Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013797.1 Kokia drynarioides strain JFW-HI SEQ_128825, 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: 16391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:8708 original size:118 final size:117
Alignment explanation
Indices: 8494--9298 Score: 567
Period size: 119 Copynumber: 6.8 Consensus size: 117
8484 ACAGAAAAAA
* * * * * * **
8494 TTTTGGTGTTGACCAT-TGCATGACCGACACCTCCTTTTAATATGATAAAAAATCAAATTTTTGA
1 TTTTTGTGTTGGCCATGT-CATGGCCGACACC-CCTTTTTATTTGATAAAAAATCAATTTTTTTT
* * *
8558 GTGTTGGCCATGCAATGGCCGACACCCTCTTTTTGTCAAATAAAAAATTTAATTT
64 GTGTTGGCCATGCAATAGCCGACACCC-CTTTTTATCAAATAAAAAATTCAATTT
* * *
8613 TTTTTGTGTTAGCCATGTCATGGTCGACACCCCTGTTTATTTGATAAAAAATCAATTTTTTTTGT
1 TTTTTGTGTTGGCCATGTCATGGCCGACACCCCTTTTTATTTGATAAAAAATCAATTTTTTTTGT
* **
8678 GTTGGCCATGCAATAACTAACACCTCCTTTTT-TCAAATAAAAAAATTTCGAA-TT
66 GTTGGCCATGCAATAGCCGACACC-CCTTTTTATCAAAT-AAAAAA-TTC-AATTT
* * ** ** **
8732 TTTTTGTGTTGGCCAT-TGCATGACTGACACTTCTTTTTATCTAAATAAAAAATCAATTTTTTGG
1 TTTTTGTGTTGGCCATGT-CATGGCCGACACCCCTTTTTAT-TTGATAAAAAATCAATTTTTTTT
* * * * * *
8796 GTATTGGTCATGCCATGGCCAACACCCCATTTTTGTCAAAT-AAAAATTCGAATTT
64 GTGTTGGCCATGCAATAGCCGACACCCC-TTTTTATCAAATAAAAAATTC-AATTT
* * * *
8851 TTTTTATGTTGGTCATGTCATGGCCGACA-CTCTTATTTATCTGATAAAAAAATCAA-TTTTTTT
1 TTTTTGTGTTGGCCATGTCATGGCCGACACCCCTT-TTTATTTGAT-AAAAAATCAATTTTTTTT
* * *
8914 GTGTTGGCCATGCAATGGTCGACACCCCTTTTTATCTAAATAAAAAA-TCAAATT
64 GTGTTGGCCATGCAATAGCCGACACCCCTTTTTATC-AAATAAAAAATTCAATTT
** * * * *
8968 TTTGGGTGTTGGTCATGCCATGACCGACACCCCTTTTTAGTTAGATAAAAAATTCGAATTTTTTT
1 TTTTTGTGTTGGCCATGTCATGGCCGACACCCCTTTTTA-TTTGATAAAAAA-TC-AATTTTTTT
* * * ** *
9033 TATGTTGGCCATGCCATAGCCGACACCCCTATTTATCTGATAAAAAAAATCAATTT
63 TGTGTTGGCCATGCAATAGCCGACACCCCTTTTTATCAAAT-AAAAAATTCAATTT
* * * ** *
9089 TTTTTGTGTTGGCCATG-CAATAGCTGACACCTCTTTTT-TCAGATAAAAAAATTTCAAATTTTT
1 TTTTTGTGTTGGCCATGTC-ATGGCCGACACCCCTTTTTATTTGAT-AAAAAA--TCAATTTTTT
* * ** * * * * *
9152 TTGTGTTGGTCATTGC-ATGGCTTATACTCTTTTTTATCTGAATAAAAAA-TCAA-AT
62 TTGTGTTGGCCA-TGCAATAGCCGACACCCCTTTTTATC-AAATAAAAAATTCAATTT
* * ** * * ***
9207 TTTTGGATGTTGGCCATGCCATGTTCTACACCCTCTTTTTGTCAAATAAAAAATTCGAA-TTTTT
1 TTTTTG-TGTTGGCCATGTCATGGCCGACACCC-CTTTTTATTTGATAAAAAA-TC-AATTTTTT
* * *
9271 TTGTGTTGGCAATGAAATGGCCGACACC
62 TTGTGTTGGCCATGCAATAGCCGACACC
9299 AACTTTCTCT
Statistics
Matches: 551, Mismatches: 102, Indels: 66
0.77 0.14 0.09
Matches are distributed among these distances:
117 51 0.09
118 125 0.23
119 169 0.31
120 152 0.28
121 54 0.10
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.39
Consensus pattern (117 bp):
TTTTTGTGTTGGCCATGTCATGGCCGACACCCCTTTTTATTTGATAAAAAATCAATTTTTTTTGT
GTTGGCCATGCAATAGCCGACACCCCTTTTTATCAAATAAAAAATTCAATTT
Found at i:8745 original size:61 final size:58
Alignment explanation
Indices: 8494--9298 Score: 560
Period size: 59 Copynumber: 13.5 Consensus size: 58
8484 ACAGAAAAAA
* * * * *
8494 TTTTGGTGTTGACCATTGC-ATGACCGACACCTCCTTTTAAT-ATGATAAAAAA-TCAAATT
1 TTTTTGTGTTGGCCA-TGCAATGGCCGACACC-CCTTTTTATCA-AATAAAAAATTC-AATT
** * *
8553 TTTGAGTGTTGGCCATGCAATGGCCGACACCCTCTTTTTGTCAAATAAAAAATTTAATTT
1 TTTTTGTGTTGGCCATGCAATGGCCGACACCC-CTTTTTATCAAATAAAAAATTCAA-TT
* * * ***
8613 TTTTTGTGTTAGCCATGTC-ATGGTCGACACCCCTGTTTATTTGATAAAAAA-TCAATTT
1 TTTTTGTGTTGGCCATG-CAATGGCCGACACCCCTTTTTATCAAATAAAAAATTCAA-TT
** **
8671 TTTTTGTGTTGGCCATGCAATAACTAACACCTCCTTTTT-TCAAATAAAAAAATTTCGAATT
1 TTTTTGTGTTGGCCATGCAATGGCCGACACC-CCTTTTTATCAAAT-AAAAAA-TTC-AATT
* * **
8732 TTTTTGTGTTGGCCATTGC-ATGACTGACACTTCTTTTTATCTAAATAAAAAA-TCAATT
1 TTTTTGTGTTGGCCA-TGCAATGGCCGACACCCCTTTTTATC-AAATAAAAAATTCAATT
* * * * * *
8790 TTTTGGGTATTGGTCATGCCATGGCCAACACCCCATTTTTGTCAAAT-AAAAATTCGAATTT
1 TTTT-TGTGTTGGCCATGCAATGGCCGACACCCC-TTTTTATCAAATAAAAAATTC-AA-TT
* * * ** *
8851 TTTTTATGTTGGTCATGTC-ATGGCCGACA-CTCTTATTTATCTGATAAAAAAATCAATT
1 TTTTTGTGTTGGCCATG-CAATGGCCGACACCCCTT-TTTATCAAATAAAAAATTCAATT
*
8909 TTTTTGTGTTGGCCATGCAATGGTCGACACCCCTTTTTATCTAAATAAAAAA-TCAAATT
1 TTTTTGTGTTGGCCATGCAATGGCCGACACCCCTTTTTATC-AAATAAAAAATTC-AATT
** * * * * *
8968 TTTGGGTGTTGGTCATGCCATGACCGACACCCCTTTTTAGTTAGATAAAAAATTCGAATTT
1 TTTTTGTGTTGGCCATGCAATGGCCGACACCCCTTTTTA-TCAAATAAAAAATTC-AA-TT
* * * * ** *
9029 TTTTTATGTTGGCCATGCCATAGCCGACACCCCTATTTATCTGATAAAAAAAATCAATTT
1 TTTTTGTGTTGGCCATGCAATGGCCGACACCCCTTTTTATCAAAT-AAAAAATTCAA-TT
* * * *
9089 TTTTTGTGTTGGCCATGCAATAGCTGACACCTCTTTTT-TCAGATAAAAAAATTTCAAATT
1 TTTTTGTGTTGGCCATGCAATGGCCGACACCCCTTTTTATCAAAT-AAAAAA-TTC-AATT
* ** * * * * *
9149 TTTTTGTGTTGGTCATTGC-ATGGCTTATACTCTTTTTTATCTGAATAAAAAA-TCAAAT
1 TTTTTGTGTTGGCCA-TGCAATGGCCGACACCCCTTTTTATC-AAATAAAAAATTCAATT
* * ** * *
9207 TTTTGGATGTTGGCCATGCCATGTTCTACACCCTCTTTTTGTCAAATAAAAAATTCGAATT
1 TTTTTG-TGTTGGCCATGCAATGGCCGACACCC-CTTTTTATCAAATAAAAAATTC-AATT
* *
9268 TTTTTGTGTTGGCAATGAAATGGCCGACACC
1 TTTTTGTGTTGGCCATGCAATGGCCGACACC
9299 AACTTTCTCT
Statistics
Matches: 594, Mismatches: 110, Indels: 83
0.75 0.14 0.11
Matches are distributed among these distances:
57 2 0.00
58 99 0.17
59 198 0.33
60 177 0.30
61 107 0.18
62 11 0.02
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.39
Consensus pattern (58 bp):
TTTTTGTGTTGGCCATGCAATGGCCGACACCCCTTTTTATCAAATAAAAAATTCAATT
Found at i:8924 original size:238 final size:233
Alignment explanation
Indices: 8494--9298 Score: 735
Period size: 238 Copynumber: 3.4 Consensus size: 233
8484 ACAGAAAAAA
* * * *
8494 TTTTGGTGTTGACCATTGCATGACCGACACCTCCTTTTAATATGATAAAAAATCAAATTTTTGAG
1 TTTTGGTGTTGGCCATTGCATGACCGACACCTCTTTTTATTA-GATAAAAAATCAATTTTTTGAG
* *
8559 TGTTGGCCATGCAATGGCCGACACCCTC-TTTTTGTCAAATAAAAAATTTAATTTTTTTTGTGTT
65 TGTTGGCCATGCCATGGCCGACACCC-CATTTTTGTCAAAT-AAAAATTCAATTTTTTTTGTGTT
* * * * *
8623 AGCCATGTCATGGTCGACACCCCTGTTTATTTGAT-AAAAAATCAATTTTTTTTGTGTTGGCCAT
128 GGCCATGTCATGGCCGACA-CTCTTTTTATCTGATAAAAAAATCAA-TTTTTTTGTGTTGGCCAT
*
8687 GCAATAACT-AACACCTCCTTTTT-TC-AAATAAAAAAATTTCGAATT
191 GCAAT-ACTCAACACC-CCTTTTTATCTAAAT-AAAAAA--TCAAATT
* * * * *
8732 TTTTTGTGTTGGCCATTGCATGACTGACACTTCTTTTTATCTAAATAAAAAATCAATTTTTTGGG
1 TTTTGGTGTTGGCCATTGCATGACCGACACCTCTTTTTAT-TAGATAAAAAATCAATTTTTTGAG
* * * *
8797 TATTGGTCATGCCATGGCCAACACCCCATTTTTGTCAAATAAAAATTCGAATTTTTTTTATGTTG
65 TGTTGGCCATGCCATGGCCGACACCCCATTTTTGTCAAATAAAAATTC-AATTTTTTTTGTGTTG
*
8862 GTCATGTCATGGCCGACACTCTTATTTATCTGATAAAAAAATCAATTTTTTTGTGTTGGCCATGC
129 GCCATGTCATGGCCGACACTCTT-TTTATCTGATAAAAAAATCAATTTTTTTGTGTTGGCCATGC
** *
8927 AATGGTCGACACCCCTTTTTATCTAAATAAAAAATCAAATT
193 AATACTCAACACCCCTTTTTATCTAAATAAAAAATCAAATT
* * *
8968 TTTGGGTGTTGGTCA-TGCCATGACCGACACCCCTTTTTAGTTAGATAAAAAATTCGAATTTTTT
1 TTTTGGTGTTGGCCATTG-CATGACCGACACCTCTTTTTA-TTAGATAAAAAA-TC-AA-TTTTT
* *
9032 TTA-TGTTGGCCATGCCATAGCCGACACCCCTATTTATCTGAT-AAA-AAAAA-TCAATTTTTTT
61 TGAGTGTTGGCCATGCCATGGCCGACACCCC-ATTT-T-TG-TCAAATAAAAATTCAATTTTTTT
* * *
9093 TGTGTTGGCCATG-CAATAGCTGACACCTCTTTTT-TCAGATAAAAAAATTTCAAATTTTTTTGT
122 TGTGTTGGCCATGTC-ATGGCCGACA-CTCTTTTTATCTGATAAAAAAA--TC-AATTTTTTTGT
* * * * * * *
9156 GTTGGTCATTGC-ATGGCT-TATACTCTTTTTTATCTGAATAAAAAATCAAA-T
182 GTTGGCCA-TGCAAT-ACTCAACACCCCTTTTTATCTAAATAAAAAATCAAATT
** * * * *
9207 TTTTGGATGTTGGCCA-TGCCATGTTCTACACCCTCTTTTTGTCAAATAAAAAATTCGAATTTTT
1 TTTTGG-TGTTGGCCATTG-CATGACCGACA-CCTCTTTTTATTAGATAAAAAA-TC-AATTTTT
* * **
9271 T-TGTGTTGGCAATGAAATGGCCGACACC
61 TGAGTGTTGGCCATGCCATGGCCGACACC
9299 AACTTTCTCT
Statistics
Matches: 476, Mismatches: 64, Indels: 53
0.80 0.11 0.09
Matches are distributed among these distances:
235 2 0.00
236 46 0.10
237 35 0.07
238 218 0.46
239 68 0.14
240 88 0.18
241 18 0.04
242 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.39
Consensus pattern (233 bp):
TTTTGGTGTTGGCCATTGCATGACCGACACCTCTTTTTATTAGATAAAAAATCAATTTTTTGAGT
GTTGGCCATGCCATGGCCGACACCCCATTTTTGTCAAATAAAAATTCAATTTTTTTTGTGTTGGC
CATGTCATGGCCGACACTCTTTTTATCTGATAAAAAAATCAATTTTTTTGTGTTGGCCATGCAAT
ACTCAACACCCCTTTTTATCTAAATAAAAAATCAAATT
Found at i:13399 original size:84 final size:85
Alignment explanation
Indices: 13155--13712 Score: 827
Period size: 84 Copynumber: 6.5 Consensus size: 85
13145 AATTTAACAT
*
13155 TATTTAAATAAAAAAGATTATTATTATATTACAATTTATATCAAATAATGTGTTGATTTGATAAT
1 TATTTAAAT-AAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGATAAT
13220 ACATTATTTATCAAATTTTAA
65 ACATTATTTATCAAATTTTAA
* *
13241 TATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAATAGTGTGTTGATTTGACAAT
1 TATTTAAAT-AAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGATAAT
13306 ACATTATTTATCAAATTTTAA
65 ACATTATTTATCAAATTTTAA
* * *
13327 TATTTAAATAAAAA-ATTATTATTATATTACAATTTTTATTAAATAATGTGTTTATTTGATAACA
1 TATTTAAATAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGATAATA
*
13391 CATAATTTATC-AATTTTAA
66 CATTATTTATCAAATTTTAA
* * *
13410 TATTTAAATAAAAAGATTATTATTATATTATAATTTTTATTAAATAATGAGTTGATTTGATAATA
1 TATTTAAATAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGATAATA
13475 CATTATTTATCAAATTTTAATA
66 CATTATTTATCAAATTTT-A-A
* *** *
13497 TATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAATAAAAAGTTGATTTGACACA
1 TATTTAAATAAAAA-GATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTG--ATA
* *
13562 ATACATTATTTACCAAATTTGAA
63 ATACATTATTTATCAAATTTTAA
* * *
13585 TATTTTAATTAAAA-ATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGAAAATA
1 TATTTAAATAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGATAATA
13649 CATTATTTATCAAATTTTAA
66 CATTATTTATCAAATTTTAA
* *
13669 TATTTAAATTAAAA-ATTATTATTATATTACAAATTTTATCAAAT
1 TATTTAAATAAAAAGATTATTATTATATTACAATTTTTATCAAAT
13713 TTTAAATTTA
Statistics
Matches: 433, Mismatches: 32, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
83 22 0.05
84 176 0.41
85 11 0.03
86 134 0.31
87 15 0.03
88 53 0.12
89 1 0.00
90 21 0.05
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (85 bp):
TATTTAAATAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGATAATA
CATTATTTATCAAATTTTAA
Found at i:14748 original size:10 final size:10
Alignment explanation
Indices: 14731--14759 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
14721 ATATTTTTTA
14731 AATT-TTATT
1 AATTATTATT
14740 AATTATTATT
1 AATTATTATT
14750 AATTATTATT
1 AATTATTATT
14760 TTTATTCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
AATTATTATT
Found at i:14938 original size:19 final size:19
Alignment explanation
Indices: 14901--14943 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
14891 TTTTATAATA
* *
14901 TTTTTTCTATTTTAGAAAT
1 TTTTTTATATTTTACAAAT
14920 GTTTTTTATATTTT-CAAAT
1 -TTTTTTATATTTTACAAAT
14939 TTTTT
1 TTTTT
14944 AAAAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 4 0.19
20 12 0.57
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTTTTATATTTTACAAAT
Found at i:14994 original size:21 final size:21
Alignment explanation
Indices: 14970--15019 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
14960 ATATTTTTAC
*
14970 AAATATTTTTTTACATTTTCG
1 AAATATTTTTTTACATTATCG
14991 AAATA-TTTTTTACATTATCG
1 AAATATTTTTTTACATTATCG
15011 AAAT-TTTTT
1 AAATATTTTT
15020 AACTAAACTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (21 bp):
AAATATTTTTTTACATTATCG
Found at i:15921 original size:120 final size:121
Alignment explanation
Indices: 15783--16031 Score: 437
Period size: 120 Copynumber: 2.1 Consensus size: 121
15773 TCATTTTCGT
* * *
15783 AAATAATAAAAAATTTTGAGTTACTTGAATAAATTACTCGTTACTTGGATAAAGGACAAATTGAT
1 AAATAATAAAAAAATTTGAGTTACTTGAATAAATTACCCGATACTTGGATAAAGGACAAATTGAT
15848 AAGAAGAATTCTACGC-TTTCTACAAATATAATATAAAATAAATAAATAATTACCA
66 AAGAAGAATTCTACGCTTTTCTACAAATATAATATAAAATAAATAAATAATTACCA
*
15903 AAATAATAAAAAAATTTGAGTTACTTGAATAAATTACCCGATACTTGGATAAAGGACAAATTGGT
1 AAATAATAAAAAAATTTGAGTTACTTGAATAAATTACCCGATACTTGGATAAAGGACAAATTGAT
* *
15968 AAGAAGAATTCTAGGCTTTTTTACAAATATAATATAAAATAAATAAATAATTACCA
66 AAGAAGAATTCTACGCTTTTCTACAAATATAATATAAAATAAATAAATAATTACCA
16024 AAATAATA
1 AAATAATA
16032 TTTCATCCCA
Statistics
Matches: 122, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
120 76 0.62
121 46 0.38
ACGTcount: A:0.49, C:0.09, G:0.10, T:0.31
Consensus pattern (121 bp):
AAATAATAAAAAAATTTGAGTTACTTGAATAAATTACCCGATACTTGGATAAAGGACAAATTGAT
AAGAAGAATTCTACGCTTTTCTACAAATATAATATAAAATAAATAAATAATTACCA
Done.