Multiple sequence alignment - TraesCS6A01G011400

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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 TraesCS6A01G011400 chr6A 100.000 4309 0 0 1 4309 5322608 5318300 0.000000e+00 7958
1 TraesCS6A01G011400 chr6A 91.421 373 25 3 2770 3135 5762025 5762397 4.970000e-139 505
2 TraesCS6A01G011400 chr6A 91.153 373 26 3 2770 3135 5663825 5664197 2.310000e-137 499
3 TraesCS6A01G011400 chr6A 86.957 299 29 9 1674 1965 370232964 370233259 1.160000e-85 327
4 TraesCS6A01G011400 chr6A 84.768 151 16 5 3133 3281 5664236 5664381 1.250000e-30 145
5 TraesCS6A01G011400 chr6A 84.106 151 17 5 3133 3281 5762436 5762581 5.810000e-29 139
6 TraesCS6A01G011400 chr6B 88.955 2508 173 51 706 3138 11289147 11286669 0.000000e+00 3001
7 TraesCS6A01G011400 chr6B 86.551 632 43 15 3133 3754 11286633 11286034 0.000000e+00 658
8 TraesCS6A01G011400 chr6B 85.647 634 62 12 2522 3134 125020692 125021317 1.310000e-179 640
9 TraesCS6A01G011400 chr6B 91.569 427 28 3 3883 4309 11284127 11283709 2.230000e-162 582
10 TraesCS6A01G011400 chr6B 84.211 304 39 8 368 669 11289440 11289144 1.960000e-73 287
11 TraesCS6A01G011400 chr6B 80.000 205 29 6 2311 2513 159090894 159090700 1.620000e-29 141
12 TraesCS6A01G011400 chr6B 81.034 174 24 7 1294 1464 70047718 70047551 3.500000e-26 130
13 TraesCS6A01G011400 chr6D 88.775 2138 146 49 6 2077 5979586 5977477 0.000000e+00 2532
14 TraesCS6A01G011400 chr6D 92.172 792 51 9 2305 3094 5977434 5976652 0.000000e+00 1109
15 TraesCS6A01G011400 chr6D 88.099 563 37 7 3187 3741 5976653 5976113 3.630000e-180 641
16 TraesCS6A01G011400 chr6D 76.232 345 56 16 3883 4223 5864720 5864398 4.460000e-35 159
17 TraesCS6A01G011400 chr6D 90.196 102 9 1 992 1093 471075284 471075384 9.720000e-27 132
18 TraesCS6A01G011400 chr2D 84.893 1218 131 37 994 2182 131277189 131278382 0.000000e+00 1181
19 TraesCS6A01G011400 chr2D 81.818 385 51 11 3178 3552 131279342 131279717 5.410000e-79 305
20 TraesCS6A01G011400 chr2A 84.372 1235 125 32 992 2182 137931820 137933030 0.000000e+00 1149
21 TraesCS6A01G011400 chr2A 83.430 1032 127 29 2518 3515 137933339 137934360 0.000000e+00 918
22 TraesCS6A01G011400 chr2A 82.909 275 38 4 2241 2513 137933033 137933300 5.570000e-59 239
23 TraesCS6A01G011400 chr2B 84.241 1212 139 36 992 2182 184772874 184774054 0.000000e+00 1133
24 TraesCS6A01G011400 chr2B 85.621 612 54 18 2513 3095 184774288 184774894 2.850000e-171 612
25 TraesCS6A01G011400 chr2B 83.158 380 49 10 3184 3552 184774952 184775327 2.480000e-87 333
26 TraesCS6A01G011400 chr2B 85.098 255 25 5 1561 1805 64814568 64814317 9.250000e-62 248
27 TraesCS6A01G011400 chr1D 85.381 643 65 12 2513 3134 360102712 360103346 1.310000e-179 640
28 TraesCS6A01G011400 chr1D 80.000 205 29 6 2311 2513 360102484 360102678 1.620000e-29 141
29 TraesCS6A01G011400 chr7D 84.858 634 67 12 2522 3134 636113417 636112792 2.850000e-171 612
30 TraesCS6A01G011400 chr7D 84.700 634 68 12 2522 3134 636195689 636195064 1.330000e-169 606
31 TraesCS6A01G011400 chr7D 85.433 508 51 9 2522 3008 636062976 636062471 1.380000e-139 507
32 TraesCS6A01G011400 chr7D 81.884 276 38 6 2241 2513 329820751 329821017 5.610000e-54 222
33 TraesCS6A01G011400 chr7D 80.000 205 29 6 2311 2513 64418813 64418619 1.620000e-29 141
34 TraesCS6A01G011400 chr7D 79.612 206 28 8 2311 2513 636113654 636113460 7.520000e-28 135
35 TraesCS6A01G011400 chr4B 80.167 600 80 22 993 1570 146016880 146016298 3.100000e-111 412
36 TraesCS6A01G011400 chr4B 86.622 299 30 9 1674 1965 626991695 626991990 5.380000e-84 322
37 TraesCS6A01G011400 chr7B 87.291 299 28 9 1674 1965 645437113 645436818 2.480000e-87 333
38 TraesCS6A01G011400 chr7B 87.291 299 28 9 1674 1965 701399778 701400073 2.480000e-87 333
39 TraesCS6A01G011400 chrUn 79.612 206 28 8 2311 2513 317270086 317269892 7.520000e-28 135


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 TraesCS6A01G011400 chr6A 5318300 5322608 4308 True 7958.000000 7958 100.000000 1 4309 1 chr6A.!!$R1 4308
1 TraesCS6A01G011400 chr6A 5663825 5664381 556 False 322.000000 499 87.960500 2770 3281 2 chr6A.!!$F2 511
2 TraesCS6A01G011400 chr6A 5762025 5762581 556 False 322.000000 505 87.763500 2770 3281 2 chr6A.!!$F3 511
3 TraesCS6A01G011400 chr6B 11283709 11289440 5731 True 1132.000000 3001 87.821500 368 4309 4 chr6B.!!$R3 3941
4 TraesCS6A01G011400 chr6B 125020692 125021317 625 False 640.000000 640 85.647000 2522 3134 1 chr6B.!!$F1 612
5 TraesCS6A01G011400 chr6D 5976113 5979586 3473 True 1427.333333 2532 89.682000 6 3741 3 chr6D.!!$R2 3735
6 TraesCS6A01G011400 chr2D 131277189 131279717 2528 False 743.000000 1181 83.355500 994 3552 2 chr2D.!!$F1 2558
7 TraesCS6A01G011400 chr2A 137931820 137934360 2540 False 768.666667 1149 83.570333 992 3515 3 chr2A.!!$F1 2523
8 TraesCS6A01G011400 chr2B 184772874 184775327 2453 False 692.666667 1133 84.340000 992 3552 3 chr2B.!!$F1 2560
9 TraesCS6A01G011400 chr1D 360102484 360103346 862 False 390.500000 640 82.690500 2311 3134 2 chr1D.!!$F1 823
10 TraesCS6A01G011400 chr7D 636195064 636195689 625 True 606.000000 606 84.700000 2522 3134 1 chr7D.!!$R3 612
11 TraesCS6A01G011400 chr7D 636062471 636062976 505 True 507.000000 507 85.433000 2522 3008 1 chr7D.!!$R2 486
12 TraesCS6A01G011400 chr7D 636112792 636113654 862 True 373.500000 612 82.235000 2311 3134 2 chr7D.!!$R4 823
13 TraesCS6A01G011400 chr4B 146016298 146016880 582 True 412.000000 412 80.167000 993 1570 1 chr4B.!!$R1 577

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
73 79 0.107654 AGCCGTCAGCCCATTAGTTC 60.108 55.0 0.00 0.00 45.47 3.01 F
91 115 0.246635 TCAAGACCTAAGTCAGCCGC 59.753 55.0 0.00 0.00 46.15 6.53 F
931 983 0.318441 TCACACTCACCTACAGCTGC 59.682 55.0 15.27 0.00 0.00 5.25 F
1125 1198 0.441145 GAACCGAATCGAACCCAACG 59.559 55.0 3.36 0.00 0.00 4.10 F
2037 2186 0.607217 CACTCCATTGCACAGCTGGA 60.607 55.0 19.93 3.31 37.50 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1006 1062 2.027653 GGTTCCTCTTCTTGTCCCTCAG 60.028 54.545 0.00 0.00 0.00 3.35 R
2084 2244 0.518636 ACGCAATCAGCACACATCAC 59.481 50.000 0.00 0.00 46.13 3.06 R
2089 2270 1.262950 TGTGTAACGCAATCAGCACAC 59.737 47.619 0.00 0.00 43.89 3.82 R
2614 2857 1.723003 GTGTTCCGGTTGTAGTTAGCG 59.277 52.381 0.00 0.00 36.35 4.26 R
3554 3903 0.034476 CTGCAGTGACAGCTGAAGGA 59.966 55.000 23.35 5.26 38.26 3.36 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
27 28 1.056700 TTAGGAGGAGATGGGCTGGC 61.057 60.000 0.00 0.00 0.00 4.85
47 48 1.335496 CTGGGCCGAAAAGAACGAAAA 59.665 47.619 0.00 0.00 0.00 2.29
49 50 1.335810 GGGCCGAAAAGAACGAAAAGT 59.664 47.619 0.00 0.00 0.00 2.66
73 79 0.107654 AGCCGTCAGCCCATTAGTTC 60.108 55.000 0.00 0.00 45.47 3.01
86 92 5.570844 GCCCATTAGTTCAAGACCTAAGTCA 60.571 44.000 0.00 0.00 46.15 3.41
87 93 6.109359 CCCATTAGTTCAAGACCTAAGTCAG 58.891 44.000 0.00 0.00 46.15 3.51
91 115 0.246635 TCAAGACCTAAGTCAGCCGC 59.753 55.000 0.00 0.00 46.15 6.53
140 164 0.766131 CCTCCCTCTACTCCTCGCTA 59.234 60.000 0.00 0.00 0.00 4.26
168 192 1.819905 CTCGGCCTCCTTTCCTCTC 59.180 63.158 0.00 0.00 0.00 3.20
171 195 2.379459 GGCCTCCTTTCCTCTCCCC 61.379 68.421 0.00 0.00 0.00 4.81
173 197 1.631071 GCCTCCTTTCCTCTCCCCTG 61.631 65.000 0.00 0.00 0.00 4.45
175 199 0.911525 CTCCTTTCCTCTCCCCTGCA 60.912 60.000 0.00 0.00 0.00 4.41
176 200 0.475632 TCCTTTCCTCTCCCCTGCAA 60.476 55.000 0.00 0.00 0.00 4.08
178 202 0.695347 CTTTCCTCTCCCCTGCAACT 59.305 55.000 0.00 0.00 0.00 3.16
180 204 1.201429 TTCCTCTCCCCTGCAACTCC 61.201 60.000 0.00 0.00 0.00 3.85
181 205 2.581354 CTCTCCCCTGCAACTCCG 59.419 66.667 0.00 0.00 0.00 4.63
183 207 4.785453 CTCCCCTGCAACTCCGCC 62.785 72.222 0.00 0.00 0.00 6.13
190 214 4.070552 GCAACTCCGCCGTCCTCT 62.071 66.667 0.00 0.00 0.00 3.69
228 253 2.758737 CGCCCCTCCTCCGTAAGT 60.759 66.667 0.00 0.00 0.00 2.24
233 258 1.335882 CCCTCCTCCGTAAGTTCCCC 61.336 65.000 0.00 0.00 0.00 4.81
253 278 4.778143 GCCCCTCATTCACCGCGT 62.778 66.667 4.92 0.00 0.00 6.01
255 280 2.511600 CCCTCATTCACCGCGTCC 60.512 66.667 4.92 0.00 0.00 4.79
269 294 1.661341 GCGTCCTCTTCATTGATGCT 58.339 50.000 0.00 0.00 37.89 3.79
277 302 4.384537 CCTCTTCATTGATGCTACCCAGAA 60.385 45.833 0.00 0.00 0.00 3.02
289 314 3.244596 GCTACCCAGAAAACAGTCTTCCT 60.245 47.826 0.00 0.00 0.00 3.36
294 319 4.319177 CCAGAAAACAGTCTTCCTGGTAG 58.681 47.826 0.00 0.00 41.45 3.18
361 390 4.872664 CTTGGTACTCGAGGATGGAATAC 58.127 47.826 18.41 7.90 0.00 1.89
388 417 6.872920 TGCCAAATGTTTACTTGAGAAAGTT 58.127 32.000 0.00 0.00 34.37 2.66
415 446 3.423154 CCTGTTCCCGTTGCTCGC 61.423 66.667 0.00 0.00 38.35 5.03
431 462 0.802222 TCGCTAAGCATGCTCACGTC 60.802 55.000 22.93 7.90 0.00 4.34
437 468 2.791383 AGCATGCTCACGTCTCTATC 57.209 50.000 16.30 0.00 0.00 2.08
440 471 2.645163 CATGCTCACGTCTCTATCGAC 58.355 52.381 0.00 0.00 0.00 4.20
460 491 6.552629 TCGACTGATTGATTCTATATACGGC 58.447 40.000 0.00 0.00 0.00 5.68
462 493 6.404844 CGACTGATTGATTCTATATACGGCCT 60.405 42.308 0.00 0.00 0.00 5.19
466 497 8.918202 TGATTGATTCTATATACGGCCTTTTT 57.082 30.769 0.00 0.00 0.00 1.94
467 498 8.999431 TGATTGATTCTATATACGGCCTTTTTC 58.001 33.333 0.00 0.00 0.00 2.29
468 499 7.739498 TTGATTCTATATACGGCCTTTTTCC 57.261 36.000 0.00 0.00 0.00 3.13
470 501 8.197592 TGATTCTATATACGGCCTTTTTCCTA 57.802 34.615 0.00 0.00 0.00 2.94
494 526 0.531090 TACGCGGTGCTTCTGTGTTT 60.531 50.000 12.47 0.00 42.69 2.83
495 527 1.082756 CGCGGTGCTTCTGTGTTTC 60.083 57.895 0.00 0.00 0.00 2.78
508 541 3.138304 CTGTGTTTCCCAGATTCGTCAA 58.862 45.455 0.00 0.00 31.38 3.18
515 548 6.072728 TGTTTCCCAGATTCGTCAATTACTTG 60.073 38.462 0.00 0.00 0.00 3.16
520 553 8.210946 TCCCAGATTCGTCAATTACTTGAATAT 58.789 33.333 0.00 0.00 42.85 1.28
521 554 9.489084 CCCAGATTCGTCAATTACTTGAATATA 57.511 33.333 0.00 0.00 42.85 0.86
559 593 6.976088 TGTAAATTTGTCTGGTTGGTATGTG 58.024 36.000 0.00 0.00 0.00 3.21
560 594 6.773200 TGTAAATTTGTCTGGTTGGTATGTGA 59.227 34.615 0.00 0.00 0.00 3.58
567 606 3.073798 TCTGGTTGGTATGTGACATGGTT 59.926 43.478 8.61 0.00 0.00 3.67
598 637 6.973843 TCCAGAAGAATTTTGTGTCAGAATG 58.026 36.000 0.00 0.00 37.54 2.67
609 648 2.417933 GTGTCAGAATGGTGCAGCTAAG 59.582 50.000 18.08 2.99 36.16 2.18
611 650 1.003464 TCAGAATGGTGCAGCTAAGCA 59.997 47.619 18.08 3.24 38.53 3.91
616 655 5.623951 GAATGGTGCAGCTAAGCATTCGG 62.624 52.174 25.46 0.00 46.48 4.30
677 717 2.026641 CCCAGCTGTATGAATGGGTTG 58.973 52.381 13.81 0.00 46.19 3.77
694 734 3.366679 GGGTTGACAGCAATGATTGACTG 60.367 47.826 20.29 20.29 39.25 3.51
696 736 4.261741 GGTTGACAGCAATGATTGACTGTT 60.262 41.667 24.92 14.99 43.19 3.16
698 738 4.136051 TGACAGCAATGATTGACTGTTGA 58.864 39.130 24.92 16.81 43.19 3.18
714 754 7.047891 TGACTGTTGAAGTTTCTATGTTGTCT 58.952 34.615 0.00 0.00 40.07 3.41
746 786 9.049523 CATCATCATTTACTTATATCCCGATGG 57.950 37.037 0.00 0.00 0.00 3.51
755 795 0.679505 TATCCCGATGGTACTGCTGC 59.320 55.000 0.00 0.00 0.00 5.25
793 837 1.067821 GCCATAGTTGTCTCTCCGAGG 59.932 57.143 0.00 0.00 0.00 4.63
931 983 0.318441 TCACACTCACCTACAGCTGC 59.682 55.000 15.27 0.00 0.00 5.25
939 991 4.651503 ACTCACCTACAGCTGCTATATTGT 59.348 41.667 15.27 3.06 0.00 2.71
942 994 4.917998 CACCTACAGCTGCTATATTGTACG 59.082 45.833 15.27 0.00 0.00 3.67
974 1026 5.215252 CTGACTTCTTCAGTTACAGGGAA 57.785 43.478 0.00 0.00 46.12 3.97
1006 1062 0.464373 TTGATTGAGCGAGATGGGGC 60.464 55.000 0.00 0.00 0.00 5.80
1125 1198 0.441145 GAACCGAATCGAACCCAACG 59.559 55.000 3.36 0.00 0.00 4.10
1126 1199 0.952010 AACCGAATCGAACCCAACGG 60.952 55.000 3.36 0.00 44.77 4.44
1131 1204 2.419667 GAATCGAACCCAACGGAAAGA 58.580 47.619 0.00 0.00 0.00 2.52
1331 1437 2.865670 GCAAGGTCTGTCTGTCTCAGTG 60.866 54.545 0.00 0.00 34.86 3.66
1672 1813 1.135286 GCTTACAAGTTCCTGGCATGC 60.135 52.381 9.90 9.90 0.00 4.06
1825 1968 8.661352 ATGCTGGTTATATGTTTATTTTTGCC 57.339 30.769 0.00 0.00 0.00 4.52
1951 2099 6.533730 TCTGTGTTTCTGTCATGGAATACTT 58.466 36.000 0.00 0.00 0.00 2.24
2009 2158 6.349300 ACACTCAGTTAATATTACCAGGCTG 58.651 40.000 7.75 7.75 0.00 4.85
2022 2171 1.338020 CCAGGCTGTTTGTTTCCACTC 59.662 52.381 14.43 0.00 0.00 3.51
2037 2186 0.607217 CACTCCATTGCACAGCTGGA 60.607 55.000 19.93 3.31 37.50 3.86
2089 2270 6.796705 TGATGCAAGCTATAATCAGTGATG 57.203 37.500 6.34 0.00 0.00 3.07
2091 2272 5.996669 TGCAAGCTATAATCAGTGATGTG 57.003 39.130 6.34 0.00 0.00 3.21
2107 2288 1.587547 TGTGTGCTGATTGCGTTACA 58.412 45.000 0.00 0.00 46.63 2.41
2175 2361 6.072112 AGTGGTATGTGAATGTCAAAACAC 57.928 37.500 0.00 0.00 38.48 3.32
2215 2401 9.455847 GAATTCACTATGATGATAAAAACAGGC 57.544 33.333 0.00 0.00 0.00 4.85
2216 2402 6.942532 TCACTATGATGATAAAAACAGGCC 57.057 37.500 0.00 0.00 0.00 5.19
2217 2403 6.422333 TCACTATGATGATAAAAACAGGCCA 58.578 36.000 5.01 0.00 0.00 5.36
2218 2404 7.062322 TCACTATGATGATAAAAACAGGCCAT 58.938 34.615 5.01 0.00 0.00 4.40
2219 2405 8.217111 TCACTATGATGATAAAAACAGGCCATA 58.783 33.333 5.01 0.00 0.00 2.74
2222 2408 5.448654 TGATGATAAAAACAGGCCATAGCT 58.551 37.500 5.01 0.00 39.73 3.32
2231 2417 4.833478 ACAGGCCATAGCTATAATGGAG 57.167 45.455 16.73 8.52 45.77 3.86
2234 2420 3.777522 AGGCCATAGCTATAATGGAGGAC 59.222 47.826 16.73 10.24 45.77 3.85
2363 2558 9.007901 CAAGGTTCTTGTCTTAGATCTCATTTT 57.992 33.333 0.00 0.00 0.00 1.82
2425 2626 7.333423 TGTGTACTTTATTATGAACACAGAGGC 59.667 37.037 2.21 0.00 41.48 4.70
2429 2630 6.942576 ACTTTATTATGAACACAGAGGCTGTT 59.057 34.615 0.00 0.00 42.59 3.16
2443 2648 7.549134 CACAGAGGCTGTTGTAATTCTTACATA 59.451 37.037 0.00 0.00 42.59 2.29
2472 2680 8.209917 ACAGTTCTGTTTTCCTGTACTTTTAG 57.790 34.615 0.00 0.00 36.44 1.85
2501 2709 5.473931 AGCTGTATGTAGTCACTGTTTCTG 58.526 41.667 0.00 0.00 0.00 3.02
2502 2710 5.243954 AGCTGTATGTAGTCACTGTTTCTGA 59.756 40.000 0.00 0.00 0.00 3.27
2503 2711 6.071108 AGCTGTATGTAGTCACTGTTTCTGAT 60.071 38.462 0.00 0.00 0.00 2.90
2527 2769 7.757941 TGTTTTGATTCCACATCTTGTATCA 57.242 32.000 0.00 0.00 0.00 2.15
2614 2857 4.049869 GCGGCTTAGTAAGGTAATCTGTC 58.950 47.826 11.84 0.00 0.00 3.51
2694 2939 5.411669 GTGTTACCAGGATAAAACAGTGGAG 59.588 44.000 0.00 0.00 32.83 3.86
2728 2973 5.734720 AGATGCTCGAAGGAATTGTAAAGA 58.265 37.500 0.00 0.00 0.00 2.52
2942 3212 4.144297 AGTGTTCTAGAGCCAATTTTGCA 58.856 39.130 3.94 0.00 0.00 4.08
3155 3485 2.861360 GCTTTTGCTTTCTGCCTGTCTG 60.861 50.000 0.00 0.00 43.35 3.51
3161 3491 4.397420 TGCTTTCTGCCTGTCTGATTTTA 58.603 39.130 0.00 0.00 42.00 1.52
3168 3498 5.643777 TCTGCCTGTCTGATTTTAGCTAAAC 59.356 40.000 18.45 8.94 0.00 2.01
3174 3504 7.225538 CCTGTCTGATTTTAGCTAAACGATGAT 59.774 37.037 18.45 9.05 0.00 2.45
3176 3506 7.549134 TGTCTGATTTTAGCTAAACGATGATGT 59.451 33.333 18.45 0.00 0.00 3.06
3236 3568 3.834231 ACAAGATATTTGCCTGGTTGCTT 59.166 39.130 0.00 0.00 0.00 3.91
3240 3572 5.448654 AGATATTTGCCTGGTTGCTTATGA 58.551 37.500 0.00 0.00 0.00 2.15
3251 3586 6.024552 TGGTTGCTTATGATTTTCTTGGTC 57.975 37.500 0.00 0.00 0.00 4.02
3470 3812 9.787435 TGTAAGTTAAATGACTGGTTTATGTCT 57.213 29.630 0.00 0.00 34.57 3.41
3498 3840 0.524862 GCATCAAGCTGTGGTGGAAG 59.475 55.000 10.03 0.00 38.94 3.46
3539 3888 6.357367 TCTTTCCTGCTCCCTTATTTACATC 58.643 40.000 0.00 0.00 0.00 3.06
3540 3889 4.706842 TCCTGCTCCCTTATTTACATCC 57.293 45.455 0.00 0.00 0.00 3.51
3541 3890 4.307259 TCCTGCTCCCTTATTTACATCCT 58.693 43.478 0.00 0.00 0.00 3.24
3542 3891 4.726825 TCCTGCTCCCTTATTTACATCCTT 59.273 41.667 0.00 0.00 0.00 3.36
3543 3892 5.066593 CCTGCTCCCTTATTTACATCCTTC 58.933 45.833 0.00 0.00 0.00 3.46
3544 3893 5.397899 CCTGCTCCCTTATTTACATCCTTCA 60.398 44.000 0.00 0.00 0.00 3.02
3545 3894 5.684704 TGCTCCCTTATTTACATCCTTCAG 58.315 41.667 0.00 0.00 0.00 3.02
3546 3895 4.517075 GCTCCCTTATTTACATCCTTCAGC 59.483 45.833 0.00 0.00 0.00 4.26
3547 3896 5.688766 GCTCCCTTATTTACATCCTTCAGCT 60.689 44.000 0.00 0.00 0.00 4.24
3548 3897 5.684704 TCCCTTATTTACATCCTTCAGCTG 58.315 41.667 7.63 7.63 0.00 4.24
3549 3898 5.191722 TCCCTTATTTACATCCTTCAGCTGT 59.808 40.000 14.67 0.00 0.00 4.40
3550 3899 5.529060 CCCTTATTTACATCCTTCAGCTGTC 59.471 44.000 14.67 0.00 0.00 3.51
3551 3900 6.115446 CCTTATTTACATCCTTCAGCTGTCA 58.885 40.000 14.67 0.52 0.00 3.58
3552 3901 6.037610 CCTTATTTACATCCTTCAGCTGTCAC 59.962 42.308 14.67 0.00 0.00 3.67
3553 3902 4.623932 TTTACATCCTTCAGCTGTCACT 57.376 40.909 14.67 0.00 0.00 3.41
3554 3903 4.623932 TTACATCCTTCAGCTGTCACTT 57.376 40.909 14.67 0.00 0.00 3.16
3619 3968 6.997239 ATTCGTCTCCCAAGGTTTAATAAC 57.003 37.500 0.00 0.00 0.00 1.89
3660 4011 7.486407 ACCTTGAATGCCATCTTAAGAAAAT 57.514 32.000 9.71 0.00 0.00 1.82
3729 4085 5.176590 GCTACTTCAGCGATCATTTCTTAGG 59.823 44.000 0.00 0.00 41.37 2.69
3754 4110 9.909043 GGTTAATTTGTGTTTCAACATTTACAC 57.091 29.630 0.00 0.00 41.59 2.90
3755 4111 9.909043 GTTAATTTGTGTTTCAACATTTACACC 57.091 29.630 0.00 0.00 41.59 4.16
3757 4113 8.785329 AATTTGTGTTTCAACATTTACACCTT 57.215 26.923 0.00 0.00 41.59 3.50
3758 4114 7.588143 TTTGTGTTTCAACATTTACACCTTG 57.412 32.000 0.00 0.00 41.59 3.61
3761 4117 7.476667 TGTGTTTCAACATTTACACCTTGTAG 58.523 34.615 0.00 0.00 41.59 2.74
3762 4118 7.337184 TGTGTTTCAACATTTACACCTTGTAGA 59.663 33.333 0.00 0.00 41.59 2.59
3768 5605 9.295825 TCAACATTTACACCTTGTAGATCATTT 57.704 29.630 0.00 0.00 33.92 2.32
3775 5612 4.096382 CACCTTGTAGATCATTTTTCGGGG 59.904 45.833 0.00 0.00 0.00 5.73
3776 5613 4.018779 ACCTTGTAGATCATTTTTCGGGGA 60.019 41.667 0.00 0.00 0.00 4.81
3777 5614 5.133221 CCTTGTAGATCATTTTTCGGGGAT 58.867 41.667 0.00 0.00 0.00 3.85
3778 5615 5.009010 CCTTGTAGATCATTTTTCGGGGATG 59.991 44.000 0.00 0.00 0.00 3.51
3779 5616 3.882888 TGTAGATCATTTTTCGGGGATGC 59.117 43.478 0.00 0.00 0.00 3.91
3782 5619 3.319972 AGATCATTTTTCGGGGATGCATG 59.680 43.478 2.46 0.00 0.00 4.06
3783 5620 1.136695 TCATTTTTCGGGGATGCATGC 59.863 47.619 11.82 11.82 0.00 4.06
3784 5621 1.137479 CATTTTTCGGGGATGCATGCT 59.863 47.619 20.33 4.11 0.00 3.79
3786 5623 1.321805 TTTTCGGGGATGCATGCTGG 61.322 55.000 20.33 10.09 0.00 4.85
3789 5626 2.910994 GGGGATGCATGCTGGAGC 60.911 66.667 20.33 0.48 42.50 4.70
3790 5627 2.910994 GGGATGCATGCTGGAGCC 60.911 66.667 20.33 10.90 43.92 4.70
3791 5628 2.195139 GGATGCATGCTGGAGCCT 59.805 61.111 20.33 0.00 41.29 4.58
3792 5629 1.897615 GGATGCATGCTGGAGCCTC 60.898 63.158 20.33 4.24 41.29 4.70
3793 5630 1.153025 GATGCATGCTGGAGCCTCA 60.153 57.895 20.33 0.00 41.18 3.86
3795 5632 0.106167 ATGCATGCTGGAGCCTCAAT 60.106 50.000 20.33 0.00 41.18 2.57
3796 5633 0.547553 TGCATGCTGGAGCCTCAATA 59.452 50.000 20.33 0.00 41.18 1.90
3797 5634 1.144298 TGCATGCTGGAGCCTCAATAT 59.856 47.619 20.33 0.00 41.18 1.28
3798 5635 1.540267 GCATGCTGGAGCCTCAATATG 59.460 52.381 11.37 0.00 41.18 1.78
3799 5636 2.812983 GCATGCTGGAGCCTCAATATGA 60.813 50.000 11.37 0.00 41.18 2.15
3802 5639 2.707257 TGCTGGAGCCTCAATATGATCA 59.293 45.455 0.00 0.00 41.18 2.92
3803 5640 3.244457 TGCTGGAGCCTCAATATGATCAG 60.244 47.826 0.09 0.00 41.18 2.90
3804 5641 3.869140 GCTGGAGCCTCAATATGATCAGG 60.869 52.174 0.09 0.00 34.31 3.86
3806 5643 2.305343 GGAGCCTCAATATGATCAGGCT 59.695 50.000 20.48 20.48 44.92 4.58
3807 5644 3.336468 GAGCCTCAATATGATCAGGCTG 58.664 50.000 24.14 8.58 43.10 4.85
3808 5645 1.811359 GCCTCAATATGATCAGGCTGC 59.189 52.381 10.34 0.00 33.81 5.25
3809 5646 2.552591 GCCTCAATATGATCAGGCTGCT 60.553 50.000 10.34 0.00 33.81 4.24
3810 5647 3.752665 CCTCAATATGATCAGGCTGCTT 58.247 45.455 10.34 0.00 0.00 3.91
3812 5649 2.882761 TCAATATGATCAGGCTGCTTGC 59.117 45.455 10.34 0.00 41.94 4.01
3813 5650 2.621526 CAATATGATCAGGCTGCTTGCA 59.378 45.455 10.34 5.29 45.15 4.08
3814 5651 2.651382 TATGATCAGGCTGCTTGCAT 57.349 45.000 10.34 12.10 45.15 3.96
3818 5655 2.126071 CAGGCTGCTTGCATGCAC 60.126 61.111 22.58 17.66 46.51 4.57
3819 5656 3.744719 AGGCTGCTTGCATGCACG 61.745 61.111 22.58 20.69 45.15 5.34
3821 5658 4.710695 GCTGCTTGCATGCACGCA 62.711 61.111 38.97 38.97 46.45 5.24
3822 5659 2.803670 CTGCTTGCATGCACGCAC 60.804 61.111 38.69 21.07 44.36 5.34
3823 5660 4.686722 TGCTTGCATGCACGCACG 62.687 61.111 38.69 18.54 44.36 5.34
3825 5662 2.251963 CTTGCATGCACGCACGAA 59.748 55.556 22.58 2.30 42.87 3.85
3826 5663 1.154169 CTTGCATGCACGCACGAAT 60.154 52.632 22.58 0.00 42.87 3.34
3828 5665 2.127634 TTGCATGCACGCACGAATGT 62.128 50.000 22.58 0.00 42.87 2.71
3830 5667 1.512522 CATGCACGCACGAATGTGG 60.513 57.895 0.00 0.00 46.51 4.17
3831 5668 1.965930 ATGCACGCACGAATGTGGT 60.966 52.632 0.00 0.00 46.51 4.16
3832 5669 1.514678 ATGCACGCACGAATGTGGTT 61.515 50.000 0.00 0.00 46.51 3.67
3834 5671 0.236187 GCACGCACGAATGTGGTTAA 59.764 50.000 0.00 0.00 46.51 2.01
3837 5674 3.425094 GCACGCACGAATGTGGTTAATAA 60.425 43.478 0.00 0.00 46.51 1.40
3838 5675 4.331137 CACGCACGAATGTGGTTAATAAG 58.669 43.478 0.00 0.00 46.51 1.73
3839 5676 4.092237 CACGCACGAATGTGGTTAATAAGA 59.908 41.667 0.00 0.00 46.51 2.10
3842 5679 6.128117 ACGCACGAATGTGGTTAATAAGATTT 60.128 34.615 0.00 0.00 46.51 2.17
3843 5680 6.410914 CGCACGAATGTGGTTAATAAGATTTC 59.589 38.462 0.00 0.00 46.51 2.17
3845 5682 6.410914 CACGAATGTGGTTAATAAGATTTCGC 59.589 38.462 0.00 0.00 42.59 4.70
3846 5683 5.907391 CGAATGTGGTTAATAAGATTTCGCC 59.093 40.000 0.00 0.00 0.00 5.54
3847 5684 6.457663 CGAATGTGGTTAATAAGATTTCGCCA 60.458 38.462 0.00 0.00 0.00 5.69
3849 5686 6.767524 TGTGGTTAATAAGATTTCGCCATT 57.232 33.333 0.00 0.00 0.00 3.16
3852 5689 6.019881 GTGGTTAATAAGATTTCGCCATTTGC 60.020 38.462 0.00 0.00 0.00 3.68
3853 5690 6.127479 TGGTTAATAAGATTTCGCCATTTGCT 60.127 34.615 0.00 0.00 38.05 3.91
3854 5691 7.067615 TGGTTAATAAGATTTCGCCATTTGCTA 59.932 33.333 0.00 0.00 38.05 3.49
3855 5692 8.082242 GGTTAATAAGATTTCGCCATTTGCTAT 58.918 33.333 0.00 0.00 38.05 2.97
3856 5693 8.905702 GTTAATAAGATTTCGCCATTTGCTATG 58.094 33.333 0.00 0.00 38.05 2.23
3857 5694 3.996150 AGATTTCGCCATTTGCTATGG 57.004 42.857 12.46 12.46 41.99 2.74
3873 5710 6.178607 TGCTATGGCACCCATGATATATAG 57.821 41.667 0.00 0.00 44.84 1.31
3874 5711 4.999950 GCTATGGCACCCATGATATATAGC 59.000 45.833 7.00 0.00 44.84 2.97
3877 5714 5.455392 TGGCACCCATGATATATAGCATT 57.545 39.130 10.76 0.00 28.37 3.56
3878 5715 6.573712 TGGCACCCATGATATATAGCATTA 57.426 37.500 10.76 0.00 28.37 1.90
3879 5716 6.356556 TGGCACCCATGATATATAGCATTAC 58.643 40.000 10.76 0.02 28.37 1.89
3881 5718 6.484643 GGCACCCATGATATATAGCATTACTG 59.515 42.308 10.76 7.29 28.37 2.74
3898 6032 8.035394 AGCATTACTGTATAAATATCCAGACGG 58.965 37.037 0.64 0.00 0.00 4.79
3917 6051 2.289444 CGGAAGCTTTCACTAGGAACCA 60.289 50.000 5.39 0.00 34.56 3.67
3943 6077 3.773667 TCATCTTGAGCTCTCAGAATGGT 59.226 43.478 16.19 0.00 41.13 3.55
3988 6122 3.367395 GGTTTTATTGCCCTCTTGAGCAC 60.367 47.826 0.00 0.00 39.10 4.40
3998 6132 2.559440 CTCTTGAGCACTGGATTAGCC 58.441 52.381 0.00 0.00 37.10 3.93
4060 6194 3.511934 TCCAACTCTAGCTCTGAAGGAAC 59.488 47.826 0.00 0.00 0.00 3.62
4065 6199 1.830477 CTAGCTCTGAAGGAACAGGCT 59.170 52.381 0.00 0.00 42.38 4.58
4067 6201 1.830477 AGCTCTGAAGGAACAGGCTAG 59.170 52.381 0.00 0.00 40.10 3.42
4069 6203 0.905357 TCTGAAGGAACAGGCTAGGC 59.095 55.000 8.55 8.55 38.31 3.93
4102 6236 0.603975 GGTGGAGAAGTGAGTGGTGC 60.604 60.000 0.00 0.00 0.00 5.01
4123 6257 0.615331 GGCTCATGTTCTGGGACTGA 59.385 55.000 0.00 0.00 26.64 3.41
4154 6288 0.742635 GCCAGAGTTCTAGCAGTGGC 60.743 60.000 0.00 0.00 43.43 5.01
4155 6289 0.610174 CCAGAGTTCTAGCAGTGGCA 59.390 55.000 0.00 0.00 44.61 4.92
4156 6290 1.674221 CCAGAGTTCTAGCAGTGGCAC 60.674 57.143 10.29 10.29 44.61 5.01
4174 6308 3.437795 ACATGCAAGCGCTGGAGC 61.438 61.111 18.24 18.86 39.64 4.70
4184 6318 3.071206 GCTGGAGCTCGAGGTGGA 61.071 66.667 23.97 6.93 38.21 4.02
4187 6321 3.151022 GGAGCTCGAGGTGGAGGG 61.151 72.222 23.97 0.00 34.56 4.30
4188 6322 3.151022 GAGCTCGAGGTGGAGGGG 61.151 72.222 23.97 0.00 34.56 4.79
4189 6323 4.787280 AGCTCGAGGTGGAGGGGG 62.787 72.222 17.85 0.00 34.56 5.40
4191 6325 3.077556 CTCGAGGTGGAGGGGGTG 61.078 72.222 3.91 0.00 0.00 4.61
4192 6326 4.715130 TCGAGGTGGAGGGGGTGG 62.715 72.222 0.00 0.00 0.00 4.61
4222 6356 4.009675 CAATATGGTGGTAATGGATCCGG 58.990 47.826 7.39 0.00 0.00 5.14
4248 6382 2.158696 GGCTCAGCCTTCCAGTCAATAT 60.159 50.000 9.09 0.00 46.69 1.28
4262 6396 4.528596 CAGTCAATATAGTGTAGGAGGGGG 59.471 50.000 0.00 0.00 0.00 5.40
4268 6402 1.326055 AGTGTAGGAGGGGGTGGATA 58.674 55.000 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.422093 CCCATCTCCTCCTAACAAAGCC 60.422 54.545 0.00 0.00 0.00 4.35
4 5 2.239654 CAGCCCATCTCCTCCTAACAAA 59.760 50.000 0.00 0.00 0.00 2.83
5 6 1.839994 CAGCCCATCTCCTCCTAACAA 59.160 52.381 0.00 0.00 0.00 2.83
6 7 1.500474 CAGCCCATCTCCTCCTAACA 58.500 55.000 0.00 0.00 0.00 2.41
7 8 0.761802 CCAGCCCATCTCCTCCTAAC 59.238 60.000 0.00 0.00 0.00 2.34
8 9 1.056700 GCCAGCCCATCTCCTCCTAA 61.057 60.000 0.00 0.00 0.00 2.69
27 28 0.948678 TTTCGTTCTTTTCGGCCCAG 59.051 50.000 0.00 0.00 0.00 4.45
47 48 2.659610 GGCTGACGGCTGAGAACT 59.340 61.111 6.16 0.00 41.46 3.01
49 50 1.841302 AATGGGCTGACGGCTGAGAA 61.841 55.000 6.16 0.00 41.46 2.87
50 51 0.975556 TAATGGGCTGACGGCTGAGA 60.976 55.000 6.16 0.00 41.46 3.27
52 53 1.264749 ACTAATGGGCTGACGGCTGA 61.265 55.000 6.16 0.00 41.46 4.26
73 79 0.037326 TGCGGCTGACTTAGGTCTTG 60.037 55.000 6.54 0.94 42.54 3.02
125 149 1.444836 CCGATAGCGAGGAGTAGAGG 58.555 60.000 0.00 0.00 40.82 3.69
126 150 0.800012 GCCGATAGCGAGGAGTAGAG 59.200 60.000 0.00 0.00 40.82 2.43
127 151 0.605860 GGCCGATAGCGAGGAGTAGA 60.606 60.000 0.00 0.00 45.17 2.59
128 152 0.889638 TGGCCGATAGCGAGGAGTAG 60.890 60.000 0.00 0.00 45.17 2.57
153 177 2.379459 GGGGAGAGGAAAGGAGGCC 61.379 68.421 0.00 0.00 0.00 5.19
171 195 4.379243 AGGACGGCGGAGTTGCAG 62.379 66.667 13.24 0.00 36.28 4.41
173 197 3.991536 GAGAGGACGGCGGAGTTGC 62.992 68.421 13.24 0.00 0.00 4.17
175 199 3.069318 GGAGAGGACGGCGGAGTT 61.069 66.667 13.24 0.00 0.00 3.01
233 258 4.856801 CGGTGAATGAGGGGCGGG 62.857 72.222 0.00 0.00 0.00 6.13
238 263 2.511600 GGACGCGGTGAATGAGGG 60.512 66.667 12.47 0.00 0.00 4.30
243 268 0.537188 ATGAAGAGGACGCGGTGAAT 59.463 50.000 12.47 0.00 0.00 2.57
247 272 0.537188 ATCAATGAAGAGGACGCGGT 59.463 50.000 12.47 0.00 0.00 5.68
251 276 3.126831 GGTAGCATCAATGAAGAGGACG 58.873 50.000 0.00 0.00 0.00 4.79
253 278 3.114606 TGGGTAGCATCAATGAAGAGGA 58.885 45.455 0.00 0.00 0.00 3.71
255 280 4.412796 TCTGGGTAGCATCAATGAAGAG 57.587 45.455 0.00 0.00 0.00 2.85
269 294 3.072476 CCAGGAAGACTGTTTTCTGGGTA 59.928 47.826 16.21 0.00 46.06 3.69
277 302 3.648545 AGAAGCTACCAGGAAGACTGTTT 59.351 43.478 0.00 0.00 46.06 2.83
289 314 1.824852 TGCATCGAGAAGAAGCTACCA 59.175 47.619 0.00 0.00 43.41 3.25
290 315 2.586258 TGCATCGAGAAGAAGCTACC 57.414 50.000 0.00 0.00 43.41 3.18
294 319 0.729690 GGGTTGCATCGAGAAGAAGC 59.270 55.000 0.00 0.00 43.32 3.86
344 373 4.262463 GGCAATGTATTCCATCCTCGAGTA 60.262 45.833 12.31 0.00 31.75 2.59
361 390 7.439056 ACTTTCTCAAGTAAACATTTGGCAATG 59.561 33.333 0.00 4.48 41.81 2.82
388 417 3.007473 ACGGGAACAGGAAAAAGAACA 57.993 42.857 0.00 0.00 0.00 3.18
415 446 2.575694 AGAGACGTGAGCATGCTTAG 57.424 50.000 23.61 17.79 0.00 2.18
437 468 5.744345 GGCCGTATATAGAATCAATCAGTCG 59.256 44.000 0.00 0.00 0.00 4.18
440 471 8.553459 AAAAGGCCGTATATAGAATCAATCAG 57.447 34.615 0.00 0.00 0.00 2.90
458 489 3.242641 CGCGTAGAATTAGGAAAAAGGCC 60.243 47.826 0.00 0.00 0.00 5.19
460 491 3.937079 ACCGCGTAGAATTAGGAAAAAGG 59.063 43.478 4.92 0.00 0.00 3.11
462 493 3.125658 GCACCGCGTAGAATTAGGAAAAA 59.874 43.478 4.92 0.00 0.00 1.94
466 497 1.108776 AGCACCGCGTAGAATTAGGA 58.891 50.000 4.92 0.00 0.00 2.94
467 498 1.859080 GAAGCACCGCGTAGAATTAGG 59.141 52.381 4.92 0.00 0.00 2.69
468 499 2.535984 CAGAAGCACCGCGTAGAATTAG 59.464 50.000 4.92 0.00 0.00 1.73
470 501 1.337823 ACAGAAGCACCGCGTAGAATT 60.338 47.619 4.92 0.00 0.00 2.17
494 526 5.414789 TCAAGTAATTGACGAATCTGGGA 57.585 39.130 0.56 0.00 0.00 4.37
495 527 6.683974 ATTCAAGTAATTGACGAATCTGGG 57.316 37.500 4.86 0.00 0.00 4.45
520 553 9.891828 GACAAATTTACAACAACATCATCAGTA 57.108 29.630 0.00 0.00 0.00 2.74
521 554 8.632679 AGACAAATTTACAACAACATCATCAGT 58.367 29.630 0.00 0.00 0.00 3.41
522 555 8.908678 CAGACAAATTTACAACAACATCATCAG 58.091 33.333 0.00 0.00 0.00 2.90
530 564 6.103330 ACCAACCAGACAAATTTACAACAAC 58.897 36.000 0.00 0.00 0.00 3.32
532 566 5.923733 ACCAACCAGACAAATTTACAACA 57.076 34.783 0.00 0.00 0.00 3.33
572 611 6.624352 TCTGACACAAAATTCTTCTGGAAG 57.376 37.500 4.13 4.13 37.36 3.46
573 612 7.428020 CATTCTGACACAAAATTCTTCTGGAA 58.572 34.615 0.00 0.00 38.41 3.53
577 616 6.736794 GCACCATTCTGACACAAAATTCTTCT 60.737 38.462 0.00 0.00 0.00 2.85
598 637 1.718757 CCCGAATGCTTAGCTGCACC 61.719 60.000 5.60 0.00 46.33 5.01
609 648 3.311486 TTTGATTTCCAACCCGAATGC 57.689 42.857 0.00 0.00 33.85 3.56
611 650 7.047271 CCATTAATTTGATTTCCAACCCGAAT 58.953 34.615 0.00 0.00 33.85 3.34
616 655 6.654582 AGCAACCATTAATTTGATTTCCAACC 59.345 34.615 4.40 0.00 33.85 3.77
677 717 4.754372 TCAACAGTCAATCATTGCTGTC 57.246 40.909 20.71 2.17 42.73 3.51
739 779 0.676466 TTTGCAGCAGTACCATCGGG 60.676 55.000 0.00 0.00 41.29 5.14
746 786 2.351726 CCGGACTAATTTGCAGCAGTAC 59.648 50.000 0.00 0.00 0.00 2.73
755 795 7.103641 ACTATGGCATATACCGGACTAATTTG 58.896 38.462 9.46 2.89 0.00 2.32
793 837 6.389906 CCACACTATTCTGACAAAAATTCCC 58.610 40.000 0.00 0.00 0.00 3.97
901 949 9.823647 CTGTAGGTGAGTGTGAATTATAAGATT 57.176 33.333 0.00 0.00 0.00 2.40
902 950 7.928706 GCTGTAGGTGAGTGTGAATTATAAGAT 59.071 37.037 0.00 0.00 0.00 2.40
915 967 4.862902 ATATAGCAGCTGTAGGTGAGTG 57.137 45.455 16.64 0.00 45.66 3.51
931 983 7.544566 AGTCAGGTTGTCAAACGTACAATATAG 59.455 37.037 5.72 0.00 38.95 1.31
939 991 4.395959 AGAAGTCAGGTTGTCAAACGTA 57.604 40.909 0.00 0.00 37.15 3.57
974 1026 5.127194 TCGCTCAATCAAACCTCTATGTAGT 59.873 40.000 0.00 0.00 0.00 2.73
1006 1062 2.027653 GGTTCCTCTTCTTGTCCCTCAG 60.028 54.545 0.00 0.00 0.00 3.35
1125 1198 3.878160 TGTGTGGGTGTTTTTCTTTCC 57.122 42.857 0.00 0.00 0.00 3.13
1126 1199 4.142049 TGGATGTGTGGGTGTTTTTCTTTC 60.142 41.667 0.00 0.00 0.00 2.62
1131 1204 4.769345 AAATGGATGTGTGGGTGTTTTT 57.231 36.364 0.00 0.00 0.00 1.94
1499 1629 3.189285 GCTTGCAGAAAACACAACACAT 58.811 40.909 0.00 0.00 0.00 3.21
1533 1667 4.216257 CCCTGTCTAAACACATCACCAAAG 59.784 45.833 0.00 0.00 0.00 2.77
1628 1769 3.020274 ACAACAAACATACAGTGTGCCA 58.980 40.909 5.88 0.00 41.14 4.92
1672 1813 2.628178 TCGCCACCTGATATACCAAGAG 59.372 50.000 0.00 0.00 0.00 2.85
1811 1953 9.482627 TCGTTATCAAAAGGCAAAAATAAACAT 57.517 25.926 0.00 0.00 0.00 2.71
1825 1968 6.124088 AGGCTATGCTTTCGTTATCAAAAG 57.876 37.500 0.00 0.00 35.93 2.27
1910 2055 5.625150 ACACAGATTAGACAGCTTTTTCCT 58.375 37.500 0.00 0.00 0.00 3.36
1917 2063 5.220710 ACAGAAACACAGATTAGACAGCT 57.779 39.130 0.00 0.00 0.00 4.24
1926 2072 6.715280 AGTATTCCATGACAGAAACACAGAT 58.285 36.000 0.00 0.00 0.00 2.90
1966 2114 4.650131 AGTGTCTGTAGCCTATAGGGAAAC 59.350 45.833 20.58 12.90 37.23 2.78
2009 2158 3.123050 GTGCAATGGAGTGGAAACAAAC 58.877 45.455 0.00 0.00 46.06 2.93
2022 2171 3.713288 CATAAATCCAGCTGTGCAATGG 58.287 45.455 13.81 0.00 35.30 3.16
2082 2242 1.465187 CGCAATCAGCACACATCACTG 60.465 52.381 0.00 0.00 46.13 3.66
2084 2244 0.518636 ACGCAATCAGCACACATCAC 59.481 50.000 0.00 0.00 46.13 3.06
2089 2270 1.262950 TGTGTAACGCAATCAGCACAC 59.737 47.619 0.00 0.00 43.89 3.82
2091 2272 2.679355 TTGTGTAACGCAATCAGCAC 57.321 45.000 0.00 0.00 46.13 4.40
2107 2288 6.952773 TTTCTAACATGGCTTACAGTTTGT 57.047 33.333 0.00 0.00 0.00 2.83
2213 2399 3.777522 AGTCCTCCATTATAGCTATGGCC 59.222 47.826 16.77 0.00 41.90 5.36
2214 2400 5.181748 CAAGTCCTCCATTATAGCTATGGC 58.818 45.833 16.77 0.00 41.90 4.40
2215 2401 6.014242 TCACAAGTCCTCCATTATAGCTATGG 60.014 42.308 16.77 11.93 43.22 2.74
2216 2402 6.997655 TCACAAGTCCTCCATTATAGCTATG 58.002 40.000 16.77 2.00 0.00 2.23
2217 2403 6.784969 ACTCACAAGTCCTCCATTATAGCTAT 59.215 38.462 11.77 11.77 0.00 2.97
2218 2404 6.136857 ACTCACAAGTCCTCCATTATAGCTA 58.863 40.000 0.00 0.00 0.00 3.32
2219 2405 4.965532 ACTCACAAGTCCTCCATTATAGCT 59.034 41.667 0.00 0.00 0.00 3.32
2411 2612 3.769739 ACAACAGCCTCTGTGTTCATA 57.230 42.857 0.00 0.00 44.62 2.15
2412 2613 2.645838 ACAACAGCCTCTGTGTTCAT 57.354 45.000 0.00 0.00 44.62 2.57
2413 2614 3.552132 TTACAACAGCCTCTGTGTTCA 57.448 42.857 0.00 0.00 44.62 3.18
2414 2615 4.757149 AGAATTACAACAGCCTCTGTGTTC 59.243 41.667 0.00 2.10 44.62 3.18
2415 2616 4.718961 AGAATTACAACAGCCTCTGTGTT 58.281 39.130 0.00 0.00 44.62 3.32
2416 2617 4.357918 AGAATTACAACAGCCTCTGTGT 57.642 40.909 0.00 4.30 44.62 3.72
2443 2648 6.885922 AGTACAGGAAAACAGAACTGTAGTT 58.114 36.000 7.90 5.83 43.73 2.24
2472 2680 6.682746 ACAGTGACTACATACAGCTATATGC 58.317 40.000 11.97 0.00 43.29 3.14
2485 2693 6.821160 TCAAAACATCAGAAACAGTGACTACA 59.179 34.615 0.00 0.00 0.00 2.74
2486 2694 7.246674 TCAAAACATCAGAAACAGTGACTAC 57.753 36.000 0.00 0.00 0.00 2.73
2501 2709 8.461222 TGATACAAGATGTGGAATCAAAACATC 58.539 33.333 12.25 12.25 46.86 3.06
2502 2710 8.246180 GTGATACAAGATGTGGAATCAAAACAT 58.754 33.333 0.00 0.00 36.23 2.71
2503 2711 7.448161 AGTGATACAAGATGTGGAATCAAAACA 59.552 33.333 0.00 0.00 36.23 2.83
2527 2769 3.617531 CGCACACCTTTCCATCTAGAAGT 60.618 47.826 0.00 0.00 0.00 3.01
2614 2857 1.723003 GTGTTCCGGTTGTAGTTAGCG 59.277 52.381 0.00 0.00 36.35 4.26
2728 2973 1.888436 TTGCGACGCTTCTCATCCCT 61.888 55.000 22.08 0.00 0.00 4.20
2942 3212 6.050432 TCAACGACCTACAAAGTAACACATT 58.950 36.000 0.00 0.00 0.00 2.71
3182 3512 6.671190 TCACACAGCATACAATCAGAAAAAG 58.329 36.000 0.00 0.00 0.00 2.27
3240 3572 7.500559 GCTTCCTATCTGTATGACCAAGAAAAT 59.499 37.037 0.00 0.00 0.00 1.82
3251 3586 3.738282 GCTGAACGCTTCCTATCTGTATG 59.262 47.826 0.00 0.00 35.14 2.39
3260 3595 0.321122 CTGAAGGCTGAACGCTTCCT 60.321 55.000 0.00 0.00 39.13 3.36
3341 3677 0.252421 AGCAGAGTCCCATCACTCCA 60.252 55.000 0.00 0.00 43.53 3.86
3388 3726 1.270518 CGAAATCGCCATCTCATCCCT 60.271 52.381 0.00 0.00 0.00 4.20
3498 3840 7.062722 GCAGGAAAGAAAGCAAGTTCATTAATC 59.937 37.037 0.00 0.00 0.00 1.75
3539 3888 2.224378 TGAAGGAAGTGACAGCTGAAGG 60.224 50.000 23.35 0.00 0.00 3.46
3540 3889 3.065655 CTGAAGGAAGTGACAGCTGAAG 58.934 50.000 23.35 0.00 0.00 3.02
3541 3890 3.117491 CTGAAGGAAGTGACAGCTGAA 57.883 47.619 23.35 5.08 0.00 3.02
3542 3891 2.827800 CTGAAGGAAGTGACAGCTGA 57.172 50.000 23.35 0.00 0.00 4.26
3546 3895 2.224137 TGACAGCTGAAGGAAGTGACAG 60.224 50.000 23.35 0.00 0.00 3.51
3547 3896 1.762370 TGACAGCTGAAGGAAGTGACA 59.238 47.619 23.35 1.85 0.00 3.58
3548 3897 2.139118 GTGACAGCTGAAGGAAGTGAC 58.861 52.381 23.35 0.00 0.00 3.67
3549 3898 2.042464 AGTGACAGCTGAAGGAAGTGA 58.958 47.619 23.35 0.00 0.00 3.41
3550 3899 2.141517 CAGTGACAGCTGAAGGAAGTG 58.858 52.381 23.35 9.61 38.70 3.16
3551 3900 1.542108 GCAGTGACAGCTGAAGGAAGT 60.542 52.381 23.35 0.00 38.70 3.01
3552 3901 1.155042 GCAGTGACAGCTGAAGGAAG 58.845 55.000 23.35 6.59 38.70 3.46
3553 3902 0.469494 TGCAGTGACAGCTGAAGGAA 59.531 50.000 23.35 0.00 38.70 3.36
3554 3903 0.034476 CTGCAGTGACAGCTGAAGGA 59.966 55.000 23.35 5.26 38.26 3.36
3604 3953 7.998964 AGATGGAGTATGTTATTAAACCTTGGG 59.001 37.037 0.00 0.00 34.49 4.12
3619 3968 8.834465 CATTCAAGGTTCTTAAGATGGAGTATG 58.166 37.037 5.89 2.46 0.00 2.39
3664 4016 7.430502 GCAACAAATCCAGAATCTAGAAAATCG 59.569 37.037 0.00 0.00 0.00 3.34
3729 4085 9.909043 GGTGTAAATGTTGAAACACAAATTAAC 57.091 29.630 0.00 0.00 43.13 2.01
3743 4099 9.912634 AAAATGATCTACAAGGTGTAAATGTTG 57.087 29.630 0.00 0.00 31.67 3.33
3746 4102 9.277565 CGAAAAATGATCTACAAGGTGTAAATG 57.722 33.333 0.00 0.00 31.67 2.32
3747 4103 8.458843 CCGAAAAATGATCTACAAGGTGTAAAT 58.541 33.333 0.00 0.00 31.67 1.40
3754 4110 4.523083 TCCCCGAAAAATGATCTACAAGG 58.477 43.478 0.00 0.00 0.00 3.61
3755 4111 5.506317 GCATCCCCGAAAAATGATCTACAAG 60.506 44.000 0.00 0.00 0.00 3.16
3757 4113 3.882888 GCATCCCCGAAAAATGATCTACA 59.117 43.478 0.00 0.00 0.00 2.74
3758 4114 3.882888 TGCATCCCCGAAAAATGATCTAC 59.117 43.478 0.00 0.00 0.00 2.59
3761 4117 3.645884 CATGCATCCCCGAAAAATGATC 58.354 45.455 0.00 0.00 0.00 2.92
3762 4118 2.224113 GCATGCATCCCCGAAAAATGAT 60.224 45.455 14.21 0.00 0.00 2.45
3768 5605 1.753848 CCAGCATGCATCCCCGAAA 60.754 57.895 21.98 0.00 31.97 3.46
3775 5612 0.750546 TTGAGGCTCCAGCATGCATC 60.751 55.000 21.98 6.40 44.36 3.91
3776 5613 0.106167 ATTGAGGCTCCAGCATGCAT 60.106 50.000 21.98 1.69 44.36 3.96
3777 5614 0.547553 TATTGAGGCTCCAGCATGCA 59.452 50.000 21.98 0.00 44.36 3.96
3778 5615 1.540267 CATATTGAGGCTCCAGCATGC 59.460 52.381 10.51 10.51 44.36 4.06
3779 5616 3.136009 TCATATTGAGGCTCCAGCATG 57.864 47.619 12.86 10.09 44.36 4.06
3782 5619 3.336468 CTGATCATATTGAGGCTCCAGC 58.664 50.000 12.86 0.00 41.14 4.85
3783 5620 3.869140 GCCTGATCATATTGAGGCTCCAG 60.869 52.174 12.86 8.92 33.81 3.86
3784 5621 2.039480 GCCTGATCATATTGAGGCTCCA 59.961 50.000 12.86 0.12 33.81 3.86
3786 5623 3.336468 CAGCCTGATCATATTGAGGCTC 58.664 50.000 18.32 7.79 41.75 4.70
3789 5626 3.420300 AGCAGCCTGATCATATTGAGG 57.580 47.619 0.00 0.00 0.00 3.86
3790 5627 3.058155 GCAAGCAGCCTGATCATATTGAG 60.058 47.826 0.00 0.00 37.23 3.02
3791 5628 2.882761 GCAAGCAGCCTGATCATATTGA 59.117 45.455 0.00 0.00 37.23 2.57
3792 5629 2.621526 TGCAAGCAGCCTGATCATATTG 59.378 45.455 0.00 0.00 44.83 1.90
3793 5630 2.940158 TGCAAGCAGCCTGATCATATT 58.060 42.857 0.00 0.00 44.83 1.28
3795 5632 2.227194 CATGCAAGCAGCCTGATCATA 58.773 47.619 0.00 0.00 44.83 2.15
3796 5633 1.032794 CATGCAAGCAGCCTGATCAT 58.967 50.000 0.00 0.00 44.83 2.45
3797 5634 1.663379 GCATGCAAGCAGCCTGATCA 61.663 55.000 14.21 0.00 44.83 2.92
3798 5635 1.065928 GCATGCAAGCAGCCTGATC 59.934 57.895 14.21 0.00 44.83 2.92
3799 5636 1.680989 TGCATGCAAGCAGCCTGAT 60.681 52.632 20.30 0.00 44.83 2.90
3802 5639 3.744719 CGTGCATGCAAGCAGCCT 61.745 61.111 24.58 0.00 46.69 4.58
3810 5647 2.176300 CATTCGTGCGTGCATGCA 59.824 55.556 29.30 29.30 43.95 3.96
3812 5649 1.512522 CCACATTCGTGCGTGCATG 60.513 57.895 7.74 7.74 42.17 4.06
3813 5650 1.514678 AACCACATTCGTGCGTGCAT 61.515 50.000 0.00 0.00 42.17 3.96
3814 5651 0.880718 TAACCACATTCGTGCGTGCA 60.881 50.000 0.00 0.00 42.17 4.57
3815 5652 0.236187 TTAACCACATTCGTGCGTGC 59.764 50.000 0.00 0.00 42.17 5.34
3816 5653 2.892373 ATTAACCACATTCGTGCGTG 57.108 45.000 0.00 0.00 42.17 5.34
3817 5654 4.247258 TCTTATTAACCACATTCGTGCGT 58.753 39.130 0.00 0.00 42.17 5.24
3818 5655 4.850859 TCTTATTAACCACATTCGTGCG 57.149 40.909 0.00 0.00 42.17 5.34
3819 5656 6.410914 CGAAATCTTATTAACCACATTCGTGC 59.589 38.462 0.00 0.00 42.17 5.34
3820 5657 6.410914 GCGAAATCTTATTAACCACATTCGTG 59.589 38.462 0.00 0.00 43.21 4.35
3821 5658 6.457799 GGCGAAATCTTATTAACCACATTCGT 60.458 38.462 0.00 0.00 39.28 3.85
3822 5659 5.907391 GGCGAAATCTTATTAACCACATTCG 59.093 40.000 0.00 0.00 39.85 3.34
3823 5660 6.791303 TGGCGAAATCTTATTAACCACATTC 58.209 36.000 0.00 0.00 0.00 2.67
3825 5662 6.959639 ATGGCGAAATCTTATTAACCACAT 57.040 33.333 0.00 0.00 0.00 3.21
3826 5663 6.767524 AATGGCGAAATCTTATTAACCACA 57.232 33.333 0.00 0.00 0.00 4.17
3828 5665 6.039616 GCAAATGGCGAAATCTTATTAACCA 58.960 36.000 0.00 0.00 0.00 3.67
3829 5666 6.510746 GCAAATGGCGAAATCTTATTAACC 57.489 37.500 0.00 0.00 0.00 2.85
3852 5689 6.178607 TGCTATATATCATGGGTGCCATAG 57.821 41.667 0.00 0.00 43.15 2.23
3853 5690 6.768641 ATGCTATATATCATGGGTGCCATA 57.231 37.500 0.00 0.00 43.15 2.74
3854 5691 5.658198 ATGCTATATATCATGGGTGCCAT 57.342 39.130 0.00 0.00 46.37 4.40
3855 5692 5.455392 AATGCTATATATCATGGGTGCCA 57.545 39.130 0.00 0.00 38.19 4.92
3856 5693 6.484643 CAGTAATGCTATATATCATGGGTGCC 59.515 42.308 0.00 0.00 0.00 5.01
3857 5694 7.050377 ACAGTAATGCTATATATCATGGGTGC 58.950 38.462 0.00 0.00 0.00 5.01
3872 5709 8.035394 CCGTCTGGATATTTATACAGTAATGCT 58.965 37.037 9.17 0.00 43.62 3.79
3873 5710 8.033038 TCCGTCTGGATATTTATACAGTAATGC 58.967 37.037 9.17 0.00 43.62 3.56
3874 5711 9.923143 TTCCGTCTGGATATTTATACAGTAATG 57.077 33.333 9.17 0.00 45.91 1.90
3877 5714 7.450634 AGCTTCCGTCTGGATATTTATACAGTA 59.549 37.037 9.17 0.00 45.91 2.74
3878 5715 6.267928 AGCTTCCGTCTGGATATTTATACAGT 59.732 38.462 9.17 0.00 45.91 3.55
3879 5716 6.692486 AGCTTCCGTCTGGATATTTATACAG 58.308 40.000 3.74 3.74 45.91 2.74
3881 5718 7.656137 TGAAAGCTTCCGTCTGGATATTTATAC 59.344 37.037 0.00 0.00 45.91 1.47
3890 6024 1.048601 AGTGAAAGCTTCCGTCTGGA 58.951 50.000 0.00 0.00 44.61 3.86
3898 6032 4.134563 TGTTGGTTCCTAGTGAAAGCTTC 58.865 43.478 0.00 0.00 33.94 3.86
3917 6051 5.417754 TTCTGAGAGCTCAAGATGATGTT 57.582 39.130 17.77 0.00 39.39 2.71
3943 6077 5.393135 CCGAGAGATGCTAGTTTTGTGTCTA 60.393 44.000 0.00 0.00 0.00 2.59
3960 6094 2.838202 AGAGGGCAATAAAACCGAGAGA 59.162 45.455 0.00 0.00 0.00 3.10
4013 6147 1.132554 CCTCCCCATGGATCTCCCTG 61.133 65.000 15.22 0.00 40.80 4.45
4030 6164 0.689412 GCTAGAGTTGGAGCCTCCCT 60.689 60.000 8.62 0.00 35.03 4.20
4031 6165 0.689412 AGCTAGAGTTGGAGCCTCCC 60.689 60.000 8.62 0.00 39.65 4.30
4060 6194 2.139484 CCTCCCTCTGCCTAGCCTG 61.139 68.421 0.00 0.00 0.00 4.85
4065 6199 2.958739 ACCCCCTCCCTCTGCCTA 60.959 66.667 0.00 0.00 0.00 3.93
4069 6203 3.011517 CACCACCCCCTCCCTCTG 61.012 72.222 0.00 0.00 0.00 3.35
4102 6236 0.617413 AGTCCCAGAACATGAGCCAG 59.383 55.000 0.00 0.00 0.00 4.85
4128 6262 1.069978 GCTAGAACTCTGGCCAGATCC 59.930 57.143 35.11 24.55 43.58 3.36
4143 6277 0.674581 GCATGTGTGCCACTGCTAGA 60.675 55.000 15.49 0.00 45.76 2.43
4154 6288 2.126618 CCAGCGCTTGCATGTGTG 60.127 61.111 7.50 10.54 42.66 3.82
4155 6289 2.281692 TCCAGCGCTTGCATGTGT 60.282 55.556 7.50 0.00 42.66 3.72
4156 6290 2.483745 CTCCAGCGCTTGCATGTG 59.516 61.111 7.50 8.70 42.66 3.21
4174 6308 3.077556 CACCCCCTCCACCTCGAG 61.078 72.222 5.13 5.13 0.00 4.04
4180 6314 2.609610 TACTGCCACCCCCTCCAC 60.610 66.667 0.00 0.00 0.00 4.02
4181 6315 2.285368 CTACTGCCACCCCCTCCA 60.285 66.667 0.00 0.00 0.00 3.86
4192 6326 2.348411 ACCACCATATTGGCTACTGC 57.652 50.000 0.00 0.00 42.67 4.40
4193 6327 4.761739 CCATTACCACCATATTGGCTACTG 59.238 45.833 0.00 0.00 42.67 2.74
4194 6328 4.663120 TCCATTACCACCATATTGGCTACT 59.337 41.667 0.00 0.00 42.67 2.57
4195 6329 4.980573 TCCATTACCACCATATTGGCTAC 58.019 43.478 0.00 0.00 42.67 3.58
4234 6368 6.015010 CCTCCTACACTATATTGACTGGAAGG 60.015 46.154 0.00 0.00 39.30 3.46
4236 6370 5.839063 CCCTCCTACACTATATTGACTGGAA 59.161 44.000 0.00 0.00 0.00 3.53
4241 6375 4.283722 CACCCCCTCCTACACTATATTGAC 59.716 50.000 0.00 0.00 0.00 3.18
4248 6382 1.326055 ATCCACCCCCTCCTACACTA 58.674 55.000 0.00 0.00 0.00 2.74
4262 6396 3.686016 ACACCAAGTTCACCATATCCAC 58.314 45.455 0.00 0.00 0.00 4.02
4268 6402 5.505181 AGAAGATACACCAAGTTCACCAT 57.495 39.130 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.