Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011235.1 Kokia drynarioides strain JFW-HI SEQ_126213, 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: 7044
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Found at i:720 original size:24 final size:23
Alignment explanation
Indices: 683--729 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
673 TTGGACTTTG
*
683 ATTTAAATAGATTTAAACTTTAA
1 ATTTAAATAAATTTAAACTTTAA
*
706 ATTTATAATAAATTTAAATTTTAA
1 ATTTA-AATAAATTTAAACTTTAA
730 GTAAATCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTTAAATAAATTTAAACTTTAA
Found at i:721 original size:17 final size:17
Alignment explanation
Indices: 696--775 Score: 97
Period size: 17 Copynumber: 4.6 Consensus size: 17
686 TAAATAGATT
*
696 TAAACTTTAAATTTATAA
1 TAAA-TTTAAATTTAAAA
* *
714 TAAATTTAAATTTTAAG
1 TAAATTTAAATTTAAAA
* *
731 TAAATCTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
748 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
765 TAAATTTAAAT
1 TAAATTTAAAT
776 CCTATTGGGC
Statistics
Matches: 51, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
17 47 0.92
18 4 0.08
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:723 original size:6 final size:6
Alignment explanation
Indices: 693--775 Score: 50
Period size: 6 Copynumber: 14.3 Consensus size: 6
683 ATTTAAATAG
* * *
693 ATTTAA ACTTTAA ATTTATA A--TAA ATTTAA ATTTTA A-GTAA ATCTAA
1 ATTTAA A-TTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * * *
740 ACTTAA A-ATAA ATTTAA TTTTAA A-ATAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT
776 CCTATTGGGC
Statistics
Matches: 58, Mismatches: 12, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
4 2 0.03
5 13 0.22
6 35 0.60
7 8 0.14
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (6 bp):
ATTTAA
Found at i:1454 original size:193 final size:198
Alignment explanation
Indices: 1111--1748 Score: 664
Period size: 193 Copynumber: 3.2 Consensus size: 198
1101 ACTTGGCCTT
* * * * * * * * *
1111 CTTCTCAGTATCTCATCAAGAAGACGACCGCATCGCTTGTTTTGATCCACTTCTCTGTGTTTCCT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTAGTTTTAATCCGCTTCTCTGTATCTCAT
* * * *
1176 CAAGAAGACGGATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTCGC
66 CAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTCGA
* * * *
1241 CCTGTTTCTCTG-TATCTCATCAGGAGGCTGGGG-TCGAAGATTTG-T-TT-GC-ATTGAGTTGG
131 CCTGCTTCTC-GATGTCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTATTGGCGATTGAGTTGG
1300 TATA
195 TATA
* * *
1304 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTAGTTTCAATCCGCTTCTCTGTATCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTAGTTTTAATCCGCTTCTCTGTATCTCAT
* ** *
1369 CAAAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAAAAGCTAACCTTTTTATTGTTTCGA
66 CAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTCGA
*
1434 CCTGCTTCTCGATGTCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTCACATTGAGCGCGGGTTT
131 CCTGCTTCTCGATGTCTCATCAGGAAGTTGGGGTTCGAAGATTTGCT---ATT--G-GC--GATT
* * *
1499 GATTTGGTCTT
188 GAGTTGGTATA
** ** *
1510 CTTCTCAGTATCTCATCAGGAAGATGACCGTGTCGTTTA-TTTTAATCCGCTTCTCTATATCTCA
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATC-ACTAGTTTTAATCCGCTTCTCTGTATCTCA
* * * *
1574 TCAAGAAGACGAATTTGGTCCAATTCTCAGTATCTCATTAGGAAGCAAACC-TTTTATTGCTTCA
65 TCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTCG
* *
1638 ACCTGCTTCTC-AGTGTCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTTACATCGAGCGTGGGT
130 ACCTGCTTCTCGA-TGTCTCATCAGGAAGTTGGGGTTCGAAGATTTGC-T--ATTG-GC----GA
* * *
1702 TTGATTTGGTCTT
186 TTGAGTTGGTATA
1715 CTTCTCAGTATCTCATCAGGAAGATGACCGCATC
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATC
1749 GTTTGTGGAT
Statistics
Matches: 379, Mismatches: 47, Indels: 26
0.84 0.10 0.06
Matches are distributed among these distances:
192 1 0.00
193 137 0.36
194 11 0.03
195 1 0.00
199 2 0.01
203 5 0.01
204 1 0.00
205 109 0.29
206 110 0.29
207 2 0.01
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (198 bp):
CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTAGTTTTAATCCGCTTCTCTGTATCTCAT
CAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTCGA
CCTGCTTCTCGATGTCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTATTGGCGATTGAGTTGGT
ATA
Found at i:1730 original size:205 final size:206
Alignment explanation
Indices: 1304--1745 Score: 683
Period size: 205 Copynumber: 2.2 Consensus size: 206
1294 AGTTGGTATA
* *
1304 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTAGTTTCAATCCGCTTCTCTGTATCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCCTCACTAGTTTCAATCCGCTTCTCTATATCTCAT
* * * *
1369 CAAAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAAAAGCTAACCTTTTTATTGTTTCGA
66 CAAAAAGACGAATTTGGTCCAATTCTCAGTATCTCATCAAAAAGCAAACCTTTTTATTGCTTCAA
*
1434 CCTGCTTCTCGATGTCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTCACATTGAGCGCGGGTTT
131 CCTGCTTCTCGATGTCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTCACATCGAGCGCGGGTTT
1499 GATTTGGTCTT
196 GATTTGGTCTT
** ** *
1510 CTTCTCAGTATCTCATCAGGAAGATGACCGTGTCGTTTA-TTTTAATCCGCTTCTCTATATCTCA
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCCTC-ACTAGTTTCAATCCGCTTCTCTATATCTCA
* * **
1574 TCAAGAAGACGAATTTGGTCCAATTCTCAGTATCTCATTAGGAAGCAAACC-TTTTATTGCTTCA
65 TCAAAAAGACGAATTTGGTCCAATTCTCAGTATCTCATCAAAAAGCAAACCTTTTTATTGCTTCA
* *
1638 ACCTGCTTCTC-AGTGTCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTTACATCGAGCGTGGGT
130 ACCTGCTTCTCGA-TGTCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTCACATCGAGCGCGGGT
1702 TTGATTTGGTCTT
194 TTGATTTGGTCTT
1715 CTTCTCAGTATCTCATCAGGAAGATGACCGC
1 CTTCTCAGTATCTCATCAGGAAGATGACCGC
1746 ATCGTTTGTG
Statistics
Matches: 215, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
204 1 0.00
205 113 0.53
206 99 0.46
207 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (206 bp):
CTTCTCAGTATCTCATCAGGAAGATGACCGCCTCACTAGTTTCAATCCGCTTCTCTATATCTCAT
CAAAAAGACGAATTTGGTCCAATTCTCAGTATCTCATCAAAAAGCAAACCTTTTTATTGCTTCAA
CCTGCTTCTCGATGTCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTCACATCGAGCGCGGGTTT
GATTTGGTCTT
Done.