Multiple sequence alignment - TraesCS3B01G109900

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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 TraesCS3B01G109900 chr3B 100.000 2603 0 0 1 2603 75958264 75955662 0.000000e+00 4807.0
1 TraesCS3B01G109900 chr3B 90.166 1688 107 31 1 1649 76115091 76116758 0.000000e+00 2143.0
2 TraesCS3B01G109900 chr3A 91.141 1885 85 22 1 1820 60442977 60441110 0.000000e+00 2481.0
3 TraesCS3B01G109900 chr3A 92.801 1139 71 7 1 1137 60471524 60472653 0.000000e+00 1639.0
4 TraesCS3B01G109900 chr3A 93.654 520 26 3 1131 1647 60472678 60473193 0.000000e+00 771.0
5 TraesCS3B01G109900 chr3A 93.210 324 21 1 2072 2394 670666947 670666624 2.340000e-130 475.0
6 TraesCS3B01G109900 chr3A 90.000 260 24 2 1817 2074 60439949 60439690 4.150000e-88 335.0
7 TraesCS3B01G109900 chr3A 89.450 218 17 4 2387 2603 60439675 60439463 1.190000e-68 270.0
8 TraesCS3B01G109900 chr3D 91.785 1692 90 23 1 1647 48348672 48350359 0.000000e+00 2309.0
9 TraesCS3B01G109900 chr3D 91.866 1672 64 21 1 1609 48252272 48250610 0.000000e+00 2268.0
10 TraesCS3B01G109900 chr3D 89.216 408 37 2 1131 1534 48295756 48295352 1.080000e-138 503.0
11 TraesCS3B01G109900 chr3D 93.711 318 20 0 2072 2389 441430718 441431035 6.520000e-131 477.0
12 TraesCS3B01G109900 chr3D 86.514 393 45 6 1690 2074 48295115 48294723 2.390000e-115 425.0
13 TraesCS3B01G109900 chr3D 85.116 215 23 6 2387 2600 48294708 48294502 7.300000e-51 211.0
14 TraesCS3B01G109900 chr7B 79.050 821 144 22 114 929 682283706 682282909 2.950000e-149 538.0
15 TraesCS3B01G109900 chr6A 79.050 821 144 22 114 929 205114773 205115570 2.950000e-149 538.0
16 TraesCS3B01G109900 chr5A 95.312 320 15 0 2075 2394 106686671 106686990 2.310000e-140 508.0
17 TraesCS3B01G109900 chr5A 76.147 436 78 19 109 534 520209662 520209243 3.400000e-49 206.0
18 TraesCS3B01G109900 chr5A 76.648 364 67 13 1133 1487 520208590 520208236 4.420000e-43 185.0
19 TraesCS3B01G109900 chr7D 94.984 319 16 0 2073 2391 393041071 393041389 3.870000e-138 501.0
20 TraesCS3B01G109900 chr7D 85.321 109 12 4 2497 2603 390857408 390857302 2.740000e-20 110.0
21 TraesCS3B01G109900 chr4D 94.984 319 13 1 2073 2391 309628806 309629121 5.000000e-137 497.0
22 TraesCS3B01G109900 chr6D 94.118 323 19 0 2072 2394 317480514 317480192 2.330000e-135 492.0
23 TraesCS3B01G109900 chr6D 81.598 413 65 9 112 523 142989963 142989561 5.370000e-87 331.0
24 TraesCS3B01G109900 chr4A 94.118 323 19 0 2072 2394 554641810 554641488 2.330000e-135 492.0
25 TraesCS3B01G109900 chr4A 93.498 323 21 0 2072 2394 85901080 85900758 5.040000e-132 481.0
26 TraesCS3B01G109900 chr5B 93.417 319 20 1 2073 2391 456975824 456976141 3.030000e-129 472.0
27 TraesCS3B01G109900 chr5B 76.860 363 68 11 1133 1487 491083033 491082679 9.510000e-45 191.0
28 TraesCS3B01G109900 chr6B 76.127 821 146 43 114 929 255211338 255210563 4.060000e-103 385.0
29 TraesCS3B01G109900 chr1D 75.654 612 120 25 114 716 337217326 337217917 7.090000e-71 278.0
30 TraesCS3B01G109900 chrUn 72.857 350 83 11 1139 1482 24901500 24901843 2.740000e-20 110.0
31 TraesCS3B01G109900 chr5D 76.974 152 30 5 1263 1413 380076340 380076193 5.970000e-12 82.4


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 TraesCS3B01G109900 chr3B 75955662 75958264 2602 True 4807.000000 4807 100.000000 1 2603 1 chr3B.!!$R1 2602
1 TraesCS3B01G109900 chr3B 76115091 76116758 1667 False 2143.000000 2143 90.166000 1 1649 1 chr3B.!!$F1 1648
2 TraesCS3B01G109900 chr3A 60471524 60473193 1669 False 1205.000000 1639 93.227500 1 1647 2 chr3A.!!$F1 1646
3 TraesCS3B01G109900 chr3A 60439463 60442977 3514 True 1028.666667 2481 90.197000 1 2603 3 chr3A.!!$R2 2602
4 TraesCS3B01G109900 chr3D 48348672 48350359 1687 False 2309.000000 2309 91.785000 1 1647 1 chr3D.!!$F1 1646
5 TraesCS3B01G109900 chr3D 48250610 48252272 1662 True 2268.000000 2268 91.866000 1 1609 1 chr3D.!!$R1 1608
6 TraesCS3B01G109900 chr3D 48294502 48295756 1254 True 379.666667 503 86.948667 1131 2600 3 chr3D.!!$R2 1469
7 TraesCS3B01G109900 chr7B 682282909 682283706 797 True 538.000000 538 79.050000 114 929 1 chr7B.!!$R1 815
8 TraesCS3B01G109900 chr6A 205114773 205115570 797 False 538.000000 538 79.050000 114 929 1 chr6A.!!$F1 815
9 TraesCS3B01G109900 chr6B 255210563 255211338 775 True 385.000000 385 76.127000 114 929 1 chr6B.!!$R1 815
10 TraesCS3B01G109900 chr1D 337217326 337217917 591 False 278.000000 278 75.654000 114 716 1 chr1D.!!$F1 602

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
22 23 0.547075 TACTACTCGCTCCTCCTGCT 59.453 55.0 0.0 0.0 0.0 4.24 F
26 27 0.902516 ACTCGCTCCTCCTGCTTCTT 60.903 55.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1009 1057 0.108851 TCGCTGCTCGCACTAATCAA 60.109 50.000 0.0 0.0 39.08 2.57 R
1878 3231 1.529826 GGAAGCTAATCAAGTTGCGCG 60.530 52.381 0.0 0.0 0.00 6.86 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
22 23 0.547075 TACTACTCGCTCCTCCTGCT 59.453 55.000 0.00 0.00 0.00 4.24
26 27 0.902516 ACTCGCTCCTCCTGCTTCTT 60.903 55.000 0.00 0.00 0.00 2.52
45 46 4.401022 TCTTCTTCTGGTCGTGGTAACTA 58.599 43.478 0.00 0.00 37.61 2.24
59 60 3.054434 TGGTAACTACGCTCTACCTGGTA 60.054 47.826 6.36 6.36 36.76 3.25
539 540 2.874664 CGTGAACTTGACCCGGGGA 61.875 63.158 27.92 8.15 0.00 4.81
638 639 3.399181 CTGCTGCGGGAGGGGTTA 61.399 66.667 6.08 0.00 0.00 2.85
800 804 2.354503 GGACAAGAAGAGATCAGCAGCA 60.355 50.000 0.00 0.00 0.00 4.41
960 979 4.998672 CCGATCCTGTTTAGTGTTTACCAA 59.001 41.667 0.00 0.00 0.00 3.67
1661 1833 1.135546 TGTTTGTGCTTTGTGGTGACG 60.136 47.619 0.00 0.00 0.00 4.35
1669 1841 1.455786 CTTTGTGGTGACGATCGTGAC 59.544 52.381 28.12 27.38 0.00 3.67
1670 1842 0.671796 TTGTGGTGACGATCGTGACT 59.328 50.000 31.54 6.74 32.89 3.41
1671 1843 1.525941 TGTGGTGACGATCGTGACTA 58.474 50.000 31.54 25.81 32.89 2.59
1672 1844 1.198408 TGTGGTGACGATCGTGACTAC 59.802 52.381 35.09 35.09 42.07 2.73
1673 1845 1.198408 GTGGTGACGATCGTGACTACA 59.802 52.381 36.07 24.67 41.57 2.74
1674 1846 1.881324 TGGTGACGATCGTGACTACAA 59.119 47.619 31.54 15.77 32.89 2.41
1675 1847 2.293955 TGGTGACGATCGTGACTACAAA 59.706 45.455 31.54 13.64 32.89 2.83
1676 1848 3.243468 TGGTGACGATCGTGACTACAAAA 60.243 43.478 31.54 12.13 32.89 2.44
1677 1849 3.120782 GGTGACGATCGTGACTACAAAAC 59.879 47.826 31.54 13.66 32.89 2.43
1678 1850 3.120782 GTGACGATCGTGACTACAAAACC 59.879 47.826 27.31 9.11 29.75 3.27
1680 1852 3.314553 ACGATCGTGACTACAAAACCTG 58.685 45.455 22.06 0.00 0.00 4.00
1682 1854 4.022935 ACGATCGTGACTACAAAACCTGTA 60.023 41.667 22.06 0.00 39.64 2.74
1683 1855 4.322804 CGATCGTGACTACAAAACCTGTAC 59.677 45.833 7.03 0.00 39.64 2.90
1684 1856 4.924305 TCGTGACTACAAAACCTGTACT 57.076 40.909 0.00 0.00 39.64 2.73
1720 1903 2.028748 TCTTGGCTACCGTTGTAAGGAC 60.029 50.000 0.00 0.00 0.00 3.85
1743 1927 5.523552 ACCTGCAGTTTTATTTTGCTGTTTC 59.476 36.000 13.81 0.00 38.60 2.78
1833 3183 4.571176 GGTTCCCTAAGACAATGATCGAAC 59.429 45.833 0.00 0.00 0.00 3.95
1839 3189 3.340814 AGACAATGATCGAACTTGGCT 57.659 42.857 7.34 7.34 33.39 4.75
1878 3231 7.907214 TCCTCAGAATTACAAGCTAAAAGAC 57.093 36.000 0.00 0.00 0.00 3.01
1892 3245 3.889196 AAAAGACGCGCAACTTGATTA 57.111 38.095 5.73 0.00 0.00 1.75
1909 3262 7.406104 ACTTGATTAGCTTCCCTAAGACAATT 58.594 34.615 0.00 0.00 39.29 2.32
1910 3263 7.337942 ACTTGATTAGCTTCCCTAAGACAATTG 59.662 37.037 3.24 3.24 39.29 2.32
1989 3344 5.562696 GCAGCTGCTACAAAAAGATGTGTTA 60.563 40.000 31.33 0.00 38.21 2.41
1994 3349 7.341445 TGCTACAAAAAGATGTGTTAGGTTT 57.659 32.000 0.00 0.00 34.75 3.27
2043 3398 5.745312 TCTGTGTCTGGTTGAGTGAATAT 57.255 39.130 0.00 0.00 0.00 1.28
2045 3400 7.239763 TCTGTGTCTGGTTGAGTGAATATAA 57.760 36.000 0.00 0.00 0.00 0.98
2102 3457 9.997482 TTTTGCGGATAGAAATTTGTATTACTC 57.003 29.630 9.06 2.77 0.00 2.59
2103 3458 8.725405 TTGCGGATAGAAATTTGTATTACTCA 57.275 30.769 9.06 4.94 0.00 3.41
2104 3459 8.725405 TGCGGATAGAAATTTGTATTACTCAA 57.275 30.769 9.06 0.00 0.00 3.02
2105 3460 9.168451 TGCGGATAGAAATTTGTATTACTCAAA 57.832 29.630 9.06 0.00 38.77 2.69
2106 3461 9.997482 GCGGATAGAAATTTGTATTACTCAAAA 57.003 29.630 9.06 0.00 38.11 2.44
2116 3471 7.739498 TTGTATTACTCAAAACCTCAAGTCC 57.261 36.000 0.00 0.00 0.00 3.85
2117 3472 7.074653 TGTATTACTCAAAACCTCAAGTCCT 57.925 36.000 0.00 0.00 0.00 3.85
2118 3473 7.514721 TGTATTACTCAAAACCTCAAGTCCTT 58.485 34.615 0.00 0.00 0.00 3.36
2119 3474 8.653191 TGTATTACTCAAAACCTCAAGTCCTTA 58.347 33.333 0.00 0.00 0.00 2.69
2120 3475 7.981102 ATTACTCAAAACCTCAAGTCCTTAC 57.019 36.000 0.00 0.00 0.00 2.34
2121 3476 5.367945 ACTCAAAACCTCAAGTCCTTACA 57.632 39.130 0.00 0.00 0.00 2.41
2122 3477 5.751586 ACTCAAAACCTCAAGTCCTTACAA 58.248 37.500 0.00 0.00 0.00 2.41
2123 3478 6.365520 ACTCAAAACCTCAAGTCCTTACAAT 58.634 36.000 0.00 0.00 0.00 2.71
2124 3479 6.486993 ACTCAAAACCTCAAGTCCTTACAATC 59.513 38.462 0.00 0.00 0.00 2.67
2125 3480 5.768164 TCAAAACCTCAAGTCCTTACAATCC 59.232 40.000 0.00 0.00 0.00 3.01
2126 3481 4.993705 AACCTCAAGTCCTTACAATCCA 57.006 40.909 0.00 0.00 0.00 3.41
2127 3482 5.520748 AACCTCAAGTCCTTACAATCCAT 57.479 39.130 0.00 0.00 0.00 3.41
2128 3483 5.104259 ACCTCAAGTCCTTACAATCCATC 57.896 43.478 0.00 0.00 0.00 3.51
2129 3484 4.122776 CCTCAAGTCCTTACAATCCATCG 58.877 47.826 0.00 0.00 0.00 3.84
2130 3485 3.531538 TCAAGTCCTTACAATCCATCGC 58.468 45.455 0.00 0.00 0.00 4.58
2131 3486 3.055458 TCAAGTCCTTACAATCCATCGCA 60.055 43.478 0.00 0.00 0.00 5.10
2132 3487 3.185246 AGTCCTTACAATCCATCGCAG 57.815 47.619 0.00 0.00 0.00 5.18
2133 3488 1.599542 GTCCTTACAATCCATCGCAGC 59.400 52.381 0.00 0.00 0.00 5.25
2134 3489 0.947244 CCTTACAATCCATCGCAGCC 59.053 55.000 0.00 0.00 0.00 4.85
2135 3490 1.667236 CTTACAATCCATCGCAGCCA 58.333 50.000 0.00 0.00 0.00 4.75
2136 3491 2.016318 CTTACAATCCATCGCAGCCAA 58.984 47.619 0.00 0.00 0.00 4.52
2137 3492 2.121291 TACAATCCATCGCAGCCAAA 57.879 45.000 0.00 0.00 0.00 3.28
2138 3493 1.477553 ACAATCCATCGCAGCCAAAT 58.522 45.000 0.00 0.00 0.00 2.32
2139 3494 1.826720 ACAATCCATCGCAGCCAAATT 59.173 42.857 0.00 0.00 0.00 1.82
2140 3495 2.159198 ACAATCCATCGCAGCCAAATTC 60.159 45.455 0.00 0.00 0.00 2.17
2141 3496 1.766494 ATCCATCGCAGCCAAATTCA 58.234 45.000 0.00 0.00 0.00 2.57
2142 3497 1.543607 TCCATCGCAGCCAAATTCAA 58.456 45.000 0.00 0.00 0.00 2.69
2143 3498 1.891811 TCCATCGCAGCCAAATTCAAA 59.108 42.857 0.00 0.00 0.00 2.69
2144 3499 2.094597 TCCATCGCAGCCAAATTCAAAG 60.095 45.455 0.00 0.00 0.00 2.77
2145 3500 1.657094 CATCGCAGCCAAATTCAAAGC 59.343 47.619 0.00 0.00 0.00 3.51
2146 3501 0.672889 TCGCAGCCAAATTCAAAGCA 59.327 45.000 0.00 0.00 0.00 3.91
2147 3502 1.273048 TCGCAGCCAAATTCAAAGCAT 59.727 42.857 0.00 0.00 0.00 3.79
2148 3503 1.657094 CGCAGCCAAATTCAAAGCATC 59.343 47.619 0.00 0.00 0.00 3.91
2149 3504 2.673043 CGCAGCCAAATTCAAAGCATCT 60.673 45.455 0.00 0.00 0.00 2.90
2150 3505 2.671396 GCAGCCAAATTCAAAGCATCTG 59.329 45.455 0.00 0.00 0.00 2.90
2151 3506 3.259064 CAGCCAAATTCAAAGCATCTGG 58.741 45.455 0.00 0.00 0.00 3.86
2152 3507 3.056393 CAGCCAAATTCAAAGCATCTGGA 60.056 43.478 0.00 0.00 0.00 3.86
2153 3508 3.194968 AGCCAAATTCAAAGCATCTGGAG 59.805 43.478 0.00 0.00 0.00 3.86
2154 3509 3.677976 GCCAAATTCAAAGCATCTGGAGG 60.678 47.826 0.00 0.00 0.00 4.30
2155 3510 3.512724 CCAAATTCAAAGCATCTGGAGGT 59.487 43.478 0.00 0.00 0.00 3.85
2156 3511 4.381292 CCAAATTCAAAGCATCTGGAGGTC 60.381 45.833 0.00 0.00 0.00 3.85
2157 3512 2.496899 TTCAAAGCATCTGGAGGTCC 57.503 50.000 0.00 0.00 0.00 4.46
2158 3513 0.620556 TCAAAGCATCTGGAGGTCCC 59.379 55.000 0.00 0.00 34.29 4.46
2159 3514 0.745845 CAAAGCATCTGGAGGTCCCG 60.746 60.000 0.00 0.00 37.93 5.14
2160 3515 0.909610 AAAGCATCTGGAGGTCCCGA 60.910 55.000 0.00 0.00 37.93 5.14
2161 3516 0.909610 AAGCATCTGGAGGTCCCGAA 60.910 55.000 0.00 0.00 37.93 4.30
2162 3517 1.153349 GCATCTGGAGGTCCCGAAC 60.153 63.158 0.00 0.00 37.93 3.95
2171 3526 3.668386 GTCCCGAACCAAGCCAAG 58.332 61.111 0.00 0.00 0.00 3.61
2172 3527 1.228154 GTCCCGAACCAAGCCAAGT 60.228 57.895 0.00 0.00 0.00 3.16
2173 3528 1.072505 TCCCGAACCAAGCCAAGTC 59.927 57.895 0.00 0.00 0.00 3.01
2174 3529 1.228124 CCCGAACCAAGCCAAGTCA 60.228 57.895 0.00 0.00 0.00 3.41
2175 3530 0.609131 CCCGAACCAAGCCAAGTCAT 60.609 55.000 0.00 0.00 0.00 3.06
2176 3531 0.523072 CCGAACCAAGCCAAGTCATG 59.477 55.000 0.00 0.00 0.00 3.07
2187 3542 3.268023 CCAAGTCATGGTTCTACCCTC 57.732 52.381 0.00 0.00 44.85 4.30
2188 3543 2.418746 CCAAGTCATGGTTCTACCCTCG 60.419 54.545 0.00 0.00 44.85 4.63
2189 3544 0.824759 AGTCATGGTTCTACCCTCGC 59.175 55.000 0.00 0.00 37.50 5.03
2190 3545 0.824759 GTCATGGTTCTACCCTCGCT 59.175 55.000 0.00 0.00 37.50 4.93
2191 3546 2.029623 GTCATGGTTCTACCCTCGCTA 58.970 52.381 0.00 0.00 37.50 4.26
2192 3547 2.029623 TCATGGTTCTACCCTCGCTAC 58.970 52.381 0.00 0.00 37.50 3.58
2193 3548 1.030457 ATGGTTCTACCCTCGCTACG 58.970 55.000 0.00 0.00 37.50 3.51
2194 3549 0.035152 TGGTTCTACCCTCGCTACGA 60.035 55.000 0.00 0.00 37.50 3.43
2209 3564 7.618964 CTCGCTACGAGCAAAATATACTAAA 57.381 36.000 3.83 0.00 46.75 1.85
2210 3565 7.385668 TCGCTACGAGCAAAATATACTAAAC 57.614 36.000 7.47 0.00 42.58 2.01
2211 3566 7.198390 TCGCTACGAGCAAAATATACTAAACT 58.802 34.615 7.47 0.00 42.58 2.66
2212 3567 8.344831 TCGCTACGAGCAAAATATACTAAACTA 58.655 33.333 7.47 0.00 42.58 2.24
2213 3568 9.125906 CGCTACGAGCAAAATATACTAAACTAT 57.874 33.333 7.47 0.00 42.58 2.12
2235 3590 9.095065 ACTATCACTAACTTTATTTTGGCTACG 57.905 33.333 0.00 0.00 0.00 3.51
2236 3591 9.309516 CTATCACTAACTTTATTTTGGCTACGA 57.690 33.333 0.00 0.00 0.00 3.43
2237 3592 8.732746 ATCACTAACTTTATTTTGGCTACGAT 57.267 30.769 0.00 0.00 0.00 3.73
2238 3593 8.556213 TCACTAACTTTATTTTGGCTACGATT 57.444 30.769 0.00 0.00 0.00 3.34
2239 3594 9.005777 TCACTAACTTTATTTTGGCTACGATTT 57.994 29.630 0.00 0.00 0.00 2.17
2244 3599 9.567848 AACTTTATTTTGGCTACGATTTACATG 57.432 29.630 0.00 0.00 0.00 3.21
2245 3600 8.952278 ACTTTATTTTGGCTACGATTTACATGA 58.048 29.630 0.00 0.00 0.00 3.07
2246 3601 9.438291 CTTTATTTTGGCTACGATTTACATGAG 57.562 33.333 0.00 0.00 0.00 2.90
2247 3602 8.500753 TTATTTTGGCTACGATTTACATGAGT 57.499 30.769 0.00 0.00 0.00 3.41
2248 3603 9.602568 TTATTTTGGCTACGATTTACATGAGTA 57.397 29.630 0.00 0.00 0.00 2.59
2249 3604 7.908827 TTTTGGCTACGATTTACATGAGTAA 57.091 32.000 0.00 0.00 38.40 2.24
2250 3605 8.500753 TTTTGGCTACGATTTACATGAGTAAT 57.499 30.769 0.00 0.00 39.78 1.89
2251 3606 9.602568 TTTTGGCTACGATTTACATGAGTAATA 57.397 29.630 0.00 0.00 39.78 0.98
2252 3607 8.583810 TTGGCTACGATTTACATGAGTAATAC 57.416 34.615 0.00 0.00 39.78 1.89
2253 3608 7.718525 TGGCTACGATTTACATGAGTAATACA 58.281 34.615 0.00 0.00 39.78 2.29
2254 3609 8.198778 TGGCTACGATTTACATGAGTAATACAA 58.801 33.333 0.00 0.00 39.78 2.41
2255 3610 9.037737 GGCTACGATTTACATGAGTAATACAAA 57.962 33.333 0.00 0.00 39.78 2.83
2266 3621 8.450964 ACATGAGTAATACAAAAATCACGAAGG 58.549 33.333 0.00 0.00 0.00 3.46
2267 3622 8.664798 CATGAGTAATACAAAAATCACGAAGGA 58.335 33.333 0.00 0.00 0.00 3.36
2268 3623 8.610248 TGAGTAATACAAAAATCACGAAGGAA 57.390 30.769 0.00 0.00 0.00 3.36
2269 3624 8.500773 TGAGTAATACAAAAATCACGAAGGAAC 58.499 33.333 0.00 0.00 0.00 3.62
2270 3625 8.385898 AGTAATACAAAAATCACGAAGGAACA 57.614 30.769 0.00 0.00 0.00 3.18
2271 3626 8.842280 AGTAATACAAAAATCACGAAGGAACAA 58.158 29.630 0.00 0.00 0.00 2.83
2272 3627 9.453325 GTAATACAAAAATCACGAAGGAACAAA 57.547 29.630 0.00 0.00 0.00 2.83
2273 3628 8.934507 AATACAAAAATCACGAAGGAACAAAA 57.065 26.923 0.00 0.00 0.00 2.44
2274 3629 6.885735 ACAAAAATCACGAAGGAACAAAAG 57.114 33.333 0.00 0.00 0.00 2.27
2275 3630 6.626302 ACAAAAATCACGAAGGAACAAAAGA 58.374 32.000 0.00 0.00 0.00 2.52
2276 3631 7.264947 ACAAAAATCACGAAGGAACAAAAGAT 58.735 30.769 0.00 0.00 0.00 2.40
2277 3632 8.410141 ACAAAAATCACGAAGGAACAAAAGATA 58.590 29.630 0.00 0.00 0.00 1.98
2278 3633 9.410556 CAAAAATCACGAAGGAACAAAAGATAT 57.589 29.630 0.00 0.00 0.00 1.63
2279 3634 9.626045 AAAAATCACGAAGGAACAAAAGATATC 57.374 29.630 0.00 0.00 0.00 1.63
2280 3635 8.567285 AAATCACGAAGGAACAAAAGATATCT 57.433 30.769 0.00 0.00 0.00 1.98
2281 3636 9.667107 AAATCACGAAGGAACAAAAGATATCTA 57.333 29.630 5.46 0.00 0.00 1.98
2282 3637 9.667107 AATCACGAAGGAACAAAAGATATCTAA 57.333 29.630 5.46 0.00 0.00 2.10
2283 3638 9.838339 ATCACGAAGGAACAAAAGATATCTAAT 57.162 29.630 5.46 0.00 0.00 1.73
2284 3639 9.314321 TCACGAAGGAACAAAAGATATCTAATC 57.686 33.333 5.46 0.74 0.00 1.75
2285 3640 9.319143 CACGAAGGAACAAAAGATATCTAATCT 57.681 33.333 5.46 0.00 0.00 2.40
2286 3641 9.892130 ACGAAGGAACAAAAGATATCTAATCTT 57.108 29.630 5.46 3.85 39.82 2.40
2303 3658 8.239038 TCTAATCTTCTTTATGATGGACGAGT 57.761 34.615 0.00 0.00 0.00 4.18
2304 3659 9.350951 TCTAATCTTCTTTATGATGGACGAGTA 57.649 33.333 0.00 0.00 0.00 2.59
2305 3660 9.967346 CTAATCTTCTTTATGATGGACGAGTAA 57.033 33.333 0.00 0.00 0.00 2.24
2307 3662 8.649973 ATCTTCTTTATGATGGACGAGTAAAC 57.350 34.615 0.00 0.00 0.00 2.01
2308 3663 7.039882 TCTTCTTTATGATGGACGAGTAAACC 58.960 38.462 0.00 0.00 0.00 3.27
2309 3664 5.345702 TCTTTATGATGGACGAGTAAACCG 58.654 41.667 0.00 0.00 0.00 4.44
2310 3665 4.987408 TTATGATGGACGAGTAAACCGA 57.013 40.909 0.00 0.00 0.00 4.69
2311 3666 5.524971 TTATGATGGACGAGTAAACCGAT 57.475 39.130 0.00 0.00 0.00 4.18
2312 3667 3.431922 TGATGGACGAGTAAACCGATC 57.568 47.619 0.00 0.00 0.00 3.69
2313 3668 3.021695 TGATGGACGAGTAAACCGATCT 58.978 45.455 0.00 0.00 0.00 2.75
2314 3669 2.933495 TGGACGAGTAAACCGATCTG 57.067 50.000 0.00 0.00 0.00 2.90
2315 3670 2.165167 TGGACGAGTAAACCGATCTGT 58.835 47.619 0.00 0.00 0.00 3.41
2316 3671 2.163010 TGGACGAGTAAACCGATCTGTC 59.837 50.000 0.00 0.00 0.00 3.51
2329 3684 3.435105 GATCTGTCGACATCTGAAGCT 57.565 47.619 20.40 0.00 0.00 3.74
2330 3685 3.779759 GATCTGTCGACATCTGAAGCTT 58.220 45.455 20.40 0.00 0.00 3.74
2331 3686 2.951726 TCTGTCGACATCTGAAGCTTG 58.048 47.619 20.40 3.10 0.00 4.01
2332 3687 2.558359 TCTGTCGACATCTGAAGCTTGA 59.442 45.455 20.40 5.69 0.00 3.02
2333 3688 3.005791 TCTGTCGACATCTGAAGCTTGAA 59.994 43.478 20.40 0.00 0.00 2.69
2334 3689 3.930336 TGTCGACATCTGAAGCTTGAAT 58.070 40.909 15.76 0.00 0.00 2.57
2335 3690 3.928992 TGTCGACATCTGAAGCTTGAATC 59.071 43.478 15.76 0.00 0.00 2.52
2336 3691 3.928992 GTCGACATCTGAAGCTTGAATCA 59.071 43.478 11.55 0.00 0.00 2.57
2337 3692 4.389992 GTCGACATCTGAAGCTTGAATCAA 59.610 41.667 11.55 0.00 0.00 2.57
2338 3693 5.064452 GTCGACATCTGAAGCTTGAATCAAT 59.936 40.000 11.55 0.00 0.00 2.57
2339 3694 5.645067 TCGACATCTGAAGCTTGAATCAATT 59.355 36.000 2.10 0.00 0.00 2.32
2340 3695 6.149973 TCGACATCTGAAGCTTGAATCAATTT 59.850 34.615 2.10 0.00 0.00 1.82
2341 3696 6.805271 CGACATCTGAAGCTTGAATCAATTTT 59.195 34.615 2.10 0.00 0.00 1.82
2342 3697 7.964559 CGACATCTGAAGCTTGAATCAATTTTA 59.035 33.333 2.10 0.00 0.00 1.52
2343 3698 8.976986 ACATCTGAAGCTTGAATCAATTTTAC 57.023 30.769 2.10 0.00 0.00 2.01
2344 3699 8.800332 ACATCTGAAGCTTGAATCAATTTTACT 58.200 29.630 2.10 0.00 0.00 2.24
2345 3700 9.073368 CATCTGAAGCTTGAATCAATTTTACTG 57.927 33.333 2.10 0.00 0.00 2.74
2346 3701 7.086376 TCTGAAGCTTGAATCAATTTTACTGC 58.914 34.615 2.10 0.00 0.00 4.40
2347 3702 6.158598 TGAAGCTTGAATCAATTTTACTGCC 58.841 36.000 2.10 0.00 0.00 4.85
2348 3703 5.726980 AGCTTGAATCAATTTTACTGCCA 57.273 34.783 0.00 0.00 0.00 4.92
2349 3704 6.290294 AGCTTGAATCAATTTTACTGCCAT 57.710 33.333 0.00 0.00 0.00 4.40
2350 3705 6.704310 AGCTTGAATCAATTTTACTGCCATT 58.296 32.000 0.00 0.00 0.00 3.16
2351 3706 7.839907 AGCTTGAATCAATTTTACTGCCATTA 58.160 30.769 0.00 0.00 0.00 1.90
2352 3707 7.977853 AGCTTGAATCAATTTTACTGCCATTAG 59.022 33.333 0.00 0.00 0.00 1.73
2353 3708 7.975616 GCTTGAATCAATTTTACTGCCATTAGA 59.024 33.333 0.00 0.00 0.00 2.10
2354 3709 9.512435 CTTGAATCAATTTTACTGCCATTAGAG 57.488 33.333 0.00 0.00 0.00 2.43
2355 3710 8.806429 TGAATCAATTTTACTGCCATTAGAGA 57.194 30.769 0.00 0.00 0.00 3.10
2356 3711 8.896744 TGAATCAATTTTACTGCCATTAGAGAG 58.103 33.333 0.00 0.00 0.00 3.20
2357 3712 8.814038 AATCAATTTTACTGCCATTAGAGAGT 57.186 30.769 0.00 0.00 0.00 3.24
2358 3713 7.849804 TCAATTTTACTGCCATTAGAGAGTC 57.150 36.000 0.00 0.00 0.00 3.36
2359 3714 6.823689 TCAATTTTACTGCCATTAGAGAGTCC 59.176 38.462 0.00 0.00 0.00 3.85
2360 3715 5.755409 TTTTACTGCCATTAGAGAGTCCA 57.245 39.130 0.00 0.00 0.00 4.02
2361 3716 5.957771 TTTACTGCCATTAGAGAGTCCAT 57.042 39.130 0.00 0.00 0.00 3.41
2362 3717 5.537300 TTACTGCCATTAGAGAGTCCATC 57.463 43.478 0.00 0.00 0.00 3.51
2363 3718 3.652055 ACTGCCATTAGAGAGTCCATCT 58.348 45.455 0.00 0.00 42.61 2.90
2372 3727 1.649321 AGAGTCCATCTCAACCTGCA 58.351 50.000 0.00 0.00 44.98 4.41
2373 3728 1.277557 AGAGTCCATCTCAACCTGCAC 59.722 52.381 0.00 0.00 44.98 4.57
2374 3729 1.277557 GAGTCCATCTCAACCTGCACT 59.722 52.381 0.00 0.00 42.34 4.40
2375 3730 1.002888 AGTCCATCTCAACCTGCACTG 59.997 52.381 0.00 0.00 0.00 3.66
2376 3731 0.325933 TCCATCTCAACCTGCACTGG 59.674 55.000 0.00 0.00 0.00 4.00
2377 3732 1.310933 CCATCTCAACCTGCACTGGC 61.311 60.000 0.00 0.00 41.68 4.85
2393 3748 1.474478 CTGGCAAGTCGCTTCTCTAGA 59.526 52.381 0.00 0.00 41.91 2.43
2399 3754 0.811915 GTCGCTTCTCTAGACTGGCA 59.188 55.000 0.00 0.00 32.58 4.92
2409 3764 5.268387 TCTCTAGACTGGCAGAGAAGAAAT 58.732 41.667 23.66 0.00 43.29 2.17
2453 3808 4.872691 ACAAGCATTTTCTCCTCAGATACG 59.127 41.667 0.00 0.00 0.00 3.06
2468 3823 7.491372 TCCTCAGATACGACATATTGTTGTTTC 59.509 37.037 5.88 7.81 42.03 2.78
2473 3828 9.309516 AGATACGACATATTGTTGTTTCGTTAT 57.690 29.630 5.88 0.00 42.03 1.89
2547 3903 2.955614 ACTTATCTCACGTGGAAACCG 58.044 47.619 17.00 3.59 0.00 4.44
2561 3917 0.106419 AAACCGGGTGCTGAAGGAAA 60.106 50.000 6.32 0.00 0.00 3.13
2589 3945 1.044611 GGCTAGCTCCAGGTAGAAGG 58.955 60.000 15.72 0.00 46.05 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.640029 AGTTACCACGACCAGAAGAAGAA 59.360 43.478 0.00 0.00 0.00 2.52
26 27 2.485426 CGTAGTTACCACGACCAGAAGA 59.515 50.000 0.00 0.00 41.91 2.87
45 46 0.752376 GCTCCTACCAGGTAGAGCGT 60.752 60.000 26.32 0.00 38.29 5.07
93 94 3.961729 CGGAGGAAACCGTTGTCC 58.038 61.111 0.00 5.00 46.70 4.02
539 540 2.484203 GCGACGAACGAGGCTAGT 59.516 61.111 0.00 0.00 45.77 2.57
960 979 0.030908 GACGCCTTTCGATCGAGGAT 59.969 55.000 23.49 12.44 41.67 3.24
1009 1057 0.108851 TCGCTGCTCGCACTAATCAA 60.109 50.000 0.00 0.00 39.08 2.57
1551 1633 2.280797 GCGAACACCACCAGCTCA 60.281 61.111 0.00 0.00 0.00 4.26
1557 1639 2.668550 GGGACAGCGAACACCACC 60.669 66.667 0.00 0.00 0.00 4.61
1661 1833 5.467705 AGTACAGGTTTTGTAGTCACGATC 58.532 41.667 0.00 0.00 41.09 3.69
1720 1903 5.754890 AGAAACAGCAAAATAAAACTGCAGG 59.245 36.000 19.93 0.00 38.58 4.85
1768 1954 8.834465 AGCACAGTTAGCAATTCTTCATAATAG 58.166 33.333 0.00 0.00 0.00 1.73
1854 3204 6.590292 CGTCTTTTAGCTTGTAATTCTGAGGA 59.410 38.462 0.00 0.00 0.00 3.71
1878 3231 1.529826 GGAAGCTAATCAAGTTGCGCG 60.530 52.381 0.00 0.00 0.00 6.86
1892 3245 4.640771 TGACAATTGTCTTAGGGAAGCT 57.359 40.909 32.57 0.00 44.99 3.74
1913 3266 8.997323 TGTCAAGTTTTTGTCAATGTCAAATTT 58.003 25.926 6.50 0.91 35.25 1.82
1932 3285 7.505585 TGAAGAATGGTCCTTTTTATGTCAAGT 59.494 33.333 0.00 0.00 0.00 3.16
1989 3344 4.734398 TCAAAAGTGATGCAACAAACCT 57.266 36.364 0.00 0.00 0.00 3.50
2018 3373 2.965147 TCACTCAACCAGACACAGATGA 59.035 45.455 0.00 0.00 0.00 2.92
2043 3398 6.990798 TGTGATGAACATGATTTTTGGCTTA 58.009 32.000 0.00 0.00 32.36 3.09
2045 3400 5.471556 TGTGATGAACATGATTTTTGGCT 57.528 34.783 0.00 0.00 32.36 4.75
2078 3433 8.725405 TGAGTAATACAAATTTCTATCCGCAA 57.275 30.769 0.00 0.00 0.00 4.85
2079 3434 8.725405 TTGAGTAATACAAATTTCTATCCGCA 57.275 30.769 0.00 0.00 0.00 5.69
2080 3435 9.997482 TTTTGAGTAATACAAATTTCTATCCGC 57.003 29.630 0.00 0.00 37.15 5.54
2090 3445 8.793592 GGACTTGAGGTTTTGAGTAATACAAAT 58.206 33.333 0.00 0.00 37.15 2.32
2091 3446 7.996644 AGGACTTGAGGTTTTGAGTAATACAAA 59.003 33.333 0.00 0.00 35.81 2.83
2092 3447 7.514721 AGGACTTGAGGTTTTGAGTAATACAA 58.485 34.615 0.00 0.00 0.00 2.41
2093 3448 7.074653 AGGACTTGAGGTTTTGAGTAATACA 57.925 36.000 0.00 0.00 0.00 2.29
2094 3449 7.981102 AAGGACTTGAGGTTTTGAGTAATAC 57.019 36.000 0.00 0.00 0.00 1.89
2095 3450 8.653191 TGTAAGGACTTGAGGTTTTGAGTAATA 58.347 33.333 0.00 0.00 0.00 0.98
2096 3451 7.514721 TGTAAGGACTTGAGGTTTTGAGTAAT 58.485 34.615 0.00 0.00 0.00 1.89
2097 3452 6.891388 TGTAAGGACTTGAGGTTTTGAGTAA 58.109 36.000 0.00 0.00 0.00 2.24
2098 3453 6.488769 TGTAAGGACTTGAGGTTTTGAGTA 57.511 37.500 0.00 0.00 0.00 2.59
2099 3454 5.367945 TGTAAGGACTTGAGGTTTTGAGT 57.632 39.130 0.00 0.00 0.00 3.41
2100 3455 6.072452 GGATTGTAAGGACTTGAGGTTTTGAG 60.072 42.308 0.00 0.00 0.00 3.02
2101 3456 5.768164 GGATTGTAAGGACTTGAGGTTTTGA 59.232 40.000 0.00 0.00 0.00 2.69
2102 3457 5.534654 TGGATTGTAAGGACTTGAGGTTTTG 59.465 40.000 0.00 0.00 0.00 2.44
2103 3458 5.701224 TGGATTGTAAGGACTTGAGGTTTT 58.299 37.500 0.00 0.00 0.00 2.43
2104 3459 5.319043 TGGATTGTAAGGACTTGAGGTTT 57.681 39.130 0.00 0.00 0.00 3.27
2105 3460 4.993705 TGGATTGTAAGGACTTGAGGTT 57.006 40.909 0.00 0.00 0.00 3.50
2106 3461 4.383118 CGATGGATTGTAAGGACTTGAGGT 60.383 45.833 0.00 0.00 0.00 3.85
2107 3462 4.122776 CGATGGATTGTAAGGACTTGAGG 58.877 47.826 0.00 0.00 0.00 3.86
2108 3463 3.557595 GCGATGGATTGTAAGGACTTGAG 59.442 47.826 0.00 0.00 0.00 3.02
2109 3464 3.055458 TGCGATGGATTGTAAGGACTTGA 60.055 43.478 0.00 0.00 0.00 3.02
2110 3465 3.270027 TGCGATGGATTGTAAGGACTTG 58.730 45.455 0.00 0.00 0.00 3.16
2111 3466 3.535561 CTGCGATGGATTGTAAGGACTT 58.464 45.455 0.00 0.00 0.00 3.01
2112 3467 2.743183 GCTGCGATGGATTGTAAGGACT 60.743 50.000 0.00 0.00 0.00 3.85
2113 3468 1.599542 GCTGCGATGGATTGTAAGGAC 59.400 52.381 0.00 0.00 0.00 3.85
2114 3469 1.475034 GGCTGCGATGGATTGTAAGGA 60.475 52.381 0.00 0.00 0.00 3.36
2115 3470 0.947244 GGCTGCGATGGATTGTAAGG 59.053 55.000 0.00 0.00 0.00 2.69
2116 3471 1.667236 TGGCTGCGATGGATTGTAAG 58.333 50.000 0.00 0.00 0.00 2.34
2117 3472 2.121291 TTGGCTGCGATGGATTGTAA 57.879 45.000 0.00 0.00 0.00 2.41
2118 3473 2.121291 TTTGGCTGCGATGGATTGTA 57.879 45.000 0.00 0.00 0.00 2.41
2119 3474 1.477553 ATTTGGCTGCGATGGATTGT 58.522 45.000 0.00 0.00 0.00 2.71
2120 3475 2.159212 TGAATTTGGCTGCGATGGATTG 60.159 45.455 0.00 0.00 0.00 2.67
2121 3476 2.101783 TGAATTTGGCTGCGATGGATT 58.898 42.857 0.00 0.00 0.00 3.01
2122 3477 1.766494 TGAATTTGGCTGCGATGGAT 58.234 45.000 0.00 0.00 0.00 3.41
2123 3478 1.543607 TTGAATTTGGCTGCGATGGA 58.456 45.000 0.00 0.00 0.00 3.41
2124 3479 2.264813 CTTTGAATTTGGCTGCGATGG 58.735 47.619 0.00 0.00 0.00 3.51
2125 3480 1.657094 GCTTTGAATTTGGCTGCGATG 59.343 47.619 0.00 0.00 0.00 3.84
2126 3481 1.273048 TGCTTTGAATTTGGCTGCGAT 59.727 42.857 0.00 0.00 0.00 4.58
2127 3482 0.672889 TGCTTTGAATTTGGCTGCGA 59.327 45.000 0.00 0.00 0.00 5.10
2128 3483 1.657094 GATGCTTTGAATTTGGCTGCG 59.343 47.619 0.00 0.00 0.00 5.18
2129 3484 2.671396 CAGATGCTTTGAATTTGGCTGC 59.329 45.455 0.00 0.00 0.00 5.25
2130 3485 3.056393 TCCAGATGCTTTGAATTTGGCTG 60.056 43.478 0.00 0.00 31.02 4.85
2131 3486 3.167485 TCCAGATGCTTTGAATTTGGCT 58.833 40.909 0.00 0.00 31.02 4.75
2132 3487 3.518590 CTCCAGATGCTTTGAATTTGGC 58.481 45.455 0.00 0.00 31.02 4.52
2133 3488 3.512724 ACCTCCAGATGCTTTGAATTTGG 59.487 43.478 0.00 0.00 31.96 3.28
2134 3489 4.381292 GGACCTCCAGATGCTTTGAATTTG 60.381 45.833 0.00 0.00 35.64 2.32
2135 3490 3.766051 GGACCTCCAGATGCTTTGAATTT 59.234 43.478 0.00 0.00 35.64 1.82
2136 3491 3.359950 GGACCTCCAGATGCTTTGAATT 58.640 45.455 0.00 0.00 35.64 2.17
2137 3492 2.357569 GGGACCTCCAGATGCTTTGAAT 60.358 50.000 0.00 0.00 37.91 2.57
2138 3493 1.004745 GGGACCTCCAGATGCTTTGAA 59.995 52.381 0.00 0.00 37.91 2.69
2139 3494 0.620556 GGGACCTCCAGATGCTTTGA 59.379 55.000 0.00 0.00 37.91 2.69
2140 3495 0.745845 CGGGACCTCCAGATGCTTTG 60.746 60.000 0.00 0.00 37.91 2.77
2141 3496 0.909610 TCGGGACCTCCAGATGCTTT 60.910 55.000 0.00 0.00 35.30 3.51
2142 3497 0.909610 TTCGGGACCTCCAGATGCTT 60.910 55.000 0.00 0.00 39.87 3.91
2143 3498 1.306141 TTCGGGACCTCCAGATGCT 60.306 57.895 0.00 0.00 39.87 3.79
2144 3499 1.153349 GTTCGGGACCTCCAGATGC 60.153 63.158 0.00 0.00 39.87 3.91
2145 3500 1.522569 GGTTCGGGACCTCCAGATG 59.477 63.158 0.00 0.00 45.55 2.90
2146 3501 4.051932 GGTTCGGGACCTCCAGAT 57.948 61.111 0.00 0.00 45.55 2.90
2154 3509 1.228154 ACTTGGCTTGGTTCGGGAC 60.228 57.895 0.00 0.00 0.00 4.46
2155 3510 1.072505 GACTTGGCTTGGTTCGGGA 59.927 57.895 0.00 0.00 0.00 5.14
2156 3511 0.609131 ATGACTTGGCTTGGTTCGGG 60.609 55.000 0.00 0.00 0.00 5.14
2157 3512 0.523072 CATGACTTGGCTTGGTTCGG 59.477 55.000 0.00 0.00 0.00 4.30
2158 3513 0.523072 CCATGACTTGGCTTGGTTCG 59.477 55.000 0.00 0.00 39.09 3.95
2168 3523 2.893637 CGAGGGTAGAACCATGACTTG 58.106 52.381 0.00 0.00 41.02 3.16
2169 3524 1.207329 GCGAGGGTAGAACCATGACTT 59.793 52.381 0.00 0.00 41.02 3.01
2170 3525 0.824759 GCGAGGGTAGAACCATGACT 59.175 55.000 0.00 0.00 41.02 3.41
2171 3526 0.824759 AGCGAGGGTAGAACCATGAC 59.175 55.000 0.00 0.00 41.02 3.06
2172 3527 2.029623 GTAGCGAGGGTAGAACCATGA 58.970 52.381 0.00 0.00 41.02 3.07
2173 3528 1.269102 CGTAGCGAGGGTAGAACCATG 60.269 57.143 0.00 0.00 41.02 3.66
2174 3529 1.030457 CGTAGCGAGGGTAGAACCAT 58.970 55.000 0.00 0.00 41.02 3.55
2175 3530 0.035152 TCGTAGCGAGGGTAGAACCA 60.035 55.000 0.00 0.00 41.02 3.67
2176 3531 2.785868 TCGTAGCGAGGGTAGAACC 58.214 57.895 0.00 0.00 37.60 3.62
2186 3541 7.198390 AGTTTAGTATATTTTGCTCGTAGCGA 58.802 34.615 0.00 0.00 46.26 4.93
2187 3542 7.390918 AGTTTAGTATATTTTGCTCGTAGCG 57.609 36.000 3.08 0.00 46.26 4.26
2209 3564 9.095065 CGTAGCCAAAATAAAGTTAGTGATAGT 57.905 33.333 0.00 0.00 0.00 2.12
2210 3565 9.309516 TCGTAGCCAAAATAAAGTTAGTGATAG 57.690 33.333 0.00 0.00 0.00 2.08
2211 3566 9.826574 ATCGTAGCCAAAATAAAGTTAGTGATA 57.173 29.630 0.00 0.00 0.00 2.15
2212 3567 8.732746 ATCGTAGCCAAAATAAAGTTAGTGAT 57.267 30.769 0.00 0.00 0.00 3.06
2213 3568 8.556213 AATCGTAGCCAAAATAAAGTTAGTGA 57.444 30.769 0.00 0.00 0.00 3.41
2218 3573 9.567848 CATGTAAATCGTAGCCAAAATAAAGTT 57.432 29.630 0.00 0.00 0.00 2.66
2219 3574 8.952278 TCATGTAAATCGTAGCCAAAATAAAGT 58.048 29.630 0.00 0.00 0.00 2.66
2220 3575 9.438291 CTCATGTAAATCGTAGCCAAAATAAAG 57.562 33.333 0.00 0.00 0.00 1.85
2221 3576 8.952278 ACTCATGTAAATCGTAGCCAAAATAAA 58.048 29.630 0.00 0.00 0.00 1.40
2222 3577 8.500753 ACTCATGTAAATCGTAGCCAAAATAA 57.499 30.769 0.00 0.00 0.00 1.40
2223 3578 9.602568 TTACTCATGTAAATCGTAGCCAAAATA 57.397 29.630 0.00 0.00 35.90 1.40
2224 3579 8.500753 TTACTCATGTAAATCGTAGCCAAAAT 57.499 30.769 0.00 0.00 35.90 1.82
2225 3580 7.908827 TTACTCATGTAAATCGTAGCCAAAA 57.091 32.000 0.00 0.00 35.90 2.44
2226 3581 9.037737 GTATTACTCATGTAAATCGTAGCCAAA 57.962 33.333 0.00 0.00 41.36 3.28
2227 3582 8.198778 TGTATTACTCATGTAAATCGTAGCCAA 58.801 33.333 0.00 0.00 41.36 4.52
2228 3583 7.718525 TGTATTACTCATGTAAATCGTAGCCA 58.281 34.615 0.00 0.00 41.36 4.75
2229 3584 8.583810 TTGTATTACTCATGTAAATCGTAGCC 57.416 34.615 0.00 0.00 41.36 3.93
2240 3595 8.450964 CCTTCGTGATTTTTGTATTACTCATGT 58.549 33.333 0.00 0.00 0.00 3.21
2241 3596 8.664798 TCCTTCGTGATTTTTGTATTACTCATG 58.335 33.333 0.00 0.00 0.00 3.07
2242 3597 8.786826 TCCTTCGTGATTTTTGTATTACTCAT 57.213 30.769 0.00 0.00 0.00 2.90
2243 3598 8.500773 GTTCCTTCGTGATTTTTGTATTACTCA 58.499 33.333 0.00 0.00 0.00 3.41
2244 3599 8.500773 TGTTCCTTCGTGATTTTTGTATTACTC 58.499 33.333 0.00 0.00 0.00 2.59
2245 3600 8.385898 TGTTCCTTCGTGATTTTTGTATTACT 57.614 30.769 0.00 0.00 0.00 2.24
2246 3601 9.453325 TTTGTTCCTTCGTGATTTTTGTATTAC 57.547 29.630 0.00 0.00 0.00 1.89
2248 3603 8.934507 TTTTGTTCCTTCGTGATTTTTGTATT 57.065 26.923 0.00 0.00 0.00 1.89
2249 3604 8.410141 TCTTTTGTTCCTTCGTGATTTTTGTAT 58.590 29.630 0.00 0.00 0.00 2.29
2250 3605 7.763356 TCTTTTGTTCCTTCGTGATTTTTGTA 58.237 30.769 0.00 0.00 0.00 2.41
2251 3606 6.626302 TCTTTTGTTCCTTCGTGATTTTTGT 58.374 32.000 0.00 0.00 0.00 2.83
2252 3607 7.698836 ATCTTTTGTTCCTTCGTGATTTTTG 57.301 32.000 0.00 0.00 0.00 2.44
2253 3608 9.626045 GATATCTTTTGTTCCTTCGTGATTTTT 57.374 29.630 0.00 0.00 0.00 1.94
2254 3609 9.014297 AGATATCTTTTGTTCCTTCGTGATTTT 57.986 29.630 0.00 0.00 0.00 1.82
2255 3610 8.567285 AGATATCTTTTGTTCCTTCGTGATTT 57.433 30.769 0.00 0.00 0.00 2.17
2256 3611 9.667107 TTAGATATCTTTTGTTCCTTCGTGATT 57.333 29.630 11.25 0.00 0.00 2.57
2257 3612 9.838339 ATTAGATATCTTTTGTTCCTTCGTGAT 57.162 29.630 11.25 0.00 0.00 3.06
2258 3613 9.314321 GATTAGATATCTTTTGTTCCTTCGTGA 57.686 33.333 11.25 0.00 0.00 4.35
2259 3614 9.319143 AGATTAGATATCTTTTGTTCCTTCGTG 57.681 33.333 11.25 0.00 0.00 4.35
2260 3615 9.892130 AAGATTAGATATCTTTTGTTCCTTCGT 57.108 29.630 11.25 0.00 34.99 3.85
2277 3632 8.865090 ACTCGTCCATCATAAAGAAGATTAGAT 58.135 33.333 0.00 0.00 0.00 1.98
2278 3633 8.239038 ACTCGTCCATCATAAAGAAGATTAGA 57.761 34.615 0.00 0.00 0.00 2.10
2279 3634 9.967346 TTACTCGTCCATCATAAAGAAGATTAG 57.033 33.333 0.00 0.00 0.00 1.73
2281 3636 9.099454 GTTTACTCGTCCATCATAAAGAAGATT 57.901 33.333 0.00 0.00 0.00 2.40
2282 3637 7.711339 GGTTTACTCGTCCATCATAAAGAAGAT 59.289 37.037 0.00 0.00 0.00 2.40
2283 3638 7.039882 GGTTTACTCGTCCATCATAAAGAAGA 58.960 38.462 0.00 0.00 0.00 2.87
2284 3639 6.019801 CGGTTTACTCGTCCATCATAAAGAAG 60.020 42.308 0.00 0.00 0.00 2.85
2285 3640 5.808540 CGGTTTACTCGTCCATCATAAAGAA 59.191 40.000 0.00 0.00 0.00 2.52
2286 3641 5.125900 TCGGTTTACTCGTCCATCATAAAGA 59.874 40.000 0.00 0.00 0.00 2.52
2287 3642 5.345702 TCGGTTTACTCGTCCATCATAAAG 58.654 41.667 0.00 0.00 0.00 1.85
2288 3643 5.327616 TCGGTTTACTCGTCCATCATAAA 57.672 39.130 0.00 0.00 0.00 1.40
2289 3644 4.987408 TCGGTTTACTCGTCCATCATAA 57.013 40.909 0.00 0.00 0.00 1.90
2290 3645 4.825634 AGATCGGTTTACTCGTCCATCATA 59.174 41.667 0.00 0.00 0.00 2.15
2291 3646 3.637229 AGATCGGTTTACTCGTCCATCAT 59.363 43.478 0.00 0.00 0.00 2.45
2292 3647 3.021695 AGATCGGTTTACTCGTCCATCA 58.978 45.455 0.00 0.00 0.00 3.07
2293 3648 3.181489 ACAGATCGGTTTACTCGTCCATC 60.181 47.826 0.00 0.00 0.00 3.51
2294 3649 2.758979 ACAGATCGGTTTACTCGTCCAT 59.241 45.455 0.00 0.00 0.00 3.41
2295 3650 2.163010 GACAGATCGGTTTACTCGTCCA 59.837 50.000 0.00 0.00 0.00 4.02
2296 3651 2.790468 CGACAGATCGGTTTACTCGTCC 60.790 54.545 0.00 0.00 44.99 4.79
2297 3652 2.438583 CGACAGATCGGTTTACTCGTC 58.561 52.381 0.00 0.00 44.99 4.20
2298 3653 2.539346 CGACAGATCGGTTTACTCGT 57.461 50.000 0.00 0.00 44.99 4.18
2309 3664 3.435105 AGCTTCAGATGTCGACAGATC 57.565 47.619 24.41 17.05 0.00 2.75
2310 3665 3.194329 TCAAGCTTCAGATGTCGACAGAT 59.806 43.478 24.41 11.86 0.00 2.90
2311 3666 2.558359 TCAAGCTTCAGATGTCGACAGA 59.442 45.455 24.41 12.99 0.00 3.41
2312 3667 2.951726 TCAAGCTTCAGATGTCGACAG 58.048 47.619 24.41 10.66 0.00 3.51
2313 3668 3.385193 TTCAAGCTTCAGATGTCGACA 57.615 42.857 22.48 22.48 0.00 4.35
2314 3669 3.928992 TGATTCAAGCTTCAGATGTCGAC 59.071 43.478 9.11 9.11 0.00 4.20
2315 3670 4.192429 TGATTCAAGCTTCAGATGTCGA 57.808 40.909 0.00 0.00 0.00 4.20
2316 3671 4.934075 TTGATTCAAGCTTCAGATGTCG 57.066 40.909 0.00 0.00 0.00 4.35
2317 3672 9.070149 GTAAAATTGATTCAAGCTTCAGATGTC 57.930 33.333 5.21 0.00 0.00 3.06
2318 3673 8.800332 AGTAAAATTGATTCAAGCTTCAGATGT 58.200 29.630 5.21 0.00 0.00 3.06
2319 3674 9.073368 CAGTAAAATTGATTCAAGCTTCAGATG 57.927 33.333 5.21 0.00 0.00 2.90
2320 3675 7.758528 GCAGTAAAATTGATTCAAGCTTCAGAT 59.241 33.333 5.21 0.00 0.00 2.90
2321 3676 7.086376 GCAGTAAAATTGATTCAAGCTTCAGA 58.914 34.615 5.21 0.00 0.00 3.27
2322 3677 6.309737 GGCAGTAAAATTGATTCAAGCTTCAG 59.690 38.462 5.21 0.00 0.00 3.02
2323 3678 6.158598 GGCAGTAAAATTGATTCAAGCTTCA 58.841 36.000 5.21 0.00 0.00 3.02
2324 3679 6.158598 TGGCAGTAAAATTGATTCAAGCTTC 58.841 36.000 5.21 0.00 0.00 3.86
2325 3680 6.100404 TGGCAGTAAAATTGATTCAAGCTT 57.900 33.333 5.21 0.00 0.00 3.74
2326 3681 5.726980 TGGCAGTAAAATTGATTCAAGCT 57.273 34.783 5.21 0.00 0.00 3.74
2327 3682 6.973229 AATGGCAGTAAAATTGATTCAAGC 57.027 33.333 5.21 1.12 0.00 4.01
2328 3683 9.512435 CTCTAATGGCAGTAAAATTGATTCAAG 57.488 33.333 5.21 0.00 0.00 3.02
2329 3684 9.241919 TCTCTAATGGCAGTAAAATTGATTCAA 57.758 29.630 0.75 0.75 0.00 2.69
2330 3685 8.806429 TCTCTAATGGCAGTAAAATTGATTCA 57.194 30.769 0.00 0.00 0.00 2.57
2331 3686 8.897752 ACTCTCTAATGGCAGTAAAATTGATTC 58.102 33.333 0.00 0.00 0.00 2.52
2332 3687 8.814038 ACTCTCTAATGGCAGTAAAATTGATT 57.186 30.769 0.00 0.00 0.00 2.57
2333 3688 7.500559 GGACTCTCTAATGGCAGTAAAATTGAT 59.499 37.037 0.00 0.00 0.00 2.57
2334 3689 6.823689 GGACTCTCTAATGGCAGTAAAATTGA 59.176 38.462 0.00 0.00 0.00 2.57
2335 3690 6.599244 TGGACTCTCTAATGGCAGTAAAATTG 59.401 38.462 0.00 0.00 0.00 2.32
2336 3691 6.721318 TGGACTCTCTAATGGCAGTAAAATT 58.279 36.000 0.00 0.00 0.00 1.82
2337 3692 6.313519 TGGACTCTCTAATGGCAGTAAAAT 57.686 37.500 0.00 0.00 0.00 1.82
2338 3693 5.755409 TGGACTCTCTAATGGCAGTAAAA 57.245 39.130 0.00 0.00 0.00 1.52
2339 3694 5.663106 AGATGGACTCTCTAATGGCAGTAAA 59.337 40.000 0.00 0.00 0.00 2.01
2340 3695 5.211973 AGATGGACTCTCTAATGGCAGTAA 58.788 41.667 0.00 0.00 0.00 2.24
2341 3696 4.809193 AGATGGACTCTCTAATGGCAGTA 58.191 43.478 0.00 0.00 0.00 2.74
2342 3697 3.640967 GAGATGGACTCTCTAATGGCAGT 59.359 47.826 0.00 0.00 45.97 4.40
2343 3698 4.255833 GAGATGGACTCTCTAATGGCAG 57.744 50.000 0.00 0.00 45.97 4.85
2352 3707 4.941461 AGTGCAGGTTGAGATGGACTCTC 61.941 52.174 0.00 0.00 43.62 3.20
2353 3708 1.277557 GTGCAGGTTGAGATGGACTCT 59.722 52.381 0.00 0.00 45.13 3.24
2354 3709 1.277557 AGTGCAGGTTGAGATGGACTC 59.722 52.381 0.00 0.00 43.62 3.36
2355 3710 1.356124 AGTGCAGGTTGAGATGGACT 58.644 50.000 0.00 0.00 42.45 3.85
2356 3711 1.446907 CAGTGCAGGTTGAGATGGAC 58.553 55.000 0.00 0.00 37.97 4.02
2357 3712 0.325933 CCAGTGCAGGTTGAGATGGA 59.674 55.000 0.00 0.00 0.00 3.41
2358 3713 1.310933 GCCAGTGCAGGTTGAGATGG 61.311 60.000 0.00 0.00 37.47 3.51
2359 3714 0.607217 TGCCAGTGCAGGTTGAGATG 60.607 55.000 0.00 0.00 44.23 2.90
2360 3715 1.763120 TGCCAGTGCAGGTTGAGAT 59.237 52.632 0.00 0.00 44.23 2.75
2361 3716 3.239464 TGCCAGTGCAGGTTGAGA 58.761 55.556 0.00 0.00 44.23 3.27
2376 3731 2.525055 CAGTCTAGAGAAGCGACTTGC 58.475 52.381 0.00 0.00 46.98 4.01
2377 3732 2.733858 GCCAGTCTAGAGAAGCGACTTG 60.734 54.545 0.00 0.00 35.95 3.16
2378 3733 1.474879 GCCAGTCTAGAGAAGCGACTT 59.525 52.381 0.00 0.00 35.95 3.01
2379 3734 1.099689 GCCAGTCTAGAGAAGCGACT 58.900 55.000 0.00 0.00 38.47 4.18
2380 3735 0.811915 TGCCAGTCTAGAGAAGCGAC 59.188 55.000 0.00 0.00 0.00 5.19
2381 3736 1.098869 CTGCCAGTCTAGAGAAGCGA 58.901 55.000 0.00 0.00 0.00 4.93
2382 3737 1.065401 CTCTGCCAGTCTAGAGAAGCG 59.935 57.143 0.00 0.00 42.34 4.68
2383 3738 2.374184 TCTCTGCCAGTCTAGAGAAGC 58.626 52.381 0.00 0.00 44.63 3.86
2393 3748 2.157738 GCACATTTCTTCTCTGCCAGT 58.842 47.619 0.00 0.00 0.00 4.00
2399 3754 2.802816 GTCGTGTGCACATTTCTTCTCT 59.197 45.455 24.69 0.00 0.00 3.10
2409 3764 2.248280 ACCAAATAGTCGTGTGCACA 57.752 45.000 17.42 17.42 0.00 4.57
2473 3828 2.617774 TGTGTGTACTGTACTGCGTACA 59.382 45.455 17.98 16.75 45.20 2.90
2482 3837 8.027189 GTGAGTTAATCATCTGTGTGTACTGTA 58.973 37.037 0.00 0.00 40.92 2.74
2483 3838 6.868864 GTGAGTTAATCATCTGTGTGTACTGT 59.131 38.462 0.00 0.00 40.92 3.55
2484 3839 6.311445 GGTGAGTTAATCATCTGTGTGTACTG 59.689 42.308 0.00 0.00 40.92 2.74
2485 3840 6.398918 GGTGAGTTAATCATCTGTGTGTACT 58.601 40.000 0.00 0.00 40.92 2.73
2486 3841 6.648725 GGTGAGTTAATCATCTGTGTGTAC 57.351 41.667 0.00 0.00 40.92 2.90
2547 3903 2.863809 TCTCTTTTTCCTTCAGCACCC 58.136 47.619 0.00 0.00 0.00 4.61
2561 3917 1.836802 CTGGAGCTAGCCCTTCTCTTT 59.163 52.381 12.13 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.