Multiple sequence alignment - TraesCS3B01G290100

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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 TraesCS3B01G290100 chr3B 100.000 2519 0 0 1 2519 465694663 465697181 0.000000e+00 4652.0
1 TraesCS3B01G290100 chr3B 96.966 857 26 0 599 1455 465657662 465658518 0.000000e+00 1439.0
2 TraesCS3B01G290100 chr3B 89.372 414 16 6 213 598 465657219 465657632 1.740000e-136 496.0
3 TraesCS3B01G290100 chr3B 91.250 240 19 2 2177 2415 465672302 465672540 2.420000e-85 326.0
4 TraesCS3B01G290100 chr3B 85.959 292 28 9 1453 1741 465671485 465671766 1.460000e-77 300.0
5 TraesCS3B01G290100 chr3B 89.041 73 8 0 2100 2172 126919153 126919081 9.600000e-15 91.6
6 TraesCS3B01G290100 chr3A 93.850 1187 51 12 649 1827 478954041 478955213 0.000000e+00 1768.0
7 TraesCS3B01G290100 chr3A 88.825 698 51 16 1825 2519 478955375 478956048 0.000000e+00 832.0
8 TraesCS3B01G290100 chr3A 86.942 582 56 18 23 593 478953346 478953918 9.830000e-179 636.0
9 TraesCS3B01G290100 chr3A 96.825 63 2 0 599 661 478953953 478954015 3.430000e-19 106.0
10 TraesCS3B01G290100 chrUn 96.616 857 29 0 599 1455 339538965 339539821 0.000000e+00 1423.0
11 TraesCS3B01G290100 chrUn 93.023 258 11 1 348 598 339538678 339538935 1.100000e-98 370.0
12 TraesCS3B01G290100 chrUn 84.615 78 12 0 2100 2177 67392775 67392698 7.470000e-11 78.7
13 TraesCS3B01G290100 chr3D 88.312 1232 71 28 827 2051 359527973 359529138 0.000000e+00 1410.0
14 TraesCS3B01G290100 chr3D 93.333 240 15 1 2177 2415 359529151 359529390 1.110000e-93 353.0
15 TraesCS3B01G290100 chr3D 82.079 279 25 10 15 280 359523581 359523847 5.460000e-52 215.0
16 TraesCS3B01G290100 chr3D 96.970 66 2 0 387 452 359527878 359527943 7.370000e-21 111.0
17 TraesCS3B01G290100 chr3D 95.238 42 1 1 2061 2102 563581334 563581374 5.820000e-07 65.8
18 TraesCS3B01G290100 chr6B 82.787 122 9 6 2062 2172 462161594 462161714 5.730000e-17 99.0
19 TraesCS3B01G290100 chr6B 87.342 79 10 0 2441 2519 417237262 417237184 9.600000e-15 91.6
20 TraesCS3B01G290100 chr6B 83.146 89 13 2 2085 2172 611126400 611126487 2.080000e-11 80.5
21 TraesCS3B01G290100 chr5B 87.952 83 10 0 2437 2519 314290348 314290266 5.730000e-17 99.0
22 TraesCS3B01G290100 chr4B 88.462 78 9 0 2100 2177 91056662 91056739 7.420000e-16 95.3
23 TraesCS3B01G290100 chr4D 86.047 86 12 0 2434 2519 116521933 116522018 2.670000e-15 93.5
24 TraesCS3B01G290100 chr5A 86.585 82 11 0 2100 2181 519883110 519883191 9.600000e-15 91.6
25 TraesCS3B01G290100 chr2B 86.747 83 10 1 2100 2181 394938734 394938652 9.600000e-15 91.6
26 TraesCS3B01G290100 chr1B 85.057 87 13 0 2433 2519 561301823 561301909 3.450000e-14 89.8
27 TraesCS3B01G290100 chr6D 85.542 83 12 0 2437 2519 269122120 269122038 1.240000e-13 87.9
28 TraesCS3B01G290100 chr6D 86.301 73 10 0 2100 2172 193447229 193447157 2.080000e-11 80.5
29 TraesCS3B01G290100 chr6D 86.301 73 10 0 2100 2172 431762163 431762091 2.080000e-11 80.5
30 TraesCS3B01G290100 chr7B 83.908 87 14 0 2433 2519 587238819 587238905 1.610000e-12 84.2
31 TraesCS3B01G290100 chr7B 83.908 87 14 0 2433 2519 587428204 587428290 1.610000e-12 84.2
32 TraesCS3B01G290100 chr1D 85.542 83 8 1 2437 2519 415191818 415191896 1.610000e-12 84.2
33 TraesCS3B01G290100 chr5D 81.250 112 10 1 2062 2162 395959104 395959215 2.080000e-11 80.5
34 TraesCS3B01G290100 chr5D 96.970 33 1 0 2067 2099 472570161 472570129 3.500000e-04 56.5


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 TraesCS3B01G290100 chr3B 465694663 465697181 2518 False 4652.000000 4652 100.000000 1 2519 1 chr3B.!!$F1 2518
1 TraesCS3B01G290100 chr3B 465657219 465658518 1299 False 967.500000 1439 93.169000 213 1455 2 chr3B.!!$F2 1242
2 TraesCS3B01G290100 chr3B 465671485 465672540 1055 False 313.000000 326 88.604500 1453 2415 2 chr3B.!!$F3 962
3 TraesCS3B01G290100 chr3A 478953346 478956048 2702 False 835.500000 1768 91.610500 23 2519 4 chr3A.!!$F1 2496
4 TraesCS3B01G290100 chrUn 339538678 339539821 1143 False 896.500000 1423 94.819500 348 1455 2 chrUn.!!$F1 1107
5 TraesCS3B01G290100 chr3D 359527878 359529390 1512 False 624.666667 1410 92.871667 387 2415 3 chr3D.!!$F3 2028

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
292 297 0.812811 CCCGAGTCGTAGGATCGTCA 60.813 60.0 12.31 0.0 34.71 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 2452 0.254462 TGTGTTTGTGAGGGTCTGCA 59.746 50.0 0.0 0.0 0.0 4.41 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
20 21 4.531351 GGCCAGGTTTGCCCTTAA 57.469 55.556 0.00 0.00 42.73 1.85
21 22 2.276869 GGCCAGGTTTGCCCTTAAG 58.723 57.895 0.00 0.00 42.73 1.85
90 93 9.939424 ATACAGAGAATACTACTAAAAGGACCT 57.061 33.333 0.00 0.00 0.00 3.85
94 97 9.994017 AGAGAATACTACTAAAAGGACCTAAGT 57.006 33.333 0.00 1.76 0.00 2.24
99 102 7.868792 ACTACTAAAAGGACCTAAGTTTCCT 57.131 36.000 8.83 0.00 44.69 3.36
120 123 5.674958 TCCTTTTATACCTCCTTATTGCCCT 59.325 40.000 0.00 0.00 0.00 5.19
146 150 6.292150 GGGGATAGCTTATATAATGGCTCAC 58.708 44.000 11.37 7.91 36.40 3.51
147 151 6.126768 GGGGATAGCTTATATAATGGCTCACA 60.127 42.308 11.37 0.00 36.40 3.58
153 157 5.107065 GCTTATATAATGGCTCACAACGGTC 60.107 44.000 0.00 0.00 0.00 4.79
176 180 7.152645 GTCAACAATAGTAAGAGACAAGTCCA 58.847 38.462 0.00 0.00 0.00 4.02
212 216 9.525409 AGTTACACGATGATAAACACTAATACC 57.475 33.333 0.00 0.00 0.00 2.73
213 217 8.758715 GTTACACGATGATAAACACTAATACCC 58.241 37.037 0.00 0.00 0.00 3.69
234 238 4.217550 CCCGACAACAAGTGAAATGGTATT 59.782 41.667 0.00 0.00 0.00 1.89
292 297 0.812811 CCCGAGTCGTAGGATCGTCA 60.813 60.000 12.31 0.00 34.71 4.35
300 305 1.607148 CGTAGGATCGTCATAGTGGCA 59.393 52.381 0.00 0.00 0.00 4.92
363 388 7.740805 AGTTTTCTGAATCCTGAAACTAGTCT 58.259 34.615 0.00 0.00 39.08 3.24
366 391 4.712337 TCTGAATCCTGAAACTAGTCTCCC 59.288 45.833 0.00 0.00 0.00 4.30
477 502 6.611642 TGGAGTTCTAGTTGGCTTACATCTAT 59.388 38.462 0.00 0.00 32.48 1.98
488 514 5.934043 TGGCTTACATCTATCGATTGGATTG 59.066 40.000 1.71 3.76 36.55 2.67
513 539 7.383029 TGTCGAATTTAGTCTTTCGTGTTATGT 59.617 33.333 5.35 0.00 43.81 2.29
572 605 7.648142 TCTTCAGTGTAACATTGTGGAAAATC 58.352 34.615 0.00 0.00 41.43 2.17
589 622 5.124617 GGAAAATCAAGCCTCCTTCACTAAG 59.875 44.000 0.00 0.00 0.00 2.18
665 765 7.048629 TGGCATCAAATCAACTTTCAACTTA 57.951 32.000 0.00 0.00 0.00 2.24
702 802 1.924731 ATCAACTCTCCCGACTCACA 58.075 50.000 0.00 0.00 0.00 3.58
703 803 1.924731 TCAACTCTCCCGACTCACAT 58.075 50.000 0.00 0.00 0.00 3.21
774 874 3.551846 ACCTTCTCGCAAGGAAGAAAAA 58.448 40.909 17.30 0.00 43.12 1.94
1561 1669 2.732289 GGCAAGGCCTTGAGAAACA 58.268 52.632 42.96 0.00 46.69 2.83
1568 1676 2.093447 AGGCCTTGAGAAACATCGTAGG 60.093 50.000 0.00 0.00 0.00 3.18
1570 1678 2.280628 CCTTGAGAAACATCGTAGGGC 58.719 52.381 0.00 0.00 0.00 5.19
1611 1744 4.907582 GGGTCGTTTCGTTAGTTTCATTTG 59.092 41.667 0.00 0.00 0.00 2.32
1612 1745 4.377738 GGTCGTTTCGTTAGTTTCATTTGC 59.622 41.667 0.00 0.00 0.00 3.68
1613 1746 5.202640 GTCGTTTCGTTAGTTTCATTTGCT 58.797 37.500 0.00 0.00 0.00 3.91
1614 1747 5.679792 GTCGTTTCGTTAGTTTCATTTGCTT 59.320 36.000 0.00 0.00 0.00 3.91
1615 1748 5.905181 TCGTTTCGTTAGTTTCATTTGCTTC 59.095 36.000 0.00 0.00 0.00 3.86
1616 1749 5.679355 CGTTTCGTTAGTTTCATTTGCTTCA 59.321 36.000 0.00 0.00 0.00 3.02
1617 1750 6.359617 CGTTTCGTTAGTTTCATTTGCTTCAT 59.640 34.615 0.00 0.00 0.00 2.57
1618 1751 7.408290 CGTTTCGTTAGTTTCATTTGCTTCATC 60.408 37.037 0.00 0.00 0.00 2.92
1619 1752 6.801539 TCGTTAGTTTCATTTGCTTCATCT 57.198 33.333 0.00 0.00 0.00 2.90
1620 1753 7.202016 TCGTTAGTTTCATTTGCTTCATCTT 57.798 32.000 0.00 0.00 0.00 2.40
1621 1754 7.077605 TCGTTAGTTTCATTTGCTTCATCTTG 58.922 34.615 0.00 0.00 0.00 3.02
1622 1755 6.857964 CGTTAGTTTCATTTGCTTCATCTTGT 59.142 34.615 0.00 0.00 0.00 3.16
1623 1756 7.379529 CGTTAGTTTCATTTGCTTCATCTTGTT 59.620 33.333 0.00 0.00 0.00 2.83
1624 1757 9.677567 GTTAGTTTCATTTGCTTCATCTTGTTA 57.322 29.630 0.00 0.00 0.00 2.41
1625 1758 9.677567 TTAGTTTCATTTGCTTCATCTTGTTAC 57.322 29.630 0.00 0.00 0.00 2.50
1626 1759 6.857964 AGTTTCATTTGCTTCATCTTGTTACG 59.142 34.615 0.00 0.00 0.00 3.18
1627 1760 4.722194 TCATTTGCTTCATCTTGTTACGC 58.278 39.130 0.00 0.00 0.00 4.42
1628 1761 2.873170 TTGCTTCATCTTGTTACGCG 57.127 45.000 3.53 3.53 0.00 6.01
1629 1762 0.442310 TGCTTCATCTTGTTACGCGC 59.558 50.000 5.73 0.00 0.00 6.86
1630 1763 0.721718 GCTTCATCTTGTTACGCGCT 59.278 50.000 5.73 0.00 0.00 5.92
1631 1764 1.267087 GCTTCATCTTGTTACGCGCTC 60.267 52.381 5.73 0.00 0.00 5.03
1632 1765 1.324736 CTTCATCTTGTTACGCGCTCC 59.675 52.381 5.73 0.00 0.00 4.70
1633 1766 0.800683 TCATCTTGTTACGCGCTCCG 60.801 55.000 5.73 0.00 44.21 4.63
1711 1869 2.154462 GGAGGTGATGTTCCACTTGTG 58.846 52.381 0.00 0.00 37.24 3.33
1717 1875 1.886542 GATGTTCCACTTGTGGTTCCC 59.113 52.381 18.05 6.72 0.00 3.97
1720 1878 1.407618 GTTCCACTTGTGGTTCCCAAC 59.592 52.381 18.05 11.40 34.18 3.77
1797 2175 1.283736 GTCGTGTTTGTCGGTCTGTT 58.716 50.000 0.00 0.00 0.00 3.16
1813 2192 4.331168 GGTCTGTTGAGATGATAAGTGCAC 59.669 45.833 9.40 9.40 0.00 4.57
1827 2207 6.761242 TGATAAGTGCACTGTTGATACATACC 59.239 38.462 22.49 0.00 32.86 2.73
1908 2452 6.657541 TGTTCTTTTAGGAATACAAAGCGGAT 59.342 34.615 0.00 0.00 0.00 4.18
1911 2455 2.418368 AGGAATACAAAGCGGATGCA 57.582 45.000 0.00 0.00 46.23 3.96
1927 2471 0.254462 TGCAGACCCTCACAAACACA 59.746 50.000 0.00 0.00 0.00 3.72
1934 2478 5.241506 CAGACCCTCACAAACACATACAAAT 59.758 40.000 0.00 0.00 0.00 2.32
1937 2481 6.303839 ACCCTCACAAACACATACAAATACT 58.696 36.000 0.00 0.00 0.00 2.12
1964 2510 1.277326 TGAATACGCTCACGCACATC 58.723 50.000 0.00 0.00 45.53 3.06
1965 2511 1.277326 GAATACGCTCACGCACATCA 58.723 50.000 0.00 0.00 45.53 3.07
1973 2519 2.808202 GCTCACGCACATCATATCCCTT 60.808 50.000 0.00 0.00 35.78 3.95
1974 2520 2.804527 CTCACGCACATCATATCCCTTG 59.195 50.000 0.00 0.00 0.00 3.61
1979 2525 3.990469 CGCACATCATATCCCTTGAGTAC 59.010 47.826 0.00 0.00 0.00 2.73
1998 2544 4.570772 AGTACCGAAATTGATCAATCACGG 59.429 41.667 36.56 36.56 45.49 4.94
2058 2605 5.476599 TCCAACCAATATCTCACCACAAAAG 59.523 40.000 0.00 0.00 0.00 2.27
2064 2611 6.429692 CCAATATCTCACCACAAAAGTGTACA 59.570 38.462 0.00 0.00 35.72 2.90
2070 2617 2.227194 CCACAAAAGTGTACACCCTCC 58.773 52.381 22.28 0.00 35.72 4.30
2071 2618 2.422235 CCACAAAAGTGTACACCCTCCA 60.422 50.000 22.28 0.00 35.72 3.86
2131 2678 8.028938 AGTCATGTTTTAGTGTTAAATGCATCC 58.971 33.333 0.00 0.00 29.82 3.51
2139 2686 8.812147 TTAGTGTTAAATGCATCCGTATCTAG 57.188 34.615 0.00 0.00 0.00 2.43
2140 2687 6.817184 AGTGTTAAATGCATCCGTATCTAGT 58.183 36.000 0.00 0.00 0.00 2.57
2154 2701 8.515695 TCCGTATCTAGTCAAATCTAAGACAA 57.484 34.615 0.00 0.00 37.23 3.18
2155 2702 8.622157 TCCGTATCTAGTCAAATCTAAGACAAG 58.378 37.037 0.00 0.00 37.23 3.16
2156 2703 8.622157 CCGTATCTAGTCAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 37.23 3.02
2167 2714 9.322776 CAAATCTAAGACAAGAATTTTCAGACG 57.677 33.333 0.00 0.00 0.00 4.18
2168 2715 7.602517 ATCTAAGACAAGAATTTTCAGACGG 57.397 36.000 0.00 0.00 0.00 4.79
2169 2716 6.755206 TCTAAGACAAGAATTTTCAGACGGA 58.245 36.000 0.00 0.00 0.00 4.69
2170 2717 5.931441 AAGACAAGAATTTTCAGACGGAG 57.069 39.130 0.00 0.00 0.00 4.63
2171 2718 4.319177 AGACAAGAATTTTCAGACGGAGG 58.681 43.478 0.00 0.00 0.00 4.30
2313 2860 3.821033 GGTCAGTTTGTTTCTATGCACCT 59.179 43.478 0.00 0.00 0.00 4.00
2415 2964 5.416952 ACATGAGCCCAGAGTGAATAAAAAG 59.583 40.000 0.00 0.00 0.00 2.27
2417 2966 5.630121 TGAGCCCAGAGTGAATAAAAAGAA 58.370 37.500 0.00 0.00 0.00 2.52
2418 2967 6.068010 TGAGCCCAGAGTGAATAAAAAGAAA 58.932 36.000 0.00 0.00 0.00 2.52
2419 2968 6.549364 TGAGCCCAGAGTGAATAAAAAGAAAA 59.451 34.615 0.00 0.00 0.00 2.29
2420 2969 7.233348 TGAGCCCAGAGTGAATAAAAAGAAAAT 59.767 33.333 0.00 0.00 0.00 1.82
2450 2999 1.656652 ATTGCGGAGAAAGATGACCG 58.343 50.000 0.00 0.00 46.74 4.79
2451 3000 0.606096 TTGCGGAGAAAGATGACCGA 59.394 50.000 0.00 0.00 46.94 4.69
2499 3048 3.262660 AGAGCATTTGGATGTCTGAGTCA 59.737 43.478 0.00 0.00 35.63 3.41
2510 3059 4.244425 TGTCTGAGTCACTCTTAGCAAC 57.756 45.455 6.33 0.00 30.99 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.897271 TTCCTCATTGCTTAAGGGCA 57.103 45.000 4.29 0.00 40.74 5.36
13 14 4.743057 AAATTCCTCATTGCTTAAGGGC 57.257 40.909 4.29 0.00 0.00 5.19
94 97 6.837048 GGGCAATAAGGAGGTATAAAAGGAAA 59.163 38.462 0.00 0.00 0.00 3.13
99 102 5.399727 CCCAGGGCAATAAGGAGGTATAAAA 60.400 44.000 0.00 0.00 0.00 1.52
101 104 3.655777 CCCAGGGCAATAAGGAGGTATAA 59.344 47.826 0.00 0.00 0.00 0.98
116 119 1.966845 TATAAGCTATCCCCCAGGGC 58.033 55.000 0.00 0.00 43.94 5.19
120 123 5.296966 AGCCATTATATAAGCTATCCCCCA 58.703 41.667 7.30 0.00 32.73 4.96
126 129 6.818644 CCGTTGTGAGCCATTATATAAGCTAT 59.181 38.462 8.72 0.00 35.23 2.97
136 140 2.147958 GTTGACCGTTGTGAGCCATTA 58.852 47.619 0.00 0.00 0.00 1.90
137 141 0.951558 GTTGACCGTTGTGAGCCATT 59.048 50.000 0.00 0.00 0.00 3.16
138 142 0.179032 TGTTGACCGTTGTGAGCCAT 60.179 50.000 0.00 0.00 0.00 4.40
139 143 0.393132 TTGTTGACCGTTGTGAGCCA 60.393 50.000 0.00 0.00 0.00 4.75
146 150 5.924254 TGTCTCTTACTATTGTTGACCGTTG 59.076 40.000 0.00 0.00 0.00 4.10
147 151 6.092955 TGTCTCTTACTATTGTTGACCGTT 57.907 37.500 0.00 0.00 0.00 4.44
153 157 7.155328 ACTGGACTTGTCTCTTACTATTGTTG 58.845 38.462 0.61 0.00 0.00 3.33
176 180 5.386958 TCATCGTGTAACTCAGCTTAACT 57.613 39.130 0.00 0.00 31.75 2.24
193 197 6.210796 TGTCGGGTATTAGTGTTTATCATCG 58.789 40.000 0.00 0.00 0.00 3.84
212 216 5.371115 AATACCATTTCACTTGTTGTCGG 57.629 39.130 0.00 0.00 0.00 4.79
213 217 5.856455 GGAAATACCATTTCACTTGTTGTCG 59.144 40.000 12.34 0.00 38.79 4.35
292 297 1.559682 ACCATTTCGGAGTGCCACTAT 59.440 47.619 0.00 0.00 38.63 2.12
300 305 7.993183 ACTTAAATCATGATACCATTTCGGAGT 59.007 33.333 9.04 3.29 38.63 3.85
366 391 3.001406 AAGGTTCGGACGGGGAGG 61.001 66.667 0.00 0.00 0.00 4.30
477 502 6.338146 AGACTAAATTCGACAATCCAATCGA 58.662 36.000 0.00 0.00 45.17 3.59
513 539 5.013079 ACTTGAAACCAGATACATGAGTCCA 59.987 40.000 0.00 0.00 0.00 4.02
545 578 4.065088 TCCACAATGTTACACTGAAGAGC 58.935 43.478 0.00 0.00 0.00 4.09
572 605 2.479566 TGCTTAGTGAAGGAGGCTTG 57.520 50.000 0.00 0.00 32.84 4.01
637 699 4.039488 TGAAAGTTGATTTGATGCCAAGCT 59.961 37.500 0.00 0.00 33.23 3.74
695 795 3.182967 CGTAGGCTTCTTCATGTGAGTC 58.817 50.000 0.00 0.00 0.00 3.36
723 823 6.140110 TCTAAAGCGAAGAAACCGAAATTTG 58.860 36.000 0.00 0.00 0.00 2.32
774 874 3.003689 CCGTGCTCTGACAAGTGAATTTT 59.996 43.478 0.00 0.00 0.00 1.82
777 877 1.800805 CCGTGCTCTGACAAGTGAAT 58.199 50.000 0.00 0.00 0.00 2.57
1511 1619 4.148838 TGAGGAAACCAACATTTACCCAG 58.851 43.478 0.00 0.00 0.00 4.45
1555 1663 4.546829 TTAACTGCCCTACGATGTTTCT 57.453 40.909 0.00 0.00 0.00 2.52
1556 1664 5.813080 AATTAACTGCCCTACGATGTTTC 57.187 39.130 0.00 0.00 0.00 2.78
1561 1669 4.117685 GACGAAATTAACTGCCCTACGAT 58.882 43.478 0.00 0.00 0.00 3.73
1568 1676 4.638865 ACCCATTAGACGAAATTAACTGCC 59.361 41.667 0.00 0.00 0.00 4.85
1570 1678 5.579511 ACGACCCATTAGACGAAATTAACTG 59.420 40.000 0.00 0.00 0.00 3.16
1611 1744 0.721718 AGCGCGTAACAAGATGAAGC 59.278 50.000 8.43 0.00 0.00 3.86
1612 1745 1.324736 GGAGCGCGTAACAAGATGAAG 59.675 52.381 8.43 0.00 0.00 3.02
1613 1746 1.355971 GGAGCGCGTAACAAGATGAA 58.644 50.000 8.43 0.00 0.00 2.57
1614 1747 0.800683 CGGAGCGCGTAACAAGATGA 60.801 55.000 8.43 0.00 0.00 2.92
1615 1748 1.076533 ACGGAGCGCGTAACAAGATG 61.077 55.000 8.43 0.00 0.00 2.90
1616 1749 0.389426 AACGGAGCGCGTAACAAGAT 60.389 50.000 8.43 0.00 0.00 2.40
1617 1750 1.007038 AACGGAGCGCGTAACAAGA 60.007 52.632 8.43 0.00 0.00 3.02
1618 1751 1.129809 CAACGGAGCGCGTAACAAG 59.870 57.895 8.43 0.00 0.00 3.16
1619 1752 2.945615 GCAACGGAGCGCGTAACAA 61.946 57.895 8.43 0.00 0.00 2.83
1620 1753 2.475098 TAGCAACGGAGCGCGTAACA 62.475 55.000 8.43 0.00 40.15 2.41
1621 1754 1.346378 TTAGCAACGGAGCGCGTAAC 61.346 55.000 8.43 0.00 40.15 2.50
1622 1755 0.458889 ATTAGCAACGGAGCGCGTAA 60.459 50.000 8.43 0.00 40.15 3.18
1623 1756 1.140161 ATTAGCAACGGAGCGCGTA 59.860 52.632 8.43 0.00 40.15 4.42
1624 1757 2.125673 ATTAGCAACGGAGCGCGT 60.126 55.556 8.43 0.00 40.15 6.01
1625 1758 2.321060 CATTAGCAACGGAGCGCG 59.679 61.111 0.00 0.00 40.15 6.86
1626 1759 0.808453 TACCATTAGCAACGGAGCGC 60.808 55.000 0.00 0.00 40.15 5.92
1627 1760 1.647346 TTACCATTAGCAACGGAGCG 58.353 50.000 0.00 0.00 40.15 5.03
1628 1761 4.632538 ATTTTACCATTAGCAACGGAGC 57.367 40.909 0.00 0.00 0.00 4.70
1629 1762 6.537301 TGTCTATTTTACCATTAGCAACGGAG 59.463 38.462 0.00 0.00 0.00 4.63
1630 1763 6.408035 TGTCTATTTTACCATTAGCAACGGA 58.592 36.000 0.00 0.00 0.00 4.69
1631 1764 6.671614 TGTCTATTTTACCATTAGCAACGG 57.328 37.500 0.00 0.00 0.00 4.44
1632 1765 8.064222 CAGATGTCTATTTTACCATTAGCAACG 58.936 37.037 0.00 0.00 0.00 4.10
1633 1766 9.109393 TCAGATGTCTATTTTACCATTAGCAAC 57.891 33.333 0.00 0.00 0.00 4.17
1634 1767 9.330063 CTCAGATGTCTATTTTACCATTAGCAA 57.670 33.333 0.00 0.00 0.00 3.91
1635 1768 8.704668 TCTCAGATGTCTATTTTACCATTAGCA 58.295 33.333 0.00 0.00 0.00 3.49
1711 1869 5.227011 TTGTGAAGACAGATGTTGGGAACC 61.227 45.833 0.00 0.00 41.16 3.62
1717 1875 4.993584 ACTAGCTTGTGAAGACAGATGTTG 59.006 41.667 0.00 0.00 32.26 3.33
1720 1878 6.870965 AGTTAACTAGCTTGTGAAGACAGATG 59.129 38.462 6.26 0.00 32.26 2.90
1797 2175 5.151297 TCAACAGTGCACTTATCATCTCA 57.849 39.130 18.94 0.00 0.00 3.27
1813 2192 4.804139 GTCGAACCTGGTATGTATCAACAG 59.196 45.833 0.00 0.00 39.49 3.16
1827 2207 1.960689 ACCCCAAAAATGTCGAACCTG 59.039 47.619 0.00 0.00 0.00 4.00
1887 2431 5.163663 TGCATCCGCTTTGTATTCCTAAAAG 60.164 40.000 0.00 0.00 39.64 2.27
1897 2441 0.392461 GGGTCTGCATCCGCTTTGTA 60.392 55.000 0.00 0.00 39.64 2.41
1903 2447 2.512515 GTGAGGGTCTGCATCCGC 60.513 66.667 0.00 0.00 39.24 5.54
1908 2452 0.254462 TGTGTTTGTGAGGGTCTGCA 59.746 50.000 0.00 0.00 0.00 4.41
1911 2455 4.431416 TTGTATGTGTTTGTGAGGGTCT 57.569 40.909 0.00 0.00 0.00 3.85
1927 2471 9.649167 GCGTATTCATAAGGGTAGTATTTGTAT 57.351 33.333 0.00 0.00 0.00 2.29
1934 2478 5.049198 CGTGAGCGTATTCATAAGGGTAGTA 60.049 44.000 0.00 0.00 0.00 1.82
1937 2481 4.233123 CGTGAGCGTATTCATAAGGGTA 57.767 45.455 0.00 0.00 0.00 3.69
1964 2510 6.288294 TCAATTTCGGTACTCAAGGGATATG 58.712 40.000 0.00 0.00 0.00 1.78
1965 2511 6.494666 TCAATTTCGGTACTCAAGGGATAT 57.505 37.500 0.00 0.00 0.00 1.63
1973 2519 5.290885 CGTGATTGATCAATTTCGGTACTCA 59.709 40.000 21.57 10.03 38.75 3.41
1974 2520 5.276868 CCGTGATTGATCAATTTCGGTACTC 60.277 44.000 32.91 18.55 39.73 2.59
1979 2525 4.496341 CCTTCCGTGATTGATCAATTTCGG 60.496 45.833 34.13 34.13 42.59 4.30
1998 2544 8.926715 AACATAAACAAAACTTTCAGACCTTC 57.073 30.769 0.00 0.00 0.00 3.46
2025 2571 7.339466 GGTGAGATATTGGTTGGACAATAAGTT 59.661 37.037 3.14 0.00 44.01 2.66
2058 2605 4.563140 TTTTAGGATGGAGGGTGTACAC 57.437 45.455 18.01 18.01 0.00 2.90
2064 2611 7.226059 AGACAATAATTTTAGGATGGAGGGT 57.774 36.000 0.00 0.00 0.00 4.34
2106 2653 7.008266 CGGATGCATTTAACACTAAAACATGAC 59.992 37.037 0.00 0.00 32.32 3.06
2156 2703 9.847224 ACATAATATTACCTCCGTCTGAAAATT 57.153 29.630 0.00 0.00 0.00 1.82
2157 2704 9.847224 AACATAATATTACCTCCGTCTGAAAAT 57.153 29.630 0.00 0.00 0.00 1.82
2158 2705 9.675464 AAACATAATATTACCTCCGTCTGAAAA 57.325 29.630 0.00 0.00 0.00 2.29
2159 2706 9.104965 CAAACATAATATTACCTCCGTCTGAAA 57.895 33.333 0.00 0.00 0.00 2.69
2160 2707 8.479689 TCAAACATAATATTACCTCCGTCTGAA 58.520 33.333 0.00 0.00 0.00 3.02
2161 2708 8.014070 TCAAACATAATATTACCTCCGTCTGA 57.986 34.615 0.00 0.00 0.00 3.27
2162 2709 8.657074 TTCAAACATAATATTACCTCCGTCTG 57.343 34.615 0.00 0.00 0.00 3.51
2163 2710 9.847224 AATTCAAACATAATATTACCTCCGTCT 57.153 29.630 0.00 0.00 0.00 4.18
2290 2837 3.057526 GGTGCATAGAAACAAACTGACCC 60.058 47.826 0.00 0.00 0.00 4.46
2450 2999 0.671781 AGCACGGACATCAAGCACTC 60.672 55.000 0.00 0.00 0.00 3.51
2451 3000 0.608130 TAGCACGGACATCAAGCACT 59.392 50.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.