Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011794.1 Kokia drynarioides strain JFW-HI SEQ_126789, 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: 84798
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:848 original size:3 final size:3
Alignment explanation
Indices: 840--864 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
830 TAAATAACAC
840 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
865 GTCTCAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1120 original size:30 final size:30
Alignment explanation
Indices: 1084--1143 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1074 AATTAGTAAA
*
1084 AATAAAATTATATTTTAA-CTTTTTAAAAAT
1 AATAAAATTATAATTTAATC-TTTTAAAAAT
*
1114 AATAAAATTTTAATTTAATCTTTTAAAAAT
1 AATAAAATTATAATTTAATCTTTTAAAAAT
1144 TACACTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (30 bp):
AATAAAATTATAATTTAATCTTTTAAAAAT
Found at i:3975 original size:29 final size:28
Alignment explanation
Indices: 3885--4138 Score: 232
Period size: 29 Copynumber: 8.8 Consensus size: 28
3875 TTCAAGGTCG
* *
3885 AAAATGGAGTTTTTGGACA-TCCGGGGGT-
1 AAAATGGAATTTTTGGA-AGTTC-GGGGTA
* * *
3913 AAAATGGTAATTTTTGAAAGTTTCCGTGT-
1 AAAATGG-AATTTTTGGAAG-TTCGGGGTA
*
3942 CAAATGGAATTTTTGGAAGTTCGGGGTTA
1 AAAATGGAATTTTTGGAAGTTCGGGG-TA
3971 AAAAT-GAGATTTTTGGAAGTTCGGGGGTA
1 AAAATGGA-ATTTTTGGAAGTTC-GGGGTA
* *
4000 AAAATGGAATTTTTGGAAGTTTTGGGGTC
1 AAAATGGAATTTTTGGAAG-TTCGGGGTA
*
4029 AAAATAGG-ATTTTTGGAAGTTTAGGGGTA
1 AAAAT-GGAATTTTTGGAAG-TTCGGGGTA
*
4058 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAG-TTCGGGGT-A
*
4088 AAAATAGG-ATTTTTGGAAGTTCAAGGGTA
1 AAAAT-GGAATTTTTGGAAGTTC-GGGGTA
4117 AAAATGGAATTTTTGGACAGTT
1 AAAATGGAATTTTTGGA-AGTT
4139 TAGAGACCCT
Statistics
Matches: 193, Mismatches: 17, Indels: 30
0.80 0.07 0.12
Matches are distributed among these distances:
27 5 0.03
28 26 0.13
29 123 0.64
30 37 0.19
31 2 0.01
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.35
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTCGGGGTA
Found at i:4070 original size:87 final size:88
Alignment explanation
Indices: 3885--4141 Score: 278
Period size: 87 Copynumber: 2.9 Consensus size: 88
3875 TTCAAGGTCG
* * * ** *
3885 AAAATGGAGTTTTTGGACA-TCCGGGGGT-AAAATGGTAATTTTTGAAAGTTTCCGTGTC-AAAT
1 AAAATGGAATTTTTGGA-AGTTCGGGGGTAAAAATGG-AATTTTTGGAAGTTTAAGGGTCAAAAT
*
3947 GGAATTTTTGGAAG-TTCGGGGTTA
64 GGAATTTTTGGAAGTTTAGGGGTTA
**
3971 AAAAT-GAGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAATA
1 AAAATGGA-ATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTAAGGGTCAAAAT-
4035 GG-ATTTTTGGAAGTTTAGGGG-TA
64 GGAATTTTTGGAAGTTTAGGGGTTA
** * *
4058 AAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATAGG-ATTTTTGGAAGTTCAAGGGTAAAAAT
1 AAAATGGAATTTTTGGAAGTTCGGGGGT-AAAAAT-GGAATTTTTGGAAGTTTAAGGGTCAAAAT
4122 GGAATTTTTGGACAGTTTAG
64 GGAATTTTTGGA-AGTTTAG
4142 AGACCCTCGA
Statistics
Matches: 147, Mismatches: 13, Indels: 19
0.82 0.07 0.11
Matches are distributed among these distances:
85 3 0.02
86 39 0.27
87 49 0.33
88 47 0.32
89 9 0.06
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.35
Consensus pattern (88 bp):
AAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTAAGGGTCAAAATGG
AATTTTTGGAAGTTTAGGGGTTA
Found at i:4121 original size:59 final size:59
Alignment explanation
Indices: 3943--4139 Score: 310
Period size: 58 Copynumber: 3.4 Consensus size: 59
3933 TTTCCGTGTC
* * *
3943 AAATGGAATTTTTGGAAG-TTCGGGGTTAAAAAT-GAGATTTTTGGAAGTTCGGGGGTAA
1 AAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATAG-GATTTTTGGAAGTTCAGGGGTAA
*
4001 AAATGGAATTTTTGGAAGTTTTGGGGTC-AAAATAGGATTTTTGGAAGTTTAGGGGTAA
1 AAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATAGGATTTTTGGAAGTTCAGGGGTAA
*
4059 AAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATAGGATTTTTGGAAGTTCAAGGGTAA
1 AAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATAGGATTTTTGGAAGTTCAGGGGTAA
4118 AAATGGAATTTTTGGACAGTTT
1 AAATGGAATTTTTGGA-AGTTT
4140 AGAGACCCTC
Statistics
Matches: 129, Mismatches: 6, Indels: 6
0.91 0.04 0.04
Matches are distributed among these distances:
58 72 0.56
59 52 0.40
60 5 0.04
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (59 bp):
AAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATAGGATTTTTGGAAGTTCAGGGGTAA
Found at i:5221 original size:22 final size:21
Alignment explanation
Indices: 5178--5227 Score: 77
Period size: 19 Copynumber: 2.5 Consensus size: 21
5168 TTTACTTTTT
5178 TTATTATTAAAATGTTATTTA
1 TTATTATTAAAATGTTATTTA
*
5199 TTATTATTAAAA--ATATTTA
1 TTATTATTAAAATGTTATTTA
5218 TTATTATTAA
1 TTATTATTAA
5228 TATTATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 16 0.57
21 12 0.43
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TTATTATTAAAATGTTATTTA
Found at i:5234 original size:19 final size:19
Alignment explanation
Indices: 5177--5234 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
5167 ATTTACTTTT
* *
5177 TTTATTATTA-AAATGTTA
1 TTTATTATTATTAATATTA
* *
5195 TTTATTATTATTAAAAATA
1 TTTATTATTATTAATATTA
5214 TTTATTATTATTAATATTA
1 TTTATTATTATTAATATTA
5233 TT
1 TT
5235 AAAAACATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 10 0.30
19 23 0.70
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTATTATTATTAATATTA
Found at i:5305 original size:3 final size:3
Alignment explanation
Indices: 5297--5326 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5287 TTAACGTTAC
5297 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5327 ACTTATGAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5884 original size:15 final size:15
Alignment explanation
Indices: 5864--5927 Score: 101
Period size: 15 Copynumber: 4.3 Consensus size: 15
5854 ACTTTGGGTC
*
5864 ATTGGGCCGTTTGTA
1 ATTGGGCCATTTGTA
5879 ATTGGGCCATTTGTA
1 ATTGGGCCATTTGTA
* *
5894 CTTGGGCCGTTTGTA
1 ATTGGGCCATTTGTA
5909 ATTGGGCCATTTGTA
1 ATTGGGCCATTTGTA
5924 ATTG
1 ATTG
5928 TACTTTGTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.16, C:0.14, G:0.30, T:0.41
Consensus pattern (15 bp):
ATTGGGCCATTTGTA
Found at i:5899 original size:30 final size:30
Alignment explanation
Indices: 5865--5923 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
5855 CTTTGGGTCA
5865 TTGGGCCGTTTGTAATTGGGCCATTTGTAC
1 TTGGGCCGTTTGTAATTGGGCCATTTGTAC
5895 TTGGGCCGTTTGTAATTGGGCCATTTGTA
1 TTGGGCCGTTTGTAATTGGGCCATTTGTA
5924 ATTGTACTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.14, C:0.15, G:0.31, T:0.41
Consensus pattern (30 bp):
TTGGGCCGTTTGTAATTGGGCCATTTGTAC
Found at i:5982 original size:17 final size:16
Alignment explanation
Indices: 5960--6038 Score: 86
Period size: 17 Copynumber: 4.8 Consensus size: 16
5950 TTGGACTTTC
5960 TAAATTTAATTTTATAA
1 TAAATTTAATTTTA-AA
*
5977 TAAATTTAAATTTCAAA
1 TAAATTT-AATTTTAAA
*
5994 TAAATTTAAATTTAAAA
1 TAAATTT-AATTTTAAA
* *
6011 TAAACTTAAATTTAAA
1 TAAATTTAATTTTAAA
*
6027 TAAATTCAATTT
1 TAAATTTAATTT
6039 CCAATAGGTC
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
16 16 0.30
17 31 0.58
18 6 0.11
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATTTAATTTTAAA
Found at i:5998 original size:34 final size:33
Alignment explanation
Indices: 5960--6038 Score: 113
Period size: 34 Copynumber: 2.4 Consensus size: 33
5950 TTGGACTTTC
* *
5960 TAAATTTAATTTTATAATAAATTTAAATTTCAAA
1 TAAATTTAATTTTAAAATAAACTTAAATTT-AAA
*
5994 TAAATTTAAATTTAAAATAAACTTAAATTTAAA
1 TAAATTTAATTTTAAAATAAACTTAAATTTAAA
*
6027 TAAATTCAATTT
1 TAAATTTAATTT
6039 CCAATAGGTC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 13 0.32
34 27 0.68
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (33 bp):
TAAATTTAATTTTAAAATAAACTTAAATTTAAA
Found at i:6011 original size:7 final size:6
Alignment explanation
Indices: 5960--6027 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 6
5950 TTGGACTTTC
*
5960 TAAATT TAATTT TATAA-- TAAATT TAAATT TCAAA-- TAAATT TAAATT
1 TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAATT TAAATT TAAATT
* *
6006 TAAA-A TAAACT TAAATT TAAAT
1 TAAATT TAAATT TAAATT TAAAT
6028 AAATTCAATT
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
4 5 0.10
5 7 0.14
6 34 0.68
7 4 0.08
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:6760 original size:19 final size:19
Alignment explanation
Indices: 6724--6775 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
6714 ATCTATTTTT
*
6724 AATAATTTAATATCAAA-TC
1 AATAATTTTAT-TCAAATTC
6743 AATAATTTTATTCGAAATTTC
1 AATAATTTTATTC-AAA-TTC
*
6764 AATATTTTTATT
1 AATAATTTTATT
6776 TGGATTTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 2 0.07
19 13 0.46
21 13 0.46
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (19 bp):
AATAATTTTATTCAAATTC
Found at i:9816 original size:28 final size:29
Alignment explanation
Indices: 9784--9841 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
9774 TTATTTTAGA
*
9784 ATATT-TTTAAAATATTAACTTTCTTTAT
1 ATATTCTTTAAAATATTAAATTTCTTTAT
* * *
9812 ATATTCTTTAAATTTTTAAATTTTTTTAT
1 ATATTCTTTAAAATATTAAATTTCTTTAT
9841 A
1 A
9842 AATGTAAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.60
Consensus pattern (29 bp):
ATATTCTTTAAAATATTAAATTTCTTTAT
Found at i:21746 original size:18 final size:17
Alignment explanation
Indices: 21713--21750 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
21703 AATTTGATAA
21713 TTAAACTATTAGAAATGT
1 TTAAACTATTAGAAAT-T
21731 TTAAACTATTCA-AAATT
1 TTAAACTATT-AGAAATT
21748 TTA
1 TTA
21751 TTTAAGAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 14 0.74
19 1 0.05
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (17 bp):
TTAAACTATTAGAAATT
Found at i:22875 original size:80 final size:80
Alignment explanation
Indices: 22742--22897 Score: 312
Period size: 80 Copynumber: 1.9 Consensus size: 80
22732 TGGGATACAT
22742 ACCCGTATCCGACACTCACAAACAGCATAGGTATACATATCTTCATTCTGACCAAGGTAGGTCAG
1 ACCCGTATCCGACACTCACAAACAGCATAGGTATACATATCTTCATTCTGACCAAGGTAGGTCAG
22807 ATTTGTTTTAGATGA
66 ATTTGTTTTAGATGA
22822 ACCCGTATCCGACACTCACAAACAGCATAGGTATACATATCTTCATTCTGACCAAGGTAGGTCAG
1 ACCCGTATCCGACACTCACAAACAGCATAGGTATACATATCTTCATTCTGACCAAGGTAGGTCAG
22887 ATTTGTTTTAG
66 ATTTGTTTTAG
22898 TAATGTTCTT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (80 bp):
ACCCGTATCCGACACTCACAAACAGCATAGGTATACATATCTTCATTCTGACCAAGGTAGGTCAG
ATTTGTTTTAGATGA
Found at i:26498 original size:23 final size:25
Alignment explanation
Indices: 26472--26519 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
26462 GCTTTTGCCG
*
26472 ATTGAC-ACAAACTAA-ATTAGATA
1 ATTGACTACAAACTAATAATAGATA
*
26495 ATTGACTAGAAACTAATAATAGATA
1 ATTGACTACAAACTAATAATAGATA
26520 TCCATTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 8 0.38
25 7 0.33
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.27
Consensus pattern (25 bp):
ATTGACTACAAACTAATAATAGATA
Found at i:28512 original size:3 final size:3
Alignment explanation
Indices: 28506--28534 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28496 AGGTATAGAC
28506 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
28535 ATATGCGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:33879 original size:14 final size:14
Alignment explanation
Indices: 33860--33893 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
33850 AGGTCTACAA
33860 AGGTTTCAGATTGG
1 AGGTTTCAGATTGG
33874 AGGTTTCAGATTGG
1 AGGTTTCAGATTGG
*
33888 GGGTTT
1 AGGTTT
33894 ACCTCTAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.18, C:0.06, G:0.38, T:0.38
Consensus pattern (14 bp):
AGGTTTCAGATTGG
Found at i:39235 original size:145 final size:141
Alignment explanation
Indices: 39069--39389 Score: 360
Period size: 143 Copynumber: 2.2 Consensus size: 141
39059 AAGGGTGAGA
* * ** **
39069 AGTAAAAGTTTAGGGGAAAAATAAAAAGTTTT-GGAATTTTAGGG-AGTAAGATTTTGAGGAGTA
1 AGTAAAAGTTTTGGGGGAAAATAAAAAGTTTTAGGAATTTTAGGGAAGTAA-A-TGGGAAAAGTA
* * * *
39132 AAGCTTTGAAGGGAAAATATTTTTAAAAAAAAAATTGAGGGGGGAATGGGTTTGAGGTAAATGGG
64 AAACTTTGAAGGGAAAATA---TTAAAAAAAAAATTG-GAGGGAAATGAGTTTGAGGTAAATGGG
39197 GGGTGGGATGAGA-ATAG
125 GGGTGGGATGAGAGA-AG
**
39214 AGTAAAAGTTTTGGGGGAAAATAAAAAGTTTTGAGGGTTTTTAGGGAAAGTAAATGGGAAAAGTA
1 AGTAAAAGTTTTGGGGGAAAATAAAAAGTTTT-AGGAATTTTAGGG-AAGTAAATGGGAAAAGTA
* * * * * *
39279 AAATTTTGGAGGGAAAATATTAAAAAAACAATTGGAGGGAAATGAGTTTGGGGTAGATTGGGGGT
64 AAACTTTGAAGGGAAAATATTAAAAAAAAAATTGGAGGGAAATGAGTTTGAGGTAAATGGGGGGT
39344 GGGATGAGAGAAG
129 GGGATGAGAGAAG
39357 AGTAAAAGTTTTGGGGGAAAAGTAAAAATGTTT
1 AGTAAAAGTTTTGGGGGAAAA-TAAAAA-GTTT
39390 GGGGGTTTGA
Statistics
Matches: 151, Mismatches: 18, Indels: 14
0.83 0.10 0.08
Matches are distributed among these distances:
143 57 0.38
144 21 0.14
145 34 0.23
147 33 0.22
148 1 0.01
149 5 0.03
ACGTcount: A:0.40, C:0.01, G:0.33, T:0.26
Consensus pattern (141 bp):
AGTAAAAGTTTTGGGGGAAAATAAAAAGTTTTAGGAATTTTAGGGAAGTAAATGGGAAAAGTAAA
ACTTTGAAGGGAAAATATTAAAAAAAAAATTGGAGGGAAATGAGTTTGAGGTAAATGGGGGGTGG
GATGAGAGAAG
Found at i:48910 original size:19 final size:19
Alignment explanation
Indices: 48886--48931 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
48876 TTATTTCATT
48886 TTAATTATTTATGATTTAA
1 TTAATTATTTATGATTTAA
48905 TTAATTATTTATGATTTAA
1 TTAATTATTTATGATTTAA
48924 TT-ATTATT
1 TTAATTATT
48932 AATGTCCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 6 0.22
19 21 0.78
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (19 bp):
TTAATTATTTATGATTTAA
Found at i:51381 original size:29 final size:29
Alignment explanation
Indices: 51331--51425 Score: 70
Period size: 29 Copynumber: 3.2 Consensus size: 29
51321 ATGTTAAGAT
* *
51331 AAATATATAAAA-AATTTCAATAAATAAAA
1 AAATATATAAAATTA-TTAAATAAATAAAA
*
51360 AAATATATAAAATTATTAAAT-ATTAAAA
1 AAATATATAAAATTATTAAATAAATAAAA
* *
51388 TAATATAATACAAATATTTTTAAA-AAAGTAAAA
1 -AA-AT-ATATAAA-ATTATTAAATAAA-TAAAA
51421 AAATA
1 AAATA
51426 ATATGGATGG
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
28 6 0.11
29 19 0.36
30 4 0.08
31 8 0.15
32 11 0.21
33 5 0.09
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.32
Consensus pattern (29 bp):
AAATATATAAAATTATTAAATAAATAAAA
Found at i:52890 original size:20 final size:20
Alignment explanation
Indices: 52867--52942 Score: 54
Period size: 19 Copynumber: 4.0 Consensus size: 20
52857 AAATTATAGG
52867 ATATTTATAAAATTTATTAT
1 ATATTTATAAAATTTATTAT
*
52887 ATA-TCATAAAATTT-TTA-
1 ATATTTATAAAATTTATTAT
* * **
52904 ATAATTACAAAAACTATT-T
1 ATATTTATAAAATTTATTAT
52923 A-ATATTATAAAATATTATTA
1 ATAT-TTATAAAAT-TTATTA
52943 ATAAGTTATG
Statistics
Matches: 41, Mismatches: 9, Indels: 11
0.67 0.15 0.18
Matches are distributed among these distances:
17 3 0.07
18 11 0.27
19 20 0.49
20 7 0.17
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATTTATAAAATTTATTAT
Found at i:56627 original size:6 final size:6
Alignment explanation
Indices: 56616--56646 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
56606 TTGGACACGA
*
56616 CGATGG CGATGG CGATGG CGATGG CTATGG C
1 CGATGG CGATGG CGATGG CGATGG CGATGG C
56647 ATCGACATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.16, C:0.19, G:0.45, T:0.19
Consensus pattern (6 bp):
CGATGG
Found at i:63018 original size:10 final size:10
Alignment explanation
Indices: 63003--63035 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
62993 AATGAAAATT
63003 TTTTTTAAAA
1 TTTTTTAAAA
63013 TTTTTTAAAA
1 TTTTTTAAAA
*
63023 -ATTTTAAAA
1 TTTTTTAAAA
63032 TTTT
1 TTTT
63036 AAATTAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TTTTTTAAAA
Found at i:68045 original size:2 final size:2
Alignment explanation
Indices: 68038--68062 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
68028 TATGTCTTGT
68038 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
68063 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Done.