Multiple sequence alignment - TraesCS2B01G119400

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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 TraesCS2B01G119400 chr2B 100.000 4796 0 0 1 4796 86209735 86214530 0.000000e+00 8857
1 TraesCS2B01G119400 chr2B 93.123 349 10 8 3951 4292 765341717 765341376 2.580000e-137 499
2 TraesCS2B01G119400 chr2D 91.135 4918 173 100 1 4781 55056112 55060903 0.000000e+00 6423
3 TraesCS2B01G119400 chr2A 90.508 4309 156 86 548 4719 55850493 55854685 0.000000e+00 5457
4 TraesCS2B01G119400 chr2A 83.468 496 28 21 1 478 55849807 55850266 3.450000e-111 412
5 TraesCS2B01G119400 chr7B 91.098 820 26 16 3951 4730 502266511 502265699 0.000000e+00 1066
6 TraesCS2B01G119400 chr7B 89.866 819 37 13 3952 4730 66954583 66953771 0.000000e+00 1011
7 TraesCS2B01G119400 chr4A 89.691 194 20 0 2352 2545 469513112 469513305 1.030000e-61 248
8 TraesCS2B01G119400 chr4B 89.175 194 21 0 2352 2545 149938152 149937959 4.800000e-60 243
9 TraesCS2B01G119400 chr5D 92.233 103 8 0 2876 2978 236662764 236662662 3.870000e-31 147
10 TraesCS2B01G119400 chr5A 92.233 103 8 0 2876 2978 318756941 318757043 3.870000e-31 147
11 TraesCS2B01G119400 chr5B 91.262 103 9 0 2876 2978 268432472 268432574 1.800000e-29 141


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 TraesCS2B01G119400 chr2B 86209735 86214530 4795 False 8857.0 8857 100.000 1 4796 1 chr2B.!!$F1 4795
1 TraesCS2B01G119400 chr2D 55056112 55060903 4791 False 6423.0 6423 91.135 1 4781 1 chr2D.!!$F1 4780
2 TraesCS2B01G119400 chr2A 55849807 55854685 4878 False 2934.5 5457 86.988 1 4719 2 chr2A.!!$F1 4718
3 TraesCS2B01G119400 chr7B 502265699 502266511 812 True 1066.0 1066 91.098 3951 4730 1 chr7B.!!$R2 779
4 TraesCS2B01G119400 chr7B 66953771 66954583 812 True 1011.0 1011 89.866 3952 4730 1 chr7B.!!$R1 778

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
533 747 0.106217 CCTCCCTCCCTCACTCTCTC 60.106 65.0 0.00 0.0 0.00 3.20 F
638 853 0.106419 TTTTGCAGAAACCCCCTCGT 60.106 50.0 0.00 0.0 0.00 4.18 F
977 1258 0.179234 GTTTGGTTGGGTTGGGTTGG 59.821 55.0 0.00 0.0 0.00 3.77 F
2319 2634 0.320771 TCCGCTCTGCCTGAAAGTTC 60.321 55.0 0.00 0.0 0.00 3.01 F
3105 3434 0.254462 TGTGGCCAACAGAGAACACA 59.746 50.0 7.24 0.0 36.59 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1980 2285 1.133884 GTGGGTATTTACCTCTGGCCC 60.134 57.143 0.0 0.0 45.72 5.80 R
2594 2912 0.035439 GGTCATGGGGATGTTGTCGT 60.035 55.000 0.0 0.0 0.00 4.34 R
2595 2913 0.035534 TGGTCATGGGGATGTTGTCG 60.036 55.000 0.0 0.0 0.00 4.35 R
3582 3924 1.310216 GGTTAATGCCGCCGTTCCTT 61.310 55.000 0.0 0.0 0.00 3.36 R
4715 5151 0.959372 GTGAGCTGAATGGTGCTGCT 60.959 55.000 0.0 0.0 42.19 4.24 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
256 271 2.209273 CGTTCCAGTCAATCACACACA 58.791 47.619 0.00 0.00 0.00 3.72
257 272 2.221749 CGTTCCAGTCAATCACACACAG 59.778 50.000 0.00 0.00 0.00 3.66
272 291 1.990060 ACAGACAGATCCACCCCGG 60.990 63.158 0.00 0.00 0.00 5.73
313 336 6.862209 ACAGTAAAAACTCAAAATCACAGCA 58.138 32.000 0.00 0.00 0.00 4.41
316 339 6.751888 AGTAAAAACTCAAAATCACAGCACAC 59.248 34.615 0.00 0.00 0.00 3.82
349 372 5.499139 TTTTACCGCCAGATTGATTGATC 57.501 39.130 0.00 0.00 0.00 2.92
352 375 0.870393 CGCCAGATTGATTGATCGGG 59.130 55.000 0.51 0.51 42.22 5.14
366 392 2.620115 TGATCGGGTGACGGTACTATTC 59.380 50.000 0.00 0.00 44.45 1.75
369 395 1.939934 CGGGTGACGGTACTATTCGTA 59.060 52.381 0.00 0.00 39.88 3.43
370 396 2.354510 CGGGTGACGGTACTATTCGTAA 59.645 50.000 0.00 0.00 39.88 3.18
371 397 3.003689 CGGGTGACGGTACTATTCGTAAT 59.996 47.826 0.00 0.00 39.88 1.89
372 398 4.498009 CGGGTGACGGTACTATTCGTAATT 60.498 45.833 0.00 0.00 39.88 1.40
373 399 5.351458 GGGTGACGGTACTATTCGTAATTT 58.649 41.667 0.00 0.00 39.88 1.82
374 400 5.460091 GGGTGACGGTACTATTCGTAATTTC 59.540 44.000 0.00 0.00 39.88 2.17
393 419 6.811634 ATTTCAATTTGGCATTCCTATCCA 57.188 33.333 0.00 0.00 0.00 3.41
395 421 5.794726 TCAATTTGGCATTCCTATCCATG 57.205 39.130 0.00 0.00 0.00 3.66
398 424 0.473755 TGGCATTCCTATCCATGCGT 59.526 50.000 0.00 0.00 45.81 5.24
399 425 1.160137 GGCATTCCTATCCATGCGTC 58.840 55.000 0.00 0.00 45.81 5.19
400 426 1.543208 GGCATTCCTATCCATGCGTCA 60.543 52.381 0.00 0.00 45.81 4.35
433 464 6.016443 ACAGGAAGAATGCAGAGAAAAGAAAG 60.016 38.462 0.00 0.00 0.00 2.62
436 467 4.085009 AGAATGCAGAGAAAAGAAAGGGG 58.915 43.478 0.00 0.00 0.00 4.79
437 468 2.292828 TGCAGAGAAAAGAAAGGGGG 57.707 50.000 0.00 0.00 0.00 5.40
528 742 4.787280 CCGCCTCCCTCCCTCACT 62.787 72.222 0.00 0.00 0.00 3.41
529 743 3.151022 CGCCTCCCTCCCTCACTC 61.151 72.222 0.00 0.00 0.00 3.51
530 744 2.366570 GCCTCCCTCCCTCACTCT 59.633 66.667 0.00 0.00 0.00 3.24
531 745 1.760480 GCCTCCCTCCCTCACTCTC 60.760 68.421 0.00 0.00 0.00 3.20
532 746 2.015081 CCTCCCTCCCTCACTCTCT 58.985 63.158 0.00 0.00 0.00 3.10
533 747 0.106217 CCTCCCTCCCTCACTCTCTC 60.106 65.000 0.00 0.00 0.00 3.20
549 763 2.047560 TCCTGAGACGACGAGCGA 60.048 61.111 0.00 0.00 44.57 4.93
550 764 2.031044 CTCCTGAGACGACGAGCGAG 62.031 65.000 0.00 0.00 44.57 5.03
551 765 2.276994 CTGAGACGACGAGCGAGC 60.277 66.667 0.00 0.00 44.57 5.03
565 780 1.582610 GCGAGCGGGGAAAAACATCA 61.583 55.000 0.00 0.00 0.00 3.07
566 781 0.168128 CGAGCGGGGAAAAACATCAC 59.832 55.000 0.00 0.00 0.00 3.06
567 782 1.243902 GAGCGGGGAAAAACATCACA 58.756 50.000 0.00 0.00 0.00 3.58
568 783 1.200020 GAGCGGGGAAAAACATCACAG 59.800 52.381 0.00 0.00 0.00 3.66
569 784 0.388520 GCGGGGAAAAACATCACAGC 60.389 55.000 0.00 0.00 36.79 4.40
570 785 0.958091 CGGGGAAAAACATCACAGCA 59.042 50.000 0.00 0.00 0.00 4.41
571 786 1.068333 CGGGGAAAAACATCACAGCAG 60.068 52.381 0.00 0.00 0.00 4.24
572 787 1.337167 GGGGAAAAACATCACAGCAGC 60.337 52.381 0.00 0.00 0.00 5.25
573 788 1.340889 GGGAAAAACATCACAGCAGCA 59.659 47.619 0.00 0.00 0.00 4.41
579 794 2.033602 ATCACAGCAGCAGCAGCA 59.966 55.556 12.92 0.00 45.49 4.41
613 828 3.114616 CAGGACAGAACGCGGCAG 61.115 66.667 12.47 0.99 0.00 4.85
614 829 4.379243 AGGACAGAACGCGGCAGG 62.379 66.667 12.47 0.00 0.00 4.85
638 853 0.106419 TTTTGCAGAAACCCCCTCGT 60.106 50.000 0.00 0.00 0.00 4.18
677 892 3.827898 GGCACCCTCGTCCTCTCG 61.828 72.222 0.00 0.00 0.00 4.04
835 1097 0.526662 CTAACCCACGAACGAGCTCT 59.473 55.000 12.85 0.00 0.00 4.09
951 1223 1.040339 GGGGTGTGAGGTTGTTTGCA 61.040 55.000 0.00 0.00 0.00 4.08
953 1225 1.202405 GGGTGTGAGGTTGTTTGCAAG 60.202 52.381 0.00 0.00 34.94 4.01
954 1226 1.476488 GGTGTGAGGTTGTTTGCAAGT 59.524 47.619 0.00 0.00 34.94 3.16
955 1227 2.094234 GGTGTGAGGTTGTTTGCAAGTT 60.094 45.455 0.00 0.00 34.94 2.66
956 1228 3.129638 GGTGTGAGGTTGTTTGCAAGTTA 59.870 43.478 0.00 0.00 34.94 2.24
957 1229 4.351192 GTGTGAGGTTGTTTGCAAGTTAG 58.649 43.478 0.00 0.00 34.94 2.34
958 1230 3.380004 TGTGAGGTTGTTTGCAAGTTAGG 59.620 43.478 0.00 0.00 34.94 2.69
959 1231 3.380320 GTGAGGTTGTTTGCAAGTTAGGT 59.620 43.478 0.00 0.00 34.94 3.08
960 1232 4.020543 TGAGGTTGTTTGCAAGTTAGGTT 58.979 39.130 0.00 0.00 34.94 3.50
961 1233 4.464597 TGAGGTTGTTTGCAAGTTAGGTTT 59.535 37.500 0.00 0.00 34.94 3.27
962 1234 4.754322 AGGTTGTTTGCAAGTTAGGTTTG 58.246 39.130 0.00 0.00 34.94 2.93
963 1235 3.868661 GGTTGTTTGCAAGTTAGGTTTGG 59.131 43.478 0.00 0.00 34.94 3.28
964 1236 4.500127 GTTGTTTGCAAGTTAGGTTTGGT 58.500 39.130 0.00 0.00 34.94 3.67
965 1237 4.810191 TGTTTGCAAGTTAGGTTTGGTT 57.190 36.364 0.00 0.00 0.00 3.67
966 1238 4.499183 TGTTTGCAAGTTAGGTTTGGTTG 58.501 39.130 0.00 0.00 0.00 3.77
971 1243 3.739830 GCAAGTTAGGTTTGGTTGGGTTG 60.740 47.826 0.00 0.00 0.00 3.77
977 1258 0.179234 GTTTGGTTGGGTTGGGTTGG 59.821 55.000 0.00 0.00 0.00 3.77
1323 1613 4.816984 TCGGTCTCCTCGCCCTCC 62.817 72.222 0.00 0.00 0.00 4.30
1326 1616 3.213402 GTCTCCTCGCCCTCCTCG 61.213 72.222 0.00 0.00 0.00 4.63
1380 1673 3.364441 GTCAGCAATGGCACCGCA 61.364 61.111 12.01 0.00 44.61 5.69
1470 1766 3.372554 CTTCTTCGGCGGGGACTCC 62.373 68.421 7.21 0.00 0.00 3.85
1908 2213 3.680196 TACTCCCCCACCGGCTCT 61.680 66.667 0.00 0.00 0.00 4.09
1980 2285 1.728426 GCAGCAGCAGCAAAACGAG 60.728 57.895 4.63 0.00 45.49 4.18
1986 2291 2.956987 CAGCAAAACGAGGGCCAG 59.043 61.111 6.18 0.96 0.00 4.85
2044 2352 0.802607 CGCTCTCGTTTCTACCAGCC 60.803 60.000 0.00 0.00 0.00 4.85
2145 2453 0.586319 CGCACAAGTTCATGAACCGT 59.414 50.000 30.34 24.89 42.06 4.83
2296 2611 3.767230 CTCGCACACCGCAGTTCG 61.767 66.667 0.00 0.00 42.60 3.95
2313 2628 3.071206 GACCTCCGCTCTGCCTGA 61.071 66.667 0.00 0.00 0.00 3.86
2318 2633 0.321122 CTCCGCTCTGCCTGAAAGTT 60.321 55.000 0.00 0.00 0.00 2.66
2319 2634 0.320771 TCCGCTCTGCCTGAAAGTTC 60.321 55.000 0.00 0.00 0.00 3.01
2321 2636 0.603707 CGCTCTGCCTGAAAGTTCCA 60.604 55.000 0.00 0.00 0.00 3.53
2368 2683 4.227134 CGCAGCATCTACGGCCCT 62.227 66.667 0.00 0.00 0.00 5.19
2413 2728 2.390599 GCAGAAGCGCATGTTCGGA 61.391 57.895 11.47 0.00 0.00 4.55
2590 2908 2.695359 CTTCCGGCAGCAGTAACTAAA 58.305 47.619 0.00 0.00 0.00 1.85
2592 2910 2.419667 TCCGGCAGCAGTAACTAAAAC 58.580 47.619 0.00 0.00 0.00 2.43
2594 2912 2.550606 CCGGCAGCAGTAACTAAAACAA 59.449 45.455 0.00 0.00 0.00 2.83
2595 2913 3.551551 CGGCAGCAGTAACTAAAACAAC 58.448 45.455 0.00 0.00 0.00 3.32
2596 2914 3.551551 GGCAGCAGTAACTAAAACAACG 58.448 45.455 0.00 0.00 0.00 4.10
2597 2915 3.249080 GGCAGCAGTAACTAAAACAACGA 59.751 43.478 0.00 0.00 0.00 3.85
2598 2916 4.209112 GCAGCAGTAACTAAAACAACGAC 58.791 43.478 0.00 0.00 0.00 4.34
2599 2917 4.260456 GCAGCAGTAACTAAAACAACGACA 60.260 41.667 0.00 0.00 0.00 4.35
2752 3070 3.488384 GGTTCGTCATTGTTGCAACTTCA 60.488 43.478 28.61 14.14 0.00 3.02
2816 3139 3.501445 GCTGAGCTGAGATTCTTGTGTTT 59.499 43.478 3.62 0.00 0.00 2.83
2821 3144 6.263842 TGAGCTGAGATTCTTGTGTTTGATTT 59.736 34.615 0.00 0.00 0.00 2.17
2824 3147 6.515531 GCTGAGATTCTTGTGTTTGATTTGGA 60.516 38.462 0.00 0.00 0.00 3.53
2826 3149 7.954835 TGAGATTCTTGTGTTTGATTTGGATT 58.045 30.769 0.00 0.00 0.00 3.01
2827 3150 8.423349 TGAGATTCTTGTGTTTGATTTGGATTT 58.577 29.630 0.00 0.00 0.00 2.17
3102 3431 0.663153 GTGTGTGGCCAACAGAGAAC 59.337 55.000 7.24 0.00 40.26 3.01
3104 3433 0.663153 GTGTGGCCAACAGAGAACAC 59.337 55.000 7.24 4.82 40.26 3.32
3105 3434 0.254462 TGTGGCCAACAGAGAACACA 59.746 50.000 7.24 0.00 36.59 3.72
3106 3435 1.133823 TGTGGCCAACAGAGAACACAT 60.134 47.619 7.24 0.00 34.31 3.21
3122 3454 8.993424 AGAGAACACATCTTATTATTACCTGGT 58.007 33.333 4.05 4.05 38.96 4.00
3212 3544 1.177401 GCGGCTTCCTTTTTCCTCAT 58.823 50.000 0.00 0.00 0.00 2.90
3284 3616 0.687354 CCAGCCCTAACACTGACAGT 59.313 55.000 1.07 1.07 35.90 3.55
3373 3705 1.963338 GCTTTCGTCCAGCAGTGCT 60.963 57.895 13.14 13.14 40.77 4.40
3408 3740 7.231317 AGCATTTCACCAAACTGATCTTTTAGA 59.769 33.333 0.00 0.00 0.00 2.10
3412 3744 4.459337 CACCAAACTGATCTTTTAGACCCC 59.541 45.833 0.00 0.00 0.00 4.95
3423 3759 6.630203 TCTTTTAGACCCCTTGTGCTAATA 57.370 37.500 0.00 0.00 0.00 0.98
3486 3822 3.182996 ACCAAGTCGGGGGCCTTT 61.183 61.111 0.84 0.00 40.22 3.11
3899 4255 1.683385 GCTCCCCAGTAAAATCATGCC 59.317 52.381 0.00 0.00 0.00 4.40
3916 4272 4.467082 TCATGCCATGCCTTTTTCACTTAT 59.533 37.500 0.00 0.00 0.00 1.73
3939 4295 4.843728 TGGAATGATGGTGTCTTAACCTC 58.156 43.478 0.00 0.00 41.16 3.85
3949 4305 3.447944 GTGTCTTAACCTCGGATCCTTCT 59.552 47.826 10.75 0.00 0.00 2.85
4022 4379 7.396540 AAAGGAATAGTGCAACATAGGAAAG 57.603 36.000 0.00 0.00 41.43 2.62
4098 4456 4.092116 ACTTTCTTTCCCTTCACCTCTG 57.908 45.455 0.00 0.00 0.00 3.35
4133 4497 3.005554 CACCAGCTTATTCAGACCACAG 58.994 50.000 0.00 0.00 0.00 3.66
4326 4726 1.975407 CACCAAGCTCCTGGCAAGG 60.975 63.158 0.00 0.00 46.06 3.61
4348 4753 3.365969 GCAAGCCACCGCCAATATAATAC 60.366 47.826 0.00 0.00 34.57 1.89
4532 4949 2.100605 AGCTAGCTAGTTGTGTTGGC 57.899 50.000 17.69 5.22 0.00 4.52
4587 5017 5.104941 TGAAGATATTGAACAGGTCCGTCAT 60.105 40.000 0.00 0.00 0.00 3.06
4711 5147 2.743183 CGTGGATCATGGTCCCTTCTTC 60.743 54.545 22.55 5.19 37.48 2.87
4715 5151 2.342406 TCATGGTCCCTTCTTCCTCA 57.658 50.000 0.00 0.00 0.00 3.86
4723 5159 0.676151 CCTTCTTCCTCAGCAGCACC 60.676 60.000 0.00 0.00 0.00 5.01
4733 5169 0.958876 CAGCAGCACCATTCAGCTCA 60.959 55.000 0.00 0.00 39.50 4.26
4734 5170 0.959372 AGCAGCACCATTCAGCTCAC 60.959 55.000 0.00 0.00 39.50 3.51
4738 5174 0.890542 GCACCATTCAGCTCACCACA 60.891 55.000 0.00 0.00 0.00 4.17
4781 5217 8.575649 TTCTTGGTTTTTCACTTTCTACTTCT 57.424 30.769 0.00 0.00 0.00 2.85
4782 5218 8.575649 TCTTGGTTTTTCACTTTCTACTTCTT 57.424 30.769 0.00 0.00 0.00 2.52
4783 5219 8.458843 TCTTGGTTTTTCACTTTCTACTTCTTG 58.541 33.333 0.00 0.00 0.00 3.02
4784 5220 7.696992 TGGTTTTTCACTTTCTACTTCTTGT 57.303 32.000 0.00 0.00 0.00 3.16
4785 5221 8.117813 TGGTTTTTCACTTTCTACTTCTTGTT 57.882 30.769 0.00 0.00 0.00 2.83
4786 5222 8.241367 TGGTTTTTCACTTTCTACTTCTTGTTC 58.759 33.333 0.00 0.00 0.00 3.18
4787 5223 7.428472 GGTTTTTCACTTTCTACTTCTTGTTCG 59.572 37.037 0.00 0.00 0.00 3.95
4788 5224 6.598753 TTTCACTTTCTACTTCTTGTTCGG 57.401 37.500 0.00 0.00 0.00 4.30
4789 5225 5.272283 TCACTTTCTACTTCTTGTTCGGT 57.728 39.130 0.00 0.00 0.00 4.69
4790 5226 5.287226 TCACTTTCTACTTCTTGTTCGGTC 58.713 41.667 0.00 0.00 0.00 4.79
4791 5227 5.068723 TCACTTTCTACTTCTTGTTCGGTCT 59.931 40.000 0.00 0.00 0.00 3.85
4792 5228 5.175856 CACTTTCTACTTCTTGTTCGGTCTG 59.824 44.000 0.00 0.00 0.00 3.51
4793 5229 4.931661 TTCTACTTCTTGTTCGGTCTGT 57.068 40.909 0.00 0.00 0.00 3.41
4794 5230 4.238761 TCTACTTCTTGTTCGGTCTGTG 57.761 45.455 0.00 0.00 0.00 3.66
4795 5231 1.583054 ACTTCTTGTTCGGTCTGTGC 58.417 50.000 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 144 4.735132 TCCTTTGCCTCGTCGCCG 62.735 66.667 0.00 0.00 0.00 6.46
142 152 1.903404 CCCGCTTTGTCCTTTGCCT 60.903 57.895 0.00 0.00 0.00 4.75
256 271 3.083997 GCCGGGGTGGATCTGTCT 61.084 66.667 2.18 0.00 42.00 3.41
257 272 4.176752 GGCCGGGGTGGATCTGTC 62.177 72.222 2.18 0.00 42.00 3.51
337 360 2.483714 CCGTCACCCGATCAATCAATCT 60.484 50.000 0.00 0.00 39.56 2.40
349 372 0.734889 ACGAATAGTACCGTCACCCG 59.265 55.000 0.00 0.00 33.23 5.28
352 375 7.510428 TTGAAATTACGAATAGTACCGTCAC 57.490 36.000 3.10 0.00 39.86 3.67
366 392 7.382218 GGATAGGAATGCCAAATTGAAATTACG 59.618 37.037 0.00 0.00 36.29 3.18
369 395 7.197901 TGGATAGGAATGCCAAATTGAAATT 57.802 32.000 0.00 0.00 36.29 1.82
370 396 6.811634 TGGATAGGAATGCCAAATTGAAAT 57.188 33.333 0.00 0.00 36.29 2.17
371 397 6.584488 CATGGATAGGAATGCCAAATTGAAA 58.416 36.000 0.00 0.00 34.95 2.69
372 398 5.453621 GCATGGATAGGAATGCCAAATTGAA 60.454 40.000 0.00 0.00 42.73 2.69
373 399 4.039488 GCATGGATAGGAATGCCAAATTGA 59.961 41.667 0.00 0.00 42.73 2.57
374 400 4.312443 GCATGGATAGGAATGCCAAATTG 58.688 43.478 0.00 0.00 42.73 2.32
393 419 1.217511 CTGTGCTCTCCTGACGCAT 59.782 57.895 0.00 0.00 35.93 4.73
395 421 2.125753 CCTGTGCTCTCCTGACGC 60.126 66.667 0.00 0.00 0.00 5.19
398 424 2.015456 TTCTTCCTGTGCTCTCCTGA 57.985 50.000 0.00 0.00 0.00 3.86
399 425 2.630158 CATTCTTCCTGTGCTCTCCTG 58.370 52.381 0.00 0.00 0.00 3.86
400 426 1.065564 GCATTCTTCCTGTGCTCTCCT 60.066 52.381 0.00 0.00 36.02 3.69
436 467 1.376037 CTGTCACCGCCTCTTTCCC 60.376 63.158 0.00 0.00 0.00 3.97
437 468 0.390472 CTCTGTCACCGCCTCTTTCC 60.390 60.000 0.00 0.00 0.00 3.13
438 469 0.390472 CCTCTGTCACCGCCTCTTTC 60.390 60.000 0.00 0.00 0.00 2.62
439 470 1.674057 CCTCTGTCACCGCCTCTTT 59.326 57.895 0.00 0.00 0.00 2.52
440 471 2.948720 GCCTCTGTCACCGCCTCTT 61.949 63.158 0.00 0.00 0.00 2.85
441 472 3.386237 GCCTCTGTCACCGCCTCT 61.386 66.667 0.00 0.00 0.00 3.69
442 473 4.803426 CGCCTCTGTCACCGCCTC 62.803 72.222 0.00 0.00 0.00 4.70
529 743 1.719117 GCTCGTCGTCTCAGGAGAG 59.281 63.158 0.00 0.00 43.48 3.20
530 744 2.101233 CGCTCGTCGTCTCAGGAGA 61.101 63.158 0.00 0.00 31.09 3.71
531 745 2.031044 CTCGCTCGTCGTCTCAGGAG 62.031 65.000 0.00 0.00 39.67 3.69
532 746 2.047560 TCGCTCGTCGTCTCAGGA 60.048 61.111 0.00 0.00 39.67 3.86
533 747 2.401592 CTCGCTCGTCGTCTCAGG 59.598 66.667 0.00 0.00 39.67 3.86
549 763 1.247567 CTGTGATGTTTTTCCCCGCT 58.752 50.000 0.00 0.00 0.00 5.52
550 764 0.388520 GCTGTGATGTTTTTCCCCGC 60.389 55.000 0.00 0.00 0.00 6.13
551 765 0.958091 TGCTGTGATGTTTTTCCCCG 59.042 50.000 0.00 0.00 0.00 5.73
555 769 2.056577 GCTGCTGCTGTGATGTTTTTC 58.943 47.619 8.53 0.00 36.03 2.29
569 784 1.092348 TTTATCTGCTGCTGCTGCTG 58.908 50.000 27.67 26.32 40.48 4.41
570 785 1.830279 TTTTATCTGCTGCTGCTGCT 58.170 45.000 27.67 13.59 40.48 4.24
571 786 2.257034 GTTTTTATCTGCTGCTGCTGC 58.743 47.619 22.51 22.51 40.48 5.25
572 787 3.240069 GTGTTTTTATCTGCTGCTGCTG 58.760 45.455 17.00 15.94 40.48 4.41
573 788 2.229784 GGTGTTTTTATCTGCTGCTGCT 59.770 45.455 17.00 0.00 40.48 4.24
579 794 1.812571 CCTGCGGTGTTTTTATCTGCT 59.187 47.619 0.00 0.00 34.91 4.24
618 833 1.256812 CGAGGGGGTTTCTGCAAAAT 58.743 50.000 0.00 0.00 0.00 1.82
638 853 1.861542 CGGCGATTGGCAAAACCTCA 61.862 55.000 3.01 0.00 46.16 3.86
835 1097 0.982852 AGCGACTCCATGAATCCCCA 60.983 55.000 0.00 0.00 0.00 4.96
887 1156 2.052237 CGCACAGCACAACGAACC 60.052 61.111 0.00 0.00 0.00 3.62
891 1160 2.661537 TCCTCGCACAGCACAACG 60.662 61.111 0.00 0.00 0.00 4.10
916 1185 0.692756 CCCCTTCTTCCTCCTCCCTC 60.693 65.000 0.00 0.00 0.00 4.30
917 1186 1.398234 CCCCTTCTTCCTCCTCCCT 59.602 63.158 0.00 0.00 0.00 4.20
951 1223 3.035363 CCAACCCAACCAAACCTAACTT 58.965 45.455 0.00 0.00 0.00 2.66
953 1225 1.689813 CCCAACCCAACCAAACCTAAC 59.310 52.381 0.00 0.00 0.00 2.34
954 1226 1.291335 ACCCAACCCAACCAAACCTAA 59.709 47.619 0.00 0.00 0.00 2.69
955 1227 0.935194 ACCCAACCCAACCAAACCTA 59.065 50.000 0.00 0.00 0.00 3.08
956 1228 0.043485 AACCCAACCCAACCAAACCT 59.957 50.000 0.00 0.00 0.00 3.50
957 1229 0.179234 CAACCCAACCCAACCAAACC 59.821 55.000 0.00 0.00 0.00 3.27
958 1230 0.179234 CCAACCCAACCCAACCAAAC 59.821 55.000 0.00 0.00 0.00 2.93
959 1231 0.983378 CCCAACCCAACCCAACCAAA 60.983 55.000 0.00 0.00 0.00 3.28
960 1232 1.383248 CCCAACCCAACCCAACCAA 60.383 57.895 0.00 0.00 0.00 3.67
961 1233 2.283809 CCCAACCCAACCCAACCA 59.716 61.111 0.00 0.00 0.00 3.67
962 1234 3.238497 GCCCAACCCAACCCAACC 61.238 66.667 0.00 0.00 0.00 3.77
963 1235 3.611674 CGCCCAACCCAACCCAAC 61.612 66.667 0.00 0.00 0.00 3.77
964 1236 3.801068 CTCGCCCAACCCAACCCAA 62.801 63.158 0.00 0.00 0.00 4.12
965 1237 4.278513 CTCGCCCAACCCAACCCA 62.279 66.667 0.00 0.00 0.00 4.51
971 1243 4.660938 ACCAAGCTCGCCCAACCC 62.661 66.667 0.00 0.00 0.00 4.11
977 1258 2.956964 CGATCGACCAAGCTCGCC 60.957 66.667 10.26 0.00 33.47 5.54
1008 1289 1.153823 CACCTTGGTCGCCTCGTAG 60.154 63.158 0.00 0.00 0.00 3.51
1375 1668 3.842923 CGCCATCTCCTCTGCGGT 61.843 66.667 0.00 0.00 43.08 5.68
1470 1766 1.278337 CTCGTCGAGGATCAGCGAG 59.722 63.158 14.68 6.62 42.01 5.03
1776 2081 2.750637 GCGAGGTCGTCAGGGAGA 60.751 66.667 0.69 0.00 42.22 3.71
1908 2213 4.095400 GAGGGGGAGCCAGGGAGA 62.095 72.222 0.00 0.00 0.00 3.71
1980 2285 1.133884 GTGGGTATTTACCTCTGGCCC 60.134 57.143 0.00 0.00 45.72 5.80
2022 2330 1.738350 CTGGTAGAAACGAGAGCGAGA 59.262 52.381 0.00 0.00 41.64 4.04
2313 2628 2.799017 GGTTAATCCCGGTGGAACTTT 58.201 47.619 0.00 0.00 45.98 2.66
2368 2683 4.656117 ATGCGCACGTCGTGGACA 62.656 61.111 25.70 16.57 41.07 4.02
2413 2728 1.475682 GGGTAGACGAAGGTGACGAAT 59.524 52.381 0.00 0.00 34.70 3.34
2590 2908 1.885887 CATGGGGATGTTGTCGTTGTT 59.114 47.619 0.00 0.00 0.00 2.83
2592 2910 1.468520 GTCATGGGGATGTTGTCGTTG 59.531 52.381 0.00 0.00 0.00 4.10
2594 2912 0.035439 GGTCATGGGGATGTTGTCGT 60.035 55.000 0.00 0.00 0.00 4.34
2595 2913 0.035534 TGGTCATGGGGATGTTGTCG 60.036 55.000 0.00 0.00 0.00 4.35
2596 2914 2.442236 ATGGTCATGGGGATGTTGTC 57.558 50.000 0.00 0.00 0.00 3.18
2597 2915 2.925966 AATGGTCATGGGGATGTTGT 57.074 45.000 0.00 0.00 0.00 3.32
2598 2916 5.874897 AATAAATGGTCATGGGGATGTTG 57.125 39.130 0.00 0.00 0.00 3.33
2599 2917 5.366477 GGAAATAAATGGTCATGGGGATGTT 59.634 40.000 0.00 0.00 0.00 2.71
2752 3070 7.548967 TGCATATGAACATGAACAATCAACAT 58.451 30.769 6.97 0.00 39.49 2.71
2816 3139 2.749076 CTCGCACCTGAAATCCAAATCA 59.251 45.455 0.00 0.00 0.00 2.57
2821 3144 0.911769 ATCCTCGCACCTGAAATCCA 59.088 50.000 0.00 0.00 0.00 3.41
2824 3147 0.254178 AGCATCCTCGCACCTGAAAT 59.746 50.000 0.00 0.00 0.00 2.17
2826 3149 1.078918 CAGCATCCTCGCACCTGAA 60.079 57.895 0.00 0.00 0.00 3.02
2827 3150 2.580815 CAGCATCCTCGCACCTGA 59.419 61.111 0.00 0.00 0.00 3.86
2853 3176 1.421485 CATCTCGTTGGCGCTGTTC 59.579 57.895 7.64 0.00 38.14 3.18
3102 3431 8.612619 GTTGTGACCAGGTAATAATAAGATGTG 58.387 37.037 0.00 0.00 0.00 3.21
3104 3433 8.731275 TGTTGTGACCAGGTAATAATAAGATG 57.269 34.615 0.00 0.00 0.00 2.90
3105 3434 8.768397 TCTGTTGTGACCAGGTAATAATAAGAT 58.232 33.333 0.00 0.00 0.00 2.40
3106 3435 8.141298 TCTGTTGTGACCAGGTAATAATAAGA 57.859 34.615 0.00 0.00 0.00 2.10
3122 3454 1.334556 GCAACACTGCATCTGTTGTGA 59.665 47.619 26.34 0.00 46.88 3.58
3212 3544 2.004583 CTCCGTTGACCGCATTCTTA 57.995 50.000 0.00 0.00 34.38 2.10
3284 3616 3.004944 GCGTTAAATTCCACCTTTGGTCA 59.995 43.478 0.00 0.00 44.35 4.02
3373 3705 3.517296 TGGTGAAATGCTTACTTCCCA 57.483 42.857 0.00 0.00 0.00 4.37
3408 3740 2.936202 CTGCATATTAGCACAAGGGGT 58.064 47.619 0.00 0.00 40.11 4.95
3412 3744 1.658373 CGCGCTGCATATTAGCACAAG 60.658 52.381 5.56 0.00 41.18 3.16
3423 3759 2.203056 TTATGCTCCGCGCTGCAT 60.203 55.556 29.53 29.53 43.53 3.96
3486 3822 2.435938 GCGAAAGGATCACGGGCA 60.436 61.111 0.00 0.00 0.00 5.36
3507 3843 2.704108 GGCGATCTCCGACTCAGTA 58.296 57.895 0.00 0.00 44.62 2.74
3531 3867 2.858158 GCGTTGCAACCCGTAGAC 59.142 61.111 23.42 0.00 0.00 2.59
3532 3868 2.735478 CGCGTTGCAACCCGTAGA 60.735 61.111 24.69 0.00 0.00 2.59
3582 3924 1.310216 GGTTAATGCCGCCGTTCCTT 61.310 55.000 0.00 0.00 0.00 3.36
3899 4255 7.098477 TCATTCCAATAAGTGAAAAAGGCATG 58.902 34.615 0.00 0.00 0.00 4.06
3916 4272 5.253330 GAGGTTAAGACACCATCATTCCAA 58.747 41.667 0.00 0.00 39.62 3.53
3939 4295 2.350772 GCAAAACACACAGAAGGATCCG 60.351 50.000 5.98 0.00 0.00 4.18
3949 4305 3.951037 ACATAGACAAGGCAAAACACACA 59.049 39.130 0.00 0.00 0.00 3.72
4022 4379 4.201950 TGCTGCAACTTCTTCACTCTTTTC 60.202 41.667 0.00 0.00 0.00 2.29
4098 4456 1.654954 CTGGTGCCATCAGCTTGAGC 61.655 60.000 0.00 0.00 44.23 4.26
4326 4726 1.028905 TTATATTGGCGGTGGCTTGC 58.971 50.000 0.00 0.00 39.81 4.01
4348 4753 7.876936 TTACATGAGAACTACTACTAGTGGG 57.123 40.000 11.30 3.83 33.14 4.61
4532 4949 9.022915 TCCAGTGAAATTATACATACGTAAACG 57.977 33.333 0.00 0.04 46.33 3.60
4571 5001 1.691976 AGACATGACGGACCTGTTCAA 59.308 47.619 0.00 0.00 0.00 2.69
4587 5017 4.314440 GCCCACAGCACCGAGACA 62.314 66.667 0.00 0.00 42.97 3.41
4619 5055 2.203938 TGAGTGGTCCACCCCTCC 60.204 66.667 18.80 4.00 34.49 4.30
4674 5110 3.414700 CGGCCAACGCTGACACTC 61.415 66.667 2.24 0.00 44.91 3.51
4711 5147 1.654954 GCTGAATGGTGCTGCTGAGG 61.655 60.000 0.00 0.00 0.00 3.86
4715 5151 0.959372 GTGAGCTGAATGGTGCTGCT 60.959 55.000 0.00 0.00 42.19 4.24
4723 5159 1.467734 GCTTCTGTGGTGAGCTGAATG 59.532 52.381 0.00 0.00 0.00 2.67
4754 5190 8.575649 AAGTAGAAAGTGAAAAACCAAGAAGA 57.424 30.769 0.00 0.00 0.00 2.87
4757 5193 8.458843 CAAGAAGTAGAAAGTGAAAAACCAAGA 58.541 33.333 0.00 0.00 0.00 3.02
4758 5194 8.244113 ACAAGAAGTAGAAAGTGAAAAACCAAG 58.756 33.333 0.00 0.00 0.00 3.61
4760 5196 7.696992 ACAAGAAGTAGAAAGTGAAAAACCA 57.303 32.000 0.00 0.00 0.00 3.67
4761 5197 7.428472 CGAACAAGAAGTAGAAAGTGAAAAACC 59.572 37.037 0.00 0.00 0.00 3.27
4762 5198 7.428472 CCGAACAAGAAGTAGAAAGTGAAAAAC 59.572 37.037 0.00 0.00 0.00 2.43
4767 5203 5.068723 AGACCGAACAAGAAGTAGAAAGTGA 59.931 40.000 0.00 0.00 0.00 3.41
4768 5204 5.175856 CAGACCGAACAAGAAGTAGAAAGTG 59.824 44.000 0.00 0.00 0.00 3.16
4776 5212 1.583054 GCACAGACCGAACAAGAAGT 58.417 50.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.