Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003920.1 Kokia drynarioides strain JFW-HI SEQ_116995, 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: 36911
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:3035 original size:26 final size:26
Alignment explanation
Indices: 2990--3054 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
2980 GCATTGCGCG
* *
2990 CAGAATTATCGCTGGAGGAACT-TGTT
1 CAGAATTATCGCTCGAGGAA-TATGTC
3016 CAGAATTATCGCTACG-GGAATATGTC
1 CAGAATTATCGCT-CGAGGAATATGTC
*
3042 CAGAGTTATCGCT
1 CAGAATTATCGCT
3055 GCATAAGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 1 0.03
26 32 0.94
27 1 0.03
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (26 bp):
CAGAATTATCGCTCGAGGAATATGTC
Found at i:12643 original size:30 final size:29
Alignment explanation
Indices: 12582--12659 Score: 95
Period size: 30 Copynumber: 2.7 Consensus size: 29
12572 GTGGATGTTC
* *
12582 TCTGTTATATGTGCA-CCCTAGTGCTGGAA
1 TCTGTTATATGTG-AGCCTTACTGCTGGAA
*
12611 TCTGTTATATGTGAGCCTTACTGGTGGGAA
1 TCTGTTATATGTGAGCCTTACTGCT-GGAA
*
12641 TCTGGTATATGTGAGCCTT
1 TCTGTTATATGTGAGCCTT
12660 TGTTGTGAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 1 0.02
29 20 0.47
30 22 0.51
ACGTcount: A:0.19, C:0.17, G:0.27, T:0.37
Consensus pattern (29 bp):
TCTGTTATATGTGAGCCTTACTGCTGGAA
Found at i:21961 original size:15 final size:15
Alignment explanation
Indices: 21936--21970 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
21926 ATATTAAATA
21936 GATTT-AATTGATTT
1 GATTTAAATTGATTT
21950 GATTTAAATTGATTT
1 GATTTAAATTGATTT
*
21965 AATTTA
1 GATTTA
21971 TTTAATGCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.54
Consensus pattern (15 bp):
GATTTAAATTGATTT
Found at i:23051 original size:20 final size:20
Alignment explanation
Indices: 23021--23072 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
23011 TTAAAATCTC
*
23021 AAAATTTATTACTTTAA-TT
1 AAAATTTATTAATTTAATTT
23040 AAAATATTATTAATTTAATTT
1 AAAAT-TTATTAATTTAATTT
23061 ATAAATTTATTA
1 A-AAATTTATTA
23073 TAAATATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 5 0.17
20 11 0.38
21 9 0.31
22 4 0.14
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
AAAATTTATTAATTTAATTT
Found at i:26435 original size:39 final size:39
Alignment explanation
Indices: 26381--26524 Score: 162
Period size: 39 Copynumber: 3.7 Consensus size: 39
26371 AAACACTACG
* * * * *
26381 ATGCAATGCCGAACTGACGATAACACTATAAATACCGTA
1 ATGCAATACTGAACTGATGGTAACACTGTAAATACCGTA
26420 ATGCAATACTGAACTGATGGTAACACTGTAAATACCGTA
1 ATGCAATACTGAACTGATGGTAACACTGTAAATACCGTA
*** **
26459 ACATAATACTGAACCAATGGTAACACTGTAAATACCGTA
1 ATGCAATACTGAACTGATGGTAACACTGTAAATACCGTA
* ** *
26498 TTGCAATACTGGGCCGATGGTAACACT
1 ATGCAATACTGAACTGATGGTAACACT
26525 ACAAACACCG
Statistics
Matches: 88, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 88 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (39 bp):
ATGCAATACTGAACTGATGGTAACACTGTAAATACCGTA
Found at i:34130 original size:46 final size:46
Alignment explanation
Indices: 34080--34369 Score: 259
Period size: 46 Copynumber: 6.3 Consensus size: 46
34070 TTACTCATTT
* * * *
34080 GGGTTAAACCTACATGAATCTG-ATAATAGTTCTTGGTCACCTATTA
1 GGGTTGAACCTACACGAATC-GAATAATAGTGCTTGGTCACCTGTTA
* * *
34126 GGGTTGAACATACACAAATCGAATAATAGTG-TCTGGTCACCCGTTA
1 GGGTTGAACCTACACGAATCGAATAATAGTGCT-TGGTCACCTGTTA
* * * *
34172 AGGTTGAACCTACACGAATCGAACAATAGTGCCTAGTCACCCT-TTA
1 GGGTTGAACCTACACGAATCGAATAATAGTGCTTGGTCA-CCTGTTA
* * * *
34218 AGGTTGAACCTACACGAATTGGATAATAGTGCTTGGTCATGC-GTTA
1 GGGTTGAACCTACACGAATCGAATAATAGTGCTTGGTCA-CCTGTTA
* * *
34264 GGGTTGAACGTACATGAATCGAATAATAGTGCTTGGTCACCTGTTC
1 GGGTTGAACCTACACGAATCGAATAATAGTGCTTGGTCACCTGTTA
* * * * **
34310 GGGTTGAACCTTCATGAATC-AGATAATACTACCAGGTCAACC-GTTA
1 GGGTTGAACCTACACGAATCGA-ATAATAGTGCTTGGTC-ACCTGTTA
*
34356 AGGTTGAACCTACA
1 GGGTTGAACCTACA
34370 AAACAAATAG
Statistics
Matches: 199, Mismatches: 37, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
45 4 0.02
46 190 0.95
47 5 0.03
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (46 bp):
GGGTTGAACCTACACGAATCGAATAATAGTGCTTGGTCACCTGTTA
Found at i:34315 original size:138 final size:138
Alignment explanation
Indices: 34081--34369 Score: 336
Period size: 138 Copynumber: 2.1 Consensus size: 138
34071 TACTCATTTG
* * *
34081 GGTTAAACCTACATGAATCTGATAATAGTTCTTGGTCACCTATTAGGGTTGAACATACACAAATC
1 GGTTGAACCTACACGAATCTGATAATAGTGCTTGGTCACCTATTAGGGTTGAACATACACAAATC
* *
34146 GAATAATAGTGTCTGGTCACCCGTTAAGGTTGAACCTACACGAATC-GAACAATAGTGCCTA-GT
66 GAATAATAGTGTCTGGTCACCCGTTAAGGTTGAACCTACACGAATCAG-ACAATACTACC-AGGT
* *
34209 CACCCTTTAA
129 CAACCGTTAA
* * * **
34219 GGTTGAACCTACACGAAT-TGGATAATAGTGCTTGGTCATGC-GTTAGGGTTGAACGTACATGAA
1 GGTTGAACCTACACGAATCT-GATAATAGTGCTTGGTCA-CCTATTAGGGTTGAACATACACAAA
* ** * * *
34282 TCGAATAATAGTG-CTTGGTCACCTGTTCGGGTTGAACCTTCATGAATCAGATAATACTACCAGG
64 TCGAATAATAGTGTC-TGGTCACCCGTTAAGGTTGAACCTACACGAATCAGACAATACTACCAGG
34346 TCAACCGTTAA
128 TCAACCGTTAA
34357 GGTTGAACCTACA
1 GGTTGAACCTACA
34370 AAACAAATAG
Statistics
Matches: 128, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
137 3 0.02
138 123 0.96
139 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (138 bp):
GGTTGAACCTACACGAATCTGATAATAGTGCTTGGTCACCTATTAGGGTTGAACATACACAAATC
GAATAATAGTGTCTGGTCACCCGTTAAGGTTGAACCTACACGAATCAGACAATACTACCAGGTCA
ACCGTTAA
Found at i:35394 original size:26 final size:26
Alignment explanation
Indices: 35364--35416 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
35354 AATTGTAAAT
*
35364 ATTAAGATATT-TTAAATTAAACTTTA
1 ATTAAGATATTACT-AATTAAACTTTA
**
35390 ATTAATCTATTACTAATTAAACTTTA
1 ATTAAGATATTACTAATTAAACTTTA
35416 A
1 A
35417 ACAAGATTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 22 0.96
27 1 0.04
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (26 bp):
ATTAAGATATTACTAATTAAACTTTA
Done.