Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007067.1 Kokia drynarioides strain JFW-HI SEQ_121676, 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: 2397
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Found at i:87 original size:3 final size:3
Alignment explanation
Indices: 79--134 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
69 ACCTTTCGAT
* *
79 TTA TTA TTA TTA TTA ATA TCTA TTA TTA TTA TTA -TA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
*
124 ATA TTAA TTA T
1 TTA TT-A TTA T
135 AGTTGCCATT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 2 0.04
3 38 0.83
4 6 0.13
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:866 original size:17 final size:16
Alignment explanation
Indices: 844--923 Score: 97
Period size: 17 Copynumber: 4.8 Consensus size: 16
834 TAAATAAATT
844 TAAATTTAAATTTATAA
1 TAAATTTAAATTTA-AA
861 TAAATTTAAATTTCAAA
1 TAAATTTAAATTT-AAA
878 TAAATTTAAATTTAAAA
1 TAAATTTAAATTT-AAA
* *
895 TAAACTTAATTTTAATA
1 TAAATTTAAATTTAA-A
*
912 TAAATTCAAATT
1 TAAATTTAAATT
924 CTGTTGGACC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
16 2 0.04
17 52 0.95
18 1 0.02
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:866 original size:23 final size:23
Alignment explanation
Indices: 831--878 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
821 ATTGGACATT
831 ATTTAAATAAATTTAAATTT-AA
1 ATTTAAATAAATTTAAATTTCAA
853 ATTTATAATAAATTTAAATTTCAA
1 ATTTA-AATAAATTTAAATTTCAA
877 AT
1 AT
879 AAATTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 5 0.21
23 15 0.62
24 4 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAAATAAATTTAAATTTCAA
Found at i:881 original size:11 final size:10
Alignment explanation
Indices: 831--888 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
821 ATTGGACATT
831 ATTTAAATAA
1 ATTTAAATAA
841 ATTTAAATTTAA
1 ATTTAAA--TAA
853 ATTTATAATAA
1 ATTTA-AATAA
864 ATTTAAAT--
1 ATTTAAATAA
*
872 -TTCAAATAA
1 ATTTAAATAA
881 ATTTAAAT
1 ATTTAAAT
889 TTAAAATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 6 0.15
10 16 0.40
11 8 0.20
12 8 0.20
13 2 0.05
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (10 bp):
ATTTAAATAA
Found at i:885 original size:34 final size:34
Alignment explanation
Indices: 844--923 Score: 108
Period size: 34 Copynumber: 2.4 Consensus size: 34
834 TAAATAAATT
* *
844 TAAATTTAAATTTATAATAAATTTAAATTTCAA-A
1 TAAATTTAAATTTAAAATAAACTT-AATTTCAATA
*
878 TAAATTTAAATTTAAAATAAACTTAATTTTAATA
1 TAAATTTAAATTTAAAATAAACTTAATTTCAATA
*
912 TAAATTCAAATT
1 TAAATTTAAATT
924 CTGTTGGACC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 7 0.17
34 34 0.83
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (34 bp):
TAAATTTAAATTTAAAATAAACTTAATTTCAATA
Found at i:887 original size:23 final size:23
Alignment explanation
Indices: 836--893 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
826 ACATTATTTA
**
836 AATAAATTTAAATTTAAATTTAT
1 AATAAATTTAAATTTAAATAAAT
859 AATAAATTTAAATTTCAAATAAAT
1 AATAAATTTAAATTT-AAATAAAT
*
883 -TTAAATTTAAA
1 AATAAATTTAAA
894 ATAAACTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 25 0.81
24 6 0.19
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
AATAAATTTAAATTTAAATAAAT
Found at i:895 original size:7 final size:6
Alignment explanation
Indices: 838--923 Score: 67
Period size: 6 Copynumber: 15.0 Consensus size: 6
828 ATTATTTAAA
838 TAAATT TAAATT TAAATT TATAA-- TAAATT TAAATT TCAAA-- TAAATT
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAATT TAAATT
* * * * *
884 TAAATT TAAA-A TAAACT T-AATT TTAATA TAAATT CAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
924 CTGTTGGACC
Statistics
Matches: 65, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
4 5 0.08
5 11 0.17
6 44 0.68
7 5 0.08
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:1551 original size:120 final size:121
Alignment explanation
Indices: 1381--1758 Score: 430
Period size: 115 Copynumber: 3.2 Consensus size: 121
1371 TTACTTTATC
* * *
1381 CTGCTTCTCAGTATCTTATCAAGAAGCTGGGGA-TCGAGGATTTGCTCACATCGAGCGCGGGTTT
1 CTGCTTCTCAGTATCTCATCAGGAAGCT-GGGATTCGAAGATTTGCTCACATCGAGCGCGGGTTT
*
1445 GATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACCTTACTTGTTTCAAT
65 GATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACATTACTTGTTTCAAT
* ** *
1502 CTGCTTCTCTGTATCTCATCAGGAAGCT-GGATTCGAAGATTTGAACACATCGAGC-C----CTG
1 CTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCGCGGGTTTG
* * * * * * ** * * *
1561 AGTTGGTATACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTA-TTATTTCGAC
66 ATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACATTACTTGTTTCAAT
* * *
1616 CTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTTGAAGATTTGCTCACATCGAGCGTGGGTTTG
1 CTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCGCGGGTTTG
* ** **
1681 ATTTGGTCTTCTCCTCAGTATCTCATCAGGAAGATGACTGCATCGCTTGTTTCAAT
66 ATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACATTACTTGTTTCAAT
* *
1737 CCGCTTCTCCGTATCTCATCAG
1 CTGCTTCTCAGTATCTCATCAG
1759 AAAGACGAAT
Statistics
Matches: 206, Mismatches: 43, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
114 34 0.17
115 62 0.30
119 4 0.02
120 54 0.26
121 52 0.25
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.34
Consensus pattern (121 bp):
CTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCGCGGGTTTG
ATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACATTACTTGTTTCAAT
Found at i:1772 original size:120 final size:117
Alignment explanation
Indices: 1378--1758 Score: 373
Period size: 121 Copynumber: 3.2 Consensus size: 117
1368 TTATTACTTT
* * * * *
1378 ATCCTGCTTCTCAGTATCTTATCAAGAAGCTGGGGA-TCGAGGATTTGCTCACATCGAGCGCGGG
1 ATCC-GCTTCTCAGTATCTCATCAGGAAGCT--GGATTTGAAGATTTGCTCACATCGAGCGTGGG
1442 TTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACCTTACTTGTTTCA
63 TTTGATTTGGTCTTC-TCTCAGTATCTCATCAGGAAGATGACCA--TTACTTGTTTCA
* * * ** * *
1500 ATCTGCTTCTCTGTATCTCATCAGGAAGCTGGATTCGAAGATTTGAACACATCGAGCCCTGAG-T
1 ATCCGCTTCTCAGTATCTCATCAGGAAGCTGGATTTGAAGATTTGCTCACATCGAG-CGTGGGTT
* * * * * * *
1564 TGGTAT--ACTTCTCT--GTATCTCATCAGGAAGCTAACCATTTTA-TTATTTCG
65 TGATTTGGTCTTCTCTCAGTATCTCATCAGGAAGATGACCA--TTACTTGTTTCA
*
1614 A-CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTTGAAGATTTGCTCACATCGAGCGTGGGT
1 ATCC-GCTTCTCAGTATCTCATCAGGAAGCT-GGATTTGAAGATTTGCTCACATCGAGCGTGGGT
**
1678 TTGATTTGGTCTTCTCCTCAGTATCTCATCAGGAAGATGACTGCATCGCTTGTTTCA
64 TTGATTTGGTCTTCT-CTCAGTATCTCATCAGGAAGATGAC--CATTACTTGTTTCA
*
1735 ATCCGCTTCTCCGTATCTCATCAG
1 ATCCGCTTCTCAGTATCTCATCAG
1759 AAAGACGAAT
Statistics
Matches: 208, Mismatches: 37, Indels: 29
0.76 0.14 0.11
Matches are distributed among these distances:
113 1 0.00
114 36 0.17
115 51 0.25
117 8 0.04
118 6 0.03
119 3 0.01
120 44 0.21
121 52 0.25
122 7 0.03
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (117 bp):
ATCCGCTTCTCAGTATCTCATCAGGAAGCTGGATTTGAAGATTTGCTCACATCGAGCGTGGGTTT
GATTTGGTCTTCTCTCAGTATCTCATCAGGAAGATGACCATTACTTGTTTCA
Found at i:1838 original size:206 final size:200
Alignment explanation
Indices: 1578--1957 Score: 519
Period size: 206 Copynumber: 1.9 Consensus size: 200
1568 ATACTTCTCT
* *
1578 GTATCTCATCAGGAAGCTAACCATTTTATTATTTCGACCTGCTTCTCAGTATCTCATCAGGAAGC
1 GTATCTCATCAAGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGC
* * * * *
1643 TGGGGTTTGAAGATTTGCTCACATCGAG-CGTGGGTTTGATTTGGTCTTCTCCTCAGTATCTCAT
66 T-GGGTTCGAAGATTTGCTCACATCAAGTCCTGAG-TTGATAT--TCTTCT--T-AGTATCTCAT
* ** *
1707 CAGGAAGATGACTGCATCGCTTGTTTCAATCCGCTTCTCCGTATCTCATCAGAAAGACGAATTTG
124 CAGAAAGATGACCACATCACTTGTTTCAATCCGCTTCTCCGTATCTCATCAGAAAGACGAATTTG
1772 ATTCACTTTTCA
189 ATTCACTTTTCA
* *
1784 GTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATTAGGAAGC
1 GTATCTCATCAAGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGC
* * *
1849 TGGGTTCGAAGATTTGCTCGCATCAAGTCCTGAGTTGGTATTCTTCTTTGTATCTCATCAGAAAG
66 TGGGTTCGAAGATTTGCTCACATCAAGTCCTGAGTTGATATTCTTCTTAGTATCTCATCAGAAAG
* * *
1914 ATGACCACCTTACTTGTTTCAATCCGCTTCTCTGTATCTCATCA
131 ATGACCACATCACTTGTTTCAATCCGCTTCTCCGTATCTCATCA
1958 AGAAGCTAGG
Statistics
Matches: 154, Mismatches: 19, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
200 53 0.34
201 1 0.01
203 6 0.04
205 28 0.18
206 66 0.43
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (200 bp):
GTATCTCATCAAGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGC
TGGGTTCGAAGATTTGCTCACATCAAGTCCTGAGTTGATATTCTTCTTAGTATCTCATCAGAAAG
ATGACCACATCACTTGTTTCAATCCGCTTCTCCGTATCTCATCAGAAAGACGAATTTGATTCACT
TTTCA
Found at i:2076 original size:436 final size:438
Alignment explanation
Indices: 1355--2170 Score: 1223
Period size: 436 Copynumber: 1.9 Consensus size: 438
1345 ATTTTGTCAG
* * *
1355 GAAGCTAACCATTTTATTACTTTATCCTGCTTCTCAGTATCTTATCAAGAAGCTGGGGATCGAGG
1 GAAGCTAACCATTTTATTACTTGATCCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGATCGAAG
* * * *
1420 ATTTGCTCACATCGAGCGCGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACC
66 ATTTGCTCACATCAAGCGC--G--TGAGTTGGTATTCTTCTCAGTATCTCATCAGAAAGATGACC
* * *
1485 ACCTTACTTGTTTCAATCTGCTTCTCTGTATCTCATCAGGAAGCTGGATTCGAAGATTTGAACAC
127 ACCTTACTTGTTTCAATCCGCTTCTCTGTATCTCATCAAGAAGCTGGATTCGAAGACTTGAACAC
1550 ATCGAGCCCTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTATTTCGA
192 ATCGAGCCCTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTATTTCGA
* * * *
1615 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTTGAAGATTTGCTCACATCGAGCGT-GGGT-
257 CCTACTTCTCAGTATCTCATCAGGAAACTGGGGTTCGAAGATTTGCTCACATCGAGCCTCGGGTA
*
1678 TTGATTTGGTCTTCTCCTCAGTATCTCATCAGGAAGATGA-CTGCATCGCTTGTTTCAATCCGCT
322 TTGATTTGGTCTTCTCCTCAGTATCTCATCAAGAAGATGATC-GCATCGC-TGTTTCAATCCGCT
1742 TCTCCGTATCTCATCAGAAAGACGAATTTGATTCACTTTTCAGTATCTCATCAA
385 TCTCCGTATCTCATCAGAAAGACGAATTTGATTCACTTTTCAGTATCTCATCAA
* * * *
1796 GAAGCTAACCATTTTATTGCTTCGA-CCTGCTTCTCAGTATCTCATTAGGAAGCT-GGGTTCGAA
1 GAAGCTAACCATTTTATTACTT-GATCCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGATCGAA
* **
1859 GATTTGCTCGCATCAAGTC-C-TGAGTTGGTATTCTTCTTTGTATCTCATCAGAAAGATGACCAC
65 GATTTGCTCACATCAAG-CGCGTGAGTTGGTATTCTTCTCAGTATCTCATCAGAAAGATGACCAC
*
1922 CTTACTTGTTTCAATCCGCTTCTCTGTATCTCATCAAGAAGCTAGGATTCGAAGACTTGATCACA
129 CTTACTTGTTTCAATCCGCTTCTCTGTATCTCATCAAGAAGCT-GGATTCGAAGACTTGAACACA
1987 TCGAGCCCTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTATTTCGAC
193 TCGAGCCCTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTATTTCGAC
* * * * **
2052 CTACTTCTCAGTATCTCGTCAGGAAATTGGGGTTCGAAGATTTGCTCACTTTGAGCCTCGTTTCA
258 CTACTTCTCAGTATCTCATCAGGAAACTGGGGTTCGAAGATTTGCTCACATCGAGCCTCGGGT-A
*
2117 TTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGATCGCATCGCTGTTT
322 TTGATTTGGTCTTCTCCTCAGTATCTCATCAAGAAGATGATCGCATCGCTGTTT
2171 GTGGATGGTC
Statistics
Matches: 338, Mismatches: 30, Indels: 17
0.88 0.08 0.04
Matches are distributed among these distances:
435 79 0.23
436 134 0.40
437 2 0.01
438 5 0.01
439 45 0.13
440 24 0.07
441 48 0.14
442 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (438 bp):
GAAGCTAACCATTTTATTACTTGATCCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGATCGAAG
ATTTGCTCACATCAAGCGCGTGAGTTGGTATTCTTCTCAGTATCTCATCAGAAAGATGACCACCT
TACTTGTTTCAATCCGCTTCTCTGTATCTCATCAAGAAGCTGGATTCGAAGACTTGAACACATCG
AGCCCTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTATTTCGACCTA
CTTCTCAGTATCTCATCAGGAAACTGGGGTTCGAAGATTTGCTCACATCGAGCCTCGGGTATTGA
TTTGGTCTTCTCCTCAGTATCTCATCAAGAAGATGATCGCATCGCTGTTTCAATCCGCTTCTCCG
TATCTCATCAGAAAGACGAATTTGATTCACTTTTCAGTATCTCATCAA
Done.