Multiple sequence alignment - TraesCS4D01G260400

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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 TraesCS4D01G260400 chr4D 100.000 4241 0 0 1 4241 429486393 429482153 0.000000e+00 7832.0
1 TraesCS4D01G260400 chr4A 91.917 1633 77 23 1705 3319 37045153 37046748 0.000000e+00 2233.0
2 TraesCS4D01G260400 chr4A 88.873 1393 99 26 223 1583 37043560 37044928 0.000000e+00 1663.0
3 TraesCS4D01G260400 chr4A 90.835 491 17 10 3728 4217 37046974 37047437 2.150000e-177 632.0
4 TraesCS4D01G260400 chr4A 89.474 133 9 5 3624 3752 617362938 617363069 3.390000e-36 163.0
5 TraesCS4D01G260400 chr4A 81.308 214 13 13 3431 3626 37046771 37046975 9.500000e-32 148.0
6 TraesCS4D01G260400 chr4A 96.296 54 2 0 1653 1706 37045075 37045128 5.840000e-14 89.8
7 TraesCS4D01G260400 chr4B 93.380 1420 64 19 1809 3209 527298430 527297022 0.000000e+00 2074.0
8 TraesCS4D01G260400 chr4B 88.252 1711 126 40 1 1651 527300306 527298611 0.000000e+00 1977.0
9 TraesCS4D01G260400 chr4B 93.023 430 21 6 3814 4241 527296701 527296279 1.680000e-173 619.0
10 TraesCS4D01G260400 chr4B 89.697 165 9 6 3466 3623 527296918 527296755 2.000000e-48 204.0
11 TraesCS4D01G260400 chr7A 94.643 112 4 2 3625 3734 33366009 33365898 5.640000e-39 172.0
12 TraesCS4D01G260400 chr7A 93.103 116 5 3 3620 3733 560407161 560407047 2.620000e-37 167.0
13 TraesCS4D01G260400 chr2A 93.966 116 4 3 3620 3733 394582835 394582949 5.640000e-39 172.0
14 TraesCS4D01G260400 chr1A 93.966 116 4 3 3620 3733 134973485 134973599 5.640000e-39 172.0
15 TraesCS4D01G260400 chr3D 93.913 115 4 3 3623 3734 230765643 230765757 2.030000e-38 171.0
16 TraesCS4D01G260400 chr5A 93.103 116 5 3 3620 3733 127831750 127831864 2.620000e-37 167.0
17 TraesCS4D01G260400 chr1D 93.103 116 4 3 3624 3737 11489779 11489666 2.620000e-37 167.0
18 TraesCS4D01G260400 chr2B 89.394 132 10 3 3619 3748 123063304 123063433 3.390000e-36 163.0
19 TraesCS4D01G260400 chr5B 86.667 75 7 3 632 705 599691199 599691271 3.520000e-11 80.5
20 TraesCS4D01G260400 chr5D 84.000 75 9 3 632 705 487302130 487302202 7.610000e-08 69.4
21 TraesCS4D01G260400 chr1B 100.000 29 0 0 3936 3964 258502307 258502335 2.000000e-03 54.7


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 TraesCS4D01G260400 chr4D 429482153 429486393 4240 True 7832.00 7832 100.0000 1 4241 1 chr4D.!!$R1 4240
1 TraesCS4D01G260400 chr4A 37043560 37047437 3877 False 953.16 2233 89.8458 223 4217 5 chr4A.!!$F2 3994
2 TraesCS4D01G260400 chr4B 527296279 527300306 4027 True 1218.50 2074 91.0880 1 4241 4 chr4B.!!$R1 4240

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
439 462 0.248539 GGTACATGAGAGGTCGCGAC 60.249 60.0 30.67 30.67 0.0 5.19 F
1123 1178 0.178843 AGGGGAGGAAGGGTAGCAAA 60.179 55.0 0.00 0.00 0.0 3.68 F
1405 1460 0.098025 CGTGCGGTGTTTGTCACTTT 59.902 50.0 0.00 0.00 45.5 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1405 1460 0.620556 GGGACAGAAGGCATCAAGGA 59.379 55.0 0.0 0.0 0.0 3.36 R
2727 2907 0.389948 CCTCCTTGTAGTCACCGTGC 60.390 60.0 0.0 0.0 0.0 5.34 R
3269 3452 0.106719 TCGATCCATGCCCTTTTCCC 60.107 55.0 0.0 0.0 0.0 3.97 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
25 26 4.573607 ACTAGAAAAACAAAGTCACGACCC 59.426 41.667 0.00 0.00 0.00 4.46
29 30 5.768164 AGAAAAACAAAGTCACGACCCATAT 59.232 36.000 0.00 0.00 0.00 1.78
55 56 5.366482 ACAATGCACATATACCCACACTA 57.634 39.130 0.00 0.00 0.00 2.74
75 76 3.274196 CGCATACACGCAAGACAAC 57.726 52.632 0.00 0.00 43.62 3.32
102 103 0.529833 CAACCACCAGCACAACACAA 59.470 50.000 0.00 0.00 0.00 3.33
123 124 3.643159 AAAAATGGCCTGAAACGACTC 57.357 42.857 3.32 0.00 0.00 3.36
124 125 2.270352 AAATGGCCTGAAACGACTCA 57.730 45.000 3.32 0.00 0.00 3.41
131 146 1.581934 CTGAAACGACTCAAGGCACA 58.418 50.000 0.00 0.00 0.00 4.57
174 189 0.734889 GCACGCATCTTACATGCCTT 59.265 50.000 0.00 0.00 41.71 4.35
177 192 3.364366 GCACGCATCTTACATGCCTTATC 60.364 47.826 0.00 0.00 41.71 1.75
179 194 3.059884 CGCATCTTACATGCCTTATCGT 58.940 45.455 0.00 0.00 41.71 3.73
186 201 1.277842 ACATGCCTTATCGTGTGGTGA 59.722 47.619 0.00 0.00 35.10 4.02
198 213 3.064682 TCGTGTGGTGAACAACTTTGATG 59.935 43.478 0.00 0.00 41.57 3.07
199 214 3.115554 GTGTGGTGAACAACTTTGATGC 58.884 45.455 0.00 0.00 41.57 3.91
200 215 2.100584 TGTGGTGAACAACTTTGATGCC 59.899 45.455 0.00 0.00 35.24 4.40
207 222 4.826733 TGAACAACTTTGATGCCACATAGT 59.173 37.500 0.00 0.00 34.58 2.12
437 460 1.298413 CGGTACATGAGAGGTCGCG 60.298 63.158 0.00 0.00 0.00 5.87
438 461 1.712018 CGGTACATGAGAGGTCGCGA 61.712 60.000 3.71 3.71 0.00 5.87
439 462 0.248539 GGTACATGAGAGGTCGCGAC 60.249 60.000 30.67 30.67 0.00 5.19
440 463 0.450583 GTACATGAGAGGTCGCGACA 59.549 55.000 37.26 19.58 0.00 4.35
452 479 2.856557 GGTCGCGACACTCCTATAAAAC 59.143 50.000 37.26 13.91 0.00 2.43
523 554 2.818751 AACACAACAACAAGGGGAGA 57.181 45.000 0.00 0.00 0.00 3.71
541 572 3.181510 GGAGAAACACACGCAATCCATAC 60.182 47.826 0.00 0.00 0.00 2.39
552 583 3.584834 GCAATCCATACAACCCACAAAC 58.415 45.455 0.00 0.00 0.00 2.93
651 682 5.178623 CAGAGACAAACCTTTTGCACGTATA 59.821 40.000 0.00 0.00 0.00 1.47
676 707 3.003275 ACAACAACTAATTGCGTGGTGAG 59.997 43.478 8.56 0.93 39.66 3.51
776 808 8.726988 TGTATTTATTTTCGTCTCTTCCCTTTG 58.273 33.333 0.00 0.00 0.00 2.77
778 810 6.554334 TTATTTTCGTCTCTTCCCTTTGTG 57.446 37.500 0.00 0.00 0.00 3.33
780 812 2.526304 TCGTCTCTTCCCTTTGTGTG 57.474 50.000 0.00 0.00 0.00 3.82
781 813 1.760613 TCGTCTCTTCCCTTTGTGTGT 59.239 47.619 0.00 0.00 0.00 3.72
847 900 2.701163 CTATTGGGCCGAGCGGAGTC 62.701 65.000 13.94 1.59 37.50 3.36
867 920 3.679980 GTCAGAAGCTTCAACGCAATCTA 59.320 43.478 27.57 0.00 30.45 1.98
883 936 1.218316 CTACCCGAAGAGCCCACAC 59.782 63.158 0.00 0.00 0.00 3.82
957 1011 2.194201 TGGAATGGAAACCCTCGAAC 57.806 50.000 0.00 0.00 0.00 3.95
972 1026 4.639310 CCCTCGAACCGCACTATATATACT 59.361 45.833 0.00 0.00 0.00 2.12
973 1027 5.220815 CCCTCGAACCGCACTATATATACTC 60.221 48.000 0.00 0.00 0.00 2.59
974 1028 5.220815 CCTCGAACCGCACTATATATACTCC 60.221 48.000 0.00 0.00 0.00 3.85
981 1035 3.890147 GCACTATATATACTCCCCCTCGG 59.110 52.174 0.00 0.00 0.00 4.63
997 1051 1.376812 CGGCTGTGTAGGGTTTCCC 60.377 63.158 0.00 0.00 45.90 3.97
1123 1178 0.178843 AGGGGAGGAAGGGTAGCAAA 60.179 55.000 0.00 0.00 0.00 3.68
1177 1232 1.442526 CCCTTGCAGCATCGTGATCC 61.443 60.000 0.00 0.00 0.00 3.36
1201 1256 5.187576 CAGGATCTGTTTCTTCTCCTCTTCT 59.812 44.000 0.00 0.00 34.09 2.85
1210 1265 6.835819 TTCTTCTCCTCTTCTTTCGTCATA 57.164 37.500 0.00 0.00 0.00 2.15
1219 1274 5.664457 TCTTCTTTCGTCATATGCTGATGT 58.336 37.500 0.00 0.00 41.03 3.06
1243 1298 0.468226 TCTTGCCTGGTTTCTCGTGT 59.532 50.000 0.00 0.00 0.00 4.49
1246 1301 1.305201 TGCCTGGTTTCTCGTGTTTC 58.695 50.000 0.00 0.00 0.00 2.78
1372 1427 0.249911 CCAAGGTATGCTCTACCCGC 60.250 60.000 11.14 0.00 38.33 6.13
1384 1439 2.257409 CTACCCGCCCTTGCATCTGT 62.257 60.000 0.00 0.00 37.32 3.41
1405 1460 0.098025 CGTGCGGTGTTTGTCACTTT 59.902 50.000 0.00 0.00 45.50 2.66
1407 1462 0.736053 TGCGGTGTTTGTCACTTTCC 59.264 50.000 0.00 0.00 45.50 3.13
1414 1469 4.044426 GTGTTTGTCACTTTCCTTGATGC 58.956 43.478 0.00 0.00 43.13 3.91
1426 1481 1.272092 CCTTGATGCCTTCTGTCCCAA 60.272 52.381 0.00 0.00 0.00 4.12
1427 1482 1.815003 CTTGATGCCTTCTGTCCCAAC 59.185 52.381 0.00 0.00 0.00 3.77
1454 1509 2.622436 CTGTTTAGTAGTCTGCCTGCC 58.378 52.381 0.00 0.00 0.00 4.85
1469 1526 0.249447 CTGCCCTCATACGCGATTGA 60.249 55.000 15.93 14.30 0.00 2.57
1517 1574 5.782893 AACGGATTCAACCATTTTCTCAA 57.217 34.783 0.00 0.00 0.00 3.02
1539 1596 2.100749 AGGTTGCCTTGTTGTGTTAAGC 59.899 45.455 0.00 0.00 0.00 3.09
1544 1601 1.398595 CTTGTTGTGTTAAGCGCTGC 58.601 50.000 12.58 5.16 0.00 5.25
1563 1620 1.950909 GCAGGACGTGATAGACTAGCT 59.049 52.381 0.00 0.00 0.00 3.32
1583 1640 5.303971 AGCTCTAGAATGCAATCGCTATTT 58.696 37.500 6.73 0.00 39.64 1.40
1584 1641 6.459066 AGCTCTAGAATGCAATCGCTATTTA 58.541 36.000 6.73 0.00 39.64 1.40
1640 1727 2.700371 TGTCTCACCAATGTCTCAGTGT 59.300 45.455 0.00 0.00 0.00 3.55
1653 1740 6.358118 TGTCTCAGTGTTGTAATTTGTGAC 57.642 37.500 0.00 0.00 34.57 3.67
1654 1741 5.877564 TGTCTCAGTGTTGTAATTTGTGACA 59.122 36.000 5.33 5.33 38.90 3.58
1655 1742 6.372937 TGTCTCAGTGTTGTAATTTGTGACAA 59.627 34.615 0.00 0.00 38.53 3.18
1743 1906 3.624410 AGTCGTTTGTGTTTGGTCTAACC 59.376 43.478 0.00 0.00 39.22 2.85
1749 1912 3.404899 TGTGTTTGGTCTAACCGATTCC 58.595 45.455 0.00 0.00 42.58 3.01
1753 1916 3.887621 TTGGTCTAACCGATTCCTCTG 57.112 47.619 0.00 0.00 42.58 3.35
1771 1934 3.154710 TCTGACTGTGTTCCTATGTCGT 58.845 45.455 0.00 0.00 0.00 4.34
1782 1945 4.830826 TCCTATGTCGTATGTGTAGCAG 57.169 45.455 0.00 0.00 0.00 4.24
1784 1947 5.370679 TCCTATGTCGTATGTGTAGCAGTA 58.629 41.667 0.00 0.00 0.00 2.74
1786 1949 4.569761 ATGTCGTATGTGTAGCAGTAGG 57.430 45.455 0.00 0.00 0.00 3.18
1800 1963 2.949451 AGTAGGCACACTGAATCTCG 57.051 50.000 0.00 0.00 0.00 4.04
1804 1968 2.851195 AGGCACACTGAATCTCGTTTT 58.149 42.857 0.00 0.00 0.00 2.43
1855 2019 8.334263 AGGAATTTGTTCAATGTTTGTTTGTT 57.666 26.923 0.00 0.00 0.00 2.83
1856 2020 8.235905 AGGAATTTGTTCAATGTTTGTTTGTTG 58.764 29.630 0.00 0.00 0.00 3.33
1857 2021 8.020244 GGAATTTGTTCAATGTTTGTTTGTTGT 58.980 29.630 0.00 0.00 0.00 3.32
1858 2022 9.392021 GAATTTGTTCAATGTTTGTTTGTTGTT 57.608 25.926 0.00 0.00 0.00 2.83
1862 2026 8.365399 TGTTCAATGTTTGTTTGTTGTTGTAA 57.635 26.923 0.00 0.00 0.00 2.41
1864 2028 9.312146 GTTCAATGTTTGTTTGTTGTTGTAAAG 57.688 29.630 0.00 0.00 0.00 1.85
1866 2030 9.046296 TCAATGTTTGTTTGTTGTTGTAAAGTT 57.954 25.926 0.00 0.00 0.00 2.66
1867 2031 9.100895 CAATGTTTGTTTGTTGTTGTAAAGTTG 57.899 29.630 0.00 0.00 0.00 3.16
1870 2034 7.707035 TGTTTGTTTGTTGTTGTAAAGTTGACT 59.293 29.630 0.00 0.00 0.00 3.41
1880 2044 9.767228 TTGTTGTAAAGTTGACTGTATTAGCTA 57.233 29.630 0.00 0.00 0.00 3.32
1889 2053 5.410924 TGACTGTATTAGCTAACTGCACAG 58.589 41.667 24.04 24.04 43.39 3.66
2058 2222 6.478512 AACTTCTGGGTAATGATCTCTCTC 57.521 41.667 0.00 0.00 0.00 3.20
2075 2239 1.277842 TCTCGCATTGCCTGAAACCTA 59.722 47.619 2.41 0.00 0.00 3.08
2081 2245 3.928375 GCATTGCCTGAAACCTAATGTTG 59.072 43.478 0.00 0.00 37.23 3.33
2249 2414 0.950836 TGTTCACCATTGGCTTCACG 59.049 50.000 1.54 0.00 0.00 4.35
2348 2514 8.170730 ACCTTCCTCCTTTTGTATCTTTGTATT 58.829 33.333 0.00 0.00 0.00 1.89
2591 2757 1.156095 CCTGAAGGCCCCCAAGTTT 59.844 57.895 0.00 0.00 0.00 2.66
2664 2831 6.212888 ACTGAAAATATTTTAGCTGGGCAG 57.787 37.500 13.34 15.09 0.00 4.85
2828 3008 1.609061 GGTTGCTGCTGCTGAGTAGAA 60.609 52.381 17.00 0.00 40.48 2.10
2962 3142 0.905357 ATTCCTAGCCAGCGTTCAGT 59.095 50.000 0.00 0.00 0.00 3.41
3008 3189 5.779241 TTCTGGATGGAGGTTATGAGTTT 57.221 39.130 0.00 0.00 0.00 2.66
3043 3225 2.151202 AGTTTATTCCTGCCGTGTGTG 58.849 47.619 0.00 0.00 0.00 3.82
3058 3240 5.332205 GCCGTGTGTGTTTTATGTTTGAATG 60.332 40.000 0.00 0.00 0.00 2.67
3085 3267 6.438763 ACTTATGCTCTGTTGTTTTGTTAGC 58.561 36.000 0.00 0.00 0.00 3.09
3168 3350 1.691434 GCTACAGCTTCTCCTAGCCAT 59.309 52.381 0.00 0.00 42.20 4.40
3171 3353 1.484240 ACAGCTTCTCCTAGCCATGAC 59.516 52.381 0.00 0.00 42.20 3.06
3172 3354 1.761784 CAGCTTCTCCTAGCCATGACT 59.238 52.381 0.00 0.00 42.20 3.41
3184 3367 0.176680 CCATGACTCCCTCCGTCTTG 59.823 60.000 0.00 0.00 36.72 3.02
3209 3392 4.778534 TTACTTGTAGAAGTGACGGGAG 57.221 45.455 15.18 0.00 42.66 4.30
3210 3393 1.893801 ACTTGTAGAAGTGACGGGAGG 59.106 52.381 4.15 0.00 41.12 4.30
3215 3398 3.003763 AAGTGACGGGAGGGGAGC 61.004 66.667 0.00 0.00 0.00 4.70
3253 3436 2.689983 CAATGTGCTCCCCCAATTAGTC 59.310 50.000 0.00 0.00 0.00 2.59
3277 3460 3.566351 ACAGAAAGTGAAGGGGAAAAGG 58.434 45.455 0.00 0.00 0.00 3.11
3278 3461 2.893489 CAGAAAGTGAAGGGGAAAAGGG 59.107 50.000 0.00 0.00 0.00 3.95
3279 3462 1.618837 GAAAGTGAAGGGGAAAAGGGC 59.381 52.381 0.00 0.00 0.00 5.19
3288 3474 0.106719 GGGAAAAGGGCATGGATCGA 60.107 55.000 0.00 0.00 0.00 3.59
3320 3506 0.599204 GGCGTTCGGTCTTTGAGTCA 60.599 55.000 0.00 0.00 0.00 3.41
3321 3507 1.214367 GCGTTCGGTCTTTGAGTCAA 58.786 50.000 0.08 0.08 0.00 3.18
3322 3508 1.070776 GCGTTCGGTCTTTGAGTCAAC 60.071 52.381 4.68 0.00 0.00 3.18
3323 3509 2.198406 CGTTCGGTCTTTGAGTCAACA 58.802 47.619 4.68 0.00 0.00 3.33
3324 3510 2.034001 CGTTCGGTCTTTGAGTCAACAC 60.034 50.000 4.68 5.37 0.00 3.32
3325 3511 3.195661 GTTCGGTCTTTGAGTCAACACT 58.804 45.455 4.68 0.00 34.57 3.55
3344 3530 2.351726 ACTCGTATTTTCATGCGGCTTC 59.648 45.455 0.00 0.00 38.88 3.86
3346 3532 1.400142 CGTATTTTCATGCGGCTTCCA 59.600 47.619 0.00 0.00 35.06 3.53
3347 3533 2.033299 CGTATTTTCATGCGGCTTCCAT 59.967 45.455 0.00 0.00 35.06 3.41
3348 3534 3.249799 CGTATTTTCATGCGGCTTCCATA 59.750 43.478 0.00 0.00 35.06 2.74
3349 3535 4.083324 CGTATTTTCATGCGGCTTCCATAT 60.083 41.667 0.00 0.00 35.06 1.78
3353 3539 4.829064 TTCATGCGGCTTCCATATTTAC 57.171 40.909 0.00 0.00 0.00 2.01
3354 3540 4.085357 TCATGCGGCTTCCATATTTACT 57.915 40.909 0.00 0.00 0.00 2.24
3355 3541 4.065088 TCATGCGGCTTCCATATTTACTC 58.935 43.478 0.00 0.00 0.00 2.59
3357 3543 2.159014 TGCGGCTTCCATATTTACTCGT 60.159 45.455 0.00 0.00 0.00 4.18
3358 3544 2.475487 GCGGCTTCCATATTTACTCGTC 59.525 50.000 0.00 0.00 0.00 4.20
3359 3545 3.713288 CGGCTTCCATATTTACTCGTCA 58.287 45.455 0.00 0.00 0.00 4.35
3360 3546 3.736252 CGGCTTCCATATTTACTCGTCAG 59.264 47.826 0.00 0.00 0.00 3.51
3361 3547 4.499188 CGGCTTCCATATTTACTCGTCAGA 60.499 45.833 0.00 0.00 0.00 3.27
3362 3548 5.357257 GGCTTCCATATTTACTCGTCAGAA 58.643 41.667 0.00 0.00 0.00 3.02
3363 3549 5.463724 GGCTTCCATATTTACTCGTCAGAAG 59.536 44.000 0.00 0.00 33.13 2.85
3364 3550 5.050702 GCTTCCATATTTACTCGTCAGAAGC 60.051 44.000 5.30 5.30 44.57 3.86
3365 3551 5.592104 TCCATATTTACTCGTCAGAAGCA 57.408 39.130 0.00 0.00 0.00 3.91
3366 3552 5.348986 TCCATATTTACTCGTCAGAAGCAC 58.651 41.667 0.00 0.00 0.00 4.40
3367 3553 4.508124 CCATATTTACTCGTCAGAAGCACC 59.492 45.833 0.00 0.00 0.00 5.01
3368 3554 3.678056 ATTTACTCGTCAGAAGCACCA 57.322 42.857 0.00 0.00 0.00 4.17
3379 3565 6.653320 TCGTCAGAAGCACCAAGTATTTATTT 59.347 34.615 0.00 0.00 0.00 1.40
3387 3573 7.891561 AGCACCAAGTATTTATTTACTGCAAA 58.108 30.769 0.00 0.00 32.78 3.68
3405 3591 8.712285 ACTGCAAAATTGGATAGAAATTGATG 57.288 30.769 0.00 0.00 0.00 3.07
3406 3592 8.316214 ACTGCAAAATTGGATAGAAATTGATGT 58.684 29.630 0.00 0.00 0.00 3.06
3407 3593 9.806203 CTGCAAAATTGGATAGAAATTGATGTA 57.194 29.630 0.00 0.00 0.00 2.29
3475 3661 8.391106 AGAAATTGATGTAGCGACAAGTAATTC 58.609 33.333 3.04 6.86 39.59 2.17
3477 3663 4.740268 TGATGTAGCGACAAGTAATTCGT 58.260 39.130 3.04 0.00 39.59 3.85
3512 3729 7.287810 AGTATTATATTGTGACAAGGGTTCCC 58.712 38.462 3.74 0.00 0.00 3.97
3524 3741 1.119684 GGGTTCCCAAACTGCTGTTT 58.880 50.000 15.19 15.19 46.20 2.83
3579 3813 5.927689 TGGTAAGCTGCAATGAAGAAAATTG 59.072 36.000 1.02 0.00 37.94 2.32
3617 3851 3.601443 ATGAAGTGGCACTACTGACTC 57.399 47.619 22.37 13.93 0.00 3.36
3621 3855 2.598565 AGTGGCACTACTGACTCAAGA 58.401 47.619 20.61 0.00 0.00 3.02
3624 3858 1.548269 GGCACTACTGACTCAAGAGCT 59.452 52.381 0.00 0.00 0.00 4.09
3625 3859 2.755655 GGCACTACTGACTCAAGAGCTA 59.244 50.000 0.00 0.00 0.00 3.32
3626 3860 3.428316 GGCACTACTGACTCAAGAGCTAC 60.428 52.174 0.00 0.00 0.00 3.58
3627 3861 3.442273 GCACTACTGACTCAAGAGCTACT 59.558 47.826 0.00 0.00 0.00 2.57
3628 3862 4.438200 GCACTACTGACTCAAGAGCTACTC 60.438 50.000 0.00 0.00 0.00 2.59
3629 3863 4.941263 CACTACTGACTCAAGAGCTACTCT 59.059 45.833 0.00 0.00 43.37 3.24
3630 3864 5.064707 CACTACTGACTCAAGAGCTACTCTC 59.935 48.000 0.00 0.00 40.28 3.20
3639 3873 0.658897 GAGCTACTCTCTCCGTTCGG 59.341 60.000 4.74 4.74 38.78 4.30
3640 3874 0.252479 AGCTACTCTCTCCGTTCGGA 59.748 55.000 13.34 13.34 0.00 4.55
3641 3875 1.093159 GCTACTCTCTCCGTTCGGAA 58.907 55.000 14.79 5.84 33.41 4.30
3642 3876 1.677052 GCTACTCTCTCCGTTCGGAAT 59.323 52.381 14.79 2.09 33.41 3.01
3643 3877 2.099427 GCTACTCTCTCCGTTCGGAATT 59.901 50.000 14.79 0.00 33.41 2.17
3644 3878 3.314635 GCTACTCTCTCCGTTCGGAATTA 59.685 47.826 14.79 3.46 33.41 1.40
3645 3879 3.779271 ACTCTCTCCGTTCGGAATTAC 57.221 47.619 14.79 0.00 33.41 1.89
3646 3880 3.354467 ACTCTCTCCGTTCGGAATTACT 58.646 45.455 14.79 0.00 33.41 2.24
3647 3881 3.762823 ACTCTCTCCGTTCGGAATTACTT 59.237 43.478 14.79 0.00 33.41 2.24
3648 3882 4.106029 TCTCTCCGTTCGGAATTACTTG 57.894 45.455 14.79 2.23 33.41 3.16
3649 3883 3.508793 TCTCTCCGTTCGGAATTACTTGT 59.491 43.478 14.79 0.00 33.41 3.16
3650 3884 3.841643 TCTCCGTTCGGAATTACTTGTC 58.158 45.455 14.79 0.00 33.41 3.18
3651 3885 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
3652 3886 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
3653 3887 1.266211 CGTTCGGAATTACTTGTCGCG 60.266 52.381 0.00 0.00 0.00 5.87
3654 3888 1.060122 GTTCGGAATTACTTGTCGCGG 59.940 52.381 6.13 0.00 0.00 6.46
3655 3889 0.527113 TCGGAATTACTTGTCGCGGA 59.473 50.000 6.13 0.00 0.00 5.54
3656 3890 1.067706 TCGGAATTACTTGTCGCGGAA 60.068 47.619 6.13 0.00 0.00 4.30
3657 3891 1.727880 CGGAATTACTTGTCGCGGAAA 59.272 47.619 6.13 0.00 0.00 3.13
3658 3892 2.350498 CGGAATTACTTGTCGCGGAAAT 59.650 45.455 6.13 0.00 0.00 2.17
3659 3893 3.680789 GGAATTACTTGTCGCGGAAATG 58.319 45.455 6.13 0.00 0.00 2.32
3660 3894 3.486875 GGAATTACTTGTCGCGGAAATGG 60.487 47.826 6.13 0.00 0.00 3.16
3661 3895 2.459060 TTACTTGTCGCGGAAATGGA 57.541 45.000 6.13 0.00 0.00 3.41
3662 3896 2.684001 TACTTGTCGCGGAAATGGAT 57.316 45.000 6.13 0.00 0.00 3.41
3663 3897 1.086696 ACTTGTCGCGGAAATGGATG 58.913 50.000 6.13 0.00 0.00 3.51
3664 3898 1.086696 CTTGTCGCGGAAATGGATGT 58.913 50.000 6.13 0.00 0.00 3.06
3665 3899 2.276201 CTTGTCGCGGAAATGGATGTA 58.724 47.619 6.13 0.00 0.00 2.29
3666 3900 2.613026 TGTCGCGGAAATGGATGTAT 57.387 45.000 6.13 0.00 0.00 2.29
3667 3901 2.479837 TGTCGCGGAAATGGATGTATC 58.520 47.619 6.13 0.00 0.00 2.24
3668 3902 2.159028 TGTCGCGGAAATGGATGTATCA 60.159 45.455 6.13 0.00 0.00 2.15
3669 3903 2.869801 GTCGCGGAAATGGATGTATCAA 59.130 45.455 6.13 0.00 0.00 2.57
3670 3904 2.869801 TCGCGGAAATGGATGTATCAAC 59.130 45.455 6.13 0.00 0.00 3.18
3671 3905 2.611751 CGCGGAAATGGATGTATCAACA 59.388 45.455 0.00 0.00 40.69 3.33
3673 3907 4.450757 CGCGGAAATGGATGTATCAACATA 59.549 41.667 0.00 0.00 46.49 2.29
3674 3908 5.122239 CGCGGAAATGGATGTATCAACATAT 59.878 40.000 0.00 0.00 46.49 1.78
3675 3909 6.348458 CGCGGAAATGGATGTATCAACATATT 60.348 38.462 0.00 0.00 46.49 1.28
3676 3910 7.370383 GCGGAAATGGATGTATCAACATATTT 58.630 34.615 0.00 0.00 46.49 1.40
3677 3911 7.867403 GCGGAAATGGATGTATCAACATATTTT 59.133 33.333 0.00 0.00 46.49 1.82
3701 3935 9.893634 TTTAGTTTTAGATACATCCATTTCCGA 57.106 29.630 0.00 0.00 0.00 4.55
3702 3936 9.542462 TTAGTTTTAGATACATCCATTTCCGAG 57.458 33.333 0.00 0.00 0.00 4.63
3703 3937 7.792032 AGTTTTAGATACATCCATTTCCGAGA 58.208 34.615 0.00 0.00 0.00 4.04
3704 3938 7.711339 AGTTTTAGATACATCCATTTCCGAGAC 59.289 37.037 0.00 0.00 0.00 3.36
3705 3939 6.724893 TTAGATACATCCATTTCCGAGACA 57.275 37.500 0.00 0.00 0.00 3.41
3706 3940 5.614324 AGATACATCCATTTCCGAGACAA 57.386 39.130 0.00 0.00 0.00 3.18
3707 3941 5.605534 AGATACATCCATTTCCGAGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
3708 3942 3.703001 ACATCCATTTCCGAGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
3709 3943 4.819105 ACATCCATTTCCGAGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
3710 3944 5.160607 ACATCCATTTCCGAGACAAGTAA 57.839 39.130 0.00 0.00 0.00 2.24
3711 3945 5.745227 ACATCCATTTCCGAGACAAGTAAT 58.255 37.500 0.00 0.00 0.00 1.89
3712 3946 6.180472 ACATCCATTTCCGAGACAAGTAATT 58.820 36.000 0.00 0.00 0.00 1.40
3713 3947 6.316390 ACATCCATTTCCGAGACAAGTAATTC 59.684 38.462 0.00 0.00 0.00 2.17
3714 3948 5.800296 TCCATTTCCGAGACAAGTAATTCA 58.200 37.500 0.00 0.00 0.00 2.57
3715 3949 5.874810 TCCATTTCCGAGACAAGTAATTCAG 59.125 40.000 0.00 0.00 0.00 3.02
3716 3950 5.874810 CCATTTCCGAGACAAGTAATTCAGA 59.125 40.000 0.00 0.00 0.00 3.27
3717 3951 6.371548 CCATTTCCGAGACAAGTAATTCAGAA 59.628 38.462 0.00 0.00 0.00 3.02
3718 3952 6.780706 TTTCCGAGACAAGTAATTCAGAAC 57.219 37.500 0.00 0.00 0.00 3.01
3719 3953 4.482386 TCCGAGACAAGTAATTCAGAACG 58.518 43.478 0.00 0.00 0.00 3.95
3720 3954 3.612860 CCGAGACAAGTAATTCAGAACGG 59.387 47.826 0.00 0.00 0.00 4.44
3721 3955 4.482386 CGAGACAAGTAATTCAGAACGGA 58.518 43.478 0.00 0.00 0.00 4.69
3722 3956 4.559251 CGAGACAAGTAATTCAGAACGGAG 59.441 45.833 0.00 0.00 0.00 4.63
3723 3957 4.822026 AGACAAGTAATTCAGAACGGAGG 58.178 43.478 0.00 0.00 0.00 4.30
3724 3958 3.933332 GACAAGTAATTCAGAACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
3725 3959 3.581332 ACAAGTAATTCAGAACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
3726 3960 4.184629 CAAGTAATTCAGAACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
3746 3980 7.079048 AGGGAGTAGATATCTGTGGAAATCTT 58.921 38.462 15.79 0.00 31.38 2.40
3782 4016 3.009723 TGAAGCACTTTATGTGGCTAGC 58.990 45.455 6.04 6.04 46.27 3.42
3845 4079 4.649674 ACGTCACTGGGATACTGATTGTAT 59.350 41.667 0.00 0.00 43.94 2.29
3894 4129 2.223829 ACACTCTCTTCACTTGTCCACG 60.224 50.000 0.00 0.00 0.00 4.94
3899 4134 3.485346 TTCACTTGTCCACGGCCCC 62.485 63.158 0.00 0.00 0.00 5.80
3900 4135 4.263572 CACTTGTCCACGGCCCCA 62.264 66.667 0.00 0.00 0.00 4.96
3901 4136 3.953775 ACTTGTCCACGGCCCCAG 61.954 66.667 0.00 0.00 0.00 4.45
3932 4167 4.217118 GGTGCATATCCTTTGCTTGGATAG 59.783 45.833 14.68 9.91 46.08 2.08
3966 4201 6.098679 CCAATCTATCATGATCGTCTTCCTC 58.901 44.000 12.53 0.00 0.00 3.71
4034 4270 1.615883 TCACTTCACAGAGCAGGTCTC 59.384 52.381 0.00 0.00 42.21 3.36
4092 4328 7.495606 ACCAATGAAATGTTCCTCAAAGAAAAC 59.504 33.333 0.00 0.00 0.00 2.43
4217 4453 8.347004 TCTTTATGGATGCAGTGATGTAAAAA 57.653 30.769 0.00 0.00 0.00 1.94
4218 4454 8.461222 TCTTTATGGATGCAGTGATGTAAAAAG 58.539 33.333 0.00 0.00 0.00 2.27
4223 4459 7.495901 TGGATGCAGTGATGTAAAAAGAAAAA 58.504 30.769 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.573201 TGGGTCGTGACTTTGTTTTTCTAG 59.427 41.667 0.00 0.00 0.00 2.43
22 23 8.802267 GGTATATGTGCATTGTTTTATATGGGT 58.198 33.333 0.00 0.00 0.00 4.51
25 26 9.624697 GTGGGTATATGTGCATTGTTTTATATG 57.375 33.333 0.00 0.00 0.00 1.78
29 30 6.661377 AGTGTGGGTATATGTGCATTGTTTTA 59.339 34.615 0.00 0.00 0.00 1.52
83 84 0.529833 TTGTGTTGTGCTGGTGGTTG 59.470 50.000 0.00 0.00 0.00 3.77
84 85 1.261480 TTTGTGTTGTGCTGGTGGTT 58.739 45.000 0.00 0.00 0.00 3.67
85 86 1.261480 TTTTGTGTTGTGCTGGTGGT 58.739 45.000 0.00 0.00 0.00 4.16
120 121 1.097547 GTGTGCACTGTGCCTTGAGT 61.098 55.000 28.17 0.00 44.23 3.41
121 122 1.096967 TGTGTGCACTGTGCCTTGAG 61.097 55.000 28.17 0.00 44.23 3.02
122 123 0.679321 TTGTGTGCACTGTGCCTTGA 60.679 50.000 28.17 8.38 44.23 3.02
123 124 0.248743 CTTGTGTGCACTGTGCCTTG 60.249 55.000 28.17 9.96 44.23 3.61
124 125 2.008268 GCTTGTGTGCACTGTGCCTT 62.008 55.000 28.17 0.00 44.23 4.35
131 146 1.462616 TTGTCTTGCTTGTGTGCACT 58.537 45.000 19.41 0.00 43.20 4.40
159 174 3.809832 ACACGATAAGGCATGTAAGATGC 59.190 43.478 0.16 0.16 43.85 3.91
160 175 4.212004 CCACACGATAAGGCATGTAAGATG 59.788 45.833 0.00 0.00 0.00 2.90
174 189 4.443621 TCAAAGTTGTTCACCACACGATA 58.556 39.130 0.00 0.00 33.98 2.92
177 192 3.362295 CATCAAAGTTGTTCACCACACG 58.638 45.455 0.00 0.00 33.98 4.49
179 194 2.100584 GGCATCAAAGTTGTTCACCACA 59.899 45.455 0.00 0.00 0.00 4.17
186 201 5.789643 AACTATGTGGCATCAAAGTTGTT 57.210 34.783 0.00 0.00 0.00 2.83
390 413 4.441773 GGGCTAGAAGCTTCCAACTAGTAC 60.442 50.000 22.81 13.45 41.99 2.73
437 460 2.856557 GTCGGCGTTTTATAGGAGTGTC 59.143 50.000 6.85 0.00 0.00 3.67
438 461 2.494870 AGTCGGCGTTTTATAGGAGTGT 59.505 45.455 6.85 0.00 0.00 3.55
439 462 3.114065 GAGTCGGCGTTTTATAGGAGTG 58.886 50.000 6.85 0.00 0.00 3.51
440 463 3.022406 AGAGTCGGCGTTTTATAGGAGT 58.978 45.455 6.85 0.00 0.00 3.85
452 479 1.721926 GAAAGAACTGAAGAGTCGGCG 59.278 52.381 0.00 0.00 32.86 6.46
500 528 5.017490 TCTCCCCTTGTTGTTGTGTTTTTA 58.983 37.500 0.00 0.00 0.00 1.52
519 550 1.234821 TGGATTGCGTGTGTTTCTCC 58.765 50.000 0.00 0.00 0.00 3.71
523 554 3.305064 GGTTGTATGGATTGCGTGTGTTT 60.305 43.478 0.00 0.00 0.00 2.83
651 682 5.239744 TCACCACGCAATTAGTTGTTGTTAT 59.760 36.000 0.00 0.00 37.65 1.89
676 707 9.937175 GAATTAAGTATTGCACATCTAAGTTCC 57.063 33.333 0.00 0.00 0.00 3.62
761 793 1.760613 ACACACAAAGGGAAGAGACGA 59.239 47.619 0.00 0.00 0.00 4.20
776 808 2.412937 GTTGCCTGCCACACACAC 59.587 61.111 0.00 0.00 0.00 3.82
778 810 1.954362 TTTGGTTGCCTGCCACACAC 61.954 55.000 0.00 0.00 35.46 3.82
780 812 0.530431 CTTTTGGTTGCCTGCCACAC 60.530 55.000 0.00 0.00 35.46 3.82
781 813 0.685785 TCTTTTGGTTGCCTGCCACA 60.686 50.000 0.00 0.00 35.46 4.17
847 900 3.181516 GGTAGATTGCGTTGAAGCTTCTG 60.182 47.826 26.09 16.71 38.13 3.02
867 920 4.003788 CGTGTGGGCTCTTCGGGT 62.004 66.667 0.00 0.00 0.00 5.28
935 989 1.211949 TCGAGGGTTTCCATTCCATCC 59.788 52.381 0.00 0.00 31.83 3.51
957 1011 3.890147 GAGGGGGAGTATATATAGTGCGG 59.110 52.174 11.63 0.00 0.00 5.69
972 1026 2.363795 CTACACAGCCGAGGGGGA 60.364 66.667 0.00 0.00 38.47 4.81
973 1027 3.470888 CCTACACAGCCGAGGGGG 61.471 72.222 0.00 0.00 39.58 5.40
974 1028 3.470888 CCCTACACAGCCGAGGGG 61.471 72.222 0.00 0.00 45.53 4.79
1160 1215 0.656259 CTGGATCACGATGCTGCAAG 59.344 55.000 6.36 6.68 0.00 4.01
1177 1232 5.187576 AGAAGAGGAGAAGAAACAGATCCTG 59.812 44.000 0.00 0.00 40.48 3.86
1201 1256 3.872696 ACCACATCAGCATATGACGAAA 58.127 40.909 6.97 0.00 41.91 3.46
1210 1265 1.547372 GGCAAGAAACCACATCAGCAT 59.453 47.619 0.00 0.00 0.00 3.79
1219 1274 2.306847 GAGAAACCAGGCAAGAAACCA 58.693 47.619 0.00 0.00 0.00 3.67
1243 1298 1.805539 CGGATCGACGCTGCAGAAA 60.806 57.895 20.43 0.00 0.00 2.52
1246 1301 2.507102 AACGGATCGACGCTGCAG 60.507 61.111 10.11 10.11 37.37 4.41
1367 1422 3.650950 ACAGATGCAAGGGCGGGT 61.651 61.111 0.00 0.00 45.35 5.28
1384 1439 2.820037 TGACAAACACCGCACGCA 60.820 55.556 0.00 0.00 0.00 5.24
1405 1460 0.620556 GGGACAGAAGGCATCAAGGA 59.379 55.000 0.00 0.00 0.00 3.36
1407 1462 1.815003 GTTGGGACAGAAGGCATCAAG 59.185 52.381 0.00 0.00 42.39 3.02
1414 1469 2.093447 AGCTAATCGTTGGGACAGAAGG 60.093 50.000 0.00 0.00 42.39 3.46
1426 1481 5.341617 GCAGACTACTAAACAGCTAATCGT 58.658 41.667 0.00 0.00 0.00 3.73
1427 1482 4.740695 GGCAGACTACTAAACAGCTAATCG 59.259 45.833 0.00 0.00 0.00 3.34
1454 1509 3.567576 AGATCTCAATCGCGTATGAGG 57.432 47.619 29.56 18.16 42.62 3.86
1469 1526 8.441311 TCATGCCAATAGGACTAAATAGATCT 57.559 34.615 0.00 0.00 36.89 2.75
1517 1574 3.430236 GCTTAACACAACAAGGCAACCTT 60.430 43.478 0.00 0.00 45.88 3.50
1539 1596 0.867753 GTCTATCACGTCCTGCAGCG 60.868 60.000 8.66 10.37 0.00 5.18
1544 1601 3.472652 AGAGCTAGTCTATCACGTCCTG 58.527 50.000 0.00 0.00 31.71 3.86
1563 1620 7.433680 TCAGTAAATAGCGATTGCATTCTAGA 58.566 34.615 7.90 0.00 46.23 2.43
1583 1640 8.637281 TCGCGAACTAAAATCAATTATCAGTA 57.363 30.769 6.20 0.00 0.00 2.74
1584 1641 7.534085 TCGCGAACTAAAATCAATTATCAGT 57.466 32.000 6.20 0.00 0.00 3.41
1601 1687 6.677411 GTGAGACAAAATAGTAAATCGCGAAC 59.323 38.462 15.24 7.19 0.00 3.95
1606 1692 8.450964 ACATTGGTGAGACAAAATAGTAAATCG 58.549 33.333 0.00 0.00 33.48 3.34
1614 1700 6.427853 CACTGAGACATTGGTGAGACAAAATA 59.572 38.462 0.00 0.00 33.48 1.40
1743 1906 2.232452 AGGAACACAGTCAGAGGAATCG 59.768 50.000 0.00 0.00 0.00 3.34
1749 1912 3.191581 ACGACATAGGAACACAGTCAGAG 59.808 47.826 0.00 0.00 0.00 3.35
1753 1916 4.798907 CACATACGACATAGGAACACAGTC 59.201 45.833 0.00 0.00 0.00 3.51
1771 1934 3.096852 AGTGTGCCTACTGCTACACATA 58.903 45.455 16.34 0.00 45.91 2.29
1782 1945 2.656560 ACGAGATTCAGTGTGCCTAC 57.343 50.000 0.00 0.00 0.00 3.18
1784 1947 2.550830 AAACGAGATTCAGTGTGCCT 57.449 45.000 0.00 0.00 0.00 4.75
1786 1949 4.613031 GCTTAAAAACGAGATTCAGTGTGC 59.387 41.667 0.00 0.00 0.00 4.57
1799 1962 6.517914 TGTAAATGCAAAGGCTTAAAAACG 57.482 33.333 0.00 0.00 41.91 3.60
1800 1963 8.555361 TGAATGTAAATGCAAAGGCTTAAAAAC 58.445 29.630 0.00 0.00 41.91 2.43
1804 1968 8.845413 AAATGAATGTAAATGCAAAGGCTTAA 57.155 26.923 0.00 0.00 41.91 1.85
1836 2000 7.251704 ACAACAACAAACAAACATTGAACAA 57.748 28.000 0.00 0.00 0.00 2.83
1841 2005 9.100895 CAACTTTACAACAACAAACAAACATTG 57.899 29.630 0.00 0.00 0.00 2.82
1853 2017 8.557029 AGCTAATACAGTCAACTTTACAACAAC 58.443 33.333 0.00 0.00 0.00 3.32
1855 2019 9.767228 TTAGCTAATACAGTCAACTTTACAACA 57.233 29.630 0.86 0.00 0.00 3.33
1857 2021 9.991906 AGTTAGCTAATACAGTCAACTTTACAA 57.008 29.630 9.88 0.00 30.67 2.41
1858 2022 9.419297 CAGTTAGCTAATACAGTCAACTTTACA 57.581 33.333 9.88 0.00 31.77 2.41
1862 2026 6.369065 GTGCAGTTAGCTAATACAGTCAACTT 59.631 38.462 9.88 0.00 45.94 2.66
1864 2028 5.637810 TGTGCAGTTAGCTAATACAGTCAAC 59.362 40.000 9.88 0.00 45.94 3.18
1866 2030 5.047306 ACTGTGCAGTTAGCTAATACAGTCA 60.047 40.000 26.06 15.43 42.32 3.41
1867 2031 5.411781 ACTGTGCAGTTAGCTAATACAGTC 58.588 41.667 26.06 10.53 42.32 3.51
1889 2053 9.727627 CTGAGGCAATCTAAAATAAAGATGAAC 57.272 33.333 0.00 0.00 33.95 3.18
1895 2059 6.830838 ACCCTCTGAGGCAATCTAAAATAAAG 59.169 38.462 18.51 1.37 32.73 1.85
2058 2222 2.164219 ACATTAGGTTTCAGGCAATGCG 59.836 45.455 0.00 0.00 31.28 4.73
2075 2239 5.938438 AAGCAAAAACACAACACAACATT 57.062 30.435 0.00 0.00 0.00 2.71
2081 2245 5.312838 GTTAGCAAAGCAAAAACACAACAC 58.687 37.500 0.00 0.00 0.00 3.32
2235 2400 1.347707 TCTCTTCGTGAAGCCAATGGT 59.652 47.619 0.00 0.00 38.28 3.55
2249 2414 0.955919 CCTGGTTTGGGCGTCTCTTC 60.956 60.000 0.00 0.00 0.00 2.87
2348 2514 7.123098 AGCTCAATGATCACCAAAACATTATCA 59.877 33.333 0.00 0.00 32.75 2.15
2664 2831 6.619801 AGACTGGAGAACAACAATTAACAC 57.380 37.500 0.00 0.00 0.00 3.32
2727 2907 0.389948 CCTCCTTGTAGTCACCGTGC 60.390 60.000 0.00 0.00 0.00 5.34
2828 3008 5.355350 AGCAGCAAAATAGCGACTTCTATTT 59.645 36.000 0.00 3.66 45.87 1.40
3043 3225 9.423061 AGCATAAGTTCCATTCAAACATAAAAC 57.577 29.630 0.00 0.00 0.00 2.43
3058 3240 5.831997 ACAAAACAACAGAGCATAAGTTCC 58.168 37.500 0.00 0.00 0.00 3.62
3085 3267 7.730364 ACAAAAAGTTGGTACTGAGATACAG 57.270 36.000 0.00 0.00 44.20 2.74
3168 3350 1.463375 TCCAAGACGGAGGGAGTCA 59.537 57.895 0.00 0.00 39.64 3.41
3184 3367 4.868734 CCCGTCACTTCTACAAGTAATTCC 59.131 45.833 0.00 0.00 41.24 3.01
3209 3392 5.127031 TGCTAATTTTACTTTCATGCTCCCC 59.873 40.000 0.00 0.00 0.00 4.81
3210 3393 6.207691 TGCTAATTTTACTTTCATGCTCCC 57.792 37.500 0.00 0.00 0.00 4.30
3247 3430 3.997021 CCTTCACTTTCTGTGCGACTAAT 59.003 43.478 0.00 0.00 45.81 1.73
3253 3436 0.250295 TCCCCTTCACTTTCTGTGCG 60.250 55.000 0.00 0.00 45.81 5.34
3269 3452 0.106719 TCGATCCATGCCCTTTTCCC 60.107 55.000 0.00 0.00 0.00 3.97
3270 3453 1.762708 TTCGATCCATGCCCTTTTCC 58.237 50.000 0.00 0.00 0.00 3.13
3272 3455 2.493278 CTGTTTCGATCCATGCCCTTTT 59.507 45.455 0.00 0.00 0.00 2.27
3273 3456 2.094675 CTGTTTCGATCCATGCCCTTT 58.905 47.619 0.00 0.00 0.00 3.11
3274 3457 1.755179 CTGTTTCGATCCATGCCCTT 58.245 50.000 0.00 0.00 0.00 3.95
3276 3459 1.728490 GGCTGTTTCGATCCATGCCC 61.728 60.000 11.10 0.42 33.45 5.36
3277 3460 1.031571 TGGCTGTTTCGATCCATGCC 61.032 55.000 13.49 13.49 39.33 4.40
3278 3461 0.810648 TTGGCTGTTTCGATCCATGC 59.189 50.000 0.00 0.00 0.00 4.06
3279 3462 3.788333 AATTGGCTGTTTCGATCCATG 57.212 42.857 0.00 0.00 0.00 3.66
3320 3506 2.159572 GCCGCATGAAAATACGAGTGTT 60.160 45.455 0.00 0.00 0.00 3.32
3321 3507 1.396996 GCCGCATGAAAATACGAGTGT 59.603 47.619 0.00 0.00 0.00 3.55
3322 3508 1.665679 AGCCGCATGAAAATACGAGTG 59.334 47.619 0.00 0.00 0.00 3.51
3323 3509 2.024176 AGCCGCATGAAAATACGAGT 57.976 45.000 0.00 0.00 0.00 4.18
3324 3510 2.286418 GGAAGCCGCATGAAAATACGAG 60.286 50.000 0.00 0.00 0.00 4.18
3325 3511 1.668751 GGAAGCCGCATGAAAATACGA 59.331 47.619 0.00 0.00 0.00 3.43
3326 3512 1.400142 TGGAAGCCGCATGAAAATACG 59.600 47.619 0.00 0.00 0.00 3.06
3327 3513 3.715628 ATGGAAGCCGCATGAAAATAC 57.284 42.857 0.00 0.00 0.00 1.89
3328 3514 6.403866 AAATATGGAAGCCGCATGAAAATA 57.596 33.333 0.00 0.00 0.00 1.40
3329 3515 4.942761 AATATGGAAGCCGCATGAAAAT 57.057 36.364 0.00 0.00 0.00 1.82
3330 3516 4.734398 AAATATGGAAGCCGCATGAAAA 57.266 36.364 0.00 0.00 0.00 2.29
3331 3517 4.887071 AGTAAATATGGAAGCCGCATGAAA 59.113 37.500 0.00 0.00 0.00 2.69
3332 3518 4.460263 AGTAAATATGGAAGCCGCATGAA 58.540 39.130 0.00 0.00 0.00 2.57
3344 3530 4.508124 GGTGCTTCTGACGAGTAAATATGG 59.492 45.833 0.00 0.00 0.00 2.74
3346 3532 5.339008 TGGTGCTTCTGACGAGTAAATAT 57.661 39.130 0.00 0.00 0.00 1.28
3347 3533 4.794278 TGGTGCTTCTGACGAGTAAATA 57.206 40.909 0.00 0.00 0.00 1.40
3348 3534 3.678056 TGGTGCTTCTGACGAGTAAAT 57.322 42.857 0.00 0.00 0.00 1.40
3349 3535 3.181469 ACTTGGTGCTTCTGACGAGTAAA 60.181 43.478 0.00 0.00 0.00 2.01
3353 3539 2.724977 TACTTGGTGCTTCTGACGAG 57.275 50.000 0.00 0.00 0.00 4.18
3354 3540 3.678056 AATACTTGGTGCTTCTGACGA 57.322 42.857 0.00 0.00 0.00 4.20
3355 3541 6.422776 AATAAATACTTGGTGCTTCTGACG 57.577 37.500 0.00 0.00 0.00 4.35
3357 3543 8.946085 CAGTAAATAAATACTTGGTGCTTCTGA 58.054 33.333 0.00 0.00 33.90 3.27
3358 3544 7.698130 GCAGTAAATAAATACTTGGTGCTTCTG 59.302 37.037 0.00 0.00 33.90 3.02
3359 3545 7.393234 TGCAGTAAATAAATACTTGGTGCTTCT 59.607 33.333 0.00 0.00 33.90 2.85
3360 3546 7.535139 TGCAGTAAATAAATACTTGGTGCTTC 58.465 34.615 0.00 0.00 33.90 3.86
3361 3547 7.461182 TGCAGTAAATAAATACTTGGTGCTT 57.539 32.000 0.00 0.00 33.90 3.91
3362 3548 7.461182 TTGCAGTAAATAAATACTTGGTGCT 57.539 32.000 0.00 0.00 33.90 4.40
3363 3549 8.527567 TTTTGCAGTAAATAAATACTTGGTGC 57.472 30.769 0.00 0.00 33.90 5.01
3379 3565 9.806203 CATCAATTTCTATCCAATTTTGCAGTA 57.194 29.630 0.00 0.00 0.00 2.74
3422 3608 7.672240 TCCATTTTGCGGTATGTATAGACATA 58.328 34.615 6.10 6.10 44.77 2.29
3424 3610 5.919755 TCCATTTTGCGGTATGTATAGACA 58.080 37.500 0.00 0.00 40.72 3.41
3425 3611 8.033038 TCTATCCATTTTGCGGTATGTATAGAC 58.967 37.037 0.00 0.00 29.86 2.59
3426 3612 8.129496 TCTATCCATTTTGCGGTATGTATAGA 57.871 34.615 0.00 0.00 31.37 1.98
3427 3613 8.771920 TTCTATCCATTTTGCGGTATGTATAG 57.228 34.615 0.00 0.00 0.00 1.31
3428 3614 9.733556 ATTTCTATCCATTTTGCGGTATGTATA 57.266 29.630 0.00 0.00 0.00 1.47
3429 3615 8.635765 ATTTCTATCCATTTTGCGGTATGTAT 57.364 30.769 0.00 0.00 0.00 2.29
3430 3616 8.349245 CAATTTCTATCCATTTTGCGGTATGTA 58.651 33.333 0.00 0.00 0.00 2.29
3431 3617 6.959639 ATTTCTATCCATTTTGCGGTATGT 57.040 33.333 0.00 0.00 0.00 2.29
3432 3618 7.424803 TCAATTTCTATCCATTTTGCGGTATG 58.575 34.615 0.00 0.00 0.00 2.39
3433 3619 7.581213 TCAATTTCTATCCATTTTGCGGTAT 57.419 32.000 0.00 0.00 0.00 2.73
3434 3620 7.068103 ACATCAATTTCTATCCATTTTGCGGTA 59.932 33.333 0.00 0.00 0.00 4.02
3435 3621 5.913137 TCAATTTCTATCCATTTTGCGGT 57.087 34.783 0.00 0.00 0.00 5.68
3436 3622 6.275335 ACATCAATTTCTATCCATTTTGCGG 58.725 36.000 0.00 0.00 0.00 5.69
3437 3623 7.113965 GCTACATCAATTTCTATCCATTTTGCG 59.886 37.037 0.00 0.00 0.00 4.85
3438 3624 7.113965 CGCTACATCAATTTCTATCCATTTTGC 59.886 37.037 0.00 0.00 0.00 3.68
3439 3625 8.344831 TCGCTACATCAATTTCTATCCATTTTG 58.655 33.333 0.00 0.00 0.00 2.44
3475 3661 6.813649 CACAATATAATACTCCCTCCATCACG 59.186 42.308 0.00 0.00 0.00 4.35
3477 3663 7.512402 TGTCACAATATAATACTCCCTCCATCA 59.488 37.037 0.00 0.00 0.00 3.07
3524 3741 6.475504 TCTCTTCAAAATAACCTGCTGATGA 58.524 36.000 0.00 0.00 0.00 2.92
3579 3813 9.143631 CCACTTCATTGAAACTTTGATTTATCC 57.856 33.333 0.01 0.00 0.00 2.59
3621 3855 0.252479 TCCGAACGGAGAGAGTAGCT 59.748 55.000 12.04 0.00 39.76 3.32
3624 3858 4.521146 AGTAATTCCGAACGGAGAGAGTA 58.479 43.478 15.34 3.20 46.06 2.59
3625 3859 3.354467 AGTAATTCCGAACGGAGAGAGT 58.646 45.455 15.34 4.12 46.06 3.24
3626 3860 4.106197 CAAGTAATTCCGAACGGAGAGAG 58.894 47.826 15.34 1.49 46.06 3.20
3627 3861 3.508793 ACAAGTAATTCCGAACGGAGAGA 59.491 43.478 15.34 2.49 46.06 3.10
3628 3862 3.846360 ACAAGTAATTCCGAACGGAGAG 58.154 45.455 15.34 5.41 46.06 3.20
3629 3863 3.671433 CGACAAGTAATTCCGAACGGAGA 60.671 47.826 15.34 8.02 46.06 3.71
3630 3864 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
3631 3865 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
3632 3866 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
3633 3867 1.266211 CGCGACAAGTAATTCCGAACG 60.266 52.381 0.00 0.00 0.00 3.95
3634 3868 1.060122 CCGCGACAAGTAATTCCGAAC 59.940 52.381 8.23 0.00 0.00 3.95
3635 3869 1.067706 TCCGCGACAAGTAATTCCGAA 60.068 47.619 8.23 0.00 0.00 4.30
3636 3870 0.527113 TCCGCGACAAGTAATTCCGA 59.473 50.000 8.23 0.00 0.00 4.55
3637 3871 1.352114 TTCCGCGACAAGTAATTCCG 58.648 50.000 8.23 0.00 0.00 4.30
3638 3872 3.486875 CCATTTCCGCGACAAGTAATTCC 60.487 47.826 8.23 0.00 0.00 3.01
3639 3873 3.372822 TCCATTTCCGCGACAAGTAATTC 59.627 43.478 8.23 0.00 0.00 2.17
3640 3874 3.340034 TCCATTTCCGCGACAAGTAATT 58.660 40.909 8.23 0.00 0.00 1.40
3641 3875 2.980568 TCCATTTCCGCGACAAGTAAT 58.019 42.857 8.23 0.00 0.00 1.89
3642 3876 2.459060 TCCATTTCCGCGACAAGTAA 57.541 45.000 8.23 0.00 0.00 2.24
3643 3877 2.276201 CATCCATTTCCGCGACAAGTA 58.724 47.619 8.23 0.00 0.00 2.24
3644 3878 1.086696 CATCCATTTCCGCGACAAGT 58.913 50.000 8.23 0.00 0.00 3.16
3645 3879 1.086696 ACATCCATTTCCGCGACAAG 58.913 50.000 8.23 0.00 0.00 3.16
3646 3880 2.388310 TACATCCATTTCCGCGACAA 57.612 45.000 8.23 0.00 0.00 3.18
3647 3881 2.159028 TGATACATCCATTTCCGCGACA 60.159 45.455 8.23 0.00 0.00 4.35
3648 3882 2.479837 TGATACATCCATTTCCGCGAC 58.520 47.619 8.23 0.00 0.00 5.19
3649 3883 2.869801 GTTGATACATCCATTTCCGCGA 59.130 45.455 8.23 0.00 0.00 5.87
3650 3884 2.611751 TGTTGATACATCCATTTCCGCG 59.388 45.455 0.00 0.00 0.00 6.46
3651 3885 4.836125 ATGTTGATACATCCATTTCCGC 57.164 40.909 0.00 0.00 41.07 5.54
3675 3909 9.893634 TCGGAAATGGATGTATCTAAAACTAAA 57.106 29.630 0.00 0.00 0.00 1.85
3676 3910 9.542462 CTCGGAAATGGATGTATCTAAAACTAA 57.458 33.333 0.00 0.00 0.00 2.24
3677 3911 8.920174 TCTCGGAAATGGATGTATCTAAAACTA 58.080 33.333 0.00 0.00 0.00 2.24
3678 3912 7.711339 GTCTCGGAAATGGATGTATCTAAAACT 59.289 37.037 0.00 0.00 0.00 2.66
3679 3913 7.494625 TGTCTCGGAAATGGATGTATCTAAAAC 59.505 37.037 0.00 0.00 0.00 2.43
3680 3914 7.561251 TGTCTCGGAAATGGATGTATCTAAAA 58.439 34.615 0.00 0.00 0.00 1.52
3681 3915 7.119709 TGTCTCGGAAATGGATGTATCTAAA 57.880 36.000 0.00 0.00 0.00 1.85
3682 3916 6.724893 TGTCTCGGAAATGGATGTATCTAA 57.275 37.500 0.00 0.00 0.00 2.10
3683 3917 6.323996 ACTTGTCTCGGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 0.00 1.98
3684 3918 5.129485 ACTTGTCTCGGAAATGGATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
3685 3919 5.360591 ACTTGTCTCGGAAATGGATGTATC 58.639 41.667 0.00 0.00 0.00 2.24
3686 3920 5.359194 ACTTGTCTCGGAAATGGATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
3687 3921 4.819105 ACTTGTCTCGGAAATGGATGTA 57.181 40.909 0.00 0.00 0.00 2.29
3688 3922 3.703001 ACTTGTCTCGGAAATGGATGT 57.297 42.857 0.00 0.00 0.00 3.06
3689 3923 6.316140 TGAATTACTTGTCTCGGAAATGGATG 59.684 38.462 0.00 0.00 0.00 3.51
3690 3924 6.414732 TGAATTACTTGTCTCGGAAATGGAT 58.585 36.000 0.00 0.00 0.00 3.41
3691 3925 5.800296 TGAATTACTTGTCTCGGAAATGGA 58.200 37.500 0.00 0.00 0.00 3.41
3692 3926 5.874810 TCTGAATTACTTGTCTCGGAAATGG 59.125 40.000 0.00 0.00 0.00 3.16
3693 3927 6.968131 TCTGAATTACTTGTCTCGGAAATG 57.032 37.500 0.00 0.00 0.00 2.32
3694 3928 6.090898 CGTTCTGAATTACTTGTCTCGGAAAT 59.909 38.462 0.00 0.00 35.51 2.17
3695 3929 5.404366 CGTTCTGAATTACTTGTCTCGGAAA 59.596 40.000 0.00 0.00 35.51 3.13
3696 3930 4.921515 CGTTCTGAATTACTTGTCTCGGAA 59.078 41.667 0.00 0.00 32.16 4.30
3697 3931 4.482386 CGTTCTGAATTACTTGTCTCGGA 58.518 43.478 0.00 0.00 0.00 4.55
3698 3932 3.612860 CCGTTCTGAATTACTTGTCTCGG 59.387 47.826 0.00 0.00 0.00 4.63
3699 3933 4.482386 TCCGTTCTGAATTACTTGTCTCG 58.518 43.478 0.00 0.00 0.00 4.04
3700 3934 4.865365 CCTCCGTTCTGAATTACTTGTCTC 59.135 45.833 0.00 0.00 0.00 3.36
3701 3935 4.322801 CCCTCCGTTCTGAATTACTTGTCT 60.323 45.833 0.00 0.00 0.00 3.41
3702 3936 3.933332 CCCTCCGTTCTGAATTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
3703 3937 3.581332 TCCCTCCGTTCTGAATTACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
3704 3938 4.184629 CTCCCTCCGTTCTGAATTACTTG 58.815 47.826 0.00 0.00 0.00 3.16
3705 3939 3.838903 ACTCCCTCCGTTCTGAATTACTT 59.161 43.478 0.00 0.00 0.00 2.24
3706 3940 3.442076 ACTCCCTCCGTTCTGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
3707 3941 3.889520 ACTCCCTCCGTTCTGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
3708 3942 4.863548 TCTACTCCCTCCGTTCTGAATTA 58.136 43.478 0.00 0.00 0.00 1.40
3709 3943 3.709587 TCTACTCCCTCCGTTCTGAATT 58.290 45.455 0.00 0.00 0.00 2.17
3710 3944 3.383698 TCTACTCCCTCCGTTCTGAAT 57.616 47.619 0.00 0.00 0.00 2.57
3711 3945 2.893215 TCTACTCCCTCCGTTCTGAA 57.107 50.000 0.00 0.00 0.00 3.02
3712 3946 4.351407 AGATATCTACTCCCTCCGTTCTGA 59.649 45.833 2.53 0.00 0.00 3.27
3713 3947 4.457603 CAGATATCTACTCCCTCCGTTCTG 59.542 50.000 4.54 0.00 0.00 3.02
3714 3948 4.105057 ACAGATATCTACTCCCTCCGTTCT 59.895 45.833 4.54 0.00 0.00 3.01
3715 3949 4.216687 CACAGATATCTACTCCCTCCGTTC 59.783 50.000 4.54 0.00 0.00 3.95
3716 3950 4.145807 CACAGATATCTACTCCCTCCGTT 58.854 47.826 4.54 0.00 0.00 4.44
3717 3951 3.498841 CCACAGATATCTACTCCCTCCGT 60.499 52.174 4.54 0.00 0.00 4.69
3718 3952 3.085533 CCACAGATATCTACTCCCTCCG 58.914 54.545 4.54 0.00 0.00 4.63
3719 3953 4.390129 TCCACAGATATCTACTCCCTCC 57.610 50.000 4.54 0.00 0.00 4.30
3720 3954 6.723977 AGATTTCCACAGATATCTACTCCCTC 59.276 42.308 4.54 0.00 38.55 4.30
3721 3955 6.629156 AGATTTCCACAGATATCTACTCCCT 58.371 40.000 4.54 0.00 38.55 4.20
3722 3956 6.926630 AGATTTCCACAGATATCTACTCCC 57.073 41.667 4.54 0.00 38.55 4.30
3723 3957 9.699703 GTAAAGATTTCCACAGATATCTACTCC 57.300 37.037 4.54 0.00 39.16 3.85
3726 3960 9.699703 GGAGTAAAGATTTCCACAGATATCTAC 57.300 37.037 4.54 0.00 39.16 2.59
3845 4079 5.594725 GTGATGTCTCCATCTTACCAGAGTA 59.405 44.000 4.51 0.00 46.38 2.59
3876 4111 1.937108 GCCGTGGACAAGTGAAGAGAG 60.937 57.143 0.00 0.00 0.00 3.20
3899 4134 2.093288 AGGATATGCACCACACTGACTG 60.093 50.000 0.00 0.00 0.00 3.51
3900 4135 2.191400 AGGATATGCACCACACTGACT 58.809 47.619 0.00 0.00 0.00 3.41
3901 4136 2.698855 AGGATATGCACCACACTGAC 57.301 50.000 0.00 0.00 0.00 3.51
3932 4167 6.872628 TCATGATAGATTGGTGAATGAAGC 57.127 37.500 0.00 0.00 0.00 3.86
3966 4201 3.492102 TCTGTTCAGTTGAGGAAAGGG 57.508 47.619 0.00 0.00 0.00 3.95
4034 4270 7.602645 CACTTAACCCGAAAAGTTTTAAAACG 58.397 34.615 22.04 11.96 43.51 3.60


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

AutoCloner maintained by Alex Coulton.