Multiple sequence alignment - TraesCS2B01G440200

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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 TraesCS2B01G440200 chr2B 100.000 9190 0 0 1 9190 632173837 632164648 0.000000e+00 16971.0
1 TraesCS2B01G440200 chr2B 97.484 2027 35 8 6664 8679 632012099 632010078 0.000000e+00 3446.0
2 TraesCS2B01G440200 chr2B 95.789 190 8 0 9001 9190 632159900 632159711 3.220000e-79 307.0
3 TraesCS2B01G440200 chr2B 92.147 191 14 1 9001 9190 14539323 14539513 1.520000e-67 268.0
4 TraesCS2B01G440200 chr2B 98.261 115 2 0 6545 6659 632018586 632018472 1.560000e-47 202.0
5 TraesCS2B01G440200 chr2D 95.311 8807 303 44 1 8777 532185438 532176712 0.000000e+00 13874.0
6 TraesCS2B01G440200 chr2D 96.018 226 6 2 8776 9001 532176555 532176333 1.890000e-96 364.0
7 TraesCS2B01G440200 chr2D 88.112 143 12 3 8807 8949 532154706 532154569 2.050000e-36 165.0
8 TraesCS2B01G440200 chr2A 94.736 8359 344 48 562 8878 676722934 676714630 0.000000e+00 12911.0
9 TraesCS2B01G440200 chr2A 89.981 539 32 13 1 521 676723465 676722931 0.000000e+00 676.0
10 TraesCS2B01G440200 chr2A 90.217 92 2 4 8916 9000 676714633 676714542 7.540000e-21 113.0
11 TraesCS2B01G440200 chr2A 97.436 39 1 0 8877 8915 676452792 676452754 5.960000e-07 67.6
12 TraesCS2B01G440200 chr5B 89.070 796 61 13 5370 6154 530694598 530693818 0.000000e+00 965.0
13 TraesCS2B01G440200 chr5B 91.398 186 13 2 6260 6443 530693825 530693641 1.530000e-62 252.0
14 TraesCS2B01G440200 chr7B 95.767 189 8 0 9002 9190 697483658 697483470 1.160000e-78 305.0
15 TraesCS2B01G440200 chr7B 93.750 192 9 3 9001 9190 697482858 697482668 1.510000e-72 285.0
16 TraesCS2B01G440200 chr3B 93.717 191 11 1 9001 9190 760335558 760335368 1.510000e-72 285.0
17 TraesCS2B01G440200 chr3B 93.684 190 11 1 9002 9190 760340500 760340311 5.430000e-72 283.0
18 TraesCS2B01G440200 chr3B 91.667 192 13 3 9001 9190 751840154 751840344 7.080000e-66 263.0
19 TraesCS2B01G440200 chr5A 91.099 191 15 2 9001 9190 114933355 114933544 3.290000e-64 257.0
20 TraesCS2B01G440200 chr1A 89.175 194 10 9 9002 9190 563247611 563247798 2.000000e-56 231.0
21 TraesCS2B01G440200 chr4D 97.368 38 1 0 523 560 502536238 502536201 2.140000e-06 65.8


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 TraesCS2B01G440200 chr2B 632164648 632173837 9189 True 16971.000000 16971 100.000000 1 9190 1 chr2B.!!$R4 9189
1 TraesCS2B01G440200 chr2B 632010078 632012099 2021 True 3446.000000 3446 97.484000 6664 8679 1 chr2B.!!$R1 2015
2 TraesCS2B01G440200 chr2D 532176333 532185438 9105 True 7119.000000 13874 95.664500 1 9001 2 chr2D.!!$R2 9000
3 TraesCS2B01G440200 chr2A 676714542 676723465 8923 True 4566.666667 12911 91.644667 1 9000 3 chr2A.!!$R2 8999
4 TraesCS2B01G440200 chr5B 530693641 530694598 957 True 608.500000 965 90.234000 5370 6443 2 chr5B.!!$R1 1073
5 TraesCS2B01G440200 chr7B 697482668 697483658 990 True 295.000000 305 94.758500 9001 9190 2 chr7B.!!$R1 189

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
473 483 0.174389 CAGTGTGACCTCGGATCAGG 59.826 60.000 0.00 0.00 39.80 3.86 F
648 674 0.412244 TGACTGGTAGGTGGTAGCCT 59.588 55.000 0.00 0.00 42.43 4.58 F
650 676 0.617820 ACTGGTAGGTGGTAGCCTGG 60.618 60.000 0.00 0.00 39.60 4.45 F
1391 1429 0.835543 TGAAAATGGGGGCCAAGTGG 60.836 55.000 4.39 0.00 36.95 4.00 F
2130 2172 1.303799 AAGAGCTGGCTGATGCAACG 61.304 55.000 0.00 0.00 41.91 4.10 F
2684 2726 3.015327 AGATGAAACTGGAAGAGCATGC 58.985 45.455 10.51 10.51 37.43 4.06 F
3895 3937 1.351350 AGTTGGAGTCCCAGTTAAGCC 59.649 52.381 6.74 0.00 44.60 4.35 F
4535 4577 0.535780 CAGCTTGAGCACAGTGGGAA 60.536 55.000 0.00 0.00 45.16 3.97 F
4639 4681 0.755327 GCAAGTGGGGGACAACTTGT 60.755 55.000 14.46 0.00 38.90 3.16 F
6078 6131 0.250295 CAGAAAAGCAGGGGTCGTCA 60.250 55.000 0.00 0.00 0.00 4.35 F
6763 6818 0.464452 AGGCTGCTTACCGTACCATC 59.536 55.000 0.00 0.00 0.00 3.51 F
8065 8132 3.768757 GACATATCTCAGGCTCCTAGCAT 59.231 47.826 0.78 0.00 44.75 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1860 1902 0.804989 CCAGCTCAAAACCATCGGAC 59.195 55.000 0.00 0.0 0.00 4.79 R
2274 2316 1.228245 TTCTGCAGCCCTTTTCGCT 60.228 52.632 9.47 0.0 36.91 4.93 R
2684 2726 5.734855 TTCACTTGTCTCTTTTTCCTTCG 57.265 39.130 0.00 0.0 0.00 3.79 R
2730 2772 3.194329 CAGACTGCAGGTTGAGTATCTGA 59.806 47.826 19.93 0.0 34.92 3.27 R
3865 3907 0.953727 GACTCCAACTGCATGCACAA 59.046 50.000 18.46 0.0 0.00 3.33 R
4269 4311 3.126073 CTCTTTTTGGTTTGCTTCTGCC 58.874 45.455 0.00 0.0 38.71 4.85 R
4873 4915 0.542467 TGATTTGCTGCACCCATGGT 60.542 50.000 11.73 0.0 35.62 3.55 R
5352 5394 0.962855 GGAGCTCCAAGCCCTTTGAC 60.963 60.000 28.43 0.0 43.77 3.18 R
6610 6665 1.632409 ACTTGCATGGTCTGGATCTGT 59.368 47.619 4.44 0.0 0.00 3.41 R
7919 7985 4.100035 TGCTGATAACTACTGATCAGGGTG 59.900 45.833 26.08 16.8 46.13 4.61 R
8145 8212 0.320683 CCGATGACCACTGACAGCAA 60.321 55.000 1.25 0.0 0.00 3.91 R
8941 9181 1.062047 CATGCATGCTGTGTCGCTC 59.938 57.895 20.33 0.0 0.00 5.03 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
117 119 1.004560 CTGTCCGCCTCTGCTTTCA 60.005 57.895 0.00 0.00 34.43 2.69
123 125 1.678728 CCGCCTCTGCTTTCACCATTA 60.679 52.381 0.00 0.00 34.43 1.90
149 151 4.830765 TCCCGCCCGATTTCGCTG 62.831 66.667 0.00 0.00 38.18 5.18
155 163 2.187946 CCGATTTCGCTGGGAGCT 59.812 61.111 0.00 0.00 39.60 4.09
335 345 1.152819 CGATCGTGGTAGGGAGGGA 60.153 63.158 7.03 0.00 0.00 4.20
336 346 1.173444 CGATCGTGGTAGGGAGGGAG 61.173 65.000 7.03 0.00 0.00 4.30
337 347 0.828343 GATCGTGGTAGGGAGGGAGG 60.828 65.000 0.00 0.00 0.00 4.30
338 348 2.313749 ATCGTGGTAGGGAGGGAGGG 62.314 65.000 0.00 0.00 0.00 4.30
387 397 1.410882 TGTCTTTTGCCTTTTTCCGGG 59.589 47.619 0.00 0.00 0.00 5.73
420 430 4.213482 GGACTATTTGGTGGATATTGCGTC 59.787 45.833 0.00 0.00 0.00 5.19
462 472 5.499139 TGTTCTCCAAAATTCAGTGTGAC 57.501 39.130 0.00 0.00 0.00 3.67
473 483 0.174389 CAGTGTGACCTCGGATCAGG 59.826 60.000 0.00 0.00 39.80 3.86
533 552 4.109675 CGATCCAACCCCGGCCTT 62.110 66.667 0.00 0.00 0.00 4.35
543 562 2.182537 CCGGCCTTTGCATCAAGC 59.817 61.111 0.00 0.00 45.96 4.01
603 622 5.357878 GCAACATAATTCTGGTCCTGATTGA 59.642 40.000 10.20 0.00 0.00 2.57
626 648 1.128200 TGTGTGGAGTTGGTACTGCT 58.872 50.000 0.00 0.00 42.66 4.24
644 670 2.706723 TGCTTTTGACTGGTAGGTGGTA 59.293 45.455 0.00 0.00 0.00 3.25
645 671 3.244422 TGCTTTTGACTGGTAGGTGGTAG 60.244 47.826 0.00 0.00 0.00 3.18
646 672 3.335579 CTTTTGACTGGTAGGTGGTAGC 58.664 50.000 0.00 0.00 0.00 3.58
647 673 1.272807 TTGACTGGTAGGTGGTAGCC 58.727 55.000 0.00 0.00 0.00 3.93
648 674 0.412244 TGACTGGTAGGTGGTAGCCT 59.588 55.000 0.00 0.00 42.43 4.58
649 675 0.824759 GACTGGTAGGTGGTAGCCTG 59.175 60.000 0.00 0.00 39.60 4.85
650 676 0.617820 ACTGGTAGGTGGTAGCCTGG 60.618 60.000 0.00 0.00 39.60 4.45
651 677 0.617820 CTGGTAGGTGGTAGCCTGGT 60.618 60.000 0.00 0.00 39.60 4.00
670 696 5.721960 CCTGGTAGGCTATGTATACAGGAAT 59.278 44.000 11.91 0.00 0.00 3.01
760 786 1.448717 GAGCTGTCGCCTTTCCTCC 60.449 63.158 0.00 0.00 36.60 4.30
915 941 8.680039 TCATCATTACACATTATCTTGATGCA 57.320 30.769 0.00 0.00 39.05 3.96
918 944 7.364970 TCATTACACATTATCTTGATGCATGC 58.635 34.615 11.82 11.82 0.00 4.06
930 956 4.823790 TGATGCATGCATACTCATTCAC 57.176 40.909 32.27 16.86 36.70 3.18
968 996 6.403866 TGCCAGTATTTCTTGTTGTGAATT 57.596 33.333 0.00 0.00 0.00 2.17
1011 1039 1.227497 GCCCGAGATGGAAGCAGAG 60.227 63.158 0.00 0.00 42.00 3.35
1029 1057 2.577059 CAGGCGGCGGAAGTAAGA 59.423 61.111 9.78 0.00 0.00 2.10
1041 1069 3.648739 GGAAGTAAGATCTGGGGAGACT 58.351 50.000 0.00 0.00 0.00 3.24
1069 1097 5.041940 GTCTTAAGTCGCCTGATACGATTT 58.958 41.667 1.63 0.00 42.26 2.17
1070 1098 5.173492 GTCTTAAGTCGCCTGATACGATTTC 59.827 44.000 1.63 0.00 42.26 2.17
1079 1107 4.738541 GCCTGATACGATTTCGGTAAGGAA 60.739 45.833 12.59 0.00 44.95 3.36
1086 1114 6.321848 ACGATTTCGGTAAGGAAAACATTT 57.678 33.333 4.84 0.00 44.95 2.32
1098 1133 4.084013 AGGAAAACATTTAAGTCGAGTGCG 60.084 41.667 0.00 0.00 39.35 5.34
1102 1137 2.729882 ACATTTAAGTCGAGTGCGTGTC 59.270 45.455 0.00 0.00 38.98 3.67
1103 1138 2.787601 TTTAAGTCGAGTGCGTGTCT 57.212 45.000 0.00 0.00 38.98 3.41
1133 1168 5.416639 TCCAGCGTACTTACAGAAATGAGTA 59.583 40.000 0.00 0.00 0.00 2.59
1201 1236 3.980775 CAGTTTTGTTATTTGGCGTCCAG 59.019 43.478 0.00 0.00 33.81 3.86
1221 1256 5.241506 TCCAGTACTTCTTGATGCCAAAAAG 59.758 40.000 0.00 0.00 36.63 2.27
1231 1266 6.538381 TCTTGATGCCAAAAAGGAAAAGAAAC 59.462 34.615 0.00 0.00 41.22 2.78
1281 1317 6.377146 GGTGGGTGACTGAAATATATGTTGTT 59.623 38.462 0.00 0.00 0.00 2.83
1391 1429 0.835543 TGAAAATGGGGGCCAAGTGG 60.836 55.000 4.39 0.00 36.95 4.00
1418 1456 8.992073 CCCCTTTCATAAAAAGAAACATTTGAG 58.008 33.333 0.00 0.00 32.09 3.02
1437 1475 4.093743 TGAGTATGTAGAAGCTTGGGTCA 58.906 43.478 2.10 0.00 0.00 4.02
1455 1493 2.297033 GTCAATGATAATTGGCGGGCAT 59.703 45.455 4.64 0.00 32.65 4.40
1544 1585 5.748402 TGATCAGCATAACTTTCAGACCAT 58.252 37.500 0.00 0.00 0.00 3.55
1546 1587 7.337938 TGATCAGCATAACTTTCAGACCATTA 58.662 34.615 0.00 0.00 0.00 1.90
1771 1813 4.978083 ATTCTGACAATGCCAATGTCTC 57.022 40.909 13.67 0.00 45.81 3.36
1845 1887 4.280677 GTGAAGGAAACACCCAATGATGAA 59.719 41.667 0.00 0.00 40.05 2.57
2130 2172 1.303799 AAGAGCTGGCTGATGCAACG 61.304 55.000 0.00 0.00 41.91 4.10
2196 2238 4.703575 CAGAGGATTCAAGAAATTGAGGCA 59.296 41.667 0.00 0.00 31.87 4.75
2684 2726 3.015327 AGATGAAACTGGAAGAGCATGC 58.985 45.455 10.51 10.51 37.43 4.06
2753 2795 3.056250 CAGATACTCAACCTGCAGTCTGT 60.056 47.826 13.81 0.00 0.00 3.41
2806 2848 4.742012 TCTCAAAGGGACTCTAGTTGACT 58.258 43.478 0.00 0.00 38.49 3.41
2909 2951 4.697352 AGAAGCATTGTCGCATAAAGAAGT 59.303 37.500 0.00 0.00 0.00 3.01
3282 3324 8.294954 AGATGAATGAATTGCAATCTTCTCTT 57.705 30.769 13.38 6.63 36.65 2.85
3401 3443 6.423905 CACGAAAGAAGTATTGAACTGGAGAA 59.576 38.462 0.00 0.00 38.88 2.87
3636 3678 3.709141 AGGAGAAAGAGCTTATGGACTCC 59.291 47.826 13.72 13.72 41.74 3.85
3865 3907 5.316167 TGCAACTGTCCAATAAGAATGACT 58.684 37.500 0.00 0.00 0.00 3.41
3895 3937 1.351350 AGTTGGAGTCCCAGTTAAGCC 59.649 52.381 6.74 0.00 44.60 4.35
3897 3939 1.440618 TGGAGTCCCAGTTAAGCCAA 58.559 50.000 6.74 0.00 37.58 4.52
4198 4240 3.511146 AGATGAATGCAATGGTTTCCGTT 59.489 39.130 0.00 0.00 32.22 4.44
4269 4311 3.063180 CAGCAAGTCTCGAGGCTTTATTG 59.937 47.826 29.02 21.35 33.60 1.90
4428 4470 1.342819 GCTGATCTAGAATCTGCCCGT 59.657 52.381 16.25 0.00 37.12 5.28
4467 4509 2.224499 GGAGAATGATCTTCAGGCCCTC 60.224 54.545 0.00 0.00 35.54 4.30
4535 4577 0.535780 CAGCTTGAGCACAGTGGGAA 60.536 55.000 0.00 0.00 45.16 3.97
4548 4590 1.348036 AGTGGGAAGGCACTAGAACAC 59.652 52.381 0.00 0.00 38.49 3.32
4626 4668 2.075338 GAGAAGAAGCTCCAGCAAGTG 58.925 52.381 0.48 0.00 45.16 3.16
4639 4681 0.755327 GCAAGTGGGGGACAACTTGT 60.755 55.000 14.46 0.00 38.90 3.16
4873 4915 2.125552 CATTGGCCGAGAGCACGA 60.126 61.111 0.00 0.00 46.50 4.35
5269 5311 4.084287 TGATGAGCTGCAGGAGAAATTTT 58.916 39.130 17.12 0.00 0.00 1.82
5314 5356 1.220206 GCTGCAGAGAAGCTGGCTA 59.780 57.895 20.43 0.00 45.03 3.93
5352 5394 7.864379 ACAATAAAACATTTGACAGAAGAGCAG 59.136 33.333 0.00 0.00 0.00 4.24
5874 5923 9.305925 GCCAATGAAGAAAATCATAAGGTTAAG 57.694 33.333 9.18 0.00 39.08 1.85
6078 6131 0.250295 CAGAAAAGCAGGGGTCGTCA 60.250 55.000 0.00 0.00 0.00 4.35
6308 6361 1.068472 AGAACTGACGAGCAAGTACCG 60.068 52.381 0.00 0.00 0.00 4.02
6331 6384 1.805869 CACACTGGAAGAGAAGCAGG 58.194 55.000 0.00 0.00 37.43 4.85
6535 6590 6.691255 AACTAATTTGGGTCCTACAGTACA 57.309 37.500 0.00 0.00 0.00 2.90
6561 6616 1.271762 TGTCGAGCTGTACAGTAGGGT 60.272 52.381 23.44 4.44 0.00 4.34
6566 6621 5.297776 GTCGAGCTGTACAGTAGGGTAATTA 59.702 44.000 23.44 0.00 0.00 1.40
6582 6637 5.752472 GGGTAATTAGTCCTACTTTCGAAGC 59.248 44.000 0.00 0.00 0.00 3.86
6763 6818 0.464452 AGGCTGCTTACCGTACCATC 59.536 55.000 0.00 0.00 0.00 3.51
7215 7274 4.194640 GCAAGAAGCTGAGATCCATTACA 58.805 43.478 0.00 0.00 41.15 2.41
7919 7985 7.684937 AAAGATGCTATGAAATATCCTGAGC 57.315 36.000 0.00 0.00 0.00 4.26
8065 8132 3.768757 GACATATCTCAGGCTCCTAGCAT 59.231 47.826 0.78 0.00 44.75 3.79
8287 8354 8.117956 TCCCATGAACCTAAACTACTACTCTAA 58.882 37.037 0.00 0.00 0.00 2.10
8310 8377 4.580167 ACTGAACAAAACATAGCTTGCTCA 59.420 37.500 0.00 0.00 0.00 4.26
8339 8406 2.253603 GATTGCAATTGAACGGACTGC 58.746 47.619 14.33 0.00 0.00 4.40
8569 8641 8.664211 AGGAAGTCCGTCAGAAATATTAATTC 57.336 34.615 0.00 0.00 42.08 2.17
8634 8716 7.621428 ATCACTCCAGTGTTTTTGATCTATG 57.379 36.000 6.61 0.00 45.76 2.23
8803 9043 0.232303 GTATCTGTAACCGCATGCGC 59.768 55.000 34.00 20.53 38.24 6.09
8863 9103 2.024176 GCCATATGATACGGGCGAAT 57.976 50.000 3.65 0.00 36.58 3.34
8881 9121 5.335191 GGCGAATTGGATCTGGTCATATTTC 60.335 44.000 0.00 0.00 0.00 2.17
8941 9181 3.195698 GAAAGCGCCCAGGCTACG 61.196 66.667 2.29 0.00 43.93 3.51
9001 9248 5.720202 GGAGAAAGTCCAAAACAAAGTTGT 58.280 37.500 0.00 0.00 46.10 3.32
9002 9249 5.576774 GGAGAAAGTCCAAAACAAAGTTGTG 59.423 40.000 0.00 0.00 46.10 3.33
9003 9250 6.096673 AGAAAGTCCAAAACAAAGTTGTGT 57.903 33.333 0.00 0.00 41.31 3.72
9004 9251 6.521162 AGAAAGTCCAAAACAAAGTTGTGTT 58.479 32.000 0.00 0.00 43.58 3.32
9028 9275 9.694137 GTTGGAATAGATGTATAGGAGTTGTAC 57.306 37.037 0.00 0.00 0.00 2.90
9085 9332 7.898636 TCTTCTCTATCCCTTCTTCTCTTTCTT 59.101 37.037 0.00 0.00 0.00 2.52
9119 9366 1.454111 CCGTCCTGGTCGATCTCCT 60.454 63.158 14.81 0.00 0.00 3.69
9183 9430 3.712016 TGCCCAATATATACATGCGGT 57.288 42.857 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 68 2.956964 CGGCAGAATCGGAGCGAC 60.957 66.667 0.00 0.00 39.18 5.19
150 152 4.173924 GAGCAGAGGGGCAGCTCC 62.174 72.222 1.54 1.54 46.88 4.70
260 268 1.572085 CCGCAGCACCTCAAAGTCAG 61.572 60.000 0.00 0.00 0.00 3.51
326 336 2.577757 AACCAGCCCTCCCTCCCTA 61.578 63.158 0.00 0.00 0.00 3.53
338 348 4.947147 TCGTGCCCACCAACCAGC 62.947 66.667 0.00 0.00 0.00 4.85
387 397 0.451783 CAAATAGTCCAGCAACCGGC 59.548 55.000 0.00 0.00 45.30 6.13
388 398 1.094785 CCAAATAGTCCAGCAACCGG 58.905 55.000 0.00 0.00 0.00 5.28
462 472 1.204146 TTTTCCTCCCTGATCCGAGG 58.796 55.000 12.33 12.33 46.07 4.63
486 505 7.957484 CGATCAACAAGTAGTCGATTGAATTTT 59.043 33.333 3.59 0.00 33.29 1.82
488 507 6.811665 TCGATCAACAAGTAGTCGATTGAATT 59.188 34.615 3.59 0.00 36.52 2.17
490 509 5.705902 TCGATCAACAAGTAGTCGATTGAA 58.294 37.500 3.59 0.00 36.52 2.69
543 562 0.732538 TCGTATGGCTATGCGCATCG 60.733 55.000 29.11 22.46 41.38 3.84
552 571 2.492088 CAAGGATCCGATCGTATGGCTA 59.508 50.000 15.09 0.00 0.00 3.93
603 622 2.124411 AGTACCAACTCCACACAAGGT 58.876 47.619 0.00 0.00 0.00 3.50
626 648 2.039348 GGCTACCACCTACCAGTCAAAA 59.961 50.000 0.00 0.00 0.00 2.44
646 672 4.673968 TCCTGTATACATAGCCTACCAGG 58.326 47.826 5.91 0.13 38.80 4.45
647 673 6.859112 ATTCCTGTATACATAGCCTACCAG 57.141 41.667 5.91 0.00 0.00 4.00
648 674 8.174757 TCTTATTCCTGTATACATAGCCTACCA 58.825 37.037 5.91 0.00 0.00 3.25
649 675 8.591114 TCTTATTCCTGTATACATAGCCTACC 57.409 38.462 5.91 0.00 0.00 3.18
760 786 4.438880 CCACTTCACTACAGACTGGATACG 60.439 50.000 7.51 0.00 42.51 3.06
915 941 4.696455 TCACATCGTGAATGAGTATGCAT 58.304 39.130 3.79 3.79 39.78 3.96
930 956 3.461061 ACTGGCATCAATACTCACATCG 58.539 45.455 0.00 0.00 0.00 3.84
968 996 5.805486 CACTAGCTTAGTATTCGTTTCTGCA 59.195 40.000 0.00 0.00 37.23 4.41
1011 1039 2.925162 ATCTTACTTCCGCCGCCTGC 62.925 60.000 0.00 0.00 0.00 4.85
1041 1069 2.799017 TCAGGCGACTTAAGACTGGTA 58.201 47.619 10.09 0.00 40.21 3.25
1069 1097 6.222389 TCGACTTAAATGTTTTCCTTACCGA 58.778 36.000 0.00 0.00 0.00 4.69
1070 1098 6.146673 ACTCGACTTAAATGTTTTCCTTACCG 59.853 38.462 0.00 0.00 0.00 4.02
1079 1107 3.558418 ACACGCACTCGACTTAAATGTTT 59.442 39.130 0.00 0.00 39.41 2.83
1086 1114 1.197036 CTCAGACACGCACTCGACTTA 59.803 52.381 0.00 0.00 39.41 2.24
1098 1133 2.164624 AGTACGCTGGAATCTCAGACAC 59.835 50.000 3.47 0.00 36.93 3.67
1102 1137 4.096532 TCTGTAAGTACGCTGGAATCTCAG 59.903 45.833 0.00 0.00 34.85 3.35
1103 1138 4.014406 TCTGTAAGTACGCTGGAATCTCA 58.986 43.478 0.00 0.00 33.76 3.27
1133 1168 8.340618 AGAAAGTAACAAGATATGCACACATT 57.659 30.769 0.00 0.00 37.74 2.71
1201 1236 5.705609 TCCTTTTTGGCATCAAGAAGTAC 57.294 39.130 7.56 0.00 41.05 2.73
1231 1266 4.637483 AACATGTTCAGAAACCACACTG 57.363 40.909 4.92 0.00 34.28 3.66
1391 1429 7.443879 TCAAATGTTTCTTTTTATGAAAGGGGC 59.556 33.333 4.26 0.00 34.58 5.80
1418 1456 5.428253 TCATTGACCCAAGCTTCTACATAC 58.572 41.667 0.00 0.00 0.00 2.39
1428 1466 3.721035 GCCAATTATCATTGACCCAAGC 58.279 45.455 1.02 0.00 42.35 4.01
1437 1475 2.596346 TCATGCCCGCCAATTATCATT 58.404 42.857 0.00 0.00 0.00 2.57
1845 1887 0.833287 CGGACCCTGTTCCATCATCT 59.167 55.000 0.00 0.00 35.04 2.90
1860 1902 0.804989 CCAGCTCAAAACCATCGGAC 59.195 55.000 0.00 0.00 0.00 4.79
2065 2107 5.698089 TCTGTGCTTCTTGTAGAGAATTGTG 59.302 40.000 0.00 0.00 43.23 3.33
2130 2172 1.703438 CCAGCTCGCTCAGTGATTGC 61.703 60.000 0.00 0.00 0.00 3.56
2196 2238 6.760770 GCTTATCAGCTGATGAACTTAACTCT 59.239 38.462 34.48 10.82 43.51 3.24
2274 2316 1.228245 TTCTGCAGCCCTTTTCGCT 60.228 52.632 9.47 0.00 36.91 4.93
2684 2726 5.734855 TTCACTTGTCTCTTTTTCCTTCG 57.265 39.130 0.00 0.00 0.00 3.79
2730 2772 3.194329 CAGACTGCAGGTTGAGTATCTGA 59.806 47.826 19.93 0.00 34.92 3.27
2753 2795 5.879777 TGTTCATCCTTTAATTCATCGAGCA 59.120 36.000 0.00 0.00 0.00 4.26
2806 2848 8.465999 GTCTCTCTCTGATAGTTTTGATTCAGA 58.534 37.037 0.00 0.00 41.60 3.27
2883 2925 4.877823 TCTTTATGCGACAATGCTTCTGAT 59.122 37.500 0.00 0.00 35.36 2.90
2909 2951 9.434275 TGATAGATTTCAGATTTACCTCCAGTA 57.566 33.333 0.00 0.00 0.00 2.74
3282 3324 4.081142 TGAGTTTTAGATGCCGAGGAATCA 60.081 41.667 12.39 0.00 32.60 2.57
3401 3443 7.692460 TCAGACTTTGATGTATGAAGCAAAT 57.308 32.000 0.00 0.00 35.58 2.32
3636 3678 5.627499 TTTCTTCGGTGATTTGAATCAGG 57.373 39.130 6.66 3.20 45.38 3.86
3865 3907 0.953727 GACTCCAACTGCATGCACAA 59.046 50.000 18.46 0.00 0.00 3.33
3895 3937 3.824133 TGCTATGATCATCCCCAACTTG 58.176 45.455 12.53 0.00 0.00 3.16
3897 3939 4.524802 TTTGCTATGATCATCCCCAACT 57.475 40.909 12.53 0.00 0.00 3.16
4198 4240 5.445069 TCCAGAAAGTTCATCAACCTTCAA 58.555 37.500 0.00 0.00 35.97 2.69
4269 4311 3.126073 CTCTTTTTGGTTTGCTTCTGCC 58.874 45.455 0.00 0.00 38.71 4.85
4428 4470 3.913799 TCTCCACCTCTTCCATTTTACCA 59.086 43.478 0.00 0.00 0.00 3.25
4467 4509 3.305398 ACTGAGCTTTCTCTAACACCG 57.695 47.619 0.00 0.00 40.03 4.94
4548 4590 3.641437 TCAATTTTCTTGGAAGTGGCG 57.359 42.857 0.00 0.00 0.00 5.69
4863 4905 2.202797 CCCATGGTCGTGCTCTCG 60.203 66.667 11.73 0.00 0.00 4.04
4873 4915 0.542467 TGATTTGCTGCACCCATGGT 60.542 50.000 11.73 0.00 35.62 3.55
5012 5054 4.937620 GCACCTCAGTCAAATGTTCTATCA 59.062 41.667 0.00 0.00 0.00 2.15
5269 5311 3.068165 TCTTTCTCAGAACTCGCAGACAA 59.932 43.478 0.00 0.00 0.00 3.18
5352 5394 0.962855 GGAGCTCCAAGCCCTTTGAC 60.963 60.000 28.43 0.00 43.77 3.18
5805 5854 8.659527 TGCTCTTCATAATATCCCAACTCAATA 58.340 33.333 0.00 0.00 0.00 1.90
5874 5923 3.332761 TTGTGCACGACTTCATCAAAC 57.667 42.857 13.13 0.00 0.00 2.93
6055 6108 1.743996 GACCCCTGCTTTTCTGCTAG 58.256 55.000 0.00 0.00 0.00 3.42
6078 6131 4.462508 TCGCAATGAGTGAATCTCTTCT 57.537 40.909 0.00 0.00 43.13 2.85
6285 6338 1.772182 ACTTGCTCGTCAGTTCTTCG 58.228 50.000 0.00 0.00 0.00 3.79
6308 6361 1.803555 GCTTCTCTTCCAGTGTGCTTC 59.196 52.381 0.00 0.00 0.00 3.86
6366 6421 5.927281 ATTTGGCTATTGCTTCATCAAGT 57.073 34.783 0.00 0.00 39.59 3.16
6610 6665 1.632409 ACTTGCATGGTCTGGATCTGT 59.368 47.619 4.44 0.00 0.00 3.41
6763 6818 1.063469 CGCCAATTTACCTGGTTAGCG 59.937 52.381 3.84 3.59 36.24 4.26
7342 7402 6.440328 AGCAGGCTTCCAAATTTAAGGATTTA 59.560 34.615 0.00 0.00 33.10 1.40
7919 7985 4.100035 TGCTGATAACTACTGATCAGGGTG 59.900 45.833 26.08 16.80 46.13 4.61
8145 8212 0.320683 CCGATGACCACTGACAGCAA 60.321 55.000 1.25 0.00 0.00 3.91
8287 8354 4.580167 TGAGCAAGCTATGTTTTGTTCAGT 59.420 37.500 0.00 0.00 38.86 3.41
8310 8377 4.379652 GTTCAATTGCAATCCACCAAACT 58.620 39.130 13.38 0.00 0.00 2.66
8339 8406 1.349026 TGACTTCTCCCTGAAAGCCAG 59.651 52.381 0.00 0.00 42.55 4.85
8569 8641 3.486108 GCTTACACTCGACCATATGAACG 59.514 47.826 3.65 9.48 0.00 3.95
8634 8716 3.380320 GCCAACCAACAACCCAGATATAC 59.620 47.826 0.00 0.00 0.00 1.47
8803 9043 4.840911 CAGAATCTGCAAATACATCACCG 58.159 43.478 0.00 0.00 0.00 4.94
8863 9103 5.951148 TGCAAAGAAATATGACCAGATCCAA 59.049 36.000 0.00 0.00 0.00 3.53
8938 9178 1.805539 GCATGCTGTGTCGCTCGTA 60.806 57.895 11.37 0.00 0.00 3.43
8941 9181 1.062047 CATGCATGCTGTGTCGCTC 59.938 57.895 20.33 0.00 0.00 5.03
9001 9248 8.319057 ACAACTCCTATACATCTATTCCAACA 57.681 34.615 0.00 0.00 0.00 3.33
9002 9249 9.694137 GTACAACTCCTATACATCTATTCCAAC 57.306 37.037 0.00 0.00 0.00 3.77
9003 9250 9.429109 TGTACAACTCCTATACATCTATTCCAA 57.571 33.333 0.00 0.00 0.00 3.53
9004 9251 9.078990 CTGTACAACTCCTATACATCTATTCCA 57.921 37.037 0.00 0.00 0.00 3.53
9005 9252 8.524487 CCTGTACAACTCCTATACATCTATTCC 58.476 40.741 0.00 0.00 0.00 3.01
9052 9299 7.896496 AGAAGAAGGGATAGAGAAGAAGTACAA 59.104 37.037 0.00 0.00 0.00 2.41
9061 9308 9.722317 ATAAGAAAGAGAAGAAGGGATAGAGAA 57.278 33.333 0.00 0.00 0.00 2.87
9085 9332 2.684881 GGACGGTCGTTACAAGGAGATA 59.315 50.000 1.43 0.00 0.00 1.98
9128 9375 3.024547 CAAGTTACAGGGGAGATCGAGA 58.975 50.000 0.00 0.00 0.00 4.04
9136 9383 2.270858 TGGCATACAAGTTACAGGGGA 58.729 47.619 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.