Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001688.1 Kokia drynarioides strain JFW-HI SEQ_113364, 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: 45906
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 7 characters in sequence are not A, C, G, or T
Found at i:11139 original size:36 final size:36
Alignment explanation
Indices: 11089--11223 Score: 198
Period size: 36 Copynumber: 3.8 Consensus size: 36
11079 ATGGTCATGC
* *
11089 TTACTCCTTATTGACCCAAAGGTAATGATGCTCATT
1 TTACTCCCTATTGACCCAAAGGTCATGATGCTCATT
* *
11125 TTACTCCCTGTTGACCCAAAGGTCATTATGCTCATT
1 TTACTCCCTATTGACCCAAAGGTCATGATGCTCATT
* *
11161 TTACTACCTGTTGACCCAAAGGTCATGATGCTCATT
1 TTACTCCCTATTGACCCAAAGGTCATGATGCTCATT
* *
11197 TAAATCCCTATTGACCCAAAGGTCATG
1 TTACTCCCTATTGACCCAAAGGTCATG
11224 CCTATTACCA
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 89 1.00
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (36 bp):
TTACTCCCTATTGACCCAAAGGTCATGATGCTCATT
Found at i:17170 original size:29 final size:29
Alignment explanation
Indices: 17127--17193 Score: 107
Period size: 30 Copynumber: 2.3 Consensus size: 29
17117 AATTATCTAT
*
17127 AATTTTATAATTTTTAAATAATTAAATTAA
1 AATTTTATAATTTTTAAA-AATTAAAGTAA
*
17157 AATTTTATAATTTTTAAAAATTAAAGTAT
1 AATTTTATAATTTTTAAAAATTAAAGTAA
17186 AATTTTAT
1 AATTTTAT
17194 TTTTATTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 17 0.49
30 18 0.51
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (29 bp):
AATTTTATAATTTTTAAAAATTAAAGTAA
Found at i:20105 original size:30 final size:29
Alignment explanation
Indices: 20064--20263 Score: 158
Period size: 30 Copynumber: 6.8 Consensus size: 29
20054 CACAATGAAA
20064 TTTTGGAAAGTTCGGGGG-CTAAATTCAATT
1 TTTTGGAAAGTTCGGGGGTC-AAATTCAA-T
* * *
20094 TTTTGGGAAGTTTGGGGGTCAAATCTGAA-
1 TTTTGGAAAGTTCGGGGGTCAAAT-TCAAT
* *
20123 TTTTGGAAAGTTCAGGGGTCAAATTTAAAT
1 TTTTGGAAAGTTCGGGGGTCAAA-TTCAAT
* * * *
20153 TTTTGGGAAGTTTGAGGGTCAAATGT-GAT
1 TTTTGGAAAGTTCGGGGGTCAAAT-TCAAT
* * * *
20182 GTTTGGAAAGTTC-GAGGACAAGATAT-GAT
1 TTTTGGAAAGTTCGGGGGTCAA-AT-TCAAT
20211 TTTTGGAAAGTTCGGGGGTCAAATTCTAAT
1 TTTTGGAAAGTTCGGGGGTCAAATTC-AAT
* *
20241 TTTTGGAAAGTTCGAGAGTCAAA
1 TTTTGGAAAGTTCGGGGGTCAAA
20264 ATGTAATTTC
Statistics
Matches: 136, Mismatches: 25, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
28 6 0.04
29 56 0.41
30 70 0.51
31 4 0.03
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.34
Consensus pattern (29 bp):
TTTTGGAAAGTTCGGGGGTCAAATTCAAT
Found at i:20127 original size:59 final size:57
Alignment explanation
Indices: 20062--20254 Score: 196
Period size: 59 Copynumber: 3.3 Consensus size: 57
20052 GTCACAATGA
20062 AATTTTGGAAAGTTCGGGGGCTAAATTCAATTTTTTGGGAAGTTTGGGGGTCAAATCTG
1 AATTTTGGAAAGTTCGGGGGCTAAATT-AA-TTTTTGGGAAGTTTGGGGGTCAAATCTG
* * *
20121 AATTTTGGAAAGTTCAGGGG-TCAAATTTAAATTTTTGGGAAGTTTGAGGGTCAAATGTG
1 AATTTTGGAAAGTTCGGGGGCT-AAA-TT-AATTTTTGGGAAGTTTGGGGGTCAAATCTG
* * * * *
20180 -ATGTTTGGAAAGTTCGAGGAC-AAGATATGATTTTTGGAAAGTTCGGGGGTCAAATTCT-
1 AAT-TTTGGAAAGTTCGGGGGCTAA-AT-TAATTTTTGGGAAGTTTGGGGGTCAAA-TCTG
20238 AATTTTTGGAAAGTTCG
1 AA-TTTTGGAAAGTTCG
20255 AGAGTCAAAA
Statistics
Matches: 113, Mismatches: 12, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
58 28 0.25
59 80 0.71
60 5 0.04
ACGTcount: A:0.28, C:0.07, G:0.29, T:0.35
Consensus pattern (57 bp):
AATTTTGGAAAGTTCGGGGGCTAAATTAATTTTTGGGAAGTTTGGGGGTCAAATCTG
Found at i:20271 original size:30 final size:30
Alignment explanation
Indices: 20050--20272 Score: 149
Period size: 30 Copynumber: 7.6 Consensus size: 30
20040 AGGAAAAACG
* *
20050 GGGTCACAATG-AAATTTTGGAAAGTTCG-
1 GGGTCAAAATGTAATTTTTGGAAAGTTCGA
* * * * *
20078 GGGGCTAAAT-TCAATTTTTTGGGAAGTTTGG
1 GGGTCAAAATGT-AA-TTTTTGGAAAGTTCGA
*
20109 GGGTC-AAATCTGAA-TTTTGGAAAGTTC-A
1 GGGTCAAAATGT-AATTTTTGGAAAGTTCGA
* * *
20137 GGGGTC-AAATTTAAATTTTTGGGAAGTTTGA
1 -GGGTCAAAATGT-AATTTTTGGAAAGTTCGA
* *
20168 GGGTC-AAATGTGATGTTTGGAAAGTTCGA
1 GGGTCAAAATGTAATTTTTGGAAAGTTCGA
* * * * *
20197 -GGACAAGATATGATTTTTGGAAAGTTCGG
1 GGGTCAAAATGTAATTTTTGGAAAGTTCGA
* *
20226 GGGTCAAATTCTAATTTTTGGAAAGTTCGA
1 GGGTCAAAATGTAATTTTTGGAAAGTTCGA
*
20256 GAGTCAAAATGTAATTT
1 GGGTCAAAATGTAATTT
20273 CTAAAAAGTT
Statistics
Matches: 151, Mismatches: 34, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
28 10 0.07
29 59 0.39
30 74 0.49
31 8 0.05
ACGTcount: A:0.30, C:0.08, G:0.28, T:0.34
Consensus pattern (30 bp):
GGGTCAAAATGTAATTTTTGGAAAGTTCGA
Found at i:22077 original size:85 final size:85
Alignment explanation
Indices: 21942--22099 Score: 237
Period size: 85 Copynumber: 1.9 Consensus size: 85
21932 GATTTGGTCT
* *
21942 ACTTCTCTGTATCTCATCAAGAAGATGACCGCCTCATTGTTTCAATCCACTTCTCTATATCTCAT
1 ACTTCTCTGTATCTCATCAAGAAAATGACCGCCTCATTGTTTCAACCCACTTCTCTATATCTCAT
22007 CAAGAAGACGAATTTGATTC
66 CAAGAAGACGAATTTGATTC
* * * * *
22027 ACTTCTTTGTATCTCATCAAGAAAATGATCGCTTTATTGCTTT-GACCCACTTCTCTATATCTCA
1 ACTTCTCTGTATCTCATCAAGAAAATGACCGCCTCATTG-TTTCAACCCACTTCTCTATATCTCA
22091 TCAAGAAGA
65 TCAAGAAGA
22100 TGAGGTTTGA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
85 62 0.95
86 3 0.05
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.35
Consensus pattern (85 bp):
ACTTCTCTGTATCTCATCAAGAAAATGACCGCCTCATTGTTTCAACCCACTTCTCTATATCTCAT
CAAGAAGACGAATTTGATTC
Found at i:22225 original size:208 final size:208
Alignment explanation
Indices: 21867--22898 Score: 1197
Period size: 208 Copynumber: 5.0 Consensus size: 208
21857 CTCTTGGTCT
* *
21867 ACTTCTCTGTATCTCAT-AAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCTCTTCAT
1 ACTTCTCTGTATCTCATCAA-GAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCAT
* *
21931 TGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCCTCATTGTTTCAATCCACTTCT
65 TGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTATTTCAATCCACTTCT
* * * * *
21996 CTATATCTCATCA-AGAAGACGAATTTGATTCACTTCTTTGTATCTCATCAAGAAAATGATCGCT
130 CTGTATCTCATCAGA-AAGACGAATTTGGTTCACTTCTCTGTATCTCATCAAGAAAATGACCACT
22060 TTATTGCTTTGACCC
194 TTATTGCTTTGACCC
* *
22075 ACTTCTCTATATCTCATCAAGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCATCGCTTCATT
1 ACTTCTCTGTATCTCATCAAGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATT
* * * * * *
22140 GATTTGGTCTACTTCGCTGTATCTTATCAGGAAGATGGCTGCCTCATTGTTTCAATCCATTTCTC
66 GATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTATTTCAATCCACTTCTC
* * * * * *
22205 TGTATTTCATCAGGAAGACGAATTTGG-TCTACTTCTCTATATCTCATCAGGAAGATGGCCACTT
131 TGTATCTCATCAGAAAGACGAATTTGGTTC-ACTTCTCTGTATCTCATCAAGAAAATGACCACTT
22269 TATTGCTTTGACCC
195 TATTGCTTTGACCC
* * * *
22283 ACTTCTCCGTATATCATCAAGAAGGT-AGGGTTTGAAGTCTCATTCGTATTGAGCTTTGCTTCAT
1 ACTTCTCTGTATCTCATCAAGAAGATGA-GGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCAT
* *
22347 TGATTTGGTCTACTTCTCTGTATCTCATTAGGAAGATGACCACCTCATTATTTCAATCCACTTCT
65 TGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTATTTCAATCCACTTCT
* * * * * * *
22412 TTGTAGCTCATCAGAAAGATGGATTTGGTCCACTTCTTTGTATCTCATC-AGAAAGATGACCGCT
130 CTGTATCTCATCAGAAAGACGAATTTGGTTCACTTCTCTGTATCTCATCAAGAAA-ATGACCACT
*
22476 TTATTGCTTTGACTC
194 TTATTGCTTTGACCC
*
22491 ACTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATT
1 ACTTCTCTGTATCTCATCAAGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATT
* * * *
22556 GAATTGGTCTACTTCTCTGTATCTCATCAGGAATATGACCG--TACATTATTTTAATTCACTTCT
66 GATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCT-CATTATTTCAATCCACTTCT
* * * * * ** * * *
22619 TTGTATCTCAACAGAAAGACGGATTTGGTTCACTTCTCTGCATATTGTCAGGAAGATGATCACTT
130 CTGTATCTCATCAGAAAGACGAATTTGGTTCACTTCTCTGTATCTCATCAAGAAAATGACCACTT
*
22684 TATTGCTTCGACCC
195 TATTGCTTTGACCC
* * * * * *
22698 ACTTCTCTATATCTCACCAAGAAGATGGGGTTTGAAGTCTCATTCGTGTTAAGCTTCACTTCATA
1 ACTTCTCTGTATCTCATCAAGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCAT-
* * * * * * * * * *
22763 T-ATTT-G-ATA-TACTCTATATCTCATTAGAAAGATGATCGCTTCATTGTTTTAATTCACTTCT
65 TGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTATTTCAATCCACTTCT
* * * * ** * * *
22824 CTATATCTTATCA-AGAAGATGGATTTGGTTCACTTCTCTACATCTTATCAGGAAGATGACCACT
130 CTGTATCTCATCAGA-AAGACGAATTTGGTTCACTTCTCTGTATCTCATCAAGAAAATGACCACT
*
22888 TTATTACTTTG
194 TTATTGCTTTG
22899 GATGACTGGA
Statistics
Matches: 709, Mismatches: 102, Indels: 29
0.84 0.12 0.03
Matches are distributed among these distances:
204 24 0.03
205 83 0.12
206 3 0.00
207 144 0.20
208 451 0.64
209 4 0.01
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (208 bp):
ACTTCTCTGTATCTCATCAAGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATT
GATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTATTTCAATCCACTTCTC
TGTATCTCATCAGAAAGACGAATTTGGTTCACTTCTCTGTATCTCATCAAGAAAATGACCACTTT
ATTGCTTTGACCC
Found at i:22289 original size:85 final size:85
Alignment explanation
Indices: 22141--22306 Score: 199
Period size: 85 Copynumber: 2.0 Consensus size: 85
22131 CGCTTCATTG
* * ** * * *
22141 ATTTGGTCTACTTCGCTGTATCTTATCAGGAAGATGGCTGCCTCATTGTTTCAATCCATTTCTCT
1 ATTTGGTCTACTTCGCTATATCTCATCAGGAAGATGGCCACCTCATTGTTTCAACCCACTTCTCC
* *
22206 GTATTTCATCAGGAAGACGA
66 GTATATCATCAAGAAGACGA
* * * *
22226 ATTTGGTCTACTTCTCTATATCTCATCAGGAAGATGGCCACTTTATTGCTTT-GACCCACTTCTC
1 ATTTGGTCTACTTCGCTATATCTCATCAGGAAGATGGCCACCTCATTG-TTTCAACCCACTTCTC
22290 CGTATATCATCAAGAAG
65 CGTATATCATCAAGAAG
22307 GTAGGGTTTG
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
85 64 0.96
86 3 0.04
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (85 bp):
ATTTGGTCTACTTCGCTATATCTCATCAGGAAGATGGCCACCTCATTGTTTCAACCCACTTCTCC
GTATATCATCAAGAAGACGA
Found at i:22494 original size:85 final size:85
Alignment explanation
Indices: 22348--22517 Score: 207
Period size: 85 Copynumber: 2.0 Consensus size: 85
22338 TTGCTTCATT
* * * *
22348 GATTTGGTCTACTTCTCTGTATCTCATTAGGAAGATGACCACCTCATTATTTCAATCCACTTCTT
1 GATTTGGTCCACTTCTCTGTATCTCATCAGAAAGATGACCACCTCATTATTTCAATCCACTTCTC
22413 TGTAGCTCATCAGAAAGATG
66 TGTAGCTCATCAGAAAGATG
* * * * * * *
22433 GATTTGGTCCACTTCTTTGTATCTCATCAGAAAGATGACCGCTTTATTGCTTTGACT-CACTTCT
1 GATTTGGTCCACTTCTCTGTATCTCATCAGAAAGATGACCACCTCATT-ATTTCAATCCACTTCT
* *
22497 CTGTATCTCATCAGGAAGATG
65 CTGTAGCTCATCAGAAAGATG
22518 AGGTTTGAAG
Statistics
Matches: 71, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
85 66 0.93
86 5 0.07
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.37
Consensus pattern (85 bp):
GATTTGGTCCACTTCTCTGTATCTCATCAGAAAGATGACCACCTCATTATTTCAATCCACTTCTC
TGTAGCTCATCAGAAAGATG
Found at i:22999 original size:39 final size:39
Alignment explanation
Indices: 22896--23180 Score: 284
Period size: 42 Copynumber: 7.1 Consensus size: 39
22886 CTTTATTACT
* *
22896 TTGGATGACTGGAATTTGCCCCATGATCGAGGTAAGAGA
1 TTGGATGACTGCAATTTGCCCCATGATCGGGGTAAGAGA
* * * *
22935 TTAGATGATGGCTGTAATTTGCCCCATGATTGGGTTAAGAGA
1 TT-G--GATGACTGCAATTTGCCCCATGATCGGGGTAAGAGA
* * * *
22977 TTGGATGGCTGCAATCTACCCCATGATCGGGGTAAAAGA
1 TTGGATGACTGCAATTTGCCCCATGATCGGGGTAAGAGA
* *
23016 TCGGATGACTGCAATCTGCCCCATGATCGGGGTAAGAGA
1 TTGGATGACTGCAATTTGCCCCATGATCGGGGTAAGAGA
** * *
23055 TTGGATAATGACTATAATTTGCCCCATGATTGGGCTAAGAGA
1 TTGG---ATGACTGCAATTTGCCCCATGATCGGGGTAAGAGA
*
23097 TTGGATAATGACTGCAATTTGCCCCATGATCGGGGTAAGATA
1 TTGG---ATGACTGCAATTTGCCCCATGATCGGGGTAAGAGA
* * * * *
23139 TTAGATG-CTTCAATCTGCCCCGTGATCGGGGTAAGATA
1 TTGGATGACTGCAATTTGCCCCATGATCGGGGTAAGAGA
23177 TTGG
1 TTGG
23181 TGCCTTCAAT
Statistics
Matches: 209, Mismatches: 31, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
38 31 0.15
39 73 0.35
40 1 0.00
41 1 0.00
42 103 0.49
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (39 bp):
TTGGATGACTGCAATTTGCCCCATGATCGGGGTAAGAGA
Found at i:31298 original size:30 final size:30
Alignment explanation
Indices: 31198--31387 Score: 126
Period size: 29 Copynumber: 6.4 Consensus size: 30
31188 AAAAATGAAA
* * *
31198 TTTTGGAAAGTTCG-GGGGCTAAATTCAAAT
1 TTTTGGAAAGTTCGAGGGTC-AAAATCTAAT
* *
31228 TTTT-GAGAAGTTTTG-GCGTC-AAATCTGAA-
1 TTTTGGA-AAG-TTCGAGGGTCAAAATCT-AAT
* * * *
31257 TTTTGGGAAGTTCAAGGGTCAAAATGTGAT
1 TTTTGGAAAGTTCGAGGGTCAAAATCTAAT
* * *
31287 TTTTGGAAAGTTCGA-GGACAAAATGTTAT
1 TTTTGGAAAGTTCGAGGGTCAAAATCTAAT
*
31316 TTTTGGAAAGTTCGA-GGTC-AAATCCAAAT
1 TTTTGGAAAGTTCGAGGGTCAAAAT-CTAAT
* *
31345 TTTTGGAAAGTTTGAGGGTCAAAATATAAT
1 TTTTGGAAAGTTCGAGGGTCAAAATCTAAT
* *
31375 TTATAGAAAGTTC
1 TTTTGGAAAGTTC
31388 AAGGACCTCT
Statistics
Matches: 125, Mismatches: 25, Indels: 20
0.74 0.15 0.12
Matches are distributed among these distances:
28 6 0.05
29 64 0.51
30 45 0.36
31 10 0.08
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.35
Consensus pattern (30 bp):
TTTTGGAAAGTTCGAGGGTCAAAATCTAAT
Found at i:33264 original size:16 final size:16
Alignment explanation
Indices: 33243--33273 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33233 AATCATATAA
33243 TCAATCAATTTAGCAT
1 TCAATCAATTTAGCAT
*
33259 TCAATCATTTTAGCA
1 TCAATCAATTTAGCA
33274 ACAATCTTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.39
Consensus pattern (16 bp):
TCAATCAATTTAGCAT
Found at i:37157 original size:26 final size:26
Alignment explanation
Indices: 37126--37175 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
37116 ATATAAACCA
*
37126 TTTCATACTCTTTATAAACTTTTTTT
1 TTTCATACTCTTTATAAACATTTTTT
*
37152 TTTCATATTCTTTATAAACATTTT
1 TTTCATACTCTTTATAAACATTTT
37176 AAGAGAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (26 bp):
TTTCATACTCTTTATAAACATTTTTT
Done.