Multiple sequence alignment - TraesCS7A01G168200

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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 TraesCS7A01G168200 chr7A 100.000 2871 0 0 1 2871 124788877 124791747 0.000000e+00 5302.0
1 TraesCS7A01G168200 chr7A 86.364 66 7 2 2043 2107 11090772 11090708 1.430000e-08 71.3
2 TraesCS7A01G168200 chr7A 97.297 37 1 0 2045 2081 309906905 309906869 2.390000e-06 63.9
3 TraesCS7A01G168200 chr7D 92.677 2185 74 33 744 2871 119891007 119893162 0.000000e+00 3070.0
4 TraesCS7A01G168200 chr7D 85.670 642 69 9 25 655 119889400 119890029 0.000000e+00 654.0
5 TraesCS7A01G168200 chr7B 88.872 1339 56 25 732 2001 81421901 81423215 0.000000e+00 1561.0
6 TraesCS7A01G168200 chr7B 88.154 726 41 20 2166 2871 81423320 81424020 0.000000e+00 822.0
7 TraesCS7A01G168200 chr7B 91.795 195 16 0 207 401 81419995 81420189 3.650000e-69 272.0
8 TraesCS7A01G168200 chr7B 88.312 154 17 1 1 154 81419839 81419991 1.760000e-42 183.0
9 TraesCS7A01G168200 chr5D 82.353 85 9 4 2049 2132 53874023 53873944 5.130000e-08 69.4
10 TraesCS7A01G168200 chr4A 80.952 84 11 3 2041 2123 71105208 71105129 8.590000e-06 62.1
11 TraesCS7A01G168200 chr6A 79.070 86 13 3 2049 2134 260323597 260323517 1.000000e-03 54.7


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 TraesCS7A01G168200 chr7A 124788877 124791747 2870 False 5302.0 5302 100.00000 1 2871 1 chr7A.!!$F1 2870
1 TraesCS7A01G168200 chr7D 119889400 119893162 3762 False 1862.0 3070 89.17350 25 2871 2 chr7D.!!$F1 2846
2 TraesCS7A01G168200 chr7B 81419839 81424020 4181 False 709.5 1561 89.28325 1 2871 4 chr7B.!!$F1 2870

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
675 1193 0.035534 TGTTGCTGGTGTGTGTGACT 60.036 50.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2206 3832 0.178975 GGTGGGTTCATGGTTGTGGA 60.179 55.0 0.0 0.0 0.0 4.02 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
49 50 0.532573 CAGTGTGCGTCTCCCTATGT 59.467 55.000 0.00 0.00 0.00 2.29
60 61 4.618965 GTCTCCCTATGTGTTATTCGGAC 58.381 47.826 0.00 0.00 0.00 4.79
72 74 4.449743 TGTTATTCGGACAACTTGCTGTAC 59.550 41.667 0.00 0.00 0.00 2.90
74 76 1.491563 CGGACAACTTGCTGTACGC 59.508 57.895 0.00 3.22 45.98 4.42
75 77 1.866925 GGACAACTTGCTGTACGCC 59.133 57.895 7.13 0.00 38.05 5.68
77 79 0.602905 GACAACTTGCTGTACGCCCT 60.603 55.000 7.13 0.00 38.05 5.19
78 80 0.602905 ACAACTTGCTGTACGCCCTC 60.603 55.000 7.13 0.00 38.05 4.30
85 87 1.715585 CTGTACGCCCTCGCAAATG 59.284 57.895 0.00 0.00 39.84 2.32
120 122 1.244019 ATGGCCTCGCAGTGAAAACC 61.244 55.000 3.32 0.00 0.00 3.27
128 130 1.032014 GCAGTGAAAACCAAGAGGCA 58.968 50.000 0.00 0.00 39.06 4.75
138 140 0.390735 CCAAGAGGCAAATTGGCAGC 60.391 55.000 21.49 12.55 46.46 5.25
142 144 4.032653 GGCAAATTGGCAGCCCTA 57.967 55.556 14.91 0.00 43.14 3.53
145 147 1.202568 GGCAAATTGGCAGCCCTATTC 60.203 52.381 14.91 0.00 43.14 1.75
154 156 3.052944 TGGCAGCCCTATTCCAACTAAAT 60.053 43.478 9.64 0.00 0.00 1.40
157 159 3.891366 CAGCCCTATTCCAACTAAATGGG 59.109 47.826 0.00 0.00 41.05 4.00
168 170 6.785076 TCCAACTAAATGGGAGATTTACACA 58.215 36.000 0.00 0.00 41.05 3.72
192 194 1.001974 CACCACTCGACCCAAATCTCA 59.998 52.381 0.00 0.00 0.00 3.27
195 197 2.093500 CCACTCGACCCAAATCTCATGA 60.093 50.000 0.00 0.00 0.00 3.07
202 204 7.012704 ACTCGACCCAAATCTCATGAATAAATG 59.987 37.037 0.00 0.00 0.00 2.32
220 222 2.544844 TGAGAGAGGTACCGGGAAAT 57.455 50.000 6.32 0.00 0.00 2.17
235 237 1.908619 GGAAATGTTTTGAGGGCCCAT 59.091 47.619 27.56 9.36 0.00 4.00
237 239 3.132824 GGAAATGTTTTGAGGGCCCATAG 59.867 47.826 27.56 0.00 0.00 2.23
267 269 5.237996 CACCAACATGATGTCAGTGGATATC 59.762 44.000 18.79 0.00 40.82 1.63
368 372 6.554334 TTCGCCTGCAATAAATAATCCTAC 57.446 37.500 0.00 0.00 0.00 3.18
440 945 3.054802 TCCAAGCCCAAACAACACAAATT 60.055 39.130 0.00 0.00 0.00 1.82
445 950 7.390162 CCAAGCCCAAACAACACAAATTATAAT 59.610 33.333 0.00 0.00 0.00 1.28
447 952 8.916628 AGCCCAAACAACACAAATTATAATTT 57.083 26.923 16.15 16.15 39.07 1.82
498 1003 2.143876 AATGAAGTGGCCCATGTACC 57.856 50.000 0.00 0.00 0.00 3.34
512 1017 0.249120 TGTACCATCAAGCCCTGTCG 59.751 55.000 0.00 0.00 0.00 4.35
516 1021 0.321564 CCATCAAGCCCTGTCGTGAA 60.322 55.000 0.00 0.00 0.00 3.18
587 1105 2.224867 ACCCATCCAAGGTCAAAGAGTG 60.225 50.000 0.00 0.00 28.99 3.51
588 1106 2.440409 CCATCCAAGGTCAAAGAGTGG 58.560 52.381 0.00 0.00 0.00 4.00
602 1120 1.425066 AGAGTGGGTTTGATTCCTGCA 59.575 47.619 0.00 0.00 0.00 4.41
605 1123 0.776810 TGGGTTTGATTCCTGCAGGA 59.223 50.000 32.00 32.00 43.73 3.86
627 1145 1.882352 GCAAGGTTGGTGGTCCAGTAG 60.882 57.143 0.00 0.00 45.22 2.57
631 1149 0.605589 GTTGGTGGTCCAGTAGTGCC 60.606 60.000 0.00 0.00 45.22 5.01
640 1158 0.960364 CCAGTAGTGCCGCAACCAAT 60.960 55.000 0.00 0.00 0.00 3.16
643 1161 0.170339 GTAGTGCCGCAACCAATTCC 59.830 55.000 0.00 0.00 0.00 3.01
646 1164 4.794439 GCCGCAACCAATTCCGCC 62.794 66.667 0.00 0.00 0.00 6.13
655 1173 5.356426 GCAACCAATTCCGCCTAAATAAAT 58.644 37.500 0.00 0.00 0.00 1.40
656 1174 5.815222 GCAACCAATTCCGCCTAAATAAATT 59.185 36.000 0.00 0.00 0.00 1.82
657 1175 6.238076 GCAACCAATTCCGCCTAAATAAATTG 60.238 38.462 0.00 0.00 37.17 2.32
658 1176 6.538945 ACCAATTCCGCCTAAATAAATTGT 57.461 33.333 0.00 0.00 36.20 2.71
659 1177 6.941857 ACCAATTCCGCCTAAATAAATTGTT 58.058 32.000 0.00 0.00 36.20 2.83
660 1178 6.816140 ACCAATTCCGCCTAAATAAATTGTTG 59.184 34.615 0.00 0.00 36.20 3.33
661 1179 6.238076 CCAATTCCGCCTAAATAAATTGTTGC 60.238 38.462 0.00 0.00 36.20 4.17
662 1180 5.652994 TTCCGCCTAAATAAATTGTTGCT 57.347 34.783 0.00 0.00 0.00 3.91
663 1181 4.992688 TCCGCCTAAATAAATTGTTGCTG 58.007 39.130 0.00 0.00 0.00 4.41
664 1182 4.111916 CCGCCTAAATAAATTGTTGCTGG 58.888 43.478 0.00 0.00 0.00 4.85
665 1183 4.381505 CCGCCTAAATAAATTGTTGCTGGT 60.382 41.667 0.00 0.00 0.00 4.00
666 1184 4.562394 CGCCTAAATAAATTGTTGCTGGTG 59.438 41.667 0.00 0.00 0.00 4.17
667 1185 5.478407 GCCTAAATAAATTGTTGCTGGTGT 58.522 37.500 0.00 0.00 0.00 4.16
668 1186 5.348451 GCCTAAATAAATTGTTGCTGGTGTG 59.652 40.000 0.00 0.00 0.00 3.82
669 1187 6.454795 CCTAAATAAATTGTTGCTGGTGTGT 58.545 36.000 0.00 0.00 0.00 3.72
670 1188 6.365789 CCTAAATAAATTGTTGCTGGTGTGTG 59.634 38.462 0.00 0.00 0.00 3.82
671 1189 4.935352 ATAAATTGTTGCTGGTGTGTGT 57.065 36.364 0.00 0.00 0.00 3.72
672 1190 2.582728 AATTGTTGCTGGTGTGTGTG 57.417 45.000 0.00 0.00 0.00 3.82
673 1191 1.761449 ATTGTTGCTGGTGTGTGTGA 58.239 45.000 0.00 0.00 0.00 3.58
674 1192 0.808125 TTGTTGCTGGTGTGTGTGAC 59.192 50.000 0.00 0.00 0.00 3.67
675 1193 0.035534 TGTTGCTGGTGTGTGTGACT 60.036 50.000 0.00 0.00 0.00 3.41
676 1194 0.378257 GTTGCTGGTGTGTGTGACTG 59.622 55.000 0.00 0.00 0.00 3.51
677 1195 0.035534 TTGCTGGTGTGTGTGACTGT 60.036 50.000 0.00 0.00 0.00 3.55
678 1196 0.744057 TGCTGGTGTGTGTGACTGTG 60.744 55.000 0.00 0.00 0.00 3.66
679 1197 0.744414 GCTGGTGTGTGTGACTGTGT 60.744 55.000 0.00 0.00 0.00 3.72
680 1198 1.009078 CTGGTGTGTGTGACTGTGTG 58.991 55.000 0.00 0.00 0.00 3.82
681 1199 0.610687 TGGTGTGTGTGACTGTGTGA 59.389 50.000 0.00 0.00 0.00 3.58
682 1200 1.006832 GGTGTGTGTGACTGTGTGAC 58.993 55.000 0.00 0.00 0.00 3.67
683 1201 1.405526 GGTGTGTGTGACTGTGTGACT 60.406 52.381 0.00 0.00 0.00 3.41
684 1202 1.660607 GTGTGTGTGACTGTGTGACTG 59.339 52.381 0.00 0.00 0.00 3.51
685 1203 1.275010 TGTGTGTGACTGTGTGACTGT 59.725 47.619 0.00 0.00 32.79 3.55
686 1204 1.660607 GTGTGTGACTGTGTGACTGTG 59.339 52.381 0.00 0.00 30.17 3.66
687 1205 1.275010 TGTGTGACTGTGTGACTGTGT 59.725 47.619 0.00 0.00 30.17 3.72
688 1206 1.660607 GTGTGACTGTGTGACTGTGTG 59.339 52.381 0.00 0.00 30.17 3.82
689 1207 1.275010 TGTGACTGTGTGACTGTGTGT 59.725 47.619 0.00 0.00 30.17 3.72
690 1208 1.660607 GTGACTGTGTGACTGTGTGTG 59.339 52.381 0.00 0.00 30.17 3.82
691 1209 1.275010 TGACTGTGTGACTGTGTGTGT 59.725 47.619 0.00 0.00 30.17 3.72
692 1210 1.927174 GACTGTGTGACTGTGTGTGTC 59.073 52.381 0.00 0.00 30.17 3.67
693 1211 1.550524 ACTGTGTGACTGTGTGTGTCT 59.449 47.619 0.00 0.00 35.63 3.41
694 1212 2.196749 CTGTGTGACTGTGTGTGTCTC 58.803 52.381 0.00 0.00 35.63 3.36
695 1213 1.824852 TGTGTGACTGTGTGTGTCTCT 59.175 47.619 0.00 0.00 35.63 3.10
696 1214 2.159240 TGTGTGACTGTGTGTGTCTCTC 60.159 50.000 0.00 0.00 35.63 3.20
697 1215 2.099921 GTGTGACTGTGTGTGTCTCTCT 59.900 50.000 0.00 0.00 35.63 3.10
698 1216 2.359214 TGTGACTGTGTGTGTCTCTCTC 59.641 50.000 0.00 0.00 35.63 3.20
699 1217 2.621055 GTGACTGTGTGTGTCTCTCTCT 59.379 50.000 0.00 0.00 35.63 3.10
700 1218 2.881513 TGACTGTGTGTGTCTCTCTCTC 59.118 50.000 0.00 0.00 35.63 3.20
701 1219 3.146066 GACTGTGTGTGTCTCTCTCTCT 58.854 50.000 0.00 0.00 0.00 3.10
702 1220 3.561143 ACTGTGTGTGTCTCTCTCTCTT 58.439 45.455 0.00 0.00 0.00 2.85
703 1221 3.957497 ACTGTGTGTGTCTCTCTCTCTTT 59.043 43.478 0.00 0.00 0.00 2.52
704 1222 4.202101 ACTGTGTGTGTCTCTCTCTCTTTG 60.202 45.833 0.00 0.00 0.00 2.77
705 1223 3.954258 TGTGTGTGTCTCTCTCTCTTTGA 59.046 43.478 0.00 0.00 0.00 2.69
706 1224 4.402474 TGTGTGTGTCTCTCTCTCTTTGAA 59.598 41.667 0.00 0.00 0.00 2.69
707 1225 5.105351 TGTGTGTGTCTCTCTCTCTTTGAAA 60.105 40.000 0.00 0.00 0.00 2.69
708 1226 5.461737 GTGTGTGTCTCTCTCTCTTTGAAAG 59.538 44.000 0.00 0.00 0.00 2.62
709 1227 4.987912 GTGTGTCTCTCTCTCTTTGAAAGG 59.012 45.833 4.94 0.00 0.00 3.11
710 1228 4.895889 TGTGTCTCTCTCTCTTTGAAAGGA 59.104 41.667 4.94 0.96 0.00 3.36
713 1231 5.600484 TGTCTCTCTCTCTTTGAAAGGAGTT 59.400 40.000 17.15 0.00 31.69 3.01
715 1233 5.835819 TCTCTCTCTCTTTGAAAGGAGTTGA 59.164 40.000 17.15 15.36 31.69 3.18
717 1235 6.696411 TCTCTCTCTTTGAAAGGAGTTGATC 58.304 40.000 17.15 0.00 31.69 2.92
731 1249 6.106673 AGGAGTTGATCGTGTTGTTATTAGG 58.893 40.000 0.00 0.00 0.00 2.69
732 1250 5.220605 GGAGTTGATCGTGTTGTTATTAGGC 60.221 44.000 0.00 0.00 0.00 3.93
734 1252 3.537580 TGATCGTGTTGTTATTAGGCCC 58.462 45.455 0.00 0.00 0.00 5.80
737 1255 1.741145 CGTGTTGTTATTAGGCCCACC 59.259 52.381 0.00 0.00 0.00 4.61
739 1257 1.629353 TGTTGTTATTAGGCCCACCGA 59.371 47.619 0.00 0.00 42.76 4.69
742 2267 0.542805 GTTATTAGGCCCACCGACCA 59.457 55.000 0.00 0.00 42.76 4.02
836 2362 0.953960 AAACCCGCAAGCGAACTAGG 60.954 55.000 16.97 10.41 42.83 3.02
892 2419 3.370231 CCGTTGCCTTTTCCCCCG 61.370 66.667 0.00 0.00 0.00 5.73
960 2523 1.687563 AACCACCACGGAAAAGGAAG 58.312 50.000 0.00 0.00 38.63 3.46
1074 2646 4.504916 CGTGCGGGGAGAGAGCAG 62.505 72.222 0.00 0.00 41.93 4.24
1227 2799 1.293267 TTCGCCCGATTTCCGTTGAC 61.293 55.000 0.00 0.00 36.31 3.18
1228 2800 1.740296 CGCCCGATTTCCGTTGACT 60.740 57.895 0.00 0.00 36.31 3.41
1229 2801 1.296056 CGCCCGATTTCCGTTGACTT 61.296 55.000 0.00 0.00 36.31 3.01
1230 2802 0.879090 GCCCGATTTCCGTTGACTTT 59.121 50.000 0.00 0.00 36.31 2.66
1231 2803 1.401018 GCCCGATTTCCGTTGACTTTG 60.401 52.381 0.00 0.00 36.31 2.77
1232 2804 2.147958 CCCGATTTCCGTTGACTTTGA 58.852 47.619 0.00 0.00 36.31 2.69
1447 3025 4.457496 CTCACGGTGAGCGCCCAT 62.457 66.667 23.81 0.00 37.72 4.00
1460 3043 2.325082 GCCCATCTGCGTTCGTTGT 61.325 57.895 0.00 0.00 0.00 3.32
1464 3047 0.586319 CATCTGCGTTCGTTGTGGTT 59.414 50.000 0.00 0.00 0.00 3.67
1470 3053 1.924191 GCGTTCGTTGTGGTTTGGATG 60.924 52.381 0.00 0.00 0.00 3.51
1478 3061 2.315176 TGTGGTTTGGATGGAACTTGG 58.685 47.619 0.00 0.00 0.00 3.61
1557 3150 0.179037 TCGTATCAGATCGACGGGGT 60.179 55.000 5.99 0.00 37.20 4.95
1570 3163 2.663196 GGGGTGGTGAAGGAGTCG 59.337 66.667 0.00 0.00 0.00 4.18
1729 3322 3.419759 CCGTGCCCGTACAGCAAC 61.420 66.667 9.01 3.98 43.02 4.17
1855 3448 6.810888 TTCCTTGCGTACGTACAATAATAC 57.189 37.500 24.50 5.94 0.00 1.89
1883 3479 4.056050 TCTGTTCTTTACGACTTTGCTCC 58.944 43.478 0.00 0.00 0.00 4.70
1945 3550 5.416947 GGATACGAACCTCACAAATACAGT 58.583 41.667 0.00 0.00 0.00 3.55
1946 3551 5.291128 GGATACGAACCTCACAAATACAGTG 59.709 44.000 0.00 0.00 38.32 3.66
1984 3589 4.946157 AGTCTGATTTTGGGATGCTACTTG 59.054 41.667 0.00 0.00 0.00 3.16
1986 3591 2.760092 TGATTTTGGGATGCTACTTGGC 59.240 45.455 0.00 0.00 0.00 4.52
1989 3594 0.034186 TTGGGATGCTACTTGGCCAG 60.034 55.000 5.11 2.72 0.00 4.85
2019 3624 7.009179 ACATCTCTTCTTACTCATTTGGACA 57.991 36.000 0.00 0.00 0.00 4.02
2020 3625 6.876257 ACATCTCTTCTTACTCATTTGGACAC 59.124 38.462 0.00 0.00 0.00 3.67
2022 3627 7.067496 TCTCTTCTTACTCATTTGGACACTT 57.933 36.000 0.00 0.00 0.00 3.16
2023 3628 7.155328 TCTCTTCTTACTCATTTGGACACTTC 58.845 38.462 0.00 0.00 0.00 3.01
2026 3631 7.442364 TCTTCTTACTCATTTGGACACTTCAAG 59.558 37.037 0.00 0.00 0.00 3.02
2027 3632 6.826668 TCTTACTCATTTGGACACTTCAAGA 58.173 36.000 0.00 0.00 0.00 3.02
2028 3633 6.931281 TCTTACTCATTTGGACACTTCAAGAG 59.069 38.462 0.00 0.00 0.00 2.85
2029 3634 3.817647 ACTCATTTGGACACTTCAAGAGC 59.182 43.478 0.00 0.00 0.00 4.09
2031 3636 3.565482 TCATTTGGACACTTCAAGAGCAC 59.435 43.478 0.00 0.00 0.00 4.40
2043 3651 6.002704 ACTTCAAGAGCACAAGAGAATGATT 58.997 36.000 0.00 0.00 0.00 2.57
2085 3696 2.818130 GCAAAAGAATTGCCTCACCA 57.182 45.000 1.80 0.00 39.38 4.17
2153 3764 4.404507 ACATGACGCACAAATAGTTCAC 57.595 40.909 0.00 0.00 0.00 3.18
2155 3766 4.455533 ACATGACGCACAAATAGTTCACAT 59.544 37.500 0.00 0.00 0.00 3.21
2179 3801 5.580022 ACAAAGCATAAAACCCTATGACCT 58.420 37.500 0.00 0.00 31.94 3.85
2187 3809 1.035932 ACCCTATGACCTCACCGTCG 61.036 60.000 0.00 0.00 35.40 5.12
2206 3832 0.247736 GACCCGACACTCTGAATGCT 59.752 55.000 0.00 0.00 0.00 3.79
2255 3881 4.948341 ACATTACAAAGGAAACCCCAAC 57.052 40.909 0.00 0.00 37.41 3.77
2258 3884 5.163353 ACATTACAAAGGAAACCCCAACAAG 60.163 40.000 0.00 0.00 37.41 3.16
2264 3890 2.024369 AGGAAACCCCAACAAGAACACT 60.024 45.455 0.00 0.00 37.41 3.55
2265 3891 2.764010 GGAAACCCCAACAAGAACACTT 59.236 45.455 0.00 0.00 34.14 3.16
2280 3906 6.222038 AGAACACTTAGACTGAAGACAACA 57.778 37.500 0.00 0.00 0.00 3.33
2314 3944 9.578576 CCAAATCCATAGAAGAGAATAATGGAA 57.421 33.333 6.45 0.00 46.73 3.53
2329 3959 2.937469 TGGAAATAACAATGGCTGCG 57.063 45.000 0.00 0.00 0.00 5.18
2763 4406 0.108138 CGTTCAGGGTCAGCTTAGGG 60.108 60.000 0.00 0.00 0.00 3.53
2773 4419 4.552278 GCTTAGGGCGCAAAACAC 57.448 55.556 10.83 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 3.472652 ACAGCAAGTTGTCCGAATAACA 58.527 40.909 4.48 0.00 0.00 2.41
72 74 1.656818 AATCCACATTTGCGAGGGCG 61.657 55.000 0.00 0.00 44.10 6.13
73 75 1.065551 GTAATCCACATTTGCGAGGGC 59.934 52.381 0.00 0.00 40.52 5.19
74 76 1.676006 GGTAATCCACATTTGCGAGGG 59.324 52.381 0.00 0.00 0.00 4.30
75 77 2.364632 TGGTAATCCACATTTGCGAGG 58.635 47.619 0.00 0.00 39.03 4.63
77 79 2.490115 GGTTGGTAATCCACATTTGCGA 59.510 45.455 0.00 0.00 44.22 5.10
78 80 2.230025 TGGTTGGTAATCCACATTTGCG 59.770 45.455 0.00 0.00 44.22 4.85
120 122 0.390735 GGCTGCCAATTTGCCTCTTG 60.391 55.000 15.17 0.00 43.05 3.02
128 130 2.501316 GTTGGAATAGGGCTGCCAATTT 59.499 45.455 22.05 9.90 41.89 1.82
138 140 5.646692 TCTCCCATTTAGTTGGAATAGGG 57.353 43.478 0.00 0.00 39.25 3.53
142 144 7.893302 TGTGTAAATCTCCCATTTAGTTGGAAT 59.107 33.333 0.00 0.00 39.25 3.01
145 147 7.461182 TTGTGTAAATCTCCCATTTAGTTGG 57.539 36.000 0.00 0.00 36.46 3.77
168 170 2.649531 TTTGGGTCGAGTGGTGATTT 57.350 45.000 0.00 0.00 0.00 2.17
173 175 1.348064 TGAGATTTGGGTCGAGTGGT 58.652 50.000 0.00 0.00 0.00 4.16
192 194 5.012148 CCCGGTACCTCTCTCATTTATTCAT 59.988 44.000 10.90 0.00 0.00 2.57
195 197 4.553678 TCCCGGTACCTCTCTCATTTATT 58.446 43.478 10.90 0.00 0.00 1.40
202 204 2.108970 ACATTTCCCGGTACCTCTCTC 58.891 52.381 10.90 0.00 0.00 3.20
205 207 3.073356 TCAAAACATTTCCCGGTACCTCT 59.927 43.478 10.90 0.00 0.00 3.69
220 222 2.580322 TGATCTATGGGCCCTCAAAACA 59.420 45.455 25.70 13.78 0.00 2.83
256 258 5.302059 CCCGTCTAGAAAAGATATCCACTGA 59.698 44.000 0.00 0.00 36.36 3.41
259 261 4.202223 TGCCCGTCTAGAAAAGATATCCAC 60.202 45.833 0.00 0.00 36.36 4.02
267 269 5.470845 CAACTTATGCCCGTCTAGAAAAG 57.529 43.478 0.00 0.00 0.00 2.27
293 297 7.808381 GCAAAGTCTTTAAATACAGAGGAAACC 59.192 37.037 6.51 0.00 0.00 3.27
368 372 6.136071 CAGTCTGAAAAACAGTGTAAATCCG 58.864 40.000 0.00 0.00 45.86 4.18
440 945 9.856162 AAGGGACCTAAAGCGAATTAAATTATA 57.144 29.630 0.00 0.00 0.00 0.98
445 950 6.294843 CCAAAAGGGACCTAAAGCGAATTAAA 60.295 38.462 0.00 0.00 40.01 1.52
447 952 4.703093 CCAAAAGGGACCTAAAGCGAATTA 59.297 41.667 0.00 0.00 40.01 1.40
498 1003 0.798776 GTTCACGACAGGGCTTGATG 59.201 55.000 2.65 0.00 0.00 3.07
512 1017 2.617274 GGCAGAAGCACCGGTTCAC 61.617 63.158 2.97 0.00 41.76 3.18
516 1021 4.643387 GGTGGCAGAAGCACCGGT 62.643 66.667 0.00 0.00 44.61 5.28
587 1105 3.670105 TCCTGCAGGAATCAAACCC 57.330 52.632 33.41 0.00 42.18 4.11
602 1120 0.251341 GACCACCAACCTTGCATCCT 60.251 55.000 0.00 0.00 0.00 3.24
605 1123 0.540365 CTGGACCACCAACCTTGCAT 60.540 55.000 0.00 0.00 46.32 3.96
610 1128 1.056660 CACTACTGGACCACCAACCT 58.943 55.000 0.00 0.00 46.32 3.50
616 1134 2.434359 GCGGCACTACTGGACCAC 60.434 66.667 0.00 0.00 0.00 4.16
627 1145 2.126502 CGGAATTGGTTGCGGCAC 60.127 61.111 0.05 0.00 44.20 5.01
640 1158 5.406649 CAGCAACAATTTATTTAGGCGGAA 58.593 37.500 0.00 0.00 0.00 4.30
643 1161 4.562394 CACCAGCAACAATTTATTTAGGCG 59.438 41.667 0.00 0.00 0.00 5.52
646 1164 6.922957 ACACACACCAGCAACAATTTATTTAG 59.077 34.615 0.00 0.00 0.00 1.85
655 1173 0.808125 GTCACACACACCAGCAACAA 59.192 50.000 0.00 0.00 0.00 2.83
656 1174 0.035534 AGTCACACACACCAGCAACA 60.036 50.000 0.00 0.00 0.00 3.33
657 1175 0.378257 CAGTCACACACACCAGCAAC 59.622 55.000 0.00 0.00 0.00 4.17
658 1176 0.035534 ACAGTCACACACACCAGCAA 60.036 50.000 0.00 0.00 0.00 3.91
659 1177 0.744057 CACAGTCACACACACCAGCA 60.744 55.000 0.00 0.00 0.00 4.41
660 1178 0.744414 ACACAGTCACACACACCAGC 60.744 55.000 0.00 0.00 0.00 4.85
661 1179 1.009078 CACACAGTCACACACACCAG 58.991 55.000 0.00 0.00 0.00 4.00
662 1180 0.610687 TCACACAGTCACACACACCA 59.389 50.000 0.00 0.00 0.00 4.17
663 1181 1.006832 GTCACACAGTCACACACACC 58.993 55.000 0.00 0.00 0.00 4.16
664 1182 1.660607 CAGTCACACAGTCACACACAC 59.339 52.381 0.00 0.00 0.00 3.82
665 1183 1.275010 ACAGTCACACAGTCACACACA 59.725 47.619 0.00 0.00 0.00 3.72
666 1184 1.660607 CACAGTCACACAGTCACACAC 59.339 52.381 0.00 0.00 0.00 3.82
667 1185 1.275010 ACACAGTCACACAGTCACACA 59.725 47.619 0.00 0.00 0.00 3.72
668 1186 1.660607 CACACAGTCACACAGTCACAC 59.339 52.381 0.00 0.00 0.00 3.82
669 1187 1.275010 ACACACAGTCACACAGTCACA 59.725 47.619 0.00 0.00 0.00 3.58
670 1188 1.660607 CACACACAGTCACACAGTCAC 59.339 52.381 0.00 0.00 0.00 3.67
671 1189 1.275010 ACACACACAGTCACACAGTCA 59.725 47.619 0.00 0.00 0.00 3.41
672 1190 1.927174 GACACACACAGTCACACAGTC 59.073 52.381 0.00 0.00 36.06 3.51
673 1191 1.550524 AGACACACACAGTCACACAGT 59.449 47.619 0.00 0.00 38.46 3.55
674 1192 2.159184 AGAGACACACACAGTCACACAG 60.159 50.000 0.00 0.00 38.46 3.66
675 1193 1.824852 AGAGACACACACAGTCACACA 59.175 47.619 0.00 0.00 38.46 3.72
676 1194 2.099921 AGAGAGACACACACAGTCACAC 59.900 50.000 0.00 0.00 38.46 3.82
677 1195 2.359214 GAGAGAGACACACACAGTCACA 59.641 50.000 0.00 0.00 38.46 3.58
678 1196 2.621055 AGAGAGAGACACACACAGTCAC 59.379 50.000 0.00 0.00 38.46 3.67
679 1197 2.881513 GAGAGAGAGACACACACAGTCA 59.118 50.000 0.00 0.00 38.46 3.41
680 1198 3.146066 AGAGAGAGAGACACACACAGTC 58.854 50.000 0.00 0.00 36.26 3.51
681 1199 3.222173 AGAGAGAGAGACACACACAGT 57.778 47.619 0.00 0.00 0.00 3.55
682 1200 4.037327 TCAAAGAGAGAGAGACACACACAG 59.963 45.833 0.00 0.00 0.00 3.66
683 1201 3.954258 TCAAAGAGAGAGAGACACACACA 59.046 43.478 0.00 0.00 0.00 3.72
684 1202 4.576216 TCAAAGAGAGAGAGACACACAC 57.424 45.455 0.00 0.00 0.00 3.82
685 1203 5.452496 CCTTTCAAAGAGAGAGAGACACACA 60.452 44.000 0.00 0.00 30.18 3.72
686 1204 4.987912 CCTTTCAAAGAGAGAGAGACACAC 59.012 45.833 0.00 0.00 30.18 3.82
687 1205 4.895889 TCCTTTCAAAGAGAGAGAGACACA 59.104 41.667 0.00 0.00 30.18 3.72
688 1206 5.010617 ACTCCTTTCAAAGAGAGAGAGACAC 59.989 44.000 17.66 0.00 33.09 3.67
689 1207 5.144100 ACTCCTTTCAAAGAGAGAGAGACA 58.856 41.667 17.66 0.00 33.09 3.41
690 1208 5.722021 ACTCCTTTCAAAGAGAGAGAGAC 57.278 43.478 17.66 0.00 33.09 3.36
691 1209 5.835819 TCAACTCCTTTCAAAGAGAGAGAGA 59.164 40.000 17.66 11.13 33.09 3.10
692 1210 6.095432 TCAACTCCTTTCAAAGAGAGAGAG 57.905 41.667 17.66 9.68 33.09 3.20
693 1211 6.571344 CGATCAACTCCTTTCAAAGAGAGAGA 60.571 42.308 17.66 14.90 33.09 3.10
694 1212 5.576384 CGATCAACTCCTTTCAAAGAGAGAG 59.424 44.000 17.66 10.26 33.09 3.20
695 1213 5.011125 ACGATCAACTCCTTTCAAAGAGAGA 59.989 40.000 17.66 9.29 33.09 3.10
696 1214 5.119898 CACGATCAACTCCTTTCAAAGAGAG 59.880 44.000 11.89 11.89 34.21 3.20
697 1215 4.991056 CACGATCAACTCCTTTCAAAGAGA 59.009 41.667 0.00 0.00 0.00 3.10
698 1216 4.752101 ACACGATCAACTCCTTTCAAAGAG 59.248 41.667 0.00 0.00 0.00 2.85
699 1217 4.703897 ACACGATCAACTCCTTTCAAAGA 58.296 39.130 0.00 0.00 0.00 2.52
700 1218 5.207768 CAACACGATCAACTCCTTTCAAAG 58.792 41.667 0.00 0.00 0.00 2.77
701 1219 4.638421 ACAACACGATCAACTCCTTTCAAA 59.362 37.500 0.00 0.00 0.00 2.69
702 1220 4.196193 ACAACACGATCAACTCCTTTCAA 58.804 39.130 0.00 0.00 0.00 2.69
703 1221 3.804036 ACAACACGATCAACTCCTTTCA 58.196 40.909 0.00 0.00 0.00 2.69
704 1222 4.813296 AACAACACGATCAACTCCTTTC 57.187 40.909 0.00 0.00 0.00 2.62
705 1223 6.877611 AATAACAACACGATCAACTCCTTT 57.122 33.333 0.00 0.00 0.00 3.11
706 1224 6.594159 CCTAATAACAACACGATCAACTCCTT 59.406 38.462 0.00 0.00 0.00 3.36
707 1225 6.106673 CCTAATAACAACACGATCAACTCCT 58.893 40.000 0.00 0.00 0.00 3.69
708 1226 5.220605 GCCTAATAACAACACGATCAACTCC 60.221 44.000 0.00 0.00 0.00 3.85
709 1227 5.220605 GGCCTAATAACAACACGATCAACTC 60.221 44.000 0.00 0.00 0.00 3.01
710 1228 4.634443 GGCCTAATAACAACACGATCAACT 59.366 41.667 0.00 0.00 0.00 3.16
713 1231 3.055021 TGGGCCTAATAACAACACGATCA 60.055 43.478 4.53 0.00 0.00 2.92
715 1233 3.275999 GTGGGCCTAATAACAACACGAT 58.724 45.455 4.53 0.00 0.00 3.73
717 1235 1.741145 GGTGGGCCTAATAACAACACG 59.259 52.381 4.53 0.00 0.00 4.49
755 2281 1.686052 GGAGCCTTCTGATGAGATCGT 59.314 52.381 0.00 0.00 0.00 3.73
860 2386 0.317519 AACGGCTACTTTTTGTGCGC 60.318 50.000 0.00 0.00 0.00 6.09
892 2419 4.271291 GCTTGTTTATGGGTCGAGAGATTC 59.729 45.833 0.00 0.00 45.19 2.52
960 2523 2.595172 TTTTCGGGGGTGGTTCGC 60.595 61.111 0.00 0.00 0.00 4.70
1074 2646 1.269831 CGATCTCGACCATTCCCCTTC 60.270 57.143 0.00 0.00 43.02 3.46
1227 2799 3.499918 ACCGCAGAGAGTCAAAATCAAAG 59.500 43.478 0.00 0.00 0.00 2.77
1228 2800 3.250762 CACCGCAGAGAGTCAAAATCAAA 59.749 43.478 0.00 0.00 0.00 2.69
1229 2801 2.807967 CACCGCAGAGAGTCAAAATCAA 59.192 45.455 0.00 0.00 0.00 2.57
1230 2802 2.416747 CACCGCAGAGAGTCAAAATCA 58.583 47.619 0.00 0.00 0.00 2.57
1231 2803 1.129437 GCACCGCAGAGAGTCAAAATC 59.871 52.381 0.00 0.00 0.00 2.17
1232 2804 1.160137 GCACCGCAGAGAGTCAAAAT 58.840 50.000 0.00 0.00 0.00 1.82
1446 3024 1.002900 CAAACCACAACGAACGCAGAT 60.003 47.619 0.00 0.00 0.00 2.90
1447 3025 0.375454 CAAACCACAACGAACGCAGA 59.625 50.000 0.00 0.00 0.00 4.26
1460 3043 3.320610 TTCCAAGTTCCATCCAAACCA 57.679 42.857 0.00 0.00 0.00 3.67
1464 3047 3.509575 CCGATTTTCCAAGTTCCATCCAA 59.490 43.478 0.00 0.00 0.00 3.53
1470 3053 3.561503 CGTTTCCGATTTTCCAAGTTCC 58.438 45.455 0.00 0.00 35.63 3.62
1478 3061 5.399013 ACATCAATTCCGTTTCCGATTTTC 58.601 37.500 0.00 0.00 35.63 2.29
1855 3448 6.461816 CAAAGTCGTAAAGAACAGATCGATG 58.538 40.000 0.54 0.00 0.00 3.84
1883 3479 1.115467 ATCTCCTGGAGCTTACACCG 58.885 55.000 19.08 0.00 0.00 4.94
1945 3550 1.341209 AGACTCGATGATAATGGCGCA 59.659 47.619 10.83 0.00 0.00 6.09
1946 3551 1.723542 CAGACTCGATGATAATGGCGC 59.276 52.381 0.00 0.00 0.00 6.53
1984 3589 5.799827 AAGAAGAGATGTATAGACTGGCC 57.200 43.478 0.00 0.00 0.00 5.36
1986 3591 8.684386 TGAGTAAGAAGAGATGTATAGACTGG 57.316 38.462 0.00 0.00 0.00 4.00
2018 3623 4.753610 TCATTCTCTTGTGCTCTTGAAGTG 59.246 41.667 0.00 0.00 0.00 3.16
2019 3624 4.965814 TCATTCTCTTGTGCTCTTGAAGT 58.034 39.130 0.00 0.00 0.00 3.01
2020 3625 6.497785 AATCATTCTCTTGTGCTCTTGAAG 57.502 37.500 0.00 0.00 0.00 3.02
2022 3627 8.571461 AATAAATCATTCTCTTGTGCTCTTGA 57.429 30.769 0.00 0.00 0.00 3.02
2023 3628 9.635520 AAAATAAATCATTCTCTTGTGCTCTTG 57.364 29.630 0.00 0.00 0.00 3.02
2072 3680 5.075858 TCAATCAATTGGTGAGGCAATTC 57.924 39.130 5.42 0.00 40.43 2.17
2083 3694 8.991243 TCTTTTCTGCTTAATCAATCAATTGG 57.009 30.769 5.42 0.00 38.30 3.16
2140 3751 9.838975 TTATGCTTTGTATGTGAACTATTTGTG 57.161 29.630 0.00 0.00 0.00 3.33
2150 3761 7.831690 TCATAGGGTTTTATGCTTTGTATGTGA 59.168 33.333 0.00 0.00 32.31 3.58
2153 3764 7.285401 AGGTCATAGGGTTTTATGCTTTGTATG 59.715 37.037 0.00 0.00 32.31 2.39
2155 3766 6.727394 AGGTCATAGGGTTTTATGCTTTGTA 58.273 36.000 0.00 0.00 32.31 2.41
2187 3809 0.247736 AGCATTCAGAGTGTCGGGTC 59.752 55.000 0.00 0.00 0.00 4.46
2206 3832 0.178975 GGTGGGTTCATGGTTGTGGA 60.179 55.000 0.00 0.00 0.00 4.02
2255 3881 6.535150 TGTTGTCTTCAGTCTAAGTGTTCTTG 59.465 38.462 0.00 0.00 35.36 3.02
2258 3884 6.199342 GTCTGTTGTCTTCAGTCTAAGTGTTC 59.801 42.308 0.00 0.00 34.86 3.18
2264 3890 4.404394 TGGTGTCTGTTGTCTTCAGTCTAA 59.596 41.667 0.00 0.00 34.86 2.10
2265 3891 3.958147 TGGTGTCTGTTGTCTTCAGTCTA 59.042 43.478 0.00 0.00 34.86 2.59
2280 3906 4.536090 TCTTCTATGGATTTGGTGGTGTCT 59.464 41.667 0.00 0.00 0.00 3.41
2314 3944 1.832883 TGTCCGCAGCCATTGTTATT 58.167 45.000 0.00 0.00 0.00 1.40
2320 3950 0.968405 AATGTTTGTCCGCAGCCATT 59.032 45.000 0.00 0.00 0.00 3.16
2329 3959 3.874392 CCATGAGGGAAATGTTTGTCC 57.126 47.619 0.00 0.00 40.01 4.02
2763 4406 1.130955 CCATGTGAAGTGTTTTGCGC 58.869 50.000 0.00 0.00 0.00 6.09
2765 4408 3.435105 TGTCCATGTGAAGTGTTTTGC 57.565 42.857 0.00 0.00 0.00 3.68
2773 4419 3.128242 GCTTCCAAGATGTCCATGTGAAG 59.872 47.826 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.