Multiple sequence alignment - TraesCS2D01G325400

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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 TraesCS2D01G325400 chr2D 100.000 3463 0 0 1 3463 419028403 419024941 0.000000e+00 6396.0
1 TraesCS2D01G325400 chr2B 95.295 1998 84 8 1469 3463 491024717 491022727 0.000000e+00 3160.0
2 TraesCS2D01G325400 chr2B 90.134 598 24 18 838 1418 491025295 491024716 0.000000e+00 745.0
3 TraesCS2D01G325400 chr2B 82.724 793 73 33 1 743 491050469 491049691 0.000000e+00 647.0
4 TraesCS2D01G325400 chr2B 85.083 181 24 2 1 179 139004644 139004465 7.630000e-42 182.0
5 TraesCS2D01G325400 chr2B 93.750 112 7 0 734 845 491049528 491049417 5.940000e-38 169.0
6 TraesCS2D01G325400 chr2B 90.476 63 6 0 39 101 382737273 382737335 2.210000e-12 84.2
7 TraesCS2D01G325400 chr2A 92.235 1159 68 10 1444 2587 571148315 571149466 0.000000e+00 1622.0
8 TraesCS2D01G325400 chr2A 91.124 890 58 9 2575 3463 571149481 571150350 0.000000e+00 1186.0
9 TraesCS2D01G325400 chr2A 91.850 638 32 8 734 1352 571147647 571148283 0.000000e+00 872.0
10 TraesCS2D01G325400 chr2A 91.176 204 18 0 18 221 570934859 570935062 9.470000e-71 278.0
11 TraesCS2D01G325400 chr2A 88.158 228 27 0 516 743 571147256 571147483 4.400000e-69 272.0
12 TraesCS2D01G325400 chr2A 78.519 135 21 7 39 170 285592706 285592577 7.970000e-12 82.4
13 TraesCS2D01G325400 chr5B 82.456 285 45 4 1 284 703505065 703505345 9.600000e-61 244.0
14 TraesCS2D01G325400 chr5B 81.849 292 45 5 1 291 699393550 699393834 4.470000e-59 239.0
15 TraesCS2D01G325400 chr4A 83.026 271 43 3 1 269 631383602 631383333 3.450000e-60 243.0


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 TraesCS2D01G325400 chr2D 419024941 419028403 3462 True 6396.0 6396 100.00000 1 3463 1 chr2D.!!$R1 3462
1 TraesCS2D01G325400 chr2B 491022727 491025295 2568 True 1952.5 3160 92.71450 838 3463 2 chr2B.!!$R2 2625
2 TraesCS2D01G325400 chr2B 491049417 491050469 1052 True 408.0 647 88.23700 1 845 2 chr2B.!!$R3 844
3 TraesCS2D01G325400 chr2A 571147256 571150350 3094 False 988.0 1622 90.84175 516 3463 4 chr2A.!!$F2 2947

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
372 386 0.108424 TGTTGTTGCCCTTTGTGTGC 60.108 50.0 0.0 0.0 0.0 4.57 F
1573 1816 0.036952 AAGCCACGATCACTGACCTG 60.037 55.0 0.0 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 2153 0.534412 CATCTGTGAAGAGGAGCGGT 59.466 55.0 0.00 0.0 0.0 5.68 R
3096 3385 0.469917 CGGCCAGGGAATCTACACAT 59.530 55.0 2.24 0.0 0.0 3.21 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
37 38 0.395724 CCTTGCTGGTATTCACCCCC 60.396 60.000 0.00 0.00 45.11 5.40
38 39 0.331278 CTTGCTGGTATTCACCCCCA 59.669 55.000 0.00 0.00 45.11 4.96
39 40 0.331278 TTGCTGGTATTCACCCCCAG 59.669 55.000 0.00 0.00 45.11 4.45
40 41 4.986467 CTGGTATTCACCCCCAGC 57.014 61.111 0.00 0.00 45.11 4.85
54 55 0.249120 CCCAGCATGACACCTAACGA 59.751 55.000 0.00 0.00 39.69 3.85
85 86 3.857052 TGCTTTTGTCCTATACCGTCAG 58.143 45.455 0.00 0.00 0.00 3.51
87 88 3.793559 CTTTTGTCCTATACCGTCAGGG 58.206 50.000 0.41 0.00 43.47 4.45
101 102 3.056749 CCGTCAGGGTTAGGTATGATAGC 60.057 52.174 0.00 0.00 0.00 2.97
108 109 5.243283 AGGGTTAGGTATGATAGCGTTGTAG 59.757 44.000 0.00 0.00 0.00 2.74
111 112 2.963101 AGGTATGATAGCGTTGTAGCCA 59.037 45.455 0.00 0.00 38.01 4.75
116 117 4.665833 TGATAGCGTTGTAGCCACTATT 57.334 40.909 0.00 0.00 38.01 1.73
117 118 5.018539 TGATAGCGTTGTAGCCACTATTT 57.981 39.130 0.00 0.00 38.01 1.40
118 119 4.808895 TGATAGCGTTGTAGCCACTATTTG 59.191 41.667 0.00 0.00 38.01 2.32
119 120 1.737793 AGCGTTGTAGCCACTATTTGC 59.262 47.619 0.00 0.00 38.01 3.68
120 121 1.202143 GCGTTGTAGCCACTATTTGCC 60.202 52.381 0.00 0.00 0.00 4.52
121 122 1.400494 CGTTGTAGCCACTATTTGCCC 59.600 52.381 0.00 0.00 0.00 5.36
122 123 2.723273 GTTGTAGCCACTATTTGCCCT 58.277 47.619 0.00 0.00 0.00 5.19
123 124 2.683362 GTTGTAGCCACTATTTGCCCTC 59.317 50.000 0.00 0.00 0.00 4.30
124 125 1.211949 TGTAGCCACTATTTGCCCTCC 59.788 52.381 0.00 0.00 0.00 4.30
125 126 0.468226 TAGCCACTATTTGCCCTCCG 59.532 55.000 0.00 0.00 0.00 4.63
126 127 1.077716 GCCACTATTTGCCCTCCGT 60.078 57.895 0.00 0.00 0.00 4.69
169 170 6.395780 TGGTGACCCCTTTCATCTATAAAA 57.604 37.500 0.00 0.00 0.00 1.52
191 192 1.063942 AGGGCCCATTGCTACCTTTAC 60.064 52.381 27.56 0.00 40.92 2.01
196 197 3.876156 GCCCATTGCTACCTTTACAAGGA 60.876 47.826 9.60 0.00 43.88 3.36
198 199 6.949392 GCCCATTGCTACCTTTACAAGGATC 61.949 48.000 9.60 0.00 43.88 3.36
218 219 1.463674 GACACCCTGCCCATTTACAG 58.536 55.000 0.00 0.00 0.00 2.74
226 227 3.134804 CCTGCCCATTTACAGTAGCTAGT 59.865 47.826 0.00 0.00 31.76 2.57
237 238 0.902531 GTAGCTAGTTGCACCTCCCA 59.097 55.000 0.00 0.00 45.94 4.37
246 247 1.673665 GCACCTCCCAAGCACTCTG 60.674 63.158 0.00 0.00 0.00 3.35
259 260 1.598130 ACTCTGCCGACAAGGTTGC 60.598 57.895 0.00 0.00 43.70 4.17
260 261 1.597854 CTCTGCCGACAAGGTTGCA 60.598 57.895 0.00 0.00 43.70 4.08
272 273 3.964909 CAAGGTTGCACTCTTGTAAACC 58.035 45.455 16.07 5.40 35.73 3.27
276 277 3.211045 GTTGCACTCTTGTAAACCCAGA 58.789 45.455 0.00 0.00 0.00 3.86
284 285 4.985538 TCTTGTAAACCCAGAGCTCAAAT 58.014 39.130 17.77 0.00 0.00 2.32
297 311 6.766944 CCAGAGCTCAAATTCATCAAGAGTAT 59.233 38.462 17.77 0.00 0.00 2.12
306 320 9.825972 CAAATTCATCAAGAGTATGTTTTACGT 57.174 29.630 0.00 0.00 0.00 3.57
320 334 2.661840 TTACGTTTCACAGCGGCCCA 62.662 55.000 0.00 0.00 0.00 5.36
322 336 2.625823 CGTTTCACAGCGGCCCAAT 61.626 57.895 0.00 0.00 0.00 3.16
323 337 1.665442 GTTTCACAGCGGCCCAATT 59.335 52.632 0.00 0.00 0.00 2.32
346 360 2.067013 GGGTAAACTCTTCGTGTGCTC 58.933 52.381 0.00 0.00 0.00 4.26
348 362 3.057033 GGGTAAACTCTTCGTGTGCTCTA 60.057 47.826 0.00 0.00 0.00 2.43
358 372 1.578583 GTGTGCTCTACGGTTGTTGT 58.421 50.000 0.00 0.00 0.00 3.32
371 385 1.999024 GTTGTTGTTGCCCTTTGTGTG 59.001 47.619 0.00 0.00 0.00 3.82
372 386 0.108424 TGTTGTTGCCCTTTGTGTGC 60.108 50.000 0.00 0.00 0.00 4.57
374 388 1.260538 TTGTTGCCCTTTGTGTGCCA 61.261 50.000 0.00 0.00 0.00 4.92
378 392 1.591327 GCCCTTTGTGTGCCAAACG 60.591 57.895 0.00 0.00 38.12 3.60
389 403 2.044555 GCCAAACGTAGAAGGGCCC 61.045 63.158 16.46 16.46 38.70 5.80
411 425 0.457035 TGGCCCGTAGATTGTCGTAC 59.543 55.000 0.00 0.00 0.00 3.67
415 429 0.927083 CCGTAGATTGTCGTACGCCG 60.927 60.000 11.24 3.97 40.55 6.46
433 447 3.071459 GACACGGACGCGCATCTTG 62.071 63.158 5.73 6.13 0.00 3.02
442 456 2.456119 GCGCATCTTGTCCTGGTCG 61.456 63.158 0.30 0.00 0.00 4.79
466 494 2.357517 CAGCTCGCCCTTGTCGTT 60.358 61.111 0.00 0.00 0.00 3.85
469 497 2.030562 CTCGCCCTTGTCGTTGGT 59.969 61.111 0.00 0.00 0.00 3.67
471 499 3.411351 CGCCCTTGTCGTTGGTCG 61.411 66.667 0.00 0.00 41.41 4.79
482 510 3.608662 TTGGTCGGACCGTTCGCT 61.609 61.111 21.52 0.00 42.58 4.93
490 518 2.665185 ACCGTTCGCTGCAAGGTC 60.665 61.111 0.00 0.00 0.00 3.85
508 536 2.445654 CAGGCTCCCTCCCTCCTC 60.446 72.222 0.00 0.00 0.00 3.71
509 537 3.773154 AGGCTCCCTCCCTCCTCC 61.773 72.222 0.00 0.00 0.00 4.30
532 582 2.234168 GTCACCAGTACTCTCTTTCCCC 59.766 54.545 0.00 0.00 0.00 4.81
560 610 1.093159 CTGCTCTCCTTCCATTGCAC 58.907 55.000 0.00 0.00 0.00 4.57
568 618 1.880819 CTTCCATTGCACCCACTGGC 61.881 60.000 0.00 0.00 40.54 4.85
601 651 3.311106 CGAAGCAGACACCGTAACTTTA 58.689 45.455 0.00 0.00 0.00 1.85
611 661 8.225777 CAGACACCGTAACTTTAATTCCTTTAC 58.774 37.037 0.00 0.00 0.00 2.01
627 677 3.564511 CTTTACAGGCATCAACCAAACG 58.435 45.455 0.00 0.00 0.00 3.60
652 702 7.306632 CGGAACAGAGATTTATCCATTACGTTC 60.307 40.741 0.00 0.00 0.00 3.95
674 724 3.005050 CCCGTTACCAGCGTGATCTAATA 59.995 47.826 0.00 0.00 0.00 0.98
783 1007 0.454452 GGCTCGTGCGAAAATTGACC 60.454 55.000 3.02 0.00 40.82 4.02
789 1013 2.041244 GTGCGAAAATTGACCGTTGAC 58.959 47.619 0.00 0.00 0.00 3.18
878 1105 6.875948 TTGTATAATGCTGTTGAAGTGTGT 57.124 33.333 0.00 0.00 0.00 3.72
1121 1363 2.456119 CGATGGTCTCGCCTTGCAC 61.456 63.158 0.00 0.00 41.14 4.57
1208 1450 4.117661 AGGCGAGGCGTCTTCGAC 62.118 66.667 13.68 11.28 39.37 4.20
1224 1466 3.899545 GACTGACGGGGAGGGGACA 62.900 68.421 0.00 0.00 0.00 4.02
1273 1515 2.943978 GCCGAGGCCGCCTACATAT 61.944 63.158 13.29 0.00 31.76 1.78
1371 1614 4.261280 GCTCCAATGCAAGCAAATTTTGTT 60.261 37.500 10.65 1.80 38.42 2.83
1394 1637 3.249559 CACTTTCTTCTGTGAACTGGAGC 59.750 47.826 0.00 0.00 36.38 4.70
1404 1647 5.645067 TCTGTGAACTGGAGCATCATTTAAG 59.355 40.000 0.00 0.00 36.25 1.85
1407 1650 5.012239 TGAACTGGAGCATCATTTAAGCTT 58.988 37.500 3.48 3.48 39.02 3.74
1408 1651 6.094048 GTGAACTGGAGCATCATTTAAGCTTA 59.906 38.462 0.86 0.86 39.02 3.09
1409 1652 6.317140 TGAACTGGAGCATCATTTAAGCTTAG 59.683 38.462 6.24 0.00 39.02 2.18
1410 1653 4.578105 ACTGGAGCATCATTTAAGCTTAGC 59.422 41.667 6.24 5.69 39.02 3.09
1411 1654 3.885297 TGGAGCATCATTTAAGCTTAGCC 59.115 43.478 6.24 0.78 39.02 3.93
1412 1655 3.885297 GGAGCATCATTTAAGCTTAGCCA 59.115 43.478 6.24 0.00 39.02 4.75
1413 1656 4.522022 GGAGCATCATTTAAGCTTAGCCAT 59.478 41.667 6.24 0.00 39.02 4.40
1414 1657 5.335504 GGAGCATCATTTAAGCTTAGCCATC 60.336 44.000 6.24 0.96 39.02 3.51
1415 1658 4.214971 AGCATCATTTAAGCTTAGCCATCG 59.785 41.667 6.24 0.00 34.37 3.84
1416 1659 4.023707 GCATCATTTAAGCTTAGCCATCGT 60.024 41.667 6.24 0.00 0.00 3.73
1417 1660 5.506317 GCATCATTTAAGCTTAGCCATCGTT 60.506 40.000 6.24 0.00 0.00 3.85
1418 1661 6.293407 GCATCATTTAAGCTTAGCCATCGTTA 60.293 38.462 6.24 0.00 0.00 3.18
1419 1662 7.639039 CATCATTTAAGCTTAGCCATCGTTAA 58.361 34.615 6.24 0.00 0.00 2.01
1420 1663 7.801716 TCATTTAAGCTTAGCCATCGTTAAT 57.198 32.000 6.24 0.00 0.00 1.40
1421 1664 7.861630 TCATTTAAGCTTAGCCATCGTTAATC 58.138 34.615 6.24 0.00 0.00 1.75
1422 1665 5.900339 TTAAGCTTAGCCATCGTTAATCG 57.100 39.130 6.24 0.00 41.41 3.34
1423 1666 2.755650 AGCTTAGCCATCGTTAATCGG 58.244 47.619 0.00 0.00 40.32 4.18
1424 1667 2.364324 AGCTTAGCCATCGTTAATCGGA 59.636 45.455 0.00 0.00 40.32 4.55
1425 1668 3.128349 GCTTAGCCATCGTTAATCGGAA 58.872 45.455 0.00 0.00 40.32 4.30
1426 1669 3.558418 GCTTAGCCATCGTTAATCGGAAA 59.442 43.478 0.00 0.00 40.32 3.13
1427 1670 4.034742 GCTTAGCCATCGTTAATCGGAAAA 59.965 41.667 0.00 0.00 40.32 2.29
1428 1671 5.448089 GCTTAGCCATCGTTAATCGGAAAAA 60.448 40.000 0.00 0.00 40.32 1.94
1467 1710 4.009675 GCTCTGTGGTTACCAATCATTCA 58.990 43.478 5.33 0.00 34.18 2.57
1468 1711 4.641989 GCTCTGTGGTTACCAATCATTCAT 59.358 41.667 5.33 0.00 34.18 2.57
1469 1712 5.126061 GCTCTGTGGTTACCAATCATTCATT 59.874 40.000 5.33 0.00 34.18 2.57
1470 1713 6.678900 GCTCTGTGGTTACCAATCATTCATTC 60.679 42.308 5.33 0.00 34.18 2.67
1500 1743 4.843220 AGATGAAAAGAAAGTGTGCCAG 57.157 40.909 0.00 0.00 0.00 4.85
1573 1816 0.036952 AAGCCACGATCACTGACCTG 60.037 55.000 0.00 0.00 0.00 4.00
1610 1853 1.283321 ACTTCTTCTTCATCCTGCCCC 59.717 52.381 0.00 0.00 0.00 5.80
1691 1934 1.948834 CAGCATTACGGCCATGATTCA 59.051 47.619 2.24 0.00 0.00 2.57
1707 1950 3.890756 TGATTCATGGTGAGTTTGCTTGT 59.109 39.130 0.00 0.00 0.00 3.16
1846 2106 1.602165 CGTCAGTCGTTGCTTAGGTGT 60.602 52.381 0.00 0.00 34.52 4.16
1869 2129 6.979817 TGTCAGAAGGATTGTTCAATTTTGTG 59.020 34.615 0.00 6.89 0.00 3.33
1908 2168 2.038814 TTGCACCGCTCCTCTTCACA 62.039 55.000 0.00 0.00 0.00 3.58
2013 2273 2.229784 GACCCAAAATGAACCAGCTGAG 59.770 50.000 17.39 8.04 0.00 3.35
2380 2640 4.272504 TCAGAACGTGAAACCAAAAGCTAG 59.727 41.667 0.00 0.00 29.64 3.42
2415 2675 4.331968 TGTAGCAAGGTTTATCCCAGTTG 58.668 43.478 0.00 0.00 36.75 3.16
2611 2900 3.423539 AGATAGTGCTTGGCTGAAACA 57.576 42.857 0.00 0.00 0.00 2.83
2755 3044 7.592938 TGTTACAGATGCTAAGAAAAACATGG 58.407 34.615 0.00 0.00 0.00 3.66
2805 3094 5.473931 TGCTAGTTTGCAGAAAGTCTAGAG 58.526 41.667 0.00 0.00 38.12 2.43
3070 3359 4.783227 AGGAGCCCTTCAAGACAGTTATTA 59.217 41.667 0.00 0.00 0.00 0.98
3073 3362 6.261158 GGAGCCCTTCAAGACAGTTATTAATC 59.739 42.308 0.00 0.00 0.00 1.75
3077 3366 7.628580 GCCCTTCAAGACAGTTATTAATCCAAC 60.629 40.741 0.00 0.00 0.00 3.77
3091 3380 7.687941 ATTAATCCAACGAGACATTTCAGTT 57.312 32.000 0.00 0.00 0.00 3.16
3093 3382 4.066646 TCCAACGAGACATTTCAGTTCA 57.933 40.909 0.00 0.00 0.00 3.18
3094 3383 4.058124 TCCAACGAGACATTTCAGTTCAG 58.942 43.478 0.00 0.00 0.00 3.02
3095 3384 3.809832 CCAACGAGACATTTCAGTTCAGT 59.190 43.478 0.00 0.00 0.00 3.41
3096 3385 4.988540 CCAACGAGACATTTCAGTTCAGTA 59.011 41.667 0.00 0.00 0.00 2.74
3097 3386 5.639506 CCAACGAGACATTTCAGTTCAGTAT 59.360 40.000 0.00 0.00 0.00 2.12
3099 3388 5.784177 ACGAGACATTTCAGTTCAGTATGT 58.216 37.500 0.00 0.00 37.40 2.29
3101 3390 5.635280 CGAGACATTTCAGTTCAGTATGTGT 59.365 40.000 0.00 0.00 37.40 3.72
3102 3391 6.806739 CGAGACATTTCAGTTCAGTATGTGTA 59.193 38.462 0.00 0.00 37.40 2.90
3103 3392 7.008719 CGAGACATTTCAGTTCAGTATGTGTAG 59.991 40.741 0.00 0.00 37.40 2.74
3104 3393 7.896811 AGACATTTCAGTTCAGTATGTGTAGA 58.103 34.615 0.00 0.00 37.40 2.59
3105 3394 8.535335 AGACATTTCAGTTCAGTATGTGTAGAT 58.465 33.333 0.00 0.00 37.40 1.98
3146 3435 2.078849 TTTGCAGAAAGAGATCGCGA 57.921 45.000 13.09 13.09 0.00 5.87
3181 3470 1.136305 GCGCTGAGTTATGGTACCTGA 59.864 52.381 14.36 0.00 0.00 3.86
3220 3509 2.026879 GAGATCGAGCCGGCAGAC 59.973 66.667 31.54 18.19 0.00 3.51
3260 3549 0.104304 GGGACATATTCACGGCGACT 59.896 55.000 16.62 0.00 0.00 4.18
3436 3725 4.400109 GCAGCTGGACGACGACGA 62.400 66.667 17.12 0.00 42.66 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.328680 GCATCGTTAGGTGTCATGCTG 59.671 52.381 0.00 0.00 37.47 4.41
38 39 1.066215 TGCATCGTTAGGTGTCATGCT 60.066 47.619 4.03 0.00 40.48 3.79
39 40 1.368641 TGCATCGTTAGGTGTCATGC 58.631 50.000 0.00 0.00 40.29 4.06
40 41 4.621068 AAATGCATCGTTAGGTGTCATG 57.379 40.909 0.00 0.00 0.00 3.07
85 86 4.332428 ACAACGCTATCATACCTAACCC 57.668 45.455 0.00 0.00 0.00 4.11
87 88 4.922103 GGCTACAACGCTATCATACCTAAC 59.078 45.833 0.00 0.00 0.00 2.34
111 112 4.374399 CGTAATTACGGAGGGCAAATAGT 58.626 43.478 26.65 0.00 45.30 2.12
133 134 5.140454 AGGGGTCACCATAATAGCAAAATC 58.860 41.667 0.00 0.00 43.89 2.17
141 142 7.888514 ATAGATGAAAGGGGTCACCATAATA 57.111 36.000 0.00 0.00 43.89 0.98
143 144 7.699709 TTATAGATGAAAGGGGTCACCATAA 57.300 36.000 0.00 0.00 43.89 1.90
169 170 0.413434 AAGGTAGCAATGGGCCCTTT 59.587 50.000 25.70 21.12 46.50 3.11
172 173 1.341581 TGTAAAGGTAGCAATGGGCCC 60.342 52.381 17.59 17.59 46.50 5.80
191 192 1.450312 GGCAGGGTGTCGATCCTTG 60.450 63.158 14.25 14.25 35.56 3.61
196 197 0.916086 TAAATGGGCAGGGTGTCGAT 59.084 50.000 0.00 0.00 0.00 3.59
198 199 0.322098 TGTAAATGGGCAGGGTGTCG 60.322 55.000 0.00 0.00 0.00 4.35
201 202 2.643551 CTACTGTAAATGGGCAGGGTG 58.356 52.381 0.00 0.00 37.07 4.61
218 219 0.902531 TGGGAGGTGCAACTAGCTAC 59.097 55.000 2.94 0.00 45.94 3.58
226 227 1.228245 GAGTGCTTGGGAGGTGCAA 60.228 57.895 0.00 0.00 38.50 4.08
237 238 1.302033 CCTTGTCGGCAGAGTGCTT 60.302 57.895 0.00 0.00 44.28 3.91
246 247 1.166531 AAGAGTGCAACCTTGTCGGC 61.167 55.000 0.00 0.00 37.80 5.54
259 260 3.244215 TGAGCTCTGGGTTTACAAGAGTG 60.244 47.826 16.19 0.00 0.00 3.51
260 261 2.972713 TGAGCTCTGGGTTTACAAGAGT 59.027 45.455 16.19 0.00 0.00 3.24
272 273 4.942483 ACTCTTGATGAATTTGAGCTCTGG 59.058 41.667 16.19 0.00 0.00 3.86
276 277 7.934855 AACATACTCTTGATGAATTTGAGCT 57.065 32.000 0.00 0.00 0.00 4.09
284 285 9.047371 TGAAACGTAAAACATACTCTTGATGAA 57.953 29.630 0.00 0.00 0.00 2.57
297 311 1.268133 GCCGCTGTGAAACGTAAAACA 60.268 47.619 0.00 0.00 42.39 2.83
306 320 0.539438 AGAATTGGGCCGCTGTGAAA 60.539 50.000 0.00 0.00 0.00 2.69
307 321 1.074775 AGAATTGGGCCGCTGTGAA 59.925 52.632 0.00 0.00 0.00 3.18
320 334 4.755123 CACACGAAGAGTTTACCCAGAATT 59.245 41.667 0.00 0.00 0.00 2.17
322 336 3.724374 CACACGAAGAGTTTACCCAGAA 58.276 45.455 0.00 0.00 0.00 3.02
323 337 2.547218 GCACACGAAGAGTTTACCCAGA 60.547 50.000 0.00 0.00 0.00 3.86
338 352 0.506932 CAACAACCGTAGAGCACACG 59.493 55.000 0.00 0.00 39.10 4.49
346 360 1.314730 AAGGGCAACAACAACCGTAG 58.685 50.000 0.00 0.00 39.74 3.51
348 362 0.174617 CAAAGGGCAACAACAACCGT 59.825 50.000 0.00 0.00 39.74 4.83
371 385 2.044555 GGGCCCTTCTACGTTTGGC 61.045 63.158 17.04 0.00 41.42 4.52
372 386 0.676782 CAGGGCCCTTCTACGTTTGG 60.677 60.000 26.10 1.99 0.00 3.28
374 388 0.036306 CACAGGGCCCTTCTACGTTT 59.964 55.000 26.10 0.00 0.00 3.60
389 403 0.806102 CGACAATCTACGGGCCACAG 60.806 60.000 4.39 0.00 0.00 3.66
415 429 2.809601 AAGATGCGCGTCCGTGTC 60.810 61.111 25.54 0.29 36.67 3.67
423 437 2.434884 ACCAGGACAAGATGCGCG 60.435 61.111 0.00 0.00 0.00 6.86
426 440 2.109126 GGCGACCAGGACAAGATGC 61.109 63.158 0.00 0.00 0.00 3.91
460 488 2.682256 GAACGGTCCGACCAACGACA 62.682 60.000 20.51 0.00 45.77 4.35
461 489 2.018324 GAACGGTCCGACCAACGAC 61.018 63.158 20.51 0.65 45.77 4.34
466 494 4.351938 CAGCGAACGGTCCGACCA 62.352 66.667 20.51 0.00 38.47 4.02
469 497 4.287781 TTGCAGCGAACGGTCCGA 62.288 61.111 20.51 0.00 0.00 4.55
471 499 3.423154 CCTTGCAGCGAACGGTCC 61.423 66.667 0.00 0.00 0.00 4.46
482 510 3.650950 GGGAGCCTGGACCTTGCA 61.651 66.667 0.00 0.00 0.00 4.08
490 518 4.101077 AGGAGGGAGGGAGCCTGG 62.101 72.222 0.00 0.00 31.76 4.45
532 582 1.206849 GAAGGAGAGCAGACAAGGGAG 59.793 57.143 0.00 0.00 0.00 4.30
574 624 2.049063 GTGTCTGCTTCGGCGTCT 60.049 61.111 6.85 0.00 45.37 4.18
578 628 1.373748 TTACGGTGTCTGCTTCGGC 60.374 57.895 0.00 0.00 42.19 5.54
594 644 8.871629 TGATGCCTGTAAAGGAATTAAAGTTA 57.128 30.769 1.93 0.00 28.09 2.24
601 651 4.415596 TGGTTGATGCCTGTAAAGGAATT 58.584 39.130 1.93 0.00 0.00 2.17
611 661 0.958091 TTCCGTTTGGTTGATGCCTG 59.042 50.000 0.00 0.00 36.30 4.85
627 677 7.041984 GGAACGTAATGGATAAATCTCTGTTCC 60.042 40.741 0.00 0.00 42.29 3.62
652 702 0.742505 TAGATCACGCTGGTAACGGG 59.257 55.000 0.00 0.00 45.89 5.28
674 724 9.106070 GAAAGTGGTAATGTAAACGATAAGGAT 57.894 33.333 0.00 0.00 0.00 3.24
783 1007 2.672188 TGGTTGCAATAACGTCAACG 57.328 45.000 0.59 0.12 40.53 4.10
789 1013 7.810766 AAAGACATTTATGGTTGCAATAACG 57.189 32.000 0.59 0.00 0.00 3.18
1208 1450 3.391382 GTGTCCCCTCCCCGTCAG 61.391 72.222 0.00 0.00 0.00 3.51
1273 1515 0.618968 GGGAGGAGGAAGAGCCAGAA 60.619 60.000 0.00 0.00 40.02 3.02
1371 1614 4.697514 CTCCAGTTCACAGAAGAAAGTGA 58.302 43.478 0.00 0.00 42.55 3.41
1394 1637 5.679734 ACGATGGCTAAGCTTAAATGATG 57.320 39.130 7.74 0.00 0.00 3.07
1404 1647 2.750948 TCCGATTAACGATGGCTAAGC 58.249 47.619 0.00 0.00 45.77 3.09
1425 1668 3.014623 GCACGATAACTAGCCCCTTTTT 58.985 45.455 0.00 0.00 0.00 1.94
1426 1669 2.238898 AGCACGATAACTAGCCCCTTTT 59.761 45.455 0.00 0.00 0.00 2.27
1427 1670 1.838077 AGCACGATAACTAGCCCCTTT 59.162 47.619 0.00 0.00 0.00 3.11
1428 1671 1.413077 GAGCACGATAACTAGCCCCTT 59.587 52.381 0.00 0.00 0.00 3.95
1429 1672 1.041437 GAGCACGATAACTAGCCCCT 58.959 55.000 0.00 0.00 0.00 4.79
1430 1673 1.041437 AGAGCACGATAACTAGCCCC 58.959 55.000 0.00 0.00 0.00 5.80
1431 1674 1.409427 ACAGAGCACGATAACTAGCCC 59.591 52.381 0.00 0.00 0.00 5.19
1432 1675 2.464865 CACAGAGCACGATAACTAGCC 58.535 52.381 0.00 0.00 0.00 3.93
1433 1676 2.159226 ACCACAGAGCACGATAACTAGC 60.159 50.000 0.00 0.00 0.00 3.42
1434 1677 3.784701 ACCACAGAGCACGATAACTAG 57.215 47.619 0.00 0.00 0.00 2.57
1435 1678 4.142315 GGTAACCACAGAGCACGATAACTA 60.142 45.833 0.00 0.00 0.00 2.24
1436 1679 3.368116 GGTAACCACAGAGCACGATAACT 60.368 47.826 0.00 0.00 0.00 2.24
1437 1680 2.928116 GGTAACCACAGAGCACGATAAC 59.072 50.000 0.00 0.00 0.00 1.89
1438 1681 2.563620 TGGTAACCACAGAGCACGATAA 59.436 45.455 0.00 0.00 0.00 1.75
1439 1682 2.172679 TGGTAACCACAGAGCACGATA 58.827 47.619 0.00 0.00 0.00 2.92
1440 1683 0.973632 TGGTAACCACAGAGCACGAT 59.026 50.000 0.00 0.00 0.00 3.73
1441 1684 0.753867 TTGGTAACCACAGAGCACGA 59.246 50.000 0.00 0.00 30.78 4.35
1442 1685 1.732259 GATTGGTAACCACAGAGCACG 59.268 52.381 0.00 0.00 30.78 5.34
1468 1711 9.316730 CACTTTCTTTTCATCTTTTGAATGGAA 57.683 29.630 0.00 0.00 43.73 3.53
1469 1712 8.477256 ACACTTTCTTTTCATCTTTTGAATGGA 58.523 29.630 0.00 0.00 43.73 3.41
1470 1713 8.545420 CACACTTTCTTTTCATCTTTTGAATGG 58.455 33.333 0.00 0.00 43.73 3.16
1495 1738 4.702831 TGCTAATTAATCGATGACTGGCA 58.297 39.130 0.00 3.46 0.00 4.92
1496 1739 5.445142 CGATGCTAATTAATCGATGACTGGC 60.445 44.000 12.26 0.67 46.70 4.85
1500 1743 6.690704 TCACGATGCTAATTAATCGATGAC 57.309 37.500 20.85 0.00 46.70 3.06
1573 1816 4.373116 TTGAGCGACAGGCCGACC 62.373 66.667 0.00 0.00 45.17 4.79
1610 1853 0.866061 CGCGTACCGGAGTTGATCAG 60.866 60.000 9.46 0.00 0.00 2.90
1629 1872 3.368843 CGCCTGAAAATTCTGGAATTTGC 59.631 43.478 19.59 17.07 46.76 3.68
1691 1934 2.620115 CACTGACAAGCAAACTCACCAT 59.380 45.455 0.00 0.00 0.00 3.55
1846 2106 7.345422 TCACAAAATTGAACAATCCTTCTGA 57.655 32.000 0.00 0.27 0.00 3.27
1869 2129 0.607489 ACAGCAGTGTCCAGGCAATC 60.607 55.000 0.00 0.00 26.76 2.67
1893 2153 0.534412 CATCTGTGAAGAGGAGCGGT 59.466 55.000 0.00 0.00 0.00 5.68
1908 2168 1.152440 CCGGTCCCTCCTAGCATCT 60.152 63.158 0.00 0.00 0.00 2.90
1930 2190 0.671251 AAGATGTCGAGCGATCCCTC 59.329 55.000 0.00 0.00 0.00 4.30
2013 2273 8.894768 AATAGATGTAAGATAACCTGAACTGC 57.105 34.615 0.00 0.00 0.00 4.40
2380 2640 4.757149 ACCTTGCTACATTCACAAACTCTC 59.243 41.667 0.00 0.00 0.00 3.20
2582 2870 6.261603 TCAGCCAAGCACTATCTTGATAAATG 59.738 38.462 5.19 0.00 44.61 2.32
2611 2900 1.688197 CCATTTGTGCACTGGGTTCTT 59.312 47.619 19.41 0.00 0.00 2.52
2755 3044 7.672122 TTCCTAGAGAACTTAGTTATTCCCC 57.328 40.000 0.00 0.00 0.00 4.81
2782 3071 5.468540 TCTAGACTTTCTGCAAACTAGCA 57.531 39.130 0.00 0.00 43.35 3.49
2783 3072 4.867608 CCTCTAGACTTTCTGCAAACTAGC 59.132 45.833 0.00 0.00 0.00 3.42
2805 3094 4.033472 GCTTCTAGCGTTCTGAAAAGATCC 59.967 45.833 0.00 0.00 0.00 3.36
3028 3317 1.701031 TTCCAGCGGGACAAGAACCA 61.701 55.000 4.56 0.00 44.89 3.67
3070 3359 5.063204 TGAACTGAAATGTCTCGTTGGATT 58.937 37.500 0.00 0.00 0.00 3.01
3073 3362 3.809832 ACTGAACTGAAATGTCTCGTTGG 59.190 43.478 0.00 0.00 0.00 3.77
3077 3366 5.635280 ACACATACTGAACTGAAATGTCTCG 59.365 40.000 0.00 0.00 0.00 4.04
3091 3380 3.388024 GCCAGGGAATCTACACATACTGA 59.612 47.826 0.00 0.00 0.00 3.41
3093 3382 2.706190 GGCCAGGGAATCTACACATACT 59.294 50.000 0.00 0.00 0.00 2.12
3094 3383 2.548067 CGGCCAGGGAATCTACACATAC 60.548 54.545 2.24 0.00 0.00 2.39
3095 3384 1.691976 CGGCCAGGGAATCTACACATA 59.308 52.381 2.24 0.00 0.00 2.29
3096 3385 0.469917 CGGCCAGGGAATCTACACAT 59.530 55.000 2.24 0.00 0.00 3.21
3097 3386 0.616395 TCGGCCAGGGAATCTACACA 60.616 55.000 2.24 0.00 0.00 3.72
3099 3388 0.830648 CTTCGGCCAGGGAATCTACA 59.169 55.000 2.24 0.00 0.00 2.74
3101 3390 1.874129 TTCTTCGGCCAGGGAATCTA 58.126 50.000 2.24 0.00 0.00 1.98
3102 3391 0.991920 TTTCTTCGGCCAGGGAATCT 59.008 50.000 2.24 0.00 0.00 2.40
3103 3392 1.834188 TTTTCTTCGGCCAGGGAATC 58.166 50.000 2.24 0.00 0.00 2.52
3104 3393 2.291540 TGATTTTCTTCGGCCAGGGAAT 60.292 45.455 2.24 0.00 0.00 3.01
3105 3394 1.074727 TGATTTTCTTCGGCCAGGGAA 59.925 47.619 2.24 0.00 0.00 3.97
3146 3435 2.432146 TCAGCGCTGAATACTCTCCATT 59.568 45.455 36.62 0.00 36.53 3.16
3248 3537 3.000819 TCCCCAGTCGCCGTGAAT 61.001 61.111 0.00 0.00 0.00 2.57
3436 3725 2.841044 AACCACAGACGACGGGGT 60.841 61.111 0.00 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.