Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008436.1 Kokia drynarioides strain JFW-HI SEQ_123107, 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: 37138
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:1067 original size:16 final size:16
Alignment explanation
Indices: 1046--1076 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1036 AGTTAAAATT
*
1046 TAATTTTATGAATTTA
1 TAATTTGATGAATTTA
1062 TAATTTGATGAATTT
1 TAATTTGATGAATTT
1077 TTTAAAAAAA
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:0.00, G:0.10, T:0.55
Consensus pattern (16 bp):
TAATTTGATGAATTTA
Found at i:1790 original size:21 final size:21
Alignment explanation
Indices: 1753--1792 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1743 GAAACCATGC
*
1753 ATGTATTTAAAACACATATTT
1 ATGTATTTAAAAAACATATTT
1774 ATGT-TTTAAAATAACATAT
1 ATGTATTTAAAA-AACATAT
1793 AATAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
ATGTATTTAAAAAACATATTT
Found at i:2295 original size:18 final size:18
Alignment explanation
Indices: 2265--2299 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2255 TAAAATGTGC
2265 ATAATAAAATTAAAATAT
1 ATAATAAAATTAAAATAT
2283 ATAA-AAAATTTAAAATA
1 ATAATAAAA-TTAAAATA
2300 AAGTTTTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAATAAAATTAAAATAT
Found at i:4786 original size:21 final size:21
Alignment explanation
Indices: 4760--4813 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
4750 ATTCTTTGGT
*
4760 CACTGGCACAAAACTCAATTA
1 CACTGGCACAAAACCCAATTA
* *
4781 CACTGGCACAAAGCCCGATTA
1 CACTGGCACAAAACCCAATTA
*
4802 CACCGGCACAAA
1 CACTGGCACAAA
4814 GCCTACTAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.39, C:0.33, G:0.15, T:0.13
Consensus pattern (21 bp):
CACTGGCACAAAACCCAATTA
Found at i:9661 original size:9 final size:9
Alignment explanation
Indices: 9599--9661 Score: 54
Period size: 9 Copynumber: 7.0 Consensus size: 9
9589 AATCGTTCTG
*
9599 TTATCATCA
1 TTATCATTA
*
9608 TTATCATCA
1 TTATCATTA
* *
9617 TCATCATCA
1 TTATCATTA
* *
9626 TCATTATTA
1 TTATCATTA
*
9635 TTATTATTA
1 TTATCATTA
*
9644 TTATTATTA
1 TTATCATTA
9653 TTATCATTA
1 TTATCATTA
9662 GTGCTTATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 49 1.00
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.52
Consensus pattern (9 bp):
TTATCATTA
Found at i:9673 original size:3 final size:3
Alignment explanation
Indices: 9628--9661 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
9618 CATCATCATC
*
9628 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
9662 GTGCTTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:10566 original size:4 final size:4
Alignment explanation
Indices: 10557--10621 Score: 121
Period size: 4 Copynumber: 16.2 Consensus size: 4
10547 ATTTTACTAA
10557 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
10605 TATG TATG TACG TATG T
1 TATG TATG TATG TATG T
10622 GTACATGATA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 59 1.00
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:23031 original size:22 final size:23
Alignment explanation
Indices: 22990--23036 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
22980 AATATTTATA
* *
22990 TAATCTTAATTATATTAAATACT
1 TAATATTAATTATATGAAATACT
23013 TAATATTAA-TATATGAAATACT
1 TAATATTAATTATATGAAATACT
23035 TA
1 TA
23037 TATGCTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (23 bp):
TAATATTAATTATATGAAATACT
Found at i:27432 original size:15 final size:15
Alignment explanation
Indices: 27412--27449 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
27402 GGTAATATGA
27412 TAATTTAAAT-TTCGT
1 TAATTTAAATATT-GT
27427 TAATTTAAATATTGT
1 TAATTTAAATATTGT
27442 TACATTTA
1 TA-ATTTA
27450 TTTTTATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (15 bp):
TAATTTAAATATTGT
Found at i:29802 original size:4 final size:4
Alignment explanation
Indices: 29785--29934 Score: 86
Period size: 4 Copynumber: 36.5 Consensus size: 4
29775 TTTAACTAAG
* * * * * *
29785 TAAA TAAG TAAA TAAA TAAC TGAA TAAA AAAA TAAA CAAAA TAAA TAAC
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA -TAAA TAAA TAAA
* * * * * *
29834 TAAA TAAT TAAC TAAA TAAAA TAAA TAAT TAAC TAAA -AATA TATA TATA
1 TAAA TAAA TAAA TAAA T-AAA TAAA TAAA TAAA TAAA TAA-A TAAA TAAA
* * * * * *
29883 TATA TAAT TAAC TAAT TAAA TAAAA CAAA TAAT TAAA TAAA TAAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA T-AAA TAAA TAAA TAAA TAAA T-AAA TAAA
29933 TA
1 TA
29935 TTTTTAAATT
Statistics
Matches: 112, Mismatches: 28, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
3 2 0.02
4 95 0.85
5 15 0.13
ACGTcount: A:0.66, C:0.05, G:0.01, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:29829 original size:29 final size:29
Alignment explanation
Indices: 29794--29872 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
29784 GTAAATAAGT
*
29794 AAATAAATAACTGAATAAAAAAATAAACA
1 AAATAAATAACTAAATAAAAAAATAAACA
** * *
29823 AAATAAATAACTAAATAATTAACTAAATA
1 AAATAAATAACTAAATAAAAAAATAAACA
* *
29852 AAATAAATAATTAACTAAAAA
1 AAATAAATAACTAAATAAAAA
29873 TATATATATA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.70, C:0.06, G:0.01, T:0.23
Consensus pattern (29 bp):
AAATAAATAACTAAATAAAAAAATAAACA
Found at i:29855 original size:17 final size:17
Alignment explanation
Indices: 29786--29931 Score: 77
Period size: 17 Copynumber: 8.4 Consensus size: 17
29776 TTAACTAAGT
*
29786 AAATAAGTAAATAAAT-
1 AAATAATTAAATAAATA
* *
29802 AACTGAA-TAAAAAAATA
1 AAAT-AATTAAATAAATA
* *
29819 AACA-AAATAAATAACT-
1 AA-ATAATTAAATAAATA
*
29835 AAATAATTAACTAAATA
1 AAATAATTAAATAAATA
* * *
29852 AAATAAATAATTAACTAA
1 AAATAATTAAATAAAT-A
*
29870 AAATATATATATATATATAATT
1 AAATA-AT-TA-A-ATA-AATA
*
29892 AACTAATTAAATAAA-A
1 AAATAATTAAATAAATA
29908 CAAATAATTAAATAAATA
1 -AAATAATTAAATAAATA
29926 AAATAA
1 AAATAA
29932 ATATTTTTAA
Statistics
Matches: 98, Mismatches: 18, Indels: 27
0.69 0.13 0.19
Matches are distributed among these distances:
15 1 0.01
16 24 0.24
17 46 0.47
18 10 0.10
19 2 0.02
20 4 0.04
21 3 0.03
22 6 0.06
23 2 0.02
ACGTcount: A:0.66, C:0.05, G:0.01, T:0.27
Consensus pattern (17 bp):
AAATAATTAAATAAATA
Found at i:30796 original size:80 final size:80
Alignment explanation
Indices: 30646--30866 Score: 252
Period size: 80 Copynumber: 2.8 Consensus size: 80
30636 CCAGTATACA
* ** * * * ** *
30646 ATGCTGCTCATACAAGCTGTTGAGAATCCGCAACATATGACA-GA-CTCAGCCATCGATACAGTC
1 ATGCTGCTCACACAAGCTGTCAAGAATCTGCAACATATG-CAGGATCTTAGCCATCG-GAGGGTT
*
30709 CATTTTATCCACTCACG
64 CACTTTATCCACTCACG
* *
30726 ATG-TAGCTCACACAAGCTGTCAAGAAT-TCGCAACGTATGTAGGATCTTAGCCATCGGAGGGTT
1 ATGCT-GCTCACACAAGCTGTCAAGAATCT-GCAACATATGCAGGATCTTAGCCATCGGAGGGTT
30789 CACTTTATCCACTCACG
64 CACTTTATCCACTCACG
* *
30806 ATGCTGCTCACACAAGCTGTCAAGAATCTGCAACATATGCAGGATCTTGGCTATCGGAGGG
1 ATGCTGCTCACACAAGCTGTCAAGAATCTGCAACATATGCAGGATCTTAGCCATCGGAGGG
30867 CCCTTACATT
Statistics
Matches: 119, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
79 2 0.02
80 105 0.88
81 12 0.10
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.25
Consensus pattern (80 bp):
ATGCTGCTCACACAAGCTGTCAAGAATCTGCAACATATGCAGGATCTTAGCCATCGGAGGGTTCA
CTTTATCCACTCACG
Found at i:32846 original size:30 final size:30
Alignment explanation
Indices: 32799--33011 Score: 143
Period size: 30 Copynumber: 7.2 Consensus size: 30
32789 TTACATTTTA
* *
32799 ACCCCCAAACTAT-CCAAAAATTTAGATTAG
1 ACCCTCAAACT-TCCCAAAAATTTAGATTTG
*
32829 ACCCTCGAACTTCCCAAAAATTTAGATTTG
1 ACCCTCAAACTTCCCAAAAATTTAGATTTG
* *
32859 ACCCT-TAACTTCCCAAAAATTCAGATTTG
1 ACCCTCAAACTTCCCAAAAATTTAGATTTG
* *
32888 ACCC-CTAAACTT-CCAAAAAATTAGGATTTA
1 ACCCTC-AAACTTCCCAAAAATTTA-GATTTG
* * *
32918 ACCCCCAAACTTTCCAAAAAAAATT--ATTTG
1 ACCCTCAAAC-TTCC-CAAAAATTTAGATTTG
** * * * *
32948 ACCCTCGTACTTACTAAAAATTCAAATTTG
1 ACCCTCAAACTTCCCAAAAATTTAGATTTG
* * * * *
32978 GCCCCCAAACTTTCC-AAAATTTTGTTTTG
1 ACCCTCAAACTTCCCAAAAATTTAGATTTG
33007 ACCCT
1 ACCCT
33012 ATTTTTCCTT
Statistics
Matches: 143, Mismatches: 30, Indels: 21
0.74 0.15 0.11
Matches are distributed among these distances:
28 6 0.04
29 52 0.36
30 73 0.51
31 3 0.02
32 1 0.01
33 8 0.06
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (30 bp):
ACCCTCAAACTTCCCAAAAATTTAGATTTG
Done.