Multiple sequence alignment - TraesCS1A01G124000

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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 TraesCS1A01G124000 chr1A 100.000 2521 0 0 1 2521 145875666 145878186 0.000000e+00 4656.0
1 TraesCS1A01G124000 chr6A 93.137 1428 85 7 824 2243 341434654 341433232 0.000000e+00 2082.0
2 TraesCS1A01G124000 chr6A 93.841 828 39 4 3 819 341435436 341434610 0.000000e+00 1236.0
3 TraesCS1A01G124000 chr6A 91.870 123 8 1 2248 2368 361696087 361695965 1.200000e-38 171.0
4 TraesCS1A01G124000 chr5A 93.048 1424 84 9 824 2243 130250045 130251457 0.000000e+00 2067.0
5 TraesCS1A01G124000 chr5A 93.960 745 32 5 1 733 130248983 130249726 0.000000e+00 1114.0
6 TraesCS1A01G124000 chr5A 91.111 135 7 4 2240 2372 255885069 255884938 7.170000e-41 178.0
7 TraesCS1A01G124000 chr7D 93.658 1293 78 3 824 2113 343752058 343753349 0.000000e+00 1930.0
8 TraesCS1A01G124000 chr7D 93.020 831 44 6 1 819 276974697 276973869 0.000000e+00 1201.0
9 TraesCS1A01G124000 chr7D 94.562 331 16 1 824 1152 276973913 276973583 6.220000e-141 510.0
10 TraesCS1A01G124000 chr6D 93.245 829 40 5 1 819 252748650 252749472 0.000000e+00 1206.0
11 TraesCS1A01G124000 chr4A 93.108 827 41 7 4 819 236202170 236201349 0.000000e+00 1197.0
12 TraesCS1A01G124000 chr4A 92.875 800 35 10 33 819 311252118 311251328 0.000000e+00 1142.0
13 TraesCS1A01G124000 chr7A 92.892 830 47 4 1 819 245728918 245728090 0.000000e+00 1195.0
14 TraesCS1A01G124000 chr7A 94.260 331 17 1 824 1152 245728134 245727804 2.890000e-139 505.0
15 TraesCS1A01G124000 chr7A 81.208 298 44 7 1955 2243 604789967 604789673 1.950000e-56 230.0
16 TraesCS1A01G124000 chr7A 84.286 210 24 3 2310 2519 347255999 347255799 1.980000e-46 196.0
17 TraesCS1A01G124000 chr6B 94.250 713 37 4 108 818 128543312 128544022 0.000000e+00 1086.0
18 TraesCS1A01G124000 chr6B 93.318 434 26 2 824 1255 142538616 142539048 2.730000e-179 638.0
19 TraesCS1A01G124000 chr6B 87.805 451 37 8 1796 2243 401020990 401021425 1.730000e-141 512.0
20 TraesCS1A01G124000 chr6B 90.191 367 33 2 824 1188 128543980 128544345 2.270000e-130 475.0
21 TraesCS1A01G124000 chr6B 84.586 266 31 3 1152 1408 381169338 381169602 3.220000e-64 255.0
22 TraesCS1A01G124000 chr6B 93.865 163 5 2 2081 2243 492779873 492780030 9.010000e-60 241.0
23 TraesCS1A01G124000 chr7B 93.417 714 43 4 108 819 40671592 40672303 0.000000e+00 1055.0
24 TraesCS1A01G124000 chr7B 90.308 454 40 3 1791 2243 478022460 478022010 2.160000e-165 592.0
25 TraesCS1A01G124000 chr7B 91.553 367 28 2 824 1188 40672260 40672625 1.040000e-138 503.0
26 TraesCS1A01G124000 chr7B 93.080 289 18 2 1513 1800 78283731 78284018 3.000000e-114 422.0
27 TraesCS1A01G124000 chr7B 92.388 289 20 2 1513 1800 155546111 155546398 6.490000e-111 411.0
28 TraesCS1A01G124000 chr7B 90.977 133 8 3 2242 2372 90423539 90423409 2.580000e-40 176.0
29 TraesCS1A01G124000 chr3B 93.417 714 43 4 108 819 94306839 94307550 0.000000e+00 1055.0
30 TraesCS1A01G124000 chr3B 90.749 454 38 4 1791 2243 422106512 422106062 9.980000e-169 603.0
31 TraesCS1A01G124000 chr3B 90.372 457 41 3 1788 2243 354366039 354365585 4.640000e-167 597.0
32 TraesCS1A01G124000 chr3B 92.096 291 19 3 1513 1800 379947280 379947569 8.400000e-110 407.0
33 TraesCS1A01G124000 chr3B 82.857 210 27 2 2311 2519 410370060 410370261 1.990000e-41 180.0
34 TraesCS1A01G124000 chr1B 93.318 434 27 1 824 1255 521343877 521343444 7.600000e-180 640.0
35 TraesCS1A01G124000 chr1B 95.706 163 7 0 2081 2243 484056823 484056985 1.920000e-66 263.0
36 TraesCS1A01G124000 chr1B 91.848 184 13 2 1091 1274 346285872 346285691 3.220000e-64 255.0
37 TraesCS1A01G124000 chr1B 80.383 209 32 2 2311 2519 484059127 484059326 1.560000e-32 150.0
38 TraesCS1A01G124000 chr4B 91.724 290 21 3 1513 1800 341243769 341244057 1.400000e-107 399.0
39 TraesCS1A01G124000 chr4B 91.724 290 21 2 1513 1800 370756828 370757116 1.400000e-107 399.0
40 TraesCS1A01G124000 chr4B 91.815 281 14 1 1 272 338488788 338489068 1.410000e-102 383.0
41 TraesCS1A01G124000 chr4B 96.319 163 6 0 2081 2243 560902298 560902136 4.130000e-68 268.0
42 TraesCS1A01G124000 chr4B 81.818 209 29 2 2311 2519 560900041 560899842 1.550000e-37 167.0
43 TraesCS1A01G124000 chrUn 91.349 289 21 3 1513 1800 261370189 261369904 2.350000e-105 392.0
44 TraesCS1A01G124000 chrUn 83.761 234 30 1 1201 1426 48738521 48738288 5.460000e-52 215.0
45 TraesCS1A01G124000 chrUn 95.918 49 2 0 1796 1844 116800694 116800742 2.080000e-11 80.5
46 TraesCS1A01G124000 chr3D 84.890 364 46 2 1152 1506 145294477 145294840 2.380000e-95 359.0
47 TraesCS1A01G124000 chr3D 84.282 369 49 2 1152 1511 146086936 146086568 3.990000e-93 351.0
48 TraesCS1A01G124000 chr2B 81.955 133 15 3 2310 2442 294607278 294607155 1.230000e-18 104.0
49 TraesCS1A01G124000 chr2B 81.955 133 15 3 2310 2442 560812882 560812759 1.230000e-18 104.0
50 TraesCS1A01G124000 chr1D 95.918 49 2 0 1796 1844 42484274 42484322 2.080000e-11 80.5


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 TraesCS1A01G124000 chr1A 145875666 145878186 2520 False 4656.0 4656 100.0000 1 2521 1 chr1A.!!$F1 2520
1 TraesCS1A01G124000 chr6A 341433232 341435436 2204 True 1659.0 2082 93.4890 3 2243 2 chr6A.!!$R2 2240
2 TraesCS1A01G124000 chr5A 130248983 130251457 2474 False 1590.5 2067 93.5040 1 2243 2 chr5A.!!$F1 2242
3 TraesCS1A01G124000 chr7D 343752058 343753349 1291 False 1930.0 1930 93.6580 824 2113 1 chr7D.!!$F1 1289
4 TraesCS1A01G124000 chr7D 276973583 276974697 1114 True 855.5 1201 93.7910 1 1152 2 chr7D.!!$R1 1151
5 TraesCS1A01G124000 chr6D 252748650 252749472 822 False 1206.0 1206 93.2450 1 819 1 chr6D.!!$F1 818
6 TraesCS1A01G124000 chr4A 236201349 236202170 821 True 1197.0 1197 93.1080 4 819 1 chr4A.!!$R1 815
7 TraesCS1A01G124000 chr4A 311251328 311252118 790 True 1142.0 1142 92.8750 33 819 1 chr4A.!!$R2 786
8 TraesCS1A01G124000 chr7A 245727804 245728918 1114 True 850.0 1195 93.5760 1 1152 2 chr7A.!!$R3 1151
9 TraesCS1A01G124000 chr6B 128543312 128544345 1033 False 780.5 1086 92.2205 108 1188 2 chr6B.!!$F5 1080
10 TraesCS1A01G124000 chr7B 40671592 40672625 1033 False 779.0 1055 92.4850 108 1188 2 chr7B.!!$F3 1080
11 TraesCS1A01G124000 chr3B 94306839 94307550 711 False 1055.0 1055 93.4170 108 819 1 chr3B.!!$F1 711
12 TraesCS1A01G124000 chr1B 484056823 484059326 2503 False 206.5 263 88.0445 2081 2519 2 chr1B.!!$F1 438
13 TraesCS1A01G124000 chr4B 560899842 560902298 2456 True 217.5 268 89.0685 2081 2519 2 chr4B.!!$R1 438

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
815 1109 0.171007 CGCAAATGCCCTTAGTGGTG 59.829 55.0 0.0 0.0 37.91 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2201 2506 0.447801 AGCTCGTAAAAATGCGCCAG 59.552 50.0 4.18 0.0 0.0 4.85 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
87 88 8.523658 TCACTATCACCATAACTAGATACATGC 58.476 37.037 0.00 0.00 0.00 4.06
90 91 6.478512 TCACCATAACTAGATACATGCACA 57.521 37.500 0.00 0.00 0.00 4.57
299 311 3.758554 ACCAAAAGCTTGCGATGAACTAT 59.241 39.130 0.00 0.00 0.00 2.12
402 415 6.151648 CACAAAAGAGTGACCATGAATACCAT 59.848 38.462 0.00 0.00 42.05 3.55
578 592 1.672881 GCGCAATAAAGCATCTGGACT 59.327 47.619 0.30 0.00 0.00 3.85
580 594 2.032550 CGCAATAAAGCATCTGGACTGG 59.967 50.000 0.00 0.00 0.00 4.00
652 666 8.957466 GGTTCCTCATATAGCAACTAAAACTTT 58.043 33.333 0.00 0.00 0.00 2.66
677 692 9.835389 TTAGTACAACTACACCTTTATTGTTGT 57.165 29.630 12.70 12.70 46.11 3.32
773 1067 4.947147 GGCAGTGTGGAACCGCCA 62.947 66.667 1.86 0.00 46.96 5.69
780 1074 2.115052 TGGAACCGCCAAGCATGT 59.885 55.556 0.00 0.00 45.87 3.21
781 1075 1.376848 TGGAACCGCCAAGCATGTA 59.623 52.632 0.00 0.00 45.87 2.29
782 1076 0.676466 TGGAACCGCCAAGCATGTAG 60.676 55.000 0.00 0.00 45.87 2.74
783 1077 1.429423 GAACCGCCAAGCATGTAGC 59.571 57.895 0.00 0.00 46.19 3.58
792 1086 4.823276 GCATGTAGCTCGAGTGCT 57.177 55.556 15.13 9.46 46.11 4.40
793 1087 3.946950 GCATGTAGCTCGAGTGCTA 57.053 52.632 15.13 8.34 43.74 3.49
794 1088 1.764851 GCATGTAGCTCGAGTGCTAG 58.235 55.000 15.13 1.09 44.93 3.42
795 1089 1.335182 GCATGTAGCTCGAGTGCTAGA 59.665 52.381 15.13 10.04 44.93 2.43
796 1090 2.856720 GCATGTAGCTCGAGTGCTAGAC 60.857 54.545 15.13 3.60 44.93 2.59
797 1091 1.007580 TGTAGCTCGAGTGCTAGACG 58.992 55.000 15.13 0.00 44.93 4.18
798 1092 0.316360 GTAGCTCGAGTGCTAGACGC 60.316 60.000 15.13 0.00 44.93 5.19
807 1101 4.225497 GCTAGACGCAAATGCCCT 57.775 55.556 0.00 0.41 38.92 5.19
808 1102 2.482326 GCTAGACGCAAATGCCCTT 58.518 52.632 0.00 0.00 38.92 3.95
809 1103 1.663695 GCTAGACGCAAATGCCCTTA 58.336 50.000 0.00 0.00 38.92 2.69
810 1104 1.599542 GCTAGACGCAAATGCCCTTAG 59.400 52.381 0.00 0.95 38.92 2.18
811 1105 2.906354 CTAGACGCAAATGCCCTTAGT 58.094 47.619 0.00 0.00 37.91 2.24
812 1106 1.453155 AGACGCAAATGCCCTTAGTG 58.547 50.000 0.00 0.00 37.91 2.74
813 1107 0.451783 GACGCAAATGCCCTTAGTGG 59.548 55.000 0.00 0.00 37.91 4.00
814 1108 0.251165 ACGCAAATGCCCTTAGTGGT 60.251 50.000 0.00 0.00 37.91 4.16
815 1109 0.171007 CGCAAATGCCCTTAGTGGTG 59.829 55.000 0.00 0.00 37.91 4.17
816 1110 0.532115 GCAAATGCCCTTAGTGGTGG 59.468 55.000 0.00 0.00 34.31 4.61
817 1111 0.532115 CAAATGCCCTTAGTGGTGGC 59.468 55.000 0.00 0.00 45.56 5.01
818 1112 0.614697 AAATGCCCTTAGTGGTGGCC 60.615 55.000 0.00 0.00 44.72 5.36
819 1113 1.509548 AATGCCCTTAGTGGTGGCCT 61.510 55.000 3.32 0.00 44.72 5.19
820 1114 1.926426 ATGCCCTTAGTGGTGGCCTC 61.926 60.000 3.32 0.00 44.72 4.70
822 1116 1.923395 CCCTTAGTGGTGGCCTCCA 60.923 63.158 22.73 22.73 34.85 3.86
846 1140 3.402110 CATGTAGCTTGAGTGTTGGACA 58.598 45.455 0.00 0.00 0.00 4.02
919 1213 3.285484 CCAGCTAGCATCCATGAAAACT 58.715 45.455 18.83 0.00 0.00 2.66
1028 1323 1.685355 GCAAAGGGGCTGGTGTGTTT 61.685 55.000 0.00 0.00 0.00 2.83
1082 1381 0.478072 TGCTTGGTGAAGATGGTGGT 59.522 50.000 0.00 0.00 0.00 4.16
1086 1385 2.100631 GGTGAAGATGGTGGTCGCG 61.101 63.158 0.00 0.00 0.00 5.87
1171 1470 4.037446 TGGAATTCAAGCTACAACCAACAC 59.963 41.667 7.93 0.00 0.00 3.32
1177 1476 3.485463 AGCTACAACCAACACTAGCAA 57.515 42.857 0.00 0.00 35.10 3.91
1195 1494 5.186996 AGCAAGAATTCAAGCGAAAGAAA 57.813 34.783 8.44 0.00 34.01 2.52
1279 1578 0.955428 CAAACTCCTAAGCTGCGGCA 60.955 55.000 21.93 1.29 41.70 5.69
1295 1594 1.874019 GCATCGCATGACTCGACGT 60.874 57.895 0.00 0.00 38.88 4.34
1343 1642 1.588404 GTAGTGAATGATGTCGTGCCG 59.412 52.381 0.00 0.00 0.00 5.69
1376 1675 4.135153 ACCGAGGCTAGCACGCAG 62.135 66.667 18.24 11.64 0.00 5.18
1415 1714 3.770040 CGTCGGACCTGGATGGCA 61.770 66.667 0.00 0.00 40.22 4.92
1435 1734 1.735198 TAAAGAGAACACGGCGGCG 60.735 57.895 31.06 31.06 0.00 6.46
1452 1751 2.265739 GCTGCGATGTGGACCTGA 59.734 61.111 0.00 0.00 0.00 3.86
1456 1755 2.103042 GCGATGTGGACCTGAGTGC 61.103 63.158 0.00 0.00 34.33 4.40
1511 1810 3.524606 GGATTCTCGGGGCGTCGA 61.525 66.667 0.00 1.92 37.60 4.20
1521 1820 1.805120 CGGGGCGTCGATTCAATTAGT 60.805 52.381 0.00 0.00 0.00 2.24
1636 1937 5.962433 TGTGTGTATAAGAAGCTAGTGGTC 58.038 41.667 0.00 0.00 0.00 4.02
1654 1955 7.219484 AGTGGTCTAAATTGAAAACATGGAG 57.781 36.000 0.00 0.00 0.00 3.86
1674 1975 1.680735 GAGTGCCACCACACATTTTCA 59.319 47.619 0.00 0.00 44.53 2.69
1721 2025 6.314784 GTCCTATAGTGCATGTTTTGTGTTC 58.685 40.000 0.00 0.00 0.00 3.18
1724 2028 7.333423 TCCTATAGTGCATGTTTTGTGTTCTAC 59.667 37.037 0.00 0.00 0.00 2.59
1807 2111 3.704566 AGCTTACATTAGATGGTGGTCGA 59.295 43.478 0.00 0.00 33.60 4.20
1886 2190 1.900016 CCTGGCTGCTGCAAGTTCA 60.900 57.895 17.74 5.41 38.56 3.18
2029 2333 4.974368 GCTCTTAGAGTCTGAGCTGTTA 57.026 45.455 20.09 0.00 46.69 2.41
2035 2339 8.582657 TCTTAGAGTCTGAGCTGTTATTTAGT 57.417 34.615 7.06 0.00 0.00 2.24
2189 2493 7.553334 TGTGAAATGGTAGTCCTAGTGTATTC 58.447 38.462 0.00 0.00 34.23 1.75
2201 2506 7.040494 GTCCTAGTGTATTCTTCCTTTGTACC 58.960 42.308 0.00 0.00 0.00 3.34
2203 2508 7.042335 CCTAGTGTATTCTTCCTTTGTACCTG 58.958 42.308 0.00 0.00 0.00 4.00
2243 2548 8.766476 AGCTACATAGGCAAGATATACATGATT 58.234 33.333 0.00 0.00 0.00 2.57
2244 2549 9.388506 GCTACATAGGCAAGATATACATGATTT 57.611 33.333 0.00 0.00 0.00 2.17
2251 2556 9.851686 AGGCAAGATATACATGATTTTGTTCTA 57.148 29.630 0.00 0.00 0.00 2.10
2269 2574 9.647797 TTTGTTCTATCATTGTACTATTGTCGT 57.352 29.630 0.00 0.00 0.00 4.34
2271 2576 8.248253 TGTTCTATCATTGTACTATTGTCGTGT 58.752 33.333 0.00 0.00 0.00 4.49
2273 2578 9.946165 TTCTATCATTGTACTATTGTCGTGTAG 57.054 33.333 0.00 0.00 0.00 2.74
2275 2580 5.898174 TCATTGTACTATTGTCGTGTAGGG 58.102 41.667 0.00 0.00 0.00 3.53
2276 2581 4.724074 TTGTACTATTGTCGTGTAGGGG 57.276 45.455 0.00 0.00 0.00 4.79
2288 3180 3.000727 CGTGTAGGGGAATTGAACTGAC 58.999 50.000 0.00 0.00 0.00 3.51
2307 4618 1.903860 ACAATACCCGCTACCAAGTCA 59.096 47.619 0.00 0.00 0.00 3.41
2308 4619 2.303600 ACAATACCCGCTACCAAGTCAA 59.696 45.455 0.00 0.00 0.00 3.18
2330 4712 7.275341 GTCAACATGAACAGTTCAACAATTCAA 59.725 33.333 19.92 0.00 43.95 2.69
2363 4745 3.061322 GCAAAGCTCACATGAATGCAAA 58.939 40.909 0.00 0.00 32.80 3.68
2364 4746 3.682858 GCAAAGCTCACATGAATGCAAAT 59.317 39.130 0.00 0.00 32.80 2.32
2365 4747 4.435518 GCAAAGCTCACATGAATGCAAATG 60.436 41.667 0.00 0.00 32.80 2.32
2366 4748 3.520290 AGCTCACATGAATGCAAATGG 57.480 42.857 0.00 2.56 0.00 3.16
2367 4749 3.093814 AGCTCACATGAATGCAAATGGA 58.906 40.909 0.00 5.77 0.00 3.41
2368 4750 3.512329 AGCTCACATGAATGCAAATGGAA 59.488 39.130 0.00 0.38 0.00 3.53
2369 4751 4.161565 AGCTCACATGAATGCAAATGGAAT 59.838 37.500 0.00 0.00 0.00 3.01
2370 4752 5.361571 AGCTCACATGAATGCAAATGGAATA 59.638 36.000 0.00 0.00 0.00 1.75
2379 4761 7.289310 TGAATGCAAATGGAATAGTGGAGATA 58.711 34.615 0.00 0.00 0.00 1.98
2388 4770 5.010933 GGAATAGTGGAGATACTCGATCCA 58.989 45.833 0.45 0.45 40.80 3.41
2394 4776 3.648545 TGGAGATACTCGATCCAGAGAGA 59.351 47.826 0.45 0.00 38.19 3.10
2403 4785 1.303423 ATCCAGAGAGAGGAGGGGCT 61.303 60.000 0.00 0.00 38.83 5.19
2404 4786 1.457455 CCAGAGAGAGGAGGGGCTC 60.457 68.421 0.00 0.00 0.00 4.70
2437 4819 2.896801 CTTGTGCTTGCGAACGGCT 61.897 57.895 0.00 0.00 44.05 5.52
2443 4825 0.301987 GCTTGCGAACGGCTAGAATC 59.698 55.000 0.00 0.00 45.77 2.52
2444 4826 1.640428 CTTGCGAACGGCTAGAATCA 58.360 50.000 0.00 0.00 45.77 2.57
2449 4831 0.933796 GAACGGCTAGAATCAGCAGC 59.066 55.000 0.00 1.10 43.67 5.25
2452 4834 1.443407 GGCTAGAATCAGCAGCGGA 59.557 57.895 0.00 0.00 43.67 5.54
2477 4859 3.399181 GGTGCGGGAGGTGGATGA 61.399 66.667 0.00 0.00 0.00 2.92
2481 4863 4.227134 CGGGAGGTGGATGAGGCG 62.227 72.222 0.00 0.00 0.00 5.52
2490 4872 4.489771 GATGAGGCGGGGGTGGTG 62.490 72.222 0.00 0.00 0.00 4.17
2508 4890 2.906897 CGCCAGCAGGTTGGTGTT 60.907 61.111 7.47 0.00 43.78 3.32
2509 4891 1.599518 CGCCAGCAGGTTGGTGTTA 60.600 57.895 7.47 0.00 43.78 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 7.915397 AGTGCTTGTTATAGTCAAAAAGTTGTG 59.085 33.333 0.00 0.00 36.07 3.33
90 91 8.290325 GCTAGTGCTTGTTATAGTCAAAAAGTT 58.710 33.333 0.00 0.00 36.03 2.66
169 180 7.129457 ACAATCTTATAGAGAGCACCATTCA 57.871 36.000 0.00 0.00 37.93 2.57
186 197 5.290158 GCGATTTTCATGCATCAACAATCTT 59.710 36.000 0.00 0.00 0.00 2.40
402 415 5.700832 CCTGTAGAGTGCATTTTTGTAGTGA 59.299 40.000 0.00 0.00 0.00 3.41
573 587 3.808728 CTTGTCTGTTCTTTCCAGTCCA 58.191 45.455 0.00 0.00 0.00 4.02
578 592 3.558931 TCAGCTTGTCTGTTCTTTCCA 57.441 42.857 0.00 0.00 43.32 3.53
580 594 4.572389 TCAGTTCAGCTTGTCTGTTCTTTC 59.428 41.667 8.13 0.00 43.32 2.62
765 1059 1.429423 GCTACATGCTTGGCGGTTC 59.571 57.895 4.44 0.00 38.95 3.62
775 1069 1.335182 TCTAGCACTCGAGCTACATGC 59.665 52.381 13.61 14.51 44.50 4.06
776 1070 2.601029 CGTCTAGCACTCGAGCTACATG 60.601 54.545 13.61 3.76 44.50 3.21
777 1071 1.600013 CGTCTAGCACTCGAGCTACAT 59.400 52.381 13.61 0.00 44.50 2.29
778 1072 1.007580 CGTCTAGCACTCGAGCTACA 58.992 55.000 13.61 0.00 44.50 2.74
779 1073 0.316360 GCGTCTAGCACTCGAGCTAC 60.316 60.000 13.61 1.63 44.50 3.58
780 1074 2.015382 GCGTCTAGCACTCGAGCTA 58.985 57.895 13.61 9.32 44.50 3.32
791 1085 2.609459 CACTAAGGGCATTTGCGTCTAG 59.391 50.000 0.00 0.21 43.26 2.43
792 1086 2.627945 CACTAAGGGCATTTGCGTCTA 58.372 47.619 0.00 0.00 43.26 2.59
793 1087 1.453155 CACTAAGGGCATTTGCGTCT 58.547 50.000 0.00 0.00 43.26 4.18
794 1088 0.451783 CCACTAAGGGCATTTGCGTC 59.548 55.000 0.00 0.00 43.26 5.19
795 1089 0.251165 ACCACTAAGGGCATTTGCGT 60.251 50.000 0.00 0.00 43.89 5.24
796 1090 0.171007 CACCACTAAGGGCATTTGCG 59.829 55.000 0.00 0.00 43.89 4.85
797 1091 0.532115 CCACCACTAAGGGCATTTGC 59.468 55.000 0.00 0.00 43.89 3.68
798 1092 0.532115 GCCACCACTAAGGGCATTTG 59.468 55.000 0.00 0.00 46.92 2.32
799 1093 2.976099 GCCACCACTAAGGGCATTT 58.024 52.632 0.00 0.00 46.92 2.32
800 1094 4.764143 GCCACCACTAAGGGCATT 57.236 55.556 0.00 0.00 46.92 3.56
804 1098 1.497309 TTGGAGGCCACCACTAAGGG 61.497 60.000 22.87 0.00 43.89 3.95
805 1099 0.035056 CTTGGAGGCCACCACTAAGG 60.035 60.000 22.87 6.21 45.67 2.69
806 1100 0.678048 GCTTGGAGGCCACCACTAAG 60.678 60.000 22.87 17.46 39.85 2.18
807 1101 1.378762 GCTTGGAGGCCACCACTAA 59.621 57.895 22.87 6.66 39.85 2.24
808 1102 1.207488 ATGCTTGGAGGCCACCACTA 61.207 55.000 22.87 11.32 39.85 2.74
809 1103 2.541907 ATGCTTGGAGGCCACCACT 61.542 57.895 22.87 4.19 39.85 4.00
810 1104 2.036256 ATGCTTGGAGGCCACCAC 59.964 61.111 22.87 12.12 39.85 4.16
811 1105 1.496444 TACATGCTTGGAGGCCACCA 61.496 55.000 19.11 19.11 38.24 4.17
812 1106 0.749454 CTACATGCTTGGAGGCCACC 60.749 60.000 13.09 13.09 30.78 4.61
813 1107 1.379642 GCTACATGCTTGGAGGCCAC 61.380 60.000 13.40 0.00 34.01 5.01
814 1108 1.077501 GCTACATGCTTGGAGGCCA 60.078 57.895 13.40 0.00 34.01 5.36
815 1109 3.833304 GCTACATGCTTGGAGGCC 58.167 61.111 13.40 0.00 34.01 5.19
846 1140 1.923356 CCACCACTAAGGGCATTTGT 58.077 50.000 0.00 0.00 43.89 2.83
879 1173 0.457853 GCAATACGTCCAGCACTCGA 60.458 55.000 0.00 0.00 0.00 4.04
883 1177 2.089854 CTGGCAATACGTCCAGCAC 58.910 57.895 7.97 0.00 42.79 4.40
919 1213 4.639755 TGTGCAAGACTCAATTTTGTCTCA 59.360 37.500 9.67 3.78 42.02 3.27
987 1282 4.309099 CTTTGCACATTGCTTGGTTATGT 58.691 39.130 0.00 0.00 45.31 2.29
1028 1323 1.069090 GTCGAGCACACACAGGGAA 59.931 57.895 0.00 0.00 0.00 3.97
1086 1385 4.421948 CAGTACAAGTAGAATCGTGGGTC 58.578 47.826 0.00 0.00 0.00 4.46
1171 1470 5.536554 TCTTTCGCTTGAATTCTTGCTAG 57.463 39.130 16.76 12.37 0.00 3.42
1177 1476 6.708054 TCTCTCTTTTCTTTCGCTTGAATTCT 59.292 34.615 7.05 0.00 0.00 2.40
1195 1494 5.014755 TCCTCTCTTCACTAACCTCTCTCTT 59.985 44.000 0.00 0.00 0.00 2.85
1279 1578 0.109272 ACAACGTCGAGTCATGCGAT 60.109 50.000 0.00 0.00 40.19 4.58
1295 1594 0.466372 TGGGCCGTTCAATGACACAA 60.466 50.000 0.00 0.00 0.00 3.33
1415 1714 0.669625 GCCGCCGTGTTCTCTTTACT 60.670 55.000 0.00 0.00 0.00 2.24
1435 1734 1.812922 CTCAGGTCCACATCGCAGC 60.813 63.158 0.00 0.00 0.00 5.25
1508 1807 9.459640 GCTACTATGTGTTACTAATTGAATCGA 57.540 33.333 0.00 0.00 0.00 3.59
1614 1914 6.210287 AGACCACTAGCTTCTTATACACAC 57.790 41.667 0.00 0.00 0.00 3.82
1624 1924 7.871853 TGTTTTCAATTTAGACCACTAGCTTC 58.128 34.615 0.00 0.00 0.00 3.86
1636 1937 6.095377 GGCACTCTCCATGTTTTCAATTTAG 58.905 40.000 0.00 0.00 0.00 1.85
1654 1955 1.680735 TGAAAATGTGTGGTGGCACTC 59.319 47.619 18.45 11.53 39.89 3.51
1697 1998 5.880054 ACACAAAACATGCACTATAGGAC 57.120 39.130 4.43 0.00 0.00 3.85
1701 2005 6.869388 TCGTAGAACACAAAACATGCACTATA 59.131 34.615 0.00 0.00 0.00 1.31
1702 2006 5.699001 TCGTAGAACACAAAACATGCACTAT 59.301 36.000 0.00 0.00 0.00 2.12
1703 2007 5.051153 TCGTAGAACACAAAACATGCACTA 58.949 37.500 0.00 0.00 0.00 2.74
1724 2028 8.220755 TCCCTATATGTTTTCCATTTTCTTCG 57.779 34.615 0.00 0.00 34.86 3.79
1886 2190 2.363306 TGCACCATCTTCACCAAGTT 57.637 45.000 0.00 0.00 0.00 2.66
2013 2317 9.998106 AAAAACTAAATAACAGCTCAGACTCTA 57.002 29.630 0.00 0.00 0.00 2.43
2073 2377 8.625651 TCGGTTCATTGGTTTTATGTTATATGG 58.374 33.333 0.00 0.00 0.00 2.74
2164 2468 7.399191 AGAATACACTAGGACTACCATTTCACA 59.601 37.037 0.00 0.00 38.94 3.58
2177 2481 6.958192 AGGTACAAAGGAAGAATACACTAGGA 59.042 38.462 0.00 0.00 0.00 2.94
2189 2493 0.605319 TGCGCCAGGTACAAAGGAAG 60.605 55.000 4.18 0.00 0.00 3.46
2201 2506 0.447801 AGCTCGTAAAAATGCGCCAG 59.552 50.000 4.18 0.00 0.00 4.85
2203 2508 1.395608 TGTAGCTCGTAAAAATGCGCC 59.604 47.619 4.18 0.00 0.00 6.53
2243 2548 9.647797 ACGACAATAGTACAATGATAGAACAAA 57.352 29.630 0.00 0.00 0.00 2.83
2244 2549 9.083080 CACGACAATAGTACAATGATAGAACAA 57.917 33.333 0.00 0.00 0.00 2.83
2246 2551 8.630278 ACACGACAATAGTACAATGATAGAAC 57.370 34.615 0.00 0.00 0.00 3.01
2248 2553 8.565416 CCTACACGACAATAGTACAATGATAGA 58.435 37.037 0.00 0.00 0.00 1.98
2249 2554 7.808381 CCCTACACGACAATAGTACAATGATAG 59.192 40.741 0.00 0.00 0.00 2.08
2251 2556 6.462487 CCCCTACACGACAATAGTACAATGAT 60.462 42.308 0.00 0.00 0.00 2.45
2252 2557 5.163488 CCCCTACACGACAATAGTACAATGA 60.163 44.000 0.00 0.00 0.00 2.57
2253 2558 5.047847 CCCCTACACGACAATAGTACAATG 58.952 45.833 0.00 0.00 0.00 2.82
2255 2560 4.343231 TCCCCTACACGACAATAGTACAA 58.657 43.478 0.00 0.00 0.00 2.41
2256 2561 3.966979 TCCCCTACACGACAATAGTACA 58.033 45.455 0.00 0.00 0.00 2.90
2257 2562 4.989279 TTCCCCTACACGACAATAGTAC 57.011 45.455 0.00 0.00 0.00 2.73
2258 2563 5.657745 TCAATTCCCCTACACGACAATAGTA 59.342 40.000 0.00 0.00 0.00 1.82
2259 2564 4.468510 TCAATTCCCCTACACGACAATAGT 59.531 41.667 0.00 0.00 0.00 2.12
2260 2565 5.018539 TCAATTCCCCTACACGACAATAG 57.981 43.478 0.00 0.00 0.00 1.73
2262 2567 3.992943 TCAATTCCCCTACACGACAAT 57.007 42.857 0.00 0.00 0.00 2.71
2265 2570 3.000727 CAGTTCAATTCCCCTACACGAC 58.999 50.000 0.00 0.00 0.00 4.34
2266 2571 2.901192 TCAGTTCAATTCCCCTACACGA 59.099 45.455 0.00 0.00 0.00 4.35
2267 2572 3.000727 GTCAGTTCAATTCCCCTACACG 58.999 50.000 0.00 0.00 0.00 4.49
2268 2573 4.015872 TGTCAGTTCAATTCCCCTACAC 57.984 45.455 0.00 0.00 0.00 2.90
2269 2574 4.715534 TTGTCAGTTCAATTCCCCTACA 57.284 40.909 0.00 0.00 0.00 2.74
2271 2576 5.751586 GGTATTGTCAGTTCAATTCCCCTA 58.248 41.667 0.00 0.00 38.46 3.53
2273 2578 4.983671 GGTATTGTCAGTTCAATTCCCC 57.016 45.455 0.00 0.00 38.46 4.81
2275 2580 3.181500 GCGGGTATTGTCAGTTCAATTCC 60.181 47.826 6.55 6.55 41.38 3.01
2276 2581 3.689649 AGCGGGTATTGTCAGTTCAATTC 59.310 43.478 0.00 0.00 38.68 2.17
2288 3180 2.676342 GTTGACTTGGTAGCGGGTATTG 59.324 50.000 0.00 0.00 0.00 1.90
2307 4618 7.322664 ACTTGAATTGTTGAACTGTTCATGTT 58.677 30.769 22.60 14.56 39.84 2.71
2308 4619 6.866480 ACTTGAATTGTTGAACTGTTCATGT 58.134 32.000 22.60 18.90 39.84 3.21
2330 4712 3.004106 GTGAGCTTTGCACTGATGAAACT 59.996 43.478 0.00 0.00 33.57 2.66
2363 4745 5.654650 GGATCGAGTATCTCCACTATTCCAT 59.345 44.000 0.00 0.00 34.75 3.41
2364 4746 5.010933 GGATCGAGTATCTCCACTATTCCA 58.989 45.833 0.00 0.00 34.75 3.53
2365 4747 5.010933 TGGATCGAGTATCTCCACTATTCC 58.989 45.833 0.45 0.00 34.85 3.01
2366 4748 5.941058 TCTGGATCGAGTATCTCCACTATTC 59.059 44.000 4.53 0.00 34.85 1.75
2367 4749 5.882040 TCTGGATCGAGTATCTCCACTATT 58.118 41.667 4.53 0.00 34.85 1.73
2368 4750 5.249622 TCTCTGGATCGAGTATCTCCACTAT 59.750 44.000 4.53 0.00 34.85 2.12
2369 4751 4.593634 TCTCTGGATCGAGTATCTCCACTA 59.406 45.833 4.53 0.00 34.85 2.74
2370 4752 3.392947 TCTCTGGATCGAGTATCTCCACT 59.607 47.826 4.53 0.00 34.85 4.00
2379 4761 1.142870 CCTCCTCTCTCTGGATCGAGT 59.857 57.143 4.53 0.00 32.56 4.18
2388 4770 0.850784 GTAGAGCCCCTCCTCTCTCT 59.149 60.000 0.00 0.00 41.15 3.10
2394 4776 4.159108 CCCGGTAGAGCCCCTCCT 62.159 72.222 0.00 0.00 0.00 3.69
2418 4800 2.427410 CCGTTCGCAAGCACAAGC 60.427 61.111 0.00 0.00 42.56 4.01
2430 4812 0.933796 GCTGCTGATTCTAGCCGTTC 59.066 55.000 0.00 0.00 43.02 3.95
2431 4813 0.807667 CGCTGCTGATTCTAGCCGTT 60.808 55.000 0.00 0.00 43.02 4.44
2433 4815 1.953138 CCGCTGCTGATTCTAGCCG 60.953 63.158 0.00 0.00 43.02 5.52
2437 4819 1.066422 CGCTCCGCTGCTGATTCTA 59.934 57.895 0.00 0.00 0.00 2.10
2464 4846 4.227134 CGCCTCATCCACCTCCCG 62.227 72.222 0.00 0.00 0.00 5.14
2465 4847 3.866582 CCGCCTCATCCACCTCCC 61.867 72.222 0.00 0.00 0.00 4.30
2470 4852 4.489771 CACCCCCGCCTCATCCAC 62.490 72.222 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.