Multiple sequence alignment - TraesCS2B01G244600

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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 TraesCS2B01G244600 chr2B 100.000 4200 0 0 1 4200 248654270 248658469 0.000000e+00 7757
1 TraesCS2B01G244600 chr2D 93.330 4138 167 42 113 4200 191240484 191236406 0.000000e+00 6011
2 TraesCS2B01G244600 chr2A 92.757 3341 152 45 113 3408 206403129 206406424 0.000000e+00 4747
3 TraesCS2B01G244600 chr2A 92.796 819 29 13 3394 4200 206409432 206410232 0.000000e+00 1158
4 TraesCS2B01G244600 chr2A 90.351 114 10 1 5 117 206402990 206403103 9.410000e-32 148


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 TraesCS2B01G244600 chr2B 248654270 248658469 4199 False 7757.000000 7757 100.000 1 4200 1 chr2B.!!$F1 4199
1 TraesCS2B01G244600 chr2D 191236406 191240484 4078 True 6011.000000 6011 93.330 113 4200 1 chr2D.!!$R1 4087
2 TraesCS2B01G244600 chr2A 206402990 206410232 7242 False 2017.666667 4747 91.968 5 4200 3 chr2A.!!$F1 4195

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
171 202 0.393820 TAGGGTGTTCGGTTGTGGTC 59.606 55.000 0.00 0.00 0.0 4.02 F
1148 1186 0.326048 ATCCTACAGGTGCCAGAGCT 60.326 55.000 0.00 0.00 40.8 4.09 F
1246 1295 0.179124 GGAGAGTGTCTGATCGTGGC 60.179 60.000 0.00 0.00 0.0 5.01 F
2668 2724 1.593209 GTTCAACTGGGACGCGTCA 60.593 57.895 37.26 20.13 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1168 1210 0.105913 ACCAAAGAAGGGGCGGAAAA 60.106 50.000 0.00 0.00 0.00 2.29 R
2329 2385 0.798776 CCTGGAGCTTACGTTGCTTG 59.201 55.000 15.21 9.67 41.30 4.01 R
3157 3216 1.066858 ACATGTTGACTACTGCCCTCG 60.067 52.381 0.00 0.00 0.00 4.63 R
3893 7014 1.402613 GTAAACCACGTGCAAACTGGT 59.597 47.619 10.91 5.55 40.17 4.00 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
17 18 4.757773 ACCGGGACAGAAGATCGA 57.242 55.556 6.32 0.00 0.00 3.59
50 51 3.021695 CCTAGAGTGGTGGATGTCGTTA 58.978 50.000 0.00 0.00 0.00 3.18
69 70 1.068753 CCAGAGTGGCCTGCGATAG 59.931 63.158 3.32 0.00 32.97 2.08
100 101 1.373748 GGCTGACGTTGCCGAAGTA 60.374 57.895 15.87 0.00 41.03 2.24
101 102 0.739813 GGCTGACGTTGCCGAAGTAT 60.740 55.000 15.87 0.00 41.03 2.12
104 105 2.540515 CTGACGTTGCCGAAGTATCAT 58.459 47.619 0.00 0.00 37.88 2.45
153 184 4.359105 AGGCTAGTGGTAGAATGGTGTTA 58.641 43.478 0.00 0.00 0.00 2.41
171 202 0.393820 TAGGGTGTTCGGTTGTGGTC 59.606 55.000 0.00 0.00 0.00 4.02
186 217 4.538746 TGTGGTCGTATCATGGTTTGTA 57.461 40.909 0.00 0.00 0.00 2.41
212 243 3.359695 TTATAAAGCGGGGCAAGAAGT 57.640 42.857 0.00 0.00 0.00 3.01
276 307 2.519780 GGAGAGTCTCGGCCCGAT 60.520 66.667 6.16 0.00 34.61 4.18
315 346 1.933021 ACGTCCTGGATAACTGTCCA 58.067 50.000 0.00 0.00 45.78 4.02
337 368 4.317530 TCTGCTTCTACCACTTCCTCTA 57.682 45.455 0.00 0.00 0.00 2.43
343 374 1.822990 CTACCACTTCCTCTACGGCAA 59.177 52.381 0.00 0.00 0.00 4.52
424 455 6.611613 TGAACTCTCATGTTATGAACCTCT 57.388 37.500 0.00 0.00 39.11 3.69
567 598 7.973388 TGAAAAATGCCTAATTTCCTAACATCG 59.027 33.333 0.00 0.00 37.51 3.84
624 655 9.449719 AGACTTTCTATGGGTAAATGTGTAAAG 57.550 33.333 0.00 0.00 0.00 1.85
684 715 4.811969 TTTGGCATCAGAAAATGAGCAT 57.188 36.364 0.00 0.00 42.53 3.79
689 720 5.419788 TGGCATCAGAAAATGAGCATAAACT 59.580 36.000 0.00 0.00 42.53 2.66
706 741 8.454106 AGCATAAACTATAAGTTGTTCTGCAAG 58.546 33.333 13.66 0.00 38.66 4.01
719 754 4.823442 TGTTCTGCAAGTTGATGTCTTGAT 59.177 37.500 7.16 0.00 43.17 2.57
726 761 5.616424 GCAAGTTGATGTCTTGATGTCAGTC 60.616 44.000 7.16 0.00 43.17 3.51
759 794 4.558226 AGCATGGATCACAGTTCAGTTA 57.442 40.909 0.00 0.00 0.00 2.24
765 800 6.550938 TGGATCACAGTTCAGTTATGAGAT 57.449 37.500 0.00 0.00 36.61 2.75
850 885 2.166870 TGTCCAAACTACGCGTGGATAT 59.833 45.455 30.06 11.79 43.19 1.63
852 887 4.038282 TGTCCAAACTACGCGTGGATATAT 59.962 41.667 30.06 2.78 43.19 0.86
862 897 4.510340 ACGCGTGGATATATTTTTGTCCTC 59.490 41.667 12.93 0.00 0.00 3.71
864 899 4.510340 GCGTGGATATATTTTTGTCCTCGT 59.490 41.667 13.81 0.00 44.82 4.18
985 1020 2.290641 GCGAAATCCCACGATAAGCATT 59.709 45.455 0.00 0.00 0.00 3.56
1005 1040 4.703645 TTGAACGATCGAAGAGATGAGT 57.296 40.909 24.34 0.00 43.63 3.41
1052 1087 2.884827 CACGCATGAAGAGTCATCTCA 58.115 47.619 0.00 0.00 42.88 3.27
1053 1088 3.455327 CACGCATGAAGAGTCATCTCAT 58.545 45.455 0.00 0.00 42.88 2.90
1054 1089 3.490155 CACGCATGAAGAGTCATCTCATC 59.510 47.826 0.00 0.00 42.88 2.92
1055 1090 3.384146 ACGCATGAAGAGTCATCTCATCT 59.616 43.478 0.00 0.00 42.88 2.90
1056 1091 3.982701 CGCATGAAGAGTCATCTCATCTC 59.017 47.826 0.00 0.00 42.88 2.75
1057 1092 4.499357 CGCATGAAGAGTCATCTCATCTCA 60.499 45.833 0.00 0.00 42.88 3.27
1061 1096 5.829829 TGAAGAGTCATCTCATCTCATTCG 58.170 41.667 0.00 0.00 42.66 3.34
1077 1112 6.755206 TCTCATTCGTATAAATACAGTGGGG 58.245 40.000 0.00 0.00 32.87 4.96
1142 1180 1.133136 TCCTCCTATCCTACAGGTGCC 60.133 57.143 0.00 0.00 34.56 5.01
1143 1181 1.413082 CCTCCTATCCTACAGGTGCCA 60.413 57.143 0.00 0.00 34.56 4.92
1144 1182 1.967066 CTCCTATCCTACAGGTGCCAG 59.033 57.143 0.00 0.00 34.56 4.85
1145 1183 1.573857 TCCTATCCTACAGGTGCCAGA 59.426 52.381 0.00 0.00 34.56 3.86
1146 1184 1.967066 CCTATCCTACAGGTGCCAGAG 59.033 57.143 0.00 0.00 36.34 3.35
1147 1185 1.342819 CTATCCTACAGGTGCCAGAGC 59.657 57.143 0.00 0.00 40.48 4.09
1148 1186 0.326048 ATCCTACAGGTGCCAGAGCT 60.326 55.000 0.00 0.00 40.80 4.09
1149 1187 0.972983 TCCTACAGGTGCCAGAGCTC 60.973 60.000 5.27 5.27 40.80 4.09
1150 1188 1.260538 CCTACAGGTGCCAGAGCTCA 61.261 60.000 17.77 0.00 40.80 4.26
1151 1189 0.610174 CTACAGGTGCCAGAGCTCAA 59.390 55.000 17.77 0.00 40.80 3.02
1152 1190 1.002430 CTACAGGTGCCAGAGCTCAAA 59.998 52.381 17.77 0.00 40.80 2.69
1207 1249 4.131596 GGTTAGTGTTGCTACCTTGTCAA 58.868 43.478 0.00 0.00 0.00 3.18
1236 1285 2.533266 TTGAACTGCAGGAGAGTGTC 57.467 50.000 19.93 4.10 0.00 3.67
1241 1290 1.824230 ACTGCAGGAGAGTGTCTGATC 59.176 52.381 19.93 0.00 33.11 2.92
1242 1291 0.813821 TGCAGGAGAGTGTCTGATCG 59.186 55.000 0.00 0.00 33.11 3.69
1246 1295 0.179124 GGAGAGTGTCTGATCGTGGC 60.179 60.000 0.00 0.00 0.00 5.01
1250 1299 1.996191 GAGTGTCTGATCGTGGCTTTC 59.004 52.381 0.00 0.00 0.00 2.62
1252 1301 2.037772 AGTGTCTGATCGTGGCTTTCTT 59.962 45.455 0.00 0.00 0.00 2.52
1253 1302 3.258372 AGTGTCTGATCGTGGCTTTCTTA 59.742 43.478 0.00 0.00 0.00 2.10
1254 1303 4.081420 AGTGTCTGATCGTGGCTTTCTTAT 60.081 41.667 0.00 0.00 0.00 1.73
1255 1304 4.033358 GTGTCTGATCGTGGCTTTCTTATG 59.967 45.833 0.00 0.00 0.00 1.90
1256 1305 4.184629 GTCTGATCGTGGCTTTCTTATGT 58.815 43.478 0.00 0.00 0.00 2.29
1257 1306 4.033358 GTCTGATCGTGGCTTTCTTATGTG 59.967 45.833 0.00 0.00 0.00 3.21
1258 1307 4.081697 TCTGATCGTGGCTTTCTTATGTGA 60.082 41.667 0.00 0.00 0.00 3.58
1259 1308 4.769688 TGATCGTGGCTTTCTTATGTGAT 58.230 39.130 0.00 0.00 0.00 3.06
1260 1309 4.571984 TGATCGTGGCTTTCTTATGTGATG 59.428 41.667 0.00 0.00 0.00 3.07
1261 1310 3.270027 TCGTGGCTTTCTTATGTGATGG 58.730 45.455 0.00 0.00 0.00 3.51
1262 1311 3.055458 TCGTGGCTTTCTTATGTGATGGA 60.055 43.478 0.00 0.00 0.00 3.41
1263 1312 3.063997 CGTGGCTTTCTTATGTGATGGAC 59.936 47.826 0.00 0.00 0.00 4.02
1264 1313 3.378427 GTGGCTTTCTTATGTGATGGACC 59.622 47.826 0.00 0.00 0.00 4.46
1265 1314 3.266772 TGGCTTTCTTATGTGATGGACCT 59.733 43.478 0.00 0.00 0.00 3.85
1266 1315 3.629398 GGCTTTCTTATGTGATGGACCTG 59.371 47.826 0.00 0.00 0.00 4.00
1267 1316 4.265073 GCTTTCTTATGTGATGGACCTGT 58.735 43.478 0.00 0.00 0.00 4.00
1268 1317 5.428253 GCTTTCTTATGTGATGGACCTGTA 58.572 41.667 0.00 0.00 0.00 2.74
1269 1318 5.294552 GCTTTCTTATGTGATGGACCTGTAC 59.705 44.000 0.00 0.00 0.00 2.90
1270 1319 4.649088 TCTTATGTGATGGACCTGTACG 57.351 45.455 0.00 0.00 0.00 3.67
1535 1584 2.030562 AGGTACGCAGCGCACTTT 59.969 55.556 16.61 2.11 0.00 2.66
1536 1585 2.027625 AGGTACGCAGCGCACTTTC 61.028 57.895 16.61 0.00 0.00 2.62
1537 1586 2.093983 GTACGCAGCGCACTTTCG 59.906 61.111 16.61 7.71 0.00 3.46
1538 1587 2.355363 TACGCAGCGCACTTTCGT 60.355 55.556 16.61 13.42 36.72 3.85
1550 1602 3.312421 CGCACTTTCGTTATCCCATGATT 59.688 43.478 0.00 0.00 32.18 2.57
1556 1608 4.665833 TCGTTATCCCATGATTCGTTCT 57.334 40.909 0.00 0.00 32.71 3.01
1574 1630 4.153117 CGTTCTACCTGTACTGTACGTCTT 59.847 45.833 12.87 0.88 0.00 3.01
1581 1637 4.486090 CTGTACTGTACGTCTTGCTGAAT 58.514 43.478 12.87 0.00 0.00 2.57
1582 1638 4.878439 TGTACTGTACGTCTTGCTGAATT 58.122 39.130 12.87 0.00 0.00 2.17
1583 1639 5.294356 TGTACTGTACGTCTTGCTGAATTT 58.706 37.500 12.87 0.00 0.00 1.82
1584 1640 4.732285 ACTGTACGTCTTGCTGAATTTG 57.268 40.909 0.00 0.00 0.00 2.32
1588 1644 5.270083 TGTACGTCTTGCTGAATTTGTTTG 58.730 37.500 0.00 0.00 0.00 2.93
1589 1645 4.370364 ACGTCTTGCTGAATTTGTTTGT 57.630 36.364 0.00 0.00 0.00 2.83
1590 1646 4.743493 ACGTCTTGCTGAATTTGTTTGTT 58.257 34.783 0.00 0.00 0.00 2.83
1747 1803 2.155194 CGAGCACCTCTTCTTCGCG 61.155 63.158 0.00 0.00 0.00 5.87
1969 2025 2.617274 GGTGACCAAGAAGTGCGGC 61.617 63.158 0.00 0.00 0.00 6.53
2316 2372 2.169789 CCATCGCGAGGCTCAACAG 61.170 63.158 16.59 0.00 0.00 3.16
2329 2385 1.961277 CAACAGCACCGACCTGGAC 60.961 63.158 0.00 0.00 42.00 4.02
2647 2703 2.656069 GGCCTACAACCTCTCGCCA 61.656 63.158 0.00 0.00 36.38 5.69
2668 2724 1.593209 GTTCAACTGGGACGCGTCA 60.593 57.895 37.26 20.13 0.00 4.35
2993 3049 9.330063 TGCCATTAAATCTTAATCTAGTGACTG 57.670 33.333 0.00 0.00 0.00 3.51
3157 3216 0.905357 TCTGGACTAAGCCTGGAAGC 59.095 55.000 0.00 0.00 0.00 3.86
3161 3220 0.179097 GACTAAGCCTGGAAGCGAGG 60.179 60.000 0.00 0.00 38.01 4.63
3223 3282 8.277197 TGATGAAGGTTGAGAAGGAATAATGAT 58.723 33.333 0.00 0.00 0.00 2.45
3224 3283 9.129532 GATGAAGGTTGAGAAGGAATAATGATT 57.870 33.333 0.00 0.00 0.00 2.57
3225 3284 8.884124 TGAAGGTTGAGAAGGAATAATGATTT 57.116 30.769 0.00 0.00 0.00 2.17
3226 3285 8.742777 TGAAGGTTGAGAAGGAATAATGATTTG 58.257 33.333 0.00 0.00 0.00 2.32
3227 3286 7.651027 AGGTTGAGAAGGAATAATGATTTGG 57.349 36.000 0.00 0.00 0.00 3.28
3272 3331 4.799564 TTGGATAAAAGAAAAGCGGCAT 57.200 36.364 1.45 0.00 0.00 4.40
3277 3336 1.620822 AAAGAAAAGCGGCATGAGGT 58.379 45.000 1.45 0.00 0.00 3.85
3360 3442 6.906157 ATTATGTTAGGCTCCAATTGGATG 57.094 37.500 27.20 20.43 44.46 3.51
3408 6512 2.035449 ACGATGTCTTTCAGGTCGTCAA 59.965 45.455 0.00 0.00 41.11 3.18
3418 6522 3.334691 TCAGGTCGTCAATGAATTGGAC 58.665 45.455 3.31 4.10 38.30 4.02
3428 6532 6.642131 CGTCAATGAATTGGACAAGTCAATTT 59.358 34.615 17.45 7.26 46.41 1.82
3429 6533 7.169645 CGTCAATGAATTGGACAAGTCAATTTT 59.830 33.333 17.45 6.64 46.41 1.82
3441 6545 9.528018 GGACAAGTCAATTTTTATTGAAACTCA 57.472 29.630 2.29 0.00 41.61 3.41
3581 6694 8.732531 TGGTTCCACCTTATAGATTTAAAAACG 58.267 33.333 0.00 0.00 39.58 3.60
3605 6718 1.202132 GCATGCCAAATCGCGACTTAA 60.202 47.619 12.93 0.00 0.00 1.85
3619 6732 4.353737 GCGACTTAACCATACGTATCACA 58.646 43.478 4.74 0.00 0.00 3.58
3660 6773 7.961326 ATAAATGATTAAAAGCACCCTCAGT 57.039 32.000 0.00 0.00 0.00 3.41
3698 6811 1.417517 TCAGAAAGGCTCACTGCAAGA 59.582 47.619 13.59 0.00 45.15 3.02
3823 6944 0.108186 ACCGCGATGATGAGAAGCAA 60.108 50.000 8.23 0.00 0.00 3.91
3991 7115 2.294791 AGAATTCTCAGTAGGATCGGCG 59.705 50.000 0.88 0.00 0.00 6.46
4190 7318 5.642063 TCTTGATTTTGGACCAACGATCTAC 59.358 40.000 21.64 7.24 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.818296 CTTCGATCTTCTGTCCCGGT 59.182 55.000 0.00 0.00 0.00 5.28
1 2 0.818296 ACTTCGATCTTCTGTCCCGG 59.182 55.000 0.00 0.00 0.00 5.73
2 3 1.472878 TCACTTCGATCTTCTGTCCCG 59.527 52.381 0.00 0.00 0.00 5.14
3 4 3.594603 TTCACTTCGATCTTCTGTCCC 57.405 47.619 0.00 0.00 0.00 4.46
4 5 4.750098 TGTTTTCACTTCGATCTTCTGTCC 59.250 41.667 0.00 0.00 0.00 4.02
5 6 5.671074 GTGTTTTCACTTCGATCTTCTGTC 58.329 41.667 0.00 0.00 46.30 3.51
50 51 1.680522 CTATCGCAGGCCACTCTGGT 61.681 60.000 5.01 0.00 40.46 4.00
69 70 0.393132 GTCAGCCACCTAAAGCTCCC 60.393 60.000 0.00 0.00 37.18 4.30
74 75 0.517316 GCAACGTCAGCCACCTAAAG 59.483 55.000 1.76 0.00 0.00 1.85
95 96 2.996621 GCCGCCTGACATATGATACTTC 59.003 50.000 10.38 0.00 0.00 3.01
96 97 2.610479 CGCCGCCTGACATATGATACTT 60.610 50.000 10.38 0.00 0.00 2.24
100 101 1.004560 CCGCCGCCTGACATATGAT 60.005 57.895 10.38 0.00 0.00 2.45
101 102 2.421314 CCGCCGCCTGACATATGA 59.579 61.111 10.38 0.00 0.00 2.15
104 105 2.023414 CTAACCCGCCGCCTGACATA 62.023 60.000 0.00 0.00 0.00 2.29
153 184 1.147600 GACCACAACCGAACACCCT 59.852 57.895 0.00 0.00 0.00 4.34
186 217 6.969993 TCTTGCCCCGCTTTATAAATAAAT 57.030 33.333 0.00 0.00 32.36 1.40
212 243 4.000988 GGTGCAGGTTCTATCGAAAAAGA 58.999 43.478 0.00 0.00 0.00 2.52
276 307 1.154488 GTCGATTTTGAGCGCGCAA 60.154 52.632 35.10 23.01 0.00 4.85
315 346 3.718723 AGAGGAAGTGGTAGAAGCAGAT 58.281 45.455 0.00 0.00 0.00 2.90
337 368 0.181824 ACAAGGTACTGGTTTGCCGT 59.818 50.000 0.00 0.00 41.93 5.68
343 374 3.314693 TGGAGAAGACAAGGTACTGGTT 58.685 45.455 0.00 0.00 41.93 3.67
409 440 5.882000 TCAACATGGAGAGGTTCATAACATG 59.118 40.000 0.00 0.00 39.88 3.21
424 455 6.718699 GACCAAAGTCACATGTCAACATGGA 61.719 44.000 24.66 15.64 44.24 3.41
477 508 0.730155 CGCAAATCGCATGCAACAGT 60.730 50.000 19.57 0.00 44.01 3.55
496 527 8.430801 AGCATCATCAGAAGTTTACTAACATC 57.569 34.615 0.00 0.00 36.70 3.06
624 655 4.505742 CCTCCCTGCCTCCAAATATTACTC 60.506 50.000 0.00 0.00 0.00 2.59
684 715 9.332502 TCAACTTGCAGAACAACTTATAGTTTA 57.667 29.630 0.00 0.00 36.03 2.01
689 720 7.661437 AGACATCAACTTGCAGAACAACTTATA 59.339 33.333 0.00 0.00 33.68 0.98
693 728 4.202441 AGACATCAACTTGCAGAACAACT 58.798 39.130 0.00 0.00 33.68 3.16
696 731 4.198530 TCAAGACATCAACTTGCAGAACA 58.801 39.130 0.00 0.00 42.76 3.18
706 741 4.153117 GGTGACTGACATCAAGACATCAAC 59.847 45.833 0.00 0.00 0.00 3.18
719 754 1.204704 CTATGGCTTCGGTGACTGACA 59.795 52.381 0.00 0.00 0.00 3.58
726 761 2.324215 CCATGCTATGGCTTCGGTG 58.676 57.895 1.68 0.00 44.70 4.94
759 794 3.192422 GCGTGCTACTCCTATCATCTCAT 59.808 47.826 0.00 0.00 0.00 2.90
765 800 0.380733 CGTGCGTGCTACTCCTATCA 59.619 55.000 0.00 0.00 0.00 2.15
850 885 3.432933 GGTTACGCACGAGGACAAAAATA 59.567 43.478 0.00 0.00 0.00 1.40
852 887 1.598601 GGTTACGCACGAGGACAAAAA 59.401 47.619 0.00 0.00 0.00 1.94
862 897 0.918619 ATTTCGATCGGTTACGCACG 59.081 50.000 16.41 0.00 40.69 5.34
864 899 1.135527 AGGATTTCGATCGGTTACGCA 59.864 47.619 16.41 0.00 40.69 5.24
894 929 4.388080 TACGTCGACGGTGCCACG 62.388 66.667 37.89 14.84 44.95 4.94
895 930 2.503375 CTACGTCGACGGTGCCAC 60.503 66.667 37.89 0.00 44.95 5.01
896 931 4.409218 GCTACGTCGACGGTGCCA 62.409 66.667 37.89 18.09 44.95 4.92
985 1020 3.065510 GGACTCATCTCTTCGATCGTTCA 59.934 47.826 15.94 0.00 0.00 3.18
1005 1040 1.218047 GTGCATGGTAGCGTCTGGA 59.782 57.895 0.00 0.00 37.31 3.86
1052 1087 7.016268 ACCCCACTGTATTTATACGAATGAGAT 59.984 37.037 0.00 0.00 36.06 2.75
1053 1088 6.325545 ACCCCACTGTATTTATACGAATGAGA 59.674 38.462 0.00 0.00 36.06 3.27
1054 1089 6.522054 ACCCCACTGTATTTATACGAATGAG 58.478 40.000 0.00 0.00 36.06 2.90
1055 1090 6.488769 ACCCCACTGTATTTATACGAATGA 57.511 37.500 0.00 0.00 36.06 2.57
1056 1091 7.517734 CGAAACCCCACTGTATTTATACGAATG 60.518 40.741 0.00 0.00 36.06 2.67
1057 1092 6.480981 CGAAACCCCACTGTATTTATACGAAT 59.519 38.462 0.00 0.00 36.06 3.34
1061 1096 5.756833 CCTCGAAACCCCACTGTATTTATAC 59.243 44.000 0.00 0.00 0.00 1.47
1077 1112 1.960994 GCTCTGCTTCGCCTCGAAAC 61.961 60.000 3.24 0.00 45.23 2.78
1115 1151 4.530161 CCTGTAGGATAGGAGGATCAAAGG 59.470 50.000 0.00 0.00 37.52 3.11
1142 1180 1.807886 GCCATGGCTTTGAGCTCTG 59.192 57.895 29.98 6.44 41.99 3.35
1143 1181 1.748122 CGCCATGGCTTTGAGCTCT 60.748 57.895 33.07 0.00 41.99 4.09
1144 1182 1.986575 GACGCCATGGCTTTGAGCTC 61.987 60.000 33.07 6.82 41.99 4.09
1145 1183 2.034687 ACGCCATGGCTTTGAGCT 59.965 55.556 33.07 6.51 41.99 4.09
1146 1184 2.486966 GACGCCATGGCTTTGAGC 59.513 61.111 33.07 9.49 41.46 4.26
1147 1185 2.787249 CGACGCCATGGCTTTGAG 59.213 61.111 33.07 19.95 39.32 3.02
1148 1186 3.430862 GCGACGCCATGGCTTTGA 61.431 61.111 33.07 0.00 39.32 2.69
1168 1210 0.105913 ACCAAAGAAGGGGCGGAAAA 60.106 50.000 0.00 0.00 0.00 2.29
1170 1212 0.772384 TAACCAAAGAAGGGGCGGAA 59.228 50.000 0.00 0.00 0.00 4.30
1228 1277 0.814457 AGCCACGATCAGACACTCTC 59.186 55.000 0.00 0.00 0.00 3.20
1229 1278 1.261480 AAGCCACGATCAGACACTCT 58.739 50.000 0.00 0.00 0.00 3.24
1230 1279 1.996191 GAAAGCCACGATCAGACACTC 59.004 52.381 0.00 0.00 0.00 3.51
1236 1285 4.183865 TCACATAAGAAAGCCACGATCAG 58.816 43.478 0.00 0.00 0.00 2.90
1241 1290 3.063997 GTCCATCACATAAGAAAGCCACG 59.936 47.826 0.00 0.00 0.00 4.94
1242 1291 3.378427 GGTCCATCACATAAGAAAGCCAC 59.622 47.826 0.00 0.00 0.00 5.01
1246 1295 5.520288 CGTACAGGTCCATCACATAAGAAAG 59.480 44.000 0.00 0.00 0.00 2.62
1250 1299 4.386867 ACGTACAGGTCCATCACATAAG 57.613 45.455 0.00 0.00 0.00 1.73
1252 1301 3.313249 CGTACGTACAGGTCCATCACATA 59.687 47.826 24.50 0.00 0.00 2.29
1253 1302 2.098607 CGTACGTACAGGTCCATCACAT 59.901 50.000 24.50 0.00 0.00 3.21
1254 1303 1.469703 CGTACGTACAGGTCCATCACA 59.530 52.381 24.50 0.00 0.00 3.58
1255 1304 1.470098 ACGTACGTACAGGTCCATCAC 59.530 52.381 21.41 0.00 0.00 3.06
1256 1305 1.469703 CACGTACGTACAGGTCCATCA 59.530 52.381 22.34 0.00 0.00 3.07
1257 1306 1.796617 GCACGTACGTACAGGTCCATC 60.797 57.143 22.34 2.00 0.00 3.51
1258 1307 0.171903 GCACGTACGTACAGGTCCAT 59.828 55.000 22.34 0.00 0.00 3.41
1259 1308 1.171549 TGCACGTACGTACAGGTCCA 61.172 55.000 22.34 9.61 0.00 4.02
1260 1309 0.455633 CTGCACGTACGTACAGGTCC 60.456 60.000 32.01 12.24 36.23 4.46
1261 1310 0.518636 TCTGCACGTACGTACAGGTC 59.481 55.000 35.98 16.86 39.34 3.85
1262 1311 1.131883 GATCTGCACGTACGTACAGGT 59.868 52.381 35.98 33.12 39.34 4.00
1263 1312 1.131693 TGATCTGCACGTACGTACAGG 59.868 52.381 35.98 23.00 39.34 4.00
1264 1313 2.537639 TGATCTGCACGTACGTACAG 57.462 50.000 33.22 33.22 40.01 2.74
1265 1314 2.478879 CCATGATCTGCACGTACGTACA 60.479 50.000 22.34 20.83 0.00 2.90
1266 1315 2.117137 CCATGATCTGCACGTACGTAC 58.883 52.381 22.34 16.78 0.00 3.67
1267 1316 2.018515 TCCATGATCTGCACGTACGTA 58.981 47.619 22.34 5.72 0.00 3.57
1268 1317 0.815095 TCCATGATCTGCACGTACGT 59.185 50.000 16.72 16.72 0.00 3.57
1269 1318 1.481240 CTCCATGATCTGCACGTACG 58.519 55.000 15.01 15.01 0.00 3.67
1270 1319 1.409064 TCCTCCATGATCTGCACGTAC 59.591 52.381 0.00 0.00 0.00 3.67
1521 1570 2.355363 ACGAAAGTGCGCTGCGTA 60.355 55.556 24.04 17.28 46.97 4.42
1535 1584 4.665833 AGAACGAATCATGGGATAACGA 57.334 40.909 0.00 0.00 37.11 3.85
1536 1585 4.684703 GGTAGAACGAATCATGGGATAACG 59.315 45.833 0.00 0.00 38.49 3.18
1537 1586 5.696724 CAGGTAGAACGAATCATGGGATAAC 59.303 44.000 0.00 0.00 32.09 1.89
1538 1587 5.365605 ACAGGTAGAACGAATCATGGGATAA 59.634 40.000 0.00 0.00 32.09 1.75
1550 1602 3.664107 ACGTACAGTACAGGTAGAACGA 58.336 45.455 11.37 0.00 0.00 3.85
1556 1608 3.189910 CAGCAAGACGTACAGTACAGGTA 59.810 47.826 11.37 0.00 0.00 3.08
1574 1630 2.857152 GCACGAACAAACAAATTCAGCA 59.143 40.909 0.00 0.00 0.00 4.41
1581 1637 1.813178 TCACCTGCACGAACAAACAAA 59.187 42.857 0.00 0.00 0.00 2.83
1582 1638 1.131504 GTCACCTGCACGAACAAACAA 59.868 47.619 0.00 0.00 0.00 2.83
1583 1639 0.730265 GTCACCTGCACGAACAAACA 59.270 50.000 0.00 0.00 0.00 2.83
1584 1640 0.315869 CGTCACCTGCACGAACAAAC 60.316 55.000 0.00 0.00 39.75 2.93
1747 1803 2.809601 CGGTCGTGGTACTGCTGC 60.810 66.667 0.00 0.00 0.00 5.25
1969 2025 4.047125 ACCTTCCCCGCCATGTGG 62.047 66.667 0.00 0.00 38.53 4.17
2125 2181 1.073763 CCAAGGATGAACTGGTGGTCA 59.926 52.381 0.00 0.00 0.00 4.02
2308 2364 2.031163 AGGTCGGTGCTGTTGAGC 59.969 61.111 0.00 0.00 46.44 4.26
2316 2372 3.050275 GCTTGTCCAGGTCGGTGC 61.050 66.667 0.00 0.00 35.57 5.01
2329 2385 0.798776 CCTGGAGCTTACGTTGCTTG 59.201 55.000 15.21 9.67 41.30 4.01
2359 2415 1.741770 CTTGTCGTAGCTGGTGGCC 60.742 63.158 0.00 0.00 43.05 5.36
2545 2601 1.226717 GCTCGACGTCTCCATCCAC 60.227 63.158 14.70 0.00 0.00 4.02
2647 2703 1.736645 CGCGTCCCAGTTGAACGAT 60.737 57.895 0.00 0.00 38.65 3.73
2715 2771 4.065281 GCCACACGTACCCGAGCT 62.065 66.667 0.00 0.00 37.88 4.09
3010 3066 6.932400 ACAAAACATGCATGAACAATTGAGAT 59.068 30.769 32.75 10.70 0.00 2.75
3090 3149 8.327429 CAAGCAACACCAAACATTTAGTTAAAG 58.673 33.333 0.00 0.00 40.26 1.85
3157 3216 1.066858 ACATGTTGACTACTGCCCTCG 60.067 52.381 0.00 0.00 0.00 4.63
3161 3220 3.365364 GCAAGAACATGTTGACTACTGCC 60.365 47.826 17.58 0.00 0.00 4.85
3258 3317 1.541588 GACCTCATGCCGCTTTTCTTT 59.458 47.619 0.00 0.00 0.00 2.52
3261 3320 0.169009 GTGACCTCATGCCGCTTTTC 59.831 55.000 0.00 0.00 0.00 2.29
3272 3331 0.900421 CCAGAGCTGATGTGACCTCA 59.100 55.000 0.00 0.00 0.00 3.86
3277 3336 7.446319 CCAATTATATTTCCAGAGCTGATGTGA 59.554 37.037 0.00 0.00 0.00 3.58
3360 3442 4.007659 ACAGTTTACCCCGATTTGACATC 58.992 43.478 0.00 0.00 0.00 3.06
3441 6545 7.686438 TGCTTGTTTGAGTTGACATACATAT 57.314 32.000 0.00 0.00 33.42 1.78
3506 6617 9.525826 AAGAACTTCATTGTCCTGATTAGAAAT 57.474 29.630 0.00 0.00 0.00 2.17
3510 6621 9.311916 CTCTAAGAACTTCATTGTCCTGATTAG 57.688 37.037 0.00 0.00 0.00 1.73
3581 6694 2.278142 GCGATTTGGCATGCGACC 60.278 61.111 12.44 0.00 0.00 4.79
3599 6712 8.186821 AGTTACTGTGATACGTATGGTTAAGTC 58.813 37.037 13.97 0.00 0.00 3.01
3605 6718 7.636150 ACTTAGTTACTGTGATACGTATGGT 57.364 36.000 13.97 8.71 0.00 3.55
3646 6759 5.306114 ACTACTTAACTGAGGGTGCTTTT 57.694 39.130 0.00 0.00 0.00 2.27
3660 6773 9.186837 CCTTTCTGATGTACTCCTACTACTTAA 57.813 37.037 0.00 0.00 0.00 1.85
3761 6881 1.532238 GCCTTGGGCTAAGTAGGGG 59.468 63.158 9.87 0.00 46.69 4.79
3797 6918 2.036346 TCTCATCATCGCGGTGATCATT 59.964 45.455 31.15 9.88 36.72 2.57
3823 6944 5.001874 AGTGCATGATGATCGCAATTATCT 58.998 37.500 0.00 0.00 37.41 1.98
3893 7014 1.402613 GTAAACCACGTGCAAACTGGT 59.597 47.619 10.91 5.55 40.17 4.00
3991 7115 7.278646 ACATCTTTTCCTTTTGCTTTCTGTTTC 59.721 33.333 0.00 0.00 0.00 2.78


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

AutoCloner maintained by Alex Coulton.