Multiple sequence alignment - TraesCS2B01G578700

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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 TraesCS2B01G578700 chr2B 100.000 5558 0 0 1 5558 767013644 767019201 0.000000e+00 10264.0
1 TraesCS2B01G578700 chr2D 92.534 5143 223 79 3 5060 624549969 624555035 0.000000e+00 7221.0
2 TraesCS2B01G578700 chr2D 86.626 329 34 6 1 327 624549028 624549348 6.850000e-94 355.0
3 TraesCS2B01G578700 chr2D 93.627 204 10 3 5354 5555 624555301 624555503 9.050000e-78 302.0
4 TraesCS2B01G578700 chr2D 93.478 184 6 5 5065 5247 624555108 624555286 9.180000e-68 268.0
5 TraesCS2B01G578700 chr2D 91.200 125 11 0 5243 5367 71577052 71576928 2.660000e-38 171.0
6 TraesCS2B01G578700 chr2D 91.837 49 4 0 377 425 522984070 522984118 9.990000e-08 69.4
7 TraesCS2B01G578700 chr2A 91.948 5129 277 73 18 5057 755784726 755789807 0.000000e+00 7059.0
8 TraesCS2B01G578700 chr2A 93.301 209 8 4 5352 5555 755790074 755790281 2.520000e-78 303.0
9 TraesCS2B01G578700 chr2A 92.655 177 8 3 5071 5247 755789890 755790061 3.320000e-62 250.0
10 TraesCS2B01G578700 chr2A 94.068 118 6 1 5236 5352 410279682 410279565 1.590000e-40 178.0
11 TraesCS2B01G578700 chr4A 96.491 114 4 0 5243 5356 692072611 692072498 7.350000e-44 189.0
12 TraesCS2B01G578700 chr1B 94.872 117 4 2 5246 5361 187465665 187465550 1.230000e-41 182.0
13 TraesCS2B01G578700 chr1B 94.737 114 6 0 5246 5359 533752140 533752027 1.590000e-40 178.0
14 TraesCS2B01G578700 chr6B 94.737 114 6 0 5246 5359 714341351 714341464 1.590000e-40 178.0
15 TraesCS2B01G578700 chr5A 93.333 120 7 1 5245 5364 368170798 368170680 5.720000e-40 176.0
16 TraesCS2B01G578700 chr5A 88.889 54 5 1 372 424 707705967 707706020 1.290000e-06 65.8
17 TraesCS2B01G578700 chr7D 92.000 125 8 2 5243 5366 34225091 34224968 2.060000e-39 174.0
18 TraesCS2B01G578700 chr5B 91.200 125 10 1 5238 5361 572978508 572978384 9.580000e-38 169.0
19 TraesCS2B01G578700 chr6D 93.478 46 3 0 379 424 132661087 132661132 9.990000e-08 69.4
20 TraesCS2B01G578700 chr5D 91.489 47 4 0 378 424 302333584 302333630 1.290000e-06 65.8
21 TraesCS2B01G578700 chr5D 89.796 49 5 0 376 424 467775149 467775197 4.650000e-06 63.9
22 TraesCS2B01G578700 chr5D 89.583 48 5 0 375 422 125286889 125286842 1.670000e-05 62.1
23 TraesCS2B01G578700 chr3D 88.679 53 5 1 372 424 11578656 11578605 4.650000e-06 63.9


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 TraesCS2B01G578700 chr2B 767013644 767019201 5557 False 10264.000000 10264 100.000000 1 5558 1 chr2B.!!$F1 5557
1 TraesCS2B01G578700 chr2D 624549028 624555503 6475 False 2036.500000 7221 91.566250 1 5555 4 chr2D.!!$F2 5554
2 TraesCS2B01G578700 chr2A 755784726 755790281 5555 False 2537.333333 7059 92.634667 18 5555 3 chr2A.!!$F1 5537

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
683 1638 0.039617 CGCAACGCAAAATTGGGAGA 60.040 50.000 15.96 0.0 43.04 3.71 F
1520 2517 0.679640 TAGTTTGAATGCGCCCCCAG 60.680 55.000 4.18 0.0 0.00 4.45 F
2981 4049 1.006998 TCAGCAAGGTGGCCCAATAAT 59.993 47.619 0.00 0.0 0.00 1.28 F
3162 4230 0.034616 CTTCAGGCGAGGATCATCCC 59.965 60.000 0.00 4.4 37.19 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1550 2548 0.958876 CCTTGTCCCCACGGCTAAAC 60.959 60.0 0.00 0.0 0.0 2.01 R
2984 4052 0.249911 AACTGACTTGGACCTGTCGC 60.250 55.0 11.62 0.0 36.1 5.19 R
4515 5583 0.035915 TCCGGGCAAAATCATCGTCA 60.036 50.0 0.00 0.0 0.0 4.35 R
4567 5636 0.595095 AGAAGCGCCAAGAAAAGCAG 59.405 50.0 2.29 0.0 0.0 4.24 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
30 31 3.055891 GCAGATACTTTGCACCCCATTTT 60.056 43.478 0.00 0.00 41.17 1.82
46 47 3.939592 CCATTTTCGGGAAGAGGAGTTAC 59.060 47.826 0.00 0.00 0.00 2.50
61 1002 5.186198 AGGAGTTACATGTATGCTGGTTTC 58.814 41.667 6.36 0.00 0.00 2.78
89 1030 2.291354 ACACTCCCACCTACCTACCTA 58.709 52.381 0.00 0.00 0.00 3.08
90 1031 2.244252 ACACTCCCACCTACCTACCTAG 59.756 54.545 0.00 0.00 0.00 3.02
118 1059 5.595885 AGAGGTGAAGATGATGTACATTCG 58.404 41.667 10.30 0.00 39.56 3.34
158 1099 1.410153 ACTGCCTGCAAAGGTGAAAAG 59.590 47.619 0.00 0.00 0.00 2.27
161 1102 2.499289 TGCCTGCAAAGGTGAAAAGAAA 59.501 40.909 0.00 0.00 0.00 2.52
163 1104 3.938334 GCCTGCAAAGGTGAAAAGAAAAA 59.062 39.130 0.00 0.00 0.00 1.94
167 1108 6.074356 CCTGCAAAGGTGAAAAGAAAAATACG 60.074 38.462 0.00 0.00 0.00 3.06
170 1111 6.639279 GCAAAGGTGAAAAGAAAAATACGCTA 59.361 34.615 0.00 0.00 0.00 4.26
172 1113 7.506328 AAGGTGAAAAGAAAAATACGCTACT 57.494 32.000 0.00 0.00 0.00 2.57
173 1114 7.130303 AGGTGAAAAGAAAAATACGCTACTC 57.870 36.000 0.00 0.00 0.00 2.59
248 1189 0.896940 AGTTACCTTCTCGTCCGCCA 60.897 55.000 0.00 0.00 0.00 5.69
255 1196 2.279252 CTCGTCCGCCATTACCCG 60.279 66.667 0.00 0.00 0.00 5.28
268 1213 3.687698 CCATTACCCGTCACGAGAAAATT 59.312 43.478 0.00 0.00 0.00 1.82
317 1262 0.872388 CACACTCCGCCCACTAAAAC 59.128 55.000 0.00 0.00 0.00 2.43
328 1274 4.390264 GCCCACTAAAACTCAAGAGAAGT 58.610 43.478 3.73 0.00 0.00 3.01
343 1290 8.798748 TCAAGAGAAGTCGTAGTTTTCTAAAG 57.201 34.615 0.00 0.00 33.23 1.85
348 1295 9.623350 GAGAAGTCGTAGTTTTCTAAAGTACAT 57.377 33.333 14.22 0.00 33.23 2.29
380 1327 9.790344 ATAGAGAATCAAGCTGCAAAATACTAT 57.210 29.630 1.02 0.00 37.82 2.12
387 1334 4.464947 AGCTGCAAAATACTATTCCCTCC 58.535 43.478 1.02 0.00 0.00 4.30
405 1352 4.513442 CCTCCGATCCAAAATAAGTGTCA 58.487 43.478 0.00 0.00 0.00 3.58
412 1359 5.975693 TCCAAAATAAGTGTCATGGGTTC 57.024 39.130 0.00 0.00 0.00 3.62
417 1364 1.892209 AAGTGTCATGGGTTCGGTTC 58.108 50.000 0.00 0.00 0.00 3.62
432 1381 6.313164 GGGTTCGGTTCAAATTTTGTTAACAA 59.687 34.615 17.01 17.01 0.00 2.83
465 1414 2.999331 AGATACCGGGTTCATTGGTTG 58.001 47.619 4.31 0.00 37.20 3.77
467 1416 0.772384 TACCGGGTTCATTGGTTGGT 59.228 50.000 4.31 0.00 37.20 3.67
468 1417 0.538746 ACCGGGTTCATTGGTTGGTC 60.539 55.000 6.32 0.00 29.87 4.02
469 1418 1.248101 CCGGGTTCATTGGTTGGTCC 61.248 60.000 0.00 0.00 0.00 4.46
470 1419 0.538516 CGGGTTCATTGGTTGGTCCA 60.539 55.000 0.00 0.00 45.60 4.02
494 1443 4.007940 CCAACACCGACGCAACCG 62.008 66.667 0.00 0.00 41.14 4.44
540 1490 0.887933 GCAACCCATTTCACCGTCAT 59.112 50.000 0.00 0.00 0.00 3.06
546 1496 2.615240 CCCATTTCACCGTCATGTCTCA 60.615 50.000 0.00 0.00 0.00 3.27
576 1527 8.527567 TTCAAGTCAAACTTTGTTAAACTTGG 57.472 30.769 21.85 11.51 41.36 3.61
584 1535 9.914923 CAAACTTTGTTAAACTTGGCTAAATTC 57.085 29.630 0.00 0.00 0.00 2.17
642 1597 9.573166 TGGTATATAAGGATCACAAAATTGGAG 57.427 33.333 0.00 0.00 0.00 3.86
643 1598 9.793259 GGTATATAAGGATCACAAAATTGGAGA 57.207 33.333 0.00 0.00 0.00 3.71
647 1602 8.884124 ATAAGGATCACAAAATTGGAGAGAAA 57.116 30.769 0.00 0.00 0.00 2.52
648 1603 6.830873 AGGATCACAAAATTGGAGAGAAAG 57.169 37.500 0.00 0.00 0.00 2.62
649 1604 6.546484 AGGATCACAAAATTGGAGAGAAAGA 58.454 36.000 0.00 0.00 0.00 2.52
650 1605 6.658391 AGGATCACAAAATTGGAGAGAAAGAG 59.342 38.462 0.00 0.00 0.00 2.85
680 1635 0.933796 AAACGCAACGCAAAATTGGG 59.066 45.000 8.47 8.47 45.49 4.12
681 1636 0.103208 AACGCAACGCAAAATTGGGA 59.897 45.000 15.96 0.00 43.04 4.37
682 1637 0.318614 ACGCAACGCAAAATTGGGAG 60.319 50.000 15.96 9.33 43.04 4.30
683 1638 0.039617 CGCAACGCAAAATTGGGAGA 60.040 50.000 15.96 0.00 43.04 3.71
684 1639 1.701704 GCAACGCAAAATTGGGAGAG 58.298 50.000 15.96 6.97 43.04 3.20
686 1641 2.288152 GCAACGCAAAATTGGGAGAGAA 60.288 45.455 15.96 0.00 43.04 2.87
687 1642 3.568538 CAACGCAAAATTGGGAGAGAAG 58.431 45.455 15.96 0.00 43.04 2.85
688 1643 3.140325 ACGCAAAATTGGGAGAGAAGA 57.860 42.857 15.96 0.00 43.04 2.87
689 1644 3.077359 ACGCAAAATTGGGAGAGAAGAG 58.923 45.455 15.96 0.00 43.04 2.85
723 1694 3.254617 GGTTCCGTCCCCAACCCT 61.255 66.667 0.00 0.00 36.76 4.34
1155 2146 1.076192 GCTCCCTCGTTCCTCCCTA 60.076 63.158 0.00 0.00 0.00 3.53
1159 2151 0.756070 CCCTCGTTCCTCCCTACCTC 60.756 65.000 0.00 0.00 0.00 3.85
1181 2178 1.615384 CCTTCCCTTCCTTCCAAGCTG 60.615 57.143 0.00 0.00 0.00 4.24
1302 2299 3.326747 CACCGGAGAGAAAGATTTCGTT 58.673 45.455 9.46 0.00 41.92 3.85
1314 2311 4.730949 AGATTTCGTTACCCAAGATCGA 57.269 40.909 0.00 0.00 0.00 3.59
1317 2314 0.819582 TCGTTACCCAAGATCGACCC 59.180 55.000 0.00 0.00 0.00 4.46
1318 2315 0.822164 CGTTACCCAAGATCGACCCT 59.178 55.000 0.00 0.00 0.00 4.34
1338 2335 4.253685 CCTGTATCCACGATGTTCTTTGT 58.746 43.478 0.00 0.00 0.00 2.83
1346 2343 2.157668 ACGATGTTCTTTGTCGATGTGC 59.842 45.455 0.69 0.00 38.63 4.57
1396 2393 0.811616 CGATGCTAGGGCTTGGTCAC 60.812 60.000 0.00 0.00 39.59 3.67
1398 2395 2.820037 GCTAGGGCTTGGTCACGC 60.820 66.667 0.00 0.00 35.22 5.34
1424 2421 1.084370 CCTGTTGCTCGACGGGAATC 61.084 60.000 9.11 0.00 46.98 2.52
1488 2485 3.636300 TGAAGGTGAAGACAACCCATTTG 59.364 43.478 0.00 0.00 41.49 2.32
1489 2486 3.593442 AGGTGAAGACAACCCATTTGA 57.407 42.857 0.00 0.00 38.73 2.69
1490 2487 3.490348 AGGTGAAGACAACCCATTTGAG 58.510 45.455 0.00 0.00 38.73 3.02
1504 2501 4.467769 CCATTTGAGGAGGCATCATTAGT 58.532 43.478 0.00 0.00 0.00 2.24
1520 2517 0.679640 TAGTTTGAATGCGCCCCCAG 60.680 55.000 4.18 0.00 0.00 4.45
1550 2548 4.906618 ACTATTGCCTTGATTATACCCCG 58.093 43.478 0.00 0.00 0.00 5.73
1651 2649 6.491745 GGGGAGGATTTCTTGATAGGAATTTC 59.508 42.308 0.00 0.00 29.31 2.17
1692 2691 3.966665 TGCTTCCCCTGTCTGAAAATTTT 59.033 39.130 2.28 2.28 0.00 1.82
1711 2710 2.260844 TGTTTGCTCCTGAAGACCTG 57.739 50.000 0.00 0.00 0.00 4.00
1720 2719 2.834549 TCCTGAAGACCTGAACATCTCC 59.165 50.000 0.00 0.00 0.00 3.71
1721 2720 2.836981 CCTGAAGACCTGAACATCTCCT 59.163 50.000 0.00 0.00 0.00 3.69
1722 2721 3.262915 CCTGAAGACCTGAACATCTCCTT 59.737 47.826 0.00 0.00 0.00 3.36
1723 2722 4.502962 CTGAAGACCTGAACATCTCCTTC 58.497 47.826 0.00 0.00 0.00 3.46
1816 2859 7.731720 TGTTTTTGTATGTATTTAGACGTCGG 58.268 34.615 10.46 0.00 0.00 4.79
1827 2870 4.935885 TTAGACGTCGGTAGTCTCTTTC 57.064 45.455 10.46 0.00 44.87 2.62
1887 2930 5.279106 CCTTTGAAACATCCTGCAATTCAGA 60.279 40.000 6.50 0.00 45.72 3.27
2053 3101 3.730215 ACCCTATGTGGTGTAAATGCA 57.270 42.857 0.00 0.00 37.20 3.96
2061 3109 4.657013 TGTGGTGTAAATGCAGTAATGGA 58.343 39.130 0.00 0.00 0.00 3.41
2136 3184 8.768955 TGTTTCAAAATTTATGTTTGATTCCCG 58.231 29.630 0.81 0.00 42.82 5.14
2181 3229 7.168135 CCTGTTAAATTTCTGTGCTTCAGTTTC 59.832 37.037 0.00 0.00 43.97 2.78
2392 3440 2.016905 CCCGGATGAACCCTAGAGAT 57.983 55.000 0.73 0.00 34.64 2.75
2457 3505 2.243602 TTTCGCCATCCGGTAATACC 57.756 50.000 0.00 0.00 37.59 2.73
2460 3508 1.477685 CGCCATCCGGTAATACCCCT 61.478 60.000 0.00 0.00 33.75 4.79
2511 3567 6.992123 CACCATAAGACCTTGTAATATCTGCA 59.008 38.462 0.00 0.00 0.00 4.41
2517 3573 5.587844 AGACCTTGTAATATCTGCAAGCAAG 59.412 40.000 0.00 0.00 44.10 4.01
2572 3630 8.552034 GTTCATAGTAACTAACAAGGCATGATC 58.448 37.037 0.00 0.00 0.00 2.92
2573 3631 6.923508 TCATAGTAACTAACAAGGCATGATCG 59.076 38.462 0.00 0.00 0.00 3.69
2582 3640 3.270027 CAAGGCATGATCGTAGAAACCA 58.730 45.455 0.00 0.00 43.58 3.67
2591 3649 3.293311 TCGTAGAAACCACTGTAGTGC 57.707 47.619 6.50 0.00 44.34 4.40
2603 3661 3.696548 CACTGTAGTGCTCCTAGTCATGA 59.303 47.826 0.00 0.00 39.39 3.07
2608 3666 4.669206 AGTGCTCCTAGTCATGATCTTG 57.331 45.455 0.00 2.18 0.00 3.02
2609 3667 3.129871 GTGCTCCTAGTCATGATCTTGC 58.870 50.000 0.00 0.20 0.00 4.01
2610 3668 2.767960 TGCTCCTAGTCATGATCTTGCA 59.232 45.455 0.00 2.95 0.00 4.08
2611 3669 3.181468 TGCTCCTAGTCATGATCTTGCAG 60.181 47.826 0.00 0.00 0.00 4.41
2628 3696 7.428282 TCTTGCAGTTCGTTTTGACATTATA 57.572 32.000 0.00 0.00 0.00 0.98
2704 3772 4.989279 ATTGATGGTATGTTTGGTGCTC 57.011 40.909 0.00 0.00 0.00 4.26
2727 3795 2.269940 ACTCCTGGAATACCTGCAGTT 58.730 47.619 13.81 0.00 41.77 3.16
2919 3987 3.011032 AGCCTCAGACCCAAAAGAATGAT 59.989 43.478 0.00 0.00 0.00 2.45
2943 4011 1.600023 TGGGTGTTAAGGAGTTTGCG 58.400 50.000 0.00 0.00 0.00 4.85
2981 4049 1.006998 TCAGCAAGGTGGCCCAATAAT 59.993 47.619 0.00 0.00 0.00 1.28
3011 4079 4.225267 CAGGTCCAAGTCAGTTAATAGGGT 59.775 45.833 0.00 0.00 0.00 4.34
3024 4092 3.782889 AATAGGGTTGCAGCGAATTTC 57.217 42.857 0.00 0.00 0.00 2.17
3036 4104 1.298157 CGAATTTCGCCAGGACAGCA 61.298 55.000 5.78 0.00 31.14 4.41
3162 4230 0.034616 CTTCAGGCGAGGATCATCCC 59.965 60.000 0.00 4.40 37.19 3.85
3215 4283 4.970711 ACTGATCCTATGCAAGATTGGAG 58.029 43.478 0.00 0.00 30.13 3.86
3333 4401 2.410469 GCCAACGATGCAGATGCC 59.590 61.111 1.72 0.00 41.18 4.40
3424 4492 2.493278 CCGGCTGATTTTGAAATCCAGT 59.507 45.455 12.51 0.00 43.19 4.00
3447 4515 7.711772 CAGTCTCATCATGAAAGAGAGCTATTT 59.288 37.037 23.80 9.17 38.93 1.40
3600 4668 1.072965 GGCCCTGTTGAGATAGATGGG 59.927 57.143 0.00 0.00 36.41 4.00
3834 4902 4.002982 CTGATAGAGTAGATGCTCGCTCT 58.997 47.826 13.20 13.20 40.26 4.09
3903 4971 6.032039 AGTTATGCCTATGGATATTCAGGGA 58.968 40.000 9.32 0.00 32.67 4.20
3999 5067 0.677414 TCGCTGATGGCAAGCATTCA 60.677 50.000 11.42 0.00 41.91 2.57
4116 5184 2.632512 TCTTGATTTTGAAGGCCCAACC 59.367 45.455 0.00 0.00 39.61 3.77
4211 5279 7.934855 ATGTGAAAGAAGATAAATCTGCTGT 57.065 32.000 1.03 0.00 42.05 4.40
4231 5299 1.217779 GTCTCTCACAGGCAGGCTC 59.782 63.158 0.00 0.00 0.00 4.70
4238 5306 0.747283 CACAGGCAGGCTCAATCTCC 60.747 60.000 0.00 0.00 0.00 3.71
4241 5309 2.899339 GCAGGCTCAATCTCCGGC 60.899 66.667 0.00 0.00 36.48 6.13
4260 5328 1.965754 CTGAAGCCGAGAAGGAGGGG 61.966 65.000 0.00 0.00 45.00 4.79
4281 5349 4.321452 GGGTACGACAACACTATCAGTTCA 60.321 45.833 0.00 0.00 0.00 3.18
4428 5496 0.326048 ACTATGAGCAGAGGCAGGGT 60.326 55.000 0.00 0.00 44.61 4.34
4515 5583 2.164624 CGACGAGGAAGAGTTTGAGGAT 59.835 50.000 0.00 0.00 0.00 3.24
4661 5734 0.322816 ATTCTTGTGGCGCTCCATGT 60.323 50.000 7.64 0.00 45.62 3.21
4777 5850 5.070770 AGCGAGGTAGATGATGATGATTC 57.929 43.478 0.00 0.00 0.00 2.52
4822 5895 2.388121 GTGTAAAAACAGCTGCTGCAG 58.612 47.619 28.39 24.80 42.74 4.41
4957 6031 3.075283 TCCAACTTGGAGGGCATCTTTTA 59.925 43.478 6.39 0.00 42.67 1.52
4965 6040 6.284891 TGGAGGGCATCTTTTATTTTCTTG 57.715 37.500 0.00 0.00 0.00 3.02
5040 6117 6.578172 TGTGCATATATTTGATTGCGAAATCG 59.422 34.615 11.55 0.00 43.27 3.34
5060 6137 7.858052 AATCGTTTTGTTTCATCAGTTGATC 57.142 32.000 0.00 0.00 33.34 2.92
5074 6151 5.807909 TCAGTTGATCTGATCCATGTTTCA 58.192 37.500 14.71 0.00 46.77 2.69
5075 6152 5.878669 TCAGTTGATCTGATCCATGTTTCAG 59.121 40.000 14.71 13.38 46.77 3.02
5076 6153 4.639310 AGTTGATCTGATCCATGTTTCAGC 59.361 41.667 14.71 0.00 39.36 4.26
5078 6155 4.851843 TGATCTGATCCATGTTTCAGCTT 58.148 39.130 14.71 7.02 39.36 3.74
5079 6156 5.258841 TGATCTGATCCATGTTTCAGCTTT 58.741 37.500 14.71 5.16 39.36 3.51
5080 6157 6.417258 TGATCTGATCCATGTTTCAGCTTTA 58.583 36.000 14.71 2.05 39.36 1.85
5082 6159 8.212995 TGATCTGATCCATGTTTCAGCTTTATA 58.787 33.333 14.71 1.21 39.36 0.98
5127 6271 0.034574 TCAGTGGTGCTGTTGGTTGT 60.035 50.000 0.00 0.00 45.23 3.32
5128 6272 1.210722 TCAGTGGTGCTGTTGGTTGTA 59.789 47.619 0.00 0.00 45.23 2.41
5129 6273 1.333619 CAGTGGTGCTGTTGGTTGTAC 59.666 52.381 0.00 0.00 40.27 2.90
5132 6276 2.546789 GTGGTGCTGTTGGTTGTACTAC 59.453 50.000 0.00 0.00 0.00 2.73
5138 6282 6.350780 GGTGCTGTTGGTTGTACTACTACTAT 60.351 42.308 7.38 0.00 0.00 2.12
5247 6391 6.255020 CGGGACACAAGTTGAGTATAATGTAC 59.745 42.308 10.54 2.01 0.00 2.90
5248 6392 7.328737 GGGACACAAGTTGAGTATAATGTACT 58.671 38.462 10.54 0.00 0.00 2.73
5249 6393 7.491696 GGGACACAAGTTGAGTATAATGTACTC 59.508 40.741 10.54 9.80 43.06 2.59
5250 6394 7.491696 GGACACAAGTTGAGTATAATGTACTCC 59.508 40.741 10.54 1.07 42.32 3.85
5251 6395 7.328737 ACACAAGTTGAGTATAATGTACTCCC 58.671 38.462 10.54 5.55 42.32 4.30
5253 6397 7.707035 CACAAGTTGAGTATAATGTACTCCCTC 59.293 40.741 10.54 5.38 42.32 4.30
5254 6398 6.980416 AGTTGAGTATAATGTACTCCCTCC 57.020 41.667 13.39 1.11 42.32 4.30
5255 6399 5.535406 AGTTGAGTATAATGTACTCCCTCCG 59.465 44.000 13.39 0.00 42.32 4.63
5256 6400 5.057843 TGAGTATAATGTACTCCCTCCGT 57.942 43.478 13.39 0.00 42.32 4.69
5259 6403 4.518211 AGTATAATGTACTCCCTCCGTTCG 59.482 45.833 0.00 0.00 0.00 3.95
5260 6404 0.822164 AATGTACTCCCTCCGTTCGG 59.178 55.000 4.74 4.74 0.00 4.30
5261 6405 0.033796 ATGTACTCCCTCCGTTCGGA 60.034 55.000 13.34 13.34 0.00 4.55
5262 6406 0.251297 TGTACTCCCTCCGTTCGGAA 60.251 55.000 14.79 0.04 33.41 4.30
5263 6407 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
5264 6408 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
5265 6409 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
5266 6410 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
5267 6411 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
5268 6412 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
5269 6413 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
5270 6414 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
5271 6415 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
5272 6416 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
5273 6417 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
5274 6418 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
5275 6419 3.495193 CGTTCGGAATTACTTGTCTCGA 58.505 45.455 0.00 0.00 0.00 4.04
5276 6420 3.916172 CGTTCGGAATTACTTGTCTCGAA 59.084 43.478 0.00 0.00 33.66 3.71
5277 6421 4.383649 CGTTCGGAATTACTTGTCTCGAAA 59.616 41.667 0.00 0.00 37.00 3.46
5278 6422 5.107760 CGTTCGGAATTACTTGTCTCGAAAA 60.108 40.000 0.00 0.00 37.00 2.29
5279 6423 6.400727 CGTTCGGAATTACTTGTCTCGAAAAT 60.401 38.462 0.00 0.00 37.00 1.82
5280 6424 6.403333 TCGGAATTACTTGTCTCGAAAATG 57.597 37.500 0.00 0.00 0.00 2.32
5281 6425 5.350365 TCGGAATTACTTGTCTCGAAAATGG 59.650 40.000 0.00 0.00 0.00 3.16
5282 6426 5.350365 CGGAATTACTTGTCTCGAAAATGGA 59.650 40.000 0.00 0.00 0.00 3.41
5283 6427 6.037172 CGGAATTACTTGTCTCGAAAATGGAT 59.963 38.462 0.00 0.00 0.00 3.41
5284 6428 7.189512 GGAATTACTTGTCTCGAAAATGGATG 58.810 38.462 0.00 0.00 0.00 3.51
5285 6429 7.148239 GGAATTACTTGTCTCGAAAATGGATGT 60.148 37.037 0.00 0.00 0.00 3.06
5286 6430 8.786826 AATTACTTGTCTCGAAAATGGATGTA 57.213 30.769 0.00 0.00 0.00 2.29
5287 6431 8.964476 ATTACTTGTCTCGAAAATGGATGTAT 57.036 30.769 0.00 0.00 0.00 2.29
5288 6432 6.910536 ACTTGTCTCGAAAATGGATGTATC 57.089 37.500 0.00 0.00 0.00 2.24
5289 6433 6.644347 ACTTGTCTCGAAAATGGATGTATCT 58.356 36.000 0.00 0.00 0.00 1.98
5290 6434 7.782049 ACTTGTCTCGAAAATGGATGTATCTA 58.218 34.615 0.00 0.00 0.00 1.98
5291 6435 7.923344 ACTTGTCTCGAAAATGGATGTATCTAG 59.077 37.037 0.00 0.00 0.00 2.43
5292 6436 7.582667 TGTCTCGAAAATGGATGTATCTAGA 57.417 36.000 0.00 0.00 0.00 2.43
5293 6437 8.007405 TGTCTCGAAAATGGATGTATCTAGAA 57.993 34.615 0.00 0.00 0.00 2.10
5294 6438 7.921214 TGTCTCGAAAATGGATGTATCTAGAAC 59.079 37.037 0.00 0.00 0.00 3.01
5295 6439 8.138712 GTCTCGAAAATGGATGTATCTAGAACT 58.861 37.037 0.00 0.00 0.00 3.01
5296 6440 9.350951 TCTCGAAAATGGATGTATCTAGAACTA 57.649 33.333 0.00 0.00 0.00 2.24
5297 6441 9.967346 CTCGAAAATGGATGTATCTAGAACTAA 57.033 33.333 0.00 0.00 0.00 2.24
5327 6471 8.407457 TGTCTAGATACATTCATTTTCACGAC 57.593 34.615 0.00 0.00 0.00 4.34
5328 6472 8.032451 TGTCTAGATACATTCATTTTCACGACA 58.968 33.333 0.00 0.00 0.00 4.35
5329 6473 8.869897 GTCTAGATACATTCATTTTCACGACAA 58.130 33.333 0.00 0.00 0.00 3.18
5330 6474 9.087424 TCTAGATACATTCATTTTCACGACAAG 57.913 33.333 0.00 0.00 0.00 3.16
5331 6475 7.672983 AGATACATTCATTTTCACGACAAGT 57.327 32.000 0.00 0.00 0.00 3.16
5332 6476 8.771920 AGATACATTCATTTTCACGACAAGTA 57.228 30.769 0.00 0.00 0.00 2.24
5333 6477 9.214957 AGATACATTCATTTTCACGACAAGTAA 57.785 29.630 0.00 0.00 0.00 2.24
5334 6478 9.988350 GATACATTCATTTTCACGACAAGTAAT 57.012 29.630 0.00 0.00 0.00 1.89
5336 6480 8.728088 ACATTCATTTTCACGACAAGTAATTC 57.272 30.769 0.00 0.00 0.00 2.17
5337 6481 7.807907 ACATTCATTTTCACGACAAGTAATTCC 59.192 33.333 0.00 0.00 0.00 3.01
5338 6482 5.922546 TCATTTTCACGACAAGTAATTCCG 58.077 37.500 0.00 0.00 0.00 4.30
5339 6483 5.697178 TCATTTTCACGACAAGTAATTCCGA 59.303 36.000 0.00 0.00 0.00 4.55
5340 6484 5.987777 TTTTCACGACAAGTAATTCCGAA 57.012 34.783 0.00 0.00 0.00 4.30
5341 6485 4.977741 TTCACGACAAGTAATTCCGAAC 57.022 40.909 0.00 0.00 0.00 3.95
5342 6486 3.979948 TCACGACAAGTAATTCCGAACA 58.020 40.909 0.00 0.00 0.00 3.18
5343 6487 3.985279 TCACGACAAGTAATTCCGAACAG 59.015 43.478 0.00 0.00 0.00 3.16
5344 6488 3.985279 CACGACAAGTAATTCCGAACAGA 59.015 43.478 0.00 0.00 0.00 3.41
5345 6489 4.090066 CACGACAAGTAATTCCGAACAGAG 59.910 45.833 0.00 0.00 0.00 3.35
5346 6490 3.612860 CGACAAGTAATTCCGAACAGAGG 59.387 47.826 0.00 0.00 0.00 3.69
5347 6491 3.933332 GACAAGTAATTCCGAACAGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
5348 6492 3.581332 ACAAGTAATTCCGAACAGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
5349 6493 4.184629 CAAGTAATTCCGAACAGAGGGAG 58.815 47.826 0.00 0.00 33.01 4.30
5350 6494 3.442076 AGTAATTCCGAACAGAGGGAGT 58.558 45.455 0.00 0.00 33.01 3.85
5398 6542 1.529010 TGGGCAGACCAGCAACTTG 60.529 57.895 0.00 0.00 46.80 3.16
5416 6560 6.019801 GCAACTTGGTAAGATATGACAGTACG 60.020 42.308 0.00 0.00 0.00 3.67
5417 6561 6.770746 ACTTGGTAAGATATGACAGTACGT 57.229 37.500 0.00 0.00 0.00 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.816411 ACATGTAACTCCTCTTCCCGA 58.184 47.619 0.00 0.00 0.00 5.14
35 36 4.471386 ACCAGCATACATGTAACTCCTCTT 59.529 41.667 10.14 0.00 0.00 2.85
38 39 4.844349 AACCAGCATACATGTAACTCCT 57.156 40.909 10.14 1.24 0.00 3.69
46 47 4.985413 ACATTTCGAAACCAGCATACATG 58.015 39.130 13.81 6.02 0.00 3.21
61 1002 2.762535 AGGTGGGAGTGTACATTTCG 57.237 50.000 0.00 0.00 0.00 3.46
89 1030 4.296912 ACATCATCTTCACCTCTCCATCT 58.703 43.478 0.00 0.00 0.00 2.90
90 1031 4.686191 ACATCATCTTCACCTCTCCATC 57.314 45.455 0.00 0.00 0.00 3.51
118 1059 4.935808 CAGTTAGGTGGGAGTGTACATTTC 59.064 45.833 0.00 0.00 0.00 2.17
158 1099 4.375272 GGGTAGGGAGTAGCGTATTTTTC 58.625 47.826 0.00 0.00 0.00 2.29
161 1102 1.959282 CGGGTAGGGAGTAGCGTATTT 59.041 52.381 0.00 0.00 0.00 1.40
163 1104 0.892814 GCGGGTAGGGAGTAGCGTAT 60.893 60.000 0.00 0.00 0.00 3.06
167 1108 3.232483 GGGCGGGTAGGGAGTAGC 61.232 72.222 0.00 0.00 0.00 3.58
170 1111 2.803593 TTTACGGGCGGGTAGGGAGT 62.804 60.000 0.00 0.00 0.00 3.85
172 1113 2.038651 TTTACGGGCGGGTAGGGA 59.961 61.111 0.00 0.00 0.00 4.20
173 1114 2.059786 TCTTTACGGGCGGGTAGGG 61.060 63.158 0.00 0.00 0.00 3.53
241 1182 1.812507 GTGACGGGTAATGGCGGAC 60.813 63.158 0.00 0.00 0.00 4.79
248 1189 4.571919 TGAATTTTCTCGTGACGGGTAAT 58.428 39.130 4.20 3.46 0.00 1.89
317 1262 8.798748 TTTAGAAAACTACGACTTCTCTTGAG 57.201 34.615 0.00 0.00 31.91 3.02
356 1303 8.517062 AATAGTATTTTGCAGCTTGATTCTCT 57.483 30.769 0.00 0.00 0.00 3.10
380 1327 4.018779 ACACTTATTTTGGATCGGAGGGAA 60.019 41.667 0.00 0.00 0.00 3.97
387 1334 4.640201 ACCCATGACACTTATTTTGGATCG 59.360 41.667 0.00 0.00 0.00 3.69
405 1352 4.681074 ACAAAATTTGAACCGAACCCAT 57.319 36.364 13.19 0.00 0.00 4.00
412 1359 7.218583 ACGTAGTTGTTAACAAAATTTGAACCG 59.781 33.333 22.14 14.84 37.78 4.44
465 1414 1.895231 GTGTTGGTTCCGGTGGACC 60.895 63.158 14.71 14.71 0.00 4.46
467 1416 2.511900 GGTGTTGGTTCCGGTGGA 59.488 61.111 0.00 0.00 0.00 4.02
468 1417 2.975799 CGGTGTTGGTTCCGGTGG 60.976 66.667 0.00 0.00 42.61 4.61
469 1418 2.109387 TCGGTGTTGGTTCCGGTG 59.891 61.111 0.00 0.00 45.79 4.94
470 1419 2.109593 GTCGGTGTTGGTTCCGGT 59.890 61.111 0.00 0.00 45.79 5.28
471 1420 3.039588 CGTCGGTGTTGGTTCCGG 61.040 66.667 0.00 0.00 45.79 5.14
472 1421 3.708734 GCGTCGGTGTTGGTTCCG 61.709 66.667 0.00 0.00 46.93 4.30
475 1424 2.474612 GGTTGCGTCGGTGTTGGTT 61.475 57.895 0.00 0.00 0.00 3.67
507 1456 0.671796 GGTTGCGGTTTTTACTGCCT 59.328 50.000 6.64 0.00 41.09 4.75
540 1490 8.397906 CAAAGTTTGACTTGAAATAGTGAGACA 58.602 33.333 10.19 0.00 38.66 3.41
594 1545 6.269307 ACCATCTAGACTAGAGAGGAGTAGTC 59.731 46.154 27.90 1.95 43.77 2.59
627 1579 7.678947 TCTCTTTCTCTCCAATTTTGTGATC 57.321 36.000 0.00 0.00 0.00 2.92
640 1595 6.364976 CGTTTCTTTCCTCTTCTCTTTCTCTC 59.635 42.308 0.00 0.00 0.00 3.20
641 1596 6.220201 CGTTTCTTTCCTCTTCTCTTTCTCT 58.780 40.000 0.00 0.00 0.00 3.10
642 1597 5.107259 GCGTTTCTTTCCTCTTCTCTTTCTC 60.107 44.000 0.00 0.00 0.00 2.87
643 1598 4.752604 GCGTTTCTTTCCTCTTCTCTTTCT 59.247 41.667 0.00 0.00 0.00 2.52
644 1599 4.511826 TGCGTTTCTTTCCTCTTCTCTTTC 59.488 41.667 0.00 0.00 0.00 2.62
645 1600 4.451900 TGCGTTTCTTTCCTCTTCTCTTT 58.548 39.130 0.00 0.00 0.00 2.52
646 1601 4.073293 TGCGTTTCTTTCCTCTTCTCTT 57.927 40.909 0.00 0.00 0.00 2.85
647 1602 3.753294 TGCGTTTCTTTCCTCTTCTCT 57.247 42.857 0.00 0.00 0.00 3.10
648 1603 3.363084 CGTTGCGTTTCTTTCCTCTTCTC 60.363 47.826 0.00 0.00 0.00 2.87
649 1604 2.544267 CGTTGCGTTTCTTTCCTCTTCT 59.456 45.455 0.00 0.00 0.00 2.85
650 1605 2.904915 CGTTGCGTTTCTTTCCTCTTC 58.095 47.619 0.00 0.00 0.00 2.87
680 1635 5.420739 TCCTAGCCTTTTCTTCTCTTCTCTC 59.579 44.000 0.00 0.00 0.00 3.20
681 1636 5.186992 GTCCTAGCCTTTTCTTCTCTTCTCT 59.813 44.000 0.00 0.00 0.00 3.10
682 1637 5.416083 GTCCTAGCCTTTTCTTCTCTTCTC 58.584 45.833 0.00 0.00 0.00 2.87
683 1638 4.081917 CGTCCTAGCCTTTTCTTCTCTTCT 60.082 45.833 0.00 0.00 0.00 2.85
684 1639 4.177783 CGTCCTAGCCTTTTCTTCTCTTC 58.822 47.826 0.00 0.00 0.00 2.87
686 1641 2.498078 CCGTCCTAGCCTTTTCTTCTCT 59.502 50.000 0.00 0.00 0.00 3.10
687 1642 2.234168 ACCGTCCTAGCCTTTTCTTCTC 59.766 50.000 0.00 0.00 0.00 2.87
688 1643 2.258109 ACCGTCCTAGCCTTTTCTTCT 58.742 47.619 0.00 0.00 0.00 2.85
689 1644 2.764439 ACCGTCCTAGCCTTTTCTTC 57.236 50.000 0.00 0.00 0.00 2.87
718 1689 6.417503 AACAAATATAAAGGGAGGAGGGTT 57.582 37.500 0.00 0.00 0.00 4.11
723 1694 6.954232 ACTCGAAACAAATATAAAGGGAGGA 58.046 36.000 0.00 0.00 0.00 3.71
962 1950 4.548513 CTCCCCCTCCTCCTCCGG 62.549 77.778 0.00 0.00 0.00 5.14
963 1951 4.548513 CCTCCCCCTCCTCCTCCG 62.549 77.778 0.00 0.00 0.00 4.63
1143 2134 1.309006 GGGAGGTAGGGAGGAACGA 59.691 63.158 0.00 0.00 0.00 3.85
1155 2146 0.550393 GAAGGAAGGGAAGGGGAGGT 60.550 60.000 0.00 0.00 0.00 3.85
1159 2151 0.332972 CTTGGAAGGAAGGGAAGGGG 59.667 60.000 0.00 0.00 0.00 4.79
1302 2299 2.832643 TACAGGGTCGATCTTGGGTA 57.167 50.000 12.87 0.00 0.00 3.69
1318 2315 4.321378 TCGACAAAGAACATCGTGGATACA 60.321 41.667 0.00 0.00 38.41 2.29
1338 2335 2.520465 ATTCACGCCCTGCACATCGA 62.520 55.000 4.09 0.00 0.00 3.59
1396 2393 1.571460 GAGCAACAGGAACACAGCG 59.429 57.895 0.00 0.00 0.00 5.18
1398 2395 0.861837 GTCGAGCAACAGGAACACAG 59.138 55.000 0.00 0.00 0.00 3.66
1424 2421 2.856222 AGGTATAAGTCTACCGTCCCG 58.144 52.381 0.00 0.00 44.94 5.14
1488 2485 5.506982 GCATTCAAACTAATGATGCCTCCTC 60.507 44.000 0.91 0.00 38.84 3.71
1489 2486 4.340381 GCATTCAAACTAATGATGCCTCCT 59.660 41.667 0.91 0.00 38.84 3.69
1490 2487 4.614946 GCATTCAAACTAATGATGCCTCC 58.385 43.478 0.91 0.00 38.84 4.30
1504 2501 3.381136 GCTGGGGGCGCATTCAAA 61.381 61.111 10.83 0.00 0.00 2.69
1520 2517 9.185192 GTATAATCAAGGCAATAGTCAATTTGC 57.815 33.333 0.00 0.00 0.00 3.68
1550 2548 0.958876 CCTTGTCCCCACGGCTAAAC 60.959 60.000 0.00 0.00 0.00 2.01
1586 2584 1.608590 CATCTTGGGCAAACAGACGTT 59.391 47.619 0.00 0.00 36.73 3.99
1692 2691 1.768275 TCAGGTCTTCAGGAGCAAACA 59.232 47.619 0.00 0.00 44.16 2.83
1827 2870 8.627208 AAAGCAGGTACCAATATGATATTCAG 57.373 34.615 15.94 0.00 0.00 3.02
2053 3101 6.213600 ACTGGTGAGAACATAAGTCCATTACT 59.786 38.462 0.00 0.00 41.49 2.24
2061 3109 9.614792 GGATAATTAACTGGTGAGAACATAAGT 57.385 33.333 0.00 0.00 0.00 2.24
2123 3171 1.895131 AGCAAAGCGGGAATCAAACAT 59.105 42.857 0.00 0.00 0.00 2.71
2127 3175 4.776349 TCTAATAGCAAAGCGGGAATCAA 58.224 39.130 0.00 0.00 0.00 2.57
2135 3183 7.016361 ACAGGTAAAATCTAATAGCAAAGCG 57.984 36.000 0.00 0.00 0.00 4.68
2392 3440 7.768807 ATTGCCATTTAACCAGTAGTAACAA 57.231 32.000 0.00 0.00 0.00 2.83
2457 3505 5.013079 AGCAGGGAAAATAAAGGAAAAAGGG 59.987 40.000 0.00 0.00 0.00 3.95
2460 3508 9.719355 GAATAAGCAGGGAAAATAAAGGAAAAA 57.281 29.630 0.00 0.00 0.00 1.94
2511 3567 3.756933 AATTGTTGATGCCACTTGCTT 57.243 38.095 0.00 0.00 42.00 3.91
2551 3609 6.216801 ACGATCATGCCTTGTTAGTTACTA 57.783 37.500 0.00 0.00 0.00 1.82
2582 3640 3.969553 TCATGACTAGGAGCACTACAGT 58.030 45.455 0.00 0.00 0.00 3.55
2591 3649 4.669206 ACTGCAAGATCATGACTAGGAG 57.331 45.455 1.25 1.88 37.43 3.69
2603 3661 4.836125 ATGTCAAAACGAACTGCAAGAT 57.164 36.364 0.00 0.00 37.43 2.40
2608 3666 7.801315 TCAACTTATAATGTCAAAACGAACTGC 59.199 33.333 0.00 0.00 0.00 4.40
2609 3667 9.658475 TTCAACTTATAATGTCAAAACGAACTG 57.342 29.630 0.00 0.00 0.00 3.16
2704 3772 5.209318 ACTGCAGGTATTCCAGGAGTTGG 62.209 52.174 19.93 0.00 46.16 3.77
2727 3795 7.331026 AGTTATAAGCAGCATAGTGTGAAGAA 58.669 34.615 0.00 0.00 0.00 2.52
2931 3999 2.248280 TTGTCTGCGCAAACTCCTTA 57.752 45.000 15.97 0.00 0.00 2.69
2943 4011 6.127810 TGCTGAATTAGATGATTTGTCTGC 57.872 37.500 0.00 0.00 0.00 4.26
2981 4049 1.070786 GACTTGGACCTGTCGCCAA 59.929 57.895 0.00 0.00 41.61 4.52
2984 4052 0.249911 AACTGACTTGGACCTGTCGC 60.250 55.000 11.62 0.00 36.10 5.19
3036 4104 3.915575 GCTGGTATTGCAGCTGCT 58.084 55.556 36.61 21.93 43.82 4.24
3103 4171 0.601841 GCTGCTGGCATGCTGTTTTT 60.602 50.000 18.92 0.00 41.35 1.94
3162 4230 4.505922 GGAAGATTGTTCTGATAGCACTCG 59.494 45.833 0.00 0.00 30.72 4.18
3215 4283 2.882761 GGAGGTGTTTGGTAAGGTTGAC 59.117 50.000 0.00 0.00 0.00 3.18
3351 4419 1.982226 TCCCTTCCAAAATCGTCAGGA 59.018 47.619 0.00 0.00 0.00 3.86
3424 4492 9.539825 GTTAAATAGCTCTCTTTCATGATGAGA 57.460 33.333 20.63 20.63 36.51 3.27
3447 4515 1.339631 CCTTGCTCACCCATTCCGTTA 60.340 52.381 0.00 0.00 0.00 3.18
3576 4644 1.833630 TCTATCTCAACAGGGCCAGTG 59.166 52.381 6.18 3.45 0.00 3.66
3652 4720 4.681978 ACTGCGTTCCGGGCTGAC 62.682 66.667 13.52 2.33 34.03 3.51
3834 4902 4.141824 TGTCTTCTATCTCGCTCTCTCTCA 60.142 45.833 0.00 0.00 0.00 3.27
3999 5067 5.794894 AGTGAATCTGTTACATTCCGTCTT 58.205 37.500 0.00 0.00 30.30 3.01
4116 5184 4.019858 TCTGTAAGATGACACTGAGAGGG 58.980 47.826 0.00 0.00 38.67 4.30
4211 5279 2.587247 GCCTGCCTGTGAGAGACCA 61.587 63.158 0.00 0.00 0.00 4.02
4241 5309 1.519719 CCCTCCTTCTCGGCTTCAG 59.480 63.158 0.00 0.00 0.00 3.02
4248 5316 0.679002 TGTCGTACCCCTCCTTCTCG 60.679 60.000 0.00 0.00 0.00 4.04
4260 5328 5.696822 TCTGAACTGATAGTGTTGTCGTAC 58.303 41.667 0.00 0.00 0.00 3.67
4281 5349 7.836685 TCACCTGATCTACTCTTGTATTCTTCT 59.163 37.037 0.00 0.00 0.00 2.85
4428 5496 2.017782 GTCGCCTCATACTCTGACTCA 58.982 52.381 0.00 0.00 0.00 3.41
4515 5583 0.035915 TCCGGGCAAAATCATCGTCA 60.036 50.000 0.00 0.00 0.00 4.35
4567 5636 0.595095 AGAAGCGCCAAGAAAAGCAG 59.405 50.000 2.29 0.00 0.00 4.24
4599 5668 5.420104 CACTAGAGGGGAAATCAAGCATTTT 59.580 40.000 0.00 0.00 34.60 1.82
4661 5734 4.320202 GCGCTATCAACTTGAAACAGGAAA 60.320 41.667 0.00 0.00 0.00 3.13
4777 5850 8.792538 ACGTAAAGATTACTTTCTCGTTTATCG 58.207 33.333 14.44 0.00 44.78 2.92
4822 5895 2.695359 TCCAGGATACGCTCAACAAAC 58.305 47.619 0.00 0.00 46.39 2.93
4890 5964 5.951148 TCTCAGGCACAAAAATATCAATGGA 59.049 36.000 0.00 0.00 0.00 3.41
5013 6090 6.375945 TTCGCAATCAAATATATGCACACT 57.624 33.333 0.00 0.00 38.69 3.55
5019 6096 9.768125 CAAAACGATTTCGCAATCAAATATATG 57.232 29.630 8.49 0.00 44.43 1.78
5060 6137 8.680903 AGTTTATAAAGCTGAAACATGGATCAG 58.319 33.333 19.97 19.97 44.66 2.90
5063 6140 7.615365 TCCAGTTTATAAAGCTGAAACATGGAT 59.385 33.333 20.27 0.00 36.52 3.41
5064 6141 6.945435 TCCAGTTTATAAAGCTGAAACATGGA 59.055 34.615 20.27 18.29 37.66 3.41
5065 6142 7.156876 TCCAGTTTATAAAGCTGAAACATGG 57.843 36.000 20.27 14.89 35.88 3.66
5068 6145 7.121168 CCAGATCCAGTTTATAAAGCTGAAACA 59.879 37.037 20.27 8.72 35.88 2.83
5069 6146 7.336931 TCCAGATCCAGTTTATAAAGCTGAAAC 59.663 37.037 20.27 13.65 34.05 2.78
5070 6147 7.402054 TCCAGATCCAGTTTATAAAGCTGAAA 58.598 34.615 20.27 12.78 32.39 2.69
5072 6149 6.560003 TCCAGATCCAGTTTATAAAGCTGA 57.440 37.500 20.27 9.73 32.39 4.26
5073 6150 7.172875 CAGATCCAGATCCAGTTTATAAAGCTG 59.827 40.741 15.31 15.31 38.58 4.24
5074 6151 7.222872 CAGATCCAGATCCAGTTTATAAAGCT 58.777 38.462 0.00 0.00 38.58 3.74
5075 6152 6.429385 CCAGATCCAGATCCAGTTTATAAAGC 59.571 42.308 0.00 0.00 38.58 3.51
5076 6153 6.939163 CCCAGATCCAGATCCAGTTTATAAAG 59.061 42.308 0.00 0.00 38.58 1.85
5078 6155 5.911178 ACCCAGATCCAGATCCAGTTTATAA 59.089 40.000 4.01 0.00 38.58 0.98
5079 6156 5.307976 CACCCAGATCCAGATCCAGTTTATA 59.692 44.000 4.01 0.00 38.58 0.98
5080 6157 4.103785 CACCCAGATCCAGATCCAGTTTAT 59.896 45.833 4.01 0.00 38.58 1.40
5082 6159 2.240667 CACCCAGATCCAGATCCAGTTT 59.759 50.000 4.01 0.00 38.58 2.66
5132 6276 9.429359 GACAGTCATGGATGGATAAAATAGTAG 57.571 37.037 0.00 0.00 0.00 2.57
5138 6282 6.065976 ACAGACAGTCATGGATGGATAAAA 57.934 37.500 2.66 0.00 0.00 1.52
5247 6391 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
5248 6392 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
5249 6393 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
5250 6394 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
5251 6395 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
5253 6397 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
5254 6398 3.495193 TCGAGACAAGTAATTCCGAACG 58.505 45.455 0.00 0.00 0.00 3.95
5255 6399 5.834239 TTTCGAGACAAGTAATTCCGAAC 57.166 39.130 0.00 0.00 34.86 3.95
5256 6400 6.128391 CCATTTTCGAGACAAGTAATTCCGAA 60.128 38.462 0.00 0.00 33.57 4.30
5259 6403 6.737254 TCCATTTTCGAGACAAGTAATTCC 57.263 37.500 0.00 0.00 0.00 3.01
5260 6404 7.752695 ACATCCATTTTCGAGACAAGTAATTC 58.247 34.615 0.00 0.00 0.00 2.17
5261 6405 7.687941 ACATCCATTTTCGAGACAAGTAATT 57.312 32.000 0.00 0.00 0.00 1.40
5262 6406 8.964476 ATACATCCATTTTCGAGACAAGTAAT 57.036 30.769 0.00 0.00 0.00 1.89
5263 6407 8.258007 AGATACATCCATTTTCGAGACAAGTAA 58.742 33.333 0.00 0.00 0.00 2.24
5264 6408 7.782049 AGATACATCCATTTTCGAGACAAGTA 58.218 34.615 0.00 0.00 0.00 2.24
5265 6409 6.644347 AGATACATCCATTTTCGAGACAAGT 58.356 36.000 0.00 0.00 0.00 3.16
5266 6410 8.138074 TCTAGATACATCCATTTTCGAGACAAG 58.862 37.037 0.00 0.00 0.00 3.16
5267 6411 8.007405 TCTAGATACATCCATTTTCGAGACAA 57.993 34.615 0.00 0.00 0.00 3.18
5268 6412 7.582667 TCTAGATACATCCATTTTCGAGACA 57.417 36.000 0.00 0.00 0.00 3.41
5269 6413 8.138712 AGTTCTAGATACATCCATTTTCGAGAC 58.861 37.037 0.00 0.00 0.00 3.36
5270 6414 8.239038 AGTTCTAGATACATCCATTTTCGAGA 57.761 34.615 0.00 0.00 0.00 4.04
5271 6415 9.967346 TTAGTTCTAGATACATCCATTTTCGAG 57.033 33.333 0.00 0.00 0.00 4.04
5301 6445 9.035607 GTCGTGAAAATGAATGTATCTAGACAT 57.964 33.333 0.00 0.00 41.92 3.06
5302 6446 8.032451 TGTCGTGAAAATGAATGTATCTAGACA 58.968 33.333 0.00 0.00 0.00 3.41
5303 6447 8.407457 TGTCGTGAAAATGAATGTATCTAGAC 57.593 34.615 0.00 0.00 0.00 2.59
5304 6448 8.996024 TTGTCGTGAAAATGAATGTATCTAGA 57.004 30.769 0.00 0.00 0.00 2.43
5305 6449 8.873830 ACTTGTCGTGAAAATGAATGTATCTAG 58.126 33.333 0.00 0.00 0.00 2.43
5306 6450 8.771920 ACTTGTCGTGAAAATGAATGTATCTA 57.228 30.769 0.00 0.00 0.00 1.98
5307 6451 7.672983 ACTTGTCGTGAAAATGAATGTATCT 57.327 32.000 0.00 0.00 0.00 1.98
5308 6452 9.988350 ATTACTTGTCGTGAAAATGAATGTATC 57.012 29.630 0.00 0.00 0.00 2.24
5310 6454 9.820229 GAATTACTTGTCGTGAAAATGAATGTA 57.180 29.630 0.00 0.00 0.00 2.29
5311 6455 7.807907 GGAATTACTTGTCGTGAAAATGAATGT 59.192 33.333 0.00 0.00 0.00 2.71
5312 6456 7.007367 CGGAATTACTTGTCGTGAAAATGAATG 59.993 37.037 0.00 0.00 0.00 2.67
5313 6457 7.021196 CGGAATTACTTGTCGTGAAAATGAAT 58.979 34.615 0.00 0.00 0.00 2.57
5314 6458 6.203145 TCGGAATTACTTGTCGTGAAAATGAA 59.797 34.615 0.00 0.00 0.00 2.57
5315 6459 5.697178 TCGGAATTACTTGTCGTGAAAATGA 59.303 36.000 0.00 0.00 0.00 2.57
5316 6460 5.922546 TCGGAATTACTTGTCGTGAAAATG 58.077 37.500 0.00 0.00 0.00 2.32
5317 6461 6.017770 TGTTCGGAATTACTTGTCGTGAAAAT 60.018 34.615 0.00 0.00 0.00 1.82
5318 6462 5.293814 TGTTCGGAATTACTTGTCGTGAAAA 59.706 36.000 0.00 0.00 0.00 2.29
5319 6463 4.809958 TGTTCGGAATTACTTGTCGTGAAA 59.190 37.500 0.00 0.00 0.00 2.69
5320 6464 4.370049 TGTTCGGAATTACTTGTCGTGAA 58.630 39.130 0.00 0.00 0.00 3.18
5321 6465 3.979948 TGTTCGGAATTACTTGTCGTGA 58.020 40.909 0.00 0.00 0.00 4.35
5322 6466 3.985279 TCTGTTCGGAATTACTTGTCGTG 59.015 43.478 0.00 0.00 0.00 4.35
5323 6467 4.235360 CTCTGTTCGGAATTACTTGTCGT 58.765 43.478 0.00 0.00 0.00 4.34
5324 6468 3.612860 CCTCTGTTCGGAATTACTTGTCG 59.387 47.826 0.00 0.00 0.00 4.35
5325 6469 3.933332 CCCTCTGTTCGGAATTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
5326 6470 3.581332 TCCCTCTGTTCGGAATTACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
5327 6471 4.184629 CTCCCTCTGTTCGGAATTACTTG 58.815 47.826 0.00 0.00 0.00 3.16
5328 6472 3.838903 ACTCCCTCTGTTCGGAATTACTT 59.161 43.478 0.00 0.00 0.00 2.24
5329 6473 3.442076 ACTCCCTCTGTTCGGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
5330 6474 3.889520 ACTCCCTCTGTTCGGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
5331 6475 5.266788 TCTTACTCCCTCTGTTCGGAATTA 58.733 41.667 0.00 0.00 0.00 1.40
5332 6476 4.094476 TCTTACTCCCTCTGTTCGGAATT 58.906 43.478 0.00 0.00 0.00 2.17
5333 6477 3.702045 CTCTTACTCCCTCTGTTCGGAAT 59.298 47.826 0.00 0.00 0.00 3.01
5334 6478 3.090037 CTCTTACTCCCTCTGTTCGGAA 58.910 50.000 0.00 0.00 0.00 4.30
5335 6479 2.041350 ACTCTTACTCCCTCTGTTCGGA 59.959 50.000 0.00 0.00 0.00 4.55
5336 6480 2.448453 ACTCTTACTCCCTCTGTTCGG 58.552 52.381 0.00 0.00 0.00 4.30
5337 6481 4.522722 AAACTCTTACTCCCTCTGTTCG 57.477 45.455 0.00 0.00 0.00 3.95
5338 6482 4.998033 CCAAAACTCTTACTCCCTCTGTTC 59.002 45.833 0.00 0.00 0.00 3.18
5339 6483 4.747009 GCCAAAACTCTTACTCCCTCTGTT 60.747 45.833 0.00 0.00 0.00 3.16
5340 6484 3.244596 GCCAAAACTCTTACTCCCTCTGT 60.245 47.826 0.00 0.00 0.00 3.41
5341 6485 3.008485 AGCCAAAACTCTTACTCCCTCTG 59.992 47.826 0.00 0.00 0.00 3.35
5342 6486 3.252351 AGCCAAAACTCTTACTCCCTCT 58.748 45.455 0.00 0.00 0.00 3.69
5343 6487 3.704800 AGCCAAAACTCTTACTCCCTC 57.295 47.619 0.00 0.00 0.00 4.30
5344 6488 5.780958 AATAGCCAAAACTCTTACTCCCT 57.219 39.130 0.00 0.00 0.00 4.20
5345 6489 6.835819 AAAATAGCCAAAACTCTTACTCCC 57.164 37.500 0.00 0.00 0.00 4.30
5346 6490 6.586463 GCAAAAATAGCCAAAACTCTTACTCC 59.414 38.462 0.00 0.00 0.00 3.85
5347 6491 7.114953 GTGCAAAAATAGCCAAAACTCTTACTC 59.885 37.037 0.00 0.00 0.00 2.59
5348 6492 6.923508 GTGCAAAAATAGCCAAAACTCTTACT 59.076 34.615 0.00 0.00 0.00 2.24
5349 6493 6.923508 AGTGCAAAAATAGCCAAAACTCTTAC 59.076 34.615 0.00 0.00 0.00 2.34
5350 6494 6.922957 CAGTGCAAAAATAGCCAAAACTCTTA 59.077 34.615 0.00 0.00 0.00 2.10
5416 6560 8.592998 CGAGGTCGGATTATAGCAATTATTTAC 58.407 37.037 0.00 0.00 35.37 2.01
5417 6561 7.277098 GCGAGGTCGGATTATAGCAATTATTTA 59.723 37.037 0.89 0.00 40.23 1.40


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

AutoCloner maintained by Alex Coulton.