Multiple sequence alignment - TraesCS3A01G523000

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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 TraesCS3A01G523000 chr3A 100.000 2503 0 0 1 2503 738695017 738692515 0.000000e+00 4623.0
1 TraesCS3A01G523000 chr3A 84.427 1631 215 18 875 2479 738307643 738306026 0.000000e+00 1568.0
2 TraesCS3A01G523000 chr3A 81.454 949 142 19 883 1804 738250953 738250012 0.000000e+00 747.0
3 TraesCS3A01G523000 chr3A 84.548 686 78 14 930 1594 738808085 738807407 0.000000e+00 654.0
4 TraesCS3A01G523000 chr3A 77.728 1109 195 29 1417 2496 738856954 738855869 1.520000e-177 632.0
5 TraesCS3A01G523000 chr3A 89.738 458 26 10 501 939 738808857 738808402 1.560000e-157 566.0
6 TraesCS3A01G523000 chr3A 90.135 446 26 11 42 481 738820133 738819700 5.620000e-157 564.0
7 TraesCS3A01G523000 chr3A 100.000 302 0 0 2704 3005 738692314 738692013 2.620000e-155 558.0
8 TraesCS3A01G523000 chr3A 78.596 883 97 42 55 868 738308541 738307682 1.610000e-137 499.0
9 TraesCS3A01G523000 chr3A 94.361 266 15 0 1957 2222 738760412 738760147 2.790000e-110 409.0
10 TraesCS3A01G523000 chr3A 87.415 294 31 4 2215 2503 738759359 738759067 1.730000e-87 333.0
11 TraesCS3A01G523000 chr3A 78.669 511 76 17 1984 2487 738709572 738709088 2.910000e-80 309.0
12 TraesCS3A01G523000 chr3A 82.308 260 30 8 146 396 738593915 738593663 8.440000e-51 211.0
13 TraesCS3A01G523000 chr3A 82.308 260 30 8 146 396 738672410 738672158 8.440000e-51 211.0
14 TraesCS3A01G523000 chr3A 81.154 260 37 8 1031 1281 738225367 738225111 6.570000e-47 198.0
15 TraesCS3A01G523000 chr3A 81.323 257 36 4 1034 1281 738240241 738239988 6.570000e-47 198.0
16 TraesCS3A01G523000 chr3A 92.437 119 9 0 2887 3005 738758887 738758769 1.430000e-38 171.0
17 TraesCS3A01G523000 chr3A 83.420 193 20 5 213 397 738907853 738907665 5.150000e-38 169.0
18 TraesCS3A01G523000 chr3A 81.818 209 20 11 213 412 738319174 738318975 3.100000e-35 159.0
19 TraesCS3A01G523000 chr3A 86.620 142 10 4 880 1012 738663345 738663204 6.710000e-32 148.0
20 TraesCS3A01G523000 chr3A 86.290 124 11 3 132 250 738685516 738685394 2.430000e-26 130.0
21 TraesCS3A01G523000 chr3A 88.776 98 9 2 154 250 738215973 738215877 5.260000e-23 119.0
22 TraesCS3A01G523000 chr3A 90.164 61 6 0 139 199 738338575 738338515 2.480000e-11 80.5
23 TraesCS3A01G523000 chr3A 90.164 61 6 0 139 199 738720222 738720162 2.480000e-11 80.5
24 TraesCS3A01G523000 chr5B 81.517 633 98 11 1881 2503 621479176 621478553 1.240000e-138 503.0
25 TraesCS3A01G523000 chr5B 78.635 674 116 11 889 1536 621480144 621479473 3.580000e-114 422.0
26 TraesCS3A01G523000 chr5B 81.285 529 82 12 1982 2498 621470277 621469754 2.160000e-111 412.0
27 TraesCS3A01G523000 chr5B 76.253 838 150 30 882 1681 621471351 621470525 1.680000e-107 399.0
28 TraesCS3A01G523000 chr5A 84.000 525 66 9 1982 2503 624724891 624724382 3.480000e-134 488.0
29 TraesCS3A01G523000 chr5A 81.474 529 81 12 1982 2498 624712974 624712451 4.630000e-113 418.0
30 TraesCS3A01G523000 chr5A 76.570 828 151 27 889 1683 624725967 624725150 5.990000e-112 414.0
31 TraesCS3A01G523000 chr5A 75.685 839 155 22 882 1681 624714050 624713222 1.020000e-99 374.0
32 TraesCS3A01G523000 chr5A 89.888 89 9 0 2917 3005 624723764 624723676 6.810000e-22 115.0
33 TraesCS3A01G523000 chr5A 90.541 74 7 0 2921 2994 624712173 624712100 6.860000e-17 99.0
34 TraesCS3A01G523000 chr5D 79.656 639 99 22 1876 2499 500134333 500133711 5.950000e-117 431.0
35 TraesCS3A01G523000 chr5D 76.335 824 155 21 889 1680 500140284 500139469 3.610000e-109 405.0
36 TraesCS3A01G523000 chr3D 78.864 634 102 17 918 1525 605953201 605953828 1.680000e-107 399.0
37 TraesCS3A01G523000 chr3D 77.540 187 28 8 2817 2993 606002116 606002298 1.910000e-17 100.0
38 TraesCS3A01G523000 chr3D 88.889 81 8 1 2913 2993 606773669 606773590 6.860000e-17 99.0
39 TraesCS3A01G523000 chr3D 94.231 52 3 0 139 190 605344447 605344498 2.480000e-11 80.5
40 TraesCS3A01G523000 chrUn 83.838 198 30 2 2307 2503 42327464 42327268 1.420000e-43 187.0
41 TraesCS3A01G523000 chrUn 83.838 198 30 2 2307 2503 367633526 367633330 1.420000e-43 187.0
42 TraesCS3A01G523000 chrUn 82.787 122 16 4 2872 2993 42327137 42327021 1.470000e-18 104.0
43 TraesCS3A01G523000 chrUn 82.787 122 16 4 2872 2993 367633199 367633083 1.470000e-18 104.0
44 TraesCS3A01G523000 chrUn 78.022 182 29 8 2818 2993 399337167 399337343 1.470000e-18 104.0
45 TraesCS3A01G523000 chr3B 82.787 122 16 4 2872 2993 816172371 816172255 1.470000e-18 104.0


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 TraesCS3A01G523000 chr3A 738692013 738695017 3004 True 2590.500000 4623 100.000000 1 3005 2 chr3A.!!$R17 3004
1 TraesCS3A01G523000 chr3A 738306026 738308541 2515 True 1033.500000 1568 81.511500 55 2479 2 chr3A.!!$R16 2424
2 TraesCS3A01G523000 chr3A 738250012 738250953 941 True 747.000000 747 81.454000 883 1804 1 chr3A.!!$R4 921
3 TraesCS3A01G523000 chr3A 738855869 738856954 1085 True 632.000000 632 77.728000 1417 2496 1 chr3A.!!$R14 1079
4 TraesCS3A01G523000 chr3A 738807407 738808857 1450 True 610.000000 654 87.143000 501 1594 2 chr3A.!!$R19 1093
5 TraesCS3A01G523000 chr3A 738758769 738760412 1643 True 304.333333 409 91.404333 1957 3005 3 chr3A.!!$R18 1048
6 TraesCS3A01G523000 chr5B 621478553 621480144 1591 True 462.500000 503 80.076000 889 2503 2 chr5B.!!$R2 1614
7 TraesCS3A01G523000 chr5B 621469754 621471351 1597 True 405.500000 412 78.769000 882 2498 2 chr5B.!!$R1 1616
8 TraesCS3A01G523000 chr5A 624723676 624725967 2291 True 339.000000 488 83.486000 889 3005 3 chr5A.!!$R2 2116
9 TraesCS3A01G523000 chr5A 624712100 624714050 1950 True 297.000000 418 82.566667 882 2994 3 chr5A.!!$R1 2112
10 TraesCS3A01G523000 chr5D 500133711 500134333 622 True 431.000000 431 79.656000 1876 2499 1 chr5D.!!$R1 623
11 TraesCS3A01G523000 chr5D 500139469 500140284 815 True 405.000000 405 76.335000 889 1680 1 chr5D.!!$R2 791
12 TraesCS3A01G523000 chr3D 605953201 605953828 627 False 399.000000 399 78.864000 918 1525 1 chr3D.!!$F2 607

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
34 35 0.035152 TACCATGGCTGTGCTCCTTG 60.035 55.0 13.04 0.0 0.00 3.61 F
760 839 0.245539 ACGACATACAAGGTCACGGG 59.754 55.0 0.00 0.0 34.97 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1225 1692 0.799917 CTCGGTCGATGAGCAGTGTG 60.800 60.0 4.91 0.00 0.0 3.82 R
2200 2739 0.037605 AATGGTCCCTTCGTCGACAC 60.038 55.0 17.16 4.58 0.0 3.67 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
22 23 5.964958 AACTGTCAGAACATTTACCATGG 57.035 39.130 11.19 11.19 34.13 3.66
23 24 3.758554 ACTGTCAGAACATTTACCATGGC 59.241 43.478 13.04 0.00 34.13 4.40
24 25 4.012374 CTGTCAGAACATTTACCATGGCT 58.988 43.478 13.04 1.45 34.13 4.75
25 26 3.758023 TGTCAGAACATTTACCATGGCTG 59.242 43.478 13.04 8.52 0.00 4.85
26 27 3.758554 GTCAGAACATTTACCATGGCTGT 59.241 43.478 13.04 7.83 31.78 4.40
27 28 3.758023 TCAGAACATTTACCATGGCTGTG 59.242 43.478 13.04 8.52 31.78 3.66
28 29 2.493278 AGAACATTTACCATGGCTGTGC 59.507 45.455 13.04 9.29 0.00 4.57
29 30 2.220653 ACATTTACCATGGCTGTGCT 57.779 45.000 13.04 0.00 0.00 4.40
30 31 2.094675 ACATTTACCATGGCTGTGCTC 58.905 47.619 13.04 0.00 0.00 4.26
31 32 1.406539 CATTTACCATGGCTGTGCTCC 59.593 52.381 13.04 0.00 0.00 4.70
32 33 0.698238 TTTACCATGGCTGTGCTCCT 59.302 50.000 13.04 0.00 0.00 3.69
33 34 0.698238 TTACCATGGCTGTGCTCCTT 59.302 50.000 13.04 0.00 0.00 3.36
34 35 0.035152 TACCATGGCTGTGCTCCTTG 60.035 55.000 13.04 0.00 0.00 3.61
35 36 2.050350 CCATGGCTGTGCTCCTTGG 61.050 63.158 0.00 0.00 40.89 3.61
36 37 1.303888 CATGGCTGTGCTCCTTGGT 60.304 57.895 0.00 0.00 0.00 3.67
37 38 0.896940 CATGGCTGTGCTCCTTGGTT 60.897 55.000 0.00 0.00 0.00 3.67
38 39 0.896940 ATGGCTGTGCTCCTTGGTTG 60.897 55.000 0.00 0.00 0.00 3.77
39 40 1.529244 GGCTGTGCTCCTTGGTTGT 60.529 57.895 0.00 0.00 0.00 3.32
40 41 0.250727 GGCTGTGCTCCTTGGTTGTA 60.251 55.000 0.00 0.00 0.00 2.41
41 42 1.160137 GCTGTGCTCCTTGGTTGTAG 58.840 55.000 0.00 0.00 0.00 2.74
42 43 1.160137 CTGTGCTCCTTGGTTGTAGC 58.840 55.000 0.00 0.00 35.51 3.58
43 44 0.764890 TGTGCTCCTTGGTTGTAGCT 59.235 50.000 0.00 0.00 35.95 3.32
44 45 1.142870 TGTGCTCCTTGGTTGTAGCTT 59.857 47.619 0.00 0.00 35.95 3.74
45 46 2.370519 TGTGCTCCTTGGTTGTAGCTTA 59.629 45.455 0.00 0.00 35.95 3.09
46 47 3.181449 TGTGCTCCTTGGTTGTAGCTTAA 60.181 43.478 0.00 0.00 35.95 1.85
47 48 3.437049 GTGCTCCTTGGTTGTAGCTTAAG 59.563 47.826 0.00 0.00 35.95 1.85
48 49 2.420372 GCTCCTTGGTTGTAGCTTAAGC 59.580 50.000 20.09 20.09 42.49 3.09
49 50 3.674997 CTCCTTGGTTGTAGCTTAAGCA 58.325 45.455 28.39 12.31 45.16 3.91
50 51 4.072131 CTCCTTGGTTGTAGCTTAAGCAA 58.928 43.478 28.39 19.97 45.16 3.91
51 52 4.465886 TCCTTGGTTGTAGCTTAAGCAAA 58.534 39.130 28.39 16.51 42.68 3.68
52 53 5.076873 TCCTTGGTTGTAGCTTAAGCAAAT 58.923 37.500 28.39 11.37 42.68 2.32
53 54 5.048083 TCCTTGGTTGTAGCTTAAGCAAATG 60.048 40.000 28.39 16.65 42.68 2.32
107 108 4.854924 CGGGGATGCGACATGCCA 62.855 66.667 23.90 0.00 45.60 4.92
135 136 3.058914 GCTTTGCGCTCAAGTCTTCTTTA 60.059 43.478 9.73 0.00 33.12 1.85
144 146 5.986135 GCTCAAGTCTTCTTTACACTCAAGA 59.014 40.000 0.00 0.00 0.00 3.02
149 151 9.050601 CAAGTCTTCTTTACACTCAAGATTCTT 57.949 33.333 0.00 0.00 30.26 2.52
152 154 9.477484 GTCTTCTTTACACTCAAGATTCTTACA 57.523 33.333 0.00 0.00 30.26 2.41
178 180 3.339547 GCTGTGTAGCCCTTTTCCA 57.660 52.632 0.00 0.00 44.33 3.53
180 182 1.817740 GCTGTGTAGCCCTTTTCCACA 60.818 52.381 0.00 0.00 44.33 4.17
201 203 2.485795 GGAACACTGCCCGCACAAA 61.486 57.895 0.00 0.00 0.00 2.83
203 205 3.137637 AACACTGCCCGCACAAAGC 62.138 57.895 0.00 0.00 40.87 3.51
211 213 2.249309 CGCACAAAGCACCAGACG 59.751 61.111 0.00 0.00 46.13 4.18
212 214 2.050985 GCACAAAGCACCAGACGC 60.051 61.111 0.00 0.00 44.79 5.19
231 233 5.070446 AGACGCACCAGATTCTTGGAATATA 59.930 40.000 8.56 0.00 40.87 0.86
275 277 6.114187 TCATGTACCTGATTCTTTGTCTGT 57.886 37.500 0.00 0.00 0.00 3.41
276 278 5.934043 TCATGTACCTGATTCTTTGTCTGTG 59.066 40.000 0.00 0.00 0.00 3.66
312 314 5.221880 CAATCACAATGTTTACCCTGTGTG 58.778 41.667 9.75 0.00 40.07 3.82
313 315 3.892284 TCACAATGTTTACCCTGTGTGT 58.108 40.909 9.75 0.00 40.07 3.72
314 316 3.629855 TCACAATGTTTACCCTGTGTGTG 59.370 43.478 9.75 0.00 40.07 3.82
315 317 2.360801 ACAATGTTTACCCTGTGTGTGC 59.639 45.455 0.00 0.00 0.00 4.57
324 326 1.202758 CCCTGTGTGTGCTCTTGGTTA 60.203 52.381 0.00 0.00 0.00 2.85
334 336 3.126000 GTGCTCTTGGTTACATCTTGAGC 59.874 47.826 0.00 0.00 43.73 4.26
339 341 2.076100 TGGTTACATCTTGAGCAAGCG 58.924 47.619 5.37 2.33 38.28 4.68
342 344 2.736721 GTTACATCTTGAGCAAGCGACA 59.263 45.455 5.37 0.00 38.28 4.35
343 345 2.105006 ACATCTTGAGCAAGCGACAT 57.895 45.000 5.37 0.00 38.28 3.06
382 389 7.217906 ACTTTAGTTACTGTTGCTTAGCTCTT 58.782 34.615 5.60 0.00 0.00 2.85
383 390 7.715686 ACTTTAGTTACTGTTGCTTAGCTCTTT 59.284 33.333 5.60 0.00 0.00 2.52
424 431 5.873146 TTTTTGTTACCCCTCGGAAAAAT 57.127 34.783 0.00 0.00 0.00 1.82
425 432 4.857509 TTTGTTACCCCTCGGAAAAATG 57.142 40.909 0.00 0.00 0.00 2.32
426 433 3.512219 TGTTACCCCTCGGAAAAATGT 57.488 42.857 0.00 0.00 0.00 2.71
427 434 3.150767 TGTTACCCCTCGGAAAAATGTG 58.849 45.455 0.00 0.00 0.00 3.21
428 435 3.151554 GTTACCCCTCGGAAAAATGTGT 58.848 45.455 0.00 0.00 0.00 3.72
429 436 1.616159 ACCCCTCGGAAAAATGTGTG 58.384 50.000 0.00 0.00 0.00 3.82
430 437 1.133606 ACCCCTCGGAAAAATGTGTGT 60.134 47.619 0.00 0.00 0.00 3.72
431 438 1.960689 CCCCTCGGAAAAATGTGTGTT 59.039 47.619 0.00 0.00 0.00 3.32
432 439 3.150767 CCCCTCGGAAAAATGTGTGTTA 58.849 45.455 0.00 0.00 0.00 2.41
462 469 5.705609 ATGTTGGTGATGGTTTCAGTTAC 57.294 39.130 0.00 0.00 34.17 2.50
463 470 4.787551 TGTTGGTGATGGTTTCAGTTACT 58.212 39.130 0.00 0.00 34.17 2.24
475 482 4.785511 TTCAGTTACTGTCACCTAGCTC 57.214 45.455 12.41 0.00 32.61 4.09
476 483 3.763057 TCAGTTACTGTCACCTAGCTCA 58.237 45.455 12.41 0.00 32.61 4.26
481 488 2.320781 ACTGTCACCTAGCTCAGTTGT 58.679 47.619 0.00 0.00 37.81 3.32
483 490 3.508012 ACTGTCACCTAGCTCAGTTGTAG 59.492 47.826 0.00 0.00 37.81 2.74
484 491 3.759086 CTGTCACCTAGCTCAGTTGTAGA 59.241 47.826 0.00 0.00 0.00 2.59
485 492 3.506455 TGTCACCTAGCTCAGTTGTAGAC 59.494 47.826 0.00 0.00 0.00 2.59
486 493 2.747989 TCACCTAGCTCAGTTGTAGACG 59.252 50.000 0.00 0.00 0.00 4.18
488 495 3.011119 ACCTAGCTCAGTTGTAGACGAG 58.989 50.000 0.00 0.00 34.32 4.18
491 498 2.065993 GCTCAGTTGTAGACGAGCAA 57.934 50.000 5.42 0.00 45.59 3.91
492 499 1.989165 GCTCAGTTGTAGACGAGCAAG 59.011 52.381 5.42 0.00 45.59 4.01
493 500 2.351835 GCTCAGTTGTAGACGAGCAAGA 60.352 50.000 5.42 0.00 45.59 3.02
494 501 3.674682 GCTCAGTTGTAGACGAGCAAGAT 60.675 47.826 5.42 0.00 45.59 2.40
498 505 0.894835 TGTAGACGAGCAAGATGGCA 59.105 50.000 0.00 0.00 35.83 4.92
499 506 1.281899 GTAGACGAGCAAGATGGCAC 58.718 55.000 0.00 0.00 35.83 5.01
512 544 3.290710 AGATGGCACTCACAACAGTTTT 58.709 40.909 0.00 0.00 0.00 2.43
632 686 9.528489 TTCCTTTCTATGTTAGTAATGCCTTTT 57.472 29.630 0.00 0.00 0.00 2.27
681 736 6.223120 CCAGAAAATCGACAAGGGAAATTTT 58.777 36.000 0.00 0.00 33.49 1.82
760 839 0.245539 ACGACATACAAGGTCACGGG 59.754 55.000 0.00 0.00 34.97 5.28
771 850 4.184439 TCACGGGCTGACAGTACA 57.816 55.556 0.00 0.00 0.00 2.90
772 851 2.666085 TCACGGGCTGACAGTACAT 58.334 52.632 0.00 0.00 0.00 2.29
773 852 1.842052 TCACGGGCTGACAGTACATA 58.158 50.000 0.00 0.00 0.00 2.29
774 853 1.475280 TCACGGGCTGACAGTACATAC 59.525 52.381 0.00 0.00 0.00 2.39
775 854 1.203758 CACGGGCTGACAGTACATACA 59.796 52.381 0.00 0.00 0.00 2.29
776 855 1.897133 ACGGGCTGACAGTACATACAA 59.103 47.619 0.00 0.00 0.00 2.41
777 856 2.094182 ACGGGCTGACAGTACATACAAG 60.094 50.000 0.00 0.00 0.00 3.16
778 857 2.738643 CGGGCTGACAGTACATACAAGG 60.739 54.545 3.99 0.00 0.00 3.61
780 859 3.522553 GGCTGACAGTACATACAAGGTC 58.477 50.000 3.99 0.00 0.00 3.85
781 860 3.056107 GGCTGACAGTACATACAAGGTCA 60.056 47.826 3.99 9.42 34.88 4.02
782 861 3.927142 GCTGACAGTACATACAAGGTCAC 59.073 47.826 3.99 3.34 33.59 3.67
783 862 4.560716 GCTGACAGTACATACAAGGTCACA 60.561 45.833 3.99 0.00 33.59 3.58
788 867 6.631016 ACAGTACATACAAGGTCACATACAG 58.369 40.000 0.00 0.00 0.00 2.74
790 869 4.551702 ACATACAAGGTCACATACAGCA 57.448 40.909 0.00 0.00 0.00 4.41
791 870 4.905429 ACATACAAGGTCACATACAGCAA 58.095 39.130 0.00 0.00 0.00 3.91
792 871 4.937620 ACATACAAGGTCACATACAGCAAG 59.062 41.667 0.00 0.00 0.00 4.01
1038 1490 8.307483 CCGATGATGTTCTATCTATTGGTACTT 58.693 37.037 0.00 0.00 0.00 2.24
1104 1556 2.296365 CCAGCAGAGCCCTGAAGGA 61.296 63.158 0.00 0.00 43.02 3.36
1109 1561 1.948144 GCAGAGCCCTGAAGGAAACTC 60.948 57.143 0.00 2.28 43.02 3.01
1170 1637 0.905357 ACGTGAGCTTTGCCTATCCT 59.095 50.000 0.00 0.00 0.00 3.24
1225 1692 3.068024 TGACTTCAACCTCATTTGCAACC 59.932 43.478 0.00 0.00 0.00 3.77
1230 1697 2.071778 ACCTCATTTGCAACCACACT 57.928 45.000 0.00 0.00 0.00 3.55
1238 1705 1.229975 TGCAACCACACTGCTCATCG 61.230 55.000 0.00 0.00 40.59 3.84
1239 1706 0.950555 GCAACCACACTGCTCATCGA 60.951 55.000 0.00 0.00 36.84 3.59
1294 1761 6.851222 AGGTGATCGAATTTAGCAATACTG 57.149 37.500 0.00 0.00 0.00 2.74
1299 1766 8.551205 GTGATCGAATTTAGCAATACTGATTCA 58.449 33.333 0.00 0.00 34.45 2.57
1342 1818 0.957395 CTCGCATACCATCCCCATGC 60.957 60.000 0.00 0.00 41.29 4.06
1344 1820 0.609957 CGCATACCATCCCCATGCAT 60.610 55.000 0.00 0.00 44.19 3.96
1345 1821 1.180029 GCATACCATCCCCATGCATC 58.820 55.000 0.00 0.00 43.59 3.91
1352 1828 0.995132 ATCCCCATGCATCCTGGTGA 60.995 55.000 0.00 0.00 31.44 4.02
1353 1829 1.152819 CCCCATGCATCCTGGTGAG 60.153 63.158 0.00 0.00 31.44 3.51
1377 1853 7.975750 AGAGTGTCTACAACTTTTCTTTGAAC 58.024 34.615 0.00 0.00 0.00 3.18
1407 1889 1.435168 AGGTCCTTCTCCCTTGAGTCT 59.565 52.381 0.00 0.00 39.75 3.24
1528 2010 1.140452 CAGAGATGGTGGCTATGCACT 59.860 52.381 0.00 0.00 0.00 4.40
1561 2043 2.061773 CATCCGGATGCTGTCGTATTC 58.938 52.381 30.53 0.00 31.39 1.75
1564 2046 2.061773 CCGGATGCTGTCGTATTCATC 58.938 52.381 0.00 0.00 35.74 2.92
1567 2049 3.550842 CGGATGCTGTCGTATTCATCTGA 60.551 47.826 11.17 0.00 42.13 3.27
1570 2052 3.521560 TGCTGTCGTATTCATCTGAACC 58.478 45.455 0.00 0.00 36.80 3.62
1571 2053 3.195610 TGCTGTCGTATTCATCTGAACCT 59.804 43.478 0.00 0.00 36.80 3.50
1575 2060 6.312918 GCTGTCGTATTCATCTGAACCTTAAA 59.687 38.462 0.00 0.00 36.80 1.52
1601 2086 6.313658 GGCAGTTTTCAGTTCAAATTTGTCTT 59.686 34.615 17.47 2.17 0.00 3.01
1619 2104 2.694628 TCTTCAACCACAGCAAAAGCAT 59.305 40.909 0.00 0.00 0.00 3.79
1626 2111 1.730064 CACAGCAAAAGCATCATTGGC 59.270 47.619 0.00 0.00 0.00 4.52
1641 2126 2.904866 GGCGCACACTCCAACCAA 60.905 61.111 10.83 0.00 0.00 3.67
1702 2187 3.487576 CCGGGTGGCTTTATGCTAA 57.512 52.632 0.00 0.00 42.39 3.09
1719 2204 4.445453 TGCTAATGTGGCAGATAGTTGAG 58.555 43.478 0.00 0.00 34.56 3.02
1733 2224 0.955428 GTTGAGCCATCCAACTGCGA 60.955 55.000 0.00 0.00 40.37 5.10
1757 2248 1.136695 TGCCAAGCAAAACAGGACAAG 59.863 47.619 0.00 0.00 34.76 3.16
1808 2302 1.000385 CAACGACCGTACACCCAGTTA 60.000 52.381 0.00 0.00 0.00 2.24
1809 2303 1.549203 ACGACCGTACACCCAGTTAT 58.451 50.000 0.00 0.00 0.00 1.89
1813 2307 3.256558 GACCGTACACCCAGTTATTGTC 58.743 50.000 0.00 0.00 0.00 3.18
1818 2312 3.764237 ACACCCAGTTATTGTCTCGTT 57.236 42.857 0.00 0.00 0.00 3.85
1862 2359 1.138247 GCAATGGCTACAGCTGCAC 59.862 57.895 15.27 2.79 38.55 4.57
1879 2382 1.927174 GCACGTGCAGGACTAACTATG 59.073 52.381 34.52 0.00 41.59 2.23
1887 2390 3.813443 CAGGACTAACTATGCAGGCAAT 58.187 45.455 0.00 0.00 0.00 3.56
1898 2401 1.284491 TGCAGGCAATCCCTACATTCA 59.716 47.619 0.00 0.00 44.09 2.57
1910 2413 4.019174 CCCTACATTCAAGATGGTTGCTT 58.981 43.478 0.00 0.00 0.00 3.91
1919 2422 7.649533 TTCAAGATGGTTGCTTCAATGATAT 57.350 32.000 0.00 0.00 0.00 1.63
1926 2429 5.822519 TGGTTGCTTCAATGATATAGGTGAC 59.177 40.000 0.00 0.00 0.00 3.67
1931 2434 6.162777 GCTTCAATGATATAGGTGACTCCTC 58.837 44.000 0.00 0.00 44.42 3.71
1933 2437 7.177568 GCTTCAATGATATAGGTGACTCCTCTA 59.822 40.741 0.00 0.00 44.42 2.43
1945 2456 6.325286 AGGTGACTCCTCTATTCCTAATCAAC 59.675 42.308 0.00 0.00 44.42 3.18
2134 2652 3.498774 AGAGTTTCACCTCAACTGCAT 57.501 42.857 0.00 0.00 34.49 3.96
2137 2655 4.999950 AGAGTTTCACCTCAACTGCATAAG 59.000 41.667 0.00 0.00 34.49 1.73
2171 2695 0.962356 CTGCCCTGGTCATGTTGGAC 60.962 60.000 0.00 0.00 37.06 4.02
2172 2696 1.380302 GCCCTGGTCATGTTGGACT 59.620 57.895 0.00 0.00 37.91 3.85
2173 2697 0.251341 GCCCTGGTCATGTTGGACTT 60.251 55.000 0.00 0.00 37.91 3.01
2174 2698 1.538047 CCCTGGTCATGTTGGACTTG 58.462 55.000 0.00 0.00 37.91 3.16
2175 2699 1.202927 CCCTGGTCATGTTGGACTTGT 60.203 52.381 0.00 0.00 37.91 3.16
2176 2700 1.881973 CCTGGTCATGTTGGACTTGTG 59.118 52.381 0.00 0.00 37.91 3.33
2200 2739 5.355350 GGGAGAAACAGGTCATTGACATAAG 59.645 44.000 18.09 3.45 33.68 1.73
2241 3575 3.524095 ATGTCACCATTCCTGACCAAA 57.476 42.857 0.00 0.00 37.79 3.28
2243 3577 3.843422 TGTCACCATTCCTGACCAAAAT 58.157 40.909 0.00 0.00 37.79 1.82
2262 3596 3.695830 ATTCTGCGAACTCCCTGTTTA 57.304 42.857 0.00 0.00 39.30 2.01
2268 3602 6.278363 TCTGCGAACTCCCTGTTTATATTAC 58.722 40.000 0.00 0.00 39.30 1.89
2269 3603 5.979993 TGCGAACTCCCTGTTTATATTACA 58.020 37.500 0.00 0.00 39.30 2.41
2270 3604 6.046593 TGCGAACTCCCTGTTTATATTACAG 58.953 40.000 9.56 9.56 42.06 2.74
2271 3605 5.050295 GCGAACTCCCTGTTTATATTACAGC 60.050 44.000 10.61 0.00 41.28 4.40
2272 3606 5.465724 CGAACTCCCTGTTTATATTACAGCC 59.534 44.000 10.61 0.00 41.28 4.85
2359 3696 0.255890 GCAGAGGCCCAACAGGATAA 59.744 55.000 0.00 0.00 38.24 1.75
2401 3738 1.808411 ACGAACAGCAAGTGTATGGG 58.192 50.000 0.00 0.00 39.03 4.00
2796 4304 5.614324 ACATGTATAGAAGTTGCCAGCTA 57.386 39.130 0.00 0.00 0.00 3.32
2800 4308 6.978674 TGTATAGAAGTTGCCAGCTACTAT 57.021 37.500 7.15 2.82 32.21 2.12
2803 4311 8.920174 TGTATAGAAGTTGCCAGCTACTATAAA 58.080 33.333 7.15 0.00 32.21 1.40
2804 4312 9.413048 GTATAGAAGTTGCCAGCTACTATAAAG 57.587 37.037 7.15 0.00 32.21 1.85
2805 4313 6.546428 AGAAGTTGCCAGCTACTATAAAGA 57.454 37.500 7.15 0.00 32.21 2.52
2806 4314 6.342111 AGAAGTTGCCAGCTACTATAAAGAC 58.658 40.000 7.15 0.00 32.21 3.01
2807 4315 4.683832 AGTTGCCAGCTACTATAAAGACG 58.316 43.478 4.90 0.00 30.83 4.18
2808 4316 3.728076 TGCCAGCTACTATAAAGACGG 57.272 47.619 0.00 0.00 0.00 4.79
2811 4319 3.067742 GCCAGCTACTATAAAGACGGTGA 59.932 47.826 0.00 0.00 0.00 4.02
2812 4320 4.608951 CCAGCTACTATAAAGACGGTGAC 58.391 47.826 0.00 0.00 0.00 3.67
2814 4322 5.530171 CCAGCTACTATAAAGACGGTGACTA 59.470 44.000 0.00 0.00 0.00 2.59
2815 4323 6.428799 CAGCTACTATAAAGACGGTGACTAC 58.571 44.000 0.00 0.00 0.00 2.73
2818 4376 7.338957 AGCTACTATAAAGACGGTGACTACTTT 59.661 37.037 0.00 0.00 37.24 2.66
2820 4378 9.286946 CTACTATAAAGACGGTGACTACTTTTG 57.713 37.037 0.00 0.00 35.85 2.44
2824 4382 3.910648 AGACGGTGACTACTTTTGCTAC 58.089 45.455 0.00 0.00 0.00 3.58
2834 4392 8.488764 GTGACTACTTTTGCTACTTCTAGTTTG 58.511 37.037 0.00 0.00 0.00 2.93
2853 4411 7.671495 AGTTTGTTTTATCATTCATTTGGGC 57.329 32.000 0.00 0.00 0.00 5.36
2855 4413 7.938490 AGTTTGTTTTATCATTCATTTGGGCTT 59.062 29.630 0.00 0.00 0.00 4.35
2856 4414 7.903995 TTGTTTTATCATTCATTTGGGCTTC 57.096 32.000 0.00 0.00 0.00 3.86
2857 4415 7.002250 TGTTTTATCATTCATTTGGGCTTCA 57.998 32.000 0.00 0.00 0.00 3.02
2858 4416 6.873076 TGTTTTATCATTCATTTGGGCTTCAC 59.127 34.615 0.00 0.00 0.00 3.18
2859 4417 6.855763 TTTATCATTCATTTGGGCTTCACT 57.144 33.333 0.00 0.00 0.00 3.41
2860 4418 6.855763 TTATCATTCATTTGGGCTTCACTT 57.144 33.333 0.00 0.00 0.00 3.16
2861 4419 7.953005 TTATCATTCATTTGGGCTTCACTTA 57.047 32.000 0.00 0.00 0.00 2.24
2862 4420 6.855763 ATCATTCATTTGGGCTTCACTTAA 57.144 33.333 0.00 0.00 0.00 1.85
2863 4421 6.855763 TCATTCATTTGGGCTTCACTTAAT 57.144 33.333 0.00 0.00 0.00 1.40
2864 4422 7.243604 TCATTCATTTGGGCTTCACTTAATT 57.756 32.000 0.00 0.00 0.00 1.40
2865 4423 7.098477 TCATTCATTTGGGCTTCACTTAATTG 58.902 34.615 0.00 0.00 0.00 2.32
2866 4424 6.662865 TTCATTTGGGCTTCACTTAATTGA 57.337 33.333 0.00 0.00 0.00 2.57
2869 4427 8.537728 TCATTTGGGCTTCACTTAATTGATAT 57.462 30.769 0.00 0.00 0.00 1.63
2903 4461 8.097038 TGTTAGCTGAATGAAGTACAATCTTCT 58.903 33.333 0.00 0.00 42.76 2.85
2936 4744 7.228308 TGTGTCATAGATTTTGTCAACACATCA 59.772 33.333 0.00 0.00 40.37 3.07
2949 4757 9.844790 TTGTCAACACATCATATCAAGATTTTC 57.155 29.630 0.00 0.00 30.55 2.29
2984 4792 4.963276 TTAATGAATGCCTTCAACCGAG 57.037 40.909 8.55 0.00 44.29 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.012374 AGCCATGGTAAATGTTCTGACAG 58.988 43.478 14.67 0.00 39.58 3.51
3 4 3.758023 CAGCCATGGTAAATGTTCTGACA 59.242 43.478 14.67 0.00 40.71 3.58
5 6 3.758023 CACAGCCATGGTAAATGTTCTGA 59.242 43.478 14.67 0.00 0.00 3.27
6 7 3.674138 GCACAGCCATGGTAAATGTTCTG 60.674 47.826 14.67 11.54 0.00 3.02
7 8 2.493278 GCACAGCCATGGTAAATGTTCT 59.507 45.455 14.67 0.00 0.00 3.01
8 9 2.493278 AGCACAGCCATGGTAAATGTTC 59.507 45.455 14.67 8.13 0.00 3.18
9 10 2.493278 GAGCACAGCCATGGTAAATGTT 59.507 45.455 14.67 5.10 0.00 2.71
10 11 2.094675 GAGCACAGCCATGGTAAATGT 58.905 47.619 14.67 10.58 0.00 2.71
11 12 1.406539 GGAGCACAGCCATGGTAAATG 59.593 52.381 14.67 9.93 0.00 2.32
12 13 1.285962 AGGAGCACAGCCATGGTAAAT 59.714 47.619 14.67 0.00 0.00 1.40
13 14 0.698238 AGGAGCACAGCCATGGTAAA 59.302 50.000 14.67 0.00 0.00 2.01
14 15 0.698238 AAGGAGCACAGCCATGGTAA 59.302 50.000 14.67 0.00 0.00 2.85
15 16 0.035152 CAAGGAGCACAGCCATGGTA 60.035 55.000 14.67 0.00 0.00 3.25
16 17 1.303888 CAAGGAGCACAGCCATGGT 60.304 57.895 14.67 0.00 0.00 3.55
17 18 2.050350 CCAAGGAGCACAGCCATGG 61.050 63.158 7.63 7.63 0.00 3.66
18 19 0.896940 AACCAAGGAGCACAGCCATG 60.897 55.000 0.00 0.00 0.00 3.66
19 20 0.896940 CAACCAAGGAGCACAGCCAT 60.897 55.000 0.00 0.00 0.00 4.40
20 21 1.529010 CAACCAAGGAGCACAGCCA 60.529 57.895 0.00 0.00 0.00 4.75
21 22 0.250727 TACAACCAAGGAGCACAGCC 60.251 55.000 0.00 0.00 0.00 4.85
22 23 1.160137 CTACAACCAAGGAGCACAGC 58.840 55.000 0.00 0.00 0.00 4.40
23 24 1.160137 GCTACAACCAAGGAGCACAG 58.840 55.000 0.00 0.00 34.96 3.66
24 25 0.764890 AGCTACAACCAAGGAGCACA 59.235 50.000 0.55 0.00 37.40 4.57
25 26 1.897560 AAGCTACAACCAAGGAGCAC 58.102 50.000 0.55 0.00 37.40 4.40
26 27 3.674997 CTTAAGCTACAACCAAGGAGCA 58.325 45.455 0.55 0.00 37.40 4.26
27 28 2.420372 GCTTAAGCTACAACCAAGGAGC 59.580 50.000 20.38 0.00 38.21 4.70
28 29 3.674997 TGCTTAAGCTACAACCAAGGAG 58.325 45.455 26.90 0.00 42.66 3.69
29 30 3.780804 TGCTTAAGCTACAACCAAGGA 57.219 42.857 26.90 0.23 42.66 3.36
30 31 4.846779 TTTGCTTAAGCTACAACCAAGG 57.153 40.909 26.90 0.00 42.66 3.61
31 32 5.858581 GTCATTTGCTTAAGCTACAACCAAG 59.141 40.000 26.90 8.45 42.66 3.61
32 33 5.561919 CGTCATTTGCTTAAGCTACAACCAA 60.562 40.000 26.90 9.33 42.66 3.67
33 34 4.083537 CGTCATTTGCTTAAGCTACAACCA 60.084 41.667 26.90 5.89 42.66 3.67
34 35 4.153475 TCGTCATTTGCTTAAGCTACAACC 59.847 41.667 26.90 10.92 42.66 3.77
35 36 5.080068 GTCGTCATTTGCTTAAGCTACAAC 58.920 41.667 26.90 16.68 42.66 3.32
36 37 4.143200 CGTCGTCATTTGCTTAAGCTACAA 60.143 41.667 26.90 17.10 42.66 2.41
37 38 3.366724 CGTCGTCATTTGCTTAAGCTACA 59.633 43.478 26.90 11.98 42.66 2.74
38 39 3.241995 CCGTCGTCATTTGCTTAAGCTAC 60.242 47.826 26.90 15.48 42.66 3.58
39 40 2.927477 CCGTCGTCATTTGCTTAAGCTA 59.073 45.455 26.90 17.93 42.66 3.32
40 41 1.732259 CCGTCGTCATTTGCTTAAGCT 59.268 47.619 26.90 5.41 42.66 3.74
41 42 1.463444 ACCGTCGTCATTTGCTTAAGC 59.537 47.619 20.84 20.84 42.50 3.09
42 43 2.159707 CCACCGTCGTCATTTGCTTAAG 60.160 50.000 0.00 0.00 0.00 1.85
43 44 1.801771 CCACCGTCGTCATTTGCTTAA 59.198 47.619 0.00 0.00 0.00 1.85
44 45 1.434555 CCACCGTCGTCATTTGCTTA 58.565 50.000 0.00 0.00 0.00 3.09
45 46 1.234615 CCCACCGTCGTCATTTGCTT 61.235 55.000 0.00 0.00 0.00 3.91
46 47 1.671054 CCCACCGTCGTCATTTGCT 60.671 57.895 0.00 0.00 0.00 3.91
47 48 1.231958 TTCCCACCGTCGTCATTTGC 61.232 55.000 0.00 0.00 0.00 3.68
48 49 1.069500 GTTTCCCACCGTCGTCATTTG 60.069 52.381 0.00 0.00 0.00 2.32
49 50 1.232119 GTTTCCCACCGTCGTCATTT 58.768 50.000 0.00 0.00 0.00 2.32
50 51 0.604511 GGTTTCCCACCGTCGTCATT 60.605 55.000 0.00 0.00 35.12 2.57
51 52 1.004200 GGTTTCCCACCGTCGTCAT 60.004 57.895 0.00 0.00 35.12 3.06
52 53 2.422591 GGTTTCCCACCGTCGTCA 59.577 61.111 0.00 0.00 35.12 4.35
89 90 4.856801 GGCATGTCGCATCCCCGT 62.857 66.667 0.00 0.00 45.17 5.28
90 91 4.854924 TGGCATGTCGCATCCCCG 62.855 66.667 0.00 0.00 45.17 5.73
93 94 1.650912 GATGTGGCATGTCGCATCC 59.349 57.895 33.69 20.26 44.44 3.51
97 98 1.651240 AAGCTGATGTGGCATGTCGC 61.651 55.000 3.29 3.29 41.28 5.19
135 136 7.547370 GCTGAAGTATGTAAGAATCTTGAGTGT 59.453 37.037 5.64 0.00 0.00 3.55
144 146 6.758886 GCTACACAGCTGAAGTATGTAAGAAT 59.241 38.462 23.35 0.00 44.93 2.40
178 180 2.111043 CGGGCAGTGTTCCAGTGT 59.889 61.111 5.69 0.00 37.16 3.55
180 182 3.872603 TGCGGGCAGTGTTCCAGT 61.873 61.111 5.69 0.00 0.00 4.00
189 191 4.347453 GGTGCTTTGTGCGGGCAG 62.347 66.667 0.00 0.00 46.63 4.85
201 203 2.116983 AATCTGGTGCGTCTGGTGCT 62.117 55.000 0.00 0.00 0.00 4.40
203 205 0.036952 AGAATCTGGTGCGTCTGGTG 60.037 55.000 0.00 0.00 0.00 4.17
211 213 7.663081 TCTGAATATATTCCAAGAATCTGGTGC 59.337 37.037 20.29 0.00 37.74 5.01
212 214 9.565090 TTCTGAATATATTCCAAGAATCTGGTG 57.435 33.333 20.29 0.00 37.74 4.17
231 233 8.692710 ACATGAAGTGCAATGATTATTCTGAAT 58.307 29.630 8.14 8.14 0.00 2.57
250 252 6.652481 ACAGACAAAGAATCAGGTACATGAAG 59.348 38.462 15.00 3.56 31.76 3.02
251 253 6.427853 CACAGACAAAGAATCAGGTACATGAA 59.572 38.462 15.00 0.00 31.76 2.57
275 277 2.239402 TGTGATTGCTGGAGATAAGCCA 59.761 45.455 0.00 0.00 40.06 4.75
276 278 2.923121 TGTGATTGCTGGAGATAAGCC 58.077 47.619 0.00 0.00 40.06 4.35
312 314 3.126000 GCTCAAGATGTAACCAAGAGCAC 59.874 47.826 0.00 0.00 44.60 4.40
313 315 3.338249 GCTCAAGATGTAACCAAGAGCA 58.662 45.455 0.00 0.00 44.60 4.26
314 316 3.338249 TGCTCAAGATGTAACCAAGAGC 58.662 45.455 0.00 0.00 45.23 4.09
315 317 4.142730 GCTTGCTCAAGATGTAACCAAGAG 60.143 45.833 13.33 0.00 40.79 2.85
324 326 2.005451 GATGTCGCTTGCTCAAGATGT 58.995 47.619 13.33 0.00 40.79 3.06
334 336 4.576053 TCCATTCCAATTAGATGTCGCTTG 59.424 41.667 0.00 0.00 0.00 4.01
339 341 8.738645 ACTAAAGTCCATTCCAATTAGATGTC 57.261 34.615 0.00 0.00 0.00 3.06
343 345 9.667107 CAGTAACTAAAGTCCATTCCAATTAGA 57.333 33.333 0.00 0.00 0.00 2.10
402 409 5.128991 ACATTTTTCCGAGGGGTAACAAAAA 59.871 36.000 0.00 0.00 32.87 1.94
403 410 4.650131 ACATTTTTCCGAGGGGTAACAAAA 59.350 37.500 0.00 0.00 39.74 2.44
404 411 4.038162 CACATTTTTCCGAGGGGTAACAAA 59.962 41.667 0.00 0.00 39.74 2.83
405 412 3.570550 CACATTTTTCCGAGGGGTAACAA 59.429 43.478 0.00 0.00 39.74 2.83
406 413 3.150767 CACATTTTTCCGAGGGGTAACA 58.849 45.455 0.00 0.00 39.74 2.41
407 414 3.057806 CACACATTTTTCCGAGGGGTAAC 60.058 47.826 0.00 0.00 33.83 2.50
408 415 3.150767 CACACATTTTTCCGAGGGGTAA 58.849 45.455 0.00 0.00 33.83 2.85
409 416 2.106857 ACACACATTTTTCCGAGGGGTA 59.893 45.455 0.00 0.00 33.83 3.69
410 417 1.133606 ACACACATTTTTCCGAGGGGT 60.134 47.619 0.00 0.00 33.83 4.95
411 418 1.616159 ACACACATTTTTCCGAGGGG 58.384 50.000 0.00 0.00 0.00 4.79
412 419 3.818773 AGTAACACACATTTTTCCGAGGG 59.181 43.478 0.00 0.00 0.00 4.30
413 420 5.238650 AGAAGTAACACACATTTTTCCGAGG 59.761 40.000 0.00 0.00 0.00 4.63
414 421 6.300354 AGAAGTAACACACATTTTTCCGAG 57.700 37.500 0.00 0.00 0.00 4.63
415 422 6.687081 AAGAAGTAACACACATTTTTCCGA 57.313 33.333 0.00 0.00 0.00 4.55
416 423 8.901748 CATTAAGAAGTAACACACATTTTTCCG 58.098 33.333 0.00 0.00 0.00 4.30
417 424 9.744468 ACATTAAGAAGTAACACACATTTTTCC 57.256 29.630 0.00 0.00 0.00 3.13
420 427 9.528018 CCAACATTAAGAAGTAACACACATTTT 57.472 29.630 0.00 0.00 0.00 1.82
421 428 8.691797 ACCAACATTAAGAAGTAACACACATTT 58.308 29.630 0.00 0.00 0.00 2.32
422 429 8.134895 CACCAACATTAAGAAGTAACACACATT 58.865 33.333 0.00 0.00 0.00 2.71
423 430 7.500892 TCACCAACATTAAGAAGTAACACACAT 59.499 33.333 0.00 0.00 0.00 3.21
424 431 6.824196 TCACCAACATTAAGAAGTAACACACA 59.176 34.615 0.00 0.00 0.00 3.72
425 432 7.254227 TCACCAACATTAAGAAGTAACACAC 57.746 36.000 0.00 0.00 0.00 3.82
426 433 7.040755 CCATCACCAACATTAAGAAGTAACACA 60.041 37.037 0.00 0.00 0.00 3.72
427 434 7.040686 ACCATCACCAACATTAAGAAGTAACAC 60.041 37.037 0.00 0.00 0.00 3.32
428 435 7.001674 ACCATCACCAACATTAAGAAGTAACA 58.998 34.615 0.00 0.00 0.00 2.41
429 436 7.448748 ACCATCACCAACATTAAGAAGTAAC 57.551 36.000 0.00 0.00 0.00 2.50
430 437 8.472007 AAACCATCACCAACATTAAGAAGTAA 57.528 30.769 0.00 0.00 0.00 2.24
431 438 7.721842 TGAAACCATCACCAACATTAAGAAGTA 59.278 33.333 0.00 0.00 31.50 2.24
432 439 6.549364 TGAAACCATCACCAACATTAAGAAGT 59.451 34.615 0.00 0.00 31.50 3.01
475 482 2.926200 CCATCTTGCTCGTCTACAACTG 59.074 50.000 0.00 0.00 0.00 3.16
476 483 2.675317 GCCATCTTGCTCGTCTACAACT 60.675 50.000 0.00 0.00 0.00 3.16
481 488 1.135139 GAGTGCCATCTTGCTCGTCTA 59.865 52.381 0.00 0.00 0.00 2.59
483 490 0.390340 TGAGTGCCATCTTGCTCGTC 60.390 55.000 0.00 0.00 0.00 4.20
484 491 0.671781 GTGAGTGCCATCTTGCTCGT 60.672 55.000 0.00 0.00 0.00 4.18
485 492 0.671472 TGTGAGTGCCATCTTGCTCG 60.671 55.000 0.00 0.00 0.00 5.03
486 493 1.198637 GTTGTGAGTGCCATCTTGCTC 59.801 52.381 0.00 0.00 0.00 4.26
488 495 0.953727 TGTTGTGAGTGCCATCTTGC 59.046 50.000 0.00 0.00 0.00 4.01
491 498 2.645838 AACTGTTGTGAGTGCCATCT 57.354 45.000 0.00 0.00 0.00 2.90
492 499 3.066621 TGAAAACTGTTGTGAGTGCCATC 59.933 43.478 0.00 0.00 0.00 3.51
493 500 3.023119 TGAAAACTGTTGTGAGTGCCAT 58.977 40.909 0.00 0.00 0.00 4.40
494 501 2.441410 TGAAAACTGTTGTGAGTGCCA 58.559 42.857 0.00 0.00 0.00 4.92
498 505 4.201910 CGTTCCATGAAAACTGTTGTGAGT 60.202 41.667 0.00 0.00 0.00 3.41
499 506 4.282068 CGTTCCATGAAAACTGTTGTGAG 58.718 43.478 0.00 0.00 0.00 3.51
681 736 4.250464 CTGTTCCTGATAAACCACGCTAA 58.750 43.478 0.00 0.00 0.00 3.09
746 817 2.678786 TCAGCCCGTGACCTTGTAT 58.321 52.632 0.00 0.00 0.00 2.29
760 839 3.927142 GTGACCTTGTATGTACTGTCAGC 59.073 47.826 0.00 0.00 33.80 4.26
769 848 4.551702 TGCTGTATGTGACCTTGTATGT 57.448 40.909 0.00 0.00 0.00 2.29
770 849 5.178061 TCTTGCTGTATGTGACCTTGTATG 58.822 41.667 0.00 0.00 0.00 2.39
771 850 5.420725 TCTTGCTGTATGTGACCTTGTAT 57.579 39.130 0.00 0.00 0.00 2.29
772 851 4.882842 TCTTGCTGTATGTGACCTTGTA 57.117 40.909 0.00 0.00 0.00 2.41
773 852 3.769739 TCTTGCTGTATGTGACCTTGT 57.230 42.857 0.00 0.00 0.00 3.16
774 853 6.425114 GGTATATCTTGCTGTATGTGACCTTG 59.575 42.308 0.00 0.00 0.00 3.61
775 854 6.464465 GGGTATATCTTGCTGTATGTGACCTT 60.464 42.308 0.00 0.00 0.00 3.50
776 855 5.012148 GGGTATATCTTGCTGTATGTGACCT 59.988 44.000 0.00 0.00 0.00 3.85
777 856 5.238583 GGGTATATCTTGCTGTATGTGACC 58.761 45.833 0.00 0.00 0.00 4.02
778 857 5.238583 GGGGTATATCTTGCTGTATGTGAC 58.761 45.833 0.00 0.00 0.00 3.67
780 859 4.041567 TGGGGGTATATCTTGCTGTATGTG 59.958 45.833 0.00 0.00 0.00 3.21
781 860 4.041691 GTGGGGGTATATCTTGCTGTATGT 59.958 45.833 0.00 0.00 0.00 2.29
782 861 4.287067 AGTGGGGGTATATCTTGCTGTATG 59.713 45.833 0.00 0.00 0.00 2.39
783 862 4.287067 CAGTGGGGGTATATCTTGCTGTAT 59.713 45.833 0.00 0.00 0.00 2.29
788 867 1.545651 GGCAGTGGGGGTATATCTTGC 60.546 57.143 0.00 0.00 0.00 4.01
790 869 1.774856 GTGGCAGTGGGGGTATATCTT 59.225 52.381 0.00 0.00 0.00 2.40
791 870 1.345009 TGTGGCAGTGGGGGTATATCT 60.345 52.381 0.00 0.00 0.00 1.98
792 871 1.136828 TGTGGCAGTGGGGGTATATC 58.863 55.000 0.00 0.00 0.00 1.63
821 904 4.631377 TGAAAGGAGATGCTTCGTACATTG 59.369 41.667 0.00 0.00 0.00 2.82
822 905 4.631813 GTGAAAGGAGATGCTTCGTACATT 59.368 41.667 0.00 0.00 0.00 2.71
1038 1490 3.069586 CAGTTGGTTGTCCTAGTGACTCA 59.930 47.826 11.21 6.02 44.75 3.41
1104 1556 1.599518 TGATGGTTGCGCCGAGTTT 60.600 52.632 4.18 0.00 41.21 2.66
1109 1561 3.853330 CGAGTGATGGTTGCGCCG 61.853 66.667 4.18 0.00 41.21 6.46
1170 1637 1.146041 CCTGGATCCGATGCCGAAA 59.854 57.895 7.39 0.00 38.22 3.46
1225 1692 0.799917 CTCGGTCGATGAGCAGTGTG 60.800 60.000 4.91 0.00 0.00 3.82
1230 1697 2.755876 AGCCTCGGTCGATGAGCA 60.756 61.111 11.08 0.00 31.98 4.26
1238 1705 1.016653 GCACAAGAAGAGCCTCGGTC 61.017 60.000 0.00 0.00 0.00 4.79
1239 1706 1.004440 GCACAAGAAGAGCCTCGGT 60.004 57.895 0.00 0.00 0.00 4.69
1292 1759 6.927381 GGCCCAGATTGAATTAAATGAATCAG 59.073 38.462 5.65 0.00 0.00 2.90
1293 1760 6.612456 AGGCCCAGATTGAATTAAATGAATCA 59.388 34.615 0.00 0.00 0.00 2.57
1294 1761 7.059202 AGGCCCAGATTGAATTAAATGAATC 57.941 36.000 0.00 0.00 0.00 2.52
1299 1766 5.148225 AGGAGGCCCAGATTGAATTAAAT 57.852 39.130 0.00 0.00 33.88 1.40
1305 1781 1.561542 GAGAAGGAGGCCCAGATTGAA 59.438 52.381 0.00 0.00 33.88 2.69
1342 1818 3.092301 TGTAGACACTCTCACCAGGATG 58.908 50.000 0.00 0.00 0.00 3.51
1344 1820 2.891580 GTTGTAGACACTCTCACCAGGA 59.108 50.000 0.00 0.00 0.00 3.86
1345 1821 2.894126 AGTTGTAGACACTCTCACCAGG 59.106 50.000 0.00 0.00 0.00 4.45
1352 1828 7.824779 AGTTCAAAGAAAAGTTGTAGACACTCT 59.175 33.333 0.00 0.00 0.00 3.24
1353 1829 7.975750 AGTTCAAAGAAAAGTTGTAGACACTC 58.024 34.615 0.00 0.00 0.00 3.51
1407 1889 9.278978 TCACAGCTTGTAATGTTTAGAACAATA 57.721 29.630 0.00 0.00 45.86 1.90
1448 1930 1.621317 TGGTAGCATCGTCTCCAACAA 59.379 47.619 0.00 0.00 0.00 2.83
1452 1934 0.963856 ACGTGGTAGCATCGTCTCCA 60.964 55.000 14.01 0.00 32.26 3.86
1528 2010 6.481976 CAGCATCCGGATGTATTTTTACAGTA 59.518 38.462 37.88 0.00 40.80 2.74
1561 2043 5.712152 AAACTGCCTTTAAGGTTCAGATG 57.288 39.130 20.31 1.68 37.80 2.90
1564 2046 5.067805 ACTGAAAACTGCCTTTAAGGTTCAG 59.932 40.000 26.16 26.16 41.72 3.02
1567 2049 5.420739 TGAACTGAAAACTGCCTTTAAGGTT 59.579 36.000 13.03 0.00 37.80 3.50
1570 2052 8.424274 AATTTGAACTGAAAACTGCCTTTAAG 57.576 30.769 0.00 0.00 0.00 1.85
1571 2053 8.663911 CAAATTTGAACTGAAAACTGCCTTTAA 58.336 29.630 13.08 0.00 0.00 1.52
1575 2060 5.733676 ACAAATTTGAACTGAAAACTGCCT 58.266 33.333 24.64 0.00 0.00 4.75
1619 2104 1.228094 TTGGAGTGTGCGCCAATGA 60.228 52.632 4.18 0.00 46.99 2.57
1626 2111 1.101049 AGGTTTGGTTGGAGTGTGCG 61.101 55.000 0.00 0.00 0.00 5.34
1641 2126 3.791320 TCTATCCCACAGTTGAGAGGTT 58.209 45.455 0.00 0.00 0.00 3.50
1702 2187 2.338577 GGCTCAACTATCTGCCACAT 57.661 50.000 0.00 0.00 44.34 3.21
1719 2204 2.117156 AGCATCGCAGTTGGATGGC 61.117 57.895 4.19 0.00 41.22 4.40
1721 2206 1.063649 GCAGCATCGCAGTTGGATG 59.936 57.895 0.00 0.00 43.23 3.51
1757 2248 1.000283 ACTCGCTCATACAGGCATAGC 60.000 52.381 0.00 0.00 0.00 2.97
1808 2302 2.002586 CGGCATCTTCAACGAGACAAT 58.997 47.619 0.00 0.00 0.00 2.71
1809 2303 1.428448 CGGCATCTTCAACGAGACAA 58.572 50.000 0.00 0.00 0.00 3.18
1813 2307 2.094659 ACGCGGCATCTTCAACGAG 61.095 57.895 12.47 0.00 0.00 4.18
1862 2359 2.196749 CTGCATAGTTAGTCCTGCACG 58.803 52.381 0.00 0.00 39.54 5.34
1873 2376 2.509548 TGTAGGGATTGCCTGCATAGTT 59.490 45.455 10.89 0.00 0.00 2.24
1874 2377 2.126882 TGTAGGGATTGCCTGCATAGT 58.873 47.619 10.89 0.00 0.00 2.12
1879 2382 2.057137 TGAATGTAGGGATTGCCTGC 57.943 50.000 7.03 6.14 0.00 4.85
1887 2390 3.266772 AGCAACCATCTTGAATGTAGGGA 59.733 43.478 0.00 0.00 0.00 4.20
1898 2401 7.230108 CACCTATATCATTGAAGCAACCATCTT 59.770 37.037 0.00 0.00 0.00 2.40
1926 2429 6.485830 TGGTGTTGATTAGGAATAGAGGAG 57.514 41.667 0.00 0.00 0.00 3.69
1931 2434 9.173021 TGTATGTTTGGTGTTGATTAGGAATAG 57.827 33.333 0.00 0.00 0.00 1.73
1933 2437 7.122650 CCTGTATGTTTGGTGTTGATTAGGAAT 59.877 37.037 0.00 0.00 0.00 3.01
2134 2652 3.490933 GGCAGCTGATGATGTCGTACTTA 60.491 47.826 20.43 0.00 31.27 2.24
2137 2655 1.212616 GGCAGCTGATGATGTCGTAC 58.787 55.000 20.43 0.00 31.27 3.67
2171 2695 2.638480 TGACCTGTTTCTCCCACAAG 57.362 50.000 0.00 0.00 0.00 3.16
2172 2696 3.117701 TCAATGACCTGTTTCTCCCACAA 60.118 43.478 0.00 0.00 0.00 3.33
2173 2697 2.441375 TCAATGACCTGTTTCTCCCACA 59.559 45.455 0.00 0.00 0.00 4.17
2174 2698 2.814336 GTCAATGACCTGTTTCTCCCAC 59.186 50.000 1.10 0.00 0.00 4.61
2175 2699 2.441375 TGTCAATGACCTGTTTCTCCCA 59.559 45.455 11.24 0.00 0.00 4.37
2176 2700 3.140325 TGTCAATGACCTGTTTCTCCC 57.860 47.619 11.24 0.00 0.00 4.30
2200 2739 0.037605 AATGGTCCCTTCGTCGACAC 60.038 55.000 17.16 4.58 0.00 3.67
2204 2743 2.864343 GACATTAATGGTCCCTTCGTCG 59.136 50.000 19.37 0.00 0.00 5.12
2241 3575 2.568623 AACAGGGAGTTCGCAGAATT 57.431 45.000 0.00 0.00 45.90 2.17
2243 3577 3.695830 ATAAACAGGGAGTTCGCAGAA 57.304 42.857 0.00 0.00 45.90 3.02
2315 3652 3.878778 ACTTAGATTAGCAGCAACCCAG 58.121 45.455 0.00 0.00 0.00 4.45
2355 3692 7.443575 ACTCACACAAGCATATCCAGATTTATC 59.556 37.037 0.00 0.00 0.00 1.75
2359 3696 5.108187 ACTCACACAAGCATATCCAGATT 57.892 39.130 0.00 0.00 0.00 2.40
2401 3738 5.587289 CATAGACTCCTTCAGCACTTACTC 58.413 45.833 0.00 0.00 0.00 2.59
2704 4060 9.982651 GATAGATGGTATAGTACAAAGCTTTGA 57.017 33.333 38.78 22.52 40.55 2.69
2705 4061 9.988815 AGATAGATGGTATAGTACAAAGCTTTG 57.011 33.333 32.53 32.53 43.62 2.77
2724 4080 4.621747 GCGGCATAGGCAGTTAAGATAGAT 60.622 45.833 0.15 0.00 43.71 1.98
2729 4085 0.830648 AGCGGCATAGGCAGTTAAGA 59.169 50.000 0.15 0.00 43.71 2.10
2782 4281 6.342111 GTCTTTATAGTAGCTGGCAACTTCT 58.658 40.000 0.00 0.00 37.61 2.85
2783 4282 5.232414 CGTCTTTATAGTAGCTGGCAACTTC 59.768 44.000 0.00 0.00 37.61 3.01
2796 4304 6.589139 GCAAAAGTAGTCACCGTCTTTATAGT 59.411 38.462 0.00 0.00 31.24 2.12
2800 4308 4.952460 AGCAAAAGTAGTCACCGTCTTTA 58.048 39.130 0.00 0.00 31.24 1.85
2803 4311 3.573110 AGTAGCAAAAGTAGTCACCGTCT 59.427 43.478 0.00 0.00 0.00 4.18
2804 4312 3.910648 AGTAGCAAAAGTAGTCACCGTC 58.089 45.455 0.00 0.00 0.00 4.79
2805 4313 4.038883 AGAAGTAGCAAAAGTAGTCACCGT 59.961 41.667 0.00 0.00 0.00 4.83
2806 4314 4.557205 AGAAGTAGCAAAAGTAGTCACCG 58.443 43.478 0.00 0.00 0.00 4.94
2807 4315 6.689554 ACTAGAAGTAGCAAAAGTAGTCACC 58.310 40.000 0.00 0.00 0.00 4.02
2808 4316 8.488764 CAAACTAGAAGTAGCAAAAGTAGTCAC 58.511 37.037 0.00 0.00 0.00 3.67
2811 4319 8.959705 AACAAACTAGAAGTAGCAAAAGTAGT 57.040 30.769 0.00 0.00 0.00 2.73
2834 4392 7.099120 AGTGAAGCCCAAATGAATGATAAAAC 58.901 34.615 0.00 0.00 0.00 2.43
2838 4396 7.953005 TTAAGTGAAGCCCAAATGAATGATA 57.047 32.000 0.00 0.00 0.00 2.15
2839 4397 6.855763 TTAAGTGAAGCCCAAATGAATGAT 57.144 33.333 0.00 0.00 0.00 2.45
2840 4398 6.855763 ATTAAGTGAAGCCCAAATGAATGA 57.144 33.333 0.00 0.00 0.00 2.57
2841 4399 7.098477 TCAATTAAGTGAAGCCCAAATGAATG 58.902 34.615 2.54 0.00 0.00 2.67
2842 4400 7.243604 TCAATTAAGTGAAGCCCAAATGAAT 57.756 32.000 2.54 0.00 0.00 2.57
2844 4402 6.855763 ATCAATTAAGTGAAGCCCAAATGA 57.144 33.333 9.98 0.00 0.00 2.57
2845 4403 9.037737 CAATATCAATTAAGTGAAGCCCAAATG 57.962 33.333 9.98 0.00 0.00 2.32
2848 4406 7.716799 ACAATATCAATTAAGTGAAGCCCAA 57.283 32.000 9.98 0.00 0.00 4.12
2850 4408 8.250332 TGAAACAATATCAATTAAGTGAAGCCC 58.750 33.333 9.98 0.00 0.00 5.19
2851 4409 9.807649 ATGAAACAATATCAATTAAGTGAAGCC 57.192 29.630 9.98 0.00 0.00 4.35
2863 4421 9.791820 CATTCAGCTAACATGAAACAATATCAA 57.208 29.630 0.00 0.00 39.92 2.57
2864 4422 9.176460 TCATTCAGCTAACATGAAACAATATCA 57.824 29.630 0.00 0.00 39.92 2.15
2869 4427 7.275888 ACTTCATTCAGCTAACATGAAACAA 57.724 32.000 0.00 0.22 39.92 2.83
2879 4437 8.314021 TCAGAAGATTGTACTTCATTCAGCTAA 58.686 33.333 0.00 0.00 45.83 3.09
2882 4440 6.974932 TCAGAAGATTGTACTTCATTCAGC 57.025 37.500 0.00 0.00 45.83 4.26
2883 4441 9.985318 GAAATCAGAAGATTGTACTTCATTCAG 57.015 33.333 0.00 0.00 43.52 3.02
2885 4443 9.985318 CAGAAATCAGAAGATTGTACTTCATTC 57.015 33.333 0.00 0.00 43.52 2.67
2891 4449 7.445121 TGACACAGAAATCAGAAGATTGTACT 58.555 34.615 0.00 0.00 43.52 2.73
2903 4461 8.620116 TGACAAAATCTATGACACAGAAATCA 57.380 30.769 0.00 0.00 0.00 2.57
2984 4792 1.469079 GGCATGTCCCGTTACAATTGC 60.469 52.381 5.05 5.02 35.56 3.56


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

AutoCloner maintained by Alex Coulton.