Multiple sequence alignment - TraesCS2B01G113900

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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 TraesCS2B01G113900 chr2B 100.000 3645 0 0 1 3645 77170302 77173946 0.000000e+00 6732
1 TraesCS2B01G113900 chr2B 84.579 214 26 4 2479 2686 1678618 1678830 4.770000e-49 206
2 TraesCS2B01G113900 chr2A 91.925 3294 167 45 1 3245 51583552 51586795 0.000000e+00 4518
3 TraesCS2B01G113900 chr2A 94.634 410 16 2 3241 3645 51586874 51587282 6.640000e-177 630
4 TraesCS2B01G113900 chr2D 93.128 2372 98 25 1299 3645 49878723 49881054 0.000000e+00 3417
5 TraesCS2B01G113900 chr2D 90.787 1335 50 26 1 1302 49877349 49878643 0.000000e+00 1716
6 TraesCS2B01G113900 chr4D 92.412 369 28 0 1 369 312800692 312800324 8.960000e-146 527
7 TraesCS2B01G113900 chr4A 91.057 369 33 0 1 369 163818742 163819110 1.950000e-137 499
8 TraesCS2B01G113900 chr3B 88.108 370 41 1 1 370 578401432 578401798 1.550000e-118 436
9 TraesCS2B01G113900 chr3D 87.838 370 45 0 1 370 441147402 441147771 5.590000e-118 435
10 TraesCS2B01G113900 chr3A 87.838 370 45 0 1 370 581274024 581274393 5.590000e-118 435
11 TraesCS2B01G113900 chr1B 87.838 370 45 0 1 370 543498111 543497742 5.590000e-118 435
12 TraesCS2B01G113900 chr1A 87.838 370 45 0 1 370 499785368 499784999 5.590000e-118 435
13 TraesCS2B01G113900 chr4B 85.514 214 24 4 2479 2686 391595363 391595575 2.200000e-52 217
14 TraesCS2B01G113900 chr7B 85.047 214 25 4 2479 2686 654701732 654701520 1.030000e-50 211
15 TraesCS2B01G113900 chr7A 84.906 212 25 4 2479 2684 605163720 605163510 1.330000e-49 207
16 TraesCS2B01G113900 chr7A 84.038 213 27 3 2480 2686 694564538 694564749 7.980000e-47 198


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 TraesCS2B01G113900 chr2B 77170302 77173946 3644 False 6732.0 6732 100.0000 1 3645 1 chr2B.!!$F2 3644
1 TraesCS2B01G113900 chr2A 51583552 51587282 3730 False 2574.0 4518 93.2795 1 3645 2 chr2A.!!$F1 3644
2 TraesCS2B01G113900 chr2D 49877349 49881054 3705 False 2566.5 3417 91.9575 1 3645 2 chr2D.!!$F1 3644

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
380 381 0.322456 CCAAATGAGCTCCGACCCAA 60.322 55.0 12.15 0.00 0.00 4.12 F
841 852 0.537143 CAGCTGGGTAGGTTGCAACA 60.537 55.0 29.55 8.78 30.85 3.33 F
1323 1436 0.673644 AACCAGGACCGAAATCAGCG 60.674 55.0 0.00 0.00 0.00 5.18 F
1640 1774 1.032014 TGCAACACTTTCAGCCCTTC 58.968 50.0 0.00 0.00 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1511 1624 0.109597 CGCCTCAAACAGTTGGATGC 60.110 55.0 7.69 7.69 35.29 3.91 R
2257 2398 0.685131 TCGCCTTGATCGGGTCCTTA 60.685 55.0 6.44 0.00 0.00 2.69 R
2586 2730 1.007336 CACGCCGACACTGTCCTTAC 61.007 60.0 3.50 0.00 0.00 2.34 R
2673 2817 1.157870 AGGTTTCAGACACCAACGCG 61.158 55.0 3.53 3.53 36.67 6.01 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
89 90 5.055144 CAGGACATGATCAATGAAGTCGAT 58.945 41.667 0.00 0.00 38.72 3.59
242 243 4.853050 GCTGCTGAGCTCCGCCAT 62.853 66.667 24.95 0.00 42.52 4.40
260 261 0.895530 ATGTCATGACGAACCTCGGT 59.104 50.000 20.54 0.00 45.59 4.69
371 372 2.029623 GTCATGATGGCCAAATGAGCT 58.970 47.619 26.67 3.60 31.21 4.09
376 377 0.749454 ATGGCCAAATGAGCTCCGAC 60.749 55.000 10.96 0.00 0.00 4.79
378 379 2.115291 GCCAAATGAGCTCCGACCC 61.115 63.158 12.15 0.00 0.00 4.46
379 380 1.299648 CCAAATGAGCTCCGACCCA 59.700 57.895 12.15 0.00 0.00 4.51
380 381 0.322456 CCAAATGAGCTCCGACCCAA 60.322 55.000 12.15 0.00 0.00 4.12
381 382 1.533625 CAAATGAGCTCCGACCCAAA 58.466 50.000 12.15 0.00 0.00 3.28
388 389 1.815421 CTCCGACCCAAATGCTCCG 60.815 63.158 0.00 0.00 0.00 4.63
590 591 4.012374 CTGGTGTATCCTGATTGCTGTTT 58.988 43.478 0.00 0.00 37.33 2.83
666 668 1.270947 TGGAAAGCCGGTGTTTCGTAT 60.271 47.619 19.21 0.00 35.16 3.06
710 712 6.741992 TTTACAGATGTTATCCTGTGCTTG 57.258 37.500 0.00 0.00 42.88 4.01
714 725 5.536161 ACAGATGTTATCCTGTGCTTGTTTT 59.464 36.000 0.00 0.00 41.59 2.43
717 728 2.979813 GTTATCCTGTGCTTGTTTTGCG 59.020 45.455 0.00 0.00 0.00 4.85
741 752 5.530171 GTGTGAATGGCAGATGAAGATACAT 59.470 40.000 0.00 0.00 0.00 2.29
744 755 7.774625 TGTGAATGGCAGATGAAGATACATTTA 59.225 33.333 0.00 0.00 0.00 1.40
745 756 8.790718 GTGAATGGCAGATGAAGATACATTTAT 58.209 33.333 0.00 0.00 0.00 1.40
795 806 9.767684 GAAATTTGAAATTTAAATTTAGCCGGG 57.232 29.630 22.82 0.00 43.76 5.73
801 812 6.451064 AATTTAAATTTAGCCGGGACAGAG 57.549 37.500 7.64 0.00 0.00 3.35
823 834 5.500234 AGAAGTATCAGGCTTAAATGTGCA 58.500 37.500 0.00 0.00 0.00 4.57
841 852 0.537143 CAGCTGGGTAGGTTGCAACA 60.537 55.000 29.55 8.78 30.85 3.33
847 858 3.034635 TGGGTAGGTTGCAACAAACAAT 58.965 40.909 29.55 11.04 0.00 2.71
862 873 6.594788 ACAAACAATTTGCTGGATGATAGT 57.405 33.333 1.23 0.00 44.39 2.12
887 898 4.655647 CAGCCTGTGCCTGTGCCT 62.656 66.667 0.00 0.00 38.69 4.75
888 899 4.655647 AGCCTGTGCCTGTGCCTG 62.656 66.667 0.00 0.00 38.69 4.85
889 900 4.962836 GCCTGTGCCTGTGCCTGT 62.963 66.667 0.00 0.00 36.33 4.00
890 901 2.981909 CCTGTGCCTGTGCCTGTG 60.982 66.667 0.00 0.00 36.33 3.66
891 902 2.203252 CTGTGCCTGTGCCTGTGT 60.203 61.111 0.00 0.00 36.33 3.72
929 942 1.412453 TACCACCGTGCTTGGTCCTT 61.412 55.000 0.00 0.00 44.54 3.36
945 958 3.195610 GGTCCTTTTAAGGCCTGGAATTG 59.804 47.826 5.69 0.78 46.06 2.32
984 997 1.160989 GGAACACACACACACACACA 58.839 50.000 0.00 0.00 0.00 3.72
985 998 1.135803 GGAACACACACACACACACAC 60.136 52.381 0.00 0.00 0.00 3.82
986 999 1.533299 GAACACACACACACACACACA 59.467 47.619 0.00 0.00 0.00 3.72
987 1000 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
988 1001 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
989 1002 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
990 1003 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
991 1004 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
992 1005 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
993 1006 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
994 1007 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
995 1008 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
996 1009 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
997 1010 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
998 1011 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
999 1012 1.265365 CACACACACACACACACACAA 59.735 47.619 0.00 0.00 0.00 3.33
1083 1096 2.678836 CCTGAAGAAGCAGATCAGCAAG 59.321 50.000 13.03 0.42 39.36 4.01
1136 1150 2.295885 GGTTCTTCCCTCGACTCGATA 58.704 52.381 0.62 0.00 34.61 2.92
1137 1151 2.885894 GGTTCTTCCCTCGACTCGATAT 59.114 50.000 0.62 0.00 34.61 1.63
1138 1152 3.058085 GGTTCTTCCCTCGACTCGATATC 60.058 52.174 0.62 0.00 34.61 1.63
1143 1157 4.022413 TCCCTCGACTCGATATCAGATT 57.978 45.455 0.62 0.00 34.61 2.40
1145 1159 3.127895 CCCTCGACTCGATATCAGATTCC 59.872 52.174 0.62 0.00 34.61 3.01
1146 1160 3.753797 CCTCGACTCGATATCAGATTCCA 59.246 47.826 0.62 0.00 34.61 3.53
1149 1163 5.944013 TCGACTCGATATCAGATTCCATTC 58.056 41.667 3.12 0.00 0.00 2.67
1150 1164 5.098893 CGACTCGATATCAGATTCCATTCC 58.901 45.833 3.12 0.00 0.00 3.01
1151 1165 5.065704 ACTCGATATCAGATTCCATTCCG 57.934 43.478 3.12 0.00 0.00 4.30
1152 1166 4.524714 ACTCGATATCAGATTCCATTCCGT 59.475 41.667 3.12 0.00 0.00 4.69
1154 1168 4.767409 TCGATATCAGATTCCATTCCGTCT 59.233 41.667 3.12 0.00 0.00 4.18
1159 1190 2.611292 CAGATTCCATTCCGTCTTCTGC 59.389 50.000 0.00 0.00 0.00 4.26
1164 1195 1.135575 CCATTCCGTCTTCTGCTTTGC 60.136 52.381 0.00 0.00 0.00 3.68
1167 1198 0.681733 TCCGTCTTCTGCTTTGCTCT 59.318 50.000 0.00 0.00 0.00 4.09
1177 1208 3.313526 TCTGCTTTGCTCTCAAGTTCAAC 59.686 43.478 0.00 0.00 33.12 3.18
1294 1326 5.120363 GGTTTCAGTTCGACAAGGTATCTTC 59.880 44.000 0.00 0.00 0.00 2.87
1313 1426 4.283722 TCTTCTTCAGTAGAAACCAGGACC 59.716 45.833 0.00 0.00 42.19 4.46
1323 1436 0.673644 AACCAGGACCGAAATCAGCG 60.674 55.000 0.00 0.00 0.00 5.18
1356 1469 3.486383 CTTCAGTTTGGTTCCCTGCTAA 58.514 45.455 0.00 0.00 0.00 3.09
1365 1478 2.271800 GTTCCCTGCTAACATCACTCG 58.728 52.381 0.00 0.00 0.00 4.18
1376 1489 4.537135 AACATCACTCGTGTGTTCCTAT 57.463 40.909 16.49 0.69 44.14 2.57
1492 1605 6.474440 TGGATTCTCCCAGGTAAAGGAAACT 61.474 44.000 0.00 0.00 37.99 2.66
1493 1606 5.191124 GGATTCTCCCAGGTAAAGGAAACTA 59.809 44.000 0.00 0.00 42.68 2.24
1494 1607 5.494390 TTCTCCCAGGTAAAGGAAACTAC 57.506 43.478 0.00 0.00 42.68 2.73
1498 1611 5.872963 TCCCAGGTAAAGGAAACTACTTTC 58.127 41.667 0.00 0.00 42.68 2.62
1511 1624 6.373186 AAACTACTTTCTCCAAAAGAACCG 57.627 37.500 4.64 0.00 43.75 4.44
1559 1689 3.620061 CACAGGATCTGCTGTGTGT 57.380 52.632 19.97 0.00 44.07 3.72
1640 1774 1.032014 TGCAACACTTTCAGCCCTTC 58.968 50.000 0.00 0.00 0.00 3.46
1681 1815 5.544176 ACAGGTATTCCTCTTGAACTCTCAA 59.456 40.000 0.00 0.00 43.07 3.02
1689 1823 4.155644 CCTCTTGAACTCTCAAATTCTGCC 59.844 45.833 0.00 0.00 41.05 4.85
1701 1836 3.904136 AATTCTGCCAACTTTGAGTCG 57.096 42.857 0.00 0.00 0.00 4.18
1807 1946 6.596497 CCCATCTACCGTTATTAAACAACAGT 59.404 38.462 4.71 2.23 35.16 3.55
1964 2104 9.930693 TCTAGGAAAGAGAAAGTTATTCTTCAC 57.069 33.333 3.14 1.05 35.02 3.18
2078 2218 4.964262 ACATGGACATGGAAATTTAGGCAT 59.036 37.500 15.94 0.00 42.91 4.40
2081 2221 4.646040 TGGACATGGAAATTTAGGCATGAG 59.354 41.667 0.00 0.00 0.00 2.90
2093 2233 3.674528 AGGCATGAGATATGGTTCTCG 57.325 47.619 0.00 0.00 44.22 4.04
2179 2320 1.616159 TTTAGGGCAAGGTGCTGAAC 58.384 50.000 0.00 0.00 44.28 3.18
2257 2398 1.068083 CATCTGCGACGTGGCCTAT 59.932 57.895 20.26 10.24 0.00 2.57
2284 2425 1.594862 CCGATCAAGGCGAAATCTGTC 59.405 52.381 0.00 0.00 0.00 3.51
2395 2536 1.157513 TCACACTGTCCCCAGGCTA 59.842 57.895 0.00 0.00 43.36 3.93
2536 2680 2.093216 CGCAAGCATCCTGGAAGAC 58.907 57.895 0.00 0.00 34.07 3.01
2586 2730 5.157940 TCAAATTCAGAGAGTTCAGGAGG 57.842 43.478 0.00 0.00 0.00 4.30
2595 2739 3.436243 AGAGTTCAGGAGGTAAGGACAG 58.564 50.000 0.00 0.00 0.00 3.51
2664 2808 1.362406 GGCAGTAGCTGAACTTCGCC 61.362 60.000 0.00 0.00 41.70 5.54
2673 2817 0.599204 TGAACTTCGCCGGTTGAGTC 60.599 55.000 1.90 1.83 0.00 3.36
2734 2882 3.007940 CAGATGGTAGACCTTGTTCACCA 59.992 47.826 0.00 0.00 43.10 4.17
2771 2919 7.911130 TGAGAGATGAGAATAAATCAGTCCT 57.089 36.000 0.00 0.00 0.00 3.85
2966 3115 7.090953 GCCTAAAGCTCTATATACATCGAGT 57.909 40.000 0.00 0.00 38.99 4.18
2995 3144 5.617252 ACGAATCTACAAGGAACAAAGGAA 58.383 37.500 0.00 0.00 0.00 3.36
2996 3145 5.469084 ACGAATCTACAAGGAACAAAGGAAC 59.531 40.000 0.00 0.00 0.00 3.62
3063 3212 2.404995 GCAGCTGCCTCATGTGGAC 61.405 63.158 28.76 9.26 34.31 4.02
3262 3496 6.183361 TGGGTACTTGATTGTGTTCTAAGTCA 60.183 38.462 0.00 0.00 33.93 3.41
3275 3509 8.342634 TGTGTTCTAAGTCACTTGCTTAAATTC 58.657 33.333 0.00 0.00 35.82 2.17
3279 3513 5.767816 AAGTCACTTGCTTAAATTCCGTT 57.232 34.783 0.00 0.00 0.00 4.44
3310 3552 4.101585 TCCTTCATGGGCACTTGTATAGAG 59.898 45.833 1.28 0.00 36.20 2.43
3514 3761 9.715123 CTTGATCAATAATTGCATTACGTTGTA 57.285 29.630 8.96 0.00 0.00 2.41
3530 3777 9.878599 ATTACGTTGTAAAAGACATTTCTCAAG 57.121 29.630 0.00 0.00 38.07 3.02
3627 3874 9.684448 TTCGCATCTAGAAAGAACAAGATATAG 57.316 33.333 0.00 0.00 34.73 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.089239 TGCCCCAGCGAACGCATA 62.089 61.111 20.66 0.00 44.31 3.14
215 216 1.735386 GCTCAGCAGCAGAGATGAAA 58.265 50.000 18.59 0.00 46.06 2.69
242 243 0.038618 CACCGAGGTTCGTCATGACA 60.039 55.000 24.93 9.94 38.40 3.58
260 261 1.587043 CCTCGTCGGTGAGCTTCTCA 61.587 60.000 0.00 0.00 38.25 3.27
371 372 2.267642 CGGAGCATTTGGGTCGGA 59.732 61.111 0.00 0.00 44.40 4.55
376 377 1.089920 CTGTCTTCGGAGCATTTGGG 58.910 55.000 0.00 0.00 0.00 4.12
378 379 2.005451 CTCCTGTCTTCGGAGCATTTG 58.995 52.381 0.00 0.00 41.39 2.32
379 380 1.065854 CCTCCTGTCTTCGGAGCATTT 60.066 52.381 0.58 0.00 45.37 2.32
380 381 0.539051 CCTCCTGTCTTCGGAGCATT 59.461 55.000 0.58 0.00 45.37 3.56
381 382 0.324738 TCCTCCTGTCTTCGGAGCAT 60.325 55.000 0.58 0.00 45.37 3.79
388 389 3.006247 GCACAATTCTCCTCCTGTCTTC 58.994 50.000 0.00 0.00 0.00 2.87
640 642 1.176527 ACACCGGCTTTCCATTGATG 58.823 50.000 0.00 0.00 0.00 3.07
710 712 1.130955 CTGCCATTCACACGCAAAAC 58.869 50.000 0.00 0.00 30.85 2.43
714 725 0.321475 TCATCTGCCATTCACACGCA 60.321 50.000 0.00 0.00 0.00 5.24
717 728 4.877823 TGTATCTTCATCTGCCATTCACAC 59.122 41.667 0.00 0.00 0.00 3.82
741 752 9.237187 TCCAGCATCACAAAGTACATTAATAAA 57.763 29.630 0.00 0.00 0.00 1.40
744 755 7.557358 TCATCCAGCATCACAAAGTACATTAAT 59.443 33.333 0.00 0.00 0.00 1.40
745 756 6.883756 TCATCCAGCATCACAAAGTACATTAA 59.116 34.615 0.00 0.00 0.00 1.40
747 758 5.255687 TCATCCAGCATCACAAAGTACATT 58.744 37.500 0.00 0.00 0.00 2.71
748 759 4.847198 TCATCCAGCATCACAAAGTACAT 58.153 39.130 0.00 0.00 0.00 2.29
749 760 4.284829 TCATCCAGCATCACAAAGTACA 57.715 40.909 0.00 0.00 0.00 2.90
750 761 5.627499 TTTCATCCAGCATCACAAAGTAC 57.373 39.130 0.00 0.00 0.00 2.73
751 762 6.839124 AATTTCATCCAGCATCACAAAGTA 57.161 33.333 0.00 0.00 0.00 2.24
752 763 5.733620 AATTTCATCCAGCATCACAAAGT 57.266 34.783 0.00 0.00 0.00 2.66
753 764 6.160684 TCAAATTTCATCCAGCATCACAAAG 58.839 36.000 0.00 0.00 0.00 2.77
754 765 6.099159 TCAAATTTCATCCAGCATCACAAA 57.901 33.333 0.00 0.00 0.00 2.83
755 766 5.725325 TCAAATTTCATCCAGCATCACAA 57.275 34.783 0.00 0.00 0.00 3.33
793 804 2.393646 AGCCTGATACTTCTCTGTCCC 58.606 52.381 0.00 0.00 0.00 4.46
794 805 5.599999 TTAAGCCTGATACTTCTCTGTCC 57.400 43.478 0.00 0.00 0.00 4.02
795 806 7.010923 CACATTTAAGCCTGATACTTCTCTGTC 59.989 40.741 0.00 0.00 0.00 3.51
801 812 5.731686 GCTGCACATTTAAGCCTGATACTTC 60.732 44.000 0.00 0.00 0.00 3.01
823 834 0.184933 TTGTTGCAACCTACCCAGCT 59.815 50.000 26.14 0.00 0.00 4.24
841 852 7.094377 ACGTTACTATCATCCAGCAAATTGTTT 60.094 33.333 0.00 0.00 0.00 2.83
847 858 4.094294 GCAACGTTACTATCATCCAGCAAA 59.906 41.667 0.00 0.00 0.00 3.68
862 873 3.339731 GCACAGGCTGCAACGTTA 58.660 55.556 15.89 0.00 46.29 3.18
885 896 2.688958 GCTACCTACTACTCCACACAGG 59.311 54.545 0.00 0.00 39.47 4.00
886 897 3.353557 TGCTACCTACTACTCCACACAG 58.646 50.000 0.00 0.00 0.00 3.66
887 898 3.444792 TGCTACCTACTACTCCACACA 57.555 47.619 0.00 0.00 0.00 3.72
888 899 3.762823 AGTTGCTACCTACTACTCCACAC 59.237 47.826 0.00 0.00 0.00 3.82
889 900 4.043608 AGTTGCTACCTACTACTCCACA 57.956 45.455 0.00 0.00 0.00 4.17
890 901 5.497635 GTAGTTGCTACCTACTACTCCAC 57.502 47.826 0.00 0.00 42.88 4.02
945 958 0.536006 ACTCTTCCACAAGCACAGGC 60.536 55.000 0.00 0.00 41.61 4.85
974 987 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
984 997 2.423185 CTCCATTTGTGTGTGTGTGTGT 59.577 45.455 0.00 0.00 0.00 3.72
985 998 2.795681 GCTCCATTTGTGTGTGTGTGTG 60.796 50.000 0.00 0.00 0.00 3.82
986 999 1.405105 GCTCCATTTGTGTGTGTGTGT 59.595 47.619 0.00 0.00 0.00 3.72
987 1000 1.404748 TGCTCCATTTGTGTGTGTGTG 59.595 47.619 0.00 0.00 0.00 3.82
988 1001 1.677576 CTGCTCCATTTGTGTGTGTGT 59.322 47.619 0.00 0.00 0.00 3.72
989 1002 1.001048 CCTGCTCCATTTGTGTGTGTG 60.001 52.381 0.00 0.00 0.00 3.82
990 1003 1.133823 TCCTGCTCCATTTGTGTGTGT 60.134 47.619 0.00 0.00 0.00 3.72
991 1004 1.538512 CTCCTGCTCCATTTGTGTGTG 59.461 52.381 0.00 0.00 0.00 3.82
992 1005 1.421268 TCTCCTGCTCCATTTGTGTGT 59.579 47.619 0.00 0.00 0.00 3.72
993 1006 2.189594 TCTCCTGCTCCATTTGTGTG 57.810 50.000 0.00 0.00 0.00 3.82
994 1007 2.373169 TCTTCTCCTGCTCCATTTGTGT 59.627 45.455 0.00 0.00 0.00 3.72
995 1008 3.063510 TCTTCTCCTGCTCCATTTGTG 57.936 47.619 0.00 0.00 0.00 3.33
996 1009 3.683802 CTTCTTCTCCTGCTCCATTTGT 58.316 45.455 0.00 0.00 0.00 2.83
997 1010 2.422832 GCTTCTTCTCCTGCTCCATTTG 59.577 50.000 0.00 0.00 0.00 2.32
998 1011 2.308275 AGCTTCTTCTCCTGCTCCATTT 59.692 45.455 0.00 0.00 0.00 2.32
999 1012 1.914798 AGCTTCTTCTCCTGCTCCATT 59.085 47.619 0.00 0.00 0.00 3.16
1023 1036 3.699894 CCGTGGAGGCAGAGCACT 61.700 66.667 0.00 0.00 0.00 4.40
1083 1096 1.077429 GAGGATGGAAGGGTGCCAC 60.077 63.158 0.00 0.00 38.44 5.01
1136 1150 4.701765 CAGAAGACGGAATGGAATCTGAT 58.298 43.478 0.00 0.00 35.91 2.90
1137 1151 3.679917 GCAGAAGACGGAATGGAATCTGA 60.680 47.826 4.20 0.00 35.91 3.27
1138 1152 2.611292 GCAGAAGACGGAATGGAATCTG 59.389 50.000 0.00 0.00 36.71 2.90
1143 1157 2.426522 CAAAGCAGAAGACGGAATGGA 58.573 47.619 0.00 0.00 0.00 3.41
1145 1159 1.808945 AGCAAAGCAGAAGACGGAATG 59.191 47.619 0.00 0.00 0.00 2.67
1146 1160 2.079925 GAGCAAAGCAGAAGACGGAAT 58.920 47.619 0.00 0.00 0.00 3.01
1149 1163 1.074752 GAGAGCAAAGCAGAAGACGG 58.925 55.000 0.00 0.00 0.00 4.79
1150 1164 1.788258 TGAGAGCAAAGCAGAAGACG 58.212 50.000 0.00 0.00 0.00 4.18
1151 1165 3.137533 ACTTGAGAGCAAAGCAGAAGAC 58.862 45.455 0.00 0.00 32.73 3.01
1152 1166 3.482156 ACTTGAGAGCAAAGCAGAAGA 57.518 42.857 0.00 0.00 32.73 2.87
1154 1168 3.544684 TGAACTTGAGAGCAAAGCAGAA 58.455 40.909 0.00 0.00 32.73 3.02
1159 1190 4.554330 GCAGAGTTGAACTTGAGAGCAAAG 60.554 45.833 0.00 0.00 32.73 2.77
1164 1195 3.065655 CCAGCAGAGTTGAACTTGAGAG 58.934 50.000 0.00 0.00 0.00 3.20
1167 1198 3.281727 AACCAGCAGAGTTGAACTTGA 57.718 42.857 0.00 0.00 0.00 3.02
1177 1208 2.856222 AGACCTGAAAAACCAGCAGAG 58.144 47.619 0.00 0.00 32.97 3.35
1294 1326 2.561419 TCGGTCCTGGTTTCTACTGAAG 59.439 50.000 0.00 0.00 33.28 3.02
1313 1426 1.061711 CTGGAAGAAGCGCTGATTTCG 59.938 52.381 12.58 0.86 34.07 3.46
1323 1436 1.902938 AACTGAAGGCTGGAAGAAGC 58.097 50.000 0.00 0.00 42.75 3.86
1376 1489 5.069318 TGTGTATTCAGTGAAATCCTGCAA 58.931 37.500 10.14 0.00 0.00 4.08
1390 1503 7.386059 TGCACTCTTCTAGATTTGTGTATTCA 58.614 34.615 15.87 7.12 0.00 2.57
1492 1605 3.811083 TGCGGTTCTTTTGGAGAAAGTA 58.189 40.909 0.00 0.00 45.59 2.24
1493 1606 2.650322 TGCGGTTCTTTTGGAGAAAGT 58.350 42.857 0.00 0.00 45.59 2.66
1494 1607 3.366374 GGATGCGGTTCTTTTGGAGAAAG 60.366 47.826 0.00 0.00 45.59 2.62
1498 1611 1.533625 TGGATGCGGTTCTTTTGGAG 58.466 50.000 0.00 0.00 0.00 3.86
1511 1624 0.109597 CGCCTCAAACAGTTGGATGC 60.110 55.000 7.69 7.69 35.29 3.91
1551 1681 5.229887 CACAACTATGTTTTCAACACACAGC 59.770 40.000 0.00 0.00 45.50 4.40
1664 1798 5.471456 GCAGAATTTGAGAGTTCAAGAGGAA 59.529 40.000 0.00 0.00 43.76 3.36
1681 1815 3.214328 ACGACTCAAAGTTGGCAGAATT 58.786 40.909 0.00 0.00 33.85 2.17
1689 1823 4.738740 ACTTAACTCGACGACTCAAAGTTG 59.261 41.667 7.84 0.00 35.70 3.16
1701 1836 7.928103 TGTATATCTCTGGAACTTAACTCGAC 58.072 38.462 0.00 0.00 0.00 4.20
1782 1921 6.596497 ACTGTTGTTTAATAACGGTAGATGGG 59.404 38.462 15.62 0.00 43.71 4.00
1807 1946 1.399744 ATTGCTAGATCGCGGGGACA 61.400 55.000 6.13 0.00 0.00 4.02
1881 2021 2.329267 ACTGTTCTGTCAGGATGGACA 58.671 47.619 0.00 0.00 45.06 4.02
1882 2022 4.537135 TTACTGTTCTGTCAGGATGGAC 57.463 45.455 0.00 0.00 39.48 4.02
1964 2104 3.774066 TGATATCTTCGGCATATGCTCG 58.226 45.455 26.12 24.91 41.70 5.03
2048 2188 9.965824 CTAAATTTCCATGTCCATGTAAATACC 57.034 33.333 10.13 0.00 36.67 2.73
2057 2197 5.210430 TCATGCCTAAATTTCCATGTCCAT 58.790 37.500 18.22 3.80 37.09 3.41
2058 2198 4.608269 TCATGCCTAAATTTCCATGTCCA 58.392 39.130 18.22 5.10 37.09 4.02
2078 2218 3.595190 TCCTCCGAGAACCATATCTCA 57.405 47.619 0.00 0.00 44.98 3.27
2081 2221 4.282195 ACATCTTCCTCCGAGAACCATATC 59.718 45.833 0.00 0.00 0.00 1.63
2115 2255 2.727123 TGGAACCAGAAGCAGAACAA 57.273 45.000 0.00 0.00 0.00 2.83
2179 2320 4.006989 TGAACTTAATTGGTGGGTGATCG 58.993 43.478 0.00 0.00 0.00 3.69
2248 2389 1.111116 TCGGGTCCTTATAGGCCACG 61.111 60.000 5.01 0.00 34.52 4.94
2257 2398 0.685131 TCGCCTTGATCGGGTCCTTA 60.685 55.000 6.44 0.00 0.00 2.69
2284 2425 5.125097 CCAGTCTTTCTCTCCAATGAAATGG 59.875 44.000 0.00 0.00 42.12 3.16
2395 2536 1.062488 ACAGGGGAGAGTGCAAACCT 61.062 55.000 0.00 0.00 0.00 3.50
2536 2680 3.159984 GCGTCTGCGTTCTTGAGG 58.840 61.111 0.00 0.00 40.81 3.86
2586 2730 1.007336 CACGCCGACACTGTCCTTAC 61.007 60.000 3.50 0.00 0.00 2.34
2595 2739 2.430921 CTGACTCCACGCCGACAC 60.431 66.667 0.00 0.00 0.00 3.67
2664 2808 2.660552 ACCAACGCGACTCAACCG 60.661 61.111 15.93 0.00 0.00 4.44
2673 2817 1.157870 AGGTTTCAGACACCAACGCG 61.158 55.000 3.53 3.53 36.67 6.01
2771 2919 3.573967 GGAGGAAAAGAACAGGCAAATCA 59.426 43.478 0.00 0.00 0.00 2.57
2879 3028 2.039084 CCAGTAGGTTCAAGTGCCTCTT 59.961 50.000 0.00 0.00 36.38 2.85
2966 3115 3.003394 TCCTTGTAGATTCGTCCGGTA 57.997 47.619 0.00 0.00 0.00 4.02
3063 3212 1.627834 AGTGAGGCTGAAGAAAGAGGG 59.372 52.381 0.00 0.00 0.00 4.30
3262 3496 5.257082 ACACAAACGGAATTTAAGCAAGT 57.743 34.783 0.00 0.00 0.00 3.16
3275 3509 2.742053 CCATGAAGGACTACACAAACGG 59.258 50.000 0.00 0.00 41.22 4.44
3279 3513 1.702401 TGCCCATGAAGGACTACACAA 59.298 47.619 0.00 0.00 41.22 3.33
3350 3597 8.324163 TCTTTAGCTCTTTTACTCATTTCACC 57.676 34.615 0.00 0.00 0.00 4.02
3366 3613 8.268850 TCTTGAATATTGTGGTTCTTTAGCTC 57.731 34.615 0.00 0.00 0.00 4.09
3514 3761 4.340381 ACAGCAGCTTGAGAAATGTCTTTT 59.660 37.500 0.00 0.00 32.80 2.27


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

AutoCloner maintained by Alex Coulton.