Multiple sequence alignment - TraesCS2B01G574200

Loading Multiple Alignment...

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 TraesCS2B01G574200 chr2B 100.000 3814 0 0 1 3814 763837923 763841736 0.000000e+00 7044.0
1 TraesCS2B01G574200 chr2B 88.258 528 48 8 1884 2403 52188129 52187608 1.510000e-173 619.0
2 TraesCS2B01G574200 chr2B 86.667 405 38 13 1142 1538 785860452 785860848 5.850000e-118 435.0
3 TraesCS2B01G574200 chr2B 91.864 295 21 3 1426 1717 559331390 559331096 3.550000e-110 409.0
4 TraesCS2B01G574200 chr2B 85.827 381 45 5 1162 1541 719635513 719635141 2.760000e-106 396.0
5 TraesCS2B01G574200 chr2B 88.474 321 33 4 1400 1717 52188555 52188236 5.980000e-103 385.0
6 TraesCS2B01G574200 chr2B 92.424 264 20 0 1142 1405 312364523 312364260 1.000000e-100 377.0
7 TraesCS2B01G574200 chr2B 88.462 260 23 1 1611 1870 312363450 312363198 1.330000e-79 307.0
8 TraesCS2B01G574200 chr2B 86.792 265 20 7 1118 1381 70860598 70860848 8.070000e-72 281.0
9 TraesCS2B01G574200 chr2B 87.931 232 21 2 1611 1842 737641486 737641710 2.260000e-67 267.0
10 TraesCS2B01G574200 chr2B 94.118 102 6 0 1112 1213 737640894 737640995 5.100000e-34 156.0
11 TraesCS2B01G574200 chr2A 89.260 3175 194 53 13 3155 753612979 753616038 0.000000e+00 3838.0
12 TraesCS2B01G574200 chr2A 96.617 473 16 0 3342 3814 753616022 753616494 0.000000e+00 785.0
13 TraesCS2B01G574200 chr2D 89.848 2167 138 41 749 2879 621954300 621952180 0.000000e+00 2708.0
14 TraesCS2B01G574200 chr2D 92.291 467 16 4 3348 3814 621951809 621951363 0.000000e+00 645.0
15 TraesCS2B01G574200 chr2D 87.612 557 52 13 987 1537 582869037 582869582 6.950000e-177 630.0
16 TraesCS2B01G574200 chr2D 93.382 272 16 2 2888 3158 621952066 621951796 5.930000e-108 401.0
17 TraesCS2B01G574200 chr2D 93.333 60 4 0 48 107 621955073 621955014 5.250000e-14 89.8
18 TraesCS2B01G574200 chr3D 83.012 830 104 22 953 1765 570096792 570095983 0.000000e+00 717.0
19 TraesCS2B01G574200 chr3D 88.656 573 50 9 1884 2448 436318527 436319092 0.000000e+00 684.0
20 TraesCS2B01G574200 chr3D 92.197 346 24 3 1372 1714 436318072 436318417 1.590000e-133 486.0
21 TraesCS2B01G574200 chr3D 83.301 515 57 12 1440 1937 277239998 277240500 7.520000e-122 448.0
22 TraesCS2B01G574200 chr4B 88.908 577 48 9 1884 2452 378837115 378836547 0.000000e+00 697.0
23 TraesCS2B01G574200 chr4B 89.720 321 30 3 1400 1717 378837542 378837222 1.280000e-109 407.0
24 TraesCS2B01G574200 chr4B 96.714 213 4 3 3141 3353 423055704 423055495 6.060000e-93 351.0
25 TraesCS2B01G574200 chr7B 88.235 578 51 10 1884 2452 608285942 608286511 0.000000e+00 675.0
26 TraesCS2B01G574200 chr7B 88.442 398 37 7 1142 1538 744691954 744691565 4.460000e-129 472.0
27 TraesCS2B01G574200 chr7B 89.720 321 30 3 1400 1717 608285515 608285835 1.280000e-109 407.0
28 TraesCS2B01G574200 chr7B 80.620 516 69 14 1440 1937 234761545 234762047 1.670000e-98 370.0
29 TraesCS2B01G574200 chr7B 99.485 194 1 0 3158 3351 246011555 246011362 1.690000e-93 353.0
30 TraesCS2B01G574200 chr7B 100.000 191 0 0 3158 3348 443081576 443081766 1.690000e-93 353.0
31 TraesCS2B01G574200 chr7B 86.923 260 27 1 1611 1870 278031110 278031362 6.240000e-73 285.0
32 TraesCS2B01G574200 chr7B 86.829 205 14 7 1013 1213 744692153 744691958 2.310000e-52 217.0
33 TraesCS2B01G574200 chr5B 87.522 577 56 9 1884 2452 645187290 645187858 0.000000e+00 652.0
34 TraesCS2B01G574200 chr5B 89.937 318 29 3 1400 1714 645186863 645187180 1.280000e-109 407.0
35 TraesCS2B01G574200 chr5B 98.492 199 1 2 3159 3357 458934570 458934374 2.180000e-92 350.0
36 TraesCS2B01G574200 chr5D 82.913 515 59 11 1440 1937 511351815 511351313 1.630000e-118 436.0
37 TraesCS2B01G574200 chr4D 82.524 515 61 15 1440 1937 289495035 289495537 3.520000e-115 425.0
38 TraesCS2B01G574200 chr7A 82.330 515 59 13 1440 1937 305581928 305581429 5.890000e-113 418.0
39 TraesCS2B01G574200 chr7A 90.847 295 24 3 1426 1717 633539946 633539652 3.570000e-105 392.0
40 TraesCS2B01G574200 chr5A 91.438 292 22 3 1426 1714 546946614 546946905 7.680000e-107 398.0
41 TraesCS2B01G574200 chr1B 91.438 292 22 3 1426 1714 21657685 21657976 7.680000e-107 398.0
42 TraesCS2B01G574200 chr1B 97.561 205 3 2 3152 3354 466262899 466263103 2.180000e-92 350.0
43 TraesCS2B01G574200 chr6B 99.485 194 0 1 3158 3351 422696833 422697025 6.060000e-93 351.0
44 TraesCS2B01G574200 chr6B 99.462 186 1 0 3159 3344 387145161 387144976 4.720000e-89 339.0
45 TraesCS2B01G574200 chr6B 88.701 177 14 4 1884 2059 54644999 54645170 1.070000e-50 211.0
46 TraesCS2B01G574200 chr6A 94.690 226 8 4 3156 3379 310143743 310143966 7.840000e-92 348.0
47 TraesCS2B01G574200 chr3A 98.485 198 1 2 3159 3356 437863747 437863552 7.840000e-92 348.0
48 TraesCS2B01G574200 chr7D 87.059 255 19 6 1118 1372 41261792 41262032 3.750000e-70 276.0
49 TraesCS2B01G574200 chr3B 88.701 177 13 5 1884 2059 789066536 789066366 3.860000e-50 209.0


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 TraesCS2B01G574200 chr2B 763837923 763841736 3813 False 7044.00 7044 100.0000 1 3814 1 chr2B.!!$F2 3813
1 TraesCS2B01G574200 chr2B 52187608 52188555 947 True 502.00 619 88.3660 1400 2403 2 chr2B.!!$R3 1003
2 TraesCS2B01G574200 chr2B 312363198 312364523 1325 True 342.00 377 90.4430 1142 1870 2 chr2B.!!$R4 728
3 TraesCS2B01G574200 chr2B 737640894 737641710 816 False 211.50 267 91.0245 1112 1842 2 chr2B.!!$F4 730
4 TraesCS2B01G574200 chr2A 753612979 753616494 3515 False 2311.50 3838 92.9385 13 3814 2 chr2A.!!$F1 3801
5 TraesCS2B01G574200 chr2D 621951363 621955073 3710 True 960.95 2708 92.2135 48 3814 4 chr2D.!!$R1 3766
6 TraesCS2B01G574200 chr2D 582869037 582869582 545 False 630.00 630 87.6120 987 1537 1 chr2D.!!$F1 550
7 TraesCS2B01G574200 chr3D 570095983 570096792 809 True 717.00 717 83.0120 953 1765 1 chr3D.!!$R1 812
8 TraesCS2B01G574200 chr3D 436318072 436319092 1020 False 585.00 684 90.4265 1372 2448 2 chr3D.!!$F2 1076
9 TraesCS2B01G574200 chr3D 277239998 277240500 502 False 448.00 448 83.3010 1440 1937 1 chr3D.!!$F1 497
10 TraesCS2B01G574200 chr4B 378836547 378837542 995 True 552.00 697 89.3140 1400 2452 2 chr4B.!!$R2 1052
11 TraesCS2B01G574200 chr7B 608285515 608286511 996 False 541.00 675 88.9775 1400 2452 2 chr7B.!!$F4 1052
12 TraesCS2B01G574200 chr7B 234761545 234762047 502 False 370.00 370 80.6200 1440 1937 1 chr7B.!!$F1 497
13 TraesCS2B01G574200 chr7B 744691565 744692153 588 True 344.50 472 87.6355 1013 1538 2 chr7B.!!$R2 525
14 TraesCS2B01G574200 chr5B 645186863 645187858 995 False 529.50 652 88.7295 1400 2452 2 chr5B.!!$F1 1052
15 TraesCS2B01G574200 chr5D 511351313 511351815 502 True 436.00 436 82.9130 1440 1937 1 chr5D.!!$R1 497
16 TraesCS2B01G574200 chr4D 289495035 289495537 502 False 425.00 425 82.5240 1440 1937 1 chr4D.!!$F1 497

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
558 768 0.034186 ATCAATCCCTTTGCCGCTCA 60.034 50.0 0.0 0.0 35.16 4.26 F
918 1148 0.035056 CAGTCCACCACAATCCCCTC 60.035 60.0 0.0 0.0 0.00 4.30 F
919 1149 0.178861 AGTCCACCACAATCCCCTCT 60.179 55.0 0.0 0.0 0.00 3.69 F
920 1150 0.253327 GTCCACCACAATCCCCTCTC 59.747 60.0 0.0 0.0 0.00 3.20 F
1767 2927 0.548031 TCAAGGATGGATCTGCCCAC 59.452 55.0 0.0 0.0 39.34 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1949 3127 0.396435 AAGAGCCCACACGTCATGAA 59.604 50.000 0.00 0.0 0.00 2.57 R
1951 3129 1.300971 CCAAGAGCCCACACGTCATG 61.301 60.000 0.00 0.0 0.00 3.07 R
2073 3252 1.381165 AACCCACGTTGTGACCAAGC 61.381 55.000 0.00 0.0 35.23 4.01 R
2362 3549 2.111384 AGTGATGGGTACGCAAGAGAT 58.889 47.619 17.26 0.0 43.62 2.75 R
3189 4483 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.0 44.78 4.85 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
24 25 3.670055 CAGTTTGCGCAAGGTAATTTCTG 59.330 43.478 23.68 16.28 38.28 3.02
38 39 8.554835 AGGTAATTTCTGCTCTCTTTCTTAAC 57.445 34.615 0.00 0.00 0.00 2.01
46 47 6.146184 TCTGCTCTCTTTCTTAACAAATCACG 59.854 38.462 0.00 0.00 0.00 4.35
107 109 7.230510 TGCTACTCTTGTAATTGTTTGTCCATT 59.769 33.333 0.00 0.00 0.00 3.16
169 356 8.846211 AGTACTTTGTTACAGTTATTGCAACAT 58.154 29.630 0.00 0.00 41.47 2.71
199 386 7.313646 AGTTTGCTGCTATTATCGATATACGT 58.686 34.615 5.84 0.00 43.13 3.57
295 485 8.349568 ACAAGAATACTAAGGACCAAATTTCC 57.650 34.615 0.00 0.00 0.00 3.13
299 490 2.041216 ACTAAGGACCAAATTTCCGGCT 59.959 45.455 0.00 0.00 38.29 5.52
303 494 1.304962 ACCAAATTTCCGGCTCCCC 60.305 57.895 0.00 0.00 0.00 4.81
479 672 8.610248 TGTATGATCAAAGAAGAAAACGGTTA 57.390 30.769 0.00 0.00 0.00 2.85
499 692 6.038825 CGGTTATTTTACCAACCATATGCAGA 59.961 38.462 0.00 0.00 43.70 4.26
500 693 7.255451 CGGTTATTTTACCAACCATATGCAGAT 60.255 37.037 0.00 0.00 43.70 2.90
501 694 8.082242 GGTTATTTTACCAACCATATGCAGATC 58.918 37.037 0.00 0.00 43.13 2.75
502 695 8.629158 GTTATTTTACCAACCATATGCAGATCA 58.371 33.333 0.00 0.00 0.00 2.92
503 696 7.658525 ATTTTACCAACCATATGCAGATCAA 57.341 32.000 0.00 0.00 0.00 2.57
504 697 7.473735 TTTTACCAACCATATGCAGATCAAA 57.526 32.000 0.00 0.00 0.00 2.69
505 698 6.698008 TTACCAACCATATGCAGATCAAAG 57.302 37.500 0.00 0.00 0.00 2.77
506 699 3.382546 ACCAACCATATGCAGATCAAAGC 59.617 43.478 0.00 0.00 0.00 3.51
507 700 3.382227 CCAACCATATGCAGATCAAAGCA 59.618 43.478 9.46 9.46 45.92 3.91
508 701 4.357142 CAACCATATGCAGATCAAAGCAC 58.643 43.478 9.27 0.00 44.49 4.40
520 730 7.130917 GCAGATCAAAGCACATCTTACAATAG 58.869 38.462 0.00 0.00 33.88 1.73
554 764 0.944386 CGGTATCAATCCCTTTGCCG 59.056 55.000 0.00 0.00 33.93 5.69
558 768 0.034186 ATCAATCCCTTTGCCGCTCA 60.034 50.000 0.00 0.00 35.16 4.26
562 772 0.257039 ATCCCTTTGCCGCTCATTCT 59.743 50.000 0.00 0.00 0.00 2.40
563 773 0.392998 TCCCTTTGCCGCTCATTCTC 60.393 55.000 0.00 0.00 0.00 2.87
565 775 1.012841 CCTTTGCCGCTCATTCTCTC 58.987 55.000 0.00 0.00 0.00 3.20
573 783 3.122297 CCGCTCATTCTCTCAGAATCAC 58.878 50.000 0.00 0.00 42.67 3.06
578 788 6.183360 CGCTCATTCTCTCAGAATCACAAAAT 60.183 38.462 0.00 0.00 42.67 1.82
579 789 7.188157 GCTCATTCTCTCAGAATCACAAAATC 58.812 38.462 0.00 0.00 42.67 2.17
580 790 7.621428 TCATTCTCTCAGAATCACAAAATCC 57.379 36.000 0.00 0.00 42.67 3.01
600 813 3.994392 TCCTTCGAGTTTCCATTTCTTCG 59.006 43.478 0.00 0.00 0.00 3.79
650 865 2.156051 AACGGCCCTCGAGTCAGTTC 62.156 60.000 12.31 0.00 42.43 3.01
659 874 1.199327 TCGAGTCAGTTCGAGCGAAAT 59.801 47.619 6.91 3.07 44.00 2.17
660 875 2.417586 TCGAGTCAGTTCGAGCGAAATA 59.582 45.455 6.91 0.00 44.00 1.40
739 955 2.856720 GCGTTCGGATTCAAGCAACAAA 60.857 45.455 0.00 0.00 0.00 2.83
740 956 3.367607 CGTTCGGATTCAAGCAACAAAA 58.632 40.909 0.00 0.00 0.00 2.44
741 957 3.794028 CGTTCGGATTCAAGCAACAAAAA 59.206 39.130 0.00 0.00 0.00 1.94
805 1021 3.119388 CCACATGTCATTGACCAACCATC 60.119 47.826 14.05 0.00 0.00 3.51
838 1054 0.683973 CTCCTGAATCCCCGATCCAG 59.316 60.000 0.00 0.00 0.00 3.86
913 1143 2.086869 CATCACCAGTCCACCACAATC 58.913 52.381 0.00 0.00 0.00 2.67
914 1144 0.400213 TCACCAGTCCACCACAATCC 59.600 55.000 0.00 0.00 0.00 3.01
915 1145 0.609131 CACCAGTCCACCACAATCCC 60.609 60.000 0.00 0.00 0.00 3.85
916 1146 1.000896 CCAGTCCACCACAATCCCC 60.001 63.158 0.00 0.00 0.00 4.81
917 1147 1.500783 CCAGTCCACCACAATCCCCT 61.501 60.000 0.00 0.00 0.00 4.79
918 1148 0.035056 CAGTCCACCACAATCCCCTC 60.035 60.000 0.00 0.00 0.00 4.30
919 1149 0.178861 AGTCCACCACAATCCCCTCT 60.179 55.000 0.00 0.00 0.00 3.69
920 1150 0.253327 GTCCACCACAATCCCCTCTC 59.747 60.000 0.00 0.00 0.00 3.20
921 1151 0.914417 TCCACCACAATCCCCTCTCC 60.914 60.000 0.00 0.00 0.00 3.71
922 1152 1.609783 CACCACAATCCCCTCTCCC 59.390 63.158 0.00 0.00 0.00 4.30
923 1153 0.916358 CACCACAATCCCCTCTCCCT 60.916 60.000 0.00 0.00 0.00 4.20
932 1162 0.926220 CCCCTCTCCCTCCCCATTTT 60.926 60.000 0.00 0.00 0.00 1.82
949 1179 3.430333 TTTTCCAAAGCTCGACCAAAC 57.570 42.857 0.00 0.00 0.00 2.93
1274 1756 2.266055 GTCCTCTCCAACGCCCTG 59.734 66.667 0.00 0.00 0.00 4.45
1414 2566 2.025898 GTCCAGAGTAGGAGTAGCACC 58.974 57.143 0.00 0.00 38.64 5.01
1478 2630 1.424493 GCTGTGGTCGTATGCTCTGC 61.424 60.000 0.00 0.00 0.00 4.26
1573 2728 0.822164 AATCATGCCCTGCTTTGCTC 59.178 50.000 0.00 0.00 0.00 4.26
1633 2788 3.118920 TGTTCAAACTGAAGTCGTCCAGA 60.119 43.478 0.00 0.00 37.00 3.86
1703 2863 0.957888 GGCCTGAGCACTTTGGAGTC 60.958 60.000 0.00 0.00 42.56 3.36
1723 2883 6.407525 GGAGTCTGGCTGTAGTTTGAGATTAT 60.408 42.308 0.00 0.00 0.00 1.28
1737 2897 7.559170 AGTTTGAGATTATTCTTTGGGAGATGG 59.441 37.037 0.00 0.00 33.49 3.51
1746 2906 2.642171 TTGGGAGATGGTAGAGTGGT 57.358 50.000 0.00 0.00 0.00 4.16
1767 2927 0.548031 TCAAGGATGGATCTGCCCAC 59.452 55.000 0.00 0.00 39.34 4.61
1773 2933 0.835941 ATGGATCTGCCCACTCAGTC 59.164 55.000 0.00 0.00 39.34 3.51
1780 2940 1.375268 GCCCACTCAGTCTGCAGAC 60.375 63.158 34.82 34.82 45.08 3.51
1861 3028 6.936968 ACATACTCCCTTCTCTACAAAGTT 57.063 37.500 0.00 0.00 0.00 2.66
1877 3044 9.760077 TCTACAAAGTTAAGACTAAAGAGGTTG 57.240 33.333 0.00 0.00 34.21 3.77
1933 3111 5.869649 TGCTAGCACATGTCCTTTATCTA 57.130 39.130 14.93 0.00 0.00 1.98
1939 3117 6.234177 AGCACATGTCCTTTATCTATTAGCC 58.766 40.000 0.00 0.00 0.00 3.93
2109 3288 4.069304 TGGGTTTCTGTTAACTTGATCGG 58.931 43.478 7.22 0.00 0.00 4.18
2168 3353 8.841300 TGATTATTGTGTAGCACTGTTTTGTAA 58.159 29.630 0.90 0.00 35.11 2.41
2342 3529 0.976641 TTGCCATCAAGAGAGACCGT 59.023 50.000 0.00 0.00 0.00 4.83
2362 3549 9.189156 AGACCGTACAGTTTTTATACAGGTATA 57.811 33.333 0.00 0.00 30.88 1.47
2466 3654 6.037786 TCATGTACGATCTCCTTTTGTCTT 57.962 37.500 0.00 0.00 0.00 3.01
2469 3657 7.921214 TCATGTACGATCTCCTTTTGTCTTATC 59.079 37.037 0.00 0.00 0.00 1.75
2527 3715 4.277476 GGTGGTTTCATGTATTGGGATGA 58.723 43.478 0.00 0.00 0.00 2.92
2568 3756 7.224753 ACGCTCATTTACATTGGTGAGTTATAG 59.775 37.037 0.00 0.00 40.08 1.31
2606 3794 1.742268 GTCCTCTTGGATTTCTGCAGC 59.258 52.381 9.47 0.00 45.29 5.25
2667 3855 4.288626 TGGGCTTTCTTTCAGGTGTACTAT 59.711 41.667 0.00 0.00 0.00 2.12
2949 4242 2.549754 CCTTAGCATATTTCTGGGCGTG 59.450 50.000 0.00 0.00 0.00 5.34
3124 4418 4.472496 ACTAGAGTTTAGTAGGGCCTAGC 58.528 47.826 15.05 9.19 0.00 3.42
3125 4419 3.399952 AGAGTTTAGTAGGGCCTAGCA 57.600 47.619 15.05 1.14 0.00 3.49
3161 4455 8.635877 AATTGTTAGAAGCTACTACGATGAAG 57.364 34.615 0.00 0.00 0.00 3.02
3162 4456 6.132791 TGTTAGAAGCTACTACGATGAAGG 57.867 41.667 0.00 0.00 0.00 3.46
3163 4457 5.067413 TGTTAGAAGCTACTACGATGAAGGG 59.933 44.000 0.00 0.00 0.00 3.95
3164 4458 2.959707 AGAAGCTACTACGATGAAGGGG 59.040 50.000 0.00 0.00 0.00 4.79
3165 4459 2.750141 AGCTACTACGATGAAGGGGA 57.250 50.000 0.00 0.00 0.00 4.81
3166 4460 2.588620 AGCTACTACGATGAAGGGGAG 58.411 52.381 0.00 0.00 0.00 4.30
3167 4461 1.000052 GCTACTACGATGAAGGGGAGC 60.000 57.143 0.00 0.00 0.00 4.70
3168 4462 1.614413 CTACTACGATGAAGGGGAGCC 59.386 57.143 0.00 0.00 0.00 4.70
3169 4463 0.032017 ACTACGATGAAGGGGAGCCT 60.032 55.000 0.00 0.00 0.00 4.58
3170 4464 1.123928 CTACGATGAAGGGGAGCCTT 58.876 55.000 0.00 0.00 0.00 4.35
3171 4465 0.830648 TACGATGAAGGGGAGCCTTG 59.169 55.000 0.00 0.00 0.00 3.61
3172 4466 1.153086 CGATGAAGGGGAGCCTTGG 60.153 63.158 0.00 0.00 0.00 3.61
3173 4467 1.454663 GATGAAGGGGAGCCTTGGC 60.455 63.158 2.97 2.97 0.00 4.52
3174 4468 3.350031 ATGAAGGGGAGCCTTGGCG 62.350 63.158 5.95 0.00 0.00 5.69
3182 4476 3.605749 GAGCCTTGGCGCAGTGGTA 62.606 63.158 10.83 0.00 0.00 3.25
3183 4477 2.671619 GCCTTGGCGCAGTGGTAA 60.672 61.111 10.83 0.00 0.00 2.85
3184 4478 2.265182 GCCTTGGCGCAGTGGTAAA 61.265 57.895 10.83 0.00 0.00 2.01
3185 4479 1.875963 CCTTGGCGCAGTGGTAAAG 59.124 57.895 10.83 0.71 0.00 1.85
3186 4480 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
3187 4481 1.228124 TTGGCGCAGTGGTAAAGCT 60.228 52.632 10.83 0.00 0.00 3.74
3188 4482 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
3193 4487 1.878775 CAGTGGTAAAGCTGCTGCC 59.121 57.895 12.44 7.07 40.80 4.85
3194 4488 0.607489 CAGTGGTAAAGCTGCTGCCT 60.607 55.000 12.44 2.45 40.80 4.75
3195 4489 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35
3196 4490 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
3197 4491 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
3198 4492 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
3199 4493 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
3200 4494 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
3201 4495 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
3202 4496 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
3203 4497 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
3204 4498 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
3205 4499 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
3206 4500 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
3207 4501 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
3222 4516 2.859165 TGAGGTCATGGGTTCAAGTC 57.141 50.000 0.00 0.00 0.00 3.01
3223 4517 1.351017 TGAGGTCATGGGTTCAAGTCC 59.649 52.381 0.00 0.00 0.00 3.85
3224 4518 1.630878 GAGGTCATGGGTTCAAGTCCT 59.369 52.381 0.00 0.00 0.00 3.85
3225 4519 1.352352 AGGTCATGGGTTCAAGTCCTG 59.648 52.381 0.00 0.00 0.00 3.86
3226 4520 1.614317 GGTCATGGGTTCAAGTCCTGG 60.614 57.143 0.00 0.00 0.00 4.45
3227 4521 1.351017 GTCATGGGTTCAAGTCCTGGA 59.649 52.381 0.00 0.00 0.00 3.86
3228 4522 2.061848 TCATGGGTTCAAGTCCTGGAA 58.938 47.619 0.00 0.00 0.00 3.53
3229 4523 2.445145 TCATGGGTTCAAGTCCTGGAAA 59.555 45.455 0.00 0.00 0.00 3.13
3230 4524 2.358322 TGGGTTCAAGTCCTGGAAAC 57.642 50.000 0.00 0.00 0.00 2.78
3231 4525 1.566703 TGGGTTCAAGTCCTGGAAACA 59.433 47.619 0.00 0.00 32.36 2.83
3245 4539 4.431416 TGGAAACAGCCTCTTACAGAAA 57.569 40.909 0.00 0.00 35.01 2.52
3246 4540 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
3247 4541 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
3248 4542 4.762251 GGAAACAGCCTCTTACAGAAATGT 59.238 41.667 0.00 0.00 0.00 2.71
3249 4543 5.938125 GGAAACAGCCTCTTACAGAAATGTA 59.062 40.000 0.00 0.00 0.00 2.29
3250 4544 6.092807 GGAAACAGCCTCTTACAGAAATGTAG 59.907 42.308 0.00 0.00 0.00 2.74
3251 4545 5.091261 ACAGCCTCTTACAGAAATGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
3252 4546 4.080863 ACAGCCTCTTACAGAAATGTAGGG 60.081 45.833 0.00 0.66 0.00 3.53
3253 4547 4.162320 CAGCCTCTTACAGAAATGTAGGGA 59.838 45.833 0.00 0.00 0.00 4.20
3254 4548 4.783227 AGCCTCTTACAGAAATGTAGGGAA 59.217 41.667 0.00 0.00 0.00 3.97
3255 4549 5.250774 AGCCTCTTACAGAAATGTAGGGAAA 59.749 40.000 0.00 0.00 0.00 3.13
3256 4550 5.586643 GCCTCTTACAGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
3257 4551 6.116126 CCTCTTACAGAAATGTAGGGAAAGG 58.884 44.000 0.00 0.00 0.00 3.11
3258 4552 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
3259 4553 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
3260 4554 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
3261 4555 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
3262 4556 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
3263 4557 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
3264 4558 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
3265 4559 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
3266 4560 0.535797 GTAGGGAAAGGCTGCGTACT 59.464 55.000 0.00 0.00 34.81 2.73
3267 4561 1.753073 GTAGGGAAAGGCTGCGTACTA 59.247 52.381 0.00 0.00 34.81 1.82
3268 4562 1.497161 AGGGAAAGGCTGCGTACTAT 58.503 50.000 0.00 0.00 0.00 2.12
3269 4563 2.674420 AGGGAAAGGCTGCGTACTATA 58.326 47.619 0.00 0.00 0.00 1.31
3270 4564 2.628657 AGGGAAAGGCTGCGTACTATAG 59.371 50.000 0.00 0.00 0.00 1.31
3271 4565 2.626743 GGGAAAGGCTGCGTACTATAGA 59.373 50.000 6.78 0.00 0.00 1.98
3272 4566 3.552478 GGGAAAGGCTGCGTACTATAGAC 60.552 52.174 6.78 0.00 0.00 2.59
3273 4567 3.552478 GGAAAGGCTGCGTACTATAGACC 60.552 52.174 6.78 0.00 0.00 3.85
3274 4568 1.618487 AGGCTGCGTACTATAGACCC 58.382 55.000 6.78 0.00 0.00 4.46
3275 4569 1.133575 AGGCTGCGTACTATAGACCCA 60.134 52.381 6.78 0.00 0.00 4.51
3276 4570 1.684983 GGCTGCGTACTATAGACCCAA 59.315 52.381 6.78 0.00 0.00 4.12
3277 4571 2.101917 GGCTGCGTACTATAGACCCAAA 59.898 50.000 6.78 0.00 0.00 3.28
3278 4572 3.381949 GCTGCGTACTATAGACCCAAAG 58.618 50.000 6.78 0.00 0.00 2.77
3279 4573 3.181478 GCTGCGTACTATAGACCCAAAGT 60.181 47.826 6.78 0.00 0.00 2.66
3280 4574 4.360563 CTGCGTACTATAGACCCAAAGTG 58.639 47.826 6.78 0.00 0.00 3.16
3281 4575 3.131577 TGCGTACTATAGACCCAAAGTGG 59.868 47.826 6.78 0.00 37.25 4.00
3282 4576 3.131755 GCGTACTATAGACCCAAAGTGGT 59.868 47.826 6.78 0.00 42.79 4.16
3287 4581 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
3288 4582 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
3289 4583 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
3290 4584 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
3291 4585 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
3292 4586 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
3293 4587 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
3294 4588 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
3295 4589 2.606826 GTGGTCGGACCCTTCCCT 60.607 66.667 23.81 0.00 38.99 4.20
3296 4590 2.606519 TGGTCGGACCCTTCCCTG 60.607 66.667 23.81 0.00 38.99 4.45
3297 4591 3.400054 GGTCGGACCCTTCCCTGG 61.400 72.222 16.55 0.00 38.99 4.45
3298 4592 2.284405 GTCGGACCCTTCCCTGGA 60.284 66.667 0.00 0.00 38.99 3.86
3299 4593 2.284405 TCGGACCCTTCCCTGGAC 60.284 66.667 0.00 0.00 38.99 4.02
3300 4594 3.400054 CGGACCCTTCCCTGGACC 61.400 72.222 0.00 0.00 38.99 4.46
3301 4595 3.015753 GGACCCTTCCCTGGACCC 61.016 72.222 0.00 0.00 35.57 4.46
3302 4596 2.125225 GACCCTTCCCTGGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
3303 4597 2.204151 ACCCTTCCCTGGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
3304 4598 3.732849 CCCTTCCCTGGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
3305 4599 4.101448 CCTTCCCTGGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
3306 4600 4.785453 CTTCCCTGGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
3331 4625 3.558674 GAGCTACATGCACCAGGTT 57.441 52.632 0.00 0.00 45.94 3.50
3332 4626 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
3333 4627 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
3334 4628 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
3335 4629 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
3336 4630 1.788518 TACATGCACCAGGTTGCCCT 61.789 55.000 10.46 0.00 42.25 5.19
3337 4631 1.909781 CATGCACCAGGTTGCCCTT 60.910 57.895 10.46 0.00 42.25 3.95
3338 4632 1.152269 ATGCACCAGGTTGCCCTTT 60.152 52.632 10.46 0.00 42.25 3.11
3339 4633 0.763986 ATGCACCAGGTTGCCCTTTT 60.764 50.000 10.46 0.00 42.25 2.27
3340 4634 0.980231 TGCACCAGGTTGCCCTTTTT 60.980 50.000 10.46 0.00 42.25 1.94
3669 4963 9.167311 GTTTATCAACATCAATGAGTCTACCTT 57.833 33.333 0.00 0.00 32.54 3.50
3720 5014 0.108089 TCACCGCTAGCCGCATTTTA 60.108 50.000 9.66 0.00 39.08 1.52
3804 5098 6.663953 TGATTCTCCTACTACTGTAGCTTGTT 59.336 38.462 14.55 0.00 43.51 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.958091 ATTACCTTGCGCAAACTGCA 59.042 45.000 25.01 7.69 45.36 4.41
1 2 2.064573 AATTACCTTGCGCAAACTGC 57.935 45.000 25.01 0.00 40.69 4.40
2 3 3.670055 CAGAAATTACCTTGCGCAAACTG 59.330 43.478 25.01 17.16 0.00 3.16
3 4 3.857010 GCAGAAATTACCTTGCGCAAACT 60.857 43.478 25.01 13.95 0.00 2.66
4 5 2.408368 GCAGAAATTACCTTGCGCAAAC 59.592 45.455 25.01 7.96 0.00 2.93
5 6 2.295909 AGCAGAAATTACCTTGCGCAAA 59.704 40.909 25.01 9.74 0.00 3.68
6 7 1.885887 AGCAGAAATTACCTTGCGCAA 59.114 42.857 23.48 23.48 0.00 4.85
7 8 1.468520 GAGCAGAAATTACCTTGCGCA 59.531 47.619 5.66 5.66 0.00 6.09
8 9 1.740025 AGAGCAGAAATTACCTTGCGC 59.260 47.619 0.00 0.00 0.00 6.09
9 10 3.265791 AGAGAGCAGAAATTACCTTGCG 58.734 45.455 0.00 0.00 0.00 4.85
10 11 5.414144 AGAAAGAGAGCAGAAATTACCTTGC 59.586 40.000 0.00 0.00 0.00 4.01
11 12 7.446001 AAGAAAGAGAGCAGAAATTACCTTG 57.554 36.000 0.00 0.00 0.00 3.61
24 25 6.074005 CACGTGATTTGTTAAGAAAGAGAGC 58.926 40.000 10.90 0.00 0.00 4.09
38 39 3.354089 AAAGAAGTGGCACGTGATTTG 57.646 42.857 22.23 0.00 0.00 2.32
107 109 7.829725 ACAAATATAGCAAAGCAATCAGTGAA 58.170 30.769 0.00 0.00 0.00 3.18
169 356 9.875691 ATATCGATAATAGCAGCAAACTATCAA 57.124 29.630 9.61 0.00 30.00 2.57
197 384 9.935682 ATAGCAACATCAATGAGTTAATAAACG 57.064 29.630 0.00 0.00 40.73 3.60
387 580 1.874466 GTCGTCTCTAGGCAAGCGC 60.874 63.158 0.00 0.00 37.44 5.92
399 592 2.050351 CGACTTGCCACGTCGTCT 60.050 61.111 14.79 0.00 46.56 4.18
450 643 8.883731 CCGTTTTCTTCTTTGATCATACAGTAT 58.116 33.333 0.00 0.00 0.00 2.12
451 644 7.876068 ACCGTTTTCTTCTTTGATCATACAGTA 59.124 33.333 0.00 0.00 0.00 2.74
452 645 6.710744 ACCGTTTTCTTCTTTGATCATACAGT 59.289 34.615 0.00 0.00 0.00 3.55
453 646 7.133891 ACCGTTTTCTTCTTTGATCATACAG 57.866 36.000 0.00 0.00 0.00 2.74
454 647 7.504924 AACCGTTTTCTTCTTTGATCATACA 57.495 32.000 0.00 0.00 0.00 2.29
479 672 7.658525 TTGATCTGCATATGGTTGGTAAAAT 57.341 32.000 4.56 0.00 0.00 1.82
499 692 8.049117 TCTTCCTATTGTAAGATGTGCTTTGAT 58.951 33.333 0.00 0.00 38.05 2.57
500 693 7.394016 TCTTCCTATTGTAAGATGTGCTTTGA 58.606 34.615 0.00 0.00 38.05 2.69
501 694 7.615582 TCTTCCTATTGTAAGATGTGCTTTG 57.384 36.000 0.00 0.00 38.05 2.77
502 695 8.515414 GTTTCTTCCTATTGTAAGATGTGCTTT 58.485 33.333 0.00 0.00 38.05 3.51
503 696 7.665559 TGTTTCTTCCTATTGTAAGATGTGCTT 59.334 33.333 0.00 0.00 40.68 3.91
504 697 7.168219 TGTTTCTTCCTATTGTAAGATGTGCT 58.832 34.615 0.00 0.00 32.05 4.40
505 698 7.377766 TGTTTCTTCCTATTGTAAGATGTGC 57.622 36.000 0.00 0.00 32.05 4.57
520 730 5.873179 TGATACCGACAAATGTTTCTTCC 57.127 39.130 0.00 0.00 0.00 3.46
554 764 6.492007 TTTTGTGATTCTGAGAGAATGAGC 57.508 37.500 3.55 0.00 44.41 4.26
558 768 7.065563 CGAAGGATTTTGTGATTCTGAGAGAAT 59.934 37.037 0.00 0.00 46.84 2.40
562 772 5.793817 TCGAAGGATTTTGTGATTCTGAGA 58.206 37.500 0.00 0.00 0.00 3.27
563 773 5.641209 ACTCGAAGGATTTTGTGATTCTGAG 59.359 40.000 0.00 0.00 32.23 3.35
565 775 5.869753 ACTCGAAGGATTTTGTGATTCTG 57.130 39.130 0.00 0.00 0.00 3.02
573 783 6.681777 AGAAATGGAAACTCGAAGGATTTTG 58.318 36.000 0.00 0.00 0.00 2.44
578 788 3.994392 CGAAGAAATGGAAACTCGAAGGA 59.006 43.478 0.00 0.00 0.00 3.36
579 789 3.746492 ACGAAGAAATGGAAACTCGAAGG 59.254 43.478 0.00 0.00 0.00 3.46
580 790 4.992381 ACGAAGAAATGGAAACTCGAAG 57.008 40.909 0.00 0.00 0.00 3.79
619 834 2.434185 GCCGTTGGATCGAGTGCA 60.434 61.111 0.00 0.00 0.00 4.57
622 837 2.683933 AGGGCCGTTGGATCGAGT 60.684 61.111 0.00 0.00 0.00 4.18
650 865 0.643820 GTGGGAACGTATTTCGCTCG 59.356 55.000 4.67 0.00 45.39 5.03
659 874 4.400251 AGAACTGATATTCGTGGGAACGTA 59.600 41.667 0.00 0.00 34.37 3.57
660 875 3.194968 AGAACTGATATTCGTGGGAACGT 59.805 43.478 0.00 0.00 34.37 3.99
711 927 3.786048 GCTTGAATCCGAACGCTAAAATG 59.214 43.478 0.00 0.00 0.00 2.32
712 928 3.438781 TGCTTGAATCCGAACGCTAAAAT 59.561 39.130 0.00 0.00 0.00 1.82
713 929 2.809119 TGCTTGAATCCGAACGCTAAAA 59.191 40.909 0.00 0.00 0.00 1.52
714 930 2.418692 TGCTTGAATCCGAACGCTAAA 58.581 42.857 0.00 0.00 0.00 1.85
715 931 2.087501 TGCTTGAATCCGAACGCTAA 57.912 45.000 0.00 0.00 0.00 3.09
716 932 1.730064 GTTGCTTGAATCCGAACGCTA 59.270 47.619 0.00 0.00 0.00 4.26
717 933 0.517316 GTTGCTTGAATCCGAACGCT 59.483 50.000 0.00 0.00 0.00 5.07
718 934 0.237235 TGTTGCTTGAATCCGAACGC 59.763 50.000 0.00 0.00 0.00 4.84
740 956 5.435291 TCCTTTGGCATGAACATTGTTTTT 58.565 33.333 3.08 0.00 0.00 1.94
741 957 5.033589 TCCTTTGGCATGAACATTGTTTT 57.966 34.783 3.08 0.00 0.00 2.43
742 958 4.686191 TCCTTTGGCATGAACATTGTTT 57.314 36.364 3.08 0.00 0.00 2.83
743 959 4.686191 TTCCTTTGGCATGAACATTGTT 57.314 36.364 0.63 0.63 0.00 2.83
744 960 4.686191 TTTCCTTTGGCATGAACATTGT 57.314 36.364 0.00 0.00 0.00 2.71
745 961 5.759273 TCTTTTTCCTTTGGCATGAACATTG 59.241 36.000 0.00 0.00 0.00 2.82
746 962 5.759763 GTCTTTTTCCTTTGGCATGAACATT 59.240 36.000 0.00 0.00 0.00 2.71
747 963 5.299949 GTCTTTTTCCTTTGGCATGAACAT 58.700 37.500 0.00 0.00 0.00 2.71
838 1054 0.174617 CCTCTCGGTCTCTGCCTTTC 59.825 60.000 0.00 0.00 0.00 2.62
913 1143 0.926220 AAAATGGGGAGGGAGAGGGG 60.926 60.000 0.00 0.00 0.00 4.79
914 1144 0.553333 GAAAATGGGGAGGGAGAGGG 59.447 60.000 0.00 0.00 0.00 4.30
915 1145 0.553333 GGAAAATGGGGAGGGAGAGG 59.447 60.000 0.00 0.00 0.00 3.69
916 1146 1.298953 TGGAAAATGGGGAGGGAGAG 58.701 55.000 0.00 0.00 0.00 3.20
917 1147 1.766951 TTGGAAAATGGGGAGGGAGA 58.233 50.000 0.00 0.00 0.00 3.71
918 1148 2.460669 CTTTGGAAAATGGGGAGGGAG 58.539 52.381 0.00 0.00 0.00 4.30
919 1149 1.552254 GCTTTGGAAAATGGGGAGGGA 60.552 52.381 0.00 0.00 0.00 4.20
920 1150 0.904649 GCTTTGGAAAATGGGGAGGG 59.095 55.000 0.00 0.00 0.00 4.30
921 1151 1.827344 GAGCTTTGGAAAATGGGGAGG 59.173 52.381 0.00 0.00 0.00 4.30
922 1152 1.474077 CGAGCTTTGGAAAATGGGGAG 59.526 52.381 0.00 0.00 0.00 4.30
923 1153 1.074727 TCGAGCTTTGGAAAATGGGGA 59.925 47.619 0.00 0.00 0.00 4.81
932 1162 0.536460 GGGTTTGGTCGAGCTTTGGA 60.536 55.000 16.64 0.00 0.00 3.53
1253 1735 2.182030 GCGTTGGAGAGGACCGAG 59.818 66.667 0.00 0.00 0.00 4.63
1274 1756 1.357334 GATGACGACGAGGAGGAGC 59.643 63.158 0.00 0.00 0.00 4.70
1344 1832 0.251077 AGAGCAAAGTGGGGAGCAAG 60.251 55.000 0.00 0.00 0.00 4.01
1347 1835 2.338785 GCAGAGCAAAGTGGGGAGC 61.339 63.158 0.00 0.00 0.00 4.70
1414 2566 5.231702 TCTAGTAGATCAGATCTCGAACGG 58.768 45.833 16.70 8.35 40.76 4.44
1529 2684 6.531594 TCAGTTATAATCTGCACGACTGAAAG 59.468 38.462 0.00 0.00 39.06 2.62
1573 2728 5.895928 TCAGCAGTAAGAGCATACAACTAG 58.104 41.667 0.00 0.00 0.00 2.57
1633 2788 6.423905 CAGTAATATACATTGTAGCAAGCCGT 59.576 38.462 2.53 0.00 0.00 5.68
1703 2863 7.856145 AAGAATAATCTCAAACTACAGCCAG 57.144 36.000 0.00 0.00 33.77 4.85
1723 2883 3.519510 CCACTCTACCATCTCCCAAAGAA 59.480 47.826 0.00 0.00 37.61 2.52
1737 2897 4.553330 TCCATCCTTGAAACCACTCTAC 57.447 45.455 0.00 0.00 0.00 2.59
1746 2906 1.640149 TGGGCAGATCCATCCTTGAAA 59.360 47.619 0.00 0.00 36.21 2.69
1780 2940 5.066593 GGTAAATTAGAAGATCCCCTGCAG 58.933 45.833 6.78 6.78 0.00 4.41
1781 2941 4.476846 TGGTAAATTAGAAGATCCCCTGCA 59.523 41.667 0.00 0.00 0.00 4.41
1782 2942 4.822350 GTGGTAAATTAGAAGATCCCCTGC 59.178 45.833 0.00 0.00 0.00 4.85
1783 2943 6.253946 AGTGGTAAATTAGAAGATCCCCTG 57.746 41.667 0.00 0.00 0.00 4.45
1784 2944 6.217693 ACAAGTGGTAAATTAGAAGATCCCCT 59.782 38.462 0.00 0.00 0.00 4.79
1785 2945 6.424032 ACAAGTGGTAAATTAGAAGATCCCC 58.576 40.000 0.00 0.00 0.00 4.81
1786 2946 6.542735 GGACAAGTGGTAAATTAGAAGATCCC 59.457 42.308 0.00 0.00 0.00 3.85
1842 3009 6.783482 AGTCTTAACTTTGTAGAGAAGGGAGT 59.217 38.462 0.00 0.00 28.74 3.85
1861 3028 6.827727 ACTTGAAGCAACCTCTTTAGTCTTA 58.172 36.000 0.00 0.00 0.00 2.10
1877 3044 4.756084 AACTGCTGTCATAACTTGAAGC 57.244 40.909 0.00 0.00 38.19 3.86
1933 3111 8.029522 CACGTCATGAATACAGTATAGGCTAAT 58.970 37.037 0.00 0.00 0.00 1.73
1939 3117 5.920840 CCCACACGTCATGAATACAGTATAG 59.079 44.000 0.00 0.00 0.00 1.31
1949 3127 0.396435 AAGAGCCCACACGTCATGAA 59.604 50.000 0.00 0.00 0.00 2.57
1951 3129 1.300971 CCAAGAGCCCACACGTCATG 61.301 60.000 0.00 0.00 0.00 3.07
2073 3252 1.381165 AACCCACGTTGTGACCAAGC 61.381 55.000 0.00 0.00 35.23 4.01
2130 3309 9.390795 GCTACACAATAATCAATTAAGATGCAG 57.609 33.333 0.00 0.00 0.00 4.41
2168 3353 9.709495 ATTGCGGTATTGCATAAATAAATGAAT 57.291 25.926 0.00 0.00 45.78 2.57
2362 3549 2.111384 AGTGATGGGTACGCAAGAGAT 58.889 47.619 17.26 0.00 43.62 2.75
2403 3590 3.315191 AGTTTGTGTGTGTGCAAGTATCC 59.685 43.478 0.00 0.00 0.00 2.59
2527 3715 7.440523 AAATGAGCGTAAAGAAGTTGAAGAT 57.559 32.000 0.00 0.00 0.00 2.40
2826 4014 2.683211 AAGAACTCACCAAATGGGCT 57.317 45.000 4.17 0.00 42.05 5.19
2949 4242 6.512297 ACAAATTCCACAGACAATGTTAACC 58.488 36.000 2.48 0.00 41.41 2.85
2999 4292 1.004277 AGGGATTTTTAGCGACTGCCA 59.996 47.619 0.00 0.00 44.31 4.92
3164 4458 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
3165 4459 2.690653 TTTACCACTGCGCCAAGGCT 62.691 55.000 4.18 0.00 39.32 4.58
3166 4460 2.200170 CTTTACCACTGCGCCAAGGC 62.200 60.000 4.18 0.00 37.85 4.35
3167 4461 1.875963 CTTTACCACTGCGCCAAGG 59.124 57.895 4.18 6.21 0.00 3.61
3168 4462 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
3169 4463 1.228124 AGCTTTACCACTGCGCCAA 60.228 52.632 4.18 0.00 0.00 4.52
3170 4464 1.965930 CAGCTTTACCACTGCGCCA 60.966 57.895 4.18 0.00 0.00 5.69
3171 4465 2.870372 CAGCTTTACCACTGCGCC 59.130 61.111 4.18 0.00 0.00 6.53
3175 4469 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.00 41.70 3.66
3176 4470 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
3177 4471 0.242017 CAAGGCAGCAGCTTTACCAC 59.758 55.000 0.00 0.00 38.07 4.16
3178 4472 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
3179 4473 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
3180 4474 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
3181 4475 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
3182 4476 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
3183 4477 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
3184 4478 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
3185 4479 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
3186 4480 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
3187 4481 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
3188 4482 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
3189 4483 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
3190 4484 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
3202 4496 2.025887 GGACTTGAACCCATGACCTCAT 60.026 50.000 0.00 0.00 36.96 2.90
3203 4497 1.351017 GGACTTGAACCCATGACCTCA 59.649 52.381 0.00 0.00 32.45 3.86
3204 4498 1.630878 AGGACTTGAACCCATGACCTC 59.369 52.381 0.00 0.00 37.82 3.85
3205 4499 1.352352 CAGGACTTGAACCCATGACCT 59.648 52.381 0.00 0.00 40.96 3.85
3206 4500 1.614317 CCAGGACTTGAACCCATGACC 60.614 57.143 0.00 0.00 34.29 4.02
3207 4501 1.351017 TCCAGGACTTGAACCCATGAC 59.649 52.381 0.00 0.00 0.00 3.06
3208 4502 1.741028 TCCAGGACTTGAACCCATGA 58.259 50.000 0.00 0.00 0.00 3.07
3209 4503 2.558359 GTTTCCAGGACTTGAACCCATG 59.442 50.000 0.00 0.00 0.00 3.66
3210 4504 2.176798 TGTTTCCAGGACTTGAACCCAT 59.823 45.455 0.00 0.00 0.00 4.00
3211 4505 1.566703 TGTTTCCAGGACTTGAACCCA 59.433 47.619 0.00 0.00 0.00 4.51
3212 4506 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
3213 4507 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
3214 4508 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
3215 4509 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
3216 4510 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
3217 4511 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
3218 4512 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
3219 4513 1.439543 AAGAGGCTGTTTCCAGGACT 58.560 50.000 0.00 0.00 39.22 3.85
3220 4514 2.038557 TGTAAGAGGCTGTTTCCAGGAC 59.961 50.000 0.90 0.00 39.22 3.85
3221 4515 2.303022 CTGTAAGAGGCTGTTTCCAGGA 59.697 50.000 0.90 0.00 35.89 3.86
3222 4516 2.303022 TCTGTAAGAGGCTGTTTCCAGG 59.697 50.000 17.71 5.83 38.67 4.45
3223 4517 3.685139 TCTGTAAGAGGCTGTTTCCAG 57.315 47.619 0.90 9.48 38.67 3.86
3235 4529 5.250774 AGCCTTTCCCTACATTTCTGTAAGA 59.749 40.000 0.00 0.00 44.68 2.10
3236 4530 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
3237 4531 5.253330 CAGCCTTTCCCTACATTTCTGTAA 58.747 41.667 0.00 0.00 37.41 2.41
3238 4532 4.843728 CAGCCTTTCCCTACATTTCTGTA 58.156 43.478 0.00 0.00 36.79 2.74
3239 4533 3.690460 CAGCCTTTCCCTACATTTCTGT 58.310 45.455 0.00 0.00 39.49 3.41
3240 4534 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
3241 4535 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
3242 4536 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
3243 4537 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
3244 4538 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
3245 4539 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
3246 4540 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
3247 4541 0.535797 AGTACGCAGCCTTTCCCTAC 59.464 55.000 0.00 0.00 0.00 3.18
3248 4542 2.148446 TAGTACGCAGCCTTTCCCTA 57.852 50.000 0.00 0.00 0.00 3.53
3249 4543 1.497161 ATAGTACGCAGCCTTTCCCT 58.503 50.000 0.00 0.00 0.00 4.20
3250 4544 2.626743 TCTATAGTACGCAGCCTTTCCC 59.373 50.000 0.00 0.00 0.00 3.97
3251 4545 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
3252 4546 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
3253 4547 2.364647 GGGTCTATAGTACGCAGCCTTT 59.635 50.000 0.00 0.00 0.00 3.11
3254 4548 1.962100 GGGTCTATAGTACGCAGCCTT 59.038 52.381 0.00 0.00 0.00 4.35
3255 4549 1.133575 TGGGTCTATAGTACGCAGCCT 60.134 52.381 13.98 0.00 35.18 4.58
3256 4550 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
3257 4551 3.181478 ACTTTGGGTCTATAGTACGCAGC 60.181 47.826 16.00 2.07 40.36 5.25
3258 4552 4.360563 CACTTTGGGTCTATAGTACGCAG 58.639 47.826 16.00 11.29 40.36 5.18
3259 4553 3.131577 CCACTTTGGGTCTATAGTACGCA 59.868 47.826 13.98 13.98 37.94 5.24
3260 4554 3.131755 ACCACTTTGGGTCTATAGTACGC 59.868 47.826 0.00 6.13 43.37 4.42
3261 4555 4.996788 ACCACTTTGGGTCTATAGTACG 57.003 45.455 0.00 0.00 43.37 3.67
3271 4565 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
3272 4566 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
3273 4567 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
3274 4568 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
3275 4569 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
3276 4570 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
3277 4571 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
3278 4572 2.606826 AGGGAAGGGTCCGACCAC 60.607 66.667 19.43 8.70 46.04 4.16
3279 4573 2.606519 CAGGGAAGGGTCCGACCA 60.607 66.667 19.43 0.00 46.04 4.02
3280 4574 3.400054 CCAGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
3281 4575 2.284405 TCCAGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
3282 4576 2.284405 GTCCAGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
3283 4577 3.400054 GGTCCAGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
3284 4578 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
3285 4579 2.125225 AGGGTCCAGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
3286 4580 2.204151 CAGGGTCCAGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
3287 4581 3.732849 GCAGGGTCCAGGGAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
3288 4582 4.101448 CGCAGGGTCCAGGGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
3289 4583 4.785453 GCGCAGGGTCCAGGGAAG 62.785 72.222 0.30 0.00 0.00 3.46
3301 4595 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
3304 4598 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
3305 4599 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
3306 4600 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
3307 4601 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
3313 4607 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
3314 4608 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
3315 4609 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
3316 4610 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
3317 4611 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
3341 4635 8.964772 AGGAGTTATCGTAGTAGCTTCTAAAAA 58.035 33.333 1.13 0.00 0.00 1.94
3342 4636 8.517062 AGGAGTTATCGTAGTAGCTTCTAAAA 57.483 34.615 1.13 0.00 0.00 1.52
3343 4637 8.517062 AAGGAGTTATCGTAGTAGCTTCTAAA 57.483 34.615 1.13 0.00 0.00 1.85
3344 4638 8.517062 AAAGGAGTTATCGTAGTAGCTTCTAA 57.483 34.615 1.13 0.00 0.00 2.10
3345 4639 8.517062 AAAAGGAGTTATCGTAGTAGCTTCTA 57.483 34.615 0.00 0.00 0.00 2.10
3346 4640 7.407393 AAAAGGAGTTATCGTAGTAGCTTCT 57.593 36.000 0.00 0.00 0.00 2.85
3347 4641 7.758528 TCAAAAAGGAGTTATCGTAGTAGCTTC 59.241 37.037 0.00 0.00 0.00 3.86
3348 4642 7.609056 TCAAAAAGGAGTTATCGTAGTAGCTT 58.391 34.615 0.00 0.00 0.00 3.74
3349 4643 7.166691 TCAAAAAGGAGTTATCGTAGTAGCT 57.833 36.000 0.00 0.00 0.00 3.32
3350 4644 7.330208 TGTTCAAAAAGGAGTTATCGTAGTAGC 59.670 37.037 0.00 0.00 0.00 3.58
3351 4645 8.752766 TGTTCAAAAAGGAGTTATCGTAGTAG 57.247 34.615 0.00 0.00 0.00 2.57
3353 4647 9.886132 ATATGTTCAAAAAGGAGTTATCGTAGT 57.114 29.630 0.00 0.00 0.00 2.73
3356 4650 9.449719 AGAATATGTTCAAAAAGGAGTTATCGT 57.550 29.630 4.92 0.00 36.79 3.73
3357 4651 9.708222 CAGAATATGTTCAAAAAGGAGTTATCG 57.292 33.333 4.92 0.00 36.79 2.92
3685 4979 4.766970 GAGCCCGACTCATGATGG 57.233 61.111 0.00 0.00 45.49 3.51
3706 5000 2.690683 TGCCCATAAAATGCGGCTAGC 61.691 52.381 6.04 6.04 43.02 3.42
3745 5039 2.540265 ACTATGTGAGCAGCATAGGC 57.460 50.000 19.29 0.00 45.98 3.93


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

AutoCloner maintained by Alex Coulton.