Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014156.1 Kokia drynarioides strain JFW-HI SEQ_129189, 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: 8108
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Found at i:811 original size:24 final size:26
Alignment explanation
Indices: 784--831 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
774 AGAGAAATGT
784 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
808 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
832 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:920 original size:23 final size:23
Alignment explanation
Indices: 894--1125 Score: 205
Period size: 23 Copynumber: 10.1 Consensus size: 23
884 ACACTAGCGC
894 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
917 GCTCTTTGTTTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
940 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
963 GCTCTCTGTTTAGCTCT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
986 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
*
1009 GCTCTCTGTTTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
* *
1032 GCT-TACTGTTTCGCACT-TCGTGT
1 GCTCT-CTGATTAGCACTGT-GTGT
* * * *
1055 GC-CTACTGATTTGCGCTATGTGC
1 GCTCT-CTGATTAGCACTGTGTGT
*
1078 GC-CTACTGATT-GCACTGTGTAT
1 GCTCT-CTGATTAGCACTGTGTGT
1100 GCT-TACTGGATT-GCACTGTGTGT
1 GCTCT-CT-GATTAGCACTGTGTGT
1123 GCT
1 GCT
1126 TACTGTTTCC
Statistics
Matches: 180, Mismatches: 19, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.09
23 160 0.89
24 3 0.02
ACGTcount: A:0.11, C:0.23, G:0.25, T:0.41
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:1056 original size:46 final size:46
Alignment explanation
Indices: 894--1034 Score: 264
Period size: 46 Copynumber: 3.1 Consensus size: 46
884 ACACTAGCGC
*
894 GCTCTCTGATTAGCACTGTGTGTGCTCTTTGTTTAGCACTTCGTGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACTTCGTGT
*
940 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCTCTTCGTGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACTTCGTGT
986 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACTTCGTGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACTTCGTGT
1032 GCT
1 GCT
1035 TACTGTTTCG
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 92 1.00
ACGTcount: A:0.10, C:0.23, G:0.24, T:0.43
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACTTCGTGT
Found at i:1126 original size:23 final size:23
Alignment explanation
Indices: 899--1156 Score: 171
Period size: 23 Copynumber: 11.1 Consensus size: 23
889 AGCGCGCTCT
899 CTGATTAGCACTGTGTGTGCTCT-
1 CTGATTAGCACTGTGTGTGCT-TA
* *
922 TTGTTTAGCACT-TCGTGTGCTCT-
1 CTGATTAGCACTGT-GTGTGCT-TA
945 CTGATTAGCACTGTGTGTGCTCT-
1 CTGATTAGCACTGTGTGTGCT-TA
* *
968 CTGTTTAGCTCT-TCGTGTGCTCT-
1 CTGATTAGCACTGT-GTGTGCT-TA
991 CTGATTAGCACTGTGTGTGCTCT-
1 CTGATTAGCACTGTGTGTGCT-TA
*
1014 CTGTTTAGCACT-TCGTGTGCTTA
1 CTGATTAGCACTGT-GTGTGCTTA
* * *
1037 CTGTTTCGCACT-TCGTGTGCCTA
1 CTGATTAGCACTGT-GTGTGCTTA
* * * * *
1060 CTGATTTGCGCTATGTGCGCCTA
1 CTGATTAGCACTGTGTGTGCTTA
*
1083 CTGATT-GCACTGTGTATGCTTA
1 CTGATTAGCACTGTGTGTGCTTA
1105 CTGGATT-GCACTGTGTGTGCTTA
1 CT-GATTAGCACTGTGTGTGCTTA
*
1128 CTGTTTCCCTAGCACT-TGTGTGCTTA
1 CTG-AT---TAGCACTGTGTGTGCTTA
1154 CTG
1 CTG
1157 TTAAGTACTT
Statistics
Matches: 200, Mismatches: 22, Indels: 23
0.82 0.09 0.09
Matches are distributed among these distances:
22 18 0.09
23 160 0.80
24 3 0.01
26 14 0.07
27 5 0.03
ACGTcount: A:0.12, C:0.23, G:0.24, T:0.41
Consensus pattern (23 bp):
CTGATTAGCACTGTGTGTGCTTA
Found at i:5182 original size:23 final size:23
Alignment explanation
Indices: 5111--5237 Score: 116
Period size: 23 Copynumber: 5.4 Consensus size: 23
5101 GAACACCAGC
* * *
5111 GTGCTCTCTGTTTAGCACGTCT-C
1 GTGCTCTCTGATTAGCAC-TTTGT
5134 GTGCTCTCTGTTATTAGCA-TTGTGT
1 GTGCTCTCTG--ATTAGCACTT-TGT
5159 GTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
* *
5182 GTGCTTTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
* * *
5205 GTACTATCT-ATTTAGCACTGTGT
1 GTGCTCTCTGA-TTAGCACTTTGT
5228 GTGCTCTCTG
1 GTGCTCTCTG
5238 TTGCCCAGCA
Statistics
Matches: 86, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
22 1 0.01
23 66 0.77
24 3 0.03
25 16 0.19
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTTTGT
Done.