Multiple sequence alignment - TraesCS2B01G466500

Loading Multiple Alignment...

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 TraesCS2B01G466500 chr2B 100.000 3770 0 0 1 3770 662372014 662375783 0.000000e+00 6962
1 TraesCS2B01G466500 chr2B 85.904 2263 154 64 167 2367 661850338 661852497 0.000000e+00 2259
2 TraesCS2B01G466500 chr2D 90.484 3615 197 65 1 3554 555575417 555578945 0.000000e+00 4634
3 TraesCS2B01G466500 chr2D 86.572 2383 147 65 1 2288 555394079 555396383 0.000000e+00 2468
4 TraesCS2B01G466500 chr2D 88.000 150 13 3 3622 3770 555613116 555613261 5.010000e-39 172
5 TraesCS2B01G466500 chr2D 86.861 137 17 1 1386 1522 636638923 636639058 6.520000e-33 152
6 TraesCS2B01G466500 chr2A 85.503 3518 231 117 1 3393 695149036 695152399 0.000000e+00 3413
7 TraesCS2B01G466500 chr2A 85.520 221 21 7 3560 3770 695152704 695152923 1.760000e-53 220
8 TraesCS2B01G466500 chr2A 86.429 140 18 1 1383 1522 625243570 625243708 6.520000e-33 152
9 TraesCS2B01G466500 chr6D 93.023 129 8 1 1141 1269 352835526 352835653 1.790000e-43 187
10 TraesCS2B01G466500 chr6D 90.000 130 13 0 1397 1526 352835668 352835797 6.480000e-38 169
11 TraesCS2B01G466500 chr6D 94.444 90 5 0 1627 1716 352835881 352835970 5.080000e-29 139
12 TraesCS2B01G466500 chr6A 93.023 129 8 1 1141 1269 490301789 490301916 1.790000e-43 187
13 TraesCS2B01G466500 chr6A 91.538 130 11 0 1397 1526 490301931 490302060 2.990000e-41 180
14 TraesCS2B01G466500 chr6A 95.349 86 4 0 1627 1712 490302137 490302222 1.830000e-28 137
15 TraesCS2B01G466500 chr6B 90.909 132 11 1 1141 1272 526101297 526101167 3.870000e-40 176
16 TraesCS2B01G466500 chr6B 90.769 130 12 0 1397 1526 526101155 526101026 1.390000e-39 174
17 TraesCS2B01G466500 chr6B 95.349 86 4 0 1627 1712 526100919 526100834 1.830000e-28 137


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 TraesCS2B01G466500 chr2B 662372014 662375783 3769 False 6962.0 6962 100.0000 1 3770 1 chr2B.!!$F2 3769
1 TraesCS2B01G466500 chr2B 661850338 661852497 2159 False 2259.0 2259 85.9040 167 2367 1 chr2B.!!$F1 2200
2 TraesCS2B01G466500 chr2D 555575417 555578945 3528 False 4634.0 4634 90.4840 1 3554 1 chr2D.!!$F2 3553
3 TraesCS2B01G466500 chr2D 555394079 555396383 2304 False 2468.0 2468 86.5720 1 2288 1 chr2D.!!$F1 2287
4 TraesCS2B01G466500 chr2A 695149036 695152923 3887 False 1816.5 3413 85.5115 1 3770 2 chr2A.!!$F2 3769


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
814 922 0.178301 GGCCGGGGTTTTGTTTTTGA 59.822 50.0 2.18 0.0 0.00 2.69 F
1116 1267 0.107654 GAAGCAGCCGGATTGGTAGT 60.108 55.0 5.05 0.0 41.21 2.73 F
1972 2159 0.388520 TCGACATGCTTCTGGACACG 60.389 55.0 0.00 0.0 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 2135 0.247460 CCAGAAGCATGTCGAGGTCA 59.753 55.0 0.0 0.00 0.00 4.02 R
2463 2677 0.745468 AACTAAGAGATCGGACGGGC 59.255 55.0 0.0 0.00 0.00 6.13 R
3318 3561 0.036164 TCCACCACGTGAGATTTGGG 59.964 55.0 19.3 7.36 35.23 4.12 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
120 144 2.166829 ACTGTTTGTTGTGAGGTTGCA 58.833 42.857 0.00 0.00 0.00 4.08
121 145 2.164219 ACTGTTTGTTGTGAGGTTGCAG 59.836 45.455 0.00 0.00 0.00 4.41
143 167 3.414700 GCACCGTCCTGCAGTTCG 61.415 66.667 13.81 15.78 37.11 3.95
162 191 1.812324 CGCCGGGGCTGTTATAATTGA 60.812 52.381 5.22 0.00 39.32 2.57
189 227 6.461110 AAAATGGGATGAATTAGACAGCAG 57.539 37.500 0.00 0.00 0.00 4.24
238 280 2.541762 GCTCTGTTGATTCACCTATCGC 59.458 50.000 0.00 0.00 0.00 4.58
243 285 2.515926 TGATTCACCTATCGCAGCTC 57.484 50.000 0.00 0.00 0.00 4.09
272 319 1.165270 GCGTACTGTTGCCCAATCTT 58.835 50.000 0.00 0.00 0.00 2.40
330 378 1.818674 GCTTACTGTTCCCCACCATTG 59.181 52.381 0.00 0.00 0.00 2.82
351 400 3.493129 TGAAAACTGATTTGGACGAGTCG 59.507 43.478 11.85 11.85 0.00 4.18
361 410 0.389948 GGACGAGTCGTGCAAAGGAT 60.390 55.000 29.25 0.00 46.80 3.24
548 622 3.537874 GATCCCGTCGGTCCCAGG 61.538 72.222 11.06 0.00 0.00 4.45
582 656 3.753294 AGGCACGAAAGAAGAGAAGAA 57.247 42.857 0.00 0.00 0.00 2.52
583 657 3.394719 AGGCACGAAAGAAGAGAAGAAC 58.605 45.455 0.00 0.00 0.00 3.01
584 658 2.480802 GGCACGAAAGAAGAGAAGAACC 59.519 50.000 0.00 0.00 0.00 3.62
587 661 2.704065 ACGAAAGAAGAGAAGAACCCCA 59.296 45.455 0.00 0.00 0.00 4.96
590 664 4.657013 GAAAGAAGAGAAGAACCCCACAT 58.343 43.478 0.00 0.00 0.00 3.21
591 665 3.990959 AGAAGAGAAGAACCCCACATC 57.009 47.619 0.00 0.00 0.00 3.06
592 666 2.573915 AGAAGAGAAGAACCCCACATCC 59.426 50.000 0.00 0.00 0.00 3.51
593 667 2.044793 AGAGAAGAACCCCACATCCA 57.955 50.000 0.00 0.00 0.00 3.41
594 668 1.630878 AGAGAAGAACCCCACATCCAC 59.369 52.381 0.00 0.00 0.00 4.02
595 669 0.698818 AGAAGAACCCCACATCCACC 59.301 55.000 0.00 0.00 0.00 4.61
596 670 0.698818 GAAGAACCCCACATCCACCT 59.301 55.000 0.00 0.00 0.00 4.00
597 671 1.913419 GAAGAACCCCACATCCACCTA 59.087 52.381 0.00 0.00 0.00 3.08
598 672 1.584724 AGAACCCCACATCCACCTAG 58.415 55.000 0.00 0.00 0.00 3.02
605 689 2.564947 CCCACATCCACCTAGCTAGATC 59.435 54.545 22.70 0.00 0.00 2.75
617 701 1.442857 CTAGATCGCGCCGATGACC 60.443 63.158 17.23 5.65 47.00 4.02
618 702 3.249973 TAGATCGCGCCGATGACCG 62.250 63.158 17.23 0.00 47.00 4.79
717 801 2.591715 ACAGACACACGCAAGGCC 60.592 61.111 0.00 0.00 46.39 5.19
807 915 4.614036 AGTGGGGCCGGGGTTTTG 62.614 66.667 2.18 0.00 0.00 2.44
813 921 0.816018 GGGCCGGGGTTTTGTTTTTG 60.816 55.000 2.18 0.00 0.00 2.44
814 922 0.178301 GGCCGGGGTTTTGTTTTTGA 59.822 50.000 2.18 0.00 0.00 2.69
815 923 1.292061 GCCGGGGTTTTGTTTTTGAC 58.708 50.000 2.18 0.00 0.00 3.18
1006 1133 2.669569 CCAGTGTCCCGGTTGCAG 60.670 66.667 0.00 0.00 0.00 4.41
1027 1170 1.464608 CTTGCACATGTCCGGTACAAG 59.535 52.381 0.00 4.54 42.70 3.16
1030 1173 1.067142 GCACATGTCCGGTACAAGAGA 60.067 52.381 13.66 0.00 42.70 3.10
1031 1174 2.881074 CACATGTCCGGTACAAGAGAG 58.119 52.381 13.66 5.04 42.70 3.20
1102 1249 2.350522 GCTAGCTAGCTGTTTGAAGCA 58.649 47.619 33.71 2.47 46.08 3.91
1110 1261 0.883833 CTGTTTGAAGCAGCCGGATT 59.116 50.000 5.05 0.00 0.00 3.01
1113 1264 0.539438 TTTGAAGCAGCCGGATTGGT 60.539 50.000 5.05 5.27 41.21 3.67
1116 1267 0.107654 GAAGCAGCCGGATTGGTAGT 60.108 55.000 5.05 0.00 41.21 2.73
1344 1505 5.119743 GCTCTTTGAGTTCATGCCAATTTTC 59.880 40.000 0.00 0.00 31.39 2.29
1374 1536 3.854666 AGAACTCGACTGATTCATGTGG 58.145 45.455 0.00 0.00 0.00 4.17
1542 1704 4.242475 CAAGTACGTTCATCACTTGCCTA 58.758 43.478 13.54 0.00 41.75 3.93
1543 1705 4.530710 AGTACGTTCATCACTTGCCTAA 57.469 40.909 0.00 0.00 0.00 2.69
1544 1706 4.243270 AGTACGTTCATCACTTGCCTAAC 58.757 43.478 0.00 0.00 0.00 2.34
1545 1707 2.066262 ACGTTCATCACTTGCCTAACG 58.934 47.619 0.00 0.00 43.76 3.18
1546 1708 2.288579 ACGTTCATCACTTGCCTAACGA 60.289 45.455 11.79 0.00 41.48 3.85
1552 1714 2.499197 TCACTTGCCTAACGATTGCAA 58.501 42.857 0.00 0.00 42.28 4.08
1573 1735 2.089980 CACCCTGAAGAAAGCTCCATG 58.910 52.381 0.00 0.00 0.00 3.66
1887 2068 3.485431 CGGCGAGCAGAGCAACAG 61.485 66.667 0.00 0.00 36.08 3.16
1963 2150 1.160137 GCTTTGACCTCGACATGCTT 58.840 50.000 0.00 0.00 0.00 3.91
1972 2159 0.388520 TCGACATGCTTCTGGACACG 60.389 55.000 0.00 0.00 0.00 4.49
2197 2393 1.975327 CAAGGGAACAGAGGCGAGA 59.025 57.895 0.00 0.00 0.00 4.04
2374 2585 1.745489 GTGCTACTTCCAAGCCGGG 60.745 63.158 2.18 0.00 39.30 5.73
2419 2633 4.821589 GGACCCGAAGCCTCTGCG 62.822 72.222 0.00 0.00 44.33 5.18
2425 2639 1.511305 CGAAGCCTCTGCGGTTCTA 59.489 57.895 0.00 0.00 44.33 2.10
2426 2640 0.526524 CGAAGCCTCTGCGGTTCTAG 60.527 60.000 0.00 0.00 44.33 2.43
2429 2643 1.079127 GCCTCTGCGGTTCTAGCAA 60.079 57.895 0.00 0.00 44.67 3.91
2437 2651 1.006832 CGGTTCTAGCAAACATCCCG 58.993 55.000 0.00 0.00 0.00 5.14
2456 2670 6.546428 TCCCGATGGATTTATAAGATCTCC 57.454 41.667 0.00 0.00 35.03 3.71
2457 2671 6.022958 TCCCGATGGATTTATAAGATCTCCA 58.977 40.000 0.00 0.00 40.12 3.86
2458 2672 6.673978 TCCCGATGGATTTATAAGATCTCCAT 59.326 38.462 15.32 15.32 46.70 3.41
2463 2677 6.701340 TGGATTTATAAGATCTCCATCACCG 58.299 40.000 0.00 0.00 31.19 4.94
2464 2678 5.582665 GGATTTATAAGATCTCCATCACCGC 59.417 44.000 0.00 0.00 0.00 5.68
2482 2701 0.745468 GCCCGTCCGATCTCTTAGTT 59.255 55.000 0.00 0.00 0.00 2.24
2495 2714 7.117812 CCGATCTCTTAGTTTAGAAACAAGCAA 59.882 37.037 7.82 2.68 41.30 3.91
2709 2933 0.101759 ACACACTGCGACTACGTTGT 59.898 50.000 1.24 1.24 41.98 3.32
2740 2964 0.530288 AAAGTGGTGCAACGCAAACT 59.470 45.000 19.16 1.74 41.47 2.66
2910 3137 5.540911 TCGAAATTCCTACTACGGTTTTGT 58.459 37.500 0.00 0.00 0.00 2.83
2978 3207 0.110486 TTTGGTGAAGCCTGTCTCCC 59.890 55.000 0.00 0.00 38.35 4.30
3070 3299 0.315251 CGTGTCCTTGAGTGAGCAGA 59.685 55.000 0.00 0.00 0.00 4.26
3148 3377 1.832998 GGTTACCTAACACGGGATCCA 59.167 52.381 15.23 0.00 37.92 3.41
3235 3465 0.108898 CTCCTGGACTTGAGTGCTCG 60.109 60.000 4.31 0.00 37.28 5.03
3296 3532 8.405531 TCTTTGATAAAACATATGTAAGCTGCC 58.594 33.333 9.21 0.00 0.00 4.85
3298 3534 7.880160 TGATAAAACATATGTAAGCTGCCTT 57.120 32.000 9.21 0.00 35.05 4.35
3318 3561 1.134521 TGTTGTCGATGGACTATGGCC 60.135 52.381 9.41 0.00 43.79 5.36
3349 3592 2.771943 ACGTGGTGGAGATGAATGGTAT 59.228 45.455 0.00 0.00 0.00 2.73
3357 3600 3.258372 GGAGATGAATGGTATGCCTCGTA 59.742 47.826 0.16 0.00 35.27 3.43
3370 3613 1.337821 CCTCGTAGAATATTCCGCGC 58.662 55.000 18.64 0.00 34.09 6.86
3393 3636 3.368531 CCCTCACCTAAGCTGAAGTACAC 60.369 52.174 0.00 0.00 0.00 2.90
3394 3637 3.511934 CCTCACCTAAGCTGAAGTACACT 59.488 47.826 0.00 0.00 0.00 3.55
3397 3640 6.546403 CCTCACCTAAGCTGAAGTACACTATA 59.454 42.308 0.00 0.00 0.00 1.31
3398 3641 7.231722 CCTCACCTAAGCTGAAGTACACTATAT 59.768 40.741 0.00 0.00 0.00 0.86
3403 3646 9.250624 CCTAAGCTGAAGTACACTATATGTTTC 57.749 37.037 0.00 0.00 43.19 2.78
3455 3701 1.067635 CGCAGCAGCAACCCTTATTTT 60.068 47.619 0.82 0.00 42.27 1.82
3491 3737 2.356069 CCGGAGCAAGAAAATAGGCTTC 59.644 50.000 0.00 0.00 36.59 3.86
3513 3759 7.168637 GCTTCATCATTATGTCGCAAATGATTT 59.831 33.333 16.99 0.00 45.90 2.17
3599 4012 5.952526 TTTCTTATTTCCCGGAACAAGAC 57.047 39.130 17.50 0.00 28.83 3.01
3600 4013 4.903045 TCTTATTTCCCGGAACAAGACT 57.097 40.909 15.18 0.00 0.00 3.24
3601 4014 5.237236 TCTTATTTCCCGGAACAAGACTT 57.763 39.130 15.18 0.00 0.00 3.01
3602 4015 5.243207 TCTTATTTCCCGGAACAAGACTTC 58.757 41.667 15.18 0.00 0.00 3.01
3603 4016 3.502123 ATTTCCCGGAACAAGACTTCA 57.498 42.857 0.73 0.00 0.00 3.02
3604 4017 2.249844 TTCCCGGAACAAGACTTCAC 57.750 50.000 0.73 0.00 0.00 3.18
3605 4018 1.124780 TCCCGGAACAAGACTTCACA 58.875 50.000 0.73 0.00 0.00 3.58
3607 4020 1.873591 CCCGGAACAAGACTTCACAAG 59.126 52.381 0.73 0.00 0.00 3.16
3608 4021 1.264288 CCGGAACAAGACTTCACAAGC 59.736 52.381 0.00 0.00 0.00 4.01
3609 4022 1.070577 CGGAACAAGACTTCACAAGCG 60.071 52.381 0.00 0.00 0.00 4.68
3633 4047 7.128331 CGCAATAAAATTCATCTACACTGGAG 58.872 38.462 0.00 0.00 0.00 3.86
3639 4053 8.425577 AAAATTCATCTACACTGGAGTTATCG 57.574 34.615 0.00 0.00 0.00 2.92
3641 4055 6.769134 TTCATCTACACTGGAGTTATCGAA 57.231 37.500 0.00 0.00 0.00 3.71
3676 4091 7.118723 TCATCCACACTGGCTAATCTTATTTT 58.881 34.615 0.00 0.00 37.47 1.82
3677 4092 7.615365 TCATCCACACTGGCTAATCTTATTTTT 59.385 33.333 0.00 0.00 37.47 1.94
3722 4137 0.331616 ATCTAACCACTGGGCCAACC 59.668 55.000 8.04 0.00 37.90 3.77
3723 4138 0.770557 TCTAACCACTGGGCCAACCT 60.771 55.000 8.04 0.00 41.11 3.50
3724 4139 0.112412 CTAACCACTGGGCCAACCTT 59.888 55.000 8.04 0.00 41.11 3.50
3725 4140 1.353022 CTAACCACTGGGCCAACCTTA 59.647 52.381 8.04 0.20 41.11 2.69
3726 4141 0.783850 AACCACTGGGCCAACCTTAT 59.216 50.000 8.04 0.00 41.11 1.73
3727 4142 0.039618 ACCACTGGGCCAACCTTATG 59.960 55.000 8.04 0.00 41.11 1.90
3728 4143 0.684153 CCACTGGGCCAACCTTATGG 60.684 60.000 8.04 4.98 43.70 2.74
3766 4186 1.621814 CGACTTTAGGTCCACCAAGGA 59.378 52.381 0.00 0.00 46.75 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 144 4.008933 GCAGGACGGTGCTGGACT 62.009 66.667 27.42 0.00 40.54 3.85
121 145 4.314440 TGCAGGACGGTGCTGGAC 62.314 66.667 27.42 14.46 44.32 4.02
143 167 1.975660 TCAATTATAACAGCCCCGGC 58.024 50.000 0.00 0.00 42.33 6.13
146 170 7.495606 CCATTTTTCTTCAATTATAACAGCCCC 59.504 37.037 0.00 0.00 0.00 5.80
149 173 9.822185 ATCCCATTTTTCTTCAATTATAACAGC 57.178 29.630 0.00 0.00 0.00 4.40
162 191 7.178983 TGCTGTCTAATTCATCCCATTTTTCTT 59.821 33.333 0.00 0.00 0.00 2.52
189 227 6.913873 TTTGCACCTACGATTTATTAGACC 57.086 37.500 0.00 0.00 0.00 3.85
238 280 0.602638 TACGCACTGTTTGGGAGCTG 60.603 55.000 0.00 0.00 40.70 4.24
272 319 3.426963 GCTTCGAACCAAATTTATCGCCA 60.427 43.478 12.69 4.58 35.39 5.69
330 378 3.493503 ACGACTCGTCCAAATCAGTTTTC 59.506 43.478 0.00 0.00 33.69 2.29
351 400 4.783461 GGAACGGATCTCATCCTTTGCAC 61.783 52.174 7.99 0.00 44.72 4.57
378 435 0.252789 TTAACCGGGACAGGGATGGA 60.253 55.000 6.32 0.00 35.02 3.41
522 595 3.186047 GACGGGATCGCGTGGTTG 61.186 66.667 37.95 10.32 40.63 3.77
548 622 2.436115 GCCTAGTTGGGTGTCCGC 60.436 66.667 0.00 0.00 36.00 5.54
582 656 0.341961 TAGCTAGGTGGATGTGGGGT 59.658 55.000 4.27 0.00 0.00 4.95
583 657 1.051812 CTAGCTAGGTGGATGTGGGG 58.948 60.000 13.32 0.00 0.00 4.96
584 658 2.088104 TCTAGCTAGGTGGATGTGGG 57.912 55.000 20.58 0.00 0.00 4.61
587 661 1.889829 GCGATCTAGCTAGGTGGATGT 59.110 52.381 23.50 3.32 0.00 3.06
590 664 1.516365 GCGCGATCTAGCTAGGTGGA 61.516 60.000 19.19 10.61 34.40 4.02
591 665 1.081108 GCGCGATCTAGCTAGGTGG 60.081 63.158 20.58 15.95 34.40 4.61
592 666 1.081108 GGCGCGATCTAGCTAGGTG 60.081 63.158 20.58 12.04 34.40 4.00
593 667 2.618219 CGGCGCGATCTAGCTAGGT 61.618 63.158 20.58 14.33 34.40 3.08
594 668 1.649390 ATCGGCGCGATCTAGCTAGG 61.649 60.000 20.58 6.04 43.45 3.02
595 669 0.522286 CATCGGCGCGATCTAGCTAG 60.522 60.000 12.10 15.01 45.19 3.42
596 670 0.953960 TCATCGGCGCGATCTAGCTA 60.954 55.000 12.10 0.00 45.19 3.32
597 671 2.256764 CATCGGCGCGATCTAGCT 59.743 61.111 12.10 0.00 45.19 3.32
598 672 2.083522 GTCATCGGCGCGATCTAGC 61.084 63.158 12.10 1.21 45.19 3.42
666 750 1.847328 AATTCATTTCCCGGTCACCC 58.153 50.000 0.00 0.00 0.00 4.61
717 801 1.519455 GACGAGAAGGTGGCGGATG 60.519 63.158 0.00 0.00 0.00 3.51
803 911 2.996621 CACTTGGCCGTCAAAAACAAAA 59.003 40.909 0.00 0.00 34.56 2.44
804 912 2.611518 CACTTGGCCGTCAAAAACAAA 58.388 42.857 0.00 0.00 34.56 2.83
807 915 0.249280 CCCACTTGGCCGTCAAAAAC 60.249 55.000 0.00 0.00 34.56 2.43
1006 1133 0.953471 TGTACCGGACATGTGCAAGC 60.953 55.000 18.05 4.90 31.20 4.01
1015 1142 1.174783 GCTCTCTCTTGTACCGGACA 58.825 55.000 9.46 5.40 35.78 4.02
1102 1249 1.407979 CTACGAACTACCAATCCGGCT 59.592 52.381 0.00 0.00 39.03 5.52
1110 1261 1.471119 CTCCCAGCTACGAACTACCA 58.529 55.000 0.00 0.00 0.00 3.25
1113 1264 0.627451 TCCCTCCCAGCTACGAACTA 59.373 55.000 0.00 0.00 0.00 2.24
1116 1267 1.381327 CCTCCCTCCCAGCTACGAA 60.381 63.158 0.00 0.00 0.00 3.85
1202 1357 3.781770 GAGGCGCATGTCCTCCTCG 62.782 68.421 19.38 4.04 43.32 4.63
1344 1505 5.828299 ATCAGTCGAGTTCTCTCTTAAGG 57.172 43.478 1.85 0.00 38.45 2.69
1374 1536 1.741145 ACCTGTCGAACCAAAACACAC 59.259 47.619 0.00 0.00 0.00 3.82
1542 1704 1.608590 CTTCAGGGTGTTGCAATCGTT 59.391 47.619 0.59 0.00 0.00 3.85
1543 1705 1.202758 TCTTCAGGGTGTTGCAATCGT 60.203 47.619 0.59 0.00 0.00 3.73
1544 1706 1.522668 TCTTCAGGGTGTTGCAATCG 58.477 50.000 0.59 0.00 0.00 3.34
1545 1707 3.858503 GCTTTCTTCAGGGTGTTGCAATC 60.859 47.826 0.59 0.00 0.00 2.67
1546 1708 2.036346 GCTTTCTTCAGGGTGTTGCAAT 59.964 45.455 0.59 0.00 0.00 3.56
1552 1714 1.140312 TGGAGCTTTCTTCAGGGTGT 58.860 50.000 0.00 0.00 0.00 4.16
1573 1735 3.189910 AGTTGATCACACATGACACATGC 59.810 43.478 0.00 0.00 37.79 4.06
1887 2068 4.673841 GCTCAAATTCTAGTTCCTTGCTGC 60.674 45.833 0.00 0.00 0.00 5.25
1948 2135 0.247460 CCAGAAGCATGTCGAGGTCA 59.753 55.000 0.00 0.00 0.00 4.02
1963 2150 1.331399 TGTTGGTGACCGTGTCCAGA 61.331 55.000 0.00 0.00 32.63 3.86
1972 2159 3.022287 CAGTGCGTGTTGGTGACC 58.978 61.111 0.00 0.00 0.00 4.02
2077 2264 3.909312 GGCACGATGTCGATCTCG 58.091 61.111 15.40 15.40 43.02 4.04
2209 2405 1.795177 CTTTCCGTCGTCGTCGTCC 60.795 63.158 10.76 0.00 38.33 4.79
2419 2633 2.396590 TCGGGATGTTTGCTAGAACC 57.603 50.000 0.00 0.00 0.00 3.62
2442 2656 5.491982 GGCGGTGATGGAGATCTTATAAAT 58.508 41.667 0.00 0.00 0.00 1.40
2444 2658 3.260884 GGGCGGTGATGGAGATCTTATAA 59.739 47.826 0.00 0.00 0.00 0.98
2448 2662 1.832912 GGGCGGTGATGGAGATCTT 59.167 57.895 0.00 0.00 0.00 2.40
2456 2670 4.221422 ATCGGACGGGCGGTGATG 62.221 66.667 1.11 0.00 0.00 3.07
2457 2671 3.912907 GATCGGACGGGCGGTGAT 61.913 66.667 1.11 0.00 0.00 3.06
2459 2673 4.570663 GAGATCGGACGGGCGGTG 62.571 72.222 1.11 0.00 0.00 4.94
2460 2674 2.898920 TAAGAGATCGGACGGGCGGT 62.899 60.000 0.00 0.00 0.00 5.68
2461 2675 2.131294 CTAAGAGATCGGACGGGCGG 62.131 65.000 0.00 0.00 0.00 6.13
2462 2676 1.283181 CTAAGAGATCGGACGGGCG 59.717 63.158 0.00 0.00 0.00 6.13
2463 2677 0.745468 AACTAAGAGATCGGACGGGC 59.255 55.000 0.00 0.00 0.00 6.13
2464 2678 3.881688 TCTAAACTAAGAGATCGGACGGG 59.118 47.826 0.00 0.00 0.00 5.28
2482 2701 2.159894 CGATCGCGTTGCTTGTTTCTAA 60.160 45.455 5.77 0.00 0.00 2.10
2589 2808 1.529865 GTCTTCGTGCTGGGTTTGTAC 59.470 52.381 0.00 0.00 0.00 2.90
2682 2906 1.334556 AGTCGCAGTGTGTACAACGTA 59.665 47.619 0.00 0.00 0.00 3.57
2740 2964 3.564053 ACCTTGACCCGTTTTTGACTA 57.436 42.857 0.00 0.00 0.00 2.59
2978 3207 2.555199 CAGCGAATGGGAAAGGTAGAG 58.445 52.381 0.00 0.00 0.00 2.43
3148 3377 2.163601 GACCCGGCCGTAACTTGTCT 62.164 60.000 26.12 0.00 0.00 3.41
3235 3465 4.095211 AGTGGTACTCTAGTTTCTTCCCC 58.905 47.826 0.00 0.00 0.00 4.81
3296 3532 2.609459 GCCATAGTCCATCGACAACAAG 59.391 50.000 0.00 0.00 41.87 3.16
3298 3534 1.134521 GGCCATAGTCCATCGACAACA 60.135 52.381 0.00 0.00 41.87 3.33
3318 3561 0.036164 TCCACCACGTGAGATTTGGG 59.964 55.000 19.30 7.36 35.23 4.12
3349 3592 1.335597 CGCGGAATATTCTACGAGGCA 60.336 52.381 19.36 0.00 0.00 4.75
3357 3600 1.371558 GAGGGGCGCGGAATATTCT 59.628 57.895 14.95 0.00 0.00 2.40
3370 3613 1.280457 ACTTCAGCTTAGGTGAGGGG 58.720 55.000 23.53 15.55 40.56 4.79
3410 3653 7.254556 CGCTATGCTTGATGATGTTCTTCTAAA 60.255 37.037 0.00 0.00 0.00 1.85
3413 3656 4.510711 CGCTATGCTTGATGATGTTCTTCT 59.489 41.667 0.00 0.00 0.00 2.85
3451 3697 3.202906 CGGTATCGGTGGATGACAAAAT 58.797 45.455 0.00 0.00 34.00 1.82
3566 3977 5.445939 CGGGAAATAAGAAATCGTGTCACAG 60.446 44.000 3.42 0.00 0.00 3.66
3573 3984 4.581868 TGTTCCGGGAAATAAGAAATCGT 58.418 39.130 11.82 0.00 0.00 3.73
3574 3985 5.353123 TCTTGTTCCGGGAAATAAGAAATCG 59.647 40.000 24.29 8.38 30.04 3.34
3576 3987 6.246163 AGTCTTGTTCCGGGAAATAAGAAAT 58.754 36.000 26.44 19.45 32.73 2.17
3599 4012 6.529125 AGATGAATTTTATTGCGCTTGTGAAG 59.471 34.615 9.73 0.00 0.00 3.02
3600 4013 6.389091 AGATGAATTTTATTGCGCTTGTGAA 58.611 32.000 9.73 0.00 0.00 3.18
3601 4014 5.953183 AGATGAATTTTATTGCGCTTGTGA 58.047 33.333 9.73 0.00 0.00 3.58
3602 4015 6.746822 TGTAGATGAATTTTATTGCGCTTGTG 59.253 34.615 9.73 0.00 0.00 3.33
3603 4016 6.747280 GTGTAGATGAATTTTATTGCGCTTGT 59.253 34.615 9.73 0.00 0.00 3.16
3604 4017 6.968904 AGTGTAGATGAATTTTATTGCGCTTG 59.031 34.615 9.73 0.00 0.00 4.01
3605 4018 6.968904 CAGTGTAGATGAATTTTATTGCGCTT 59.031 34.615 9.73 0.00 0.00 4.68
3607 4020 5.682862 CCAGTGTAGATGAATTTTATTGCGC 59.317 40.000 0.00 0.00 0.00 6.09
3608 4021 7.015226 TCCAGTGTAGATGAATTTTATTGCG 57.985 36.000 0.00 0.00 0.00 4.85
3609 4022 7.989826 ACTCCAGTGTAGATGAATTTTATTGC 58.010 34.615 0.00 0.00 0.00 3.56
3646 4060 5.954150 AGATTAGCCAGTGTGGATGATTTTT 59.046 36.000 0.00 0.00 40.96 1.94
3650 4064 4.785346 AAGATTAGCCAGTGTGGATGAT 57.215 40.909 0.00 0.00 40.96 2.45
3676 4091 0.334676 ATCCTTCCGGCCCATCAAAA 59.665 50.000 0.00 0.00 0.00 2.44
3677 4092 0.334676 AATCCTTCCGGCCCATCAAA 59.665 50.000 0.00 0.00 0.00 2.69
3687 4102 5.878116 TGGTTAGATGTGTTAAATCCTTCCG 59.122 40.000 0.00 0.00 0.00 4.30
3701 4116 1.072266 TTGGCCCAGTGGTTAGATGT 58.928 50.000 8.74 0.00 0.00 3.06
3722 4137 7.279981 TCGGAATACAATTCTGTTGTCCATAAG 59.720 37.037 8.03 0.00 37.23 1.73
3723 4138 7.065324 GTCGGAATACAATTCTGTTGTCCATAA 59.935 37.037 8.03 0.00 37.23 1.90
3724 4139 6.537301 GTCGGAATACAATTCTGTTGTCCATA 59.463 38.462 8.03 0.00 37.23 2.74
3725 4140 5.354234 GTCGGAATACAATTCTGTTGTCCAT 59.646 40.000 8.03 0.00 37.23 3.41
3726 4141 4.693566 GTCGGAATACAATTCTGTTGTCCA 59.306 41.667 8.03 0.00 37.23 4.02
3727 4142 4.935808 AGTCGGAATACAATTCTGTTGTCC 59.064 41.667 8.03 0.00 36.96 4.02
3728 4143 6.481954 AAGTCGGAATACAATTCTGTTGTC 57.518 37.500 8.03 0.00 36.96 3.18



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

AutoCloner maintained by Alex Coulton.