Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011427.1 Kokia drynarioides strain JFW-HI SEQ_126411, 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: 5387
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Found at i:35 original size:18 final size:17
Alignment explanation
Indices: 1--124 Score: 140
Period size: 17 Copynumber: 7.1 Consensus size: 17
* *
1 AATTTATAATAATTTTA
1 AATTTAAAATAAATTTA
18 AATTTGAAAATAAATTTA
1 AATTT-AAAATAAATTTA
* *
36 AACTTAAATTAAATTTA
1 AATTTAAAATAAATTTA
*
53 AATTCAAAATAAATTTA
1 AATTTAAAATAAATTTA
*
70 AATTTAAAATAAATTAA
1 AATTTAAAATAAATTTA
** *
87 AATTTTTTAACAAATTTA
1 AA-TTTAAAATAAATTTA
105 AATTTTAAAATAAATTTA
1 AA-TTTAAAATAAATTTA
123 AA
1 AA
125 GGGAGTTTGG
Statistics
Matches: 89, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
17 47 0.53
18 42 0.47
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:53 original size:11 final size:12
Alignment explanation
Indices: 14--91 Score: 65
Period size: 11 Copynumber: 6.8 Consensus size: 12
4 TTATAATAAT
14 TTTAAATTTGAAA
1 TTTAAATTT-AAA
*
27 -ATAAATTTAAA
1 TTTAAATTTAAA
*
38 CTTAAA-TTAAA
1 TTTAAATTTAAA
*
49 TTTAAATTCAAA
1 TTTAAATTTAAA
*
61 -ATAAATTTAAA
1 TTTAAATTTAAA
*
72 TTTAAA-ATAAA
1 TTTAAATTTAAA
*
83 TTAAAATTT
1 TTTAAATTT
92 TTTAACAAAT
Statistics
Matches: 51, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
11 31 0.61
12 20 0.39
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:91 original size:23 final size:23
Alignment explanation
Indices: 40--87 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
30 AATTTAAACT
*
40 TAAA-TTAAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAATCAAAA
*
62 TAAATTTAAATTTAAAAT-AAAT
1 TAAATTTAAATTTAAAATCAAAA
84 TAAA
1 TAAA
88 ATTTTTTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAATTTAAATTTAAAATCAAAA
Found at i:109 original size:6 final size:6
Alignment explanation
Indices: 14--91 Score: 65
Period size: 6 Copynumber: 13.5 Consensus size: 6
4 TTATAATAAT
* * *
14 TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA -TTAAA TTTAAA TTCAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
61 -ATAAA TTTAAA TTTAAA -ATAAA TTAAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
92 TTTAACAAAT
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
5 15 0.27
6 38 0.68
7 3 0.05
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:920 original size:206 final size:207
Alignment explanation
Indices: 459--1115 Score: 719
Period size: 207 Copynumber: 3.2 Consensus size: 207
449 TTTCATTGAC
*
459 TTGGCCTTCTTC-CTAGTATCTCATTGGGAAGATGACTGCATAGTTTGTTTCAATTCGCTTCTCT
1 TTGGCCTTCTTCTC-AGTATCTCATTGGGAAGATGACCGCATAGTTTGTTTCAATTCGCTTCTCT
* * * *
523 GTATCTCATCAAGAAGACGAATTTTGATCAACTTCTCCGTATCTCATC-AAGAAGCTAACCGTTT
65 GTATCTCATCAGGAAGACGAA-TTTGTTC-ACTTCTCAGTATCTCATCTAATAAGCTAACCGTTT
* ** * * * * *
587 TATTATTTCGCCCTGCTTCTCAATATCTTATCAAGAAGCTGGGGTTCGAAG-GTTTG-TT-CATC
128 TATTATTTCGACCTGCTTCTCGGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTTGCTTT
* * ** *
649 GTGCGTGGGTTTGGT
193 GAGCGTAGGCCTGAT
* * * * * *
664 TTGGCCTTCTTCTCAGTATCTCATCGGGAAGATGACCACATCGCTTGTTTCAATCCGCCTCT-TC
1 TTGGCCTTCTTCTCAGTATCTCATTGGGAAGATGACCGCATAGTTTGTTTCAATTCGCTTCTCT-
* *
728 GCATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCTGA-AAGCTAACCG-TTT
65 GTATCTCATCAGGAAGACGAATTT-GTTCACTTCTCAGTATCTCATCTAATAAGCTAACCGTTTT
**
791 ATTGCTTCGACCTGCTTCTCGGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTTGCTTTG
129 ATTATTTCGACCTGCTTCTCGGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTTGCTTTG
856 AGCGTAGGCCTGAT
194 AGCGTAGGCCTGAT
* * *
870 TTGGTCTTCTTCTCAGTATCTCATTGGGAAGATGACTGCGTAGTTTGTTTCAATTCGCTTCTCTG
1 TTGGCCTTCTTCTCAGTATCTCATTGGGAAGATGACCGCATAGTTTGTTTCAATTCGCTTCTCTG
* ** * * **
935 TATCTCATCAGGAAGACGAATTTCTT-A--TCAGGAAGCTAATCGT--TTTATTATTCTAACCGT
66 TATCTCATCAGGAAGACGAATTTGTTCACTTC--TCAG-T-ATC-TCATCTAATAAGCTAACCGT
* *
995 TTTATTATTTCGACCTGGTTCTCGGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCGCT
126 TTTATTATTTCGACCTGCTTCTCGGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTTGCT
1060 TTGAGCGTAGGCCTGAT
191 TTGAGCGTAGGCCTGAT
* * * * * *
1077 TTGGTCTCCTTTTCAGCATCTCACTAGGAAGATGACCGC
1 TTGGCCTTCTTCTCAGTATCTCATTGGGAAGATGACCGC
1116 GTCGTTTATG
Statistics
Matches: 382, Mismatches: 55, Indels: 28
0.82 0.12 0.06
Matches are distributed among these distances:
202 2 0.01
203 46 0.12
204 38 0.10
205 83 0.22
206 100 0.26
207 113 0.30
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (207 bp):
TTGGCCTTCTTCTCAGTATCTCATTGGGAAGATGACCGCATAGTTTGTTTCAATTCGCTTCTCTG
TATCTCATCAGGAAGACGAATTTGTTCACTTCTCAGTATCTCATCTAATAAGCTAACCGTTTTAT
TATTTCGACCTGCTTCTCGGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTTGCTTTGAG
CGTAGGCCTGAT
Found at i:995 original size:17 final size:17
Alignment explanation
Indices: 970--1003 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
960 TATCAGGAAG
*
970 CTAATCGTTTTATTATT
1 CTAACCGTTTTATTATT
987 CTAACCGTTTTATTATT
1 CTAACCGTTTTATTATT
1004 TCGACCTGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.15, G:0.06, T:0.56
Consensus pattern (17 bp):
CTAACCGTTTTATTATT
Done.