Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002532.1 Kokia drynarioides strain JFW-HI SEQ_114707, 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: 40173
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5622 original size:83 final size:83
Alignment explanation
Indices: 5507--5718 Score: 309
Period size: 83 Copynumber: 2.5 Consensus size: 83
5497 TTTTACTTGT
* *
5507 GTTGTGTACACTTGCACAT-TTACGATTGCAATATTATTTTACACACGATAGTACGATACTCTAC
1 GTTGTGTACACTTGCACATGCTAC-A--ACAATATTATTTTACACACGATAGTACGATACTCTAC
5571 TTATCACTTCATTACTTGAAC
63 TTATCACTTCATTACTTGAAC
* * *
5592 GTTGTGTACACTTGCACATGCTACCACAATATTATTTTACACGCGATAGTATGATACTCTACTTA
1 GTTGTGTACACTTGCACATGCTACAACAATATTATTTTACACACGATAGTACGATACTCTACTTA
*
5657 TCACTTTATTACTTGAAC
66 TCACTTCATTACTTGAAC
*
5675 GTTGTGTACACTTGAACATTTGCTACAACAATATTATTTTACAC
1 GTTGTGTACACTTGCACA--TGCTACAACAATATTATTTTACAC
5719 GGGACAGTAA
Statistics
Matches: 116, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
83 71 0.61
85 42 0.36
86 3 0.03
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.38
Consensus pattern (83 bp):
GTTGTGTACACTTGCACATGCTACAACAATATTATTTTACACACGATAGTACGATACTCTACTTA
TCACTTCATTACTTGAAC
Found at i:15963 original size:16 final size:17
Alignment explanation
Indices: 15942--15975 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
15932 TTTTAAACCC
*
15942 TAAATA-CTAACCATTA
1 TAAATATCTAAACATTA
15958 TAAATATCTAAACATTA
1 TAAATATCTAAACATTA
15975 T
1 T
15976 TATAACTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAATATCTAAACATTA
Found at i:20514 original size:27 final size:28
Alignment explanation
Indices: 20466--20523 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
20456 CGTGCATTGG
* *
20466 AATTTAGTTTTAGCTTTAAC-TTAGACT
1 AATTTAGTTTTAGATTAAACTTTAGACT
*
20493 AATTTAG-TTTAGATTAATACTTTAGATT
1 AATTTAGTTTTAGATTAA-ACTTTAGACT
20521 AAT
1 AAT
20524 ATCCTTAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 8 0.31
27 9 0.35
28 9 0.35
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.48
Consensus pattern (28 bp):
AATTTAGTTTTAGATTAAACTTTAGACT
Found at i:20518 original size:13 final size:13
Alignment explanation
Indices: 20500--20524 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20490 ACTAATTTAG
20500 TTTAGATTAATAC
1 TTTAGATTAATAC
20513 TTTAGATTAATA
1 TTTAGATTAATA
20525 TCCTTAACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
TTTAGATTAATAC
Found at i:27306 original size:16 final size:16
Alignment explanation
Indices: 27285--27346 Score: 54
Period size: 16 Copynumber: 3.7 Consensus size: 16
27275 GGTGTTAAGA
27285 TATTAATTTTTTTAAT
1 TATTAATTTTTTTAAT
*
27301 TATTAA-TTTATTAACT
1 TATTAATTTTTTTAA-T
*
27317 TTTTAATTTATTTTAAAT
1 TATTAATTT-TTTT-AAT
*
27335 TGTTAATATTTT
1 TATTAAT-TTTT
27347 ATACTAATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
15 7 0.19
16 12 0.32
17 2 0.05
18 12 0.32
19 4 0.11
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TATTAATTTTTTTAAT
Found at i:27306 original size:24 final size:23
Alignment explanation
Indices: 27279--27324 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
27269 TCAAAAGGTG
*
27279 TTAAGATATTAATTTTTTTAATTA
1 TTAAGATATTAA-CTTTTTAATTA
**
27303 TTAATTTATTAACTTTTTAATT
1 TTAAGATATTAACTTTTTAATT
27325 TATTTTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (23 bp):
TTAAGATATTAACTTTTTAATTA
Found at i:31105 original size:36 final size:36
Alignment explanation
Indices: 31035--31309 Score: 245
Period size: 36 Copynumber: 7.6 Consensus size: 36
31025 AGAATGGCCT
* * *
31035 TATGCTCTAACCGAGACATAAG-AGATCA-CTTAGCAT
1 TATGCTCTAACCGAGACATATGCA-AT-ATCATAGCAA
31071 TATGCTCTAACCGAGACATATGCAATATCATAGCAA
1 TATGCTCTAACCGAGACATATGCAATATCATAGCAA
* * * * *
31107 TACGCTCTAATCGAGACGTATACAACATCATAGCAA
1 TATGCTCTAACCGAGACATATGCAATATCATAGCAA
* * ** * *
31143 TATGTTTTAACCGAGACATATGCAGCATAATAGAAA
1 TATGCTCTAACCGAGACATATGCAATATCATAGCAA
* *
31179 TATGCTCTAACCAAGACATATACAACT-TCATAGCAA
1 TATGCTCTAACCGAGACATATGCAA-TATCATAGCAA
* * *
31215 TATTCTCTAATCGAGACATATGCAACT-TCATAGCGA
1 TATGCTCTAACCGAGACATATGCAA-TATCATAGCAA
* * * *
31251 TATGCTCTAACTGAGACATATGTAACT-TCATGGTAA
1 TATGCTCTAACCGAGACATATGCAA-TATCATAGCAA
* *
31287 TACGCTCTAACCGAGACGTATGC
1 TATGCTCTAACCGAGACATATGC
31310 TTCCTTTGAA
Statistics
Matches: 195, Mismatches: 41, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
35 1 0.01
36 193 0.99
37 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.27
Consensus pattern (36 bp):
TATGCTCTAACCGAGACATATGCAATATCATAGCAA
Found at i:31231 original size:108 final size:108
Alignment explanation
Indices: 31035--31272 Score: 293
Period size: 108 Copynumber: 2.2 Consensus size: 108
31025 AGAATGGCCT
* * * * * *
31035 TATGCTCTAACCGAGACATAAG-AG-ATCACTTAGCATTATGCTCTAACCGAGACATATGCAATA
1 TATGCTCTAACCGAGACATATGCAGCAT-A-ATAGAAATATGCTCTAACCAAGACATATACAATA
*
31098 TCATAGCAATACGCTCTAATCGAGACGTATACAACATCATAGCAA
64 TCATAGCAATACGCTCTAATCGAGACATATACAACATCATAGCAA
* *
31143 TATGTTTTAACCGAGACATATGCAGCATAATAGAAATATGCTCTAACCAAGACATATACAACT-T
1 TATGCTCTAACCGAGACATATGCAGCATAATAGAAATATGCTCTAACCAAGACATATACAA-TAT
** * * *
31207 CATAGCAATATTCTCTAATCGAGACATATGCAACTTCATAGCGA
65 CATAGCAATACGCTCTAATCGAGACATATACAACATCATAGCAA
*
31251 TATGCTCTAACTGAGACATATG
1 TATGCTCTAACCGAGACATATG
31273 TAACTTCATG
Statistics
Matches: 110, Mismatches: 17, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
108 104 0.95
109 4 0.04
110 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.26
Consensus pattern (108 bp):
TATGCTCTAACCGAGACATATGCAGCATAATAGAAATATGCTCTAACCAAGACATATACAATATC
ATAGCAATACGCTCTAATCGAGACATATACAACATCATAGCAA
Found at i:31294 original size:108 final size:108
Alignment explanation
Indices: 31074--31303 Score: 282
Period size: 108 Copynumber: 2.1 Consensus size: 108
31064 TTAGCATTAT
* *
31074 GCTCTAACCGAGACATATGCAATATCATAGCAATACGCTCTAATCGAGACGTATACAACATCATA
1 GCTCTAACCGAGACATATACAATATCATAGCAATACGCTCTAATCGAGACATATACAACATCATA
* * * *
31139 GCAATATGTTTTAACCGAGACATATGCAGCATAATAGAAATAT
66 GCAATATGCTCTAACCGAGACATATGCAACATAATAGAAATAC
* ** * *
31182 GCTCTAACCAAGACATATACAACT-TCATAGCAATATTCTCTAATCGAGACATATGCAACTTCAT
1 GCTCTAACCGAGACATATACAA-TATCATAGCAATACGCTCTAATCGAGACATATACAACATCAT
* * * * * * *
31246 AGCGATATGCTCTAACTGAGACATATGTAACTTCATGGTAATAC
65 AGCAATATGCTCTAACCGAGACATATGCAACATAATAGAAATAC
31290 GCTCTAACCGAGAC
1 GCTCTAACCGAGAC
31304 GTATGCTTCC
Statistics
Matches: 102, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
108 101 0.99
109 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.26
Consensus pattern (108 bp):
GCTCTAACCGAGACATATACAATATCATAGCAATACGCTCTAATCGAGACATATACAACATCATA
GCAATATGCTCTAACCGAGACATATGCAACATAATAGAAATAC
Found at i:39563 original size:41 final size:44
Alignment explanation
Indices: 39513--39593 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 44
39503 GTCTTGAGAT
*
39513 GAGAATGAG-A-A-TGTGATAAAGGAAGACTTATGACTCGAAAG
1 GAGAATGAGAATATTGTGAAAAAGGAAGACTTATGACTCGAAAG
* *
39554 GAGAGTGAGAATATTGTTAAAAAGGAAGACTTATGACTCG
1 GAGAATGAGAATATTGTGAAAAAGGAAGACTTATGACTCG
39594 GTAAACCATA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 8 0.24
42 1 0.03
43 1 0.03
44 24 0.71
ACGTcount: A:0.42, C:0.07, G:0.28, T:0.22
Consensus pattern (44 bp):
GAGAATGAGAATATTGTGAAAAAGGAAGACTTATGACTCGAAAG
Found at i:39621 original size:40 final size:40
Alignment explanation
Indices: 39566--39661 Score: 174
Period size: 40 Copynumber: 2.4 Consensus size: 40
39556 GAGTGAGAAT
39566 ATTGTTAAAAAGGAAGACTTATGACTCGGTAAACCATAAG
1 ATTGTTAAAAAGGAAGACTTATGACTCGGTAAACCATAAG
* *
39606 ATTGTTAAAAAGGAAGACTTATGACTCGGTAGAGCATAAG
1 ATTGTTAAAAAGGAAGACTTATGACTCGGTAAACCATAAG
39646 ATTGTTAAAAAGGAAG
1 ATTGTTAAAAAGGAAG
39662 TCACATGAAC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.43, C:0.09, G:0.23, T:0.25
Consensus pattern (40 bp):
ATTGTTAAAAAGGAAGACTTATGACTCGGTAAACCATAAG
Done.