Multiple sequence alignment - TraesCS6B01G339200

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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 TraesCS6B01G339200 chr6B 100.000 3488 0 0 1 3488 597555732 597559219 0.000000e+00 6442.0
1 TraesCS6B01G339200 chr6B 75.332 904 195 28 1005 1897 127040916 127040030 3.240000e-110 409.0
2 TraesCS6B01G339200 chr6D 91.209 3151 122 58 1 3059 399217825 399220912 0.000000e+00 4141.0
3 TraesCS6B01G339200 chr6D 75.774 904 191 28 1005 1897 56553109 56552223 6.920000e-117 431.0
4 TraesCS6B01G339200 chr6D 88.406 345 28 7 3060 3403 399220950 399221283 4.190000e-109 405.0
5 TraesCS6B01G339200 chr6D 90.909 77 6 1 3412 3488 399221267 399221342 6.160000e-18 102.0
6 TraesCS6B01G339200 chr6A 90.452 3163 139 68 1 3059 545317852 545320955 0.000000e+00 4017.0
7 TraesCS6B01G339200 chr6A 75.938 906 186 30 1005 1897 71067867 71066981 1.490000e-118 436.0
8 TraesCS6B01G339200 chr6A 88.539 349 16 8 3060 3403 545320993 545321322 5.420000e-108 401.0
9 TraesCS6B01G339200 chr7D 82.842 1154 175 15 1005 2140 198502379 198501231 0.000000e+00 1013.0
10 TraesCS6B01G339200 chr7A 82.476 1147 180 14 1005 2133 207548560 207547417 0.000000e+00 985.0
11 TraesCS6B01G339200 chr7A 74.642 698 147 27 1217 1902 602232851 602232172 7.370000e-72 281.0
12 TraesCS6B01G339200 chr7B 81.787 1153 189 14 999 2133 162923054 162924203 0.000000e+00 946.0
13 TraesCS6B01G339200 chr3A 88.333 60 4 3 228 286 484992180 484992123 6.250000e-08 69.4
14 TraesCS6B01G339200 chr2A 88.333 60 4 2 228 287 510302704 510302648 6.250000e-08 69.4
15 TraesCS6B01G339200 chr5B 97.436 39 1 0 247 285 289802199 289802237 2.250000e-07 67.6
16 TraesCS6B01G339200 chr4A 87.931 58 4 3 228 284 89418407 89418462 8.080000e-07 65.8
17 TraesCS6B01G339200 chr4D 95.000 40 2 0 247 286 375151055 375151016 2.910000e-06 63.9


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 TraesCS6B01G339200 chr6B 597555732 597559219 3487 False 6442.000000 6442 100.000000 1 3488 1 chr6B.!!$F1 3487
1 TraesCS6B01G339200 chr6B 127040030 127040916 886 True 409.000000 409 75.332000 1005 1897 1 chr6B.!!$R1 892
2 TraesCS6B01G339200 chr6D 399217825 399221342 3517 False 1549.333333 4141 90.174667 1 3488 3 chr6D.!!$F1 3487
3 TraesCS6B01G339200 chr6D 56552223 56553109 886 True 431.000000 431 75.774000 1005 1897 1 chr6D.!!$R1 892
4 TraesCS6B01G339200 chr6A 545317852 545321322 3470 False 2209.000000 4017 89.495500 1 3403 2 chr6A.!!$F1 3402
5 TraesCS6B01G339200 chr6A 71066981 71067867 886 True 436.000000 436 75.938000 1005 1897 1 chr6A.!!$R1 892
6 TraesCS6B01G339200 chr7D 198501231 198502379 1148 True 1013.000000 1013 82.842000 1005 2140 1 chr7D.!!$R1 1135
7 TraesCS6B01G339200 chr7A 207547417 207548560 1143 True 985.000000 985 82.476000 1005 2133 1 chr7A.!!$R1 1128
8 TraesCS6B01G339200 chr7A 602232172 602232851 679 True 281.000000 281 74.642000 1217 1902 1 chr7A.!!$R2 685
9 TraesCS6B01G339200 chr7B 162923054 162924203 1149 False 946.000000 946 81.787000 999 2133 1 chr7B.!!$F1 1134

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
198 199 0.770008 GCAAATTCGCGTGTGTGAAC 59.230 50.000 5.77 0.0 46.57 3.18 F
208 209 1.004292 CGTGTGTGAACGGAGGAAAAC 60.004 52.381 0.00 0.0 39.89 2.43 F
620 647 1.988293 TGCCTCCATTTTGAAACGGA 58.012 45.000 0.00 0.0 0.00 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1105 1161 0.674581 CGCTCTCCATCCACAAGCAA 60.675 55.000 0.0 0.0 33.21 3.91 R
1147 1203 1.295423 GAGCGAGCAGTACCCCAAA 59.705 57.895 0.0 0.0 0.00 3.28 R
2542 2631 0.107993 CGCCATCAAAGCAGAGGAGA 60.108 55.000 0.0 0.0 0.00 3.71 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
73 74 6.754675 GCAAGACAAGGCTGTTTTTAGTTTTA 59.245 34.615 0.00 0.00 35.30 1.52
127 128 1.045407 AGTGGTCGTAGCCAAAGACA 58.955 50.000 5.38 0.00 40.68 3.41
188 189 1.024579 TTCCTCGGGAGCAAATTCGC 61.025 55.000 0.00 0.00 31.21 4.70
198 199 0.770008 GCAAATTCGCGTGTGTGAAC 59.230 50.000 5.77 0.00 46.57 3.18
208 209 1.004292 CGTGTGTGAACGGAGGAAAAC 60.004 52.381 0.00 0.00 39.89 2.43
219 220 2.095263 CGGAGGAAAACGAAATGCATGT 60.095 45.455 0.00 0.00 0.00 3.21
240 241 8.991026 GCATGTACACGGGTGTAATTTATATTA 58.009 33.333 12.85 0.00 46.33 0.98
243 244 9.409312 TGTACACGGGTGTAATTTATATTATCG 57.591 33.333 12.85 0.00 46.33 2.92
244 245 9.410556 GTACACGGGTGTAATTTATATTATCGT 57.589 33.333 12.85 0.00 46.33 3.73
245 246 8.524870 ACACGGGTGTAATTTATATTATCGTC 57.475 34.615 1.96 0.00 42.90 4.20
249 250 8.644619 CGGGTGTAATTTATATTATCGTCTGTG 58.355 37.037 0.00 0.00 0.00 3.66
284 285 7.210718 TGCCATGATGTTTGATGAATAGATC 57.789 36.000 0.00 0.00 0.00 2.75
287 288 7.623715 GCCATGATGTTTGATGAATAGATCGAG 60.624 40.741 0.00 0.00 0.00 4.04
288 289 6.775939 TGATGTTTGATGAATAGATCGAGC 57.224 37.500 0.00 0.00 0.00 5.03
289 290 6.282930 TGATGTTTGATGAATAGATCGAGCA 58.717 36.000 2.38 0.00 33.10 4.26
294 318 2.381752 TGAATAGATCGAGCAGGGGA 57.618 50.000 2.38 0.00 0.00 4.81
297 321 3.070159 TGAATAGATCGAGCAGGGGAAAG 59.930 47.826 2.38 0.00 0.00 2.62
346 371 7.756722 CCTCTTTCGCTTATTGATTTGAAATGT 59.243 33.333 0.00 0.00 0.00 2.71
395 420 7.448161 TCTGTTTTGACAATGTCTACCATCATT 59.552 33.333 14.97 0.00 35.08 2.57
405 430 5.614308 TGTCTACCATCATTCTATGCAAGG 58.386 41.667 0.00 0.00 0.00 3.61
497 522 6.663523 AGCAATGTTATACAAGGGCTTTAGTT 59.336 34.615 0.00 0.00 31.76 2.24
499 524 7.275560 GCAATGTTATACAAGGGCTTTAGTTTG 59.724 37.037 0.00 0.00 0.00 2.93
501 526 7.443259 TGTTATACAAGGGCTTTAGTTTGTC 57.557 36.000 0.00 0.00 35.55 3.18
512 537 6.461092 GGGCTTTAGTTTGTCTTTGTTAGCTT 60.461 38.462 0.00 0.00 0.00 3.74
513 538 6.637254 GGCTTTAGTTTGTCTTTGTTAGCTTC 59.363 38.462 0.00 0.00 0.00 3.86
514 539 7.418408 GCTTTAGTTTGTCTTTGTTAGCTTCT 58.582 34.615 0.00 0.00 0.00 2.85
515 540 7.588123 GCTTTAGTTTGTCTTTGTTAGCTTCTC 59.412 37.037 0.00 0.00 0.00 2.87
516 541 8.732746 TTTAGTTTGTCTTTGTTAGCTTCTCT 57.267 30.769 0.00 0.00 0.00 3.10
517 542 8.732746 TTAGTTTGTCTTTGTTAGCTTCTCTT 57.267 30.769 0.00 0.00 0.00 2.85
518 543 7.631717 AGTTTGTCTTTGTTAGCTTCTCTTT 57.368 32.000 0.00 0.00 0.00 2.52
519 544 7.698628 AGTTTGTCTTTGTTAGCTTCTCTTTC 58.301 34.615 0.00 0.00 0.00 2.62
520 545 7.554476 AGTTTGTCTTTGTTAGCTTCTCTTTCT 59.446 33.333 0.00 0.00 0.00 2.52
521 546 7.865706 TTGTCTTTGTTAGCTTCTCTTTCTT 57.134 32.000 0.00 0.00 0.00 2.52
522 547 7.484035 TGTCTTTGTTAGCTTCTCTTTCTTC 57.516 36.000 0.00 0.00 0.00 2.87
523 548 7.047891 TGTCTTTGTTAGCTTCTCTTTCTTCA 58.952 34.615 0.00 0.00 0.00 3.02
524 549 7.225538 TGTCTTTGTTAGCTTCTCTTTCTTCAG 59.774 37.037 0.00 0.00 0.00 3.02
525 550 5.931441 TTGTTAGCTTCTCTTTCTTCAGC 57.069 39.130 0.00 0.00 0.00 4.26
526 551 5.220710 TGTTAGCTTCTCTTTCTTCAGCT 57.779 39.130 0.00 0.00 43.33 4.24
530 555 3.324556 AGCTTCTCTTTCTTCAGCTCTGT 59.675 43.478 0.00 0.00 35.95 3.41
542 567 7.891183 TCTTCAGCTCTGTTTGTTATAACTC 57.109 36.000 16.33 7.82 0.00 3.01
543 568 7.671302 TCTTCAGCTCTGTTTGTTATAACTCT 58.329 34.615 16.33 0.00 0.00 3.24
544 569 7.815068 TCTTCAGCTCTGTTTGTTATAACTCTC 59.185 37.037 16.33 7.21 0.00 3.20
545 570 7.233389 TCAGCTCTGTTTGTTATAACTCTCT 57.767 36.000 16.33 0.92 0.00 3.10
546 571 7.671302 TCAGCTCTGTTTGTTATAACTCTCTT 58.329 34.615 16.33 0.00 0.00 2.85
547 572 8.150945 TCAGCTCTGTTTGTTATAACTCTCTTT 58.849 33.333 16.33 0.00 0.00 2.52
548 573 8.439286 CAGCTCTGTTTGTTATAACTCTCTTTC 58.561 37.037 16.33 1.13 0.00 2.62
593 620 6.153680 ACTCTCTCTTAGTTAGGAATGGTGTG 59.846 42.308 0.00 0.00 0.00 3.82
617 644 6.482973 TGAATCTTTTGCCTCCATTTTGAAAC 59.517 34.615 0.00 0.00 0.00 2.78
620 647 1.988293 TGCCTCCATTTTGAAACGGA 58.012 45.000 0.00 0.00 0.00 4.69
800 854 4.609691 GCTAAGCGCAGGTATAAAACAA 57.390 40.909 11.47 0.00 37.06 2.83
801 855 4.340263 GCTAAGCGCAGGTATAAAACAAC 58.660 43.478 11.47 0.00 37.06 3.32
861 915 9.716556 ACCCCTATATATGTTCTTCTACCTATG 57.283 37.037 0.00 0.00 0.00 2.23
891 945 7.231925 CAGGATTAACCATCATGGAATTGATCA 59.768 37.037 11.90 0.00 40.96 2.92
959 1015 2.729383 TCCATGATCAGATAGGCCCT 57.271 50.000 0.00 0.00 0.00 5.19
1129 1185 2.060980 GTGGATGGAGAGCGGGTCT 61.061 63.158 9.87 9.87 38.71 3.85
1198 1254 0.824109 CGAGCTGGATCTTGTACCCA 59.176 55.000 0.00 0.00 0.00 4.51
1733 1795 0.737715 CACCTCGTACTTGCTCAGCC 60.738 60.000 0.00 0.00 0.00 4.85
1778 1840 0.602905 GGTCCACCACGACTTGAAGG 60.603 60.000 0.00 0.00 35.64 3.46
2020 2091 1.066143 CAGTACGGCTTCACCTTCCAT 60.066 52.381 0.00 0.00 35.61 3.41
2186 2257 3.276091 TGTTTGTGCTCACGGGCG 61.276 61.111 0.00 0.00 34.52 6.13
2261 2332 0.556380 TTCCTCCTCCTCCTCCTCCT 60.556 60.000 0.00 0.00 0.00 3.69
2262 2333 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
2263 2334 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
2350 2422 5.061721 ACCCATTAATTCACTCCCCATAC 57.938 43.478 0.00 0.00 0.00 2.39
2383 2455 6.061441 ACATCAAATTTCCTGCCGTATCATA 58.939 36.000 0.00 0.00 0.00 2.15
2391 2463 0.313987 TGCCGTATCATACAGCTCCG 59.686 55.000 4.65 0.00 33.36 4.63
2458 2541 2.358737 AAGGAAGCAAGGGTCGCG 60.359 61.111 0.00 0.00 0.00 5.87
2459 2542 3.901797 AAGGAAGCAAGGGTCGCGG 62.902 63.158 6.13 0.00 0.00 6.46
2500 2583 2.693797 GTTGTGACCACAGCTTCATG 57.306 50.000 9.29 0.00 42.94 3.07
2501 2584 2.221169 GTTGTGACCACAGCTTCATGA 58.779 47.619 9.29 0.00 42.94 3.07
2529 2618 1.611673 CCATCTTGACGCTTCCCTTGT 60.612 52.381 0.00 0.00 0.00 3.16
2537 2626 1.032114 CGCTTCCCTTGTTCATCCCC 61.032 60.000 0.00 0.00 0.00 4.81
2542 2631 1.693640 CCTTGTTCATCCCCTGCCT 59.306 57.895 0.00 0.00 0.00 4.75
2583 2672 0.391395 CCCTGTCTTCTCTGCAGCAG 60.391 60.000 17.10 17.10 0.00 4.24
2777 2894 1.616187 CCTCTCGACAGGTTCCTGGTA 60.616 57.143 20.88 6.79 38.30 3.25
2794 2911 0.543749 GTAGACTTCATGGCCTGCCT 59.456 55.000 9.97 0.00 36.94 4.75
2797 2914 0.747283 GACTTCATGGCCTGCCTCTG 60.747 60.000 9.97 7.28 36.94 3.35
2808 2925 1.392589 CTGCCTCTGTCTCTCTCTCC 58.607 60.000 0.00 0.00 0.00 3.71
2812 2935 1.133792 CCTCTGTCTCTCTCTCCCTCC 60.134 61.905 0.00 0.00 0.00 4.30
2841 2964 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
2850 2973 1.610673 TCTCTCTCTGTGGGTGCCC 60.611 63.158 0.00 0.00 0.00 5.36
2870 2993 1.739067 GCTACCGGCAATCTTTGTCT 58.261 50.000 0.00 0.00 41.35 3.41
2871 2994 2.737359 CGCTACCGGCAATCTTTGTCTA 60.737 50.000 0.00 0.00 41.91 2.59
2872 2995 2.866762 GCTACCGGCAATCTTTGTCTAG 59.133 50.000 0.00 0.00 41.35 2.43
2935 3076 1.180456 TGGCGGACGGAACAGAACTA 61.180 55.000 0.00 0.00 0.00 2.24
2938 3079 1.336609 GCGGACGGAACAGAACTAACT 60.337 52.381 0.00 0.00 0.00 2.24
3015 3156 3.948086 GACCGCGTGGACAGAGACG 62.948 68.421 24.59 0.00 39.21 4.18
3018 3159 2.179517 GCGTGGACAGAGACGAGG 59.820 66.667 0.00 0.00 37.81 4.63
3130 3316 2.734723 CGCCGTCAGTGACCAGTG 60.735 66.667 17.57 11.73 0.00 3.66
3133 3319 2.421314 CGTCAGTGACCAGTGCCA 59.579 61.111 17.57 0.00 0.00 4.92
3135 3321 1.963338 GTCAGTGACCAGTGCCAGC 60.963 63.158 12.54 0.00 0.00 4.85
3144 3330 4.827087 AGTGCCAGCGCTCCATCG 62.827 66.667 7.13 0.00 35.36 3.84
3145 3331 4.819761 GTGCCAGCGCTCCATCGA 62.820 66.667 7.13 0.00 35.36 3.59
3146 3332 4.519437 TGCCAGCGCTCCATCGAG 62.519 66.667 7.13 0.00 39.33 4.04
3210 3401 2.805353 CTGTCGTCCGTTGGCTCG 60.805 66.667 0.00 0.00 0.00 5.03
3224 3415 2.125350 CTCGGGAGCTTGCTCACC 60.125 66.667 21.97 18.32 0.00 4.02
3230 3421 1.589113 GAGCTTGCTCACCTCGAGT 59.411 57.895 16.71 0.00 44.33 4.18
3237 3428 1.064946 CTCACCTCGAGTCGGATGC 59.935 63.158 13.54 0.00 36.94 3.91
3246 3437 1.202417 CGAGTCGGATGCCATACTGTT 60.202 52.381 4.10 0.00 0.00 3.16
3248 3439 3.490249 CGAGTCGGATGCCATACTGTTAA 60.490 47.826 4.10 0.00 0.00 2.01
3272 3463 3.209410 AGCTGACAGACTTCCAAGTTTG 58.791 45.455 6.65 8.14 44.22 2.93
3293 3484 2.378806 CTGTTGAAAAGTGCTTGCTCG 58.621 47.619 0.00 0.00 0.00 5.03
3319 3510 6.358974 TCAGTGTGAAGTCCAAGATTATCA 57.641 37.500 0.00 0.00 0.00 2.15
3350 3541 1.208293 TGCAAAACCAACCCCAAACTC 59.792 47.619 0.00 0.00 0.00 3.01
3394 3585 6.642540 GCACTTCCTTGAACTTCTAAAAATGG 59.357 38.462 0.00 0.00 0.00 3.16
3398 3589 7.510549 TCCTTGAACTTCTAAAAATGGAGTG 57.489 36.000 0.00 0.00 0.00 3.51
3403 3594 8.477419 TGAACTTCTAAAAATGGAGTGGAATT 57.523 30.769 0.00 0.00 0.00 2.17
3404 3595 8.359642 TGAACTTCTAAAAATGGAGTGGAATTG 58.640 33.333 0.00 0.00 0.00 2.32
3405 3596 7.839680 ACTTCTAAAAATGGAGTGGAATTGT 57.160 32.000 0.00 0.00 0.00 2.71
3406 3597 7.661040 ACTTCTAAAAATGGAGTGGAATTGTG 58.339 34.615 0.00 0.00 0.00 3.33
3407 3598 7.287696 ACTTCTAAAAATGGAGTGGAATTGTGT 59.712 33.333 0.00 0.00 0.00 3.72
3408 3599 7.595819 TCTAAAAATGGAGTGGAATTGTGTT 57.404 32.000 0.00 0.00 0.00 3.32
3409 3600 8.698973 TCTAAAAATGGAGTGGAATTGTGTTA 57.301 30.769 0.00 0.00 0.00 2.41
3410 3601 9.137459 TCTAAAAATGGAGTGGAATTGTGTTAA 57.863 29.630 0.00 0.00 0.00 2.01
3411 3602 9.757227 CTAAAAATGGAGTGGAATTGTGTTAAA 57.243 29.630 0.00 0.00 0.00 1.52
3413 3604 9.454859 AAAAATGGAGTGGAATTGTGTTAAAAA 57.545 25.926 0.00 0.00 0.00 1.94
3481 3672 5.841957 AGGCAGTTGAATCAATTACATCC 57.158 39.130 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 2.653766 CAACGCGCGGCAGTTTTT 60.654 55.556 35.22 14.60 0.00 1.94
174 175 2.098298 CACGCGAATTTGCTCCCG 59.902 61.111 15.93 2.65 0.00 5.14
188 189 1.004292 GTTTTCCTCCGTTCACACACG 60.004 52.381 0.00 0.00 40.02 4.49
198 199 2.095263 ACATGCATTTCGTTTTCCTCCG 60.095 45.455 0.00 0.00 0.00 4.63
208 209 1.083489 ACCCGTGTACATGCATTTCG 58.917 50.000 9.72 1.19 0.00 3.46
219 220 9.624697 GACGATAATATAAATTACACCCGTGTA 57.375 33.333 3.57 3.57 44.42 2.90
240 241 3.684788 GCAATACAAGGAACACAGACGAT 59.315 43.478 0.00 0.00 0.00 3.73
241 242 3.064207 GCAATACAAGGAACACAGACGA 58.936 45.455 0.00 0.00 0.00 4.20
242 243 2.159627 GGCAATACAAGGAACACAGACG 59.840 50.000 0.00 0.00 0.00 4.18
243 244 3.146066 TGGCAATACAAGGAACACAGAC 58.854 45.455 0.00 0.00 0.00 3.51
244 245 3.500448 TGGCAATACAAGGAACACAGA 57.500 42.857 0.00 0.00 0.00 3.41
245 246 3.758023 TCATGGCAATACAAGGAACACAG 59.242 43.478 0.00 0.00 0.00 3.66
249 250 4.989279 ACATCATGGCAATACAAGGAAC 57.011 40.909 0.00 0.00 0.00 3.62
253 254 6.566141 TCATCAAACATCATGGCAATACAAG 58.434 36.000 0.00 0.00 0.00 3.16
259 260 7.520937 CGATCTATTCATCAAACATCATGGCAA 60.521 37.037 0.00 0.00 0.00 4.52
284 285 3.984193 CTGCCCTTTCCCCTGCTCG 62.984 68.421 0.00 0.00 0.00 5.03
287 288 2.677875 CACTGCCCTTTCCCCTGC 60.678 66.667 0.00 0.00 0.00 4.85
288 289 2.036256 CCACTGCCCTTTCCCCTG 59.964 66.667 0.00 0.00 0.00 4.45
289 290 3.268032 CCCACTGCCCTTTCCCCT 61.268 66.667 0.00 0.00 0.00 4.79
294 318 3.086764 AAGGTGCCCACTGCCCTTT 62.087 57.895 0.00 0.00 43.76 3.11
297 321 4.284550 TGAAGGTGCCCACTGCCC 62.285 66.667 0.00 0.00 40.16 5.36
316 340 6.429692 TCAAATCAATAAGCGAAAGAGGACAA 59.570 34.615 0.00 0.00 0.00 3.18
320 344 7.756722 ACATTTCAAATCAATAAGCGAAAGAGG 59.243 33.333 0.00 0.00 0.00 3.69
361 386 6.769822 AGACATTGTCAAAACAGATGAAGACT 59.230 34.615 18.57 0.00 36.57 3.24
369 394 6.295249 TGATGGTAGACATTGTCAAAACAGA 58.705 36.000 18.57 4.20 40.72 3.41
395 420 5.714333 TGCCTCAATTTTAACCTTGCATAGA 59.286 36.000 0.00 0.00 0.00 1.98
405 430 3.662186 CACGTCGTTGCCTCAATTTTAAC 59.338 43.478 0.00 0.00 0.00 2.01
497 522 7.552687 TGAAGAAAGAGAAGCTAACAAAGACAA 59.447 33.333 0.00 0.00 0.00 3.18
499 524 7.484035 TGAAGAAAGAGAAGCTAACAAAGAC 57.516 36.000 0.00 0.00 0.00 3.01
501 526 6.204495 AGCTGAAGAAAGAGAAGCTAACAAAG 59.796 38.462 0.00 0.00 42.25 2.77
512 537 5.028549 ACAAACAGAGCTGAAGAAAGAGA 57.971 39.130 4.21 0.00 0.00 3.10
513 538 5.747951 AACAAACAGAGCTGAAGAAAGAG 57.252 39.130 4.21 0.00 0.00 2.85
514 539 8.774586 GTTATAACAAACAGAGCTGAAGAAAGA 58.225 33.333 10.81 0.00 0.00 2.52
515 540 8.778358 AGTTATAACAAACAGAGCTGAAGAAAG 58.222 33.333 17.65 0.00 0.00 2.62
516 541 8.677148 AGTTATAACAAACAGAGCTGAAGAAA 57.323 30.769 17.65 0.00 0.00 2.52
517 542 8.150945 AGAGTTATAACAAACAGAGCTGAAGAA 58.849 33.333 17.65 0.00 0.00 2.52
518 543 7.671302 AGAGTTATAACAAACAGAGCTGAAGA 58.329 34.615 17.65 0.00 0.00 2.87
519 544 7.816995 AGAGAGTTATAACAAACAGAGCTGAAG 59.183 37.037 17.65 0.00 0.00 3.02
520 545 7.671302 AGAGAGTTATAACAAACAGAGCTGAA 58.329 34.615 17.65 0.00 0.00 3.02
521 546 7.233389 AGAGAGTTATAACAAACAGAGCTGA 57.767 36.000 17.65 0.00 0.00 4.26
522 547 7.897575 AAGAGAGTTATAACAAACAGAGCTG 57.102 36.000 17.65 0.00 0.00 4.24
523 548 8.371699 AGAAAGAGAGTTATAACAAACAGAGCT 58.628 33.333 17.65 0.00 0.00 4.09
524 549 8.541133 AGAAAGAGAGTTATAACAAACAGAGC 57.459 34.615 17.65 1.46 0.00 4.09
579 604 5.863935 GCAAAAGATTCACACCATTCCTAAC 59.136 40.000 0.00 0.00 0.00 2.34
583 608 3.259123 AGGCAAAAGATTCACACCATTCC 59.741 43.478 0.00 0.00 0.00 3.01
589 616 4.525912 AATGGAGGCAAAAGATTCACAC 57.474 40.909 0.00 0.00 0.00 3.82
593 620 6.346838 CGTTTCAAAATGGAGGCAAAAGATTC 60.347 38.462 0.00 0.00 0.00 2.52
763 817 0.542938 TAGCGGCTATCCCTGCATCT 60.543 55.000 5.42 0.00 36.16 2.90
798 852 5.636837 TCTTTCGTTCAGTTTCTTTGGTTG 58.363 37.500 0.00 0.00 0.00 3.77
799 853 5.890424 TCTTTCGTTCAGTTTCTTTGGTT 57.110 34.783 0.00 0.00 0.00 3.67
800 854 5.182380 TGTTCTTTCGTTCAGTTTCTTTGGT 59.818 36.000 0.00 0.00 0.00 3.67
801 855 5.636837 TGTTCTTTCGTTCAGTTTCTTTGG 58.363 37.500 0.00 0.00 0.00 3.28
861 915 4.464008 TCCATGATGGTTAATCCTGAAGC 58.536 43.478 11.87 0.00 39.03 3.86
864 918 6.671605 TCAATTCCATGATGGTTAATCCTGA 58.328 36.000 11.87 4.14 39.03 3.86
959 1015 3.120385 CTGAGCGCGTCAATGGCA 61.120 61.111 8.43 0.00 33.60 4.92
967 1023 3.649986 GCCAACAACTGAGCGCGT 61.650 61.111 8.43 0.00 0.00 6.01
997 1053 3.664888 AAGCTGCTGCCCCATGGA 61.665 61.111 15.22 0.00 40.80 3.41
1105 1161 0.674581 CGCTCTCCATCCACAAGCAA 60.675 55.000 0.00 0.00 33.21 3.91
1147 1203 1.295423 GAGCGAGCAGTACCCCAAA 59.705 57.895 0.00 0.00 0.00 3.28
1778 1840 4.386413 CCAGTTCCTGGTGAGCAC 57.614 61.111 1.99 0.00 45.82 4.40
2224 2295 1.209747 GAAGAAACTCCGCCCATACCT 59.790 52.381 0.00 0.00 0.00 3.08
2228 2299 0.253327 GAGGAAGAAACTCCGCCCAT 59.747 55.000 0.00 0.00 40.75 4.00
2350 2422 2.417243 GGAAATTTGATGTTCCTGGCCG 60.417 50.000 0.00 0.00 40.24 6.13
2391 2463 1.750193 TGTTTCCATCTCCATTCGGC 58.250 50.000 0.00 0.00 0.00 5.54
2458 2541 1.312815 GGATTCAGCTGGTATGTGCC 58.687 55.000 15.13 2.58 0.00 5.01
2459 2542 0.940126 CGGATTCAGCTGGTATGTGC 59.060 55.000 15.13 0.33 0.00 4.57
2460 2543 1.138859 TCCGGATTCAGCTGGTATGTG 59.861 52.381 15.13 0.00 35.72 3.21
2500 2583 0.526524 CGTCAAGATGGAGGTCGCTC 60.527 60.000 0.00 0.00 0.00 5.03
2501 2584 1.513158 CGTCAAGATGGAGGTCGCT 59.487 57.895 0.00 0.00 0.00 4.93
2529 2618 0.692419 GAGGAGAGGCAGGGGATGAA 60.692 60.000 0.00 0.00 0.00 2.57
2537 2626 0.612229 TCAAAGCAGAGGAGAGGCAG 59.388 55.000 0.00 0.00 0.00 4.85
2542 2631 0.107993 CGCCATCAAAGCAGAGGAGA 60.108 55.000 0.00 0.00 0.00 3.71
2583 2672 1.372128 CTTTCTTTGCGTGCCTGCC 60.372 57.895 0.00 0.00 0.00 4.85
2777 2894 0.913451 AGAGGCAGGCCATGAAGTCT 60.913 55.000 13.63 2.34 38.92 3.24
2794 2911 0.923358 GGGAGGGAGAGAGAGACAGA 59.077 60.000 0.00 0.00 0.00 3.41
2797 2914 1.143073 GAGAGGGAGGGAGAGAGAGAC 59.857 61.905 0.00 0.00 0.00 3.36
2808 2925 2.370189 GAGAGAGAGAGAGAGAGGGAGG 59.630 59.091 0.00 0.00 0.00 4.30
2812 2935 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
2859 2982 4.946157 ACCATTCCTGCTAGACAAAGATTG 59.054 41.667 0.00 0.00 0.00 2.67
2870 2993 1.757118 CCTCGAGAACCATTCCTGCTA 59.243 52.381 15.71 0.00 0.00 3.49
2871 2994 0.539051 CCTCGAGAACCATTCCTGCT 59.461 55.000 15.71 0.00 0.00 4.24
2872 2995 0.462759 CCCTCGAGAACCATTCCTGC 60.463 60.000 15.71 0.00 0.00 4.85
2902 3033 2.241880 CGCCACCGCCGGTATAAAG 61.242 63.158 9.25 0.00 32.11 1.85
2903 3034 2.202905 CGCCACCGCCGGTATAAA 60.203 61.111 9.25 0.00 32.11 1.40
2920 3061 4.780275 ACTAGTTAGTTCTGTTCCGTCC 57.220 45.455 0.00 0.00 31.13 4.79
2935 3076 3.378339 CCGTTCAACGACAGAACTAGTT 58.622 45.455 12.68 8.13 46.05 2.24
2938 3079 1.000060 CCCCGTTCAACGACAGAACTA 60.000 52.381 12.68 0.00 46.05 2.24
3004 3145 1.025113 CGCTACCTCGTCTCTGTCCA 61.025 60.000 0.00 0.00 0.00 4.02
3141 3327 2.941210 GAGCTCGGAGATCCTCGAT 58.059 57.895 12.13 0.00 33.89 3.59
3220 3411 2.415608 GGCATCCGACTCGAGGTGA 61.416 63.158 18.41 10.19 0.00 4.02
3221 3412 2.021068 ATGGCATCCGACTCGAGGTG 62.021 60.000 18.41 8.31 0.00 4.00
3224 3415 0.955178 AGTATGGCATCCGACTCGAG 59.045 55.000 11.84 11.84 0.00 4.04
3230 3421 4.693283 CTTCTTAACAGTATGGCATCCGA 58.307 43.478 1.65 0.00 43.62 4.55
3237 3428 5.578727 GTCTGTCAGCTTCTTAACAGTATGG 59.421 44.000 0.00 0.00 43.62 2.74
3246 3437 4.345257 ACTTGGAAGTCTGTCAGCTTCTTA 59.655 41.667 24.01 16.21 40.49 2.10
3248 3439 2.703007 ACTTGGAAGTCTGTCAGCTTCT 59.297 45.455 24.01 10.03 40.49 2.85
3272 3463 2.122564 GAGCAAGCACTTTTCAACAGC 58.877 47.619 0.00 0.00 0.00 4.40
3319 3510 4.500127 GTTGGTTTTGCAGTTACTTGGTT 58.500 39.130 0.00 0.00 0.00 3.67
3350 3541 0.316204 CTTGCTTCAGCCACCCAAAG 59.684 55.000 0.00 0.00 41.18 2.77
3412 3603 6.648192 TGTTGTTGATTCCACTCCAATTTTT 58.352 32.000 0.00 0.00 0.00 1.94
3413 3604 6.232581 TGTTGTTGATTCCACTCCAATTTT 57.767 33.333 0.00 0.00 0.00 1.82
3414 3605 5.867903 TGTTGTTGATTCCACTCCAATTT 57.132 34.783 0.00 0.00 0.00 1.82
3415 3606 5.335897 CGATGTTGTTGATTCCACTCCAATT 60.336 40.000 0.00 0.00 0.00 2.32
3416 3607 4.156556 CGATGTTGTTGATTCCACTCCAAT 59.843 41.667 0.00 0.00 0.00 3.16
3417 3608 3.501828 CGATGTTGTTGATTCCACTCCAA 59.498 43.478 0.00 0.00 0.00 3.53
3420 3611 4.393062 ACATCGATGTTGTTGATTCCACTC 59.607 41.667 25.18 0.00 37.90 3.51
3446 3637 8.865090 TGATTCAACTGCCTTAATTTTTAAGGA 58.135 29.630 23.75 11.69 45.24 3.36


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

AutoCloner maintained by Alex Coulton.