Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009081.1 Kokia drynarioides strain JFW-HI SEQ_123781, 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: 35358
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:4944 original size:41 final size:41
Alignment explanation
Indices: 4898--4993 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
4888 TTAGCGGCGT
* *
4898 TTTTCTCATAAACGCCACTAATGCTCTTACCTTTTGCTGCA
1 TTTTCTCATAAACGCCACTAATGCTCTTACCTTTTCCGGCA
* * * *
4939 TTTTCTCATAAACGCCGCTAGTGCTCTTACTTTTTCCGGCG
1 TTTTCTCATAAACGCCACTAATGCTCTTACCTTTTCCGGCA
4980 TTTTCTCATAAACG
1 TTTTCTCATAAACG
4994 TCGTTATTGC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.20, C:0.28, G:0.12, T:0.40
Consensus pattern (41 bp):
TTTTCTCATAAACGCCACTAATGCTCTTACCTTTTCCGGCA
Found at i:5013 original size:41 final size:40
Alignment explanation
Indices: 4892--5022 Score: 136
Period size: 41 Copynumber: 3.2 Consensus size: 40
4882 TAACCTTTAG
* * *
4892 CGGCGTTTTTCTCATAAACGCCACTAATGCTCTTACCTTTTG
1 CGGCG-TTTTCTCATAAACGCCGCTAGTGCTCTTA-CTTTTC
* *
4934 CTGCATTTTCTCATAAACGCCGCTAGTGCTCTTACTTTTTC
1 CGGCGTTTTCTCATAAACGCCGCTAGTGCTCTTAC-TTTTC
* * * * * *
4975 CGGCGTTTTCTCATAAACGTCGTTATTGCTTTTCCTTTTG
1 CGGCGTTTTCTCATAAACGCCGCTAGTGCTCTTACTTTTC
5015 CGGCGTTT
1 CGGCGTTT
5023 ATGAAAAAAC
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 13 0.17
41 59 0.79
42 3 0.04
ACGTcount: A:0.15, C:0.27, G:0.16, T:0.42
Consensus pattern (40 bp):
CGGCGTTTTCTCATAAACGCCGCTAGTGCTCTTACTTTTC
Found at i:12714 original size:82 final size:81
Alignment explanation
Indices: 12568--12728 Score: 250
Period size: 82 Copynumber: 2.0 Consensus size: 81
12558 GTTGACTTAG
* *
12568 ATCACAAGTGAGCGGCAAATCATGGAAAAGGGAAAACGCAAAATAATCCCTAGAGTTTCATTTTT
1 ATCACAAGCGAGCAGCAAATCATGGAAAAGGGAAAACGCAAAATAATCCCTAGAGTTTCATTTTT
12633 GCTACAAATTCGTCTA
66 GCTACAAATTCGTCTA
* * * * *
12649 ATCACGAGCGAGCAGCAGATCATGGAAAAGGGAAAATCGTAGAATAATCCCTAGAGTTTTATTTT
1 ATCACAAGCGAGCAGCAAATCATGGAAAAGGGAAAA-CGCAAAATAATCCCTAGAGTTTCATTTT
12714 TGCTACAAATTCGTC
65 TGCTACAAATTCGTC
12729 CAATAAGTTC
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
81 32 0.44
82 40 0.56
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (81 bp):
ATCACAAGCGAGCAGCAAATCATGGAAAAGGGAAAACGCAAAATAATCCCTAGAGTTTCATTTTT
GCTACAAATTCGTCTA
Found at i:12857 original size:19 final size:19
Alignment explanation
Indices: 12835--12934 Score: 110
Period size: 19 Copynumber: 5.2 Consensus size: 19
12825 GGAATTAGCA
12835 AATACTAGCTCGTAAGAGC
1 AATACTAGCTCGTAAGAGC
*
12854 AATACTAGCTCGTAAGGGC
1 AATACTAGCTCGTAAGAGC
* *
12873 AATACTGGCTCGTAAGAGT
1 AATACTAGCTCGTAAGAGC
* * *
12892 AATATTAGTTCGTGAGAGC
1 AATACTAGCTCGTAAGAGC
* * *
12911 AAATACTGGCTCATGAGAGC
1 -AATACTAGCTCGTAAGAGC
12931 AATA
1 AATA
12935 TGCTGTACTG
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
19 52 0.78
20 15 0.22
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (19 bp):
AATACTAGCTCGTAAGAGC
Found at i:12886 original size:38 final size:39
Alignment explanation
Indices: 12831--12934 Score: 129
Period size: 38 Copynumber: 2.7 Consensus size: 39
12821 AAAAGGAATT
*
12831 AGCAAATACTAGCTCGTAAGAGCAATACTAGCTCGTAAG
1 AGCAAATACTGGCTCGTAAGAGCAATACTAGCTCGTAAG
* * * * *
12870 GGC-AATACTGGCTCGTAAGAGTAATATTAGTTCGTGAG
1 AGCAAATACTGGCTCGTAAGAGCAATACTAGCTCGTAAG
* *
12908 AGCAAATACTGGCTCATGAGAGCAATA
1 AGCAAATACTGGCTCGTAAGAGCAATA
12935 TGCTGTACTG
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 32 0.59
39 22 0.41
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (39 bp):
AGCAAATACTGGCTCGTAAGAGCAATACTAGCTCGTAAG
Found at i:18529 original size:219 final size:214
Alignment explanation
Indices: 18149--18977 Score: 851
Period size: 213 Copynumber: 3.9 Consensus size: 214
18139 TTTTAGGGAT
* * * * * * * *
18149 ATGAGTGACAACCTTGAATGGTCAATTGGTAC-TATGATTAACGTACGTTATGAACATGTGTGGT
1 ATGAGTGACGACCTTGAA-AGTCAATTGATACTTATAATTAGCGTATGTTAGGAACATGCGTGGT
* * * * * * **
18213 AATAAGCATTTTGATTTTTTGGGTTTTGTGACTTTTGCATTAATGAAAGTTACACATGTTTCCAT
65 AATAAGCGTTTCGATGTTTTGGGATTTGCGACTTTTGCATTAAT-AAAGTGACACACATTTCCAT
* *
18278 GTGATTAAGTATTGAAGCGATATGACAATCATTAACTTTTCCACATATATATTAATAGTTTGTTA
129 GTGATTAAGTATTGAAGCGATATGACAATCATTAACTTTTCCACATATTTATT-GTAGTTTGTTA
*
18343 GTGAGCAGCCATTAAATTGGAAAC
193 GTGA-CAGCCA-TAAATTGGGAAC
* * * * *
18367 AAGAGTGACGACCTTGAAAGGTTAATTGGTACTTATGATTAGCATATGTTAGGAACATGCGTGGT
1 ATGAGTGACGACCTTGAAA-GTCAATTGATACTTATAATTAGCGTATGTTAGGAACATGCGTGGT
* * * * * *
18432 AATAAGCGTTTCAATGTTTTGGGTTTTGCGAATTTTACATTAATAAATGTGATACACGTTTCCAT
65 AATAAGCGTTTCGATGTTTTGGGATTTGCGACTTTTGCATTAATAAA-GTGACACACATTTCCAT
* ** *
18497 GTGATTGAGTATTGAAGCGATATGACAATC----A-TTTTCCTTATATTTATTGTCGATTTGTTA
129 GTGATTAAGTATTGAAGCGATATGACAATCATTAACTTTTCCACATATTTATTGTAG-TTTGTTA
* *
18557 ATGAACAGCCAGAAAGTTGGGAAC
193 GTG-ACAGCCATAAA-TTGGGAAC
* *
18581 ATGAGTGACGACCTTGAAAGTCAATTGATAATTATAATTAGCGTATGTTAGGAACATGTGTGGTA
1 ATGAGTGACGACCTTGAAAGTCAATTGATACTTATAATTAGCGTATGTTAGGAACATGCGTGGTA
* * ** * *
18646 ATAAGCGTTTTG-GGTTTTTGGGATTTGCGACTTTTGTGTTAATAAATGTGATACACATTTTCAT
66 ATAAGCGTTTCGATG-TTTTGGGATTTGCGACTTTTGCATTAATAAA-GTGACACACATTTCCAT
* * * *
18710 GTGACTAAGTATTGAAGCGATATGACAATCATTAACTTTTCCTCATATTTATTGTCAATTTGCTA
129 GTGATTAAGTATTGAAGCGATATGACAATCATTAACTTTTCCACATATTTATTGT-AGTTTGTTA
*
18775 GTGACAGCCATAATGTTGGGAAC
193 GTGACAGCCATAA-ATTGGGAAC
* * *
18798 ATGAGTGACGACCTTG-AAGT-TATCTGATACTTATAATTAGCGTATGCTAGGAACATGCATGGT
1 ATGAGTGACGACCTTGAAAGTCAAT-TGATACTTATAATTAGCGTATGTTAGGAACATGCGTGGT
* * * *
18861 AATAAGCG-TTCTGAT-TTTTGGGGATTTGTGACTTTTCCATTAATGAA-T--CACACATTTCTA
65 AATAAGCGTTTC-GATGTTTT-GGGATTTGCGACTTTTGCATTAATAAAGTGACACACATTTCCA
* * *
18921 TGTGATTGAA-TATTGAAGCGATACGATAATCATTAACTTTTCTACATATTTTATTGT
128 TGTGATT-AAGTATTGAAGCGATATGACAATCATTAACTTTTCCACATA-TTTATTGT
18978 CGACCTATTA
Statistics
Matches: 517, Mismatches: 74, Indels: 45
0.81 0.12 0.07
Matches are distributed among these distances:
212 50 0.10
213 135 0.26
214 55 0.11
215 10 0.02
216 70 0.14
217 34 0.07
218 56 0.11
219 107 0.21
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.37
Consensus pattern (214 bp):
ATGAGTGACGACCTTGAAAGTCAATTGATACTTATAATTAGCGTATGTTAGGAACATGCGTGGTA
ATAAGCGTTTCGATGTTTTGGGATTTGCGACTTTTGCATTAATAAAGTGACACACATTTCCATGT
GATTAAGTATTGAAGCGATATGACAATCATTAACTTTTCCACATATTTATTGTAGTTTGTTAGTG
ACAGCCATAAATTGGGAAC
Found at i:24026 original size:20 final size:20
Alignment explanation
Indices: 24001--24053 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
23991 TTGGCCTGAG
*
24001 ACTTCTACCGATAGAACTTC
1 ACTTCTACCGATAAAACTTC
* *
24021 ACTTCTACAGACAAAACTTC
1 ACTTCTACCGATAAAACTTC
* *
24041 AGTTTTACCGATA
1 ACTTCTACCGATA
24054 TCTTGAAGAC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.30
Consensus pattern (20 bp):
ACTTCTACCGATAAAACTTC
Found at i:24265 original size:20 final size:20
Alignment explanation
Indices: 24240--24295 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
24230 CTACCCTAGG
* *
24240 ACTTCTACTGGTAGAACTTC
1 ACTTCTACTGATACAACTTC
*
24260 ACTTCTATTGATACAACTTC
1 ACTTCTACTGATACAACTTC
*
24280 AATTCTACTGATACAA
1 ACTTCTACTGATACAA
24296 GTATGCTTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (20 bp):
ACTTCTACTGATACAACTTC
Found at i:25772 original size:21 final size:21
Alignment explanation
Indices: 25748--25793 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
25738 GAAAACAATG
* *
25748 ATAACGATGAGATTAATTATA
1 ATAACAATGAGATTAAATATA
* *
25769 ATAATAATGAGATTAAATATT
1 ATAACAATGAGATTAAATATA
25790 ATAA
1 ATAA
25794 AAATAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.35
Consensus pattern (21 bp):
ATAACAATGAGATTAAATATA
Found at i:26854 original size:72 final size:72
Alignment explanation
Indices: 26737--26881 Score: 281
Period size: 72 Copynumber: 2.0 Consensus size: 72
26727 AAAGAATATG
*
26737 CCCTTAAGATTCCATGATGGAATGCAGAGGACCTTGTTCTACTTGCAGTAAACTGTTCTAAACTA
1 CCCTTAAGATTCCATGATGGAATGCAGAGGACCTTATTCTACTTGCAGTAAACTGTTCTAAACTA
26802 AATCAGA
66 AATCAGA
26809 CCCTTAAGATTCCATGATGGAATGCAGAGGACCTTATTCTACTTGCAGTAAACTGTTCTAAACTA
1 CCCTTAAGATTCCATGATGGAATGCAGAGGACCTTATTCTACTTGCAGTAAACTGTTCTAAACTA
26874 AATCAGA
66 AATCAGA
26881 C
1 C
26882 TGAATAGTGA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.29
Consensus pattern (72 bp):
CCCTTAAGATTCCATGATGGAATGCAGAGGACCTTATTCTACTTGCAGTAAACTGTTCTAAACTA
AATCAGA
Done.