Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012148.1 Kokia drynarioides strain JFW-HI SEQ_127147, 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: 10333
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.37
Found at i:1025 original size:23 final size:23
Alignment explanation
Indices: 997--1096 Score: 98
Period size: 23 Copynumber: 4.3 Consensus size: 23
987 ACACTAGTGC
997 GCCCTCTGTTTAGCACGTTTC-GT
1 GCCCTCTGTTTAGCAC-TTTCTGT
* *
1020 GCCCTCTGTTCAGCACTATCTGT
1 GCCCTCTGTTTAGCACTTTCTGT
*
1043 GCCCTTTGTTATTAGCAC-TTCGTGT
1 GCCCTCTG-T-TTAGCACTTTC-TGT
* *
1068 GCCCTCTGATTAGCACTTTATGT
1 GCCCTCTGTTTAGCACTTTCTGT
1091 -CCCTCT
1 GCCCTCT
1097 ATTAAGTACT
Statistics
Matches: 64, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
22 9 0.14
23 34 0.53
24 5 0.08
25 16 0.25
ACGTcount: A:0.12, C:0.31, G:0.18, T:0.39
Consensus pattern (23 bp):
GCCCTCTGTTTAGCACTTTCTGT
Found at i:6668 original size:87 final size:87
Alignment explanation
Indices: 6522--6708 Score: 275
Period size: 87 Copynumber: 2.1 Consensus size: 87
6512 TTTTGTTACA
* * * ** * *
6522 TATTATGTGACACGATCATTCTGATTCTGATTTTCTGACGAACGTAAACATTTTGACCGAGCTCC
1 TATTATGTGACACAATCATTCAGATTCTAATTAGCTGACGAACGTAAACATTCTGACCGAGCTCA
6587 TGCATATGTTACGGACTCGAGT
66 TGCATATGTTACGGACTCGAGT
* *
6609 TATTATGTGACACAATCATTCAGATTGTAATTAGCTGACGAGCGTAAACATTCTGACCGAGCTCA
1 TATTATGTGACACAATCATTCAGATTCTAATTAGCTGACGAACGTAAACATTCTGACCGAGCTCA
*
6674 TGCATGTGTTACGGACTCGAGT
66 TGCATATGTTACGGACTCGAGT
*
6696 TATTATGAGACAC
1 TATTATGTGACAC
6709 GGATTTAGCT
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 89 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (87 bp):
TATTATGTGACACAATCATTCAGATTCTAATTAGCTGACGAACGTAAACATTCTGACCGAGCTCA
TGCATATGTTACGGACTCGAGT
Found at i:9025 original size:43 final size:43
Alignment explanation
Indices: 8953--9495 Score: 414
Period size: 43 Copynumber: 12.7 Consensus size: 43
8943 ACAAGTGATC
*
8953 CTTCGGTTTATCCGATGATGCA-TTGTGTGTGCCAGTATAGTTG
1 CTTCGGTTTATCCGATGATGCACTT-TGTGTGCCAGTATATTTG
* * * * *
8996 CTTCAGTTTATCTGATGATGTACTTTGTGTGCCAATATATTTT
1 CTTCGGTTTATCCGATGATGCACTTTGTGTGCCAGTATATTTG
* * * ** * * * * *
9039 CTTTGATTTCTTTGATGATGTACTGTGTGTTCTAGTATAATTG
1 CTTCGGTTTATCCGATGATGCACTTTGTGTGCCAGTATATTTG
* * *
9082 CTTTGGTTTATCCGATGATGCACTTTGTGTTCCAATATATTTG
1 CTTCGGTTTATCCGATGATGCACTTTGTGTGCCAGTATATTTG
* * * ** *
9125 CTTCAGTTTATCGGATGATGCACTATGTGTTTCAATATATTTG
1 CTTCGGTTTATCCGATGATGCACTTTGTGTGCCAGTATATTTG
* *
9168 TTTCGGTATATCCGATGATGCACTTTGTGTGCCAGTATAGTTT-
1 CTTCGGTTTATCCGATGATGCACTTTGTGTGCCAGTATA-TTTG
* * ** * **
9211 CTTTGTTTTATTTGATGGTGCACTTTGTGTGTGAGTAT-TTT-
1 CTTCGGTTTATCCGATGATGCACTTTGTGTGCCAGTATATTTG
* * * *
9252 TTTCGGTTTATCCAATGATGAATTTTGTGTGCCAGTATATTTG
1 CTTCGGTTTATCCGATGATGCACTTTGTGTGCCAGTATATTTG
* * * * * * * * **
9295 CTTCGATTTAGCTGATGATGTAGTGTATATGTTAGTATATTTG
1 CTTCGGTTTATCCGATGATGCACTTTGTGTGCCAGTATATTTG
** * * *
9338 CTTCAATTTATCCGATGATGCAATGTGTGTGCTAGTATATTTG
1 CTTCGGTTTATCCGATGATGCACTTTGTGTGCCAGTATATTTG
* ** * * *
9381 CTTCGTTTTATCAAATGATGCACTGTGTGTGGCCA-TGTAGTTG
1 CTTCGGTTTATCCGATGATGCACTTTGTGT-GCCAGTATATTTG
* ** * *
9424 CTTCGATTTATCCGATGATGCAC-TTACGTGCCAATATAATTG
1 CTTCGGTTTATCCGATGATGCACTTTGTGTGCCAGTATATTTG
* *
9466 CGTCGGTTTATCTGATGATGCACTTATGTG
1 CTTCGGTTTATCCGATGATGCACTT-TGTG
9496 CTAGTATGGT
Statistics
Matches: 392, Mismatches: 100, Indels: 15
0.77 0.20 0.03
Matches are distributed among these distances:
41 34 0.09
42 32 0.08
43 316 0.81
44 10 0.03
ACGTcount: A:0.20, C:0.14, G:0.22, T:0.45
Consensus pattern (43 bp):
CTTCGGTTTATCCGATGATGCACTTTGTGTGCCAGTATATTTG
Done.