Multiple sequence alignment - TraesCS7B01G087800

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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 TraesCS7B01G087800 chr7B 100.000 3155 0 0 1 3155 103081072 103077918 0.000000e+00 5827
1 TraesCS7B01G087800 chr7B 88.021 384 36 5 2622 3000 102647243 102646865 2.230000e-121 446
2 TraesCS7B01G087800 chr7B 88.489 278 29 3 2724 3000 102805708 102805433 1.810000e-87 333
3 TraesCS7B01G087800 chr7B 86.154 130 12 5 571 699 328589542 328589418 5.490000e-28 135
4 TraesCS7B01G087800 chr7A 94.058 2373 99 22 813 3155 137800453 137798093 0.000000e+00 3563
5 TraesCS7B01G087800 chr7A 87.175 577 52 17 260 826 137801062 137800498 1.230000e-178 636
6 TraesCS7B01G087800 chr7A 84.940 166 19 5 571 734 610191140 610191301 2.520000e-36 163
7 TraesCS7B01G087800 chr7D 95.721 2197 82 8 962 3155 137790127 137787940 0.000000e+00 3526
8 TraesCS7B01G087800 chr7D 89.239 381 36 3 2622 3000 137716020 137715643 3.680000e-129 472
9 TraesCS7B01G087800 chr7D 89.005 382 36 3 2622 3000 137605560 137605182 4.760000e-128 468
10 TraesCS7B01G087800 chr7D 89.524 315 26 5 519 831 137790649 137790340 2.950000e-105 392
11 TraesCS7B01G087800 chr7D 86.469 303 29 7 2855 3155 137784502 137784210 3.930000e-84 322
12 TraesCS7B01G087800 chr7D 90.083 242 20 3 4 244 137793019 137792781 8.500000e-81 311
13 TraesCS7B01G087800 chr7D 88.213 263 23 7 260 519 137792793 137792536 1.100000e-79 307
14 TraesCS7B01G087800 chr7D 89.691 97 0 1 813 899 137790303 137790207 7.150000e-22 115
15 TraesCS7B01G087800 chr7D 90.588 85 7 1 650 734 5173706 5173623 9.250000e-21 111
16 TraesCS7B01G087800 chrUn 88.976 381 37 3 2622 3000 330791215 330791592 1.710000e-127 466
17 TraesCS7B01G087800 chrUn 74.793 242 50 8 1064 1295 102006573 102006333 7.200000e-17 99
18 TraesCS7B01G087800 chr2B 85.366 164 19 4 571 734 583417238 583417396 7.000000e-37 165
19 TraesCS7B01G087800 chr2B 85.417 144 20 1 354 497 209136639 209136497 7.050000e-32 148
20 TraesCS7B01G087800 chr6D 85.185 162 19 4 574 734 115633574 115633417 9.060000e-36 161
21 TraesCS7B01G087800 chr6D 73.651 315 67 12 1085 1391 7728528 7728834 1.200000e-19 108
22 TraesCS7B01G087800 chr4B 84.146 164 19 6 572 734 559158625 559158468 5.450000e-33 152
23 TraesCS7B01G087800 chr5A 73.684 361 70 18 1062 1405 650824603 650824955 1.990000e-22 117
24 TraesCS7B01G087800 chr6B 74.448 317 51 19 976 1284 14340434 14340728 3.330000e-20 110
25 TraesCS7B01G087800 chr6A 75.207 242 49 7 1064 1295 34303845 34303605 1.550000e-18 104
26 TraesCS7B01G087800 chr6A 75.207 242 49 7 1064 1295 34414549 34414309 1.550000e-18 104
27 TraesCS7B01G087800 chr5D 78.212 179 28 8 1062 1230 524577577 524577754 1.550000e-18 104
28 TraesCS7B01G087800 chr1B 77.976 168 31 5 568 734 470550982 470551144 2.000000e-17 100


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 TraesCS7B01G087800 chr7B 103077918 103081072 3154 True 5827.000000 5827 100.000000 1 3155 1 chr7B.!!$R3 3154
1 TraesCS7B01G087800 chr7A 137798093 137801062 2969 True 2099.500000 3563 90.616500 260 3155 2 chr7A.!!$R1 2895
2 TraesCS7B01G087800 chr7D 137784210 137793019 8809 True 828.833333 3526 89.950167 4 3155 6 chr7D.!!$R4 3151

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
944 2958 0.09820 GCATACGTTTCCGCTTTCCC 59.902 55.0 0.0 0.0 37.7 3.97 F
948 2962 0.17904 ACGTTTCCGCTTTCCCTCAA 60.179 50.0 0.0 0.0 37.7 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1765 3779 0.106918 TCCTGTGAAAACCCAAGCGT 60.107 50.0 0.0 0.0 0.00 5.07 R
2592 4606 0.383949 GTGTTTGCACAATGGACGGT 59.616 50.0 0.0 0.0 44.64 4.83 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
39 40 5.588246 ACATGTGTTCAATATATGTCCGCAA 59.412 36.000 0.00 0.00 0.00 4.85
50 51 0.597568 TGTCCGCAATTCAAGGCTTG 59.402 50.000 21.17 21.17 0.00 4.01
84 85 4.332828 ACACTATTTCCCAAAGGCTACAC 58.667 43.478 0.00 0.00 0.00 2.90
88 89 5.652452 ACTATTTCCCAAAGGCTACACAATC 59.348 40.000 0.00 0.00 0.00 2.67
89 90 3.517296 TTCCCAAAGGCTACACAATCA 57.483 42.857 0.00 0.00 0.00 2.57
102 103 6.749118 GGCTACACAATCATTTTAGCTTTGAG 59.251 38.462 0.00 0.00 36.28 3.02
161 163 4.038642 TGGTTCTTTAGTTGGCAACCATTC 59.961 41.667 25.81 10.48 41.26 2.67
162 164 4.556233 GTTCTTTAGTTGGCAACCATTCC 58.444 43.478 25.81 5.64 31.53 3.01
163 165 2.817258 TCTTTAGTTGGCAACCATTCCG 59.183 45.455 25.81 10.53 31.53 4.30
164 166 2.279935 TTAGTTGGCAACCATTCCGT 57.720 45.000 25.81 8.88 31.53 4.69
165 167 1.529226 TAGTTGGCAACCATTCCGTG 58.471 50.000 25.81 0.00 31.53 4.94
185 187 2.287308 TGAAACTCCACGGCAAAATTCG 60.287 45.455 0.00 0.00 0.00 3.34
212 214 6.546428 TCTTTCGAGAATAATGGAGAGGTT 57.454 37.500 0.00 0.00 0.00 3.50
215 217 8.537016 TCTTTCGAGAATAATGGAGAGGTTAAA 58.463 33.333 0.00 0.00 0.00 1.52
227 229 7.875327 TGGAGAGGTTAAATATTTTACTGCC 57.125 36.000 14.94 11.70 0.00 4.85
234 236 8.630037 AGGTTAAATATTTTACTGCCATAGTGC 58.370 33.333 14.94 0.00 40.65 4.40
235 237 8.630037 GGTTAAATATTTTACTGCCATAGTGCT 58.370 33.333 14.94 0.00 40.65 4.40
239 241 8.980481 AATATTTTACTGCCATAGTGCTAAGT 57.020 30.769 0.00 0.00 40.65 2.24
240 242 6.927294 ATTTTACTGCCATAGTGCTAAGTC 57.073 37.500 0.00 0.00 40.65 3.01
241 243 5.677319 TTTACTGCCATAGTGCTAAGTCT 57.323 39.130 0.00 0.00 40.65 3.24
242 244 5.677319 TTACTGCCATAGTGCTAAGTCTT 57.323 39.130 0.00 0.00 40.65 3.01
243 245 4.559862 ACTGCCATAGTGCTAAGTCTTT 57.440 40.909 0.00 0.00 38.49 2.52
244 246 4.508662 ACTGCCATAGTGCTAAGTCTTTC 58.491 43.478 0.00 0.00 38.49 2.62
245 247 3.873910 TGCCATAGTGCTAAGTCTTTCC 58.126 45.455 0.00 0.00 0.00 3.13
246 248 3.206964 GCCATAGTGCTAAGTCTTTCCC 58.793 50.000 0.00 0.00 0.00 3.97
247 249 3.809905 CCATAGTGCTAAGTCTTTCCCC 58.190 50.000 0.00 0.00 0.00 4.81
248 250 3.433740 CCATAGTGCTAAGTCTTTCCCCC 60.434 52.174 0.00 0.00 0.00 5.40
249 251 0.613777 AGTGCTAAGTCTTTCCCCCG 59.386 55.000 0.00 0.00 0.00 5.73
250 252 1.025113 GTGCTAAGTCTTTCCCCCGC 61.025 60.000 0.00 0.00 0.00 6.13
251 253 1.298667 GCTAAGTCTTTCCCCCGCA 59.701 57.895 0.00 0.00 0.00 5.69
252 254 0.744771 GCTAAGTCTTTCCCCCGCAG 60.745 60.000 0.00 0.00 0.00 5.18
253 255 0.902531 CTAAGTCTTTCCCCCGCAGA 59.097 55.000 0.00 0.00 0.00 4.26
254 256 1.278127 CTAAGTCTTTCCCCCGCAGAA 59.722 52.381 0.00 0.00 0.00 3.02
255 257 0.476771 AAGTCTTTCCCCCGCAGAAA 59.523 50.000 0.00 0.00 0.00 2.52
256 258 0.476771 AGTCTTTCCCCCGCAGAAAA 59.523 50.000 0.00 0.00 33.06 2.29
257 259 1.133606 AGTCTTTCCCCCGCAGAAAAA 60.134 47.619 0.00 0.00 33.06 1.94
258 260 1.269723 GTCTTTCCCCCGCAGAAAAAG 59.730 52.381 0.00 0.00 33.06 2.27
274 276 6.019559 GCAGAAAAAGGTGCTAAGTCTTTTTG 60.020 38.462 14.93 6.47 45.16 2.44
276 278 7.545615 CAGAAAAAGGTGCTAAGTCTTTTTGTT 59.454 33.333 14.93 4.07 45.16 2.83
277 279 8.094548 AGAAAAAGGTGCTAAGTCTTTTTGTTT 58.905 29.630 14.93 2.21 45.16 2.83
278 280 8.615878 AAAAAGGTGCTAAGTCTTTTTGTTTT 57.384 26.923 10.84 0.00 44.19 2.43
279 281 7.595311 AAAGGTGCTAAGTCTTTTTGTTTTG 57.405 32.000 0.00 0.00 0.00 2.44
280 282 5.109210 AGGTGCTAAGTCTTTTTGTTTTGC 58.891 37.500 0.00 0.00 0.00 3.68
310 312 0.731855 GTGCTAAGTCGACCGACCAC 60.732 60.000 17.62 14.23 45.59 4.16
315 317 1.861971 AAGTCGACCGACCACTTTTC 58.138 50.000 17.62 0.00 45.59 2.29
362 366 7.521871 TTTTTAAAGTCGGGCCACTTTATTA 57.478 32.000 26.98 19.91 44.55 0.98
363 367 6.499234 TTTAAAGTCGGGCCACTTTATTAC 57.501 37.500 26.98 2.98 44.55 1.89
405 409 4.847198 TCATTACAAGATCATGTGGCACT 58.153 39.130 19.83 0.00 34.75 4.40
454 458 6.183360 ACCTAATGTTTAAGCATGCTTAGCAG 60.183 38.462 32.55 24.14 43.65 4.24
455 459 4.644103 ATGTTTAAGCATGCTTAGCAGG 57.356 40.909 32.55 14.92 43.65 4.85
457 461 3.440173 TGTTTAAGCATGCTTAGCAGGAC 59.560 43.478 32.55 25.59 43.36 3.85
460 464 2.205022 AGCATGCTTAGCAGGACAAA 57.795 45.000 23.33 0.00 43.36 2.83
461 465 1.815003 AGCATGCTTAGCAGGACAAAC 59.185 47.619 23.33 4.18 43.36 2.93
462 466 1.466360 GCATGCTTAGCAGGACAAACG 60.466 52.381 23.33 0.00 43.36 3.60
463 467 2.076100 CATGCTTAGCAGGACAAACGA 58.924 47.619 14.03 0.00 43.36 3.85
464 468 2.472695 TGCTTAGCAGGACAAACGAT 57.527 45.000 1.39 0.00 33.32 3.73
465 469 2.346803 TGCTTAGCAGGACAAACGATC 58.653 47.619 1.39 0.00 33.32 3.69
466 470 1.666189 GCTTAGCAGGACAAACGATCC 59.334 52.381 0.00 0.00 36.38 3.36
507 511 6.705863 ACCCTCATGAATATTGAGAAAAGC 57.294 37.500 4.73 0.00 42.63 3.51
526 2417 4.148128 AGCCAACTGATCATTAGGACAG 57.852 45.455 10.62 0.00 36.58 3.51
531 2422 2.437281 ACTGATCATTAGGACAGGCAGG 59.563 50.000 0.00 0.00 35.08 4.85
539 2430 2.267324 GACAGGCAGGCCAGAGAC 59.733 66.667 13.63 0.00 38.92 3.36
559 2450 6.448714 AGAGACCAGGCCTGTATAGATAGATA 59.551 42.308 30.63 0.00 0.00 1.98
560 2451 7.130285 AGAGACCAGGCCTGTATAGATAGATAT 59.870 40.741 30.63 4.99 0.00 1.63
565 2456 9.509956 CCAGGCCTGTATAGATAGATATAGTAC 57.490 40.741 30.63 0.00 0.00 2.73
594 2485 4.260170 GAGAATATCATGTGCTCCCATCC 58.740 47.826 0.00 0.00 0.00 3.51
595 2486 3.654321 AGAATATCATGTGCTCCCATCCA 59.346 43.478 0.00 0.00 0.00 3.41
640 2531 9.206870 CCAGTTTTCAAAATGCACATTTATAGT 57.793 29.630 8.92 0.00 39.88 2.12
644 2535 9.900710 TTTTCAAAATGCACATTTATAGTACGT 57.099 25.926 8.92 0.00 39.88 3.57
703 2601 6.149973 CACATCACATGAGTGTACAATTCCTT 59.850 38.462 0.00 0.00 46.01 3.36
707 2605 8.684386 TCACATGAGTGTACAATTCCTTAAAA 57.316 30.769 0.00 0.00 46.01 1.52
708 2606 9.126151 TCACATGAGTGTACAATTCCTTAAAAA 57.874 29.630 0.00 0.00 46.01 1.94
790 2688 6.144241 TCAAAATTCAAAATGTGATGTCAGCG 59.856 34.615 0.00 0.00 35.70 5.18
793 2691 2.157474 TCAAAATGTGATGTCAGCGTCG 59.843 45.455 0.00 0.00 33.44 5.12
809 2707 3.680937 AGCGTCGACAAATATTTTCGGAA 59.319 39.130 17.16 9.58 33.50 4.30
913 2927 1.571215 CTTTGTACCCACGTTCCGCC 61.571 60.000 0.00 0.00 0.00 6.13
935 2949 3.173853 TGCCGCTGCATACGTTTC 58.826 55.556 0.00 0.00 44.23 2.78
936 2950 2.395360 TGCCGCTGCATACGTTTCC 61.395 57.895 0.00 0.00 44.23 3.13
937 2951 2.701006 CCGCTGCATACGTTTCCG 59.299 61.111 0.00 0.00 40.83 4.30
938 2952 2.021380 CGCTGCATACGTTTCCGC 59.979 61.111 0.00 0.00 37.70 5.54
939 2953 2.452813 CGCTGCATACGTTTCCGCT 61.453 57.895 0.00 0.00 37.70 5.52
940 2954 1.794222 GCTGCATACGTTTCCGCTT 59.206 52.632 0.00 0.00 37.70 4.68
941 2955 0.168128 GCTGCATACGTTTCCGCTTT 59.832 50.000 0.00 0.00 37.70 3.51
942 2956 1.790481 GCTGCATACGTTTCCGCTTTC 60.790 52.381 0.00 0.00 37.70 2.62
943 2957 0.800012 TGCATACGTTTCCGCTTTCC 59.200 50.000 0.00 0.00 37.70 3.13
944 2958 0.098200 GCATACGTTTCCGCTTTCCC 59.902 55.000 0.00 0.00 37.70 3.97
945 2959 1.734163 CATACGTTTCCGCTTTCCCT 58.266 50.000 0.00 0.00 37.70 4.20
946 2960 1.664151 CATACGTTTCCGCTTTCCCTC 59.336 52.381 0.00 0.00 37.70 4.30
947 2961 0.680618 TACGTTTCCGCTTTCCCTCA 59.319 50.000 0.00 0.00 37.70 3.86
948 2962 0.179040 ACGTTTCCGCTTTCCCTCAA 60.179 50.000 0.00 0.00 37.70 3.02
949 2963 0.948678 CGTTTCCGCTTTCCCTCAAA 59.051 50.000 0.00 0.00 0.00 2.69
950 2964 1.069227 CGTTTCCGCTTTCCCTCAAAG 60.069 52.381 0.00 0.00 44.10 2.77
951 2965 2.227194 GTTTCCGCTTTCCCTCAAAGA 58.773 47.619 0.00 0.00 44.02 2.52
952 2966 2.621526 GTTTCCGCTTTCCCTCAAAGAA 59.378 45.455 0.00 0.00 44.02 2.52
953 2967 2.649531 TCCGCTTTCCCTCAAAGAAA 57.350 45.000 0.00 0.00 44.02 2.52
954 2968 2.938838 TCCGCTTTCCCTCAAAGAAAA 58.061 42.857 0.00 0.00 44.02 2.29
955 2969 3.292460 TCCGCTTTCCCTCAAAGAAAAA 58.708 40.909 0.00 0.00 44.02 1.94
1061 3075 1.456287 GCTACCCACCATCCCATCC 59.544 63.158 0.00 0.00 0.00 3.51
1090 3104 2.606826 ACCTCGTTCCCCTCCACC 60.607 66.667 0.00 0.00 0.00 4.61
1215 3229 0.980423 GAAGGCTCTCCAACCTCACT 59.020 55.000 0.00 0.00 34.31 3.41
1224 3238 0.247736 CCAACCTCACTTCCCTCTCG 59.752 60.000 0.00 0.00 0.00 4.04
1231 3245 1.990614 ACTTCCCTCTCGAAGCCCC 60.991 63.158 0.00 0.00 42.57 5.80
1257 3271 1.460699 GGTGGCCTTTCTCTTGGGT 59.539 57.895 3.32 0.00 0.00 4.51
1485 3499 0.251077 ACCCCAAGCTGCTCTTTCTG 60.251 55.000 1.00 0.00 31.27 3.02
1546 3560 1.026718 GGTGATCAAGCCGAACCTGG 61.027 60.000 0.00 0.00 0.00 4.45
1577 3591 3.567478 AGAATGTGGGATAAGTGCTCC 57.433 47.619 0.00 0.00 0.00 4.70
1589 3603 3.641434 AAGTGCTCCTGATATTGCAGT 57.359 42.857 0.00 0.00 40.32 4.40
1765 3779 8.740906 TCGCCAGGAAAATACAATTTTTACATA 58.259 29.630 0.00 0.00 32.76 2.29
1845 3859 8.907885 GTCCTGGCTTTATCTGATAAAAAGATT 58.092 33.333 20.00 0.00 35.92 2.40
1939 3953 4.584743 TGATCATGTATAGCGTTGAGAGGT 59.415 41.667 0.00 0.00 0.00 3.85
2015 4029 6.518493 TGGACGTGGAATTGGACTATTATAC 58.482 40.000 0.00 0.00 0.00 1.47
2146 4160 1.464997 CAAAAGGAAGTGCTCGGCTAC 59.535 52.381 0.00 0.00 0.00 3.58
2150 4164 1.352156 GGAAGTGCTCGGCTACAACG 61.352 60.000 0.00 0.00 0.00 4.10
2174 4188 2.831685 AACTGTGGTGTGCGAGAATA 57.168 45.000 0.00 0.00 0.00 1.75
2257 4271 1.248486 TCGGTTCAGAGTCAGAGTGG 58.752 55.000 0.00 0.00 0.00 4.00
2592 4606 6.378745 TGCAGATCCTACCCATTAGTTACTA 58.621 40.000 0.00 0.00 0.00 1.82
2593 4607 6.267014 TGCAGATCCTACCCATTAGTTACTAC 59.733 42.308 0.00 0.00 0.00 2.73
2594 4608 6.295180 GCAGATCCTACCCATTAGTTACTACC 60.295 46.154 0.00 0.00 0.00 3.18
2677 4694 9.305110 CGATTGCTACAAAAACAATTCATTTTC 57.695 29.630 0.00 0.00 34.28 2.29
2726 4743 9.820725 CATGTTCAAATTTTGGATATGTGGTAT 57.179 29.630 15.47 0.00 34.22 2.73
2793 4810 2.439507 CCAGTACTTATCCCTGCCACAT 59.560 50.000 0.00 0.00 0.00 3.21
2821 4838 7.156876 TCAAGGTTATGCTTTAGTTGGAATG 57.843 36.000 0.00 0.00 0.00 2.67
2878 4895 2.875094 AGCTGCCTCTTTTGTCTCAT 57.125 45.000 0.00 0.00 0.00 2.90
2962 4979 2.053627 CTTTGAGGCGTTGTCATTTGC 58.946 47.619 0.00 0.00 0.00 3.68
3012 5029 6.206634 TCCAACTGTTGTTTTATCTGTCCATC 59.793 38.462 18.38 0.00 33.52 3.51
3067 5085 3.944055 GTGGCAAGAGTCACTAGAGAA 57.056 47.619 0.00 0.00 46.70 2.87
3068 5086 3.843999 GTGGCAAGAGTCACTAGAGAAG 58.156 50.000 0.00 0.00 46.70 2.85
3069 5087 2.828520 TGGCAAGAGTCACTAGAGAAGG 59.171 50.000 0.00 0.00 0.00 3.46
3070 5088 2.829120 GGCAAGAGTCACTAGAGAAGGT 59.171 50.000 0.00 0.00 0.00 3.50
3089 5109 7.652727 AGAAGGTTTTTCTTATCAAGCACTTC 58.347 34.615 0.00 0.00 0.00 3.01
3124 5144 4.338118 TGGTGTTCTAAGGAGCAACAAAAG 59.662 41.667 0.00 0.00 45.01 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.774354 AACACATGTTCATTTTGCTCATTC 57.226 33.333 0.00 0.00 31.64 2.67
16 17 5.671742 TGCGGACATATATTGAACACATG 57.328 39.130 0.00 0.00 0.00 3.21
21 22 6.857964 CCTTGAATTGCGGACATATATTGAAC 59.142 38.462 0.00 0.00 0.00 3.18
25 26 5.072741 AGCCTTGAATTGCGGACATATATT 58.927 37.500 0.00 0.00 0.00 1.28
36 37 3.928375 CCACAATACAAGCCTTGAATTGC 59.072 43.478 12.25 0.00 0.00 3.56
39 40 6.183360 TGTTTTCCACAATACAAGCCTTGAAT 60.183 34.615 12.25 0.00 29.87 2.57
72 73 5.807011 GCTAAAATGATTGTGTAGCCTTTGG 59.193 40.000 5.09 0.00 32.74 3.28
77 78 6.620678 TCAAAGCTAAAATGATTGTGTAGCC 58.379 36.000 10.42 0.00 38.33 3.93
78 79 6.252228 GCTCAAAGCTAAAATGATTGTGTAGC 59.748 38.462 7.37 7.37 38.45 3.58
84 85 4.560035 CGGTGCTCAAAGCTAAAATGATTG 59.440 41.667 0.11 0.00 42.97 2.67
88 89 3.829886 TCGGTGCTCAAAGCTAAAATG 57.170 42.857 0.11 0.00 42.97 2.32
89 90 4.458989 TGAATCGGTGCTCAAAGCTAAAAT 59.541 37.500 0.11 0.00 42.97 1.82
102 103 5.803020 AGAGACTTTATTTGAATCGGTGC 57.197 39.130 0.00 0.00 0.00 5.01
163 165 2.793278 ATTTTGCCGTGGAGTTTCAC 57.207 45.000 0.00 0.00 0.00 3.18
164 166 2.287308 CGAATTTTGCCGTGGAGTTTCA 60.287 45.455 0.00 0.00 0.00 2.69
165 167 2.031508 TCGAATTTTGCCGTGGAGTTTC 60.032 45.455 0.00 0.00 0.00 2.78
185 187 7.713073 ACCTCTCCATTATTCTCGAAAGAAATC 59.287 37.037 0.00 0.00 44.49 2.17
201 203 8.914011 GGCAGTAAAATATTTAACCTCTCCATT 58.086 33.333 0.01 0.00 0.00 3.16
215 217 8.432805 AGACTTAGCACTATGGCAGTAAAATAT 58.567 33.333 0.00 0.00 34.98 1.28
221 223 5.395324 GGAAAGACTTAGCACTATGGCAGTA 60.395 44.000 0.00 0.00 34.98 2.74
227 229 3.741388 CGGGGGAAAGACTTAGCACTATG 60.741 52.174 0.00 0.00 0.00 2.23
231 233 1.025113 GCGGGGGAAAGACTTAGCAC 61.025 60.000 0.00 0.00 0.00 4.40
232 234 1.298667 GCGGGGGAAAGACTTAGCA 59.701 57.895 0.00 0.00 0.00 3.49
233 235 0.744771 CTGCGGGGGAAAGACTTAGC 60.745 60.000 0.00 0.00 0.00 3.09
234 236 0.902531 TCTGCGGGGGAAAGACTTAG 59.097 55.000 0.00 0.00 0.00 2.18
235 237 1.354101 TTCTGCGGGGGAAAGACTTA 58.646 50.000 0.00 0.00 0.00 2.24
236 238 0.476771 TTTCTGCGGGGGAAAGACTT 59.523 50.000 0.00 0.00 0.00 3.01
237 239 0.476771 TTTTCTGCGGGGGAAAGACT 59.523 50.000 0.00 0.00 34.73 3.24
238 240 1.269723 CTTTTTCTGCGGGGGAAAGAC 59.730 52.381 9.28 0.00 34.73 3.01
239 241 1.616159 CTTTTTCTGCGGGGGAAAGA 58.384 50.000 9.28 0.00 34.73 2.52
240 242 0.603065 CCTTTTTCTGCGGGGGAAAG 59.397 55.000 0.00 1.27 34.73 2.62
241 243 0.105913 ACCTTTTTCTGCGGGGGAAA 60.106 50.000 0.00 0.00 0.00 3.13
242 244 0.825840 CACCTTTTTCTGCGGGGGAA 60.826 55.000 0.00 0.00 0.00 3.97
243 245 1.228429 CACCTTTTTCTGCGGGGGA 60.228 57.895 0.00 0.00 0.00 4.81
244 246 2.931068 GCACCTTTTTCTGCGGGGG 61.931 63.158 0.00 0.00 0.00 5.40
245 247 0.608035 TAGCACCTTTTTCTGCGGGG 60.608 55.000 0.00 0.00 38.51 5.73
246 248 1.200020 CTTAGCACCTTTTTCTGCGGG 59.800 52.381 0.00 0.00 38.51 6.13
247 249 1.880027 ACTTAGCACCTTTTTCTGCGG 59.120 47.619 0.00 0.00 38.51 5.69
248 250 2.808543 AGACTTAGCACCTTTTTCTGCG 59.191 45.455 0.00 0.00 38.51 5.18
249 251 4.837896 AAGACTTAGCACCTTTTTCTGC 57.162 40.909 0.00 0.00 0.00 4.26
250 252 7.035612 ACAAAAAGACTTAGCACCTTTTTCTG 58.964 34.615 13.39 9.42 43.85 3.02
251 253 7.170393 ACAAAAAGACTTAGCACCTTTTTCT 57.830 32.000 13.39 4.62 43.85 2.52
252 254 7.827819 AACAAAAAGACTTAGCACCTTTTTC 57.172 32.000 13.39 0.00 43.85 2.29
253 255 8.503196 CAAAACAAAAAGACTTAGCACCTTTTT 58.497 29.630 11.63 11.63 45.47 1.94
254 256 7.360861 GCAAAACAAAAAGACTTAGCACCTTTT 60.361 33.333 0.00 0.00 40.57 2.27
255 257 6.092122 GCAAAACAAAAAGACTTAGCACCTTT 59.908 34.615 0.00 0.00 0.00 3.11
256 258 5.580691 GCAAAACAAAAAGACTTAGCACCTT 59.419 36.000 0.00 0.00 0.00 3.50
257 259 5.109210 GCAAAACAAAAAGACTTAGCACCT 58.891 37.500 0.00 0.00 0.00 4.00
258 260 4.026886 CGCAAAACAAAAAGACTTAGCACC 60.027 41.667 0.00 0.00 0.00 5.01
274 276 3.195661 AGCACTATAGCTACCGCAAAAC 58.804 45.455 0.00 0.00 44.50 2.43
276 278 4.098960 ACTTAGCACTATAGCTACCGCAAA 59.901 41.667 0.00 0.00 46.07 3.68
277 279 3.635373 ACTTAGCACTATAGCTACCGCAA 59.365 43.478 0.00 0.00 46.07 4.85
278 280 3.220110 ACTTAGCACTATAGCTACCGCA 58.780 45.455 0.00 0.00 46.07 5.69
279 281 3.667430 CGACTTAGCACTATAGCTACCGC 60.667 52.174 0.00 0.00 46.07 5.68
280 282 3.744942 TCGACTTAGCACTATAGCTACCG 59.255 47.826 0.00 2.37 46.07 4.02
340 342 6.149807 CAGTAATAAAGTGGCCCGACTTTAAA 59.850 38.462 24.45 16.22 46.43 1.52
343 345 4.007659 CAGTAATAAAGTGGCCCGACTTT 58.992 43.478 21.17 21.17 45.87 2.66
346 348 3.195661 CTCAGTAATAAAGTGGCCCGAC 58.804 50.000 0.00 0.00 0.00 4.79
351 355 5.567138 ACATTGCTCAGTAATAAAGTGGC 57.433 39.130 0.00 0.00 0.00 5.01
362 366 3.354948 TGCCTATGAACATTGCTCAGT 57.645 42.857 0.00 0.00 0.00 3.41
363 367 3.881089 TGATGCCTATGAACATTGCTCAG 59.119 43.478 0.00 0.00 0.00 3.35
430 434 6.135290 TGCTAAGCATGCTTAAACATTAGG 57.865 37.500 33.51 22.49 37.97 2.69
439 443 3.348647 TTGTCCTGCTAAGCATGCTTA 57.651 42.857 32.44 32.44 38.13 3.09
454 458 5.709966 AGCAATTTTAAGGATCGTTTGTCC 58.290 37.500 5.89 0.00 35.94 4.02
455 459 7.527457 AGTAGCAATTTTAAGGATCGTTTGTC 58.473 34.615 5.89 0.00 0.00 3.18
457 461 8.237267 AGAAGTAGCAATTTTAAGGATCGTTTG 58.763 33.333 5.89 0.00 0.00 2.93
460 464 7.494952 GGTAGAAGTAGCAATTTTAAGGATCGT 59.505 37.037 0.00 0.00 0.00 3.73
461 465 7.041984 GGGTAGAAGTAGCAATTTTAAGGATCG 60.042 40.741 0.00 0.00 0.00 3.69
462 466 7.993758 AGGGTAGAAGTAGCAATTTTAAGGATC 59.006 37.037 0.00 0.00 0.00 3.36
463 467 7.873195 AGGGTAGAAGTAGCAATTTTAAGGAT 58.127 34.615 0.00 0.00 0.00 3.24
464 468 7.037873 TGAGGGTAGAAGTAGCAATTTTAAGGA 60.038 37.037 0.00 0.00 0.00 3.36
465 469 7.110155 TGAGGGTAGAAGTAGCAATTTTAAGG 58.890 38.462 0.00 0.00 0.00 2.69
466 470 8.616076 CATGAGGGTAGAAGTAGCAATTTTAAG 58.384 37.037 0.00 0.00 0.00 1.85
507 511 3.209410 GCCTGTCCTAATGATCAGTTGG 58.791 50.000 16.14 16.14 0.00 3.77
526 2417 4.106925 CCTGGTCTCTGGCCTGCC 62.107 72.222 3.32 0.00 0.00 4.85
539 2430 9.509956 GTACTATATCTATCTATACAGGCCTGG 57.490 40.741 35.42 18.44 34.19 4.45
559 2450 8.756927 CACATGATATTCTCCCATCTGTACTAT 58.243 37.037 0.00 0.00 0.00 2.12
560 2451 7.310052 GCACATGATATTCTCCCATCTGTACTA 60.310 40.741 0.00 0.00 0.00 1.82
565 2456 4.907809 AGCACATGATATTCTCCCATCTG 58.092 43.478 0.00 0.00 0.00 2.90
582 2473 0.409092 ACCAAATGGATGGGAGCACA 59.591 50.000 6.42 0.00 45.18 4.57
641 2532 9.849166 ATTGTTTTCGGAATTATTTTGATACGT 57.151 25.926 0.00 0.00 0.00 3.57
646 2537 8.768955 CCACAATTGTTTTCGGAATTATTTTGA 58.231 29.630 8.77 0.00 0.00 2.69
647 2538 8.768955 TCCACAATTGTTTTCGGAATTATTTTG 58.231 29.630 8.77 0.00 0.00 2.44
649 2540 8.934825 CATCCACAATTGTTTTCGGAATTATTT 58.065 29.630 16.72 0.35 0.00 1.40
650 2541 8.093927 ACATCCACAATTGTTTTCGGAATTATT 58.906 29.630 16.72 0.95 0.00 1.40
651 2542 7.610865 ACATCCACAATTGTTTTCGGAATTAT 58.389 30.769 16.72 1.27 0.00 1.28
652 2543 6.987386 ACATCCACAATTGTTTTCGGAATTA 58.013 32.000 16.72 0.00 0.00 1.40
788 2686 3.644805 TCCGAAAATATTTGTCGACGC 57.355 42.857 22.84 0.00 36.92 5.19
935 2949 3.726291 TTTTTCTTTGAGGGAAAGCGG 57.274 42.857 0.00 0.00 40.95 5.52
1003 3017 2.738480 CGTTCGGAGGTGGTGGAA 59.262 61.111 0.00 0.00 0.00 3.53
1090 3104 3.775654 GGTGGTGGAGAGGAGGCG 61.776 72.222 0.00 0.00 0.00 5.52
1215 3229 1.990060 CTGGGGCTTCGAGAGGGAA 60.990 63.158 0.00 0.00 0.00 3.97
1485 3499 1.082104 CTCGCGGTTTGACTTTGCC 60.082 57.895 6.13 0.00 0.00 4.52
1519 3533 1.202463 CGGCTTGATCACCTTCTCGAT 60.202 52.381 0.00 0.00 0.00 3.59
1546 3560 0.967380 CCACATTCTTGGAGGGTGGC 60.967 60.000 0.00 0.00 42.11 5.01
1577 3591 8.454106 AGTACAAGCTTAAAACTGCAATATCAG 58.546 33.333 0.00 0.00 39.86 2.90
1589 3603 4.202284 ACCGACAGGAGTACAAGCTTAAAA 60.202 41.667 0.00 0.00 41.02 1.52
1657 3671 1.320344 TGCACGCCTAACTCCTCGAT 61.320 55.000 0.00 0.00 0.00 3.59
1686 3700 3.799755 GCACGGCGGAACATCCAC 61.800 66.667 13.24 0.00 35.91 4.02
1765 3779 0.106918 TCCTGTGAAAACCCAAGCGT 60.107 50.000 0.00 0.00 0.00 5.07
1770 3784 3.577848 CCAAATCATCCTGTGAAAACCCA 59.422 43.478 0.00 0.00 40.97 4.51
1845 3859 0.904865 AGAACCCCACAGATCGCTGA 60.905 55.000 0.00 0.00 45.17 4.26
1939 3953 2.113562 GTACCGGGGCAACAACCA 59.886 61.111 6.32 0.00 39.74 3.67
2015 4029 3.592814 CAGCCAGCGATGCCATGG 61.593 66.667 7.63 7.63 37.15 3.66
2146 4160 0.732571 ACACCACAGTTTCAGCGTTG 59.267 50.000 0.00 0.00 0.00 4.10
2150 4164 1.009675 CGCACACCACAGTTTCAGC 60.010 57.895 0.00 0.00 0.00 4.26
2174 4188 5.523916 CCTCGGATAATCTCAAAATGAACGT 59.476 40.000 0.00 0.00 0.00 3.99
2245 4259 2.666272 TCACAGTCCACTCTGACTCT 57.334 50.000 0.65 0.00 43.63 3.24
2257 4271 6.899114 ACGGACTTTTTATCAATTCACAGTC 58.101 36.000 0.00 0.00 0.00 3.51
2592 4606 0.383949 GTGTTTGCACAATGGACGGT 59.616 50.000 0.00 0.00 44.64 4.83
2593 4607 3.177883 GTGTTTGCACAATGGACGG 57.822 52.632 0.00 0.00 44.64 4.79
2677 4694 7.320443 TGGATTGTAATCGATTCCTCAAAAG 57.680 36.000 15.25 0.00 36.27 2.27
2726 4743 6.823689 GGCAATAAGACAATCTAGTTCCTTCA 59.176 38.462 0.00 0.00 0.00 3.02
2793 4810 4.301072 ACTAAAGCATAACCTTGAGCCA 57.699 40.909 0.00 0.00 27.90 4.75
2821 4838 6.110707 TCCGGTGACCAATCTATAAAAGAAC 58.889 40.000 1.11 0.00 37.89 3.01
2830 4847 4.098960 GTCAATACTCCGGTGACCAATCTA 59.901 45.833 11.17 0.00 36.48 1.98
2872 4889 6.083098 ACACTATGAGCAGATACATGAGAC 57.917 41.667 0.00 0.00 0.00 3.36
2878 4895 7.744087 AACAAAAACACTATGAGCAGATACA 57.256 32.000 0.00 0.00 0.00 2.29
2962 4979 4.200092 GGGAGTGGTCCATTAGCTAAAAG 58.800 47.826 10.85 6.30 46.07 2.27
2977 4994 1.888512 CAACAGTTGGAATGGGAGTGG 59.111 52.381 5.25 0.00 0.00 4.00
3012 5029 5.299279 CCCATTAGTAAGCCTTAATGGTGTG 59.701 44.000 17.37 4.10 44.43 3.82
3063 5081 7.208225 AGTGCTTGATAAGAAAAACCTTCTC 57.792 36.000 0.00 0.00 0.00 2.87
3067 5085 8.157476 TCTAGAAGTGCTTGATAAGAAAAACCT 58.843 33.333 0.00 0.00 0.00 3.50
3068 5086 8.324163 TCTAGAAGTGCTTGATAAGAAAAACC 57.676 34.615 0.00 0.00 0.00 3.27
3124 5144 2.876550 AGTTCGTAAACAGGCAGGAAAC 59.123 45.455 0.00 0.00 37.88 2.78


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

AutoCloner maintained by Alex Coulton.