Multiple sequence alignment - TraesCS2A01G092800

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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 TraesCS2A01G092800 chr2A 100.000 3903 0 0 1 3903 46116598 46112696 0.000000e+00 7208.0
1 TraesCS2A01G092800 chr2A 74.062 320 72 9 417 731 113602841 113603154 1.900000e-23 121.0
2 TraesCS2A01G092800 chr2D 93.193 2747 137 26 345 3063 43800530 43797806 0.000000e+00 3991.0
3 TraesCS2A01G092800 chr2D 91.772 474 29 7 3312 3780 43793235 43792767 0.000000e+00 651.0
4 TraesCS2A01G092800 chr2D 80.540 704 123 13 2181 2879 407226443 407225749 2.670000e-146 529.0
5 TraesCS2A01G092800 chr2D 80.000 225 13 12 3083 3307 43793519 43793327 1.890000e-28 137.0
6 TraesCS2A01G092800 chr2B 91.943 2718 145 33 368 3043 68425103 68422418 0.000000e+00 3738.0
7 TraesCS2A01G092800 chr2B 89.205 176 15 3 3032 3206 68416778 68416606 2.360000e-52 217.0
8 TraesCS2A01G092800 chr2B 78.846 260 49 6 2226 2482 486986804 486986548 1.860000e-38 171.0
9 TraesCS2A01G092800 chr2B 76.949 295 64 4 2190 2482 747310699 747310407 8.680000e-37 165.0
10 TraesCS2A01G092800 chr2B 88.525 61 6 1 575 635 84742446 84742505 5.410000e-09 73.1
11 TraesCS2A01G092800 chr4A 78.208 982 187 16 1001 1967 141131937 141130968 1.550000e-168 603.0
12 TraesCS2A01G092800 chr4A 80.256 704 129 10 2181 2879 141130968 141130270 4.470000e-144 521.0
13 TraesCS2A01G092800 chr4A 80.269 223 32 11 272 486 670145260 670145478 1.450000e-34 158.0
14 TraesCS2A01G092800 chr4B 77.620 983 197 16 998 1967 408949850 408950822 3.380000e-160 575.0
15 TraesCS2A01G092800 chr4B 79.915 707 126 14 2181 2879 408950822 408951520 4.500000e-139 505.0
16 TraesCS2A01G092800 chr4B 71.581 468 114 15 21 478 13359819 13360277 4.120000e-20 110.0
17 TraesCS2A01G092800 chr1B 77.475 990 188 21 1001 1967 135964412 135963435 9.470000e-156 560.0
18 TraesCS2A01G092800 chr1B 80.141 710 126 10 2181 2879 135963435 135962730 2.080000e-142 516.0
19 TraesCS2A01G092800 chr1B 84.337 249 36 3 3288 3535 670391785 670392031 1.400000e-59 241.0
20 TraesCS2A01G092800 chr4D 80.824 704 125 10 2181 2879 328998267 328998965 9.540000e-151 544.0
21 TraesCS2A01G092800 chr7B 75.920 652 135 15 6 644 100005170 100004528 8.140000e-82 315.0
22 TraesCS2A01G092800 chr7B 84.030 263 36 3 3288 3548 213247822 213248080 8.370000e-62 248.0
23 TraesCS2A01G092800 chr7B 70.935 695 152 34 24 699 470525760 470525097 6.850000e-23 119.0
24 TraesCS2A01G092800 chr5B 74.476 764 154 27 2 747 707471999 707471259 3.810000e-75 292.0
25 TraesCS2A01G092800 chr5B 74.131 259 54 8 327 577 243347581 243347328 1.150000e-15 95.3
26 TraesCS2A01G092800 chr5B 90.476 63 5 1 3296 3357 577244668 577244730 8.990000e-12 82.4
27 TraesCS2A01G092800 chr7A 84.030 263 36 3 3288 3548 251743257 251743515 8.370000e-62 248.0
28 TraesCS2A01G092800 chr7A 76.689 296 50 14 371 660 732945300 732945018 3.140000e-31 147.0
29 TraesCS2A01G092800 chr7A 70.677 532 135 15 210 733 681020406 681019888 8.920000e-17 99.0
30 TraesCS2A01G092800 chr7D 83.650 263 37 3 3288 3548 236640338 236640596 3.900000e-60 243.0
31 TraesCS2A01G092800 chr6D 78.028 355 69 6 2 351 311903459 311903809 8.490000e-52 215.0
32 TraesCS2A01G092800 chr5A 72.921 469 102 19 24 476 79208139 79207680 5.260000e-29 139.0
33 TraesCS2A01G092800 chr5A 80.208 96 16 3 3445 3539 96982699 96982606 7.000000e-08 69.4
34 TraesCS2A01G092800 chr6B 77.003 287 37 16 3288 3548 579551961 579552244 1.890000e-28 137.0
35 TraesCS2A01G092800 chr6B 97.297 37 1 0 574 610 126917945 126917981 3.260000e-06 63.9
36 TraesCS2A01G092800 chrUn 75.510 245 51 8 395 635 32258653 32258892 1.150000e-20 111.0
37 TraesCS2A01G092800 chrUn 71.795 468 102 26 24 476 64337310 64337762 5.330000e-19 106.0
38 TraesCS2A01G092800 chr3D 79.355 155 27 4 328 478 580017238 580017391 1.920000e-18 104.0
39 TraesCS2A01G092800 chr3B 77.397 146 30 3 318 462 691657524 691657381 2.500000e-12 84.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G092800 chr2A 46112696 46116598 3902 True 7208 7208 100.0000 1 3903 1 chr2A.!!$R1 3902
1 TraesCS2A01G092800 chr2D 43797806 43800530 2724 True 3991 3991 93.1930 345 3063 1 chr2D.!!$R1 2718
2 TraesCS2A01G092800 chr2D 407225749 407226443 694 True 529 529 80.5400 2181 2879 1 chr2D.!!$R2 698
3 TraesCS2A01G092800 chr2D 43792767 43793519 752 True 394 651 85.8860 3083 3780 2 chr2D.!!$R3 697
4 TraesCS2A01G092800 chr2B 68422418 68425103 2685 True 3738 3738 91.9430 368 3043 1 chr2B.!!$R2 2675
5 TraesCS2A01G092800 chr4A 141130270 141131937 1667 True 562 603 79.2320 1001 2879 2 chr4A.!!$R1 1878
6 TraesCS2A01G092800 chr4B 408949850 408951520 1670 False 540 575 78.7675 998 2879 2 chr4B.!!$F2 1881
7 TraesCS2A01G092800 chr1B 135962730 135964412 1682 True 538 560 78.8080 1001 2879 2 chr1B.!!$R1 1878
8 TraesCS2A01G092800 chr4D 328998267 328998965 698 False 544 544 80.8240 2181 2879 1 chr4D.!!$F1 698
9 TraesCS2A01G092800 chr7B 100004528 100005170 642 True 315 315 75.9200 6 644 1 chr7B.!!$R1 638
10 TraesCS2A01G092800 chr5B 707471259 707471999 740 True 292 292 74.4760 2 747 1 chr5B.!!$R2 745

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
693 718 0.318107 CGGTTACTGTTCACGGACGT 60.318 55.0 0.00 0.00 0.0 4.34 F
2086 2173 0.108804 TGAAAGACTAAGCCGGCTCG 60.109 55.0 32.93 25.58 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2185 2275 0.323629 TGAAGAAGCCGTTCCCGATT 59.676 50.0 0.0 0.0 35.63 3.34 R
3719 3910 1.016627 CCATCCACTACAATGCCGTG 58.983 55.0 0.0 0.0 0.00 4.94 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
19 20 1.443407 CGAGGAGAATGCCCGACAT 59.557 57.895 0.00 0.00 42.30 3.06
35 36 1.405821 GACATCGGTCGGACTCAATCT 59.594 52.381 8.23 0.00 33.68 2.40
40 41 0.741221 GGTCGGACTCAATCTGCCAC 60.741 60.000 8.23 0.00 32.82 5.01
46 47 1.590238 GACTCAATCTGCCACGAATCG 59.410 52.381 0.00 0.00 0.00 3.34
68 69 1.901464 GTGTCCGCCCAAATGGTGT 60.901 57.895 0.00 0.00 43.57 4.16
77 78 0.810648 CCAAATGGTGTGTGGATCCG 59.189 55.000 7.39 0.00 34.05 4.18
80 81 2.135903 AATGGTGTGTGGATCCGGCA 62.136 55.000 7.39 5.97 0.00 5.69
83 84 1.078497 GTGTGTGGATCCGGCATGA 60.078 57.895 7.39 0.00 0.00 3.07
106 107 4.175489 GTCGTCGCTGCCTCGCTA 62.175 66.667 6.31 0.00 0.00 4.26
117 118 3.288484 CTCGCTAGAGGTGGTGCA 58.712 61.111 0.00 0.00 40.75 4.57
121 122 1.877576 CGCTAGAGGTGGTGCACTCA 61.878 60.000 17.98 10.37 34.40 3.41
122 123 0.321671 GCTAGAGGTGGTGCACTCAA 59.678 55.000 17.98 0.00 34.40 3.02
124 125 2.616510 GCTAGAGGTGGTGCACTCAATT 60.617 50.000 17.98 4.86 34.40 2.32
130 131 0.821301 TGGTGCACTCAATTTGGCGA 60.821 50.000 17.98 0.00 0.00 5.54
132 133 0.593128 GTGCACTCAATTTGGCGACT 59.407 50.000 10.32 0.00 0.00 4.18
167 168 1.826487 GTGCAACCCCTTCGTTGGT 60.826 57.895 0.00 0.00 42.78 3.67
170 171 1.826054 CAACCCCTTCGTTGGTGCA 60.826 57.895 0.00 0.00 39.58 4.57
193 194 1.348008 ATGATGAGGCCATCCGTGGT 61.348 55.000 5.01 0.00 46.64 4.16
242 243 4.057428 GTCGTGCGAGGCAGAGGT 62.057 66.667 0.00 0.00 40.08 3.85
243 244 3.303135 TCGTGCGAGGCAGAGGTT 61.303 61.111 0.00 0.00 40.08 3.50
245 246 2.343758 GTGCGAGGCAGAGGTTGA 59.656 61.111 0.00 0.00 40.08 3.18
252 253 1.920835 GGCAGAGGTTGAGGGAGGT 60.921 63.158 0.00 0.00 0.00 3.85
253 254 1.492993 GGCAGAGGTTGAGGGAGGTT 61.493 60.000 0.00 0.00 0.00 3.50
254 255 0.322008 GCAGAGGTTGAGGGAGGTTG 60.322 60.000 0.00 0.00 0.00 3.77
255 256 0.322008 CAGAGGTTGAGGGAGGTTGC 60.322 60.000 0.00 0.00 0.00 4.17
256 257 0.768221 AGAGGTTGAGGGAGGTTGCA 60.768 55.000 0.00 0.00 0.00 4.08
257 258 0.322008 GAGGTTGAGGGAGGTTGCAG 60.322 60.000 0.00 0.00 0.00 4.41
258 259 1.973812 GGTTGAGGGAGGTTGCAGC 60.974 63.158 0.00 0.00 0.00 5.25
259 260 1.228245 GTTGAGGGAGGTTGCAGCA 60.228 57.895 2.05 0.00 0.00 4.41
260 261 1.073722 TTGAGGGAGGTTGCAGCAG 59.926 57.895 2.05 0.00 0.00 4.24
261 262 2.749441 GAGGGAGGTTGCAGCAGC 60.749 66.667 2.05 0.00 42.57 5.25
262 263 4.357279 AGGGAGGTTGCAGCAGCC 62.357 66.667 20.35 20.35 41.13 4.85
264 265 4.357279 GGAGGTTGCAGCAGCCCT 62.357 66.667 23.80 18.65 41.13 5.19
299 312 1.309499 CGAGGAGGAGTCGCACTCTT 61.309 60.000 13.59 8.04 44.46 2.85
304 317 2.569134 GAGTCGCACTCTTCGGCT 59.431 61.111 8.50 0.00 45.28 5.52
364 385 2.531428 TGGTGGACATGGCCTCCA 60.531 61.111 33.28 33.28 46.36 3.86
486 507 4.057428 GTGAGCCGGTGCGAGTCT 62.057 66.667 1.90 0.00 44.33 3.24
499 524 1.104630 CGAGTCTTCCCACTCTACCC 58.895 60.000 0.00 0.00 40.75 3.69
510 535 4.790962 TCTACCCCGCGAGCGACT 62.791 66.667 19.72 3.10 42.83 4.18
523 548 3.305964 CGAGCGACTGAAGAAACACTTA 58.694 45.455 0.00 0.00 39.13 2.24
524 549 3.119792 CGAGCGACTGAAGAAACACTTAC 59.880 47.826 0.00 0.00 39.13 2.34
525 550 4.299978 GAGCGACTGAAGAAACACTTACT 58.700 43.478 0.00 0.00 39.13 2.24
526 551 4.694339 AGCGACTGAAGAAACACTTACTT 58.306 39.130 0.00 0.00 39.13 2.24
528 553 4.506654 GCGACTGAAGAAACACTTACTTCA 59.493 41.667 0.00 0.00 44.66 3.02
534 559 4.790718 AGAAACACTTACTTCAAGGGGT 57.209 40.909 0.00 0.00 40.23 4.95
559 584 1.515954 GACCGTCGGACATGGACAT 59.484 57.895 20.51 0.00 34.76 3.06
678 703 2.093306 TGTTTGAGATGCGATCGGTT 57.907 45.000 18.30 0.00 0.00 4.44
684 709 2.165641 TGAGATGCGATCGGTTACTGTT 59.834 45.455 18.30 0.00 0.00 3.16
693 718 0.318107 CGGTTACTGTTCACGGACGT 60.318 55.000 0.00 0.00 0.00 4.34
718 749 1.646540 ACACGTGTGTCGGCATTTG 59.353 52.632 22.71 0.00 40.24 2.32
738 769 7.466996 GCATTTGAGAGGTCAGATTTGATGTAG 60.467 40.741 0.00 0.00 35.39 2.74
739 770 6.857437 TTGAGAGGTCAGATTTGATGTAGA 57.143 37.500 0.00 0.00 35.39 2.59
740 771 7.429374 TTGAGAGGTCAGATTTGATGTAGAT 57.571 36.000 0.00 0.00 35.39 1.98
742 773 6.382282 TGAGAGGTCAGATTTGATGTAGATGT 59.618 38.462 0.00 0.00 35.39 3.06
744 775 7.046652 AGAGGTCAGATTTGATGTAGATGTTG 58.953 38.462 0.00 0.00 35.39 3.33
856 896 1.511464 GTGCGACTCTCCGTACACG 60.511 63.158 0.00 0.00 43.06 4.49
909 949 2.636830 CATCCATTTCTTCACCTCGCT 58.363 47.619 0.00 0.00 0.00 4.93
911 951 1.623311 TCCATTTCTTCACCTCGCTGA 59.377 47.619 0.00 0.00 0.00 4.26
915 955 4.437239 CATTTCTTCACCTCGCTGACTAT 58.563 43.478 0.00 0.00 0.00 2.12
930 970 0.666913 ACTATGTCGCCGCTCGTTAT 59.333 50.000 0.00 0.00 39.67 1.89
935 975 1.299620 TCGCCGCTCGTTATAAGCC 60.300 57.895 0.00 0.00 39.67 4.35
1134 1175 1.372997 CACCTCCGTCAAGTCCGTG 60.373 63.158 0.00 0.00 0.00 4.94
1422 1471 3.057019 CGAGATGACCGACTTCAACAAA 58.943 45.455 0.00 0.00 0.00 2.83
1618 1676 2.268920 GCAGCCTCAACATCGGGA 59.731 61.111 0.00 0.00 0.00 5.14
1619 1677 1.377202 GCAGCCTCAACATCGGGAA 60.377 57.895 0.00 0.00 0.00 3.97
1620 1678 1.372087 GCAGCCTCAACATCGGGAAG 61.372 60.000 0.00 0.00 0.00 3.46
1671 1729 1.470979 CCTTACTGGATGAACGACGGG 60.471 57.143 0.00 0.00 38.35 5.28
2004 2080 9.999009 TGTTTTAACACATAGATAGACGTAGAG 57.001 33.333 0.00 0.00 33.17 2.43
2016 2092 3.622630 AGACGTAGAGGCTCATACACTT 58.377 45.455 18.26 2.47 25.16 3.16
2034 2117 3.104512 ACTTGATCACCCCTATGAACGA 58.895 45.455 0.00 0.00 30.82 3.85
2037 2120 2.835156 TGATCACCCCTATGAACGAACA 59.165 45.455 0.00 0.00 30.82 3.18
2040 2123 2.569853 TCACCCCTATGAACGAACACAT 59.430 45.455 0.00 0.00 0.00 3.21
2042 2125 4.407621 TCACCCCTATGAACGAACACATAT 59.592 41.667 0.00 0.00 0.00 1.78
2047 2130 6.070767 CCCCTATGAACGAACACATATCCTAT 60.071 42.308 0.00 0.00 0.00 2.57
2083 2170 3.636282 TTTTTGAAAGACTAAGCCGGC 57.364 42.857 21.89 21.89 0.00 6.13
2084 2171 2.561478 TTTGAAAGACTAAGCCGGCT 57.439 45.000 27.08 27.08 0.00 5.52
2086 2173 0.108804 TGAAAGACTAAGCCGGCTCG 60.109 55.000 32.93 25.58 0.00 5.03
2094 2181 1.337071 CTAAGCCGGCTCGTCATCTTA 59.663 52.381 32.93 14.88 0.00 2.10
2096 2183 0.535335 AGCCGGCTCGTCATCTTAAA 59.465 50.000 27.08 0.00 0.00 1.52
2100 2187 3.558418 GCCGGCTCGTCATCTTAAAATTA 59.442 43.478 22.15 0.00 0.00 1.40
2125 2212 2.771089 AGTCATCACAGACGCACAATT 58.229 42.857 0.00 0.00 43.24 2.32
2140 2227 4.513581 GCACAATTAACCAAAGCAAAACG 58.486 39.130 0.00 0.00 0.00 3.60
2605 2695 1.501582 GGCCATGGAAGGAGTACTCT 58.498 55.000 21.88 3.41 0.00 3.24
2782 2879 1.617322 TCAAGACTGTCACCTACGCT 58.383 50.000 10.88 0.00 0.00 5.07
2788 2885 2.257371 GTCACCTACGCTGACGCA 59.743 61.111 0.00 0.00 45.53 5.24
2856 2953 2.574929 CAAGTACGGCGTGCCCTA 59.425 61.111 24.86 0.00 0.00 3.53
2918 3015 4.948847 TCATTAACTCATCACTCCATCCG 58.051 43.478 0.00 0.00 0.00 4.18
2920 3017 4.819105 TTAACTCATCACTCCATCCGTT 57.181 40.909 0.00 0.00 0.00 4.44
2925 3022 2.167693 TCATCACTCCATCCGTTACCAC 59.832 50.000 0.00 0.00 0.00 4.16
2934 3031 3.189702 CCATCCGTTACCACGTTTCATTT 59.810 43.478 0.00 0.00 45.62 2.32
2935 3032 4.399978 CATCCGTTACCACGTTTCATTTC 58.600 43.478 0.00 0.00 45.62 2.17
2936 3033 2.807392 TCCGTTACCACGTTTCATTTCC 59.193 45.455 0.00 0.00 45.62 3.13
2939 3036 2.203470 TACCACGTTTCATTTCCCCC 57.797 50.000 0.00 0.00 0.00 5.40
2953 3050 3.399181 CCCCCTGCTCCGTTGCTA 61.399 66.667 0.00 0.00 0.00 3.49
2957 3054 0.535335 CCCTGCTCCGTTGCTACTTA 59.465 55.000 0.00 0.00 0.00 2.24
2987 3084 7.225538 GCAATTAGCTGAGTTGACATATACTGT 59.774 37.037 0.00 0.00 39.88 3.55
2988 3085 9.102757 CAATTAGCTGAGTTGACATATACTGTT 57.897 33.333 0.00 0.00 38.54 3.16
3008 3105 8.433421 ACTGTTAATTATACACTATGGTGCAC 57.567 34.615 8.80 8.80 46.57 4.57
3067 3166 9.668497 ACTTACTAACTAGCTTTAATTTGGAGG 57.332 33.333 0.00 0.00 0.00 4.30
3068 3167 9.886132 CTTACTAACTAGCTTTAATTTGGAGGA 57.114 33.333 0.00 0.00 0.00 3.71
3069 3168 9.886132 TTACTAACTAGCTTTAATTTGGAGGAG 57.114 33.333 0.00 0.00 0.00 3.69
3070 3169 8.147244 ACTAACTAGCTTTAATTTGGAGGAGA 57.853 34.615 0.00 0.00 0.00 3.71
3071 3170 8.261522 ACTAACTAGCTTTAATTTGGAGGAGAG 58.738 37.037 0.00 0.00 0.00 3.20
3072 3171 6.875972 ACTAGCTTTAATTTGGAGGAGAGA 57.124 37.500 0.00 0.00 0.00 3.10
3073 3172 7.259088 ACTAGCTTTAATTTGGAGGAGAGAA 57.741 36.000 0.00 0.00 0.00 2.87
3074 3173 7.690256 ACTAGCTTTAATTTGGAGGAGAGAAA 58.310 34.615 0.00 0.00 0.00 2.52
3075 3174 7.826744 ACTAGCTTTAATTTGGAGGAGAGAAAG 59.173 37.037 0.00 0.00 0.00 2.62
3076 3175 6.784031 AGCTTTAATTTGGAGGAGAGAAAGA 58.216 36.000 0.00 0.00 0.00 2.52
3077 3176 7.409358 AGCTTTAATTTGGAGGAGAGAAAGAT 58.591 34.615 0.00 0.00 0.00 2.40
3078 3177 7.338957 AGCTTTAATTTGGAGGAGAGAAAGATG 59.661 37.037 0.00 0.00 0.00 2.90
3079 3178 7.121907 GCTTTAATTTGGAGGAGAGAAAGATGT 59.878 37.037 0.00 0.00 0.00 3.06
3080 3179 7.928307 TTAATTTGGAGGAGAGAAAGATGTG 57.072 36.000 0.00 0.00 0.00 3.21
3081 3180 3.340814 TTGGAGGAGAGAAAGATGTGC 57.659 47.619 0.00 0.00 0.00 4.57
3094 3193 7.607607 AGAGAAAGATGTGCATGTGTATGTAAA 59.392 33.333 0.00 0.00 36.65 2.01
3101 3200 3.009584 TGCATGTGTATGTAAACCTGGGA 59.990 43.478 0.00 0.00 36.65 4.37
3103 3202 4.036734 GCATGTGTATGTAAACCTGGGATG 59.963 45.833 0.00 0.00 36.65 3.51
3114 3213 7.371936 TGTAAACCTGGGATGTTTATTTTTCG 58.628 34.615 0.00 0.00 39.56 3.46
3118 3217 7.095695 ACCTGGGATGTTTATTTTTCGTATG 57.904 36.000 0.00 0.00 0.00 2.39
3128 3227 9.991388 TGTTTATTTTTCGTATGTATACCTTGC 57.009 29.630 0.00 0.00 0.00 4.01
3154 3253 4.659111 TTCTTTACTCGGTGTGTCTTCA 57.341 40.909 0.00 0.00 0.00 3.02
3161 3260 1.068541 TCGGTGTGTCTTCACGATGAG 60.069 52.381 0.00 0.00 46.49 2.90
3162 3261 1.714794 GGTGTGTCTTCACGATGAGG 58.285 55.000 0.00 0.00 46.49 3.86
3163 3262 1.000955 GGTGTGTCTTCACGATGAGGT 59.999 52.381 0.00 0.00 46.49 3.85
3164 3263 2.061773 GTGTGTCTTCACGATGAGGTG 58.938 52.381 0.00 0.00 46.49 4.00
3165 3264 1.071605 GTGTCTTCACGATGAGGTGC 58.928 55.000 0.00 0.00 37.83 5.01
3166 3265 0.969149 TGTCTTCACGATGAGGTGCT 59.031 50.000 0.00 0.00 37.83 4.40
3167 3266 1.067565 TGTCTTCACGATGAGGTGCTC 60.068 52.381 0.00 0.00 37.83 4.26
3168 3267 0.532573 TCTTCACGATGAGGTGCTCC 59.467 55.000 0.00 0.00 37.83 4.70
3170 3269 0.976641 TTCACGATGAGGTGCTCCTT 59.023 50.000 9.08 0.00 45.24 3.36
3171 3270 0.247460 TCACGATGAGGTGCTCCTTG 59.753 55.000 9.08 2.94 45.24 3.61
3172 3271 0.036952 CACGATGAGGTGCTCCTTGT 60.037 55.000 9.08 0.54 45.24 3.16
3173 3272 1.204704 CACGATGAGGTGCTCCTTGTA 59.795 52.381 9.08 0.00 45.24 2.41
3174 3273 1.204941 ACGATGAGGTGCTCCTTGTAC 59.795 52.381 9.08 0.00 45.24 2.90
3175 3274 1.478510 CGATGAGGTGCTCCTTGTACT 59.521 52.381 9.08 0.00 45.24 2.73
3176 3275 2.093973 CGATGAGGTGCTCCTTGTACTT 60.094 50.000 9.08 0.00 45.24 2.24
3177 3276 3.617531 CGATGAGGTGCTCCTTGTACTTT 60.618 47.826 9.08 0.00 45.24 2.66
3178 3277 3.857157 TGAGGTGCTCCTTGTACTTTT 57.143 42.857 9.08 0.00 45.24 2.27
3179 3278 4.164843 TGAGGTGCTCCTTGTACTTTTT 57.835 40.909 9.08 0.00 45.24 1.94
3200 3299 2.404559 TGTTGGTGGGTTGTACTCTCT 58.595 47.619 0.00 0.00 0.00 3.10
3244 3343 6.253512 TCGTGAAATGAATATCGTCTTCAGTG 59.746 38.462 0.00 0.00 36.16 3.66
3259 3358 3.319137 TCAGTGATGTGAAGGCAGTAC 57.681 47.619 0.00 0.00 0.00 2.73
3260 3359 2.028112 TCAGTGATGTGAAGGCAGTACC 60.028 50.000 0.00 0.00 39.61 3.34
3296 3395 5.892686 ACAAGGTTAGAGTCATACTACCTCC 59.107 44.000 0.00 0.00 0.00 4.30
3307 3406 6.555360 AGTCATACTACCTCCTTCCCAAATAG 59.445 42.308 0.00 0.00 0.00 1.73
3308 3407 6.553852 GTCATACTACCTCCTTCCCAAATAGA 59.446 42.308 0.00 0.00 0.00 1.98
3309 3408 7.235812 GTCATACTACCTCCTTCCCAAATAGAT 59.764 40.741 0.00 0.00 0.00 1.98
3310 3409 5.896073 ACTACCTCCTTCCCAAATAGATG 57.104 43.478 0.00 0.00 0.00 2.90
3504 3690 5.996644 TGGTCAAACTTAGGAAGAACTGAA 58.003 37.500 0.00 0.00 0.00 3.02
3506 3692 6.710744 TGGTCAAACTTAGGAAGAACTGAATC 59.289 38.462 0.00 0.00 0.00 2.52
3542 3728 1.454847 GCCATGTATTTGGGGCCGA 60.455 57.895 0.00 0.00 40.55 5.54
3543 3729 1.455383 GCCATGTATTTGGGGCCGAG 61.455 60.000 0.00 0.00 40.55 4.63
3544 3730 0.106719 CCATGTATTTGGGGCCGAGT 60.107 55.000 0.00 0.00 32.80 4.18
3546 3732 0.916086 ATGTATTTGGGGCCGAGTGA 59.084 50.000 0.00 0.00 0.00 3.41
3547 3733 0.251916 TGTATTTGGGGCCGAGTGAG 59.748 55.000 0.00 0.00 0.00 3.51
3548 3734 0.539986 GTATTTGGGGCCGAGTGAGA 59.460 55.000 0.00 0.00 0.00 3.27
3550 3736 0.625849 ATTTGGGGCCGAGTGAGAAT 59.374 50.000 0.00 0.00 0.00 2.40
3551 3737 1.281419 TTTGGGGCCGAGTGAGAATA 58.719 50.000 0.00 0.00 0.00 1.75
3647 3838 6.438186 AAAATCCCAAAAGGTGAATGTCAT 57.562 33.333 0.00 0.00 36.75 3.06
3648 3839 5.410355 AATCCCAAAAGGTGAATGTCATG 57.590 39.130 0.00 0.00 36.75 3.07
3650 3841 4.676109 TCCCAAAAGGTGAATGTCATGAT 58.324 39.130 0.00 0.00 36.75 2.45
3652 3843 6.434302 TCCCAAAAGGTGAATGTCATGATAT 58.566 36.000 0.00 0.00 36.75 1.63
3756 3947 8.699130 AGTGGATGGGAATTTTCTTATGAAATC 58.301 33.333 4.77 1.46 41.24 2.17
3758 3949 9.934784 TGGATGGGAATTTTCTTATGAAATCTA 57.065 29.630 4.77 0.00 41.24 1.98
3805 3996 6.861065 TTTTCTGAGTTGTGATCTTGTACC 57.139 37.500 0.00 0.00 0.00 3.34
3806 3997 5.545063 TTCTGAGTTGTGATCTTGTACCA 57.455 39.130 0.00 0.00 0.00 3.25
3807 3998 5.545063 TCTGAGTTGTGATCTTGTACCAA 57.455 39.130 0.00 0.00 0.00 3.67
3808 3999 5.924356 TCTGAGTTGTGATCTTGTACCAAA 58.076 37.500 0.00 0.00 0.00 3.28
3809 4000 6.533730 TCTGAGTTGTGATCTTGTACCAAAT 58.466 36.000 0.00 0.00 0.00 2.32
3810 4001 6.427853 TCTGAGTTGTGATCTTGTACCAAATG 59.572 38.462 0.00 0.00 0.00 2.32
3811 4002 6.061441 TGAGTTGTGATCTTGTACCAAATGT 58.939 36.000 0.00 0.00 0.00 2.71
3812 4003 7.220740 TGAGTTGTGATCTTGTACCAAATGTA 58.779 34.615 0.00 0.00 0.00 2.29
3824 4015 4.957759 ACCAAATGTACGTGCTTAATCC 57.042 40.909 4.97 0.00 0.00 3.01
3825 4016 4.328536 ACCAAATGTACGTGCTTAATCCA 58.671 39.130 4.97 0.00 0.00 3.41
3826 4017 4.947388 ACCAAATGTACGTGCTTAATCCAT 59.053 37.500 4.97 0.00 0.00 3.41
3827 4018 5.065988 ACCAAATGTACGTGCTTAATCCATC 59.934 40.000 4.97 0.00 0.00 3.51
3828 4019 5.065859 CCAAATGTACGTGCTTAATCCATCA 59.934 40.000 4.97 0.00 0.00 3.07
3829 4020 5.734855 AATGTACGTGCTTAATCCATCAC 57.265 39.130 4.97 0.00 0.00 3.06
3830 4021 3.527533 TGTACGTGCTTAATCCATCACC 58.472 45.455 4.97 0.00 0.00 4.02
3831 4022 2.779755 ACGTGCTTAATCCATCACCA 57.220 45.000 0.00 0.00 0.00 4.17
3832 4023 3.066291 ACGTGCTTAATCCATCACCAA 57.934 42.857 0.00 0.00 0.00 3.67
3833 4024 3.417101 ACGTGCTTAATCCATCACCAAA 58.583 40.909 0.00 0.00 0.00 3.28
3834 4025 3.823873 ACGTGCTTAATCCATCACCAAAA 59.176 39.130 0.00 0.00 0.00 2.44
3835 4026 4.462483 ACGTGCTTAATCCATCACCAAAAT 59.538 37.500 0.00 0.00 0.00 1.82
3836 4027 5.650266 ACGTGCTTAATCCATCACCAAAATA 59.350 36.000 0.00 0.00 0.00 1.40
3837 4028 6.151985 ACGTGCTTAATCCATCACCAAAATAA 59.848 34.615 0.00 0.00 0.00 1.40
3838 4029 6.692681 CGTGCTTAATCCATCACCAAAATAAG 59.307 38.462 0.00 0.00 0.00 1.73
3839 4030 7.547227 GTGCTTAATCCATCACCAAAATAAGT 58.453 34.615 0.00 0.00 0.00 2.24
3840 4031 8.682710 GTGCTTAATCCATCACCAAAATAAGTA 58.317 33.333 0.00 0.00 0.00 2.24
3841 4032 9.249053 TGCTTAATCCATCACCAAAATAAGTAA 57.751 29.630 0.00 0.00 0.00 2.24
3847 4038 7.771183 TCCATCACCAAAATAAGTAATCTTGC 58.229 34.615 0.00 0.00 35.36 4.01
3848 4039 7.395772 TCCATCACCAAAATAAGTAATCTTGCA 59.604 33.333 0.00 0.00 35.36 4.08
3849 4040 8.199449 CCATCACCAAAATAAGTAATCTTGCAT 58.801 33.333 0.00 0.00 35.36 3.96
3852 4043 8.682710 TCACCAAAATAAGTAATCTTGCATACC 58.317 33.333 0.00 0.00 35.36 2.73
3853 4044 7.643764 CACCAAAATAAGTAATCTTGCATACCG 59.356 37.037 0.00 0.00 35.36 4.02
3854 4045 7.554835 ACCAAAATAAGTAATCTTGCATACCGA 59.445 33.333 0.00 0.00 35.36 4.69
3855 4046 8.402472 CCAAAATAAGTAATCTTGCATACCGAA 58.598 33.333 0.00 0.00 35.36 4.30
3856 4047 9.781834 CAAAATAAGTAATCTTGCATACCGAAA 57.218 29.630 0.00 0.00 35.36 3.46
3858 4049 5.485662 AAGTAATCTTGCATACCGAAAGC 57.514 39.130 0.00 0.00 32.09 3.51
3859 4050 4.513442 AGTAATCTTGCATACCGAAAGCA 58.487 39.130 0.00 0.00 36.32 3.91
3860 4051 5.126067 AGTAATCTTGCATACCGAAAGCAT 58.874 37.500 0.00 0.00 38.19 3.79
3861 4052 6.288294 AGTAATCTTGCATACCGAAAGCATA 58.712 36.000 0.00 0.00 38.19 3.14
3862 4053 5.679734 AATCTTGCATACCGAAAGCATAG 57.320 39.130 0.00 0.00 38.19 2.23
3863 4054 3.466836 TCTTGCATACCGAAAGCATAGG 58.533 45.455 0.00 0.00 38.19 2.57
3864 4055 2.254546 TGCATACCGAAAGCATAGGG 57.745 50.000 0.00 0.00 32.55 3.53
3865 4056 1.765904 TGCATACCGAAAGCATAGGGA 59.234 47.619 0.00 0.00 32.55 4.20
3866 4057 2.371841 TGCATACCGAAAGCATAGGGAT 59.628 45.455 0.00 0.00 32.55 3.85
3867 4058 2.744202 GCATACCGAAAGCATAGGGATG 59.256 50.000 8.85 8.85 46.55 3.51
3868 4059 3.807209 GCATACCGAAAGCATAGGGATGT 60.807 47.826 13.11 0.00 45.77 3.06
3869 4060 4.562757 GCATACCGAAAGCATAGGGATGTA 60.563 45.833 13.11 0.00 45.77 2.29
3870 4061 5.734720 CATACCGAAAGCATAGGGATGTAT 58.265 41.667 5.92 0.00 40.59 2.29
3871 4062 4.273148 ACCGAAAGCATAGGGATGTATC 57.727 45.455 0.00 0.00 35.30 2.24
3872 4063 3.008049 ACCGAAAGCATAGGGATGTATCC 59.992 47.826 2.17 2.17 46.41 2.59
3882 4073 1.312815 GGATGTATCCACCAGCTTGC 58.687 55.000 6.03 0.00 46.38 4.01
3883 4074 1.408683 GGATGTATCCACCAGCTTGCA 60.409 52.381 6.03 0.00 46.38 4.08
3884 4075 1.945394 GATGTATCCACCAGCTTGCAG 59.055 52.381 0.00 0.00 0.00 4.41
3885 4076 0.983467 TGTATCCACCAGCTTGCAGA 59.017 50.000 0.00 0.00 0.00 4.26
3886 4077 1.350684 TGTATCCACCAGCTTGCAGAA 59.649 47.619 0.00 0.00 0.00 3.02
3887 4078 2.224744 TGTATCCACCAGCTTGCAGAAA 60.225 45.455 0.00 0.00 0.00 2.52
3888 4079 2.226962 ATCCACCAGCTTGCAGAAAT 57.773 45.000 0.00 0.00 0.00 2.17
3889 4080 1.538047 TCCACCAGCTTGCAGAAATC 58.462 50.000 0.00 0.00 0.00 2.17
3890 4081 1.074405 TCCACCAGCTTGCAGAAATCT 59.926 47.619 0.00 0.00 0.00 2.40
3891 4082 1.471684 CCACCAGCTTGCAGAAATCTC 59.528 52.381 0.00 0.00 0.00 2.75
3892 4083 2.434428 CACCAGCTTGCAGAAATCTCT 58.566 47.619 0.00 0.00 0.00 3.10
3893 4084 3.603532 CACCAGCTTGCAGAAATCTCTA 58.396 45.455 0.00 0.00 0.00 2.43
3894 4085 4.005650 CACCAGCTTGCAGAAATCTCTAA 58.994 43.478 0.00 0.00 0.00 2.10
3895 4086 4.456911 CACCAGCTTGCAGAAATCTCTAAA 59.543 41.667 0.00 0.00 0.00 1.85
3896 4087 4.699257 ACCAGCTTGCAGAAATCTCTAAAG 59.301 41.667 0.00 0.00 31.83 1.85
3897 4088 4.096081 CCAGCTTGCAGAAATCTCTAAAGG 59.904 45.833 0.00 0.00 30.40 3.11
3898 4089 4.096081 CAGCTTGCAGAAATCTCTAAAGGG 59.904 45.833 0.00 0.00 30.40 3.95
3899 4090 4.018960 AGCTTGCAGAAATCTCTAAAGGGA 60.019 41.667 0.00 0.00 30.40 4.20
3900 4091 4.702131 GCTTGCAGAAATCTCTAAAGGGAA 59.298 41.667 0.00 0.00 30.40 3.97
3901 4092 5.183904 GCTTGCAGAAATCTCTAAAGGGAAA 59.816 40.000 0.00 0.00 30.40 3.13
3902 4093 6.127507 GCTTGCAGAAATCTCTAAAGGGAAAT 60.128 38.462 0.00 0.00 30.40 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.032860 ATGTCGGGCATTCTCCTCGG 62.033 60.000 0.00 0.00 33.14 4.63
19 20 1.511305 GCAGATTGAGTCCGACCGA 59.489 57.895 0.00 0.00 0.00 4.69
46 47 1.714899 CCATTTGGGCGGACACGATC 61.715 60.000 0.00 0.00 44.60 3.69
51 52 1.900981 CACACCATTTGGGCGGACA 60.901 57.895 0.96 0.00 42.05 4.02
68 69 2.910360 CCTCATGCCGGATCCACA 59.090 61.111 13.41 9.86 0.00 4.17
77 78 2.456119 CGACGACTTGCCTCATGCC 61.456 63.158 0.00 0.00 40.16 4.40
80 81 1.446792 CAGCGACGACTTGCCTCAT 60.447 57.895 0.00 0.00 0.00 2.90
105 106 3.411446 CAAATTGAGTGCACCACCTCTA 58.589 45.455 14.63 1.54 34.49 2.43
106 107 2.233271 CAAATTGAGTGCACCACCTCT 58.767 47.619 14.63 0.00 34.49 3.69
111 112 0.821301 TCGCCAAATTGAGTGCACCA 60.821 50.000 14.63 8.65 0.00 4.17
117 118 2.290641 GTGTTCAGTCGCCAAATTGAGT 59.709 45.455 0.00 0.00 0.00 3.41
121 122 0.591170 CGGTGTTCAGTCGCCAAATT 59.409 50.000 0.00 0.00 37.81 1.82
122 123 0.534203 ACGGTGTTCAGTCGCCAAAT 60.534 50.000 0.00 0.00 37.81 2.32
124 125 1.885388 CACGGTGTTCAGTCGCCAA 60.885 57.895 0.00 0.00 37.81 4.52
148 149 1.826054 CCAACGAAGGGGTTGCACA 60.826 57.895 0.00 0.00 44.58 4.57
150 151 1.826054 CACCAACGAAGGGGTTGCA 60.826 57.895 0.00 0.00 44.58 4.08
167 168 1.986632 ATGGCCTCATCATCGGTGCA 61.987 55.000 3.32 0.00 0.00 4.57
193 194 2.125326 CATACCCTCAGCGGACGGA 61.125 63.158 8.74 0.00 33.16 4.69
225 226 3.575351 AACCTCTGCCTCGCACGAC 62.575 63.158 0.00 0.00 33.79 4.34
242 243 1.073722 CTGCTGCAACCTCCCTCAA 59.926 57.895 3.02 0.00 0.00 3.02
243 244 2.752358 CTGCTGCAACCTCCCTCA 59.248 61.111 3.02 0.00 0.00 3.86
245 246 4.357279 GGCTGCTGCAACCTCCCT 62.357 66.667 17.89 0.00 41.91 4.20
270 283 3.522731 CCTCCTCGCCGACCTCTG 61.523 72.222 0.00 0.00 0.00 3.35
274 287 3.519930 GACTCCTCCTCGCCGACC 61.520 72.222 0.00 0.00 0.00 4.79
285 298 2.995872 GCCGAAGAGTGCGACTCCT 61.996 63.158 11.24 1.02 46.18 3.69
299 312 1.734137 GCTATCCGTCTTGAGCCGA 59.266 57.895 0.00 0.00 0.00 5.54
304 317 0.901827 TTGCAGGCTATCCGTCTTGA 59.098 50.000 0.00 0.00 37.47 3.02
355 371 1.077501 CATCGTGGTTGGAGGCCAT 60.078 57.895 5.01 0.00 38.40 4.40
364 385 0.323629 ACAACGGATCCATCGTGGTT 59.676 50.000 13.41 3.50 41.41 3.67
419 440 2.630158 CCTACTCTTCCTCGTCGAAGA 58.370 52.381 13.67 13.67 44.67 2.87
422 443 0.747283 GCCCTACTCTTCCTCGTCGA 60.747 60.000 0.00 0.00 0.00 4.20
482 503 0.324460 CGGGGTAGAGTGGGAAGACT 60.324 60.000 0.00 0.00 0.00 3.24
486 507 3.072468 CGCGGGGTAGAGTGGGAA 61.072 66.667 0.00 0.00 0.00 3.97
499 524 1.733041 TTTCTTCAGTCGCTCGCGG 60.733 57.895 6.13 0.00 40.25 6.46
510 535 5.130350 CCCCTTGAAGTAAGTGTTTCTTCA 58.870 41.667 5.03 5.03 43.44 3.02
523 548 2.116125 GGCTGCACCCCTTGAAGT 59.884 61.111 0.50 0.00 32.44 3.01
524 549 3.058160 CGGCTGCACCCCTTGAAG 61.058 66.667 0.50 0.00 33.14 3.02
525 550 3.565214 TCGGCTGCACCCCTTGAA 61.565 61.111 0.50 0.00 33.26 2.69
526 551 4.329545 GTCGGCTGCACCCCTTGA 62.330 66.667 0.50 0.00 33.26 3.02
546 571 2.186644 CGCCATGTCCATGTCCGA 59.813 61.111 6.53 0.00 37.11 4.55
559 584 2.124983 GCTCATTCAGCTCCGCCA 60.125 61.111 0.00 0.00 45.83 5.69
611 636 9.169468 CGCAATTAAGAAACCACATATTCATAC 57.831 33.333 0.00 0.00 0.00 2.39
619 644 5.067283 GGATACCGCAATTAAGAAACCACAT 59.933 40.000 0.00 0.00 0.00 3.21
702 727 0.249699 TCTCAAATGCCGACACACGT 60.250 50.000 0.00 0.00 40.78 4.49
710 735 2.322355 ATCTGACCTCTCAAATGCCG 57.678 50.000 0.00 0.00 0.00 5.69
718 749 6.815089 ACATCTACATCAAATCTGACCTCTC 58.185 40.000 0.00 0.00 33.30 3.20
738 769 1.173913 GGGCAGGTGGTTACAACATC 58.826 55.000 0.00 0.00 36.52 3.06
739 770 0.251608 GGGGCAGGTGGTTACAACAT 60.252 55.000 0.00 0.00 36.52 2.71
740 771 1.151908 GGGGCAGGTGGTTACAACA 59.848 57.895 0.00 0.00 36.52 3.33
742 773 0.251564 CATGGGGCAGGTGGTTACAA 60.252 55.000 0.00 0.00 0.00 2.41
744 775 2.052104 GCATGGGGCAGGTGGTTAC 61.052 63.158 0.00 0.00 43.97 2.50
819 859 3.517602 CACGACGAAAATAGATGGTCCA 58.482 45.455 0.00 0.00 0.00 4.02
820 860 2.284417 GCACGACGAAAATAGATGGTCC 59.716 50.000 0.00 0.00 0.00 4.46
882 922 2.939103 GTGAAGAAATGGATGGACCGAG 59.061 50.000 0.00 0.00 42.61 4.63
909 949 1.929806 AACGAGCGGCGACATAGTCA 61.930 55.000 12.98 0.00 44.57 3.41
911 951 0.666913 ATAACGAGCGGCGACATAGT 59.333 50.000 12.98 0.00 44.57 2.12
915 955 0.868602 GCTTATAACGAGCGGCGACA 60.869 55.000 12.98 0.00 44.57 4.35
930 970 3.915575 GACGGAGGAGACGGCTTA 58.084 61.111 0.00 0.00 36.18 3.09
935 975 2.174969 CGGAGAGACGGAGGAGACG 61.175 68.421 0.00 0.00 37.36 4.18
999 1040 3.426859 CGATGATCGCACCTTTACTCATC 59.573 47.826 0.41 0.00 36.99 2.92
1618 1676 1.383803 CCCCTAGCAGCCTCCTCTT 60.384 63.158 0.00 0.00 0.00 2.85
1619 1677 2.285180 CCCCTAGCAGCCTCCTCT 59.715 66.667 0.00 0.00 0.00 3.69
1620 1678 1.836604 CTCCCCTAGCAGCCTCCTC 60.837 68.421 0.00 0.00 0.00 3.71
1671 1729 4.087892 TCCAGCAGCCGCCTCTTC 62.088 66.667 0.00 0.00 39.83 2.87
1704 1762 1.228154 GTTGGGCTTGAACTCCGGT 60.228 57.895 0.00 0.00 0.00 5.28
1707 1765 0.534203 TGACGTTGGGCTTGAACTCC 60.534 55.000 0.00 0.00 0.00 3.85
1863 1921 1.536940 TGACGACGAGGTTGGTGATA 58.463 50.000 0.00 0.00 0.00 2.15
1998 2074 4.036852 TGATCAAGTGTATGAGCCTCTACG 59.963 45.833 0.00 0.00 34.89 3.51
2004 2080 2.565841 GGGTGATCAAGTGTATGAGCC 58.434 52.381 0.00 0.00 34.89 4.70
2016 2092 2.835156 TGTTCGTTCATAGGGGTGATCA 59.165 45.455 0.00 0.00 0.00 2.92
2064 2147 2.812011 GAGCCGGCTTAGTCTTTCAAAA 59.188 45.455 33.34 0.00 0.00 2.44
2070 2157 1.248785 TGACGAGCCGGCTTAGTCTT 61.249 55.000 40.20 23.59 35.04 3.01
2083 2170 8.717821 TGACTTGGTTAATTTTAAGATGACGAG 58.282 33.333 0.00 0.00 0.00 4.18
2084 2171 8.610248 TGACTTGGTTAATTTTAAGATGACGA 57.390 30.769 0.00 0.00 0.00 4.20
2094 2181 6.668323 CGTCTGTGATGACTTGGTTAATTTT 58.332 36.000 0.00 0.00 35.00 1.82
2096 2183 4.154195 GCGTCTGTGATGACTTGGTTAATT 59.846 41.667 0.00 0.00 35.00 1.40
2100 2187 1.202639 TGCGTCTGTGATGACTTGGTT 60.203 47.619 0.00 0.00 35.00 3.67
2125 2212 4.705337 ACAGTTCGTTTTGCTTTGGTTA 57.295 36.364 0.00 0.00 0.00 2.85
2140 2227 7.254932 GCATTTCCTCCATTATCAGTACAGTTC 60.255 40.741 0.00 0.00 0.00 3.01
2185 2275 0.323629 TGAAGAAGCCGTTCCCGATT 59.676 50.000 0.00 0.00 35.63 3.34
2605 2695 3.889538 CGTTCTGGATGTAGATGGTCCTA 59.110 47.826 0.00 0.00 33.15 2.94
2734 2831 4.465480 TTGGCGCGCTGGCTCATA 62.465 61.111 32.29 7.91 45.14 2.15
2782 2879 2.206750 GTGTACTCCTTTTGTGCGTCA 58.793 47.619 0.00 0.00 0.00 4.35
2788 2885 1.682854 TCGACGGTGTACTCCTTTTGT 59.317 47.619 11.98 2.52 0.00 2.83
2918 3015 2.229543 GGGGGAAATGAAACGTGGTAAC 59.770 50.000 0.00 0.00 0.00 2.50
2920 3017 2.203470 GGGGGAAATGAAACGTGGTA 57.797 50.000 0.00 0.00 0.00 3.25
2936 3033 3.399181 TAGCAACGGAGCAGGGGG 61.399 66.667 4.18 0.00 36.85 5.40
2939 3036 2.604046 ATAAGTAGCAACGGAGCAGG 57.396 50.000 4.18 0.00 36.85 4.85
2953 3050 7.770433 TGTCAACTCAGCTAATTGCATATAAGT 59.230 33.333 0.00 0.00 45.94 2.24
2957 3054 8.859236 ATATGTCAACTCAGCTAATTGCATAT 57.141 30.769 16.89 16.89 45.94 1.78
2987 3084 6.201997 CGCAGTGCACCATAGTGTATAATTAA 59.798 38.462 16.83 0.00 46.35 1.40
2988 3085 5.694458 CGCAGTGCACCATAGTGTATAATTA 59.306 40.000 16.83 0.00 46.35 1.40
2989 3086 4.511454 CGCAGTGCACCATAGTGTATAATT 59.489 41.667 16.83 0.00 46.35 1.40
3008 3105 4.126437 TGGTTAATCATCATGGTACGCAG 58.874 43.478 0.00 0.00 0.00 5.18
3063 3162 3.204526 CATGCACATCTTTCTCTCCTCC 58.795 50.000 0.00 0.00 0.00 4.30
3064 3163 3.622163 CACATGCACATCTTTCTCTCCTC 59.378 47.826 0.00 0.00 0.00 3.71
3065 3164 3.008813 ACACATGCACATCTTTCTCTCCT 59.991 43.478 0.00 0.00 0.00 3.69
3066 3165 3.341823 ACACATGCACATCTTTCTCTCC 58.658 45.455 0.00 0.00 0.00 3.71
3067 3166 5.583854 ACATACACATGCACATCTTTCTCTC 59.416 40.000 0.00 0.00 35.39 3.20
3068 3167 5.494724 ACATACACATGCACATCTTTCTCT 58.505 37.500 0.00 0.00 35.39 3.10
3069 3168 5.808042 ACATACACATGCACATCTTTCTC 57.192 39.130 0.00 0.00 35.39 2.87
3070 3169 7.362056 GGTTTACATACACATGCACATCTTTCT 60.362 37.037 0.00 0.00 35.39 2.52
3071 3170 6.747280 GGTTTACATACACATGCACATCTTTC 59.253 38.462 0.00 0.00 35.39 2.62
3072 3171 6.434028 AGGTTTACATACACATGCACATCTTT 59.566 34.615 0.00 0.00 35.39 2.52
3073 3172 5.945784 AGGTTTACATACACATGCACATCTT 59.054 36.000 0.00 0.00 35.39 2.40
3074 3173 5.355071 CAGGTTTACATACACATGCACATCT 59.645 40.000 0.00 0.00 35.39 2.90
3075 3174 5.449041 CCAGGTTTACATACACATGCACATC 60.449 44.000 0.00 0.00 35.39 3.06
3076 3175 4.398988 CCAGGTTTACATACACATGCACAT 59.601 41.667 0.00 0.00 35.39 3.21
3077 3176 3.755905 CCAGGTTTACATACACATGCACA 59.244 43.478 0.00 0.00 35.39 4.57
3078 3177 3.128589 CCCAGGTTTACATACACATGCAC 59.871 47.826 0.00 0.00 35.39 4.57
3079 3178 3.009584 TCCCAGGTTTACATACACATGCA 59.990 43.478 0.00 0.00 35.39 3.96
3080 3179 3.616219 TCCCAGGTTTACATACACATGC 58.384 45.455 0.00 0.00 35.39 4.06
3081 3180 5.192927 ACATCCCAGGTTTACATACACATG 58.807 41.667 0.00 0.00 38.21 3.21
3094 3193 6.661805 ACATACGAAAAATAAACATCCCAGGT 59.338 34.615 0.00 0.00 0.00 4.00
3118 3217 8.762426 CCGAGTAAAGAAATTAGCAAGGTATAC 58.238 37.037 0.00 0.00 0.00 1.47
3128 3227 7.384115 TGAAGACACACCGAGTAAAGAAATTAG 59.616 37.037 0.00 0.00 0.00 1.73
3176 3275 4.345854 AGAGTACAACCCACCAACAAAAA 58.654 39.130 0.00 0.00 0.00 1.94
3177 3276 3.949113 GAGAGTACAACCCACCAACAAAA 59.051 43.478 0.00 0.00 0.00 2.44
3178 3277 3.201266 AGAGAGTACAACCCACCAACAAA 59.799 43.478 0.00 0.00 0.00 2.83
3179 3278 2.775384 AGAGAGTACAACCCACCAACAA 59.225 45.455 0.00 0.00 0.00 2.83
3180 3279 2.404559 AGAGAGTACAACCCACCAACA 58.595 47.619 0.00 0.00 0.00 3.33
3181 3280 3.577415 ACTAGAGAGTACAACCCACCAAC 59.423 47.826 0.00 0.00 32.65 3.77
3182 3281 3.853207 ACTAGAGAGTACAACCCACCAA 58.147 45.455 0.00 0.00 32.65 3.67
3183 3282 3.537795 ACTAGAGAGTACAACCCACCA 57.462 47.619 0.00 0.00 32.65 4.17
3184 3283 5.015515 ACTAACTAGAGAGTACAACCCACC 58.984 45.833 0.00 0.00 33.58 4.61
3194 3293 6.639590 TGGGAGAGTAACTAACTAGAGAGT 57.360 41.667 0.00 0.00 39.07 3.24
3195 3294 7.041644 CGAATGGGAGAGTAACTAACTAGAGAG 60.042 44.444 0.00 0.00 39.07 3.20
3196 3295 6.766944 CGAATGGGAGAGTAACTAACTAGAGA 59.233 42.308 0.00 0.00 39.07 3.10
3200 3299 6.182627 TCACGAATGGGAGAGTAACTAACTA 58.817 40.000 0.00 0.00 39.07 2.24
3237 3336 2.775890 ACTGCCTTCACATCACTGAAG 58.224 47.619 2.49 2.49 44.72 3.02
3240 3339 2.350522 GGTACTGCCTTCACATCACTG 58.649 52.381 0.00 0.00 0.00 3.66
3264 3363 5.006896 TGACTCTAACCTTGTCCTAAGGA 57.993 43.478 12.32 0.00 39.81 3.36
3265 3364 5.941555 ATGACTCTAACCTTGTCCTAAGG 57.058 43.478 4.23 4.23 43.05 2.69
3266 3365 7.648039 AGTATGACTCTAACCTTGTCCTAAG 57.352 40.000 0.00 0.00 0.00 2.18
3267 3366 7.559170 GGTAGTATGACTCTAACCTTGTCCTAA 59.441 40.741 0.00 0.00 0.00 2.69
3491 3677 6.270000 TCCAGTCAAAGATTCAGTTCTTCCTA 59.730 38.462 0.00 0.00 34.89 2.94
3500 3686 7.348201 GCGTATAAATCCAGTCAAAGATTCAG 58.652 38.462 0.00 0.00 31.54 3.02
3504 3690 5.680619 TGGCGTATAAATCCAGTCAAAGAT 58.319 37.500 0.00 0.00 0.00 2.40
3506 3692 5.296780 ACATGGCGTATAAATCCAGTCAAAG 59.703 40.000 0.00 0.00 32.78 2.77
3594 3782 4.873827 TCGTGCCCTTTTGACATTCTATAC 59.126 41.667 0.00 0.00 0.00 1.47
3598 3786 2.154462 CTCGTGCCCTTTTGACATTCT 58.846 47.619 0.00 0.00 0.00 2.40
3628 3816 4.111255 TCATGACATTCACCTTTTGGGA 57.889 40.909 0.00 0.00 46.08 4.37
3629 3817 6.720112 ATATCATGACATTCACCTTTTGGG 57.280 37.500 0.00 0.00 46.08 4.12
3681 3872 7.771183 TGCTTTTCTTAGTTCACAATCAAACT 58.229 30.769 0.00 0.00 39.07 2.66
3719 3910 1.016627 CCATCCACTACAATGCCGTG 58.983 55.000 0.00 0.00 0.00 4.94
3781 3972 6.826231 TGGTACAAGATCACAACTCAGAAAAA 59.174 34.615 0.00 0.00 31.92 1.94
3782 3973 6.353323 TGGTACAAGATCACAACTCAGAAAA 58.647 36.000 0.00 0.00 31.92 2.29
3783 3974 5.924356 TGGTACAAGATCACAACTCAGAAA 58.076 37.500 0.00 0.00 31.92 2.52
3784 3975 5.545063 TGGTACAAGATCACAACTCAGAA 57.455 39.130 0.00 0.00 31.92 3.02
3802 3993 5.489249 TGGATTAAGCACGTACATTTGGTA 58.511 37.500 0.00 0.00 0.00 3.25
3803 3994 4.328536 TGGATTAAGCACGTACATTTGGT 58.671 39.130 0.00 0.00 0.00 3.67
3804 3995 4.955925 TGGATTAAGCACGTACATTTGG 57.044 40.909 0.00 0.00 0.00 3.28
3805 3996 5.965334 GTGATGGATTAAGCACGTACATTTG 59.035 40.000 0.00 0.00 0.00 2.32
3806 3997 5.065988 GGTGATGGATTAAGCACGTACATTT 59.934 40.000 0.00 0.00 32.24 2.32
3807 3998 4.574828 GGTGATGGATTAAGCACGTACATT 59.425 41.667 0.00 0.00 32.24 2.71
3808 3999 4.127171 GGTGATGGATTAAGCACGTACAT 58.873 43.478 0.00 0.00 32.24 2.29
3809 4000 3.055747 TGGTGATGGATTAAGCACGTACA 60.056 43.478 0.00 0.00 32.24 2.90
3810 4001 3.527533 TGGTGATGGATTAAGCACGTAC 58.472 45.455 0.00 0.00 32.24 3.67
3811 4002 3.897141 TGGTGATGGATTAAGCACGTA 57.103 42.857 0.00 0.00 32.24 3.57
3812 4003 2.779755 TGGTGATGGATTAAGCACGT 57.220 45.000 0.00 0.00 32.24 4.49
3813 4004 4.433186 TTTTGGTGATGGATTAAGCACG 57.567 40.909 0.00 0.00 32.24 5.34
3814 4005 7.547227 ACTTATTTTGGTGATGGATTAAGCAC 58.453 34.615 0.00 0.00 0.00 4.40
3815 4006 7.716799 ACTTATTTTGGTGATGGATTAAGCA 57.283 32.000 0.00 0.00 0.00 3.91
3821 4012 8.416329 GCAAGATTACTTATTTTGGTGATGGAT 58.584 33.333 0.00 0.00 34.70 3.41
3822 4013 7.395772 TGCAAGATTACTTATTTTGGTGATGGA 59.604 33.333 0.00 0.00 34.70 3.41
3823 4014 7.546358 TGCAAGATTACTTATTTTGGTGATGG 58.454 34.615 0.00 0.00 34.70 3.51
3826 4017 8.682710 GGTATGCAAGATTACTTATTTTGGTGA 58.317 33.333 0.00 0.00 34.70 4.02
3827 4018 7.643764 CGGTATGCAAGATTACTTATTTTGGTG 59.356 37.037 0.00 0.00 34.70 4.17
3828 4019 7.554835 TCGGTATGCAAGATTACTTATTTTGGT 59.445 33.333 0.00 0.00 34.70 3.67
3829 4020 7.925993 TCGGTATGCAAGATTACTTATTTTGG 58.074 34.615 0.00 0.00 34.70 3.28
3830 4021 9.781834 TTTCGGTATGCAAGATTACTTATTTTG 57.218 29.630 0.00 0.00 34.70 2.44
3832 4023 8.129211 GCTTTCGGTATGCAAGATTACTTATTT 58.871 33.333 0.00 0.00 34.70 1.40
3833 4024 7.282224 TGCTTTCGGTATGCAAGATTACTTATT 59.718 33.333 0.00 0.00 34.33 1.40
3834 4025 6.765989 TGCTTTCGGTATGCAAGATTACTTAT 59.234 34.615 0.00 0.00 34.33 1.73
3835 4026 6.110033 TGCTTTCGGTATGCAAGATTACTTA 58.890 36.000 0.00 0.00 34.33 2.24
3836 4027 4.941263 TGCTTTCGGTATGCAAGATTACTT 59.059 37.500 0.00 0.00 34.33 2.24
3837 4028 4.513442 TGCTTTCGGTATGCAAGATTACT 58.487 39.130 0.00 0.00 34.33 2.24
3838 4029 4.875544 TGCTTTCGGTATGCAAGATTAC 57.124 40.909 0.00 0.00 34.33 1.89
3839 4030 5.700832 CCTATGCTTTCGGTATGCAAGATTA 59.299 40.000 0.00 0.00 39.94 1.75
3840 4031 4.516698 CCTATGCTTTCGGTATGCAAGATT 59.483 41.667 0.00 0.00 39.94 2.40
3841 4032 4.067896 CCTATGCTTTCGGTATGCAAGAT 58.932 43.478 0.00 0.00 39.94 2.40
3842 4033 3.466836 CCTATGCTTTCGGTATGCAAGA 58.533 45.455 0.00 0.00 39.94 3.02
3843 4034 2.549754 CCCTATGCTTTCGGTATGCAAG 59.450 50.000 0.00 0.00 39.94 4.01
3844 4035 2.171659 TCCCTATGCTTTCGGTATGCAA 59.828 45.455 0.00 0.00 39.94 4.08
3845 4036 1.765904 TCCCTATGCTTTCGGTATGCA 59.234 47.619 0.00 0.00 40.69 3.96
3846 4037 2.543777 TCCCTATGCTTTCGGTATGC 57.456 50.000 0.00 0.00 0.00 3.14
3847 4038 4.008074 ACATCCCTATGCTTTCGGTATG 57.992 45.455 0.00 0.00 36.50 2.39
3848 4039 5.104900 GGATACATCCCTATGCTTTCGGTAT 60.105 44.000 0.00 0.00 41.20 2.73
3849 4040 4.222145 GGATACATCCCTATGCTTTCGGTA 59.778 45.833 0.00 0.00 41.20 4.02
3850 4041 3.008049 GGATACATCCCTATGCTTTCGGT 59.992 47.826 0.00 0.00 41.20 4.69
3851 4042 3.007940 TGGATACATCCCTATGCTTTCGG 59.992 47.826 5.80 0.00 46.59 4.30
3852 4043 4.271696 TGGATACATCCCTATGCTTTCG 57.728 45.455 5.80 0.00 46.59 3.46
3865 4056 8.776956 AGATTTCTGCAAGCTGGTGGATACAT 62.777 42.308 0.00 0.00 38.38 2.29
3866 4057 7.560379 AGATTTCTGCAAGCTGGTGGATACA 62.560 44.000 0.00 0.00 34.60 2.29
3867 4058 2.113860 TTCTGCAAGCTGGTGGATAC 57.886 50.000 0.00 0.00 0.00 2.24
3868 4059 2.877097 TTTCTGCAAGCTGGTGGATA 57.123 45.000 0.00 0.00 0.00 2.59
3869 4060 2.097825 GATTTCTGCAAGCTGGTGGAT 58.902 47.619 0.00 0.00 0.00 3.41
3870 4061 1.074405 AGATTTCTGCAAGCTGGTGGA 59.926 47.619 0.00 0.00 26.66 4.02
3871 4062 1.471684 GAGATTTCTGCAAGCTGGTGG 59.528 52.381 0.00 0.00 28.47 4.61
3872 4063 2.434428 AGAGATTTCTGCAAGCTGGTG 58.566 47.619 0.00 0.00 28.47 4.17
3873 4064 2.875094 AGAGATTTCTGCAAGCTGGT 57.125 45.000 0.00 0.00 28.47 4.00
3874 4065 4.096081 CCTTTAGAGATTTCTGCAAGCTGG 59.904 45.833 0.00 0.00 34.79 4.85
3875 4066 4.096081 CCCTTTAGAGATTTCTGCAAGCTG 59.904 45.833 0.00 0.00 34.79 4.24
3876 4067 4.018960 TCCCTTTAGAGATTTCTGCAAGCT 60.019 41.667 0.00 0.00 34.79 3.74
3877 4068 4.265073 TCCCTTTAGAGATTTCTGCAAGC 58.735 43.478 0.00 0.00 34.79 4.01
3878 4069 6.824305 TTTCCCTTTAGAGATTTCTGCAAG 57.176 37.500 0.00 0.00 34.79 4.01


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

AutoCloner maintained by Alex Coulton.