Multiple sequence alignment - TraesCS1D01G380500

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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 TraesCS1D01G380500 chr1D 100.000 2768 0 0 1 2768 455994872 455997639 0.000000e+00 5112
1 TraesCS1D01G380500 chr1D 83.815 346 54 2 1016 1360 65889669 65889325 7.390000e-86 327
2 TraesCS1D01G380500 chr1A 95.551 899 29 7 846 1737 549560120 549561014 0.000000e+00 1428
3 TraesCS1D01G380500 chr1A 87.347 735 53 16 120 853 549555139 549555834 0.000000e+00 806
4 TraesCS1D01G380500 chr1A 96.063 381 14 1 2101 2481 549561593 549561972 1.090000e-173 619
5 TraesCS1D01G380500 chr1A 92.903 310 11 4 1773 2072 549561009 549561317 9.100000e-120 440
6 TraesCS1D01G380500 chr1A 94.186 258 11 1 2515 2768 549561973 549562230 9.290000e-105 390
7 TraesCS1D01G380500 chr1A 80.371 377 68 4 2395 2768 554571370 554570997 5.840000e-72 281
8 TraesCS1D01G380500 chr1B 93.189 969 38 12 970 1918 626348845 626349805 0.000000e+00 1399
9 TraesCS1D01G380500 chr1B 86.119 353 47 2 995 1346 105736043 105735692 2.010000e-101 379
10 TraesCS1D01G380500 chr1B 81.818 385 62 6 2388 2768 637894160 637893780 1.600000e-82 316
11 TraesCS1D01G380500 chr1B 95.035 141 7 0 1917 2057 626397765 626397905 3.590000e-54 222
12 TraesCS1D01G380500 chr1B 92.742 124 9 0 2089 2212 626398155 626398278 2.190000e-41 180
13 TraesCS1D01G380500 chr7D 87.173 421 47 4 120 537 182613184 182613600 3.230000e-129 472
14 TraesCS1D01G380500 chr7D 85.194 412 54 5 120 528 185113910 185114317 1.530000e-112 416
15 TraesCS1D01G380500 chr7D 88.281 128 8 2 1 122 150763467 150763341 2.220000e-31 147
16 TraesCS1D01G380500 chr5D 85.851 417 52 5 120 533 411155451 411155863 1.180000e-118 436
17 TraesCS1D01G380500 chr5D 84.524 420 60 3 120 537 552044304 552044720 7.130000e-111 411
18 TraesCS1D01G380500 chr3A 85.308 422 56 3 120 537 693124873 693124454 5.480000e-117 431
19 TraesCS1D01G380500 chr5A 85.337 416 56 3 120 533 492629288 492629700 2.550000e-115 425
20 TraesCS1D01G380500 chr2D 84.561 421 59 4 120 537 591268503 591268920 1.980000e-111 412
21 TraesCS1D01G380500 chr2D 87.591 137 9 4 1 130 11036293 11036158 4.770000e-33 152
22 TraesCS1D01G380500 chr3D 84.323 421 60 5 120 537 401012175 401011758 9.230000e-110 407
23 TraesCS1D01G380500 chr6D 84.323 421 59 5 120 537 303446040 303445624 3.320000e-109 405
24 TraesCS1D01G380500 chr6D 89.706 136 7 4 1 130 310404325 310404459 1.710000e-37 167
25 TraesCS1D01G380500 chr4B 80.163 368 64 7 998 1361 657159413 657159775 1.630000e-67 267
26 TraesCS1D01G380500 chr4B 78.474 367 72 5 998 1361 657142167 657142529 1.660000e-57 233
27 TraesCS1D01G380500 chr4B 88.976 127 13 1 1 126 73691322 73691196 3.690000e-34 156
28 TraesCS1D01G380500 chr6A 89.683 126 6 3 1 119 19265047 19265172 1.330000e-33 154
29 TraesCS1D01G380500 chr6A 87.200 125 9 4 1 119 450092540 450092663 4.810000e-28 135
30 TraesCS1D01G380500 chr7A 86.719 128 10 5 1 122 287183086 287182960 4.810000e-28 135
31 TraesCS1D01G380500 chr7A 86.992 123 9 4 3 119 669517577 669517698 6.220000e-27 132
32 TraesCS1D01G380500 chr5B 87.200 125 9 2 1 119 425872992 425873115 4.810000e-28 135
33 TraesCS1D01G380500 chr4D 80.451 133 23 2 1222 1354 509679106 509678977 6.310000e-17 99


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 TraesCS1D01G380500 chr1D 455994872 455997639 2767 False 5112.00 5112 100.00000 1 2768 1 chr1D.!!$F1 2767
1 TraesCS1D01G380500 chr1A 549555139 549555834 695 False 806.00 806 87.34700 120 853 1 chr1A.!!$F1 733
2 TraesCS1D01G380500 chr1A 549560120 549562230 2110 False 719.25 1428 94.67575 846 2768 4 chr1A.!!$F2 1922
3 TraesCS1D01G380500 chr1B 626348845 626349805 960 False 1399.00 1399 93.18900 970 1918 1 chr1B.!!$F1 948
4 TraesCS1D01G380500 chr1B 626397765 626398278 513 False 201.00 222 93.88850 1917 2212 2 chr1B.!!$F2 295

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
331 332 0.100682 GCTACTCTTCATCGGCGACA 59.899 55.0 13.76 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2098 2382 0.108756 GCAGGTAGACGAAGACCCAC 60.109 60.0 0.0 0.0 36.27 4.61 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
57 58 4.918201 GCGGCGGAAGGAGGGATG 62.918 72.222 9.78 0.00 0.00 3.51
58 59 4.241555 CGGCGGAAGGAGGGATGG 62.242 72.222 0.00 0.00 0.00 3.51
59 60 2.768344 GGCGGAAGGAGGGATGGA 60.768 66.667 0.00 0.00 0.00 3.41
60 61 2.375345 GGCGGAAGGAGGGATGGAA 61.375 63.158 0.00 0.00 0.00 3.53
61 62 1.147153 GCGGAAGGAGGGATGGAAG 59.853 63.158 0.00 0.00 0.00 3.46
62 63 1.832912 CGGAAGGAGGGATGGAAGG 59.167 63.158 0.00 0.00 0.00 3.46
63 64 0.691078 CGGAAGGAGGGATGGAAGGA 60.691 60.000 0.00 0.00 0.00 3.36
64 65 0.840617 GGAAGGAGGGATGGAAGGAC 59.159 60.000 0.00 0.00 0.00 3.85
65 66 0.466124 GAAGGAGGGATGGAAGGACG 59.534 60.000 0.00 0.00 0.00 4.79
66 67 0.983378 AAGGAGGGATGGAAGGACGG 60.983 60.000 0.00 0.00 0.00 4.79
67 68 2.444256 GGAGGGATGGAAGGACGGG 61.444 68.421 0.00 0.00 0.00 5.28
68 69 3.090532 AGGGATGGAAGGACGGGC 61.091 66.667 0.00 0.00 0.00 6.13
69 70 4.547367 GGGATGGAAGGACGGGCG 62.547 72.222 0.00 0.00 0.00 6.13
70 71 4.547367 GGATGGAAGGACGGGCGG 62.547 72.222 0.00 0.00 0.00 6.13
86 87 4.547367 GGCGGCTAGGGTTGCGAT 62.547 66.667 0.00 0.00 0.00 4.58
87 88 2.967615 GCGGCTAGGGTTGCGATC 60.968 66.667 0.00 0.00 0.00 3.69
88 89 2.280186 CGGCTAGGGTTGCGATCC 60.280 66.667 0.00 0.00 0.00 3.36
89 90 2.111251 GGCTAGGGTTGCGATCCC 59.889 66.667 0.00 1.34 44.90 3.85
139 140 2.885113 CGAGACGGTGATGGCTCA 59.115 61.111 0.00 0.00 0.00 4.26
156 157 7.500227 TGATGGCTCACTAAAGATGAAATAAGG 59.500 37.037 0.00 0.00 0.00 2.69
158 159 7.175104 TGGCTCACTAAAGATGAAATAAGGTT 58.825 34.615 0.00 0.00 0.00 3.50
164 165 7.283354 CACTAAAGATGAAATAAGGTTCTCCCC 59.717 40.741 0.00 0.00 0.00 4.81
168 169 5.608860 AGATGAAATAAGGTTCTCCCCCTAG 59.391 44.000 0.00 0.00 0.00 3.02
169 170 4.706616 TGAAATAAGGTTCTCCCCCTAGT 58.293 43.478 0.00 0.00 0.00 2.57
171 172 2.862850 TAAGGTTCTCCCCCTAGTCC 57.137 55.000 0.00 0.00 0.00 3.85
179 180 3.152400 CCCCTAGTCCCCGTTCCG 61.152 72.222 0.00 0.00 0.00 4.30
199 200 0.577269 GTGATGCGCCTAACATCGTC 59.423 55.000 4.18 0.00 45.61 4.20
206 207 0.596859 GCCTAACATCGTCGGTAGGC 60.597 60.000 21.48 21.48 42.47 3.93
223 224 1.664965 GCGTGTGGAGGTGTGTCTC 60.665 63.158 0.00 0.00 0.00 3.36
230 231 2.997897 AGGTGTGTCTCCGAGGGC 60.998 66.667 0.00 0.00 0.00 5.19
237 238 2.043852 TCTCCGAGGGCTCTGTCC 60.044 66.667 0.00 0.00 0.00 4.02
243 244 2.363147 AGGGCTCTGTCCTCGGTC 60.363 66.667 0.00 0.00 27.34 4.79
331 332 0.100682 GCTACTCTTCATCGGCGACA 59.899 55.000 13.76 0.00 0.00 4.35
336 337 1.014044 TCTTCATCGGCGACAGTTGC 61.014 55.000 13.76 3.86 0.00 4.17
337 338 1.005037 TTCATCGGCGACAGTTGCT 60.005 52.632 13.76 0.00 0.00 3.91
338 339 1.291184 TTCATCGGCGACAGTTGCTG 61.291 55.000 13.76 14.95 40.13 4.41
340 341 1.301716 ATCGGCGACAGTTGCTGTT 60.302 52.632 19.57 10.07 45.44 3.16
341 342 1.291877 ATCGGCGACAGTTGCTGTTC 61.292 55.000 19.57 0.00 45.44 3.18
342 343 1.956170 CGGCGACAGTTGCTGTTCT 60.956 57.895 13.08 0.00 45.44 3.01
343 344 1.571460 GGCGACAGTTGCTGTTCTG 59.429 57.895 12.78 0.00 45.44 3.02
344 345 0.880278 GGCGACAGTTGCTGTTCTGA 60.880 55.000 12.78 0.00 45.44 3.27
349 350 1.150827 CAGTTGCTGTTCTGATGCGA 58.849 50.000 0.00 0.00 34.02 5.10
360 361 1.620323 TCTGATGCGATGGTCCTATGG 59.380 52.381 0.00 0.00 0.00 2.74
363 364 0.768221 ATGCGATGGTCCTATGGGGT 60.768 55.000 0.00 0.00 36.25 4.95
380 381 1.615502 GGTCTTAGCACGACGACTTC 58.384 55.000 0.00 0.00 32.24 3.01
405 406 3.714391 ACTGTCGACTACAACAAGGTTC 58.286 45.455 17.92 0.00 37.74 3.62
407 408 1.454653 GTCGACTACAACAAGGTTCGC 59.545 52.381 8.70 0.00 0.00 4.70
409 410 1.154197 GACTACAACAAGGTTCGCCC 58.846 55.000 0.00 0.00 38.27 6.13
411 412 1.296056 CTACAACAAGGTTCGCCCGG 61.296 60.000 0.00 0.00 38.74 5.73
412 413 4.038080 CAACAAGGTTCGCCCGGC 62.038 66.667 0.00 0.00 38.74 6.13
413 414 4.265056 AACAAGGTTCGCCCGGCT 62.265 61.111 8.05 0.00 38.74 5.52
414 415 3.785122 AACAAGGTTCGCCCGGCTT 62.785 57.895 8.05 0.00 38.74 4.35
426 427 2.492090 CGGCTTCGGTGAGAGAGG 59.508 66.667 0.00 0.00 0.00 3.69
461 462 2.155194 CGTCTTCCGCTCGCTTCAG 61.155 63.158 0.00 0.00 0.00 3.02
475 476 2.538449 CGCTTCAGTGTTTGTAGTCGTT 59.462 45.455 0.00 0.00 0.00 3.85
484 485 2.735134 GTTTGTAGTCGTTGCTAGGTGG 59.265 50.000 0.00 0.00 0.00 4.61
496 497 2.023404 TGCTAGGTGGTCTAAGGATCCA 60.023 50.000 15.82 0.00 0.00 3.41
538 539 6.594788 TTTAGTGTTCGTTATACTCCCACT 57.405 37.500 0.00 0.00 35.92 4.00
541 542 6.388435 AGTGTTCGTTATACTCCCACTATC 57.612 41.667 0.00 0.00 30.45 2.08
542 543 6.127793 AGTGTTCGTTATACTCCCACTATCT 58.872 40.000 0.00 0.00 30.45 1.98
543 544 6.606395 AGTGTTCGTTATACTCCCACTATCTT 59.394 38.462 0.00 0.00 30.45 2.40
544 545 7.123847 AGTGTTCGTTATACTCCCACTATCTTT 59.876 37.037 0.00 0.00 30.45 2.52
545 546 7.763071 GTGTTCGTTATACTCCCACTATCTTTT 59.237 37.037 0.00 0.00 0.00 2.27
546 547 8.316214 TGTTCGTTATACTCCCACTATCTTTTT 58.684 33.333 0.00 0.00 0.00 1.94
632 633 4.039245 TCCTAGCCATAGTTAGCACATCAC 59.961 45.833 0.00 0.00 0.00 3.06
646 647 3.375299 GCACATCACTGATACTTTCACCC 59.625 47.826 0.00 0.00 0.00 4.61
686 687 7.094549 ACGCTGATACTTTCCTGAGATATACTC 60.095 40.741 0.00 0.00 45.11 2.59
703 704 8.669243 AGATATACTCTTTCTTTCTTTTTGGCG 58.331 33.333 0.00 0.00 0.00 5.69
705 706 5.774498 ACTCTTTCTTTCTTTTTGGCGAT 57.226 34.783 0.00 0.00 0.00 4.58
706 707 6.149129 ACTCTTTCTTTCTTTTTGGCGATT 57.851 33.333 0.00 0.00 0.00 3.34
707 708 6.573434 ACTCTTTCTTTCTTTTTGGCGATTT 58.427 32.000 0.00 0.00 0.00 2.17
708 709 7.041721 ACTCTTTCTTTCTTTTTGGCGATTTT 58.958 30.769 0.00 0.00 0.00 1.82
709 710 7.010460 ACTCTTTCTTTCTTTTTGGCGATTTTG 59.990 33.333 0.00 0.00 0.00 2.44
710 711 5.982465 TTCTTTCTTTTTGGCGATTTTGG 57.018 34.783 0.00 0.00 0.00 3.28
711 712 3.807071 TCTTTCTTTTTGGCGATTTTGGC 59.193 39.130 0.00 0.00 0.00 4.52
712 713 1.777101 TCTTTTTGGCGATTTTGGCG 58.223 45.000 0.00 0.00 37.19 5.69
713 714 1.338337 TCTTTTTGGCGATTTTGGCGA 59.662 42.857 0.00 0.00 37.19 5.54
714 715 2.131183 CTTTTTGGCGATTTTGGCGAA 58.869 42.857 0.00 0.00 36.14 4.70
715 716 2.225068 TTTTGGCGATTTTGGCGAAA 57.775 40.000 1.66 1.66 43.25 3.46
716 717 2.225068 TTTGGCGATTTTGGCGAAAA 57.775 40.000 9.15 9.15 35.61 2.29
717 718 2.225068 TTGGCGATTTTGGCGAAAAA 57.775 40.000 10.78 4.64 41.88 1.94
721 722 3.862267 TGGCGATTTTGGCGAAAAATATG 59.138 39.130 10.78 7.02 46.29 1.78
735 736 6.855914 GCGAAAAATATGTGTGTCTTTCTGAA 59.144 34.615 0.00 0.00 0.00 3.02
847 848 5.625150 AGACAAAAGTTGCTCTGGTAGATT 58.375 37.500 0.00 0.00 0.00 2.40
877 878 6.522946 AGAAAGCCCTACCGATCTTATTTAC 58.477 40.000 0.00 0.00 0.00 2.01
892 893 5.359009 TCTTATTTACCGGATCTTCGTCACT 59.641 40.000 9.46 0.00 0.00 3.41
896 897 1.215382 CGGATCTTCGTCACTGCCA 59.785 57.895 0.00 0.00 0.00 4.92
910 911 1.155889 CTGCCATCGTAACAACAGCA 58.844 50.000 0.00 0.00 0.00 4.41
933 934 7.443575 AGCATATTATATCGAAATGGCATCTCC 59.556 37.037 0.00 0.00 0.00 3.71
941 942 2.556840 AATGGCATCTCCCACCCACG 62.557 60.000 0.00 0.00 37.79 4.94
943 944 2.363975 GGCATCTCCCACCCACGTA 61.364 63.158 0.00 0.00 0.00 3.57
944 945 1.144057 GCATCTCCCACCCACGTAG 59.856 63.158 0.00 0.00 0.00 3.51
945 946 1.144057 CATCTCCCACCCACGTAGC 59.856 63.158 0.00 0.00 0.00 3.58
946 947 1.001760 ATCTCCCACCCACGTAGCT 59.998 57.895 0.00 0.00 0.00 3.32
947 948 1.043673 ATCTCCCACCCACGTAGCTC 61.044 60.000 0.00 0.00 0.00 4.09
948 949 1.982395 CTCCCACCCACGTAGCTCA 60.982 63.158 0.00 0.00 0.00 4.26
965 968 3.648545 AGCTCAAGGTTAGGTTTCTGAGT 59.351 43.478 0.00 0.00 0.00 3.41
968 971 3.971305 TCAAGGTTAGGTTTCTGAGTCCA 59.029 43.478 0.00 0.00 0.00 4.02
991 994 1.683790 GGTCGATCGAACGCAACCAG 61.684 60.000 21.31 0.00 32.77 4.00
1139 1145 0.387565 GGCGAGAAGATCTCCTCCAC 59.612 60.000 3.02 0.00 40.34 4.02
1389 1410 2.105766 GACGACCATTACTACCACCCT 58.894 52.381 0.00 0.00 0.00 4.34
1550 1571 3.177249 GTGCGACGTCGGCCTTAC 61.177 66.667 36.13 20.21 40.23 2.34
1608 1629 3.452264 TCGACAACTGGGAAGATGATGAT 59.548 43.478 0.00 0.00 0.00 2.45
1609 1630 3.558829 CGACAACTGGGAAGATGATGATG 59.441 47.826 0.00 0.00 0.00 3.07
1610 1631 4.681512 CGACAACTGGGAAGATGATGATGA 60.682 45.833 0.00 0.00 0.00 2.92
1616 1637 3.117776 TGGGAAGATGATGATGAAGGTGG 60.118 47.826 0.00 0.00 0.00 4.61
1641 1662 1.309006 GGAGGAGGGGTACTTCGGA 59.691 63.158 0.00 0.00 0.00 4.55
1644 1665 1.684734 GGAGGGGTACTTCGGAGCA 60.685 63.158 0.00 0.00 0.00 4.26
1856 1879 3.245441 TCCTTCCTTTCTTACTCCCGTT 58.755 45.455 0.00 0.00 0.00 4.44
1968 2001 8.193438 CGTGAGAATGCTCCTGATATATTCATA 58.807 37.037 0.00 0.00 40.55 2.15
2027 2060 6.482308 TGCAAAGTCTTTGTCTTCTAGGTTAC 59.518 38.462 23.07 5.71 42.56 2.50
2030 2063 8.365647 CAAAGTCTTTGTCTTCTAGGTTACCTA 58.634 37.037 15.93 11.02 35.94 3.08
2173 2690 1.769098 CTGTCATGGCGCGATTCAGG 61.769 60.000 12.10 6.57 0.00 3.86
2216 2733 1.360551 CGAGAGGTGCCATCCTACG 59.639 63.158 0.00 0.00 38.02 3.51
2226 2743 0.103208 CCATCCTACGGCAGACAGTC 59.897 60.000 0.00 0.00 0.00 3.51
2288 2805 2.512515 GCCGCTTCATCGAGGCTT 60.513 61.111 3.98 0.00 45.07 4.35
2408 2925 4.201679 CAGCGGCCCGTCATCGTA 62.202 66.667 4.45 0.00 35.01 3.43
2460 2977 2.415825 CTATTGAGGAGCGGACGGA 58.584 57.895 0.00 0.00 0.00 4.69
2482 2999 4.353437 GGACGTGGCGTTCTCGGT 62.353 66.667 0.00 0.00 41.37 4.69
2483 3000 3.103911 GACGTGGCGTTCTCGGTG 61.104 66.667 0.00 0.00 41.37 4.94
2484 3001 4.657824 ACGTGGCGTTCTCGGTGG 62.658 66.667 0.00 0.00 36.35 4.61
2510 3027 4.724697 CTGTTCGCGGCGCACAAG 62.725 66.667 32.61 18.46 32.38 3.16
2512 3029 3.408020 GTTCGCGGCGCACAAGTA 61.408 61.111 32.61 6.18 0.00 2.24
2513 3030 3.408020 TTCGCGGCGCACAAGTAC 61.408 61.111 32.61 0.00 0.00 2.73
2571 3088 4.713735 TCGGCCCAATGCAAGCGA 62.714 61.111 0.00 0.00 43.89 4.93
2577 3094 0.597568 CCCAATGCAAGCGAAGAACA 59.402 50.000 0.00 0.00 0.00 3.18
2635 3152 2.185350 CGAGGCCATGCTCGAGTT 59.815 61.111 15.13 0.00 44.85 3.01
2664 3185 3.815569 GACTCGCTGCCGGAGATCG 62.816 68.421 5.05 2.03 38.88 3.69
2666 3187 3.815569 CTCGCTGCCGGAGATCGAC 62.816 68.421 5.05 0.00 42.43 4.20
2668 3189 4.194720 GCTGCCGGAGATCGACGT 62.195 66.667 5.05 0.00 42.43 4.34
2696 3217 2.048603 GCTGGAGATGGCCCAACAC 61.049 63.158 0.00 0.00 32.53 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.357517 ACGCTGCCGGCATATAGC 60.358 61.111 32.87 27.86 41.91 2.97
14 15 1.738099 GGACGCTGCCGGCATATAG 60.738 63.158 32.87 22.51 46.86 1.31
15 16 1.754380 AAGGACGCTGCCGGCATATA 61.754 55.000 32.87 6.85 46.86 0.86
16 17 2.996168 GAAGGACGCTGCCGGCATAT 62.996 60.000 32.87 18.75 46.86 1.78
17 18 3.733344 GAAGGACGCTGCCGGCATA 62.733 63.158 32.87 8.24 46.86 3.14
40 41 4.918201 CATCCCTCCTTCCGCCGC 62.918 72.222 0.00 0.00 0.00 6.53
41 42 4.241555 CCATCCCTCCTTCCGCCG 62.242 72.222 0.00 0.00 0.00 6.46
42 43 2.330924 CTTCCATCCCTCCTTCCGCC 62.331 65.000 0.00 0.00 0.00 6.13
43 44 1.147153 CTTCCATCCCTCCTTCCGC 59.853 63.158 0.00 0.00 0.00 5.54
44 45 0.691078 TCCTTCCATCCCTCCTTCCG 60.691 60.000 0.00 0.00 0.00 4.30
45 46 0.840617 GTCCTTCCATCCCTCCTTCC 59.159 60.000 0.00 0.00 0.00 3.46
46 47 0.466124 CGTCCTTCCATCCCTCCTTC 59.534 60.000 0.00 0.00 0.00 3.46
47 48 0.983378 CCGTCCTTCCATCCCTCCTT 60.983 60.000 0.00 0.00 0.00 3.36
48 49 1.383248 CCGTCCTTCCATCCCTCCT 60.383 63.158 0.00 0.00 0.00 3.69
49 50 2.444256 CCCGTCCTTCCATCCCTCC 61.444 68.421 0.00 0.00 0.00 4.30
50 51 3.108288 GCCCGTCCTTCCATCCCTC 62.108 68.421 0.00 0.00 0.00 4.30
51 52 3.090532 GCCCGTCCTTCCATCCCT 61.091 66.667 0.00 0.00 0.00 4.20
52 53 4.547367 CGCCCGTCCTTCCATCCC 62.547 72.222 0.00 0.00 0.00 3.85
53 54 4.547367 CCGCCCGTCCTTCCATCC 62.547 72.222 0.00 0.00 0.00 3.51
69 70 4.547367 ATCGCAACCCTAGCCGCC 62.547 66.667 0.00 0.00 0.00 6.13
70 71 2.967615 GATCGCAACCCTAGCCGC 60.968 66.667 0.00 0.00 0.00 6.53
71 72 2.280186 GGATCGCAACCCTAGCCG 60.280 66.667 0.00 0.00 0.00 5.52
72 73 2.111251 GGGATCGCAACCCTAGCC 59.889 66.667 4.64 0.00 43.65 3.93
73 74 2.280186 CGGGATCGCAACCCTAGC 60.280 66.667 10.70 0.00 44.72 3.42
116 117 4.194720 ATCACCGTCTCGCCTCGC 62.195 66.667 0.00 0.00 0.00 5.03
117 118 2.278206 CATCACCGTCTCGCCTCG 60.278 66.667 0.00 0.00 0.00 4.63
118 119 2.105128 CCATCACCGTCTCGCCTC 59.895 66.667 0.00 0.00 0.00 4.70
139 140 7.347252 GGGGAGAACCTTATTTCATCTTTAGT 58.653 38.462 0.00 0.00 40.03 2.24
149 150 4.045736 GGACTAGGGGGAGAACCTTATTT 58.954 47.826 0.00 0.00 39.54 1.40
156 157 1.761271 CGGGGACTAGGGGGAGAAC 60.761 68.421 0.00 0.00 0.00 3.01
158 159 2.234246 GAACGGGGACTAGGGGGAGA 62.234 65.000 0.00 0.00 0.00 3.71
179 180 0.810031 ACGATGTTAGGCGCATCACC 60.810 55.000 10.83 0.00 41.91 4.02
188 189 0.317603 CGCCTACCGACGATGTTAGG 60.318 60.000 0.00 2.09 40.02 2.69
199 200 3.379445 ACCTCCACACGCCTACCG 61.379 66.667 0.00 0.00 44.21 4.02
206 207 4.655527 GAGACACACCTCCACACG 57.344 61.111 0.00 0.00 0.00 4.49
230 231 1.914634 CAAATCGACCGAGGACAGAG 58.085 55.000 0.00 0.00 0.00 3.35
311 312 0.930742 GTCGCCGATGAAGAGTAGCG 60.931 60.000 0.00 0.00 44.61 4.26
331 332 1.736126 CATCGCATCAGAACAGCAACT 59.264 47.619 0.00 0.00 0.00 3.16
336 337 1.134580 AGGACCATCGCATCAGAACAG 60.135 52.381 0.00 0.00 0.00 3.16
337 338 0.904649 AGGACCATCGCATCAGAACA 59.095 50.000 0.00 0.00 0.00 3.18
338 339 2.890808 TAGGACCATCGCATCAGAAC 57.109 50.000 0.00 0.00 0.00 3.01
339 340 2.037641 CCATAGGACCATCGCATCAGAA 59.962 50.000 0.00 0.00 0.00 3.02
340 341 1.620323 CCATAGGACCATCGCATCAGA 59.380 52.381 0.00 0.00 0.00 3.27
341 342 1.338484 CCCATAGGACCATCGCATCAG 60.338 57.143 0.00 0.00 33.47 2.90
342 343 0.686789 CCCATAGGACCATCGCATCA 59.313 55.000 0.00 0.00 33.47 3.07
343 344 0.036010 CCCCATAGGACCATCGCATC 60.036 60.000 0.00 0.00 38.24 3.91
344 345 0.768221 ACCCCATAGGACCATCGCAT 60.768 55.000 0.00 0.00 39.89 4.73
349 350 2.339769 GCTAAGACCCCATAGGACCAT 58.660 52.381 0.00 0.00 39.89 3.55
360 361 0.243095 AAGTCGTCGTGCTAAGACCC 59.757 55.000 0.00 0.00 35.33 4.46
363 364 0.524862 GGGAAGTCGTCGTGCTAAGA 59.475 55.000 0.00 0.00 0.00 2.10
380 381 0.594602 TGTTGTAGTCGACAGTCGGG 59.405 55.000 22.66 0.00 40.88 5.14
390 391 1.154197 GGGCGAACCTTGTTGTAGTC 58.846 55.000 0.00 0.00 35.85 2.59
409 410 2.492090 CCTCTCTCACCGAAGCCG 59.508 66.667 0.00 0.00 0.00 5.52
411 412 2.896443 CCCCTCTCTCACCGAAGC 59.104 66.667 0.00 0.00 0.00 3.86
412 413 2.896443 GCCCCTCTCTCACCGAAG 59.104 66.667 0.00 0.00 0.00 3.79
413 414 2.856039 ATCGCCCCTCTCTCACCGAA 62.856 60.000 0.00 0.00 0.00 4.30
414 415 3.360423 ATCGCCCCTCTCTCACCGA 62.360 63.158 0.00 0.00 0.00 4.69
419 420 2.725008 CGTCATCGCCCCTCTCTC 59.275 66.667 0.00 0.00 0.00 3.20
450 451 1.125021 CTACAAACACTGAAGCGAGCG 59.875 52.381 0.00 0.00 0.00 5.03
461 462 3.183775 CACCTAGCAACGACTACAAACAC 59.816 47.826 0.00 0.00 0.00 3.32
475 476 2.023404 TGGATCCTTAGACCACCTAGCA 60.023 50.000 14.23 0.00 0.00 3.49
518 519 6.127793 AGATAGTGGGAGTATAACGAACACT 58.872 40.000 0.00 0.00 40.41 3.55
598 599 5.930135 ACTATGGCTAGGAAAATTCATCGT 58.070 37.500 0.00 0.00 0.00 3.73
632 633 2.672961 TCTGCGGGTGAAAGTATCAG 57.327 50.000 0.00 0.00 39.19 2.90
686 687 6.421405 CCAAAATCGCCAAAAAGAAAGAAAG 58.579 36.000 0.00 0.00 0.00 2.62
696 697 2.225068 TTTCGCCAAAATCGCCAAAA 57.775 40.000 0.00 0.00 0.00 2.44
697 698 2.225068 TTTTCGCCAAAATCGCCAAA 57.775 40.000 0.00 0.00 0.00 3.28
700 701 3.862845 ACATATTTTTCGCCAAAATCGCC 59.137 39.130 8.03 0.00 43.00 5.54
701 702 4.326009 ACACATATTTTTCGCCAAAATCGC 59.674 37.500 8.03 0.00 43.00 4.58
703 704 6.586082 AGACACACATATTTTTCGCCAAAATC 59.414 34.615 8.03 0.00 43.00 2.17
705 706 5.837437 AGACACACATATTTTTCGCCAAAA 58.163 33.333 0.00 0.00 38.76 2.44
706 707 5.446143 AGACACACATATTTTTCGCCAAA 57.554 34.783 0.00 0.00 0.00 3.28
707 708 5.446143 AAGACACACATATTTTTCGCCAA 57.554 34.783 0.00 0.00 0.00 4.52
708 709 5.240623 AGAAAGACACACATATTTTTCGCCA 59.759 36.000 0.00 0.00 31.67 5.69
709 710 5.569059 CAGAAAGACACACATATTTTTCGCC 59.431 40.000 0.00 0.00 31.67 5.54
710 711 6.370593 TCAGAAAGACACACATATTTTTCGC 58.629 36.000 0.00 0.00 31.67 4.70
711 712 8.282592 TCTTCAGAAAGACACACATATTTTTCG 58.717 33.333 0.00 0.00 36.59 3.46
712 713 9.950680 TTCTTCAGAAAGACACACATATTTTTC 57.049 29.630 0.00 0.00 41.23 2.29
713 714 9.956720 CTTCTTCAGAAAGACACACATATTTTT 57.043 29.630 0.00 0.00 41.23 1.94
714 715 9.342308 TCTTCTTCAGAAAGACACACATATTTT 57.658 29.630 0.00 0.00 41.23 1.82
715 716 8.908786 TCTTCTTCAGAAAGACACACATATTT 57.091 30.769 0.00 0.00 41.23 1.40
716 717 8.908786 TTCTTCTTCAGAAAGACACACATATT 57.091 30.769 0.00 0.00 41.23 1.28
717 718 8.908786 TTTCTTCTTCAGAAAGACACACATAT 57.091 30.769 0.00 0.00 45.12 1.78
816 817 2.360165 AGCAACTTTTGTCTCAAGGCTG 59.640 45.455 0.00 0.00 0.00 4.85
877 878 1.519455 GGCAGTGACGAAGATCCGG 60.519 63.158 0.00 0.00 0.00 5.14
892 893 1.819928 ATGCTGTTGTTACGATGGCA 58.180 45.000 0.00 0.00 0.00 4.92
896 897 9.634163 TTCGATATAATATGCTGTTGTTACGAT 57.366 29.630 0.00 0.00 0.00 3.73
910 911 7.716998 GTGGGAGATGCCATTTCGATATAATAT 59.283 37.037 0.00 0.00 38.95 1.28
926 927 1.144057 CTACGTGGGTGGGAGATGC 59.856 63.158 0.00 0.00 0.00 3.91
933 934 1.079127 CCTTGAGCTACGTGGGTGG 60.079 63.158 8.83 0.00 0.00 4.61
941 942 5.148651 TCAGAAACCTAACCTTGAGCTAC 57.851 43.478 0.00 0.00 0.00 3.58
943 944 3.648545 ACTCAGAAACCTAACCTTGAGCT 59.351 43.478 0.00 0.00 0.00 4.09
944 945 3.997681 GACTCAGAAACCTAACCTTGAGC 59.002 47.826 0.00 0.00 0.00 4.26
945 946 4.040461 TGGACTCAGAAACCTAACCTTGAG 59.960 45.833 0.00 0.00 0.00 3.02
946 947 3.971305 TGGACTCAGAAACCTAACCTTGA 59.029 43.478 0.00 0.00 0.00 3.02
947 948 4.065789 GTGGACTCAGAAACCTAACCTTG 58.934 47.826 0.00 0.00 0.00 3.61
948 949 3.072622 GGTGGACTCAGAAACCTAACCTT 59.927 47.826 0.00 0.00 0.00 3.50
965 968 1.888018 GTTCGATCGACCTGGTGGA 59.112 57.895 19.26 14.09 37.04 4.02
968 971 2.149803 TTGCGTTCGATCGACCTGGT 62.150 55.000 19.26 0.00 0.00 4.00
991 994 1.721487 CGGCGGACATGGTTTGATC 59.279 57.895 0.00 0.00 0.00 2.92
1273 1279 0.320771 AGCAGGCTGAACTTGTACCG 60.321 55.000 20.86 0.00 0.00 4.02
1550 1571 2.951745 GCGAGCACGTCATCTCCG 60.952 66.667 5.23 0.00 41.98 4.63
1608 1629 2.525629 TCCGCCTCACCACCTTCA 60.526 61.111 0.00 0.00 0.00 3.02
1609 1630 2.266055 CTCCGCCTCACCACCTTC 59.734 66.667 0.00 0.00 0.00 3.46
1610 1631 3.322466 CCTCCGCCTCACCACCTT 61.322 66.667 0.00 0.00 0.00 3.50
1616 1637 3.674050 TACCCCTCCTCCGCCTCAC 62.674 68.421 0.00 0.00 0.00 3.51
1641 1662 3.138468 GGGGAGGATAATAAGTTGGTGCT 59.862 47.826 0.00 0.00 0.00 4.40
1644 1665 4.354087 GGATGGGGAGGATAATAAGTTGGT 59.646 45.833 0.00 0.00 0.00 3.67
1702 1723 0.313043 CACCACTTGACGTACTCGGT 59.687 55.000 0.00 0.00 41.85 4.69
1765 1786 1.369692 CATATTGGCCGCCGACCTA 59.630 57.895 0.00 0.00 0.00 3.08
1767 1788 3.660111 GCATATTGGCCGCCGACC 61.660 66.667 0.00 0.00 0.00 4.79
1856 1879 7.118723 AGCCCACAGAATTATTAAGATCAACA 58.881 34.615 0.00 0.00 0.00 3.33
1896 1922 1.592669 CTATTGCGCTAGCTGCCGT 60.593 57.895 22.62 15.60 45.42 5.68
1968 2001 6.430000 GGCGTATATATTGTTGGTTTCCATCT 59.570 38.462 0.00 0.00 31.53 2.90
2027 2060 3.429547 CGAGACCCTGATTGAACTGTAGG 60.430 52.174 0.00 0.00 0.00 3.18
2030 2063 1.971357 ACGAGACCCTGATTGAACTGT 59.029 47.619 0.00 0.00 0.00 3.55
2098 2382 0.108756 GCAGGTAGACGAAGACCCAC 60.109 60.000 0.00 0.00 36.27 4.61
2106 2623 1.101635 CCGGATCTGCAGGTAGACGA 61.102 60.000 15.13 0.00 0.00 4.20
2148 2665 1.446099 CGCGCCATGACAGTGTAGT 60.446 57.895 0.00 0.00 0.00 2.73
2173 2690 1.137086 TCTTGGCCGAGTAAGCAGATC 59.863 52.381 19.96 0.00 0.00 2.75
2216 2733 4.767255 CTGGCCCGACTGTCTGCC 62.767 72.222 23.43 23.43 44.27 4.85
2270 2787 4.880537 AGCCTCGATGAAGCGGCG 62.881 66.667 0.51 0.51 45.93 6.46
2392 2909 3.900892 CTACGATGACGGGCCGCT 61.901 66.667 28.71 13.81 44.46 5.52
2434 2951 0.839946 GCTCCTCAATAGGGCAAGGA 59.160 55.000 0.00 0.00 43.84 3.36
2444 2961 1.379977 TCTCCGTCCGCTCCTCAAT 60.380 57.895 0.00 0.00 0.00 2.57
2460 2977 3.692406 GAACGCCACGTCCCCTCT 61.692 66.667 0.00 0.00 39.99 3.69
2493 3010 4.724697 CTTGTGCGCCGCGAACAG 62.725 66.667 25.00 15.88 46.54 3.16
2495 3012 3.408020 TACTTGTGCGCCGCGAAC 61.408 61.111 17.45 17.45 35.71 3.95
2496 3013 3.408020 GTACTTGTGCGCCGCGAA 61.408 61.111 18.91 1.76 0.00 4.70
2497 3014 3.925362 ATGTACTTGTGCGCCGCGA 62.925 57.895 18.91 0.00 0.00 5.87
2498 3015 3.487202 ATGTACTTGTGCGCCGCG 61.487 61.111 8.83 8.83 0.00 6.46
2499 3016 2.098298 CATGTACTTGTGCGCCGC 59.902 61.111 4.18 0.00 0.00 6.53
2500 3017 2.098298 GCATGTACTTGTGCGCCG 59.902 61.111 4.18 0.00 0.00 6.46
2501 3018 1.425428 GAGCATGTACTTGTGCGCC 59.575 57.895 4.18 0.00 45.69 6.53
2502 3019 1.059369 CGAGCATGTACTTGTGCGC 59.941 57.895 0.00 0.00 45.69 6.09
2503 3020 1.059369 GCGAGCATGTACTTGTGCG 59.941 57.895 10.17 13.41 45.69 5.34
2504 3021 1.425428 GGCGAGCATGTACTTGTGC 59.575 57.895 10.17 9.80 41.57 4.57
2505 3022 1.709760 CGGCGAGCATGTACTTGTG 59.290 57.895 0.00 0.61 0.00 3.33
2506 3023 4.185413 CGGCGAGCATGTACTTGT 57.815 55.556 0.00 0.00 0.00 3.16
2534 3051 2.434884 AGCTCCGCCATGAACACG 60.435 61.111 0.00 0.00 0.00 4.49
2537 3054 1.424493 CGAAGAGCTCCGCCATGAAC 61.424 60.000 10.93 0.00 0.00 3.18
2571 3088 1.000955 CCGCACTACAGGACTGTTCTT 59.999 52.381 10.57 0.00 41.83 2.52
2577 3094 0.330604 TCTACCCGCACTACAGGACT 59.669 55.000 0.00 0.00 0.00 3.85
2719 3240 4.756642 TCGACTTCAAACTTTGCAGATCAT 59.243 37.500 8.00 0.00 0.00 2.45
2726 3247 3.229552 GCAGATCGACTTCAAACTTTGC 58.770 45.455 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.