCS4A01G406600 chr4D 82.895 456 38 7 29 450 472529867 472529418 1.660000e-99 374.0
5 TraesCS4A01G406600 chr7D 91.250 3897 203 66 789 4635 78505160 78501352 0.000000e+00 5180.0
6 TraesCS4A01G406600 chr7D 87.838 444 42 8 4436 4870 511194450 511194010 1.210000e-140 510.0
7 TraesCS4A01G406600 chr7D 91.176 204 14 3 480 683 78505868 78505669 1.730000e-69 274.0
8 TraesCS4A01G406600 chr7D 86.466 133 16 1 4231 4361 407792828 407792696 1.410000e-30 145.0
9 TraesCS4A01G406600 chr4B 90.778 3524 180 72 785 4244 594875867 594872425 0.000000e+00 4573.0
10 TraesCS4A01G406600 chr4B 88.648 599 51 10 4282 4870 594872422 594871831 0.000000e+00 713.0
11 TraesCS4A01G406600 chr4B 81.235 405 42 19 29 405 594876606 594876208 3.690000e-76 296.0
12 TraesCS4A01G406600 chr4B 90.323 155 8 4 521 674 594876121 594875973 3.850000e-46 196.0
13 TraesCS4A01G406600 chr2B 85.914 930 71 26 865 1768 70753542 70754437 0.000000e+00 937.0
14 TraesCS4A01G406600 chr2B 86.290 124 15 2 997 1119 482740236 482740114 3.060000e-27 134.0
15 TraesCS4A01G406600 chr3D 87.640 445 42 8 4436 4870 581945332 581944891 5.630000e-139 505.0
16 TraesCS4A01G406600 chr3D 88.550 131 15 0 4231 4361 464061401 464061271 5.050000e-35 159.0
17 TraesCS4A01G406600 chr6A 82.129 263 36 10 191 450 54413761 54414015 1.060000e-51 215.0
18 TraesCS4A01G406600 chr6A 89.796 49 5 0 38 86 459599842 459599890 4.070000e-06 63.9
19 TraesCS4A01G406600 chr5D 81.739 230 38 2 2324 2553 190271580 190271355 6.430000e-44 189.0
20 TraesCS4A01G406600 chr5D 88.550 131 15 0 4231 4361 367592008 367591878 5.050000e-35 159.0
21 TraesCS4A01G406600 chr5A 80.932 236 41 2 2318 2553 229524032 229524263 2.990000e-42 183.0
22 TraesCS4A01G406600 chr2D 76.577 333 72 6 3468 3797 406955964 406955635 1.390000e-40 178.0
23 TraesCS4A01G406600 chr2D 89.062 128 14 0 4231 4358 538390887 538391014 5.050000e-35 159.0
24 TraesCS4A01G406600 chr2D 87.097 124 14 2 997 1119 406959626 406959504 6.570000e-29 139.0
25 TraesCS4A01G406600 chr2A 75.976 333 74 6 3468 3797 574976833 574976504 3.020000e-37 167.0
26 TraesCS4A01G406600 chr2A 86.290 124 15 2 997 1119 574980457 574980335 3.060000e-27 134.0
27 TraesCS4A01G406600 chrUn 89.062 128 14 0 4231 4358 477284097 477284224 5.050000e-35 159.0
28 TraesCS4A01G406600 chr5B 87.786 131 16 0 4231 4361 434924098 434923968 2.350000e-33 154.0


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 TraesCS4A01G406600 chr4A 679273336 679278205 4869 True 8994.00 8994 100.000 1 4870 1 chr4A.!!$R1 4869
1 TraesCS4A01G406600 chr4A 679310636 679311939 1303 True 237.25 418 92.215 3 450 2 chr4A.!!$R2 447
2 TraesCS4A01G406600 chr4D 472518779 472522791 4012 True 5517.00 5517 91.513 815 4869 1 chr4D.!!$R1 4054
3 TraesCS4A01G406600 chr7D 78501352 78505868 4516 True 2727.00 5180 91.213 480 4635 2 chr7D.!!$R3 4155
4 TraesCS4A01G406600 chr4B 594871831 594876606 4775 True 1444.50 4573 87.746 29 4870 4 chr4B.!!$R1 4841
5 TraesCS4A01G406600 chr2B 70753542 70754437 895 False 937.00 937 85.914 865 1768 1 chr2B.!!$F1 903

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
697 1620 0.034089 CCTTGAAATCCGAGCCCCTT 60.034 55.000 0.0 0.0 0.0 3.95 F
780 2101 0.324285 CTCTTCCTTCCTGTGCTGCT 59.676 55.000 0.0 0.0 0.0 4.24 F
854 2227 0.533755 CTCCAAGCCATCCATCCGTC 60.534 60.000 0.0 0.0 0.0 4.79 F
1342 2748 1.079750 GGAGCGAGTGGTGAGGTTC 60.080 63.158 0.0 0.0 0.0 3.62 F
1991 3413 1.977854 AGGCTTATGGTGTGAGTGTGA 59.022 47.619 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1669 3087 1.195448 CACAGAAGTAAAGTGCCTGCG 59.805 52.381 0.0 0.0 0.00 5.18 R
2367 3791 1.347378 TCAGTGTAATCCAGCACAGCA 59.653 47.619 0.0 0.0 38.02 4.41 R
2371 3795 2.417933 CTGCTTCAGTGTAATCCAGCAC 59.582 50.000 0.0 0.0 33.75 4.40 R
2859 4304 2.012673 CCCAGACTGCAATAAGAGCAC 58.987 52.381 0.0 0.0 37.02 4.40 R
3913 5358 0.109723 GCAGTAGGTGTGGGGACAAA 59.890 55.000 0.0 0.0 46.06 2.83 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
122 953 0.381801 TACGACGTCCTATTTCCGCC 59.618 55.000 10.58 0.00 0.00 6.13
150 981 1.990060 CCATGAGGGTCGTCCAGGT 60.990 63.158 0.04 0.00 38.24 4.00
181 1012 1.737793 GTCTTGGATAACACCTTGGCG 59.262 52.381 0.00 0.00 0.00 5.69
182 1013 1.094785 CTTGGATAACACCTTGGCGG 58.905 55.000 0.00 0.00 39.35 6.13
193 1052 1.361668 CCTTGGCGGTCTGATGTTCG 61.362 60.000 0.00 0.00 0.00 3.95
198 1057 1.970917 GCGGTCTGATGTTCGGCAAG 61.971 60.000 0.00 0.00 0.00 4.01
200 1059 1.403647 CGGTCTGATGTTCGGCAAGTA 60.404 52.381 0.00 0.00 0.00 2.24
205 1064 1.804151 TGATGTTCGGCAAGTAACAGC 59.196 47.619 0.00 0.00 41.24 4.40
264 1123 6.998673 GGATGGGCAATACTACTGAAAACTAT 59.001 38.462 0.00 0.00 0.00 2.12
333 1192 1.738099 CTGCTCCTTTGCGTACGCT 60.738 57.895 36.99 0.00 42.51 5.07
334 1193 0.457853 CTGCTCCTTTGCGTACGCTA 60.458 55.000 36.99 29.17 42.51 4.26
335 1194 0.174845 TGCTCCTTTGCGTACGCTAT 59.825 50.000 36.99 0.00 42.51 2.97
336 1195 1.406180 TGCTCCTTTGCGTACGCTATA 59.594 47.619 36.99 21.39 42.51 1.31
337 1196 2.035449 TGCTCCTTTGCGTACGCTATAT 59.965 45.455 36.99 0.00 42.51 0.86
376 1235 9.970395 GCTCCATCAACATTAATTTTCATCATA 57.030 29.630 0.00 0.00 0.00 2.15
382 1241 6.084326 ACATTAATTTTCATCATACCCGCC 57.916 37.500 0.00 0.00 0.00 6.13
420 1279 2.521708 AGCCGCAAACCAGCCTTT 60.522 55.556 0.00 0.00 0.00 3.11
421 1280 2.356194 GCCGCAAACCAGCCTTTG 60.356 61.111 0.00 0.00 34.71 2.77
425 1284 0.385390 CGCAAACCAGCCTTTGAGTT 59.615 50.000 3.84 0.00 33.61 3.01
428 1287 2.884639 GCAAACCAGCCTTTGAGTTCTA 59.115 45.455 3.84 0.00 33.61 2.10
433 1294 2.354259 CAGCCTTTGAGTTCTAGCTGG 58.646 52.381 0.00 0.00 43.05 4.85
440 1301 2.729194 TGAGTTCTAGCTGGGAGACTC 58.271 52.381 16.48 16.48 0.00 3.36
445 1306 2.370349 TCTAGCTGGGAGACTCTTTCG 58.630 52.381 1.74 0.00 0.00 3.46
450 1311 2.184579 GGAGACTCTTTCGCCGGG 59.815 66.667 2.18 0.00 34.05 5.73
451 1312 2.509561 GAGACTCTTTCGCCGGGC 60.510 66.667 9.54 9.54 0.00 6.13
452 1313 3.296709 GAGACTCTTTCGCCGGGCA 62.297 63.158 20.71 3.24 0.00 5.36
453 1314 2.125106 GACTCTTTCGCCGGGCAT 60.125 61.111 20.71 0.00 0.00 4.40
454 1315 2.436646 ACTCTTTCGCCGGGCATG 60.437 61.111 20.71 3.40 0.00 4.06
455 1316 3.204827 CTCTTTCGCCGGGCATGG 61.205 66.667 20.71 2.57 0.00 3.66
456 1317 3.976701 CTCTTTCGCCGGGCATGGT 62.977 63.158 20.71 0.00 0.00 3.55
457 1318 3.814268 CTTTCGCCGGGCATGGTG 61.814 66.667 20.71 1.74 40.98 4.17
458 1319 4.337177 TTTCGCCGGGCATGGTGA 62.337 61.111 20.71 4.50 46.43 4.02
463 1324 3.402681 CCGGGCATGGTGAGGACT 61.403 66.667 0.00 0.00 0.00 3.85
464 1325 2.671070 CGGGCATGGTGAGGACTT 59.329 61.111 0.00 0.00 0.00 3.01
465 1326 1.002134 CGGGCATGGTGAGGACTTT 60.002 57.895 0.00 0.00 0.00 2.66
466 1327 1.308069 CGGGCATGGTGAGGACTTTG 61.308 60.000 0.00 0.00 0.00 2.77
467 1328 0.038166 GGGCATGGTGAGGACTTTGA 59.962 55.000 0.00 0.00 0.00 2.69
468 1329 1.547675 GGGCATGGTGAGGACTTTGAA 60.548 52.381 0.00 0.00 0.00 2.69
469 1330 2.238521 GGCATGGTGAGGACTTTGAAA 58.761 47.619 0.00 0.00 0.00 2.69
470 1331 2.827921 GGCATGGTGAGGACTTTGAAAT 59.172 45.455 0.00 0.00 0.00 2.17
471 1332 3.367703 GGCATGGTGAGGACTTTGAAATG 60.368 47.826 0.00 0.00 0.00 2.32
472 1333 3.841643 CATGGTGAGGACTTTGAAATGC 58.158 45.455 0.00 0.00 0.00 3.56
473 1334 3.228188 TGGTGAGGACTTTGAAATGCT 57.772 42.857 0.00 0.00 0.00 3.79
474 1335 2.886523 TGGTGAGGACTTTGAAATGCTG 59.113 45.455 0.00 0.00 0.00 4.41
475 1336 3.149196 GGTGAGGACTTTGAAATGCTGA 58.851 45.455 0.00 0.00 0.00 4.26
476 1337 3.760684 GGTGAGGACTTTGAAATGCTGAT 59.239 43.478 0.00 0.00 0.00 2.90
477 1338 4.219288 GGTGAGGACTTTGAAATGCTGATT 59.781 41.667 0.00 0.00 0.00 2.57
478 1339 5.397326 GTGAGGACTTTGAAATGCTGATTC 58.603 41.667 0.00 0.00 0.00 2.52
486 1347 4.929819 TGAAATGCTGATTCATGGATGG 57.070 40.909 0.00 0.00 32.10 3.51
497 1358 2.858745 TCATGGATGGATGATGTGCTG 58.141 47.619 0.00 0.00 0.00 4.41
519 1380 6.073440 GCTGGTAGTGATTTAAAACGTCTTGA 60.073 38.462 0.00 0.00 0.00 3.02
527 1449 8.679385 GTGATTTAAAACGTCTTGAAAAGTAGC 58.321 33.333 0.00 0.00 46.34 3.58
544 1466 4.053295 AGTAGCACAAAACGTCACGTAAT 58.947 39.130 1.57 0.00 39.99 1.89
545 1467 5.221880 AGTAGCACAAAACGTCACGTAATA 58.778 37.500 1.57 0.00 39.99 0.98
559 1481 6.406042 CGTCACGTAATAAGGATTTTTAACGC 59.594 38.462 0.00 0.00 0.00 4.84
683 1606 1.112113 GATAGACACGAGCCCCTTGA 58.888 55.000 0.00 0.00 0.00 3.02
684 1607 1.480954 GATAGACACGAGCCCCTTGAA 59.519 52.381 0.00 0.00 0.00 2.69
685 1608 1.344065 TAGACACGAGCCCCTTGAAA 58.656 50.000 0.00 0.00 0.00 2.69
686 1609 0.693049 AGACACGAGCCCCTTGAAAT 59.307 50.000 0.00 0.00 0.00 2.17
687 1610 1.087501 GACACGAGCCCCTTGAAATC 58.912 55.000 0.00 0.00 0.00 2.17
688 1611 0.322546 ACACGAGCCCCTTGAAATCC 60.323 55.000 0.00 0.00 0.00 3.01
689 1612 1.078426 ACGAGCCCCTTGAAATCCG 60.078 57.895 0.00 0.00 0.00 4.18
690 1613 1.220749 CGAGCCCCTTGAAATCCGA 59.779 57.895 0.00 0.00 0.00 4.55
691 1614 0.811616 CGAGCCCCTTGAAATCCGAG 60.812 60.000 0.00 0.00 0.00 4.63
692 1615 1.077429 AGCCCCTTGAAATCCGAGC 60.077 57.895 0.00 0.00 0.00 5.03
693 1616 2.121538 GCCCCTTGAAATCCGAGCC 61.122 63.158 0.00 0.00 0.00 4.70
694 1617 1.453928 CCCCTTGAAATCCGAGCCC 60.454 63.158 0.00 0.00 0.00 5.19
695 1618 1.453928 CCCTTGAAATCCGAGCCCC 60.454 63.158 0.00 0.00 0.00 5.80
696 1619 1.609783 CCTTGAAATCCGAGCCCCT 59.390 57.895 0.00 0.00 0.00 4.79
697 1620 0.034089 CCTTGAAATCCGAGCCCCTT 60.034 55.000 0.00 0.00 0.00 3.95
698 1621 1.211949 CCTTGAAATCCGAGCCCCTTA 59.788 52.381 0.00 0.00 0.00 2.69
730 2051 0.597637 CATGGGTCGGTCGCAGATAC 60.598 60.000 0.00 0.00 42.07 2.24
764 2085 3.394836 GCAGCGTCCCCTTCCTCT 61.395 66.667 0.00 0.00 0.00 3.69
765 2086 2.960688 GCAGCGTCCCCTTCCTCTT 61.961 63.158 0.00 0.00 0.00 2.85
766 2087 1.219393 CAGCGTCCCCTTCCTCTTC 59.781 63.158 0.00 0.00 0.00 2.87
768 2089 1.990614 GCGTCCCCTTCCTCTTCCT 60.991 63.158 0.00 0.00 0.00 3.36
769 2090 1.554583 GCGTCCCCTTCCTCTTCCTT 61.555 60.000 0.00 0.00 0.00 3.36
770 2091 0.537653 CGTCCCCTTCCTCTTCCTTC 59.462 60.000 0.00 0.00 0.00 3.46
771 2092 0.913205 GTCCCCTTCCTCTTCCTTCC 59.087 60.000 0.00 0.00 0.00 3.46
772 2093 0.800239 TCCCCTTCCTCTTCCTTCCT 59.200 55.000 0.00 0.00 0.00 3.36
774 2095 1.662686 CCCTTCCTCTTCCTTCCTGT 58.337 55.000 0.00 0.00 0.00 4.00
775 2096 1.280421 CCCTTCCTCTTCCTTCCTGTG 59.720 57.143 0.00 0.00 0.00 3.66
776 2097 1.339535 CCTTCCTCTTCCTTCCTGTGC 60.340 57.143 0.00 0.00 0.00 4.57
777 2098 1.627834 CTTCCTCTTCCTTCCTGTGCT 59.372 52.381 0.00 0.00 0.00 4.40
780 2101 0.324285 CTCTTCCTTCCTGTGCTGCT 59.676 55.000 0.00 0.00 0.00 4.24
781 2102 1.552337 CTCTTCCTTCCTGTGCTGCTA 59.448 52.381 0.00 0.00 0.00 3.49
784 2105 1.451028 CCTTCCTGTGCTGCTAGCC 60.451 63.158 13.29 0.00 41.51 3.93
786 2148 2.189191 CTTCCTGTGCTGCTAGCCCA 62.189 60.000 13.29 6.67 41.51 5.36
787 2149 2.124819 CCTGTGCTGCTAGCCCAG 60.125 66.667 13.29 12.27 44.67 4.45
841 2206 0.887387 TTTCGCCCGTTTCCTCCAAG 60.887 55.000 0.00 0.00 0.00 3.61
854 2227 0.533755 CTCCAAGCCATCCATCCGTC 60.534 60.000 0.00 0.00 0.00 4.79
855 2228 1.526917 CCAAGCCATCCATCCGTCC 60.527 63.158 0.00 0.00 0.00 4.79
856 2229 1.889105 CAAGCCATCCATCCGTCCG 60.889 63.158 0.00 0.00 0.00 4.79
857 2230 2.367202 AAGCCATCCATCCGTCCGT 61.367 57.895 0.00 0.00 0.00 4.69
1284 2687 3.286576 CTTGAATTCGATCTTGCGATGC 58.713 45.455 0.04 0.00 40.35 3.91
1340 2746 3.374402 CGGAGCGAGTGGTGAGGT 61.374 66.667 0.00 0.00 0.00 3.85
1341 2747 2.932234 CGGAGCGAGTGGTGAGGTT 61.932 63.158 0.00 0.00 0.00 3.50
1342 2748 1.079750 GGAGCGAGTGGTGAGGTTC 60.080 63.158 0.00 0.00 0.00 3.62
1414 2829 5.512576 CCTGATGGATGATGAGATGCTGTTA 60.513 44.000 0.00 0.00 34.57 2.41
1416 2831 4.077300 TGGATGATGAGATGCTGTTACC 57.923 45.455 0.00 0.00 0.00 2.85
1427 2842 4.565564 AGATGCTGTTACCGTTTCGATTAC 59.434 41.667 0.00 0.00 0.00 1.89
1428 2843 2.662637 TGCTGTTACCGTTTCGATTACG 59.337 45.455 12.17 12.17 41.26 3.18
1442 2857 5.555190 TCGATTACGATGTTATGCTTTCG 57.445 39.130 0.00 0.00 43.81 3.46
1443 2858 5.275494 TCGATTACGATGTTATGCTTTCGA 58.725 37.500 0.00 0.00 43.81 3.71
1451 2866 4.661993 TGTTATGCTTTCGATGTGTGTC 57.338 40.909 0.00 0.00 0.00 3.67
1452 2867 4.314961 TGTTATGCTTTCGATGTGTGTCT 58.685 39.130 0.00 0.00 0.00 3.41
1460 2875 5.730568 GCTTTCGATGTGTGTCTGAACTTTT 60.731 40.000 0.00 0.00 0.00 2.27
1470 2885 5.163488 TGTGTCTGAACTTTTAACCGAGAGA 60.163 40.000 0.00 0.00 0.00 3.10
1519 2936 3.728373 GGGATTGGGGGCACTCGT 61.728 66.667 0.00 0.00 0.00 4.18
1527 2944 2.124695 GGGCACTCGTGGATTCCC 60.125 66.667 0.00 0.00 0.00 3.97
1566 2983 5.417580 TGAGTTTTGCCCTGTATAATTGACC 59.582 40.000 0.00 0.00 0.00 4.02
1618 3035 8.435982 CAAGGGAGAGGATAATATGTTTTCTCT 58.564 37.037 0.00 0.00 32.34 3.10
1638 3055 9.582431 TTTCTCTATTTGTATTTGTACTCCTCG 57.418 33.333 0.00 0.00 0.00 4.63
1665 3083 7.038729 TGGGATTGGCTAAATTGTTTGTGATTA 60.039 33.333 0.00 0.00 0.00 1.75
1809 3227 3.136763 CAGGTACCATTGCAGCTATCTG 58.863 50.000 15.94 0.00 43.16 2.90
1814 3232 2.751259 ACCATTGCAGCTATCTGTTGTG 59.249 45.455 0.00 0.00 42.29 3.33
1850 3268 3.822735 TCTGCCTCAGTTTCCTTCATTTG 59.177 43.478 0.00 0.00 32.61 2.32
1910 3332 7.448469 ACATATTAAGTCTGAACTGGCACTTTT 59.552 33.333 0.00 0.00 35.36 2.27
1911 3333 8.946085 CATATTAAGTCTGAACTGGCACTTTTA 58.054 33.333 0.00 0.00 35.36 1.52
1912 3334 9.686683 ATATTAAGTCTGAACTGGCACTTTTAT 57.313 29.630 0.00 0.00 35.36 1.40
1913 3335 7.817418 TTAAGTCTGAACTGGCACTTTTATT 57.183 32.000 0.00 0.00 35.36 1.40
1914 3336 8.911918 TTAAGTCTGAACTGGCACTTTTATTA 57.088 30.769 0.00 0.00 35.36 0.98
1918 3340 7.023575 GTCTGAACTGGCACTTTTATTACATG 58.976 38.462 0.00 0.00 0.00 3.21
1957 3379 5.252863 TGGGATTTCCTCTGGTTTATTGAGA 59.747 40.000 0.00 0.00 36.20 3.27
1986 3408 3.133542 TCATCAGAGGCTTATGGTGTGAG 59.866 47.826 3.46 0.00 28.85 3.51
1987 3409 2.540383 TCAGAGGCTTATGGTGTGAGT 58.460 47.619 0.00 0.00 0.00 3.41
1988 3410 2.234661 TCAGAGGCTTATGGTGTGAGTG 59.765 50.000 0.00 0.00 0.00 3.51
1989 3411 2.027745 CAGAGGCTTATGGTGTGAGTGT 60.028 50.000 0.00 0.00 0.00 3.55
1990 3412 2.027745 AGAGGCTTATGGTGTGAGTGTG 60.028 50.000 0.00 0.00 0.00 3.82
1991 3413 1.977854 AGGCTTATGGTGTGAGTGTGA 59.022 47.619 0.00 0.00 0.00 3.58
1992 3414 2.573462 AGGCTTATGGTGTGAGTGTGAT 59.427 45.455 0.00 0.00 0.00 3.06
1993 3415 2.679837 GGCTTATGGTGTGAGTGTGATG 59.320 50.000 0.00 0.00 0.00 3.07
1994 3416 2.096496 GCTTATGGTGTGAGTGTGATGC 59.904 50.000 0.00 0.00 0.00 3.91
1995 3417 2.008752 TATGGTGTGAGTGTGATGCG 57.991 50.000 0.00 0.00 0.00 4.73
2009 3431 5.238432 AGTGTGATGCGTATGTTTCTTGAAA 59.762 36.000 0.00 0.00 0.00 2.69
2046 3469 3.896272 CAGTATCTAGTAACCCCCTGGAC 59.104 52.174 0.00 0.00 34.81 4.02
2085 3508 4.705110 TCAAGAATTTGGACTGTGGAGA 57.295 40.909 0.00 0.00 34.97 3.71
2102 3525 2.572104 GGAGAAAGCCCAGGAGTCTTTA 59.428 50.000 0.00 0.00 30.97 1.85
2232 3655 6.033966 CAGGGTTTGTTTGTGTTTAACTCTC 58.966 40.000 0.00 0.00 27.40 3.20
2286 3709 6.178239 TGCTTTCCTCGTTTATCTTTTAGC 57.822 37.500 0.00 0.00 0.00 3.09
2297 3720 7.064609 TCGTTTATCTTTTAGCCTGAACATCAG 59.935 37.037 0.32 0.32 43.91 2.90
2351 3775 4.691216 GGCCTTCTACTAGTTTCAGTTGTG 59.309 45.833 0.00 0.00 0.00 3.33
2367 3791 9.868277 TTTCAGTTGTGTGATTTGATAAAAGTT 57.132 25.926 0.00 0.00 0.00 2.66
2371 3795 7.436080 AGTTGTGTGATTTGATAAAAGTTGCTG 59.564 33.333 0.00 0.00 0.00 4.41
2385 3809 2.154462 GTTGCTGTGCTGGATTACACT 58.846 47.619 0.00 0.00 37.68 3.55
2397 3821 4.922206 TGGATTACACTGAAGCAGGAATT 58.078 39.130 0.00 0.00 35.51 2.17
2468 3901 6.941436 AGATCAGCAATCAGAAGAAGAAAACT 59.059 34.615 0.00 0.00 36.79 2.66
2641 4086 6.855836 TGTTTTACAGGATGCTCATGAATTC 58.144 36.000 0.00 0.00 42.53 2.17
2725 4170 7.138692 AGAACCTTCTCAAAATTCATCTTCG 57.861 36.000 0.00 0.00 29.94 3.79
2748 4193 6.015350 TCGAATAAGACTTCTAATGGCCCTAG 60.015 42.308 0.00 0.76 0.00 3.02
2782 4227 4.574828 CCCAATGGTAGTCATAAAGAACCG 59.425 45.833 0.00 0.00 34.44 4.44
2785 4230 5.888982 ATGGTAGTCATAAAGAACCGGAT 57.111 39.130 9.46 0.00 33.61 4.18
2842 4287 7.449704 AGTTTTCATCCATTTCTGCCTATATCC 59.550 37.037 0.00 0.00 0.00 2.59
2843 4288 6.708885 TTCATCCATTTCTGCCTATATCCT 57.291 37.500 0.00 0.00 0.00 3.24
2844 4289 6.708885 TCATCCATTTCTGCCTATATCCTT 57.291 37.500 0.00 0.00 0.00 3.36
2856 4301 7.715249 TCTGCCTATATCCTTTTTGTGTATGAC 59.285 37.037 0.00 0.00 0.00 3.06
2859 4304 7.095607 GCCTATATCCTTTTTGTGTATGACTCG 60.096 40.741 0.00 0.00 0.00 4.18
3024 4469 4.708726 AAATAGTTCAATCACCAGCTGC 57.291 40.909 8.66 0.00 0.00 5.25
3111 4556 6.514048 GCTGCAGGTATGTTATTCCATTTCTC 60.514 42.308 17.12 0.00 0.00 2.87
3120 4565 7.465353 TGTTATTCCATTTCTCTTGATTGCA 57.535 32.000 0.00 0.00 0.00 4.08
3137 4582 5.476254 TGATTGCATGTTGTTTCCTCATGTA 59.524 36.000 0.00 0.00 40.40 2.29
3140 4585 6.814644 ATTGCATGTTGTTTCCTCATGTAATG 59.185 34.615 15.57 0.00 45.50 1.90
3144 4589 7.148255 GCATGTTGTTTCCTCATGTAATGTCTA 60.148 37.037 0.00 0.00 46.80 2.59
3177 4622 1.134280 CCTCCTGGTCCACATCATGAC 60.134 57.143 0.00 0.00 0.00 3.06
3647 5092 5.063564 GGTCGACAATTCAGACTTGGAATAC 59.936 44.000 18.91 0.00 34.02 1.89
3743 5188 2.930826 ACCACTGGTTGTTCTTCGAT 57.069 45.000 0.00 0.00 27.29 3.59
3799 5244 0.108615 CAGACATTCTTCGGCTCGGT 60.109 55.000 0.00 0.00 0.00 4.69
3960 5408 7.811236 CCGTGCTATATAGAAGATTCGGTAAAA 59.189 37.037 14.16 0.00 0.00 1.52
4018 5467 0.546122 TGCTTTGGTGGAGTCAGTGT 59.454 50.000 0.00 0.00 0.00 3.55
4146 5606 9.534565 TCGATCTGGAATAATGTTTCTTAAGAG 57.465 33.333 5.12 0.00 0.00 2.85
4322 5787 7.329471 GCCTTCCTTTCTTTGTCATTTGTATTC 59.671 37.037 0.00 0.00 0.00 1.75
4323 5788 8.359642 CCTTCCTTTCTTTGTCATTTGTATTCA 58.640 33.333 0.00 0.00 0.00 2.57
4384 5852 1.745653 GCTAAGCTCCCGAAAATTGCT 59.254 47.619 0.00 0.00 35.30 3.91
4408 5876 7.659390 GCTAGAAGCCAAATTCAGATATGTACT 59.341 37.037 0.00 0.00 34.48 2.73
4415 5883 6.263842 CCAAATTCAGATATGTACTGCCACAT 59.736 38.462 0.00 1.89 41.88 3.21
4416 5884 7.445096 CCAAATTCAGATATGTACTGCCACATA 59.555 37.037 5.64 5.64 43.60 2.29
4417 5885 8.501580 CAAATTCAGATATGTACTGCCACATAG 58.498 37.037 8.36 0.00 42.93 2.23
4495 5963 6.826668 CCACATGGATACTATAAGTGGTGAA 58.173 40.000 0.00 0.00 40.00 3.18
4496 5964 6.931281 CCACATGGATACTATAAGTGGTGAAG 59.069 42.308 0.00 0.00 40.00 3.02
4503 5971 8.880750 GGATACTATAAGTGGTGAAGTTTGTTC 58.119 37.037 0.00 0.00 0.00 3.18
4510 5978 1.673920 GGTGAAGTTTGTTCGGCAAGA 59.326 47.619 0.00 0.00 38.47 3.02
4519 5987 2.554142 TGTTCGGCAAGATAGCATGAG 58.446 47.619 0.00 0.00 35.83 2.90
4540 6009 0.954452 CCCAAGTGAGGAAGCAACAC 59.046 55.000 0.00 0.00 35.15 3.32
4584 6055 1.340399 CCTATCTGGGCAGCTGGACA 61.340 60.000 17.12 0.00 0.00 4.02
4623 6094 0.764369 ACTGTTCTCCTCCAGCCACA 60.764 55.000 0.00 0.00 31.76 4.17
4630 6101 1.072965 CTCCTCCAGCCACAAAGTTCT 59.927 52.381 0.00 0.00 0.00 3.01
4635 6106 1.610522 CCAGCCACAAAGTTCTTCCTG 59.389 52.381 0.00 0.00 0.00 3.86
4636 6107 2.575532 CAGCCACAAAGTTCTTCCTGA 58.424 47.619 0.00 0.00 0.00 3.86
4643 6114 5.534654 CCACAAAGTTCTTCCTGATTACCAA 59.465 40.000 0.00 0.00 0.00 3.67
4648 6119 8.792633 CAAAGTTCTTCCTGATTACCAATACAA 58.207 33.333 0.00 0.00 0.00 2.41
4664 6135 6.897413 ACCAATACAAGCAAGATATTTTCCCT 59.103 34.615 0.00 0.00 0.00 4.20
4707 6179 2.294233 GCACAAGCTCAAACTGGAATCA 59.706 45.455 0.00 0.00 37.91 2.57
4708 6180 3.611057 GCACAAGCTCAAACTGGAATCAG 60.611 47.826 0.00 0.00 41.34 2.90
4718 6191 1.271597 ACTGGAATCAGCAGTTCACCC 60.272 52.381 0.00 0.00 44.59 4.61
4721 6194 2.238521 GGAATCAGCAGTTCACCCAAA 58.761 47.619 0.00 0.00 0.00 3.28
4736 6215 2.203401 CCCAAACGACAACAGTTACGA 58.797 47.619 15.76 0.00 0.00 3.43
4737 6216 2.803956 CCCAAACGACAACAGTTACGAT 59.196 45.455 15.76 4.60 0.00 3.73
4738 6217 3.989167 CCCAAACGACAACAGTTACGATA 59.011 43.478 15.76 0.00 0.00 2.92
4739 6218 4.143263 CCCAAACGACAACAGTTACGATAC 60.143 45.833 15.76 0.00 0.00 2.24
4742 6221 5.756950 AACGACAACAGTTACGATACATG 57.243 39.130 15.76 0.00 0.00 3.21
4753 6232 1.299541 CGATACATGCACTGGGGAAC 58.700 55.000 0.00 0.00 0.00 3.62
4830 6309 3.689347 ACTGGCATAGCAAAGTGAATCA 58.311 40.909 0.00 0.00 0.00 2.57
4837 6316 1.098050 GCAAAGTGAATCATCCGGCT 58.902 50.000 0.00 0.00 0.00 5.52
4838 6317 1.064654 GCAAAGTGAATCATCCGGCTC 59.935 52.381 0.00 0.00 0.00 4.70
4842 6321 1.202734 AGTGAATCATCCGGCTCCATG 60.203 52.381 0.00 0.00 0.00 3.66
4846 6325 2.060567 ATCATCCGGCTCCATGGGTG 62.061 60.000 13.02 6.60 37.73 4.61
4861 6340 0.037232 GGGTGAACGGGAACAGAGAG 60.037 60.000 0.00 0.00 0.00 3.20
4862 6341 0.966920 GGTGAACGGGAACAGAGAGA 59.033 55.000 0.00 0.00 0.00 3.10
4863 6342 1.550976 GGTGAACGGGAACAGAGAGAT 59.449 52.381 0.00 0.00 0.00 2.75
4864 6343 2.028020 GGTGAACGGGAACAGAGAGATT 60.028 50.000 0.00 0.00 0.00 2.40
4866 6345 2.897326 TGAACGGGAACAGAGAGATTCA 59.103 45.455 0.00 0.00 0.00 2.57
4867 6346 3.254892 GAACGGGAACAGAGAGATTCAC 58.745 50.000 0.00 0.00 0.00 3.18
4868 6347 2.530701 ACGGGAACAGAGAGATTCACT 58.469 47.619 0.00 0.00 0.00 3.41
4869 6348 2.232452 ACGGGAACAGAGAGATTCACTG 59.768 50.000 2.60 2.60 40.27 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.991606 CCTTCTTGAAGTACACATGAACTCA 59.008 40.000 0.00 0.00 31.54 3.41
1 2 5.106908 GCCTTCTTGAAGTACACATGAACTC 60.107 44.000 0.00 7.69 31.54 3.01
36 867 7.858052 ATTTTAGTTTTGAAGCTCACAATCG 57.142 32.000 7.04 0.00 0.00 3.34
122 953 0.395686 ACCCTCATGGAGCGATCATG 59.604 55.000 1.84 4.93 42.28 3.07
150 981 4.224147 TGTTATCCAAGACAATCTTCGGGA 59.776 41.667 1.38 1.38 33.78 5.14
181 1012 2.380084 TACTTGCCGAACATCAGACC 57.620 50.000 0.00 0.00 0.00 3.85
182 1013 3.064207 TGTTACTTGCCGAACATCAGAC 58.936 45.455 0.00 0.00 30.72 3.51
193 1052 1.502190 GGAAGCGCTGTTACTTGCC 59.498 57.895 12.58 0.00 0.00 4.52
198 1057 0.739813 ATGTCGGGAAGCGCTGTTAC 60.740 55.000 12.58 6.17 0.00 2.50
200 1059 2.034879 CATGTCGGGAAGCGCTGTT 61.035 57.895 12.58 0.00 0.00 3.16
205 1064 0.523968 CATTTGCATGTCGGGAAGCG 60.524 55.000 0.00 0.00 0.00 4.68
264 1123 1.938585 CTACCTTGGGTCCTCACTGA 58.061 55.000 0.00 0.00 37.09 3.41
326 1185 7.432545 AGCTTTTGAGCATATATATAGCGTACG 59.567 37.037 11.84 11.84 37.25 3.67
334 1193 8.954350 GTTGATGGAGCTTTTGAGCATATATAT 58.046 33.333 0.88 0.00 37.25 0.86
335 1194 7.938490 TGTTGATGGAGCTTTTGAGCATATATA 59.062 33.333 0.88 0.00 37.25 0.86
336 1195 6.774170 TGTTGATGGAGCTTTTGAGCATATAT 59.226 34.615 0.88 0.00 37.25 0.86
337 1196 6.121590 TGTTGATGGAGCTTTTGAGCATATA 58.878 36.000 0.88 0.00 37.25 0.86
420 1279 2.310349 AGAGTCTCCCAGCTAGAACTCA 59.690 50.000 19.05 0.00 0.00 3.41
421 1280 3.012934 AGAGTCTCCCAGCTAGAACTC 57.987 52.381 0.00 14.04 0.00 3.01
425 1284 2.370349 CGAAAGAGTCTCCCAGCTAGA 58.630 52.381 0.00 0.00 0.00 2.43
428 1287 1.594310 GCGAAAGAGTCTCCCAGCT 59.406 57.895 0.00 0.00 0.00 4.24
433 1294 2.184579 CCCGGCGAAAGAGTCTCC 59.815 66.667 9.30 0.00 0.00 3.71
440 1301 3.814268 CACCATGCCCGGCGAAAG 61.814 66.667 9.30 0.00 0.00 2.62
450 1311 3.841643 CATTTCAAAGTCCTCACCATGC 58.158 45.455 0.00 0.00 0.00 4.06
451 1312 3.508793 AGCATTTCAAAGTCCTCACCATG 59.491 43.478 0.00 0.00 0.00 3.66
452 1313 3.508793 CAGCATTTCAAAGTCCTCACCAT 59.491 43.478 0.00 0.00 0.00 3.55
453 1314 2.886523 CAGCATTTCAAAGTCCTCACCA 59.113 45.455 0.00 0.00 0.00 4.17
454 1315 3.149196 TCAGCATTTCAAAGTCCTCACC 58.851 45.455 0.00 0.00 0.00 4.02
455 1316 5.048504 TGAATCAGCATTTCAAAGTCCTCAC 60.049 40.000 0.00 0.00 30.44 3.51
456 1317 5.072055 TGAATCAGCATTTCAAAGTCCTCA 58.928 37.500 0.00 0.00 30.44 3.86
457 1318 5.633830 TGAATCAGCATTTCAAAGTCCTC 57.366 39.130 0.00 0.00 30.44 3.71
458 1319 5.105473 CCATGAATCAGCATTTCAAAGTCCT 60.105 40.000 0.00 0.00 36.72 3.85
459 1320 5.105635 TCCATGAATCAGCATTTCAAAGTCC 60.106 40.000 0.00 0.00 36.72 3.85
460 1321 5.957798 TCCATGAATCAGCATTTCAAAGTC 58.042 37.500 0.00 0.00 36.72 3.01
461 1322 5.988310 TCCATGAATCAGCATTTCAAAGT 57.012 34.783 0.00 0.00 36.72 2.66
462 1323 5.753438 CCATCCATGAATCAGCATTTCAAAG 59.247 40.000 0.00 0.00 36.72 2.77
463 1324 5.422650 TCCATCCATGAATCAGCATTTCAAA 59.577 36.000 0.00 0.00 36.72 2.69
464 1325 4.957327 TCCATCCATGAATCAGCATTTCAA 59.043 37.500 0.00 0.00 36.72 2.69
465 1326 4.538738 TCCATCCATGAATCAGCATTTCA 58.461 39.130 0.00 0.00 37.49 2.69
466 1327 5.243060 TCATCCATCCATGAATCAGCATTTC 59.757 40.000 0.00 0.00 29.41 2.17
467 1328 5.144832 TCATCCATCCATGAATCAGCATTT 58.855 37.500 0.00 0.00 29.41 2.32
468 1329 4.736473 TCATCCATCCATGAATCAGCATT 58.264 39.130 0.00 0.00 29.41 3.56
469 1330 4.382386 TCATCCATCCATGAATCAGCAT 57.618 40.909 0.00 0.00 29.41 3.79
470 1331 3.868619 TCATCCATCCATGAATCAGCA 57.131 42.857 0.00 0.00 29.41 4.41
471 1332 4.079970 ACATCATCCATCCATGAATCAGC 58.920 43.478 0.00 0.00 36.36 4.26
472 1333 4.082733 GCACATCATCCATCCATGAATCAG 60.083 45.833 0.00 0.00 36.36 2.90
473 1334 3.824443 GCACATCATCCATCCATGAATCA 59.176 43.478 0.00 0.00 36.36 2.57
474 1335 4.079970 AGCACATCATCCATCCATGAATC 58.920 43.478 0.00 0.00 36.36 2.52
475 1336 3.826729 CAGCACATCATCCATCCATGAAT 59.173 43.478 0.00 0.00 36.36 2.57
476 1337 3.219281 CAGCACATCATCCATCCATGAA 58.781 45.455 0.00 0.00 36.36 2.57
477 1338 2.488347 CCAGCACATCATCCATCCATGA 60.488 50.000 0.00 0.00 37.20 3.07
478 1339 1.886542 CCAGCACATCATCCATCCATG 59.113 52.381 0.00 0.00 0.00 3.66
486 1347 6.925610 TTAAATCACTACCAGCACATCATC 57.074 37.500 0.00 0.00 0.00 2.92
497 1358 9.166126 CTTTTCAAGACGTTTTAAATCACTACC 57.834 33.333 0.00 0.00 0.00 3.18
519 1380 3.125658 ACGTGACGTTTTGTGCTACTTTT 59.874 39.130 4.10 0.00 36.35 2.27
525 1447 4.084223 CCTTATTACGTGACGTTTTGTGCT 60.084 41.667 18.28 0.00 41.54 4.40
527 1449 5.579384 TCCTTATTACGTGACGTTTTGTG 57.421 39.130 18.28 4.58 41.54 3.33
544 1466 2.162008 GCCACGGCGTTAAAAATCCTTA 59.838 45.455 11.19 0.00 0.00 2.69
545 1467 1.068125 GCCACGGCGTTAAAAATCCTT 60.068 47.619 11.19 0.00 0.00 3.36
683 1606 0.837940 GGAGTAAGGGGCTCGGATTT 59.162 55.000 0.00 0.00 34.00 2.17
684 1607 1.054978 GGGAGTAAGGGGCTCGGATT 61.055 60.000 0.00 0.00 34.00 3.01
685 1608 1.459730 GGGAGTAAGGGGCTCGGAT 60.460 63.158 0.00 0.00 34.00 4.18
686 1609 2.042230 GGGAGTAAGGGGCTCGGA 60.042 66.667 0.00 0.00 34.00 4.55
687 1610 1.766461 ATGGGAGTAAGGGGCTCGG 60.766 63.158 0.00 0.00 34.00 4.63
688 1611 1.048724 TCATGGGAGTAAGGGGCTCG 61.049 60.000 0.00 0.00 34.00 5.03
689 1612 0.470341 GTCATGGGAGTAAGGGGCTC 59.530 60.000 0.00 0.00 0.00 4.70
690 1613 1.338136 CGTCATGGGAGTAAGGGGCT 61.338 60.000 0.00 0.00 0.00 5.19
691 1614 1.146263 CGTCATGGGAGTAAGGGGC 59.854 63.158 0.00 0.00 0.00 5.80
692 1615 0.464452 GTCGTCATGGGAGTAAGGGG 59.536 60.000 0.00 0.00 0.00 4.79
693 1616 1.191535 TGTCGTCATGGGAGTAAGGG 58.808 55.000 0.00 0.00 0.00 3.95
694 1617 2.826428 CATGTCGTCATGGGAGTAAGG 58.174 52.381 13.92 0.00 45.30 2.69
756 2077 1.339535 GCACAGGAAGGAAGAGGAAGG 60.340 57.143 0.00 0.00 0.00 3.46
758 2079 1.349026 CAGCACAGGAAGGAAGAGGAA 59.651 52.381 0.00 0.00 0.00 3.36
762 2083 1.552337 CTAGCAGCACAGGAAGGAAGA 59.448 52.381 0.00 0.00 0.00 2.87
764 2085 0.036010 GCTAGCAGCACAGGAAGGAA 60.036 55.000 10.63 0.00 41.89 3.36
765 2086 1.599047 GCTAGCAGCACAGGAAGGA 59.401 57.895 10.63 0.00 41.89 3.36
766 2087 1.451028 GGCTAGCAGCACAGGAAGG 60.451 63.158 18.24 0.00 44.75 3.46
768 2089 2.671070 GGGCTAGCAGCACAGGAA 59.329 61.111 18.24 0.00 45.95 3.36
806 2168 2.515912 CGAAATAAAAAGGGAGCGTGC 58.484 47.619 0.00 0.00 0.00 5.34
812 2174 2.203470 ACGGGCGAAATAAAAAGGGA 57.797 45.000 0.00 0.00 0.00 4.20
813 2175 3.247442 GAAACGGGCGAAATAAAAAGGG 58.753 45.455 0.00 0.00 0.00 3.95
841 2206 2.280186 GACGGACGGATGGATGGC 60.280 66.667 0.00 0.00 0.00 4.40
854 2227 0.912486 AGGAGGAAGAAATGGGACGG 59.088 55.000 0.00 0.00 0.00 4.79
855 2228 2.014068 GCAGGAGGAAGAAATGGGACG 61.014 57.143 0.00 0.00 0.00 4.79
856 2229 1.283321 AGCAGGAGGAAGAAATGGGAC 59.717 52.381 0.00 0.00 0.00 4.46
857 2230 1.561542 GAGCAGGAGGAAGAAATGGGA 59.438 52.381 0.00 0.00 0.00 4.37
887 2261 4.856801 CTTGGGGATCGGTGGGCG 62.857 72.222 0.00 0.00 0.00 6.13
975 2364 2.350458 CCAACTCCCATTTGCCCGG 61.350 63.158 0.00 0.00 0.00 5.73
1062 2451 0.810016 AGTTCTCGAGGCCGAAGTAC 59.190 55.000 13.56 0.27 45.04 2.73
1162 2551 2.047179 GGCGAAGGAAACGAGGCT 60.047 61.111 0.00 0.00 0.00 4.58
1206 2609 1.209127 CGGGGAACGCATTGAACAC 59.791 57.895 0.00 0.00 43.53 3.32
1284 2687 1.366111 CGCACACAAATCTACCCCGG 61.366 60.000 0.00 0.00 0.00 5.73
1321 2724 4.056125 CTCACCACTCGCTCCGCA 62.056 66.667 0.00 0.00 0.00 5.69
1334 2740 0.959553 TGACTGGACTCGAACCTCAC 59.040 55.000 9.25 2.64 0.00 3.51
1335 2741 1.248486 CTGACTGGACTCGAACCTCA 58.752 55.000 9.25 5.39 0.00 3.86
1337 2743 1.536943 GGCTGACTGGACTCGAACCT 61.537 60.000 9.25 0.00 0.00 3.50
1338 2744 1.079750 GGCTGACTGGACTCGAACC 60.080 63.158 1.87 1.87 0.00 3.62
1339 2745 1.079750 GGGCTGACTGGACTCGAAC 60.080 63.158 0.00 0.00 0.00 3.95
1340 2746 2.283529 GGGGCTGACTGGACTCGAA 61.284 63.158 0.00 0.00 0.00 3.71
1341 2747 2.680352 GGGGCTGACTGGACTCGA 60.680 66.667 0.00 0.00 0.00 4.04
1342 2748 3.775654 GGGGGCTGACTGGACTCG 61.776 72.222 0.00 0.00 0.00 4.18
1388 2803 2.347731 CATCTCATCATCCATCAGGCG 58.652 52.381 0.00 0.00 33.74 5.52
1427 2842 4.201714 ACACACATCGAAAGCATAACATCG 60.202 41.667 0.00 0.00 36.67 3.84
1428 2843 5.063944 AGACACACATCGAAAGCATAACATC 59.936 40.000 0.00 0.00 0.00 3.06
1429 2844 4.937620 AGACACACATCGAAAGCATAACAT 59.062 37.500 0.00 0.00 0.00 2.71
1430 2845 4.152223 CAGACACACATCGAAAGCATAACA 59.848 41.667 0.00 0.00 0.00 2.41
1431 2846 4.388773 TCAGACACACATCGAAAGCATAAC 59.611 41.667 0.00 0.00 0.00 1.89
1432 2847 4.565022 TCAGACACACATCGAAAGCATAA 58.435 39.130 0.00 0.00 0.00 1.90
1433 2848 4.186856 TCAGACACACATCGAAAGCATA 57.813 40.909 0.00 0.00 0.00 3.14
1434 2849 3.044235 TCAGACACACATCGAAAGCAT 57.956 42.857 0.00 0.00 0.00 3.79
1435 2850 2.524569 TCAGACACACATCGAAAGCA 57.475 45.000 0.00 0.00 0.00 3.91
1436 2851 2.802816 AGTTCAGACACACATCGAAAGC 59.197 45.455 0.00 0.00 0.00 3.51
1437 2852 5.409643 AAAGTTCAGACACACATCGAAAG 57.590 39.130 0.00 0.00 0.00 2.62
1438 2853 5.811399 AAAAGTTCAGACACACATCGAAA 57.189 34.783 0.00 0.00 0.00 3.46
1439 2854 6.238266 GGTTAAAAGTTCAGACACACATCGAA 60.238 38.462 0.00 0.00 0.00 3.71
1440 2855 5.235616 GGTTAAAAGTTCAGACACACATCGA 59.764 40.000 0.00 0.00 0.00 3.59
1441 2856 5.440685 GGTTAAAAGTTCAGACACACATCG 58.559 41.667 0.00 0.00 0.00 3.84
1442 2857 5.235616 TCGGTTAAAAGTTCAGACACACATC 59.764 40.000 0.00 0.00 0.00 3.06
1443 2858 5.120399 TCGGTTAAAAGTTCAGACACACAT 58.880 37.500 0.00 0.00 0.00 3.21
1451 2866 5.179368 TGCAATCTCTCGGTTAAAAGTTCAG 59.821 40.000 0.00 0.00 0.00 3.02
1452 2867 5.060506 TGCAATCTCTCGGTTAAAAGTTCA 58.939 37.500 0.00 0.00 0.00 3.18
1460 2875 8.050778 ACATTAAAAATGCAATCTCTCGGTTA 57.949 30.769 0.00 0.00 0.00 2.85
1527 2944 5.391310 GCAAAACTCACACATCAGTCTATGG 60.391 44.000 0.00 0.00 0.00 2.74
1566 2983 7.377928 GTCACAAAGTTTCTGATGAGAACATTG 59.622 37.037 0.00 3.45 37.97 2.82
1618 3035 6.154877 TCCCACGAGGAGTACAAATACAAATA 59.845 38.462 0.00 0.00 40.93 1.40
1638 3055 4.690280 CACAAACAATTTAGCCAATCCCAC 59.310 41.667 0.00 0.00 0.00 4.61
1665 3083 4.122776 CAGAAGTAAAGTGCCTGCGATAT 58.877 43.478 0.00 0.00 0.00 1.63
1669 3087 1.195448 CACAGAAGTAAAGTGCCTGCG 59.805 52.381 0.00 0.00 0.00 5.18
1809 3227 6.705825 AGGCAGAATAAACAATTTTCCACAAC 59.294 34.615 0.00 0.00 0.00 3.32
1814 3232 6.691508 ACTGAGGCAGAATAAACAATTTTCC 58.308 36.000 0.82 0.00 35.18 3.13
1893 3315 6.554334 TGTAATAAAAGTGCCAGTTCAGAC 57.446 37.500 0.00 0.00 0.00 3.51
1910 3332 7.230747 CCATGTTATTCAGGGGACATGTAATA 58.769 38.462 0.00 0.00 44.79 0.98
1911 3333 6.070656 CCATGTTATTCAGGGGACATGTAAT 58.929 40.000 0.00 0.00 44.79 1.89
1912 3334 5.445069 CCATGTTATTCAGGGGACATGTAA 58.555 41.667 0.00 0.00 44.79 2.41
1913 3335 5.047566 CCATGTTATTCAGGGGACATGTA 57.952 43.478 0.00 0.00 44.79 2.29
1914 3336 3.902218 CCATGTTATTCAGGGGACATGT 58.098 45.455 0.00 0.00 44.79 3.21
1975 3397 2.289382 ACGCATCACACTCACACCATAA 60.289 45.455 0.00 0.00 0.00 1.90
1979 3401 1.660607 CATACGCATCACACTCACACC 59.339 52.381 0.00 0.00 0.00 4.16
1986 3408 4.661993 TCAAGAAACATACGCATCACAC 57.338 40.909 0.00 0.00 0.00 3.82
1987 3409 5.681337 TTTCAAGAAACATACGCATCACA 57.319 34.783 0.00 0.00 0.00 3.58
1988 3410 5.569059 CCTTTTCAAGAAACATACGCATCAC 59.431 40.000 0.00 0.00 0.00 3.06
1989 3411 5.240623 ACCTTTTCAAGAAACATACGCATCA 59.759 36.000 0.00 0.00 0.00 3.07
1990 3412 5.699839 ACCTTTTCAAGAAACATACGCATC 58.300 37.500 0.00 0.00 0.00 3.91
1991 3413 5.240623 TGACCTTTTCAAGAAACATACGCAT 59.759 36.000 0.00 0.00 0.00 4.73
1992 3414 4.576873 TGACCTTTTCAAGAAACATACGCA 59.423 37.500 0.00 0.00 0.00 5.24
1993 3415 5.103290 TGACCTTTTCAAGAAACATACGC 57.897 39.130 0.00 0.00 0.00 4.42
1994 3416 5.147162 GCTGACCTTTTCAAGAAACATACG 58.853 41.667 0.00 0.00 32.21 3.06
1995 3417 6.072112 TGCTGACCTTTTCAAGAAACATAC 57.928 37.500 0.00 0.00 32.21 2.39
2009 3431 2.584835 TACTGCCAAATGCTGACCTT 57.415 45.000 0.00 0.00 41.11 3.50
2011 3433 2.648059 AGATACTGCCAAATGCTGACC 58.352 47.619 0.00 0.00 41.11 4.02
2046 3469 4.756642 TCTTGAATTTGACACTAGCACCAG 59.243 41.667 0.00 0.00 0.00 4.00
2232 3655 6.832520 AGCACCTACATATCATCTCACTAG 57.167 41.667 0.00 0.00 0.00 2.57
2246 3669 3.981071 AGCAATTGACTAGCACCTACA 57.019 42.857 10.34 0.00 0.00 2.74
2247 3670 4.095036 GGAAAGCAATTGACTAGCACCTAC 59.905 45.833 10.34 0.00 0.00 3.18
2297 3720 2.514803 AGGCACTACCCAAATGAACAC 58.485 47.619 0.00 0.00 40.58 3.32
2304 3727 4.043561 TCCAGATAAAAGGCACTACCCAAA 59.956 41.667 0.00 0.00 38.49 3.28
2334 3758 8.365399 TCAAATCACACAACTGAAACTAGTAG 57.635 34.615 0.00 0.00 0.00 2.57
2351 3775 5.922544 AGCACAGCAACTTTTATCAAATCAC 59.077 36.000 0.00 0.00 0.00 3.06
2367 3791 1.347378 TCAGTGTAATCCAGCACAGCA 59.653 47.619 0.00 0.00 38.02 4.41
2371 3795 2.417933 CTGCTTCAGTGTAATCCAGCAC 59.582 50.000 0.00 0.00 33.75 4.40
2385 3809 3.429492 TGTGCCATTAATTCCTGCTTCA 58.571 40.909 0.00 0.00 0.00 3.02
2397 3821 8.256605 ACAATTATACTTTGCAATGTGCCATTA 58.743 29.630 24.00 6.97 44.23 1.90
2705 4150 9.713740 CTTATTCGAAGATGAATTTTGAGAAGG 57.286 33.333 3.35 0.00 39.27 3.46
2708 4153 9.658799 AGTCTTATTCGAAGATGAATTTTGAGA 57.341 29.630 9.63 0.00 39.27 3.27
2725 4170 7.068686 ACTAGGGCCATTAGAAGTCTTATTC 57.931 40.000 17.64 0.00 0.00 1.75
2733 4178 5.071788 TGACCATTACTAGGGCCATTAGAAG 59.928 44.000 17.64 2.10 31.11 2.85
2782 4227 4.497291 TTTGTGGACCCATGTAGTATCC 57.503 45.455 0.00 0.00 0.00 2.59
2785 4230 3.265737 AGCATTTGTGGACCCATGTAGTA 59.734 43.478 0.00 0.00 0.00 1.82
2842 4287 4.449068 AGAGCACGAGTCATACACAAAAAG 59.551 41.667 0.00 0.00 0.00 2.27
2843 4288 4.377021 AGAGCACGAGTCATACACAAAAA 58.623 39.130 0.00 0.00 0.00 1.94
2844 4289 3.990092 AGAGCACGAGTCATACACAAAA 58.010 40.909 0.00 0.00 0.00 2.44
2856 4301 2.602211 CAGACTGCAATAAGAGCACGAG 59.398 50.000 0.00 0.00 37.02 4.18
2859 4304 2.012673 CCCAGACTGCAATAAGAGCAC 58.987 52.381 0.00 0.00 37.02 4.40
2905 4350 9.967451 TGTTTGATTAGTCAATATTCCCTACAA 57.033 29.630 1.06 0.00 43.49 2.41
3024 4469 6.377327 TCTGTTGAGCTGAAGTTTTTAAGG 57.623 37.500 0.00 0.00 0.00 2.69
3111 4556 4.873817 TGAGGAAACAACATGCAATCAAG 58.126 39.130 0.00 0.00 0.00 3.02
3120 4565 8.103305 ACTAGACATTACATGAGGAAACAACAT 58.897 33.333 0.00 0.00 0.00 2.71
3137 4582 7.016072 CAGGAGGAAATGGAGATACTAGACATT 59.984 40.741 0.00 0.00 33.55 2.71
3140 4585 5.245075 CCAGGAGGAAATGGAGATACTAGAC 59.755 48.000 0.00 0.00 39.02 2.59
3144 4589 3.970640 GACCAGGAGGAAATGGAGATACT 59.029 47.826 0.00 0.00 39.02 2.12
3177 4622 4.136796 AGCTCTGATGCTACTCTACTGAG 58.863 47.826 0.00 0.00 42.10 3.35
3647 5092 1.277557 ACTAGCACAGCAAAGAGGGAG 59.722 52.381 0.00 0.00 0.00 4.30
3743 5188 3.119352 CGGTCATCTCAACAGTCTCATCA 60.119 47.826 0.00 0.00 0.00 3.07
3799 5244 3.322828 GGTGTTACCACTGAACTCCTGTA 59.677 47.826 0.00 0.00 41.53 2.74
3910 5355 2.819608 CAGTAGGTGTGGGGACAAAATG 59.180 50.000 0.00 0.00 46.06 2.32
3911 5356 2.817839 GCAGTAGGTGTGGGGACAAAAT 60.818 50.000 0.00 0.00 46.06 1.82
3913 5358 0.109723 GCAGTAGGTGTGGGGACAAA 59.890 55.000 0.00 0.00 46.06 2.83
3914 5359 0.766674 AGCAGTAGGTGTGGGGACAA 60.767 55.000 0.00 0.00 46.06 3.18
3916 5361 1.597461 GAGCAGTAGGTGTGGGGAC 59.403 63.158 0.00 0.00 0.00 4.46
3918 5363 2.990479 GGAGCAGTAGGTGTGGGG 59.010 66.667 0.00 0.00 0.00 4.96
3919 5364 2.283529 ACGGAGCAGTAGGTGTGGG 61.284 63.158 0.00 0.00 0.00 4.61
3960 5408 7.502226 TGGTCTTGCCATTCGAATTATTCTAAT 59.498 33.333 8.21 1.42 43.61 1.73
4018 5467 5.699001 TCGTCACAGCTTCTTTATTGCTAAA 59.301 36.000 0.00 0.00 35.05 1.85
4070 5524 2.034305 CAGCAAGAAGACTGCAAGCTTT 59.966 45.455 0.00 0.00 37.60 3.51
4146 5606 7.118101 GCATCTCTTCTTCACATGATAAGATCC 59.882 40.741 12.93 0.00 32.05 3.36
4164 5624 4.880696 GGCTTCAAGATACAAGCATCTCTT 59.119 41.667 6.04 0.00 45.85 2.85
4165 5625 4.163839 AGGCTTCAAGATACAAGCATCTCT 59.836 41.667 6.04 0.00 45.85 3.10
4166 5626 4.450053 AGGCTTCAAGATACAAGCATCTC 58.550 43.478 6.04 0.00 45.85 2.75
4251 5716 4.084328 GCAAACAGCGGCTACATATAAGAG 60.084 45.833 0.26 0.00 0.00 2.85
4322 5787 9.376075 CCCAAATAAGAGCAGACAGTATATATG 57.624 37.037 0.00 0.00 0.00 1.78
4323 5788 9.326489 TCCCAAATAAGAGCAGACAGTATATAT 57.674 33.333 0.00 0.00 0.00 0.86
4341 5806 2.706890 GTCGGAACAAGCTCCCAAATA 58.293 47.619 0.00 0.00 31.03 1.40
4384 5852 7.442364 GCAGTACATATCTGAATTTGGCTTCTA 59.558 37.037 0.00 0.00 35.20 2.10
4415 5883 5.623596 GCAGTCACACACCACATATGTACTA 60.624 44.000 8.32 0.00 0.00 1.82
4416 5884 4.820897 CAGTCACACACCACATATGTACT 58.179 43.478 8.32 2.92 0.00 2.73
4417 5885 3.370978 GCAGTCACACACCACATATGTAC 59.629 47.826 8.32 0.38 0.00 2.90
4495 5963 2.778299 TGCTATCTTGCCGAACAAACT 58.222 42.857 0.00 0.00 37.96 2.66
4496 5964 3.126858 TCATGCTATCTTGCCGAACAAAC 59.873 43.478 0.00 0.00 37.96 2.93
4503 5971 1.233285 GGCCTCATGCTATCTTGCCG 61.233 60.000 0.00 0.00 40.92 5.69
4510 5978 1.142465 CTCACTTGGGCCTCATGCTAT 59.858 52.381 4.53 0.00 40.92 2.97
4519 5987 1.228552 TTGCTTCCTCACTTGGGCC 60.229 57.895 0.00 0.00 0.00 5.80
4540 6009 2.477357 CCACGAAATGCAGAATCAGCTG 60.477 50.000 7.63 7.63 38.91 4.24
4584 6055 2.492090 GTCGAGATCAGCAGCGGT 59.508 61.111 0.00 0.00 0.00 5.68
4591 6062 1.740585 AGAACAGTCGGTCGAGATCAG 59.259 52.381 0.00 0.00 0.00 2.90
4623 6094 8.934023 TTGTATTGGTAATCAGGAAGAACTTT 57.066 30.769 0.00 0.00 0.00 2.66
4630 6101 6.480763 TCTTGCTTGTATTGGTAATCAGGAA 58.519 36.000 0.00 0.00 0.00 3.36
4643 6114 9.920946 TTTCTAGGGAAAATATCTTGCTTGTAT 57.079 29.630 0.00 0.00 38.35 2.29
4648 6119 6.731467 TGGTTTCTAGGGAAAATATCTTGCT 58.269 36.000 0.00 0.00 42.22 3.91
4664 6135 3.373748 CACTTGCGTGCATATGGTTTCTA 59.626 43.478 4.56 0.00 33.82 2.10
4707 6179 0.107410 TGTCGTTTGGGTGAACTGCT 60.107 50.000 0.00 0.00 0.00 4.24
4708 6180 0.736053 TTGTCGTTTGGGTGAACTGC 59.264 50.000 0.00 0.00 0.00 4.40
4718 6191 5.564213 TGTATCGTAACTGTTGTCGTTTG 57.436 39.130 2.69 0.00 0.00 2.93
4721 6194 3.611113 GCATGTATCGTAACTGTTGTCGT 59.389 43.478 2.69 2.86 0.00 4.34
4736 6215 0.998928 TGGTTCCCCAGTGCATGTAT 59.001 50.000 0.00 0.00 35.17 2.29
4737 6216 2.469162 TGGTTCCCCAGTGCATGTA 58.531 52.632 0.00 0.00 35.17 2.29
4738 6217 3.260297 TGGTTCCCCAGTGCATGT 58.740 55.556 0.00 0.00 35.17 3.21
4753 6232 4.500603 GCCATCAGCTGAAATATTCTGG 57.499 45.455 22.50 21.60 38.99 3.86
4780 6259 5.954150 AGTGCAGGGACAAATCTAAATCAAT 59.046 36.000 0.00 0.00 0.00 2.57
4781 6260 5.183713 CAGTGCAGGGACAAATCTAAATCAA 59.816 40.000 0.00 0.00 0.00 2.57
4830 6309 2.000701 TTCACCCATGGAGCCGGAT 61.001 57.895 15.22 0.00 0.00 4.18
4837 6316 1.377229 GTTCCCGTTCACCCATGGA 59.623 57.895 15.22 0.00 0.00 3.41
4838 6317 0.960364 CTGTTCCCGTTCACCCATGG 60.960 60.000 4.14 4.14 0.00 3.66
4842 6321 0.037232 CTCTCTGTTCCCGTTCACCC 60.037 60.000 0.00 0.00 0.00 4.61
4846 6325 3.056465 AGTGAATCTCTCTGTTCCCGTTC 60.056 47.826 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.