Multiple sequence alignment - TraesCS3A01G090800

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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 TraesCS3A01G090800 chr3A 100.000 3879 0 0 1 3879 57705568 57701690 0.000000e+00 7164.0
1 TraesCS3A01G090800 chr3A 89.167 240 24 2 1055 1294 57466065 57466302 8.150000e-77 298.0
2 TraesCS3A01G090800 chr3A 86.842 76 5 5 355 428 597543557 597543485 3.210000e-11 80.5
3 TraesCS3A01G090800 chr3D 90.834 1571 61 25 414 1959 45946502 45944990 0.000000e+00 2026.0
4 TraesCS3A01G090800 chr3D 97.542 1139 22 3 1960 3098 45944842 45943710 0.000000e+00 1943.0
5 TraesCS3A01G090800 chr3D 95.806 620 22 3 3261 3879 45943715 45943099 0.000000e+00 998.0
6 TraesCS3A01G090800 chr3D 97.384 344 9 0 1 344 45946844 45946501 1.550000e-163 586.0
7 TraesCS3A01G090800 chr3D 91.129 248 14 6 1055 1302 45904570 45904809 2.890000e-86 329.0
8 TraesCS3A01G090800 chr3D 87.500 264 25 3 2041 2304 45905168 45905423 8.150000e-77 298.0
9 TraesCS3A01G090800 chr3D 96.491 57 1 1 1960 2016 45905111 45905166 4.130000e-15 93.5
10 TraesCS3A01G090800 chr3D 90.769 65 6 0 355 419 333321814 333321878 1.920000e-13 87.9
11 TraesCS3A01G090800 chr4D 96.552 58 0 2 359 415 430817073 430817017 1.150000e-15 95.3
12 TraesCS3A01G090800 chr5D 93.443 61 4 0 355 415 74715743 74715683 1.480000e-14 91.6
13 TraesCS3A01G090800 chr3B 93.548 62 2 2 359 419 802601617 802601557 1.480000e-14 91.6
14 TraesCS3A01G090800 chr7A 91.935 62 5 0 358 419 629780078 629780017 1.920000e-13 87.9
15 TraesCS3A01G090800 chr2D 90.769 65 6 0 355 419 545854311 545854375 1.920000e-13 87.9
16 TraesCS3A01G090800 chr7D 88.889 72 4 4 359 428 163634756 163634825 6.910000e-13 86.1
17 TraesCS3A01G090800 chr1A 88.732 71 6 2 355 424 578209704 578209773 6.910000e-13 86.1


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 TraesCS3A01G090800 chr3A 57701690 57705568 3878 True 7164.000000 7164 100.000000 1 3879 1 chr3A.!!$R1 3878
1 TraesCS3A01G090800 chr3D 45943099 45946844 3745 True 1388.250000 2026 95.391500 1 3879 4 chr3D.!!$R1 3878
2 TraesCS3A01G090800 chr3D 45904570 45905423 853 False 240.166667 329 91.706667 1055 2304 3 chr3D.!!$F2 1249

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
891 892 0.031043 CCCACACACACGTCTCGTAA 59.969 55.0 0.00 0.0 38.32 3.18 F
978 988 0.841289 GTCCAATCCCCGGATACCAA 59.159 55.0 0.73 0.0 34.32 3.67 F
2517 2738 0.319900 GCTCTGTTTGTCAGCCGAGA 60.320 55.0 0.00 0.0 43.32 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2024 2245 0.482446 TTGACCTTGTCCCTGGCAAT 59.518 50.0 0.00 0.00 0.00 3.56 R
2792 3013 1.029681 GGGCGTACCAAATCAATCCC 58.970 55.0 0.00 0.00 39.85 3.85 R
3753 3975 0.673022 GATGGCGAGCCTGGATGATC 60.673 60.0 15.75 5.01 36.94 2.92 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
55 56 2.161808 GCTACTGACGCAGACTTCTACA 59.838 50.000 12.77 0.00 35.18 2.74
298 299 0.385029 GTGCAAGCACACATGACCAA 59.615 50.000 19.47 0.00 45.53 3.67
342 343 8.970859 TCACAAAAGAAAGAAAGATCTCTTCT 57.029 30.769 11.90 11.90 34.49 2.85
349 350 9.533831 AAGAAAGAAAGATCTCTTCTACTCTCT 57.466 33.333 15.85 13.05 34.49 3.10
350 351 9.533831 AGAAAGAAAGATCTCTTCTACTCTCTT 57.466 33.333 15.85 8.85 34.49 2.85
351 352 9.788960 GAAAGAAAGATCTCTTCTACTCTCTTC 57.211 37.037 15.85 12.23 34.49 2.87
352 353 7.553881 AGAAAGATCTCTTCTACTCTCTTCG 57.446 40.000 14.63 0.00 34.61 3.79
353 354 7.110155 AGAAAGATCTCTTCTACTCTCTTCGT 58.890 38.462 14.63 0.00 34.61 3.85
354 355 7.610305 AGAAAGATCTCTTCTACTCTCTTCGTT 59.390 37.037 14.63 0.00 34.61 3.85
355 356 8.795842 AAAGATCTCTTCTACTCTCTTCGTTA 57.204 34.615 0.00 0.00 34.61 3.18
356 357 8.974060 AAGATCTCTTCTACTCTCTTCGTTAT 57.026 34.615 0.00 0.00 33.05 1.89
357 358 8.974060 AGATCTCTTCTACTCTCTTCGTTATT 57.026 34.615 0.00 0.00 30.96 1.40
361 362 9.669887 TCTCTTCTACTCTCTTCGTTATTAACT 57.330 33.333 5.11 0.00 0.00 2.24
402 403 9.762381 ATACAAAGTTGGGTTATCTATTTTGGA 57.238 29.630 0.00 0.00 0.00 3.53
403 404 8.485578 ACAAAGTTGGGTTATCTATTTTGGAA 57.514 30.769 0.00 0.00 0.00 3.53
404 405 8.364894 ACAAAGTTGGGTTATCTATTTTGGAAC 58.635 33.333 0.00 0.00 0.00 3.62
405 406 6.753107 AGTTGGGTTATCTATTTTGGAACG 57.247 37.500 0.00 0.00 0.00 3.95
406 407 5.650703 AGTTGGGTTATCTATTTTGGAACGG 59.349 40.000 0.00 0.00 0.00 4.44
407 408 5.438698 TGGGTTATCTATTTTGGAACGGA 57.561 39.130 0.00 0.00 0.00 4.69
408 409 5.433526 TGGGTTATCTATTTTGGAACGGAG 58.566 41.667 0.00 0.00 0.00 4.63
409 410 4.820173 GGGTTATCTATTTTGGAACGGAGG 59.180 45.833 0.00 0.00 0.00 4.30
410 411 4.820173 GGTTATCTATTTTGGAACGGAGGG 59.180 45.833 0.00 0.00 0.00 4.30
411 412 5.397109 GGTTATCTATTTTGGAACGGAGGGA 60.397 44.000 0.00 0.00 0.00 4.20
412 413 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
470 471 7.158697 CCGATGAATGGTAGTTATCATGGTTA 58.841 38.462 0.00 0.00 32.90 2.85
484 485 8.821894 GTTATCATGGTTAACACTGATCTCTTC 58.178 37.037 19.55 8.39 32.94 2.87
507 508 0.455633 CTGAAACTACGACGGGTCCG 60.456 60.000 7.97 7.97 46.03 4.79
519 520 1.012486 CGGGTCCGCAAGAAGTACAC 61.012 60.000 0.00 0.00 43.02 2.90
545 546 2.693074 TCGTGATGCTATTGCCACTCTA 59.307 45.455 0.00 0.00 38.71 2.43
548 549 4.635223 GTGATGCTATTGCCACTCTATCA 58.365 43.478 0.00 0.00 38.71 2.15
556 557 3.988976 TGCCACTCTATCAGCTTCTTT 57.011 42.857 0.00 0.00 0.00 2.52
561 562 5.007528 GCCACTCTATCAGCTTCTTTTCATC 59.992 44.000 0.00 0.00 0.00 2.92
578 579 4.063998 TCATCGTGATGAATCTCCAAGG 57.936 45.455 10.01 0.00 44.14 3.61
581 582 2.159043 TCGTGATGAATCTCCAAGGAGC 60.159 50.000 11.31 0.00 41.71 4.70
627 628 1.483827 CCATGCAGTCAGCTTCTCCTA 59.516 52.381 0.00 0.00 45.94 2.94
644 645 6.544928 TCTCCTAACACATTCTCTGCATAA 57.455 37.500 0.00 0.00 0.00 1.90
646 647 7.568349 TCTCCTAACACATTCTCTGCATAATT 58.432 34.615 0.00 0.00 0.00 1.40
686 687 2.089201 CCCAAATTTAGGACACCCGTC 58.911 52.381 0.00 0.00 41.80 4.79
737 738 1.454201 TGTCGGCACAAACTCAAACA 58.546 45.000 0.00 0.00 0.00 2.83
738 739 1.813178 TGTCGGCACAAACTCAAACAA 59.187 42.857 0.00 0.00 0.00 2.83
781 782 7.878477 CATCTGTGCATTGTAGTTTTCATTT 57.122 32.000 0.00 0.00 0.00 2.32
784 785 9.979578 ATCTGTGCATTGTAGTTTTCATTTTTA 57.020 25.926 0.00 0.00 0.00 1.52
859 860 1.815408 GCATCGGATATGTGGGCTGTT 60.815 52.381 0.00 0.00 0.00 3.16
891 892 0.031043 CCCACACACACGTCTCGTAA 59.969 55.000 0.00 0.00 38.32 3.18
909 910 1.739067 AAAGTTGCCAGGATACGAGC 58.261 50.000 0.00 0.00 46.39 5.03
977 987 1.404479 CGTCCAATCCCCGGATACCA 61.404 60.000 0.73 0.00 34.32 3.25
978 988 0.841289 GTCCAATCCCCGGATACCAA 59.159 55.000 0.73 0.00 34.32 3.67
994 1004 1.450312 CAACCCGCCTCCTCACATC 60.450 63.158 0.00 0.00 0.00 3.06
1035 1053 4.162690 GCCTCTCCAATCCCGCGT 62.163 66.667 4.92 0.00 0.00 6.01
1039 1057 2.202932 CTCCAATCCCGCGTCCTG 60.203 66.667 4.92 0.00 0.00 3.86
1052 1070 1.857318 CGTCCTGTGCGACTCTGAGT 61.857 60.000 10.66 10.66 0.00 3.41
1320 1342 3.822735 AGTTCTTTGTGTGTCCATGGATG 59.177 43.478 19.62 1.66 0.00 3.51
1369 1433 4.537135 TTTCTACTGCCAGGTACTCTTG 57.463 45.455 0.00 0.00 34.60 3.02
1385 1449 6.757478 GGTACTCTTGTGTATTTCTTAGGAGC 59.243 42.308 0.00 0.00 0.00 4.70
1397 1461 3.366396 TCTTAGGAGCTCACAAGGGTAG 58.634 50.000 17.19 1.23 0.00 3.18
1398 1462 3.011369 TCTTAGGAGCTCACAAGGGTAGA 59.989 47.826 17.19 3.56 0.00 2.59
1399 1463 2.559381 AGGAGCTCACAAGGGTAGAT 57.441 50.000 17.19 0.00 0.00 1.98
1400 1464 3.689872 AGGAGCTCACAAGGGTAGATA 57.310 47.619 17.19 0.00 0.00 1.98
1401 1465 3.995636 AGGAGCTCACAAGGGTAGATAA 58.004 45.455 17.19 0.00 0.00 1.75
1402 1466 4.362677 AGGAGCTCACAAGGGTAGATAAA 58.637 43.478 17.19 0.00 0.00 1.40
1493 1562 8.934023 ATTGAGGAACCAAAGTATGAAAACTA 57.066 30.769 0.00 0.00 0.00 2.24
1494 1563 8.754991 TTGAGGAACCAAAGTATGAAAACTAA 57.245 30.769 0.00 0.00 0.00 2.24
1495 1564 8.754991 TGAGGAACCAAAGTATGAAAACTAAA 57.245 30.769 0.00 0.00 0.00 1.85
1496 1565 9.362151 TGAGGAACCAAAGTATGAAAACTAAAT 57.638 29.630 0.00 0.00 0.00 1.40
1506 1575 9.606631 AAGTATGAAAACTAAATTTTGGTTGCA 57.393 25.926 12.62 12.62 40.73 4.08
1568 1641 8.103305 ACCATGAACTATACTGTGAGAATGTTT 58.897 33.333 0.00 0.00 0.00 2.83
1576 1649 7.759489 ATACTGTGAGAATGTTTTGCCTAAA 57.241 32.000 0.00 0.00 0.00 1.85
1580 1653 6.446318 TGTGAGAATGTTTTGCCTAAATGTC 58.554 36.000 0.00 0.00 0.00 3.06
1581 1654 5.569059 GTGAGAATGTTTTGCCTAAATGTCG 59.431 40.000 0.00 0.00 0.00 4.35
1587 1660 5.302360 TGTTTTGCCTAAATGTCGTAGTCT 58.698 37.500 0.00 0.00 0.00 3.24
1593 1666 5.109903 GCCTAAATGTCGTAGTCTTGTGAT 58.890 41.667 0.00 0.00 0.00 3.06
1689 1762 4.039124 TCTTCAGTGTTATGACTGCTGTGA 59.961 41.667 0.00 0.00 42.74 3.58
1729 1802 9.559958 CTCATGTTAAATAACTTGTCCATGTTC 57.440 33.333 14.91 0.00 40.30 3.18
1732 1805 8.458573 TGTTAAATAACTTGTCCATGTTCAGT 57.541 30.769 5.05 0.00 37.12 3.41
1771 1844 5.182487 TGTTCAACAACTTGTTCAGAGCTA 58.818 37.500 4.06 0.00 38.77 3.32
1774 1847 4.574828 TCAACAACTTGTTCAGAGCTAACC 59.425 41.667 4.06 0.00 38.77 2.85
1775 1848 4.423625 ACAACTTGTTCAGAGCTAACCT 57.576 40.909 0.00 0.00 0.00 3.50
1776 1849 4.130118 ACAACTTGTTCAGAGCTAACCTG 58.870 43.478 0.00 0.00 0.00 4.00
1777 1850 4.141711 ACAACTTGTTCAGAGCTAACCTGA 60.142 41.667 0.00 0.00 38.74 3.86
1778 1851 4.689612 ACTTGTTCAGAGCTAACCTGAA 57.310 40.909 11.27 11.27 45.30 3.02
1782 1855 3.988976 TTCAGAGCTAACCTGAAGCAT 57.011 42.857 11.27 0.00 43.39 3.79
1783 1856 3.257469 TCAGAGCTAACCTGAAGCATG 57.743 47.619 1.27 0.00 42.62 4.06
1784 1857 2.833943 TCAGAGCTAACCTGAAGCATGA 59.166 45.455 0.00 0.00 42.62 3.07
1785 1858 2.935201 CAGAGCTAACCTGAAGCATGAC 59.065 50.000 0.00 0.00 42.62 3.06
1786 1859 2.836981 AGAGCTAACCTGAAGCATGACT 59.163 45.455 0.00 0.00 42.62 3.41
1787 1860 2.935201 GAGCTAACCTGAAGCATGACTG 59.065 50.000 0.00 0.00 42.62 3.51
1803 1876 2.224281 TGACTGCATCGTGACTTCCTTT 60.224 45.455 0.00 0.00 0.00 3.11
1813 1886 7.679638 GCATCGTGACTTCCTTTGCTTTAATAT 60.680 37.037 0.00 0.00 0.00 1.28
1814 1887 7.681939 TCGTGACTTCCTTTGCTTTAATATT 57.318 32.000 0.00 0.00 0.00 1.28
1815 1888 8.780846 TCGTGACTTCCTTTGCTTTAATATTA 57.219 30.769 0.00 0.00 0.00 0.98
1816 1889 9.221933 TCGTGACTTCCTTTGCTTTAATATTAA 57.778 29.630 3.71 3.71 0.00 1.40
1830 1903 7.165812 GCTTTAATATTAATTGCAGGTGACACG 59.834 37.037 19.89 0.00 0.00 4.49
1835 1908 4.927782 TGCAGGTGACACGGGCAC 62.928 66.667 16.09 3.95 35.56 5.01
1873 1946 2.203224 TTCCTCGCGCCAAAACCA 60.203 55.556 0.00 0.00 0.00 3.67
1881 1954 2.029743 CGCCAAAACCATATCCCCG 58.970 57.895 0.00 0.00 0.00 5.73
1924 1997 3.664495 GTCCTCCGTGACGAGACA 58.336 61.111 6.54 0.00 30.97 3.41
2024 2245 4.399303 TGTCTGATAAGATTGTCGCTCTCA 59.601 41.667 0.00 0.00 0.00 3.27
2031 2252 1.329906 GATTGTCGCTCTCATTGCCAG 59.670 52.381 0.00 0.00 0.00 4.85
2285 2506 0.537188 ACCAAGAGATCGCGTGGAAT 59.463 50.000 31.59 12.56 35.04 3.01
2517 2738 0.319900 GCTCTGTTTGTCAGCCGAGA 60.320 55.000 0.00 0.00 43.32 4.04
2530 2751 2.041115 CCGAGACTGCTCCGAGTCA 61.041 63.158 4.89 0.00 44.25 3.41
2770 2991 7.278424 GCCAATGTTTGAGTTACATATGCATTT 59.722 33.333 3.54 0.00 35.26 2.32
2792 3013 3.134623 TGGAAGTGCCATACTACCATCTG 59.865 47.826 0.00 0.00 43.33 2.90
2794 3015 2.050144 AGTGCCATACTACCATCTGGG 58.950 52.381 0.54 0.00 38.04 4.45
3007 3228 2.351726 GTCGCAAACTGTGTTCTTGACT 59.648 45.455 0.00 0.00 0.00 3.41
3041 3262 2.884894 ATGCGGCTACTTGGTAGTAC 57.115 50.000 0.00 0.00 38.30 2.73
3098 3319 7.178573 TGAGGTCCATACAATCTCTATAGGAG 58.821 42.308 0.00 0.00 43.12 3.69
3099 3320 7.109901 AGGTCCATACAATCTCTATAGGAGT 57.890 40.000 0.00 0.00 42.40 3.85
3100 3321 6.951198 AGGTCCATACAATCTCTATAGGAGTG 59.049 42.308 13.62 13.62 42.40 3.51
3101 3322 6.153680 GGTCCATACAATCTCTATAGGAGTGG 59.846 46.154 17.27 9.19 42.40 4.00
3102 3323 5.717178 TCCATACAATCTCTATAGGAGTGGC 59.283 44.000 17.27 0.00 42.40 5.01
3103 3324 5.393569 CCATACAATCTCTATAGGAGTGGCG 60.394 48.000 17.27 8.91 42.40 5.69
3104 3325 2.894126 ACAATCTCTATAGGAGTGGCGG 59.106 50.000 17.27 0.68 42.40 6.13
3105 3326 3.157881 CAATCTCTATAGGAGTGGCGGA 58.842 50.000 0.00 0.00 42.40 5.54
3106 3327 2.570415 TCTCTATAGGAGTGGCGGAG 57.430 55.000 0.00 0.00 42.40 4.63
3107 3328 0.885196 CTCTATAGGAGTGGCGGAGC 59.115 60.000 0.00 0.00 44.99 4.70
3108 3329 1.546773 CTCTATAGGAGTGGCGGAGCT 60.547 57.143 0.00 0.00 45.04 4.09
3109 3330 3.078471 CTCTATAGGAGTGGCGGAGCTT 61.078 54.545 0.00 0.00 45.04 3.74
3110 3331 5.165234 CTCTATAGGAGTGGCGGAGCTTG 62.165 56.522 0.00 0.00 45.04 4.01
3125 3346 2.896745 GCTTGGGCTAAATTCATGGG 57.103 50.000 0.00 0.00 35.22 4.00
3126 3347 1.413812 GCTTGGGCTAAATTCATGGGG 59.586 52.381 0.00 0.00 35.22 4.96
3127 3348 2.041701 CTTGGGCTAAATTCATGGGGG 58.958 52.381 0.00 0.00 0.00 5.40
3150 3371 2.203625 TTGGCTGGAGGGGCAAAC 60.204 61.111 1.14 0.00 46.16 2.93
3151 3372 2.777960 TTGGCTGGAGGGGCAAACT 61.778 57.895 1.14 0.00 46.16 2.66
3152 3373 2.361737 GGCTGGAGGGGCAAACTC 60.362 66.667 0.00 0.00 0.00 3.01
3153 3374 2.436109 GCTGGAGGGGCAAACTCA 59.564 61.111 5.64 0.00 36.70 3.41
3154 3375 1.676967 GCTGGAGGGGCAAACTCAG 60.677 63.158 5.64 0.00 36.70 3.35
3155 3376 1.763770 CTGGAGGGGCAAACTCAGT 59.236 57.895 5.64 0.00 36.70 3.41
3156 3377 0.322008 CTGGAGGGGCAAACTCAGTC 60.322 60.000 5.64 0.00 36.70 3.51
3157 3378 1.059584 TGGAGGGGCAAACTCAGTCA 61.060 55.000 5.64 0.00 36.70 3.41
3158 3379 0.606673 GGAGGGGCAAACTCAGTCAC 60.607 60.000 5.64 0.00 36.70 3.67
3159 3380 0.398318 GAGGGGCAAACTCAGTCACT 59.602 55.000 0.00 0.00 35.09 3.41
3160 3381 1.623811 GAGGGGCAAACTCAGTCACTA 59.376 52.381 0.00 0.00 35.09 2.74
3161 3382 2.237392 GAGGGGCAAACTCAGTCACTAT 59.763 50.000 0.00 0.00 35.09 2.12
3162 3383 3.450904 AGGGGCAAACTCAGTCACTATA 58.549 45.455 0.00 0.00 0.00 1.31
3163 3384 3.844211 AGGGGCAAACTCAGTCACTATAA 59.156 43.478 0.00 0.00 0.00 0.98
3164 3385 4.080863 AGGGGCAAACTCAGTCACTATAAG 60.081 45.833 0.00 0.00 0.00 1.73
3165 3386 3.623510 GGGCAAACTCAGTCACTATAAGC 59.376 47.826 0.00 0.00 0.00 3.09
3166 3387 4.508662 GGCAAACTCAGTCACTATAAGCT 58.491 43.478 0.00 0.00 0.00 3.74
3167 3388 4.938226 GGCAAACTCAGTCACTATAAGCTT 59.062 41.667 3.48 3.48 0.00 3.74
3168 3389 5.412904 GGCAAACTCAGTCACTATAAGCTTT 59.587 40.000 3.20 0.00 0.00 3.51
3169 3390 6.072452 GGCAAACTCAGTCACTATAAGCTTTT 60.072 38.462 3.20 0.00 0.00 2.27
3170 3391 7.363431 GCAAACTCAGTCACTATAAGCTTTTT 58.637 34.615 3.20 0.00 0.00 1.94
3195 3416 9.515020 TTTTTAGTGGATAAATTGATCGAATGC 57.485 29.630 0.00 0.00 33.40 3.56
3196 3417 7.800155 TTAGTGGATAAATTGATCGAATGCA 57.200 32.000 0.00 0.00 0.00 3.96
3197 3418 6.698008 AGTGGATAAATTGATCGAATGCAA 57.302 33.333 0.00 0.00 0.00 4.08
3198 3419 7.099266 AGTGGATAAATTGATCGAATGCAAA 57.901 32.000 0.00 0.00 0.00 3.68
3199 3420 7.198390 AGTGGATAAATTGATCGAATGCAAAG 58.802 34.615 0.00 0.00 0.00 2.77
3200 3421 7.067372 AGTGGATAAATTGATCGAATGCAAAGA 59.933 33.333 0.00 0.00 0.00 2.52
3201 3422 7.864379 GTGGATAAATTGATCGAATGCAAAGAT 59.136 33.333 0.00 0.00 0.00 2.40
3202 3423 9.065798 TGGATAAATTGATCGAATGCAAAGATA 57.934 29.630 0.00 0.00 0.00 1.98
3208 3429 9.888878 AATTGATCGAATGCAAAGATATACAAG 57.111 29.630 0.00 0.00 0.00 3.16
3209 3430 8.661352 TTGATCGAATGCAAAGATATACAAGA 57.339 30.769 0.00 0.00 0.00 3.02
3210 3431 8.661352 TGATCGAATGCAAAGATATACAAGAA 57.339 30.769 0.00 0.00 0.00 2.52
3211 3432 8.768019 TGATCGAATGCAAAGATATACAAGAAG 58.232 33.333 0.00 0.00 0.00 2.85
3212 3433 6.948353 TCGAATGCAAAGATATACAAGAAGC 58.052 36.000 0.00 0.00 0.00 3.86
3213 3434 6.763135 TCGAATGCAAAGATATACAAGAAGCT 59.237 34.615 0.00 0.00 0.00 3.74
3214 3435 7.042456 TCGAATGCAAAGATATACAAGAAGCTC 60.042 37.037 0.00 0.00 0.00 4.09
3215 3436 7.254556 CGAATGCAAAGATATACAAGAAGCTCA 60.255 37.037 0.00 0.00 0.00 4.26
3216 3437 6.915544 TGCAAAGATATACAAGAAGCTCAG 57.084 37.500 0.00 0.00 0.00 3.35
3217 3438 5.819379 TGCAAAGATATACAAGAAGCTCAGG 59.181 40.000 0.00 0.00 0.00 3.86
3218 3439 5.819901 GCAAAGATATACAAGAAGCTCAGGT 59.180 40.000 0.00 0.00 0.00 4.00
3219 3440 6.317391 GCAAAGATATACAAGAAGCTCAGGTT 59.683 38.462 0.00 0.00 0.00 3.50
3220 3441 7.678218 GCAAAGATATACAAGAAGCTCAGGTTG 60.678 40.741 0.00 0.00 0.00 3.77
3221 3442 5.923204 AGATATACAAGAAGCTCAGGTTGG 58.077 41.667 0.00 0.00 0.00 3.77
3222 3443 2.185004 TACAAGAAGCTCAGGTTGGC 57.815 50.000 0.00 0.00 0.00 4.52
3223 3444 0.538287 ACAAGAAGCTCAGGTTGGCC 60.538 55.000 0.00 0.00 0.00 5.36
3224 3445 0.538057 CAAGAAGCTCAGGTTGGCCA 60.538 55.000 0.00 0.00 37.19 5.36
3225 3446 0.538287 AAGAAGCTCAGGTTGGCCAC 60.538 55.000 3.88 0.00 37.19 5.01
3246 3467 3.691342 CCAGGTCGCCCTCACGAA 61.691 66.667 0.00 0.00 44.93 3.85
3247 3468 2.125912 CAGGTCGCCCTCACGAAG 60.126 66.667 0.00 0.00 44.93 3.79
3248 3469 4.070552 AGGTCGCCCTCACGAAGC 62.071 66.667 0.00 0.00 44.93 3.86
3249 3470 4.070552 GGTCGCCCTCACGAAGCT 62.071 66.667 0.00 0.00 44.93 3.74
3250 3471 2.507324 GTCGCCCTCACGAAGCTC 60.507 66.667 0.00 0.00 44.93 4.09
3251 3472 3.760035 TCGCCCTCACGAAGCTCC 61.760 66.667 0.00 0.00 39.54 4.70
3254 3475 4.821589 CCCTCACGAAGCTCCGCC 62.822 72.222 0.00 0.00 0.00 6.13
3255 3476 4.069232 CCTCACGAAGCTCCGCCA 62.069 66.667 0.00 0.00 0.00 5.69
3256 3477 2.048222 CTCACGAAGCTCCGCCAA 60.048 61.111 0.00 0.00 0.00 4.52
3257 3478 2.357034 TCACGAAGCTCCGCCAAC 60.357 61.111 0.00 0.00 0.00 3.77
3258 3479 2.357517 CACGAAGCTCCGCCAACT 60.358 61.111 0.00 0.00 0.00 3.16
3259 3480 2.357517 ACGAAGCTCCGCCAACTG 60.358 61.111 0.00 0.00 0.00 3.16
3260 3481 2.048222 CGAAGCTCCGCCAACTGA 60.048 61.111 0.00 0.00 0.00 3.41
3261 3482 1.448540 CGAAGCTCCGCCAACTGAT 60.449 57.895 0.00 0.00 0.00 2.90
3262 3483 0.179111 CGAAGCTCCGCCAACTGATA 60.179 55.000 0.00 0.00 0.00 2.15
3263 3484 1.576356 GAAGCTCCGCCAACTGATAG 58.424 55.000 0.00 0.00 0.00 2.08
3264 3485 0.179000 AAGCTCCGCCAACTGATAGG 59.821 55.000 0.00 0.00 0.00 2.57
3265 3486 0.687757 AGCTCCGCCAACTGATAGGA 60.688 55.000 0.00 0.00 0.00 2.94
3325 3546 9.967346 TGAAGTATACAAGAAGATAGCACATAC 57.033 33.333 5.50 0.00 0.00 2.39
3355 3576 7.102993 ACAGTGCATTTTATTTACATTTCCCC 58.897 34.615 0.00 0.00 0.00 4.81
3359 3580 6.597280 TGCATTTTATTTACATTTCCCCTTGC 59.403 34.615 0.00 0.00 0.00 4.01
3403 3624 7.119709 TGCTGCTACCAATAGTCAATAACTA 57.880 36.000 0.00 0.00 44.49 2.24
3489 3710 5.627499 TGTATCTCATTGTGTTTGAAGGC 57.373 39.130 0.00 0.00 0.00 4.35
3577 3798 3.433615 AGATTTCGAGCTTCTTTGAACCG 59.566 43.478 0.00 0.00 0.00 4.44
3582 3803 2.677037 CGAGCTTCTTTGAACCGGGTAT 60.677 50.000 6.32 0.00 0.00 2.73
3584 3805 2.304761 AGCTTCTTTGAACCGGGTATCA 59.695 45.455 6.32 4.35 0.00 2.15
3599 3820 3.676646 GGGTATCAGAACACACACGTTAC 59.323 47.826 0.00 0.00 0.00 2.50
3605 3827 2.159198 AGAACACACACGTTACCGTCTT 60.159 45.455 0.00 0.00 46.28 3.01
3638 3860 7.119699 CACTCAAAGCACAAGAAGGAATACATA 59.880 37.037 0.00 0.00 0.00 2.29
3647 3869 8.177663 CACAAGAAGGAATACATACAATGTCAC 58.822 37.037 0.00 0.00 43.67 3.67
3753 3975 1.227639 GCCTCATGCTCAGCACATAG 58.772 55.000 0.00 0.00 43.04 2.23
3790 4012 4.201990 GCCATCTTTGCTCTAATGTCCTTG 60.202 45.833 0.00 0.00 0.00 3.61
3820 4042 6.466812 CATACTACTGGTGCCATGATATTCA 58.533 40.000 0.00 0.00 0.00 2.57
3822 4044 2.936202 ACTGGTGCCATGATATTCACC 58.064 47.619 0.00 4.35 46.78 4.02
3845 4067 0.599204 AAGGTGTTGTACAGTCGCCG 60.599 55.000 19.61 0.00 36.92 6.46
3871 4093 1.266718 CCGTCACCACATGAACCTTTG 59.733 52.381 0.00 0.00 39.72 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 1.771255 AGACAGCTCCTGACCAAACTT 59.229 47.619 0.00 0.00 35.18 2.66
251 252 6.348458 CCGTTGCATTGACTTGAGAAATAGAA 60.348 38.462 0.00 0.00 0.00 2.10
323 324 9.533831 AGAGAGTAGAAGAGATCTTTCTTTCTT 57.466 33.333 18.85 8.40 39.71 2.52
376 377 9.762381 TCCAAAATAGATAACCCAACTTTGTAT 57.238 29.630 0.00 0.00 0.00 2.29
377 378 9.589461 TTCCAAAATAGATAACCCAACTTTGTA 57.411 29.630 0.00 0.00 0.00 2.41
378 379 8.364894 GTTCCAAAATAGATAACCCAACTTTGT 58.635 33.333 0.00 0.00 0.00 2.83
379 380 7.540745 CGTTCCAAAATAGATAACCCAACTTTG 59.459 37.037 0.00 0.00 0.00 2.77
380 381 7.309560 CCGTTCCAAAATAGATAACCCAACTTT 60.310 37.037 0.00 0.00 0.00 2.66
381 382 6.152154 CCGTTCCAAAATAGATAACCCAACTT 59.848 38.462 0.00 0.00 0.00 2.66
382 383 5.650703 CCGTTCCAAAATAGATAACCCAACT 59.349 40.000 0.00 0.00 0.00 3.16
383 384 5.648960 TCCGTTCCAAAATAGATAACCCAAC 59.351 40.000 0.00 0.00 0.00 3.77
384 385 5.817784 TCCGTTCCAAAATAGATAACCCAA 58.182 37.500 0.00 0.00 0.00 4.12
385 386 5.433526 CTCCGTTCCAAAATAGATAACCCA 58.566 41.667 0.00 0.00 0.00 4.51
386 387 4.820173 CCTCCGTTCCAAAATAGATAACCC 59.180 45.833 0.00 0.00 0.00 4.11
387 388 4.820173 CCCTCCGTTCCAAAATAGATAACC 59.180 45.833 0.00 0.00 0.00 2.85
388 389 5.677567 TCCCTCCGTTCCAAAATAGATAAC 58.322 41.667 0.00 0.00 0.00 1.89
389 390 5.427481 ACTCCCTCCGTTCCAAAATAGATAA 59.573 40.000 0.00 0.00 0.00 1.75
390 391 4.966805 ACTCCCTCCGTTCCAAAATAGATA 59.033 41.667 0.00 0.00 0.00 1.98
391 392 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
392 393 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
393 394 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
394 395 4.098894 ACTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
395 396 2.910977 ACTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
396 397 2.332117 ACTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
397 398 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
398 399 1.897802 GAACTACTCCCTCCGTTCCAA 59.102 52.381 0.00 0.00 31.89 3.53
399 400 1.076677 AGAACTACTCCCTCCGTTCCA 59.923 52.381 0.00 0.00 37.15 3.53
400 401 1.849977 AGAACTACTCCCTCCGTTCC 58.150 55.000 0.00 0.00 37.15 3.62
401 402 4.643784 TGATTAGAACTACTCCCTCCGTTC 59.356 45.833 0.00 0.00 36.81 3.95
402 403 4.401837 GTGATTAGAACTACTCCCTCCGTT 59.598 45.833 0.00 0.00 0.00 4.44
403 404 3.952967 GTGATTAGAACTACTCCCTCCGT 59.047 47.826 0.00 0.00 0.00 4.69
404 405 3.952323 TGTGATTAGAACTACTCCCTCCG 59.048 47.826 0.00 0.00 0.00 4.63
405 406 5.598830 TCATGTGATTAGAACTACTCCCTCC 59.401 44.000 0.00 0.00 0.00 4.30
406 407 6.716934 TCATGTGATTAGAACTACTCCCTC 57.283 41.667 0.00 0.00 0.00 4.30
407 408 8.643324 GTTATCATGTGATTAGAACTACTCCCT 58.357 37.037 0.19 0.00 36.05 4.20
408 409 8.643324 AGTTATCATGTGATTAGAACTACTCCC 58.357 37.037 0.19 0.00 32.25 4.30
470 471 2.902486 TCAGCAGGAAGAGATCAGTGTT 59.098 45.455 0.00 0.00 0.00 3.32
484 485 0.736325 CCCGTCGTAGTTTCAGCAGG 60.736 60.000 0.00 0.00 0.00 4.85
507 508 3.057736 TCACGAGTAGGTGTACTTCTTGC 60.058 47.826 0.00 0.00 39.78 4.01
519 520 2.224042 TGGCAATAGCATCACGAGTAGG 60.224 50.000 0.00 0.00 44.61 3.18
545 546 5.181009 TCATCACGATGAAAAGAAGCTGAT 58.819 37.500 7.26 0.00 44.14 2.90
561 562 2.208431 GCTCCTTGGAGATTCATCACG 58.792 52.381 19.85 0.00 0.00 4.35
581 582 0.179161 CGTTAGGAGCAGAGGACGTG 60.179 60.000 0.00 0.00 0.00 4.49
627 628 6.327934 GCAAGAATTATGCAGAGAATGTGTT 58.672 36.000 10.07 0.00 43.29 3.32
686 687 0.368907 CAACGCGTCGATACAAAGGG 59.631 55.000 14.44 0.00 0.00 3.95
737 738 1.268845 GCATTTGGTCCGTTCACGTTT 60.269 47.619 0.00 0.00 37.74 3.60
738 739 0.309612 GCATTTGGTCCGTTCACGTT 59.690 50.000 0.00 0.00 37.74 3.99
801 802 1.133598 TCATCACCTACTACGGCGTTG 59.866 52.381 21.24 20.17 0.00 4.10
808 809 5.070446 TGGATGGATGTTCATCACCTACTAC 59.930 44.000 13.64 0.00 43.82 2.73
809 810 5.070446 GTGGATGGATGTTCATCACCTACTA 59.930 44.000 13.64 0.00 43.82 1.82
810 811 4.040047 TGGATGGATGTTCATCACCTACT 58.960 43.478 13.64 0.00 43.82 2.57
859 860 3.618750 GTGGGTTCGACGTGGGGA 61.619 66.667 0.00 0.00 0.00 4.81
891 892 0.460284 CGCTCGTATCCTGGCAACTT 60.460 55.000 0.00 0.00 37.61 2.66
909 910 2.382519 CGCTCCTCGACCTAATAAACG 58.617 52.381 0.00 0.00 41.67 3.60
977 987 2.670148 GGATGTGAGGAGGCGGGTT 61.670 63.158 0.00 0.00 0.00 4.11
978 988 3.083997 GGATGTGAGGAGGCGGGT 61.084 66.667 0.00 0.00 0.00 5.28
1035 1053 2.258317 GACTCAGAGTCGCACAGGA 58.742 57.895 14.96 0.00 35.28 3.86
1052 1070 0.984995 TGAGTCGAGGAGGTCAGAGA 59.015 55.000 0.00 0.00 0.00 3.10
1320 1342 5.277442 CCAATTCACCAAGAACACAAATTGC 60.277 40.000 0.00 0.00 39.49 3.56
1369 1433 5.582665 CCTTGTGAGCTCCTAAGAAATACAC 59.417 44.000 21.92 7.51 0.00 2.90
1439 1508 5.565509 TCTGACTATCTACCAGCTATCAGG 58.434 45.833 0.00 0.00 34.43 3.86
1529 1598 9.116067 GTATAGTTCATGGTAAAGTAATGCCAA 57.884 33.333 0.00 0.00 34.39 4.52
1568 1641 4.688879 CACAAGACTACGACATTTAGGCAA 59.311 41.667 0.00 0.00 0.00 4.52
1576 1649 4.021456 TGGACAATCACAAGACTACGACAT 60.021 41.667 0.00 0.00 0.00 3.06
1580 1653 2.668457 GCTGGACAATCACAAGACTACG 59.332 50.000 0.00 0.00 0.00 3.51
1581 1654 3.664107 TGCTGGACAATCACAAGACTAC 58.336 45.455 0.00 0.00 0.00 2.73
1587 1660 3.243805 CCACATTTGCTGGACAATCACAA 60.244 43.478 0.00 0.00 38.31 3.33
1593 1666 1.117994 TTGCCACATTTGCTGGACAA 58.882 45.000 0.00 0.00 36.13 3.18
1633 1706 9.303537 GAGTACATTGGTTTTAGCTAAGAGTAG 57.696 37.037 6.24 0.00 0.00 2.57
1780 1853 1.662629 GGAAGTCACGATGCAGTCATG 59.337 52.381 0.00 0.00 31.96 3.07
1781 1854 1.552337 AGGAAGTCACGATGCAGTCAT 59.448 47.619 0.00 0.00 35.17 3.06
1782 1855 0.969149 AGGAAGTCACGATGCAGTCA 59.031 50.000 0.00 0.00 0.00 3.41
1783 1856 2.086054 AAGGAAGTCACGATGCAGTC 57.914 50.000 0.00 0.00 0.00 3.51
1784 1857 2.146342 CAAAGGAAGTCACGATGCAGT 58.854 47.619 0.00 0.00 0.00 4.40
1785 1858 1.135859 GCAAAGGAAGTCACGATGCAG 60.136 52.381 0.00 0.00 32.80 4.41
1786 1859 0.874390 GCAAAGGAAGTCACGATGCA 59.126 50.000 0.00 0.00 32.80 3.96
1787 1860 1.160137 AGCAAAGGAAGTCACGATGC 58.840 50.000 0.00 0.00 0.00 3.91
1788 1861 3.904136 AAAGCAAAGGAAGTCACGATG 57.096 42.857 0.00 0.00 0.00 3.84
1789 1862 7.865706 ATATTAAAGCAAAGGAAGTCACGAT 57.134 32.000 0.00 0.00 0.00 3.73
1790 1863 7.681939 AATATTAAAGCAAAGGAAGTCACGA 57.318 32.000 0.00 0.00 0.00 4.35
1803 1876 7.973388 GTGTCACCTGCAATTAATATTAAAGCA 59.027 33.333 24.93 24.93 36.75 3.91
1813 1886 1.529226 CCCGTGTCACCTGCAATTAA 58.471 50.000 0.00 0.00 0.00 1.40
1814 1887 0.958382 GCCCGTGTCACCTGCAATTA 60.958 55.000 6.52 0.00 0.00 1.40
1815 1888 2.268076 GCCCGTGTCACCTGCAATT 61.268 57.895 6.52 0.00 0.00 2.32
1816 1889 2.672996 GCCCGTGTCACCTGCAAT 60.673 61.111 6.52 0.00 0.00 3.56
1850 1923 0.802494 TTTGGCGCGAGGAAGAATTC 59.198 50.000 12.10 0.00 46.67 2.17
1873 1946 2.529389 GGGTGGAGCCGGGGATAT 60.529 66.667 2.18 0.00 38.44 1.63
1919 1992 1.763545 GGGGAAGGTGAGGTATGTCTC 59.236 57.143 0.00 0.00 0.00 3.36
1924 1997 0.981277 CGTGGGGGAAGGTGAGGTAT 60.981 60.000 0.00 0.00 0.00 2.73
2024 2245 0.482446 TTGACCTTGTCCCTGGCAAT 59.518 50.000 0.00 0.00 0.00 3.56
2031 2252 3.321968 AGCAAAGATTTTGACCTTGTCCC 59.678 43.478 5.77 0.00 0.00 4.46
2285 2506 3.749064 GCCGGCAGTCGAGTCAGA 61.749 66.667 24.80 0.00 42.43 3.27
2354 2575 2.668550 GACCTGCCGTTCCACCAC 60.669 66.667 0.00 0.00 0.00 4.16
2517 2738 1.979693 GGGAGTGACTCGGAGCAGT 60.980 63.158 6.50 7.16 0.00 4.40
2635 2856 2.153057 CACGTTGTACATGACACAGTCG 59.847 50.000 18.87 18.87 37.96 4.18
2711 2932 2.579657 TAGGATGCCATACCCCGCG 61.580 63.158 0.00 0.00 0.00 6.46
2792 3013 1.029681 GGGCGTACCAAATCAATCCC 58.970 55.000 0.00 0.00 39.85 3.85
2794 3015 2.639065 TCAGGGCGTACCAAATCAATC 58.361 47.619 1.21 0.00 43.89 2.67
2860 3081 9.472361 TGTCAGAACAAGTAAACTAGTCATTAC 57.528 33.333 8.76 8.76 30.70 1.89
2862 3083 8.958119 TTGTCAGAACAAGTAAACTAGTCATT 57.042 30.769 0.00 0.00 40.45 2.57
3007 3228 3.321968 AGCCGCATAGATCAGTACATTCA 59.678 43.478 0.00 0.00 0.00 2.57
3041 3262 5.005971 CACAAACAAAGAAGTGAAGCAATGG 59.994 40.000 0.00 0.00 33.99 3.16
3106 3327 1.413812 CCCCATGAATTTAGCCCAAGC 59.586 52.381 0.00 0.00 40.32 4.01
3107 3328 2.041701 CCCCCATGAATTTAGCCCAAG 58.958 52.381 0.00 0.00 0.00 3.61
3108 3329 2.173126 CCCCCATGAATTTAGCCCAA 57.827 50.000 0.00 0.00 0.00 4.12
3109 3330 3.944061 CCCCCATGAATTTAGCCCA 57.056 52.632 0.00 0.00 0.00 5.36
3131 3352 1.610086 TTTGCCCCTCCAGCCAATG 60.610 57.895 0.00 0.00 0.00 2.82
3132 3353 1.610379 GTTTGCCCCTCCAGCCAAT 60.610 57.895 0.00 0.00 0.00 3.16
3133 3354 2.203625 GTTTGCCCCTCCAGCCAA 60.204 61.111 0.00 0.00 0.00 4.52
3134 3355 3.185203 AGTTTGCCCCTCCAGCCA 61.185 61.111 0.00 0.00 0.00 4.75
3135 3356 2.361737 GAGTTTGCCCCTCCAGCC 60.362 66.667 0.00 0.00 0.00 4.85
3136 3357 1.676967 CTGAGTTTGCCCCTCCAGC 60.677 63.158 0.00 0.00 0.00 4.85
3137 3358 0.322008 GACTGAGTTTGCCCCTCCAG 60.322 60.000 0.00 0.00 0.00 3.86
3138 3359 1.059584 TGACTGAGTTTGCCCCTCCA 61.060 55.000 0.00 0.00 0.00 3.86
3139 3360 0.606673 GTGACTGAGTTTGCCCCTCC 60.607 60.000 0.00 0.00 0.00 4.30
3140 3361 0.398318 AGTGACTGAGTTTGCCCCTC 59.602 55.000 0.00 0.00 0.00 4.30
3141 3362 1.729586 TAGTGACTGAGTTTGCCCCT 58.270 50.000 0.00 0.00 0.00 4.79
3142 3363 2.789409 ATAGTGACTGAGTTTGCCCC 57.211 50.000 0.00 0.00 0.00 5.80
3143 3364 3.623510 GCTTATAGTGACTGAGTTTGCCC 59.376 47.826 0.00 0.00 0.00 5.36
3144 3365 4.508662 AGCTTATAGTGACTGAGTTTGCC 58.491 43.478 0.00 0.00 0.00 4.52
3145 3366 6.487689 AAAGCTTATAGTGACTGAGTTTGC 57.512 37.500 0.00 0.00 0.00 3.68
3169 3390 9.515020 GCATTCGATCAATTTATCCACTAAAAA 57.485 29.630 0.00 0.00 33.15 1.94
3170 3391 8.681806 TGCATTCGATCAATTTATCCACTAAAA 58.318 29.630 0.00 0.00 33.15 1.52
3171 3392 8.219546 TGCATTCGATCAATTTATCCACTAAA 57.780 30.769 0.00 0.00 33.92 1.85
3172 3393 7.800155 TGCATTCGATCAATTTATCCACTAA 57.200 32.000 0.00 0.00 0.00 2.24
3173 3394 7.800155 TTGCATTCGATCAATTTATCCACTA 57.200 32.000 0.00 0.00 0.00 2.74
3174 3395 6.698008 TTGCATTCGATCAATTTATCCACT 57.302 33.333 0.00 0.00 0.00 4.00
3175 3396 7.195646 TCTTTGCATTCGATCAATTTATCCAC 58.804 34.615 0.00 0.00 0.00 4.02
3176 3397 7.332213 TCTTTGCATTCGATCAATTTATCCA 57.668 32.000 0.00 0.00 0.00 3.41
3182 3403 9.888878 CTTGTATATCTTTGCATTCGATCAATT 57.111 29.630 0.00 0.00 0.00 2.32
3183 3404 9.276590 TCTTGTATATCTTTGCATTCGATCAAT 57.723 29.630 0.00 0.00 0.00 2.57
3184 3405 8.661352 TCTTGTATATCTTTGCATTCGATCAA 57.339 30.769 0.00 0.00 0.00 2.57
3185 3406 8.661352 TTCTTGTATATCTTTGCATTCGATCA 57.339 30.769 0.00 0.00 0.00 2.92
3186 3407 7.743838 GCTTCTTGTATATCTTTGCATTCGATC 59.256 37.037 0.00 0.00 0.00 3.69
3187 3408 7.443575 AGCTTCTTGTATATCTTTGCATTCGAT 59.556 33.333 0.00 0.00 0.00 3.59
3188 3409 6.763135 AGCTTCTTGTATATCTTTGCATTCGA 59.237 34.615 0.00 0.00 0.00 3.71
3189 3410 6.952743 AGCTTCTTGTATATCTTTGCATTCG 58.047 36.000 0.00 0.00 0.00 3.34
3190 3411 7.923888 TGAGCTTCTTGTATATCTTTGCATTC 58.076 34.615 0.00 0.00 0.00 2.67
3191 3412 7.013083 CCTGAGCTTCTTGTATATCTTTGCATT 59.987 37.037 0.00 0.00 0.00 3.56
3192 3413 6.485984 CCTGAGCTTCTTGTATATCTTTGCAT 59.514 38.462 0.00 0.00 0.00 3.96
3193 3414 5.819379 CCTGAGCTTCTTGTATATCTTTGCA 59.181 40.000 0.00 0.00 0.00 4.08
3194 3415 5.819901 ACCTGAGCTTCTTGTATATCTTTGC 59.180 40.000 0.00 0.00 0.00 3.68
3195 3416 7.201679 CCAACCTGAGCTTCTTGTATATCTTTG 60.202 40.741 0.00 0.00 0.00 2.77
3196 3417 6.825721 CCAACCTGAGCTTCTTGTATATCTTT 59.174 38.462 0.00 0.00 0.00 2.52
3197 3418 6.352516 CCAACCTGAGCTTCTTGTATATCTT 58.647 40.000 0.00 0.00 0.00 2.40
3198 3419 5.686124 GCCAACCTGAGCTTCTTGTATATCT 60.686 44.000 0.00 0.00 0.00 1.98
3199 3420 4.513318 GCCAACCTGAGCTTCTTGTATATC 59.487 45.833 0.00 0.00 0.00 1.63
3200 3421 4.455606 GCCAACCTGAGCTTCTTGTATAT 58.544 43.478 0.00 0.00 0.00 0.86
3201 3422 3.370527 GGCCAACCTGAGCTTCTTGTATA 60.371 47.826 0.00 0.00 0.00 1.47
3202 3423 2.619074 GGCCAACCTGAGCTTCTTGTAT 60.619 50.000 0.00 0.00 0.00 2.29
3203 3424 1.271379 GGCCAACCTGAGCTTCTTGTA 60.271 52.381 0.00 0.00 0.00 2.41
3204 3425 0.538287 GGCCAACCTGAGCTTCTTGT 60.538 55.000 0.00 0.00 0.00 3.16
3205 3426 0.538057 TGGCCAACCTGAGCTTCTTG 60.538 55.000 0.61 0.00 36.63 3.02
3206 3427 0.538287 GTGGCCAACCTGAGCTTCTT 60.538 55.000 7.24 0.00 36.63 2.52
3207 3428 1.073897 GTGGCCAACCTGAGCTTCT 59.926 57.895 7.24 0.00 36.63 2.85
3208 3429 1.973812 GGTGGCCAACCTGAGCTTC 60.974 63.158 10.67 0.00 46.55 3.86
3209 3430 2.116125 GGTGGCCAACCTGAGCTT 59.884 61.111 10.67 0.00 46.55 3.74
3233 3454 2.507324 GAGCTTCGTGAGGGCGAC 60.507 66.667 0.00 0.00 40.85 5.19
3234 3455 3.760035 GGAGCTTCGTGAGGGCGA 61.760 66.667 0.00 0.00 39.28 5.54
3248 3469 2.555199 CTTTCCTATCAGTTGGCGGAG 58.445 52.381 0.00 0.00 0.00 4.63
3249 3470 1.406887 GCTTTCCTATCAGTTGGCGGA 60.407 52.381 0.00 0.00 0.00 5.54
3250 3471 1.017387 GCTTTCCTATCAGTTGGCGG 58.983 55.000 0.00 0.00 0.00 6.13
3251 3472 1.667724 CAGCTTTCCTATCAGTTGGCG 59.332 52.381 0.00 0.00 0.00 5.69
3252 3473 2.019984 CCAGCTTTCCTATCAGTTGGC 58.980 52.381 0.00 0.00 34.96 4.52
3253 3474 2.019984 GCCAGCTTTCCTATCAGTTGG 58.980 52.381 0.00 0.00 42.72 3.77
3254 3475 2.996631 AGCCAGCTTTCCTATCAGTTG 58.003 47.619 0.00 0.00 0.00 3.16
3255 3476 3.615155 GAAGCCAGCTTTCCTATCAGTT 58.385 45.455 6.31 0.00 36.26 3.16
3256 3477 2.092699 GGAAGCCAGCTTTCCTATCAGT 60.093 50.000 6.31 0.00 36.26 3.41
3257 3478 2.570135 GGAAGCCAGCTTTCCTATCAG 58.430 52.381 6.31 0.00 36.26 2.90
3258 3479 1.134401 CGGAAGCCAGCTTTCCTATCA 60.134 52.381 12.70 0.00 36.26 2.15
3259 3480 1.587547 CGGAAGCCAGCTTTCCTATC 58.412 55.000 12.70 0.00 36.26 2.08
3260 3481 3.788672 CGGAAGCCAGCTTTCCTAT 57.211 52.632 12.70 0.00 36.26 2.57
3335 3556 6.038161 GGCAAGGGGAAATGTAAATAAAATGC 59.962 38.462 0.00 0.00 0.00 3.56
3355 3576 4.678840 GCTCCATGTAATTTTCAGGGCAAG 60.679 45.833 2.22 0.00 36.79 4.01
3359 3580 3.181483 GCAGCTCCATGTAATTTTCAGGG 60.181 47.826 0.75 0.75 37.99 4.45
3497 3718 8.684386 TTGAATTTACATGTCCACTTTGAGTA 57.316 30.769 0.00 0.00 0.00 2.59
3498 3719 7.581213 TTGAATTTACATGTCCACTTTGAGT 57.419 32.000 0.00 0.00 0.00 3.41
3499 3720 7.920151 TGTTTGAATTTACATGTCCACTTTGAG 59.080 33.333 0.00 0.00 0.00 3.02
3500 3721 7.776107 TGTTTGAATTTACATGTCCACTTTGA 58.224 30.769 0.00 0.00 0.00 2.69
3501 3722 7.169645 CCTGTTTGAATTTACATGTCCACTTTG 59.830 37.037 0.00 0.00 0.00 2.77
3502 3723 7.209475 CCTGTTTGAATTTACATGTCCACTTT 58.791 34.615 0.00 0.00 0.00 2.66
3503 3724 6.239289 CCCTGTTTGAATTTACATGTCCACTT 60.239 38.462 0.00 0.00 0.00 3.16
3577 3798 2.450609 ACGTGTGTGTTCTGATACCC 57.549 50.000 0.00 0.00 0.00 3.69
3599 3820 5.625311 GTGCTTTGAGTGAAAATAAAGACGG 59.375 40.000 0.00 0.00 33.18 4.79
3605 3827 7.068103 TCCTTCTTGTGCTTTGAGTGAAAATAA 59.932 33.333 0.00 0.00 0.00 1.40
3638 3860 5.336134 GGCTTTTAAATACCCGTGACATTGT 60.336 40.000 0.00 0.00 0.00 2.71
3647 3869 4.156922 TCATGTGTGGCTTTTAAATACCCG 59.843 41.667 4.94 0.00 0.00 5.28
3753 3975 0.673022 GATGGCGAGCCTGGATGATC 60.673 60.000 15.75 5.01 36.94 2.92
3822 4044 2.221055 GCGACTGTACAACACCTTCAAG 59.779 50.000 0.00 0.00 0.00 3.02
3832 4054 1.135199 GGATTCTCGGCGACTGTACAA 60.135 52.381 4.99 0.00 0.00 2.41
3845 4067 2.672961 TCATGTGGTGACGGATTCTC 57.327 50.000 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.