Multiple sequence alignment - TraesCS2B01G520700

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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 TraesCS2B01G520700 chr2B 100.000 2964 0 0 1 2964 715598390 715601353 0.000000e+00 5474.0
1 TraesCS2B01G520700 chr2D 94.364 1455 57 10 1524 2964 590366768 590368211 0.000000e+00 2209.0
2 TraesCS2B01G520700 chr2D 85.505 1090 85 39 432 1461 590365618 590366694 0.000000e+00 1070.0
3 TraesCS2B01G520700 chr2D 91.166 283 13 5 65 341 590344112 590344388 1.000000e-99 374.0
4 TraesCS2B01G520700 chr2D 85.000 200 24 5 332 529 590344423 590344618 6.480000e-47 198.0
5 TraesCS2B01G520700 chr2A 88.767 1825 112 35 358 2139 724745157 724746931 0.000000e+00 2148.0
6 TraesCS2B01G520700 chr2A 96.191 1024 26 5 1944 2964 724747170 724748183 0.000000e+00 1663.0
7 TraesCS2B01G520700 chr2A 91.459 281 9 6 53 328 724744894 724745164 3.610000e-99 372.0
8 TraesCS2B01G520700 chr2A 97.959 196 4 0 1944 2139 724746954 724747149 1.020000e-89 340.0
9 TraesCS2B01G520700 chr3B 83.189 577 73 15 2396 2955 188701915 188702484 9.480000e-140 507.0
10 TraesCS2B01G520700 chr3B 97.917 48 1 0 1918 1965 188614945 188614992 1.890000e-12 84.2
11 TraesCS2B01G520700 chr3A 83.761 468 48 16 2514 2964 145620246 145620702 4.570000e-113 418.0


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 TraesCS2B01G520700 chr2B 715598390 715601353 2963 False 5474.00 5474 100.0000 1 2964 1 chr2B.!!$F1 2963
1 TraesCS2B01G520700 chr2D 590365618 590368211 2593 False 1639.50 2209 89.9345 432 2964 2 chr2D.!!$F2 2532
2 TraesCS2B01G520700 chr2D 590344112 590344618 506 False 286.00 374 88.0830 65 529 2 chr2D.!!$F1 464
3 TraesCS2B01G520700 chr2A 724744894 724748183 3289 False 1130.75 2148 93.5940 53 2964 4 chr2A.!!$F1 2911
4 TraesCS2B01G520700 chr3B 188701915 188702484 569 False 507.00 507 83.1890 2396 2955 1 chr3B.!!$F2 559

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
647 716 0.036765 GTGTAGTTCACATGCCCCGA 60.037 55.0 0.0 0.0 45.51 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2240 2840 0.111639 GGTTCCCCTAACTTGTGGCA 59.888 55.0 0.0 0.0 38.23 4.92 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 2.259618 CGTGAGACAAATAGTGACCCG 58.740 52.381 0.00 0.00 0.00 5.28
21 22 2.000447 GTGAGACAAATAGTGACCCGC 59.000 52.381 0.00 0.00 0.00 6.13
22 23 1.621317 TGAGACAAATAGTGACCCGCA 59.379 47.619 0.00 0.00 0.00 5.69
30 31 2.202623 GTGACCCGCACGAGCTAG 60.203 66.667 2.73 0.00 37.83 3.42
31 32 4.129737 TGACCCGCACGAGCTAGC 62.130 66.667 6.62 6.62 39.10 3.42
32 33 4.129737 GACCCGCACGAGCTAGCA 62.130 66.667 18.83 0.00 39.10 3.49
33 34 3.642778 GACCCGCACGAGCTAGCAA 62.643 63.158 18.83 0.00 39.10 3.91
34 35 2.202932 CCCGCACGAGCTAGCAAT 60.203 61.111 18.83 0.00 39.10 3.56
35 36 2.240500 CCCGCACGAGCTAGCAATC 61.241 63.158 18.83 5.64 39.10 2.67
36 37 1.519234 CCGCACGAGCTAGCAATCA 60.519 57.895 18.83 0.00 39.10 2.57
37 38 0.877649 CCGCACGAGCTAGCAATCAT 60.878 55.000 18.83 0.00 39.10 2.45
38 39 0.231534 CGCACGAGCTAGCAATCATG 59.768 55.000 18.83 6.58 39.10 3.07
39 40 0.585357 GCACGAGCTAGCAATCATGG 59.415 55.000 18.83 0.00 37.91 3.66
40 41 0.585357 CACGAGCTAGCAATCATGGC 59.415 55.000 18.83 0.00 0.00 4.40
41 42 0.467384 ACGAGCTAGCAATCATGGCT 59.533 50.000 18.83 0.00 45.18 4.75
42 43 1.688735 ACGAGCTAGCAATCATGGCTA 59.311 47.619 18.83 0.00 42.62 3.93
48 49 1.516110 AGCAATCATGGCTAGGGTCT 58.484 50.000 0.00 0.00 40.47 3.85
49 50 1.849039 AGCAATCATGGCTAGGGTCTT 59.151 47.619 0.00 0.00 40.47 3.01
50 51 3.048600 AGCAATCATGGCTAGGGTCTTA 58.951 45.455 0.00 0.00 40.47 2.10
51 52 3.459598 AGCAATCATGGCTAGGGTCTTAA 59.540 43.478 0.00 0.00 40.47 1.85
56 57 4.160329 TCATGGCTAGGGTCTTAATCGAT 58.840 43.478 0.00 0.00 0.00 3.59
81 82 5.598416 TTCGAATAGACTGTGGATGATGT 57.402 39.130 0.00 0.00 0.00 3.06
113 114 9.349713 TGTTTGAGTTGGAATAAAACTAGTCAT 57.650 29.630 0.00 0.00 37.98 3.06
114 115 9.612620 GTTTGAGTTGGAATAAAACTAGTCATG 57.387 33.333 0.00 0.00 37.98 3.07
115 116 7.921786 TGAGTTGGAATAAAACTAGTCATGG 57.078 36.000 0.00 0.00 37.98 3.66
187 190 2.303175 TCAAGCCACACCAAGTAAACC 58.697 47.619 0.00 0.00 0.00 3.27
227 235 2.956386 CAACTCACGTCGACAAAGTTG 58.044 47.619 26.58 26.58 40.39 3.16
236 244 3.259902 GTCGACAAAGTTGGTATCTCCC 58.740 50.000 11.55 0.00 34.77 4.30
237 245 2.901192 TCGACAAAGTTGGTATCTCCCA 59.099 45.455 0.00 0.00 34.77 4.37
238 246 3.325425 TCGACAAAGTTGGTATCTCCCAA 59.675 43.478 0.00 0.00 42.16 4.12
239 247 4.069304 CGACAAAGTTGGTATCTCCCAAA 58.931 43.478 0.00 0.00 45.72 3.28
308 317 5.723672 AATCGAGTCTGAGACCAGTTAAA 57.276 39.130 9.33 0.00 41.16 1.52
338 347 2.160219 TGTTTGAGACAGCAATCGCATC 59.840 45.455 0.00 0.00 42.27 3.91
339 348 2.097680 TTGAGACAGCAATCGCATCA 57.902 45.000 0.00 0.00 42.27 3.07
340 349 2.320745 TGAGACAGCAATCGCATCAT 57.679 45.000 0.00 0.00 42.27 2.45
343 395 0.234106 GACAGCAATCGCATCATCCG 59.766 55.000 0.00 0.00 42.27 4.18
346 398 0.105593 AGCAATCGCATCATCCGTCT 59.894 50.000 0.00 0.00 42.27 4.18
356 408 4.377943 CGCATCATCCGTCTTGTACAAAAA 60.378 41.667 10.03 0.00 0.00 1.94
359 411 6.033831 GCATCATCCGTCTTGTACAAAAATTG 59.966 38.462 10.03 3.63 0.00 2.32
382 434 7.439157 TGAGACACTTATTTTGAGATGTTGG 57.561 36.000 0.00 0.00 0.00 3.77
454 508 4.892880 CGAATAAACAAAGCTAATCTCGCG 59.107 41.667 0.00 0.00 0.00 5.87
466 520 2.907897 ATCTCGCGGCAGCAGTTACC 62.908 60.000 10.08 0.00 45.49 2.85
474 528 1.589716 GCAGCAGTTACCAGCCCTTG 61.590 60.000 0.00 0.00 0.00 3.61
495 549 6.378280 CCTTGGCATAAATCAAACTCCTAACT 59.622 38.462 0.00 0.00 0.00 2.24
598 652 1.726533 GATCGGTCGACAGAGTCCCC 61.727 65.000 22.45 6.77 0.00 4.81
619 673 6.670027 TCCCCTAAGATAAGATGCTTATCCTC 59.330 42.308 18.57 2.14 33.11 3.71
620 674 6.406400 CCCCTAAGATAAGATGCTTATCCTCG 60.406 46.154 18.57 10.06 33.11 4.63
647 716 0.036765 GTGTAGTTCACATGCCCCGA 60.037 55.000 0.00 0.00 45.51 5.14
648 717 0.908910 TGTAGTTCACATGCCCCGAT 59.091 50.000 0.00 0.00 30.04 4.18
649 718 1.280710 TGTAGTTCACATGCCCCGATT 59.719 47.619 0.00 0.00 30.04 3.34
661 730 6.374053 CACATGCCCCGATTATACATAATTGA 59.626 38.462 9.80 0.00 36.62 2.57
670 739 7.336679 CCGATTATACATAATTGATTGCTCCCA 59.663 37.037 9.80 0.00 36.62 4.37
699 768 1.136252 CACATGTTTCCGTCTCTTGCG 60.136 52.381 0.00 0.00 0.00 4.85
703 772 3.894547 TTTCCGTCTCTTGCGCCCC 62.895 63.158 4.18 0.00 0.00 5.80
772 865 0.100682 TGATAAGACCGACGCTCTGC 59.899 55.000 0.00 0.00 0.00 4.26
773 866 0.100682 GATAAGACCGACGCTCTGCA 59.899 55.000 0.00 0.00 0.00 4.41
774 867 0.179134 ATAAGACCGACGCTCTGCAC 60.179 55.000 0.00 0.00 0.00 4.57
775 868 2.523184 TAAGACCGACGCTCTGCACG 62.523 60.000 0.00 0.00 0.00 5.34
780 873 3.782244 GACGCTCTGCACGGCAAG 61.782 66.667 0.00 3.02 38.41 4.01
783 876 3.426568 GCTCTGCACGGCAAGGTC 61.427 66.667 0.35 0.00 38.41 3.85
899 1015 2.440796 CCCACCCCTCGCGTAGTA 60.441 66.667 5.77 0.00 0.00 1.82
900 1016 2.053865 CCCACCCCTCGCGTAGTAA 61.054 63.158 5.77 0.00 0.00 2.24
901 1017 1.606885 CCCACCCCTCGCGTAGTAAA 61.607 60.000 5.77 0.00 0.00 2.01
977 1093 1.949525 CCAAGAGATAACCATTGCCCG 59.050 52.381 0.00 0.00 0.00 6.13
992 1108 2.046892 CCGTGCCTCCTGTTCAGG 60.047 66.667 12.20 12.20 0.00 3.86
998 1114 1.920325 CCTCCTGTTCAGGCCCTGA 60.920 63.158 10.05 10.05 38.87 3.86
1007 1123 0.259647 TCAGGCCCTGAAATGGATGG 59.740 55.000 12.03 0.00 37.57 3.51
1009 1125 0.259938 AGGCCCTGAAATGGATGGAC 59.740 55.000 0.00 0.00 0.00 4.02
1027 1143 1.288127 CCTTGCAACAAGGCTCTGC 59.712 57.895 13.10 8.73 36.60 4.26
1064 1180 1.293498 GCGTCTGCCAAGGAGAAGA 59.707 57.895 3.44 0.00 33.98 2.87
1065 1181 0.107945 GCGTCTGCCAAGGAGAAGAT 60.108 55.000 3.44 0.00 33.98 2.40
1101 1226 2.454832 CTTCTTGCACCTCGCCCTCA 62.455 60.000 0.00 0.00 41.33 3.86
1141 1266 3.853330 CGTGCTCATTGGCGTCGG 61.853 66.667 0.00 0.00 34.52 4.79
1170 1295 1.041447 ATGGGTCGAGTTACTCCCCG 61.041 60.000 17.72 4.30 35.58 5.73
1185 1310 1.672356 CCCGCCCGATGATCATTCC 60.672 63.158 10.14 0.00 0.00 3.01
1206 1331 2.649034 GGGTCGTCTTCAGCGTCA 59.351 61.111 0.00 0.00 0.00 4.35
1288 1413 3.655211 CCCAGCTTCCTGCCAGGT 61.655 66.667 11.27 0.00 44.23 4.00
1289 1414 2.300967 CCCAGCTTCCTGCCAGGTA 61.301 63.158 11.27 0.00 44.23 3.08
1290 1415 1.222936 CCAGCTTCCTGCCAGGTAG 59.777 63.158 12.70 12.70 44.23 3.18
1291 1416 1.267574 CCAGCTTCCTGCCAGGTAGA 61.268 60.000 20.39 3.12 44.23 2.59
1316 1441 3.573538 ACATGCTTTGCACCTTGATAACA 59.426 39.130 0.00 0.00 43.04 2.41
1334 1459 1.077915 CATGGAATTTGCCCGTTTGC 58.922 50.000 0.00 0.00 0.00 3.68
1382 1508 4.736126 AAACTTTGTCACCCTTTCCAAG 57.264 40.909 0.00 0.00 0.00 3.61
1396 1522 4.418392 CTTTCCAAGAACATGCATGCTAC 58.582 43.478 26.53 16.80 0.00 3.58
1397 1523 2.009051 TCCAAGAACATGCATGCTACG 58.991 47.619 26.53 11.16 0.00 3.51
1398 1524 1.532505 CCAAGAACATGCATGCTACGC 60.533 52.381 26.53 11.10 0.00 4.42
1418 1544 3.596214 GCTAACAGGTCTTCAAATCGGA 58.404 45.455 0.00 0.00 0.00 4.55
1453 1579 8.579850 TTAAAATGACATGCTCCTAAGTGATT 57.420 30.769 0.00 0.00 0.00 2.57
1466 1592 5.105310 TCCTAAGTGATTAGCTTGTGAGGTC 60.105 44.000 0.00 0.00 34.88 3.85
1555 1707 3.318017 ACTAGAGAACACAATGTCACGC 58.682 45.455 0.00 0.00 0.00 5.34
1606 1759 9.976511 ATCCACTTCATATTGCAAATTATTCAG 57.023 29.630 1.71 0.00 0.00 3.02
1608 1761 9.241317 CCACTTCATATTGCAAATTATTCAGAC 57.759 33.333 1.71 0.00 0.00 3.51
1619 1778 7.496920 TGCAAATTATTCAGACTACCATCTCTG 59.503 37.037 0.00 0.00 36.07 3.35
1806 1965 1.464997 GAACCAGCGGTCAAATCACTC 59.535 52.381 0.69 0.00 33.12 3.51
1899 2058 0.106519 AGCAGCACCAACCTCTTGTT 60.107 50.000 0.00 0.00 37.80 2.83
2206 2799 4.461081 GTGTTAAACTTGCCCATGATGGTA 59.539 41.667 11.09 0.00 35.17 3.25
2207 2800 4.704540 TGTTAAACTTGCCCATGATGGTAG 59.295 41.667 11.09 7.26 35.17 3.18
2208 2801 2.442236 AACTTGCCCATGATGGTAGG 57.558 50.000 11.09 2.31 35.17 3.18
2209 2802 1.298953 ACTTGCCCATGATGGTAGGT 58.701 50.000 11.09 2.96 35.17 3.08
2210 2803 1.064463 ACTTGCCCATGATGGTAGGTG 60.064 52.381 11.09 0.00 35.17 4.00
2211 2804 0.258484 TTGCCCATGATGGTAGGTGG 59.742 55.000 11.09 0.00 35.17 4.61
2212 2805 0.918799 TGCCCATGATGGTAGGTGGT 60.919 55.000 11.09 0.00 35.17 4.16
2240 2840 8.300286 CACCATCTATTCTCTTATACACACGAT 58.700 37.037 0.00 0.00 0.00 3.73
2305 2905 3.876914 TGTTCCTGAAAGCAACTGTACAG 59.123 43.478 21.44 21.44 0.00 2.74
2388 2988 1.526464 GGCCACAACATTCGCAAAAAG 59.474 47.619 0.00 0.00 0.00 2.27
2494 3098 3.058846 GCTCGTCTGGTTTTCTTTTCTCC 60.059 47.826 0.00 0.00 0.00 3.71
2750 3359 7.012894 CAGACCACAATACCTTGTCTTTTGTAA 59.987 37.037 0.00 0.00 43.76 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.621317 TGCGGGTCACTATTTGTCTCA 59.379 47.619 0.00 0.00 0.00 3.27
3 4 2.000447 GTGCGGGTCACTATTTGTCTC 59.000 52.381 0.00 0.00 42.38 3.36
4 5 1.671850 CGTGCGGGTCACTATTTGTCT 60.672 52.381 0.00 0.00 43.46 3.41
5 6 0.719465 CGTGCGGGTCACTATTTGTC 59.281 55.000 0.00 0.00 43.46 3.18
6 7 0.319083 TCGTGCGGGTCACTATTTGT 59.681 50.000 0.00 0.00 43.46 2.83
7 8 0.999406 CTCGTGCGGGTCACTATTTG 59.001 55.000 0.00 0.00 43.46 2.32
8 9 0.739813 GCTCGTGCGGGTCACTATTT 60.740 55.000 0.00 0.00 43.46 1.40
9 10 1.153628 GCTCGTGCGGGTCACTATT 60.154 57.895 0.00 0.00 43.46 1.73
10 11 0.750546 TAGCTCGTGCGGGTCACTAT 60.751 55.000 3.48 0.00 43.46 2.12
11 12 1.374343 CTAGCTCGTGCGGGTCACTA 61.374 60.000 3.48 0.00 43.46 2.74
12 13 2.675423 TAGCTCGTGCGGGTCACT 60.675 61.111 3.48 0.00 43.46 3.41
13 14 2.202623 CTAGCTCGTGCGGGTCAC 60.203 66.667 3.48 0.00 45.42 3.67
14 15 4.129737 GCTAGCTCGTGCGGGTCA 62.130 66.667 7.70 0.00 45.42 4.02
15 16 2.907897 ATTGCTAGCTCGTGCGGGTC 62.908 60.000 17.23 0.00 45.42 4.46
16 17 2.907897 GATTGCTAGCTCGTGCGGGT 62.908 60.000 17.23 0.00 45.42 5.28
17 18 2.202932 ATTGCTAGCTCGTGCGGG 60.203 61.111 17.23 2.35 45.42 6.13
18 19 0.877649 ATGATTGCTAGCTCGTGCGG 60.878 55.000 17.23 2.70 45.42 5.69
19 20 0.231534 CATGATTGCTAGCTCGTGCG 59.768 55.000 17.23 0.00 45.42 5.34
20 21 0.585357 CCATGATTGCTAGCTCGTGC 59.415 55.000 17.23 0.07 40.05 5.34
21 22 0.585357 GCCATGATTGCTAGCTCGTG 59.415 55.000 17.23 16.39 0.00 4.35
22 23 0.467384 AGCCATGATTGCTAGCTCGT 59.533 50.000 17.23 4.48 37.28 4.18
23 24 2.445565 TAGCCATGATTGCTAGCTCG 57.554 50.000 17.23 0.00 40.23 5.03
28 29 2.694397 AGACCCTAGCCATGATTGCTA 58.306 47.619 0.00 0.00 40.23 3.49
29 30 1.516110 AGACCCTAGCCATGATTGCT 58.484 50.000 0.00 0.00 42.81 3.91
30 31 2.355010 AAGACCCTAGCCATGATTGC 57.645 50.000 0.00 0.00 0.00 3.56
31 32 4.692625 CGATTAAGACCCTAGCCATGATTG 59.307 45.833 0.00 0.00 0.00 2.67
32 33 4.593206 TCGATTAAGACCCTAGCCATGATT 59.407 41.667 0.00 0.00 0.00 2.57
33 34 4.160329 TCGATTAAGACCCTAGCCATGAT 58.840 43.478 0.00 0.00 0.00 2.45
34 35 3.572642 TCGATTAAGACCCTAGCCATGA 58.427 45.455 0.00 0.00 0.00 3.07
35 36 4.021104 TGATCGATTAAGACCCTAGCCATG 60.021 45.833 0.00 0.00 0.00 3.66
36 37 4.160329 TGATCGATTAAGACCCTAGCCAT 58.840 43.478 0.00 0.00 0.00 4.40
37 38 3.572642 TGATCGATTAAGACCCTAGCCA 58.427 45.455 0.00 0.00 0.00 4.75
38 39 4.810191 ATGATCGATTAAGACCCTAGCC 57.190 45.455 0.00 0.00 0.00 3.93
56 57 5.852282 TCATCCACAGTCTATTCGAATGA 57.148 39.130 20.87 12.62 40.01 2.57
66 67 5.207354 ACAGAGATACATCATCCACAGTCT 58.793 41.667 0.00 0.00 33.75 3.24
69 70 6.343703 TCAAACAGAGATACATCATCCACAG 58.656 40.000 0.00 0.00 33.75 3.66
115 116 1.745653 GCCTTTTCTAGGTGGCATCAC 59.254 52.381 0.00 0.00 46.61 3.06
133 136 2.079925 CCTAGCAGAGTCAAACTTGCC 58.920 52.381 0.00 0.00 34.82 4.52
227 235 5.508994 CCTGTTTGTTTGTTTGGGAGATACC 60.509 44.000 0.00 0.00 38.08 2.73
236 244 6.073003 TGGTTTAAAGCCTGTTTGTTTGTTTG 60.073 34.615 14.49 0.00 0.00 2.93
237 245 5.998363 TGGTTTAAAGCCTGTTTGTTTGTTT 59.002 32.000 14.49 0.00 0.00 2.83
238 246 5.552178 TGGTTTAAAGCCTGTTTGTTTGTT 58.448 33.333 14.49 0.00 0.00 2.83
239 247 5.153950 TGGTTTAAAGCCTGTTTGTTTGT 57.846 34.783 14.49 0.00 0.00 2.83
313 322 3.548818 GCGATTGCTGTCTCAAACAAAGT 60.549 43.478 0.00 0.00 37.45 2.66
314 323 2.975851 GCGATTGCTGTCTCAAACAAAG 59.024 45.455 0.00 0.00 37.45 2.77
315 324 2.357323 TGCGATTGCTGTCTCAAACAAA 59.643 40.909 6.47 0.00 43.34 2.83
338 347 6.797033 GTCTCAATTTTTGTACAAGACGGATG 59.203 38.462 8.56 5.35 0.00 3.51
339 348 6.485313 TGTCTCAATTTTTGTACAAGACGGAT 59.515 34.615 8.56 0.00 35.01 4.18
340 349 5.818336 TGTCTCAATTTTTGTACAAGACGGA 59.182 36.000 8.56 4.05 35.01 4.69
356 408 8.517878 CCAACATCTCAAAATAAGTGTCTCAAT 58.482 33.333 0.00 0.00 0.00 2.57
359 411 6.655003 TCCCAACATCTCAAAATAAGTGTCTC 59.345 38.462 0.00 0.00 0.00 3.36
374 426 6.650807 CACGCAAATATATACTCCCAACATCT 59.349 38.462 0.00 0.00 0.00 2.90
377 429 5.919755 TCACGCAAATATATACTCCCAACA 58.080 37.500 0.00 0.00 0.00 3.33
379 431 7.450074 AGAATCACGCAAATATATACTCCCAA 58.550 34.615 0.00 0.00 0.00 4.12
380 432 7.004555 AGAATCACGCAAATATATACTCCCA 57.995 36.000 0.00 0.00 0.00 4.37
382 434 9.209175 AGAAAGAATCACGCAAATATATACTCC 57.791 33.333 0.00 0.00 0.00 3.85
421 475 5.187186 AGCTTTGTTTATTCGGGTCTCTAGA 59.813 40.000 0.00 0.00 0.00 2.43
474 528 7.391148 TTCAGTTAGGAGTTTGATTTATGCC 57.609 36.000 0.00 0.00 0.00 4.40
478 532 7.040686 GGTGCTTTCAGTTAGGAGTTTGATTTA 60.041 37.037 0.00 0.00 0.00 1.40
479 533 6.239036 GGTGCTTTCAGTTAGGAGTTTGATTT 60.239 38.462 0.00 0.00 0.00 2.17
495 549 1.228094 TGGCGACATGGTGCTTTCA 60.228 52.632 10.68 0.00 33.40 2.69
598 652 7.821652 TCACGAGGATAAGCATCTTATCTTAG 58.178 38.462 19.81 16.41 33.20 2.18
619 673 1.419374 GTGAACTACACTGGCTCACG 58.581 55.000 0.00 0.00 45.13 4.35
647 716 8.059798 GCTGGGAGCAATCAATTATGTATAAT 57.940 34.615 0.00 0.00 41.89 1.28
648 717 7.452880 GCTGGGAGCAATCAATTATGTATAA 57.547 36.000 0.00 0.00 41.89 0.98
670 739 1.269206 CGGAAACATGTGTTGCTTGCT 60.269 47.619 0.00 0.00 38.44 3.91
675 744 1.873591 AGAGACGGAAACATGTGTTGC 59.126 47.619 0.00 0.71 38.44 4.17
699 768 3.837570 AACACTCGTTTCCGGGGGC 62.838 63.158 0.00 0.00 43.69 5.80
772 865 3.726517 CCTTGCGACCTTGCCGTG 61.727 66.667 0.00 0.00 0.00 4.94
773 866 1.895020 TATCCTTGCGACCTTGCCGT 61.895 55.000 0.00 0.00 0.00 5.68
774 867 1.153449 TATCCTTGCGACCTTGCCG 60.153 57.895 0.00 0.00 0.00 5.69
775 868 0.815615 CCTATCCTTGCGACCTTGCC 60.816 60.000 0.00 0.00 0.00 4.52
776 869 1.440145 GCCTATCCTTGCGACCTTGC 61.440 60.000 0.00 0.00 0.00 4.01
777 870 0.179000 AGCCTATCCTTGCGACCTTG 59.821 55.000 0.00 0.00 0.00 3.61
778 871 0.912486 AAGCCTATCCTTGCGACCTT 59.088 50.000 0.00 0.00 0.00 3.50
779 872 0.179000 CAAGCCTATCCTTGCGACCT 59.821 55.000 0.00 0.00 36.18 3.85
780 873 0.815615 CCAAGCCTATCCTTGCGACC 60.816 60.000 0.00 0.00 40.62 4.79
781 874 0.107654 ACCAAGCCTATCCTTGCGAC 60.108 55.000 0.00 0.00 40.62 5.19
782 875 0.618458 AACCAAGCCTATCCTTGCGA 59.382 50.000 0.00 0.00 40.62 5.10
783 876 1.463674 AAACCAAGCCTATCCTTGCG 58.536 50.000 0.00 0.00 40.62 4.85
875 979 1.977009 GCGAGGGGTGGGGAAAAAG 60.977 63.158 0.00 0.00 0.00 2.27
895 1011 8.911018 ACCCCATATATATGCAGACTTTACTA 57.089 34.615 16.08 0.00 32.40 1.82
899 1015 5.792712 AGGACCCCATATATATGCAGACTTT 59.207 40.000 16.08 0.00 32.40 2.66
900 1016 5.353986 AGGACCCCATATATATGCAGACTT 58.646 41.667 16.08 4.84 32.40 3.01
901 1017 4.965352 AGGACCCCATATATATGCAGACT 58.035 43.478 16.08 7.90 32.40 3.24
992 1108 0.259938 AGGTCCATCCATTTCAGGGC 59.740 55.000 0.00 0.00 39.02 5.19
993 1109 2.381911 CAAGGTCCATCCATTTCAGGG 58.618 52.381 0.00 0.00 39.02 4.45
998 1114 2.607499 TGTTGCAAGGTCCATCCATTT 58.393 42.857 0.00 0.00 39.02 2.32
1007 1123 0.595095 CAGAGCCTTGTTGCAAGGTC 59.405 55.000 23.69 19.31 39.60 3.85
1009 1125 1.288127 GCAGAGCCTTGTTGCAAGG 59.712 57.895 20.21 20.21 40.39 3.61
1050 1166 3.204526 GTGATCATCTTCTCCTTGGCAG 58.795 50.000 0.00 0.00 0.00 4.85
1141 1266 0.390860 CTCGACCCATCACCCAGATC 59.609 60.000 0.00 0.00 33.72 2.75
1185 1310 2.182030 GCTGAAGACGACCCCGAG 59.818 66.667 0.00 0.00 39.50 4.63
1190 1315 1.134530 CGATGACGCTGAAGACGACC 61.135 60.000 0.00 0.00 0.00 4.79
1287 1412 3.600388 AGGTGCAAAGCATGTACTCTAC 58.400 45.455 9.81 0.00 41.91 2.59
1288 1413 3.981071 AGGTGCAAAGCATGTACTCTA 57.019 42.857 9.81 0.00 41.91 2.43
1289 1414 2.816087 CAAGGTGCAAAGCATGTACTCT 59.184 45.455 9.81 4.21 41.91 3.24
1290 1415 2.813754 TCAAGGTGCAAAGCATGTACTC 59.186 45.455 9.81 2.40 41.91 2.59
1291 1416 2.862541 TCAAGGTGCAAAGCATGTACT 58.137 42.857 9.81 0.00 41.91 2.73
1316 1441 0.389687 CGCAAACGGGCAAATTCCAT 60.390 50.000 0.00 0.00 34.97 3.41
1334 1459 4.998672 TGTTTTCATACAGGTAGGGAAACG 59.001 41.667 17.98 0.00 44.10 3.60
1396 1522 2.348666 CCGATTTGAAGACCTGTTAGCG 59.651 50.000 0.00 0.00 0.00 4.26
1397 1523 3.596214 TCCGATTTGAAGACCTGTTAGC 58.404 45.455 0.00 0.00 0.00 3.09
1398 1524 4.572389 CCATCCGATTTGAAGACCTGTTAG 59.428 45.833 0.00 0.00 0.00 2.34
1418 1544 4.810491 GCATGTCATTTTAAATTCGGCCAT 59.190 37.500 2.24 0.00 0.00 4.40
1453 1579 1.729586 AAGTGGGACCTCACAAGCTA 58.270 50.000 13.53 0.00 39.93 3.32
1466 1592 0.670162 CTTGTCCTGTGCAAAGTGGG 59.330 55.000 2.51 0.00 0.00 4.61
1590 1743 9.851686 AGATGGTAGTCTGAATAATTTGCAATA 57.148 29.630 0.00 0.00 0.00 1.90
1774 1933 1.105759 GCTGGTTCATGCCTGATCCC 61.106 60.000 14.36 8.42 39.57 3.85
1806 1965 0.518636 CTTGTTGCATGTCCTCGGTG 59.481 55.000 0.00 0.00 0.00 4.94
1899 2058 2.879756 GCAGGTAAATTGGCACTCCTGA 60.880 50.000 19.47 0.00 43.28 3.86
2210 2803 8.857098 TGTGTATAAGAGAATAGATGGTGTACC 58.143 37.037 0.00 0.00 0.00 3.34
2211 2804 9.680315 GTGTGTATAAGAGAATAGATGGTGTAC 57.320 37.037 0.00 0.00 0.00 2.90
2212 2805 8.565416 CGTGTGTATAAGAGAATAGATGGTGTA 58.435 37.037 0.00 0.00 0.00 2.90
2240 2840 0.111639 GGTTCCCCTAACTTGTGGCA 59.888 55.000 0.00 0.00 38.23 4.92
2305 2905 7.196331 GCAATACTGATTTTCCACAGAATACC 58.804 38.462 0.00 0.00 37.54 2.73
2388 2988 1.779061 TTGTGGCCCTTGACTCCCTC 61.779 60.000 0.00 0.00 0.00 4.30
2597 3202 4.381292 GGCAAATTTGATCTCCTTCAGGTG 60.381 45.833 22.31 0.00 36.34 4.00


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

AutoCloner maintained by Alex Coulton.