Multiple sequence alignment - TraesCS4B01G213400

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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 TraesCS4B01G213400 chr4B 100.000 3655 0 0 1 3655 451901491 451905145 0.000000e+00 6750
1 TraesCS4B01G213400 chr4B 91.982 898 46 9 2756 3652 622314544 622315416 0.000000e+00 1236
2 TraesCS4B01G213400 chr4B 83.784 259 36 4 1572 1828 30595269 30595015 1.310000e-59 241
3 TraesCS4B01G213400 chr4D 93.817 1973 99 10 752 2713 367042013 367043973 0.000000e+00 2946
4 TraesCS4B01G213400 chr4D 92.487 772 28 13 1 747 367041201 367041967 0.000000e+00 1077
5 TraesCS4B01G213400 chr4D 86.053 380 46 7 1541 1917 154924617 154924992 5.690000e-108 401
6 TraesCS4B01G213400 chr4A 90.291 2235 115 35 1 2185 97876979 97874797 0.000000e+00 2832
7 TraesCS4B01G213400 chr4A 93.214 501 28 1 2222 2716 97874796 97874296 0.000000e+00 732
8 TraesCS4B01G213400 chr7D 92.239 902 43 11 2756 3655 438692015 438691139 0.000000e+00 1253
9 TraesCS4B01G213400 chr7D 89.556 900 49 9 2755 3652 189433054 189433910 0.000000e+00 1099
10 TraesCS4B01G213400 chr7D 84.833 778 92 16 1147 1917 31931016 31931774 0.000000e+00 760
11 TraesCS4B01G213400 chr7D 87.277 393 24 5 2756 3147 189435450 189435817 3.370000e-115 425
12 TraesCS4B01G213400 chr7B 91.898 901 47 8 2756 3655 744245680 744244805 0.000000e+00 1236
13 TraesCS4B01G213400 chr7B 91.473 903 49 10 2755 3655 459116801 459115925 0.000000e+00 1216
14 TraesCS4B01G213400 chr7B 91.232 901 43 6 2756 3655 742267723 742266858 0.000000e+00 1194
15 TraesCS4B01G213400 chr7B 87.692 390 22 5 2756 3145 706113453 706113816 7.250000e-117 431
16 TraesCS4B01G213400 chr3D 91.898 901 45 10 2754 3652 606920565 606921439 0.000000e+00 1234
17 TraesCS4B01G213400 chr3D 87.212 391 24 5 2756 3145 606922978 606923343 4.360000e-114 422
18 TraesCS4B01G213400 chr2D 92.152 892 43 9 2756 3645 16240431 16241297 0.000000e+00 1234
19 TraesCS4B01G213400 chr2D 95.461 749 33 1 2908 3655 537456188 537455440 0.000000e+00 1194
20 TraesCS4B01G213400 chr2D 85.032 775 89 17 1150 1917 325249143 325248389 0.000000e+00 763
21 TraesCS4B01G213400 chr2B 91.759 898 46 13 2756 3652 45562544 45563414 0.000000e+00 1223
22 TraesCS4B01G213400 chr2B 84.496 258 35 4 1572 1828 311671658 311671911 2.180000e-62 250
23 TraesCS4B01G213400 chr6A 91.648 898 49 8 2756 3652 2224140 2225012 0.000000e+00 1219
24 TraesCS4B01G213400 chr6A 86.701 391 26 10 2756 3145 106683683 106684048 9.450000e-111 411
25 TraesCS4B01G213400 chr6D 90.344 901 60 6 2754 3652 30415770 30416645 0.000000e+00 1157
26 TraesCS4B01G213400 chr5D 89.767 645 41 4 2752 3396 491429942 491429323 0.000000e+00 802
27 TraesCS4B01G213400 chr6B 88.780 615 43 8 2756 3370 347744191 347744779 0.000000e+00 730
28 TraesCS4B01G213400 chr6B 82.699 289 43 6 1542 1828 259709512 259709795 2.180000e-62 250
29 TraesCS4B01G213400 chr5A 86.310 336 39 6 1584 1917 492682043 492681713 3.470000e-95 359
30 TraesCS4B01G213400 chr5B 86.552 290 35 4 1148 1434 620779783 620779495 2.120000e-82 316
31 TraesCS4B01G213400 chr5B 84.255 235 32 4 1595 1828 704602745 704602515 1.320000e-54 224


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 TraesCS4B01G213400 chr4B 451901491 451905145 3654 False 6750.0 6750 100.0000 1 3655 1 chr4B.!!$F1 3654
1 TraesCS4B01G213400 chr4B 622314544 622315416 872 False 1236.0 1236 91.9820 2756 3652 1 chr4B.!!$F2 896
2 TraesCS4B01G213400 chr4D 367041201 367043973 2772 False 2011.5 2946 93.1520 1 2713 2 chr4D.!!$F2 2712
3 TraesCS4B01G213400 chr4A 97874296 97876979 2683 True 1782.0 2832 91.7525 1 2716 2 chr4A.!!$R1 2715
4 TraesCS4B01G213400 chr7D 438691139 438692015 876 True 1253.0 1253 92.2390 2756 3655 1 chr7D.!!$R1 899
5 TraesCS4B01G213400 chr7D 189433054 189435817 2763 False 762.0 1099 88.4165 2755 3652 2 chr7D.!!$F2 897
6 TraesCS4B01G213400 chr7D 31931016 31931774 758 False 760.0 760 84.8330 1147 1917 1 chr7D.!!$F1 770
7 TraesCS4B01G213400 chr7B 744244805 744245680 875 True 1236.0 1236 91.8980 2756 3655 1 chr7B.!!$R3 899
8 TraesCS4B01G213400 chr7B 459115925 459116801 876 True 1216.0 1216 91.4730 2755 3655 1 chr7B.!!$R1 900
9 TraesCS4B01G213400 chr7B 742266858 742267723 865 True 1194.0 1194 91.2320 2756 3655 1 chr7B.!!$R2 899
10 TraesCS4B01G213400 chr3D 606920565 606923343 2778 False 828.0 1234 89.5550 2754 3652 2 chr3D.!!$F1 898
11 TraesCS4B01G213400 chr2D 16240431 16241297 866 False 1234.0 1234 92.1520 2756 3645 1 chr2D.!!$F1 889
12 TraesCS4B01G213400 chr2D 537455440 537456188 748 True 1194.0 1194 95.4610 2908 3655 1 chr2D.!!$R2 747
13 TraesCS4B01G213400 chr2D 325248389 325249143 754 True 763.0 763 85.0320 1150 1917 1 chr2D.!!$R1 767
14 TraesCS4B01G213400 chr2B 45562544 45563414 870 False 1223.0 1223 91.7590 2756 3652 1 chr2B.!!$F1 896
15 TraesCS4B01G213400 chr6A 2224140 2225012 872 False 1219.0 1219 91.6480 2756 3652 1 chr6A.!!$F1 896
16 TraesCS4B01G213400 chr6D 30415770 30416645 875 False 1157.0 1157 90.3440 2754 3652 1 chr6D.!!$F1 898
17 TraesCS4B01G213400 chr5D 491429323 491429942 619 True 802.0 802 89.7670 2752 3396 1 chr5D.!!$R1 644
18 TraesCS4B01G213400 chr6B 347744191 347744779 588 False 730.0 730 88.7800 2756 3370 1 chr6B.!!$F2 614

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
971 1082 0.611062 TACGAGTCCTCTGGTGGGTG 60.611 60.0 0.0 0.0 34.61 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2888 3027 0.174845 CACCTTGCGGTATCTCGGAA 59.825 55.0 0.0 0.0 43.24 4.3 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
148 153 0.973632 TCGCAGGTGGTAACTGACAT 59.026 50.000 0.00 0.00 38.20 3.06
341 362 6.827586 AGGTTTGATTTGGCGATAGTTTTA 57.172 33.333 0.00 0.00 39.35 1.52
366 392 1.480789 TACAGCTCATAACCCGCAGA 58.519 50.000 0.00 0.00 0.00 4.26
369 395 1.123077 AGCTCATAACCCGCAGATCA 58.877 50.000 0.00 0.00 0.00 2.92
389 415 2.783379 TAGAGAGCCATGAGACCCAT 57.217 50.000 0.00 0.00 35.44 4.00
402 428 2.103263 GAGACCCATACTTGCCAGTAGG 59.897 54.545 3.81 3.29 38.96 3.18
443 469 3.746751 CGGAGGCTGATTGATCCTCAATT 60.747 47.826 9.40 0.00 46.20 2.32
444 470 4.213513 GGAGGCTGATTGATCCTCAATTT 58.786 43.478 9.40 0.00 46.20 1.82
445 471 4.648307 GGAGGCTGATTGATCCTCAATTTT 59.352 41.667 9.40 0.00 46.20 1.82
446 472 5.128335 GGAGGCTGATTGATCCTCAATTTTT 59.872 40.000 9.40 0.00 46.20 1.94
520 567 7.881775 AGCAAATTAAACCGAGAATTCCTAT 57.118 32.000 0.65 0.00 0.00 2.57
527 574 5.880054 AACCGAGAATTCCTATGTTGTTG 57.120 39.130 0.65 0.00 0.00 3.33
601 650 2.723209 CGATTGTACCTAACGCGATGA 58.277 47.619 15.93 0.00 0.00 2.92
604 653 1.753930 TGTACCTAACGCGATGAGGA 58.246 50.000 25.14 11.20 34.24 3.71
616 665 4.876107 ACGCGATGAGGAAAACAGATTTAT 59.124 37.500 15.93 0.00 0.00 1.40
617 666 5.006746 ACGCGATGAGGAAAACAGATTTATC 59.993 40.000 15.93 0.00 0.00 1.75
618 667 5.006649 CGCGATGAGGAAAACAGATTTATCA 59.993 40.000 0.00 0.00 33.66 2.15
619 668 6.195165 GCGATGAGGAAAACAGATTTATCAC 58.805 40.000 0.00 0.00 32.60 3.06
620 669 6.037610 GCGATGAGGAAAACAGATTTATCACT 59.962 38.462 0.00 0.00 32.60 3.41
621 670 7.404985 CGATGAGGAAAACAGATTTATCACTG 58.595 38.462 0.00 0.00 39.65 3.66
622 671 7.278646 CGATGAGGAAAACAGATTTATCACTGA 59.721 37.037 0.00 0.00 37.54 3.41
623 672 8.868522 ATGAGGAAAACAGATTTATCACTGAA 57.131 30.769 0.00 0.00 37.54 3.02
626 675 6.434340 AGGAAAACAGATTTATCACTGAACCC 59.566 38.462 0.00 0.00 37.54 4.11
633 682 4.895668 TTTATCACTGAACCCCGTAACT 57.104 40.909 0.00 0.00 0.00 2.24
638 687 3.062042 CACTGAACCCCGTAACTTGTAC 58.938 50.000 0.00 0.00 0.00 2.90
737 807 5.253330 TGTATTAGGTCTCCAAGCTTTTGG 58.747 41.667 0.00 0.00 43.40 3.28
750 820 1.786579 GCTTTTGGACACGCAACAATC 59.213 47.619 0.00 0.00 0.00 2.67
775 886 0.855349 CCACATATCTTCGACGCTGC 59.145 55.000 0.00 0.00 0.00 5.25
790 901 2.031683 ACGCTGCAAAGTGTAAACTGAC 59.968 45.455 0.00 0.00 0.00 3.51
833 944 1.153958 CGAGCTGTCGCAGTGATCA 60.154 57.895 0.00 0.00 39.88 2.92
944 1055 8.967918 TGTAGTTACATGCTACTTATCTGAGTT 58.032 33.333 5.72 0.00 39.47 3.01
948 1059 9.974750 GTTACATGCTACTTATCTGAGTTTTTC 57.025 33.333 0.00 0.00 0.00 2.29
971 1082 0.611062 TACGAGTCCTCTGGTGGGTG 60.611 60.000 0.00 0.00 34.61 4.61
972 1083 2.665603 GAGTCCTCTGGTGGGTGC 59.334 66.667 0.00 0.00 0.00 5.01
1128 1241 5.359194 TCTGGCTCTAATTTTAGGGAGTG 57.641 43.478 1.31 0.00 32.90 3.51
1269 1388 5.531753 TTCTCTACAGAGGGAGAGGTAAA 57.468 43.478 6.41 0.00 42.30 2.01
1295 1416 4.320608 TGGAAATGTTTGCTGAGGAAAC 57.679 40.909 20.64 20.64 34.48 2.78
1302 1425 2.552743 GTTTGCTGAGGAAACTGGTACC 59.447 50.000 20.25 4.43 44.43 3.34
1347 1470 7.615365 ACAATTCCACTTATTTATCTTGCTGGA 59.385 33.333 0.00 0.00 0.00 3.86
1352 1475 6.238842 CCACTTATTTATCTTGCTGGATGTGG 60.239 42.308 0.00 0.00 31.14 4.17
1412 1535 2.225267 ACAAGGGAATCACGGGGATTTT 60.225 45.455 6.97 0.00 46.17 1.82
1449 1572 3.195825 GCTACTCTTAAGGAGGCAGAACA 59.804 47.826 1.85 0.00 45.83 3.18
1724 1850 4.184629 AGATCGAAACAATGCTACCTCAC 58.815 43.478 0.00 0.00 0.00 3.51
1792 1921 5.887598 TGTGTTCTTCAGATCCCCAATAATG 59.112 40.000 0.00 0.00 0.00 1.90
1797 1926 8.571336 GTTCTTCAGATCCCCAATAATGTATTG 58.429 37.037 1.70 1.70 43.94 1.90
1799 1928 8.501904 TCTTCAGATCCCCAATAATGTATTGAA 58.498 33.333 9.13 0.00 46.52 2.69
1861 1990 0.843309 TTCTCCACCACAGGCAAAGA 59.157 50.000 0.00 0.00 0.00 2.52
1872 2001 0.036858 AGGCAAAGAGAAGACGAGGC 60.037 55.000 0.00 0.00 0.00 4.70
1955 2084 6.313658 TGACATGATTTATCTTCGACACCTTG 59.686 38.462 0.00 0.00 0.00 3.61
2015 2144 7.654923 GCTGACACTTCATATCACATCTGATTA 59.345 37.037 0.00 0.00 38.21 1.75
2186 2315 1.429687 AGGCGTAGATCATACTCCCCT 59.570 52.381 0.00 0.00 0.00 4.79
2187 2316 1.546476 GGCGTAGATCATACTCCCCTG 59.454 57.143 0.00 0.00 0.00 4.45
2195 2324 4.596643 AGATCATACTCCCCTGATGAAAGG 59.403 45.833 0.00 0.00 33.50 3.11
2200 2329 1.153086 CCCCTGATGAAAGGAGGCG 60.153 63.158 0.00 0.00 40.02 5.52
2203 2332 1.694150 CCCTGATGAAAGGAGGCGATA 59.306 52.381 0.00 0.00 40.02 2.92
2291 2420 2.488710 GCGTAGGTCCTACTCACCCTAT 60.489 54.545 23.74 0.00 35.06 2.57
2300 2435 1.867363 ACTCACCCTATGACAGGTCC 58.133 55.000 0.00 0.00 43.80 4.46
2359 2494 2.167693 CTCCATACCGTTACAGAAGGCA 59.832 50.000 0.00 0.00 0.00 4.75
2368 2503 0.898326 TACAGAAGGCAGAGGTCGCA 60.898 55.000 0.00 0.00 0.00 5.10
2526 2661 1.339151 GCTGTTCTCCACGGAAAGGAT 60.339 52.381 0.00 0.00 33.99 3.24
2576 2711 2.348998 CCTGGCAAGAGGCGTTCT 59.651 61.111 0.00 0.00 46.16 3.01
2624 2759 1.000993 ATGCTCCAGGTCCGTCTCT 59.999 57.895 0.00 0.00 0.00 3.10
2625 2760 1.040339 ATGCTCCAGGTCCGTCTCTC 61.040 60.000 0.00 0.00 0.00 3.20
2651 2786 1.168407 GCTCAACCTCAGCAAGCACA 61.168 55.000 0.00 0.00 36.82 4.57
2671 2806 1.803334 TGATGTTTTACGAAGCGCCT 58.197 45.000 2.29 0.00 0.00 5.52
2672 2807 2.147958 TGATGTTTTACGAAGCGCCTT 58.852 42.857 2.29 0.00 0.00 4.35
2718 2853 9.965824 AATGTTGGAATTTTAGTAACTCTGTTG 57.034 29.630 0.00 0.00 0.00 3.33
2719 2854 8.514330 TGTTGGAATTTTAGTAACTCTGTTGT 57.486 30.769 0.00 0.00 0.00 3.32
2720 2855 9.616156 TGTTGGAATTTTAGTAACTCTGTTGTA 57.384 29.630 0.00 0.00 0.00 2.41
2732 2867 7.921214 AGTAACTCTGTTGTAATGGTATGATCG 59.079 37.037 0.00 0.00 0.00 3.69
2733 2868 6.222038 ACTCTGTTGTAATGGTATGATCGT 57.778 37.500 0.00 0.00 0.00 3.73
2734 2869 6.042777 ACTCTGTTGTAATGGTATGATCGTG 58.957 40.000 0.00 0.00 0.00 4.35
2735 2870 4.808895 TCTGTTGTAATGGTATGATCGTGC 59.191 41.667 0.00 0.00 0.00 5.34
2736 2871 4.508662 TGTTGTAATGGTATGATCGTGCA 58.491 39.130 5.34 0.00 0.00 4.57
2737 2872 4.331443 TGTTGTAATGGTATGATCGTGCAC 59.669 41.667 6.82 6.82 0.00 4.57
2738 2873 3.462982 TGTAATGGTATGATCGTGCACC 58.537 45.455 12.15 2.79 0.00 5.01
2739 2874 3.133901 TGTAATGGTATGATCGTGCACCT 59.866 43.478 12.15 0.00 32.04 4.00
2740 2875 2.245159 ATGGTATGATCGTGCACCTG 57.755 50.000 12.15 0.00 32.04 4.00
2741 2876 0.901827 TGGTATGATCGTGCACCTGT 59.098 50.000 12.15 0.00 32.04 4.00
2742 2877 2.104170 TGGTATGATCGTGCACCTGTA 58.896 47.619 12.15 0.00 32.04 2.74
2743 2878 2.698274 TGGTATGATCGTGCACCTGTAT 59.302 45.455 12.15 4.00 32.04 2.29
2744 2879 3.133901 TGGTATGATCGTGCACCTGTATT 59.866 43.478 12.15 0.00 32.04 1.89
2745 2880 4.127171 GGTATGATCGTGCACCTGTATTT 58.873 43.478 12.15 0.00 0.00 1.40
2746 2881 4.211374 GGTATGATCGTGCACCTGTATTTC 59.789 45.833 12.15 0.00 0.00 2.17
2747 2882 2.267426 TGATCGTGCACCTGTATTTCG 58.733 47.619 12.15 0.00 0.00 3.46
2748 2883 2.268298 GATCGTGCACCTGTATTTCGT 58.732 47.619 12.15 0.00 0.00 3.85
2749 2884 1.705256 TCGTGCACCTGTATTTCGTC 58.295 50.000 12.15 0.00 0.00 4.20
2750 2885 1.000052 TCGTGCACCTGTATTTCGTCA 60.000 47.619 12.15 0.00 0.00 4.35
2839 2978 4.370049 TGACACCGAGATTTGTTAACGAA 58.630 39.130 10.70 10.70 0.00 3.85
2882 3021 0.806102 CGAGGCAATGACTACGGGTG 60.806 60.000 0.00 0.00 0.00 4.61
2883 3022 1.078426 AGGCAATGACTACGGGTGC 60.078 57.895 0.00 0.00 34.42 5.01
2884 3023 1.078426 GGCAATGACTACGGGTGCT 60.078 57.895 0.00 0.00 35.53 4.40
2885 3024 1.090052 GGCAATGACTACGGGTGCTC 61.090 60.000 0.00 0.00 35.53 4.26
2886 3025 1.090052 GCAATGACTACGGGTGCTCC 61.090 60.000 0.00 0.00 32.43 4.70
2887 3026 0.537188 CAATGACTACGGGTGCTCCT 59.463 55.000 4.53 0.00 0.00 3.69
2888 3027 1.066143 CAATGACTACGGGTGCTCCTT 60.066 52.381 4.53 0.00 0.00 3.36
2889 3028 1.276622 ATGACTACGGGTGCTCCTTT 58.723 50.000 4.53 0.00 0.00 3.11
2890 3029 0.606604 TGACTACGGGTGCTCCTTTC 59.393 55.000 4.53 0.00 0.00 2.62
2891 3030 0.108281 GACTACGGGTGCTCCTTTCC 60.108 60.000 4.53 0.00 0.00 3.13
2892 3031 1.153628 CTACGGGTGCTCCTTTCCG 60.154 63.158 4.53 2.27 46.95 4.30
2893 3032 1.601419 CTACGGGTGCTCCTTTCCGA 61.601 60.000 4.53 0.00 44.69 4.55
2894 3033 1.601419 TACGGGTGCTCCTTTCCGAG 61.601 60.000 4.53 0.00 44.69 4.63
2895 3034 2.646175 CGGGTGCTCCTTTCCGAGA 61.646 63.158 4.53 0.00 44.69 4.04
2896 3035 1.908483 GGGTGCTCCTTTCCGAGAT 59.092 57.895 4.53 0.00 30.97 2.75
2897 3036 1.120530 GGGTGCTCCTTTCCGAGATA 58.879 55.000 4.53 0.00 30.97 1.98
2898 3037 1.202545 GGGTGCTCCTTTCCGAGATAC 60.203 57.143 4.53 0.00 30.97 2.24
2899 3038 1.202545 GGTGCTCCTTTCCGAGATACC 60.203 57.143 0.00 0.00 33.98 2.73
2900 3039 0.744874 TGCTCCTTTCCGAGATACCG 59.255 55.000 0.00 0.00 30.97 4.02
2901 3040 0.597898 GCTCCTTTCCGAGATACCGC 60.598 60.000 0.00 0.00 30.97 5.68
2902 3041 0.744874 CTCCTTTCCGAGATACCGCA 59.255 55.000 0.00 0.00 30.97 5.69
2903 3042 1.136305 CTCCTTTCCGAGATACCGCAA 59.864 52.381 0.00 0.00 30.97 4.85
2904 3043 1.136305 TCCTTTCCGAGATACCGCAAG 59.864 52.381 0.00 0.00 0.00 4.01
3000 3140 5.100259 CCTGTCGTTATTTAGTCGTCATGT 58.900 41.667 0.00 0.00 0.00 3.21
3017 3157 0.252479 TGTGTTACAACGTGGGGTGT 59.748 50.000 0.00 0.00 0.00 4.16
3159 3299 2.752354 CACAACAAACTCCACCTTGACA 59.248 45.455 0.00 0.00 0.00 3.58
3221 3361 1.067142 TCATGTACTCCGGACTTGTGC 60.067 52.381 0.00 1.03 0.00 4.57
3458 3599 5.530915 CACAACGGAATACCATACCATCATT 59.469 40.000 0.00 0.00 35.59 2.57
3654 3795 3.971032 GAGAACCACTCTTGTTGGTTG 57.029 47.619 11.42 0.00 44.94 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
189 194 2.022240 GACTGCGATCCTGTCCTCCC 62.022 65.000 8.89 0.00 36.67 4.30
341 362 2.483714 CGGGTTATGAGCTGTATGTGCT 60.484 50.000 0.00 0.00 44.24 4.40
366 392 3.172339 GGGTCTCATGGCTCTCTATGAT 58.828 50.000 0.00 0.00 33.25 2.45
369 395 2.783379 TGGGTCTCATGGCTCTCTAT 57.217 50.000 0.00 0.00 0.00 1.98
389 415 3.756933 ACGTTTTCCTACTGGCAAGTA 57.243 42.857 0.00 0.00 37.88 2.24
402 428 2.095617 CCGAACCCCAACATACGTTTTC 60.096 50.000 0.00 0.00 31.13 2.29
446 472 5.475220 TGCGAACCAGAATTGAGGATAAAAA 59.525 36.000 0.00 0.00 0.00 1.94
447 473 5.007034 TGCGAACCAGAATTGAGGATAAAA 58.993 37.500 0.00 0.00 0.00 1.52
448 474 4.584874 TGCGAACCAGAATTGAGGATAAA 58.415 39.130 0.00 0.00 0.00 1.40
449 475 4.214986 TGCGAACCAGAATTGAGGATAA 57.785 40.909 0.00 0.00 0.00 1.75
450 476 3.904800 TGCGAACCAGAATTGAGGATA 57.095 42.857 0.00 0.00 0.00 2.59
451 477 2.787473 TGCGAACCAGAATTGAGGAT 57.213 45.000 0.00 0.00 0.00 3.24
452 478 2.559698 TTGCGAACCAGAATTGAGGA 57.440 45.000 0.00 0.00 0.00 3.71
453 479 3.504863 CATTTGCGAACCAGAATTGAGG 58.495 45.455 0.00 0.00 0.00 3.86
454 480 2.919229 GCATTTGCGAACCAGAATTGAG 59.081 45.455 0.00 0.00 0.00 3.02
455 481 2.945278 GCATTTGCGAACCAGAATTGA 58.055 42.857 0.00 0.00 0.00 2.57
520 567 2.034812 GGAAACATAACCGCCAACAACA 59.965 45.455 0.00 0.00 0.00 3.33
527 574 1.480789 ATTGGGGAAACATAACCGCC 58.519 50.000 0.00 0.00 38.15 6.13
601 650 6.434340 GGGTTCAGTGATAAATCTGTTTTCCT 59.566 38.462 0.00 0.00 33.89 3.36
604 653 5.183140 CGGGGTTCAGTGATAAATCTGTTTT 59.817 40.000 0.00 0.00 33.89 2.43
616 665 1.764134 ACAAGTTACGGGGTTCAGTGA 59.236 47.619 0.00 0.00 0.00 3.41
617 666 2.249844 ACAAGTTACGGGGTTCAGTG 57.750 50.000 0.00 0.00 0.00 3.66
618 667 2.288395 CGTACAAGTTACGGGGTTCAGT 60.288 50.000 0.00 0.00 37.29 3.41
619 668 2.331194 CGTACAAGTTACGGGGTTCAG 58.669 52.381 0.00 0.00 37.29 3.02
620 669 2.437200 CGTACAAGTTACGGGGTTCA 57.563 50.000 0.00 0.00 37.29 3.18
638 687 0.239879 CCACCAATTCAACGTTCCCG 59.760 55.000 0.00 0.00 40.83 5.14
737 807 3.000041 TGGTCATAGATTGTTGCGTGTC 59.000 45.455 0.00 0.00 0.00 3.67
750 820 3.914966 GCGTCGAAGATATGTGGTCATAG 59.085 47.826 1.37 0.00 40.67 2.23
775 886 6.183360 ACAATCCACTGTCAGTTTACACTTTG 60.183 38.462 1.67 3.90 0.00 2.77
790 901 2.029739 TCAAGCATGCAACAATCCACTG 60.030 45.455 21.98 1.30 0.00 3.66
833 944 4.873010 TCTAACCTGACCATAGAAGCTCT 58.127 43.478 0.00 0.00 0.00 4.09
944 1055 4.401519 CACCAGAGGACTCGTATAGGAAAA 59.598 45.833 0.00 0.00 34.09 2.29
948 1059 2.231529 CCACCAGAGGACTCGTATAGG 58.768 57.143 0.00 0.00 34.09 2.57
971 1082 2.490903 ACAGACAGGCAAATGAATCAGC 59.509 45.455 0.00 0.00 0.00 4.26
972 1083 4.008330 AGACAGACAGGCAAATGAATCAG 58.992 43.478 0.00 0.00 0.00 2.90
1087 1200 4.952335 CCAGAAATGCCTAGACTCCAAAAT 59.048 41.667 0.00 0.00 0.00 1.82
1128 1241 9.725019 TCCTAACACATTACATGGATATCAATC 57.275 33.333 4.83 0.00 33.60 2.67
1269 1388 5.324409 TCCTCAGCAAACATTTCCATAAGT 58.676 37.500 0.00 0.00 0.00 2.24
1302 1425 5.885230 TTGTTAGCAATCTTCTCACATGG 57.115 39.130 0.00 0.00 0.00 3.66
1347 1470 2.097036 CATCAATCACCTGTGCCACAT 58.903 47.619 0.00 0.00 0.00 3.21
1352 1475 1.542915 ACTTGCATCAATCACCTGTGC 59.457 47.619 0.00 0.00 36.39 4.57
1449 1572 3.181475 ACGGTCGAGATATTTGATGCAGT 60.181 43.478 0.00 0.00 0.00 4.40
1758 1886 7.987458 GGGATCTGAAGAACACAAATAGTATGA 59.013 37.037 0.00 0.00 0.00 2.15
1797 1926 8.351495 TGTGTTTTATGTCAAAAGCAAGATTC 57.649 30.769 0.00 0.00 32.41 2.52
1799 1928 7.981225 ACTTGTGTTTTATGTCAAAAGCAAGAT 59.019 29.630 20.97 10.90 37.10 2.40
1861 1990 2.647158 GGGTTCGGCCTCGTCTTCT 61.647 63.158 0.00 0.00 37.43 2.85
1872 2001 2.282180 CCTGGTGTTGGGGTTCGG 60.282 66.667 0.00 0.00 0.00 4.30
1955 2084 7.499232 ACTTTCTAGCACATAATTCATGGTACC 59.501 37.037 4.43 4.43 39.13 3.34
2015 2144 8.632679 GGTATCACCACATAATCAAATGTCAAT 58.367 33.333 0.00 0.00 38.01 2.57
2031 2160 1.486726 CCTCCTTCCTGGTATCACCAC 59.513 57.143 0.00 0.00 44.79 4.16
2186 2315 4.215908 AGTAGTATCGCCTCCTTTCATCA 58.784 43.478 0.00 0.00 0.00 3.07
2187 2316 4.521256 AGAGTAGTATCGCCTCCTTTCATC 59.479 45.833 0.00 0.00 0.00 2.92
2195 2324 2.572209 AGGGAGAGTAGTATCGCCTC 57.428 55.000 5.69 0.00 39.00 4.70
2200 2329 4.924625 TCTGCCATAGGGAGAGTAGTATC 58.075 47.826 2.92 0.00 45.03 2.24
2243 2372 1.304217 GGGAGACTCCGACCTGTCA 60.304 63.158 15.46 0.00 37.43 3.58
2273 2402 3.789840 TGTCATAGGGTGAGTAGGACCTA 59.210 47.826 0.00 0.00 37.56 3.08
2291 2420 0.252103 GGGGTGAGTAGGACCTGTCA 60.252 60.000 3.53 4.18 33.58 3.58
2300 2435 2.311688 GACCATGGCGGGGTGAGTAG 62.312 65.000 13.04 0.00 39.19 2.57
2359 2494 3.374402 CGTGGGAGTGCGACCTCT 61.374 66.667 0.00 0.00 0.00 3.69
2368 2503 1.397390 AACAGAACGGTCGTGGGAGT 61.397 55.000 0.00 0.00 0.00 3.85
2488 2623 4.978099 ACAGCTCCTTGATTCTTCTGAAA 58.022 39.130 0.00 0.00 35.63 2.69
2489 2624 4.630644 ACAGCTCCTTGATTCTTCTGAA 57.369 40.909 0.00 0.00 36.54 3.02
2541 2676 2.046988 TGACCTGCTGCGTGATGG 60.047 61.111 0.00 0.00 0.00 3.51
2564 2699 2.926838 GCTTTCTCTAGAACGCCTCTTG 59.073 50.000 9.41 0.00 41.63 3.02
2576 2711 3.181471 GGCTGTGAGCATAGCTTTCTCTA 60.181 47.826 16.85 0.00 44.75 2.43
2624 2759 3.760035 GAGGTTGAGCGCTCCCGA 61.760 66.667 33.23 17.19 36.29 5.14
2625 2760 3.997064 CTGAGGTTGAGCGCTCCCG 62.997 68.421 33.23 12.45 37.57 5.14
2651 2786 2.356135 AGGCGCTTCGTAAAACATCAT 58.644 42.857 7.64 0.00 0.00 2.45
2671 2806 3.325902 AACGGAAATACGGTGGCAA 57.674 47.368 0.00 0.00 38.39 4.52
2713 2848 4.570369 TGCACGATCATACCATTACAACAG 59.430 41.667 0.00 0.00 0.00 3.16
2716 2851 3.874543 GGTGCACGATCATACCATTACAA 59.125 43.478 11.45 0.00 33.42 2.41
2717 2852 3.133901 AGGTGCACGATCATACCATTACA 59.866 43.478 11.45 0.00 35.66 2.41
2718 2853 3.494626 CAGGTGCACGATCATACCATTAC 59.505 47.826 11.45 0.00 35.66 1.89
2719 2854 3.133901 ACAGGTGCACGATCATACCATTA 59.866 43.478 11.45 0.00 35.66 1.90
2720 2855 2.092968 ACAGGTGCACGATCATACCATT 60.093 45.455 11.45 0.00 35.66 3.16
2721 2856 1.486310 ACAGGTGCACGATCATACCAT 59.514 47.619 11.45 0.00 35.66 3.55
2722 2857 0.901827 ACAGGTGCACGATCATACCA 59.098 50.000 11.45 0.00 35.66 3.25
2723 2858 2.882927 TACAGGTGCACGATCATACC 57.117 50.000 11.45 0.00 0.00 2.73
2724 2859 4.085055 CGAAATACAGGTGCACGATCATAC 60.085 45.833 11.45 0.00 0.00 2.39
2725 2860 4.048504 CGAAATACAGGTGCACGATCATA 58.951 43.478 11.45 0.00 0.00 2.15
2726 2861 2.866156 CGAAATACAGGTGCACGATCAT 59.134 45.455 11.45 0.00 0.00 2.45
2727 2862 2.267426 CGAAATACAGGTGCACGATCA 58.733 47.619 11.45 0.00 0.00 2.92
2728 2863 2.268298 ACGAAATACAGGTGCACGATC 58.732 47.619 11.45 0.00 0.00 3.69
2729 2864 2.268298 GACGAAATACAGGTGCACGAT 58.732 47.619 11.45 0.00 0.00 3.73
2730 2865 1.000052 TGACGAAATACAGGTGCACGA 60.000 47.619 11.45 0.00 0.00 4.35
2731 2866 1.424403 TGACGAAATACAGGTGCACG 58.576 50.000 11.45 0.00 0.00 5.34
2732 2867 3.000041 TCATGACGAAATACAGGTGCAC 59.000 45.455 8.80 8.80 0.00 4.57
2733 2868 3.000041 GTCATGACGAAATACAGGTGCA 59.000 45.455 10.69 0.00 0.00 4.57
2734 2869 3.062639 CAGTCATGACGAAATACAGGTGC 59.937 47.826 19.85 0.00 36.20 5.01
2735 2870 4.245660 ACAGTCATGACGAAATACAGGTG 58.754 43.478 19.85 10.91 36.20 4.00
2736 2871 4.537135 ACAGTCATGACGAAATACAGGT 57.463 40.909 19.85 5.92 36.20 4.00
2737 2872 6.330278 TCTAACAGTCATGACGAAATACAGG 58.670 40.000 19.85 6.12 36.20 4.00
2738 2873 7.812309 TTCTAACAGTCATGACGAAATACAG 57.188 36.000 19.85 11.58 36.20 2.74
2739 2874 9.863845 TTATTCTAACAGTCATGACGAAATACA 57.136 29.630 19.85 4.63 36.20 2.29
2743 2878 8.879759 GGATTTATTCTAACAGTCATGACGAAA 58.120 33.333 19.85 9.50 36.20 3.46
2744 2879 7.222031 CGGATTTATTCTAACAGTCATGACGAA 59.778 37.037 19.85 16.13 36.20 3.85
2745 2880 6.695713 CGGATTTATTCTAACAGTCATGACGA 59.304 38.462 19.85 8.16 36.20 4.20
2746 2881 6.695713 TCGGATTTATTCTAACAGTCATGACG 59.304 38.462 19.85 16.37 36.20 4.35
2747 2882 7.169982 CCTCGGATTTATTCTAACAGTCATGAC 59.830 40.741 18.47 18.47 0.00 3.06
2748 2883 7.147724 ACCTCGGATTTATTCTAACAGTCATGA 60.148 37.037 0.00 0.00 0.00 3.07
2749 2884 6.986817 ACCTCGGATTTATTCTAACAGTCATG 59.013 38.462 0.00 0.00 0.00 3.07
2750 2885 7.125792 ACCTCGGATTTATTCTAACAGTCAT 57.874 36.000 0.00 0.00 0.00 3.06
2796 2934 6.128200 TGTCATCATTGTCTGTGATTACTTGC 60.128 38.462 0.00 0.00 34.21 4.01
2882 3021 0.597898 GCGGTATCTCGGAAAGGAGC 60.598 60.000 0.00 0.00 33.98 4.70
2883 3022 0.744874 TGCGGTATCTCGGAAAGGAG 59.255 55.000 0.00 0.00 35.32 3.69
2884 3023 1.136305 CTTGCGGTATCTCGGAAAGGA 59.864 52.381 0.00 0.00 39.74 3.36
2885 3024 1.571919 CTTGCGGTATCTCGGAAAGG 58.428 55.000 0.00 0.00 39.74 3.11
2886 3025 1.134788 ACCTTGCGGTATCTCGGAAAG 60.135 52.381 0.00 0.00 43.29 2.62
2887 3026 0.899720 ACCTTGCGGTATCTCGGAAA 59.100 50.000 0.00 0.00 43.29 3.13
2888 3027 0.174845 CACCTTGCGGTATCTCGGAA 59.825 55.000 0.00 0.00 43.24 4.30
2889 3028 1.813859 CACCTTGCGGTATCTCGGA 59.186 57.895 0.00 0.00 43.24 4.55
2890 3029 1.883084 GCACCTTGCGGTATCTCGG 60.883 63.158 0.00 0.00 43.24 4.63
2891 3030 3.706140 GCACCTTGCGGTATCTCG 58.294 61.111 0.00 0.00 43.24 4.04
2904 3043 1.202545 GGTATCTCGGAAAGGAGCACC 60.203 57.143 0.00 0.00 34.15 5.01
2905 3044 1.536284 CGGTATCTCGGAAAGGAGCAC 60.536 57.143 0.00 0.00 33.98 4.40
2906 3045 0.744874 CGGTATCTCGGAAAGGAGCA 59.255 55.000 0.00 0.00 33.98 4.26
2984 3124 7.381948 ACGTTGTAACACATGACGACTAAATAA 59.618 33.333 0.00 0.00 35.12 1.40
2988 3128 4.441744 CACGTTGTAACACATGACGACTAA 59.558 41.667 0.00 0.00 35.12 2.24
3000 3140 0.831966 AGACACCCCACGTTGTAACA 59.168 50.000 0.00 0.00 0.00 2.41
3159 3299 8.650490 ACAAATTCAAGGTGGTGAAGAATATTT 58.350 29.630 0.00 0.00 40.72 1.40
3221 3361 3.126514 TCGGTAAGCTACGAAGAAGACAG 59.873 47.826 5.72 0.00 36.01 3.51
3342 3483 5.543714 TCGCATCTTTACAAGTTACAAGGA 58.456 37.500 0.00 0.00 0.00 3.36
3348 3489 3.369756 CGGCTTCGCATCTTTACAAGTTA 59.630 43.478 0.00 0.00 0.00 2.24
3373 3514 2.831526 TGACCGTGATGATTGGAGAGAA 59.168 45.455 0.00 0.00 0.00 2.87
3458 3599 5.957842 AATTTCGCTTGGTGTTCTTCATA 57.042 34.783 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.