Multiple sequence alignment - TraesCS6B01G332800

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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 TraesCS6B01G332800 chr6B 100.000 5051 0 0 1 5051 584219267 584224317 0.000000e+00 9328
1 TraesCS6B01G332800 chr6B 84.248 711 87 9 3389 4093 46625826 46626517 0.000000e+00 669
2 TraesCS6B01G332800 chr6B 82.190 758 97 20 4313 5051 46648561 46649299 7.180000e-173 617
3 TraesCS6B01G332800 chr6B 82.058 758 98 16 4313 5051 38621549 38620811 3.340000e-171 612
4 TraesCS6B01G332800 chr6B 85.806 465 46 17 2866 3327 38623486 38623039 4.580000e-130 475
5 TraesCS6B01G332800 chr6B 85.542 415 50 3 1595 2001 38624125 38623713 4.670000e-115 425
6 TraesCS6B01G332800 chr6B 80.366 382 40 15 2965 3317 46621469 46621844 1.800000e-64 257
7 TraesCS6B01G332800 chr6B 91.176 136 10 2 658 792 584035632 584035766 3.110000e-42 183
8 TraesCS6B01G332800 chr6D 94.821 3688 139 24 418 4090 389987635 389983985 0.000000e+00 5705
9 TraesCS6B01G332800 chr6D 95.440 921 41 1 4129 5049 389983982 389983063 0.000000e+00 1467
10 TraesCS6B01G332800 chr6D 82.988 964 112 25 3363 4319 23740916 23739998 0.000000e+00 824
11 TraesCS6B01G332800 chr6D 83.944 710 77 23 2617 3320 23746855 23746177 0.000000e+00 645
12 TraesCS6B01G332800 chr6D 81.520 763 97 19 4313 5051 23739973 23739231 5.630000e-164 588
13 TraesCS6B01G332800 chr6D 87.373 491 42 9 1528 2001 23747361 23746874 3.440000e-151 545
14 TraesCS6B01G332800 chr6D 87.537 337 39 2 1 334 389988059 389987723 2.210000e-103 387
15 TraesCS6B01G332800 chr6D 91.603 131 9 2 661 791 390232671 390232543 4.020000e-41 180
16 TraesCS6B01G332800 chr6A 94.870 1501 64 8 1448 2942 536439586 536438093 0.000000e+00 2333
17 TraesCS6B01G332800 chr6A 94.672 976 38 6 3151 4118 536437742 536436773 0.000000e+00 1502
18 TraesCS6B01G332800 chr6A 91.873 1009 61 15 417 1406 536440668 536439662 0.000000e+00 1389
19 TraesCS6B01G332800 chr6A 92.212 886 42 14 4164 5049 536436774 536435916 0.000000e+00 1229
20 TraesCS6B01G332800 chr6A 83.194 958 121 22 3368 4319 22350414 22349491 0.000000e+00 841
21 TraesCS6B01G332800 chr6A 82.122 867 108 25 2450 3308 22274852 22274025 0.000000e+00 699
22 TraesCS6B01G332800 chr6A 81.842 760 97 23 4313 5051 22349466 22348727 7.240000e-168 601
23 TraesCS6B01G332800 chr6A 82.063 630 84 18 4313 4921 22265339 22264718 1.250000e-140 510
24 TraesCS6B01G332800 chr6A 94.872 234 11 1 2922 3154 536438078 536437845 1.030000e-96 364
25 TraesCS6B01G332800 chr6A 84.699 366 39 8 1513 1862 22275528 22275164 2.890000e-92 350
26 TraesCS6B01G332800 chr6A 91.810 232 13 6 683 911 536769473 536769245 8.160000e-83 318
27 TraesCS6B01G332800 chr6A 88.542 192 20 2 2111 2302 22275097 22274908 1.090000e-56 231
28 TraesCS6B01G332800 chr6A 93.939 132 7 1 661 791 603342229 603342360 1.110000e-46 198
29 TraesCS6B01G332800 chr3B 82.523 658 92 13 4313 4951 745006715 745006062 1.590000e-154 556
30 TraesCS6B01G332800 chr7A 84.656 189 19 6 683 864 700821380 700821565 4.020000e-41 180
31 TraesCS6B01G332800 chr7D 86.310 168 18 3 679 842 610915624 610915790 1.450000e-40 178
32 TraesCS6B01G332800 chr7D 86.667 150 19 1 1144 1293 610920233 610920381 1.130000e-36 165
33 TraesCS6B01G332800 chr7B 84.239 184 27 2 681 864 699932937 699933118 1.450000e-40 178


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 TraesCS6B01G332800 chr6B 584219267 584224317 5050 False 9328.000000 9328 100.000000 1 5051 1 chr6B.!!$F3 5050
1 TraesCS6B01G332800 chr6B 46648561 46649299 738 False 617.000000 617 82.190000 4313 5051 1 chr6B.!!$F1 738
2 TraesCS6B01G332800 chr6B 38620811 38624125 3314 True 504.000000 612 84.468667 1595 5051 3 chr6B.!!$R1 3456
3 TraesCS6B01G332800 chr6B 46621469 46626517 5048 False 463.000000 669 82.307000 2965 4093 2 chr6B.!!$F4 1128
4 TraesCS6B01G332800 chr6D 389983063 389988059 4996 True 2519.666667 5705 92.599333 1 5049 3 chr6D.!!$R4 5048
5 TraesCS6B01G332800 chr6D 23739231 23740916 1685 True 706.000000 824 82.254000 3363 5051 2 chr6D.!!$R2 1688
6 TraesCS6B01G332800 chr6D 23746177 23747361 1184 True 595.000000 645 85.658500 1528 3320 2 chr6D.!!$R3 1792
7 TraesCS6B01G332800 chr6A 536435916 536440668 4752 True 1363.400000 2333 93.699800 417 5049 5 chr6A.!!$R5 4632
8 TraesCS6B01G332800 chr6A 22348727 22350414 1687 True 721.000000 841 82.518000 3368 5051 2 chr6A.!!$R4 1683
9 TraesCS6B01G332800 chr6A 22264718 22265339 621 True 510.000000 510 82.063000 4313 4921 1 chr6A.!!$R1 608
10 TraesCS6B01G332800 chr6A 22274025 22275528 1503 True 426.666667 699 85.121000 1513 3308 3 chr6A.!!$R3 1795
11 TraesCS6B01G332800 chr3B 745006062 745006715 653 True 556.000000 556 82.523000 4313 4951 1 chr3B.!!$R1 638

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
411 415 0.108329 AGAATAACGACGCCACTGGG 60.108 55.000 0.0 0.0 37.18 4.45 F
881 919 0.629571 AAACCCCCTAATCCCCTCCC 60.630 60.000 0.0 0.0 0.00 4.30 F
2160 2278 0.321034 GACCTACCCACCCAACGTTC 60.321 60.000 0.0 0.0 0.00 3.95 F
2874 2997 0.032130 TAGCTTCTTGATAGGGCGCG 59.968 55.000 0.0 0.0 0.00 6.86 F
3505 7770 2.487934 CCAATCGTCCTATGCTTCCAG 58.512 52.381 0.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2013 2131 1.137404 CCGCTTGCTTTTCATCCGG 59.863 57.895 0.00 0.00 34.14 5.14 R
2589 2708 0.901580 AGGTGCCAAATGCTTCCAGG 60.902 55.000 0.00 0.00 42.00 4.45 R
3381 4192 0.032403 ATGTGCAGCGCATGTGTTTT 59.968 45.000 20.85 0.00 41.91 2.43 R
3679 7944 0.032815 GTGCCGGATCTAGAGAAGGC 59.967 60.000 21.41 21.41 40.82 4.35 R
4349 8648 1.072173 TCATCTGGTGGGTGTTGACAG 59.928 52.381 0.00 0.00 0.00 3.51 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
48 49 6.942532 TTGAATTTGTTGCTTAGACTGTCT 57.057 33.333 15.57 15.57 0.00 3.41
61 62 8.758829 TGCTTAGACTGTCTCATAAATCCTTTA 58.241 33.333 14.62 0.00 0.00 1.85
113 114 2.529780 TGTTTGATTGGCTGCAAAGG 57.470 45.000 0.50 0.00 34.95 3.11
124 125 2.613725 GGCTGCAAAGGAAGAAAATGGG 60.614 50.000 0.50 0.00 0.00 4.00
126 127 3.258123 GCTGCAAAGGAAGAAAATGGGTA 59.742 43.478 0.00 0.00 0.00 3.69
128 129 5.127031 GCTGCAAAGGAAGAAAATGGGTATA 59.873 40.000 0.00 0.00 0.00 1.47
131 132 6.667414 TGCAAAGGAAGAAAATGGGTATATGT 59.333 34.615 0.00 0.00 0.00 2.29
136 137 9.588096 AAGGAAGAAAATGGGTATATGTAATCC 57.412 33.333 0.00 0.00 0.00 3.01
137 138 8.960064 AGGAAGAAAATGGGTATATGTAATCCT 58.040 33.333 0.00 0.00 0.00 3.24
148 149 7.646526 GGGTATATGTAATCCTTTTCGTTTTGC 59.353 37.037 0.00 0.00 0.00 3.68
156 157 5.004922 TCCTTTTCGTTTTGCTGATGTTT 57.995 34.783 0.00 0.00 0.00 2.83
157 158 6.137794 TCCTTTTCGTTTTGCTGATGTTTA 57.862 33.333 0.00 0.00 0.00 2.01
171 172 6.092122 TGCTGATGTTTAGACCTTACGAAATG 59.908 38.462 0.00 0.00 0.00 2.32
176 177 6.161381 TGTTTAGACCTTACGAAATGGACTC 58.839 40.000 0.00 0.00 0.00 3.36
189 190 3.806949 ATGGACTCTTTTTACAGGCCA 57.193 42.857 5.01 0.00 0.00 5.36
230 231 2.436417 TGTGTCATTGGGAAGCTAAGC 58.564 47.619 0.00 0.00 0.00 3.09
237 238 1.376037 GGGAAGCTAAGCGTGCACT 60.376 57.895 16.19 0.00 29.61 4.40
239 240 0.875059 GGAAGCTAAGCGTGCACTTT 59.125 50.000 16.19 11.61 0.00 2.66
247 249 1.890876 AGCGTGCACTTTACCAATGA 58.109 45.000 16.19 0.00 0.00 2.57
284 286 0.742505 ATGCTCAACCGGCATTGATG 59.257 50.000 0.00 0.94 46.62 3.07
290 292 2.102749 CCGGCATTGATGTTGCGG 59.897 61.111 0.00 0.00 41.07 5.69
297 299 3.510719 GCATTGATGTTGCGGTGTTTAT 58.489 40.909 0.00 0.00 0.00 1.40
298 300 3.304026 GCATTGATGTTGCGGTGTTTATG 59.696 43.478 0.00 0.00 0.00 1.90
305 307 2.093306 TGCGGTGTTTATGTCTCCTG 57.907 50.000 0.00 0.00 0.00 3.86
312 314 6.038271 GCGGTGTTTATGTCTCCTGAATAATT 59.962 38.462 0.00 0.00 0.00 1.40
315 317 8.739972 GGTGTTTATGTCTCCTGAATAATTGTT 58.260 33.333 0.00 0.00 0.00 2.83
334 338 1.511613 TGGGGGAACTCCAGATGATC 58.488 55.000 0.00 0.00 37.91 2.92
336 340 1.846439 GGGGGAACTCCAGATGATCAA 59.154 52.381 0.00 0.00 37.91 2.57
337 341 2.444766 GGGGGAACTCCAGATGATCAAT 59.555 50.000 0.00 0.00 37.91 2.57
338 342 3.117360 GGGGGAACTCCAGATGATCAATT 60.117 47.826 0.00 0.00 37.91 2.32
339 343 4.540715 GGGGAACTCCAGATGATCAATTT 58.459 43.478 0.00 0.00 37.91 1.82
340 344 4.958581 GGGGAACTCCAGATGATCAATTTT 59.041 41.667 0.00 0.00 37.91 1.82
341 345 5.423290 GGGGAACTCCAGATGATCAATTTTT 59.577 40.000 0.00 0.00 37.91 1.94
368 372 5.410355 AACAAGATGATCATTTGGGGTTG 57.590 39.130 22.95 16.16 0.00 3.77
376 380 3.100207 TCATTTGGGGTTGATCTTCCC 57.900 47.619 14.61 14.61 42.73 3.97
380 384 2.674754 GGGTTGATCTTCCCGCCA 59.325 61.111 9.38 0.00 33.97 5.69
382 386 1.452108 GGTTGATCTTCCCGCCAGG 60.452 63.158 0.00 0.00 37.24 4.45
403 407 3.223157 GTGCAACCAAAGAATAACGACG 58.777 45.455 0.00 0.00 0.00 5.12
404 408 2.239201 GCAACCAAAGAATAACGACGC 58.761 47.619 0.00 0.00 0.00 5.19
407 411 1.802365 ACCAAAGAATAACGACGCCAC 59.198 47.619 0.00 0.00 0.00 5.01
409 413 2.159707 CCAAAGAATAACGACGCCACTG 60.160 50.000 0.00 0.00 0.00 3.66
411 415 0.108329 AGAATAACGACGCCACTGGG 60.108 55.000 0.00 0.00 37.18 4.45
427 458 3.444742 CACTGGGCTGCAAATTGATCTAA 59.555 43.478 0.50 0.00 0.00 2.10
444 475 5.721960 TGATCTAACTTCTGACCTAGGCTTT 59.278 40.000 9.30 0.00 0.00 3.51
465 496 2.162608 TGTAGCGTTTTGTGCTTGTGTT 59.837 40.909 0.00 0.00 43.71 3.32
472 503 2.292103 TTGTGCTTGTGTTGCCTTTC 57.708 45.000 0.00 0.00 0.00 2.62
502 534 8.597662 TCGGATGGTAATAACTAATAAGCAAC 57.402 34.615 0.00 0.00 0.00 4.17
526 558 6.070309 ACAATTCTTTCTGATCAGCTACTCCT 60.070 38.462 18.36 0.00 0.00 3.69
530 562 5.481824 TCTTTCTGATCAGCTACTCCTTTCA 59.518 40.000 18.36 0.00 0.00 2.69
559 591 9.474920 CCGTTGTGGATATTTTATGCATTTTAT 57.525 29.630 3.54 0.00 42.00 1.40
642 676 5.934402 AGTCAAGGGTAATACTGATTCGT 57.066 39.130 0.00 0.00 0.00 3.85
645 679 6.606395 AGTCAAGGGTAATACTGATTCGTAGT 59.394 38.462 0.00 0.00 0.00 2.73
659 693 4.346734 TTCGTAGTTCCGTACTGTGATC 57.653 45.455 0.00 0.00 37.73 2.92
675 709 9.453325 GTACTGTGATCTAGCTTAATTAGTGAC 57.547 37.037 0.00 0.00 0.00 3.67
815 853 1.385528 ACGCCGATTTTAATCCCACC 58.614 50.000 0.00 0.00 31.68 4.61
845 883 0.965363 CGTCCATCCCCCAAACCAAG 60.965 60.000 0.00 0.00 0.00 3.61
881 919 0.629571 AAACCCCCTAATCCCCTCCC 60.630 60.000 0.00 0.00 0.00 4.30
913 951 1.394151 CCCAGAACCTCTCCCTCCT 59.606 63.158 0.00 0.00 0.00 3.69
914 952 0.689412 CCCAGAACCTCTCCCTCCTC 60.689 65.000 0.00 0.00 0.00 3.71
994 1043 2.225791 CTCCATTGACTCCCGCACGA 62.226 60.000 0.00 0.00 0.00 4.35
1199 1248 1.630244 CGGTTCTTCCTGCGCAAGAG 61.630 60.000 13.05 9.79 43.02 2.85
1409 1461 2.159043 GCTAGAGCCAGTGTCATGCTTA 60.159 50.000 0.00 0.00 34.99 3.09
1410 1462 3.679917 GCTAGAGCCAGTGTCATGCTTAA 60.680 47.826 0.00 0.00 34.99 1.85
1446 1532 3.696051 GTGCCTTGATTTAGGATTGCTCA 59.304 43.478 0.00 0.00 37.50 4.26
1459 1548 8.991243 TTAGGATTGCTCAAAAATTCTTGATG 57.009 30.769 0.00 0.00 34.86 3.07
1475 1564 5.678583 TCTTGATGAGATTTCAGATGTCCC 58.321 41.667 0.00 0.00 36.61 4.46
1510 1600 6.438259 AGATTCTGATTTGTGAAGCTGATG 57.562 37.500 0.00 0.00 37.51 3.07
1511 1601 5.944599 AGATTCTGATTTGTGAAGCTGATGT 59.055 36.000 0.00 0.00 37.51 3.06
1512 1602 6.433404 AGATTCTGATTTGTGAAGCTGATGTT 59.567 34.615 0.00 0.00 37.51 2.71
1513 1603 6.395426 TTCTGATTTGTGAAGCTGATGTTT 57.605 33.333 0.00 0.00 30.82 2.83
1514 1604 5.765176 TCTGATTTGTGAAGCTGATGTTTG 58.235 37.500 0.00 0.00 0.00 2.93
1515 1605 5.532032 TCTGATTTGTGAAGCTGATGTTTGA 59.468 36.000 0.00 0.00 0.00 2.69
1516 1606 5.522456 TGATTTGTGAAGCTGATGTTTGAC 58.478 37.500 0.00 0.00 0.00 3.18
1517 1607 5.300034 TGATTTGTGAAGCTGATGTTTGACT 59.700 36.000 0.00 0.00 0.00 3.41
1623 1716 2.279741 GCTGACAACGGCATCTATTCA 58.720 47.619 0.00 0.00 46.56 2.57
1734 1828 3.000727 CACTTCGGTGTACAATTCCCTC 58.999 50.000 0.00 0.00 40.78 4.30
1947 2065 6.183360 GCATAGTCTCTCCAGATATCTACACG 60.183 46.154 4.54 0.00 0.00 4.49
2013 2131 4.942852 CAGAGATGGAGTCTGTATTGGTC 58.057 47.826 0.00 0.00 37.29 4.02
2160 2278 0.321034 GACCTACCCACCCAACGTTC 60.321 60.000 0.00 0.00 0.00 3.95
2438 2556 2.111384 AGATCGGCTGTTGGATAGTGT 58.889 47.619 0.00 0.00 0.00 3.55
2571 2689 4.451900 AGCAGGGTATTGTTCCGAATAAG 58.548 43.478 0.00 0.00 0.00 1.73
2589 2708 6.457528 CGAATAAGAAGTTCTTCCTTGATGCC 60.458 42.308 21.25 5.08 37.89 4.40
2615 2734 1.318158 GCATTTGGCACCTCTCCCAG 61.318 60.000 0.00 0.00 43.97 4.45
2676 2795 5.480073 AGAGTCAAGTAGAGATTCTGCAAGT 59.520 40.000 0.00 0.00 31.82 3.16
2790 2913 0.179009 ACTCTGCAAGCAAGCCAGAA 60.179 50.000 0.00 0.00 0.00 3.02
2871 2994 2.875317 GCAAGTAGCTTCTTGATAGGGC 59.125 50.000 30.50 14.35 45.11 5.19
2874 2997 0.032130 TAGCTTCTTGATAGGGCGCG 59.968 55.000 0.00 0.00 0.00 6.86
2925 3085 3.134985 TGTCCAGTTGCTTGTACCAAGTA 59.865 43.478 5.92 0.00 0.00 2.24
3203 3499 7.941919 TGCTATACCTTCTGTTACTAGTGATG 58.058 38.462 5.39 0.00 0.00 3.07
3361 4172 7.608761 TCTCGGTGCTTTAGGTAAATTTAATGT 59.391 33.333 0.00 0.00 0.00 2.71
3392 7654 8.889000 GTTAGTCTACTTTTTAAAACACATGCG 58.111 33.333 0.00 0.00 0.00 4.73
3505 7770 2.487934 CCAATCGTCCTATGCTTCCAG 58.512 52.381 0.00 0.00 0.00 3.86
3679 7944 0.538057 TGCCAACTTTCTCCCTGCAG 60.538 55.000 6.78 6.78 0.00 4.41
3936 8202 9.772973 TCAAACAAGAGTGCTACTTAGATAAAA 57.227 29.630 0.00 0.00 0.00 1.52
4033 8299 4.006319 ACAATCCTGAGTAGCTGCTTTTC 58.994 43.478 7.79 6.81 0.00 2.29
4083 8349 2.234414 CCTGCAGTTGTTATGGGCAAAT 59.766 45.455 13.81 0.00 33.58 2.32
4107 8373 2.942376 TGATCAATCGCGGCATAAGTTT 59.058 40.909 6.13 0.00 0.00 2.66
4120 8386 5.856455 CGGCATAAGTTTACTTCCAAAGTTG 59.144 40.000 0.00 0.00 42.81 3.16
4152 8418 1.732917 CCAGTTTTTGGCTGTCGCA 59.267 52.632 0.00 0.00 40.87 5.10
4168 8434 4.430007 TGTCGCAACAGGTAAATAGCTAG 58.570 43.478 0.00 0.00 31.93 3.42
4170 8436 2.544267 CGCAACAGGTAAATAGCTAGGC 59.456 50.000 0.00 0.00 31.93 3.93
4176 8442 4.344102 ACAGGTAAATAGCTAGGCGAATCA 59.656 41.667 0.00 0.00 31.93 2.57
4398 8697 0.681733 TGGTCTTCCTCACTGCTCAC 59.318 55.000 0.00 0.00 34.23 3.51
4594 8894 6.489700 TGCAAATGTGATCTTTTGAGGAACTA 59.510 34.615 15.80 0.00 41.55 2.24
4696 9014 2.834549 AGACTGTTCATCGGGTTCTGAT 59.165 45.455 0.00 0.00 0.00 2.90
4784 9103 0.034767 TTGCAGCAGGAATCTCCAGG 60.035 55.000 0.00 0.00 39.61 4.45
4797 9116 7.503566 CAGGAATCTCCAGGCTTCAATTAATAA 59.496 37.037 0.00 0.00 39.61 1.40
4870 9189 3.579151 GAGTAGGGTGGGTGATTAGATCC 59.421 52.174 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 6.942005 TGCGATATCCAAATTGAATAGACCAT 59.058 34.615 0.00 0.00 0.00 3.55
64 65 7.639039 TGTTGCGATATCCAAATTGAATAGAC 58.361 34.615 7.84 0.00 0.00 2.59
97 98 2.596346 TCTTCCTTTGCAGCCAATCAA 58.404 42.857 0.00 0.00 0.00 2.57
124 125 9.221775 CAGCAAAACGAAAAGGATTACATATAC 57.778 33.333 0.00 0.00 0.00 1.47
126 127 8.050778 TCAGCAAAACGAAAAGGATTACATAT 57.949 30.769 0.00 0.00 0.00 1.78
128 129 6.325919 TCAGCAAAACGAAAAGGATTACAT 57.674 33.333 0.00 0.00 0.00 2.29
131 132 6.325919 ACATCAGCAAAACGAAAAGGATTA 57.674 33.333 0.00 0.00 0.00 1.75
136 137 6.142320 GGTCTAAACATCAGCAAAACGAAAAG 59.858 38.462 0.00 0.00 0.00 2.27
137 138 5.974751 GGTCTAAACATCAGCAAAACGAAAA 59.025 36.000 0.00 0.00 0.00 2.29
141 142 4.749245 AGGTCTAAACATCAGCAAAACG 57.251 40.909 0.00 0.00 0.00 3.60
148 149 6.816640 TCCATTTCGTAAGGTCTAAACATCAG 59.183 38.462 0.00 0.00 38.47 2.90
156 157 6.600882 AAAGAGTCCATTTCGTAAGGTCTA 57.399 37.500 0.00 0.00 38.47 2.59
157 158 5.485209 AAAGAGTCCATTTCGTAAGGTCT 57.515 39.130 0.00 0.00 38.47 3.85
171 172 1.813178 GCTGGCCTGTAAAAAGAGTCC 59.187 52.381 11.69 0.00 0.00 3.85
176 177 2.097466 CCATACGCTGGCCTGTAAAAAG 59.903 50.000 11.69 0.00 38.47 2.27
189 190 5.755375 CACATGAAATACTTCTCCATACGCT 59.245 40.000 0.00 0.00 32.33 5.07
197 198 6.599244 TCCCAATGACACATGAAATACTTCTC 59.401 38.462 0.00 0.00 32.33 2.87
206 207 3.159213 AGCTTCCCAATGACACATGAA 57.841 42.857 0.00 0.00 0.00 2.57
230 231 4.481930 TCTTTCATTGGTAAAGTGCACG 57.518 40.909 12.01 0.00 35.79 5.34
237 238 8.634335 TCACATTGAGATCTTTCATTGGTAAA 57.366 30.769 0.00 0.00 34.41 2.01
239 240 8.102676 TCTTCACATTGAGATCTTTCATTGGTA 58.897 33.333 0.00 0.00 34.41 3.25
247 249 6.178324 TGAGCATCTTCACATTGAGATCTTT 58.822 36.000 0.00 0.00 34.92 2.52
279 281 3.818210 AGACATAAACACCGCAACATCAA 59.182 39.130 0.00 0.00 0.00 2.57
284 286 2.159627 CAGGAGACATAAACACCGCAAC 59.840 50.000 0.00 0.00 0.00 4.17
290 292 9.559958 CAACAATTATTCAGGAGACATAAACAC 57.440 33.333 0.00 0.00 0.00 3.32
297 299 4.569653 CCCCCAACAATTATTCAGGAGACA 60.570 45.833 0.00 0.00 0.00 3.41
298 300 3.954258 CCCCCAACAATTATTCAGGAGAC 59.046 47.826 0.00 0.00 0.00 3.36
305 307 4.349365 TGGAGTTCCCCCAACAATTATTC 58.651 43.478 0.00 0.00 37.48 1.75
312 314 0.698238 CATCTGGAGTTCCCCCAACA 59.302 55.000 0.00 0.00 37.48 3.33
315 317 1.274358 TGATCATCTGGAGTTCCCCCA 60.274 52.381 0.00 0.00 34.29 4.96
338 342 9.709495 CCCAAATGATCATCTTGTTTAGAAAAA 57.291 29.630 9.06 0.00 36.22 1.94
339 343 8.313292 CCCCAAATGATCATCTTGTTTAGAAAA 58.687 33.333 9.06 0.00 36.22 2.29
340 344 7.454380 ACCCCAAATGATCATCTTGTTTAGAAA 59.546 33.333 9.06 0.00 36.22 2.52
341 345 6.953520 ACCCCAAATGATCATCTTGTTTAGAA 59.046 34.615 9.06 0.00 36.22 2.10
342 346 6.493166 ACCCCAAATGATCATCTTGTTTAGA 58.507 36.000 9.06 0.00 37.28 2.10
343 347 6.780457 ACCCCAAATGATCATCTTGTTTAG 57.220 37.500 9.06 6.73 0.00 1.85
344 348 6.723515 TCAACCCCAAATGATCATCTTGTTTA 59.276 34.615 9.06 0.00 0.00 2.01
345 349 5.543405 TCAACCCCAAATGATCATCTTGTTT 59.457 36.000 9.06 0.00 0.00 2.83
346 350 5.085920 TCAACCCCAAATGATCATCTTGTT 58.914 37.500 9.06 6.03 0.00 2.83
347 351 4.676109 TCAACCCCAAATGATCATCTTGT 58.324 39.130 9.06 0.00 0.00 3.16
348 352 5.864418 ATCAACCCCAAATGATCATCTTG 57.136 39.130 9.06 14.32 30.62 3.02
355 359 3.646534 GGGAAGATCAACCCCAAATGAT 58.353 45.455 14.05 0.00 40.19 2.45
356 360 2.620367 CGGGAAGATCAACCCCAAATGA 60.620 50.000 17.69 0.00 42.86 2.57
357 361 1.750778 CGGGAAGATCAACCCCAAATG 59.249 52.381 17.69 4.01 42.86 2.32
358 362 1.959989 GCGGGAAGATCAACCCCAAAT 60.960 52.381 17.69 0.00 42.86 2.32
359 363 0.610785 GCGGGAAGATCAACCCCAAA 60.611 55.000 17.69 0.00 42.86 3.28
368 372 2.514824 GCACCTGGCGGGAAGATC 60.515 66.667 21.81 0.00 38.76 2.75
380 384 3.252458 GTCGTTATTCTTTGGTTGCACCT 59.748 43.478 6.83 0.00 39.58 4.00
382 386 3.223157 CGTCGTTATTCTTTGGTTGCAC 58.777 45.455 0.00 0.00 0.00 4.57
389 393 2.159707 CCAGTGGCGTCGTTATTCTTTG 60.160 50.000 0.00 0.00 0.00 2.77
390 394 2.073816 CCAGTGGCGTCGTTATTCTTT 58.926 47.619 0.00 0.00 0.00 2.52
392 396 0.108329 CCCAGTGGCGTCGTTATTCT 60.108 55.000 2.61 0.00 0.00 2.40
404 408 0.899720 ATCAATTTGCAGCCCAGTGG 59.100 50.000 0.63 0.63 0.00 4.00
407 411 3.698040 AGTTAGATCAATTTGCAGCCCAG 59.302 43.478 0.00 0.00 0.00 4.45
409 413 4.400567 AGAAGTTAGATCAATTTGCAGCCC 59.599 41.667 0.00 0.00 0.00 5.19
411 415 6.026513 GTCAGAAGTTAGATCAATTTGCAGC 58.973 40.000 0.00 0.00 0.00 5.25
413 417 6.240894 AGGTCAGAAGTTAGATCAATTTGCA 58.759 36.000 0.00 0.00 0.00 4.08
414 418 6.749923 AGGTCAGAAGTTAGATCAATTTGC 57.250 37.500 0.00 0.00 0.00 3.68
415 419 7.011857 GCCTAGGTCAGAAGTTAGATCAATTTG 59.988 40.741 11.31 0.00 0.00 2.32
427 458 3.055747 GCTACAAAGCCTAGGTCAGAAGT 60.056 47.826 11.31 4.95 43.40 3.01
444 475 1.740585 ACACAAGCACAAAACGCTACA 59.259 42.857 0.00 0.00 39.29 2.74
502 534 6.347696 AGGAGTAGCTGATCAGAAAGAATTG 58.652 40.000 27.04 0.00 0.00 2.32
506 538 5.481824 TGAAAGGAGTAGCTGATCAGAAAGA 59.518 40.000 27.04 4.60 0.00 2.52
526 558 5.398603 AAAATATCCACAACGGCATGAAA 57.601 34.783 0.00 0.00 33.14 2.69
530 562 4.340666 TGCATAAAATATCCACAACGGCAT 59.659 37.500 0.00 0.00 33.14 4.40
559 591 6.074648 AGGTGTTTCCCTCATTACATTTCAA 58.925 36.000 0.00 0.00 36.75 2.69
617 649 6.070995 ACGAATCAGTATTACCCTTGACTTCA 60.071 38.462 0.00 0.00 0.00 3.02
618 650 6.338937 ACGAATCAGTATTACCCTTGACTTC 58.661 40.000 0.00 0.00 0.00 3.01
619 651 6.295719 ACGAATCAGTATTACCCTTGACTT 57.704 37.500 0.00 0.00 0.00 3.01
642 676 4.778579 AGCTAGATCACAGTACGGAACTA 58.221 43.478 0.00 1.69 35.76 2.24
645 679 6.710597 ATTAAGCTAGATCACAGTACGGAA 57.289 37.500 0.00 0.00 0.00 4.30
659 693 7.759886 TGTGCTGTTAGTCACTAATTAAGCTAG 59.240 37.037 21.30 7.22 34.21 3.42
675 709 0.806102 CGGATCCGGTGTGCTGTTAG 60.806 60.000 26.95 0.00 35.56 2.34
792 827 4.037089 GGTGGGATTAAAATCGGCGTAAAT 59.963 41.667 6.85 0.77 36.27 1.40
794 829 2.944349 GGTGGGATTAAAATCGGCGTAA 59.056 45.455 6.85 0.00 36.27 3.18
795 830 2.563702 GGTGGGATTAAAATCGGCGTA 58.436 47.619 6.85 0.00 36.27 4.42
796 831 1.385528 GGTGGGATTAAAATCGGCGT 58.614 50.000 6.85 0.00 36.27 5.68
797 832 0.666374 GGGTGGGATTAAAATCGGCG 59.334 55.000 0.00 0.00 36.27 6.46
798 833 1.770294 TGGGTGGGATTAAAATCGGC 58.230 50.000 0.00 0.00 36.27 5.54
799 834 4.810191 TTTTGGGTGGGATTAAAATCGG 57.190 40.909 0.00 0.00 36.27 4.18
802 837 5.045213 GGTGGATTTTGGGTGGGATTAAAAT 60.045 40.000 0.00 0.00 35.95 1.82
803 838 4.287326 GGTGGATTTTGGGTGGGATTAAAA 59.713 41.667 0.00 0.00 0.00 1.52
815 853 1.102978 GGATGGACGGTGGATTTTGG 58.897 55.000 0.00 0.00 0.00 3.28
845 883 3.936772 TTTGGACGGCTGGGATGGC 62.937 63.158 0.00 0.00 0.00 4.40
881 919 0.030092 TCTGGGTTCTGGATAGGGGG 60.030 60.000 0.00 0.00 0.00 5.40
926 964 4.918201 GGAATGGCGAGGGGCGAG 62.918 72.222 0.00 0.00 44.92 5.03
959 1005 0.106967 GGAGGATGGGTTTCTGGAGC 60.107 60.000 0.00 0.00 0.00 4.70
994 1043 2.435693 GGTAGGCGAGCATCTGGGT 61.436 63.158 0.00 0.00 0.00 4.51
1409 1461 8.823220 AATCAAGGCACCTTATGTAAGTTATT 57.177 30.769 0.61 0.00 34.50 1.40
1410 1462 8.823220 AAATCAAGGCACCTTATGTAAGTTAT 57.177 30.769 0.61 0.00 34.50 1.89
1426 1478 4.989279 TTGAGCAATCCTAAATCAAGGC 57.011 40.909 0.00 0.00 36.51 4.35
1455 1544 4.472470 ACAGGGACATCTGAAATCTCATCA 59.528 41.667 0.00 0.00 38.11 3.07
1459 1548 3.539604 CCACAGGGACATCTGAAATCTC 58.460 50.000 0.00 0.00 38.11 2.75
1475 1564 6.207417 ACAAATCAGAATCTGTTAACCCACAG 59.793 38.462 10.36 0.00 44.96 3.66
1489 1579 6.585695 AACATCAGCTTCACAAATCAGAAT 57.414 33.333 0.00 0.00 0.00 2.40
1492 1582 5.628193 GTCAAACATCAGCTTCACAAATCAG 59.372 40.000 0.00 0.00 0.00 2.90
1510 1600 9.118236 GCAGAAATATCTAACAAACAGTCAAAC 57.882 33.333 0.00 0.00 33.50 2.93
1511 1601 9.066892 AGCAGAAATATCTAACAAACAGTCAAA 57.933 29.630 0.00 0.00 33.50 2.69
1512 1602 8.621532 AGCAGAAATATCTAACAAACAGTCAA 57.378 30.769 0.00 0.00 33.50 3.18
1513 1603 7.063426 CGAGCAGAAATATCTAACAAACAGTCA 59.937 37.037 0.00 0.00 33.50 3.41
1514 1604 7.063544 ACGAGCAGAAATATCTAACAAACAGTC 59.936 37.037 0.00 0.00 33.50 3.51
1515 1605 6.874134 ACGAGCAGAAATATCTAACAAACAGT 59.126 34.615 0.00 0.00 33.50 3.55
1516 1606 7.295952 ACGAGCAGAAATATCTAACAAACAG 57.704 36.000 0.00 0.00 33.50 3.16
1517 1607 7.667043 AACGAGCAGAAATATCTAACAAACA 57.333 32.000 0.00 0.00 33.50 2.83
1623 1716 5.131642 TCTTCCCATCACAGATATCAGCTTT 59.868 40.000 5.32 0.00 0.00 3.51
1734 1828 2.055310 AATGCAGATGCGCACCGATG 62.055 55.000 14.90 10.57 46.56 3.84
1947 2065 4.761235 TCCGTCGATCACTCCATTATAC 57.239 45.455 0.00 0.00 0.00 1.47
2013 2131 1.137404 CCGCTTGCTTTTCATCCGG 59.863 57.895 0.00 0.00 34.14 5.14
2160 2278 8.236585 TCCCATAGTTTGTTATCATGGAATTG 57.763 34.615 0.50 0.00 38.77 2.32
2438 2556 3.559171 GGGCACTACACCTTTCTCAATCA 60.559 47.826 0.00 0.00 0.00 2.57
2505 2623 5.592104 TCTGGACAAGCATCTTATCGTTA 57.408 39.130 0.00 0.00 0.00 3.18
2541 2659 5.049405 CGGAACAATACCCTGCTTATTCATC 60.049 44.000 0.00 0.00 0.00 2.92
2571 2689 2.751806 CAGGGCATCAAGGAAGAACTTC 59.248 50.000 6.06 6.06 38.80 3.01
2589 2708 0.901580 AGGTGCCAAATGCTTCCAGG 60.902 55.000 0.00 0.00 42.00 4.45
2611 2730 1.657804 ACTCTCCTGGGTTTACTGGG 58.342 55.000 0.00 0.00 0.00 4.45
2615 2734 4.041321 AGGTTTGTACTCTCCTGGGTTTAC 59.959 45.833 0.00 0.00 0.00 2.01
2676 2795 5.065988 GCTTGAACTAGCCATTTCCGAATTA 59.934 40.000 0.00 0.00 35.06 1.40
2790 2913 3.620488 TGAACTGCTTTCAGAACCTGTT 58.380 40.909 0.00 5.46 42.95 3.16
2871 2994 1.835483 AAGCAGTTCAGAACAGCGCG 61.835 55.000 21.22 0.00 46.98 6.86
2874 2997 1.942657 TGTGAAGCAGTTCAGAACAGC 59.057 47.619 20.22 20.22 43.55 4.40
2901 3024 0.865769 GGTACAAGCAACTGGACACG 59.134 55.000 0.00 0.00 31.07 4.49
3203 3499 1.876156 CTCTGAAGCACAACCAAGACC 59.124 52.381 0.00 0.00 0.00 3.85
3366 4177 8.889000 CGCATGTGTTTTAAAAAGTAGACTAAC 58.111 33.333 1.31 0.00 0.00 2.34
3380 4191 0.665298 TGTGCAGCGCATGTGTTTTA 59.335 45.000 11.47 0.00 41.91 1.52
3381 4192 0.032403 ATGTGCAGCGCATGTGTTTT 59.968 45.000 20.85 0.00 41.91 2.43
3382 4193 0.880441 TATGTGCAGCGCATGTGTTT 59.120 45.000 28.33 7.19 41.91 2.83
3392 7654 2.679837 ACTAGCAATGTGTATGTGCAGC 59.320 45.455 0.00 0.00 40.83 5.25
3453 7716 9.750125 AATTCTTTAGTTGTTGTCAATCCTTTC 57.250 29.630 0.00 0.00 35.92 2.62
3505 7770 0.804989 CGCCAGTTCATCTTGGAACC 59.195 55.000 2.68 0.00 46.52 3.62
3679 7944 0.032815 GTGCCGGATCTAGAGAAGGC 59.967 60.000 21.41 21.41 40.82 4.35
3936 8202 7.754924 CGAGTCACCACAAATTAATTGCTATTT 59.245 33.333 0.39 0.00 43.13 1.40
3943 8209 7.392113 TCCATAACGAGTCACCACAAATTAATT 59.608 33.333 0.00 0.00 0.00 1.40
4033 8299 2.673368 GCTAACGGAGAATGGACAACTG 59.327 50.000 0.00 0.00 0.00 3.16
4083 8349 4.314961 ACTTATGCCGCGATTGATCATAA 58.685 39.130 8.23 10.03 0.00 1.90
4107 8373 7.122055 ACACTTGTTCATTCAACTTTGGAAGTA 59.878 33.333 0.00 0.00 41.91 2.24
4120 8386 6.573617 CAAAAACTGGACACTTGTTCATTC 57.426 37.500 0.00 0.00 32.18 2.67
4152 8418 4.748277 TTCGCCTAGCTATTTACCTGTT 57.252 40.909 0.00 0.00 0.00 3.16
4168 8434 2.704725 TGAAGTTGCTTTGATTCGCC 57.295 45.000 0.00 0.00 0.00 5.54
4170 8436 4.786507 TGTCATGAAGTTGCTTTGATTCG 58.213 39.130 0.00 0.00 0.00 3.34
4349 8648 1.072173 TCATCTGGTGGGTGTTGACAG 59.928 52.381 0.00 0.00 0.00 3.51
4356 8655 1.806542 CGAAGTTTCATCTGGTGGGTG 59.193 52.381 0.00 0.00 0.00 4.61
4398 8697 1.473434 GCTTCAGGGATGGAGTTACCG 60.473 57.143 0.00 0.00 42.61 4.02
4696 9014 6.774673 TGGTTATATTCACAGTGAAAGGACA 58.225 36.000 19.92 11.28 40.12 4.02
4797 9116 7.775053 AACAACATGGAGGTAAACAATGTAT 57.225 32.000 0.00 0.00 0.00 2.29
4800 9119 7.784633 AAAAACAACATGGAGGTAAACAATG 57.215 32.000 0.00 0.00 0.00 2.82


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

AutoCloner maintained by Alex Coulton.