Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010522.1 Kokia drynarioides strain JFW-HI SEQ_125434, 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: 1719
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.24
Warning! 71 characters in sequence are not A, C, G, or T
Found at i:1130 original size:139 final size:139
Alignment explanation
Indices: 661--1126 Score: 758
Period size: 139 Copynumber: 3.3 Consensus size: 139
651 AAACGGTTAG
* * *
661 CTTCCTGATGAGATACTGAG-AGATGAACCAAATTCGTATTCCTGATGAAATACAGAGAAGCAGA
1 CTTCCAGATGAGGTACTGAGAAG-TGAACCAAATTCGTCTTCCTGATGAAATACAGAGAAGCAGA
725 TTGAAACAGTGATGGGATCATCTTCTTGATGAGACACTGAGAAAAAGACCCAAACGAGGCTCGAA
65 TTGAAACAGTGATGGGATCATCTTCTTGATGAGACACTGAGAAAAAGACCCAAACGAGGCTCGAA
790 ACGAGCAGAT
130 ACGAGCAGAT
800 CTTCCAGATGAGGTACTGAGAAGTGAACCAAATTTCGTCTTCCTGATGAAATACAGAGAAGCAGA
1 CTTCCAGATGAGGTACTGAGAAGTGAACCAAA-TTCGTCTTCCTGATGAAATACAGAGAAGCAGA
* * *
865 TTGAAACAGTGATGGGATCATATTCCTGATGAGACACTGATAAAAAGACCCAAACGAGGCTCGAA
65 TTGAAACAGTGATGGGATCATCTTCTTGATGAGACACTGAGAAAAAGACCCAAACGAGGCTCGAA
* *
930 ACTAGCAAAT
130 ACGAGCAGAT
* *
940 CTTCCAAAT-AGGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGC-GA
1 CTTCCAGATGAGG-TACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAAATACAGAGAAGCAG-
* *
1003 ATTGAAACAGTGATGGGATCATCTTCTTGATGAGACACTAAGAAGAAGACCCAAACGAGGCTCGA
64 ATTGAAACAGTGATGGGATCATCTTCTTGATGAGACACTGAGAAAAAGACCCAAACGAGGCTCGA
1068 AACGAGCAGAT
129 AACGAGCAGAT
*
1079 CTTCTAGATGAGGTACTGAGAAGTGAACCAAATTCGTCTTCCTGATGA
1 CTTCCAGATGAGGTACTGAGAAGTGAACCAAATTCGTCTTCCTGATGA
1127 GATAAGCGAA
Statistics
Matches: 303, Mismatches: 19, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
138 1 0.00
139 169 0.56
140 133 0.44
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (139 bp):
CTTCCAGATGAGGTACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAAATACAGAGAAGCAGAT
TGAAACAGTGATGGGATCATCTTCTTGATGAGACACTGAGAAAAAGACCCAAACGAGGCTCGAAA
CGAGCAGAT
Found at i:1206 original size:139 final size:135
Alignment explanation
Indices: 661--1191 Score: 528
Period size: 139 Copynumber: 3.9 Consensus size: 135
651 AAACGGTTAG
* * * * *
661 CTTCCTGATGAGATACTGAG-AGATGAACCAAATTCGTATTCCTGATGAAATACAGAGAA--GCA
1 CTTCCAGATGAGGTACTGAGAAG-TGAACCAAATTCGTCTTCCTGATGAGATA-AGCGAATTG-A
* * * * *
723 GATTGAAAC-AGTGATGGGATCATCTTCTTGATGAGACACTGAGAAAAAGACCCAAACGAGGCTC
63 GA--CAAACGA-TG-T-GGATCATATTCCTGATGAGACACTAAGAAGAAGACCCAAACGAGGCTC
787 GAAACGAGCAGAT
123 GAAACGAGCAGAT
* *
800 CTTCCAGATGAGGTACTGAGAAGTGAACCAAATTTCGTCTTCCTGATGAAATACAGAGAA--GCA
1 CTTCCAGATGAGGTACTGAGAAGTGAACCAAA-TTCGTCTTCCTGATGAGATA-AGCGAATTG-A
* * * *
863 GATTGAAAC-AGTGATGGGATCATATTCCTGATGAGACACTGATAAAAAGACCCAAACGAGGCTC
63 GA--CAAACGA-TG-T-GGATCATATTCCTGATGAGACACTAAGAAGAAGACCCAAACGAGGCTC
* *
927 GAAACTAGCAAAT
123 GAAACGAGCAGAT
*
940 CTTCCAAAT-AGGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAA
1 CTTCCAGATGAGG-TACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGAT------AAGCGAA
* ** * *
1004 TTGAAAC-AGTGATG-GGATCATCTTCTTGATGAGACACTAAGAAGAAGACCCAAACGAGGCTCG
59 TTGAGACAAACGATGTGGATCATATTCCTGATGAGACACTAAGAAGAAGACCCAAACGAGGCTCG
1067 AAACGAGCAGAT
124 AAACGAGCAGAT
*
1079 CTTCTAGATGAGGTACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATAAGCGAATTGAGAC
1 CTTCCAGATGAGGTACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATAAGCGAATTGAGAC
* *
1144 AAACGACGTGG-TCATATTCCTGATGAGATACTAAGAAGAAGA-CCAAAC
66 AAACGATGTGGATCATATTCCTGATGAGACACTAAGAAGAAGACCCAAAC
1192 CAAACCCACG
Statistics
Matches: 346, Mismatches: 31, Indels: 36
0.84 0.08 0.09
Matches are distributed among these distances:
133 19 0.05
134 32 0.09
135 2 0.01
139 147 0.42
140 133 0.38
142 3 0.01
143 1 0.00
144 5 0.01
145 3 0.01
146 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.21
Consensus pattern (135 bp):
CTTCCAGATGAGGTACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATAAGCGAATTGAGAC
AAACGATGTGGATCATATTCCTGATGAGACACTAAGAAGAAGACCCAAACGAGGCTCGAAACGAG
CAGAT
Found at i:1669 original size:17 final size:17
Alignment explanation
Indices: 1643--1715 Score: 103
Period size: 17 Copynumber: 4.4 Consensus size: 17
1633 TTAAAAATTG
1643 AATTTA-TTTAAATTTA
1 AATTTATTTTAAATTTA
*
1659 AGTTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
1676 AATTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
* *
1693 AATTTATTATAAAATTA
1 AATTTATTTTAAATTTA
1710 AATTTA
1 AATTTA
1716 GAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
16 5 0.10
17 45 0.90
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:1690 original size:34 final size:33
Alignment explanation
Indices: 1630--1715 Score: 120
Period size: 34 Copynumber: 2.6 Consensus size: 33
1620 TTATCTGGAC
* *
1630 TTATTA-AAAATTGAATTTATTTAAATTTAAGT
1 TTATTATAAAATTAAATTTATTTAAATTTAAAT
* *
1662 TTATTTTAAATTTAAATTTATTTGAAATTTAAAT
1 TTATTATAAAATTAAATTTATTT-AAATTTAAAT
1696 TTATTATAAAATTAAATTTA
1 TTATTATAAAATTAAATTTA
1716 GAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 5 0.11
33 14 0.30
34 27 0.59
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (33 bp):
TTATTATAAAATTAAATTTATTTAAATTTAAAT
Found at i:1691 original size:7 final size:6
Alignment explanation
Indices: 1648--1715 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 6
1638 AATTGAATTT
* *
1648 ATTTAA ATTTAA GTTT-A TTTTAA ATTTAA ATTT-- ATTTGAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA
*
1694 ATTT-- ATTATAA AATTAA ATTTA
1 ATTTAA ATT-TAA ATTTAA ATTTA
1716 GAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
4 7 0.14
5 5 0.10
6 32 0.64
7 6 0.12
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
ATTTAA
Done.