Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011404.1 Kokia drynarioides strain JFW-HI SEQ_126386, 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: 50696
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:9025 original size:15 final size:15
Alignment explanation
Indices: 9005--9054 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
8995 TGGGTTCAGA
*
9005 TTTTTTGAGTTAGAT
1 TTTTTTAAGTTAGAT
* *
9020 TTTTTTAAATTTGAT
1 TTTTTTAAGTTAGAT
* *
9035 TTTTTAAAGTTCGAT
1 TTTTTTAAGTTAGAT
9050 TTTTT
1 TTTTT
9055 GATTTTTAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.22, C:0.02, G:0.12, T:0.64
Consensus pattern (15 bp):
TTTTTTAAGTTAGAT
Found at i:9353 original size:25 final size:25
Alignment explanation
Indices: 9311--9359 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
9301 AAATTTTTAT
*
9311 TTTTGTATTTTTATTTTTAGAAATTG
1 TTTTGTATTTTTAATTTTA-AAATTG
9337 TTTT-TATTTTTAATTTTAAAATT
1 TTTTGTATTTTTAATTTTAAAATT
9360 TAGATTTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.23
25 13 0.59
26 4 0.18
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (25 bp):
TTTTGTATTTTTAATTTTAAAATTG
Found at i:10197 original size:19 final size:19
Alignment explanation
Indices: 10175--10211 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
10165 TAAATTTTGA
10175 AATTTAAAAAATAAAAATT
1 AATTTAAAAAATAAAAATT
* *
10194 AATTTATAAAATAGAAAT
1 AATTTAAAAAATAAAAAT
10212 ATAGAACTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
AATTTAAAAAATAAAAATT
Found at i:10823 original size:29 final size:29
Alignment explanation
Indices: 10791--10846 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
10781 AACATTTTAA
*
10791 AAATTGTAAAAAAATTTAAAAATTATTAG
1 AAATTGTAAAAAAATTTAAAAAATATTAG
* *
10820 AAATTGTAAAAGATTTTAAAAAATATT
1 AAATTGTAAAAAAATTTAAAAAATATT
10847 TTAAAATGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (29 bp):
AAATTGTAAAAAAATTTAAAAAATATTAG
Found at i:10853 original size:10 final size:9
Alignment explanation
Indices: 10784--10841 Score: 53
Period size: 10 Copynumber: 6.1 Consensus size: 9
10774 ATGTTGGAAC
10784 ATTTTAAAA
1 ATTTTAAAA
*
10793 ATTGTAAAAA
1 ATT-TTAAAA
*
10803 AATTTAAAA
1 ATTTTAAAA
*
10812 ATTATTAGAA
1 ATT-TTAAAA
*
10822 ATTGTAAAA
1 ATTTTAAAA
10831 GATTTTAAAA
1 -ATTTTAAAA
10841 A
1 A
10842 ATATTTTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
9 15 0.39
10 23 0.61
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (9 bp):
ATTTTAAAA
Found at i:11612 original size:2 final size:2
Alignment explanation
Indices: 11603--11631 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
11593 TTTTATTACT
11603 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11632 ATTTTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:12849 original size:38 final size:37
Alignment explanation
Indices: 12782--12853 Score: 99
Period size: 38 Copynumber: 1.9 Consensus size: 37
12772 AATAATAACT
* *
12782 AATTTAATCATATTTTAATATAATTATTATTAAATAC
1 AATTTAATCATATCTTAATATAATAATTATTAAATAC
* *
12819 AATTTAATTATATGCTTGATATAATAATTATTAAA
1 AATTTAATCATAT-CTTAATATAATAATTATTAAA
12854 ATATGACTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 12 0.40
38 18 0.60
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (37 bp):
AATTTAATCATATCTTAATATAATAATTATTAAATAC
Found at i:21102 original size:120 final size:120
Alignment explanation
Indices: 20889--21131 Score: 450
Period size: 120 Copynumber: 2.0 Consensus size: 120
20879 ACTAGCCACA
20889 CAAATCTCATGTATTAGTAGCTTATCGTAGATAAGGGCATCGCAAGCCCTATCCCAAACACAAGG
1 CAAATCTCATGTATTAGTAGCTTATCGTAGATAAGGGCATCGCAAGCCCTATCCCAAACACAAGG
20954 ATCTAAAGATCTGTTCATATTTCTCCGACCAACTCAAACTCAAGGGACCTCCAAC
66 ATCTAAAGATCTGTTCATATTTCTCCGACCAACTCAAACTCAAGGGACCTCCAAC
*
21009 CAAATCTCATGTATTAGTAGCTTATCGTAGATAAGGGCATCGTAAGCCCTATCCCAAACACAAGG
1 CAAATCTCATGTATTAGTAGCTTATCGTAGATAAGGGCATCGCAAGCCCTATCCCAAACACAAGG
***
21074 ATCTAGCTATCTGTTCATATTTCTCCGACCAACTCAAACTCAAGGGACCTCCAAC
66 ATCTAAAGATCTGTTCATATTTCTCCGACCAACTCAAACTCAAGGGACCTCCAAC
21129 CAA
1 CAA
21132 CTCAAATAGG
Statistics
Matches: 119, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 119 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.25
Consensus pattern (120 bp):
CAAATCTCATGTATTAGTAGCTTATCGTAGATAAGGGCATCGCAAGCCCTATCCCAAACACAAGG
ATCTAAAGATCTGTTCATATTTCTCCGACCAACTCAAACTCAAGGGACCTCCAAC
Found at i:31896 original size:14 final size:14
Alignment explanation
Indices: 31867--31914 Score: 59
Period size: 13 Copynumber: 3.6 Consensus size: 14
31857 TTTGAGAAGC
31867 TTTT-AAAAAGTG-
1 TTTTGAAAAAGTGA
31879 TTTTGAAAAAGTGA
1 TTTTGAAAAAGTGA
31893 TTTTG-AAAAGT-A
1 TTTTGAAAAAGTGA
31905 TTTTTGAAAA
1 -TTTTGAAAA
31915 GCTTGATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
12 5 0.16
13 19 0.59
14 8 0.25
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.42
Consensus pattern (14 bp):
TTTTGAAAAAGTGA
Found at i:33111 original size:17 final size:17
Alignment explanation
Indices: 33066--33105 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
33056 ACCGAGTATG
33066 AGGCTTGATGTGGATCA
1 AGGCTTGATGTGGATCA
33083 AGGCTTGATGTGGATCA
1 AGGCTTGATGTGGATCA
33100 AGGCTT
1 AGGCTT
33106 TCTGTGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.35, T:0.30
Consensus pattern (17 bp):
AGGCTTGATGTGGATCA
Found at i:35610 original size:23 final size:23
Alignment explanation
Indices: 35578--35624 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
35568 CAACTTCCAC
*
35578 TTGTTCATGATAGTAACAGTAAG
1 TTGTTCATGACAGTAACAGTAAG
*
35601 TTGTTTATGACAGTAACAGTAAG
1 TTGTTCATGACAGTAACAGTAAG
35624 T
1 T
35625 ATCACACGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (23 bp):
TTGTTCATGACAGTAACAGTAAG
Found at i:49351 original size:18 final size:19
Alignment explanation
Indices: 49315--49359 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
49305 TTAAATTAAA
*
49315 TAATTCGAGTTATTTGAAT
1 TAATTCGAGTTATTCGAAT
*
49334 TAATT-GAGTTGTTCGAAT
1 TAATTCGAGTTATTCGAAT
*
49352 CAATTCGA
1 TAATTCGA
49360 ATAAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (19 bp):
TAATTCGAGTTATTCGAAT
Found at i:49967 original size:24 final size:25
Alignment explanation
Indices: 49916--49967 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
49906 TTCATCATTT
*
49916 ATAAATGTCGAAACCATTTTTTTAAA
1 ATAAATGTCGAAA-CATTATTTTAAA
*
49942 ATAAATTTCGAAA-ATTATTTTAAA
1 ATAAATGTCGAAACATTATTTTAAA
49966 AT
1 AT
49968 TGAAAATGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 12 0.50
26 12 0.50
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (25 bp):
ATAAATGTCGAAACATTATTTTAAA
Done.