Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010629.1 Kokia drynarioides strain JFW-HI SEQ_125565, 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: 3445
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.25
Warning! 170 characters in sequence are not A, C, G, or T
Found at i:679 original size:43 final size:43
Alignment explanation
Indices: 632--761 Score: 108
Period size: 43 Copynumber: 3.0 Consensus size: 43
622 TTCCCGACGA
*
632 TCCCGCACCATCATCAGCCTAAGTTACCGATGGTGTTCGATGC
1 TCCCGCACCATCATCAGCCAAAGTTACCGATGGTGTTCGATGC
* * *
675 TCCCGCA-CATC--CGAGGCACCAAGGTACCGATGCT-TCTCGATGC
1 TCCCGCACCATCATC-A-GC-CAAAGTTACCGATGGTGT-TCGATGC
** * *
718 TCCCATACCACCATCGGCCAAAGTTACCGATGGTG-TCTGATGC
1 TCCCGCACCATCATCAGCCAAAGTTACCGATGGTGTTC-GATGC
761 T
1 T
762 ATCGCACATC
Statistics
Matches: 68, Mismatches: 10, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
40 1 0.01
41 1 0.01
42 9 0.13
43 51 0.75
44 5 0.07
46 1 0.01
ACGTcount: A:0.22, C:0.34, G:0.22, T:0.23
Consensus pattern (43 bp):
TCCCGCACCATCATCAGCCAAAGTTACCGATGGTGTTCGATGC
Found at i:742 original size:86 final size:85
Alignment explanation
Indices: 585--871 Score: 337
Period size: 86 Copynumber: 3.3 Consensus size: 85
575 ATAGTGTCCC
* * * * * * *
585 ATGCTCCAGCACATGCAAGGCACCAAGGTACCGATACTTCCCGACGATCCCGCACCATCATCAGC
1 ATGCTCCCGCACATCCAAGGCACCAAGGTACCGATGCTTCCCGATG-TCCCGTACCACCATCGGC
650 CTAAGTTACCGATGGTGT-TCG
65 CTAAGTTACCGATGGTGTCT-G
* * *
671 ATGCTCCCGCACATCCGAGGCACCAAGGTACCGATGCTTCTCGATGCTCCCATACCACCATCGGC
1 ATGCTCCCGCACATCCAAGGCACCAAGGTACCGATGCTTCCCGATG-TCCCGTACCACCATCGGC
*
736 CAAAGTTACCGATGGTGTCTG
65 CTAAGTTACCGATGGTGTCTG
** * * *
757 ATGCTATCGCACATCCAAGGCACCAAGGTGTCAAGA-GC-TCCCGATTGTCCTGTACCACCATCG
1 ATGCTCCCGCACATCCAAGGCACCAAGGT-AC-CGATGCTTCCCGA-TGTCCCGTACCACCATCG
*
820 GTCTAAGTTACCGATGGTGTCTG
63 GCCTAAGTTACCGATGGTGTCTG
*
843 ATGCTCTCGCACATCCAAGGCACCAAGGT
1 ATGCTCCCGCACATCCAAGGCACCAAGGT
872 GTCNNNNNNN
Statistics
Matches: 174, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
86 166 0.95
87 6 0.03
88 2 0.01
ACGTcount: A:0.24, C:0.33, G:0.22, T:0.21
Consensus pattern (85 bp):
ATGCTCCCGCACATCCAAGGCACCAAGGTACCGATGCTTCCCGATGTCCCGTACCACCATCGGCC
TAAGTTACCGATGGTGTCTG
Found at i:1261 original size:86 final size:86
Alignment explanation
Indices: 1116--1474 Score: 459
Period size: 86 Copynumber: 4.2 Consensus size: 86
1106 NNNNNNNNNN
* ** * *
1116 AAGGTACCGATGGATCCCGATGATCTCGCACCACCATCGGCCTAAGTTACCGATGGTGTCTGATG
1 AAGGTGCCGATGCTTCCCGATGATCCCGCACCACCATCGGCCTAAGTTACCGATGGTGTCCGATG
*
1181 CTCCCACATATCAAAGGCACC
66 CTCCCACACATCAAAGGCACC
* * * *
1202 AAGGTACCGATGCTTCCCGATGGTCCCGCACCACCATCGGTCTCAGTTACCGATGGTGTCCGATG
1 AAGGTGCCGATGCTTCCCGATGATCCCGCACCACCATCGGCCTAAGTTACCGATGGTGTCCGATG
* *
1267 CTCCAACACATCGAAGGCACC
66 CTCCCACACATCAAAGGCACC
* * * *
1288 ATGGTGCCGATACTTCCCGATGATCCCGCACCACCATCGCCCTAAGTTACCGATAGTGTCCGATG
1 AAGGTGCCGATGCTTCCCGATGATCCCGCACCACCATCGGCCTAAGTTACCGATGGTGTCCGATG
* *
1353 CTCTCGCACATCAAAGGCACC
66 CTCCCACACATCAAAGGCACC
* * * * * ** *
1374 AAGGTGTCGATAG-ATCTCGATGGTCCCGCACTACCATCGGCCTAAGTTGTCGATGGTGTACGAT
1 AAGGTGCCGAT-GCTTCCCGATGATCCCGCACCACCATCGGCCTAAGTTACCGATGGTGTCCGAT
*
1438 GCTCCCGCACATCAAAGGCACC
65 GCTCCCACACATCAAAGGCACC
1460 AAGGTGCCGATGCTT
1 AAGGTGCCGATGCTT
1475 TCNNNNNNNN
Statistics
Matches: 234, Mismatches: 37, Indels: 4
0.85 0.13 0.01
Matches are distributed among these distances:
85 1 0.00
86 233 1.00
ACGTcount: A:0.23, C:0.32, G:0.23, T:0.21
Consensus pattern (86 bp):
AAGGTGCCGATGCTTCCCGATGATCCCGCACCACCATCGGCCTAAGTTACCGATGGTGTCCGATG
CTCCCACACATCAAAGGCACC
Found at i:1385 original size:43 final size:43
Alignment explanation
Indices: 1338--1470 Score: 135
Period size: 43 Copynumber: 3.1 Consensus size: 43
1328 CCTAAGTTAC
*
1338 CGATAGTGTCCGATGCTCTCGCACATCAAAGGCACCAAGGTGT
1 CGATAGTGTCCGATGCTCCCGCACATCAAAGGCACCAAGGTGT
* * * ** * *
1381 CGATAG-ATCTCGATGGTCCCGCACTACCATCGGC-CTAAGTTGT
1 CGATAGTGTC-CGATGCTCCCGCAC-ATCAAAGGCACCAAGGTGT
* * *
1424 CGATGGTGTACGATGCTCCCGCACATCAAAGGCACCAAGGTGC
1 CGATAGTGTCCGATGCTCCCGCACATCAAAGGCACCAAGGTGT
1467 CGAT
1 CGAT
1471 GCTTTCNNNN
Statistics
Matches: 68, Mismatches: 18, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
42 8 0.12
43 53 0.78
44 7 0.10
ACGTcount: A:0.24, C:0.29, G:0.26, T:0.21
Consensus pattern (43 bp):
CGATAGTGTCCGATGCTCCCGCACATCAAAGGCACCAAGGTGT
Found at i:1471 original size:43 final size:42
Alignment explanation
Indices: 1165--1471 Score: 124
Period size: 43 Copynumber: 7.1 Consensus size: 42
1155 GCCTAAGTTA
* * *
1165 CCGATGGTGTCTGATGCTCCCACATATCAAAGGCACCAAGGTA
1 CCGATGGTGTC-GATGCTCCCGCACATCAAAGGCACCAAGGTG
* * * ** * * *
1208 CCGATGCT-TCCCGATGGTCCCGCACCACCATCGGTC-TC-AGTTA
1 CCGATGGTGT--CGATGCTCCCGCA-CATCAAAGG-CACCAAGGTG
** * *
1251 CCGATGGTGTCCGATGCTCCAACACATCGAAGGCACCATGGTG
1 CCGATGGTGT-CGATGCTCCCGCACATCAAAGGCACCAAGGTG
** * * ** * *
1294 CCGATACT-TCCCGATGATCCCGCACCA-CCATCGC-CCTAAGTTA
1 CCGATGGTGT--CGATGCTCCCGCA-CATCAAAGGCACC-AAGGTG
* *
1337 CCGATAGTGTCCGATGCTCTCGCACATCAAAGGCACCAAGGTG
1 CCGATGGTGT-CGATGCTCCCGCACATCAAAGGCACCAAGGTG
* * * * * ** * *
1380 TCGATAGATCTCGATGGTCCCGCACTACCATCGGC-CTAAGTTG
1 CCGAT-GGTGTCGATGCTCCCGCAC-ATCAAAGGCACCAAGGTG
*
1423 TCGATGGTGTACGATGCTCCCGCACATCAAAGGCACCAAGGTG
1 CCGATGGTGT-CGATGCTCCCGCACATCAAAGGCACCAAGGTG
1466 CCGATG
1 CCGATG
1472 CTTTCNNNNN
Statistics
Matches: 187, Mismatches: 60, Indels: 34
0.67 0.21 0.12
Matches are distributed among these distances:
41 1 0.01
42 21 0.11
43 143 0.76
44 21 0.11
45 1 0.01
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.21
Consensus pattern (42 bp):
CCGATGGTGTCGATGCTCCCGCACATCAAAGGCACCAAGGTG
Found at i:1676 original size:86 final size:85
Alignment explanation
Indices: 1537--1747 Score: 271
Period size: 86 Copynumber: 2.4 Consensus size: 85
1527 NNTGGTCCTA
* ** *
1537 CACCACCATCGACCTAAGTTGTCGATTGTGTCCGATGCTCTCGCACATCCAAGGCACCAAGGTGC
1 CACCACCATAGACCTAAGTTACCGATAGTGT-CGATGCTCTCGCACATCCAAGGCACCAAGGTGC
*
1602 CGATGGATCCCGATGGTCCCG
65 CGATGCATCCCGATGGTCCCG
* *
1623 CACCACCGTTAG-CCTAAGTTACCGATAGTGTCTGATGCTCTCGCACATTCAAGGCACCAAGGTG
1 CACCACC-ATAGACCTAAGTTACCGATAGTGTC-GATGCTCTCGCACATCCAAGGCACCAAGGTG
* * *
1687 CCTATGCTTCCCGATGGTCTCG
64 CCGATGCATCCCGATGGTCCCG
* *
1709 CACCACCATCGACCTAAGTTACCGATGGTGTACGATGCT
1 CACCACCATAGACCTAAGTTACCGATAGTGT-CGATGCT
1748 TCCCAGTGGT
Statistics
Matches: 108, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
85 3 0.03
86 102 0.94
87 3 0.03
ACGTcount: A:0.22, C:0.32, G:0.23, T:0.23
Consensus pattern (85 bp):
CACCACCATAGACCTAAGTTACCGATAGTGTCGATGCTCTCGCACATCCAAGGCACCAAGGTGCC
GATGCATCCCGATGGTCCCG
Found at i:1770 original size:53 final size:53
Alignment explanation
Indices: 1690--1800 Score: 181
Period size: 53 Copynumber: 2.1 Consensus size: 53
1680 CAAGGTGCCT
*
1690 ATGCTTCCCGATGGTCTCGCACCACCATCGACCTAAGTTACCGATGGTGTAC-G
1 ATGCTTCCCGATGGTCCCGCACCACCATCGACCTAAGTTACCGATGGTGT-CTG
1743 ATGCTTCCC-AGTGGTCCCGCACCACCATCGACCTAAGTTACCGATGGTGTCTG
1 ATGCTTCCCGA-TGGTCCCGCACCACCATCGACCTAAGTTACCGATGGTGTCTG
1796 ATGCT
1 ATGCT
1801 CTCACACATC
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
52 2 0.04
53 53 0.96
ACGTcount: A:0.20, C:0.32, G:0.23, T:0.25
Consensus pattern (53 bp):
ATGCTTCCCGATGGTCCCGCACCACCATCGACCTAAGTTACCGATGGTGTCTG
Found at i:1853 original size:139 final size:139
Alignment explanation
Indices: 1615--1886 Score: 379
Period size: 139 Copynumber: 2.0 Consensus size: 139
1605 TGGATCCCGA
* * *
1615 TGGTCCCGCACCACCGTTAGCCTAAGTTACCGATAGTGTCTGATGCTCTCGCACATTCAAGGCAC
1 TGGTCCCGCACCACCATGAGCCTAAGTTACCGATAGTGTCTGATGCTCTCACACATTCAAGGCAC
* * * *
1680 CAAGGTGCCTATGCTTCCCGATGGTCTCGCACCACCATCGACCTAAGTTACCGATGGTGTAC-GA
66 CAAGGTACCGATGCATCCCGATGGTCCCGCACCACCATCGACCTAAGTTACCGATGGTGT-CTGA
1744 TGCTTCCCAG
130 TGCTTCCCAG
*
1754 TGGTCCCGCACCACCATCGA-CCTAAGTTACCGATGGTGTCTGATGCTCTCACACA-TCTAAGGC
1 TGGTCCCGCACCACCAT-GAGCCTAAGTTACCGATAGTGTCTGATGCTCTCACACATTC-AAGGC
* * * * *
1817 ACCAAGGTACCGGTGGATCCCGATTGTCCCGTACCACCATCGGCCTAAGTTACCGATGGTGTCTG
64 ACCAAGGTACCGATGCATCCCGATGGTCCCGCACCACCATCGACCTAAGTTACCGATGGTGTCTG
1882 ATGCT
129 ATGCT
1887 CCCGCACATC
Statistics
Matches: 117, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
138 3 0.03
139 113 0.97
140 1 0.01
ACGTcount: A:0.21, C:0.32, G:0.23, T:0.24
Consensus pattern (139 bp):
TGGTCCCGCACCACCATGAGCCTAAGTTACCGATAGTGTCTGATGCTCTCACACATTCAAGGCAC
CAAGGTACCGATGCATCCCGATGGTCCCGCACCACCATCGACCTAAGTTACCGATGGTGTCTGAT
GCTTCCCAG
Found at i:1926 original size:86 final size:86
Alignment explanation
Indices: 1741--2100 Score: 361
Period size: 86 Copynumber: 4.2 Consensus size: 86
1731 CGATGGTGTA
* * * *
1741 CGATGCTTCCC-AGTGGTCCCGCACCACCATCGACCTAAGTTACCGATGGTGTCTGATGCTCTCA
1 CGATACTTCCCGA-TGGTCCCGCACCACCATCGGCCTAAGTTACCGATGGTGTCTGATGCTCCCG
* *
1805 CACATCTAAGGCACCAAGGTAC
65 CACATCGAAGGCACCAAGGTGC
* *** * *
1827 CGGTGGATCCCGATTGTCCCGTACCACCATCGGCCTAAGTTACCGATGGTGTCTGATGCTCCCGC
1 CGATACTTCCCGATGGTCCCGCACCACCATCGGCCTAAGTTACCGATGGTGTCTGATGCTCCCGC
*
1892 ACATCGAAGGCACCATGGTGC
66 ACATCGAAGGCACCAAGGTGC
* ** ** *
1913 CGATACTTTCCGATGGTCCCGCACCACCATCGGCCTCTGTTGTCGAT-G-GTCTGATGCTCCCTC
1 CGATACTTCCCGATGGTCCCGCACCACCATCGGCCTAAGTTACCGATGGTGTCTGATGCTCCCGC
* * * *
1976 ACATCGTAGGCACCATGATTC
66 ACATCGAAGGCACCAAGGTGC
* ** * * * ** *
1997 TGATACTTCCCGATGGTCCTACGCCATCATCGGCCTCAGTTGTCGATGGTGTCCGATGCTCCCGC
1 CGATACTTCCCGATGGTCCCGCACCACCATCGGCCTAAGTTACCGATGGTGTCTGATGCTCCCGC
*
2062 ACATCCG-AGACACCAAGGTGC
66 ACAT-CGAAGGCACCAAGGTGC
2083 CGATGA-TTCCCGATGGTC
1 CGAT-ACTTCCCGATGGTC
2101 TCGNNNNNNN
Statistics
Matches: 229, Mismatches: 40, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
84 72 0.31
85 2 0.01
86 151 0.66
87 4 0.02
ACGTcount: A:0.19, C:0.33, G:0.24, T:0.24
Consensus pattern (86 bp):
CGATACTTCCCGATGGTCCCGCACCACCATCGGCCTAAGTTACCGATGGTGTCTGATGCTCCCGC
ACATCGAAGGCACCAAGGTGC
Found at i:1962 original size:225 final size:225
Alignment explanation
Indices: 1537--1944 Score: 620
Period size: 225 Copynumber: 1.8 Consensus size: 225
1527 NNTGGTCCTA
** * * *
1537 CACCACCATCGACCTAAGTTGTCGATTGTGTCCGATGCTCTCGCACATCCAAGGCACCAAGGTGC
1 CACCACCATCGACCTAAGTTACCGATGGTGTCCGATGCTCTCACACATCCAAGGCACCAAGGTAC
* * *
1602 CGATGGATCCCGATGGTCCCGCACCACCGTTAGCCTAAGTTACCGATAGTGTCTGATGCTCTCGC
66 CGATGGATCCCGATGGTCCCGCACCACCATCAGCCTAAGTTACCGATAGTGTCTGATGCTCCCGC
* * *
1667 ACATTCAAGGCACCAAGGTGCCTATGCTTCCCGATGGTCTCGCACCACCATCGACCTAAGTTACC
131 ACATTCAAGGCACCAAGGTGCCGATACTTCCCGATGGTCCCGCACCACCATCGACCTAAGTTACC
1732 GATGGTGTACGATGCTTCCCAGTGGTCCCG
196 GATGGTGTACGATGCTTCCCAGTGGTCCCG
* *
1762 CACCACCATCGACCTAAGTTACCGATGGTGTCTGATGCTCTCACACATCTAAGGCACCAAGGTAC
1 CACCACCATCGACCTAAGTTACCGATGGTGTCCGATGCTCTCACACATCCAAGGCACCAAGGTAC
* * * * *
1827 CGGTGGATCCCGATTGTCCCGTACCACCATCGGCCTAAGTTACCGATGGTGTCTGATGCTCCCGC
66 CGATGGATCCCGATGGTCCCGCACCACCATCAGCCTAAGTTACCGATAGTGTCTGATGCTCCCGC
* *
1892 ACA-TCGAAGGCACCATGGTGCCGATACTTTCCGATGGTCCCGCACCACCATCG
131 ACATTC-AAGGCACCAAGGTGCCGATACTTCCCGATGGTCCCGCACCACCATCG
1945 GCCTCTGTTG
Statistics
Matches: 162, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
224 2 0.01
225 160 0.99
ACGTcount: A:0.21, C:0.33, G:0.23, T:0.23
Consensus pattern (225 bp):
CACCACCATCGACCTAAGTTACCGATGGTGTCCGATGCTCTCACACATCCAAGGCACCAAGGTAC
CGATGGATCCCGATGGTCCCGCACCACCATCAGCCTAAGTTACCGATAGTGTCTGATGCTCCCGC
ACATTCAAGGCACCAAGGTGCCGATACTTCCCGATGGTCCCGCACCACCATCGACCTAAGTTACC
GATGGTGTACGATGCTTCCCAGTGGTCCCG
Done.