Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012832.1 Kokia drynarioides strain JFW-HI SEQ_127845, 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: 23807
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:668 original size:30 final size:29
Alignment explanation
Indices: 608--1011 Score: 341
Period size: 29 Copynumber: 13.7 Consensus size: 29
598 CTAAATTGTT
** *
608 CAAAAATTTCATTTTTA-CCCACAGACTTC
1 CAAAAATCCCATTTTTACCCCA-AAACTTC
* *
637 CAAAAATCTCATTTTTGACCTCAAAACTTC
1 CAAAAATCCCATTTTT-ACCCCAAAACTTC
* * *
667 CAAAAATCTCATTTTTATCCTC-GAACTTC
1 CAAAAATCCCATTTTTA-CCCCAAAACTTC
*
696 TAAAAATCCCATTTTTAACCCCAAAACTTC
1 CAAAAATCCCATTTTT-ACCCCAAAACTTC
* *
726 CAAAAAACCCATTTTTACCCCTAAACTTC
1 CAAAAATCCCATTTTTACCCCAAAACTTC
* *
755 TAAAAATCCCATTTTTAACCTCAAAACTTC
1 CAAAAATCCCATTTTT-ACCCCAAAACTTC
***
785 CAAAAATCCCATTTTTACCCTTGAACTTC
1 CAAAAATCCCATTTTTACCCCAAAACTTC
* * *
814 TAAAAAATCCTATTTTTAACCCCGAAACTTC
1 -CAAAAATCCCATTTTT-ACCCCAAAACTTC
* * *
845 CAAAAATCTCATTTTTACCCTC-GAACTTT
1 CAAAAATCCCATTTTTACCC-CAAAACTTC
* * * *
874 TAAAAATCTCATTTTTAACCTCGAAACTT-
1 CAAAAATCCCATTTTT-ACCCCAAAACTTC
* * **
903 AAAAAATCCCATTTTGACCCCAAAACCAC
1 CAAAAATCCCATTTTTACCCCAAAACTTC
* *
932 CAAAAATCCCATTTTTAACCCAAAAACTTT
1 CAAAAATCCCATTTTT-ACCCCAAAACTTC
* **
962 CAAAAGGT-CCATTTTTACCCCCGAACTTC
1 CAAAA-ATCCCATTTTTACCCCAAAACTTC
*
991 TAAAAATCCCATTTTTGACCC
1 CAAAAATCCCATTTTT-ACCC
1012 TGAATTTTCC
Statistics
Matches: 306, Mismatches: 53, Indels: 31
0.78 0.14 0.08
Matches are distributed among these distances:
28 9 0.03
29 147 0.48
30 136 0.44
31 14 0.05
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (29 bp):
CAAAAATCCCATTTTTACCCCAAAACTTC
Found at i:701 original size:59 final size:59
Alignment explanation
Indices: 608--1006 Score: 446
Period size: 59 Copynumber: 6.8 Consensus size: 59
598 CTAAATTGTT
** * * * *
608 CAAAAATTTCATTTTTACCCAC-AGACTTCCAAAAATCTCATTTTTGACCTCAAAACTTC
1 CAAAAATCCCATTTTTACCCCCGA-ACTTCTAAAAATCCCATTTTTAACCTCAAAACTTC
* * * *
667 CAAAAATCTCATTTTTATCCTCGAACTTCTAAAAATCCCATTTTTAACCCCAAAACTTC
1 CAAAAATCCCATTTTTACCCCCGAACTTCTAAAAATCCCATTTTTAACCTCAAAACTTC
* **
726 CAAAAAACCCATTTTTACCCCTAAACTTCTAAAAATCCCATTTTTAACCTCAAAACTTC
1 CAAAAATCCCATTTTTACCCCCGAACTTCTAAAAATCCCATTTTTAACCTCAAAACTTC
** * * *
785 CAAAAATCCCATTTTTACCCTTGAACTTCTAAAAAATCCTATTTTTAACCCCGAAACTTC
1 CAAAAATCCCATTTTTACCCCCGAACTTCT-AAAAATCCCATTTTTAACCTCAAAACTTC
* * * * *
845 CAAAAATCTCATTTTTACCCTCGAACTTTTAAAAATCTCATTTTTAACCTCGAAACTT-
1 CAAAAATCCCATTTTTACCCCCGAACTTCTAAAAATCCCATTTTTAACCTCAAAACTTC
* * ** ** * *
903 AAAAAATCCCATTTTGACCCCAAAACCACCAAAAATCCCATTTTTAACC-CAAAAACTTT
1 CAAAAATCCCATTTTTACCCCCGAACTTCTAAAAATCCCATTTTTAACCTC-AAAACTTC
*
962 CAAAAGGT-CCATTTTTACCCCCGAACTTCTAAAAATCCCATTTTT
1 CAAAA-ATCCCATTTTTACCCCCGAACTTCTAAAAATCCCATTTTT
1007 GACCCTGAAT
Statistics
Matches: 289, Mismatches: 46, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
57 1 0.00
58 44 0.15
59 189 0.65
60 55 0.19
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.32
Consensus pattern (59 bp):
CAAAAATCCCATTTTTACCCCCGAACTTCTAAAAATCCCATTTTTAACCTCAAAACTTC
Found at i:12394 original size:16 final size:18
Alignment explanation
Indices: 12362--12394 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12352 TGACTAAATT
12362 TTTATAATAAAATAATGC
1 TTTATAATAAAATAATGC
12380 TTTATAA-AAAA-AATG
1 TTTATAATAAAATAATG
12395 AAAAGAAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 4 0.27
18 7 0.47
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (18 bp):
TTTATAATAAAATAATGC
Found at i:13983 original size:23 final size:22
Alignment explanation
Indices: 13957--14036 Score: 97
Period size: 23 Copynumber: 3.5 Consensus size: 22
13947 AAGTAATTAA
13957 CAGTAAGCACACATAATGCAAT
1 CAGTAAGCACACATAATGCAAT
* *
13979 CCAGTAAGCACACACAGTGCAAT
1 -CAGTAAGCACACATAATGCAAT
* * *
14002 CAGTAGGCGCACATAACGCAAAT
1 CAGTAAGCACACATAATGC-AAT
14025 CAGTAAGCACAC
1 CAGTAAGCACAC
14037 GAAGTGCGAA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
22 14 0.30
23 33 0.70
ACGTcount: A:0.41, C:0.28, G:0.17, T:0.14
Consensus pattern (22 bp):
CAGTAAGCACACATAATGCAAT
Found at i:14043 original size:45 final size:45
Alignment explanation
Indices: 13955--14056 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 45
13945 CGAAGTAATT
* *
13955 AACAGTAAGCACACATAATGCAATCCAGTAAGCACACACAGTGC-
1 AACAGTAAGCGCACATAACGCAATCCAGTAAGCACACACAGTGCG
*
13999 AATCAGTAGGCGCACATAACGCAAAT-CAGTAAGCACACGA-AGTGCG
1 AA-CAGTAAGCGCACATAACGC-AATCCAGTAAGCACAC-ACAGTGCG
*
14045 AACAGTATGCGC
1 AACAGTAAGCGC
14057 GCTAGCGTTC
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
44 2 0.04
45 42 0.84
46 6 0.12
ACGTcount: A:0.40, C:0.25, G:0.21, T:0.14
Consensus pattern (45 bp):
AACAGTAAGCGCACATAACGCAATCCAGTAAGCACACACAGTGCG
Found at i:16296 original size:14 final size:14
Alignment explanation
Indices: 16277--16304 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16267 GAAATCGGGA
16277 AAAGTTTGAATTAT
1 AAAGTTTGAATTAT
16291 AAAGTTTGAATTAT
1 AAAGTTTGAATTAT
16305 GGCACGGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (14 bp):
AAAGTTTGAATTAT
Found at i:18249 original size:25 final size:25
Alignment explanation
Indices: 18221--18274 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
18211 GTCATTTTGT
18221 TATTATATTACTACTATTTTGTTGA
1 TATTATATTACTACTATTTTGTTGA
* ** *
18246 TATTATATTGCTGTTATTTTGTTGG
1 TATTATATTACTACTATTTTGTTGA
18271 TATT
1 TATT
18275 GTTTTGATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.22, C:0.06, G:0.13, T:0.59
Consensus pattern (25 bp):
TATTATATTACTACTATTTTGTTGA
Found at i:19110 original size:8 final size:8
Alignment explanation
Indices: 19099--19139 Score: 52
Period size: 7 Copynumber: 5.5 Consensus size: 8
19089 ATTTTTTTAC
*
19099 ATATATAA
1 ATATAAAA
19107 ATATAAAA
1 ATATAAAA
19115 ATA-AAAA
1 ATATAAAA
19122 ATA-AAAA
1 ATATAAAA
19129 ATA-AAAA
1 ATATAAAA
19136 ATAT
1 ATAT
19140 TTTTATTGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
7 21 0.68
8 10 0.32
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
ATATAAAA
Found at i:19123 original size:7 final size:7
Alignment explanation
Indices: 19105--19138 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
19095 TTACATATAT
19105 AAATATAA
1 AAATA-AA
19113 AAATAAA
1 AAATAAA
19120 AAATAAA
1 AAATAAA
19127 AAATAAA
1 AAATAAA
19134 AAATA
1 AAATA
19139 TTTTTATTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.81
8 5 0.19
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (7 bp):
AAATAAA
Done.