Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011422.1 Kokia drynarioides strain JFW-HI SEQ_126406, 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: 80551
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:7642 original size:12 final size:12
Alignment explanation
Indices: 7625--7655 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
7615 TCGACACCTA
7625 TTTCTTCATCTT
1 TTTCTTCATCTT
7637 TTTCTTCATCTT
1 TTTCTTCATCTT
7649 TTTCTTC
1 TTTCTTC
7656 CTCCACATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.26, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTCTTCATCTT
Found at i:13080 original size:3 final size:3
Alignment explanation
Indices: 13074--13104 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
13064 TTTTATGTTA
13074 TAT TAT TAT TAT TATT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
13105 CTAATATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:13085 original size:16 final size:16
Alignment explanation
Indices: 13072--13104 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
13062 TTTTTTATGT
13072 TATATTATTATTATTA
1 TATATTATTATTATTA
*
13088 TTTATTATTATTATTA
1 TATATTATTATTATTA
13104 T
1 T
13105 CTAATATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATATTATTATTATTA
Found at i:13112 original size:13 final size:12
Alignment explanation
Indices: 13074--13104 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
13064 TTTTATGTTA
13074 TATTATTATTAT
1 TATTATTATTAT
13086 TATTTATTATTAT
1 TA-TTATTATTAT
13099 TATTAT
1 TATTAT
13105 CTAATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTATTATTAT
Found at i:13112 original size:16 final size:16
Alignment explanation
Indices: 13077--13112 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
13067 TATGTTATAT
* *
13077 TATTATTATTATTTAT
1 TATTATTATTATCTAA
13093 TATTATTATTATCTAA
1 TATTATTATTATCTAA
13109 TATT
1 TATT
13113 TAGTTTTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTATTATTATCTAA
Found at i:33483 original size:15 final size:17
Alignment explanation
Indices: 33453--33487 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
33443 TATTTTCTAA
33453 TCTTAGAGCAATATTTT
1 TCTTAGAGCAATATTTT
33470 TCTTAG-GC-ATATTTT
1 TCTTAGAGCAATATTTT
33485 TCT
1 TCT
33488 ACACTCCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
16 2 0.11
17 6 0.33
ACGTcount: A:0.23, C:0.14, G:0.11, T:0.51
Consensus pattern (17 bp):
TCTTAGAGCAATATTTT
Found at i:35960 original size:9 final size:8
Alignment explanation
Indices: 35932--36002 Score: 54
Period size: 9 Copynumber: 8.2 Consensus size: 8
35922 CAGTCACTTG
35932 AAAAGAAA
1 AAAAGAAA
*
35940 AATCA-AAA
1 AA-AAGAAA
35948 AAAAGAAA
1 AAAAGAAA
35956 GAAAAGAAA
1 -AAAAGAAA
**
35965 ATGAGAAA
1 AAAAGAAA
35973 AAATGAGAAA
1 AAA--AGAAA
35983 AAGAAGAAA
1 AA-AAGAAA
35992 GAAAAGAAA
1 -AAAAGAAA
36001 AA
1 AA
36003 GAAAAATAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
7 1 0.02
8 19 0.38
9 20 0.40
10 9 0.18
11 1 0.02
ACGTcount: A:0.77, C:0.01, G:0.17, T:0.04
Consensus pattern (8 bp):
AAAAGAAA
Found at i:35973 original size:24 final size:23
Alignment explanation
Indices: 35931--36007 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 23
35921 TCAGTCACTT
*
35931 GAAAAGAAAAATCAAAAAAAAGAAA
1 GAAAAG-AAAAT-AGAAAAAAGAAA
*
35956 GAAAAGAAAATGAGAAAAAATGAGA
1 GAAAAGAAAAT-AGAAAAAA-GAAA
35981 -AAAAGAAGAA-AGAAAAGAA-AAA
1 GAAAAGAA-AATAGAAAA-AAGAAA
36003 GAAAA
1 GAAAA
36008 ATAAATTGCT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
22 2 0.05
23 10 0.23
24 21 0.48
25 11 0.25
ACGTcount: A:0.77, C:0.01, G:0.18, T:0.04
Consensus pattern (23 bp):
GAAAAGAAAATAGAAAAAAGAAA
Found at i:35999 original size:18 final size:18
Alignment explanation
Indices: 35944--36005 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 18
35934 AAGAAAAATC
*
35944 AAAAAAAAGAAAGAAAAG
1 AAAAAGAAGAAAGAAAAG
*
35962 AAAATG-AGAAA-AAATGAG
1 AAAAAGAAGAAAGAAA--AG
35980 AAAAAGAAGAAAGAAAAG
1 AAAAAGAAGAAAGAAAAG
35998 AAAAAGAA
1 AAAAAGAA
36006 AAATAAATTG
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
16 3 0.08
17 5 0.14
18 21 0.57
19 5 0.14
20 3 0.08
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.03
Consensus pattern (18 bp):
AAAAAGAAGAAAGAAAAG
Found at i:49360 original size:2 final size:2
Alignment explanation
Indices: 49353--49380 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
49343 ATTAGAAAGA
49353 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49381 GCTAATGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60580 original size:13 final size:13
Alignment explanation
Indices: 60562--60607 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
60552 ATGAGTTAGA
60562 AAATATAAATACT
1 AAATATAAATACT
**
60575 AAATATGAAATAGA
1 AAATAT-AAATACT
60589 AAATATAAATACT
1 AAATATAAATACT
60602 AAATAT
1 AAATAT
60608 GAAAGGCCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.28
Consensus pattern (13 bp):
AAATATAAATACT
Found at i:60582 original size:27 final size:27
Alignment explanation
Indices: 60558--60611 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
60548 AACAATGAGT
60558 TAGAAAATATAAATACTAAATATGAAA
1 TAGAAAATATAAATACTAAATATGAAA
60585 TAGAAAATATAAATACTAAATATGAAA
1 TAGAAAATATAAATACTAAATATGAAA
60612 GGCCTATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.63, C:0.04, G:0.07, T:0.26
Consensus pattern (27 bp):
TAGAAAATATAAATACTAAATATGAAA
Found at i:60605 original size:20 final size:22
Alignment explanation
Indices: 60568--60611 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
60558 TAGAAAATAT
60568 AAATACTAAATATGAAATA-GA
1 AAATACTAAATATGAAATATGA
60589 AAATA-TAAATACT-AAATATGA
1 AAATACTAAATA-TGAAATATGA
60610 AA
1 AA
60612 GGCCTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.64, C:0.05, G:0.07, T:0.25
Consensus pattern (22 bp):
AAATACTAAATATGAAATATGA
Found at i:60971 original size:10 final size:10
Alignment explanation
Indices: 60934--60977 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
60924 AATATATTTA
60934 TTTTCTTT-T
1 TTTTCTTTCT
*
60943 GTTTCTTTCCT
1 TTTTCTTT-CT
*
60954 TCTTCTTTCT
1 TTTTCTTTCT
60964 TTTTCTTTCT
1 TTTTCTTTCT
60974 TTTT
1 TTTT
60978 GAGAATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 7 0.24
10 15 0.52
11 7 0.24
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.77
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:63561 original size:199 final size:199
Alignment explanation
Indices: 63221--63617 Score: 650
Period size: 199 Copynumber: 2.0 Consensus size: 199
63211 ACCATGGTAG
*
63221 GGGAATATCCGTCTAGGTGCTCGCAGAAGAATTCCCAACCCAAACCAGTGATTGTTCTTGCGATT
1 GGGAATATCCGGCTAGGTGCTCGCAGAAGAATTCCCAACCCAAACCAGTGATTGTTCTTGCGATT
63286 TGTTTCCCCAATGTCTGGTGTAGGGACAACTGTATACCCTACTATGGGTGGCAATTTCGTTTAAG
66 TGTTTCCCCAATGTCTGGTGTAGGGACAACTGTATACCCTACTATGGGTGGCAATTTCGTTTAAG
*
63351 CACAGTGTCATGGTAGCGGTCCTTAGCCACCTTGGACAAAAATAAGACAGGTTCGTTTGGTTAGG
131 CACAGTGTCATGGTAGCGGTCCTTAGCCACCTTAGACAAAAATAAGACAGGTTCGTTTGGTTAGG
63416 GTTA
196 GTTA
* * * * * *
63420 GGGAATATCCGGCTGGGTGCTCGTAGAAGAATTCCTACCCCAGACCAGTTATTGTTCTTGCGATT
1 GGGAATATCCGGCTAGGTGCTCGCAGAAGAATTCCCAACCCAAACCAGTGATTGTTCTTGCGATT
* * * *
63485 TGTTTCCCCAATGTCTGGTGTGGGGACAACTGTATACCCTGCTATGGGTGGTAATTTCGTTTGAG
66 TGTTTCCCCAATGTCTGGTGTAGGGACAACTGTATACCCTACTATGGGTGGCAATTTCGTTTAAG
* * * *
63550 CATATTGTCATGGTAGCGGTCCTTAGCCGCCTTAGACAAAAATAAGACAGGTTCGTTTGGTTGGG
131 CACAGTGTCATGGTAGCGGTCCTTAGCCACCTTAGACAAAAATAAGACAGGTTCGTTTGGTTAGG
63615 GTT
196 GTT
63618 GGTCTATGGT
Statistics
Matches: 182, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
199 182 1.00
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.30
Consensus pattern (199 bp):
GGGAATATCCGGCTAGGTGCTCGCAGAAGAATTCCCAACCCAAACCAGTGATTGTTCTTGCGATT
TGTTTCCCCAATGTCTGGTGTAGGGACAACTGTATACCCTACTATGGGTGGCAATTTCGTTTAAG
CACAGTGTCATGGTAGCGGTCCTTAGCCACCTTAGACAAAAATAAGACAGGTTCGTTTGGTTAGG
GTTA
Found at i:73001 original size:38 final size:38
Alignment explanation
Indices: 72959--73033 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
72949 AAACGAACCT
*
72959 TAAACTCTCAAGGGTTTCTCAAATAATTTCCACCTTTC
1 TAAACTCTCAAGGGTTTCTAAAATAATTTCCACCTTTC
72997 TAAACTCTCAAGGGTTTCTAAAATAATTTCCACCTTT
1 TAAACTCTCAAGGGTTTCTAAAATAATTTCCACCTTT
73034 TTGCAATTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.31, C:0.24, G:0.08, T:0.37
Consensus pattern (38 bp):
TAAACTCTCAAGGGTTTCTAAAATAATTTCCACCTTTC
Done.