Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009971.1 Kokia drynarioides strain JFW-HI SEQ_124720, 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: 75180
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:843 original size:30 final size:29
Alignment explanation
Indices: 768--1099 Score: 343
Period size: 29 Copynumber: 11.4 Consensus size: 29
758 CGAAGATTAT
* *
768 ATTTTTACCCCTAAACTTCTAAAAATTCC
1 ATTTTTACCCCGAAACTTCCAAAAATTCC
* *
797 ATTTTTACCCCTAAACTTCCAAAATTTCC
1 ATTTTTACCCCGAAACTTCCAAAAATTCC
*
826 ATTTTTGACCCCGAAACTTCCAAAAATTTC
1 ATTTTT-ACCCCGAAACTTCCAAAAATTCC
856 ATTTTTACCCCG-AACTTCCAAAAATTCC
1 ATTTTTACCCCGAAACTTCCAAAAATTCC
*
884 ATTTTTGACCTCGAAACTTCCAAAAATTCC
1 ATTTTT-ACCCCGAAACTTCCAAAAATTCC
* **
914 ATTTTTATCGTG-AACTTCCAAAAATTCC
1 ATTTTTACCCCGAAACTTCCAAAAATTCC
*
942 ATTTTTACCCTCG-AACTTCCAAAATTTCC
1 ATTTTTACCC-CGAAACTTCCAAAAATTCC
* ** **
971 ATTTTTGA-CCCAAAACTTTAAAAAATTAT
1 ATTTTT-ACCCCGAAACTTCCAAAAATTCC
* *
1000 ATTTTTAACCCCAAAACTTCCAAAAATTAC
1 ATTTTT-ACCCCGAAACTTCCAAAAATTCC
* *
1030 ATTTTTACCCTCG-AACCTCCAAAATTTCC
1 ATTTTTACCC-CGAAACTTCCAAAAATTCC
* ** *
1059 ATTTTTGATCTTGAAACTTTCAAAAATTACC
1 ATTTTT-ACCCCGAAACTTCCAAAAATT-CC
1090 A-TTTTACCCC
1 ATTTTTACCCC
1100 TGGATGTCCA
Statistics
Matches: 255, Mismatches: 37, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
28 46 0.18
29 115 0.45
30 91 0.36
31 3 0.01
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.36
Consensus pattern (29 bp):
ATTTTTACCCCGAAACTTCCAAAAATTCC
Found at i:884 original size:58 final size:58
Alignment explanation
Indices: 768--1190 Score: 387
Period size: 58 Copynumber: 7.3 Consensus size: 58
758 CGAAGATTAT
* * * *
768 ATTTTT-ACCCCTAAACTTCTAAAAATTCCATTTTTACCCCTAAACTTCCAAAATTTCC
1 ATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCC-GAACTTCCAAAAATTCC
*
826 ATTTTTGACCCCGAAACTTCCAAAAATTTCATTTTTACCCCGAACTTCCAAAAATTCC
1 ATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATTCC
* * **
884 ATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTATCGTGAACTTCCAAAAATTCC
1 ATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATTCC
* ** ** **
942 ATTTTT-ACCCTCG-AACTTCCAAAATTTCCATTTTTGACCCAAAACTTTAAAAAATTAT
1 ATTTTTGACCC-CGAAACTTCCAAAAATTCCATTTTT-ACCCCGAACTTCCAAAAATTCC
* * * * *
1000 ATTTTTAACCCCAAAACTTCCAAAAATTACATTTTTACCCTCGAACCTCCAAAATTTCC
1 ATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCC-CGAACTTCCAAAAATTCC
* ** * * *
1059 ATTTTTGATCTTGAAACTTTCAAAAATTACCA-TTTTACCCCTGGA-TGTCCAAAAACTCC
1 ATTTTTGACCCCGAAACTTCCAAAAATT-CCATTTTTACCCC-GAACT-TCCAAAAATTCC
* * * * *
1118 ATTTTCGATCTCGAAAC-TCTC-AAAATTACCA-TTTTACCATCGAA-TGCCGAAAAATTCC
1 ATTTTTGACCCCGAAACTTC-CAAAAATT-CCATTTTTACC-CCGAACTTCC-AAAAATTCC
*
1176 ATTTTTAACCCCGAA
1 ATTTTTGACCCCGAA
1191 CTTTCCTAAA
Statistics
Matches: 300, Mismatches: 53, Indels: 24
0.80 0.14 0.06
Matches are distributed among these distances:
57 26 0.09
58 148 0.49
59 124 0.41
60 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (58 bp):
ATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATTCC
Found at i:1110 original size:88 final size:88
Alignment explanation
Indices: 768--1122 Score: 361
Period size: 88 Copynumber: 4.1 Consensus size: 88
758 CGAAGATTAT
* * * * * * *
768 ATTTTTACCC-CTAAACTTCTAAAAATTCCATTTTT-ACCCCTAAAC-TTCCAAAATTTCCATTT
1 ATTTTTACCCTC-GAACTTCCAAAATTTCCATTTTTGA-CTCGAAACTTTCAAAAATTACCATTT
*
830 TTGACCCC-GAAACTTCCAAAAATTTC
64 TT-ACCCCTG-AACTTCCAAAAATTCC
* *
856 ATTTTTACCC-CGAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATT-CCATTTT
1 ATTTTTACCCTCGAACTTCCAAAATTTCCATTTTTGA-CTCGAAACTTTCAAAAATTACCATTTT
* *
919 TA-TCGTGAACTTCCAAAAATTCC
65 TACCCCTGAACTTCCAAAAATTCC
* * * *
942 ATTTTTACCCTCGAACTTCCAAAATTTCCATTTTTGACCCAAAACTTTAAAAAATTA-TATTTTT
1 ATTTTTACCCTCGAACTTCCAAAATTTCCATTTTTGACTCGAAACTTTCAAAAATTACCATTTTT
** *
1006 AACCCCAAAACTTCCAAAAATTAC
66 -ACCCCTGAACTTCCAAAAATTCC
* *
1030 ATTTTTACCCTCGAACCTCCAAAATTTCCATTTTTGATCTTGAAACTTTCAAAAATTACCA-TTT
1 ATTTTTACCCTCGAACTTCCAAAATTTCCATTTTTGA-CTCGAAACTTTCAAAAATTACCATTTT
* *
1094 TACCCCTGGA-TGTCCAAAAACTCC
65 TACCCCTGAACT-TCCAAAAATTCC
1118 ATTTT
1 ATTTT
1123 CGATCTCGAA
Statistics
Matches: 226, Mismatches: 31, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
86 47 0.21
87 50 0.22
88 100 0.44
89 28 0.12
90 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (88 bp):
ATTTTTACCCTCGAACTTCCAAAATTTCCATTTTTGACTCGAAACTTTCAAAAATTACCATTTTT
ACCCCTGAACTTCCAAAAATTCC
Found at i:22671 original size:11 final size:11
Alignment explanation
Indices: 22655--22684 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
22645 GTAAGGCTCC
22655 TAAAAAAAAAA
1 TAAAAAAAAAA
22666 TAAAAAAAAAA
1 TAAAAAAAAAA
22677 -AAAAAAAA
1 TAAAAAAAA
22685 CTTTGATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.42
11 11 0.58
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (11 bp):
TAAAAAAAAAA
Found at i:46877 original size:30 final size:31
Alignment explanation
Indices: 46843--46900 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
46833 ATTGAGTTGA
*
46843 AATCAAA-TTTAATATATACATTTAAACCAC
1 AATCAAAGTTTAATATATACAATTAAACCAC
* *
46873 AATCAAAGTTTCATATGTACAATTAAAC
1 AATCAAAGTTTAATATATACAATTAAAC
46901 AAAATAACGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 7 0.29
31 17 0.71
ACGTcount: A:0.48, C:0.16, G:0.03, T:0.33
Consensus pattern (31 bp):
AATCAAAGTTTAATATATACAATTAAACCAC
Found at i:59520 original size:23 final size:23
Alignment explanation
Indices: 59493--59541 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
59483 CTTAAAATTA
59493 AATATAAACATGGTTGTCTTAGC
1 AATATAAACATGGTTGTCTTAGC
59516 AATATAAACATGGTTGTCTTAGC
1 AATATAAACATGGTTGTCTTAGC
59539 AAT
1 AAT
59542 TTAGGCTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (23 bp):
AATATAAACATGGTTGTCTTAGC
Found at i:70045 original size:18 final size:18
Alignment explanation
Indices: 70022--70063 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
70012 AGGATGTTTT
70022 TTATTT-CTAAAAATAAGA
1 TTATTTACT-AAAATAAGA
* *
70040 TTATTTAGTCAAATAAGA
1 TTATTTACTAAAATAAGA
70058 TTATTT
1 TTATTT
70064 TTTTAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (18 bp):
TTATTTACTAAAATAAGA
Found at i:71525 original size:15 final size:16
Alignment explanation
Indices: 71498--71536 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
71488 TTTTTATATA
71498 TTATTTTTAATAAATT
1 TTATTTTTAATAAATT
*
71514 TTATTTTT-ATAATTT
1 TTATTTTTAATAAATT
71529 TTATTTTT
1 TTATTTTT
71537 TTTTAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTATTTTTAATAAATT
Found at i:71529 original size:14 final size:14
Alignment explanation
Indices: 71487--71536 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
71477 AAGGTTTAAG
*
71487 ATTTTTAT-ATATT
1 ATTTTTATAATTTT
71500 ATTTTTAATAAATTTT
1 ATTTTT-AT-AATTTT
71516 ATTTTTATAATTTTT
1 ATTTTTATAA-TTTT
71531 ATTTTT
1 ATTTTT
71537 TTTTAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 6 0.19
14 4 0.12
15 12 0.38
16 10 0.31
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
ATTTTTATAATTTT
Found at i:71537 original size:16 final size:16
Alignment explanation
Indices: 71498--71547 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
71488 TTTTTATATA
* *
71498 TTATTTTTAATAAATT
1 TTATTTTTTATAATTT
71514 TTA-TTTTTATAATTT
1 TTATTTTTTATAATTT
*
71529 TTATTTTTTTTTAATTT
1 TTA-TTTTTTATAATTT
71546 TT
1 TT
71548 TTGAGACATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.45
16 3 0.10
17 13 0.45
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTATTTTTTATAATTT
Done.