Multiple sequence alignment - TraesCS6D01G183000

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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 TraesCS6D01G183000 chr6D 100.000 4164 0 0 1 4164 219093127 219088964 0.000000e+00 7690.0
1 TraesCS6D01G183000 chr6D 86.026 229 32 0 3759 3987 186544634 186544862 3.220000e-61 246.0
2 TraesCS6D01G183000 chr6A 96.754 1941 36 13 1771 3709 298563199 298565114 0.000000e+00 3210.0
3 TraesCS6D01G183000 chr6A 94.718 1382 59 5 1 1377 298561307 298562679 0.000000e+00 2135.0
4 TraesCS6D01G183000 chr6A 91.538 390 21 7 3783 4164 298565112 298565497 1.030000e-145 527.0
5 TraesCS6D01G183000 chr6A 97.778 135 0 1 1375 1509 298562936 298563067 3.240000e-56 230.0
6 TraesCS6D01G183000 chr6A 96.053 76 3 0 1514 1589 298563132 298563207 1.570000e-24 124.0
7 TraesCS6D01G183000 chr6B 95.773 1869 60 13 1977 3838 306798848 306800704 0.000000e+00 2996.0
8 TraesCS6D01G183000 chr6B 90.392 1072 39 29 435 1470 306797324 306798367 0.000000e+00 1351.0
9 TraesCS6D01G183000 chr6B 87.699 439 33 3 1 438 306796872 306797290 3.740000e-135 492.0
10 TraesCS6D01G183000 chr6B 83.114 456 43 16 3742 4164 306800688 306801142 6.530000e-103 385.0
11 TraesCS6D01G183000 chr6B 98.565 209 3 0 1771 1979 306798527 306798735 1.830000e-98 370.0
12 TraesCS6D01G183000 chr6B 96.257 187 7 0 1590 1776 627025444 627025258 1.450000e-79 307.0
13 TraesCS6D01G183000 chr6B 94.764 191 8 2 1590 1780 266910875 266910687 3.150000e-76 296.0
14 TraesCS6D01G183000 chr6B 96.053 76 3 0 1514 1589 306798460 306798535 1.570000e-24 124.0
15 TraesCS6D01G183000 chr4D 91.733 375 29 1 1 373 163790493 163790119 1.720000e-143 520.0
16 TraesCS6D01G183000 chr7D 97.268 183 5 0 1590 1772 31996742 31996924 1.120000e-80 311.0
17 TraesCS6D01G183000 chr7D 79.021 286 51 8 3047 3331 369172977 369172700 1.980000e-43 187.0
18 TraesCS6D01G183000 chr7D 100.000 30 0 0 1515 1544 139223391 139223420 5.820000e-04 56.5
19 TraesCS6D01G183000 chr7D 94.444 36 2 0 1516 1551 601407394 601407359 5.820000e-04 56.5
20 TraesCS6D01G183000 chr7D 96.875 32 1 0 1520 1551 601436235 601436204 2.000000e-03 54.7
21 TraesCS6D01G183000 chr1A 97.268 183 5 0 1590 1772 589956633 589956815 1.120000e-80 311.0
22 TraesCS6D01G183000 chr1A 93.909 197 11 1 1582 1778 540673019 540673214 3.150000e-76 296.0
23 TraesCS6D01G183000 chr1A 85.232 237 34 1 3751 3987 64940188 64940423 4.160000e-60 243.0
24 TraesCS6D01G183000 chr1A 89.394 66 4 2 3602 3664 210720886 210720951 3.450000e-11 80.5
25 TraesCS6D01G183000 chr3B 94.819 193 10 0 1581 1773 255299238 255299430 6.770000e-78 302.0
26 TraesCS6D01G183000 chr5B 94.301 193 11 0 1581 1773 328653792 328653984 3.150000e-76 296.0
27 TraesCS6D01G183000 chr5B 87.773 229 28 0 3759 3987 217916213 217916441 6.860000e-68 268.0
28 TraesCS6D01G183000 chr1D 92.308 208 14 2 1577 1783 470861943 470861737 1.130000e-75 294.0
29 TraesCS6D01G183000 chr3D 92.611 203 13 2 1576 1778 533955502 533955702 1.460000e-74 291.0
30 TraesCS6D01G183000 chr3D 98.734 79 1 0 1140 1218 24745358 24745436 1.560000e-29 141.0
31 TraesCS6D01G183000 chr3D 98.551 69 1 0 1150 1218 306007134 306007202 5.650000e-24 122.0
32 TraesCS6D01G183000 chr2B 88.646 229 25 1 3762 3990 114506289 114506062 1.140000e-70 278.0
33 TraesCS6D01G183000 chr2B 86.885 61 6 1 3602 3660 360045469 360045409 2.690000e-07 67.6
34 TraesCS6D01G183000 chr7B 88.261 230 27 0 3758 3987 290835542 290835771 4.100000e-70 276.0
35 TraesCS6D01G183000 chr7B 87.013 231 30 0 3758 3988 290731952 290732182 1.150000e-65 261.0
36 TraesCS6D01G183000 chr7B 94.444 36 2 0 1516 1551 680523255 680523220 5.820000e-04 56.5
37 TraesCS6D01G183000 chr7B 94.286 35 2 0 1516 1550 680523671 680523637 2.000000e-03 54.7
38 TraesCS6D01G183000 chr5D 86.937 222 29 0 3766 3987 449668348 449668569 2.490000e-62 250.0
39 TraesCS6D01G183000 chr5D 96.875 32 1 0 1511 1542 509138213 509138244 2.000000e-03 54.7
40 TraesCS6D01G183000 chrUn 97.436 78 2 0 1141 1218 389316159 389316236 2.610000e-27 134.0
41 TraesCS6D01G183000 chrUn 98.667 75 1 0 1144 1218 389367731 389367657 2.610000e-27 134.0
42 TraesCS6D01G183000 chr4A 98.667 75 1 0 1144 1218 605364661 605364587 2.610000e-27 134.0
43 TraesCS6D01G183000 chr2A 89.394 66 4 2 3602 3664 328923090 328923155 3.450000e-11 80.5
44 TraesCS6D01G183000 chr2A 89.394 66 4 2 3602 3664 328926136 328926201 3.450000e-11 80.5
45 TraesCS6D01G183000 chr3A 90.164 61 4 1 3602 3660 291939650 291939710 1.240000e-10 78.7
46 TraesCS6D01G183000 chr7A 86.364 66 4 4 3602 3664 288829676 288829739 2.690000e-07 67.6
47 TraesCS6D01G183000 chr7A 94.444 36 2 0 1516 1551 693184165 693184130 5.820000e-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 TraesCS6D01G183000 chr6D 219088964 219093127 4163 True 7690.0 7690 100.000000 1 4164 1 chr6D.!!$R1 4163
1 TraesCS6D01G183000 chr6A 298561307 298565497 4190 False 1245.2 3210 95.368200 1 4164 5 chr6A.!!$F1 4163
2 TraesCS6D01G183000 chr6B 306796872 306801142 4270 False 953.0 2996 91.932667 1 4164 6 chr6B.!!$F1 4163

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
531 570 0.037975 GGTTGTCCTTGCCATGCTTG 60.038 55.0 0.00 0.0 0.00 4.01 F
749 819 1.347320 CCGGAAAGACGCTCAGTTAC 58.653 55.0 0.00 0.0 0.00 2.50 F
1771 2185 0.178903 TGTGTCCTAGGCAGACCCTT 60.179 55.0 2.96 0.0 43.06 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1751 2165 0.043334 AGGGTCTGCCTAGGACACAT 59.957 55.000 14.75 0.0 39.36 3.21 R
1777 2191 0.175073 GTCGTGGATCTAGCGGGTTT 59.825 55.000 0.00 0.0 0.00 3.27 R
3367 3897 4.393062 CGTCATTACTGCAAGGTTCATCTT 59.607 41.667 0.00 0.0 39.30 2.40 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
77 78 5.187381 TGGCATCAATGAAAATTCAAGGCTA 59.813 36.000 0.00 0.00 41.13 3.93
198 200 2.530151 AGCTGCACCTTGAGGGGA 60.530 61.111 2.79 0.00 42.67 4.81
202 204 1.928868 CTGCACCTTGAGGGGAAAAT 58.071 50.000 2.79 0.00 42.67 1.82
231 233 4.452733 AAGTAGGCGGCGACTGGC 62.453 66.667 28.54 18.31 42.51 4.85
242 244 2.087009 CGACTGGCCGAAGACGAAC 61.087 63.158 8.87 0.00 42.66 3.95
251 253 1.466167 CCGAAGACGAACGAGTCCTTA 59.534 52.381 0.14 0.00 41.83 2.69
288 290 2.235016 GATGATAGAGGACTGCTCCGT 58.765 52.381 0.00 0.00 42.22 4.69
316 318 1.202879 TGTGAGCCAAAAGGGAACGAT 60.203 47.619 0.00 0.00 40.01 3.73
438 477 1.560860 GCTGTGATCCGATTAGGCGC 61.561 60.000 0.00 0.00 40.77 6.53
477 516 1.202348 CGAGATCATGAGCGACTGGTT 60.202 52.381 5.12 0.00 0.00 3.67
504 543 1.095600 GGATGAAGAAACGGAAGGGC 58.904 55.000 0.00 0.00 0.00 5.19
505 544 1.095600 GATGAAGAAACGGAAGGGCC 58.904 55.000 0.00 0.00 0.00 5.80
523 562 0.804989 CCGAATGAGGTTGTCCTTGC 59.195 55.000 0.00 0.00 45.24 4.01
531 570 0.037975 GGTTGTCCTTGCCATGCTTG 60.038 55.000 0.00 0.00 0.00 4.01
623 662 1.741327 GCGGCCCACTACGGATTCTA 61.741 60.000 0.00 0.00 36.56 2.10
702 741 2.425143 TCATCCCAAACTGCTGATCC 57.575 50.000 0.00 0.00 0.00 3.36
708 747 2.242043 CCAAACTGCTGATCCAAAGGT 58.758 47.619 0.00 0.00 0.00 3.50
731 801 3.696051 TGAAAATGCTAACTGAGATGGCC 59.304 43.478 0.00 0.00 0.00 5.36
749 819 1.347320 CCGGAAAGACGCTCAGTTAC 58.653 55.000 0.00 0.00 0.00 2.50
1261 1335 9.452287 CATCAAATCAAAATTCCCCTTATTTGT 57.548 29.630 0.00 0.00 35.43 2.83
1295 1369 3.156293 TGATGGAATGACAGGGTTGTTG 58.844 45.455 0.00 0.00 37.76 3.33
1510 1864 9.851686 ACTACATCTTTTGGAATGCTTATATCA 57.148 29.630 0.00 0.00 0.00 2.15
1518 1932 7.946655 TTGGAATGCTTATATCACTAAGACG 57.053 36.000 0.00 0.00 31.58 4.18
1531 1945 5.741011 TCACTAAGACGCTTATTTTGGGAT 58.259 37.500 0.79 0.00 0.00 3.85
1597 2011 9.836076 AAACTTAGTTTACAAGAACAGTTTGTC 57.164 29.630 8.76 0.00 39.36 3.18
1598 2012 8.788325 ACTTAGTTTACAAGAACAGTTTGTCT 57.212 30.769 0.00 0.00 39.36 3.41
1599 2013 9.880157 ACTTAGTTTACAAGAACAGTTTGTCTA 57.120 29.630 0.00 0.00 39.36 2.59
1604 2018 9.997482 GTTTACAAGAACAGTTTGTCTAATTCA 57.003 29.630 0.00 0.00 39.36 2.57
1605 2019 9.997482 TTTACAAGAACAGTTTGTCTAATTCAC 57.003 29.630 0.00 0.00 39.36 3.18
1606 2020 7.624360 ACAAGAACAGTTTGTCTAATTCACA 57.376 32.000 0.00 0.00 33.72 3.58
1607 2021 8.225603 ACAAGAACAGTTTGTCTAATTCACAT 57.774 30.769 0.00 0.00 33.72 3.21
1608 2022 8.345565 ACAAGAACAGTTTGTCTAATTCACATC 58.654 33.333 0.00 0.00 33.72 3.06
1609 2023 8.562892 CAAGAACAGTTTGTCTAATTCACATCT 58.437 33.333 0.00 0.00 0.00 2.90
1610 2024 9.778741 AAGAACAGTTTGTCTAATTCACATCTA 57.221 29.630 0.00 0.00 0.00 1.98
1611 2025 9.429359 AGAACAGTTTGTCTAATTCACATCTAG 57.571 33.333 0.00 0.00 0.00 2.43
1612 2026 9.424319 GAACAGTTTGTCTAATTCACATCTAGA 57.576 33.333 0.00 0.00 0.00 2.43
1613 2027 9.950496 AACAGTTTGTCTAATTCACATCTAGAT 57.050 29.630 0.00 0.00 0.00 1.98
1614 2028 9.376075 ACAGTTTGTCTAATTCACATCTAGATG 57.624 33.333 27.63 27.63 44.15 2.90
1641 2055 7.849804 TTTTAAGGATGTCACATCTAAGCTC 57.150 36.000 17.46 0.00 0.00 4.09
1642 2056 4.414337 AAGGATGTCACATCTAAGCTCC 57.586 45.455 17.46 0.18 0.00 4.70
1643 2057 3.652055 AGGATGTCACATCTAAGCTCCT 58.348 45.455 17.46 2.78 0.00 3.69
1644 2058 4.809193 AGGATGTCACATCTAAGCTCCTA 58.191 43.478 17.46 0.00 30.26 2.94
1645 2059 4.586841 AGGATGTCACATCTAAGCTCCTAC 59.413 45.833 17.46 0.00 30.26 3.18
1646 2060 4.342378 GGATGTCACATCTAAGCTCCTACA 59.658 45.833 17.46 0.00 0.00 2.74
1647 2061 5.163405 GGATGTCACATCTAAGCTCCTACAA 60.163 44.000 17.46 0.00 0.00 2.41
1648 2062 5.330455 TGTCACATCTAAGCTCCTACAAG 57.670 43.478 0.00 0.00 0.00 3.16
1649 2063 4.772624 TGTCACATCTAAGCTCCTACAAGT 59.227 41.667 0.00 0.00 0.00 3.16
1650 2064 5.949952 TGTCACATCTAAGCTCCTACAAGTA 59.050 40.000 0.00 0.00 0.00 2.24
1651 2065 6.607600 TGTCACATCTAAGCTCCTACAAGTAT 59.392 38.462 0.00 0.00 0.00 2.12
1652 2066 7.778382 TGTCACATCTAAGCTCCTACAAGTATA 59.222 37.037 0.00 0.00 0.00 1.47
1653 2067 8.798402 GTCACATCTAAGCTCCTACAAGTATAT 58.202 37.037 0.00 0.00 0.00 0.86
1662 2076 8.651589 AGCTCCTACAAGTATATAATGTAGCA 57.348 34.615 21.13 12.51 43.21 3.49
1663 2077 9.090103 AGCTCCTACAAGTATATAATGTAGCAA 57.910 33.333 21.13 14.44 43.21 3.91
1664 2078 9.141400 GCTCCTACAAGTATATAATGTAGCAAC 57.859 37.037 21.13 13.24 43.21 4.17
1680 2094 9.816354 AATGTAGCAACAAGAAATAACAAAACT 57.184 25.926 0.00 0.00 39.58 2.66
1682 2096 9.944663 TGTAGCAACAAGAAATAACAAAACTAG 57.055 29.630 0.00 0.00 30.91 2.57
1683 2097 9.394477 GTAGCAACAAGAAATAACAAAACTAGG 57.606 33.333 0.00 0.00 0.00 3.02
1684 2098 8.232913 AGCAACAAGAAATAACAAAACTAGGA 57.767 30.769 0.00 0.00 0.00 2.94
1685 2099 8.860088 AGCAACAAGAAATAACAAAACTAGGAT 58.140 29.630 0.00 0.00 0.00 3.24
1720 2134 2.225019 CACAAACAGAGTGGACATCAGC 59.775 50.000 0.00 0.00 33.43 4.26
1721 2135 2.105477 ACAAACAGAGTGGACATCAGCT 59.895 45.455 0.00 0.00 0.00 4.24
1722 2136 3.144506 CAAACAGAGTGGACATCAGCTT 58.855 45.455 0.00 0.00 0.00 3.74
1723 2137 4.202357 ACAAACAGAGTGGACATCAGCTTA 60.202 41.667 0.00 0.00 0.00 3.09
1724 2138 3.883830 ACAGAGTGGACATCAGCTTAG 57.116 47.619 0.00 0.00 0.00 2.18
1725 2139 3.435275 ACAGAGTGGACATCAGCTTAGA 58.565 45.455 0.00 0.00 0.00 2.10
1726 2140 4.029520 ACAGAGTGGACATCAGCTTAGAT 58.970 43.478 0.00 0.00 0.00 1.98
1740 2154 8.923683 CATCAGCTTAGATGTGACATAACTATG 58.076 37.037 0.00 0.92 40.35 2.23
1765 2179 4.517952 CATCTAGATGTGTCCTAGGCAG 57.482 50.000 22.42 0.00 35.50 4.85
1766 2180 3.953542 TCTAGATGTGTCCTAGGCAGA 57.046 47.619 2.96 4.66 35.50 4.26
1767 2181 3.556999 TCTAGATGTGTCCTAGGCAGAC 58.443 50.000 2.96 2.81 35.50 3.51
1768 2182 1.490574 AGATGTGTCCTAGGCAGACC 58.509 55.000 2.96 0.00 33.09 3.85
1769 2183 0.466124 GATGTGTCCTAGGCAGACCC 59.534 60.000 2.96 0.00 36.11 4.46
1771 2185 0.178903 TGTGTCCTAGGCAGACCCTT 60.179 55.000 2.96 0.00 43.06 3.95
1772 2186 1.078159 TGTGTCCTAGGCAGACCCTTA 59.922 52.381 2.96 0.00 43.06 2.69
1773 2187 1.481363 GTGTCCTAGGCAGACCCTTAC 59.519 57.143 2.96 0.00 43.06 2.34
1774 2188 1.078159 TGTCCTAGGCAGACCCTTACA 59.922 52.381 2.96 0.00 43.06 2.41
1775 2189 2.185387 GTCCTAGGCAGACCCTTACAA 58.815 52.381 2.96 0.00 43.06 2.41
1776 2190 2.168728 GTCCTAGGCAGACCCTTACAAG 59.831 54.545 2.96 0.00 43.06 3.16
1777 2191 2.043939 TCCTAGGCAGACCCTTACAAGA 59.956 50.000 2.96 0.00 43.06 3.02
1778 2192 2.838202 CCTAGGCAGACCCTTACAAGAA 59.162 50.000 0.00 0.00 43.06 2.52
1863 2277 4.563580 GCCCAGAGACAATACAAGACTTCA 60.564 45.833 0.00 0.00 0.00 3.02
2191 2721 3.243839 TGCAAATGGCCTTTTGAGTTCTC 60.244 43.478 35.84 22.12 43.89 2.87
2257 2787 5.335191 CCAAAGACAATGAAGCAACTCTACC 60.335 44.000 0.00 0.00 0.00 3.18
2553 3083 2.175878 ACAGGATTATCCAGCGATGC 57.824 50.000 14.30 0.00 39.61 3.91
2565 3095 8.703604 TTATCCAGCGATGCTTATAGAATAAC 57.296 34.615 0.00 0.00 36.40 1.89
2766 3296 4.877823 TCAACTATCTGGCACATAAGCAAG 59.122 41.667 0.00 0.00 38.20 4.01
3185 3715 1.107114 TTGGGCAATTTGACGTGTGT 58.893 45.000 0.00 0.00 0.00 3.72
3350 3880 3.252400 TGCTTTGTTGTTCTTTGCTGTG 58.748 40.909 0.00 0.00 0.00 3.66
3367 3897 6.769134 TGCTGTGTACTAAGAGTTATAGCA 57.231 37.500 9.38 9.38 36.64 3.49
3406 3936 7.116948 CAGTAATGACGATCAGATCAAATACCC 59.883 40.741 11.12 0.00 0.00 3.69
3462 3992 7.755373 GGACATCTTTATTCGATCGATATGTCA 59.245 37.037 29.64 16.68 41.40 3.58
3503 4033 6.680810 CATAACACAGACAAACATCCAACAT 58.319 36.000 0.00 0.00 0.00 2.71
3670 4206 5.961396 ATCTGACTACAACGTGTCTTAGT 57.039 39.130 5.49 2.58 34.57 2.24
3707 4243 5.892568 ACTCTAAGAAGTTATTGATCGCGT 58.107 37.500 5.77 0.00 0.00 6.01
3713 4249 1.404391 AGTTATTGATCGCGTCGGAGT 59.596 47.619 5.77 0.00 0.00 3.85
3720 4256 1.197036 GATCGCGTCGGAGTATGATCA 59.803 52.381 5.77 0.00 34.00 2.92
3722 4258 1.121240 CGCGTCGGAGTATGATCAAC 58.879 55.000 0.00 0.00 0.00 3.18
3724 4260 1.067212 GCGTCGGAGTATGATCAACCT 59.933 52.381 0.00 0.00 0.00 3.50
3725 4261 2.292569 GCGTCGGAGTATGATCAACCTA 59.707 50.000 0.00 0.00 0.00 3.08
3727 4263 4.558898 GCGTCGGAGTATGATCAACCTAAT 60.559 45.833 0.00 0.00 0.00 1.73
3745 4281 9.965824 CAACCTAATGAAGAACAAACAATAACT 57.034 29.630 0.00 0.00 0.00 2.24
3853 4470 7.325821 ACAATACGTTAATGCATGTCAACAAAG 59.674 33.333 0.00 0.00 0.00 2.77
3864 4481 7.630026 TGCATGTCAACAAAGATTATATCGTC 58.370 34.615 0.00 0.00 0.00 4.20
3870 4487 8.548721 GTCAACAAAGATTATATCGTCGGATTT 58.451 33.333 0.00 0.00 34.00 2.17
3973 4591 5.698741 TGACATGGAATACAATGAGGACT 57.301 39.130 0.00 0.00 0.00 3.85
3983 4601 9.057089 GGAATACAATGAGGACTAATAAACCAG 57.943 37.037 0.00 0.00 0.00 4.00
4040 4693 9.005777 ACGAGATTGATCTACTTCTATAAGACC 57.994 37.037 0.00 0.00 37.25 3.85
4041 4694 9.226606 CGAGATTGATCTACTTCTATAAGACCT 57.773 37.037 0.00 0.00 37.25 3.85
4097 4750 1.138661 CCCAAGGCAGCAAAACTCAAA 59.861 47.619 0.00 0.00 0.00 2.69
4106 4759 3.058914 CAGCAAAACTCAAACCTAGGTCG 60.059 47.826 16.64 10.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.094494 CAGAGTTGCAGGTACATCTCGT 60.094 50.000 0.00 0.00 40.03 4.18
50 51 3.513662 TGAATTTTCATTGATGCCAGCG 58.486 40.909 0.00 0.00 31.01 5.18
77 78 0.179100 CGTGCCATTCTCGATCTGGT 60.179 55.000 9.11 0.00 33.89 4.00
124 126 0.904649 AAGAGCGACATCCCACATCA 59.095 50.000 0.00 0.00 0.00 3.07
127 129 3.055458 TGATTTAAGAGCGACATCCCACA 60.055 43.478 0.00 0.00 0.00 4.17
198 200 4.382793 GCCTACTTCCGTCTCCTGTATTTT 60.383 45.833 0.00 0.00 0.00 1.82
202 204 1.760192 GCCTACTTCCGTCTCCTGTA 58.240 55.000 0.00 0.00 0.00 2.74
231 233 0.240411 AAGGACTCGTTCGTCTTCGG 59.760 55.000 0.00 0.00 37.69 4.30
242 244 0.797249 CTTCGTGGCGTAAGGACTCG 60.797 60.000 0.00 0.00 41.91 4.18
251 253 1.686325 ATCCCTATGCTTCGTGGCGT 61.686 55.000 3.14 3.14 35.47 5.68
288 290 2.517959 CTTTTGGCTCACATCCCTTCA 58.482 47.619 0.00 0.00 0.00 3.02
316 318 0.031716 CCTCCTCCTGGTCATCTCCA 60.032 60.000 0.00 0.00 36.00 3.86
341 343 1.980772 CCGTTCCCGTGGGTAGAGT 60.981 63.158 4.53 0.00 36.47 3.24
438 477 2.028476 TCGTGATTAGGGTTGTGTCTGG 60.028 50.000 0.00 0.00 0.00 3.86
477 516 1.879380 CGTTTCTTCATCCTTGCCACA 59.121 47.619 0.00 0.00 0.00 4.17
523 562 3.980775 CGGAAAAAGTACAACAAGCATGG 59.019 43.478 0.00 0.00 0.00 3.66
531 570 1.268625 CCCAGCCGGAAAAAGTACAAC 59.731 52.381 5.05 0.00 0.00 3.32
623 662 3.635373 TCACTTCGTTAGCTATCCCGAAT 59.365 43.478 18.02 9.82 38.48 3.34
663 702 4.340617 TGATTTTGGCCGTTAGATTTCCT 58.659 39.130 0.00 0.00 0.00 3.36
702 741 6.738114 TCTCAGTTAGCATTTTCAACCTTTG 58.262 36.000 0.00 0.00 0.00 2.77
708 747 4.158394 GGCCATCTCAGTTAGCATTTTCAA 59.842 41.667 0.00 0.00 0.00 2.69
731 801 2.060326 TGTAACTGAGCGTCTTTCCG 57.940 50.000 0.00 0.00 0.00 4.30
769 839 4.450976 CGGTCAAATCACTATTCCATGGA 58.549 43.478 11.44 11.44 0.00 3.41
1261 1335 6.266330 TGTCATTCCATCAATTTTGTACACCA 59.734 34.615 0.00 0.00 0.00 4.17
1295 1369 5.061920 AGCAGCAAGTACAGTACTAACTC 57.938 43.478 13.87 8.33 38.26 3.01
1486 1840 9.851686 AGTGATATAAGCATTCCAAAAGATGTA 57.148 29.630 0.00 0.00 0.00 2.29
1487 1841 8.757982 AGTGATATAAGCATTCCAAAAGATGT 57.242 30.769 0.00 0.00 0.00 3.06
1509 1863 5.220854 CCATCCCAAAATAAGCGTCTTAGTG 60.221 44.000 5.72 4.27 0.00 2.74
1510 1864 4.881850 CCATCCCAAAATAAGCGTCTTAGT 59.118 41.667 5.72 0.92 0.00 2.24
1518 1932 3.225940 CTCCCTCCATCCCAAAATAAGC 58.774 50.000 0.00 0.00 0.00 3.09
1531 1945 5.432390 AGATGTTAGTCTAGTACTCCCTCCA 59.568 44.000 0.00 0.00 39.80 3.86
1616 2030 7.336931 GGAGCTTAGATGTGACATCCTTAAAAA 59.663 37.037 21.05 6.46 0.00 1.94
1617 2031 6.823689 GGAGCTTAGATGTGACATCCTTAAAA 59.176 38.462 21.05 8.00 0.00 1.52
1618 2032 6.156949 AGGAGCTTAGATGTGACATCCTTAAA 59.843 38.462 21.05 10.18 31.97 1.52
1619 2033 5.663106 AGGAGCTTAGATGTGACATCCTTAA 59.337 40.000 21.05 13.11 31.97 1.85
1620 2034 5.211973 AGGAGCTTAGATGTGACATCCTTA 58.788 41.667 21.05 6.22 31.97 2.69
1621 2035 4.036518 AGGAGCTTAGATGTGACATCCTT 58.963 43.478 21.05 7.22 31.97 3.36
1622 2036 3.652055 AGGAGCTTAGATGTGACATCCT 58.348 45.455 21.05 11.37 0.00 3.24
1623 2037 4.342378 TGTAGGAGCTTAGATGTGACATCC 59.658 45.833 21.05 6.49 0.00 3.51
1624 2038 5.521906 TGTAGGAGCTTAGATGTGACATC 57.478 43.478 17.46 17.46 0.00 3.06
1625 2039 5.423610 ACTTGTAGGAGCTTAGATGTGACAT 59.576 40.000 0.00 0.00 0.00 3.06
1626 2040 4.772624 ACTTGTAGGAGCTTAGATGTGACA 59.227 41.667 0.00 0.00 0.00 3.58
1627 2041 5.331876 ACTTGTAGGAGCTTAGATGTGAC 57.668 43.478 0.00 0.00 0.00 3.67
1628 2042 8.941995 ATATACTTGTAGGAGCTTAGATGTGA 57.058 34.615 0.00 0.00 0.00 3.58
1636 2050 9.090103 TGCTACATTATATACTTGTAGGAGCTT 57.910 33.333 22.07 0.00 41.89 3.74
1637 2051 8.651589 TGCTACATTATATACTTGTAGGAGCT 57.348 34.615 22.07 0.00 41.89 4.09
1638 2052 9.141400 GTTGCTACATTATATACTTGTAGGAGC 57.859 37.037 22.07 19.41 42.61 4.70
1654 2068 9.816354 AGTTTTGTTATTTCTTGTTGCTACATT 57.184 25.926 0.81 0.00 33.44 2.71
1656 2070 9.944663 CTAGTTTTGTTATTTCTTGTTGCTACA 57.055 29.630 0.00 0.00 0.00 2.74
1657 2071 9.394477 CCTAGTTTTGTTATTTCTTGTTGCTAC 57.606 33.333 0.00 0.00 0.00 3.58
1658 2072 9.344772 TCCTAGTTTTGTTATTTCTTGTTGCTA 57.655 29.630 0.00 0.00 0.00 3.49
1659 2073 8.232913 TCCTAGTTTTGTTATTTCTTGTTGCT 57.767 30.769 0.00 0.00 0.00 3.91
1699 2113 2.225019 GCTGATGTCCACTCTGTTTGTG 59.775 50.000 0.00 0.00 35.39 3.33
1700 2114 2.105477 AGCTGATGTCCACTCTGTTTGT 59.895 45.455 0.00 0.00 0.00 2.83
1701 2115 2.775890 AGCTGATGTCCACTCTGTTTG 58.224 47.619 0.00 0.00 0.00 2.93
1702 2116 3.498774 AAGCTGATGTCCACTCTGTTT 57.501 42.857 0.00 0.00 0.00 2.83
1703 2117 3.834813 TCTAAGCTGATGTCCACTCTGTT 59.165 43.478 0.00 0.00 0.00 3.16
1704 2118 3.435275 TCTAAGCTGATGTCCACTCTGT 58.565 45.455 0.00 0.00 0.00 3.41
1705 2119 4.370049 CATCTAAGCTGATGTCCACTCTG 58.630 47.826 5.99 0.00 39.05 3.35
1706 2120 4.669206 CATCTAAGCTGATGTCCACTCT 57.331 45.455 5.99 0.00 39.05 3.24
1714 2128 8.923683 CATAGTTATGTCACATCTAAGCTGATG 58.076 37.037 11.48 11.48 46.61 3.07
1715 2129 8.646004 ACATAGTTATGTCACATCTAAGCTGAT 58.354 33.333 0.00 0.00 42.96 2.90
1716 2130 8.011844 ACATAGTTATGTCACATCTAAGCTGA 57.988 34.615 0.00 0.00 42.96 4.26
1744 2158 4.022416 GTCTGCCTAGGACACATCTAGATG 60.022 50.000 27.63 27.63 44.15 2.90
1745 2159 4.148838 GTCTGCCTAGGACACATCTAGAT 58.851 47.826 14.75 0.00 37.08 1.98
1746 2160 3.556999 GTCTGCCTAGGACACATCTAGA 58.443 50.000 14.75 0.00 37.08 2.43
1747 2161 2.625790 GGTCTGCCTAGGACACATCTAG 59.374 54.545 14.75 0.00 35.61 2.43
1748 2162 2.667470 GGTCTGCCTAGGACACATCTA 58.333 52.381 14.75 0.00 35.61 1.98
1749 2163 1.490574 GGTCTGCCTAGGACACATCT 58.509 55.000 14.75 0.00 35.61 2.90
1750 2164 0.466124 GGGTCTGCCTAGGACACATC 59.534 60.000 14.75 0.00 37.11 3.06
1751 2165 0.043334 AGGGTCTGCCTAGGACACAT 59.957 55.000 14.75 0.00 39.36 3.21
1752 2166 0.178903 AAGGGTCTGCCTAGGACACA 60.179 55.000 14.75 0.00 39.36 3.72
1753 2167 1.481363 GTAAGGGTCTGCCTAGGACAC 59.519 57.143 14.75 2.52 37.38 3.67
1754 2168 1.078159 TGTAAGGGTCTGCCTAGGACA 59.922 52.381 14.75 9.37 35.61 4.02
1755 2169 1.861982 TGTAAGGGTCTGCCTAGGAC 58.138 55.000 14.75 4.44 34.45 3.85
1756 2170 2.043939 TCTTGTAAGGGTCTGCCTAGGA 59.956 50.000 14.75 0.00 34.45 2.94
1757 2171 2.467880 TCTTGTAAGGGTCTGCCTAGG 58.532 52.381 3.67 3.67 34.45 3.02
1758 2172 4.254492 GTTTCTTGTAAGGGTCTGCCTAG 58.746 47.826 0.00 0.00 34.45 3.02
1759 2173 3.008704 GGTTTCTTGTAAGGGTCTGCCTA 59.991 47.826 0.00 0.00 34.45 3.93
1760 2174 2.224793 GGTTTCTTGTAAGGGTCTGCCT 60.225 50.000 0.00 0.00 34.45 4.75
1761 2175 2.160205 GGTTTCTTGTAAGGGTCTGCC 58.840 52.381 0.00 0.00 0.00 4.85
1762 2176 2.160205 GGGTTTCTTGTAAGGGTCTGC 58.840 52.381 0.00 0.00 0.00 4.26
1763 2177 2.423577 CGGGTTTCTTGTAAGGGTCTG 58.576 52.381 0.00 0.00 0.00 3.51
1764 2178 1.271217 GCGGGTTTCTTGTAAGGGTCT 60.271 52.381 0.00 0.00 0.00 3.85
1765 2179 1.162698 GCGGGTTTCTTGTAAGGGTC 58.837 55.000 0.00 0.00 0.00 4.46
1766 2180 0.769247 AGCGGGTTTCTTGTAAGGGT 59.231 50.000 0.00 0.00 0.00 4.34
1767 2181 2.235402 TCTAGCGGGTTTCTTGTAAGGG 59.765 50.000 0.00 0.00 0.00 3.95
1768 2182 3.604875 TCTAGCGGGTTTCTTGTAAGG 57.395 47.619 0.00 0.00 0.00 2.69
1769 2183 4.120589 GGATCTAGCGGGTTTCTTGTAAG 58.879 47.826 0.00 0.00 0.00 2.34
1770 2184 3.516300 TGGATCTAGCGGGTTTCTTGTAA 59.484 43.478 0.00 0.00 0.00 2.41
1771 2185 3.101437 TGGATCTAGCGGGTTTCTTGTA 58.899 45.455 0.00 0.00 0.00 2.41
1772 2186 1.906574 TGGATCTAGCGGGTTTCTTGT 59.093 47.619 0.00 0.00 0.00 3.16
1773 2187 2.280628 GTGGATCTAGCGGGTTTCTTG 58.719 52.381 0.00 0.00 0.00 3.02
1774 2188 1.134788 CGTGGATCTAGCGGGTTTCTT 60.135 52.381 0.00 0.00 0.00 2.52
1775 2189 0.460311 CGTGGATCTAGCGGGTTTCT 59.540 55.000 0.00 0.00 0.00 2.52
1776 2190 0.458669 TCGTGGATCTAGCGGGTTTC 59.541 55.000 0.00 0.00 0.00 2.78
1777 2191 0.175073 GTCGTGGATCTAGCGGGTTT 59.825 55.000 0.00 0.00 0.00 3.27
1778 2192 1.673808 GGTCGTGGATCTAGCGGGTT 61.674 60.000 0.00 0.00 0.00 4.11
1863 2277 6.602009 TGAATCTCTTGTGATTGCATCTGAAT 59.398 34.615 3.12 0.00 36.86 2.57
1980 2509 4.991472 AGGTAAGCTAAGTACGCTGTTAC 58.009 43.478 0.00 0.00 37.87 2.50
2257 2787 7.388224 CCCAGATATGAAAGAGAATGATGTCAG 59.612 40.741 0.00 0.00 0.00 3.51
2565 3095 6.917533 ACAGCCAAGAAGAAGTATCAAATTG 58.082 36.000 0.00 0.00 0.00 2.32
2766 3296 4.889995 CAGGGATTTTCAAGGTAATCCTCC 59.110 45.833 12.19 0.00 45.89 4.30
2986 3516 6.653526 TGAATCTTCCAGAAAGCATCAAAA 57.346 33.333 0.00 0.00 34.76 2.44
3045 3575 6.064717 GGCATGAATTAAGATAGACTGGGTT 58.935 40.000 0.00 0.00 0.00 4.11
3185 3715 7.466746 AAAAGGAAATAGCATAACAAGCAGA 57.533 32.000 0.00 0.00 0.00 4.26
3350 3880 9.465985 GGTTCATCTTGCTATAACTCTTAGTAC 57.534 37.037 0.00 0.00 0.00 2.73
3367 3897 4.393062 CGTCATTACTGCAAGGTTCATCTT 59.607 41.667 0.00 0.00 39.30 2.40
3462 3992 4.796495 GCGGGCCGGGTTCATCTT 62.796 66.667 29.48 0.00 0.00 2.40
3559 4090 7.129425 AGGATCTACTCATCTTAAGTTGGACT 58.871 38.462 12.51 0.52 0.00 3.85
3670 4206 7.609056 ACTTCTTAGAGTTGGCTTAACGATTA 58.391 34.615 0.00 0.00 44.15 1.75
3707 4243 6.549736 TCTTCATTAGGTTGATCATACTCCGA 59.450 38.462 0.00 0.00 0.00 4.55
3713 4249 9.513906 TGTTTGTTCTTCATTAGGTTGATCATA 57.486 29.630 0.00 0.00 0.00 2.15
3745 4281 8.921205 GGATGGAGGTAGTAAAAGTTAGTGATA 58.079 37.037 0.00 0.00 0.00 2.15
3957 4575 8.974060 TGGTTTATTAGTCCTCATTGTATTCC 57.026 34.615 0.00 0.00 0.00 3.01
3983 4601 6.947644 TCTTTGGGTTTTGTTAGTTAGTCC 57.052 37.500 0.00 0.00 0.00 3.85
4040 4693 2.716017 GGTCGCCACCTCTCAGGAG 61.716 68.421 0.00 0.00 37.67 3.69
4041 4694 2.680352 GGTCGCCACCTCTCAGGA 60.680 66.667 0.00 0.00 37.67 3.86
4042 4695 1.903877 ATTGGTCGCCACCTCTCAGG 61.904 60.000 1.09 0.00 44.17 3.86


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

AutoCloner maintained by Alex Coulton.