Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007742.1 Kokia drynarioides strain JFW-HI SEQ_122375, 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: 2617
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.35
Found at i:920 original size:86 final size:86
Alignment explanation
Indices: 743--909 Score: 239
Period size: 86 Copynumber: 2.0 Consensus size: 86
733 CCTTCATTTG
* * *
743 ATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCATTACTTCTTTTAATCCGCTTCTC
1 ATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCATTACTTCTTTCAACCCGCTTCTC
* *
808 TGTATCTCATCAGGAAGACGA
66 AGTATCTCATCAAGAAGACGA
* * *
829 ATTTGGTCCACTTCTCTGTGTCTCATCAGGAAGATGACCGCTTTA-TTGC-TTCGACCCGCTTCT
1 ATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCATTACTT-CTTTCAACCCGCTTCT
892 CAGTATCTCATCAAGAAG
65 CAGTATCTCATCAAGAAG
910 CTGGGGTTTG
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
85 29 0.40
86 43 0.60
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (86 bp):
ATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCATTACTTCTTTCAACCCGCTTCTC
AGTATCTCATCAAGAAGACGA
Found at i:1010 original size:208 final size:209
Alignment explanation
Indices: 630--1454 Score: 973
Period size: 209 Copynumber: 4.0 Consensus size: 209
620 CTCTCAGTCT
* * * * * ** * *
630 ACTTCTCTGTATCTCACCAAGAAGATGATCGATTTATTGCTTCAACCCACTTCTCTGTATCTTAT
1 ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
** * * * ** *
695 CAGGAAAATAGGGGTTTTTGAAGCTTCACTCACA-T----TTTCCTTCATTTGATTTGGTCTACT
66 CAGGAAGCTA-GGG--TTCGAAGTTTCGCTCACATTAAGCTTTGTTTCA-TTGATTTGGTATACT
* * * *
755 TCTCTGTATCTCATCAGGAAGATGACCGCATTACTTCTTTTAATCCGCTTCTCTGTATCTCATCA
127 TCTCTATATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTATCTCATCA
*
820 GGAAGACGAATTTGGTCC
192 AGAAGACGAATTTGGTCC
* *
838 ACTTCTCTGTGTCTCATCAGGAAGATGACCGCTTTATTGCTTCGACCCGCTTCTCAGTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
* * * * * * * *
903 CAAGAAGCTGGGGTTTGGAGTTTCGCTCATATTAAGCTTTATTTCGTTGATTTGGTATTCTTCTC
66 CAGGAAGCTAGGGTTCGAAGTTTCGCTCACATTAAGCTTTGTTTCATTGATTTGGTATACTTCTC
* * * *
968 TATATCTCATTAGGAAGATGATCGCATCAC-TGTTTCAATCCGCTTCTCTGTATCTCATCAAGAA
131 TATATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTATCTCATCAAGAA
**
1032 GACGAATTTGGTTT
196 GACGAATTTGGTCC
* * ** ** * *
1046 ACTTCTCTGTATCTCATCAGGAAGTTGATCATTTTATTGCTTTAACATGCTTCTCAATATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
*
1111 CAGGAAGCTAGGGTTCGAAGTTTCGCTCACA-TAGAGCTTTGCTTCATTGATTTGGTATACTTCT
66 CAGGAAGCTAGGGTTCGAAGTTTCGCTCACATTA-AGCTTTGTTTCATTGATTTGGTATACTTCT
* ** * * *
1175 CCATATCTCATCAGGAAGATGACTACCTCACTTGTTTTAATCTACTTCTCTGTATCTCATCAGGA
130 CTATATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTATCTCATCAAGA
*
1240 AGACGGATTTGGTCC
195 AGACGAATTTGGTCC
* * * *
1255 ACTTCTCTGTATCTCATCAAGAAGACGACAGCTTTATTGCTTCGACCTG-TCTCTCAGTACCTCA
1 ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTCGACCTGCT-TCTCAGTATCTCA
* * *
1319 TCAGGAAGCTAGGGTTCGAAGTTTCACTCACATTGAGCTTTGTTTCATTAATTTGGTATACTTCT
65 TCAGGAAGCTAGGGTTCGAAGTTTCGCTCACATTAAGCTTTGTTTCATTGATTTGGTATACTTCT
* *
1384 CTGTATCTCATCAGGAAGAGGACCGCATCACTTGTTTTAATCCACTTCTCTGTATCTCATCAAGA
130 CTATATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTATCTCATCAAGA
1449 AGACGA
195 AGACGA
1455 CCGCTTTATT
Statistics
Matches: 520, Mismatches: 88, Indels: 17
0.83 0.14 0.03
Matches are distributed among these distances:
205 14 0.03
206 1 0.00
207 5 0.01
208 238 0.46
209 255 0.49
210 7 0.01
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.37
Consensus pattern (209 bp):
ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
CAGGAAGCTAGGGTTCGAAGTTTCGCTCACATTAAGCTTTGTTTCATTGATTTGGTATACTTCTC
TATATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCTCTGTATCTCATCAAGAA
GACGAATTTGGTCC
Found at i:1538 original size:172 final size:170
Alignment explanation
Indices: 1252--1641 Score: 597
Period size: 172 Copynumber: 2.3 Consensus size: 170
1242 ACGGATTTGG
1252 TCCACTTCTCTGTATCTCATCAAGAAGACGACAGCTTTATTGCTTCGACCTGTCTCTCAGTACCT
1 TCCACTTCTCTGTATCTCATCAAGAAGACGACAGCTTTATTGCTTCGACCTGTCTCTCAGTACCT
*
1317 CATCAGGAAGCTAGGGTTCGAAGTTTCACTCACATTGAGCTTTGTTTCATTAATTTGGTATACTT
66 CATCAGGAAGCTAGGGTTCGAAGTTTCACTCACATTGAACTTTGTTTCATTAATTTGGTATACTT
* *
1382 CTCTGTATCTCATCAGGAAGAGGACCGCATCACTTGTTTTAA
131 CTCTGTATCTCATCAAGAAGA-GACCGCATCAC-TGTTTCAA
* *
1424 TCCACTTCTCTGTATCTCATCAAGAAGACGACCGCTTTATTGCTTCGACCTG-CTTCTCAGTATC
1 TCCACTTCTCTGTATCTCATCAAGAAGACGACAGCTTTATTGCTTCGACCTGTC-TCTCAGTACC
* *
1488 TCATCCGGAAGCT-GGGATTCGAAGTTTCACTCACATTGAACTTTGTTTCATTAATTTGGTATGC
65 TCATCAGGAAGCTAGGG-TTCGAAGTTTCACTCACATTGAACTTTGTTTCATTAATTTGGTATAC
* ** *
1552 TTCTCTGTATCTCATCAAGAAGATATTGCATCACTGTTTCCA
129 TTCTCTGTATCTCATCAAGAAGAGACCGCATCACTGTTTCAA
* *
1594 TCCACTTCTCTGTATCTCATCAGGAAGACAACTA-CTTTATTGCTTCGA
1 TCCACTTCTCTGTATCTCATCAAGAAGACGAC-AGCTTTATTGCTTCGA
1642 TAACTACAAT
Statistics
Matches: 201, Mismatches: 14, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
170 50 0.25
171 12 0.06
172 139 0.69
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.36
Consensus pattern (170 bp):
TCCACTTCTCTGTATCTCATCAAGAAGACGACAGCTTTATTGCTTCGACCTGTCTCTCAGTACCT
CATCAGGAAGCTAGGGTTCGAAGTTTCACTCACATTGAACTTTGTTTCATTAATTTGGTATACTT
CTCTGTATCTCATCAAGAAGAGACCGCATCACTGTTTCAA
Found at i:1775 original size:78 final size:77
Alignment explanation
Indices: 1644--1872 Score: 207
Period size: 78 Copynumber: 2.9 Consensus size: 77
1634 TGCTTCGATA
* * * * * * **
1644 ACTACAATCTGCCCCAT-GATC-GGGTAAGAGATTGGATGGCTGTGATCTACCCCATAGTTGGGG
1 ACTACAATCTGCCCC-TGGCTCGGGGTAAGAGATTGG-TTGATGTGATCTGCCCCAGACTCAGGG
1707 TAAAAGATC-AGATG
64 TAAAAGATCGA-ATG
1721 ACTACAATCTGCCCCTGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAGACTCAGGGT
1 ACTACAATCTGCCCCTGGCTCGGGGTAAGAGATTGGTTGAT-GTGATCTGCCCCAGACTCAGGGT
1786 AAAAGATCGAATG
65 AAAAGATCGAATG
* * * * * * * *
1799 GCTACCATCTGCCTC-GAGCTCGGGATAAGAGATTGGCTAATAGTGATCTGCCTCA-AGCTCGGG
1 ACTACAATCTGCCCCTG-GCTCGGGGTAAGAGATTGGTTGAT-GTGATCTGCCCCAGA-CTCAGG
*
1862 GTAAGAGATCG
63 GTAAAAGATCG
1873 GAATCTTCAA
Statistics
Matches: 128, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
76 1 0.01
77 23 0.18
78 103 0.80
79 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (77 bp):
ACTACAATCTGCCCCTGGCTCGGGGTAAGAGATTGGTTGATGTGATCTGCCCCAGACTCAGGGTA
AAAGATCGAATG
Done.