Multiple sequence alignment - TraesCS6B01G173500

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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 TraesCS6B01G173500 chr6B 100.000 6198 0 0 1 6198 187838039 187844236 0.000000e+00 11446.0
1 TraesCS6B01G173500 chr6B 86.940 513 53 7 5698 6198 157236740 157236230 1.170000e-156 564.0
2 TraesCS6B01G173500 chr6B 84.118 510 60 10 5698 6198 594958471 594958968 2.020000e-129 473.0
3 TraesCS6B01G173500 chr6B 94.326 141 7 1 3674 3813 191198138 191197998 1.350000e-51 215.0
4 TraesCS6B01G173500 chr6B 90.446 157 11 4 3679 3833 52982763 52982609 2.930000e-48 204.0
5 TraesCS6B01G173500 chr6D 92.751 3352 149 37 1 3302 102121487 102124794 0.000000e+00 4758.0
6 TraesCS6B01G173500 chr6D 93.956 728 21 6 4578 5297 102125820 102126532 0.000000e+00 1079.0
7 TraesCS6B01G173500 chr6D 96.745 553 11 3 3966 4517 102125280 102125826 0.000000e+00 915.0
8 TraesCS6B01G173500 chr6D 99.317 293 2 0 3390 3682 102124793 102125085 1.180000e-146 531.0
9 TraesCS6B01G173500 chr6D 89.055 402 28 11 5281 5668 102126548 102126947 9.340000e-133 484.0
10 TraesCS6B01G173500 chr6D 97.093 172 2 1 3802 3970 102125081 102125252 2.830000e-73 287.0
11 TraesCS6B01G173500 chr6D 85.870 92 3 3 6117 6198 422229147 422229238 8.560000e-14 89.8
12 TraesCS6B01G173500 chr6A 94.954 2497 78 18 852 3302 123455636 123458130 0.000000e+00 3869.0
13 TraesCS6B01G173500 chr6A 96.449 1577 35 10 3802 5368 123458417 123459982 0.000000e+00 2582.0
14 TraesCS6B01G173500 chr6A 93.352 722 32 10 100 814 123454924 123455636 0.000000e+00 1053.0
15 TraesCS6B01G173500 chr6A 100.000 293 0 0 3390 3682 123458129 123458421 5.470000e-150 542.0
16 TraesCS6B01G173500 chr6A 88.218 331 22 8 5388 5701 123460305 123460635 4.530000e-101 379.0
17 TraesCS6B01G173500 chr6A 94.231 104 6 0 1 104 123454683 123454786 6.430000e-35 159.0
18 TraesCS6B01G173500 chr7B 85.799 507 54 15 5705 6196 693458679 693459182 7.120000e-144 521.0
19 TraesCS6B01G173500 chr7B 84.971 519 60 16 5691 6196 698987830 698988343 1.540000e-140 510.0
20 TraesCS6B01G173500 chr7B 85.039 508 52 10 5705 6196 698516155 698516654 4.320000e-136 496.0
21 TraesCS6B01G173500 chr4A 85.396 404 46 6 5802 6196 661730422 661730821 2.080000e-109 407.0
22 TraesCS6B01G173500 chr3B 91.030 301 24 1 5901 6198 722584372 722584072 2.690000e-108 403.0
23 TraesCS6B01G173500 chr3B 89.634 164 9 6 3654 3811 115549487 115549648 1.050000e-47 202.0
24 TraesCS6B01G173500 chr3B 92.199 141 8 2 6061 6198 481648879 481648739 4.900000e-46 196.0
25 TraesCS6B01G173500 chr5B 91.228 228 17 1 5974 6198 550237941 550238168 2.170000e-79 307.0
26 TraesCS6B01G173500 chr5B 84.783 92 4 3 6117 6198 369249867 369249776 3.980000e-12 84.2
27 TraesCS6B01G173500 chr5B 95.455 44 2 0 6153 6196 636510910 636510953 3.100000e-08 71.3
28 TraesCS6B01G173500 chr3A 97.710 131 2 1 3675 3804 703272631 703272501 2.250000e-54 224.0
29 TraesCS6B01G173500 chr2D 95.620 137 5 1 3677 3812 622315786 622315650 1.050000e-52 219.0
30 TraesCS6B01G173500 chr2D 84.091 88 7 4 6117 6198 343540933 343541019 1.850000e-10 78.7
31 TraesCS6B01G173500 chr7A 91.195 159 9 5 3674 3831 663538192 663538346 1.750000e-50 211.0
32 TraesCS6B01G173500 chr3D 93.151 146 7 3 3668 3811 588394896 588394752 1.750000e-50 211.0
33 TraesCS6B01G173500 chr3D 87.273 110 6 5 3301 3407 182423397 182423293 1.090000e-22 119.0
34 TraesCS6B01G173500 chr1D 90.361 166 7 8 3678 3837 368493812 368493650 6.300000e-50 209.0
35 TraesCS6B01G173500 chr1D 84.615 91 4 3 6118 6198 61383123 61383213 1.430000e-11 82.4
36 TraesCS6B01G173500 chr2B 92.517 147 7 4 3673 3816 305317234 305317089 2.260000e-49 207.0
37 TraesCS6B01G173500 chr2B 89.796 98 7 1 3301 3395 129659860 129659763 8.440000e-24 122.0
38 TraesCS6B01G173500 chr2B 89.796 98 5 3 3297 3391 26724667 26724762 3.030000e-23 121.0
39 TraesCS6B01G173500 chr2B 90.426 94 5 2 3301 3391 26724762 26724670 3.030000e-23 121.0
40 TraesCS6B01G173500 chr5D 92.157 102 5 1 3300 3398 34445611 34445510 2.330000e-29 141.0
41 TraesCS6B01G173500 chr5D 90.526 95 6 1 3301 3392 34445517 34445611 8.440000e-24 122.0
42 TraesCS6B01G173500 chr5D 88.350 103 7 3 3301 3400 129166089 129166189 1.090000e-22 119.0
43 TraesCS6B01G173500 chr5D 84.146 82 13 0 6117 6198 333233229 333233310 5.150000e-11 80.5
44 TraesCS6B01G173500 chr4D 89.691 97 7 1 3301 3394 71381008 71380912 3.030000e-23 121.0
45 TraesCS6B01G173500 chr4D 89.583 96 7 1 3299 3391 71380913 71381008 1.090000e-22 119.0
46 TraesCS6B01G173500 chr1B 85.106 94 4 5 6115 6198 89962742 89962835 3.080000e-13 87.9
47 TraesCS6B01G173500 chr1A 82.796 93 5 4 6117 6198 467150294 467150202 8.620000e-09 73.1


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 TraesCS6B01G173500 chr6B 187838039 187844236 6197 False 11446.000000 11446 100.0000 1 6198 1 chr6B.!!$F1 6197
1 TraesCS6B01G173500 chr6B 157236230 157236740 510 True 564.000000 564 86.9400 5698 6198 1 chr6B.!!$R2 500
2 TraesCS6B01G173500 chr6D 102121487 102126947 5460 False 1342.333333 4758 94.8195 1 5668 6 chr6D.!!$F2 5667
3 TraesCS6B01G173500 chr6A 123454683 123460635 5952 False 1430.666667 3869 94.5340 1 5701 6 chr6A.!!$F1 5700
4 TraesCS6B01G173500 chr7B 693458679 693459182 503 False 521.000000 521 85.7990 5705 6196 1 chr7B.!!$F1 491
5 TraesCS6B01G173500 chr7B 698987830 698988343 513 False 510.000000 510 84.9710 5691 6196 1 chr7B.!!$F3 505

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
851 1014 0.108992 TCTCGCGCGATTGGTAAACT 60.109 50.0 34.86 0.00 0.0 2.66 F
1561 1762 0.032615 ACCCTCAAAACTGGCCAACA 60.033 50.0 7.01 0.00 0.0 3.33 F
2378 2597 0.402504 TGCTGTTAACCCCGGATGTT 59.597 50.0 0.73 8.95 0.0 2.71 F
3387 3611 0.774908 ACAATTTTGGGACGGAGGGA 59.225 50.0 0.00 0.00 0.0 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1858 2065 3.246699 CACGTCTTCCACAAAACGTACAT 59.753 43.478 0.00 0.0 45.67 2.29 R
3373 3597 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.0 0.00 3.28 R
3678 3902 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.0 46.06 2.59 R
5276 5547 0.654683 GAACCAATAGCAGAGCAGCG 59.345 55.000 0.00 0.0 40.15 5.18 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
93 94 5.276224 ATTCTCCAGGAAACACGACAAGTG 61.276 45.833 0.00 0.00 44.78 3.16
105 248 4.762956 ACGACAAGTGAGTAGTAAGTCC 57.237 45.455 0.00 0.00 0.00 3.85
140 284 0.409092 AATCATGTCTGCACCCCCAA 59.591 50.000 0.00 0.00 0.00 4.12
163 307 1.838112 ACAACATGCCATCGGTTCAT 58.162 45.000 0.00 0.00 0.00 2.57
226 370 1.301623 CCATGGCCGGGTAAACTCA 59.698 57.895 2.18 0.00 0.00 3.41
241 385 4.479786 AAACTCAGAACTAGGCTCATCC 57.520 45.455 0.00 0.00 0.00 3.51
259 403 2.114616 TCCTCTGAATTCTGAGAGCCC 58.885 52.381 32.44 0.00 42.37 5.19
317 461 4.806330 TCGTAAGTTCATGAACAGAGTCC 58.194 43.478 33.92 17.10 43.47 3.85
338 482 4.042311 TCCAGCACCTCATACCTAACAAAA 59.958 41.667 0.00 0.00 0.00 2.44
365 509 0.612229 CTGAGCACTCCACCATCTGT 59.388 55.000 0.00 0.00 0.00 3.41
477 631 6.579666 ACTATCCAGTGTCAGTAACGTAAA 57.420 37.500 0.00 0.00 32.25 2.01
615 771 3.850173 TCTACTTGGAAAATACTGGCCCT 59.150 43.478 0.00 0.00 0.00 5.19
639 795 1.461127 CTCTGCGGCTTTGACTTACAC 59.539 52.381 0.00 0.00 0.00 2.90
646 802 2.808543 GGCTTTGACTTACACAGGTGAG 59.191 50.000 6.40 0.00 36.73 3.51
648 804 3.495001 GCTTTGACTTACACAGGTGAGAC 59.505 47.826 6.40 0.00 34.86 3.36
849 1012 1.647346 ATTCTCGCGCGATTGGTAAA 58.353 45.000 34.86 19.38 0.00 2.01
851 1014 0.108992 TCTCGCGCGATTGGTAAACT 60.109 50.000 34.86 0.00 0.00 2.66
859 1022 4.670621 GCGCGATTGGTAAACTAAATCATG 59.329 41.667 12.10 0.00 31.88 3.07
860 1023 4.670621 CGCGATTGGTAAACTAAATCATGC 59.329 41.667 0.00 0.00 31.88 4.06
878 1041 1.202475 TGCACGCCATCGCTTTATCTA 60.202 47.619 0.00 0.00 39.84 1.98
1049 1219 3.839432 CCCTTCCGCGTCTCCCTC 61.839 72.222 4.92 0.00 0.00 4.30
1059 1229 2.045242 TCTCCCTCCTCGTCCACG 60.045 66.667 0.00 0.00 41.45 4.94
1218 1409 7.151976 CCTGTTCTAGGGTTTTGTATTTTTGG 58.848 38.462 0.00 0.00 43.33 3.28
1233 1424 2.697431 TTTGGCTGTTCGTGTATTGC 57.303 45.000 0.00 0.00 0.00 3.56
1261 1452 2.100410 CTCTAACGCTCGCTCGCA 59.900 61.111 0.00 0.00 0.00 5.10
1517 1718 2.466846 TCAGTTTCCTCGATCCCATCA 58.533 47.619 0.00 0.00 0.00 3.07
1540 1741 8.165239 TCATTTGTTGTGCTGTATTAGACTTT 57.835 30.769 0.00 0.00 0.00 2.66
1561 1762 0.032615 ACCCTCAAAACTGGCCAACA 60.033 50.000 7.01 0.00 0.00 3.33
1594 1797 1.403323 GGGCTTGAGCTACTTTGATGC 59.597 52.381 2.66 0.00 41.70 3.91
1601 1804 0.524180 GCTACTTTGATGCAAGCGCC 60.524 55.000 2.29 0.00 37.32 6.53
1608 1811 1.587088 GATGCAAGCGCCGATTTGG 60.587 57.895 2.29 0.00 42.50 3.28
1609 1812 1.992233 GATGCAAGCGCCGATTTGGA 61.992 55.000 2.29 3.29 42.00 3.53
1621 1828 4.513692 CGCCGATTTGGAGTATTAATTGGA 59.486 41.667 0.00 0.00 42.00 3.53
1747 1954 1.277557 AGTTCTCATCACTGGAGGTGC 59.722 52.381 0.00 0.00 44.98 5.01
1757 1964 1.215423 ACTGGAGGTGCTGGTTTCTTT 59.785 47.619 0.00 0.00 0.00 2.52
1759 1966 2.294512 CTGGAGGTGCTGGTTTCTTTTC 59.705 50.000 0.00 0.00 0.00 2.29
1766 1973 4.202151 GGTGCTGGTTTCTTTTCATTCTGT 60.202 41.667 0.00 0.00 0.00 3.41
1858 2065 2.622942 GTTTGCAGGGTGATGTTTCTCA 59.377 45.455 0.00 0.00 0.00 3.27
1907 2114 1.596260 ACTCAATTGATCGAGCATGCG 59.404 47.619 13.01 0.00 32.21 4.73
2087 2296 7.902920 ATGATTAGAATGTTTGCCTAACCAT 57.097 32.000 0.00 0.00 35.81 3.55
2088 2297 7.099266 TGATTAGAATGTTTGCCTAACCATG 57.901 36.000 0.00 0.00 35.81 3.66
2102 2311 6.663093 TGCCTAACCATGTTTCTGAATTATGT 59.337 34.615 11.17 1.01 0.00 2.29
2167 2376 4.034048 GCTGATGTTAGGATGTAAACCACG 59.966 45.833 0.00 0.00 0.00 4.94
2287 2506 6.128363 ACGTTAAGTTTTCACCTAATGCTAGC 60.128 38.462 8.10 8.10 0.00 3.42
2308 2527 4.461081 AGCGCTGTTGAATATTTAAACCCA 59.539 37.500 10.39 0.00 0.00 4.51
2378 2597 0.402504 TGCTGTTAACCCCGGATGTT 59.597 50.000 0.73 8.95 0.00 2.71
2502 2721 7.491682 CCATATAGTTTTAAGCACTTTGGCAT 58.508 34.615 0.00 0.00 35.83 4.40
2594 2813 8.453681 TCATGATATAGAGGTGTTACTCCCTTA 58.546 37.037 0.00 0.00 38.26 2.69
2986 3209 2.061028 GATGGAAACTTTGCTTTGCCG 58.939 47.619 0.00 0.00 0.00 5.69
3008 3232 6.539324 CCGAGTTGATAGCGTTTTGAAATAA 58.461 36.000 0.00 0.00 0.00 1.40
3028 3252 2.537863 GCACTCAGCCACTCTGTTC 58.462 57.895 0.00 0.00 43.32 3.18
3126 3350 4.965119 ATCAACGCAAATAGTCCCTTTC 57.035 40.909 0.00 0.00 0.00 2.62
3302 3526 9.329913 CATTCTGTAAGTTGCAAATGTTACTAC 57.670 33.333 20.11 11.73 32.42 2.73
3303 3527 8.671384 TTCTGTAAGTTGCAAATGTTACTACT 57.329 30.769 20.11 3.38 32.42 2.57
3304 3528 8.306680 TCTGTAAGTTGCAAATGTTACTACTC 57.693 34.615 20.11 0.00 32.42 2.59
3305 3529 7.386848 TCTGTAAGTTGCAAATGTTACTACTCC 59.613 37.037 20.11 0.00 32.42 3.85
3306 3530 5.959618 AAGTTGCAAATGTTACTACTCCC 57.040 39.130 0.00 0.00 0.00 4.30
3307 3531 5.242795 AGTTGCAAATGTTACTACTCCCT 57.757 39.130 0.00 0.00 0.00 4.20
3308 3532 5.631119 AGTTGCAAATGTTACTACTCCCTT 58.369 37.500 0.00 0.00 0.00 3.95
3309 3533 5.705905 AGTTGCAAATGTTACTACTCCCTTC 59.294 40.000 0.00 0.00 0.00 3.46
3310 3534 4.250464 TGCAAATGTTACTACTCCCTTCG 58.750 43.478 0.00 0.00 0.00 3.79
3311 3535 4.251268 GCAAATGTTACTACTCCCTTCGT 58.749 43.478 0.00 0.00 0.00 3.85
3312 3536 4.329256 GCAAATGTTACTACTCCCTTCGTC 59.671 45.833 0.00 0.00 0.00 4.20
3313 3537 4.732672 AATGTTACTACTCCCTTCGTCC 57.267 45.455 0.00 0.00 0.00 4.79
3314 3538 2.450476 TGTTACTACTCCCTTCGTCCC 58.550 52.381 0.00 0.00 0.00 4.46
3315 3539 2.225091 TGTTACTACTCCCTTCGTCCCA 60.225 50.000 0.00 0.00 0.00 4.37
3316 3540 2.827921 GTTACTACTCCCTTCGTCCCAA 59.172 50.000 0.00 0.00 0.00 4.12
3317 3541 2.019807 ACTACTCCCTTCGTCCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
3318 3542 2.332117 ACTACTCCCTTCGTCCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
3319 3543 2.910977 ACTACTCCCTTCGTCCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
3320 3544 2.971901 ACTCCCTTCGTCCCAAAATT 57.028 45.000 0.00 0.00 0.00 1.82
3321 3545 2.791655 ACTCCCTTCGTCCCAAAATTC 58.208 47.619 0.00 0.00 0.00 2.17
3322 3546 2.375509 ACTCCCTTCGTCCCAAAATTCT 59.624 45.455 0.00 0.00 0.00 2.40
3323 3547 3.181433 ACTCCCTTCGTCCCAAAATTCTT 60.181 43.478 0.00 0.00 0.00 2.52
3324 3548 3.153919 TCCCTTCGTCCCAAAATTCTTG 58.846 45.455 0.00 0.00 0.00 3.02
3325 3549 2.890945 CCCTTCGTCCCAAAATTCTTGT 59.109 45.455 0.00 0.00 0.00 3.16
3326 3550 3.057526 CCCTTCGTCCCAAAATTCTTGTC 60.058 47.826 0.00 0.00 0.00 3.18
3327 3551 3.821033 CCTTCGTCCCAAAATTCTTGTCT 59.179 43.478 0.00 0.00 0.00 3.41
3328 3552 4.278419 CCTTCGTCCCAAAATTCTTGTCTT 59.722 41.667 0.00 0.00 0.00 3.01
3329 3553 5.472137 CCTTCGTCCCAAAATTCTTGTCTTA 59.528 40.000 0.00 0.00 0.00 2.10
3330 3554 6.348540 CCTTCGTCCCAAAATTCTTGTCTTAG 60.349 42.308 0.00 0.00 0.00 2.18
3331 3555 5.860611 TCGTCCCAAAATTCTTGTCTTAGA 58.139 37.500 0.00 0.00 0.00 2.10
3332 3556 6.472887 TCGTCCCAAAATTCTTGTCTTAGAT 58.527 36.000 0.00 0.00 0.00 1.98
3333 3557 6.940298 TCGTCCCAAAATTCTTGTCTTAGATT 59.060 34.615 0.00 0.00 0.00 2.40
3334 3558 7.447238 TCGTCCCAAAATTCTTGTCTTAGATTT 59.553 33.333 0.00 0.00 0.00 2.17
3335 3559 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
3336 3560 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
3337 3561 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
3338 3562 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
3380 3604 8.887036 AGACAAATTTAAGACAATTTTGGGAC 57.113 30.769 0.00 0.00 34.70 4.46
3381 3605 7.651704 AGACAAATTTAAGACAATTTTGGGACG 59.348 33.333 0.00 0.00 34.70 4.79
3382 3606 6.704050 ACAAATTTAAGACAATTTTGGGACGG 59.296 34.615 0.00 0.00 34.70 4.79
3383 3607 6.658188 AATTTAAGACAATTTTGGGACGGA 57.342 33.333 0.00 0.00 0.00 4.69
3384 3608 5.699097 TTTAAGACAATTTTGGGACGGAG 57.301 39.130 0.00 0.00 0.00 4.63
3385 3609 2.200373 AGACAATTTTGGGACGGAGG 57.800 50.000 0.00 0.00 0.00 4.30
3386 3610 1.173913 GACAATTTTGGGACGGAGGG 58.826 55.000 0.00 0.00 0.00 4.30
3387 3611 0.774908 ACAATTTTGGGACGGAGGGA 59.225 50.000 0.00 0.00 0.00 4.20
3388 3612 1.271926 ACAATTTTGGGACGGAGGGAG 60.272 52.381 0.00 0.00 0.00 4.30
3389 3613 1.073098 AATTTTGGGACGGAGGGAGT 58.927 50.000 0.00 0.00 0.00 3.85
3390 3614 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
3677 3901 9.599322 CTAAACAGTAAAGTTGAAGCTGTAATG 57.401 33.333 0.00 0.00 39.19 1.90
3678 3902 7.568199 AACAGTAAAGTTGAAGCTGTAATGT 57.432 32.000 0.00 0.00 38.62 2.71
3679 3903 8.671384 AACAGTAAAGTTGAAGCTGTAATGTA 57.329 30.769 0.00 0.00 36.74 2.29
3680 3904 8.084590 ACAGTAAAGTTGAAGCTGTAATGTAC 57.915 34.615 0.00 0.00 36.21 2.90
3681 3905 7.931948 ACAGTAAAGTTGAAGCTGTAATGTACT 59.068 33.333 0.00 0.00 36.21 2.73
3682 3906 8.436200 CAGTAAAGTTGAAGCTGTAATGTACTC 58.564 37.037 0.00 0.00 0.00 2.59
3683 3907 6.803154 AAAGTTGAAGCTGTAATGTACTCC 57.197 37.500 0.00 0.00 0.00 3.85
3684 3908 4.833390 AGTTGAAGCTGTAATGTACTCCC 58.167 43.478 0.00 0.00 0.00 4.30
3685 3909 4.532521 AGTTGAAGCTGTAATGTACTCCCT 59.467 41.667 0.00 0.00 0.00 4.20
3686 3910 4.737855 TGAAGCTGTAATGTACTCCCTC 57.262 45.455 0.00 0.00 0.00 4.30
3687 3911 3.451178 TGAAGCTGTAATGTACTCCCTCC 59.549 47.826 0.00 0.00 0.00 4.30
3688 3912 2.032620 AGCTGTAATGTACTCCCTCCG 58.967 52.381 0.00 0.00 0.00 4.63
3689 3913 1.755380 GCTGTAATGTACTCCCTCCGT 59.245 52.381 0.00 0.00 0.00 4.69
3690 3914 2.223758 GCTGTAATGTACTCCCTCCGTC 60.224 54.545 0.00 0.00 0.00 4.79
3691 3915 2.361438 CTGTAATGTACTCCCTCCGTCC 59.639 54.545 0.00 0.00 0.00 4.79
3692 3916 1.336125 GTAATGTACTCCCTCCGTCCG 59.664 57.143 0.00 0.00 0.00 4.79
3693 3917 1.041447 AATGTACTCCCTCCGTCCGG 61.041 60.000 0.00 0.00 0.00 5.14
3694 3918 1.929860 ATGTACTCCCTCCGTCCGGA 61.930 60.000 0.00 0.00 42.90 5.14
3695 3919 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
3696 3920 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
3697 3921 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
3698 3922 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
3699 3923 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
3700 3924 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
3701 3925 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
3702 3926 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
3703 3927 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
3704 3928 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
3705 3929 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
3706 3930 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
3707 3931 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
3708 3932 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
3709 3933 4.119862 CGTCCGGAAATACTTGTCATCAT 58.880 43.478 5.23 0.00 0.00 2.45
3710 3934 5.286438 CGTCCGGAAATACTTGTCATCATA 58.714 41.667 5.23 0.00 0.00 2.15
3711 3935 5.751509 CGTCCGGAAATACTTGTCATCATAA 59.248 40.000 5.23 0.00 0.00 1.90
3712 3936 6.423905 CGTCCGGAAATACTTGTCATCATAAT 59.576 38.462 5.23 0.00 0.00 1.28
3713 3937 7.569408 CGTCCGGAAATACTTGTCATCATAATG 60.569 40.741 5.23 0.00 0.00 1.90
3714 3938 7.441157 GTCCGGAAATACTTGTCATCATAATGA 59.559 37.037 5.23 0.00 39.63 2.57
3715 3939 7.990314 TCCGGAAATACTTGTCATCATAATGAA 59.010 33.333 0.00 0.00 43.42 2.57
3716 3940 8.786898 CCGGAAATACTTGTCATCATAATGAAT 58.213 33.333 0.00 0.00 43.42 2.57
3724 3948 9.699410 ACTTGTCATCATAATGAATAAAAGGGA 57.301 29.630 0.00 0.00 43.42 4.20
3727 3951 9.645128 TGTCATCATAATGAATAAAAGGGATGT 57.355 29.630 0.00 0.00 43.42 3.06
3790 4014 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
3791 4015 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
3792 4016 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
3793 4017 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
3794 4018 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
3795 4019 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
3796 4020 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
3797 4021 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
3798 4022 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
3799 4023 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
3800 4024 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
3976 4235 3.641437 TGTATGTTTTTGTGGCTGCTC 57.359 42.857 0.00 0.00 0.00 4.26
4033 4292 8.662781 ATTGTTGACATATAGTATTTGAGCGT 57.337 30.769 7.49 0.00 0.00 5.07
4034 4293 8.487313 TTGTTGACATATAGTATTTGAGCGTT 57.513 30.769 7.49 0.00 0.00 4.84
4219 4478 9.230932 CTTGAAGAGAAAAGTTTTCTTGATGAC 57.769 33.333 27.27 15.67 40.37 3.06
4249 4508 8.478877 AGCACTATAGTATTTGTTGAAGCTAGT 58.521 33.333 4.74 0.00 0.00 2.57
4471 4731 9.404848 CTCATGATATTAATATGGGATTGCAGT 57.595 33.333 12.74 0.00 0.00 4.40
4486 4746 5.176223 GGATTGCAGTTGTGAAAGTTTCATG 59.824 40.000 20.72 15.35 42.47 3.07
4487 4747 3.446799 TGCAGTTGTGAAAGTTTCATGC 58.553 40.909 24.98 24.98 42.47 4.06
4488 4748 3.119209 TGCAGTTGTGAAAGTTTCATGCA 60.119 39.130 28.26 28.26 44.81 3.96
4489 4749 3.243643 GCAGTTGTGAAAGTTTCATGCAC 59.756 43.478 26.04 19.67 42.47 4.57
4490 4750 4.422840 CAGTTGTGAAAGTTTCATGCACA 58.577 39.130 20.72 11.93 42.47 4.57
4814 5075 7.281098 TGTGTTGGTTCAAATAGTAACCTGTA 58.719 34.615 5.88 0.00 44.55 2.74
4951 5214 6.148811 ACACACACATTACTATGCTGTTTACC 59.851 38.462 0.00 0.00 35.03 2.85
5141 5406 2.289694 ACAATTCTTCCTGGACCGTCTG 60.290 50.000 0.00 0.00 0.00 3.51
5222 5487 6.385467 AGATCTGCTTACCCTGACTAGATTTT 59.615 38.462 0.00 0.00 0.00 1.82
5223 5488 6.374417 TCTGCTTACCCTGACTAGATTTTT 57.626 37.500 0.00 0.00 0.00 1.94
5225 5490 8.090788 TCTGCTTACCCTGACTAGATTTTTAT 57.909 34.615 0.00 0.00 0.00 1.40
5229 5494 9.343539 GCTTACCCTGACTAGATTTTTATGATT 57.656 33.333 0.00 0.00 0.00 2.57
5264 5535 7.349859 ACTGATAGGGTACATTCTTATCCCAAA 59.650 37.037 0.00 0.00 40.48 3.28
5276 5547 4.166144 TCTTATCCCAAATCTCCACCCTTC 59.834 45.833 0.00 0.00 0.00 3.46
5286 5557 3.123620 CACCCTTCGCTGCTCTGC 61.124 66.667 0.00 0.00 0.00 4.26
5287 5558 3.317571 ACCCTTCGCTGCTCTGCT 61.318 61.111 0.00 0.00 0.00 4.24
5299 5602 3.196463 CTGCTCTGCTATTGGTTCTCAG 58.804 50.000 0.00 0.00 0.00 3.35
5317 5620 1.000233 GGTCCATGTCCATTGGGCA 60.000 57.895 13.33 13.33 0.00 5.36
5338 5641 5.163652 GGCACTTATGAATTGACAGTTACCC 60.164 44.000 0.00 0.00 0.00 3.69
5368 5671 1.347378 GGTGGCATTTGGTGTGGAAAT 59.653 47.619 0.00 0.00 0.00 2.17
5371 5674 3.258123 GTGGCATTTGGTGTGGAAATAGT 59.742 43.478 0.00 0.00 0.00 2.12
5372 5675 3.509575 TGGCATTTGGTGTGGAAATAGTC 59.490 43.478 0.00 0.00 0.00 2.59
5412 6018 3.609175 CGACGTTTGATTGGACATTTGCT 60.609 43.478 0.00 0.00 0.00 3.91
5417 6023 4.459390 TTGATTGGACATTTGCTCATGG 57.541 40.909 0.00 0.00 0.00 3.66
5446 6052 9.993454 TTTTTCATTGTCCATGATGTTGATAAA 57.007 25.926 0.00 0.00 41.82 1.40
5459 6065 9.820725 ATGATGTTGATAAAATATTTGTGTGGG 57.179 29.630 0.39 0.00 0.00 4.61
5473 6081 1.001406 GTGTGGGAAGTCTCACTGAGG 59.999 57.143 12.39 0.00 35.15 3.86
5480 6088 3.007398 GGAAGTCTCACTGAGGTTGTGAT 59.993 47.826 6.20 0.00 42.57 3.06
5586 6194 2.053984 GATGTATGCACGCACGCG 60.054 61.111 10.36 10.36 46.03 6.01
5612 6220 1.791555 GCAGTGCGAATTGATTGTCGG 60.792 52.381 0.00 0.00 37.73 4.79
5613 6221 1.464608 CAGTGCGAATTGATTGTCGGT 59.535 47.619 0.00 0.00 37.73 4.69
5614 6222 2.670905 CAGTGCGAATTGATTGTCGGTA 59.329 45.455 0.00 0.00 37.73 4.02
5616 6224 3.555956 AGTGCGAATTGATTGTCGGTATC 59.444 43.478 0.00 0.00 37.73 2.24
5620 6231 4.374707 GCGAATTGATTGTCGGTATCGTAC 60.375 45.833 0.00 0.00 37.73 3.67
5652 6265 8.773033 ACATTTCTAAATCAAATAGATGGCCT 57.227 30.769 3.32 0.00 36.96 5.19
5668 6281 1.134670 GGCCTAGGTGACACATGTCTC 60.135 57.143 11.31 9.23 44.99 3.36
5669 6282 1.469940 GCCTAGGTGACACATGTCTCG 60.470 57.143 11.31 0.00 44.99 4.04
5702 6326 1.956297 TGACCAAAATTCACGGACGT 58.044 45.000 0.00 0.00 0.00 4.34
5717 6341 3.760035 CGTGTCTAGTGGGCGGCT 61.760 66.667 9.56 0.00 0.00 5.52
5720 6344 3.075005 GTCTAGTGGGCGGCTGGA 61.075 66.667 9.56 0.00 0.00 3.86
5723 6347 2.687200 TAGTGGGCGGCTGGATGT 60.687 61.111 9.56 0.00 0.00 3.06
5741 6366 0.733729 GTCCACTAGTGCGATCGAGT 59.266 55.000 21.57 10.53 0.00 4.18
5772 6397 1.842699 AAAGGTAAACCCCTGTCCCT 58.157 50.000 0.00 0.00 34.19 4.20
5776 6402 2.295602 TAAACCCCTGTCCCTCGCC 61.296 63.158 0.00 0.00 0.00 5.54
5782 6408 2.642254 CCTGTCCCTCGCCGTACAA 61.642 63.158 0.00 0.00 0.00 2.41
5803 6429 0.623617 AAAGGAAGGGGATAGGCGGT 60.624 55.000 0.00 0.00 0.00 5.68
5806 6432 1.342672 GGAAGGGGATAGGCGGTCAA 61.343 60.000 0.00 0.00 0.00 3.18
5836 6462 1.218316 GATCGAGCGTCCAAACCCT 59.782 57.895 0.00 0.00 0.00 4.34
5841 6467 1.874739 CGAGCGTCCAAACCCTAACAA 60.875 52.381 0.00 0.00 0.00 2.83
5842 6468 1.804748 GAGCGTCCAAACCCTAACAAG 59.195 52.381 0.00 0.00 0.00 3.16
5848 6474 2.304761 TCCAAACCCTAACAAGATCGCT 59.695 45.455 0.00 0.00 0.00 4.93
5873 6506 4.052518 GTGGCCAGCTGTCCCCAT 62.053 66.667 12.07 0.00 0.00 4.00
5874 6507 3.731728 TGGCCAGCTGTCCCCATC 61.732 66.667 12.07 0.00 0.00 3.51
5875 6508 3.415087 GGCCAGCTGTCCCCATCT 61.415 66.667 13.81 0.00 0.00 2.90
5876 6509 2.072487 GGCCAGCTGTCCCCATCTA 61.072 63.158 13.81 0.00 0.00 1.98
5877 6510 1.449353 GCCAGCTGTCCCCATCTAG 59.551 63.158 13.81 0.00 0.00 2.43
5878 6511 1.449353 CCAGCTGTCCCCATCTAGC 59.551 63.158 13.81 0.00 36.45 3.42
5879 6512 1.449353 CAGCTGTCCCCATCTAGCC 59.551 63.158 5.25 0.00 36.86 3.93
5880 6513 1.053264 CAGCTGTCCCCATCTAGCCT 61.053 60.000 5.25 0.00 36.86 4.58
5919 6559 3.350163 CCCCAGCCCCTTCCATGT 61.350 66.667 0.00 0.00 0.00 3.21
5942 6594 3.080319 GCCTTCTTCTTCTTCTGCATGT 58.920 45.455 0.00 0.00 0.00 3.21
5967 6619 3.652057 AATGGGATCCAACAGAATCGT 57.348 42.857 15.23 0.00 36.95 3.73
5988 6640 1.210885 CCAGGCCCTTCTTCCTCCTT 61.211 60.000 0.00 0.00 0.00 3.36
5998 6650 3.176924 TCTTCCTCCTTCTGTACAGCT 57.823 47.619 18.45 0.00 0.00 4.24
6022 6674 4.158394 GCCATGGCAATTCAAGAGTAGAAA 59.842 41.667 32.08 0.00 41.49 2.52
6065 6717 1.961133 ACGGTAGAAGGGGATCCAAA 58.039 50.000 15.23 0.00 34.83 3.28
6115 6767 0.539518 GCCTTCTTCCTCCTCCTGAC 59.460 60.000 0.00 0.00 0.00 3.51
6162 6817 3.295093 TCTTCCTCCTCTAGTGCATCTG 58.705 50.000 0.00 0.00 0.00 2.90
6188 6843 3.263724 CCCCCTTCTCCATGGATCTATT 58.736 50.000 16.63 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.182001 GCTTATTTTGTCACTGTCAGGATGT 59.818 40.000 4.53 0.00 37.40 3.06
58 59 6.433847 TTCCTGGAGAATTCACTTAGAACA 57.566 37.500 8.44 0.00 39.49 3.18
93 94 8.132362 CAGTTGACAGATATGGACTTACTACTC 58.868 40.741 0.00 0.00 0.00 2.59
105 248 8.336080 CAGACATGATTTCAGTTGACAGATATG 58.664 37.037 0.00 0.00 0.00 1.78
140 284 3.181471 TGAACCGATGGCATGTTGTTTTT 60.181 39.130 3.81 0.00 0.00 1.94
163 307 2.436417 GCTGGTTGCAGTGGATAAGAA 58.564 47.619 0.00 0.00 42.31 2.52
241 385 2.235650 TGTGGGCTCTCAGAATTCAGAG 59.764 50.000 19.03 19.03 39.44 3.35
259 403 2.413239 GCCGATGAGTGAAATGTGTGTG 60.413 50.000 0.00 0.00 0.00 3.82
317 461 5.003804 AGTTTTGTTAGGTATGAGGTGCTG 58.996 41.667 0.00 0.00 0.00 4.41
338 482 2.224305 GGTGGAGTGCTCAGTGTTAAGT 60.224 50.000 1.41 0.00 0.00 2.24
420 574 1.000506 AGTGGTCGACGTAATGCTGTT 59.999 47.619 9.92 0.00 0.00 3.16
464 618 2.346545 GGTCGGCATTTACGTTACTGAC 59.653 50.000 0.00 0.00 36.19 3.51
477 631 1.789576 AAGGTTGGGAAGGTCGGCAT 61.790 55.000 0.00 0.00 0.00 4.40
576 732 2.988010 AGAAATGCACATCGCCTCTA 57.012 45.000 0.00 0.00 41.33 2.43
615 771 0.106708 AGTCAAAGCCGCAGAGAACA 59.893 50.000 0.00 0.00 0.00 3.18
639 795 0.249868 TTCGGCTGTTGTCTCACCTG 60.250 55.000 0.00 0.00 0.00 4.00
822 985 1.200483 TCGCGCGAGAATTCTCATTC 58.800 50.000 31.40 18.64 43.00 2.67
823 986 1.858091 ATCGCGCGAGAATTCTCATT 58.142 45.000 36.99 14.25 43.00 2.57
824 987 1.524355 CAATCGCGCGAGAATTCTCAT 59.476 47.619 36.99 15.07 43.00 2.90
825 988 0.923403 CAATCGCGCGAGAATTCTCA 59.077 50.000 36.99 11.94 43.00 3.27
826 989 0.230769 CCAATCGCGCGAGAATTCTC 59.769 55.000 36.99 23.20 39.55 2.87
836 999 4.267357 TGATTTAGTTTACCAATCGCGC 57.733 40.909 0.00 0.00 30.69 6.86
849 1012 1.599071 CGATGGCGTGCATGATTTAGT 59.401 47.619 10.93 0.00 0.00 2.24
851 1014 0.307453 GCGATGGCGTGCATGATTTA 59.693 50.000 10.93 0.00 40.36 1.40
859 1022 1.497991 TAGATAAAGCGATGGCGTGC 58.502 50.000 0.00 0.00 46.35 5.34
860 1023 3.060272 CAGTTAGATAAAGCGATGGCGTG 60.060 47.826 0.00 0.00 46.35 5.34
1035 1205 2.754658 GAGGAGGGAGACGCGGAA 60.755 66.667 12.47 0.00 0.00 4.30
1041 1211 2.408241 CGTGGACGAGGAGGGAGAC 61.408 68.421 0.00 0.00 43.02 3.36
1158 1328 3.490793 ATGAGATGACGAGGCGGCG 62.491 63.158 0.51 0.51 37.93 6.46
1218 1409 1.577616 CGCGCAATACACGAACAGC 60.578 57.895 8.75 0.00 0.00 4.40
1233 1424 2.059575 CGTTAGAGGTGACAACGCG 58.940 57.895 3.53 3.53 38.63 6.01
1261 1452 1.959226 CTGCCTACAAACACGCCGT 60.959 57.895 0.00 0.00 0.00 5.68
1455 1656 1.482593 ACTCGGATTGGACCAAGCTAG 59.517 52.381 21.23 19.39 29.93 3.42
1517 1718 9.893305 GTAAAAGTCTAATACAGCACAACAAAT 57.107 29.630 0.00 0.00 0.00 2.32
1540 1741 2.312390 GTTGGCCAGTTTTGAGGGTAA 58.688 47.619 5.11 0.00 0.00 2.85
1594 1797 1.299541 ATACTCCAAATCGGCGCTTG 58.700 50.000 7.64 8.33 33.14 4.01
1601 1804 6.483307 TGAGCTCCAATTAATACTCCAAATCG 59.517 38.462 12.15 0.00 0.00 3.34
1609 1812 9.950496 CCTACATTATGAGCTCCAATTAATACT 57.050 33.333 12.15 0.00 0.00 2.12
1621 1828 6.692849 TCCATCAATCCTACATTATGAGCT 57.307 37.500 0.00 0.00 0.00 4.09
1747 1954 9.918630 ATATTCAACAGAATGAAAAGAAACCAG 57.081 29.630 1.21 0.00 42.22 4.00
1858 2065 3.246699 CACGTCTTCCACAAAACGTACAT 59.753 43.478 0.00 0.00 45.67 2.29
1998 2207 8.835439 ACAAACAAAATGTGGTATTCCAATTTC 58.165 29.630 0.00 0.00 46.15 2.17
2004 2213 6.983890 AGACAACAAACAAAATGTGGTATTCC 59.016 34.615 0.00 0.00 35.10 3.01
2125 2334 3.344904 GCACACTGCAATCATGTATCC 57.655 47.619 0.00 0.00 44.26 2.59
2206 2423 5.511234 AGATACATGCTTCAAAATCAGGC 57.489 39.130 0.00 0.00 0.00 4.85
2287 2506 7.826260 AATTGGGTTTAAATATTCAACAGCG 57.174 32.000 10.93 0.00 0.00 5.18
2347 2566 4.024302 GGGTTAACAGCAGTTACAAGACAC 60.024 45.833 8.10 0.00 39.80 3.67
2502 2721 5.504853 TGTAAAGATGCATATGACACCCAA 58.495 37.500 6.97 0.00 0.00 4.12
2578 2797 4.876679 GCAATCTTAAGGGAGTAACACCTC 59.123 45.833 1.85 0.00 35.64 3.85
2986 3209 7.537306 TGCTTTATTTCAAAACGCTATCAACTC 59.463 33.333 0.00 0.00 0.00 3.01
3028 3252 4.437390 GCCAAATTCTACAGTGATGAACGG 60.437 45.833 0.00 4.28 0.00 4.44
3116 3340 5.155278 TCAAACATAAGCGAAAGGGACTA 57.845 39.130 0.00 0.00 38.49 2.59
3126 3350 6.598525 TGTGTGATACTTTCAAACATAAGCG 58.401 36.000 0.00 0.00 45.73 4.68
3302 3526 3.073274 AGAATTTTGGGACGAAGGGAG 57.927 47.619 0.00 0.00 0.00 4.30
3303 3527 3.153919 CAAGAATTTTGGGACGAAGGGA 58.846 45.455 0.00 0.00 0.00 4.20
3304 3528 2.890945 ACAAGAATTTTGGGACGAAGGG 59.109 45.455 0.00 0.00 0.00 3.95
3305 3529 3.821033 AGACAAGAATTTTGGGACGAAGG 59.179 43.478 0.00 0.00 0.00 3.46
3306 3530 5.438761 AAGACAAGAATTTTGGGACGAAG 57.561 39.130 0.00 0.00 0.00 3.79
3307 3531 6.292923 TCTAAGACAAGAATTTTGGGACGAA 58.707 36.000 0.00 0.00 0.00 3.85
3308 3532 5.860611 TCTAAGACAAGAATTTTGGGACGA 58.139 37.500 0.00 0.00 0.00 4.20
3309 3533 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
3310 3534 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
3311 3535 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
3312 3536 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
3354 3578 9.974980 GTCCCAAAATTGTCTTAAATTTGTCTA 57.025 29.630 0.00 0.00 39.20 2.59
3355 3579 7.651704 CGTCCCAAAATTGTCTTAAATTTGTCT 59.348 33.333 0.00 0.00 39.20 3.41
3356 3580 7.095816 CCGTCCCAAAATTGTCTTAAATTTGTC 60.096 37.037 0.00 0.00 39.20 3.18
3357 3581 6.704050 CCGTCCCAAAATTGTCTTAAATTTGT 59.296 34.615 0.00 0.00 39.20 2.83
3358 3582 6.926272 TCCGTCCCAAAATTGTCTTAAATTTG 59.074 34.615 0.00 0.00 39.20 2.32
3359 3583 7.056844 TCCGTCCCAAAATTGTCTTAAATTT 57.943 32.000 0.00 0.00 40.60 1.82
3360 3584 6.295067 CCTCCGTCCCAAAATTGTCTTAAATT 60.295 38.462 0.00 0.00 0.00 1.82
3361 3585 5.185056 CCTCCGTCCCAAAATTGTCTTAAAT 59.815 40.000 0.00 0.00 0.00 1.40
3362 3586 4.521256 CCTCCGTCCCAAAATTGTCTTAAA 59.479 41.667 0.00 0.00 0.00 1.52
3363 3587 4.076394 CCTCCGTCCCAAAATTGTCTTAA 58.924 43.478 0.00 0.00 0.00 1.85
3364 3588 3.560453 CCCTCCGTCCCAAAATTGTCTTA 60.560 47.826 0.00 0.00 0.00 2.10
3365 3589 2.514803 CCTCCGTCCCAAAATTGTCTT 58.485 47.619 0.00 0.00 0.00 3.01
3366 3590 1.271926 CCCTCCGTCCCAAAATTGTCT 60.272 52.381 0.00 0.00 0.00 3.41
3367 3591 1.173913 CCCTCCGTCCCAAAATTGTC 58.826 55.000 0.00 0.00 0.00 3.18
3368 3592 0.774908 TCCCTCCGTCCCAAAATTGT 59.225 50.000 0.00 0.00 0.00 2.71
3369 3593 1.271926 ACTCCCTCCGTCCCAAAATTG 60.272 52.381 0.00 0.00 0.00 2.32
3370 3594 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
3371 3595 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
3372 3596 1.272807 CTACTCCCTCCGTCCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
3373 3597 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
3374 3598 0.115745 AACTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
3375 3599 1.002069 TAACTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
3376 3600 1.753649 GTTAACTACTCCCTCCGTCCC 59.246 57.143 0.00 0.00 0.00 4.46
3377 3601 2.732763 AGTTAACTACTCCCTCCGTCC 58.267 52.381 6.26 0.00 28.23 4.79
3378 3602 6.462552 AATAAGTTAACTACTCCCTCCGTC 57.537 41.667 8.92 0.00 35.54 4.79
3379 3603 7.776107 GTTAATAAGTTAACTACTCCCTCCGT 58.224 38.462 8.92 0.00 43.99 4.69
3677 3901 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
3678 3902 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
3679 3903 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
3680 3904 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
3681 3905 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
3682 3906 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
3683 3907 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
3684 3908 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
3685 3909 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
3686 3910 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
3687 3911 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
3688 3912 7.441157 TCATTATGATGACAAGTATTTCCGGAC 59.559 37.037 1.83 0.00 37.37 4.79
3689 3913 7.505258 TCATTATGATGACAAGTATTTCCGGA 58.495 34.615 0.00 0.00 37.37 5.14
3690 3914 7.728847 TCATTATGATGACAAGTATTTCCGG 57.271 36.000 0.00 0.00 37.37 5.14
3698 3922 9.699410 TCCCTTTTATTCATTATGATGACAAGT 57.301 29.630 0.00 0.00 41.84 3.16
3701 3925 9.645128 ACATCCCTTTTATTCATTATGATGACA 57.355 29.630 0.00 0.00 41.84 3.58
3765 3989 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
3766 3990 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
3767 3991 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
3768 3992 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
3769 3993 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
3770 3994 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
3771 3995 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
3772 3996 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
3773 3997 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
3774 3998 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
3775 3999 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
3776 4000 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
3777 4001 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
3778 4002 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
3779 4003 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
3780 4004 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
3781 4005 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
3782 4006 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
3783 4007 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
3784 4008 1.479730 GTACTCCCTCCGTCCGAAAAT 59.520 52.381 0.00 0.00 0.00 1.82
3785 4009 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
3786 4010 0.038744 AGTACTCCCTCCGTCCGAAA 59.961 55.000 0.00 0.00 0.00 3.46
3787 4011 0.911769 TAGTACTCCCTCCGTCCGAA 59.088 55.000 0.00 0.00 0.00 4.30
3788 4012 0.911769 TTAGTACTCCCTCCGTCCGA 59.088 55.000 0.00 0.00 0.00 4.55
3789 4013 1.307097 CTTAGTACTCCCTCCGTCCG 58.693 60.000 0.00 0.00 0.00 4.79
3790 4014 2.433662 ACTTAGTACTCCCTCCGTCC 57.566 55.000 0.00 0.00 0.00 4.79
3791 4015 7.573968 TTATTTACTTAGTACTCCCTCCGTC 57.426 40.000 0.00 0.00 0.00 4.79
3792 4016 8.003629 AGATTATTTACTTAGTACTCCCTCCGT 58.996 37.037 0.00 0.00 0.00 4.69
3793 4017 8.406730 AGATTATTTACTTAGTACTCCCTCCG 57.593 38.462 0.00 0.00 0.00 4.63
4031 4290 9.946165 AAAGAAAGTCAGAATTTACCTTAAACG 57.054 29.630 0.00 0.00 0.00 3.60
4219 4478 7.520119 TTCAACAAATACTATAGTGCTCACG 57.480 36.000 15.90 2.04 36.20 4.35
4471 4731 3.119209 TGCTGTGCATGAAACTTTCACAA 60.119 39.130 6.35 0.00 43.48 3.33
4486 4746 2.286294 GTCATGTATAGCTGTGCTGTGC 59.714 50.000 0.00 0.00 40.10 4.57
4487 4747 3.524541 TGTCATGTATAGCTGTGCTGTG 58.475 45.455 0.00 0.00 40.10 3.66
4488 4748 3.893326 TGTCATGTATAGCTGTGCTGT 57.107 42.857 0.00 0.00 40.10 4.40
4489 4749 5.746307 AATTGTCATGTATAGCTGTGCTG 57.254 39.130 0.00 0.00 40.10 4.41
4490 4750 6.764308 AAAATTGTCATGTATAGCTGTGCT 57.236 33.333 0.00 0.00 43.41 4.40
4615 4876 4.778213 AGATATTTCAACAGCTAGGGCA 57.222 40.909 0.00 0.00 41.70 5.36
4679 4940 5.543507 AATCTAGCCACTTCAGATCGAAT 57.456 39.130 0.00 0.00 31.69 3.34
4680 4941 5.344743 AAATCTAGCCACTTCAGATCGAA 57.655 39.130 0.00 0.00 0.00 3.71
4814 5075 5.600696 TGACATGCAGTATCGTAACATGAT 58.399 37.500 0.00 0.00 40.39 2.45
4951 5214 5.418310 AACAGAAAGAAATGGTGTGTACG 57.582 39.130 0.00 0.00 0.00 3.67
4978 5241 6.551601 AGGCTAACAACTATGCATACTACTCT 59.448 38.462 1.16 0.00 0.00 3.24
4979 5242 6.750148 AGGCTAACAACTATGCATACTACTC 58.250 40.000 1.16 0.00 0.00 2.59
5141 5406 2.894387 GCTGCTCGAGGATGGTGC 60.894 66.667 15.58 7.38 33.82 5.01
5222 5487 9.213777 ACCCTATCAGTCTAAAGTCAATCATAA 57.786 33.333 0.00 0.00 0.00 1.90
5223 5488 8.783660 ACCCTATCAGTCTAAAGTCAATCATA 57.216 34.615 0.00 0.00 0.00 2.15
5225 5490 7.618117 TGTACCCTATCAGTCTAAAGTCAATCA 59.382 37.037 0.00 0.00 0.00 2.57
5229 5494 7.839705 AGAATGTACCCTATCAGTCTAAAGTCA 59.160 37.037 0.00 0.00 37.26 3.41
5230 5495 8.240267 AGAATGTACCCTATCAGTCTAAAGTC 57.760 38.462 0.00 0.00 37.26 3.01
5242 5513 8.525729 AGATTTGGGATAAGAATGTACCCTAT 57.474 34.615 0.00 0.00 40.98 2.57
5264 5535 1.965754 GAGCAGCGAAGGGTGGAGAT 61.966 60.000 0.00 0.00 41.91 2.75
5276 5547 0.654683 GAACCAATAGCAGAGCAGCG 59.345 55.000 0.00 0.00 40.15 5.18
5286 5557 4.446371 GACATGGACCTGAGAACCAATAG 58.554 47.826 0.00 0.00 37.24 1.73
5287 5558 3.199946 GGACATGGACCTGAGAACCAATA 59.800 47.826 0.00 0.00 37.24 1.90
5299 5602 1.000233 TGCCCAATGGACATGGACC 60.000 57.895 0.00 0.49 40.56 4.46
5446 6052 5.707298 CAGTGAGACTTCCCACACAAATATT 59.293 40.000 0.00 0.00 35.84 1.28
5459 6065 3.735237 TCACAACCTCAGTGAGACTTC 57.265 47.619 22.09 0.00 40.80 3.01
5473 6081 4.989168 AGTACCTTTCGTCTTCATCACAAC 59.011 41.667 0.00 0.00 0.00 3.32
5480 6088 2.561419 CCTCCAGTACCTTTCGTCTTCA 59.439 50.000 0.00 0.00 0.00 3.02
5586 6194 0.787787 TCAATTCGCACTGCACGTAC 59.212 50.000 1.11 0.00 0.00 3.67
5594 6202 1.808411 ACCGACAATCAATTCGCACT 58.192 45.000 0.00 0.00 33.78 4.40
5612 6220 4.427312 AGAAATGTCCAACCGTACGATAC 58.573 43.478 18.76 7.57 0.00 2.24
5613 6221 4.724074 AGAAATGTCCAACCGTACGATA 57.276 40.909 18.76 0.00 0.00 2.92
5614 6222 3.604875 AGAAATGTCCAACCGTACGAT 57.395 42.857 18.76 0.00 0.00 3.73
5616 6224 5.349270 TGATTTAGAAATGTCCAACCGTACG 59.651 40.000 8.69 8.69 0.00 3.67
5620 6231 8.673711 TCTATTTGATTTAGAAATGTCCAACCG 58.326 33.333 0.00 0.00 0.00 4.44
5668 6281 1.407258 TGGTCAAAAGAAAACCTGCCG 59.593 47.619 0.00 0.00 34.05 5.69
5669 6282 3.535280 TTGGTCAAAAGAAAACCTGCC 57.465 42.857 0.00 0.00 34.05 4.85
5702 6326 3.390521 CCAGCCGCCCACTAGACA 61.391 66.667 0.00 0.00 0.00 3.41
5717 6341 1.409064 GATCGCACTAGTGGACATCCA 59.591 52.381 23.95 0.00 45.30 3.41
5720 6344 1.335182 CTCGATCGCACTAGTGGACAT 59.665 52.381 23.95 6.16 0.00 3.06
5723 6347 0.733150 CACTCGATCGCACTAGTGGA 59.267 55.000 23.95 18.44 36.53 4.02
5782 6408 1.063942 CCGCCTATCCCCTTCCTTTTT 60.064 52.381 0.00 0.00 0.00 1.94
5803 6429 1.428448 CGATCAGCTCGGTTTGTTGA 58.572 50.000 0.00 0.00 43.82 3.18
5817 6443 1.079405 GGGTTTGGACGCTCGATCA 60.079 57.895 0.00 0.00 35.94 2.92
5827 6453 2.304761 AGCGATCTTGTTAGGGTTTGGA 59.695 45.455 0.00 0.00 0.00 3.53
5836 6462 1.140852 CATGGGGGAGCGATCTTGTTA 59.859 52.381 0.00 0.00 0.00 2.41
5841 6467 2.446848 CCACATGGGGGAGCGATCT 61.447 63.158 5.91 0.00 0.00 2.75
5842 6468 2.111878 CCACATGGGGGAGCGATC 59.888 66.667 5.91 0.00 0.00 3.69
5873 6506 2.122813 GGGGGCTAGCAGGCTAGA 60.123 66.667 27.69 0.00 46.56 2.43
5874 6507 2.446610 TGGGGGCTAGCAGGCTAG 60.447 66.667 21.12 21.12 46.41 3.42
5875 6508 2.768344 GTGGGGGCTAGCAGGCTA 60.768 66.667 18.24 0.49 41.09 3.93
5913 6553 3.795688 AGAAGAAGAAGGCAACATGGA 57.204 42.857 0.00 0.00 41.41 3.41
5917 6557 2.880890 GCAGAAGAAGAAGAAGGCAACA 59.119 45.455 0.00 0.00 41.41 3.33
5919 6559 3.213206 TGCAGAAGAAGAAGAAGGCAA 57.787 42.857 0.00 0.00 0.00 4.52
5942 6594 4.656100 TTCTGTTGGATCCCATTTCTGA 57.344 40.909 9.90 2.32 31.53 3.27
5949 6601 1.209504 GGACGATTCTGTTGGATCCCA 59.790 52.381 9.90 0.00 0.00 4.37
5967 6619 1.616628 GAGGAAGAAGGGCCTGGGA 60.617 63.158 6.92 0.00 33.84 4.37
5988 6640 1.078214 GCCATGGCAGCTGTACAGA 60.078 57.895 32.08 5.29 41.49 3.41
6022 6674 9.240159 CGTTTGTATGGCTTTTTAAGTAGTTTT 57.760 29.630 0.00 0.00 0.00 2.43
6032 6684 5.048294 CCTTCTACCGTTTGTATGGCTTTTT 60.048 40.000 0.00 0.00 33.37 1.94
6035 6687 3.606687 CCTTCTACCGTTTGTATGGCTT 58.393 45.455 0.00 0.00 33.37 4.35
6044 6696 1.961133 TGGATCCCCTTCTACCGTTT 58.039 50.000 9.90 0.00 0.00 3.60
6047 6699 1.475213 GCTTTGGATCCCCTTCTACCG 60.475 57.143 9.90 0.00 0.00 4.02
6065 6717 3.710722 CTGGCGTGGAGAAGGGCT 61.711 66.667 0.00 0.00 39.79 5.19
6115 6767 0.253327 GAGGGGAGTTACTTGCCTGG 59.747 60.000 0.00 0.00 0.00 4.45
6162 6817 1.920351 TCCATGGAGAAGGGGGTTTAC 59.080 52.381 11.44 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.