Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007088.1 Kokia drynarioides strain JFW-HI SEQ_121697, 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: 22336
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3236 original size:17 final size:17
Alignment explanation
Indices: 3216--3252 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
3206 TTTTATTGAA
*
3216 ATTGTCATTGCATTTTT
1 ATTGTCATTGCACTTTT
*
3233 ATTGTCCTTGCACTTTT
1 ATTGTCATTGCACTTTT
3250 ATT
1 ATT
3253 TGTTTTCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.16, C:0.16, G:0.11, T:0.57
Consensus pattern (17 bp):
ATTGTCATTGCACTTTT
Found at i:3236 original size:23 final size:20
Alignment explanation
Indices: 3195--3236 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 20
3185 TTCAATAGTT
3195 AATTGCATGCATTTTATTGA
1 AATTGCATGCATTTTATTGA
3215 AATTGTCATTGCATTTTTATTG
1 AATTG-CA-TGCA-TTTTATTG
3237 TCCTTGCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 2 0.11
22 4 0.21
23 8 0.42
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.50
Consensus pattern (20 bp):
AATTGCATGCATTTTATTGA
Found at i:9315 original size:17 final size:17
Alignment explanation
Indices: 9293--9325 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
9283 CAAACCATGG
9293 ACCCA-TGACTCGACCTA
1 ACCCATTGACT-GACCTA
9310 ACCCATTGACTGACCT
1 ACCCATTGACTGACCT
9326 GTTAACTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.27, C:0.39, G:0.12, T:0.21
Consensus pattern (17 bp):
ACCCATTGACTGACCTA
Found at i:13611 original size:26 final size:26
Alignment explanation
Indices: 13575--13628 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
13565 CATGTAAAGG
13575 TAAATAAAAGTTTAATTTTAAGTACT
1 TAAATAAAAGTTTAATTTTAAGTACT
13601 TAAATAAAAGTTTAATTTTAAGTACT
1 TAAATAAAAGTTTAATTTTAAGTACT
13627 TA
1 TA
13629 GTTTTGCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (26 bp):
TAAATAAAAGTTTAATTTTAAGTACT
Found at i:14262 original size:20 final size:20
Alignment explanation
Indices: 14237--14279 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
14227 TTTTTAACTC
14237 TTTATATTT-TCTTTAGAATT
1 TTTATATTTAT-TTTAGAATT
*
14257 TTTATATTTATTTTATAATT
1 TTTATATTTATTTTAGAATT
14277 TTT
1 TTT
14280 TTAAAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTATATTTATTTTAGAATT
Found at i:14434 original size:18 final size:18
Alignment explanation
Indices: 14411--14448 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
14401 CACCAATCTG
14411 TTATTCAAATTATTTGAA
1 TTATTCAAATTATTTGAA
* *
14429 TTATTCGAGTTATTTGAA
1 TTATTCAAATTATTTGAA
14447 TT
1 TT
14449 GTAAAATTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.53
Consensus pattern (18 bp):
TTATTCAAATTATTTGAA
Found at i:20133 original size:75 final size:75
Alignment explanation
Indices: 20039--20187 Score: 289
Period size: 75 Copynumber: 2.0 Consensus size: 75
20029 CTAATATTGG
20039 TACCTAGGTGCAAGAGAGCCTAAAATAAGCCTGAAATCACCATAAAACATATAAAAATGTTCCTT
1 TACCTAGGTGCAAGAGAGCCTAAAATAAGCCTGAAATCACCATAAAACATATAAAAATGTTCCTT
20104 AAACATTTTT
66 AAACATTTTT
*
20114 TACCTAGGTGTAAGAGAGCCTAAAATAAGCCTGAAATCACCATAAAACATATAAAAATGTTCCTT
1 TACCTAGGTGCAAGAGAGCCTAAAATAAGCCTGAAATCACCATAAAACATATAAAAATGTTCCTT
20179 AAACATTTT
66 AAACATTTT
20188 CAATAATTCT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (75 bp):
TACCTAGGTGCAAGAGAGCCTAAAATAAGCCTGAAATCACCATAAAACATATAAAAATGTTCCTT
AAACATTTTT
Found at i:21198 original size:105 final size:105
Alignment explanation
Indices: 21064--21276 Score: 390
Period size: 105 Copynumber: 2.0 Consensus size: 105
21054 AAGAAAAAGG
*
21064 ATTAAACAAACATGAAATGAAAGAGAGAGGACTCAAAGGGATAATTATACCCTAGTCTAGGATTA
1 ATTAAACAAACATGAAATGAAAGAGAGAGGACTCAAAGGGATAATTATACCATAGTCTAGGATTA
*
21129 ATGGTGGTGGGTGAACCACTATCTAGATTTTATGGTTAAA
66 ATGGTGGTGGGTGAACCACTATCAAGATTTTATGGTTAAA
21169 ATTAAACAAACATGAAATGAAAGAGAGAGGACTCAAAGGGATAATTATACCATAGTCTAGGATTA
1 ATTAAACAAACATGAAATGAAAGAGAGAGGACTCAAAGGGATAATTATACCATAGTCTAGGATTA
* *
21234 GTGGTGGTGGGTGAACCACTATCAAGATTTTGTGGTTAAA
66 ATGGTGGTGGGTGAACCACTATCAAGATTTTATGGTTAAA
21274 ATT
1 ATT
21277 TTAGTAAACA
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 104 1.00
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (105 bp):
ATTAAACAAACATGAAATGAAAGAGAGAGGACTCAAAGGGATAATTATACCATAGTCTAGGATTA
ATGGTGGTGGGTGAACCACTATCAAGATTTTATGGTTAAA
Done.