Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001312.1 Kokia drynarioides strain JFW-HI SEQ_112729, 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: 11838
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:943 original size:12 final size:12
Alignment explanation
Indices: 918--1092 Score: 59
Period size: 12 Copynumber: 14.8 Consensus size: 12
908 TTTATCAAGA
918 TAAATATTAAAT
1 TAAATATTAAAT
930 TAAAT-TTAATAT
1 TAAATATTAA-AT
*
942 TAAATCTT--AT
1 TAAATATTAAAT
952 TAAA-A-T-AAT
1 TAAATATTAAAT
* *
961 AAAATATT-TAT
1 TAAATATTAAAT
* *
972 CTACAAGATAAATAT
1 -TA-AATATTAA-AT
987 TAAA--TTAAAT
1 TAAATATTAAAT
*
997 TAAATATTAAAA
1 TAAATATTAAAT
*
1009 TAATTACTTTAATAT
1 TAAATA--TTAA-AT
* *
1024 TAAATTAATAAAA
1 TAAA-TATTAAAT
* *
1037 T-ACTATTAAAA
1 TAAATATTAAAT
1048 TAAATATTAAAT
1 TAAATATTAAAT
*
1060 TTAAT-TTAATAT
1 TAAATATTAA-AT
*
1072 TAAAATATTAAAA
1 T-AAATATTAAAT
1085 T-AATATTA
1 TAAATATTA
1093 TTTTTGGAAT
Statistics
Matches: 123, Mismatches: 21, Indels: 39
0.67 0.11 0.21
Matches are distributed among these distances:
8 1 0.01
9 5 0.04
10 13 0.11
11 29 0.24
12 39 0.32
13 15 0.12
14 13 0.11
15 6 0.05
16 2 0.02
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (12 bp):
TAAATATTAAAT
Found at i:1025 original size:37 final size:36
Alignment explanation
Indices: 980--1092 Score: 115
Period size: 37 Copynumber: 3.1 Consensus size: 36
970 ATCTACAAGA
980 TAAATATTAAATTAAATTAAATATTAAAATAATTACT
1 TAAATATTAAATTAAATTAAATATTAAAATAATTA-T
* * *
1017 TTAATATTAAATT-AATAAAATACTATTAAAATAAATAT
1 TAAATATTAAATTAAAT-TAA-A-TATTAAAATAATTAT
*
1055 TAAAT-TTAATTTAATATTAAAATATTAAAATAA-TAT
1 TAAATATTAAATTAA-ATT-AAATATTAAAATAATTAT
1091 TA
1 TA
1093 TTTTTGGAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
36 8 0.12
37 31 0.48
38 8 0.12
39 17 0.27
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (36 bp):
TAAATATTAAATTAAATTAAATATTAAAATAATTAT
Found at i:1031 original size:11 final size:11
Alignment explanation
Indices: 985--1092 Score: 59
Period size: 11 Copynumber: 9.9 Consensus size: 11
975 CAAGATAAAT
985 ATTAA-ATTAA
1 ATTAATATTAA
995 ATTAAATATTAA
1 ATT-AATATTAA
* *
1007 AAT-A-ATTAC
1 ATTAATATTAA
*
1016 TTTAATATTAA
1 ATTAATATTAA
1027 ATTAATA--AA
1 ATTAATATTAA
*
1036 A-TACTATTAAA
1 ATTAATATT-AA
*
1047 ATAAATATTAA
1 ATTAATATTAA
1058 ATTTAAT-TTAA
1 A-TTAATATTAA
1069 TATTAAAATATTAA
1 -ATT--AATATTAA
*
1083 AATAATATTA
1 ATTAATATTA
1093 TTTTTGGAAT
Statistics
Matches: 74, Mismatches: 11, Indels: 25
0.67 0.10 0.23
Matches are distributed among these distances:
8 4 0.05
9 8 0.11
10 5 0.07
11 31 0.42
12 17 0.23
13 5 0.07
14 4 0.05
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (11 bp):
ATTAATATTAA
Found at i:1092 original size:48 final size:50
Alignment explanation
Indices: 990--1092 Score: 138
Period size: 48 Copynumber: 2.1 Consensus size: 50
980 TAAATATTAA
* * * *
990 ATTAAATTAAATATTAAAATAATTACTTTAATATTAAATTAATAAAATACT
1 ATTAAAATAAATATTAAAAT-ATTAATTTAATATTAAAATAATAAAATAAT
*
1041 ATTAAAATAAATATT-AAAT-TTAATTTAATATTAAAATATTAAAATAAT
1 ATTAAAATAAATATTAAAATATTAATTTAATATTAAAATAATAAAATAAT
1089 ATTA
1 ATTA
1093 TTTTTGGAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
48 29 0.62
50 4 0.09
51 14 0.30
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (50 bp):
ATTAAAATAAATATTAAAATATTAATTTAATATTAAAATAATAAAATAAT
Found at i:1794 original size:10 final size:12
Alignment explanation
Indices: 1766--1797 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1756 TGAAAAGCAT
1766 AAAATAAAAGAG
1 AAAATAAAAGAG
1778 AAAATAAAAG-G
1 AAAATAAAAGAG
1789 -AAATAAAAG
1 AAAATAAAAG
1798 CAAGATTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 9 0.45
11 1 0.05
12 10 0.50
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (12 bp):
AAAATAAAAGAG
Found at i:11055 original size:102 final size:102
Alignment explanation
Indices: 10874--11098 Score: 360
Period size: 102 Copynumber: 2.2 Consensus size: 102
10864 TGAGTCCTCG
*
10874 ATAGCTCGTGTGAGCAGCATCGTGACTCGAAAAAGAGATATGGATCCTATATGGATTATAGGTCC
1 ATAGCTCGTGTGAGCAGCATCATGACTCGAAAAAGAGATATGGATCCTATATGGATTATAGGTCC
* *
10939 TACGATGGCTAGGACTTATGCTTTACGCATACTCCTA
66 TACGATGACAAGGACTTATGCTTTACGCATACTCCTA
* * *
10976 ATAGCTTGTGTGAGCAGTATCATGACTCGAAAAAGAGATATGGATCCTATGTGGATTATAGGTCC
1 ATAGCTCGTGTGAGCAGCATCATGACTCGAAAAAGAGATATGGATCCTATATGGATTATAGGTCC
* * *
11041 TATGATGACAAGGACTTATGCTTTATGCATACTCCTC
66 TACGATGACAAGGACTTATGCTTTACGCATACTCCTA
*
11078 ACAGCTCGTGTGAGCAGCATC
1 ATAGCTCGTGTGAGCAGCATC
11099 GTTAGGAAAT
Statistics
Matches: 111, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
102 111 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (102 bp):
ATAGCTCGTGTGAGCAGCATCATGACTCGAAAAAGAGATATGGATCCTATATGGATTATAGGTCC
TACGATGACAAGGACTTATGCTTTACGCATACTCCTA
Done.