Multiple sequence alignment - TraesCS5B01G130400

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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 TraesCS5B01G130400 chr5B 100.000 4123 0 0 1 4123 242139271 242135149 0.000000e+00 7614
1 TraesCS5B01G130400 chr5B 95.273 3406 62 21 797 4123 238314870 238318255 0.000000e+00 5306
2 TraesCS5B01G130400 chr5B 93.274 565 25 7 1 565 238312317 238312868 0.000000e+00 821
3 TraesCS5B01G130400 chr5B 100.000 150 0 0 571 720 602841827 602841678 1.130000e-70 278
4 TraesCS5B01G130400 chr5A 91.775 3477 168 48 728 4123 292861871 292858432 0.000000e+00 4728
5 TraesCS5B01G130400 chr5A 92.650 517 24 6 1 508 292862797 292862286 0.000000e+00 732
6 TraesCS5B01G130400 chr5D 91.719 3369 145 48 821 4114 219526664 219523355 0.000000e+00 4553
7 TraesCS5B01G130400 chr5D 90.925 584 26 14 1 570 219527444 219526874 0.000000e+00 760
8 TraesCS5B01G130400 chr5D 97.030 101 0 3 721 821 219526881 219526784 2.550000e-37 167
9 TraesCS5B01G130400 chr7B 100.000 152 0 0 571 722 271250162 271250011 8.730000e-72 281
10 TraesCS5B01G130400 chr7B 99.338 151 1 0 571 721 577232778 577232628 1.460000e-69 274
11 TraesCS5B01G130400 chr7B 98.667 150 2 0 571 720 77430009 77430158 2.440000e-67 267
12 TraesCS5B01G130400 chr2B 99.342 152 1 0 571 722 452597578 452597427 4.060000e-70 276
13 TraesCS5B01G130400 chr1A 98.667 150 2 0 571 720 45587268 45587417 2.440000e-67 267
14 TraesCS5B01G130400 chr1A 98.667 150 2 0 571 720 552838118 552838267 2.440000e-67 267
15 TraesCS5B01G130400 chr6A 92.771 166 12 0 561 726 136546659 136546824 1.480000e-59 241
16 TraesCS5B01G130400 chr3B 94.805 154 8 0 571 724 40214098 40214251 1.480000e-59 241
17 TraesCS5B01G130400 chr3D 93.421 76 5 0 3533 3608 19210039 19209964 3.370000e-21 113


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 TraesCS5B01G130400 chr5B 242135149 242139271 4122 True 7614.000000 7614 100.000000 1 4123 1 chr5B.!!$R1 4122
1 TraesCS5B01G130400 chr5B 238312317 238318255 5938 False 3063.500000 5306 94.273500 1 4123 2 chr5B.!!$F1 4122
2 TraesCS5B01G130400 chr5A 292858432 292862797 4365 True 2730.000000 4728 92.212500 1 4123 2 chr5A.!!$R1 4122
3 TraesCS5B01G130400 chr5D 219523355 219527444 4089 True 1826.666667 4553 93.224667 1 4114 3 chr5D.!!$R1 4113

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
602 984 0.038618 CACACGACAAGGATGGACGA 60.039 55.0 0.00 0.0 35.53 4.20 F
684 1066 0.041576 CAATCAGCGATCGTGCATGG 60.042 55.0 17.81 0.0 37.31 3.66 F
2262 4633 0.306533 TTTCCTTCAAGAACGCGCAC 59.693 50.0 5.73 0.0 0.00 5.34 F
2267 4638 1.098712 TTCAAGAACGCGCACCCTTT 61.099 50.0 5.73 0.0 0.00 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2262 4633 0.324645 ATAGGCAGGCAACCAAAGGG 60.325 55.0 0.00 0.0 41.29 3.95 R
2264 4635 1.549203 ACATAGGCAGGCAACCAAAG 58.451 50.0 0.00 0.0 37.17 2.77 R
3067 5493 0.038166 GGAAAGCCTGTGACCCATGA 59.962 55.0 0.00 0.0 0.00 3.07 R
3418 5846 0.108585 TGGAAACAGGCCACAGACTC 59.891 55.0 5.01 0.0 35.01 3.36 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
29 30 3.880490 AGTTGCGGTTTGAGTTGTAATGA 59.120 39.130 0.00 0.00 0.00 2.57
77 78 3.695825 GGAGGGAGGGGTGGGAGA 61.696 72.222 0.00 0.00 0.00 3.71
142 144 1.988293 TTGAATTTGTTCTCGGGGCA 58.012 45.000 0.00 0.00 0.00 5.36
149 159 3.378911 TTGTTCTCGGGGCAATTTTTC 57.621 42.857 0.00 0.00 0.00 2.29
174 191 3.191162 TGTAAATCTGCATTGCCACTGAC 59.809 43.478 6.12 0.00 0.00 3.51
242 259 1.689273 GCACCACACCATTAAACCCAA 59.311 47.619 0.00 0.00 0.00 4.12
519 545 1.211703 TGGGTGTTTCTTGTGCAGAGA 59.788 47.619 0.00 0.00 31.12 3.10
520 546 1.876156 GGGTGTTTCTTGTGCAGAGAG 59.124 52.381 0.00 0.00 31.12 3.20
521 547 2.485479 GGGTGTTTCTTGTGCAGAGAGA 60.485 50.000 0.00 0.00 31.12 3.10
522 548 2.805099 GGTGTTTCTTGTGCAGAGAGAG 59.195 50.000 0.00 0.00 31.12 3.20
523 549 3.493350 GGTGTTTCTTGTGCAGAGAGAGA 60.493 47.826 0.00 0.00 31.12 3.10
524 550 3.740321 GTGTTTCTTGTGCAGAGAGAGAG 59.260 47.826 0.00 0.00 31.12 3.20
565 947 2.287788 CGCCATTCTTGTGCAGTTTCTT 60.288 45.455 0.00 0.00 0.00 2.52
566 948 3.054878 GCCATTCTTGTGCAGTTTCTTG 58.945 45.455 0.00 0.00 0.00 3.02
570 952 0.318107 CTTGTGCAGTTTCTTGCCCG 60.318 55.000 0.00 0.00 43.43 6.13
573 955 0.317854 GTGCAGTTTCTTGCCCGAAC 60.318 55.000 0.00 0.00 43.43 3.95
574 956 1.082104 GCAGTTTCTTGCCCGAACG 60.082 57.895 0.00 0.00 38.13 3.95
575 957 1.082104 CAGTTTCTTGCCCGAACGC 60.082 57.895 0.00 0.00 0.00 4.84
576 958 1.227853 AGTTTCTTGCCCGAACGCT 60.228 52.632 0.00 0.00 0.00 5.07
578 960 2.903547 TTTCTTGCCCGAACGCTGC 61.904 57.895 0.00 0.00 0.00 5.25
579 961 3.825160 TTCTTGCCCGAACGCTGCT 62.825 57.895 0.00 0.00 0.00 4.24
580 962 2.434185 CTTGCCCGAACGCTGCTA 60.434 61.111 0.00 0.00 0.00 3.49
581 963 1.815421 CTTGCCCGAACGCTGCTAT 60.815 57.895 0.00 0.00 0.00 2.97
584 966 1.227147 GCCCGAACGCTGCTATACA 60.227 57.895 0.00 0.00 0.00 2.29
586 968 0.179121 CCCGAACGCTGCTATACACA 60.179 55.000 0.00 0.00 0.00 3.72
587 969 0.921347 CCGAACGCTGCTATACACAC 59.079 55.000 0.00 0.00 0.00 3.82
588 970 0.566136 CGAACGCTGCTATACACACG 59.434 55.000 0.00 0.00 0.00 4.49
589 971 1.792632 CGAACGCTGCTATACACACGA 60.793 52.381 0.00 0.00 0.00 4.35
590 972 1.582502 GAACGCTGCTATACACACGAC 59.417 52.381 0.00 0.00 0.00 4.34
591 973 0.524414 ACGCTGCTATACACACGACA 59.476 50.000 0.00 0.00 0.00 4.35
592 974 1.068125 ACGCTGCTATACACACGACAA 60.068 47.619 0.00 0.00 0.00 3.18
593 975 1.583856 CGCTGCTATACACACGACAAG 59.416 52.381 0.00 0.00 0.00 3.16
596 978 3.738281 GCTGCTATACACACGACAAGGAT 60.738 47.826 0.00 0.00 0.00 3.24
597 979 3.780902 TGCTATACACACGACAAGGATG 58.219 45.455 0.00 0.00 0.00 3.51
598 980 3.123804 GCTATACACACGACAAGGATGG 58.876 50.000 0.00 0.00 0.00 3.51
599 981 3.181479 GCTATACACACGACAAGGATGGA 60.181 47.826 0.00 0.00 0.00 3.41
600 982 2.736144 TACACACGACAAGGATGGAC 57.264 50.000 0.00 0.00 0.00 4.02
601 983 0.319555 ACACACGACAAGGATGGACG 60.320 55.000 0.00 0.00 36.83 4.79
602 984 0.038618 CACACGACAAGGATGGACGA 60.039 55.000 0.00 0.00 35.53 4.20
603 985 0.895530 ACACGACAAGGATGGACGAT 59.104 50.000 0.00 0.00 35.53 3.73
605 987 2.289444 ACACGACAAGGATGGACGATTT 60.289 45.455 0.00 0.00 35.53 2.17
606 988 3.056393 ACACGACAAGGATGGACGATTTA 60.056 43.478 0.00 0.00 35.53 1.40
607 989 3.306166 CACGACAAGGATGGACGATTTAC 59.694 47.826 0.00 0.00 35.53 2.01
608 990 3.056393 ACGACAAGGATGGACGATTTACA 60.056 43.478 0.00 0.00 35.53 2.41
609 991 3.306166 CGACAAGGATGGACGATTTACAC 59.694 47.826 0.00 0.00 34.21 2.90
610 992 4.250464 GACAAGGATGGACGATTTACACA 58.750 43.478 0.00 0.00 0.00 3.72
612 994 2.888594 AGGATGGACGATTTACACACG 58.111 47.619 0.00 0.00 0.00 4.49
613 995 2.494471 AGGATGGACGATTTACACACGA 59.506 45.455 0.00 0.00 0.00 4.35
616 998 1.996898 TGGACGATTTACACACGATGC 59.003 47.619 0.00 0.00 0.00 3.91
617 999 2.268298 GGACGATTTACACACGATGCT 58.732 47.619 0.00 0.00 0.00 3.79
618 1000 3.119424 TGGACGATTTACACACGATGCTA 60.119 43.478 0.00 0.00 0.00 3.49
619 1001 3.242248 GGACGATTTACACACGATGCTAC 59.758 47.826 0.00 0.00 0.00 3.58
620 1002 3.184541 ACGATTTACACACGATGCTACC 58.815 45.455 0.00 0.00 0.00 3.18
621 1003 2.538449 CGATTTACACACGATGCTACCC 59.462 50.000 0.00 0.00 0.00 3.69
622 1004 3.527533 GATTTACACACGATGCTACCCA 58.472 45.455 0.00 0.00 0.00 4.51
623 1005 3.620427 TTTACACACGATGCTACCCAT 57.380 42.857 0.00 0.00 36.70 4.00
624 1006 2.882927 TACACACGATGCTACCCATC 57.117 50.000 0.00 0.00 45.58 3.51
632 1014 2.604046 ATGCTACCCATCAAGACGTC 57.396 50.000 7.70 7.70 0.00 4.34
633 1015 0.535335 TGCTACCCATCAAGACGTCC 59.465 55.000 13.01 0.00 0.00 4.79
635 1017 1.139058 GCTACCCATCAAGACGTCCAT 59.861 52.381 13.01 0.00 0.00 3.41
636 1018 2.420129 GCTACCCATCAAGACGTCCATT 60.420 50.000 13.01 0.00 0.00 3.16
637 1019 2.879103 ACCCATCAAGACGTCCATTT 57.121 45.000 13.01 0.00 0.00 2.32
639 1021 3.606687 ACCCATCAAGACGTCCATTTAC 58.393 45.455 13.01 0.00 0.00 2.01
640 1022 3.008594 ACCCATCAAGACGTCCATTTACA 59.991 43.478 13.01 0.00 0.00 2.41
641 1023 3.374058 CCCATCAAGACGTCCATTTACAC 59.626 47.826 13.01 0.00 0.00 2.90
643 1025 4.454161 CCATCAAGACGTCCATTTACACAA 59.546 41.667 13.01 0.00 0.00 3.33
645 1027 4.951254 TCAAGACGTCCATTTACACAAGA 58.049 39.130 13.01 0.00 0.00 3.02
646 1028 5.547465 TCAAGACGTCCATTTACACAAGAT 58.453 37.500 13.01 0.00 0.00 2.40
649 1031 6.032956 AGACGTCCATTTACACAAGATGTA 57.967 37.500 13.01 0.00 43.19 2.29
651 1033 5.790593 ACGTCCATTTACACAAGATGTACT 58.209 37.500 0.00 0.00 43.71 2.73
653 1035 5.637810 CGTCCATTTACACAAGATGTACTGT 59.362 40.000 0.00 0.00 43.71 3.55
654 1036 6.809689 CGTCCATTTACACAAGATGTACTGTA 59.190 38.462 0.00 0.00 43.71 2.74
655 1037 7.491372 CGTCCATTTACACAAGATGTACTGTAT 59.509 37.037 0.00 0.00 43.71 2.29
656 1038 8.818057 GTCCATTTACACAAGATGTACTGTATC 58.182 37.037 0.00 0.00 43.71 2.24
657 1039 8.536175 TCCATTTACACAAGATGTACTGTATCA 58.464 33.333 0.00 0.00 43.71 2.15
658 1040 9.161629 CCATTTACACAAGATGTACTGTATCAA 57.838 33.333 0.00 0.00 43.71 2.57
661 1043 5.178797 ACACAAGATGTACTGTATCAAGCC 58.821 41.667 0.00 0.00 40.88 4.35
664 1046 4.737855 AGATGTACTGTATCAAGCCGTT 57.262 40.909 0.00 0.00 0.00 4.44
668 1050 4.827692 TGTACTGTATCAAGCCGTTCAAT 58.172 39.130 0.00 0.00 0.00 2.57
670 1052 3.937814 ACTGTATCAAGCCGTTCAATCA 58.062 40.909 0.00 0.00 0.00 2.57
671 1053 3.935203 ACTGTATCAAGCCGTTCAATCAG 59.065 43.478 0.00 0.00 0.00 2.90
672 1054 2.677836 TGTATCAAGCCGTTCAATCAGC 59.322 45.455 0.00 0.00 0.00 4.26
673 1055 0.729116 ATCAAGCCGTTCAATCAGCG 59.271 50.000 0.00 0.00 0.00 5.18
674 1056 0.320334 TCAAGCCGTTCAATCAGCGA 60.320 50.000 0.00 0.00 0.00 4.93
676 1058 1.009829 AAGCCGTTCAATCAGCGATC 58.990 50.000 0.00 0.00 0.00 3.69
679 1061 0.298707 CCGTTCAATCAGCGATCGTG 59.701 55.000 17.81 13.42 0.00 4.35
681 1063 0.721154 GTTCAATCAGCGATCGTGCA 59.279 50.000 17.81 0.42 37.31 4.57
683 1065 0.932399 TCAATCAGCGATCGTGCATG 59.068 50.000 17.81 14.01 37.31 4.06
684 1066 0.041576 CAATCAGCGATCGTGCATGG 60.042 55.000 17.81 0.00 37.31 3.66
686 1068 0.462581 ATCAGCGATCGTGCATGGTT 60.463 50.000 17.81 0.00 37.31 3.67
687 1069 1.083806 TCAGCGATCGTGCATGGTTC 61.084 55.000 17.81 3.05 37.31 3.62
689 1071 3.005898 CGATCGTGCATGGTTCGG 58.994 61.111 18.62 6.04 0.00 4.30
710 1092 4.980805 GGCAGTGTCGTTCGCCCA 62.981 66.667 0.00 0.00 38.67 5.36
712 1094 2.029073 CAGTGTCGTTCGCCCAGT 59.971 61.111 0.00 0.00 0.00 4.00
714 1096 0.732880 CAGTGTCGTTCGCCCAGTAG 60.733 60.000 0.00 0.00 0.00 2.57
715 1097 1.177256 AGTGTCGTTCGCCCAGTAGT 61.177 55.000 0.00 0.00 0.00 2.73
716 1098 0.319297 GTGTCGTTCGCCCAGTAGTT 60.319 55.000 0.00 0.00 0.00 2.24
718 1100 1.066136 GTCGTTCGCCCAGTAGTTTC 58.934 55.000 0.00 0.00 0.00 2.78
720 1102 0.665369 CGTTCGCCCAGTAGTTTCGT 60.665 55.000 0.00 0.00 0.00 3.85
721 1103 1.505425 GTTCGCCCAGTAGTTTCGTT 58.495 50.000 0.00 0.00 0.00 3.85
723 1105 0.963962 TCGCCCAGTAGTTTCGTTCT 59.036 50.000 0.00 0.00 0.00 3.01
724 1106 1.342174 TCGCCCAGTAGTTTCGTTCTT 59.658 47.619 0.00 0.00 0.00 2.52
726 1108 1.197036 GCCCAGTAGTTTCGTTCTTGC 59.803 52.381 0.00 0.00 0.00 4.01
727 1109 1.804748 CCCAGTAGTTTCGTTCTTGCC 59.195 52.381 0.00 0.00 0.00 4.52
728 1110 1.804748 CCAGTAGTTTCGTTCTTGCCC 59.195 52.381 0.00 0.00 0.00 5.36
729 1111 1.804748 CAGTAGTTTCGTTCTTGCCCC 59.195 52.381 0.00 0.00 0.00 5.80
730 1112 1.162698 GTAGTTTCGTTCTTGCCCCC 58.837 55.000 0.00 0.00 0.00 5.40
731 1113 0.766131 TAGTTTCGTTCTTGCCCCCA 59.234 50.000 0.00 0.00 0.00 4.96
733 1115 0.536460 GTTTCGTTCTTGCCCCCAGA 60.536 55.000 0.00 0.00 0.00 3.86
1453 3766 0.316841 TCCATTTTTGCTGTTCGGGC 59.683 50.000 0.00 0.00 0.00 6.13
1558 3877 3.922910 TCTGCTGTTCTTGACTCTCATG 58.077 45.455 0.00 0.00 0.00 3.07
1779 4148 2.167281 TCATGCTCTCCAGTAGTTCAGC 59.833 50.000 0.00 0.00 0.00 4.26
1923 4292 8.648693 GTCCCAGCTAGAGAGGTAATTAATTAA 58.351 37.037 9.48 0.00 0.00 1.40
1924 4293 9.393786 TCCCAGCTAGAGAGGTAATTAATTAAT 57.606 33.333 9.48 4.81 0.00 1.40
1982 4353 8.805175 TCCATTACATTGTGAATTTGTGATCTT 58.195 29.630 0.00 0.00 0.00 2.40
2200 4571 5.762825 CCTACGAGGTACTACTATGCAAA 57.237 43.478 0.00 0.00 41.55 3.68
2262 4633 0.306533 TTTCCTTCAAGAACGCGCAC 59.693 50.000 5.73 0.00 0.00 5.34
2264 4635 2.556287 CTTCAAGAACGCGCACCC 59.444 61.111 5.73 0.00 0.00 4.61
2265 4636 1.961277 CTTCAAGAACGCGCACCCT 60.961 57.895 5.73 0.00 0.00 4.34
2266 4637 1.507141 CTTCAAGAACGCGCACCCTT 61.507 55.000 5.73 3.57 0.00 3.95
2267 4638 1.098712 TTCAAGAACGCGCACCCTTT 61.099 50.000 5.73 0.00 0.00 3.11
2274 4645 4.662961 GCGCACCCTTTGGTTGCC 62.663 66.667 0.30 0.00 44.75 4.52
2314 4711 4.322567 AGAGAGAGAGCAACCAAACATTC 58.677 43.478 0.00 0.00 0.00 2.67
2358 4755 7.383029 TGAATCTCTGTTGAATGTTTCATTTGC 59.617 33.333 0.00 0.00 39.84 3.68
2512 4933 9.941325 ATTCAAACTGAAAATATTTGGTGCATA 57.059 25.926 0.39 0.00 40.12 3.14
2573 4994 1.209504 TCCTTTACAATGGCCGAGGAG 59.790 52.381 0.00 0.00 0.00 3.69
2742 5164 7.249186 TGCATTTTGAAACCATCTTTTCTTG 57.751 32.000 0.00 0.00 36.58 3.02
3069 5495 2.203408 TTGGCGCACAACCCATCA 60.203 55.556 10.83 0.00 33.18 3.07
3082 5508 1.611419 CCATCATGGGTCACAGGCT 59.389 57.895 0.00 0.00 32.67 4.58
3204 5630 5.540719 ACTGGGTTCTATCCTAATCAGCTAC 59.459 44.000 0.00 0.00 0.00 3.58
3373 5800 5.390145 CCATTGCTGTAACGGTTACTTGTAC 60.390 44.000 26.22 14.16 37.06 2.90
3374 5801 4.589216 TGCTGTAACGGTTACTTGTACT 57.411 40.909 26.22 0.00 37.06 2.73
3375 5802 5.703978 TGCTGTAACGGTTACTTGTACTA 57.296 39.130 26.22 8.27 37.06 1.82
3418 5846 3.868757 TCTAACTCCATGTCTGAACGG 57.131 47.619 0.00 0.00 0.00 4.44
3480 5913 8.645730 TGACGTGTGTTACTTTTGATTTAGTA 57.354 30.769 0.00 0.00 0.00 1.82
3595 6040 5.238432 TGAATTTGTATATGCACTTAGGGCG 59.762 40.000 0.76 0.00 0.00 6.13
3605 6050 2.159382 CACTTAGGGCGTGTTTGGATT 58.841 47.619 0.00 0.00 0.00 3.01
3644 6089 5.359860 CCCTACCAAAATCCTATTGTTGACC 59.640 44.000 0.00 0.00 0.00 4.02
3944 6390 7.830940 ATTGGTATACACAATTGCACATTTG 57.169 32.000 5.05 0.00 35.11 2.32
3961 6407 9.033481 TGCACATTTGATTCTTGTTTTTAGAAG 57.967 29.630 0.00 0.00 35.28 2.85
4002 6450 9.677567 TGCTCGGCTTTAAATTAATAAATCATC 57.322 29.630 0.00 0.00 0.00 2.92
4110 6559 4.564940 GCTCCTTCATGCCATAAAAGAG 57.435 45.455 1.61 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.846124 CACCACCCCCTACCACTGT 60.846 63.158 0.00 0.00 0.00 3.55
142 144 8.291740 GGCAATGCAGATTTACAAAGAAAAATT 58.708 29.630 7.79 0.00 0.00 1.82
149 159 4.624024 CAGTGGCAATGCAGATTTACAAAG 59.376 41.667 7.79 0.00 0.00 2.77
404 430 6.163476 TGCAAAAGTGTACTGGAGTATACAG 58.837 40.000 14.04 0.00 42.66 2.74
519 545 2.481441 TCCTGCTCTCTCTCTCTCTCT 58.519 52.381 0.00 0.00 0.00 3.10
520 546 2.945668 GTTCCTGCTCTCTCTCTCTCTC 59.054 54.545 0.00 0.00 0.00 3.20
521 547 2.357154 GGTTCCTGCTCTCTCTCTCTCT 60.357 54.545 0.00 0.00 0.00 3.10
522 548 2.024414 GGTTCCTGCTCTCTCTCTCTC 58.976 57.143 0.00 0.00 0.00 3.20
523 549 1.341976 GGGTTCCTGCTCTCTCTCTCT 60.342 57.143 0.00 0.00 0.00 3.10
524 550 1.111277 GGGTTCCTGCTCTCTCTCTC 58.889 60.000 0.00 0.00 0.00 3.20
565 947 1.227147 GTATAGCAGCGTTCGGGCA 60.227 57.895 0.00 0.00 34.64 5.36
566 948 1.227147 TGTATAGCAGCGTTCGGGC 60.227 57.895 0.00 0.00 0.00 6.13
570 952 1.582502 GTCGTGTGTATAGCAGCGTTC 59.417 52.381 0.00 0.00 0.00 3.95
573 955 1.583856 CTTGTCGTGTGTATAGCAGCG 59.416 52.381 0.00 0.00 0.00 5.18
574 956 1.927174 CCTTGTCGTGTGTATAGCAGC 59.073 52.381 0.00 0.00 0.00 5.25
575 957 3.503827 TCCTTGTCGTGTGTATAGCAG 57.496 47.619 0.00 0.00 0.00 4.24
576 958 3.430236 CCATCCTTGTCGTGTGTATAGCA 60.430 47.826 0.00 0.00 0.00 3.49
578 960 4.360563 GTCCATCCTTGTCGTGTGTATAG 58.639 47.826 0.00 0.00 0.00 1.31
579 961 3.181494 CGTCCATCCTTGTCGTGTGTATA 60.181 47.826 0.00 0.00 0.00 1.47
580 962 2.416836 CGTCCATCCTTGTCGTGTGTAT 60.417 50.000 0.00 0.00 0.00 2.29
581 963 1.068125 CGTCCATCCTTGTCGTGTGTA 60.068 52.381 0.00 0.00 0.00 2.90
584 966 0.895530 ATCGTCCATCCTTGTCGTGT 59.104 50.000 0.00 0.00 0.00 4.49
586 968 2.762535 AAATCGTCCATCCTTGTCGT 57.237 45.000 0.00 0.00 0.00 4.34
587 969 3.306166 GTGTAAATCGTCCATCCTTGTCG 59.694 47.826 0.00 0.00 0.00 4.35
588 970 4.092968 GTGTGTAAATCGTCCATCCTTGTC 59.907 45.833 0.00 0.00 0.00 3.18
589 971 4.000988 GTGTGTAAATCGTCCATCCTTGT 58.999 43.478 0.00 0.00 0.00 3.16
590 972 3.062099 CGTGTGTAAATCGTCCATCCTTG 59.938 47.826 0.00 0.00 0.00 3.61
591 973 3.056393 TCGTGTGTAAATCGTCCATCCTT 60.056 43.478 0.00 0.00 0.00 3.36
592 974 2.494471 TCGTGTGTAAATCGTCCATCCT 59.506 45.455 0.00 0.00 0.00 3.24
593 975 2.883574 TCGTGTGTAAATCGTCCATCC 58.116 47.619 0.00 0.00 0.00 3.51
596 978 1.996898 GCATCGTGTGTAAATCGTCCA 59.003 47.619 0.00 0.00 0.00 4.02
597 979 2.268298 AGCATCGTGTGTAAATCGTCC 58.732 47.619 0.00 0.00 0.00 4.79
598 980 3.242248 GGTAGCATCGTGTGTAAATCGTC 59.758 47.826 0.00 0.00 0.00 4.20
599 981 3.184541 GGTAGCATCGTGTGTAAATCGT 58.815 45.455 0.00 0.00 0.00 3.73
600 982 2.538449 GGGTAGCATCGTGTGTAAATCG 59.462 50.000 0.00 0.00 0.00 3.34
601 983 3.527533 TGGGTAGCATCGTGTGTAAATC 58.472 45.455 0.00 0.00 0.00 2.17
602 984 3.620427 TGGGTAGCATCGTGTGTAAAT 57.380 42.857 0.00 0.00 0.00 1.40
603 985 3.055747 TGATGGGTAGCATCGTGTGTAAA 60.056 43.478 0.00 0.00 32.04 2.01
605 987 2.104170 TGATGGGTAGCATCGTGTGTA 58.896 47.619 0.00 0.00 32.04 2.90
606 988 0.901827 TGATGGGTAGCATCGTGTGT 59.098 50.000 0.00 0.00 32.04 3.72
607 989 1.935873 CTTGATGGGTAGCATCGTGTG 59.064 52.381 0.00 0.00 32.04 3.82
608 990 1.831106 TCTTGATGGGTAGCATCGTGT 59.169 47.619 0.00 0.00 32.04 4.49
609 991 2.205074 GTCTTGATGGGTAGCATCGTG 58.795 52.381 0.00 0.00 32.04 4.35
610 992 1.202417 CGTCTTGATGGGTAGCATCGT 60.202 52.381 0.00 0.00 32.04 3.73
612 994 2.474816 GACGTCTTGATGGGTAGCATC 58.525 52.381 8.70 0.00 0.00 3.91
613 995 1.139058 GGACGTCTTGATGGGTAGCAT 59.861 52.381 16.46 0.00 0.00 3.79
616 998 3.543680 AATGGACGTCTTGATGGGTAG 57.456 47.619 16.46 0.00 0.00 3.18
617 999 3.992943 AAATGGACGTCTTGATGGGTA 57.007 42.857 16.46 0.00 0.00 3.69
618 1000 2.879103 AAATGGACGTCTTGATGGGT 57.121 45.000 16.46 0.00 0.00 4.51
619 1001 3.374058 GTGTAAATGGACGTCTTGATGGG 59.626 47.826 16.46 0.00 0.00 4.00
620 1002 4.000325 TGTGTAAATGGACGTCTTGATGG 59.000 43.478 16.46 0.00 0.00 3.51
621 1003 5.408299 TCTTGTGTAAATGGACGTCTTGATG 59.592 40.000 16.46 0.00 0.00 3.07
622 1004 5.547465 TCTTGTGTAAATGGACGTCTTGAT 58.453 37.500 16.46 2.50 0.00 2.57
623 1005 4.951254 TCTTGTGTAAATGGACGTCTTGA 58.049 39.130 16.46 0.00 0.00 3.02
624 1006 5.179368 ACATCTTGTGTAAATGGACGTCTTG 59.821 40.000 16.46 0.00 39.91 3.02
625 1007 5.305585 ACATCTTGTGTAAATGGACGTCTT 58.694 37.500 16.46 4.56 39.91 3.01
626 1008 4.894784 ACATCTTGTGTAAATGGACGTCT 58.105 39.130 16.46 0.00 39.91 4.18
627 1009 5.867716 AGTACATCTTGTGTAAATGGACGTC 59.132 40.000 7.13 7.13 44.52 4.34
629 1011 5.637810 ACAGTACATCTTGTGTAAATGGACG 59.362 40.000 0.00 0.00 44.52 4.79
630 1012 8.718102 ATACAGTACATCTTGTGTAAATGGAC 57.282 34.615 0.00 0.00 44.52 4.02
631 1013 8.536175 TGATACAGTACATCTTGTGTAAATGGA 58.464 33.333 0.00 0.00 44.52 3.41
632 1014 8.716646 TGATACAGTACATCTTGTGTAAATGG 57.283 34.615 0.00 0.00 44.52 3.16
635 1017 7.333423 GGCTTGATACAGTACATCTTGTGTAAA 59.667 37.037 0.00 0.00 44.52 2.01
636 1018 6.816640 GGCTTGATACAGTACATCTTGTGTAA 59.183 38.462 0.00 0.00 44.52 2.41
637 1019 6.338146 GGCTTGATACAGTACATCTTGTGTA 58.662 40.000 0.00 0.00 42.29 2.90
639 1021 4.268644 CGGCTTGATACAGTACATCTTGTG 59.731 45.833 0.00 0.00 0.00 3.33
640 1022 4.081642 ACGGCTTGATACAGTACATCTTGT 60.082 41.667 0.00 0.00 0.00 3.16
641 1023 4.433615 ACGGCTTGATACAGTACATCTTG 58.566 43.478 0.00 0.00 0.00 3.02
643 1025 4.159693 TGAACGGCTTGATACAGTACATCT 59.840 41.667 0.00 0.00 0.00 2.90
645 1027 4.465632 TGAACGGCTTGATACAGTACAT 57.534 40.909 0.00 0.00 0.00 2.29
646 1028 3.945981 TGAACGGCTTGATACAGTACA 57.054 42.857 0.00 0.00 0.00 2.90
649 1031 3.935203 CTGATTGAACGGCTTGATACAGT 59.065 43.478 0.00 0.00 0.00 3.55
651 1033 2.677836 GCTGATTGAACGGCTTGATACA 59.322 45.455 0.00 0.00 38.89 2.29
653 1035 1.933181 CGCTGATTGAACGGCTTGATA 59.067 47.619 0.00 0.00 39.69 2.15
654 1036 0.729116 CGCTGATTGAACGGCTTGAT 59.271 50.000 0.00 0.00 39.69 2.57
655 1037 0.320334 TCGCTGATTGAACGGCTTGA 60.320 50.000 0.00 0.00 39.69 3.02
656 1038 0.729116 ATCGCTGATTGAACGGCTTG 59.271 50.000 0.00 0.00 39.69 4.01
657 1039 1.009829 GATCGCTGATTGAACGGCTT 58.990 50.000 0.00 0.00 39.69 4.35
658 1040 1.148157 CGATCGCTGATTGAACGGCT 61.148 55.000 0.26 0.00 39.69 5.52
659 1041 1.273887 CGATCGCTGATTGAACGGC 59.726 57.895 0.26 0.00 38.62 5.68
661 1043 0.314578 GCACGATCGCTGATTGAACG 60.315 55.000 16.60 0.00 37.60 3.95
664 1046 0.932399 CATGCACGATCGCTGATTGA 59.068 50.000 16.60 0.00 0.00 2.57
668 1050 1.079197 AACCATGCACGATCGCTGA 60.079 52.632 16.60 0.00 0.00 4.26
670 1052 2.167219 CGAACCATGCACGATCGCT 61.167 57.895 16.60 0.00 0.00 4.93
671 1053 2.321060 CGAACCATGCACGATCGC 59.679 61.111 16.60 0.00 0.00 4.58
672 1054 3.005898 CCGAACCATGCACGATCG 58.994 61.111 14.88 14.88 0.00 3.69
673 1055 2.709475 GCCGAACCATGCACGATC 59.291 61.111 0.00 0.00 0.00 3.69
674 1056 2.824041 GGCCGAACCATGCACGAT 60.824 61.111 0.00 0.00 38.86 3.73
694 1076 2.758770 TACTGGGCGAACGACACTGC 62.759 60.000 1.79 0.00 0.00 4.40
696 1078 1.177256 ACTACTGGGCGAACGACACT 61.177 55.000 1.79 0.00 0.00 3.55
697 1079 0.319297 AACTACTGGGCGAACGACAC 60.319 55.000 1.79 0.00 0.00 3.67
698 1080 0.390124 AAACTACTGGGCGAACGACA 59.610 50.000 1.79 0.00 0.00 4.35
699 1081 1.066136 GAAACTACTGGGCGAACGAC 58.934 55.000 0.00 0.00 0.00 4.34
700 1082 0.387622 CGAAACTACTGGGCGAACGA 60.388 55.000 0.00 0.00 0.00 3.85
702 1084 1.458445 GAACGAAACTACTGGGCGAAC 59.542 52.381 0.00 0.00 0.00 3.95
705 1087 1.459592 CAAGAACGAAACTACTGGGCG 59.540 52.381 0.00 0.00 0.00 6.13
706 1088 1.197036 GCAAGAACGAAACTACTGGGC 59.803 52.381 0.00 0.00 0.00 5.36
707 1089 1.804748 GGCAAGAACGAAACTACTGGG 59.195 52.381 0.00 0.00 0.00 4.45
708 1090 1.804748 GGGCAAGAACGAAACTACTGG 59.195 52.381 0.00 0.00 0.00 4.00
709 1091 1.804748 GGGGCAAGAACGAAACTACTG 59.195 52.381 0.00 0.00 0.00 2.74
710 1092 1.271217 GGGGGCAAGAACGAAACTACT 60.271 52.381 0.00 0.00 0.00 2.57
712 1094 0.766131 TGGGGGCAAGAACGAAACTA 59.234 50.000 0.00 0.00 0.00 2.24
714 1096 0.536460 TCTGGGGGCAAGAACGAAAC 60.536 55.000 0.00 0.00 0.00 2.78
715 1097 0.404040 ATCTGGGGGCAAGAACGAAA 59.596 50.000 0.00 0.00 0.00 3.46
716 1098 1.281419 TATCTGGGGGCAAGAACGAA 58.719 50.000 0.00 0.00 0.00 3.85
718 1100 2.158755 AGATTATCTGGGGGCAAGAACG 60.159 50.000 0.00 0.00 0.00 3.95
720 1102 3.392616 GAGAGATTATCTGGGGGCAAGAA 59.607 47.826 0.00 0.00 38.84 2.52
721 1103 2.975489 GAGAGATTATCTGGGGGCAAGA 59.025 50.000 0.00 0.00 38.84 3.02
723 1105 2.975489 GAGAGAGATTATCTGGGGGCAA 59.025 50.000 0.00 0.00 38.84 4.52
724 1106 2.180973 AGAGAGAGATTATCTGGGGGCA 59.819 50.000 0.00 0.00 38.84 5.36
726 1108 3.855668 ACAGAGAGAGATTATCTGGGGG 58.144 50.000 0.00 0.00 46.96 5.40
727 1109 5.885449 AAACAGAGAGAGATTATCTGGGG 57.115 43.478 0.00 0.00 46.96 4.96
728 1110 8.869109 AGATAAAACAGAGAGAGATTATCTGGG 58.131 37.037 0.00 0.00 46.96 4.45
729 1111 9.912634 GAGATAAAACAGAGAGAGATTATCTGG 57.087 37.037 0.00 0.00 46.96 3.86
733 1115 8.367156 GGCAGAGATAAAACAGAGAGAGATTAT 58.633 37.037 0.00 0.00 0.00 1.28
1453 3766 0.529378 GGGAGCAAACATGGCAAGAG 59.471 55.000 0.00 0.00 0.00 2.85
1500 3813 1.229177 GCCCAAACTGGACCCCATT 60.229 57.895 0.00 0.00 40.96 3.16
1558 3877 2.890808 TAGGAGATGGATGCGACAAC 57.109 50.000 0.00 0.00 0.00 3.32
1923 4292 6.879458 AGGTTTAAGATGTCAAAGACGCTAAT 59.121 34.615 0.00 0.00 34.95 1.73
1924 4293 6.228258 AGGTTTAAGATGTCAAAGACGCTAA 58.772 36.000 0.00 0.00 34.95 3.09
1925 4294 5.790593 AGGTTTAAGATGTCAAAGACGCTA 58.209 37.500 0.00 0.00 34.95 4.26
1926 4295 4.642429 AGGTTTAAGATGTCAAAGACGCT 58.358 39.130 0.00 0.00 34.95 5.07
1982 4353 1.769716 TACAACACCCATCCGCCACA 61.770 55.000 0.00 0.00 0.00 4.17
2262 4633 0.324645 ATAGGCAGGCAACCAAAGGG 60.325 55.000 0.00 0.00 41.29 3.95
2264 4635 1.549203 ACATAGGCAGGCAACCAAAG 58.451 50.000 0.00 0.00 37.17 2.77
2265 4636 2.889170 TACATAGGCAGGCAACCAAA 57.111 45.000 0.00 0.00 37.17 3.28
2266 4637 3.380471 AATACATAGGCAGGCAACCAA 57.620 42.857 0.00 0.00 37.17 3.67
2267 4638 4.165180 TCTTAATACATAGGCAGGCAACCA 59.835 41.667 0.00 0.00 37.17 3.67
2274 4645 7.882791 TCTCTCTCTCTCTTAATACATAGGCAG 59.117 40.741 0.00 0.00 0.00 4.85
2314 4711 9.107177 AGAGATTCACAATAGCAATTCTTGTAG 57.893 33.333 0.00 0.00 32.14 2.74
2358 4755 2.354203 GCAGAGTCCAAACTACTCAGGG 60.354 54.545 6.06 0.00 44.77 4.45
2505 4926 1.615392 GCCCTGGAAATCATATGCACC 59.385 52.381 0.00 0.00 0.00 5.01
2512 4933 2.181975 CAAACAGGCCCTGGAAATCAT 58.818 47.619 16.70 0.00 35.51 2.45
2573 4994 4.097361 GTCCTCTTCCGGCCACCC 62.097 72.222 2.24 0.00 0.00 4.61
2703 5124 5.302568 TCAAAATGCAAAAGGTGTGAGAGAT 59.697 36.000 0.00 0.00 0.00 2.75
2742 5164 3.866910 TGTTCAGACGGTTTGTGTTAGAC 59.133 43.478 0.00 0.00 0.00 2.59
3067 5493 0.038166 GGAAAGCCTGTGACCCATGA 59.962 55.000 0.00 0.00 0.00 3.07
3068 5494 0.967380 GGGAAAGCCTGTGACCCATG 60.967 60.000 0.00 0.00 40.20 3.66
3069 5495 1.384191 GGGAAAGCCTGTGACCCAT 59.616 57.895 0.00 0.00 40.20 4.00
3082 5508 3.117888 GCAGAGGTTGATATCAGGGGAAA 60.118 47.826 5.39 0.00 0.00 3.13
3204 5630 0.679002 CCCCAACTGGACTGCTGATG 60.679 60.000 0.00 0.00 37.39 3.07
3373 5800 9.583765 GAAGGTAACCACTGATTAAAGTACTAG 57.416 37.037 0.00 0.00 37.17 2.57
3374 5801 9.317827 AGAAGGTAACCACTGATTAAAGTACTA 57.682 33.333 0.00 0.00 37.17 1.82
3375 5802 8.203681 AGAAGGTAACCACTGATTAAAGTACT 57.796 34.615 0.00 0.00 37.17 2.73
3418 5846 0.108585 TGGAAACAGGCCACAGACTC 59.891 55.000 5.01 0.00 35.01 3.36
3595 6040 0.675633 ACTGGCTGCAATCCAAACAC 59.324 50.000 0.50 0.00 32.41 3.32
3605 6050 0.838554 TAGGGTGGTTACTGGCTGCA 60.839 55.000 0.50 0.00 0.00 4.41
3785 6230 6.183360 ACAACAACGTTGTAGAAATGACACAT 60.183 34.615 32.47 10.76 41.31 3.21
3796 6241 1.305201 AGCCCACAACAACGTTGTAG 58.695 50.000 32.47 23.50 41.31 2.74
3944 6390 7.440523 TGCCTCTCTTCTAAAAACAAGAATC 57.559 36.000 0.00 0.00 32.72 2.52
3961 6407 2.402305 CGAGCACATCTTATGCCTCTC 58.598 52.381 0.00 0.00 44.53 3.20
4002 6450 5.581605 ACACTTGACTACTTTGCATGTTTG 58.418 37.500 0.00 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.