Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001984.1 Kokia drynarioides strain JFW-HI SEQ_113836, 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: 23900
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:405 original size:3 final size:3
Alignment explanation
Indices: 394--453 Score: 59
Period size: 3 Copynumber: 20.3 Consensus size: 3
384 TTCTCTTTTT
* * * * *
394 TTA TT- TTA TTA TCA TTA ATA TTA TTA TTA TTA CTG TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
441 TTA ATA TTA TTA T
1 TTA TTA TTA TTA T
454 CAATGTTATC
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1147 original size:6 final size:6
Alignment explanation
Indices: 1138--1202 Score: 64
Period size: 6 Copynumber: 11.2 Consensus size: 6
1128 AATTTTATTT
* ** *
1138 ATTTAA ATTTATA A--TAA TTTTAA ATTTAA AGATAA ATTTAA ACTTAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
1185 A-TTAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA A
1203 ATCAATTTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
4 1 0.02
5 7 0.15
6 38 0.79
7 2 0.04
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:1161 original size:17 final size:17
Alignment explanation
Indices: 1138--1214 Score: 100
Period size: 17 Copynumber: 4.5 Consensus size: 17
1128 AATTTTATTT
*
1138 ATTTAAATTTATAATAA
1 ATTTAAATTTAAAATAA
*
1155 TTTTAAATTTAAAGATAA
1 ATTTAAATTTAAA-ATAA
* *
1173 ATTTAAACTTAAATTAA
1 ATTTAAATTTAAAATAA
*
1190 ATTTAAATTTAAAATCA
1 ATTTAAATTTAAAATAA
1207 ATTTAAAT
1 ATTTAAAT
1215 GAGTTTGGTT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
17 36 0.71
18 15 0.29
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:1175 original size:12 final size:11
Alignment explanation
Indices: 1158--1213 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
1148 ATAATAATTT
1158 TAAATTTAAAGA
1 TAAATTTAAA-A
*
1170 TAAATTTAAACT
1 TAAATTTAAA-A
*
1182 TAAA-TTAAATT
1 TAAATTTAAA-A
1193 TAAATTTAAAA
1 TAAATTTAAAA
*
1204 TCAATTTAAA
1 TAAATTTAAA
1214 TGAGTTTGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
11 19 0.50
12 19 0.50
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:1212 original size:23 final size:23
Alignment explanation
Indices: 1160--1214 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
1150 AATAATTTTA
* * *
1160 AATTTAAAGATAAATTTAAACTT
1 AATTTAAATATAAATTTAAAATC
* *
1183 AAATTAAATTTAAATTTAAAATC
1 AATTTAAATATAAATTTAAAATC
1206 AATTTAAAT
1 AATTTAAAT
1215 GAGTTTGGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (23 bp):
AATTTAAATATAAATTTAAAATC
Found at i:1261 original size:3 final size:3
Alignment explanation
Indices: 1253--1302 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
1243 GGCTCCAACA
1253 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1301 AT
1 AT
1303 AAGGTTAGGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:7897 original size:5 final size:5
Alignment explanation
Indices: 7887--7912 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
7877 GAAGGGATAC
7887 GGTGG GGTGG GGTGG GGTGG GGTGG G
1 GGTGG GGTGG GGTGG GGTGG GGTGG G
7913 TGCGAGGGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.81, T:0.19
Consensus pattern (5 bp):
GGTGG
Found at i:8674 original size:61 final size:61
Alignment explanation
Indices: 8560--8686 Score: 145
Period size: 60 Copynumber: 2.1 Consensus size: 61
8550 TTTTTTAAAT
* *
8560 GTGTATAATTAAATCAAAATTAAAATTTCAAGTATACATTTGAACCACAATTAAAGTTTCAC
1 GTGTATAATTAAATCAAAATTAAAATTTCAAGTATACAATTGAACCAAAATTAAAG-TTCAC
* * *
8622 GTGTATAATTACATC-AAATTAAAA-TTCATA-TATACAATTGCA-CATTAAATTAAAGTTCAT
1 GTGTATAATTAAATCAAAATTAAAATTTCA-AGTATACAATTGAACCA--AAATTAAAGTTCAC
8682 GTGTA
1 GTGTA
8687 ATTTTAAGAA
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
59 2 0.04
60 23 0.40
61 18 0.32
62 14 0.25
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (61 bp):
GTGTATAATTAAATCAAAATTAAAATTTCAAGTATACAATTGAACCAAAATTAAAGTTCAC
Found at i:9051 original size:15 final size:14
Alignment explanation
Indices: 9023--9081 Score: 59
Period size: 13 Copynumber: 4.2 Consensus size: 14
9013 ACATAATAAT
*
9023 AATTAAATTGTATTA
1 AATTAAA-TATATTA
9038 AATTAAAATATATT-
1 AATT-AAATATATTA
*
9052 AATTATATAT-TTA
1 AATTAAATATATTA
*
9065 AATTAAATATAATA
1 AATTAAATATATTA
9079 AAT
1 AAT
9082 CCTAACTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
12 2 0.05
13 14 0.38
14 9 0.24
15 9 0.24
16 3 0.08
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (14 bp):
AATTAAATATATTA
Found at i:10355 original size:25 final size:22
Alignment explanation
Indices: 10331--10390 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
10321 TCAGATTTTA
10331 TTATTTAATAATAAAAATATGT
1 TTATTTAATAATAAAAATATGT
*
10353 TTATTTAATTATAAAAATATG-
1 TTATTTAATAATAAAAATATGT
* *
10374 ATATTTAA-AAAAAAAAT
1 TTATTTAATAATAAAAAT
10391 TCGTAGGTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.21
21 7 0.21
22 20 0.59
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (22 bp):
TTATTTAATAATAAAAATATGT
Found at i:14731 original size:37 final size:37
Alignment explanation
Indices: 14681--14781 Score: 175
Period size: 37 Copynumber: 2.7 Consensus size: 37
14671 ACTACAAGTT
* *
14681 GATGAGGCACTGGGTGCCAAGTTATTTTGGTTTAACC
1 GATGAGACACTGGGTGTCAAGTTATTTTGGTTTAACC
14718 GATGAGACACTGGGTGTCAAGTTATTTTGGTTTAACC
1 GATGAGACACTGGGTGTCAAGTTATTTTGGTTTAACC
*
14755 GATGAGACACTGGGTGTCAATTTATTT
1 GATGAGACACTGGGTGTCAAGTTATTT
14782 ATAGCGCTGG
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.35
Consensus pattern (37 bp):
GATGAGACACTGGGTGTCAAGTTATTTTGGTTTAACC
Found at i:14824 original size:61 final size:61
Alignment explanation
Indices: 14727--14853 Score: 218
Period size: 61 Copynumber: 2.1 Consensus size: 61
14717 CGATGAGACA
* * * *
14727 CTGGGTGTCAAGTTATTTTGGTTTAACCGATGAGACACTGGGTGTCAATTTATTTATAGCG
1 CTGGGCGTCAAGTTACTTTGGTTTAACCGATAAGACACTGGGTGTCAATTTATTTATAACG
14788 CTGGGCGTCAAGTTACTTTGGTTTAACCGATAAGACACTGGGTGTCAATTTATTTATAACG
1 CTGGGCGTCAAGTTACTTTGGTTTAACCGATAAGACACTGGGTGTCAATTTATTTATAACG
14849 CTGGG
1 CTGGG
14854 TGCGATTTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (61 bp):
CTGGGCGTCAAGTTACTTTGGTTTAACCGATAAGACACTGGGTGTCAATTTATTTATAACG
Found at i:15081 original size:15 final size:15
Alignment explanation
Indices: 15058--15087 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15048 ATTATGCATA
15058 ATGGGTATGGAAATG
1 ATGGGTATGGAAATG
*
15073 ATGGTTATGGAAATG
1 ATGGGTATGGAAATG
15088 GAAATGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.37, T:0.30
Consensus pattern (15 bp):
ATGGGTATGGAAATG
Found at i:17003 original size:21 final size:20
Alignment explanation
Indices: 16963--17001 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
16953 CTTAAAGGAA
16963 GTATCGATACTTTGAGTTTG
1 GTATCGATACTTTGAGTTTG
16983 GTATCGATACCTTTG-GTTT
1 GTATCGATA-CTTTGAGTTT
17002 TGAACTGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (20 bp):
GTATCGATACTTTGAGTTTG
Found at i:19282 original size:20 final size:21
Alignment explanation
Indices: 19235--19283 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
19225 CCATGTATCA
*
19235 ATACATGACCTAGTGGTATTT
1 ATACATGACCTAGTGGTATTG
*
19256 ATGCATG-CCTA-TAGGTATTG
1 ATACATGACCTAGT-GGTATTG
19276 ATACATGA
1 ATACATGA
19284 GTGTTAAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 1 0.04
20 16 0.70
21 6 0.26
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (21 bp):
ATACATGACCTAGTGGTATTG
Done.