Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001745.1 Kokia drynarioides strain JFW-HI SEQ_113456, 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: 58976
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--36 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
* *
1 AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37 TATTATACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5305 original size:25 final size:25
Alignment explanation
Indices: 5262--5506 Score: 214
Period size: 25 Copynumber: 9.8 Consensus size: 25
5252 AGTTTAGGTT
5262 TTACGAGCCCAGACA-AATATCGCTC
1 TTACGAG-CCAGACAGAATATCGCTC
* *
5287 TTACAAGCCAGTCAGAATATCGCTC
1 TTACGAGCCAGACAGAATATCGCTC
* *
5312 TTACGAGCTAGACATAATATCGCTC
1 TTACGAGCCAGACAGAATATCGCTC
*
5337 TTACGAGCCAGACAGAATATCACTC
1 TTACGAGCCAGACAGAATATCGCTC
* * *
5362 TTACGAGACAAAATCAG-A-ATCTCTC
1 TTACGAG-CCAGA-CAGAATATCGCTC
* * *
5387 TTATGAGCCAAACA-AATATTGCTC
1 TTACGAGCCAGACAGAATATCGCTC
*
5411 TTACAAGCCAGACAGAATATCGCTC
1 TTACGAGCCAGACAGAATATCGCTC
* *
5436 TTATGAGCCAAACAGAATAAT-GCTCC
1 TTACGAGCCAGACAGAAT-ATCGCT-C
* * * * *
5462 TT-TGAGACAAAATTAGAATATCACTC
1 TTACGAG-CCAGA-CAGAATATCGCTC
5488 TTACGAGCCAGACAGAATA
1 TTACGAGCCAGACAGAATA
5507 AAGCTCCTTT
Statistics
Matches: 178, Mismatches: 30, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
23 3 0.02
24 26 0.15
25 115 0.65
26 21 0.12
27 13 0.07
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (25 bp):
TTACGAGCCAGACAGAATATCGCTC
Found at i:5420 original size:74 final size:75
Alignment explanation
Indices: 5309--5447 Score: 199
Period size: 74 Copynumber: 1.9 Consensus size: 75
5299 CAGAATATCG
* * *
5309 CTCTTACGAGCTAGACATAATATCGCTCTTACGAGCCAGACAGAATATCACTCTTACGAGACAAA
1 CTCTTACGAGCCAAACATAATATCGCTCTTACAAGCCAGACAGAATATCACTCTTACGAGACAAA
5374 ATCAGAATCT
66 ATCAGAATCT
* * * * *
5384 CTCTTATGAGCCAAACA-AATATTGCTCTTACAAGCCAGACAGAATATCGCTCTTATGAGCCAAA
1 CTCTTACGAGCCAAACATAATATCGCTCTTACAAGCCAGACAGAATATCACTCTTACGAGACAAA
5448 CAGAATAATG
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
74 42 0.75
75 14 0.25
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.24
Consensus pattern (75 bp):
CTCTTACGAGCCAAACATAATATCGCTCTTACAAGCCAGACAGAATATCACTCTTACGAGACAAA
ATCAGAATCT
Found at i:5496 original size:52 final size:52
Alignment explanation
Indices: 5424--5526 Score: 161
Period size: 52 Copynumber: 2.0 Consensus size: 52
5414 CAAGCCAGAC
* * *
5424 AGAATATCGCTCTTATGAGCCAAACAGAATAATGCTCCTTTGAGACAAAATT
1 AGAATATCACTCTTACGAGCCAAACAGAATAAAGCTCCTTTGAGACAAAATT
* *
5476 AGAATATCACTCTTACGAGCCAGACAGAATAAAGCTCCTTTGAGCCAAAAT
1 AGAATATCACTCTTACGAGCCAAACAGAATAAAGCTCCTTTGAGACAAAAT
5527 CAGATTACTC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (52 bp):
AGAATATCACTCTTACGAGCCAAACAGAATAAAGCTCCTTTGAGACAAAATT
Found at i:5520 original size:25 final size:25
Alignment explanation
Indices: 5384--5524 Score: 92
Period size: 25 Copynumber: 5.6 Consensus size: 25
5374 ATCAGAATCT
**
5384 CTCTTATGAGCCAAACA-AATATTG
1 CTCTTATGAGCCAAACAGAATAAAG
** * **
5408 CTCTTACAAGCCAGACAGAATATCG
1 CTCTTATGAGCCAAACAGAATAAAG
*
5433 CTCTTATGAGCCAAACAGAATAATG
1 CTCTTATGAGCCAAACAGAATAAAG
* * *
5458 CTCCTT-TGAGACAAAATTAGAATATCA-
1 CT-CTTATGAG-CCAAA-CAGAATA-AAG
* *
5485 CTCTTACGAGCCAGACAGAATAAAG
1 CTCTTATGAGCCAAACAGAATAAAG
5510 CTCCTT-TGAGCCAAA
1 CT-CTTATGAGCCAAA
5525 ATCAGATTAC
Statistics
Matches: 89, Mismatches: 20, Indels: 15
0.72 0.16 0.12
Matches are distributed among these distances:
24 15 0.17
25 47 0.53
26 16 0.18
27 11 0.12
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (25 bp):
CTCTTATGAGCCAAACAGAATAAAG
Found at i:26137 original size:18 final size:19
Alignment explanation
Indices: 26116--26169 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
26106 TATAACACAT
26116 TAAAAAT-TAA-ACCTACAC
1 TAAAAATATAATA-CTACAC
*
26134 TAAATATATAATACTACAC
1 TAAAAATATAATACTACAC
*
26153 TAAACATATAATACTAC
1 TAAAAATATAATACTAC
26170 TTTAAAGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 6 0.19
19 25 0.78
20 1 0.03
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAAATATAATACTACAC
Found at i:26175 original size:19 final size:19
Alignment explanation
Indices: 26128--26169 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
26118 AAAATTAAAC
*
26128 CTACACTAAATATATAATA
1 CTACACTAAACATATAATA
26147 CTACACTAAACATATAATA
1 CTACACTAAACATATAATA
26166 CTAC
1 CTAC
26170 TTTAAAGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (19 bp):
CTACACTAAACATATAATA
Found at i:26256 original size:32 final size:32
Alignment explanation
Indices: 26184--26261 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 32
26174 AAGTAAACAT
*
26184 TAAAATAATGTTAAGATGACTATATAAAAAAATA
1 TAAAA-AATGTTAA-ATGACTAAATAAAAAAATA
* *
26218 T-TAAAATGTTAAAT-ACTAAATTAAAATAATA
1 TAAAAAATGTTAAATGACTAAA-TAAAAAAATA
26249 TAAAAAAT-TTAAA
1 TAAAAAATGTTAAA
26262 AATAATATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
30 5 0.13
31 17 0.45
32 13 0.34
33 2 0.05
34 1 0.03
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (32 bp):
TAAAAAATGTTAAATGACTAAATAAAAAAATA
Found at i:28881 original size:31 final size:30
Alignment explanation
Indices: 28816--28902 Score: 115
Period size: 31 Copynumber: 2.9 Consensus size: 30
28806 GTCTTACCCC
*
28816 ATGTTTATTGTCCCAGTAGAC--TCTATCT
1 ATGTTTATTGTCCCAGCAGACTATCTATCT
* *
28844 ATGTTTATTGTCCCAACGGACTATCTATCTT
1 ATGTTTATTGTCCCAGCAGACTATCTATC-T
*
28875 ATGTTTATTGTCCTAGCAGACTATCTAT
1 ATGTTTATTGTCCCAGCAGACTATCTAT
28903 TTTGTGGATG
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
28 18 0.36
30 6 0.12
31 26 0.52
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.43
Consensus pattern (30 bp):
ATGTTTATTGTCCCAGCAGACTATCTATCT
Found at i:31153 original size:24 final size:24
Alignment explanation
Indices: 31111--31157 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
31101 TCGATAGTTG
31111 CATAGTAAGTATCAATAGTTCTGCT
1 CATAGTAAGTATCAATAG-TCTGCT
**
31136 CATAG-AAGTATCGGTAGTCTGC
1 CATAGTAAGTATCAATAGTCTGC
31158 GTACTTGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 10 0.50
25 5 0.25
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (24 bp):
CATAGTAAGTATCAATAGTCTGCT
Found at i:31272 original size:21 final size:21
Alignment explanation
Indices: 31248--31302 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
31238 TTGGTAAAAA
*
31248 CTTCACTTGTTTCAATAGAAG
1 CTTCACTTGTATCAATAGAAG
*
31269 CTTCACTTGTATCGATAGAA-
1 CTTCACTTGTATCAATAGAAG
*
31289 CTGTCACATGTATC
1 CT-TCACTTGTATC
31303 GGTAGAAGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (21 bp):
CTTCACTTGTATCAATAGAAG
Found at i:31303 original size:21 final size:21
Alignment explanation
Indices: 31248--31310 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
31238 TTGGTAAAAA
* * *
31248 CTTCACTTGTTTCAATAGAAG
1 CTTCACATGTATCGATAGAAG
*
31269 CTTCACTTGTATCGATAGAA-
1 CTTCACATGTATCGATAGAAG
*
31289 CTGTCACATGTATCGGTAGAAG
1 CT-TCACATGTATCGATAGAAG
31311 TCTGCACTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 2 0.06
21 34 0.94
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (21 bp):
CTTCACATGTATCGATAGAAG
Found at i:40519 original size:30 final size:31
Alignment explanation
Indices: 40480--40550 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 31
40470 CATTTAACAC
40480 AACAGTCACTCAAC-TT-T-GAAAATGTGACAA
1 AACAGTCACT-AACATTATCGAAAA-GTGACAA
*
40510 AACAATCACTAACATTATCGAAAAGTGACAA
1 AACAGTCACTAACATTATCGAAAAGTGACAA
40541 AACAGTCACT
1 AACAGTCACT
40551 GATTAATAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 3 0.08
30 11 0.31
31 17 0.47
32 5 0.14
ACGTcount: A:0.46, C:0.21, G:0.11, T:0.21
Consensus pattern (31 bp):
AACAGTCACTAACATTATCGAAAAGTGACAA
Found at i:40914 original size:21 final size:21
Alignment explanation
Indices: 40870--40916 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
40860 ATACTTGTTA
**
40870 CATCTACTGTATCAACATTTC
1 CATCTACTGTATCAACATAGC
*
40891 CATCTACTGTATTAACATAGC
1 CATCTACTGTATCAACATAGC
40912 CATCT
1 CATCT
40917 TCTCATCCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (21 bp):
CATCTACTGTATCAACATAGC
Found at i:41203 original size:30 final size:30
Alignment explanation
Indices: 41132--41204 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 30
41122 CCATTCGATT
41132 TTAGTGACTGTTTTGTCACTTTTCGATAATG
1 TTAGTGACTGTTTTGTCACTTTTC-ATAATG
*
41163 TTACTGACTGTTTTGTCACTTTT-ATGAA-G
1 TTAGTGACTGTTTTGTCACTTTTCAT-AATG
41192 TTGAGTGACTGTT
1 TT-AGTGACTGTT
41205 GTGTTAAATG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
29 5 0.13
30 11 0.29
31 22 0.58
ACGTcount: A:0.19, C:0.12, G:0.21, T:0.48
Consensus pattern (30 bp):
TTAGTGACTGTTTTGTCACTTTTCATAATG
Done.