Multiple sequence alignment - TraesCS5A01G450700

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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 TraesCS5A01G450700 chr5A 100.000 3296 0 0 1 3296 632662821 632666116 0.000000e+00 6087.0
1 TraesCS5A01G450700 chr5A 89.030 237 8 13 2357 2592 315842271 315842490 9.010000e-71 278.0
2 TraesCS5A01G450700 chr5A 93.048 187 11 2 6 190 632650714 632650900 4.190000e-69 272.0
3 TraesCS5A01G450700 chr5A 83.505 97 16 0 1395 1491 623644240 623644336 1.260000e-14 91.6
4 TraesCS5A01G450700 chr5D 89.760 3369 182 62 1 3294 505122748 505126028 0.000000e+00 4159.0
5 TraesCS5A01G450700 chr5D 87.458 893 41 26 2357 3241 29466105 29466934 0.000000e+00 963.0
6 TraesCS5A01G450700 chr5D 89.299 542 20 15 2404 2939 447516218 447515709 0.000000e+00 645.0
7 TraesCS5A01G450700 chr5D 85.039 635 55 19 2669 3294 182438764 182438161 7.820000e-171 610.0
8 TraesCS5A01G450700 chr5B 86.480 3432 202 100 1 3294 634980545 634983852 0.000000e+00 3526.0
9 TraesCS5A01G450700 chr1D 88.341 892 36 26 2357 3241 288277468 288278298 0.000000e+00 1009.0
10 TraesCS5A01G450700 chr3D 87.570 893 42 26 2357 3241 47562858 47563689 0.000000e+00 970.0
11 TraesCS5A01G450700 chr3D 89.154 544 18 16 2404 2939 562942030 562941520 9.970000e-180 640.0
12 TraesCS5A01G450700 chr3D 85.504 407 34 13 2896 3294 313254609 313254998 5.120000e-108 401.0
13 TraesCS5A01G450700 chr7D 87.374 895 45 24 2357 3244 577029787 577028954 0.000000e+00 965.0
14 TraesCS5A01G450700 chr7D 88.555 533 17 11 2404 2930 453203239 453202745 1.010000e-169 606.0
15 TraesCS5A01G450700 chr7D 87.454 542 23 14 2401 2936 42719219 42719721 1.700000e-162 582.0
16 TraesCS5A01G450700 chr7D 87.873 503 18 11 2443 2939 28303999 28303534 4.810000e-153 551.0
17 TraesCS5A01G450700 chr7D 82.474 97 17 0 1395 1491 514909793 514909697 5.860000e-13 86.1
18 TraesCS5A01G450700 chr6D 87.108 892 44 25 2357 3241 227946482 227947309 0.000000e+00 944.0
19 TraesCS5A01G450700 chr6D 85.859 297 15 7 2645 2936 449087615 449087889 1.160000e-74 291.0
20 TraesCS5A01G450700 chr6D 88.667 150 4 4 2795 2939 471156940 471156799 1.570000e-38 171.0
21 TraesCS5A01G450700 chr7A 86.050 638 48 19 2666 3294 360266678 360267283 0.000000e+00 647.0
22 TraesCS5A01G450700 chr7A 89.451 237 10 7 2357 2592 676177802 676178024 5.380000e-73 285.0
23 TraesCS5A01G450700 chr4D 88.192 542 19 13 2404 2939 224454102 224453600 3.640000e-169 604.0
24 TraesCS5A01G450700 chr2D 87.085 542 24 15 2404 2939 581699098 581698597 3.690000e-159 571.0
25 TraesCS5A01G450700 chr2D 86.241 407 33 12 2896 3294 121235065 121235456 1.410000e-113 420.0
26 TraesCS5A01G450700 chr2A 85.714 427 34 18 2878 3294 405140685 405141094 3.040000e-115 425.0
27 TraesCS5A01G450700 chr2A 85.246 427 36 18 2878 3294 396000664 396000255 6.580000e-112 414.0
28 TraesCS5A01G450700 chr2A 82.295 305 36 10 1203 1491 775611482 775611180 7.060000e-62 248.0
29 TraesCS5A01G450700 chr6B 81.967 305 37 9 1203 1491 497825513 497825211 3.290000e-60 243.0
30 TraesCS5A01G450700 chr6B 79.070 258 36 10 1250 1491 103157891 103157636 9.470000e-36 161.0
31 TraesCS5A01G450700 chr4B 81.967 305 37 10 1203 1491 624392984 624393286 3.290000e-60 243.0
32 TraesCS5A01G450700 chrUn 82.437 279 31 10 1203 1465 478759970 478760246 9.200000e-56 228.0
33 TraesCS5A01G450700 chr2B 80.065 306 37 12 1203 1491 136271142 136270844 4.310000e-49 206.0
34 TraesCS5A01G450700 chr6A 83.505 97 16 0 1395 1491 392215274 392215178 1.260000e-14 91.6
35 TraesCS5A01G450700 chr7B 88.889 63 3 3 1431 1491 58746921 58746981 1.270000e-09 75.0
36 TraesCS5A01G450700 chr7B 80.412 97 19 0 1395 1491 666202574 666202478 1.270000e-09 75.0
37 TraesCS5A01G450700 chr1A 81.928 83 15 0 1409 1491 2521215 2521133 1.640000e-08 71.3


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 TraesCS5A01G450700 chr5A 632662821 632666116 3295 False 6087 6087 100.000 1 3296 1 chr5A.!!$F4 3295
1 TraesCS5A01G450700 chr5D 505122748 505126028 3280 False 4159 4159 89.760 1 3294 1 chr5D.!!$F2 3293
2 TraesCS5A01G450700 chr5D 29466105 29466934 829 False 963 963 87.458 2357 3241 1 chr5D.!!$F1 884
3 TraesCS5A01G450700 chr5D 447515709 447516218 509 True 645 645 89.299 2404 2939 1 chr5D.!!$R2 535
4 TraesCS5A01G450700 chr5D 182438161 182438764 603 True 610 610 85.039 2669 3294 1 chr5D.!!$R1 625
5 TraesCS5A01G450700 chr5B 634980545 634983852 3307 False 3526 3526 86.480 1 3294 1 chr5B.!!$F1 3293
6 TraesCS5A01G450700 chr1D 288277468 288278298 830 False 1009 1009 88.341 2357 3241 1 chr1D.!!$F1 884
7 TraesCS5A01G450700 chr3D 47562858 47563689 831 False 970 970 87.570 2357 3241 1 chr3D.!!$F1 884
8 TraesCS5A01G450700 chr3D 562941520 562942030 510 True 640 640 89.154 2404 2939 1 chr3D.!!$R1 535
9 TraesCS5A01G450700 chr7D 577028954 577029787 833 True 965 965 87.374 2357 3244 1 chr7D.!!$R4 887
10 TraesCS5A01G450700 chr7D 42719219 42719721 502 False 582 582 87.454 2401 2936 1 chr7D.!!$F1 535
11 TraesCS5A01G450700 chr6D 227946482 227947309 827 False 944 944 87.108 2357 3241 1 chr6D.!!$F1 884
12 TraesCS5A01G450700 chr7A 360266678 360267283 605 False 647 647 86.050 2666 3294 1 chr7A.!!$F1 628
13 TraesCS5A01G450700 chr4D 224453600 224454102 502 True 604 604 88.192 2404 2939 1 chr4D.!!$R1 535
14 TraesCS5A01G450700 chr2D 581698597 581699098 501 True 571 571 87.085 2404 2939 1 chr2D.!!$R1 535

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
151 152 0.035247 TAATCCGGACCCCCAAAACG 60.035 55.0 6.12 0.0 0.00 3.60 F
599 650 0.037882 CAGCGCCAACTCAGAGAAGA 60.038 55.0 2.29 0.0 0.00 2.87 F
1163 1273 0.106419 GACGGAGGAGAGACCAGGAT 60.106 60.0 0.00 0.0 42.04 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1188 1298 0.250234 CGCTGTCCTGGAAAGGATCA 59.750 55.000 15.64 0.0 40.51 2.92 R
2262 2415 1.218047 CGATCTTCCGGACTTGCCA 59.782 57.895 1.83 0.0 35.94 4.92 R
2766 2954 0.105964 GTTTCCCCTGTGGCAAAACC 59.894 55.000 0.00 0.0 33.20 3.27 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
55 56 5.535783 TCTGAAACCAATGAGCTGATTTTCA 59.464 36.000 10.00 10.00 32.13 2.69
60 61 3.863424 CCAATGAGCTGATTTTCACATGC 59.137 43.478 0.00 0.00 0.00 4.06
83 84 2.268920 GGCACCAGGATGAAGCGA 59.731 61.111 0.00 0.00 39.69 4.93
84 85 1.153086 GGCACCAGGATGAAGCGAT 60.153 57.895 0.00 0.00 39.69 4.58
85 86 0.106708 GGCACCAGGATGAAGCGATA 59.893 55.000 0.00 0.00 39.69 2.92
86 87 1.475034 GGCACCAGGATGAAGCGATAA 60.475 52.381 0.00 0.00 39.69 1.75
87 88 2.498167 GCACCAGGATGAAGCGATAAT 58.502 47.619 0.00 0.00 39.69 1.28
91 92 3.136443 ACCAGGATGAAGCGATAATCCAA 59.864 43.478 15.41 0.00 42.04 3.53
151 152 0.035247 TAATCCGGACCCCCAAAACG 60.035 55.000 6.12 0.00 0.00 3.60
226 228 0.752054 TCACTTTGGGGCTTGCTTTG 59.248 50.000 0.00 0.00 0.00 2.77
308 333 0.321653 GTCTCTTTCGCCACCCACAT 60.322 55.000 0.00 0.00 0.00 3.21
314 339 1.169661 TTCGCCACCCACATGACAAC 61.170 55.000 0.00 0.00 0.00 3.32
324 354 1.514087 CATGACAACATGCAGCCCC 59.486 57.895 0.00 0.00 45.51 5.80
325 355 1.077086 ATGACAACATGCAGCCCCA 59.923 52.632 0.00 0.00 35.21 4.96
329 359 0.835941 ACAACATGCAGCCCCAAAAA 59.164 45.000 0.00 0.00 0.00 1.94
377 421 1.197264 CTACATCTACGTAGCCCGAGC 59.803 57.143 18.00 0.00 40.70 5.03
491 542 6.531923 ACTACAACTTTACTTTCTTCCTCCC 58.468 40.000 0.00 0.00 0.00 4.30
492 543 4.726583 ACAACTTTACTTTCTTCCTCCCC 58.273 43.478 0.00 0.00 0.00 4.81
493 544 4.079970 CAACTTTACTTTCTTCCTCCCCC 58.920 47.826 0.00 0.00 0.00 5.40
494 545 3.610260 ACTTTACTTTCTTCCTCCCCCT 58.390 45.455 0.00 0.00 0.00 4.79
495 546 3.587951 ACTTTACTTTCTTCCTCCCCCTC 59.412 47.826 0.00 0.00 0.00 4.30
496 547 3.579742 TTACTTTCTTCCTCCCCCTCT 57.420 47.619 0.00 0.00 0.00 3.69
497 548 1.959710 ACTTTCTTCCTCCCCCTCTC 58.040 55.000 0.00 0.00 0.00 3.20
498 549 1.152271 ACTTTCTTCCTCCCCCTCTCA 59.848 52.381 0.00 0.00 0.00 3.27
499 550 1.557371 CTTTCTTCCTCCCCCTCTCAC 59.443 57.143 0.00 0.00 0.00 3.51
500 551 0.793617 TTCTTCCTCCCCCTCTCACT 59.206 55.000 0.00 0.00 0.00 3.41
525 576 5.810095 TCACTCTCACTCTCTCACTCAATA 58.190 41.667 0.00 0.00 0.00 1.90
526 577 6.241645 TCACTCTCACTCTCTCACTCAATAA 58.758 40.000 0.00 0.00 0.00 1.40
527 578 6.889177 TCACTCTCACTCTCTCACTCAATAAT 59.111 38.462 0.00 0.00 0.00 1.28
553 604 0.951558 TTTGCTCGCAGGAAGAAACC 59.048 50.000 0.00 0.00 0.00 3.27
599 650 0.037882 CAGCGCCAACTCAGAGAAGA 60.038 55.000 2.29 0.00 0.00 2.87
602 653 0.891373 CGCCAACTCAGAGAAGAGGA 59.109 55.000 3.79 0.00 39.97 3.71
603 654 1.273606 CGCCAACTCAGAGAAGAGGAA 59.726 52.381 3.79 0.00 39.97 3.36
662 725 2.490993 AAAGAAAAGCGGGCATGGCG 62.491 55.000 13.76 9.77 35.00 5.69
909 1000 4.681978 AAGCCAGCGTCGTCACCC 62.682 66.667 0.00 0.00 0.00 4.61
943 1047 3.560239 GGGGAAAGAAGAAACAGAGGAGG 60.560 52.174 0.00 0.00 0.00 4.30
944 1048 3.560239 GGGAAAGAAGAAACAGAGGAGGG 60.560 52.174 0.00 0.00 0.00 4.30
945 1049 3.560239 GGAAAGAAGAAACAGAGGAGGGG 60.560 52.174 0.00 0.00 0.00 4.79
946 1050 2.723530 AGAAGAAACAGAGGAGGGGA 57.276 50.000 0.00 0.00 0.00 4.81
947 1051 2.261729 AGAAGAAACAGAGGAGGGGAC 58.738 52.381 0.00 0.00 0.00 4.46
1080 1190 2.420722 TCTTGTTTTGGTGTCGTTGGTC 59.579 45.455 0.00 0.00 0.00 4.02
1140 1250 4.172512 CGGAGGATGCTGCTGGCT 62.173 66.667 3.89 0.00 42.39 4.75
1143 1253 3.013327 AGGATGCTGCTGGCTGGA 61.013 61.111 0.00 0.00 42.39 3.86
1156 1266 1.077357 GCTGGAGACGGAGGAGAGA 60.077 63.158 0.00 0.00 39.98 3.10
1163 1273 0.106419 GACGGAGGAGAGACCAGGAT 60.106 60.000 0.00 0.00 42.04 3.24
1188 1298 1.839894 GGAGGATTTCCGGGCTGAT 59.160 57.895 0.00 0.00 42.08 2.90
1236 1346 2.199535 CCCAATGGCCCTGATCCC 59.800 66.667 0.00 0.00 0.00 3.85
1306 1416 3.370061 GCAAGATTGGCTCTGAATTTTGC 59.630 43.478 7.46 7.46 41.12 3.68
1308 1418 2.165030 AGATTGGCTCTGAATTTTGCGG 59.835 45.455 0.00 0.00 31.12 5.69
1313 1423 0.457337 CTCTGAATTTTGCGGGCTGC 60.457 55.000 12.43 12.43 46.70 5.25
1329 1463 1.952839 GCTGCTTTCCCCTCCTCTTTC 60.953 57.143 0.00 0.00 0.00 2.62
1351 1485 4.058124 CTGTTCATCCAACTTCAGTTCGA 58.942 43.478 0.00 0.00 35.83 3.71
1384 1518 2.308570 TGAGTCATGTGGCCCTGTAAAT 59.691 45.455 0.00 0.00 0.00 1.40
1474 1608 4.370364 TCTTGAAGTTTGGTTCTGTTGC 57.630 40.909 0.00 0.00 0.00 4.17
1495 1629 9.033481 TGTTGCTTTGAAATCTGAAAATGTTAG 57.967 29.630 0.00 0.00 0.00 2.34
1562 1706 2.834549 CAGTGGGGTGACAGACTCTATT 59.165 50.000 0.00 0.00 0.00 1.73
1563 1707 2.834549 AGTGGGGTGACAGACTCTATTG 59.165 50.000 0.00 0.00 0.00 1.90
1564 1708 2.832129 GTGGGGTGACAGACTCTATTGA 59.168 50.000 0.00 0.00 0.00 2.57
1566 1710 4.080863 GTGGGGTGACAGACTCTATTGAAT 60.081 45.833 0.00 0.00 0.00 2.57
1567 1711 4.536090 TGGGGTGACAGACTCTATTGAATT 59.464 41.667 0.00 0.00 0.00 2.17
1609 1753 2.191128 AAAGCACTCTTACTGCCTGG 57.809 50.000 0.00 0.00 35.01 4.45
1651 1795 6.959639 ACAAGTTCTTGGTTTATGACATGT 57.040 33.333 15.51 0.00 0.00 3.21
1659 1803 9.906660 TTCTTGGTTTATGACATGTTTAATGTC 57.093 29.630 10.77 10.77 46.28 3.06
1680 1824 6.199376 TGTCCCATGAAATAGGTCTAGTGTA 58.801 40.000 0.00 0.00 0.00 2.90
1699 1843 7.544804 AGTGTATAATGTGCCATCTGATAGA 57.455 36.000 0.00 0.00 0.00 1.98
1706 1850 3.384789 TGTGCCATCTGATAGACTACACC 59.615 47.826 0.00 0.00 0.00 4.16
1731 1875 6.423302 CAGTTCACTCTGTAGCATTCCATATC 59.577 42.308 0.00 0.00 0.00 1.63
1747 1891 6.387192 TCCATATCCTCTGTTTTCCTGAAA 57.613 37.500 0.00 0.00 0.00 2.69
1760 1904 7.950512 TGTTTTCCTGAAATTTCTTATGCTGA 58.049 30.769 18.64 3.06 0.00 4.26
1801 1945 5.382618 AAGAATTCAGGAACTCAACATGC 57.617 39.130 8.44 0.00 34.60 4.06
1807 1951 5.947228 TCAGGAACTCAACATGCTTTAAG 57.053 39.130 0.00 0.00 34.60 1.85
1808 1952 5.620206 TCAGGAACTCAACATGCTTTAAGA 58.380 37.500 0.00 0.00 34.60 2.10
1809 1953 5.470098 TCAGGAACTCAACATGCTTTAAGAC 59.530 40.000 0.00 0.00 34.60 3.01
1910 2054 1.074775 GCCTCACACCCACATTCCA 59.925 57.895 0.00 0.00 0.00 3.53
1915 2059 3.561097 CCTCACACCCACATTCCACAATA 60.561 47.826 0.00 0.00 0.00 1.90
2016 2160 8.425577 TCTTTCAGCTATAGCAAGTTGATTAC 57.574 34.615 26.07 0.00 45.16 1.89
2227 2380 1.590932 CTGCTCCAATCCCTTCATCG 58.409 55.000 0.00 0.00 0.00 3.84
2240 2393 2.630098 CCTTCATCGCCCTCTAATCTGA 59.370 50.000 0.00 0.00 0.00 3.27
2247 2400 4.887748 TCGCCCTCTAATCTGATGATTTC 58.112 43.478 0.00 0.00 42.37 2.17
2259 2412 3.624777 TGATGATTTCTTCTTCAGGGGC 58.375 45.455 0.00 0.00 34.53 5.80
2262 2415 0.329596 ATTTCTTCTTCAGGGGCGCT 59.670 50.000 7.64 0.00 0.00 5.92
2440 2623 1.691801 GGTGTAACTAGGGAGGGGGAG 60.692 61.905 0.00 0.00 36.74 4.30
2546 2731 0.604780 CAGAGGCTGTGTTCTGGTGG 60.605 60.000 2.99 0.00 37.70 4.61
2547 2732 1.056700 AGAGGCTGTGTTCTGGTGGT 61.057 55.000 0.00 0.00 0.00 4.16
2554 2739 1.101049 GTGTTCTGGTGGTGTGGTGG 61.101 60.000 0.00 0.00 0.00 4.61
2629 2815 2.718073 GCAATGGGGGCAAGAGCTG 61.718 63.158 0.00 0.00 41.70 4.24
2641 2828 2.512705 CAAGAGCTGCTTTCCCTTTCT 58.487 47.619 2.53 0.00 33.60 2.52
2642 2829 2.889678 CAAGAGCTGCTTTCCCTTTCTT 59.110 45.455 2.53 0.00 33.60 2.52
2643 2830 3.235750 AGAGCTGCTTTCCCTTTCTTT 57.764 42.857 2.53 0.00 0.00 2.52
2644 2831 3.570540 AGAGCTGCTTTCCCTTTCTTTT 58.429 40.909 2.53 0.00 0.00 2.27
2728 2916 4.511454 GGTTTTGATGCCCACTTTCTTTTC 59.489 41.667 0.00 0.00 0.00 2.29
2729 2917 4.335400 TTTGATGCCCACTTTCTTTTCC 57.665 40.909 0.00 0.00 0.00 3.13
2766 2954 4.693283 TCAGTTTCAGAACCACACAGTAG 58.307 43.478 0.00 0.00 36.39 2.57
2779 2967 1.608590 CACAGTAGGTTTTGCCACAGG 59.391 52.381 0.00 0.00 40.61 4.00
2783 2971 0.854218 TAGGTTTTGCCACAGGGGAA 59.146 50.000 0.00 0.00 43.49 3.97
2868 3061 5.486063 TCACCTAATAAAGTAACCCTGCTCA 59.514 40.000 0.00 0.00 0.00 4.26
2869 3062 5.585047 CACCTAATAAAGTAACCCTGCTCAC 59.415 44.000 0.00 0.00 0.00 3.51
2870 3063 5.487845 ACCTAATAAAGTAACCCTGCTCACT 59.512 40.000 0.00 0.00 0.00 3.41
2871 3064 6.670902 ACCTAATAAAGTAACCCTGCTCACTA 59.329 38.462 0.00 0.00 0.00 2.74
2872 3065 7.147707 ACCTAATAAAGTAACCCTGCTCACTAG 60.148 40.741 0.00 0.00 0.00 2.57
2873 3066 6.869206 AATAAAGTAACCCTGCTCACTAGA 57.131 37.500 0.00 0.00 0.00 2.43
2874 3067 4.810191 AAAGTAACCCTGCTCACTAGAG 57.190 45.455 0.00 0.00 44.96 2.43
2914 3107 1.250154 TTCCCCATCTTGCTTTGCCG 61.250 55.000 0.00 0.00 0.00 5.69
2958 3156 7.397892 TTTTTCCCCTCCAAAATTTCAAAAC 57.602 32.000 0.00 0.00 0.00 2.43
2961 3159 5.679601 TCCCCTCCAAAATTTCAAAACTTG 58.320 37.500 0.00 0.00 0.00 3.16
3115 3331 1.002868 CAGAGGAACACCAGCCAGG 60.003 63.158 0.00 0.00 45.67 4.45
3134 3350 4.918278 TGCCAGCCAAAGCAGCCA 62.918 61.111 0.00 0.00 43.56 4.75
3187 3404 1.211457 CACCCTTCTGATTCCCTCCTG 59.789 57.143 0.00 0.00 0.00 3.86
3206 3423 6.488344 CCTCCTGCTCTCTTTAACTTCTTTTT 59.512 38.462 0.00 0.00 0.00 1.94
3257 3474 3.752339 CGAGCCCCCAAAGCAAGC 61.752 66.667 0.00 0.00 0.00 4.01
3294 3511 2.610694 CGCTGTTGCTGTGGGACTG 61.611 63.158 0.00 0.00 36.97 3.51
3295 3512 1.227943 GCTGTTGCTGTGGGACTGA 60.228 57.895 0.00 0.00 36.03 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 6.551385 AATCTGTTGGATTATCGCTTCATC 57.449 37.500 0.00 0.00 42.28 2.92
76 77 4.507756 CGAATCTGTTGGATTATCGCTTCA 59.492 41.667 0.00 0.00 43.90 3.02
77 78 4.745125 TCGAATCTGTTGGATTATCGCTTC 59.255 41.667 0.00 0.00 43.90 3.86
78 79 4.693283 TCGAATCTGTTGGATTATCGCTT 58.307 39.130 0.00 0.00 43.90 4.68
79 80 4.322080 TCGAATCTGTTGGATTATCGCT 57.678 40.909 0.00 0.00 43.90 4.93
80 81 5.403897 TTTCGAATCTGTTGGATTATCGC 57.596 39.130 0.00 0.00 43.90 4.58
81 82 6.202762 TCCATTTCGAATCTGTTGGATTATCG 59.797 38.462 0.00 0.00 43.90 2.92
82 83 7.496529 TCCATTTCGAATCTGTTGGATTATC 57.503 36.000 0.00 0.00 43.90 1.75
83 84 7.040201 CCATCCATTTCGAATCTGTTGGATTAT 60.040 37.037 17.38 3.85 43.90 1.28
84 85 6.262944 CCATCCATTTCGAATCTGTTGGATTA 59.737 38.462 17.38 0.00 43.90 1.75
85 86 5.068198 CCATCCATTTCGAATCTGTTGGATT 59.932 40.000 17.38 0.00 46.24 3.01
86 87 4.581824 CCATCCATTTCGAATCTGTTGGAT 59.418 41.667 15.56 15.56 43.06 3.41
87 88 3.947196 CCATCCATTTCGAATCTGTTGGA 59.053 43.478 15.34 14.37 37.63 3.53
91 92 4.446371 GAGTCCATCCATTTCGAATCTGT 58.554 43.478 0.00 0.00 0.00 3.41
151 152 3.552890 GCCTTGTGTCACCATCCTTTTTC 60.553 47.826 0.00 0.00 0.00 2.29
226 228 0.817654 GGGGCATGGTAAAAGTGAGC 59.182 55.000 0.00 0.00 0.00 4.26
308 333 0.758310 TTTGGGGCTGCATGTTGTCA 60.758 50.000 0.50 0.00 0.00 3.58
314 339 3.439825 GGTAAAATTTTTGGGGCTGCATG 59.560 43.478 9.06 0.00 0.00 4.06
324 354 4.083565 TCTCGGGAGGGGTAAAATTTTTG 58.916 43.478 9.06 0.00 0.00 2.44
325 355 4.043686 TCTCTCGGGAGGGGTAAAATTTTT 59.956 41.667 13.54 0.00 39.86 1.94
329 359 2.023307 TCTCTCTCGGGAGGGGTAAAAT 60.023 50.000 13.51 0.00 40.35 1.82
491 542 2.091541 GTGAGAGTGAGAGTGAGAGGG 58.908 57.143 0.00 0.00 0.00 4.30
492 543 3.009723 GAGTGAGAGTGAGAGTGAGAGG 58.990 54.545 0.00 0.00 0.00 3.69
493 544 3.935203 GAGAGTGAGAGTGAGAGTGAGAG 59.065 52.174 0.00 0.00 0.00 3.20
494 545 3.582647 AGAGAGTGAGAGTGAGAGTGAGA 59.417 47.826 0.00 0.00 0.00 3.27
495 546 3.935203 GAGAGAGTGAGAGTGAGAGTGAG 59.065 52.174 0.00 0.00 0.00 3.51
496 547 3.326297 TGAGAGAGTGAGAGTGAGAGTGA 59.674 47.826 0.00 0.00 0.00 3.41
497 548 3.436704 GTGAGAGAGTGAGAGTGAGAGTG 59.563 52.174 0.00 0.00 0.00 3.51
498 549 3.327757 AGTGAGAGAGTGAGAGTGAGAGT 59.672 47.826 0.00 0.00 0.00 3.24
499 550 3.935203 GAGTGAGAGAGTGAGAGTGAGAG 59.065 52.174 0.00 0.00 0.00 3.20
500 551 3.326297 TGAGTGAGAGAGTGAGAGTGAGA 59.674 47.826 0.00 0.00 0.00 3.27
537 588 0.320771 TCTGGTTTCTTCCTGCGAGC 60.321 55.000 0.00 0.00 0.00 5.03
543 594 4.104738 TCCAACAATCTCTGGTTTCTTCCT 59.895 41.667 0.00 0.00 34.11 3.36
544 595 4.398319 TCCAACAATCTCTGGTTTCTTCC 58.602 43.478 0.00 0.00 34.11 3.46
553 604 7.042797 TCCTTTTTCTTTCCAACAATCTCTG 57.957 36.000 0.00 0.00 0.00 3.35
603 654 2.604382 ATGGCGCCCCTGCTTTTT 60.604 55.556 26.77 0.00 34.43 1.94
624 675 4.034258 GCCATCGCCATCGCCATG 62.034 66.667 0.00 0.00 35.26 3.66
625 676 4.567488 TGCCATCGCCATCGCCAT 62.567 61.111 0.00 0.00 35.26 4.40
626 677 4.792804 TTGCCATCGCCATCGCCA 62.793 61.111 0.00 0.00 35.26 5.69
627 678 2.941964 CTTTTGCCATCGCCATCGCC 62.942 60.000 0.00 0.00 35.26 5.54
628 679 1.587088 CTTTTGCCATCGCCATCGC 60.587 57.895 0.00 0.00 35.26 4.58
629 680 0.451383 TTCTTTTGCCATCGCCATCG 59.549 50.000 0.00 0.00 0.00 3.84
630 681 2.652941 TTTCTTTTGCCATCGCCATC 57.347 45.000 0.00 0.00 0.00 3.51
662 725 2.464459 CCAAAGCGAGCGACCCATC 61.464 63.158 0.00 0.00 0.00 3.51
703 783 0.465460 TGCCGTGCTTTTCAAGGACT 60.465 50.000 6.58 0.00 46.33 3.85
892 975 4.681978 GGGTGACGACGCTGGCTT 62.682 66.667 0.00 0.00 32.30 4.35
915 1006 1.142060 TTTCTTCTTTCCCCGGTGGA 58.858 50.000 7.51 7.51 43.18 4.02
921 1012 3.560239 CCTCCTCTGTTTCTTCTTTCCCC 60.560 52.174 0.00 0.00 0.00 4.81
922 1013 3.560239 CCCTCCTCTGTTTCTTCTTTCCC 60.560 52.174 0.00 0.00 0.00 3.97
923 1014 3.560239 CCCCTCCTCTGTTTCTTCTTTCC 60.560 52.174 0.00 0.00 0.00 3.13
925 1016 3.073209 GTCCCCTCCTCTGTTTCTTCTTT 59.927 47.826 0.00 0.00 0.00 2.52
943 1047 2.041405 CCTCCTCCTCCCTGTCCC 60.041 72.222 0.00 0.00 0.00 4.46
944 1048 2.766229 GCCTCCTCCTCCCTGTCC 60.766 72.222 0.00 0.00 0.00 4.02
945 1049 3.151022 CGCCTCCTCCTCCCTGTC 61.151 72.222 0.00 0.00 0.00 3.51
946 1050 3.670629 CTCGCCTCCTCCTCCCTGT 62.671 68.421 0.00 0.00 0.00 4.00
947 1051 2.837291 CTCGCCTCCTCCTCCCTG 60.837 72.222 0.00 0.00 0.00 4.45
1080 1190 4.778415 CTCTCCGCCACCACGACG 62.778 72.222 0.00 0.00 34.06 5.12
1117 1227 4.598894 CAGCATCCTCCGCCCTCG 62.599 72.222 0.00 0.00 0.00 4.63
1140 1250 1.303615 GGTCTCTCCTCCGTCTCCA 59.696 63.158 0.00 0.00 0.00 3.86
1143 1253 1.208844 TCCTGGTCTCTCCTCCGTCT 61.209 60.000 0.00 0.00 37.07 4.18
1163 1273 1.195115 CCGGAAATCCTCCAGAGTCA 58.805 55.000 0.00 0.00 45.74 3.41
1185 1295 2.092753 GCTGTCCTGGAAAGGATCATCA 60.093 50.000 15.64 0.00 40.51 3.07
1188 1298 0.250234 CGCTGTCCTGGAAAGGATCA 59.750 55.000 15.64 0.00 40.51 2.92
1236 1346 3.074412 GGTGAAGTACCTGTTGTGGATG 58.926 50.000 0.00 0.00 46.51 3.51
1271 1381 3.051327 CAATCTTGCAATGCAACGAACA 58.949 40.909 17.55 0.00 43.99 3.18
1273 1383 2.674954 CCAATCTTGCAATGCAACGAA 58.325 42.857 17.55 6.00 43.99 3.85
1308 1418 1.857638 AAGAGGAGGGGAAAGCAGCC 61.858 60.000 0.00 0.00 0.00 4.85
1313 1423 3.073062 TGAACAGAAAGAGGAGGGGAAAG 59.927 47.826 0.00 0.00 0.00 2.62
1329 1463 4.058124 TCGAACTGAAGTTGGATGAACAG 58.942 43.478 0.00 0.00 37.74 3.16
1351 1485 5.182001 GCCACATGACTCAGAAACTAACATT 59.818 40.000 0.00 0.00 0.00 2.71
1474 1608 6.308766 CCGGCTAACATTTTCAGATTTCAAAG 59.691 38.462 0.00 0.00 0.00 2.77
1495 1629 1.966451 CTCAGACCAACCAACCGGC 60.966 63.158 0.00 0.00 34.57 6.13
1575 1719 7.951530 AGAGTGCTTTATTTCAAATTTGGTG 57.048 32.000 17.90 0.00 0.00 4.17
1609 1753 3.686016 TGTTCTTGGTAAAGAGCCATCC 58.314 45.455 0.73 0.00 43.27 3.51
1659 1803 9.658799 CATTATACACTAGACCTATTTCATGGG 57.341 37.037 0.00 0.00 36.88 4.00
1699 1843 3.256136 GCTACAGAGTGAACTGGTGTAGT 59.744 47.826 20.47 0.00 39.73 2.73
1706 1850 3.930336 TGGAATGCTACAGAGTGAACTG 58.070 45.455 0.00 0.00 42.78 3.16
1731 1875 7.543520 GCATAAGAAATTTCAGGAAAACAGAGG 59.456 37.037 19.99 0.00 33.56 3.69
1747 1891 7.458409 TCTCTTTTTGCTCAGCATAAGAAAT 57.542 32.000 19.67 0.00 38.30 2.17
1782 1926 5.796424 AAAGCATGTTGAGTTCCTGAATT 57.204 34.783 0.00 0.00 0.00 2.17
1807 1951 9.150348 CCCTTTATGGTCAAACAAAATTATGTC 57.850 33.333 0.00 0.00 31.81 3.06
1808 1952 8.100164 CCCCTTTATGGTCAAACAAAATTATGT 58.900 33.333 0.00 0.00 34.24 2.29
1809 1953 8.100164 ACCCCTTTATGGTCAAACAAAATTATG 58.900 33.333 0.00 0.00 0.00 1.90
2016 2160 8.839310 TCTTGAACAGAAAAGAGGAATAAGAG 57.161 34.615 0.00 0.00 0.00 2.85
2227 2380 6.532826 AGAAGAAATCATCAGATTAGAGGGC 58.467 40.000 0.00 0.00 43.52 5.19
2240 2393 2.648059 CGCCCCTGAAGAAGAAATCAT 58.352 47.619 0.00 0.00 0.00 2.45
2247 2400 2.437359 CCAGCGCCCCTGAAGAAG 60.437 66.667 2.29 0.00 44.64 2.85
2259 2412 2.859273 ATCTTCCGGACTTGCCAGCG 62.859 60.000 1.83 0.00 35.94 5.18
2262 2415 1.218047 CGATCTTCCGGACTTGCCA 59.782 57.895 1.83 0.00 35.94 4.92
2354 2535 4.206375 TGTTTGTTCCTTCTTGAGATGCA 58.794 39.130 0.00 0.00 0.00 3.96
2355 2536 4.836125 TGTTTGTTCCTTCTTGAGATGC 57.164 40.909 0.00 0.00 0.00 3.91
2399 2581 1.283029 ACAACATCCATCCAGACCCAG 59.717 52.381 0.00 0.00 0.00 4.45
2440 2623 4.366684 CCCAAGTCCAGGCCACCC 62.367 72.222 5.01 0.00 0.00 4.61
2523 2708 1.876156 CCAGAACACAGCCTCTGTTTC 59.124 52.381 0.00 5.56 42.59 2.78
2678 2865 6.750148 ACAATGTGCTAATAGTAGTAGGAGC 58.250 40.000 6.76 6.57 0.00 4.70
2728 2916 1.909302 ACTGATACAGTGACAAGGGGG 59.091 52.381 0.00 0.00 43.63 5.40
2729 2917 3.703001 AACTGATACAGTGACAAGGGG 57.297 47.619 5.17 0.00 44.62 4.79
2766 2954 0.105964 GTTTCCCCTGTGGCAAAACC 59.894 55.000 0.00 0.00 33.20 3.27
2779 2967 4.515567 TGTTTGTTTGTTTGTTGGTTTCCC 59.484 37.500 0.00 0.00 0.00 3.97
2783 2971 5.008118 CCTGTTGTTTGTTTGTTTGTTGGTT 59.992 36.000 0.00 0.00 0.00 3.67
2784 2972 4.513318 CCTGTTGTTTGTTTGTTTGTTGGT 59.487 37.500 0.00 0.00 0.00 3.67
2785 2973 4.513318 ACCTGTTGTTTGTTTGTTTGTTGG 59.487 37.500 0.00 0.00 0.00 3.77
2786 2974 5.235186 TGACCTGTTGTTTGTTTGTTTGTTG 59.765 36.000 0.00 0.00 0.00 3.33
2868 3061 4.401202 GCAAAAGCCTCTCTACTCTCTAGT 59.599 45.833 0.00 0.00 39.91 2.57
2869 3062 4.202111 GGCAAAAGCCTCTCTACTCTCTAG 60.202 50.000 0.00 0.00 0.00 2.43
2870 3063 3.702045 GGCAAAAGCCTCTCTACTCTCTA 59.298 47.826 0.00 0.00 0.00 2.43
2871 3064 2.499693 GGCAAAAGCCTCTCTACTCTCT 59.500 50.000 0.00 0.00 0.00 3.10
2872 3065 2.234908 TGGCAAAAGCCTCTCTACTCTC 59.765 50.000 8.11 0.00 0.00 3.20
2873 3066 2.235898 CTGGCAAAAGCCTCTCTACTCT 59.764 50.000 8.11 0.00 0.00 3.24
2874 3067 2.027653 ACTGGCAAAAGCCTCTCTACTC 60.028 50.000 8.11 0.00 0.00 2.59
2939 3137 5.296531 CACAAGTTTTGAAATTTTGGAGGGG 59.703 40.000 0.00 0.00 0.00 4.79
2990 3202 5.477510 TGTTGGATGCAAATGTGTTATTCC 58.522 37.500 0.00 0.00 0.00 3.01
3122 3338 1.666872 CTTGCTTGGCTGCTTTGGC 60.667 57.895 0.00 0.23 39.26 4.52
3123 3339 1.666872 GCTTGCTTGGCTGCTTTGG 60.667 57.895 0.00 0.00 0.00 3.28
3206 3423 5.860611 TCAAAGCTACTACTAAGCCACAAA 58.139 37.500 0.00 0.00 41.02 2.83
3211 3428 4.330347 GCTGTTCAAAGCTACTACTAAGCC 59.670 45.833 0.00 0.00 41.02 4.35
3257 3474 4.767255 GCTCTCACCACCCCAGCG 62.767 72.222 0.00 0.00 0.00 5.18


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

AutoCloner maintained by Alex Coulton.