Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012325.1 Kokia drynarioides strain JFW-HI SEQ_127327, 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: 40774
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:1000 original size:30 final size:33
Alignment explanation
Indices: 960--1029 Score: 101
Period size: 30 Copynumber: 2.2 Consensus size: 33
950 GGTCTATATC
*
960 ATTATAATTTTTAAAGGATT-AAAT-TAATTA-
1 ATTATTATTTTTAAAGGATTAAAATGTAATTAT
*
990 ATTATTATTTTTAAAGGGTTAAAATGTAATTAT
1 ATTATTATTTTTAAAGGATTAAAATGTAATTAT
1023 ATTATTA
1 ATTATTA
1030 CTAATTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
30 18 0.51
31 4 0.11
32 6 0.17
33 7 0.20
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (33 bp):
ATTATTATTTTTAAAGGATTAAAATGTAATTAT
Found at i:1320 original size:21 final size:18
Alignment explanation
Indices: 1273--1320 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 18
1263 TTTATATATG
1273 AATTAAATATTTTTTAAA
1 AATTAAATATTTTTTAAA
*
1291 ACTTAAAATATTACTTTTAAA
1 AATT-AAATATT--TTTTAAA
1312 AATTGAAAT
1 AATT-AAAT
1321 TAAACCCGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 3 0.12
19 7 0.29
21 14 0.58
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (18 bp):
AATTAAATATTTTTTAAA
Found at i:7078 original size:19 final size:21
Alignment explanation
Indices: 7036--7079 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
7026 CCCGAATTTT
*
7036 GAACCCTAAACCTTGAACATC
1 GAACCCTAAACCTTGAACACC
*
7057 GAACCC-AAA-CTTGAACCCC
1 GAACCCTAAACCTTGAACACC
7076 GAAC
1 GAAC
7080 ATTGATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
20 3 0.14
21 6 0.29
ACGTcount: A:0.39, C:0.36, G:0.11, T:0.14
Consensus pattern (21 bp):
GAACCCTAAACCTTGAACACC
Found at i:8863 original size:21 final size:18
Alignment explanation
Indices: 8816--8863 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 18
8806 TTTATATATG
8816 AATTAAATATTTTTTAAA
1 AATTAAATATTTTTTAAA
*
8834 ACTTAAAATATTACTTTTAAA
1 AATT-AAATATT--TTTTAAA
8855 AATTGAAAT
1 AATT-AAAT
8864 TAAACCCGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 3 0.12
19 7 0.29
21 14 0.58
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (18 bp):
AATTAAATATTTTTTAAA
Found at i:8972 original size:6 final size:6
Alignment explanation
Indices: 8961--9024 Score: 64
Period size: 6 Copynumber: 11.2 Consensus size: 6
8951 ATTTGTTTAG
* *
8961 AAATTT AAATTT ATA-TT AAATTT AAATTT --ATTT CGAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT -AAATTT AAATTT
*
9007 -AATTT AAGTTT AAATTT A
1 AAATTT AAATTT AAATTT A
9025 TTTTCCAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
4 4 0.08
5 9 0.19
6 31 0.65
7 4 0.08
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:8983 original size:17 final size:16
Alignment explanation
Indices: 8929--9056 Score: 98
Period size: 17 Copynumber: 7.4 Consensus size: 16
8919 TCAAACTCCC
8929 TTTAAATTTATTTTAAGA
1 TTTAAATTTA-TTTAA-A
* *
8947 -ATAAATTTGTTTAGAAA
1 TTTAAATTTATTT--AAA
8964 TTTAAATTTATATTAAA
1 TTTAAATTTAT-TTAAA
*
8981 TTTAAATTTATTTCGAA
1 TTTAAATTTATTT-AAA
*
8998 TTTAAATTTAATTTAAG
1 TTTAAATTT-ATTTAAA
9015 TTTAAATTTATTTTCCAAA
1 TTTAAATTTA-TTT--AAA
9034 TTTAAGA-TTATTATAAA
1 TTTAA-ATTTATT-TAAA
9051 TTTAAA
1 TTTAAA
9057 ATAAATAAGA
Statistics
Matches: 91, Mismatches: 8, Indels: 24
0.74 0.07 0.20
Matches are distributed among these distances:
16 7 0.08
17 54 0.59
18 16 0.18
19 13 0.14
20 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:9005 original size:34 final size:35
Alignment explanation
Indices: 8929--9027 Score: 114
Period size: 34 Copynumber: 2.9 Consensus size: 35
8919 TCAAACTCCC
* * *
8929 TTTAAATTTATTTTAAGA-ATAAATTTGTTTAGAAA
1 TTTAAATTTATATTAA-ATTTAAATTTATTTAGAAA
*
8964 TTTAAATTTATATTAAATTTAAATTTATTTCG-AA
1 TTTAAATTTATATTAAATTTAAATTTATTTAGAAA
*
8998 TTTAAATTTA-ATTTAAGTTTAAATTTATTT
1 TTTAAATTTATA-TTAAATTTAAATTTATTT
9028 TCCAAATTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
33 1 0.02
34 30 0.53
35 26 0.46
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (35 bp):
TTTAAATTTATATTAAATTTAAATTTATTTAGAAA
Found at i:11070 original size:58 final size:58
Alignment explanation
Indices: 10937--11232 Score: 393
Period size: 58 Copynumber: 5.0 Consensus size: 58
10927 CCCCGAAGGT
* ** *
10937 CCCT-AAACTTTCCAAAAATTCTGTTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
1 CCCTAAAAC-TTCCAAAAATCCCATTTTTACCC-CAAACTTCCAAAAATCCCATTTTTGA
* *
10996 CCCTAAAACTTTCAAAAATCCCCTTTTTGACCCCAAACTTCCAAAAA-CCCATTTTTGA
1 CCCTAAAACTTCCAAAAATCCCATTTTT-ACCCCAAACTTCCAAAAATCCCATTTTTGA
11054 CCCTAAAACTTCCAAAAATCCCATTTTTACCCCCAAACTTCCAAAAATCCCA-TTTTGA
1 CCCTAAAACTTCCAAAAATCCCATTTTTA-CCCCAAACTTCCAAAAATCCCATTTTTGA
* *
11112 CCCTAAAACTTCCAAAAATTCCA-TTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
1 CCCTAAAACTTCCAAAAATCCCATTTTTACCC-CAAACTTCCAAAAATCCCATTTTTGA
* * *
11170 CCCTAAAACTTCAAAAAAAATCCTATTTTTACCCCCAAACTTTCAAAAATCCCATTTTTGA
1 CCCTAAAACTTC--CAAAAATCCCATTTTTA-CCCCAAACTTCCAAAAATCCCATTTTTGA
11231 CC
1 CC
11233 TCGAATTTTC
Statistics
Matches: 213, Mismatches: 14, Indels: 18
0.87 0.06 0.07
Matches are distributed among these distances:
56 3 0.01
57 24 0.11
58 100 0.47
59 36 0.17
60 16 0.08
61 31 0.15
62 3 0.01
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.31
Consensus pattern (58 bp):
CCCTAAAACTTCCAAAAATCCCATTTTTACCCCAAACTTCCAAAAATCCCATTTTTGA
Found at i:11242 original size:29 final size:30
Alignment explanation
Indices: 10937--11232 Score: 349
Period size: 29 Copynumber: 10.1 Consensus size: 30
10927 CCCCGAAGGT
* **
10937 CCCT-AAACTTTCCAAAAATTCTGTTTTT-A
1 CCCTCAAAC-TTCCAAAAATCCCATTTTTGA
*
10966 CCCTCGAACTTCCAAAAATCCCATTTTTGA
1 CCCTCAAACTTCCAAAAATCCCATTTTTGA
* * *
10996 CCCTAAAACTTTCAAAAATCCCCTTTTTGA
1 CCCTCAAACTTCCAAAAATCCCATTTTTGA
11026 CCC-CAAACTTCCAAAAA-CCCATTTTTGA
1 CCCTCAAACTTCCAAAAATCCCATTTTTGA
*
11054 CCCTAAAACTTCCAAAAATCCCATTTTT-A
1 CCCTCAAACTTCCAAAAATCCCATTTTTGA
*
11083 CCCCCAAACTTCCAAAAATCCCA-TTTTGA
1 CCCTCAAACTTCCAAAAATCCCATTTTTGA
* *
11112 CCCTAAAACTTCCAAAAATTCCA-TTTT-A
1 CCCTCAAACTTCCAAAAATCCCATTTTTGA
*
11140 CCCTCGAACTTCCAAAAATCCCATTTTTGA
1 CCCTCAAACTTCCAAAAATCCCATTTTTGA
* * *
11170 CCCTAAAACTTCAAAAAAAATCCTATTTTT-A
1 CCCTCAAACTTC--CAAAAATCCCATTTTTGA
* *
11201 CCCCCAAACTTTCAAAAATCCCATTTTTGA
1 CCCTCAAACTTCCAAAAATCCCATTTTTGA
11231 CC
1 CC
11233 TCGAATTTTC
Statistics
Matches: 228, Mismatches: 29, Indels: 19
0.83 0.11 0.07
Matches are distributed among these distances:
28 38 0.17
29 110 0.48
30 56 0.25
31 10 0.04
32 14 0.06
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.31
Consensus pattern (30 bp):
CCCTCAAACTTCCAAAAATCCCATTTTTGA
Found at i:13094 original size:21 final size:21
Alignment explanation
Indices: 13068--13116 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
13058 TATTTAAAAT
13068 TTTTTTTATATTGTACTTGAA
1 TTTTTTTATATTGTACTTGAA
13089 TTTTTTTATATTGTACTTGAA
1 TTTTTTTATATTGTACTTGAA
13110 TTTTTTT
1 TTTTTTT
13117 GAACAGAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.04, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTTTTTATATTGTACTTGAA
Found at i:18730 original size:13 final size:14
Alignment explanation
Indices: 18712--18749 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
18702 AACAATAATT
18712 TAAATATTATT-TA
1 TAAATATTATTATA
18725 TAAATATTATTATA
1 TAAATATTATTATA
*
18739 TTAA-ATTATTA
1 TAAATATTATTA
18750 AATGTCATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 18 0.78
14 5 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAAATATTATTATA
Found at i:21564 original size:292 final size:289
Alignment explanation
Indices: 21040--21617 Score: 1068
Period size: 292 Copynumber: 2.0 Consensus size: 289
21030 GTAATTCGAA
21040 ACAAATTCAACAATAATAAACCCTAAATTTTGAAATAAAAAAATTCACTTTATAATCATATAATT
1 ACAAATTCAACAATAATAAACCCTAAATTTTGAAATAAAAAAATTCACTTTATAATCATATAATT
*
21105 AAAAATGATGTAATAATTAACTTGAATTTTACAAAAAGAAATTTATTAGTGTTAATAGTTGGACC
66 AAAAATGATGTAATAATTAACTTGAATTTTACAAAAAGAAATTTATTAGTGTTAATAATTGGACC
21170 TGAATTTTAAAATTTGAAAAATAAATAAACTAAATTTATAAAAATAAAAATACGTGGACTAAATT
131 TGAATTTTAAAATTTGAAAAATAAATAAACTAAATTTATAAAAATAAAAATACGTGGACTAAATT
21235 TCAAATTTTCAAAAAGTACAAAAACTTCTAAAAGATTTTAACAAAAAAAAAAAAAACCAAATTGC
196 TCAAATTTTCAAAAAGTACAAAAACTTCTAAAAGATTTTAAC---AAAAAAAAAAACCAAATTGC
*
21300 ACAAATAGTATATTAATCCTATTCCCATTTAG
258 ACAAAAAGTATATTAATCCTATTCCCATTTAG
21332 ACAAATTCAACAATAATAAACCCTAAATTTTGAAATAAAAAAATTCA-TTTAATAATCATATAAT
1 ACAAATTCAACAATAATAAACCCTAAATTTTGAAATAAAAAAATTCACTTT-ATAATCATATAAT
*
21396 TAAAGATGATGTAATAATTAACTTGAATTTTACAAAAAGAAATTTATTAGTGTTAATAATTGGAC
65 TAAAAATGATGTAATAATTAACTTGAATTTTACAAAAAGAAATTTATTAGTGTTAATAATTGGAC
*
21461 CTGAATTTTAAAATTTGAAAAATAAATAAACTAAATTTATAAAGATAAAAATACGTGGACTAAAT
130 CTGAATTTTAAAATTTGAAAAATAAATAAACTAAATTTATAAAAATAAAAATACGTGGACTAAAT
*
21526 TTCAAATTTTCAAAAAGTACAAAAACTTCTGAAAGATTTTAACAAAAAAAAAAACCAAATTGCAC
195 TTCAAATTTTCAAAAAGTACAAAAACTTCTAAAAGATTTTAACAAAAAAAAAAACCAAATTGCAC
21591 AAAAAGTATATTAATCCTATTCCCATT
260 AAAAAGTATATTAATCCTATTCCCATT
21618 CCCATTCCCA
Statistics
Matches: 280, Mismatches: 5, Indels: 5
0.97 0.02 0.02
Matches are distributed among these distances:
289 48 0.17
291 3 0.01
292 229 0.82
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (289 bp):
ACAAATTCAACAATAATAAACCCTAAATTTTGAAATAAAAAAATTCACTTTATAATCATATAATT
AAAAATGATGTAATAATTAACTTGAATTTTACAAAAAGAAATTTATTAGTGTTAATAATTGGACC
TGAATTTTAAAATTTGAAAAATAAATAAACTAAATTTATAAAAATAAAAATACGTGGACTAAATT
TCAAATTTTCAAAAAGTACAAAAACTTCTAAAAGATTTTAACAAAAAAAAAAACCAAATTGCACA
AAAAGTATATTAATCCTATTCCCATTTAG
Found at i:21620 original size:6 final size:6
Alignment explanation
Indices: 21609--21635 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
21599 TATTAATCCT
21609 ATTCCC ATTCCC ATTCCC ATTCCC ATT
1 ATTCCC ATTCCC ATTCCC ATTCCC ATT
21636 TAGTTCTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.44, G:0.00, T:0.37
Consensus pattern (6 bp):
ATTCCC
Done.