Multiple sequence alignment - TraesCS2A01G372600

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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 TraesCS2A01G372600 chr2A 100.000 3036 0 0 1 3036 615343114 615346149 0.000000e+00 5607
1 TraesCS2A01G372600 chr2B 89.731 3126 175 47 2 3036 553611963 553615033 0.000000e+00 3860
2 TraesCS2A01G372600 chr2D 89.558 3122 178 57 2 3036 473274752 473277812 0.000000e+00 3823
3 TraesCS2A01G372600 chr1B 83.283 329 40 10 2284 2602 599469634 599469957 3.830000e-74 289


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 TraesCS2A01G372600 chr2A 615343114 615346149 3035 False 5607 5607 100.000 1 3036 1 chr2A.!!$F1 3035
1 TraesCS2A01G372600 chr2B 553611963 553615033 3070 False 3860 3860 89.731 2 3036 1 chr2B.!!$F1 3034
2 TraesCS2A01G372600 chr2D 473274752 473277812 3060 False 3823 3823 89.558 2 3036 1 chr2D.!!$F1 3034

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
609 636 0.036875 GTGGGTTCTTCAGTGGGGAG 59.963 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2540 2627 0.175302 TGCAGTTGGGCAAACACTTG 59.825 50.0 7.64 0.0 41.65 3.16 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
123 124 2.682582 GATTGGGACGGGGCATCTCC 62.683 65.000 0.00 0.00 0.00 3.71
169 190 2.777114 TGGTCTTCCATGGCTAATAGCA 59.223 45.455 14.76 3.15 40.09 3.49
171 192 3.142174 GTCTTCCATGGCTAATAGCACC 58.858 50.000 14.76 0.00 44.75 5.01
188 209 8.677148 AATAGCACCGAATATTCAATTACAGT 57.323 30.769 15.57 0.00 0.00 3.55
193 214 7.384115 GCACCGAATATTCAATTACAGTAGCTA 59.616 37.037 15.57 0.00 0.00 3.32
213 234 6.783892 GCTAGGATCAGCTTTAATCTTCTG 57.216 41.667 0.00 0.00 38.57 3.02
234 255 1.299316 CAGCACCTGCAAACGTTGG 60.299 57.895 0.00 0.00 45.16 3.77
236 257 3.119193 CACCTGCAAACGTTGGCT 58.881 55.556 27.10 5.61 0.00 4.75
237 258 1.437160 CACCTGCAAACGTTGGCTT 59.563 52.632 27.10 9.90 0.00 4.35
242 263 1.601903 CTGCAAACGTTGGCTTAGTCA 59.398 47.619 27.10 6.09 0.00 3.41
244 265 2.423892 TGCAAACGTTGGCTTAGTCAAA 59.576 40.909 27.10 2.50 0.00 2.69
245 266 2.787129 GCAAACGTTGGCTTAGTCAAAC 59.213 45.455 20.60 0.00 0.00 2.93
246 267 3.488553 GCAAACGTTGGCTTAGTCAAACT 60.489 43.478 20.60 0.00 0.00 2.66
247 268 4.260866 GCAAACGTTGGCTTAGTCAAACTA 60.261 41.667 20.60 0.00 0.00 2.24
248 269 5.562113 GCAAACGTTGGCTTAGTCAAACTAT 60.562 40.000 20.60 0.00 29.64 2.12
249 270 5.607119 AACGTTGGCTTAGTCAAACTATG 57.393 39.130 0.00 0.00 29.64 2.23
250 271 3.435671 ACGTTGGCTTAGTCAAACTATGC 59.564 43.478 0.00 13.63 45.61 3.14
257 278 5.768317 GCTTAGTCAAACTATGCAAAACCA 58.232 37.500 15.94 0.00 45.63 3.67
258 279 5.629435 GCTTAGTCAAACTATGCAAAACCAC 59.371 40.000 15.94 0.00 45.63 4.16
261 282 3.003897 GTCAAACTATGCAAAACCACGGA 59.996 43.478 0.00 0.00 0.00 4.69
263 284 3.848272 AACTATGCAAAACCACGGATG 57.152 42.857 0.00 0.00 0.00 3.51
304 325 1.200020 GTGTTCCATGCCTTTCTTCCG 59.800 52.381 0.00 0.00 0.00 4.30
358 380 3.626996 TTGAGCATGGGGGCAGTCG 62.627 63.158 0.00 0.00 35.83 4.18
378 400 2.480853 AATACTGCGGCGTGACACGA 62.481 55.000 31.08 9.52 46.05 4.35
399 421 2.999331 TGGGCATAAGCTAGTGGTTTC 58.001 47.619 0.00 0.00 41.70 2.78
400 422 2.307392 TGGGCATAAGCTAGTGGTTTCA 59.693 45.455 0.00 0.00 41.70 2.69
407 433 6.564328 CATAAGCTAGTGGTTTCATTTTCCC 58.436 40.000 0.00 0.00 35.36 3.97
444 470 4.099633 TCCCAGGAAGATATGCTAGGATG 58.900 47.826 7.05 0.00 32.52 3.51
480 507 4.018688 AACCTAAAGTGGCTTAGGGTTAGG 60.019 45.833 13.69 10.57 45.07 2.69
510 537 6.716628 ACAAAGAGGATAAAGACAGAATGCAA 59.283 34.615 0.00 0.00 42.53 4.08
564 591 3.453717 AGAAATCAGAGCATCCACAGCTA 59.546 43.478 0.00 0.00 43.58 3.32
601 628 3.394274 TGAGAAAGATGGTGGGTTCTTCA 59.606 43.478 0.00 0.00 31.09 3.02
608 635 1.423794 GGTGGGTTCTTCAGTGGGGA 61.424 60.000 0.00 0.00 0.00 4.81
609 636 0.036875 GTGGGTTCTTCAGTGGGGAG 59.963 60.000 0.00 0.00 0.00 4.30
610 637 0.401395 TGGGTTCTTCAGTGGGGAGT 60.401 55.000 0.00 0.00 0.00 3.85
611 638 0.325272 GGGTTCTTCAGTGGGGAGTC 59.675 60.000 0.00 0.00 0.00 3.36
612 639 0.325272 GGTTCTTCAGTGGGGAGTCC 59.675 60.000 0.00 0.00 0.00 3.85
613 640 1.353091 GTTCTTCAGTGGGGAGTCCT 58.647 55.000 9.58 0.00 36.20 3.85
614 641 1.276705 GTTCTTCAGTGGGGAGTCCTC 59.723 57.143 9.58 5.35 36.20 3.71
637 664 0.318120 CCATTGCTTGCGAAAAGGGT 59.682 50.000 0.00 0.00 0.00 4.34
658 694 7.506971 AGGGTAATTGGAGTGCTTATAGTTAC 58.493 38.462 0.00 0.00 0.00 2.50
671 707 5.923684 GCTTATAGTTACTCTCTGGCACATC 59.076 44.000 0.00 0.00 38.20 3.06
685 721 2.224606 GCACATCGACATGGAATCCAT 58.775 47.619 9.36 9.36 46.37 3.41
948 985 6.882140 TCCTTAAACACATGGTTATAGGTGTG 59.118 38.462 17.31 3.07 43.16 3.82
953 990 5.545658 CACATGGTTATAGGTGTGTTCAC 57.454 43.478 0.00 0.00 43.19 3.18
954 991 5.000591 CACATGGTTATAGGTGTGTTCACA 58.999 41.667 1.23 1.23 45.45 3.58
955 992 5.001232 ACATGGTTATAGGTGTGTTCACAC 58.999 41.667 22.85 22.85 45.45 3.82
976 1013 4.489493 CACGTTATCGACATTTTAAACGCC 59.511 41.667 0.00 0.00 42.38 5.68
979 1026 5.224313 CGTTATCGACATTTTAAACGCCTTG 59.776 40.000 0.00 0.00 39.71 3.61
982 1029 3.560481 TCGACATTTTAAACGCCTTGACA 59.440 39.130 0.00 0.00 0.00 3.58
1020 1070 4.276926 CCCACTTTTCTGACTTCTCCTTTG 59.723 45.833 0.00 0.00 0.00 2.77
1021 1071 4.884164 CCACTTTTCTGACTTCTCCTTTGT 59.116 41.667 0.00 0.00 0.00 2.83
1031 1081 7.819415 TCTGACTTCTCCTTTGTATTACATGTG 59.181 37.037 9.11 0.00 0.00 3.21
1053 1103 4.043059 TGTTCCTACTGTCTACTGACCTCT 59.957 45.833 0.00 0.00 42.28 3.69
1055 1105 3.118702 TCCTACTGTCTACTGACCTCTCG 60.119 52.174 0.00 0.00 42.28 4.04
1101 1151 2.352814 CCGTGAGTTCTTCGACCAGAAT 60.353 50.000 3.01 0.00 38.34 2.40
1129 1179 3.801638 GCGACAGATAGCATCCTGATTGT 60.802 47.826 6.31 0.00 34.65 2.71
1205 1255 1.338674 CCAGTGTCCGATAACAAGCCA 60.339 52.381 0.00 0.00 0.00 4.75
1334 1390 1.449353 CCATCTCTACTGCTGGCCC 59.551 63.158 0.00 0.00 0.00 5.80
1343 1399 1.351080 ACTGCTGGCCCTGCATCTAT 61.351 55.000 16.16 0.00 37.65 1.98
1355 1411 1.839598 GCATCTATGAGTGGCTGCGC 61.840 60.000 0.00 0.00 0.00 6.09
1376 1432 1.414181 CCATCGGTGGTATCAGCTTCT 59.586 52.381 6.53 0.00 40.83 2.85
1495 1551 2.947652 CGAAGAAATCACTGGATGGCAT 59.052 45.455 0.00 0.00 32.92 4.40
1580 1636 1.227645 CGATGATGACCGGCACCAT 60.228 57.895 0.00 2.83 0.00 3.55
1603 1659 3.958629 ATGTGGAGCCCAGCCCTCT 62.959 63.158 0.00 0.00 32.34 3.69
1661 1717 0.872388 GTGCCACCGAATTCGACTTT 59.128 50.000 28.76 7.37 43.02 2.66
1709 1765 2.105128 CTGATCCACTCGACGGCC 59.895 66.667 0.00 0.00 0.00 6.13
1733 1789 2.356278 GTGCTTGGAGGGATGGCA 59.644 61.111 0.00 0.00 0.00 4.92
1739 1795 3.092511 GGAGGGATGGCAGAGGCA 61.093 66.667 0.00 0.00 43.71 4.75
1818 1874 3.991051 CTGTCGCGGACCACACCT 61.991 66.667 6.13 0.00 0.00 4.00
1931 1987 0.603707 TCTTGTTCTGAAGCAGGGCG 60.604 55.000 0.00 0.00 31.51 6.13
1935 1991 0.320771 GTTCTGAAGCAGGGCGAGAA 60.321 55.000 0.00 0.00 31.51 2.87
1936 1992 0.396435 TTCTGAAGCAGGGCGAGAAA 59.604 50.000 0.00 0.00 31.51 2.52
1941 1997 0.398318 AAGCAGGGCGAGAAACTCTT 59.602 50.000 0.00 0.00 0.00 2.85
2103 2162 3.538591 TGCTCTTAACGGTCTCTATCGA 58.461 45.455 0.00 0.00 32.06 3.59
2221 2280 3.947834 GGAACTCCATTACCTGAACCATG 59.052 47.826 0.00 0.00 35.64 3.66
2224 2283 2.947652 CTCCATTACCTGAACCATGCAG 59.052 50.000 0.00 0.00 0.00 4.41
2236 2295 0.899720 CCATGCAGATGGCCTGTTTT 59.100 50.000 3.32 0.00 43.00 2.43
2262 2321 1.339055 GCCTGCATCTGTCACTACCAA 60.339 52.381 0.00 0.00 0.00 3.67
2273 2332 6.058833 TCTGTCACTACCAAGTAATGCAAAA 58.941 36.000 0.00 0.00 33.48 2.44
2282 2343 6.458210 ACCAAGTAATGCAAAATTTCCTCAG 58.542 36.000 0.00 0.00 0.00 3.35
2288 2349 2.892852 TGCAAAATTTCCTCAGTCTGGG 59.107 45.455 0.00 0.00 0.00 4.45
2293 2354 6.462347 GCAAAATTTCCTCAGTCTGGGTTTTA 60.462 38.462 0.00 0.00 0.00 1.52
2314 2375 8.992073 GTTTTATTTCCAGAATCTGCATTGTTT 58.008 29.630 4.40 0.00 0.00 2.83
2328 2390 3.066481 GCATTGTTTTTGCATTGGTTGGT 59.934 39.130 0.00 0.00 39.90 3.67
2338 2400 0.106521 ATTGGTTGGTGGTTTGCTGC 59.893 50.000 0.00 0.00 0.00 5.25
2356 2420 4.628333 TGCTGCTACTGGATTTACGTTTAC 59.372 41.667 0.00 0.00 0.00 2.01
2385 2449 2.475864 CCCATTCGTTGTTTGTGCAATG 59.524 45.455 0.00 0.00 36.87 2.82
2394 2458 5.257108 GTTGTTTGTGCAATGAATGTGTTG 58.743 37.500 0.00 0.00 0.00 3.33
2413 2478 7.694886 TGTGTTGACATTTACGTACATTTTCA 58.305 30.769 0.00 0.00 0.00 2.69
2414 2479 8.182227 TGTGTTGACATTTACGTACATTTTCAA 58.818 29.630 9.81 9.81 0.00 2.69
2463 2542 4.827304 TGCAAATTGAATGACACGAAGA 57.173 36.364 0.00 0.00 0.00 2.87
2468 2547 8.028354 TGCAAATTGAATGACACGAAGAATATT 58.972 29.630 0.00 0.00 0.00 1.28
2487 2566 7.977853 AGAATATTGCGCATCAGAAAAGAATTT 59.022 29.630 12.75 0.00 42.41 1.82
2534 2621 0.981943 AGTAGCCGTGCCCTACTTTT 59.018 50.000 0.00 0.00 41.97 2.27
2535 2622 2.181975 AGTAGCCGTGCCCTACTTTTA 58.818 47.619 0.00 0.00 41.97 1.52
2537 2624 2.327200 AGCCGTGCCCTACTTTTATC 57.673 50.000 0.00 0.00 0.00 1.75
2538 2625 0.935196 GCCGTGCCCTACTTTTATCG 59.065 55.000 0.00 0.00 0.00 2.92
2540 2627 2.199236 CCGTGCCCTACTTTTATCGAC 58.801 52.381 0.00 0.00 0.00 4.20
2571 2663 1.400629 CCAACTGCATCTTTCTGCACG 60.401 52.381 0.00 0.00 46.76 5.34
2652 2772 3.067320 CAGCAGCAGCACAGTAGTAGATA 59.933 47.826 3.17 0.00 45.49 1.98
2696 2816 7.368833 GCGGTGTACTGAACTATACTGATTAT 58.631 38.462 0.00 0.00 0.00 1.28
2723 2843 6.934645 TGTGTTCAAAAGAGGAACTATACTGG 59.065 38.462 6.80 0.00 43.84 4.00
2728 2848 9.667107 TTCAAAAGAGGAACTATACTGGTTATG 57.333 33.333 0.00 0.00 41.55 1.90
2734 2854 6.120220 AGGAACTATACTGGTTATGTTTGCC 58.880 40.000 0.00 0.00 36.02 4.52
2751 2871 1.288752 CCAACGGCGGCAAAATCTT 59.711 52.632 13.24 0.00 0.00 2.40
2757 2877 2.354821 ACGGCGGCAAAATCTTAGAATC 59.645 45.455 13.24 0.00 0.00 2.52
2814 2934 6.760440 AGTGATAATCATCCCACAAGAGAT 57.240 37.500 0.00 0.00 32.35 2.75
2820 2940 2.905736 TCATCCCACAAGAGATGACACA 59.094 45.455 0.00 0.00 42.98 3.72
2842 2962 4.556942 TCAATAGCTCAATCCATTTGCG 57.443 40.909 0.00 0.00 35.16 4.85
2867 2987 1.825474 AGTACGGTTACATGAGCTGCT 59.175 47.619 0.00 0.00 0.00 4.24
2950 3070 3.686916 GGAGAAAGGTTCTACTGCTGT 57.313 47.619 0.66 0.66 40.87 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.819632 GGTGGGGATCGTGATGTGC 60.820 63.158 0.00 0.00 0.00 4.57
169 190 8.088981 CCTAGCTACTGTAATTGAATATTCGGT 58.911 37.037 10.80 0.73 0.00 4.69
171 192 9.862371 ATCCTAGCTACTGTAATTGAATATTCG 57.138 33.333 10.80 0.00 0.00 3.34
193 214 4.459330 GCCAGAAGATTAAAGCTGATCCT 58.541 43.478 0.00 0.00 0.00 3.24
213 234 4.347453 CGTTTGCAGGTGCTGGCC 62.347 66.667 0.00 0.00 42.66 5.36
234 255 5.629435 GTGGTTTTGCATAGTTTGACTAAGC 59.371 40.000 8.03 8.03 43.46 3.09
236 257 5.278071 CCGTGGTTTTGCATAGTTTGACTAA 60.278 40.000 0.00 0.00 33.89 2.24
237 258 4.214545 CCGTGGTTTTGCATAGTTTGACTA 59.785 41.667 0.00 0.00 34.82 2.59
242 263 3.613910 GCATCCGTGGTTTTGCATAGTTT 60.614 43.478 0.00 0.00 35.22 2.66
244 265 1.472480 GCATCCGTGGTTTTGCATAGT 59.528 47.619 0.00 0.00 35.22 2.12
245 266 1.472082 TGCATCCGTGGTTTTGCATAG 59.528 47.619 8.93 0.00 39.98 2.23
246 267 1.539157 TGCATCCGTGGTTTTGCATA 58.461 45.000 8.93 0.00 39.98 3.14
247 268 2.349701 TGCATCCGTGGTTTTGCAT 58.650 47.368 8.93 0.00 39.98 3.96
248 269 3.847621 TGCATCCGTGGTTTTGCA 58.152 50.000 8.93 8.93 42.41 4.08
249 270 2.869233 ATATGCATCCGTGGTTTTGC 57.131 45.000 0.19 4.90 35.67 3.68
250 271 7.433708 TCTATAATATGCATCCGTGGTTTTG 57.566 36.000 0.19 0.00 0.00 2.44
251 272 8.514594 CATTCTATAATATGCATCCGTGGTTTT 58.485 33.333 0.19 0.00 0.00 2.43
263 284 9.173939 GAACACAGTTTGCATTCTATAATATGC 57.826 33.333 10.37 10.37 45.66 3.14
304 325 0.104487 GGCGGCTTAGAGTTACCTCC 59.896 60.000 0.00 0.00 38.58 4.30
344 366 1.148273 TATTCGACTGCCCCCATGC 59.852 57.895 0.00 0.00 0.00 4.06
358 380 1.708027 GTGTCACGCCGCAGTATTC 59.292 57.895 0.00 0.00 0.00 1.75
378 400 3.053693 TGAAACCACTAGCTTATGCCCAT 60.054 43.478 0.00 0.00 40.80 4.00
444 470 4.154195 CACTTTAGGTTGTACTGACATGCC 59.846 45.833 0.00 0.00 34.86 4.40
510 537 6.561519 AATTAGTACAAGGGCTACAGATGT 57.438 37.500 0.00 0.00 0.00 3.06
601 628 1.079438 GGACTGAGGACTCCCCACT 59.921 63.158 0.00 0.00 37.41 4.00
608 635 1.612726 GCAAGCAATGGACTGAGGACT 60.613 52.381 0.00 0.00 0.00 3.85
609 636 0.807496 GCAAGCAATGGACTGAGGAC 59.193 55.000 0.00 0.00 0.00 3.85
610 637 0.674581 CGCAAGCAATGGACTGAGGA 60.675 55.000 0.00 0.00 0.00 3.71
611 638 0.674581 TCGCAAGCAATGGACTGAGG 60.675 55.000 0.00 0.00 37.18 3.86
612 639 1.159285 TTCGCAAGCAATGGACTGAG 58.841 50.000 0.00 0.00 37.18 3.35
613 640 1.603456 TTTCGCAAGCAATGGACTGA 58.397 45.000 0.00 0.00 37.18 3.41
614 641 2.322161 CTTTTCGCAAGCAATGGACTG 58.678 47.619 0.00 0.00 37.18 3.51
637 664 9.422681 AGAGAGTAACTATAAGCACTCCAATTA 57.577 33.333 0.00 0.00 38.53 1.40
658 694 1.568606 CATGTCGATGTGCCAGAGAG 58.431 55.000 0.00 0.00 0.00 3.20
685 721 1.407712 GCGGATGTTAGGTAAAGCCCA 60.408 52.381 0.00 0.00 38.26 5.36
948 985 7.201008 CGTTTAAAATGTCGATAACGTGTGAAC 60.201 37.037 0.00 0.00 40.69 3.18
949 986 6.786573 CGTTTAAAATGTCGATAACGTGTGAA 59.213 34.615 0.00 0.00 40.69 3.18
950 987 6.290643 CGTTTAAAATGTCGATAACGTGTGA 58.709 36.000 0.00 0.00 40.69 3.58
951 988 5.000901 GCGTTTAAAATGTCGATAACGTGTG 59.999 40.000 0.00 0.00 40.12 3.82
952 989 5.074791 GCGTTTAAAATGTCGATAACGTGT 58.925 37.500 0.00 0.00 40.12 4.49
953 990 4.489493 GGCGTTTAAAATGTCGATAACGTG 59.511 41.667 0.00 0.00 40.12 4.49
954 991 4.389687 AGGCGTTTAAAATGTCGATAACGT 59.610 37.500 0.00 0.00 40.12 3.99
955 992 4.889241 AGGCGTTTAAAATGTCGATAACG 58.111 39.130 0.00 0.00 40.71 3.18
956 993 6.247791 GTCAAGGCGTTTAAAATGTCGATAAC 59.752 38.462 0.00 0.00 0.00 1.89
957 994 6.073167 TGTCAAGGCGTTTAAAATGTCGATAA 60.073 34.615 0.00 0.00 0.00 1.75
958 995 5.408909 TGTCAAGGCGTTTAAAATGTCGATA 59.591 36.000 0.00 0.00 0.00 2.92
959 996 4.214545 TGTCAAGGCGTTTAAAATGTCGAT 59.785 37.500 0.00 0.00 0.00 3.59
960 997 3.560481 TGTCAAGGCGTTTAAAATGTCGA 59.440 39.130 0.60 0.00 0.00 4.20
961 998 3.879427 TGTCAAGGCGTTTAAAATGTCG 58.121 40.909 0.00 0.00 0.00 4.35
962 999 3.668656 GCTGTCAAGGCGTTTAAAATGTC 59.331 43.478 0.00 0.00 0.00 3.06
963 1000 3.317993 AGCTGTCAAGGCGTTTAAAATGT 59.682 39.130 0.00 0.00 34.52 2.71
964 1001 3.900941 AGCTGTCAAGGCGTTTAAAATG 58.099 40.909 0.00 0.00 34.52 2.32
965 1002 4.037446 TGAAGCTGTCAAGGCGTTTAAAAT 59.963 37.500 0.00 0.00 31.51 1.82
966 1003 3.378742 TGAAGCTGTCAAGGCGTTTAAAA 59.621 39.130 0.00 0.00 31.51 1.52
976 1013 4.574013 GGGACTAATCATGAAGCTGTCAAG 59.426 45.833 17.19 0.00 40.50 3.02
979 1026 3.873952 GTGGGACTAATCATGAAGCTGTC 59.126 47.826 0.00 6.26 0.00 3.51
982 1029 4.851639 AAGTGGGACTAATCATGAAGCT 57.148 40.909 0.00 0.00 0.00 3.74
1020 1070 8.684520 AGTAGACAGTAGGAACACATGTAATAC 58.315 37.037 0.00 0.00 0.00 1.89
1021 1071 8.683615 CAGTAGACAGTAGGAACACATGTAATA 58.316 37.037 0.00 0.00 0.00 0.98
1031 1081 4.591929 AGAGGTCAGTAGACAGTAGGAAC 58.408 47.826 0.00 0.00 46.80 3.62
1053 1103 8.492673 ACTGCAATCAAATAGAAATAGAACGA 57.507 30.769 0.00 0.00 0.00 3.85
1055 1105 9.937175 GGTACTGCAATCAAATAGAAATAGAAC 57.063 33.333 0.00 0.00 0.00 3.01
1101 1151 2.677836 GGATGCTATCTGTCGCAAACAA 59.322 45.455 0.00 0.00 39.89 2.83
1129 1179 1.573376 CCATTCCCCCACCTTCCATAA 59.427 52.381 0.00 0.00 0.00 1.90
1205 1255 3.588842 TCTCCCCACTGATGTTCTTCATT 59.411 43.478 0.00 0.00 36.83 2.57
1334 1390 1.227639 GCAGCCACTCATAGATGCAG 58.772 55.000 0.00 0.00 33.92 4.41
1355 1411 5.912184 CAGAAGCTGATACCACCGATGGG 62.912 56.522 0.00 0.00 41.42 4.00
1495 1551 4.467084 GCCGTCGAGGAATGGCCA 62.467 66.667 8.56 8.56 45.00 5.36
1523 1579 2.032634 GTGCGCAACATTCTCCCGA 61.033 57.895 14.00 0.00 0.00 5.14
1550 1606 2.353889 GTCATCATCGATGCTGCTTTGT 59.646 45.455 21.53 0.00 39.63 2.83
1580 1636 1.303561 GCTGGGCTCCACATTGTGA 60.304 57.895 18.33 3.87 35.23 3.58
1661 1717 0.543410 TTGGCGAAGGAGGGTAGACA 60.543 55.000 0.00 0.00 0.00 3.41
1709 1765 4.101448 CCTCCAAGCACCCCTCCG 62.101 72.222 0.00 0.00 0.00 4.63
1733 1789 2.345244 CACGGAAGCACTGCCTCT 59.655 61.111 0.00 0.00 0.00 3.69
1739 1795 4.250305 AACGCCCACGGAAGCACT 62.250 61.111 0.00 0.00 46.04 4.40
1886 1942 2.814919 ACACAAGACCACAAACACGAAA 59.185 40.909 0.00 0.00 0.00 3.46
1927 1983 1.801178 CAGAACAAGAGTTTCTCGCCC 59.199 52.381 0.00 0.00 38.30 6.13
1931 1987 6.758886 TCTTCAGTTCAGAACAAGAGTTTCTC 59.241 38.462 15.85 0.00 38.30 2.87
1935 1991 5.363939 CCTCTTCAGTTCAGAACAAGAGTT 58.636 41.667 26.65 4.31 38.70 3.01
1936 1992 4.742138 GCCTCTTCAGTTCAGAACAAGAGT 60.742 45.833 26.65 4.90 38.70 3.24
1941 1997 1.270305 CCGCCTCTTCAGTTCAGAACA 60.270 52.381 15.85 0.00 0.00 3.18
2224 2283 1.511850 GCAAACCAAAACAGGCCATC 58.488 50.000 5.01 0.00 0.00 3.51
2236 2295 0.178995 TGACAGATGCAGGCAAACCA 60.179 50.000 0.00 0.00 39.06 3.67
2262 2321 6.071728 CCAGACTGAGGAAATTTTGCATTACT 60.072 38.462 3.32 0.00 0.00 2.24
2273 2332 6.437477 GGAAATAAAACCCAGACTGAGGAAAT 59.563 38.462 14.71 4.92 0.00 2.17
2288 2349 8.538409 AACAATGCAGATTCTGGAAATAAAAC 57.462 30.769 12.12 0.00 35.08 2.43
2293 2354 6.072893 GCAAAAACAATGCAGATTCTGGAAAT 60.073 34.615 12.12 1.74 43.29 2.17
2314 2375 2.636830 CAAACCACCAACCAATGCAAA 58.363 42.857 0.00 0.00 0.00 3.68
2328 2390 2.584835 AATCCAGTAGCAGCAAACCA 57.415 45.000 0.00 0.00 0.00 3.67
2338 2400 7.167136 GGAGATTCGTAAACGTAAATCCAGTAG 59.833 40.741 11.22 0.00 40.80 2.57
2402 2467 9.782028 CATTTTGAGATGTTTTGAAAATGTACG 57.218 29.630 0.00 0.00 38.40 3.67
2403 2468 9.584839 GCATTTTGAGATGTTTTGAAAATGTAC 57.415 29.630 0.00 0.00 42.24 2.90
2413 2478 8.143193 TCTACAATGTGCATTTTGAGATGTTTT 58.857 29.630 15.89 0.00 0.00 2.43
2414 2479 7.660112 TCTACAATGTGCATTTTGAGATGTTT 58.340 30.769 15.89 0.00 0.00 2.83
2463 2542 8.483307 AAAATTCTTTTCTGATGCGCAATATT 57.517 26.923 17.11 0.00 0.00 1.28
2497 2576 7.491696 ACGGCTACTAATTGAAATGTCTCTAAC 59.508 37.037 0.00 0.00 0.00 2.34
2500 2579 5.812642 CACGGCTACTAATTGAAATGTCTCT 59.187 40.000 0.00 0.00 0.00 3.10
2534 2621 2.550606 GTTGGGCAAACACTTGTCGATA 59.449 45.455 0.00 0.00 38.09 2.92
2535 2622 1.336755 GTTGGGCAAACACTTGTCGAT 59.663 47.619 0.00 0.00 38.09 3.59
2537 2624 0.738389 AGTTGGGCAAACACTTGTCG 59.262 50.000 7.64 0.00 41.61 4.35
2538 2625 1.802508 GCAGTTGGGCAAACACTTGTC 60.803 52.381 7.64 0.00 41.61 3.18
2540 2627 0.175302 TGCAGTTGGGCAAACACTTG 59.825 50.000 7.64 0.00 41.65 3.16
2571 2663 1.808945 CACATGACTTCTCCTTGCACC 59.191 52.381 0.00 0.00 0.00 5.01
2696 2816 9.653287 CAGTATAGTTCCTCTTTTGAACACATA 57.347 33.333 5.99 1.21 43.57 2.29
2734 2854 1.466950 TCTAAGATTTTGCCGCCGTTG 59.533 47.619 0.00 0.00 0.00 4.10
2751 2871 8.521176 GGTCAGTGTTACTCTGTTAAGATTCTA 58.479 37.037 13.12 0.00 34.86 2.10
2757 2877 8.873830 CATATTGGTCAGTGTTACTCTGTTAAG 58.126 37.037 13.12 0.00 34.86 1.85
2814 2934 5.101648 TGGATTGAGCTATTGATGTGTCA 57.898 39.130 0.00 0.00 0.00 3.58
2817 2937 5.690409 GCAAATGGATTGAGCTATTGATGTG 59.310 40.000 0.00 0.00 41.85 3.21
2818 2938 5.506815 CGCAAATGGATTGAGCTATTGATGT 60.507 40.000 0.00 0.00 41.85 3.06
2820 2940 5.117355 CGCAAATGGATTGAGCTATTGAT 57.883 39.130 0.00 0.00 41.85 2.57
2842 2962 4.209288 CAGCTCATGTAACCGTACTATTGC 59.791 45.833 0.00 0.00 0.00 3.56
2867 2987 8.740123 TCTTGACTGGTACAAAAACTGAATTA 57.260 30.769 0.00 0.00 38.70 1.40
2950 3070 2.435938 GGCGATCCAGCGGAACAA 60.436 61.111 1.44 0.00 34.34 2.83


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

AutoCloner maintained by Alex Coulton.