Multiple sequence alignment - TraesCS7A01G390300

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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 TraesCS7A01G390300 chr7A 100.000 6434 0 0 1 6434 566536814 566543247 0.000000e+00 11882
1 TraesCS7A01G390300 chr7D 93.654 3057 133 25 588 3610 500626149 500629178 0.000000e+00 4514
2 TraesCS7A01G390300 chr7D 93.813 2392 96 13 3620 5981 500629225 500631594 0.000000e+00 3550
3 TraesCS7A01G390300 chr7D 92.135 356 25 3 6080 6434 500744873 500745226 3.460000e-137 499
4 TraesCS7A01G390300 chr7D 80.680 559 65 20 24 549 500625298 500625846 1.680000e-105 394
5 TraesCS7A01G390300 chr7D 77.597 308 58 7 106 408 164641879 164642180 6.630000e-40 176
6 TraesCS7A01G390300 chr7B 92.461 2414 124 22 3620 5981 528765910 528768317 0.000000e+00 3397
7 TraesCS7A01G390300 chr7B 93.275 2275 107 26 1361 3623 528763632 528765872 0.000000e+00 3312
8 TraesCS7A01G390300 chr7B 88.261 1397 94 32 2 1360 528762230 528763594 0.000000e+00 1607
9 TraesCS7A01G390300 chr7B 90.000 390 32 3 6051 6434 528769395 528769783 1.250000e-136 497
10 TraesCS7A01G390300 chr7B 90.000 80 3 4 5973 6051 528769289 528769364 1.480000e-16 99
11 TraesCS7A01G390300 chr6D 75.937 507 101 13 4073 4575 139311702 139311213 2.320000e-59 241
12 TraesCS7A01G390300 chr6D 87.755 147 18 0 4672 4818 139311134 139310988 8.580000e-39 172
13 TraesCS7A01G390300 chr6D 89.744 117 12 0 3827 3943 139312196 139312080 4.020000e-32 150
14 TraesCS7A01G390300 chr6D 74.194 310 71 6 106 411 286783957 286783653 3.150000e-23 121
15 TraesCS7A01G390300 chr6B 76.019 417 74 19 4661 5071 239286225 239285829 6.580000e-45 193
16 TraesCS7A01G390300 chr6B 82.390 159 24 2 1150 1308 239290311 239290157 1.130000e-27 135
17 TraesCS7A01G390300 chr6A 87.075 147 19 0 4672 4818 181897430 181897284 3.990000e-37 167
18 TraesCS7A01G390300 chr6A 76.768 297 60 5 113 408 85133026 85133314 2.400000e-34 158
19 TraesCS7A01G390300 chr3D 74.432 352 71 13 63 402 593802468 593802124 4.050000e-27 134
20 TraesCS7A01G390300 chr1A 77.928 222 44 2 191 411 559048544 559048327 4.050000e-27 134
21 TraesCS7A01G390300 chr4A 77.434 226 43 7 185 408 55562396 55562615 1.880000e-25 128
22 TraesCS7A01G390300 chr5D 73.410 346 68 17 117 450 90298960 90299293 2.450000e-19 108


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 TraesCS7A01G390300 chr7A 566536814 566543247 6433 False 11882.000000 11882 100.000000 1 6434 1 chr7A.!!$F1 6433
1 TraesCS7A01G390300 chr7D 500625298 500631594 6296 False 2819.333333 4514 89.382333 24 5981 3 chr7D.!!$F3 5957
2 TraesCS7A01G390300 chr7B 528762230 528769783 7553 False 1782.400000 3397 90.799400 2 6434 5 chr7B.!!$F1 6432

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
690 998 0.034863 TCCCCCACATTTACGAAGCC 60.035 55.000 0.00 0.00 0.00 4.35 F
1390 1742 0.108041 CATGAAGGGTTTGGCATGGC 60.108 55.000 13.29 13.29 35.64 4.40 F
1825 2178 0.618458 TGATACACCCTGCTTCCACC 59.382 55.000 0.00 0.00 0.00 4.61 F
3260 3627 1.133262 CCAAATGGCCCTGAGGATGAT 60.133 52.381 0.00 0.00 33.47 2.45 F
3821 4233 2.677765 TAAAAGTTCCCGGTGCGGCA 62.678 55.000 0.00 0.00 46.86 5.69 F
5006 5449 0.187117 TGGTTGACCCAGCAATGGAA 59.813 50.000 0.00 0.00 38.72 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1802 2155 1.279271 GGAAGCAGGGTGTATCAGTGT 59.721 52.381 0.00 0.0 0.00 3.55 R
3215 3582 1.267806 GTTGTCGGTACTTGAGGACGA 59.732 52.381 0.00 0.0 32.17 4.20 R
3812 4224 1.326548 GTATAAGAAGTTGCCGCACCG 59.673 52.381 0.00 0.0 0.00 4.94 R
4155 4589 0.522626 TAAGCGACACGATGTTCGGA 59.477 50.000 1.69 0.0 45.59 4.55 R
5030 5473 0.737019 TTATGTCGGCGAAACGGGAC 60.737 55.000 12.92 0.0 0.00 4.46 R
6330 7817 0.034767 CCTGCCCTCTTGATCTGCAA 60.035 55.000 0.00 0.0 34.73 4.08 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
18 19 3.854669 CCAGGAAGGCGAGGCGAT 61.855 66.667 0.00 0.00 0.00 4.58
19 20 2.498941 CCAGGAAGGCGAGGCGATA 61.499 63.158 0.00 0.00 0.00 2.92
20 21 1.441729 CAGGAAGGCGAGGCGATAA 59.558 57.895 0.00 0.00 0.00 1.75
49 50 8.719648 GCTATCTGAAGATGAAATAAGGTCATG 58.280 37.037 2.99 0.00 35.84 3.07
60 62 1.495579 AAGGTCATGCACTCTGCCCT 61.496 55.000 0.00 0.00 44.23 5.19
74 76 3.249961 CCCTTCTATCCCCCGCCC 61.250 72.222 0.00 0.00 0.00 6.13
75 77 3.626924 CCTTCTATCCCCCGCCCG 61.627 72.222 0.00 0.00 0.00 6.13
76 78 2.523412 CTTCTATCCCCCGCCCGA 60.523 66.667 0.00 0.00 0.00 5.14
77 79 1.913762 CTTCTATCCCCCGCCCGAT 60.914 63.158 0.00 0.00 0.00 4.18
78 80 0.613853 CTTCTATCCCCCGCCCGATA 60.614 60.000 0.00 0.00 0.00 2.92
80 82 1.305046 CTATCCCCCGCCCGATAGT 60.305 63.158 0.00 0.00 35.32 2.12
81 83 1.605058 CTATCCCCCGCCCGATAGTG 61.605 65.000 0.00 0.00 35.32 2.74
87 89 3.028130 CGCCCGATAGTGCGTCTA 58.972 61.111 0.00 0.00 45.43 2.59
88 90 1.082038 CGCCCGATAGTGCGTCTAG 60.082 63.158 0.00 0.00 45.43 2.43
99 101 3.171705 GCGTCTAGCTCATCGAAGG 57.828 57.895 0.00 0.00 44.04 3.46
101 103 0.318275 CGTCTAGCTCATCGAAGGGC 60.318 60.000 3.84 3.84 0.00 5.19
102 104 0.747255 GTCTAGCTCATCGAAGGGCA 59.253 55.000 15.85 0.00 0.00 5.36
113 125 3.934391 GAAGGGCACGTGTCTCCGG 62.934 68.421 21.13 0.00 0.00 5.14
121 133 1.064946 CGTGTCTCCGGCAGATCTC 59.935 63.158 0.00 0.00 32.08 2.75
134 146 4.150359 GGCAGATCTCATGGGATTCAATT 58.850 43.478 10.06 0.00 0.00 2.32
137 149 4.022242 CAGATCTCATGGGATTCAATTGGC 60.022 45.833 10.06 0.00 0.00 4.52
148 160 1.243902 TCAATTGGCGTTGGTCTTCC 58.756 50.000 5.42 0.00 0.00 3.46
187 199 9.207042 GGATACAATCTTCGTTCGTTTTAATTC 57.793 33.333 0.00 0.00 0.00 2.17
188 200 9.749490 GATACAATCTTCGTTCGTTTTAATTCA 57.251 29.630 0.00 0.00 0.00 2.57
189 201 7.831750 ACAATCTTCGTTCGTTTTAATTCAC 57.168 32.000 0.00 0.00 0.00 3.18
190 202 6.572254 ACAATCTTCGTTCGTTTTAATTCACG 59.428 34.615 0.00 0.00 37.77 4.35
198 210 5.970140 TCGTTTTAATTCACGTGTCTTCA 57.030 34.783 16.51 0.00 37.66 3.02
199 211 5.969741 TCGTTTTAATTCACGTGTCTTCAG 58.030 37.500 16.51 0.82 37.66 3.02
200 212 5.749588 TCGTTTTAATTCACGTGTCTTCAGA 59.250 36.000 16.51 3.17 37.66 3.27
213 225 5.423015 GTGTCTTCAGATTGCATCCTTCTA 58.577 41.667 0.00 0.00 0.00 2.10
226 238 6.835174 TGCATCCTTCTAATCTATGCTTCTT 58.165 36.000 0.00 0.00 42.63 2.52
287 299 2.429610 GGGGTCTTAGCACGATGACTTA 59.570 50.000 0.00 0.00 0.00 2.24
293 305 5.232414 GTCTTAGCACGATGACTTATTGACC 59.768 44.000 0.00 0.00 0.00 4.02
324 336 0.882927 CAAGTTTTGTCCGGCTCCGA 60.883 55.000 10.28 0.00 42.83 4.55
341 353 1.117749 CGATGAGGGAGGATCAGGCA 61.118 60.000 0.00 0.00 36.25 4.75
375 389 0.321122 CCTTCGGCTTGCTCAAGAGT 60.321 55.000 13.33 0.00 40.79 3.24
381 395 2.158449 CGGCTTGCTCAAGAGTTTGTAG 59.842 50.000 13.33 0.00 40.79 2.74
386 400 4.054780 TGCTCAAGAGTTTGTAGTCGTT 57.945 40.909 0.00 0.00 35.73 3.85
400 414 5.131067 TGTAGTCGTTGCTAGATGGTCTAT 58.869 41.667 0.00 0.00 0.00 1.98
401 415 4.576216 AGTCGTTGCTAGATGGTCTATG 57.424 45.455 0.00 0.00 0.00 2.23
402 416 3.319405 AGTCGTTGCTAGATGGTCTATGG 59.681 47.826 0.00 0.00 0.00 2.74
488 511 3.558931 AAAAACCCCAAAGAGGCTTTG 57.441 42.857 11.83 11.83 35.39 2.77
489 512 2.174685 AAACCCCAAAGAGGCTTTGT 57.825 45.000 16.11 0.00 35.39 2.83
490 513 3.322191 AAACCCCAAAGAGGCTTTGTA 57.678 42.857 16.11 0.00 35.39 2.41
492 515 1.497286 ACCCCAAAGAGGCTTTGTACA 59.503 47.619 16.11 0.00 35.39 2.90
493 516 1.886542 CCCCAAAGAGGCTTTGTACAC 59.113 52.381 16.11 0.00 35.39 2.90
494 517 2.489073 CCCCAAAGAGGCTTTGTACACT 60.489 50.000 16.11 0.00 35.39 3.55
495 518 3.222603 CCCAAAGAGGCTTTGTACACTT 58.777 45.455 16.11 0.00 35.39 3.16
496 519 3.636764 CCCAAAGAGGCTTTGTACACTTT 59.363 43.478 16.11 0.00 35.39 2.66
497 520 4.099419 CCCAAAGAGGCTTTGTACACTTTT 59.901 41.667 16.11 0.00 35.39 2.27
498 521 5.281727 CCAAAGAGGCTTTGTACACTTTTC 58.718 41.667 16.11 0.00 0.00 2.29
499 522 5.281727 CAAAGAGGCTTTGTACACTTTTCC 58.718 41.667 10.84 0.00 0.00 3.13
500 523 4.164843 AGAGGCTTTGTACACTTTTCCA 57.835 40.909 0.00 0.00 0.00 3.53
501 524 4.729868 AGAGGCTTTGTACACTTTTCCAT 58.270 39.130 0.00 0.00 0.00 3.41
502 525 5.140454 AGAGGCTTTGTACACTTTTCCATT 58.860 37.500 0.00 0.00 0.00 3.16
503 526 5.598417 AGAGGCTTTGTACACTTTTCCATTT 59.402 36.000 0.00 0.00 0.00 2.32
504 527 5.600696 AGGCTTTGTACACTTTTCCATTTG 58.399 37.500 0.00 0.00 0.00 2.32
524 554 1.308998 CCCTGAAATATGTCACCCGC 58.691 55.000 0.00 0.00 0.00 6.13
529 559 1.940613 GAAATATGTCACCCGCACCTC 59.059 52.381 0.00 0.00 0.00 3.85
549 579 2.104451 TCGTCCTCTCTAGCCGTTAGAT 59.896 50.000 0.00 0.00 37.75 1.98
552 858 1.889829 CCTCTCTAGCCGTTAGATGGG 59.110 57.143 0.00 0.00 37.75 4.00
601 907 5.527214 GCATAATAGATGTGCCTTGTGTGTA 59.473 40.000 0.00 0.00 32.88 2.90
602 908 6.038161 GCATAATAGATGTGCCTTGTGTGTAA 59.962 38.462 0.00 0.00 32.88 2.41
603 909 7.415095 GCATAATAGATGTGCCTTGTGTGTAAA 60.415 37.037 0.00 0.00 32.88 2.01
604 910 5.880054 ATAGATGTGCCTTGTGTGTAAAC 57.120 39.130 0.00 0.00 0.00 2.01
605 911 3.820557 AGATGTGCCTTGTGTGTAAACT 58.179 40.909 0.00 0.00 0.00 2.66
689 997 1.092348 GTCCCCCACATTTACGAAGC 58.908 55.000 0.00 0.00 0.00 3.86
690 998 0.034863 TCCCCCACATTTACGAAGCC 60.035 55.000 0.00 0.00 0.00 4.35
691 999 1.373590 CCCCCACATTTACGAAGCCG 61.374 60.000 0.00 0.00 42.50 5.52
692 1000 1.427819 CCCACATTTACGAAGCCGC 59.572 57.895 0.00 0.00 39.95 6.53
855 1163 2.466982 CGAGCAAGCATGGCATCGT 61.467 57.895 0.00 0.00 37.68 3.73
909 1217 4.085733 AGATAGATAAGAGCGAGGCATGT 58.914 43.478 0.00 0.00 0.00 3.21
1181 1496 3.058160 CAGTTGCGGCTCTTGGGG 61.058 66.667 0.00 0.00 0.00 4.96
1314 1629 2.838202 TCACCTCAATGTAAGGGTCTCC 59.162 50.000 0.00 0.00 38.29 3.71
1329 1644 3.134985 GGGTCTCCCTCTTGTCCTAAATC 59.865 52.174 0.00 0.00 41.34 2.17
1390 1742 0.108041 CATGAAGGGTTTGGCATGGC 60.108 55.000 13.29 13.29 35.64 4.40
1501 1854 3.006217 GCTGGCCAGAAAAATCTCTGTTT 59.994 43.478 37.21 0.00 41.15 2.83
1591 1944 1.428869 ACCCTGCTCTGAAACTGACT 58.571 50.000 0.00 0.00 0.00 3.41
1592 1945 2.609747 ACCCTGCTCTGAAACTGACTA 58.390 47.619 0.00 0.00 0.00 2.59
1593 1946 2.300437 ACCCTGCTCTGAAACTGACTAC 59.700 50.000 0.00 0.00 0.00 2.73
1594 1947 2.600731 CCTGCTCTGAAACTGACTACG 58.399 52.381 0.00 0.00 0.00 3.51
1664 2017 9.643693 CCTCTATGTATTTGTGCTTTTCAATTT 57.356 29.630 0.00 0.00 0.00 1.82
1674 2027 7.232945 TGTGCTTTTCAATTTAAAGTTGCTC 57.767 32.000 10.11 6.73 35.52 4.26
1706 2059 8.715191 ATCAAGATGTTACTGACAGAAGATTC 57.285 34.615 10.08 0.79 42.62 2.52
1728 2081 7.593875 TTCTGCATATTTGTGCCAATTTTAC 57.406 32.000 0.00 0.00 44.43 2.01
1738 2091 4.039852 TGTGCCAATTTTACTTTCCCCTTC 59.960 41.667 0.00 0.00 0.00 3.46
1747 2100 3.532641 ACTTTCCCCTTCATTCTGCTT 57.467 42.857 0.00 0.00 0.00 3.91
1825 2178 0.618458 TGATACACCCTGCTTCCACC 59.382 55.000 0.00 0.00 0.00 4.61
1923 2276 5.660460 TGACAACGATGTATGAGCTAACAT 58.340 37.500 0.00 8.20 40.74 2.71
1963 2316 9.565213 CTTCATTGCTCTATGTTTTCCTTAAAG 57.435 33.333 0.00 0.00 0.00 1.85
2079 2432 2.421424 CTGTAATGCTTCTCACCTTGCC 59.579 50.000 0.00 0.00 0.00 4.52
2097 2450 5.341872 TTGCCCATCTTCATTACCATTTG 57.658 39.130 0.00 0.00 0.00 2.32
2165 2518 8.314021 AGGAATTTGGCGAGAAATAATTTTTCT 58.686 29.630 12.49 12.49 41.08 2.52
2239 2592 4.035208 AGTTGCTTACTACCGCAAATATGC 59.965 41.667 0.00 0.00 46.40 3.14
2240 2593 6.373117 AGTTGCTTACTACCGCAAATATGCA 61.373 40.000 1.42 0.00 46.40 3.96
2389 2744 5.955959 TCTGTATTGTAAGGCCTACTGAGAA 59.044 40.000 5.16 0.00 0.00 2.87
2391 2746 7.783119 TCTGTATTGTAAGGCCTACTGAGAATA 59.217 37.037 5.16 4.11 27.25 1.75
2393 2748 9.596308 TGTATTGTAAGGCCTACTGAGAATATA 57.404 33.333 5.16 2.71 30.71 0.86
2544 2909 3.880490 AGTTTTACCTGTGAAATGTGCGA 59.120 39.130 0.00 0.00 0.00 5.10
2633 3000 7.252612 TCCCTGTTACATGACTTCATCTTAA 57.747 36.000 0.00 0.00 33.61 1.85
2855 3222 1.204704 TCAACTATCGGGCACAGTCAG 59.795 52.381 0.00 0.00 0.00 3.51
2949 3316 3.159472 TGCCTGCTTTTTCATCTGATGT 58.841 40.909 16.66 0.00 0.00 3.06
3045 3412 3.697045 CTCGATTCCAGACTTGAGGTAGT 59.303 47.826 0.00 0.00 0.00 2.73
3212 3579 3.240134 GAGTCCGGTTGCTCAGCCA 62.240 63.158 0.00 0.00 0.00 4.75
3215 3582 2.270205 CCGGTTGCTCAGCCAGAT 59.730 61.111 0.00 0.00 0.00 2.90
3260 3627 1.133262 CCAAATGGCCCTGAGGATGAT 60.133 52.381 0.00 0.00 33.47 2.45
3582 3953 8.352201 TGAGGTAAAGTGAATCAGATTTTGTTG 58.648 33.333 0.00 0.00 0.00 3.33
3583 3954 8.237811 AGGTAAAGTGAATCAGATTTTGTTGT 57.762 30.769 0.00 0.00 0.00 3.32
3686 4098 3.753842 TCTCGTTTCTTTTTGTGTGTGC 58.246 40.909 0.00 0.00 0.00 4.57
3700 4112 3.985279 TGTGTGTGCGTAGATTCTAACAC 59.015 43.478 15.58 15.58 38.66 3.32
3806 4218 9.520515 AATAGTTCTCCAGCAAAGAAGATAAAA 57.479 29.630 0.00 0.00 33.57 1.52
3812 4224 5.476945 TCCAGCAAAGAAGATAAAAGTTCCC 59.523 40.000 0.00 0.00 0.00 3.97
3821 4233 2.677765 TAAAAGTTCCCGGTGCGGCA 62.678 55.000 0.00 0.00 46.86 5.69
4004 4420 5.745294 GCATAGCATTGTTTACATGTTCAGG 59.255 40.000 2.30 0.15 0.00 3.86
4007 4441 3.056607 GCATTGTTTACATGTTCAGGCCT 60.057 43.478 2.30 0.00 0.00 5.19
4012 4446 6.716934 TGTTTACATGTTCAGGCCTTTTTA 57.283 33.333 0.00 0.00 0.00 1.52
4013 4447 7.296628 TGTTTACATGTTCAGGCCTTTTTAT 57.703 32.000 0.00 0.00 0.00 1.40
4134 4568 7.405292 AGGATCATTTTCTTGAGGTTGTATCA 58.595 34.615 0.00 0.00 0.00 2.15
4155 4589 2.717639 ACATTTCTCGGCTTAGGCAT 57.282 45.000 6.60 0.00 40.87 4.40
4343 4777 3.369147 CGAGCTTTGGAGTATGTTGTCTG 59.631 47.826 0.00 0.00 0.00 3.51
4346 4780 4.757149 AGCTTTGGAGTATGTTGTCTGAAC 59.243 41.667 0.00 0.00 0.00 3.18
4347 4781 4.757149 GCTTTGGAGTATGTTGTCTGAACT 59.243 41.667 0.00 0.00 0.00 3.01
4401 4836 4.272748 ACTTTTCTGGTGAAGCGAACTTAC 59.727 41.667 0.00 0.00 35.82 2.34
4537 4972 1.376553 GTCTGACTCTGGGCTTGCC 60.377 63.158 2.49 2.49 0.00 4.52
4595 5030 4.876107 ACATAGTAGCAACATACTGCCAAC 59.124 41.667 0.00 0.00 43.73 3.77
4651 5089 6.374333 TCATTGTTAGTTGGACTAAATCAGGC 59.626 38.462 2.37 0.00 41.80 4.85
4743 5181 2.017049 GCCATGTCAGGAACACATACC 58.983 52.381 0.00 0.00 41.75 2.73
4868 5310 9.383519 TGCTGTAAATTTGAACCAAAAATTACA 57.616 25.926 20.30 20.30 41.54 2.41
5006 5449 0.187117 TGGTTGACCCAGCAATGGAA 59.813 50.000 0.00 0.00 38.72 3.53
5030 5473 3.629398 GGATGTACCCTGCAAAATCTCTG 59.371 47.826 0.00 0.00 0.00 3.35
5148 5591 6.417044 GCAGCTAAAATATGAACAGCATTCAG 59.583 38.462 9.06 0.00 38.44 3.02
5219 5676 7.164122 AGTGGCTATGTTGATATATGAACTGG 58.836 38.462 14.88 7.17 0.00 4.00
5251 5716 4.986054 TCAGAGAGGTAGAGTAGGATCC 57.014 50.000 2.48 2.48 0.00 3.36
5480 5948 5.528043 ACCAGAGCTGTATCAGAACATAG 57.472 43.478 0.00 0.00 32.44 2.23
5481 5949 4.959210 ACCAGAGCTGTATCAGAACATAGT 59.041 41.667 0.00 0.00 32.44 2.12
5482 5950 6.129874 ACCAGAGCTGTATCAGAACATAGTA 58.870 40.000 0.00 0.00 32.44 1.82
5510 5978 9.689075 CATTTTGTGAGTATTAGTATGTGTTCG 57.311 33.333 0.00 0.00 0.00 3.95
5527 5995 6.631962 TGTGTTCGGTTTTTACTCCATTTTT 58.368 32.000 0.00 0.00 0.00 1.94
5691 6159 3.670055 GGATTTGTGACAAGTTGAATGCG 59.330 43.478 10.54 0.00 0.00 4.73
5714 6182 2.336478 CCTCTGTCAGACGGCGACT 61.336 63.158 16.62 10.89 34.37 4.18
5752 6220 1.271543 TGTGGGAAGCCTCACTGATTG 60.272 52.381 0.00 0.00 35.15 2.67
5833 6305 1.206578 CGTGCCATGTCAAACGTCC 59.793 57.895 0.00 0.00 0.00 4.79
5845 6317 1.061131 CAAACGTCCGAGCACATCATC 59.939 52.381 0.00 0.00 0.00 2.92
5893 6365 5.398603 TGTTGAAGGCTCTTTTGTTTTCA 57.601 34.783 0.00 0.00 0.00 2.69
5915 6387 0.762461 CTTTTGTTGGGGCCTTGGGA 60.762 55.000 0.84 0.00 0.00 4.37
5920 6393 1.861656 TTGGGGCCTTGGGAGGATT 60.862 57.895 0.84 0.00 46.74 3.01
5955 6428 4.328983 GCTCAACGTTTCGAATCCTGATAA 59.671 41.667 0.00 0.00 0.00 1.75
5973 6448 6.090223 CCTGATAACATGGTTTTTAAAACCGC 59.910 38.462 27.74 11.28 43.15 5.68
6009 7463 4.156556 GCACTCAAGCATCTTTGACCATAA 59.843 41.667 0.00 0.00 33.71 1.90
6010 7464 5.335897 GCACTCAAGCATCTTTGACCATAAA 60.336 40.000 0.00 0.00 33.71 1.40
6065 7551 3.373565 GTGCCCGGGAGCCAAAAG 61.374 66.667 29.31 0.00 0.00 2.27
6124 7610 6.603095 AGTTTACTTTGCTTGCTAGAAATCG 58.397 36.000 0.00 0.00 0.00 3.34
6127 7613 2.489938 TTGCTTGCTAGAAATCGGGT 57.510 45.000 0.00 0.00 0.00 5.28
6135 7621 2.356135 CTAGAAATCGGGTGTTGTGGG 58.644 52.381 0.00 0.00 0.00 4.61
6171 7657 0.811616 GCGTGCATGTCCCCTCTTAG 60.812 60.000 7.93 0.00 0.00 2.18
6182 7668 1.209504 CCCCTCTTAGCAATCGACCAA 59.790 52.381 0.00 0.00 0.00 3.67
6203 7689 2.376518 ACTCCCTTTTCTCCTGCATTGA 59.623 45.455 0.00 0.00 0.00 2.57
6215 7701 4.454678 TCCTGCATTGATCCAATCTGTAC 58.545 43.478 0.00 0.00 31.05 2.90
6226 7712 1.124297 CAATCTGTACGTGCGTGTGTC 59.876 52.381 7.55 0.00 0.00 3.67
6239 7725 2.599848 GCGTGTGTCATGTGTTCACTTC 60.600 50.000 4.59 0.00 33.82 3.01
6258 7744 2.496817 GCCCTCAGCTAGTCACCG 59.503 66.667 0.00 0.00 38.99 4.94
6262 7748 1.599606 CCTCAGCTAGTCACCGCAGT 61.600 60.000 0.00 0.00 0.00 4.40
6265 7751 1.071605 CAGCTAGTCACCGCAGTTTC 58.928 55.000 0.00 0.00 0.00 2.78
6274 7760 0.685097 ACCGCAGTTTCTCTTGCCTA 59.315 50.000 0.00 0.00 0.00 3.93
6291 7777 1.270305 CCTAGCCCATACGTCCATGTG 60.270 57.143 0.00 0.00 0.00 3.21
6293 7779 2.534019 GCCCATACGTCCATGTGCG 61.534 63.158 0.00 4.87 0.00 5.34
6296 7782 0.739462 CCATACGTCCATGTGCGTGT 60.739 55.000 18.10 11.09 41.68 4.49
6304 7790 0.036952 CCATGTGCGTGTCCTCTTCT 60.037 55.000 0.00 0.00 0.00 2.85
6307 7793 1.444553 GTGCGTGTCCTCTTCTCGG 60.445 63.158 0.00 0.00 0.00 4.63
6324 7810 5.801350 TCTCGGTTCTTGCATATCTTTTG 57.199 39.130 0.00 0.00 0.00 2.44
6330 7817 6.260936 CGGTTCTTGCATATCTTTTGATACCT 59.739 38.462 0.00 0.00 43.41 3.08
6342 7829 7.114754 ATCTTTTGATACCTTGCAGATCAAGA 58.885 34.615 6.25 9.45 44.78 3.02
6352 7839 1.695597 AGATCAAGAGGGCAGGGGG 60.696 63.158 0.00 0.00 0.00 5.40
6383 7875 1.383523 TGCATTTGTTGTGTCCGTCA 58.616 45.000 0.00 0.00 0.00 4.35
6391 7883 0.462937 TTGTGTCCGTCAGTTGGTGG 60.463 55.000 0.00 0.00 0.00 4.61
6427 7919 5.706916 CAGTGTTACATACTACCGTTGAGT 58.293 41.667 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 7.872993 CCTTATTTCATCTTCAGATAGCCGTTA 59.127 37.037 0.00 0.00 32.63 3.18
19 20 6.708054 CCTTATTTCATCTTCAGATAGCCGTT 59.292 38.462 0.00 0.00 32.63 4.44
20 21 6.183361 ACCTTATTTCATCTTCAGATAGCCGT 60.183 38.462 0.00 0.00 32.63 5.68
49 50 0.107643 GGGATAGAAGGGCAGAGTGC 59.892 60.000 0.00 0.00 44.08 4.40
60 62 0.613853 CTATCGGGCGGGGGATAGAA 60.614 60.000 2.66 0.00 42.99 2.10
74 76 2.723314 CGATGAGCTAGACGCACTATCG 60.723 54.545 0.00 0.00 42.61 2.92
75 77 2.480802 TCGATGAGCTAGACGCACTATC 59.519 50.000 0.00 0.00 42.61 2.08
76 78 2.495084 TCGATGAGCTAGACGCACTAT 58.505 47.619 0.00 0.00 42.61 2.12
77 79 1.949465 TCGATGAGCTAGACGCACTA 58.051 50.000 0.00 0.00 42.61 2.74
78 80 1.064803 CTTCGATGAGCTAGACGCACT 59.935 52.381 0.00 0.00 42.61 4.40
80 82 0.382158 CCTTCGATGAGCTAGACGCA 59.618 55.000 0.00 0.00 42.61 5.24
81 83 0.318275 CCCTTCGATGAGCTAGACGC 60.318 60.000 0.00 0.00 39.57 5.19
82 84 0.318275 GCCCTTCGATGAGCTAGACG 60.318 60.000 0.00 0.00 0.00 4.18
83 85 0.747255 TGCCCTTCGATGAGCTAGAC 59.253 55.000 6.38 0.00 0.00 2.59
84 86 0.747255 GTGCCCTTCGATGAGCTAGA 59.253 55.000 6.38 0.00 0.00 2.43
85 87 0.596083 CGTGCCCTTCGATGAGCTAG 60.596 60.000 6.38 0.00 0.00 3.42
86 88 1.320344 ACGTGCCCTTCGATGAGCTA 61.320 55.000 6.38 0.00 0.00 3.32
87 89 2.185350 CGTGCCCTTCGATGAGCT 59.815 61.111 6.38 0.00 0.00 4.09
88 90 2.125512 ACGTGCCCTTCGATGAGC 60.126 61.111 0.00 0.00 0.00 4.26
89 91 1.078759 GACACGTGCCCTTCGATGAG 61.079 60.000 17.22 0.00 0.00 2.90
90 92 1.080093 GACACGTGCCCTTCGATGA 60.080 57.895 17.22 0.00 0.00 2.92
91 93 1.078759 GAGACACGTGCCCTTCGATG 61.079 60.000 17.22 0.00 0.00 3.84
92 94 1.215647 GAGACACGTGCCCTTCGAT 59.784 57.895 17.22 0.00 0.00 3.59
93 95 2.649034 GAGACACGTGCCCTTCGA 59.351 61.111 17.22 0.00 0.00 3.71
94 96 2.432628 GGAGACACGTGCCCTTCG 60.433 66.667 17.22 0.00 0.00 3.79
95 97 2.432628 CGGAGACACGTGCCCTTC 60.433 66.667 17.22 11.01 0.00 3.46
96 98 4.003788 CCGGAGACACGTGCCCTT 62.004 66.667 17.22 0.00 0.00 3.95
101 103 1.517257 GATCTGCCGGAGACACGTG 60.517 63.158 15.48 15.48 31.75 4.49
102 104 1.658686 GAGATCTGCCGGAGACACGT 61.659 60.000 5.05 0.00 31.75 4.49
113 125 4.022242 CCAATTGAATCCCATGAGATCTGC 60.022 45.833 7.12 0.00 0.00 4.26
121 133 2.542597 CAACGCCAATTGAATCCCATG 58.457 47.619 7.12 0.00 0.00 3.66
134 146 2.280524 CACGGAAGACCAACGCCA 60.281 61.111 0.00 0.00 35.59 5.69
137 149 0.246635 AGATCCACGGAAGACCAACG 59.753 55.000 0.00 0.00 35.59 4.10
148 160 5.545588 AGATTGTATCCATGAAGATCCACG 58.454 41.667 0.00 0.00 0.00 4.94
187 199 2.094894 GGATGCAATCTGAAGACACGTG 59.905 50.000 15.48 15.48 44.71 4.49
188 200 2.027745 AGGATGCAATCTGAAGACACGT 60.028 45.455 0.00 0.00 44.71 4.49
189 201 2.625737 AGGATGCAATCTGAAGACACG 58.374 47.619 0.00 0.00 44.71 4.49
190 202 4.260170 AGAAGGATGCAATCTGAAGACAC 58.740 43.478 0.00 0.00 44.71 3.67
198 210 7.018487 AGCATAGATTAGAAGGATGCAATCT 57.982 36.000 7.79 0.00 44.71 2.40
199 211 7.607223 AGAAGCATAGATTAGAAGGATGCAATC 59.393 37.037 7.79 5.65 44.26 2.67
200 212 7.460071 AGAAGCATAGATTAGAAGGATGCAAT 58.540 34.615 7.79 0.00 44.26 3.56
213 225 9.404848 TCTCATTGATGAAAAGAAGCATAGATT 57.595 29.630 0.00 0.00 36.18 2.40
234 246 5.016051 ACGTAGCAGAACATCAATCTCAT 57.984 39.130 0.00 0.00 0.00 2.90
237 249 3.935203 CCAACGTAGCAGAACATCAATCT 59.065 43.478 0.00 0.00 0.00 2.40
248 260 1.468520 CCCAAATGACCAACGTAGCAG 59.531 52.381 0.00 0.00 0.00 4.24
253 265 0.476771 AGACCCCAAATGACCAACGT 59.523 50.000 0.00 0.00 0.00 3.99
287 299 3.007614 ACTTGTTGTAGTAGCCGGTCAAT 59.992 43.478 1.90 0.00 0.00 2.57
293 305 4.319261 GGACAAAACTTGTTGTAGTAGCCG 60.319 45.833 0.00 0.00 45.52 5.52
324 336 1.424302 CATTGCCTGATCCTCCCTCAT 59.576 52.381 0.00 0.00 0.00 2.90
334 346 2.117156 GCTGCCGTCATTGCCTGAT 61.117 57.895 0.00 0.00 35.97 2.90
370 384 5.449107 TCTAGCAACGACTACAAACTCTT 57.551 39.130 0.00 0.00 0.00 2.85
375 389 4.219944 AGACCATCTAGCAACGACTACAAA 59.780 41.667 0.00 0.00 0.00 2.83
381 395 3.318275 TCCATAGACCATCTAGCAACGAC 59.682 47.826 0.00 0.00 31.67 4.34
413 427 7.162761 TGATAGTACAAGGAACATCGGAAAAA 58.837 34.615 0.00 0.00 0.00 1.94
418 432 5.692204 GTCATGATAGTACAAGGAACATCGG 59.308 44.000 0.00 0.00 0.00 4.18
419 433 6.273071 TGTCATGATAGTACAAGGAACATCG 58.727 40.000 0.00 0.00 0.00 3.84
420 434 8.492673 TTTGTCATGATAGTACAAGGAACATC 57.507 34.615 0.00 0.00 34.80 3.06
421 435 8.896744 CATTTGTCATGATAGTACAAGGAACAT 58.103 33.333 0.00 0.00 34.80 2.71
473 496 1.886542 GTGTACAAAGCCTCTTTGGGG 59.113 52.381 19.55 0.37 36.00 4.96
474 497 2.863809 AGTGTACAAAGCCTCTTTGGG 58.136 47.619 19.55 0.97 36.00 4.12
475 498 4.918810 AAAGTGTACAAAGCCTCTTTGG 57.081 40.909 19.55 5.96 39.35 3.28
476 499 5.163561 TGGAAAAGTGTACAAAGCCTCTTTG 60.164 40.000 15.40 15.40 35.64 2.77
478 501 4.532834 TGGAAAAGTGTACAAAGCCTCTT 58.467 39.130 0.00 0.00 0.00 2.85
479 502 4.164843 TGGAAAAGTGTACAAAGCCTCT 57.835 40.909 0.00 0.00 0.00 3.69
480 503 5.453567 AATGGAAAAGTGTACAAAGCCTC 57.546 39.130 0.00 0.00 0.00 4.70
481 504 5.600696 CAAATGGAAAAGTGTACAAAGCCT 58.399 37.500 0.00 0.00 0.00 4.58
482 505 4.211164 GCAAATGGAAAAGTGTACAAAGCC 59.789 41.667 0.00 0.00 0.00 4.35
484 507 4.749598 GGGCAAATGGAAAAGTGTACAAAG 59.250 41.667 0.00 0.00 0.00 2.77
485 508 4.407296 AGGGCAAATGGAAAAGTGTACAAA 59.593 37.500 0.00 0.00 0.00 2.83
486 509 3.964031 AGGGCAAATGGAAAAGTGTACAA 59.036 39.130 0.00 0.00 0.00 2.41
487 510 3.320541 CAGGGCAAATGGAAAAGTGTACA 59.679 43.478 0.00 0.00 0.00 2.90
488 511 3.572255 TCAGGGCAAATGGAAAAGTGTAC 59.428 43.478 0.00 0.00 0.00 2.90
489 512 3.838565 TCAGGGCAAATGGAAAAGTGTA 58.161 40.909 0.00 0.00 0.00 2.90
490 513 2.676748 TCAGGGCAAATGGAAAAGTGT 58.323 42.857 0.00 0.00 0.00 3.55
492 515 4.980339 ATTTCAGGGCAAATGGAAAAGT 57.020 36.364 0.00 0.00 33.47 2.66
493 516 6.408869 ACATATTTCAGGGCAAATGGAAAAG 58.591 36.000 0.00 0.00 33.47 2.27
494 517 6.013898 TGACATATTTCAGGGCAAATGGAAAA 60.014 34.615 0.00 0.00 33.47 2.29
495 518 5.483231 TGACATATTTCAGGGCAAATGGAAA 59.517 36.000 0.00 0.00 34.17 3.13
496 519 5.022122 TGACATATTTCAGGGCAAATGGAA 58.978 37.500 0.00 0.00 0.00 3.53
497 520 4.402155 GTGACATATTTCAGGGCAAATGGA 59.598 41.667 0.00 0.00 0.00 3.41
498 521 4.441913 GGTGACATATTTCAGGGCAAATGG 60.442 45.833 0.00 0.00 0.00 3.16
499 522 4.441913 GGGTGACATATTTCAGGGCAAATG 60.442 45.833 0.00 0.00 0.00 2.32
500 523 3.706086 GGGTGACATATTTCAGGGCAAAT 59.294 43.478 0.00 0.00 0.00 2.32
501 524 3.096092 GGGTGACATATTTCAGGGCAAA 58.904 45.455 0.00 0.00 0.00 3.68
502 525 2.733956 GGGTGACATATTTCAGGGCAA 58.266 47.619 0.00 0.00 0.00 4.52
503 526 1.408127 CGGGTGACATATTTCAGGGCA 60.408 52.381 0.00 0.00 0.00 5.36
504 527 1.308998 CGGGTGACATATTTCAGGGC 58.691 55.000 0.00 0.00 0.00 5.19
524 554 1.440938 CGGCTAGAGAGGACGAGGTG 61.441 65.000 0.00 0.00 0.00 4.00
529 559 1.950828 TCTAACGGCTAGAGAGGACG 58.049 55.000 0.00 0.00 32.56 4.79
549 579 5.476091 ACTTTAAATCAAAATTCGGCCCA 57.524 34.783 0.00 0.00 0.00 5.36
552 858 7.068955 CCACAAACTTTAAATCAAAATTCGGC 58.931 34.615 0.00 0.00 0.00 5.54
581 887 6.003950 AGTTTACACACAAGGCACATCTATT 58.996 36.000 0.00 0.00 0.00 1.73
582 888 5.560724 AGTTTACACACAAGGCACATCTAT 58.439 37.500 0.00 0.00 0.00 1.98
583 889 4.968259 AGTTTACACACAAGGCACATCTA 58.032 39.130 0.00 0.00 0.00 1.98
855 1163 7.442656 GGCTAGTTAATATAGAAAGGAGTGCA 58.557 38.462 0.00 0.00 0.00 4.57
909 1217 2.587322 GATCACCATTCCCGACGGCA 62.587 60.000 8.86 0.00 0.00 5.69
1102 1411 2.173782 TGCCTACCAAGAAACCAAGACA 59.826 45.455 0.00 0.00 0.00 3.41
1103 1412 2.858745 TGCCTACCAAGAAACCAAGAC 58.141 47.619 0.00 0.00 0.00 3.01
1181 1496 1.826096 GTTCCAGGAGGTGTAGAGGTC 59.174 57.143 0.00 0.00 35.89 3.85
1314 1629 6.395629 TCAGTAAACGATTTAGGACAAGAGG 58.604 40.000 0.00 0.00 0.00 3.69
1329 1644 7.413438 CCCTCTTCAATTCTTCATCAGTAAACG 60.413 40.741 0.00 0.00 0.00 3.60
1377 1729 4.440127 CGCTGCCATGCCAAACCC 62.440 66.667 0.00 0.00 0.00 4.11
1390 1742 0.883833 ATTTTCCCTGCAAGACGCTG 59.116 50.000 0.00 0.00 43.06 5.18
1501 1854 6.610830 AGGAGAACTTTTTGTCCCAGAAATA 58.389 36.000 0.00 0.00 44.79 1.40
1553 1906 6.095377 CAGGGTTGCATAAATCTCTGTTTTC 58.905 40.000 0.00 0.00 0.00 2.29
1570 1923 1.876156 GTCAGTTTCAGAGCAGGGTTG 59.124 52.381 0.00 0.00 0.00 3.77
1591 1944 5.058490 AGCTTAGCCAAACAAAACTACGTA 58.942 37.500 0.00 0.00 0.00 3.57
1592 1945 3.881089 AGCTTAGCCAAACAAAACTACGT 59.119 39.130 0.00 0.00 0.00 3.57
1593 1946 4.483476 AGCTTAGCCAAACAAAACTACG 57.517 40.909 0.00 0.00 0.00 3.51
1594 1947 6.019075 CCAAAAGCTTAGCCAAACAAAACTAC 60.019 38.462 0.00 0.00 0.00 2.73
1664 2017 8.972127 ACATCTTGATAGTCTAGAGCAACTTTA 58.028 33.333 0.00 0.00 32.23 1.85
1674 2027 9.114952 TCTGTCAGTAACATCTTGATAGTCTAG 57.885 37.037 0.00 0.00 37.23 2.43
1728 2081 4.879197 AAAAGCAGAATGAAGGGGAAAG 57.121 40.909 0.00 0.00 39.69 2.62
1738 2091 8.184192 ACGGTAAAATCAGATAAAAGCAGAATG 58.816 33.333 0.00 0.00 40.87 2.67
1747 2100 8.155821 TGACAACAACGGTAAAATCAGATAAA 57.844 30.769 0.00 0.00 0.00 1.40
1802 2155 1.279271 GGAAGCAGGGTGTATCAGTGT 59.721 52.381 0.00 0.00 0.00 3.55
1811 2164 1.281925 ATAGGGGTGGAAGCAGGGTG 61.282 60.000 0.00 0.00 34.77 4.61
1825 2178 3.259123 AGAAAGGTTGCTGCAAAATAGGG 59.741 43.478 17.80 0.00 0.00 3.53
1923 2276 7.615403 AGAGCAATGAAGATTTGTACTACTGA 58.385 34.615 0.00 0.00 0.00 3.41
2079 2432 5.969423 ACTTGCAAATGGTAATGAAGATGG 58.031 37.500 0.00 0.00 0.00 3.51
2165 2518 5.189736 GGATATAGAGTATGGGATGTTGCCA 59.810 44.000 0.00 0.00 43.78 4.92
2397 2752 9.793259 ATGATGTACTCTAAAAAGGACAAAGAA 57.207 29.630 0.00 0.00 43.24 2.52
2402 2757 8.375506 AGTGAATGATGTACTCTAAAAAGGACA 58.624 33.333 0.00 0.00 44.12 4.02
2494 2859 9.263538 GATAATTAAATTCATCTTTGGCATGCA 57.736 29.630 21.36 2.54 0.00 3.96
2496 2861 9.767228 TGGATAATTAAATTCATCTTTGGCATG 57.233 29.630 0.00 0.00 0.00 4.06
2544 2909 4.395625 AGTGCCGATGATCATCATTTCAT 58.604 39.130 30.13 12.13 37.20 2.57
2855 3222 1.443802 GCTTAGGTTGCTGAGGACAC 58.556 55.000 0.00 0.00 0.00 3.67
2949 3316 4.948608 TTAAAGGCGCAATTATCGAACA 57.051 36.364 10.83 0.00 0.00 3.18
3212 3579 2.015587 GTCGGTACTTGAGGACGATCT 58.984 52.381 0.00 0.00 35.90 2.75
3215 3582 1.267806 GTTGTCGGTACTTGAGGACGA 59.732 52.381 0.00 0.00 32.17 4.20
3260 3627 4.800023 TGTCACCTTCTTCGATAGGGATA 58.200 43.478 11.91 4.25 35.79 2.59
3272 3639 2.856222 CCTTGCTTCTTGTCACCTTCT 58.144 47.619 0.00 0.00 0.00 2.85
3612 3983 9.892130 CAGACAGAATCTAGTAATTTTTACCCT 57.108 33.333 0.00 0.00 35.15 4.34
3613 3984 9.110502 CCAGACAGAATCTAGTAATTTTTACCC 57.889 37.037 0.00 0.00 35.15 3.69
3628 4040 6.817765 TTGAATTACCAACCAGACAGAATC 57.182 37.500 0.00 0.00 0.00 2.52
3686 4098 5.416083 TGGATGTTGGTGTTAGAATCTACG 58.584 41.667 0.00 0.00 0.00 3.51
3700 4112 3.199508 AGGAGAGTCTTGATGGATGTTGG 59.800 47.826 0.00 0.00 0.00 3.77
3812 4224 1.326548 GTATAAGAAGTTGCCGCACCG 59.673 52.381 0.00 0.00 0.00 4.94
4012 4446 7.831193 AGTTCTAGTGTATGATGAAGCCAAAAT 59.169 33.333 0.00 0.00 0.00 1.82
4013 4447 7.119699 CAGTTCTAGTGTATGATGAAGCCAAAA 59.880 37.037 0.00 0.00 0.00 2.44
4134 4568 2.790433 TGCCTAAGCCGAGAAATGTTT 58.210 42.857 0.00 0.00 38.69 2.83
4155 4589 0.522626 TAAGCGACACGATGTTCGGA 59.477 50.000 1.69 0.00 45.59 4.55
4247 4681 2.354259 CCTCATCAGAGAAGTGCAACC 58.646 52.381 0.00 0.00 44.98 3.77
4291 4725 3.077519 GCGCTATCCTCACACGGGT 62.078 63.158 0.00 0.00 0.00 5.28
4343 4777 7.519032 AGGCACTAGATTCAGTAGATAGTTC 57.481 40.000 0.00 0.00 36.02 3.01
4346 4780 7.865385 GTGAAAGGCACTAGATTCAGTAGATAG 59.135 40.741 0.00 0.00 44.27 2.08
4347 4781 7.717568 GTGAAAGGCACTAGATTCAGTAGATA 58.282 38.462 0.00 0.00 44.27 1.98
4401 4836 4.574828 ACAAAGGTTAGCAGTACACTGTTG 59.425 41.667 10.87 7.83 45.45 3.33
4537 4972 1.089920 CAGGATTTGGTGAGAAGGCG 58.910 55.000 0.00 0.00 0.00 5.52
4651 5089 6.427547 ACCTGGCAAAACATAACAAAATGATG 59.572 34.615 0.00 0.00 0.00 3.07
4683 5121 1.302033 AAGTGAGCCAAGCACCTCG 60.302 57.895 0.00 0.00 36.95 4.63
4743 5181 3.881795 ACTGTACACGTCACTCTTTACG 58.118 45.455 0.00 0.00 44.47 3.18
4885 5328 5.851720 TGCACAACACAATGGTTCAAATAT 58.148 33.333 0.00 0.00 0.00 1.28
4886 5329 5.068329 TCTGCACAACACAATGGTTCAAATA 59.932 36.000 0.00 0.00 0.00 1.40
5030 5473 0.737019 TTATGTCGGCGAAACGGGAC 60.737 55.000 12.92 0.00 0.00 4.46
5141 5584 5.943706 ATGATCAGATTGCTACTGAATGC 57.056 39.130 0.09 6.03 45.44 3.56
5148 5591 3.817647 GGGGTGAATGATCAGATTGCTAC 59.182 47.826 0.09 0.00 35.88 3.58
5246 5711 4.339530 GGGCAGACAGAAAATTTAGGATCC 59.660 45.833 2.48 2.48 0.00 3.36
5251 5716 5.474876 ACAGAAGGGCAGACAGAAAATTTAG 59.525 40.000 0.00 0.00 0.00 1.85
5502 5970 6.399639 AAATGGAGTAAAAACCGAACACAT 57.600 33.333 0.00 0.00 0.00 3.21
5527 5995 4.041567 TGAAGCTCCTGAAATACCAGACAA 59.958 41.667 0.00 0.00 36.29 3.18
5691 6159 2.807045 CGTCTGACAGAGGCGTGC 60.807 66.667 11.93 0.00 45.17 5.34
5714 6182 3.594775 CTGGCAAGGCACACGCAA 61.595 61.111 0.00 0.00 41.24 4.85
5833 6305 3.005554 ACTCAAAAGGATGATGTGCTCG 58.994 45.455 0.00 0.00 0.00 5.03
5845 6317 6.150976 TCACCAATATACAAGCACTCAAAAGG 59.849 38.462 0.00 0.00 0.00 3.11
5893 6365 1.699083 CCAAGGCCCCAACAAAAGAAT 59.301 47.619 0.00 0.00 0.00 2.40
5955 6428 3.459145 GGTGCGGTTTTAAAAACCATGT 58.541 40.909 10.35 0.00 40.28 3.21
5973 6448 2.048222 AGTGCGTGATGTCCGGTG 60.048 61.111 0.00 0.00 0.00 4.94
6107 7593 2.487762 CACCCGATTTCTAGCAAGCAAA 59.512 45.455 0.00 0.00 0.00 3.68
6108 7594 2.083774 CACCCGATTTCTAGCAAGCAA 58.916 47.619 0.00 0.00 0.00 3.91
6113 7599 2.422597 CACAACACCCGATTTCTAGCA 58.577 47.619 0.00 0.00 0.00 3.49
6124 7610 4.678743 GGGGAGCCCACAACACCC 62.679 72.222 8.02 0.00 44.65 4.61
6135 7621 2.115291 GCAAGACAATCCGGGGAGC 61.115 63.158 0.00 0.00 0.00 4.70
6142 7628 0.523072 ACATGCACGCAAGACAATCC 59.477 50.000 0.63 0.00 43.62 3.01
6171 7657 1.534729 AAAGGGAGTTGGTCGATTGC 58.465 50.000 0.00 0.00 0.00 3.56
6182 7668 2.376518 TCAATGCAGGAGAAAAGGGAGT 59.623 45.455 0.00 0.00 0.00 3.85
6203 7689 1.067142 ACACGCACGTACAGATTGGAT 60.067 47.619 0.00 0.00 0.00 3.41
6215 7701 0.383002 GAACACATGACACACGCACG 60.383 55.000 0.00 0.00 0.00 5.34
6226 7712 0.606401 AGGGCCGAAGTGAACACATG 60.606 55.000 7.68 0.00 0.00 3.21
6239 7725 2.496817 GTGACTAGCTGAGGGCCG 59.503 66.667 0.00 0.00 43.05 6.13
6258 7744 1.090728 GGCTAGGCAAGAGAAACTGC 58.909 55.000 12.16 0.00 0.00 4.40
6262 7748 2.158957 CGTATGGGCTAGGCAAGAGAAA 60.159 50.000 19.14 0.00 0.00 2.52
6265 7751 0.753262 ACGTATGGGCTAGGCAAGAG 59.247 55.000 19.14 7.47 0.00 2.85
6291 7777 0.733223 GAACCGAGAAGAGGACACGC 60.733 60.000 0.00 0.00 0.00 5.34
6293 7779 2.678324 CAAGAACCGAGAAGAGGACAC 58.322 52.381 0.00 0.00 0.00 3.67
6296 7782 1.338107 TGCAAGAACCGAGAAGAGGA 58.662 50.000 0.00 0.00 0.00 3.71
6304 7790 6.260050 GGTATCAAAAGATATGCAAGAACCGA 59.740 38.462 0.00 0.00 0.00 4.69
6307 7793 7.433425 GCAAGGTATCAAAAGATATGCAAGAAC 59.567 37.037 0.00 0.00 0.00 3.01
6330 7817 0.034767 CCTGCCCTCTTGATCTGCAA 60.035 55.000 0.00 0.00 34.73 4.08
6342 7829 2.091283 AACACTTTCCCCCTGCCCT 61.091 57.895 0.00 0.00 0.00 5.19
6346 7833 1.039856 CAACCAACACTTTCCCCCTG 58.960 55.000 0.00 0.00 0.00 4.45
6352 7839 4.391523 ACAACAAATGCAACCAACACTTTC 59.608 37.500 0.00 0.00 0.00 2.62
6383 7875 1.109323 GCAAAGCAGGACCACCAACT 61.109 55.000 0.00 0.00 38.94 3.16
6405 7897 5.709164 AGACTCAACGGTAGTATGTAACACT 59.291 40.000 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.