Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024186.1 Corchorus olitorius cultivar O-4 contig24219, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 79097
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:5752 original size:40 final size:40
Alignment explanation
Indices: 5703--5783 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
5693 TATAACAACC
*
5703 GATATAAAAGGTTCGTAACCAATTTACTCGTTTGTTTAAT
1 GATACAAAAGGTTCGTAACCAATTTACTCGTTTGTTTAAT
5743 GATACAAAAGGTTCGTAACCAATTTACTCGTTTGTTTAAT
1 GATACAAAAGGTTCGTAACCAATTTACTCGTTTGTTTAAT
5783 G
1 G
5784 TTAGACCCGC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (40 bp):
GATACAAAAGGTTCGTAACCAATTTACTCGTTTGTTTAAT
Found at i:7211 original size:51 final size:50
Alignment explanation
Indices: 7130--7233 Score: 145
Period size: 51 Copynumber: 2.1 Consensus size: 50
7120 AGTTATCTAA
* * *
7130 CTTAGAAACAATGTTAACCTGAGACAATGTTATTGTTTATTATTGGTTTTG
1 CTTAAAAACAATGTTAACCTGAGACAATGTTACTGTTT-TTATTGATTTTG
** *
7181 CTTAAAAACAATGTTAAGTTGAGACTATGTTACTGTTTTTATTGATTTTG
1 CTTAAAAACAATGTTAACCTGAGACAATGTTACTGTTTTTATTGATTTTG
7231 CTT
1 CTT
7234 TACTTATTAG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 14 0.30
51 33 0.70
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (50 bp):
CTTAAAAACAATGTTAACCTGAGACAATGTTACTGTTTTTATTGATTTTG
Found at i:7946 original size:32 final size:32
Alignment explanation
Indices: 7905--7983 Score: 122
Period size: 32 Copynumber: 2.5 Consensus size: 32
7895 GTGGCGTTTT
*
7905 GTTCATAAAACGCCCCTATATGGAGGCGCTTC
1 GTTCATAAAACGCCCCTATATAGAGGCGCTTC
* * *
7937 GTTCATAAAACGCCCCTATATAGTGGCGTTTT
1 GTTCATAAAACGCCCCTATATAGAGGCGCTTC
7969 GTTCATAAAACGCCC
1 GTTCATAAAACGCCC
7984 TGATTTTGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28
Consensus pattern (32 bp):
GTTCATAAAACGCCCCTATATAGAGGCGCTTC
Found at i:9752 original size:43 final size:45
Alignment explanation
Indices: 9691--9781 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 45
9681 ATGGTAGATA
9691 ACAGAATTATGTAACACAATT-GC-AAAAGTAGTTAGTCCAAATT
1 ACAGAATTATGTAACACAATTAGCAAAAAGTAGTTAGTCCAAATT
9734 ACAGAATTATGTAACACAATTAGCAGAAAAGTAGTTAGTCCAAATT
1 ACAGAATTATGTAACACAATTAGCA-AAAAGTAGTTAGTCCAAATT
9780 AC
1 AC
9782 TTACCATCTC
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
43 21 0.47
44 2 0.04
46 22 0.49
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.26
Consensus pattern (45 bp):
ACAGAATTATGTAACACAATTAGCAAAAAGTAGTTAGTCCAAATT
Found at i:9761 original size:22 final size:22
Alignment explanation
Indices: 9692--9761 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
9682 TGGTAGATAA
9692 CAGAATTATGTAACACAATT-G
1 CAGAATTATGTAACACAATTAG
* * *
9713 CAAAAGTA-GTTAGTC-CAAATTA-
1 CAGAATTATG-TA-ACAC-AATTAG
9735 CAGAATTATGTAACACAATTAG
1 CAGAATTATGTAACACAATTAG
9757 CAGAA
1 CAGAA
9762 AAGTAGTTAG
Statistics
Matches: 36, Mismatches: 6, Indels: 13
0.65 0.11 0.24
Matches are distributed among these distances:
20 1 0.03
21 15 0.42
22 19 0.53
23 1 0.03
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (22 bp):
CAGAATTATGTAACACAATTAG
Found at i:15143 original size:25 final size:26
Alignment explanation
Indices: 15078--15145 Score: 93
Period size: 26 Copynumber: 2.7 Consensus size: 26
15068 AGACCAAAAC
* * * *
15078 ACAACAACAACACCAAATTTAGGTCA
1 ACAAAAACAGCACCAAATATAGCTCA
15104 ACAAAAACAGCACCAAATATAGCTCA
1 ACAAAAACAGCACCAAATATAGCTCA
15130 ACAAAAACAG-ACCAAA
1 ACAAAAACAGCACCAAA
15146 ACAGTTTCCA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
25 6 0.16
26 32 0.84
ACGTcount: A:0.56, C:0.26, G:0.07, T:0.10
Consensus pattern (26 bp):
ACAAAAACAGCACCAAATATAGCTCA
Found at i:16938 original size:26 final size:26
Alignment explanation
Indices: 16879--16939 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
16869 AAGGAGAAGG
* *
16879 AAAGAAGAAGAAAAAGTTGGGAAAGA
1 AAAGAAGAAGAAAAAGATGGGAAACA
* * * *
16905 TAACAAGAAGAAAAGGATGGGAATCA
1 AAAGAAGAAGAAAAAGATGGGAAACA
16931 AAAGAAGAA
1 AAAGAAGAA
16940 ACGATGAGTT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.61, C:0.03, G:0.28, T:0.08
Consensus pattern (26 bp):
AAAGAAGAAGAAAAAGATGGGAAACA
Found at i:17974 original size:10 final size:10
Alignment explanation
Indices: 17961--18011 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
17951 GGTGTTATAT
17961 TTGTGAATTA
1 TTGTGAATTA
* *
17971 TTGTG-CTAA
1 TTGTGAATTA
*
17980 TTGTTAATTA
1 TTGTGAATTA
*
17990 TTTGTGAATTT
1 -TTGTGAATTA
18001 TTGTGAATTA
1 TTGTGAATTA
18011 T
1 T
18012 ATTTGTTAGA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
9 6 0.19
10 17 0.55
11 8 0.26
ACGTcount: A:0.25, C:0.02, G:0.18, T:0.55
Consensus pattern (10 bp):
TTGTGAATTA
Found at i:18826 original size:14 final size:15
Alignment explanation
Indices: 18795--18827 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
18785 TTGGTTCGTC
*
18795 AAAACTATTTTCCAG
1 AAAACAATTTTCCAG
18810 AAAACAATTTT-CAG
1 AAAACAATTTTCCAG
18824 AAAA
1 AAAA
18828 GAGATCCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.52, C:0.15, G:0.06, T:0.27
Consensus pattern (15 bp):
AAAACAATTTTCCAG
Found at i:23091 original size:12 final size:12
Alignment explanation
Indices: 23074--23100 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
23064 GTTTGGGGTA
23074 TAACTCTAAACC
1 TAACTCTAAACC
23086 TAACTCTAAACC
1 TAACTCTAAACC
23098 TAA
1 TAA
23101 TCATGCTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (12 bp):
TAACTCTAAACC
Found at i:24569 original size:36 final size:37
Alignment explanation
Indices: 24511--24599 Score: 126
Period size: 37 Copynumber: 2.4 Consensus size: 37
24501 GAAATATTGA
*
24511 TTTTAGTTCGTTCAATTTCCAC-TTTTTGTCAAATTCAG
1 TTTT-GTTC-TTCAATTACCACTTTTTTGTCAAATTCAG
* *
24549 TTTTGTTCTTCAATTACCACTTTTTTGTCAATTTCAT
1 TTTTGTTCTTCAATTACCACTTTTTTGTCAAATTCAG
24586 TTTTGTTCTTCAAT
1 TTTTGTTCTTCAAT
24600 CTTCATTACA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
36 11 0.23
37 32 0.68
38 4 0.09
ACGTcount: A:0.19, C:0.18, G:0.08, T:0.55
Consensus pattern (37 bp):
TTTTGTTCTTCAATTACCACTTTTTTGTCAAATTCAG
Found at i:27490 original size:22 final size:22
Alignment explanation
Indices: 27447--27490 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
27437 GTGCCAAAAG
*
27447 TTGTGGAGTCAGTTTTACTATT
1 TTGTGGAGTCAGTTTCACTATT
*
27469 TTGTAGGAGTTAGTTTCA-TATT
1 TTGT-GGAGTCAGTTTCACTATT
27491 GTTATTGATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.20, C:0.07, G:0.23, T:0.50
Consensus pattern (22 bp):
TTGTGGAGTCAGTTTCACTATT
Found at i:32694 original size:30 final size:29
Alignment explanation
Indices: 32626--32697 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 29
32616 TGGCAAGAAA
* *
32626 TACAATGGTATGGGAATTAATTTTAAAAG
1 TACAATGGTTTGGGAATTAATTTTAAAAC
*
32655 TACAATGGTTTGGGAATTATTTTTAAAAAC
1 TACAATGGTTTGGGAATTAATTTT-AAAAC
*
32685 TATAATGGTTTGG
1 TACAATGGTTTGG
32698 TCAAAAACTC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
29 22 0.58
30 16 0.42
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.39
Consensus pattern (29 bp):
TACAATGGTTTGGGAATTAATTTTAAAAC
Found at i:40101 original size:3 final size:3
Alignment explanation
Indices: 40093--40144 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
40083 GAAATTACGA
40093 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
40141 AAT A
1 AAT A
40145 TACCAAAATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:47580 original size:13 final size:13
Alignment explanation
Indices: 47562--47590 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
47552 TACTCACAAT
47562 TAGATTCAATTAC
1 TAGATTCAATTAC
47575 TAGATTCAATTAC
1 TAGATTCAATTAC
47588 TAG
1 TAG
47591 GGTTAGTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (13 bp):
TAGATTCAATTAC
Found at i:50928 original size:4 final size:4
Alignment explanation
Indices: 50916--50984 Score: 52
Period size: 4 Copynumber: 17.0 Consensus size: 4
50906 AAAAAAAAGT
* * * *
50916 AATA GATA AATA AATA AGTA AATA GATA GAA-A AATA AATA AAAA TAATA
1 AATA AATA AATA AATA AATA AATA AATA -AATA AATA AATA AATA -AATA
*
50965 GATA AATA AA-A AGATA AATA
1 AATA AATA AATA A-ATA AATA
50985 GGTATATAGA
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
3 4 0.08
4 40 0.80
5 6 0.12
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.22
Consensus pattern (4 bp):
AATA
Found at i:50937 original size:12 final size:13
Alignment explanation
Indices: 50919--50984 Score: 58
Period size: 12 Copynumber: 5.7 Consensus size: 13
50909 AAAAAGTAAT
50919 AGATAAATAAATA
1 AGATAAATAAATA
*
50932 AG-TAAATAGAT-
1 AGATAAATAAATA
*
50943 AGAAAAATAAAT-
1 AGATAAATAAATA
50955 A-A-AAAT-AAT-
1 AGATAAATAAATA
50964 AGATAAATAAA-A
1 AGATAAATAAATA
50976 AGATAAATA
1 AGATAAATA
50985 GGTATATAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
9 4 0.09
10 5 0.11
11 7 0.16
12 27 0.60
13 2 0.04
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (13 bp):
AGATAAATAAATA
Found at i:51003 original size:24 final size:24
Alignment explanation
Indices: 50970--51077 Score: 84
Period size: 24 Copynumber: 4.6 Consensus size: 24
50960 TAATAGATAA
* *
50970 ATAAAAAGATAAATAGGTATATAG
1 ATAAATAGATAAATAGGTATAAAG
* *
50994 ATAAGTAGATAAAGAGGTATAAAG
1 ATAAATAGATAAATAGGTATAAAG
* *
51018 ATAAATAGAAAAATAAGTAGGTAAA-
1 ATAAATAGATAAATAGGTA--TAAAG
*
51043 A-AAATAGAT-AATA-GTA-AATAA
1 ATAAATAGATAAATAGGTATAA-AG
51064 AT-AATAGATAAATA
1 ATAAATAGATAAATA
51078 ACTATAATAA
Statistics
Matches: 69, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
19 2 0.03
20 1 0.01
21 8 0.12
22 7 0.10
23 4 0.06
24 42 0.61
25 1 0.01
26 4 0.06
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (24 bp):
ATAAATAGATAAATAGGTATAAAG
Found at i:51061 original size:14 final size:15
Alignment explanation
Indices: 51044--51078 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
51034 GTAGGTAAAA
*
51044 AAATAGATAATAG-T
1 AAATAAATAATAGAT
51058 AAATAAATAATAGAT
1 AAATAAATAATAGAT
51073 AAATAA
1 AAATAA
51079 CTATAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (15 bp):
AAATAAATAATAGAT
Found at i:52480 original size:55 final size:54
Alignment explanation
Indices: 52416--52605 Score: 172
Period size: 54 Copynumber: 3.5 Consensus size: 54
52406 TAACTAACCT
* *
52416 CACTGGATC-ATTTAAGATTCAAC-CTTGATCA-CAGAAACTTCTCTTGGAATGACCG
1 CACTGGATCAATTTAAGA-TCAACTC-TAATCATCAAAAAC-T-TCTTGGAATGACCG
*
52471 CACTGGATCAAATTTAAGATCAACTCTAATCATCAAAAACTTCTTGGAATGACTG
1 CACTGGATC-AATTTAAGATCAACTCTAATCATCAAAAACTTCTTGGAATGACCG
* * * ** * ** * *
52526 CATTGTATCAGTTGGAGATCAACTCTGATCATTGAAAACTTCTTGGAATGATCA
1 CACTGGATCAATTTAAGATCAACTCTAATCATCAAAAACTTCTTGGAATGACCG
*
52580 CACTGGATC-ATCTAAGGATCAACTCT
1 CACTGGATCAATTTAA-GATCAACTCT
52606 GATCTCTAAA
Statistics
Matches: 110, Mismatches: 20, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
53 2 0.02
54 53 0.48
55 29 0.26
56 11 0.10
57 15 0.14
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (54 bp):
CACTGGATCAATTTAAGATCAACTCTAATCATCAAAAACTTCTTGGAATGACCG
Found at i:59249 original size:26 final size:27
Alignment explanation
Indices: 59192--59242 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
59182 GAAAAAATTT
*
59192 TTTTTTTTTATTTATGACGCAGAAAAAC
1 TTTTTTTTTA-TTATAACGCAGAAAAAC
59220 TTTTTTTTTA-TATAACGCA-AAAA
1 TTTTTTTTTATTATAACGCAGAAAA
59243 CTCTTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 8 0.36
28 10 0.45
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (27 bp):
TTTTTTTTTATTATAACGCAGAAAAAC
Found at i:62197 original size:15 final size:16
Alignment explanation
Indices: 62167--62199 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
62157 CTCTTGCATG
*
62167 AAAACACTTCTTTTTT
1 AAAACAATTCTTTTTT
62183 AAAACAATT-TTTTTT
1 AAAACAATTCTTTTTT
62198 AA
1 AA
62200 CTACCCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.48
Consensus pattern (16 bp):
AAAACAATTCTTTTTT
Found at i:63597 original size:36 final size:36
Alignment explanation
Indices: 63557--63629 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
63547 TATATAGAGA
*
63557 ATAAACTATGATTATGATTAGGAATTCAAGAAATTT
1 ATAAACTAAGATTATGATTAGGAATTCAAGAAATTT
* *
63593 ATAAACTAAGGTTATGATTAGGAATTCAGGAAATTT
1 ATAAACTAAGATTATGATTAGGAATTCAAGAAATTT
63629 A
1 A
63630 AAAAGAAACG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.34
Consensus pattern (36 bp):
ATAAACTAAGATTATGATTAGGAATTCAAGAAATTT
Found at i:64125 original size:36 final size:36
Alignment explanation
Indices: 64085--64177 Score: 141
Period size: 36 Copynumber: 2.6 Consensus size: 36
64075 ACGAAATCTA
*
64085 AACAGAGACCTAAACAGGTTTCTAAACGAAACATTG
1 AACAGAGACCTAAGCAGGTTTCTAAACGAAACATTG
* * *
64121 AACAGAGACCTAAGCAAGTTTCTAAACGAAGCTTTG
1 AACAGAGACCTAAGCAGGTTTCTAAACGAAACATTG
*
64157 AACCGAGACCTAAGCAGGTTT
1 AACAGAGACCTAAGCAGGTTT
64178 AATCAAACGA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.20
Consensus pattern (36 bp):
AACAGAGACCTAAGCAGGTTTCTAAACGAAACATTG
Found at i:64205 original size:38 final size:38
Alignment explanation
Indices: 64161--64587 Score: 222
Period size: 38 Copynumber: 11.0 Consensus size: 38
64151 GCTTTGAACC
* * *
64161 GAGACCTAAGCAGGTTTAATCAAACGAGATTCTAAGCG
1 GAGACCTAAGCAGGTTTAATTAAACGAGACTCTAAGCA
* ** *
64199 GGGACCTAAGCAGGTTTTCTTAAAC-AGAATTTCTAAGCA
1 GAGACCTAAGCAGGTTTAATTAAACGAG-A-CTCTAAGCA
* * * **
64238 GAGACCTAAGCAGGTTTACTTGAATG-GCAACTCTAAATA
1 GAGACCTAAGCAGGTTTAATTAAACGAG--ACTCTAAGCA
* * * *
64277 GGGACCTAAGCAAGTTTGATTAAACGAAACTCTAAGCA
1 GAGACCTAAGCAGGTTTAATTAAACGAGACTCTAAGCA
* * *
64315 GAGACCTAAGCAGGTTTGATTAGACGA-AGCTCTAAGTA
1 GAGACCTAAGCAGGTTTAATTAAACGAGA-CTCTAAGCA
* * * * * *
64353 GAGTCCTAAGCAGGTTTACTCAAATGAAATTCTAA--A
1 GAGACCTAAGCAGGTTTAATTAAACGAGACTCTAAGCA
* *
64389 TGAGGACCTAAGCAGGTTTGATTAAACGA-AGCTCTAAGTA
1 -GA-GACCTAAGCAGGTTTAATTAAACGAGA-CTCTAAGCA
* * * * *
64429 GAGATCCTAAGTAGGTTTACTTGAATG-GCACTTCTAAAC-
1 GAGA-CCTAAGCAGGTTTAATTAAACGAG-AC-TCTAAGCA
* * * *
64468 GAGGACCTAAGCAGGTTTTACTTAAATGAAACTTCTAAACA
1 GA-GACCTAAGCAGG-TTTAATTAAACGAGAC-TCTAAGCA
* * * **
64509 GAGACCTAAGTAGGTTTTACTTAAACGAAAACTCTAAATA
1 GAGACCTAAGCAGG-TTTAATTAAACG-AGACTCTAAGCA
* * * * * * *
64549 AAGACCTAAACATGTTTACTTAAATGAAACTATAAGCA
1 GAGACCTAAGCAGGTTTAATTAAACGAGACTCTAAGCA
64587 G
1 G
64588 GTTCTTCTTA
Statistics
Matches: 308, Mismatches: 60, Indels: 42
0.75 0.15 0.10
Matches are distributed among these distances:
36 1 0.00
37 6 0.02
38 124 0.40
39 99 0.32
40 72 0.23
41 6 0.02
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (38 bp):
GAGACCTAAGCAGGTTTAATTAAACGAGACTCTAAGCA
Found at i:64244 original size:39 final size:37
Alignment explanation
Indices: 64074--64537 Score: 263
Period size: 38 Copynumber: 12.2 Consensus size: 37
64064 AAATATTTTG
* * *
64074 AACGAAATCTAAACAGAGACCTAAACAGGTTT-C-TA
1 AACGAATTCTAAGCAGAGACCTAAGCAGGTTTACTTA
* *
64109 AACGAAACATT-GAA-CAGAGACCTAAGCAAGTTT-C-TA
1 AACG--A-ATTCTAAGCAGAGACCTAAGCAGGTTTACTTA
* * *
64145 AACGAAGCTT-TGAA-CCGAGACCTAAGCAGGTTTAATCA
1 AACGAA--TTCT-AAGCAGAGACCTAAGCAGGTTTACTTA
* * *
64183 AACGAGATTCTAAGCGGGGACCTAAGCAGGTTTTCTTA
1 AACGA-ATTCTAAGCAGAGACCTAAGCAGGTTTACTTA
64221 AACAGAATTTCTAAGCAGAGACCTAAGCAGGTTTACTTGA
1 AAC-GAA-TTCTAAGCAGAGACCTAAGCAGGTTTACTT-A
** * ** * *
64261 ATGGCAACTCTAAATAGGGACCTAAGCAAGTTTGA-TTA
1 AACG-AATTCTAAGCAGAGACCTAAGCAGGTTT-ACTTA
*
64299 AACGAAACTCTAAGCAGAGACCTAAGCAGGTTTGA-TTA
1 AACG-AATTCTAAGCAGAGACCTAAGCAGGTTT-ACTTA
* * * * *
64337 GACGAAGCTCTAAGTAGAGTCCTAAGCAGGTTTACTCA
1 AACGAA-TTCTAAGCAGAGACCTAAGCAGGTTTACTTA
*
64375 AATGAAATTCTAA--ATGAGGACCTAAGCAGGTTTGA-TTA
1 AACG-AATTCTAAGCA-GA-GACCTAAGCAGGTTT-ACTTA
* * *
64413 AACGAAGCTCTAAGTAGAGATCCTAAGTAGGTTTACTTGA
1 AACGAA-TTCTAAGCAGAGA-CCTAAGCAGGTTTACTT-A
** * *
64453 ATGGCACTTCTAAAC-GAGGACCTAAGCAGGTTTTACTTA
1 AACG-AATTCTAAGCAGA-GACCTAAGCAGG-TTTACTTA
* * *
64492 AATGAAACTTCTAAACAGAGACCTAAGTAGGTTTTACTTA
1 AACG-AA-TTCTAAGCAGAGACCTAAGCAGG-TTTACTTA
64532 AACGAA
1 AACGAA
64538 AACTCTAAAT
Statistics
Matches: 340, Mismatches: 56, Indels: 62
0.74 0.12 0.14
Matches are distributed among these distances:
33 1 0.00
34 1 0.00
35 6 0.02
36 44 0.13
37 14 0.04
38 127 0.37
39 90 0.26
40 54 0.16
41 3 0.01
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.25
Consensus pattern (37 bp):
AACGAATTCTAAGCAGAGACCTAAGCAGGTTTACTTA
Found at i:64253 original size:77 final size:76
Alignment explanation
Indices: 64074--64331 Score: 208
Period size: 77 Copynumber: 3.4 Consensus size: 76
64064 AAATATTTTG
* * * * * *
64074 AACGAAA-TCTAAACAGAGACCTAAACAGGTTT-CT-AAACGAAACAT-TGAACAGAGACCTAAG
1 AACGAAACTCTAAGCAGAGACCTAAGCAGGTTTAATCAAACGGAAC-TCTAAACAGGGACCTAAG
*
64135 CAAGTTT--CTA
65 CAAGTTTGATTA
* * * * * *
64145 AACGAAGCTTTGAA-CCGAGACCTAAGCAGGTTTAATCAAAC-GAGATTCTAAGCGGGGACCTAA
1 AACGAAACTCT-AAGCAGAGACCTAAGCAGGTTTAATCAAACGGA-ACTCTAAACAGGGACCTAA
* **
64208 GCAGGTTTTCTTA
64 GCAAGTTTGATTA
** * ** * *
64221 AACAGAATTTCTAAGCAGAGACCTAAGCAGGTTTACTTGAATGGCAACTCTAAATAGGGACCTAA
1 AAC-GAAACTCTAAGCAGAGACCTAAGCAGGTTTAATCAAACGG-AACTCTAAACAGGGACCTAA
64286 GCAAGTTTGATTA
64 GCAAGTTTGATTA
64299 AACGAAACTCTAAGCAGAGACCTAAGCAGGTTT
1 AACGAAACTCTAAGCAGAGACCTAAGCAGGTTT
64332 GATTAGACGA
Statistics
Matches: 145, Mismatches: 30, Indels: 18
0.75 0.16 0.09
Matches are distributed among these distances:
71 6 0.04
72 19 0.13
73 5 0.03
74 23 0.16
76 7 0.05
77 55 0.38
78 29 0.20
79 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.22
Consensus pattern (76 bp):
AACGAAACTCTAAGCAGAGACCTAAGCAGGTTTAATCAAACGGAACTCTAAACAGGGACCTAAGC
AAGTTTGATTA
Found at i:64447 original size:192 final size:196
Alignment explanation
Indices: 64162--64577 Score: 513
Period size: 192 Copynumber: 2.1 Consensus size: 196
64152 CTTTGAACCG
* * * * * **
64162 AGACCTAAGCAGGTTTAATCAAACGAGATTCTAAGCGGGGACCTAAGCAGGTTTTCTTAAACAGA
1 AGACCTAAGCAGGTTTACTCAAATGAAATTCTAAACGAGGACCTAAGCAGGTTTGATTAAACAGA
**
64227 ATTTCTAAGCAGAGACCTAAGCAGGTTTACTTGAATGGCAAC-TCTAAATAG-GGACCTAAGCAA
66 AGCTCTAAGCAGAGACCTAAGCAGGTTTACTTGAATGGC-ACTTCTAAA-AGAGGACCTAAGCAA
* * * *
64290 GTTTGA-TTAAACGAAAC-TCTAAGCAGAGACCTAAGCAGGTTTGA-TTAGACG-AAGCTCTAAG
129 GTTTGACTTAAACGAAACTTCTAAACAGAGACCTAAGCAGGTTTGACTTAAACGAAAACTCTAAA
*
64351 TAG
194 TAA
* *
64354 AGTCCTAAGCAGGTTTACTCAAATGAAATTCTAAATGAGGACCTAAGCAGGTTTGATTAAAC-GA
1 AGACCTAAGCAGGTTTACTCAAATGAAATTCTAAACGAGGACCTAAGCAGGTTTGATTAAACAGA
* * * *
64418 AGCTCTAAGTAGAGATCCTAAGTAGGTTTACTTGAATGGCACTTCTAAACGAGGACCTAAGCAGG
66 AGCTCTAAGCAGAGA-CCTAAGCAGGTTTACTTGAATGGCACTTCTAAAAGAGGACCTAAGCAAG
* * * *
64483 TTTTACTTAAATGAAACTTCTAAACAGAGACCTAAGTAGGTTTTACTTAAACGAAAACTCTAAAT
130 TTTGACTTAAACGAAACTTCTAAACAGAGACCTAAGCAGGTTTGACTTAAACGAAAACTCTAAAT
64548 AA
195 AA
* * *
64550 AGACCTAAACATGTTTACTTAAATGAAA
1 AGACCTAAGCAGGTTTACTCAAATGAAA
64578 CTATAAGCAG
Statistics
Matches: 189, Mismatches: 28, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
191 17 0.09
192 98 0.52
193 10 0.05
194 24 0.13
195 6 0.03
196 34 0.18
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.26
Consensus pattern (196 bp):
AGACCTAAGCAGGTTTACTCAAATGAAATTCTAAACGAGGACCTAAGCAGGTTTGATTAAACAGA
AGCTCTAAGCAGAGACCTAAGCAGGTTTACTTGAATGGCACTTCTAAAAGAGGACCTAAGCAAGT
TTGACTTAAACGAAACTTCTAAACAGAGACCTAAGCAGGTTTGACTTAAACGAAAACTCTAAATA
A
Found at i:70634 original size:24 final size:24
Alignment explanation
Indices: 70601--70661 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
70591 CGAAGTCCAA
*
70601 GATGGAAAACTCAGCATGGAATTT
1 GATGGGAAACTCAGCATGGAATTT
70625 GATGGGAAACTCAGCATGGAATTT
1 GATGGGAAACTCAGCATGGAATTT
70649 GATGGGAAACTCA
1 GATGGGAAACTCA
70662 TTGAATTCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (24 bp):
GATGGGAAACTCAGCATGGAATTT
Found at i:78801 original size:28 final size:28
Alignment explanation
Indices: 78761--78835 Score: 114
Period size: 28 Copynumber: 2.6 Consensus size: 28
78751 GTCACTTAAG
* *
78761 GGGGCATTCTGGTCATTTTACATGTCCA
1 GGGGCATTTTGGTCATTTTACATATCCA
*
78789 GGGGCATTTTGGTCATTTTGCATATCCA
1 GGGGCATTTTGGTCATTTTACATATCCA
78817 GGGGCATTTTGGGTCATTT
1 GGGGCATTTT-GGTCATTT
78836 CAAATGCACT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
28 35 0.81
29 8 0.19
ACGTcount: A:0.16, C:0.17, G:0.28, T:0.39
Consensus pattern (28 bp):
GGGGCATTTTGGTCATTTTACATATCCA
Done.