Multiple sequence alignment - TraesCS2B01G572800

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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 TraesCS2B01G572800 chr2B 100.000 4626 0 0 1 4626 762506917 762502292 0.000000e+00 8543
1 TraesCS2B01G572800 chr2B 88.276 290 19 5 1944 2232 762504815 762504540 2.670000e-87 333
2 TraesCS2B01G572800 chr2B 88.276 290 19 5 2103 2378 762504974 762504686 2.670000e-87 333
3 TraesCS2B01G572800 chr2B 77.419 620 78 43 8 591 762789765 762789172 3.480000e-81 313
4 TraesCS2B01G572800 chr2B 79.638 442 72 13 7 431 762915695 762915255 7.520000e-78 302
5 TraesCS2B01G572800 chr2B 78.440 436 69 17 1 416 762800631 762800201 1.280000e-65 261
6 TraesCS2B01G572800 chr2B 77.108 498 70 25 9 472 762885311 762884824 9.940000e-62 248
7 TraesCS2B01G572800 chr2B 82.609 253 32 7 9 250 762793611 762793360 3.630000e-51 213
8 TraesCS2B01G572800 chr2B 89.855 138 14 0 1944 2081 762504669 762504532 1.320000e-40 178
9 TraesCS2B01G572800 chr2B 89.855 138 14 0 2249 2386 762504974 762504837 1.320000e-40 178
10 TraesCS2B01G572800 chr2D 91.439 3691 198 54 1 3629 621551095 621547461 0.000000e+00 4957
11 TraesCS2B01G572800 chr2D 91.086 359 25 4 3679 4036 621547163 621546811 3.240000e-131 479
12 TraesCS2B01G572800 chr2D 92.308 234 16 2 3 235 499308807 499309039 9.590000e-87 331
13 TraesCS2B01G572800 chr2D 86.120 317 22 6 1917 2232 621548998 621548703 5.770000e-84 322
14 TraesCS2B01G572800 chr2D 84.548 343 28 7 420 762 499309065 499309382 2.690000e-82 316
15 TraesCS2B01G572800 chr2D 85.449 323 22 11 2079 2378 621549169 621548849 3.480000e-81 313
16 TraesCS2B01G572800 chr2D 88.406 138 16 0 1944 2081 621548832 621548695 2.860000e-37 167
17 TraesCS2B01G572800 chr2D 91.379 116 8 2 1956 2070 166797521 166797635 1.720000e-34 158
18 TraesCS2B01G572800 chr2D 89.167 120 11 2 2262 2380 166797522 166797640 1.040000e-31 148
19 TraesCS2B01G572800 chr2A 89.210 3698 223 58 916 4561 753255171 753251598 0.000000e+00 4457
20 TraesCS2B01G572800 chr2A 91.514 766 42 5 1 762 753255966 753255220 0.000000e+00 1033
21 TraesCS2B01G572800 chr2A 79.123 479 68 19 1 460 753402732 753402267 7.520000e-78 302
22 TraesCS2B01G572800 chr2A 88.971 136 15 0 1946 2081 753253866 753253731 7.960000e-38 169
23 TraesCS2B01G572800 chr2A 86.822 129 14 3 2257 2383 515483544 515483417 1.740000e-29 141
24 TraesCS2B01G572800 chr2A 88.034 117 12 2 2117 2232 515483537 515483422 2.240000e-28 137
25 TraesCS2B01G572800 chr4A 86.589 343 30 6 420 762 153777221 153776895 9.460000e-97 364
26 TraesCS2B01G572800 chr4A 91.525 236 18 2 1 235 153777481 153777247 1.610000e-84 324
27 TraesCS2B01G572800 chr1D 86.034 179 20 5 2281 2458 415318184 415318358 2.200000e-43 187
28 TraesCS2B01G572800 chr1B 83.824 204 26 7 2257 2458 561622882 561623080 2.200000e-43 187
29 TraesCS2B01G572800 chr3B 89.600 125 11 2 2109 2232 754027332 754027455 1.720000e-34 158
30 TraesCS2B01G572800 chr3B 90.164 122 10 2 1950 2070 754027332 754027452 1.720000e-34 158
31 TraesCS2B01G572800 chr3A 85.366 123 16 2 2111 2232 136519551 136519672 4.860000e-25 126
32 TraesCS2B01G572800 chr5B 85.321 109 15 1 2350 2458 594258900 594258793 1.360000e-20 111
33 TraesCS2B01G572800 chr1A 86.598 97 11 2 2126 2221 6019624 6019719 6.330000e-19 106


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 TraesCS2B01G572800 chr2B 762502292 762506917 4625 True 1913.000000 8543 91.252400 1 4626 5 chr2B.!!$R4 4625
1 TraesCS2B01G572800 chr2B 762789172 762793611 4439 True 263.000000 313 80.014000 8 591 2 chr2B.!!$R5 583
2 TraesCS2B01G572800 chr2D 621546811 621551095 4284 True 1247.600000 4957 88.500000 1 4036 5 chr2D.!!$R1 4035
3 TraesCS2B01G572800 chr2D 499308807 499309382 575 False 323.500000 331 88.428000 3 762 2 chr2D.!!$F2 759
4 TraesCS2B01G572800 chr2A 753251598 753255966 4368 True 1886.333333 4457 89.898333 1 4561 3 chr2A.!!$R3 4560
5 TraesCS2B01G572800 chr4A 153776895 153777481 586 True 344.000000 364 89.057000 1 762 2 chr4A.!!$R1 761

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
186 198 0.103572 TACTATTCGAAGCCGGGCAC 59.896 55.0 23.09 13.62 36.24 5.01 F
762 841 0.530288 TGGCTCGTCGATGATGTTCA 59.470 50.0 7.99 1.94 0.00 3.18 F
1360 3245 0.753262 ATCTCGAGGGGATTGGTTCG 59.247 55.0 13.56 0.00 34.56 3.95 F
2443 4934 0.403304 ATGGCCATACCCAGGATCCA 60.403 55.0 19.18 0.00 38.50 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1309 3193 0.041833 TGAAGGTGGGAGAGAGGAGG 59.958 60.0 0.00 0.0 0.00 4.30 R
2039 4522 0.112995 AAGGCAATGACAAGGCAGGA 59.887 50.0 7.42 0.0 0.00 3.86 R
3157 5650 0.889186 TTTCTCGGCAAGTGCTTCCC 60.889 55.0 2.85 0.0 41.70 3.97 R
4037 6799 0.107410 TGGTACATCCAATGTCGGGC 60.107 55.0 0.00 0.0 44.12 6.13 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
41 42 2.054799 AGCCAGGAAGGTAACAACAGA 58.945 47.619 0.00 0.00 40.61 3.41
89 90 9.646427 AAATATATTTCGTAGCTGAATCCTCTC 57.354 33.333 4.81 0.00 0.00 3.20
186 198 0.103572 TACTATTCGAAGCCGGGCAC 59.896 55.000 23.09 13.62 36.24 5.01
261 273 5.106673 GGTACAAAAGCATACCTGAAGTCAC 60.107 44.000 0.00 0.00 38.28 3.67
346 392 5.186021 ACTTATCTGACTCTTGGACATTCGT 59.814 40.000 0.00 0.00 0.00 3.85
547 602 4.073293 ACGTGACCTGAATCTCAGTTTT 57.927 40.909 3.15 0.00 42.80 2.43
674 753 1.291877 GCCGTCTCAATTCGTGTGCT 61.292 55.000 0.00 0.00 0.00 4.40
731 810 5.116180 TCCGATTAACTGTCATGTGAATCC 58.884 41.667 0.00 0.00 35.41 3.01
762 841 0.530288 TGGCTCGTCGATGATGTTCA 59.470 50.000 7.99 1.94 0.00 3.18
763 842 1.136891 TGGCTCGTCGATGATGTTCAT 59.863 47.619 7.99 0.00 40.34 2.57
769 859 3.546271 TCGTCGATGATGTTCATTTCGTC 59.454 43.478 2.39 10.18 37.20 4.20
778 868 9.643652 GATGATGTTCATTTCGTCTTATCTTTC 57.356 33.333 0.00 0.00 37.20 2.62
974 2600 1.095600 CACAGGCTGACGAGCTACTA 58.904 55.000 23.66 0.00 45.44 1.82
1030 2656 1.518302 GTCCGCTTCCTCTTCTCCC 59.482 63.158 0.00 0.00 0.00 4.30
1285 3169 1.669115 CCCGTCTCCTGCAACAGTG 60.669 63.158 0.00 0.00 0.00 3.66
1309 3193 3.400054 CCCTCCGTCCACCCCTTC 61.400 72.222 0.00 0.00 0.00 3.46
1310 3194 3.400054 CCTCCGTCCACCCCTTCC 61.400 72.222 0.00 0.00 0.00 3.46
1311 3195 2.284699 CTCCGTCCACCCCTTCCT 60.285 66.667 0.00 0.00 0.00 3.36
1312 3196 2.284405 TCCGTCCACCCCTTCCTC 60.284 66.667 0.00 0.00 0.00 3.71
1313 3197 3.400054 CCGTCCACCCCTTCCTCC 61.400 72.222 0.00 0.00 0.00 4.30
1336 3220 2.046892 CCCACCTTCACAGCCTCG 60.047 66.667 0.00 0.00 0.00 4.63
1343 3227 1.272781 CTTCACAGCCTCGTCGAATC 58.727 55.000 0.00 0.00 0.00 2.52
1358 3243 1.139058 CGAATCTCGAGGGGATTGGTT 59.861 52.381 13.56 0.00 43.74 3.67
1360 3245 0.753262 ATCTCGAGGGGATTGGTTCG 59.247 55.000 13.56 0.00 34.56 3.95
1384 3269 6.238211 CGTCGCTTCATCTAATTTTGAGGAAT 60.238 38.462 8.05 0.00 34.46 3.01
1538 3718 9.778741 AACTGTAACATTAGAAACTGATCTTGA 57.221 29.630 0.00 0.00 0.00 3.02
1549 3729 8.041829 AGAAACTGATCTTGATGAAATCTGTG 57.958 34.615 0.00 0.00 45.81 3.66
1691 4173 2.314852 TCAGTCAGGGAGGTAGGATTGA 59.685 50.000 0.00 0.00 0.00 2.57
1720 4202 6.830912 TGGGTGTTGGATATATTCTGAAGAG 58.169 40.000 0.00 0.00 0.00 2.85
1742 4224 2.239201 GCAAATTCTCGTGCCGTAAAC 58.761 47.619 0.00 0.00 34.58 2.01
1747 4229 1.990799 TCTCGTGCCGTAAACTGATG 58.009 50.000 0.00 0.00 0.00 3.07
1748 4230 1.271379 TCTCGTGCCGTAAACTGATGT 59.729 47.619 0.00 0.00 0.00 3.06
1766 4248 5.937187 TGATGTGTATTGGATTTTGTGTCG 58.063 37.500 0.00 0.00 0.00 4.35
1903 4385 2.009774 CCGAAGCAAGGAAGGTATGTG 58.990 52.381 0.00 0.00 0.00 3.21
1937 4419 4.195416 CCTTGATGCCTTCTCCTTAGTTC 58.805 47.826 0.00 0.00 0.00 3.01
1941 4423 1.977854 TGCCTTCTCCTTAGTTCAGCA 59.022 47.619 0.00 0.00 0.00 4.41
1942 4424 2.371841 TGCCTTCTCCTTAGTTCAGCAA 59.628 45.455 0.00 0.00 0.00 3.91
1943 4425 3.009473 TGCCTTCTCCTTAGTTCAGCAAT 59.991 43.478 0.00 0.00 0.00 3.56
1944 4426 4.013050 GCCTTCTCCTTAGTTCAGCAATT 58.987 43.478 0.00 0.00 0.00 2.32
1945 4427 5.186198 GCCTTCTCCTTAGTTCAGCAATTA 58.814 41.667 0.00 0.00 0.00 1.40
1946 4428 5.295540 GCCTTCTCCTTAGTTCAGCAATTAG 59.704 44.000 0.00 0.00 0.00 1.73
1947 4429 5.295540 CCTTCTCCTTAGTTCAGCAATTAGC 59.704 44.000 0.00 0.00 46.19 3.09
1964 4446 6.237648 GCAATTAGCACACAATAACAAGATGC 60.238 38.462 0.00 0.00 44.79 3.91
1965 4447 3.476295 AGCACACAATAACAAGATGCG 57.524 42.857 0.00 0.00 36.71 4.73
1966 4448 3.073678 AGCACACAATAACAAGATGCGA 58.926 40.909 0.00 0.00 36.71 5.10
1975 4458 1.446907 ACAAGATGCGAGGAAGCTTG 58.553 50.000 2.10 0.22 41.15 4.01
1980 4463 2.681848 AGATGCGAGGAAGCTTGAATTG 59.318 45.455 2.10 0.00 38.13 2.32
1993 4476 7.147915 GGAAGCTTGAATTGATTGGTTGGTATA 60.148 37.037 2.10 0.00 0.00 1.47
2006 4489 7.450124 TTGGTTGGTATAAAATTGAACGCTA 57.550 32.000 0.00 0.00 0.00 4.26
2039 4522 5.324409 AGATGTGGTTGGTGATGTTTATGT 58.676 37.500 0.00 0.00 0.00 2.29
2041 4524 3.823873 TGTGGTTGGTGATGTTTATGTCC 59.176 43.478 0.00 0.00 0.00 4.02
2060 4551 1.345415 CCTGCCTTGTCATTGCCTTTT 59.655 47.619 0.00 0.00 0.00 2.27
2070 4561 7.116805 CCTTGTCATTGCCTTTTGAATAGAAAC 59.883 37.037 0.00 0.00 0.00 2.78
2072 4563 7.495901 TGTCATTGCCTTTTGAATAGAAACAA 58.504 30.769 0.00 0.00 0.00 2.83
2192 4683 2.681848 CAAGAGATGAGGTTGGTGATGC 59.318 50.000 0.00 0.00 0.00 3.91
2285 4776 6.585416 ACAAGATGTGAGAAAGCCAAAATTT 58.415 32.000 0.00 0.00 0.00 1.82
2348 4839 5.828328 TGTGGTTGGTGATGTTTATGTACAA 59.172 36.000 0.00 0.00 0.00 2.41
2352 4843 6.977213 GTTGGTGATGTTTATGTACAACCTT 58.023 36.000 0.00 0.00 32.53 3.50
2361 4852 5.637006 TTATGTACAACCTTGTCATTGCC 57.363 39.130 0.00 0.00 42.35 4.52
2443 4934 0.403304 ATGGCCATACCCAGGATCCA 60.403 55.000 19.18 0.00 38.50 3.41
2454 4945 3.654806 ACCCAGGATCCATCATCTAAAGG 59.345 47.826 15.82 1.65 0.00 3.11
2712 5204 8.672823 GGTACCTAAAACTTAATATCCAGTGG 57.327 38.462 4.06 1.40 0.00 4.00
2753 5245 8.995027 AAATATGGCAATATTCCTACTGTGAA 57.005 30.769 6.80 0.00 37.89 3.18
2754 5246 9.592196 AAATATGGCAATATTCCTACTGTGAAT 57.408 29.630 6.80 0.00 37.89 2.57
2755 5247 8.798859 ATATGGCAATATTCCTACTGTGAATC 57.201 34.615 0.00 0.00 34.43 2.52
2756 5248 6.252599 TGGCAATATTCCTACTGTGAATCT 57.747 37.500 0.00 0.00 34.43 2.40
2757 5249 6.057533 TGGCAATATTCCTACTGTGAATCTG 58.942 40.000 0.00 0.00 34.43 2.90
2758 5250 6.058183 GGCAATATTCCTACTGTGAATCTGT 58.942 40.000 0.00 0.00 34.43 3.41
2759 5251 6.017605 GGCAATATTCCTACTGTGAATCTGTG 60.018 42.308 0.00 0.00 34.43 3.66
2760 5252 6.763135 GCAATATTCCTACTGTGAATCTGTGA 59.237 38.462 0.00 0.00 34.43 3.58
2766 5258 5.105187 TCCTACTGTGAATCTGTGATCCAAG 60.105 44.000 0.00 0.00 0.00 3.61
2768 5260 3.244665 ACTGTGAATCTGTGATCCAAGCA 60.245 43.478 0.00 0.00 0.00 3.91
2877 5369 8.705048 TTTTGTATTTTAACCAGTCAACAACC 57.295 30.769 0.00 0.00 0.00 3.77
2880 5372 5.784578 ATTTTAACCAGTCAACAACCCTC 57.215 39.130 0.00 0.00 0.00 4.30
2945 5437 6.738352 GCCATCAGCATTTTTATTTACTCG 57.262 37.500 0.00 0.00 42.97 4.18
2946 5438 6.265577 GCCATCAGCATTTTTATTTACTCGT 58.734 36.000 0.00 0.00 42.97 4.18
2967 5459 4.860352 CGTGTGATGTTCCTTTCGTATGTA 59.140 41.667 0.00 0.00 0.00 2.29
3008 5500 6.183360 TGTGAGTGATATGATCTCTGACACTG 60.183 42.308 14.09 0.00 40.35 3.66
3010 5502 6.039159 TGAGTGATATGATCTCTGACACTGTC 59.961 42.308 14.09 1.86 37.27 3.51
3066 5559 6.423905 TCTTGGCAGTAAAATCATATAGCGTC 59.576 38.462 0.00 0.00 0.00 5.19
3090 5583 9.138062 GTCGACTCTTCTATACGAGAATGTATA 57.862 37.037 8.70 0.00 43.39 1.47
3157 5650 3.811497 TGCAATTAGCCTGATTGATCGAG 59.189 43.478 12.92 0.00 44.83 4.04
3420 5913 9.831737 CAGTTGTGAATTTAAGGTAATCTTCTG 57.168 33.333 0.00 0.00 36.93 3.02
3462 5956 1.667724 CAGGCAAGCTTCGGTTCTATG 59.332 52.381 0.00 0.00 0.00 2.23
3507 6004 2.224018 CCTATCTGAGCTCTCAACTGCC 60.224 54.545 16.19 0.00 39.39 4.85
3629 6134 5.049954 TCGCAAGATAAGCAAAGTTAACGTT 60.050 36.000 5.88 5.88 45.01 3.99
3647 6152 2.597217 CTTCAGTTTGGGCCGCCA 60.597 61.111 12.58 0.00 0.00 5.69
3707 6460 4.037684 CCGTACTGAACCTGTATTCCCTAG 59.962 50.000 0.00 0.00 0.00 3.02
3708 6461 4.643784 CGTACTGAACCTGTATTCCCTAGT 59.356 45.833 0.00 0.00 0.00 2.57
3709 6462 5.824624 CGTACTGAACCTGTATTCCCTAGTA 59.175 44.000 0.00 0.00 0.00 1.82
3871 6632 4.644685 GGTACTACCTGGATACCGTTGTAA 59.355 45.833 0.00 0.00 34.73 2.41
3971 6732 8.969260 ATCATTACATCGGTTGCATATCATAT 57.031 30.769 0.00 0.00 0.00 1.78
3983 6744 5.807909 TGCATATCATATGGTGTATGCACT 58.192 37.500 28.05 0.00 44.01 4.40
4036 6798 3.567478 AAGATACCACTGGGATTCTGC 57.433 47.619 0.00 0.00 38.05 4.26
4037 6799 1.414181 AGATACCACTGGGATTCTGCG 59.586 52.381 0.00 0.00 38.05 5.18
4038 6800 0.179045 ATACCACTGGGATTCTGCGC 60.179 55.000 0.00 0.00 38.05 6.09
4044 6806 4.467084 GGGATTCTGCGCCCGACA 62.467 66.667 4.18 0.00 34.00 4.35
4056 6818 0.107410 GCCCGACATTGGATGTACCA 60.107 55.000 0.00 0.00 45.03 3.25
4066 6828 3.426787 TGGATGTACCAAAATCCGTGT 57.573 42.857 5.70 0.00 46.75 4.49
4074 6836 2.884639 ACCAAAATCCGTGTCCTTTCTG 59.115 45.455 0.00 0.00 0.00 3.02
4101 6863 3.120321 TGTGTAAATGGAGCTCGTGTT 57.880 42.857 7.83 3.71 0.00 3.32
4110 6872 1.136336 GGAGCTCGTGTTTTTGCTACG 60.136 52.381 7.83 0.00 35.76 3.51
4115 6877 3.784488 CTCGTGTTTTTGCTACGAAGAC 58.216 45.455 0.00 0.00 44.90 3.01
4121 6883 6.199393 GTGTTTTTGCTACGAAGACAAGAAT 58.801 36.000 0.00 0.00 0.00 2.40
4123 6885 6.910433 TGTTTTTGCTACGAAGACAAGAATTC 59.090 34.615 0.00 0.00 0.00 2.17
4147 6909 0.547471 TCCTCTTCCCTGTGGATGCA 60.547 55.000 0.00 0.00 41.40 3.96
4151 6913 2.686915 CTCTTCCCTGTGGATGCATTTC 59.313 50.000 0.00 0.00 41.40 2.17
4165 6927 4.173036 TGCATTTCTTCCGGACAAAATC 57.827 40.909 16.65 12.97 0.00 2.17
4170 6932 6.375377 CATTTCTTCCGGACAAAATCGTTTA 58.625 36.000 16.65 0.00 0.00 2.01
4195 6957 1.982073 GCGGATGCGTTTCTTCTGGG 61.982 60.000 8.84 0.00 0.00 4.45
4206 6968 3.915437 TTCTTCTGGGCAAAATCGTTC 57.085 42.857 0.00 0.00 0.00 3.95
4209 6971 2.107950 TCTGGGCAAAATCGTTCGAT 57.892 45.000 1.68 1.68 0.00 3.59
4218 6980 1.651987 AATCGTTCGATGGCGTTGAT 58.348 45.000 8.46 0.00 38.98 2.57
4235 6997 5.730568 GCGTTGATGATTATGGTTCTGGTTC 60.731 44.000 0.00 0.00 0.00 3.62
4250 7012 1.818060 TGGTTCGCATCATTTTCCCTG 59.182 47.619 0.00 0.00 0.00 4.45
4266 7028 0.824109 CCTGTCTATGGCCGAGTCAA 59.176 55.000 0.00 0.00 0.00 3.18
4293 7055 4.035441 CCTTTGCCATTTTGTGTTCCTTTG 59.965 41.667 0.00 0.00 0.00 2.77
4294 7056 3.191078 TGCCATTTTGTGTTCCTTTGG 57.809 42.857 0.00 0.00 0.00 3.28
4306 7077 2.303311 GTTCCTTTGGAGAGCTACAGGT 59.697 50.000 0.00 0.00 31.21 4.00
4324 7095 4.832266 ACAGGTAGTTTGATTGATTTGCCA 59.168 37.500 0.00 0.00 0.00 4.92
4334 7105 1.164411 TGATTTGCCACGCTTACCAG 58.836 50.000 0.00 0.00 0.00 4.00
4335 7106 1.271108 TGATTTGCCACGCTTACCAGA 60.271 47.619 0.00 0.00 0.00 3.86
4336 7107 1.398390 GATTTGCCACGCTTACCAGAG 59.602 52.381 0.00 0.00 0.00 3.35
4337 7108 0.394938 TTTGCCACGCTTACCAGAGA 59.605 50.000 0.00 0.00 0.00 3.10
4339 7110 1.448013 GCCACGCTTACCAGAGACC 60.448 63.158 0.00 0.00 0.00 3.85
4340 7111 1.972198 CCACGCTTACCAGAGACCA 59.028 57.895 0.00 0.00 0.00 4.02
4341 7112 0.108615 CCACGCTTACCAGAGACCAG 60.109 60.000 0.00 0.00 0.00 4.00
4342 7113 0.737715 CACGCTTACCAGAGACCAGC 60.738 60.000 0.00 0.00 0.00 4.85
4343 7114 1.517257 CGCTTACCAGAGACCAGCG 60.517 63.158 0.00 0.00 46.46 5.18
4345 7116 0.179124 GCTTACCAGAGACCAGCGAG 60.179 60.000 0.00 0.00 0.00 5.03
4346 7117 0.457851 CTTACCAGAGACCAGCGAGG 59.542 60.000 0.00 0.00 45.67 4.63
4347 7118 1.605058 TTACCAGAGACCAGCGAGGC 61.605 60.000 0.00 0.00 43.14 4.70
4350 7121 2.036414 AGAGACCAGCGAGGCAGA 59.964 61.111 0.00 0.00 43.14 4.26
4351 7122 2.051518 AGAGACCAGCGAGGCAGAG 61.052 63.158 0.00 0.00 43.14 3.35
4352 7123 3.073735 AGACCAGCGAGGCAGAGG 61.074 66.667 0.00 0.00 43.14 3.69
4353 7124 4.154347 GACCAGCGAGGCAGAGGG 62.154 72.222 0.00 0.00 43.14 4.30
4355 7126 4.463879 CCAGCGAGGCAGAGGGTG 62.464 72.222 0.00 0.00 0.00 4.61
4356 7127 3.385384 CAGCGAGGCAGAGGGTGA 61.385 66.667 0.00 0.00 0.00 4.02
4357 7128 3.386237 AGCGAGGCAGAGGGTGAC 61.386 66.667 0.00 0.00 0.00 3.67
4359 7130 2.948720 GCGAGGCAGAGGGTGACTT 61.949 63.158 0.00 0.00 45.31 3.01
4362 7133 0.321122 GAGGCAGAGGGTGACTTGTG 60.321 60.000 0.00 0.00 45.31 3.33
4363 7134 0.764369 AGGCAGAGGGTGACTTGTGA 60.764 55.000 0.00 0.00 45.31 3.58
4373 7144 2.959516 GTGACTTGTGATGATCACCGA 58.040 47.619 21.68 10.27 46.40 4.69
4375 7146 2.094026 TGACTTGTGATGATCACCGAGG 60.094 50.000 21.68 8.11 46.40 4.63
4376 7147 1.293924 CTTGTGATGATCACCGAGGC 58.706 55.000 21.68 0.00 46.40 4.70
4381 7152 1.228063 ATGATCACCGAGGCATGCC 60.228 57.895 30.12 30.12 0.00 4.40
4405 7177 1.812571 CCTGACTTTTGTTGCGGCTAT 59.187 47.619 0.00 0.00 0.00 2.97
4411 7183 2.394930 TTTGTTGCGGCTATGAGCTA 57.605 45.000 0.00 0.00 41.99 3.32
4412 7184 1.939974 TTGTTGCGGCTATGAGCTAG 58.060 50.000 0.00 0.00 41.99 3.42
4413 7185 0.824109 TGTTGCGGCTATGAGCTAGT 59.176 50.000 0.00 0.00 41.99 2.57
4414 7186 2.028876 TGTTGCGGCTATGAGCTAGTA 58.971 47.619 0.00 0.00 41.99 1.82
4440 7212 6.418585 AGATATGAATGAATATGCGTGCAG 57.581 37.500 0.00 0.00 0.00 4.41
4450 7222 1.539560 ATGCGTGCAGTGGAGACTCT 61.540 55.000 1.74 0.00 33.64 3.24
4451 7223 1.005630 GCGTGCAGTGGAGACTCTT 60.006 57.895 1.74 0.00 30.18 2.85
4457 7229 2.035961 TGCAGTGGAGACTCTTGTGTAC 59.964 50.000 1.74 0.00 30.18 2.90
4460 7232 2.814919 AGTGGAGACTCTTGTGTACTCG 59.185 50.000 1.74 0.00 0.00 4.18
4488 7260 4.447138 ACTTTGGAGTAATGGTGGAACA 57.553 40.909 0.00 0.00 33.76 3.18
4526 7298 3.074412 CACCAGTAACATTGACCAGGAC 58.926 50.000 0.00 0.00 0.00 3.85
4527 7299 2.289444 ACCAGTAACATTGACCAGGACG 60.289 50.000 0.00 0.00 0.00 4.79
4528 7300 2.028476 CCAGTAACATTGACCAGGACGA 60.028 50.000 0.00 0.00 0.00 4.20
4534 7306 2.305927 ACATTGACCAGGACGAGGAAAT 59.694 45.455 0.00 0.00 0.00 2.17
4561 7333 8.917414 ATCCACCCACAGTATGATATAAGTAT 57.083 34.615 0.00 0.00 39.69 2.12
4562 7334 8.134202 TCCACCCACAGTATGATATAAGTATG 57.866 38.462 0.00 0.00 39.69 2.39
4563 7335 7.733047 TCCACCCACAGTATGATATAAGTATGT 59.267 37.037 0.00 0.00 39.69 2.29
4564 7336 7.819415 CCACCCACAGTATGATATAAGTATGTG 59.181 40.741 0.00 0.00 39.69 3.21
4565 7337 8.367911 CACCCACAGTATGATATAAGTATGTGT 58.632 37.037 0.00 0.00 39.69 3.72
4566 7338 8.367911 ACCCACAGTATGATATAAGTATGTGTG 58.632 37.037 0.00 0.00 39.69 3.82
4567 7339 7.331934 CCCACAGTATGATATAAGTATGTGTGC 59.668 40.741 0.00 0.00 39.69 4.57
4568 7340 7.331934 CCACAGTATGATATAAGTATGTGTGCC 59.668 40.741 0.00 0.00 39.69 5.01
4569 7341 7.872483 CACAGTATGATATAAGTATGTGTGCCA 59.128 37.037 0.00 0.00 39.69 4.92
4570 7342 8.428852 ACAGTATGATATAAGTATGTGTGCCAA 58.571 33.333 0.00 0.00 39.69 4.52
4571 7343 8.929746 CAGTATGATATAAGTATGTGTGCCAAG 58.070 37.037 0.00 0.00 39.69 3.61
4572 7344 8.870116 AGTATGATATAAGTATGTGTGCCAAGA 58.130 33.333 0.00 0.00 0.00 3.02
4573 7345 9.144747 GTATGATATAAGTATGTGTGCCAAGAG 57.855 37.037 0.00 0.00 0.00 2.85
4574 7346 6.524734 TGATATAAGTATGTGTGCCAAGAGG 58.475 40.000 0.00 0.00 38.23 3.69
4575 7347 2.496899 AAGTATGTGTGCCAAGAGGG 57.503 50.000 0.00 0.00 40.85 4.30
4576 7348 1.656587 AGTATGTGTGCCAAGAGGGA 58.343 50.000 0.00 0.00 40.01 4.20
4577 7349 1.556911 AGTATGTGTGCCAAGAGGGAG 59.443 52.381 0.00 0.00 40.01 4.30
4578 7350 0.911769 TATGTGTGCCAAGAGGGAGG 59.088 55.000 0.00 0.00 40.01 4.30
4579 7351 1.856539 ATGTGTGCCAAGAGGGAGGG 61.857 60.000 0.00 0.00 40.01 4.30
4580 7352 2.206900 TGTGCCAAGAGGGAGGGA 59.793 61.111 0.00 0.00 40.01 4.20
4581 7353 1.920325 TGTGCCAAGAGGGAGGGAG 60.920 63.158 0.00 0.00 40.01 4.30
4582 7354 2.285668 TGCCAAGAGGGAGGGAGG 60.286 66.667 0.00 0.00 40.01 4.30
4583 7355 3.093172 GCCAAGAGGGAGGGAGGG 61.093 72.222 0.00 0.00 40.01 4.30
4584 7356 2.787866 CCAAGAGGGAGGGAGGGA 59.212 66.667 0.00 0.00 40.01 4.20
4585 7357 1.383803 CCAAGAGGGAGGGAGGGAG 60.384 68.421 0.00 0.00 40.01 4.30
4586 7358 1.383803 CAAGAGGGAGGGAGGGAGG 60.384 68.421 0.00 0.00 0.00 4.30
4587 7359 3.339951 AAGAGGGAGGGAGGGAGGC 62.340 68.421 0.00 0.00 0.00 4.70
4588 7360 4.890306 GAGGGAGGGAGGGAGGCC 62.890 77.778 0.00 0.00 0.00 5.19
4599 7371 4.416738 GGAGGCCAGCCACCACTC 62.417 72.222 18.97 3.44 44.71 3.51
4600 7372 3.325753 GAGGCCAGCCACCACTCT 61.326 66.667 12.03 0.00 38.92 3.24
4601 7373 3.322318 GAGGCCAGCCACCACTCTC 62.322 68.421 12.03 0.00 38.92 3.20
4602 7374 3.640407 GGCCAGCCACCACTCTCA 61.640 66.667 3.12 0.00 35.81 3.27
4603 7375 2.359230 GCCAGCCACCACTCTCAC 60.359 66.667 0.00 0.00 0.00 3.51
4604 7376 2.348998 CCAGCCACCACTCTCACC 59.651 66.667 0.00 0.00 0.00 4.02
4605 7377 2.519622 CCAGCCACCACTCTCACCA 61.520 63.158 0.00 0.00 0.00 4.17
4606 7378 1.681666 CAGCCACCACTCTCACCAT 59.318 57.895 0.00 0.00 0.00 3.55
4607 7379 0.904649 CAGCCACCACTCTCACCATA 59.095 55.000 0.00 0.00 0.00 2.74
4608 7380 1.487976 CAGCCACCACTCTCACCATAT 59.512 52.381 0.00 0.00 0.00 1.78
4609 7381 2.700371 CAGCCACCACTCTCACCATATA 59.300 50.000 0.00 0.00 0.00 0.86
4610 7382 3.326006 CAGCCACCACTCTCACCATATAT 59.674 47.826 0.00 0.00 0.00 0.86
4611 7383 4.528206 CAGCCACCACTCTCACCATATATA 59.472 45.833 0.00 0.00 0.00 0.86
4612 7384 5.188555 CAGCCACCACTCTCACCATATATAT 59.811 44.000 0.00 0.00 0.00 0.86
4613 7385 6.381133 CAGCCACCACTCTCACCATATATATA 59.619 42.308 0.00 0.00 0.00 0.86
4614 7386 7.070447 CAGCCACCACTCTCACCATATATATAT 59.930 40.741 0.00 0.00 0.00 0.86
4615 7387 7.288852 AGCCACCACTCTCACCATATATATATC 59.711 40.741 2.03 0.00 0.00 1.63
4616 7388 7.288852 GCCACCACTCTCACCATATATATATCT 59.711 40.741 2.03 0.00 0.00 1.98
4617 7389 8.855110 CCACCACTCTCACCATATATATATCTC 58.145 40.741 2.03 0.00 0.00 2.75
4618 7390 9.639563 CACCACTCTCACCATATATATATCTCT 57.360 37.037 2.03 0.00 0.00 3.10
4619 7391 9.860650 ACCACTCTCACCATATATATATCTCTC 57.139 37.037 2.03 0.00 0.00 3.20
4623 7395 9.739276 CTCTCACCATATATATATCTCTCTCCC 57.261 40.741 2.03 0.00 0.00 4.30
4624 7396 9.472347 TCTCACCATATATATATCTCTCTCCCT 57.528 37.037 2.03 0.00 0.00 4.20
4625 7397 9.739276 CTCACCATATATATATCTCTCTCCCTC 57.261 40.741 2.03 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.846193 TGCTGGTCTGTTGTTACCTTC 58.154 47.619 0.00 0.00 36.67 3.46
89 90 4.675190 ATTCAGAGACAAGACATTTGCG 57.325 40.909 0.00 0.00 0.00 4.85
192 204 0.737219 GCTCTTGGAGAAATGCGCAT 59.263 50.000 19.28 19.28 0.00 4.73
261 273 2.665519 CGAAGCTCCAATTCAACGGTTG 60.666 50.000 14.62 14.62 0.00 3.77
329 375 2.104111 ACCAACGAATGTCCAAGAGTCA 59.896 45.455 0.00 0.00 0.00 3.41
339 385 3.338249 CTCTTCATCCACCAACGAATGT 58.662 45.455 0.00 0.00 0.00 2.71
342 388 1.347707 AGCTCTTCATCCACCAACGAA 59.652 47.619 0.00 0.00 0.00 3.85
346 392 1.280133 CTGGAGCTCTTCATCCACCAA 59.720 52.381 14.64 0.00 40.70 3.67
547 602 2.401583 AGCATTCGTGTGGCAAGATA 57.598 45.000 0.00 0.00 0.00 1.98
674 753 7.413328 CGAATAACAGAGCAAGTCATCAATCAA 60.413 37.037 0.00 0.00 0.00 2.57
749 828 5.456192 AAGACGAAATGAACATCATCGAC 57.544 39.130 20.92 16.80 35.76 4.20
762 841 7.648510 GGTACGATCAGAAAGATAAGACGAAAT 59.351 37.037 0.00 0.00 37.00 2.17
763 842 6.971184 GGTACGATCAGAAAGATAAGACGAAA 59.029 38.462 0.00 0.00 37.00 3.46
778 868 7.442656 AGGGTTAAATATCTTGGTACGATCAG 58.557 38.462 0.00 0.00 0.00 2.90
905 2505 2.816087 TGCCAATCAGAACTTCAGAAGC 59.184 45.455 10.33 0.00 0.00 3.86
913 2513 4.298103 AGAATCACTGCCAATCAGAACT 57.702 40.909 0.00 0.00 45.72 3.01
997 2623 1.589196 GGACGCGTCTACTCATGGC 60.589 63.158 35.50 14.31 0.00 4.40
1305 3189 0.689412 GGTGGGAGAGAGGAGGAAGG 60.689 65.000 0.00 0.00 0.00 3.46
1306 3190 0.338120 AGGTGGGAGAGAGGAGGAAG 59.662 60.000 0.00 0.00 0.00 3.46
1307 3191 0.793617 AAGGTGGGAGAGAGGAGGAA 59.206 55.000 0.00 0.00 0.00 3.36
1308 3192 0.336737 GAAGGTGGGAGAGAGGAGGA 59.663 60.000 0.00 0.00 0.00 3.71
1309 3193 0.041833 TGAAGGTGGGAGAGAGGAGG 59.958 60.000 0.00 0.00 0.00 4.30
1310 3194 1.190643 GTGAAGGTGGGAGAGAGGAG 58.809 60.000 0.00 0.00 0.00 3.69
1311 3195 0.487325 TGTGAAGGTGGGAGAGAGGA 59.513 55.000 0.00 0.00 0.00 3.71
1312 3196 0.901124 CTGTGAAGGTGGGAGAGAGG 59.099 60.000 0.00 0.00 0.00 3.69
1313 3197 0.248843 GCTGTGAAGGTGGGAGAGAG 59.751 60.000 0.00 0.00 0.00 3.20
1336 3220 1.269831 CCAATCCCCTCGAGATTCGAC 60.270 57.143 15.71 0.00 44.82 4.20
1343 3227 0.179108 GACGAACCAATCCCCTCGAG 60.179 60.000 5.13 5.13 35.34 4.04
1353 3238 3.306917 TTAGATGAAGCGACGAACCAA 57.693 42.857 0.00 0.00 0.00 3.67
1358 3243 4.566759 CCTCAAAATTAGATGAAGCGACGA 59.433 41.667 0.00 0.00 0.00 4.20
1360 3245 6.422776 TTCCTCAAAATTAGATGAAGCGAC 57.577 37.500 0.00 0.00 0.00 5.19
1384 3269 3.995705 GCCATCTGCAAAAACAGCAATTA 59.004 39.130 0.00 0.00 42.17 1.40
1390 3289 1.010419 GGCGCCATCTGCAAAAACAG 61.010 55.000 24.80 0.00 41.33 3.16
1538 3718 7.041098 GCGAACCCTAATATTCACAGATTTCAT 60.041 37.037 0.00 0.00 0.00 2.57
1549 3729 1.873698 TGCGGCGAACCCTAATATTC 58.126 50.000 12.98 0.00 0.00 1.75
1647 4127 3.252215 ACCCACACACAAATATGTTGTCG 59.748 43.478 1.73 0.00 37.82 4.35
1691 4173 5.713389 CAGAATATATCCAACACCCATGCAT 59.287 40.000 0.00 0.00 0.00 3.96
1739 4221 7.725251 ACACAAAATCCAATACACATCAGTTT 58.275 30.769 0.00 0.00 0.00 2.66
1742 4224 6.023435 CGACACAAAATCCAATACACATCAG 58.977 40.000 0.00 0.00 0.00 2.90
1747 4229 5.851177 CAGTTCGACACAAAATCCAATACAC 59.149 40.000 0.00 0.00 0.00 2.90
1748 4230 5.561919 GCAGTTCGACACAAAATCCAATACA 60.562 40.000 0.00 0.00 0.00 2.29
1766 4248 0.250038 TGTCAGAGCACCTGCAGTTC 60.250 55.000 13.81 4.90 45.16 3.01
1903 4385 0.962356 CATCAAGGGGTGACTGTGGC 60.962 60.000 0.00 0.00 39.72 5.01
1937 4419 6.380995 TCTTGTTATTGTGTGCTAATTGCTG 58.619 36.000 0.00 0.00 43.37 4.41
1941 4423 6.029607 CGCATCTTGTTATTGTGTGCTAATT 58.970 36.000 0.00 0.00 0.00 1.40
1942 4424 5.353956 TCGCATCTTGTTATTGTGTGCTAAT 59.646 36.000 0.00 0.00 0.00 1.73
1943 4425 4.693095 TCGCATCTTGTTATTGTGTGCTAA 59.307 37.500 0.00 0.00 0.00 3.09
1944 4426 4.249661 TCGCATCTTGTTATTGTGTGCTA 58.750 39.130 0.00 0.00 0.00 3.49
1945 4427 3.073678 TCGCATCTTGTTATTGTGTGCT 58.926 40.909 0.00 0.00 0.00 4.40
1946 4428 3.419915 CTCGCATCTTGTTATTGTGTGC 58.580 45.455 0.00 0.00 0.00 4.57
1947 4429 3.684305 TCCTCGCATCTTGTTATTGTGTG 59.316 43.478 0.00 0.00 0.00 3.82
1948 4430 3.937814 TCCTCGCATCTTGTTATTGTGT 58.062 40.909 0.00 0.00 0.00 3.72
1958 4440 2.479566 TTCAAGCTTCCTCGCATCTT 57.520 45.000 0.00 0.00 0.00 2.40
1964 4446 3.441572 ACCAATCAATTCAAGCTTCCTCG 59.558 43.478 0.00 0.00 0.00 4.63
1965 4447 5.166398 CAACCAATCAATTCAAGCTTCCTC 58.834 41.667 0.00 0.00 0.00 3.71
1966 4448 4.020839 CCAACCAATCAATTCAAGCTTCCT 60.021 41.667 0.00 0.00 0.00 3.36
1980 4463 7.033185 AGCGTTCAATTTTATACCAACCAATC 58.967 34.615 0.00 0.00 0.00 2.67
1993 4476 6.260050 TCTCTTGTTGACTAGCGTTCAATTTT 59.740 34.615 0.00 0.00 0.00 1.82
2006 4489 3.117888 ACCAACCACATCTCTTGTTGACT 60.118 43.478 0.00 0.00 40.30 3.41
2039 4522 0.112995 AAGGCAATGACAAGGCAGGA 59.887 50.000 7.42 0.00 0.00 3.86
2041 4524 2.036217 TCAAAAGGCAATGACAAGGCAG 59.964 45.455 7.42 0.00 0.00 4.85
2070 4561 9.054922 GGAGAAGGAATCAAGAGATAAGAATTG 57.945 37.037 0.00 0.00 33.08 2.32
2072 4563 8.565780 AGGAGAAGGAATCAAGAGATAAGAAT 57.434 34.615 0.00 0.00 33.08 2.40
2088 4579 4.591498 TGTGTGCTAAACTAAGGAGAAGGA 59.409 41.667 0.00 0.00 0.00 3.36
2192 4683 4.201950 GGCAATGACAAGGCTGTACATAAG 60.202 45.833 0.00 0.00 35.30 1.73
2285 4776 6.655848 AGCGTTCAAGTTTATACCAACCAATA 59.344 34.615 0.00 0.00 0.00 1.90
2348 4839 4.961438 ATTCAAAAGGCAATGACAAGGT 57.039 36.364 0.00 0.00 0.00 3.50
2403 4894 3.170991 ACTAGTGTAGGCAGAGTTCCA 57.829 47.619 0.00 0.00 0.00 3.53
2478 4969 3.118702 TCGTTTTGTTCCAGGTGTAGACA 60.119 43.478 0.00 0.00 0.00 3.41
2514 5005 7.994911 AGTATGCTCATGTTGATCAGGAATTAA 59.005 33.333 0.00 0.00 36.41 1.40
2547 5038 7.552687 TGCCAAAACTATACTTCCATAAGTCAG 59.447 37.037 0.00 0.00 42.42 3.51
2551 5042 6.828785 AGGTGCCAAAACTATACTTCCATAAG 59.171 38.462 0.00 0.00 38.77 1.73
2686 5178 7.718314 CCACTGGATATTAAGTTTTAGGTACCC 59.282 40.741 8.74 0.00 0.00 3.69
2712 5204 7.224297 TGCCATATTTCTAATCCAAGAGGTAC 58.776 38.462 0.00 0.00 35.89 3.34
2714 5206 6.266131 TGCCATATTTCTAATCCAAGAGGT 57.734 37.500 0.00 0.00 35.89 3.85
2742 5234 4.352893 TGGATCACAGATTCACAGTAGGA 58.647 43.478 0.00 0.00 0.00 2.94
2753 5245 9.797642 TTTTATATGTATGCTTGGATCACAGAT 57.202 29.630 0.00 0.00 0.00 2.90
2754 5246 9.797642 ATTTTATATGTATGCTTGGATCACAGA 57.202 29.630 0.00 0.00 0.00 3.41
2891 5383 8.761575 TCAAAGTTCAATGCCATTTATCTTTC 57.238 30.769 5.20 0.00 0.00 2.62
2938 5430 4.446385 CGAAAGGAACATCACACGAGTAAA 59.554 41.667 0.00 0.00 0.00 2.01
2941 5433 2.223971 ACGAAAGGAACATCACACGAGT 60.224 45.455 0.00 0.00 0.00 4.18
2942 5434 2.404215 ACGAAAGGAACATCACACGAG 58.596 47.619 0.00 0.00 0.00 4.18
2943 5435 2.519377 ACGAAAGGAACATCACACGA 57.481 45.000 0.00 0.00 0.00 4.35
2944 5436 3.678072 ACATACGAAAGGAACATCACACG 59.322 43.478 0.00 0.00 0.00 4.49
2945 5437 6.715344 TTACATACGAAAGGAACATCACAC 57.285 37.500 0.00 0.00 0.00 3.82
2946 5438 7.308109 GGTTTTACATACGAAAGGAACATCACA 60.308 37.037 0.00 0.00 0.00 3.58
2967 5459 4.339247 CACTCACAGGTTCATGAAGGTTTT 59.661 41.667 8.80 0.00 0.00 2.43
3008 5500 7.857885 GCATTGCTGAATGTAATAGGTTAAGAC 59.142 37.037 0.16 0.00 41.09 3.01
3010 5502 7.934457 AGCATTGCTGAATGTAATAGGTTAAG 58.066 34.615 11.09 0.00 41.09 1.85
3090 5583 5.204409 TGCAATCTGCTTGTTTTTCATCT 57.796 34.783 0.00 0.00 45.31 2.90
3094 5587 2.477754 GCCTGCAATCTGCTTGTTTTTC 59.522 45.455 0.00 0.00 45.31 2.29
3157 5650 0.889186 TTTCTCGGCAAGTGCTTCCC 60.889 55.000 2.85 0.00 41.70 3.97
3420 5913 3.020274 GAGAAGGGGAAAAAGAGGATGC 58.980 50.000 0.00 0.00 0.00 3.91
3462 5956 5.684550 ACCGGAAAGTTGTATGAAGAAAC 57.315 39.130 9.46 0.00 0.00 2.78
3507 6004 4.321452 GGTATGCCTGATAAATGTGCATGG 60.321 45.833 5.60 0.00 42.25 3.66
3629 6134 2.282180 GGCGGCCCAAACTGAAGA 60.282 61.111 8.12 0.00 0.00 2.87
3647 6152 1.047034 GCTATAGTGGGGGACGTGGT 61.047 60.000 0.00 0.00 0.00 4.16
3654 6159 2.654863 CCAGTTTTGCTATAGTGGGGG 58.345 52.381 0.84 0.00 32.31 5.40
3661 6166 5.756195 CTGCATTAGCCAGTTTTGCTATA 57.244 39.130 0.00 0.00 40.75 1.31
3707 6460 6.895898 TCGTCCGAGTTCATCAATATAGTAC 58.104 40.000 0.00 0.00 0.00 2.73
3708 6461 7.148289 GGATCGTCCGAGTTCATCAATATAGTA 60.148 40.741 0.00 0.00 0.00 1.82
3709 6462 6.349445 GGATCGTCCGAGTTCATCAATATAGT 60.349 42.308 0.00 0.00 0.00 2.12
3871 6632 6.267471 CAGATTCTAAGCAGAGAGGATACCTT 59.733 42.308 0.00 0.00 31.76 3.50
3983 6744 5.483685 AAGGACAAGTTCTACTACATGCA 57.516 39.130 0.00 0.00 0.00 3.96
4036 6798 1.157870 GGTACATCCAATGTCGGGCG 61.158 60.000 0.00 0.00 43.67 6.13
4037 6799 0.107410 TGGTACATCCAATGTCGGGC 60.107 55.000 0.00 0.00 44.12 6.13
4056 6818 3.146847 GACCAGAAAGGACACGGATTTT 58.853 45.455 0.00 0.00 41.22 1.82
4063 6825 3.632145 ACACAAATGACCAGAAAGGACAC 59.368 43.478 0.00 0.00 44.67 3.67
4097 6859 5.151632 TCTTGTCTTCGTAGCAAAAACAC 57.848 39.130 0.00 0.00 0.00 3.32
4101 6863 5.529430 TGGAATTCTTGTCTTCGTAGCAAAA 59.471 36.000 5.23 1.31 0.00 2.44
4110 6872 5.495640 AGAGGACATGGAATTCTTGTCTTC 58.504 41.667 27.39 27.39 46.96 2.87
4115 6877 3.950395 GGGAAGAGGACATGGAATTCTTG 59.050 47.826 5.23 6.42 0.00 3.02
4121 6883 1.630369 CACAGGGAAGAGGACATGGAA 59.370 52.381 0.00 0.00 0.00 3.53
4123 6885 0.254178 CCACAGGGAAGAGGACATGG 59.746 60.000 0.00 0.00 35.59 3.66
4147 6909 5.447624 AAACGATTTTGTCCGGAAGAAAT 57.552 34.783 20.37 20.37 0.00 2.17
4151 6913 4.905269 GGATAAACGATTTTGTCCGGAAG 58.095 43.478 5.23 0.00 41.54 3.46
4183 6945 2.031157 ACGATTTTGCCCAGAAGAAACG 60.031 45.455 0.00 0.00 0.00 3.60
4191 6953 1.202177 CCATCGAACGATTTTGCCCAG 60.202 52.381 6.98 0.00 31.62 4.45
4193 6955 0.525455 GCCATCGAACGATTTTGCCC 60.525 55.000 6.98 0.00 31.62 5.36
4195 6957 0.179200 ACGCCATCGAACGATTTTGC 60.179 50.000 12.05 9.31 39.41 3.68
4206 6968 2.807967 ACCATAATCATCAACGCCATCG 59.192 45.455 0.00 0.00 42.43 3.84
4209 6971 3.627123 CAGAACCATAATCATCAACGCCA 59.373 43.478 0.00 0.00 0.00 5.69
4218 6980 3.342377 TGCGAACCAGAACCATAATCA 57.658 42.857 0.00 0.00 0.00 2.57
4235 6997 3.251729 CCATAGACAGGGAAAATGATGCG 59.748 47.826 0.00 0.00 0.00 4.73
4250 7012 1.941325 CCTTTGACTCGGCCATAGAC 58.059 55.000 2.24 0.04 0.00 2.59
4271 7033 4.035441 CCAAAGGAACACAAAATGGCAAAG 59.965 41.667 0.00 0.00 0.00 2.77
4274 7036 2.768527 TCCAAAGGAACACAAAATGGCA 59.231 40.909 0.00 0.00 0.00 4.92
4293 7055 5.105310 TCAATCAAACTACCTGTAGCTCTCC 60.105 44.000 4.25 0.00 36.66 3.71
4294 7056 5.967088 TCAATCAAACTACCTGTAGCTCTC 58.033 41.667 4.25 0.00 36.66 3.20
4306 7077 3.505680 AGCGTGGCAAATCAATCAAACTA 59.494 39.130 0.00 0.00 0.00 2.24
4324 7095 1.592223 GCTGGTCTCTGGTAAGCGT 59.408 57.895 0.00 0.00 0.00 5.07
4334 7105 2.493973 CTCTGCCTCGCTGGTCTC 59.506 66.667 0.00 0.00 38.35 3.36
4335 7106 3.073735 CCTCTGCCTCGCTGGTCT 61.074 66.667 0.00 0.00 38.35 3.85
4336 7107 4.154347 CCCTCTGCCTCGCTGGTC 62.154 72.222 0.00 0.00 38.35 4.02
4339 7110 3.385384 TCACCCTCTGCCTCGCTG 61.385 66.667 0.00 0.00 0.00 5.18
4340 7111 3.386237 GTCACCCTCTGCCTCGCT 61.386 66.667 0.00 0.00 0.00 4.93
4341 7112 2.948720 AAGTCACCCTCTGCCTCGC 61.949 63.158 0.00 0.00 0.00 5.03
4342 7113 1.079543 CAAGTCACCCTCTGCCTCG 60.080 63.158 0.00 0.00 0.00 4.63
4343 7114 0.321122 CACAAGTCACCCTCTGCCTC 60.321 60.000 0.00 0.00 0.00 4.70
4345 7116 0.326264 ATCACAAGTCACCCTCTGCC 59.674 55.000 0.00 0.00 0.00 4.85
4346 7117 1.002430 TCATCACAAGTCACCCTCTGC 59.998 52.381 0.00 0.00 0.00 4.26
4347 7118 3.055602 TGATCATCACAAGTCACCCTCTG 60.056 47.826 0.00 0.00 0.00 3.35
4350 7121 3.340814 GTGATCATCACAAGTCACCCT 57.659 47.619 13.26 0.00 46.22 4.34
4362 7133 1.233285 GGCATGCCTCGGTGATCATC 61.233 60.000 29.98 0.00 0.00 2.92
4363 7134 1.228063 GGCATGCCTCGGTGATCAT 60.228 57.895 29.98 0.00 0.00 2.45
4372 7143 1.451028 GTCAGGTCAGGCATGCCTC 60.451 63.158 36.65 25.26 46.28 4.70
4375 7146 1.068055 CAAAAGTCAGGTCAGGCATGC 60.068 52.381 9.90 9.90 0.00 4.06
4376 7147 2.233271 ACAAAAGTCAGGTCAGGCATG 58.767 47.619 0.00 0.00 0.00 4.06
4381 7152 1.002468 CCGCAACAAAAGTCAGGTCAG 60.002 52.381 0.00 0.00 0.00 3.51
4384 7155 0.751643 AGCCGCAACAAAAGTCAGGT 60.752 50.000 0.00 0.00 0.00 4.00
4411 7183 9.794685 CACGCATATTCATTCATATCTACTACT 57.205 33.333 0.00 0.00 0.00 2.57
4412 7184 8.535592 GCACGCATATTCATTCATATCTACTAC 58.464 37.037 0.00 0.00 0.00 2.73
4413 7185 8.250332 TGCACGCATATTCATTCATATCTACTA 58.750 33.333 0.00 0.00 0.00 1.82
4414 7186 7.099120 TGCACGCATATTCATTCATATCTACT 58.901 34.615 0.00 0.00 0.00 2.57
4433 7205 1.005630 AAGAGTCTCCACTGCACGC 60.006 57.895 0.00 0.00 30.63 5.34
4440 7212 2.553172 ACGAGTACACAAGAGTCTCCAC 59.447 50.000 0.00 0.00 0.00 4.02
4450 7222 4.093703 CCAAAGTTGAACACGAGTACACAA 59.906 41.667 0.00 0.00 0.00 3.33
4451 7223 3.619483 CCAAAGTTGAACACGAGTACACA 59.381 43.478 0.00 0.00 0.00 3.72
4457 7229 5.334105 CCATTACTCCAAAGTTGAACACGAG 60.334 44.000 0.00 0.00 36.92 4.18
4460 7232 5.507315 CCACCATTACTCCAAAGTTGAACAC 60.507 44.000 0.00 0.00 36.92 3.32
4488 7260 2.705658 TGGTGAGATCTGGACTGTTTGT 59.294 45.455 0.00 0.00 0.00 2.83
4500 7272 4.832248 TGGTCAATGTTACTGGTGAGATC 58.168 43.478 0.00 0.00 0.00 2.75
4526 7298 1.065491 TGTGGGTGGATCATTTCCTCG 60.065 52.381 0.00 0.00 45.68 4.63
4527 7299 2.025887 ACTGTGGGTGGATCATTTCCTC 60.026 50.000 0.00 0.00 45.68 3.71
4528 7300 1.995542 ACTGTGGGTGGATCATTTCCT 59.004 47.619 0.00 0.00 45.68 3.36
4534 7306 6.787458 ACTTATATCATACTGTGGGTGGATCA 59.213 38.462 0.00 0.00 0.00 2.92
4542 7314 7.331934 GGCACACATACTTATATCATACTGTGG 59.668 40.741 0.00 0.00 37.62 4.17
4545 7317 8.831715 TTGGCACACATACTTATATCATACTG 57.168 34.615 0.00 0.00 39.29 2.74
4546 7318 8.870116 TCTTGGCACACATACTTATATCATACT 58.130 33.333 0.00 0.00 39.29 2.12
4561 7333 2.528818 CCCTCCCTCTTGGCACACA 61.529 63.158 0.00 0.00 39.29 3.72
4562 7334 2.190488 CTCCCTCCCTCTTGGCACAC 62.190 65.000 0.00 0.00 39.29 3.82
4563 7335 1.920325 CTCCCTCCCTCTTGGCACA 60.920 63.158 0.00 0.00 0.00 4.57
4564 7336 2.674220 CCTCCCTCCCTCTTGGCAC 61.674 68.421 0.00 0.00 0.00 5.01
4565 7337 2.285668 CCTCCCTCCCTCTTGGCA 60.286 66.667 0.00 0.00 0.00 4.92
4566 7338 3.093172 CCCTCCCTCCCTCTTGGC 61.093 72.222 0.00 0.00 0.00 4.52
4567 7339 1.383803 CTCCCTCCCTCCCTCTTGG 60.384 68.421 0.00 0.00 0.00 3.61
4568 7340 1.383803 CCTCCCTCCCTCCCTCTTG 60.384 68.421 0.00 0.00 0.00 3.02
4569 7341 3.124088 CCTCCCTCCCTCCCTCTT 58.876 66.667 0.00 0.00 0.00 2.85
4570 7342 3.773154 GCCTCCCTCCCTCCCTCT 61.773 72.222 0.00 0.00 0.00 3.69
4571 7343 4.890306 GGCCTCCCTCCCTCCCTC 62.890 77.778 0.00 0.00 0.00 4.30
4582 7354 4.416738 GAGTGGTGGCTGGCCTCC 62.417 72.222 21.62 21.62 46.78 4.30
4583 7355 3.322318 GAGAGTGGTGGCTGGCCTC 62.322 68.421 13.05 9.03 36.94 4.70
4584 7356 3.325753 GAGAGTGGTGGCTGGCCT 61.326 66.667 13.05 0.00 36.94 5.19
4585 7357 3.640407 TGAGAGTGGTGGCTGGCC 61.640 66.667 4.43 4.43 0.00 5.36
4586 7358 2.359230 GTGAGAGTGGTGGCTGGC 60.359 66.667 0.00 0.00 0.00 4.85
4587 7359 1.845627 ATGGTGAGAGTGGTGGCTGG 61.846 60.000 0.00 0.00 0.00 4.85
4588 7360 0.904649 TATGGTGAGAGTGGTGGCTG 59.095 55.000 0.00 0.00 0.00 4.85
4589 7361 1.885049 ATATGGTGAGAGTGGTGGCT 58.115 50.000 0.00 0.00 0.00 4.75
4590 7362 5.683876 ATATATATGGTGAGAGTGGTGGC 57.316 43.478 0.00 0.00 0.00 5.01
4591 7363 8.774546 AGATATATATATGGTGAGAGTGGTGG 57.225 38.462 10.03 0.00 0.00 4.61
4592 7364 9.639563 AGAGATATATATATGGTGAGAGTGGTG 57.360 37.037 10.03 0.00 0.00 4.17
4593 7365 9.860650 GAGAGATATATATATGGTGAGAGTGGT 57.139 37.037 10.03 0.00 0.00 4.16
4597 7369 9.739276 GGGAGAGAGATATATATATGGTGAGAG 57.261 40.741 10.03 0.00 0.00 3.20
4598 7370 9.472347 AGGGAGAGAGATATATATATGGTGAGA 57.528 37.037 10.03 0.00 0.00 3.27
4599 7371 9.739276 GAGGGAGAGAGATATATATATGGTGAG 57.261 40.741 10.03 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.