Multiple sequence alignment - TraesCS1D01G013200

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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 TraesCS1D01G013200 chr1D 100.000 5419 0 0 1 5419 6773629 6779047 0.000000e+00 10008.0
1 TraesCS1D01G013200 chr1D 87.923 207 20 3 2582 2787 6775686 6775888 7.010000e-59 239.0
2 TraesCS1D01G013200 chr1D 87.923 207 20 3 2058 2260 6776210 6776415 7.010000e-59 239.0
3 TraesCS1D01G013200 chr1B 88.558 3557 250 90 3 3491 9074017 9070550 0.000000e+00 4169.0
4 TraesCS1D01G013200 chr1B 94.788 518 23 2 4901 5418 8948544 8948031 0.000000e+00 804.0
5 TraesCS1D01G013200 chr1B 83.693 417 53 13 3485 3900 9070518 9070116 3.960000e-101 379.0
6 TraesCS1D01G013200 chr1B 81.818 363 42 20 4107 4459 9070085 9069737 3.200000e-72 283.0
7 TraesCS1D01G013200 chr1B 82.946 129 17 3 4848 4975 486351941 486352065 1.600000e-20 111.0
8 TraesCS1D01G013200 chr1A 85.076 2640 248 68 1 2583 8246410 8248960 0.000000e+00 2558.0
9 TraesCS1D01G013200 chr1A 92.718 975 41 14 3481 4429 8249977 8250947 0.000000e+00 1380.0
10 TraesCS1D01G013200 chr1A 88.958 643 47 12 4794 5419 8264057 8264692 0.000000e+00 773.0
11 TraesCS1D01G013200 chr1A 91.597 476 33 5 2578 3051 8248985 8249455 0.000000e+00 651.0
12 TraesCS1D01G013200 chr1A 87.111 450 33 13 3043 3476 8249500 8249940 2.270000e-133 486.0
13 TraesCS1D01G013200 chr1A 83.641 434 59 9 1829 2254 8248756 8249185 1.090000e-106 398.0
14 TraesCS1D01G013200 chr1A 82.819 227 27 8 2566 2785 8248416 8248637 5.540000e-45 193.0
15 TraesCS1D01G013200 chr1A 100.000 28 0 0 4586 4613 8251638 8251665 1.000000e-02 52.8
16 TraesCS1D01G013200 chr4A 90.573 541 46 4 1904 2443 68460326 68459790 0.000000e+00 712.0
17 TraesCS1D01G013200 chr4A 82.895 228 29 8 2566 2787 68460193 68459970 4.280000e-46 196.0
18 TraesCS1D01G013200 chr5B 90.388 541 46 5 1904 2443 56554399 56554934 0.000000e+00 706.0
19 TraesCS1D01G013200 chr5B 83.406 229 26 10 2566 2787 56554532 56554755 9.200000e-48 202.0
20 TraesCS1D01G013200 chr5B 81.250 240 45 0 5178 5417 689223584 689223823 1.540000e-45 195.0
21 TraesCS1D01G013200 chr7B 86.712 587 65 8 1460 2034 632610216 632610801 1.650000e-179 640.0
22 TraesCS1D01G013200 chr7B 85.520 587 68 9 1460 2034 421500529 421499948 1.000000e-166 597.0
23 TraesCS1D01G013200 chr2D 77.448 1011 158 45 3482 4451 448217500 448218481 1.720000e-149 540.0
24 TraesCS1D01G013200 chr2D 80.000 395 44 20 2714 3097 547519013 547518643 5.380000e-65 259.0
25 TraesCS1D01G013200 chr2A 76.598 1017 156 51 3482 4451 5091653 5092634 8.160000e-133 484.0
26 TraesCS1D01G013200 chrUn 76.683 995 147 47 3482 4438 81836638 81837585 1.770000e-129 473.0
27 TraesCS1D01G013200 chrUn 83.582 201 19 5 2817 3009 81836254 81836448 5.580000e-40 176.0
28 TraesCS1D01G013200 chr6A 76.660 994 149 45 3482 4438 12105467 12106414 1.770000e-129 473.0
29 TraesCS1D01G013200 chr6A 84.865 185 15 7 2817 2994 12105100 12105278 2.010000e-39 174.0
30 TraesCS1D01G013200 chr3A 76.459 994 151 45 3482 4438 102673082 102672135 3.820000e-126 462.0
31 TraesCS1D01G013200 chr3A 81.860 215 26 4 2817 3024 102673465 102673257 9.330000e-38 169.0
32 TraesCS1D01G013200 chr5D 82.479 234 41 0 5184 5417 546075399 546075632 7.110000e-49 206.0
33 TraesCS1D01G013200 chr2B 92.771 83 6 0 1121 1203 470057846 470057928 2.650000e-23 121.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G013200 chr1D 6773629 6779047 5418 False 3495.333333 10008 91.948667 1 5419 3 chr1D.!!$F1 5418
1 TraesCS1D01G013200 chr1B 9069737 9074017 4280 True 1610.333333 4169 84.689667 3 4459 3 chr1B.!!$R2 4456
2 TraesCS1D01G013200 chr1B 8948031 8948544 513 True 804.000000 804 94.788000 4901 5418 1 chr1B.!!$R1 517
3 TraesCS1D01G013200 chr1A 8246410 8251665 5255 False 816.971429 2558 88.994571 1 4613 7 chr1A.!!$F2 4612
4 TraesCS1D01G013200 chr1A 8264057 8264692 635 False 773.000000 773 88.958000 4794 5419 1 chr1A.!!$F1 625
5 TraesCS1D01G013200 chr4A 68459790 68460326 536 True 454.000000 712 86.734000 1904 2787 2 chr4A.!!$R1 883
6 TraesCS1D01G013200 chr5B 56554399 56554934 535 False 454.000000 706 86.897000 1904 2787 2 chr5B.!!$F2 883
7 TraesCS1D01G013200 chr7B 632610216 632610801 585 False 640.000000 640 86.712000 1460 2034 1 chr7B.!!$F1 574
8 TraesCS1D01G013200 chr7B 421499948 421500529 581 True 597.000000 597 85.520000 1460 2034 1 chr7B.!!$R1 574
9 TraesCS1D01G013200 chr2D 448217500 448218481 981 False 540.000000 540 77.448000 3482 4451 1 chr2D.!!$F1 969
10 TraesCS1D01G013200 chr2A 5091653 5092634 981 False 484.000000 484 76.598000 3482 4451 1 chr2A.!!$F1 969
11 TraesCS1D01G013200 chrUn 81836254 81837585 1331 False 324.500000 473 80.132500 2817 4438 2 chrUn.!!$F1 1621
12 TraesCS1D01G013200 chr6A 12105100 12106414 1314 False 323.500000 473 80.762500 2817 4438 2 chr6A.!!$F1 1621
13 TraesCS1D01G013200 chr3A 102672135 102673465 1330 True 315.500000 462 79.159500 2817 4438 2 chr3A.!!$R1 1621

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
137 145 0.039180 TCCCCTGACTCACGCTTCTA 59.961 55.0 0.00 0.00 0.00 2.10 F
1573 1634 0.037975 GCCAGTTCATTTGCCTGGTG 60.038 55.0 13.94 0.00 46.09 4.17 F
2338 2431 0.181114 CTCGAGGGATTGGATGGCAA 59.819 55.0 3.91 0.00 0.00 4.52 F
2509 2606 0.242825 TTACTCCGTTGAGCTGTCGG 59.757 55.0 12.69 12.69 42.74 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1900 1989 0.391130 GCATGCTCCACAGACGGTAA 60.391 55.0 11.37 0.0 0.00 2.85 R
2955 3102 0.040692 CAATGATTCCATGCGCTCCG 60.041 55.0 9.73 0.0 32.36 4.63 R
3338 3547 0.477795 AGGGGTTTACCTTGGCCTCT 60.478 55.0 3.32 0.0 37.69 3.69 R
4499 4878 0.035439 TCCAATTCACCGCCTTCTCC 60.035 55.0 0.00 0.0 0.00 3.71 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
91 95 3.118408 CCTAACTACCCAAGCATAGCACA 60.118 47.826 0.00 0.00 0.00 4.57
97 101 3.696045 ACCCAAGCATAGCACACATTTA 58.304 40.909 0.00 0.00 0.00 1.40
103 107 7.927629 CCCAAGCATAGCACACATTTATATTTT 59.072 33.333 0.00 0.00 0.00 1.82
137 145 0.039180 TCCCCTGACTCACGCTTCTA 59.961 55.000 0.00 0.00 0.00 2.10
152 160 6.071784 TCACGCTTCTAGTGTTACCATAGAAA 60.072 38.462 7.47 0.00 36.71 2.52
161 169 9.256477 CTAGTGTTACCATAGAAATTATCGCAA 57.744 33.333 0.00 0.00 0.00 4.85
194 209 4.276926 ACACCTTCTTCAAGATGTTGCTTC 59.723 41.667 0.00 0.00 31.45 3.86
200 215 2.783135 TCAAGATGTTGCTTCTGACCC 58.217 47.619 0.00 0.00 33.23 4.46
209 224 6.084326 TGTTGCTTCTGACCCTTATTTTTC 57.916 37.500 0.00 0.00 0.00 2.29
216 231 8.563732 GCTTCTGACCCTTATTTTTCTATCATC 58.436 37.037 0.00 0.00 0.00 2.92
217 232 8.662781 TTCTGACCCTTATTTTTCTATCATCG 57.337 34.615 0.00 0.00 0.00 3.84
219 234 5.465390 TGACCCTTATTTTTCTATCATCGCG 59.535 40.000 0.00 0.00 0.00 5.87
335 350 4.855531 AGCAGTCAAAATTGTTACGGTTC 58.144 39.130 0.00 0.00 0.00 3.62
336 351 4.336993 AGCAGTCAAAATTGTTACGGTTCA 59.663 37.500 0.00 0.00 0.00 3.18
338 353 5.212194 CAGTCAAAATTGTTACGGTTCAGG 58.788 41.667 0.00 0.00 0.00 3.86
340 355 3.632604 TCAAAATTGTTACGGTTCAGGCA 59.367 39.130 0.00 0.00 0.00 4.75
342 357 4.434713 AAATTGTTACGGTTCAGGCATC 57.565 40.909 0.00 0.00 0.00 3.91
360 380 0.892755 TCCGGCTCACAGTAATTCGT 59.107 50.000 0.00 0.00 0.00 3.85
384 404 7.041303 CGTCCATGAATCTTGATTCATCTTCAT 60.041 37.037 26.63 10.92 46.24 2.57
401 421 7.502226 TCATCTTCATTTGTCTTGTAAACACCT 59.498 33.333 0.00 0.00 0.00 4.00
405 425 6.353323 TCATTTGTCTTGTAAACACCTGAGA 58.647 36.000 0.00 0.00 0.00 3.27
408 428 5.353394 TGTCTTGTAAACACCTGAGACTT 57.647 39.130 11.79 0.00 33.45 3.01
415 435 9.450807 CTTGTAAACACCTGAGACTTAAATTTG 57.549 33.333 0.00 0.00 0.00 2.32
422 442 8.052748 ACACCTGAGACTTAAATTTGCCATATA 58.947 33.333 0.00 0.00 0.00 0.86
424 444 9.646522 ACCTGAGACTTAAATTTGCCATATAAT 57.353 29.630 0.00 0.00 0.00 1.28
458 480 6.058183 ACTCATCAACCAATCTATGTTAGGC 58.942 40.000 0.00 0.00 0.00 3.93
461 483 5.092554 TCAACCAATCTATGTTAGGCGAA 57.907 39.130 0.00 0.00 0.00 4.70
462 484 5.492895 TCAACCAATCTATGTTAGGCGAAA 58.507 37.500 0.00 0.00 0.00 3.46
463 485 5.584649 TCAACCAATCTATGTTAGGCGAAAG 59.415 40.000 0.00 0.00 0.00 2.62
464 486 5.353394 ACCAATCTATGTTAGGCGAAAGA 57.647 39.130 0.00 0.00 0.00 2.52
476 498 7.653647 TGTTAGGCGAAAGACAAAAACAATAT 58.346 30.769 0.00 0.00 46.78 1.28
488 510 6.000840 ACAAAAACAATATCCCGCCAAAATT 58.999 32.000 0.00 0.00 0.00 1.82
494 516 4.724279 ATATCCCGCCAAAATTAGACCT 57.276 40.909 0.00 0.00 0.00 3.85
536 561 9.239551 AGACAATGTGATACCTACGCTAATATA 57.760 33.333 0.00 0.00 0.00 0.86
537 562 9.850628 GACAATGTGATACCTACGCTAATATAA 57.149 33.333 0.00 0.00 0.00 0.98
608 636 5.219587 CGAATCGAAACGCATTAACTTTGTG 60.220 40.000 0.00 0.00 0.00 3.33
612 640 2.415697 ACGCATTAACTTTGTGCCAC 57.584 45.000 0.00 0.00 35.51 5.01
634 662 7.041440 GCCACCACAACAAAAATTAAAGCTAAT 60.041 33.333 0.00 0.00 0.00 1.73
690 718 9.745880 GGCTAAAAACTCTTTATTTTATAGCCC 57.254 33.333 19.46 10.60 41.93 5.19
776 806 1.054406 TTAGCCGCTAAGCCATCCCT 61.054 55.000 8.84 0.00 0.00 4.20
777 807 1.472662 TAGCCGCTAAGCCATCCCTC 61.473 60.000 0.00 0.00 0.00 4.30
1028 1058 0.107017 TCCGAGTAGTAAGTCCCCGG 60.107 60.000 0.00 0.00 37.08 5.73
1057 1087 1.084370 CGCCGCCGATCTTTCTTTCT 61.084 55.000 0.00 0.00 36.29 2.52
1060 1090 2.476352 GCCGCCGATCTTTCTTTCTTTC 60.476 50.000 0.00 0.00 0.00 2.62
1061 1091 3.003480 CCGCCGATCTTTCTTTCTTTCT 58.997 45.455 0.00 0.00 0.00 2.52
1063 1093 3.241804 CGCCGATCTTTCTTTCTTTCTCG 60.242 47.826 0.00 0.00 0.00 4.04
1065 1095 3.929610 CCGATCTTTCTTTCTTTCTCGCT 59.070 43.478 0.00 0.00 0.00 4.93
1067 1097 5.312054 CGATCTTTCTTTCTTTCTCGCTTG 58.688 41.667 0.00 0.00 0.00 4.01
1069 1099 6.183360 CGATCTTTCTTTCTTTCTCGCTTGAT 60.183 38.462 0.00 0.00 0.00 2.57
1072 1102 7.134815 TCTTTCTTTCTTTCTCGCTTGATTTG 58.865 34.615 0.00 0.00 0.00 2.32
1073 1103 6.377327 TTCTTTCTTTCTCGCTTGATTTGT 57.623 33.333 0.00 0.00 0.00 2.83
1074 1104 5.990408 TCTTTCTTTCTCGCTTGATTTGTC 58.010 37.500 0.00 0.00 0.00 3.18
1078 1108 1.070821 TCTCGCTTGATTTGTCTGCG 58.929 50.000 0.00 0.00 46.71 5.18
1079 1109 0.792640 CTCGCTTGATTTGTCTGCGT 59.207 50.000 0.00 0.00 45.69 5.24
1082 1118 1.971962 CGCTTGATTTGTCTGCGTTTC 59.028 47.619 0.00 0.00 41.45 2.78
1087 1123 5.555069 GCTTGATTTGTCTGCGTTTCTTTTG 60.555 40.000 0.00 0.00 0.00 2.44
1090 1126 5.514914 TGATTTGTCTGCGTTTCTTTTGTTC 59.485 36.000 0.00 0.00 0.00 3.18
1264 1315 2.676016 TTCTTTTGCGCGTGCCAAGG 62.676 55.000 19.87 14.51 41.78 3.61
1283 1334 7.105588 GCCAAGGAAATTTATGAGGTTTGATT 58.894 34.615 0.00 0.00 0.00 2.57
1286 1337 9.143631 CAAGGAAATTTATGAGGTTTGATTGAC 57.856 33.333 0.00 0.00 0.00 3.18
1293 1344 5.909621 ATGAGGTTTGATTGACTGATTGG 57.090 39.130 0.00 0.00 0.00 3.16
1295 1346 4.761739 TGAGGTTTGATTGACTGATTGGTC 59.238 41.667 0.00 0.00 36.81 4.02
1296 1347 3.753272 AGGTTTGATTGACTGATTGGTCG 59.247 43.478 0.00 0.00 38.91 4.79
1297 1348 3.751175 GGTTTGATTGACTGATTGGTCGA 59.249 43.478 0.00 0.00 38.91 4.20
1298 1349 4.396166 GGTTTGATTGACTGATTGGTCGAT 59.604 41.667 0.00 0.00 41.48 3.59
1302 1353 1.866015 TGACTGATTGGTCGATCCCT 58.134 50.000 0.00 0.00 38.91 4.20
1398 1454 2.613691 CCCTTTTGCTGTGATTGATGC 58.386 47.619 0.00 0.00 0.00 3.91
1418 1475 2.629336 AGCTCCATTAAGTAGCTGCC 57.371 50.000 0.00 0.00 44.67 4.85
1427 1484 0.736325 AAGTAGCTGCCGCAAGTACG 60.736 55.000 2.05 0.00 39.10 3.67
1448 1505 2.617532 GGGCTTCTGACTGAATCTGCTT 60.618 50.000 0.00 0.00 33.71 3.91
1567 1628 1.636988 GCTGATGCCAGTTCATTTGC 58.363 50.000 0.00 0.00 42.35 3.68
1568 1629 1.738030 GCTGATGCCAGTTCATTTGCC 60.738 52.381 0.00 0.00 42.35 4.52
1573 1634 0.037975 GCCAGTTCATTTGCCTGGTG 60.038 55.000 13.94 0.00 46.09 4.17
1575 1636 1.331214 CAGTTCATTTGCCTGGTGGT 58.669 50.000 0.00 0.00 35.27 4.16
1616 1677 2.154462 GGGATATGGTGCTTGGATTCG 58.846 52.381 0.00 0.00 0.00 3.34
1696 1764 4.192317 GCTAGATCTTGGTGTTAGGTTGG 58.808 47.826 0.00 0.00 0.00 3.77
1700 1768 3.775261 TCTTGGTGTTAGGTTGGTACC 57.225 47.619 4.43 4.43 45.39 3.34
1714 1782 5.442391 GGTTGGTACCTGGATTGCTTTATA 58.558 41.667 14.36 0.00 41.53 0.98
1768 1836 1.065418 AGGGGTTTCTGATTGGCGTAG 60.065 52.381 0.00 0.00 0.00 3.51
1853 1941 4.320844 CCAGGGAGGTGGGGATAG 57.679 66.667 0.00 0.00 33.46 2.08
1862 1950 4.490706 GGAGGTGGGGATAGTTACAGTAT 58.509 47.826 0.00 0.00 0.00 2.12
1876 1965 7.941053 AGTTACAGTATTATATTGTGGGGGA 57.059 36.000 10.08 0.00 30.84 4.81
1894 1983 2.027192 GGGAAATGCAGTGACACCTAGA 60.027 50.000 0.84 0.00 0.00 2.43
1898 1987 5.183904 GGAAATGCAGTGACACCTAGAAAAT 59.816 40.000 0.84 0.00 0.00 1.82
1899 1988 6.374333 GGAAATGCAGTGACACCTAGAAAATA 59.626 38.462 0.84 0.00 0.00 1.40
1900 1989 7.067494 GGAAATGCAGTGACACCTAGAAAATAT 59.933 37.037 0.84 0.00 0.00 1.28
1984 2074 7.221838 GTGCGCCATTTTTAGCTGATTTTATTA 59.778 33.333 4.18 0.00 0.00 0.98
2077 2167 3.502211 GCTGCACCAACTAAAGCTCTTAA 59.498 43.478 0.00 0.00 0.00 1.85
2078 2168 4.613850 GCTGCACCAACTAAAGCTCTTAAC 60.614 45.833 0.00 0.00 0.00 2.01
2114 2207 9.981460 AGGAATTGCTTTATATTATAAGGGAGG 57.019 33.333 0.00 0.00 0.00 4.30
2134 2227 6.062749 GGAGGTCTTTTATGATAAACCCCTC 58.937 44.000 18.94 18.94 32.81 4.30
2147 2240 2.327325 ACCCCTCTGTGTACATCACT 57.673 50.000 0.00 0.00 46.27 3.41
2174 2267 1.922447 AGATTGGGCCAATGTACTCCA 59.078 47.619 35.23 3.44 33.90 3.86
2175 2268 2.515429 AGATTGGGCCAATGTACTCCAT 59.485 45.455 35.23 9.91 33.90 3.41
2176 2269 2.142356 TTGGGCCAATGTACTCCATG 57.858 50.000 16.66 0.00 32.82 3.66
2198 2291 9.871238 CCATGAGTAATTACTTACTGTACAACT 57.129 33.333 18.96 0.00 45.97 3.16
2254 2347 4.337836 TGCAAATAATTGGAAGCTATCGCA 59.662 37.500 0.00 0.00 36.39 5.10
2264 2357 1.242076 AGCTATCGCATTGATTGGGC 58.758 50.000 0.00 0.00 38.57 5.36
2338 2431 0.181114 CTCGAGGGATTGGATGGCAA 59.819 55.000 3.91 0.00 0.00 4.52
2339 2432 0.846015 TCGAGGGATTGGATGGCAAT 59.154 50.000 0.00 0.00 0.00 3.56
2468 2565 2.028420 TGTACCATCTGTGCAGCATC 57.972 50.000 0.00 0.00 34.39 3.91
2508 2605 1.337821 GTTACTCCGTTGAGCTGTCG 58.662 55.000 0.00 0.00 42.74 4.35
2509 2606 0.242825 TTACTCCGTTGAGCTGTCGG 59.757 55.000 12.69 12.69 42.74 4.79
2510 2607 0.892358 TACTCCGTTGAGCTGTCGGT 60.892 55.000 16.64 5.40 42.74 4.69
2511 2608 1.734477 CTCCGTTGAGCTGTCGGTG 60.734 63.158 16.64 12.28 43.94 4.94
2512 2609 2.029073 CCGTTGAGCTGTCGGTGT 59.971 61.111 11.21 0.00 39.51 4.16
2513 2610 2.310233 CCGTTGAGCTGTCGGTGTG 61.310 63.158 11.21 0.00 39.51 3.82
2514 2611 2.939022 GTTGAGCTGTCGGTGTGC 59.061 61.111 0.00 0.00 0.00 4.57
2577 2685 3.576550 GGAAAGTAAAATGGCCTGGTTGA 59.423 43.478 3.32 0.00 0.00 3.18
2623 2763 4.664150 TTGTTTCGAGGGAAATTGCTTT 57.336 36.364 0.00 0.00 43.58 3.51
2624 2764 5.776173 TTGTTTCGAGGGAAATTGCTTTA 57.224 34.783 0.00 0.00 43.58 1.85
2663 2803 6.012858 AGGTCTTTTATGATGAACCCTGTGTA 60.013 38.462 0.00 0.00 0.00 2.90
2675 2815 3.178046 ACCCTGTGTATGTACATCACCA 58.822 45.455 23.70 13.90 38.63 4.17
2767 2907 8.572185 TGCTAAGCAGTCATAATTACAAACAAA 58.428 29.630 0.00 0.00 33.32 2.83
2775 2915 8.034804 AGTCATAATTACAAACAAATGGAAGCC 58.965 33.333 0.00 0.00 0.00 4.35
2798 2938 2.222213 TCGCGTTGATGGTTAGTTGTTG 59.778 45.455 5.77 0.00 0.00 3.33
2857 2997 7.581213 ACAAAATCTACCTGTGTTCATTCAA 57.419 32.000 0.00 0.00 0.00 2.69
2955 3102 4.390909 ACAATAACAAGCAGTTACTACCGC 59.609 41.667 4.20 0.00 44.95 5.68
3080 3282 7.225538 AGTTTCACTCTAGTCATTGTTGAACTG 59.774 37.037 0.00 0.00 32.48 3.16
3085 3287 6.926272 ACTCTAGTCATTGTTGAACTGAACTC 59.074 38.462 0.00 0.00 32.48 3.01
3112 3314 8.685536 GTTCATTTTCGCTCTGCATTATTTATC 58.314 33.333 0.00 0.00 0.00 1.75
3150 3352 7.050377 TCAGGAATGAGGATCTACATTTTCAC 58.950 38.462 15.06 9.08 36.94 3.18
3184 3393 9.209048 TCATGGTGTTAATACTCCTTACTACAT 57.791 33.333 2.17 0.00 38.47 2.29
3230 3439 4.762251 ACAGATAGGGAAAGCTTCAACAAC 59.238 41.667 0.00 0.00 0.00 3.32
3293 3502 2.478134 CAGTGTGTGCAAGCTTCTAGTC 59.522 50.000 0.00 0.00 0.00 2.59
3338 3547 6.051074 TGATAGTAAGGTCGTCGATACAGAA 58.949 40.000 0.00 0.00 0.00 3.02
3356 3565 0.408309 AAGAGGCCAAGGTAAACCCC 59.592 55.000 5.01 0.00 36.42 4.95
3378 3588 5.320277 CCTTCTCTCTTTCTTGGTTCCATT 58.680 41.667 0.00 0.00 0.00 3.16
3383 3593 5.445069 TCTCTTTCTTGGTTCCATTGACAA 58.555 37.500 0.00 0.00 0.00 3.18
3385 3596 7.230747 TCTCTTTCTTGGTTCCATTGACAATA 58.769 34.615 0.00 0.00 0.00 1.90
3395 3606 7.230510 TGGTTCCATTGACAATATTAGCCATAC 59.769 37.037 0.00 0.00 0.00 2.39
3435 3650 0.807667 CCTGCGACCATGCTACAGTC 60.808 60.000 0.00 0.00 35.36 3.51
3476 3700 7.121759 ACAGCTTGCTGTTATCAACATTTAGAT 59.878 33.333 20.95 0.00 41.26 1.98
3477 3701 7.431376 CAGCTTGCTGTTATCAACATTTAGATG 59.569 37.037 13.89 0.00 41.26 2.90
3478 3702 6.694411 GCTTGCTGTTATCAACATTTAGATGG 59.306 38.462 0.00 0.00 41.26 3.51
3479 3703 7.415541 GCTTGCTGTTATCAACATTTAGATGGA 60.416 37.037 0.00 0.00 41.26 3.41
3559 3826 6.801539 TCTCTAGTTGCCACAATAAAACAG 57.198 37.500 0.00 0.00 0.00 3.16
3603 3870 9.630098 TTTCATTCTTGATAAATTGACAAGCTC 57.370 29.630 11.93 0.00 40.20 4.09
3641 3909 4.917906 ACTCCTCTTCCTAATGCAGTTT 57.082 40.909 0.00 0.00 0.00 2.66
3650 3918 7.327975 TCTTCCTAATGCAGTTTCGATCTTTA 58.672 34.615 0.00 0.00 0.00 1.85
3661 3934 7.439655 GCAGTTTCGATCTTTACTATTCAGGAT 59.560 37.037 0.00 0.00 0.00 3.24
3891 4166 7.445121 TCTCTGTTATATTTGGCACTGATAGG 58.555 38.462 0.00 0.00 0.00 2.57
3900 4176 3.609853 TGGCACTGATAGGTCATCAAAC 58.390 45.455 0.00 0.00 43.15 2.93
3905 4181 3.195610 ACTGATAGGTCATCAAACGAGCA 59.804 43.478 0.00 0.00 43.15 4.26
4024 4308 2.103432 CTCTGCATCATCAAGAGAGGCT 59.897 50.000 0.00 0.00 42.74 4.58
4080 4371 3.427638 CCAGCAAGAGCAATGATGAACAG 60.428 47.826 3.62 0.00 45.49 3.16
4091 4386 7.439381 AGCAATGATGAACAGTTTCTCAAAAT 58.561 30.769 3.59 0.00 32.36 1.82
4117 4448 4.440808 TCCCATGGGAGTTTTCTAGGTTA 58.559 43.478 30.62 1.60 39.76 2.85
4431 4810 2.015588 GCTCATAAGCTCAGCAAGGCA 61.016 52.381 0.00 0.00 45.55 4.75
4438 4817 1.246056 GCTCAGCAAGGCACCATTCA 61.246 55.000 0.00 0.00 0.00 2.57
4451 4830 3.313526 GCACCATTCATACACCTCATGAC 59.686 47.826 0.00 0.00 32.23 3.06
4455 4834 4.758674 CCATTCATACACCTCATGACATCC 59.241 45.833 0.00 0.00 32.23 3.51
4459 4838 0.984230 ACACCTCATGACATCCGGTT 59.016 50.000 0.00 0.00 0.00 4.44
4460 4839 1.339055 ACACCTCATGACATCCGGTTG 60.339 52.381 11.06 11.06 0.00 3.77
4461 4840 0.984230 ACCTCATGACATCCGGTTGT 59.016 50.000 18.02 18.02 0.00 3.32
4462 4841 1.339055 ACCTCATGACATCCGGTTGTG 60.339 52.381 22.62 12.21 0.00 3.33
4463 4842 1.066215 CCTCATGACATCCGGTTGTGA 60.066 52.381 22.62 15.08 0.00 3.58
4464 4843 2.274437 CTCATGACATCCGGTTGTGAG 58.726 52.381 22.62 17.54 36.00 3.51
4465 4844 1.623311 TCATGACATCCGGTTGTGAGT 59.377 47.619 22.62 5.65 0.00 3.41
4466 4845 2.038426 TCATGACATCCGGTTGTGAGTT 59.962 45.455 22.62 0.00 0.00 3.01
4467 4846 1.877637 TGACATCCGGTTGTGAGTTG 58.122 50.000 22.62 1.54 0.00 3.16
4468 4847 1.140052 TGACATCCGGTTGTGAGTTGT 59.860 47.619 22.62 4.59 0.00 3.32
4469 4848 2.218603 GACATCCGGTTGTGAGTTGTT 58.781 47.619 22.62 0.00 0.00 2.83
4470 4849 1.946768 ACATCCGGTTGTGAGTTGTTG 59.053 47.619 17.33 0.00 0.00 3.33
4471 4850 1.266718 CATCCGGTTGTGAGTTGTTGG 59.733 52.381 0.00 0.00 0.00 3.77
4472 4851 0.542333 TCCGGTTGTGAGTTGTTGGA 59.458 50.000 0.00 0.00 0.00 3.53
4473 4852 0.944386 CCGGTTGTGAGTTGTTGGAG 59.056 55.000 0.00 0.00 0.00 3.86
4474 4853 0.944386 CGGTTGTGAGTTGTTGGAGG 59.056 55.000 0.00 0.00 0.00 4.30
4475 4854 0.668535 GGTTGTGAGTTGTTGGAGGC 59.331 55.000 0.00 0.00 0.00 4.70
4476 4855 1.680338 GTTGTGAGTTGTTGGAGGCT 58.320 50.000 0.00 0.00 0.00 4.58
4477 4856 1.334869 GTTGTGAGTTGTTGGAGGCTG 59.665 52.381 0.00 0.00 0.00 4.85
4478 4857 0.179020 TGTGAGTTGTTGGAGGCTGG 60.179 55.000 0.00 0.00 0.00 4.85
4479 4858 0.108585 GTGAGTTGTTGGAGGCTGGA 59.891 55.000 0.00 0.00 0.00 3.86
4480 4859 0.843309 TGAGTTGTTGGAGGCTGGAA 59.157 50.000 0.00 0.00 0.00 3.53
4481 4860 1.214175 TGAGTTGTTGGAGGCTGGAAA 59.786 47.619 0.00 0.00 0.00 3.13
4482 4861 2.306847 GAGTTGTTGGAGGCTGGAAAA 58.693 47.619 0.00 0.00 0.00 2.29
4483 4862 2.893489 GAGTTGTTGGAGGCTGGAAAAT 59.107 45.455 0.00 0.00 0.00 1.82
4484 4863 3.308401 AGTTGTTGGAGGCTGGAAAATT 58.692 40.909 0.00 0.00 0.00 1.82
4485 4864 3.321968 AGTTGTTGGAGGCTGGAAAATTC 59.678 43.478 0.00 0.00 0.00 2.17
4486 4865 2.956132 TGTTGGAGGCTGGAAAATTCA 58.044 42.857 0.00 0.00 0.00 2.57
4487 4866 2.627699 TGTTGGAGGCTGGAAAATTCAC 59.372 45.455 0.00 0.00 0.00 3.18
4488 4867 1.923356 TGGAGGCTGGAAAATTCACC 58.077 50.000 0.00 0.00 0.00 4.02
4489 4868 1.146774 TGGAGGCTGGAAAATTCACCA 59.853 47.619 0.00 4.01 34.81 4.17
4490 4869 2.225343 TGGAGGCTGGAAAATTCACCAT 60.225 45.455 0.00 0.00 35.54 3.55
4491 4870 2.428530 GGAGGCTGGAAAATTCACCATC 59.571 50.000 0.00 1.34 35.54 3.51
4492 4871 3.091545 GAGGCTGGAAAATTCACCATCA 58.908 45.455 0.00 0.00 35.54 3.07
4493 4872 3.509442 AGGCTGGAAAATTCACCATCAA 58.491 40.909 4.42 0.00 35.54 2.57
4494 4873 3.903090 AGGCTGGAAAATTCACCATCAAA 59.097 39.130 4.42 0.00 35.54 2.69
4495 4874 4.020839 AGGCTGGAAAATTCACCATCAAAG 60.021 41.667 4.42 0.00 35.54 2.77
4496 4875 4.248058 GCTGGAAAATTCACCATCAAAGG 58.752 43.478 4.42 0.00 35.54 3.11
4497 4876 4.248058 CTGGAAAATTCACCATCAAAGGC 58.752 43.478 4.42 0.00 35.54 4.35
4498 4877 3.903090 TGGAAAATTCACCATCAAAGGCT 59.097 39.130 0.27 0.00 0.00 4.58
4499 4878 4.248058 GGAAAATTCACCATCAAAGGCTG 58.752 43.478 0.00 0.00 0.00 4.85
4500 4879 3.967332 AAATTCACCATCAAAGGCTGG 57.033 42.857 0.00 0.00 38.55 4.85
4501 4880 2.905415 ATTCACCATCAAAGGCTGGA 57.095 45.000 0.00 0.00 36.35 3.86
4502 4881 2.205022 TTCACCATCAAAGGCTGGAG 57.795 50.000 0.00 0.00 36.35 3.86
4503 4882 1.361204 TCACCATCAAAGGCTGGAGA 58.639 50.000 0.00 0.00 36.35 3.71
4504 4883 1.704628 TCACCATCAAAGGCTGGAGAA 59.295 47.619 0.00 0.00 36.35 2.87
4505 4884 2.089980 CACCATCAAAGGCTGGAGAAG 58.910 52.381 0.00 0.00 36.35 2.85
4506 4885 1.005215 ACCATCAAAGGCTGGAGAAGG 59.995 52.381 0.00 0.00 36.35 3.46
4528 4907 4.213482 GGCGGTGAATTGGATATACTGAAC 59.787 45.833 0.00 0.00 0.00 3.18
4535 4914 8.391106 GTGAATTGGATATACTGAACACAGAAC 58.609 37.037 0.00 0.00 35.80 3.01
4546 4925 9.944376 ATACTGAACACAGAACTTGTATACAAT 57.056 29.630 18.35 5.09 38.16 2.71
4550 4929 9.990360 TGAACACAGAACTTGTATACAATAGAA 57.010 29.630 18.35 0.00 38.16 2.10
4552 4931 9.998106 AACACAGAACTTGTATACAATAGAACT 57.002 29.630 18.35 10.71 38.16 3.01
4604 4983 2.869801 CCGTCACAGTTTGAGCTTGTTA 59.130 45.455 0.00 0.00 33.71 2.41
4628 5007 9.534565 TTATGCAATCTCACTAGTCATTACTTC 57.465 33.333 0.00 0.00 37.15 3.01
4650 5029 3.638484 GTCAGTGTTTTAGGCGCATTTT 58.362 40.909 10.83 0.00 0.00 1.82
4657 5036 5.458779 GTGTTTTAGGCGCATTTTATGGATC 59.541 40.000 10.83 0.00 0.00 3.36
4664 5043 4.320494 GGCGCATTTTATGGATCTTAGGTG 60.320 45.833 10.83 0.00 0.00 4.00
4665 5044 4.320494 GCGCATTTTATGGATCTTAGGTGG 60.320 45.833 0.30 0.00 0.00 4.61
4684 5063 7.437793 AGGTGGCAAAAATTGTATGAAAATG 57.562 32.000 0.00 0.00 0.00 2.32
4696 5080 6.631971 TGTATGAAAATGTGAGCTTGTCAA 57.368 33.333 0.00 0.00 36.74 3.18
4722 5106 7.865820 TCATCCTGTTATCTTTCAGAAAGGAT 58.134 34.615 20.70 12.49 39.01 3.24
4733 5117 7.765307 TCTTTCAGAAAGGATCATATTGTTGC 58.235 34.615 20.70 0.00 39.01 4.17
4734 5118 7.613022 TCTTTCAGAAAGGATCATATTGTTGCT 59.387 33.333 20.70 0.00 39.01 3.91
4735 5119 6.688637 TCAGAAAGGATCATATTGTTGCTG 57.311 37.500 0.00 0.00 0.00 4.41
4736 5120 6.417258 TCAGAAAGGATCATATTGTTGCTGA 58.583 36.000 0.00 0.00 0.00 4.26
4737 5121 6.541278 TCAGAAAGGATCATATTGTTGCTGAG 59.459 38.462 0.00 0.00 0.00 3.35
4739 5123 7.066645 CAGAAAGGATCATATTGTTGCTGAGAA 59.933 37.037 0.00 0.00 0.00 2.87
4754 5178 8.461222 TGTTGCTGAGAATATGGTTAATTCAAG 58.539 33.333 0.00 0.00 36.09 3.02
4762 5186 9.023962 AGAATATGGTTAATTCAAGCTTGTCAA 57.976 29.630 25.19 14.14 36.09 3.18
4770 5194 9.017669 GTTAATTCAAGCTTGTCAATCATCATC 57.982 33.333 25.19 5.07 0.00 2.92
4775 5199 4.597004 AGCTTGTCAATCATCATCCTGTT 58.403 39.130 0.00 0.00 0.00 3.16
4777 5201 5.587844 AGCTTGTCAATCATCATCCTGTTAC 59.412 40.000 0.00 0.00 0.00 2.50
4778 5202 5.355071 GCTTGTCAATCATCATCCTGTTACA 59.645 40.000 0.00 0.00 0.00 2.41
4784 5208 8.341173 GTCAATCATCATCCTGTTACATTTCTC 58.659 37.037 0.00 0.00 0.00 2.87
4785 5209 7.500227 TCAATCATCATCCTGTTACATTTCTCC 59.500 37.037 0.00 0.00 0.00 3.71
4786 5210 6.566079 TCATCATCCTGTTACATTTCTCCT 57.434 37.500 0.00 0.00 0.00 3.69
4866 5290 6.653020 ACCTTGAATGCTGACTGATGTAATA 58.347 36.000 0.00 0.00 0.00 0.98
4867 5291 7.112122 ACCTTGAATGCTGACTGATGTAATAA 58.888 34.615 0.00 0.00 0.00 1.40
4868 5292 7.066284 ACCTTGAATGCTGACTGATGTAATAAC 59.934 37.037 0.00 0.00 0.00 1.89
4890 5314 6.739331 ACTCTTATAATGGACAAGAGGAGG 57.261 41.667 13.44 0.00 46.22 4.30
4891 5315 5.071115 ACTCTTATAATGGACAAGAGGAGGC 59.929 44.000 13.44 0.00 46.22 4.70
4892 5316 4.348168 TCTTATAATGGACAAGAGGAGGCC 59.652 45.833 0.00 0.00 0.00 5.19
4893 5317 1.965414 TAATGGACAAGAGGAGGCCA 58.035 50.000 5.01 0.00 0.00 5.36
4903 5331 2.800250 AGAGGAGGCCAGAAACATTTG 58.200 47.619 5.01 0.00 0.00 2.32
5065 5617 3.541950 ATCCGCTGGGCATCATCCG 62.542 63.158 0.00 0.00 0.00 4.18
5111 5663 1.741401 CTTCTCGCCGCCATTGTCA 60.741 57.895 0.00 0.00 0.00 3.58
5156 5708 4.778143 CCTTCCTTGACCCCGGCG 62.778 72.222 0.00 0.00 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 74 3.871594 GTGTGCTATGCTTGGGTAGTTAG 59.128 47.826 0.00 0.00 0.00 2.34
91 95 9.801873 CAAACGAGGGATGAAAAATATAAATGT 57.198 29.630 0.00 0.00 0.00 2.71
97 101 5.359860 GGGACAAACGAGGGATGAAAAATAT 59.640 40.000 0.00 0.00 0.00 1.28
103 107 0.326927 GGGGACAAACGAGGGATGAA 59.673 55.000 0.00 0.00 0.00 2.57
161 169 6.182627 TCTTGAAGAAGGTGTTGATGCATAT 58.817 36.000 0.00 0.00 0.00 1.78
164 172 3.819368 TCTTGAAGAAGGTGTTGATGCA 58.181 40.909 0.00 0.00 0.00 3.96
165 173 4.730657 CATCTTGAAGAAGGTGTTGATGC 58.269 43.478 0.00 0.00 35.80 3.91
194 209 6.346919 CGCGATGATAGAAAAATAAGGGTCAG 60.347 42.308 0.00 0.00 0.00 3.51
262 277 9.739276 AGAATCTTACATGTGGACTTATTTGAA 57.261 29.630 9.11 0.00 0.00 2.69
309 324 6.225318 ACCGTAACAATTTTGACTGCTAGTA 58.775 36.000 0.00 0.00 0.00 1.82
314 329 4.602995 TGAACCGTAACAATTTTGACTGC 58.397 39.130 0.00 0.00 0.00 4.40
317 332 3.978855 GCCTGAACCGTAACAATTTTGAC 59.021 43.478 0.00 0.00 0.00 3.18
328 343 2.897207 CCGGATGCCTGAACCGTA 59.103 61.111 0.00 0.00 44.34 4.02
330 345 4.473520 AGCCGGATGCCTGAACCG 62.474 66.667 5.05 0.00 45.24 4.44
335 350 1.960040 TACTGTGAGCCGGATGCCTG 61.960 60.000 5.05 0.00 42.71 4.85
336 351 1.264749 TTACTGTGAGCCGGATGCCT 61.265 55.000 5.05 0.00 42.71 4.75
338 353 1.599542 GAATTACTGTGAGCCGGATGC 59.400 52.381 5.05 0.00 41.71 3.91
340 355 1.480954 ACGAATTACTGTGAGCCGGAT 59.519 47.619 5.05 0.00 0.00 4.18
342 357 1.278238 GACGAATTACTGTGAGCCGG 58.722 55.000 0.00 0.00 0.00 6.13
344 359 2.380084 TGGACGAATTACTGTGAGCC 57.620 50.000 0.00 0.00 0.00 4.70
346 361 6.045318 AGATTCATGGACGAATTACTGTGAG 58.955 40.000 0.00 0.00 35.74 3.51
384 404 5.741011 AGTCTCAGGTGTTTACAAGACAAA 58.259 37.500 12.45 0.00 36.06 2.83
426 446 6.560253 AGATTGGTTGATGAGTTGTACAAC 57.440 37.500 27.72 27.72 40.90 3.32
434 456 6.058183 GCCTAACATAGATTGGTTGATGAGT 58.942 40.000 0.00 0.00 0.00 3.41
458 480 4.557301 GCGGGATATTGTTTTTGTCTTTCG 59.443 41.667 0.00 0.00 0.00 3.46
461 483 3.829601 TGGCGGGATATTGTTTTTGTCTT 59.170 39.130 0.00 0.00 0.00 3.01
462 484 3.426615 TGGCGGGATATTGTTTTTGTCT 58.573 40.909 0.00 0.00 0.00 3.41
463 485 3.859411 TGGCGGGATATTGTTTTTGTC 57.141 42.857 0.00 0.00 0.00 3.18
464 486 4.608948 TTTGGCGGGATATTGTTTTTGT 57.391 36.364 0.00 0.00 0.00 2.83
476 498 2.040545 TGAAGGTCTAATTTTGGCGGGA 59.959 45.455 0.00 0.00 0.00 5.14
488 510 6.152323 GTCTAACCAGTACATGTGAAGGTCTA 59.848 42.308 9.11 7.56 0.00 2.59
494 516 6.426633 CACATTGTCTAACCAGTACATGTGAA 59.573 38.462 9.11 0.00 36.20 3.18
608 636 4.574421 AGCTTTAATTTTTGTTGTGGTGGC 59.426 37.500 0.00 0.00 0.00 5.01
612 640 9.862585 GTTGATTAGCTTTAATTTTTGTTGTGG 57.137 29.630 0.00 0.00 0.00 4.17
694 722 9.586435 TTCACATTTCCTCTTTTTCTTCTTTTC 57.414 29.630 0.00 0.00 0.00 2.29
954 984 3.937372 TTCGGGGGAGAAGGGGGAC 62.937 68.421 0.00 0.00 0.00 4.46
955 985 2.909292 GATTCGGGGGAGAAGGGGGA 62.909 65.000 0.00 0.00 33.19 4.81
956 986 2.368329 ATTCGGGGGAGAAGGGGG 60.368 66.667 0.00 0.00 33.19 5.40
957 987 2.452937 GGATTCGGGGGAGAAGGGG 61.453 68.421 0.00 0.00 33.19 4.79
958 988 2.808206 CGGATTCGGGGGAGAAGGG 61.808 68.421 0.00 0.00 33.19 3.95
959 989 2.822399 CGGATTCGGGGGAGAAGG 59.178 66.667 0.00 0.00 33.19 3.46
960 990 2.109181 GCGGATTCGGGGGAGAAG 59.891 66.667 0.00 0.00 36.79 2.85
961 991 3.476419 GGCGGATTCGGGGGAGAA 61.476 66.667 0.00 0.00 36.79 2.87
1037 1067 2.036764 GAAAGAAAGATCGGCGGCGG 62.037 60.000 31.73 13.01 0.00 6.13
1057 1087 3.542712 GCAGACAAATCAAGCGAGAAA 57.457 42.857 0.00 0.00 0.00 2.52
1063 1093 3.273919 AGAAACGCAGACAAATCAAGC 57.726 42.857 0.00 0.00 0.00 4.01
1065 1095 5.406649 ACAAAAGAAACGCAGACAAATCAA 58.593 33.333 0.00 0.00 0.00 2.57
1067 1097 5.051708 GGAACAAAAGAAACGCAGACAAATC 60.052 40.000 0.00 0.00 0.00 2.17
1069 1099 4.170256 GGAACAAAAGAAACGCAGACAAA 58.830 39.130 0.00 0.00 0.00 2.83
1072 1102 2.372350 CGGAACAAAAGAAACGCAGAC 58.628 47.619 0.00 0.00 0.00 3.51
1073 1103 1.332375 CCGGAACAAAAGAAACGCAGA 59.668 47.619 0.00 0.00 0.00 4.26
1074 1104 1.599419 CCCGGAACAAAAGAAACGCAG 60.599 52.381 0.73 0.00 0.00 5.18
1078 1108 4.048504 CAATCACCCGGAACAAAAGAAAC 58.951 43.478 0.73 0.00 0.00 2.78
1079 1109 3.954904 TCAATCACCCGGAACAAAAGAAA 59.045 39.130 0.73 0.00 0.00 2.52
1082 1118 4.022416 TCAATCAATCACCCGGAACAAAAG 60.022 41.667 0.73 0.00 0.00 2.27
1087 1123 3.016736 ACATCAATCAATCACCCGGAAC 58.983 45.455 0.73 0.00 0.00 3.62
1090 1126 1.066002 GCACATCAATCAATCACCCGG 59.934 52.381 0.00 0.00 0.00 5.73
1283 1334 1.866015 AGGGATCGACCAATCAGTCA 58.134 50.000 6.41 0.00 41.20 3.41
1286 1337 3.428045 GCAAAAAGGGATCGACCAATCAG 60.428 47.826 6.41 0.00 41.20 2.90
1293 1344 1.468914 GTCCTGCAAAAAGGGATCGAC 59.531 52.381 0.00 0.00 37.96 4.20
1295 1346 0.447801 CGTCCTGCAAAAAGGGATCG 59.552 55.000 0.00 0.00 37.96 3.69
1296 1347 1.468914 GTCGTCCTGCAAAAAGGGATC 59.531 52.381 0.00 0.00 37.96 3.36
1297 1348 1.534729 GTCGTCCTGCAAAAAGGGAT 58.465 50.000 0.00 0.00 37.96 3.85
1298 1349 0.882927 CGTCGTCCTGCAAAAAGGGA 60.883 55.000 0.00 0.00 37.96 4.20
1299 1350 1.574428 CGTCGTCCTGCAAAAAGGG 59.426 57.895 0.00 0.00 37.96 3.95
1302 1353 0.875040 TACGCGTCGTCCTGCAAAAA 60.875 50.000 18.63 0.00 41.54 1.94
1418 1475 1.080093 TCAGAAGCCCGTACTTGCG 60.080 57.895 0.00 0.00 0.00 4.85
1427 1484 1.065564 AGCAGATTCAGTCAGAAGCCC 60.066 52.381 0.00 0.00 43.58 5.19
1428 1485 2.399916 AGCAGATTCAGTCAGAAGCC 57.600 50.000 0.00 0.00 43.58 4.35
1430 1487 5.486526 AGGTAAAGCAGATTCAGTCAGAAG 58.513 41.667 0.00 0.00 40.15 2.85
1448 1505 6.040278 TGCAGACACATTCATGAAAAAGGTAA 59.960 34.615 13.09 0.00 0.00 2.85
1567 1628 3.703001 ACAGATAACAGAACCACCAGG 57.297 47.619 0.00 0.00 42.21 4.45
1568 1629 8.786826 TTATTAACAGATAACAGAACCACCAG 57.213 34.615 0.00 0.00 0.00 4.00
1573 1634 9.403583 TCCCAATTATTAACAGATAACAGAACC 57.596 33.333 0.00 0.00 0.00 3.62
1696 1764 6.964934 CGTTTTGTATAAAGCAATCCAGGTAC 59.035 38.462 0.19 0.00 0.00 3.34
1700 1768 5.799936 CACCGTTTTGTATAAAGCAATCCAG 59.200 40.000 0.19 0.00 0.00 3.86
1768 1836 6.888430 AGTTTTGTCAGAACAATGTATCGAC 58.112 36.000 8.79 0.00 44.59 4.20
1853 1941 8.983702 TTTCCCCCACAATATAATACTGTAAC 57.016 34.615 0.00 0.00 0.00 2.50
1862 1950 4.648762 CACTGCATTTCCCCCACAATATAA 59.351 41.667 0.00 0.00 0.00 0.98
1876 1965 7.944729 ATATTTTCTAGGTGTCACTGCATTT 57.055 32.000 2.35 0.00 0.00 2.32
1894 1983 4.839121 TGCTCCACAGACGGTAATATTTT 58.161 39.130 0.00 0.00 0.00 1.82
1898 1987 2.483013 GCATGCTCCACAGACGGTAATA 60.483 50.000 11.37 0.00 0.00 0.98
1899 1988 1.743772 GCATGCTCCACAGACGGTAAT 60.744 52.381 11.37 0.00 0.00 1.89
1900 1989 0.391130 GCATGCTCCACAGACGGTAA 60.391 55.000 11.37 0.00 0.00 2.85
1984 2074 2.600439 GGTAAGTACCCGCCTTCCT 58.400 57.895 0.00 0.00 40.53 3.36
2077 2167 3.515602 AGCAATTCCTCTCCAAACAGT 57.484 42.857 0.00 0.00 0.00 3.55
2078 2168 4.861102 AAAGCAATTCCTCTCCAAACAG 57.139 40.909 0.00 0.00 0.00 3.16
2114 2207 6.884836 ACACAGAGGGGTTTATCATAAAAGAC 59.115 38.462 0.00 0.00 0.00 3.01
2147 2240 4.046286 ACATTGGCCCAATCTAAGTTCA 57.954 40.909 5.84 0.00 31.05 3.18
2254 2347 2.173519 CAGAGTTGGTGCCCAATCAAT 58.826 47.619 9.49 0.00 45.80 2.57
2356 2449 5.833131 ACCACTGGACAAATTTAACACAGAT 59.167 36.000 0.71 1.96 0.00 2.90
2468 2565 0.529378 GCAATTGTTGAGCTCAGGGG 59.471 55.000 17.43 6.08 0.00 4.79
2541 2649 6.827586 TTTACTTTCCAAGCAAATATCCGT 57.172 33.333 0.00 0.00 0.00 4.69
2560 2668 4.747810 CAAGATCAACCAGGCCATTTTAC 58.252 43.478 5.01 0.00 0.00 2.01
2577 2685 2.171003 GGGCTTTAGTTGGTGCAAGAT 58.829 47.619 0.00 0.00 0.00 2.40
2631 2771 7.775561 GGGTTCATCATAAAAGACCTCACTTAT 59.224 37.037 0.00 0.00 0.00 1.73
2652 2792 4.189231 GGTGATGTACATACACAGGGTTC 58.811 47.826 25.90 13.03 39.30 3.62
2663 2803 6.547141 CCCAATCTATGTTTGGTGATGTACAT 59.453 38.462 8.43 8.43 41.74 2.29
2675 2815 3.456380 ACAGTGGCCCAATCTATGTTT 57.544 42.857 0.00 0.00 0.00 2.83
2798 2938 4.642429 ACCTAACACATCAAGTCTCAACC 58.358 43.478 0.00 0.00 0.00 3.77
2955 3102 0.040692 CAATGATTCCATGCGCTCCG 60.041 55.000 9.73 0.00 32.36 4.63
2997 3144 8.416329 GTGCCAAAAGATCAGGATAAACATTAT 58.584 33.333 0.00 0.00 0.00 1.28
3000 3147 5.127682 GGTGCCAAAAGATCAGGATAAACAT 59.872 40.000 0.00 0.00 0.00 2.71
3080 3282 3.726436 CAGAGCGAAAATGAACGAGTTC 58.274 45.455 8.89 8.89 39.91 3.01
3085 3287 2.532531 ATGCAGAGCGAAAATGAACG 57.467 45.000 0.00 0.00 0.00 3.95
3150 3352 9.784531 AGGAGTATTAACACCATGATAATTCTG 57.215 33.333 0.00 0.00 38.71 3.02
3158 3360 8.598202 TGTAGTAAGGAGTATTAACACCATGA 57.402 34.615 0.00 0.00 38.71 3.07
3184 3393 8.940768 TGTCACATCATATACGATCTGAAAAA 57.059 30.769 0.00 0.00 0.00 1.94
3203 3412 3.582647 TGAAGCTTTCCCTATCTGTCACA 59.417 43.478 0.00 0.00 0.00 3.58
3230 3439 0.583438 CACTCAACCACTGCTTGACG 59.417 55.000 0.00 0.00 0.00 4.35
3293 3502 3.658757 ACCAAATCACATTTGTTCCCG 57.341 42.857 7.92 0.00 46.22 5.14
3338 3547 0.477795 AGGGGTTTACCTTGGCCTCT 60.478 55.000 3.32 0.00 37.69 3.69
3356 3565 6.000219 TCAATGGAACCAAGAAAGAGAGAAG 59.000 40.000 0.00 0.00 0.00 2.85
3378 3588 6.493189 TGGACTGTATGGCTAATATTGTCA 57.507 37.500 0.00 0.00 32.25 3.58
3383 3593 7.986085 GTCATTTGGACTGTATGGCTAATAT 57.014 36.000 0.00 0.00 43.46 1.28
3412 3627 1.065491 TGTAGCATGGTCGCAGGAATT 60.065 47.619 0.00 0.00 0.00 2.17
3435 3650 6.089016 CAGCAAGCTGTGAAATTGAGTAATTG 59.911 38.462 13.72 0.00 36.71 2.32
3476 3700 4.882427 TCAAACTAAAATCACGGTTGTCCA 59.118 37.500 0.00 0.00 0.00 4.02
3477 3701 5.427036 TCAAACTAAAATCACGGTTGTCC 57.573 39.130 0.00 0.00 0.00 4.02
3478 3702 4.909880 GCTCAAACTAAAATCACGGTTGTC 59.090 41.667 0.00 0.00 0.00 3.18
3479 3703 4.336993 TGCTCAAACTAAAATCACGGTTGT 59.663 37.500 0.00 0.00 0.00 3.32
3559 3826 5.957842 TGAAACAGATTCATGGTGGTTAC 57.042 39.130 0.00 0.00 43.08 2.50
3599 3866 7.346960 AGGAGTATCAAGAAGAATAAAGGAGCT 59.653 37.037 0.00 0.00 36.25 4.09
3603 3870 9.541143 GAAGAGGAGTATCAAGAAGAATAAAGG 57.459 37.037 0.00 0.00 36.25 3.11
3891 4166 3.310303 GCATACTGCTCGTTTGATGAC 57.690 47.619 0.00 0.00 40.96 3.06
3905 4181 4.829492 AGCTTTTCTTTCCACAAGCATACT 59.171 37.500 5.60 0.00 43.48 2.12
4038 4322 3.130633 GGCGAATTTGAAAAGCAAGGTT 58.869 40.909 0.00 0.00 37.87 3.50
4039 4323 2.102252 TGGCGAATTTGAAAAGCAAGGT 59.898 40.909 0.00 0.00 37.87 3.50
4080 4371 5.714806 TCCCATGGGAAGTATTTTGAGAAAC 59.285 40.000 32.09 0.00 42.05 2.78
4091 4386 4.473559 CCTAGAAAACTCCCATGGGAAGTA 59.526 45.833 33.13 12.43 44.66 2.24
4429 4808 3.313526 GTCATGAGGTGTATGAATGGTGC 59.686 47.826 0.00 0.00 36.41 5.01
4431 4810 4.842531 TGTCATGAGGTGTATGAATGGT 57.157 40.909 0.00 0.00 36.41 3.55
4438 4817 2.398588 ACCGGATGTCATGAGGTGTAT 58.601 47.619 9.46 0.00 33.37 2.29
4451 4830 1.266718 CCAACAACTCACAACCGGATG 59.733 52.381 9.46 10.13 0.00 3.51
4455 4834 0.944386 CCTCCAACAACTCACAACCG 59.056 55.000 0.00 0.00 0.00 4.44
4459 4838 0.179020 CCAGCCTCCAACAACTCACA 60.179 55.000 0.00 0.00 0.00 3.58
4460 4839 0.108585 TCCAGCCTCCAACAACTCAC 59.891 55.000 0.00 0.00 0.00 3.51
4461 4840 0.843309 TTCCAGCCTCCAACAACTCA 59.157 50.000 0.00 0.00 0.00 3.41
4462 4841 1.981256 TTTCCAGCCTCCAACAACTC 58.019 50.000 0.00 0.00 0.00 3.01
4463 4842 2.452600 TTTTCCAGCCTCCAACAACT 57.547 45.000 0.00 0.00 0.00 3.16
4464 4843 3.069443 TGAATTTTCCAGCCTCCAACAAC 59.931 43.478 0.00 0.00 0.00 3.32
4465 4844 3.069443 GTGAATTTTCCAGCCTCCAACAA 59.931 43.478 0.00 0.00 0.00 2.83
4466 4845 2.627699 GTGAATTTTCCAGCCTCCAACA 59.372 45.455 0.00 0.00 0.00 3.33
4467 4846 2.029020 GGTGAATTTTCCAGCCTCCAAC 60.029 50.000 0.00 0.00 0.00 3.77
4468 4847 2.247358 GGTGAATTTTCCAGCCTCCAA 58.753 47.619 0.00 0.00 0.00 3.53
4469 4848 1.146774 TGGTGAATTTTCCAGCCTCCA 59.853 47.619 0.00 0.00 0.00 3.86
4470 4849 1.923356 TGGTGAATTTTCCAGCCTCC 58.077 50.000 0.00 0.00 0.00 4.30
4471 4850 3.091545 TGATGGTGAATTTTCCAGCCTC 58.908 45.455 13.01 4.99 39.09 4.70
4472 4851 3.173953 TGATGGTGAATTTTCCAGCCT 57.826 42.857 13.01 0.00 39.09 4.58
4473 4852 3.959535 TTGATGGTGAATTTTCCAGCC 57.040 42.857 13.01 6.78 39.09 4.85
4474 4853 4.248058 CCTTTGATGGTGAATTTTCCAGC 58.752 43.478 9.98 9.98 40.09 4.85
4475 4854 4.020839 AGCCTTTGATGGTGAATTTTCCAG 60.021 41.667 8.19 0.00 37.14 3.86
4476 4855 3.903090 AGCCTTTGATGGTGAATTTTCCA 59.097 39.130 5.28 5.28 38.14 3.53
4477 4856 4.248058 CAGCCTTTGATGGTGAATTTTCC 58.752 43.478 0.00 0.00 0.00 3.13
4478 4857 4.248058 CCAGCCTTTGATGGTGAATTTTC 58.752 43.478 0.00 0.00 43.25 2.29
4479 4858 4.276058 CCAGCCTTTGATGGTGAATTTT 57.724 40.909 0.00 0.00 43.25 1.82
4480 4859 3.967332 CCAGCCTTTGATGGTGAATTT 57.033 42.857 0.00 0.00 43.25 1.82
4488 4867 1.101331 GCCTTCTCCAGCCTTTGATG 58.899 55.000 0.00 0.00 0.00 3.07
4489 4868 0.393537 CGCCTTCTCCAGCCTTTGAT 60.394 55.000 0.00 0.00 0.00 2.57
4490 4869 1.003355 CGCCTTCTCCAGCCTTTGA 60.003 57.895 0.00 0.00 0.00 2.69
4491 4870 2.042831 CCGCCTTCTCCAGCCTTTG 61.043 63.158 0.00 0.00 0.00 2.77
4492 4871 2.352805 CCGCCTTCTCCAGCCTTT 59.647 61.111 0.00 0.00 0.00 3.11
4493 4872 2.930562 ACCGCCTTCTCCAGCCTT 60.931 61.111 0.00 0.00 0.00 4.35
4494 4873 3.710722 CACCGCCTTCTCCAGCCT 61.711 66.667 0.00 0.00 0.00 4.58
4495 4874 2.543067 ATTCACCGCCTTCTCCAGCC 62.543 60.000 0.00 0.00 0.00 4.85
4496 4875 0.678048 AATTCACCGCCTTCTCCAGC 60.678 55.000 0.00 0.00 0.00 4.85
4497 4876 1.089920 CAATTCACCGCCTTCTCCAG 58.910 55.000 0.00 0.00 0.00 3.86
4498 4877 0.322456 CCAATTCACCGCCTTCTCCA 60.322 55.000 0.00 0.00 0.00 3.86
4499 4878 0.035439 TCCAATTCACCGCCTTCTCC 60.035 55.000 0.00 0.00 0.00 3.71
4500 4879 2.044123 ATCCAATTCACCGCCTTCTC 57.956 50.000 0.00 0.00 0.00 2.87
4501 4880 3.864789 ATATCCAATTCACCGCCTTCT 57.135 42.857 0.00 0.00 0.00 2.85
4502 4881 4.452455 CAGTATATCCAATTCACCGCCTTC 59.548 45.833 0.00 0.00 0.00 3.46
4503 4882 4.102524 TCAGTATATCCAATTCACCGCCTT 59.897 41.667 0.00 0.00 0.00 4.35
4504 4883 3.646162 TCAGTATATCCAATTCACCGCCT 59.354 43.478 0.00 0.00 0.00 5.52
4505 4884 4.002906 TCAGTATATCCAATTCACCGCC 57.997 45.455 0.00 0.00 0.00 6.13
4506 4885 4.814234 TGTTCAGTATATCCAATTCACCGC 59.186 41.667 0.00 0.00 0.00 5.68
4507 4886 5.815222 TGTGTTCAGTATATCCAATTCACCG 59.185 40.000 0.00 0.00 0.00 4.94
4508 4887 7.047891 TCTGTGTTCAGTATATCCAATTCACC 58.952 38.462 0.00 0.00 41.91 4.02
4569 4948 6.290294 ACTGTGACGGGTATATTAAACAGT 57.710 37.500 0.00 0.00 41.48 3.55
4570 4949 7.332430 TCAAACTGTGACGGGTATATTAAACAG 59.668 37.037 0.00 0.00 39.67 3.16
4571 4950 7.160049 TCAAACTGTGACGGGTATATTAAACA 58.840 34.615 0.00 0.00 0.00 2.83
4572 4951 7.599630 TCAAACTGTGACGGGTATATTAAAC 57.400 36.000 0.00 0.00 0.00 2.01
4583 4962 1.299541 ACAAGCTCAAACTGTGACGG 58.700 50.000 0.00 0.00 31.13 4.79
4584 4963 4.457810 CATAACAAGCTCAAACTGTGACG 58.542 43.478 0.00 0.00 31.13 4.35
4604 4983 6.699204 CGAAGTAATGACTAGTGAGATTGCAT 59.301 38.462 0.00 0.00 33.58 3.96
4628 5007 0.796312 ATGCGCCTAAAACACTGACG 59.204 50.000 4.18 0.00 0.00 4.35
4650 5029 6.667414 ACAATTTTTGCCACCTAAGATCCATA 59.333 34.615 0.00 0.00 0.00 2.74
4657 5036 8.600449 TTTTCATACAATTTTTGCCACCTAAG 57.400 30.769 0.00 0.00 0.00 2.18
4664 5043 7.017055 GCTCACATTTTCATACAATTTTTGCC 58.983 34.615 0.00 0.00 0.00 4.52
4665 5044 7.799784 AGCTCACATTTTCATACAATTTTTGC 58.200 30.769 0.00 0.00 0.00 3.68
4684 5063 3.341823 ACAGGATGATTGACAAGCTCAC 58.658 45.455 4.88 0.00 39.69 3.51
4696 5080 7.865820 TCCTTTCTGAAAGATAACAGGATGAT 58.134 34.615 27.21 0.00 46.36 2.45
4722 5106 9.625747 TTAACCATATTCTCAGCAACAATATGA 57.374 29.630 14.52 0.00 40.63 2.15
4728 5112 7.936496 TGAATTAACCATATTCTCAGCAACA 57.064 32.000 0.00 0.00 34.00 3.33
4729 5113 7.433425 GCTTGAATTAACCATATTCTCAGCAAC 59.567 37.037 0.00 0.00 38.06 4.17
4731 5115 6.830324 AGCTTGAATTAACCATATTCTCAGCA 59.170 34.615 15.93 0.00 39.22 4.41
4732 5116 7.269477 AGCTTGAATTAACCATATTCTCAGC 57.731 36.000 0.00 0.00 38.24 4.26
4733 5117 8.680903 ACAAGCTTGAATTAACCATATTCTCAG 58.319 33.333 32.50 0.00 34.00 3.35
4734 5118 8.579850 ACAAGCTTGAATTAACCATATTCTCA 57.420 30.769 32.50 0.00 34.00 3.27
4735 5119 8.677300 TGACAAGCTTGAATTAACCATATTCTC 58.323 33.333 32.50 13.55 34.00 2.87
4736 5120 8.579850 TGACAAGCTTGAATTAACCATATTCT 57.420 30.769 32.50 4.02 34.00 2.40
4737 5121 9.807649 ATTGACAAGCTTGAATTAACCATATTC 57.192 29.630 32.50 14.58 33.58 1.75
4739 5123 8.970020 TGATTGACAAGCTTGAATTAACCATAT 58.030 29.630 32.50 5.43 0.00 1.78
4754 5178 4.978083 AACAGGATGATGATTGACAAGC 57.022 40.909 0.00 0.00 39.69 4.01
4762 5186 7.146715 AGGAGAAATGTAACAGGATGATGAT 57.853 36.000 0.00 0.00 39.69 2.45
4792 5216 4.832266 TCCAGCCAATTAACAACACAAGAT 59.168 37.500 0.00 0.00 0.00 2.40
4809 5233 1.269778 GCCAAAAGACAAACTCCAGCC 60.270 52.381 0.00 0.00 0.00 4.85
4841 5265 3.341823 ACATCAGTCAGCATTCAAGGTC 58.658 45.455 0.00 0.00 0.00 3.85
4866 5290 6.408662 GCCTCCTCTTGTCCATTATAAGAGTT 60.409 42.308 11.05 0.00 46.61 3.01
4867 5291 5.071115 GCCTCCTCTTGTCCATTATAAGAGT 59.929 44.000 11.05 0.00 46.61 3.24
4874 5298 1.839994 CTGGCCTCCTCTTGTCCATTA 59.160 52.381 3.32 0.00 0.00 1.90
4883 5307 2.556114 CCAAATGTTTCTGGCCTCCTCT 60.556 50.000 3.32 0.00 0.00 3.69
4891 5315 7.572523 TTATATCTCAGCCAAATGTTTCTGG 57.427 36.000 0.00 0.00 35.67 3.86
4892 5316 7.917505 GGTTTATATCTCAGCCAAATGTTTCTG 59.082 37.037 0.00 0.00 0.00 3.02
4893 5317 7.615365 TGGTTTATATCTCAGCCAAATGTTTCT 59.385 33.333 0.00 0.00 0.00 2.52
4903 5331 7.283127 TCAAGTTCATTGGTTTATATCTCAGCC 59.717 37.037 0.00 0.00 39.54 4.85
4955 5385 7.038302 TCCTACATTGTTAGACCTGAAACTCAT 60.038 37.037 0.00 0.00 0.00 2.90
5065 5617 2.237393 CTGCTCAGCTTAGGATGGAC 57.763 55.000 0.00 0.00 0.00 4.02
5087 5639 3.191539 GGCGGCGAGAAGAAGCAG 61.192 66.667 12.98 0.00 34.54 4.24
5096 5648 3.869272 GCTGACAATGGCGGCGAG 61.869 66.667 12.98 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.