Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002459.1 Kokia drynarioides strain JFW-HI SEQ_114580, 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: 37536
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Found at i:968 original size:30 final size:29
Alignment explanation
Indices: 847--1094 Score: 122
Period size: 30 Copynumber: 8.5 Consensus size: 29
837 TAAAATGTCT
*
847 AAAAATTACATTTTT-ACTCCTAAACTTTCC
1 AAAAATTACATTTTTGAC-CCGAAAC-TTCC
* * *
877 -AAAATTATATTTTTTGACCTCG-AGCTTTC
1 AAAAATTACA-TTTTTGACC-CGAAACTTCC
* *
906 AAAAATTACATTTAT-ACCTCG-GACTTCC
1 AAAAATTACATTTTTGACC-CGAAACTTCC
* *
934 AAAAATTCCATTTTTGATCCCGAAACTTTC
1 AAAAATTACATTTTTGA-CCCGAAACTTCC
* *
964 AAAAATTACATTTTT-ACCTTCG-GACCTCC
1 AAAAATTACATTTTTGACC--CGAAACTTCC
* * **
993 AAAAATTCCATTTTTTGACCCCAAAACTTTT
1 AAAAATTACA-TTTTTGA-CCCGAAACTTCC
*
1024 AAAAATTACATTTTT-ACCCCTAAAACTT--
1 AAAAATTACATTTTTGA-CCC-GAAACTTCC
* * * **
1052 AAAAACTCCA-TTTTGACCCCAATTTTCC
1 AAAAATTACATTTTTGACCCGAAACTTCC
1080 AAAAATTAACATTTT
1 AAAAATT-ACATTTT
1095 ACCCTCGAAT
Statistics
Matches: 168, Mismatches: 31, Indels: 38
0.71 0.13 0.16
Matches are distributed among these distances:
26 4 0.02
27 7 0.04
28 40 0.24
29 39 0.23
30 60 0.36
31 16 0.10
32 2 0.01
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.37
Consensus pattern (29 bp):
AAAAATTACATTTTTGACCCGAAACTTCC
Found at i:995 original size:29 final size:28
Alignment explanation
Indices: 847--1007 Score: 114
Period size: 29 Copynumber: 5.5 Consensus size: 28
837 TAAAATGTCT
**
847 AAAAATTACATTTTTA-CTCCTAAACTTTCC
1 AAAAATTACATTTTTACCT-C-GGAC-TTCC
* *
877 -AAAATTATATTTTTTGACCTC-GAGCTTTC
1 AAAAATTACA-TTTTT-ACCTCGGA-CTTCC
*
906 AAAAATTACATTTATACCTCGGACTTCC
1 AAAAATTACATTTTTACCTCGGACTTCC
* * *
934 AAAAATTCCATTTTTGATCC-CGAAACTTTC
1 AAAAATTACATTTTT-A-CCTCG-GACTTCC
*
964 AAAAATTACATTTTTACCTTCGGACCTCC
1 AAAAATTACATTTTTACC-TCGGACTTCC
*
993 AAAAATTCCATTTTT
1 AAAAATTACATTTTT
1008 TGACCCCAAA
Statistics
Matches: 105, Mismatches: 15, Indels: 23
0.73 0.10 0.16
Matches are distributed among these distances:
28 24 0.23
29 40 0.38
30 37 0.35
31 2 0.02
32 2 0.02
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.39
Consensus pattern (28 bp):
AAAAATTACATTTTTACCTCGGACTTCC
Found at i:1006 original size:59 final size:59
Alignment explanation
Indices: 901--1041 Score: 221
Period size: 60 Copynumber: 2.4 Consensus size: 59
891 TGACCTCGAG
* * * *
901 CTTTCAAAAATTACATTTATACCTCGGACTTCCAAAAATTCCA-TTTTTGATCCCGAAA
1 CTTTCAAAAATTACATTTTTACCTCGGACCTCCAAAAATTCCATTTTTTGACCCCAAAA
959 CTTTCAAAAATTACATTTTTACCTTCGGACCTCCAAAAATTCCATTTTTTGACCCCAAAA
1 CTTTCAAAAATTACATTTTTACC-TCGGACCTCCAAAAATTCCATTTTTTGACCCCAAAA
*
1019 CTTTTAAAAATTACATTTTTACC
1 CTTTCAAAAATTACATTTTTACC
1042 CCTAAAACTT
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
58 22 0.29
59 19 0.25
60 35 0.46
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (59 bp):
CTTTCAAAAATTACATTTTTACCTCGGACCTCCAAAAATTCCATTTTTTGACCCCAAAA
Found at i:1056 original size:59 final size:57
Alignment explanation
Indices: 847--1099 Score: 187
Period size: 60 Copynumber: 4.4 Consensus size: 57
837 TAAAATGTCT
* ** * * *
847 AAAAATTACATTTTTACTCCTAAACTTTCCAAAATTATATTTTTTGACCTC-GAGCTTTC
1 AAAAATTACATTTTTAC-CCTAAAC-TTCAAAAATTCCA-TTTTTGACCCCAAAACTTTC
* ** * *
906 AAAAATTACATTTATA-CCTCGGACTTCCAAAAATTCCATTTTTGATCCCGAAACTTTC
1 AAAAATTACATTTTTACCCT-AAACTT-CAAAAATTCCATTTTTGACCCCAAAACTTTC
** * * *
964 AAAAATTACATTTTTACCTTCGGACCTCCAAAAATTCCATTTTTTGACCCCAAAACTTTT
1 AAAAATTACATTTTTACC--CTAAACTTCAAAAATTCCA-TTTTTGACCCCAAAACTTTC
* *
1024 AAAAATTACATTTTTACCCCTAAAACTT-AAAAACTCCA-TTTTGACCCC--AATTTTCC
1 AAAAATTACATTTTTA-CCCT-AAACTTCAAAAATTCCATTTTTGACCCCAAAACTTT-C
1080 AAAAATTAACA-TTTTACCCT
1 AAAAATT-ACATTTTTACCCT
1100 CGAATTTCTA
Statistics
Matches: 158, Mismatches: 25, Indels: 26
0.76 0.12 0.12
Matches are distributed among these distances:
55 9 0.06
56 12 0.08
57 27 0.17
58 31 0.20
59 37 0.23
60 39 0.25
61 3 0.02
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (57 bp):
AAAAATTACATTTTTACCCTAAACTTCAAAAATTCCATTTTTGACCCCAAAACTTTC
Found at i:1094 original size:29 final size:29
Alignment explanation
Indices: 1060--1153 Score: 79
Period size: 29 Copynumber: 3.2 Consensus size: 29
1050 TTAAAAACTC
1060 CATTTTGACCC-CAATTTTCCAAAAATTAA
1 CATTTTGACCCACAATTTTCCAAAAATT-A
* *
1089 CATTTT-ACCCTCGAA-TTTCTAAAAATCT-
1 CATTTTGACCCAC-AATTTTCCAAAAAT-TA
* * *
1117 CATTTTAACCCAAAATTTTCCCAAAATTA
1 CATTTTGACCCACAATTTTCCAAAAATTA
1146 CCATTTTG
1 -CATTTTG
1154 CCCCCGAGAG
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
28 13 0.25
29 30 0.58
30 9 0.17
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.37
Consensus pattern (29 bp):
CATTTTGACCCACAATTTTCCAAAAATTA
Found at i:1226 original size:28 final size:28
Alignment explanation
Indices: 1137--1211 Score: 123
Period size: 28 Copynumber: 2.7 Consensus size: 28
1127 CAAAATTTTC
1137 CCAAAATTACCATTTTGCCCCCGAGAGT
1 CCAAAATTACCATTTTGCCCCCGAGAGT
* *
1165 CCAAAATTACCATTTTACCCCCAAGAGT
1 CCAAAATTACCATTTTGCCCCCGAGAGT
*
1193 CCAAAATTATCATTTTGCC
1 CCAAAATTACCATTTTGCC
1212 TCCGGGTATC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.32, C:0.31, G:0.09, T:0.28
Consensus pattern (28 bp):
CCAAAATTACCATTTTGCCCCCGAGAGT
Found at i:2097 original size:2 final size:2
Alignment explanation
Indices: 2092--2116 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2082 ATATATACAT
2092 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
2117 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3968 original size:12 final size:12
Alignment explanation
Indices: 3953--3977 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3943 ATATTCATTC
3953 ACATACATATAT
1 ACATACATATAT
3965 ACATACATATAT
1 ACATACATATAT
3977 A
1 A
3978 TATAATTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
ACATACATATAT
Found at i:9100 original size:89 final size:89
Alignment explanation
Indices: 8993--9172 Score: 306
Period size: 89 Copynumber: 2.0 Consensus size: 89
8983 AAGAATGGAT
*
8993 TACAAGCCCTACGATGGCTGAGATTTATGCTTGATTTGCATATTCTCGTCAGCTTAGTGTGAGCA
1 TACAAGCCCTACGATGGCTGAGATTTATGCTTGATATGCATATTCTCGTCAGCTTAGTGTGAGCA
*
9058 ACATCGTTAGGGAACAATTATATG
66 ACATCATTAGGGAACAATTATATG
* *
9082 TACAGGCCCTACGATGGCTGATATTTATGCTTGATATGCATATTCTCGTCAGCTTAGTGTGAGCA
1 TACAAGCCCTACGATGGCTGAGATTTATGCTTGATATGCATATTCTCGTCAGCTTAGTGTGAGCA
**
9147 ACATCATTAGGGAACTGTTATATG
66 ACATCATTAGGGAACAATTATATG
9171 TA
1 TA
9173 TAGATACCGT
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
89 85 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (89 bp):
TACAAGCCCTACGATGGCTGAGATTTATGCTTGATATGCATATTCTCGTCAGCTTAGTGTGAGCA
ACATCATTAGGGAACAATTATATG
Found at i:12978 original size:15 final size:16
Alignment explanation
Indices: 12943--12980 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
12933 TAGAAAAATG
12943 CCGCCACCAGGATGGGGA
1 CCGCCACCAGGA--GGGA
12961 CCGCCACCAGGA-GGA
1 CCGCCACCAGGAGGGA
12976 CCGCC
1 CCGCC
12981 GGGGCCTCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.40
18 12 0.60
ACGTcount: A:0.21, C:0.42, G:0.34, T:0.03
Consensus pattern (16 bp):
CCGCCACCAGGAGGGA
Found at i:14220 original size:18 final size:18
Alignment explanation
Indices: 14197--14234 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
14187 GACCAATATG
*
14197 TTATTTGCA-TTATTCGAA
1 TTATTTG-AGTTATTCAAA
14215 TTATTTGAGTTATTCAAA
1 TTATTTGAGTTATTCAAA
14233 TT
1 TT
14235 GTAAACTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.29, C:0.08, G:0.11, T:0.53
Consensus pattern (18 bp):
TTATTTGAGTTATTCAAA
Found at i:20338 original size:12 final size:12
Alignment explanation
Indices: 20316--20425 Score: 55
Period size: 12 Copynumber: 8.9 Consensus size: 12
20306 ATAACATCCA
*
20316 AACAACCAAAAT
1 AACAACAAAAAT
*
20328 AACAACAAAAAC
1 AACAACAAAAAT
*
20340 AGCAGA-AAAAAT
1 AACA-ACAAAAAT
* *
20352 AACAGCAAAAAAAAA
1 -A-A-CAACAAAAAT
20367 AAGCAACAAAAAT
1 AA-CAACAAAAAT
* *
20380 AACAGCAAAAAC
1 AACAACAAAAAT
**
20392 AGTATA-AAAAAT
1 AACA-ACAAAAAT
*
20404 AGCAACAAAAAT
1 AACAACAAAAAT
20416 AACAA-AAAAA
1 AACAACAAAAA
20426 GCACCAAAAC
Statistics
Matches: 75, Mismatches: 16, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
11 6 0.08
12 46 0.61
13 14 0.19
14 2 0.03
15 7 0.09
ACGTcount: A:0.72, C:0.15, G:0.06, T:0.06
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:20354 original size:24 final size:23
Alignment explanation
Indices: 20323--20425 Score: 80
Period size: 24 Copynumber: 4.2 Consensus size: 23
20313 CCAAACAACC
20323 AAAATAACAACAAAAACAGCAGAA
1 AAAATAACAACAAAAACAGCA-AA
* *
20347 AAAATAACAGCAAAAAAAAAAAGCAACA
1 AAAAT-A-A-C-AACAAAAACAGCAA-A
* *
20375 AAAATAACAGCAAAAACAGTATAA
1 AAAATAACAACAAAAACAGCA-AA
* * *
20399 AAAATAGCAACAAAAATAACAAA
1 AAAATAACAACAAAAACAGCAAA
20422 AAAA
1 AAAA
20426 GCACCAAAAC
Statistics
Matches: 62, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
23 6 0.10
24 31 0.50
25 3 0.05
26 2 0.03
27 3 0.05
28 17 0.27
ACGTcount: A:0.73, C:0.14, G:0.07, T:0.07
Consensus pattern (23 bp):
AAAATAACAACAAAAACAGCAAA
Found at i:20357 original size:15 final size:14
Alignment explanation
Indices: 20337--20390 Score: 74
Period size: 14 Copynumber: 3.8 Consensus size: 14
20327 TAACAACAAA
20337 AACAGCAGAAAAAAT
1 AACAGCA-AAAAAAT
20352 AACAGCAAAAAAA-
1 AACAGCAAAAAAAT
*
20365 AAAAGCAACAAAAAT
1 AACAGCAA-AAAAAT
20380 AACAGCAAAAA
1 AACAGCAAAAA
20391 CAGTATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
13 7 0.20
14 14 0.40
15 14 0.40
ACGTcount: A:0.72, C:0.15, G:0.09, T:0.04
Consensus pattern (14 bp):
AACAGCAAAAAAAT
Found at i:20444 original size:19 final size:19
Alignment explanation
Indices: 20420--20497 Score: 74
Period size: 19 Copynumber: 4.1 Consensus size: 19
20410 AAAAATAACA
20420 AAAAAAGCACCAAAACAAT
1 AAAAAAGCACCAAAACAAT
*
20439 AAAAAATCA--AAACAGCAA-
1 AAAAAAGCACCAAA-A-CAAT
*
20457 AAAACAA-CAACTAAAACAAT
1 AAAA-AAGC-ACCAAAACAAT
20477 AAAAAAGCACCAAAACAAT
1 AAAAAAGCACCAAAACAAT
20496 AA
1 AA
20498 TATAATTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
17 3 0.06
18 6 0.12
19 31 0.63
20 6 0.12
21 3 0.06
ACGTcount: A:0.71, C:0.19, G:0.04, T:0.06
Consensus pattern (19 bp):
AAAAAAGCACCAAAACAAT
Found at i:26683 original size:36 final size:36
Alignment explanation
Indices: 26636--26715 Score: 160
Period size: 36 Copynumber: 2.2 Consensus size: 36
26626 CTTTAGACAA
26636 CCCCTTCCTAAGCCCGTAGCCACCAACCTTAGCCTT
1 CCCCTTCCTAAGCCCGTAGCCACCAACCTTAGCCTT
26672 CCCCTTCCTAAGCCCGTAGCCACCAACCTTAGCCTT
1 CCCCTTCCTAAGCCCGTAGCCACCAACCTTAGCCTT
26708 CCCCTTCC
1 CCCCTTCC
26716 CCTTCCCTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.17, C:0.50, G:0.10, T:0.23
Consensus pattern (36 bp):
CCCCTTCCTAAGCCCGTAGCCACCAACCTTAGCCTT
Done.