Multiple sequence alignment - TraesCS7A01G504000

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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 TraesCS7A01G504000 chr7A 100.000 2707 0 0 1 2707 692510607 692507901 0.000000e+00 5000.0
1 TraesCS7A01G504000 chr7A 95.127 985 44 2 1725 2707 671820777 671819795 0.000000e+00 1550.0
2 TraesCS7A01G504000 chr7A 80.940 383 39 16 1054 1422 692683645 692683283 3.430000e-69 272.0
3 TraesCS7A01G504000 chr2A 96.259 989 34 2 1722 2707 750534711 750533723 0.000000e+00 1618.0
4 TraesCS7A01G504000 chr2A 95.040 988 41 5 1725 2707 118230658 118229674 0.000000e+00 1546.0
5 TraesCS7A01G504000 chr2A 94.944 989 43 5 1723 2707 726747311 726746326 0.000000e+00 1543.0
6 TraesCS7A01G504000 chr5A 96.053 988 34 4 1723 2707 502601480 502600495 0.000000e+00 1604.0
7 TraesCS7A01G504000 chr5A 95.846 987 33 5 1723 2707 671200021 671201001 0.000000e+00 1589.0
8 TraesCS7A01G504000 chr5A 95.436 986 41 2 1724 2707 394268754 394267771 0.000000e+00 1568.0
9 TraesCS7A01G504000 chr6A 95.335 986 39 5 1725 2707 133799693 133800674 0.000000e+00 1559.0
10 TraesCS7A01G504000 chr6A 95.233 986 42 3 1725 2707 45000136 44999153 0.000000e+00 1555.0
11 TraesCS7A01G504000 chr7D 88.363 1014 56 30 698 1673 600502819 600501830 0.000000e+00 1162.0
12 TraesCS7A01G504000 chr7D 87.070 727 37 30 1 703 600504651 600503958 0.000000e+00 769.0
13 TraesCS7A01G504000 chr7D 84.293 382 35 13 1054 1422 600848738 600848369 1.540000e-92 350.0
14 TraesCS7A01G504000 chr7D 84.392 378 31 18 1054 1422 600467194 600466836 2.000000e-91 346.0
15 TraesCS7A01G504000 chr7B 87.476 1022 51 42 698 1670 679884375 679883382 0.000000e+00 1107.0
16 TraesCS7A01G504000 chr7B 82.083 480 57 14 3 481 679890400 679889949 1.520000e-102 383.0
17 TraesCS7A01G504000 chr7B 85.470 351 39 11 1054 1401 680013765 680013424 3.320000e-94 355.0
18 TraesCS7A01G504000 chr7B 85.143 350 40 9 1057 1401 679814199 679813857 5.550000e-92 348.0
19 TraesCS7A01G504000 chr7B 92.063 63 2 2 616 677 679885671 679885611 4.800000e-13 86.1


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 TraesCS7A01G504000 chr7A 692507901 692510607 2706 True 5000.00 5000 100.0000 1 2707 1 chr7A.!!$R2 2706
1 TraesCS7A01G504000 chr7A 671819795 671820777 982 True 1550.00 1550 95.1270 1725 2707 1 chr7A.!!$R1 982
2 TraesCS7A01G504000 chr2A 750533723 750534711 988 True 1618.00 1618 96.2590 1722 2707 1 chr2A.!!$R3 985
3 TraesCS7A01G504000 chr2A 118229674 118230658 984 True 1546.00 1546 95.0400 1725 2707 1 chr2A.!!$R1 982
4 TraesCS7A01G504000 chr2A 726746326 726747311 985 True 1543.00 1543 94.9440 1723 2707 1 chr2A.!!$R2 984
5 TraesCS7A01G504000 chr5A 502600495 502601480 985 True 1604.00 1604 96.0530 1723 2707 1 chr5A.!!$R2 984
6 TraesCS7A01G504000 chr5A 671200021 671201001 980 False 1589.00 1589 95.8460 1723 2707 1 chr5A.!!$F1 984
7 TraesCS7A01G504000 chr5A 394267771 394268754 983 True 1568.00 1568 95.4360 1724 2707 1 chr5A.!!$R1 983
8 TraesCS7A01G504000 chr6A 133799693 133800674 981 False 1559.00 1559 95.3350 1725 2707 1 chr6A.!!$F1 982
9 TraesCS7A01G504000 chr6A 44999153 45000136 983 True 1555.00 1555 95.2330 1725 2707 1 chr6A.!!$R1 982
10 TraesCS7A01G504000 chr7D 600501830 600504651 2821 True 965.50 1162 87.7165 1 1673 2 chr7D.!!$R3 1672
11 TraesCS7A01G504000 chr7B 679883382 679885671 2289 True 596.55 1107 89.7695 616 1670 2 chr7B.!!$R4 1054

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
90 91 0.025898 CGATGTGACGAAGCAGCATG 59.974 55.0 0.00 0.0 35.39 4.06 F
1427 3431 0.108138 AGCTCCTTCGTGCACATACC 60.108 55.0 18.64 0.0 0.00 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1677 3693 0.179129 GCAGTTGATTTCCGGCATGG 60.179 55.0 0.0 0.0 40.09 3.66 R
2228 4254 1.107945 GAGAGGAGAAGGAGGAACGG 58.892 60.0 0.0 0.0 0.00 4.44 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
58 59 1.378531 GCAATGGCGAGTACCAATCA 58.621 50.000 0.00 0.00 44.65 2.57
69 70 5.399858 CGAGTACCAATCATAAGGGATACG 58.600 45.833 0.00 0.00 37.60 3.06
71 72 6.342338 AGTACCAATCATAAGGGATACGAC 57.658 41.667 0.00 0.00 37.60 4.34
90 91 0.025898 CGATGTGACGAAGCAGCATG 59.974 55.000 0.00 0.00 35.39 4.06
118 119 2.689553 TAGCCGAAGATGAACATGCA 57.310 45.000 0.00 0.00 0.00 3.96
121 122 1.199789 GCCGAAGATGAACATGCACAA 59.800 47.619 0.00 0.00 0.00 3.33
140 141 6.201615 TGCACAAATATGAGTCGAGATGAATC 59.798 38.462 0.00 0.00 41.99 2.52
201 202 1.867233 GTGTGTGTCAGTGTTGGCTAG 59.133 52.381 0.00 0.00 0.00 3.42
210 211 1.277557 AGTGTTGGCTAGCTCTTCCAG 59.722 52.381 15.72 0.00 0.00 3.86
225 226 3.444034 TCTTCCAGTGTCCATCTAAGACG 59.556 47.826 0.00 0.00 37.04 4.18
249 250 1.429463 GATGTATCCATCGAACCGGC 58.571 55.000 0.00 0.00 38.28 6.13
254 255 1.762708 ATCCATCGAACCGGCAAATT 58.237 45.000 0.00 0.00 0.00 1.82
256 257 0.525761 CCATCGAACCGGCAAATTGT 59.474 50.000 0.00 0.00 0.00 2.71
295 296 0.326595 TGGGCCGCTTCTGAATACAA 59.673 50.000 0.00 0.00 0.00 2.41
296 297 0.733150 GGGCCGCTTCTGAATACAAC 59.267 55.000 0.00 0.00 0.00 3.32
298 299 2.419574 GGGCCGCTTCTGAATACAACTA 60.420 50.000 0.00 0.00 0.00 2.24
299 300 3.467803 GGCCGCTTCTGAATACAACTAT 58.532 45.455 0.00 0.00 0.00 2.12
301 302 4.448060 GGCCGCTTCTGAATACAACTATAC 59.552 45.833 0.00 0.00 0.00 1.47
302 303 5.290386 GCCGCTTCTGAATACAACTATACT 58.710 41.667 0.00 0.00 0.00 2.12
303 304 5.175856 GCCGCTTCTGAATACAACTATACTG 59.824 44.000 0.00 0.00 0.00 2.74
304 305 6.504398 CCGCTTCTGAATACAACTATACTGA 58.496 40.000 0.00 0.00 0.00 3.41
305 306 6.418226 CCGCTTCTGAATACAACTATACTGAC 59.582 42.308 0.00 0.00 0.00 3.51
307 308 7.166638 CGCTTCTGAATACAACTATACTGACAG 59.833 40.741 0.00 0.00 0.00 3.51
308 309 8.191446 GCTTCTGAATACAACTATACTGACAGA 58.809 37.037 10.08 0.00 0.00 3.41
316 317 7.704578 ACAACTATACTGACAGATAGTGTGT 57.295 36.000 19.53 19.62 40.56 3.72
317 318 8.803397 ACAACTATACTGACAGATAGTGTGTA 57.197 34.615 19.53 0.61 40.56 2.90
318 319 9.409918 ACAACTATACTGACAGATAGTGTGTAT 57.590 33.333 19.53 6.63 40.56 2.29
384 385 3.429043 TTGGTAACGAGATCCGCAC 57.571 52.632 0.00 3.03 43.32 5.34
389 390 1.135489 GTAACGAGATCCGCACAGTCA 60.135 52.381 0.00 0.00 43.32 3.41
399 400 3.521560 TCCGCACAGTCATAAGTTCATC 58.478 45.455 0.00 0.00 0.00 2.92
403 404 4.807834 CGCACAGTCATAAGTTCATCTCAT 59.192 41.667 0.00 0.00 0.00 2.90
423 424 9.984190 ATCTCATGATATATGGATTGAAGATCG 57.016 33.333 0.00 0.00 0.00 3.69
427 428 9.760077 CATGATATATGGATTGAAGATCGATCA 57.240 33.333 26.47 5.58 38.71 2.92
431 432 9.948964 ATATATGGATTGAAGATCGATCAAACA 57.051 29.630 26.47 18.68 38.71 2.83
432 433 8.681486 ATATGGATTGAAGATCGATCAAACAA 57.319 30.769 26.47 24.56 38.71 2.83
433 434 6.816134 TGGATTGAAGATCGATCAAACAAA 57.184 33.333 26.47 13.35 38.71 2.83
464 465 6.436261 CCTAAGCTTGCAAATGATATGACAG 58.564 40.000 9.86 0.00 0.00 3.51
482 483 6.194796 TGACAGCAATTGAGTAATAAAGGC 57.805 37.500 10.34 0.00 0.00 4.35
487 488 7.393234 ACAGCAATTGAGTAATAAAGGCAGTTA 59.607 33.333 10.34 0.00 0.00 2.24
539 540 4.214980 CAACTACCTTGCTGAAACAGTG 57.785 45.455 0.00 0.00 33.43 3.66
576 577 2.894919 GCCAATGGCCTTGCGAAT 59.105 55.556 14.47 0.00 44.06 3.34
590 591 0.645868 GCGAATCGAACGAAGAAGGG 59.354 55.000 6.91 0.00 0.00 3.95
592 593 1.736032 CGAATCGAACGAAGAAGGGCT 60.736 52.381 0.00 0.00 0.00 5.19
595 596 1.830279 TCGAACGAAGAAGGGCTCTA 58.170 50.000 0.00 0.00 32.46 2.43
736 2691 1.200020 CCGCATCTCCACCAGAAAAAC 59.800 52.381 0.00 0.00 33.62 2.43
737 2692 1.879380 CGCATCTCCACCAGAAAAACA 59.121 47.619 0.00 0.00 33.62 2.83
738 2693 2.095567 CGCATCTCCACCAGAAAAACAG 60.096 50.000 0.00 0.00 33.62 3.16
739 2694 2.352127 GCATCTCCACCAGAAAAACAGC 60.352 50.000 0.00 0.00 33.62 4.40
740 2695 3.152341 CATCTCCACCAGAAAAACAGCT 58.848 45.455 0.00 0.00 33.62 4.24
743 2698 3.391296 TCTCCACCAGAAAAACAGCTACT 59.609 43.478 0.00 0.00 0.00 2.57
745 2700 2.814336 CCACCAGAAAAACAGCTACTCC 59.186 50.000 0.00 0.00 0.00 3.85
746 2701 3.496870 CCACCAGAAAAACAGCTACTCCT 60.497 47.826 0.00 0.00 0.00 3.69
747 2702 4.262894 CCACCAGAAAAACAGCTACTCCTA 60.263 45.833 0.00 0.00 0.00 2.94
748 2703 4.691216 CACCAGAAAAACAGCTACTCCTAC 59.309 45.833 0.00 0.00 0.00 3.18
750 2705 4.932200 CCAGAAAAACAGCTACTCCTACAG 59.068 45.833 0.00 0.00 0.00 2.74
752 2707 5.635700 CAGAAAAACAGCTACTCCTACAGAC 59.364 44.000 0.00 0.00 0.00 3.51
753 2708 3.851976 AAACAGCTACTCCTACAGACG 57.148 47.619 0.00 0.00 0.00 4.18
754 2709 2.783609 ACAGCTACTCCTACAGACGA 57.216 50.000 0.00 0.00 0.00 4.20
755 2710 2.634600 ACAGCTACTCCTACAGACGAG 58.365 52.381 0.00 0.00 0.00 4.18
756 2711 1.944024 CAGCTACTCCTACAGACGAGG 59.056 57.143 0.00 0.00 35.17 4.63
791 2746 0.109597 CCAGAAATTCGCACACAGCC 60.110 55.000 0.00 0.00 41.38 4.85
797 2752 2.216750 ATTCGCACACAGCCATTGCC 62.217 55.000 0.00 0.00 41.38 4.52
912 2867 1.270518 CCGATTCCGCATCATTCCTCT 60.271 52.381 0.00 0.00 0.00 3.69
913 2868 2.064762 CGATTCCGCATCATTCCTCTC 58.935 52.381 0.00 0.00 0.00 3.20
914 2869 2.421619 GATTCCGCATCATTCCTCTCC 58.578 52.381 0.00 0.00 0.00 3.71
915 2870 1.203237 TTCCGCATCATTCCTCTCCA 58.797 50.000 0.00 0.00 0.00 3.86
970 2939 1.619807 TAAAGCTACGCCACCTCCCC 61.620 60.000 0.00 0.00 0.00 4.81
1009 2978 2.891941 TACGACATACTCCCCGGCGT 62.892 60.000 6.01 0.00 0.00 5.68
1035 3004 0.321298 TTTGTCAGTTAGCCGAGGCC 60.321 55.000 10.95 0.00 43.17 5.19
1039 3008 3.148279 AGTTAGCCGAGGCCCGAG 61.148 66.667 10.95 6.50 43.17 4.63
1096 3068 1.657751 CTCGACGTGCCTGGAGATCA 61.658 60.000 0.00 0.00 0.00 2.92
1177 3149 0.545309 CAACCACTCCTCCTCCTCCA 60.545 60.000 0.00 0.00 0.00 3.86
1192 3164 1.339610 CCTCCAGATTCAGCTACCTCG 59.660 57.143 0.00 0.00 0.00 4.63
1403 3407 0.390860 ACTACATCCTCGCCTGATGC 59.609 55.000 8.09 0.00 42.68 3.91
1427 3431 0.108138 AGCTCCTTCGTGCACATACC 60.108 55.000 18.64 0.00 0.00 2.73
1450 3454 1.275291 TGTAGTGGAGCTTGCTGTACC 59.725 52.381 0.00 0.00 0.00 3.34
1469 3483 1.113788 CGCCATTGTTGGGATTGGAT 58.886 50.000 0.00 0.00 43.84 3.41
1470 3484 1.481772 CGCCATTGTTGGGATTGGATT 59.518 47.619 0.00 0.00 43.84 3.01
1471 3485 2.093553 CGCCATTGTTGGGATTGGATTT 60.094 45.455 0.00 0.00 43.84 2.17
1472 3486 3.272581 GCCATTGTTGGGATTGGATTTG 58.727 45.455 0.00 0.00 43.84 2.32
1473 3487 3.876341 CCATTGTTGGGATTGGATTTGG 58.124 45.455 0.00 0.00 39.56 3.28
1474 3488 3.518705 CCATTGTTGGGATTGGATTTGGA 59.481 43.478 0.00 0.00 39.56 3.53
1517 3531 1.393883 GCCGTAGCTAGTTGTTTGAGC 59.606 52.381 0.00 0.00 36.42 4.26
1555 3570 4.376615 CGGTGGTTGTACATGTAGTTTTCG 60.377 45.833 5.62 1.69 0.00 3.46
1605 3621 4.744631 TCGTGATGTATGATTGGTTCATCG 59.255 41.667 0.00 0.00 44.13 3.84
1606 3622 4.744631 CGTGATGTATGATTGGTTCATCGA 59.255 41.667 0.00 0.00 44.13 3.59
1611 3627 4.821260 TGTATGATTGGTTCATCGATTGGG 59.179 41.667 0.00 0.00 44.13 4.12
1670 3686 4.514441 GGAGCTAGCGATTAGTGTACTGTA 59.486 45.833 9.55 0.00 0.00 2.74
1673 3689 6.264088 AGCTAGCGATTAGTGTACTGTAAAC 58.736 40.000 9.55 0.00 0.00 2.01
1674 3690 6.095160 AGCTAGCGATTAGTGTACTGTAAACT 59.905 38.462 14.69 14.69 0.00 2.66
1675 3691 6.196724 GCTAGCGATTAGTGTACTGTAAACTG 59.803 42.308 18.74 5.14 0.00 3.16
1676 3692 6.022163 AGCGATTAGTGTACTGTAAACTGT 57.978 37.500 18.74 8.77 0.00 3.55
1677 3693 6.091437 AGCGATTAGTGTACTGTAAACTGTC 58.909 40.000 18.74 14.88 0.00 3.51
1678 3694 5.287992 GCGATTAGTGTACTGTAAACTGTCC 59.712 44.000 18.74 7.78 0.00 4.02
1679 3695 6.384224 CGATTAGTGTACTGTAAACTGTCCA 58.616 40.000 18.74 0.00 0.00 4.02
1680 3696 7.033791 CGATTAGTGTACTGTAAACTGTCCAT 58.966 38.462 18.74 7.13 0.00 3.41
1681 3697 7.009265 CGATTAGTGTACTGTAAACTGTCCATG 59.991 40.741 18.74 2.76 0.00 3.66
1682 3698 4.315803 AGTGTACTGTAAACTGTCCATGC 58.684 43.478 9.82 0.00 0.00 4.06
1683 3699 3.435671 GTGTACTGTAAACTGTCCATGCC 59.564 47.826 0.77 0.00 0.00 4.40
1684 3700 1.808411 ACTGTAAACTGTCCATGCCG 58.192 50.000 0.00 0.00 0.00 5.69
1685 3701 1.086696 CTGTAAACTGTCCATGCCGG 58.913 55.000 0.00 0.00 0.00 6.13
1686 3702 0.687920 TGTAAACTGTCCATGCCGGA 59.312 50.000 5.05 0.00 43.61 5.14
1694 3710 3.976704 TCCATGCCGGAAATCAACT 57.023 47.368 5.05 0.00 42.52 3.16
1695 3711 1.462616 TCCATGCCGGAAATCAACTG 58.537 50.000 5.05 0.00 42.52 3.16
1696 3712 0.179129 CCATGCCGGAAATCAACTGC 60.179 55.000 5.05 0.00 36.56 4.40
1697 3713 0.813184 CATGCCGGAAATCAACTGCT 59.187 50.000 5.05 0.00 0.00 4.24
1698 3714 0.813184 ATGCCGGAAATCAACTGCTG 59.187 50.000 5.05 0.00 0.00 4.41
1699 3715 1.243342 TGCCGGAAATCAACTGCTGG 61.243 55.000 5.05 0.00 0.00 4.85
1700 3716 1.244019 GCCGGAAATCAACTGCTGGT 61.244 55.000 5.05 0.00 0.00 4.00
1701 3717 1.948611 GCCGGAAATCAACTGCTGGTA 60.949 52.381 5.05 0.00 0.00 3.25
1702 3718 2.643551 CCGGAAATCAACTGCTGGTAT 58.356 47.619 0.00 0.00 0.00 2.73
1703 3719 3.016736 CCGGAAATCAACTGCTGGTATT 58.983 45.455 0.00 0.00 0.00 1.89
1704 3720 3.181497 CCGGAAATCAACTGCTGGTATTG 60.181 47.826 0.00 0.00 0.00 1.90
1705 3721 3.440173 CGGAAATCAACTGCTGGTATTGT 59.560 43.478 0.00 0.00 0.00 2.71
1706 3722 4.082787 CGGAAATCAACTGCTGGTATTGTT 60.083 41.667 0.00 0.00 0.00 2.83
1707 3723 5.564651 CGGAAATCAACTGCTGGTATTGTTT 60.565 40.000 0.00 0.00 0.00 2.83
1708 3724 5.634859 GGAAATCAACTGCTGGTATTGTTTG 59.365 40.000 0.00 0.00 0.00 2.93
1709 3725 3.641437 TCAACTGCTGGTATTGTTTGC 57.359 42.857 0.00 0.00 0.00 3.68
1710 3726 2.954989 TCAACTGCTGGTATTGTTTGCA 59.045 40.909 0.00 0.00 0.00 4.08
1711 3727 3.382865 TCAACTGCTGGTATTGTTTGCAA 59.617 39.130 0.00 0.00 39.16 4.08
1712 3728 4.039004 TCAACTGCTGGTATTGTTTGCAAT 59.961 37.500 0.00 0.00 46.14 3.56
1713 3729 3.916761 ACTGCTGGTATTGTTTGCAATG 58.083 40.909 0.00 0.00 44.32 2.82
1714 3730 3.255725 CTGCTGGTATTGTTTGCAATGG 58.744 45.455 0.00 0.00 44.32 3.16
1715 3731 2.896044 TGCTGGTATTGTTTGCAATGGA 59.104 40.909 0.00 0.00 44.32 3.41
1716 3732 3.514706 TGCTGGTATTGTTTGCAATGGAT 59.485 39.130 0.00 0.00 44.32 3.41
1717 3733 3.866910 GCTGGTATTGTTTGCAATGGATG 59.133 43.478 0.00 0.00 44.32 3.51
1718 3734 4.435425 CTGGTATTGTTTGCAATGGATGG 58.565 43.478 0.00 0.00 44.32 3.51
1719 3735 3.197333 TGGTATTGTTTGCAATGGATGGG 59.803 43.478 0.00 0.00 44.32 4.00
1720 3736 3.197549 GGTATTGTTTGCAATGGATGGGT 59.802 43.478 0.00 0.00 44.32 4.51
1967 3991 0.106419 CTCTACCCTCTTCTCGGCCT 60.106 60.000 0.00 0.00 0.00 5.19
2158 4184 0.531200 GCCGGCCTATATAAGACGCT 59.469 55.000 18.11 0.00 0.00 5.07
2228 4254 2.334653 CCTCTCTCTCGCCATCGC 59.665 66.667 0.00 0.00 35.26 4.58
2415 4441 4.148825 GGCGTGGAGGATCAGCGT 62.149 66.667 0.00 0.00 36.44 5.07
2604 4630 2.663852 CAACGGCGTCGAACCCTT 60.664 61.111 20.03 0.00 40.11 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.873698 TTGCGGTGTCACCTAGAAAC 58.126 50.000 19.82 3.27 35.66 2.78
58 59 3.058432 CGTCACATCGTCGTATCCCTTAT 60.058 47.826 0.00 0.00 0.00 1.73
69 70 1.008875 TGCTGCTTCGTCACATCGTC 61.009 55.000 0.00 0.00 0.00 4.20
71 72 0.025898 CATGCTGCTTCGTCACATCG 59.974 55.000 0.00 0.00 0.00 3.84
118 119 6.739112 TCGATTCATCTCGACTCATATTTGT 58.261 36.000 0.00 0.00 42.38 2.83
173 174 0.812811 ACTGACACACACAGCAGCAG 60.813 55.000 0.00 0.00 38.74 4.24
174 175 1.091197 CACTGACACACACAGCAGCA 61.091 55.000 0.00 0.00 38.74 4.41
175 176 1.091771 ACACTGACACACACAGCAGC 61.092 55.000 0.00 0.00 38.74 5.25
176 177 1.063027 CAACACTGACACACACAGCAG 59.937 52.381 0.00 0.00 38.74 4.24
177 178 1.085893 CAACACTGACACACACAGCA 58.914 50.000 0.00 0.00 38.74 4.41
178 179 0.378257 CCAACACTGACACACACAGC 59.622 55.000 0.00 0.00 38.74 4.40
179 180 0.378257 GCCAACACTGACACACACAG 59.622 55.000 0.00 0.00 40.68 3.66
201 202 3.449018 TCTTAGATGGACACTGGAAGAGC 59.551 47.826 0.00 0.00 37.43 4.09
210 211 4.436242 TCTGAACGTCTTAGATGGACAC 57.564 45.455 6.39 0.00 33.73 3.67
249 250 0.904394 CTGGGGGTGGGGACAATTTG 60.904 60.000 0.00 0.00 46.06 2.32
301 302 8.633561 TCCAGAAATATACACACTATCTGTCAG 58.366 37.037 0.00 0.00 32.86 3.51
302 303 8.533569 TCCAGAAATATACACACTATCTGTCA 57.466 34.615 0.00 0.00 32.86 3.58
316 317 9.366216 GCGTGTGTATCATTATCCAGAAATATA 57.634 33.333 0.00 0.00 0.00 0.86
317 318 7.877612 TGCGTGTGTATCATTATCCAGAAATAT 59.122 33.333 0.00 0.00 0.00 1.28
318 319 7.213678 TGCGTGTGTATCATTATCCAGAAATA 58.786 34.615 0.00 0.00 0.00 1.40
319 320 6.054941 TGCGTGTGTATCATTATCCAGAAAT 58.945 36.000 0.00 0.00 0.00 2.17
320 321 5.423886 TGCGTGTGTATCATTATCCAGAAA 58.576 37.500 0.00 0.00 0.00 2.52
321 322 5.017294 TGCGTGTGTATCATTATCCAGAA 57.983 39.130 0.00 0.00 0.00 3.02
322 323 4.664150 TGCGTGTGTATCATTATCCAGA 57.336 40.909 0.00 0.00 0.00 3.86
323 324 4.811024 AGTTGCGTGTGTATCATTATCCAG 59.189 41.667 0.00 0.00 0.00 3.86
324 325 4.765273 AGTTGCGTGTGTATCATTATCCA 58.235 39.130 0.00 0.00 0.00 3.41
325 326 5.734855 AAGTTGCGTGTGTATCATTATCC 57.265 39.130 0.00 0.00 0.00 2.59
368 369 0.172803 ACTGTGCGGATCTCGTTACC 59.827 55.000 5.66 0.00 41.72 2.85
399 400 9.984190 ATCGATCTTCAATCCATATATCATGAG 57.016 33.333 0.09 0.00 0.00 2.90
423 424 5.105063 GCTTAGGCAGGAATTTGTTTGATC 58.895 41.667 0.00 0.00 38.54 2.92
427 428 4.800582 GCAAGCTTAGGCAGGAATTTGTTT 60.801 41.667 0.00 0.00 41.70 2.83
430 431 2.231964 TGCAAGCTTAGGCAGGAATTTG 59.768 45.455 7.34 0.00 41.70 2.32
431 432 2.528564 TGCAAGCTTAGGCAGGAATTT 58.471 42.857 7.34 0.00 41.70 1.82
432 433 2.220653 TGCAAGCTTAGGCAGGAATT 57.779 45.000 7.34 0.00 41.70 2.17
433 434 2.220653 TTGCAAGCTTAGGCAGGAAT 57.779 45.000 10.90 0.00 41.68 3.01
464 465 9.665264 GTATAACTGCCTTTATTACTCAATTGC 57.335 33.333 0.00 0.00 0.00 3.56
573 574 1.927838 GAGCCCTTCTTCGTTCGATTC 59.072 52.381 0.00 0.00 0.00 2.52
576 577 1.471684 GTAGAGCCCTTCTTCGTTCGA 59.528 52.381 0.00 0.00 37.36 3.71
736 2691 1.944024 CCTCGTCTGTAGGAGTAGCTG 59.056 57.143 0.00 0.00 36.15 4.24
737 2692 1.134037 CCCTCGTCTGTAGGAGTAGCT 60.134 57.143 0.00 0.00 36.15 3.32
738 2693 1.134159 TCCCTCGTCTGTAGGAGTAGC 60.134 57.143 0.00 0.00 36.15 3.58
739 2694 2.485835 CCTCCCTCGTCTGTAGGAGTAG 60.486 59.091 4.34 0.00 43.73 2.57
740 2695 1.489649 CCTCCCTCGTCTGTAGGAGTA 59.510 57.143 4.34 0.00 43.73 2.59
743 2698 0.997363 TTCCTCCCTCGTCTGTAGGA 59.003 55.000 0.00 0.00 36.08 2.94
745 2700 5.074115 AGAATATTCCTCCCTCGTCTGTAG 58.926 45.833 11.92 0.00 0.00 2.74
746 2701 5.063017 AGAATATTCCTCCCTCGTCTGTA 57.937 43.478 11.92 0.00 0.00 2.74
747 2702 3.892588 GAGAATATTCCTCCCTCGTCTGT 59.107 47.826 11.92 0.00 0.00 3.41
748 2703 3.891977 TGAGAATATTCCTCCCTCGTCTG 59.108 47.826 11.92 0.00 0.00 3.51
750 2705 3.305744 GCTGAGAATATTCCTCCCTCGTC 60.306 52.174 11.92 1.46 0.00 4.20
752 2707 2.028567 GGCTGAGAATATTCCTCCCTCG 60.029 54.545 11.92 1.74 0.00 4.63
753 2708 2.975489 TGGCTGAGAATATTCCTCCCTC 59.025 50.000 11.92 3.53 0.00 4.30
754 2709 2.978278 CTGGCTGAGAATATTCCTCCCT 59.022 50.000 11.92 0.00 0.00 4.20
755 2710 2.975489 TCTGGCTGAGAATATTCCTCCC 59.025 50.000 11.92 8.16 0.00 4.30
756 2711 4.696479 TTCTGGCTGAGAATATTCCTCC 57.304 45.455 11.92 8.49 35.64 4.30
826 2781 4.662961 TGTGCTGTCGCTGACCGG 62.663 66.667 0.00 0.00 37.59 5.28
827 2782 2.661537 TTGTGCTGTCGCTGACCG 60.662 61.111 6.30 1.99 36.97 4.79
828 2783 2.320587 CCTTGTGCTGTCGCTGACC 61.321 63.158 6.30 0.00 36.97 4.02
829 2784 2.959357 GCCTTGTGCTGTCGCTGAC 61.959 63.158 2.32 2.32 36.87 3.51
842 2797 4.722700 CACCGTGGAGGGGCCTTG 62.723 72.222 0.84 0.00 46.96 3.61
912 2867 4.424711 GCAAGCCGGGTGGATGGA 62.425 66.667 13.59 0.00 37.49 3.41
913 2868 4.431131 AGCAAGCCGGGTGGATGG 62.431 66.667 13.59 0.00 37.49 3.51
914 2869 3.136123 CAGCAAGCCGGGTGGATG 61.136 66.667 12.59 12.59 37.49 3.51
1009 2978 1.508632 GCTAACTGACAAACTCGGCA 58.491 50.000 0.00 0.00 0.00 5.69
1047 3016 4.201122 CTCATCCTGCCCCCTGCC 62.201 72.222 0.00 0.00 40.16 4.85
1048 3017 4.891037 GCTCATCCTGCCCCCTGC 62.891 72.222 0.00 0.00 41.77 4.85
1049 3018 3.095163 AGCTCATCCTGCCCCCTG 61.095 66.667 0.00 0.00 0.00 4.45
1050 3019 2.771762 GAGCTCATCCTGCCCCCT 60.772 66.667 9.40 0.00 0.00 4.79
1177 3149 2.295909 GCAGATCGAGGTAGCTGAATCT 59.704 50.000 0.00 4.52 0.00 2.40
1403 3407 1.664649 TGCACGAAGGAGCTTGTCG 60.665 57.895 11.65 11.65 40.56 4.35
1427 3431 1.079543 AGCAAGCTCCACTACAGCG 60.080 57.895 0.00 0.00 42.14 5.18
1450 3454 1.113788 ATCCAATCCCAACAATGGCG 58.886 50.000 0.00 0.00 46.09 5.69
1469 3483 5.449862 GCACAACTTACAAGTCATGTCCAAA 60.450 40.000 0.00 0.00 42.70 3.28
1470 3484 4.036262 GCACAACTTACAAGTCATGTCCAA 59.964 41.667 0.00 0.00 42.70 3.53
1471 3485 3.563808 GCACAACTTACAAGTCATGTCCA 59.436 43.478 0.00 0.00 42.70 4.02
1472 3486 3.363970 CGCACAACTTACAAGTCATGTCC 60.364 47.826 0.00 0.00 42.70 4.02
1473 3487 3.247648 ACGCACAACTTACAAGTCATGTC 59.752 43.478 0.00 0.00 42.70 3.06
1474 3488 3.202906 ACGCACAACTTACAAGTCATGT 58.797 40.909 0.00 0.00 46.36 3.21
1509 3523 5.288804 GGCACTAAAGAATTTGCTCAAACA 58.711 37.500 0.00 0.00 39.63 2.83
1517 3531 2.556622 ACCACCGGCACTAAAGAATTTG 59.443 45.455 0.00 0.00 39.63 2.32
1555 3570 6.379988 ACCAATATACCCAACCAATCAAGAAC 59.620 38.462 0.00 0.00 0.00 3.01
1605 3621 4.034285 TCTTTTCCTCAAGGACCCAATC 57.966 45.455 0.00 0.00 45.39 2.67
1606 3622 4.469469 TTCTTTTCCTCAAGGACCCAAT 57.531 40.909 0.00 0.00 45.39 3.16
1611 3627 5.073428 ACCAAGATTCTTTTCCTCAAGGAC 58.927 41.667 0.00 0.00 45.39 3.85
1677 3693 0.179129 GCAGTTGATTTCCGGCATGG 60.179 55.000 0.00 0.00 40.09 3.66
1678 3694 0.813184 AGCAGTTGATTTCCGGCATG 59.187 50.000 0.00 0.00 0.00 4.06
1679 3695 0.813184 CAGCAGTTGATTTCCGGCAT 59.187 50.000 0.00 0.00 0.00 4.40
1680 3696 1.243342 CCAGCAGTTGATTTCCGGCA 61.243 55.000 0.00 0.00 0.00 5.69
1681 3697 1.244019 ACCAGCAGTTGATTTCCGGC 61.244 55.000 0.00 0.00 0.00 6.13
1682 3698 2.107950 TACCAGCAGTTGATTTCCGG 57.892 50.000 0.00 0.00 0.00 5.14
1683 3699 3.440173 ACAATACCAGCAGTTGATTTCCG 59.560 43.478 0.00 0.00 0.00 4.30
1684 3700 5.391312 AACAATACCAGCAGTTGATTTCC 57.609 39.130 0.00 0.00 0.00 3.13
1685 3701 5.119125 GCAAACAATACCAGCAGTTGATTTC 59.881 40.000 0.00 0.00 0.00 2.17
1686 3702 4.990426 GCAAACAATACCAGCAGTTGATTT 59.010 37.500 0.00 0.00 0.00 2.17
1687 3703 4.039004 TGCAAACAATACCAGCAGTTGATT 59.961 37.500 0.00 0.00 0.00 2.57
1688 3704 3.573538 TGCAAACAATACCAGCAGTTGAT 59.426 39.130 0.00 0.00 0.00 2.57
1689 3705 2.954989 TGCAAACAATACCAGCAGTTGA 59.045 40.909 0.00 0.00 0.00 3.18
1690 3706 3.367992 TGCAAACAATACCAGCAGTTG 57.632 42.857 0.00 0.00 0.00 3.16
1691 3707 4.309099 CATTGCAAACAATACCAGCAGTT 58.691 39.130 1.71 0.00 44.83 3.16
1692 3708 3.306225 CCATTGCAAACAATACCAGCAGT 60.306 43.478 1.71 0.00 44.83 4.40
1693 3709 3.056678 TCCATTGCAAACAATACCAGCAG 60.057 43.478 1.71 0.00 44.83 4.24
1694 3710 2.896044 TCCATTGCAAACAATACCAGCA 59.104 40.909 1.71 0.00 44.83 4.41
1695 3711 3.591196 TCCATTGCAAACAATACCAGC 57.409 42.857 1.71 0.00 44.83 4.85
1696 3712 4.435425 CCATCCATTGCAAACAATACCAG 58.565 43.478 1.71 0.00 44.83 4.00
1697 3713 3.197333 CCCATCCATTGCAAACAATACCA 59.803 43.478 1.71 0.00 44.83 3.25
1698 3714 3.197549 ACCCATCCATTGCAAACAATACC 59.802 43.478 1.71 0.00 44.83 2.73
1699 3715 4.183101 CACCCATCCATTGCAAACAATAC 58.817 43.478 1.71 0.00 44.83 1.89
1700 3716 3.837146 ACACCCATCCATTGCAAACAATA 59.163 39.130 1.71 0.00 44.83 1.90
1702 3718 2.045524 ACACCCATCCATTGCAAACAA 58.954 42.857 1.71 0.00 40.87 2.83
1703 3719 1.714541 ACACCCATCCATTGCAAACA 58.285 45.000 1.71 0.00 0.00 2.83
1704 3720 3.368323 CCTTACACCCATCCATTGCAAAC 60.368 47.826 1.71 0.00 0.00 2.93
1705 3721 2.830923 CCTTACACCCATCCATTGCAAA 59.169 45.455 1.71 0.00 0.00 3.68
1706 3722 2.455557 CCTTACACCCATCCATTGCAA 58.544 47.619 0.00 0.00 0.00 4.08
1707 3723 1.341877 CCCTTACACCCATCCATTGCA 60.342 52.381 0.00 0.00 0.00 4.08
1708 3724 1.402787 CCCTTACACCCATCCATTGC 58.597 55.000 0.00 0.00 0.00 3.56
1709 3725 1.341877 TGCCCTTACACCCATCCATTG 60.342 52.381 0.00 0.00 0.00 2.82
1710 3726 1.006813 TGCCCTTACACCCATCCATT 58.993 50.000 0.00 0.00 0.00 3.16
1711 3727 1.145738 GATGCCCTTACACCCATCCAT 59.854 52.381 0.00 0.00 0.00 3.41
1712 3728 0.550914 GATGCCCTTACACCCATCCA 59.449 55.000 0.00 0.00 0.00 3.41
1713 3729 0.846693 AGATGCCCTTACACCCATCC 59.153 55.000 0.00 0.00 35.78 3.51
1714 3730 1.202818 GGAGATGCCCTTACACCCATC 60.203 57.143 0.00 0.00 35.49 3.51
1715 3731 0.846693 GGAGATGCCCTTACACCCAT 59.153 55.000 0.00 0.00 0.00 4.00
1716 3732 0.548926 TGGAGATGCCCTTACACCCA 60.549 55.000 0.00 0.00 34.97 4.51
1717 3733 0.181350 CTGGAGATGCCCTTACACCC 59.819 60.000 0.00 0.00 34.97 4.61
1718 3734 0.464554 GCTGGAGATGCCCTTACACC 60.465 60.000 0.00 0.00 34.97 4.16
1719 3735 0.464554 GGCTGGAGATGCCCTTACAC 60.465 60.000 0.00 0.00 44.32 2.90
1720 3736 1.915228 GGCTGGAGATGCCCTTACA 59.085 57.895 0.00 0.00 44.32 2.41
1807 3825 0.460284 GCGAAAATCGAGCTCCTGGA 60.460 55.000 8.47 0.00 43.74 3.86
1816 3834 2.395360 CCAAGCCGGCGAAAATCGA 61.395 57.895 23.20 0.00 43.74 3.59
1967 3991 1.153901 GGCGATGAGGACGACGAAA 60.154 57.895 0.00 0.00 0.00 3.46
2228 4254 1.107945 GAGAGGAGAAGGAGGAACGG 58.892 60.000 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.